Multiple sequence alignment - TraesCS4B01G240100

Loading Multiple Alignment...

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 TraesCS4B01G240100 chr4B 100.000 7260 0 0 1 7260 497868930 497861671 0.000000e+00 13407
1 TraesCS4B01G240100 chr4A 94.044 4181 155 26 2 4128 59679123 59674983 0.000000e+00 6255
2 TraesCS4B01G240100 chr4A 95.521 2590 74 17 4484 7034 59674319 59671733 0.000000e+00 4102
3 TraesCS4B01G240100 chr4A 92.935 368 15 5 4127 4485 59674912 59674547 6.450000e-145 525
4 TraesCS4B01G240100 chr4D 95.938 2511 84 11 1989 4485 402239257 402236751 0.000000e+00 4056
5 TraesCS4B01G240100 chr4D 95.147 2081 59 7 4484 6543 402236533 402234474 0.000000e+00 3245
6 TraesCS4B01G240100 chr4D 93.597 1999 60 23 2 1957 402241231 402239258 0.000000e+00 2920
7 TraesCS4B01G240100 chr4D 91.068 459 18 9 6577 7034 402234474 402234038 3.750000e-167 599
8 TraesCS4B01G240100 chr4D 86.207 116 8 5 7001 7116 402234031 402233924 1.280000e-22 119
9 TraesCS4B01G240100 chr3D 77.974 227 41 8 4611 4833 515551804 515552025 4.570000e-27 134


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 TraesCS4B01G240100 chr4B 497861671 497868930 7259 True 13407.000000 13407 100.000000 1 7260 1 chr4B.!!$R1 7259
1 TraesCS4B01G240100 chr4A 59671733 59679123 7390 True 3627.333333 6255 94.166667 2 7034 3 chr4A.!!$R1 7032
2 TraesCS4B01G240100 chr4D 402233924 402241231 7307 True 2187.800000 4056 92.391400 2 7116 5 chr4D.!!$R1 7114

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
359 368 0.099968 GTATGCAGCTCGTACCGTCA 59.900 55.000 0.00 0.00 32.29 4.35 F
431 440 0.598065 GCCACGTTTCAAATCCAGCT 59.402 50.000 0.00 0.00 0.00 4.24 F
1171 1224 1.957695 TCTCGCTTGCTGTGCTGTG 60.958 57.895 0.00 0.00 0.00 3.66 F
2552 2605 1.002134 CCGGTTCAGCATCCTTGGT 60.002 57.895 0.00 0.00 0.00 3.67 F
2993 3048 0.371645 GCTTGTAGCGTCTGTGATGC 59.628 55.000 3.80 3.80 44.07 3.91 F
3177 3232 2.500098 GTCATGTGGTAGAAGCACCCTA 59.500 50.000 6.77 0.00 45.33 3.53 F
4513 4886 2.021457 TGGATTGATGCTGACATGCTG 58.979 47.619 0.00 0.00 36.35 4.41 F
5533 5917 1.612442 TTTCCCAGCTAGCGAGGGT 60.612 57.895 33.58 7.78 43.31 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1893 0.035152 ATTGGGTTGAGCGAGCATCA 60.035 50.0 0.00 0.00 33.17 3.07 R
2034 2087 0.107703 CGCAATCAGGAGCCTGGTTA 60.108 55.0 14.31 0.00 44.67 2.85 R
2970 3025 1.073216 CACAGACGCTACAAGCTCCG 61.073 60.0 0.00 0.00 39.60 4.63 R
4496 4869 2.139323 ACCAGCATGTCAGCATCAAT 57.861 45.0 0.00 0.00 36.85 2.57 R
4513 4886 2.354821 GGAATGCACAACGGAGATAACC 59.645 50.0 0.00 0.00 0.00 2.85 R
4623 4996 4.636648 TCCAAAAACGTCACTTATGTGTGT 59.363 37.5 8.46 6.21 44.14 3.72 R
5818 6202 0.044092 TAGAGCCCACTCCCATTGGA 59.956 55.0 3.62 0.00 44.65 3.53 R
7137 7609 0.031111 TGCTACTGGGGTAGATGGCT 60.031 55.0 7.28 0.00 46.01 4.75 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
110 111 4.825634 GCAACCTTTACAAGACCTAGGTTT 59.174 41.667 17.53 7.69 44.57 3.27
225 230 1.007721 AGGAGATGGAGTGGCTAGTGT 59.992 52.381 0.00 0.00 0.00 3.55
227 232 3.031736 GGAGATGGAGTGGCTAGTGTAA 58.968 50.000 0.00 0.00 0.00 2.41
274 279 1.210931 CCGCTCTCGTTACGTGGAA 59.789 57.895 4.24 0.00 0.00 3.53
277 282 0.109226 GCTCTCGTTACGTGGAAGCT 60.109 55.000 4.24 0.00 0.00 3.74
278 283 1.897641 CTCTCGTTACGTGGAAGCTC 58.102 55.000 4.24 0.00 0.00 4.09
279 284 0.167470 TCTCGTTACGTGGAAGCTCG 59.833 55.000 4.24 0.00 0.00 5.03
280 285 0.797249 CTCGTTACGTGGAAGCTCGG 60.797 60.000 4.24 0.00 0.00 4.63
281 286 1.210931 CGTTACGTGGAAGCTCGGA 59.789 57.895 0.00 0.00 0.00 4.55
332 341 4.200283 GCGAGGAGGACCGCTCTG 62.200 72.222 0.00 0.00 46.96 3.35
359 368 0.099968 GTATGCAGCTCGTACCGTCA 59.900 55.000 0.00 0.00 32.29 4.35
418 427 3.829601 TCTTTGGAAATTTATGGCCACGT 59.170 39.130 8.16 0.00 0.00 4.49
431 440 0.598065 GCCACGTTTCAAATCCAGCT 59.402 50.000 0.00 0.00 0.00 4.24
444 453 8.752005 TTCAAATCCAGCTAATATTAACAGCT 57.248 30.769 5.54 5.54 46.36 4.24
452 461 7.464830 AGCTAATATTAACAGCTGTTACACG 57.535 36.000 33.52 20.33 43.82 4.49
455 464 7.436080 GCTAATATTAACAGCTGTTACACGGTA 59.564 37.037 33.52 20.81 39.92 4.02
456 465 9.472361 CTAATATTAACAGCTGTTACACGGTAT 57.528 33.333 33.52 25.07 39.92 2.73
459 468 4.796038 AACAGCTGTTACACGGTATACT 57.204 40.909 30.25 1.16 36.32 2.12
466 475 2.340210 TACACGGTATACTACGCCCA 57.660 50.000 2.25 0.00 0.00 5.36
494 503 7.196331 GGAAGGAAAGTTAATCAATTCCATCG 58.804 38.462 6.21 0.00 43.03 3.84
1167 1220 3.782244 CCGTCTCGCTTGCTGTGC 61.782 66.667 0.00 0.00 0.00 4.57
1169 1222 2.858868 GTCTCGCTTGCTGTGCTG 59.141 61.111 0.00 0.00 0.00 4.41
1170 1223 1.958205 GTCTCGCTTGCTGTGCTGT 60.958 57.895 0.00 0.00 0.00 4.40
1171 1224 1.957695 TCTCGCTTGCTGTGCTGTG 60.958 57.895 0.00 0.00 0.00 3.66
1189 1242 2.251642 GGTGGTGTCGTGTTGCTCC 61.252 63.158 0.00 0.00 0.00 4.70
1206 1259 4.776322 CGGTGCCGCCTGATTGGA 62.776 66.667 0.00 0.00 38.35 3.53
1418 1471 4.726317 TGTCTGGGGAATGGATTTCTGATA 59.274 41.667 0.00 0.00 34.56 2.15
1458 1511 3.055458 TGGTAATTGCGTTGGAGATCTGA 60.055 43.478 0.00 0.00 0.00 3.27
1470 1523 3.131223 TGGAGATCTGACTGGATTCGTTC 59.869 47.826 0.00 0.00 0.00 3.95
1471 1524 3.491792 GGAGATCTGACTGGATTCGTTCC 60.492 52.174 0.00 0.88 45.69 3.62
1507 1560 2.751259 AGCAGGCTCATGTGTATTGTTG 59.249 45.455 0.00 0.00 0.00 3.33
1544 1597 4.081586 TGCAATGCTTAATCCATTTGCAGA 60.082 37.500 6.82 0.00 37.07 4.26
1722 1775 5.048991 ACCGAAAATGGTTGATGTACAGTTC 60.049 40.000 0.33 0.00 39.99 3.01
1785 1838 5.428253 ACACGCTGTCAATATAATCCAACT 58.572 37.500 0.00 0.00 0.00 3.16
1840 1893 4.250305 AGTGTTTCCCGGCGCTGT 62.250 61.111 16.49 0.00 0.00 4.40
1979 2032 7.661536 TCATATGTATCCCTTGCCTATAGAC 57.338 40.000 0.00 0.00 0.00 2.59
1986 2039 5.405063 TCCCTTGCCTATAGACTCTACTT 57.595 43.478 0.00 0.00 0.00 2.24
2052 2105 2.158696 AGATAACCAGGCTCCTGATTGC 60.159 50.000 17.08 3.90 46.30 3.56
2184 2237 1.073629 TGTGGAGGTTGTACCCCCA 60.074 57.895 0.00 0.00 39.75 4.96
2216 2269 6.019237 CAGTAAGTGTGCTATGAATGCTAGTG 60.019 42.308 0.00 0.00 0.00 2.74
2292 2345 9.076596 GGACATAATGTTTGAGAAAATTAGCAC 57.923 33.333 0.00 0.00 0.00 4.40
2394 2447 1.195448 CCAGCATTCTTGACACACGTC 59.805 52.381 0.00 0.00 42.93 4.34
2423 2476 1.369689 GTGCTTGCTTGTGTCGCAG 60.370 57.895 0.00 0.00 38.80 5.18
2424 2477 1.819208 TGCTTGCTTGTGTCGCAGT 60.819 52.632 0.00 0.00 38.80 4.40
2552 2605 1.002134 CCGGTTCAGCATCCTTGGT 60.002 57.895 0.00 0.00 0.00 3.67
2692 2745 5.596361 TGGGTGCATGGGTATATGTTTTTAG 59.404 40.000 0.00 0.00 0.00 1.85
2730 2783 1.752753 TGTTGCTTTTCAATCGCACG 58.247 45.000 0.00 0.00 36.99 5.34
2803 2858 9.880157 TTCAAATATAGACCCACTTGTACTTAC 57.120 33.333 0.00 0.00 0.00 2.34
2815 2870 7.095187 CCCACTTGTACTTACTTCAGTGAAATC 60.095 40.741 7.06 0.00 34.36 2.17
2816 2871 7.359264 CCACTTGTACTTACTTCAGTGAAATCG 60.359 40.741 7.06 0.00 34.36 3.34
2878 2933 2.348666 CAGTTGGTAGCGAGCATTACAC 59.651 50.000 0.00 0.00 31.88 2.90
2904 2959 5.934043 TCATGTCGTCTTTGATGAATGAGTT 59.066 36.000 0.00 0.00 30.17 3.01
2970 3025 1.966451 CAAAGGCCCGTGACTCCAC 60.966 63.158 0.00 0.00 39.86 4.02
2993 3048 0.371645 GCTTGTAGCGTCTGTGATGC 59.628 55.000 3.80 3.80 44.07 3.91
3100 3155 7.398024 AGCAGATACAAAAGAAAGACCAGTAT 58.602 34.615 0.00 0.00 0.00 2.12
3177 3232 2.500098 GTCATGTGGTAGAAGCACCCTA 59.500 50.000 6.77 0.00 45.33 3.53
3250 3308 4.160252 ACAGGACAGCTCAAAACATTTTGT 59.840 37.500 14.95 0.00 45.77 2.83
3259 3317 5.655488 CTCAAAACATTTTGTACACCCACA 58.345 37.500 14.95 0.00 45.77 4.17
3265 3323 5.983540 ACATTTTGTACACCCACAAACATT 58.016 33.333 0.00 0.00 45.52 2.71
3297 3355 6.419116 CGTTCTGTCTGGATATACATGACTTG 59.581 42.308 14.68 9.81 0.00 3.16
3332 3390 3.133691 CGCATTATACTGTCACTGCCAT 58.866 45.455 0.00 0.00 0.00 4.40
3333 3391 3.561310 CGCATTATACTGTCACTGCCATT 59.439 43.478 0.00 0.00 0.00 3.16
3386 3446 7.230510 TGTTACTGTATTGTTTTCTGCTCCATT 59.769 33.333 0.00 0.00 0.00 3.16
3391 3451 9.888878 CTGTATTGTTTTCTGCTCCATTATATG 57.111 33.333 0.00 0.00 0.00 1.78
3399 3459 9.425248 TTTTCTGCTCCATTATATGATCCTTTT 57.575 29.630 0.00 0.00 0.00 2.27
3663 3723 4.260784 GGATGCGATACTAAAGCTTGTTGG 60.261 45.833 0.00 0.00 0.00 3.77
3706 3766 5.049167 GCTGATTCAAGGACAGATCTAGTG 58.951 45.833 0.00 0.00 34.07 2.74
4024 4084 3.971032 CCAAGAGTTGTTTGGTCAGTC 57.029 47.619 0.00 0.00 40.15 3.51
4193 4325 6.554334 TTTATCAAGCAAGTGTGGTTACTC 57.446 37.500 0.00 0.00 43.55 2.59
4206 4338 6.495872 AGTGTGGTTACTCTTGAACACCTATA 59.504 38.462 0.00 0.00 38.91 1.31
4381 4523 8.990163 TGTCTTCAACCTTTTTAGTATCCTTT 57.010 30.769 0.00 0.00 0.00 3.11
4432 4575 6.702329 ACTGGTGACTTCTCTATTTTACTGG 58.298 40.000 0.00 0.00 0.00 4.00
4461 4604 4.161565 ACGCTCCTGGATGTTAGTAATTGA 59.838 41.667 0.00 0.00 0.00 2.57
4462 4605 5.163301 ACGCTCCTGGATGTTAGTAATTGAT 60.163 40.000 0.00 0.00 0.00 2.57
4485 4628 8.768397 TGATTACATTTTACACCTCAGTATCCT 58.232 33.333 0.00 0.00 0.00 3.24
4496 4869 6.901300 ACACCTCAGTATCCTATTTTAGTGGA 59.099 38.462 0.00 0.00 0.00 4.02
4513 4886 2.021457 TGGATTGATGCTGACATGCTG 58.979 47.619 0.00 0.00 36.35 4.41
4523 4896 2.477825 CTGACATGCTGGTTATCTCCG 58.522 52.381 0.00 0.00 0.00 4.63
4623 4996 8.523658 CAGATTCATCATATACTCCTTCCGTAA 58.476 37.037 0.00 0.00 0.00 3.18
4899 5283 2.030805 GCTGAGTTGATTTCTTGCGGTT 60.031 45.455 0.00 0.00 0.00 4.44
4904 5288 5.049680 TGAGTTGATTTCTTGCGGTTACTTC 60.050 40.000 0.00 0.00 0.00 3.01
5218 5602 3.760684 CTGCAGTCAAAGGAAATAAGCCT 59.239 43.478 5.25 0.00 37.35 4.58
5491 5875 2.224670 TGTCAAACCTTCCGGCATAGTT 60.225 45.455 0.00 0.00 0.00 2.24
5533 5917 1.612442 TTTCCCAGCTAGCGAGGGT 60.612 57.895 33.58 7.78 43.31 4.34
5741 6125 6.595682 GGAAATCTTCCTGGTCTCATGAATA 58.404 40.000 0.00 0.00 46.57 1.75
5743 6127 7.419518 GGAAATCTTCCTGGTCTCATGAATAGA 60.420 40.741 0.00 0.00 46.57 1.98
5759 6143 9.234827 TCATGAATAGAAACTCAAATGTGATGT 57.765 29.630 0.00 0.00 31.85 3.06
5791 6175 5.416013 AGGAATAAGTAGCTTTCAAACTGGC 59.584 40.000 0.00 0.00 0.00 4.85
5821 6205 7.293299 ACTCCATATCTGGTTAATCAGAATCCA 59.707 37.037 21.87 8.52 45.54 3.41
5828 6212 5.533903 CTGGTTAATCAGAATCCAATGGGAG 59.466 44.000 10.40 0.00 40.90 4.30
5886 6270 4.636249 AGCACTGACTCTCTTAACCAAAG 58.364 43.478 0.00 0.00 36.45 2.77
5908 6292 4.946157 AGCTATGCTTATGCCAACCATATC 59.054 41.667 0.00 0.00 33.89 1.63
5998 6382 1.215423 ACAGGTGGCTGGTCTTCTTTT 59.785 47.619 0.00 0.00 0.00 2.27
6013 6397 6.758416 GGTCTTCTTTTCAAAATATGGATGGC 59.242 38.462 0.00 0.00 0.00 4.40
6085 6469 1.201647 CAGAGTTCAAATGCAGCCCTG 59.798 52.381 0.00 0.00 0.00 4.45
6324 6711 8.099364 AGTCAACTTTGTTGTATTCATGGTAG 57.901 34.615 9.78 0.00 0.00 3.18
6509 6910 3.688235 AGTCTAGCCGTAGCCTATTAGG 58.312 50.000 5.28 5.28 41.25 2.69
6515 6931 1.264295 CGTAGCCTATTAGGGACCCC 58.736 60.000 7.00 1.17 35.37 4.95
6530 6946 3.487372 GGACCCCTGTTAATTATGCTCC 58.513 50.000 0.00 0.00 0.00 4.70
6575 7004 7.275920 ACTCTCTTTTCTAACATGTGTTCACT 58.724 34.615 0.00 0.00 39.31 3.41
6646 7075 2.749621 GTGCAGGGTAATCACTGGAAAG 59.250 50.000 0.00 0.00 46.33 2.62
6839 7269 4.528920 TGGCCTAGTTAACTTGTGTGTTT 58.471 39.130 14.49 0.00 0.00 2.83
6857 7287 6.261381 GTGTGTTTGTTTAGTCCCATCTAACA 59.739 38.462 0.00 0.00 30.87 2.41
6858 7288 6.485313 TGTGTTTGTTTAGTCCCATCTAACAG 59.515 38.462 0.00 0.00 30.87 3.16
6990 7422 8.457238 AGTTTAGAGGATTAAGAATTGCATCC 57.543 34.615 0.00 0.00 38.75 3.51
7036 7508 4.321974 GCTGTAAAGCCTGTAAATTGCCTT 60.322 41.667 0.00 0.00 0.00 4.35
7041 7513 2.041620 AGCCTGTAAATTGCCTTCCTGA 59.958 45.455 0.00 0.00 0.00 3.86
7046 7518 1.928868 AAATTGCCTTCCTGAGTGGG 58.071 50.000 0.00 0.00 36.20 4.61
7057 7529 1.886542 CCTGAGTGGGCCTACAAAAAC 59.113 52.381 22.57 7.61 0.00 2.43
7065 7537 5.650703 AGTGGGCCTACAAAAACATATACAC 59.349 40.000 22.57 5.79 0.00 2.90
7066 7538 5.416326 GTGGGCCTACAAAAACATATACACA 59.584 40.000 15.42 0.00 0.00 3.72
7070 7542 8.038351 GGGCCTACAAAAACATATACACATTTT 58.962 33.333 0.84 0.00 0.00 1.82
7079 7551 9.995003 AAAACATATACACATTTTTGTCCATGT 57.005 25.926 0.00 0.00 36.38 3.21
7082 7554 8.405531 ACATATACACATTTTTGTCCATGTAGC 58.594 33.333 0.00 0.00 34.58 3.58
7083 7555 4.519540 ACACATTTTTGTCCATGTAGCC 57.480 40.909 0.00 0.00 32.16 3.93
7084 7556 3.894427 ACACATTTTTGTCCATGTAGCCA 59.106 39.130 0.00 0.00 32.16 4.75
7085 7557 4.343526 ACACATTTTTGTCCATGTAGCCAA 59.656 37.500 0.00 0.00 32.16 4.52
7086 7558 4.925054 CACATTTTTGTCCATGTAGCCAAG 59.075 41.667 0.00 0.00 32.16 3.61
7087 7559 4.588528 ACATTTTTGTCCATGTAGCCAAGT 59.411 37.500 0.00 0.00 31.60 3.16
7088 7560 4.846779 TTTTTGTCCATGTAGCCAAGTC 57.153 40.909 0.00 0.00 0.00 3.01
7089 7561 3.788227 TTTGTCCATGTAGCCAAGTCT 57.212 42.857 0.00 0.00 0.00 3.24
7093 7565 1.555075 TCCATGTAGCCAAGTCTGTCC 59.445 52.381 0.00 0.00 0.00 4.02
7095 7567 2.419297 CCATGTAGCCAAGTCTGTCCTC 60.419 54.545 0.00 0.00 0.00 3.71
7116 7588 6.040955 TCCTCGATATGTTGCTAGTCATTTCT 59.959 38.462 0.00 0.00 0.00 2.52
7117 7589 6.145209 CCTCGATATGTTGCTAGTCATTTCTG 59.855 42.308 0.00 0.00 0.00 3.02
7118 7590 5.985530 TCGATATGTTGCTAGTCATTTCTGG 59.014 40.000 0.00 0.00 0.00 3.86
7119 7591 5.333645 CGATATGTTGCTAGTCATTTCTGGC 60.334 44.000 0.00 0.00 41.26 4.85
7120 7592 3.423539 TGTTGCTAGTCATTTCTGGCT 57.576 42.857 4.02 0.00 41.41 4.75
7121 7593 4.551702 TGTTGCTAGTCATTTCTGGCTA 57.448 40.909 4.02 0.00 41.41 3.93
7128 7600 2.686915 AGTCATTTCTGGCTAGCAATGC 59.313 45.455 18.24 11.51 37.43 3.56
7138 7610 4.234530 GGCTAGCAATGCCTGATTTAAG 57.765 45.455 18.24 0.00 46.38 1.85
7139 7611 3.551659 GGCTAGCAATGCCTGATTTAAGC 60.552 47.826 18.24 0.00 46.38 3.09
7140 7612 3.551659 GCTAGCAATGCCTGATTTAAGCC 60.552 47.826 10.63 0.00 0.00 4.35
7141 7613 2.459644 AGCAATGCCTGATTTAAGCCA 58.540 42.857 0.00 0.00 0.00 4.75
7142 7614 3.036091 AGCAATGCCTGATTTAAGCCAT 58.964 40.909 0.00 0.00 0.00 4.40
7143 7615 3.069158 AGCAATGCCTGATTTAAGCCATC 59.931 43.478 0.00 0.00 0.00 3.51
7144 7616 3.069158 GCAATGCCTGATTTAAGCCATCT 59.931 43.478 0.00 0.00 0.00 2.90
7145 7617 4.279169 GCAATGCCTGATTTAAGCCATCTA 59.721 41.667 0.00 0.00 0.00 1.98
7146 7618 5.766222 CAATGCCTGATTTAAGCCATCTAC 58.234 41.667 0.00 0.00 0.00 2.59
7147 7619 3.820557 TGCCTGATTTAAGCCATCTACC 58.179 45.455 0.00 0.00 0.00 3.18
7148 7620 3.149981 GCCTGATTTAAGCCATCTACCC 58.850 50.000 0.00 0.00 0.00 3.69
7149 7621 3.756117 CCTGATTTAAGCCATCTACCCC 58.244 50.000 0.00 0.00 0.00 4.95
7150 7622 3.138283 CCTGATTTAAGCCATCTACCCCA 59.862 47.826 0.00 0.00 0.00 4.96
7151 7623 4.392940 CTGATTTAAGCCATCTACCCCAG 58.607 47.826 0.00 0.00 0.00 4.45
7152 7624 3.785887 TGATTTAAGCCATCTACCCCAGT 59.214 43.478 0.00 0.00 0.00 4.00
7153 7625 4.972568 TGATTTAAGCCATCTACCCCAGTA 59.027 41.667 0.00 0.00 0.00 2.74
7154 7626 5.071788 TGATTTAAGCCATCTACCCCAGTAG 59.928 44.000 0.00 0.00 46.34 2.57
7155 7627 1.132500 AAGCCATCTACCCCAGTAGC 58.868 55.000 0.00 0.00 44.87 3.58
7156 7628 0.031111 AGCCATCTACCCCAGTAGCA 60.031 55.000 0.00 0.00 44.87 3.49
7157 7629 0.394565 GCCATCTACCCCAGTAGCAG 59.605 60.000 0.00 0.00 44.87 4.24
7158 7630 1.794714 CCATCTACCCCAGTAGCAGT 58.205 55.000 0.00 0.00 44.87 4.40
7159 7631 2.958818 CCATCTACCCCAGTAGCAGTA 58.041 52.381 0.00 0.00 44.87 2.74
7160 7632 2.628657 CCATCTACCCCAGTAGCAGTAC 59.371 54.545 0.00 0.00 44.87 2.73
7161 7633 3.567397 CATCTACCCCAGTAGCAGTACT 58.433 50.000 0.00 0.00 44.87 2.73
7162 7634 4.447325 CCATCTACCCCAGTAGCAGTACTA 60.447 50.000 0.00 0.00 44.87 1.82
7163 7635 4.434545 TCTACCCCAGTAGCAGTACTAG 57.565 50.000 0.00 0.00 44.87 2.57
7164 7636 4.042884 TCTACCCCAGTAGCAGTACTAGA 58.957 47.826 0.00 0.00 44.87 2.43
7165 7637 3.752359 ACCCCAGTAGCAGTACTAGAA 57.248 47.619 0.00 0.00 37.40 2.10
7166 7638 4.267341 ACCCCAGTAGCAGTACTAGAAT 57.733 45.455 0.00 0.00 37.40 2.40
7167 7639 4.621769 ACCCCAGTAGCAGTACTAGAATT 58.378 43.478 0.00 0.00 37.40 2.17
7168 7640 5.774179 ACCCCAGTAGCAGTACTAGAATTA 58.226 41.667 0.00 0.00 37.40 1.40
7169 7641 5.834204 ACCCCAGTAGCAGTACTAGAATTAG 59.166 44.000 0.00 0.00 37.40 1.73
7170 7642 5.279056 CCCCAGTAGCAGTACTAGAATTAGC 60.279 48.000 0.00 0.00 37.40 3.09
7171 7643 5.302059 CCCAGTAGCAGTACTAGAATTAGCA 59.698 44.000 0.00 0.00 37.40 3.49
7172 7644 6.015010 CCCAGTAGCAGTACTAGAATTAGCAT 60.015 42.308 0.00 0.00 37.40 3.79
7173 7645 7.437748 CCAGTAGCAGTACTAGAATTAGCATT 58.562 38.462 0.00 0.00 37.40 3.56
7174 7646 7.928706 CCAGTAGCAGTACTAGAATTAGCATTT 59.071 37.037 0.00 0.00 37.40 2.32
7175 7647 9.319143 CAGTAGCAGTACTAGAATTAGCATTTT 57.681 33.333 0.00 0.00 37.40 1.82
7176 7648 9.535878 AGTAGCAGTACTAGAATTAGCATTTTC 57.464 33.333 0.00 0.00 37.76 2.29
7177 7649 9.314321 GTAGCAGTACTAGAATTAGCATTTTCA 57.686 33.333 0.00 0.00 0.00 2.69
7178 7650 8.202745 AGCAGTACTAGAATTAGCATTTTCAC 57.797 34.615 0.00 0.00 0.00 3.18
7179 7651 7.824289 AGCAGTACTAGAATTAGCATTTTCACA 59.176 33.333 0.00 0.00 0.00 3.58
7180 7652 8.119226 GCAGTACTAGAATTAGCATTTTCACAG 58.881 37.037 0.00 0.00 0.00 3.66
7181 7653 9.155975 CAGTACTAGAATTAGCATTTTCACAGT 57.844 33.333 0.00 0.00 0.00 3.55
7182 7654 9.372369 AGTACTAGAATTAGCATTTTCACAGTC 57.628 33.333 0.00 0.00 0.00 3.51
7183 7655 7.617041 ACTAGAATTAGCATTTTCACAGTCC 57.383 36.000 0.00 0.00 0.00 3.85
7184 7656 7.398024 ACTAGAATTAGCATTTTCACAGTCCT 58.602 34.615 0.00 0.00 0.00 3.85
7185 7657 6.506500 AGAATTAGCATTTTCACAGTCCTG 57.493 37.500 0.00 0.00 0.00 3.86
7186 7658 6.240894 AGAATTAGCATTTTCACAGTCCTGA 58.759 36.000 0.40 0.00 0.00 3.86
7187 7659 6.888632 AGAATTAGCATTTTCACAGTCCTGAT 59.111 34.615 0.40 0.00 0.00 2.90
7188 7660 6.690194 ATTAGCATTTTCACAGTCCTGATC 57.310 37.500 0.40 0.00 0.00 2.92
7189 7661 4.298103 AGCATTTTCACAGTCCTGATCT 57.702 40.909 0.40 0.00 0.00 2.75
7190 7662 4.660168 AGCATTTTCACAGTCCTGATCTT 58.340 39.130 0.40 0.00 0.00 2.40
7191 7663 4.699257 AGCATTTTCACAGTCCTGATCTTC 59.301 41.667 0.40 0.00 0.00 2.87
7192 7664 4.699257 GCATTTTCACAGTCCTGATCTTCT 59.301 41.667 0.40 0.00 0.00 2.85
7193 7665 5.391736 GCATTTTCACAGTCCTGATCTTCTG 60.392 44.000 0.40 0.36 0.00 3.02
7194 7666 3.969287 TTCACAGTCCTGATCTTCTGG 57.031 47.619 0.40 0.00 36.89 3.86
7195 7667 1.552337 TCACAGTCCTGATCTTCTGGC 59.448 52.381 0.40 0.00 35.69 4.85
7196 7668 0.534412 ACAGTCCTGATCTTCTGGCG 59.466 55.000 0.40 0.00 35.69 5.69
7197 7669 0.809241 CAGTCCTGATCTTCTGGCGC 60.809 60.000 0.00 0.00 35.69 6.53
7198 7670 1.219124 GTCCTGATCTTCTGGCGCA 59.781 57.895 10.83 0.00 35.69 6.09
7199 7671 0.391661 GTCCTGATCTTCTGGCGCAA 60.392 55.000 10.83 0.00 35.69 4.85
7200 7672 0.391661 TCCTGATCTTCTGGCGCAAC 60.392 55.000 10.83 0.00 35.69 4.17
7201 7673 1.372087 CCTGATCTTCTGGCGCAACC 61.372 60.000 10.83 0.00 39.84 3.77
7213 7685 3.435186 GCAACCAGAGCCGCCTTC 61.435 66.667 0.00 0.00 0.00 3.46
7214 7686 2.348998 CAACCAGAGCCGCCTTCT 59.651 61.111 0.00 0.00 0.00 2.85
7215 7687 2.037136 CAACCAGAGCCGCCTTCTG 61.037 63.158 3.21 3.21 41.34 3.02
7216 7688 3.909086 AACCAGAGCCGCCTTCTGC 62.909 63.158 4.46 0.00 40.54 4.26
7237 7709 4.504916 CGCTCTCTGTCCGCTGGG 62.505 72.222 0.00 0.00 0.00 4.45
7238 7710 3.386237 GCTCTCTGTCCGCTGGGT 61.386 66.667 0.00 0.00 33.83 4.51
7239 7711 2.052690 GCTCTCTGTCCGCTGGGTA 61.053 63.158 0.00 0.00 33.83 3.69
7240 7712 1.810532 CTCTCTGTCCGCTGGGTAC 59.189 63.158 0.00 0.00 33.83 3.34
7241 7713 1.994507 CTCTCTGTCCGCTGGGTACG 61.995 65.000 0.00 0.00 33.83 3.67
7242 7714 2.282674 TCTGTCCGCTGGGTACGT 60.283 61.111 0.00 0.00 33.83 3.57
7243 7715 2.126071 CTGTCCGCTGGGTACGTG 60.126 66.667 0.00 0.00 33.83 4.49
7244 7716 4.367023 TGTCCGCTGGGTACGTGC 62.367 66.667 0.00 0.00 33.83 5.34
7245 7717 4.367023 GTCCGCTGGGTACGTGCA 62.367 66.667 5.86 0.00 33.83 4.57
7246 7718 4.063967 TCCGCTGGGTACGTGCAG 62.064 66.667 5.86 0.00 33.83 4.41
7247 7719 4.373116 CCGCTGGGTACGTGCAGT 62.373 66.667 5.86 0.00 0.00 4.40
7248 7720 2.569657 CGCTGGGTACGTGCAGTA 59.430 61.111 5.86 0.00 0.00 2.74
7249 7721 1.516386 CGCTGGGTACGTGCAGTAG 60.516 63.158 5.86 1.47 35.72 2.57
7250 7722 1.888018 GCTGGGTACGTGCAGTAGA 59.112 57.895 5.86 0.00 35.72 2.59
7251 7723 0.179134 GCTGGGTACGTGCAGTAGAG 60.179 60.000 5.86 0.00 35.72 2.43
7252 7724 0.179134 CTGGGTACGTGCAGTAGAGC 60.179 60.000 5.86 0.00 35.72 4.09
7253 7725 0.896479 TGGGTACGTGCAGTAGAGCA 60.896 55.000 5.86 0.00 43.35 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.813152 CACCAAATCAAAGATTCGGCTTTAAT 59.187 34.615 0.00 0.00 36.39 1.40
10 11 4.686191 TGTTGCCACCAAATCAAAGATT 57.314 36.364 0.00 0.00 31.68 2.40
33 34 1.574263 GGTGTCTTCCTAGCCTCCTT 58.426 55.000 0.00 0.00 0.00 3.36
161 166 3.254060 GCTTGACAAATCTGAGCGACTA 58.746 45.455 0.00 0.00 0.00 2.59
201 206 1.144936 GCCACTCCATCTCCTTCCG 59.855 63.158 0.00 0.00 0.00 4.30
241 246 4.933064 CGGTCATCCTCGCCGCTC 62.933 72.222 0.00 0.00 38.99 5.03
253 258 1.208358 CACGTAACGAGAGCGGTCA 59.792 57.895 18.15 0.00 43.17 4.02
277 282 4.988716 ACTGGCGTGACCCTCCGA 62.989 66.667 0.00 0.00 37.83 4.55
278 283 4.003788 AACTGGCGTGACCCTCCG 62.004 66.667 0.00 0.00 37.83 4.63
279 284 2.358737 CAACTGGCGTGACCCTCC 60.359 66.667 0.00 0.00 37.83 4.30
280 285 1.668151 GACAACTGGCGTGACCCTC 60.668 63.158 0.00 0.00 37.83 4.30
281 286 0.830444 TAGACAACTGGCGTGACCCT 60.830 55.000 0.00 0.00 37.83 4.34
332 341 1.209275 CGAGCTGCATACACGTAGCC 61.209 60.000 1.02 0.00 44.76 3.93
359 368 3.487120 AAAGGACTAGAAAACTGGCGT 57.513 42.857 0.00 0.00 0.00 5.68
392 401 5.046663 GTGGCCATAAATTTCCAAAGAAGGA 60.047 40.000 9.72 0.00 35.41 3.36
418 427 9.189156 AGCTGTTAATATTAGCTGGATTTGAAA 57.811 29.630 9.87 0.00 45.40 2.69
444 453 2.357637 GGGCGTAGTATACCGTGTAACA 59.642 50.000 0.00 0.00 38.71 2.41
466 475 5.125578 GGAATTGATTAACTTTCCTTCCGCT 59.874 40.000 0.00 0.00 35.74 5.52
469 478 7.196331 CGATGGAATTGATTAACTTTCCTTCC 58.804 38.462 10.44 0.00 38.35 3.46
494 503 0.109919 CTGTTTACGCCTTTTCGCCC 60.110 55.000 0.00 0.00 0.00 6.13
1167 1220 2.013807 CAACACGACACCACCACAG 58.986 57.895 0.00 0.00 0.00 3.66
1169 1222 1.772063 GAGCAACACGACACCACCAC 61.772 60.000 0.00 0.00 0.00 4.16
1170 1223 1.522806 GAGCAACACGACACCACCA 60.523 57.895 0.00 0.00 0.00 4.17
1171 1224 2.251642 GGAGCAACACGACACCACC 61.252 63.158 0.00 0.00 0.00 4.61
1189 1242 4.776322 TCCAATCAGGCGGCACCG 62.776 66.667 13.08 4.30 46.52 4.94
1206 1259 0.745845 AGACCTACGTACGTCGGCAT 60.746 55.000 32.04 20.88 44.69 4.40
1284 1337 8.680903 CAAATCAAACTCCTAATAAGCATGAGT 58.319 33.333 0.00 0.00 37.88 3.41
1418 1471 8.522830 CAATTACCAGTCCTTAATCAAACACAT 58.477 33.333 0.00 0.00 0.00 3.21
1470 1523 2.573369 CTGCTCAGATTCTTCCCATGG 58.427 52.381 4.14 4.14 0.00 3.66
1471 1524 2.573369 CCTGCTCAGATTCTTCCCATG 58.427 52.381 0.00 0.00 0.00 3.66
1472 1525 1.133853 GCCTGCTCAGATTCTTCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
1657 1710 8.658499 AAGATTACTACGGTAATAAAAGGCAG 57.342 34.615 2.02 0.00 45.39 4.85
1722 1775 5.243207 ACTTACTGTTCCCAAATAGAACCG 58.757 41.667 1.53 0.00 42.41 4.44
1785 1838 2.365941 TCAGACGGTACATGTGTTTCCA 59.634 45.455 9.11 0.00 0.00 3.53
1790 1843 2.166459 CCTGATCAGACGGTACATGTGT 59.834 50.000 24.62 0.00 0.00 3.72
1791 1844 2.481969 CCCTGATCAGACGGTACATGTG 60.482 54.545 24.62 2.38 0.00 3.21
1840 1893 0.035152 ATTGGGTTGAGCGAGCATCA 60.035 50.000 0.00 0.00 33.17 3.07
1979 2032 1.468054 GCATTTGCGCCCAAAGTAGAG 60.468 52.381 4.18 0.00 43.60 2.43
2034 2087 0.107703 CGCAATCAGGAGCCTGGTTA 60.108 55.000 14.31 0.00 44.67 2.85
2052 2105 6.075415 GCAATAGCAGCAATAACAATACAACG 60.075 38.462 0.00 0.00 41.58 4.10
2216 2269 6.597562 TCCCCACATATTAGATTTGTACCAC 58.402 40.000 0.00 0.00 0.00 4.16
2278 2331 3.009473 AGCCTCTGGTGCTAATTTTCTCA 59.991 43.478 0.00 0.00 37.28 3.27
2309 2362 5.819379 GGAGCAACATCAGATAAGACAATCA 59.181 40.000 0.00 0.00 0.00 2.57
2423 2476 7.494298 ACAATCAAATCCAACACCTTGTTTAAC 59.506 33.333 0.00 0.00 38.77 2.01
2424 2477 7.560368 ACAATCAAATCCAACACCTTGTTTAA 58.440 30.769 0.00 0.00 38.77 1.52
2552 2605 2.899838 GTGCCACGTGTCAAGCCA 60.900 61.111 15.65 0.00 0.00 4.75
2803 2858 2.076863 GGACCACCGATTTCACTGAAG 58.923 52.381 0.00 0.00 0.00 3.02
2815 2870 2.046892 CAGAAGGCAGGACCACCG 60.047 66.667 0.00 0.00 43.14 4.94
2816 2871 2.360475 GCAGAAGGCAGGACCACC 60.360 66.667 0.00 0.00 43.14 4.61
2878 2933 4.872124 TCATTCATCAAAGACGACATGAGG 59.128 41.667 0.00 0.00 0.00 3.86
2936 2991 3.681313 GCCTTTGGCCTTTCAACTTTTCA 60.681 43.478 3.32 0.00 44.06 2.69
2970 3025 1.073216 CACAGACGCTACAAGCTCCG 61.073 60.000 0.00 0.00 39.60 4.63
2991 3046 6.168270 AGTAAACCTTGCCAAATAAAAGCA 57.832 33.333 0.00 0.00 33.97 3.91
2993 3048 7.041440 CCCAAAGTAAACCTTGCCAAATAAAAG 60.041 37.037 0.00 0.00 32.32 2.27
3100 3155 3.842007 TCTGGTTCCCGAGTGTTTTTA 57.158 42.857 0.00 0.00 0.00 1.52
3107 3162 3.502123 TTCATTTTCTGGTTCCCGAGT 57.498 42.857 0.00 0.00 0.00 4.18
3177 3232 2.357836 CTCCAGGCAGCCAACCAT 59.642 61.111 15.80 0.00 0.00 3.55
3250 3308 5.103000 CGTTTCAAAATGTTTGTGGGTGTA 58.897 37.500 0.98 0.00 0.00 2.90
3259 3317 5.804979 CCAGACAGAACGTTTCAAAATGTTT 59.195 36.000 12.87 0.14 45.37 2.83
3265 3323 7.156000 TGTATATCCAGACAGAACGTTTCAAA 58.844 34.615 0.46 0.00 0.00 2.69
3297 3355 5.919141 AGTATAATGCGTCTACCGAATGAAC 59.081 40.000 0.00 0.00 34.10 3.18
3332 3390 5.675684 TGGATAGAGCAACATACACTGAA 57.324 39.130 0.00 0.00 0.00 3.02
3333 3391 5.675684 TTGGATAGAGCAACATACACTGA 57.324 39.130 0.00 0.00 0.00 3.41
3399 3459 4.448537 ACAAGTTGTAGCTGCACAAAAA 57.551 36.364 6.75 0.00 39.98 1.94
3706 3766 6.866480 TGCTCCATGTTTTATTCCTTTCATC 58.134 36.000 0.00 0.00 0.00 2.92
4024 4084 3.837213 ACAAATTGTTGATGGAGCTCG 57.163 42.857 7.83 0.00 38.20 5.03
4206 4338 9.466497 TGAAGAGAATTGGCATACTTCTAAATT 57.534 29.630 0.00 8.74 36.00 1.82
4327 4461 2.596923 TGCAAATGGCTGGCGACA 60.597 55.556 0.00 0.00 45.15 4.35
4432 4575 2.674796 ACATCCAGGAGCGTAGAAAC 57.325 50.000 0.00 0.00 0.00 2.78
4485 4628 7.469043 GCATGTCAGCATCAATCCACTAAAATA 60.469 37.037 0.00 0.00 31.99 1.40
4486 4629 6.682113 GCATGTCAGCATCAATCCACTAAAAT 60.682 38.462 0.00 0.00 31.99 1.82
4496 4869 2.139323 ACCAGCATGTCAGCATCAAT 57.861 45.000 0.00 0.00 36.85 2.57
4513 4886 2.354821 GGAATGCACAACGGAGATAACC 59.645 50.000 0.00 0.00 0.00 2.85
4523 4896 4.782019 TGGAACTAATGGAATGCACAAC 57.218 40.909 0.00 0.00 0.00 3.32
4623 4996 4.636648 TCCAAAAACGTCACTTATGTGTGT 59.363 37.500 8.46 6.21 44.14 3.72
4871 5255 5.106396 GCAAGAAATCAACTCAGCATACTGT 60.106 40.000 0.00 0.00 44.77 3.55
5218 5602 4.340097 CCAAATGCTATTTGCTCTCCATGA 59.660 41.667 13.09 0.00 43.37 3.07
5491 5875 9.851686 AAAGTATTTAATGACTGAGATGGCATA 57.148 29.630 0.00 0.00 35.86 3.14
5533 5917 8.150827 TCAAGGAATTTTGATTAGGAGAGAGA 57.849 34.615 0.00 0.00 32.39 3.10
5759 6143 7.394016 TGAAAGCTACTTATTCCTTGTGATGA 58.606 34.615 0.00 0.00 0.00 2.92
5818 6202 0.044092 TAGAGCCCACTCCCATTGGA 59.956 55.000 3.62 0.00 44.65 3.53
5819 6203 0.918983 TTAGAGCCCACTCCCATTGG 59.081 55.000 0.00 0.00 44.65 3.16
5821 6205 1.285078 GGTTTAGAGCCCACTCCCATT 59.715 52.381 0.00 0.00 44.65 3.16
5845 6229 3.246619 GCTCTCAGTCTTTAGAACACCG 58.753 50.000 0.00 0.00 0.00 4.94
5886 6270 4.201851 CGATATGGTTGGCATAAGCATAGC 60.202 45.833 20.85 20.85 41.88 2.97
5908 6292 1.021390 AAGACAGCAAGCCGGAATCG 61.021 55.000 5.05 0.00 0.00 3.34
6013 6397 6.357367 ACTTGGCCCAACAGTATTTCTATAG 58.643 40.000 0.00 0.00 0.00 1.31
6085 6469 1.758862 CCTTGATCTGGCAATTTCCCC 59.241 52.381 0.00 0.00 0.00 4.81
6509 6910 3.138468 AGGAGCATAATTAACAGGGGTCC 59.862 47.826 0.00 0.00 41.83 4.46
6646 7075 7.148590 GCAACCATTCATCAAACCACTAAATTC 60.149 37.037 0.00 0.00 0.00 2.17
6839 7269 8.934023 AAAAATCTGTTAGATGGGACTAAACA 57.066 30.769 0.00 0.00 34.65 2.83
6990 7422 5.050499 GCCATATGTTCAAGACAAGATCTCG 60.050 44.000 0.00 0.00 42.62 4.04
7036 7508 1.440618 TTTTGTAGGCCCACTCAGGA 58.559 50.000 2.16 0.00 41.22 3.86
7041 7513 5.650703 GTGTATATGTTTTTGTAGGCCCACT 59.349 40.000 2.16 0.00 0.00 4.00
7057 7529 7.862372 GGCTACATGGACAAAAATGTGTATATG 59.138 37.037 0.00 0.00 37.57 1.78
7065 7537 5.047802 AGACTTGGCTACATGGACAAAAATG 60.048 40.000 0.00 0.00 33.44 2.32
7066 7538 5.047802 CAGACTTGGCTACATGGACAAAAAT 60.048 40.000 0.00 0.00 33.44 1.82
7070 7542 2.371841 ACAGACTTGGCTACATGGACAA 59.628 45.455 0.00 0.00 32.77 3.18
7072 7544 2.622436 GACAGACTTGGCTACATGGAC 58.378 52.381 0.00 0.00 0.00 4.02
7073 7545 1.555075 GGACAGACTTGGCTACATGGA 59.445 52.381 0.00 0.00 30.93 3.41
7074 7546 1.556911 AGGACAGACTTGGCTACATGG 59.443 52.381 0.00 0.00 30.93 3.66
7075 7547 2.736719 CGAGGACAGACTTGGCTACATG 60.737 54.545 0.00 0.00 30.93 3.21
7076 7548 1.478510 CGAGGACAGACTTGGCTACAT 59.521 52.381 0.00 0.00 30.93 2.29
7079 7551 2.145397 ATCGAGGACAGACTTGGCTA 57.855 50.000 0.00 0.00 30.93 3.93
7080 7552 2.145397 TATCGAGGACAGACTTGGCT 57.855 50.000 0.00 0.00 30.93 4.75
7081 7553 2.101582 ACATATCGAGGACAGACTTGGC 59.898 50.000 0.00 0.00 0.00 4.52
7082 7554 4.115516 CAACATATCGAGGACAGACTTGG 58.884 47.826 0.00 0.00 0.00 3.61
7083 7555 3.553511 GCAACATATCGAGGACAGACTTG 59.446 47.826 0.00 0.00 0.00 3.16
7084 7556 3.449018 AGCAACATATCGAGGACAGACTT 59.551 43.478 0.00 0.00 0.00 3.01
7085 7557 3.027412 AGCAACATATCGAGGACAGACT 58.973 45.455 0.00 0.00 0.00 3.24
7086 7558 3.444703 AGCAACATATCGAGGACAGAC 57.555 47.619 0.00 0.00 0.00 3.51
7087 7559 4.207955 ACTAGCAACATATCGAGGACAGA 58.792 43.478 0.00 0.00 0.00 3.41
7088 7560 4.036852 TGACTAGCAACATATCGAGGACAG 59.963 45.833 0.00 0.00 0.00 3.51
7089 7561 3.951680 TGACTAGCAACATATCGAGGACA 59.048 43.478 0.00 0.00 0.00 4.02
7093 7565 6.145209 CCAGAAATGACTAGCAACATATCGAG 59.855 42.308 0.00 0.00 0.00 4.04
7095 7567 5.333645 GCCAGAAATGACTAGCAACATATCG 60.334 44.000 0.00 0.00 0.00 2.92
7118 7590 3.551659 GGCTTAAATCAGGCATTGCTAGC 60.552 47.826 8.10 8.10 39.20 3.42
7119 7591 3.633525 TGGCTTAAATCAGGCATTGCTAG 59.366 43.478 8.82 1.64 44.06 3.42
7120 7592 3.630168 TGGCTTAAATCAGGCATTGCTA 58.370 40.909 8.82 0.00 44.06 3.49
7121 7593 2.459644 TGGCTTAAATCAGGCATTGCT 58.540 42.857 8.82 0.00 44.06 3.91
7122 7594 2.965572 TGGCTTAAATCAGGCATTGC 57.034 45.000 0.00 0.00 44.06 3.56
7127 7599 3.149981 GGGTAGATGGCTTAAATCAGGC 58.850 50.000 0.00 0.00 39.83 4.85
7128 7600 3.138283 TGGGGTAGATGGCTTAAATCAGG 59.862 47.826 0.00 0.00 0.00 3.86
7129 7601 4.141390 ACTGGGGTAGATGGCTTAAATCAG 60.141 45.833 0.00 0.00 0.00 2.90
7130 7602 3.785887 ACTGGGGTAGATGGCTTAAATCA 59.214 43.478 0.00 0.00 0.00 2.57
7131 7603 4.439253 ACTGGGGTAGATGGCTTAAATC 57.561 45.455 0.00 0.00 0.00 2.17
7132 7604 4.202472 GCTACTGGGGTAGATGGCTTAAAT 60.202 45.833 7.28 0.00 46.01 1.40
7133 7605 3.135895 GCTACTGGGGTAGATGGCTTAAA 59.864 47.826 7.28 0.00 46.01 1.52
7134 7606 2.704065 GCTACTGGGGTAGATGGCTTAA 59.296 50.000 7.28 0.00 46.01 1.85
7135 7607 2.326428 GCTACTGGGGTAGATGGCTTA 58.674 52.381 7.28 0.00 46.01 3.09
7136 7608 1.132500 GCTACTGGGGTAGATGGCTT 58.868 55.000 7.28 0.00 46.01 4.35
7137 7609 0.031111 TGCTACTGGGGTAGATGGCT 60.031 55.000 7.28 0.00 46.01 4.75
7138 7610 0.394565 CTGCTACTGGGGTAGATGGC 59.605 60.000 7.28 0.00 46.01 4.40
7139 7611 1.794714 ACTGCTACTGGGGTAGATGG 58.205 55.000 7.28 0.12 46.01 3.51
7140 7612 3.567397 AGTACTGCTACTGGGGTAGATG 58.433 50.000 0.00 2.13 46.01 2.90
7141 7613 3.975479 AGTACTGCTACTGGGGTAGAT 57.025 47.619 0.00 0.00 46.01 1.98
7142 7614 4.042884 TCTAGTACTGCTACTGGGGTAGA 58.957 47.826 5.39 0.00 46.01 2.59
7143 7615 4.434545 TCTAGTACTGCTACTGGGGTAG 57.565 50.000 5.39 0.00 45.91 3.18
7144 7616 4.868172 TTCTAGTACTGCTACTGGGGTA 57.132 45.455 5.39 0.00 34.79 3.69
7145 7617 3.752359 TTCTAGTACTGCTACTGGGGT 57.248 47.619 5.39 0.00 34.79 4.95
7146 7618 5.279056 GCTAATTCTAGTACTGCTACTGGGG 60.279 48.000 5.39 0.00 34.79 4.96
7147 7619 5.302059 TGCTAATTCTAGTACTGCTACTGGG 59.698 44.000 5.39 0.00 34.79 4.45
7148 7620 6.392625 TGCTAATTCTAGTACTGCTACTGG 57.607 41.667 5.39 0.00 34.79 4.00
7149 7621 8.879342 AAATGCTAATTCTAGTACTGCTACTG 57.121 34.615 5.39 0.00 34.79 2.74
7150 7622 9.535878 GAAAATGCTAATTCTAGTACTGCTACT 57.464 33.333 5.39 0.00 37.04 2.57
7151 7623 9.314321 TGAAAATGCTAATTCTAGTACTGCTAC 57.686 33.333 5.39 0.00 0.00 3.58
7152 7624 9.314321 GTGAAAATGCTAATTCTAGTACTGCTA 57.686 33.333 5.39 0.00 0.00 3.49
7153 7625 7.824289 TGTGAAAATGCTAATTCTAGTACTGCT 59.176 33.333 5.39 0.00 0.00 4.24
7154 7626 7.974675 TGTGAAAATGCTAATTCTAGTACTGC 58.025 34.615 5.39 0.00 0.00 4.40
7155 7627 9.155975 ACTGTGAAAATGCTAATTCTAGTACTG 57.844 33.333 5.39 0.00 0.00 2.74
7156 7628 9.372369 GACTGTGAAAATGCTAATTCTAGTACT 57.628 33.333 0.00 0.00 0.00 2.73
7157 7629 8.604890 GGACTGTGAAAATGCTAATTCTAGTAC 58.395 37.037 0.00 0.00 0.00 2.73
7158 7630 8.540388 AGGACTGTGAAAATGCTAATTCTAGTA 58.460 33.333 0.00 0.00 0.00 1.82
7159 7631 7.335422 CAGGACTGTGAAAATGCTAATTCTAGT 59.665 37.037 0.00 0.00 0.00 2.57
7160 7632 7.550551 TCAGGACTGTGAAAATGCTAATTCTAG 59.449 37.037 0.00 0.00 0.00 2.43
7161 7633 7.394016 TCAGGACTGTGAAAATGCTAATTCTA 58.606 34.615 0.00 0.00 0.00 2.10
7162 7634 6.240894 TCAGGACTGTGAAAATGCTAATTCT 58.759 36.000 0.00 0.00 0.00 2.40
7163 7635 6.500684 TCAGGACTGTGAAAATGCTAATTC 57.499 37.500 0.00 0.00 0.00 2.17
7164 7636 6.888632 AGATCAGGACTGTGAAAATGCTAATT 59.111 34.615 0.00 0.00 0.00 1.40
7165 7637 6.421485 AGATCAGGACTGTGAAAATGCTAAT 58.579 36.000 0.00 0.00 0.00 1.73
7166 7638 5.809001 AGATCAGGACTGTGAAAATGCTAA 58.191 37.500 0.00 0.00 0.00 3.09
7167 7639 5.426689 AGATCAGGACTGTGAAAATGCTA 57.573 39.130 0.00 0.00 0.00 3.49
7168 7640 4.298103 AGATCAGGACTGTGAAAATGCT 57.702 40.909 0.00 0.00 0.00 3.79
7169 7641 4.699257 AGAAGATCAGGACTGTGAAAATGC 59.301 41.667 0.00 0.00 0.00 3.56
7170 7642 5.123502 CCAGAAGATCAGGACTGTGAAAATG 59.876 44.000 0.00 0.00 0.00 2.32
7171 7643 5.251764 CCAGAAGATCAGGACTGTGAAAAT 58.748 41.667 0.00 0.00 0.00 1.82
7172 7644 4.645535 CCAGAAGATCAGGACTGTGAAAA 58.354 43.478 0.00 0.00 0.00 2.29
7173 7645 3.557898 GCCAGAAGATCAGGACTGTGAAA 60.558 47.826 0.00 0.00 0.00 2.69
7174 7646 2.027745 GCCAGAAGATCAGGACTGTGAA 60.028 50.000 0.00 0.00 0.00 3.18
7175 7647 1.552337 GCCAGAAGATCAGGACTGTGA 59.448 52.381 0.00 0.00 0.00 3.58
7176 7648 1.738365 CGCCAGAAGATCAGGACTGTG 60.738 57.143 0.00 0.00 0.00 3.66
7177 7649 0.534412 CGCCAGAAGATCAGGACTGT 59.466 55.000 0.00 0.00 0.00 3.55
7178 7650 0.809241 GCGCCAGAAGATCAGGACTG 60.809 60.000 0.00 0.00 0.00 3.51
7179 7651 1.260538 TGCGCCAGAAGATCAGGACT 61.261 55.000 4.18 0.00 0.00 3.85
7180 7652 0.391661 TTGCGCCAGAAGATCAGGAC 60.392 55.000 4.18 0.00 0.00 3.85
7181 7653 0.391661 GTTGCGCCAGAAGATCAGGA 60.392 55.000 4.18 0.00 0.00 3.86
7182 7654 1.372087 GGTTGCGCCAGAAGATCAGG 61.372 60.000 4.18 0.00 37.17 3.86
7183 7655 0.674581 TGGTTGCGCCAGAAGATCAG 60.675 55.000 4.18 0.00 43.61 2.90
7184 7656 1.374568 TGGTTGCGCCAGAAGATCA 59.625 52.632 4.18 0.00 43.61 2.92
7185 7657 4.301505 TGGTTGCGCCAGAAGATC 57.698 55.556 4.18 0.00 43.61 2.75
7196 7668 3.435186 GAAGGCGGCTCTGGTTGC 61.435 66.667 13.70 0.00 0.00 4.17
7197 7669 2.037136 CAGAAGGCGGCTCTGGTTG 61.037 63.158 22.23 10.61 37.29 3.77
7198 7670 2.348998 CAGAAGGCGGCTCTGGTT 59.651 61.111 22.23 5.32 37.29 3.67
7199 7671 4.400961 GCAGAAGGCGGCTCTGGT 62.401 66.667 27.19 10.02 40.62 4.00
7220 7692 4.504916 CCCAGCGGACAGAGAGCG 62.505 72.222 0.00 0.00 35.78 5.03
7221 7693 2.052690 TACCCAGCGGACAGAGAGC 61.053 63.158 0.00 0.00 0.00 4.09
7222 7694 1.810532 GTACCCAGCGGACAGAGAG 59.189 63.158 0.00 0.00 0.00 3.20
7223 7695 2.044555 CGTACCCAGCGGACAGAGA 61.045 63.158 0.00 0.00 0.00 3.10
7224 7696 2.341101 ACGTACCCAGCGGACAGAG 61.341 63.158 0.00 0.00 0.00 3.35
7225 7697 2.282674 ACGTACCCAGCGGACAGA 60.283 61.111 0.00 0.00 0.00 3.41
7226 7698 2.126071 CACGTACCCAGCGGACAG 60.126 66.667 0.00 0.00 0.00 3.51
7227 7699 4.367023 GCACGTACCCAGCGGACA 62.367 66.667 0.00 0.00 0.00 4.02
7228 7700 4.367023 TGCACGTACCCAGCGGAC 62.367 66.667 0.00 0.00 0.00 4.79
7229 7701 4.063967 CTGCACGTACCCAGCGGA 62.064 66.667 0.00 0.00 36.79 5.54
7230 7702 2.884087 CTACTGCACGTACCCAGCGG 62.884 65.000 9.23 6.11 40.41 5.52
7231 7703 1.516386 CTACTGCACGTACCCAGCG 60.516 63.158 9.23 0.00 32.37 5.18
7232 7704 0.179134 CTCTACTGCACGTACCCAGC 60.179 60.000 9.23 0.00 32.37 4.85
7233 7705 0.179134 GCTCTACTGCACGTACCCAG 60.179 60.000 8.09 8.09 35.26 4.45
7234 7706 0.896479 TGCTCTACTGCACGTACCCA 60.896 55.000 0.00 0.00 38.12 4.51
7235 7707 0.245539 TTGCTCTACTGCACGTACCC 59.754 55.000 0.00 0.00 43.20 3.69
7236 7708 1.630148 CTTGCTCTACTGCACGTACC 58.370 55.000 0.00 0.00 43.20 3.34
7237 7709 1.201647 TCCTTGCTCTACTGCACGTAC 59.798 52.381 0.00 0.00 43.20 3.67
7238 7710 1.472878 CTCCTTGCTCTACTGCACGTA 59.527 52.381 0.00 0.00 43.20 3.57
7239 7711 0.244994 CTCCTTGCTCTACTGCACGT 59.755 55.000 0.00 0.00 43.20 4.49
7240 7712 0.244994 ACTCCTTGCTCTACTGCACG 59.755 55.000 0.00 0.00 43.20 5.34


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

AutoCloner maintained by Alex Coulton.