Multiple sequence alignment - TraesCS2B01G487600

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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 TraesCS2B01G487600 chr2B 100.000 2606 0 0 1 2606 683748450 683751055 0.000000e+00 4813.0
1 TraesCS2B01G487600 chr2B 100.000 1356 0 0 2927 4282 683751376 683752731 0.000000e+00 2505.0
2 TraesCS2B01G487600 chr2B 90.099 101 8 1 1 99 43209543 43209643 3.470000e-26 130.0
3 TraesCS2B01G487600 chr2B 87.879 99 10 1 1 97 214004108 214004206 9.730000e-22 115.0
4 TraesCS2B01G487600 chr2D 96.686 1358 32 7 2934 4282 571876841 571878194 0.000000e+00 2246.0
5 TraesCS2B01G487600 chr2D 90.587 1158 64 16 810 1955 571875041 571876165 0.000000e+00 1493.0
6 TraesCS2B01G487600 chr2D 92.796 819 44 8 1 809 571874197 571875010 0.000000e+00 1171.0
7 TraesCS2B01G487600 chr2D 94.577 461 19 1 1956 2416 571876283 571876737 0.000000e+00 708.0
8 TraesCS2B01G487600 chr2D 88.406 138 12 4 2395 2531 441085749 441085883 3.430000e-36 163.0
9 TraesCS2B01G487600 chr2D 98.765 81 0 1 2527 2606 571876733 571876813 4.460000e-30 143.0
10 TraesCS2B01G487600 chr2A 95.788 1021 26 10 3275 4282 710354804 710355820 0.000000e+00 1631.0
11 TraesCS2B01G487600 chr2A 89.991 1169 57 19 810 1960 710352740 710353866 0.000000e+00 1456.0
12 TraesCS2B01G487600 chr2A 89.769 821 71 7 1 809 710351883 710352702 0.000000e+00 1038.0
13 TraesCS2B01G487600 chr2A 91.789 341 25 1 2947 3287 710354447 710354784 5.010000e-129 472.0
14 TraesCS2B01G487600 chr7D 81.616 359 38 11 1 331 545224394 545224752 5.460000e-69 272.0
15 TraesCS2B01G487600 chr7D 88.800 125 13 1 2408 2531 4241694 4241818 7.420000e-33 152.0
16 TraesCS2B01G487600 chr7D 85.714 98 14 0 4166 4263 638648195 638648098 2.110000e-18 104.0
17 TraesCS2B01G487600 chr7D 81.633 98 18 0 4166 4263 631060306 631060209 9.870000e-12 82.4
18 TraesCS2B01G487600 chr7D 84.146 82 13 0 4167 4248 631231691 631231772 3.550000e-11 80.5
19 TraesCS2B01G487600 chr6D 81.739 345 38 12 1 321 410168888 410169231 9.130000e-67 265.0
20 TraesCS2B01G487600 chr6D 76.301 346 55 20 2 336 456565584 456565255 4.430000e-35 159.0
21 TraesCS2B01G487600 chr6A 80.756 291 31 13 4 270 555665642 555665931 2.020000e-48 204.0
22 TraesCS2B01G487600 chr6B 77.746 355 44 16 1 321 617107003 617107356 7.310000e-43 185.0
23 TraesCS2B01G487600 chr6B 90.323 124 10 2 2415 2537 708072301 708072179 1.230000e-35 161.0
24 TraesCS2B01G487600 chr6B 91.071 56 5 0 418 473 693829376 693829321 4.590000e-10 76.8
25 TraesCS2B01G487600 chr3B 90.909 121 11 0 2411 2531 740547463 740547583 3.430000e-36 163.0
26 TraesCS2B01G487600 chr3B 84.459 148 20 3 659 805 823969087 823969232 4.460000e-30 143.0
27 TraesCS2B01G487600 chr1D 90.323 124 11 1 2411 2534 391734205 391734083 1.230000e-35 161.0
28 TraesCS2B01G487600 chr7B 90.678 118 11 0 2414 2531 586306766 586306883 1.590000e-34 158.0
29 TraesCS2B01G487600 chr7B 89.831 118 12 0 2415 2532 749556292 749556175 7.420000e-33 152.0
30 TraesCS2B01G487600 chr4D 90.598 117 11 0 2415 2531 400680566 400680682 5.730000e-34 156.0
31 TraesCS2B01G487600 chr5A 85.430 151 18 2 659 809 78977176 78977030 2.060000e-33 154.0
32 TraesCS2B01G487600 chr5D 88.710 124 13 1 2415 2537 501074107 501073984 2.670000e-32 150.0
33 TraesCS2B01G487600 chr5D 90.909 110 10 0 700 809 84342994 84342885 9.590000e-32 148.0
34 TraesCS2B01G487600 chr1B 88.288 111 7 2 2201 2305 441395305 441395195 1.250000e-25 128.0
35 TraesCS2B01G487600 chr1B 97.619 42 1 0 2122 2163 441425210 441425169 5.940000e-09 73.1
36 TraesCS2B01G487600 chr3D 86.555 119 9 3 2194 2305 84635865 84635747 1.620000e-24 124.0
37 TraesCS2B01G487600 chr3D 100.000 42 0 0 2122 2163 84635908 84635867 1.280000e-10 78.7
38 TraesCS2B01G487600 chr7A 76.503 183 38 4 4070 4248 726737474 726737655 1.270000e-15 95.3
39 TraesCS2B01G487600 chrUn 86.747 83 11 0 4166 4248 248487392 248487474 4.560000e-15 93.5
40 TraesCS2B01G487600 chrUn 84.337 83 13 0 4166 4248 88657835 88657753 9.870000e-12 82.4


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 TraesCS2B01G487600 chr2B 683748450 683752731 4281 False 3659.00 4813 100.00000 1 4282 2 chr2B.!!$F3 4281
1 TraesCS2B01G487600 chr2D 571874197 571878194 3997 False 1152.20 2246 94.68220 1 4282 5 chr2D.!!$F2 4281
2 TraesCS2B01G487600 chr2A 710351883 710355820 3937 False 1149.25 1631 91.83425 1 4282 4 chr2A.!!$F1 4281

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
263 267 0.036010 ACTCGGATTTGCCACCTCTG 60.036 55.0 0.00 0.0 35.94 3.35 F
1289 1349 0.100146 GTCCAAGGAGGTACGCGTAG 59.900 60.0 21.25 5.8 39.02 3.51 F
1927 2009 0.033642 TACCGAAATGTGGCACGACA 59.966 50.0 13.77 0.0 0.00 4.35 F
2098 2300 0.107897 AGCGGACTCACAAACACACA 60.108 50.0 0.00 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1456 0.390860 ACACTATCGGGATGCTGCTC 59.609 55.000 0.00 0.00 0.00 4.26 R
3170 3374 0.904865 TCCCTCTGTCACTTCCGCAT 60.905 55.000 0.00 0.00 0.00 4.73 R
3234 3438 1.372683 GCTGGTCAGTTGCTCTGGA 59.627 57.895 8.98 0.00 43.76 3.86 R
3851 4100 1.401409 CCAATTACAACAGGTGCAGCG 60.401 52.381 10.78 8.17 0.00 5.18 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
156 159 4.537936 AAGAAGTGTCTTCGTTTTCAGC 57.462 40.909 4.24 0.00 40.18 4.26
183 186 4.022849 GCTAAGCACAAGTGTGGAATCTTT 60.023 41.667 13.10 0.00 45.72 2.52
186 189 2.350772 GCACAAGTGTGGAATCTTTCGG 60.351 50.000 13.10 0.00 45.72 4.30
249 252 1.402456 CCAACGGTCAAGACTACTCGG 60.402 57.143 0.00 0.00 0.00 4.63
262 266 1.482593 CTACTCGGATTTGCCACCTCT 59.517 52.381 0.00 0.00 35.94 3.69
263 267 0.036010 ACTCGGATTTGCCACCTCTG 60.036 55.000 0.00 0.00 35.94 3.35
268 272 0.804989 GATTTGCCACCTCTGAACCG 59.195 55.000 0.00 0.00 0.00 4.44
271 275 0.759959 TTGCCACCTCTGAACCGTTA 59.240 50.000 0.00 0.00 0.00 3.18
288 292 2.289072 CGTTAGATCGGCTCCATCCAAT 60.289 50.000 0.00 0.00 0.00 3.16
300 304 4.330074 GCTCCATCCAATAACCGATATTCG 59.670 45.833 0.00 0.00 40.07 3.34
316 320 8.139350 ACCGATATTCGAAGTTAATCATACACA 58.861 33.333 3.35 0.00 43.74 3.72
370 380 5.429957 AGATATTTTCATTCCTTCTGCGC 57.570 39.130 0.00 0.00 0.00 6.09
412 425 2.930826 AATTATGCCCGTACCTCTGG 57.069 50.000 0.00 0.00 0.00 3.86
506 519 4.880537 ATCTCTCAAGCGGCGGCG 62.881 66.667 28.70 28.70 46.35 6.46
524 537 1.045350 CGCCTCTCCTCTTCCCATCA 61.045 60.000 0.00 0.00 0.00 3.07
586 599 1.185618 TTGGTCTCTGGACGTGGAGG 61.186 60.000 0.00 0.00 42.97 4.30
623 643 1.464734 TGATCTCACGACCTGTCCTC 58.535 55.000 0.00 0.00 0.00 3.71
651 671 5.040635 TGAATTGTTTTTCTTCGGACTTGC 58.959 37.500 0.00 0.00 0.00 4.01
656 676 7.441890 TTGTTTTTCTTCGGACTTGCATATA 57.558 32.000 0.00 0.00 0.00 0.86
691 711 5.014202 GGCCCCACAAATAAACCGATATAT 58.986 41.667 0.00 0.00 0.00 0.86
874 934 4.212004 CGCTGAAGTTCATCTCACTGAAAA 59.788 41.667 5.91 0.00 36.92 2.29
946 1006 0.999712 TGTTCTTCTTCCCCATCCCC 59.000 55.000 0.00 0.00 0.00 4.81
1006 1066 0.106015 TCTGCCGGATCTGATGGAGA 60.106 55.000 5.05 0.26 34.25 3.71
1010 1070 1.662608 CGGATCTGATGGAGACCGG 59.337 63.158 0.00 0.00 39.64 5.28
1120 1180 4.742649 AGAGGCTCCGGTGCGAGA 62.743 66.667 21.34 0.00 30.97 4.04
1130 1190 2.026879 GTGCGAGATCGAGAGGGC 59.973 66.667 6.39 0.00 43.02 5.19
1184 1244 4.717629 CGTGAACGAGCCGCTGGA 62.718 66.667 9.64 0.00 43.02 3.86
1289 1349 0.100146 GTCCAAGGAGGTACGCGTAG 59.900 60.000 21.25 5.80 39.02 3.51
1323 1383 4.343814 TCCATCATATGCGGTACAAAGAGA 59.656 41.667 9.93 0.00 0.00 3.10
1393 1456 7.306167 GCGCATTTACCATGTCAATTTGATAAG 60.306 37.037 0.30 0.00 0.00 1.73
1405 1468 2.245159 TTGATAAGAGCAGCATCCCG 57.755 50.000 0.00 0.00 0.00 5.14
1479 1542 5.958380 TCTGCTCTTATTTCTACCCTTCAGA 59.042 40.000 0.00 0.00 0.00 3.27
1484 1547 7.184067 TCTTATTTCTACCCTTCAGACTTCC 57.816 40.000 0.00 0.00 0.00 3.46
1499 1562 2.716969 GACTTCCCTAAATAGGCCCCAT 59.283 50.000 0.00 0.00 42.26 4.00
1500 1563 3.914435 GACTTCCCTAAATAGGCCCCATA 59.086 47.826 0.00 0.00 42.26 2.74
1501 1564 4.523304 ACTTCCCTAAATAGGCCCCATAT 58.477 43.478 0.00 0.00 42.26 1.78
1510 1573 9.670442 CCTAAATAGGCCCCATATATAACTCTA 57.330 37.037 0.00 0.00 36.53 2.43
1517 1580 7.080353 GGCCCCATATATAACTCTATCCCTAA 58.920 42.308 0.00 0.00 0.00 2.69
1530 1593 5.694995 TCTATCCCTAAAGAAAATGGCAGG 58.305 41.667 0.00 0.00 0.00 4.85
1535 1598 3.826157 CCTAAAGAAAATGGCAGGTCACA 59.174 43.478 0.00 0.00 0.00 3.58
1536 1599 4.463891 CCTAAAGAAAATGGCAGGTCACAT 59.536 41.667 0.00 0.00 0.00 3.21
1537 1600 3.947910 AAGAAAATGGCAGGTCACATG 57.052 42.857 0.00 0.00 0.00 3.21
1538 1601 3.159213 AGAAAATGGCAGGTCACATGA 57.841 42.857 0.00 0.00 0.00 3.07
1539 1602 3.705051 AGAAAATGGCAGGTCACATGAT 58.295 40.909 0.00 0.00 0.00 2.45
1540 1603 3.698040 AGAAAATGGCAGGTCACATGATC 59.302 43.478 0.00 0.00 0.00 2.92
1541 1604 2.812836 AATGGCAGGTCACATGATCA 57.187 45.000 0.00 0.00 0.00 2.92
1542 1605 3.308035 AATGGCAGGTCACATGATCAT 57.692 42.857 1.18 1.18 0.00 2.45
1543 1606 2.336945 TGGCAGGTCACATGATCATC 57.663 50.000 4.86 0.00 0.00 2.92
1544 1607 1.841919 TGGCAGGTCACATGATCATCT 59.158 47.619 4.86 0.00 0.00 2.90
1545 1608 2.240414 TGGCAGGTCACATGATCATCTT 59.760 45.455 4.86 0.00 0.00 2.40
1546 1609 3.285484 GGCAGGTCACATGATCATCTTT 58.715 45.455 4.86 0.00 0.00 2.52
1547 1610 3.066342 GGCAGGTCACATGATCATCTTTG 59.934 47.826 4.86 3.77 0.00 2.77
1548 1611 3.943381 GCAGGTCACATGATCATCTTTGA 59.057 43.478 4.86 6.18 36.00 2.69
1549 1612 4.579340 GCAGGTCACATGATCATCTTTGAT 59.421 41.667 4.86 0.00 45.39 2.57
1550 1613 5.067413 GCAGGTCACATGATCATCTTTGATT 59.933 40.000 4.86 0.10 42.73 2.57
1551 1614 6.726230 CAGGTCACATGATCATCTTTGATTC 58.274 40.000 4.86 6.10 42.73 2.52
1552 1615 6.542735 CAGGTCACATGATCATCTTTGATTCT 59.457 38.462 4.86 7.95 42.73 2.40
1553 1616 7.067129 CAGGTCACATGATCATCTTTGATTCTT 59.933 37.037 4.86 0.00 42.73 2.52
1554 1617 7.614583 AGGTCACATGATCATCTTTGATTCTTT 59.385 33.333 4.86 0.00 42.73 2.52
1555 1618 8.248945 GGTCACATGATCATCTTTGATTCTTTT 58.751 33.333 4.86 0.00 42.73 2.27
1556 1619 9.635520 GTCACATGATCATCTTTGATTCTTTTT 57.364 29.630 4.86 0.00 42.73 1.94
1557 1620 9.850628 TCACATGATCATCTTTGATTCTTTTTC 57.149 29.630 4.86 0.00 42.73 2.29
1558 1621 9.634163 CACATGATCATCTTTGATTCTTTTTCA 57.366 29.630 4.86 0.00 42.73 2.69
1559 1622 9.635520 ACATGATCATCTTTGATTCTTTTTCAC 57.364 29.630 4.86 0.00 42.73 3.18
1560 1623 9.856488 CATGATCATCTTTGATTCTTTTTCACT 57.144 29.630 4.86 0.00 42.73 3.41
1591 1654 5.865085 TCAATAGCAGTGAAACAAGTAGGT 58.135 37.500 0.00 0.00 41.43 3.08
1604 1667 4.579869 ACAAGTAGGTCCAAATAGCACTG 58.420 43.478 0.00 0.00 0.00 3.66
1624 1697 5.528690 CACTGAATAGTCAATACCATGTGGG 59.471 44.000 3.77 0.00 37.66 4.61
1625 1698 5.047566 TGAATAGTCAATACCATGTGGGG 57.952 43.478 3.77 0.00 42.91 4.96
1626 1699 4.724293 TGAATAGTCAATACCATGTGGGGA 59.276 41.667 3.77 0.00 42.91 4.81
1627 1700 5.192722 TGAATAGTCAATACCATGTGGGGAA 59.807 40.000 3.77 0.00 42.91 3.97
1657 1735 3.516615 GAACTGATAGAGCACTGGACAC 58.483 50.000 0.00 0.00 0.00 3.67
1696 1777 6.094881 TCACATCCGTGTTCTTTCTTTTCTTT 59.905 34.615 0.00 0.00 44.02 2.52
1836 1918 6.310941 TCTACCTGGTCAAATTTCATTGGAA 58.689 36.000 0.63 0.00 0.00 3.53
1858 1940 6.183360 GGAAAAGTGGGCATATGATATGATCG 60.183 42.308 16.22 0.00 0.00 3.69
1877 1959 7.315247 TGATCGAAGTCAAAACTTTTGAGAA 57.685 32.000 15.81 2.88 45.80 2.87
1893 1975 5.571784 TTGAGAAGCATGTGATCAAATCC 57.428 39.130 0.00 0.00 0.00 3.01
1912 1994 0.885596 CCTAGTCGCTCTCCCTACCG 60.886 65.000 0.00 0.00 0.00 4.02
1927 2009 0.033642 TACCGAAATGTGGCACGACA 59.966 50.000 13.77 0.00 0.00 4.35
1930 2012 1.579429 GAAATGTGGCACGACACCC 59.421 57.895 13.77 0.00 40.62 4.61
2054 2256 0.847373 TGGGGTCAACTTGTTAGCCA 59.153 50.000 0.00 0.00 32.32 4.75
2098 2300 0.107897 AGCGGACTCACAAACACACA 60.108 50.000 0.00 0.00 0.00 3.72
2148 2350 4.681942 CACCGAGTTAACTGAACAAGAGAG 59.318 45.833 14.14 0.00 40.86 3.20
2150 2352 5.068723 ACCGAGTTAACTGAACAAGAGAGAA 59.931 40.000 14.14 0.00 40.86 2.87
2182 2384 6.097839 AGAGAAAACAGAGTAACCTGTACACA 59.902 38.462 0.00 0.00 45.82 3.72
2199 2401 5.825679 TGTACACAGTAGTTTTTCAGGCAAT 59.174 36.000 0.00 0.00 0.00 3.56
2313 2515 1.066215 TGTTGAGCTGGCATACATCGT 60.066 47.619 0.00 0.00 0.00 3.73
2326 2528 2.930826 ACATCGTTCTGGACCAAGTT 57.069 45.000 0.00 0.00 0.00 2.66
2334 2536 1.211703 TCTGGACCAAGTTCAGCACAA 59.788 47.619 0.00 0.00 38.92 3.33
2337 2539 1.748493 GGACCAAGTTCAGCACAACAA 59.252 47.619 1.13 0.00 0.00 2.83
2386 2588 5.063312 CCAACAAATGAAACCTGTCACAAAC 59.937 40.000 0.00 0.00 0.00 2.93
2398 2600 4.414852 CTGTCACAAACCAACTTGTTCAG 58.585 43.478 0.00 0.00 37.43 3.02
2416 2618 2.734606 TCAGTTGCGCAACACATAGTAC 59.265 45.455 44.07 23.00 43.47 2.73
2417 2619 2.736721 CAGTTGCGCAACACATAGTACT 59.263 45.455 44.07 24.76 43.47 2.73
2418 2620 2.993899 AGTTGCGCAACACATAGTACTC 59.006 45.455 44.07 20.81 43.47 2.59
2420 2622 1.287425 GCGCAACACATAGTACTCCC 58.713 55.000 0.30 0.00 0.00 4.30
2421 2623 1.134788 GCGCAACACATAGTACTCCCT 60.135 52.381 0.30 0.00 0.00 4.20
2422 2624 2.810650 CGCAACACATAGTACTCCCTC 58.189 52.381 0.00 0.00 0.00 4.30
2423 2625 2.165641 CGCAACACATAGTACTCCCTCA 59.834 50.000 0.00 0.00 0.00 3.86
2424 2626 3.735208 CGCAACACATAGTACTCCCTCAG 60.735 52.174 0.00 0.00 0.00 3.35
2425 2627 3.195825 GCAACACATAGTACTCCCTCAGT 59.804 47.826 0.00 0.00 39.41 3.41
2426 2628 4.678309 GCAACACATAGTACTCCCTCAGTC 60.678 50.000 0.00 0.00 36.43 3.51
2427 2629 3.633418 ACACATAGTACTCCCTCAGTCC 58.367 50.000 0.00 0.00 36.43 3.85
2428 2630 2.619177 CACATAGTACTCCCTCAGTCCG 59.381 54.545 0.00 0.00 36.43 4.79
2429 2631 2.231529 CATAGTACTCCCTCAGTCCGG 58.768 57.143 0.00 0.00 36.43 5.14
2430 2632 1.588239 TAGTACTCCCTCAGTCCGGA 58.412 55.000 0.00 0.00 36.43 5.14
2431 2633 0.702902 AGTACTCCCTCAGTCCGGAA 59.297 55.000 5.23 0.00 36.43 4.30
2432 2634 1.076677 AGTACTCCCTCAGTCCGGAAA 59.923 52.381 5.23 0.00 36.43 3.13
2433 2635 2.108970 GTACTCCCTCAGTCCGGAAAT 58.891 52.381 5.23 0.00 36.43 2.17
2434 2636 2.544844 ACTCCCTCAGTCCGGAAATA 57.455 50.000 5.23 0.00 0.00 1.40
2435 2637 2.108970 ACTCCCTCAGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
2436 2638 2.292323 ACTCCCTCAGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
2437 2639 2.766828 CTCCCTCAGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
2438 2640 2.500098 TCCCTCAGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
2439 2641 2.236395 CCCTCAGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
2440 2642 3.522553 CCTCAGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
2441 2643 3.179830 CTCAGTCCGGAAATACTTGTCG 58.820 50.000 5.23 0.00 0.00 4.35
2442 2644 1.659098 CAGTCCGGAAATACTTGTCGC 59.341 52.381 5.23 0.00 0.00 5.19
2443 2645 1.274167 AGTCCGGAAATACTTGTCGCA 59.726 47.619 5.23 0.00 0.00 5.10
2444 2646 2.093658 AGTCCGGAAATACTTGTCGCAT 60.094 45.455 5.23 0.00 0.00 4.73
2445 2647 3.131577 AGTCCGGAAATACTTGTCGCATA 59.868 43.478 5.23 0.00 0.00 3.14
2446 2648 3.866910 GTCCGGAAATACTTGTCGCATAA 59.133 43.478 5.23 0.00 0.00 1.90
2447 2649 4.330620 GTCCGGAAATACTTGTCGCATAAA 59.669 41.667 5.23 0.00 0.00 1.40
2448 2650 5.007332 GTCCGGAAATACTTGTCGCATAAAT 59.993 40.000 5.23 0.00 0.00 1.40
2449 2651 5.007234 TCCGGAAATACTTGTCGCATAAATG 59.993 40.000 0.00 0.00 0.00 2.32
2450 2652 5.204833 CGGAAATACTTGTCGCATAAATGG 58.795 41.667 0.00 0.00 0.00 3.16
2451 2653 5.007234 CGGAAATACTTGTCGCATAAATGGA 59.993 40.000 0.00 0.00 0.00 3.41
2452 2654 6.293407 CGGAAATACTTGTCGCATAAATGGAT 60.293 38.462 0.00 0.00 0.00 3.41
2453 2655 7.095397 CGGAAATACTTGTCGCATAAATGGATA 60.095 37.037 0.00 0.00 0.00 2.59
2454 2656 8.230486 GGAAATACTTGTCGCATAAATGGATAG 58.770 37.037 0.00 0.00 0.00 2.08
2455 2657 8.902540 AAATACTTGTCGCATAAATGGATAGA 57.097 30.769 0.00 0.00 0.00 1.98
2456 2658 8.902540 AATACTTGTCGCATAAATGGATAGAA 57.097 30.769 0.00 0.00 0.00 2.10
2457 2659 8.902540 ATACTTGTCGCATAAATGGATAGAAA 57.097 30.769 0.00 0.00 0.00 2.52
2458 2660 7.807977 ACTTGTCGCATAAATGGATAGAAAT 57.192 32.000 0.00 0.00 0.00 2.17
2459 2661 8.225603 ACTTGTCGCATAAATGGATAGAAATT 57.774 30.769 0.00 0.00 0.00 1.82
2460 2662 8.131100 ACTTGTCGCATAAATGGATAGAAATTG 58.869 33.333 0.00 0.00 0.00 2.32
2461 2663 7.800155 TGTCGCATAAATGGATAGAAATTGA 57.200 32.000 0.00 0.00 0.00 2.57
2462 2664 8.394971 TGTCGCATAAATGGATAGAAATTGAT 57.605 30.769 0.00 0.00 0.00 2.57
2463 2665 8.291740 TGTCGCATAAATGGATAGAAATTGATG 58.708 33.333 0.00 0.00 30.56 3.07
2464 2666 7.272084 GTCGCATAAATGGATAGAAATTGATGC 59.728 37.037 7.40 7.40 43.17 3.91
2465 2667 7.040548 TCGCATAAATGGATAGAAATTGATGCA 60.041 33.333 14.86 0.00 45.35 3.96
2466 2668 7.758076 CGCATAAATGGATAGAAATTGATGCAT 59.242 33.333 14.86 0.00 45.35 3.96
2467 2669 9.084164 GCATAAATGGATAGAAATTGATGCATC 57.916 33.333 20.14 20.14 44.82 3.91
2471 2673 9.803507 AAATGGATAGAAATTGATGCATCTAGA 57.196 29.630 26.32 13.33 33.50 2.43
2472 2674 9.803507 AATGGATAGAAATTGATGCATCTAGAA 57.196 29.630 26.32 13.68 33.50 2.10
2473 2675 8.613060 TGGATAGAAATTGATGCATCTAGAAC 57.387 34.615 26.32 14.85 0.00 3.01
2474 2676 8.435187 TGGATAGAAATTGATGCATCTAGAACT 58.565 33.333 26.32 20.05 0.00 3.01
2475 2677 9.935241 GGATAGAAATTGATGCATCTAGAACTA 57.065 33.333 26.32 21.24 0.00 2.24
2483 2685 8.942338 TTGATGCATCTAGAACTAAAATACGT 57.058 30.769 26.32 0.00 0.00 3.57
2484 2686 8.575565 TGATGCATCTAGAACTAAAATACGTC 57.424 34.615 26.32 0.00 0.00 4.34
2485 2687 8.414003 TGATGCATCTAGAACTAAAATACGTCT 58.586 33.333 26.32 0.00 0.00 4.18
2486 2688 9.894783 GATGCATCTAGAACTAAAATACGTCTA 57.105 33.333 19.70 0.00 0.00 2.59
2487 2689 9.900710 ATGCATCTAGAACTAAAATACGTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
2488 2690 9.117183 TGCATCTAGAACTAAAATACGTCTAGA 57.883 33.333 10.27 10.27 38.94 2.43
2492 2694 9.117183 TCTAGAACTAAAATACGTCTAGATGCA 57.883 33.333 12.04 0.00 32.48 3.96
2493 2695 9.900710 CTAGAACTAAAATACGTCTAGATGCAT 57.099 33.333 12.04 0.00 0.00 3.96
2494 2696 8.804688 AGAACTAAAATACGTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
2495 2697 7.868415 AGAACTAAAATACGTCTAGATGCATCC 59.132 37.037 23.06 6.84 0.00 3.51
2496 2698 7.050970 ACTAAAATACGTCTAGATGCATCCA 57.949 36.000 23.06 9.05 0.00 3.41
2497 2699 7.671302 ACTAAAATACGTCTAGATGCATCCAT 58.329 34.615 23.06 8.39 0.00 3.41
2498 2700 8.150945 ACTAAAATACGTCTAGATGCATCCATT 58.849 33.333 23.06 7.62 0.00 3.16
2499 2701 7.807977 AAAATACGTCTAGATGCATCCATTT 57.192 32.000 23.06 13.11 0.00 2.32
2500 2702 7.807977 AAATACGTCTAGATGCATCCATTTT 57.192 32.000 23.06 6.85 0.00 1.82
2501 2703 7.807977 AATACGTCTAGATGCATCCATTTTT 57.192 32.000 23.06 6.10 0.00 1.94
2502 2704 5.741388 ACGTCTAGATGCATCCATTTTTC 57.259 39.130 23.06 6.86 0.00 2.29
2503 2705 4.576463 ACGTCTAGATGCATCCATTTTTCC 59.424 41.667 23.06 2.88 0.00 3.13
2504 2706 4.319046 CGTCTAGATGCATCCATTTTTCCG 60.319 45.833 23.06 10.66 0.00 4.30
2505 2707 4.816385 GTCTAGATGCATCCATTTTTCCGA 59.184 41.667 23.06 0.00 0.00 4.55
2506 2708 4.816385 TCTAGATGCATCCATTTTTCCGAC 59.184 41.667 23.06 0.00 0.00 4.79
2507 2709 3.355378 AGATGCATCCATTTTTCCGACA 58.645 40.909 23.06 0.00 0.00 4.35
2508 2710 3.763360 AGATGCATCCATTTTTCCGACAA 59.237 39.130 23.06 0.00 0.00 3.18
2509 2711 3.574284 TGCATCCATTTTTCCGACAAG 57.426 42.857 0.00 0.00 0.00 3.16
2510 2712 2.890311 TGCATCCATTTTTCCGACAAGT 59.110 40.909 0.00 0.00 0.00 3.16
2511 2713 4.075682 TGCATCCATTTTTCCGACAAGTA 58.924 39.130 0.00 0.00 0.00 2.24
2512 2714 4.704540 TGCATCCATTTTTCCGACAAGTAT 59.295 37.500 0.00 0.00 0.00 2.12
2513 2715 5.184864 TGCATCCATTTTTCCGACAAGTATT 59.815 36.000 0.00 0.00 0.00 1.89
2514 2716 6.099341 GCATCCATTTTTCCGACAAGTATTT 58.901 36.000 0.00 0.00 0.00 1.40
2515 2717 6.253512 GCATCCATTTTTCCGACAAGTATTTC 59.746 38.462 0.00 0.00 0.00 2.17
2516 2718 6.262193 TCCATTTTTCCGACAAGTATTTCC 57.738 37.500 0.00 0.00 0.00 3.13
2517 2719 5.092781 CCATTTTTCCGACAAGTATTTCCG 58.907 41.667 0.00 0.00 0.00 4.30
2518 2720 4.752661 TTTTTCCGACAAGTATTTCCGG 57.247 40.909 0.00 0.00 41.36 5.14
2519 2721 3.681593 TTTCCGACAAGTATTTCCGGA 57.318 42.857 0.00 0.00 46.18 5.14
2520 2722 2.660189 TCCGACAAGTATTTCCGGAC 57.340 50.000 1.83 0.00 43.47 4.79
2521 2723 2.173519 TCCGACAAGTATTTCCGGACT 58.826 47.619 1.83 0.00 43.47 3.85
2522 2724 2.094390 TCCGACAAGTATTTCCGGACTG 60.094 50.000 1.83 0.00 43.47 3.51
2523 2725 2.094390 CCGACAAGTATTTCCGGACTGA 60.094 50.000 1.83 0.00 42.49 3.41
2524 2726 3.179830 CGACAAGTATTTCCGGACTGAG 58.820 50.000 1.83 0.00 0.00 3.35
2525 2727 3.522553 GACAAGTATTTCCGGACTGAGG 58.477 50.000 1.83 0.00 0.00 3.86
2526 2728 2.904434 ACAAGTATTTCCGGACTGAGGT 59.096 45.455 1.83 0.00 0.00 3.85
2527 2729 4.091549 ACAAGTATTTCCGGACTGAGGTA 58.908 43.478 1.83 0.00 0.00 3.08
2528 2730 4.159879 ACAAGTATTTCCGGACTGAGGTAG 59.840 45.833 1.83 0.00 0.00 3.18
2529 2731 3.978610 AGTATTTCCGGACTGAGGTAGT 58.021 45.455 1.83 0.00 44.02 2.73
2530 2732 5.121380 AGTATTTCCGGACTGAGGTAGTA 57.879 43.478 1.83 0.00 40.53 1.82
2531 2733 5.703310 AGTATTTCCGGACTGAGGTAGTAT 58.297 41.667 1.83 0.00 40.53 2.12
2532 2734 6.845908 AGTATTTCCGGACTGAGGTAGTATA 58.154 40.000 1.83 0.00 40.53 1.47
2533 2735 7.468496 AGTATTTCCGGACTGAGGTAGTATAT 58.532 38.462 1.83 0.00 40.53 0.86
2534 2736 6.837471 ATTTCCGGACTGAGGTAGTATATC 57.163 41.667 1.83 0.00 40.53 1.63
2535 2737 4.987963 TCCGGACTGAGGTAGTATATCA 57.012 45.455 0.00 0.00 40.53 2.15
3170 3374 9.477484 TTTAAACACTGTCAAAAAGCAGTTAAA 57.523 25.926 0.00 0.00 43.27 1.52
3199 3403 1.546029 TGACAGAGGGACGTCAATCTG 59.454 52.381 31.67 31.67 43.81 2.90
3219 3423 3.476552 TGGAACAACCATGTCAAGAGTC 58.523 45.455 0.00 0.00 44.64 3.36
3234 3438 4.654262 TCAAGAGTCAGGGTTGTAAGAACT 59.346 41.667 0.00 0.00 0.00 3.01
3347 3584 3.302415 GCGCACCTGTTTTCATTTTCAAC 60.302 43.478 0.30 0.00 0.00 3.18
3512 3751 4.812626 TGCATGTATACATTGTGCTCTGAG 59.187 41.667 23.49 0.00 33.61 3.35
3519 3758 4.833478 ACATTGTGCTCTGAGAGGTAAT 57.167 40.909 12.01 0.48 0.00 1.89
3533 3772 5.659971 TGAGAGGTAATAGGTAACCTTGGAC 59.340 44.000 0.00 0.00 46.22 4.02
3554 3793 5.523552 GGACAATTTTATGCTAAATGTGGCC 59.476 40.000 0.00 0.00 32.14 5.36
3611 3856 3.947868 ACCATGAAGATTGGAGAGTGTG 58.052 45.455 0.00 0.00 37.69 3.82
3715 3964 3.079578 AGCATGATGTTTGTCTGGACAG 58.920 45.455 0.00 0.00 42.94 3.51
3987 4236 9.832445 TTCAATAGGATACAGGAAATAACTCAC 57.168 33.333 0.00 0.00 41.41 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.826274 TCCATACTTCAGTTCTCCCAAG 57.174 45.455 0.00 0.00 0.00 3.61
156 159 2.618241 TCCACACTTGTGCTTAGCAAAG 59.382 45.455 9.05 16.22 44.34 2.77
183 186 3.449377 TCTGCCACATGTTACTAATCCGA 59.551 43.478 0.00 0.00 0.00 4.55
186 189 5.822519 TGGATTCTGCCACATGTTACTAATC 59.177 40.000 0.00 2.66 31.66 1.75
225 228 4.670347 GAGTAGTCTTGACCGTTGGATAC 58.330 47.826 0.00 0.00 0.00 2.24
249 252 0.804989 CGGTTCAGAGGTGGCAAATC 59.195 55.000 0.00 0.00 0.00 2.17
268 272 2.910688 TTGGATGGAGCCGATCTAAC 57.089 50.000 0.00 0.00 0.00 2.34
271 275 2.039084 GGTTATTGGATGGAGCCGATCT 59.961 50.000 0.00 0.00 33.95 2.75
349 359 4.214437 CGCGCAGAAGGAATGAAAATATC 58.786 43.478 8.75 0.00 0.00 1.63
370 380 4.481930 TTTTCAGGTAACACAAGATGCG 57.518 40.909 0.00 0.00 41.41 4.73
411 424 2.185608 GCAGAAGGAGAGACCGCC 59.814 66.667 0.00 0.00 44.74 6.13
412 425 2.185608 GGCAGAAGGAGAGACCGC 59.814 66.667 0.00 0.00 44.74 5.68
506 519 0.758123 CTGATGGGAAGAGGAGAGGC 59.242 60.000 0.00 0.00 0.00 4.70
524 537 2.048127 GCGAGCACGAAAGACCCT 60.048 61.111 8.01 0.00 42.66 4.34
623 643 5.342259 GTCCGAAGAAAAACAATTCATTCGG 59.658 40.000 21.29 21.29 46.75 4.30
651 671 6.070251 TGTGGGGCCAGATAACTGTATATATG 60.070 42.308 4.39 0.00 42.05 1.78
656 676 2.487775 TGTGGGGCCAGATAACTGTAT 58.512 47.619 4.39 0.00 42.05 2.29
725 745 8.149973 TGGTCTTTTTGTGTTGTATAAGACTC 57.850 34.615 0.00 0.00 40.60 3.36
874 934 0.868406 CAGCGGCGACTTCTCTTTTT 59.132 50.000 12.98 0.00 0.00 1.94
878 938 2.513026 AATGCAGCGGCGACTTCTCT 62.513 55.000 12.98 0.00 45.35 3.10
880 940 2.046892 AATGCAGCGGCGACTTCT 60.047 55.556 12.98 0.00 45.35 2.85
946 1006 2.027625 GTCGGTGGAGGAAAGTGCG 61.028 63.158 0.00 0.00 0.00 5.34
1006 1066 2.034066 CAGCCACACAATCCCGGT 59.966 61.111 0.00 0.00 0.00 5.28
1010 1070 1.870055 CTGCACCAGCCACACAATCC 61.870 60.000 0.00 0.00 41.13 3.01
1120 1180 2.835431 CACCTCGGCCCTCTCGAT 60.835 66.667 0.00 0.00 36.01 3.59
1289 1349 3.683847 GCATATGATGGATCTACAGGGGC 60.684 52.174 6.97 0.00 0.00 5.80
1323 1383 3.693085 GTGTGAGGCATGTGATGAAATCT 59.307 43.478 0.00 0.00 45.81 2.40
1393 1456 0.390860 ACACTATCGGGATGCTGCTC 59.609 55.000 0.00 0.00 0.00 4.26
1405 1468 3.752665 TGGTCTCCTCCGATACACTATC 58.247 50.000 0.00 0.00 0.00 2.08
1479 1542 2.296943 TGGGGCCTATTTAGGGAAGT 57.703 50.000 0.84 0.00 43.82 3.01
1484 1547 8.568617 AGAGTTATATATGGGGCCTATTTAGG 57.431 38.462 8.02 0.00 46.42 2.69
1510 1573 4.264352 TGACCTGCCATTTTCTTTAGGGAT 60.264 41.667 0.00 0.00 0.00 3.85
1517 1580 3.499338 TCATGTGACCTGCCATTTTCTT 58.501 40.909 0.00 0.00 0.00 2.52
1530 1593 9.635520 AAAAAGAATCAAAGATGATCATGTGAC 57.364 29.630 14.30 0.00 45.60 3.67
1539 1602 9.630098 GCATTAGTGAAAAAGAATCAAAGATGA 57.370 29.630 0.00 0.00 40.57 2.92
1540 1603 9.414295 TGCATTAGTGAAAAAGAATCAAAGATG 57.586 29.630 0.00 0.00 0.00 2.90
1541 1604 9.415544 GTGCATTAGTGAAAAAGAATCAAAGAT 57.584 29.630 0.00 0.00 0.00 2.40
1542 1605 8.632679 AGTGCATTAGTGAAAAAGAATCAAAGA 58.367 29.630 0.00 0.00 0.00 2.52
1543 1606 8.807667 AGTGCATTAGTGAAAAAGAATCAAAG 57.192 30.769 0.00 0.00 0.00 2.77
1544 1607 8.412456 TGAGTGCATTAGTGAAAAAGAATCAAA 58.588 29.630 0.00 0.00 0.00 2.69
1545 1608 7.939782 TGAGTGCATTAGTGAAAAAGAATCAA 58.060 30.769 0.00 0.00 0.00 2.57
1546 1609 7.509141 TGAGTGCATTAGTGAAAAAGAATCA 57.491 32.000 0.00 0.00 0.00 2.57
1547 1610 8.976986 ATTGAGTGCATTAGTGAAAAAGAATC 57.023 30.769 0.00 0.00 0.00 2.52
1549 1612 8.023128 GCTATTGAGTGCATTAGTGAAAAAGAA 58.977 33.333 0.00 0.00 32.93 2.52
1550 1613 7.174772 TGCTATTGAGTGCATTAGTGAAAAAGA 59.825 33.333 0.00 0.00 33.94 2.52
1551 1614 7.307694 TGCTATTGAGTGCATTAGTGAAAAAG 58.692 34.615 0.00 0.00 33.94 2.27
1552 1615 7.040478 ACTGCTATTGAGTGCATTAGTGAAAAA 60.040 33.333 0.00 0.00 38.59 1.94
1553 1616 6.430925 ACTGCTATTGAGTGCATTAGTGAAAA 59.569 34.615 0.00 0.00 38.59 2.29
1554 1617 5.939883 ACTGCTATTGAGTGCATTAGTGAAA 59.060 36.000 0.00 0.00 38.59 2.69
1555 1618 5.352293 CACTGCTATTGAGTGCATTAGTGAA 59.648 40.000 0.00 0.00 38.59 3.18
1556 1619 4.872124 CACTGCTATTGAGTGCATTAGTGA 59.128 41.667 0.00 0.00 38.59 3.41
1557 1620 4.872124 TCACTGCTATTGAGTGCATTAGTG 59.128 41.667 0.00 0.00 40.64 2.74
1558 1621 5.089970 TCACTGCTATTGAGTGCATTAGT 57.910 39.130 0.00 0.00 40.64 2.24
1559 1622 6.128200 TGTTTCACTGCTATTGAGTGCATTAG 60.128 38.462 0.00 0.00 40.64 1.73
1560 1623 5.704978 TGTTTCACTGCTATTGAGTGCATTA 59.295 36.000 0.00 0.00 40.64 1.90
1561 1624 4.520111 TGTTTCACTGCTATTGAGTGCATT 59.480 37.500 0.00 0.00 40.64 3.56
1562 1625 4.074259 TGTTTCACTGCTATTGAGTGCAT 58.926 39.130 0.00 0.00 40.64 3.96
1563 1626 3.475575 TGTTTCACTGCTATTGAGTGCA 58.524 40.909 0.00 0.00 40.64 4.57
1591 1654 7.715249 GGTATTGACTATTCAGTGCTATTTGGA 59.285 37.037 0.00 0.00 34.21 3.53
1604 1667 5.304686 TCCCCACATGGTATTGACTATTC 57.695 43.478 0.00 0.00 0.00 1.75
1633 1711 3.027412 TCCAGTGCTCTATCAGTTCCTC 58.973 50.000 0.00 0.00 0.00 3.71
1643 1721 0.881796 CGACAGTGTCCAGTGCTCTA 59.118 55.000 17.57 0.00 35.19 2.43
1657 1735 3.121279 CGGATGTGAACACTTAACGACAG 59.879 47.826 6.51 0.00 0.00 3.51
1696 1777 0.608035 GTTCGCCTGATCCAAACCCA 60.608 55.000 0.00 0.00 0.00 4.51
1836 1918 6.053632 TCGATCATATCATATGCCCACTTT 57.946 37.500 0.00 0.00 0.00 2.66
1858 1940 6.753744 ACATGCTTCTCAAAAGTTTTGACTTC 59.246 34.615 23.91 14.48 0.00 3.01
1877 1959 4.712476 GACTAGGGATTTGATCACATGCT 58.288 43.478 12.37 2.88 34.29 3.79
1893 1975 0.885596 CGGTAGGGAGAGCGACTAGG 60.886 65.000 0.00 0.00 42.83 3.02
1912 1994 0.889186 AGGGTGTCGTGCCACATTTC 60.889 55.000 0.00 0.00 37.06 2.17
1927 2009 7.855784 AGAAAAATAAATCTTTGGTGAGGGT 57.144 32.000 0.00 0.00 0.00 4.34
1930 2012 9.762933 TTGGAAGAAAAATAAATCTTTGGTGAG 57.237 29.630 0.00 0.00 36.08 3.51
1999 2200 9.843334 CGAAATCCTTCACTATATTAGTACTCC 57.157 37.037 0.00 0.00 37.23 3.85
2090 2292 4.856487 CACAAATTCACTTCGTGTGTGTTT 59.144 37.500 10.10 9.44 46.27 2.83
2092 2294 3.687212 TCACAAATTCACTTCGTGTGTGT 59.313 39.130 12.24 5.70 46.27 3.72
2098 2300 4.821805 AGGACAATCACAAATTCACTTCGT 59.178 37.500 0.00 0.00 0.00 3.85
2114 2316 1.056660 AACTCGGTGTGGAGGACAAT 58.943 50.000 0.00 0.00 38.39 2.71
2148 2350 5.208463 ACTCTGTTTTCTCTCCTCTGTTC 57.792 43.478 0.00 0.00 0.00 3.18
2150 2352 5.011227 GGTTACTCTGTTTTCTCTCCTCTGT 59.989 44.000 0.00 0.00 0.00 3.41
2182 2384 5.473039 GCATTCATTGCCTGAAAAACTACT 58.527 37.500 3.26 0.00 46.62 2.57
2199 2401 4.764823 AGTAGAACGGAAATTTGGCATTCA 59.235 37.500 0.00 0.00 0.00 2.57
2215 2417 5.693814 CATTTGTTGCTGGAGAAGTAGAAC 58.306 41.667 0.00 0.00 0.00 3.01
2241 2443 7.825270 TCGGTTGTGTCCATGTATAAATAAACT 59.175 33.333 0.00 0.00 0.00 2.66
2313 2515 1.211703 TGTGCTGAACTTGGTCCAGAA 59.788 47.619 0.00 0.00 0.00 3.02
2326 2528 5.049060 GTGTATTACATGGTTGTTGTGCTGA 60.049 40.000 0.00 0.00 37.28 4.26
2334 2536 6.472016 TGTCATGAGTGTATTACATGGTTGT 58.528 36.000 0.00 0.00 40.86 3.32
2337 2539 6.299805 ACTGTCATGAGTGTATTACATGGT 57.700 37.500 0.00 0.00 40.86 3.55
2398 2600 2.093783 GGAGTACTATGTGTTGCGCAAC 59.906 50.000 39.38 39.38 41.50 4.17
2416 2618 2.389715 AGTATTTCCGGACTGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
2417 2619 2.500098 CAAGTATTTCCGGACTGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
2418 2620 2.236395 ACAAGTATTTCCGGACTGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
2420 2622 3.179830 CGACAAGTATTTCCGGACTGAG 58.820 50.000 1.83 0.00 0.00 3.35
2421 2623 2.673043 GCGACAAGTATTTCCGGACTGA 60.673 50.000 1.83 0.00 0.00 3.41
2422 2624 1.659098 GCGACAAGTATTTCCGGACTG 59.341 52.381 1.83 0.00 0.00 3.51
2423 2625 1.274167 TGCGACAAGTATTTCCGGACT 59.726 47.619 1.83 0.00 0.00 3.85
2424 2626 1.717194 TGCGACAAGTATTTCCGGAC 58.283 50.000 1.83 0.00 0.00 4.79
2425 2627 2.684001 ATGCGACAAGTATTTCCGGA 57.316 45.000 0.00 0.00 0.00 5.14
2426 2628 4.868450 TTTATGCGACAAGTATTTCCGG 57.132 40.909 0.00 0.00 0.00 5.14
2427 2629 5.007234 TCCATTTATGCGACAAGTATTTCCG 59.993 40.000 0.00 0.00 0.00 4.30
2428 2630 6.371809 TCCATTTATGCGACAAGTATTTCC 57.628 37.500 0.00 0.00 0.00 3.13
2429 2631 8.988934 TCTATCCATTTATGCGACAAGTATTTC 58.011 33.333 0.00 0.00 0.00 2.17
2430 2632 8.902540 TCTATCCATTTATGCGACAAGTATTT 57.097 30.769 0.00 0.00 0.00 1.40
2431 2633 8.902540 TTCTATCCATTTATGCGACAAGTATT 57.097 30.769 0.00 0.00 0.00 1.89
2432 2634 8.902540 TTTCTATCCATTTATGCGACAAGTAT 57.097 30.769 0.00 0.00 0.00 2.12
2433 2635 8.902540 ATTTCTATCCATTTATGCGACAAGTA 57.097 30.769 0.00 0.00 0.00 2.24
2434 2636 7.807977 ATTTCTATCCATTTATGCGACAAGT 57.192 32.000 0.00 0.00 0.00 3.16
2435 2637 8.344831 TCAATTTCTATCCATTTATGCGACAAG 58.655 33.333 0.00 0.00 0.00 3.16
2436 2638 8.219546 TCAATTTCTATCCATTTATGCGACAA 57.780 30.769 0.00 0.00 0.00 3.18
2437 2639 7.800155 TCAATTTCTATCCATTTATGCGACA 57.200 32.000 0.00 0.00 0.00 4.35
2438 2640 7.272084 GCATCAATTTCTATCCATTTATGCGAC 59.728 37.037 0.00 0.00 32.91 5.19
2439 2641 7.040548 TGCATCAATTTCTATCCATTTATGCGA 60.041 33.333 0.00 0.00 40.55 5.10
2440 2642 7.085746 TGCATCAATTTCTATCCATTTATGCG 58.914 34.615 0.00 0.00 40.55 4.73
2441 2643 8.997621 ATGCATCAATTTCTATCCATTTATGC 57.002 30.769 0.00 0.00 39.15 3.14
2445 2647 9.803507 TCTAGATGCATCAATTTCTATCCATTT 57.196 29.630 27.81 4.45 0.00 2.32
2446 2648 9.803507 TTCTAGATGCATCAATTTCTATCCATT 57.196 29.630 27.81 5.10 0.00 3.16
2447 2649 9.228949 GTTCTAGATGCATCAATTTCTATCCAT 57.771 33.333 27.81 5.53 0.00 3.41
2448 2650 8.435187 AGTTCTAGATGCATCAATTTCTATCCA 58.565 33.333 27.81 0.00 0.00 3.41
2449 2651 8.845413 AGTTCTAGATGCATCAATTTCTATCC 57.155 34.615 27.81 5.66 0.00 2.59
2457 2659 9.547753 ACGTATTTTAGTTCTAGATGCATCAAT 57.452 29.630 27.81 16.55 0.00 2.57
2458 2660 8.942338 ACGTATTTTAGTTCTAGATGCATCAA 57.058 30.769 27.81 11.42 0.00 2.57
2459 2661 8.414003 AGACGTATTTTAGTTCTAGATGCATCA 58.586 33.333 27.81 13.12 0.00 3.07
2460 2662 8.804688 AGACGTATTTTAGTTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
2461 2663 9.900710 CTAGACGTATTTTAGTTCTAGATGCAT 57.099 33.333 0.00 0.00 0.00 3.96
2462 2664 9.117183 TCTAGACGTATTTTAGTTCTAGATGCA 57.883 33.333 0.00 0.00 32.48 3.96
2466 2668 9.117183 TGCATCTAGACGTATTTTAGTTCTAGA 57.883 33.333 8.64 8.64 38.94 2.43
2467 2669 9.900710 ATGCATCTAGACGTATTTTAGTTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
2468 2670 9.894783 GATGCATCTAGACGTATTTTAGTTCTA 57.105 33.333 19.70 0.00 0.00 2.10
2469 2671 7.868415 GGATGCATCTAGACGTATTTTAGTTCT 59.132 37.037 25.28 0.00 0.00 3.01
2470 2672 7.652105 TGGATGCATCTAGACGTATTTTAGTTC 59.348 37.037 25.28 3.59 0.00 3.01
2471 2673 7.497595 TGGATGCATCTAGACGTATTTTAGTT 58.502 34.615 25.28 0.00 0.00 2.24
2472 2674 7.050970 TGGATGCATCTAGACGTATTTTAGT 57.949 36.000 25.28 0.00 0.00 2.24
2473 2675 8.539770 AATGGATGCATCTAGACGTATTTTAG 57.460 34.615 25.28 0.00 0.00 1.85
2474 2676 8.902540 AAATGGATGCATCTAGACGTATTTTA 57.097 30.769 25.28 0.00 0.00 1.52
2475 2677 7.807977 AAATGGATGCATCTAGACGTATTTT 57.192 32.000 25.28 12.25 0.00 1.82
2476 2678 7.807977 AAAATGGATGCATCTAGACGTATTT 57.192 32.000 25.28 12.91 0.00 1.40
2477 2679 7.041098 GGAAAAATGGATGCATCTAGACGTATT 60.041 37.037 25.28 7.52 0.00 1.89
2478 2680 6.428159 GGAAAAATGGATGCATCTAGACGTAT 59.572 38.462 25.28 6.16 0.00 3.06
2479 2681 5.758296 GGAAAAATGGATGCATCTAGACGTA 59.242 40.000 25.28 5.08 0.00 3.57
2480 2682 4.576463 GGAAAAATGGATGCATCTAGACGT 59.424 41.667 25.28 8.02 0.00 4.34
2481 2683 4.319046 CGGAAAAATGGATGCATCTAGACG 60.319 45.833 25.28 14.35 0.00 4.18
2482 2684 4.816385 TCGGAAAAATGGATGCATCTAGAC 59.184 41.667 25.28 9.96 0.00 2.59
2483 2685 4.816385 GTCGGAAAAATGGATGCATCTAGA 59.184 41.667 25.28 9.00 0.00 2.43
2484 2686 4.576053 TGTCGGAAAAATGGATGCATCTAG 59.424 41.667 25.28 6.75 0.00 2.43
2485 2687 4.522114 TGTCGGAAAAATGGATGCATCTA 58.478 39.130 25.28 20.79 0.00 1.98
2486 2688 3.355378 TGTCGGAAAAATGGATGCATCT 58.645 40.909 25.28 5.06 0.00 2.90
2487 2689 3.781079 TGTCGGAAAAATGGATGCATC 57.219 42.857 18.81 18.81 0.00 3.91
2488 2690 3.511146 ACTTGTCGGAAAAATGGATGCAT 59.489 39.130 0.00 0.00 0.00 3.96
2489 2691 2.890311 ACTTGTCGGAAAAATGGATGCA 59.110 40.909 0.00 0.00 0.00 3.96
2490 2692 3.575965 ACTTGTCGGAAAAATGGATGC 57.424 42.857 0.00 0.00 0.00 3.91
2491 2693 6.751888 GGAAATACTTGTCGGAAAAATGGATG 59.248 38.462 0.00 0.00 0.00 3.51
2492 2694 6.404293 CGGAAATACTTGTCGGAAAAATGGAT 60.404 38.462 0.00 0.00 0.00 3.41
2493 2695 5.106475 CGGAAATACTTGTCGGAAAAATGGA 60.106 40.000 0.00 0.00 0.00 3.41
2494 2696 5.092781 CGGAAATACTTGTCGGAAAAATGG 58.907 41.667 0.00 0.00 0.00 3.16
2495 2697 5.092781 CCGGAAATACTTGTCGGAAAAATG 58.907 41.667 0.00 0.00 42.94 2.32
2496 2698 5.005094 TCCGGAAATACTTGTCGGAAAAAT 58.995 37.500 0.00 0.00 45.40 1.82
2497 2699 4.387598 TCCGGAAATACTTGTCGGAAAAA 58.612 39.130 0.00 0.00 45.40 1.94
2498 2700 4.005487 TCCGGAAATACTTGTCGGAAAA 57.995 40.909 0.00 0.00 45.40 2.29
2499 2701 3.681593 TCCGGAAATACTTGTCGGAAA 57.318 42.857 0.00 0.00 45.40 3.13
2501 2703 2.094390 CAGTCCGGAAATACTTGTCGGA 60.094 50.000 5.23 0.00 46.06 4.55
2502 2704 2.094390 TCAGTCCGGAAATACTTGTCGG 60.094 50.000 5.23 0.00 41.80 4.79
2503 2705 3.179830 CTCAGTCCGGAAATACTTGTCG 58.820 50.000 5.23 0.00 0.00 4.35
2504 2706 3.056035 ACCTCAGTCCGGAAATACTTGTC 60.056 47.826 5.23 0.00 0.00 3.18
2505 2707 2.904434 ACCTCAGTCCGGAAATACTTGT 59.096 45.455 5.23 0.00 0.00 3.16
2506 2708 3.611766 ACCTCAGTCCGGAAATACTTG 57.388 47.619 5.23 0.00 0.00 3.16
2507 2709 4.351127 ACTACCTCAGTCCGGAAATACTT 58.649 43.478 5.23 0.00 28.33 2.24
2508 2710 3.978610 ACTACCTCAGTCCGGAAATACT 58.021 45.455 5.23 0.00 28.33 2.12
2509 2711 7.392673 TGATATACTACCTCAGTCCGGAAATAC 59.607 40.741 5.23 0.00 38.80 1.89
2510 2712 7.464273 TGATATACTACCTCAGTCCGGAAATA 58.536 38.462 5.23 0.00 38.80 1.40
2511 2713 6.312529 TGATATACTACCTCAGTCCGGAAAT 58.687 40.000 5.23 0.00 38.80 2.17
2512 2714 5.698104 TGATATACTACCTCAGTCCGGAAA 58.302 41.667 5.23 0.00 38.80 3.13
2513 2715 5.314718 TGATATACTACCTCAGTCCGGAA 57.685 43.478 5.23 0.00 38.80 4.30
2514 2716 4.987963 TGATATACTACCTCAGTCCGGA 57.012 45.455 0.00 0.00 38.80 5.14
2515 2717 5.768662 TCTTTGATATACTACCTCAGTCCGG 59.231 44.000 0.00 0.00 38.80 5.14
2516 2718 6.294065 GGTCTTTGATATACTACCTCAGTCCG 60.294 46.154 0.00 0.00 38.80 4.79
2517 2719 6.550108 TGGTCTTTGATATACTACCTCAGTCC 59.450 42.308 0.00 0.00 38.80 3.85
2518 2720 7.502895 TCTGGTCTTTGATATACTACCTCAGTC 59.497 40.741 0.00 0.00 38.80 3.51
2519 2721 7.355101 TCTGGTCTTTGATATACTACCTCAGT 58.645 38.462 0.00 0.00 41.62 3.41
2520 2722 7.825331 TCTGGTCTTTGATATACTACCTCAG 57.175 40.000 0.00 0.00 0.00 3.35
2521 2723 7.618117 TGTTCTGGTCTTTGATATACTACCTCA 59.382 37.037 0.00 0.00 0.00 3.86
2522 2724 8.008513 TGTTCTGGTCTTTGATATACTACCTC 57.991 38.462 0.00 0.00 0.00 3.85
2523 2725 7.973048 TGTTCTGGTCTTTGATATACTACCT 57.027 36.000 0.00 0.00 0.00 3.08
2524 2726 7.711339 CCTTGTTCTGGTCTTTGATATACTACC 59.289 40.741 0.00 0.00 0.00 3.18
2525 2727 8.258708 ACCTTGTTCTGGTCTTTGATATACTAC 58.741 37.037 0.00 0.00 31.03 2.73
2526 2728 8.375493 ACCTTGTTCTGGTCTTTGATATACTA 57.625 34.615 0.00 0.00 31.03 1.82
2527 2729 7.259088 ACCTTGTTCTGGTCTTTGATATACT 57.741 36.000 0.00 0.00 31.03 2.12
2528 2730 7.923414 AACCTTGTTCTGGTCTTTGATATAC 57.077 36.000 0.00 0.00 36.69 1.47
2531 2733 9.444600 GTATAAACCTTGTTCTGGTCTTTGATA 57.555 33.333 0.00 0.00 36.69 2.15
2532 2734 8.164070 AGTATAAACCTTGTTCTGGTCTTTGAT 58.836 33.333 0.00 0.00 36.69 2.57
2533 2735 7.514721 AGTATAAACCTTGTTCTGGTCTTTGA 58.485 34.615 0.00 0.00 36.69 2.69
2534 2736 7.745620 AGTATAAACCTTGTTCTGGTCTTTG 57.254 36.000 0.00 0.00 36.69 2.77
2535 2737 9.281371 GTTAGTATAAACCTTGTTCTGGTCTTT 57.719 33.333 0.00 0.00 36.69 2.52
2926 3128 3.243501 TGCATGCTTGACAAAAACTCTCC 60.244 43.478 20.33 0.00 0.00 3.71
2927 3129 3.968649 TGCATGCTTGACAAAAACTCTC 58.031 40.909 20.33 0.00 0.00 3.20
2928 3130 4.304110 CATGCATGCTTGACAAAAACTCT 58.696 39.130 25.15 0.00 0.00 3.24
2929 3131 4.640805 CATGCATGCTTGACAAAAACTC 57.359 40.909 25.15 0.00 0.00 3.01
2984 3188 1.442526 GCATTCTGCCAGGATCACCG 61.443 60.000 0.00 0.00 38.20 4.94
2987 3191 1.213430 TCATGCATTCTGCCAGGATCA 59.787 47.619 0.00 0.00 44.23 2.92
3170 3374 0.904865 TCCCTCTGTCACTTCCGCAT 60.905 55.000 0.00 0.00 0.00 4.73
3179 3383 1.546029 CAGATTGACGTCCCTCTGTCA 59.454 52.381 25.22 1.48 42.98 3.58
3199 3403 3.476552 TGACTCTTGACATGGTTGTTCC 58.523 45.455 0.00 0.00 35.79 3.62
3219 3423 3.866449 GCTCTGGAGTTCTTACAACCCTG 60.866 52.174 0.00 0.00 0.00 4.45
3234 3438 1.372683 GCTGGTCAGTTGCTCTGGA 59.627 57.895 8.98 0.00 43.76 3.86
3485 3724 6.416750 CAGAGCACAATGTATACATGCAAATG 59.583 38.462 24.55 18.19 36.56 2.32
3512 3751 5.945144 TGTCCAAGGTTACCTATTACCTC 57.055 43.478 3.55 0.00 43.88 3.85
3519 3758 7.179269 AGCATAAAATTGTCCAAGGTTACCTA 58.821 34.615 3.55 0.00 31.13 3.08
3533 3772 8.836268 ATATGGCCACATTTAGCATAAAATTG 57.164 30.769 8.16 0.00 38.53 2.32
3611 3856 3.485947 TTTTGTGCACTCTGAACACAC 57.514 42.857 19.41 2.93 43.57 3.82
3851 4100 1.401409 CCAATTACAACAGGTGCAGCG 60.401 52.381 10.78 8.17 0.00 5.18
3892 4141 2.442413 CAACTCCTCGTCTCTTCTCCT 58.558 52.381 0.00 0.00 0.00 3.69
3987 4236 4.956700 TCCTCTAGGATGTCTTGTAACTGG 59.043 45.833 0.00 0.00 39.78 4.00


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

AutoCloner maintained by Alex Coulton.