Multiple sequence alignment - TraesCS2B01G400900

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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 TraesCS2B01G400900 chr2B 100.000 5361 0 0 1 5361 569133408 569128048 0.000000e+00 9901.0
1 TraesCS2B01G400900 chr2B 96.078 204 6 2 2422 2624 438929385 438929183 1.110000e-86 331.0
2 TraesCS2B01G400900 chr2D 93.003 1858 80 20 2622 4459 484375844 484377671 0.000000e+00 2665.0
3 TraesCS2B01G400900 chr2D 94.612 928 43 3 1504 2424 484374901 484375828 0.000000e+00 1430.0
4 TraesCS2B01G400900 chr2D 91.142 937 39 12 541 1441 484373840 484374768 0.000000e+00 1230.0
5 TraesCS2B01G400900 chr2D 88.480 625 33 14 1 622 484373294 484373882 0.000000e+00 719.0
6 TraesCS2B01G400900 chr2D 86.833 600 45 14 4500 5089 484377671 484378246 1.630000e-179 640.0
7 TraesCS2B01G400900 chr2D 85.787 197 22 2 5168 5358 484378269 484378465 2.530000e-48 204.0
8 TraesCS2B01G400900 chr2D 88.430 121 13 1 206 325 484373367 484373487 1.560000e-30 145.0
9 TraesCS2B01G400900 chr2D 97.059 34 1 0 4880 4913 548745229 548745262 2.090000e-04 58.4
10 TraesCS2B01G400900 chr2A 89.116 1957 153 35 2622 4543 628673640 628675571 0.000000e+00 2379.0
11 TraesCS2B01G400900 chr2A 90.305 1444 58 21 1 1407 628670720 628672118 0.000000e+00 1816.0
12 TraesCS2B01G400900 chr2A 86.026 780 63 23 4587 5358 628675568 628676309 0.000000e+00 795.0
13 TraesCS2B01G400900 chr2A 86.694 248 18 4 1557 1789 628672571 628672818 1.480000e-65 261.0
14 TraesCS2B01G400900 chr2A 84.064 251 20 5 1873 2119 628672813 628673047 1.940000e-54 224.0
15 TraesCS2B01G400900 chr2A 90.400 125 11 1 206 329 628670791 628670915 4.300000e-36 163.0
16 TraesCS2B01G400900 chr7A 88.291 743 52 19 3840 4558 357233840 357234571 0.000000e+00 857.0
17 TraesCS2B01G400900 chr7A 87.399 746 60 23 3835 4558 380407053 380407786 0.000000e+00 826.0
18 TraesCS2B01G400900 chr4D 98.985 197 2 0 2425 2621 470124420 470124616 2.380000e-93 353.0
19 TraesCS2B01G400900 chr4D 100.000 32 0 0 4884 4915 27157482 27157451 5.800000e-05 60.2
20 TraesCS2B01G400900 chr7B 97.073 205 5 1 2422 2626 88283911 88283708 1.430000e-90 344.0
21 TraesCS2B01G400900 chr7B 97.487 199 5 0 2424 2622 554524154 554524352 1.850000e-89 340.0
22 TraesCS2B01G400900 chr7B 87.719 57 7 0 5146 5202 518401497 518401553 3.470000e-07 67.6
23 TraesCS2B01G400900 chr7B 87.719 57 7 0 5146 5202 518409605 518409661 3.470000e-07 67.6
24 TraesCS2B01G400900 chr3D 97.938 194 4 0 2427 2620 254079389 254079196 2.390000e-88 337.0
25 TraesCS2B01G400900 chr6D 96.040 202 6 2 2422 2622 43060425 43060625 1.440000e-85 327.0
26 TraesCS2B01G400900 chr5B 96.447 197 5 2 2426 2622 44464413 44464219 1.860000e-84 324.0
27 TraesCS2B01G400900 chr5D 95.545 202 5 2 2421 2622 530795037 530794840 2.410000e-83 320.0
28 TraesCS2B01G400900 chr3B 95.500 200 8 1 2423 2622 518618201 518618399 8.660000e-83 318.0
29 TraesCS2B01G400900 chr6B 78.673 211 31 5 5154 5358 549082137 549081935 1.570000e-25 128.0
30 TraesCS2B01G400900 chr4A 80.645 155 26 4 5121 5273 670845209 670845361 3.390000e-22 117.0
31 TraesCS2B01G400900 chr4A 78.161 174 33 2 5152 5320 575803670 575803843 7.340000e-19 106.0
32 TraesCS2B01G400900 chr3A 88.571 70 8 0 5131 5200 688882793 688882862 9.570000e-13 86.1
33 TraesCS2B01G400900 chr7D 88.889 63 7 0 5137 5199 489905678 489905740 1.600000e-10 78.7


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 TraesCS2B01G400900 chr2B 569128048 569133408 5360 True 9901.000000 9901 100.000000 1 5361 1 chr2B.!!$R2 5360
1 TraesCS2B01G400900 chr2D 484373294 484378465 5171 False 1004.714286 2665 89.755286 1 5358 7 chr2D.!!$F2 5357
2 TraesCS2B01G400900 chr2A 628670720 628676309 5589 False 939.666667 2379 87.767500 1 5358 6 chr2A.!!$F1 5357
3 TraesCS2B01G400900 chr7A 357233840 357234571 731 False 857.000000 857 88.291000 3840 4558 1 chr7A.!!$F1 718
4 TraesCS2B01G400900 chr7A 380407053 380407786 733 False 826.000000 826 87.399000 3835 4558 1 chr7A.!!$F2 723

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
259 265 0.107752 CTCCTGGCTCCTGCTTCTTC 60.108 60.0 0.0 0.0 39.59 2.87 F
1042 1109 0.324614 CCACACCACAGCATACAGGA 59.675 55.0 0.0 0.0 0.00 3.86 F
2528 3224 0.110486 TTGGTTCTTGCCCACCTCTC 59.890 55.0 0.0 0.0 33.76 3.20 F
2615 3311 0.102120 CAAACTTTGGCAGCGAACCA 59.898 50.0 0.0 0.0 34.65 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2674 0.451783 GGCAATTCCAGTAAGGCGTG 59.548 55.0 0.00 0.00 37.29 5.34 R
2596 3292 0.102120 TGGTTCGCTGCCAAAGTTTG 59.898 50.0 8.73 8.73 32.29 2.93 R
4025 4755 0.379669 GATGGGAGTCATGCTTTGCG 59.620 55.0 0.00 0.00 35.97 4.85 R
4569 5326 0.249657 CCAGCTCTATTCTGCCCGAC 60.250 60.0 0.00 0.00 0.00 4.79 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
41 44 9.469097 AGGCGACTTATTCTATCTATAATGAGT 57.531 33.333 0.00 0.00 37.44 3.41
77 80 5.427036 TGGAGTTCCATTTCGTGTAAAAC 57.573 39.130 0.00 0.00 42.01 2.43
140 146 1.903955 GCTCCTTCTTCTTCCTCCCCT 60.904 57.143 0.00 0.00 0.00 4.79
155 161 1.422161 CCCCTGCTCCTATTCCCCAG 61.422 65.000 0.00 0.00 0.00 4.45
205 211 1.611965 GCCTCCCTTCTGCTCCAAT 59.388 57.895 0.00 0.00 0.00 3.16
252 258 4.463879 CGCACCTCCTGGCTCCTG 62.464 72.222 0.00 0.00 36.63 3.86
253 259 4.792804 GCACCTCCTGGCTCCTGC 62.793 72.222 0.00 0.00 36.63 4.85
254 260 3.007920 CACCTCCTGGCTCCTGCT 61.008 66.667 0.00 0.00 39.59 4.24
255 261 2.204059 ACCTCCTGGCTCCTGCTT 60.204 61.111 0.00 0.00 39.59 3.91
256 262 2.297129 ACCTCCTGGCTCCTGCTTC 61.297 63.158 0.00 0.00 39.59 3.86
257 263 1.994507 CCTCCTGGCTCCTGCTTCT 60.995 63.158 0.00 0.00 39.59 2.85
258 264 1.560866 CCTCCTGGCTCCTGCTTCTT 61.561 60.000 0.00 0.00 39.59 2.52
259 265 0.107752 CTCCTGGCTCCTGCTTCTTC 60.108 60.000 0.00 0.00 39.59 2.87
265 271 1.004161 GGCTCCTGCTTCTTCTTCCTT 59.996 52.381 0.00 0.00 39.59 3.36
269 275 1.632920 CCTGCTTCTTCTTCCTTCCCT 59.367 52.381 0.00 0.00 0.00 4.20
325 331 4.410400 CCACCACCGCCTCCTTCC 62.410 72.222 0.00 0.00 0.00 3.46
638 657 4.415332 GTCGTCTCCGCCGCTGAA 62.415 66.667 0.00 0.00 0.00 3.02
731 783 1.733399 GGAGACGAGCCGTTGTGTC 60.733 63.158 1.80 0.00 41.37 3.67
744 796 1.004292 GTTGTGTCCCGCAATATACGC 60.004 52.381 0.00 0.00 36.26 4.42
918 977 1.891150 CTTGCTGGAAAGCAGTGGATT 59.109 47.619 0.16 0.00 46.21 3.01
939 998 2.103771 TGATGAGAGCCCTTAGATGCAC 59.896 50.000 0.00 0.00 0.00 4.57
1042 1109 0.324614 CCACACCACAGCATACAGGA 59.675 55.000 0.00 0.00 0.00 3.86
1044 1111 0.615331 ACACCACAGCATACAGGAGG 59.385 55.000 0.00 0.00 0.00 4.30
1045 1112 0.745845 CACCACAGCATACAGGAGGC 60.746 60.000 0.00 0.00 34.09 4.70
1046 1113 1.522355 CCACAGCATACAGGAGGCG 60.522 63.158 0.00 0.00 40.72 5.52
1047 1114 1.522355 CACAGCATACAGGAGGCGG 60.522 63.158 0.00 0.00 40.72 6.13
1048 1115 2.590007 CAGCATACAGGAGGCGGC 60.590 66.667 0.00 0.00 40.72 6.53
1049 1116 3.083349 AGCATACAGGAGGCGGCA 61.083 61.111 13.08 0.00 40.72 5.69
1221 1288 2.002505 CCTCATGACCCGAGGTATCT 57.997 55.000 0.00 0.00 44.35 1.98
1222 1289 1.889829 CCTCATGACCCGAGGTATCTC 59.110 57.143 0.00 0.00 44.35 2.75
1228 1297 0.398664 ACCCGAGGTATCTCCCCTTG 60.399 60.000 0.00 0.00 36.70 3.61
1321 1417 0.826672 CTAGGCGGGTCCTATTCCGT 60.827 60.000 0.00 0.00 45.99 4.69
1340 1436 2.805671 CGTGTTCCTATCTGTTGTGCAA 59.194 45.455 0.00 0.00 0.00 4.08
1396 1492 1.402325 GGCTTGGTAATTCGTGTTGCC 60.402 52.381 0.00 0.00 34.80 4.52
1432 1630 4.461781 CACCTCCTCTTTGATCTTTGCATT 59.538 41.667 0.00 0.00 0.00 3.56
1433 1631 5.047519 CACCTCCTCTTTGATCTTTGCATTT 60.048 40.000 0.00 0.00 0.00 2.32
1506 1736 7.198306 ACTACAAACCTTCTTGGAATAAACG 57.802 36.000 0.00 0.00 39.71 3.60
1511 1741 7.490079 ACAAACCTTCTTGGAATAAACGTTTTC 59.510 33.333 20.19 11.43 39.71 2.29
1521 1792 8.624367 TGGAATAAACGTTTTCAATCCTCTAA 57.376 30.769 20.19 3.86 0.00 2.10
1529 1800 7.752695 ACGTTTTCAATCCTCTAAATGACATC 58.247 34.615 0.00 0.00 0.00 3.06
1705 2123 7.179338 AGACAGTTTGGTACAGAGAGAACATAT 59.821 37.037 0.00 0.00 42.39 1.78
1764 2185 7.171678 GGTTACAATCTGCCATATACAACTCTC 59.828 40.741 0.00 0.00 0.00 3.20
1859 2280 6.672147 ACAAAATCTTGTAGCATCAGTTCAC 58.328 36.000 0.00 0.00 44.14 3.18
1860 2281 5.886960 AAATCTTGTAGCATCAGTTCACC 57.113 39.130 0.00 0.00 0.00 4.02
2017 2439 5.957798 AGTATGTGCATTTCAACCATGAAG 58.042 37.500 0.00 0.00 45.82 3.02
2069 2491 8.870160 TTTGTCATTTTCACTCATTTGGTTAG 57.130 30.769 0.00 0.00 0.00 2.34
2256 2800 3.554934 TGAGCAATCAGGTCTGTGTTTT 58.445 40.909 0.00 0.00 44.98 2.43
2260 2804 4.646492 AGCAATCAGGTCTGTGTTTTCTTT 59.354 37.500 0.00 0.00 0.00 2.52
2426 3122 8.815565 TGGCACATTATATCAAAGGTTTAAGA 57.184 30.769 0.00 0.00 0.00 2.10
2427 3123 8.902806 TGGCACATTATATCAAAGGTTTAAGAG 58.097 33.333 0.00 0.00 0.00 2.85
2429 3125 7.862873 GCACATTATATCAAAGGTTTAAGAGCC 59.137 37.037 0.00 0.00 0.00 4.70
2430 3126 9.125026 CACATTATATCAAAGGTTTAAGAGCCT 57.875 33.333 0.00 0.00 38.25 4.58
2436 3132 6.834168 TCAAAGGTTTAAGAGCCTAATTGG 57.166 37.500 0.00 0.00 35.11 3.16
2437 3133 6.311735 TCAAAGGTTTAAGAGCCTAATTGGT 58.688 36.000 0.00 0.00 35.11 3.67
2438 3134 6.780522 TCAAAGGTTTAAGAGCCTAATTGGTT 59.219 34.615 0.00 0.00 35.11 3.67
2439 3135 7.289084 TCAAAGGTTTAAGAGCCTAATTGGTTT 59.711 33.333 0.00 0.00 35.11 3.27
2440 3136 6.590234 AGGTTTAAGAGCCTAATTGGTTTG 57.410 37.500 0.00 0.00 34.31 2.93
2441 3137 6.311735 AGGTTTAAGAGCCTAATTGGTTTGA 58.688 36.000 0.00 0.00 34.31 2.69
2442 3138 6.954102 AGGTTTAAGAGCCTAATTGGTTTGAT 59.046 34.615 0.00 0.00 34.31 2.57
2443 3139 7.035612 GGTTTAAGAGCCTAATTGGTTTGATG 58.964 38.462 0.00 0.00 38.35 3.07
2444 3140 4.725790 AAGAGCCTAATTGGTTTGATGC 57.274 40.909 0.00 0.00 38.35 3.91
2445 3141 3.026694 AGAGCCTAATTGGTTTGATGCC 58.973 45.455 0.00 0.00 38.35 4.40
2446 3142 2.760092 GAGCCTAATTGGTTTGATGCCA 59.240 45.455 0.00 0.00 38.35 4.92
2483 3179 7.495135 CCAATTGTTGGCAAGTCTAAAAATT 57.505 32.000 0.00 0.00 45.17 1.82
2484 3180 7.929159 CCAATTGTTGGCAAGTCTAAAAATTT 58.071 30.769 0.00 0.00 45.17 1.82
2485 3181 7.856894 CCAATTGTTGGCAAGTCTAAAAATTTG 59.143 33.333 0.00 0.00 45.17 2.32
2486 3182 6.917217 TTGTTGGCAAGTCTAAAAATTTGG 57.083 33.333 0.00 0.00 0.00 3.28
2487 3183 4.813697 TGTTGGCAAGTCTAAAAATTTGGC 59.186 37.500 0.00 3.09 43.80 4.52
2488 3184 4.953940 TGGCAAGTCTAAAAATTTGGCT 57.046 36.364 10.28 0.00 43.85 4.75
2489 3185 4.881920 TGGCAAGTCTAAAAATTTGGCTC 58.118 39.130 10.28 0.00 43.85 4.70
2490 3186 4.588528 TGGCAAGTCTAAAAATTTGGCTCT 59.411 37.500 10.28 0.00 43.85 4.09
2491 3187 5.164233 GGCAAGTCTAAAAATTTGGCTCTC 58.836 41.667 0.00 0.00 41.31 3.20
2492 3188 5.278957 GGCAAGTCTAAAAATTTGGCTCTCA 60.279 40.000 0.00 0.00 41.31 3.27
2493 3189 6.215845 GCAAGTCTAAAAATTTGGCTCTCAA 58.784 36.000 0.00 0.00 0.00 3.02
2494 3190 6.870439 GCAAGTCTAAAAATTTGGCTCTCAAT 59.130 34.615 0.00 0.00 34.98 2.57
2495 3191 7.386025 GCAAGTCTAAAAATTTGGCTCTCAATT 59.614 33.333 0.00 0.00 34.98 2.32
2496 3192 8.706035 CAAGTCTAAAAATTTGGCTCTCAATTG 58.294 33.333 0.00 0.00 34.98 2.32
2497 3193 7.381323 AGTCTAAAAATTTGGCTCTCAATTGG 58.619 34.615 5.42 0.00 34.98 3.16
2498 3194 7.015584 AGTCTAAAAATTTGGCTCTCAATTGGT 59.984 33.333 5.42 0.00 34.98 3.67
2499 3195 7.657354 GTCTAAAAATTTGGCTCTCAATTGGTT 59.343 33.333 5.42 0.00 34.98 3.67
2500 3196 6.622833 AAAAATTTGGCTCTCAATTGGTTG 57.377 33.333 5.42 0.00 34.98 3.77
2501 3197 3.967332 ATTTGGCTCTCAATTGGTTGG 57.033 42.857 5.42 0.00 35.99 3.77
2502 3198 0.968405 TTGGCTCTCAATTGGTTGGC 59.032 50.000 5.42 8.56 35.99 4.52
2503 3199 0.112995 TGGCTCTCAATTGGTTGGCT 59.887 50.000 5.42 0.00 35.99 4.75
2504 3200 1.354031 TGGCTCTCAATTGGTTGGCTA 59.646 47.619 5.42 1.08 35.99 3.93
2505 3201 1.745653 GGCTCTCAATTGGTTGGCTAC 59.254 52.381 5.42 0.00 35.99 3.58
2523 3219 3.912899 CCAATTGGTTCTTGCCCAC 57.087 52.632 16.90 0.00 0.00 4.61
2524 3220 0.321346 CCAATTGGTTCTTGCCCACC 59.679 55.000 16.90 0.00 0.00 4.61
2525 3221 1.341080 CAATTGGTTCTTGCCCACCT 58.659 50.000 0.00 0.00 33.76 4.00
2526 3222 1.273327 CAATTGGTTCTTGCCCACCTC 59.727 52.381 0.00 0.00 33.76 3.85
2527 3223 0.779997 ATTGGTTCTTGCCCACCTCT 59.220 50.000 0.00 0.00 33.76 3.69
2528 3224 0.110486 TTGGTTCTTGCCCACCTCTC 59.890 55.000 0.00 0.00 33.76 3.20
2529 3225 1.059584 TGGTTCTTGCCCACCTCTCA 61.060 55.000 0.00 0.00 33.76 3.27
2530 3226 0.110486 GGTTCTTGCCCACCTCTCAA 59.890 55.000 0.00 0.00 0.00 3.02
2531 3227 1.478654 GGTTCTTGCCCACCTCTCAAA 60.479 52.381 0.00 0.00 0.00 2.69
2532 3228 2.306847 GTTCTTGCCCACCTCTCAAAA 58.693 47.619 0.00 0.00 0.00 2.44
2533 3229 2.693074 GTTCTTGCCCACCTCTCAAAAA 59.307 45.455 0.00 0.00 0.00 1.94
2534 3230 2.586425 TCTTGCCCACCTCTCAAAAAG 58.414 47.619 0.00 0.00 0.00 2.27
2535 3231 2.091885 TCTTGCCCACCTCTCAAAAAGT 60.092 45.455 0.00 0.00 0.00 2.66
2536 3232 2.452600 TGCCCACCTCTCAAAAAGTT 57.547 45.000 0.00 0.00 0.00 2.66
2537 3233 2.031120 TGCCCACCTCTCAAAAAGTTG 58.969 47.619 0.00 0.00 35.95 3.16
2538 3234 1.269778 GCCCACCTCTCAAAAAGTTGC 60.270 52.381 0.00 0.00 34.50 4.17
2539 3235 1.341209 CCCACCTCTCAAAAAGTTGCC 59.659 52.381 0.00 0.00 34.50 4.52
2540 3236 2.031120 CCACCTCTCAAAAAGTTGCCA 58.969 47.619 0.00 0.00 34.50 4.92
2541 3237 2.430332 CCACCTCTCAAAAAGTTGCCAA 59.570 45.455 0.00 0.00 34.50 4.52
2542 3238 3.070015 CCACCTCTCAAAAAGTTGCCAAT 59.930 43.478 0.00 0.00 34.50 3.16
2543 3239 4.443315 CCACCTCTCAAAAAGTTGCCAATT 60.443 41.667 0.00 0.00 34.50 2.32
2544 3240 5.118286 CACCTCTCAAAAAGTTGCCAATTT 58.882 37.500 0.00 0.00 34.50 1.82
2545 3241 5.585844 CACCTCTCAAAAAGTTGCCAATTTT 59.414 36.000 0.00 0.00 34.50 1.82
2546 3242 6.093909 CACCTCTCAAAAAGTTGCCAATTTTT 59.906 34.615 4.98 4.98 38.74 1.94
2559 3255 4.979943 CCAATTTTTGGCAACTTTTGGT 57.020 36.364 18.95 0.00 45.17 3.67
2560 3256 5.321959 CCAATTTTTGGCAACTTTTGGTT 57.678 34.783 18.95 0.73 45.17 3.67
2561 3257 5.718146 CCAATTTTTGGCAACTTTTGGTTT 58.282 33.333 18.95 0.00 45.17 3.27
2562 3258 6.162079 CCAATTTTTGGCAACTTTTGGTTTT 58.838 32.000 18.95 0.00 45.17 2.43
2563 3259 6.090493 CCAATTTTTGGCAACTTTTGGTTTTG 59.910 34.615 18.95 7.01 45.17 2.44
2564 3260 3.839051 TTTGGCAACTTTTGGTTTTGC 57.161 38.095 0.00 0.00 44.05 3.68
2582 3278 3.702147 CCAAATGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
2583 3279 1.964552 CCAAATGTTGGCTTGCCAAA 58.035 45.000 26.12 17.09 45.17 3.28
2584 3280 2.506444 CCAAATGTTGGCTTGCCAAAT 58.494 42.857 26.12 18.32 45.17 2.32
2585 3281 3.672808 CCAAATGTTGGCTTGCCAAATA 58.327 40.909 26.12 18.73 45.17 1.40
2586 3282 4.263435 CCAAATGTTGGCTTGCCAAATAT 58.737 39.130 26.12 19.92 45.17 1.28
2587 3283 4.701171 CCAAATGTTGGCTTGCCAAATATT 59.299 37.500 26.12 23.52 45.17 1.28
2588 3284 5.392165 CCAAATGTTGGCTTGCCAAATATTG 60.392 40.000 26.12 25.13 45.17 1.90
2613 3309 2.885502 CCAAACTTTGGCAGCGAAC 58.114 52.632 7.63 0.00 45.17 3.95
2614 3310 0.597377 CCAAACTTTGGCAGCGAACC 60.597 55.000 7.63 0.00 45.17 3.62
2615 3311 0.102120 CAAACTTTGGCAGCGAACCA 59.898 50.000 0.00 0.00 34.65 3.67
2616 3312 0.820871 AAACTTTGGCAGCGAACCAA 59.179 45.000 4.28 4.28 45.37 3.67
2617 3313 1.039856 AACTTTGGCAGCGAACCAAT 58.960 45.000 8.64 0.00 46.25 3.16
2618 3314 1.039856 ACTTTGGCAGCGAACCAATT 58.960 45.000 8.64 0.00 46.25 2.32
2619 3315 2.235016 ACTTTGGCAGCGAACCAATTA 58.765 42.857 8.64 0.00 46.25 1.40
2620 3316 2.228822 ACTTTGGCAGCGAACCAATTAG 59.771 45.455 8.64 7.12 46.25 1.73
2628 3324 3.127548 CAGCGAACCAATTAGCATTCACT 59.872 43.478 0.00 0.00 38.79 3.41
2814 3512 8.721478 TCTAGTTTACAATTTGATCACTTCTGC 58.279 33.333 2.79 0.00 0.00 4.26
2892 3590 9.554395 TGTTCAAACATCTGTAACTTGAATCTA 57.446 29.630 10.29 1.84 35.81 1.98
2905 3603 6.388619 ACTTGAATCTATTGTAGGGTTGGT 57.611 37.500 0.00 0.00 0.00 3.67
2906 3604 6.415573 ACTTGAATCTATTGTAGGGTTGGTC 58.584 40.000 0.00 0.00 0.00 4.02
2987 3685 7.416964 AGATTGGATATGCTATGGTCTAGAC 57.583 40.000 14.87 14.87 0.00 2.59
3005 3703 7.427214 GTCTAGACTGGGTTATTGATGTAGAC 58.573 42.308 15.91 0.00 0.00 2.59
3077 3775 3.462205 GGTAGGATTATGGTGGAAAGGGT 59.538 47.826 0.00 0.00 0.00 4.34
3102 3800 9.769093 GTAAAGATGTTTACATGTGTGGATTAC 57.231 33.333 17.99 4.58 45.15 1.89
3110 3808 3.188460 ACATGTGTGGATTACGTTTGAGC 59.812 43.478 0.00 0.00 0.00 4.26
3117 3815 5.645929 TGTGGATTACGTTTGAGCACATATT 59.354 36.000 0.00 0.00 0.00 1.28
3281 3983 1.001068 TGGTTGCCAATGTTGCATCTG 59.999 47.619 0.00 0.00 38.76 2.90
3342 4044 5.344743 TCCTTAGCCTAGTCTCAAACATG 57.655 43.478 0.00 0.00 0.00 3.21
3343 4045 5.023452 TCCTTAGCCTAGTCTCAAACATGA 58.977 41.667 0.00 0.00 0.00 3.07
3455 4174 9.232388 CTGTCCCCAGTTTCATCATCTTTGATG 62.232 44.444 9.20 9.20 44.83 3.07
3715 4438 5.352284 ACCTTCAGTTGATAACGATAGCTG 58.648 41.667 0.00 0.00 42.67 4.24
3751 4474 5.367352 ACCTGTCCCGTGATATTGGTATAAA 59.633 40.000 0.00 0.00 0.00 1.40
3753 4476 6.204108 CCTGTCCCGTGATATTGGTATAAAAC 59.796 42.308 0.00 0.00 0.00 2.43
3783 4506 8.297426 CAGTTTGAATTCATAGCATCATAGCAT 58.703 33.333 9.40 0.00 36.85 3.79
3983 4710 4.864704 TTCATTTACTCCTTTTGGCACC 57.135 40.909 0.00 0.00 40.12 5.01
4013 4743 9.434420 GAGCTTACTTGATTGCAATATATCTCT 57.566 33.333 12.97 3.34 32.68 3.10
4025 4755 8.327941 TGCAATATATCTCTTCAATTGTAGGC 57.672 34.615 11.64 5.10 31.65 3.93
4278 5025 5.761234 ACAGTAATAGAAGTTTTGTTCGCCA 59.239 36.000 0.00 0.00 0.00 5.69
4439 5196 1.188863 GTTACGGGCTGGTAGAGGAA 58.811 55.000 0.00 0.00 0.00 3.36
4451 5208 2.297597 GGTAGAGGAATAGCGCACATCT 59.702 50.000 11.47 12.66 0.00 2.90
4472 5229 3.344703 CATGGTTTGCAGGTGGAGA 57.655 52.632 0.00 0.00 0.00 3.71
4473 5230 1.171308 CATGGTTTGCAGGTGGAGAG 58.829 55.000 0.00 0.00 0.00 3.20
4474 5231 1.067295 ATGGTTTGCAGGTGGAGAGA 58.933 50.000 0.00 0.00 0.00 3.10
4475 5232 1.067295 TGGTTTGCAGGTGGAGAGAT 58.933 50.000 0.00 0.00 0.00 2.75
4476 5233 1.271543 TGGTTTGCAGGTGGAGAGATG 60.272 52.381 0.00 0.00 0.00 2.90
4477 5234 1.457346 GTTTGCAGGTGGAGAGATGG 58.543 55.000 0.00 0.00 0.00 3.51
4478 5235 1.003580 GTTTGCAGGTGGAGAGATGGA 59.996 52.381 0.00 0.00 0.00 3.41
4479 5236 0.907486 TTGCAGGTGGAGAGATGGAG 59.093 55.000 0.00 0.00 0.00 3.86
4480 5237 0.041684 TGCAGGTGGAGAGATGGAGA 59.958 55.000 0.00 0.00 0.00 3.71
4481 5238 0.463620 GCAGGTGGAGAGATGGAGAC 59.536 60.000 0.00 0.00 0.00 3.36
4522 5279 0.680280 TGGTAGAGTGAGGCGAGACC 60.680 60.000 0.00 0.00 39.61 3.85
4554 5311 3.717294 GGTGGCACCGTGGGAGAT 61.717 66.667 22.83 0.00 0.00 2.75
4558 5315 4.101448 GCACCGTGGGAGATGGCT 62.101 66.667 0.00 0.00 33.31 4.75
4565 5322 4.496336 GGGAGATGGCTGGCGCTT 62.496 66.667 7.64 0.00 36.09 4.68
4566 5323 3.207669 GGAGATGGCTGGCGCTTG 61.208 66.667 7.64 0.90 36.09 4.01
4567 5324 3.207669 GAGATGGCTGGCGCTTGG 61.208 66.667 7.64 0.00 36.09 3.61
4585 5342 1.951631 GCGTCGGGCAGAATAGAGC 60.952 63.158 0.00 0.00 42.87 4.09
4635 5392 7.641249 AGAAGAAAAATGGGATTGAGAGAGAT 58.359 34.615 0.00 0.00 0.00 2.75
4637 5394 6.363882 AGAAAAATGGGATTGAGAGAGATCC 58.636 40.000 0.00 0.00 40.90 3.36
4699 5456 1.368641 CCGAGGATGAAATTGCGTGA 58.631 50.000 0.00 0.00 0.00 4.35
4718 5475 2.776072 GCCACCGTGAAACGATCG 59.224 61.111 14.88 14.88 0.00 3.69
4734 5491 1.421410 ATCGCGTGCAATCGAGGTTC 61.421 55.000 5.77 0.00 38.17 3.62
4765 5527 4.436584 CGTGATCTGAAGGCTTGTCAAATC 60.437 45.833 3.46 0.00 0.00 2.17
4787 5549 1.677820 CGGAGATGCCCCGTAAGTTTT 60.678 52.381 0.00 0.00 41.91 2.43
4789 5551 2.941064 GGAGATGCCCCGTAAGTTTTAC 59.059 50.000 0.00 0.00 0.00 2.01
4790 5552 2.606272 GAGATGCCCCGTAAGTTTTACG 59.394 50.000 12.92 12.92 40.30 3.18
4791 5553 2.027837 AGATGCCCCGTAAGTTTTACGT 60.028 45.455 17.04 0.00 39.09 3.57
4792 5554 3.195396 AGATGCCCCGTAAGTTTTACGTA 59.805 43.478 17.04 0.00 39.09 3.57
4793 5555 2.682836 TGCCCCGTAAGTTTTACGTAC 58.317 47.619 17.04 8.72 39.09 3.67
4937 5704 3.664107 TCTTCGCTGCAAATCACTACTT 58.336 40.909 0.00 0.00 0.00 2.24
5017 5784 5.765182 CCAACTTAGAAAGGTCATGTGAAGT 59.235 40.000 0.00 0.00 0.00 3.01
5024 5791 4.357918 AAGGTCATGTGAAGTAAGTGCT 57.642 40.909 0.00 0.00 0.00 4.40
5027 5794 3.815401 GGTCATGTGAAGTAAGTGCTTGT 59.185 43.478 0.00 0.00 0.00 3.16
5082 5849 1.157870 CGACCAGCCACAACTTTCGT 61.158 55.000 0.00 0.00 0.00 3.85
5136 5905 2.206750 GAAAACCCAACCCGAAAAAGC 58.793 47.619 0.00 0.00 0.00 3.51
5147 5916 0.602905 CGAAAAAGCCCGACCAGACT 60.603 55.000 0.00 0.00 0.00 3.24
5149 5918 0.602905 AAAAAGCCCGACCAGACTCG 60.603 55.000 0.00 0.00 0.00 4.18
5157 5926 4.371417 ACCAGACTCGGCCCGGTA 62.371 66.667 1.90 0.00 0.00 4.02
5158 5927 2.838225 CCAGACTCGGCCCGGTAT 60.838 66.667 1.90 0.00 0.00 2.73
5159 5928 2.432300 CCAGACTCGGCCCGGTATT 61.432 63.158 1.90 0.00 0.00 1.89
5160 5929 1.227263 CAGACTCGGCCCGGTATTG 60.227 63.158 1.90 0.00 0.00 1.90
5161 5930 2.588034 GACTCGGCCCGGTATTGC 60.588 66.667 1.90 0.00 0.00 3.56
5162 5931 4.171103 ACTCGGCCCGGTATTGCC 62.171 66.667 1.90 9.25 44.41 4.52
5163 5932 4.929707 CTCGGCCCGGTATTGCCC 62.930 72.222 13.14 0.00 45.07 5.36
5221 5996 4.684134 GGCTGGGCTTGGGCTTGA 62.684 66.667 0.00 0.00 38.73 3.02
5227 6002 1.035139 GGGCTTGGGCTTGACATATG 58.965 55.000 0.00 0.00 38.73 1.78
5229 6004 2.422803 GGGCTTGGGCTTGACATATGTA 60.423 50.000 8.71 0.00 38.73 2.29
5231 6006 3.278574 GCTTGGGCTTGACATATGTACA 58.721 45.455 8.71 0.00 35.22 2.90
5310 6085 3.903208 GGCTTCAAATCTAGGCCCA 57.097 52.632 0.00 0.00 37.12 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 40 4.954202 ACTCCACGGATACTCAATTACTCA 59.046 41.667 0.00 0.00 0.00 3.41
38 41 5.517322 ACTCCACGGATACTCAATTACTC 57.483 43.478 0.00 0.00 0.00 2.59
39 42 5.163437 GGAACTCCACGGATACTCAATTACT 60.163 44.000 0.00 0.00 35.64 2.24
40 43 5.048507 GGAACTCCACGGATACTCAATTAC 58.951 45.833 0.00 0.00 35.64 1.89
41 44 4.712829 TGGAACTCCACGGATACTCAATTA 59.287 41.667 0.00 0.00 42.01 1.40
42 45 3.517901 TGGAACTCCACGGATACTCAATT 59.482 43.478 0.00 0.00 42.01 2.32
43 46 3.104512 TGGAACTCCACGGATACTCAAT 58.895 45.455 0.00 0.00 42.01 2.57
44 47 2.531771 TGGAACTCCACGGATACTCAA 58.468 47.619 0.00 0.00 42.01 3.02
77 80 3.532542 GCCCTAGTGCACTACTTTTAGG 58.467 50.000 22.67 21.14 40.89 2.69
115 118 0.254462 GGAAGAAGAAGGAGCCAGGG 59.746 60.000 0.00 0.00 0.00 4.45
140 146 1.382557 TCGCTGGGGAATAGGAGCA 60.383 57.895 0.00 0.00 0.00 4.26
205 211 3.343941 AGCCCTAGTGCATTCGTTTTA 57.656 42.857 0.00 0.00 0.00 1.52
247 253 2.355615 GGGAAGGAAGAAGAAGCAGGAG 60.356 54.545 0.00 0.00 0.00 3.69
248 254 1.630878 GGGAAGGAAGAAGAAGCAGGA 59.369 52.381 0.00 0.00 0.00 3.86
249 255 1.632920 AGGGAAGGAAGAAGAAGCAGG 59.367 52.381 0.00 0.00 0.00 4.85
250 256 2.709213 CAGGGAAGGAAGAAGAAGCAG 58.291 52.381 0.00 0.00 0.00 4.24
251 257 1.271597 GCAGGGAAGGAAGAAGAAGCA 60.272 52.381 0.00 0.00 0.00 3.91
252 258 1.004161 AGCAGGGAAGGAAGAAGAAGC 59.996 52.381 0.00 0.00 0.00 3.86
253 259 2.355615 GGAGCAGGGAAGGAAGAAGAAG 60.356 54.545 0.00 0.00 0.00 2.85
254 260 1.630878 GGAGCAGGGAAGGAAGAAGAA 59.369 52.381 0.00 0.00 0.00 2.52
255 261 1.203364 AGGAGCAGGGAAGGAAGAAGA 60.203 52.381 0.00 0.00 0.00 2.87
256 262 1.209261 GAGGAGCAGGGAAGGAAGAAG 59.791 57.143 0.00 0.00 0.00 2.85
257 263 1.203364 AGAGGAGCAGGGAAGGAAGAA 60.203 52.381 0.00 0.00 0.00 2.52
258 264 0.415429 AGAGGAGCAGGGAAGGAAGA 59.585 55.000 0.00 0.00 0.00 2.87
259 265 1.284313 AAGAGGAGCAGGGAAGGAAG 58.716 55.000 0.00 0.00 0.00 3.46
265 271 0.617820 GTGGGTAAGAGGAGCAGGGA 60.618 60.000 0.00 0.00 0.00 4.20
269 275 1.159905 TGGGTGGGTAAGAGGAGCA 59.840 57.895 0.00 0.00 0.00 4.26
297 303 4.436998 GTGGTGGGCGAGAGGACG 62.437 72.222 0.00 0.00 0.00 4.79
298 304 4.083862 GGTGGTGGGCGAGAGGAC 62.084 72.222 0.00 0.00 0.00 3.85
307 313 4.410400 GAAGGAGGCGGTGGTGGG 62.410 72.222 0.00 0.00 0.00 4.61
308 314 4.410400 GGAAGGAGGCGGTGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
309 315 4.760047 CGGAAGGAGGCGGTGGTG 62.760 72.222 0.00 0.00 0.00 4.17
453 459 2.107552 TCTCCGTTTTGTCTGGGGAAAT 59.892 45.455 0.00 0.00 0.00 2.17
547 553 3.520862 GGATACGACCCGCCGACA 61.521 66.667 0.00 0.00 0.00 4.35
561 567 3.854669 CCTTCCTCAGCCGCGGAT 61.855 66.667 33.48 23.90 0.00 4.18
638 657 4.070552 GCAGACGACCCGCCTTCT 62.071 66.667 0.00 0.00 0.00 2.85
918 977 2.103771 GTGCATCTAAGGGCTCTCATCA 59.896 50.000 0.00 0.00 0.00 3.07
939 998 3.624861 GTCACAGTATCTGCCATCCAAAG 59.375 47.826 0.00 0.00 34.37 2.77
1178 1245 2.994417 GGCACCCCGAAAATGGCA 60.994 61.111 0.00 0.00 38.69 4.92
1221 1288 2.738587 TTTTGTGTGTAGCAAGGGGA 57.261 45.000 0.00 0.00 0.00 4.81
1244 1321 0.608640 CACGGTAGCAAGAGGAGGTT 59.391 55.000 0.00 0.00 0.00 3.50
1321 1417 4.065088 GAGTTGCACAACAGATAGGAACA 58.935 43.478 15.40 0.00 43.47 3.18
1340 1436 2.423660 CCTAGTTCCCCTCATCGAGAGT 60.424 54.545 9.90 0.00 43.12 3.24
1396 1492 3.639094 AGAGGAGGTGGAAGATAACATCG 59.361 47.826 0.00 0.00 0.00 3.84
1473 1703 5.500645 AGAAGGTTTGTAGTTGCAGAAAC 57.499 39.130 0.00 0.00 39.24 2.78
1506 1736 9.780413 GAAGATGTCATTTAGAGGATTGAAAAC 57.220 33.333 0.00 0.00 0.00 2.43
1511 1741 8.396390 CAACTGAAGATGTCATTTAGAGGATTG 58.604 37.037 0.00 0.00 35.07 2.67
1525 1796 6.174720 TCCTAACTTGACAACTGAAGATGT 57.825 37.500 0.00 0.00 33.59 3.06
1529 1800 7.065803 TCTGTTTTCCTAACTTGACAACTGAAG 59.934 37.037 0.00 0.00 31.65 3.02
1705 2123 9.699410 AAACCATCATCTATTTATGAACAGGAA 57.301 29.630 0.00 0.00 39.25 3.36
1764 2185 9.961265 AGCATATTCATGTGAAAAATATCAGTG 57.039 29.630 0.00 0.00 37.61 3.66
2017 2439 3.068165 AGCCCACAAAACTAGTTTTCTGC 59.932 43.478 26.90 23.64 40.45 4.26
2131 2670 3.425758 GCAATTCCAGTAAGGCGTGTAAC 60.426 47.826 0.00 0.00 37.29 2.50
2132 2671 2.745281 GCAATTCCAGTAAGGCGTGTAA 59.255 45.455 0.00 0.00 37.29 2.41
2134 2673 1.165270 GCAATTCCAGTAAGGCGTGT 58.835 50.000 0.00 0.00 37.29 4.49
2135 2674 0.451783 GGCAATTCCAGTAAGGCGTG 59.548 55.000 0.00 0.00 37.29 5.34
2138 2678 1.135402 CAACGGCAATTCCAGTAAGGC 60.135 52.381 0.00 0.00 37.29 4.35
2424 3120 3.026694 GGCATCAAACCAATTAGGCTCT 58.973 45.455 0.00 0.00 43.14 4.09
2425 3121 2.760092 TGGCATCAAACCAATTAGGCTC 59.240 45.455 0.00 0.00 43.14 4.70
2426 3122 2.818921 TGGCATCAAACCAATTAGGCT 58.181 42.857 0.00 0.00 43.14 4.58
2427 3123 3.608316 TTGGCATCAAACCAATTAGGC 57.392 42.857 0.00 0.00 42.23 3.93
2460 3156 7.856894 CCAAATTTTTAGACTTGCCAACAATTG 59.143 33.333 3.24 3.24 34.61 2.32
2461 3157 7.468494 GCCAAATTTTTAGACTTGCCAACAATT 60.468 33.333 0.00 0.00 34.61 2.32
2462 3158 6.017192 GCCAAATTTTTAGACTTGCCAACAAT 60.017 34.615 0.00 0.00 34.61 2.71
2463 3159 5.295540 GCCAAATTTTTAGACTTGCCAACAA 59.704 36.000 0.00 0.00 0.00 2.83
2464 3160 4.813697 GCCAAATTTTTAGACTTGCCAACA 59.186 37.500 0.00 0.00 0.00 3.33
2465 3161 5.056480 AGCCAAATTTTTAGACTTGCCAAC 58.944 37.500 0.00 0.00 0.00 3.77
2466 3162 5.070313 AGAGCCAAATTTTTAGACTTGCCAA 59.930 36.000 0.00 0.00 0.00 4.52
2467 3163 4.588528 AGAGCCAAATTTTTAGACTTGCCA 59.411 37.500 0.00 0.00 0.00 4.92
2468 3164 5.139435 AGAGCCAAATTTTTAGACTTGCC 57.861 39.130 0.00 0.00 0.00 4.52
2469 3165 5.772521 TGAGAGCCAAATTTTTAGACTTGC 58.227 37.500 0.00 0.00 0.00 4.01
2470 3166 8.706035 CAATTGAGAGCCAAATTTTTAGACTTG 58.294 33.333 0.00 0.00 38.43 3.16
2471 3167 7.874528 CCAATTGAGAGCCAAATTTTTAGACTT 59.125 33.333 7.12 0.00 38.43 3.01
2472 3168 7.015584 ACCAATTGAGAGCCAAATTTTTAGACT 59.984 33.333 7.12 0.00 38.43 3.24
2473 3169 7.154656 ACCAATTGAGAGCCAAATTTTTAGAC 58.845 34.615 7.12 0.00 38.43 2.59
2474 3170 7.301868 ACCAATTGAGAGCCAAATTTTTAGA 57.698 32.000 7.12 0.00 38.43 2.10
2475 3171 7.095102 CCAACCAATTGAGAGCCAAATTTTTAG 60.095 37.037 7.12 0.00 38.15 1.85
2476 3172 6.709846 CCAACCAATTGAGAGCCAAATTTTTA 59.290 34.615 7.12 0.00 38.15 1.52
2477 3173 5.532032 CCAACCAATTGAGAGCCAAATTTTT 59.468 36.000 7.12 0.00 38.15 1.94
2478 3174 5.065235 CCAACCAATTGAGAGCCAAATTTT 58.935 37.500 7.12 0.00 38.15 1.82
2479 3175 4.644498 CCAACCAATTGAGAGCCAAATTT 58.356 39.130 7.12 0.00 38.15 1.82
2480 3176 3.557686 GCCAACCAATTGAGAGCCAAATT 60.558 43.478 7.12 0.00 38.15 1.82
2481 3177 2.027837 GCCAACCAATTGAGAGCCAAAT 60.028 45.455 7.12 0.00 38.15 2.32
2482 3178 1.344114 GCCAACCAATTGAGAGCCAAA 59.656 47.619 7.12 0.00 38.15 3.28
2483 3179 0.968405 GCCAACCAATTGAGAGCCAA 59.032 50.000 7.12 0.00 38.15 4.52
2484 3180 0.112995 AGCCAACCAATTGAGAGCCA 59.887 50.000 7.12 0.00 38.15 4.75
2485 3181 1.745653 GTAGCCAACCAATTGAGAGCC 59.254 52.381 7.12 0.00 38.15 4.70
2505 3201 0.321346 GGTGGGCAAGAACCAATTGG 59.679 55.000 23.31 23.31 40.24 3.16
2506 3202 1.273327 GAGGTGGGCAAGAACCAATTG 59.727 52.381 0.00 0.00 40.24 2.32
2507 3203 1.147817 AGAGGTGGGCAAGAACCAATT 59.852 47.619 0.00 0.00 40.24 2.32
2508 3204 0.779997 AGAGGTGGGCAAGAACCAAT 59.220 50.000 0.00 0.00 40.24 3.16
2509 3205 0.110486 GAGAGGTGGGCAAGAACCAA 59.890 55.000 0.00 0.00 40.24 3.67
2510 3206 1.059584 TGAGAGGTGGGCAAGAACCA 61.060 55.000 0.00 0.00 39.05 3.67
2511 3207 0.110486 TTGAGAGGTGGGCAAGAACC 59.890 55.000 0.00 0.00 36.66 3.62
2512 3208 1.981256 TTTGAGAGGTGGGCAAGAAC 58.019 50.000 0.00 0.00 0.00 3.01
2513 3209 2.746279 TTTTGAGAGGTGGGCAAGAA 57.254 45.000 0.00 0.00 0.00 2.52
2514 3210 2.091885 ACTTTTTGAGAGGTGGGCAAGA 60.092 45.455 0.00 0.00 0.00 3.02
2515 3211 2.310538 ACTTTTTGAGAGGTGGGCAAG 58.689 47.619 0.00 0.00 0.00 4.01
2516 3212 2.430332 CAACTTTTTGAGAGGTGGGCAA 59.570 45.455 0.00 0.00 34.24 4.52
2517 3213 2.031120 CAACTTTTTGAGAGGTGGGCA 58.969 47.619 0.00 0.00 34.24 5.36
2518 3214 1.269778 GCAACTTTTTGAGAGGTGGGC 60.270 52.381 0.00 0.00 34.24 5.36
2519 3215 1.341209 GGCAACTTTTTGAGAGGTGGG 59.659 52.381 0.00 0.00 34.24 4.61
2520 3216 2.031120 TGGCAACTTTTTGAGAGGTGG 58.969 47.619 0.00 0.00 34.24 4.61
2521 3217 3.799281 TTGGCAACTTTTTGAGAGGTG 57.201 42.857 0.00 0.00 34.24 4.00
2522 3218 5.357742 AAATTGGCAACTTTTTGAGAGGT 57.642 34.783 0.00 0.00 34.24 3.85
2523 3219 6.682423 AAAAATTGGCAACTTTTTGAGAGG 57.318 33.333 21.38 0.00 34.26 3.69
2538 3234 5.718146 AAACCAAAAGTTGCCAAAAATTGG 58.282 33.333 12.33 12.33 45.80 3.16
2539 3235 6.400834 GCAAAACCAAAAGTTGCCAAAAATTG 60.401 34.615 0.00 0.00 41.41 2.32
2540 3236 5.636965 GCAAAACCAAAAGTTGCCAAAAATT 59.363 32.000 0.00 0.00 41.41 1.82
2541 3237 5.167121 GCAAAACCAAAAGTTGCCAAAAAT 58.833 33.333 0.00 0.00 41.41 1.82
2542 3238 4.550422 GCAAAACCAAAAGTTGCCAAAAA 58.450 34.783 0.00 0.00 41.41 1.94
2543 3239 4.166187 GCAAAACCAAAAGTTGCCAAAA 57.834 36.364 0.00 0.00 41.41 2.44
2544 3240 3.839051 GCAAAACCAAAAGTTGCCAAA 57.161 38.095 0.00 0.00 41.41 3.28
2596 3292 0.102120 TGGTTCGCTGCCAAAGTTTG 59.898 50.000 8.73 8.73 32.29 2.93
2597 3293 0.820871 TTGGTTCGCTGCCAAAGTTT 59.179 45.000 0.00 0.00 42.39 2.66
2598 3294 2.499214 TTGGTTCGCTGCCAAAGTT 58.501 47.368 0.00 0.00 42.39 2.66
2599 3295 4.251246 TTGGTTCGCTGCCAAAGT 57.749 50.000 0.00 0.00 42.39 2.66
2603 3299 0.607762 TGCTAATTGGTTCGCTGCCA 60.608 50.000 0.00 0.00 0.00 4.92
2604 3300 0.740737 ATGCTAATTGGTTCGCTGCC 59.259 50.000 0.00 0.00 0.00 4.85
2605 3301 2.159393 TGAATGCTAATTGGTTCGCTGC 60.159 45.455 0.00 0.00 0.00 5.25
2606 3302 3.127548 AGTGAATGCTAATTGGTTCGCTG 59.872 43.478 7.23 0.00 39.26 5.18
2607 3303 3.347216 AGTGAATGCTAATTGGTTCGCT 58.653 40.909 3.37 3.37 36.80 4.93
2608 3304 3.764885 AGTGAATGCTAATTGGTTCGC 57.235 42.857 0.00 0.00 0.00 4.70
2609 3305 5.295431 TCAAGTGAATGCTAATTGGTTCG 57.705 39.130 0.00 0.00 0.00 3.95
2610 3306 7.761409 TGTATCAAGTGAATGCTAATTGGTTC 58.239 34.615 0.00 0.00 0.00 3.62
2611 3307 7.148018 CCTGTATCAAGTGAATGCTAATTGGTT 60.148 37.037 0.00 0.00 0.00 3.67
2612 3308 6.319658 CCTGTATCAAGTGAATGCTAATTGGT 59.680 38.462 0.00 0.00 0.00 3.67
2613 3309 6.543465 TCCTGTATCAAGTGAATGCTAATTGG 59.457 38.462 0.00 0.00 0.00 3.16
2614 3310 7.412853 GTCCTGTATCAAGTGAATGCTAATTG 58.587 38.462 0.00 0.00 0.00 2.32
2615 3311 6.543831 GGTCCTGTATCAAGTGAATGCTAATT 59.456 38.462 0.00 0.00 0.00 1.40
2616 3312 6.058183 GGTCCTGTATCAAGTGAATGCTAAT 58.942 40.000 0.00 0.00 0.00 1.73
2617 3313 5.045942 TGGTCCTGTATCAAGTGAATGCTAA 60.046 40.000 0.00 0.00 0.00 3.09
2618 3314 4.469586 TGGTCCTGTATCAAGTGAATGCTA 59.530 41.667 0.00 0.00 0.00 3.49
2619 3315 3.264193 TGGTCCTGTATCAAGTGAATGCT 59.736 43.478 0.00 0.00 0.00 3.79
2620 3316 3.609853 TGGTCCTGTATCAAGTGAATGC 58.390 45.455 0.00 0.00 0.00 3.56
2628 3324 5.497464 TCTTGTCATTGGTCCTGTATCAA 57.503 39.130 0.00 0.00 31.20 2.57
2665 3361 3.054802 AGGGATGATTCTGGTGAAGACAC 60.055 47.826 0.00 0.00 45.27 3.67
2892 3590 0.322187 GCACCGACCAACCCTACAAT 60.322 55.000 0.00 0.00 0.00 2.71
2906 3604 1.330521 CCTATCAATGTTTCGGCACCG 59.669 52.381 1.73 1.73 41.35 4.94
2987 3685 5.359194 ACCAGTCTACATCAATAACCCAG 57.641 43.478 0.00 0.00 0.00 4.45
3077 3775 8.661257 CGTAATCCACACATGTAAACATCTTTA 58.339 33.333 0.00 0.00 33.61 1.85
3102 3800 4.818534 ATGCCTAATATGTGCTCAAACG 57.181 40.909 0.00 0.00 0.00 3.60
3110 3808 8.613060 AAGTCAGACATAATGCCTAATATGTG 57.387 34.615 2.66 0.00 41.53 3.21
3117 3815 7.282585 AGCAAATAAGTCAGACATAATGCCTA 58.717 34.615 17.00 0.00 0.00 3.93
3243 3944 1.068055 CCAGAAAGCAAGCATGTGACC 60.068 52.381 0.00 0.00 0.00 4.02
3281 3983 9.797556 AGTATTTACCAAGACAAAGAAAACAAC 57.202 29.630 0.00 0.00 0.00 3.32
3342 4044 8.724229 CAAAGATTCCATCCCAAAAAGAAAATC 58.276 33.333 0.00 0.00 0.00 2.17
3343 4045 7.666804 CCAAAGATTCCATCCCAAAAAGAAAAT 59.333 33.333 0.00 0.00 0.00 1.82
3455 4174 4.392921 AGTCACACACATATAGACCTGC 57.607 45.455 0.00 0.00 0.00 4.85
3556 4275 6.994421 AGGAAATCAAACTTGTAATGGGTT 57.006 33.333 0.00 0.00 0.00 4.11
3557 4276 6.994421 AAGGAAATCAAACTTGTAATGGGT 57.006 33.333 0.00 0.00 0.00 4.51
3693 4415 5.233050 CACAGCTATCGTTATCAACTGAAGG 59.767 44.000 0.00 0.00 0.00 3.46
3715 4438 1.160137 GGACAGGTCAAGCATCACAC 58.840 55.000 1.41 0.00 0.00 3.82
3751 4474 4.523943 TGCTATGAATTCAAACTGCAGGTT 59.476 37.500 19.93 16.37 40.28 3.50
3753 4476 4.707030 TGCTATGAATTCAAACTGCAGG 57.293 40.909 19.93 0.00 0.00 4.85
3754 4477 5.886992 TGATGCTATGAATTCAAACTGCAG 58.113 37.500 22.53 13.48 32.65 4.41
3755 4478 5.900865 TGATGCTATGAATTCAAACTGCA 57.099 34.783 21.35 21.35 0.00 4.41
3756 4479 6.581542 GCTATGATGCTATGAATTCAAACTGC 59.418 38.462 13.09 13.86 0.00 4.40
3757 4480 7.645402 TGCTATGATGCTATGAATTCAAACTG 58.355 34.615 13.09 4.32 0.00 3.16
3806 4529 4.186159 GGGGTGATGAATGCAGAAAATTG 58.814 43.478 0.00 0.00 0.00 2.32
3983 4710 2.621338 TGCAATCAAGTAAGCTCTCCG 58.379 47.619 0.00 0.00 0.00 4.63
4013 4743 1.611006 TGCTTTGCGCCTACAATTGAA 59.389 42.857 13.59 0.00 38.05 2.69
4021 4751 0.744414 GGAGTCATGCTTTGCGCCTA 60.744 55.000 4.18 0.00 38.05 3.93
4025 4755 0.379669 GATGGGAGTCATGCTTTGCG 59.620 55.000 0.00 0.00 35.97 4.85
4266 5013 3.498397 TCTGAGATTCTGGCGAACAAAAC 59.502 43.478 0.00 0.00 30.67 2.43
4278 5025 5.480073 AGCAAAGACACTACTCTGAGATTCT 59.520 40.000 12.44 2.55 0.00 2.40
4462 5219 0.463620 GTCTCCATCTCTCCACCTGC 59.536 60.000 0.00 0.00 0.00 4.85
4463 5220 1.755959 CTGTCTCCATCTCTCCACCTG 59.244 57.143 0.00 0.00 0.00 4.00
4464 5221 1.360852 ACTGTCTCCATCTCTCCACCT 59.639 52.381 0.00 0.00 0.00 4.00
4465 5222 1.480137 CACTGTCTCCATCTCTCCACC 59.520 57.143 0.00 0.00 0.00 4.61
4467 5224 1.359130 TCCACTGTCTCCATCTCTCCA 59.641 52.381 0.00 0.00 0.00 3.86
4468 5225 2.031120 CTCCACTGTCTCCATCTCTCC 58.969 57.143 0.00 0.00 0.00 3.71
4470 5227 2.358090 CCTCTCCACTGTCTCCATCTCT 60.358 54.545 0.00 0.00 0.00 3.10
4472 5229 1.643286 TCCTCTCCACTGTCTCCATCT 59.357 52.381 0.00 0.00 0.00 2.90
4473 5230 2.151502 TCCTCTCCACTGTCTCCATC 57.848 55.000 0.00 0.00 0.00 3.51
4474 5231 2.630889 TTCCTCTCCACTGTCTCCAT 57.369 50.000 0.00 0.00 0.00 3.41
4475 5232 2.251818 CTTTCCTCTCCACTGTCTCCA 58.748 52.381 0.00 0.00 0.00 3.86
4476 5233 1.552792 CCTTTCCTCTCCACTGTCTCC 59.447 57.143 0.00 0.00 0.00 3.71
4477 5234 1.552792 CCCTTTCCTCTCCACTGTCTC 59.447 57.143 0.00 0.00 0.00 3.36
4478 5235 1.150135 TCCCTTTCCTCTCCACTGTCT 59.850 52.381 0.00 0.00 0.00 3.41
4479 5236 1.552792 CTCCCTTTCCTCTCCACTGTC 59.447 57.143 0.00 0.00 0.00 3.51
4480 5237 1.150135 TCTCCCTTTCCTCTCCACTGT 59.850 52.381 0.00 0.00 0.00 3.55
4481 5238 1.944177 TCTCCCTTTCCTCTCCACTG 58.056 55.000 0.00 0.00 0.00 3.66
4482 5239 2.723530 TTCTCCCTTTCCTCTCCACT 57.276 50.000 0.00 0.00 0.00 4.00
4483 5240 3.615155 CAATTCTCCCTTTCCTCTCCAC 58.385 50.000 0.00 0.00 0.00 4.02
4563 5320 1.153449 TATTCTGCCCGACGCCAAG 60.153 57.895 0.00 0.00 36.24 3.61
4564 5321 1.153449 CTATTCTGCCCGACGCCAA 60.153 57.895 0.00 0.00 36.24 4.52
4565 5322 2.016393 CTCTATTCTGCCCGACGCCA 62.016 60.000 0.00 0.00 36.24 5.69
4566 5323 1.300233 CTCTATTCTGCCCGACGCC 60.300 63.158 0.00 0.00 36.24 5.68
4567 5324 1.951631 GCTCTATTCTGCCCGACGC 60.952 63.158 0.00 0.00 38.31 5.19
4568 5325 0.596083 CAGCTCTATTCTGCCCGACG 60.596 60.000 0.00 0.00 0.00 5.12
4569 5326 0.249657 CCAGCTCTATTCTGCCCGAC 60.250 60.000 0.00 0.00 0.00 4.79
4570 5327 2.032860 GCCAGCTCTATTCTGCCCGA 62.033 60.000 0.00 0.00 0.00 5.14
4571 5328 1.596477 GCCAGCTCTATTCTGCCCG 60.596 63.158 0.00 0.00 0.00 6.13
4579 5336 3.610669 CTCCGCCGCCAGCTCTAT 61.611 66.667 0.00 0.00 40.39 1.98
4601 5358 3.359950 CCATTTTTCTTCTCCCTCCCTG 58.640 50.000 0.00 0.00 0.00 4.45
4602 5359 2.313041 CCCATTTTTCTTCTCCCTCCCT 59.687 50.000 0.00 0.00 0.00 4.20
4635 5392 2.927856 ATGCCACCCACTCACGGA 60.928 61.111 0.00 0.00 0.00 4.69
4637 5394 0.179100 CTAGATGCCACCCACTCACG 60.179 60.000 0.00 0.00 0.00 4.35
4658 5415 3.631686 GCAAGGGGCAATTTTGTCTTTTT 59.368 39.130 0.00 0.00 43.97 1.94
4699 5456 2.025418 GATCGTTTCACGGTGGCGT 61.025 57.895 8.50 2.80 42.81 5.68
4718 5475 1.696832 GGAGAACCTCGATTGCACGC 61.697 60.000 0.00 0.00 0.00 5.34
4734 5491 1.202394 CCTTCAGATCACGCTCTGGAG 60.202 57.143 10.26 10.26 45.12 3.86
4844 5606 2.223433 GCTGAGCATTTGACCTACATGC 60.223 50.000 0.00 0.00 35.48 4.06
4937 5704 6.895756 AGGTGTAGTGTATTATCAACTCTCCA 59.104 38.462 0.00 0.00 0.00 3.86
5009 5776 5.825679 TGGTTTACAAGCACTTACTTCACAT 59.174 36.000 0.00 0.00 33.29 3.21
5017 5784 3.754323 CGGGATTGGTTTACAAGCACTTA 59.246 43.478 0.00 0.00 46.45 2.24
5082 5849 1.938585 CTCAGGTAGGAGGTGACCAA 58.061 55.000 3.63 0.00 38.27 3.67
5103 5870 2.025226 TGGGTTTTCCATGGCCGTATAA 60.025 45.455 6.96 0.00 41.46 0.98
5124 5893 1.900016 GGTCGGGCTTTTTCGGGTT 60.900 57.895 0.00 0.00 0.00 4.11
5221 5996 6.998673 GCCTCTTCCCTAAAATGTACATATGT 59.001 38.462 13.93 13.93 0.00 2.29
5227 6002 4.200092 CAGGCCTCTTCCCTAAAATGTAC 58.800 47.826 0.00 0.00 0.00 2.90
5229 6004 2.024941 CCAGGCCTCTTCCCTAAAATGT 60.025 50.000 0.00 0.00 0.00 2.71
5231 6006 2.242452 GTCCAGGCCTCTTCCCTAAAAT 59.758 50.000 0.00 0.00 0.00 1.82
5260 6035 4.200092 CCCATTAGTAGAAAAGCCTGTCC 58.800 47.826 0.00 0.00 0.00 4.02
5264 6039 2.580783 TGGCCCATTAGTAGAAAAGCCT 59.419 45.455 0.00 0.00 39.90 4.58


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

AutoCloner maintained by Alex Coulton.