Multiple sequence alignment - TraesCS1D01G066100

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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 TraesCS1D01G066100 chr1D 100.000 8451 0 0 1 8451 47871946 47880396 0.000000e+00 15607.0
1 TraesCS1D01G066100 chr1D 78.192 697 99 34 6 680 475529446 475528781 6.150000e-106 396.0
2 TraesCS1D01G066100 chr1D 87.778 90 10 1 3687 3775 253346848 253346937 4.170000e-18 104.0
3 TraesCS1D01G066100 chr1A 93.565 3248 122 38 1281 4467 47799691 47802912 0.000000e+00 4759.0
4 TraesCS1D01G066100 chr1A 96.429 2744 76 12 4635 7372 47802962 47805689 0.000000e+00 4505.0
5 TraesCS1D01G066100 chr1A 88.619 905 67 20 363 1245 47798802 47799692 0.000000e+00 1068.0
6 TraesCS1D01G066100 chr1A 88.419 544 31 10 7502 8021 47805877 47806412 2.000000e-175 627.0
7 TraesCS1D01G066100 chr1A 77.361 667 109 32 44 680 3641905 3642559 2.900000e-94 357.0
8 TraesCS1D01G066100 chr1A 85.449 323 20 10 8035 8341 47806462 47806773 2.290000e-80 311.0
9 TraesCS1D01G066100 chr1A 84.375 224 17 9 2054 2274 47800586 47800794 4.000000e-48 204.0
10 TraesCS1D01G066100 chr1B 93.709 2766 69 13 4635 7375 67537616 67540301 0.000000e+00 4047.0
11 TraesCS1D01G066100 chr1B 95.760 1934 59 13 2714 4635 67535611 67537533 0.000000e+00 3096.0
12 TraesCS1D01G066100 chr1B 91.850 1043 53 14 802 1817 67533575 67534612 0.000000e+00 1426.0
13 TraesCS1D01G066100 chr1B 97.512 643 16 0 2189 2831 67534969 67535611 0.000000e+00 1099.0
14 TraesCS1D01G066100 chr1B 91.370 533 23 10 7498 8021 67540566 67541084 0.000000e+00 708.0
15 TraesCS1D01G066100 chr1B 93.454 443 23 2 1920 2359 67534616 67535055 0.000000e+00 652.0
16 TraesCS1D01G066100 chr1B 91.413 361 20 6 8035 8388 67541138 67541494 1.280000e-132 484.0
17 TraesCS1D01G066100 chr1B 85.811 148 8 6 679 818 67533320 67533462 2.460000e-30 145.0
18 TraesCS1D01G066100 chr1B 82.270 141 9 8 7361 7499 67540394 67540520 3.230000e-19 108.0
19 TraesCS1D01G066100 chr5A 91.787 1315 62 23 4635 5945 456503206 456504478 0.000000e+00 1788.0
20 TraesCS1D01G066100 chr5A 93.241 1006 50 12 3590 4580 456502116 456503118 0.000000e+00 1465.0
21 TraesCS1D01G066100 chr5A 93.906 640 28 7 3590 4219 474538146 474538784 0.000000e+00 955.0
22 TraesCS1D01G066100 chr5A 92.661 654 38 6 5618 6266 474539220 474539868 0.000000e+00 933.0
23 TraesCS1D01G066100 chr5A 94.860 428 19 1 5145 5569 474538796 474539223 0.000000e+00 665.0
24 TraesCS1D01G066100 chr5A 92.982 285 17 3 6814 7097 427869712 427869994 6.100000e-111 412.0
25 TraesCS1D01G066100 chr5A 92.672 232 7 5 6263 6493 474540181 474540403 8.180000e-85 326.0
26 TraesCS1D01G066100 chr5A 81.325 332 49 10 6 330 666693501 666693826 3.030000e-64 257.0
27 TraesCS1D01G066100 chr5A 94.898 98 4 1 6666 6762 474540593 474540690 1.470000e-32 152.0
28 TraesCS1D01G066100 chr5A 83.750 160 8 7 7396 7554 427870129 427870271 1.480000e-27 135.0
29 TraesCS1D01G066100 chr5A 89.474 95 8 1 3693 3785 444560855 444560949 1.490000e-22 119.0
30 TraesCS1D01G066100 chr5A 85.333 75 4 1 7277 7351 427870050 427870117 4.230000e-08 71.3
31 TraesCS1D01G066100 chr5D 91.635 1315 55 19 4635 5945 371443563 371444826 0.000000e+00 1768.0
32 TraesCS1D01G066100 chr5D 93.819 1003 47 10 3590 4580 371442475 371443474 0.000000e+00 1495.0
33 TraesCS1D01G066100 chr5D 91.148 723 32 11 6377 7097 371468131 371468823 0.000000e+00 952.0
34 TraesCS1D01G066100 chr5D 92.551 443 26 4 5947 6386 371465343 371465781 5.570000e-176 628.0
35 TraesCS1D01G066100 chr5D 81.659 229 34 8 456 680 531657421 531657645 5.210000e-42 183.0
36 TraesCS1D01G066100 chr5D 95.455 44 2 0 7277 7320 371468848 371468891 4.230000e-08 71.3
37 TraesCS1D01G066100 chr5B 78.644 693 118 22 3 680 80635450 80636127 4.690000e-117 433.0
38 TraesCS1D01G066100 chr5B 91.489 94 8 0 4542 4635 694912685 694912592 6.880000e-26 130.0
39 TraesCS1D01G066100 chr5B 90.426 94 9 0 4542 4635 694734159 694734066 3.200000e-24 124.0
40 TraesCS1D01G066100 chr3D 79.179 682 97 28 6 652 334638907 334639578 1.690000e-116 431.0
41 TraesCS1D01G066100 chr3D 81.273 534 74 19 6 536 393069243 393068733 7.900000e-110 409.0
42 TraesCS1D01G066100 chr3D 77.580 562 93 27 9 557 592808136 592807595 8.240000e-80 309.0
43 TraesCS1D01G066100 chr6B 84.687 431 35 12 5465 5894 711737127 711737527 1.320000e-107 401.0
44 TraesCS1D01G066100 chr6B 78.898 635 80 30 90 680 123839729 123839105 1.720000e-101 381.0
45 TraesCS1D01G066100 chr6B 88.889 135 11 3 5296 5426 711736986 711737120 6.790000e-36 163.0
46 TraesCS1D01G066100 chr6B 92.632 95 7 0 4541 4635 30306966 30307060 4.110000e-28 137.0
47 TraesCS1D01G066100 chr2A 79.091 660 81 30 6 640 726769706 726769079 1.320000e-107 401.0
48 TraesCS1D01G066100 chr2A 78.883 573 82 26 6 552 749658880 749658321 1.350000e-92 351.0
49 TraesCS1D01G066100 chr2D 78.398 699 87 37 10 680 512839145 512838483 6.150000e-106 396.0
50 TraesCS1D01G066100 chr2D 78.492 358 47 17 201 536 109728574 109728225 3.090000e-49 207.0
51 TraesCS1D01G066100 chr6A 84.223 431 38 11 5465 5895 613089975 613090375 7.950000e-105 392.0
52 TraesCS1D01G066100 chr6A 88.281 128 12 2 5302 5426 613089841 613089968 5.280000e-32 150.0
53 TraesCS1D01G066100 chr6A 86.139 101 12 2 3679 3778 33306992 33306893 3.230000e-19 108.0
54 TraesCS1D01G066100 chr7D 79.892 557 89 19 6 552 618768491 618767948 3.700000e-103 387.0
55 TraesCS1D01G066100 chr7D 91.579 95 8 0 4541 4635 537285752 537285658 1.910000e-26 132.0
56 TraesCS1D01G066100 chr4A 77.856 709 94 40 6 680 614421606 614420927 1.720000e-101 381.0
57 TraesCS1D01G066100 chr3B 76.835 695 99 36 6 651 433686361 433687042 1.360000e-87 335.0
58 TraesCS1D01G066100 chr3B 85.393 89 13 0 3690 3778 428702187 428702275 9.030000e-15 93.5
59 TraesCS1D01G066100 chr7A 78.030 528 93 21 30 553 146754798 146754290 2.290000e-80 311.0
60 TraesCS1D01G066100 chr7A 92.473 93 7 0 4543 4635 105169738 105169830 5.320000e-27 134.0
61 TraesCS1D01G066100 chr4B 79.226 491 67 18 200 684 466690822 466691283 8.240000e-80 309.0
62 TraesCS1D01G066100 chr4B 92.632 95 7 0 4541 4635 142521062 142520968 4.110000e-28 137.0
63 TraesCS1D01G066100 chr4B 91.667 96 7 1 4539 4634 672039771 672039677 1.910000e-26 132.0
64 TraesCS1D01G066100 chrUn 75.249 703 127 35 11 686 29209219 29208537 2.980000e-74 291.0
65 TraesCS1D01G066100 chr2B 83.193 238 35 5 446 680 548669231 548669466 6.650000e-51 213.0
66 TraesCS1D01G066100 chr4D 91.579 95 8 0 4541 4635 100229657 100229563 1.910000e-26 132.0
67 TraesCS1D01G066100 chr3A 86.905 84 11 0 3695 3778 358268437 358268354 2.510000e-15 95.3


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 TraesCS1D01G066100 chr1D 47871946 47880396 8450 False 15607.000000 15607 100.000000 1 8451 1 chr1D.!!$F1 8450
1 TraesCS1D01G066100 chr1D 475528781 475529446 665 True 396.000000 396 78.192000 6 680 1 chr1D.!!$R1 674
2 TraesCS1D01G066100 chr1A 47798802 47806773 7971 False 1912.333333 4759 89.476000 363 8341 6 chr1A.!!$F2 7978
3 TraesCS1D01G066100 chr1A 3641905 3642559 654 False 357.000000 357 77.361000 44 680 1 chr1A.!!$F1 636
4 TraesCS1D01G066100 chr1B 67533320 67541494 8174 False 1307.222222 4047 91.461000 679 8388 9 chr1B.!!$F1 7709
5 TraesCS1D01G066100 chr5A 456502116 456504478 2362 False 1626.500000 1788 92.514000 3590 5945 2 chr5A.!!$F4 2355
6 TraesCS1D01G066100 chr5A 474538146 474540690 2544 False 606.200000 955 93.799400 3590 6762 5 chr5A.!!$F5 3172
7 TraesCS1D01G066100 chr5A 427869712 427870271 559 False 206.100000 412 87.355000 6814 7554 3 chr5A.!!$F3 740
8 TraesCS1D01G066100 chr5D 371442475 371444826 2351 False 1631.500000 1768 92.727000 3590 5945 2 chr5D.!!$F2 2355
9 TraesCS1D01G066100 chr5D 371465343 371468891 3548 False 550.433333 952 93.051333 5947 7320 3 chr5D.!!$F3 1373
10 TraesCS1D01G066100 chr5B 80635450 80636127 677 False 433.000000 433 78.644000 3 680 1 chr5B.!!$F1 677
11 TraesCS1D01G066100 chr3D 334638907 334639578 671 False 431.000000 431 79.179000 6 652 1 chr3D.!!$F1 646
12 TraesCS1D01G066100 chr3D 393068733 393069243 510 True 409.000000 409 81.273000 6 536 1 chr3D.!!$R1 530
13 TraesCS1D01G066100 chr3D 592807595 592808136 541 True 309.000000 309 77.580000 9 557 1 chr3D.!!$R2 548
14 TraesCS1D01G066100 chr6B 123839105 123839729 624 True 381.000000 381 78.898000 90 680 1 chr6B.!!$R1 590
15 TraesCS1D01G066100 chr6B 711736986 711737527 541 False 282.000000 401 86.788000 5296 5894 2 chr6B.!!$F2 598
16 TraesCS1D01G066100 chr2A 726769079 726769706 627 True 401.000000 401 79.091000 6 640 1 chr2A.!!$R1 634
17 TraesCS1D01G066100 chr2A 749658321 749658880 559 True 351.000000 351 78.883000 6 552 1 chr2A.!!$R2 546
18 TraesCS1D01G066100 chr2D 512838483 512839145 662 True 396.000000 396 78.398000 10 680 1 chr2D.!!$R2 670
19 TraesCS1D01G066100 chr6A 613089841 613090375 534 False 271.000000 392 86.252000 5302 5895 2 chr6A.!!$F1 593
20 TraesCS1D01G066100 chr7D 618767948 618768491 543 True 387.000000 387 79.892000 6 552 1 chr7D.!!$R2 546
21 TraesCS1D01G066100 chr4A 614420927 614421606 679 True 381.000000 381 77.856000 6 680 1 chr4A.!!$R1 674
22 TraesCS1D01G066100 chr3B 433686361 433687042 681 False 335.000000 335 76.835000 6 651 1 chr3B.!!$F2 645
23 TraesCS1D01G066100 chr7A 146754290 146754798 508 True 311.000000 311 78.030000 30 553 1 chr7A.!!$R1 523
24 TraesCS1D01G066100 chrUn 29208537 29209219 682 True 291.000000 291 75.249000 11 686 1 chrUn.!!$R1 675

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
718 913 0.472471 ACGGTGGCTTTTCCTCAAGA 59.528 50.000 0.00 0.00 35.26 3.02 F
2286 2750 1.064685 GGGATCCTCGTTTGGTTCCAT 60.065 52.381 12.58 0.00 44.08 3.41 F
2598 3062 1.202651 AGTGTCTTCCCCTGTTTGACG 60.203 52.381 0.00 0.00 0.00 4.35 F
3107 3688 1.301677 GGCTGCAAGTGGTACTCTGC 61.302 60.000 0.50 0.00 34.84 4.26 F
3129 3710 1.526575 CCAGGAGCACGCCATTTTGT 61.527 55.000 0.00 0.00 0.00 2.83 F
4974 5659 1.214305 AGCCCCCAGTGAATGCCTTA 61.214 55.000 0.00 0.00 0.00 2.69 F
6664 10136 1.051008 TCACCATCATCAGGATCCGG 58.949 55.000 5.98 5.68 32.57 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 3062 0.031994 GTTCACCCAACACATGCACC 59.968 55.000 0.00 0.00 34.76 5.01 R
3107 3688 2.826777 AAATGGCGTGCTCCTGGGAG 62.827 60.000 11.97 11.97 44.56 4.30 R
3653 4234 4.154918 GCTGAAAATGTAAGAGACTGGGTG 59.845 45.833 0.00 0.00 0.00 4.61 R
4911 5596 1.787462 AAGCCCAAGGAGCTCTGCTT 61.787 55.000 14.64 15.81 39.88 3.91 R
5090 5776 3.054434 TGAGAATAATGGTGACTGGGGTG 60.054 47.826 0.00 0.00 0.00 4.61 R
6950 10424 1.371558 GCGGTCCTTGAACTCCACT 59.628 57.895 0.00 0.00 0.00 4.00 R
7655 11318 0.179067 ACGGCCGTGAAGAACAAGAA 60.179 50.000 33.75 0.00 0.00 2.52 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
114 122 8.599876 AAATGTTCGCAATTTTGAAAAGAAAC 57.400 26.923 0.00 0.00 0.00 2.78
268 301 6.224420 ACTGTTCGTGACTTACAAAATAGC 57.776 37.500 0.00 0.00 0.00 2.97
298 332 7.378966 TGATTTATAAAATGTTTGCCGGTTCA 58.621 30.769 1.90 0.00 0.00 3.18
334 389 9.438228 TCATGCATTTTAAAACATGTTCATGAT 57.562 25.926 21.83 4.90 40.57 2.45
389 482 8.880768 AAAATGTTCGTTGATTCTAGAAATCG 57.119 30.769 9.71 11.44 0.00 3.34
473 576 9.422196 GCAAATAGTATAAAGTGTTCACGAATC 57.578 33.333 0.00 0.00 0.00 2.52
519 644 8.967218 TGAAAATGCTCGAAAATCTGTAAAAAG 58.033 29.630 0.00 0.00 0.00 2.27
621 808 1.401530 CGATGCAGCAAAATATGGCG 58.598 50.000 1.53 0.00 34.54 5.69
644 831 6.127925 GCGATGGCCATTGAAGATTATGATTA 60.128 38.462 33.51 0.00 0.00 1.75
680 874 2.874751 GCACGGCCGTTTTGCTAT 59.125 55.556 32.11 0.00 33.26 2.97
686 880 1.268539 CGGCCGTTTTGCTATTGATCC 60.269 52.381 19.50 0.00 0.00 3.36
692 886 5.687285 GCCGTTTTGCTATTGATCCATAAAG 59.313 40.000 0.00 0.00 0.00 1.85
700 894 6.018262 TGCTATTGATCCATAAAGTGCGTTAC 60.018 38.462 0.00 0.00 0.00 2.50
717 912 2.178912 TACGGTGGCTTTTCCTCAAG 57.821 50.000 0.00 0.00 35.26 3.02
718 913 0.472471 ACGGTGGCTTTTCCTCAAGA 59.528 50.000 0.00 0.00 35.26 3.02
743 945 3.418684 AAACCACGGCACTCTTAGATT 57.581 42.857 0.00 0.00 0.00 2.40
751 953 3.131223 CGGCACTCTTAGATTGGAGAGAA 59.869 47.826 7.32 0.00 41.49 2.87
752 954 4.438148 GGCACTCTTAGATTGGAGAGAAC 58.562 47.826 7.32 0.00 41.49 3.01
753 955 4.438148 GCACTCTTAGATTGGAGAGAACC 58.562 47.826 7.32 0.00 41.49 3.62
754 956 4.161377 GCACTCTTAGATTGGAGAGAACCT 59.839 45.833 7.32 0.00 41.49 3.50
755 957 5.337975 GCACTCTTAGATTGGAGAGAACCTT 60.338 44.000 7.32 0.00 41.49 3.50
910 1244 3.094572 TGTAAGCTACTGTACCACTCCC 58.905 50.000 0.00 0.00 0.00 4.30
1187 1524 1.884756 GCGATTCTATCTACTCGCGG 58.115 55.000 6.13 0.00 45.65 6.46
1217 1554 1.516603 GTCAAGTCCGACGCTAGGC 60.517 63.158 0.00 0.00 0.00 3.93
1381 1727 1.885850 AACCGCGTGCGTTTTCTCT 60.886 52.632 13.70 0.00 37.81 3.10
1382 1728 1.828331 AACCGCGTGCGTTTTCTCTC 61.828 55.000 13.70 0.00 37.81 3.20
1484 1842 1.173913 GGTCCCACTGTATTTGCACC 58.826 55.000 0.00 0.00 0.00 5.01
1494 1852 3.411446 TGTATTTGCACCTGTTCCTCTG 58.589 45.455 0.00 0.00 0.00 3.35
1495 1853 2.957402 ATTTGCACCTGTTCCTCTGA 57.043 45.000 0.00 0.00 0.00 3.27
1556 1916 5.688621 GGTTCGTTTGTTGGGTTTTCTTATC 59.311 40.000 0.00 0.00 0.00 1.75
1642 2010 4.283722 AGCGGGGTAGATAAACTAATGAGG 59.716 45.833 0.00 0.00 32.49 3.86
1675 2043 6.075315 AGAGTTAACAAATTTGGTAGGCCTT 58.925 36.000 21.74 7.96 30.99 4.35
1715 2083 9.860898 AAGAATTACTTTATGGTTTCTGAATGC 57.139 29.630 0.00 0.00 34.94 3.56
1752 2120 1.609208 AATGCACCCACTCAGTGAAC 58.391 50.000 6.30 0.00 37.42 3.18
1819 2187 2.529780 TGCAATTTTGGCAAGGAGTG 57.470 45.000 0.00 4.49 38.54 3.51
1837 2205 4.368808 CACCGCGTGCCTTCGTTG 62.369 66.667 4.92 0.00 0.00 4.10
1869 2237 5.877012 CCTAGCAATTAGTGTCTTGTGTGAT 59.123 40.000 0.00 0.00 0.00 3.06
1873 2241 5.853282 GCAATTAGTGTCTTGTGTGATTGAC 59.147 40.000 0.00 0.00 0.00 3.18
1913 2281 4.819630 TGCTTAGGCGTTAATTAGGGATTG 59.180 41.667 0.00 0.00 42.25 2.67
1914 2282 4.820173 GCTTAGGCGTTAATTAGGGATTGT 59.180 41.667 0.00 0.00 0.00 2.71
1915 2283 5.298527 GCTTAGGCGTTAATTAGGGATTGTT 59.701 40.000 0.00 0.00 0.00 2.83
1916 2284 6.484308 GCTTAGGCGTTAATTAGGGATTGTTA 59.516 38.462 0.00 0.00 0.00 2.41
1917 2285 7.012610 GCTTAGGCGTTAATTAGGGATTGTTAA 59.987 37.037 0.00 0.00 0.00 2.01
1918 2286 6.937436 AGGCGTTAATTAGGGATTGTTAAG 57.063 37.500 0.00 0.00 0.00 1.85
1919 2287 6.655930 AGGCGTTAATTAGGGATTGTTAAGA 58.344 36.000 0.00 0.00 0.00 2.10
1920 2288 7.287810 AGGCGTTAATTAGGGATTGTTAAGAT 58.712 34.615 0.00 0.00 0.00 2.40
1921 2289 7.778382 AGGCGTTAATTAGGGATTGTTAAGATT 59.222 33.333 0.00 0.00 0.00 2.40
2208 2660 1.597027 CCTCGTTTGGTTCCACGCT 60.597 57.895 0.00 0.00 36.32 5.07
2245 2700 3.874383 TTTCCATCCTCTGGTTTCACA 57.126 42.857 0.00 0.00 46.08 3.58
2286 2750 1.064685 GGGATCCTCGTTTGGTTCCAT 60.065 52.381 12.58 0.00 44.08 3.41
2299 2763 2.297895 TTCCATGCCGGTAGCCACT 61.298 57.895 1.90 0.00 42.71 4.00
2349 2813 1.673665 CTTCCTCTGGTGCAGCCAC 60.674 63.158 14.36 0.00 43.61 5.01
2479 2943 1.270907 AGTAGCCTTCTGTCCACCAG 58.729 55.000 0.00 0.00 42.97 4.00
2598 3062 1.202651 AGTGTCTTCCCCTGTTTGACG 60.203 52.381 0.00 0.00 0.00 4.35
2861 3442 8.450385 TTTGACGTTTTTGGTTAACAGTTAAG 57.550 30.769 8.10 0.00 0.00 1.85
2862 3443 7.143514 TGACGTTTTTGGTTAACAGTTAAGT 57.856 32.000 8.10 0.00 0.00 2.24
2863 3444 8.261492 TGACGTTTTTGGTTAACAGTTAAGTA 57.739 30.769 8.10 0.00 0.00 2.24
3030 3611 4.870991 GCTGATACTACAGGGTCTTTTGTC 59.129 45.833 0.00 0.00 38.22 3.18
3060 3641 6.331369 TGGAAGATCTGTTTTTGAATGGAC 57.669 37.500 0.00 0.00 0.00 4.02
3099 3680 2.366916 AGCTATAGTAGGCTGCAAGTGG 59.633 50.000 5.14 0.00 37.41 4.00
3107 3688 1.301677 GGCTGCAAGTGGTACTCTGC 61.302 60.000 0.50 0.00 34.84 4.26
3129 3710 1.526575 CCAGGAGCACGCCATTTTGT 61.527 55.000 0.00 0.00 0.00 2.83
3935 4527 9.832445 GATCTACTTTGTCTATTTGTTATGGGA 57.168 33.333 0.00 0.00 0.00 4.37
3967 4559 7.717875 TGCCTTCTATACAATAACAATACACCC 59.282 37.037 0.00 0.00 0.00 4.61
4056 4648 2.771089 GCTGGTCAAATGAGTCTGACA 58.229 47.619 10.88 0.00 43.11 3.58
4107 4699 8.617290 AGGTTTAGTTGACTTATTGGTACTTG 57.383 34.615 0.00 0.00 0.00 3.16
4201 4795 9.950680 TTCACTGTTTCTTTTTCACATCTTATC 57.049 29.630 0.00 0.00 0.00 1.75
4343 4937 3.055891 TCATGAGGAGCTTCGACATGAAA 60.056 43.478 24.96 11.58 42.38 2.69
4390 4984 9.614792 GGTAAGATATTGAGTATTTCCAACACT 57.385 33.333 0.00 0.00 0.00 3.55
4467 5062 3.421919 TGCTGTGATGGTCAAGATCAA 57.578 42.857 0.00 0.00 31.65 2.57
4505 5100 4.534103 AGGAGAAGGATAACTTGCAACTCT 59.466 41.667 0.00 0.00 40.21 3.24
4911 5596 4.204012 CAGGTGGTTTCAACTTACAGGAA 58.796 43.478 0.00 0.00 39.26 3.36
4919 5604 3.403038 TCAACTTACAGGAAAGCAGAGC 58.597 45.455 0.00 0.00 0.00 4.09
4974 5659 1.214305 AGCCCCCAGTGAATGCCTTA 61.214 55.000 0.00 0.00 0.00 2.69
5011 5696 7.177216 TCAAGCCATCATTGTTTTCATACTCTT 59.823 33.333 0.00 0.00 0.00 2.85
5135 5824 1.153289 CTCCCGAGCCAATCCACAG 60.153 63.158 0.00 0.00 0.00 3.66
5247 5939 8.741101 CAGATACATCTTCTGCTGTAAGTATC 57.259 38.462 0.00 0.00 37.76 2.24
5367 6060 5.606505 TGTTTAGCCAAAATTTGTTCCCTC 58.393 37.500 4.92 0.00 0.00 4.30
5395 6090 5.923733 TCTACTCAATCTGGAGGAAGTTC 57.076 43.478 0.00 0.00 39.27 3.01
6034 6733 5.946298 TCGTATCAGTTTCTTAGCTTTCGA 58.054 37.500 0.00 0.00 0.00 3.71
6498 9877 2.653890 CAATTCTTCACTGGCACGTTG 58.346 47.619 0.00 0.00 0.00 4.10
6515 9902 4.393062 CACGTTGCAATGAAGAATCCTAGT 59.607 41.667 25.13 0.00 0.00 2.57
6549 9936 4.072131 GTTCTCCATTAGCACTTGTGGAA 58.928 43.478 2.81 0.00 40.03 3.53
6664 10136 1.051008 TCACCATCATCAGGATCCGG 58.949 55.000 5.98 5.68 32.57 5.14
6839 10312 2.632643 TGCTGCACGAGAAAGCAAT 58.367 47.368 0.00 0.00 43.65 3.56
6935 10409 2.039084 AGAAACCGATGTGAGGAAGCTT 59.961 45.455 0.00 0.00 0.00 3.74
6950 10424 2.988010 AGCTTGACATCGCTTCCATA 57.012 45.000 0.00 0.00 31.17 2.74
7253 10727 7.577303 TCTTGGCAATATTAAGATTCCAGTCT 58.423 34.615 0.00 0.00 0.00 3.24
7256 10730 7.345691 TGGCAATATTAAGATTCCAGTCTCAA 58.654 34.615 8.84 0.00 0.00 3.02
7257 10731 7.500227 TGGCAATATTAAGATTCCAGTCTCAAG 59.500 37.037 8.84 0.00 0.00 3.02
7258 10732 7.716998 GGCAATATTAAGATTCCAGTCTCAAGA 59.283 37.037 0.00 0.00 0.00 3.02
7259 10733 9.282569 GCAATATTAAGATTCCAGTCTCAAGAT 57.717 33.333 0.00 0.00 0.00 2.40
7263 10737 8.789767 ATTAAGATTCCAGTCTCAAGATAGGA 57.210 34.615 0.76 0.76 0.00 2.94
7264 10738 6.729690 AAGATTCCAGTCTCAAGATAGGAG 57.270 41.667 4.33 0.00 33.48 3.69
7265 10739 6.024563 AGATTCCAGTCTCAAGATAGGAGA 57.975 41.667 0.00 0.00 39.01 3.71
7266 10740 6.070656 AGATTCCAGTCTCAAGATAGGAGAG 58.929 44.000 0.00 0.00 41.77 3.20
7267 10741 4.871871 TCCAGTCTCAAGATAGGAGAGT 57.128 45.455 0.00 0.00 43.95 3.24
7383 10890 5.649782 AACAATTTTAGATCTGTGGCTGG 57.350 39.130 5.18 0.00 0.00 4.85
7386 11002 2.698855 TTTAGATCTGTGGCTGGAGC 57.301 50.000 5.18 0.00 41.14 4.70
7400 11016 4.467082 TGGCTGGAGCATATTTGATTGTTT 59.533 37.500 0.20 0.00 44.36 2.83
7402 11018 4.807304 GCTGGAGCATATTTGATTGTTTGG 59.193 41.667 0.00 0.00 41.59 3.28
7409 11025 5.291614 GCATATTTGATTGTTTGGCGTTGAT 59.708 36.000 0.00 0.00 0.00 2.57
7418 11034 3.380004 TGTTTGGCGTTGATTGATATCCC 59.620 43.478 0.00 0.00 0.00 3.85
7618 11281 2.047655 GCGGTGGTCCACGAATCA 60.048 61.111 15.93 0.00 34.83 2.57
7654 11317 4.498241 TGATCTTGTCTTCTTCACCGATG 58.502 43.478 0.00 0.00 0.00 3.84
7655 11318 4.021104 TGATCTTGTCTTCTTCACCGATGT 60.021 41.667 0.00 0.00 0.00 3.06
7666 11329 4.750098 TCTTCACCGATGTTCTTGTTCTTC 59.250 41.667 0.00 0.00 0.00 2.87
7667 11330 4.066646 TCACCGATGTTCTTGTTCTTCA 57.933 40.909 0.00 0.00 0.00 3.02
7668 11331 3.807622 TCACCGATGTTCTTGTTCTTCAC 59.192 43.478 0.00 0.00 0.00 3.18
7669 11332 2.800544 ACCGATGTTCTTGTTCTTCACG 59.199 45.455 0.00 0.00 0.00 4.35
7670 11333 2.157668 CCGATGTTCTTGTTCTTCACGG 59.842 50.000 0.00 0.00 0.00 4.94
7671 11334 2.411547 CGATGTTCTTGTTCTTCACGGC 60.412 50.000 0.00 0.00 0.00 5.68
7710 11379 1.067295 TGTTGGTTGATCCTCTGCCT 58.933 50.000 0.00 0.00 37.07 4.75
7811 11485 1.960689 CAGGCTAGCTACCTTCCTCTC 59.039 57.143 15.72 0.00 34.42 3.20
7823 11497 6.041069 GCTACCTTCCTCTCTAAGCAAGATAA 59.959 42.308 0.00 0.00 32.41 1.75
7824 11498 7.256154 GCTACCTTCCTCTCTAAGCAAGATAAT 60.256 40.741 0.00 0.00 32.41 1.28
7826 11500 8.554490 ACCTTCCTCTCTAAGCAAGATAATAA 57.446 34.615 0.00 0.00 32.41 1.40
7828 11502 9.651913 CCTTCCTCTCTAAGCAAGATAATAATC 57.348 37.037 0.00 0.00 32.41 1.75
7890 11565 3.072476 ACAGCCGGGTGTATTTATATGCT 59.928 43.478 36.56 8.39 0.00 3.79
7958 11644 2.100197 CGGTGTGGACTTATCTCCTCA 58.900 52.381 0.00 0.00 32.53 3.86
8012 11701 3.495806 GGAGAGGATTCGGAAGCAATCAT 60.496 47.826 8.39 0.00 32.75 2.45
8021 11710 2.095853 CGGAAGCAATCATAAACAGCGT 59.904 45.455 0.00 0.00 0.00 5.07
8131 11868 2.458006 CTTTCGCCGTTTGTGCCTCC 62.458 60.000 0.00 0.00 0.00 4.30
8133 11870 3.055719 CGCCGTTTGTGCCTCCAT 61.056 61.111 0.00 0.00 0.00 3.41
8191 11935 5.915758 CACTGAGGCGTCTATATTTGTCTAC 59.084 44.000 8.06 0.00 0.00 2.59
8293 12041 4.641541 CCATGTATGCTTTGGTGATTCTGA 59.358 41.667 0.00 0.00 0.00 3.27
8322 12074 3.869832 GCGAGGTTAAGTAATGGAAGGAC 59.130 47.826 0.00 0.00 0.00 3.85
8323 12075 4.110482 CGAGGTTAAGTAATGGAAGGACG 58.890 47.826 0.00 0.00 0.00 4.79
8382 12134 4.218417 ACGCTGATAATTGAGCAAACCTTT 59.782 37.500 0.00 0.00 34.69 3.11
8392 12144 3.778954 AGCAAACCTTTAGCTCAGACT 57.221 42.857 0.00 0.00 32.05 3.24
8393 12145 4.092116 AGCAAACCTTTAGCTCAGACTT 57.908 40.909 0.00 0.00 32.05 3.01
8394 12146 4.464947 AGCAAACCTTTAGCTCAGACTTT 58.535 39.130 0.00 0.00 32.05 2.66
8395 12147 4.889995 AGCAAACCTTTAGCTCAGACTTTT 59.110 37.500 0.00 0.00 32.05 2.27
8396 12148 5.360999 AGCAAACCTTTAGCTCAGACTTTTT 59.639 36.000 0.00 0.00 32.05 1.94
8397 12149 5.460091 GCAAACCTTTAGCTCAGACTTTTTG 59.540 40.000 0.00 0.00 0.00 2.44
8398 12150 4.837896 ACCTTTAGCTCAGACTTTTTGC 57.162 40.909 0.00 0.00 0.00 3.68
8399 12151 4.464947 ACCTTTAGCTCAGACTTTTTGCT 58.535 39.130 0.00 0.00 37.72 3.91
8400 12152 4.889995 ACCTTTAGCTCAGACTTTTTGCTT 59.110 37.500 0.00 0.00 35.47 3.91
8401 12153 5.218139 CCTTTAGCTCAGACTTTTTGCTTG 58.782 41.667 0.00 0.00 35.47 4.01
8402 12154 5.009010 CCTTTAGCTCAGACTTTTTGCTTGA 59.991 40.000 0.00 0.00 35.47 3.02
8403 12155 6.294397 CCTTTAGCTCAGACTTTTTGCTTGAT 60.294 38.462 0.00 0.00 35.47 2.57
8404 12156 7.094634 CCTTTAGCTCAGACTTTTTGCTTGATA 60.095 37.037 0.00 0.00 35.47 2.15
8405 12157 7.928307 TTAGCTCAGACTTTTTGCTTGATAT 57.072 32.000 0.00 0.00 35.47 1.63
8406 12158 9.448438 TTTAGCTCAGACTTTTTGCTTGATATA 57.552 29.630 0.00 0.00 35.47 0.86
8407 12159 7.313951 AGCTCAGACTTTTTGCTTGATATAC 57.686 36.000 0.00 0.00 0.00 1.47
8408 12160 6.317391 AGCTCAGACTTTTTGCTTGATATACC 59.683 38.462 0.00 0.00 0.00 2.73
8409 12161 6.317391 GCTCAGACTTTTTGCTTGATATACCT 59.683 38.462 0.00 0.00 0.00 3.08
8410 12162 7.615582 TCAGACTTTTTGCTTGATATACCTG 57.384 36.000 0.00 0.00 0.00 4.00
8411 12163 7.394016 TCAGACTTTTTGCTTGATATACCTGA 58.606 34.615 0.00 0.00 0.00 3.86
8412 12164 8.049117 TCAGACTTTTTGCTTGATATACCTGAT 58.951 33.333 0.00 0.00 0.00 2.90
8413 12165 9.330063 CAGACTTTTTGCTTGATATACCTGATA 57.670 33.333 0.00 0.00 0.00 2.15
8422 12174 9.987272 TGCTTGATATACCTGATATATACATGC 57.013 33.333 0.00 0.00 36.72 4.06
8423 12175 9.133627 GCTTGATATACCTGATATATACATGCG 57.866 37.037 0.00 0.00 36.72 4.73
8430 12182 9.755804 ATACCTGATATATACATGCGAATGAAG 57.244 33.333 11.32 0.00 0.00 3.02
8431 12183 6.536582 ACCTGATATATACATGCGAATGAAGC 59.463 38.462 11.32 0.00 0.00 3.86
8432 12184 6.760298 CCTGATATATACATGCGAATGAAGCT 59.240 38.462 11.32 0.00 35.28 3.74
8433 12185 7.922811 CCTGATATATACATGCGAATGAAGCTA 59.077 37.037 11.32 0.00 35.28 3.32
8434 12186 8.634475 TGATATATACATGCGAATGAAGCTAC 57.366 34.615 11.32 0.00 35.28 3.58
8435 12187 8.470002 TGATATATACATGCGAATGAAGCTACT 58.530 33.333 11.32 0.00 35.28 2.57
8436 12188 6.957984 ATATACATGCGAATGAAGCTACTG 57.042 37.500 11.32 0.00 35.28 2.74
8437 12189 3.251479 ACATGCGAATGAAGCTACTGA 57.749 42.857 11.32 0.00 35.28 3.41
8438 12190 2.932614 ACATGCGAATGAAGCTACTGAC 59.067 45.455 11.32 0.00 35.28 3.51
8439 12191 2.741759 TGCGAATGAAGCTACTGACA 57.258 45.000 0.00 0.00 35.28 3.58
8440 12192 2.337583 TGCGAATGAAGCTACTGACAC 58.662 47.619 0.00 0.00 35.28 3.67
8441 12193 2.288763 TGCGAATGAAGCTACTGACACA 60.289 45.455 0.00 0.00 35.28 3.72
8442 12194 2.736721 GCGAATGAAGCTACTGACACAA 59.263 45.455 0.00 0.00 0.00 3.33
8443 12195 3.186409 GCGAATGAAGCTACTGACACAAA 59.814 43.478 0.00 0.00 0.00 2.83
8444 12196 4.667668 GCGAATGAAGCTACTGACACAAAG 60.668 45.833 0.00 0.00 0.00 2.77
8445 12197 4.667668 CGAATGAAGCTACTGACACAAAGC 60.668 45.833 0.00 0.00 35.16 3.51
8446 12198 2.494059 TGAAGCTACTGACACAAAGCC 58.506 47.619 0.00 0.00 35.54 4.35
8447 12199 1.807142 GAAGCTACTGACACAAAGCCC 59.193 52.381 0.00 0.00 35.54 5.19
8448 12200 0.320771 AGCTACTGACACAAAGCCCG 60.321 55.000 0.00 0.00 35.54 6.13
8449 12201 0.602905 GCTACTGACACAAAGCCCGT 60.603 55.000 0.00 0.00 0.00 5.28
8450 12202 1.429463 CTACTGACACAAAGCCCGTC 58.571 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 261 8.812329 TCACGAACAGTTTTTGAATATTTTTGG 58.188 29.630 0.00 0.00 0.00 3.28
231 263 9.581099 AGTCACGAACAGTTTTTGAATATTTTT 57.419 25.926 0.00 0.00 0.00 1.94
236 268 8.199176 TGTAAGTCACGAACAGTTTTTGAATA 57.801 30.769 0.00 0.00 0.00 1.75
501 625 7.110216 CGTGAACACTTTTTACAGATTTTCGAG 59.890 37.037 3.51 0.00 0.00 4.04
644 831 0.511221 CGTTGCGACGTGAGGAAAAT 59.489 50.000 18.62 0.00 44.08 1.82
680 874 3.619483 CCGTAACGCACTTTATGGATCAA 59.381 43.478 0.00 0.00 39.61 2.57
686 880 1.201987 GCCACCGTAACGCACTTTATG 60.202 52.381 0.00 0.00 0.00 1.90
692 886 0.385098 GAAAAGCCACCGTAACGCAC 60.385 55.000 0.00 0.00 0.00 5.34
700 894 1.604604 TTCTTGAGGAAAAGCCACCG 58.395 50.000 0.00 0.00 40.02 4.94
736 938 7.436673 CGAATGTAAGGTTCTCTCCAATCTAAG 59.563 40.741 0.00 0.00 0.00 2.18
743 945 3.170717 ACCGAATGTAAGGTTCTCTCCA 58.829 45.455 0.00 0.00 37.49 3.86
751 953 6.045072 TGAAAGATGTACCGAATGTAAGGT 57.955 37.500 0.00 0.00 44.08 3.50
752 954 6.538742 ACATGAAAGATGTACCGAATGTAAGG 59.461 38.462 0.00 0.00 0.00 2.69
753 955 7.539712 ACATGAAAGATGTACCGAATGTAAG 57.460 36.000 0.00 0.00 0.00 2.34
754 956 7.065324 GGAACATGAAAGATGTACCGAATGTAA 59.935 37.037 0.00 0.00 0.00 2.41
755 957 6.537301 GGAACATGAAAGATGTACCGAATGTA 59.463 38.462 0.00 0.00 0.00 2.29
1101 1438 1.224870 GGCTTACAGGGAGGAAGGC 59.775 63.158 0.00 0.00 38.40 4.35
1187 1524 1.615502 GACTTGACCTACGAGCGAAC 58.384 55.000 0.00 0.00 33.49 3.95
1398 1756 1.117234 ACAAACGAAAAATCGTGCGC 58.883 45.000 0.00 0.00 46.41 6.09
1463 1821 0.958382 TGCAAATACAGTGGGACCGC 60.958 55.000 0.00 0.00 0.00 5.68
1474 1832 3.674997 TCAGAGGAACAGGTGCAAATAC 58.325 45.455 0.00 0.00 0.00 1.89
1484 1842 3.862267 CGCTTCTAACATCAGAGGAACAG 59.138 47.826 0.00 0.00 0.00 3.16
1494 1852 4.806247 ACATAGAACAGCGCTTCTAACATC 59.194 41.667 19.78 6.37 36.54 3.06
1495 1853 4.568359 CACATAGAACAGCGCTTCTAACAT 59.432 41.667 19.78 5.23 36.54 2.71
1619 1979 4.283722 CCTCATTAGTTTATCTACCCCGCT 59.716 45.833 0.00 0.00 0.00 5.52
1666 2034 0.106894 CTCCGGATTGAAGGCCTACC 59.893 60.000 5.16 0.96 0.00 3.18
1675 2043 4.469945 AGTAATTCTTCACCTCCGGATTGA 59.530 41.667 3.57 8.36 0.00 2.57
1715 2083 3.782250 GCATTTTCTCATACGTCGTGCTG 60.782 47.826 8.47 5.81 0.00 4.41
1752 2120 2.628178 TCCGTCTATCCTGGCAGTTATG 59.372 50.000 14.43 0.00 0.00 1.90
1820 2188 4.368808 CAACGAAGGCACGCGGTG 62.369 66.667 12.47 7.75 41.36 4.94
1822 2190 4.072088 GACAACGAAGGCACGCGG 62.072 66.667 12.47 0.00 35.53 6.46
1834 2202 5.581085 CACTAATTGCTAGGTACCAGACAAC 59.419 44.000 15.94 0.00 31.14 3.32
1837 2205 5.127356 AGACACTAATTGCTAGGTACCAGAC 59.873 44.000 15.94 2.70 31.14 3.51
1869 2237 4.379394 GCATGGAAGATAAAACTGCGTCAA 60.379 41.667 0.00 0.00 0.00 3.18
1873 2241 4.361451 AAGCATGGAAGATAAAACTGCG 57.639 40.909 0.00 0.00 33.54 5.18
2028 2396 2.611292 GAGAACAATGATGAAGAGCCCG 59.389 50.000 0.00 0.00 0.00 6.13
2258 2713 1.987807 AACGAGGATCCCATGGCTGG 61.988 60.000 8.55 1.68 42.73 4.85
2299 2763 0.404040 ACGAGGATGGAAAAAGGCCA 59.596 50.000 5.01 0.00 40.24 5.36
2303 2767 3.059352 ACCAGACGAGGATGGAAAAAG 57.941 47.619 0.00 0.00 39.02 2.27
2349 2813 0.179062 CCAAGATGAAGAGGAGCCCG 60.179 60.000 0.00 0.00 0.00 6.13
2598 3062 0.031994 GTTCACCCAACACATGCACC 59.968 55.000 0.00 0.00 34.76 5.01
2861 3442 8.932791 TCATAAGTCACGAGGAAAGAAAAATAC 58.067 33.333 0.00 0.00 0.00 1.89
2862 3443 9.667107 ATCATAAGTCACGAGGAAAGAAAAATA 57.333 29.630 0.00 0.00 0.00 1.40
2863 3444 7.979444 TCATAAGTCACGAGGAAAGAAAAAT 57.021 32.000 0.00 0.00 0.00 1.82
2911 3492 9.468532 AGAGAAAATCAAAAGTCAATGCTAAAC 57.531 29.630 0.00 0.00 0.00 2.01
3060 3641 8.191446 ACTATAGCTGTTTATATAGCGTCCATG 58.809 37.037 0.00 0.00 42.72 3.66
3107 3688 2.826777 AAATGGCGTGCTCCTGGGAG 62.827 60.000 11.97 11.97 44.56 4.30
3350 3931 6.716628 ACATTGCCAAATAGTTCAGAGAAGAA 59.283 34.615 0.00 0.00 0.00 2.52
3351 3932 6.240894 ACATTGCCAAATAGTTCAGAGAAGA 58.759 36.000 0.00 0.00 0.00 2.87
3653 4234 4.154918 GCTGAAAATGTAAGAGACTGGGTG 59.845 45.833 0.00 0.00 0.00 4.61
3967 4559 9.307121 CTACTTCAATTACTAATCACCACTGAG 57.693 37.037 0.00 0.00 0.00 3.35
4056 4648 7.493367 TGAACCAACCGTATTCAAAGAAAAAT 58.507 30.769 0.00 0.00 29.56 1.82
4467 5062 4.346418 CCTTCTCCTGTGCATAACTCCTAT 59.654 45.833 0.00 0.00 0.00 2.57
4911 5596 1.787462 AAGCCCAAGGAGCTCTGCTT 61.787 55.000 14.64 15.81 39.88 3.91
4919 5604 3.749226 GAGGAATGATAAGCCCAAGGAG 58.251 50.000 0.00 0.00 0.00 3.69
4974 5659 3.499338 TGATGGCTTGACAGGATTTGTT 58.501 40.909 0.00 0.00 41.05 2.83
5090 5776 3.054434 TGAGAATAATGGTGACTGGGGTG 60.054 47.826 0.00 0.00 0.00 4.61
5135 5824 1.551883 AGCTTGAAAACCATGATGGCC 59.448 47.619 12.25 0.00 42.67 5.36
5321 6014 1.252904 GGCCTTGCTGCTTCCATCAA 61.253 55.000 0.00 0.00 0.00 2.57
5367 6060 5.994250 TCCTCCAGATTGAGTAGATTTTGG 58.006 41.667 0.00 0.00 0.00 3.28
5395 6090 1.803519 GCGACCGAAGAGCTGAGTG 60.804 63.158 0.00 0.00 0.00 3.51
6034 6733 9.298250 TCAGAAGTCTACAGAACAAACTAGTAT 57.702 33.333 0.00 0.00 0.00 2.12
6396 9773 6.017192 ACTCCTAGGAATCTTCACTGTAACA 58.983 40.000 13.77 0.00 0.00 2.41
6498 9877 6.458888 GGTTTGCTACTAGGATTCTTCATTGC 60.459 42.308 0.00 0.00 0.00 3.56
6515 9902 3.806949 ATGGAGAACTTGGGTTTGCTA 57.193 42.857 0.00 0.00 35.58 3.49
6664 10136 4.165372 TGATATACCCTTTCTGTTCCCCAC 59.835 45.833 0.00 0.00 0.00 4.61
6935 10409 2.107366 TCCACTATGGAAGCGATGTCA 58.893 47.619 0.00 0.00 45.00 3.58
6950 10424 1.371558 GCGGTCCTTGAACTCCACT 59.628 57.895 0.00 0.00 0.00 4.00
7253 10727 6.679542 TGGTATTGGTACTCTCCTATCTTGA 58.320 40.000 0.00 0.00 0.00 3.02
7256 10730 6.019748 CCATGGTATTGGTACTCTCCTATCT 58.980 44.000 2.57 0.00 31.74 1.98
7257 10731 5.337652 GCCATGGTATTGGTACTCTCCTATC 60.338 48.000 14.67 0.00 39.11 2.08
7258 10732 4.532521 GCCATGGTATTGGTACTCTCCTAT 59.467 45.833 14.67 0.00 39.11 2.57
7259 10733 3.901844 GCCATGGTATTGGTACTCTCCTA 59.098 47.826 14.67 0.00 39.11 2.94
7260 10734 2.706190 GCCATGGTATTGGTACTCTCCT 59.294 50.000 14.67 0.00 39.11 3.69
7261 10735 2.706190 AGCCATGGTATTGGTACTCTCC 59.294 50.000 14.67 0.00 39.11 3.71
7262 10736 3.643792 AGAGCCATGGTATTGGTACTCTC 59.356 47.826 14.67 7.07 39.11 3.20
7263 10737 3.658725 AGAGCCATGGTATTGGTACTCT 58.341 45.455 14.67 10.77 39.11 3.24
7264 10738 5.482908 CATAGAGCCATGGTATTGGTACTC 58.517 45.833 14.67 8.54 39.11 2.59
7265 10739 4.287067 CCATAGAGCCATGGTATTGGTACT 59.713 45.833 14.67 0.00 40.62 2.73
7266 10740 4.579869 CCATAGAGCCATGGTATTGGTAC 58.420 47.826 14.67 0.00 40.62 3.34
7267 10741 3.009033 GCCATAGAGCCATGGTATTGGTA 59.991 47.826 14.67 0.00 46.21 3.25
7383 10890 4.423732 ACGCCAAACAATCAAATATGCTC 58.576 39.130 0.00 0.00 0.00 4.26
7386 11002 6.890663 ATCAACGCCAAACAATCAAATATG 57.109 33.333 0.00 0.00 0.00 1.78
7400 11016 1.492599 TGGGGATATCAATCAACGCCA 59.507 47.619 4.83 0.00 40.29 5.69
7402 11018 3.214328 ACTTGGGGATATCAATCAACGC 58.786 45.455 4.83 0.00 33.41 4.84
7440 11056 9.851686 AAGGAAATAAAGATGTGTGCTCATATA 57.148 29.630 0.00 0.00 0.00 0.86
7567 11230 4.695993 TGCGCATCTTCCACGGCA 62.696 61.111 5.66 0.00 0.00 5.69
7605 11268 2.631160 AAACTGTGATTCGTGGACCA 57.369 45.000 0.00 0.00 0.00 4.02
7612 11275 7.134815 AGATCAACAAGAAAAACTGTGATTCG 58.865 34.615 0.00 0.00 0.00 3.34
7615 11278 7.775120 ACAAGATCAACAAGAAAAACTGTGAT 58.225 30.769 0.00 0.00 0.00 3.06
7618 11281 7.396540 AGACAAGATCAACAAGAAAAACTGT 57.603 32.000 0.00 0.00 0.00 3.55
7654 11317 0.234884 CGGCCGTGAAGAACAAGAAC 59.765 55.000 19.50 0.00 0.00 3.01
7655 11318 0.179067 ACGGCCGTGAAGAACAAGAA 60.179 50.000 33.75 0.00 0.00 2.52
7666 11329 4.025401 GCCAACAAGACGGCCGTG 62.025 66.667 39.65 24.61 42.82 4.94
7710 11379 2.922503 TGCGGCAGGAGAAGGTCA 60.923 61.111 0.00 0.00 0.00 4.02
7811 11485 9.416794 ACACGATCTGATTATTATCTTGCTTAG 57.583 33.333 0.00 0.00 0.00 2.18
7823 11497 6.338214 AGCATCTACACACGATCTGATTAT 57.662 37.500 0.00 0.00 0.00 1.28
7824 11498 5.774498 AGCATCTACACACGATCTGATTA 57.226 39.130 0.00 0.00 0.00 1.75
7826 11500 4.142071 ACAAGCATCTACACACGATCTGAT 60.142 41.667 0.00 0.00 0.00 2.90
7828 11502 3.305361 CACAAGCATCTACACACGATCTG 59.695 47.826 0.00 0.00 0.00 2.90
7829 11503 3.056536 ACACAAGCATCTACACACGATCT 60.057 43.478 0.00 0.00 0.00 2.75
7870 11545 3.616560 CGAGCATATAAATACACCCGGCT 60.617 47.826 0.00 0.00 0.00 5.52
7890 11565 0.754957 CCCCAATAATTGCAGCCCGA 60.755 55.000 0.00 0.00 0.00 5.14
7954 11630 0.833287 CCTACCACCACCAGATGAGG 59.167 60.000 0.00 0.00 0.00 3.86
7958 11644 2.367202 CCGCCTACCACCACCAGAT 61.367 63.158 0.00 0.00 0.00 2.90
8109 11846 1.508808 GGCACAAACGGCGAAAGGTA 61.509 55.000 16.62 0.00 0.00 3.08
8131 11868 2.880822 ACATCGAAACTTGTCGCATG 57.119 45.000 0.00 0.00 40.88 4.06
8133 11870 1.333702 GCAACATCGAAACTTGTCGCA 60.334 47.619 0.00 0.00 40.88 5.10
8165 11902 3.704566 ACAAATATAGACGCCTCAGTGGA 59.295 43.478 0.00 0.00 38.35 4.02
8191 11935 8.820933 CCATTCATGCATTATTATACTACTCCG 58.179 37.037 0.00 0.00 0.00 4.63
8234 11978 4.712051 TCCTTTCCACCAGGATATCATG 57.288 45.455 10.43 10.43 45.26 3.07
8293 12041 5.070446 TCCATTACTTAACCTCGCTCATCAT 59.930 40.000 0.00 0.00 0.00 2.45
8348 12100 2.378445 TATCAGCGTGCAAGCAAGTA 57.622 45.000 26.30 12.22 40.15 2.24
8352 12104 2.083002 TCAATTATCAGCGTGCAAGCA 58.917 42.857 26.30 7.28 40.15 3.91
8382 12134 7.495934 GGTATATCAAGCAAAAAGTCTGAGCTA 59.504 37.037 0.00 0.00 34.66 3.32
8396 12148 9.987272 GCATGTATATATCAGGTATATCAAGCA 57.013 33.333 0.00 0.00 37.25 3.91
8397 12149 9.133627 CGCATGTATATATCAGGTATATCAAGC 57.866 37.037 0.00 4.21 37.25 4.01
8404 12156 9.755804 CTTCATTCGCATGTATATATCAGGTAT 57.244 33.333 0.00 0.00 0.00 2.73
8405 12157 7.706607 GCTTCATTCGCATGTATATATCAGGTA 59.293 37.037 0.00 0.00 0.00 3.08
8406 12158 6.536582 GCTTCATTCGCATGTATATATCAGGT 59.463 38.462 0.00 0.00 0.00 4.00
8407 12159 6.760298 AGCTTCATTCGCATGTATATATCAGG 59.240 38.462 0.00 0.00 0.00 3.86
8408 12160 7.767745 AGCTTCATTCGCATGTATATATCAG 57.232 36.000 0.00 0.00 0.00 2.90
8409 12161 8.470002 AGTAGCTTCATTCGCATGTATATATCA 58.530 33.333 0.00 0.00 0.00 2.15
8410 12162 8.750416 CAGTAGCTTCATTCGCATGTATATATC 58.250 37.037 0.00 0.00 0.00 1.63
8411 12163 8.470002 TCAGTAGCTTCATTCGCATGTATATAT 58.530 33.333 0.00 0.00 0.00 0.86
8412 12164 7.755373 GTCAGTAGCTTCATTCGCATGTATATA 59.245 37.037 0.00 0.00 0.00 0.86
8413 12165 6.587990 GTCAGTAGCTTCATTCGCATGTATAT 59.412 38.462 0.00 0.00 0.00 0.86
8414 12166 5.920840 GTCAGTAGCTTCATTCGCATGTATA 59.079 40.000 0.00 0.00 0.00 1.47
8415 12167 4.747108 GTCAGTAGCTTCATTCGCATGTAT 59.253 41.667 0.00 0.00 0.00 2.29
8416 12168 4.112634 GTCAGTAGCTTCATTCGCATGTA 58.887 43.478 0.00 0.00 0.00 2.29
8417 12169 2.932614 GTCAGTAGCTTCATTCGCATGT 59.067 45.455 0.00 0.00 0.00 3.21
8418 12170 2.931969 TGTCAGTAGCTTCATTCGCATG 59.068 45.455 0.00 0.00 0.00 4.06
8419 12171 2.932614 GTGTCAGTAGCTTCATTCGCAT 59.067 45.455 0.00 0.00 0.00 4.73
8420 12172 2.288763 TGTGTCAGTAGCTTCATTCGCA 60.289 45.455 0.00 0.00 0.00 5.10
8421 12173 2.337583 TGTGTCAGTAGCTTCATTCGC 58.662 47.619 0.00 0.00 0.00 4.70
8422 12174 4.667668 GCTTTGTGTCAGTAGCTTCATTCG 60.668 45.833 0.00 0.00 0.00 3.34
8423 12175 4.378874 GGCTTTGTGTCAGTAGCTTCATTC 60.379 45.833 0.00 0.00 34.16 2.67
8424 12176 3.503748 GGCTTTGTGTCAGTAGCTTCATT 59.496 43.478 0.00 0.00 34.16 2.57
8425 12177 3.077359 GGCTTTGTGTCAGTAGCTTCAT 58.923 45.455 0.00 0.00 34.16 2.57
8426 12178 2.494059 GGCTTTGTGTCAGTAGCTTCA 58.506 47.619 0.00 0.00 34.16 3.02
8427 12179 1.807142 GGGCTTTGTGTCAGTAGCTTC 59.193 52.381 0.00 0.00 34.16 3.86
8428 12180 1.878102 CGGGCTTTGTGTCAGTAGCTT 60.878 52.381 0.00 0.00 34.16 3.74
8429 12181 0.320771 CGGGCTTTGTGTCAGTAGCT 60.321 55.000 0.00 0.00 34.16 3.32
8430 12182 0.602905 ACGGGCTTTGTGTCAGTAGC 60.603 55.000 0.00 0.00 0.00 3.58
8431 12183 1.429463 GACGGGCTTTGTGTCAGTAG 58.571 55.000 0.00 0.00 32.91 2.57
8432 12184 3.599412 GACGGGCTTTGTGTCAGTA 57.401 52.632 0.00 0.00 32.91 2.74
8433 12185 4.456806 GACGGGCTTTGTGTCAGT 57.543 55.556 0.00 0.00 32.91 3.41


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

AutoCloner maintained by Alex Coulton.