Multiple sequence alignment - TraesCS2B01G599000

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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 TraesCS2B01G599000 chr2B 100.000 5553 0 0 1 5553 781800119 781805671 0.000000e+00 10255
1 TraesCS2B01G599000 chr2B 88.443 2267 213 27 1006 3248 781790134 781792375 0.000000e+00 2689
2 TraesCS2B01G599000 chr2B 86.739 1478 156 25 981 2432 784273521 784274984 0.000000e+00 1607
3 TraesCS2B01G599000 chr2B 82.780 1475 177 36 2431 3877 784275019 784276444 0.000000e+00 1245
4 TraesCS2B01G599000 chr2B 87.762 286 15 11 3803 4069 781793128 781793412 3.230000e-82 316
5 TraesCS2B01G599000 chr2B 91.216 148 13 0 5403 5550 781794658 781794805 9.430000e-48 202
6 TraesCS2B01G599000 chr2B 85.340 191 20 4 5362 5547 781827018 781827205 2.040000e-44 191
7 TraesCS2B01G599000 chr2B 82.692 156 22 3 3921 4075 784276416 784276567 3.490000e-27 134
8 TraesCS2B01G599000 chr2D 93.761 3927 151 47 981 4840 648115421 648111522 0.000000e+00 5808
9 TraesCS2B01G599000 chr2D 88.626 2242 205 25 1030 3249 648126638 648124425 0.000000e+00 2682
10 TraesCS2B01G599000 chr2D 86.703 1474 164 19 981 2432 648352257 648353720 0.000000e+00 1607
11 TraesCS2B01G599000 chr2D 83.014 1460 179 31 2431 3869 648353755 648355166 0.000000e+00 1258
12 TraesCS2B01G599000 chr2D 86.615 904 57 27 18 914 648116590 648115744 0.000000e+00 941
13 TraesCS2B01G599000 chr2D 81.481 513 79 9 3316 3823 648124256 648123755 1.860000e-109 407
14 TraesCS2B01G599000 chr2D 95.213 188 5 3 5367 5553 648104264 648104080 1.510000e-75 294
15 TraesCS2B01G599000 chr2D 74.086 903 137 57 6 847 648128049 648127183 1.180000e-71 281
16 TraesCS2B01G599000 chr2D 87.137 241 19 5 3838 4069 648123689 648123452 4.270000e-66 263
17 TraesCS2B01G599000 chr2D 89.062 192 18 1 5362 5553 648122310 648122122 9.300000e-58 235
18 TraesCS2B01G599000 chr2D 83.974 156 20 3 3921 4075 648355146 648355297 1.610000e-30 145
19 TraesCS2B01G599000 chrUn 93.605 3925 158 43 976 4840 31320674 31324565 0.000000e+00 5771
20 TraesCS2B01G599000 chrUn 89.686 2007 180 15 1258 3249 31306608 31308602 0.000000e+00 2534
21 TraesCS2B01G599000 chrUn 86.073 1472 168 20 981 2432 31091733 31090279 0.000000e+00 1548
22 TraesCS2B01G599000 chrUn 82.707 1463 181 32 2431 3869 31090244 31088830 0.000000e+00 1234
23 TraesCS2B01G599000 chrUn 88.946 588 49 8 393 977 31319529 31320103 0.000000e+00 712
24 TraesCS2B01G599000 chrUn 88.221 399 33 7 12 407 31319125 31319512 1.090000e-126 464
25 TraesCS2B01G599000 chrUn 83.364 535 39 25 3803 4309 31309294 31309806 3.050000e-122 449
26 TraesCS2B01G599000 chrUn 76.805 914 114 53 12 847 31304692 31305585 1.850000e-114 424
27 TraesCS2B01G599000 chrUn 81.168 531 81 10 3316 3838 31308771 31309290 5.180000e-110 409
28 TraesCS2B01G599000 chrUn 89.051 274 15 6 1013 1277 31306318 31306585 5.360000e-85 326
29 TraesCS2B01G599000 chrUn 95.745 188 4 3 5367 5553 31325388 31325572 3.250000e-77 300
30 TraesCS2B01G599000 chrUn 89.583 192 17 1 5362 5553 31369802 31369990 2.000000e-59 241
31 TraesCS2B01G599000 chrUn 87.234 188 21 1 5362 5549 31311457 31311641 1.570000e-50 211
32 TraesCS2B01G599000 chrUn 82.803 157 22 3 3921 4076 31088850 31088698 9.700000e-28 135
33 TraesCS2B01G599000 chr5D 80.220 182 31 4 5368 5548 6712042 6712219 1.260000e-26 132


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 TraesCS2B01G599000 chr2B 781800119 781805671 5552 False 10255.000000 10255 100.000000 1 5553 1 chr2B.!!$F1 5552
1 TraesCS2B01G599000 chr2B 781790134 781794805 4671 False 1069.000000 2689 89.140333 1006 5550 3 chr2B.!!$F3 4544
2 TraesCS2B01G599000 chr2B 784273521 784276567 3046 False 995.333333 1607 84.070333 981 4075 3 chr2B.!!$F4 3094
3 TraesCS2B01G599000 chr2D 648111522 648116590 5068 True 3374.500000 5808 90.188000 18 4840 2 chr2D.!!$R2 4822
4 TraesCS2B01G599000 chr2D 648352257 648355297 3040 False 1003.333333 1607 84.563667 981 4075 3 chr2D.!!$F1 3094
5 TraesCS2B01G599000 chr2D 648122122 648128049 5927 True 773.600000 2682 84.078400 6 5553 5 chr2D.!!$R3 5547
6 TraesCS2B01G599000 chrUn 31319125 31325572 6447 False 1811.750000 5771 91.629250 12 5553 4 chrUn.!!$F3 5541
7 TraesCS2B01G599000 chrUn 31088698 31091733 3035 True 972.333333 1548 83.861000 981 4076 3 chrUn.!!$R1 3095
8 TraesCS2B01G599000 chrUn 31304692 31311641 6949 False 725.500000 2534 84.551333 12 5549 6 chrUn.!!$F2 5537

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
242 306 0.032952 GTTTTTGGCCCCCTCGTTTC 59.967 55.000 0.00 0.0 0.00 2.78 F
466 576 0.107214 GCTGGGATGGATTGTTCCGA 60.107 55.000 0.00 0.0 45.89 4.55 F
470 580 0.177141 GGATGGATTGTTCCGACCGA 59.823 55.000 0.00 0.0 45.89 4.69 F
1322 2342 0.524862 CACAAGCTGTGGATCCTTGC 59.475 55.000 14.23 13.9 44.27 4.01 F
2726 3836 1.079543 CTCACCAACTCCCTCGCTG 60.080 63.158 0.00 0.0 0.00 5.18 F
3574 4810 1.009829 GTTCATCCGAGTGACATGGC 58.990 55.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 2465 0.037790 GCTCGCCACTGTCTTCTTCT 60.038 55.000 0.00 0.0 0.00 2.85 R
1832 2870 0.951040 CACCGTCCTGAGGCAAAGAC 60.951 60.000 0.00 0.0 0.00 3.01 R
2342 3392 2.194212 GGCCTGAGCTGCATGATGG 61.194 63.158 1.02 0.0 39.73 3.51 R
3266 4382 0.251354 CCTGTGGTGCTGCTAGACAT 59.749 55.000 0.00 0.0 0.00 3.06 R
4515 5982 2.822561 TCACTCAAACACAAAACTGGCA 59.177 40.909 0.00 0.0 0.00 4.92 R
5271 7778 0.039798 CTCATGTTGTGCCTGTGTGC 60.040 55.000 0.00 0.0 0.00 4.57 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
116 127 1.859302 CACTACTGCTCCTCCCTCTT 58.141 55.000 0.00 0.00 0.00 2.85
119 130 1.760029 CTACTGCTCCTCCCTCTTTCC 59.240 57.143 0.00 0.00 0.00 3.13
120 131 0.118144 ACTGCTCCTCCCTCTTTCCT 59.882 55.000 0.00 0.00 0.00 3.36
203 232 4.933064 GCGGCCGATCCTCGTCTG 62.933 72.222 33.48 0.00 38.40 3.51
204 233 4.933064 CGGCCGATCCTCGTCTGC 62.933 72.222 24.07 0.00 38.40 4.26
205 234 3.532155 GGCCGATCCTCGTCTGCT 61.532 66.667 0.00 0.00 38.40 4.24
207 236 2.725008 CCGATCCTCGTCTGCTCC 59.275 66.667 0.00 0.00 38.40 4.70
208 237 1.826054 CCGATCCTCGTCTGCTCCT 60.826 63.158 0.00 0.00 38.40 3.69
209 238 1.358402 CGATCCTCGTCTGCTCCTG 59.642 63.158 0.00 0.00 34.72 3.86
210 239 1.067250 GATCCTCGTCTGCTCCTGC 59.933 63.158 0.00 0.00 40.20 4.85
242 306 0.032952 GTTTTTGGCCCCCTCGTTTC 59.967 55.000 0.00 0.00 0.00 2.78
302 366 3.646162 ACCAAAACAAAAGGGGGAGATTC 59.354 43.478 0.00 0.00 0.00 2.52
419 521 7.543172 TGAATGAAAGAAATAAAGTGCAGATGC 59.457 33.333 0.00 0.00 42.50 3.91
466 576 0.107214 GCTGGGATGGATTGTTCCGA 60.107 55.000 0.00 0.00 45.89 4.55
470 580 0.177141 GGATGGATTGTTCCGACCGA 59.823 55.000 0.00 0.00 45.89 4.69
486 596 2.159382 ACCGACCATGGATTGTTGTTC 58.841 47.619 21.47 1.17 0.00 3.18
487 597 2.224769 ACCGACCATGGATTGTTGTTCT 60.225 45.455 21.47 0.00 0.00 3.01
496 606 2.796593 GGATTGTTGTTCTTGCTGTTGC 59.203 45.455 0.00 0.00 40.20 4.17
497 607 2.292103 TTGTTGTTCTTGCTGTTGCC 57.708 45.000 0.00 0.00 38.71 4.52
570 690 1.378250 AGCCCTTGATCTGCACTGC 60.378 57.895 0.00 0.00 0.00 4.40
584 704 3.719121 CTGCTAGCAGGGACAGGT 58.281 61.111 33.06 0.00 40.17 4.00
639 764 1.203013 GGCACCCCTCTAAAACCACTT 60.203 52.381 0.00 0.00 0.00 3.16
640 765 2.040679 GGCACCCCTCTAAAACCACTTA 59.959 50.000 0.00 0.00 0.00 2.24
652 777 8.959676 TCTAAAACCACTTATAAAACCCCAAT 57.040 30.769 0.00 0.00 0.00 3.16
713 844 2.159707 GCTGTTCGATTTATGTGTGCGT 60.160 45.455 0.00 0.00 0.00 5.24
725 856 7.901874 TTTATGTGTGCGTCTTTTAGTTTTC 57.098 32.000 0.00 0.00 0.00 2.29
743 874 6.314917 AGTTTTCTGGATGGATACCAAAGTT 58.685 36.000 0.00 0.00 36.95 2.66
744 875 6.782494 AGTTTTCTGGATGGATACCAAAGTTT 59.218 34.615 0.00 0.00 36.95 2.66
745 876 7.290014 AGTTTTCTGGATGGATACCAAAGTTTT 59.710 33.333 0.00 0.00 36.95 2.43
746 877 8.581578 GTTTTCTGGATGGATACCAAAGTTTTA 58.418 33.333 0.00 0.00 36.95 1.52
747 878 8.893563 TTTCTGGATGGATACCAAAGTTTTAT 57.106 30.769 0.00 0.00 36.95 1.40
748 879 7.880160 TCTGGATGGATACCAAAGTTTTATG 57.120 36.000 0.00 0.00 36.95 1.90
753 884 3.129638 GGATACCAAAGTTTTATGGCGCA 59.870 43.478 10.83 0.00 40.51 6.09
754 885 4.381079 GGATACCAAAGTTTTATGGCGCAA 60.381 41.667 10.83 0.00 40.51 4.85
778 915 1.337728 ACATTGTGTGCCTCGATTCGA 60.338 47.619 8.70 8.70 0.00 3.71
851 998 4.946157 AGGTCTCTACTGGCATTTGATTTG 59.054 41.667 0.00 0.00 0.00 2.32
853 1000 4.943705 GTCTCTACTGGCATTTGATTTGGA 59.056 41.667 0.00 0.00 0.00 3.53
860 1007 3.189285 GGCATTTGATTTGGATGTTCCG 58.811 45.455 0.00 0.00 40.17 4.30
970 1140 7.603180 TCATGTATATGTCTGCTCCTTTACT 57.397 36.000 0.00 0.00 35.73 2.24
973 1143 7.278461 TGTATATGTCTGCTCCTTTACTCTC 57.722 40.000 0.00 0.00 0.00 3.20
1129 2089 3.981071 TCTCCTATGTGAACCAGTTGG 57.019 47.619 0.00 0.00 42.17 3.77
1226 2204 6.111382 TGAATATGAAGAAGGCAGTGAAGAG 58.889 40.000 0.00 0.00 0.00 2.85
1227 2205 2.847327 TGAAGAAGGCAGTGAAGAGG 57.153 50.000 0.00 0.00 0.00 3.69
1228 2206 2.329267 TGAAGAAGGCAGTGAAGAGGA 58.671 47.619 0.00 0.00 0.00 3.71
1277 2255 7.256286 TCTACGATGATGATGATGATGATGAC 58.744 38.462 0.00 0.00 0.00 3.06
1288 2308 2.282407 TGATGATGACGACAGCAATGG 58.718 47.619 10.24 0.00 45.44 3.16
1322 2342 0.524862 CACAAGCTGTGGATCCTTGC 59.475 55.000 14.23 13.90 44.27 4.01
1357 2377 3.133721 GCAGAAGAAGAGGAGGCTAATGA 59.866 47.826 0.00 0.00 0.00 2.57
1362 2382 4.877773 AGAAGAGGAGGCTAATGAAGAGA 58.122 43.478 0.00 0.00 0.00 3.10
1364 2384 5.363580 AGAAGAGGAGGCTAATGAAGAGAAG 59.636 44.000 0.00 0.00 0.00 2.85
1374 2394 2.479566 TGAAGAGAAGCCTTGCGATT 57.520 45.000 0.00 0.00 0.00 3.34
1376 2396 1.399791 GAAGAGAAGCCTTGCGATTGG 59.600 52.381 0.00 0.00 0.00 3.16
1401 2421 3.455910 CACCCCACTTGAAGATGAGGATA 59.544 47.826 0.00 0.00 0.00 2.59
1409 2429 7.419518 CCACTTGAAGATGAGGATACCAGTTAT 60.420 40.741 0.00 0.00 37.17 1.89
1442 2465 8.352201 CCTTTTGTTGATGAACTCTGTTATGAA 58.648 33.333 0.00 0.00 32.79 2.57
1514 2549 1.376553 GCTCTGTGAAGTGGAGCCC 60.377 63.158 0.00 0.00 44.46 5.19
1605 2643 4.352298 AGGAACAAAATGAGGAAGAGGTCT 59.648 41.667 0.00 0.00 0.00 3.85
1796 2834 3.057946 GGAAAGCTCAGTTTGATGACCAC 60.058 47.826 0.00 0.00 0.00 4.16
1832 2870 1.959042 AGAGGCAAGAACACACAGTG 58.041 50.000 0.00 0.00 39.75 3.66
2342 3392 4.393371 GGCTTTGTGAAGTACTCTGATTCC 59.607 45.833 0.00 0.00 35.25 3.01
2726 3836 1.079543 CTCACCAACTCCCTCGCTG 60.080 63.158 0.00 0.00 0.00 5.18
2938 4048 5.391256 TGGTGGAAAGAGTCTAGTAGTCAA 58.609 41.667 0.00 0.00 0.00 3.18
2948 4058 5.373222 AGTCTAGTAGTCAAGCGATCAGAT 58.627 41.667 0.00 0.00 0.00 2.90
2960 4076 3.055530 AGCGATCAGATTCTTGTCCAACT 60.056 43.478 0.00 0.00 0.00 3.16
3202 4318 5.772825 ATTGATCAAATGGATGGTTACCG 57.227 39.130 13.09 0.00 36.00 4.02
3266 4382 4.019681 CCTAATATAATGCCTCGGGTGGAA 60.020 45.833 0.00 0.00 0.00 3.53
3569 4805 1.398390 GCCAATGTTCATCCGAGTGAC 59.602 52.381 0.00 0.00 0.00 3.67
3574 4810 1.009829 GTTCATCCGAGTGACATGGC 58.990 55.000 0.00 0.00 0.00 4.40
3995 5387 1.349259 CCACCGCGACTAAACCTTCG 61.349 60.000 8.23 0.00 38.31 3.79
4411 5822 3.162666 CCATTCCCATGCTATCAATGCT 58.837 45.455 0.00 0.00 0.00 3.79
4426 5837 1.624336 ATGCTTTGCTGGTGTGATGT 58.376 45.000 0.00 0.00 0.00 3.06
4515 5982 0.889994 TCATGCGCCTGCTGAATTTT 59.110 45.000 4.18 0.00 43.34 1.82
4518 5985 2.096442 GCGCCTGCTGAATTTTGCC 61.096 57.895 0.00 0.00 38.39 4.52
4519 5986 1.289694 CGCCTGCTGAATTTTGCCA 59.710 52.632 0.00 0.00 0.00 4.92
4528 5995 3.622612 GCTGAATTTTGCCAGTTTTGTGT 59.377 39.130 0.00 0.00 33.19 3.72
4541 6027 6.459573 GCCAGTTTTGTGTTTGAGTGAAGATA 60.460 38.462 0.00 0.00 0.00 1.98
4639 6153 8.073467 TCAAATAGTTTTTCTTCCAGGTGTTT 57.927 30.769 0.00 0.00 0.00 2.83
4663 6177 0.906066 TTGCATTGCCCAATCAGCAT 59.094 45.000 6.12 0.00 40.59 3.79
4667 6181 0.906066 ATTGCCCAATCAGCATTGCA 59.094 45.000 11.91 0.00 40.59 4.08
4675 6189 4.049186 CCAATCAGCATTGCAATTCTAGC 58.951 43.478 11.35 10.95 38.53 3.42
4676 6190 4.202121 CCAATCAGCATTGCAATTCTAGCT 60.202 41.667 11.35 13.05 38.53 3.32
4700 6214 2.557924 CCTAAGTTTCACTGGCATGCAA 59.442 45.455 21.36 7.49 0.00 4.08
4711 6225 3.324556 ACTGGCATGCAACCTACATTTTT 59.675 39.130 21.36 0.00 0.00 1.94
4712 6226 3.924144 TGGCATGCAACCTACATTTTTC 58.076 40.909 21.36 0.00 0.00 2.29
4714 6228 4.176271 GGCATGCAACCTACATTTTTCTC 58.824 43.478 21.36 0.00 0.00 2.87
4715 6229 4.176271 GCATGCAACCTACATTTTTCTCC 58.824 43.478 14.21 0.00 0.00 3.71
4716 6230 4.747810 CATGCAACCTACATTTTTCTCCC 58.252 43.478 0.00 0.00 0.00 4.30
4717 6231 4.112634 TGCAACCTACATTTTTCTCCCT 57.887 40.909 0.00 0.00 0.00 4.20
4718 6232 3.826157 TGCAACCTACATTTTTCTCCCTG 59.174 43.478 0.00 0.00 0.00 4.45
4720 6234 5.007682 GCAACCTACATTTTTCTCCCTGTA 58.992 41.667 0.00 0.00 0.00 2.74
4722 6236 6.238648 CAACCTACATTTTTCTCCCTGTAGT 58.761 40.000 7.54 0.00 39.47 2.73
4723 6237 6.449830 ACCTACATTTTTCTCCCTGTAGTT 57.550 37.500 7.54 0.00 39.47 2.24
4724 6238 6.473758 ACCTACATTTTTCTCCCTGTAGTTC 58.526 40.000 7.54 0.00 39.47 3.01
4725 6239 6.043938 ACCTACATTTTTCTCCCTGTAGTTCA 59.956 38.462 7.54 0.00 39.47 3.18
4727 6241 7.281100 CCTACATTTTTCTCCCTGTAGTTCATC 59.719 40.741 7.54 0.00 39.47 2.92
4789 6328 5.552870 TGAAGTAGAGCTCTGTTTCCTTT 57.447 39.130 26.78 9.25 0.00 3.11
4806 6345 5.078411 TCCTTTCAGTGAGCTATTCAGTC 57.922 43.478 0.00 0.00 37.36 3.51
4810 6349 2.159324 TCAGTGAGCTATTCAGTCGCTG 60.159 50.000 5.90 5.90 45.95 5.18
4818 6384 4.390297 AGCTATTCAGTCGCTGTTTTCTTC 59.610 41.667 6.72 0.00 32.61 2.87
4819 6385 4.436183 GCTATTCAGTCGCTGTTTTCTTCC 60.436 45.833 6.72 0.00 32.61 3.46
4820 6386 1.878953 TCAGTCGCTGTTTTCTTCCC 58.121 50.000 6.72 0.00 32.61 3.97
4822 6388 2.158813 TCAGTCGCTGTTTTCTTCCCTT 60.159 45.455 6.72 0.00 32.61 3.95
4823 6389 3.070446 TCAGTCGCTGTTTTCTTCCCTTA 59.930 43.478 6.72 0.00 32.61 2.69
4830 6396 6.070653 TCGCTGTTTTCTTCCCTTATAACCTA 60.071 38.462 0.00 0.00 0.00 3.08
4867 6433 8.986477 AAATTGTAAATTCAGGTTGTAGATGC 57.014 30.769 0.00 0.00 0.00 3.91
4868 6434 7.944729 ATTGTAAATTCAGGTTGTAGATGCT 57.055 32.000 0.00 0.00 0.00 3.79
4869 6435 6.985188 TGTAAATTCAGGTTGTAGATGCTC 57.015 37.500 0.00 0.00 0.00 4.26
4870 6436 6.711277 TGTAAATTCAGGTTGTAGATGCTCT 58.289 36.000 0.00 0.00 0.00 4.09
4872 6438 8.318412 TGTAAATTCAGGTTGTAGATGCTCTTA 58.682 33.333 0.00 0.00 0.00 2.10
4873 6439 7.856145 AAATTCAGGTTGTAGATGCTCTTAG 57.144 36.000 0.00 0.00 0.00 2.18
4874 6440 4.392921 TCAGGTTGTAGATGCTCTTAGC 57.607 45.455 0.00 0.00 42.82 3.09
4885 6659 1.414181 TGCTCTTAGCCACTGGATAGC 59.586 52.381 0.00 0.00 41.51 2.97
4893 6698 3.733337 AGCCACTGGATAGCTAAATTCG 58.267 45.455 0.00 0.00 34.38 3.34
4894 6699 2.224314 GCCACTGGATAGCTAAATTCGC 59.776 50.000 0.00 0.00 0.00 4.70
4921 7091 4.324267 AGGTCTTGCATGTGTTAAGGTAC 58.676 43.478 0.00 0.00 0.00 3.34
4926 7096 6.975772 GTCTTGCATGTGTTAAGGTACAAAAA 59.024 34.615 0.00 0.00 0.00 1.94
4928 7098 8.200792 TCTTGCATGTGTTAAGGTACAAAAATT 58.799 29.630 0.00 0.00 0.00 1.82
4934 7104 7.714703 TGTGTTAAGGTACAAAAATTACCCAC 58.285 34.615 0.00 0.00 40.08 4.61
4943 7113 7.175293 GGTACAAAAATTACCCACACATCAGTA 59.825 37.037 0.00 0.00 33.98 2.74
4966 7467 3.204526 TGCATTTTCCAAAAGCACAAGG 58.795 40.909 0.00 0.00 31.76 3.61
4999 7500 6.909550 AATGTACAAAGTGAAAGCCCATAA 57.090 33.333 0.00 0.00 0.00 1.90
5002 7503 8.766994 ATGTACAAAGTGAAAGCCCATAATAT 57.233 30.769 0.00 0.00 0.00 1.28
5028 7529 1.202976 ACAGAGGCCAACTGCTCATTT 60.203 47.619 23.62 6.35 40.92 2.32
5031 7532 2.298163 AGAGGCCAACTGCTCATTTTTG 59.702 45.455 5.01 0.00 40.92 2.44
5032 7533 1.150827 GGCCAACTGCTCATTTTTGC 58.849 50.000 0.00 0.00 40.92 3.68
5044 7550 2.500910 TCATTTTTGCCCCCATCACATC 59.499 45.455 0.00 0.00 0.00 3.06
5054 7560 3.577848 CCCCCATCACATCAAAGTTGAAA 59.422 43.478 0.00 0.00 41.13 2.69
5060 7566 6.971184 CCATCACATCAAAGTTGAAAGATAGC 59.029 38.462 0.00 0.00 41.13 2.97
5073 7579 6.203808 TGAAAGATAGCTAGTCAAACGCTA 57.796 37.500 0.00 0.00 40.18 4.26
5075 7581 6.095021 TGAAAGATAGCTAGTCAAACGCTAGA 59.905 38.462 0.00 0.00 39.36 2.43
5099 7605 8.971073 AGATAATTTATTTTGTGGAAGACTGGG 58.029 33.333 0.00 0.00 0.00 4.45
5101 7608 6.840780 ATTTATTTTGTGGAAGACTGGGAG 57.159 37.500 0.00 0.00 0.00 4.30
5126 7633 8.376270 AGTTGATAGCTAATATAACTGGGGAAC 58.624 37.037 0.00 0.00 0.00 3.62
5156 7663 4.883083 TCGCTAATAATTCGGAAGCTCAT 58.117 39.130 0.00 0.00 0.00 2.90
5161 7668 6.017934 GCTAATAATTCGGAAGCTCATGTTCA 60.018 38.462 0.00 0.00 0.00 3.18
5167 7674 2.096496 CGGAAGCTCATGTTCACATTCC 59.904 50.000 0.00 0.00 33.61 3.01
5173 7680 3.676646 GCTCATGTTCACATTCCAAAAGC 59.323 43.478 0.00 0.00 33.61 3.51
5190 7697 1.230324 AGCTTTTCTCAGCCGTTGTC 58.770 50.000 0.00 0.00 41.12 3.18
5192 7699 0.512952 CTTTTCTCAGCCGTTGTCCG 59.487 55.000 0.00 0.00 0.00 4.79
5203 7710 4.150994 TTGTCCGGACAAGGCAAC 57.849 55.556 39.59 12.24 45.42 4.17
5215 7722 2.738213 AAGGCAACGCTCCAGGTCTG 62.738 60.000 0.00 0.00 46.39 3.51
5224 7731 2.671070 CCAGGTCTGGGCATCGTT 59.329 61.111 9.08 0.00 46.81 3.85
5234 7741 4.157817 GCATCGTTGCTGCAAAGG 57.842 55.556 24.20 16.16 45.77 3.11
5235 7742 2.090524 GCATCGTTGCTGCAAAGGC 61.091 57.895 24.20 16.34 45.77 4.35
5247 7754 1.251251 GCAAAGGCATGGACTGAAGT 58.749 50.000 0.00 0.00 40.72 3.01
5248 7755 1.615392 GCAAAGGCATGGACTGAAGTT 59.385 47.619 0.00 0.00 40.72 2.66
5250 7757 2.886523 CAAAGGCATGGACTGAAGTTCA 59.113 45.455 5.25 5.25 38.04 3.18
5251 7758 2.191128 AGGCATGGACTGAAGTTCAC 57.809 50.000 0.08 0.00 36.16 3.18
5252 7759 1.701847 AGGCATGGACTGAAGTTCACT 59.298 47.619 0.08 0.00 36.16 3.41
5253 7760 1.808945 GGCATGGACTGAAGTTCACTG 59.191 52.381 0.08 0.00 36.16 3.66
5254 7761 2.550855 GGCATGGACTGAAGTTCACTGA 60.551 50.000 0.08 0.00 36.16 3.41
5255 7762 3.141398 GCATGGACTGAAGTTCACTGAA 58.859 45.455 0.08 0.00 36.16 3.02
5256 7763 3.058639 GCATGGACTGAAGTTCACTGAAC 60.059 47.826 13.25 13.25 42.25 3.18
5270 7777 5.525378 GTTCACTGAACTTCACAAGAGTGAT 59.475 40.000 13.77 0.00 42.75 3.06
5287 7794 4.256462 TGCACACAGGCACAACAT 57.744 50.000 0.00 0.00 39.25 2.71
5288 7795 1.734748 TGCACACAGGCACAACATG 59.265 52.632 0.00 0.00 39.25 3.21
5289 7796 0.750911 TGCACACAGGCACAACATGA 60.751 50.000 0.00 0.00 39.25 3.07
5290 7797 0.039798 GCACACAGGCACAACATGAG 60.040 55.000 0.00 0.00 0.00 2.90
5291 7798 1.596603 CACACAGGCACAACATGAGA 58.403 50.000 0.00 0.00 0.00 3.27
5293 7800 2.031420 CACACAGGCACAACATGAGAAG 60.031 50.000 0.00 0.00 0.00 2.85
5294 7801 2.158769 ACACAGGCACAACATGAGAAGA 60.159 45.455 0.00 0.00 0.00 2.87
5296 7803 2.880890 ACAGGCACAACATGAGAAGAAC 59.119 45.455 0.00 0.00 0.00 3.01
5297 7804 2.880268 CAGGCACAACATGAGAAGAACA 59.120 45.455 0.00 0.00 0.00 3.18
5298 7805 3.316029 CAGGCACAACATGAGAAGAACAA 59.684 43.478 0.00 0.00 0.00 2.83
5299 7806 4.022589 CAGGCACAACATGAGAAGAACAAT 60.023 41.667 0.00 0.00 0.00 2.71
5300 7807 5.181811 CAGGCACAACATGAGAAGAACAATA 59.818 40.000 0.00 0.00 0.00 1.90
5301 7808 5.769662 AGGCACAACATGAGAAGAACAATAA 59.230 36.000 0.00 0.00 0.00 1.40
5302 7809 6.265196 AGGCACAACATGAGAAGAACAATAAA 59.735 34.615 0.00 0.00 0.00 1.40
5303 7810 6.922957 GGCACAACATGAGAAGAACAATAAAA 59.077 34.615 0.00 0.00 0.00 1.52
5304 7811 7.599998 GGCACAACATGAGAAGAACAATAAAAT 59.400 33.333 0.00 0.00 0.00 1.82
5305 7812 9.624697 GCACAACATGAGAAGAACAATAAAATA 57.375 29.630 0.00 0.00 0.00 1.40
5340 7847 8.515473 AAAACCTATAAAATGTTTCAGCGAAC 57.485 30.769 0.00 0.00 31.37 3.95
5341 7848 5.864986 ACCTATAAAATGTTTCAGCGAACG 58.135 37.500 0.00 0.00 32.18 3.95
5342 7849 5.163794 ACCTATAAAATGTTTCAGCGAACGG 60.164 40.000 0.00 0.00 32.18 4.44
5343 7850 4.759516 ATAAAATGTTTCAGCGAACGGT 57.240 36.364 0.00 0.00 32.18 4.83
5344 7851 5.866335 ATAAAATGTTTCAGCGAACGGTA 57.134 34.783 0.00 0.00 32.18 4.02
5346 7853 2.157834 ATGTTTCAGCGAACGGTACA 57.842 45.000 0.00 1.09 32.18 2.90
5348 7855 3.300852 TGTTTCAGCGAACGGTACATA 57.699 42.857 0.00 0.00 32.18 2.29
5350 7857 4.996344 TGTTTCAGCGAACGGTACATATA 58.004 39.130 0.00 0.00 32.18 0.86
5352 7859 4.906065 TTCAGCGAACGGTACATATACT 57.094 40.909 0.00 0.00 0.00 2.12
5353 7860 4.219143 TCAGCGAACGGTACATATACTG 57.781 45.455 0.00 0.00 42.60 2.74
5354 7861 2.724690 CAGCGAACGGTACATATACTGC 59.275 50.000 0.00 0.00 40.86 4.40
5355 7862 1.712350 GCGAACGGTACATATACTGCG 59.288 52.381 0.00 0.00 40.86 5.18
5357 7864 2.056577 GAACGGTACATATACTGCGCC 58.943 52.381 4.18 0.00 40.86 6.53
5358 7865 0.039798 ACGGTACATATACTGCGCCG 60.040 55.000 4.18 0.00 45.40 6.46
5359 7866 0.239082 CGGTACATATACTGCGCCGA 59.761 55.000 4.18 0.00 43.78 5.54
5360 7867 1.135489 CGGTACATATACTGCGCCGAT 60.135 52.381 4.18 0.00 43.78 4.18
5386 7915 1.727335 GAACGAGGTCTTGCTTAGCAC 59.273 52.381 6.34 0.00 38.71 4.40
5397 7926 1.227674 CTTAGCACGGATCAGGGCC 60.228 63.158 16.93 0.00 42.61 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.292178 GATGGGAGAGGAGGCGCG 62.292 72.222 0.00 0.00 0.00 6.86
2 3 3.934962 GGATGGGAGAGGAGGCGC 61.935 72.222 0.00 0.00 0.00 6.53
3 4 3.237741 GGGATGGGAGAGGAGGCG 61.238 72.222 0.00 0.00 0.00 5.52
4 5 2.851588 GGGGATGGGAGAGGAGGC 60.852 72.222 0.00 0.00 0.00 4.70
10 11 2.628465 AGGGGAGGGGATGGGAGA 60.628 66.667 0.00 0.00 0.00 3.71
107 118 0.692756 GGAGGGAGGAAAGAGGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
116 127 2.768344 GGCCATCGGAGGGAGGAA 60.768 66.667 13.78 0.00 0.00 3.36
135 147 0.181350 ATGATCTGCCGGGGAAGAAC 59.819 55.000 2.18 0.00 32.78 3.01
171 200 2.325082 CCGCGGAAAGAACACCCAG 61.325 63.158 24.07 0.00 0.00 4.45
207 236 3.944250 AACCCCATTCCTGCCGCAG 62.944 63.158 13.82 13.82 0.00 5.18
208 237 3.521765 AAACCCCATTCCTGCCGCA 62.522 57.895 0.00 0.00 0.00 5.69
209 238 1.826340 AAAAACCCCATTCCTGCCGC 61.826 55.000 0.00 0.00 0.00 6.53
210 239 0.037419 CAAAAACCCCATTCCTGCCG 60.037 55.000 0.00 0.00 0.00 5.69
242 306 1.201921 CGAAACAAGAAGAATCGGCCG 60.202 52.381 22.12 22.12 0.00 6.13
316 380 4.598894 CTGGGGCAGCGGAGATCG 62.599 72.222 0.00 0.00 42.76 3.69
317 381 4.247380 CCTGGGGCAGCGGAGATC 62.247 72.222 0.00 0.00 0.00 2.75
419 521 3.270877 GTGGCAACCATCCTACTTACTG 58.729 50.000 0.00 0.00 35.28 2.74
431 533 2.904866 GCACTTCCGTGGCAACCA 60.905 61.111 0.00 0.00 41.51 3.67
466 576 2.159382 GAACAACAATCCATGGTCGGT 58.841 47.619 12.58 5.38 0.00 4.69
470 580 3.006110 CAGCAAGAACAACAATCCATGGT 59.994 43.478 12.58 0.00 0.00 3.55
570 690 1.482593 CAACCTACCTGTCCCTGCTAG 59.517 57.143 0.00 0.00 0.00 3.42
605 730 1.226686 GGTGCCAGATATCTGCAGCG 61.227 60.000 27.58 17.52 42.47 5.18
652 777 3.023045 GCTAGTCCCCTCCCTCCCA 62.023 68.421 0.00 0.00 0.00 4.37
713 844 7.695055 TGGTATCCATCCAGAAAACTAAAAGA 58.305 34.615 0.00 0.00 0.00 2.52
725 856 6.461509 GCCATAAAACTTTGGTATCCATCCAG 60.462 42.308 0.00 0.00 36.28 3.86
743 874 3.492383 CACAATGTGTTTTGCGCCATAAA 59.508 39.130 4.18 0.00 0.00 1.40
744 875 3.055591 CACAATGTGTTTTGCGCCATAA 58.944 40.909 4.18 0.00 0.00 1.90
745 876 2.035193 ACACAATGTGTTTTGCGCCATA 59.965 40.909 13.98 0.00 45.08 2.74
746 877 1.202510 ACACAATGTGTTTTGCGCCAT 60.203 42.857 13.98 0.00 45.08 4.40
747 878 0.174389 ACACAATGTGTTTTGCGCCA 59.826 45.000 13.98 0.00 45.08 5.69
748 879 0.576328 CACACAATGTGTTTTGCGCC 59.424 50.000 17.31 0.00 45.08 6.53
778 915 7.394359 ACATGCATGTTTCCTACATTCTTAAGT 59.606 33.333 26.61 0.00 45.19 2.24
851 998 5.008316 AGTCACAAAACTAAACGGAACATCC 59.992 40.000 0.00 0.00 0.00 3.51
853 1000 5.732247 GCAGTCACAAAACTAAACGGAACAT 60.732 40.000 0.00 0.00 0.00 2.71
860 1007 6.312672 ACAATTTGGCAGTCACAAAACTAAAC 59.687 34.615 0.78 0.00 40.74 2.01
1088 2048 9.301897 AGGAGAAGATTATTGTTTAGCAAAAGT 57.698 29.630 0.00 0.00 40.91 2.66
1129 2089 2.973082 GCCCCATTCTTGCACCAC 59.027 61.111 0.00 0.00 0.00 4.16
1226 2204 4.274950 TCACGTTCAAATGGTTCTTCTTCC 59.725 41.667 0.00 0.00 0.00 3.46
1227 2205 5.418310 TCACGTTCAAATGGTTCTTCTTC 57.582 39.130 0.00 0.00 0.00 2.87
1228 2206 5.828299 TTCACGTTCAAATGGTTCTTCTT 57.172 34.783 0.00 0.00 0.00 2.52
1277 2255 1.746615 CTCACCCCCATTGCTGTCG 60.747 63.158 0.00 0.00 0.00 4.35
1288 2308 0.467290 TTGTGTTTCTGGCTCACCCC 60.467 55.000 0.00 0.00 33.59 4.95
1322 2342 2.977914 TCTTCTGCCAAAGGATCTTCG 58.022 47.619 0.00 0.00 0.00 3.79
1357 2377 1.457346 CCAATCGCAAGGCTTCTCTT 58.543 50.000 0.00 0.00 38.47 2.85
1362 2382 3.070576 GGCCCAATCGCAAGGCTT 61.071 61.111 0.00 0.00 46.31 4.35
1364 2384 4.133796 GTGGCCCAATCGCAAGGC 62.134 66.667 0.00 0.00 46.37 4.35
1376 2396 0.967380 CATCTTCAAGTGGGGTGGCC 60.967 60.000 0.00 0.00 0.00 5.36
1401 2421 6.549364 TCAACAAAAGGTTCATCATAACTGGT 59.451 34.615 0.00 0.00 37.72 4.00
1409 2429 6.547141 AGAGTTCATCAACAAAAGGTTCATCA 59.453 34.615 0.00 0.00 37.72 3.07
1442 2465 0.037790 GCTCGCCACTGTCTTCTTCT 60.038 55.000 0.00 0.00 0.00 2.85
1490 2513 2.496871 CTCCACTTCACAGAGCTGATCT 59.503 50.000 4.21 0.00 39.56 2.75
1514 2549 1.446907 GAGCCACCTCAACATCACAG 58.553 55.000 0.00 0.00 38.03 3.66
1605 2643 4.131596 CCCTTTCTCAGTGTCCGTTTTAA 58.868 43.478 0.00 0.00 0.00 1.52
1796 2834 2.061773 CTCTTACACAAGTGGCTGTCG 58.938 52.381 5.08 0.00 33.20 4.35
1832 2870 0.951040 CACCGTCCTGAGGCAAAGAC 60.951 60.000 0.00 0.00 0.00 3.01
2252 3302 3.731652 TCAGTTACTTTCCCGAAACGA 57.268 42.857 0.00 0.00 0.00 3.85
2254 3304 8.610035 CCTTTATATCAGTTACTTTCCCGAAAC 58.390 37.037 0.00 0.00 0.00 2.78
2342 3392 2.194212 GGCCTGAGCTGCATGATGG 61.194 63.158 1.02 0.00 39.73 3.51
2669 3776 1.187567 ATGCAAGTGGTGAAAGGCCC 61.188 55.000 0.00 0.00 0.00 5.80
2726 3836 7.760340 ACGTACAGTCTAGATTTCTTCATTTCC 59.240 37.037 0.00 0.00 0.00 3.13
2754 3864 2.624437 ATCGACCGCGGAAGGTTAGC 62.624 60.000 35.90 8.88 46.09 3.09
2938 4048 3.055530 AGTTGGACAAGAATCTGATCGCT 60.056 43.478 0.00 0.00 0.00 4.93
2948 4058 1.311859 CTGCAGCAGTTGGACAAGAA 58.688 50.000 14.90 0.00 0.00 2.52
3202 4318 1.473434 CCAGGGTACTTGCTCCGATTC 60.473 57.143 0.00 0.00 0.00 2.52
3266 4382 0.251354 CCTGTGGTGCTGCTAGACAT 59.749 55.000 0.00 0.00 0.00 3.06
3313 4549 6.516718 CCTACATATAGGTTGGTCAAGTCTG 58.483 44.000 9.48 0.00 42.95 3.51
3574 4810 3.264897 GACGCGCCATGTAGCTGG 61.265 66.667 5.73 0.00 39.45 4.85
4173 5571 6.201425 CCAAATGATGCTAATTAACACATGGC 59.799 38.462 0.00 0.00 0.00 4.40
4411 5822 4.397420 ACAGAATACATCACACCAGCAAA 58.603 39.130 0.00 0.00 0.00 3.68
4515 5982 2.822561 TCACTCAAACACAAAACTGGCA 59.177 40.909 0.00 0.00 0.00 4.92
4518 5985 9.520204 AAATATCTTCACTCAAACACAAAACTG 57.480 29.630 0.00 0.00 0.00 3.16
4519 5986 9.520204 CAAATATCTTCACTCAAACACAAAACT 57.480 29.630 0.00 0.00 0.00 2.66
4590 6086 5.030874 ACTCGGTTGAAAAATTAGAAGCG 57.969 39.130 0.00 0.00 39.88 4.68
4639 6153 3.679361 GCTGATTGGGCAATGCAAACATA 60.679 43.478 7.79 0.00 34.62 2.29
4663 6177 5.683876 ACTTAGGAGAGCTAGAATTGCAA 57.316 39.130 0.00 0.00 0.00 4.08
4700 6214 6.043938 TGAACTACAGGGAGAAAAATGTAGGT 59.956 38.462 13.88 8.49 46.18 3.08
4711 6225 4.871871 AGAGAGATGAACTACAGGGAGA 57.128 45.455 0.00 0.00 0.00 3.71
4712 6226 4.952957 TCAAGAGAGATGAACTACAGGGAG 59.047 45.833 0.00 0.00 0.00 4.30
4714 6228 5.667539 TTCAAGAGAGATGAACTACAGGG 57.332 43.478 0.00 0.00 32.10 4.45
4715 6229 7.969536 TTTTTCAAGAGAGATGAACTACAGG 57.030 36.000 0.00 0.00 36.57 4.00
4723 6237 9.948964 TCACAAGATATTTTTCAAGAGAGATGA 57.051 29.630 0.00 0.00 0.00 2.92
4753 6269 5.298989 TCTACTTCAACCACCTAAAGCAA 57.701 39.130 0.00 0.00 0.00 3.91
4755 6271 3.685272 GCTCTACTTCAACCACCTAAAGC 59.315 47.826 0.00 0.00 0.00 3.51
4758 6274 4.220821 CAGAGCTCTACTTCAACCACCTAA 59.779 45.833 17.75 0.00 0.00 2.69
4759 6275 3.764434 CAGAGCTCTACTTCAACCACCTA 59.236 47.826 17.75 0.00 0.00 3.08
4762 6301 3.669251 ACAGAGCTCTACTTCAACCAC 57.331 47.619 17.75 0.00 0.00 4.16
4789 6328 2.095461 AGCGACTGAATAGCTCACTGA 58.905 47.619 0.00 0.00 33.30 3.41
4806 6345 4.941873 AGGTTATAAGGGAAGAAAACAGCG 59.058 41.667 0.00 0.00 0.00 5.18
4843 6409 8.353423 AGCATCTACAACCTGAATTTACAATT 57.647 30.769 0.00 0.00 0.00 2.32
4861 6427 8.901676 AGCTATCCAGTGGCTAAGAGCATCTA 62.902 46.154 15.91 0.00 43.84 1.98
4862 6428 8.901676 TAGCTATCCAGTGGCTAAGAGCATCT 62.902 46.154 15.91 1.45 46.98 2.90
4863 6429 2.926778 ATCCAGTGGCTAAGAGCATC 57.073 50.000 3.51 0.00 44.75 3.91
4864 6430 2.038295 GCTATCCAGTGGCTAAGAGCAT 59.962 50.000 3.51 0.00 44.75 3.79
4865 6431 1.414181 GCTATCCAGTGGCTAAGAGCA 59.586 52.381 3.51 0.00 44.75 4.26
4866 6432 1.691434 AGCTATCCAGTGGCTAAGAGC 59.309 52.381 3.51 6.05 43.59 4.09
4873 6439 2.224314 GCGAATTTAGCTATCCAGTGGC 59.776 50.000 3.51 0.00 33.92 5.01
4874 6440 3.466836 TGCGAATTTAGCTATCCAGTGG 58.533 45.455 1.40 1.40 35.28 4.00
4885 6659 4.346129 GCAAGACCTCATTGCGAATTTAG 58.654 43.478 0.00 0.00 43.15 1.85
4894 6699 3.928727 AACACATGCAAGACCTCATTG 57.071 42.857 0.00 0.00 0.00 2.82
4921 7091 7.063308 GCATTACTGATGTGTGGGTAATTTTTG 59.937 37.037 0.00 0.00 38.07 2.44
4926 7096 4.854173 TGCATTACTGATGTGTGGGTAAT 58.146 39.130 0.00 0.00 38.07 1.89
4928 7098 3.990959 TGCATTACTGATGTGTGGGTA 57.009 42.857 0.00 0.00 38.07 3.69
4934 7104 7.622672 GCTTTTGGAAAATGCATTACTGATGTG 60.623 37.037 13.39 2.51 38.07 3.21
4943 7113 4.276431 CCTTGTGCTTTTGGAAAATGCATT 59.724 37.500 5.99 5.99 35.83 3.56
4966 7467 9.665264 CTTTCACTTTGTACATTAAAGAGTTCC 57.335 33.333 11.79 0.00 38.26 3.62
5009 7510 1.542492 AAATGAGCAGTTGGCCTCTG 58.458 50.000 19.30 19.30 46.50 3.35
5013 7514 1.150827 GCAAAAATGAGCAGTTGGCC 58.849 50.000 0.00 0.00 46.50 5.36
5028 7529 1.901159 CTTTGATGTGATGGGGGCAAA 59.099 47.619 0.00 0.00 0.00 3.68
5031 7532 1.205417 CAACTTTGATGTGATGGGGGC 59.795 52.381 0.00 0.00 0.00 5.80
5032 7533 2.806434 TCAACTTTGATGTGATGGGGG 58.194 47.619 0.00 0.00 31.01 5.40
5044 7550 7.742089 CGTTTGACTAGCTATCTTTCAACTTTG 59.258 37.037 0.00 0.00 0.00 2.77
5054 7560 7.747155 TTATCTAGCGTTTGACTAGCTATCT 57.253 36.000 0.00 0.00 41.84 1.98
5073 7579 8.971073 CCCAGTCTTCCACAAAATAAATTATCT 58.029 33.333 0.00 0.00 0.00 1.98
5075 7581 8.893563 TCCCAGTCTTCCACAAAATAAATTAT 57.106 30.769 0.00 0.00 0.00 1.28
5099 7605 8.135382 TCCCCAGTTATATTAGCTATCAACTC 57.865 38.462 0.00 0.00 0.00 3.01
5101 7608 7.606839 GGTTCCCCAGTTATATTAGCTATCAAC 59.393 40.741 0.00 0.00 0.00 3.18
5126 7633 3.906008 CCGAATTATTAGCGAATTTGCGG 59.094 43.478 12.05 2.59 40.67 5.69
5129 7636 6.430451 AGCTTCCGAATTATTAGCGAATTTG 58.570 36.000 0.00 0.00 36.96 2.32
5135 7642 4.449068 ACATGAGCTTCCGAATTATTAGCG 59.551 41.667 0.00 0.00 36.96 4.26
5156 7663 5.976458 AGAAAAGCTTTTGGAATGTGAACA 58.024 33.333 28.42 0.00 0.00 3.18
5161 7668 4.502087 GGCTGAGAAAAGCTTTTGGAATGT 60.502 41.667 28.42 2.95 43.06 2.71
5167 7674 2.781945 ACGGCTGAGAAAAGCTTTTG 57.218 45.000 28.42 14.92 43.06 2.44
5173 7680 0.512952 CGGACAACGGCTGAGAAAAG 59.487 55.000 0.00 0.00 39.42 2.27
5190 7697 3.423154 GAGCGTTGCCTTGTCCGG 61.423 66.667 0.00 0.00 0.00 5.14
5192 7699 2.281484 TGGAGCGTTGCCTTGTCC 60.281 61.111 0.00 0.00 0.00 4.02
5194 7701 2.281761 CCTGGAGCGTTGCCTTGT 60.282 61.111 0.00 0.00 0.00 3.16
5217 7724 2.752322 TGCCTTTGCAGCAACGATGC 62.752 55.000 13.10 10.01 45.81 3.91
5218 7725 1.286570 TGCCTTTGCAGCAACGATG 59.713 52.632 13.10 1.10 44.23 3.84
5219 7726 3.762293 TGCCTTTGCAGCAACGAT 58.238 50.000 13.10 0.00 44.23 3.73
5228 7735 1.251251 ACTTCAGTCCATGCCTTTGC 58.749 50.000 0.00 0.00 38.26 3.68
5229 7736 2.886523 TGAACTTCAGTCCATGCCTTTG 59.113 45.455 0.00 0.00 0.00 2.77
5230 7737 2.887152 GTGAACTTCAGTCCATGCCTTT 59.113 45.455 0.00 0.00 0.00 3.11
5231 7738 2.107204 AGTGAACTTCAGTCCATGCCTT 59.893 45.455 0.00 0.00 0.00 4.35
5233 7740 1.808945 CAGTGAACTTCAGTCCATGCC 59.191 52.381 0.00 0.00 0.00 4.40
5234 7741 2.771089 TCAGTGAACTTCAGTCCATGC 58.229 47.619 0.00 0.00 0.00 4.06
5235 7742 4.739046 GTTCAGTGAACTTCAGTCCATG 57.261 45.455 25.56 0.00 39.23 3.66
5246 7753 5.149054 CACTCTTGTGAAGTTCAGTGAAC 57.851 43.478 25.51 25.51 46.55 3.18
5259 7766 1.534163 CCTGTGTGCATCACTCTTGTG 59.466 52.381 16.70 0.00 46.27 3.33
5262 7769 0.109153 TGCCTGTGTGCATCACTCTT 59.891 50.000 16.70 0.00 46.27 2.85
5263 7770 0.604780 GTGCCTGTGTGCATCACTCT 60.605 55.000 16.70 0.00 46.27 3.24
5264 7771 0.886043 TGTGCCTGTGTGCATCACTC 60.886 55.000 16.70 9.10 46.27 3.51
5265 7772 0.466007 TTGTGCCTGTGTGCATCACT 60.466 50.000 16.70 0.00 46.27 3.41
5266 7773 0.318107 GTTGTGCCTGTGTGCATCAC 60.318 55.000 11.13 11.13 44.30 3.06
5267 7774 0.750911 TGTTGTGCCTGTGTGCATCA 60.751 50.000 0.00 0.00 44.30 3.07
5270 7777 0.750911 TCATGTTGTGCCTGTGTGCA 60.751 50.000 0.00 0.00 39.37 4.57
5271 7778 0.039798 CTCATGTTGTGCCTGTGTGC 60.040 55.000 0.00 0.00 0.00 4.57
5273 7780 2.158769 TCTTCTCATGTTGTGCCTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
5274 7781 2.497138 TCTTCTCATGTTGTGCCTGTG 58.503 47.619 0.00 0.00 0.00 3.66
5275 7782 2.880890 GTTCTTCTCATGTTGTGCCTGT 59.119 45.455 0.00 0.00 0.00 4.00
5278 7785 3.988379 TTGTTCTTCTCATGTTGTGCC 57.012 42.857 0.00 0.00 0.00 5.01
5279 7786 7.928908 TTTTATTGTTCTTCTCATGTTGTGC 57.071 32.000 0.00 0.00 0.00 4.57
5315 7822 7.325097 CGTTCGCTGAAACATTTTATAGGTTTT 59.675 33.333 0.00 0.00 35.08 2.43
5316 7823 6.799925 CGTTCGCTGAAACATTTTATAGGTTT 59.200 34.615 0.00 0.00 37.44 3.27
5318 7825 5.163794 CCGTTCGCTGAAACATTTTATAGGT 60.164 40.000 0.00 0.00 0.00 3.08
5320 7827 5.864986 ACCGTTCGCTGAAACATTTTATAG 58.135 37.500 0.00 0.00 0.00 1.31
5321 7828 5.866335 ACCGTTCGCTGAAACATTTTATA 57.134 34.783 0.00 0.00 0.00 0.98
5323 7830 4.510711 TGTACCGTTCGCTGAAACATTTTA 59.489 37.500 0.00 0.00 0.00 1.52
5324 7831 3.312973 TGTACCGTTCGCTGAAACATTTT 59.687 39.130 0.00 0.00 0.00 1.82
5325 7832 2.873472 TGTACCGTTCGCTGAAACATTT 59.127 40.909 0.00 0.00 0.00 2.32
5327 7834 2.157834 TGTACCGTTCGCTGAAACAT 57.842 45.000 0.00 0.00 0.00 2.71
5328 7835 2.157834 ATGTACCGTTCGCTGAAACA 57.842 45.000 0.00 0.00 0.00 2.83
5330 7837 5.038683 CAGTATATGTACCGTTCGCTGAAA 58.961 41.667 0.00 0.00 0.00 2.69
5331 7838 4.603985 CAGTATATGTACCGTTCGCTGAA 58.396 43.478 0.00 0.00 0.00 3.02
5332 7839 3.549423 GCAGTATATGTACCGTTCGCTGA 60.549 47.826 0.00 0.00 0.00 4.26
5333 7840 2.724690 GCAGTATATGTACCGTTCGCTG 59.275 50.000 0.00 0.00 0.00 5.18
5336 7843 1.712350 GCGCAGTATATGTACCGTTCG 59.288 52.381 0.30 0.00 0.00 3.95
5337 7844 2.056577 GGCGCAGTATATGTACCGTTC 58.943 52.381 10.83 0.00 0.00 3.95
5339 7846 0.039798 CGGCGCAGTATATGTACCGT 60.040 55.000 10.83 0.00 41.67 4.83
5340 7847 0.239082 TCGGCGCAGTATATGTACCG 59.761 55.000 10.83 0.00 45.42 4.02
5341 7848 2.649331 ATCGGCGCAGTATATGTACC 57.351 50.000 10.83 0.00 0.00 3.34
5342 7849 4.698276 CAAAATCGGCGCAGTATATGTAC 58.302 43.478 10.83 0.00 0.00 2.90
5343 7850 3.185594 GCAAAATCGGCGCAGTATATGTA 59.814 43.478 10.83 0.00 0.00 2.29
5344 7851 2.032030 GCAAAATCGGCGCAGTATATGT 60.032 45.455 10.83 0.00 0.00 2.29
5346 7853 2.969443 GCAAAATCGGCGCAGTATAT 57.031 45.000 10.83 0.00 0.00 0.86
5355 7862 1.226018 CCTCGTTCGCAAAATCGGC 60.226 57.895 0.00 0.00 0.00 5.54
5357 7864 1.068474 AGACCTCGTTCGCAAAATCG 58.932 50.000 0.00 0.00 0.00 3.34
5358 7865 2.839474 CAAGACCTCGTTCGCAAAATC 58.161 47.619 0.00 0.00 0.00 2.17
5359 7866 1.069227 GCAAGACCTCGTTCGCAAAAT 60.069 47.619 0.00 0.00 0.00 1.82
5360 7867 0.306533 GCAAGACCTCGTTCGCAAAA 59.693 50.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.