Multiple sequence alignment - TraesCS2D01G284800

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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 TraesCS2D01G284800 chr2D 100.000 9610 0 0 1 9610 360298461 360308070 0.000000e+00 17747
1 TraesCS2D01G284800 chr2D 85.059 589 68 11 60 631 452408013 452408598 5.000000e-162 582
2 TraesCS2D01G284800 chr2D 83.293 413 55 9 2486 2897 222195726 222195327 1.520000e-97 368
3 TraesCS2D01G284800 chr2D 100.000 80 0 0 1 80 482784445 482784524 2.160000e-31 148
4 TraesCS2D01G284800 chr2A 96.537 5227 128 20 76 5273 485753881 485759083 0.000000e+00 8600
5 TraesCS2D01G284800 chr2A 97.825 2207 37 8 6750 8951 485762710 485764910 0.000000e+00 3799
6 TraesCS2D01G284800 chr2A 96.752 1139 15 10 5620 6753 485759535 485760656 0.000000e+00 1879
7 TraesCS2D01G284800 chr2A 97.727 264 5 1 5280 5542 485759267 485759530 4.090000e-123 453
8 TraesCS2D01G284800 chr2A 87.879 264 16 3 9362 9609 485765391 485765654 7.300000e-76 296
9 TraesCS2D01G284800 chr2B 95.300 4617 140 27 700 5273 429261373 429256791 0.000000e+00 7252
10 TraesCS2D01G284800 chr2B 95.318 3140 94 23 5978 9094 429255719 429252610 0.000000e+00 4935
11 TraesCS2D01G284800 chr2B 91.310 725 35 13 5280 5999 429256601 429255900 0.000000e+00 965
12 TraesCS2D01G284800 chr2B 81.906 619 86 12 79 677 498411907 498411295 5.180000e-137 499
13 TraesCS2D01G284800 chr2B 94.510 255 14 0 9092 9346 637570194 637570448 2.520000e-105 394
14 TraesCS2D01G284800 chr2B 84.058 414 50 10 2487 2898 184374349 184374748 1.510000e-102 385
15 TraesCS2D01G284800 chr2B 91.566 249 20 1 9362 9609 429252612 429252364 9.240000e-90 342
16 TraesCS2D01G284800 chr2B 96.512 86 1 2 1 86 71220498 71220581 3.620000e-29 141
17 TraesCS2D01G284800 chr5D 86.246 618 70 2 76 678 266287380 266287997 0.000000e+00 656
18 TraesCS2D01G284800 chr5D 85.413 617 71 6 79 678 427168969 427168355 2.950000e-174 623
19 TraesCS2D01G284800 chr5D 95.276 254 12 0 9093 9346 520896802 520897055 4.180000e-108 403
20 TraesCS2D01G284800 chr5D 84.746 413 49 9 2487 2898 20990786 20991185 1.500000e-107 401
21 TraesCS2D01G284800 chr5D 91.000 100 7 2 1 98 292012465 292012366 6.050000e-27 134
22 TraesCS2D01G284800 chr6D 86.201 616 68 8 79 678 401756324 401755710 0.000000e+00 651
23 TraesCS2D01G284800 chr6D 81.618 408 54 9 290 679 346771495 346771091 1.560000e-82 318
24 TraesCS2D01G284800 chr6D 98.718 78 1 0 1 78 304915417 304915494 1.300000e-28 139
25 TraesCS2D01G284800 chr3D 85.854 615 70 5 80 678 371911685 371912298 1.050000e-178 638
26 TraesCS2D01G284800 chr3D 85.644 613 72 7 81 678 469144472 469143861 1.760000e-176 630
27 TraesCS2D01G284800 chr3D 85.318 613 73 3 76 672 343496522 343497133 1.370000e-172 617
28 TraesCS2D01G284800 chr3D 84.032 620 73 14 79 678 487833393 487832780 3.010000e-159 573
29 TraesCS2D01G284800 chr3D 73.289 453 94 20 3654 4099 463537670 463538102 3.620000e-29 141
30 TraesCS2D01G284800 chr4B 89.542 459 46 2 79 536 99263281 99262824 1.800000e-161 580
31 TraesCS2D01G284800 chr4B 94.163 257 15 0 9090 9346 92021456 92021712 9.050000e-105 392
32 TraesCS2D01G284800 chr1D 83.495 618 80 11 79 678 95940374 95939761 3.030000e-154 556
33 TraesCS2D01G284800 chr1D 87.991 458 55 0 79 536 338866744 338866287 8.490000e-150 542
34 TraesCS2D01G284800 chr1D 82.448 621 86 14 76 677 473143435 473144051 1.110000e-143 521
35 TraesCS2D01G284800 chr1D 94.253 261 14 1 9086 9346 2447169 2446910 1.940000e-106 398
36 TraesCS2D01G284800 chr1D 93.617 94 4 2 2 94 339241881 339241789 1.300000e-28 139
37 TraesCS2D01G284800 chr1A 85.714 413 44 11 2557 2964 557973803 557973401 1.150000e-113 422
38 TraesCS2D01G284800 chr1A 95.720 257 11 0 9090 9346 424518613 424518869 1.930000e-111 414
39 TraesCS2D01G284800 chr1A 83.803 426 53 10 2487 2910 522435970 522435559 3.250000e-104 390
40 TraesCS2D01G284800 chr1A 87.719 114 12 2 1511 1622 58928840 58928953 2.180000e-26 132
41 TraesCS2D01G284800 chr3B 84.235 425 52 9 2487 2910 817960077 817959667 5.410000e-107 399
42 TraesCS2D01G284800 chr3B 93.536 263 15 2 9086 9346 463459879 463460141 3.250000e-104 390
43 TraesCS2D01G284800 chr3B 80.115 523 78 12 176 678 475051348 475051864 5.480000e-97 366
44 TraesCS2D01G284800 chr3B 74.017 458 93 18 3654 4099 616893933 616894376 7.720000e-36 163
45 TraesCS2D01G284800 chr3B 77.377 305 50 15 7836 8123 616895518 616895820 7.720000e-36 163
46 TraesCS2D01G284800 chrUn 94.208 259 15 0 9088 9346 88026064 88025806 6.990000e-106 396
47 TraesCS2D01G284800 chrUn 93.822 259 16 0 9088 9346 88029014 88028756 3.250000e-104 390
48 TraesCS2D01G284800 chr1B 92.727 275 16 4 9074 9346 623837217 623837489 2.520000e-105 394
49 TraesCS2D01G284800 chr7A 84.058 414 51 9 2487 2898 150885702 150886102 1.510000e-102 385
50 TraesCS2D01G284800 chr7A 98.750 80 1 0 1 80 129744471 129744550 1.010000e-29 143
51 TraesCS2D01G284800 chr7D 78.678 605 101 18 79 678 537232579 537231998 2.530000e-100 377
52 TraesCS2D01G284800 chr5A 83.535 413 53 9 2487 2898 30097170 30097568 1.180000e-98 372
53 TraesCS2D01G284800 chr5A 97.590 83 1 1 1 83 291111324 291111405 3.620000e-29 141
54 TraesCS2D01G284800 chr5A 95.455 88 3 1 1 87 268501276 268501189 1.300000e-28 139
55 TraesCS2D01G284800 chr3A 73.510 453 104 13 3654 4099 606671132 606671575 3.590000e-34 158
56 TraesCS2D01G284800 chr6B 96.429 84 3 0 1 84 279484431 279484514 1.300000e-28 139


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 TraesCS2D01G284800 chr2D 360298461 360308070 9609 False 17747.0 17747 100.0000 1 9610 1 chr2D.!!$F1 9609
1 TraesCS2D01G284800 chr2D 452408013 452408598 585 False 582.0 582 85.0590 60 631 1 chr2D.!!$F2 571
2 TraesCS2D01G284800 chr2A 485753881 485765654 11773 False 3005.4 8600 95.3440 76 9609 5 chr2A.!!$F1 9533
3 TraesCS2D01G284800 chr2B 429252364 429261373 9009 True 3373.5 7252 93.3735 700 9609 4 chr2B.!!$R2 8909
4 TraesCS2D01G284800 chr2B 498411295 498411907 612 True 499.0 499 81.9060 79 677 1 chr2B.!!$R1 598
5 TraesCS2D01G284800 chr5D 266287380 266287997 617 False 656.0 656 86.2460 76 678 1 chr5D.!!$F2 602
6 TraesCS2D01G284800 chr5D 427168355 427168969 614 True 623.0 623 85.4130 79 678 1 chr5D.!!$R2 599
7 TraesCS2D01G284800 chr6D 401755710 401756324 614 True 651.0 651 86.2010 79 678 1 chr6D.!!$R2 599
8 TraesCS2D01G284800 chr3D 371911685 371912298 613 False 638.0 638 85.8540 80 678 1 chr3D.!!$F2 598
9 TraesCS2D01G284800 chr3D 469143861 469144472 611 True 630.0 630 85.6440 81 678 1 chr3D.!!$R1 597
10 TraesCS2D01G284800 chr3D 343496522 343497133 611 False 617.0 617 85.3180 76 672 1 chr3D.!!$F1 596
11 TraesCS2D01G284800 chr3D 487832780 487833393 613 True 573.0 573 84.0320 79 678 1 chr3D.!!$R2 599
12 TraesCS2D01G284800 chr1D 95939761 95940374 613 True 556.0 556 83.4950 79 678 1 chr1D.!!$R2 599
13 TraesCS2D01G284800 chr1D 473143435 473144051 616 False 521.0 521 82.4480 76 677 1 chr1D.!!$F1 601
14 TraesCS2D01G284800 chr3B 475051348 475051864 516 False 366.0 366 80.1150 176 678 1 chr3B.!!$F2 502
15 TraesCS2D01G284800 chrUn 88025806 88029014 3208 True 393.0 396 94.0150 9088 9346 2 chrUn.!!$R1 258
16 TraesCS2D01G284800 chr7D 537231998 537232579 581 True 377.0 377 78.6780 79 678 1 chr7D.!!$R1 599

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
19 20 0.035458 CTTCTGCTCCTCGTTGGGTT 59.965 55.000 0.00 0.0 36.20 4.11 F
21 22 0.250295 TCTGCTCCTCGTTGGGTTTG 60.250 55.000 0.00 0.0 36.20 2.93 F
1352 1374 0.250513 ATCAAACTCCAGCGAGGGAC 59.749 55.000 0.00 0.0 40.77 4.46 F
1414 1437 4.160736 TCTATATGCGTGAGGATGAACG 57.839 45.455 0.00 0.0 44.06 3.95 F
1680 1704 4.713824 AACTTGGCTGATGATTGTGATG 57.286 40.909 0.00 0.0 0.00 3.07 F
2551 2583 0.872388 GACAACGGTGCCCAAGTAAG 59.128 55.000 0.00 0.0 0.00 2.34 F
3337 3373 1.679139 TTTGGCTGTGGTTGTCTCAG 58.321 50.000 0.00 0.0 0.00 3.35 F
5161 5234 0.038166 GCTGGGGTTTCCACATGAGA 59.962 55.000 0.00 0.0 41.46 3.27 F
5468 5727 0.612174 AGACTAAGGCACTGGCTCGA 60.612 55.000 5.42 0.0 40.86 4.04 F
5924 6191 1.200519 TGCCGCCCTGTCTATTAGTT 58.799 50.000 0.00 0.0 0.00 2.24 F
7896 10432 2.233431 CCTGCAGCTTTAGACACTCTCT 59.767 50.000 8.66 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2041 0.596600 TCCTTCATTATCGCCGCGTC 60.597 55.000 13.39 0.00 0.00 5.19 R
2138 2170 4.541973 TTGAGATTCACTGCTTGCTAGA 57.458 40.909 0.00 0.00 0.00 2.43 R
2525 2557 1.310216 GGGCACCGTTGTCCCATTAC 61.310 60.000 7.43 0.00 42.35 1.89 R
2551 2583 5.031578 CGAGCACACACTCTCTATTAGAAC 58.968 45.833 0.00 0.00 34.35 3.01 R
3295 3331 5.948992 AAGATCAAACCTCTACAACTTGC 57.051 39.130 0.00 0.00 0.00 4.01 R
4648 4717 1.715519 GCAATTCACATGTTGCGACAC 59.284 47.619 9.51 0.00 40.95 3.67 R
5277 5353 1.352083 AGAGTTGTGCCTTCCAGCTA 58.648 50.000 0.00 0.00 0.00 3.32 R
7268 9804 2.185608 GGCTTCACTCGAGGAGCC 59.814 66.667 28.89 28.89 32.04 4.70 R
7896 10432 0.780637 TATCCAACCAAACCAGGCCA 59.219 50.000 5.01 0.00 0.00 5.36 R
8158 10703 8.100791 TGGTGTCTATAGTTGTTTCTGCTATTT 58.899 33.333 0.00 0.00 0.00 1.40 R
9191 12088 0.888736 CGGGCGCATTAATGATCCCA 60.889 55.000 29.37 0.00 39.39 4.37 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
17 18 4.606071 CTTCTGCTCCTCGTTGGG 57.394 61.111 0.00 0.00 36.20 4.12
18 19 1.674057 CTTCTGCTCCTCGTTGGGT 59.326 57.895 0.00 0.00 36.20 4.51
19 20 0.035458 CTTCTGCTCCTCGTTGGGTT 59.965 55.000 0.00 0.00 36.20 4.11
20 21 0.472471 TTCTGCTCCTCGTTGGGTTT 59.528 50.000 0.00 0.00 36.20 3.27
21 22 0.250295 TCTGCTCCTCGTTGGGTTTG 60.250 55.000 0.00 0.00 36.20 2.93
22 23 0.250295 CTGCTCCTCGTTGGGTTTGA 60.250 55.000 0.00 0.00 36.20 2.69
23 24 0.534203 TGCTCCTCGTTGGGTTTGAC 60.534 55.000 0.00 0.00 36.20 3.18
24 25 0.534203 GCTCCTCGTTGGGTTTGACA 60.534 55.000 0.00 0.00 36.20 3.58
25 26 1.226746 CTCCTCGTTGGGTTTGACAC 58.773 55.000 0.00 0.00 36.20 3.67
26 27 0.834612 TCCTCGTTGGGTTTGACACT 59.165 50.000 0.00 0.00 36.20 3.55
27 28 1.202604 TCCTCGTTGGGTTTGACACTC 60.203 52.381 0.00 0.00 36.20 3.51
28 29 1.202651 CCTCGTTGGGTTTGACACTCT 60.203 52.381 0.00 0.00 0.00 3.24
29 30 2.561569 CTCGTTGGGTTTGACACTCTT 58.438 47.619 0.00 0.00 0.00 2.85
30 31 3.493699 CCTCGTTGGGTTTGACACTCTTA 60.494 47.826 0.00 0.00 0.00 2.10
31 32 3.460103 TCGTTGGGTTTGACACTCTTAC 58.540 45.455 0.00 0.00 0.00 2.34
32 33 3.133362 TCGTTGGGTTTGACACTCTTACT 59.867 43.478 0.00 0.00 0.00 2.24
33 34 3.875134 CGTTGGGTTTGACACTCTTACTT 59.125 43.478 0.00 0.00 0.00 2.24
34 35 5.051816 CGTTGGGTTTGACACTCTTACTTA 58.948 41.667 0.00 0.00 0.00 2.24
35 36 5.699458 CGTTGGGTTTGACACTCTTACTTAT 59.301 40.000 0.00 0.00 0.00 1.73
36 37 6.128634 CGTTGGGTTTGACACTCTTACTTATC 60.129 42.308 0.00 0.00 0.00 1.75
37 38 6.428083 TGGGTTTGACACTCTTACTTATCA 57.572 37.500 0.00 0.00 0.00 2.15
38 39 6.833041 TGGGTTTGACACTCTTACTTATCAA 58.167 36.000 0.00 0.00 0.00 2.57
39 40 7.284074 TGGGTTTGACACTCTTACTTATCAAA 58.716 34.615 0.00 0.00 34.57 2.69
40 41 7.776030 TGGGTTTGACACTCTTACTTATCAAAA 59.224 33.333 0.00 0.00 37.69 2.44
41 42 8.626526 GGGTTTGACACTCTTACTTATCAAAAA 58.373 33.333 0.00 0.00 37.69 1.94
42 43 9.665264 GGTTTGACACTCTTACTTATCAAAAAG 57.335 33.333 0.00 0.00 37.69 2.27
45 46 8.311650 TGACACTCTTACTTATCAAAAAGAGC 57.688 34.615 10.10 0.00 45.71 4.09
46 47 8.150945 TGACACTCTTACTTATCAAAAAGAGCT 58.849 33.333 10.10 0.00 45.71 4.09
47 48 9.640963 GACACTCTTACTTATCAAAAAGAGCTA 57.359 33.333 10.10 0.00 45.71 3.32
48 49 9.425577 ACACTCTTACTTATCAAAAAGAGCTAC 57.574 33.333 10.10 0.00 45.71 3.58
49 50 9.424319 CACTCTTACTTATCAAAAAGAGCTACA 57.576 33.333 10.10 0.00 45.71 2.74
50 51 9.998106 ACTCTTACTTATCAAAAAGAGCTACAA 57.002 29.630 10.10 0.00 45.71 2.41
57 58 9.727627 CTTATCAAAAAGAGCTACAATTGATCC 57.272 33.333 13.59 0.00 38.21 3.36
58 59 6.515272 TCAAAAAGAGCTACAATTGATCCC 57.485 37.500 13.59 0.00 0.00 3.85
59 60 6.009589 TCAAAAAGAGCTACAATTGATCCCA 58.990 36.000 13.59 0.00 0.00 4.37
60 61 6.664816 TCAAAAAGAGCTACAATTGATCCCAT 59.335 34.615 13.59 0.00 0.00 4.00
61 62 7.833682 TCAAAAAGAGCTACAATTGATCCCATA 59.166 33.333 13.59 0.00 0.00 2.74
62 63 8.636213 CAAAAAGAGCTACAATTGATCCCATAT 58.364 33.333 13.59 0.00 0.00 1.78
63 64 9.866655 AAAAAGAGCTACAATTGATCCCATATA 57.133 29.630 13.59 0.00 0.00 0.86
64 65 8.854614 AAAGAGCTACAATTGATCCCATATAC 57.145 34.615 13.59 0.00 0.00 1.47
65 66 7.805083 AGAGCTACAATTGATCCCATATACT 57.195 36.000 13.59 0.00 0.00 2.12
66 67 8.212259 AGAGCTACAATTGATCCCATATACTT 57.788 34.615 13.59 0.00 0.00 2.24
67 68 8.099537 AGAGCTACAATTGATCCCATATACTTG 58.900 37.037 13.59 0.00 0.00 3.16
68 69 7.749666 AGCTACAATTGATCCCATATACTTGT 58.250 34.615 13.59 0.00 0.00 3.16
69 70 7.663081 AGCTACAATTGATCCCATATACTTGTG 59.337 37.037 13.59 0.00 0.00 3.33
70 71 7.094634 GCTACAATTGATCCCATATACTTGTGG 60.095 40.741 13.59 0.00 34.04 4.17
77 78 4.705110 CCCATATACTTGTGGGTCATCA 57.295 45.455 2.25 0.00 46.53 3.07
97 98 8.540492 GTCATCAGTAATACAACATCGTAAAGG 58.460 37.037 0.00 0.00 0.00 3.11
226 227 2.933906 TCGAATCTCGGGCAATTAACAC 59.066 45.455 0.00 0.00 40.88 3.32
259 260 5.885912 ACGAAGGGAACTGCATATAACATTT 59.114 36.000 0.00 0.00 42.68 2.32
283 284 3.750371 TGAATCCTTGACATCGTGGTTT 58.250 40.909 0.00 0.00 0.00 3.27
431 432 4.919211 CGTTTAACGTTCGGTGACGCTAA 61.919 47.826 2.82 3.62 45.35 3.09
445 446 5.235831 GGTGACGCTAAAGTAATATTGGGAC 59.764 44.000 0.00 0.00 0.00 4.46
489 492 1.407258 GTTCGGAGTCCTGGATGAGAG 59.593 57.143 7.77 0.00 0.00 3.20
490 493 0.626382 TCGGAGTCCTGGATGAGAGT 59.374 55.000 7.77 0.00 0.00 3.24
631 650 3.165875 TCGGAGAAGTCTGAAAGTCCAT 58.834 45.455 0.00 0.00 34.95 3.41
678 697 3.496160 CATGGGCTGAGGGGAGGG 61.496 72.222 0.00 0.00 0.00 4.30
929 948 4.081917 TGTCAAACAAGAAACAAACCTCCC 60.082 41.667 0.00 0.00 0.00 4.30
1107 1126 2.254651 GACAACCTCGTCGACGCT 59.745 61.111 32.19 14.41 39.60 5.07
1131 1150 0.686769 AGGTTTCGCCGACTCCCTAT 60.687 55.000 3.59 0.00 43.70 2.57
1138 1157 0.389757 GCCGACTCCCTATTCTGACC 59.610 60.000 0.00 0.00 0.00 4.02
1177 1196 1.060937 CATTACGCGCTGCTGGTTC 59.939 57.895 5.73 0.00 0.00 3.62
1305 1327 1.526464 CTGCGGTGAATTGTTTTTGCC 59.474 47.619 0.00 0.00 0.00 4.52
1352 1374 0.250513 ATCAAACTCCAGCGAGGGAC 59.749 55.000 0.00 0.00 40.77 4.46
1397 1420 5.186021 TCTTCGTCTGCCTTTCTTCTTCTAT 59.814 40.000 0.00 0.00 0.00 1.98
1398 1421 6.377429 TCTTCGTCTGCCTTTCTTCTTCTATA 59.623 38.462 0.00 0.00 0.00 1.31
1399 1422 6.716934 TCGTCTGCCTTTCTTCTTCTATAT 57.283 37.500 0.00 0.00 0.00 0.86
1414 1437 4.160736 TCTATATGCGTGAGGATGAACG 57.839 45.455 0.00 0.00 44.06 3.95
1677 1701 5.633830 ACTTAACTTGGCTGATGATTGTG 57.366 39.130 0.00 0.00 0.00 3.33
1680 1704 4.713824 AACTTGGCTGATGATTGTGATG 57.286 40.909 0.00 0.00 0.00 3.07
1892 1924 5.301555 GGGATTTTAGTCATGGCTAGAGTC 58.698 45.833 7.19 9.27 0.00 3.36
1949 1981 8.397906 TCTGATTAATCCGCAAGAAGTATTTTG 58.602 33.333 12.90 0.00 43.02 2.44
1982 2014 7.389803 AGTTTTTCTTTTTGATGTTTTGGGG 57.610 32.000 0.00 0.00 0.00 4.96
2009 2041 7.463469 AAGAATAAAAAGTTGACGCTTTTGG 57.537 32.000 4.82 0.00 44.88 3.28
2388 2420 9.778993 CAGTCTGATGGAAATATGTTTTTGTAG 57.221 33.333 0.00 0.00 0.00 2.74
2551 2583 0.872388 GACAACGGTGCCCAAGTAAG 59.128 55.000 0.00 0.00 0.00 2.34
3295 3331 3.091545 AGAGTCTCTTCTCAAGGAGCTG 58.908 50.000 0.00 0.00 36.97 4.24
3337 3373 1.679139 TTTGGCTGTGGTTGTCTCAG 58.321 50.000 0.00 0.00 0.00 3.35
3846 3886 6.146347 CAGGTACTTTAACTCTTCTTCACAGC 59.854 42.308 0.00 0.00 34.60 4.40
4280 4330 5.446473 CGAAGATTTATCTGTGCTGGTCAAC 60.446 44.000 0.00 0.00 37.19 3.18
4648 4717 0.615331 TCCCTAGCCTGCTGAACTTG 59.385 55.000 0.97 0.00 0.00 3.16
5083 5154 4.081309 GGCTGGTAACTGTATGGTTAGACA 60.081 45.833 0.00 0.00 37.92 3.41
5117 5188 1.296715 CAGTAGTGGTGGTGGCCTC 59.703 63.158 3.32 0.00 0.00 4.70
5161 5234 0.038166 GCTGGGGTTTCCACATGAGA 59.962 55.000 0.00 0.00 41.46 3.27
5162 5235 1.952367 GCTGGGGTTTCCACATGAGAG 60.952 57.143 0.00 0.00 41.46 3.20
5164 5237 1.780309 TGGGGTTTCCACATGAGAGTT 59.220 47.619 0.00 0.00 41.46 3.01
5165 5238 2.176798 TGGGGTTTCCACATGAGAGTTT 59.823 45.455 0.00 0.00 41.46 2.66
5167 5240 4.141135 TGGGGTTTCCACATGAGAGTTTAA 60.141 41.667 0.00 0.00 41.46 1.52
5468 5727 0.612174 AGACTAAGGCACTGGCTCGA 60.612 55.000 5.42 0.00 40.86 4.04
5535 5795 2.200067 CGAAGCTGAGCTGGTTCTATG 58.800 52.381 8.16 0.00 39.62 2.23
5615 5875 2.260844 TTTGCCAGAACACTCAGAGG 57.739 50.000 1.53 0.00 0.00 3.69
5628 5888 4.082679 ACACTCAGAGGACGTAGATTGAAC 60.083 45.833 1.53 0.00 0.00 3.18
5740 6006 4.549458 GCACTTTCAAATAGCTGAGCAAA 58.451 39.130 7.39 0.00 0.00 3.68
5747 6013 9.362539 CTTTCAAATAGCTGAGCAAAAATATGT 57.637 29.630 7.39 0.00 0.00 2.29
5778 6044 6.605471 TGTCTAGAATGCTCAGGAAACTAA 57.395 37.500 0.00 0.00 40.21 2.24
5839 6106 6.949352 ATGAAACTTTTTCAGAAGAGCTCA 57.051 33.333 17.77 0.00 0.00 4.26
5840 6107 6.949352 TGAAACTTTTTCAGAAGAGCTCAT 57.051 33.333 17.77 2.97 0.00 2.90
5846 6113 6.204495 ACTTTTTCAGAAGAGCTCATTGAGAC 59.796 38.462 17.77 9.99 0.00 3.36
5924 6191 1.200519 TGCCGCCCTGTCTATTAGTT 58.799 50.000 0.00 0.00 0.00 2.24
6106 6576 7.306574 GCAACTTTCAGCAAATTAAACACTACC 60.307 37.037 0.00 0.00 0.00 3.18
6489 6959 5.191722 TGTTAAAATGCCTGTCCTATCTCCT 59.808 40.000 0.00 0.00 0.00 3.69
6621 7092 3.130516 TGAACTTCTAGTCATGCTACCCG 59.869 47.826 0.00 0.00 0.00 5.28
6930 9462 8.267183 TCATCATCTTTTTAGCCTACAGATTGA 58.733 33.333 0.00 0.00 0.00 2.57
7268 9804 6.183359 GCAAACAAATAGAGACTGATTTTGCG 60.183 38.462 0.00 0.00 31.99 4.85
7896 10432 2.233431 CCTGCAGCTTTAGACACTCTCT 59.767 50.000 8.66 0.00 0.00 3.10
8158 10703 0.881118 GCAGATGTTTCCCGCAAAGA 59.119 50.000 0.00 0.00 0.00 2.52
8423 10968 6.472016 TCATGGCATTGTGAGTAGTTTTAGA 58.528 36.000 0.00 0.00 0.00 2.10
8429 10974 7.018235 GCATTGTGAGTAGTTTTAGAGAAAGC 58.982 38.462 0.00 0.00 0.00 3.51
8678 11224 6.715344 CGTAAGTAGTTTGCATTCTTGGTA 57.285 37.500 0.00 0.00 0.00 3.25
8835 11382 5.823861 TTACTCCATGGCTTGCATATCTA 57.176 39.130 6.96 0.00 0.00 1.98
8882 11430 4.141287 CTGTCCACCATTGTCCTTGTTTA 58.859 43.478 0.00 0.00 0.00 2.01
8885 11433 4.339814 GTCCACCATTGTCCTTGTTTACAA 59.660 41.667 0.00 0.00 39.73 2.41
8896 11444 7.054124 TGTCCTTGTTTACAAAGAGATTCAGT 58.946 34.615 0.00 0.00 35.15 3.41
8936 11484 9.751542 GGGATGATATATAACTCGAATGGTTAG 57.248 37.037 2.72 0.00 33.50 2.34
8992 11543 6.772078 ACTGTTTTGTAAGAACTTCACTTCG 58.228 36.000 0.00 0.00 0.00 3.79
9001 11552 6.560253 AAGAACTTCACTTCGCAATTATGT 57.440 33.333 0.00 0.00 0.00 2.29
9002 11553 5.931532 AGAACTTCACTTCGCAATTATGTG 58.068 37.500 0.00 0.00 38.44 3.21
9013 11910 7.769044 ACTTCGCAATTATGTGGTCTACTAAAT 59.231 33.333 0.00 0.00 37.65 1.40
9130 12027 6.239176 CCTTATACAAGGCCACAAACTCAAAA 60.239 38.462 5.01 0.00 44.90 2.44
9151 12048 9.895138 TCAAAATACAGGTACCTAGGTAAAATC 57.105 33.333 23.40 10.71 31.86 2.17
9171 12068 8.707938 AAAATCTAATGACTATTTTGCAAGCC 57.292 30.769 0.00 0.00 32.93 4.35
9182 12079 5.739752 ATTTTGCAAGCCAACTTTTCTTC 57.260 34.783 0.00 0.00 32.29 2.87
9185 12082 5.590530 TTGCAAGCCAACTTTTCTTCTTA 57.409 34.783 0.00 0.00 32.29 2.10
9191 12088 7.867909 GCAAGCCAACTTTTCTTCTTATTAACT 59.132 33.333 0.00 0.00 32.29 2.24
9234 12131 2.291089 TGCATGCAAGGAAGGAATGAGA 60.291 45.455 20.30 0.00 0.00 3.27
9246 12143 5.397334 GGAAGGAATGAGAAGGAAGTAGCAT 60.397 44.000 0.00 0.00 0.00 3.79
9260 12157 8.200024 AGGAAGTAGCATAGTGTCATTATGAT 57.800 34.615 17.10 13.80 32.46 2.45
9292 12189 9.173939 GCATGCAAGTATTAAATAAGTTGCTAG 57.826 33.333 14.21 15.65 37.62 3.42
9337 12269 2.005560 GCCTCGGTTACTGTTAGTGGC 61.006 57.143 0.00 0.00 34.94 5.01
9340 12272 1.274167 TCGGTTACTGTTAGTGGCCTG 59.726 52.381 3.32 0.00 0.00 4.85
9352 12284 1.844497 AGTGGCCTGGTATAAGGGAAC 59.156 52.381 3.32 0.00 37.84 3.62
9367 12299 0.464452 GGAACGGAGGGAGTACATGG 59.536 60.000 0.00 0.00 0.00 3.66
9377 12309 6.365520 GGAGGGAGTACATGGTAATGATTTT 58.634 40.000 0.00 0.00 37.24 1.82
9388 12320 7.781693 ACATGGTAATGATTTTATGCTCTCCTT 59.218 33.333 0.00 0.00 37.24 3.36
9426 12358 3.012518 CCATTCGTCCTGAGCTGAATTT 58.987 45.455 0.00 0.00 0.00 1.82
9435 12367 0.244721 GAGCTGAATTTGTGGTGGGC 59.755 55.000 0.00 0.00 0.00 5.36
9438 12370 1.606224 GCTGAATTTGTGGTGGGCTTG 60.606 52.381 0.00 0.00 0.00 4.01
9449 12381 4.339814 TGTGGTGGGCTTGTAAGTAAAAAG 59.660 41.667 0.00 0.00 0.00 2.27
9452 12384 6.208007 GTGGTGGGCTTGTAAGTAAAAAGTAT 59.792 38.462 0.00 0.00 0.00 2.12
9462 12394 9.562408 TTGTAAGTAAAAAGTATCACATGGTGA 57.438 29.630 1.05 1.05 46.90 4.02
9469 12401 4.679373 AGTATCACATGGTGAAGCTAGG 57.321 45.455 2.87 0.00 45.96 3.02
9510 12442 5.242615 TCGTTTCCATGATTGTGATCCAAAA 59.757 36.000 0.00 0.00 36.44 2.44
9609 13697 6.803320 CGCATTAATTGGTAGGAATATGCTTG 59.197 38.462 0.00 0.00 36.04 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.035458 AACCCAACGAGGAGCAGAAG 59.965 55.000 0.00 0.00 41.22 2.85
2 3 0.250295 CAAACCCAACGAGGAGCAGA 60.250 55.000 0.00 0.00 41.22 4.26
3 4 0.250295 TCAAACCCAACGAGGAGCAG 60.250 55.000 0.00 0.00 41.22 4.24
4 5 0.534203 GTCAAACCCAACGAGGAGCA 60.534 55.000 0.00 0.00 41.22 4.26
5 6 0.534203 TGTCAAACCCAACGAGGAGC 60.534 55.000 0.00 0.00 41.22 4.70
6 7 1.202651 AGTGTCAAACCCAACGAGGAG 60.203 52.381 0.00 0.00 41.22 3.69
8 9 1.202651 AGAGTGTCAAACCCAACGAGG 60.203 52.381 0.00 0.00 37.03 4.63
9 10 2.240493 AGAGTGTCAAACCCAACGAG 57.760 50.000 0.00 0.00 0.00 4.18
10 11 2.702592 AAGAGTGTCAAACCCAACGA 57.297 45.000 0.00 0.00 0.00 3.85
12 13 6.708949 TGATAAGTAAGAGTGTCAAACCCAAC 59.291 38.462 0.00 0.00 0.00 3.77
13 14 6.833041 TGATAAGTAAGAGTGTCAAACCCAA 58.167 36.000 0.00 0.00 0.00 4.12
15 16 7.739498 TTTGATAAGTAAGAGTGTCAAACCC 57.261 36.000 0.00 0.00 32.50 4.11
16 17 9.665264 CTTTTTGATAAGTAAGAGTGTCAAACC 57.335 33.333 0.00 0.00 35.89 3.27
19 20 8.774586 GCTCTTTTTGATAAGTAAGAGTGTCAA 58.225 33.333 11.12 0.00 43.39 3.18
20 21 8.150945 AGCTCTTTTTGATAAGTAAGAGTGTCA 58.849 33.333 11.12 0.00 43.39 3.58
21 22 8.541133 AGCTCTTTTTGATAAGTAAGAGTGTC 57.459 34.615 11.12 0.00 43.39 3.67
22 23 9.425577 GTAGCTCTTTTTGATAAGTAAGAGTGT 57.574 33.333 11.12 3.83 43.39 3.55
23 24 9.424319 TGTAGCTCTTTTTGATAAGTAAGAGTG 57.576 33.333 11.12 0.00 43.39 3.51
24 25 9.998106 TTGTAGCTCTTTTTGATAAGTAAGAGT 57.002 29.630 11.12 3.21 43.39 3.24
31 32 9.727627 GGATCAATTGTAGCTCTTTTTGATAAG 57.272 33.333 5.13 0.00 34.81 1.73
32 33 8.686334 GGGATCAATTGTAGCTCTTTTTGATAA 58.314 33.333 5.13 0.00 34.81 1.75
33 34 7.833682 TGGGATCAATTGTAGCTCTTTTTGATA 59.166 33.333 5.13 0.00 34.81 2.15
34 35 6.664816 TGGGATCAATTGTAGCTCTTTTTGAT 59.335 34.615 5.13 12.18 36.73 2.57
35 36 6.009589 TGGGATCAATTGTAGCTCTTTTTGA 58.990 36.000 5.13 0.00 0.00 2.69
36 37 6.271488 TGGGATCAATTGTAGCTCTTTTTG 57.729 37.500 5.13 0.00 0.00 2.44
37 38 8.773033 ATATGGGATCAATTGTAGCTCTTTTT 57.227 30.769 5.13 0.00 0.00 1.94
38 39 9.289782 GTATATGGGATCAATTGTAGCTCTTTT 57.710 33.333 5.13 0.00 0.00 2.27
39 40 8.664079 AGTATATGGGATCAATTGTAGCTCTTT 58.336 33.333 5.13 0.00 0.00 2.52
40 41 8.212259 AGTATATGGGATCAATTGTAGCTCTT 57.788 34.615 5.13 0.00 0.00 2.85
41 42 7.805083 AGTATATGGGATCAATTGTAGCTCT 57.195 36.000 5.13 0.00 0.00 4.09
42 43 7.880195 ACAAGTATATGGGATCAATTGTAGCTC 59.120 37.037 5.13 0.00 0.00 4.09
43 44 7.663081 CACAAGTATATGGGATCAATTGTAGCT 59.337 37.037 5.13 0.00 0.00 3.32
44 45 7.094634 CCACAAGTATATGGGATCAATTGTAGC 60.095 40.741 5.13 0.00 31.83 3.58
45 46 8.327941 CCACAAGTATATGGGATCAATTGTAG 57.672 38.462 5.13 0.00 31.83 2.74
57 58 5.296151 ACTGATGACCCACAAGTATATGG 57.704 43.478 0.00 0.00 35.59 2.74
58 59 9.424319 GTATTACTGATGACCCACAAGTATATG 57.576 37.037 0.00 0.00 0.00 1.78
59 60 9.154632 TGTATTACTGATGACCCACAAGTATAT 57.845 33.333 0.00 0.00 0.00 0.86
60 61 8.541899 TGTATTACTGATGACCCACAAGTATA 57.458 34.615 0.00 0.00 0.00 1.47
61 62 7.432148 TGTATTACTGATGACCCACAAGTAT 57.568 36.000 0.00 0.00 0.00 2.12
62 63 6.860790 TGTATTACTGATGACCCACAAGTA 57.139 37.500 0.00 0.00 0.00 2.24
63 64 5.755409 TGTATTACTGATGACCCACAAGT 57.245 39.130 0.00 0.00 0.00 3.16
64 65 5.937540 TGTTGTATTACTGATGACCCACAAG 59.062 40.000 0.00 0.00 0.00 3.16
65 66 5.870706 TGTTGTATTACTGATGACCCACAA 58.129 37.500 0.00 0.00 0.00 3.33
66 67 5.491323 TGTTGTATTACTGATGACCCACA 57.509 39.130 0.00 0.00 0.00 4.17
67 68 5.234329 CGATGTTGTATTACTGATGACCCAC 59.766 44.000 0.00 0.00 0.00 4.61
68 69 5.105106 ACGATGTTGTATTACTGATGACCCA 60.105 40.000 0.00 0.00 0.00 4.51
69 70 5.357257 ACGATGTTGTATTACTGATGACCC 58.643 41.667 0.00 0.00 0.00 4.46
70 71 7.997107 TTACGATGTTGTATTACTGATGACC 57.003 36.000 0.00 0.00 0.00 4.02
71 72 8.540492 CCTTTACGATGTTGTATTACTGATGAC 58.460 37.037 0.00 0.00 0.00 3.06
72 73 7.709182 CCCTTTACGATGTTGTATTACTGATGA 59.291 37.037 0.00 0.00 0.00 2.92
73 74 7.518370 GCCCTTTACGATGTTGTATTACTGATG 60.518 40.741 0.00 0.00 0.00 3.07
74 75 6.482308 GCCCTTTACGATGTTGTATTACTGAT 59.518 38.462 0.00 0.00 0.00 2.90
77 78 5.985911 AGCCCTTTACGATGTTGTATTACT 58.014 37.500 0.00 0.00 0.00 2.24
120 121 9.234384 CGTAATACAAGATCTCGTGACTAAATT 57.766 33.333 0.00 0.00 0.00 1.82
122 123 7.066163 TCCGTAATACAAGATCTCGTGACTAAA 59.934 37.037 0.00 0.00 0.00 1.85
259 260 3.513912 ACCACGATGTCAAGGATTCAGTA 59.486 43.478 0.00 0.00 0.00 2.74
364 365 8.012957 AGAATTATTTAGACATGACCGAGACT 57.987 34.615 0.00 0.00 0.00 3.24
411 412 2.414058 TAGCGTCACCGAACGTTAAA 57.586 45.000 0.00 0.00 44.38 1.52
431 432 9.200817 ACTAAAATGCATGTCCCAATATTACTT 57.799 29.630 0.00 0.00 0.00 2.24
445 446 9.577110 AACAATATTCAGTCACTAAAATGCATG 57.423 29.630 0.00 0.00 0.00 4.06
489 492 3.036783 CTCCTCGTGACGTCCGGAC 62.037 68.421 25.28 25.28 0.00 4.79
490 493 2.745100 CTCCTCGTGACGTCCGGA 60.745 66.667 20.97 0.00 0.00 5.14
631 650 1.275291 GAGACGTGATGGAACCCTTGA 59.725 52.381 0.00 0.00 0.00 3.02
678 697 3.317149 GGGTATTATTTCCGCAACCTTCC 59.683 47.826 0.00 0.00 0.00 3.46
929 948 0.692756 GGGGAGAGGAGGGAGAAAGG 60.693 65.000 0.00 0.00 0.00 3.11
1131 1150 4.515191 CAGGAAAAGAAATCGTGGTCAGAA 59.485 41.667 0.00 0.00 0.00 3.02
1138 1157 5.627499 TGATTCCAGGAAAAGAAATCGTG 57.373 39.130 5.81 0.00 33.60 4.35
1177 1196 3.207778 TCCAATTTAAGGGCGTATTCCG 58.792 45.455 0.00 0.00 40.40 4.30
1305 1327 2.061773 GATCTCACATAATCGCCACGG 58.938 52.381 0.00 0.00 0.00 4.94
1397 1420 2.809446 CTTCGTTCATCCTCACGCATA 58.191 47.619 0.00 0.00 36.32 3.14
1398 1421 1.645034 CTTCGTTCATCCTCACGCAT 58.355 50.000 0.00 0.00 36.32 4.73
1399 1422 1.014044 GCTTCGTTCATCCTCACGCA 61.014 55.000 0.00 0.00 36.32 5.24
1414 1437 3.305629 CAGTCGCATAGAACTCTTGCTTC 59.694 47.826 10.22 5.48 34.23 3.86
1892 1924 1.022735 ATCCACCGTACTGCTCTACG 58.977 55.000 6.75 6.75 39.41 3.51
1982 2014 9.829637 CAAAAGCGTCAACTTTTTATTCTTTAC 57.170 29.630 0.00 0.00 45.29 2.01
2009 2041 0.596600 TCCTTCATTATCGCCGCGTC 60.597 55.000 13.39 0.00 0.00 5.19
2138 2170 4.541973 TTGAGATTCACTGCTTGCTAGA 57.458 40.909 0.00 0.00 0.00 2.43
2232 2264 2.095604 AAAGCTAAGGTTTGGCCCAA 57.904 45.000 0.00 0.00 37.96 4.12
2388 2420 3.073274 AGAACCTCACATAAGTTGGGC 57.927 47.619 0.00 0.00 0.00 5.36
2525 2557 1.310216 GGGCACCGTTGTCCCATTAC 61.310 60.000 7.43 0.00 42.35 1.89
2551 2583 5.031578 CGAGCACACACTCTCTATTAGAAC 58.968 45.833 0.00 0.00 34.35 3.01
3295 3331 5.948992 AAGATCAAACCTCTACAACTTGC 57.051 39.130 0.00 0.00 0.00 4.01
4648 4717 1.715519 GCAATTCACATGTTGCGACAC 59.284 47.619 9.51 0.00 40.95 3.67
4746 4815 2.868899 CAGGCCCATCTAATTCTTCCC 58.131 52.381 0.00 0.00 0.00 3.97
5014 5085 4.828072 AGTTCTGGGATGGTAGTTCTTC 57.172 45.455 0.00 0.00 0.00 2.87
5117 5188 8.867935 GCACTATCATACTTTGAGCATACATAG 58.132 37.037 0.00 0.00 37.89 2.23
5273 5349 2.106511 AGTTGTGCCTTCCAGCTAAGAA 59.893 45.455 0.00 0.00 0.00 2.52
5274 5350 1.699634 AGTTGTGCCTTCCAGCTAAGA 59.300 47.619 0.00 0.00 0.00 2.10
5276 5352 1.699634 AGAGTTGTGCCTTCCAGCTAA 59.300 47.619 0.00 0.00 0.00 3.09
5277 5353 1.352083 AGAGTTGTGCCTTCCAGCTA 58.648 50.000 0.00 0.00 0.00 3.32
5468 5727 2.919971 GCTCAAGCCGAAAGTGAGT 58.080 52.632 0.00 0.00 40.76 3.41
5535 5795 6.153756 ACATATTTTGTAACTTCCGGCAAAC 58.846 36.000 0.00 0.00 36.57 2.93
5697 5961 5.575218 GTGCCGACCTATTTTGTAAATTTGG 59.425 40.000 0.00 0.00 0.00 3.28
5698 5962 6.386654 AGTGCCGACCTATTTTGTAAATTTG 58.613 36.000 0.00 0.00 0.00 2.32
5699 5963 6.584185 AGTGCCGACCTATTTTGTAAATTT 57.416 33.333 0.00 0.00 0.00 1.82
5747 6013 6.942005 TCCTGAGCATTCTAGACAAATTTCAA 59.058 34.615 0.00 0.00 0.00 2.69
5821 6088 6.204495 GTCTCAATGAGCTCTTCTGAAAAAGT 59.796 38.462 16.19 0.00 0.00 2.66
5822 6089 6.601264 GTCTCAATGAGCTCTTCTGAAAAAG 58.399 40.000 16.19 3.66 0.00 2.27
5846 6113 3.609703 AGCCTGTAGGTGAGCTCG 58.390 61.111 9.64 0.00 37.57 5.03
6106 6576 3.486108 AGTCGTTGATATTTAGCGCGAAG 59.514 43.478 12.10 0.00 0.00 3.79
7003 9537 7.881751 AGTGTGCTGCATTGAGTGATATTATAT 59.118 33.333 5.27 0.00 0.00 0.86
7021 9555 4.573900 AGGAAGTTCAGATTAGTGTGCTG 58.426 43.478 5.01 0.00 0.00 4.41
7243 9779 6.183359 CGCAAAATCAGTCTCTATTTGTTTGC 60.183 38.462 7.11 7.11 42.89 3.68
7268 9804 2.185608 GGCTTCACTCGAGGAGCC 59.814 66.667 28.89 28.89 32.04 4.70
7896 10432 0.780637 TATCCAACCAAACCAGGCCA 59.219 50.000 5.01 0.00 0.00 5.36
8158 10703 8.100791 TGGTGTCTATAGTTGTTTCTGCTATTT 58.899 33.333 0.00 0.00 0.00 1.40
8367 10912 3.981211 TGAAACCATTGAAAAGAGCAGC 58.019 40.909 0.00 0.00 0.00 5.25
8458 11003 7.388437 AGTGGATTGCATTTTATTCACATGTT 58.612 30.769 9.64 0.00 33.51 2.71
8532 11078 3.249799 TGTGTGTAGTAGCATTTGTGCAC 59.750 43.478 10.75 10.75 37.25 4.57
8683 11229 8.458573 TCACAAAATACACCAAAGACTATTGT 57.541 30.769 0.00 0.00 0.00 2.71
8754 11300 7.200434 AGCCAAGGATAGAAGTCTTTCATAA 57.800 36.000 0.00 0.00 35.70 1.90
8810 11357 5.893255 AGATATGCAAGCCATGGAGTAAAAA 59.107 36.000 18.40 0.00 35.34 1.94
8904 11452 5.527951 TCGAGTTATATATCATCCCGCTCTC 59.472 44.000 0.00 0.00 0.00 3.20
8970 11518 5.122554 TGCGAAGTGAAGTTCTTACAAAACA 59.877 36.000 4.17 0.00 0.00 2.83
9024 11921 5.804979 CACAGATTTGTTTTTCGAACTTGGT 59.195 36.000 0.00 0.00 34.62 3.67
9124 12021 9.901172 ATTTTACCTAGGTACCTGTATTTTGAG 57.099 33.333 25.33 10.73 0.00 3.02
9151 12048 6.624423 AGTTGGCTTGCAAAATAGTCATTAG 58.376 36.000 0.00 0.00 0.00 1.73
9161 12058 4.831107 AGAAGAAAAGTTGGCTTGCAAAA 58.169 34.783 0.00 0.00 34.71 2.44
9166 12063 9.185192 CAGTTAATAAGAAGAAAAGTTGGCTTG 57.815 33.333 0.00 0.00 34.71 4.01
9182 12079 7.023575 GCGCATTAATGATCCCAGTTAATAAG 58.976 38.462 19.73 0.00 0.00 1.73
9185 12082 4.218417 GGCGCATTAATGATCCCAGTTAAT 59.782 41.667 19.73 0.00 0.00 1.40
9191 12088 0.888736 CGGGCGCATTAATGATCCCA 60.889 55.000 29.37 0.00 39.39 4.37
9234 12131 8.023021 TCATAATGACACTATGCTACTTCCTT 57.977 34.615 0.00 0.00 0.00 3.36
9246 12143 7.444792 TGCATGCATGTAATCATAATGACACTA 59.555 33.333 26.79 0.00 33.13 2.74
9282 12179 7.372714 TGATGTTTTCTCGTACTAGCAACTTA 58.627 34.615 9.33 0.00 0.00 2.24
9292 12189 9.937577 GCAAAATTTAATGATGTTTTCTCGTAC 57.062 29.630 0.00 0.00 0.00 3.67
9337 12269 1.692519 CCTCCGTTCCCTTATACCAGG 59.307 57.143 0.00 0.00 0.00 4.45
9340 12272 1.969208 CTCCCTCCGTTCCCTTATACC 59.031 57.143 0.00 0.00 0.00 2.73
9352 12284 2.963101 TCATTACCATGTACTCCCTCCG 59.037 50.000 0.00 0.00 0.00 4.63
9377 12309 7.394641 CCATCAGTACTATGTAAGGAGAGCATA 59.605 40.741 0.00 0.00 0.00 3.14
9388 12320 5.831525 ACGAATGGACCATCAGTACTATGTA 59.168 40.000 7.63 0.00 0.00 2.29
9426 12358 3.579534 TTTACTTACAAGCCCACCACA 57.420 42.857 0.00 0.00 0.00 4.17
9435 12367 9.825972 CACCATGTGATACTTTTTACTTACAAG 57.174 33.333 0.00 0.00 35.23 3.16
9449 12381 3.134458 GCCTAGCTTCACCATGTGATAC 58.866 50.000 0.00 0.00 42.40 2.24
9452 12384 1.279496 AGCCTAGCTTCACCATGTGA 58.721 50.000 0.00 0.00 41.09 3.58
9462 12394 2.103263 CGTCCCATTTCTAGCCTAGCTT 59.897 50.000 0.00 0.00 40.44 3.74
9469 12401 1.480219 CGACGCGTCCCATTTCTAGC 61.480 60.000 31.84 4.84 0.00 3.42
9510 12442 5.437060 ACTCACAACGCCCAATTATTAGAT 58.563 37.500 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.