Multiple sequence alignment - TraesCS5A01G456100

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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 TraesCS5A01G456100 chr5A 100.000 6488 0 0 1 6488 636419964 636413477 0.000000e+00 11982.0
1 TraesCS5A01G456100 chr5A 91.135 282 24 1 6067 6348 636305949 636306229 1.320000e-101 381.0
2 TraesCS5A01G456100 chr5A 82.051 429 41 18 2468 2890 378671846 378672244 3.750000e-87 333.0
3 TraesCS5A01G456100 chr5A 93.182 44 3 0 6445 6488 636306289 636306332 1.510000e-06 65.8
4 TraesCS5A01G456100 chr5A 94.595 37 2 0 570 606 224700812 224700848 2.530000e-04 58.4
5 TraesCS5A01G456100 chr5D 92.755 2664 129 29 944 3555 509142191 509139540 0.000000e+00 3792.0
6 TraesCS5A01G456100 chr5D 93.995 1682 93 6 4811 6488 509138184 509136507 0.000000e+00 2540.0
7 TraesCS5A01G456100 chr5D 96.696 1271 35 5 3548 4812 509139512 509138243 0.000000e+00 2108.0
8 TraesCS5A01G456100 chr5D 85.452 763 68 22 90 829 509142978 509142236 0.000000e+00 754.0
9 TraesCS5A01G456100 chr5D 92.473 279 21 0 6080 6358 509020294 509020572 3.640000e-107 399.0
10 TraesCS5A01G456100 chr5D 95.327 107 3 2 1 106 509144328 509144223 1.120000e-37 169.0
11 TraesCS5A01G456100 chr5D 98.039 51 1 0 853 903 509142243 509142193 8.960000e-14 89.8
12 TraesCS5A01G456100 chr5D 93.617 47 3 0 6442 6488 509020631 509020677 3.250000e-08 71.3
13 TraesCS5A01G456100 chr5B 94.360 2181 94 15 4319 6487 639679608 639677445 0.000000e+00 3319.0
14 TraesCS5A01G456100 chr5B 91.584 2020 111 26 942 2924 639683270 639681273 0.000000e+00 2734.0
15 TraesCS5A01G456100 chr5B 96.005 776 28 3 3548 4321 639680495 639679721 0.000000e+00 1258.0
16 TraesCS5A01G456100 chr5B 95.833 456 12 1 3107 3555 639680978 639680523 0.000000e+00 730.0
17 TraesCS5A01G456100 chr5B 89.619 289 28 2 6070 6358 639620076 639620362 3.700000e-97 366.0
18 TraesCS5A01G456100 chr5B 96.914 162 5 0 2908 3069 639681138 639680977 8.290000e-69 272.0
19 TraesCS5A01G456100 chr5B 90.476 126 5 3 798 923 639683377 639683259 6.730000e-35 159.0
20 TraesCS5A01G456100 chr3A 82.650 732 106 16 2167 2884 328751039 328751763 4.270000e-176 628.0
21 TraesCS5A01G456100 chr3A 82.093 430 42 17 2467 2890 646305127 646305527 1.040000e-87 335.0
22 TraesCS5A01G456100 chr3A 92.857 168 10 2 4666 4831 607058405 607058572 6.500000e-60 243.0
23 TraesCS5A01G456100 chr3A 97.436 39 0 1 568 606 40144817 40144780 1.510000e-06 65.8
24 TraesCS5A01G456100 chr2D 83.488 430 35 20 2467 2890 465956230 465955831 1.030000e-97 368.0
25 TraesCS5A01G456100 chr6B 82.558 430 39 19 2467 2890 301624370 301624769 4.820000e-91 346.0
26 TraesCS5A01G456100 chr7A 82.093 430 41 18 2467 2890 9404864 9405263 1.040000e-87 335.0
27 TraesCS5A01G456100 chr7A 92.771 166 10 2 4672 4835 494786990 494786825 8.410000e-59 239.0
28 TraesCS5A01G456100 chr6A 81.860 430 43 18 2467 2890 61180869 61181269 4.850000e-86 329.0
29 TraesCS5A01G456100 chr6A 92.727 165 10 2 4672 4834 442395555 442395719 3.020000e-58 237.0
30 TraesCS5A01G456100 chr7D 84.091 264 40 2 6082 6344 88149857 88149595 3.000000e-63 254.0
31 TraesCS5A01G456100 chr4B 95.031 161 7 1 4672 4831 103804479 103804639 1.080000e-62 252.0
32 TraesCS5A01G456100 chr4B 93.827 162 8 2 4672 4831 28724143 28724304 6.500000e-60 243.0
33 TraesCS5A01G456100 chr4B 88.000 50 3 3 570 617 646248625 646248577 1.000000e-03 56.5
34 TraesCS5A01G456100 chr4D 93.827 162 8 2 4672 4831 75266909 75266748 6.500000e-60 243.0
35 TraesCS5A01G456100 chr2A 91.011 178 14 2 4664 4839 184561323 184561146 8.410000e-59 239.0
36 TraesCS5A01G456100 chr1B 100.000 36 0 0 573 608 31829692 31829657 4.200000e-07 67.6
37 TraesCS5A01G456100 chr4A 97.297 37 1 0 570 606 696290939 696290903 5.430000e-06 63.9
38 TraesCS5A01G456100 chr2B 100.000 34 0 0 575 608 799591088 799591121 5.430000e-06 63.9
39 TraesCS5A01G456100 chrUn 100.000 32 0 0 575 606 60419604 60419573 7.030000e-05 60.2
40 TraesCS5A01G456100 chr7B 100.000 31 0 0 577 607 15022202 15022232 2.530000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G456100 chr5A 636413477 636419964 6487 True 11982.000000 11982 100.000000 1 6488 1 chr5A.!!$R1 6487
1 TraesCS5A01G456100 chr5D 509136507 509144328 7821 True 1575.466667 3792 93.710667 1 6488 6 chr5D.!!$R1 6487
2 TraesCS5A01G456100 chr5B 639677445 639683377 5932 True 1412.000000 3319 94.195333 798 6487 6 chr5B.!!$R1 5689
3 TraesCS5A01G456100 chr3A 328751039 328751763 724 False 628.000000 628 82.650000 2167 2884 1 chr3A.!!$F1 717

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
333 1596 0.321996 GTGTTGTCCACTCCCTCCTC 59.678 60.000 0.00 0.00 41.11 3.71 F
906 2216 0.391661 CAATCCGAGGTCACCCTGTG 60.392 60.000 0.00 0.00 42.86 3.66 F
1283 2620 0.107312 CTGTTATGGCTCCTGCTGCT 60.107 55.000 0.00 0.00 39.59 4.24 F
1672 3012 0.251341 GGAGGCTTCCAGCTTTCCAA 60.251 55.000 10.56 0.00 43.45 3.53 F
1675 3015 0.533951 GGCTTCCAGCTTTCCAATGG 59.466 55.000 0.00 0.00 41.99 3.16 F
1679 3019 1.075601 TCCAGCTTTCCAATGGTCCT 58.924 50.000 0.00 0.00 35.51 3.85 F
2716 4078 1.204231 GAGTACGAACACTCCTTCCCC 59.796 57.143 0.00 0.00 39.26 4.81 F
3669 5239 1.869767 GCTGCATATCTGAAAGGTCCG 59.130 52.381 0.00 0.00 0.00 4.79 F
3947 5520 1.971695 GCCATGTATTAGCGGGCCC 60.972 63.158 13.57 13.57 38.70 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 2582 0.440371 GTGCACGAGCTTAGCAGAAC 59.560 55.000 7.07 0.00 42.74 3.01 R
2143 3487 0.911525 TGGCTCCTCCTCTTCCTTGG 60.912 60.000 0.00 0.00 35.26 3.61 R
2261 3605 1.204467 GATGCAAGGAAAAATCCGGCA 59.796 47.619 15.90 15.90 44.48 5.69 R
3275 4802 1.351350 AGTTGGGTAGCCAGGAGTTTC 59.649 52.381 14.38 0.95 0.00 2.78 R
3375 4909 3.676646 ACGACTGTACGCTTTCCAAATAC 59.323 43.478 0.00 0.00 36.70 1.89 R
3669 5239 8.999431 TCTTCTGGTTGTCAATTAATACTGTTC 58.001 33.333 0.00 0.00 0.00 3.18 R
3947 5520 3.553917 TGCACGTGTATCGGATATGTTTG 59.446 43.478 18.38 0.00 44.69 2.93 R
5412 7172 0.319297 AAAGTACAGACGACCCGCAC 60.319 55.000 0.00 0.00 0.00 5.34 R
5828 7588 2.290641 GGTGCTATTACCAGGCAAATCG 59.709 50.000 0.00 0.00 40.54 3.34 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
36 37 9.465199 TGATGACTTCAAAATTCATCCAGATTA 57.535 29.630 13.95 0.00 43.21 1.75
159 1422 4.451096 TCTCAACATTTTAAGGCGTGACTC 59.549 41.667 0.00 0.00 0.00 3.36
175 1438 2.289820 TGACTCATACGCGTCATAGGAC 59.710 50.000 18.63 10.45 40.77 3.85
197 1460 3.741245 AGAGAGCTAACTAGTCCACCA 57.259 47.619 0.00 0.00 0.00 4.17
200 1463 5.134661 AGAGAGCTAACTAGTCCACCATAC 58.865 45.833 0.00 0.00 0.00 2.39
201 1464 4.216708 AGAGCTAACTAGTCCACCATACC 58.783 47.826 0.00 0.00 0.00 2.73
227 1490 7.070571 CCATCTTCCTCAACTAATAGTCTTCCT 59.929 40.741 0.00 0.00 0.00 3.36
230 1493 8.881262 TCTTCCTCAACTAATAGTCTTCCTTTT 58.119 33.333 0.00 0.00 0.00 2.27
234 1497 9.152595 CCTCAACTAATAGTCTTCCTTTTACAC 57.847 37.037 0.00 0.00 0.00 2.90
235 1498 9.930693 CTCAACTAATAGTCTTCCTTTTACACT 57.069 33.333 0.00 0.00 0.00 3.55
241 1504 4.377897 AGTCTTCCTTTTACACTTGACCG 58.622 43.478 0.00 0.00 0.00 4.79
245 1508 1.796459 CCTTTTACACTTGACCGTCCG 59.204 52.381 0.00 0.00 0.00 4.79
251 1514 2.432628 CTTGACCGTCCGCTCACC 60.433 66.667 0.00 0.00 0.00 4.02
291 1554 4.873827 GTGTGTTCTCCTACTGTGTTTTCA 59.126 41.667 0.00 0.00 0.00 2.69
292 1555 5.527582 GTGTGTTCTCCTACTGTGTTTTCAT 59.472 40.000 0.00 0.00 0.00 2.57
293 1556 5.758296 TGTGTTCTCCTACTGTGTTTTCATC 59.242 40.000 0.00 0.00 0.00 2.92
294 1557 5.992217 GTGTTCTCCTACTGTGTTTTCATCT 59.008 40.000 0.00 0.00 0.00 2.90
295 1558 6.146347 GTGTTCTCCTACTGTGTTTTCATCTC 59.854 42.308 0.00 0.00 0.00 2.75
296 1559 6.042093 TGTTCTCCTACTGTGTTTTCATCTCT 59.958 38.462 0.00 0.00 0.00 3.10
297 1560 6.274157 TCTCCTACTGTGTTTTCATCTCTC 57.726 41.667 0.00 0.00 0.00 3.20
299 1562 7.175797 TCTCCTACTGTGTTTTCATCTCTCTA 58.824 38.462 0.00 0.00 0.00 2.43
300 1563 7.670140 TCTCCTACTGTGTTTTCATCTCTCTAA 59.330 37.037 0.00 0.00 0.00 2.10
301 1564 7.603651 TCCTACTGTGTTTTCATCTCTCTAAC 58.396 38.462 0.00 0.00 0.00 2.34
302 1565 7.451877 TCCTACTGTGTTTTCATCTCTCTAACT 59.548 37.037 0.00 0.00 0.00 2.24
303 1566 8.091449 CCTACTGTGTTTTCATCTCTCTAACTT 58.909 37.037 0.00 0.00 0.00 2.66
306 1569 9.832445 ACTGTGTTTTCATCTCTCTAACTTAAA 57.168 29.630 0.00 0.00 0.00 1.52
308 1571 9.607988 TGTGTTTTCATCTCTCTAACTTAAACA 57.392 29.630 0.00 0.00 32.47 2.83
310 1573 9.832445 TGTTTTCATCTCTCTAACTTAAACACT 57.168 29.630 0.00 0.00 30.64 3.55
313 1576 9.477484 TTTCATCTCTCTAACTTAAACACTGTC 57.523 33.333 0.00 0.00 0.00 3.51
314 1577 7.306213 TCATCTCTCTAACTTAAACACTGTCG 58.694 38.462 0.00 0.00 0.00 4.35
315 1578 6.630444 TCTCTCTAACTTAAACACTGTCGT 57.370 37.500 0.00 0.00 0.00 4.34
316 1579 6.436261 TCTCTCTAACTTAAACACTGTCGTG 58.564 40.000 0.00 0.00 46.63 4.35
328 1591 0.600255 CTGTCGTGTTGTCCACTCCC 60.600 60.000 0.00 0.00 42.20 4.30
333 1596 0.321996 GTGTTGTCCACTCCCTCCTC 59.678 60.000 0.00 0.00 41.11 3.71
354 1617 4.973168 TCTGTGCTTGAATTCTACTTGGT 58.027 39.130 7.05 0.00 0.00 3.67
355 1618 5.376625 TCTGTGCTTGAATTCTACTTGGTT 58.623 37.500 7.05 0.00 0.00 3.67
356 1619 5.827797 TCTGTGCTTGAATTCTACTTGGTTT 59.172 36.000 7.05 0.00 0.00 3.27
358 1621 5.827797 TGTGCTTGAATTCTACTTGGTTTCT 59.172 36.000 7.05 0.00 0.00 2.52
363 1643 9.561270 GCTTGAATTCTACTTGGTTTCTTAATC 57.439 33.333 7.05 0.00 0.00 1.75
371 1651 1.271488 TGGTTTCTTAATCGGGGCGTT 60.271 47.619 0.00 0.00 0.00 4.84
376 1656 1.170442 CTTAATCGGGGCGTTGGTTT 58.830 50.000 0.00 0.00 0.00 3.27
398 1678 6.590656 TTCCTAATCAACCACCCATCTAAT 57.409 37.500 0.00 0.00 0.00 1.73
466 1748 0.527565 GCCATTGTCGCCAATCACTT 59.472 50.000 0.00 0.00 39.28 3.16
467 1749 1.742831 GCCATTGTCGCCAATCACTTA 59.257 47.619 0.00 0.00 39.28 2.24
475 1757 5.294356 TGTCGCCAATCACTTATATACACC 58.706 41.667 0.00 0.00 0.00 4.16
498 1783 1.801178 CCTTTGTCGCTTCTTCTCCAC 59.199 52.381 0.00 0.00 0.00 4.02
562 1872 4.082463 CCTCTCTTCTTCTTCTAGTTGCGT 60.082 45.833 0.00 0.00 0.00 5.24
563 1873 4.799678 TCTCTTCTTCTTCTAGTTGCGTG 58.200 43.478 0.00 0.00 0.00 5.34
569 1879 3.319137 TCTTCTAGTTGCGTGCTCATT 57.681 42.857 0.00 0.00 0.00 2.57
570 1880 4.450082 TCTTCTAGTTGCGTGCTCATTA 57.550 40.909 0.00 0.00 0.00 1.90
574 1884 2.185004 AGTTGCGTGCTCATTAGGTT 57.815 45.000 0.00 0.00 0.00 3.50
575 1885 3.328382 AGTTGCGTGCTCATTAGGTTA 57.672 42.857 0.00 0.00 0.00 2.85
576 1886 3.262420 AGTTGCGTGCTCATTAGGTTAG 58.738 45.455 0.00 0.00 0.00 2.34
577 1887 3.000727 GTTGCGTGCTCATTAGGTTAGT 58.999 45.455 0.00 0.00 0.00 2.24
578 1888 2.616960 TGCGTGCTCATTAGGTTAGTG 58.383 47.619 0.00 0.00 0.00 2.74
579 1889 1.933853 GCGTGCTCATTAGGTTAGTGG 59.066 52.381 0.00 0.00 0.00 4.00
580 1890 2.550978 CGTGCTCATTAGGTTAGTGGG 58.449 52.381 0.00 0.00 0.00 4.61
582 1892 2.504175 GTGCTCATTAGGTTAGTGGGGA 59.496 50.000 0.00 0.00 0.00 4.81
584 1894 3.136443 TGCTCATTAGGTTAGTGGGGATG 59.864 47.826 0.00 0.00 0.00 3.51
585 1895 3.391296 GCTCATTAGGTTAGTGGGGATGA 59.609 47.826 0.00 0.00 0.00 2.92
586 1896 4.743955 GCTCATTAGGTTAGTGGGGATGAC 60.744 50.000 0.00 0.00 0.00 3.06
587 1897 3.714798 TCATTAGGTTAGTGGGGATGACC 59.285 47.826 0.00 0.00 39.11 4.02
588 1898 3.502051 TTAGGTTAGTGGGGATGACCT 57.498 47.619 0.00 0.00 42.93 3.85
589 1899 4.630382 TTAGGTTAGTGGGGATGACCTA 57.370 45.455 0.00 0.00 40.90 3.08
590 1900 3.726837 AGGTTAGTGGGGATGACCTAT 57.273 47.619 0.00 0.00 38.88 2.57
591 1901 4.022359 AGGTTAGTGGGGATGACCTATT 57.978 45.455 0.00 0.00 38.88 1.73
592 1902 4.380791 AGGTTAGTGGGGATGACCTATTT 58.619 43.478 0.00 0.00 38.88 1.40
593 1903 5.544682 AGGTTAGTGGGGATGACCTATTTA 58.455 41.667 0.00 0.00 38.88 1.40
594 1904 5.607171 AGGTTAGTGGGGATGACCTATTTAG 59.393 44.000 0.00 0.00 38.88 1.85
664 1974 9.802039 TGTTTGGTAGGTATTTCTTCAATAACT 57.198 29.630 0.00 0.00 45.84 2.24
791 2101 8.504812 AAAAACTGAAATGTAAATGCAAACCT 57.495 26.923 0.00 0.00 0.00 3.50
794 2104 6.996509 ACTGAAATGTAAATGCAAACCTGAT 58.003 32.000 0.00 0.00 0.00 2.90
795 2105 7.092716 ACTGAAATGTAAATGCAAACCTGATC 58.907 34.615 0.00 0.00 0.00 2.92
796 2106 6.397272 TGAAATGTAAATGCAAACCTGATCC 58.603 36.000 0.00 0.00 0.00 3.36
813 2123 3.588842 TGATCCTCCACCACAAAAGAGAT 59.411 43.478 0.00 0.00 0.00 2.75
821 2131 5.047377 TCCACCACAAAAGAGATAAAATGGC 60.047 40.000 0.00 0.00 0.00 4.40
836 2146 3.249986 AATGGCACATTTTCCATTCCG 57.750 42.857 0.00 0.00 46.90 4.30
837 2147 0.894141 TGGCACATTTTCCATTCCGG 59.106 50.000 0.00 0.00 0.00 5.14
843 2153 1.944234 ATTTTCCATTCCGGGCGCAC 61.944 55.000 10.83 3.71 34.36 5.34
903 2213 1.995626 CCCAATCCGAGGTCACCCT 60.996 63.158 0.00 0.00 46.66 4.34
904 2214 1.221840 CCAATCCGAGGTCACCCTG 59.778 63.158 0.00 0.00 42.86 4.45
905 2215 1.553690 CCAATCCGAGGTCACCCTGT 61.554 60.000 0.00 0.00 42.86 4.00
906 2216 0.391661 CAATCCGAGGTCACCCTGTG 60.392 60.000 0.00 0.00 42.86 3.66
907 2217 2.185310 AATCCGAGGTCACCCTGTGC 62.185 60.000 0.00 0.00 42.86 4.57
908 2218 4.394712 CCGAGGTCACCCTGTGCC 62.395 72.222 0.00 0.00 42.86 5.01
909 2219 4.394712 CGAGGTCACCCTGTGCCC 62.395 72.222 0.00 0.00 42.86 5.36
910 2220 3.249189 GAGGTCACCCTGTGCCCA 61.249 66.667 0.00 0.00 42.86 5.36
911 2221 2.532715 AGGTCACCCTGTGCCCAT 60.533 61.111 0.00 0.00 40.58 4.00
912 2222 2.142292 GAGGTCACCCTGTGCCCATT 62.142 60.000 0.00 0.00 42.86 3.16
913 2223 1.678970 GGTCACCCTGTGCCCATTC 60.679 63.158 0.00 0.00 31.26 2.67
914 2224 1.678970 GTCACCCTGTGCCCATTCC 60.679 63.158 0.00 0.00 32.98 3.01
915 2225 2.159490 TCACCCTGTGCCCATTCCA 61.159 57.895 0.00 0.00 32.98 3.53
916 2226 1.228831 CACCCTGTGCCCATTCCAA 60.229 57.895 0.00 0.00 0.00 3.53
917 2227 0.831288 CACCCTGTGCCCATTCCAAA 60.831 55.000 0.00 0.00 0.00 3.28
918 2228 0.831711 ACCCTGTGCCCATTCCAAAC 60.832 55.000 0.00 0.00 0.00 2.93
919 2229 1.543944 CCCTGTGCCCATTCCAAACC 61.544 60.000 0.00 0.00 0.00 3.27
920 2230 0.542702 CCTGTGCCCATTCCAAACCT 60.543 55.000 0.00 0.00 0.00 3.50
921 2231 1.272425 CCTGTGCCCATTCCAAACCTA 60.272 52.381 0.00 0.00 0.00 3.08
922 2232 1.818674 CTGTGCCCATTCCAAACCTAC 59.181 52.381 0.00 0.00 0.00 3.18
923 2233 1.427368 TGTGCCCATTCCAAACCTACT 59.573 47.619 0.00 0.00 0.00 2.57
924 2234 2.158385 TGTGCCCATTCCAAACCTACTT 60.158 45.455 0.00 0.00 0.00 2.24
925 2235 2.897326 GTGCCCATTCCAAACCTACTTT 59.103 45.455 0.00 0.00 0.00 2.66
926 2236 3.323691 GTGCCCATTCCAAACCTACTTTT 59.676 43.478 0.00 0.00 0.00 2.27
927 2237 3.323403 TGCCCATTCCAAACCTACTTTTG 59.677 43.478 0.00 0.00 36.40 2.44
928 2238 3.323691 GCCCATTCCAAACCTACTTTTGT 59.676 43.478 0.00 0.00 35.09 2.83
929 2239 4.560716 GCCCATTCCAAACCTACTTTTGTC 60.561 45.833 0.00 0.00 35.09 3.18
930 2240 4.832823 CCCATTCCAAACCTACTTTTGTCT 59.167 41.667 0.00 0.00 35.09 3.41
931 2241 6.007703 CCCATTCCAAACCTACTTTTGTCTA 58.992 40.000 0.00 0.00 35.09 2.59
932 2242 6.492087 CCCATTCCAAACCTACTTTTGTCTAA 59.508 38.462 0.00 0.00 35.09 2.10
933 2243 7.014808 CCCATTCCAAACCTACTTTTGTCTAAA 59.985 37.037 0.00 0.00 35.09 1.85
934 2244 8.417884 CCATTCCAAACCTACTTTTGTCTAAAA 58.582 33.333 0.00 0.00 35.09 1.52
935 2245 9.810545 CATTCCAAACCTACTTTTGTCTAAAAA 57.189 29.630 0.00 0.00 35.50 1.94
1014 2324 2.419198 GCGATGCAGATCCTCCGT 59.581 61.111 0.00 0.00 0.00 4.69
1240 2577 2.349755 GGCCGCACAGGGTTTAGA 59.650 61.111 0.00 0.00 41.48 2.10
1245 2582 1.202651 CCGCACAGGGTTTAGATAGGG 60.203 57.143 0.00 0.00 35.97 3.53
1254 2591 5.130477 CAGGGTTTAGATAGGGTTCTGCTAA 59.870 44.000 0.00 0.00 0.00 3.09
1283 2620 0.107312 CTGTTATGGCTCCTGCTGCT 60.107 55.000 0.00 0.00 39.59 4.24
1294 2631 1.155042 CCTGCTGCTCTGTTCAGTTC 58.845 55.000 0.00 0.00 34.21 3.01
1327 2664 1.379642 GGGAGAATTCGCTTGGCAGG 61.380 60.000 9.15 0.00 33.73 4.85
1354 2691 5.126396 GCAGTTCCTTGCTATTTTGTTCT 57.874 39.130 0.00 0.00 40.89 3.01
1376 2713 5.647658 TCTGTGGTTCCATTGATATGTTCAC 59.352 40.000 0.00 0.00 32.84 3.18
1386 2723 5.432885 TTGATATGTTCACTAGCGATCGA 57.567 39.130 21.57 0.00 32.84 3.59
1387 2724 5.432885 TGATATGTTCACTAGCGATCGAA 57.567 39.130 21.57 4.71 0.00 3.71
1399 2736 2.352651 AGCGATCGAACAAATGTCATGG 59.647 45.455 21.57 0.00 0.00 3.66
1402 2739 4.671508 GCGATCGAACAAATGTCATGGAAA 60.672 41.667 21.57 0.00 0.00 3.13
1405 2742 3.057596 TCGAACAAATGTCATGGAAAGCC 60.058 43.478 0.00 0.00 0.00 4.35
1407 2744 4.559300 CGAACAAATGTCATGGAAAGCCTT 60.559 41.667 0.00 0.00 34.31 4.35
1416 2754 5.221601 TGTCATGGAAAGCCTTTTGCAATTA 60.222 36.000 0.00 0.00 45.78 1.40
1419 2757 6.941436 TCATGGAAAGCCTTTTGCAATTATTT 59.059 30.769 0.00 0.00 45.78 1.40
1423 2761 6.857451 GGAAAGCCTTTTGCAATTATTTTGTG 59.143 34.615 0.00 0.00 44.83 3.33
1433 2773 6.779117 TGCAATTATTTTGTGTTTGTTGTGG 58.221 32.000 0.00 0.00 0.00 4.17
1436 2776 8.127954 GCAATTATTTTGTGTTTGTTGTGGAAT 58.872 29.630 0.00 0.00 0.00 3.01
1446 2786 5.293814 TGTTTGTTGTGGAATGCTCAAATTG 59.706 36.000 0.00 0.00 0.00 2.32
1462 2802 7.594758 TGCTCAAATTGTATGTTCTACTTTTGC 59.405 33.333 0.00 0.00 0.00 3.68
1463 2803 7.594758 GCTCAAATTGTATGTTCTACTTTTGCA 59.405 33.333 0.00 0.00 0.00 4.08
1467 2807 7.701539 ATTGTATGTTCTACTTTTGCATCCA 57.298 32.000 0.00 0.00 0.00 3.41
1491 2831 0.392461 ATCGTGGTGTGAATTCCCCG 60.392 55.000 2.27 3.88 0.00 5.73
1509 2849 1.640428 CGTGCGACCAACAGTCATAT 58.360 50.000 0.00 0.00 46.69 1.78
1513 2853 1.737236 GCGACCAACAGTCATATTGCA 59.263 47.619 0.00 0.00 46.69 4.08
1517 2857 4.083324 CGACCAACAGTCATATTGCAACTT 60.083 41.667 0.00 0.00 46.69 2.66
1563 2903 5.122396 GCATATTCCAACCTAGATTTAGCCG 59.878 44.000 0.00 0.00 0.00 5.52
1567 2907 3.773119 TCCAACCTAGATTTAGCCGAGTT 59.227 43.478 0.00 0.00 0.00 3.01
1568 2908 4.957954 TCCAACCTAGATTTAGCCGAGTTA 59.042 41.667 0.00 0.00 0.00 2.24
1569 2909 5.422970 TCCAACCTAGATTTAGCCGAGTTAA 59.577 40.000 0.00 0.00 0.00 2.01
1583 2923 6.885922 AGCCGAGTTAATTAGTATTTGGTCT 58.114 36.000 0.00 0.00 0.00 3.85
1602 2942 2.037641 TCTATCGGCTTGACATGGATGG 59.962 50.000 0.00 0.00 0.00 3.51
1642 2982 9.781834 TGTTATTGAAGTTGTTTTCTACAGTTG 57.218 29.630 0.00 0.00 38.19 3.16
1672 3012 0.251341 GGAGGCTTCCAGCTTTCCAA 60.251 55.000 10.56 0.00 43.45 3.53
1673 3013 1.618074 GGAGGCTTCCAGCTTTCCAAT 60.618 52.381 10.56 0.00 43.45 3.16
1674 3014 1.475682 GAGGCTTCCAGCTTTCCAATG 59.524 52.381 0.00 0.00 41.99 2.82
1675 3015 0.533951 GGCTTCCAGCTTTCCAATGG 59.466 55.000 0.00 0.00 41.99 3.16
1676 3016 1.260544 GCTTCCAGCTTTCCAATGGT 58.739 50.000 0.00 0.00 38.45 3.55
1677 3017 1.203287 GCTTCCAGCTTTCCAATGGTC 59.797 52.381 0.00 0.00 38.45 4.02
1678 3018 1.821136 CTTCCAGCTTTCCAATGGTCC 59.179 52.381 0.00 0.00 35.51 4.46
1679 3019 1.075601 TCCAGCTTTCCAATGGTCCT 58.924 50.000 0.00 0.00 35.51 3.85
1680 3020 2.274542 TCCAGCTTTCCAATGGTCCTA 58.725 47.619 0.00 0.00 35.51 2.94
1692 3032 6.013379 TCCAATGGTCCTAAAAATAACTGCA 58.987 36.000 0.00 0.00 0.00 4.41
1715 3058 8.035394 TGCAAAACTTCTGGTGTACATTTTTAA 58.965 29.630 0.00 0.00 0.00 1.52
1764 3107 8.435430 GTCTTAATTTTGCTAATGCCTTTTCAC 58.565 33.333 0.00 0.00 38.71 3.18
1769 3112 6.892658 TTTGCTAATGCCTTTTCACTTCTA 57.107 33.333 0.00 0.00 38.71 2.10
1824 3167 4.271776 CGATGCTTGCATTGACTTGAGATA 59.728 41.667 15.68 0.00 0.00 1.98
1868 3211 8.463930 AAACTTGGAAATGTGATACAGAGAAA 57.536 30.769 0.00 0.00 0.00 2.52
1882 3225 7.819415 TGATACAGAGAAAAGGTGTGTGATTAG 59.181 37.037 0.00 0.00 0.00 1.73
1895 3238 6.540189 GGTGTGTGATTAGCTGATTACATCTT 59.460 38.462 17.33 0.00 29.78 2.40
2036 3380 4.582240 CCCTCCATATTTCCTCAAGCTTTC 59.418 45.833 0.00 0.00 0.00 2.62
2053 3397 7.121168 TCAAGCTTTCTGGTTTATATTCACCTG 59.879 37.037 0.00 4.66 33.63 4.00
2100 3444 7.711772 AGAGCAATCACTCTTATCATTTCTGAG 59.288 37.037 0.00 0.00 44.76 3.35
2143 3487 5.682862 GGTGATAAAATCGCATCATTCACAC 59.317 40.000 0.00 0.00 41.46 3.82
2261 3605 6.515035 GCAAGCTAATGTTGGTCTTGTTACTT 60.515 38.462 0.00 0.00 37.17 2.24
2265 3609 1.944024 TGTTGGTCTTGTTACTTGCCG 59.056 47.619 0.00 0.00 0.00 5.69
2285 3629 4.518970 GCCGGATTTTTCCTTGCATCTATA 59.481 41.667 5.05 0.00 0.00 1.31
2324 3674 6.369890 TCACACAAAATGCTCTCATCTTAGAC 59.630 38.462 0.00 0.00 31.27 2.59
2368 3726 2.627699 AGGACATGCCAACAACGAAAAT 59.372 40.909 8.58 0.00 40.02 1.82
2376 3734 7.870445 ACATGCCAACAACGAAAATATAACTTT 59.130 29.630 0.00 0.00 0.00 2.66
2716 4078 1.204231 GAGTACGAACACTCCTTCCCC 59.796 57.143 0.00 0.00 39.26 4.81
2809 4182 6.453926 TTTGTACCCTGTCCTTGTTAAAAC 57.546 37.500 0.00 0.00 0.00 2.43
2834 4209 3.861689 GCTCCTGTGCAATTTTTCATAGC 59.138 43.478 0.00 0.00 0.00 2.97
2872 4248 6.519679 TTCTGGTTACATCTTACGAAGCTA 57.480 37.500 0.00 0.00 0.00 3.32
2946 4473 2.432456 CGAGCAGTGTTAGCCGCA 60.432 61.111 0.00 0.00 0.00 5.69
2968 4495 5.578776 CACTGAAGGTACCAAACAAAGTTC 58.421 41.667 15.94 6.98 0.00 3.01
3275 4802 3.996363 GGCCAAATTAACCTGCTTTTGAG 59.004 43.478 0.00 0.00 32.17 3.02
3544 5078 3.496331 TCCCTGTTTTCTTGTCATTCCC 58.504 45.455 0.00 0.00 0.00 3.97
3581 5150 7.225538 CCATGTAGTAATGACTTCATCTGGAAC 59.774 40.741 4.21 0.00 40.57 3.62
3669 5239 1.869767 GCTGCATATCTGAAAGGTCCG 59.130 52.381 0.00 0.00 0.00 4.79
3830 5400 6.038825 AGTGCTGCTGTAGACATAGTAGTTAG 59.961 42.308 0.00 0.00 29.96 2.34
3870 5440 7.433131 CAGTGGACAAAATTATCAATTCCGATG 59.567 37.037 0.00 0.00 0.00 3.84
3947 5520 1.971695 GCCATGTATTAGCGGGCCC 60.972 63.158 13.57 13.57 38.70 5.80
3964 5537 2.812011 GGCCCAAACATATCCGATACAC 59.188 50.000 0.00 0.00 0.00 2.90
3976 5549 3.331150 TCCGATACACGTGCATTTTTCT 58.669 40.909 17.22 0.00 40.78 2.52
3984 5557 4.915085 ACACGTGCATTTTTCTTAATTCGG 59.085 37.500 17.22 0.00 0.00 4.30
4152 5725 9.974980 GGTTAAAGTAAATTTTGATTGAGACCA 57.025 29.630 0.00 0.00 32.01 4.02
4440 6129 9.880157 TTATGGGTTGAGTATTAGTAAGTCAAC 57.120 33.333 18.60 18.60 44.08 3.18
4482 6171 5.880332 GGTACTTCTCATATTTTGTGGCTCA 59.120 40.000 0.00 0.00 0.00 4.26
4493 6182 4.935352 TTTGTGGCTCAAAATAAGCACT 57.065 36.364 11.93 0.00 42.18 4.40
4505 6194 7.939782 TCAAAATAAGCACTCTTGTCAAATGA 58.060 30.769 0.00 0.00 33.85 2.57
4508 6197 4.675190 AAGCACTCTTGTCAAATGATCG 57.325 40.909 0.00 0.00 0.00 3.69
4588 6277 6.572509 GCTTGGAGTGAGTGATAGTGTTCTAA 60.573 42.308 0.00 0.00 0.00 2.10
4642 6332 8.893219 ACATACCTGATGGATAATTATATGCG 57.107 34.615 0.00 0.00 40.18 4.73
4920 6678 7.639039 CAAAAGCAGTAAACAGTAGTTCATGA 58.361 34.615 0.00 0.00 36.84 3.07
5006 6764 7.114754 TCTCTTATCATCAATTGTTTGAGGCT 58.885 34.615 15.51 0.00 44.75 4.58
5086 6844 3.714280 TGCTGGATAATGGCCTTACAGTA 59.286 43.478 3.32 0.00 0.00 2.74
5111 6870 7.001674 ACTTGTAAGTTGATGGTACCATTTCA 58.998 34.615 27.97 20.24 35.21 2.69
5321 7081 3.118075 TGTTGAAGTGGGTGAGAACATCA 60.118 43.478 0.00 0.00 34.79 3.07
5412 7172 8.162878 AGCTGTATTATTCTGAACATGAATGG 57.837 34.615 0.00 0.00 35.90 3.16
5433 7193 1.012486 GCGGGTCGTCTGTACTTTGG 61.012 60.000 0.00 0.00 0.00 3.28
5447 7207 7.116519 GTCTGTACTTTGGTAGCTAAGTTCTTG 59.883 40.741 23.14 15.53 36.16 3.02
5473 7233 9.366216 GGTAAAAATTCACTGAAACTGTTTTCT 57.634 29.630 7.28 0.00 41.64 2.52
5492 7252 3.470868 TCTATTTCAGGGCCTAAGGGTT 58.529 45.455 5.28 0.00 34.45 4.11
5526 7286 2.926586 GCTTTGTTCTCCGAAATTGGGC 60.927 50.000 0.00 0.00 0.00 5.36
5698 7458 4.625311 TGTACACGCTGACATTAAGATGTG 59.375 41.667 0.00 0.00 46.27 3.21
5775 7535 5.280164 TGTGCAAAACGCCAATCATATATG 58.720 37.500 6.36 6.36 41.33 1.78
5813 7573 5.923733 TGTTGTTCCTTGTATGGTTTTGT 57.076 34.783 0.00 0.00 0.00 2.83
5919 7679 6.838198 CATTTATGCACTGGATTTGAATGG 57.162 37.500 0.00 0.00 0.00 3.16
5949 7709 1.937223 GCCGGTTTTGGTTTGAAAAGG 59.063 47.619 1.90 0.00 0.00 3.11
6031 7792 4.388773 TGTACACTTTCTAAAGCTGCATCG 59.611 41.667 1.02 0.00 39.63 3.84
6033 7794 4.256920 ACACTTTCTAAAGCTGCATCGAT 58.743 39.130 1.02 0.00 39.63 3.59
6246 8007 4.047059 GCGAGGAACCCGACGACA 62.047 66.667 0.00 0.00 32.43 4.35
6385 8147 1.780309 TCAGGTGGGGTTCACTGAATT 59.220 47.619 0.00 0.00 45.38 2.17
6405 8175 3.350219 TCTCAGGTATTCAGGTTTGGC 57.650 47.619 0.00 0.00 0.00 4.52
6406 8176 2.009774 CTCAGGTATTCAGGTTTGGCG 58.990 52.381 0.00 0.00 0.00 5.69
6407 8177 1.349688 TCAGGTATTCAGGTTTGGCGT 59.650 47.619 0.00 0.00 0.00 5.68
6408 8178 1.468520 CAGGTATTCAGGTTTGGCGTG 59.531 52.381 0.00 0.00 0.00 5.34
6409 8179 0.808755 GGTATTCAGGTTTGGCGTGG 59.191 55.000 0.00 0.00 34.05 4.94
6410 8180 0.808755 GTATTCAGGTTTGGCGTGGG 59.191 55.000 0.00 0.00 34.05 4.61
6440 8210 8.555361 GGAGAAGAGTTAGAATGTTGCATTATC 58.445 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 1380 9.921637 TGTTGAGAGAAACTTGTTACAAATTTT 57.078 25.926 6.00 5.23 0.00 1.82
133 1396 5.049680 GTCACGCCTTAAAATGTTGAGAGAA 60.050 40.000 0.00 0.00 0.00 2.87
140 1403 5.163893 CGTATGAGTCACGCCTTAAAATGTT 60.164 40.000 0.00 0.00 31.94 2.71
159 1422 3.995048 TCTCTAGTCCTATGACGCGTATG 59.005 47.826 13.97 2.16 46.51 2.39
175 1438 4.783055 TGGTGGACTAGTTAGCTCTCTAG 58.217 47.826 17.89 17.89 39.37 2.43
195 1458 5.630415 TTAGTTGAGGAAGATGGGTATGG 57.370 43.478 0.00 0.00 0.00 2.74
197 1460 8.013667 AGACTATTAGTTGAGGAAGATGGGTAT 58.986 37.037 0.00 0.00 0.00 2.73
200 1463 6.739331 AGACTATTAGTTGAGGAAGATGGG 57.261 41.667 0.00 0.00 0.00 4.00
201 1464 7.070571 AGGAAGACTATTAGTTGAGGAAGATGG 59.929 40.741 0.00 0.00 0.00 3.51
227 1490 1.202557 AGCGGACGGTCAAGTGTAAAA 60.203 47.619 10.76 0.00 0.00 1.52
230 1493 1.582968 GAGCGGACGGTCAAGTGTA 59.417 57.895 17.75 0.00 41.72 2.90
238 1501 3.692406 GAAGGGTGAGCGGACGGT 61.692 66.667 0.00 0.00 0.00 4.83
241 1504 0.034896 TCAAAGAAGGGTGAGCGGAC 59.965 55.000 0.00 0.00 0.00 4.79
245 1508 4.378874 CGAAAGATTCAAAGAAGGGTGAGC 60.379 45.833 0.00 0.00 0.00 4.26
251 1514 5.424121 ACACACGAAAGATTCAAAGAAGG 57.576 39.130 0.00 0.00 0.00 3.46
291 1554 7.085116 CACGACAGTGTTTAAGTTAGAGAGAT 58.915 38.462 0.00 0.00 43.15 2.75
292 1555 6.436261 CACGACAGTGTTTAAGTTAGAGAGA 58.564 40.000 0.00 0.00 43.15 3.10
293 1556 6.677027 CACGACAGTGTTTAAGTTAGAGAG 57.323 41.667 0.00 0.00 43.15 3.20
315 1578 0.191064 AGAGGAGGGAGTGGACAACA 59.809 55.000 0.00 0.00 0.00 3.33
316 1579 0.610687 CAGAGGAGGGAGTGGACAAC 59.389 60.000 0.00 0.00 0.00 3.32
328 1591 5.083533 AGTAGAATTCAAGCACAGAGGAG 57.916 43.478 8.44 0.00 0.00 3.69
333 1596 5.695851 AACCAAGTAGAATTCAAGCACAG 57.304 39.130 8.44 0.00 0.00 3.66
354 1617 1.271488 ACCAACGCCCCGATTAAGAAA 60.271 47.619 0.00 0.00 0.00 2.52
355 1618 0.325602 ACCAACGCCCCGATTAAGAA 59.674 50.000 0.00 0.00 0.00 2.52
356 1619 0.325602 AACCAACGCCCCGATTAAGA 59.674 50.000 0.00 0.00 0.00 2.10
358 1621 1.166989 GAAACCAACGCCCCGATTAA 58.833 50.000 0.00 0.00 0.00 1.40
363 1643 0.678684 ATTAGGAAACCAACGCCCCG 60.679 55.000 0.00 0.00 0.00 5.73
376 1656 5.073144 GGATTAGATGGGTGGTTGATTAGGA 59.927 44.000 0.00 0.00 0.00 2.94
398 1678 2.234414 GGACAACATACACCCTAACGGA 59.766 50.000 0.00 0.00 34.64 4.69
475 1757 0.036875 AGAAGAAGCGACAAAGGGGG 59.963 55.000 0.00 0.00 0.00 5.40
481 1763 0.319555 CGGTGGAGAAGAAGCGACAA 60.320 55.000 0.00 0.00 39.55 3.18
482 1764 1.289066 CGGTGGAGAAGAAGCGACA 59.711 57.895 0.00 0.00 39.55 4.35
498 1783 3.252974 AGAGGTACATGAAGAAAGCGG 57.747 47.619 0.00 0.00 0.00 5.52
526 1811 6.843333 AGAAGAAGAGAGGACCATTATGATGA 59.157 38.462 0.00 0.00 35.16 2.92
535 1821 5.263872 ACTAGAAGAAGAAGAGAGGACCA 57.736 43.478 0.00 0.00 0.00 4.02
536 1822 5.623596 GCAACTAGAAGAAGAAGAGAGGACC 60.624 48.000 0.00 0.00 0.00 4.46
562 1872 2.840511 TCCCCACTAACCTAATGAGCA 58.159 47.619 0.00 0.00 0.00 4.26
563 1873 3.391296 TCATCCCCACTAACCTAATGAGC 59.609 47.826 0.00 0.00 0.00 4.26
569 1879 4.845530 ATAGGTCATCCCCACTAACCTA 57.154 45.455 2.32 2.32 44.41 3.08
570 1880 3.726837 ATAGGTCATCCCCACTAACCT 57.273 47.619 0.00 0.00 42.78 3.50
614 1924 9.047928 ACATTTGGCAAAAGGTCTTATGGAACA 62.048 37.037 17.70 0.00 38.25 3.18
615 1925 4.864704 TTGGCAAAAGGTCTTATGGAAC 57.135 40.909 0.00 0.00 0.00 3.62
616 1926 5.306678 ACATTTGGCAAAAGGTCTTATGGAA 59.693 36.000 17.70 0.00 35.46 3.53
617 1927 4.837860 ACATTTGGCAAAAGGTCTTATGGA 59.162 37.500 17.70 0.00 35.46 3.41
618 1928 5.151297 ACATTTGGCAAAAGGTCTTATGG 57.849 39.130 17.70 0.00 35.46 2.74
661 1971 8.414003 GGAAAGGAAGAACATAAGACAAAAGTT 58.586 33.333 0.00 0.00 0.00 2.66
664 1974 7.230712 GGAGGAAAGGAAGAACATAAGACAAAA 59.769 37.037 0.00 0.00 0.00 2.44
670 1980 4.944317 GTGGGAGGAAAGGAAGAACATAAG 59.056 45.833 0.00 0.00 0.00 1.73
671 1981 4.601857 AGTGGGAGGAAAGGAAGAACATAA 59.398 41.667 0.00 0.00 0.00 1.90
789 2099 2.040278 TCTTTTGTGGTGGAGGATCAGG 59.960 50.000 0.00 0.00 36.25 3.86
791 2101 2.978978 TCTCTTTTGTGGTGGAGGATCA 59.021 45.455 0.00 0.00 36.25 2.92
794 2104 5.576563 TTTATCTCTTTTGTGGTGGAGGA 57.423 39.130 0.00 0.00 0.00 3.71
795 2105 6.350445 CCATTTTATCTCTTTTGTGGTGGAGG 60.350 42.308 0.00 0.00 0.00 4.30
796 2106 6.624423 CCATTTTATCTCTTTTGTGGTGGAG 58.376 40.000 0.00 0.00 0.00 3.86
821 2131 0.179140 CGCCCGGAATGGAAAATGTG 60.179 55.000 0.73 0.00 42.00 3.21
843 2153 1.748591 GCCTAAGATGTGGGCTGAAGG 60.749 57.143 0.00 0.00 42.31 3.46
903 2213 1.427368 AGTAGGTTTGGAATGGGCACA 59.573 47.619 0.00 0.00 0.00 4.57
904 2214 2.215942 AGTAGGTTTGGAATGGGCAC 57.784 50.000 0.00 0.00 0.00 5.01
905 2215 2.990740 AAGTAGGTTTGGAATGGGCA 57.009 45.000 0.00 0.00 0.00 5.36
906 2216 3.323691 ACAAAAGTAGGTTTGGAATGGGC 59.676 43.478 3.02 0.00 41.82 5.36
907 2217 4.832823 AGACAAAAGTAGGTTTGGAATGGG 59.167 41.667 3.02 0.00 41.82 4.00
908 2218 7.519032 TTAGACAAAAGTAGGTTTGGAATGG 57.481 36.000 3.02 0.00 41.82 3.16
909 2219 9.810545 TTTTTAGACAAAAGTAGGTTTGGAATG 57.189 29.630 3.02 0.00 41.82 2.67
935 2245 3.553302 CGCCGGTAGGTTTGGAAATTTTT 60.553 43.478 1.90 0.00 40.50 1.94
936 2246 2.029739 CGCCGGTAGGTTTGGAAATTTT 60.030 45.455 1.90 0.00 40.50 1.82
937 2247 1.542472 CGCCGGTAGGTTTGGAAATTT 59.458 47.619 1.90 0.00 40.50 1.82
938 2248 1.170442 CGCCGGTAGGTTTGGAAATT 58.830 50.000 1.90 0.00 40.50 1.82
939 2249 1.310216 GCGCCGGTAGGTTTGGAAAT 61.310 55.000 1.90 0.00 40.50 2.17
940 2250 1.967494 GCGCCGGTAGGTTTGGAAA 60.967 57.895 1.90 0.00 40.50 3.13
967 2277 4.980805 GGTGGTTCGCCGTCTGCA 62.981 66.667 0.00 0.00 41.33 4.41
1014 2324 2.654802 AGCTTCGAGAAGGTTCCGA 58.345 52.632 11.29 0.00 45.80 4.55
1240 2577 2.101582 CACGAGCTTAGCAGAACCCTAT 59.898 50.000 7.07 0.00 0.00 2.57
1245 2582 0.440371 GTGCACGAGCTTAGCAGAAC 59.560 55.000 7.07 0.00 42.74 3.01
1254 2591 1.021390 GCCATAACAGTGCACGAGCT 61.021 55.000 12.01 2.25 42.74 4.09
1294 2631 2.004583 TCTCCCACAAATTCGCTACG 57.995 50.000 0.00 0.00 0.00 3.51
1354 2691 5.569355 AGTGAACATATCAATGGAACCACA 58.431 37.500 0.00 0.00 40.50 4.17
1376 2713 4.318333 CCATGACATTTGTTCGATCGCTAG 60.318 45.833 11.09 0.00 0.00 3.42
1386 2723 4.961438 AAGGCTTTCCATGACATTTGTT 57.039 36.364 0.00 0.00 33.74 2.83
1387 2724 4.961438 AAAGGCTTTCCATGACATTTGT 57.039 36.364 6.68 0.00 33.74 2.83
1399 2736 7.416817 ACACAAAATAATTGCAAAAGGCTTTC 58.583 30.769 13.76 2.15 45.15 2.62
1402 2739 6.940831 AACACAAAATAATTGCAAAAGGCT 57.059 29.167 1.71 0.00 45.15 4.58
1405 2742 9.339492 ACAACAAACACAAAATAATTGCAAAAG 57.661 25.926 1.71 0.00 0.00 2.27
1407 2744 7.752239 CCACAACAAACACAAAATAATTGCAAA 59.248 29.630 1.71 0.00 0.00 3.68
1416 2754 5.184711 AGCATTCCACAACAAACACAAAAT 58.815 33.333 0.00 0.00 0.00 1.82
1419 2757 3.194329 TGAGCATTCCACAACAAACACAA 59.806 39.130 0.00 0.00 0.00 3.33
1423 2761 5.294060 ACAATTTGAGCATTCCACAACAAAC 59.706 36.000 2.79 0.00 31.77 2.93
1433 2773 9.846248 AAAGTAGAACATACAATTTGAGCATTC 57.154 29.630 2.79 2.45 0.00 2.67
1436 2776 7.594758 GCAAAAGTAGAACATACAATTTGAGCA 59.405 33.333 2.79 0.00 32.86 4.26
1446 2786 6.494893 TGTGGATGCAAAAGTAGAACATAC 57.505 37.500 0.00 0.00 0.00 2.39
1467 2807 3.005367 GGGAATTCACACCACGATTTTGT 59.995 43.478 7.93 0.00 0.00 2.83
1481 2821 2.046700 GGTCGCACGGGGAATTCA 60.047 61.111 7.93 0.00 0.00 2.57
1513 2853 1.597663 GCTACACGTTCTGCACAAGTT 59.402 47.619 0.00 0.00 0.00 2.66
1517 2857 0.599991 CTGGCTACACGTTCTGCACA 60.600 55.000 5.91 1.83 0.00 4.57
1524 2864 4.369182 GAATATGCTACTGGCTACACGTT 58.631 43.478 0.00 0.00 42.39 3.99
1526 2866 3.243737 TGGAATATGCTACTGGCTACACG 60.244 47.826 0.00 0.00 42.39 4.49
1541 2881 6.270231 ACTCGGCTAAATCTAGGTTGGAATAT 59.730 38.462 0.00 0.00 0.00 1.28
1547 2887 7.787725 AATTAACTCGGCTAAATCTAGGTTG 57.212 36.000 0.00 0.00 0.00 3.77
1549 2889 8.247666 ACTAATTAACTCGGCTAAATCTAGGT 57.752 34.615 0.00 0.00 0.00 3.08
1563 2903 8.923683 GCCGATAGACCAAATACTAATTAACTC 58.076 37.037 0.00 0.00 39.76 3.01
1567 2907 8.644216 TCAAGCCGATAGACCAAATACTAATTA 58.356 33.333 0.00 0.00 39.76 1.40
1568 2908 7.441458 GTCAAGCCGATAGACCAAATACTAATT 59.559 37.037 0.00 0.00 39.76 1.40
1569 2909 6.929606 GTCAAGCCGATAGACCAAATACTAAT 59.070 38.462 0.00 0.00 39.76 1.73
1580 2920 2.890808 TCCATGTCAAGCCGATAGAC 57.109 50.000 0.00 0.00 39.76 2.59
1583 2923 1.768275 ACCATCCATGTCAAGCCGATA 59.232 47.619 0.00 0.00 0.00 2.92
1617 2957 9.783256 ACAACTGTAGAAAACAACTTCAATAAC 57.217 29.630 0.00 0.00 37.74 1.89
1642 2982 1.139256 GGAAGCCTCCCTGCTAACTAC 59.861 57.143 0.00 0.00 41.80 2.73
1672 3012 7.962441 AGTTTTGCAGTTATTTTTAGGACCAT 58.038 30.769 0.00 0.00 0.00 3.55
1673 3013 7.354751 AGTTTTGCAGTTATTTTTAGGACCA 57.645 32.000 0.00 0.00 0.00 4.02
1674 3014 8.141909 AGAAGTTTTGCAGTTATTTTTAGGACC 58.858 33.333 0.00 0.00 0.00 4.46
1675 3015 8.968242 CAGAAGTTTTGCAGTTATTTTTAGGAC 58.032 33.333 0.00 0.00 0.00 3.85
1676 3016 8.141268 CCAGAAGTTTTGCAGTTATTTTTAGGA 58.859 33.333 0.00 0.00 0.00 2.94
1677 3017 7.926018 ACCAGAAGTTTTGCAGTTATTTTTAGG 59.074 33.333 0.00 0.00 0.00 2.69
1678 3018 8.755018 CACCAGAAGTTTTGCAGTTATTTTTAG 58.245 33.333 0.00 0.00 0.00 1.85
1679 3019 8.254508 ACACCAGAAGTTTTGCAGTTATTTTTA 58.745 29.630 0.00 0.00 0.00 1.52
1680 3020 7.102993 ACACCAGAAGTTTTGCAGTTATTTTT 58.897 30.769 0.00 0.00 0.00 1.94
1715 3058 7.460402 AGACCCAGGATATAATCAAGATGTCAT 59.540 37.037 0.00 0.00 0.00 3.06
1718 3061 7.639062 AAGACCCAGGATATAATCAAGATGT 57.361 36.000 0.00 0.00 0.00 3.06
1824 3167 6.814954 AGTTTCACCTACACATATGAGGAT 57.185 37.500 10.38 0.00 34.24 3.24
1868 3211 5.804639 TGTAATCAGCTAATCACACACCTT 58.195 37.500 0.00 0.00 0.00 3.50
2036 3380 7.362056 CCAGAAACACAGGTGAATATAAACCAG 60.362 40.741 6.40 4.16 39.05 4.00
2053 3397 6.807720 GCTCTTACTTAGTAGACCAGAAACAC 59.192 42.308 0.00 0.00 0.00 3.32
2100 3444 4.816385 TCACCTGAACAGAAGACATTCAAC 59.184 41.667 3.19 0.00 37.94 3.18
2143 3487 0.911525 TGGCTCCTCCTCTTCCTTGG 60.912 60.000 0.00 0.00 35.26 3.61
2187 3531 4.504097 GTGGTGCAACAGATTGAAAGAAAC 59.496 41.667 3.59 0.00 39.98 2.78
2261 3605 1.204467 GATGCAAGGAAAAATCCGGCA 59.796 47.619 15.90 15.90 44.48 5.69
2285 3629 7.549839 CATTTTGTGTGATTGGGTCTGATAAT 58.450 34.615 0.00 0.00 0.00 1.28
2324 3674 6.403636 CCTGTTGCTGTTGCTAAAATAGGTAG 60.404 42.308 0.00 0.00 40.48 3.18
2496 3855 2.691409 TCGTCATTTGAGGGGACATC 57.309 50.000 0.87 0.00 0.00 3.06
2716 4078 4.074970 AGTCCTAGAATGCCTTTTGTGTG 58.925 43.478 0.00 0.00 0.00 3.82
2809 4182 2.053627 GAAAAATTGCACAGGAGCACG 58.946 47.619 0.00 0.00 45.61 5.34
2834 4209 4.105754 ACCAGAAAAAGGGAAGAGAAGG 57.894 45.455 0.00 0.00 0.00 3.46
2946 4473 5.258051 TGAACTTTGTTTGGTACCTTCAGT 58.742 37.500 14.36 3.91 0.00 3.41
3146 4673 6.567959 TGTGCAAAACTAATGTCAAATGTCA 58.432 32.000 0.00 0.00 0.00 3.58
3223 4750 2.096980 GCAAAACCTAGTTCCATACGGC 59.903 50.000 0.00 0.00 0.00 5.68
3275 4802 1.351350 AGTTGGGTAGCCAGGAGTTTC 59.649 52.381 14.38 0.95 0.00 2.78
3375 4909 3.676646 ACGACTGTACGCTTTCCAAATAC 59.323 43.478 0.00 0.00 36.70 1.89
3544 5078 9.770097 AGTCATTACTACATGGATGTTAATGAG 57.230 33.333 18.68 6.21 43.68 2.90
3669 5239 8.999431 TCTTCTGGTTGTCAATTAATACTGTTC 58.001 33.333 0.00 0.00 0.00 3.18
3764 5334 4.976116 GCTACAGGCACAAAAGTAAACAAG 59.024 41.667 0.00 0.00 41.35 3.16
3830 5400 8.641499 TTTTGTCCACTGTGATCATTTAAAAC 57.359 30.769 9.86 0.00 0.00 2.43
3947 5520 3.553917 TGCACGTGTATCGGATATGTTTG 59.446 43.478 18.38 0.00 44.69 2.93
3964 5537 4.323336 CCACCGAATTAAGAAAAATGCACG 59.677 41.667 0.00 0.00 0.00 5.34
3976 5549 6.383415 GTCTTTATTGTTGCCACCGAATTAA 58.617 36.000 0.00 0.00 0.00 1.40
3984 5557 3.810373 CTGACGTCTTTATTGTTGCCAC 58.190 45.455 17.92 0.00 0.00 5.01
4482 6171 7.752239 CGATCATTTGACAAGAGTGCTTATTTT 59.248 33.333 0.00 0.00 31.81 1.82
4493 6182 4.009002 TCATTGCCGATCATTTGACAAGA 58.991 39.130 0.00 0.00 0.00 3.02
4505 6194 7.450074 TCTATTACCATAACTTCATTGCCGAT 58.550 34.615 0.00 0.00 0.00 4.18
4508 6197 9.555727 TTACTCTATTACCATAACTTCATTGCC 57.444 33.333 0.00 0.00 0.00 4.52
4588 6277 8.055181 ACTCCAGACAAAATATCACATTATGGT 58.945 33.333 0.00 0.00 0.00 3.55
4642 6332 8.962111 CAATTAACTTTCAAGTTTCTTCTCTGC 58.038 33.333 10.15 0.00 46.52 4.26
4711 6402 5.386958 TTGCTCCGTATGTAGTCCATATC 57.613 43.478 0.00 0.00 38.29 1.63
5006 6764 5.307204 AGTTTAGTTACCGCATAACACCAA 58.693 37.500 9.79 0.28 45.00 3.67
5086 6844 7.001674 TGAAATGGTACCATCAACTTACAAGT 58.998 34.615 27.49 4.65 36.87 3.16
5123 6882 6.122277 ACACCATTCCATAAAGGTCTATGTG 58.878 40.000 0.00 0.00 39.02 3.21
5136 6895 3.706086 GGCTTTTCCATACACCATTCCAT 59.294 43.478 0.00 0.00 34.01 3.41
5234 6994 4.826274 AATACTTCAAGCTGCAGGACTA 57.174 40.909 17.12 0.00 0.00 2.59
5412 7172 0.319297 AAAGTACAGACGACCCGCAC 60.319 55.000 0.00 0.00 0.00 5.34
5433 7193 9.608617 GTGAATTTTTACCAAGAACTTAGCTAC 57.391 33.333 0.00 0.00 0.00 3.58
5447 7207 9.366216 AGAAAACAGTTTCAGTGAATTTTTACC 57.634 29.630 6.36 0.12 44.82 2.85
5473 7233 2.923629 ACAACCCTTAGGCCCTGAAATA 59.076 45.455 0.00 0.00 36.11 1.40
5492 7252 4.397420 AGAACAAAGCACCATATGACACA 58.603 39.130 3.65 0.00 0.00 3.72
5526 7286 4.506886 AGAAGGTGAGTACAAGTCGAAG 57.493 45.455 0.00 0.00 0.00 3.79
5698 7458 6.829229 ACTACCAAGTTATAAAAGGGCAAC 57.171 37.500 0.00 0.00 29.00 4.17
5813 7573 3.795150 GCAAATCGAGAAACTTGTTGCCA 60.795 43.478 0.00 0.00 35.09 4.92
5828 7588 2.290641 GGTGCTATTACCAGGCAAATCG 59.709 50.000 0.00 0.00 40.54 3.34
6031 7792 3.956744 AGGGTTTTGTAGCTCCTGAATC 58.043 45.455 0.00 0.00 0.00 2.52
6033 7794 3.307480 GCTAGGGTTTTGTAGCTCCTGAA 60.307 47.826 0.00 0.00 38.92 3.02
6150 7911 3.653009 GTGCTGTGCTTCGCTGCA 61.653 61.111 0.00 7.64 44.06 4.41
6264 8025 4.118584 GCATTGGAGGTTGCCCTT 57.881 55.556 0.00 0.00 42.86 3.95
6278 8039 1.760192 GCTGAAGACCATGAAGGCAT 58.240 50.000 0.00 0.00 43.14 4.40
6279 8040 0.674581 CGCTGAAGACCATGAAGGCA 60.675 55.000 0.00 0.00 43.14 4.75
6385 8147 2.354704 CGCCAAACCTGAATACCTGAGA 60.355 50.000 0.00 0.00 0.00 3.27
6406 8176 0.606604 TAACTCTTCTCCACGCCCAC 59.393 55.000 0.00 0.00 0.00 4.61
6407 8177 0.895530 CTAACTCTTCTCCACGCCCA 59.104 55.000 0.00 0.00 0.00 5.36
6408 8178 1.183549 TCTAACTCTTCTCCACGCCC 58.816 55.000 0.00 0.00 0.00 6.13
6409 8179 3.190874 CATTCTAACTCTTCTCCACGCC 58.809 50.000 0.00 0.00 0.00 5.68
6410 8180 3.851098 ACATTCTAACTCTTCTCCACGC 58.149 45.455 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.