Multiple sequence alignment - TraesCS5D01G508700

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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 TraesCS5D01G508700 chr5D 100.000 7049 0 0 1 7049 533869956 533862908 0.000000e+00 13018.0
1 TraesCS5D01G508700 chr5D 85.220 1908 226 35 1648 3546 533666038 533664178 0.000000e+00 1910.0
2 TraesCS5D01G508700 chr5D 84.168 1358 178 22 1648 2995 533644751 533643421 0.000000e+00 1282.0
3 TraesCS5D01G508700 chr5D 82.962 1121 129 35 2993 4110 533643164 533642103 0.000000e+00 955.0
4 TraesCS5D01G508700 chr5D 84.722 504 43 6 4230 4732 533660300 533659830 2.300000e-129 473.0
5 TraesCS5D01G508700 chr5D 89.796 343 30 4 5452 5790 533641169 533640828 1.090000e-117 435.0
6 TraesCS5D01G508700 chr5D 88.921 343 33 4 5452 5790 533659463 533659122 1.090000e-112 418.0
7 TraesCS5D01G508700 chr5D 80.952 504 72 14 4954 5443 219765675 219766168 1.860000e-100 377.0
8 TraesCS5D01G508700 chr5D 84.135 416 35 8 4223 4637 533642094 533641709 2.400000e-99 374.0
9 TraesCS5D01G508700 chr5D 87.405 262 28 4 4819 5077 533659823 533659564 5.350000e-76 296.0
10 TraesCS5D01G508700 chr5D 95.327 107 5 0 4111 4217 500862548 500862442 3.380000e-38 171.0
11 TraesCS5D01G508700 chr5D 85.294 170 15 8 915 1084 533666525 533666366 4.370000e-37 167.0
12 TraesCS5D01G508700 chr5B 93.934 3330 107 36 833 4113 673939827 673936544 0.000000e+00 4942.0
13 TraesCS5D01G508700 chr5B 92.991 2454 106 30 4207 6643 673936545 673934141 0.000000e+00 3518.0
14 TraesCS5D01G508700 chr5B 81.826 1150 149 32 1663 2798 673691565 673690462 0.000000e+00 911.0
15 TraesCS5D01G508700 chr5B 86.853 753 85 9 2779 3529 673690443 673689703 0.000000e+00 830.0
16 TraesCS5D01G508700 chr5B 85.110 591 69 12 2959 3546 673769789 673769215 2.830000e-163 586.0
17 TraesCS5D01G508700 chr5B 83.542 559 78 6 3547 4105 597233617 597234161 1.750000e-140 510.0
18 TraesCS5D01G508700 chr5B 89.717 389 19 7 18 393 673940682 673940302 1.780000e-130 477.0
19 TraesCS5D01G508700 chr5B 89.250 400 15 12 6675 7049 673934142 673933746 6.400000e-130 475.0
20 TraesCS5D01G508700 chr5B 82.523 555 69 15 4818 5356 345975994 345976536 4.980000e-126 462.0
21 TraesCS5D01G508700 chr5B 85.275 455 35 4 4230 4684 673765477 673765055 2.330000e-119 440.0
22 TraesCS5D01G508700 chr5B 89.796 343 30 4 5452 5790 673688239 673687898 1.090000e-117 435.0
23 TraesCS5D01G508700 chr5B 84.597 409 33 8 4230 4637 673689156 673688777 5.160000e-101 379.0
24 TraesCS5D01G508700 chr5B 89.668 271 6 7 411 659 673940218 673939948 6.820000e-85 326.0
25 TraesCS5D01G508700 chr5B 87.786 262 27 4 4819 5077 673765042 673764783 1.150000e-77 302.0
26 TraesCS5D01G508700 chr4A 95.604 2252 71 12 1479 3711 638170081 638172323 0.000000e+00 3585.0
27 TraesCS5D01G508700 chr4A 95.478 2145 67 12 4207 6324 638172833 638174974 0.000000e+00 3397.0
28 TraesCS5D01G508700 chr4A 83.468 2474 314 48 1648 4110 638213921 638216310 0.000000e+00 2215.0
29 TraesCS5D01G508700 chr4A 89.525 716 43 13 758 1470 638169296 638169982 0.000000e+00 878.0
30 TraesCS5D01G508700 chr4A 97.304 408 6 3 3710 4113 638172428 638172834 0.000000e+00 688.0
31 TraesCS5D01G508700 chr4A 82.720 706 67 21 6365 7049 638175041 638175712 1.700000e-160 577.0
32 TraesCS5D01G508700 chr4A 85.129 464 26 22 1 422 638134757 638135219 1.090000e-117 435.0
33 TraesCS5D01G508700 chr4A 84.804 408 32 15 4230 4637 638216325 638216702 3.990000e-102 383.0
34 TraesCS5D01G508700 chr4A 86.431 339 20 15 411 736 638135260 638135585 1.460000e-91 348.0
35 TraesCS5D01G508700 chr4B 90.832 1527 116 15 1576 3097 14392074 14393581 0.000000e+00 2023.0
36 TraesCS5D01G508700 chr4B 88.266 1159 97 25 4874 5998 14395237 14396390 0.000000e+00 1351.0
37 TraesCS5D01G508700 chr4B 86.855 1027 81 24 3090 4110 14393728 14394706 0.000000e+00 1099.0
38 TraesCS5D01G508700 chr4B 93.373 498 28 5 4230 4726 14394721 14395214 0.000000e+00 732.0
39 TraesCS5D01G508700 chr4B 88.276 290 19 7 6496 6771 14396626 14396914 4.070000e-87 333.0
40 TraesCS5D01G508700 chr4B 82.857 385 35 16 994 1365 14391439 14391805 4.100000e-82 316.0
41 TraesCS5D01G508700 chr4B 95.192 104 5 0 4105 4208 186741664 186741767 1.570000e-36 165.0
42 TraesCS5D01G508700 chr4B 80.342 234 30 11 6099 6324 14396393 14396618 5.660000e-36 163.0
43 TraesCS5D01G508700 chr4B 92.857 112 8 0 4109 4220 498378510 498378621 5.660000e-36 163.0
44 TraesCS5D01G508700 chr4B 100.000 28 0 0 6957 6984 626454076 626454103 1.300000e-02 52.8
45 TraesCS5D01G508700 chr6D 85.570 1587 159 31 1998 3546 352908670 352907116 0.000000e+00 1598.0
46 TraesCS5D01G508700 chr6D 85.911 582 65 14 3535 4113 352907154 352906587 7.820000e-169 604.0
47 TraesCS5D01G508700 chr6D 85.636 550 67 3 3556 4105 406560092 406559555 1.030000e-157 568.0
48 TraesCS5D01G508700 chr6D 83.114 456 42 13 4230 4685 406559534 406559114 3.990000e-102 383.0
49 TraesCS5D01G508700 chr6D 88.213 263 28 3 4818 5077 352906095 352905833 1.910000e-80 311.0
50 TraesCS5D01G508700 chr6D 86.047 172 17 3 959 1130 352910038 352909874 2.020000e-40 178.0
51 TraesCS5D01G508700 chr6D 90.244 123 8 4 4100 4218 362051536 362051414 2.630000e-34 158.0
52 TraesCS5D01G508700 chr3B 84.844 739 40 21 955 1668 820882004 820882695 0.000000e+00 678.0
53 TraesCS5D01G508700 chr3B 84.409 558 67 11 3556 4105 631522147 631522692 1.350000e-146 531.0
54 TraesCS5D01G508700 chr3B 83.717 565 76 8 3547 4110 144790155 144790704 2.910000e-143 520.0
55 TraesCS5D01G508700 chr3B 81.337 643 85 18 4818 5443 631523005 631523629 2.280000e-134 490.0
56 TraesCS5D01G508700 chr3B 81.838 457 68 11 4230 4685 735952124 735951682 3.110000e-98 370.0
57 TraesCS5D01G508700 chr3B 84.085 377 50 4 3738 4113 7079821 7080188 8.700000e-94 355.0
58 TraesCS5D01G508700 chr3B 95.238 105 5 0 4112 4216 766128276 766128172 4.370000e-37 167.0
59 TraesCS5D01G508700 chr3B 90.909 88 6 2 4731 4817 60259750 60259664 4.470000e-22 117.0
60 TraesCS5D01G508700 chr3B 90.588 85 8 0 4732 4816 60259655 60259739 5.780000e-21 113.0
61 TraesCS5D01G508700 chr6B 82.334 634 86 16 4818 5443 687250800 687251415 1.740000e-145 527.0
62 TraesCS5D01G508700 chr6B 83.542 559 78 6 3547 4105 504290736 504291280 1.750000e-140 510.0
63 TraesCS5D01G508700 chr6B 84.557 531 62 10 3556 4080 687249784 687250300 6.310000e-140 508.0
64 TraesCS5D01G508700 chr6B 100.000 28 0 0 6957 6984 75984909 75984936 1.300000e-02 52.8
65 TraesCS5D01G508700 chr7A 82.047 635 90 15 4818 5446 82160324 82159708 2.910000e-143 520.0
66 TraesCS5D01G508700 chr7A 81.917 647 81 21 4818 5446 94703936 94703308 1.360000e-141 514.0
67 TraesCS5D01G508700 chr7A 83.503 491 60 11 3556 4040 82161897 82161422 8.390000e-119 438.0
68 TraesCS5D01G508700 chr7A 85.263 285 33 3 3821 4105 94704708 94704433 1.160000e-72 285.0
69 TraesCS5D01G508700 chr7B 81.947 637 89 16 4818 5446 606781712 606781094 3.770000e-142 516.0
70 TraesCS5D01G508700 chr1A 82.178 606 75 18 4818 5407 10814554 10815142 2.280000e-134 490.0
71 TraesCS5D01G508700 chr1A 89.655 87 9 0 4730 4816 481924518 481924432 2.080000e-20 111.0
72 TraesCS5D01G508700 chr1A 83.607 122 16 4 4695 4816 516728799 516728916 2.080000e-20 111.0
73 TraesCS5D01G508700 chr1A 87.912 91 9 2 4727 4816 481924417 481924506 9.670000e-19 106.0
74 TraesCS5D01G508700 chr3D 86.810 326 35 7 4230 4554 554073161 554072843 2.420000e-94 357.0
75 TraesCS5D01G508700 chr3D 95.238 105 5 0 4112 4216 23081175 23081279 4.370000e-37 167.0
76 TraesCS5D01G508700 chr2D 93.694 111 7 0 4104 4214 7661711 7661601 4.370000e-37 167.0
77 TraesCS5D01G508700 chr2B 94.495 109 4 2 4109 4216 159487891 159487998 4.370000e-37 167.0
78 TraesCS5D01G508700 chr2B 90.000 120 8 4 4094 4210 674033923 674034041 1.220000e-32 152.0
79 TraesCS5D01G508700 chr2B 100.000 28 0 0 6957 6984 357951478 357951505 1.300000e-02 52.8
80 TraesCS5D01G508700 chr5A 90.698 86 8 0 4731 4816 533944187 533944272 1.610000e-21 115.0
81 TraesCS5D01G508700 chr4D 88.636 88 10 0 4730 4817 210457865 210457778 2.690000e-19 108.0
82 TraesCS5D01G508700 chrUn 100.000 28 0 0 6957 6984 38370693 38370720 1.300000e-02 52.8
83 TraesCS5D01G508700 chr2A 100.000 28 0 0 6957 6984 496468969 496468996 1.300000e-02 52.8
84 TraesCS5D01G508700 chr1B 100.000 28 0 0 6957 6984 26668548 26668575 1.300000e-02 52.8
85 TraesCS5D01G508700 chr1B 100.000 28 0 0 6957 6984 54914349 54914376 1.300000e-02 52.8


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 TraesCS5D01G508700 chr5D 533862908 533869956 7048 True 13018.000000 13018 100.000000 1 7049 1 chr5D.!!$R2 7048
1 TraesCS5D01G508700 chr5D 533640828 533644751 3923 True 761.500000 1282 85.265250 1648 5790 4 chr5D.!!$R3 4142
2 TraesCS5D01G508700 chr5D 533659122 533666525 7403 True 652.800000 1910 86.312400 915 5790 5 chr5D.!!$R4 4875
3 TraesCS5D01G508700 chr5B 673933746 673940682 6936 True 1947.600000 4942 91.112000 18 7049 5 chr5B.!!$R3 7031
4 TraesCS5D01G508700 chr5B 673687898 673691565 3667 True 638.750000 911 85.768000 1663 5790 4 chr5B.!!$R1 4127
5 TraesCS5D01G508700 chr5B 597233617 597234161 544 False 510.000000 510 83.542000 3547 4105 1 chr5B.!!$F2 558
6 TraesCS5D01G508700 chr5B 345975994 345976536 542 False 462.000000 462 82.523000 4818 5356 1 chr5B.!!$F1 538
7 TraesCS5D01G508700 chr5B 673764783 673769789 5006 True 442.666667 586 86.057000 2959 5077 3 chr5B.!!$R2 2118
8 TraesCS5D01G508700 chr4A 638169296 638175712 6416 False 1825.000000 3585 92.126200 758 7049 5 chr4A.!!$F2 6291
9 TraesCS5D01G508700 chr4A 638213921 638216702 2781 False 1299.000000 2215 84.136000 1648 4637 2 chr4A.!!$F3 2989
10 TraesCS5D01G508700 chr4A 638134757 638135585 828 False 391.500000 435 85.780000 1 736 2 chr4A.!!$F1 735
11 TraesCS5D01G508700 chr4B 14391439 14396914 5475 False 859.571429 2023 87.257286 994 6771 7 chr4B.!!$F4 5777
12 TraesCS5D01G508700 chr6D 352905833 352910038 4205 True 672.750000 1598 86.435250 959 5077 4 chr6D.!!$R2 4118
13 TraesCS5D01G508700 chr6D 406559114 406560092 978 True 475.500000 568 84.375000 3556 4685 2 chr6D.!!$R3 1129
14 TraesCS5D01G508700 chr3B 820882004 820882695 691 False 678.000000 678 84.844000 955 1668 1 chr3B.!!$F4 713
15 TraesCS5D01G508700 chr3B 144790155 144790704 549 False 520.000000 520 83.717000 3547 4110 1 chr3B.!!$F3 563
16 TraesCS5D01G508700 chr3B 631522147 631523629 1482 False 510.500000 531 82.873000 3556 5443 2 chr3B.!!$F5 1887
17 TraesCS5D01G508700 chr6B 687249784 687251415 1631 False 517.500000 527 83.445500 3556 5443 2 chr6B.!!$F3 1887
18 TraesCS5D01G508700 chr6B 504290736 504291280 544 False 510.000000 510 83.542000 3547 4105 1 chr6B.!!$F2 558
19 TraesCS5D01G508700 chr7A 82159708 82161897 2189 True 479.000000 520 82.775000 3556 5446 2 chr7A.!!$R1 1890
20 TraesCS5D01G508700 chr7A 94703308 94704708 1400 True 399.500000 514 83.590000 3821 5446 2 chr7A.!!$R2 1625
21 TraesCS5D01G508700 chr7B 606781094 606781712 618 True 516.000000 516 81.947000 4818 5446 1 chr7B.!!$R1 628
22 TraesCS5D01G508700 chr1A 10814554 10815142 588 False 490.000000 490 82.178000 4818 5407 1 chr1A.!!$F1 589

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
397 449 0.179006 GCCAGATCTCCAACCATCCC 60.179 60.000 0.00 0.0 0.00 3.85 F
738 869 0.260523 GGCCTGGCCCAACCTAATAA 59.739 55.000 27.77 0.0 44.06 1.40 F
1477 1735 0.108281 TTGCACTTTGCTTTGCTGCA 60.108 45.000 0.00 0.0 45.31 4.41 F
1672 2078 1.066136 GAACCGTCGCCTCTGTTTAC 58.934 55.000 0.00 0.0 0.00 2.01 F
2025 2960 3.320541 TGGTGTTTTGGTGCTTATTCTGG 59.679 43.478 0.00 0.0 0.00 3.86 F
3399 4837 4.261405 CGATCACTTGGTTTAACTTTGCCA 60.261 41.667 0.00 0.0 0.00 4.92 F
4437 10110 0.036105 CAGGCCCCCAGAAATTTTGC 60.036 55.000 0.00 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1639 0.674581 CCAGGAGTTGAGATGCGCAA 60.675 55.000 17.11 0.0 0.00 4.85 R
1643 2049 2.671177 CGACGGTTCAAGCAGGCAG 61.671 63.158 0.00 0.0 0.00 4.85 R
2406 3349 4.157105 TGCTGCTCTTATACACGACAAGTA 59.843 41.667 0.00 0.0 0.00 2.24 R
3366 4804 4.471904 ACCAAGTGATCGCTCTGAAATA 57.528 40.909 9.70 0.0 0.00 1.40 R
3809 5443 7.171630 AGTCGATGATTAACTACTTGGAAGT 57.828 36.000 0.00 0.0 42.91 3.01 R
4523 10199 0.764890 TGTGTCTTCTGAACCCCCAG 59.235 55.000 0.00 0.0 35.55 4.45 R
6107 12001 0.320421 ATCTAACACGCAAGCACGGT 60.320 50.000 0.00 0.0 45.62 4.83 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
54 59 3.003480 GCAAACGAGCTCCAGAAATAGT 58.997 45.455 8.47 0.00 0.00 2.12
70 75 7.225397 CAGAAATAGTCGGTCGTTCTTTTAAC 58.775 38.462 0.00 0.00 0.00 2.01
121 129 2.236644 GGAAAGAAGTACTCCCACTCCC 59.763 54.545 0.00 0.00 0.00 4.30
237 255 2.401766 CGGCAACATCAGCAGGGTC 61.402 63.158 0.00 0.00 0.00 4.46
254 272 0.518764 GTCGCAGTCGTAGTCTCGTG 60.519 60.000 0.00 0.00 36.96 4.35
311 345 2.662596 GAGATCACGGCCCACACA 59.337 61.111 0.00 0.00 0.00 3.72
393 445 0.982852 ATCCGCCAGATCTCCAACCA 60.983 55.000 0.00 0.00 0.00 3.67
397 449 0.179006 GCCAGATCTCCAACCATCCC 60.179 60.000 0.00 0.00 0.00 3.85
682 813 0.460987 CTCAAGGTGCATCGACCCTC 60.461 60.000 0.00 0.00 36.56 4.30
689 820 3.083349 CATCGACCCTCCTGCCCA 61.083 66.667 0.00 0.00 0.00 5.36
690 821 3.083997 ATCGACCCTCCTGCCCAC 61.084 66.667 0.00 0.00 0.00 4.61
707 838 1.270518 CCACCACTTGACCAGTCAGAG 60.271 57.143 0.09 4.88 41.13 3.35
738 869 0.260523 GGCCTGGCCCAACCTAATAA 59.739 55.000 27.77 0.00 44.06 1.40
752 883 5.532664 ACCTAATAAGCGTCTAGAAAGGG 57.467 43.478 0.00 0.00 0.00 3.95
753 884 5.206587 ACCTAATAAGCGTCTAGAAAGGGA 58.793 41.667 0.00 0.00 0.00 4.20
799 940 4.988598 ACAAGTGTCGCAGGCCCG 62.989 66.667 0.00 0.00 0.00 6.13
820 961 4.676444 CGTTGCCGCATGAAGATG 57.324 55.556 0.00 0.00 0.00 2.90
821 962 1.063006 CGTTGCCGCATGAAGATGG 59.937 57.895 0.00 0.00 0.00 3.51
822 963 1.434696 GTTGCCGCATGAAGATGGG 59.565 57.895 0.00 0.00 41.21 4.00
823 964 2.417257 TTGCCGCATGAAGATGGGC 61.417 57.895 0.00 0.00 42.19 5.36
824 965 2.517875 GCCGCATGAAGATGGGCT 60.518 61.111 0.00 0.00 40.30 5.19
825 966 2.842256 GCCGCATGAAGATGGGCTG 61.842 63.158 0.00 0.00 40.30 4.85
826 967 2.191513 CCGCATGAAGATGGGCTGG 61.192 63.158 0.00 0.00 40.41 4.85
827 968 2.842256 CGCATGAAGATGGGCTGGC 61.842 63.158 0.00 0.00 35.90 4.85
828 969 1.755395 GCATGAAGATGGGCTGGCA 60.755 57.895 2.88 0.00 0.00 4.92
829 970 1.113517 GCATGAAGATGGGCTGGCAT 61.114 55.000 2.88 0.00 0.00 4.40
830 971 0.673985 CATGAAGATGGGCTGGCATG 59.326 55.000 2.88 0.00 35.36 4.06
831 972 0.469331 ATGAAGATGGGCTGGCATGG 60.469 55.000 2.88 0.00 0.00 3.66
892 1036 4.297299 TGCGTACGATAAACCCTAGAAG 57.703 45.455 21.65 0.00 0.00 2.85
895 1039 3.317430 CGTACGATAAACCCTAGAAGGCT 59.683 47.826 10.44 0.00 32.73 4.58
896 1040 4.516698 CGTACGATAAACCCTAGAAGGCTA 59.483 45.833 10.44 0.00 32.73 3.93
897 1041 5.334724 CGTACGATAAACCCTAGAAGGCTAG 60.335 48.000 10.44 0.00 43.08 3.42
903 1047 2.657143 ACCCTAGAAGGCTAGAACGAG 58.343 52.381 0.00 0.00 45.71 4.18
923 1067 3.322466 AACCAGTCCCGGCCTCTG 61.322 66.667 0.00 3.76 0.00 3.35
1193 1370 1.153449 TCGCTGCCAAGGTATTCCG 60.153 57.895 0.00 0.00 39.05 4.30
1196 1373 1.095807 GCTGCCAAGGTATTCCGTCC 61.096 60.000 0.00 0.00 39.05 4.79
1382 1625 3.344904 TTTACGCTATCCGCTCTGTAC 57.655 47.619 0.00 0.00 41.76 2.90
1395 1638 1.596260 CTCTGTACGCTCCGATTACGA 59.404 52.381 0.00 0.00 42.66 3.43
1396 1639 2.216046 TCTGTACGCTCCGATTACGAT 58.784 47.619 0.00 0.00 42.66 3.73
1466 1724 5.964758 TGTTCAAAGTTCAGATTGCACTTT 58.035 33.333 1.85 1.85 42.82 2.66
1469 1727 4.660789 AAAGTTCAGATTGCACTTTGCT 57.339 36.364 6.14 0.00 41.08 3.91
1470 1728 4.660789 AAGTTCAGATTGCACTTTGCTT 57.339 36.364 0.00 0.00 45.31 3.91
1471 1729 4.660789 AGTTCAGATTGCACTTTGCTTT 57.339 36.364 0.00 0.00 45.31 3.51
1472 1730 4.365723 AGTTCAGATTGCACTTTGCTTTG 58.634 39.130 0.00 0.00 45.31 2.77
1473 1731 2.746269 TCAGATTGCACTTTGCTTTGC 58.254 42.857 0.00 0.00 45.31 3.68
1475 1733 2.475111 CAGATTGCACTTTGCTTTGCTG 59.525 45.455 0.00 0.00 45.31 4.41
1477 1735 0.108281 TTGCACTTTGCTTTGCTGCA 60.108 45.000 0.00 0.00 45.31 4.41
1558 1936 9.823647 TCTGAGTATTACATCTTCTGGATTTTC 57.176 33.333 0.00 0.00 31.27 2.29
1608 2010 3.058293 TGATAGTGAAGCAAAAACTGGCG 60.058 43.478 0.00 0.00 34.54 5.69
1643 2049 6.481434 AATCCCAGTAATAGACAGTACCAC 57.519 41.667 0.00 0.00 0.00 4.16
1672 2078 1.066136 GAACCGTCGCCTCTGTTTAC 58.934 55.000 0.00 0.00 0.00 2.01
1947 2358 3.959495 ATTGCTGGATCCCATGTAACT 57.041 42.857 9.90 0.00 30.82 2.24
2025 2960 3.320541 TGGTGTTTTGGTGCTTATTCTGG 59.679 43.478 0.00 0.00 0.00 3.86
2406 3349 5.489637 TGTGTTATTGTCATAAGGGGTAGGT 59.510 40.000 0.00 0.00 0.00 3.08
2447 3390 4.640201 GCAGCAGGAGTTAATGGTTGAATA 59.360 41.667 0.00 0.00 0.00 1.75
2479 3422 7.969536 ACTCATGCGTTTCTATTTGCTATAT 57.030 32.000 0.00 0.00 0.00 0.86
2804 3796 6.183360 TGGCTGCAGTTATTTGTTTAGTTCAA 60.183 34.615 16.64 0.00 0.00 2.69
2805 3797 6.868339 GGCTGCAGTTATTTGTTTAGTTCAAT 59.132 34.615 16.64 0.00 0.00 2.57
3399 4837 4.261405 CGATCACTTGGTTTAACTTTGCCA 60.261 41.667 0.00 0.00 0.00 4.92
3409 4848 5.009610 GGTTTAACTTTGCCAACTCATCTGA 59.990 40.000 0.00 0.00 0.00 3.27
3546 4985 6.624423 TCTTTTCATTCTTGCTTATTCCAGC 58.376 36.000 0.00 0.00 40.55 4.85
3600 5045 6.756074 CAGTGTGGTTTTGTCATTTAACATGT 59.244 34.615 0.00 0.00 0.00 3.21
3695 5140 7.661437 GTGATTATGGATGCCTTGTAAGTGATA 59.339 37.037 0.00 0.00 0.00 2.15
3809 5443 9.967451 TCCACAGTAATTTCAGATGGTTTTATA 57.033 29.630 0.00 0.00 0.00 0.98
4119 9432 8.926092 ATCCTTATTTTATTTGCTACTCCCTC 57.074 34.615 0.00 0.00 0.00 4.30
4120 9433 7.287810 TCCTTATTTTATTTGCTACTCCCTCC 58.712 38.462 0.00 0.00 0.00 4.30
4121 9434 6.204882 CCTTATTTTATTTGCTACTCCCTCCG 59.795 42.308 0.00 0.00 0.00 4.63
4122 9435 4.563140 TTTTATTTGCTACTCCCTCCGT 57.437 40.909 0.00 0.00 0.00 4.69
4123 9436 3.814005 TTATTTGCTACTCCCTCCGTC 57.186 47.619 0.00 0.00 0.00 4.79
4124 9437 1.867363 ATTTGCTACTCCCTCCGTCT 58.133 50.000 0.00 0.00 0.00 4.18
4125 9438 1.183549 TTTGCTACTCCCTCCGTCTC 58.816 55.000 0.00 0.00 0.00 3.36
4126 9439 0.039180 TTGCTACTCCCTCCGTCTCA 59.961 55.000 0.00 0.00 0.00 3.27
4127 9440 0.039180 TGCTACTCCCTCCGTCTCAA 59.961 55.000 0.00 0.00 0.00 3.02
4128 9441 1.183549 GCTACTCCCTCCGTCTCAAA 58.816 55.000 0.00 0.00 0.00 2.69
4129 9442 1.549170 GCTACTCCCTCCGTCTCAAAA 59.451 52.381 0.00 0.00 0.00 2.44
4130 9443 2.168728 GCTACTCCCTCCGTCTCAAAAT 59.831 50.000 0.00 0.00 0.00 1.82
4131 9444 3.383825 GCTACTCCCTCCGTCTCAAAATA 59.616 47.826 0.00 0.00 0.00 1.40
4132 9445 4.142004 GCTACTCCCTCCGTCTCAAAATAA 60.142 45.833 0.00 0.00 0.00 1.40
4133 9446 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
4134 9447 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
4135 9448 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
4136 9449 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
4137 9450 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
4138 9451 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
4139 9452 5.238583 CCTCCGTCTCAAAATAAGTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
4140 9453 5.120830 CCTCCGTCTCAAAATAAGTGTCTTG 59.879 44.000 0.00 0.00 0.00 3.02
4141 9454 5.849510 TCCGTCTCAAAATAAGTGTCTTGA 58.150 37.500 0.00 0.00 0.00 3.02
4142 9455 5.926542 TCCGTCTCAAAATAAGTGTCTTGAG 59.073 40.000 4.63 4.63 43.97 3.02
4143 9456 5.389935 CCGTCTCAAAATAAGTGTCTTGAGC 60.390 44.000 5.91 1.95 42.87 4.26
4144 9457 5.406780 CGTCTCAAAATAAGTGTCTTGAGCT 59.593 40.000 5.91 0.00 42.87 4.09
4145 9458 6.073548 CGTCTCAAAATAAGTGTCTTGAGCTT 60.074 38.462 5.91 0.00 42.87 3.74
4146 9459 7.116376 CGTCTCAAAATAAGTGTCTTGAGCTTA 59.884 37.037 5.91 0.00 42.87 3.09
4147 9460 8.439286 GTCTCAAAATAAGTGTCTTGAGCTTAG 58.561 37.037 5.91 0.00 42.87 2.18
4148 9461 8.150945 TCTCAAAATAAGTGTCTTGAGCTTAGT 58.849 33.333 5.91 0.00 42.87 2.24
4149 9462 9.424319 CTCAAAATAAGTGTCTTGAGCTTAGTA 57.576 33.333 0.00 0.00 38.63 1.82
4150 9463 9.204570 TCAAAATAAGTGTCTTGAGCTTAGTAC 57.795 33.333 0.00 0.00 0.00 2.73
4151 9464 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
4152 9465 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
4153 9466 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
4154 9467 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
4155 9468 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
4156 9469 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
4157 9470 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
4158 9471 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
4159 9472 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
4182 9495 5.817784 ACTAGAGCTAGTACAAAGTCCAGA 58.182 41.667 8.35 0.00 43.98 3.86
4183 9496 5.648960 ACTAGAGCTAGTACAAAGTCCAGAC 59.351 44.000 8.35 0.00 43.98 3.51
4184 9497 4.408276 AGAGCTAGTACAAAGTCCAGACA 58.592 43.478 0.00 0.00 0.00 3.41
4185 9498 4.218852 AGAGCTAGTACAAAGTCCAGACAC 59.781 45.833 0.00 0.00 0.00 3.67
4186 9499 4.153411 AGCTAGTACAAAGTCCAGACACT 58.847 43.478 0.00 0.00 0.00 3.55
4187 9500 4.589374 AGCTAGTACAAAGTCCAGACACTT 59.411 41.667 0.00 0.00 38.30 3.16
4188 9501 5.773680 AGCTAGTACAAAGTCCAGACACTTA 59.226 40.000 0.00 0.00 35.45 2.24
4189 9502 6.437793 AGCTAGTACAAAGTCCAGACACTTAT 59.562 38.462 0.00 0.00 35.45 1.73
4190 9503 7.038941 AGCTAGTACAAAGTCCAGACACTTATT 60.039 37.037 0.00 0.00 35.45 1.40
4191 9504 7.603024 GCTAGTACAAAGTCCAGACACTTATTT 59.397 37.037 0.00 0.00 35.45 1.40
4192 9505 9.490379 CTAGTACAAAGTCCAGACACTTATTTT 57.510 33.333 0.00 0.00 35.45 1.82
4193 9506 8.154649 AGTACAAAGTCCAGACACTTATTTTG 57.845 34.615 0.00 3.93 35.45 2.44
4194 9507 6.391227 ACAAAGTCCAGACACTTATTTTGG 57.609 37.500 0.00 0.00 35.45 3.28
4195 9508 5.301805 ACAAAGTCCAGACACTTATTTTGGG 59.698 40.000 0.00 0.00 35.45 4.12
4196 9509 4.993705 AGTCCAGACACTTATTTTGGGA 57.006 40.909 0.00 0.00 0.00 4.37
4197 9510 5.520748 AGTCCAGACACTTATTTTGGGAT 57.479 39.130 0.00 0.00 0.00 3.85
4198 9511 5.256474 AGTCCAGACACTTATTTTGGGATG 58.744 41.667 0.00 0.00 0.00 3.51
4199 9512 4.399303 GTCCAGACACTTATTTTGGGATGG 59.601 45.833 0.00 0.00 0.00 3.51
4200 9513 4.290985 TCCAGACACTTATTTTGGGATGGA 59.709 41.667 0.00 0.00 0.00 3.41
4201 9514 4.641989 CCAGACACTTATTTTGGGATGGAG 59.358 45.833 0.00 0.00 0.00 3.86
4202 9515 4.641989 CAGACACTTATTTTGGGATGGAGG 59.358 45.833 0.00 0.00 0.00 4.30
4203 9516 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
4204 9517 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
4205 9518 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
4436 10109 1.276138 GACAGGCCCCCAGAAATTTTG 59.724 52.381 0.00 0.00 0.00 2.44
4437 10110 0.036105 CAGGCCCCCAGAAATTTTGC 60.036 55.000 0.00 0.00 0.00 3.68
4438 10111 0.178894 AGGCCCCCAGAAATTTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
4523 10199 4.333926 GGATGATGTAGCTGACAAAGAACC 59.666 45.833 0.00 0.00 42.78 3.62
4768 10529 9.445786 ACAAAAATAAGTGTCGTTGATTTAGTG 57.554 29.630 0.00 0.00 0.00 2.74
4816 10585 3.950397 TCAGCGACACTTATTTTGGGAT 58.050 40.909 0.00 0.00 0.00 3.85
4931 10730 0.100682 CTCCCACAGTCACGTATCCG 59.899 60.000 0.00 0.00 40.83 4.18
5195 11011 1.068588 CCACGACCTTCACAAGAGACA 59.931 52.381 0.00 0.00 0.00 3.41
5359 11194 2.028930 AGAAAACGGCACTCCAGTCTAG 60.029 50.000 0.00 0.00 0.00 2.43
5380 11218 8.747471 GTCTAGACACAAACCTACCTTAACTAT 58.253 37.037 18.20 0.00 0.00 2.12
5563 11437 2.024414 TGCTATAGCTTCTGACGCAGA 58.976 47.619 24.61 5.59 42.66 4.26
5591 11473 3.678252 CGAGGACAGAAGATGTTGAGCAT 60.678 47.826 0.00 0.00 44.17 3.79
5807 11691 8.666573 TGCAAATGCGATGAATAAAATTTCAAT 58.333 25.926 0.35 0.00 45.83 2.57
5824 11708 8.608844 AATTTCAATTACCCGTTGCAATTTAA 57.391 26.923 0.59 0.00 31.53 1.52
5829 11713 7.175293 TCAATTACCCGTTGCAATTTAAGTACT 59.825 33.333 0.59 0.00 0.00 2.73
5860 11748 6.272318 CACTGCTGAGTTGGTATTTTGAAAA 58.728 36.000 0.00 0.00 0.00 2.29
5891 11785 1.114627 ACCATGCGCTGATACTCTGA 58.885 50.000 9.73 0.00 0.00 3.27
5947 11841 2.130193 TGGCTGCCTATCTGGAATCTT 58.870 47.619 21.03 0.00 38.35 2.40
6090 11984 1.106351 ACCATCGCCAGCAACACAAA 61.106 50.000 0.00 0.00 0.00 2.83
6123 12017 2.304401 CGACCGTGCTTGCGTGTTA 61.304 57.895 0.00 0.00 0.00 2.41
6164 12060 0.319040 CATCCGCGGTCATCCTACTG 60.319 60.000 27.15 6.10 0.00 2.74
6189 12085 3.993736 GGTGTATGTTCAATTTTGGCACC 59.006 43.478 0.00 0.00 37.33 5.01
6201 12097 1.034838 TTGGCACCGGATACCAATGC 61.035 55.000 19.11 11.96 38.52 3.56
6399 12333 1.134907 GCCATGCATTTTCCACCTGAG 60.135 52.381 0.00 0.00 0.00 3.35
6451 12386 7.321153 GGTGTTTAGAATGTTACTCTAGCTGA 58.679 38.462 0.00 0.00 0.00 4.26
6480 12415 5.781210 TTGTTGTTGCCATATCAGTTGAA 57.219 34.783 0.00 0.00 0.00 2.69
6481 12416 5.981088 TGTTGTTGCCATATCAGTTGAAT 57.019 34.783 0.00 0.00 0.00 2.57
6482 12417 5.953183 TGTTGTTGCCATATCAGTTGAATC 58.047 37.500 0.00 0.00 0.00 2.52
6484 12419 6.153170 TGTTGTTGCCATATCAGTTGAATCAT 59.847 34.615 0.00 0.00 0.00 2.45
6485 12420 6.139048 TGTTGCCATATCAGTTGAATCATG 57.861 37.500 0.00 0.00 0.00 3.07
6487 12422 6.377712 TGTTGCCATATCAGTTGAATCATGAA 59.622 34.615 0.00 0.00 0.00 2.57
6488 12423 7.093858 TGTTGCCATATCAGTTGAATCATGAAA 60.094 33.333 0.00 0.00 0.00 2.69
6489 12424 7.591421 TGCCATATCAGTTGAATCATGAAAT 57.409 32.000 0.00 0.00 0.00 2.17
6490 12425 8.014070 TGCCATATCAGTTGAATCATGAAATT 57.986 30.769 0.00 0.00 0.00 1.82
6491 12426 8.479689 TGCCATATCAGTTGAATCATGAAATTT 58.520 29.630 0.00 0.00 0.00 1.82
6492 12427 9.970395 GCCATATCAGTTGAATCATGAAATTTA 57.030 29.630 0.00 0.00 0.00 1.40
6651 12598 3.893521 AGCATGACATCAACATGATCCA 58.106 40.909 0.00 0.00 45.22 3.41
6773 12726 2.941064 CGAGTTGCCTCATGACATGAAT 59.059 45.455 18.49 0.00 39.11 2.57
6777 12730 5.503927 AGTTGCCTCATGACATGAATAGTT 58.496 37.500 18.49 1.69 39.11 2.24
6778 12731 5.356190 AGTTGCCTCATGACATGAATAGTTG 59.644 40.000 18.49 6.39 39.11 3.16
6781 12734 6.413892 TGCCTCATGACATGAATAGTTGTTA 58.586 36.000 18.49 0.00 39.11 2.41
6855 12823 5.337813 GGCTCCTCAAATGTCCAAAAATCAT 60.338 40.000 0.00 0.00 0.00 2.45
6902 12870 3.870538 TGAGCATCTTGGATGCCTAAT 57.129 42.857 23.37 9.55 45.59 1.73
7018 12997 6.656270 TGTGTGACATTTGAGAAGAAGCATAT 59.344 34.615 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.361201 CGTTTGCTGGTTGGATATCTATAATGG 60.361 40.741 2.05 0.00 0.00 3.16
16 17 6.822442 TCGTTTGCTGGTTGGATATCTATAA 58.178 36.000 2.05 0.00 0.00 0.98
24 29 0.250901 AGCTCGTTTGCTGGTTGGAT 60.251 50.000 0.00 0.00 42.33 3.41
70 75 2.715864 CTTGCGTGCGTGAAGGGTTG 62.716 60.000 0.00 0.00 0.00 3.77
154 162 3.108144 CGTTTGTTGCAGGTTTCTCTTG 58.892 45.455 0.00 0.00 0.00 3.02
209 218 0.249398 GATGTTGCCGGGTCACTAGT 59.751 55.000 2.18 0.00 0.00 2.57
237 255 1.226046 CCACGAGACTACGACTGCG 60.226 63.158 0.00 0.00 44.79 5.18
254 272 3.155167 CGGGGTCTGGGCTAGTCC 61.155 72.222 6.37 6.37 34.30 3.85
490 600 0.960861 GCCTCTTTTTGGGCGCTAGT 60.961 55.000 7.64 0.00 38.91 2.57
664 791 1.596934 GAGGGTCGATGCACCTTGA 59.403 57.895 0.00 0.00 36.57 3.02
677 808 4.599500 AGTGGTGGGCAGGAGGGT 62.599 66.667 0.00 0.00 0.00 4.34
682 813 2.282462 GGTCAAGTGGTGGGCAGG 60.282 66.667 0.00 0.00 0.00 4.85
689 820 1.051812 CCTCTGACTGGTCAAGTGGT 58.948 55.000 4.94 0.00 40.07 4.16
690 821 0.321122 GCCTCTGACTGGTCAAGTGG 60.321 60.000 4.94 9.67 40.07 4.00
691 822 0.668706 CGCCTCTGACTGGTCAAGTG 60.669 60.000 4.94 0.80 40.07 3.16
692 823 0.827925 TCGCCTCTGACTGGTCAAGT 60.828 55.000 4.94 0.00 43.85 3.16
723 854 0.621609 ACGCTTATTAGGTTGGGCCA 59.378 50.000 0.00 0.00 40.61 5.36
809 950 2.842256 GCCAGCCCATCTTCATGCG 61.842 63.158 0.00 0.00 0.00 4.73
812 953 0.469331 CCATGCCAGCCCATCTTCAT 60.469 55.000 0.00 0.00 0.00 2.57
895 1039 0.606604 GGACTGGTTGGCTCGTTCTA 59.393 55.000 0.00 0.00 0.00 2.10
896 1040 1.371558 GGACTGGTTGGCTCGTTCT 59.628 57.895 0.00 0.00 0.00 3.01
897 1041 1.671379 GGGACTGGTTGGCTCGTTC 60.671 63.158 0.00 0.00 0.00 3.95
1098 1248 2.563427 GTCTTCTTGCGCTTGGCC 59.437 61.111 9.73 0.00 42.61 5.36
1179 1356 1.219664 CGGACGGAATACCTTGGCA 59.780 57.895 0.00 0.00 0.00 4.92
1193 1370 2.483106 GCAAAAGGAAAGGAGTACGGAC 59.517 50.000 0.00 0.00 0.00 4.79
1196 1373 3.058914 CACAGCAAAAGGAAAGGAGTACG 60.059 47.826 0.00 0.00 0.00 3.67
1229 1406 2.488153 GCACTCTAAACCAACACCCATC 59.512 50.000 0.00 0.00 0.00 3.51
1382 1625 1.482955 CGCAATCGTAATCGGAGCG 59.517 57.895 0.00 0.00 41.68 5.03
1395 1638 1.376543 CAGGAGTTGAGATGCGCAAT 58.623 50.000 17.11 6.08 0.00 3.56
1396 1639 0.674581 CCAGGAGTTGAGATGCGCAA 60.675 55.000 17.11 0.00 0.00 4.85
1467 1725 8.752766 ATTGATTATTATGTATGCAGCAAAGC 57.247 30.769 0.00 0.00 0.00 3.51
1468 1726 9.902196 TGATTGATTATTATGTATGCAGCAAAG 57.098 29.630 0.00 0.00 0.00 2.77
1469 1727 9.681692 GTGATTGATTATTATGTATGCAGCAAA 57.318 29.630 0.00 0.00 0.00 3.68
1470 1728 9.070179 AGTGATTGATTATTATGTATGCAGCAA 57.930 29.630 0.00 0.00 0.00 3.91
1471 1729 8.625786 AGTGATTGATTATTATGTATGCAGCA 57.374 30.769 0.00 0.00 0.00 4.41
1571 1962 9.237846 GCTTCACTATCAAAATTAAGTAATGCC 57.762 33.333 0.00 0.00 0.00 4.40
1608 2010 3.933861 ACTGGGATTACTGGGATCAAC 57.066 47.619 0.00 0.00 0.00 3.18
1643 2049 2.671177 CGACGGTTCAAGCAGGCAG 61.671 63.158 0.00 0.00 0.00 4.85
1672 2078 5.050490 CCAAGGTAGGTTACTGAATCATCG 58.950 45.833 0.00 0.00 0.00 3.84
1947 2358 3.527533 ACTTACTTGAAGAACACGTGCA 58.472 40.909 17.22 1.47 38.65 4.57
2406 3349 4.157105 TGCTGCTCTTATACACGACAAGTA 59.843 41.667 0.00 0.00 0.00 2.24
2450 3393 5.258622 CAAATAGAAACGCATGAGTACAGC 58.741 41.667 1.37 0.00 0.00 4.40
2451 3394 5.063944 AGCAAATAGAAACGCATGAGTACAG 59.936 40.000 1.37 0.00 0.00 2.74
2479 3422 6.949117 TTACCATGTACCCCTTTACTTGTA 57.051 37.500 0.00 0.00 0.00 2.41
2480 3423 5.846528 TTACCATGTACCCCTTTACTTGT 57.153 39.130 0.00 0.00 0.00 3.16
3043 4297 6.676456 GCGATATGCTGAAGAAACATTTCACT 60.676 38.462 7.10 0.00 41.73 3.41
3366 4804 4.471904 ACCAAGTGATCGCTCTGAAATA 57.528 40.909 9.70 0.00 0.00 1.40
3438 4877 9.743057 CTATTTAGTGTCTCTGAAATCTACAGG 57.257 37.037 0.00 0.00 36.22 4.00
3600 5045 8.821686 TTTCTTCCTATCCTGAAATGCATTAA 57.178 30.769 13.39 3.40 0.00 1.40
3769 5402 8.738645 AATTACTGTGGATTAGGAGAATGTTC 57.261 34.615 0.00 0.00 0.00 3.18
3809 5443 7.171630 AGTCGATGATTAACTACTTGGAAGT 57.828 36.000 0.00 0.00 42.91 3.01
4106 9419 1.183549 GAGACGGAGGGAGTAGCAAA 58.816 55.000 0.00 0.00 0.00 3.68
4110 9423 5.127356 ACTTATTTTGAGACGGAGGGAGTAG 59.873 44.000 0.00 0.00 0.00 2.57
4112 9425 3.838903 ACTTATTTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
4113 9426 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
4114 9427 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
4115 9428 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4116 9429 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
4117 9430 5.926542 TCAAGACACTTATTTTGAGACGGAG 59.073 40.000 0.00 0.00 0.00 4.63
4118 9431 5.849510 TCAAGACACTTATTTTGAGACGGA 58.150 37.500 0.00 0.00 0.00 4.69
4119 9432 5.389935 GCTCAAGACACTTATTTTGAGACGG 60.390 44.000 15.10 0.00 45.82 4.79
4120 9433 5.406780 AGCTCAAGACACTTATTTTGAGACG 59.593 40.000 15.10 0.00 45.82 4.18
4121 9434 6.793492 AGCTCAAGACACTTATTTTGAGAC 57.207 37.500 15.10 7.85 45.82 3.36
4122 9435 8.150945 ACTAAGCTCAAGACACTTATTTTGAGA 58.849 33.333 15.10 0.00 45.82 3.27
4123 9436 8.316640 ACTAAGCTCAAGACACTTATTTTGAG 57.683 34.615 8.33 8.33 45.75 3.02
4124 9437 9.204570 GTACTAAGCTCAAGACACTTATTTTGA 57.795 33.333 3.19 0.00 0.00 2.69
4125 9438 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
4126 9439 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
4127 9440 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
4128 9441 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
4129 9442 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
4130 9443 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
4131 9444 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
4132 9445 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
4133 9446 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
4134 9447 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
4158 9471 6.822676 GTCTGGACTTTGTACTAGCTCTAGTA 59.177 42.308 11.59 11.59 43.98 1.82
4160 9473 5.648526 TGTCTGGACTTTGTACTAGCTCTAG 59.351 44.000 0.00 2.55 39.04 2.43
4161 9474 5.415077 GTGTCTGGACTTTGTACTAGCTCTA 59.585 44.000 0.00 0.00 0.00 2.43
4162 9475 4.218852 GTGTCTGGACTTTGTACTAGCTCT 59.781 45.833 0.00 0.00 0.00 4.09
4163 9476 4.218852 AGTGTCTGGACTTTGTACTAGCTC 59.781 45.833 0.00 0.00 0.00 4.09
4164 9477 4.153411 AGTGTCTGGACTTTGTACTAGCT 58.847 43.478 0.00 0.00 0.00 3.32
4165 9478 4.522722 AGTGTCTGGACTTTGTACTAGC 57.477 45.455 2.38 0.00 0.00 3.42
4166 9479 9.490379 AAAATAAGTGTCTGGACTTTGTACTAG 57.510 33.333 2.38 0.00 37.38 2.57
4167 9480 9.268268 CAAAATAAGTGTCTGGACTTTGTACTA 57.732 33.333 2.38 0.00 37.38 1.82
4168 9481 7.228706 CCAAAATAAGTGTCTGGACTTTGTACT 59.771 37.037 2.38 0.00 37.38 2.73
4169 9482 7.360361 CCAAAATAAGTGTCTGGACTTTGTAC 58.640 38.462 2.38 0.00 37.38 2.90
4170 9483 6.488683 CCCAAAATAAGTGTCTGGACTTTGTA 59.511 38.462 2.38 0.00 37.38 2.41
4171 9484 5.301805 CCCAAAATAAGTGTCTGGACTTTGT 59.698 40.000 2.38 0.00 37.38 2.83
4172 9485 5.534654 TCCCAAAATAAGTGTCTGGACTTTG 59.465 40.000 2.38 3.84 37.38 2.77
4173 9486 5.701224 TCCCAAAATAAGTGTCTGGACTTT 58.299 37.500 2.38 0.56 37.38 2.66
4174 9487 5.319043 TCCCAAAATAAGTGTCTGGACTT 57.681 39.130 2.38 0.00 39.54 3.01
4175 9488 4.993705 TCCCAAAATAAGTGTCTGGACT 57.006 40.909 2.38 0.00 0.00 3.85
4176 9489 4.399303 CCATCCCAAAATAAGTGTCTGGAC 59.601 45.833 0.00 0.00 0.00 4.02
4177 9490 4.290985 TCCATCCCAAAATAAGTGTCTGGA 59.709 41.667 0.00 0.00 0.00 3.86
4178 9491 4.599041 TCCATCCCAAAATAAGTGTCTGG 58.401 43.478 0.00 0.00 0.00 3.86
4179 9492 4.641989 CCTCCATCCCAAAATAAGTGTCTG 59.358 45.833 0.00 0.00 0.00 3.51
4180 9493 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
4181 9494 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
4182 9495 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
4183 9496 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
4184 9497 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
4185 9498 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
4186 9499 6.606241 AATACTCCCTCCATCCCAAAATAA 57.394 37.500 0.00 0.00 0.00 1.40
4187 9500 6.855061 ACTAATACTCCCTCCATCCCAAAATA 59.145 38.462 0.00 0.00 0.00 1.40
4188 9501 5.676811 ACTAATACTCCCTCCATCCCAAAAT 59.323 40.000 0.00 0.00 0.00 1.82
4189 9502 5.043762 ACTAATACTCCCTCCATCCCAAAA 58.956 41.667 0.00 0.00 0.00 2.44
4190 9503 4.641868 ACTAATACTCCCTCCATCCCAAA 58.358 43.478 0.00 0.00 0.00 3.28
4191 9504 4.295905 ACTAATACTCCCTCCATCCCAA 57.704 45.455 0.00 0.00 0.00 4.12
4192 9505 4.295905 AACTAATACTCCCTCCATCCCA 57.704 45.455 0.00 0.00 0.00 4.37
4193 9506 6.383436 GGTATAACTAATACTCCCTCCATCCC 59.617 46.154 0.00 0.00 40.40 3.85
4194 9507 6.383436 GGGTATAACTAATACTCCCTCCATCC 59.617 46.154 0.00 0.00 40.40 3.51
4195 9508 6.958192 TGGGTATAACTAATACTCCCTCCATC 59.042 42.308 0.00 0.00 40.39 3.51
4196 9509 6.729569 GTGGGTATAACTAATACTCCCTCCAT 59.270 42.308 0.00 0.00 40.39 3.41
4197 9510 6.080009 GTGGGTATAACTAATACTCCCTCCA 58.920 44.000 0.00 0.00 40.39 3.86
4198 9511 6.080009 TGTGGGTATAACTAATACTCCCTCC 58.920 44.000 0.00 0.00 40.39 4.30
4199 9512 7.453752 TCATGTGGGTATAACTAATACTCCCTC 59.546 40.741 0.00 0.00 40.39 4.30
4200 9513 7.310634 TCATGTGGGTATAACTAATACTCCCT 58.689 38.462 0.00 0.00 40.39 4.20
4201 9514 7.453752 TCTCATGTGGGTATAACTAATACTCCC 59.546 40.741 0.00 0.00 40.39 4.30
4202 9515 8.418597 TCTCATGTGGGTATAACTAATACTCC 57.581 38.462 0.00 0.00 40.39 3.85
4203 9516 9.298250 TCTCTCATGTGGGTATAACTAATACTC 57.702 37.037 0.00 0.00 41.35 2.59
4204 9517 9.830186 ATCTCTCATGTGGGTATAACTAATACT 57.170 33.333 0.00 0.00 40.40 2.12
4205 9518 9.862371 CATCTCTCATGTGGGTATAACTAATAC 57.138 37.037 0.00 0.00 39.92 1.89
4523 10199 0.764890 TGTGTCTTCTGAACCCCCAG 59.235 55.000 0.00 0.00 35.55 4.45
4931 10730 6.263168 ACACCTACATTATTGCTTGGATTAGC 59.737 38.462 0.00 0.00 41.59 3.09
4970 10770 3.089284 TGCAAGTCTCGATGAGAACCTA 58.911 45.455 0.00 0.00 40.59 3.08
5095 10896 7.663081 TGAATGAATATTCTCCCAAGATACTGC 59.337 37.037 16.24 0.00 42.56 4.40
5178 10990 1.795286 GCTTGTCTCTTGTGAAGGTCG 59.205 52.381 0.00 0.00 0.00 4.79
5195 11011 8.416329 GTCAAATAATAATCAGGGACAATGCTT 58.584 33.333 0.00 0.00 0.00 3.91
5359 11194 7.974482 ACAATAGTTAAGGTAGGTTTGTGTC 57.026 36.000 0.00 0.00 0.00 3.67
5387 11225 9.388506 CTCATTTGTATCAAGAGTTAGACCAAT 57.611 33.333 0.00 0.00 0.00 3.16
5563 11437 1.258445 ATCTTCTGTCCTCGGGCGTT 61.258 55.000 0.00 0.00 0.00 4.84
5591 11473 3.512329 TCGAGTGGTAGTTATCAAAGGCA 59.488 43.478 0.00 0.00 0.00 4.75
5807 11691 6.485984 TGAAGTACTTAAATTGCAACGGGTAA 59.514 34.615 8.42 0.00 0.00 2.85
5810 11694 5.365403 TGAAGTACTTAAATTGCAACGGG 57.635 39.130 8.42 0.00 0.00 5.28
5811 11695 6.183359 GCAATGAAGTACTTAAATTGCAACGG 60.183 38.462 35.75 18.61 44.12 4.44
5824 11708 3.244353 ACTCAGCAGTGCAATGAAGTACT 60.244 43.478 20.00 1.41 34.66 2.73
5829 11713 1.610038 CCAACTCAGCAGTGCAATGAA 59.390 47.619 20.00 1.03 31.06 2.57
5872 11766 1.114627 TCAGAGTATCAGCGCATGGT 58.885 50.000 11.47 3.77 37.82 3.55
5873 11767 2.067013 CATCAGAGTATCAGCGCATGG 58.933 52.381 11.47 0.00 37.82 3.66
5891 11785 1.888512 AGCAGCGACCAACAAATTCAT 59.111 42.857 0.00 0.00 0.00 2.57
5947 11841 1.651737 TCCTTCACCTTGGAATCCGA 58.348 50.000 0.00 0.00 0.00 4.55
6059 11953 2.990479 GATGGTGAGAGGCCCGTT 59.010 61.111 0.00 0.00 0.00 4.44
6107 12001 0.320421 ATCTAACACGCAAGCACGGT 60.320 50.000 0.00 0.00 45.62 4.83
6123 12017 9.988815 GGATGTATGTATTACACTCTTTCATCT 57.011 33.333 0.00 0.00 43.46 2.90
6164 12060 4.021544 TGCCAAAATTGAACATACACCTCC 60.022 41.667 0.00 0.00 0.00 4.30
6189 12085 1.934589 TTCGAGTGCATTGGTATCCG 58.065 50.000 0.00 0.00 0.00 4.18
6201 12097 3.688272 ACGACCGTATGTATTTCGAGTG 58.312 45.455 0.00 0.00 33.87 3.51
6328 12236 1.681780 GGATCAGGTGGAAAATGCCGA 60.682 52.381 0.00 0.00 0.00 5.54
6444 12379 5.393962 GCAACAACAAACCTTATCAGCTAG 58.606 41.667 0.00 0.00 0.00 3.42
6481 12416 9.187996 TGTTCCATCAATAGCTAAATTTCATGA 57.812 29.630 0.00 0.00 0.00 3.07
6482 12417 9.976511 ATGTTCCATCAATAGCTAAATTTCATG 57.023 29.630 0.00 0.00 0.00 3.07
6484 12419 7.922278 GCATGTTCCATCAATAGCTAAATTTCA 59.078 33.333 0.00 0.00 0.00 2.69
6485 12420 7.922278 TGCATGTTCCATCAATAGCTAAATTTC 59.078 33.333 0.00 0.00 0.00 2.17
6487 12422 7.350744 TGCATGTTCCATCAATAGCTAAATT 57.649 32.000 0.00 0.00 0.00 1.82
6488 12423 6.964807 TGCATGTTCCATCAATAGCTAAAT 57.035 33.333 0.00 0.00 0.00 1.40
6489 12424 6.964807 ATGCATGTTCCATCAATAGCTAAA 57.035 33.333 0.00 0.00 0.00 1.85
6490 12425 6.016024 GGAATGCATGTTCCATCAATAGCTAA 60.016 38.462 13.21 0.00 45.63 3.09
6491 12426 5.474532 GGAATGCATGTTCCATCAATAGCTA 59.525 40.000 13.21 0.00 45.63 3.32
6492 12427 4.280174 GGAATGCATGTTCCATCAATAGCT 59.720 41.667 13.21 0.00 45.63 3.32
6493 12428 4.553323 GGAATGCATGTTCCATCAATAGC 58.447 43.478 13.21 0.00 45.63 2.97
6545 12485 8.485976 AACGGAATTGAAGATTTTAGAGAGAG 57.514 34.615 0.00 0.00 0.00 3.20
6700 12652 2.755103 AGATGACACGTGAGCTGACATA 59.245 45.455 25.01 0.00 32.01 2.29
6855 12823 2.674954 CAAGGTGCATGCGAAATTTCA 58.325 42.857 17.99 0.43 0.00 2.69
6944 12916 6.294473 CCAGGCTCATCTGTGAATAGTAATT 58.706 40.000 0.00 0.00 33.05 1.40
6945 12917 5.221803 CCCAGGCTCATCTGTGAATAGTAAT 60.222 44.000 0.00 0.00 33.05 1.89
7018 12997 9.827198 AAATAGATGATTTATAAATGCCCCTGA 57.173 29.630 15.39 0.00 35.91 3.86


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

AutoCloner maintained by Alex Coulton.