Multiple sequence alignment - TraesCS2A01G580900

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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 TraesCS2A01G580900 chr2A 100.000 4385 0 0 1 4385 773217915 773222299 0.000000e+00 8098
1 TraesCS2A01G580900 chr2D 94.051 4303 193 24 112 4385 646595687 646591419 0.000000e+00 6469
2 TraesCS2A01G580900 chr2D 88.904 1469 137 18 2928 4385 647110100 647111553 0.000000e+00 1786
3 TraesCS2A01G580900 chr2D 84.762 315 41 7 4074 4384 118118036 118118347 4.260000e-80 309
4 TraesCS2A01G580900 chr4A 85.220 318 40 7 4073 4384 684997493 684997177 1.970000e-83 320
5 TraesCS2A01G580900 chr4D 84.790 309 41 4 4079 4383 509800895 509801201 5.510000e-79 305
6 TraesCS2A01G580900 chr4D 84.564 298 40 6 4074 4367 40116795 40117090 1.540000e-74 291
7 TraesCS2A01G580900 chr5B 83.923 311 46 4 4077 4383 491086270 491085960 1.190000e-75 294
8 TraesCS2A01G580900 chr5B 83.121 314 47 5 4074 4383 530963498 530963187 9.290000e-72 281
9 TraesCS2A01G580900 chr1B 83.125 320 45 9 4070 4384 612859766 612859451 2.580000e-72 283
10 TraesCS2A01G580900 chr1B 82.958 311 45 7 4077 4383 1184073 1183767 1.550000e-69 274


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 TraesCS2A01G580900 chr2A 773217915 773222299 4384 False 8098 8098 100.000 1 4385 1 chr2A.!!$F1 4384
1 TraesCS2A01G580900 chr2D 646591419 646595687 4268 True 6469 6469 94.051 112 4385 1 chr2D.!!$R1 4273
2 TraesCS2A01G580900 chr2D 647110100 647111553 1453 False 1786 1786 88.904 2928 4385 1 chr2D.!!$F2 1457

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
249 251 0.178924 AAAGATGTGGCCCAGGCTTT 60.179 50.0 8.89 9.22 41.60 3.51 F
333 358 0.755079 TGAGCTCAATCCCCATCTCG 59.245 55.0 15.67 0.00 0.00 4.04 F
1806 1834 0.396417 ACGAGATGCAGGGCTACTCT 60.396 55.0 0.00 0.00 32.84 3.24 F
2025 2053 0.108138 ATCAGTTGCTACCACTCGGC 60.108 55.0 0.00 0.00 34.57 5.54 F
3138 3166 0.035458 ACTTAGTGGACAGTGGCAGC 59.965 55.0 0.00 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1333 0.040058 TCAACATGGCATCCTGGCTT 59.960 50.000 0.0 0.00 44.10 4.35 R
1857 1885 1.523711 ACCGCATGCGAATGGGTAG 60.524 57.895 39.9 22.63 42.83 3.18 R
3120 3148 0.035317 TGCTGCCACTGTCCACTAAG 59.965 55.000 0.0 0.00 0.00 2.18 R
3157 3185 0.842635 GCTTCCATGACCTCCTCCAT 59.157 55.000 0.0 0.00 0.00 3.41 R
4300 4335 2.548057 TCAGAGCCAAAAACATCGACAC 59.452 45.455 0.0 0.00 0.00 3.67 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
17 18 4.063967 TACGCTGTGCAGACCCCG 62.064 66.667 3.02 0.00 0.00 5.73
21 22 3.636231 CTGTGCAGACCCCGGGAA 61.636 66.667 26.32 0.00 0.00 3.97
22 23 3.172106 TGTGCAGACCCCGGGAAA 61.172 61.111 26.32 0.00 0.00 3.13
23 24 2.359975 GTGCAGACCCCGGGAAAG 60.360 66.667 26.32 8.13 0.00 2.62
24 25 2.528127 TGCAGACCCCGGGAAAGA 60.528 61.111 26.32 0.00 0.00 2.52
25 26 1.923395 TGCAGACCCCGGGAAAGAT 60.923 57.895 26.32 0.53 0.00 2.40
26 27 1.452108 GCAGACCCCGGGAAAGATG 60.452 63.158 26.32 14.18 0.00 2.90
27 28 1.991230 CAGACCCCGGGAAAGATGT 59.009 57.895 26.32 10.40 0.00 3.06
28 29 0.328258 CAGACCCCGGGAAAGATGTT 59.672 55.000 26.32 0.00 0.00 2.71
29 30 0.618981 AGACCCCGGGAAAGATGTTC 59.381 55.000 26.32 4.67 0.00 3.18
30 31 0.393944 GACCCCGGGAAAGATGTTCC 60.394 60.000 26.32 0.00 37.86 3.62
31 32 1.137594 ACCCCGGGAAAGATGTTCCA 61.138 55.000 26.32 0.00 40.32 3.53
32 33 0.258774 CCCCGGGAAAGATGTTCCAT 59.741 55.000 26.32 0.00 40.32 3.41
33 34 1.680338 CCCGGGAAAGATGTTCCATC 58.320 55.000 18.48 0.00 40.32 3.51
34 35 1.299541 CCGGGAAAGATGTTCCATCG 58.700 55.000 7.39 2.79 40.32 3.84
35 36 1.406887 CCGGGAAAGATGTTCCATCGT 60.407 52.381 7.39 0.00 40.32 3.73
36 37 1.665679 CGGGAAAGATGTTCCATCGTG 59.334 52.381 7.39 0.00 40.32 4.35
37 38 2.711542 GGGAAAGATGTTCCATCGTGT 58.288 47.619 7.39 0.00 40.32 4.49
38 39 3.677700 CGGGAAAGATGTTCCATCGTGTA 60.678 47.826 7.39 0.00 40.32 2.90
39 40 4.451900 GGGAAAGATGTTCCATCGTGTAT 58.548 43.478 7.39 0.00 40.32 2.29
40 41 4.881850 GGGAAAGATGTTCCATCGTGTATT 59.118 41.667 7.39 0.00 40.32 1.89
41 42 5.357032 GGGAAAGATGTTCCATCGTGTATTT 59.643 40.000 7.39 0.00 40.32 1.40
42 43 6.458342 GGGAAAGATGTTCCATCGTGTATTTC 60.458 42.308 7.39 3.55 40.32 2.17
43 44 6.093495 GGAAAGATGTTCCATCGTGTATTTCA 59.907 38.462 13.33 0.00 38.45 2.69
44 45 7.201732 GGAAAGATGTTCCATCGTGTATTTCAT 60.202 37.037 13.33 0.00 38.45 2.57
45 46 6.851222 AGATGTTCCATCGTGTATTTCATC 57.149 37.500 0.00 0.00 0.00 2.92
46 47 6.348498 AGATGTTCCATCGTGTATTTCATCA 58.652 36.000 0.00 0.00 33.83 3.07
47 48 6.481313 AGATGTTCCATCGTGTATTTCATCAG 59.519 38.462 0.00 0.00 33.83 2.90
48 49 5.729510 TGTTCCATCGTGTATTTCATCAGA 58.270 37.500 0.00 0.00 0.00 3.27
49 50 5.812127 TGTTCCATCGTGTATTTCATCAGAG 59.188 40.000 0.00 0.00 0.00 3.35
50 51 5.598416 TCCATCGTGTATTTCATCAGAGT 57.402 39.130 0.00 0.00 0.00 3.24
51 52 5.351458 TCCATCGTGTATTTCATCAGAGTG 58.649 41.667 0.00 0.00 0.00 3.51
52 53 5.105351 TCCATCGTGTATTTCATCAGAGTGT 60.105 40.000 0.00 0.00 0.00 3.55
53 54 5.582269 CCATCGTGTATTTCATCAGAGTGTT 59.418 40.000 0.00 0.00 0.00 3.32
54 55 6.456047 CCATCGTGTATTTCATCAGAGTGTTG 60.456 42.308 0.00 0.00 0.00 3.33
55 56 4.388773 TCGTGTATTTCATCAGAGTGTTGC 59.611 41.667 0.00 0.00 0.00 4.17
56 57 4.436050 CGTGTATTTCATCAGAGTGTTGCC 60.436 45.833 0.00 0.00 0.00 4.52
57 58 4.455533 GTGTATTTCATCAGAGTGTTGCCA 59.544 41.667 0.00 0.00 0.00 4.92
58 59 4.696877 TGTATTTCATCAGAGTGTTGCCAG 59.303 41.667 0.00 0.00 0.00 4.85
59 60 3.490439 TTTCATCAGAGTGTTGCCAGA 57.510 42.857 0.00 0.00 0.00 3.86
60 61 3.708403 TTCATCAGAGTGTTGCCAGAT 57.292 42.857 0.00 0.00 0.00 2.90
61 62 3.257469 TCATCAGAGTGTTGCCAGATC 57.743 47.619 0.00 0.00 0.00 2.75
62 63 2.836372 TCATCAGAGTGTTGCCAGATCT 59.164 45.455 0.00 0.00 0.00 2.75
63 64 2.756840 TCAGAGTGTTGCCAGATCTG 57.243 50.000 16.24 16.24 37.13 2.90
77 78 5.068234 CCAGATCTGGTACTCGTAAAACA 57.932 43.478 30.55 0.00 45.53 2.83
78 79 5.661458 CCAGATCTGGTACTCGTAAAACAT 58.339 41.667 30.55 0.00 45.53 2.71
79 80 5.749109 CCAGATCTGGTACTCGTAAAACATC 59.251 44.000 30.55 0.00 45.53 3.06
80 81 6.405953 CCAGATCTGGTACTCGTAAAACATCT 60.406 42.308 30.55 0.00 45.53 2.90
81 82 7.036220 CAGATCTGGTACTCGTAAAACATCTT 58.964 38.462 15.38 0.00 0.00 2.40
82 83 7.221067 CAGATCTGGTACTCGTAAAACATCTTC 59.779 40.741 15.38 0.00 0.00 2.87
83 84 6.585695 TCTGGTACTCGTAAAACATCTTCT 57.414 37.500 0.00 0.00 0.00 2.85
84 85 6.618811 TCTGGTACTCGTAAAACATCTTCTC 58.381 40.000 0.00 0.00 0.00 2.87
85 86 5.717119 TGGTACTCGTAAAACATCTTCTCC 58.283 41.667 0.00 0.00 0.00 3.71
86 87 5.107824 GGTACTCGTAAAACATCTTCTCCC 58.892 45.833 0.00 0.00 0.00 4.30
87 88 5.105432 GGTACTCGTAAAACATCTTCTCCCT 60.105 44.000 0.00 0.00 0.00 4.20
88 89 5.074584 ACTCGTAAAACATCTTCTCCCTC 57.925 43.478 0.00 0.00 0.00 4.30
89 90 4.527038 ACTCGTAAAACATCTTCTCCCTCA 59.473 41.667 0.00 0.00 0.00 3.86
90 91 4.817517 TCGTAAAACATCTTCTCCCTCAC 58.182 43.478 0.00 0.00 0.00 3.51
91 92 3.933332 CGTAAAACATCTTCTCCCTCACC 59.067 47.826 0.00 0.00 0.00 4.02
92 93 4.562757 CGTAAAACATCTTCTCCCTCACCA 60.563 45.833 0.00 0.00 0.00 4.17
93 94 3.425162 AAACATCTTCTCCCTCACCAC 57.575 47.619 0.00 0.00 0.00 4.16
94 95 0.898320 ACATCTTCTCCCTCACCACG 59.102 55.000 0.00 0.00 0.00 4.94
95 96 0.898320 CATCTTCTCCCTCACCACGT 59.102 55.000 0.00 0.00 0.00 4.49
96 97 1.276421 CATCTTCTCCCTCACCACGTT 59.724 52.381 0.00 0.00 0.00 3.99
97 98 1.420430 TCTTCTCCCTCACCACGTTT 58.580 50.000 0.00 0.00 0.00 3.60
98 99 1.343465 TCTTCTCCCTCACCACGTTTC 59.657 52.381 0.00 0.00 0.00 2.78
99 100 1.344763 CTTCTCCCTCACCACGTTTCT 59.655 52.381 0.00 0.00 0.00 2.52
100 101 2.297698 TCTCCCTCACCACGTTTCTA 57.702 50.000 0.00 0.00 0.00 2.10
101 102 1.891150 TCTCCCTCACCACGTTTCTAC 59.109 52.381 0.00 0.00 0.00 2.59
102 103 1.893801 CTCCCTCACCACGTTTCTACT 59.106 52.381 0.00 0.00 0.00 2.57
103 104 1.891150 TCCCTCACCACGTTTCTACTC 59.109 52.381 0.00 0.00 0.00 2.59
104 105 1.402456 CCCTCACCACGTTTCTACTCG 60.402 57.143 0.00 0.00 0.00 4.18
105 106 1.268899 CCTCACCACGTTTCTACTCGT 59.731 52.381 0.00 0.00 40.99 4.18
147 148 7.624360 TGATTTTTAGTCGTAGCCATTCAAT 57.376 32.000 0.00 0.00 0.00 2.57
208 209 2.779755 TTCACGTTGGATATGTGGCT 57.220 45.000 0.00 0.00 42.83 4.75
210 211 1.831106 TCACGTTGGATATGTGGCTCT 59.169 47.619 0.00 0.00 42.83 4.09
215 216 3.310774 CGTTGGATATGTGGCTCTGAAAG 59.689 47.826 0.00 0.00 0.00 2.62
233 235 6.490040 TCTGAAAGTATCCCCACAAAGAAAAG 59.510 38.462 0.00 0.00 33.76 2.27
247 249 0.613012 GAAAAGATGTGGCCCAGGCT 60.613 55.000 8.89 0.00 41.60 4.58
249 251 0.178924 AAAGATGTGGCCCAGGCTTT 60.179 50.000 8.89 9.22 41.60 3.51
282 300 6.252441 CGCGATGTAAATATTTTTGCCAAAGA 59.748 34.615 0.00 0.00 0.00 2.52
303 328 1.620822 AAAAGACCACATCCCAGCAC 58.379 50.000 0.00 0.00 0.00 4.40
318 343 2.392821 CAGCACATCTATCGTCTGAGC 58.607 52.381 0.00 0.00 0.00 4.26
322 347 3.489908 GCACATCTATCGTCTGAGCTCAA 60.490 47.826 18.85 2.60 0.00 3.02
333 358 0.755079 TGAGCTCAATCCCCATCTCG 59.245 55.000 15.67 0.00 0.00 4.04
467 492 4.077982 TCCAGAGGGATACATAAGGGAAGT 60.078 45.833 0.00 0.00 38.64 3.01
479 504 1.187087 AGGGAAGTAGCCGACTCTTG 58.813 55.000 0.00 0.00 37.44 3.02
553 578 7.603024 TCCTCGAGGTAAATCTTTTTCTTCTTC 59.397 37.037 30.17 0.00 36.34 2.87
567 592 7.510549 TTTTCTTCTTCCAAACACTAGGATG 57.489 36.000 0.00 0.00 33.10 3.51
629 654 9.827198 TTATTCCATGGATTAAGCTATTCCATT 57.173 29.630 17.06 9.58 42.99 3.16
635 660 6.128486 TGGATTAAGCTATTCCATTTGCAGA 58.872 36.000 7.85 0.00 34.32 4.26
636 661 6.779049 TGGATTAAGCTATTCCATTTGCAGAT 59.221 34.615 7.85 0.00 34.32 2.90
670 695 3.731728 GTCCATGGCCTCCCTGCA 61.732 66.667 6.96 0.00 0.00 4.41
727 752 7.282585 TGCATGCCTAACTTATCAAGAGTAAT 58.717 34.615 16.68 0.00 0.00 1.89
754 782 8.233190 GCTCTTCATATCATGGCAACTAAATAC 58.767 37.037 0.00 0.00 37.61 1.89
759 787 7.661437 TCATATCATGGCAACTAAATACTGGAC 59.339 37.037 0.00 0.00 37.61 4.02
764 792 7.343574 TCATGGCAACTAAATACTGGACTACTA 59.656 37.037 0.00 0.00 37.61 1.82
801 829 5.964758 ACAACTCTGCTATCTTCTCTTCAG 58.035 41.667 0.00 0.00 0.00 3.02
832 860 7.013083 TCTCAACGAGTATAAGTATCAACCCTC 59.987 40.741 0.00 0.00 0.00 4.30
895 923 5.659440 TTTTTCTCTTTGTGCTTGGAGTT 57.341 34.783 0.00 0.00 0.00 3.01
963 991 5.616270 TGTTAATATATTTCTGGCAGCGGA 58.384 37.500 10.34 0.00 0.00 5.54
1036 1064 2.349590 TGAACATGCTGAGTTCCATCG 58.650 47.619 11.90 0.00 43.57 3.84
1048 1076 4.994852 TGAGTTCCATCGTTTTCCTACTTG 59.005 41.667 0.00 0.00 0.00 3.16
1051 1079 4.884668 TCCATCGTTTTCCTACTTGTCT 57.115 40.909 0.00 0.00 0.00 3.41
1092 1120 3.009115 GCCTACCCCTCCACTGCA 61.009 66.667 0.00 0.00 0.00 4.41
1181 1209 3.808618 GCCCTTGTCATTCTTGAGAGTGT 60.809 47.826 3.84 0.00 34.01 3.55
1305 1333 1.784358 CTAACCCTGGTGATCCCGTA 58.216 55.000 0.00 0.00 35.15 4.02
1400 1428 1.002033 GTCAACAGCCACAAAGAGCAG 60.002 52.381 0.00 0.00 0.00 4.24
1407 1435 1.972872 CCACAAAGAGCAGGTCAGTT 58.027 50.000 1.66 0.00 0.00 3.16
1428 1456 0.745845 CAGGCTTGCGGCTAGATGTT 60.746 55.000 15.54 0.00 45.39 2.71
1431 1459 1.086696 GCTTGCGGCTAGATGTTTCA 58.913 50.000 15.54 0.00 38.06 2.69
1483 1511 1.264288 CCTCTGTTTGGCAGTCGTTTC 59.736 52.381 0.00 0.00 45.23 2.78
1665 1693 2.169832 TCACTGAAGTTGCTAGCACC 57.830 50.000 19.17 11.34 0.00 5.01
1806 1834 0.396417 ACGAGATGCAGGGCTACTCT 60.396 55.000 0.00 0.00 32.84 3.24
1857 1885 4.082026 AGCCTAGCCATGAAATTTTGTGAC 60.082 41.667 0.00 0.00 0.00 3.67
2025 2053 0.108138 ATCAGTTGCTACCACTCGGC 60.108 55.000 0.00 0.00 34.57 5.54
2130 2158 6.404074 GCTTAATAGATTGTGCTTGCAGAGTT 60.404 38.462 0.00 0.00 0.00 3.01
2131 2159 4.959596 ATAGATTGTGCTTGCAGAGTTG 57.040 40.909 0.00 0.00 0.00 3.16
2152 2180 4.787551 TGCCATTTTCCAGTATTACGGAT 58.212 39.130 7.80 0.00 0.00 4.18
2158 2186 7.360101 CCATTTTCCAGTATTACGGATCGAATC 60.360 40.741 0.00 0.00 0.00 2.52
2197 2225 5.122396 GGTAACTGCTTGTTGTTATCAGAGG 59.878 44.000 6.04 0.00 39.55 3.69
2305 2333 6.344500 AGGATCACAGCTATAGTTTGTTCAG 58.656 40.000 0.84 0.00 0.00 3.02
2347 2375 0.984230 AGGAATCTTGTTCTCCGCCA 59.016 50.000 0.00 0.00 34.22 5.69
2413 2441 1.029947 CATACCCGGGACACCAAAGC 61.030 60.000 32.02 0.00 36.13 3.51
2458 2486 2.758736 AGCTACCAGCAACTTCTCTG 57.241 50.000 0.38 0.00 45.56 3.35
2478 2506 0.843309 TGAAGCTTGGAAGTGGTGGA 59.157 50.000 2.10 0.00 0.00 4.02
2486 2514 1.203001 TGGAAGTGGTGGATTTGGGTC 60.203 52.381 0.00 0.00 0.00 4.46
2556 2584 2.034685 GGAAAGTGTTCAGCAAGGAACC 59.965 50.000 11.73 5.40 45.12 3.62
2599 2627 4.098807 TCATGACAATTGGGAGAATGCATG 59.901 41.667 10.83 9.54 33.06 4.06
2650 2678 2.386660 GCAGAGAAGTCGCACAGGC 61.387 63.158 0.00 0.00 0.00 4.85
2668 2696 2.754002 AGGCTTCTTGTCTACGAGTACC 59.246 50.000 0.00 0.00 0.00 3.34
2676 2704 2.030540 TGTCTACGAGTACCTGTGCAAC 60.031 50.000 0.00 0.00 37.35 4.17
2691 2719 3.190327 TGTGCAACGGTTCATTGGATAAG 59.810 43.478 0.00 0.00 42.39 1.73
2721 2749 5.518848 TTCATGCATGTTCAGTTTTCACT 57.481 34.783 25.43 0.00 0.00 3.41
2722 2750 5.518848 TCATGCATGTTCAGTTTTCACTT 57.481 34.783 25.43 0.00 0.00 3.16
2727 2755 5.101628 GCATGTTCAGTTTTCACTTTGTCA 58.898 37.500 0.00 0.00 0.00 3.58
2775 2803 1.559682 TCCATAGCCAGAGGTTTGTCC 59.440 52.381 0.00 0.00 0.00 4.02
2829 2857 2.489329 CCACTTGGACATAAAGCCACAG 59.511 50.000 0.00 0.00 37.39 3.66
2832 2860 4.460382 CACTTGGACATAAAGCCACAGAAT 59.540 41.667 0.00 0.00 33.01 2.40
2898 2926 5.476599 TGGACTGTCCAAAATGATAAACTGG 59.523 40.000 26.54 0.00 45.00 4.00
2925 2953 5.277683 CCAGAGCAAAATTATGACTCGGATG 60.278 44.000 0.00 0.00 32.39 3.51
3022 3050 4.850680 TGGTATTGTAGTGGTGGAAATCC 58.149 43.478 0.00 0.00 0.00 3.01
3052 3080 2.034507 CGAGAGAATTTGGACGAATCGC 60.035 50.000 1.15 0.00 0.00 4.58
3069 3097 2.048603 GCTGCCCGAGGAAAGCATT 61.049 57.895 9.99 0.00 35.11 3.56
3087 3115 3.559242 GCATTCACCTGATAAGTCTGCTC 59.441 47.826 0.00 0.00 0.00 4.26
3096 3124 5.290643 CCTGATAAGTCTGCTCGAAGAAAAG 59.709 44.000 0.00 0.00 34.09 2.27
3108 3136 3.077359 CGAAGAAAAGGCAAGATCTGGT 58.923 45.455 0.00 0.00 0.00 4.00
3111 3139 3.416156 AGAAAAGGCAAGATCTGGTCAC 58.584 45.455 4.11 0.00 0.00 3.67
3120 3148 0.179124 GATCTGGTCACCTGCTCGAC 60.179 60.000 0.00 0.00 0.00 4.20
3138 3166 0.035458 ACTTAGTGGACAGTGGCAGC 59.965 55.000 0.00 0.00 0.00 5.25
3357 3385 3.185246 ACTTCTTCCTATGTGCCATCG 57.815 47.619 0.00 0.00 0.00 3.84
3363 3391 2.046292 TCCTATGTGCCATCGGAATCA 58.954 47.619 6.12 0.00 0.00 2.57
3415 3443 7.372260 ACTTCAGCTTTCCATATCTGACTAT 57.628 36.000 0.00 0.00 35.55 2.12
3496 3524 6.971726 ATTTGGTGCATCACTATTCATGAT 57.028 33.333 0.00 0.00 37.27 2.45
3501 3529 6.016610 TGGTGCATCACTATTCATGATTCATG 60.017 38.462 18.71 18.71 37.57 3.07
3502 3530 6.016527 GGTGCATCACTATTCATGATTCATGT 60.017 38.462 22.64 10.05 37.53 3.21
3503 3531 7.173735 GGTGCATCACTATTCATGATTCATGTA 59.826 37.037 22.64 15.75 37.53 2.29
3567 3595 4.340381 GGCAAAAGACAGATGGCAAGATAT 59.660 41.667 0.00 0.00 39.25 1.63
3568 3596 5.163478 GGCAAAAGACAGATGGCAAGATATT 60.163 40.000 0.00 0.00 39.25 1.28
3589 3617 9.823098 GATATTCTATTCATTGCACATTCTCAC 57.177 33.333 0.00 0.00 0.00 3.51
3682 3710 7.102993 TCATTTCTACTGCTACAATTGCACTA 58.897 34.615 5.05 0.00 36.37 2.74
3702 3730 5.692204 CACTAACTTTGACATCAACGAGACT 59.308 40.000 5.22 0.00 35.28 3.24
3729 3757 3.934068 TGTACTACTAGGCCTTGTTTGC 58.066 45.455 24.94 15.54 0.00 3.68
3735 3763 3.146847 ACTAGGCCTTGTTTGCAACTAC 58.853 45.455 12.58 0.00 0.00 2.73
3744 3772 6.621596 GCCTTGTTTGCAACTACTTATCTGAG 60.622 42.308 0.00 0.00 0.00 3.35
3765 3793 9.784531 TCTGAGAAGTTTCATATGTTTCTTCTT 57.215 29.630 24.34 15.79 40.69 2.52
3766 3794 9.823098 CTGAGAAGTTTCATATGTTTCTTCTTG 57.177 33.333 24.34 19.55 40.69 3.02
3767 3795 9.342308 TGAGAAGTTTCATATGTTTCTTCTTGT 57.658 29.630 24.34 13.09 40.69 3.16
3813 3842 5.465532 TTGCATCAATTTAGCAACTGGAA 57.534 34.783 5.18 0.00 42.71 3.53
3817 3846 7.609960 TGCATCAATTTAGCAACTGGAAATTA 58.390 30.769 0.00 0.00 34.97 1.40
3846 3875 5.039920 TGGATCATGTACATTCAGAAGGG 57.960 43.478 5.37 0.00 0.00 3.95
3854 3883 7.451255 TCATGTACATTCAGAAGGGAAAAACAT 59.549 33.333 5.37 0.00 32.44 2.71
3855 3884 7.214467 TGTACATTCAGAAGGGAAAAACATC 57.786 36.000 0.00 0.00 0.00 3.06
3888 3917 8.808529 CAACTCACATACTAAAATAAGAGACGG 58.191 37.037 0.00 0.00 0.00 4.79
3913 3942 2.183478 TATGCTTGTGTGGGTGACTG 57.817 50.000 0.00 0.00 0.00 3.51
3956 3986 7.677276 GCATAGTTCACAGAATATTCCACACAC 60.677 40.741 11.92 4.52 0.00 3.82
3959 3989 2.095853 CACAGAATATTCCACACACGCC 59.904 50.000 11.92 0.00 0.00 5.68
3962 3992 4.126437 CAGAATATTCCACACACGCCATA 58.874 43.478 11.92 0.00 0.00 2.74
3991 4021 7.703621 TGCATCTTCTTTTTCTTCTTCACAAAG 59.296 33.333 0.00 0.00 0.00 2.77
3994 4024 8.348285 TCTTCTTTTTCTTCTTCACAAAGGAA 57.652 30.769 0.00 0.00 33.03 3.36
4033 4063 7.799081 TGAGATTTGAGAATCCACACATCTAT 58.201 34.615 6.66 0.00 42.16 1.98
4038 4068 9.722184 ATTTGAGAATCCACACATCTATGATAG 57.278 33.333 0.00 0.00 0.00 2.08
4039 4069 8.482852 TTGAGAATCCACACATCTATGATAGA 57.517 34.615 4.40 4.40 39.50 1.98
4092 4122 4.274794 TCTATACTAGAAGGGTTGGGCA 57.725 45.455 0.00 0.00 0.00 5.36
4118 4148 1.892862 CCGCGGGTTGGTGTTGTTA 60.893 57.895 20.10 0.00 0.00 2.41
4128 4158 5.395879 GGGTTGGTGTTGTTAGGTTTTCATT 60.396 40.000 0.00 0.00 0.00 2.57
4129 4159 6.110033 GGTTGGTGTTGTTAGGTTTTCATTT 58.890 36.000 0.00 0.00 0.00 2.32
4130 4160 6.256975 GGTTGGTGTTGTTAGGTTTTCATTTC 59.743 38.462 0.00 0.00 0.00 2.17
4132 4162 6.801575 TGGTGTTGTTAGGTTTTCATTTCTC 58.198 36.000 0.00 0.00 0.00 2.87
4133 4163 6.605594 TGGTGTTGTTAGGTTTTCATTTCTCT 59.394 34.615 0.00 0.00 0.00 3.10
4134 4164 7.776030 TGGTGTTGTTAGGTTTTCATTTCTCTA 59.224 33.333 0.00 0.00 0.00 2.43
4144 4174 7.984617 AGGTTTTCATTTCTCTACTATCTCTGC 59.015 37.037 0.00 0.00 0.00 4.26
4228 4263 9.436957 AATTGGTAGACAAATATATCGACATCC 57.563 33.333 0.00 0.00 43.46 3.51
4230 4265 8.134202 TGGTAGACAAATATATCGACATCCAT 57.866 34.615 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.063967 CGGGGTCTGCACAGCGTA 62.064 66.667 0.00 0.00 0.00 4.42
4 5 3.190738 TTTCCCGGGGTCTGCACAG 62.191 63.158 23.50 0.00 0.00 3.66
5 6 3.172106 TTTCCCGGGGTCTGCACA 61.172 61.111 23.50 0.00 0.00 4.57
6 7 2.198304 ATCTTTCCCGGGGTCTGCAC 62.198 60.000 23.50 0.00 0.00 4.57
7 8 1.923395 ATCTTTCCCGGGGTCTGCA 60.923 57.895 23.50 0.00 0.00 4.41
8 9 1.452108 CATCTTTCCCGGGGTCTGC 60.452 63.158 23.50 0.00 0.00 4.26
9 10 0.328258 AACATCTTTCCCGGGGTCTG 59.672 55.000 23.50 13.71 0.00 3.51
10 11 0.618981 GAACATCTTTCCCGGGGTCT 59.381 55.000 23.50 0.00 0.00 3.85
11 12 0.393944 GGAACATCTTTCCCGGGGTC 60.394 60.000 23.50 0.00 32.48 4.46
12 13 1.137594 TGGAACATCTTTCCCGGGGT 61.138 55.000 23.50 6.27 37.79 4.95
13 14 1.688811 TGGAACATCTTTCCCGGGG 59.311 57.895 23.50 6.77 37.79 5.73
26 27 5.812642 ACTCTGATGAAATACACGATGGAAC 59.187 40.000 0.00 0.00 0.00 3.62
27 28 5.812127 CACTCTGATGAAATACACGATGGAA 59.188 40.000 0.00 0.00 0.00 3.53
28 29 5.105351 ACACTCTGATGAAATACACGATGGA 60.105 40.000 0.00 0.00 0.00 3.41
29 30 5.111989 ACACTCTGATGAAATACACGATGG 58.888 41.667 0.00 0.00 0.00 3.51
30 31 6.472680 CAACACTCTGATGAAATACACGATG 58.527 40.000 0.00 0.00 0.00 3.84
31 32 5.063944 GCAACACTCTGATGAAATACACGAT 59.936 40.000 0.00 0.00 0.00 3.73
32 33 4.388773 GCAACACTCTGATGAAATACACGA 59.611 41.667 0.00 0.00 0.00 4.35
33 34 4.436050 GGCAACACTCTGATGAAATACACG 60.436 45.833 0.00 0.00 0.00 4.49
34 35 4.455533 TGGCAACACTCTGATGAAATACAC 59.544 41.667 0.00 0.00 46.17 2.90
35 36 4.650734 TGGCAACACTCTGATGAAATACA 58.349 39.130 0.00 0.00 46.17 2.29
36 37 4.937620 TCTGGCAACACTCTGATGAAATAC 59.062 41.667 0.00 0.00 46.17 1.89
37 38 5.164620 TCTGGCAACACTCTGATGAAATA 57.835 39.130 0.00 0.00 46.17 1.40
38 39 4.025040 TCTGGCAACACTCTGATGAAAT 57.975 40.909 0.00 0.00 46.17 2.17
39 40 3.490439 TCTGGCAACACTCTGATGAAA 57.510 42.857 0.00 0.00 46.17 2.69
40 41 3.262660 AGATCTGGCAACACTCTGATGAA 59.737 43.478 0.00 0.00 46.17 2.57
41 42 2.836372 AGATCTGGCAACACTCTGATGA 59.164 45.455 0.00 0.00 46.17 2.92
42 43 2.937149 CAGATCTGGCAACACTCTGATG 59.063 50.000 15.38 0.00 46.80 3.07
43 44 2.093075 CCAGATCTGGCAACACTCTGAT 60.093 50.000 28.45 0.84 46.80 2.90
44 45 1.277273 CCAGATCTGGCAACACTCTGA 59.723 52.381 28.45 0.00 46.80 3.27
45 46 1.735386 CCAGATCTGGCAACACTCTG 58.265 55.000 28.45 1.31 46.17 3.35
56 57 6.565234 AGATGTTTTACGAGTACCAGATCTG 58.435 40.000 16.24 16.24 0.00 2.90
57 58 6.777213 AGATGTTTTACGAGTACCAGATCT 57.223 37.500 0.00 0.00 0.00 2.75
58 59 7.259161 AGAAGATGTTTTACGAGTACCAGATC 58.741 38.462 0.00 0.00 0.00 2.75
59 60 7.171630 AGAAGATGTTTTACGAGTACCAGAT 57.828 36.000 0.00 0.00 0.00 2.90
60 61 6.349944 GGAGAAGATGTTTTACGAGTACCAGA 60.350 42.308 0.00 0.00 0.00 3.86
61 62 5.805994 GGAGAAGATGTTTTACGAGTACCAG 59.194 44.000 0.00 0.00 0.00 4.00
62 63 5.337009 GGGAGAAGATGTTTTACGAGTACCA 60.337 44.000 0.00 0.00 0.00 3.25
63 64 5.105432 AGGGAGAAGATGTTTTACGAGTACC 60.105 44.000 0.00 0.00 0.00 3.34
64 65 5.963594 AGGGAGAAGATGTTTTACGAGTAC 58.036 41.667 0.00 0.00 0.00 2.73
65 66 5.713389 TGAGGGAGAAGATGTTTTACGAGTA 59.287 40.000 0.00 0.00 0.00 2.59
66 67 4.527038 TGAGGGAGAAGATGTTTTACGAGT 59.473 41.667 0.00 0.00 0.00 4.18
67 68 4.865365 GTGAGGGAGAAGATGTTTTACGAG 59.135 45.833 0.00 0.00 0.00 4.18
68 69 4.322499 GGTGAGGGAGAAGATGTTTTACGA 60.322 45.833 0.00 0.00 0.00 3.43
69 70 3.933332 GGTGAGGGAGAAGATGTTTTACG 59.067 47.826 0.00 0.00 0.00 3.18
70 71 4.695928 GTGGTGAGGGAGAAGATGTTTTAC 59.304 45.833 0.00 0.00 0.00 2.01
71 72 4.562757 CGTGGTGAGGGAGAAGATGTTTTA 60.563 45.833 0.00 0.00 0.00 1.52
72 73 3.756117 GTGGTGAGGGAGAAGATGTTTT 58.244 45.455 0.00 0.00 0.00 2.43
73 74 2.289694 CGTGGTGAGGGAGAAGATGTTT 60.290 50.000 0.00 0.00 0.00 2.83
74 75 1.276421 CGTGGTGAGGGAGAAGATGTT 59.724 52.381 0.00 0.00 0.00 2.71
75 76 0.898320 CGTGGTGAGGGAGAAGATGT 59.102 55.000 0.00 0.00 0.00 3.06
76 77 0.898320 ACGTGGTGAGGGAGAAGATG 59.102 55.000 0.00 0.00 0.00 2.90
77 78 1.645710 AACGTGGTGAGGGAGAAGAT 58.354 50.000 0.00 0.00 0.00 2.40
78 79 1.343465 GAAACGTGGTGAGGGAGAAGA 59.657 52.381 0.00 0.00 0.00 2.87
79 80 1.344763 AGAAACGTGGTGAGGGAGAAG 59.655 52.381 0.00 0.00 0.00 2.85
80 81 1.420430 AGAAACGTGGTGAGGGAGAA 58.580 50.000 0.00 0.00 0.00 2.87
81 82 1.891150 GTAGAAACGTGGTGAGGGAGA 59.109 52.381 0.00 0.00 0.00 3.71
82 83 1.893801 AGTAGAAACGTGGTGAGGGAG 59.106 52.381 0.00 0.00 0.00 4.30
83 84 1.891150 GAGTAGAAACGTGGTGAGGGA 59.109 52.381 0.00 0.00 0.00 4.20
84 85 1.402456 CGAGTAGAAACGTGGTGAGGG 60.402 57.143 0.00 0.00 0.00 4.30
85 86 1.268899 ACGAGTAGAAACGTGGTGAGG 59.731 52.381 0.00 0.00 41.17 3.86
86 87 2.701073 ACGAGTAGAAACGTGGTGAG 57.299 50.000 0.00 0.00 41.17 3.51
92 93 1.268899 CAGGACCACGAGTAGAAACGT 59.731 52.381 0.00 0.00 43.50 3.99
93 94 1.538512 TCAGGACCACGAGTAGAAACG 59.461 52.381 0.00 0.00 0.00 3.60
94 95 3.005578 AGTTCAGGACCACGAGTAGAAAC 59.994 47.826 0.00 0.00 0.00 2.78
95 96 3.228453 AGTTCAGGACCACGAGTAGAAA 58.772 45.455 0.00 0.00 0.00 2.52
96 97 2.872732 AGTTCAGGACCACGAGTAGAA 58.127 47.619 0.00 0.00 0.00 2.10
97 98 2.581216 AGTTCAGGACCACGAGTAGA 57.419 50.000 0.00 0.00 0.00 2.59
98 99 3.425892 CGTTAGTTCAGGACCACGAGTAG 60.426 52.174 0.00 0.00 37.54 2.57
99 100 2.485426 CGTTAGTTCAGGACCACGAGTA 59.515 50.000 0.00 0.00 37.54 2.59
100 101 1.268899 CGTTAGTTCAGGACCACGAGT 59.731 52.381 0.00 0.00 37.54 4.18
101 102 1.268899 ACGTTAGTTCAGGACCACGAG 59.731 52.381 7.98 0.00 38.30 4.18
102 103 1.321474 ACGTTAGTTCAGGACCACGA 58.679 50.000 7.98 0.00 38.30 4.35
103 104 2.144482 AACGTTAGTTCAGGACCACG 57.856 50.000 0.00 0.33 39.89 4.94
104 105 3.460103 TCAAACGTTAGTTCAGGACCAC 58.540 45.455 0.00 0.00 40.18 4.16
105 106 3.823281 TCAAACGTTAGTTCAGGACCA 57.177 42.857 0.00 0.00 40.18 4.02
106 107 5.684550 AAATCAAACGTTAGTTCAGGACC 57.315 39.130 0.00 0.00 40.18 4.46
107 108 8.340443 ACTAAAAATCAAACGTTAGTTCAGGAC 58.660 33.333 0.00 0.00 40.18 3.85
108 109 8.441312 ACTAAAAATCAAACGTTAGTTCAGGA 57.559 30.769 0.00 0.00 40.18 3.86
109 110 7.529519 CGACTAAAAATCAAACGTTAGTTCAGG 59.470 37.037 0.00 0.00 40.18 3.86
110 111 8.060090 ACGACTAAAAATCAAACGTTAGTTCAG 58.940 33.333 0.00 0.00 40.18 3.02
147 148 4.651503 TGGGCTGGAACTAAAAATCAAACA 59.348 37.500 0.00 0.00 0.00 2.83
208 209 5.576563 TTCTTTGTGGGGATACTTTCAGA 57.423 39.130 0.00 0.00 0.00 3.27
210 211 6.369629 TCTTTTCTTTGTGGGGATACTTTCA 58.630 36.000 0.00 0.00 0.00 2.69
215 216 5.954335 CACATCTTTTCTTTGTGGGGATAC 58.046 41.667 0.00 0.00 37.64 2.24
233 235 2.353610 CCAAAGCCTGGGCCACATC 61.354 63.158 0.00 0.00 42.17 3.06
247 249 2.749706 TTACATCGCGGGTGGCCAAA 62.750 55.000 7.24 0.00 38.94 3.28
249 251 2.544590 ATTTACATCGCGGGTGGCCA 62.545 55.000 0.00 0.00 38.94 5.36
251 253 1.519408 ATATTTACATCGCGGGTGGC 58.481 50.000 6.13 0.00 38.69 5.01
252 254 4.561735 AAAATATTTACATCGCGGGTGG 57.438 40.909 6.13 0.00 0.00 4.61
292 310 2.036475 GACGATAGATGTGCTGGGATGT 59.964 50.000 0.00 0.00 41.38 3.06
297 315 2.861750 GCTCAGACGATAGATGTGCTGG 60.862 54.545 0.00 0.00 40.19 4.85
303 328 4.484236 GGATTGAGCTCAGACGATAGATG 58.516 47.826 17.43 0.00 41.38 2.90
337 362 2.197465 GGTGATTCAGTAGGGGAGGTT 58.803 52.381 0.00 0.00 0.00 3.50
398 423 2.869503 AATCGACCACCGTGGATGCC 62.870 60.000 24.80 8.87 40.96 4.40
446 471 5.046950 GCTACTTCCCTTATGTATCCCTCTG 60.047 48.000 0.00 0.00 0.00 3.35
467 492 0.898326 TGGAGCACAAGAGTCGGCTA 60.898 55.000 0.00 0.00 36.59 3.93
479 504 0.676151 CCTGCTTCCTCTTGGAGCAC 60.676 60.000 0.00 0.00 44.24 4.40
514 539 1.977544 CGAGGAGAGGAACCGTGGT 60.978 63.158 0.00 0.00 0.00 4.16
515 540 1.658686 CTCGAGGAGAGGAACCGTGG 61.659 65.000 3.91 0.00 43.20 4.94
542 567 7.014230 CCATCCTAGTGTTTGGAAGAAGAAAAA 59.986 37.037 0.00 0.00 35.81 1.94
553 578 3.433306 TGGAACCATCCTAGTGTTTGG 57.567 47.619 0.00 0.00 46.70 3.28
622 647 5.644644 GACGAAGAAATCTGCAAATGGAAT 58.355 37.500 0.00 0.00 0.00 3.01
629 654 2.987149 GAGACGACGAAGAAATCTGCAA 59.013 45.455 0.00 0.00 0.00 4.08
635 660 3.005472 TGGACTTGAGACGACGAAGAAAT 59.995 43.478 0.00 0.00 0.00 2.17
636 661 2.359848 TGGACTTGAGACGACGAAGAAA 59.640 45.455 0.00 0.00 0.00 2.52
670 695 4.104383 TCAGGTTCTTGGCTTCTTCAAT 57.896 40.909 0.00 0.00 0.00 2.57
727 752 4.160642 AGTTGCCATGATATGAAGAGCA 57.839 40.909 0.00 0.00 0.00 4.26
738 766 5.435686 AGTCCAGTATTTAGTTGCCATGA 57.564 39.130 0.00 0.00 0.00 3.07
754 782 3.570550 GCCTGGTGATACTAGTAGTCCAG 59.429 52.174 26.72 26.72 40.13 3.86
759 787 5.105310 AGTTGTTGCCTGGTGATACTAGTAG 60.105 44.000 8.85 0.00 0.00 2.57
764 792 2.639839 AGAGTTGTTGCCTGGTGATACT 59.360 45.455 0.00 0.00 0.00 2.12
771 799 2.012673 GATAGCAGAGTTGTTGCCTGG 58.987 52.381 0.00 0.00 42.48 4.45
832 860 1.100510 TCGGAGGACTTACGATGTGG 58.899 55.000 0.00 0.00 0.00 4.17
938 966 5.470098 CCGCTGCCAGAAATATATTAACAGT 59.530 40.000 0.00 0.00 0.00 3.55
963 991 1.679898 CTCGAAGAAGGGCCCTGTT 59.320 57.895 29.50 22.70 34.09 3.16
971 999 6.159293 TGTGCTTATATATGCTCGAAGAAGG 58.841 40.000 18.37 0.00 34.09 3.46
1036 1064 6.070136 AGGATAGGGAAGACAAGTAGGAAAAC 60.070 42.308 0.00 0.00 0.00 2.43
1048 1076 1.072965 CATGGGCAGGATAGGGAAGAC 59.927 57.143 0.00 0.00 0.00 3.01
1051 1079 0.328450 ACCATGGGCAGGATAGGGAA 60.328 55.000 18.09 0.00 0.00 3.97
1092 1120 2.260639 TCCAGAGATTTGAGGGAGCT 57.739 50.000 0.00 0.00 0.00 4.09
1181 1209 1.476891 GAAGTCGGTATGAGGTGCTGA 59.523 52.381 0.00 0.00 0.00 4.26
1305 1333 0.040058 TCAACATGGCATCCTGGCTT 59.960 50.000 0.00 0.00 44.10 4.35
1428 1456 4.524714 TCAAACAACACAAGGTTTCCTGAA 59.475 37.500 0.00 0.00 37.72 3.02
1431 1459 4.709397 TGATCAAACAACACAAGGTTTCCT 59.291 37.500 0.00 0.00 37.72 3.36
1483 1511 2.754552 CCAATGTATCTGTTGGGTGGTG 59.245 50.000 0.00 0.00 40.90 4.17
1665 1693 7.085746 TGACAAATGCATAACAGTCTGATTTG 58.914 34.615 6.91 12.67 36.08 2.32
1857 1885 1.523711 ACCGCATGCGAATGGGTAG 60.524 57.895 39.90 22.63 42.83 3.18
2002 2030 2.165641 CGAGTGGTAGCAACTGATGGTA 59.834 50.000 0.00 0.00 40.93 3.25
2025 2053 5.712217 TGTCACTGAAGTAAGAAACGTTG 57.288 39.130 0.00 0.00 0.00 4.10
2130 2158 4.223556 TCCGTAATACTGGAAAATGGCA 57.776 40.909 0.00 0.00 0.00 4.92
2131 2159 4.084013 CGATCCGTAATACTGGAAAATGGC 60.084 45.833 7.76 0.00 37.90 4.40
2152 2180 5.984725 ACCACCATTACTGTAATGATTCGA 58.015 37.500 31.87 0.00 46.52 3.71
2158 2186 5.880332 AGCAGTTACCACCATTACTGTAATG 59.120 40.000 26.25 26.25 43.94 1.90
2197 2225 4.794169 TCTGCCAGCGAAATTAGTTTTTC 58.206 39.130 0.00 0.00 33.24 2.29
2236 2264 7.637229 CCTTGTATCTTGATGTATGCTGAAAG 58.363 38.462 0.00 0.00 0.00 2.62
2237 2265 6.038603 GCCTTGTATCTTGATGTATGCTGAAA 59.961 38.462 0.00 0.00 0.00 2.69
2290 2318 7.148239 ACCTGCAATTACTGAACAAACTATAGC 60.148 37.037 0.00 0.00 0.00 2.97
2347 2375 8.070034 TCTTTCTTGCACATTTTCCATATGAT 57.930 30.769 3.65 0.00 0.00 2.45
2458 2486 0.954452 CCACCACTTCCAAGCTTCAC 59.046 55.000 0.00 0.00 0.00 3.18
2478 2506 4.453480 TCCTTTGAAGACTGACCCAAAT 57.547 40.909 0.00 0.00 0.00 2.32
2486 2514 5.248640 TGCCTATCTTTCCTTTGAAGACTG 58.751 41.667 0.00 0.00 36.08 3.51
2556 2584 2.096248 ACCTCTGCTAAGAACTCCTCG 58.904 52.381 0.00 0.00 30.03 4.63
2599 2627 6.708054 CCTATCAACCTGACAAGATTATGGTC 59.292 42.308 0.00 0.00 0.00 4.02
2650 2678 4.724303 CACAGGTACTCGTAGACAAGAAG 58.276 47.826 0.00 0.00 34.60 2.85
2668 2696 0.950836 TCCAATGAACCGTTGCACAG 59.049 50.000 0.00 0.00 0.00 3.66
2676 2704 4.708177 AGATCCACTTATCCAATGAACCG 58.292 43.478 0.00 0.00 0.00 4.44
2691 2719 4.157289 ACTGAACATGCATGAAAGATCCAC 59.843 41.667 32.75 12.13 0.00 4.02
2721 2749 6.762187 TGTTACGTCTAGTTTTCCATGACAAA 59.238 34.615 0.00 0.00 0.00 2.83
2722 2750 6.282167 TGTTACGTCTAGTTTTCCATGACAA 58.718 36.000 0.00 0.00 0.00 3.18
2727 2755 9.832445 ATTATGATGTTACGTCTAGTTTTCCAT 57.168 29.630 6.13 0.00 0.00 3.41
2756 2784 2.044123 GGACAAACCTCTGGCTATGG 57.956 55.000 0.00 0.00 35.41 2.74
2775 2803 3.881688 CCTTGCATTCTTCATGGAGGTAG 59.118 47.826 0.00 0.00 34.17 3.18
2829 2857 9.956640 ATGAACCTATCATCAAGGAGAATATTC 57.043 33.333 7.41 7.41 45.91 1.75
2855 2883 3.317711 TCCAAAATCAGAAAGCTTTGCGA 59.682 39.130 18.30 12.79 0.00 5.10
2896 2924 4.016444 GTCATAATTTTGCTCTGGTCCCA 58.984 43.478 0.00 0.00 0.00 4.37
2898 2926 4.034510 CGAGTCATAATTTTGCTCTGGTCC 59.965 45.833 13.78 0.00 0.00 4.46
2925 2953 3.165160 ATATCCACGGGTGCCTCGC 62.165 63.158 0.00 0.00 0.00 5.03
3003 3031 6.432783 CACAAAGGATTTCCACCACTACAATA 59.567 38.462 0.00 0.00 35.03 1.90
3009 3037 2.597455 CCACAAAGGATTTCCACCACT 58.403 47.619 0.00 0.00 41.22 4.00
3022 3050 2.095059 CCAAATTCTCTCGGCCACAAAG 60.095 50.000 2.24 0.00 0.00 2.77
3052 3080 0.677731 TGAATGCTTTCCTCGGGCAG 60.678 55.000 9.63 0.00 39.38 4.85
3069 3097 2.723273 TCGAGCAGACTTATCAGGTGA 58.277 47.619 0.00 0.00 0.00 4.02
3087 3115 3.077359 ACCAGATCTTGCCTTTTCTTCG 58.923 45.455 0.00 0.00 0.00 3.79
3096 3124 1.028868 GCAGGTGACCAGATCTTGCC 61.029 60.000 3.63 0.00 0.00 4.52
3108 3136 0.888619 CCACTAAGTCGAGCAGGTGA 59.111 55.000 9.22 0.00 0.00 4.02
3111 3139 0.888619 TGTCCACTAAGTCGAGCAGG 59.111 55.000 0.00 0.00 0.00 4.85
3120 3148 0.035317 TGCTGCCACTGTCCACTAAG 59.965 55.000 0.00 0.00 0.00 2.18
3138 3166 7.338449 TCCTCCATATGACATTGCATATCATTG 59.662 37.037 3.65 9.94 38.94 2.82
3157 3185 0.842635 GCTTCCATGACCTCCTCCAT 59.157 55.000 0.00 0.00 0.00 3.41
3282 3310 3.507411 ACTAGGGACAAAGCTGTAGTCA 58.493 45.455 13.40 0.00 35.30 3.41
3357 3385 3.837355 AGGCCCTGATAAATGTGATTCC 58.163 45.455 0.00 0.00 0.00 3.01
3363 3391 5.912149 TTCATCTAGGCCCTGATAAATGT 57.088 39.130 0.00 0.00 0.00 2.71
3415 3443 4.559300 GCAAAACAGCAAAAGCTATCCTCA 60.559 41.667 0.00 0.00 0.00 3.86
3567 3595 7.451501 TTGTGAGAATGTGCAATGAATAGAA 57.548 32.000 0.00 0.00 0.00 2.10
3568 3596 7.634671 ATTGTGAGAATGTGCAATGAATAGA 57.365 32.000 0.00 0.00 31.29 1.98
3606 3634 8.840833 TTTGCAAGGCATAAATACGATCTATA 57.159 30.769 0.00 0.00 38.76 1.31
3610 3638 7.434897 TCATTTTTGCAAGGCATAAATACGATC 59.565 33.333 15.68 0.00 44.01 3.69
3654 3682 8.562892 GTGCAATTGTAGCAGTAGAAATGATAT 58.437 33.333 7.40 0.00 43.63 1.63
3672 3700 6.129378 CGTTGATGTCAAAGTTAGTGCAATTG 60.129 38.462 0.00 0.00 37.63 2.32
3682 3710 8.827177 TTATAAGTCTCGTTGATGTCAAAGTT 57.173 30.769 8.20 1.11 37.63 2.66
3702 3730 9.826574 CAAACAAGGCCTAGTAGTACATTATAA 57.173 33.333 5.16 0.00 0.00 0.98
3791 3819 5.465532 TTCCAGTTGCTAAATTGATGCAA 57.534 34.783 8.35 8.35 43.25 4.08
3817 3846 8.812513 TCTGAATGTACATGATCCAAAAATCT 57.187 30.769 9.63 0.00 0.00 2.40
3834 3863 6.550854 TGAAGATGTTTTTCCCTTCTGAATGT 59.449 34.615 0.00 0.00 36.78 2.71
3846 3875 7.810766 TGTGAGTTGTTTGAAGATGTTTTTC 57.189 32.000 0.00 0.00 0.00 2.29
3888 3917 4.009675 TCACCCACACAAGCATATTCTTC 58.990 43.478 0.00 0.00 0.00 2.87
3913 3942 7.873739 AACTATGCAGTTCAAAATTACAAGC 57.126 32.000 0.00 0.00 41.25 4.01
3942 3971 3.874543 TGTATGGCGTGTGTGGAATATTC 59.125 43.478 6.93 6.93 0.00 1.75
3945 3975 3.202097 CATGTATGGCGTGTGTGGAATA 58.798 45.455 0.00 0.00 0.00 1.75
3956 3986 3.976793 AAAGAAGATGCATGTATGGCG 57.023 42.857 2.46 0.00 0.00 5.69
3959 3989 9.286946 GAAGAAGAAAAAGAAGATGCATGTATG 57.713 33.333 2.46 0.00 0.00 2.39
3962 3992 7.144000 GTGAAGAAGAAAAAGAAGATGCATGT 58.856 34.615 2.46 0.00 0.00 3.21
3991 4021 7.816031 TCAAATCTCAATTCAAGAAGCATTTCC 59.184 33.333 0.00 0.00 33.64 3.13
3994 4024 8.118976 TCTCAAATCTCAATTCAAGAAGCATT 57.881 30.769 0.00 0.00 0.00 3.56
4118 4148 7.984617 GCAGAGATAGTAGAGAAATGAAAACCT 59.015 37.037 0.00 0.00 0.00 3.50
4222 4257 7.441157 TGATACCGACTTGATTTTATGGATGTC 59.559 37.037 0.00 0.00 0.00 3.06
4224 4259 7.728847 TGATACCGACTTGATTTTATGGATG 57.271 36.000 0.00 0.00 0.00 3.51
4227 4262 9.489084 TCTAATGATACCGACTTGATTTTATGG 57.511 33.333 0.00 0.00 0.00 2.74
4233 4268 9.429359 GATGAATCTAATGATACCGACTTGATT 57.571 33.333 0.00 0.00 31.70 2.57
4239 4274 8.763049 TTCATGATGAATCTAATGATACCGAC 57.237 34.615 3.29 0.00 30.26 4.79
4284 4319 4.562082 TCGACACCCACAATACTAAACAG 58.438 43.478 0.00 0.00 0.00 3.16
4286 4321 4.933400 ACATCGACACCCACAATACTAAAC 59.067 41.667 0.00 0.00 0.00 2.01
4300 4335 2.548057 TCAGAGCCAAAAACATCGACAC 59.452 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.