Multiple sequence alignment - TraesCS7D01G010900

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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 TraesCS7D01G010900 chr7D 100.000 3452 0 0 1 3452 5023600 5027051 0.000000e+00 6375.0
1 TraesCS7D01G010900 chr7D 91.980 611 31 10 2442 3036 406334618 406334010 0.000000e+00 841.0
2 TraesCS7D01G010900 chr7D 97.746 488 7 4 2441 2927 8967566 8968050 0.000000e+00 837.0
3 TraesCS7D01G010900 chr4A 86.268 1755 211 15 711 2441 738393005 738391257 0.000000e+00 1879.0
4 TraesCS7D01G010900 chr4A 87.422 1598 159 22 645 2211 738350370 738351956 0.000000e+00 1799.0
5 TraesCS7D01G010900 chr4A 86.227 1532 144 27 711 2227 737847087 737845608 0.000000e+00 1598.0
6 TraesCS7D01G010900 chr4A 88.370 1049 93 13 1006 2025 737855294 737854246 0.000000e+00 1234.0
7 TraesCS7D01G010900 chr4A 90.621 789 69 5 1376 2162 737639140 737638355 0.000000e+00 1042.0
8 TraesCS7D01G010900 chr4A 86.983 653 59 11 744 1380 737647868 737647226 0.000000e+00 712.0
9 TraesCS7D01G010900 chr4A 88.800 500 37 9 645 1126 738070445 738070943 2.290000e-166 595.0
10 TraesCS7D01G010900 chr4A 95.062 324 14 2 1 322 738056607 738056930 3.070000e-140 508.0
11 TraesCS7D01G010900 chr4A 85.865 474 61 6 1741 2211 738524001 738523531 1.850000e-137 499.0
12 TraesCS7D01G010900 chr4A 90.000 340 20 7 645 972 737855628 737855291 8.850000e-116 427.0
13 TraesCS7D01G010900 chr4A 96.026 151 6 0 423 573 738062158 738062308 2.660000e-61 246.0
14 TraesCS7D01G010900 chr4A 85.714 224 30 2 2219 2441 738351892 738352114 5.760000e-58 235.0
15 TraesCS7D01G010900 chr4A 94.702 151 7 1 423 573 737859324 737859175 2.070000e-57 233.0
16 TraesCS7D01G010900 chr4A 93.377 151 9 1 423 573 737855949 737855800 4.480000e-54 222.0
17 TraesCS7D01G010900 chr4A 92.208 154 11 1 420 573 738058827 738058979 2.090000e-52 217.0
18 TraesCS7D01G010900 chr4A 96.203 79 3 0 645 723 738059374 738059452 2.800000e-26 130.0
19 TraesCS7D01G010900 chr4A 94.872 78 4 0 646 723 737858759 737858682 4.680000e-24 122.0
20 TraesCS7D01G010900 chr4A 94.915 59 3 0 586 644 738350272 738350330 3.670000e-15 93.5
21 TraesCS7D01G010900 chr7A 87.062 1569 143 23 664 2211 5749174 5747645 0.000000e+00 1718.0
22 TraesCS7D01G010900 chr7A 86.490 1584 158 30 645 2211 5354475 5352931 0.000000e+00 1688.0
23 TraesCS7D01G010900 chr7A 86.558 1592 140 29 645 2211 5609680 5611222 0.000000e+00 1687.0
24 TraesCS7D01G010900 chr7A 85.438 1600 163 28 645 2211 4999215 5000777 0.000000e+00 1600.0
25 TraesCS7D01G010900 chr7A 87.170 1325 109 27 950 2227 5778021 5776711 0.000000e+00 1448.0
26 TraesCS7D01G010900 chr7A 88.270 844 93 5 1385 2227 5022401 5023239 0.000000e+00 1005.0
27 TraesCS7D01G010900 chr7A 89.354 789 75 5 1331 2118 5515948 5516728 0.000000e+00 983.0
28 TraesCS7D01G010900 chr7A 84.820 639 59 11 645 1272 5014591 5015202 2.950000e-170 608.0
29 TraesCS7D01G010900 chr7A 89.849 463 44 3 1981 2441 6103365 6103826 2.970000e-165 592.0
30 TraesCS7D01G010900 chr7A 86.122 245 26 5 124 366 5602738 5602976 1.230000e-64 257.0
31 TraesCS7D01G010900 chr7A 84.848 231 35 0 2219 2449 5776790 5776560 2.070000e-57 233.0
32 TraesCS7D01G010900 chr7A 84.375 224 33 2 2219 2441 5352995 5352773 5.800000e-53 219.0
33 TraesCS7D01G010900 chr7A 93.939 99 5 1 475 573 5609423 5609520 7.720000e-32 148.0
34 TraesCS7D01G010900 chr7A 98.305 59 1 0 586 644 5609579 5609637 1.690000e-18 104.0
35 TraesCS7D01G010900 chr7A 96.552 58 2 0 586 643 5778374 5778317 2.840000e-16 97.1
36 TraesCS7D01G010900 chr7A 93.333 60 4 0 586 645 5354570 5354511 4.750000e-14 89.8
37 TraesCS7D01G010900 chr7A 96.226 53 2 0 420 472 5603182 5603234 1.710000e-13 87.9
38 TraesCS7D01G010900 chr7A 100.000 42 0 0 603 644 5014510 5014551 1.030000e-10 78.7
39 TraesCS7D01G010900 chr7A 90.385 52 2 1 269 317 5233801 5233852 8.000000e-07 65.8
40 TraesCS7D01G010900 chr7A 90.385 52 2 1 269 317 5250998 5251049 8.000000e-07 65.8
41 TraesCS7D01G010900 chr7A 90.385 52 2 1 269 317 5263799 5263850 8.000000e-07 65.8
42 TraesCS7D01G010900 chrUn 86.599 1082 87 26 947 1982 382627554 382628623 0.000000e+00 1142.0
43 TraesCS7D01G010900 chrUn 86.182 550 44 23 2700 3231 337111227 337111762 1.800000e-157 566.0
44 TraesCS7D01G010900 chrUn 96.552 58 2 0 586 643 382627204 382627261 2.840000e-16 97.1
45 TraesCS7D01G010900 chrUn 96.552 58 2 0 586 643 474005590 474005533 2.840000e-16 97.1
46 TraesCS7D01G010900 chr4D 86.900 916 80 27 2441 3346 42116346 42117231 0.000000e+00 990.0
47 TraesCS7D01G010900 chr4D 86.776 915 79 28 2442 3346 234083613 234082731 0.000000e+00 981.0
48 TraesCS7D01G010900 chr2D 86.928 918 75 29 2442 3346 165186502 165185617 0.000000e+00 989.0
49 TraesCS7D01G010900 chr2D 90.145 761 53 18 2700 3446 21649385 21650137 0.000000e+00 970.0
50 TraesCS7D01G010900 chr2D 87.391 571 52 9 645 1195 614347450 614348020 3.760000e-179 638.0
51 TraesCS7D01G010900 chr2D 86.339 549 45 22 2700 3231 590222876 590223411 3.870000e-159 571.0
52 TraesCS7D01G010900 chr2D 88.706 425 25 5 13 426 614327859 614328271 6.650000e-137 497.0
53 TraesCS7D01G010900 chr2D 86.747 415 41 5 1256 1670 614352934 614353334 1.890000e-122 449.0
54 TraesCS7D01G010900 chr2D 93.600 125 8 0 449 573 614328454 614328578 1.640000e-43 187.0
55 TraesCS7D01G010900 chr1D 92.343 653 23 17 2442 3093 467044288 467044914 0.000000e+00 904.0
56 TraesCS7D01G010900 chr1D 87.614 767 54 23 2710 3446 273905051 273904296 0.000000e+00 852.0
57 TraesCS7D01G010900 chr1D 87.126 668 53 22 2442 3096 372547987 372547340 0.000000e+00 726.0
58 TraesCS7D01G010900 chr1D 94.479 163 8 1 3223 3385 404264725 404264886 2.060000e-62 250.0
59 TraesCS7D01G010900 chr1A 83.154 1021 129 29 2442 3446 472534410 472533417 0.000000e+00 893.0
60 TraesCS7D01G010900 chr5D 89.158 701 48 20 2442 3125 307471103 307471792 0.000000e+00 848.0
61 TraesCS7D01G010900 chr3D 97.723 483 7 4 2442 2923 453159852 453160331 0.000000e+00 828.0
62 TraesCS7D01G010900 chr6D 83.191 940 83 54 2441 3359 448041939 448042824 0.000000e+00 791.0
63 TraesCS7D01G010900 chr6D 87.443 661 40 20 2711 3358 301473829 301474459 0.000000e+00 721.0
64 TraesCS7D01G010900 chr2A 91.071 56 2 1 265 317 222670419 222670364 4.780000e-09 73.1
65 TraesCS7D01G010900 chr6B 89.286 56 3 1 265 317 269781971 269781916 2.220000e-07 67.6
66 TraesCS7D01G010900 chr6B 89.286 56 3 1 265 317 610416552 610416607 2.220000e-07 67.6
67 TraesCS7D01G010900 chr4B 89.286 56 3 1 265 317 351799286 351799341 2.220000e-07 67.6


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 TraesCS7D01G010900 chr7D 5023600 5027051 3451 False 6375.000000 6375 100.000000 1 3452 1 chr7D.!!$F1 3451
1 TraesCS7D01G010900 chr7D 406334010 406334618 608 True 841.000000 841 91.980000 2442 3036 1 chr7D.!!$R1 594
2 TraesCS7D01G010900 chr4A 738391257 738393005 1748 True 1879.000000 1879 86.268000 711 2441 1 chr4A.!!$R4 1730
3 TraesCS7D01G010900 chr4A 737845608 737847087 1479 True 1598.000000 1598 86.227000 711 2227 1 chr4A.!!$R3 1516
4 TraesCS7D01G010900 chr4A 737638355 737639140 785 True 1042.000000 1042 90.621000 1376 2162 1 chr4A.!!$R1 786
5 TraesCS7D01G010900 chr4A 737647226 737647868 642 True 712.000000 712 86.983000 744 1380 1 chr4A.!!$R2 636
6 TraesCS7D01G010900 chr4A 738350272 738352114 1842 False 709.166667 1799 89.350333 586 2441 3 chr4A.!!$F3 1855
7 TraesCS7D01G010900 chr4A 737854246 737859324 5078 True 447.600000 1234 92.264200 423 2025 5 chr4A.!!$R6 1602
8 TraesCS7D01G010900 chr4A 738056607 738062308 5701 False 275.250000 508 94.874750 1 723 4 chr4A.!!$F2 722
9 TraesCS7D01G010900 chr7A 5747645 5749174 1529 True 1718.000000 1718 87.062000 664 2211 1 chr7A.!!$R1 1547
10 TraesCS7D01G010900 chr7A 4999215 5000777 1562 False 1600.000000 1600 85.438000 645 2211 1 chr7A.!!$F1 1566
11 TraesCS7D01G010900 chr7A 5022401 5023239 838 False 1005.000000 1005 88.270000 1385 2227 1 chr7A.!!$F2 842
12 TraesCS7D01G010900 chr7A 5515948 5516728 780 False 983.000000 983 89.354000 1331 2118 1 chr7A.!!$F6 787
13 TraesCS7D01G010900 chr7A 5352773 5354570 1797 True 665.600000 1688 88.066000 586 2441 3 chr7A.!!$R2 1855
14 TraesCS7D01G010900 chr7A 5609423 5611222 1799 False 646.333333 1687 92.934000 475 2211 3 chr7A.!!$F10 1736
15 TraesCS7D01G010900 chr7A 5776560 5778374 1814 True 592.700000 1448 89.523333 586 2449 3 chr7A.!!$R3 1863
16 TraesCS7D01G010900 chr7A 5014510 5015202 692 False 343.350000 608 92.410000 603 1272 2 chr7A.!!$F8 669
17 TraesCS7D01G010900 chrUn 382627204 382628623 1419 False 619.550000 1142 91.575500 586 1982 2 chrUn.!!$F2 1396
18 TraesCS7D01G010900 chrUn 337111227 337111762 535 False 566.000000 566 86.182000 2700 3231 1 chrUn.!!$F1 531
19 TraesCS7D01G010900 chr4D 42116346 42117231 885 False 990.000000 990 86.900000 2441 3346 1 chr4D.!!$F1 905
20 TraesCS7D01G010900 chr4D 234082731 234083613 882 True 981.000000 981 86.776000 2442 3346 1 chr4D.!!$R1 904
21 TraesCS7D01G010900 chr2D 165185617 165186502 885 True 989.000000 989 86.928000 2442 3346 1 chr2D.!!$R1 904
22 TraesCS7D01G010900 chr2D 21649385 21650137 752 False 970.000000 970 90.145000 2700 3446 1 chr2D.!!$F1 746
23 TraesCS7D01G010900 chr2D 614347450 614348020 570 False 638.000000 638 87.391000 645 1195 1 chr2D.!!$F3 550
24 TraesCS7D01G010900 chr2D 590222876 590223411 535 False 571.000000 571 86.339000 2700 3231 1 chr2D.!!$F2 531
25 TraesCS7D01G010900 chr2D 614327859 614328578 719 False 342.000000 497 91.153000 13 573 2 chr2D.!!$F5 560
26 TraesCS7D01G010900 chr1D 467044288 467044914 626 False 904.000000 904 92.343000 2442 3093 1 chr1D.!!$F2 651
27 TraesCS7D01G010900 chr1D 273904296 273905051 755 True 852.000000 852 87.614000 2710 3446 1 chr1D.!!$R1 736
28 TraesCS7D01G010900 chr1D 372547340 372547987 647 True 726.000000 726 87.126000 2442 3096 1 chr1D.!!$R2 654
29 TraesCS7D01G010900 chr1A 472533417 472534410 993 True 893.000000 893 83.154000 2442 3446 1 chr1A.!!$R1 1004
30 TraesCS7D01G010900 chr5D 307471103 307471792 689 False 848.000000 848 89.158000 2442 3125 1 chr5D.!!$F1 683
31 TraesCS7D01G010900 chr6D 448041939 448042824 885 False 791.000000 791 83.191000 2441 3359 1 chr6D.!!$F2 918
32 TraesCS7D01G010900 chr6D 301473829 301474459 630 False 721.000000 721 87.443000 2711 3358 1 chr6D.!!$F1 647

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
384 387 0.317160 ACGTCTCAGAAATGGCACGA 59.683 50.0 0.00 0.0 0.0 4.35 F
2248 8100 0.176449 CGGACATGTGCCATCTGAGA 59.824 55.0 12.15 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 8123 0.683412 TGCCTCCGAGATCCATCATG 59.317 55.000 0.0 0.0 0.0 3.07 R
3360 10745 4.443266 AGAGAGTCGGGCTTGCGC 62.443 66.667 0.0 0.0 0.0 6.09 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
46 47 1.218854 GAATGGTTGGGGCATGTGC 59.781 57.895 0.00 0.00 41.14 4.57
60 61 2.737359 GCATGTGCATTGTTCCATGGAG 60.737 50.000 15.53 3.89 41.59 3.86
77 78 3.585862 TGGAGCTCGTACTTGAAATGAC 58.414 45.455 7.83 0.00 0.00 3.06
78 79 2.930682 GGAGCTCGTACTTGAAATGACC 59.069 50.000 7.83 0.00 0.00 4.02
184 186 1.547820 CTGTCCAGTGAAGAGCTAGCA 59.452 52.381 18.83 0.00 0.00 3.49
222 224 2.028567 AGTAGTCAGAAACAGAGCAGCC 60.029 50.000 0.00 0.00 0.00 4.85
224 226 0.871057 GTCAGAAACAGAGCAGCCAC 59.129 55.000 0.00 0.00 0.00 5.01
263 266 1.439679 CTTCCGGAGTACTTGTTGCC 58.560 55.000 3.34 0.00 0.00 4.52
328 331 2.178912 GACTGAATCCACCGGTGAAA 57.821 50.000 36.07 22.91 0.00 2.69
329 332 1.804748 GACTGAATCCACCGGTGAAAC 59.195 52.381 36.07 21.84 0.00 2.78
330 333 1.420138 ACTGAATCCACCGGTGAAACT 59.580 47.619 36.07 16.59 36.74 2.66
331 334 1.806542 CTGAATCCACCGGTGAAACTG 59.193 52.381 36.07 18.48 44.86 3.16
343 346 5.682943 CGGTGAAACTGGTTGAGAAAATA 57.317 39.130 0.00 0.00 40.35 1.40
344 347 6.067263 CGGTGAAACTGGTTGAGAAAATAA 57.933 37.500 0.00 0.00 40.35 1.40
345 348 6.142817 CGGTGAAACTGGTTGAGAAAATAAG 58.857 40.000 0.00 0.00 40.35 1.73
347 350 7.468084 CGGTGAAACTGGTTGAGAAAATAAGAA 60.468 37.037 0.00 0.00 40.35 2.52
348 351 8.194769 GGTGAAACTGGTTGAGAAAATAAGAAA 58.805 33.333 0.00 0.00 36.74 2.52
350 353 8.744652 TGAAACTGGTTGAGAAAATAAGAAACA 58.255 29.630 0.00 0.00 0.00 2.83
351 354 9.581099 GAAACTGGTTGAGAAAATAAGAAACAA 57.419 29.630 0.00 0.00 0.00 2.83
352 355 9.936759 AAACTGGTTGAGAAAATAAGAAACAAA 57.063 25.926 0.00 0.00 0.00 2.83
353 356 9.936759 AACTGGTTGAGAAAATAAGAAACAAAA 57.063 25.926 0.00 0.00 0.00 2.44
364 367 9.620660 AAAATAAGAAACAAAATACTAGCGGTG 57.379 29.630 0.00 0.00 0.00 4.94
380 383 1.079503 GGTGACGTCTCAGAAATGGC 58.920 55.000 17.92 0.00 0.00 4.40
383 386 0.716108 GACGTCTCAGAAATGGCACG 59.284 55.000 8.70 0.00 0.00 5.34
384 387 0.317160 ACGTCTCAGAAATGGCACGA 59.683 50.000 0.00 0.00 0.00 4.35
385 388 0.994995 CGTCTCAGAAATGGCACGAG 59.005 55.000 0.00 0.00 0.00 4.18
386 389 1.402852 CGTCTCAGAAATGGCACGAGA 60.403 52.381 0.00 0.00 0.00 4.04
390 393 3.196469 TCTCAGAAATGGCACGAGATCTT 59.804 43.478 0.00 0.00 0.00 2.40
391 394 3.937706 CTCAGAAATGGCACGAGATCTTT 59.062 43.478 0.00 0.00 0.00 2.52
393 396 4.393062 TCAGAAATGGCACGAGATCTTTTC 59.607 41.667 0.00 1.10 0.00 2.29
394 397 4.394300 CAGAAATGGCACGAGATCTTTTCT 59.606 41.667 9.50 9.50 36.20 2.52
397 400 5.344743 AATGGCACGAGATCTTTTCTAGA 57.655 39.130 0.00 0.00 33.74 2.43
398 401 4.801330 TGGCACGAGATCTTTTCTAGAA 57.199 40.909 0.00 0.00 36.22 2.10
399 402 5.147330 TGGCACGAGATCTTTTCTAGAAA 57.853 39.130 13.99 13.99 36.22 2.52
400 403 4.929808 TGGCACGAGATCTTTTCTAGAAAC 59.070 41.667 17.51 6.44 36.22 2.78
401 404 4.330347 GGCACGAGATCTTTTCTAGAAACC 59.670 45.833 17.51 7.76 36.22 3.27
402 405 4.929808 GCACGAGATCTTTTCTAGAAACCA 59.070 41.667 17.51 7.50 36.22 3.67
404 407 6.092807 GCACGAGATCTTTTCTAGAAACCAAT 59.907 38.462 17.51 10.88 36.22 3.16
405 408 7.459486 CACGAGATCTTTTCTAGAAACCAATG 58.541 38.462 17.51 7.31 36.22 2.82
406 409 6.092807 ACGAGATCTTTTCTAGAAACCAATGC 59.907 38.462 17.51 5.93 36.22 3.56
407 410 6.457528 CGAGATCTTTTCTAGAAACCAATGCC 60.458 42.308 17.51 4.42 36.22 4.40
408 411 6.488715 AGATCTTTTCTAGAAACCAATGCCT 58.511 36.000 17.51 6.20 36.22 4.75
409 412 6.601217 AGATCTTTTCTAGAAACCAATGCCTC 59.399 38.462 17.51 6.52 36.22 4.70
411 414 5.707298 TCTTTTCTAGAAACCAATGCCTCTG 59.293 40.000 17.51 0.00 0.00 3.35
413 416 4.640771 TCTAGAAACCAATGCCTCTGTT 57.359 40.909 0.00 0.00 0.00 3.16
414 417 4.579869 TCTAGAAACCAATGCCTCTGTTC 58.420 43.478 0.00 0.00 0.00 3.18
415 418 2.154462 AGAAACCAATGCCTCTGTTCG 58.846 47.619 0.00 0.00 0.00 3.95
418 421 2.409870 CCAATGCCTCTGTTCGCCC 61.410 63.158 0.00 0.00 0.00 6.13
419 422 2.436646 AATGCCTCTGTTCGCCCG 60.437 61.111 0.00 0.00 0.00 6.13
421 424 3.665675 ATGCCTCTGTTCGCCCGTC 62.666 63.158 0.00 0.00 0.00 4.79
476 5653 9.888878 CAATGCTGATAAACTGTTAGGATTATG 57.111 33.333 7.25 0.00 29.99 1.90
559 5736 1.341209 CTCCCTTGCCAGTTTTGTTCC 59.659 52.381 0.00 0.00 0.00 3.62
579 5780 0.873054 GCTCATCCTGGATCATTGCG 59.127 55.000 6.13 0.00 0.00 4.85
709 5999 2.022129 CGTCGGTGCTTGTGGACTC 61.022 63.158 0.00 0.00 34.78 3.36
899 6495 4.274602 TGCCATAAACTCCAGTTCGTAA 57.725 40.909 0.00 0.00 37.25 3.18
901 6497 3.998341 GCCATAAACTCCAGTTCGTAACA 59.002 43.478 0.00 0.00 37.25 2.41
902 6498 4.142966 GCCATAAACTCCAGTTCGTAACAC 60.143 45.833 0.00 0.00 37.25 3.32
960 6558 0.976641 CACCACTACCAAGCTCCTGA 59.023 55.000 0.00 0.00 0.00 3.86
980 6578 2.375173 TCATATGCATCCTAGCTGCG 57.625 50.000 0.19 0.00 42.62 5.18
1207 6828 2.385013 TCGTAATGTGCATGCAGACT 57.615 45.000 23.41 13.26 0.00 3.24
1220 6865 2.447443 TGCAGACTACCTCGATGAGTT 58.553 47.619 0.00 0.00 0.00 3.01
1225 6870 4.025563 CAGACTACCTCGATGAGTTCTACG 60.026 50.000 0.00 0.00 0.00 3.51
1226 6871 3.204526 ACTACCTCGATGAGTTCTACGG 58.795 50.000 0.00 0.00 0.00 4.02
1235 6895 4.438880 CGATGAGTTCTACGGAGACAACAT 60.439 45.833 0.00 2.93 0.00 2.71
1299 6959 1.230324 GTCTTGTGCACCTTGACCTC 58.770 55.000 15.69 0.00 0.00 3.85
1603 7373 5.707298 GTCAACATGATCCCTTCTTTGAAGA 59.293 40.000 0.00 0.00 0.00 2.87
1738 7508 2.549992 GCAAGGGGTTGGTTTTGGAATC 60.550 50.000 0.00 0.00 0.00 2.52
1774 7544 3.056250 ACATCTCTACCTTGCTGACACTG 60.056 47.826 0.00 0.00 0.00 3.66
1870 7643 6.269077 TCGTAACATGGGGATAATGACTACAT 59.731 38.462 0.00 0.00 38.50 2.29
1922 7702 4.217118 CCTGGACCTTTCTTCATGTCAAAG 59.783 45.833 0.00 0.11 0.00 2.77
1932 7712 6.317789 TCTTCATGTCAAAGTGATGGAAAC 57.682 37.500 0.00 0.00 0.00 2.78
2030 7810 2.442236 ACTGGAATCATGCCGGATTT 57.558 45.000 5.05 0.00 37.61 2.17
2043 7823 3.202906 GCCGGATTTGATAGCACACTTA 58.797 45.455 5.05 0.00 0.00 2.24
2126 7906 2.910319 TGGGGCTGCTCTCTAGTTTAAA 59.090 45.455 0.00 0.00 0.00 1.52
2188 8040 2.094286 CCATCTGAGATCGGTATGCTCC 60.094 54.545 0.00 0.00 0.00 4.70
2203 8055 5.105310 GGTATGCTCCGTAATCTGACCATAT 60.105 44.000 0.00 0.00 0.00 1.78
2216 8068 6.813293 TCTGACCATATTGGATCTTGAAGA 57.187 37.500 0.00 0.00 40.96 2.87
2217 8069 7.384524 TCTGACCATATTGGATCTTGAAGAT 57.615 36.000 7.53 7.53 40.96 2.40
2229 8081 8.668510 TGGATCTTGAAGATAACAATCTTAGC 57.331 34.615 7.82 0.00 40.67 3.09
2230 8082 7.439356 TGGATCTTGAAGATAACAATCTTAGCG 59.561 37.037 7.82 0.00 40.67 4.26
2231 8083 7.095439 GGATCTTGAAGATAACAATCTTAGCGG 60.095 40.741 7.82 0.00 40.67 5.52
2232 8084 6.873997 TCTTGAAGATAACAATCTTAGCGGA 58.126 36.000 0.79 0.00 40.67 5.54
2233 8085 6.757010 TCTTGAAGATAACAATCTTAGCGGAC 59.243 38.462 0.79 0.00 40.67 4.79
2234 8086 5.972935 TGAAGATAACAATCTTAGCGGACA 58.027 37.500 0.79 0.00 40.67 4.02
2235 8087 6.582636 TGAAGATAACAATCTTAGCGGACAT 58.417 36.000 0.79 0.00 40.67 3.06
2236 8088 6.479990 TGAAGATAACAATCTTAGCGGACATG 59.520 38.462 0.79 0.00 40.67 3.21
2237 8089 5.918608 AGATAACAATCTTAGCGGACATGT 58.081 37.500 0.00 0.00 0.00 3.21
2238 8090 5.755375 AGATAACAATCTTAGCGGACATGTG 59.245 40.000 1.15 0.00 0.00 3.21
2239 8091 2.009774 ACAATCTTAGCGGACATGTGC 58.990 47.619 1.15 4.73 0.00 4.57
2240 8092 1.331756 CAATCTTAGCGGACATGTGCC 59.668 52.381 12.15 7.91 0.00 5.01
2241 8093 0.541392 ATCTTAGCGGACATGTGCCA 59.459 50.000 12.15 0.00 0.00 4.92
2242 8094 0.541392 TCTTAGCGGACATGTGCCAT 59.459 50.000 12.15 3.00 0.00 4.40
2243 8095 0.940126 CTTAGCGGACATGTGCCATC 59.060 55.000 12.15 1.46 0.00 3.51
2244 8096 0.541392 TTAGCGGACATGTGCCATCT 59.459 50.000 12.15 8.90 0.00 2.90
2245 8097 0.179076 TAGCGGACATGTGCCATCTG 60.179 55.000 12.15 0.00 0.00 2.90
2246 8098 1.450134 GCGGACATGTGCCATCTGA 60.450 57.895 12.15 0.00 0.00 3.27
2247 8099 1.434622 GCGGACATGTGCCATCTGAG 61.435 60.000 12.15 0.00 0.00 3.35
2248 8100 0.176449 CGGACATGTGCCATCTGAGA 59.824 55.000 12.15 0.00 0.00 3.27
2249 8101 1.202615 CGGACATGTGCCATCTGAGAT 60.203 52.381 12.15 0.00 0.00 2.75
2250 8102 2.492012 GGACATGTGCCATCTGAGATC 58.508 52.381 1.15 0.00 0.00 2.75
2251 8103 2.133553 GACATGTGCCATCTGAGATCG 58.866 52.381 1.15 0.00 0.00 3.69
2252 8104 1.202615 ACATGTGCCATCTGAGATCGG 60.203 52.381 0.00 0.00 0.00 4.18
2253 8105 1.126488 ATGTGCCATCTGAGATCGGT 58.874 50.000 10.97 0.00 0.00 4.69
2254 8106 1.775385 TGTGCCATCTGAGATCGGTA 58.225 50.000 10.97 5.55 0.00 4.02
2255 8107 2.319844 TGTGCCATCTGAGATCGGTAT 58.680 47.619 10.97 0.00 0.00 2.73
2256 8108 2.036346 TGTGCCATCTGAGATCGGTATG 59.964 50.000 10.97 0.00 0.00 2.39
2257 8109 1.001293 TGCCATCTGAGATCGGTATGC 59.999 52.381 10.97 1.51 0.00 3.14
2258 8110 1.274728 GCCATCTGAGATCGGTATGCT 59.725 52.381 10.97 0.00 0.00 3.79
2259 8111 2.289320 GCCATCTGAGATCGGTATGCTT 60.289 50.000 10.97 0.00 0.00 3.91
2260 8112 3.805108 GCCATCTGAGATCGGTATGCTTT 60.805 47.826 10.97 0.00 0.00 3.51
2261 8113 3.744942 CCATCTGAGATCGGTATGCTTTG 59.255 47.826 0.00 0.00 0.00 2.77
2262 8114 2.826428 TCTGAGATCGGTATGCTTTGC 58.174 47.619 0.00 0.00 0.00 3.68
2263 8115 2.168313 TCTGAGATCGGTATGCTTTGCA 59.832 45.455 0.00 0.00 44.86 4.08
2264 8116 2.938451 CTGAGATCGGTATGCTTTGCAA 59.062 45.455 0.00 0.00 43.62 4.08
2265 8117 3.544684 TGAGATCGGTATGCTTTGCAAT 58.455 40.909 0.00 0.00 43.62 3.56
2266 8118 3.947196 TGAGATCGGTATGCTTTGCAATT 59.053 39.130 0.00 0.00 43.62 2.32
2267 8119 4.398988 TGAGATCGGTATGCTTTGCAATTT 59.601 37.500 0.00 0.00 43.62 1.82
2268 8120 5.588246 TGAGATCGGTATGCTTTGCAATTTA 59.412 36.000 0.00 0.00 43.62 1.40
2269 8121 6.094742 TGAGATCGGTATGCTTTGCAATTTAA 59.905 34.615 0.00 0.00 43.62 1.52
2270 8122 7.042797 AGATCGGTATGCTTTGCAATTTAAT 57.957 32.000 0.00 0.00 43.62 1.40
2271 8123 7.141363 AGATCGGTATGCTTTGCAATTTAATC 58.859 34.615 0.00 0.00 43.62 1.75
2272 8124 6.201226 TCGGTATGCTTTGCAATTTAATCA 57.799 33.333 0.00 0.00 43.62 2.57
2273 8125 6.804677 TCGGTATGCTTTGCAATTTAATCAT 58.195 32.000 0.00 0.00 43.62 2.45
2274 8126 6.696583 TCGGTATGCTTTGCAATTTAATCATG 59.303 34.615 0.00 0.00 43.62 3.07
2275 8127 6.696583 CGGTATGCTTTGCAATTTAATCATGA 59.303 34.615 0.00 0.00 43.62 3.07
2276 8128 7.383029 CGGTATGCTTTGCAATTTAATCATGAT 59.617 33.333 1.18 1.18 43.62 2.45
2277 8129 8.492748 GGTATGCTTTGCAATTTAATCATGATG 58.507 33.333 9.46 0.00 43.62 3.07
2278 8130 6.912203 TGCTTTGCAATTTAATCATGATGG 57.088 33.333 9.46 0.00 34.76 3.51
2279 8131 6.641474 TGCTTTGCAATTTAATCATGATGGA 58.359 32.000 9.46 0.00 34.76 3.41
2280 8132 7.276658 TGCTTTGCAATTTAATCATGATGGAT 58.723 30.769 9.46 1.04 34.76 3.41
2281 8133 7.439955 TGCTTTGCAATTTAATCATGATGGATC 59.560 33.333 9.46 0.00 34.76 3.36
2282 8134 7.656137 GCTTTGCAATTTAATCATGATGGATCT 59.344 33.333 9.46 0.00 0.00 2.75
2283 8135 9.193133 CTTTGCAATTTAATCATGATGGATCTC 57.807 33.333 9.46 0.00 0.00 2.75
2284 8136 6.905578 TGCAATTTAATCATGATGGATCTCG 58.094 36.000 9.46 0.00 0.00 4.04
2285 8137 6.072342 TGCAATTTAATCATGATGGATCTCGG 60.072 38.462 9.46 0.00 0.00 4.63
2286 8138 6.149973 GCAATTTAATCATGATGGATCTCGGA 59.850 38.462 9.46 0.00 0.00 4.55
2287 8139 7.625817 GCAATTTAATCATGATGGATCTCGGAG 60.626 40.741 9.46 0.00 0.00 4.63
2288 8140 3.977134 AATCATGATGGATCTCGGAGG 57.023 47.619 9.46 0.00 0.00 4.30
2289 8141 0.972134 TCATGATGGATCTCGGAGGC 59.028 55.000 4.96 0.00 0.00 4.70
2290 8142 0.683412 CATGATGGATCTCGGAGGCA 59.317 55.000 4.96 0.00 0.00 4.75
2291 8143 1.071228 CATGATGGATCTCGGAGGCAA 59.929 52.381 4.96 0.00 0.00 4.52
2292 8144 1.427809 TGATGGATCTCGGAGGCAAT 58.572 50.000 4.96 0.00 0.00 3.56
2293 8145 2.608623 TGATGGATCTCGGAGGCAATA 58.391 47.619 4.96 0.00 0.00 1.90
2294 8146 2.972021 TGATGGATCTCGGAGGCAATAA 59.028 45.455 4.96 0.00 0.00 1.40
2295 8147 3.390967 TGATGGATCTCGGAGGCAATAAA 59.609 43.478 4.96 0.00 0.00 1.40
2336 8188 8.504005 CACCGAAGAACATTTTACAAGTCTAAT 58.496 33.333 0.00 0.00 0.00 1.73
2360 8212 5.944007 TGAGGTTAAAGGAGCTGGATTTAAC 59.056 40.000 19.78 19.78 43.63 2.01
2380 8232 3.973425 ACTGGGAATTCCTTGAGGATTG 58.027 45.455 23.63 6.55 44.98 2.67
2419 8271 5.491078 TGGATACCACCCTTCAGTTTAGAAT 59.509 40.000 0.00 0.00 0.00 2.40
2421 8273 6.990939 GGATACCACCCTTCAGTTTAGAATAC 59.009 42.308 0.00 0.00 0.00 1.89
2425 8277 5.411669 CCACCCTTCAGTTTAGAATACACAC 59.588 44.000 0.00 0.00 0.00 3.82
2788 8653 0.877071 CTGCTGCACAAGGTAGGTTG 59.123 55.000 0.00 0.00 0.00 3.77
2789 8654 0.182537 TGCTGCACAAGGTAGGTTGT 59.817 50.000 0.00 0.00 41.47 3.32
2790 8655 1.418264 TGCTGCACAAGGTAGGTTGTA 59.582 47.619 0.00 0.00 38.65 2.41
2876 8745 7.857885 GGCTAGATGATTTTCGGTAAAAAGATG 59.142 37.037 0.00 0.00 40.09 2.90
2888 8859 9.730420 TTCGGTAAAAAGATGAAAAAGAGAAAG 57.270 29.630 0.00 0.00 0.00 2.62
2899 8870 9.457110 GATGAAAAAGAGAAAGAAAAGAACTCC 57.543 33.333 0.00 0.00 0.00 3.85
3360 10745 1.079503 CGAAGGGAAGAAAAGGAGCG 58.920 55.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.602878 TCGGTCATTTCAAGTACGAGC 58.397 47.619 0.00 0.00 0.00 5.03
77 78 3.142951 TGAACAACATTACCCACTTCGG 58.857 45.455 0.00 0.00 0.00 4.30
78 79 4.822036 TTGAACAACATTACCCACTTCG 57.178 40.909 0.00 0.00 0.00 3.79
184 186 7.009179 TGACTACTTCTGATCCAGTTTCATT 57.991 36.000 0.00 0.00 32.61 2.57
222 224 0.620556 AGCTACATGGAAGGGGTGTG 59.379 55.000 0.00 0.00 0.00 3.82
224 226 0.749454 GCAGCTACATGGAAGGGGTG 60.749 60.000 0.00 0.00 0.00 4.61
326 329 9.936759 TTTGTTTCTTATTTTCTCAACCAGTTT 57.063 25.926 0.00 0.00 0.00 2.66
337 340 9.836076 ACCGCTAGTATTTTGTTTCTTATTTTC 57.164 29.630 0.00 0.00 0.00 2.29
339 342 9.005777 TCACCGCTAGTATTTTGTTTCTTATTT 57.994 29.630 0.00 0.00 0.00 1.40
340 343 8.448615 GTCACCGCTAGTATTTTGTTTCTTATT 58.551 33.333 0.00 0.00 0.00 1.40
343 346 5.107220 CGTCACCGCTAGTATTTTGTTTCTT 60.107 40.000 0.00 0.00 0.00 2.52
344 347 4.387862 CGTCACCGCTAGTATTTTGTTTCT 59.612 41.667 0.00 0.00 0.00 2.52
345 348 4.151157 ACGTCACCGCTAGTATTTTGTTTC 59.849 41.667 0.00 0.00 37.70 2.78
347 350 3.656559 ACGTCACCGCTAGTATTTTGTT 58.343 40.909 0.00 0.00 37.70 2.83
348 351 3.057033 AGACGTCACCGCTAGTATTTTGT 60.057 43.478 19.50 0.00 37.70 2.83
350 353 3.192001 TGAGACGTCACCGCTAGTATTTT 59.808 43.478 19.50 0.00 37.70 1.82
351 354 2.751259 TGAGACGTCACCGCTAGTATTT 59.249 45.455 19.50 0.00 37.70 1.40
352 355 2.355132 CTGAGACGTCACCGCTAGTATT 59.645 50.000 19.50 0.00 37.70 1.89
353 356 1.941294 CTGAGACGTCACCGCTAGTAT 59.059 52.381 19.50 0.00 37.70 2.12
354 357 1.066645 TCTGAGACGTCACCGCTAGTA 60.067 52.381 19.50 0.00 37.70 1.82
355 358 0.321387 TCTGAGACGTCACCGCTAGT 60.321 55.000 19.50 0.00 37.70 2.57
356 359 0.803117 TTCTGAGACGTCACCGCTAG 59.197 55.000 19.50 5.05 37.70 3.42
358 361 0.603569 ATTTCTGAGACGTCACCGCT 59.396 50.000 19.50 0.00 37.70 5.52
360 363 1.350193 CCATTTCTGAGACGTCACCG 58.650 55.000 19.50 8.28 40.83 4.94
361 364 1.079503 GCCATTTCTGAGACGTCACC 58.920 55.000 19.50 9.65 0.00 4.02
362 365 1.461127 GTGCCATTTCTGAGACGTCAC 59.539 52.381 19.50 12.69 0.00 3.67
364 367 0.716108 CGTGCCATTTCTGAGACGTC 59.284 55.000 7.70 7.70 0.00 4.34
367 370 2.370281 TCTCGTGCCATTTCTGAGAC 57.630 50.000 0.00 0.00 31.14 3.36
368 371 2.762887 AGATCTCGTGCCATTTCTGAGA 59.237 45.455 0.00 0.00 39.75 3.27
369 372 3.176552 AGATCTCGTGCCATTTCTGAG 57.823 47.619 0.00 0.00 0.00 3.35
370 373 3.616956 AAGATCTCGTGCCATTTCTGA 57.383 42.857 0.00 0.00 0.00 3.27
371 374 4.394300 AGAAAAGATCTCGTGCCATTTCTG 59.606 41.667 13.11 0.00 35.13 3.02
375 378 5.344743 TCTAGAAAAGATCTCGTGCCATT 57.655 39.130 0.00 0.00 39.71 3.16
376 379 5.344743 TTCTAGAAAAGATCTCGTGCCAT 57.655 39.130 1.68 0.00 39.71 4.40
377 380 4.801330 TTCTAGAAAAGATCTCGTGCCA 57.199 40.909 1.68 0.00 39.71 4.92
380 383 7.459486 CATTGGTTTCTAGAAAAGATCTCGTG 58.541 38.462 19.30 7.22 39.71 4.35
383 386 6.601217 AGGCATTGGTTTCTAGAAAAGATCTC 59.399 38.462 19.30 6.14 39.71 2.75
384 387 6.488715 AGGCATTGGTTTCTAGAAAAGATCT 58.511 36.000 19.30 8.24 42.48 2.75
385 388 6.601217 AGAGGCATTGGTTTCTAGAAAAGATC 59.399 38.462 19.30 7.19 33.05 2.75
386 389 6.376581 CAGAGGCATTGGTTTCTAGAAAAGAT 59.623 38.462 19.30 10.62 33.05 2.40
390 393 4.985538 ACAGAGGCATTGGTTTCTAGAAA 58.014 39.130 13.99 13.99 0.00 2.52
391 394 4.640771 ACAGAGGCATTGGTTTCTAGAA 57.359 40.909 0.00 0.00 0.00 2.10
393 396 3.372206 CGAACAGAGGCATTGGTTTCTAG 59.628 47.826 0.00 0.00 0.00 2.43
394 397 3.334691 CGAACAGAGGCATTGGTTTCTA 58.665 45.455 0.00 0.00 0.00 2.10
397 400 0.598065 GCGAACAGAGGCATTGGTTT 59.402 50.000 0.00 0.00 0.00 3.27
398 401 1.244019 GGCGAACAGAGGCATTGGTT 61.244 55.000 0.00 0.00 0.00 3.67
399 402 1.675641 GGCGAACAGAGGCATTGGT 60.676 57.895 0.00 0.00 0.00 3.67
400 403 2.409870 GGGCGAACAGAGGCATTGG 61.410 63.158 0.00 0.00 35.71 3.16
401 404 2.753966 CGGGCGAACAGAGGCATTG 61.754 63.158 0.00 0.00 35.71 2.82
402 405 2.436646 CGGGCGAACAGAGGCATT 60.437 61.111 0.00 0.00 35.71 3.56
404 407 4.373116 GACGGGCGAACAGAGGCA 62.373 66.667 0.00 0.00 35.71 4.75
406 409 4.796231 CGGACGGGCGAACAGAGG 62.796 72.222 0.00 0.00 0.00 3.69
414 417 4.735132 TTTGAGAGCGGACGGGCG 62.735 66.667 0.00 0.00 38.18 6.13
415 418 2.815647 CTTTGAGAGCGGACGGGC 60.816 66.667 0.00 0.00 0.00 6.13
507 5684 2.094854 GGTGCTTTTCTCATGCTCCTTG 60.095 50.000 0.00 0.00 36.63 3.61
519 5696 1.745653 GCTCAGGGTATGGTGCTTTTC 59.254 52.381 0.00 0.00 0.00 2.29
559 5736 0.873054 GCAATGATCCAGGATGAGCG 59.127 55.000 6.70 0.00 39.69 5.03
709 5999 3.614616 GCCTGAATTCGTCTACTTGTGAG 59.385 47.826 0.04 0.00 0.00 3.51
899 6495 0.039764 TGGATCCGTCTCTGAGGTGT 59.960 55.000 7.39 0.00 0.00 4.16
901 6497 1.698506 GATGGATCCGTCTCTGAGGT 58.301 55.000 24.39 0.00 0.00 3.85
902 6498 0.595588 CGATGGATCCGTCTCTGAGG 59.404 60.000 27.55 10.49 0.00 3.86
960 6558 2.419713 CCGCAGCTAGGATGCATATGAT 60.420 50.000 6.97 0.00 44.05 2.45
1207 6828 3.133542 TCTCCGTAGAACTCATCGAGGTA 59.866 47.826 0.00 0.00 33.35 3.08
1220 6865 4.081862 CCAAACCTATGTTGTCTCCGTAGA 60.082 45.833 0.00 0.00 34.13 2.59
1225 6870 3.506067 CCAACCAAACCTATGTTGTCTCC 59.494 47.826 0.00 0.00 38.10 3.71
1226 6871 3.057526 GCCAACCAAACCTATGTTGTCTC 60.058 47.826 0.00 0.00 38.10 3.36
1235 6895 3.262405 ACTTATCTCGCCAACCAAACCTA 59.738 43.478 0.00 0.00 0.00 3.08
1299 6959 1.688772 CCTCCAGGGAATTCATGCTG 58.311 55.000 7.93 1.62 37.23 4.41
1314 6974 3.256960 TGACCACTTGGGCCCTCC 61.257 66.667 25.70 4.56 44.80 4.30
1738 7508 2.027377 AGAGATGTTGGAGGCTTGTCAG 60.027 50.000 0.00 0.00 0.00 3.51
1774 7544 1.272769 AGGAGCTTGACCGTACAGTTC 59.727 52.381 0.00 0.00 0.00 3.01
1870 7643 4.397103 CAGATTGCATAGGTTTCTGAAGCA 59.603 41.667 6.58 1.46 36.72 3.91
1949 7729 1.379044 GGACACTGGGGCATCCTTG 60.379 63.158 0.00 0.00 36.20 3.61
1950 7730 2.616458 GGGACACTGGGGCATCCTT 61.616 63.158 0.00 0.00 36.20 3.36
2030 7810 3.981071 AGCTGGTTAAGTGTGCTATCA 57.019 42.857 0.00 0.00 31.71 2.15
2043 7823 3.746045 TCAAGAACGACTAAGCTGGTT 57.254 42.857 0.00 0.00 0.00 3.67
2126 7906 6.179906 TGTTGGAAGAGAGATCAAGTTCTT 57.820 37.500 0.00 0.00 32.87 2.52
2188 8040 7.154656 TCAAGATCCAATATGGTCAGATTACG 58.845 38.462 0.00 0.00 39.03 3.18
2194 8046 8.997323 GTTATCTTCAAGATCCAATATGGTCAG 58.003 37.037 2.18 0.00 39.03 3.51
2203 8055 9.113838 GCTAAGATTGTTATCTTCAAGATCCAA 57.886 33.333 2.18 8.82 45.82 3.53
2216 8068 4.273480 GCACATGTCCGCTAAGATTGTTAT 59.727 41.667 0.00 0.00 0.00 1.89
2217 8069 3.621268 GCACATGTCCGCTAAGATTGTTA 59.379 43.478 0.00 0.00 0.00 2.41
2224 8076 4.615901 TGGCACATGTCCGCTAAG 57.384 55.556 7.96 0.00 0.00 2.18
2236 8088 2.681706 CATACCGATCTCAGATGGCAC 58.318 52.381 0.00 0.00 0.00 5.01
2237 8089 1.001293 GCATACCGATCTCAGATGGCA 59.999 52.381 0.00 0.00 0.00 4.92
2238 8090 1.274728 AGCATACCGATCTCAGATGGC 59.725 52.381 0.00 0.00 0.00 4.40
2239 8091 3.674528 AAGCATACCGATCTCAGATGG 57.325 47.619 0.00 0.00 0.00 3.51
2240 8092 3.186001 GCAAAGCATACCGATCTCAGATG 59.814 47.826 0.00 0.00 0.00 2.90
2241 8093 3.181462 TGCAAAGCATACCGATCTCAGAT 60.181 43.478 0.00 0.00 31.71 2.90
2242 8094 2.168313 TGCAAAGCATACCGATCTCAGA 59.832 45.455 0.00 0.00 31.71 3.27
2243 8095 2.554142 TGCAAAGCATACCGATCTCAG 58.446 47.619 0.00 0.00 31.71 3.35
2244 8096 2.689553 TGCAAAGCATACCGATCTCA 57.310 45.000 0.00 0.00 31.71 3.27
2245 8097 4.558538 AATTGCAAAGCATACCGATCTC 57.441 40.909 1.71 0.00 38.76 2.75
2246 8098 4.989279 AAATTGCAAAGCATACCGATCT 57.011 36.364 1.71 0.00 38.76 2.75
2247 8099 6.917477 TGATTAAATTGCAAAGCATACCGATC 59.083 34.615 1.71 0.00 38.76 3.69
2248 8100 6.804677 TGATTAAATTGCAAAGCATACCGAT 58.195 32.000 1.71 0.00 38.76 4.18
2249 8101 6.201226 TGATTAAATTGCAAAGCATACCGA 57.799 33.333 1.71 0.00 38.76 4.69
2250 8102 6.696583 TCATGATTAAATTGCAAAGCATACCG 59.303 34.615 1.71 0.00 38.76 4.02
2251 8103 8.492748 CATCATGATTAAATTGCAAAGCATACC 58.507 33.333 5.16 0.00 38.76 2.73
2252 8104 8.492748 CCATCATGATTAAATTGCAAAGCATAC 58.507 33.333 5.16 0.00 38.76 2.39
2253 8105 8.422566 TCCATCATGATTAAATTGCAAAGCATA 58.577 29.630 5.16 0.00 38.76 3.14
2254 8106 7.276658 TCCATCATGATTAAATTGCAAAGCAT 58.723 30.769 5.16 0.00 38.76 3.79
2255 8107 6.641474 TCCATCATGATTAAATTGCAAAGCA 58.359 32.000 5.16 0.00 36.47 3.91
2256 8108 7.656137 AGATCCATCATGATTAAATTGCAAAGC 59.344 33.333 5.16 0.00 0.00 3.51
2257 8109 9.193133 GAGATCCATCATGATTAAATTGCAAAG 57.807 33.333 5.16 0.00 0.00 2.77
2258 8110 7.863877 CGAGATCCATCATGATTAAATTGCAAA 59.136 33.333 5.16 0.00 0.00 3.68
2259 8111 7.364970 CGAGATCCATCATGATTAAATTGCAA 58.635 34.615 5.16 0.00 0.00 4.08
2260 8112 6.072342 CCGAGATCCATCATGATTAAATTGCA 60.072 38.462 5.16 0.00 0.00 4.08
2261 8113 6.149973 TCCGAGATCCATCATGATTAAATTGC 59.850 38.462 5.16 0.00 0.00 3.56
2262 8114 7.148289 CCTCCGAGATCCATCATGATTAAATTG 60.148 40.741 5.16 0.00 0.00 2.32
2263 8115 6.883217 CCTCCGAGATCCATCATGATTAAATT 59.117 38.462 5.16 0.00 0.00 1.82
2264 8116 6.413052 CCTCCGAGATCCATCATGATTAAAT 58.587 40.000 5.16 0.00 0.00 1.40
2265 8117 5.798132 CCTCCGAGATCCATCATGATTAAA 58.202 41.667 5.16 0.00 0.00 1.52
2266 8118 4.323028 GCCTCCGAGATCCATCATGATTAA 60.323 45.833 5.16 0.00 0.00 1.40
2267 8119 3.196469 GCCTCCGAGATCCATCATGATTA 59.804 47.826 5.16 0.00 0.00 1.75
2268 8120 2.027377 GCCTCCGAGATCCATCATGATT 60.027 50.000 5.16 0.00 0.00 2.57
2269 8121 1.554160 GCCTCCGAGATCCATCATGAT 59.446 52.381 1.18 1.18 0.00 2.45
2270 8122 0.972134 GCCTCCGAGATCCATCATGA 59.028 55.000 0.00 0.00 0.00 3.07
2271 8123 0.683412 TGCCTCCGAGATCCATCATG 59.317 55.000 0.00 0.00 0.00 3.07
2272 8124 1.427809 TTGCCTCCGAGATCCATCAT 58.572 50.000 0.00 0.00 0.00 2.45
2273 8125 1.427809 ATTGCCTCCGAGATCCATCA 58.572 50.000 0.00 0.00 0.00 3.07
2274 8126 3.685139 TTATTGCCTCCGAGATCCATC 57.315 47.619 0.00 0.00 0.00 3.51
2275 8127 4.647564 ATTTATTGCCTCCGAGATCCAT 57.352 40.909 0.00 0.00 0.00 3.41
2276 8128 4.136796 CAATTTATTGCCTCCGAGATCCA 58.863 43.478 0.00 0.00 0.00 3.41
2277 8129 4.389374 TCAATTTATTGCCTCCGAGATCC 58.611 43.478 0.00 0.00 37.68 3.36
2278 8130 6.376978 CATTCAATTTATTGCCTCCGAGATC 58.623 40.000 0.00 0.00 37.68 2.75
2279 8131 5.242393 CCATTCAATTTATTGCCTCCGAGAT 59.758 40.000 0.00 0.00 37.68 2.75
2280 8132 4.580167 CCATTCAATTTATTGCCTCCGAGA 59.420 41.667 0.00 0.00 37.68 4.04
2281 8133 4.339247 ACCATTCAATTTATTGCCTCCGAG 59.661 41.667 0.00 0.00 37.68 4.63
2282 8134 4.097741 CACCATTCAATTTATTGCCTCCGA 59.902 41.667 0.00 0.00 37.68 4.55
2283 8135 4.097741 TCACCATTCAATTTATTGCCTCCG 59.902 41.667 0.00 0.00 37.68 4.63
2284 8136 5.127682 AGTCACCATTCAATTTATTGCCTCC 59.872 40.000 0.00 0.00 37.68 4.30
2285 8137 6.212888 AGTCACCATTCAATTTATTGCCTC 57.787 37.500 0.00 0.00 37.68 4.70
2286 8138 6.211184 TGAAGTCACCATTCAATTTATTGCCT 59.789 34.615 0.00 0.00 37.68 4.75
2287 8139 6.311200 GTGAAGTCACCATTCAATTTATTGCC 59.689 38.462 0.00 0.00 40.85 4.52
2288 8140 7.281991 GTGAAGTCACCATTCAATTTATTGC 57.718 36.000 0.00 0.00 40.85 3.56
2336 8188 4.657814 AAATCCAGCTCCTTTAACCTCA 57.342 40.909 0.00 0.00 0.00 3.86
2380 8232 1.002624 TCCAATCGGGACCAACTGC 60.003 57.895 0.00 0.00 42.15 4.40
2419 8271 2.426522 GCAAGAGCCAAGATGTGTGTA 58.573 47.619 0.00 0.00 33.58 2.90
2788 8653 7.227116 CACTAGGCTAGATTAGATCCGGTATAC 59.773 44.444 27.59 0.00 0.00 1.47
2789 8654 7.126879 TCACTAGGCTAGATTAGATCCGGTATA 59.873 40.741 27.59 0.00 0.00 1.47
2790 8655 6.069556 TCACTAGGCTAGATTAGATCCGGTAT 60.070 42.308 27.59 0.00 0.00 2.73
2876 8745 8.001881 AGGGAGTTCTTTTCTTTCTCTTTTTC 57.998 34.615 0.00 0.00 0.00 2.29
2888 8859 2.291024 GGAAGGGGAGGGAGTTCTTTTC 60.291 54.545 0.00 0.00 0.00 2.29
2893 8864 2.001838 GGGGAAGGGGAGGGAGTTC 61.002 68.421 0.00 0.00 0.00 3.01
2896 8867 1.543896 TTTGGGGAAGGGGAGGGAG 60.544 63.158 0.00 0.00 0.00 4.30
2897 8868 1.543896 CTTTGGGGAAGGGGAGGGA 60.544 63.158 0.00 0.00 0.00 4.20
2898 8869 1.146544 TTCTTTGGGGAAGGGGAGGG 61.147 60.000 0.00 0.00 35.98 4.30
2899 8870 0.039764 GTTCTTTGGGGAAGGGGAGG 59.960 60.000 0.00 0.00 35.98 4.30
3022 9371 0.735287 GGTAGTGTTCTTCGTCCCGC 60.735 60.000 0.00 0.00 0.00 6.13
3237 10612 4.450117 CCTTTTCCCCTTCCCCTTCTTTTA 60.450 45.833 0.00 0.00 0.00 1.52
3360 10745 4.443266 AGAGAGTCGGGCTTGCGC 62.443 66.667 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.