Multiple sequence alignment - TraesCS6B01G167200

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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 TraesCS6B01G167200 chr6B 100.000 5248 0 0 1 5248 175731014 175725767 0.000000e+00 9692.0
1 TraesCS6B01G167200 chr6B 78.043 838 131 29 26 816 526130840 526130009 3.680000e-131 479.0
2 TraesCS6B01G167200 chr6D 95.439 2412 55 20 2792 5185 91569183 91566809 0.000000e+00 3794.0
3 TraesCS6B01G167200 chr6D 90.812 1121 42 14 1535 2632 91570264 91569182 0.000000e+00 1443.0
4 TraesCS6B01G167200 chr6D 85.273 1134 119 14 22 1120 91572177 91571057 0.000000e+00 1125.0
5 TraesCS6B01G167200 chr6D 85.714 462 41 11 997 1452 91570802 91570360 1.030000e-126 464.0
6 TraesCS6B01G167200 chr6D 92.511 227 17 0 1149 1375 91570800 91570574 5.070000e-85 326.0
7 TraesCS6B01G167200 chr6D 94.152 171 7 2 2629 2797 266773116 266773285 1.880000e-64 257.0
8 TraesCS6B01G167200 chr6D 92.655 177 10 2 2621 2795 13557739 13557564 8.720000e-63 252.0
9 TraesCS6B01G167200 chr6D 77.919 394 62 13 224 597 232368353 232368741 6.840000e-54 222.0
10 TraesCS6B01G167200 chr6D 88.000 100 10 1 2146 2245 202257191 202257288 3.320000e-22 117.0
11 TraesCS6B01G167200 chr6D 95.455 66 2 1 5184 5248 91566727 91566662 2.590000e-18 104.0
12 TraesCS6B01G167200 chr6A 90.606 1682 49 30 3615 5248 110348769 110347149 0.000000e+00 2130.0
13 TraesCS6B01G167200 chr6A 85.695 1475 150 27 1 1427 110353159 110351698 0.000000e+00 1498.0
14 TraesCS6B01G167200 chr6A 96.028 856 28 3 2792 3644 110349620 110348768 0.000000e+00 1387.0
15 TraesCS6B01G167200 chr6A 95.261 633 22 2 2008 2632 110350251 110349619 0.000000e+00 996.0
16 TraesCS6B01G167200 chr6A 93.173 249 12 3 1705 1951 110351027 110350782 1.390000e-95 361.0
17 TraesCS6B01G167200 chr6A 92.529 174 10 2 2622 2793 98747571 98747399 4.060000e-61 246.0
18 TraesCS6B01G167200 chr6A 91.549 71 6 0 2181 2251 309872469 309872399 1.200000e-16 99.0
19 TraesCS6B01G167200 chr6A 92.157 51 4 0 2198 2248 27172791 27172741 7.290000e-09 73.1
20 TraesCS6B01G167200 chr7D 79.295 879 128 31 2 838 296479522 296478656 2.740000e-157 566.0
21 TraesCS6B01G167200 chr1D 80.485 784 105 19 1 749 254616931 254617701 1.650000e-154 556.0
22 TraesCS6B01G167200 chr1D 79.664 654 95 24 17 645 232436352 232436992 2.240000e-118 436.0
23 TraesCS6B01G167200 chr1D 94.152 171 7 2 2631 2799 360358387 360358218 1.880000e-64 257.0
24 TraesCS6B01G167200 chr2D 81.493 643 92 15 1 629 509120581 509121210 2.180000e-138 503.0
25 TraesCS6B01G167200 chr2D 95.210 167 5 2 2629 2793 620615644 620615809 1.450000e-65 261.0
26 TraesCS6B01G167200 chr2D 91.573 178 11 3 2621 2794 194458605 194458782 5.250000e-60 243.0
27 TraesCS6B01G167200 chr2D 87.611 113 13 1 2138 2250 271509182 271509071 4.270000e-26 130.0
28 TraesCS6B01G167200 chr5B 78.225 845 130 31 1 815 689878021 689877201 4.720000e-135 492.0
29 TraesCS6B01G167200 chr5B 91.011 178 14 1 2620 2795 622039379 622039202 6.790000e-59 239.0
30 TraesCS6B01G167200 chr5B 92.424 66 3 1 1785 1850 118522618 118522681 5.600000e-15 93.5
31 TraesCS6B01G167200 chr3A 78.761 678 107 24 1 649 58947418 58946749 2.260000e-113 420.0
32 TraesCS6B01G167200 chr3A 89.032 155 15 1 1699 1853 343232445 343232597 1.930000e-44 191.0
33 TraesCS6B01G167200 chr3B 80.866 554 62 20 1 539 774945273 774945797 3.810000e-106 396.0
34 TraesCS6B01G167200 chr3B 79.333 600 89 17 88 671 659599908 659600488 6.370000e-104 388.0
35 TraesCS6B01G167200 chr3B 93.103 174 9 2 2623 2793 120616904 120617077 8.720000e-63 252.0
36 TraesCS6B01G167200 chr2B 82.558 430 65 8 1 427 722900132 722899710 2.310000e-98 370.0
37 TraesCS6B01G167200 chr2B 92.353 170 11 1 2629 2796 736423918 736423749 1.890000e-59 241.0
38 TraesCS6B01G167200 chr5A 92.818 181 9 3 2631 2809 290391697 290391875 5.210000e-65 259.0
39 TraesCS6B01G167200 chr7B 92.697 178 10 2 2629 2804 678205438 678205614 2.430000e-63 254.0
40 TraesCS6B01G167200 chr7B 88.889 108 11 1 2141 2248 245610378 245610484 1.190000e-26 132.0
41 TraesCS6B01G167200 chr7B 80.000 180 22 5 356 522 25658396 25658218 2.570000e-23 121.0
42 TraesCS6B01G167200 chr7B 76.793 237 40 8 401 627 100195122 100195353 9.230000e-23 119.0
43 TraesCS6B01G167200 chr2A 93.143 175 8 2 2624 2796 310408105 310407933 2.430000e-63 254.0
44 TraesCS6B01G167200 chr4D 91.489 188 9 6 2630 2810 477898794 477898981 8.720000e-63 252.0
45 TraesCS6B01G167200 chr4D 88.889 108 10 2 2141 2248 362118185 362118290 1.190000e-26 132.0
46 TraesCS6B01G167200 chr4D 85.714 112 14 1 435 546 461280197 461280088 3.320000e-22 117.0
47 TraesCS6B01G167200 chr4D 84.314 102 14 1 445 546 17208449 17208548 1.200000e-16 99.0
48 TraesCS6B01G167200 chr3D 92.179 179 12 1 2631 2807 355892353 355892531 8.720000e-63 252.0
49 TraesCS6B01G167200 chr5D 90.625 192 9 8 2630 2814 206101936 206101747 4.060000e-61 246.0
50 TraesCS6B01G167200 chr5D 81.290 155 15 1 1697 1851 547712131 547711991 4.300000e-21 113.0
51 TraesCS6B01G167200 chr1A 91.573 178 10 4 2625 2799 219372622 219372797 1.890000e-59 241.0
52 TraesCS6B01G167200 chr1A 91.837 49 4 0 2198 2246 226433557 226433605 9.430000e-08 69.4
53 TraesCS6B01G167200 chr4A 85.455 220 26 5 2579 2793 712600578 712600796 1.900000e-54 224.0
54 TraesCS6B01G167200 chr4A 87.379 103 11 1 1755 1857 528053245 528053145 3.320000e-22 117.0
55 TraesCS6B01G167200 chr7A 87.421 159 16 3 1694 1851 323444958 323445113 4.180000e-41 180.0


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 TraesCS6B01G167200 chr6B 175725767 175731014 5247 True 9692.000000 9692 100.000000 1 5248 1 chr6B.!!$R1 5247
1 TraesCS6B01G167200 chr6B 526130009 526130840 831 True 479.000000 479 78.043000 26 816 1 chr6B.!!$R2 790
2 TraesCS6B01G167200 chr6D 91566662 91572177 5515 True 1209.333333 3794 90.867333 22 5248 6 chr6D.!!$R2 5226
3 TraesCS6B01G167200 chr6A 110347149 110353159 6010 True 1274.400000 2130 92.152600 1 5248 5 chr6A.!!$R4 5247
4 TraesCS6B01G167200 chr7D 296478656 296479522 866 True 566.000000 566 79.295000 2 838 1 chr7D.!!$R1 836
5 TraesCS6B01G167200 chr1D 254616931 254617701 770 False 556.000000 556 80.485000 1 749 1 chr1D.!!$F2 748
6 TraesCS6B01G167200 chr1D 232436352 232436992 640 False 436.000000 436 79.664000 17 645 1 chr1D.!!$F1 628
7 TraesCS6B01G167200 chr2D 509120581 509121210 629 False 503.000000 503 81.493000 1 629 1 chr2D.!!$F2 628
8 TraesCS6B01G167200 chr5B 689877201 689878021 820 True 492.000000 492 78.225000 1 815 1 chr5B.!!$R2 814
9 TraesCS6B01G167200 chr3A 58946749 58947418 669 True 420.000000 420 78.761000 1 649 1 chr3A.!!$R1 648
10 TraesCS6B01G167200 chr3B 774945273 774945797 524 False 396.000000 396 80.866000 1 539 1 chr3B.!!$F3 538
11 TraesCS6B01G167200 chr3B 659599908 659600488 580 False 388.000000 388 79.333000 88 671 1 chr3B.!!$F2 583

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
345 359 0.107703 GCAATCCTGGACATGGACGA 60.108 55.000 0.0 0.0 36.30 4.20 F
817 955 0.177141 GGACGAAATGGATGTCCGGA 59.823 55.000 0.0 0.0 42.42 5.14 F
1618 2389 0.404426 ACCCCTTTTCCCTTTCTCCG 59.596 55.000 0.0 0.0 0.00 4.63 F
2639 4041 0.032416 TGCTACCCACTACTCCCTCC 60.032 60.000 0.0 0.0 0.00 4.30 F
2641 4043 0.258194 CTACCCACTACTCCCTCCGT 59.742 60.000 0.0 0.0 0.00 4.69 F
2645 4047 0.324460 CCACTACTCCCTCCGTTCCT 60.324 60.000 0.0 0.0 0.00 3.36 F
2646 4048 1.064166 CCACTACTCCCTCCGTTCCTA 60.064 57.143 0.0 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 2031 0.033208 CCCTGCCTCTCTCTCTCTGT 60.033 60.000 0.00 0.00 0.00 3.41 R
1809 2729 1.015085 CGTTTTATGGCGACCGACCA 61.015 55.000 7.72 7.72 42.61 4.02 R
2777 4179 1.569548 TGATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36 R
3922 5361 0.115152 TCTTCTCAGCCCTCTGTCCA 59.885 55.000 0.00 0.00 41.10 4.02 R
4110 5550 6.153067 TCCTGGTTGCAACATTTAATAAACG 58.847 36.000 29.55 6.10 0.00 3.60 R
4112 5552 7.531857 TCTCCTGGTTGCAACATTTAATAAA 57.468 32.000 29.55 4.95 0.00 1.40 R
4510 5951 7.796838 TGAAGTCATGATTACGTCAAAAGAAG 58.203 34.615 0.00 0.00 40.97 2.85 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
23 25 4.938756 TCCCAGGCCACCCAACCT 62.939 66.667 5.01 0.00 36.45 3.50
148 160 2.467880 GTAGGTGATGAAGGACTCCCA 58.532 52.381 0.00 0.00 33.88 4.37
149 161 2.044793 AGGTGATGAAGGACTCCCAA 57.955 50.000 0.00 0.00 33.88 4.12
159 171 1.705997 GGACTCCCAACACACCCACT 61.706 60.000 0.00 0.00 0.00 4.00
174 186 1.447838 CACTACGAGCGCCAATGGT 60.448 57.895 2.29 0.00 0.00 3.55
179 191 2.590092 GAGCGCCAATGGTAGGGT 59.410 61.111 2.29 0.00 0.00 4.34
180 192 1.827394 GAGCGCCAATGGTAGGGTA 59.173 57.895 2.29 0.00 0.00 3.69
345 359 0.107703 GCAATCCTGGACATGGACGA 60.108 55.000 0.00 0.00 36.30 4.20
433 474 3.058160 GCAGGCGCCACAACAGAT 61.058 61.111 31.54 0.76 0.00 2.90
525 583 1.073216 GACGACGAGTAGGACGACGA 61.073 60.000 16.55 0.00 46.85 4.20
564 631 3.792053 ATCGGCGGCGACAATCCTC 62.792 63.158 37.06 0.00 0.00 3.71
567 634 1.069090 GGCGGCGACAATCCTCATA 59.931 57.895 12.98 0.00 0.00 2.15
710 830 8.507524 AAGTCTAAATAATAGGACAGTTTGGC 57.492 34.615 0.00 0.00 0.00 4.52
714 834 8.052748 TCTAAATAATAGGACAGTTTGGCATGT 58.947 33.333 0.00 0.00 0.00 3.21
715 835 9.337396 CTAAATAATAGGACAGTTTGGCATGTA 57.663 33.333 0.00 0.00 0.00 2.29
781 901 0.250166 GACGTGTACCTTTGCCACCT 60.250 55.000 0.00 0.00 0.00 4.00
782 902 1.001181 GACGTGTACCTTTGCCACCTA 59.999 52.381 0.00 0.00 0.00 3.08
783 903 1.417145 ACGTGTACCTTTGCCACCTAA 59.583 47.619 0.00 0.00 0.00 2.69
784 904 2.073816 CGTGTACCTTTGCCACCTAAG 58.926 52.381 0.00 0.00 0.00 2.18
786 906 3.618997 CGTGTACCTTTGCCACCTAAGAT 60.619 47.826 0.00 0.00 0.00 2.40
810 938 2.210116 CGAAATCCGGACGAAATGGAT 58.790 47.619 6.12 0.00 44.26 3.41
817 955 0.177141 GGACGAAATGGATGTCCGGA 59.823 55.000 0.00 0.00 42.42 5.14
838 976 2.594303 TGCGTTGGAGTTGCCCTG 60.594 61.111 0.00 0.00 34.97 4.45
841 979 1.966451 CGTTGGAGTTGCCCTGACC 60.966 63.158 0.00 0.00 34.97 4.02
877 1015 4.194720 GATCCGACGGCTCGCAGT 62.195 66.667 9.66 0.00 38.70 4.40
946 1084 3.242936 CGTTTTCCGACCAGACACAAATT 60.243 43.478 0.00 0.00 39.56 1.82
1066 1213 1.153745 GACATCGACGCCTTCAGCT 60.154 57.895 0.00 0.00 40.39 4.24
1067 1214 0.737715 GACATCGACGCCTTCAGCTT 60.738 55.000 0.00 0.00 40.39 3.74
1409 1934 3.470709 CGGAGTGCATAATGTGAGGAAT 58.529 45.455 0.00 0.00 0.00 3.01
1452 1977 8.410912 ACTTTTATTTTAGTCCTGCGAAGTTTT 58.589 29.630 0.00 0.00 0.00 2.43
1453 1978 9.244799 CTTTTATTTTAGTCCTGCGAAGTTTTT 57.755 29.630 0.00 0.00 0.00 1.94
1473 1998 2.325583 TTTTGACACTCCTGCGAAGT 57.674 45.000 0.00 0.00 0.00 3.01
1474 1999 2.325583 TTTGACACTCCTGCGAAGTT 57.674 45.000 0.00 0.00 0.00 2.66
1475 2000 2.325583 TTGACACTCCTGCGAAGTTT 57.674 45.000 0.00 0.00 0.00 2.66
1476 2001 3.462483 TTGACACTCCTGCGAAGTTTA 57.538 42.857 0.00 0.00 0.00 2.01
1477 2002 2.750948 TGACACTCCTGCGAAGTTTAC 58.249 47.619 0.00 0.00 0.00 2.01
1478 2003 2.101750 TGACACTCCTGCGAAGTTTACA 59.898 45.455 0.00 0.00 0.00 2.41
1479 2004 2.731976 GACACTCCTGCGAAGTTTACAG 59.268 50.000 0.00 0.30 0.00 2.74
1480 2005 2.364324 ACACTCCTGCGAAGTTTACAGA 59.636 45.455 7.46 0.00 33.10 3.41
1481 2006 3.006967 ACACTCCTGCGAAGTTTACAGAT 59.993 43.478 7.46 0.00 33.10 2.90
1482 2007 3.369147 CACTCCTGCGAAGTTTACAGATG 59.631 47.826 7.46 3.47 33.10 2.90
1483 2008 2.346803 TCCTGCGAAGTTTACAGATGC 58.653 47.619 7.46 0.00 33.10 3.91
1484 2009 2.028112 TCCTGCGAAGTTTACAGATGCT 60.028 45.455 7.46 0.00 33.10 3.79
1485 2010 2.094894 CCTGCGAAGTTTACAGATGCTG 59.905 50.000 7.46 0.00 37.52 4.41
1486 2011 2.995939 CTGCGAAGTTTACAGATGCTGA 59.004 45.455 0.82 0.00 35.18 4.26
1487 2012 2.995939 TGCGAAGTTTACAGATGCTGAG 59.004 45.455 0.82 0.00 35.18 3.35
1488 2013 3.254060 GCGAAGTTTACAGATGCTGAGA 58.746 45.455 0.82 0.00 35.18 3.27
1489 2014 3.305629 GCGAAGTTTACAGATGCTGAGAG 59.694 47.826 0.82 0.00 35.18 3.20
1490 2015 4.738124 CGAAGTTTACAGATGCTGAGAGA 58.262 43.478 0.82 0.00 35.18 3.10
1491 2016 5.347342 CGAAGTTTACAGATGCTGAGAGAT 58.653 41.667 0.82 0.00 35.18 2.75
1492 2017 6.499172 CGAAGTTTACAGATGCTGAGAGATA 58.501 40.000 0.82 0.00 35.18 1.98
1493 2018 6.636447 CGAAGTTTACAGATGCTGAGAGATAG 59.364 42.308 0.82 0.00 35.18 2.08
1494 2019 6.403866 AGTTTACAGATGCTGAGAGATAGG 57.596 41.667 0.82 0.00 35.18 2.57
1495 2020 5.304101 AGTTTACAGATGCTGAGAGATAGGG 59.696 44.000 0.82 0.00 35.18 3.53
1496 2021 3.609256 ACAGATGCTGAGAGATAGGGA 57.391 47.619 0.82 0.00 35.18 4.20
1497 2022 3.499338 ACAGATGCTGAGAGATAGGGAG 58.501 50.000 0.82 0.00 35.18 4.30
1498 2023 3.139957 ACAGATGCTGAGAGATAGGGAGA 59.860 47.826 0.82 0.00 35.18 3.71
1499 2024 3.760151 CAGATGCTGAGAGATAGGGAGAG 59.240 52.174 0.00 0.00 32.44 3.20
1500 2025 3.657239 AGATGCTGAGAGATAGGGAGAGA 59.343 47.826 0.00 0.00 0.00 3.10
1501 2026 3.961484 TGCTGAGAGATAGGGAGAGAA 57.039 47.619 0.00 0.00 0.00 2.87
1502 2027 4.256983 TGCTGAGAGATAGGGAGAGAAA 57.743 45.455 0.00 0.00 0.00 2.52
1503 2028 3.957497 TGCTGAGAGATAGGGAGAGAAAC 59.043 47.826 0.00 0.00 0.00 2.78
1504 2029 3.957497 GCTGAGAGATAGGGAGAGAAACA 59.043 47.826 0.00 0.00 0.00 2.83
1505 2030 4.202111 GCTGAGAGATAGGGAGAGAAACAC 60.202 50.000 0.00 0.00 0.00 3.32
1506 2031 4.935578 TGAGAGATAGGGAGAGAAACACA 58.064 43.478 0.00 0.00 0.00 3.72
1507 2032 4.707448 TGAGAGATAGGGAGAGAAACACAC 59.293 45.833 0.00 0.00 0.00 3.82
1512 2037 2.964209 AGGGAGAGAAACACACAGAGA 58.036 47.619 0.00 0.00 0.00 3.10
1521 2046 1.544724 ACACACAGAGAGAGAGAGGC 58.455 55.000 0.00 0.00 0.00 4.70
1538 2120 2.445654 CAGGGAGGGAGGGAGCTC 60.446 72.222 4.71 4.71 0.00 4.09
1558 2140 3.851128 GCCTCCGCACTACCTCCC 61.851 72.222 0.00 0.00 34.03 4.30
1565 2147 2.722201 GCACTACCTCCCCTCCACG 61.722 68.421 0.00 0.00 0.00 4.94
1566 2148 2.058595 CACTACCTCCCCTCCACGG 61.059 68.421 0.00 0.00 0.00 4.94
1567 2149 3.155167 CTACCTCCCCTCCACGGC 61.155 72.222 0.00 0.00 0.00 5.68
1568 2150 3.680196 TACCTCCCCTCCACGGCT 61.680 66.667 0.00 0.00 0.00 5.52
1569 2151 3.674050 TACCTCCCCTCCACGGCTC 62.674 68.421 0.00 0.00 0.00 4.70
1584 2166 3.402681 CTCCACCCCTGCCACGAT 61.403 66.667 0.00 0.00 0.00 3.73
1598 2180 3.610669 CGATCCCCTCCTCCTGCG 61.611 72.222 0.00 0.00 0.00 5.18
1618 2389 0.404426 ACCCCTTTTCCCTTTCTCCG 59.596 55.000 0.00 0.00 0.00 4.63
1621 2392 0.965866 CCTTTTCCCTTTCTCCGGCC 60.966 60.000 0.00 0.00 0.00 6.13
1627 2398 3.646715 CTTTCTCCGGCCACCCCA 61.647 66.667 2.24 0.00 0.00 4.96
1663 2434 1.857348 CACCCCCTTTCCCCTCCTT 60.857 63.158 0.00 0.00 0.00 3.36
1690 2461 1.700042 CCCCTTTCCCCTCCAGATCG 61.700 65.000 0.00 0.00 0.00 3.69
1781 2701 2.098233 GTGTCGCCACACCATACGG 61.098 63.158 2.81 0.00 46.49 4.02
1868 2788 6.991938 ACATTGGTGTTTATGTATTTGCAGT 58.008 32.000 0.00 0.00 34.01 4.40
1986 3350 4.955811 TGCCGATACTTCATGGATACTT 57.044 40.909 0.00 0.00 37.61 2.24
2013 3407 0.782384 GCGTTTCGGATATGTAGCGG 59.218 55.000 0.00 0.00 0.00 5.52
2158 3552 4.222810 GCTCCTCTTCTCCTTTCTCTTCTT 59.777 45.833 0.00 0.00 0.00 2.52
2159 3553 5.279960 GCTCCTCTTCTCCTTTCTCTTCTTT 60.280 44.000 0.00 0.00 0.00 2.52
2176 3578 7.399765 TCTCTTCTTTTGATCTCATCTCCTCTT 59.600 37.037 0.00 0.00 0.00 2.85
2187 3589 6.778821 TCTCATCTCCTCTTATACTCTCCTG 58.221 44.000 0.00 0.00 0.00 3.86
2409 3811 1.279496 TCTGTGCATTCTAGGTGCCT 58.721 50.000 15.41 0.00 41.83 4.75
2412 3814 4.223144 TCTGTGCATTCTAGGTGCCTATA 58.777 43.478 15.41 0.00 41.83 1.31
2506 3908 9.989869 GTAGGTTTTAATTTAGCTGATTCAGTC 57.010 33.333 14.90 7.60 33.43 3.51
2632 4034 1.477295 GTCTCCTGTGCTACCCACTAC 59.523 57.143 0.00 0.00 44.92 2.73
2633 4035 1.358103 TCTCCTGTGCTACCCACTACT 59.642 52.381 0.00 0.00 44.92 2.57
2634 4036 1.751924 CTCCTGTGCTACCCACTACTC 59.248 57.143 0.00 0.00 44.92 2.59
2636 4038 0.824759 CTGTGCTACCCACTACTCCC 59.175 60.000 0.00 0.00 44.92 4.30
2638 4040 1.112950 GTGCTACCCACTACTCCCTC 58.887 60.000 0.00 0.00 41.35 4.30
2639 4041 0.032416 TGCTACCCACTACTCCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
2640 4042 1.108132 GCTACCCACTACTCCCTCCG 61.108 65.000 0.00 0.00 0.00 4.63
2641 4043 0.258194 CTACCCACTACTCCCTCCGT 59.742 60.000 0.00 0.00 0.00 4.69
2644 4046 1.328430 CCCACTACTCCCTCCGTTCC 61.328 65.000 0.00 0.00 0.00 3.62
2645 4047 0.324460 CCACTACTCCCTCCGTTCCT 60.324 60.000 0.00 0.00 0.00 3.36
2646 4048 1.064166 CCACTACTCCCTCCGTTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
2647 4049 2.622452 CCACTACTCCCTCCGTTCCTAA 60.622 54.545 0.00 0.00 0.00 2.69
2648 4050 3.094572 CACTACTCCCTCCGTTCCTAAA 58.905 50.000 0.00 0.00 0.00 1.85
2649 4051 3.705072 CACTACTCCCTCCGTTCCTAAAT 59.295 47.826 0.00 0.00 0.00 1.40
2650 4052 4.891756 CACTACTCCCTCCGTTCCTAAATA 59.108 45.833 0.00 0.00 0.00 1.40
2651 4053 5.539193 CACTACTCCCTCCGTTCCTAAATAT 59.461 44.000 0.00 0.00 0.00 1.28
2652 4054 6.041751 CACTACTCCCTCCGTTCCTAAATATT 59.958 42.308 0.00 0.00 0.00 1.28
2653 4055 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2654 4056 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2655 4057 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2656 4058 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2657 4059 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2658 4060 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2659 4061 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2660 4062 7.415206 CCCTCCGTTCCTAAATATTTGTCTTTG 60.415 40.741 11.05 0.00 0.00 2.77
2661 4063 7.120726 CCTCCGTTCCTAAATATTTGTCTTTGT 59.879 37.037 11.05 0.00 0.00 2.83
2662 4064 9.158233 CTCCGTTCCTAAATATTTGTCTTTGTA 57.842 33.333 11.05 0.00 0.00 2.41
2663 4065 9.158233 TCCGTTCCTAAATATTTGTCTTTGTAG 57.842 33.333 11.05 0.00 0.00 2.74
2664 4066 9.158233 CCGTTCCTAAATATTTGTCTTTGTAGA 57.842 33.333 11.05 0.00 0.00 2.59
2676 4078 9.956720 ATTTGTCTTTGTAGAGATTTCAACAAG 57.043 29.630 0.00 0.00 33.70 3.16
2677 4079 8.506168 TTGTCTTTGTAGAGATTTCAACAAGT 57.494 30.769 0.00 0.00 33.70 3.16
2678 4080 7.919690 TGTCTTTGTAGAGATTTCAACAAGTG 58.080 34.615 0.00 0.00 33.70 3.16
2679 4081 7.768582 TGTCTTTGTAGAGATTTCAACAAGTGA 59.231 33.333 0.00 0.00 33.70 3.41
2680 4082 8.064814 GTCTTTGTAGAGATTTCAACAAGTGAC 58.935 37.037 0.00 0.00 35.39 3.67
2681 4083 7.987458 TCTTTGTAGAGATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
2682 4084 9.261180 CTTTGTAGAGATTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 35.39 2.59
2683 4085 8.589335 TTGTAGAGATTTCAACAAGTGACTAC 57.411 34.615 0.00 0.00 35.39 2.73
2684 4086 7.722363 TGTAGAGATTTCAACAAGTGACTACA 58.278 34.615 0.00 0.00 37.97 2.74
2685 4087 8.367911 TGTAGAGATTTCAACAAGTGACTACAT 58.632 33.333 0.00 0.00 36.58 2.29
2686 4088 9.856488 GTAGAGATTTCAACAAGTGACTACATA 57.144 33.333 0.00 0.00 35.39 2.29
2687 4089 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2688 4090 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2689 4091 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2690 4092 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2691 4093 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2692 4094 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2693 4095 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2694 4096 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2695 4097 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2696 4098 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2697 4099 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2698 4100 6.216801 AGTGACTACATACGGAGCAAAATA 57.783 37.500 0.00 0.00 0.00 1.40
2699 4101 6.636705 AGTGACTACATACGGAGCAAAATAA 58.363 36.000 0.00 0.00 0.00 1.40
2700 4102 6.757010 AGTGACTACATACGGAGCAAAATAAG 59.243 38.462 0.00 0.00 0.00 1.73
2701 4103 6.534079 GTGACTACATACGGAGCAAAATAAGT 59.466 38.462 0.00 0.00 0.00 2.24
2702 4104 6.533723 TGACTACATACGGAGCAAAATAAGTG 59.466 38.462 0.00 0.00 0.00 3.16
2703 4105 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
2704 4106 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
2705 4107 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
2706 4108 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
2707 4109 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
2708 4110 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
2709 4111 6.663944 ACGGAGCAAAATAAGTGAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
2710 4112 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
2711 4113 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
2750 4152 5.838529 CATACATTCGTATGTGGTACTCCA 58.161 41.667 16.91 0.00 46.70 3.86
2751 4153 6.455647 CATACATTCGTATGTGGTACTCCAT 58.544 40.000 16.91 0.00 46.70 3.41
2752 4154 5.353394 ACATTCGTATGTGGTACTCCATT 57.647 39.130 6.89 0.00 46.20 3.16
2753 4155 5.741011 ACATTCGTATGTGGTACTCCATTT 58.259 37.500 6.89 0.00 46.20 2.32
2754 4156 6.880484 ACATTCGTATGTGGTACTCCATTTA 58.120 36.000 6.89 0.00 46.20 1.40
2755 4157 7.332557 ACATTCGTATGTGGTACTCCATTTAA 58.667 34.615 6.89 0.00 46.20 1.52
2756 4158 7.825270 ACATTCGTATGTGGTACTCCATTTAAA 59.175 33.333 6.89 0.00 46.20 1.52
2757 4159 8.670135 CATTCGTATGTGGTACTCCATTTAAAA 58.330 33.333 0.00 0.00 46.20 1.52
2758 4160 8.795842 TTCGTATGTGGTACTCCATTTAAAAT 57.204 30.769 0.00 0.00 46.20 1.82
2759 4161 8.203937 TCGTATGTGGTACTCCATTTAAAATG 57.796 34.615 0.00 0.00 46.20 2.32
2760 4162 7.825270 TCGTATGTGGTACTCCATTTAAAATGT 59.175 33.333 0.00 0.00 46.20 2.71
2761 4163 8.120465 CGTATGTGGTACTCCATTTAAAATGTC 58.880 37.037 0.00 0.00 46.20 3.06
2762 4164 9.174166 GTATGTGGTACTCCATTTAAAATGTCT 57.826 33.333 0.00 0.00 46.20 3.41
2764 4166 8.786826 TGTGGTACTCCATTTAAAATGTCTAG 57.213 34.615 0.00 0.00 46.20 2.43
2765 4167 8.598916 TGTGGTACTCCATTTAAAATGTCTAGA 58.401 33.333 0.00 0.00 46.20 2.43
2766 4168 9.444600 GTGGTACTCCATTTAAAATGTCTAGAA 57.555 33.333 0.00 0.00 46.20 2.10
2785 4187 8.529424 TCTAGAAAGACATATTTAGGAACGGA 57.471 34.615 0.00 0.00 0.00 4.69
2786 4188 8.630917 TCTAGAAAGACATATTTAGGAACGGAG 58.369 37.037 0.00 0.00 0.00 4.63
2787 4189 6.583562 AGAAAGACATATTTAGGAACGGAGG 58.416 40.000 0.00 0.00 0.00 4.30
2788 4190 4.957684 AGACATATTTAGGAACGGAGGG 57.042 45.455 0.00 0.00 0.00 4.30
2789 4191 4.553678 AGACATATTTAGGAACGGAGGGA 58.446 43.478 0.00 0.00 0.00 4.20
2790 4192 4.589374 AGACATATTTAGGAACGGAGGGAG 59.411 45.833 0.00 0.00 0.00 4.30
2791 4193 4.296056 ACATATTTAGGAACGGAGGGAGT 58.704 43.478 0.00 0.00 0.00 3.85
2792 4194 5.461327 ACATATTTAGGAACGGAGGGAGTA 58.539 41.667 0.00 0.00 0.00 2.59
2793 4195 5.539193 ACATATTTAGGAACGGAGGGAGTAG 59.461 44.000 0.00 0.00 0.00 2.57
2794 4196 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
2795 4197 3.967467 TTAGGAACGGAGGGAGTAGAT 57.033 47.619 0.00 0.00 0.00 1.98
2796 4198 2.368311 AGGAACGGAGGGAGTAGATC 57.632 55.000 0.00 0.00 0.00 2.75
2797 4199 1.569548 AGGAACGGAGGGAGTAGATCA 59.430 52.381 0.00 0.00 0.00 2.92
2798 4200 2.178106 AGGAACGGAGGGAGTAGATCAT 59.822 50.000 0.00 0.00 0.00 2.45
2799 4201 3.398292 AGGAACGGAGGGAGTAGATCATA 59.602 47.826 0.00 0.00 0.00 2.15
2800 4202 4.044825 AGGAACGGAGGGAGTAGATCATAT 59.955 45.833 0.00 0.00 0.00 1.78
2801 4203 5.253330 AGGAACGGAGGGAGTAGATCATATA 59.747 44.000 0.00 0.00 0.00 0.86
2855 4257 6.701340 TCAATCTTCAGTGTAGCTGTTGTAT 58.299 36.000 0.00 0.00 45.23 2.29
2916 4318 5.324409 TCCAATCTGAATTGCAGGTTTAGT 58.676 37.500 0.00 0.00 45.60 2.24
3014 4416 4.349342 AGTCCTCCAGAAGTTTCAACAGAT 59.651 41.667 0.00 0.00 0.00 2.90
3104 4506 1.200948 GAAACCTCAAGTCCAGCATGC 59.799 52.381 10.51 10.51 31.97 4.06
3129 4531 6.348458 CGTCAGTGCTGGAGAATCAAAATTTA 60.348 38.462 0.00 0.00 36.25 1.40
3338 4740 4.165779 ACAGTTTTGTGAAGCTTTCAACG 58.834 39.130 14.56 8.52 42.15 4.10
3416 4818 4.949856 ACAATGAGTTCCTTGACTTGTTGT 59.050 37.500 4.49 0.00 35.03 3.32
3417 4819 5.418840 ACAATGAGTTCCTTGACTTGTTGTT 59.581 36.000 4.49 0.00 35.70 2.83
3418 4820 6.601613 ACAATGAGTTCCTTGACTTGTTGTTA 59.398 34.615 4.49 0.00 35.70 2.41
3516 4918 7.885399 ACTGTCCTTTAGCAAGAGTCATAATTT 59.115 33.333 0.00 0.00 30.57 1.82
3674 5104 4.323417 TGGCGAGTAGAACATGAAATTGT 58.677 39.130 0.00 0.00 0.00 2.71
3698 5128 5.705441 TGTCACTTGGCTATTTACCTCTTTG 59.295 40.000 0.00 0.00 0.00 2.77
3699 5129 5.938125 GTCACTTGGCTATTTACCTCTTTGA 59.062 40.000 0.00 0.00 0.00 2.69
3700 5130 6.430000 GTCACTTGGCTATTTACCTCTTTGAA 59.570 38.462 0.00 0.00 0.00 2.69
3701 5131 6.655003 TCACTTGGCTATTTACCTCTTTGAAG 59.345 38.462 0.00 0.00 0.00 3.02
3729 5168 3.366679 CCAATGGAATCTTGTGAGCACAC 60.367 47.826 7.39 7.39 46.09 3.82
4038 5477 5.423015 TGCACATGCTTCCTTTTACAAAAA 58.577 33.333 5.31 0.00 42.66 1.94
4154 5594 5.477984 CAGGAGAATCTGGATTTTGGTTCAA 59.522 40.000 0.00 0.00 33.73 2.69
4218 5658 3.606886 ACGAAGTGTGTCCATGGAC 57.393 52.632 33.97 33.97 42.51 4.02
4447 5888 9.817809 TGAGAATAGAGCACGAAATTAACTTAT 57.182 29.630 0.00 0.00 0.00 1.73
4510 5951 9.346725 GATTGGTAATCATGAGTTGTTTCTTTC 57.653 33.333 0.00 0.00 37.83 2.62
4648 6089 2.812011 GCCCAAACTCAAACGTCAGTAT 59.188 45.455 0.00 0.00 0.00 2.12
4871 6321 3.111098 GCTGAACACACTTTCTTTGCAG 58.889 45.455 0.00 0.00 0.00 4.41
5048 6498 9.685276 TCATTTCACATTATATCTTTCCAGTGT 57.315 29.630 0.00 0.00 0.00 3.55
5102 6552 9.474920 GGAATATAGCATCTCATAGCAGATTAC 57.525 37.037 0.00 0.00 30.07 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 50 1.357258 GCGACGACGTAGGAGTGAGA 61.357 60.000 10.16 0.00 41.98 3.27
86 95 3.799755 GTCGTCATTGGCACGGGC 61.800 66.667 0.00 0.00 37.85 6.13
91 100 2.225791 CTCCTCGGTCGTCATTGGCA 62.226 60.000 0.00 0.00 0.00 4.92
138 150 0.991355 TGGGTGTGTTGGGAGTCCTT 60.991 55.000 9.58 0.00 0.00 3.36
148 160 1.006571 CGCTCGTAGTGGGTGTGTT 60.007 57.895 0.00 0.00 0.00 3.32
149 161 2.649034 CGCTCGTAGTGGGTGTGT 59.351 61.111 0.00 0.00 0.00 3.72
159 171 1.440060 CCTACCATTGGCGCTCGTA 59.560 57.895 7.64 0.00 0.00 3.43
174 186 3.878131 GCCATCATCTCCTCGATACCCTA 60.878 52.174 0.00 0.00 0.00 3.53
179 191 1.077828 AGGGCCATCATCTCCTCGATA 59.922 52.381 6.18 0.00 0.00 2.92
180 192 0.178909 AGGGCCATCATCTCCTCGAT 60.179 55.000 6.18 0.00 0.00 3.59
220 232 1.374252 GCGTCGAGCTTTGGGAAGA 60.374 57.895 0.00 0.00 44.04 2.87
329 342 1.482593 GTCTTCGTCCATGTCCAGGAT 59.517 52.381 0.00 0.00 37.52 3.24
345 359 2.317609 GCATGCACGACACGGTCTT 61.318 57.895 14.21 0.00 0.00 3.01
386 400 1.594833 CCGTGACGGGGAAGATGAA 59.405 57.895 17.80 0.00 44.15 2.57
465 506 0.630673 TATGGAGGTGGCTGCCAAAT 59.369 50.000 25.23 15.10 34.18 2.32
525 583 1.432251 CGCCATCGTCTTCCGTAGT 59.568 57.895 0.00 0.00 37.94 2.73
585 671 9.651913 AAGTTCAACACATCAAAACATAAACTT 57.348 25.926 0.00 0.00 0.00 2.66
587 673 9.081997 TCAAGTTCAACACATCAAAACATAAAC 57.918 29.630 0.00 0.00 0.00 2.01
591 683 6.866480 AGTCAAGTTCAACACATCAAAACAT 58.134 32.000 0.00 0.00 0.00 2.71
593 685 7.429340 CAGTAGTCAAGTTCAACACATCAAAAC 59.571 37.037 0.00 0.00 0.00 2.43
710 830 2.114670 CCAACCAGCCCGCTACATG 61.115 63.158 0.00 0.00 0.00 3.21
738 858 2.049248 TTTACCGTCGTGCGACCC 60.049 61.111 17.47 0.00 44.77 4.46
758 878 1.134340 TGGCAAAGGTACACGTCTGTT 60.134 47.619 0.00 0.00 0.00 3.16
769 889 3.118738 CGTCTATCTTAGGTGGCAAAGGT 60.119 47.826 0.00 0.00 0.00 3.50
771 891 4.386867 TCGTCTATCTTAGGTGGCAAAG 57.613 45.455 0.00 0.00 0.00 2.77
781 901 4.129380 TCGTCCGGATTTCGTCTATCTTA 58.871 43.478 7.81 0.00 37.11 2.10
782 902 2.947652 TCGTCCGGATTTCGTCTATCTT 59.052 45.455 7.81 0.00 37.11 2.40
783 903 2.569059 TCGTCCGGATTTCGTCTATCT 58.431 47.619 7.81 0.00 37.11 1.98
784 904 3.344904 TTCGTCCGGATTTCGTCTATC 57.655 47.619 7.81 0.00 37.11 2.08
786 906 3.441163 CATTTCGTCCGGATTTCGTCTA 58.559 45.455 7.81 0.00 37.11 2.59
810 938 2.431771 CAACGCACGATCCGGACA 60.432 61.111 6.12 0.00 0.00 4.02
817 955 2.325082 GGCAACTCCAACGCACGAT 61.325 57.895 0.00 0.00 34.01 3.73
841 979 1.347097 CGTGCACTCACTGATCGTGG 61.347 60.000 16.19 9.68 43.94 4.94
946 1084 1.485294 TAGGGTTTGGGCGCTGAGAA 61.485 55.000 7.64 0.00 33.59 2.87
1047 1194 1.153745 GCTGAAGGCGTCGATGTCT 60.154 57.895 5.77 5.77 0.00 3.41
1090 1237 4.129148 GGCGAGGATGGGGGCTTT 62.129 66.667 0.00 0.00 0.00 3.51
1453 1978 2.639065 ACTTCGCAGGAGTGTCAAAAA 58.361 42.857 0.00 0.00 0.00 1.94
1454 1979 2.325583 ACTTCGCAGGAGTGTCAAAA 57.674 45.000 0.00 0.00 0.00 2.44
1455 1980 2.325583 AACTTCGCAGGAGTGTCAAA 57.674 45.000 0.00 0.00 0.00 2.69
1456 1981 2.325583 AAACTTCGCAGGAGTGTCAA 57.674 45.000 0.00 0.00 0.00 3.18
1457 1982 2.101750 TGTAAACTTCGCAGGAGTGTCA 59.898 45.455 0.00 0.00 0.00 3.58
1459 1984 2.364324 TCTGTAAACTTCGCAGGAGTGT 59.636 45.455 0.00 0.00 0.00 3.55
1460 1985 3.026630 TCTGTAAACTTCGCAGGAGTG 57.973 47.619 0.00 0.00 0.00 3.51
1461 1986 3.589988 CATCTGTAAACTTCGCAGGAGT 58.410 45.455 0.00 0.00 0.00 3.85
1462 1987 2.349886 GCATCTGTAAACTTCGCAGGAG 59.650 50.000 0.00 0.00 0.00 3.69
1463 1988 2.028112 AGCATCTGTAAACTTCGCAGGA 60.028 45.455 0.00 0.00 0.00 3.86
1464 1989 2.094894 CAGCATCTGTAAACTTCGCAGG 59.905 50.000 0.00 0.00 0.00 4.85
1465 1990 2.995939 TCAGCATCTGTAAACTTCGCAG 59.004 45.455 0.00 0.00 32.61 5.18
1466 1991 2.995939 CTCAGCATCTGTAAACTTCGCA 59.004 45.455 0.00 0.00 32.61 5.10
1467 1992 3.254060 TCTCAGCATCTGTAAACTTCGC 58.746 45.455 0.00 0.00 32.61 4.70
1468 1993 4.738124 TCTCTCAGCATCTGTAAACTTCG 58.262 43.478 0.00 0.00 32.61 3.79
1469 1994 6.922957 CCTATCTCTCAGCATCTGTAAACTTC 59.077 42.308 0.00 0.00 32.61 3.01
1470 1995 6.183360 CCCTATCTCTCAGCATCTGTAAACTT 60.183 42.308 0.00 0.00 32.61 2.66
1471 1996 5.304101 CCCTATCTCTCAGCATCTGTAAACT 59.696 44.000 0.00 0.00 32.61 2.66
1472 1997 5.303078 TCCCTATCTCTCAGCATCTGTAAAC 59.697 44.000 0.00 0.00 32.61 2.01
1473 1998 5.458595 TCCCTATCTCTCAGCATCTGTAAA 58.541 41.667 0.00 0.00 32.61 2.01
1474 1999 5.066913 TCCCTATCTCTCAGCATCTGTAA 57.933 43.478 0.00 0.00 32.61 2.41
1475 2000 4.352298 TCTCCCTATCTCTCAGCATCTGTA 59.648 45.833 0.00 0.00 32.61 2.74
1476 2001 3.139957 TCTCCCTATCTCTCAGCATCTGT 59.860 47.826 0.00 0.00 32.61 3.41
1477 2002 3.760151 CTCTCCCTATCTCTCAGCATCTG 59.240 52.174 0.00 0.00 0.00 2.90
1478 2003 3.657239 TCTCTCCCTATCTCTCAGCATCT 59.343 47.826 0.00 0.00 0.00 2.90
1479 2004 4.032960 TCTCTCCCTATCTCTCAGCATC 57.967 50.000 0.00 0.00 0.00 3.91
1480 2005 4.467861 TTCTCTCCCTATCTCTCAGCAT 57.532 45.455 0.00 0.00 0.00 3.79
1481 2006 3.957497 GTTTCTCTCCCTATCTCTCAGCA 59.043 47.826 0.00 0.00 0.00 4.41
1482 2007 3.957497 TGTTTCTCTCCCTATCTCTCAGC 59.043 47.826 0.00 0.00 0.00 4.26
1483 2008 4.952957 TGTGTTTCTCTCCCTATCTCTCAG 59.047 45.833 0.00 0.00 0.00 3.35
1484 2009 4.707448 GTGTGTTTCTCTCCCTATCTCTCA 59.293 45.833 0.00 0.00 0.00 3.27
1485 2010 4.707448 TGTGTGTTTCTCTCCCTATCTCTC 59.293 45.833 0.00 0.00 0.00 3.20
1486 2011 4.678256 TGTGTGTTTCTCTCCCTATCTCT 58.322 43.478 0.00 0.00 0.00 3.10
1487 2012 4.707448 TCTGTGTGTTTCTCTCCCTATCTC 59.293 45.833 0.00 0.00 0.00 2.75
1488 2013 4.678256 TCTGTGTGTTTCTCTCCCTATCT 58.322 43.478 0.00 0.00 0.00 1.98
1489 2014 4.707448 TCTCTGTGTGTTTCTCTCCCTATC 59.293 45.833 0.00 0.00 0.00 2.08
1490 2015 4.678256 TCTCTGTGTGTTTCTCTCCCTAT 58.322 43.478 0.00 0.00 0.00 2.57
1491 2016 4.082845 CTCTCTGTGTGTTTCTCTCCCTA 58.917 47.826 0.00 0.00 0.00 3.53
1492 2017 2.896685 CTCTCTGTGTGTTTCTCTCCCT 59.103 50.000 0.00 0.00 0.00 4.20
1493 2018 2.894126 TCTCTCTGTGTGTTTCTCTCCC 59.106 50.000 0.00 0.00 0.00 4.30
1494 2019 3.823873 TCTCTCTCTGTGTGTTTCTCTCC 59.176 47.826 0.00 0.00 0.00 3.71
1495 2020 4.759693 TCTCTCTCTCTGTGTGTTTCTCTC 59.240 45.833 0.00 0.00 0.00 3.20
1496 2021 4.724399 TCTCTCTCTCTGTGTGTTTCTCT 58.276 43.478 0.00 0.00 0.00 3.10
1497 2022 4.082787 CCTCTCTCTCTCTGTGTGTTTCTC 60.083 50.000 0.00 0.00 0.00 2.87
1498 2023 3.826157 CCTCTCTCTCTCTGTGTGTTTCT 59.174 47.826 0.00 0.00 0.00 2.52
1499 2024 3.613910 GCCTCTCTCTCTCTGTGTGTTTC 60.614 52.174 0.00 0.00 0.00 2.78
1500 2025 2.298729 GCCTCTCTCTCTCTGTGTGTTT 59.701 50.000 0.00 0.00 0.00 2.83
1501 2026 1.892474 GCCTCTCTCTCTCTGTGTGTT 59.108 52.381 0.00 0.00 0.00 3.32
1502 2027 1.202989 TGCCTCTCTCTCTCTGTGTGT 60.203 52.381 0.00 0.00 0.00 3.72
1503 2028 1.473677 CTGCCTCTCTCTCTCTGTGTG 59.526 57.143 0.00 0.00 0.00 3.82
1504 2029 1.616725 CCTGCCTCTCTCTCTCTGTGT 60.617 57.143 0.00 0.00 0.00 3.72
1505 2030 1.105457 CCTGCCTCTCTCTCTCTGTG 58.895 60.000 0.00 0.00 0.00 3.66
1506 2031 0.033208 CCCTGCCTCTCTCTCTCTGT 60.033 60.000 0.00 0.00 0.00 3.41
1507 2032 0.258484 TCCCTGCCTCTCTCTCTCTG 59.742 60.000 0.00 0.00 0.00 3.35
1512 2037 1.938596 TCCCTCCCTGCCTCTCTCT 60.939 63.158 0.00 0.00 0.00 3.10
1521 2046 2.445654 GAGCTCCCTCCCTCCCTG 60.446 72.222 0.87 0.00 31.68 4.45
1538 2120 3.077556 AGGTAGTGCGGAGGCTGG 61.078 66.667 0.00 0.00 40.82 4.85
1567 2149 3.391665 GATCGTGGCAGGGGTGGAG 62.392 68.421 7.42 0.00 0.00 3.86
1568 2150 3.399181 GATCGTGGCAGGGGTGGA 61.399 66.667 7.42 0.00 0.00 4.02
1569 2151 4.489771 GGATCGTGGCAGGGGTGG 62.490 72.222 7.42 0.00 0.00 4.61
1570 2152 4.489771 GGGATCGTGGCAGGGGTG 62.490 72.222 7.42 0.00 0.00 4.61
1573 2155 3.866582 GAGGGGATCGTGGCAGGG 61.867 72.222 7.42 0.00 0.00 4.45
1584 2166 4.779733 GGTCGCAGGAGGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
1598 2180 1.613520 CGGAGAAAGGGAAAAGGGGTC 60.614 57.143 0.00 0.00 0.00 4.46
1618 2389 4.696805 GGGGAAAGTGGGGTGGCC 62.697 72.222 0.00 0.00 0.00 5.36
1621 2392 1.852626 AGGAGGGGAAAGTGGGGTG 60.853 63.158 0.00 0.00 0.00 4.61
1627 2398 4.083862 GCGCGAGGAGGGGAAAGT 62.084 66.667 12.10 0.00 0.00 2.66
1663 2434 2.204244 GGGAAAGGGGGTGGAGGA 60.204 66.667 0.00 0.00 0.00 3.71
1690 2461 5.855740 AGACATAACCTAACTCTGTAGCC 57.144 43.478 0.00 0.00 0.00 3.93
1802 2722 2.264794 GCGACCGACCACCTTCAT 59.735 61.111 0.00 0.00 0.00 2.57
1803 2723 3.998672 GGCGACCGACCACCTTCA 61.999 66.667 0.00 0.00 0.00 3.02
1809 2729 1.015085 CGTTTTATGGCGACCGACCA 61.015 55.000 7.72 7.72 42.61 4.02
1895 2815 4.503296 GGACATATTGGAGCAGTATCCGTT 60.503 45.833 0.00 0.00 42.77 4.44
1986 3350 2.173758 TATCCGAAACGCACTGGCCA 62.174 55.000 4.71 4.71 36.38 5.36
2013 3407 1.829849 GTCAGGGGACTAGGGTTGTAC 59.170 57.143 0.00 0.00 40.21 2.90
2128 3522 1.437160 GAGAAGAGGAGCAGCTCGG 59.563 63.158 16.47 0.00 0.00 4.63
2158 3552 9.295825 GAGAGTATAAGAGGAGATGAGATCAAA 57.704 37.037 0.00 0.00 0.00 2.69
2159 3553 7.888021 GGAGAGTATAAGAGGAGATGAGATCAA 59.112 40.741 0.00 0.00 0.00 2.57
2176 3578 3.161067 GAGCCATCTGCAGGAGAGTATA 58.839 50.000 15.13 0.00 44.83 1.47
2187 3589 2.203181 GCAGGAGGAGCCATCTGC 60.203 66.667 14.88 14.88 44.34 4.26
2412 3814 7.016153 TGGTTACTCCAGAAATTCATACAGT 57.984 36.000 0.00 0.00 41.93 3.55
2506 3908 3.648009 TGAAGGCGCCAAAAATTAACAG 58.352 40.909 31.54 0.00 0.00 3.16
2632 4034 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2633 4035 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2634 4036 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2636 4038 8.040716 ACAAAGACAAATATTTAGGAACGGAG 57.959 34.615 0.00 0.00 0.00 4.63
2638 4040 9.158233 TCTACAAAGACAAATATTTAGGAACGG 57.842 33.333 0.00 0.00 0.00 4.44
2650 4052 9.956720 CTTGTTGAAATCTCTACAAAGACAAAT 57.043 29.630 0.00 0.00 43.56 2.32
2651 4053 8.956426 ACTTGTTGAAATCTCTACAAAGACAAA 58.044 29.630 0.00 0.00 43.56 2.83
2652 4054 8.397906 CACTTGTTGAAATCTCTACAAAGACAA 58.602 33.333 0.00 0.00 43.56 3.18
2653 4055 7.768582 TCACTTGTTGAAATCTCTACAAAGACA 59.231 33.333 0.00 0.00 43.56 3.41
2654 4056 8.064814 GTCACTTGTTGAAATCTCTACAAAGAC 58.935 37.037 10.49 10.49 43.56 3.01
2655 4057 7.987458 AGTCACTTGTTGAAATCTCTACAAAGA 59.013 33.333 0.00 0.00 43.56 2.52
2656 4058 8.147642 AGTCACTTGTTGAAATCTCTACAAAG 57.852 34.615 0.00 0.00 43.56 2.77
2657 4059 9.042008 GTAGTCACTTGTTGAAATCTCTACAAA 57.958 33.333 0.00 0.00 43.56 2.83
2658 4060 8.201464 TGTAGTCACTTGTTGAAATCTCTACAA 58.799 33.333 0.00 0.00 42.53 2.41
2659 4061 7.722363 TGTAGTCACTTGTTGAAATCTCTACA 58.278 34.615 0.00 0.00 36.87 2.74
2660 4062 8.764524 ATGTAGTCACTTGTTGAAATCTCTAC 57.235 34.615 0.00 0.00 35.39 2.59
2661 4063 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2662 4064 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2663 4065 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2664 4066 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2665 4067 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2666 4068 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2667 4069 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2668 4070 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2669 4071 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2670 4072 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2671 4073 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2672 4074 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2673 4075 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2674 4076 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2675 4077 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2676 4078 6.534079 ACTTATTTTGCTCCGTATGTAGTCAC 59.466 38.462 0.00 0.00 0.00 3.67
2677 4079 6.533723 CACTTATTTTGCTCCGTATGTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
2678 4080 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
2679 4081 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
2680 4082 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
2681 4083 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
2682 4084 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
2683 4085 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
2684 4086 7.985184 TGTAGATTCACTTATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
2685 4087 7.277098 GTGTAGATTCACTTATTTTGCTCCGTA 59.723 37.037 0.00 0.00 35.68 4.02
2686 4088 6.092259 GTGTAGATTCACTTATTTTGCTCCGT 59.908 38.462 0.00 0.00 35.68 4.69
2687 4089 6.313905 AGTGTAGATTCACTTATTTTGCTCCG 59.686 38.462 0.00 0.00 44.92 4.63
2688 4090 7.550906 AGAGTGTAGATTCACTTATTTTGCTCC 59.449 37.037 0.98 0.00 46.81 4.70
2689 4091 8.485976 AGAGTGTAGATTCACTTATTTTGCTC 57.514 34.615 0.98 0.00 46.81 4.26
2690 4092 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
2760 4162 8.529424 TCCGTTCCTAAATATGTCTTTCTAGA 57.471 34.615 0.00 0.00 0.00 2.43
2761 4163 7.868415 CCTCCGTTCCTAAATATGTCTTTCTAG 59.132 40.741 0.00 0.00 0.00 2.43
2762 4164 7.201974 CCCTCCGTTCCTAAATATGTCTTTCTA 60.202 40.741 0.00 0.00 0.00 2.10
2763 4165 6.408206 CCCTCCGTTCCTAAATATGTCTTTCT 60.408 42.308 0.00 0.00 0.00 2.52
2764 4166 5.758784 CCCTCCGTTCCTAAATATGTCTTTC 59.241 44.000 0.00 0.00 0.00 2.62
2765 4167 5.427481 TCCCTCCGTTCCTAAATATGTCTTT 59.573 40.000 0.00 0.00 0.00 2.52
2766 4168 4.966805 TCCCTCCGTTCCTAAATATGTCTT 59.033 41.667 0.00 0.00 0.00 3.01
2767 4169 4.553678 TCCCTCCGTTCCTAAATATGTCT 58.446 43.478 0.00 0.00 0.00 3.41
2768 4170 4.344390 ACTCCCTCCGTTCCTAAATATGTC 59.656 45.833 0.00 0.00 0.00 3.06
2769 4171 4.296056 ACTCCCTCCGTTCCTAAATATGT 58.704 43.478 0.00 0.00 0.00 2.29
2770 4172 4.957684 ACTCCCTCCGTTCCTAAATATG 57.042 45.455 0.00 0.00 0.00 1.78
2771 4173 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2772 4174 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2773 4175 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2774 4176 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2775 4177 3.203710 TGATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
2776 4178 2.781757 TGATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
2777 4179 1.569548 TGATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
2778 4180 2.068834 TGATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
2779 4181 7.994334 AGTATATATGATCTACTCCCTCCGTTC 59.006 40.741 0.00 0.00 0.00 3.95
2780 4182 7.776030 CAGTATATATGATCTACTCCCTCCGTT 59.224 40.741 0.00 0.00 0.00 4.44
2781 4183 7.092354 ACAGTATATATGATCTACTCCCTCCGT 60.092 40.741 0.00 0.00 0.00 4.69
2782 4184 7.284074 ACAGTATATATGATCTACTCCCTCCG 58.716 42.308 0.00 0.00 0.00 4.63
2783 4185 9.482175 AAACAGTATATATGATCTACTCCCTCC 57.518 37.037 0.00 0.00 0.00 4.30
2791 4193 9.929180 GCCAAGTCAAACAGTATATATGATCTA 57.071 33.333 0.00 0.00 0.00 1.98
2792 4194 8.432013 TGCCAAGTCAAACAGTATATATGATCT 58.568 33.333 0.00 0.00 0.00 2.75
2793 4195 8.607441 TGCCAAGTCAAACAGTATATATGATC 57.393 34.615 0.00 0.00 0.00 2.92
2794 4196 9.578576 AATGCCAAGTCAAACAGTATATATGAT 57.421 29.630 0.00 0.00 0.00 2.45
2795 4197 8.978874 AATGCCAAGTCAAACAGTATATATGA 57.021 30.769 0.00 0.00 0.00 2.15
2799 4201 8.190784 GCTTAAATGCCAAGTCAAACAGTATAT 58.809 33.333 0.00 0.00 0.00 0.86
2800 4202 7.535139 GCTTAAATGCCAAGTCAAACAGTATA 58.465 34.615 0.00 0.00 0.00 1.47
2801 4203 6.389906 GCTTAAATGCCAAGTCAAACAGTAT 58.610 36.000 0.00 0.00 0.00 2.12
2916 4318 1.622811 CCATTAAGGCAAAAGCCCACA 59.377 47.619 2.33 0.00 0.00 4.17
3014 4416 5.628797 TGAACCATAGTCATAGGCATTCA 57.371 39.130 0.00 0.00 0.00 2.57
3025 4427 4.697352 AGTTGTGCTTGATGAACCATAGTC 59.303 41.667 0.00 0.00 0.00 2.59
3104 4506 2.084610 TTGATTCTCCAGCACTGACG 57.915 50.000 0.00 0.00 0.00 4.35
3416 4818 5.130477 AGAAGACGGGAAGCATAAGGAATAA 59.870 40.000 0.00 0.00 0.00 1.40
3417 4819 4.654262 AGAAGACGGGAAGCATAAGGAATA 59.346 41.667 0.00 0.00 0.00 1.75
3418 4820 3.456277 AGAAGACGGGAAGCATAAGGAAT 59.544 43.478 0.00 0.00 0.00 3.01
3674 5104 5.499004 AAGAGGTAAATAGCCAAGTGACA 57.501 39.130 0.00 0.00 0.00 3.58
3698 5128 4.340381 ACAAGATTCCATTGGCATAGCTTC 59.660 41.667 0.00 0.00 31.76 3.86
3699 5129 4.098960 CACAAGATTCCATTGGCATAGCTT 59.901 41.667 0.00 0.00 31.76 3.74
3700 5130 3.635373 CACAAGATTCCATTGGCATAGCT 59.365 43.478 0.00 0.00 31.76 3.32
3701 5131 3.633525 TCACAAGATTCCATTGGCATAGC 59.366 43.478 0.00 0.00 31.76 2.97
3813 5252 7.907389 TGTGGTCTCTAGAAGATACAAATGTT 58.093 34.615 0.00 0.00 36.11 2.71
3922 5361 0.115152 TCTTCTCAGCCCTCTGTCCA 59.885 55.000 0.00 0.00 41.10 4.02
3969 5408 6.932356 TGGAATGCAAGAGAGATCATTAAC 57.068 37.500 0.00 0.00 30.19 2.01
4048 5487 7.881775 AGAACTTAGAACCACTTCAACATTT 57.118 32.000 0.00 0.00 0.00 2.32
4110 5550 6.153067 TCCTGGTTGCAACATTTAATAAACG 58.847 36.000 29.55 6.10 0.00 3.60
4112 5552 7.531857 TCTCCTGGTTGCAACATTTAATAAA 57.468 32.000 29.55 4.95 0.00 1.40
4218 5658 8.447924 AGATGGAGAATATTGAAATGACACTG 57.552 34.615 0.00 0.00 0.00 3.66
4510 5951 7.796838 TGAAGTCATGATTACGTCAAAAGAAG 58.203 34.615 0.00 0.00 40.97 2.85
4658 6099 8.458843 CAATATTTTCTTCCACTTAATGTCCGT 58.541 33.333 0.00 0.00 0.00 4.69
4659 6100 7.432252 GCAATATTTTCTTCCACTTAATGTCCG 59.568 37.037 0.00 0.00 0.00 4.79
4714 6155 6.278363 AGAAGTTTGTCGCGTTGGTATATAT 58.722 36.000 5.77 0.00 0.00 0.86
4722 6163 2.542595 AGGTTAGAAGTTTGTCGCGTTG 59.457 45.455 5.77 0.00 0.00 4.10
4723 6164 2.830104 AGGTTAGAAGTTTGTCGCGTT 58.170 42.857 5.77 0.00 0.00 4.84
4871 6321 3.323979 TCCACCACCAGTTCTAGAAGTTC 59.676 47.826 10.23 0.00 0.00 3.01
5048 6498 6.762187 CAGTGAGAAAGAGTAGTACTATCCGA 59.238 42.308 5.75 0.00 0.00 4.55
5211 6764 8.536175 CCCCTTAAAGCATAAATTAGTGGAAAA 58.464 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.