Multiple sequence alignment - TraesCS3D01G266300

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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 TraesCS3D01G266300 chr3D 100.000 9225 0 0 1 9225 369418301 369409077 0.000000e+00 17036.0
1 TraesCS3D01G266300 chr3D 86.997 323 34 8 4589 4907 394053664 394053346 3.170000e-94 357.0
2 TraesCS3D01G266300 chr3D 100.000 31 0 0 1869 1899 352113168 352113138 3.600000e-04 58.4
3 TraesCS3D01G266300 chr3B 95.448 3932 115 19 687 4597 480380378 480376490 0.000000e+00 6211.0
4 TraesCS3D01G266300 chr3B 93.623 2368 77 24 6315 8670 480374409 480372104 0.000000e+00 3469.0
5 TraesCS3D01G266300 chr3B 95.575 1401 38 8 4928 6319 480376490 480375105 0.000000e+00 2222.0
6 TraesCS3D01G266300 chr3B 87.535 353 33 8 8880 9225 480343921 480343573 1.870000e-106 398.0
7 TraesCS3D01G266300 chr3B 94.048 84 3 1 8664 8747 480369570 480369489 9.720000e-25 126.0
8 TraesCS3D01G266300 chr3B 100.000 31 0 0 1869 1899 450379472 450379442 3.600000e-04 58.4
9 TraesCS3D01G266300 chr3A 96.721 3446 86 10 698 4123 490627727 490624289 0.000000e+00 5712.0
10 TraesCS3D01G266300 chr3A 96.811 2038 35 7 5001 7025 490622353 490620333 0.000000e+00 3376.0
11 TraesCS3D01G266300 chr3A 93.882 1749 52 20 7016 8744 490619625 490617912 0.000000e+00 2586.0
12 TraesCS3D01G266300 chr3A 97.173 955 16 6 4119 5067 490623364 490622415 0.000000e+00 1604.0
13 TraesCS3D01G266300 chr3A 92.803 264 19 0 3879 4142 529849907 529850170 5.230000e-102 383.0
14 TraesCS3D01G266300 chr3A 94.091 220 11 2 9007 9225 490617523 490617305 5.340000e-87 333.0
15 TraesCS3D01G266300 chr3A 88.142 253 1 6 8742 8990 490617831 490617604 3.280000e-69 274.0
16 TraesCS3D01G266300 chr3A 97.015 67 2 0 5001 5067 490622417 490622351 7.570000e-21 113.0
17 TraesCS3D01G266300 chr2D 92.868 659 28 12 1 650 13654128 13653480 0.000000e+00 939.0
18 TraesCS3D01G266300 chr2D 90.937 662 42 11 1 652 609661831 609662484 0.000000e+00 874.0
19 TraesCS3D01G266300 chr1D 92.481 665 37 8 1 657 247134008 247133349 0.000000e+00 939.0
20 TraesCS3D01G266300 chr1D 89.701 670 47 14 1 656 355673375 355674036 0.000000e+00 835.0
21 TraesCS3D01G266300 chr7D 92.424 660 34 13 1 652 126659366 126658715 0.000000e+00 928.0
22 TraesCS3D01G266300 chr7D 91.265 664 40 11 1 650 621758873 621758214 0.000000e+00 889.0
23 TraesCS3D01G266300 chr7D 90.075 665 44 14 1 653 362360968 362360314 0.000000e+00 843.0
24 TraesCS3D01G266300 chr7D 90.852 634 41 11 26 649 80510717 80511343 0.000000e+00 833.0
25 TraesCS3D01G266300 chr7D 86.606 769 80 8 2671 3421 412160475 412159712 0.000000e+00 828.0
26 TraesCS3D01G266300 chr7D 85.096 832 99 11 4957 5774 412158916 412158096 0.000000e+00 826.0
27 TraesCS3D01G266300 chr7D 81.978 910 95 30 986 1869 412162043 412161177 0.000000e+00 708.0
28 TraesCS3D01G266300 chr7D 81.347 772 113 27 1923 2670 412161173 412160409 4.770000e-167 599.0
29 TraesCS3D01G266300 chr7D 81.818 660 74 20 6928 7563 412154723 412154086 6.390000e-141 512.0
30 TraesCS3D01G266300 chr7D 89.902 307 30 1 4594 4900 500618971 500618666 2.410000e-105 394.0
31 TraesCS3D01G266300 chr7D 91.822 269 22 0 3872 4140 499792853 499792585 8.750000e-100 375.0
32 TraesCS3D01G266300 chr7D 86.707 331 23 12 6215 6545 412155712 412155403 1.910000e-91 348.0
33 TraesCS3D01G266300 chr7D 84.179 335 35 5 4217 4535 412159333 412159001 9.000000e-80 309.0
34 TraesCS3D01G266300 chr7B 86.606 769 80 7 2671 3421 426538723 426537960 0.000000e+00 828.0
35 TraesCS3D01G266300 chr7B 86.772 635 67 11 5009 5637 426535650 426535027 0.000000e+00 691.0
36 TraesCS3D01G266300 chr7B 79.670 787 114 28 1923 2670 426539436 426538657 8.210000e-145 525.0
37 TraesCS3D01G266300 chr7B 86.311 431 51 7 7137 7563 426532678 426532252 6.530000e-126 462.0
38 TraesCS3D01G266300 chr7B 86.035 401 43 10 986 1383 426541102 426540712 1.430000e-112 418.0
39 TraesCS3D01G266300 chr7B 85.559 367 23 16 6215 6580 426533626 426533289 3.170000e-94 357.0
40 TraesCS3D01G266300 chr7B 85.542 332 38 6 1546 1869 426539769 426539440 1.150000e-88 339.0
41 TraesCS3D01G266300 chr7B 79.249 453 57 20 6621 7056 426533186 426532754 1.960000e-71 281.0
42 TraesCS3D01G266300 chr7B 84.429 289 29 4 4263 4535 426536191 426535903 4.250000e-68 270.0
43 TraesCS3D01G266300 chr7B 93.023 43 2 1 1872 1913 639041353 639041395 2.780000e-05 62.1
44 TraesCS3D01G266300 chr6D 89.238 669 46 17 1 655 329073811 329074467 0.000000e+00 813.0
45 TraesCS3D01G266300 chr6D 92.000 275 18 4 3873 4145 265182254 265182526 5.230000e-102 383.0
46 TraesCS3D01G266300 chr7A 84.856 832 95 17 4957 5774 473619041 473618227 0.000000e+00 809.0
47 TraesCS3D01G266300 chr7A 86.104 770 78 10 2671 3421 473620597 473619838 0.000000e+00 802.0
48 TraesCS3D01G266300 chr7A 81.714 875 123 24 6709 7563 473616145 473615288 0.000000e+00 695.0
49 TraesCS3D01G266300 chr7A 81.608 908 89 28 986 1869 473622167 473621314 0.000000e+00 680.0
50 TraesCS3D01G266300 chr7A 80.789 786 107 25 1923 2670 473621310 473620531 8.030000e-160 575.0
51 TraesCS3D01G266300 chr7A 92.193 269 21 0 3873 4141 646560180 646560448 1.880000e-101 381.0
52 TraesCS3D01G266300 chr7A 86.104 367 18 22 6215 6580 473616713 473616379 1.890000e-96 364.0
53 TraesCS3D01G266300 chr7A 84.731 334 31 9 4217 4535 473619454 473619126 5.380000e-82 316.0
54 TraesCS3D01G266300 chr4D 93.939 264 16 0 3879 4142 395403157 395403420 5.190000e-107 399.0
55 TraesCS3D01G266300 chr4D 90.132 304 22 8 4594 4894 421335214 421335512 1.120000e-103 388.0
56 TraesCS3D01G266300 chr4D 92.000 275 19 3 3873 4145 275616760 275616487 5.230000e-102 383.0
57 TraesCS3D01G266300 chr4D 88.217 314 26 8 4589 4894 93437065 93436755 1.890000e-96 364.0
58 TraesCS3D01G266300 chr5D 90.066 302 28 2 4594 4894 521721145 521720845 3.120000e-104 390.0
59 TraesCS3D01G266300 chr5D 90.102 293 26 3 4602 4894 317386792 317387081 2.430000e-100 377.0
60 TraesCS3D01G266300 chr2A 93.511 262 16 1 3879 4140 66802689 66802949 1.120000e-103 388.0
61 TraesCS3D01G266300 chr2B 89.037 301 29 4 4594 4894 1978744 1978448 4.070000e-98 370.0
62 TraesCS3D01G266300 chr5B 88.179 313 29 8 4591 4899 303229096 303229404 5.260000e-97 366.0
63 TraesCS3D01G266300 chr1B 100.000 28 0 0 1872 1899 336070442 336070469 1.700000e-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 TraesCS3D01G266300 chr3D 369409077 369418301 9224 True 17036.000000 17036 100.000000 1 9225 1 chr3D.!!$R2 9224
1 TraesCS3D01G266300 chr3B 480369489 480380378 10889 True 3007.000000 6211 94.673500 687 8747 4 chr3B.!!$R3 8060
2 TraesCS3D01G266300 chr3A 490617305 490627727 10422 True 1999.714286 5712 94.833571 698 9225 7 chr3A.!!$R1 8527
3 TraesCS3D01G266300 chr2D 13653480 13654128 648 True 939.000000 939 92.868000 1 650 1 chr2D.!!$R1 649
4 TraesCS3D01G266300 chr2D 609661831 609662484 653 False 874.000000 874 90.937000 1 652 1 chr2D.!!$F1 651
5 TraesCS3D01G266300 chr1D 247133349 247134008 659 True 939.000000 939 92.481000 1 657 1 chr1D.!!$R1 656
6 TraesCS3D01G266300 chr1D 355673375 355674036 661 False 835.000000 835 89.701000 1 656 1 chr1D.!!$F1 655
7 TraesCS3D01G266300 chr7D 126658715 126659366 651 True 928.000000 928 92.424000 1 652 1 chr7D.!!$R1 651
8 TraesCS3D01G266300 chr7D 621758214 621758873 659 True 889.000000 889 91.265000 1 650 1 chr7D.!!$R5 649
9 TraesCS3D01G266300 chr7D 362360314 362360968 654 True 843.000000 843 90.075000 1 653 1 chr7D.!!$R2 652
10 TraesCS3D01G266300 chr7D 80510717 80511343 626 False 833.000000 833 90.852000 26 649 1 chr7D.!!$F1 623
11 TraesCS3D01G266300 chr7D 412154086 412162043 7957 True 590.000000 828 83.961571 986 7563 7 chr7D.!!$R6 6577
12 TraesCS3D01G266300 chr7B 426532252 426541102 8850 True 463.444444 828 84.463667 986 7563 9 chr7B.!!$R1 6577
13 TraesCS3D01G266300 chr6D 329073811 329074467 656 False 813.000000 813 89.238000 1 655 1 chr6D.!!$F2 654
14 TraesCS3D01G266300 chr7A 473615288 473622167 6879 True 605.857143 809 83.700857 986 7563 7 chr7A.!!$R1 6577

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
814 856 0.175073 ATTACCCGAGCCGTGAGAAC 59.825 55.000 0.00 0.00 0.00 3.01 F
1407 1466 0.600782 GTTGGTCGACCCGTGCTAAA 60.601 55.000 31.19 14.34 35.15 1.85 F
1788 2664 2.086869 CGCCATGGAATCAGACAGTTT 58.913 47.619 18.40 0.00 0.00 2.66 F
2565 3478 1.848388 TCATGGCAACCTCATCTGGAT 59.152 47.619 0.00 0.00 0.00 3.41 F
3220 4152 3.005897 AGCTACCAGGTATGTTATCAGCG 59.994 47.826 0.00 0.00 0.00 5.18 F
4615 7325 2.700897 ACTCCCTCCGTCCATGAATAAG 59.299 50.000 0.00 0.00 0.00 1.73 F
5383 8357 0.324943 CTCGTGGATTGAAGGGTGGT 59.675 55.000 0.00 0.00 0.00 4.16 F
5771 9643 0.992431 ATCCCTTGCAGATGCTCCCT 60.992 55.000 6.35 0.00 42.66 4.20 F
6779 12751 3.399330 GGCATGTACGGTTGTATAGCAT 58.601 45.455 0.00 0.00 32.11 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 3287 2.771089 TCATCGCAAGCAGGATTATCC 58.229 47.619 2.40 2.40 34.73 2.59 R
2565 3478 6.490040 AGTGCTAGACAATTTAGAAAAAGGCA 59.510 34.615 0.00 0.00 0.00 4.75 R
3717 5361 2.057922 AGGATGAAGAAGTGGTGTGGT 58.942 47.619 0.00 0.00 0.00 4.16 R
4236 6929 1.287146 ACTACGACCCCACCACTCTAT 59.713 52.381 0.00 0.00 0.00 1.98 R
4911 7625 0.033796 AGTATTCCCTCCGTCCACGA 60.034 55.000 0.00 0.00 43.02 4.35 R
5529 8506 2.454055 GCAAAATGCTTACGATCCAGC 58.546 47.619 0.00 0.19 40.96 4.85 R
6547 12306 2.764010 TGTTAGCGATAAGAGAAGGCCA 59.236 45.455 5.01 0.00 0.00 5.36 R
7619 14459 0.388134 CAGGCACTTGCTCACAATGC 60.388 55.000 0.38 0.00 41.70 3.56 R
8298 15161 1.745232 ACGACCAACAAGTTCAGCAA 58.255 45.000 0.00 0.00 0.00 3.91 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
216 228 3.327626 ACGCGTTTTGTTTTTCCCTTTT 58.672 36.364 5.58 0.00 0.00 2.27
252 264 2.802816 GTGACTCTCACGAAAGCACAAT 59.197 45.455 0.00 0.00 37.67 2.71
529 559 1.194896 CGAAAACGCGTGCGGAAAAA 61.195 50.000 14.98 0.00 44.69 1.94
530 560 1.125270 GAAAACGCGTGCGGAAAAAT 58.875 45.000 14.98 0.00 44.69 1.82
657 697 5.766174 TCGTTAACTAGTTGCTCCCAAAATT 59.234 36.000 18.56 0.00 31.68 1.82
658 698 6.263617 TCGTTAACTAGTTGCTCCCAAAATTT 59.736 34.615 18.56 0.00 31.68 1.82
659 699 6.581166 CGTTAACTAGTTGCTCCCAAAATTTC 59.419 38.462 18.56 0.00 31.68 2.17
660 700 5.468540 AACTAGTTGCTCCCAAAATTTCC 57.531 39.130 7.48 0.00 31.68 3.13
661 701 4.740902 ACTAGTTGCTCCCAAAATTTCCT 58.259 39.130 0.00 0.00 31.68 3.36
662 702 4.524328 ACTAGTTGCTCCCAAAATTTCCTG 59.476 41.667 0.00 0.00 31.68 3.86
663 703 2.634453 AGTTGCTCCCAAAATTTCCTGG 59.366 45.455 2.36 2.36 31.68 4.45
664 704 2.368548 GTTGCTCCCAAAATTTCCTGGT 59.631 45.455 7.89 0.00 31.68 4.00
665 705 1.969923 TGCTCCCAAAATTTCCTGGTG 59.030 47.619 7.89 4.02 0.00 4.17
666 706 2.247358 GCTCCCAAAATTTCCTGGTGA 58.753 47.619 7.89 4.73 0.00 4.02
667 707 2.833943 GCTCCCAAAATTTCCTGGTGAT 59.166 45.455 7.89 0.00 0.00 3.06
668 708 3.368739 GCTCCCAAAATTTCCTGGTGATG 60.369 47.826 7.89 0.00 0.00 3.07
669 709 3.172339 TCCCAAAATTTCCTGGTGATGG 58.828 45.455 7.89 2.01 0.00 3.51
670 710 3.172339 CCCAAAATTTCCTGGTGATGGA 58.828 45.455 7.89 0.00 0.00 3.41
671 711 3.196254 CCCAAAATTTCCTGGTGATGGAG 59.804 47.826 7.89 0.00 34.76 3.86
672 712 3.834231 CCAAAATTTCCTGGTGATGGAGT 59.166 43.478 1.30 0.00 34.76 3.85
673 713 4.284234 CCAAAATTTCCTGGTGATGGAGTT 59.716 41.667 1.30 0.00 34.76 3.01
674 714 5.221702 CCAAAATTTCCTGGTGATGGAGTTT 60.222 40.000 1.30 0.00 34.76 2.66
675 715 6.014669 CCAAAATTTCCTGGTGATGGAGTTTA 60.015 38.462 1.30 0.00 34.76 2.01
676 716 7.310609 CCAAAATTTCCTGGTGATGGAGTTTAT 60.311 37.037 1.30 0.00 34.76 1.40
677 717 6.780457 AATTTCCTGGTGATGGAGTTTATG 57.220 37.500 0.00 0.00 34.76 1.90
678 718 4.927267 TTCCTGGTGATGGAGTTTATGT 57.073 40.909 0.00 0.00 34.76 2.29
679 719 4.220693 TCCTGGTGATGGAGTTTATGTG 57.779 45.455 0.00 0.00 0.00 3.21
680 720 3.587061 TCCTGGTGATGGAGTTTATGTGT 59.413 43.478 0.00 0.00 0.00 3.72
681 721 4.780554 TCCTGGTGATGGAGTTTATGTGTA 59.219 41.667 0.00 0.00 0.00 2.90
682 722 5.249622 TCCTGGTGATGGAGTTTATGTGTAA 59.750 40.000 0.00 0.00 0.00 2.41
683 723 5.586243 CCTGGTGATGGAGTTTATGTGTAAG 59.414 44.000 0.00 0.00 0.00 2.34
684 724 6.121776 TGGTGATGGAGTTTATGTGTAAGT 57.878 37.500 0.00 0.00 0.00 2.24
685 725 6.539173 TGGTGATGGAGTTTATGTGTAAGTT 58.461 36.000 0.00 0.00 0.00 2.66
809 851 2.279252 CCGATTACCCGAGCCGTG 60.279 66.667 0.00 0.00 0.00 4.94
810 852 2.777972 CCGATTACCCGAGCCGTGA 61.778 63.158 0.00 0.00 0.00 4.35
811 853 1.299165 CGATTACCCGAGCCGTGAG 60.299 63.158 0.00 0.00 0.00 3.51
812 854 1.721664 CGATTACCCGAGCCGTGAGA 61.722 60.000 0.00 0.00 0.00 3.27
813 855 0.458669 GATTACCCGAGCCGTGAGAA 59.541 55.000 0.00 0.00 0.00 2.87
814 856 0.175073 ATTACCCGAGCCGTGAGAAC 59.825 55.000 0.00 0.00 0.00 3.01
815 857 2.203972 TTACCCGAGCCGTGAGAACG 62.204 60.000 0.00 0.00 0.00 3.95
835 878 2.360852 TCGTCCTCCCGACAGTCC 60.361 66.667 0.00 0.00 42.07 3.85
1230 1289 1.933853 CGCCTGATTTAGTGGCTGTAC 59.066 52.381 0.00 0.00 44.09 2.90
1407 1466 0.600782 GTTGGTCGACCCGTGCTAAA 60.601 55.000 31.19 14.34 35.15 1.85
1420 1479 2.287915 CGTGCTAAATCTGGGGAATTCG 59.712 50.000 0.00 0.00 0.00 3.34
1576 2450 6.612247 TCGTCTGTTTTTCTTTCTAATGCA 57.388 33.333 0.00 0.00 0.00 3.96
1788 2664 2.086869 CGCCATGGAATCAGACAGTTT 58.913 47.619 18.40 0.00 0.00 2.66
1965 2847 2.091541 TCGGATCCTTGCACCAAAATC 58.908 47.619 10.75 0.00 0.00 2.17
2394 3287 8.665685 GGTACTGTCCAGTATAATTTTCACTTG 58.334 37.037 10.15 0.00 44.73 3.16
2565 3478 1.848388 TCATGGCAACCTCATCTGGAT 59.152 47.619 0.00 0.00 0.00 3.41
2635 3548 5.391523 GCTGATTATTAAGTGCCAACGTTGA 60.392 40.000 29.35 7.80 0.00 3.18
3220 4152 3.005897 AGCTACCAGGTATGTTATCAGCG 59.994 47.826 0.00 0.00 0.00 5.18
3424 4356 7.500892 TCGGTATGGTAGCAACAAAATAATCAT 59.499 33.333 0.00 0.00 0.00 2.45
3742 5386 3.584406 ACACCACTTCTTCATCCTGATGA 59.416 43.478 5.74 5.74 45.30 2.92
4367 7063 9.553064 AGTCCATACATTTCTGTAAAGATGATC 57.447 33.333 0.00 0.00 41.09 2.92
4582 7292 4.872124 TGATGACATAGTGCATCACTTGAC 59.128 41.667 4.70 5.20 42.59 3.18
4614 7324 2.759355 ACTCCCTCCGTCCATGAATAA 58.241 47.619 0.00 0.00 0.00 1.40
4615 7325 2.700897 ACTCCCTCCGTCCATGAATAAG 59.299 50.000 0.00 0.00 0.00 1.73
4838 7552 5.233689 GCATCTTTCCAATGCATTTTCTAGC 59.766 40.000 9.83 3.37 46.93 3.42
4847 7561 3.273434 TGCATTTTCTAGCTCGCTTCAT 58.727 40.909 0.00 0.00 0.00 2.57
4854 7568 3.906998 TCTAGCTCGCTTCATATTCTGC 58.093 45.455 0.00 0.00 0.00 4.26
4911 7625 6.885922 ACGGAGGTAATACTTTTAAGCAGAT 58.114 36.000 0.00 0.00 0.00 2.90
4924 7638 2.808315 CAGATCGTGGACGGAGGG 59.192 66.667 0.00 0.00 40.29 4.30
4926 7640 1.000019 AGATCGTGGACGGAGGGAA 60.000 57.895 0.00 0.00 40.29 3.97
4927 7641 0.397254 AGATCGTGGACGGAGGGAAT 60.397 55.000 0.00 0.00 40.29 3.01
4928 7642 1.133575 AGATCGTGGACGGAGGGAATA 60.134 52.381 0.00 0.00 40.29 1.75
4929 7643 1.000496 GATCGTGGACGGAGGGAATAC 60.000 57.143 0.00 0.00 40.29 1.89
5073 8039 4.122046 TCGCACTTCCATGATAACTGATG 58.878 43.478 0.00 0.00 0.00 3.07
5080 8051 4.936891 TCCATGATAACTGATGAGTGACG 58.063 43.478 0.00 0.00 30.61 4.35
5142 8113 5.041191 AGTGAGTTTGAAGAACAGTGGAT 57.959 39.130 0.00 0.00 0.00 3.41
5383 8357 0.324943 CTCGTGGATTGAAGGGTGGT 59.675 55.000 0.00 0.00 0.00 4.16
5529 8506 2.094545 GCAGCATACACCCTTGGAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
5771 9643 0.992431 ATCCCTTGCAGATGCTCCCT 60.992 55.000 6.35 0.00 42.66 4.20
5950 10925 8.947055 AGCAAGTGAACAAAATAATTGAACTT 57.053 26.923 0.00 0.44 0.00 2.66
6654 12579 9.713740 CTCATCTTACTGTTTTGCTGAATATTC 57.286 33.333 8.60 8.60 0.00 1.75
6779 12751 3.399330 GGCATGTACGGTTGTATAGCAT 58.601 45.455 0.00 0.00 32.11 3.79
6929 12919 5.513233 AGAGATGGCCATCAATTTGTTAGT 58.487 37.500 40.05 20.43 40.22 2.24
7120 13935 9.423061 ACAAATAAAGGCTCACATTTTTATGAC 57.577 29.630 0.00 0.00 0.00 3.06
7339 14158 7.558161 TCAGCATCAAATTTGGTACTAGATG 57.442 36.000 17.90 12.58 35.67 2.90
7619 14459 1.949847 CTCGGGCTCAGGGTAGTGTG 61.950 65.000 0.00 0.00 0.00 3.82
7693 14533 5.295045 CCTTTTGCTTGCTTCAGATTTTTGT 59.705 36.000 0.00 0.00 0.00 2.83
7694 14534 5.721876 TTTGCTTGCTTCAGATTTTTGTG 57.278 34.783 0.00 0.00 0.00 3.33
7755 14595 8.722394 GTTGAGTTTAACTTTCCTCAAGGATAG 58.278 37.037 13.15 13.15 44.98 2.08
7757 14597 8.095169 TGAGTTTAACTTTCCTCAAGGATAGAC 58.905 37.037 19.50 9.60 43.29 2.59
7759 14599 4.473477 AACTTTCCTCAAGGATAGACGG 57.527 45.455 19.50 0.00 43.29 4.79
7797 14637 1.217942 GGGTTTATGAAGCATCCCCCT 59.782 52.381 1.64 0.00 34.98 4.79
7856 14696 5.047306 TCACACGGATAGAAGTCATGAAACT 60.047 40.000 0.00 0.00 0.00 2.66
7967 14807 6.834168 TTGCTGAAAGAAGGTAAATTAGGG 57.166 37.500 0.00 0.00 34.07 3.53
7972 14815 8.029522 GCTGAAAGAAGGTAAATTAGGGAAAAG 58.970 37.037 0.00 0.00 34.07 2.27
8048 14891 5.512753 TGTGCTGTGTCATGTATTGTTTT 57.487 34.783 0.00 0.00 0.00 2.43
8054 14897 7.009999 TGCTGTGTCATGTATTGTTTTTGTTTC 59.990 33.333 0.00 0.00 0.00 2.78
8080 14943 5.178096 TCTCTGATTTGTATTGCCAGGAA 57.822 39.130 0.00 0.00 0.00 3.36
8086 14949 0.323302 TGTATTGCCAGGAAGCGACA 59.677 50.000 0.00 0.00 34.65 4.35
8288 15151 5.574055 CGCTAAAATCGTTGGTCTACTGTTA 59.426 40.000 0.00 0.00 0.00 2.41
8298 15161 9.128404 TCGTTGGTCTACTGTTATATTGATACT 57.872 33.333 0.00 0.00 0.00 2.12
8310 15173 9.448438 TGTTATATTGATACTTGCTGAACTTGT 57.552 29.630 0.00 0.00 0.00 3.16
8337 15200 7.534848 GTCGTTGTGACTTTTTATTAGCTTG 57.465 36.000 0.00 0.00 44.58 4.01
8378 15241 3.335579 GCACCTCGGAGTTACAATTTCT 58.664 45.455 4.02 0.00 0.00 2.52
8384 15247 6.427242 ACCTCGGAGTTACAATTTCTTTCTTC 59.573 38.462 4.02 0.00 0.00 2.87
8432 15295 2.301870 TGGTCAATCTTAGTCAGCGGTT 59.698 45.455 0.00 0.00 0.00 4.44
8507 15371 5.184892 ACCTGGAGAAAGCAATATTCTGT 57.815 39.130 0.00 0.00 37.26 3.41
8564 15428 1.896660 GGTGGGCTGAAAGTTGCGA 60.897 57.895 0.00 0.00 35.30 5.10
8584 15466 3.953766 GAGCTGTTCGATCGAAGTATGA 58.046 45.455 29.79 5.75 34.49 2.15
8585 15467 4.352039 GAGCTGTTCGATCGAAGTATGAA 58.648 43.478 29.79 4.94 34.49 2.57
8586 15468 4.938080 AGCTGTTCGATCGAAGTATGAAT 58.062 39.130 29.79 10.33 34.49 2.57
8587 15469 4.979197 AGCTGTTCGATCGAAGTATGAATC 59.021 41.667 29.79 15.95 34.49 2.52
8588 15470 4.979197 GCTGTTCGATCGAAGTATGAATCT 59.021 41.667 29.79 0.00 34.49 2.40
8589 15471 5.108065 GCTGTTCGATCGAAGTATGAATCTG 60.108 44.000 29.79 18.63 34.49 2.90
8590 15472 4.740205 TGTTCGATCGAAGTATGAATCTGC 59.260 41.667 29.79 14.09 34.49 4.26
8591 15473 4.568152 TCGATCGAAGTATGAATCTGCA 57.432 40.909 16.99 0.00 0.00 4.41
8592 15474 5.126396 TCGATCGAAGTATGAATCTGCAT 57.874 39.130 16.99 0.00 0.00 3.96
8593 15475 5.157067 TCGATCGAAGTATGAATCTGCATC 58.843 41.667 16.99 0.00 0.00 3.91
8594 15476 4.029972 CGATCGAAGTATGAATCTGCATCG 59.970 45.833 10.26 0.00 0.00 3.84
8595 15477 4.568152 TCGAAGTATGAATCTGCATCGA 57.432 40.909 0.00 0.00 0.00 3.59
8596 15478 5.126396 TCGAAGTATGAATCTGCATCGAT 57.874 39.130 0.00 0.00 0.00 3.59
8597 15479 5.157067 TCGAAGTATGAATCTGCATCGATC 58.843 41.667 0.00 0.00 0.00 3.69
8598 15480 4.029972 CGAAGTATGAATCTGCATCGATCG 59.970 45.833 9.36 9.36 0.00 3.69
8599 15481 4.511617 AGTATGAATCTGCATCGATCGT 57.488 40.909 15.94 0.00 0.00 3.73
8685 18105 6.879400 TCTCTAAGAAGCCTGGTAAAATCTC 58.121 40.000 0.00 0.00 0.00 2.75
8813 18317 5.390145 GGTTTTGCATCATTTCAGCATTGTC 60.390 40.000 0.00 0.00 38.19 3.18
8814 18318 3.513680 TGCATCATTTCAGCATTGTCC 57.486 42.857 0.00 0.00 32.55 4.02
8815 18319 2.826725 TGCATCATTTCAGCATTGTCCA 59.173 40.909 0.00 0.00 32.55 4.02
8816 18320 3.258622 TGCATCATTTCAGCATTGTCCAA 59.741 39.130 0.00 0.00 32.55 3.53
8817 18321 4.247258 GCATCATTTCAGCATTGTCCAAA 58.753 39.130 0.00 0.00 0.00 3.28
8818 18322 4.691685 GCATCATTTCAGCATTGTCCAAAA 59.308 37.500 0.00 0.00 0.00 2.44
8819 18323 5.353123 GCATCATTTCAGCATTGTCCAAAAT 59.647 36.000 0.00 0.00 0.00 1.82
8820 18324 6.674519 GCATCATTTCAGCATTGTCCAAAATG 60.675 38.462 0.00 0.00 39.98 2.32
8821 18325 5.856156 TCATTTCAGCATTGTCCAAAATGT 58.144 33.333 0.00 0.00 39.33 2.71
8822 18326 6.289834 TCATTTCAGCATTGTCCAAAATGTT 58.710 32.000 0.00 0.00 39.33 2.71
8823 18327 7.440198 TCATTTCAGCATTGTCCAAAATGTTA 58.560 30.769 0.00 0.00 39.33 2.41
8824 18328 8.095792 TCATTTCAGCATTGTCCAAAATGTTAT 58.904 29.630 0.00 0.00 39.33 1.89
8825 18329 7.887996 TTTCAGCATTGTCCAAAATGTTATC 57.112 32.000 0.00 0.00 39.33 1.75
8826 18330 6.587206 TCAGCATTGTCCAAAATGTTATCA 57.413 33.333 0.00 0.00 39.33 2.15
8827 18331 7.172868 TCAGCATTGTCCAAAATGTTATCAT 57.827 32.000 0.00 0.00 39.33 2.45
8828 18332 7.036829 TCAGCATTGTCCAAAATGTTATCATG 58.963 34.615 0.00 0.00 39.33 3.07
8829 18333 7.036829 CAGCATTGTCCAAAATGTTATCATGA 58.963 34.615 0.00 0.00 39.33 3.07
8830 18334 7.709182 CAGCATTGTCCAAAATGTTATCATGAT 59.291 33.333 13.81 13.81 39.33 2.45
8831 18335 7.924412 AGCATTGTCCAAAATGTTATCATGATC 59.076 33.333 12.53 0.00 39.33 2.92
8832 18336 7.924412 GCATTGTCCAAAATGTTATCATGATCT 59.076 33.333 12.53 0.00 39.33 2.75
8833 18337 9.244799 CATTGTCCAAAATGTTATCATGATCTG 57.755 33.333 12.53 0.03 33.65 2.90
8834 18338 7.943079 TGTCCAAAATGTTATCATGATCTGT 57.057 32.000 12.53 0.00 34.19 3.41
8835 18339 9.460019 TTGTCCAAAATGTTATCATGATCTGTA 57.540 29.630 12.53 0.00 34.19 2.74
8948 18455 2.838202 GTTATGTCTCAGAAGGGACCCA 59.162 50.000 14.60 0.00 0.00 4.51
8949 18456 2.044793 ATGTCTCAGAAGGGACCCAA 57.955 50.000 14.60 0.00 0.00 4.12
8989 18549 1.341482 TGGTTGGTGCCAAAGAACTGA 60.341 47.619 5.09 0.00 37.70 3.41
9082 18652 8.973835 TTTAGTTTTGCAGGTTATTATTTCGG 57.026 30.769 0.00 0.00 0.00 4.30
9107 18677 8.023706 GGAAGTTTTCCTACACAAATGATTCTC 58.976 37.037 0.61 0.00 46.57 2.87
9108 18678 8.697507 AAGTTTTCCTACACAAATGATTCTCT 57.302 30.769 0.00 0.00 0.00 3.10
9176 18746 7.640597 ACCAGGATAGGTTATGCTTAAAAAC 57.359 36.000 0.00 0.00 39.34 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 193 6.449448 AAACAAAACGCGTTTTCTGTTTTA 57.551 29.167 37.33 0.00 42.20 1.52
265 277 3.856267 GCGAGAGTCACGGTTTTACTTCT 60.856 47.826 11.95 0.00 0.00 2.85
437 462 3.001414 GGTCTTCCTTAGCGTTTTCTCC 58.999 50.000 0.00 0.00 0.00 3.71
438 463 2.666994 CGGTCTTCCTTAGCGTTTTCTC 59.333 50.000 0.00 0.00 33.40 2.87
439 464 2.612221 CCGGTCTTCCTTAGCGTTTTCT 60.612 50.000 0.00 0.00 36.16 2.52
603 643 1.447838 GGAGCCTCGCAACGATCAA 60.448 57.895 0.00 0.00 34.61 2.57
657 697 4.042809 ACACATAAACTCCATCACCAGGAA 59.957 41.667 0.00 0.00 34.08 3.36
658 698 3.587061 ACACATAAACTCCATCACCAGGA 59.413 43.478 0.00 0.00 0.00 3.86
659 699 3.955471 ACACATAAACTCCATCACCAGG 58.045 45.455 0.00 0.00 0.00 4.45
660 700 6.173339 ACTTACACATAAACTCCATCACCAG 58.827 40.000 0.00 0.00 0.00 4.00
661 701 6.121776 ACTTACACATAAACTCCATCACCA 57.878 37.500 0.00 0.00 0.00 4.17
662 702 6.622896 GCAACTTACACATAAACTCCATCACC 60.623 42.308 0.00 0.00 0.00 4.02
663 703 6.072728 TGCAACTTACACATAAACTCCATCAC 60.073 38.462 0.00 0.00 0.00 3.06
664 704 6.000840 TGCAACTTACACATAAACTCCATCA 58.999 36.000 0.00 0.00 0.00 3.07
665 705 6.072728 TGTGCAACTTACACATAAACTCCATC 60.073 38.462 0.00 0.00 42.88 3.51
666 706 5.767665 TGTGCAACTTACACATAAACTCCAT 59.232 36.000 0.00 0.00 42.88 3.41
667 707 5.126779 TGTGCAACTTACACATAAACTCCA 58.873 37.500 0.00 0.00 42.88 3.86
668 708 5.334879 CCTGTGCAACTTACACATAAACTCC 60.335 44.000 0.00 0.00 46.32 3.85
669 709 5.334879 CCCTGTGCAACTTACACATAAACTC 60.335 44.000 0.00 0.00 46.32 3.01
670 710 4.518970 CCCTGTGCAACTTACACATAAACT 59.481 41.667 0.00 0.00 46.32 2.66
671 711 4.517453 TCCCTGTGCAACTTACACATAAAC 59.483 41.667 0.00 0.00 46.32 2.01
672 712 4.720046 TCCCTGTGCAACTTACACATAAA 58.280 39.130 0.00 0.00 46.32 1.40
673 713 4.202419 ACTCCCTGTGCAACTTACACATAA 60.202 41.667 0.00 0.00 46.32 1.90
674 714 3.326588 ACTCCCTGTGCAACTTACACATA 59.673 43.478 0.00 0.00 46.32 2.29
675 715 2.106511 ACTCCCTGTGCAACTTACACAT 59.893 45.455 0.00 0.00 46.32 3.21
676 716 1.488812 ACTCCCTGTGCAACTTACACA 59.511 47.619 0.00 0.00 45.42 3.72
677 717 2.256117 ACTCCCTGTGCAACTTACAC 57.744 50.000 0.00 0.00 38.04 2.90
678 718 4.131596 GTTAACTCCCTGTGCAACTTACA 58.868 43.478 0.00 0.00 38.04 2.41
679 719 4.213482 CAGTTAACTCCCTGTGCAACTTAC 59.787 45.833 4.77 0.00 38.04 2.34
680 720 4.101898 TCAGTTAACTCCCTGTGCAACTTA 59.898 41.667 4.77 0.00 38.04 2.24
681 721 3.118038 TCAGTTAACTCCCTGTGCAACTT 60.118 43.478 4.77 0.00 38.04 2.66
682 722 2.438021 TCAGTTAACTCCCTGTGCAACT 59.562 45.455 4.77 0.00 38.04 3.16
683 723 2.846193 TCAGTTAACTCCCTGTGCAAC 58.154 47.619 4.77 0.00 37.35 4.17
684 724 3.411446 CATCAGTTAACTCCCTGTGCAA 58.589 45.455 4.77 0.00 0.00 4.08
685 725 2.290260 CCATCAGTTAACTCCCTGTGCA 60.290 50.000 4.77 0.00 0.00 4.57
811 853 4.493747 CGGGAGGACGAGCCGTTC 62.494 72.222 1.80 0.02 41.37 3.95
841 884 0.793104 GTTTTGAGATTTCGCGGCCG 60.793 55.000 24.05 24.05 0.00 6.13
1230 1289 3.667960 GCAGACAAGCATTACACGAAAGG 60.668 47.826 0.00 0.00 0.00 3.11
1407 1466 1.139058 CGAGTTCCGAATTCCCCAGAT 59.861 52.381 0.00 0.00 41.76 2.90
1420 1479 7.954788 AATCAATTTATCTAGCTCGAGTTCC 57.045 36.000 15.13 0.00 0.00 3.62
1468 1532 1.202382 AGTTTATCTACGCTCGCCCAC 60.202 52.381 0.00 0.00 0.00 4.61
1788 2664 3.866883 GGCTAGCATTTTGCCACTTTA 57.133 42.857 18.24 0.00 46.52 1.85
1965 2847 9.135189 TGAATAATTTGGTTTCCTATCATCCAG 57.865 33.333 0.00 0.00 0.00 3.86
2112 2994 4.523083 TGAAGTGCAGGATAACATAACCC 58.477 43.478 0.00 0.00 0.00 4.11
2394 3287 2.771089 TCATCGCAAGCAGGATTATCC 58.229 47.619 2.40 2.40 34.73 2.59
2565 3478 6.490040 AGTGCTAGACAATTTAGAAAAAGGCA 59.510 34.615 0.00 0.00 0.00 4.75
2647 3560 8.808092 AGTAGTTCTTAGCAGACAGACTTTATT 58.192 33.333 0.00 0.00 0.00 1.40
3424 4356 7.373617 TCCTTAGTTTATAGCATCCATCACA 57.626 36.000 0.00 0.00 0.00 3.58
3717 5361 2.057922 AGGATGAAGAAGTGGTGTGGT 58.942 47.619 0.00 0.00 0.00 4.16
3742 5386 6.506538 AACCTATCAATCTGGTATTCAGCT 57.493 37.500 0.00 0.00 43.06 4.24
3874 5521 3.463048 AAGGAACGGAGGGAGTACTTA 57.537 47.619 0.00 0.00 0.00 2.24
3875 5522 2.322339 AAGGAACGGAGGGAGTACTT 57.678 50.000 0.00 0.00 0.00 2.24
3876 5523 2.322339 AAAGGAACGGAGGGAGTACT 57.678 50.000 0.00 0.00 0.00 2.73
3988 5635 8.997621 ACTTTTCATGATGGATCAAATGAAAG 57.002 30.769 16.81 12.94 42.20 2.62
3990 5637 9.246670 ACTACTTTTCATGATGGATCAAATGAA 57.753 29.630 0.00 1.60 40.69 2.57
4235 6928 2.511218 ACTACGACCCCACCACTCTATA 59.489 50.000 0.00 0.00 0.00 1.31
4236 6929 1.287146 ACTACGACCCCACCACTCTAT 59.713 52.381 0.00 0.00 0.00 1.98
4367 7063 7.970061 TGCGAAATTGAAGAAAATGGAAGATAG 59.030 33.333 0.00 0.00 0.00 2.08
4582 7292 5.278858 GGACGGAGGGAGTATATAACAAGTG 60.279 48.000 0.00 0.00 0.00 3.16
4614 7324 4.846779 ATTTGAATGCCAAACGTACACT 57.153 36.364 0.00 0.00 46.41 3.55
4615 7325 5.898630 AAATTTGAATGCCAAACGTACAC 57.101 34.783 0.00 0.00 46.41 2.90
4838 7552 2.540265 AGGGCAGAATATGAAGCGAG 57.460 50.000 0.00 0.00 0.00 5.03
4911 7625 0.033796 AGTATTCCCTCCGTCCACGA 60.034 55.000 0.00 0.00 43.02 4.35
4924 7638 6.349300 TGGGTGAGATCTGCTTAAAGTATTC 58.651 40.000 0.00 0.00 0.00 1.75
4926 7640 5.957771 TGGGTGAGATCTGCTTAAAGTAT 57.042 39.130 0.00 0.00 0.00 2.12
4927 7641 5.957771 ATGGGTGAGATCTGCTTAAAGTA 57.042 39.130 0.00 0.00 0.00 2.24
4928 7642 4.851639 ATGGGTGAGATCTGCTTAAAGT 57.148 40.909 0.00 0.00 0.00 2.66
4929 7643 7.222872 AGATAATGGGTGAGATCTGCTTAAAG 58.777 38.462 0.00 0.00 0.00 1.85
4977 7699 0.827089 CAACCCACCACCAGCAATGA 60.827 55.000 0.00 0.00 0.00 2.57
5073 8039 2.991434 TTGCTAGTCAGTCGTCACTC 57.009 50.000 0.00 0.00 0.00 3.51
5142 8113 0.690192 TCCAGGAACTTCGCCATTGA 59.310 50.000 0.00 0.00 34.60 2.57
5529 8506 2.454055 GCAAAATGCTTACGATCCAGC 58.546 47.619 0.00 0.19 40.96 4.85
5771 9643 4.646040 CCAAAAGATGGCTCATTACATGGA 59.354 41.667 0.00 0.00 43.80 3.41
6147 11153 5.128335 CCGTAGTCCTACCAAGATAAAAGGT 59.872 44.000 0.00 0.00 39.41 3.50
6547 12306 2.764010 TGTTAGCGATAAGAGAAGGCCA 59.236 45.455 5.01 0.00 0.00 5.36
6779 12751 4.925054 GGTTAACTTACACGTAGCATGTCA 59.075 41.667 5.42 0.00 0.00 3.58
6819 12793 4.574599 GACAAGAGTTTGGCAATGAAGT 57.425 40.909 0.00 0.00 42.21 3.01
7524 14362 8.300286 TCACATAAACAAGACAACAGAAAAACA 58.700 29.630 0.00 0.00 0.00 2.83
7588 14428 4.513318 CCTGAGCCCGAGAAGAATATTTTC 59.487 45.833 0.00 0.00 0.00 2.29
7619 14459 0.388134 CAGGCACTTGCTCACAATGC 60.388 55.000 0.38 0.00 41.70 3.56
7755 14595 5.287226 CCTAAACATGGTATAGTGTCCGTC 58.713 45.833 0.00 0.00 0.00 4.79
7757 14597 4.100498 ACCCTAAACATGGTATAGTGTCCG 59.900 45.833 0.00 0.00 0.00 4.79
7759 14599 9.052759 CATAAACCCTAAACATGGTATAGTGTC 57.947 37.037 0.00 0.00 0.00 3.67
7837 14677 5.895928 TCTCAGTTTCATGACTTCTATCCG 58.104 41.667 0.00 0.00 0.00 4.18
7856 14696 7.621285 CCATGGTCTCCCTCTATTAATATCTCA 59.379 40.741 2.57 0.00 0.00 3.27
8054 14897 5.220989 CCTGGCAATACAAATCAGAGATGTG 60.221 44.000 0.00 0.00 0.00 3.21
8072 14935 3.939939 TGCTGTCGCTTCCTGGCA 61.940 61.111 0.00 0.00 36.97 4.92
8080 14943 2.601666 TCCCAGAGTGCTGTCGCT 60.602 61.111 0.00 0.00 40.63 4.93
8086 14949 3.107402 TGTATTCTCTCCCAGAGTGCT 57.893 47.619 0.52 0.00 42.83 4.40
8288 15151 7.394359 ACCAACAAGTTCAGCAAGTATCAATAT 59.606 33.333 0.00 0.00 0.00 1.28
8298 15161 1.745232 ACGACCAACAAGTTCAGCAA 58.255 45.000 0.00 0.00 0.00 3.91
8310 15173 6.261381 AGCTAATAAAAAGTCACAACGACCAA 59.739 34.615 0.00 0.00 46.69 3.67
8378 15241 6.767524 AATATGCAATGTAACCCGAAGAAA 57.232 33.333 0.00 0.00 0.00 2.52
8432 15295 7.519032 AGGAGATTTGGTCGAATAAACAAAA 57.481 32.000 0.00 0.00 36.53 2.44
8507 15371 6.230472 AGCATCAAACTGTCACTGTTACATA 58.770 36.000 0.00 0.00 0.00 2.29
8564 15428 4.371855 TTCATACTTCGATCGAACAGCT 57.628 40.909 25.96 11.28 0.00 4.24
8578 15460 4.511617 ACGATCGATGCAGATTCATACT 57.488 40.909 24.34 0.00 0.00 2.12
8579 15461 5.394802 ACTACGATCGATGCAGATTCATAC 58.605 41.667 24.34 0.00 0.00 2.39
8580 15462 5.629079 ACTACGATCGATGCAGATTCATA 57.371 39.130 24.34 0.00 0.00 2.15
8581 15463 4.511617 ACTACGATCGATGCAGATTCAT 57.488 40.909 24.34 0.00 0.00 2.57
8582 15464 3.990318 ACTACGATCGATGCAGATTCA 57.010 42.857 24.34 0.00 0.00 2.57
8583 15465 5.631992 TCATACTACGATCGATGCAGATTC 58.368 41.667 24.34 0.00 0.00 2.52
8584 15466 5.629079 TCATACTACGATCGATGCAGATT 57.371 39.130 24.34 0.00 0.00 2.40
8585 15467 5.629079 TTCATACTACGATCGATGCAGAT 57.371 39.130 24.34 0.00 0.00 2.90
8586 15468 5.412904 AGATTCATACTACGATCGATGCAGA 59.587 40.000 24.34 9.28 0.00 4.26
8587 15469 5.511025 CAGATTCATACTACGATCGATGCAG 59.489 44.000 24.34 14.57 0.00 4.41
8588 15470 5.393962 CAGATTCATACTACGATCGATGCA 58.606 41.667 24.34 5.69 0.00 3.96
8589 15471 4.264145 GCAGATTCATACTACGATCGATGC 59.736 45.833 24.34 9.58 0.00 3.91
8590 15472 5.393962 TGCAGATTCATACTACGATCGATG 58.606 41.667 24.34 14.84 0.00 3.84
8591 15473 5.629079 TGCAGATTCATACTACGATCGAT 57.371 39.130 24.34 8.79 0.00 3.59
8592 15474 5.432885 TTGCAGATTCATACTACGATCGA 57.567 39.130 24.34 4.52 0.00 3.59
8593 15475 5.107837 GGTTTGCAGATTCATACTACGATCG 60.108 44.000 14.88 14.88 0.00 3.69
8594 15476 5.107837 CGGTTTGCAGATTCATACTACGATC 60.108 44.000 0.00 0.00 0.00 3.69
8595 15477 4.745125 CGGTTTGCAGATTCATACTACGAT 59.255 41.667 0.00 0.00 0.00 3.73
8596 15478 4.109766 CGGTTTGCAGATTCATACTACGA 58.890 43.478 0.00 0.00 0.00 3.43
8597 15479 4.109766 TCGGTTTGCAGATTCATACTACG 58.890 43.478 0.00 0.00 0.00 3.51
8598 15480 4.508124 CCTCGGTTTGCAGATTCATACTAC 59.492 45.833 0.00 0.00 0.00 2.73
8599 15481 4.693283 CCTCGGTTTGCAGATTCATACTA 58.307 43.478 0.00 0.00 0.00 1.82
8685 18105 2.580589 CAACCAAAACGCCATAGTTCG 58.419 47.619 0.00 0.00 32.43 3.95
8815 18319 9.793252 GCTTTGTACAGATCATGATAACATTTT 57.207 29.630 8.54 0.00 34.15 1.82
8816 18320 8.959548 TGCTTTGTACAGATCATGATAACATTT 58.040 29.630 8.54 0.00 34.15 2.32
8817 18321 8.510243 TGCTTTGTACAGATCATGATAACATT 57.490 30.769 8.54 0.00 34.15 2.71
8818 18322 8.510243 TTGCTTTGTACAGATCATGATAACAT 57.490 30.769 8.54 0.00 37.19 2.71
8819 18323 7.920160 TTGCTTTGTACAGATCATGATAACA 57.080 32.000 8.54 8.20 0.00 2.41
8820 18324 9.624697 TTTTTGCTTTGTACAGATCATGATAAC 57.375 29.630 8.54 5.69 0.00 1.89
8822 18326 9.791820 CATTTTTGCTTTGTACAGATCATGATA 57.208 29.630 8.54 0.00 0.00 2.15
8823 18327 7.762615 CCATTTTTGCTTTGTACAGATCATGAT 59.237 33.333 8.25 8.25 0.00 2.45
8824 18328 7.092079 CCATTTTTGCTTTGTACAGATCATGA 58.908 34.615 0.00 0.00 0.00 3.07
8825 18329 6.183360 GCCATTTTTGCTTTGTACAGATCATG 60.183 38.462 0.00 0.00 0.00 3.07
8826 18330 5.870978 GCCATTTTTGCTTTGTACAGATCAT 59.129 36.000 0.00 0.00 0.00 2.45
8827 18331 5.229423 GCCATTTTTGCTTTGTACAGATCA 58.771 37.500 0.00 0.00 0.00 2.92
8828 18332 4.627035 GGCCATTTTTGCTTTGTACAGATC 59.373 41.667 0.00 0.00 0.00 2.75
8829 18333 4.040217 TGGCCATTTTTGCTTTGTACAGAT 59.960 37.500 0.00 0.00 0.00 2.90
8830 18334 3.386078 TGGCCATTTTTGCTTTGTACAGA 59.614 39.130 0.00 0.00 0.00 3.41
8831 18335 3.494251 GTGGCCATTTTTGCTTTGTACAG 59.506 43.478 9.72 0.00 0.00 2.74
8832 18336 3.118629 TGTGGCCATTTTTGCTTTGTACA 60.119 39.130 9.72 0.00 0.00 2.90
8833 18337 3.462021 TGTGGCCATTTTTGCTTTGTAC 58.538 40.909 9.72 0.00 0.00 2.90
8834 18338 3.827008 TGTGGCCATTTTTGCTTTGTA 57.173 38.095 9.72 0.00 0.00 2.41
8835 18339 2.706339 TGTGGCCATTTTTGCTTTGT 57.294 40.000 9.72 0.00 0.00 2.83
8955 18462 4.083003 GCACCAACCAATCGTTTCAGATTA 60.083 41.667 0.00 0.00 38.66 1.75
8986 18493 8.456471 TCTGCATTGAAATTTATTGTCTCTCAG 58.544 33.333 0.00 0.00 0.00 3.35
8989 18549 9.798994 GATTCTGCATTGAAATTTATTGTCTCT 57.201 29.630 0.00 0.00 0.00 3.10
9058 18628 8.338072 TCCGAAATAATAACCTGCAAAACTAA 57.662 30.769 0.00 0.00 0.00 2.24
9059 18629 7.925043 TCCGAAATAATAACCTGCAAAACTA 57.075 32.000 0.00 0.00 0.00 2.24
9082 18652 8.787852 AGAGAATCATTTGTGTAGGAAAACTTC 58.212 33.333 0.00 0.00 37.82 3.01


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

AutoCloner maintained by Alex Coulton.