Multiple sequence alignment - TraesCS5D01G486500

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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 TraesCS5D01G486500 chr5D 100.000 5320 0 0 1 5320 521678115 521672796 0.000000e+00 9825.0
1 TraesCS5D01G486500 chr5D 88.806 134 14 1 3705 3837 339384441 339384574 4.260000e-36 163.0
2 TraesCS5D01G486500 chr5B 88.545 2846 193 61 7 2774 658071797 658069007 0.000000e+00 3326.0
3 TraesCS5D01G486500 chr5B 90.841 1856 109 30 2774 4605 658069050 658067232 0.000000e+00 2429.0
4 TraesCS5D01G486500 chr5A 85.078 1414 134 34 294 1689 650027907 650026553 0.000000e+00 1371.0
5 TraesCS5D01G486500 chr5A 86.215 1226 122 27 3400 4609 650024778 650023584 0.000000e+00 1284.0
6 TraesCS5D01G486500 chr5A 93.398 727 34 7 4601 5320 442107904 442107185 0.000000e+00 1064.0
7 TraesCS5D01G486500 chr5A 80.383 418 68 11 2455 2865 650026406 650025996 6.690000e-79 305.0
8 TraesCS5D01G486500 chr1B 93.646 724 37 6 1220 1939 313990951 313990233 0.000000e+00 1074.0
9 TraesCS5D01G486500 chr1B 93.213 722 44 2 1220 1939 566333698 566332980 0.000000e+00 1057.0
10 TraesCS5D01G486500 chr1B 92.798 722 47 2 1220 1939 313934538 313933820 0.000000e+00 1040.0
11 TraesCS5D01G486500 chr1B 93.590 234 8 2 1213 1443 566332982 566332753 5.100000e-90 342.0
12 TraesCS5D01G486500 chr1B 93.162 234 8 2 1213 1443 313990235 313990007 2.370000e-88 337.0
13 TraesCS5D01G486500 chr4B 94.247 591 28 3 1352 1939 219450889 219451476 0.000000e+00 898.0
14 TraesCS5D01G486500 chr4B 91.954 87 7 0 3313 3399 270831756 270831670 7.240000e-24 122.0
15 TraesCS5D01G486500 chr6B 93.919 592 29 3 1352 1939 196490669 196490081 0.000000e+00 887.0
16 TraesCS5D01G486500 chr6B 92.045 88 7 0 3314 3401 278674613 278674700 2.010000e-24 124.0
17 TraesCS5D01G486500 chr6B 87.013 77 8 1 5214 5290 418152488 418152562 9.490000e-13 86.1
18 TraesCS5D01G486500 chr4A 93.729 590 29 3 1352 1939 610874372 610873789 0.000000e+00 878.0
19 TraesCS5D01G486500 chr7B 93.704 540 31 3 1352 1891 239169974 239170510 0.000000e+00 806.0
20 TraesCS5D01G486500 chr7B 91.597 238 14 3 1210 1443 239172297 239172532 1.850000e-84 324.0
21 TraesCS5D01G486500 chr7B 94.253 87 5 0 3314 3400 13801939 13801853 3.340000e-27 134.0
22 TraesCS5D01G486500 chr3A 90.049 613 51 8 4597 5202 624940314 624939705 0.000000e+00 785.0
23 TraesCS5D01G486500 chr3A 77.023 618 110 25 3713 4319 600931697 600931101 5.140000e-85 326.0
24 TraesCS5D01G486500 chr3A 88.889 108 12 0 5213 5320 624939234 624939127 3.340000e-27 134.0
25 TraesCS5D01G486500 chr6D 89.689 611 46 11 4601 5202 38536751 38536149 0.000000e+00 763.0
26 TraesCS5D01G486500 chr6D 96.070 229 7 1 1713 1939 65466117 65466345 6.510000e-99 372.0
27 TraesCS5D01G486500 chr6D 89.781 137 13 1 3705 3840 73252394 73252258 1.970000e-39 174.0
28 TraesCS5D01G486500 chr6D 93.182 88 6 0 3314 3401 155601961 155602048 4.320000e-26 130.0
29 TraesCS5D01G486500 chr2A 89.577 614 45 11 4601 5202 662937225 662937831 0.000000e+00 761.0
30 TraesCS5D01G486500 chr2A 89.251 614 47 11 4601 5202 214719708 214719102 0.000000e+00 750.0
31 TraesCS5D01G486500 chr1A 89.560 613 47 12 4601 5202 100367611 100368217 0.000000e+00 761.0
32 TraesCS5D01G486500 chr1A 89.379 612 47 14 4601 5202 53318226 53317623 0.000000e+00 754.0
33 TraesCS5D01G486500 chr1A 91.954 87 7 0 3312 3398 292767904 292767990 7.240000e-24 122.0
34 TraesCS5D01G486500 chr1A 100.000 28 0 0 2382 2409 122307226 122307253 1.000000e-02 52.8
35 TraesCS5D01G486500 chr3D 89.542 612 47 12 4601 5203 581422243 581422846 0.000000e+00 760.0
36 TraesCS5D01G486500 chr3D 80.423 378 60 12 3713 4083 458628658 458628288 5.250000e-70 276.0
37 TraesCS5D01G486500 chr3B 89.379 612 50 11 4601 5202 1267265 1267871 0.000000e+00 756.0
38 TraesCS5D01G486500 chr3B 80.851 376 60 11 3713 4083 605677381 605677013 8.720000e-73 285.0
39 TraesCS5D01G486500 chrUn 92.308 234 11 3 1213 1443 49767129 49766900 5.140000e-85 326.0
40 TraesCS5D01G486500 chrUn 93.103 87 6 0 3314 3400 84439838 84439924 1.560000e-25 128.0
41 TraesCS5D01G486500 chrUn 100.000 28 0 0 2383 2410 12873045 12873072 1.000000e-02 52.8
42 TraesCS5D01G486500 chr4D 89.552 134 13 1 3705 3837 332131721 332131854 9.160000e-38 169.0
43 TraesCS5D01G486500 chr4D 89.524 105 9 2 3295 3398 432765563 432765460 1.200000e-26 132.0
44 TraesCS5D01G486500 chr2D 89.552 134 13 1 3705 3837 147703549 147703682 9.160000e-38 169.0
45 TraesCS5D01G486500 chr2D 88.333 60 4 3 2382 2441 555111876 555111932 9.560000e-08 69.4
46 TraesCS5D01G486500 chr1D 84.516 155 23 1 4166 4319 386164350 386164196 9.230000e-33 152.0
47 TraesCS5D01G486500 chr1D 100.000 28 0 0 2389 2416 298685091 298685064 1.000000e-02 52.8
48 TraesCS5D01G486500 chr1D 100.000 28 0 0 2382 2409 431958019 431958046 1.000000e-02 52.8
49 TraesCS5D01G486500 chr6A 92.045 88 7 0 3314 3401 209391341 209391428 2.010000e-24 124.0
50 TraesCS5D01G486500 chr7D 94.444 36 2 0 2382 2417 459421539 459421574 7.440000e-04 56.5
51 TraesCS5D01G486500 chr7D 94.286 35 2 0 2381 2415 601909884 601909850 3.000000e-03 54.7
52 TraesCS5D01G486500 chr7D 94.286 35 1 1 2382 2415 101559153 101559187 1.000000e-02 52.8


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 TraesCS5D01G486500 chr5D 521672796 521678115 5319 True 9825.000000 9825 100.0000 1 5320 1 chr5D.!!$R1 5319
1 TraesCS5D01G486500 chr5B 658067232 658071797 4565 True 2877.500000 3326 89.6930 7 4605 2 chr5B.!!$R1 4598
2 TraesCS5D01G486500 chr5A 442107185 442107904 719 True 1064.000000 1064 93.3980 4601 5320 1 chr5A.!!$R1 719
3 TraesCS5D01G486500 chr5A 650023584 650027907 4323 True 986.666667 1371 83.8920 294 4609 3 chr5A.!!$R2 4315
4 TraesCS5D01G486500 chr1B 313933820 313934538 718 True 1040.000000 1040 92.7980 1220 1939 1 chr1B.!!$R1 719
5 TraesCS5D01G486500 chr1B 313990007 313990951 944 True 705.500000 1074 93.4040 1213 1939 2 chr1B.!!$R2 726
6 TraesCS5D01G486500 chr1B 566332753 566333698 945 True 699.500000 1057 93.4015 1213 1939 2 chr1B.!!$R3 726
7 TraesCS5D01G486500 chr4B 219450889 219451476 587 False 898.000000 898 94.2470 1352 1939 1 chr4B.!!$F1 587
8 TraesCS5D01G486500 chr6B 196490081 196490669 588 True 887.000000 887 93.9190 1352 1939 1 chr6B.!!$R1 587
9 TraesCS5D01G486500 chr4A 610873789 610874372 583 True 878.000000 878 93.7290 1352 1939 1 chr4A.!!$R1 587
10 TraesCS5D01G486500 chr7B 239169974 239172532 2558 False 565.000000 806 92.6505 1210 1891 2 chr7B.!!$F1 681
11 TraesCS5D01G486500 chr3A 624939127 624940314 1187 True 459.500000 785 89.4690 4597 5320 2 chr3A.!!$R2 723
12 TraesCS5D01G486500 chr3A 600931101 600931697 596 True 326.000000 326 77.0230 3713 4319 1 chr3A.!!$R1 606
13 TraesCS5D01G486500 chr6D 38536149 38536751 602 True 763.000000 763 89.6890 4601 5202 1 chr6D.!!$R1 601
14 TraesCS5D01G486500 chr2A 662937225 662937831 606 False 761.000000 761 89.5770 4601 5202 1 chr2A.!!$F1 601
15 TraesCS5D01G486500 chr2A 214719102 214719708 606 True 750.000000 750 89.2510 4601 5202 1 chr2A.!!$R1 601
16 TraesCS5D01G486500 chr1A 100367611 100368217 606 False 761.000000 761 89.5600 4601 5202 1 chr1A.!!$F1 601
17 TraesCS5D01G486500 chr1A 53317623 53318226 603 True 754.000000 754 89.3790 4601 5202 1 chr1A.!!$R1 601
18 TraesCS5D01G486500 chr3D 581422243 581422846 603 False 760.000000 760 89.5420 4601 5203 1 chr3D.!!$F1 602
19 TraesCS5D01G486500 chr3B 1267265 1267871 606 False 756.000000 756 89.3790 4601 5202 1 chr3B.!!$F1 601

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
911 963 1.298859 CCAAGAGACCTTTTCCGCCG 61.299 60.0 0.00 0.0 0.00 6.46 F
1214 1266 0.179140 CGGGCCAACAAAATCCGATG 60.179 55.0 4.39 0.0 42.94 3.84 F
2218 5168 0.182537 TGGTCAGGTTGTGGTTCAGG 59.817 55.0 0.00 0.0 0.00 3.86 F
2706 5727 0.319211 TGTGACTAGTTGAACCGGCG 60.319 55.0 0.00 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2977 1.127582 GTCGCAGATCAAGTGCTTGTC 59.872 52.381 11.17 8.49 40.67 3.18 R
2943 5965 1.241990 GGGAGAAAACCCGAGCAACC 61.242 60.000 0.00 0.00 40.49 3.77 R
4170 7271 0.818296 AGCACCTCGTCCTACACATC 59.182 55.000 0.00 0.00 0.00 3.06 R
4360 7461 0.033781 GCAAGTTTTCATGGCTGCCA 59.966 50.000 25.65 25.65 38.19 4.92 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
44 45 5.326200 TCTAGAACCTTTTGAGACCGATC 57.674 43.478 0.00 0.00 0.00 3.69
45 46 5.017490 TCTAGAACCTTTTGAGACCGATCT 58.983 41.667 0.00 0.00 38.15 2.75
49 50 5.828328 AGAACCTTTTGAGACCGATCTTTTT 59.172 36.000 0.00 0.00 34.34 1.94
81 82 7.513968 TGTTTCTTGGTTTTCAATTTTCGTTG 58.486 30.769 0.00 0.00 34.45 4.10
222 225 7.850268 AAGTTTTGTGAACATTTGTTTTTGC 57.150 28.000 0.00 0.00 38.56 3.68
225 228 7.917505 AGTTTTGTGAACATTTGTTTTTGCAAA 59.082 25.926 8.05 8.05 41.77 3.68
227 230 5.377358 TGTGAACATTTGTTTTTGCAAACG 58.623 33.333 12.39 0.00 44.76 3.60
284 287 9.474920 TTGATTTTGTGAATAGTTTTCATCCAC 57.525 29.630 0.00 0.00 0.00 4.02
285 288 8.637099 TGATTTTGTGAATAGTTTTCATCCACA 58.363 29.630 0.00 0.00 0.00 4.17
286 289 9.474920 GATTTTGTGAATAGTTTTCATCCACAA 57.525 29.630 0.00 0.00 40.06 3.33
287 290 9.829507 ATTTTGTGAATAGTTTTCATCCACAAA 57.170 25.926 12.02 12.02 45.38 2.83
288 291 8.641499 TTTGTGAATAGTTTTCATCCACAAAC 57.359 30.769 12.02 0.00 43.56 2.93
290 293 7.950512 TGTGAATAGTTTTCATCCACAAACAT 58.049 30.769 0.00 0.00 35.66 2.71
291 294 8.420222 TGTGAATAGTTTTCATCCACAAACATT 58.580 29.630 0.00 0.00 35.66 2.71
292 295 9.260002 GTGAATAGTTTTCATCCACAAACATTT 57.740 29.630 0.00 0.00 35.66 2.32
352 393 9.088512 AGCATTTTACAAAACAATTACGAACAA 57.911 25.926 0.00 0.00 0.00 2.83
370 411 8.986039 ACGAACAATATGTTTTGAAATTTTGC 57.014 26.923 0.00 0.00 41.28 3.68
396 438 8.347035 CACATTTCCTTGAATCAGCAAAATTTT 58.653 29.630 0.00 0.00 0.00 1.82
410 452 8.914654 TCAGCAAAATTTTATTGAATCGACAAG 58.085 29.630 2.44 0.00 33.22 3.16
446 489 7.970384 TGACGAACTTTTTCTATAATTCGCAT 58.030 30.769 4.25 0.00 41.91 4.73
447 490 8.447833 TGACGAACTTTTTCTATAATTCGCATT 58.552 29.630 4.25 0.00 41.91 3.56
479 524 8.931385 AATCCAAGAATATTTGTTCCAAATCG 57.069 30.769 5.53 0.00 0.00 3.34
481 526 8.568676 TCCAAGAATATTTGTTCCAAATCGTA 57.431 30.769 5.53 0.00 0.00 3.43
581 626 6.310956 TCAGTTGCAAGAACATTTTTGAACTG 59.689 34.615 19.87 19.87 39.86 3.16
712 762 3.681593 TCCCGAACAATTTTGTAGAGGG 58.318 45.455 17.62 17.62 44.03 4.30
716 766 5.010213 CCCGAACAATTTTGTAGAGGGAAAA 59.990 40.000 18.36 0.00 44.75 2.29
718 768 6.640907 CCGAACAATTTTGTAGAGGGAAAAAG 59.359 38.462 0.00 0.00 41.31 2.27
761 811 3.360867 ACGAAAATGTGGCCCAATATCA 58.639 40.909 0.00 0.00 0.00 2.15
767 817 5.697082 AATGTGGCCCAATATCACAAAAT 57.303 34.783 0.00 0.00 43.38 1.82
772 823 4.081198 TGGCCCAATATCACAAAATGGAAC 60.081 41.667 0.00 0.00 32.82 3.62
775 826 5.663456 CCCAATATCACAAAATGGAACTGG 58.337 41.667 0.00 0.00 32.82 4.00
838 890 2.263540 GTCGCCGGAGCCAAACTA 59.736 61.111 5.05 0.00 34.57 2.24
865 917 2.757980 TAAACCCTTCGCCCACCTGC 62.758 60.000 0.00 0.00 0.00 4.85
911 963 1.298859 CCAAGAGACCTTTTCCGCCG 61.299 60.000 0.00 0.00 0.00 6.46
912 964 1.671379 AAGAGACCTTTTCCGCCGC 60.671 57.895 0.00 0.00 0.00 6.53
913 965 3.125573 GAGACCTTTTCCGCCGCC 61.126 66.667 0.00 0.00 0.00 6.13
1042 1094 3.696898 CACTCTACATCTCGCCTACAAC 58.303 50.000 0.00 0.00 0.00 3.32
1107 1159 3.443037 CAGAGAGCACCTTCATCTTACG 58.557 50.000 0.00 0.00 0.00 3.18
1127 1179 3.055530 ACGATGTGCTCTTCTGGATTCTT 60.056 43.478 0.00 0.00 0.00 2.52
1170 1222 9.941664 CATGTATGAAATTTGAAGTGGACTATC 57.058 33.333 0.00 0.00 0.00 2.08
1197 1249 0.379669 GTGATCTGCATTGCTTCCGG 59.620 55.000 10.49 0.00 0.00 5.14
1208 1260 1.118356 TGCTTCCGGGCCAACAAAAT 61.118 50.000 4.39 0.00 0.00 1.82
1209 1261 0.389817 GCTTCCGGGCCAACAAAATC 60.390 55.000 4.39 0.00 0.00 2.17
1210 1262 0.246360 CTTCCGGGCCAACAAAATCC 59.754 55.000 4.39 0.00 0.00 3.01
1211 1263 1.528292 TTCCGGGCCAACAAAATCCG 61.528 55.000 4.39 0.00 40.32 4.18
1214 1266 0.179140 CGGGCCAACAAAATCCGATG 60.179 55.000 4.39 0.00 42.94 3.84
1215 1267 0.894835 GGGCCAACAAAATCCGATGT 59.105 50.000 4.39 0.00 0.00 3.06
1217 1269 1.404047 GGCCAACAAAATCCGATGTGG 60.404 52.381 0.00 0.00 40.09 4.17
1258 1310 1.544724 TGGTGGAATTGGCTTAGCAC 58.455 50.000 6.53 0.00 0.00 4.40
1293 1347 3.519510 TCACTAGTAGCATTCAAGCCCTT 59.480 43.478 0.00 0.00 34.23 3.95
1326 1380 4.159857 GCGTTTTACTTGTGTTGTTGACA 58.840 39.130 0.00 0.00 35.42 3.58
1372 1432 5.180117 CACTGTAGTCTGAAACATTCCTTGG 59.820 44.000 0.00 0.00 0.00 3.61
1415 1480 7.992295 TCCACCTTAAATCCTAAGTACCTTTT 58.008 34.615 0.00 0.00 0.00 2.27
1443 1508 1.021968 AGTTTTGCCGTCAGTTGTCC 58.978 50.000 0.00 0.00 0.00 4.02
1444 1509 0.736053 GTTTTGCCGTCAGTTGTCCA 59.264 50.000 0.00 0.00 0.00 4.02
1650 2849 1.271597 CCAAAGGTCCTTGTCCTGAGG 60.272 57.143 4.45 0.00 35.27 3.86
1745 2944 8.352942 CCTAATTTCTGTTCTAGTGCAGTTTTT 58.647 33.333 0.00 9.15 34.57 1.94
1778 2977 3.126514 GCTCATTGGGATATGAAGATGCG 59.873 47.826 0.00 0.00 34.32 4.73
1954 4897 1.280133 CAATGGTCCTTCTCCTGAGCA 59.720 52.381 0.00 0.00 42.50 4.26
1972 4915 3.012518 AGCATGGTTCCAATTTCTCGAG 58.987 45.455 5.93 5.93 0.00 4.04
1984 4927 2.342910 TTCTCGAGCGTGTACCTTTC 57.657 50.000 7.81 0.00 0.00 2.62
1985 4928 1.531423 TCTCGAGCGTGTACCTTTCT 58.469 50.000 7.81 0.00 0.00 2.52
2037 4987 6.213677 TCAACATATCCTATTGTAGTGCGTC 58.786 40.000 0.00 0.00 0.00 5.19
2046 4996 3.653539 TTGTAGTGCGTCTGTGTGTAT 57.346 42.857 0.00 0.00 0.00 2.29
2065 5015 5.182380 GTGTATCTCTAGCTCACTGGGATAC 59.818 48.000 15.90 15.90 37.66 2.24
2174 5124 6.928520 ACTTCATTGAATTGTCCTGGAAATC 58.071 36.000 0.00 0.00 0.00 2.17
2185 5135 6.627087 TGTCCTGGAAATCTAGATTCTGTT 57.373 37.500 18.19 2.71 0.00 3.16
2218 5168 0.182537 TGGTCAGGTTGTGGTTCAGG 59.817 55.000 0.00 0.00 0.00 3.86
2293 5285 6.377146 TGAGCCTTTGTTCTCCAATTTATACC 59.623 38.462 0.00 0.00 31.81 2.73
2294 5286 6.252995 AGCCTTTGTTCTCCAATTTATACCA 58.747 36.000 0.00 0.00 31.81 3.25
2295 5287 6.723977 AGCCTTTGTTCTCCAATTTATACCAA 59.276 34.615 0.00 0.00 31.81 3.67
2314 5306 5.659440 CCAAAGCTTCTTGGCCTTATAAA 57.341 39.130 3.32 0.00 39.55 1.40
2316 5308 6.276091 CCAAAGCTTCTTGGCCTTATAAATC 58.724 40.000 3.32 0.00 39.55 2.17
2337 5329 4.321718 TCCAGCTTCTTGAGAAATGACAG 58.678 43.478 7.02 0.00 33.07 3.51
2377 5369 2.551459 ACAGTGCTGAAGAATTGTCTGC 59.449 45.455 6.17 9.46 39.60 4.26
2409 5401 5.222278 ACTCCCTCCGTCCCATAATATAT 57.778 43.478 0.00 0.00 0.00 0.86
2410 5402 6.351317 ACTCCCTCCGTCCCATAATATATA 57.649 41.667 0.00 0.00 0.00 0.86
2411 5403 6.935036 ACTCCCTCCGTCCCATAATATATAT 58.065 40.000 0.00 0.00 0.00 0.86
2412 5404 6.782988 ACTCCCTCCGTCCCATAATATATATG 59.217 42.308 0.00 0.00 0.00 1.78
2413 5405 6.689561 TCCCTCCGTCCCATAATATATATGT 58.310 40.000 0.00 0.00 0.00 2.29
2447 5450 5.080969 ACGTTCATATATTATGGGACGGG 57.919 43.478 18.88 4.11 35.20 5.28
2611 5628 0.321919 TGCTCATGGCTTGACAGACC 60.322 55.000 0.00 0.00 42.39 3.85
2620 5637 3.646162 TGGCTTGACAGACCTCTCTTTTA 59.354 43.478 0.00 0.00 0.00 1.52
2630 5647 5.046304 CAGACCTCTCTTTTATTCACTGGGA 60.046 44.000 0.00 0.00 0.00 4.37
2637 5654 9.284968 CTCTCTTTTATTCACTGGGACTTTTTA 57.715 33.333 0.00 0.00 0.00 1.52
2706 5727 0.319211 TGTGACTAGTTGAACCGGCG 60.319 55.000 0.00 0.00 0.00 6.46
2745 5766 9.959721 ATGTCAACAATGGTATACTTCTTTAGT 57.040 29.630 2.25 0.00 41.04 2.24
2746 5767 9.787435 TGTCAACAATGGTATACTTCTTTAGTT 57.213 29.630 2.25 0.00 38.33 2.24
2769 5790 8.976353 AGTTTAATATGGGTGTATTTGCATTCA 58.024 29.630 0.00 0.00 0.00 2.57
2770 5791 9.762933 GTTTAATATGGGTGTATTTGCATTCAT 57.237 29.630 0.00 0.00 0.00 2.57
2771 5792 9.979578 TTTAATATGGGTGTATTTGCATTCATC 57.020 29.630 0.00 0.00 0.00 2.92
2772 5793 7.844493 AATATGGGTGTATTTGCATTCATCT 57.156 32.000 0.00 0.00 0.00 2.90
2777 5798 5.009010 GGGTGTATTTGCATTCATCTACTGG 59.991 44.000 0.00 0.00 0.00 4.00
2814 5835 8.978874 TTAGTATGGATGTAACTGCATTCATT 57.021 30.769 6.85 0.00 41.05 2.57
2820 5841 7.482474 TGGATGTAACTGCATTCATTTATGTG 58.518 34.615 0.00 0.00 29.94 3.21
2845 5866 2.143122 TCTGCTTGTAGTTTTGCCTCG 58.857 47.619 0.00 0.00 0.00 4.63
2943 5965 3.495377 TGTCTTCGTTATTTTGTCCGGTG 59.505 43.478 0.00 0.00 0.00 4.94
3011 6054 7.040409 AGCCTTTGTTTTCCACTTATACTTCAG 60.040 37.037 0.00 0.00 0.00 3.02
3026 6069 3.285484 ACTTCAGCTTCTTGGCCATATG 58.715 45.455 6.09 0.00 0.00 1.78
3055 6098 7.453393 TCAGAGTGAGAAGTTTATTCCAATGT 58.547 34.615 0.00 0.00 0.00 2.71
3176 6225 8.971073 AGAAGTGCTTTAAATTGGCTAATGTAT 58.029 29.630 0.00 0.00 0.00 2.29
3201 6250 5.133221 AGAAACTGAGGTTGTAGCAAACAT 58.867 37.500 0.00 0.00 38.10 2.71
3335 6412 6.021030 ACTACACCCTCTGTTCCTAAATGTA 58.979 40.000 0.00 0.00 33.91 2.29
3336 6413 5.836024 ACACCCTCTGTTCCTAAATGTAA 57.164 39.130 0.00 0.00 0.00 2.41
3337 6414 5.805728 ACACCCTCTGTTCCTAAATGTAAG 58.194 41.667 0.00 0.00 0.00 2.34
3340 6417 6.540189 CACCCTCTGTTCCTAAATGTAAGATG 59.460 42.308 0.00 0.00 0.00 2.90
3341 6418 6.058183 CCCTCTGTTCCTAAATGTAAGATGG 58.942 44.000 0.00 0.00 0.00 3.51
3344 6421 7.611855 CCTCTGTTCCTAAATGTAAGATGGTTT 59.388 37.037 0.00 0.00 0.00 3.27
3345 6422 8.335532 TCTGTTCCTAAATGTAAGATGGTTTG 57.664 34.615 0.00 0.00 0.00 2.93
3346 6423 7.393234 TCTGTTCCTAAATGTAAGATGGTTTGG 59.607 37.037 0.00 0.00 0.00 3.28
3347 6424 6.071616 TGTTCCTAAATGTAAGATGGTTTGGC 60.072 38.462 0.00 0.00 0.00 4.52
3348 6425 5.575157 TCCTAAATGTAAGATGGTTTGGCA 58.425 37.500 0.00 0.00 0.00 4.92
3349 6426 5.652014 TCCTAAATGTAAGATGGTTTGGCAG 59.348 40.000 0.00 0.00 0.00 4.85
3374 6465 7.986889 AGTTCAATTTAAACTGCCAAAATGTCT 59.013 29.630 2.85 0.00 35.68 3.41
3437 6528 5.493133 TGACGTTAATTGCTTGTCAAGTT 57.507 34.783 14.03 3.63 38.22 2.66
3464 6555 7.596494 TGAAAAATTGTTTCATTTTTGTGGCA 58.404 26.923 8.49 0.00 39.29 4.92
3480 6571 1.062880 TGGCAAGTTGAAACGACGAAC 59.937 47.619 7.16 0.00 0.00 3.95
3482 6573 1.005766 GCAAGTTGAAACGACGAACGA 60.006 47.619 7.16 0.00 45.77 3.85
3483 6574 2.535335 GCAAGTTGAAACGACGAACGAA 60.535 45.455 7.16 0.00 45.77 3.85
3549 6640 6.873997 TGGATGTATTCACGTTCATCTACTT 58.126 36.000 0.00 0.00 37.44 2.24
3555 6646 9.999009 TGTATTCACGTTCATCTACTTTACTAG 57.001 33.333 0.00 0.00 0.00 2.57
3602 6693 3.926821 TTCATGTACTGCAGTCGTGTA 57.073 42.857 25.56 16.20 0.00 2.90
3629 6720 8.651391 TTGTAGTTTTGAGTCGATACTTTTCA 57.349 30.769 8.57 4.65 35.56 2.69
3696 6787 7.792374 TCTCATATGTTTCCTGAATGCTAAC 57.208 36.000 1.90 0.00 0.00 2.34
3912 7009 2.359975 GCCTGTTTCCTCCGTGGG 60.360 66.667 0.00 0.00 36.20 4.61
3914 7011 1.991230 CCTGTTTCCTCCGTGGGAT 59.009 57.895 0.00 0.00 35.07 3.85
3950 7047 3.424302 CGCGAAACTGCTTGCACTTTATA 60.424 43.478 0.00 0.00 0.00 0.98
3990 7087 1.889573 GCCCAACTCTGCTATCCGC 60.890 63.158 0.00 0.00 39.77 5.54
4074 7171 2.151202 GGTTGCCTGAACTTCATCGAA 58.849 47.619 0.00 0.00 34.66 3.71
4083 7180 5.641209 CCTGAACTTCATCGAAGAGAATGTT 59.359 40.000 10.58 1.88 43.63 2.71
4087 7184 7.542477 TGAACTTCATCGAAGAGAATGTTAGTC 59.458 37.037 10.58 0.00 43.63 2.59
4102 7199 8.763601 AGAATGTTAGTCTACTATTTCTGCCTT 58.236 33.333 8.52 0.00 0.00 4.35
4105 7202 6.439375 TGTTAGTCTACTATTTCTGCCTTCCA 59.561 38.462 0.00 0.00 0.00 3.53
4114 7211 2.938354 CTGCCTTCCAGAACACCAG 58.062 57.895 0.00 0.00 44.64 4.00
4125 7222 3.748048 CCAGAACACCAGTGTCAACTATG 59.252 47.826 3.49 0.00 44.13 2.23
4128 7225 5.121298 CAGAACACCAGTGTCAACTATGATG 59.879 44.000 3.49 0.00 44.13 3.07
4129 7226 4.623932 ACACCAGTGTCAACTATGATGT 57.376 40.909 0.00 0.00 40.24 3.06
4130 7227 4.569943 ACACCAGTGTCAACTATGATGTC 58.430 43.478 0.00 0.00 40.24 3.06
4131 7228 4.040339 ACACCAGTGTCAACTATGATGTCA 59.960 41.667 0.00 0.00 40.24 3.58
4170 7271 1.337728 TGCTAACACTGTCCGTGATGG 60.338 52.381 0.93 0.00 46.81 3.51
4323 7424 3.054361 GGAGAAGCCCAGATCCTAAAACA 60.054 47.826 0.00 0.00 0.00 2.83
4341 7442 0.182299 CAGCTCCTCCCCATTCTTCC 59.818 60.000 0.00 0.00 0.00 3.46
4342 7443 0.253347 AGCTCCTCCCCATTCTTCCA 60.253 55.000 0.00 0.00 0.00 3.53
4343 7444 0.625849 GCTCCTCCCCATTCTTCCAA 59.374 55.000 0.00 0.00 0.00 3.53
4344 7445 1.005924 GCTCCTCCCCATTCTTCCAAA 59.994 52.381 0.00 0.00 0.00 3.28
4345 7446 2.947695 GCTCCTCCCCATTCTTCCAAAG 60.948 54.545 0.00 0.00 0.00 2.77
4346 7447 2.310052 CTCCTCCCCATTCTTCCAAAGT 59.690 50.000 0.00 0.00 0.00 2.66
4347 7448 2.721906 TCCTCCCCATTCTTCCAAAGTT 59.278 45.455 0.00 0.00 0.00 2.66
4348 7449 3.092301 CCTCCCCATTCTTCCAAAGTTC 58.908 50.000 0.00 0.00 0.00 3.01
4358 7459 6.579666 TTCTTCCAAAGTTCCAAGATCATG 57.420 37.500 0.00 0.00 0.00 3.07
4360 7461 4.387026 TCCAAAGTTCCAAGATCATGGT 57.613 40.909 16.26 0.00 41.46 3.55
4484 7585 8.674607 CAAGTTTCAGTTTCTACAGTAAACCTT 58.325 33.333 0.00 0.00 37.51 3.50
4518 7620 4.702247 TTTACATGTATGCGCATCGTAC 57.298 40.909 29.11 20.23 37.62 3.67
4569 7675 5.419155 GCTCCTGTTATCCTTTTTAGCCTTT 59.581 40.000 0.00 0.00 0.00 3.11
4571 7677 7.285629 GCTCCTGTTATCCTTTTTAGCCTTTAT 59.714 37.037 0.00 0.00 0.00 1.40
4579 7685 8.879427 ATCCTTTTTAGCCTTTATTACTGTGT 57.121 30.769 0.00 0.00 0.00 3.72
4582 7688 7.328493 CCTTTTTAGCCTTTATTACTGTGTTGC 59.672 37.037 0.00 0.00 0.00 4.17
4724 7836 3.941629 TGCCACTTATCCTCCTTCCTAT 58.058 45.455 0.00 0.00 0.00 2.57
4737 7849 2.483889 CCTTCCTATCCTTCTCAACGGC 60.484 54.545 0.00 0.00 0.00 5.68
4882 8000 9.962783 GCAATTGCTAATAGATGATTTCTTTCT 57.037 29.630 23.21 0.00 35.49 2.52
4976 8094 4.029625 CGTGCGTTATTGATTAAACTTGCG 60.030 41.667 0.00 0.00 0.00 4.85
5243 8829 3.181452 TGTGCTTCATGGCATATGCTCTA 60.181 43.478 26.12 13.85 44.34 2.43
5277 8863 5.191323 AGTGTCTTCCATCATCCAAGAGATT 59.809 40.000 0.00 0.00 30.59 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.675641 CCAACCTTCCCGAAGCCAG 60.676 63.158 0.00 0.00 37.11 4.85
5 6 0.250770 AGAACCAACCTTCCCGAAGC 60.251 55.000 0.00 0.00 37.11 3.86
6 7 2.565834 TCTAGAACCAACCTTCCCGAAG 59.434 50.000 0.00 0.00 38.14 3.79
7 8 2.612000 TCTAGAACCAACCTTCCCGAA 58.388 47.619 0.00 0.00 0.00 4.30
8 9 2.301009 GTTCTAGAACCAACCTTCCCGA 59.699 50.000 22.74 0.00 35.36 5.14
9 10 2.696506 GTTCTAGAACCAACCTTCCCG 58.303 52.381 22.74 0.00 35.36 5.14
33 34 6.488683 ACAAATACCAAAAAGATCGGTCTCAA 59.511 34.615 0.00 0.00 32.15 3.02
34 35 6.001460 ACAAATACCAAAAAGATCGGTCTCA 58.999 36.000 0.00 0.00 32.15 3.27
40 41 7.651704 ACCAAGAAACAAATACCAAAAAGATCG 59.348 33.333 0.00 0.00 0.00 3.69
44 45 9.767684 GAAAACCAAGAAACAAATACCAAAAAG 57.232 29.630 0.00 0.00 0.00 2.27
45 46 9.284968 TGAAAACCAAGAAACAAATACCAAAAA 57.715 25.926 0.00 0.00 0.00 1.94
49 50 9.454859 AAATTGAAAACCAAGAAACAAATACCA 57.545 25.926 0.00 0.00 38.31 3.25
259 262 8.637099 TGTGGATGAAAACTATTCACAAAATCA 58.363 29.630 0.00 0.00 40.22 2.57
265 268 7.340122 TGTTTGTGGATGAAAACTATTCACA 57.660 32.000 0.00 0.00 41.16 3.58
266 269 8.816640 AATGTTTGTGGATGAAAACTATTCAC 57.183 30.769 0.00 0.00 37.22 3.18
324 362 9.909043 GTTCGTAATTGTTTTGTAAAATGCTTT 57.091 25.926 0.00 0.00 0.00 3.51
370 411 7.429636 AATTTTGCTGATTCAAGGAAATGTG 57.570 32.000 0.00 0.00 37.34 3.21
420 463 7.970384 TGCGAATTATAGAAAAAGTTCGTCAT 58.030 30.769 7.08 0.00 40.17 3.06
421 464 7.354025 TGCGAATTATAGAAAAAGTTCGTCA 57.646 32.000 7.08 3.68 40.17 4.35
422 465 8.822105 AATGCGAATTATAGAAAAAGTTCGTC 57.178 30.769 7.08 1.52 40.17 4.20
544 589 4.329528 TCTTGCAACTGAAAACATGTTTGC 59.670 37.500 23.93 22.26 32.36 3.68
689 739 5.190132 TCCCTCTACAAAATTGTTCGGGATA 59.810 40.000 18.23 5.70 41.02 2.59
761 811 5.338300 GGCCATATTTCCAGTTCCATTTTGT 60.338 40.000 0.00 0.00 0.00 2.83
767 817 1.643286 TGGGCCATATTTCCAGTTCCA 59.357 47.619 0.00 0.00 0.00 3.53
772 823 4.768968 CCTCTATTTGGGCCATATTTCCAG 59.231 45.833 14.81 6.48 31.59 3.86
775 826 4.790765 GCCTCTATTTGGGCCATATTTC 57.209 45.455 14.81 0.00 42.30 2.17
838 890 0.177373 GCGAAGGGTTTATCGGAGGT 59.823 55.000 0.00 0.00 39.38 3.85
865 917 1.540367 TTGGAGGTGGGTAGGTGGG 60.540 63.158 0.00 0.00 0.00 4.61
866 918 0.840722 ACTTGGAGGTGGGTAGGTGG 60.841 60.000 0.00 0.00 0.00 4.61
867 919 0.613777 GACTTGGAGGTGGGTAGGTG 59.386 60.000 0.00 0.00 0.00 4.00
868 920 0.492276 AGACTTGGAGGTGGGTAGGT 59.508 55.000 0.00 0.00 0.00 3.08
869 921 1.196012 GAGACTTGGAGGTGGGTAGG 58.804 60.000 0.00 0.00 0.00 3.18
870 922 1.196012 GGAGACTTGGAGGTGGGTAG 58.804 60.000 0.00 0.00 0.00 3.18
871 923 0.490017 TGGAGACTTGGAGGTGGGTA 59.510 55.000 0.00 0.00 0.00 3.69
872 924 0.401395 TTGGAGACTTGGAGGTGGGT 60.401 55.000 0.00 0.00 0.00 4.51
994 1046 7.013834 AGAAAGTTAAATTACCCCATGTTGGA 58.986 34.615 5.57 0.00 40.96 3.53
1042 1094 3.753070 GAACGGAGTAGCGCGGGAG 62.753 68.421 8.83 0.00 45.00 4.30
1107 1159 4.332268 GTCAAGAATCCAGAAGAGCACATC 59.668 45.833 0.00 0.00 0.00 3.06
1170 1222 4.127907 AGCAATGCAGATCACTACTCATG 58.872 43.478 8.35 0.00 0.00 3.07
1197 1249 1.404047 CCACATCGGATTTTGTTGGCC 60.404 52.381 0.00 0.00 36.56 5.36
1208 1260 3.500680 GCTAAAACTCAAACCACATCGGA 59.499 43.478 0.00 0.00 38.63 4.55
1209 1261 3.502211 AGCTAAAACTCAAACCACATCGG 59.498 43.478 0.00 0.00 42.50 4.18
1210 1262 4.749245 AGCTAAAACTCAAACCACATCG 57.251 40.909 0.00 0.00 0.00 3.84
1211 1263 5.831997 ACAAGCTAAAACTCAAACCACATC 58.168 37.500 0.00 0.00 0.00 3.06
1214 1266 8.539674 CATTTTACAAGCTAAAACTCAAACCAC 58.460 33.333 0.00 0.00 30.38 4.16
1215 1267 7.708752 CCATTTTACAAGCTAAAACTCAAACCA 59.291 33.333 0.00 0.00 30.38 3.67
1217 1269 8.539674 CACCATTTTACAAGCTAAAACTCAAAC 58.460 33.333 0.00 0.00 30.38 2.93
1293 1347 4.336993 ACAAGTAAAACGCAAAGACCATCA 59.663 37.500 0.00 0.00 0.00 3.07
1326 1380 6.932960 AGTGTTGCCTCGTTTAATTAACTACT 59.067 34.615 0.00 0.00 34.46 2.57
1745 2944 7.675619 TCATATCCCAATGAGCTAGAGATACAA 59.324 37.037 0.00 0.00 32.18 2.41
1778 2977 1.127582 GTCGCAGATCAAGTGCTTGTC 59.872 52.381 11.17 8.49 40.67 3.18
1910 4853 4.511082 GTCGTCACTACTCACTAGGTATCC 59.489 50.000 0.00 0.00 0.00 2.59
1954 4897 2.009774 CGCTCGAGAAATTGGAACCAT 58.990 47.619 18.75 0.00 0.00 3.55
1972 4915 3.806625 TGGGTATAGAAAGGTACACGC 57.193 47.619 0.00 0.00 0.00 5.34
1984 4927 4.020751 AGTGCAGCTGACATATGGGTATAG 60.021 45.833 20.43 0.00 0.00 1.31
1985 4928 3.903714 AGTGCAGCTGACATATGGGTATA 59.096 43.478 20.43 0.00 0.00 1.47
2037 4987 4.202000 CCAGTGAGCTAGAGATACACACAG 60.202 50.000 0.00 0.00 34.47 3.66
2046 4996 2.438392 TCGTATCCCAGTGAGCTAGAGA 59.562 50.000 0.00 0.00 0.00 3.10
2146 5096 7.395190 TCCAGGACAATTCAATGAAGTAATG 57.605 36.000 1.10 1.16 0.00 1.90
2185 5135 6.549364 ACAACCTGACCAAATAATGAAGACAA 59.451 34.615 0.00 0.00 0.00 3.18
2293 5285 6.127366 TGGATTTATAAGGCCAAGAAGCTTTG 60.127 38.462 5.01 0.00 33.62 2.77
2294 5286 5.957774 TGGATTTATAAGGCCAAGAAGCTTT 59.042 36.000 5.01 0.00 35.97 3.51
2295 5287 5.518865 TGGATTTATAAGGCCAAGAAGCTT 58.481 37.500 5.01 0.00 0.00 3.74
2314 5306 4.914983 TGTCATTTCTCAAGAAGCTGGAT 58.085 39.130 0.00 0.00 35.21 3.41
2316 5308 3.119919 GCTGTCATTTCTCAAGAAGCTGG 60.120 47.826 0.00 0.00 35.21 4.85
2337 5329 6.524586 GCACTGTATTTTAAATCACACTGAGC 59.475 38.462 0.00 0.00 0.00 4.26
2372 5364 2.362717 AGGGAGTATTTAGCTCGCAGAC 59.637 50.000 11.00 0.00 44.93 3.51
2377 5369 1.955080 ACGGAGGGAGTATTTAGCTCG 59.045 52.381 0.00 0.00 34.00 5.03
2447 5450 4.501400 GGTGCATGCAAATAAATACTCCCC 60.501 45.833 24.58 10.72 0.00 4.81
2466 5469 4.503741 TTAAAGCAGTTCTTGATGGTGC 57.496 40.909 0.00 0.00 34.67 5.01
2598 5615 1.722034 AAGAGAGGTCTGTCAAGCCA 58.278 50.000 0.00 0.00 31.37 4.75
2600 5617 5.934625 TGAATAAAAGAGAGGTCTGTCAAGC 59.065 40.000 0.00 0.00 31.37 4.01
2611 5628 7.751768 AAAAGTCCCAGTGAATAAAAGAGAG 57.248 36.000 0.00 0.00 0.00 3.20
2652 5673 8.260114 AGAATTTTCAAGACTTGACAACCAATT 58.740 29.630 17.52 14.82 39.87 2.32
2691 5712 2.073816 CAATTCGCCGGTTCAACTAGT 58.926 47.619 1.90 0.00 0.00 2.57
2743 5764 8.976353 TGAATGCAAATACACCCATATTAAACT 58.024 29.630 0.00 0.00 0.00 2.66
2744 5765 9.762933 ATGAATGCAAATACACCCATATTAAAC 57.237 29.630 0.00 0.00 0.00 2.01
2745 5766 9.979578 GATGAATGCAAATACACCCATATTAAA 57.020 29.630 0.00 0.00 0.00 1.52
2746 5767 9.365906 AGATGAATGCAAATACACCCATATTAA 57.634 29.630 0.00 0.00 0.00 1.40
2747 5768 8.938801 AGATGAATGCAAATACACCCATATTA 57.061 30.769 0.00 0.00 0.00 0.98
2748 5769 7.844493 AGATGAATGCAAATACACCCATATT 57.156 32.000 0.00 0.00 0.00 1.28
2749 5770 8.166061 AGTAGATGAATGCAAATACACCCATAT 58.834 33.333 0.00 0.00 0.00 1.78
2750 5771 7.445096 CAGTAGATGAATGCAAATACACCCATA 59.555 37.037 0.00 0.00 0.00 2.74
2751 5772 6.263842 CAGTAGATGAATGCAAATACACCCAT 59.736 38.462 0.00 0.00 0.00 4.00
2752 5773 5.589855 CAGTAGATGAATGCAAATACACCCA 59.410 40.000 0.00 0.00 0.00 4.51
2753 5774 5.009010 CCAGTAGATGAATGCAAATACACCC 59.991 44.000 0.00 0.00 0.00 4.61
2754 5775 5.822519 TCCAGTAGATGAATGCAAATACACC 59.177 40.000 0.00 0.00 0.00 4.16
2755 5776 6.540189 AGTCCAGTAGATGAATGCAAATACAC 59.460 38.462 0.00 0.00 0.00 2.90
2756 5777 6.653020 AGTCCAGTAGATGAATGCAAATACA 58.347 36.000 0.00 0.00 0.00 2.29
2757 5778 8.662781 TTAGTCCAGTAGATGAATGCAAATAC 57.337 34.615 0.00 0.00 0.00 1.89
2758 5779 9.851686 AATTAGTCCAGTAGATGAATGCAAATA 57.148 29.630 0.00 0.00 0.00 1.40
2759 5780 8.757982 AATTAGTCCAGTAGATGAATGCAAAT 57.242 30.769 0.00 0.00 0.00 2.32
2760 5781 7.828717 TGAATTAGTCCAGTAGATGAATGCAAA 59.171 33.333 0.00 0.00 0.00 3.68
2761 5782 7.337938 TGAATTAGTCCAGTAGATGAATGCAA 58.662 34.615 0.00 0.00 0.00 4.08
2762 5783 6.888105 TGAATTAGTCCAGTAGATGAATGCA 58.112 36.000 0.00 0.00 0.00 3.96
2763 5784 7.792374 TTGAATTAGTCCAGTAGATGAATGC 57.208 36.000 0.00 0.00 0.00 3.56
2814 5835 5.420725 ACTACAAGCAGATCACCACATAA 57.579 39.130 0.00 0.00 0.00 1.90
2820 5841 3.366374 GGCAAAACTACAAGCAGATCACC 60.366 47.826 0.00 0.00 0.00 4.02
2928 5950 2.295070 AGCAACCACCGGACAAAATAAC 59.705 45.455 9.46 0.00 0.00 1.89
2935 5957 4.308458 CCGAGCAACCACCGGACA 62.308 66.667 9.46 0.00 45.58 4.02
2943 5965 1.241990 GGGAGAAAACCCGAGCAACC 61.242 60.000 0.00 0.00 40.49 3.77
3011 6054 2.363038 TGAATGCATATGGCCAAGAAGC 59.637 45.455 10.96 12.85 43.89 3.86
3026 6069 6.372659 TGGAATAAACTTCTCACTCTGAATGC 59.627 38.462 0.00 0.00 0.00 3.56
3067 6110 7.621428 ATCACACTGACCTTCATAAAATCTG 57.379 36.000 0.00 0.00 0.00 2.90
3101 6145 4.210955 GCTCACAGATAACTATTCAGCTGC 59.789 45.833 9.47 0.00 0.00 5.25
3176 6225 6.116806 TGTTTGCTACAACCTCAGTTTCTTA 58.883 36.000 0.00 0.00 32.45 2.10
3177 6226 4.947388 TGTTTGCTACAACCTCAGTTTCTT 59.053 37.500 0.00 0.00 32.45 2.52
3178 6227 4.523083 TGTTTGCTACAACCTCAGTTTCT 58.477 39.130 0.00 0.00 32.45 2.52
3179 6228 4.893424 TGTTTGCTACAACCTCAGTTTC 57.107 40.909 0.00 0.00 32.45 2.78
3180 6229 8.677300 CATATATGTTTGCTACAACCTCAGTTT 58.323 33.333 4.43 0.00 40.89 2.66
3201 6250 9.321532 ACATTACTGAGTAATACAGCCCATATA 57.678 33.333 16.73 0.00 36.70 0.86
3277 6354 1.625818 GAGGTCTTTCAAGCCCTGAGA 59.374 52.381 0.00 0.00 33.87 3.27
3335 6412 4.961438 AATTGAACTGCCAAACCATCTT 57.039 36.364 0.00 0.00 0.00 2.40
3336 6413 4.961438 AAATTGAACTGCCAAACCATCT 57.039 36.364 0.00 0.00 0.00 2.90
3337 6414 6.705825 AGTTTAAATTGAACTGCCAAACCATC 59.294 34.615 2.22 0.00 36.08 3.51
3340 6417 6.285790 CAGTTTAAATTGAACTGCCAAACC 57.714 37.500 15.89 0.00 45.02 3.27
3348 6425 7.986889 AGACATTTTGGCAGTTTAAATTGAACT 59.013 29.630 14.30 0.00 37.82 3.01
3349 6426 8.141835 AGACATTTTGGCAGTTTAAATTGAAC 57.858 30.769 14.30 6.84 0.00 3.18
3413 6504 5.885881 ACTTGACAAGCAATTAACGTCAAA 58.114 33.333 15.24 0.00 43.73 2.69
3416 6507 5.621228 CAGAACTTGACAAGCAATTAACGTC 59.379 40.000 15.24 0.04 35.59 4.34
3437 6528 7.967303 GCCACAAAAATGAAACAATTTTTCAGA 59.033 29.630 15.85 1.45 44.16 3.27
3464 6555 3.995412 TTTCGTTCGTCGTTTCAACTT 57.005 38.095 0.00 0.00 40.80 2.66
3555 6646 8.178964 TGCAGTTACATCCGTATTAAATTGAAC 58.821 33.333 0.00 0.00 0.00 3.18
3597 6688 4.971830 TCGACTCAAAACTACAAGTACACG 59.028 41.667 0.00 0.00 0.00 4.49
3602 6693 8.658499 AAAAGTATCGACTCAAAACTACAAGT 57.342 30.769 0.00 0.00 33.58 3.16
3629 6720 3.686691 GCTCCAGCTTGAACATTCCCTAT 60.687 47.826 0.00 0.00 38.21 2.57
3658 6749 9.162764 GAAACATATGAGAACAAGCTAAAGGTA 57.837 33.333 10.38 0.00 0.00 3.08
3659 6750 7.121315 GGAAACATATGAGAACAAGCTAAAGGT 59.879 37.037 10.38 0.00 0.00 3.50
3660 6751 7.337942 AGGAAACATATGAGAACAAGCTAAAGG 59.662 37.037 10.38 0.00 0.00 3.11
3912 7009 6.841286 CAGTTTCGCGTCAGTTATCAATTATC 59.159 38.462 5.77 0.00 0.00 1.75
3914 7011 5.445407 GCAGTTTCGCGTCAGTTATCAATTA 60.445 40.000 5.77 0.00 0.00 1.40
3990 7087 2.661537 TGGACACGAGCGCACTTG 60.662 61.111 11.47 10.43 0.00 3.16
4074 7171 8.417884 GGCAGAAATAGTAGACTAACATTCTCT 58.582 37.037 10.45 0.00 32.53 3.10
4083 7180 6.432581 TCTGGAAGGCAGAAATAGTAGACTA 58.567 40.000 0.00 0.00 0.00 2.59
4087 7184 5.582665 GTGTTCTGGAAGGCAGAAATAGTAG 59.417 44.000 0.00 0.00 39.96 2.57
4102 7199 1.837439 AGTTGACACTGGTGTTCTGGA 59.163 47.619 7.82 0.00 45.05 3.86
4105 7202 4.955811 TCATAGTTGACACTGGTGTTCT 57.044 40.909 7.82 9.25 45.05 3.01
4110 7207 4.563580 GGTGACATCATAGTTGACACTGGT 60.564 45.833 0.00 0.00 38.96 4.00
4111 7208 3.935203 GGTGACATCATAGTTGACACTGG 59.065 47.826 0.00 0.00 38.96 4.00
4114 7211 3.270877 GGGGTGACATCATAGTTGACAC 58.729 50.000 0.00 0.00 38.47 3.67
4170 7271 0.818296 AGCACCTCGTCCTACACATC 59.182 55.000 0.00 0.00 0.00 3.06
4235 7336 1.147376 CACCTTGAACCGGACACCA 59.853 57.895 9.46 0.00 0.00 4.17
4323 7424 0.253347 TGGAAGAATGGGGAGGAGCT 60.253 55.000 0.00 0.00 0.00 4.09
4341 7442 3.367703 GCCACCATGATCTTGGAACTTTG 60.368 47.826 29.18 17.80 39.25 2.77
4342 7443 2.827921 GCCACCATGATCTTGGAACTTT 59.172 45.455 29.18 8.05 39.25 2.66
4343 7444 2.225091 TGCCACCATGATCTTGGAACTT 60.225 45.455 29.18 8.39 39.25 2.66
4344 7445 1.355381 TGCCACCATGATCTTGGAACT 59.645 47.619 29.18 8.73 39.25 3.01
4345 7446 1.747355 CTGCCACCATGATCTTGGAAC 59.253 52.381 29.18 18.69 39.25 3.62
4346 7447 1.956636 GCTGCCACCATGATCTTGGAA 60.957 52.381 29.18 13.31 39.25 3.53
4347 7448 0.394762 GCTGCCACCATGATCTTGGA 60.395 55.000 29.18 9.95 39.25 3.53
4348 7449 1.389609 GGCTGCCACCATGATCTTGG 61.390 60.000 22.73 22.73 42.82 3.61
4358 7459 0.681175 AAGTTTTCATGGCTGCCACC 59.319 50.000 25.99 7.78 35.80 4.61
4360 7461 0.033781 GCAAGTTTTCATGGCTGCCA 59.966 50.000 25.65 25.65 38.19 4.92
4502 7604 1.139989 GCAGTACGATGCGCATACAT 58.860 50.000 25.40 14.10 36.28 2.29
4518 7620 4.778842 GGTACGTCAAATATCACAGCAG 57.221 45.455 0.00 0.00 0.00 4.24
4546 7652 8.753497 ATAAAGGCTAAAAAGGATAACAGGAG 57.247 34.615 0.00 0.00 0.00 3.69
4569 7675 5.766150 AAAACAGCAGCAACACAGTAATA 57.234 34.783 0.00 0.00 0.00 0.98
4571 7677 4.448537 AAAAACAGCAGCAACACAGTAA 57.551 36.364 0.00 0.00 0.00 2.24
4635 7746 5.475564 GGTTATTGTGTTAGGAATGTGTGGT 59.524 40.000 0.00 0.00 0.00 4.16
4636 7747 5.475220 TGGTTATTGTGTTAGGAATGTGTGG 59.525 40.000 0.00 0.00 0.00 4.17
4644 7755 6.367374 TCAGTCATGGTTATTGTGTTAGGA 57.633 37.500 0.00 0.00 0.00 2.94
4724 7836 2.654877 GGTCGCCGTTGAGAAGGA 59.345 61.111 0.00 0.00 0.00 3.36
4737 7849 3.406361 GTGTGAGCACTGCGGTCG 61.406 66.667 0.00 0.00 45.52 4.79
4786 7899 1.040339 ATGCGGAGAGAGAGACACCC 61.040 60.000 0.00 0.00 0.00 4.61
4882 8000 5.833131 ACCTCAGCAAAATAAGTTTGGAGAA 59.167 36.000 2.81 0.00 45.79 2.87
4941 8059 0.999406 AACGCACGATCCATCTTTCG 59.001 50.000 0.00 0.00 41.04 3.46
5243 8829 4.474651 TGATGGAAGACACTATGGTGGATT 59.525 41.667 14.25 7.46 46.85 3.01
5277 8863 2.362397 GACTTCCACGGCTATGAGATCA 59.638 50.000 0.00 0.00 0.00 2.92
5290 8876 3.545703 CATGGGTGATAAGGACTTCCAC 58.454 50.000 0.00 8.22 38.89 4.02


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

AutoCloner maintained by Alex Coulton.