Multiple sequence alignment - TraesCS1D01G305400

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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 TraesCS1D01G305400 chr1D 100.000 3875 0 0 932 4806 403038666 403042540 0.000000e+00 7156.0
1 TraesCS1D01G305400 chr1D 100.000 595 0 0 1 595 403037735 403038329 0.000000e+00 1099.0
2 TraesCS1D01G305400 chr1D 94.074 135 7 1 3326 3459 403041007 403041141 2.270000e-48 204.0
3 TraesCS1D01G305400 chr1D 94.074 135 7 1 3273 3407 403041060 403041193 2.270000e-48 204.0
4 TraesCS1D01G305400 chr1D 93.976 83 4 1 3378 3459 403041007 403041089 1.820000e-24 124.0
5 TraesCS1D01G305400 chr1D 93.976 83 4 1 3273 3355 403041112 403041193 1.820000e-24 124.0
6 TraesCS1D01G305400 chr1B 91.483 2313 132 18 932 3208 540991101 540993384 0.000000e+00 3120.0
7 TraesCS1D01G305400 chr1B 89.011 728 52 11 3380 4081 540993600 540994325 0.000000e+00 876.0
8 TraesCS1D01G305400 chr1B 86.116 605 54 8 1 595 540990455 540991039 4.080000e-175 625.0
9 TraesCS1D01G305400 chr1B 89.362 282 19 5 4068 4347 540994341 540994613 1.280000e-90 344.0
10 TraesCS1D01G305400 chr1B 85.185 243 31 3 232 469 25227350 25227108 1.340000e-60 244.0
11 TraesCS1D01G305400 chr1B 86.047 86 10 2 3328 3411 540993600 540993685 1.840000e-14 91.6
12 TraesCS1D01G305400 chr1B 100.000 28 0 0 3432 3459 540993600 540993627 9.000000e-03 52.8
13 TraesCS1D01G305400 chr1A 92.025 1793 104 12 932 2689 498138855 498140643 0.000000e+00 2483.0
14 TraesCS1D01G305400 chr1A 88.872 1321 89 32 2918 4233 498140870 498142137 0.000000e+00 1572.0
15 TraesCS1D01G305400 chr1A 81.306 337 45 12 4348 4673 6920861 6920532 1.720000e-64 257.0
16 TraesCS1D01G305400 chr1A 96.183 131 5 0 4676 4806 445540990 445540860 1.050000e-51 215.0
17 TraesCS1D01G305400 chr1A 93.103 87 5 1 3273 3359 498141279 498141364 5.050000e-25 126.0
18 TraesCS1D01G305400 chr1A 90.361 83 7 1 3378 3459 498141226 498141308 1.830000e-19 108.0
19 TraesCS1D01G305400 chr7D 91.549 355 27 1 1545 1899 98664903 98665254 2.010000e-133 486.0
20 TraesCS1D01G305400 chr7D 89.014 355 33 3 1545 1899 621806431 621806083 7.390000e-118 435.0
21 TraesCS1D01G305400 chr7D 95.339 236 11 0 4348 4583 633183398 633183633 4.540000e-100 375.0
22 TraesCS1D01G305400 chr7D 84.574 376 42 12 1332 1702 588622634 588622270 4.570000e-95 359.0
23 TraesCS1D01G305400 chr7D 92.000 250 14 3 1251 1500 98664656 98664899 3.560000e-91 346.0
24 TraesCS1D01G305400 chr7D 94.815 135 5 1 4674 4806 633183807 633183941 4.870000e-50 209.0
25 TraesCS1D01G305400 chr7D 97.778 90 2 0 4584 4673 633183690 633183779 6.440000e-34 156.0
26 TraesCS1D01G305400 chr7B 91.379 348 27 1 1545 1892 54314801 54315145 1.570000e-129 473.0
27 TraesCS1D01G305400 chr7B 91.600 250 15 4 1251 1500 54314554 54314797 1.660000e-89 340.0
28 TraesCS1D01G305400 chr7A 89.296 355 34 2 1545 1899 101223169 101223519 4.410000e-120 442.0
29 TraesCS1D01G305400 chr7A 93.200 250 11 3 1251 1500 101222922 101223165 3.540000e-96 363.0
30 TraesCS1D01G305400 chr7A 94.595 74 4 0 4584 4657 96530866 96530793 1.090000e-21 115.0
31 TraesCS1D01G305400 chr5A 89.326 356 30 6 1545 1899 470948474 470948126 1.590000e-119 440.0
32 TraesCS1D01G305400 chr5A 92.116 241 14 4 4343 4583 594975060 594974825 7.710000e-88 335.0
33 TraesCS1D01G305400 chr5A 91.597 238 20 0 4346 4583 324481773 324482010 3.590000e-86 329.0
34 TraesCS1D01G305400 chr5A 98.473 131 2 0 4676 4806 324487783 324487913 1.040000e-56 231.0
35 TraesCS1D01G305400 chr5A 98.889 90 1 0 4584 4673 594974768 594974679 1.380000e-35 161.0
36 TraesCS1D01G305400 chr5A 95.455 88 4 0 4586 4673 324482062 324482149 1.800000e-29 141.0
37 TraesCS1D01G305400 chr5A 86.250 80 6 2 1421 1500 13079205 13079279 1.110000e-11 82.4
38 TraesCS1D01G305400 chr3D 88.732 355 34 3 1545 1899 583603884 583603536 3.440000e-116 429.0
39 TraesCS1D01G305400 chr3A 88.451 355 35 4 1545 1899 662566779 662567127 1.600000e-114 424.0
40 TraesCS1D01G305400 chr3A 89.873 237 24 0 4347 4583 83240467 83240231 6.040000e-79 305.0
41 TraesCS1D01G305400 chr2D 94.068 236 14 0 4348 4583 450568695 450568930 4.570000e-95 359.0
42 TraesCS1D01G305400 chr2D 93.671 237 15 0 4347 4583 181211436 181211200 5.920000e-94 355.0
43 TraesCS1D01G305400 chr2D 84.921 252 9 14 4584 4806 450568987 450569238 1.350000e-55 228.0
44 TraesCS1D01G305400 chr2D 96.296 135 2 2 4674 4806 181211026 181210893 8.100000e-53 219.0
45 TraesCS1D01G305400 chr2D 96.667 90 3 0 4584 4673 181211143 181211054 3.000000e-32 150.0
46 TraesCS1D01G305400 chr3B 92.500 240 15 2 4346 4583 511624419 511624657 1.660000e-89 340.0
47 TraesCS1D01G305400 chr3B 85.897 234 29 2 229 458 798970248 798970481 3.710000e-61 246.0
48 TraesCS1D01G305400 chr3B 84.400 250 33 4 229 473 26835534 26835782 1.730000e-59 241.0
49 TraesCS1D01G305400 chr3B 93.333 135 7 1 4674 4806 511624859 511624993 1.060000e-46 198.0
50 TraesCS1D01G305400 chr3B 94.595 74 4 0 4584 4657 511624714 511624787 1.090000e-21 115.0
51 TraesCS1D01G305400 chr6A 91.949 236 19 0 4348 4583 573506080 573505845 9.970000e-87 331.0
52 TraesCS1D01G305400 chr6A 91.111 135 9 3 4674 4806 573505643 573505510 3.820000e-41 180.0
53 TraesCS1D01G305400 chr6A 97.297 74 2 0 4584 4657 573505788 573505715 5.050000e-25 126.0
54 TraesCS1D01G305400 chr2A 91.949 236 19 0 4348 4583 687499947 687499712 9.970000e-87 331.0
55 TraesCS1D01G305400 chr2A 89.630 135 11 3 4674 4806 687499511 687499378 8.270000e-38 169.0
56 TraesCS1D01G305400 chr2A 95.946 74 3 0 4584 4657 687499655 687499582 2.350000e-23 121.0
57 TraesCS1D01G305400 chr6B 84.585 253 34 3 232 480 31939847 31940098 3.710000e-61 246.0
58 TraesCS1D01G305400 chr6B 80.335 239 35 10 1332 1565 247012863 247012632 2.300000e-38 171.0
59 TraesCS1D01G305400 chr2B 84.739 249 33 3 229 472 602192291 602192539 1.340000e-60 244.0
60 TraesCS1D01G305400 chr2B 85.714 168 18 3 1333 1500 483861461 483861300 6.390000e-39 172.0
61 TraesCS1D01G305400 chrUn 84.615 247 32 4 232 474 83928654 83928410 1.730000e-59 241.0
62 TraesCS1D01G305400 chrUn 83.142 261 38 4 232 486 353243801 353243541 2.890000e-57 233.0
63 TraesCS1D01G305400 chr5B 84.337 249 33 3 228 470 586917920 586917672 6.220000e-59 239.0


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 TraesCS1D01G305400 chr1D 403037735 403042540 4805 False 1485.166667 7156 96.016667 1 4806 6 chr1D.!!$F1 4805
1 TraesCS1D01G305400 chr1B 540990455 540994613 4158 False 851.566667 3120 90.336500 1 4347 6 chr1B.!!$F1 4346
2 TraesCS1D01G305400 chr1A 498138855 498142137 3282 False 1072.250000 2483 91.090250 932 4233 4 chr1A.!!$F1 3301
3 TraesCS1D01G305400 chr7D 98664656 98665254 598 False 416.000000 486 91.774500 1251 1899 2 chr7D.!!$F1 648
4 TraesCS1D01G305400 chr7D 633183398 633183941 543 False 246.666667 375 95.977333 4348 4806 3 chr7D.!!$F2 458
5 TraesCS1D01G305400 chr7B 54314554 54315145 591 False 406.500000 473 91.489500 1251 1892 2 chr7B.!!$F1 641
6 TraesCS1D01G305400 chr7A 101222922 101223519 597 False 402.500000 442 91.248000 1251 1899 2 chr7A.!!$F1 648
7 TraesCS1D01G305400 chr2D 450568695 450569238 543 False 293.500000 359 89.494500 4348 4806 2 chr2D.!!$F1 458
8 TraesCS1D01G305400 chr2D 181210893 181211436 543 True 241.333333 355 95.544667 4347 4806 3 chr2D.!!$R1 459
9 TraesCS1D01G305400 chr3B 511624419 511624993 574 False 217.666667 340 93.476000 4346 4806 3 chr3B.!!$F3 460
10 TraesCS1D01G305400 chr6A 573505510 573506080 570 True 212.333333 331 93.452333 4348 4806 3 chr6A.!!$R1 458
11 TraesCS1D01G305400 chr2A 687499378 687499947 569 True 207.000000 331 92.508333 4348 4806 3 chr2A.!!$R1 458

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
277 278 0.179169 GGGTCTTAGCACGACGACTC 60.179 60.0 0.0 0.0 32.24 3.36 F
278 279 0.179169 GGTCTTAGCACGACGACTCC 60.179 60.0 0.0 0.0 32.24 3.85 F
312 316 0.385974 CAAGTTTTGCTCGGCTTCGG 60.386 55.0 0.0 0.0 34.13 4.30 F
1528 1585 0.450983 GCTGCTTGGATGCTGAGAAC 59.549 55.0 0.0 0.0 34.47 3.01 F
3496 3782 0.178068 CGCACCTTACACCATAGGCT 59.822 55.0 0.0 0.0 34.79 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1260 1.162800 GGCATCCACGGCATCTCTTC 61.163 60.000 0.00 0.00 0.0 2.87 R
1500 1557 1.483827 CATCCAAGCAGCCTACAGAGA 59.516 52.381 0.00 0.00 0.0 3.10 R
1573 1630 1.526464 GCAAATTTGAACTTGGCCACG 59.474 47.619 22.31 6.21 0.0 4.94 R
3499 3785 0.392336 GGTGGCTGCACATGGAAAAA 59.608 50.000 0.50 0.00 0.0 1.94 R
4730 5192 0.543749 AGAACCCACTGCTCATAGGC 59.456 55.000 0.00 0.00 0.0 3.93 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
69 70 0.976641 TTTGGAGTCACATCCGCTCT 59.023 50.000 0.00 0.00 42.77 4.09
70 71 1.847328 TTGGAGTCACATCCGCTCTA 58.153 50.000 0.00 0.00 42.77 2.43
77 78 2.621055 GTCACATCCGCTCTAGAGTGAT 59.379 50.000 30.56 22.86 41.24 3.06
79 80 1.339610 ACATCCGCTCTAGAGTGATGC 59.660 52.381 32.36 17.81 40.36 3.91
80 81 0.965439 ATCCGCTCTAGAGTGATGCC 59.035 55.000 30.56 8.59 41.24 4.40
135 136 1.141053 CGGAGAGGGTTTAGAATGGGG 59.859 57.143 0.00 0.00 0.00 4.96
136 137 2.488836 GGAGAGGGTTTAGAATGGGGA 58.511 52.381 0.00 0.00 0.00 4.81
152 153 1.677552 GGACCAGGGTGTCGAATGT 59.322 57.895 0.00 0.00 36.07 2.71
198 199 3.901797 AAAGCTCCCCCGACTTGCG 62.902 63.158 0.00 0.00 40.47 4.85
210 211 2.580589 CGACTTGCGTTTGGTTTATGG 58.419 47.619 0.00 0.00 34.64 2.74
226 227 6.659668 TGGTTTATGGGAAAACGAACATATGA 59.340 34.615 10.38 0.00 39.71 2.15
228 229 7.486870 GGTTTATGGGAAAACGAACATATGAAC 59.513 37.037 10.38 1.91 39.71 3.18
246 247 0.586319 ACGATTGTTGTTCTGGTGCG 59.414 50.000 0.00 0.00 0.00 5.34
247 248 0.865111 CGATTGTTGTTCTGGTGCGA 59.135 50.000 0.00 0.00 0.00 5.10
257 258 0.390492 TCTGGTGCGATGCTCCTATG 59.610 55.000 10.79 2.72 42.02 2.23
270 271 1.341531 CTCCTATGGGGTCTTAGCACG 59.658 57.143 0.00 0.00 36.25 5.34
272 273 1.068741 CCTATGGGGTCTTAGCACGAC 59.931 57.143 0.00 0.00 0.00 4.34
277 278 0.179169 GGGTCTTAGCACGACGACTC 60.179 60.000 0.00 0.00 32.24 3.36
278 279 0.179169 GGTCTTAGCACGACGACTCC 60.179 60.000 0.00 0.00 32.24 3.85
283 284 2.881539 TAGCACGACGACTCCCCGAT 62.882 60.000 0.00 0.00 0.00 4.18
287 288 1.226603 CGACGACTCCCCGATTGTC 60.227 63.158 0.00 0.00 0.00 3.18
306 310 4.304110 TGTCTACTACAAGTTTTGCTCGG 58.696 43.478 0.00 0.00 34.29 4.63
309 313 2.572290 ACTACAAGTTTTGCTCGGCTT 58.428 42.857 0.00 0.00 0.00 4.35
312 316 0.385974 CAAGTTTTGCTCGGCTTCGG 60.386 55.000 0.00 0.00 34.13 4.30
314 318 2.281484 TTTTGCTCGGCTTCGGCT 60.281 55.556 0.00 0.00 41.44 5.52
318 322 3.528370 GCTCGGCTTCGGCTAGGA 61.528 66.667 0.00 0.00 41.44 2.94
322 326 2.506472 GGCTTCGGCTAGGAAGGG 59.494 66.667 9.83 0.00 42.88 3.95
357 361 2.262915 CCTTCGGCTCGCTTCAGT 59.737 61.111 0.00 0.00 0.00 3.41
371 375 3.064958 CGCTTCAGTCCTTATAGTCGTCA 59.935 47.826 0.00 0.00 0.00 4.35
372 376 4.438336 CGCTTCAGTCCTTATAGTCGTCAA 60.438 45.833 0.00 0.00 0.00 3.18
379 383 7.937394 TCAGTCCTTATAGTCGTCAATAGATGA 59.063 37.037 0.00 0.00 37.45 2.92
430 439 7.809546 TTTGGTGTTTATTGTAGTGACATGA 57.190 32.000 0.00 0.00 34.86 3.07
434 443 7.094420 TGGTGTTTATTGTAGTGACATGATTGG 60.094 37.037 0.00 0.00 34.86 3.16
444 453 8.146412 TGTAGTGACATGATTGGAGATGAATAG 58.854 37.037 0.00 0.00 0.00 1.73
451 460 7.883833 ACATGATTGGAGATGAATAGATTGGAG 59.116 37.037 0.00 0.00 0.00 3.86
497 506 4.948062 AAAAAGGTAGGGTAGGCATCTT 57.052 40.909 0.00 0.00 0.00 2.40
503 514 4.358614 AGGTAGGGTAGGCATCTTATCTCT 59.641 45.833 0.00 0.00 0.00 3.10
520 531 2.617308 TCTCTACCGTCCGATCATTGAC 59.383 50.000 0.00 0.00 0.00 3.18
559 570 5.200483 TGTGAGAGAAACCAAACTTTCCAT 58.800 37.500 0.00 0.00 31.44 3.41
569 580 1.627864 AACTTTCCATCCAAACCCCG 58.372 50.000 0.00 0.00 0.00 5.73
1329 1380 2.256174 CAAAGTTGCAGCATGATTCGG 58.744 47.619 2.55 0.00 39.69 4.30
1353 1406 1.086696 TTAGTTCGCATGCTTCTGCC 58.913 50.000 17.13 0.00 39.00 4.85
1436 1493 7.201691 ACCCTCTGGACAAAATTATTTGCTCA 61.202 38.462 1.43 0.58 41.46 4.26
1528 1585 0.450983 GCTGCTTGGATGCTGAGAAC 59.549 55.000 0.00 0.00 34.47 3.01
1573 1630 5.748152 GCAGAAGAGACAGATCAGTCATAAC 59.252 44.000 19.13 8.63 40.98 1.89
1615 1672 1.893801 CTCCCGACACCTACTTCAGTT 59.106 52.381 0.00 0.00 0.00 3.16
1694 1751 7.767250 TCATATCCTGGTCTACAGTTATGAG 57.233 40.000 10.58 0.00 46.06 2.90
1751 1808 5.923684 GGAGTGAGTCGAATATTCTGATTCC 59.076 44.000 19.67 14.54 33.04 3.01
1752 1809 6.461648 GGAGTGAGTCGAATATTCTGATTCCA 60.462 42.308 19.67 12.71 33.04 3.53
1829 1886 6.847036 AGGAAGTAATCAAGCCTTATACTCCT 59.153 38.462 0.00 0.00 0.00 3.69
1913 1971 7.595819 ACATGTCCCATTTGTTTTCTTTAGA 57.404 32.000 0.00 0.00 0.00 2.10
2071 2147 6.312180 TGTCTCATCATTTTCGTGAGATGAAG 59.688 38.462 7.47 0.00 46.92 3.02
2077 2153 1.808411 TTCGTGAGATGAAGGTTGGC 58.192 50.000 0.00 0.00 41.60 4.52
2098 2174 2.417379 CGACTACATGTCTGTGAAGGGG 60.417 54.545 0.00 0.00 43.25 4.79
2116 2192 2.224793 GGGGCCAAAGGTATGTCTATCC 60.225 54.545 4.39 0.00 0.00 2.59
2146 2230 7.416154 TTGTACTTAGTTCTTGATTGTTCCG 57.584 36.000 0.00 0.00 0.00 4.30
2190 2276 3.735746 CCATTTTCGTGGTCTTTTTCTGC 59.264 43.478 0.00 0.00 34.46 4.26
2191 2277 4.499696 CCATTTTCGTGGTCTTTTTCTGCT 60.500 41.667 0.00 0.00 34.46 4.24
2193 2279 4.712122 TTTCGTGGTCTTTTTCTGCTTT 57.288 36.364 0.00 0.00 0.00 3.51
2239 2325 5.114785 TCCATGAAACATAAACAACACCG 57.885 39.130 0.00 0.00 0.00 4.94
2242 2328 5.854338 CCATGAAACATAAACAACACCGTAC 59.146 40.000 0.00 0.00 0.00 3.67
2252 2338 4.191033 ACAACACCGTACGGATCATAAA 57.809 40.909 39.52 0.00 38.96 1.40
2297 2383 4.171005 CTCACAATTCCATGCATGTTGAC 58.829 43.478 26.42 0.00 0.00 3.18
2299 2385 3.924073 CACAATTCCATGCATGTTGACAG 59.076 43.478 26.42 14.92 0.00 3.51
2303 2389 1.805943 TCCATGCATGTTGACAGTTCG 59.194 47.619 24.58 5.98 0.00 3.95
2406 2492 1.875576 GCTGGAGGATCAGGCATTACG 60.876 57.143 0.00 0.00 36.25 3.18
2614 2700 6.265196 TCTTCTGCTGGTATGATTTTGTTGTT 59.735 34.615 0.00 0.00 0.00 2.83
2637 2723 3.911661 ATTTGCTGCAGTTCTTCACTC 57.088 42.857 16.64 0.00 30.92 3.51
2720 2806 7.413446 TGTTTCCTGGAAATGGAAGAATCTAT 58.587 34.615 23.60 0.00 43.48 1.98
2730 2816 7.451731 AATGGAAGAATCTATGTGTAGGGAA 57.548 36.000 0.00 0.00 0.00 3.97
2731 2817 6.235231 TGGAAGAATCTATGTGTAGGGAAC 57.765 41.667 0.00 0.00 0.00 3.62
2740 2829 6.996509 TCTATGTGTAGGGAACTTTTTACGT 58.003 36.000 0.00 0.00 43.67 3.57
2745 2834 7.388437 TGTGTAGGGAACTTTTTACGTATCAT 58.612 34.615 0.00 0.00 43.67 2.45
2843 2932 8.012241 GGATTTTTCTTCTATAATGTGCTAGCG 58.988 37.037 10.77 0.00 0.00 4.26
2855 2944 2.100916 TGTGCTAGCGACCCTATTTCTC 59.899 50.000 10.77 0.00 0.00 2.87
2890 2979 9.512588 GTGATAAATGATTTATGGAGATGTCCT 57.487 33.333 14.63 0.00 44.30 3.85
2914 3064 4.379499 GCCATAAACACTAGCCAACAGTTC 60.379 45.833 0.00 0.00 0.00 3.01
2925 3075 9.906660 CACTAGCCAACAGTTCATTTTATTTTA 57.093 29.630 0.00 0.00 0.00 1.52
2995 3154 3.877508 CAGGTTGGCCTAATACTTAGTGC 59.122 47.826 3.32 0.00 44.97 4.40
3000 3159 3.054728 TGGCCTAATACTTAGTGCTTGCA 60.055 43.478 3.32 0.00 33.07 4.08
3007 3166 1.895131 ACTTAGTGCTTGCATTTGGGG 59.105 47.619 0.00 0.00 0.00 4.96
3010 3169 0.901580 AGTGCTTGCATTTGGGGAGG 60.902 55.000 0.00 0.00 0.00 4.30
3013 3172 0.899717 GCTTGCATTTGGGGAGGTCA 60.900 55.000 0.00 0.00 0.00 4.02
3029 3188 4.650131 GGAGGTCATTAGGCTTACAGTACT 59.350 45.833 0.00 0.00 0.00 2.73
3030 3189 5.452077 GGAGGTCATTAGGCTTACAGTACTG 60.452 48.000 21.44 21.44 0.00 2.74
3050 3209 4.523943 ACTGCTTCTTTATGGTGAATGCAA 59.476 37.500 0.00 0.00 31.49 4.08
3060 3219 9.467258 CTTTATGGTGAATGCAATTTACTATGG 57.533 33.333 0.00 0.00 42.43 2.74
3189 3348 7.782168 AGATCTACTATGTCTTGAATCAGGTGA 59.218 37.037 0.00 0.00 0.00 4.02
3205 3364 8.447924 AATCAGGTGAATATTCTGTCATGAAG 57.552 34.615 16.24 0.00 0.00 3.02
3210 3369 7.884877 AGGTGAATATTCTGTCATGAAGTTTGA 59.115 33.333 16.24 0.00 0.00 2.69
3212 3371 9.552114 GTGAATATTCTGTCATGAAGTTTGAAG 57.448 33.333 16.24 0.00 0.00 3.02
3213 3372 8.239314 TGAATATTCTGTCATGAAGTTTGAAGC 58.761 33.333 16.24 0.00 0.00 3.86
3214 3373 7.934855 ATATTCTGTCATGAAGTTTGAAGCT 57.065 32.000 0.00 0.00 0.00 3.74
3217 3376 5.824429 TCTGTCATGAAGTTTGAAGCTTTG 58.176 37.500 0.00 0.00 0.00 2.77
3218 3377 5.357878 TCTGTCATGAAGTTTGAAGCTTTGT 59.642 36.000 0.00 0.00 0.00 2.83
3219 3378 5.581605 TGTCATGAAGTTTGAAGCTTTGTC 58.418 37.500 0.00 0.00 0.00 3.18
3220 3379 5.357878 TGTCATGAAGTTTGAAGCTTTGTCT 59.642 36.000 0.00 0.00 0.00 3.41
3238 3398 5.456548 TGTCTCGTGACCTGTTATAAACA 57.543 39.130 14.57 0.00 42.28 2.83
3250 3410 1.577468 TATAAACAGCATGGCCGACG 58.423 50.000 0.00 0.00 43.62 5.12
3259 3419 1.577468 CATGGCCGACGCTTTATGTA 58.423 50.000 0.00 0.00 34.44 2.29
3282 3442 8.874156 TGTATTTCTAGCCTTGACTGATATGAT 58.126 33.333 0.00 0.00 0.00 2.45
3308 3468 2.545946 GCAATCCTTACTGAATCCTCGC 59.454 50.000 0.00 0.00 0.00 5.03
3311 3471 5.541845 CAATCCTTACTGAATCCTCGCATA 58.458 41.667 0.00 0.00 0.00 3.14
3313 3473 4.945246 TCCTTACTGAATCCTCGCATAAC 58.055 43.478 0.00 0.00 0.00 1.89
3360 3640 2.208431 CAATCCTCACTGAATCCTCGC 58.792 52.381 0.00 0.00 0.00 5.03
3371 3651 4.631813 ACTGAATCCTCGCATAACAACTTC 59.368 41.667 0.00 0.00 0.00 3.01
3402 3684 7.332926 CACTATATGATTACTGCAATCCTCACC 59.667 40.741 0.00 0.00 42.17 4.02
3412 3694 2.555199 CAATCCTCACCGAATCCTCAC 58.445 52.381 0.00 0.00 0.00 3.51
3416 3698 3.371034 TCCTCACCGAATCCTCACATAA 58.629 45.455 0.00 0.00 0.00 1.90
3419 3701 4.503910 CTCACCGAATCCTCACATAACAA 58.496 43.478 0.00 0.00 0.00 2.83
3420 3702 4.250464 TCACCGAATCCTCACATAACAAC 58.750 43.478 0.00 0.00 0.00 3.32
3421 3703 4.020573 TCACCGAATCCTCACATAACAACT 60.021 41.667 0.00 0.00 0.00 3.16
3423 3705 5.181245 CACCGAATCCTCACATAACAACTTT 59.819 40.000 0.00 0.00 0.00 2.66
3424 3706 5.411669 ACCGAATCCTCACATAACAACTTTC 59.588 40.000 0.00 0.00 0.00 2.62
3427 3709 6.963242 CGAATCCTCACATAACAACTTTCATG 59.037 38.462 0.00 0.00 0.00 3.07
3428 3710 5.627499 TCCTCACATAACAACTTTCATGC 57.373 39.130 0.00 0.00 0.00 4.06
3429 3711 5.069318 TCCTCACATAACAACTTTCATGCA 58.931 37.500 0.00 0.00 0.00 3.96
3430 3712 5.048782 TCCTCACATAACAACTTTCATGCAC 60.049 40.000 0.00 0.00 0.00 4.57
3432 3714 6.149308 CCTCACATAACAACTTTCATGCACTA 59.851 38.462 0.00 0.00 0.00 2.74
3433 3715 7.148188 CCTCACATAACAACTTTCATGCACTAT 60.148 37.037 0.00 0.00 0.00 2.12
3434 3716 8.785329 TCACATAACAACTTTCATGCACTATA 57.215 30.769 0.00 0.00 0.00 1.31
3435 3717 9.394767 TCACATAACAACTTTCATGCACTATAT 57.605 29.630 0.00 0.00 0.00 0.86
3436 3718 9.442033 CACATAACAACTTTCATGCACTATATG 57.558 33.333 0.00 0.00 0.00 1.78
3437 3719 9.394767 ACATAACAACTTTCATGCACTATATGA 57.605 29.630 0.00 0.00 33.00 2.15
3442 3724 9.618890 ACAACTTTCATGCACTATATGATTACT 57.381 29.630 0.00 0.00 34.76 2.24
3443 3725 9.874215 CAACTTTCATGCACTATATGATTACTG 57.126 33.333 0.00 0.00 34.76 2.74
3444 3726 8.092521 ACTTTCATGCACTATATGATTACTGC 57.907 34.615 0.00 0.00 34.76 4.40
3445 3727 7.716560 ACTTTCATGCACTATATGATTACTGCA 59.283 33.333 0.00 0.00 38.89 4.41
3446 3728 8.449251 TTTCATGCACTATATGATTACTGCAA 57.551 30.769 0.00 0.00 38.10 4.08
3447 3729 8.625786 TTCATGCACTATATGATTACTGCAAT 57.374 30.769 0.00 0.00 38.10 3.56
3448 3730 8.260270 TCATGCACTATATGATTACTGCAATC 57.740 34.615 0.00 0.00 43.01 2.67
3449 3731 7.335171 TCATGCACTATATGATTACTGCAATCC 59.665 37.037 0.00 0.00 42.17 3.01
3450 3732 6.772605 TGCACTATATGATTACTGCAATCCT 58.227 36.000 0.00 0.00 42.17 3.24
3451 3733 6.875726 TGCACTATATGATTACTGCAATCCTC 59.124 38.462 0.00 0.00 42.17 3.71
3452 3734 6.875726 GCACTATATGATTACTGCAATCCTCA 59.124 38.462 0.00 0.00 42.17 3.86
3453 3735 7.148507 GCACTATATGATTACTGCAATCCTCAC 60.149 40.741 0.00 0.00 42.17 3.51
3454 3736 8.093307 CACTATATGATTACTGCAATCCTCACT 58.907 37.037 0.00 0.00 42.17 3.41
3455 3737 8.093307 ACTATATGATTACTGCAATCCTCACTG 58.907 37.037 0.00 0.00 42.17 3.66
3456 3738 4.824479 TGATTACTGCAATCCTCACTGA 57.176 40.909 0.00 0.00 42.17 3.41
3457 3739 5.164620 TGATTACTGCAATCCTCACTGAA 57.835 39.130 0.00 0.00 42.17 3.02
3458 3740 5.748402 TGATTACTGCAATCCTCACTGAAT 58.252 37.500 0.00 0.00 42.17 2.57
3459 3741 6.888105 TGATTACTGCAATCCTCACTGAATA 58.112 36.000 0.00 0.00 42.17 1.75
3460 3742 6.763135 TGATTACTGCAATCCTCACTGAATAC 59.237 38.462 0.00 0.00 42.17 1.89
3461 3743 3.525537 ACTGCAATCCTCACTGAATACG 58.474 45.455 0.00 0.00 0.00 3.06
3462 3744 2.279741 TGCAATCCTCACTGAATACGC 58.720 47.619 0.00 0.00 0.00 4.42
3463 3745 1.599542 GCAATCCTCACTGAATACGCC 59.400 52.381 0.00 0.00 0.00 5.68
3464 3746 2.905075 CAATCCTCACTGAATACGCCA 58.095 47.619 0.00 0.00 0.00 5.69
3489 3775 2.356553 TCGCACGCACCTTACACC 60.357 61.111 0.00 0.00 0.00 4.16
3496 3782 0.178068 CGCACCTTACACCATAGGCT 59.822 55.000 0.00 0.00 34.79 4.58
3499 3785 3.089284 GCACCTTACACCATAGGCTTTT 58.911 45.455 0.00 0.00 34.79 2.27
3549 3835 2.588620 GATGGTGGTGTTGGGTTTGTA 58.411 47.619 0.00 0.00 0.00 2.41
3609 3896 2.158957 TGCGGACATTCAGGTAATCTCC 60.159 50.000 0.00 0.00 31.16 3.71
3610 3897 2.743938 CGGACATTCAGGTAATCTCCG 58.256 52.381 1.05 1.05 45.65 4.63
3629 3916 0.868406 GGCCTTCAGTGAACGTTGAG 59.132 55.000 5.00 0.00 0.00 3.02
3651 3938 1.726791 CCATCAGTTCTCGGTGAAACG 59.273 52.381 0.00 0.00 38.12 3.60
3689 3976 2.815503 TCCGACGAACAAGACACTGATA 59.184 45.455 0.00 0.00 0.00 2.15
3752 4039 2.086869 CTCCGATGAACAAAGCCATGT 58.913 47.619 0.00 0.00 34.24 3.21
3763 4050 2.557924 CAAAGCCATGTCTGCAAACCTA 59.442 45.455 0.00 0.00 0.00 3.08
3775 4062 2.290896 TGCAAACCTAGATGACCTTGGG 60.291 50.000 0.00 0.00 41.31 4.12
3864 4151 7.429340 GTCGCATGACCATTCTTAGTATTTTTG 59.571 37.037 0.00 0.00 39.30 2.44
3974 4264 1.076332 GATGCGTGTCCAGTGTTACC 58.924 55.000 0.00 0.00 0.00 2.85
4023 4313 7.063593 AGTATAGGAGACAACAGCTTATCAGA 58.936 38.462 0.00 0.00 0.00 3.27
4092 4411 0.810648 CTTTGGCCAAAGCATCGCTA 59.189 50.000 38.12 12.53 40.94 4.26
4142 4461 2.111878 GCCATGGCCATAGCGACT 59.888 61.111 27.24 0.00 41.24 4.18
4143 4462 1.371183 GCCATGGCCATAGCGACTA 59.629 57.895 27.24 0.00 41.24 2.59
4144 4463 0.671781 GCCATGGCCATAGCGACTAG 60.672 60.000 27.24 4.40 41.24 2.57
4145 4464 0.036952 CCATGGCCATAGCGACTAGG 60.037 60.000 20.30 9.14 41.24 3.02
4146 4465 0.671781 CATGGCCATAGCGACTAGGC 60.672 60.000 20.30 13.54 46.28 3.93
4147 4466 0.833834 ATGGCCATAGCGACTAGGCT 60.834 55.000 19.18 0.00 46.23 4.58
4182 4501 3.063485 GCACCAAAACAAAACACACACT 58.937 40.909 0.00 0.00 0.00 3.55
4256 4575 6.548441 TTAGCTACATGTGTAAAAACGCTT 57.452 33.333 9.11 0.00 32.01 4.68
4258 4577 6.548441 AGCTACATGTGTAAAAACGCTTTA 57.452 33.333 9.11 0.00 0.00 1.85
4259 4578 7.141100 AGCTACATGTGTAAAAACGCTTTAT 57.859 32.000 9.11 0.00 0.00 1.40
4306 4625 3.250744 CAAATCCGACGACACACTACAT 58.749 45.455 0.00 0.00 0.00 2.29
4314 4633 5.384787 CGACGACACACTACATTTACAGTA 58.615 41.667 0.00 0.00 0.00 2.74
4325 4644 8.186163 CACTACATTTACAGTACAACGGATCTA 58.814 37.037 0.00 0.00 0.00 1.98
4341 4660 9.017669 CAACGGATCTAGTAAGTTATTGTACAC 57.982 37.037 0.00 0.00 0.00 2.90
4438 4759 6.045072 ACGGATTTGTGGTCATCTAACTTA 57.955 37.500 0.00 0.00 0.00 2.24
4524 4845 1.738099 AGTGAGTGATGGCGTTCGC 60.738 57.895 8.75 8.75 0.00 4.70
4525 4846 2.809174 TGAGTGATGGCGTTCGCG 60.809 61.111 10.94 0.00 44.73 5.87
4653 5058 3.756434 CACACGACCCAAATTAAGGACAT 59.244 43.478 0.00 0.00 0.00 3.06
4730 5192 8.798153 GGAGCTTAAATGACATTTATTTTCGTG 58.202 33.333 18.88 7.17 34.92 4.35
4747 5209 0.035056 GTGCCTATGAGCAGTGGGTT 60.035 55.000 0.00 0.00 45.14 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.521605 CCGGTCGGCATCACTCTA 58.478 61.111 0.00 0.00 0.00 2.43
79 80 3.101209 CACATTCATGCCGGTCGG 58.899 61.111 1.90 4.85 38.57 4.79
80 81 2.404789 GCACATTCATGCCGGTCG 59.595 61.111 1.90 0.00 39.86 4.79
115 116 1.141053 CCCCATTCTAAACCCTCTCCG 59.859 57.143 0.00 0.00 0.00 4.63
135 136 0.034896 ACACATTCGACACCCTGGTC 59.965 55.000 0.00 0.00 34.42 4.02
136 137 0.250295 CACACATTCGACACCCTGGT 60.250 55.000 0.00 0.00 0.00 4.00
138 139 1.577328 GGCACACATTCGACACCCTG 61.577 60.000 0.00 0.00 0.00 4.45
140 141 1.302511 AGGCACACATTCGACACCC 60.303 57.895 0.00 0.00 0.00 4.61
141 142 1.577328 CCAGGCACACATTCGACACC 61.577 60.000 0.00 0.00 0.00 4.16
192 193 6.194039 GTTTTCCCATAAACCAAACGCAAGT 61.194 40.000 0.00 0.00 41.35 3.16
198 199 5.349809 TGTTCGTTTTCCCATAAACCAAAC 58.650 37.500 0.00 0.00 35.15 2.93
210 211 6.311723 ACAATCGTTCATATGTTCGTTTTCC 58.688 36.000 16.66 0.00 0.00 3.13
226 227 1.002900 CGCACCAGAACAACAATCGTT 60.003 47.619 0.00 0.00 35.01 3.85
228 229 0.865111 TCGCACCAGAACAACAATCG 59.135 50.000 0.00 0.00 0.00 3.34
246 247 2.027653 GCTAAGACCCCATAGGAGCATC 60.028 54.545 0.00 0.00 39.89 3.91
247 248 1.981495 GCTAAGACCCCATAGGAGCAT 59.019 52.381 0.00 0.00 39.89 3.79
257 258 1.153881 GTCGTCGTGCTAAGACCCC 60.154 63.158 0.00 0.00 35.33 4.95
270 271 1.065251 GTAGACAATCGGGGAGTCGTC 59.935 57.143 0.00 0.00 37.36 4.20
272 273 1.390565 AGTAGACAATCGGGGAGTCG 58.609 55.000 0.00 0.00 37.36 4.18
277 278 4.467198 AACTTGTAGTAGACAATCGGGG 57.533 45.455 0.00 0.00 46.95 5.73
278 279 5.390567 GCAAAACTTGTAGTAGACAATCGGG 60.391 44.000 0.00 0.00 46.95 5.14
283 284 4.748102 CCGAGCAAAACTTGTAGTAGACAA 59.252 41.667 0.00 0.00 46.03 3.18
287 288 3.326747 AGCCGAGCAAAACTTGTAGTAG 58.673 45.455 0.00 0.00 0.00 2.57
302 306 1.066587 CTTCCTAGCCGAAGCCGAG 59.933 63.158 0.00 0.00 41.25 4.63
304 308 2.107141 CCTTCCTAGCCGAAGCCG 59.893 66.667 3.83 0.00 41.25 5.52
306 310 2.506472 CCCCTTCCTAGCCGAAGC 59.494 66.667 3.83 0.00 38.35 3.86
309 313 3.751049 ATCGCCCCTTCCTAGCCGA 62.751 63.158 0.00 0.00 0.00 5.54
312 316 1.069935 GTCATCGCCCCTTCCTAGC 59.930 63.158 0.00 0.00 0.00 3.42
314 318 2.131709 CCGTCATCGCCCCTTCCTA 61.132 63.158 0.00 0.00 35.54 2.94
345 349 2.362717 ACTATAAGGACTGAAGCGAGCC 59.637 50.000 0.00 0.00 0.00 4.70
407 411 7.994425 ATCATGTCACTACAATAAACACCAA 57.006 32.000 0.00 0.00 39.58 3.67
422 431 8.504815 CAATCTATTCATCTCCAATCATGTCAC 58.495 37.037 0.00 0.00 0.00 3.67
430 439 6.776887 ACCTCCAATCTATTCATCTCCAAT 57.223 37.500 0.00 0.00 0.00 3.16
476 485 4.948062 AAGATGCCTACCCTACCTTTTT 57.052 40.909 0.00 0.00 0.00 1.94
496 505 5.048921 GTCAATGATCGGACGGTAGAGATAA 60.049 44.000 0.00 0.00 0.00 1.75
497 506 4.454847 GTCAATGATCGGACGGTAGAGATA 59.545 45.833 0.00 0.00 0.00 1.98
503 514 3.713288 GAATGTCAATGATCGGACGGTA 58.287 45.455 7.28 0.00 36.83 4.02
520 531 1.198867 TCACATTGGAAACCGCGAATG 59.801 47.619 8.23 11.19 32.99 2.67
559 570 0.399075 GGAGAAGAACGGGGTTTGGA 59.601 55.000 0.00 0.00 0.00 3.53
569 580 3.119096 GGCGCGGTGGAGAAGAAC 61.119 66.667 8.83 0.00 0.00 3.01
946 957 2.818132 GGCGGGTGAGGAGAGATG 59.182 66.667 0.00 0.00 0.00 2.90
1132 1143 5.642063 ACTAGAGCTCGAACTATCTATCTGC 59.358 44.000 8.37 0.00 0.00 4.26
1215 1260 1.162800 GGCATCCACGGCATCTCTTC 61.163 60.000 0.00 0.00 0.00 2.87
1329 1380 5.142962 GCAGAAGCATGCGAACTAAATATC 58.857 41.667 13.01 0.00 41.58 1.63
1500 1557 1.483827 CATCCAAGCAGCCTACAGAGA 59.516 52.381 0.00 0.00 0.00 3.10
1501 1558 1.950828 CATCCAAGCAGCCTACAGAG 58.049 55.000 0.00 0.00 0.00 3.35
1528 1585 7.250569 TCTGCACAAGTTTAAACTCTTTGAAG 58.749 34.615 20.78 19.05 38.57 3.02
1573 1630 1.526464 GCAAATTTGAACTTGGCCACG 59.474 47.619 22.31 6.21 0.00 4.94
1829 1886 8.727100 ATCCAATATCAGAATCCAGTGTAGTA 57.273 34.615 0.00 0.00 0.00 1.82
1942 2000 9.343994 ACACCCATAGAGGAATAGATTGATATT 57.656 33.333 0.00 0.00 41.22 1.28
1963 2021 6.178239 GTGAATTCACAACACTATACACCC 57.822 41.667 29.43 0.13 45.75 4.61
1999 2075 6.899393 ATAATGAGAAGGAAAAGTGCAACA 57.101 33.333 0.00 0.00 41.43 3.33
2000 2076 7.816640 TGTATAATGAGAAGGAAAAGTGCAAC 58.183 34.615 0.00 0.00 0.00 4.17
2001 2077 7.882791 TCTGTATAATGAGAAGGAAAAGTGCAA 59.117 33.333 0.00 0.00 0.00 4.08
2002 2078 7.394016 TCTGTATAATGAGAAGGAAAAGTGCA 58.606 34.615 0.00 0.00 0.00 4.57
2003 2079 7.849804 TCTGTATAATGAGAAGGAAAAGTGC 57.150 36.000 0.00 0.00 0.00 4.40
2004 2080 9.388506 ACATCTGTATAATGAGAAGGAAAAGTG 57.611 33.333 0.00 0.00 0.00 3.16
2009 2085 8.816894 GGGATACATCTGTATAATGAGAAGGAA 58.183 37.037 2.91 0.00 40.99 3.36
2010 2086 7.400339 GGGGATACATCTGTATAATGAGAAGGA 59.600 40.741 2.91 0.00 40.99 3.36
2011 2087 7.180946 TGGGGATACATCTGTATAATGAGAAGG 59.819 40.741 2.91 0.00 40.99 3.46
2127 2211 6.866770 TCAGTACGGAACAATCAAGAACTAAG 59.133 38.462 0.00 0.00 0.00 2.18
2128 2212 6.751157 TCAGTACGGAACAATCAAGAACTAA 58.249 36.000 0.00 0.00 0.00 2.24
2132 2216 6.464222 AGATTCAGTACGGAACAATCAAGAA 58.536 36.000 10.74 0.00 0.00 2.52
2140 2224 2.496070 CCAGGAGATTCAGTACGGAACA 59.504 50.000 10.74 0.00 0.00 3.18
2144 2228 4.122776 CAAATCCAGGAGATTCAGTACGG 58.877 47.826 0.00 0.00 44.75 4.02
2146 2230 3.879892 GCCAAATCCAGGAGATTCAGTAC 59.120 47.826 0.00 0.00 44.75 2.73
2212 2298 8.281893 GGTGTTGTTTATGTTTCATGGAATTTG 58.718 33.333 0.00 0.00 0.00 2.32
2220 2306 5.334260 CCGTACGGTGTTGTTTATGTTTCAT 60.334 40.000 26.39 0.00 0.00 2.57
2239 2325 6.755141 TCTGTTAGCAAGTTTATGATCCGTAC 59.245 38.462 0.00 0.00 0.00 3.67
2242 2328 6.662414 TTCTGTTAGCAAGTTTATGATCCG 57.338 37.500 0.00 0.00 0.00 4.18
2252 2338 7.282224 TGAGTTTACACATTTCTGTTAGCAAGT 59.718 33.333 0.00 0.00 31.62 3.16
2297 2383 5.563842 GCATTTAACCTCTGATTCGAACTG 58.436 41.667 0.00 0.00 0.00 3.16
2299 2385 4.092968 ACGCATTTAACCTCTGATTCGAAC 59.907 41.667 0.00 0.00 0.00 3.95
2303 2389 5.699839 ACAAACGCATTTAACCTCTGATTC 58.300 37.500 0.00 0.00 0.00 2.52
2406 2492 6.449635 TCACATATTACTTGGAACATTGGC 57.550 37.500 0.00 0.00 39.30 4.52
2504 2590 2.375174 AGAATTGCCCTTGTGACCTACA 59.625 45.455 0.00 0.00 37.56 2.74
2614 2700 5.560760 CGAGTGAAGAACTGCAGCAAATTTA 60.561 40.000 15.27 0.00 40.07 1.40
2637 2723 5.467735 TGGAATGATAATCAGATCAAGTGCG 59.532 40.000 0.00 0.00 39.25 5.34
2720 2806 6.757237 TGATACGTAAAAAGTTCCCTACACA 58.243 36.000 0.00 0.00 0.00 3.72
2730 2816 5.950758 TTGTGCCATGATACGTAAAAAGT 57.049 34.783 0.00 0.00 0.00 2.66
2731 2817 6.607689 TCTTTGTGCCATGATACGTAAAAAG 58.392 36.000 0.00 0.00 0.00 2.27
2740 2829 5.534278 TGTTTCTGTTCTTTGTGCCATGATA 59.466 36.000 0.00 0.00 0.00 2.15
2745 2834 5.534278 TGATATGTTTCTGTTCTTTGTGCCA 59.466 36.000 0.00 0.00 0.00 4.92
2829 2918 5.995565 AATAGGGTCGCTAGCACATTATA 57.004 39.130 16.45 0.32 0.00 0.98
2873 2962 4.090761 TGGCAGGACATCTCCATAAATC 57.909 45.455 0.00 0.00 39.39 2.17
2890 2979 3.081061 CTGTTGGCTAGTGTTTATGGCA 58.919 45.455 0.00 0.00 0.00 4.92
2925 3075 7.397192 ACCAGCAAAGAAATGGTATAACAAGAT 59.603 33.333 0.00 0.00 45.44 2.40
2927 3077 6.924111 ACCAGCAAAGAAATGGTATAACAAG 58.076 36.000 0.00 0.00 45.44 3.16
2946 3105 3.955650 TCTTGTACAGGTCTAACCAGC 57.044 47.619 4.75 0.00 41.95 4.85
2995 3154 1.856629 ATGACCTCCCCAAATGCAAG 58.143 50.000 0.00 0.00 0.00 4.01
3000 3159 2.217776 AGCCTAATGACCTCCCCAAAT 58.782 47.619 0.00 0.00 0.00 2.32
3007 3166 5.593010 CAGTACTGTAAGCCTAATGACCTC 58.407 45.833 15.06 0.00 37.60 3.85
3010 3169 5.012328 AGCAGTACTGTAAGCCTAATGAC 57.988 43.478 23.44 2.73 37.60 3.06
3013 3172 5.941555 AGAAGCAGTACTGTAAGCCTAAT 57.058 39.130 23.44 2.37 37.60 1.73
3029 3188 5.664294 ATTGCATTCACCATAAAGAAGCA 57.336 34.783 0.00 0.00 0.00 3.91
3030 3189 6.973229 AAATTGCATTCACCATAAAGAAGC 57.027 33.333 0.00 0.00 0.00 3.86
3076 3235 4.037690 GTGAACATCAGCACTCAAAACAC 58.962 43.478 0.00 0.00 32.44 3.32
3189 3348 8.345724 AGCTTCAAACTTCATGACAGAATATT 57.654 30.769 0.00 0.00 0.00 1.28
3205 3364 3.546218 GGTCACGAGACAAAGCTTCAAAC 60.546 47.826 14.98 0.00 46.80 2.93
3210 3369 1.139058 ACAGGTCACGAGACAAAGCTT 59.861 47.619 14.98 0.00 46.80 3.74
3212 3371 1.583054 AACAGGTCACGAGACAAAGC 58.417 50.000 14.98 0.00 46.80 3.51
3213 3372 6.422701 TGTTTATAACAGGTCACGAGACAAAG 59.577 38.462 14.98 6.23 40.57 2.77
3214 3373 6.282167 TGTTTATAACAGGTCACGAGACAAA 58.718 36.000 14.98 2.30 40.57 2.83
3250 3410 7.495934 TCAGTCAAGGCTAGAAATACATAAAGC 59.504 37.037 0.00 0.00 0.00 3.51
3282 3442 6.483307 CGAGGATTCAGTAAGGATTGCAATAA 59.517 38.462 12.97 0.33 30.97 1.40
3313 3473 9.874215 CAGTAATCATATAGTGCATGAAAGTTG 57.126 33.333 0.00 0.00 36.08 3.16
3360 3640 8.382030 TCATATAGTGCATGGAAGTTGTTATG 57.618 34.615 0.00 0.00 0.00 1.90
3402 3684 6.480524 TGAAAGTTGTTATGTGAGGATTCG 57.519 37.500 0.00 0.00 0.00 3.34
3416 3698 9.618890 AGTAATCATATAGTGCATGAAAGTTGT 57.381 29.630 0.00 0.00 36.08 3.32
3419 3701 8.092521 GCAGTAATCATATAGTGCATGAAAGT 57.907 34.615 0.00 0.00 46.69 2.66
3428 3710 8.093307 AGTGAGGATTGCAGTAATCATATAGTG 58.907 37.037 12.72 0.00 45.70 2.74
3429 3711 8.093307 CAGTGAGGATTGCAGTAATCATATAGT 58.907 37.037 12.72 0.22 45.70 2.12
3430 3712 8.309656 TCAGTGAGGATTGCAGTAATCATATAG 58.690 37.037 12.72 0.00 45.70 1.31
3432 3714 7.071069 TCAGTGAGGATTGCAGTAATCATAT 57.929 36.000 12.72 0.00 45.70 1.78
3433 3715 6.484364 TCAGTGAGGATTGCAGTAATCATA 57.516 37.500 12.72 0.00 45.70 2.15
3434 3716 5.363562 TCAGTGAGGATTGCAGTAATCAT 57.636 39.130 12.72 5.85 45.70 2.45
3435 3717 4.824479 TCAGTGAGGATTGCAGTAATCA 57.176 40.909 12.72 0.00 45.70 2.57
3436 3718 6.074088 CGTATTCAGTGAGGATTGCAGTAATC 60.074 42.308 2.68 2.68 43.64 1.75
3437 3719 5.755375 CGTATTCAGTGAGGATTGCAGTAAT 59.245 40.000 0.00 0.00 0.00 1.89
3438 3720 5.109210 CGTATTCAGTGAGGATTGCAGTAA 58.891 41.667 0.00 0.00 0.00 2.24
3439 3721 4.682787 CGTATTCAGTGAGGATTGCAGTA 58.317 43.478 0.00 0.00 0.00 2.74
3440 3722 3.525537 CGTATTCAGTGAGGATTGCAGT 58.474 45.455 0.00 0.00 0.00 4.40
3441 3723 2.286294 GCGTATTCAGTGAGGATTGCAG 59.714 50.000 0.00 0.00 0.00 4.41
3442 3724 2.279741 GCGTATTCAGTGAGGATTGCA 58.720 47.619 0.00 0.00 0.00 4.08
3443 3725 1.599542 GGCGTATTCAGTGAGGATTGC 59.400 52.381 0.00 0.00 0.00 3.56
3444 3726 2.905075 TGGCGTATTCAGTGAGGATTG 58.095 47.619 0.00 0.00 0.00 2.67
3445 3727 3.535561 CTTGGCGTATTCAGTGAGGATT 58.464 45.455 0.00 0.00 0.00 3.01
3446 3728 2.158900 CCTTGGCGTATTCAGTGAGGAT 60.159 50.000 0.00 0.00 0.00 3.24
3447 3729 1.207089 CCTTGGCGTATTCAGTGAGGA 59.793 52.381 0.00 0.00 0.00 3.71
3448 3730 1.066143 ACCTTGGCGTATTCAGTGAGG 60.066 52.381 0.00 0.00 0.00 3.86
3449 3731 2.386661 ACCTTGGCGTATTCAGTGAG 57.613 50.000 0.00 0.00 0.00 3.51
3450 3732 2.614481 GGAACCTTGGCGTATTCAGTGA 60.614 50.000 0.00 0.00 0.00 3.41
3451 3733 1.737793 GGAACCTTGGCGTATTCAGTG 59.262 52.381 0.00 0.00 0.00 3.66
3452 3734 1.628846 AGGAACCTTGGCGTATTCAGT 59.371 47.619 0.00 0.00 0.00 3.41
3453 3735 2.280628 GAGGAACCTTGGCGTATTCAG 58.719 52.381 0.00 0.00 0.00 3.02
3454 3736 1.404986 CGAGGAACCTTGGCGTATTCA 60.405 52.381 0.34 0.00 0.00 2.57
3455 3737 1.287425 CGAGGAACCTTGGCGTATTC 58.713 55.000 0.34 0.00 0.00 1.75
3456 3738 0.743345 GCGAGGAACCTTGGCGTATT 60.743 55.000 9.78 0.00 0.00 1.89
3457 3739 1.153429 GCGAGGAACCTTGGCGTAT 60.153 57.895 9.78 0.00 0.00 3.06
3458 3740 2.263540 GCGAGGAACCTTGGCGTA 59.736 61.111 9.78 0.00 0.00 4.42
3459 3741 3.936203 TGCGAGGAACCTTGGCGT 61.936 61.111 9.78 0.00 0.00 5.68
3460 3742 3.423154 GTGCGAGGAACCTTGGCG 61.423 66.667 9.78 3.61 0.00 5.69
3461 3743 3.423154 CGTGCGAGGAACCTTGGC 61.423 66.667 9.78 9.76 0.00 4.52
3462 3744 3.423154 GCGTGCGAGGAACCTTGG 61.423 66.667 9.78 0.31 0.00 3.61
3463 3745 2.664851 TGCGTGCGAGGAACCTTG 60.665 61.111 3.86 3.86 0.00 3.61
3464 3746 2.665185 GTGCGTGCGAGGAACCTT 60.665 61.111 0.00 0.00 0.00 3.50
3499 3785 0.392336 GGTGGCTGCACATGGAAAAA 59.608 50.000 0.50 0.00 0.00 1.94
3506 3792 0.607489 GACTTCAGGTGGCTGCACAT 60.607 55.000 0.50 0.00 0.00 3.21
3549 3835 5.126707 GTGAGCTTGGATCATTTCCTTTGAT 59.873 40.000 0.00 0.00 45.68 2.57
3609 3896 0.878523 TCAACGTTCACTGAAGGCCG 60.879 55.000 10.71 5.30 31.62 6.13
3610 3897 0.868406 CTCAACGTTCACTGAAGGCC 59.132 55.000 10.71 0.00 31.62 5.19
3629 3916 2.737252 GTTTCACCGAGAACTGATGGTC 59.263 50.000 0.00 0.00 35.56 4.02
3651 3938 5.683743 TCGTCGGATGAAAAACATTTTGAAC 59.316 36.000 0.00 0.00 39.56 3.18
3752 4039 3.307691 CCAAGGTCATCTAGGTTTGCAGA 60.308 47.826 0.00 0.00 0.00 4.26
3763 4050 2.038863 TGGTGTACCCAAGGTCATCT 57.961 50.000 0.00 0.00 41.50 2.90
3775 4062 2.770164 ACTGCATCTCCTTGGTGTAC 57.230 50.000 0.00 0.00 0.00 2.90
3864 4151 3.128242 CAGAATCAGCCCATGTCAAACTC 59.872 47.826 0.00 0.00 0.00 3.01
3974 4264 3.423907 GGCAAATAACGTTACGGACACAG 60.424 47.826 10.81 0.00 0.00 3.66
4054 4344 1.470098 AGGTGAATGAAATCGCAGTGC 59.530 47.619 4.58 4.58 0.00 4.40
4092 4411 1.373748 CGTCGGTCATTCGGTGGTT 60.374 57.895 0.00 0.00 0.00 3.67
4129 4448 1.457643 AGCCTAGTCGCTATGGCCA 60.458 57.895 8.56 8.56 45.94 5.36
4130 4449 1.290639 GAGCCTAGTCGCTATGGCC 59.709 63.158 0.00 0.00 45.94 5.36
4133 4452 1.810151 GAGAGGAGCCTAGTCGCTATG 59.190 57.143 0.00 0.00 39.87 2.23
4135 4454 1.071071 GAGAGAGGAGCCTAGTCGCTA 59.929 57.143 0.00 0.00 39.87 4.26
4136 4455 0.179029 GAGAGAGGAGCCTAGTCGCT 60.179 60.000 0.00 0.00 43.42 4.93
4137 4456 0.179029 AGAGAGAGGAGCCTAGTCGC 60.179 60.000 0.00 0.00 0.00 5.19
4138 4457 3.596214 GATAGAGAGAGGAGCCTAGTCG 58.404 54.545 0.00 0.00 0.00 4.18
4140 4459 2.304761 CCGATAGAGAGAGGAGCCTAGT 59.695 54.545 0.00 0.00 39.76 2.57
4141 4460 2.939640 GCCGATAGAGAGAGGAGCCTAG 60.940 59.091 0.00 0.00 39.76 3.02
4142 4461 1.003812 GCCGATAGAGAGAGGAGCCTA 59.996 57.143 0.00 0.00 39.76 3.93
4143 4462 0.251165 GCCGATAGAGAGAGGAGCCT 60.251 60.000 0.00 0.00 39.76 4.58
4144 4463 0.538516 TGCCGATAGAGAGAGGAGCC 60.539 60.000 0.00 0.00 39.76 4.70
4145 4464 0.596082 GTGCCGATAGAGAGAGGAGC 59.404 60.000 0.00 0.00 39.76 4.70
4146 4465 1.243902 GGTGCCGATAGAGAGAGGAG 58.756 60.000 0.00 0.00 39.76 3.69
4147 4466 0.551396 TGGTGCCGATAGAGAGAGGA 59.449 55.000 0.00 0.00 39.76 3.71
4218 4537 6.866010 TGTAGCTAAATGTATTGCCATGAG 57.134 37.500 0.00 0.00 0.00 2.90
4264 4583 9.423061 GATTTGTTACAAGCAATACTTCCAAAT 57.577 29.630 0.00 0.00 36.04 2.32
4275 4594 3.059461 GTCGTCGGATTTGTTACAAGCAA 60.059 43.478 0.00 0.00 0.00 3.91
4306 4625 8.340618 ACTTACTAGATCCGTTGTACTGTAAA 57.659 34.615 0.00 0.00 0.00 2.01
4314 4633 8.742777 TGTACAATAACTTACTAGATCCGTTGT 58.257 33.333 0.00 1.85 0.00 3.32
4325 4644 9.086758 ACCTCTACTTGTGTACAATAACTTACT 57.913 33.333 0.00 0.00 35.02 2.24
4341 4660 9.099454 GACTTTTGGTGATATTACCTCTACTTG 57.901 37.037 16.91 4.70 41.43 3.16
4371 4692 2.358898 ACTGAACATCAAGCGCAAGTTT 59.641 40.909 11.47 0.00 43.49 2.66
4438 4759 2.147958 ACCGTATTTGCACGTGATGTT 58.852 42.857 22.23 3.11 40.31 2.71
4524 4845 1.752753 TTGTGCAAAAATCAGTCGCG 58.247 45.000 0.00 0.00 0.00 5.87
4525 4846 3.305629 TGTTTTGTGCAAAAATCAGTCGC 59.694 39.130 8.72 0.00 41.37 5.19
4569 4890 2.447047 CCTATATGGGTTGGCCTTTCCT 59.553 50.000 3.32 0.00 35.26 3.36
4653 5058 1.651737 TGGTTGGCTAGAGTGGCTTA 58.348 50.000 0.00 0.00 0.00 3.09
4730 5192 0.543749 AGAACCCACTGCTCATAGGC 59.456 55.000 0.00 0.00 0.00 3.93
4747 5209 4.284829 TCAATGTGTAATGACAGGCAGA 57.715 40.909 0.00 0.00 35.82 4.26


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

AutoCloner maintained by Alex Coulton.