Multiple sequence alignment - TraesCS3D01G150500

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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 TraesCS3D01G150500 chr3D 100.000 5657 0 0 1 5657 115023772 115018116 0.000000e+00 10447
1 TraesCS3D01G150500 chr3D 95.760 566 17 2 1 560 396432001 396432565 0.000000e+00 905
2 TraesCS3D01G150500 chr3D 95.382 563 23 2 1 560 263005460 263006022 0.000000e+00 893
3 TraesCS3D01G150500 chr3D 94.386 570 23 5 1 561 462457380 462456811 0.000000e+00 867
4 TraesCS3D01G150500 chr3D 93.968 315 13 5 556 868 588790276 588790586 6.630000e-129 472
5 TraesCS3D01G150500 chr3B 94.481 3388 97 49 1395 4757 168682798 168679476 0.000000e+00 5138
6 TraesCS3D01G150500 chr3B 88.058 762 66 6 4868 5608 727397711 727398468 0.000000e+00 880
7 TraesCS3D01G150500 chr3B 96.927 423 10 1 869 1291 168683317 168682898 0.000000e+00 706
8 TraesCS3D01G150500 chr3A 91.942 2991 139 45 1894 4848 111553214 111550290 0.000000e+00 4095
9 TraesCS3D01G150500 chr3A 92.299 922 41 18 889 1802 111554111 111553212 0.000000e+00 1282
10 TraesCS3D01G150500 chr5A 88.191 796 62 11 4886 5657 632297414 632298201 0.000000e+00 920
11 TraesCS3D01G150500 chr4D 96.429 560 17 2 1 560 58652618 58653174 0.000000e+00 920
12 TraesCS3D01G150500 chr4D 94.931 217 11 0 5441 5657 69193741 69193525 1.950000e-89 340
13 TraesCS3D01G150500 chr1D 96.429 560 17 1 1 560 303307435 303306879 0.000000e+00 920
14 TraesCS3D01G150500 chr1D 95.431 569 17 7 1 560 424993268 424993836 0.000000e+00 898
15 TraesCS3D01G150500 chr1D 93.769 321 15 4 556 873 32538486 32538168 1.430000e-130 477
16 TraesCS3D01G150500 chr1D 93.987 316 16 3 556 868 415679002 415679317 5.130000e-130 475
17 TraesCS3D01G150500 chr1D 93.438 320 14 5 556 872 424994678 424994993 8.580000e-128 468
18 TraesCS3D01G150500 chr7D 87.688 796 77 17 4878 5657 187249098 187248308 0.000000e+00 907
19 TraesCS3D01G150500 chr7D 95.886 559 14 1 1 559 159077134 159077683 0.000000e+00 896
20 TraesCS3D01G150500 chr7D 94.903 569 20 7 1 560 199133710 199134278 0.000000e+00 881
21 TraesCS3D01G150500 chr7D 81.548 1008 176 9 2864 3866 425504693 425503691 0.000000e+00 822
22 TraesCS3D01G150500 chr7D 86.524 653 55 8 5038 5657 469201156 469200504 0.000000e+00 688
23 TraesCS3D01G150500 chr7D 93.458 321 17 4 556 873 565121817 565121498 1.840000e-129 473
24 TraesCS3D01G150500 chr7D 92.378 328 21 4 556 880 80195213 80195539 1.110000e-126 464
25 TraesCS3D01G150500 chr7D 84.298 363 52 5 3865 4223 425503618 425503257 3.240000e-92 350
26 TraesCS3D01G150500 chr7D 81.639 305 42 13 4365 4660 425503160 425502861 2.040000e-59 241
27 TraesCS3D01G150500 chr5D 94.903 569 20 7 1 560 117835247 117835815 0.000000e+00 881
28 TraesCS3D01G150500 chr5D 83.948 841 83 21 4864 5657 502077074 502076239 0.000000e+00 758
29 TraesCS3D01G150500 chr5D 93.730 319 15 4 556 869 117836635 117836953 1.840000e-129 473
30 TraesCS3D01G150500 chr7A 82.440 1008 167 9 2864 3866 507761325 507762327 0.000000e+00 872
31 TraesCS3D01G150500 chr7A 89.454 531 35 2 5148 5657 559364127 559364657 0.000000e+00 651
32 TraesCS3D01G150500 chr7A 84.573 363 51 5 3862 4220 507762390 507762751 6.970000e-94 355
33 TraesCS3D01G150500 chr7A 81.967 305 41 13 4365 4660 507762851 507763150 4.380000e-61 246
34 TraesCS3D01G150500 chr7B 81.647 1008 175 9 2864 3866 443294303 443293301 0.000000e+00 828
35 TraesCS3D01G150500 chr7B 84.573 363 51 5 3865 4223 443293215 443292854 6.970000e-94 355
36 TraesCS3D01G150500 chr7B 82.746 284 35 13 4386 4660 443292691 443292413 2.040000e-59 241
37 TraesCS3D01G150500 chr2D 85.472 826 83 9 4864 5657 197518978 197518158 0.000000e+00 826
38 TraesCS3D01G150500 chr2D 86.299 635 49 11 5061 5657 249898327 249898961 0.000000e+00 656
39 TraesCS3D01G150500 chr2D 93.789 322 14 5 556 871 6563087 6562766 3.960000e-131 479
40 TraesCS3D01G150500 chr2B 85.381 814 88 13 4869 5657 254519165 254518358 0.000000e+00 815
41 TraesCS3D01G150500 chr4A 84.390 820 96 16 4864 5656 435045248 435046062 0.000000e+00 776
42 TraesCS3D01G150500 chr2A 84.521 814 95 10 4871 5657 213892660 213891851 0.000000e+00 776
43 TraesCS3D01G150500 chr1A 84.664 789 91 13 4864 5627 486431412 486432195 0.000000e+00 760
44 TraesCS3D01G150500 chr6B 85.874 715 66 17 4887 5568 314511816 314511104 0.000000e+00 728
45 TraesCS3D01G150500 chr5B 83.378 740 79 17 4960 5657 409063258 409063995 0.000000e+00 645
46 TraesCS3D01G150500 chr6A 87.759 531 43 3 5148 5657 509555817 509555288 8.110000e-168 601
47 TraesCS3D01G150500 chr6D 94.953 317 11 4 556 869 27531562 27531248 5.090000e-135 492
48 TraesCS3D01G150500 chr6D 94.931 217 11 0 5441 5657 12111015 12110799 1.950000e-89 340


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 TraesCS3D01G150500 chr3D 115018116 115023772 5656 True 10447.000000 10447 100.000000 1 5657 1 chr3D.!!$R1 5656
1 TraesCS3D01G150500 chr3D 396432001 396432565 564 False 905.000000 905 95.760000 1 560 1 chr3D.!!$F2 559
2 TraesCS3D01G150500 chr3D 263005460 263006022 562 False 893.000000 893 95.382000 1 560 1 chr3D.!!$F1 559
3 TraesCS3D01G150500 chr3D 462456811 462457380 569 True 867.000000 867 94.386000 1 561 1 chr3D.!!$R2 560
4 TraesCS3D01G150500 chr3B 168679476 168683317 3841 True 2922.000000 5138 95.704000 869 4757 2 chr3B.!!$R1 3888
5 TraesCS3D01G150500 chr3B 727397711 727398468 757 False 880.000000 880 88.058000 4868 5608 1 chr3B.!!$F1 740
6 TraesCS3D01G150500 chr3A 111550290 111554111 3821 True 2688.500000 4095 92.120500 889 4848 2 chr3A.!!$R1 3959
7 TraesCS3D01G150500 chr5A 632297414 632298201 787 False 920.000000 920 88.191000 4886 5657 1 chr5A.!!$F1 771
8 TraesCS3D01G150500 chr4D 58652618 58653174 556 False 920.000000 920 96.429000 1 560 1 chr4D.!!$F1 559
9 TraesCS3D01G150500 chr1D 303306879 303307435 556 True 920.000000 920 96.429000 1 560 1 chr1D.!!$R2 559
10 TraesCS3D01G150500 chr1D 424993268 424994993 1725 False 683.000000 898 94.434500 1 872 2 chr1D.!!$F2 871
11 TraesCS3D01G150500 chr7D 187248308 187249098 790 True 907.000000 907 87.688000 4878 5657 1 chr7D.!!$R1 779
12 TraesCS3D01G150500 chr7D 159077134 159077683 549 False 896.000000 896 95.886000 1 559 1 chr7D.!!$F2 558
13 TraesCS3D01G150500 chr7D 199133710 199134278 568 False 881.000000 881 94.903000 1 560 1 chr7D.!!$F3 559
14 TraesCS3D01G150500 chr7D 469200504 469201156 652 True 688.000000 688 86.524000 5038 5657 1 chr7D.!!$R2 619
15 TraesCS3D01G150500 chr7D 425502861 425504693 1832 True 471.000000 822 82.495000 2864 4660 3 chr7D.!!$R4 1796
16 TraesCS3D01G150500 chr5D 502076239 502077074 835 True 758.000000 758 83.948000 4864 5657 1 chr5D.!!$R1 793
17 TraesCS3D01G150500 chr5D 117835247 117836953 1706 False 677.000000 881 94.316500 1 869 2 chr5D.!!$F1 868
18 TraesCS3D01G150500 chr7A 559364127 559364657 530 False 651.000000 651 89.454000 5148 5657 1 chr7A.!!$F1 509
19 TraesCS3D01G150500 chr7A 507761325 507763150 1825 False 491.000000 872 82.993333 2864 4660 3 chr7A.!!$F2 1796
20 TraesCS3D01G150500 chr7B 443292413 443294303 1890 True 474.666667 828 82.988667 2864 4660 3 chr7B.!!$R1 1796
21 TraesCS3D01G150500 chr2D 197518158 197518978 820 True 826.000000 826 85.472000 4864 5657 1 chr2D.!!$R2 793
22 TraesCS3D01G150500 chr2D 249898327 249898961 634 False 656.000000 656 86.299000 5061 5657 1 chr2D.!!$F1 596
23 TraesCS3D01G150500 chr2B 254518358 254519165 807 True 815.000000 815 85.381000 4869 5657 1 chr2B.!!$R1 788
24 TraesCS3D01G150500 chr4A 435045248 435046062 814 False 776.000000 776 84.390000 4864 5656 1 chr4A.!!$F1 792
25 TraesCS3D01G150500 chr2A 213891851 213892660 809 True 776.000000 776 84.521000 4871 5657 1 chr2A.!!$R1 786
26 TraesCS3D01G150500 chr1A 486431412 486432195 783 False 760.000000 760 84.664000 4864 5627 1 chr1A.!!$F1 763
27 TraesCS3D01G150500 chr6B 314511104 314511816 712 True 728.000000 728 85.874000 4887 5568 1 chr6B.!!$R1 681
28 TraesCS3D01G150500 chr5B 409063258 409063995 737 False 645.000000 645 83.378000 4960 5657 1 chr5B.!!$F1 697
29 TraesCS3D01G150500 chr6A 509555288 509555817 529 True 601.000000 601 87.759000 5148 5657 1 chr6A.!!$R1 509

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
717 1614 0.109689 CGTTTATTTTTGGGCGCGGA 60.110 50.0 8.83 0.00 0.0 5.54 F
1807 2748 0.037232 GAGAAGCACGCCAGGTAGTT 60.037 55.0 0.00 0.00 0.0 2.24 F
2423 3393 0.321564 TGCAGCTTTCTATGTGGCGT 60.322 50.0 0.00 0.00 0.0 5.68 F
2849 3837 0.321919 GCAGTCTTGGTCCATGCTGA 60.322 55.0 22.27 6.77 34.1 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2832 0.247460 CCGGATGCTGAGTGAGTGAA 59.753 55.0 0.00 0.0 0.00 3.18 R
3408 4396 0.913924 TCATGATCTCCTGCTTGCCA 59.086 50.0 0.00 0.0 0.00 4.92 R
4262 5342 0.605319 GAAGGTGCCCACGTTGATCA 60.605 55.0 10.65 0.0 39.23 2.92 R
4817 5912 0.110688 CACGTTGCGGAAGTGTGATG 60.111 55.0 14.41 0.0 32.39 3.07 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
57 58 2.045340 GTTCCCCCATGGACACCG 60.045 66.667 15.22 0.00 45.11 4.94
315 316 4.498520 CATGGACGCCGAGCTCGT 62.499 66.667 32.41 17.01 43.49 4.18
320 321 2.745100 ACGCCGAGCTCGTCTACA 60.745 61.111 32.41 0.00 34.84 2.74
482 531 1.421485 GCATGGAAAGTCGTCTGCG 59.579 57.895 0.00 0.00 39.92 5.18
531 580 1.371337 ATCGACACGTACTAGGCGCA 61.371 55.000 10.83 0.00 0.00 6.09
650 1547 6.189567 CGTTTCTGTTCTGATTTTTGTACGT 58.810 36.000 0.00 0.00 0.00 3.57
717 1614 0.109689 CGTTTATTTTTGGGCGCGGA 60.110 50.000 8.83 0.00 0.00 5.54
752 1655 2.399600 AATTTGCCAAGGCTGGGGGA 62.400 55.000 10.68 2.40 43.74 4.81
753 1656 2.810488 ATTTGCCAAGGCTGGGGGAG 62.810 60.000 10.68 0.00 43.74 4.30
835 1739 2.199652 CCCAGGGCGCAGTTTTTCA 61.200 57.895 10.83 0.00 0.00 2.69
836 1740 1.739049 CCAGGGCGCAGTTTTTCAA 59.261 52.632 10.83 0.00 0.00 2.69
839 1743 1.660264 GGGCGCAGTTTTTCAACGG 60.660 57.895 10.83 0.00 38.03 4.44
845 1750 1.028905 CAGTTTTTCAACGGCCTGGA 58.971 50.000 0.00 0.00 38.03 3.86
872 1777 0.599728 CGGCTGGAGATGCTCTTAGC 60.600 60.000 12.47 12.47 42.82 3.09
991 1896 1.210870 TACGTGGCGTGTCAAGTTTC 58.789 50.000 0.00 0.00 41.39 2.78
1029 1937 2.516888 CCACACCTCCCCGTTCACT 61.517 63.158 0.00 0.00 0.00 3.41
1283 2194 2.316792 CAACTTCAGACGAGTGGTACG 58.683 52.381 0.00 0.00 0.00 3.67
1286 2197 0.669619 TTCAGACGAGTGGTACGCAA 59.330 50.000 0.00 0.00 44.14 4.85
1298 2209 1.599419 GGTACGCAAGCAAACACTTGG 60.599 52.381 6.42 0.15 45.83 3.61
1302 2213 0.179103 GCAAGCAAACACTTGGCACT 60.179 50.000 6.42 0.00 45.83 4.40
1316 2227 0.807496 GGCACTGACAGAGCAATTCC 59.193 55.000 23.58 5.00 33.31 3.01
1319 2231 2.095364 GCACTGACAGAGCAATTCCTTG 60.095 50.000 18.55 0.00 31.92 3.61
1337 2249 1.375908 GATTCTCCTGCACCGCACA 60.376 57.895 0.00 0.00 33.79 4.57
1338 2250 0.745845 GATTCTCCTGCACCGCACAT 60.746 55.000 0.00 0.00 33.79 3.21
1339 2251 1.028330 ATTCTCCTGCACCGCACATG 61.028 55.000 0.00 0.00 33.79 3.21
1342 2283 3.807538 CCTGCACCGCACATGCTC 61.808 66.667 1.82 0.00 43.77 4.26
1349 2290 2.491621 CGCACATGCTCTCTCCGA 59.508 61.111 1.82 0.00 39.32 4.55
1362 2303 4.210955 GCTCTCTCCGATGATCAATCAAAC 59.789 45.833 0.00 0.00 40.69 2.93
1367 2308 4.588899 TCCGATGATCAATCAAACCAAGT 58.411 39.130 0.00 0.00 40.69 3.16
1368 2309 5.739959 TCCGATGATCAATCAAACCAAGTA 58.260 37.500 0.00 0.00 40.69 2.24
1371 2312 6.258160 CGATGATCAATCAAACCAAGTAACC 58.742 40.000 0.00 0.00 40.69 2.85
1374 2315 6.744112 TGATCAATCAAACCAAGTAACCAAC 58.256 36.000 0.00 0.00 33.08 3.77
1375 2316 5.523438 TCAATCAAACCAAGTAACCAACC 57.477 39.130 0.00 0.00 0.00 3.77
1376 2317 4.956700 TCAATCAAACCAAGTAACCAACCA 59.043 37.500 0.00 0.00 0.00 3.67
1377 2318 5.422331 TCAATCAAACCAAGTAACCAACCAA 59.578 36.000 0.00 0.00 0.00 3.67
1380 2321 2.375014 ACCAAGTAACCAACCAAGGG 57.625 50.000 0.00 0.00 0.00 3.95
1381 2322 1.854280 ACCAAGTAACCAACCAAGGGA 59.146 47.619 0.00 0.00 0.00 4.20
1386 2327 2.512476 AGTAACCAACCAAGGGACTGTT 59.488 45.455 0.00 0.00 40.86 3.16
1387 2328 1.775385 AACCAACCAAGGGACTGTTG 58.225 50.000 0.00 0.00 40.60 3.33
1388 2329 0.923358 ACCAACCAAGGGACTGTTGA 59.077 50.000 3.35 0.00 42.62 3.18
1389 2330 1.499007 ACCAACCAAGGGACTGTTGAT 59.501 47.619 3.35 0.00 42.62 2.57
1390 2331 2.091333 ACCAACCAAGGGACTGTTGATT 60.091 45.455 3.35 0.00 42.62 2.57
1391 2332 2.297033 CCAACCAAGGGACTGTTGATTG 59.703 50.000 3.35 0.00 42.62 2.67
1392 2333 1.620822 ACCAAGGGACTGTTGATTGC 58.379 50.000 0.00 0.00 40.86 3.56
1393 2334 1.145738 ACCAAGGGACTGTTGATTGCT 59.854 47.619 0.00 0.00 40.86 3.91
1805 2746 1.517257 CGAGAAGCACGCCAGGTAG 60.517 63.158 0.00 0.00 0.00 3.18
1806 2747 1.592223 GAGAAGCACGCCAGGTAGT 59.408 57.895 0.00 0.00 0.00 2.73
1807 2748 0.037232 GAGAAGCACGCCAGGTAGTT 60.037 55.000 0.00 0.00 0.00 2.24
1808 2749 0.396811 AGAAGCACGCCAGGTAGTTT 59.603 50.000 0.00 0.00 0.00 2.66
1809 2750 0.796927 GAAGCACGCCAGGTAGTTTC 59.203 55.000 0.00 0.00 0.00 2.78
1810 2751 0.949105 AAGCACGCCAGGTAGTTTCG 60.949 55.000 0.00 0.00 0.00 3.46
1811 2752 1.373748 GCACGCCAGGTAGTTTCGA 60.374 57.895 0.00 0.00 0.00 3.71
1812 2753 1.352156 GCACGCCAGGTAGTTTCGAG 61.352 60.000 0.00 0.00 0.00 4.04
1813 2754 1.080025 ACGCCAGGTAGTTTCGAGC 60.080 57.895 0.00 0.00 0.00 5.03
1815 2756 1.352156 CGCCAGGTAGTTTCGAGCAC 61.352 60.000 0.00 0.00 0.00 4.40
1816 2757 0.037232 GCCAGGTAGTTTCGAGCACT 60.037 55.000 4.86 4.86 0.00 4.40
1817 2758 1.203994 GCCAGGTAGTTTCGAGCACTA 59.796 52.381 3.09 3.09 0.00 2.74
1822 2763 5.168569 CAGGTAGTTTCGAGCACTAAATCA 58.831 41.667 7.86 0.00 0.00 2.57
1827 2768 5.168569 AGTTTCGAGCACTAAATCAATCGA 58.831 37.500 0.00 0.00 37.40 3.59
1833 2774 5.172232 CGAGCACTAAATCAATCGACACTAG 59.828 44.000 0.00 0.00 32.13 2.57
1834 2775 4.806247 AGCACTAAATCAATCGACACTAGC 59.194 41.667 0.00 0.00 0.00 3.42
1838 2779 6.090763 CACTAAATCAATCGACACTAGCAACA 59.909 38.462 0.00 0.00 0.00 3.33
1839 2780 4.928661 AATCAATCGACACTAGCAACAC 57.071 40.909 0.00 0.00 0.00 3.32
1840 2781 3.660501 TCAATCGACACTAGCAACACT 57.339 42.857 0.00 0.00 0.00 3.55
1866 2815 0.805711 TGAGTGCTGACGTGTGTGTG 60.806 55.000 0.00 0.00 0.00 3.82
1867 2816 2.094126 GAGTGCTGACGTGTGTGTGC 62.094 60.000 0.00 0.00 0.00 4.57
1868 2817 2.173669 GTGCTGACGTGTGTGTGCT 61.174 57.895 0.00 0.00 0.00 4.40
1869 2818 1.882625 TGCTGACGTGTGTGTGCTC 60.883 57.895 0.00 0.00 0.00 4.26
1883 2832 0.593128 GTGCTCTTCATGGCGTTGTT 59.407 50.000 0.00 0.00 0.00 2.83
1891 2840 1.601903 TCATGGCGTTGTTTCACTCAC 59.398 47.619 0.00 0.00 0.00 3.51
1892 2841 1.603802 CATGGCGTTGTTTCACTCACT 59.396 47.619 0.00 0.00 0.00 3.41
1893 2842 1.295792 TGGCGTTGTTTCACTCACTC 58.704 50.000 0.00 0.00 0.00 3.51
1894 2843 1.295792 GGCGTTGTTTCACTCACTCA 58.704 50.000 0.00 0.00 0.00 3.41
1968 2917 2.775856 GCAGGAGATCGACGAGGCA 61.776 63.158 3.01 0.00 0.00 4.75
1996 2945 3.371097 GAGATCCTGGCGGCGTTCA 62.371 63.158 9.37 6.84 0.00 3.18
2103 3052 2.430367 GTGCCCAAGTTCCTCCGT 59.570 61.111 0.00 0.00 0.00 4.69
2332 3281 5.411977 GTGCCATTCCTCAATCTCTATGATG 59.588 44.000 0.00 0.00 35.21 3.07
2382 3352 0.878523 TGGTTCAGTTTCTGACGGCG 60.879 55.000 4.80 4.80 40.46 6.46
2383 3353 1.204312 GTTCAGTTTCTGACGGCGC 59.796 57.895 6.90 0.00 40.46 6.53
2384 3354 1.959226 TTCAGTTTCTGACGGCGCC 60.959 57.895 19.07 19.07 40.46 6.53
2385 3355 2.652382 TTCAGTTTCTGACGGCGCCA 62.652 55.000 28.98 5.90 40.46 5.69
2400 3370 1.520787 GCCAGCCATGCATTTGCTC 60.521 57.895 15.79 4.65 42.66 4.26
2423 3393 0.321564 TGCAGCTTTCTATGTGGCGT 60.322 50.000 0.00 0.00 0.00 5.68
2426 3396 1.806542 CAGCTTTCTATGTGGCGTTGT 59.193 47.619 0.00 0.00 0.00 3.32
2517 3487 1.153524 GGTATGCATGCCCCATCCA 59.846 57.895 22.22 0.00 0.00 3.41
2518 3488 0.469705 GGTATGCATGCCCCATCCAA 60.470 55.000 22.22 0.00 0.00 3.53
2519 3489 1.636148 GTATGCATGCCCCATCCAAT 58.364 50.000 16.68 1.35 0.00 3.16
2520 3490 1.547372 GTATGCATGCCCCATCCAATC 59.453 52.381 16.68 0.00 0.00 2.67
2521 3491 0.834687 ATGCATGCCCCATCCAATCC 60.835 55.000 16.68 0.00 0.00 3.01
2522 3492 1.458020 GCATGCCCCATCCAATCCA 60.458 57.895 6.36 0.00 0.00 3.41
2523 3493 1.049855 GCATGCCCCATCCAATCCAA 61.050 55.000 6.36 0.00 0.00 3.53
2526 3496 2.267160 TGCCCCATCCAATCCAATTT 57.733 45.000 0.00 0.00 0.00 1.82
2531 3501 3.710677 CCCCATCCAATCCAATTTTGCTA 59.289 43.478 0.00 0.00 0.00 3.49
2538 3508 3.893326 ATCCAATTTTGCTAACAGCCC 57.107 42.857 0.00 0.00 41.51 5.19
2547 3517 0.673644 GCTAACAGCCCGCAGAAAGA 60.674 55.000 0.00 0.00 34.48 2.52
2548 3518 1.808411 CTAACAGCCCGCAGAAAGAA 58.192 50.000 0.00 0.00 0.00 2.52
2549 3519 2.151202 CTAACAGCCCGCAGAAAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
2553 3523 1.135286 CAGCCCGCAGAAAGAAATTCC 60.135 52.381 0.00 0.00 38.94 3.01
2554 3524 1.177401 GCCCGCAGAAAGAAATTCCT 58.823 50.000 0.00 0.00 38.94 3.36
2555 3525 1.546029 GCCCGCAGAAAGAAATTCCTT 59.454 47.619 0.00 0.00 38.94 3.36
2556 3526 2.029020 GCCCGCAGAAAGAAATTCCTTT 60.029 45.455 0.00 0.00 38.94 3.11
2557 3527 3.554960 GCCCGCAGAAAGAAATTCCTTTT 60.555 43.478 0.00 0.00 38.94 2.27
2558 3528 4.321675 GCCCGCAGAAAGAAATTCCTTTTA 60.322 41.667 0.00 0.00 38.94 1.52
2560 3530 5.633601 CCCGCAGAAAGAAATTCCTTTTAAC 59.366 40.000 0.00 0.00 38.94 2.01
2561 3531 6.447162 CCGCAGAAAGAAATTCCTTTTAACT 58.553 36.000 0.00 0.00 38.94 2.24
2562 3532 6.582672 CCGCAGAAAGAAATTCCTTTTAACTC 59.417 38.462 0.00 0.00 38.94 3.01
2563 3533 6.303259 CGCAGAAAGAAATTCCTTTTAACTCG 59.697 38.462 0.00 0.00 38.94 4.18
2564 3534 6.088217 GCAGAAAGAAATTCCTTTTAACTCGC 59.912 38.462 0.00 0.00 38.94 5.03
2565 3535 6.582672 CAGAAAGAAATTCCTTTTAACTCGCC 59.417 38.462 0.00 0.00 38.94 5.54
2566 3536 6.490381 AGAAAGAAATTCCTTTTAACTCGCCT 59.510 34.615 0.00 0.00 38.94 5.52
2567 3537 5.629079 AGAAATTCCTTTTAACTCGCCTG 57.371 39.130 0.00 0.00 0.00 4.85
2568 3538 5.313712 AGAAATTCCTTTTAACTCGCCTGA 58.686 37.500 0.00 0.00 0.00 3.86
2569 3539 5.181433 AGAAATTCCTTTTAACTCGCCTGAC 59.819 40.000 0.00 0.00 0.00 3.51
2570 3540 3.478857 TTCCTTTTAACTCGCCTGACA 57.521 42.857 0.00 0.00 0.00 3.58
2571 3541 3.478857 TCCTTTTAACTCGCCTGACAA 57.521 42.857 0.00 0.00 0.00 3.18
2572 3542 3.135994 TCCTTTTAACTCGCCTGACAAC 58.864 45.455 0.00 0.00 0.00 3.32
2573 3543 3.139077 CCTTTTAACTCGCCTGACAACT 58.861 45.455 0.00 0.00 0.00 3.16
2574 3544 3.058914 CCTTTTAACTCGCCTGACAACTG 60.059 47.826 0.00 0.00 0.00 3.16
2575 3545 3.462483 TTTAACTCGCCTGACAACTGA 57.538 42.857 0.00 0.00 0.00 3.41
2576 3546 3.462483 TTAACTCGCCTGACAACTGAA 57.538 42.857 0.00 0.00 0.00 3.02
2577 3547 2.550830 AACTCGCCTGACAACTGAAT 57.449 45.000 0.00 0.00 0.00 2.57
2578 3548 3.678056 AACTCGCCTGACAACTGAATA 57.322 42.857 0.00 0.00 0.00 1.75
2582 3552 4.393062 ACTCGCCTGACAACTGAATAATTG 59.607 41.667 0.00 0.00 0.00 2.32
2620 3600 3.225104 TGCAGAGTTTTGGAAGCAGATT 58.775 40.909 0.00 0.00 0.00 2.40
2647 3627 0.601311 GTGAGCCCTACCGCATCATC 60.601 60.000 0.00 0.00 0.00 2.92
2659 3639 1.287730 GCATCATCCTCGGCGATGTC 61.288 60.000 11.27 0.00 40.50 3.06
2772 3752 1.135689 CGAGGAGGTTGCCGAATTTTG 60.136 52.381 0.00 0.00 0.00 2.44
2773 3753 2.159382 GAGGAGGTTGCCGAATTTTGA 58.841 47.619 0.00 0.00 0.00 2.69
2776 3756 3.578282 AGGAGGTTGCCGAATTTTGATTT 59.422 39.130 0.00 0.00 0.00 2.17
2777 3757 3.926527 GGAGGTTGCCGAATTTTGATTTC 59.073 43.478 0.00 0.00 0.00 2.17
2778 3758 3.925379 AGGTTGCCGAATTTTGATTTCC 58.075 40.909 0.00 0.00 0.00 3.13
2796 3776 2.676748 TCCCCACTGCAAATGAGTTTT 58.323 42.857 0.00 0.00 0.00 2.43
2831 3819 9.922305 GAATCAAGTAGTACTACATTTTGATGC 57.078 33.333 30.35 27.54 37.93 3.91
2835 3823 8.383619 CAAGTAGTACTACATTTTGATGCAGTC 58.616 37.037 29.87 2.39 38.48 3.51
2838 3826 7.369803 AGTACTACATTTTGATGCAGTCTTG 57.630 36.000 0.00 0.00 31.21 3.02
2842 3830 3.256631 ACATTTTGATGCAGTCTTGGTCC 59.743 43.478 0.00 0.00 0.00 4.46
2847 3835 0.330604 ATGCAGTCTTGGTCCATGCT 59.669 50.000 14.68 6.37 37.76 3.79
2848 3836 0.607217 TGCAGTCTTGGTCCATGCTG 60.607 55.000 14.68 16.28 37.76 4.41
2849 3837 0.321919 GCAGTCTTGGTCCATGCTGA 60.322 55.000 22.27 6.77 34.10 4.26
2850 3838 1.446907 CAGTCTTGGTCCATGCTGAC 58.553 55.000 17.13 12.18 34.42 3.51
3408 4396 4.366267 ACTGGTACAAGGAGAGGATCAAT 58.634 43.478 1.45 0.00 38.70 2.57
4262 5342 4.080638 CCTCCTGAAGGTAAATGAGCTCTT 60.081 45.833 16.19 5.66 40.67 2.85
4267 5347 6.053632 TGAAGGTAAATGAGCTCTTGATCA 57.946 37.500 16.19 5.99 43.13 2.92
4274 5354 1.338105 TGAGCTCTTGATCAACGTGGG 60.338 52.381 16.19 0.00 35.49 4.61
4701 5794 3.135348 TCTCATGTCCTGGTCATGGATTC 59.865 47.826 26.26 0.00 41.79 2.52
4768 5863 4.379652 AGTGGAAATGTGCATTGGTTTTC 58.620 39.130 0.00 0.00 0.00 2.29
4772 5867 0.595588 ATGTGCATTGGTTTTCGCGA 59.404 45.000 3.71 3.71 0.00 5.87
4777 5872 2.728839 TGCATTGGTTTTCGCGATTTTC 59.271 40.909 10.88 0.99 0.00 2.29
4780 5875 4.432892 GCATTGGTTTTCGCGATTTTCTTC 60.433 41.667 10.88 0.00 0.00 2.87
4781 5876 4.561735 TTGGTTTTCGCGATTTTCTTCT 57.438 36.364 10.88 0.00 0.00 2.85
4782 5877 4.561735 TGGTTTTCGCGATTTTCTTCTT 57.438 36.364 10.88 0.00 0.00 2.52
4793 5888 6.953743 CGCGATTTTCTTCTTCTTCGAATTAA 59.046 34.615 0.00 0.00 0.00 1.40
4802 5897 5.977635 TCTTCTTCGAATTAATGAGCCTCA 58.022 37.500 0.00 0.00 0.00 3.86
4817 5912 1.379044 CTCAGGCCCCCAATGTCAC 60.379 63.158 0.00 0.00 0.00 3.67
4824 5919 1.176527 CCCCCAATGTCACATCACAC 58.823 55.000 0.00 0.00 0.00 3.82
4828 5923 2.489329 CCCAATGTCACATCACACTTCC 59.511 50.000 0.00 0.00 0.00 3.46
4855 5950 3.897325 GTGGTTCACGAAGGAAAAATCC 58.103 45.455 0.00 0.00 0.00 3.01
4856 5951 2.888414 TGGTTCACGAAGGAAAAATCCC 59.112 45.455 0.00 0.00 0.00 3.85
4857 5952 2.230508 GGTTCACGAAGGAAAAATCCCC 59.769 50.000 0.00 0.00 0.00 4.81
4858 5953 2.888414 GTTCACGAAGGAAAAATCCCCA 59.112 45.455 0.00 0.00 0.00 4.96
4859 5954 3.231207 TCACGAAGGAAAAATCCCCAA 57.769 42.857 0.00 0.00 0.00 4.12
4860 5955 3.567397 TCACGAAGGAAAAATCCCCAAA 58.433 40.909 0.00 0.00 0.00 3.28
4861 5956 4.156477 TCACGAAGGAAAAATCCCCAAAT 58.844 39.130 0.00 0.00 0.00 2.32
4862 5957 4.591072 TCACGAAGGAAAAATCCCCAAATT 59.409 37.500 0.00 0.00 0.00 1.82
4875 5970 3.272020 TCCCCAAATTTAAGGGCATCTCT 59.728 43.478 17.21 0.00 44.06 3.10
4945 6045 1.274167 GGTGATATATTCGGCGTGGGA 59.726 52.381 6.85 0.00 0.00 4.37
4976 6092 1.966451 CAGCCGACCCACCAAGTTC 60.966 63.158 0.00 0.00 0.00 3.01
4977 6093 3.047877 GCCGACCCACCAAGTTCG 61.048 66.667 0.00 0.00 0.00 3.95
4978 6094 3.047877 CCGACCCACCAAGTTCGC 61.048 66.667 0.00 0.00 0.00 4.70
5036 6180 0.034198 TCAGCCCAAATTCGACACGA 59.966 50.000 0.00 0.00 0.00 4.35
5042 6186 1.996898 CCAAATTCGACACGATTCGGA 59.003 47.619 11.29 2.67 39.58 4.55
5062 6207 6.316319 TCGGAACAAACTCAACAAAAAGTAC 58.684 36.000 0.00 0.00 0.00 2.73
5095 6241 9.234827 TCACATAGTTCATCACAGAAATGAATT 57.765 29.630 2.25 1.38 43.10 2.17
5333 6505 7.340122 TGAAATATGGTTCAGTGTCAAACAA 57.660 32.000 0.00 0.00 32.56 2.83
5457 6652 3.258228 AACAGCAGATGCCCGCTCA 62.258 57.895 0.14 0.00 43.38 4.26
5468 6663 1.452108 CCCGCTCAACATCCTTCCC 60.452 63.158 0.00 0.00 0.00 3.97
5642 6837 3.149196 GAGGAGCATGACCTTCAACAAA 58.851 45.455 12.07 0.00 37.93 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
262 263 2.435938 GCCTCATCCGCGGTGAAA 60.436 61.111 27.15 5.72 0.00 2.69
306 307 1.192757 CGTAGATGTAGACGAGCTCGG 59.807 57.143 36.93 20.54 44.95 4.63
315 316 1.215244 CTCGTCGCCGTAGATGTAGA 58.785 55.000 0.00 0.00 35.01 2.59
320 321 2.544698 GCTCCTCGTCGCCGTAGAT 61.545 63.158 0.00 0.00 35.01 1.98
340 341 0.032217 CCTCTTCCTCCTGCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
482 531 4.736896 GCCGGTGGTCAGGTCGAC 62.737 72.222 7.13 7.13 44.57 4.20
531 580 0.389948 GTCGAACTCGGCCTTGATGT 60.390 55.000 0.00 0.00 38.15 3.06
613 1510 2.357034 AAACGCGCATCAGACGGT 60.357 55.556 5.73 0.00 0.00 4.83
650 1547 1.924524 GGCGATCGATGAAAAGTTCGA 59.075 47.619 21.57 0.00 38.98 3.71
676 1573 1.882625 CAATCCGGCGATCAAGCGA 60.883 57.895 9.30 0.00 38.18 4.93
787 1690 2.365105 CTAGTTCGGCCCCTGGGA 60.365 66.667 16.20 0.00 37.50 4.37
872 1777 1.535204 GGGTCATTGGGTGGCTGTTG 61.535 60.000 0.00 0.00 31.47 3.33
873 1778 1.228862 GGGTCATTGGGTGGCTGTT 60.229 57.895 0.00 0.00 31.47 3.16
874 1779 2.017668 TTGGGTCATTGGGTGGCTGT 62.018 55.000 0.00 0.00 31.47 4.40
991 1896 3.056821 TGGAGGGAAATCATCGCGTATAG 60.057 47.826 5.77 0.00 45.24 1.31
1029 1937 1.683917 GGCTCGAGCTTTATCAGGAGA 59.316 52.381 34.46 0.00 41.70 3.71
1283 2194 0.179103 AGTGCCAAGTGTTTGCTTGC 60.179 50.000 0.00 0.00 43.17 4.01
1286 2197 0.740737 GTCAGTGCCAAGTGTTTGCT 59.259 50.000 0.00 0.00 32.79 3.91
1298 2209 1.818642 AGGAATTGCTCTGTCAGTGC 58.181 50.000 17.98 17.98 35.45 4.40
1302 2213 4.914983 AGAATCAAGGAATTGCTCTGTCA 58.085 39.130 0.00 0.00 0.00 3.58
1316 2227 0.674581 TGCGGTGCAGGAGAATCAAG 60.675 55.000 0.00 0.00 31.31 3.02
1319 2231 0.745845 ATGTGCGGTGCAGGAGAATC 60.746 55.000 0.00 0.00 40.08 2.52
1337 2249 3.577415 TGATTGATCATCGGAGAGAGCAT 59.423 43.478 0.00 0.00 43.63 3.79
1338 2250 2.961062 TGATTGATCATCGGAGAGAGCA 59.039 45.455 0.00 0.00 43.63 4.26
1339 2251 3.657015 TGATTGATCATCGGAGAGAGC 57.343 47.619 0.00 0.00 43.63 4.09
1342 2283 4.445453 TGGTTTGATTGATCATCGGAGAG 58.555 43.478 0.00 0.00 43.63 3.20
1349 2290 7.378181 GTTGGTTACTTGGTTTGATTGATCAT 58.622 34.615 0.00 0.00 36.56 2.45
1362 2303 2.158519 AGTCCCTTGGTTGGTTACTTGG 60.159 50.000 0.00 0.00 0.00 3.61
1367 2308 2.510382 TCAACAGTCCCTTGGTTGGTTA 59.490 45.455 0.00 0.00 41.59 2.85
1368 2309 1.286553 TCAACAGTCCCTTGGTTGGTT 59.713 47.619 0.00 0.00 41.59 3.67
1371 2312 2.288395 GCAATCAACAGTCCCTTGGTTG 60.288 50.000 0.00 0.00 41.03 3.77
1374 2315 1.542915 CAGCAATCAACAGTCCCTTGG 59.457 52.381 0.00 0.00 0.00 3.61
1375 2316 1.542915 CCAGCAATCAACAGTCCCTTG 59.457 52.381 0.00 0.00 0.00 3.61
1376 2317 1.145738 ACCAGCAATCAACAGTCCCTT 59.854 47.619 0.00 0.00 0.00 3.95
1377 2318 0.773644 ACCAGCAATCAACAGTCCCT 59.226 50.000 0.00 0.00 0.00 4.20
1380 2321 3.780925 GCACCAGCAATCAACAGTC 57.219 52.632 0.00 0.00 41.58 3.51
1391 2332 3.655810 CTCCTCGACCTGCACCAGC 62.656 68.421 0.00 0.00 42.57 4.85
1392 2333 2.279069 ACTCCTCGACCTGCACCAG 61.279 63.158 0.00 0.00 0.00 4.00
1393 2334 2.203640 ACTCCTCGACCTGCACCA 60.204 61.111 0.00 0.00 0.00 4.17
1805 2746 5.163992 TGTCGATTGATTTAGTGCTCGAAAC 60.164 40.000 0.00 0.00 36.95 2.78
1806 2747 4.926832 TGTCGATTGATTTAGTGCTCGAAA 59.073 37.500 0.00 0.00 36.95 3.46
1807 2748 4.326278 GTGTCGATTGATTTAGTGCTCGAA 59.674 41.667 0.00 0.00 36.95 3.71
1808 2749 3.857665 GTGTCGATTGATTTAGTGCTCGA 59.142 43.478 0.00 0.00 33.23 4.04
1809 2750 3.859961 AGTGTCGATTGATTTAGTGCTCG 59.140 43.478 0.00 0.00 0.00 5.03
1810 2751 5.051374 GCTAGTGTCGATTGATTTAGTGCTC 60.051 44.000 0.00 0.00 0.00 4.26
1811 2752 4.806247 GCTAGTGTCGATTGATTTAGTGCT 59.194 41.667 0.00 0.00 0.00 4.40
1812 2753 4.566759 TGCTAGTGTCGATTGATTTAGTGC 59.433 41.667 0.00 0.00 0.00 4.40
1813 2754 6.090763 TGTTGCTAGTGTCGATTGATTTAGTG 59.909 38.462 0.00 0.00 0.00 2.74
1815 2756 6.311445 AGTGTTGCTAGTGTCGATTGATTTAG 59.689 38.462 0.00 0.00 0.00 1.85
1816 2757 6.163476 AGTGTTGCTAGTGTCGATTGATTTA 58.837 36.000 0.00 0.00 0.00 1.40
1817 2758 4.997395 AGTGTTGCTAGTGTCGATTGATTT 59.003 37.500 0.00 0.00 0.00 2.17
1838 2779 1.537638 CGTCAGCACTCACTCACTAGT 59.462 52.381 0.00 0.00 35.91 2.57
1839 2780 1.537638 ACGTCAGCACTCACTCACTAG 59.462 52.381 0.00 0.00 0.00 2.57
1840 2781 1.266989 CACGTCAGCACTCACTCACTA 59.733 52.381 0.00 0.00 0.00 2.74
1842 2783 0.249073 ACACGTCAGCACTCACTCAC 60.249 55.000 0.00 0.00 0.00 3.51
1866 2815 1.266718 TGAAACAACGCCATGAAGAGC 59.733 47.619 0.00 0.00 0.00 4.09
1867 2816 2.549754 AGTGAAACAACGCCATGAAGAG 59.450 45.455 0.00 0.00 41.43 2.85
1868 2817 2.548057 GAGTGAAACAACGCCATGAAGA 59.452 45.455 0.00 0.00 41.43 2.87
1869 2818 2.290367 TGAGTGAAACAACGCCATGAAG 59.710 45.455 0.00 0.00 41.43 3.02
1883 2832 0.247460 CCGGATGCTGAGTGAGTGAA 59.753 55.000 0.00 0.00 0.00 3.18
1891 2840 2.887568 GCACGTCCGGATGCTGAG 60.888 66.667 23.85 11.99 38.84 3.35
1892 2841 4.451150 GGCACGTCCGGATGCTGA 62.451 66.667 25.15 0.00 41.74 4.26
1893 2842 4.457496 AGGCACGTCCGGATGCTG 62.457 66.667 25.15 20.82 41.74 4.41
1894 2843 4.457496 CAGGCACGTCCGGATGCT 62.457 66.667 25.15 12.33 41.74 3.79
1968 2917 0.690411 CCAGGATCTCCCTCTGCAGT 60.690 60.000 14.67 0.00 45.60 4.40
2233 3182 3.386237 GAGCAGGCAGACGTCCCT 61.386 66.667 13.01 9.91 0.00 4.20
2332 3281 2.746277 AACCGGCATCGACTTGGC 60.746 61.111 0.00 2.62 39.00 4.52
2382 3352 1.520787 GAGCAAATGCATGGCTGGC 60.521 57.895 25.65 9.27 45.16 4.85
2383 3353 1.226859 CGAGCAAATGCATGGCTGG 60.227 57.895 25.65 21.19 45.16 4.85
2384 3354 0.800683 CACGAGCAAATGCATGGCTG 60.801 55.000 25.65 19.60 45.16 4.85
2385 3355 1.246056 ACACGAGCAAATGCATGGCT 61.246 50.000 22.07 22.07 45.16 4.75
2400 3370 1.129251 CCACATAGAAAGCTGCACACG 59.871 52.381 1.02 0.00 0.00 4.49
2423 3393 1.210931 CCGGAGCTCGTCGTTACAA 59.789 57.895 7.83 0.00 37.11 2.41
2426 3396 3.818787 GCCCGGAGCTCGTCGTTA 61.819 66.667 0.73 0.00 38.99 3.18
2517 3487 3.368323 CGGGCTGTTAGCAAAATTGGATT 60.368 43.478 2.99 0.00 44.75 3.01
2518 3488 2.166254 CGGGCTGTTAGCAAAATTGGAT 59.834 45.455 2.99 0.00 44.75 3.41
2519 3489 1.543802 CGGGCTGTTAGCAAAATTGGA 59.456 47.619 2.99 0.00 44.75 3.53
2520 3490 1.994916 CGGGCTGTTAGCAAAATTGG 58.005 50.000 2.99 0.00 44.75 3.16
2521 3491 1.336702 TGCGGGCTGTTAGCAAAATTG 60.337 47.619 2.99 0.00 44.75 2.32
2522 3492 0.965439 TGCGGGCTGTTAGCAAAATT 59.035 45.000 2.99 0.00 44.75 1.82
2523 3493 0.527565 CTGCGGGCTGTTAGCAAAAT 59.472 50.000 2.99 0.00 44.75 1.82
2526 3496 0.536233 TTTCTGCGGGCTGTTAGCAA 60.536 50.000 2.99 0.00 44.75 3.91
2531 3501 1.620822 ATTTCTTTCTGCGGGCTGTT 58.379 45.000 0.00 0.00 0.00 3.16
2538 3508 6.303259 CGAGTTAAAAGGAATTTCTTTCTGCG 59.697 38.462 12.22 8.38 36.09 5.18
2547 3517 4.825085 TGTCAGGCGAGTTAAAAGGAATTT 59.175 37.500 0.00 0.00 34.92 1.82
2548 3518 4.394729 TGTCAGGCGAGTTAAAAGGAATT 58.605 39.130 0.00 0.00 0.00 2.17
2549 3519 4.015872 TGTCAGGCGAGTTAAAAGGAAT 57.984 40.909 0.00 0.00 0.00 3.01
2553 3523 3.807622 TCAGTTGTCAGGCGAGTTAAAAG 59.192 43.478 0.00 0.00 0.00 2.27
2554 3524 3.799366 TCAGTTGTCAGGCGAGTTAAAA 58.201 40.909 0.00 0.00 0.00 1.52
2555 3525 3.462483 TCAGTTGTCAGGCGAGTTAAA 57.538 42.857 0.00 0.00 0.00 1.52
2556 3526 3.462483 TTCAGTTGTCAGGCGAGTTAA 57.538 42.857 0.00 0.00 0.00 2.01
2557 3527 3.678056 ATTCAGTTGTCAGGCGAGTTA 57.322 42.857 0.00 0.00 0.00 2.24
2558 3528 2.550830 ATTCAGTTGTCAGGCGAGTT 57.449 45.000 0.00 0.00 0.00 3.01
2560 3530 4.201851 CCAATTATTCAGTTGTCAGGCGAG 60.202 45.833 0.00 0.00 0.00 5.03
2561 3531 3.689161 CCAATTATTCAGTTGTCAGGCGA 59.311 43.478 0.00 0.00 0.00 5.54
2562 3532 3.731867 GCCAATTATTCAGTTGTCAGGCG 60.732 47.826 0.00 0.00 0.00 5.52
2563 3533 3.193267 TGCCAATTATTCAGTTGTCAGGC 59.807 43.478 0.00 0.00 38.82 4.85
2564 3534 5.389859 TTGCCAATTATTCAGTTGTCAGG 57.610 39.130 0.00 0.00 0.00 3.86
2565 3535 6.215121 TGTTTGCCAATTATTCAGTTGTCAG 58.785 36.000 0.00 0.00 0.00 3.51
2566 3536 6.154203 TGTTTGCCAATTATTCAGTTGTCA 57.846 33.333 0.00 0.00 0.00 3.58
2567 3537 7.384660 TGAATGTTTGCCAATTATTCAGTTGTC 59.615 33.333 10.86 0.00 34.04 3.18
2568 3538 7.215789 TGAATGTTTGCCAATTATTCAGTTGT 58.784 30.769 10.86 0.00 34.04 3.32
2569 3539 7.655236 TGAATGTTTGCCAATTATTCAGTTG 57.345 32.000 10.86 0.00 34.04 3.16
2570 3540 7.879160 ACATGAATGTTTGCCAATTATTCAGTT 59.121 29.630 16.70 7.93 40.02 3.16
2571 3541 7.332430 CACATGAATGTTTGCCAATTATTCAGT 59.668 33.333 16.70 13.13 40.02 3.41
2572 3542 7.675403 GCACATGAATGTTTGCCAATTATTCAG 60.675 37.037 16.70 12.73 40.02 3.02
2573 3543 6.092396 GCACATGAATGTTTGCCAATTATTCA 59.908 34.615 15.00 15.00 39.39 2.57
2574 3544 6.314400 AGCACATGAATGTTTGCCAATTATTC 59.686 34.615 0.00 7.04 39.39 1.75
2575 3545 6.092944 CAGCACATGAATGTTTGCCAATTATT 59.907 34.615 0.00 0.00 39.39 1.40
2576 3546 5.583061 CAGCACATGAATGTTTGCCAATTAT 59.417 36.000 0.00 0.00 39.39 1.28
2577 3547 4.930405 CAGCACATGAATGTTTGCCAATTA 59.070 37.500 0.00 0.00 39.39 1.40
2578 3548 3.749088 CAGCACATGAATGTTTGCCAATT 59.251 39.130 0.00 0.00 39.39 2.32
2582 3552 1.073177 GCAGCACATGAATGTTTGCC 58.927 50.000 14.43 2.88 40.30 4.52
2647 3627 3.147595 TCCCTGACATCGCCGAGG 61.148 66.667 0.00 0.00 0.00 4.63
2659 3639 1.873591 GTGTTGTACAGCTTGTCCCTG 59.126 52.381 11.22 0.00 36.41 4.45
2772 3752 2.827921 ACTCATTTGCAGTGGGGAAATC 59.172 45.455 6.08 0.00 44.57 2.17
2773 3753 2.893424 ACTCATTTGCAGTGGGGAAAT 58.107 42.857 6.08 0.00 46.94 2.17
2776 3756 2.380064 AAACTCATTTGCAGTGGGGA 57.620 45.000 6.08 0.00 0.00 4.81
2777 3757 4.280677 TCTTAAAACTCATTTGCAGTGGGG 59.719 41.667 6.08 0.00 32.27 4.96
2778 3758 5.452078 TCTTAAAACTCATTTGCAGTGGG 57.548 39.130 0.00 0.00 32.27 4.61
2819 3799 4.458989 GGACCAAGACTGCATCAAAATGTA 59.541 41.667 0.00 0.00 35.18 2.29
2820 3800 3.256631 GGACCAAGACTGCATCAAAATGT 59.743 43.478 0.00 0.00 35.18 2.71
2821 3801 3.256383 TGGACCAAGACTGCATCAAAATG 59.744 43.478 0.00 0.00 35.87 2.32
2822 3802 3.499338 TGGACCAAGACTGCATCAAAAT 58.501 40.909 0.00 0.00 0.00 1.82
2831 3819 1.446907 GTCAGCATGGACCAAGACTG 58.553 55.000 13.10 13.10 36.16 3.51
2842 3830 2.746269 CAACAAACCAAGGTCAGCATG 58.254 47.619 0.00 0.00 37.54 4.06
2847 3835 1.846007 ACTGCAACAAACCAAGGTCA 58.154 45.000 0.00 0.00 0.00 4.02
2848 3836 2.427095 AGAACTGCAACAAACCAAGGTC 59.573 45.455 0.00 0.00 0.00 3.85
2849 3837 2.456577 AGAACTGCAACAAACCAAGGT 58.543 42.857 0.00 0.00 0.00 3.50
2850 3838 3.189285 CAAGAACTGCAACAAACCAAGG 58.811 45.455 0.00 0.00 0.00 3.61
2851 3839 3.119173 TCCAAGAACTGCAACAAACCAAG 60.119 43.478 0.00 0.00 0.00 3.61
2852 3840 2.828520 TCCAAGAACTGCAACAAACCAA 59.171 40.909 0.00 0.00 0.00 3.67
2853 3841 2.426738 CTCCAAGAACTGCAACAAACCA 59.573 45.455 0.00 0.00 0.00 3.67
2854 3842 2.799562 GCTCCAAGAACTGCAACAAACC 60.800 50.000 0.00 0.00 0.00 3.27
2855 3843 2.463876 GCTCCAAGAACTGCAACAAAC 58.536 47.619 0.00 0.00 0.00 2.93
3408 4396 0.913924 TCATGATCTCCTGCTTGCCA 59.086 50.000 0.00 0.00 0.00 4.92
4262 5342 0.605319 GAAGGTGCCCACGTTGATCA 60.605 55.000 10.65 0.00 39.23 2.92
4361 5441 3.118454 CGTGCCCAGCAACCTACG 61.118 66.667 0.00 0.00 41.47 3.51
4718 5811 7.175816 TCACCGATCCTCTTCTAATATTCAGAG 59.824 40.741 10.39 10.39 33.77 3.35
4727 5820 4.081642 CCACTTTCACCGATCCTCTTCTAA 60.082 45.833 0.00 0.00 0.00 2.10
4768 5863 3.972706 TCGAAGAAGAAGAAAATCGCG 57.027 42.857 0.00 0.00 0.00 5.87
4772 5867 9.780413 GCTCATTAATTCGAAGAAGAAGAAAAT 57.220 29.630 3.35 0.00 45.90 1.82
4777 5872 6.536582 TGAGGCTCATTAATTCGAAGAAGAAG 59.463 38.462 14.43 3.85 45.90 2.85
4780 5875 5.236047 CCTGAGGCTCATTAATTCGAAGAAG 59.764 44.000 19.11 0.51 45.90 2.85
4781 5876 5.118990 CCTGAGGCTCATTAATTCGAAGAA 58.881 41.667 19.11 0.48 45.90 2.52
4782 5877 4.697514 CCTGAGGCTCATTAATTCGAAGA 58.302 43.478 19.11 0.00 0.00 2.87
4802 5897 1.307647 GATGTGACATTGGGGGCCT 59.692 57.895 0.84 0.00 0.00 5.19
4807 5902 2.489329 GGAAGTGTGATGTGACATTGGG 59.511 50.000 0.00 0.00 0.00 4.12
4817 5912 0.110688 CACGTTGCGGAAGTGTGATG 60.111 55.000 14.41 0.00 32.39 3.07
4824 5919 1.278637 GTGAACCACGTTGCGGAAG 59.721 57.895 0.00 0.00 0.00 3.46
4843 5938 6.884295 CCCTTAAATTTGGGGATTTTTCCTTC 59.116 38.462 20.05 0.00 42.58 3.46
4845 5940 5.280985 GCCCTTAAATTTGGGGATTTTTCCT 60.281 40.000 25.66 0.00 43.53 3.36
4847 5942 5.565509 TGCCCTTAAATTTGGGGATTTTTC 58.434 37.500 25.66 12.85 43.53 2.29
4848 5943 5.590976 TGCCCTTAAATTTGGGGATTTTT 57.409 34.783 25.66 0.00 43.53 1.94
4854 5949 3.646534 AGAGATGCCCTTAAATTTGGGG 58.353 45.455 20.27 20.27 43.53 4.96
4855 5950 4.279420 GCTAGAGATGCCCTTAAATTTGGG 59.721 45.833 8.89 8.89 46.00 4.12
4856 5951 4.279420 GGCTAGAGATGCCCTTAAATTTGG 59.721 45.833 0.00 0.00 44.32 3.28
4857 5952 5.444663 GGCTAGAGATGCCCTTAAATTTG 57.555 43.478 0.00 0.00 44.32 2.32
4891 5991 1.017387 CGGCACTATTTCAAGCCCTC 58.983 55.000 0.00 0.00 44.18 4.30
4945 6045 4.035102 GGCTGGAAACCCGAGCCT 62.035 66.667 10.24 0.00 41.10 4.58
5036 6180 6.394809 ACTTTTTGTTGAGTTTGTTCCGAAT 58.605 32.000 0.00 0.00 0.00 3.34
5333 6505 2.188994 GCGAGCAGGAAGAGCCAT 59.811 61.111 0.00 0.00 40.02 4.40
5457 6652 1.678970 GGCTTGCGGGAAGGATGTT 60.679 57.895 11.34 0.00 31.56 2.71
5468 6663 1.302033 AAGTGTCAGGAGGCTTGCG 60.302 57.895 0.00 0.00 0.00 4.85
5511 6706 1.227823 TGTCTCAAACCCTGTGCCG 60.228 57.895 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.