Multiple sequence alignment - TraesCS4A01G331600

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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 TraesCS4A01G331600 chr4A 100.000 5742 0 0 1 5742 616229369 616235110 0.000000e+00 10604.0
1 TraesCS4A01G331600 chr4A 96.382 691 24 1 1 691 616298629 616297940 0.000000e+00 1136.0
2 TraesCS4A01G331600 chr4A 93.324 689 44 2 1 688 616211606 616212293 0.000000e+00 1016.0
3 TraesCS4A01G331600 chr4A 88.462 832 70 15 1700 2515 616313433 616312612 0.000000e+00 981.0
4 TraesCS4A01G331600 chr4A 88.776 686 68 2 7 691 616316441 616315764 0.000000e+00 832.0
5 TraesCS4A01G331600 chr4A 84.364 825 97 22 1700 2515 670382859 670382058 0.000000e+00 780.0
6 TraesCS4A01G331600 chr4A 84.256 813 86 22 3033 3836 616312086 616311307 0.000000e+00 754.0
7 TraesCS4A01G331600 chr4A 89.953 428 31 7 5236 5654 616757362 616757786 5.060000e-150 542.0
8 TraesCS4A01G331600 chr4A 90.785 293 15 5 4608 4889 616756351 616756642 1.170000e-101 381.0
9 TraesCS4A01G331600 chr4A 78.176 614 58 44 979 1552 616313861 616313284 7.180000e-84 322.0
10 TraesCS4A01G331600 chr4A 83.761 351 40 8 2646 2994 670382003 670381668 3.340000e-82 316.0
11 TraesCS4A01G331600 chr4A 84.362 243 29 5 971 1213 670383310 670383077 4.480000e-56 230.0
12 TraesCS4A01G331600 chr4A 89.344 122 8 4 793 912 616213136 616213254 1.290000e-31 148.0
13 TraesCS4A01G331600 chr4A 100.000 68 0 0 755 822 616230082 616230149 6.040000e-25 126.0
14 TraesCS4A01G331600 chr4A 100.000 68 0 0 714 781 616230123 616230190 6.040000e-25 126.0
15 TraesCS4A01G331600 chr5D 96.005 2253 79 7 1832 4074 552036999 552039250 0.000000e+00 3651.0
16 TraesCS4A01G331600 chr5D 95.785 688 29 0 1 688 552032545 552033232 0.000000e+00 1110.0
17 TraesCS4A01G331600 chr5D 90.739 853 26 14 4899 5742 552047592 552048400 0.000000e+00 1088.0
18 TraesCS4A01G331600 chr5D 90.802 848 25 9 4072 4887 552046717 552047543 0.000000e+00 1085.0
19 TraesCS4A01G331600 chr5D 88.741 826 70 12 1700 2512 551990962 551991777 0.000000e+00 989.0
20 TraesCS4A01G331600 chr5D 89.751 683 56 3 7 688 551988093 551988762 0.000000e+00 861.0
21 TraesCS4A01G331600 chr5D 82.989 1017 99 32 2863 3836 551992075 551993060 0.000000e+00 852.0
22 TraesCS4A01G331600 chr5D 88.344 326 20 9 969 1279 552036295 552036617 5.430000e-100 375.0
23 TraesCS4A01G331600 chr5D 89.037 301 18 8 1469 1765 552036615 552036904 5.470000e-95 359.0
24 TraesCS4A01G331600 chr5D 78.897 526 96 12 1 518 551058830 551058312 5.510000e-90 342.0
25 TraesCS4A01G331600 chr5D 81.922 437 40 24 902 1312 551990408 551990831 3.320000e-87 333.0
26 TraesCS4A01G331600 chr5D 80.122 493 56 19 4053 4510 552634904 552635389 4.290000e-86 329.0
27 TraesCS4A01G331600 chr5D 81.560 423 49 21 5341 5742 552323572 552323986 7.180000e-84 322.0
28 TraesCS4A01G331600 chr5D 77.799 536 106 11 1 531 543502559 543503086 9.280000e-83 318.0
29 TraesCS4A01G331600 chr5D 87.692 195 15 3 2642 2835 551991901 551992087 9.690000e-53 219.0
30 TraesCS4A01G331600 chr5D 84.324 185 20 4 1375 1552 551990929 551991111 7.650000e-39 172.0
31 TraesCS4A01G331600 chr5D 90.000 60 4 2 4882 4939 505395757 505395816 6.170000e-10 76.8
32 TraesCS4A01G331600 chr5B 94.139 1962 73 10 2121 4074 699948792 699946865 0.000000e+00 2948.0
33 TraesCS4A01G331600 chr5B 91.525 1298 69 12 2802 4074 700232796 700234077 0.000000e+00 1749.0
34 TraesCS4A01G331600 chr5B 92.221 797 24 7 4955 5742 699277038 699276271 0.000000e+00 1094.0
35 TraesCS4A01G331600 chr5B 94.186 688 40 0 4 691 699951135 699950448 0.000000e+00 1050.0
36 TraesCS4A01G331600 chr5B 80.890 1371 149 46 2642 3943 700222935 700224261 0.000000e+00 976.0
37 TraesCS4A01G331600 chr5B 92.163 689 52 2 1 688 700228465 700229152 0.000000e+00 972.0
38 TraesCS4A01G331600 chr5B 89.481 732 62 10 1891 2617 700222217 700222938 0.000000e+00 911.0
39 TraesCS4A01G331600 chr5B 92.333 600 30 10 2259 2854 700232206 700232793 0.000000e+00 839.0
40 TraesCS4A01G331600 chr5B 89.227 427 26 8 1669 2092 700231655 700232064 3.070000e-142 516.0
41 TraesCS4A01G331600 chr5B 83.978 543 59 19 4072 4608 699941645 699941125 4.000000e-136 496.0
42 TraesCS4A01G331600 chr5B 82.410 614 55 28 1165 1743 699949376 699948781 2.410000e-133 486.0
43 TraesCS4A01G331600 chr5B 83.424 549 61 20 4065 4605 700271897 700272423 3.110000e-132 483.0
44 TraesCS4A01G331600 chr5B 83.273 550 60 21 4065 4605 700247909 700248435 1.450000e-130 477.0
45 TraesCS4A01G331600 chr5B 83.152 552 63 20 4065 4608 704021615 704021086 1.450000e-130 477.0
46 TraesCS4A01G331600 chr5B 86.432 398 32 14 969 1350 700230848 700231239 3.200000e-112 416.0
47 TraesCS4A01G331600 chr5B 83.054 478 44 13 4072 4512 698274602 698274125 3.220000e-107 399.0
48 TraesCS4A01G331600 chr5B 79.310 580 57 24 4074 4606 699932024 699931461 1.180000e-91 348.0
49 TraesCS4A01G331600 chr5B 90.588 255 16 4 4608 4854 699277290 699277036 1.190000e-86 331.0
50 TraesCS4A01G331600 chr5B 78.646 576 61 16 4072 4608 699782417 699781865 5.550000e-85 326.0
51 TraesCS4A01G331600 chr5B 76.590 692 88 53 902 1553 700221247 700221904 4.320000e-81 313.0
52 TraesCS4A01G331600 chr5B 82.203 354 38 17 971 1312 700216636 700216976 1.220000e-71 281.0
53 TraesCS4A01G331600 chr5B 90.526 95 6 1 969 1060 699949476 699949382 7.810000e-24 122.0
54 TraesCS4A01G331600 chr5B 89.247 93 7 3 1678 1769 700222011 700222101 4.700000e-21 113.0
55 TraesCS4A01G331600 chr2D 84.123 1077 70 27 969 1964 420719592 420720648 0.000000e+00 948.0
56 TraesCS4A01G331600 chr6B 84.709 824 88 17 1700 2512 672450018 672450814 0.000000e+00 789.0
57 TraesCS4A01G331600 chr6B 85.019 781 83 11 1700 2467 19861337 19862096 0.000000e+00 763.0
58 TraesCS4A01G331600 chr6B 92.795 458 32 1 2787 3244 16926871 16926415 0.000000e+00 662.0
59 TraesCS4A01G331600 chr6B 87.179 156 19 1 971 1126 19846325 19846479 5.910000e-40 176.0
60 TraesCS4A01G331600 chr6B 84.211 152 15 4 1404 1552 19861336 19861481 7.760000e-29 139.0
61 TraesCS4A01G331600 chr6B 83.125 160 15 7 1404 1558 672450017 672450169 1.000000e-27 135.0
62 TraesCS4A01G331600 chr6B 82.237 152 19 3 3361 3511 239368319 239368175 2.170000e-24 124.0
63 TraesCS4A01G331600 chr6B 92.308 52 2 2 4876 4926 710798844 710798794 7.980000e-09 73.1
64 TraesCS4A01G331600 chr6B 92.308 52 2 2 4876 4926 711418677 711418727 7.980000e-09 73.1
65 TraesCS4A01G331600 chr1B 84.487 419 24 16 1572 1964 200413867 200414270 5.430000e-100 375.0
66 TraesCS4A01G331600 chr1B 85.938 64 7 2 4876 4938 349741690 349741752 3.710000e-07 67.6
67 TraesCS4A01G331600 chr7D 77.281 537 101 19 13 535 22673302 22672773 4.350000e-76 296.0
68 TraesCS4A01G331600 chr7D 94.118 51 1 1 4886 4934 401542006 401542056 6.170000e-10 76.8
69 TraesCS4A01G331600 chr3B 84.444 270 27 9 2642 2909 677386137 677386393 9.550000e-63 252.0
70 TraesCS4A01G331600 chr3B 87.111 225 20 6 1421 1638 761986768 761986546 4.440000e-61 246.0
71 TraesCS4A01G331600 chr3B 83.895 267 28 8 2645 2909 506256538 506256791 2.070000e-59 241.0
72 TraesCS4A01G331600 chr3B 87.981 208 9 6 1772 1964 761986533 761986327 1.240000e-56 231.0
73 TraesCS4A01G331600 chr3B 86.364 66 5 3 4151 4215 740886488 740886550 1.030000e-07 69.4
74 TraesCS4A01G331600 chr6D 96.429 56 1 1 5155 5210 65352139 65352193 2.200000e-14 91.6
75 TraesCS4A01G331600 chr6D 92.308 52 2 2 4876 4926 342467244 342467294 7.980000e-09 73.1
76 TraesCS4A01G331600 chr4D 95.833 48 1 1 4882 4929 348048249 348048203 6.170000e-10 76.8
77 TraesCS4A01G331600 chr4B 91.071 56 4 1 4871 4926 526896943 526896997 2.220000e-09 75.0
78 TraesCS4A01G331600 chr2A 89.583 48 5 0 4286 4333 48834037 48834084 1.730000e-05 62.1
79 TraesCS4A01G331600 chr2B 97.059 34 1 0 4298 4331 72278116 72278149 2.230000e-04 58.4
80 TraesCS4A01G331600 chr3D 97.059 34 0 1 4300 4332 32262259 32262292 8.040000e-04 56.5


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 TraesCS4A01G331600 chr4A 616229369 616235110 5741 False 10604.00 10604 100.000000 1 5742 1 chr4A.!!$F1 5741
1 TraesCS4A01G331600 chr4A 616297940 616298629 689 True 1136.00 1136 96.382000 1 691 1 chr4A.!!$R1 690
2 TraesCS4A01G331600 chr4A 616311307 616316441 5134 True 722.25 981 84.917500 7 3836 4 chr4A.!!$R2 3829
3 TraesCS4A01G331600 chr4A 616211606 616213254 1648 False 582.00 1016 91.334000 1 912 2 chr4A.!!$F2 911
4 TraesCS4A01G331600 chr4A 616756351 616757786 1435 False 461.50 542 90.369000 4608 5654 2 chr4A.!!$F4 1046
5 TraesCS4A01G331600 chr4A 670381668 670383310 1642 True 442.00 780 84.162333 971 2994 3 chr4A.!!$R3 2023
6 TraesCS4A01G331600 chr5D 552032545 552039250 6705 False 1373.75 3651 92.292750 1 4074 4 chr5D.!!$F6 4073
7 TraesCS4A01G331600 chr5D 552046717 552048400 1683 False 1086.50 1088 90.770500 4072 5742 2 chr5D.!!$F7 1670
8 TraesCS4A01G331600 chr5D 551988093 551993060 4967 False 571.00 989 85.903167 7 3836 6 chr5D.!!$F5 3829
9 TraesCS4A01G331600 chr5D 551058312 551058830 518 True 342.00 342 78.897000 1 518 1 chr5D.!!$R1 517
10 TraesCS4A01G331600 chr5D 543502559 543503086 527 False 318.00 318 77.799000 1 531 1 chr5D.!!$F2 530
11 TraesCS4A01G331600 chr5B 699946865 699951135 4270 True 1151.50 2948 90.315250 4 4074 4 chr5B.!!$R7 4070
12 TraesCS4A01G331600 chr5B 700228465 700234077 5612 False 898.40 1749 90.336000 1 4074 5 chr5B.!!$F5 4073
13 TraesCS4A01G331600 chr5B 699276271 699277290 1019 True 712.50 1094 91.404500 4608 5742 2 chr5B.!!$R6 1134
14 TraesCS4A01G331600 chr5B 700221247 700224261 3014 False 578.25 976 84.052000 902 3943 4 chr5B.!!$F4 3041
15 TraesCS4A01G331600 chr5B 699941125 699941645 520 True 496.00 496 83.978000 4072 4608 1 chr5B.!!$R4 536
16 TraesCS4A01G331600 chr5B 700271897 700272423 526 False 483.00 483 83.424000 4065 4605 1 chr5B.!!$F3 540
17 TraesCS4A01G331600 chr5B 700247909 700248435 526 False 477.00 477 83.273000 4065 4605 1 chr5B.!!$F2 540
18 TraesCS4A01G331600 chr5B 704021086 704021615 529 True 477.00 477 83.152000 4065 4608 1 chr5B.!!$R5 543
19 TraesCS4A01G331600 chr5B 699931461 699932024 563 True 348.00 348 79.310000 4074 4606 1 chr5B.!!$R3 532
20 TraesCS4A01G331600 chr5B 699781865 699782417 552 True 326.00 326 78.646000 4072 4608 1 chr5B.!!$R2 536
21 TraesCS4A01G331600 chr2D 420719592 420720648 1056 False 948.00 948 84.123000 969 1964 1 chr2D.!!$F1 995
22 TraesCS4A01G331600 chr6B 672450017 672450814 797 False 462.00 789 83.917000 1404 2512 2 chr6B.!!$F4 1108
23 TraesCS4A01G331600 chr6B 19861336 19862096 760 False 451.00 763 84.615000 1404 2467 2 chr6B.!!$F3 1063
24 TraesCS4A01G331600 chr7D 22672773 22673302 529 True 296.00 296 77.281000 13 535 1 chr7D.!!$R1 522

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
938 5444 0.540830 CTACCCATCCTCTCCTCCCG 60.541 65.000 0.00 0.00 0.00 5.14 F
1003 5552 0.103937 GGAAGAGCACGAGGAGATGG 59.896 60.000 0.00 0.00 0.00 3.51 F
1372 6074 0.389817 TGAACTCAACGCCATCTCCG 60.390 55.000 0.00 0.00 0.00 4.63 F
1642 6578 0.540923 ATTCTGGCTCTGGCTCTGTC 59.459 55.000 0.00 0.00 38.73 3.51 F
1643 6579 0.543883 TTCTGGCTCTGGCTCTGTCT 60.544 55.000 0.00 0.00 38.73 3.41 F
1721 6663 0.807496 GTCAAGTGGCAGCCATTCTC 59.193 55.000 19.75 4.23 35.28 2.87 F
2292 7321 1.000955 AGTTACTTGACCCAGCTGTCG 59.999 52.381 13.81 4.64 38.11 4.35 F
3645 8867 1.676529 TCGAGAGAATACCCAAGCTCG 59.323 52.381 0.00 0.00 44.55 5.03 F
4436 9777 1.089920 CCAAATGTCGGCTTCTCCTG 58.910 55.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 6912 0.790814 GTCGGCTGAAAGAAGGAACG 59.209 55.000 0.00 0.00 34.07 3.95 R
2292 7321 2.352960 GGAGAACATTGAGCGTTCCATC 59.647 50.000 0.00 0.00 43.07 3.51 R
2843 8016 2.561478 TCCCTGAACACTAACCAAGC 57.439 50.000 0.00 0.00 0.00 4.01 R
3578 8800 1.981495 AGGGCAAAACAGAGCTCTACT 59.019 47.619 17.75 3.08 40.45 2.57 R
3740 8963 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82 R
3780 9005 7.891712 TCATTCCAATATGGCAATATCTCACAT 59.108 33.333 0.00 0.00 37.47 3.21 R
3964 9217 8.773033 AGCTCCAAGTATCCAAATAAATGAAT 57.227 30.769 0.00 0.00 0.00 2.57 R
4452 9804 0.966179 AGCATGTGTCCACTACGTCA 59.034 50.000 0.00 0.00 0.00 4.35 R
5606 11423 2.161855 TGCAGTAATCTTTGTGGCTGG 58.838 47.619 0.00 0.00 0.00 4.85 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
261 266 4.022849 CGACTCTATGCATAGTCCATGACA 60.023 45.833 28.51 9.87 39.16 3.58
401 410 1.477700 CCGGACAATGGTGCATCAATT 59.522 47.619 2.42 0.00 34.61 2.32
551 563 4.878397 GGTGCAAATTGTAGACTAGAGCAT 59.122 41.667 0.00 0.00 0.00 3.79
641 653 2.997463 TGTGCAACACAATTGTCATCG 58.003 42.857 8.48 0.00 45.67 3.84
695 1488 2.119029 GGGCCCTGCATTACGGAAC 61.119 63.158 17.04 0.00 0.00 3.62
718 1511 2.572191 TCTAATTAGACACGTGGCCG 57.428 50.000 20.18 0.00 40.83 6.13
728 1521 2.254951 CGTGGCCGTGTACGTGTA 59.745 61.111 0.00 0.00 37.74 2.90
753 2684 2.257371 GACTGTAGACGCGTGGCA 59.743 61.111 20.70 11.78 0.00 4.92
756 2687 2.125713 TGTAGACGCGTGGCATGG 60.126 61.111 20.70 1.28 0.00 3.66
757 2688 3.564027 GTAGACGCGTGGCATGGC 61.564 66.667 20.70 13.29 0.00 4.40
768 2699 2.740826 GCATGGCCGTGTACGTGT 60.741 61.111 25.67 0.00 37.74 4.49
769 2700 1.446445 GCATGGCCGTGTACGTGTA 60.446 57.895 25.67 0.00 37.74 2.90
770 2701 1.689352 GCATGGCCGTGTACGTGTAC 61.689 60.000 25.67 3.01 37.74 2.90
771 2702 1.153978 ATGGCCGTGTACGTGTACG 60.154 57.895 16.39 16.39 46.33 3.67
776 2707 2.699910 CGTGTACGTGTACGGTGAC 58.300 57.895 15.78 4.69 44.95 3.67
778 2709 3.353731 CGTGTACGTGTACGGTGACGA 62.354 57.143 17.84 3.26 45.99 4.20
790 2721 1.206072 GTGACGACTGTAGACGCGT 59.794 57.895 13.85 13.85 39.99 6.01
791 2722 1.058590 GTGACGACTGTAGACGCGTG 61.059 60.000 20.70 3.63 37.07 5.34
869 3296 3.151554 TGAGGACGCTGACACTAGTTTA 58.848 45.455 0.00 0.00 0.00 2.01
871 3298 4.142447 TGAGGACGCTGACACTAGTTTATC 60.142 45.833 0.00 0.00 0.00 1.75
875 5374 5.238006 ACGCTGACACTAGTTTATCTCTC 57.762 43.478 0.00 0.00 0.00 3.20
921 5427 2.248248 CTCCACTCCACAGTCCAACTA 58.752 52.381 0.00 0.00 0.00 2.24
923 5429 1.002087 CCACTCCACAGTCCAACTACC 59.998 57.143 0.00 0.00 0.00 3.18
924 5430 1.002087 CACTCCACAGTCCAACTACCC 59.998 57.143 0.00 0.00 0.00 3.69
925 5431 1.348064 CTCCACAGTCCAACTACCCA 58.652 55.000 0.00 0.00 0.00 4.51
926 5432 1.909302 CTCCACAGTCCAACTACCCAT 59.091 52.381 0.00 0.00 0.00 4.00
927 5433 1.906574 TCCACAGTCCAACTACCCATC 59.093 52.381 0.00 0.00 0.00 3.51
928 5434 1.065418 CCACAGTCCAACTACCCATCC 60.065 57.143 0.00 0.00 0.00 3.51
929 5435 1.909302 CACAGTCCAACTACCCATCCT 59.091 52.381 0.00 0.00 0.00 3.24
931 5437 2.225650 ACAGTCCAACTACCCATCCTCT 60.226 50.000 0.00 0.00 0.00 3.69
932 5438 2.432510 CAGTCCAACTACCCATCCTCTC 59.567 54.545 0.00 0.00 0.00 3.20
934 5440 1.651770 TCCAACTACCCATCCTCTCCT 59.348 52.381 0.00 0.00 0.00 3.69
935 5441 2.043227 CCAACTACCCATCCTCTCCTC 58.957 57.143 0.00 0.00 0.00 3.71
936 5442 2.043227 CAACTACCCATCCTCTCCTCC 58.957 57.143 0.00 0.00 0.00 4.30
937 5443 0.563672 ACTACCCATCCTCTCCTCCC 59.436 60.000 0.00 0.00 0.00 4.30
938 5444 0.540830 CTACCCATCCTCTCCTCCCG 60.541 65.000 0.00 0.00 0.00 5.14
939 5445 0.997307 TACCCATCCTCTCCTCCCGA 60.997 60.000 0.00 0.00 0.00 5.14
940 5446 1.532794 CCCATCCTCTCCTCCCGAG 60.533 68.421 0.00 0.00 40.30 4.63
941 5447 1.231641 CCATCCTCTCCTCCCGAGT 59.768 63.158 0.00 0.00 39.84 4.18
942 5448 0.825840 CCATCCTCTCCTCCCGAGTC 60.826 65.000 0.00 0.00 39.84 3.36
943 5449 0.825840 CATCCTCTCCTCCCGAGTCC 60.826 65.000 0.00 0.00 39.84 3.85
944 5450 2.014033 ATCCTCTCCTCCCGAGTCCC 62.014 65.000 0.00 0.00 39.84 4.46
945 5451 2.517402 CTCTCCTCCCGAGTCCCG 60.517 72.222 0.00 0.00 39.84 5.14
946 5452 3.013327 TCTCCTCCCGAGTCCCGA 61.013 66.667 0.00 0.00 41.76 5.14
947 5453 2.517402 CTCCTCCCGAGTCCCGAG 60.517 72.222 0.00 0.00 41.76 4.63
948 5454 3.336568 TCCTCCCGAGTCCCGAGT 61.337 66.667 0.00 0.00 41.76 4.18
949 5455 2.829458 CCTCCCGAGTCCCGAGTC 60.829 72.222 0.00 0.00 41.76 3.36
950 5456 2.272797 CTCCCGAGTCCCGAGTCT 59.727 66.667 0.00 0.00 41.76 3.24
951 5457 2.045242 TCCCGAGTCCCGAGTCTG 60.045 66.667 0.00 0.00 41.76 3.51
952 5458 3.827898 CCCGAGTCCCGAGTCTGC 61.828 72.222 0.00 0.00 41.76 4.26
953 5459 3.062466 CCGAGTCCCGAGTCTGCA 61.062 66.667 0.00 0.00 41.76 4.41
954 5460 2.487428 CGAGTCCCGAGTCTGCAG 59.513 66.667 7.63 7.63 41.76 4.41
955 5461 2.183046 GAGTCCCGAGTCTGCAGC 59.817 66.667 9.47 4.26 0.00 5.25
956 5462 3.363844 GAGTCCCGAGTCTGCAGCC 62.364 68.421 9.47 0.00 0.00 4.85
957 5463 3.695606 GTCCCGAGTCTGCAGCCA 61.696 66.667 9.47 0.00 0.00 4.75
958 5464 2.922503 TCCCGAGTCTGCAGCCAA 60.923 61.111 9.47 0.00 0.00 4.52
959 5465 2.032528 CCCGAGTCTGCAGCCAAA 59.967 61.111 9.47 0.00 0.00 3.28
960 5466 2.037136 CCCGAGTCTGCAGCCAAAG 61.037 63.158 9.47 0.00 0.00 2.77
961 5467 2.684843 CCGAGTCTGCAGCCAAAGC 61.685 63.158 9.47 0.00 40.32 3.51
962 5468 1.962822 CGAGTCTGCAGCCAAAGCA 60.963 57.895 9.47 0.00 43.56 3.91
967 5473 2.203379 TGCAGCCAAAGCAGAGCA 60.203 55.556 0.00 0.00 43.56 4.26
1003 5552 0.103937 GGAAGAGCACGAGGAGATGG 59.896 60.000 0.00 0.00 0.00 3.51
1143 5697 1.229400 GTACTCAGGACCCCACCCA 60.229 63.158 0.00 0.00 0.00 4.51
1171 5730 1.153549 CTTCCCTTTCGCTCTCCCG 60.154 63.158 0.00 0.00 0.00 5.14
1226 5816 2.202824 TTATTGGTCTCCGCCGCG 60.203 61.111 5.59 5.59 0.00 6.46
1252 5866 1.959282 GGATTCATGGATTCAGTGGGC 59.041 52.381 0.00 0.00 0.00 5.36
1254 5868 0.617935 TTCATGGATTCAGTGGGCGA 59.382 50.000 0.00 0.00 0.00 5.54
1275 5889 2.160205 GGGACTAGGTTTTGTTCAGGC 58.840 52.381 0.00 0.00 0.00 4.85
1357 6059 1.131883 GCATGAGTGAGTGGCATGAAC 59.868 52.381 0.00 0.00 41.35 3.18
1372 6074 0.389817 TGAACTCAACGCCATCTCCG 60.390 55.000 0.00 0.00 0.00 4.63
1385 6101 5.709164 ACGCCATCTCCGTACTAGTATTATT 59.291 40.000 5.75 0.00 37.12 1.40
1386 6102 6.028368 CGCCATCTCCGTACTAGTATTATTG 58.972 44.000 5.75 0.58 0.00 1.90
1387 6103 6.349115 CGCCATCTCCGTACTAGTATTATTGT 60.349 42.308 5.75 0.00 0.00 2.71
1388 6104 7.148356 CGCCATCTCCGTACTAGTATTATTGTA 60.148 40.741 5.75 0.00 0.00 2.41
1389 6105 8.517878 GCCATCTCCGTACTAGTATTATTGTAA 58.482 37.037 5.75 0.00 0.00 2.41
1475 6216 5.771469 TGATTTTCCATAACACTGTTGCTG 58.229 37.500 4.57 2.60 0.00 4.41
1476 6217 4.582701 TTTTCCATAACACTGTTGCTGG 57.417 40.909 14.80 14.80 0.00 4.85
1477 6218 1.533625 TCCATAACACTGTTGCTGGC 58.466 50.000 15.64 0.00 0.00 4.85
1482 6223 1.312371 AACACTGTTGCTGGCGTGTT 61.312 50.000 9.63 9.63 43.47 3.32
1507 6254 3.780801 GCTGCGACAGTCAATTATTTTCG 59.219 43.478 0.41 0.00 33.43 3.46
1569 6340 7.931948 ACATAAATTCCCTTGTATTCTACCGAG 59.068 37.037 0.00 0.00 0.00 4.63
1587 6523 6.720112 ACCGAGTTAGTTACCAATAGCATA 57.280 37.500 0.00 0.00 0.00 3.14
1594 6530 8.705594 AGTTAGTTACCAATAGCATACTGTGAT 58.294 33.333 0.00 0.00 0.00 3.06
1641 6577 0.990374 AATTCTGGCTCTGGCTCTGT 59.010 50.000 0.00 0.00 38.73 3.41
1642 6578 0.540923 ATTCTGGCTCTGGCTCTGTC 59.459 55.000 0.00 0.00 38.73 3.51
1643 6579 0.543883 TTCTGGCTCTGGCTCTGTCT 60.544 55.000 0.00 0.00 38.73 3.41
1644 6580 0.969917 TCTGGCTCTGGCTCTGTCTC 60.970 60.000 0.00 0.00 38.73 3.36
1645 6581 0.971959 CTGGCTCTGGCTCTGTCTCT 60.972 60.000 0.00 0.00 38.73 3.10
1646 6582 1.256361 TGGCTCTGGCTCTGTCTCTG 61.256 60.000 0.00 0.00 38.73 3.35
1647 6583 1.257055 GGCTCTGGCTCTGTCTCTGT 61.257 60.000 0.00 0.00 38.73 3.41
1674 6610 5.251764 TGTTCACTCACTCCCTACTACTAC 58.748 45.833 0.00 0.00 0.00 2.73
1676 6612 5.100344 TCACTCACTCCCTACTACTACAG 57.900 47.826 0.00 0.00 0.00 2.74
1721 6663 0.807496 GTCAAGTGGCAGCCATTCTC 59.193 55.000 19.75 4.23 35.28 2.87
1736 6679 7.249147 CAGCCATTCTCACTTCTGAATTAAAG 58.751 38.462 0.00 0.00 31.35 1.85
1779 6734 1.704641 TAGTGTGGCTGTGACAGTCT 58.295 50.000 18.84 9.48 36.97 3.24
1844 6818 7.167924 TCAAAATCAGCATAAATTGGCACTA 57.832 32.000 0.00 0.00 0.00 2.74
1847 6821 4.235079 TCAGCATAAATTGGCACTAGGT 57.765 40.909 0.00 0.00 0.00 3.08
1878 6868 7.518731 TCTTTTTAATAAAACATCGCATGCC 57.481 32.000 13.15 0.00 0.00 4.40
1880 6870 4.991153 TTAATAAAACATCGCATGCCCA 57.009 36.364 13.15 0.00 0.00 5.36
2119 7137 4.713824 ATCATGACCATCTTGTGCAAAG 57.286 40.909 0.00 0.00 0.00 2.77
2292 7321 1.000955 AGTTACTTGACCCAGCTGTCG 59.999 52.381 13.81 4.64 38.11 4.35
2438 7470 3.953612 AGACATGGTTTTCAAGTGCAGAA 59.046 39.130 0.00 0.00 0.00 3.02
2611 7679 9.014297 CCCTTATTTTGTCTACTTGATGACTTT 57.986 33.333 0.00 0.00 34.57 2.66
2664 7735 7.327275 CGTATGCACCTCTACTGAAATAGAATC 59.673 40.741 0.00 0.00 30.76 2.52
2692 7763 7.794683 TCTTAGGATAAGAGGGTGATACCATTT 59.205 37.037 0.00 0.00 41.02 2.32
2742 7821 4.836175 TCACACAAGGATGTAGGTTGAGTA 59.164 41.667 0.00 0.00 37.82 2.59
2749 7829 6.227298 AGGATGTAGGTTGAGTACAATGAG 57.773 41.667 0.00 0.00 38.32 2.90
2863 8036 2.375174 TGCTTGGTTAGTGTTCAGGGAT 59.625 45.455 0.00 0.00 0.00 3.85
2864 8037 3.181434 TGCTTGGTTAGTGTTCAGGGATT 60.181 43.478 0.00 0.00 0.00 3.01
2865 8038 3.826729 GCTTGGTTAGTGTTCAGGGATTT 59.173 43.478 0.00 0.00 0.00 2.17
2866 8039 4.280929 GCTTGGTTAGTGTTCAGGGATTTT 59.719 41.667 0.00 0.00 0.00 1.82
2867 8040 5.221441 GCTTGGTTAGTGTTCAGGGATTTTT 60.221 40.000 0.00 0.00 0.00 1.94
2927 8102 7.574607 TGTTATAGATGGTCAGTCTCTGTCTA 58.425 38.462 0.00 0.00 32.61 2.59
3100 8311 2.198906 TAACTGGCGCATGCACTTGC 62.199 55.000 19.57 12.65 45.35 4.01
3194 8407 6.538945 TTTCTGCTTTAACAGGGTTCTTTT 57.461 33.333 0.00 0.00 38.26 2.27
3206 8419 8.661352 AACAGGGTTCTTTTGATATTTGTTTG 57.339 30.769 0.00 0.00 0.00 2.93
3311 8526 6.489127 TTTAAATCCATGGTTGACTGTACG 57.511 37.500 12.58 0.00 0.00 3.67
3553 8771 7.855904 CCGTATGTGCCTTGATAATTAACTTTC 59.144 37.037 0.00 0.00 0.00 2.62
3645 8867 1.676529 TCGAGAGAATACCCAAGCTCG 59.323 52.381 0.00 0.00 44.55 5.03
3780 9005 1.903294 TTGGCACTGGCAAAAGCAA 59.097 47.368 15.28 0.00 44.79 3.91
3809 9034 9.316594 TGAGATATTGCCATATTGGAATGATTT 57.683 29.630 4.07 0.00 40.96 2.17
3910 9162 8.408043 ACTCTGTTCAATTGGACATTTGATTA 57.592 30.769 19.90 0.00 32.74 1.75
3964 9217 1.949525 GTGTTTCTCTCTGGCTTTGCA 59.050 47.619 0.00 0.00 0.00 4.08
4259 9533 6.489127 ACGTGAAATTTGACATTATTCCGA 57.511 33.333 8.53 0.00 0.00 4.55
4260 9534 6.904498 ACGTGAAATTTGACATTATTCCGAA 58.096 32.000 8.53 0.00 0.00 4.30
4261 9535 7.535139 ACGTGAAATTTGACATTATTCCGAAT 58.465 30.769 8.53 0.00 0.00 3.34
4262 9536 8.026607 ACGTGAAATTTGACATTATTCCGAATT 58.973 29.630 8.53 0.00 0.00 2.17
4263 9537 8.859156 CGTGAAATTTGACATTATTCCGAATTT 58.141 29.630 8.53 0.00 0.00 1.82
4373 9685 7.493743 TCCACAAATTTGGAAAATGTTCATG 57.506 32.000 21.74 6.59 43.04 3.07
4374 9686 7.278135 TCCACAAATTTGGAAAATGTTCATGA 58.722 30.769 21.74 0.00 43.04 3.07
4375 9687 7.772292 TCCACAAATTTGGAAAATGTTCATGAA 59.228 29.630 21.74 3.38 43.04 2.57
4436 9777 1.089920 CCAAATGTCGGCTTCTCCTG 58.910 55.000 0.00 0.00 0.00 3.86
4486 9838 1.736126 CATGCTATAGGCCATCGCAAG 59.264 52.381 5.01 4.16 38.67 4.01
4626 9979 8.953313 TGAATCGACTTATCTAGTACAACTTCA 58.047 33.333 0.00 0.00 37.17 3.02
4889 10253 4.832248 TCAACTCCCACTGATTATGTGTC 58.168 43.478 0.00 0.00 33.92 3.67
4890 10254 3.526931 ACTCCCACTGATTATGTGTCG 57.473 47.619 0.00 0.00 33.92 4.35
4893 10257 4.020573 ACTCCCACTGATTATGTGTCGAAA 60.021 41.667 0.00 0.00 33.92 3.46
4894 10258 4.900684 TCCCACTGATTATGTGTCGAAAA 58.099 39.130 0.00 0.00 33.92 2.29
4895 10259 5.309638 TCCCACTGATTATGTGTCGAAAAA 58.690 37.500 0.00 0.00 33.92 1.94
4896 10260 5.943416 TCCCACTGATTATGTGTCGAAAAAT 59.057 36.000 0.00 0.00 33.92 1.82
4897 10261 6.029607 CCCACTGATTATGTGTCGAAAAATG 58.970 40.000 0.00 0.00 33.92 2.32
4900 10301 7.361201 CCACTGATTATGTGTCGAAAAATGTCT 60.361 37.037 0.00 0.00 33.92 3.41
4929 10330 2.225343 TGGGACGGAGGGAGTACTTTTA 60.225 50.000 0.00 0.00 0.00 1.52
5039 10548 0.752743 GGCTGCTACAATGGCCATGA 60.753 55.000 21.63 7.05 43.59 3.07
5050 10559 5.387788 ACAATGGCCATGATGTGTATGTAT 58.612 37.500 21.63 0.00 0.00 2.29
5051 10560 5.242171 ACAATGGCCATGATGTGTATGTATG 59.758 40.000 21.63 11.30 0.00 2.39
5052 10561 4.436113 TGGCCATGATGTGTATGTATGT 57.564 40.909 0.00 0.00 0.00 2.29
5053 10562 5.559148 TGGCCATGATGTGTATGTATGTA 57.441 39.130 0.00 0.00 0.00 2.29
5062 10571 8.028652 TGATGTGTATGTATGTATTCCTGGAA 57.971 34.615 12.26 12.26 0.00 3.53
5143 10652 3.199946 AGTTTCCAACACTTGTCTCCTCA 59.800 43.478 0.00 0.00 0.00 3.86
5234 11043 1.822990 CTCCCTGTTGCCTCGTACTTA 59.177 52.381 0.00 0.00 0.00 2.24
5258 11067 3.054361 CCCATGTTGCCTCCTAGTACTTT 60.054 47.826 0.00 0.00 0.00 2.66
5328 11143 3.869065 TCGTTATGTCTTGGCCTAAAGG 58.131 45.455 3.32 0.00 38.53 3.11
5390 11206 2.986019 TCATTTGAACCTCCTCTGGGAA 59.014 45.455 0.00 0.00 41.69 3.97
5392 11208 1.362224 TTGAACCTCCTCTGGGAAGG 58.638 55.000 0.00 0.00 41.69 3.46
5611 11428 6.392625 AAAAAGAGAGAACTAAAACCAGCC 57.607 37.500 0.00 0.00 0.00 4.85
5612 11429 4.706842 AAGAGAGAACTAAAACCAGCCA 57.293 40.909 0.00 0.00 0.00 4.75
5613 11430 4.009370 AGAGAGAACTAAAACCAGCCAC 57.991 45.455 0.00 0.00 0.00 5.01
5666 11510 3.565905 AAAGTACTCATTTGCTGCAGC 57.434 42.857 31.89 31.89 42.50 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
401 410 7.786030 ACTTGAGCTCTAATTGCTTATCACTA 58.214 34.615 16.19 0.00 41.30 2.74
535 547 7.873719 AGCGATATATGCTCTAGTCTACAAT 57.126 36.000 0.00 0.00 38.62 2.71
551 563 4.827284 TCTGATGTTGAGTGGAGCGATATA 59.173 41.667 0.00 0.00 0.00 0.86
641 653 0.036732 TGGGCCTTGACATGACAGAC 59.963 55.000 4.53 0.00 0.00 3.51
711 1504 2.082366 GTACACGTACACGGCCACG 61.082 63.158 11.46 11.46 44.95 4.94
718 1511 0.234625 TCGTCACCGTACACGTACAC 59.765 55.000 8.02 0.00 37.30 2.90
719 1512 0.234625 GTCGTCACCGTACACGTACA 59.765 55.000 8.02 0.00 37.30 2.90
720 1513 0.512952 AGTCGTCACCGTACACGTAC 59.487 55.000 0.58 0.00 37.30 3.67
721 1514 0.512518 CAGTCGTCACCGTACACGTA 59.487 55.000 0.58 0.00 37.30 3.57
722 1515 1.280746 CAGTCGTCACCGTACACGT 59.719 57.895 0.58 0.00 37.30 4.49
724 1517 1.800586 TCTACAGTCGTCACCGTACAC 59.199 52.381 0.00 0.00 35.01 2.90
725 1518 1.800586 GTCTACAGTCGTCACCGTACA 59.199 52.381 0.00 0.00 35.01 2.90
726 1519 1.201855 CGTCTACAGTCGTCACCGTAC 60.202 57.143 0.00 0.00 35.01 3.67
727 1520 1.070821 CGTCTACAGTCGTCACCGTA 58.929 55.000 0.00 0.00 35.01 4.02
728 1521 1.864862 CGTCTACAGTCGTCACCGT 59.135 57.895 0.00 0.00 35.01 4.83
731 1524 1.058590 CACGCGTCTACAGTCGTCAC 61.059 60.000 9.86 0.00 32.38 3.67
733 1526 1.511464 CCACGCGTCTACAGTCGTC 60.511 63.158 9.86 0.00 32.38 4.20
753 2684 1.153978 CGTACACGTACACGGCCAT 60.154 57.895 2.24 0.00 44.95 4.40
759 2690 0.234625 TCGTCACCGTACACGTACAC 59.765 55.000 8.02 0.00 37.30 2.90
761 2692 0.512952 AGTCGTCACCGTACACGTAC 59.487 55.000 0.58 0.00 37.30 3.67
762 2693 0.512518 CAGTCGTCACCGTACACGTA 59.487 55.000 0.58 0.00 37.30 3.57
763 2694 1.280746 CAGTCGTCACCGTACACGT 59.719 57.895 0.58 0.00 37.30 4.49
765 2696 1.800586 TCTACAGTCGTCACCGTACAC 59.199 52.381 0.00 0.00 35.01 2.90
766 2697 1.800586 GTCTACAGTCGTCACCGTACA 59.199 52.381 0.00 0.00 35.01 2.90
768 2699 1.070821 CGTCTACAGTCGTCACCGTA 58.929 55.000 0.00 0.00 35.01 4.02
769 2700 1.864862 CGTCTACAGTCGTCACCGT 59.135 57.895 0.00 0.00 35.01 4.83
770 2701 1.511464 GCGTCTACAGTCGTCACCG 60.511 63.158 0.00 0.00 0.00 4.94
771 2702 1.511464 CGCGTCTACAGTCGTCACC 60.511 63.158 0.00 0.00 0.00 4.02
772 2703 1.058590 CACGCGTCTACAGTCGTCAC 61.059 60.000 9.86 0.00 32.38 3.67
773 2704 1.205820 CACGCGTCTACAGTCGTCA 59.794 57.895 9.86 0.00 32.38 4.35
775 2706 2.559840 CCACGCGTCTACAGTCGT 59.440 61.111 9.86 0.00 35.35 4.34
776 2707 2.867333 ATGCCACGCGTCTACAGTCG 62.867 60.000 9.86 0.00 0.00 4.18
777 2708 1.153823 ATGCCACGCGTCTACAGTC 60.154 57.895 9.86 0.00 0.00 3.51
778 2709 1.446099 CATGCCACGCGTCTACAGT 60.446 57.895 9.86 0.00 0.00 3.55
779 2710 2.167219 CCATGCCACGCGTCTACAG 61.167 63.158 9.86 0.00 0.00 2.74
780 2711 2.125713 CCATGCCACGCGTCTACA 60.126 61.111 9.86 8.51 0.00 2.74
781 2712 3.564027 GCCATGCCACGCGTCTAC 61.564 66.667 9.86 1.47 0.00 2.59
791 2722 2.839043 TACACGTACACGGCCATGCC 62.839 60.000 0.00 0.00 46.75 4.40
848 3275 1.617322 AACTAGTGTCAGCGTCCTCA 58.383 50.000 0.00 0.00 0.00 3.86
849 3276 2.726832 AAACTAGTGTCAGCGTCCTC 57.273 50.000 0.00 0.00 0.00 3.71
869 3296 1.031112 AAGGGGAAGGGGAGAGAGAT 58.969 55.000 0.00 0.00 0.00 2.75
871 3298 1.208706 GAAAGGGGAAGGGGAGAGAG 58.791 60.000 0.00 0.00 0.00 3.20
875 5374 1.230314 AGGGAAAGGGGAAGGGGAG 60.230 63.158 0.00 0.00 0.00 4.30
921 5427 2.283809 CGGGAGGAGAGGATGGGT 59.716 66.667 0.00 0.00 0.00 4.51
923 5429 0.825840 GACTCGGGAGGAGAGGATGG 60.826 65.000 0.00 0.00 46.23 3.51
924 5430 0.825840 GGACTCGGGAGGAGAGGATG 60.826 65.000 0.00 0.00 46.23 3.51
925 5431 1.539665 GGACTCGGGAGGAGAGGAT 59.460 63.158 0.00 0.00 46.23 3.24
926 5432 2.691779 GGGACTCGGGAGGAGAGGA 61.692 68.421 0.00 0.00 46.23 3.71
927 5433 2.123640 GGGACTCGGGAGGAGAGG 60.124 72.222 0.00 0.00 46.23 3.69
928 5434 2.517402 CGGGACTCGGGAGGAGAG 60.517 72.222 0.00 0.00 46.23 3.20
929 5435 3.013327 TCGGGACTCGGGAGGAGA 61.013 66.667 0.00 0.00 46.23 3.71
931 5437 3.336568 ACTCGGGACTCGGGAGGA 61.337 66.667 0.00 0.00 43.26 3.71
932 5438 2.829458 GACTCGGGACTCGGGAGG 60.829 72.222 0.00 0.00 43.26 4.30
934 5440 2.045242 CAGACTCGGGACTCGGGA 60.045 66.667 0.00 0.00 43.26 5.14
935 5441 3.827898 GCAGACTCGGGACTCGGG 61.828 72.222 0.00 0.00 46.65 5.14
936 5442 3.057547 CTGCAGACTCGGGACTCGG 62.058 68.421 8.42 0.00 39.77 4.63
937 5443 2.487428 CTGCAGACTCGGGACTCG 59.513 66.667 8.42 0.00 40.90 4.18
938 5444 2.183046 GCTGCAGACTCGGGACTC 59.817 66.667 20.43 0.00 0.00 3.36
939 5445 3.386237 GGCTGCAGACTCGGGACT 61.386 66.667 20.43 0.00 0.00 3.85
940 5446 2.731691 TTTGGCTGCAGACTCGGGAC 62.732 60.000 22.80 0.00 0.00 4.46
941 5447 2.454832 CTTTGGCTGCAGACTCGGGA 62.455 60.000 22.80 0.00 0.00 5.14
942 5448 2.032528 TTTGGCTGCAGACTCGGG 59.967 61.111 22.80 0.00 0.00 5.14
943 5449 2.684843 GCTTTGGCTGCAGACTCGG 61.685 63.158 22.80 11.27 35.22 4.63
944 5450 1.962822 TGCTTTGGCTGCAGACTCG 60.963 57.895 22.80 10.00 39.59 4.18
945 5451 4.069869 TGCTTTGGCTGCAGACTC 57.930 55.556 22.80 7.89 39.59 3.36
950 5456 2.203379 TGCTCTGCTTTGGCTGCA 60.203 55.556 0.50 0.00 39.59 4.41
951 5457 2.257676 GTGCTCTGCTTTGGCTGC 59.742 61.111 0.00 0.00 39.59 5.25
952 5458 1.900016 TGGTGCTCTGCTTTGGCTG 60.900 57.895 0.00 0.00 39.59 4.85
953 5459 1.900498 GTGGTGCTCTGCTTTGGCT 60.900 57.895 0.00 0.00 39.59 4.75
954 5460 2.647297 GTGGTGCTCTGCTTTGGC 59.353 61.111 0.00 0.00 39.26 4.52
955 5461 2.270986 GGGTGGTGCTCTGCTTTGG 61.271 63.158 0.00 0.00 0.00 3.28
956 5462 1.521450 CTGGGTGGTGCTCTGCTTTG 61.521 60.000 0.00 0.00 0.00 2.77
957 5463 1.228367 CTGGGTGGTGCTCTGCTTT 60.228 57.895 0.00 0.00 0.00 3.51
958 5464 2.433446 CTGGGTGGTGCTCTGCTT 59.567 61.111 0.00 0.00 0.00 3.91
959 5465 4.341783 GCTGGGTGGTGCTCTGCT 62.342 66.667 0.00 0.00 39.17 4.24
1143 5697 0.784495 GAAAGGGAAGGAAGGGGGTT 59.216 55.000 0.00 0.00 0.00 4.11
1171 5730 0.614979 TCCACCACCTAGAGCAGTCC 60.615 60.000 0.00 0.00 0.00 3.85
1226 5816 1.202806 TGAATCCATGAATCCCTCGCC 60.203 52.381 0.00 0.00 0.00 5.54
1227 5817 2.149578 CTGAATCCATGAATCCCTCGC 58.850 52.381 0.00 0.00 0.00 5.03
1252 5866 3.326747 CTGAACAAAACCTAGTCCCTCG 58.673 50.000 0.00 0.00 0.00 4.63
1254 5868 2.224793 GCCTGAACAAAACCTAGTCCCT 60.225 50.000 0.00 0.00 0.00 4.20
1275 5889 7.905604 TGTACTATCAGTTCCAATTTCACAG 57.094 36.000 0.00 0.00 0.00 3.66
1357 6059 0.456221 AGTACGGAGATGGCGTTGAG 59.544 55.000 0.00 0.00 0.00 3.02
1388 6104 9.892130 CCCTTGACTATTGTAGACTTAAGATTT 57.108 33.333 10.09 0.00 0.00 2.17
1389 6105 8.487028 CCCCTTGACTATTGTAGACTTAAGATT 58.513 37.037 10.09 0.00 0.00 2.40
1391 6107 6.127140 GCCCCTTGACTATTGTAGACTTAAGA 60.127 42.308 10.09 0.00 0.00 2.10
1392 6108 6.049790 GCCCCTTGACTATTGTAGACTTAAG 58.950 44.000 0.00 0.00 0.00 1.85
1405 6138 0.255890 GAATGGCTGCCCCTTGACTA 59.744 55.000 17.53 0.00 0.00 2.59
1458 6193 1.533625 GCCAGCAACAGTGTTATGGA 58.466 50.000 30.13 0.00 30.72 3.41
1465 6206 0.179140 AAAACACGCCAGCAACAGTG 60.179 50.000 0.00 0.00 40.17 3.66
1475 6216 2.725815 GTCGCAGCAAAACACGCC 60.726 61.111 0.00 0.00 0.00 5.68
1476 6217 2.005537 CTGTCGCAGCAAAACACGC 61.006 57.895 0.00 0.00 0.00 5.34
1477 6218 0.654472 GACTGTCGCAGCAAAACACG 60.654 55.000 6.74 0.00 34.37 4.49
1482 6223 4.764679 AATAATTGACTGTCGCAGCAAA 57.235 36.364 2.98 8.15 33.78 3.68
1566 6337 7.167635 CACAGTATGCTATTGGTAACTAACTCG 59.832 40.741 0.00 0.00 42.53 4.18
1569 6340 8.888579 ATCACAGTATGCTATTGGTAACTAAC 57.111 34.615 0.00 0.00 42.53 2.34
1587 6523 2.553028 CCCCAACACTAGCAATCACAGT 60.553 50.000 0.00 0.00 0.00 3.55
1594 6530 0.690762 GGAGTCCCCAACACTAGCAA 59.309 55.000 0.00 0.00 34.14 3.91
1641 6577 3.818210 GAGTGAGTGAACAGAGACAGAGA 59.182 47.826 0.00 0.00 0.00 3.10
1642 6578 3.057596 GGAGTGAGTGAACAGAGACAGAG 60.058 52.174 0.00 0.00 0.00 3.35
1643 6579 2.887783 GGAGTGAGTGAACAGAGACAGA 59.112 50.000 0.00 0.00 0.00 3.41
1644 6580 2.029470 GGGAGTGAGTGAACAGAGACAG 60.029 54.545 0.00 0.00 0.00 3.51
1645 6581 1.964223 GGGAGTGAGTGAACAGAGACA 59.036 52.381 0.00 0.00 0.00 3.41
1646 6582 2.243810 AGGGAGTGAGTGAACAGAGAC 58.756 52.381 0.00 0.00 0.00 3.36
1647 6583 2.685106 AGGGAGTGAGTGAACAGAGA 57.315 50.000 0.00 0.00 0.00 3.10
1721 6663 9.046296 ACTTGTGTAGTCTTTAATTCAGAAGTG 57.954 33.333 0.00 0.00 37.76 3.16
1736 6679 9.509855 CTATTATGAGAACTCACTTGTGTAGTC 57.490 37.037 6.67 0.00 43.11 2.59
1880 6870 1.687123 ACGGTCAGTTCAGTTAGCACT 59.313 47.619 0.00 0.00 0.00 4.40
1898 6912 0.790814 GTCGGCTGAAAGAAGGAACG 59.209 55.000 0.00 0.00 34.07 3.95
2292 7321 2.352960 GGAGAACATTGAGCGTTCCATC 59.647 50.000 0.00 0.00 43.07 3.51
2438 7470 9.046296 CATATTACCTTATTCTTTTCGCAGACT 57.954 33.333 0.00 0.00 34.32 3.24
2639 7710 8.364142 AGATTCTATTTCAGTAGAGGTGCATAC 58.636 37.037 0.00 0.00 32.63 2.39
2664 7735 6.782988 TGGTATCACCCTCTTATCCTAAGAAG 59.217 42.308 0.00 0.00 37.50 2.85
2742 7821 7.394077 TGTGGATTATTGATTGTGTCTCATTGT 59.606 33.333 0.00 0.00 0.00 2.71
2749 7829 7.592938 TCTTGTTGTGGATTATTGATTGTGTC 58.407 34.615 0.00 0.00 0.00 3.67
2843 8016 2.561478 TCCCTGAACACTAACCAAGC 57.439 50.000 0.00 0.00 0.00 4.01
2866 8039 7.228590 AGTGCTGAGTTAACCAGGTATAAAAA 58.771 34.615 19.36 0.00 32.51 1.94
2867 8040 6.775708 AGTGCTGAGTTAACCAGGTATAAAA 58.224 36.000 19.36 0.00 32.51 1.52
2868 8041 6.368779 AGTGCTGAGTTAACCAGGTATAAA 57.631 37.500 19.36 0.00 32.51 1.40
2927 8102 7.447374 TGTTATGCAATTGCTTAGTAACAGT 57.553 32.000 29.37 6.79 42.66 3.55
3070 8281 5.178623 GCATGCGCCAGTTATACAGTAATAA 59.821 40.000 4.18 0.00 0.00 1.40
3100 8311 8.755941 CACTGAAGAACGATGTACTTATAATGG 58.244 37.037 0.00 0.00 0.00 3.16
3206 8419 8.519492 TGAAGCAATGTAATTTTCAAGTTAGC 57.481 30.769 0.00 0.00 31.98 3.09
3245 8458 8.062065 TGTGGAAGTAAAGTTTTGAGATTTGT 57.938 30.769 0.00 0.00 0.00 2.83
3578 8800 1.981495 AGGGCAAAACAGAGCTCTACT 59.019 47.619 17.75 3.08 40.45 2.57
3740 8963 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3780 9005 7.891712 TCATTCCAATATGGCAATATCTCACAT 59.108 33.333 0.00 0.00 37.47 3.21
3809 9034 9.944376 ATTAGCTAGACAAACAATGAAGAGTAA 57.056 29.630 0.00 0.00 0.00 2.24
3964 9217 8.773033 AGCTCCAAGTATCCAAATAAATGAAT 57.227 30.769 0.00 0.00 0.00 2.57
4451 9803 1.550524 AGCATGTGTCCACTACGTCAT 59.449 47.619 0.00 0.00 0.00 3.06
4452 9804 0.966179 AGCATGTGTCCACTACGTCA 59.034 50.000 0.00 0.00 0.00 4.35
4600 9953 8.953313 TGAAGTTGTACTAGATAAGTCGATTCA 58.047 33.333 0.00 0.00 39.80 2.57
4889 10253 6.905076 CGTCCCATAATGTAAGACATTTTTCG 59.095 38.462 9.92 4.65 45.80 3.46
4890 10254 7.066525 TCCGTCCCATAATGTAAGACATTTTTC 59.933 37.037 9.92 0.00 45.80 2.29
4893 10257 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
4895 10259 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
4896 10260 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
4897 10261 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
4900 10301 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
4914 10315 3.132467 ACGAGCATAAAAGTACTCCCTCC 59.868 47.826 0.00 0.00 0.00 4.30
4929 10330 3.338249 AGCAAACTGACAATACGAGCAT 58.662 40.909 0.00 0.00 0.00 3.79
5039 10548 9.866655 ATTTTCCAGGAATACATACATACACAT 57.133 29.630 1.58 0.00 0.00 3.21
5050 10559 7.779326 TCATATGCTTCATTTTCCAGGAATACA 59.221 33.333 1.58 0.00 0.00 2.29
5051 10560 8.169977 TCATATGCTTCATTTTCCAGGAATAC 57.830 34.615 1.58 0.00 0.00 1.89
5052 10561 8.765488 TTCATATGCTTCATTTTCCAGGAATA 57.235 30.769 1.58 0.00 0.00 1.75
5053 10562 7.664552 TTCATATGCTTCATTTTCCAGGAAT 57.335 32.000 1.58 0.00 0.00 3.01
5143 10652 4.204012 CGGGGTGGAATTGTGTATATTGT 58.796 43.478 0.00 0.00 0.00 2.71
5234 11043 1.372501 ACTAGGAGGCAACATGGGTT 58.627 50.000 0.00 0.00 37.87 4.11
5258 11067 4.996344 TGCGAACCGAAATAGTACATGTA 58.004 39.130 0.08 0.08 0.00 2.29
5328 11143 4.423732 TGTTCAGACTTTTGCTGCTTTTC 58.576 39.130 0.00 0.00 33.45 2.29
5390 11206 2.192263 GGTCCAATCTCTGAACTCCCT 58.808 52.381 0.00 0.00 0.00 4.20
5392 11208 3.703001 TTGGTCCAATCTCTGAACTCC 57.297 47.619 0.00 0.00 0.00 3.85
5593 11410 3.740115 TGTGGCTGGTTTTAGTTCTCTC 58.260 45.455 0.00 0.00 0.00 3.20
5594 11411 3.857157 TGTGGCTGGTTTTAGTTCTCT 57.143 42.857 0.00 0.00 0.00 3.10
5595 11412 4.578928 TCTTTGTGGCTGGTTTTAGTTCTC 59.421 41.667 0.00 0.00 0.00 2.87
5606 11423 2.161855 TGCAGTAATCTTTGTGGCTGG 58.838 47.619 0.00 0.00 0.00 4.85
5609 11426 4.215399 TGTTACTGCAGTAATCTTTGTGGC 59.785 41.667 35.13 21.73 41.85 5.01
5610 11427 5.940192 TGTTACTGCAGTAATCTTTGTGG 57.060 39.130 35.13 0.77 41.85 4.17
5611 11428 9.494479 CATAATGTTACTGCAGTAATCTTTGTG 57.506 33.333 35.13 29.21 41.85 3.33
5612 11429 9.231297 ACATAATGTTACTGCAGTAATCTTTGT 57.769 29.630 35.13 28.64 41.85 2.83
5666 11510 8.467598 ACTAGTACTACATGTCAGGTTATGTTG 58.532 37.037 0.00 0.00 38.41 3.33


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

AutoCloner maintained by Alex Coulton.