Multiple sequence alignment - TraesCS5D01G566100

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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 TraesCS5D01G566100 chr5D 100.000 6121 0 0 1 6121 564225841 564231961 0.000000e+00 11304.0
1 TraesCS5D01G566100 chr5D 85.461 3721 504 30 781 4481 563979879 563976176 0.000000e+00 3840.0
2 TraesCS5D01G566100 chr5D 89.951 408 24 5 5417 5818 564290844 564291240 1.520000e-140 510.0
3 TraesCS5D01G566100 chr5D 88.265 196 14 4 5182 5375 564290649 564290837 6.170000e-55 226.0
4 TraesCS5D01G566100 chr5D 91.503 153 11 2 782 934 564226475 564226625 6.220000e-50 209.0
5 TraesCS5D01G566100 chr5D 91.503 153 11 2 635 785 564226622 564226774 6.220000e-50 209.0
6 TraesCS5D01G566100 chr5D 92.593 54 4 0 6065 6118 564291638 564291691 1.830000e-10 78.7
7 TraesCS5D01G566100 chr4A 92.509 5473 292 50 290 5719 608271733 608266336 0.000000e+00 7727.0
8 TraesCS5D01G566100 chr4A 87.045 3520 425 20 977 4482 608481503 608478001 0.000000e+00 3945.0
9 TraesCS5D01G566100 chr4A 82.609 3657 587 40 780 4410 608234851 608231218 0.000000e+00 3184.0
10 TraesCS5D01G566100 chr4A 91.362 301 17 2 5824 6117 608265539 608265241 2.660000e-108 403.0
11 TraesCS5D01G566100 chr4A 88.889 315 26 3 5814 6121 608223461 608223149 4.480000e-101 379.0
12 TraesCS5D01G566100 chr4A 81.395 301 33 10 4989 5273 608477476 608477183 2.220000e-54 224.0
13 TraesCS5D01G566100 chr4A 90.196 153 13 1 635 785 608271264 608271112 1.350000e-46 198.0
14 TraesCS5D01G566100 chr4A 83.568 213 12 13 40 250 608272101 608271910 1.750000e-40 178.0
15 TraesCS5D01G566100 chr4A 88.489 139 12 2 799 934 608271398 608271261 1.360000e-36 165.0
16 TraesCS5D01G566100 chr4A 88.496 113 5 3 5705 5817 608265681 608265577 4.980000e-26 130.0
17 TraesCS5D01G566100 chr5B 93.793 4318 204 36 782 5081 706710064 706714335 0.000000e+00 6431.0
18 TraesCS5D01G566100 chr5B 85.647 3616 473 33 888 4481 706389074 706385483 0.000000e+00 3760.0
19 TraesCS5D01G566100 chr5B 85.246 3633 481 43 868 4474 706453378 706456981 0.000000e+00 3688.0
20 TraesCS5D01G566100 chr5B 84.678 3707 522 34 781 4465 705984670 705980988 0.000000e+00 3657.0
21 TraesCS5D01G566100 chr5B 89.474 627 45 12 5199 5818 706714507 706715119 0.000000e+00 773.0
22 TraesCS5D01G566100 chr5B 91.973 299 15 2 5825 6116 706715449 706715745 1.590000e-110 411.0
23 TraesCS5D01G566100 chr5B 82.080 452 52 15 4984 5424 706457542 706457975 5.830000e-95 359.0
24 TraesCS5D01G566100 chr5B 89.630 135 6 3 5683 5817 706715284 706715410 1.360000e-36 165.0
25 TraesCS5D01G566100 chr5B 91.964 112 4 3 4590 4696 706457137 706457248 1.060000e-32 152.0
26 TraesCS5D01G566100 chr5B 87.500 120 6 3 5895 6005 706715155 706715274 4.980000e-26 130.0
27 TraesCS5D01G566100 chr5B 81.595 163 16 9 622 782 706710051 706710201 8.330000e-24 122.0
28 TraesCS5D01G566100 chr3B 84.032 3676 535 44 858 4504 8039806 8043458 0.000000e+00 3489.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G566100 chr5D 564225841 564231961 6120 False 11304.000000 11304 100.000000 1 6121 1 chr5D.!!$F1 6120
1 TraesCS5D01G566100 chr5D 563976176 563979879 3703 True 3840.000000 3840 85.461000 781 4481 1 chr5D.!!$R1 3700
2 TraesCS5D01G566100 chr5D 564290649 564291691 1042 False 271.566667 510 90.269667 5182 6118 3 chr5D.!!$F3 936
3 TraesCS5D01G566100 chr4A 608231218 608234851 3633 True 3184.000000 3184 82.609000 780 4410 1 chr4A.!!$R2 3630
4 TraesCS5D01G566100 chr4A 608477183 608481503 4320 True 2084.500000 3945 84.220000 977 5273 2 chr4A.!!$R4 4296
5 TraesCS5D01G566100 chr4A 608265241 608272101 6860 True 1466.833333 7727 89.103333 40 6117 6 chr4A.!!$R3 6077
6 TraesCS5D01G566100 chr5B 706385483 706389074 3591 True 3760.000000 3760 85.647000 888 4481 1 chr5B.!!$R2 3593
7 TraesCS5D01G566100 chr5B 705980988 705984670 3682 True 3657.000000 3657 84.678000 781 4465 1 chr5B.!!$R1 3684
8 TraesCS5D01G566100 chr5B 706453378 706457975 4597 False 1399.666667 3688 86.430000 868 5424 3 chr5B.!!$F1 4556
9 TraesCS5D01G566100 chr5B 706710051 706715745 5694 False 1338.666667 6431 88.994167 622 6116 6 chr5B.!!$F2 5494
10 TraesCS5D01G566100 chr3B 8039806 8043458 3652 False 3489.000000 3489 84.032000 858 4504 1 chr3B.!!$F1 3646

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
305 452 0.544357 TGGACAGGGGAACTCGTGAT 60.544 55.000 1.37 0.00 0.00 3.06 F
532 679 1.750778 CAGGTGACCAACTTGCTTGTT 59.249 47.619 3.63 0.00 0.00 2.83 F
1543 1723 0.800012 GTTTGGCCGCGATGAAGTTA 59.200 50.000 8.23 0.00 0.00 2.24 F
1938 2127 1.065926 TGGGATGAGATGTGTGCTCAC 60.066 52.381 11.94 11.94 44.39 3.51 F
3334 3529 0.312729 CGGGGCAACAACTTTACCAC 59.687 55.000 0.00 0.00 39.74 4.16 F
3655 3853 0.469917 AGTGCCCAACCTATCATCCG 59.530 55.000 0.00 0.00 0.00 4.18 F
5047 5483 0.321346 TCTCGCTGGTTGATGCAGAA 59.679 50.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1656 0.252558 TAGTCTCACCCCCAACTCCC 60.253 60.000 0.00 0.00 0.00 4.30 R
2099 2289 1.472082 CAACATCGCTGGTGCCAAATA 59.528 47.619 0.00 0.00 32.26 1.40 R
2620 2813 1.217511 CAGTCGGTGATGCTCTGCT 59.782 57.895 0.00 0.00 0.00 4.24 R
3690 3888 0.310854 GTGCCTTGACAAAGTTCCCG 59.689 55.000 0.00 0.00 0.00 5.14 R
5031 5467 0.524816 GCATTCTGCATCAACCAGCG 60.525 55.000 0.00 0.00 44.26 5.18 R
5102 5552 0.675633 GCCCTTCATGTGCACAACTT 59.324 50.000 25.72 4.24 0.00 2.66 R
6025 7390 0.176680 CCCAGTGCAAGACGAGCTAT 59.823 55.000 0.00 0.00 0.00 2.97 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
18 19 3.706055 GTGCTCTGTTCCAAGTCCA 57.294 52.632 0.00 0.00 0.00 4.02
19 20 2.191128 GTGCTCTGTTCCAAGTCCAT 57.809 50.000 0.00 0.00 0.00 3.41
20 21 2.508526 GTGCTCTGTTCCAAGTCCATT 58.491 47.619 0.00 0.00 0.00 3.16
21 22 2.227388 GTGCTCTGTTCCAAGTCCATTG 59.773 50.000 0.00 0.00 38.74 2.82
22 23 2.158623 TGCTCTGTTCCAAGTCCATTGT 60.159 45.455 0.00 0.00 37.17 2.71
23 24 2.485814 GCTCTGTTCCAAGTCCATTGTC 59.514 50.000 0.00 0.00 37.17 3.18
24 25 3.808618 GCTCTGTTCCAAGTCCATTGTCT 60.809 47.826 0.00 0.00 37.17 3.41
25 26 4.392940 CTCTGTTCCAAGTCCATTGTCTT 58.607 43.478 0.00 0.00 37.17 3.01
26 27 4.792068 TCTGTTCCAAGTCCATTGTCTTT 58.208 39.130 0.00 0.00 37.17 2.52
27 28 5.200483 TCTGTTCCAAGTCCATTGTCTTTT 58.800 37.500 0.00 0.00 37.17 2.27
28 29 5.067674 TCTGTTCCAAGTCCATTGTCTTTTG 59.932 40.000 0.00 0.00 37.17 2.44
29 30 4.099266 TGTTCCAAGTCCATTGTCTTTTGG 59.901 41.667 0.00 0.00 37.17 3.28
30 31 4.177537 TCCAAGTCCATTGTCTTTTGGA 57.822 40.909 0.00 0.00 41.11 3.53
31 32 4.739793 TCCAAGTCCATTGTCTTTTGGAT 58.260 39.130 0.00 0.00 43.61 3.41
32 33 4.766891 TCCAAGTCCATTGTCTTTTGGATC 59.233 41.667 0.00 0.00 43.61 3.36
33 34 4.768968 CCAAGTCCATTGTCTTTTGGATCT 59.231 41.667 0.00 0.00 43.61 2.75
34 35 5.945784 CCAAGTCCATTGTCTTTTGGATCTA 59.054 40.000 0.00 0.00 43.61 1.98
35 36 6.434028 CCAAGTCCATTGTCTTTTGGATCTAA 59.566 38.462 0.00 0.00 43.61 2.10
36 37 7.362401 CCAAGTCCATTGTCTTTTGGATCTAAG 60.362 40.741 0.00 0.00 43.61 2.18
37 38 6.183347 AGTCCATTGTCTTTTGGATCTAAGG 58.817 40.000 0.00 0.00 43.61 2.69
38 39 5.946377 GTCCATTGTCTTTTGGATCTAAGGT 59.054 40.000 0.00 0.00 43.61 3.50
69 71 8.352137 TCATTTCTTGGAAGATTGCATCTAAA 57.648 30.769 0.00 0.00 39.08 1.85
102 105 7.520451 TCCTACATCACTACCATACATGTAC 57.480 40.000 7.96 0.00 0.00 2.90
103 106 7.064229 TCCTACATCACTACCATACATGTACA 58.936 38.462 7.96 0.00 0.00 2.90
104 107 7.230712 TCCTACATCACTACCATACATGTACAG 59.769 40.741 7.96 5.07 0.00 2.74
105 108 6.161855 ACATCACTACCATACATGTACAGG 57.838 41.667 19.59 19.59 0.00 4.00
106 109 4.665833 TCACTACCATACATGTACAGGC 57.334 45.455 20.63 0.00 0.00 4.85
107 110 4.286707 TCACTACCATACATGTACAGGCT 58.713 43.478 20.63 12.97 0.00 4.58
108 111 4.099419 TCACTACCATACATGTACAGGCTG 59.901 45.833 20.63 14.16 0.00 4.85
109 112 4.099419 CACTACCATACATGTACAGGCTGA 59.901 45.833 23.66 0.00 0.00 4.26
110 113 4.714802 ACTACCATACATGTACAGGCTGAA 59.285 41.667 23.66 6.63 0.00 3.02
111 114 3.873910 ACCATACATGTACAGGCTGAAC 58.126 45.455 23.66 1.32 0.00 3.18
112 115 3.206150 CCATACATGTACAGGCTGAACC 58.794 50.000 23.66 8.62 39.61 3.62
113 116 3.370421 CCATACATGTACAGGCTGAACCA 60.370 47.826 23.66 14.16 43.14 3.67
114 117 4.454678 CATACATGTACAGGCTGAACCAT 58.545 43.478 23.66 15.77 43.14 3.55
115 118 3.439857 ACATGTACAGGCTGAACCATT 57.560 42.857 23.66 0.00 43.14 3.16
116 119 3.084039 ACATGTACAGGCTGAACCATTG 58.916 45.455 23.66 12.52 43.14 2.82
117 120 2.949177 TGTACAGGCTGAACCATTGT 57.051 45.000 23.66 0.00 43.14 2.71
118 121 3.222173 TGTACAGGCTGAACCATTGTT 57.778 42.857 23.66 0.00 43.14 2.83
119 122 3.561143 TGTACAGGCTGAACCATTGTTT 58.439 40.909 23.66 0.00 43.14 2.83
120 123 3.957497 TGTACAGGCTGAACCATTGTTTT 59.043 39.130 23.66 0.00 43.14 2.43
121 124 3.457610 ACAGGCTGAACCATTGTTTTG 57.542 42.857 23.66 0.00 43.14 2.44
132 135 2.568509 CCATTGTTTTGCATCCTCCCTT 59.431 45.455 0.00 0.00 0.00 3.95
137 140 7.364585 CCATTGTTTTGCATCCTCCCTTATTTA 60.365 37.037 0.00 0.00 0.00 1.40
146 149 8.835734 TGCATCCTCCCTTATTTATATACACAT 58.164 33.333 0.00 0.00 0.00 3.21
176 180 8.776376 AAACAAGGAATTTTGCACATAATAGG 57.224 30.769 0.00 0.00 0.00 2.57
225 229 2.159184 TGAGCACAATCCTAGAGCTTCG 60.159 50.000 0.00 0.00 33.06 3.79
227 231 1.472376 GCACAATCCTAGAGCTTCGCT 60.472 52.381 0.00 0.00 43.88 4.93
230 234 1.410517 CAATCCTAGAGCTTCGCTGGA 59.589 52.381 0.00 0.00 39.88 3.86
235 239 3.068307 TCCTAGAGCTTCGCTGGATAAAC 59.932 47.826 0.00 0.00 39.88 2.01
249 253 8.682710 TCGCTGGATAAACAATTTTAGCTTTAT 58.317 29.630 0.00 0.00 34.56 1.40
250 254 9.301153 CGCTGGATAAACAATTTTAGCTTTATT 57.699 29.630 0.00 0.00 34.56 1.40
273 277 7.776933 TTATGCTACTTAGAATGCTCTTGTG 57.223 36.000 0.00 0.00 32.70 3.33
276 280 4.624125 GCTACTTAGAATGCTCTTGTGGGT 60.624 45.833 0.00 0.00 32.70 4.51
277 281 3.679389 ACTTAGAATGCTCTTGTGGGTG 58.321 45.455 0.00 0.00 32.70 4.61
282 286 1.238439 ATGCTCTTGTGGGTGAAACG 58.762 50.000 0.00 0.00 38.12 3.60
284 288 0.586802 GCTCTTGTGGGTGAAACGAC 59.413 55.000 0.00 0.00 38.12 4.34
285 289 1.810412 GCTCTTGTGGGTGAAACGACT 60.810 52.381 0.00 0.00 38.12 4.18
286 290 2.561569 CTCTTGTGGGTGAAACGACTT 58.438 47.619 0.00 0.00 38.12 3.01
288 292 1.333619 CTTGTGGGTGAAACGACTTGG 59.666 52.381 0.00 0.00 38.12 3.61
304 451 0.761323 TTGGACAGGGGAACTCGTGA 60.761 55.000 1.37 0.00 0.00 4.35
305 452 0.544357 TGGACAGGGGAACTCGTGAT 60.544 55.000 1.37 0.00 0.00 3.06
313 460 2.928116 GGGGAACTCGTGATTAGAAACG 59.072 50.000 0.00 0.00 41.11 3.60
314 461 3.367703 GGGGAACTCGTGATTAGAAACGA 60.368 47.826 0.00 0.00 45.86 3.85
315 462 4.430908 GGGAACTCGTGATTAGAAACGAT 58.569 43.478 0.00 0.00 46.70 3.73
328 475 4.853924 AGAAACGATTTGGCAATGTTCT 57.146 36.364 0.00 3.43 0.00 3.01
330 477 4.984161 AGAAACGATTTGGCAATGTTCTTG 59.016 37.500 0.00 0.00 0.00 3.02
332 479 4.320608 ACGATTTGGCAATGTTCTTGTT 57.679 36.364 0.00 0.00 0.00 2.83
353 500 4.790765 TGGTGTTGTTTGTTGACATTGA 57.209 36.364 0.00 0.00 0.00 2.57
360 507 8.693504 GTGTTGTTTGTTGACATTGATTAGATG 58.306 33.333 0.00 0.00 0.00 2.90
438 585 6.755542 AAAAATTGGGGGTCAGTTATTTCA 57.244 33.333 0.00 0.00 0.00 2.69
496 643 5.841957 AGCTGGTATCCAATTTGATCAAC 57.158 39.130 7.89 0.00 30.80 3.18
507 654 5.695816 CCAATTTGATCAACGACCACATTTT 59.304 36.000 7.89 0.00 0.00 1.82
510 657 4.235939 TGATCAACGACCACATTTTTGG 57.764 40.909 0.00 0.00 43.04 3.28
525 672 2.818751 TTTGGACAGGTGACCAACTT 57.181 45.000 12.58 0.00 46.32 2.66
532 679 1.750778 CAGGTGACCAACTTGCTTGTT 59.249 47.619 3.63 0.00 0.00 2.83
544 691 6.699575 AACTTGCTTGTTGACTTACTGAAT 57.300 33.333 0.00 0.00 0.00 2.57
545 692 6.064846 ACTTGCTTGTTGACTTACTGAATG 57.935 37.500 0.00 0.00 0.00 2.67
546 693 5.590259 ACTTGCTTGTTGACTTACTGAATGT 59.410 36.000 0.00 0.00 0.00 2.71
548 695 6.449635 TGCTTGTTGACTTACTGAATGTTT 57.550 33.333 0.00 0.00 0.00 2.83
580 727 7.060600 GTGACAATCACGATTCATTTGTAGA 57.939 36.000 0.00 0.00 37.67 2.59
615 762 7.013655 AGCATATTTTTGGTACTGCCTATGAAG 59.986 37.037 0.00 0.00 38.35 3.02
740 890 7.209475 AGTAAAGATCTCTTGCTAGATTGAGC 58.791 38.462 0.00 0.00 43.16 4.26
758 909 5.665916 TGAGCTCATCAGTTATCTGTTCA 57.334 39.130 13.74 0.00 41.91 3.18
796 947 9.815306 ATATAGGAGACAACTCATACATGTAGT 57.185 33.333 11.91 2.66 41.17 2.73
970 1143 4.822026 ACAGACTAACAGACATGCTAACC 58.178 43.478 0.00 0.00 0.00 2.85
974 1147 6.036517 CAGACTAACAGACATGCTAACCAATC 59.963 42.308 0.00 0.00 0.00 2.67
1134 1311 4.083590 GCTACTGAAGAGCTTTTGACCAAG 60.084 45.833 0.00 0.00 36.96 3.61
1222 1399 4.678309 GCACTAGTCTTACCAAGTGGCTAG 60.678 50.000 0.00 2.75 39.75 3.42
1488 1668 2.125225 GAGGAGGGAGTTGGGGGT 59.875 66.667 0.00 0.00 0.00 4.95
1543 1723 0.800012 GTTTGGCCGCGATGAAGTTA 59.200 50.000 8.23 0.00 0.00 2.24
1632 1815 2.039879 ACTTGGGTCAAGGTACACCATC 59.960 50.000 11.65 0.00 44.81 3.51
1647 1830 2.394930 CCATCGGTGGTGTTGATGTA 57.605 50.000 6.53 0.00 40.83 2.29
1874 2057 8.592105 ACAGTTGTCAACAATATTCAAAATGG 57.408 30.769 17.78 0.00 38.24 3.16
1938 2127 1.065926 TGGGATGAGATGTGTGCTCAC 60.066 52.381 11.94 11.94 44.39 3.51
1995 2184 2.413837 CCGGGAAGTGTAGTTCTTGTG 58.586 52.381 0.00 0.00 0.00 3.33
2023 2212 4.633980 GCAAAAGGGTTGCAGACG 57.366 55.556 6.19 0.00 44.34 4.18
2099 2289 5.435686 TGGTCAGCTTTCCAGTATTATGT 57.564 39.130 2.82 0.00 0.00 2.29
2341 2534 7.759489 AGTTATCAAGATCTACAGCCTAGAG 57.241 40.000 0.00 0.00 0.00 2.43
2367 2560 1.069636 CAGTGCTTCGCTTTCTGTTCC 60.070 52.381 0.00 0.00 0.00 3.62
2591 2784 3.992643 TGGCAATTGGTGTTTCTTCATG 58.007 40.909 7.72 0.00 0.00 3.07
2620 2813 4.708177 CTTTCTCCACAAAGAGACCTCAA 58.292 43.478 0.00 0.00 42.56 3.02
2634 2827 1.088340 CCTCAAGCAGAGCATCACCG 61.088 60.000 0.96 0.00 43.31 4.94
2852 3045 1.396653 CCTGCCCACATTTCATCCTC 58.603 55.000 0.00 0.00 0.00 3.71
3013 3206 1.535462 GGCACTTGTATGTTGACGCTT 59.465 47.619 0.00 0.00 0.00 4.68
3044 3239 3.269381 TCTTTGATTCCTGGTATTGGGCT 59.731 43.478 0.00 0.00 0.00 5.19
3273 3468 9.832445 GTATCCAAAGATGTACTTGAAGGATTA 57.168 33.333 0.00 0.00 41.42 1.75
3321 3516 1.259142 TGATCGAAGGTTACGGGGCA 61.259 55.000 0.00 0.00 0.00 5.36
3334 3529 0.312729 CGGGGCAACAACTTTACCAC 59.687 55.000 0.00 0.00 39.74 4.16
3335 3530 1.404843 GGGGCAACAACTTTACCACA 58.595 50.000 0.00 0.00 39.74 4.17
3342 3537 4.202111 GCAACAACTTTACCACACTGGATT 60.202 41.667 0.00 0.00 40.96 3.01
3570 3768 4.025040 AGATTGGTCACATGCAGAAGAA 57.975 40.909 0.00 0.00 0.00 2.52
3571 3769 4.008330 AGATTGGTCACATGCAGAAGAAG 58.992 43.478 0.00 0.00 0.00 2.85
3572 3770 3.490439 TTGGTCACATGCAGAAGAAGA 57.510 42.857 0.00 0.00 0.00 2.87
3603 3801 3.510459 TCTCCTTCCACATCTCACAAGA 58.490 45.455 0.00 0.00 35.54 3.02
3655 3853 0.469917 AGTGCCCAACCTATCATCCG 59.530 55.000 0.00 0.00 0.00 4.18
3690 3888 5.626955 GTCAGAACTTAACATTTCAGCTTGC 59.373 40.000 0.00 0.00 0.00 4.01
3789 3987 1.833630 CACCCACTGCTATTCTCTGGA 59.166 52.381 0.00 0.00 0.00 3.86
3801 3999 6.054295 GCTATTCTCTGGACATCAGTTGAAT 58.946 40.000 14.99 14.99 43.76 2.57
3933 4131 5.488919 TCTTACTGAATTCCCAGACCAATCT 59.511 40.000 2.27 0.00 37.59 2.40
3997 4195 3.686726 AGTTACAGATGTTAGCTTGCTGC 59.313 43.478 5.26 0.00 43.29 5.25
4077 4275 2.647299 TCATTTTACCCCAGAGCAGGAA 59.353 45.455 0.00 0.00 0.00 3.36
4484 4701 2.027007 AGCATGCTTTCTGCTCTCTCTT 60.027 45.455 16.30 0.00 46.79 2.85
4497 4714 8.349568 TCTGCTCTCTCTTGTTTGTACTATTA 57.650 34.615 0.00 0.00 0.00 0.98
4571 4814 3.002791 AGCTCGGTGATACACATTGTTG 58.997 45.455 0.00 0.00 35.86 3.33
4585 4862 3.837146 ACATTGTTGGATGGTTGCCAATA 59.163 39.130 0.00 0.00 46.21 1.90
4688 4970 8.902540 TGGATGGTAATGATGTTAATGTCTAC 57.097 34.615 0.00 0.00 0.00 2.59
4727 5065 1.560505 ATTCTGGAAATTGCGGGCTT 58.439 45.000 0.00 0.00 0.00 4.35
4730 5068 2.091541 TCTGGAAATTGCGGGCTTAAG 58.908 47.619 0.00 0.00 0.00 1.85
4742 5084 3.673338 GCGGGCTTAAGTGATTTGTTTTC 59.327 43.478 4.02 0.00 0.00 2.29
4775 5117 7.885922 TGGGTACTAAAATTCATGTCTGCTAAA 59.114 33.333 0.00 0.00 0.00 1.85
4777 5119 7.910683 GGTACTAAAATTCATGTCTGCTAAAGC 59.089 37.037 0.00 0.00 42.50 3.51
4798 5140 2.094286 CCCTAGGCGCTCTATCAATCAG 60.094 54.545 7.64 0.00 0.00 2.90
4860 5285 5.770162 TCTCTCCTTTCCAATTCCTGTTTTC 59.230 40.000 0.00 0.00 0.00 2.29
4982 5418 3.851098 AGCTGAAGATCGTTTACTCCAC 58.149 45.455 0.00 0.00 0.00 4.02
4987 5423 2.540515 AGATCGTTTACTCCACGCATG 58.459 47.619 0.00 0.00 37.57 4.06
5010 5446 4.577677 TGCACTTGGCCCGCAGAA 62.578 61.111 0.00 0.00 43.89 3.02
5031 5467 7.254932 GCAGAAATGGTGTATGGATAAACTCTC 60.255 40.741 0.00 0.00 0.00 3.20
5037 5473 3.704566 TGTATGGATAAACTCTCGCTGGT 59.295 43.478 0.00 0.00 0.00 4.00
5047 5483 0.321346 TCTCGCTGGTTGATGCAGAA 59.679 50.000 0.00 0.00 0.00 3.02
5084 5534 3.948473 TCAGTAGTTCCTGAGGAAGATCG 59.052 47.826 15.46 2.82 42.88 3.69
5099 5549 4.445162 GGAAGATCGAGGAGAAGGAGACTA 60.445 50.000 0.00 0.00 42.68 2.59
5102 5552 3.715638 TCGAGGAGAAGGAGACTAACA 57.284 47.619 0.00 0.00 42.68 2.41
5104 5554 4.011023 TCGAGGAGAAGGAGACTAACAAG 58.989 47.826 0.00 0.00 42.68 3.16
5105 5555 3.759618 CGAGGAGAAGGAGACTAACAAGT 59.240 47.826 0.00 0.00 42.68 3.16
5108 5558 4.902448 AGGAGAAGGAGACTAACAAGTTGT 59.098 41.667 1.64 1.64 42.68 3.32
5132 5582 2.436824 GAAGGGCGCCAAGGAGTC 60.437 66.667 30.85 8.87 0.00 3.36
5136 5586 2.656069 GGGCGCCAAGGAGTCAGTA 61.656 63.158 30.85 0.00 0.00 2.74
5138 5588 1.592223 GCGCCAAGGAGTCAGTAGT 59.408 57.895 0.00 0.00 0.00 2.73
5139 5589 0.037232 GCGCCAAGGAGTCAGTAGTT 60.037 55.000 0.00 0.00 0.00 2.24
5141 5591 2.767505 CGCCAAGGAGTCAGTAGTTTT 58.232 47.619 0.00 0.00 0.00 2.43
5168 5671 1.194121 TCTGTTGCTGCTGGGCTCTA 61.194 55.000 0.00 0.00 0.00 2.43
5222 5729 1.553248 CCGTCCTCACCAAGGTAATCA 59.447 52.381 0.00 0.00 46.32 2.57
5223 5730 2.170607 CCGTCCTCACCAAGGTAATCAT 59.829 50.000 0.00 0.00 46.32 2.45
5224 5731 3.458189 CGTCCTCACCAAGGTAATCATC 58.542 50.000 0.00 0.00 46.32 2.92
5234 5741 4.460382 CCAAGGTAATCATCAGCTTGTTGT 59.540 41.667 11.86 0.00 45.59 3.32
5314 5821 5.705441 TGTCAGGCCTATTTAGTTTGACAAG 59.295 40.000 3.98 0.00 40.07 3.16
5346 5853 2.965147 TTTGCCATGTCGTGCGAGC 61.965 57.895 0.00 0.00 0.00 5.03
5353 5860 0.443869 ATGTCGTGCGAGCATTCAAC 59.556 50.000 0.00 0.00 0.00 3.18
5354 5861 0.878086 TGTCGTGCGAGCATTCAACA 60.878 50.000 0.00 1.34 0.00 3.33
5355 5862 0.443869 GTCGTGCGAGCATTCAACAT 59.556 50.000 0.00 0.00 0.00 2.71
5356 5863 1.135972 GTCGTGCGAGCATTCAACATT 60.136 47.619 0.00 0.00 0.00 2.71
5378 5889 8.404000 ACATTGATTGATTCTTGATAGTTCTGC 58.596 33.333 0.00 0.00 0.00 4.26
5414 5925 5.592104 TTCTGGTATTGCGATGAGAGTTA 57.408 39.130 0.00 0.00 0.00 2.24
5496 6009 2.826428 CGGGATGTTTCATCGAGATGT 58.174 47.619 12.22 0.00 39.72 3.06
5538 6054 1.935327 GAGCAGCTCGACCGGTAAGT 61.935 60.000 7.34 0.00 0.00 2.24
5571 6087 1.327303 TTGCTTCACACCATGGAACC 58.673 50.000 21.47 0.00 0.00 3.62
5713 6900 4.778143 ATGTCGGCAAGGCGACCC 62.778 66.667 35.29 19.55 33.64 4.46
5747 6934 3.805108 GCTGTCCTTGATGTGTTCAGACT 60.805 47.826 0.00 0.00 35.27 3.24
5748 6935 4.384056 CTGTCCTTGATGTGTTCAGACTT 58.616 43.478 0.00 0.00 35.27 3.01
5749 6936 4.380531 TGTCCTTGATGTGTTCAGACTTC 58.619 43.478 0.00 0.00 35.27 3.01
5750 6937 4.141733 TGTCCTTGATGTGTTCAGACTTCA 60.142 41.667 0.00 0.00 35.27 3.02
5751 6938 4.450419 GTCCTTGATGTGTTCAGACTTCAG 59.550 45.833 0.00 0.00 35.27 3.02
5752 6939 4.344968 TCCTTGATGTGTTCAGACTTCAGA 59.655 41.667 0.00 0.00 35.27 3.27
5753 6940 5.012458 TCCTTGATGTGTTCAGACTTCAGAT 59.988 40.000 0.00 0.00 35.27 2.90
5754 6941 5.350914 CCTTGATGTGTTCAGACTTCAGATC 59.649 44.000 0.00 0.00 35.27 2.75
5818 7005 4.946784 AGCCGATTAGCAGTTTTGTTAG 57.053 40.909 0.00 0.00 34.23 2.34
5819 7006 4.575885 AGCCGATTAGCAGTTTTGTTAGA 58.424 39.130 0.00 0.00 34.23 2.10
5820 7007 4.392138 AGCCGATTAGCAGTTTTGTTAGAC 59.608 41.667 0.00 0.00 34.23 2.59
5821 7008 4.153475 GCCGATTAGCAGTTTTGTTAGACA 59.847 41.667 0.00 0.00 0.00 3.41
5861 7082 6.078456 ACAATTGATCCTACCTTGGATTCA 57.922 37.500 13.59 0.00 46.00 2.57
5975 7333 2.886523 CCAGCTTGAAGATGAACCAACA 59.113 45.455 12.63 0.00 32.38 3.33
6062 7427 2.335712 GCACGCCCTTTTCCTCCTG 61.336 63.158 0.00 0.00 0.00 3.86
6100 7465 3.305720 TCTATAGATGCTTTGGGTCGGT 58.694 45.455 0.00 0.00 0.00 4.69
6118 7483 2.727916 CGGTCATTTAGGTTTTCAGCGC 60.728 50.000 0.00 0.00 0.00 5.92
6119 7484 2.488153 GGTCATTTAGGTTTTCAGCGCT 59.512 45.455 2.64 2.64 0.00 5.92
6120 7485 3.492313 GTCATTTAGGTTTTCAGCGCTG 58.508 45.455 31.53 31.53 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.158623 ACAATGGACTTGGAACAGAGCA 60.159 45.455 0.00 0.00 42.39 4.26
2 3 2.485814 GACAATGGACTTGGAACAGAGC 59.514 50.000 0.00 0.00 42.39 4.09
7 8 4.340950 TCCAAAAGACAATGGACTTGGAAC 59.659 41.667 6.07 0.00 40.74 3.62
8 9 4.541705 TCCAAAAGACAATGGACTTGGAA 58.458 39.130 6.07 0.00 40.74 3.53
9 10 4.177537 TCCAAAAGACAATGGACTTGGA 57.822 40.909 4.85 4.85 40.74 3.53
16 17 6.660949 AGAACCTTAGATCCAAAAGACAATGG 59.339 38.462 0.00 0.00 38.09 3.16
17 18 7.533426 CAGAACCTTAGATCCAAAAGACAATG 58.467 38.462 0.00 0.00 0.00 2.82
18 19 6.151817 GCAGAACCTTAGATCCAAAAGACAAT 59.848 38.462 0.00 0.00 0.00 2.71
19 20 5.473504 GCAGAACCTTAGATCCAAAAGACAA 59.526 40.000 0.00 0.00 0.00 3.18
20 21 5.003804 GCAGAACCTTAGATCCAAAAGACA 58.996 41.667 0.00 0.00 0.00 3.41
21 22 5.249420 AGCAGAACCTTAGATCCAAAAGAC 58.751 41.667 0.00 0.00 0.00 3.01
22 23 5.013079 TGAGCAGAACCTTAGATCCAAAAGA 59.987 40.000 0.00 0.00 0.00 2.52
23 24 5.248640 TGAGCAGAACCTTAGATCCAAAAG 58.751 41.667 0.00 0.00 0.00 2.27
24 25 5.241403 TGAGCAGAACCTTAGATCCAAAA 57.759 39.130 0.00 0.00 0.00 2.44
25 26 4.908601 TGAGCAGAACCTTAGATCCAAA 57.091 40.909 0.00 0.00 0.00 3.28
26 27 5.441718 AATGAGCAGAACCTTAGATCCAA 57.558 39.130 0.00 0.00 0.00 3.53
27 28 5.190528 AGAAATGAGCAGAACCTTAGATCCA 59.809 40.000 0.00 0.00 0.00 3.41
28 29 5.679601 AGAAATGAGCAGAACCTTAGATCC 58.320 41.667 0.00 0.00 0.00 3.36
29 30 6.038050 CCAAGAAATGAGCAGAACCTTAGATC 59.962 42.308 0.00 0.00 0.00 2.75
30 31 5.884792 CCAAGAAATGAGCAGAACCTTAGAT 59.115 40.000 0.00 0.00 0.00 1.98
31 32 5.013079 TCCAAGAAATGAGCAGAACCTTAGA 59.987 40.000 0.00 0.00 0.00 2.10
32 33 5.248640 TCCAAGAAATGAGCAGAACCTTAG 58.751 41.667 0.00 0.00 0.00 2.18
33 34 5.241403 TCCAAGAAATGAGCAGAACCTTA 57.759 39.130 0.00 0.00 0.00 2.69
34 35 4.104383 TCCAAGAAATGAGCAGAACCTT 57.896 40.909 0.00 0.00 0.00 3.50
35 36 3.795688 TCCAAGAAATGAGCAGAACCT 57.204 42.857 0.00 0.00 0.00 3.50
36 37 4.074970 TCTTCCAAGAAATGAGCAGAACC 58.925 43.478 0.00 0.00 30.73 3.62
37 38 5.893897 ATCTTCCAAGAAATGAGCAGAAC 57.106 39.130 0.00 0.00 38.77 3.01
38 39 5.336213 GCAATCTTCCAAGAAATGAGCAGAA 60.336 40.000 8.80 0.00 38.77 3.02
88 91 4.937201 TCAGCCTGTACATGTATGGTAG 57.063 45.455 21.30 16.15 0.00 3.18
91 94 3.206150 GGTTCAGCCTGTACATGTATGG 58.794 50.000 18.16 18.16 0.00 2.74
102 105 2.137523 GCAAAACAATGGTTCAGCCTG 58.862 47.619 0.00 0.00 35.82 4.85
103 106 1.761784 TGCAAAACAATGGTTCAGCCT 59.238 42.857 6.06 0.00 35.82 4.58
104 107 2.237393 TGCAAAACAATGGTTCAGCC 57.763 45.000 6.06 0.00 35.82 4.85
105 108 2.738314 GGATGCAAAACAATGGTTCAGC 59.262 45.455 0.00 2.08 35.82 4.26
106 109 4.240096 GAGGATGCAAAACAATGGTTCAG 58.760 43.478 0.00 0.00 35.82 3.02
107 110 3.006752 GGAGGATGCAAAACAATGGTTCA 59.993 43.478 0.00 0.00 35.82 3.18
108 111 3.588955 GGAGGATGCAAAACAATGGTTC 58.411 45.455 0.00 0.00 35.82 3.62
109 112 2.302733 GGGAGGATGCAAAACAATGGTT 59.697 45.455 0.00 0.00 39.43 3.67
110 113 1.901833 GGGAGGATGCAAAACAATGGT 59.098 47.619 0.00 0.00 0.00 3.55
111 114 2.181975 AGGGAGGATGCAAAACAATGG 58.818 47.619 0.00 0.00 0.00 3.16
112 115 3.967332 AAGGGAGGATGCAAAACAATG 57.033 42.857 0.00 0.00 0.00 2.82
113 116 6.625532 AAATAAGGGAGGATGCAAAACAAT 57.374 33.333 0.00 0.00 0.00 2.71
114 117 7.732222 ATAAATAAGGGAGGATGCAAAACAA 57.268 32.000 0.00 0.00 0.00 2.83
118 121 9.515226 GTGTATATAAATAAGGGAGGATGCAAA 57.485 33.333 0.00 0.00 0.00 3.68
119 122 8.664992 TGTGTATATAAATAAGGGAGGATGCAA 58.335 33.333 0.00 0.00 0.00 4.08
120 123 8.213489 TGTGTATATAAATAAGGGAGGATGCA 57.787 34.615 0.00 0.00 0.00 3.96
121 124 9.331282 GATGTGTATATAAATAAGGGAGGATGC 57.669 37.037 0.00 0.00 0.00 3.91
142 145 6.183360 TGCAAAATTCCTTGTTTTGTGATGTG 60.183 34.615 11.52 0.00 44.40 3.21
146 149 5.240891 TGTGCAAAATTCCTTGTTTTGTGA 58.759 33.333 11.52 0.00 44.40 3.58
249 253 6.763135 CCACAAGAGCATTCTAAGTAGCATAA 59.237 38.462 0.00 0.00 31.96 1.90
250 254 6.283694 CCACAAGAGCATTCTAAGTAGCATA 58.716 40.000 0.00 0.00 31.96 3.14
251 255 5.121811 CCACAAGAGCATTCTAAGTAGCAT 58.878 41.667 0.00 0.00 31.96 3.79
252 256 4.507710 CCACAAGAGCATTCTAAGTAGCA 58.492 43.478 0.00 0.00 31.96 3.49
253 257 3.873952 CCCACAAGAGCATTCTAAGTAGC 59.126 47.826 0.00 0.00 31.96 3.58
254 258 4.872691 CACCCACAAGAGCATTCTAAGTAG 59.127 45.833 0.00 0.00 31.96 2.57
262 266 1.608590 CGTTTCACCCACAAGAGCATT 59.391 47.619 0.00 0.00 0.00 3.56
267 271 2.285083 CAAGTCGTTTCACCCACAAGA 58.715 47.619 0.00 0.00 0.00 3.02
271 275 0.942252 GTCCAAGTCGTTTCACCCAC 59.058 55.000 0.00 0.00 0.00 4.61
273 277 1.226746 CTGTCCAAGTCGTTTCACCC 58.773 55.000 0.00 0.00 0.00 4.61
276 280 0.107831 CCCCTGTCCAAGTCGTTTCA 59.892 55.000 0.00 0.00 0.00 2.69
277 281 0.395312 TCCCCTGTCCAAGTCGTTTC 59.605 55.000 0.00 0.00 0.00 2.78
282 286 0.037232 CGAGTTCCCCTGTCCAAGTC 60.037 60.000 0.00 0.00 0.00 3.01
284 288 0.320771 CACGAGTTCCCCTGTCCAAG 60.321 60.000 0.00 0.00 0.00 3.61
285 289 0.761323 TCACGAGTTCCCCTGTCCAA 60.761 55.000 0.00 0.00 0.00 3.53
286 290 0.544357 ATCACGAGTTCCCCTGTCCA 60.544 55.000 0.00 0.00 0.00 4.02
288 292 2.758979 TCTAATCACGAGTTCCCCTGTC 59.241 50.000 0.00 0.00 0.00 3.51
304 451 6.924111 AGAACATTGCCAAATCGTTTCTAAT 58.076 32.000 0.00 0.00 0.00 1.73
305 452 6.325919 AGAACATTGCCAAATCGTTTCTAA 57.674 33.333 0.00 0.00 0.00 2.10
313 460 4.211794 CACCAACAAGAACATTGCCAAATC 59.788 41.667 0.00 0.00 0.00 2.17
314 461 4.128643 CACCAACAAGAACATTGCCAAAT 58.871 39.130 0.00 0.00 0.00 2.32
315 462 3.055530 ACACCAACAAGAACATTGCCAAA 60.056 39.130 0.00 0.00 0.00 3.28
328 475 4.322080 TGTCAACAAACAACACCAACAA 57.678 36.364 0.00 0.00 0.00 2.83
330 477 4.926238 TCAATGTCAACAAACAACACCAAC 59.074 37.500 0.00 0.00 31.81 3.77
332 479 4.790765 TCAATGTCAACAAACAACACCA 57.209 36.364 0.00 0.00 31.81 4.17
353 500 5.307196 AGCGGTGACCTATTTACCATCTAAT 59.693 40.000 0.00 0.00 34.10 1.73
383 530 5.946298 TGAAGAACACGACACGATATAAGT 58.054 37.500 0.00 0.00 0.00 2.24
384 531 6.255950 TCTGAAGAACACGACACGATATAAG 58.744 40.000 0.00 0.00 0.00 1.73
385 532 6.128090 ACTCTGAAGAACACGACACGATATAA 60.128 38.462 0.00 0.00 0.00 0.98
418 565 6.611236 CCTAATGAAATAACTGACCCCCAATT 59.389 38.462 0.00 0.00 0.00 2.32
419 566 6.136155 CCTAATGAAATAACTGACCCCCAAT 58.864 40.000 0.00 0.00 0.00 3.16
421 568 4.542525 ACCTAATGAAATAACTGACCCCCA 59.457 41.667 0.00 0.00 0.00 4.96
424 571 7.881775 AATCACCTAATGAAATAACTGACCC 57.118 36.000 0.00 0.00 41.93 4.46
472 619 6.038161 CGTTGATCAAATTGGATACCAGCTTA 59.962 38.462 10.35 0.00 33.81 3.09
476 623 5.220854 GGTCGTTGATCAAATTGGATACCAG 60.221 44.000 10.35 0.00 33.81 4.00
477 624 4.638421 GGTCGTTGATCAAATTGGATACCA 59.362 41.667 10.35 0.00 0.00 3.25
485 632 6.202570 CCAAAAATGTGGTCGTTGATCAAATT 59.797 34.615 10.35 1.55 32.54 1.82
487 634 5.046529 CCAAAAATGTGGTCGTTGATCAAA 58.953 37.500 10.35 0.00 33.63 2.69
489 636 3.885901 TCCAAAAATGTGGTCGTTGATCA 59.114 39.130 0.00 0.00 39.88 2.92
496 643 1.953686 ACCTGTCCAAAAATGTGGTCG 59.046 47.619 0.00 0.00 39.88 4.79
507 654 2.021723 GCAAGTTGGTCACCTGTCCAA 61.022 52.381 4.75 0.44 40.08 3.53
510 657 1.334869 CAAGCAAGTTGGTCACCTGTC 59.665 52.381 8.24 0.00 31.82 3.51
525 672 6.449635 AAACATTCAGTAAGTCAACAAGCA 57.550 33.333 0.00 0.00 0.00 3.91
596 743 3.352648 GGCTTCATAGGCAGTACCAAAA 58.647 45.455 0.00 0.00 45.79 2.44
598 745 2.710096 GGCTTCATAGGCAGTACCAA 57.290 50.000 0.00 0.00 45.79 3.67
723 873 4.648307 TGATGAGCTCAATCTAGCAAGAGA 59.352 41.667 22.50 0.00 45.30 3.10
725 875 4.405036 ACTGATGAGCTCAATCTAGCAAGA 59.595 41.667 22.50 0.00 45.30 3.02
740 890 8.610896 GGAAAAGATGAACAGATAACTGATGAG 58.389 37.037 7.05 0.00 46.03 2.90
796 947 5.176590 GCACTTTGCCACGAAATGAATTTTA 59.823 36.000 0.00 0.00 37.42 1.52
806 961 1.098869 TTCAAGCACTTTGCCACGAA 58.901 45.000 0.00 0.00 46.52 3.85
958 1131 5.894298 TGATAGGATTGGTTAGCATGTCT 57.106 39.130 0.00 0.00 0.00 3.41
970 1143 6.491062 TGAACCCTGCAATAATGATAGGATTG 59.509 38.462 3.75 0.00 35.56 2.67
974 1147 6.713762 TTTGAACCCTGCAATAATGATAGG 57.286 37.500 0.00 0.00 34.18 2.57
1134 1311 1.968540 GGTGAGGCTTGTGTGGAGC 60.969 63.158 0.00 0.00 39.41 4.70
1222 1399 1.105759 GCAGCATCATGGAGGTTCCC 61.106 60.000 0.00 0.00 35.03 3.97
1315 1492 3.441163 CCCTAATCGACGATGAAACGAA 58.559 45.455 11.83 0.00 39.38 3.85
1476 1656 0.252558 TAGTCTCACCCCCAACTCCC 60.253 60.000 0.00 0.00 0.00 4.30
1562 1742 4.337555 CAGAGCCAGATGAACCCAAAATAG 59.662 45.833 0.00 0.00 0.00 1.73
1632 1815 2.014128 GGGATTACATCAACACCACCG 58.986 52.381 0.00 0.00 0.00 4.94
1719 1902 3.042682 TCTGTGTCCAAAGTGACCCTTA 58.957 45.455 0.00 0.00 34.25 2.69
1874 2057 1.821332 CTTCCTTCCTGCCGGATGC 60.821 63.158 5.05 0.00 39.58 3.91
1995 2184 3.245518 ACCCTTTTGCTTTGTGTTGTC 57.754 42.857 0.00 0.00 0.00 3.18
2023 2212 3.003689 ACTTGACACATTGTTGCTACTGC 59.996 43.478 0.00 0.00 40.20 4.40
2099 2289 1.472082 CAACATCGCTGGTGCCAAATA 59.528 47.619 0.00 0.00 32.26 1.40
2367 2560 9.323985 TCAAACAAGTAATTTCCTGGAAAAATG 57.676 29.630 24.44 18.90 35.11 2.32
2487 2680 6.751157 TGATCTTTGCACAAGTTCATCAAAT 58.249 32.000 13.64 0.00 0.00 2.32
2569 2762 4.141756 ACATGAAGAAACACCAATTGCCAA 60.142 37.500 0.00 0.00 0.00 4.52
2591 2784 4.516698 TCTCTTTGTGGAGAAAGCATTCAC 59.483 41.667 4.27 0.00 39.13 3.18
2620 2813 1.217511 CAGTCGGTGATGCTCTGCT 59.782 57.895 0.00 0.00 0.00 4.24
3013 3206 3.197333 CCAGGAATCAAAGAGAGAGCTGA 59.803 47.826 0.00 0.00 0.00 4.26
3044 3239 6.826668 TCCAATTCTTGAAGTTGACTCAGTA 58.173 36.000 0.00 0.00 0.00 2.74
3273 3468 3.213206 TGAAGATTTGAGTGTGGCTGT 57.787 42.857 0.00 0.00 0.00 4.40
3321 3516 6.337356 CAAAATCCAGTGTGGTAAAGTTGTT 58.663 36.000 0.00 0.00 39.03 2.83
3334 3529 2.361757 TGTGACCTTGCAAAATCCAGTG 59.638 45.455 0.00 0.00 0.00 3.66
3335 3530 2.665165 TGTGACCTTGCAAAATCCAGT 58.335 42.857 0.00 0.00 0.00 4.00
3342 3537 3.286353 TGTGAAGATGTGACCTTGCAAA 58.714 40.909 0.00 0.00 0.00 3.68
3570 3768 1.433121 GAAGGAGAGGGCCATGATCT 58.567 55.000 6.18 0.00 0.00 2.75
3571 3769 0.399833 GGAAGGAGAGGGCCATGATC 59.600 60.000 6.18 0.00 0.00 2.92
3572 3770 0.327867 TGGAAGGAGAGGGCCATGAT 60.328 55.000 6.18 0.00 0.00 2.45
3603 3801 8.695456 AGTAAAGGACAATTGTGAAGTTCAAAT 58.305 29.630 17.58 7.21 0.00 2.32
3655 3853 5.290158 TGTTAAGTTCTGACAACGAAGACAC 59.710 40.000 0.00 0.00 0.00 3.67
3690 3888 0.310854 GTGCCTTGACAAAGTTCCCG 59.689 55.000 0.00 0.00 0.00 5.14
3789 3987 8.051535 AGATAATCCAGTGAATTCAACTGATGT 58.948 33.333 26.27 17.40 33.65 3.06
3801 3999 7.582667 TCGAAGATACAGATAATCCAGTGAA 57.417 36.000 0.00 0.00 0.00 3.18
3933 4131 5.426689 AATCCTGCTCATCTTGTCTAACA 57.573 39.130 0.00 0.00 0.00 2.41
3997 4195 5.560724 TGAGGGGACAAAAGAGTTCTTATG 58.439 41.667 0.00 0.00 34.61 1.90
4077 4275 7.106239 CAGATATTAGTTGTCCAAACCACTCT 58.894 38.462 0.00 0.00 33.67 3.24
4510 4727 4.159135 GTGGTTCTGTAACGGATCCTCTTA 59.841 45.833 10.75 2.45 36.39 2.10
4521 4738 8.784043 AGATTCTAACATTTGTGGTTCTGTAAC 58.216 33.333 0.00 0.00 34.66 2.50
4585 4862 1.545651 GGTTGGACTAGCTGCCAAACT 60.546 52.381 19.62 0.00 46.03 2.66
4721 5059 4.865776 TGAAAACAAATCACTTAAGCCCG 58.134 39.130 1.29 0.00 0.00 6.13
4750 5092 7.859325 TTAGCAGACATGAATTTTAGTACCC 57.141 36.000 0.00 0.00 0.00 3.69
4754 5096 6.127619 GGGCTTTAGCAGACATGAATTTTAGT 60.128 38.462 0.00 0.00 44.36 2.24
4777 5119 1.895798 TGATTGATAGAGCGCCTAGGG 59.104 52.381 11.72 1.58 0.00 3.53
4786 5128 7.413988 CGCTCATACTAGGACTGATTGATAGAG 60.414 44.444 0.00 0.00 0.00 2.43
4798 5140 3.489398 CCACTGTTCGCTCATACTAGGAC 60.489 52.174 0.00 0.00 0.00 3.85
4959 5395 3.109619 GGAGTAAACGATCTTCAGCTCG 58.890 50.000 0.00 0.00 39.31 5.03
4965 5401 2.602878 TGCGTGGAGTAAACGATCTTC 58.397 47.619 0.00 0.00 43.68 2.87
4976 5412 1.375140 CAGTGAGCATGCGTGGAGT 60.375 57.895 13.01 0.00 0.00 3.85
4987 5423 3.368571 GGGCCAAGTGCAGTGAGC 61.369 66.667 4.39 7.38 43.89 4.26
5010 5446 5.057149 GCGAGAGTTTATCCATACACCATT 58.943 41.667 0.00 0.00 0.00 3.16
5031 5467 0.524816 GCATTCTGCATCAACCAGCG 60.525 55.000 0.00 0.00 44.26 5.18
5047 5483 1.130054 ACTGACTGTCCTGGGTGCAT 61.130 55.000 5.17 0.00 0.00 3.96
5084 5534 5.011227 ACAACTTGTTAGTCTCCTTCTCCTC 59.989 44.000 0.00 0.00 31.99 3.71
5099 5549 2.101249 CCCTTCATGTGCACAACTTGTT 59.899 45.455 25.72 2.45 35.82 2.83
5102 5552 0.675633 GCCCTTCATGTGCACAACTT 59.324 50.000 25.72 4.24 0.00 2.66
5104 5554 1.081242 CGCCCTTCATGTGCACAAC 60.081 57.895 25.72 6.55 0.00 3.32
5105 5555 2.918345 GCGCCCTTCATGTGCACAA 61.918 57.895 25.72 5.14 39.02 3.33
5108 5558 4.657408 TGGCGCCCTTCATGTGCA 62.657 61.111 26.77 0.00 40.93 4.57
5122 5572 2.814336 CCAAAACTACTGACTCCTTGGC 59.186 50.000 0.00 0.00 0.00 4.52
5132 5582 5.277538 GCAACAGAGAAGACCAAAACTACTG 60.278 44.000 0.00 0.00 0.00 2.74
5136 5586 3.629398 CAGCAACAGAGAAGACCAAAACT 59.371 43.478 0.00 0.00 0.00 2.66
5138 5588 2.358898 GCAGCAACAGAGAAGACCAAAA 59.641 45.455 0.00 0.00 0.00 2.44
5139 5589 1.949525 GCAGCAACAGAGAAGACCAAA 59.050 47.619 0.00 0.00 0.00 3.28
5141 5591 0.761187 AGCAGCAACAGAGAAGACCA 59.239 50.000 0.00 0.00 0.00 4.02
5222 5729 4.441913 CCAAAGGTTCAACAACAAGCTGAT 60.442 41.667 0.00 0.00 33.70 2.90
5223 5730 3.119173 CCAAAGGTTCAACAACAAGCTGA 60.119 43.478 0.00 0.00 33.70 4.26
5224 5731 3.189285 CCAAAGGTTCAACAACAAGCTG 58.811 45.455 0.00 0.00 33.70 4.24
5234 5741 5.824097 GGTTCAGTTAGTACCAAAGGTTCAA 59.176 40.000 0.00 0.00 37.59 2.69
5314 5821 4.155280 ACATGGCAAACGAAAGGTGTATAC 59.845 41.667 0.00 0.00 0.00 1.47
5353 5860 7.586664 CGCAGAACTATCAAGAATCAATCAATG 59.413 37.037 0.00 0.00 0.00 2.82
5354 5861 7.637229 CGCAGAACTATCAAGAATCAATCAAT 58.363 34.615 0.00 0.00 0.00 2.57
5355 5862 6.457392 GCGCAGAACTATCAAGAATCAATCAA 60.457 38.462 0.30 0.00 0.00 2.57
5356 5863 5.007039 GCGCAGAACTATCAAGAATCAATCA 59.993 40.000 0.30 0.00 0.00 2.57
5378 5889 1.098050 CCAGAATTCCCTTCTTGGCG 58.902 55.000 0.65 0.00 41.60 5.69
5571 6087 2.195096 TCAGTTTGGTACACGACAACG 58.805 47.619 0.00 0.00 39.29 4.10
5747 6934 1.219124 GCCGAGCAGGTGATCTGAA 59.781 57.895 0.00 0.00 46.18 3.02
5748 6935 1.543944 TTGCCGAGCAGGTGATCTGA 61.544 55.000 0.00 0.00 46.18 3.27
5749 6936 0.674581 TTTGCCGAGCAGGTGATCTG 60.675 55.000 0.00 0.00 46.03 2.90
5750 6937 0.674895 GTTTGCCGAGCAGGTGATCT 60.675 55.000 0.00 0.00 40.61 2.75
5751 6938 1.648467 GGTTTGCCGAGCAGGTGATC 61.648 60.000 0.17 0.00 40.61 2.92
5752 6939 1.675641 GGTTTGCCGAGCAGGTGAT 60.676 57.895 0.17 0.00 40.61 3.06
5753 6940 2.281484 GGTTTGCCGAGCAGGTGA 60.281 61.111 0.17 0.00 40.61 4.02
5930 7288 1.859427 CGTGCATCAACCAGCTTGCT 61.859 55.000 7.30 0.00 36.10 3.91
6025 7390 0.176680 CCCAGTGCAAGACGAGCTAT 59.823 55.000 0.00 0.00 0.00 2.97
6047 7412 0.250727 TTGACAGGAGGAAAAGGGCG 60.251 55.000 0.00 0.00 0.00 6.13
6062 7427 2.665185 AGAGGGTGCGCGTTTGAC 60.665 61.111 8.43 0.00 0.00 3.18
6100 7465 3.829886 CAGCGCTGAAAACCTAAATGA 57.170 42.857 33.66 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.