Multiple sequence alignment - TraesCS7A01G095300

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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 TraesCS7A01G095300 chr7A 100.000 5059 0 0 1 5059 58223602 58228660 0.000000e+00 9343.0
1 TraesCS7A01G095300 chr7A 80.783 281 37 12 2169 2440 198895676 198895404 2.390000e-48 204.0
2 TraesCS7A01G095300 chr4A 94.357 2995 119 19 801 3774 670847627 670850592 0.000000e+00 4549.0
3 TraesCS7A01G095300 chr4A 94.813 964 22 5 3770 4733 670851685 670852620 0.000000e+00 1478.0
4 TraesCS7A01G095300 chr4A 81.907 818 113 19 1 798 670844640 670845442 0.000000e+00 658.0
5 TraesCS7A01G095300 chr4A 89.205 176 15 1 4693 4864 670852621 670852796 3.070000e-52 217.0
6 TraesCS7A01G095300 chr4A 92.537 67 5 0 4849 4915 670881650 670881716 4.170000e-16 97.1
7 TraesCS7A01G095300 chr7D 94.551 2037 74 15 1703 3720 54836916 54834898 0.000000e+00 3112.0
8 TraesCS7A01G095300 chr7D 88.068 1718 128 40 1 1690 54838570 54836902 0.000000e+00 1965.0
9 TraesCS7A01G095300 chr7D 93.639 676 25 8 3903 4574 54834898 54834237 0.000000e+00 994.0
10 TraesCS7A01G095300 chr7D 93.382 136 9 0 4919 5054 19712836 19712971 8.590000e-48 202.0
11 TraesCS7A01G095300 chr7D 88.679 106 9 3 2435 2539 6744970 6744867 5.320000e-25 126.0
12 TraesCS7A01G095300 chr7D 84.874 119 16 2 4729 4846 610248164 610248281 8.900000e-23 119.0
13 TraesCS7A01G095300 chr7D 84.167 120 19 0 4730 4849 137563110 137562991 3.200000e-22 117.0
14 TraesCS7A01G095300 chr7D 94.444 54 3 0 4564 4617 459429328 459429381 3.250000e-12 84.2
15 TraesCS7A01G095300 chr7D 92.308 39 2 1 623 661 459742114 459742077 3.000000e-03 54.7
16 TraesCS7A01G095300 chr5A 95.620 137 6 0 4918 5054 504715463 504715327 2.370000e-53 220.0
17 TraesCS7A01G095300 chr5A 92.857 112 6 2 4940 5049 549315298 549315409 1.460000e-35 161.0
18 TraesCS7A01G095300 chr5A 93.458 107 7 0 4943 5049 549294682 549294788 5.240000e-35 159.0
19 TraesCS7A01G095300 chr5A 94.872 78 4 0 4918 4995 554294295 554294218 6.880000e-24 122.0
20 TraesCS7A01G095300 chr5A 80.000 165 25 5 1932 2088 455435663 455435499 1.150000e-21 115.0
21 TraesCS7A01G095300 chr5A 96.825 63 2 0 4992 5054 554294090 554294028 6.930000e-19 106.0
22 TraesCS7A01G095300 chr5A 92.982 57 4 0 4561 4617 230818227 230818171 3.250000e-12 84.2
23 TraesCS7A01G095300 chr5A 92.982 57 4 0 4561 4617 230848808 230848752 3.250000e-12 84.2
24 TraesCS7A01G095300 chr5A 94.444 36 2 0 622 657 687144437 687144402 7.080000e-04 56.5
25 TraesCS7A01G095300 chr5D 92.647 136 10 0 4919 5054 525322450 525322585 4.000000e-46 196.0
26 TraesCS7A01G095300 chr5D 95.556 90 4 0 2436 2525 310705353 310705264 1.470000e-30 145.0
27 TraesCS7A01G095300 chr5D 87.500 88 7 1 2085 2168 442203724 442203811 1.160000e-16 99.0
28 TraesCS7A01G095300 chr3D 91.549 142 12 0 4917 5058 434915598 434915739 4.000000e-46 196.0
29 TraesCS7A01G095300 chr3D 94.444 54 3 0 4564 4617 43577936 43577883 3.250000e-12 84.2
30 TraesCS7A01G095300 chr2D 89.855 138 14 0 4917 5054 314046921 314046784 1.450000e-40 178.0
31 TraesCS7A01G095300 chr2D 92.793 111 6 1 4946 5054 473292685 473292795 5.240000e-35 159.0
32 TraesCS7A01G095300 chr2D 84.615 117 18 0 4730 4846 460869567 460869451 3.200000e-22 117.0
33 TraesCS7A01G095300 chr2D 88.764 89 6 2 2088 2172 425742569 425742657 6.930000e-19 106.0
34 TraesCS7A01G095300 chr2D 92.308 39 2 1 623 661 631523757 631523794 3.000000e-03 54.7
35 TraesCS7A01G095300 chr4B 94.565 92 5 0 2432 2523 670388395 670388304 5.280000e-30 143.0
36 TraesCS7A01G095300 chr4B 95.455 88 4 0 2438 2525 277407991 277407904 1.900000e-29 141.0
37 TraesCS7A01G095300 chr4B 92.683 82 3 2 1874 1955 43739588 43739666 1.150000e-21 115.0
38 TraesCS7A01G095300 chr4B 92.500 40 2 1 622 661 498924308 498924346 7.080000e-04 56.5
39 TraesCS7A01G095300 chr5B 93.548 93 6 0 2438 2530 402737628 402737536 6.830000e-29 139.0
40 TraesCS7A01G095300 chr5B 92.473 93 7 0 2438 2530 411517379 411517287 3.180000e-27 134.0
41 TraesCS7A01G095300 chr5B 83.200 125 20 1 4730 4853 41408130 41408254 4.140000e-21 113.0
42 TraesCS7A01G095300 chr2B 94.444 90 5 0 2435 2524 483453041 483452952 6.830000e-29 139.0
43 TraesCS7A01G095300 chr2B 90.476 63 4 2 4556 4617 240186221 240186282 1.170000e-11 82.4
44 TraesCS7A01G095300 chr1A 93.548 93 6 0 2435 2527 518662849 518662757 6.830000e-29 139.0
45 TraesCS7A01G095300 chr1A 87.288 118 15 0 4730 4847 137810241 137810358 8.830000e-28 135.0
46 TraesCS7A01G095300 chr1A 78.723 235 24 9 1864 2088 462949430 462949212 3.180000e-27 134.0
47 TraesCS7A01G095300 chr4D 90.476 105 7 2 2438 2541 414221108 414221210 8.830000e-28 135.0
48 TraesCS7A01G095300 chr1D 91.837 98 4 4 2439 2535 307349155 307349249 3.180000e-27 134.0
49 TraesCS7A01G095300 chr1D 84.615 117 18 0 4730 4846 12243709 12243825 3.200000e-22 117.0
50 TraesCS7A01G095300 chr1D 89.535 86 5 1 2087 2168 279101375 279101460 6.930000e-19 106.0
51 TraesCS7A01G095300 chr7B 90.196 102 8 2 2433 2534 740996150 740996249 1.140000e-26 132.0
52 TraesCS7A01G095300 chr7B 85.714 119 17 0 4728 4846 413595491 413595609 5.320000e-25 126.0
53 TraesCS7A01G095300 chr7B 93.902 82 5 0 2087 2168 450642197 450642116 1.910000e-24 124.0
54 TraesCS7A01G095300 chr7B 90.698 43 3 1 622 664 181607714 181607673 7.080000e-04 56.5
55 TraesCS7A01G095300 chr3A 78.541 233 24 9 1864 2088 564279265 564279051 4.110000e-26 130.0
56 TraesCS7A01G095300 chr3A 88.889 90 5 2 2083 2168 151644772 151644684 6.930000e-19 106.0
57 TraesCS7A01G095300 chr2A 85.833 120 17 0 4730 4849 762756543 762756424 1.480000e-25 128.0
58 TraesCS7A01G095300 chr2A 86.316 95 7 3 2079 2168 524333395 524333488 1.160000e-16 99.0
59 TraesCS7A01G095300 chr6A 86.726 113 12 3 2439 2550 428694 428804 6.880000e-24 122.0
60 TraesCS7A01G095300 chr6A 78.027 223 24 12 1874 2088 103113004 103113209 3.200000e-22 117.0
61 TraesCS7A01G095300 chr6D 86.667 90 8 1 2083 2168 90111812 90111901 4.170000e-16 97.1
62 TraesCS7A01G095300 chr6D 96.226 53 2 0 4565 4617 30094476 30094424 2.510000e-13 87.9
63 TraesCS7A01G095300 chr6B 96.000 50 2 0 4560 4609 239055245 239055294 1.170000e-11 82.4
64 TraesCS7A01G095300 chr6B 92.857 56 2 2 4564 4617 507505885 507505830 4.200000e-11 80.5
65 TraesCS7A01G095300 chr1B 92.727 55 4 0 4560 4614 61100051 61100105 4.200000e-11 80.5
66 TraesCS7A01G095300 chr1B 92.500 40 2 1 622 661 573746596 573746634 7.080000e-04 56.5
67 TraesCS7A01G095300 chr3B 91.489 47 3 1 615 660 145319203 145319157 4.230000e-06 63.9
68 TraesCS7A01G095300 chr3B 94.286 35 1 1 630 664 441641797 441641764 9.000000e-03 52.8
69 TraesCS7A01G095300 chr3B 96.875 32 0 1 630 661 577722057 577722027 9.000000e-03 52.8


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 TraesCS7A01G095300 chr7A 58223602 58228660 5058 False 9343.000000 9343 100.0000 1 5059 1 chr7A.!!$F1 5058
1 TraesCS7A01G095300 chr4A 670844640 670852796 8156 False 1725.500000 4549 90.0705 1 4864 4 chr4A.!!$F2 4863
2 TraesCS7A01G095300 chr7D 54834237 54838570 4333 True 2023.666667 3112 92.0860 1 4574 3 chr7D.!!$R4 4573

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
580 587 0.770557 GGTATACCTGGCCATGGGGA 60.771 60.000 16.13 7.52 35.59 4.81 F
1296 3507 0.394899 GCATCTACAAGGGCAAGGCT 60.395 55.000 0.00 0.00 0.00 4.58 F
1690 3902 0.675633 GTTGGCATGTTGGAAGCTGT 59.324 50.000 0.00 0.00 0.00 4.40 F
2794 5010 1.453235 GCTATGGGCATCCTCAGCA 59.547 57.895 0.00 0.00 39.09 4.41 F
2919 5136 1.607148 GGAACTTTACAAGTGCGCCTT 59.393 47.619 4.18 4.96 41.91 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 4785 1.095228 AGAACACCTGCACCACAACG 61.095 55.000 0.00 0.0 0.00 4.10 R
2919 5136 4.415512 AGGCCAAGGGAATTACTAAGCATA 59.584 41.667 5.01 0.0 0.00 3.14 R
3680 5911 1.363807 GGCGGAAAATAGGCCATGC 59.636 57.895 5.01 0.0 46.13 4.06 R
3831 7156 0.179004 ATTGGTCCCACGCTTCACAA 60.179 50.000 0.00 0.0 0.00 3.33 R
4906 8280 0.179174 CGAACGGGGCAAAAGTATGC 60.179 55.000 0.00 0.0 45.67 3.14 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
17 18 3.309582 GGAGACCCTCCGATGCAA 58.690 61.111 0.00 0.00 41.08 4.08
43 44 8.778358 AGAATCGGTAAGATCAATAAATGAAGC 58.222 33.333 0.00 0.00 42.54 3.86
53 54 9.128404 AGATCAATAAATGAAGCACATACATGT 57.872 29.630 2.69 2.69 42.54 3.21
87 88 3.440522 GCAGGAAAATAGTGAGGTTGACC 59.559 47.826 0.00 0.00 0.00 4.02
106 107 1.676916 CCGAGAGCACATGTCCAACAT 60.677 52.381 0.00 0.00 39.91 2.71
120 121 1.666599 CCAACATGATGGCGTGTGTTG 60.667 52.381 19.84 19.84 46.66 3.33
131 132 5.446143 TGGCGTGTGTTGATAAAAAGAAT 57.554 34.783 0.00 0.00 0.00 2.40
137 138 7.591407 CGTGTGTTGATAAAAAGAATAATGCG 58.409 34.615 0.00 0.00 0.00 4.73
145 146 8.792633 TGATAAAAAGAATAATGCGGGGAATAG 58.207 33.333 0.00 0.00 0.00 1.73
175 176 4.520492 GGGGATGCTACCTTAACATGAATG 59.480 45.833 0.00 0.00 0.00 2.67
177 178 5.009010 GGGATGCTACCTTAACATGAATGTG 59.991 44.000 0.00 0.00 41.61 3.21
180 181 4.699735 TGCTACCTTAACATGAATGTGGTG 59.300 41.667 12.05 5.78 41.61 4.17
204 205 6.765036 TGATCTCATGGAGCTCATAAAAGTTC 59.235 38.462 17.19 10.33 31.17 3.01
279 280 4.268405 GCAAGGAACATCAAAACACACAAG 59.732 41.667 0.00 0.00 0.00 3.16
296 297 9.844790 AACACACAAGTAATCATGATATTGTTG 57.155 29.630 21.94 21.99 0.00 3.33
328 329 9.643693 GAATCAATGTGTTAATTCAATGTTCCT 57.356 29.630 0.00 0.00 0.00 3.36
364 365 3.071023 AGAAAGAATGTCGGGTCAACTCA 59.929 43.478 0.00 0.00 0.00 3.41
384 385 5.463061 ACTCATTTGAACGGCTTGAAAAATG 59.537 36.000 0.00 0.00 36.70 2.32
387 388 3.011949 TGAACGGCTTGAAAAATGAGC 57.988 42.857 0.00 0.00 35.71 4.26
390 391 1.336240 ACGGCTTGAAAAATGAGCTGC 60.336 47.619 0.00 0.00 44.63 5.25
393 394 2.289257 GGCTTGAAAAATGAGCTGCCTT 60.289 45.455 0.00 0.00 36.66 4.35
400 401 4.628963 AAAATGAGCTGCCTTTTTCCAT 57.371 36.364 0.00 0.00 0.00 3.41
404 405 4.032960 TGAGCTGCCTTTTTCCATCTTA 57.967 40.909 0.00 0.00 0.00 2.10
405 406 4.012374 TGAGCTGCCTTTTTCCATCTTAG 58.988 43.478 0.00 0.00 0.00 2.18
483 490 9.695155 AATAGTTTAGAAGCCCTAAAGCATAAA 57.305 29.630 8.62 0.00 45.19 1.40
486 493 7.888546 AGTTTAGAAGCCCTAAAGCATAAAGAA 59.111 33.333 8.62 0.00 45.19 2.52
514 521 7.633789 ACAGCTTATAGGAAAATTTGGAGAGA 58.366 34.615 0.00 0.00 0.00 3.10
515 522 8.109634 ACAGCTTATAGGAAAATTTGGAGAGAA 58.890 33.333 0.00 0.00 0.00 2.87
516 523 8.619546 CAGCTTATAGGAAAATTTGGAGAGAAG 58.380 37.037 0.00 0.00 0.00 2.85
517 524 8.552296 AGCTTATAGGAAAATTTGGAGAGAAGA 58.448 33.333 0.00 0.00 0.00 2.87
518 525 8.835439 GCTTATAGGAAAATTTGGAGAGAAGAG 58.165 37.037 0.00 0.00 0.00 2.85
567 574 6.753107 AAAACTGCATGTTGTAGGGTATAC 57.247 37.500 0.00 0.00 39.13 1.47
568 575 4.417426 ACTGCATGTTGTAGGGTATACC 57.583 45.455 13.99 13.99 34.23 2.73
569 576 4.473559 AACTGCATGTTGTAGGGTATACCT 59.526 41.667 21.25 10.03 44.72 3.08
570 577 5.629133 AACTGCATGTTGTAGGGTATACCTG 60.629 44.000 21.25 10.10 43.34 4.00
571 578 8.543839 AACTGCATGTTGTAGGGTATACCTGG 62.544 46.154 21.25 0.00 43.34 4.45
579 586 1.767692 GGTATACCTGGCCATGGGG 59.232 63.158 20.97 15.44 37.18 4.96
580 587 0.770557 GGTATACCTGGCCATGGGGA 60.771 60.000 16.13 7.52 35.59 4.81
581 588 1.145571 GTATACCTGGCCATGGGGAA 58.854 55.000 16.13 3.87 35.59 3.97
582 589 1.710809 GTATACCTGGCCATGGGGAAT 59.289 52.381 16.13 10.58 35.59 3.01
583 590 0.779997 ATACCTGGCCATGGGGAATC 59.220 55.000 16.13 0.00 35.59 2.52
584 591 1.360393 TACCTGGCCATGGGGAATCC 61.360 60.000 16.13 6.10 35.59 3.01
585 592 2.203394 CTGGCCATGGGGAATCCG 60.203 66.667 15.13 0.00 38.76 4.18
586 593 3.797507 CTGGCCATGGGGAATCCGG 62.798 68.421 15.13 6.83 38.76 5.14
589 596 3.501911 CCATGGGGAATCCGGCCT 61.502 66.667 2.85 0.00 38.76 5.19
590 597 2.203394 CATGGGGAATCCGGCCTG 60.203 66.667 0.00 0.00 38.76 4.85
615 622 2.281484 GGGCTTGTTCGCAGGTCA 60.281 61.111 0.00 0.00 29.64 4.02
673 689 3.244422 CGGGCTTGGGTCTAGCATATTTA 60.244 47.826 0.00 0.00 40.42 1.40
694 710 2.092914 ACATTTTAGGGAAGAGGCTCGG 60.093 50.000 9.22 0.00 0.00 4.63
728 744 3.634215 ATGGGATTTTCCATTGATGGGCT 60.634 43.478 10.00 0.00 44.55 5.19
755 771 1.393603 GCCCATGCCTAGGTTTTCTC 58.606 55.000 11.31 0.00 0.00 2.87
756 772 1.064389 GCCCATGCCTAGGTTTTCTCT 60.064 52.381 11.31 0.00 0.00 3.10
769 785 3.374367 GGTTTTCTCTCACGGGCTTTATC 59.626 47.826 0.00 0.00 0.00 1.75
799 820 2.908015 GCCCGACTTATGGCCAGA 59.092 61.111 13.05 2.53 41.97 3.86
803 824 2.500098 GCCCGACTTATGGCCAGATATA 59.500 50.000 13.05 0.00 41.97 0.86
805 826 4.697514 CCCGACTTATGGCCAGATATATG 58.302 47.826 13.05 3.46 0.00 1.78
969 3180 4.636435 CGTCCACACCCACCCACC 62.636 72.222 0.00 0.00 0.00 4.61
970 3181 4.280019 GTCCACACCCACCCACCC 62.280 72.222 0.00 0.00 0.00 4.61
971 3182 4.845307 TCCACACCCACCCACCCA 62.845 66.667 0.00 0.00 0.00 4.51
972 3183 4.596585 CCACACCCACCCACCCAC 62.597 72.222 0.00 0.00 0.00 4.61
1029 3240 3.578272 CTCTCCGTCTCGCTCCCG 61.578 72.222 0.00 0.00 0.00 5.14
1296 3507 0.394899 GCATCTACAAGGGCAAGGCT 60.395 55.000 0.00 0.00 0.00 4.58
1392 3603 3.716539 TATGCCGCCGTGCTCTGTC 62.717 63.158 0.00 0.00 0.00 3.51
1397 3608 1.421485 CGCCGTGCTCTGTCATTTC 59.579 57.895 0.00 0.00 0.00 2.17
1398 3609 1.291184 CGCCGTGCTCTGTCATTTCA 61.291 55.000 0.00 0.00 0.00 2.69
1399 3610 1.089920 GCCGTGCTCTGTCATTTCAT 58.910 50.000 0.00 0.00 0.00 2.57
1402 3613 3.612479 GCCGTGCTCTGTCATTTCATTTT 60.612 43.478 0.00 0.00 0.00 1.82
1425 3637 1.069500 GTTGATGGGTGTTTCGTTCGG 60.069 52.381 0.00 0.00 0.00 4.30
1538 3750 1.091771 CGCAAGCAGGTGATACTGGG 61.092 60.000 0.00 0.00 38.90 4.45
1644 3856 5.684704 AGAGAAAGGTGTTGAGATTCACAA 58.315 37.500 0.00 0.00 36.43 3.33
1649 3861 8.260114 AGAAAGGTGTTGAGATTCACAATTTTT 58.740 29.630 0.00 0.55 36.43 1.94
1690 3902 0.675633 GTTGGCATGTTGGAAGCTGT 59.324 50.000 0.00 0.00 0.00 4.40
1693 3905 2.161855 TGGCATGTTGGAAGCTGTTAG 58.838 47.619 0.00 0.00 0.00 2.34
1697 3909 1.896220 TGTTGGAAGCTGTTAGCCTG 58.104 50.000 0.00 0.00 43.77 4.85
1699 3911 2.230660 GTTGGAAGCTGTTAGCCTGTT 58.769 47.619 0.00 0.00 43.77 3.16
1751 3963 6.095720 TGGGTAGTTTCTTGGTTTGTAAGTTG 59.904 38.462 0.00 0.00 0.00 3.16
1783 3995 6.515512 AAACTGGGAGCATGTATTATAGGT 57.484 37.500 0.00 0.00 0.00 3.08
1819 4031 7.279615 TGTCTGGTTTCTTTGTAAGATCTTCA 58.720 34.615 12.24 7.33 37.38 3.02
1820 4032 7.939039 TGTCTGGTTTCTTTGTAAGATCTTCAT 59.061 33.333 12.24 0.00 37.38 2.57
1831 4043 9.496873 TTTGTAAGATCTTCATTCTTCCGTAAA 57.503 29.630 12.24 0.00 35.19 2.01
1835 4047 6.037098 AGATCTTCATTCTTCCGTAAACTCG 58.963 40.000 0.00 0.00 0.00 4.18
1952 4164 4.917415 ACTTTGAAAAATGAATTCCGAGCG 59.083 37.500 2.27 0.00 0.00 5.03
2050 4262 7.167468 CGGTGTCACCAAGAATTTTTCTAAAAG 59.833 37.037 21.91 0.00 38.47 2.27
2198 4414 1.834822 CTCCTCCCGGACCATCTCC 60.835 68.421 0.73 0.00 34.92 3.71
2299 4515 5.488919 TCTTCTTTTCTGGGAGGTATGATGT 59.511 40.000 0.00 0.00 0.00 3.06
2362 4578 5.172205 GTTCATAGCGAATCCCTCTAATCC 58.828 45.833 0.00 0.00 35.63 3.01
2374 4590 3.134804 CCCTCTAATCCCAGTTGTTCGAT 59.865 47.826 0.00 0.00 0.00 3.59
2389 4605 4.894784 TGTTCGATTTTAGGAGAGCAGTT 58.105 39.130 0.00 0.00 0.00 3.16
2417 4633 3.632643 TTGATGCTCTAGGTGCAATCA 57.367 42.857 13.61 13.61 44.01 2.57
2794 5010 1.453235 GCTATGGGCATCCTCAGCA 59.547 57.895 0.00 0.00 39.09 4.41
2915 5132 3.560068 AGTCTTGGAACTTTACAAGTGCG 59.440 43.478 12.68 0.00 46.80 5.34
2919 5136 1.607148 GGAACTTTACAAGTGCGCCTT 59.393 47.619 4.18 4.96 41.91 4.35
3054 5271 9.912634 CTTTGTTCAAGATACCATTGTGTTAAT 57.087 29.630 0.00 0.00 33.80 1.40
3182 5399 9.432982 ACCAGGGCTTCAATAAATTTCATATTA 57.567 29.630 0.00 0.00 0.00 0.98
3404 5629 6.486253 TCTGCTACAAATTCTACTTGCTTG 57.514 37.500 0.00 0.00 0.00 4.01
3438 5663 6.893554 TGTTCCCAAATTGATCTGATCATCTT 59.106 34.615 20.16 13.86 39.39 2.40
3566 5794 4.552378 CGCATCATTCTGCTAGAGCTTTTC 60.552 45.833 2.72 0.00 42.66 2.29
3672 5903 3.995199 TCAGAAATCACACTGTGTCCTC 58.005 45.455 11.12 5.36 34.79 3.71
3755 5986 4.275936 ACAAACTGGCAGTAGATGTGTTTC 59.724 41.667 22.37 0.00 31.58 2.78
3775 6006 6.803320 TGTTTCGGTAACAACTAGATCTAACG 59.197 38.462 3.57 0.00 43.58 3.18
3776 6007 6.500684 TTCGGTAACAACTAGATCTAACGT 57.499 37.500 3.57 0.00 0.00 3.99
3777 6008 5.872635 TCGGTAACAACTAGATCTAACGTG 58.127 41.667 3.57 4.89 0.00 4.49
3778 6009 5.412594 TCGGTAACAACTAGATCTAACGTGT 59.587 40.000 3.57 5.49 0.00 4.49
3779 6010 5.510674 CGGTAACAACTAGATCTAACGTGTG 59.489 44.000 3.57 4.08 0.00 3.82
3780 6011 6.385033 GGTAACAACTAGATCTAACGTGTGT 58.615 40.000 3.57 4.60 0.00 3.72
3782 6013 6.764877 AACAACTAGATCTAACGTGTGTTG 57.235 37.500 20.40 20.40 39.12 3.33
3898 7223 6.261158 TGCCCTTTTTAGGTAAATGCAAAAAC 59.739 34.615 0.00 0.00 0.00 2.43
3935 7260 7.539710 CCTTCATAATGTCTGAACACATTGTTG 59.460 37.037 8.72 6.83 44.92 3.33
4068 7393 2.151202 GGCGAAGGTGAAGAATGACAA 58.849 47.619 0.00 0.00 0.00 3.18
4079 7404 0.992802 GAATGACAACGCTCTCGGAC 59.007 55.000 0.00 0.00 40.69 4.79
4402 7731 4.920640 TCAGATACCCGAAGCTCTAAAG 57.079 45.455 0.00 0.00 0.00 1.85
4551 7880 0.040351 TCTGTGCTACCCTGCTCTCT 59.960 55.000 0.00 0.00 0.00 3.10
4565 7894 5.371526 CCTGCTCTCTGATTTGCCTATTTA 58.628 41.667 0.00 0.00 0.00 1.40
4571 7900 9.591792 GCTCTCTGATTTGCCTATTTAAAAATT 57.408 29.630 0.00 0.00 0.00 1.82
4581 7910 7.992008 TGCCTATTTAAAAATTACTCCCTTCG 58.008 34.615 0.00 0.00 0.00 3.79
4582 7911 7.612633 TGCCTATTTAAAAATTACTCCCTTCGT 59.387 33.333 0.00 0.00 0.00 3.85
4583 7912 8.127327 GCCTATTTAAAAATTACTCCCTTCGTC 58.873 37.037 0.00 0.00 0.00 4.20
4584 7913 8.618677 CCTATTTAAAAATTACTCCCTTCGTCC 58.381 37.037 0.00 0.00 0.00 4.79
4585 7914 6.822667 TTTAAAAATTACTCCCTTCGTCCC 57.177 37.500 0.00 0.00 0.00 4.46
4586 7915 4.376225 AAAAATTACTCCCTTCGTCCCA 57.624 40.909 0.00 0.00 0.00 4.37
4587 7916 4.586306 AAAATTACTCCCTTCGTCCCAT 57.414 40.909 0.00 0.00 0.00 4.00
4588 7917 5.703730 AAAATTACTCCCTTCGTCCCATA 57.296 39.130 0.00 0.00 0.00 2.74
4589 7918 5.703730 AAATTACTCCCTTCGTCCCATAA 57.296 39.130 0.00 0.00 0.00 1.90
4590 7919 5.906772 AATTACTCCCTTCGTCCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
4632 7961 9.077885 ACATTACACTATTTGTTTGTGATCCTT 57.922 29.630 0.00 0.00 39.91 3.36
4668 7997 7.122650 ACCAGTATTTGTAATCCAAGATGGTTG 59.877 37.037 0.00 0.00 39.03 3.77
4677 8006 6.834168 AATCCAAGATGGTTGTCGTATTTT 57.166 33.333 0.00 0.00 39.03 1.82
4737 8107 7.272144 AGGAAACTTTATGACATACTCCCTT 57.728 36.000 0.00 0.00 37.44 3.95
4739 8109 6.258068 GGAAACTTTATGACATACTCCCTTCG 59.742 42.308 0.00 0.00 0.00 3.79
4741 8111 5.903810 ACTTTATGACATACTCCCTTCGTC 58.096 41.667 0.00 0.00 0.00 4.20
4743 8113 2.225382 TGACATACTCCCTTCGTCCA 57.775 50.000 0.00 0.00 0.00 4.02
4744 8114 2.531771 TGACATACTCCCTTCGTCCAA 58.468 47.619 0.00 0.00 0.00 3.53
4750 8120 6.659824 ACATACTCCCTTCGTCCAAAATTAT 58.340 36.000 0.00 0.00 0.00 1.28
4759 8129 6.582295 CCTTCGTCCAAAATTATTTGTCACAG 59.418 38.462 0.00 0.00 43.59 3.66
4764 8138 9.619316 CGTCCAAAATTATTTGTCACAGAAATA 57.381 29.630 0.00 0.00 43.59 1.40
4831 8205 9.851686 TTATCCATTGCTATGACAAGTTATTCT 57.148 29.630 9.87 0.00 33.37 2.40
4832 8206 8.757982 ATCCATTGCTATGACAAGTTATTCTT 57.242 30.769 9.87 0.00 33.50 2.52
4873 8247 7.523293 TTTTTCACCTGCTGAGATGAATAAA 57.477 32.000 0.00 2.01 31.45 1.40
4874 8248 7.523293 TTTTCACCTGCTGAGATGAATAAAA 57.477 32.000 0.00 0.00 31.45 1.52
4875 8249 7.707624 TTTCACCTGCTGAGATGAATAAAAT 57.292 32.000 0.00 0.00 31.45 1.82
4876 8250 7.707624 TTCACCTGCTGAGATGAATAAAATT 57.292 32.000 0.00 0.00 0.00 1.82
4877 8251 7.092137 TCACCTGCTGAGATGAATAAAATTG 57.908 36.000 0.00 0.00 0.00 2.32
4878 8252 6.095860 TCACCTGCTGAGATGAATAAAATTGG 59.904 38.462 0.00 0.00 0.00 3.16
4879 8253 5.954150 ACCTGCTGAGATGAATAAAATTGGT 59.046 36.000 0.00 0.00 0.00 3.67
4880 8254 6.438425 ACCTGCTGAGATGAATAAAATTGGTT 59.562 34.615 0.00 0.00 0.00 3.67
4881 8255 6.755141 CCTGCTGAGATGAATAAAATTGGTTG 59.245 38.462 0.00 0.00 0.00 3.77
4882 8256 6.632909 TGCTGAGATGAATAAAATTGGTTGG 58.367 36.000 0.00 0.00 0.00 3.77
4883 8257 6.436847 TGCTGAGATGAATAAAATTGGTTGGA 59.563 34.615 0.00 0.00 0.00 3.53
4884 8258 7.124599 TGCTGAGATGAATAAAATTGGTTGGAT 59.875 33.333 0.00 0.00 0.00 3.41
4885 8259 7.650903 GCTGAGATGAATAAAATTGGTTGGATC 59.349 37.037 0.00 0.00 0.00 3.36
4886 8260 8.592529 TGAGATGAATAAAATTGGTTGGATCA 57.407 30.769 0.00 0.00 0.00 2.92
4887 8261 9.204337 TGAGATGAATAAAATTGGTTGGATCAT 57.796 29.630 0.00 0.00 0.00 2.45
4888 8262 9.688592 GAGATGAATAAAATTGGTTGGATCATC 57.311 33.333 0.00 0.00 0.00 2.92
4889 8263 9.430399 AGATGAATAAAATTGGTTGGATCATCT 57.570 29.630 8.25 8.25 35.88 2.90
4890 8264 9.688592 GATGAATAAAATTGGTTGGATCATCTC 57.311 33.333 0.00 0.00 0.00 2.75
4891 8265 8.592529 TGAATAAAATTGGTTGGATCATCTCA 57.407 30.769 0.00 0.00 0.00 3.27
4892 8266 9.033711 TGAATAAAATTGGTTGGATCATCTCAA 57.966 29.630 0.00 0.00 0.00 3.02
4896 8270 7.729124 AAATTGGTTGGATCATCTCAATTCT 57.271 32.000 13.06 5.51 34.86 2.40
4897 8271 8.827832 AAATTGGTTGGATCATCTCAATTCTA 57.172 30.769 13.06 0.00 34.86 2.10
4898 8272 8.827832 AATTGGTTGGATCATCTCAATTCTAA 57.172 30.769 0.00 0.00 31.68 2.10
4899 8273 8.827832 ATTGGTTGGATCATCTCAATTCTAAA 57.172 30.769 0.00 0.00 0.00 1.85
4900 8274 8.648698 TTGGTTGGATCATCTCAATTCTAAAA 57.351 30.769 0.00 0.00 0.00 1.52
4901 8275 8.827832 TGGTTGGATCATCTCAATTCTAAAAT 57.172 30.769 0.00 0.00 0.00 1.82
4902 8276 9.919416 TGGTTGGATCATCTCAATTCTAAAATA 57.081 29.630 0.00 0.00 0.00 1.40
4920 8294 8.802267 TCTAAAATATATGCATACTTTTGCCCC 58.198 33.333 25.11 0.00 42.06 5.80
4921 8295 5.643379 AATATATGCATACTTTTGCCCCG 57.357 39.130 8.99 0.00 42.06 5.73
4922 8296 2.428544 TATGCATACTTTTGCCCCGT 57.571 45.000 1.16 0.00 42.06 5.28
4923 8297 1.555967 ATGCATACTTTTGCCCCGTT 58.444 45.000 0.00 0.00 42.06 4.44
4924 8298 0.885196 TGCATACTTTTGCCCCGTTC 59.115 50.000 0.00 0.00 42.06 3.95
4925 8299 0.179174 GCATACTTTTGCCCCGTTCG 60.179 55.000 0.00 0.00 36.60 3.95
4926 8300 0.450184 CATACTTTTGCCCCGTTCGG 59.550 55.000 4.08 4.08 0.00 4.30
4927 8301 0.325602 ATACTTTTGCCCCGTTCGGA 59.674 50.000 13.08 0.00 0.00 4.55
4928 8302 0.325602 TACTTTTGCCCCGTTCGGAT 59.674 50.000 13.08 0.00 0.00 4.18
4929 8303 0.958876 ACTTTTGCCCCGTTCGGATC 60.959 55.000 13.08 4.53 0.00 3.36
4930 8304 1.654023 CTTTTGCCCCGTTCGGATCC 61.654 60.000 13.08 0.00 0.00 3.36
4931 8305 3.631952 TTTGCCCCGTTCGGATCCC 62.632 63.158 13.08 0.00 0.00 3.85
4934 8308 3.547513 CCCCGTTCGGATCCCCTC 61.548 72.222 13.08 0.00 0.00 4.30
4935 8309 3.547513 CCCGTTCGGATCCCCTCC 61.548 72.222 13.08 0.00 41.07 4.30
4936 8310 2.762459 CCGTTCGGATCCCCTCCA 60.762 66.667 6.06 0.00 45.24 3.86
4937 8311 2.499685 CGTTCGGATCCCCTCCAC 59.500 66.667 6.06 0.00 45.24 4.02
4938 8312 2.058595 CGTTCGGATCCCCTCCACT 61.059 63.158 6.06 0.00 45.24 4.00
4939 8313 1.823976 GTTCGGATCCCCTCCACTC 59.176 63.158 6.06 0.00 45.24 3.51
4940 8314 1.382695 TTCGGATCCCCTCCACTCC 60.383 63.158 6.06 0.00 45.24 3.85
4941 8315 3.227276 CGGATCCCCTCCACTCCG 61.227 72.222 6.06 0.00 45.24 4.63
4942 8316 3.551407 GGATCCCCTCCACTCCGC 61.551 72.222 0.00 0.00 44.26 5.54
4943 8317 3.551407 GATCCCCTCCACTCCGCC 61.551 72.222 0.00 0.00 0.00 6.13
4985 8359 5.470845 CGGAGCTGTAGTTAAAAAGGATG 57.529 43.478 0.00 0.00 0.00 3.51
4986 8360 4.332819 CGGAGCTGTAGTTAAAAAGGATGG 59.667 45.833 0.00 0.00 0.00 3.51
4987 8361 5.497474 GGAGCTGTAGTTAAAAAGGATGGA 58.503 41.667 0.00 0.00 0.00 3.41
4988 8362 5.586643 GGAGCTGTAGTTAAAAAGGATGGAG 59.413 44.000 0.00 0.00 0.00 3.86
4989 8363 6.128138 AGCTGTAGTTAAAAAGGATGGAGT 57.872 37.500 0.00 0.00 0.00 3.85
4990 8364 6.543735 AGCTGTAGTTAAAAAGGATGGAGTT 58.456 36.000 0.00 0.00 0.00 3.01
4991 8365 6.431234 AGCTGTAGTTAAAAAGGATGGAGTTG 59.569 38.462 0.00 0.00 0.00 3.16
4992 8366 6.206829 GCTGTAGTTAAAAAGGATGGAGTTGT 59.793 38.462 0.00 0.00 0.00 3.32
4993 8367 7.389607 GCTGTAGTTAAAAAGGATGGAGTTGTA 59.610 37.037 0.00 0.00 0.00 2.41
4994 8368 8.842358 TGTAGTTAAAAAGGATGGAGTTGTAG 57.158 34.615 0.00 0.00 0.00 2.74
4995 8369 8.434392 TGTAGTTAAAAAGGATGGAGTTGTAGT 58.566 33.333 0.00 0.00 0.00 2.73
4996 8370 7.981102 AGTTAAAAAGGATGGAGTTGTAGTC 57.019 36.000 0.00 0.00 0.00 2.59
4997 8371 6.940867 AGTTAAAAAGGATGGAGTTGTAGTCC 59.059 38.462 0.00 0.00 38.22 3.85
4998 8372 5.584551 AAAAAGGATGGAGTTGTAGTCCT 57.415 39.130 2.50 0.00 40.91 3.85
5000 8374 4.828072 AAGGATGGAGTTGTAGTCCTTC 57.172 45.455 7.55 7.55 43.85 3.46
5001 8375 2.761208 AGGATGGAGTTGTAGTCCTTCG 59.239 50.000 9.18 0.00 40.76 3.79
5002 8376 2.758979 GGATGGAGTTGTAGTCCTTCGA 59.241 50.000 9.18 0.00 40.76 3.71
5003 8377 3.429135 GGATGGAGTTGTAGTCCTTCGAC 60.429 52.174 9.18 0.00 40.76 4.20
5005 8379 2.818432 TGGAGTTGTAGTCCTTCGACTC 59.182 50.000 11.06 11.06 46.90 3.36
5006 8380 2.164017 GGAGTTGTAGTCCTTCGACTCC 59.836 54.545 18.89 18.89 46.90 3.85
5007 8381 1.811359 AGTTGTAGTCCTTCGACTCCG 59.189 52.381 0.00 0.00 46.90 4.63
5008 8382 0.524862 TTGTAGTCCTTCGACTCCGC 59.475 55.000 0.00 0.00 46.90 5.54
5009 8383 0.607217 TGTAGTCCTTCGACTCCGCA 60.607 55.000 0.00 0.00 46.90 5.69
5010 8384 0.099082 GTAGTCCTTCGACTCCGCAG 59.901 60.000 0.00 0.00 46.90 5.18
5011 8385 1.654954 TAGTCCTTCGACTCCGCAGC 61.655 60.000 0.00 0.00 46.90 5.25
5012 8386 2.676822 TCCTTCGACTCCGCAGCT 60.677 61.111 0.00 0.00 35.37 4.24
5013 8387 2.202676 CCTTCGACTCCGCAGCTC 60.203 66.667 0.00 0.00 35.37 4.09
5014 8388 2.202676 CTTCGACTCCGCAGCTCC 60.203 66.667 0.00 0.00 35.37 4.70
5015 8389 2.676822 TTCGACTCCGCAGCTCCT 60.677 61.111 0.00 0.00 35.37 3.69
5016 8390 2.606155 CTTCGACTCCGCAGCTCCTC 62.606 65.000 0.00 0.00 35.37 3.71
5017 8391 4.544689 CGACTCCGCAGCTCCTCG 62.545 72.222 0.00 0.00 0.00 4.63
5018 8392 3.444805 GACTCCGCAGCTCCTCGT 61.445 66.667 0.00 0.00 0.00 4.18
5019 8393 2.045242 ACTCCGCAGCTCCTCGTA 60.045 61.111 0.00 0.00 0.00 3.43
5020 8394 1.448922 GACTCCGCAGCTCCTCGTAT 61.449 60.000 0.00 0.00 0.00 3.06
5021 8395 1.038130 ACTCCGCAGCTCCTCGTATT 61.038 55.000 0.00 0.00 0.00 1.89
5022 8396 0.103208 CTCCGCAGCTCCTCGTATTT 59.897 55.000 0.00 0.00 0.00 1.40
5023 8397 0.535335 TCCGCAGCTCCTCGTATTTT 59.465 50.000 0.00 0.00 0.00 1.82
5024 8398 0.652592 CCGCAGCTCCTCGTATTTTG 59.347 55.000 0.00 0.00 0.00 2.44
5025 8399 1.640428 CGCAGCTCCTCGTATTTTGA 58.360 50.000 0.00 0.00 0.00 2.69
5026 8400 1.590238 CGCAGCTCCTCGTATTTTGAG 59.410 52.381 0.00 0.00 0.00 3.02
5033 8407 1.571919 CTCGTATTTTGAGGAGCCGG 58.428 55.000 0.00 0.00 0.00 6.13
5034 8408 0.461339 TCGTATTTTGAGGAGCCGGC 60.461 55.000 21.89 21.89 0.00 6.13
5035 8409 1.762222 CGTATTTTGAGGAGCCGGCG 61.762 60.000 23.20 0.00 0.00 6.46
5036 8410 1.153249 TATTTTGAGGAGCCGGCGG 60.153 57.895 24.35 24.35 0.00 6.13
5037 8411 2.602746 TATTTTGAGGAGCCGGCGGG 62.603 60.000 29.48 9.71 0.00 6.13
5050 8424 3.723348 GCGGGTTGCCGAACAGTC 61.723 66.667 0.00 0.00 37.76 3.51
5051 8425 3.047877 CGGGTTGCCGAACAGTCC 61.048 66.667 0.00 0.00 33.27 3.85
5052 8426 2.671963 GGGTTGCCGAACAGTCCC 60.672 66.667 0.00 0.00 37.19 4.46
5053 8427 2.430367 GGTTGCCGAACAGTCCCT 59.570 61.111 0.00 0.00 33.27 4.20
5054 8428 1.228154 GGTTGCCGAACAGTCCCTT 60.228 57.895 0.00 0.00 33.27 3.95
5055 8429 0.822121 GGTTGCCGAACAGTCCCTTT 60.822 55.000 0.00 0.00 33.27 3.11
5056 8430 1.543871 GGTTGCCGAACAGTCCCTTTA 60.544 52.381 0.00 0.00 33.27 1.85
5057 8431 2.433436 GTTGCCGAACAGTCCCTTTAT 58.567 47.619 0.00 0.00 31.78 1.40
5058 8432 2.107950 TGCCGAACAGTCCCTTTATG 57.892 50.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.609825 CGATTCTTGCATCGGAGGG 58.390 57.895 0.00 0.00 42.03 4.30
11 12 5.991328 TTGATCTTACCGATTCTTGCATC 57.009 39.130 0.00 0.00 30.84 3.91
17 18 8.778358 GCTTCATTTATTGATCTTACCGATTCT 58.222 33.333 0.00 0.00 33.34 2.40
42 43 5.569059 GCAAGTTAGTTTGACATGTATGTGC 59.431 40.000 0.00 0.00 41.95 4.57
43 44 6.667370 TGCAAGTTAGTTTGACATGTATGTG 58.333 36.000 0.00 0.00 41.95 3.21
53 54 7.500892 TCACTATTTTCCTGCAAGTTAGTTTGA 59.499 33.333 0.00 0.00 0.00 2.69
87 88 1.730501 ATGTTGGACATGTGCTCTCG 58.269 50.000 18.75 0.00 37.45 4.04
106 107 4.517075 TCTTTTTATCAACACACGCCATCA 59.483 37.500 0.00 0.00 0.00 3.07
107 108 5.041951 TCTTTTTATCAACACACGCCATC 57.958 39.130 0.00 0.00 0.00 3.51
113 114 7.009174 CCCGCATTATTCTTTTTATCAACACAC 59.991 37.037 0.00 0.00 0.00 3.82
120 121 8.244113 CCTATTCCCCGCATTATTCTTTTTATC 58.756 37.037 0.00 0.00 0.00 1.75
131 132 2.257207 CTCCTCCTATTCCCCGCATTA 58.743 52.381 0.00 0.00 0.00 1.90
137 138 1.151788 CCCCCTCCTCCTATTCCCC 60.152 68.421 0.00 0.00 0.00 4.81
145 146 1.843832 GGTAGCATCCCCCTCCTCC 60.844 68.421 0.00 0.00 0.00 4.30
175 176 1.483827 TGAGCTCCATGAGATCACCAC 59.516 52.381 12.15 0.00 46.02 4.16
180 181 6.991531 AGAACTTTTATGAGCTCCATGAGATC 59.008 38.462 12.15 7.22 44.25 2.75
204 205 7.096885 GCTTTGCATCGCTATTATTTTGTGTAG 60.097 37.037 0.00 0.00 0.00 2.74
219 220 1.986698 AGACAATTGCTTTGCATCGC 58.013 45.000 5.05 0.00 38.76 4.58
251 252 4.869861 GTGTTTTGATGTTCCTTGCTTGTT 59.130 37.500 0.00 0.00 0.00 2.83
294 295 9.978044 TGAATTAACACATTGATTCATGAACAA 57.022 25.926 11.07 16.27 42.66 2.83
364 365 4.448732 GCTCATTTTTCAAGCCGTTCAAAT 59.551 37.500 0.00 0.00 0.00 2.32
384 385 4.265073 TCTAAGATGGAAAAAGGCAGCTC 58.735 43.478 0.00 0.00 0.00 4.09
457 464 9.695155 TTTATGCTTTAGGGCTTCTAAACTATT 57.305 29.630 8.13 0.00 41.52 1.73
458 465 9.343539 CTTTATGCTTTAGGGCTTCTAAACTAT 57.656 33.333 8.13 8.15 41.52 2.12
483 490 8.743714 CCAAATTTTCCTATAAGCTGTCTTTCT 58.256 33.333 0.00 0.00 33.85 2.52
486 493 8.109634 TCTCCAAATTTTCCTATAAGCTGTCTT 58.890 33.333 0.00 0.00 36.35 3.01
546 553 4.473559 AGGTATACCCTACAACATGCAGTT 59.526 41.667 18.65 0.00 43.87 3.16
547 554 4.037927 AGGTATACCCTACAACATGCAGT 58.962 43.478 18.65 0.00 43.87 4.40
549 556 3.135712 CCAGGTATACCCTACAACATGCA 59.864 47.826 18.65 0.00 43.86 3.96
550 557 3.740115 CCAGGTATACCCTACAACATGC 58.260 50.000 18.65 0.00 43.86 4.06
552 559 2.709397 GGCCAGGTATACCCTACAACAT 59.291 50.000 18.65 0.00 43.86 2.71
553 560 2.121129 GGCCAGGTATACCCTACAACA 58.879 52.381 18.65 0.00 43.86 3.33
554 561 2.121129 TGGCCAGGTATACCCTACAAC 58.879 52.381 18.65 5.27 43.86 3.32
555 562 2.572229 TGGCCAGGTATACCCTACAA 57.428 50.000 18.65 0.00 43.86 2.41
556 563 2.334977 CATGGCCAGGTATACCCTACA 58.665 52.381 18.65 12.62 43.86 2.74
557 564 1.628846 CCATGGCCAGGTATACCCTAC 59.371 57.143 18.65 7.64 43.86 3.18
558 565 1.486170 CCCATGGCCAGGTATACCCTA 60.486 57.143 18.65 1.67 43.86 3.53
560 567 1.767692 CCCATGGCCAGGTATACCC 59.232 63.158 18.65 3.62 36.42 3.69
561 568 0.770557 TCCCCATGGCCAGGTATACC 60.771 60.000 17.55 14.54 0.00 2.73
563 570 1.992557 GATTCCCCATGGCCAGGTATA 59.007 52.381 17.55 0.00 0.00 1.47
564 571 0.779997 GATTCCCCATGGCCAGGTAT 59.220 55.000 17.55 8.99 0.00 2.73
565 572 1.360393 GGATTCCCCATGGCCAGGTA 61.360 60.000 17.55 3.80 34.14 3.08
566 573 2.704424 GGATTCCCCATGGCCAGGT 61.704 63.158 17.55 0.00 34.14 4.00
567 574 2.199535 GGATTCCCCATGGCCAGG 59.800 66.667 13.05 12.17 34.14 4.45
568 575 2.203394 CGGATTCCCCATGGCCAG 60.203 66.667 13.05 3.10 34.14 4.85
569 576 3.819652 CCGGATTCCCCATGGCCA 61.820 66.667 8.56 8.56 34.14 5.36
572 579 3.501911 AGGCCGGATTCCCCATGG 61.502 66.667 5.05 4.14 34.14 3.66
573 580 2.203394 CAGGCCGGATTCCCCATG 60.203 66.667 5.05 0.00 34.14 3.66
574 581 4.209866 GCAGGCCGGATTCCCCAT 62.210 66.667 5.05 0.00 34.14 4.00
597 604 3.423154 GACCTGCGAACAAGCCCG 61.423 66.667 0.00 0.00 36.02 6.13
598 605 2.281484 TGACCTGCGAACAAGCCC 60.281 61.111 0.00 0.00 36.02 5.19
599 606 2.328099 CCTGACCTGCGAACAAGCC 61.328 63.158 0.00 0.00 36.02 4.35
600 607 2.970974 GCCTGACCTGCGAACAAGC 61.971 63.158 0.00 0.00 37.71 4.01
602 609 2.281484 GGCCTGACCTGCGAACAA 60.281 61.111 0.00 0.00 34.51 2.83
664 680 7.231519 GCCTCTTCCCTAAAATGTAAATATGCT 59.768 37.037 0.00 0.00 0.00 3.79
673 689 2.092914 CCGAGCCTCTTCCCTAAAATGT 60.093 50.000 0.00 0.00 0.00 2.71
737 753 2.239654 TGAGAGAAAACCTAGGCATGGG 59.760 50.000 9.30 0.00 0.00 4.00
738 754 3.274288 GTGAGAGAAAACCTAGGCATGG 58.726 50.000 9.30 0.00 0.00 3.66
739 755 2.932614 CGTGAGAGAAAACCTAGGCATG 59.067 50.000 9.30 0.00 0.00 4.06
740 756 2.093447 CCGTGAGAGAAAACCTAGGCAT 60.093 50.000 9.30 0.00 0.00 4.40
741 757 1.275291 CCGTGAGAGAAAACCTAGGCA 59.725 52.381 9.30 0.00 0.00 4.75
755 771 0.815615 GGCCTGATAAAGCCCGTGAG 60.816 60.000 0.00 0.00 43.76 3.51
756 772 1.223487 GGCCTGATAAAGCCCGTGA 59.777 57.895 0.00 0.00 43.76 4.35
799 820 5.284861 TGCCAGACAAACCGTACATATAT 57.715 39.130 0.00 0.00 0.00 0.86
803 824 2.151202 CTTGCCAGACAAACCGTACAT 58.849 47.619 0.00 0.00 37.96 2.29
805 826 0.237498 GCTTGCCAGACAAACCGTAC 59.763 55.000 0.00 0.00 37.96 3.67
1073 3284 4.394712 CGAGGGAGTGGGTGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
1218 3429 2.123251 GGCGGATCCCTCTCCAGA 60.123 66.667 6.06 0.00 34.78 3.86
1258 3469 2.813908 GTAGCTGGCGAACACCCG 60.814 66.667 0.00 0.00 0.00 5.28
1373 3584 2.963854 CAGAGCACGGCGGCATAG 60.964 66.667 19.61 0.00 35.83 2.23
1379 3590 1.291184 TGAAATGACAGAGCACGGCG 61.291 55.000 4.80 4.80 0.00 6.46
1392 3603 5.759273 ACACCCATCAACACAAAATGAAATG 59.241 36.000 0.00 0.00 0.00 2.32
1397 3608 4.208873 CGAAACACCCATCAACACAAAATG 59.791 41.667 0.00 0.00 0.00 2.32
1398 3609 4.142049 ACGAAACACCCATCAACACAAAAT 60.142 37.500 0.00 0.00 0.00 1.82
1399 3610 3.193691 ACGAAACACCCATCAACACAAAA 59.806 39.130 0.00 0.00 0.00 2.44
1402 3613 2.045561 ACGAAACACCCATCAACACA 57.954 45.000 0.00 0.00 0.00 3.72
1425 3637 3.502572 GCCCCAGACTGCGAATTC 58.497 61.111 0.00 0.00 0.00 2.17
1500 3712 1.869754 CGAGTCCAATCATACTGCCGG 60.870 57.143 0.00 0.00 0.00 6.13
1538 3750 1.981256 TGGACAAGGCAGAGGAAAAC 58.019 50.000 0.00 0.00 0.00 2.43
1649 3861 7.296660 CAACATTTGCTTCTTTGTGTTGAAAA 58.703 30.769 9.70 0.00 45.49 2.29
1690 3902 3.831333 TCAAAATGGCATGAACAGGCTAA 59.169 39.130 0.00 1.37 38.32 3.09
1693 3905 2.613691 CTCAAAATGGCATGAACAGGC 58.386 47.619 0.00 2.78 37.39 4.85
1697 3909 3.057033 AGTCAGCTCAAAATGGCATGAAC 60.057 43.478 0.00 0.00 0.00 3.18
1699 3911 2.751259 GAGTCAGCTCAAAATGGCATGA 59.249 45.455 0.00 0.00 41.29 3.07
1751 3963 4.576463 ACATGCTCCCAGTTTCGAAATATC 59.424 41.667 14.69 1.07 0.00 1.63
1783 3995 8.527810 ACAAAGAAACCAGACAAACAAATAGAA 58.472 29.630 0.00 0.00 0.00 2.10
1831 4043 3.081061 TGCAAACATAAAGCATCCGAGT 58.919 40.909 0.00 0.00 32.55 4.18
1835 4047 5.102313 GGTAACTGCAAACATAAAGCATCC 58.898 41.667 0.00 0.00 37.68 3.51
1952 4164 9.428363 TCGCGTACATCAACAATATAAATTTTC 57.572 29.630 5.77 0.00 0.00 2.29
2050 4262 4.628766 GGGTTCCACTACGTACATCTTTTC 59.371 45.833 0.00 0.00 0.00 2.29
2362 4578 4.093556 GCTCTCCTAAAATCGAACAACTGG 59.906 45.833 0.00 0.00 0.00 4.00
2389 4605 3.323115 CACCTAGAGCATCAATCCTAGCA 59.677 47.826 0.00 0.00 37.82 3.49
2417 4633 8.848182 GGAGTACTATATAGTGTAGCAGTGTTT 58.152 37.037 23.09 0.00 37.10 2.83
2569 4785 1.095228 AGAACACCTGCACCACAACG 61.095 55.000 0.00 0.00 0.00 4.10
2915 5132 5.241728 CCAAGGGAATTACTAAGCATAAGGC 59.758 44.000 0.00 0.00 45.30 4.35
2919 5136 4.415512 AGGCCAAGGGAATTACTAAGCATA 59.584 41.667 5.01 0.00 0.00 3.14
3404 5629 8.133627 CAGATCAATTTGGGAACATAGATTCAC 58.866 37.037 0.00 0.00 42.32 3.18
3438 5663 6.103330 GGTTTTGAACACCTAGAAGCAAAAA 58.897 36.000 0.00 0.00 37.09 1.94
3443 5668 2.876550 ACGGTTTTGAACACCTAGAAGC 59.123 45.455 0.00 0.00 31.32 3.86
3447 5672 5.065474 TCAAAAGACGGTTTTGAACACCTAG 59.935 40.000 19.76 0.00 43.10 3.02
3680 5911 1.363807 GGCGGAAAATAGGCCATGC 59.636 57.895 5.01 0.00 46.13 4.06
3755 5986 5.510674 CACACGTTAGATCTAGTTGTTACCG 59.489 44.000 2.02 0.42 0.00 4.02
3774 6005 0.308684 ACAGCAAGCATCAACACACG 59.691 50.000 0.00 0.00 0.00 4.49
3775 6006 3.837213 ATACAGCAAGCATCAACACAC 57.163 42.857 0.00 0.00 0.00 3.82
3776 6007 4.520111 AGAAATACAGCAAGCATCAACACA 59.480 37.500 0.00 0.00 0.00 3.72
3777 6008 5.051891 AGAAATACAGCAAGCATCAACAC 57.948 39.130 0.00 0.00 0.00 3.32
3778 6009 5.335897 GGAAGAAATACAGCAAGCATCAACA 60.336 40.000 0.00 0.00 0.00 3.33
3779 6010 5.098211 GGAAGAAATACAGCAAGCATCAAC 58.902 41.667 0.00 0.00 0.00 3.18
3780 6011 5.012239 AGGAAGAAATACAGCAAGCATCAA 58.988 37.500 0.00 0.00 0.00 2.57
3782 6013 5.573337 AAGGAAGAAATACAGCAAGCATC 57.427 39.130 0.00 0.00 0.00 3.91
3830 7155 0.394488 TTGGTCCCACGCTTCACAAA 60.394 50.000 0.00 0.00 0.00 2.83
3831 7156 0.179004 ATTGGTCCCACGCTTCACAA 60.179 50.000 0.00 0.00 0.00 3.33
3832 7157 0.687920 TATTGGTCCCACGCTTCACA 59.312 50.000 0.00 0.00 0.00 3.58
3833 7158 1.338769 ACTATTGGTCCCACGCTTCAC 60.339 52.381 0.00 0.00 0.00 3.18
3898 7223 5.711976 AGACATTATGAAGGAACAGGTTTGG 59.288 40.000 0.00 0.00 0.00 3.28
3935 7260 5.018695 GCGGTATGATGTACTGCAAATAC 57.981 43.478 12.72 0.00 46.18 1.89
4079 7404 1.139654 TCATTCTTCCTGCCATCTCCG 59.860 52.381 0.00 0.00 0.00 4.63
4402 7731 2.032636 GCAAATGCAAAACAGTTCAGGC 60.033 45.455 0.00 0.00 41.59 4.85
4427 7756 6.642131 TCAGAATTAGCAAATGAACAACTTGC 59.358 34.615 13.42 13.42 44.61 4.01
4470 7799 6.150474 TGTGACTCGAGTTTCAGTATATGACA 59.850 38.462 21.08 5.07 37.77 3.58
4565 7894 4.376225 TGGGACGAAGGGAGTAATTTTT 57.624 40.909 0.00 0.00 0.00 1.94
4571 7900 3.649843 ACATTATGGGACGAAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
4572 7901 2.478292 ACATTATGGGACGAAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
4573 7902 4.344102 TCTTACATTATGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
4574 7903 4.100498 GTCTTACATTATGGGACGAAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
4575 7904 4.377897 GTCTTACATTATGGGACGAAGGG 58.622 47.826 0.00 0.00 0.00 3.95
4609 7938 8.349245 CACAAGGATCACAAACAAATAGTGTAA 58.651 33.333 0.00 0.00 40.60 2.41
4614 7943 6.863126 GGTTCACAAGGATCACAAACAAATAG 59.137 38.462 0.00 0.00 0.00 1.73
4616 7945 5.128499 TGGTTCACAAGGATCACAAACAAAT 59.872 36.000 0.00 0.00 0.00 2.32
4632 7961 7.255660 GGATTACAAATACTGGTTTGGTTCACA 60.256 37.037 10.93 0.00 42.07 3.58
4668 7997 6.608610 ACTTTTGCCAGTATCAAAATACGAC 58.391 36.000 0.00 0.00 42.24 4.34
4677 8006 7.394016 TCTGAAATAGACTTTTGCCAGTATCA 58.606 34.615 0.00 0.00 0.00 2.15
4727 8097 7.568199 AATAATTTTGGACGAAGGGAGTATG 57.432 36.000 0.00 0.00 0.00 2.39
4737 8107 6.869315 TCTGTGACAAATAATTTTGGACGA 57.131 33.333 0.00 0.94 45.34 4.20
4831 8205 4.903045 AAAAATCTACTCCCTCCGTCAA 57.097 40.909 0.00 0.00 0.00 3.18
4864 8238 9.688592 GAGATGATCCAACCAATTTTATTCATC 57.311 33.333 0.00 0.00 38.01 2.92
4865 8239 9.204337 TGAGATGATCCAACCAATTTTATTCAT 57.796 29.630 0.00 0.00 0.00 2.57
4866 8240 8.592529 TGAGATGATCCAACCAATTTTATTCA 57.407 30.769 0.00 0.00 0.00 2.57
4870 8244 9.258629 AGAATTGAGATGATCCAACCAATTTTA 57.741 29.630 11.75 0.00 35.26 1.52
4871 8245 8.142485 AGAATTGAGATGATCCAACCAATTTT 57.858 30.769 11.75 6.42 35.26 1.82
4872 8246 7.729124 AGAATTGAGATGATCCAACCAATTT 57.271 32.000 11.75 0.00 35.26 1.82
4873 8247 8.827832 TTAGAATTGAGATGATCCAACCAATT 57.172 30.769 10.83 10.83 37.06 2.32
4874 8248 8.827832 TTTAGAATTGAGATGATCCAACCAAT 57.172 30.769 0.00 0.00 0.00 3.16
4875 8249 8.648698 TTTTAGAATTGAGATGATCCAACCAA 57.351 30.769 0.00 0.00 0.00 3.67
4876 8250 8.827832 ATTTTAGAATTGAGATGATCCAACCA 57.172 30.769 0.00 0.00 0.00 3.67
4906 8280 0.179174 CGAACGGGGCAAAAGTATGC 60.179 55.000 0.00 0.00 45.67 3.14
4907 8281 0.450184 CCGAACGGGGCAAAAGTATG 59.550 55.000 5.25 0.00 0.00 2.39
4908 8282 0.325602 TCCGAACGGGGCAAAAGTAT 59.674 50.000 13.29 0.00 36.01 2.12
4909 8283 0.325602 ATCCGAACGGGGCAAAAGTA 59.674 50.000 13.29 0.00 36.01 2.24
4910 8284 0.958876 GATCCGAACGGGGCAAAAGT 60.959 55.000 13.29 0.00 36.01 2.66
4911 8285 1.654023 GGATCCGAACGGGGCAAAAG 61.654 60.000 13.29 0.00 36.01 2.27
4912 8286 1.676303 GGATCCGAACGGGGCAAAA 60.676 57.895 13.29 0.00 36.01 2.44
4913 8287 2.045731 GGATCCGAACGGGGCAAA 60.046 61.111 13.29 0.00 36.01 3.68
4914 8288 4.104183 GGGATCCGAACGGGGCAA 62.104 66.667 13.29 0.00 36.01 4.52
4917 8291 3.547513 GAGGGGATCCGAACGGGG 61.548 72.222 13.29 0.00 38.33 5.73
4918 8292 3.547513 GGAGGGGATCCGAACGGG 61.548 72.222 13.29 0.00 38.67 5.28
4926 8300 3.551407 GGCGGAGTGGAGGGGATC 61.551 72.222 0.00 0.00 0.00 3.36
4959 8333 2.380084 TTTAACTACAGCTCCGCCAG 57.620 50.000 0.00 0.00 0.00 4.85
4960 8334 2.843401 TTTTAACTACAGCTCCGCCA 57.157 45.000 0.00 0.00 0.00 5.69
4961 8335 2.418976 CCTTTTTAACTACAGCTCCGCC 59.581 50.000 0.00 0.00 0.00 6.13
4962 8336 3.332034 TCCTTTTTAACTACAGCTCCGC 58.668 45.455 0.00 0.00 0.00 5.54
4963 8337 4.332819 CCATCCTTTTTAACTACAGCTCCG 59.667 45.833 0.00 0.00 0.00 4.63
4964 8338 5.497474 TCCATCCTTTTTAACTACAGCTCC 58.503 41.667 0.00 0.00 0.00 4.70
4965 8339 6.174049 ACTCCATCCTTTTTAACTACAGCTC 58.826 40.000 0.00 0.00 0.00 4.09
4966 8340 6.128138 ACTCCATCCTTTTTAACTACAGCT 57.872 37.500 0.00 0.00 0.00 4.24
4967 8341 6.206829 ACAACTCCATCCTTTTTAACTACAGC 59.793 38.462 0.00 0.00 0.00 4.40
4968 8342 7.745620 ACAACTCCATCCTTTTTAACTACAG 57.254 36.000 0.00 0.00 0.00 2.74
4969 8343 8.434392 ACTACAACTCCATCCTTTTTAACTACA 58.566 33.333 0.00 0.00 0.00 2.74
4970 8344 8.843885 ACTACAACTCCATCCTTTTTAACTAC 57.156 34.615 0.00 0.00 0.00 2.73
4971 8345 8.098912 GGACTACAACTCCATCCTTTTTAACTA 58.901 37.037 0.00 0.00 0.00 2.24
4972 8346 6.940867 GGACTACAACTCCATCCTTTTTAACT 59.059 38.462 0.00 0.00 0.00 2.24
4973 8347 6.940867 AGGACTACAACTCCATCCTTTTTAAC 59.059 38.462 0.00 0.00 36.33 2.01
4974 8348 7.086685 AGGACTACAACTCCATCCTTTTTAA 57.913 36.000 0.00 0.00 36.33 1.52
4975 8349 6.697641 AGGACTACAACTCCATCCTTTTTA 57.302 37.500 0.00 0.00 36.33 1.52
4976 8350 5.584551 AGGACTACAACTCCATCCTTTTT 57.415 39.130 0.00 0.00 36.33 1.94
4977 8351 5.584551 AAGGACTACAACTCCATCCTTTT 57.415 39.130 0.00 0.00 45.50 2.27
4980 8354 2.761208 CGAAGGACTACAACTCCATCCT 59.239 50.000 0.00 0.00 41.70 3.24
4981 8355 2.758979 TCGAAGGACTACAACTCCATCC 59.241 50.000 0.00 0.00 0.00 3.51
4982 8356 3.771798 GTCGAAGGACTACAACTCCATC 58.228 50.000 0.00 0.00 40.15 3.51
4983 8357 3.870633 GTCGAAGGACTACAACTCCAT 57.129 47.619 0.00 0.00 40.15 3.41
4994 8368 2.507324 GCTGCGGAGTCGAAGGAC 60.507 66.667 5.62 0.00 42.23 3.85
4995 8369 2.676822 AGCTGCGGAGTCGAAGGA 60.677 61.111 5.62 0.00 42.23 3.36
4996 8370 2.202676 GAGCTGCGGAGTCGAAGG 60.203 66.667 5.62 0.00 42.23 3.46
4997 8371 2.202676 GGAGCTGCGGAGTCGAAG 60.203 66.667 5.62 0.00 44.72 3.79
4998 8372 2.676822 AGGAGCTGCGGAGTCGAA 60.677 61.111 5.62 0.00 39.00 3.71
4999 8373 3.134792 GAGGAGCTGCGGAGTCGA 61.135 66.667 5.62 0.00 39.00 4.20
5000 8374 4.544689 CGAGGAGCTGCGGAGTCG 62.545 72.222 5.62 2.79 39.81 4.18
5001 8375 1.448922 ATACGAGGAGCTGCGGAGTC 61.449 60.000 5.62 1.88 0.00 3.36
5002 8376 1.038130 AATACGAGGAGCTGCGGAGT 61.038 55.000 5.62 4.07 0.00 3.85
5003 8377 0.103208 AAATACGAGGAGCTGCGGAG 59.897 55.000 0.00 0.00 0.00 4.63
5004 8378 0.535335 AAAATACGAGGAGCTGCGGA 59.465 50.000 0.00 0.00 0.00 5.54
5005 8379 0.652592 CAAAATACGAGGAGCTGCGG 59.347 55.000 0.00 0.00 0.00 5.69
5006 8380 1.590238 CTCAAAATACGAGGAGCTGCG 59.410 52.381 0.00 0.00 0.00 5.18
5014 8388 1.571919 CCGGCTCCTCAAAATACGAG 58.428 55.000 0.00 0.00 0.00 4.18
5015 8389 0.461339 GCCGGCTCCTCAAAATACGA 60.461 55.000 22.15 0.00 0.00 3.43
5016 8390 1.762222 CGCCGGCTCCTCAAAATACG 61.762 60.000 26.68 0.00 0.00 3.06
5017 8391 1.436983 CCGCCGGCTCCTCAAAATAC 61.437 60.000 26.68 0.00 0.00 1.89
5018 8392 1.153249 CCGCCGGCTCCTCAAAATA 60.153 57.895 26.68 0.00 0.00 1.40
5019 8393 2.438434 CCGCCGGCTCCTCAAAAT 60.438 61.111 26.68 0.00 0.00 1.82
5020 8394 4.715523 CCCGCCGGCTCCTCAAAA 62.716 66.667 26.68 0.00 0.00 2.44
5035 8409 2.671963 GGGACTGTTCGGCAACCC 60.672 66.667 0.00 0.00 36.89 4.11
5036 8410 0.822121 AAAGGGACTGTTCGGCAACC 60.822 55.000 0.00 0.00 40.86 3.77
5037 8411 1.886886 TAAAGGGACTGTTCGGCAAC 58.113 50.000 0.00 0.00 40.86 4.17
5038 8412 2.432444 CATAAAGGGACTGTTCGGCAA 58.568 47.619 0.00 0.00 40.86 4.52
5039 8413 2.107950 CATAAAGGGACTGTTCGGCA 57.892 50.000 0.00 0.00 40.86 5.69


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

AutoCloner maintained by Alex Coulton.