Multiple sequence alignment - TraesCS2A01G051600

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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 TraesCS2A01G051600 chr2A 100.000 3549 0 0 1 3549 20276101 20272553 0.000000e+00 6554.0
1 TraesCS2A01G051600 chr2A 87.089 426 51 3 2720 3144 696279546 696279968 2.480000e-131 479.0
2 TraesCS2A01G051600 chr2A 83.520 358 48 7 3143 3490 696280357 696280713 1.230000e-84 324.0
3 TraesCS2A01G051600 chr2A 85.227 176 21 5 2720 2892 690320022 690320195 3.640000e-40 176.0
4 TraesCS2A01G051600 chr2B 89.382 1441 90 35 1 1414 33350269 33351673 0.000000e+00 1755.0
5 TraesCS2A01G051600 chr2B 91.648 874 58 9 1850 2720 33351990 33352851 0.000000e+00 1195.0
6 TraesCS2A01G051600 chr2B 86.065 897 88 25 1830 2720 32923848 32924713 0.000000e+00 929.0
7 TraesCS2A01G051600 chr2B 93.090 521 23 10 899 1413 32922477 32922990 0.000000e+00 750.0
8 TraesCS2A01G051600 chr2B 85.784 204 26 2 2721 2923 391044683 391044482 2.780000e-51 213.0
9 TraesCS2A01G051600 chr2B 82.812 192 20 8 3 182 32921684 32921874 3.670000e-35 159.0
10 TraesCS2A01G051600 chr2B 79.327 208 34 7 1617 1817 2234821 2235026 1.720000e-28 137.0
11 TraesCS2A01G051600 chrUn 91.034 1305 84 19 120 1411 24672050 24673334 0.000000e+00 1731.0
12 TraesCS2A01G051600 chrUn 95.698 860 37 0 1861 2720 24673420 24674279 0.000000e+00 1384.0
13 TraesCS2A01G051600 chrUn 87.973 898 91 14 1830 2720 16526570 16527457 0.000000e+00 1044.0
14 TraesCS2A01G051600 chrUn 84.869 1031 71 42 409 1414 16524526 16525496 0.000000e+00 961.0
15 TraesCS2A01G051600 chrUn 86.065 897 88 25 1830 2720 276927331 276928196 0.000000e+00 929.0
16 TraesCS2A01G051600 chrUn 93.090 521 23 10 899 1413 276925960 276926473 0.000000e+00 750.0
17 TraesCS2A01G051600 chrUn 78.603 687 145 2 1863 2548 338926212 338926897 1.500000e-123 453.0
18 TraesCS2A01G051600 chrUn 78.603 687 145 2 1863 2548 409660099 409660784 1.500000e-123 453.0
19 TraesCS2A01G051600 chrUn 82.812 192 20 8 3 182 276925167 276925357 3.670000e-35 159.0
20 TraesCS2A01G051600 chrUn 84.536 97 14 1 3387 3482 24945742 24945646 1.050000e-15 95.3
21 TraesCS2A01G051600 chrUn 100.000 39 0 0 200 238 16523485 16523523 4.910000e-09 73.1
22 TraesCS2A01G051600 chr2D 89.730 740 67 7 1862 2600 20061370 20062101 0.000000e+00 937.0
23 TraesCS2A01G051600 chr2D 92.101 557 29 10 869 1419 20060097 20060644 0.000000e+00 771.0
24 TraesCS2A01G051600 chr7A 87.119 427 51 4 2721 3144 692900718 692901143 6.890000e-132 481.0
25 TraesCS2A01G051600 chr5B 86.620 426 49 6 2721 3144 421501312 421501731 6.940000e-127 464.0
26 TraesCS2A01G051600 chr4A 79.016 691 135 8 1863 2548 624016490 624017175 6.940000e-127 464.0
27 TraesCS2A01G051600 chr4A 84.694 98 14 1 3386 3482 686976729 686976826 2.920000e-16 97.1
28 TraesCS2A01G051600 chr7D 92.140 229 16 2 3256 3482 520951028 520950800 4.420000e-84 322.0
29 TraesCS2A01G051600 chr5D 80.412 388 61 9 1029 1407 524259563 524259944 7.500000e-72 281.0
30 TraesCS2A01G051600 chr5D 79.841 377 64 8 1033 1400 524249477 524249850 7.550000e-67 265.0
31 TraesCS2A01G051600 chr5D 86.928 153 17 3 2720 2870 375171732 375171883 6.090000e-38 169.0
32 TraesCS2A01G051600 chr5D 85.088 114 17 0 3377 3490 375183409 375183522 2.240000e-22 117.0
33 TraesCS2A01G051600 chr5D 91.566 83 7 0 3408 3490 334308506 334308424 8.050000e-22 115.0
34 TraesCS2A01G051600 chr5D 83.333 114 18 1 3377 3490 375165576 375165688 1.740000e-18 104.0
35 TraesCS2A01G051600 chr6B 88.158 228 26 1 3256 3482 1154879 1155106 1.620000e-68 270.0
36 TraesCS2A01G051600 chr6B 88.966 145 16 0 2999 3143 1154356 1154500 2.810000e-41 180.0
37 TraesCS2A01G051600 chr4B 78.655 342 45 17 2721 3044 645475592 645475923 6.010000e-48 202.0
38 TraesCS2A01G051600 chr4B 85.161 155 20 3 2718 2870 106494315 106494468 4.740000e-34 156.0
39 TraesCS2A01G051600 chr4B 96.875 32 1 0 1774 1805 500865978 500866009 2.000000e-03 54.7
40 TraesCS2A01G051600 chr3D 83.523 176 24 4 2721 2895 590161449 590161278 3.670000e-35 159.0
41 TraesCS2A01G051600 chr1A 83.648 159 22 3 2714 2870 498800907 498801063 2.860000e-31 147.0
42 TraesCS2A01G051600 chr1A 79.487 156 26 5 1658 1807 324372804 324372649 4.850000e-19 106.0
43 TraesCS2A01G051600 chr3B 92.857 98 7 0 3393 3490 227763 227666 3.690000e-30 143.0
44 TraesCS2A01G051600 chr3B 84.524 84 9 3 1606 1687 664079390 664079471 2.940000e-11 80.5
45 TraesCS2A01G051600 chr5A 81.319 91 12 4 1611 1700 484845603 484845689 6.360000e-08 69.4


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 TraesCS2A01G051600 chr2A 20272553 20276101 3548 True 6554.000000 6554 100.000000 1 3549 1 chr2A.!!$R1 3548
1 TraesCS2A01G051600 chr2A 696279546 696280713 1167 False 401.500000 479 85.304500 2720 3490 2 chr2A.!!$F2 770
2 TraesCS2A01G051600 chr2B 33350269 33352851 2582 False 1475.000000 1755 90.515000 1 2720 2 chr2B.!!$F3 2719
3 TraesCS2A01G051600 chr2B 32921684 32924713 3029 False 612.666667 929 87.322333 3 2720 3 chr2B.!!$F2 2717
4 TraesCS2A01G051600 chrUn 24672050 24674279 2229 False 1557.500000 1731 93.366000 120 2720 2 chrUn.!!$F4 2600
5 TraesCS2A01G051600 chrUn 16523485 16527457 3972 False 692.700000 1044 90.947333 200 2720 3 chrUn.!!$F3 2520
6 TraesCS2A01G051600 chrUn 276925167 276928196 3029 False 612.666667 929 87.322333 3 2720 3 chrUn.!!$F5 2717
7 TraesCS2A01G051600 chrUn 338926212 338926897 685 False 453.000000 453 78.603000 1863 2548 1 chrUn.!!$F1 685
8 TraesCS2A01G051600 chrUn 409660099 409660784 685 False 453.000000 453 78.603000 1863 2548 1 chrUn.!!$F2 685
9 TraesCS2A01G051600 chr2D 20060097 20062101 2004 False 854.000000 937 90.915500 869 2600 2 chr2D.!!$F1 1731
10 TraesCS2A01G051600 chr4A 624016490 624017175 685 False 464.000000 464 79.016000 1863 2548 1 chr4A.!!$F1 685
11 TraesCS2A01G051600 chr6B 1154356 1155106 750 False 225.000000 270 88.562000 2999 3482 2 chr6B.!!$F1 483

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
86 89 0.104855 TGGTATCGTCTCTGCATGGC 59.895 55.0 0.0 0.0 0.00 4.40 F
350 1220 0.174617 GCGAGTGAAGGAAGAGGAGG 59.825 60.0 0.0 0.0 0.00 4.30 F
361 1231 0.397816 AAGAGGAGGGATGACCGAGG 60.398 60.0 0.0 0.0 46.96 4.63 F
1606 3440 0.103572 ACAAGACAACCGTAGTGCGT 59.896 50.0 0.0 0.0 39.32 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 3377 0.396139 AATACTCCCCGCTACGACCA 60.396 55.000 0.00 0.0 0.00 4.02 R
1586 3420 0.782384 CGCACTACGGTTGTCTTGTC 59.218 55.000 0.00 0.0 38.44 3.18 R
1897 4502 2.440980 GGGAGGCCACCATCAAGC 60.441 66.667 21.72 0.0 0.00 4.01 R
3147 6158 0.108138 GTGGCCATCGACAGCTACTT 60.108 55.000 9.72 0.0 37.49 2.24 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
25 28 1.297664 GTGGCAGACATCTCTGATGC 58.702 55.000 1.66 0.00 46.32 3.91
29 32 1.874231 GCAGACATCTCTGATGCCATG 59.126 52.381 1.66 5.50 46.32 3.66
76 79 2.024176 AAGTGGCACATGGTATCGTC 57.976 50.000 21.41 0.00 44.52 4.20
86 89 0.104855 TGGTATCGTCTCTGCATGGC 59.895 55.000 0.00 0.00 0.00 4.40
114 122 2.045708 CCAAATGGTGCCGCTGCTA 61.046 57.895 0.70 0.00 38.71 3.49
161 173 1.012086 CTCGGCCATGTTCATCACAG 58.988 55.000 2.24 0.00 39.40 3.66
166 178 3.578688 GGCCATGTTCATCACAGAAAAC 58.421 45.455 0.00 0.00 39.40 2.43
174 186 3.531538 TCATCACAGAAAACGATAGCCC 58.468 45.455 0.00 0.00 42.67 5.19
296 1166 3.060674 CGATCTCTCATTCACATGCGTTC 60.061 47.826 0.00 0.00 0.00 3.95
329 1199 1.068250 GGATACGAGGTGGAGCTGC 59.932 63.158 0.00 0.00 0.00 5.25
350 1220 0.174617 GCGAGTGAAGGAAGAGGAGG 59.825 60.000 0.00 0.00 0.00 4.30
353 1223 2.758130 GAGTGAAGGAAGAGGAGGGAT 58.242 52.381 0.00 0.00 0.00 3.85
361 1231 0.397816 AAGAGGAGGGATGACCGAGG 60.398 60.000 0.00 0.00 46.96 4.63
369 1239 1.209747 GGGATGACCGAGGTAGCTTTT 59.790 52.381 0.00 0.00 36.97 2.27
402 1272 5.957168 TCATCATGGAAACTCTCTCTCTCTT 59.043 40.000 0.00 0.00 0.00 2.85
411 1281 4.759782 ACTCTCTCTCTCTTTCTCTCTCG 58.240 47.826 0.00 0.00 0.00 4.04
414 1284 1.330521 CTCTCTCTTTCTCTCTCGCCG 59.669 57.143 0.00 0.00 0.00 6.46
416 1286 0.678366 TCTCTTTCTCTCTCGCCGCT 60.678 55.000 0.00 0.00 0.00 5.52
443 1329 4.268405 CGAGCAAAAATTCAGCACAGTTTT 59.732 37.500 0.00 0.00 0.00 2.43
459 1345 6.152831 GCACAGTTTTTAGATGATAACCCCTT 59.847 38.462 0.00 0.00 0.00 3.95
460 1346 7.309805 GCACAGTTTTTAGATGATAACCCCTTT 60.310 37.037 0.00 0.00 0.00 3.11
496 1394 4.897509 AAATCCTCTGTCATCACTCACA 57.102 40.909 0.00 0.00 0.00 3.58
499 1397 3.234353 TCCTCTGTCATCACTCACAACT 58.766 45.455 0.00 0.00 0.00 3.16
501 1399 4.218635 TCCTCTGTCATCACTCACAACTAC 59.781 45.833 0.00 0.00 0.00 2.73
524 1425 2.234661 CAAAGGAGGCCCCAGAAAAATC 59.765 50.000 12.24 0.00 37.41 2.17
615 1517 1.508632 GCTCACGTCTGGTGCTTTTA 58.491 50.000 0.00 0.00 46.56 1.52
641 1543 2.408050 GAGTAGACACAGTGCAACAGG 58.592 52.381 0.00 0.00 41.43 4.00
652 1554 3.964875 CAACAGGGCACACCACGC 61.965 66.667 0.00 0.00 43.89 5.34
761 1730 3.963733 TTCCACAGGAATGAGCCAG 57.036 52.632 0.00 0.00 36.71 4.85
777 1746 3.930634 GCCAGAAGCTCAAGAAAACAT 57.069 42.857 0.00 0.00 38.99 2.71
792 1761 4.634443 AGAAAACATAACTCCCACGCATAC 59.366 41.667 0.00 0.00 0.00 2.39
845 1853 3.934579 ACACGGTTAACTTTTGACGAACT 59.065 39.130 5.42 0.00 0.00 3.01
846 1854 5.108517 ACACGGTTAACTTTTGACGAACTA 58.891 37.500 5.42 0.00 0.00 2.24
847 1855 5.580297 ACACGGTTAACTTTTGACGAACTAA 59.420 36.000 5.42 0.00 0.00 2.24
950 2054 3.035942 GCTGCTCAGTACAAAACAAACG 58.964 45.455 0.00 0.00 0.00 3.60
954 2058 3.302610 GCTCAGTACAAAACAAACGCGTA 60.303 43.478 14.46 0.00 0.00 4.42
955 2059 4.180844 TCAGTACAAAACAAACGCGTAC 57.819 40.909 14.46 3.01 34.09 3.67
956 2060 3.864583 TCAGTACAAAACAAACGCGTACT 59.135 39.130 14.46 5.84 42.58 2.73
957 2061 5.039984 TCAGTACAAAACAAACGCGTACTA 58.960 37.500 14.46 0.00 40.49 1.82
958 2062 5.173673 TCAGTACAAAACAAACGCGTACTAG 59.826 40.000 14.46 5.30 40.49 2.57
960 2064 6.142161 CAGTACAAAACAAACGCGTACTAGTA 59.858 38.462 14.46 6.92 40.49 1.82
1129 2241 2.685017 TGGGCATGCTCGAGGTCT 60.685 61.111 18.92 0.00 0.00 3.85
1445 2750 8.659491 TGTAGTACTCTATGTTGTAGTACGTTG 58.341 37.037 0.00 0.00 46.53 4.10
1446 2751 7.678947 AGTACTCTATGTTGTAGTACGTTGT 57.321 36.000 0.00 0.00 46.53 3.32
1447 2752 8.777865 AGTACTCTATGTTGTAGTACGTTGTA 57.222 34.615 0.00 0.00 46.53 2.41
1448 2753 9.388506 AGTACTCTATGTTGTAGTACGTTGTAT 57.611 33.333 0.00 0.00 46.53 2.29
1450 2755 8.048534 ACTCTATGTTGTAGTACGTTGTATGT 57.951 34.615 0.00 0.00 0.00 2.29
1451 2756 9.166173 ACTCTATGTTGTAGTACGTTGTATGTA 57.834 33.333 0.00 0.00 0.00 2.29
1453 2758 9.166173 TCTATGTTGTAGTACGTTGTATGTAGT 57.834 33.333 0.00 0.00 0.00 2.73
1454 2759 9.218359 CTATGTTGTAGTACGTTGTATGTAGTG 57.782 37.037 0.00 0.00 0.00 2.74
1457 2762 5.252547 TGTAGTACGTTGTATGTAGTGGGA 58.747 41.667 0.00 0.00 0.00 4.37
1458 2763 4.978083 AGTACGTTGTATGTAGTGGGAG 57.022 45.455 0.00 0.00 0.00 4.30
1460 2765 1.206371 ACGTTGTATGTAGTGGGAGGC 59.794 52.381 0.00 0.00 0.00 4.70
1462 2767 2.354303 CGTTGTATGTAGTGGGAGGCAA 60.354 50.000 0.00 0.00 0.00 4.52
1463 2768 3.681594 CGTTGTATGTAGTGGGAGGCAAT 60.682 47.826 0.00 0.00 0.00 3.56
1464 2769 3.838244 TGTATGTAGTGGGAGGCAATC 57.162 47.619 0.00 0.00 0.00 2.67
1465 2770 3.111484 TGTATGTAGTGGGAGGCAATCA 58.889 45.455 0.00 0.00 0.00 2.57
1467 2772 2.489938 TGTAGTGGGAGGCAATCAAC 57.510 50.000 0.00 0.00 0.00 3.18
1469 2774 2.308570 TGTAGTGGGAGGCAATCAACAT 59.691 45.455 0.00 0.00 0.00 2.71
1471 2776 3.737559 AGTGGGAGGCAATCAACATTA 57.262 42.857 0.00 0.00 0.00 1.90
1472 2777 4.046286 AGTGGGAGGCAATCAACATTAA 57.954 40.909 0.00 0.00 0.00 1.40
1473 2778 4.613437 AGTGGGAGGCAATCAACATTAAT 58.387 39.130 0.00 0.00 0.00 1.40
1474 2779 5.765510 AGTGGGAGGCAATCAACATTAATA 58.234 37.500 0.00 0.00 0.00 0.98
1475 2780 6.194235 AGTGGGAGGCAATCAACATTAATAA 58.806 36.000 0.00 0.00 0.00 1.40
1476 2781 6.322201 AGTGGGAGGCAATCAACATTAATAAG 59.678 38.462 0.00 0.00 0.00 1.73
1481 2831 9.555727 GGAGGCAATCAACATTAATAAGTACTA 57.444 33.333 0.00 0.00 0.00 1.82
1488 2838 9.765795 ATCAACATTAATAAGTACTACCTCTGC 57.234 33.333 0.00 0.00 0.00 4.26
1532 2919 7.568199 TTTTGAAAAGGAAGGACTTACTCTG 57.432 36.000 0.00 0.00 31.17 3.35
1541 3374 6.553100 AGGAAGGACTTACTCTGATCCATAAG 59.447 42.308 0.00 0.00 33.33 1.73
1542 3375 6.239458 GGAAGGACTTACTCTGATCCATAAGG 60.239 46.154 0.00 0.00 33.33 2.69
1544 3377 4.591072 GGACTTACTCTGATCCATAAGGCT 59.409 45.833 7.68 0.00 33.81 4.58
1545 3379 5.510520 GGACTTACTCTGATCCATAAGGCTG 60.511 48.000 0.00 0.00 33.81 4.85
1549 3383 1.688735 TCTGATCCATAAGGCTGGTCG 59.311 52.381 0.00 0.00 37.57 4.79
1550 3384 1.414181 CTGATCCATAAGGCTGGTCGT 59.586 52.381 0.00 0.00 37.57 4.34
1551 3385 2.628178 CTGATCCATAAGGCTGGTCGTA 59.372 50.000 0.00 0.00 37.57 3.43
1552 3386 2.628178 TGATCCATAAGGCTGGTCGTAG 59.372 50.000 0.00 0.00 37.57 3.51
1554 3388 0.597637 CCATAAGGCTGGTCGTAGCG 60.598 60.000 0.00 0.00 44.60 4.26
1555 3389 0.597637 CATAAGGCTGGTCGTAGCGG 60.598 60.000 0.00 0.00 44.60 5.52
1556 3390 1.745320 ATAAGGCTGGTCGTAGCGGG 61.745 60.000 0.00 0.00 44.60 6.13
1560 3394 2.754658 CTGGTCGTAGCGGGGAGT 60.755 66.667 0.00 0.00 0.00 3.85
1566 3400 3.244875 TGGTCGTAGCGGGGAGTATTATA 60.245 47.826 0.00 0.00 0.00 0.98
1567 3401 3.950395 GGTCGTAGCGGGGAGTATTATAT 59.050 47.826 0.00 0.00 0.00 0.86
1568 3402 5.126067 GGTCGTAGCGGGGAGTATTATATA 58.874 45.833 0.00 0.00 0.00 0.86
1569 3403 5.008118 GGTCGTAGCGGGGAGTATTATATAC 59.992 48.000 0.00 0.00 0.00 1.47
1570 3404 5.819901 GTCGTAGCGGGGAGTATTATATACT 59.180 44.000 0.00 0.00 0.00 2.12
1571 3405 6.986817 GTCGTAGCGGGGAGTATTATATACTA 59.013 42.308 0.00 0.00 0.00 1.82
1572 3406 7.170658 GTCGTAGCGGGGAGTATTATATACTAG 59.829 44.444 0.00 0.00 0.00 2.57
1573 3407 6.989169 CGTAGCGGGGAGTATTATATACTAGT 59.011 42.308 0.00 0.00 0.00 2.57
1574 3408 8.144478 CGTAGCGGGGAGTATTATATACTAGTA 58.856 40.741 4.77 4.77 0.00 1.82
1603 3437 3.364889 TCTGACAAGACAACCGTAGTG 57.635 47.619 0.00 0.00 0.00 2.74
1604 3438 1.792949 CTGACAAGACAACCGTAGTGC 59.207 52.381 0.00 0.00 0.00 4.40
1605 3439 0.782384 GACAAGACAACCGTAGTGCG 59.218 55.000 0.00 0.00 40.95 5.34
1606 3440 0.103572 ACAAGACAACCGTAGTGCGT 59.896 50.000 0.00 0.00 39.32 5.24
1607 3441 1.337703 ACAAGACAACCGTAGTGCGTA 59.662 47.619 0.00 0.00 39.32 4.42
1608 3442 2.029649 ACAAGACAACCGTAGTGCGTAT 60.030 45.455 0.00 0.00 39.32 3.06
1609 3443 2.991190 CAAGACAACCGTAGTGCGTATT 59.009 45.455 0.00 0.00 39.32 1.89
1610 3444 4.168014 CAAGACAACCGTAGTGCGTATTA 58.832 43.478 0.00 0.00 39.32 0.98
1611 3445 4.644103 AGACAACCGTAGTGCGTATTAT 57.356 40.909 0.00 0.00 39.32 1.28
1612 3446 4.604976 AGACAACCGTAGTGCGTATTATC 58.395 43.478 0.00 0.00 39.32 1.75
1613 3447 4.096833 AGACAACCGTAGTGCGTATTATCA 59.903 41.667 0.00 0.00 39.32 2.15
1614 3448 4.940463 ACAACCGTAGTGCGTATTATCAT 58.060 39.130 0.00 0.00 39.32 2.45
1615 3449 6.016860 AGACAACCGTAGTGCGTATTATCATA 60.017 38.462 0.00 0.00 39.32 2.15
1616 3450 6.684686 ACAACCGTAGTGCGTATTATCATAT 58.315 36.000 0.00 0.00 39.32 1.78
1617 3451 7.819644 ACAACCGTAGTGCGTATTATCATATA 58.180 34.615 0.00 0.00 39.32 0.86
1618 3452 7.966753 ACAACCGTAGTGCGTATTATCATATAG 59.033 37.037 0.00 0.00 39.32 1.31
1619 3453 7.621428 ACCGTAGTGCGTATTATCATATAGT 57.379 36.000 0.00 0.00 39.32 2.12
1620 3454 7.470079 ACCGTAGTGCGTATTATCATATAGTG 58.530 38.462 0.00 0.00 39.32 2.74
1621 3455 6.414109 CCGTAGTGCGTATTATCATATAGTGC 59.586 42.308 0.00 0.00 39.32 4.40
1622 3456 6.138702 CGTAGTGCGTATTATCATATAGTGCG 59.861 42.308 0.00 0.00 35.54 5.34
1623 3457 5.950883 AGTGCGTATTATCATATAGTGCGT 58.049 37.500 0.00 0.00 0.00 5.24
1624 3458 7.080353 AGTGCGTATTATCATATAGTGCGTA 57.920 36.000 0.00 0.00 0.00 4.42
1625 3459 7.704271 AGTGCGTATTATCATATAGTGCGTAT 58.296 34.615 0.00 0.00 0.00 3.06
1626 3460 8.188799 AGTGCGTATTATCATATAGTGCGTATT 58.811 33.333 0.00 0.00 0.00 1.89
1627 3461 9.442033 GTGCGTATTATCATATAGTGCGTATTA 57.558 33.333 0.00 0.00 0.00 0.98
1643 3477 9.678941 AGTGCGTATTATCATATATTGGTATCG 57.321 33.333 0.00 0.00 0.00 2.92
1644 3478 9.459640 GTGCGTATTATCATATATTGGTATCGT 57.540 33.333 0.00 0.00 0.00 3.73
1685 3519 7.953158 ATTGACATACATGACACATAGTAGC 57.047 36.000 0.00 0.00 32.58 3.58
1686 3520 6.463995 TGACATACATGACACATAGTAGCA 57.536 37.500 0.00 0.00 0.00 3.49
1687 3521 6.273071 TGACATACATGACACATAGTAGCAC 58.727 40.000 0.00 0.00 0.00 4.40
1688 3522 6.127479 TGACATACATGACACATAGTAGCACA 60.127 38.462 0.00 0.00 0.00 4.57
1689 3523 6.820335 ACATACATGACACATAGTAGCACAT 58.180 36.000 0.00 0.00 0.00 3.21
1690 3524 6.925718 ACATACATGACACATAGTAGCACATC 59.074 38.462 0.00 0.00 0.00 3.06
1691 3525 5.343307 ACATGACACATAGTAGCACATCA 57.657 39.130 0.00 0.00 0.00 3.07
1692 3526 5.922053 ACATGACACATAGTAGCACATCAT 58.078 37.500 0.00 0.00 0.00 2.45
1693 3527 5.756833 ACATGACACATAGTAGCACATCATG 59.243 40.000 0.00 8.86 44.90 3.07
1694 3528 5.343307 TGACACATAGTAGCACATCATGT 57.657 39.130 0.00 0.00 0.00 3.21
1695 3529 6.463995 TGACACATAGTAGCACATCATGTA 57.536 37.500 0.00 0.00 0.00 2.29
1696 3530 6.872920 TGACACATAGTAGCACATCATGTAA 58.127 36.000 0.00 0.00 0.00 2.41
1697 3531 7.500141 TGACACATAGTAGCACATCATGTAAT 58.500 34.615 0.00 0.00 0.00 1.89
1698 3532 8.637986 TGACACATAGTAGCACATCATGTAATA 58.362 33.333 0.00 0.00 0.00 0.98
1699 3533 9.645059 GACACATAGTAGCACATCATGTAATAT 57.355 33.333 0.00 0.00 0.00 1.28
1782 4272 8.883954 TCAAATTTGAAAAGTTACATGCATGA 57.116 26.923 32.75 13.72 33.55 3.07
1790 4280 9.836864 TGAAAAGTTACATGCATGATACTATCT 57.163 29.630 32.75 18.91 0.00 1.98
1829 4414 5.621635 CGACATCTTAATAAGTGTCGTGG 57.378 43.478 28.64 15.16 46.08 4.94
1830 4415 5.100259 CGACATCTTAATAAGTGTCGTGGT 58.900 41.667 28.64 10.98 46.08 4.16
1831 4416 5.575606 CGACATCTTAATAAGTGTCGTGGTT 59.424 40.000 28.64 5.39 46.08 3.67
1835 4420 9.275398 ACATCTTAATAAGTGTCGTGGTTTTAA 57.725 29.630 0.00 0.00 0.00 1.52
1847 4438 8.006027 GTGTCGTGGTTTTAATCAGTAAGTAAC 58.994 37.037 0.00 0.00 0.00 2.50
1857 4448 9.787435 TTTAATCAGTAAGTAACCTGAATGTGT 57.213 29.630 0.00 0.00 0.00 3.72
1897 4502 3.003689 GGTATCATTTGAAGGATGCGGTG 59.996 47.826 1.47 0.00 33.55 4.94
2023 4628 4.388499 ACCACCATCGTCACCGGC 62.388 66.667 0.00 0.00 33.95 6.13
2173 4778 4.794439 CACGTCATCGCGGAGGCA 62.794 66.667 6.13 0.00 41.18 4.75
2465 5070 0.108567 GAACCAGAGGGAGTTCGAGC 60.109 60.000 0.00 0.00 38.05 5.03
2512 5117 3.806625 GGTGTTAAGACCGCCTACATA 57.193 47.619 5.96 0.00 0.00 2.29
2537 5142 1.000274 GCAACACCTGGGTCATTGAAC 60.000 52.381 14.12 0.00 0.00 3.18
2562 5167 3.243434 ACCAAATAGCTAGATCCGTCGTG 60.243 47.826 0.00 0.00 0.00 4.35
2587 5192 6.035112 GTCATATCTCTTCTCGTTGGTTGTTC 59.965 42.308 0.00 0.00 0.00 3.18
2638 5243 0.464373 TCCTTGATCCTGAATGGCGC 60.464 55.000 0.00 0.00 35.26 6.53
2647 5252 5.181811 TGATCCTGAATGGCGCATAATAAAG 59.818 40.000 10.83 1.25 35.26 1.85
2676 5281 5.967088 TGCTAAATCTCAGTCCACTAGAAC 58.033 41.667 0.00 0.00 0.00 3.01
2777 5382 9.880157 GAAATCATACCTACAAACTACCACTTA 57.120 33.333 0.00 0.00 0.00 2.24
2778 5383 9.662947 AAATCATACCTACAAACTACCACTTAC 57.337 33.333 0.00 0.00 0.00 2.34
2785 5391 8.626526 ACCTACAAACTACCACTTACAAATTTG 58.373 33.333 16.67 16.67 33.17 2.32
2789 5395 8.308207 ACAAACTACCACTTACAAATTTGTGTT 58.692 29.630 29.72 19.75 42.31 3.32
2790 5396 8.591312 CAAACTACCACTTACAAATTTGTGTTG 58.409 33.333 29.72 21.97 42.31 3.33
2794 5400 7.826260 ACCACTTACAAATTTGTGTTGAAAG 57.174 32.000 29.72 24.91 42.31 2.62
2795 5401 7.607250 ACCACTTACAAATTTGTGTTGAAAGA 58.393 30.769 29.72 7.95 42.31 2.52
2850 5456 0.605319 AGCGACTGATTTGGCCGAAA 60.605 50.000 10.16 6.16 0.00 3.46
2858 5464 6.096673 ACTGATTTGGCCGAAATTAAACTT 57.903 33.333 10.16 0.00 34.18 2.66
2859 5465 7.222000 ACTGATTTGGCCGAAATTAAACTTA 57.778 32.000 10.16 0.00 34.18 2.24
2872 5478 9.233232 CGAAATTAAACTTAATTATGACAGGGC 57.767 33.333 7.65 0.00 41.20 5.19
2875 5481 9.474313 AATTAAACTTAATTATGACAGGGCTGA 57.526 29.630 5.78 0.00 40.51 4.26
2889 5495 1.301401 GCTGACCCACACGTAAGCA 60.301 57.895 0.00 0.00 39.70 3.91
2892 5498 2.933492 GCTGACCCACACGTAAGCATTA 60.933 50.000 0.00 0.00 39.70 1.90
2895 5501 3.244284 TGACCCACACGTAAGCATTAACT 60.244 43.478 0.00 0.00 45.62 2.24
2898 5504 3.500680 CCCACACGTAAGCATTAACTGTT 59.499 43.478 0.00 0.00 45.62 3.16
2906 5512 7.477422 CACGTAAGCATTAACTGTTACATTGAC 59.523 37.037 0.00 0.00 45.62 3.18
2912 5518 7.335924 AGCATTAACTGTTACATTGACCGTTAT 59.664 33.333 0.00 0.00 30.44 1.89
2913 5519 7.428183 GCATTAACTGTTACATTGACCGTTATG 59.572 37.037 0.00 0.00 30.44 1.90
2923 5529 3.173668 TGACCGTTATGACATGTAGGC 57.826 47.619 0.00 0.00 0.00 3.93
2926 5532 1.542547 CCGTTATGACATGTAGGCCCC 60.543 57.143 0.00 0.00 0.00 5.80
2928 5534 2.420827 CGTTATGACATGTAGGCCCCAA 60.421 50.000 0.00 0.00 0.00 4.12
2950 5556 2.430694 TGGTCAGTGTCCCATCTAATCG 59.569 50.000 3.84 0.00 0.00 3.34
2959 5565 8.253810 CAGTGTCCCATCTAATCGTGAATATAT 58.746 37.037 0.00 0.00 0.00 0.86
3004 5610 3.259314 TGCAGGCCCAGTGGTCAT 61.259 61.111 8.74 0.00 39.40 3.06
3084 5690 0.615261 GACTCCCCTTTCCTCCTCGT 60.615 60.000 0.00 0.00 0.00 4.18
3096 5702 4.363990 CCTCGTGTCGCTGTGGCT 62.364 66.667 0.00 0.00 36.09 4.75
3147 6158 2.202479 CAGTCGAGATGCGCACGA 60.202 61.111 14.90 15.84 40.61 4.35
3150 6161 1.801913 GTCGAGATGCGCACGAAGT 60.802 57.895 21.05 1.07 41.13 3.01
3172 6183 0.172578 CTGTCGATGGCCACGTTCTA 59.827 55.000 21.61 1.80 0.00 2.10
3175 6186 0.172578 TCGATGGCCACGTTCTACAG 59.827 55.000 21.61 0.59 0.00 2.74
3178 6189 1.553690 ATGGCCACGTTCTACAGCCT 61.554 55.000 8.16 0.00 44.19 4.58
3181 6192 1.153823 CCACGTTCTACAGCCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
3182 6193 1.592400 CCACGTTCTACAGCCTCCGA 61.592 60.000 0.00 0.00 0.00 4.55
3186 6197 0.802607 GTTCTACAGCCTCCGAAGCG 60.803 60.000 0.00 0.00 34.64 4.68
3187 6198 0.963856 TTCTACAGCCTCCGAAGCGA 60.964 55.000 0.00 0.00 34.64 4.93
3225 6236 4.624293 CGGAGCTGATGTCGCTAG 57.376 61.111 0.00 0.00 37.96 3.42
3226 6237 1.659954 CGGAGCTGATGTCGCTAGC 60.660 63.158 4.06 4.06 37.96 3.42
3326 6349 6.681093 TGGGGAATTTTAGAGGAAGGAGATAA 59.319 38.462 0.00 0.00 0.00 1.75
3341 6364 6.078456 AGGAGATAAAAATGACATGTGGGA 57.922 37.500 1.15 0.00 0.00 4.37
3371 6394 2.903798 TGACGGTCAAACTTAACGGTT 58.096 42.857 8.68 0.00 0.00 4.44
3396 6420 5.123186 TGAATTTTTCAGTTCTGACGTGTGT 59.877 36.000 0.00 0.00 34.08 3.72
3406 6430 2.203153 ACGTGTGTGCCAACCCTC 60.203 61.111 0.00 0.00 0.00 4.30
3438 6462 2.989166 GTTTAAACGAGTCGAATCGGGT 59.011 45.455 34.54 24.57 46.91 5.28
3445 6469 2.097142 CGAGTCGAATCGGGTACTTTCT 59.903 50.000 26.23 0.00 39.04 2.52
3485 6509 9.887406 TTTAGTTAAAGATTAGTGAAAAAGCGG 57.113 29.630 0.00 0.00 0.00 5.52
3490 6514 6.723131 AAGATTAGTGAAAAAGCGGTAGTC 57.277 37.500 0.00 0.00 0.00 2.59
3491 6515 6.038997 AGATTAGTGAAAAAGCGGTAGTCT 57.961 37.500 0.00 0.00 0.00 3.24
3492 6516 7.166691 AGATTAGTGAAAAAGCGGTAGTCTA 57.833 36.000 0.00 0.00 0.00 2.59
3493 6517 7.783042 AGATTAGTGAAAAAGCGGTAGTCTAT 58.217 34.615 0.00 0.00 0.00 1.98
3494 6518 8.910944 AGATTAGTGAAAAAGCGGTAGTCTATA 58.089 33.333 0.00 0.00 0.00 1.31
3495 6519 9.182933 GATTAGTGAAAAAGCGGTAGTCTATAG 57.817 37.037 0.00 0.00 0.00 1.31
3496 6520 5.903810 AGTGAAAAAGCGGTAGTCTATAGG 58.096 41.667 0.00 0.00 0.00 2.57
3497 6521 4.507021 GTGAAAAAGCGGTAGTCTATAGGC 59.493 45.833 0.00 0.00 0.00 3.93
3498 6522 4.160814 TGAAAAAGCGGTAGTCTATAGGCA 59.839 41.667 7.19 0.00 0.00 4.75
3499 6523 3.729862 AAAGCGGTAGTCTATAGGCAC 57.270 47.619 7.19 2.99 0.00 5.01
3500 6524 1.236628 AGCGGTAGTCTATAGGCACG 58.763 55.000 7.19 9.17 0.00 5.34
3501 6525 0.240411 GCGGTAGTCTATAGGCACGG 59.760 60.000 7.19 8.27 0.00 4.94
3502 6526 1.602311 CGGTAGTCTATAGGCACGGT 58.398 55.000 7.19 0.00 0.00 4.83
3503 6527 1.952296 CGGTAGTCTATAGGCACGGTT 59.048 52.381 7.19 0.00 0.00 4.44
3504 6528 2.031333 CGGTAGTCTATAGGCACGGTTC 60.031 54.545 7.19 0.00 0.00 3.62
3505 6529 2.031333 GGTAGTCTATAGGCACGGTTCG 60.031 54.545 7.19 0.00 0.00 3.95
3506 6530 2.048444 AGTCTATAGGCACGGTTCGA 57.952 50.000 7.19 0.00 0.00 3.71
3507 6531 2.584236 AGTCTATAGGCACGGTTCGAT 58.416 47.619 7.19 0.00 0.00 3.59
3508 6532 2.293677 AGTCTATAGGCACGGTTCGATG 59.706 50.000 7.19 0.00 0.00 3.84
3509 6533 2.292569 GTCTATAGGCACGGTTCGATGA 59.707 50.000 0.00 0.00 0.00 2.92
3510 6534 2.953648 TCTATAGGCACGGTTCGATGAA 59.046 45.455 0.00 0.00 0.00 2.57
3511 6535 2.910688 ATAGGCACGGTTCGATGAAT 57.089 45.000 0.00 0.00 0.00 2.57
3512 6536 2.684001 TAGGCACGGTTCGATGAATT 57.316 45.000 0.00 0.00 0.00 2.17
3513 6537 1.086696 AGGCACGGTTCGATGAATTG 58.913 50.000 0.00 0.00 0.00 2.32
3514 6538 0.802494 GGCACGGTTCGATGAATTGT 59.198 50.000 0.00 0.00 0.00 2.71
3515 6539 1.465689 GGCACGGTTCGATGAATTGTG 60.466 52.381 8.74 8.74 34.77 3.33
3516 6540 1.882198 CACGGTTCGATGAATTGTGC 58.118 50.000 0.00 0.00 0.00 4.57
3517 6541 1.464608 CACGGTTCGATGAATTGTGCT 59.535 47.619 0.00 0.00 0.00 4.40
3518 6542 2.670905 CACGGTTCGATGAATTGTGCTA 59.329 45.455 0.00 0.00 0.00 3.49
3519 6543 2.930040 ACGGTTCGATGAATTGTGCTAG 59.070 45.455 0.00 0.00 0.00 3.42
3520 6544 2.930040 CGGTTCGATGAATTGTGCTAGT 59.070 45.455 0.00 0.00 0.00 2.57
3521 6545 3.370978 CGGTTCGATGAATTGTGCTAGTT 59.629 43.478 0.00 0.00 0.00 2.24
3522 6546 4.142902 CGGTTCGATGAATTGTGCTAGTTT 60.143 41.667 0.00 0.00 0.00 2.66
3523 6547 5.616866 CGGTTCGATGAATTGTGCTAGTTTT 60.617 40.000 0.00 0.00 0.00 2.43
3524 6548 6.149633 GGTTCGATGAATTGTGCTAGTTTTT 58.850 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 28 2.279582 GTGACCGACTCACTACATGG 57.720 55.000 0.00 0.00 45.38 3.66
57 60 1.555075 AGACGATACCATGTGCCACTT 59.445 47.619 0.00 0.00 0.00 3.16
62 65 1.212616 GCAGAGACGATACCATGTGC 58.787 55.000 0.00 0.00 0.00 4.57
76 79 4.172512 AGAGCGGGCCATGCAGAG 62.173 66.667 19.93 0.00 33.85 3.35
86 89 0.745845 CACCATTTGGAGAGAGCGGG 60.746 60.000 3.01 0.00 38.94 6.13
114 122 0.673985 TGCGTCAGTCTACTTGCTGT 59.326 50.000 0.00 0.00 34.57 4.40
161 173 3.477210 AGGATCAGGGCTATCGTTTTC 57.523 47.619 0.00 0.00 0.00 2.29
166 178 0.668706 CGCAAGGATCAGGGCTATCG 60.669 60.000 0.00 0.00 0.00 2.92
197 210 3.939592 GGTGAGGGAATTAGCAACACTAC 59.060 47.826 0.00 0.00 0.00 2.73
329 1199 0.891373 TCCTCTTCCTTCACTCGCAG 59.109 55.000 0.00 0.00 0.00 5.18
350 1220 2.093658 TCAAAAGCTACCTCGGTCATCC 60.094 50.000 0.00 0.00 0.00 3.51
353 1223 2.354704 CCATCAAAAGCTACCTCGGTCA 60.355 50.000 0.00 0.00 0.00 4.02
402 1272 2.701780 GGTGAGCGGCGAGAGAGAA 61.702 63.158 12.98 0.00 0.00 2.87
416 1286 1.952990 TGCTGAATTTTTGCTCGGTGA 59.047 42.857 0.00 0.00 0.00 4.02
429 1315 8.462016 GGTTATCATCTAAAAACTGTGCTGAAT 58.538 33.333 0.00 0.00 0.00 2.57
443 1329 9.847224 CTTTAGCTAAAAGGGGTTATCATCTAA 57.153 33.333 19.10 0.00 40.86 2.10
479 1365 3.674528 AGTTGTGAGTGATGACAGAGG 57.325 47.619 0.00 0.00 0.00 3.69
484 1370 3.678056 TGGGTAGTTGTGAGTGATGAC 57.322 47.619 0.00 0.00 0.00 3.06
496 1394 1.506907 GGGGCCTCCTTTGGGTAGTT 61.507 60.000 0.84 0.00 0.00 2.24
499 1397 1.928567 CTGGGGCCTCCTTTGGGTA 60.929 63.158 0.00 0.00 36.20 3.69
501 1399 2.092904 TTTCTGGGGCCTCCTTTGGG 62.093 60.000 0.00 0.00 36.20 4.12
615 1517 1.746220 GCACTGTGTCTACTCGGAGAT 59.254 52.381 12.86 0.00 33.89 2.75
652 1554 2.483188 GCTTCATAGGGTACTGTTCGGG 60.483 54.545 0.00 0.00 0.00 5.14
761 1730 5.473504 TGGGAGTTATGTTTTCTTGAGCTTC 59.526 40.000 0.00 0.00 0.00 3.86
777 1746 4.819082 GCGTATGCGTGGGAGTTA 57.181 55.556 4.81 0.00 40.81 2.24
792 1761 3.121944 GCACCGATAATATTGAGACAGCG 59.878 47.826 0.00 0.00 0.00 5.18
929 2033 3.035942 CGTTTGTTTTGTACTGAGCAGC 58.964 45.455 0.00 0.00 0.00 5.25
932 2036 2.034076 CGCGTTTGTTTTGTACTGAGC 58.966 47.619 0.00 0.00 0.00 4.26
940 2044 5.125742 GTGTACTAGTACGCGTTTGTTTTG 58.874 41.667 26.15 4.37 38.85 2.44
950 2054 0.248377 CGGCTGGTGTACTAGTACGC 60.248 60.000 30.20 30.20 43.69 4.42
954 2058 1.890894 CTGCGGCTGGTGTACTAGT 59.109 57.895 0.00 0.00 0.00 2.57
955 2059 1.519455 GCTGCGGCTGGTGTACTAG 60.519 63.158 11.21 0.00 35.22 2.57
956 2060 1.822114 TTGCTGCGGCTGGTGTACTA 61.822 55.000 20.27 0.00 39.59 1.82
957 2061 2.674563 TTTGCTGCGGCTGGTGTACT 62.675 55.000 20.27 0.00 39.59 2.73
958 2062 2.258013 TTTGCTGCGGCTGGTGTAC 61.258 57.895 20.27 0.00 39.59 2.90
960 2064 3.595758 GTTTGCTGCGGCTGGTGT 61.596 61.111 20.27 0.00 39.59 4.16
982 2094 0.984961 ATTAGCTGCCTCTGCCTCCA 60.985 55.000 0.00 0.00 36.33 3.86
1368 2480 0.602905 GGACCTTGTCGTTGGTGAGG 60.603 60.000 0.00 0.00 36.59 3.86
1420 2532 8.660373 ACAACGTACTACAACATAGAGTACTAC 58.340 37.037 0.00 0.00 42.17 2.73
1422 2534 7.678947 ACAACGTACTACAACATAGAGTACT 57.321 36.000 0.00 0.00 42.17 2.73
1423 2535 9.430838 CATACAACGTACTACAACATAGAGTAC 57.569 37.037 0.00 0.00 41.33 2.73
1424 2536 9.166173 ACATACAACGTACTACAACATAGAGTA 57.834 33.333 0.00 0.00 0.00 2.59
1429 2734 8.183536 CCACTACATACAACGTACTACAACATA 58.816 37.037 0.00 0.00 0.00 2.29
1431 2736 6.380995 CCACTACATACAACGTACTACAACA 58.619 40.000 0.00 0.00 0.00 3.33
1432 2737 5.801947 CCCACTACATACAACGTACTACAAC 59.198 44.000 0.00 0.00 0.00 3.32
1438 2743 3.736126 GCCTCCCACTACATACAACGTAC 60.736 52.174 0.00 0.00 0.00 3.67
1441 2746 1.206132 TGCCTCCCACTACATACAACG 59.794 52.381 0.00 0.00 0.00 4.10
1442 2747 3.343941 TTGCCTCCCACTACATACAAC 57.656 47.619 0.00 0.00 0.00 3.32
1445 2750 3.838244 TGATTGCCTCCCACTACATAC 57.162 47.619 0.00 0.00 0.00 2.39
1446 2751 3.521531 TGTTGATTGCCTCCCACTACATA 59.478 43.478 0.00 0.00 0.00 2.29
1447 2752 2.308570 TGTTGATTGCCTCCCACTACAT 59.691 45.455 0.00 0.00 0.00 2.29
1448 2753 1.702401 TGTTGATTGCCTCCCACTACA 59.298 47.619 0.00 0.00 0.00 2.74
1450 2755 3.737559 AATGTTGATTGCCTCCCACTA 57.262 42.857 0.00 0.00 0.00 2.74
1451 2756 2.610438 AATGTTGATTGCCTCCCACT 57.390 45.000 0.00 0.00 0.00 4.00
1453 2758 6.194235 ACTTATTAATGTTGATTGCCTCCCA 58.806 36.000 0.00 0.00 0.00 4.37
1454 2759 6.715347 ACTTATTAATGTTGATTGCCTCCC 57.285 37.500 0.00 0.00 0.00 4.30
1457 2762 9.338622 GGTAGTACTTATTAATGTTGATTGCCT 57.661 33.333 0.00 0.00 0.00 4.75
1458 2763 9.338622 AGGTAGTACTTATTAATGTTGATTGCC 57.661 33.333 0.00 0.00 0.00 4.52
1462 2767 9.765795 GCAGAGGTAGTACTTATTAATGTTGAT 57.234 33.333 0.00 0.00 0.00 2.57
1463 2768 7.919091 CGCAGAGGTAGTACTTATTAATGTTGA 59.081 37.037 0.00 0.00 0.00 3.18
1464 2769 7.705325 ACGCAGAGGTAGTACTTATTAATGTTG 59.295 37.037 0.00 0.00 0.00 3.33
1465 2770 7.779073 ACGCAGAGGTAGTACTTATTAATGTT 58.221 34.615 0.00 0.00 0.00 2.71
1467 2772 7.649973 AGACGCAGAGGTAGTACTTATTAATG 58.350 38.462 0.00 0.00 0.00 1.90
1469 2774 8.737168 TTAGACGCAGAGGTAGTACTTATTAA 57.263 34.615 0.00 0.00 0.00 1.40
1471 2776 7.479150 GTTTAGACGCAGAGGTAGTACTTATT 58.521 38.462 0.00 0.00 0.00 1.40
1472 2777 6.238320 CGTTTAGACGCAGAGGTAGTACTTAT 60.238 42.308 0.00 0.00 43.03 1.73
1473 2778 5.063944 CGTTTAGACGCAGAGGTAGTACTTA 59.936 44.000 0.00 0.00 43.03 2.24
1474 2779 4.142730 CGTTTAGACGCAGAGGTAGTACTT 60.143 45.833 0.00 0.00 43.03 2.24
1475 2780 3.373439 CGTTTAGACGCAGAGGTAGTACT 59.627 47.826 0.00 0.00 43.03 2.73
1476 2781 3.678662 CGTTTAGACGCAGAGGTAGTAC 58.321 50.000 0.00 0.00 43.03 2.73
1509 2896 6.895782 TCAGAGTAAGTCCTTCCTTTTCAAA 58.104 36.000 0.00 0.00 0.00 2.69
1512 2899 6.110033 GGATCAGAGTAAGTCCTTCCTTTTC 58.890 44.000 0.00 0.00 0.00 2.29
1514 2901 5.094387 TGGATCAGAGTAAGTCCTTCCTTT 58.906 41.667 0.00 0.00 0.00 3.11
1516 2903 4.338795 TGGATCAGAGTAAGTCCTTCCT 57.661 45.455 0.00 0.00 0.00 3.36
1517 2904 6.239458 CCTTATGGATCAGAGTAAGTCCTTCC 60.239 46.154 0.00 0.00 34.57 3.46
1519 2906 5.071115 GCCTTATGGATCAGAGTAAGTCCTT 59.929 44.000 0.00 0.00 34.57 3.36
1520 2907 4.591072 GCCTTATGGATCAGAGTAAGTCCT 59.409 45.833 0.00 0.00 34.57 3.85
1521 2908 4.591072 AGCCTTATGGATCAGAGTAAGTCC 59.409 45.833 0.00 0.00 34.57 3.85
1523 2910 4.346418 CCAGCCTTATGGATCAGAGTAAGT 59.654 45.833 0.00 0.00 43.57 2.24
1524 2911 4.346418 ACCAGCCTTATGGATCAGAGTAAG 59.654 45.833 0.00 0.00 43.57 2.34
1525 2912 4.298626 ACCAGCCTTATGGATCAGAGTAA 58.701 43.478 0.00 0.00 43.57 2.24
1526 2913 3.898123 GACCAGCCTTATGGATCAGAGTA 59.102 47.826 0.00 0.00 43.57 2.59
1527 2914 2.703007 GACCAGCCTTATGGATCAGAGT 59.297 50.000 0.00 0.00 43.57 3.24
1528 2915 2.288702 CGACCAGCCTTATGGATCAGAG 60.289 54.545 0.00 0.00 43.57 3.35
1529 2916 1.688735 CGACCAGCCTTATGGATCAGA 59.311 52.381 0.00 0.00 43.57 3.27
1530 2917 1.414181 ACGACCAGCCTTATGGATCAG 59.586 52.381 0.00 0.00 43.57 2.90
1531 2918 1.496060 ACGACCAGCCTTATGGATCA 58.504 50.000 0.00 0.00 43.57 2.92
1532 2919 2.610727 GCTACGACCAGCCTTATGGATC 60.611 54.545 0.00 0.00 43.57 3.36
1542 3375 4.208686 CTCCCCGCTACGACCAGC 62.209 72.222 0.00 0.00 38.23 4.85
1544 3377 0.396139 AATACTCCCCGCTACGACCA 60.396 55.000 0.00 0.00 0.00 4.02
1545 3379 1.609208 TAATACTCCCCGCTACGACC 58.391 55.000 0.00 0.00 0.00 4.79
1583 3417 2.545113 GCACTACGGTTGTCTTGTCAGA 60.545 50.000 0.00 0.00 0.00 3.27
1584 3418 1.792949 GCACTACGGTTGTCTTGTCAG 59.207 52.381 0.00 0.00 0.00 3.51
1585 3419 1.860676 GCACTACGGTTGTCTTGTCA 58.139 50.000 0.00 0.00 0.00 3.58
1586 3420 0.782384 CGCACTACGGTTGTCTTGTC 59.218 55.000 0.00 0.00 38.44 3.18
1587 3421 2.895039 CGCACTACGGTTGTCTTGT 58.105 52.632 0.00 0.00 38.44 3.16
1598 3432 6.965500 ACGCACTATATGATAATACGCACTAC 59.035 38.462 0.00 0.00 0.00 2.73
1599 3433 7.080353 ACGCACTATATGATAATACGCACTA 57.920 36.000 0.00 0.00 0.00 2.74
1600 3434 5.950883 ACGCACTATATGATAATACGCACT 58.049 37.500 0.00 0.00 0.00 4.40
1601 3435 7.909777 ATACGCACTATATGATAATACGCAC 57.090 36.000 0.00 0.00 0.00 5.34
1617 3451 9.678941 CGATACCAATATATGATAATACGCACT 57.321 33.333 0.00 0.00 0.00 4.40
1618 3452 9.459640 ACGATACCAATATATGATAATACGCAC 57.540 33.333 0.00 0.00 0.00 5.34
1659 3493 9.476202 GCTACTATGTGTCATGTATGTCAATAA 57.524 33.333 0.00 0.00 0.00 1.40
1660 3494 8.637986 TGCTACTATGTGTCATGTATGTCAATA 58.362 33.333 0.00 0.00 0.00 1.90
1661 3495 7.439356 GTGCTACTATGTGTCATGTATGTCAAT 59.561 37.037 0.00 0.00 0.00 2.57
1662 3496 6.756542 GTGCTACTATGTGTCATGTATGTCAA 59.243 38.462 0.00 0.00 0.00 3.18
1663 3497 6.127479 TGTGCTACTATGTGTCATGTATGTCA 60.127 38.462 0.00 0.00 0.00 3.58
1664 3498 6.273071 TGTGCTACTATGTGTCATGTATGTC 58.727 40.000 0.00 0.00 0.00 3.06
1665 3499 6.220726 TGTGCTACTATGTGTCATGTATGT 57.779 37.500 0.00 0.00 0.00 2.29
1666 3500 6.925165 TGATGTGCTACTATGTGTCATGTATG 59.075 38.462 0.00 0.00 0.00 2.39
1667 3501 7.054491 TGATGTGCTACTATGTGTCATGTAT 57.946 36.000 0.00 0.00 0.00 2.29
1668 3502 6.463995 TGATGTGCTACTATGTGTCATGTA 57.536 37.500 0.00 0.00 0.00 2.29
1669 3503 5.343307 TGATGTGCTACTATGTGTCATGT 57.657 39.130 0.00 0.00 0.00 3.21
1670 3504 5.756833 ACATGATGTGCTACTATGTGTCATG 59.243 40.000 0.00 9.67 44.29 3.07
1671 3505 5.922053 ACATGATGTGCTACTATGTGTCAT 58.078 37.500 0.00 0.00 31.34 3.06
1672 3506 5.343307 ACATGATGTGCTACTATGTGTCA 57.657 39.130 0.00 0.00 31.34 3.58
1673 3507 7.953158 ATTACATGATGTGCTACTATGTGTC 57.047 36.000 8.61 0.00 34.22 3.67
1800 4290 9.114965 CGACACTTATTAAGATGTCGGTAATAG 57.885 37.037 29.47 15.35 46.64 1.73
1808 4298 6.963049 AACCACGACACTTATTAAGATGTC 57.037 37.500 18.90 18.90 36.78 3.06
1809 4299 7.739498 AAAACCACGACACTTATTAAGATGT 57.261 32.000 10.39 10.04 0.00 3.06
1813 4398 9.755064 CTGATTAAAACCACGACACTTATTAAG 57.245 33.333 1.79 1.79 0.00 1.85
1815 4400 8.836268 ACTGATTAAAACCACGACACTTATTA 57.164 30.769 0.00 0.00 0.00 0.98
1816 4401 7.739498 ACTGATTAAAACCACGACACTTATT 57.261 32.000 0.00 0.00 0.00 1.40
1820 4405 6.285990 ACTTACTGATTAAAACCACGACACT 58.714 36.000 0.00 0.00 0.00 3.55
1823 4408 7.386025 AGGTTACTTACTGATTAAAACCACGAC 59.614 37.037 0.00 0.00 34.70 4.34
1825 4410 7.385752 TCAGGTTACTTACTGATTAAAACCACG 59.614 37.037 0.00 0.00 38.71 4.94
1826 4411 8.611654 TCAGGTTACTTACTGATTAAAACCAC 57.388 34.615 0.00 0.00 38.71 4.16
1827 4412 9.802039 ATTCAGGTTACTTACTGATTAAAACCA 57.198 29.630 0.00 0.00 42.73 3.67
1831 4416 9.787435 ACACATTCAGGTTACTTACTGATTAAA 57.213 29.630 0.00 0.00 42.73 1.52
1835 4420 8.812972 TCTTACACATTCAGGTTACTTACTGAT 58.187 33.333 0.00 0.00 42.73 2.90
1872 4477 3.879295 CGCATCCTTCAAATGATACCTGT 59.121 43.478 0.00 0.00 0.00 4.00
1891 4496 2.672651 CCACCATCAAGCACCGCA 60.673 61.111 0.00 0.00 0.00 5.69
1897 4502 2.440980 GGGAGGCCACCATCAAGC 60.441 66.667 21.72 0.00 0.00 4.01
2363 4968 4.790861 GGACGTCGCCTCCGGTTC 62.791 72.222 9.92 0.00 34.56 3.62
2512 5117 1.064003 TGACCCAGGTGTTGCTGTAT 58.936 50.000 0.00 0.00 0.00 2.29
2537 5142 4.551388 GACGGATCTAGCTATTTGGTGAG 58.449 47.826 0.00 0.00 0.00 3.51
2562 5167 5.411781 ACAACCAACGAGAAGAGATATGAC 58.588 41.667 0.00 0.00 0.00 3.06
2587 5192 2.293677 GCATCATGCAGATTTGGAGAGG 59.706 50.000 4.20 0.00 44.26 3.69
2647 5252 4.336713 GTGGACTGAGATTTAGCAAATCCC 59.663 45.833 14.21 10.22 46.65 3.85
2755 5360 7.779754 TGTAAGTGGTAGTTTGTAGGTATGA 57.220 36.000 0.00 0.00 0.00 2.15
2759 5364 8.626526 CAAATTTGTAAGTGGTAGTTTGTAGGT 58.373 33.333 10.15 0.00 0.00 3.08
2760 5365 8.626526 ACAAATTTGTAAGTGGTAGTTTGTAGG 58.373 33.333 22.10 0.00 40.16 3.18
2777 5382 9.612066 AAATGGTATCTTTCAACACAAATTTGT 57.388 25.926 18.13 18.13 43.36 2.83
2826 5432 1.009829 GCCAAATCAGTCGCTAGTGG 58.990 55.000 2.90 0.00 0.00 4.00
2830 5436 0.248012 TTCGGCCAAATCAGTCGCTA 59.752 50.000 2.24 0.00 0.00 4.26
2850 5456 8.903820 GTCAGCCCTGTCATAATTAAGTTTAAT 58.096 33.333 0.00 0.00 34.98 1.40
2872 5478 1.808411 AATGCTTACGTGTGGGTCAG 58.192 50.000 0.00 0.00 0.00 3.51
2875 5481 3.071479 CAGTTAATGCTTACGTGTGGGT 58.929 45.455 0.00 0.00 0.00 4.51
2878 5484 6.218025 TGTAACAGTTAATGCTTACGTGTG 57.782 37.500 0.00 0.00 32.56 3.82
2889 5495 8.662141 GTCATAACGGTCAATGTAACAGTTAAT 58.338 33.333 0.00 0.00 39.52 1.40
2892 5498 5.992829 TGTCATAACGGTCAATGTAACAGTT 59.007 36.000 0.00 0.00 38.35 3.16
2895 5501 5.935206 ACATGTCATAACGGTCAATGTAACA 59.065 36.000 0.00 3.25 0.00 2.41
2898 5504 6.277605 CCTACATGTCATAACGGTCAATGTA 58.722 40.000 0.00 0.00 0.00 2.29
2906 5512 1.542547 GGGGCCTACATGTCATAACGG 60.543 57.143 0.00 0.00 0.00 4.44
2912 5518 0.258484 CCATTGGGGCCTACATGTCA 59.742 55.000 0.00 0.00 0.00 3.58
2913 5519 0.258774 ACCATTGGGGCCTACATGTC 59.741 55.000 0.00 0.00 42.05 3.06
2923 5529 1.000896 GGGACACTGACCATTGGGG 60.001 63.158 7.78 0.00 44.81 4.96
3084 5690 2.970639 GTCCTAGCCACAGCGACA 59.029 61.111 0.00 0.00 46.67 4.35
3096 5702 4.382320 GTGGCCGCCAACGTCCTA 62.382 66.667 15.39 0.00 38.41 2.94
3112 5718 2.657237 GCAGTACTCCTGTGGCGT 59.343 61.111 0.00 0.00 43.55 5.68
3117 5723 0.251209 TCGACTGGCAGTACTCCTGT 60.251 55.000 22.11 17.56 43.55 4.00
3119 5725 0.328592 TCTCGACTGGCAGTACTCCT 59.671 55.000 22.11 0.00 0.00 3.69
3133 5739 0.248094 CTACTTCGTGCGCATCTCGA 60.248 55.000 15.91 16.22 41.67 4.04
3147 6158 0.108138 GTGGCCATCGACAGCTACTT 60.108 55.000 9.72 0.00 37.49 2.24
3150 6161 1.884075 AACGTGGCCATCGACAGCTA 61.884 55.000 27.07 0.00 0.00 3.32
3172 6183 4.070552 GGTCGCTTCGGAGGCTGT 62.071 66.667 10.50 0.00 0.00 4.40
3247 6258 1.154205 GGCGAATGATGGTGGAGACG 61.154 60.000 0.00 0.00 0.00 4.18
3326 6349 6.189859 ACATATGAGTCCCACATGTCATTTT 58.810 36.000 10.38 0.00 32.01 1.82
3341 6364 4.894784 AGTTTGACCGTCAACATATGAGT 58.105 39.130 13.61 0.00 39.19 3.41
3371 6394 6.027131 CACACGTCAGAACTGAAAAATTCAA 58.973 36.000 6.08 0.00 41.85 2.69
3375 6399 4.730613 GCACACACGTCAGAACTGAAAAAT 60.731 41.667 6.08 0.00 41.85 1.82
3396 6420 2.103094 CTCGATTATGAGAGGGTTGGCA 59.897 50.000 0.00 0.00 38.28 4.92
3406 6430 6.685828 TCGACTCGTTTAAACTCGATTATGAG 59.314 38.462 20.72 16.11 41.86 2.90
3465 6489 8.092687 AGACTACCGCTTTTTCACTAATCTTTA 58.907 33.333 0.00 0.00 0.00 1.85
3469 6493 9.182933 CTATAGACTACCGCTTTTTCACTAATC 57.817 37.037 0.00 0.00 0.00 1.75
3483 6507 1.602311 ACCGTGCCTATAGACTACCG 58.398 55.000 0.00 0.00 0.00 4.02
3485 6509 2.874701 TCGAACCGTGCCTATAGACTAC 59.125 50.000 0.00 0.00 0.00 2.73
3490 6514 3.364889 TTCATCGAACCGTGCCTATAG 57.635 47.619 0.00 0.00 0.00 1.31
3491 6515 4.055360 CAATTCATCGAACCGTGCCTATA 58.945 43.478 0.00 0.00 0.00 1.31
3492 6516 2.872245 CAATTCATCGAACCGTGCCTAT 59.128 45.455 0.00 0.00 0.00 2.57
3493 6517 2.276201 CAATTCATCGAACCGTGCCTA 58.724 47.619 0.00 0.00 0.00 3.93
3494 6518 1.086696 CAATTCATCGAACCGTGCCT 58.913 50.000 0.00 0.00 0.00 4.75
3495 6519 0.802494 ACAATTCATCGAACCGTGCC 59.198 50.000 0.00 0.00 0.00 5.01
3496 6520 1.882198 CACAATTCATCGAACCGTGC 58.118 50.000 0.00 0.00 0.00 5.34
3497 6521 1.464608 AGCACAATTCATCGAACCGTG 59.535 47.619 0.00 0.00 33.17 4.94
3498 6522 1.808411 AGCACAATTCATCGAACCGT 58.192 45.000 0.00 0.00 0.00 4.83
3499 6523 2.930040 ACTAGCACAATTCATCGAACCG 59.070 45.455 0.00 0.00 0.00 4.44
3500 6524 4.946784 AACTAGCACAATTCATCGAACC 57.053 40.909 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.