Multiple sequence alignment - TraesCS5B01G451500

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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 TraesCS5B01G451500 chr5B 100.000 8463 0 0 1 8463 622974359 622965897 0.000000e+00 15629.0
1 TraesCS5B01G451500 chr5B 93.968 1890 95 9 2909 4789 633309708 633311587 0.000000e+00 2841.0
2 TraesCS5B01G451500 chr5B 89.533 2293 143 38 655 2907 633307428 633309663 0.000000e+00 2815.0
3 TraesCS5B01G451500 chr5B 84.488 1515 145 33 4778 6241 633159342 633160817 0.000000e+00 1413.0
4 TraesCS5B01G451500 chr5B 83.344 1519 150 45 4778 6247 629961240 629959776 0.000000e+00 1308.0
5 TraesCS5B01G451500 chr5B 83.887 782 43 24 4778 5546 633311618 633312329 0.000000e+00 669.0
6 TraesCS5B01G451500 chr5B 80.108 930 104 29 6865 7747 629959485 629958590 1.210000e-172 617.0
7 TraesCS5B01G451500 chr5B 84.380 653 74 20 7 655 458700287 458699659 4.340000e-172 616.0
8 TraesCS5B01G451500 chr5B 84.688 640 58 16 898 1519 633156370 633156987 3.380000e-168 603.0
9 TraesCS5B01G451500 chr5B 89.095 486 47 4 4307 4789 633158829 633159311 4.370000e-167 599.0
10 TraesCS5B01G451500 chr5B 79.581 906 105 28 6865 7716 633161087 633161966 7.370000e-160 575.0
11 TraesCS5B01G451500 chr5B 88.163 490 47 8 4307 4789 629961756 629961271 2.650000e-159 573.0
12 TraesCS5B01G451500 chr5B 81.562 640 53 24 898 1519 629963305 629962713 1.290000e-127 468.0
13 TraesCS5B01G451500 chr5B 86.916 428 23 13 7391 7789 625216684 625216261 4.660000e-122 449.0
14 TraesCS5B01G451500 chr5B 86.916 428 23 13 7391 7789 628815775 628815352 4.660000e-122 449.0
15 TraesCS5B01G451500 chr5B 90.584 308 27 2 3987 4293 633158427 633158733 2.840000e-109 407.0
16 TraesCS5B01G451500 chr5B 87.193 367 27 12 2248 2594 629962609 629962243 4.760000e-107 399.0
17 TraesCS5B01G451500 chr5B 86.376 367 30 12 2248 2594 633157091 633157457 4.790000e-102 383.0
18 TraesCS5B01G451500 chr5B 88.673 309 32 2 2914 3222 633157629 633157934 2.880000e-99 374.0
19 TraesCS5B01G451500 chr5B 83.626 342 23 14 8114 8445 625216060 625215742 2.990000e-74 291.0
20 TraesCS5B01G451500 chr5B 82.935 293 28 12 8005 8295 633312327 633312599 2.360000e-60 244.0
21 TraesCS5B01G451500 chr5B 78.242 455 39 31 8006 8445 628815236 628814827 3.950000e-58 237.0
22 TraesCS5B01G451500 chr5B 88.950 181 11 5 8114 8292 629955853 629955680 1.850000e-51 215.0
23 TraesCS5B01G451500 chr5B 82.468 154 23 3 7924 8073 633162223 633162376 1.920000e-26 132.0
24 TraesCS5B01G451500 chr5B 92.593 54 0 1 8392 8441 629955630 629955577 3.280000e-09 75.0
25 TraesCS5B01G451500 chr5D 94.418 1899 79 8 2913 4789 501345245 501343352 0.000000e+00 2894.0
26 TraesCS5B01G451500 chr5D 87.603 2057 177 45 6005 8012 508276809 508274782 0.000000e+00 2314.0
27 TraesCS5B01G451500 chr5D 88.665 1641 91 26 6866 8463 501340167 501338579 0.000000e+00 1912.0
28 TraesCS5B01G451500 chr5D 92.515 1189 72 12 5694 6869 501342582 501341398 0.000000e+00 1687.0
29 TraesCS5B01G451500 chr5D 85.221 1563 152 41 1751 3291 508286747 508285242 0.000000e+00 1533.0
30 TraesCS5B01G451500 chr5D 85.335 1507 139 36 4778 6247 296922349 296923810 0.000000e+00 1483.0
31 TraesCS5B01G451500 chr5D 87.066 1152 86 22 4810 5927 296924159 296925281 0.000000e+00 1243.0
32 TraesCS5B01G451500 chr5D 84.199 1329 98 45 1491 2777 296918813 296920071 0.000000e+00 1188.0
33 TraesCS5B01G451500 chr5D 86.412 1126 86 25 1568 2660 501502859 501501768 0.000000e+00 1170.0
34 TraesCS5B01G451500 chr5D 89.290 887 65 15 850 1722 508287613 508286743 0.000000e+00 1085.0
35 TraesCS5B01G451500 chr5D 86.067 1012 84 19 653 1626 501346965 501345973 0.000000e+00 1035.0
36 TraesCS5B01G451500 chr5D 84.245 1060 95 26 6865 7881 501497370 501496340 0.000000e+00 966.0
37 TraesCS5B01G451500 chr5D 86.718 911 67 28 5371 6241 501498864 501497968 0.000000e+00 963.0
38 TraesCS5B01G451500 chr5D 88.531 776 41 19 4778 5541 501343321 501342582 0.000000e+00 896.0
39 TraesCS5B01G451500 chr5D 87.105 791 83 5 4000 4789 501500226 501499454 0.000000e+00 878.0
40 TraesCS5B01G451500 chr5D 93.214 501 30 4 4291 4789 508277621 508277123 0.000000e+00 734.0
41 TraesCS5B01G451500 chr5D 87.023 655 62 11 898 1544 501503492 501502853 0.000000e+00 717.0
42 TraesCS5B01G451500 chr5D 87.973 582 43 10 4778 5346 501499423 501498856 0.000000e+00 662.0
43 TraesCS5B01G451500 chr5D 94.686 414 14 6 2501 2907 501345702 501345290 3.330000e-178 636.0
44 TraesCS5B01G451500 chr5D 96.140 285 10 1 4779 5062 508277089 508276805 1.660000e-126 464.0
45 TraesCS5B01G451500 chr5D 89.103 312 32 1 2981 3292 501501768 501501459 3.710000e-103 387.0
46 TraesCS5B01G451500 chr5D 87.097 341 29 8 850 1178 508288989 508288652 1.040000e-98 372.0
47 TraesCS5B01G451500 chr5D 93.562 233 14 1 2138 2370 501345937 501345706 6.290000e-91 346.0
48 TraesCS5B01G451500 chr5D 89.377 273 20 7 2997 3264 296920146 296920414 1.360000e-87 335.0
49 TraesCS5B01G451500 chr5D 76.031 655 83 39 7350 7934 296929129 296929779 1.080000e-68 272.0
50 TraesCS5B01G451500 chr5D 87.192 203 23 2 4486 4688 296922135 296922334 2.380000e-55 228.0
51 TraesCS5B01G451500 chr5D 80.480 333 22 16 8114 8442 501496223 501495930 1.850000e-51 215.0
52 TraesCS5B01G451500 chr5D 87.770 139 13 3 653 789 501347594 501347458 8.790000e-35 159.0
53 TraesCS5B01G451500 chr5D 95.652 46 2 0 2936 2981 296920102 296920147 3.280000e-09 75.0
54 TraesCS5B01G451500 chr5A 90.494 2188 144 29 5694 7838 626028412 626030578 0.000000e+00 2830.0
55 TraesCS5B01G451500 chr5A 91.657 1810 104 20 2663 4462 626025983 626027755 0.000000e+00 2462.0
56 TraesCS5B01G451500 chr5A 85.462 2380 223 53 5517 7838 625707757 625710071 0.000000e+00 2364.0
57 TraesCS5B01G451500 chr5A 88.723 1809 135 32 824 2603 626024219 626025987 0.000000e+00 2146.0
58 TraesCS5B01G451500 chr5A 86.693 1518 114 38 4778 6248 599474813 599473337 0.000000e+00 1604.0
59 TraesCS5B01G451500 chr5A 87.761 1103 100 17 1567 2660 599484691 599483615 0.000000e+00 1256.0
60 TraesCS5B01G451500 chr5A 87.121 792 85 9 4000 4789 599475620 599474844 0.000000e+00 881.0
61 TraesCS5B01G451500 chr5A 89.301 701 41 13 4778 5458 625707076 625707762 0.000000e+00 848.0
62 TraesCS5B01G451500 chr5A 86.951 774 67 19 4023 4789 625706299 625707045 0.000000e+00 839.0
63 TraesCS5B01G451500 chr5A 84.644 547 52 14 999 1544 599485199 599484684 4.530000e-142 516.0
64 TraesCS5B01G451500 chr5A 81.061 660 74 31 2248 2886 625704119 625704748 5.940000e-131 479.0
65 TraesCS5B01G451500 chr5A 87.563 394 36 8 2909 3292 625704803 625705193 2.170000e-120 444.0
66 TraesCS5B01G451500 chr5A 87.387 333 22 5 5204 5535 626028093 626028406 1.740000e-96 364.0
67 TraesCS5B01G451500 chr5A 81.497 481 48 11 6865 7322 599473053 599472591 2.910000e-94 357.0
68 TraesCS5B01G451500 chr5A 83.978 362 26 13 4823 5172 626027751 626028092 1.370000e-82 318.0
69 TraesCS5B01G451500 chr5A 79.418 481 37 33 8006 8463 626030660 626031101 5.000000e-72 283.0
70 TraesCS5B01G451500 chr5A 88.995 209 21 2 3780 3987 625705184 625705391 3.030000e-64 257.0
71 TraesCS5B01G451500 chr5A 80.000 320 50 11 7501 7815 599472502 599472192 3.070000e-54 224.0
72 TraesCS5B01G451500 chr5A 81.364 220 26 8 6028 6247 577925839 577925635 1.890000e-36 165.0
73 TraesCS5B01G451500 chr5A 84.091 132 9 6 6945 7075 577925318 577925198 5.370000e-22 117.0
74 TraesCS5B01G451500 chr5A 95.556 45 2 0 7062 7106 577923898 577923854 1.180000e-08 73.1
75 TraesCS5B01G451500 chr3B 85.951 1509 125 39 4778 6248 460166705 460165246 0.000000e+00 1531.0
76 TraesCS5B01G451500 chr3B 90.343 932 50 13 7161 8054 21001495 21000566 0.000000e+00 1186.0
77 TraesCS5B01G451500 chr3B 87.690 788 88 6 4000 4784 460167522 460166741 0.000000e+00 909.0
78 TraesCS5B01G451500 chr3B 86.364 858 79 19 1808 2660 460169698 460168874 0.000000e+00 902.0
79 TraesCS5B01G451500 chr3B 89.431 492 47 4 3292 3778 490890715 490891206 4.340000e-172 616.0
80 TraesCS5B01G451500 chr3B 81.643 779 94 16 6731 7494 460165183 460164439 1.220000e-167 601.0
81 TraesCS5B01G451500 chr3B 80.119 674 78 35 918 1565 460170348 460169705 1.300000e-122 451.0
82 TraesCS5B01G451500 chr3B 87.668 373 37 3 2920 3292 460168872 460168509 7.850000e-115 425.0
83 TraesCS5B01G451500 chr2A 90.977 931 45 12 7161 8054 546773465 546772537 0.000000e+00 1218.0
84 TraesCS5B01G451500 chr2A 90.088 454 30 5 7612 8051 27110495 27110947 7.370000e-160 575.0
85 TraesCS5B01G451500 chr2A 95.973 149 6 0 7161 7309 27110352 27110500 8.490000e-60 243.0
86 TraesCS5B01G451500 chr3A 91.446 491 39 3 3291 3779 38273081 38273570 0.000000e+00 671.0
87 TraesCS5B01G451500 chr3A 83.812 661 81 13 7 654 742880727 742880080 9.400000e-169 604.0
88 TraesCS5B01G451500 chr3A 87.897 504 47 10 3292 3783 500991444 500991945 1.580000e-161 580.0
89 TraesCS5B01G451500 chr3A 94.545 55 3 0 593 647 746951857 746951803 1.510000e-12 86.1
90 TraesCS5B01G451500 chr6A 85.061 656 76 9 7 653 196337249 196336607 0.000000e+00 649.0
91 TraesCS5B01G451500 chr7B 89.496 476 48 2 3290 3763 612313107 612313582 1.220000e-167 601.0
92 TraesCS5B01G451500 chr7B 89.783 460 43 4 3291 3747 709247261 709246803 3.400000e-163 586.0
93 TraesCS5B01G451500 chr7B 82.769 650 81 21 7 644 120161811 120162441 1.240000e-152 551.0
94 TraesCS5B01G451500 chr3D 83.564 651 81 13 7 644 34048009 34048646 3.400000e-163 586.0
95 TraesCS5B01G451500 chr7A 88.889 477 48 5 3290 3763 648144751 648145225 4.400000e-162 582.0
96 TraesCS5B01G451500 chr7A 84.000 475 51 15 191 654 413113285 413113745 4.690000e-117 433.0
97 TraesCS5B01G451500 chr7A 96.296 54 2 0 594 647 543809604 543809551 1.170000e-13 89.8
98 TraesCS5B01G451500 chr7A 96.296 54 2 0 594 647 676422467 676422414 1.170000e-13 89.8
99 TraesCS5B01G451500 chr4A 85.383 561 67 8 4 563 520957284 520957830 1.230000e-157 568.0
100 TraesCS5B01G451500 chrUn 82.931 621 77 17 5 611 161630256 161630861 4.500000e-147 532.0
101 TraesCS5B01G451500 chr1A 83.721 559 77 11 7 562 355632145 355631598 4.530000e-142 516.0
102 TraesCS5B01G451500 chr4B 83.114 533 74 11 7 537 662378627 662379145 9.940000e-129 472.0
103 TraesCS5B01G451500 chr6B 87.273 220 19 4 1679 1892 42830745 42830529 8.490000e-60 243.0
104 TraesCS5B01G451500 chr1D 80.132 151 21 8 501 644 355671240 355671388 4.180000e-18 104.0


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 TraesCS5B01G451500 chr5B 622965897 622974359 8462 True 15629.000000 15629 100.000000 1 8463 1 chr5B.!!$R2 8462
1 TraesCS5B01G451500 chr5B 633307428 633312599 5171 False 1642.250000 2841 87.580750 655 8295 4 chr5B.!!$F2 7640
2 TraesCS5B01G451500 chr5B 458699659 458700287 628 True 616.000000 616 84.380000 7 655 1 chr5B.!!$R1 648
3 TraesCS5B01G451500 chr5B 633156370 633162376 6006 False 560.750000 1413 85.744125 898 8073 8 chr5B.!!$F1 7175
4 TraesCS5B01G451500 chr5B 629955577 629963305 7728 True 522.142857 1308 85.987571 898 8441 7 chr5B.!!$R5 7543
5 TraesCS5B01G451500 chr5B 625215742 625216684 942 True 370.000000 449 85.271000 7391 8445 2 chr5B.!!$R3 1054
6 TraesCS5B01G451500 chr5B 628814827 628815775 948 True 343.000000 449 82.579000 7391 8445 2 chr5B.!!$R4 1054
7 TraesCS5B01G451500 chr5D 501338579 501347594 9015 True 1195.625000 2894 90.776750 653 8463 8 chr5D.!!$R1 7810
8 TraesCS5B01G451500 chr5D 508274782 508277621 2839 True 1170.666667 2314 92.319000 4291 8012 3 chr5D.!!$R3 3721
9 TraesCS5B01G451500 chr5D 508285242 508288989 3747 True 996.666667 1533 87.202667 850 3291 3 chr5D.!!$R4 2441
10 TraesCS5B01G451500 chr5D 501495930 501503492 7562 True 744.750000 1170 86.132375 898 8442 8 chr5D.!!$R2 7544
11 TraesCS5B01G451500 chr5D 296918813 296929779 10966 False 689.142857 1483 86.407429 1491 7934 7 chr5D.!!$F1 6443
12 TraesCS5B01G451500 chr5A 626024219 626031101 6882 False 1400.500000 2830 86.942833 824 8463 6 chr5A.!!$F2 7639
13 TraesCS5B01G451500 chr5A 599483615 599485199 1584 True 886.000000 1256 86.202500 999 2660 2 chr5A.!!$R3 1661
14 TraesCS5B01G451500 chr5A 625704119 625710071 5952 False 871.833333 2364 86.555500 2248 7838 6 chr5A.!!$F1 5590
15 TraesCS5B01G451500 chr5A 599472192 599475620 3428 True 766.500000 1604 83.827750 4000 7815 4 chr5A.!!$R2 3815
16 TraesCS5B01G451500 chr3B 21000566 21001495 929 True 1186.000000 1186 90.343000 7161 8054 1 chr3B.!!$R1 893
17 TraesCS5B01G451500 chr3B 460164439 460170348 5909 True 803.166667 1531 84.905833 918 7494 6 chr3B.!!$R2 6576
18 TraesCS5B01G451500 chr2A 546772537 546773465 928 True 1218.000000 1218 90.977000 7161 8054 1 chr2A.!!$R1 893
19 TraesCS5B01G451500 chr2A 27110352 27110947 595 False 409.000000 575 93.030500 7161 8051 2 chr2A.!!$F1 890
20 TraesCS5B01G451500 chr3A 742880080 742880727 647 True 604.000000 604 83.812000 7 654 1 chr3A.!!$R1 647
21 TraesCS5B01G451500 chr3A 500991444 500991945 501 False 580.000000 580 87.897000 3292 3783 1 chr3A.!!$F2 491
22 TraesCS5B01G451500 chr6A 196336607 196337249 642 True 649.000000 649 85.061000 7 653 1 chr6A.!!$R1 646
23 TraesCS5B01G451500 chr7B 120161811 120162441 630 False 551.000000 551 82.769000 7 644 1 chr7B.!!$F1 637
24 TraesCS5B01G451500 chr3D 34048009 34048646 637 False 586.000000 586 83.564000 7 644 1 chr3D.!!$F1 637
25 TraesCS5B01G451500 chr4A 520957284 520957830 546 False 568.000000 568 85.383000 4 563 1 chr4A.!!$F1 559
26 TraesCS5B01G451500 chrUn 161630256 161630861 605 False 532.000000 532 82.931000 5 611 1 chrUn.!!$F1 606
27 TraesCS5B01G451500 chr1A 355631598 355632145 547 True 516.000000 516 83.721000 7 562 1 chr1A.!!$R1 555
28 TraesCS5B01G451500 chr4B 662378627 662379145 518 False 472.000000 472 83.114000 7 537 1 chr4B.!!$F1 530

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
150 152 1.002033 CTTGCAACTGAGCACCTGTTC 60.002 52.381 0.00 0.0 45.61 3.18 F
1432 3572 0.859232 CGTGTTCACACTGGCTACAC 59.141 55.000 8.41 0.0 44.34 2.90 F
2541 4816 0.329596 GAAGACCTCAGGGCAATGGT 59.670 55.000 0.00 0.0 35.63 3.55 F
3723 7138 0.188587 TCTCATATCGGGAGTGGCCT 59.811 55.000 3.32 0.0 36.66 5.19 F
5340 11671 0.464554 GCACAATACTCCCCTCCTGC 60.465 60.000 0.00 0.0 0.00 4.85 F
6409 12807 0.331616 GCCCACCCCACATCTAACTT 59.668 55.000 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 4054 0.320421 TAGCAACCTCAGTTCCACGC 60.320 55.000 0.00 0.00 32.45 5.34 R
2989 5361 1.211703 TCTGAAAGATATGGCGCCCAA 59.788 47.619 26.77 12.83 38.67 4.12 R
4321 8886 0.615331 TCCAGCTGGACCTTCATCAC 59.385 55.000 32.00 0.00 39.78 3.06 R
5381 11712 1.302752 GTGAGGTGCATGCCACTCA 60.303 57.895 27.62 27.62 44.08 3.41 R
6537 12936 0.535335 GTGCCAGGGATACTCGAACA 59.465 55.000 0.00 0.00 0.00 3.18 R
8221 21968 0.108992 CCTGCAAAGCCGAGTACGTA 60.109 55.000 0.00 0.00 37.88 3.57 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
40 42 1.118838 CCGCTTCTCTCCTTCATCCT 58.881 55.000 0.00 0.00 0.00 3.24
101 103 7.037802 TCCTACCTATACGTGGAATCTCATCTA 60.038 40.741 0.00 0.00 0.00 1.98
125 127 2.878429 CAGAGCGCTCCGTACTGT 59.122 61.111 32.94 10.71 31.96 3.55
150 152 1.002033 CTTGCAACTGAGCACCTGTTC 60.002 52.381 0.00 0.00 45.61 3.18
271 280 8.621532 AGTCTTGTTGCAAGAATACATAGAAA 57.378 30.769 21.65 0.00 0.00 2.52
343 353 9.921637 AGAGTCTTGTTACAGAAAAATAGAGAG 57.078 33.333 0.00 0.00 0.00 3.20
345 355 8.652290 AGTCTTGTTACAGAAAAATAGAGAGGT 58.348 33.333 0.00 0.00 0.00 3.85
359 369 8.635765 AAATAGAGAGGTAGTTTTGCATCAAA 57.364 30.769 0.00 0.00 0.00 2.69
360 370 8.814038 AATAGAGAGGTAGTTTTGCATCAAAT 57.186 30.769 0.00 0.00 33.19 2.32
394 404 9.736023 TGCAGAAAAATAGAGAAGAAAAAGTTC 57.264 29.630 0.00 0.00 0.00 3.01
413 423 4.657039 AGTTCTACAACAGGGGTCTTGTTA 59.343 41.667 0.00 0.00 34.60 2.41
414 424 5.309806 AGTTCTACAACAGGGGTCTTGTTAT 59.690 40.000 0.00 0.00 34.60 1.89
460 470 1.305201 TTTGCAACGGAGGTCTTGTC 58.695 50.000 0.00 0.00 0.00 3.18
468 478 5.335661 GCAACGGAGGTCTTGTCATAAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
514 524 1.682854 CAGGGCTCTTGTTGCAGAAAA 59.317 47.619 0.00 0.00 0.00 2.29
515 525 1.959282 AGGGCTCTTGTTGCAGAAAAG 59.041 47.619 0.00 0.00 0.00 2.27
517 527 2.287849 GGGCTCTTGTTGCAGAAAAGTC 60.288 50.000 5.38 0.00 0.00 3.01
518 528 2.358898 GGCTCTTGTTGCAGAAAAGTCA 59.641 45.455 5.38 0.00 0.00 3.41
519 529 3.549625 GGCTCTTGTTGCAGAAAAGTCAG 60.550 47.826 5.38 0.00 0.00 3.51
523 533 4.704540 TCTTGTTGCAGAAAAGTCAGGAAA 59.295 37.500 5.38 0.00 0.00 3.13
658 673 1.221840 CGTAGCACTGCCCAATCCT 59.778 57.895 0.00 0.00 0.00 3.24
684 699 1.589993 CGCATCGCTTCGATCCAGT 60.590 57.895 0.00 0.00 45.19 4.00
688 703 2.960957 ATCGCTTCGATCCAGTGGCG 62.961 60.000 3.51 3.22 43.45 5.69
778 1433 9.010029 TGACCTGGTTTATTTACAAGAGATTTC 57.990 33.333 0.00 0.00 0.00 2.17
780 1435 9.588096 ACCTGGTTTATTTACAAGAGATTTCTT 57.412 29.630 0.00 0.00 44.45 2.52
816 1471 8.857694 TTCCGTTAAAATAATCCTCTGTTTCT 57.142 30.769 0.00 0.00 0.00 2.52
819 1508 8.604890 CCGTTAAAATAATCCTCTGTTTCTCTC 58.395 37.037 0.00 0.00 0.00 3.20
883 2947 4.402528 TGGTATGGCGCCGCAGTT 62.403 61.111 23.90 6.41 0.00 3.16
1221 3317 4.452733 GGTGAGGCGACGGGGAAG 62.453 72.222 0.00 0.00 0.00 3.46
1222 3318 3.692406 GTGAGGCGACGGGGAAGT 61.692 66.667 0.00 0.00 0.00 3.01
1223 3319 3.379445 TGAGGCGACGGGGAAGTC 61.379 66.667 0.00 0.00 37.76 3.01
1224 3320 4.144703 GAGGCGACGGGGAAGTCC 62.145 72.222 0.00 0.00 37.85 3.85
1428 3568 1.591594 CGTCGTGTTCACACTGGCT 60.592 57.895 8.41 0.00 44.34 4.75
1432 3572 0.859232 CGTGTTCACACTGGCTACAC 59.141 55.000 8.41 0.00 44.34 2.90
1565 3750 9.755804 TGTCAATGCTTCATCTAGTAGATTTAG 57.244 33.333 10.09 10.95 31.32 1.85
1566 3751 9.757227 GTCAATGCTTCATCTAGTAGATTTAGT 57.243 33.333 10.09 0.00 31.32 2.24
1590 3775 2.503765 TGTCAGTTCCTCAAGGTGTTCA 59.496 45.455 0.00 0.00 36.34 3.18
1667 3852 6.360618 TGCTTGTTGAAATAAACCCCATTTT 58.639 32.000 0.00 0.00 0.00 1.82
1668 3853 6.830838 TGCTTGTTGAAATAAACCCCATTTTT 59.169 30.769 0.00 0.00 0.00 1.94
1669 3854 7.138081 GCTTGTTGAAATAAACCCCATTTTTG 58.862 34.615 0.00 0.00 0.00 2.44
1670 3855 7.201776 GCTTGTTGAAATAAACCCCATTTTTGT 60.202 33.333 0.00 0.00 0.00 2.83
1671 3856 8.581253 TTGTTGAAATAAACCCCATTTTTGTT 57.419 26.923 0.00 0.00 0.00 2.83
1672 3857 8.581253 TGTTGAAATAAACCCCATTTTTGTTT 57.419 26.923 0.00 0.00 36.30 2.83
1673 3858 9.025041 TGTTGAAATAAACCCCATTTTTGTTTT 57.975 25.926 0.00 0.00 34.33 2.43
1692 3882 9.589111 TTTGTTTTTGTATTAAACCTGAAGGAC 57.411 29.630 2.62 0.00 38.94 3.85
1731 3921 5.362430 AGAAAGGGCAACACAGTAAATCAAA 59.638 36.000 0.00 0.00 39.74 2.69
1749 3939 4.681744 TCAAATTGTGTTGCTGTCCTTTC 58.318 39.130 0.00 0.00 0.00 2.62
1760 3950 2.032178 GCTGTCCTTTCACACACAAGTC 59.968 50.000 0.00 0.00 0.00 3.01
1761 3951 3.270027 CTGTCCTTTCACACACAAGTCA 58.730 45.455 0.00 0.00 0.00 3.41
1878 4083 5.746990 ACTGAGGTTGCTACTTAACTGAT 57.253 39.130 0.00 0.00 0.00 2.90
1892 4098 0.549950 ACTGATGGCCATCTCCAAGG 59.450 55.000 38.59 24.40 39.96 3.61
1930 4136 5.175673 GTCTGTTTTTGCTCAGGTTAATTGC 59.824 40.000 0.00 0.00 33.13 3.56
1969 4175 4.695455 TGTGCATTGCTAAGGTTTAGAGAC 59.305 41.667 10.49 0.00 0.00 3.36
2006 4215 9.810231 GATTATCGCTTACTAGTTACTACAGAC 57.190 37.037 0.00 0.00 0.00 3.51
2044 4253 4.590647 TGGTATTAGAGCTGATTCTGAGGG 59.409 45.833 0.00 0.00 0.00 4.30
2128 4337 5.801531 AAGGTTTACTTTTTGCCCCTAAG 57.198 39.130 0.00 0.00 35.35 2.18
2129 4338 4.811498 AGGTTTACTTTTTGCCCCTAAGT 58.189 39.130 0.00 0.00 36.23 2.24
2130 4339 5.213519 AGGTTTACTTTTTGCCCCTAAGTT 58.786 37.500 0.00 0.00 34.26 2.66
2131 4340 6.375418 AGGTTTACTTTTTGCCCCTAAGTTA 58.625 36.000 0.00 0.00 34.26 2.24
2132 4341 6.492429 AGGTTTACTTTTTGCCCCTAAGTTAG 59.508 38.462 2.65 2.65 34.26 2.34
2216 4425 1.742308 AGTTACCTCTTTCCCTGCCA 58.258 50.000 0.00 0.00 0.00 4.92
2227 4436 5.030147 TCTTTCCCTGCCAGTTTCTCTATA 58.970 41.667 0.00 0.00 0.00 1.31
2241 4474 7.069331 CAGTTTCTCTATAGGAACATCAGGAGT 59.931 40.741 0.00 0.00 42.90 3.85
2265 4498 5.982890 CTGCTTTGAATTAAAGAAGGGGA 57.017 39.130 1.45 0.00 45.00 4.81
2356 4620 1.090052 GCCTATGCACGGAAGGTCAC 61.090 60.000 8.01 0.00 37.47 3.67
2499 4773 8.917088 CATTAGGGATTTTTACTCCATGTGAAT 58.083 33.333 0.00 0.00 34.24 2.57
2541 4816 0.329596 GAAGACCTCAGGGCAATGGT 59.670 55.000 0.00 0.00 35.63 3.55
2565 4843 5.819991 AGAAGCTCTAGGATGATAGGAGAG 58.180 45.833 0.00 0.00 37.34 3.20
2575 4853 1.839994 TGATAGGAGAGGGCAAACCAG 59.160 52.381 0.00 0.00 43.89 4.00
2680 4964 1.298993 CCAGCCTCTCACATGCAGT 59.701 57.895 0.00 0.00 0.00 4.40
2734 5022 2.230660 AGCCAGAGTTAAAACTGCACC 58.769 47.619 0.00 0.00 39.88 5.01
2907 5220 0.792640 CCACGCACTGCACTTTAGAG 59.207 55.000 1.11 0.00 0.00 2.43
2908 5221 1.502231 CACGCACTGCACTTTAGAGT 58.498 50.000 1.11 0.00 36.25 3.24
2911 5276 3.493129 CACGCACTGCACTTTAGAGTTTA 59.507 43.478 1.11 0.00 32.54 2.01
2989 5361 1.286248 AGAGGCCAACCGGAATAAGT 58.714 50.000 9.46 0.00 42.76 2.24
3034 5433 2.398554 CCATCAAGCCAACCGTCGG 61.399 63.158 10.48 10.48 0.00 4.79
3049 5452 2.190578 CGGACCAGAATGAGGCCC 59.809 66.667 0.00 0.00 39.69 5.80
3214 5622 6.749118 GCTAAAGTGCTCCAAATATTTCACTG 59.251 38.462 16.63 8.92 35.28 3.66
3547 6953 2.620234 TCCGATCTGGAAGGCCATT 58.380 52.632 5.01 0.00 46.38 3.16
3621 7029 3.009033 TGCCTAGCAGTTAATTGGTCAGT 59.991 43.478 5.89 0.00 33.32 3.41
3658 7066 5.500234 TGACAGCTGATAAATAGGCTTGTT 58.500 37.500 23.35 0.00 32.30 2.83
3681 7089 4.828829 AGACAAATTAACTGGACCTACCG 58.171 43.478 0.00 0.00 42.61 4.02
3721 7136 1.412710 TGTTCTCATATCGGGAGTGGC 59.587 52.381 0.00 0.00 34.04 5.01
3723 7138 0.188587 TCTCATATCGGGAGTGGCCT 59.811 55.000 3.32 0.00 36.66 5.19
3793 7216 2.260822 ACAGTGCTCTTATCCACACCT 58.739 47.619 0.00 0.00 34.48 4.00
3796 7219 2.906389 AGTGCTCTTATCCACACCTGAA 59.094 45.455 0.00 0.00 34.48 3.02
3872 7302 5.948992 AAGCAGTGAAGAAATAGGTTGTC 57.051 39.130 0.00 0.00 0.00 3.18
3962 7401 3.873801 GCTTCAACCTCCCAGCAATTCTA 60.874 47.826 0.00 0.00 32.17 2.10
4016 8495 1.987080 AGAATCCCAGTTAAGCCCCT 58.013 50.000 0.00 0.00 0.00 4.79
4043 8522 0.543883 TCTGGCAAGCCTCTCTGAGT 60.544 55.000 12.96 0.00 36.94 3.41
4113 8592 1.614413 ACGTCTCTTCACCCTTCAGAC 59.386 52.381 0.00 0.00 0.00 3.51
4128 8607 5.312079 CCTTCAGACTTTTCAGAACAGGAT 58.688 41.667 1.40 0.00 0.00 3.24
4162 8641 2.168521 TCCTCCAGGTCATTCGCTTTAG 59.831 50.000 0.00 0.00 36.34 1.85
4269 8748 3.590824 CCAGGCGGCTTCGATTTT 58.409 55.556 9.66 0.00 35.61 1.82
4286 8765 7.486802 TCGATTTTAAGAGAAAACGAAGGTT 57.513 32.000 0.00 0.00 39.66 3.50
4288 8767 8.066000 TCGATTTTAAGAGAAAACGAAGGTTTC 58.934 33.333 2.59 2.59 45.35 2.78
4289 8768 7.853929 CGATTTTAAGAGAAAACGAAGGTTTCA 59.146 33.333 12.32 0.00 45.35 2.69
4321 8886 1.324736 GCAAATAGCTCACGTTCCTCG 59.675 52.381 0.00 0.00 42.31 4.63
4515 9082 3.136260 GCTTCTCTCTGAATCCCTCCATT 59.864 47.826 0.00 0.00 33.71 3.16
4694 10859 1.828979 ACCGTGTTCTCTCTCTCCTC 58.171 55.000 0.00 0.00 0.00 3.71
4695 10860 0.730265 CCGTGTTCTCTCTCTCCTCG 59.270 60.000 0.00 0.00 0.00 4.63
4745 10910 3.181489 GCAATTTCCTGGAGCTCAAGATG 60.181 47.826 20.42 10.72 0.00 2.90
4763 10928 9.635520 CTCAAGATGCTCAATCAAGTTTTTAAT 57.364 29.630 0.00 0.00 37.81 1.40
4786 10997 3.764218 GGCCCATCATTCTGAGATTGAT 58.236 45.455 12.65 12.65 34.36 2.57
4829 11109 7.944729 ATCAGGCAACACACTATTCTTTATT 57.055 32.000 0.00 0.00 41.41 1.40
4868 11148 9.559732 TTGAGAAAAAGAATCTTATCACTGTCA 57.440 29.630 0.00 0.00 0.00 3.58
5019 11321 3.194755 TCTTGTACCATTAGCGCTCTGAA 59.805 43.478 16.34 2.41 0.00 3.02
5066 11373 3.197766 CAGGACCTCAGCCACAATACTTA 59.802 47.826 0.00 0.00 0.00 2.24
5137 11462 4.454504 TGAGAAAAATTTCTGTAGCGACCC 59.545 41.667 12.85 0.00 46.84 4.46
5232 11562 3.730715 CGGTGAACAAACAAGAAGATTGC 59.269 43.478 0.00 0.00 33.67 3.56
5233 11563 4.681744 GGTGAACAAACAAGAAGATTGCA 58.318 39.130 0.00 0.00 33.67 4.08
5234 11564 5.291971 GGTGAACAAACAAGAAGATTGCAT 58.708 37.500 0.00 0.00 33.67 3.96
5235 11565 5.754890 GGTGAACAAACAAGAAGATTGCATT 59.245 36.000 0.00 0.00 33.67 3.56
5236 11566 6.292488 GGTGAACAAACAAGAAGATTGCATTG 60.292 38.462 0.00 0.00 33.67 2.82
5237 11567 6.476380 GTGAACAAACAAGAAGATTGCATTGA 59.524 34.615 2.61 0.00 33.67 2.57
5238 11568 6.476380 TGAACAAACAAGAAGATTGCATTGAC 59.524 34.615 2.61 7.27 33.67 3.18
5276 11606 2.338785 GGAAGCAGCAACCAGAGCC 61.339 63.158 0.00 0.00 0.00 4.70
5277 11607 2.282745 AAGCAGCAACCAGAGCCC 60.283 61.111 0.00 0.00 0.00 5.19
5279 11609 3.060615 GCAGCAACCAGAGCCCAG 61.061 66.667 0.00 0.00 0.00 4.45
5340 11671 0.464554 GCACAATACTCCCCTCCTGC 60.465 60.000 0.00 0.00 0.00 4.85
5363 11694 1.181741 TGGCAACGGCTTTAATGGCA 61.182 50.000 14.14 6.23 44.73 4.92
5381 11712 1.338389 GCATGGCTGATGGTTTTGCTT 60.338 47.619 0.00 0.00 31.99 3.91
5463 11794 0.823460 CTCTTCCCTCCTGTCTCTGC 59.177 60.000 0.00 0.00 0.00 4.26
5550 11881 2.092646 ACACCTCGACTATCTGAGAGCT 60.093 50.000 0.00 0.00 34.04 4.09
5568 11899 2.827642 GCTGGCTGATGCACTCCC 60.828 66.667 0.00 0.00 41.91 4.30
5604 11949 1.535462 GCATGTTGCACGACTTTACCT 59.465 47.619 0.00 0.00 44.26 3.08
5686 12031 1.540146 CCATGTTGTGTCGGTGACTCA 60.540 52.381 0.00 0.00 34.85 3.41
5810 12155 4.347607 CATCCCCTCTCCTTTTGATTTGT 58.652 43.478 0.00 0.00 0.00 2.83
5811 12156 4.034285 TCCCCTCTCCTTTTGATTTGTC 57.966 45.455 0.00 0.00 0.00 3.18
5812 12157 3.657727 TCCCCTCTCCTTTTGATTTGTCT 59.342 43.478 0.00 0.00 0.00 3.41
5813 12158 4.106341 TCCCCTCTCCTTTTGATTTGTCTT 59.894 41.667 0.00 0.00 0.00 3.01
5864 12218 2.001812 ATAGATCCGTGCATGCGATC 57.998 50.000 20.25 20.25 0.00 3.69
5893 12247 3.894427 TGGTTGGAAGCAATGTGTTATGT 59.106 39.130 0.00 0.00 32.80 2.29
5978 12339 1.171308 AGATGAATGCACCACACTGC 58.829 50.000 0.00 0.00 37.70 4.40
6002 12363 3.056322 AGCATTTTCAGGAGAATTGGCAC 60.056 43.478 0.00 0.00 32.89 5.01
6064 12457 7.122353 TGAGAGAAACTAGGACATGGTACTAAC 59.878 40.741 0.00 0.00 27.51 2.34
6090 12486 5.547465 TGGAGTACAGGTATTCAGTTTGTG 58.453 41.667 0.00 0.00 0.00 3.33
6145 12542 0.912486 GCTCTTCCCTCTTAAGCCCA 59.088 55.000 0.00 0.00 0.00 5.36
6158 12555 1.145571 AAGCCCAAACCACCTGACTA 58.854 50.000 0.00 0.00 0.00 2.59
6163 12560 3.497227 GCCCAAACCACCTGACTAAACTA 60.497 47.826 0.00 0.00 0.00 2.24
6381 12779 4.451096 CCCAATATTCCCGAATCAACTACG 59.549 45.833 0.00 0.00 32.50 3.51
6409 12807 0.331616 GCCCACCCCACATCTAACTT 59.668 55.000 0.00 0.00 0.00 2.66
6458 12857 2.344203 CGACTTCCAGTCCCTCGCT 61.344 63.158 0.00 0.00 42.12 4.93
6468 12867 2.736995 CCCTCGCTTCGTCGCAAA 60.737 61.111 0.00 0.00 0.00 3.68
6488 12887 3.644966 AACCTTCTGAAGAACCACACA 57.355 42.857 18.68 0.00 0.00 3.72
6513 12912 2.127232 GAAGCCGCGCTGTTGAAC 60.127 61.111 5.56 0.00 39.62 3.18
6537 12936 0.463654 TGTCAACAAGCAAGACCGCT 60.464 50.000 0.00 0.00 46.67 5.52
6611 13022 4.452455 GTCAACCAAGTCTGTATTCAGGTG 59.548 45.833 0.00 0.00 41.59 4.00
6634 13046 1.001406 GCATCCAGTCTATCTTCCCCG 59.999 57.143 0.00 0.00 0.00 5.73
6684 13097 0.820871 GAGAGAAGACGCATCCCAGT 59.179 55.000 0.00 0.00 0.00 4.00
6692 13105 2.166664 AGACGCATCCCAGTAGAAGAAC 59.833 50.000 0.00 0.00 0.00 3.01
6711 13124 7.884877 AGAAGAACTCCAATACATCAACATTCA 59.115 33.333 0.00 0.00 0.00 2.57
6740 13190 3.338249 TCTGCACTTCCATTTCTGTAGC 58.662 45.455 0.00 0.00 0.00 3.58
6754 13204 0.673985 TGTAGCGTGCAGAAGACAGT 59.326 50.000 0.00 0.00 0.00 3.55
6760 13211 2.159310 GCGTGCAGAAGACAGTAGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
7207 17410 3.706373 TTCCAGTGGCTCGGGCTC 61.706 66.667 7.48 0.20 38.73 4.70
7370 18238 2.746362 CTCATGAACCTTGGTCTGAAGC 59.254 50.000 0.00 0.00 0.00 3.86
7496 18395 6.871844 TGAATCCACACTGAAATGTTTTGAA 58.128 32.000 0.00 0.00 0.00 2.69
7584 18513 0.599204 CCGTGCAGTAAACCGTCAGT 60.599 55.000 0.00 0.00 0.00 3.41
7588 18517 1.862201 TGCAGTAAACCGTCAGTTTCG 59.138 47.619 0.00 0.00 45.85 3.46
7678 18650 2.514458 ATCCCTTGGGTTTGTAGCAG 57.486 50.000 5.51 0.00 0.00 4.24
7922 21478 1.569479 AAAGAAGAAGACGCGGCTGC 61.569 55.000 19.28 16.46 37.91 5.25
7937 21502 3.620300 CTGCTGCACATTGGCGGTG 62.620 63.158 0.00 0.08 42.25 4.94
8073 21646 1.134753 TGGCAGCACTGTGAAAACTTG 59.865 47.619 12.86 0.87 0.00 3.16
8107 21817 3.628008 AGAAAGAAGATGGATGCATGCA 58.372 40.909 25.04 25.04 0.00 3.96
8108 21818 4.215908 AGAAAGAAGATGGATGCATGCAT 58.784 39.130 32.66 32.66 41.76 3.96
8109 21819 4.038042 AGAAAGAAGATGGATGCATGCATG 59.962 41.667 36.73 22.70 39.04 4.06
8192 21925 4.579384 CGTGTGGGTTGTGGGGCT 62.579 66.667 0.00 0.00 0.00 5.19
8214 21961 2.565391 ACCATGCATGCATTGGGATATG 59.435 45.455 32.75 21.00 33.90 1.78
8224 21971 4.177026 GCATTGGGATATGCTCTAGTACG 58.823 47.826 0.00 0.00 45.80 3.67
8227 21974 5.954296 TTGGGATATGCTCTAGTACGTAC 57.046 43.478 18.10 18.10 0.00 3.67
8230 21977 4.329528 GGGATATGCTCTAGTACGTACTCG 59.670 50.000 30.53 24.11 43.34 4.18
8369 22134 2.629098 CCAATCCCAATCCCAATCCCAA 60.629 50.000 0.00 0.00 0.00 4.12
8370 22135 3.320129 CAATCCCAATCCCAATCCCAAT 58.680 45.455 0.00 0.00 0.00 3.16
8371 22136 2.773525 TCCCAATCCCAATCCCAATC 57.226 50.000 0.00 0.00 0.00 2.67
8372 22137 1.220236 TCCCAATCCCAATCCCAATCC 59.780 52.381 0.00 0.00 0.00 3.01
8373 22138 1.720781 CCAATCCCAATCCCAATCCC 58.279 55.000 0.00 0.00 0.00 3.85
8374 22139 1.062275 CCAATCCCAATCCCAATCCCA 60.062 52.381 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.452651 CGCTGGCCCATCAGAATGT 60.453 57.895 0.00 0.00 36.93 2.71
2 3 2.517875 GCGCTGGCCCATCAGAAT 60.518 61.111 0.00 0.00 36.93 2.40
40 42 3.128349 GCGGCCATTTCGTTAGAGATAA 58.872 45.455 2.24 0.00 0.00 1.75
80 82 6.208797 TGGTTAGATGAGATTCCACGTATAGG 59.791 42.308 0.00 0.00 0.00 2.57
82 84 7.602753 CATGGTTAGATGAGATTCCACGTATA 58.397 38.462 0.00 0.00 0.00 1.47
89 91 4.965814 TCTGCATGGTTAGATGAGATTCC 58.034 43.478 0.00 0.00 0.00 3.01
125 127 2.104792 AGGTGCTCAGTTGCAAGAACTA 59.895 45.455 0.00 0.00 45.12 2.24
150 152 0.594796 GTTGCAGTGTGCCTTTTCGG 60.595 55.000 0.00 0.00 44.23 4.30
174 180 1.892819 CGTGGTCTCTGCATCACCCT 61.893 60.000 6.44 0.00 0.00 4.34
226 234 2.138596 ATTGTTGCGAAACCTTGCAG 57.861 45.000 3.18 0.00 42.89 4.41
271 280 3.108376 GGACCCAACATCTCTAGGTTCT 58.892 50.000 0.00 0.00 0.00 3.01
343 353 6.215845 ACAAGACATTTGATGCAAAACTACC 58.784 36.000 0.00 0.00 36.90 3.18
345 355 6.200665 GCAACAAGACATTTGATGCAAAACTA 59.799 34.615 14.58 0.00 44.33 2.24
359 369 7.750229 TCTCTATTTTTCTGCAACAAGACAT 57.250 32.000 0.00 0.00 0.00 3.06
360 370 7.498900 TCTTCTCTATTTTTCTGCAACAAGACA 59.501 33.333 0.00 0.00 0.00 3.41
394 404 6.295719 ACTATAACAAGACCCCTGTTGTAG 57.704 41.667 14.26 14.26 40.58 2.74
396 406 6.691255 TTACTATAACAAGACCCCTGTTGT 57.309 37.500 0.00 0.00 38.56 3.32
435 445 3.020984 AGACCTCCGTTGCAAAAGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
436 446 2.650322 AGACCTCCGTTGCAAAAGAAA 58.350 42.857 0.00 0.00 0.00 2.52
437 447 2.341846 AGACCTCCGTTGCAAAAGAA 57.658 45.000 0.00 0.00 0.00 2.52
438 448 1.946768 CAAGACCTCCGTTGCAAAAGA 59.053 47.619 0.00 0.00 0.00 2.52
439 449 1.676006 ACAAGACCTCCGTTGCAAAAG 59.324 47.619 0.00 0.00 0.00 2.27
496 506 1.683385 ACTTTTCTGCAACAAGAGCCC 59.317 47.619 6.26 0.00 0.00 5.19
523 533 3.748568 TGCTTTTGTTGCGAAACCTTTTT 59.251 34.783 3.18 0.00 0.00 1.94
563 573 2.097056 GCGAGCCGTCCGTTTTTATATC 60.097 50.000 0.00 0.00 0.00 1.63
564 574 1.862827 GCGAGCCGTCCGTTTTTATAT 59.137 47.619 0.00 0.00 0.00 0.86
565 575 1.280066 GCGAGCCGTCCGTTTTTATA 58.720 50.000 0.00 0.00 0.00 0.98
567 577 2.028733 GGCGAGCCGTCCGTTTTTA 61.029 57.895 0.00 0.00 0.00 1.52
570 580 4.736896 GAGGCGAGCCGTCCGTTT 62.737 66.667 8.63 0.00 41.95 3.60
615 630 2.425668 CGGCCGGTGGATCTTTTAAAAT 59.574 45.455 20.10 0.00 0.00 1.82
658 673 3.010585 GAAGCGATGCGTGCGTTCA 62.011 57.895 0.00 0.00 37.44 3.18
688 703 1.330655 TGAGATCGTTCAGCTCCCCC 61.331 60.000 0.00 0.00 0.00 5.40
789 1444 9.338291 GAAACAGAGGATTATTTTAACGGAAAC 57.662 33.333 0.00 0.00 0.00 2.78
802 1457 2.753452 ACGCGAGAGAAACAGAGGATTA 59.247 45.455 15.93 0.00 0.00 1.75
1565 3750 3.069729 ACACCTTGAGGAACTGACACTAC 59.930 47.826 3.59 0.00 41.55 2.73
1566 3751 3.305720 ACACCTTGAGGAACTGACACTA 58.694 45.455 3.59 0.00 41.55 2.74
1567 3752 2.119495 ACACCTTGAGGAACTGACACT 58.881 47.619 3.59 0.00 41.55 3.55
1667 3852 8.973182 AGTCCTTCAGGTTTAATACAAAAACAA 58.027 29.630 0.00 0.00 38.34 2.83
1668 3853 8.528044 AGTCCTTCAGGTTTAATACAAAAACA 57.472 30.769 0.00 0.00 38.34 2.83
1672 3857 9.498176 GTTCTAGTCCTTCAGGTTTAATACAAA 57.502 33.333 0.00 0.00 36.34 2.83
1673 3858 8.653191 TGTTCTAGTCCTTCAGGTTTAATACAA 58.347 33.333 0.00 0.00 36.34 2.41
1692 3882 3.084786 CCTTTCTTTGGGGCTGTTCTAG 58.915 50.000 0.00 0.00 0.00 2.43
1731 3921 3.023119 TGTGAAAGGACAGCAACACAAT 58.977 40.909 0.00 0.00 35.77 2.71
1749 3939 3.117794 CTGCCATTTTGACTTGTGTGTG 58.882 45.455 0.00 0.00 0.00 3.82
1849 4054 0.320421 TAGCAACCTCAGTTCCACGC 60.320 55.000 0.00 0.00 32.45 5.34
1850 4055 1.000955 AGTAGCAACCTCAGTTCCACG 59.999 52.381 0.00 0.00 32.45 4.94
1892 4098 6.129088 GCAAAAACAGACAATAGCTAAGTTGC 60.129 38.462 0.00 1.47 0.00 4.17
1969 4175 5.807520 AGTAAGCGATAATCAAGTGTCACTG 59.192 40.000 6.18 1.30 0.00 3.66
2006 4215 6.582636 TCTAATACCATGTAGGAACAGCAAG 58.417 40.000 0.00 0.00 39.49 4.01
2044 4253 5.128919 AGTTCCTTGATCATAATGTGCTCC 58.871 41.667 0.00 0.00 0.00 4.70
2068 4277 6.934645 ACAGTAGTTGCTAACTTGCTGATTTA 59.065 34.615 23.16 1.94 41.56 1.40
2162 4371 7.149973 GGGACTAAGGGTGAAAATTTGTTTAC 58.850 38.462 0.00 0.00 0.00 2.01
2216 4425 7.129425 ACTCCTGATGTTCCTATAGAGAAACT 58.871 38.462 0.00 0.00 0.00 2.66
2227 4436 2.264455 AGCAGAACTCCTGATGTTCCT 58.736 47.619 0.00 0.00 45.78 3.36
2241 4474 6.074648 TCCCCTTCTTTAATTCAAAGCAGAA 58.925 36.000 7.87 0.00 42.95 3.02
2265 4498 6.296026 TGGTTTTGAGCTATGTACAGACTTT 58.704 36.000 0.33 0.00 0.00 2.66
2356 4620 4.160065 TGAGGGCATGTGTTTAATTCATGG 59.840 41.667 13.17 0.00 39.20 3.66
2477 4750 6.256053 ACATTCACATGGAGTAAAAATCCCT 58.744 36.000 0.00 0.00 35.86 4.20
2499 4773 2.429930 CTGGCCGGTGGAGAAACA 59.570 61.111 2.29 0.00 0.00 2.83
2541 4816 6.069673 CCTCTCCTATCATCCTAGAGCTTCTA 60.070 46.154 0.00 0.00 33.80 2.10
2575 4853 6.691508 AGGATGTTCTTTTGGTAAGCAAATC 58.308 36.000 0.00 0.00 0.00 2.17
2734 5022 3.324993 GAGTGTTGAAGCTGAAGGAGAG 58.675 50.000 0.00 0.00 0.00 3.20
2892 5203 5.106908 CCTTCTAAACTCTAAAGTGCAGTGC 60.107 44.000 8.58 8.58 35.36 4.40
2907 5220 7.148222 GGAAAGTGGATAAAGAGCCTTCTAAAC 60.148 40.741 0.00 0.00 31.96 2.01
2908 5221 6.884836 GGAAAGTGGATAAAGAGCCTTCTAAA 59.115 38.462 0.00 0.00 31.96 1.85
2911 5276 4.538089 AGGAAAGTGGATAAAGAGCCTTCT 59.462 41.667 0.00 0.00 34.29 2.85
2989 5361 1.211703 TCTGAAAGATATGGCGCCCAA 59.788 47.619 26.77 12.83 38.67 4.12
3034 5433 1.683319 GGAAAGGGCCTCATTCTGGTC 60.683 57.143 6.46 0.00 0.00 4.02
3049 5452 2.818921 TCACATTGGGAATGGGGAAAG 58.181 47.619 0.00 0.00 42.63 2.62
3214 5622 8.097078 TCGTCTAAATACTGTAGAGGATTAGC 57.903 38.462 0.00 0.00 37.49 3.09
3547 6953 4.385825 CCTACTTTTCAGTGTGCAGGTTA 58.614 43.478 0.00 0.00 34.06 2.85
3621 7029 2.092968 AGCTGTCAGGCCAAATTATCGA 60.093 45.455 5.01 0.00 0.00 3.59
3658 7066 5.105228 CCGGTAGGTCCAGTTAATTTGTCTA 60.105 44.000 0.00 0.00 35.57 2.59
3701 7109 1.412710 GCCACTCCCGATATGAGAACA 59.587 52.381 0.00 0.00 33.95 3.18
3708 7116 1.734655 ATTCAGGCCACTCCCGATAT 58.265 50.000 5.01 0.00 34.51 1.63
3723 7138 6.923508 CGATATGGTCAGTTAACTGCTATTCA 59.076 38.462 27.49 19.50 43.46 2.57
3846 7269 6.547510 ACAACCTATTTCTTCACTGCTTTTCT 59.452 34.615 0.00 0.00 0.00 2.52
4016 8495 1.130054 AGGCTTGCCAGAGACCTTGA 61.130 55.000 14.54 0.00 0.00 3.02
4043 8522 3.282021 GCTGCATCACTTCAATTCCCTA 58.718 45.455 0.00 0.00 0.00 3.53
4113 8592 7.211966 AGAATCACAATCCTGTTCTGAAAAG 57.788 36.000 0.32 0.32 31.64 2.27
4128 8607 2.573462 CCTGGAGGAGGAAGAATCACAA 59.427 50.000 0.00 0.00 46.33 3.33
4172 8651 8.256605 TCAAATCTGGAGATTCAAACACAAAAA 58.743 29.630 2.36 0.00 43.41 1.94
4269 8748 7.795482 TGAATGAAACCTTCGTTTTCTCTTA 57.205 32.000 0.00 0.00 42.34 2.10
4321 8886 0.615331 TCCAGCTGGACCTTCATCAC 59.385 55.000 32.00 0.00 39.78 3.06
4515 9082 2.949177 TGAGGCTTTGTTGGCTAAGA 57.051 45.000 0.00 0.00 43.09 2.10
4745 10910 4.562789 GGCCGATTAAAAACTTGATTGAGC 59.437 41.667 0.00 0.00 0.00 4.26
4786 10997 3.269118 TGATTGGATGATTCTTGGGGACA 59.731 43.478 0.00 0.00 39.83 4.02
4829 11109 9.712305 ATTCTTTTTCTCAACGAGATTAAGAGA 57.288 29.630 13.46 6.53 38.46 3.10
4868 11148 1.383943 TGTGTATGGGCCTCCGGAT 60.384 57.895 3.57 0.00 35.24 4.18
5066 11373 9.193806 AGAAACTAAATTGGCTGATGTTGATAT 57.806 29.630 0.00 0.00 0.00 1.63
5232 11562 4.201657 TGGTGGATGCTCAATAGTCAATG 58.798 43.478 0.00 0.00 0.00 2.82
5233 11563 4.508551 TGGTGGATGCTCAATAGTCAAT 57.491 40.909 0.00 0.00 0.00 2.57
5234 11564 3.998913 TGGTGGATGCTCAATAGTCAA 57.001 42.857 0.00 0.00 0.00 3.18
5235 11565 3.264193 AGTTGGTGGATGCTCAATAGTCA 59.736 43.478 0.00 0.00 0.00 3.41
5236 11566 3.624861 CAGTTGGTGGATGCTCAATAGTC 59.375 47.826 0.00 0.00 0.00 2.59
5237 11567 3.614092 CAGTTGGTGGATGCTCAATAGT 58.386 45.455 0.00 0.00 0.00 2.12
5276 11606 1.344438 TGCTGGTTATATCGCCTCTGG 59.656 52.381 0.00 0.00 0.00 3.86
5277 11607 2.224042 TGTGCTGGTTATATCGCCTCTG 60.224 50.000 0.00 0.00 0.00 3.35
5279 11609 2.408050 CTGTGCTGGTTATATCGCCTC 58.592 52.381 0.00 0.00 0.00 4.70
5340 11671 2.736192 CCATTAAAGCCGTTGCCAAAAG 59.264 45.455 0.00 0.00 38.69 2.27
5363 11694 2.232941 CTCAAGCAAAACCATCAGCCAT 59.767 45.455 0.00 0.00 0.00 4.40
5381 11712 1.302752 GTGAGGTGCATGCCACTCA 60.303 57.895 27.62 27.62 44.08 3.41
5550 11881 2.045634 GGAGTGCATCAGCCAGCA 60.046 61.111 0.00 0.00 41.13 4.41
5563 11894 3.607370 GAGCGCCTTTTCCGGGAGT 62.607 63.158 2.29 0.00 0.00 3.85
5568 11899 3.854459 GCTCGAGCGCCTTTTCCG 61.854 66.667 23.61 0.00 0.00 4.30
5596 11941 2.351276 CGCCCAGGCAGGTAAAGT 59.649 61.111 9.78 0.00 42.06 2.66
5686 12031 3.332919 CTGTGCAGCTGACTTCAATACT 58.667 45.455 20.43 0.00 0.00 2.12
5810 12155 4.740154 TCCCCAGAATTCCTCAAAAAGA 57.260 40.909 0.65 0.00 0.00 2.52
5811 12156 5.018809 TGATCCCCAGAATTCCTCAAAAAG 58.981 41.667 0.65 0.00 0.00 2.27
5812 12157 5.009436 TGATCCCCAGAATTCCTCAAAAA 57.991 39.130 0.65 0.00 0.00 1.94
5813 12158 4.673328 TGATCCCCAGAATTCCTCAAAA 57.327 40.909 0.65 0.00 0.00 2.44
5864 12218 4.449743 CACATTGCTTCCAACCAAGAATTG 59.550 41.667 0.00 0.00 38.16 2.32
5923 12282 5.560966 TCAAAAGAAGAAACAAGTCGCTT 57.439 34.783 0.00 0.00 0.00 4.68
5978 12339 4.400251 TGCCAATTCTCCTGAAAATGCTAG 59.600 41.667 0.00 0.00 35.63 3.42
6064 12457 6.655003 ACAAACTGAATACCTGTACTCCAATG 59.345 38.462 0.00 0.00 0.00 2.82
6090 12486 4.037327 TCGACATGTTCATCTCATCCTCTC 59.963 45.833 0.00 0.00 0.00 3.20
6145 12542 4.386711 GCAGTAGTTTAGTCAGGTGGTTT 58.613 43.478 0.00 0.00 0.00 3.27
6158 12555 2.174854 AGTGAAAGGTGGGCAGTAGTTT 59.825 45.455 0.00 0.00 0.00 2.66
6163 12560 1.435256 AGTAGTGAAAGGTGGGCAGT 58.565 50.000 0.00 0.00 0.00 4.40
6363 12761 3.131577 AGTGCGTAGTTGATTCGGGAATA 59.868 43.478 0.00 0.00 0.00 1.75
6364 12762 2.093658 AGTGCGTAGTTGATTCGGGAAT 60.094 45.455 0.00 0.00 0.00 3.01
6381 12779 2.361230 GGGGTGGGCTGTTAGTGC 60.361 66.667 0.00 0.00 0.00 4.40
6409 12807 2.893441 AGCTCTGCTCTTCCGATGA 58.107 52.632 0.00 0.00 30.62 2.92
6458 12857 1.942677 TCAGAAGGTTTTGCGACGAA 58.057 45.000 0.00 0.00 0.00 3.85
6468 12867 3.279434 GTGTGTGGTTCTTCAGAAGGTT 58.721 45.455 10.42 0.00 34.27 3.50
6513 12912 3.120546 CGGTCTTGCTTGTTGACATAGTG 60.121 47.826 0.00 0.00 32.84 2.74
6537 12936 0.535335 GTGCCAGGGATACTCGAACA 59.465 55.000 0.00 0.00 0.00 3.18
6611 13022 2.301583 GGGAAGATAGACTGGATGCCTC 59.698 54.545 0.00 0.00 0.00 4.70
6684 13097 9.383519 GAATGTTGATGTATTGGAGTTCTTCTA 57.616 33.333 0.00 0.00 0.00 2.10
6692 13105 7.854557 TTCTCTGAATGTTGATGTATTGGAG 57.145 36.000 0.00 0.00 0.00 3.86
6711 13124 6.008960 AGAAATGGAAGTGCAGATTTTCTCT 58.991 36.000 0.00 0.00 28.61 3.10
6740 13190 3.773860 ATCTCTACTGTCTTCTGCACG 57.226 47.619 0.00 0.00 0.00 5.34
6754 13204 5.722290 TCTCTCACTCTCTCCCTATCTCTA 58.278 45.833 0.00 0.00 0.00 2.43
6760 13211 3.045634 CTCCTCTCTCACTCTCTCCCTA 58.954 54.545 0.00 0.00 0.00 3.53
7174 17366 1.444553 GAACTCCTCGACAGGTGCG 60.445 63.158 0.00 0.00 41.28 5.34
7285 17488 0.671781 CGGACAAGCCTGACCAGAAG 60.672 60.000 4.70 0.00 37.24 2.85
7496 18395 7.683463 GCCTCGCAAGGGTTATTATAAACAAAT 60.683 37.037 2.26 0.00 43.58 2.32
7584 18513 3.942748 ACTGCAACCAAAAGACTACGAAA 59.057 39.130 0.00 0.00 0.00 3.46
7588 18517 6.077838 CGAATAACTGCAACCAAAAGACTAC 58.922 40.000 0.00 0.00 0.00 2.73
7678 18650 1.065199 TGGATCTCAACCATCCACTGC 60.065 52.381 0.00 0.00 44.17 4.40
7716 18691 8.794335 AATTCTAGTTACAAACTTCCATCCTC 57.206 34.615 0.00 0.00 42.81 3.71
7718 18693 9.010029 TGAAATTCTAGTTACAAACTTCCATCC 57.990 33.333 0.00 0.00 42.81 3.51
7768 21215 3.682858 GCGAAAACTTACATCCTGTAGCA 59.317 43.478 0.00 0.00 33.92 3.49
7780 21240 2.481854 TGTTACGGCAGCGAAAACTTA 58.518 42.857 0.00 0.00 0.00 2.24
8073 21646 3.958147 TCTTCTTTCTTTTCCAACCACCC 59.042 43.478 0.00 0.00 0.00 4.61
8110 21820 0.947180 GTGGCCATGTGCAAAAGCTG 60.947 55.000 9.72 0.00 43.89 4.24
8111 21821 1.368579 GTGGCCATGTGCAAAAGCT 59.631 52.632 9.72 0.00 43.89 3.74
8112 21822 1.069427 TGTGGCCATGTGCAAAAGC 59.931 52.632 9.72 0.00 43.89 3.51
8192 21925 2.385135 ATCCCAATGCATGCATGGTA 57.615 45.000 32.79 21.84 36.68 3.25
8214 21961 1.580815 AGCCGAGTACGTACTAGAGC 58.419 55.000 30.17 28.01 36.50 4.09
8218 21965 1.811965 TGCAAAGCCGAGTACGTACTA 59.188 47.619 27.44 6.58 36.50 1.82
8219 21966 0.599558 TGCAAAGCCGAGTACGTACT 59.400 50.000 27.71 27.71 39.71 2.73
8220 21967 0.989890 CTGCAAAGCCGAGTACGTAC 59.010 55.000 18.10 18.10 37.88 3.67
8221 21968 0.108992 CCTGCAAAGCCGAGTACGTA 60.109 55.000 0.00 0.00 37.88 3.57
8222 21969 1.374252 CCTGCAAAGCCGAGTACGT 60.374 57.895 0.00 0.00 37.88 3.57
8223 21970 2.740714 GCCTGCAAAGCCGAGTACG 61.741 63.158 0.00 0.00 39.43 3.67
8224 21971 2.399356 GGCCTGCAAAGCCGAGTAC 61.399 63.158 11.41 0.00 41.41 2.73
8312 22073 3.443925 CGCAGGCGACAGAGGAGA 61.444 66.667 8.15 0.00 42.83 3.71
8369 22134 0.111253 GCTTCCATCGGGATTGGGAT 59.889 55.000 0.00 0.00 44.48 3.85
8370 22135 1.531748 GCTTCCATCGGGATTGGGA 59.468 57.895 0.00 0.00 44.48 4.37
8371 22136 1.529244 GGCTTCCATCGGGATTGGG 60.529 63.158 0.00 0.00 44.48 4.12
8372 22137 1.893808 CGGCTTCCATCGGGATTGG 60.894 63.158 0.00 0.00 44.48 3.16
8373 22138 1.893808 CCGGCTTCCATCGGGATTG 60.894 63.158 0.00 0.00 44.48 2.67
8374 22139 2.510906 CCGGCTTCCATCGGGATT 59.489 61.111 0.00 0.00 44.48 3.01


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

AutoCloner maintained by Alex Coulton.