Multiple sequence alignment - TraesCS4D01G078200

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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 TraesCS4D01G078200 chr4D 100.000 6519 0 0 1 6519 52491130 52497648 0.000000e+00 12039.0
1 TraesCS4D01G078200 chr4D 79.317 556 89 16 4756 5304 52753376 52753912 3.710000e-97 366.0
2 TraesCS4D01G078200 chr4D 89.116 294 31 1 5750 6043 52748559 52748851 1.340000e-96 364.0
3 TraesCS4D01G078200 chr4D 87.565 193 20 3 2697 2889 52752228 52752416 3.060000e-53 220.0
4 TraesCS4D01G078200 chr4D 88.816 152 15 2 4277 4427 52753080 52753230 1.120000e-42 185.0
5 TraesCS4D01G078200 chr4D 100.000 61 0 0 6423 6483 123337553 123337613 5.340000e-21 113.0
6 TraesCS4D01G078200 chr4D 100.000 61 0 0 6423 6483 123552008 123552068 5.340000e-21 113.0
7 TraesCS4D01G078200 chr4B 95.313 2987 104 21 2652 5632 77000621 77003577 0.000000e+00 4708.0
8 TraesCS4D01G078200 chr4B 91.370 1854 86 34 838 2635 76998800 77000635 0.000000e+00 2470.0
9 TraesCS4D01G078200 chr4B 87.867 750 42 15 5630 6375 77007101 77007805 0.000000e+00 835.0
10 TraesCS4D01G078200 chr4B 89.353 479 40 5 5899 6375 77509023 77509492 5.630000e-165 592.0
11 TraesCS4D01G078200 chr4B 78.445 566 103 16 4759 5317 77513592 77514145 1.040000e-92 351.0
12 TraesCS4D01G078200 chr4B 90.000 150 13 2 4279 4427 77513377 77513525 6.670000e-45 193.0
13 TraesCS4D01G078200 chr4A 93.611 2786 116 30 961 3708 544178653 544175892 0.000000e+00 4102.0
14 TraesCS4D01G078200 chr4A 94.458 1642 78 8 3995 5632 544175534 544173902 0.000000e+00 2516.0
15 TraesCS4D01G078200 chr4A 91.118 653 38 10 5630 6277 544172888 544172251 0.000000e+00 867.0
16 TraesCS4D01G078200 chr4A 85.784 408 42 7 5735 6139 544068035 544067641 1.010000e-112 418.0
17 TraesCS4D01G078200 chr4A 84.096 415 47 7 439 837 664168904 664169315 3.690000e-102 383.0
18 TraesCS4D01G078200 chr4A 91.489 282 15 2 3698 3979 544175849 544175577 4.770000e-101 379.0
19 TraesCS4D01G078200 chr4A 83.824 340 32 12 76 405 693523496 693523170 1.060000e-77 302.0
20 TraesCS4D01G078200 chr4A 84.337 249 31 6 2697 2945 544060139 544059899 3.040000e-58 237.0
21 TraesCS4D01G078200 chr4A 87.500 208 16 3 6135 6341 544062292 544062094 1.410000e-56 231.0
22 TraesCS4D01G078200 chr4A 97.260 73 2 0 6317 6389 544172255 544172183 2.470000e-24 124.0
23 TraesCS4D01G078200 chr4A 82.540 63 11 0 5890 5952 527004359 527004297 1.000000e-03 56.5
24 TraesCS4D01G078200 chr7D 86.284 802 83 12 59 840 625766847 625766053 0.000000e+00 846.0
25 TraesCS4D01G078200 chr6B 86.727 550 47 13 59 594 366739485 366738948 7.280000e-164 588.0
26 TraesCS4D01G078200 chr6B 87.041 463 54 3 376 837 660703994 660704451 9.690000e-143 518.0
27 TraesCS4D01G078200 chr6B 86.000 400 36 16 54 444 660703641 660704029 1.690000e-110 411.0
28 TraesCS4D01G078200 chr6D 87.387 444 39 14 410 838 239809421 239808980 1.630000e-135 494.0
29 TraesCS4D01G078200 chr6D 98.246 114 2 0 3881 3994 277272253 277272140 3.990000e-47 200.0
30 TraesCS4D01G078200 chr6D 88.966 145 16 0 270 414 239809529 239809385 5.190000e-41 180.0
31 TraesCS4D01G078200 chr6D 100.000 61 0 0 6423 6483 124519604 124519664 5.340000e-21 113.0
32 TraesCS4D01G078200 chr6D 100.000 61 0 0 6423 6483 168757172 168757232 5.340000e-21 113.0
33 TraesCS4D01G078200 chr6D 100.000 61 0 0 6423 6483 458900264 458900324 5.340000e-21 113.0
34 TraesCS4D01G078200 chr6D 100.000 37 0 0 6483 6519 99846931 99846895 1.170000e-07 69.4
35 TraesCS4D01G078200 chr2B 87.855 387 40 6 59 443 207118252 207117871 1.290000e-121 448.0
36 TraesCS4D01G078200 chr2B 83.908 435 54 11 376 796 207117905 207117473 1.020000e-107 401.0
37 TraesCS4D01G078200 chr2B 82.766 470 57 14 390 841 53906478 53906015 1.320000e-106 398.0
38 TraesCS4D01G078200 chr1A 84.000 475 57 11 376 834 587862233 587861762 7.760000e-119 438.0
39 TraesCS4D01G078200 chr1A 86.480 392 43 7 59 444 587862585 587862198 7.820000e-114 422.0
40 TraesCS4D01G078200 chr1A 83.532 419 50 9 439 841 581041813 581042228 2.220000e-99 374.0
41 TraesCS4D01G078200 chr1A 98.246 114 2 0 3881 3994 94738481 94738594 3.990000e-47 200.0
42 TraesCS4D01G078200 chr1D 84.988 433 47 10 407 839 373417640 373418054 2.170000e-114 424.0
43 TraesCS4D01G078200 chr1D 87.534 369 39 6 75 438 488613861 488613495 2.810000e-113 420.0
44 TraesCS4D01G078200 chr1D 87.989 358 35 4 59 411 373417322 373417676 3.640000e-112 416.0
45 TraesCS4D01G078200 chr1D 100.000 61 0 0 6423 6483 43234919 43234859 5.340000e-21 113.0
46 TraesCS4D01G078200 chr1D 100.000 61 0 0 6423 6483 269408882 269408942 5.340000e-21 113.0
47 TraesCS4D01G078200 chr1B 86.217 341 35 10 59 393 681050797 681051131 6.220000e-95 359.0
48 TraesCS4D01G078200 chr1B 98.246 114 2 0 3881 3994 135096695 135096808 3.990000e-47 200.0
49 TraesCS4D01G078200 chrUn 98.246 114 2 0 3881 3994 45131361 45131474 3.990000e-47 200.0
50 TraesCS4D01G078200 chrUn 98.246 114 2 0 3881 3994 267448838 267448725 3.990000e-47 200.0
51 TraesCS4D01G078200 chrUn 98.246 114 2 0 3881 3994 304293289 304293176 3.990000e-47 200.0
52 TraesCS4D01G078200 chrUn 98.246 114 2 0 3881 3994 369086944 369087057 3.990000e-47 200.0
53 TraesCS4D01G078200 chrUn 100.000 61 0 0 6423 6483 434805652 434805712 5.340000e-21 113.0
54 TraesCS4D01G078200 chrUn 80.851 141 27 0 5804 5944 54297258 54297118 1.920000e-20 111.0
55 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 45125856 45125892 1.170000e-07 69.4
56 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 86493050 86493086 1.170000e-07 69.4
57 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 186176415 186176379 1.170000e-07 69.4
58 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 247552975 247552939 1.170000e-07 69.4
59 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 345601474 345601438 1.170000e-07 69.4
60 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 400146970 400146934 1.170000e-07 69.4
61 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 454371959 454371923 1.170000e-07 69.4
62 TraesCS4D01G078200 chrUn 100.000 37 0 0 6483 6519 471890755 471890719 1.170000e-07 69.4
63 TraesCS4D01G078200 chr5D 98.246 114 2 0 3881 3994 80101065 80101178 3.990000e-47 200.0
64 TraesCS4D01G078200 chr2A 80.982 163 24 6 3029 3185 687067115 687067276 8.880000e-24 122.0
65 TraesCS4D01G078200 chr5B 98.485 66 1 0 6418 6483 701110575 701110510 4.130000e-22 117.0
66 TraesCS4D01G078200 chr5B 95.556 45 2 0 3992 4036 169041333 169041377 9.070000e-09 73.1
67 TraesCS4D01G078200 chr7A 78.528 163 24 7 3029 3185 642740791 642740948 5.380000e-16 97.1
68 TraesCS4D01G078200 chr7A 93.023 43 3 0 2413 2455 183860422 183860464 5.460000e-06 63.9
69 TraesCS4D01G078200 chr7B 86.538 52 7 0 1 52 55465436 55465487 2.540000e-04 58.4


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 TraesCS4D01G078200 chr4D 52491130 52497648 6518 False 12039.000000 12039 100.000000 1 6519 1 chr4D.!!$F1 6518
1 TraesCS4D01G078200 chr4D 52748559 52753912 5353 False 283.750000 366 86.203500 2697 6043 4 chr4D.!!$F4 3346
2 TraesCS4D01G078200 chr4B 76998800 77007805 9005 False 2671.000000 4708 91.516667 838 6375 3 chr4B.!!$F1 5537
3 TraesCS4D01G078200 chr4B 77509023 77514145 5122 False 378.666667 592 85.932667 4279 6375 3 chr4B.!!$F2 2096
4 TraesCS4D01G078200 chr4A 544172183 544178653 6470 True 1597.600000 4102 93.587200 961 6389 5 chr4A.!!$R5 5428
5 TraesCS4D01G078200 chr4A 544059899 544062292 2393 True 234.000000 237 85.918500 2697 6341 2 chr4A.!!$R4 3644
6 TraesCS4D01G078200 chr7D 625766053 625766847 794 True 846.000000 846 86.284000 59 840 1 chr7D.!!$R1 781
7 TraesCS4D01G078200 chr6B 366738948 366739485 537 True 588.000000 588 86.727000 59 594 1 chr6B.!!$R1 535
8 TraesCS4D01G078200 chr6B 660703641 660704451 810 False 464.500000 518 86.520500 54 837 2 chr6B.!!$F1 783
9 TraesCS4D01G078200 chr6D 239808980 239809529 549 True 337.000000 494 88.176500 270 838 2 chr6D.!!$R3 568
10 TraesCS4D01G078200 chr2B 207117473 207118252 779 True 424.500000 448 85.881500 59 796 2 chr2B.!!$R2 737
11 TraesCS4D01G078200 chr1A 587861762 587862585 823 True 430.000000 438 85.240000 59 834 2 chr1A.!!$R1 775
12 TraesCS4D01G078200 chr1D 373417322 373418054 732 False 420.000000 424 86.488500 59 839 2 chr1D.!!$F2 780

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
958 1130 0.105760 ATGAGAGATCCTGGTCCGCT 60.106 55.0 0.00 0.00 0.00 5.52 F
1584 1793 0.394216 TACCTAGTGTTCCGCCGCTA 60.394 55.0 0.00 0.00 0.00 4.26 F
1867 2076 0.450583 AAGCTGCAGATCATGTTGCG 59.549 50.0 20.43 9.45 43.13 4.85 F
3574 4805 0.462225 TGAACACCCTTGCGTTTCGA 60.462 50.0 0.00 0.00 0.00 3.71 F
4090 5409 0.400213 TTGTAAGCTGGTGTCCCCTG 59.600 55.0 0.00 0.00 35.34 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2602 1.304134 ATCAACTTGGGCGGGGAAC 60.304 57.895 0.00 0.00 0.00 3.62 R
3574 4805 1.963515 GTTGGAGTTTGTGGGAAGCAT 59.036 47.619 0.00 0.00 0.00 3.79 R
3750 5042 0.689623 CATCCCTCACCCTGCTATCC 59.310 60.000 0.00 0.00 0.00 2.59 R
5156 6503 0.035152 TTGCTCCGATGATGGTGCTT 60.035 50.000 8.13 0.00 46.19 3.91 R
5980 11394 0.033366 AAACTGAATTTGCCCGGTGC 59.967 50.000 0.00 4.04 41.77 5.01 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
18 19 3.238232 TTGCAGCAGAGGTGATGTC 57.762 52.632 0.00 0.00 42.40 3.06
19 20 0.671472 TTGCAGCAGAGGTGATGTCG 60.671 55.000 0.00 0.00 42.40 4.35
22 23 0.461516 CAGCAGAGGTGATGTCGCAT 60.462 55.000 0.00 0.00 35.23 4.73
24 25 1.482182 AGCAGAGGTGATGTCGCATAA 59.518 47.619 0.00 0.00 0.00 1.90
26 27 2.874701 GCAGAGGTGATGTCGCATAATT 59.125 45.455 0.00 0.00 0.00 1.40
27 28 3.313526 GCAGAGGTGATGTCGCATAATTT 59.686 43.478 0.00 0.00 0.00 1.82
28 29 4.201950 GCAGAGGTGATGTCGCATAATTTT 60.202 41.667 0.00 0.00 0.00 1.82
29 30 5.677091 GCAGAGGTGATGTCGCATAATTTTT 60.677 40.000 0.00 0.00 0.00 1.94
72 73 4.275689 CAGAAACATAGGTTGTGTTGCAGA 59.724 41.667 0.00 0.00 39.57 4.26
75 76 6.886459 AGAAACATAGGTTGTGTTGCAGATAT 59.114 34.615 0.00 0.00 39.57 1.63
78 79 7.466746 ACATAGGTTGTGTTGCAGATATTTT 57.533 32.000 0.00 0.00 37.11 1.82
79 80 7.895759 ACATAGGTTGTGTTGCAGATATTTTT 58.104 30.769 0.00 0.00 37.11 1.94
361 413 1.442769 CTGTTGTAGAAGCACGCCAT 58.557 50.000 0.00 0.00 0.00 4.40
365 417 3.000727 GTTGTAGAAGCACGCCATTACT 58.999 45.455 0.00 0.00 0.00 2.24
374 426 2.590092 GCCATTACTGGGGAGCGT 59.410 61.111 0.73 0.00 43.36 5.07
459 574 1.142688 ACCACAGCATCCCTCCCTTT 61.143 55.000 0.00 0.00 0.00 3.11
479 594 1.856629 ATTTCACCCCTGCAGGAATG 58.143 50.000 34.91 28.19 38.24 2.67
491 611 4.280819 CTGCAGGAATGGGGAAAAATCTA 58.719 43.478 5.57 0.00 0.00 1.98
529 649 2.209064 GATGCACACCTGCTGCTTGG 62.209 60.000 0.00 5.96 44.57 3.61
559 679 1.280142 CTACCTCAGATCGCGTCGG 59.720 63.158 5.77 4.21 0.00 4.79
560 680 1.437772 CTACCTCAGATCGCGTCGGT 61.438 60.000 5.77 8.67 0.00 4.69
823 982 2.186903 GAGATCGGCCGGCAGAAA 59.813 61.111 32.64 12.24 0.00 2.52
936 1108 2.317609 CGGTGCAAACGGAGACAGG 61.318 63.158 4.27 0.00 0.00 4.00
939 1111 1.305201 GTGCAAACGGAGACAGGAAA 58.695 50.000 0.00 0.00 0.00 3.13
943 1115 2.160417 GCAAACGGAGACAGGAAATGAG 59.840 50.000 0.00 0.00 0.00 2.90
949 1121 3.243704 CGGAGACAGGAAATGAGAGATCC 60.244 52.174 0.00 0.00 0.00 3.36
955 1127 3.044894 AGGAAATGAGAGATCCTGGTCC 58.955 50.000 0.00 0.00 41.96 4.46
958 1130 0.105760 ATGAGAGATCCTGGTCCGCT 60.106 55.000 0.00 0.00 0.00 5.52
998 1180 4.389576 GGCACGCTGTTGCTTCCG 62.390 66.667 2.36 0.00 42.56 4.30
1000 1182 3.349006 CACGCTGTTGCTTCCGCT 61.349 61.111 0.00 0.00 36.97 5.52
1001 1183 2.591715 ACGCTGTTGCTTCCGCTT 60.592 55.556 0.00 0.00 36.97 4.68
1002 1184 2.127118 CGCTGTTGCTTCCGCTTG 60.127 61.111 0.00 0.00 36.97 4.01
1003 1185 2.896801 CGCTGTTGCTTCCGCTTGT 61.897 57.895 0.00 0.00 36.97 3.16
1005 1187 1.785041 GCTGTTGCTTCCGCTTGTCA 61.785 55.000 0.00 0.00 36.97 3.58
1094 1278 3.066190 CTACCCGCCTCCGTCACA 61.066 66.667 0.00 0.00 0.00 3.58
1179 1363 0.691078 ACCTAGCATCCCACCATCGT 60.691 55.000 0.00 0.00 0.00 3.73
1180 1364 1.338107 CCTAGCATCCCACCATCGTA 58.662 55.000 0.00 0.00 0.00 3.43
1315 1501 4.021807 GGTTTCAAACCGTCCCATATGTTT 60.022 41.667 2.78 0.00 42.62 2.83
1376 1562 7.881643 ACGCATGCTTATTTGTCAAATTAAA 57.118 28.000 17.13 4.95 32.38 1.52
1584 1793 0.394216 TACCTAGTGTTCCGCCGCTA 60.394 55.000 0.00 0.00 0.00 4.26
1588 1797 0.533491 TAGTGTTCCGCCGCTAACAT 59.467 50.000 10.30 4.55 37.87 2.71
1609 1818 5.467399 ACATGGAAAATGATTGTTTGCTGTG 59.533 36.000 0.00 0.00 0.00 3.66
1700 1909 6.395629 TCATCCTATAGCAATAACTTACCGC 58.604 40.000 0.00 0.00 0.00 5.68
1712 1921 2.781595 CTTACCGCGGTTGACTGCCT 62.782 60.000 38.94 10.68 45.16 4.75
1867 2076 0.450583 AAGCTGCAGATCATGTTGCG 59.549 50.000 20.43 9.45 43.13 4.85
2256 2468 3.442625 GGCCCAGTTGTTTATCACCTTAC 59.557 47.826 0.00 0.00 0.00 2.34
2262 2483 7.881232 CCCAGTTGTTTATCACCTTACTCTAAA 59.119 37.037 0.00 0.00 0.00 1.85
2379 2602 6.930722 TGTGATCTGCATATATGTTACACTGG 59.069 38.462 14.14 0.00 0.00 4.00
2458 2681 8.749499 GCATTGAGCTGTTTTCATTAATGATAC 58.251 33.333 18.61 18.12 41.15 2.24
2623 2847 7.281999 TGACATGTTTGAATAGTGTCACTGAAA 59.718 33.333 16.03 6.50 42.82 2.69
2733 3884 6.040391 CCACCAAAGTTTCTGGTTATTCAGAA 59.960 38.462 3.50 3.50 45.13 3.02
2895 4093 9.525409 CATTTTGAAGATTATTCTTGCTTAGGG 57.475 33.333 4.64 0.00 42.34 3.53
2950 4149 3.863424 GCATGCACAATCATTTTCAGAGG 59.137 43.478 14.21 0.00 0.00 3.69
3185 4413 1.133199 TCAACCAAATGGAGGCCAAGT 60.133 47.619 5.01 0.00 36.95 3.16
3357 4585 2.202932 CGCTCCCACCAATCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
3360 4588 1.910580 GCTCCCACCAATCCTCGGAA 61.911 60.000 0.00 0.00 0.00 4.30
3423 4653 1.761784 ACAAAATGCCACAGCTCCAAA 59.238 42.857 0.00 0.00 40.80 3.28
3509 4739 4.338879 CCAGAGTTTCAAATCCTGATGGT 58.661 43.478 3.96 0.00 32.78 3.55
3574 4805 0.462225 TGAACACCCTTGCGTTTCGA 60.462 50.000 0.00 0.00 0.00 3.71
3602 4840 5.205056 TCCCACAAACTCCAACAAGTAATT 58.795 37.500 0.00 0.00 0.00 1.40
3693 4931 4.318332 CTCCAAGTTGTCAGTAGCAATCA 58.682 43.478 1.45 0.00 0.00 2.57
3750 5042 0.610687 GTCCTCCTCTTGGTCACAGG 59.389 60.000 0.00 0.00 34.23 4.00
3813 5105 4.080919 CCCTGTGATCAGTTGTCCAGATAA 60.081 45.833 9.65 0.00 39.82 1.75
3894 5186 2.028733 GCGCTGGCCAAAAACATGG 61.029 57.895 7.01 0.00 43.70 3.66
3966 5258 7.595819 AGAAACAGGTTACCATTTGATTTCA 57.404 32.000 3.51 0.00 0.00 2.69
4000 5319 6.749923 ACTCTTATTTGGCATTCAGTCTTC 57.250 37.500 0.00 0.00 0.00 2.87
4007 5326 1.128692 GGCATTCAGTCTTCGAAACCG 59.871 52.381 0.00 0.00 0.00 4.44
4090 5409 0.400213 TTGTAAGCTGGTGTCCCCTG 59.600 55.000 0.00 0.00 35.34 4.45
4239 5558 3.925379 TCACAGTGTATTCGAAGTGCAT 58.075 40.909 3.35 0.00 0.00 3.96
4286 5605 7.597743 CACTTTTATTGTCTGTTCTAGGTACGT 59.402 37.037 0.00 0.00 0.00 3.57
4322 5641 3.623060 CCAATGAAACCTCATACGGAGTG 59.377 47.826 0.00 0.00 41.66 3.51
4727 6074 2.337583 CGTGTGCAGCTTAGTGTGTAT 58.662 47.619 0.00 0.00 0.00 2.29
4748 6095 3.173965 TCTAATATGCTGGACCTAGCCC 58.826 50.000 11.80 0.00 43.02 5.19
4757 6104 1.281867 TGGACCTAGCCCTCATGTTTG 59.718 52.381 0.00 0.00 0.00 2.93
4758 6105 1.282157 GGACCTAGCCCTCATGTTTGT 59.718 52.381 0.00 0.00 0.00 2.83
4759 6106 2.290960 GGACCTAGCCCTCATGTTTGTT 60.291 50.000 0.00 0.00 0.00 2.83
5054 6401 7.867921 TCCTCATTTACTTCCTATTGCCTTTA 58.132 34.615 0.00 0.00 0.00 1.85
5116 6463 0.744414 CATGGGCTAACACCTGTCCG 60.744 60.000 0.00 0.00 0.00 4.79
5156 6503 2.281484 GACCGCCCTTTCACAGCA 60.281 61.111 0.00 0.00 0.00 4.41
5376 6724 1.600957 CTAGCAAGCGGACATGGATTG 59.399 52.381 0.00 0.00 34.11 2.67
5584 6935 4.385825 TCATACCATCGCCTATTTGTTCC 58.614 43.478 0.00 0.00 0.00 3.62
5628 6982 7.499563 GGGAAATTTCTAAGAGTTATCAGTCCC 59.500 40.741 17.42 1.38 0.00 4.46
5639 11049 0.038166 ATCAGTCCCGCATGTTTGGT 59.962 50.000 0.00 0.00 0.00 3.67
5668 11078 5.414789 ACACTTGTACACACTGCCATATA 57.585 39.130 0.00 0.00 0.00 0.86
5706 11116 6.721318 TCTGGGTAATGCCATATATCTTTCC 58.279 40.000 0.00 0.00 39.65 3.13
5721 11135 2.747446 TCTTTCCAGCGGCTAAATTGAC 59.253 45.455 0.26 0.00 0.00 3.18
5779 11193 0.674895 AATCAGTGAAGCACGGAGGC 60.675 55.000 0.00 0.00 41.23 4.70
5820 11234 0.181114 AGGCTGTGTGCTGAACAAGA 59.819 50.000 0.00 0.00 41.57 3.02
5892 11306 0.453950 CGGTCTCGTTTCGTCGTCAT 60.454 55.000 0.00 0.00 0.00 3.06
5931 11345 5.512749 GCTATCCTCATCTGATTCACCATGT 60.513 44.000 0.00 0.00 0.00 3.21
5955 11369 1.380403 CCACACAACGGCCAAGAACA 61.380 55.000 2.24 0.00 0.00 3.18
5971 11385 3.144506 AGAACACCTGCAGAATTCAGTG 58.855 45.455 17.39 15.64 0.00 3.66
5979 11393 4.940046 CCTGCAGAATTCAGTGAGTTACAT 59.060 41.667 17.39 0.00 0.00 2.29
5980 11394 5.163784 CCTGCAGAATTCAGTGAGTTACATG 60.164 44.000 17.39 2.76 0.00 3.21
5981 11395 4.154737 TGCAGAATTCAGTGAGTTACATGC 59.845 41.667 18.19 18.19 0.00 4.06
5982 11396 4.154737 GCAGAATTCAGTGAGTTACATGCA 59.845 41.667 19.27 0.00 0.00 3.96
6039 11453 5.470845 GCATCACGACTTGCTACTATTTT 57.529 39.130 0.00 0.00 35.95 1.82
6082 11496 4.419939 GGAAAAAGCGCCGGCAGG 62.420 66.667 28.98 12.69 43.41 4.85
6083 11497 3.361977 GAAAAAGCGCCGGCAGGA 61.362 61.111 28.98 0.00 43.41 3.86
6084 11498 3.610791 GAAAAAGCGCCGGCAGGAC 62.611 63.158 28.98 12.63 43.41 3.85
6085 11499 4.947147 AAAAGCGCCGGCAGGACA 62.947 61.111 28.98 0.00 43.41 4.02
6095 11509 2.031163 GCAGGACAGCCACTTCGT 59.969 61.111 0.00 0.00 36.29 3.85
6098 11512 3.112709 GGACAGCCACTTCGTCGC 61.113 66.667 0.00 0.00 0.00 5.19
6174 11588 3.865929 CTCAACGTCCAGCAGCGGT 62.866 63.158 0.00 0.00 0.00 5.68
6288 11702 6.453092 GGCTTTACCCTAACTTTTTCTTTCC 58.547 40.000 0.00 0.00 0.00 3.13
6289 11703 6.147581 GCTTTACCCTAACTTTTTCTTTCCG 58.852 40.000 0.00 0.00 0.00 4.30
6290 11704 5.694231 TTACCCTAACTTTTTCTTTCCGC 57.306 39.130 0.00 0.00 0.00 5.54
6291 11705 2.889045 ACCCTAACTTTTTCTTTCCGCC 59.111 45.455 0.00 0.00 0.00 6.13
6292 11706 2.230508 CCCTAACTTTTTCTTTCCGCCC 59.769 50.000 0.00 0.00 0.00 6.13
6299 11713 0.395862 TTTCTTTCCGCCCCACACAA 60.396 50.000 0.00 0.00 0.00 3.33
6395 11809 6.671614 TCATTAGGGCTTTAAATACACACG 57.328 37.500 0.00 0.00 0.00 4.49
6396 11810 4.950434 TTAGGGCTTTAAATACACACGC 57.050 40.909 0.00 0.00 0.00 5.34
6397 11811 2.785562 AGGGCTTTAAATACACACGCA 58.214 42.857 0.00 0.00 0.00 5.24
6398 11812 3.352648 AGGGCTTTAAATACACACGCAT 58.647 40.909 0.00 0.00 0.00 4.73
6399 11813 4.519213 AGGGCTTTAAATACACACGCATA 58.481 39.130 0.00 0.00 0.00 3.14
6400 11814 4.944930 AGGGCTTTAAATACACACGCATAA 59.055 37.500 0.00 0.00 0.00 1.90
6401 11815 5.065988 AGGGCTTTAAATACACACGCATAAG 59.934 40.000 0.00 0.00 0.00 1.73
6402 11816 5.065474 GGGCTTTAAATACACACGCATAAGA 59.935 40.000 0.00 0.00 0.00 2.10
6403 11817 6.192360 GGCTTTAAATACACACGCATAAGAG 58.808 40.000 0.00 0.00 0.00 2.85
6404 11818 6.192360 GCTTTAAATACACACGCATAAGAGG 58.808 40.000 0.00 0.00 0.00 3.69
6405 11819 5.728351 TTAAATACACACGCATAAGAGGC 57.272 39.130 0.00 0.00 0.00 4.70
6406 11820 2.979814 ATACACACGCATAAGAGGCA 57.020 45.000 0.00 0.00 0.00 4.75
6407 11821 2.293677 TACACACGCATAAGAGGCAG 57.706 50.000 0.00 0.00 0.00 4.85
6408 11822 1.021390 ACACACGCATAAGAGGCAGC 61.021 55.000 0.00 0.00 0.00 5.25
6409 11823 0.742281 CACACGCATAAGAGGCAGCT 60.742 55.000 0.00 0.00 0.00 4.24
6410 11824 0.742281 ACACGCATAAGAGGCAGCTG 60.742 55.000 10.11 10.11 0.00 4.24
6411 11825 1.153289 ACGCATAAGAGGCAGCTGG 60.153 57.895 17.12 0.00 0.00 4.85
6412 11826 2.541120 CGCATAAGAGGCAGCTGGC 61.541 63.158 31.58 31.58 43.74 4.85
6422 11836 3.688159 CAGCTGGCAGGGGCAAAC 61.688 66.667 17.64 0.00 43.71 2.93
6425 11839 3.058160 CTGGCAGGGGCAAACGAG 61.058 66.667 6.61 0.00 43.71 4.18
6428 11842 3.435186 GCAGGGGCAAACGAGCTC 61.435 66.667 2.73 2.73 40.72 4.09
6429 11843 2.032528 CAGGGGCAAACGAGCTCA 59.967 61.111 15.40 0.00 36.47 4.26
6430 11844 1.377725 CAGGGGCAAACGAGCTCAT 60.378 57.895 15.40 0.00 36.47 2.90
6431 11845 0.962356 CAGGGGCAAACGAGCTCATT 60.962 55.000 15.40 0.49 36.47 2.57
6432 11846 0.678048 AGGGGCAAACGAGCTCATTC 60.678 55.000 15.40 0.00 36.47 2.67
6433 11847 1.657751 GGGGCAAACGAGCTCATTCC 61.658 60.000 15.40 2.94 36.47 3.01
6434 11848 1.657751 GGGCAAACGAGCTCATTCCC 61.658 60.000 15.40 9.06 34.32 3.97
6435 11849 0.678048 GGCAAACGAGCTCATTCCCT 60.678 55.000 15.40 0.00 34.17 4.20
6436 11850 1.168714 GCAAACGAGCTCATTCCCTT 58.831 50.000 15.40 0.00 0.00 3.95
6437 11851 1.131315 GCAAACGAGCTCATTCCCTTC 59.869 52.381 15.40 0.00 0.00 3.46
6438 11852 1.394917 CAAACGAGCTCATTCCCTTCG 59.605 52.381 15.40 0.00 0.00 3.79
6439 11853 0.741221 AACGAGCTCATTCCCTTCGC 60.741 55.000 15.40 0.00 0.00 4.70
6440 11854 1.142748 CGAGCTCATTCCCTTCGCT 59.857 57.895 15.40 0.00 0.00 4.93
6441 11855 0.460987 CGAGCTCATTCCCTTCGCTT 60.461 55.000 15.40 0.00 0.00 4.68
6442 11856 1.294857 GAGCTCATTCCCTTCGCTTC 58.705 55.000 9.40 0.00 0.00 3.86
6443 11857 0.107459 AGCTCATTCCCTTCGCTTCC 60.107 55.000 0.00 0.00 0.00 3.46
6444 11858 0.107459 GCTCATTCCCTTCGCTTCCT 60.107 55.000 0.00 0.00 0.00 3.36
6445 11859 1.661341 CTCATTCCCTTCGCTTCCTG 58.339 55.000 0.00 0.00 0.00 3.86
6446 11860 0.253044 TCATTCCCTTCGCTTCCTGG 59.747 55.000 0.00 0.00 0.00 4.45
6447 11861 0.749454 CATTCCCTTCGCTTCCTGGG 60.749 60.000 0.00 0.00 40.95 4.45
6448 11862 2.558380 ATTCCCTTCGCTTCCTGGGC 62.558 60.000 0.00 0.00 39.49 5.36
6449 11863 4.803908 CCCTTCGCTTCCTGGGCC 62.804 72.222 0.00 0.00 32.49 5.80
6450 11864 4.803908 CCTTCGCTTCCTGGGCCC 62.804 72.222 17.59 17.59 0.00 5.80
6451 11865 4.033776 CTTCGCTTCCTGGGCCCA 62.034 66.667 26.67 26.67 0.00 5.36
6452 11866 3.567579 CTTCGCTTCCTGGGCCCAA 62.568 63.158 28.29 9.54 0.00 4.12
6453 11867 3.140073 TTCGCTTCCTGGGCCCAAA 62.140 57.895 28.29 17.69 0.00 3.28
6454 11868 3.064324 CGCTTCCTGGGCCCAAAG 61.064 66.667 28.29 27.00 0.00 2.77
6455 11869 3.385384 GCTTCCTGGGCCCAAAGC 61.385 66.667 34.59 34.59 42.60 3.51
6456 11870 2.118076 CTTCCTGGGCCCAAAGCA 59.882 61.111 28.29 9.93 46.50 3.91
6457 11871 1.980772 CTTCCTGGGCCCAAAGCAG 60.981 63.158 28.29 16.12 46.50 4.24
6458 11872 2.720144 CTTCCTGGGCCCAAAGCAGT 62.720 60.000 28.29 0.00 46.50 4.40
6459 11873 2.993264 CCTGGGCCCAAAGCAGTG 60.993 66.667 28.29 12.30 46.50 3.66
6460 11874 3.688159 CTGGGCCCAAAGCAGTGC 61.688 66.667 28.29 7.13 46.50 4.40
6461 11875 4.223125 TGGGCCCAAAGCAGTGCT 62.223 61.111 26.33 13.14 46.50 4.40
6472 11886 1.035139 AGCAGTGCTTTGTTTCCTGG 58.965 50.000 13.14 0.00 33.89 4.45
6473 11887 0.598419 GCAGTGCTTTGTTTCCTGGC 60.598 55.000 8.18 0.00 0.00 4.85
6474 11888 0.032540 CAGTGCTTTGTTTCCTGGCC 59.967 55.000 0.00 0.00 0.00 5.36
6475 11889 0.396974 AGTGCTTTGTTTCCTGGCCA 60.397 50.000 4.71 4.71 0.00 5.36
6476 11890 0.463620 GTGCTTTGTTTCCTGGCCAA 59.536 50.000 7.01 0.00 0.00 4.52
6477 11891 1.134551 GTGCTTTGTTTCCTGGCCAAA 60.135 47.619 7.01 0.00 0.00 3.28
6478 11892 1.767681 TGCTTTGTTTCCTGGCCAAAT 59.232 42.857 7.01 0.00 0.00 2.32
6479 11893 2.224257 TGCTTTGTTTCCTGGCCAAATC 60.224 45.455 7.01 0.00 0.00 2.17
6480 11894 2.224257 GCTTTGTTTCCTGGCCAAATCA 60.224 45.455 7.01 1.46 0.00 2.57
6481 11895 3.743899 GCTTTGTTTCCTGGCCAAATCAA 60.744 43.478 7.01 8.20 0.00 2.57
6482 11896 3.749665 TTGTTTCCTGGCCAAATCAAG 57.250 42.857 7.01 0.00 0.00 3.02
6483 11897 2.956132 TGTTTCCTGGCCAAATCAAGA 58.044 42.857 7.01 0.00 0.00 3.02
6484 11898 2.892852 TGTTTCCTGGCCAAATCAAGAG 59.107 45.455 7.01 0.00 0.00 2.85
6485 11899 1.549203 TTCCTGGCCAAATCAAGAGC 58.451 50.000 7.01 0.00 0.00 4.09
6486 11900 0.677731 TCCTGGCCAAATCAAGAGCG 60.678 55.000 7.01 0.00 0.00 5.03
6487 11901 0.677731 CCTGGCCAAATCAAGAGCGA 60.678 55.000 7.01 0.00 0.00 4.93
6488 11902 0.731417 CTGGCCAAATCAAGAGCGAG 59.269 55.000 7.01 0.00 0.00 5.03
6489 11903 0.324614 TGGCCAAATCAAGAGCGAGA 59.675 50.000 0.61 0.00 0.00 4.04
6490 11904 1.012841 GGCCAAATCAAGAGCGAGAG 58.987 55.000 0.00 0.00 0.00 3.20
6502 11916 2.125912 CGAGAGCCCTTCCACACG 60.126 66.667 0.00 0.00 0.00 4.49
6503 11917 2.266055 GAGAGCCCTTCCACACGG 59.734 66.667 0.00 0.00 0.00 4.94
6504 11918 3.316573 GAGAGCCCTTCCACACGGG 62.317 68.421 0.00 0.00 43.60 5.28
6505 11919 3.319198 GAGCCCTTCCACACGGGA 61.319 66.667 0.00 0.00 46.61 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.671472 CGACATCACCTCTGCTGCAA 60.671 55.000 3.02 0.00 0.00 4.08
1 2 1.079612 CGACATCACCTCTGCTGCA 60.080 57.895 0.88 0.88 0.00 4.41
4 5 1.114627 TATGCGACATCACCTCTGCT 58.885 50.000 0.00 0.00 0.00 4.24
5 6 1.939974 TTATGCGACATCACCTCTGC 58.060 50.000 0.00 0.00 0.00 4.26
6 7 5.490139 AAAATTATGCGACATCACCTCTG 57.510 39.130 0.00 0.00 0.00 3.35
31 32 6.587226 TGTTTCTGCAATATGATCTTTGTTGC 59.413 34.615 17.52 17.52 43.93 4.17
32 33 8.697846 ATGTTTCTGCAATATGATCTTTGTTG 57.302 30.769 0.00 0.00 0.00 3.33
37 38 8.627403 CAACCTATGTTTCTGCAATATGATCTT 58.373 33.333 0.00 0.00 30.42 2.40
38 39 7.776969 ACAACCTATGTTTCTGCAATATGATCT 59.223 33.333 0.00 0.00 40.06 2.75
39 40 7.859377 CACAACCTATGTTTCTGCAATATGATC 59.141 37.037 0.00 0.00 41.46 2.92
41 42 6.658816 ACACAACCTATGTTTCTGCAATATGA 59.341 34.615 0.00 0.00 41.46 2.15
42 43 6.855836 ACACAACCTATGTTTCTGCAATATG 58.144 36.000 0.00 0.00 41.46 1.78
44 45 6.676950 CAACACAACCTATGTTTCTGCAATA 58.323 36.000 0.00 0.00 41.46 1.90
46 47 4.736168 GCAACACAACCTATGTTTCTGCAA 60.736 41.667 0.00 0.00 41.46 4.08
50 51 4.460263 TCTGCAACACAACCTATGTTTCT 58.540 39.130 0.00 0.00 41.46 2.52
51 52 4.829064 TCTGCAACACAACCTATGTTTC 57.171 40.909 0.00 0.00 41.46 2.78
79 80 4.399004 AACACAGCCTATGTTGCAAAAA 57.601 36.364 0.00 0.00 41.41 1.94
87 88 3.439857 AATCCACAACACAGCCTATGT 57.560 42.857 0.00 0.00 45.43 2.29
88 89 4.789012 AAAATCCACAACACAGCCTATG 57.211 40.909 0.00 0.00 0.00 2.23
311 359 1.270305 GGTGCTACTGCTCTGTTGTGA 60.270 52.381 0.00 0.00 40.48 3.58
361 413 0.609662 GTTGGTACGCTCCCCAGTAA 59.390 55.000 0.00 0.00 31.04 2.24
445 528 3.373110 GGTGAAATAAAGGGAGGGATGCT 60.373 47.826 0.00 0.00 0.00 3.79
459 574 2.358090 CCATTCCTGCAGGGGTGAAATA 60.358 50.000 32.23 7.74 35.41 1.40
479 594 4.938226 CGCTAGATCCATAGATTTTTCCCC 59.062 45.833 0.00 0.00 30.90 4.81
491 611 1.059913 CCTTTCCCCGCTAGATCCAT 58.940 55.000 0.00 0.00 0.00 3.41
542 662 1.450848 ACCGACGCGATCTGAGGTA 60.451 57.895 15.93 0.00 0.00 3.08
884 1044 5.488919 AGGATGAGACTTTTAGGGTTCATCA 59.511 40.000 12.61 0.00 41.50 3.07
890 1052 2.846827 CCCAGGATGAGACTTTTAGGGT 59.153 50.000 0.00 0.00 39.69 4.34
936 1108 2.804933 GCGGACCAGGATCTCTCATTTC 60.805 54.545 0.00 0.00 0.00 2.17
939 1111 0.105760 AGCGGACCAGGATCTCTCAT 60.106 55.000 0.00 0.00 0.00 2.90
943 1115 0.103937 CTCAAGCGGACCAGGATCTC 59.896 60.000 0.00 0.00 0.00 2.75
949 1121 0.108898 CACTCTCTCAAGCGGACCAG 60.109 60.000 0.00 0.00 0.00 4.00
952 1124 1.011451 GCACACTCTCTCAAGCGGAC 61.011 60.000 0.00 0.00 0.00 4.79
953 1125 1.290324 GCACACTCTCTCAAGCGGA 59.710 57.895 0.00 0.00 0.00 5.54
955 1127 1.013005 CAGGCACACTCTCTCAAGCG 61.013 60.000 0.00 0.00 0.00 4.68
958 1130 2.061220 CCCAGGCACACTCTCTCAA 58.939 57.895 0.00 0.00 0.00 3.02
998 1180 2.946762 GTGGAAGCGGTGACAAGC 59.053 61.111 0.00 0.00 0.00 4.01
999 1181 0.878523 TTCGTGGAAGCGGTGACAAG 60.879 55.000 0.00 0.00 0.00 3.16
1000 1182 0.250124 ATTCGTGGAAGCGGTGACAA 60.250 50.000 0.00 0.00 0.00 3.18
1001 1183 0.669318 GATTCGTGGAAGCGGTGACA 60.669 55.000 0.00 0.00 0.00 3.58
1002 1184 0.389948 AGATTCGTGGAAGCGGTGAC 60.390 55.000 0.00 0.00 32.82 3.67
1003 1185 0.320374 AAGATTCGTGGAAGCGGTGA 59.680 50.000 0.00 0.00 32.82 4.02
1005 1187 1.156736 CAAAGATTCGTGGAAGCGGT 58.843 50.000 0.00 0.00 32.82 5.68
1094 1278 0.872388 GTTGGTTGCGAGAATTCCGT 59.128 50.000 14.86 0.00 0.00 4.69
1103 1287 2.664851 CTGCGAGGTTGGTTGCGA 60.665 61.111 0.00 0.00 0.00 5.10
1179 1363 2.066393 CCCTGCCTGCAGCTAGGTA 61.066 63.158 24.42 6.96 44.23 3.08
1180 1364 3.406200 CCCTGCCTGCAGCTAGGT 61.406 66.667 24.42 0.00 44.23 3.08
1315 1501 2.156098 CCGAGAATTTCCGGGAAAACA 58.844 47.619 24.83 4.11 41.89 2.83
1376 1562 7.093024 CCCCAATACTATTTCCCAGATACGTAT 60.093 40.741 8.05 8.05 0.00 3.06
1387 1574 2.445525 TCCTGCCCCCAATACTATTTCC 59.554 50.000 0.00 0.00 0.00 3.13
1461 1666 0.627451 TCTTGATCTGGCAAGCCCAT 59.373 50.000 8.89 0.18 44.33 4.00
1565 1774 0.394216 TAGCGGCGGAACACTAGGTA 60.394 55.000 9.78 0.00 0.00 3.08
1584 1793 6.017770 CACAGCAAACAATCATTTTCCATGTT 60.018 34.615 0.00 0.00 35.86 2.71
1588 1797 5.273674 TCACAGCAAACAATCATTTTCCA 57.726 34.783 0.00 0.00 0.00 3.53
1609 1818 7.035840 ACTGAAATTCCTGTTCATGCATATC 57.964 36.000 0.00 0.00 34.59 1.63
1712 1921 1.377202 GCCATCTTTGAGACCGGCA 60.377 57.895 0.00 0.00 42.63 5.69
1867 2076 7.979115 TGTAAAAGAAATGTAGCAACAACAC 57.021 32.000 0.00 0.00 39.58 3.32
2256 2468 1.723870 GCAGCGGGCATGTTTAGAG 59.276 57.895 0.00 0.00 43.97 2.43
2379 2602 1.304134 ATCAACTTGGGCGGGGAAC 60.304 57.895 0.00 0.00 0.00 3.62
2458 2681 6.140110 CGTTTATATTTATTCTGTTGGGCCG 58.860 40.000 0.00 0.00 0.00 6.13
2641 2865 6.767524 TGTTTCAGGCTTTCTCTGTTTAAA 57.232 33.333 0.00 0.00 34.15 1.52
2643 2867 6.017109 GTCATGTTTCAGGCTTTCTCTGTTTA 60.017 38.462 0.00 0.00 34.15 2.01
2644 2868 4.889409 TCATGTTTCAGGCTTTCTCTGTTT 59.111 37.500 0.00 0.00 34.15 2.83
2645 2869 4.276926 GTCATGTTTCAGGCTTTCTCTGTT 59.723 41.667 0.00 0.00 34.15 3.16
2646 2870 3.817647 GTCATGTTTCAGGCTTTCTCTGT 59.182 43.478 0.00 0.00 34.15 3.41
2647 2871 3.817084 TGTCATGTTTCAGGCTTTCTCTG 59.183 43.478 0.00 0.00 0.00 3.35
2649 2873 3.817647 AGTGTCATGTTTCAGGCTTTCTC 59.182 43.478 0.00 0.00 0.00 2.87
2652 2876 3.491447 GCAAGTGTCATGTTTCAGGCTTT 60.491 43.478 0.00 0.00 0.00 3.51
2922 4120 5.701290 TGAAAATGATTGTGCATGCATTCAA 59.299 32.000 25.64 23.30 34.03 2.69
3185 4413 6.914654 TTCAATTGATCCTCAAATGGAACA 57.085 33.333 9.40 0.00 40.12 3.18
3263 4491 3.733684 GCAAGGCTTTTGTGTTTTCTCGA 60.734 43.478 0.00 0.00 0.00 4.04
3357 4585 3.055094 TGGTTATGGAGACTCTGCTTTCC 60.055 47.826 1.74 0.20 0.00 3.13
3360 4588 2.237392 GGTGGTTATGGAGACTCTGCTT 59.763 50.000 1.74 0.00 0.00 3.91
3423 4653 4.528076 TCTCTAGGTCTTGTAGCAGGAT 57.472 45.455 0.00 0.00 0.00 3.24
3509 4739 2.049156 CGCTCTGACCGCACTCAA 60.049 61.111 0.00 0.00 0.00 3.02
3574 4805 1.963515 GTTGGAGTTTGTGGGAAGCAT 59.036 47.619 0.00 0.00 0.00 3.79
3602 4840 4.331968 GTGGTTTCAACTCCATGGTCATA 58.668 43.478 12.58 0.00 36.09 2.15
3693 4931 2.488937 TCATGCAATGCGTTCATGTTCT 59.511 40.909 20.67 0.00 46.21 3.01
3750 5042 0.689623 CATCCCTCACCCTGCTATCC 59.310 60.000 0.00 0.00 0.00 2.59
3894 5186 3.549070 GCTTTAGCAGTATGTTTGCATGC 59.451 43.478 11.82 11.82 43.92 4.06
3966 5258 5.362430 TGCCAAATAAGAGTTTCTTGTGGTT 59.638 36.000 14.26 0.00 37.29 3.67
4000 5319 1.721133 GTTTCGTGCAGCGGTTTCG 60.721 57.895 8.46 0.00 41.72 3.46
4007 5326 2.285834 CGGATAATGAGTTTCGTGCAGC 60.286 50.000 0.00 0.00 0.00 5.25
4090 5409 5.182001 AGCATTCTTACAATCAGGTTCACAC 59.818 40.000 0.00 0.00 0.00 3.82
4224 5543 5.929415 TGTTCTTGTATGCACTTCGAATACA 59.071 36.000 0.00 0.99 35.53 2.29
4239 5558 9.868277 AAAGTGATTTCAACAATTGTTCTTGTA 57.132 25.926 20.85 2.53 38.38 2.41
4322 5641 1.740025 GCAGCCTGTACAAACTCCATC 59.260 52.381 0.00 0.00 0.00 3.51
4670 6017 5.105146 ACTCTGATACCATCACCTCAAGAAC 60.105 44.000 0.00 0.00 35.06 3.01
4707 6054 1.778334 TACACACTAAGCTGCACACG 58.222 50.000 1.02 0.00 0.00 4.49
4727 6074 3.173965 GGGCTAGGTCCAGCATATTAGA 58.826 50.000 13.25 0.00 43.67 2.10
4759 6106 5.913137 ACAAGATCAACTGTGACCAAAAA 57.087 34.783 0.00 0.00 36.31 1.94
4764 6111 3.499918 CCTCAACAAGATCAACTGTGACC 59.500 47.826 0.00 0.00 36.31 4.02
5054 6401 1.156736 CGTCCGTTGCTTCCTGAAAT 58.843 50.000 0.00 0.00 0.00 2.17
5156 6503 0.035152 TTGCTCCGATGATGGTGCTT 60.035 50.000 8.13 0.00 46.19 3.91
5376 6724 7.474025 GTGTAATAAACATGAACAAAATTGCGC 59.526 33.333 0.00 0.00 41.10 6.09
5463 6811 9.597170 TCCGAGATATACTATCTGTACACATAC 57.403 37.037 1.50 0.00 33.45 2.39
5567 6918 2.348411 AGGGAACAAATAGGCGATGG 57.652 50.000 0.00 0.00 0.00 3.51
5628 6982 1.067985 TGTATGGCAACCAAACATGCG 60.068 47.619 0.00 0.00 43.47 4.73
5639 11049 3.812609 CAGTGTGTACAAGTGTATGGCAA 59.187 43.478 0.00 0.00 32.54 4.52
5668 11078 2.823959 ACCCAGATTTGTGGCATGAAT 58.176 42.857 0.00 0.00 36.11 2.57
5721 11135 3.605231 CGCTTTTACCACAAGTGTAACGG 60.605 47.826 0.00 0.00 45.86 4.44
5724 11138 2.879646 CCCGCTTTTACCACAAGTGTAA 59.120 45.455 0.00 0.00 30.98 2.41
5779 11193 0.462047 GTACCCTCCGGCACAATCTG 60.462 60.000 0.00 0.00 0.00 2.90
5820 11234 0.461339 AGTGTCGCCAACGTGTTTCT 60.461 50.000 0.00 0.00 41.18 2.52
5886 11300 2.481568 CCTATAACGCCTACGATGACGA 59.518 50.000 0.00 0.00 43.93 4.20
5892 11306 3.012518 GGATAGCCTATAACGCCTACGA 58.987 50.000 0.00 0.00 43.93 3.43
5955 11369 3.498774 AACTCACTGAATTCTGCAGGT 57.501 42.857 15.13 0.00 37.69 4.00
5971 11385 3.497879 GCCCGGTGCATGTAACTC 58.502 61.111 9.72 0.00 40.77 3.01
5980 11394 0.033366 AAACTGAATTTGCCCGGTGC 59.967 50.000 0.00 4.04 41.77 5.01
5981 11395 1.339610 TGAAACTGAATTTGCCCGGTG 59.660 47.619 0.00 0.00 0.00 4.94
5982 11396 1.613437 CTGAAACTGAATTTGCCCGGT 59.387 47.619 0.00 0.00 0.00 5.28
6090 11504 3.479269 GGCGTGGAAGCGACGAAG 61.479 66.667 0.00 0.00 37.77 3.79
6098 11512 4.096003 ACGATGGGGGCGTGGAAG 62.096 66.667 0.00 0.00 40.94 3.46
6174 11588 2.973899 GAGGCGACAGAGGAAGCA 59.026 61.111 0.00 0.00 0.00 3.91
6177 11591 2.989253 TGCGAGGCGACAGAGGAA 60.989 61.111 0.00 0.00 0.00 3.36
6284 11698 1.228124 CTCTTGTGTGGGGCGGAAA 60.228 57.895 0.00 0.00 0.00 3.13
6285 11699 1.990160 AACTCTTGTGTGGGGCGGAA 61.990 55.000 0.00 0.00 0.00 4.30
6286 11700 1.990160 AAACTCTTGTGTGGGGCGGA 61.990 55.000 0.00 0.00 0.00 5.54
6287 11701 0.250553 TAAACTCTTGTGTGGGGCGG 60.251 55.000 0.00 0.00 0.00 6.13
6288 11702 0.872388 GTAAACTCTTGTGTGGGGCG 59.128 55.000 0.00 0.00 0.00 6.13
6289 11703 2.152016 GAGTAAACTCTTGTGTGGGGC 58.848 52.381 2.81 0.00 39.81 5.80
6314 11728 2.883574 CACGCGAGGTCAATTTAGGTA 58.116 47.619 15.93 0.00 0.00 3.08
6389 11803 1.021390 GCTGCCTCTTATGCGTGTGT 61.021 55.000 0.00 0.00 0.00 3.72
6390 11804 0.742281 AGCTGCCTCTTATGCGTGTG 60.742 55.000 0.00 0.00 0.00 3.82
6391 11805 0.742281 CAGCTGCCTCTTATGCGTGT 60.742 55.000 0.00 0.00 0.00 4.49
6392 11806 1.434622 CCAGCTGCCTCTTATGCGTG 61.435 60.000 8.66 0.00 0.00 5.34
6393 11807 1.153289 CCAGCTGCCTCTTATGCGT 60.153 57.895 8.66 0.00 0.00 5.24
6394 11808 2.541120 GCCAGCTGCCTCTTATGCG 61.541 63.158 8.66 0.00 0.00 4.73
6395 11809 1.445716 CTGCCAGCTGCCTCTTATGC 61.446 60.000 8.66 4.14 40.16 3.14
6396 11810 0.818445 CCTGCCAGCTGCCTCTTATG 60.818 60.000 8.66 0.00 40.16 1.90
6397 11811 1.530771 CCTGCCAGCTGCCTCTTAT 59.469 57.895 8.66 0.00 40.16 1.73
6398 11812 2.673200 CCCTGCCAGCTGCCTCTTA 61.673 63.158 8.66 0.00 40.16 2.10
6399 11813 4.044439 CCCTGCCAGCTGCCTCTT 62.044 66.667 8.66 0.00 40.16 2.85
6405 11819 3.688159 GTTTGCCCCTGCCAGCTG 61.688 66.667 6.78 6.78 36.33 4.24
6408 11822 3.058160 CTCGTTTGCCCCTGCCAG 61.058 66.667 0.00 0.00 36.33 4.85
6411 11825 3.435186 GAGCTCGTTTGCCCCTGC 61.435 66.667 0.00 0.00 38.26 4.85
6412 11826 0.962356 AATGAGCTCGTTTGCCCCTG 60.962 55.000 15.61 0.00 0.00 4.45
6413 11827 0.678048 GAATGAGCTCGTTTGCCCCT 60.678 55.000 21.80 0.00 0.00 4.79
6414 11828 1.657751 GGAATGAGCTCGTTTGCCCC 61.658 60.000 21.80 14.37 0.00 5.80
6415 11829 1.657751 GGGAATGAGCTCGTTTGCCC 61.658 60.000 23.04 23.04 0.00 5.36
6416 11830 0.678048 AGGGAATGAGCTCGTTTGCC 60.678 55.000 23.82 23.82 0.00 4.52
6417 11831 1.131315 GAAGGGAATGAGCTCGTTTGC 59.869 52.381 21.80 15.82 0.00 3.68
6418 11832 1.394917 CGAAGGGAATGAGCTCGTTTG 59.605 52.381 21.80 0.08 0.00 2.93
6419 11833 1.726853 CGAAGGGAATGAGCTCGTTT 58.273 50.000 21.80 11.78 0.00 3.60
6420 11834 0.741221 GCGAAGGGAATGAGCTCGTT 60.741 55.000 21.10 21.10 32.23 3.85
6421 11835 1.153549 GCGAAGGGAATGAGCTCGT 60.154 57.895 9.64 5.78 32.23 4.18
6422 11836 0.460987 AAGCGAAGGGAATGAGCTCG 60.461 55.000 9.64 0.00 37.15 5.03
6423 11837 1.294857 GAAGCGAAGGGAATGAGCTC 58.705 55.000 6.82 6.82 37.15 4.09
6424 11838 0.107459 GGAAGCGAAGGGAATGAGCT 60.107 55.000 0.00 0.00 40.20 4.09
6425 11839 0.107459 AGGAAGCGAAGGGAATGAGC 60.107 55.000 0.00 0.00 0.00 4.26
6426 11840 1.661341 CAGGAAGCGAAGGGAATGAG 58.339 55.000 0.00 0.00 0.00 2.90
6427 11841 0.253044 CCAGGAAGCGAAGGGAATGA 59.747 55.000 0.00 0.00 0.00 2.57
6428 11842 0.749454 CCCAGGAAGCGAAGGGAATG 60.749 60.000 0.00 0.00 44.30 2.67
6429 11843 1.609783 CCCAGGAAGCGAAGGGAAT 59.390 57.895 0.00 0.00 44.30 3.01
6430 11844 3.077907 CCCAGGAAGCGAAGGGAA 58.922 61.111 0.00 0.00 44.30 3.97
6431 11845 3.717294 GCCCAGGAAGCGAAGGGA 61.717 66.667 0.00 0.00 44.30 4.20
6432 11846 4.803908 GGCCCAGGAAGCGAAGGG 62.804 72.222 0.00 0.00 44.37 3.95
6433 11847 4.803908 GGGCCCAGGAAGCGAAGG 62.804 72.222 19.95 0.00 0.00 3.46
6434 11848 3.567579 TTGGGCCCAGGAAGCGAAG 62.568 63.158 26.87 0.00 0.00 3.79
6435 11849 3.140073 TTTGGGCCCAGGAAGCGAA 62.140 57.895 26.87 12.07 0.00 4.70
6436 11850 3.567579 CTTTGGGCCCAGGAAGCGA 62.568 63.158 26.87 4.99 0.00 4.93
6437 11851 3.064324 CTTTGGGCCCAGGAAGCG 61.064 66.667 26.87 7.10 0.00 4.68
6438 11852 3.385384 GCTTTGGGCCCAGGAAGC 61.385 66.667 34.59 34.59 37.88 3.86
6439 11853 1.980772 CTGCTTTGGGCCCAGGAAG 60.981 63.158 26.11 26.11 40.92 3.46
6440 11854 2.118076 CTGCTTTGGGCCCAGGAA 59.882 61.111 26.87 17.01 40.92 3.36
6441 11855 3.185203 ACTGCTTTGGGCCCAGGA 61.185 61.111 26.87 15.23 40.92 3.86
6442 11856 2.993264 CACTGCTTTGGGCCCAGG 60.993 66.667 26.87 22.20 40.92 4.45
6443 11857 3.688159 GCACTGCTTTGGGCCCAG 61.688 66.667 26.87 16.29 40.92 4.45
6444 11858 4.223125 AGCACTGCTTTGGGCCCA 62.223 61.111 24.45 24.45 40.92 5.36
6453 11867 1.035139 CCAGGAAACAAAGCACTGCT 58.965 50.000 0.00 0.00 42.56 4.24
6454 11868 0.598419 GCCAGGAAACAAAGCACTGC 60.598 55.000 0.00 0.00 0.00 4.40
6455 11869 0.032540 GGCCAGGAAACAAAGCACTG 59.967 55.000 0.00 0.00 0.00 3.66
6456 11870 0.396974 TGGCCAGGAAACAAAGCACT 60.397 50.000 0.00 0.00 0.00 4.40
6457 11871 0.463620 TTGGCCAGGAAACAAAGCAC 59.536 50.000 5.11 0.00 0.00 4.40
6458 11872 1.198713 TTTGGCCAGGAAACAAAGCA 58.801 45.000 5.11 0.00 31.21 3.91
6459 11873 2.224257 TGATTTGGCCAGGAAACAAAGC 60.224 45.455 5.11 11.06 39.97 3.51
6460 11874 3.749665 TGATTTGGCCAGGAAACAAAG 57.250 42.857 5.11 0.00 37.50 2.77
6461 11875 3.708631 TCTTGATTTGGCCAGGAAACAAA 59.291 39.130 5.11 0.00 38.33 2.83
6462 11876 3.303938 TCTTGATTTGGCCAGGAAACAA 58.696 40.909 5.11 9.05 0.00 2.83
6463 11877 2.892852 CTCTTGATTTGGCCAGGAAACA 59.107 45.455 5.11 0.00 0.00 2.83
6464 11878 2.353109 GCTCTTGATTTGGCCAGGAAAC 60.353 50.000 5.11 0.00 0.00 2.78
6465 11879 1.895131 GCTCTTGATTTGGCCAGGAAA 59.105 47.619 5.11 0.00 0.00 3.13
6466 11880 1.549203 GCTCTTGATTTGGCCAGGAA 58.451 50.000 5.11 0.00 0.00 3.36
6467 11881 0.677731 CGCTCTTGATTTGGCCAGGA 60.678 55.000 5.11 0.00 0.00 3.86
6468 11882 0.677731 TCGCTCTTGATTTGGCCAGG 60.678 55.000 5.11 0.00 0.00 4.45
6469 11883 0.731417 CTCGCTCTTGATTTGGCCAG 59.269 55.000 5.11 0.00 0.00 4.85
6470 11884 0.324614 TCTCGCTCTTGATTTGGCCA 59.675 50.000 0.00 0.00 0.00 5.36
6471 11885 1.012841 CTCTCGCTCTTGATTTGGCC 58.987 55.000 0.00 0.00 0.00 5.36
6472 11886 0.376502 GCTCTCGCTCTTGATTTGGC 59.623 55.000 0.00 0.00 0.00 4.52
6473 11887 1.012841 GGCTCTCGCTCTTGATTTGG 58.987 55.000 0.00 0.00 36.09 3.28
6474 11888 1.012841 GGGCTCTCGCTCTTGATTTG 58.987 55.000 0.00 0.00 32.44 2.32
6475 11889 3.467776 GGGCTCTCGCTCTTGATTT 57.532 52.632 0.00 0.00 32.44 2.17
6482 11896 2.185608 GTGGAAGGGCTCTCGCTC 59.814 66.667 0.00 0.00 36.68 5.03
6483 11897 2.604686 TGTGGAAGGGCTCTCGCT 60.605 61.111 0.00 0.00 37.04 4.93
6484 11898 2.435059 GTGTGGAAGGGCTCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
6485 11899 2.125912 CGTGTGGAAGGGCTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
6486 11900 2.266055 CCGTGTGGAAGGGCTCTC 59.734 66.667 0.00 0.00 37.49 3.20
6487 11901 3.322466 CCCGTGTGGAAGGGCTCT 61.322 66.667 0.00 0.00 41.34 4.09


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

AutoCloner maintained by Alex Coulton.