Multiple sequence alignment - TraesCS6A01G255400

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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 TraesCS6A01G255400 chr6A 100.000 5742 0 0 1 5742 473360959 473366700 0.000000e+00 10604
1 TraesCS6A01G255400 chr6B 92.776 5177 223 41 259 5331 486518490 486513361 0.000000e+00 7348
2 TraesCS6A01G255400 chr6B 89.815 216 22 0 5330 5545 486513271 486513056 1.580000e-70 278
3 TraesCS6A01G255400 chr6B 91.566 166 9 2 96 261 486518784 486518624 2.080000e-54 224
4 TraesCS6A01G255400 chr6B 100.000 95 0 0 1 95 20186360 20186266 5.910000e-40 176
5 TraesCS6A01G255400 chr6D 94.587 4563 139 35 863 5328 333800232 333804783 0.000000e+00 6959
6 TraesCS6A01G255400 chr6D 92.771 747 38 6 98 839 333799513 333800248 0.000000e+00 1066
7 TraesCS6A01G255400 chr6D 88.235 153 17 1 5330 5481 333804876 333805028 1.270000e-41 182
8 TraesCS6A01G255400 chrUn 100.000 101 0 0 1 101 327557151 327557251 2.730000e-43 187
9 TraesCS6A01G255400 chrUn 100.000 95 0 0 1 95 369434249 369434343 5.910000e-40 176
10 TraesCS6A01G255400 chr7B 96.364 110 2 2 1 108 639919163 639919054 4.570000e-41 180
11 TraesCS6A01G255400 chr7B 100.000 96 0 0 1 96 552021290 552021385 1.640000e-40 178
12 TraesCS6A01G255400 chr1A 100.000 96 0 0 1 96 17825987 17825892 1.640000e-40 178
13 TraesCS6A01G255400 chr5B 100.000 95 0 0 1 95 118076854 118076948 5.910000e-40 176
14 TraesCS6A01G255400 chr1B 98.000 100 1 1 1 100 523333446 523333544 7.650000e-39 172
15 TraesCS6A01G255400 chr4D 95.370 108 1 4 1 105 85594079 85593973 9.890000e-38 169


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 TraesCS6A01G255400 chr6A 473360959 473366700 5741 False 10604.000000 10604 100.000000 1 5742 1 chr6A.!!$F1 5741
1 TraesCS6A01G255400 chr6B 486513056 486518784 5728 True 2616.666667 7348 91.385667 96 5545 3 chr6B.!!$R2 5449
2 TraesCS6A01G255400 chr6D 333799513 333805028 5515 False 2735.666667 6959 91.864333 98 5481 3 chr6D.!!$F1 5383

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
375 517 0.249784 CATGGAGTGCGAGATCCCAG 60.250 60.000 0.00 0.0 34.47 4.45 F
724 866 0.864377 CACGTACGCGATACTGTGGG 60.864 60.000 15.93 1.5 42.00 4.61 F
2295 2495 2.089980 ACAAGAGCTTGCCTTATGCTG 58.910 47.619 9.99 0.0 44.03 4.41 F
3315 3541 0.248661 CTACCACATCCTCTGCGACG 60.249 60.000 0.00 0.0 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 1371 1.238439 CCACAAGTCGGCACAAATCT 58.762 50.000 0.00 0.0 0.00 2.40 R
2696 2904 1.128692 GAGGATTTCGACCGTTGCAAG 59.871 52.381 0.00 0.0 0.00 4.01 R
3339 3565 1.002011 GCCCCTCCCTTCAACTGAC 60.002 63.158 0.00 0.0 0.00 3.51 R
4773 5025 0.036010 CTGCAGTTGGTACTCCCCAG 60.036 60.000 5.25 0.0 35.49 4.45 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
47 48 4.198625 CTCCAGAGCGAGCCAAAG 57.801 61.111 0.00 0.00 0.00 2.77
48 49 2.046892 TCCAGAGCGAGCCAAAGC 60.047 61.111 0.00 0.00 40.32 3.51
49 50 3.130160 CCAGAGCGAGCCAAAGCC 61.130 66.667 0.00 0.00 41.25 4.35
50 51 2.359107 CAGAGCGAGCCAAAGCCA 60.359 61.111 0.00 0.00 41.25 4.75
51 52 2.046507 AGAGCGAGCCAAAGCCAG 60.047 61.111 0.00 0.00 41.25 4.85
52 53 3.130160 GAGCGAGCCAAAGCCAGG 61.130 66.667 0.00 0.00 41.25 4.45
59 60 2.273449 CCAAAGCCAGGCTCGGAT 59.727 61.111 21.07 0.50 38.25 4.18
60 61 1.821332 CCAAAGCCAGGCTCGGATC 60.821 63.158 21.07 0.00 38.25 3.36
61 62 1.078214 CAAAGCCAGGCTCGGATCA 60.078 57.895 16.53 0.00 38.25 2.92
62 63 0.677731 CAAAGCCAGGCTCGGATCAA 60.678 55.000 16.53 0.00 38.25 2.57
63 64 0.393537 AAAGCCAGGCTCGGATCAAG 60.394 55.000 16.53 0.00 38.25 3.02
64 65 2.883267 AAGCCAGGCTCGGATCAAGC 62.883 60.000 16.53 10.12 38.25 4.01
65 66 2.906458 CCAGGCTCGGATCAAGCT 59.094 61.111 16.23 3.42 39.75 3.74
66 67 1.227497 CCAGGCTCGGATCAAGCTC 60.227 63.158 16.23 8.68 39.75 4.09
67 68 1.591059 CAGGCTCGGATCAAGCTCG 60.591 63.158 16.23 1.18 39.75 5.03
68 69 2.279784 GGCTCGGATCAAGCTCGG 60.280 66.667 16.23 0.00 39.75 4.63
69 70 2.964389 GCTCGGATCAAGCTCGGC 60.964 66.667 11.07 0.60 36.80 5.54
70 71 2.811101 CTCGGATCAAGCTCGGCT 59.189 61.111 0.00 0.00 42.56 5.52
71 72 1.299773 CTCGGATCAAGCTCGGCTC 60.300 63.158 0.00 0.00 38.25 4.70
72 73 2.656651 CGGATCAAGCTCGGCTCG 60.657 66.667 0.00 0.00 38.25 5.03
73 74 2.279784 GGATCAAGCTCGGCTCGG 60.280 66.667 0.00 0.00 38.25 4.63
74 75 2.964389 GATCAAGCTCGGCTCGGC 60.964 66.667 0.00 0.00 38.25 5.54
75 76 3.438017 GATCAAGCTCGGCTCGGCT 62.438 63.158 0.00 5.30 38.25 5.52
76 77 3.438017 ATCAAGCTCGGCTCGGCTC 62.438 63.158 9.59 0.00 38.25 4.70
86 87 4.838486 CTCGGCTCGGCTCGTGTC 62.838 72.222 0.00 0.00 0.00 3.67
89 90 4.803426 GGCTCGGCTCGTGTCCAG 62.803 72.222 0.00 0.00 0.00 3.86
196 197 2.097160 CAGAGCAACACGCATCGC 59.903 61.111 0.00 0.00 46.13 4.58
214 215 1.748122 CCTCATGCGCCTGCTTCTT 60.748 57.895 4.18 0.00 43.34 2.52
228 229 3.369175 TGCTTCTTCTCCTAGATCTGCA 58.631 45.455 5.18 0.00 0.00 4.41
231 232 4.797471 CTTCTTCTCCTAGATCTGCATCG 58.203 47.826 5.18 0.00 33.75 3.84
274 416 1.828660 TCTAGCTCCTGCCGGTAGC 60.829 63.158 15.00 12.59 40.80 3.58
275 417 1.830408 CTAGCTCCTGCCGGTAGCT 60.830 63.158 15.00 18.74 42.51 3.32
290 432 2.685388 GGTAGCTCAGGAAAATTCTGGC 59.315 50.000 0.00 0.00 33.36 4.85
375 517 0.249784 CATGGAGTGCGAGATCCCAG 60.250 60.000 0.00 0.00 34.47 4.45
415 557 5.827797 ACACTGCCTCTTGTTCTAAAAATGA 59.172 36.000 0.00 0.00 0.00 2.57
416 558 6.016777 ACACTGCCTCTTGTTCTAAAAATGAG 60.017 38.462 0.00 0.00 0.00 2.90
417 559 6.205464 CACTGCCTCTTGTTCTAAAAATGAGA 59.795 38.462 0.00 0.00 0.00 3.27
418 560 6.772716 ACTGCCTCTTGTTCTAAAAATGAGAA 59.227 34.615 0.00 0.00 0.00 2.87
419 561 7.040823 ACTGCCTCTTGTTCTAAAAATGAGAAG 60.041 37.037 0.00 0.00 33.64 2.85
420 562 6.998074 TGCCTCTTGTTCTAAAAATGAGAAGA 59.002 34.615 0.00 0.00 33.64 2.87
467 609 4.813027 TCTCAAGCCTGAATTTGCATTTC 58.187 39.130 0.00 0.00 0.00 2.17
481 623 5.888691 TTGCATTTCCGTCTGCTTAAATA 57.111 34.783 0.00 0.00 39.16 1.40
482 624 5.229921 TGCATTTCCGTCTGCTTAAATAC 57.770 39.130 0.00 0.00 39.16 1.89
483 625 4.201773 TGCATTTCCGTCTGCTTAAATACG 60.202 41.667 0.00 0.00 39.16 3.06
487 629 0.935196 CGTCTGCTTAAATACGCCCC 59.065 55.000 0.00 0.00 0.00 5.80
501 643 4.442454 CCCCTTTTCTCCCGGCCC 62.442 72.222 0.00 0.00 0.00 5.80
554 696 6.744112 AGCTTATCTGAACTCTATAGTGTGC 58.256 40.000 8.17 7.07 35.62 4.57
616 758 2.928757 AGTACACGTACGTAGCTCTCAG 59.071 50.000 22.34 8.59 40.80 3.35
618 760 1.338484 ACACGTACGTAGCTCTCAGGA 60.338 52.381 22.34 0.00 0.00 3.86
639 781 1.889170 ACTTCCTTTAGGCAGCAAAGC 59.111 47.619 0.00 0.00 31.30 3.51
724 866 0.864377 CACGTACGCGATACTGTGGG 60.864 60.000 15.93 1.50 42.00 4.61
828 970 7.851822 ACGTGTTTCTTTGCTTATTAATGTG 57.148 32.000 0.00 0.00 0.00 3.21
858 1000 6.481643 TCTTATCCACCCTTTCTCGAAAAAT 58.518 36.000 0.00 0.00 0.00 1.82
859 1001 7.626390 TCTTATCCACCCTTTCTCGAAAAATA 58.374 34.615 0.00 0.00 0.00 1.40
860 1002 8.104566 TCTTATCCACCCTTTCTCGAAAAATAA 58.895 33.333 0.00 0.00 0.00 1.40
861 1003 8.638629 TTATCCACCCTTTCTCGAAAAATAAA 57.361 30.769 0.00 0.00 0.00 1.40
862 1004 7.718334 ATCCACCCTTTCTCGAAAAATAAAT 57.282 32.000 0.00 0.00 0.00 1.40
924 1066 4.553330 TTCTCCCTGGAACTTGTACATC 57.447 45.455 0.00 0.00 0.00 3.06
932 1074 5.392767 TGGAACTTGTACATCTCAGTCTC 57.607 43.478 0.00 0.00 0.00 3.36
1015 1157 7.849804 TTCTTACCTATGATTTGCTTCTCAC 57.150 36.000 0.00 0.00 0.00 3.51
1128 1270 2.567615 AGAAGGGTATGTCACAGTGACC 59.432 50.000 27.51 14.76 46.40 4.02
1144 1286 4.154918 CAGTGACCTCCTTTTATGCTTGAC 59.845 45.833 0.00 0.00 0.00 3.18
1195 1345 7.713764 ATCTCTGTTTTAAATGGTTTTGTGC 57.286 32.000 0.00 0.00 0.00 4.57
1247 1404 4.436050 CGACTTGTGGCTAAATACTGCAAG 60.436 45.833 0.00 0.00 42.29 4.01
1371 1561 5.934935 TTTTCTCGACATTTCCTTGTACC 57.065 39.130 0.00 0.00 0.00 3.34
1412 1602 3.748048 TGCACTCAACTACTTTGCTGATC 59.252 43.478 0.00 0.00 34.88 2.92
1560 1750 9.520515 TTTCAGGTATAAATTTCTTGCTCTCTT 57.479 29.630 0.00 0.00 0.00 2.85
1565 1755 9.780413 GGTATAAATTTCTTGCTCTCTTTTCAG 57.220 33.333 0.00 0.00 0.00 3.02
1570 1760 9.473640 AAATTTCTTGCTCTCTTTTCAGATTTC 57.526 29.630 0.00 0.00 0.00 2.17
1738 1929 6.183360 ACGCATGGACATATAATTCACGTTTT 60.183 34.615 0.00 0.00 0.00 2.43
1851 2042 3.144657 TGGCAACATCAGTTCATGAGT 57.855 42.857 0.00 0.00 46.17 3.41
1960 2151 9.102757 TCTTAATGATTAGCAGAACTTGTGATC 57.897 33.333 0.00 0.00 0.00 2.92
2175 2366 9.533253 CATTGGTTCAGTCTAAAAGAATTGTTT 57.467 29.630 0.00 0.00 0.00 2.83
2215 2414 7.177216 TGAACTTTGACTGATGCCAATTCTTAT 59.823 33.333 0.00 0.00 0.00 1.73
2288 2487 2.371510 AGAGAAGAACAAGAGCTTGCCT 59.628 45.455 9.99 5.26 44.03 4.75
2295 2495 2.089980 ACAAGAGCTTGCCTTATGCTG 58.910 47.619 9.99 0.00 44.03 4.41
2303 2503 3.002759 GCTTGCCTTATGCTGTTAGCTAC 59.997 47.826 0.00 0.00 42.97 3.58
2696 2904 3.116079 TGGTTTCACTTCCTACGGAAC 57.884 47.619 0.00 0.00 36.71 3.62
2823 3031 8.739039 CACAATAGTGGTTCAGAAAATCCATTA 58.261 33.333 0.00 0.00 42.13 1.90
2824 3032 9.479549 ACAATAGTGGTTCAGAAAATCCATTAT 57.520 29.630 0.00 2.18 35.45 1.28
2921 3129 8.801299 CAATCTTCCTAGAATAGAGTATGAGCA 58.199 37.037 0.00 0.00 42.77 4.26
3048 3274 6.825610 ACCCATGTTATTTGACAACAACAAT 58.174 32.000 15.06 0.00 39.22 2.71
3155 3381 7.470009 GCCAAATGAAATATTGGTAGAACCGAT 60.470 37.037 6.43 4.29 46.29 4.18
3315 3541 0.248661 CTACCACATCCTCTGCGACG 60.249 60.000 0.00 0.00 0.00 5.12
3339 3565 3.614092 ACAGGCAAATAGTGATCCACTG 58.386 45.455 9.64 0.00 45.01 3.66
3357 3583 1.002011 GTCAGTTGAAGGGAGGGGC 60.002 63.158 0.00 0.00 0.00 5.80
3474 3700 3.857157 TTAGCTGGTTGTTTCTCAGGT 57.143 42.857 0.00 0.00 41.35 4.00
3522 3748 2.520979 CAAGACTCTTCTTACTCGGCG 58.479 52.381 0.00 0.00 40.34 6.46
3560 3786 3.230134 CACCATTGAACTTCCCTTCCAA 58.770 45.455 0.00 0.00 0.00 3.53
3593 3819 5.560722 TCTGAAAATGTACCAAGTGGAGA 57.439 39.130 3.83 0.00 38.94 3.71
3648 3874 2.910199 TCTATGGATGACAGTTGCAGC 58.090 47.619 0.00 0.00 0.00 5.25
3690 3916 0.034863 TCGGCCAGGTAACAAATCCC 60.035 55.000 2.24 0.00 41.41 3.85
3836 4062 8.046708 TGCAAAGGTATACTTATTGATCACACT 58.953 33.333 15.32 0.00 38.85 3.55
3850 4076 6.486253 TGATCACACTATGTTTCTTTCTGC 57.514 37.500 0.00 0.00 0.00 4.26
3855 4081 8.445275 TCACACTATGTTTCTTTCTGCTTAAA 57.555 30.769 0.00 0.00 0.00 1.52
3865 4091 9.548208 GTTTCTTTCTGCTTAAACTTATAGCTG 57.452 33.333 0.00 0.00 35.93 4.24
4075 4301 6.295719 TCTTAGATTTTCCCTGTACTGACC 57.704 41.667 0.60 0.00 0.00 4.02
4078 4304 4.911390 AGATTTTCCCTGTACTGACCTTG 58.089 43.478 0.60 0.00 0.00 3.61
4178 4404 5.413309 AAGATAACTCTAGTGCTGCAAGT 57.587 39.130 2.77 0.56 35.30 3.16
4311 4537 3.615849 GCGATCTGCTATTTTCCCTTG 57.384 47.619 0.00 0.00 41.73 3.61
4347 4573 7.866393 CAGAAATTTGAGACATTCTCTTTGCTT 59.134 33.333 0.00 0.00 43.73 3.91
4403 4629 5.584551 TCCTAGAGATAGCAGACACCATA 57.415 43.478 0.00 0.00 0.00 2.74
4451 4677 1.219124 GCTGATGGAGCTCCGTGAA 59.781 57.895 32.31 18.16 45.21 3.18
4755 5007 5.614308 TGAGAGATGACAGTGAACACAAAT 58.386 37.500 7.68 0.00 0.00 2.32
4790 5042 1.272807 TACTGGGGAGTACCAACTGC 58.727 55.000 0.00 0.00 42.97 4.40
4813 5065 0.798776 CATTCAGAGTGTTGACCGGC 59.201 55.000 0.00 0.00 0.00 6.13
4829 5081 1.135699 CGGCGCTTGATGTTGATTGC 61.136 55.000 7.64 0.00 0.00 3.56
4845 5097 2.032680 TTGCCAGGCGTTAATAGGAC 57.967 50.000 7.03 0.00 0.00 3.85
4918 5180 9.635520 TTTCAGTTACTAGTGCTTATACAAGTC 57.364 33.333 5.39 0.00 34.00 3.01
4923 5185 9.085250 GTTACTAGTGCTTATACAAGTCCTTTC 57.915 37.037 5.39 0.00 34.00 2.62
4924 5186 7.483580 ACTAGTGCTTATACAAGTCCTTTCT 57.516 36.000 0.00 0.00 34.00 2.52
4931 5193 8.567948 TGCTTATACAAGTCCTTTCTCTTTTTG 58.432 33.333 0.00 0.00 34.00 2.44
4932 5194 8.784043 GCTTATACAAGTCCTTTCTCTTTTTGA 58.216 33.333 0.00 0.00 34.00 2.69
4936 5198 9.971922 ATACAAGTCCTTTCTCTTTTTGAATTG 57.028 29.630 0.00 0.00 34.90 2.32
4975 5238 4.370917 TGTAACCAGTTTAGGAACGTCAC 58.629 43.478 0.00 0.00 40.75 3.67
5000 5269 7.810759 ACTGTTTCTTGTTTGTAATTGAAACGT 59.189 29.630 0.00 0.00 43.27 3.99
5031 5300 6.480651 TGAATGTACGTTATCTGTTGTGTGTT 59.519 34.615 0.00 0.00 0.00 3.32
5038 5307 6.704493 ACGTTATCTGTTGTGTGTTTAGTGAT 59.296 34.615 0.00 0.00 0.00 3.06
5040 5309 4.811555 TCTGTTGTGTGTTTAGTGATGC 57.188 40.909 0.00 0.00 0.00 3.91
5042 5311 2.621055 TGTTGTGTGTTTAGTGATGCCC 59.379 45.455 0.00 0.00 0.00 5.36
5095 5364 6.414408 AAGAATTGAGTTATCGTCTGCTTG 57.586 37.500 0.00 0.00 0.00 4.01
5123 5392 7.712204 TCTATGTCAGGTATCACAAAGTGTA 57.288 36.000 0.00 0.00 34.79 2.90
5173 5442 6.370442 TGATGTTTTAGTATGGAACTGAACGG 59.630 38.462 0.00 0.00 39.39 4.44
5181 5450 1.276989 TGGAACTGAACGGGTACATCC 59.723 52.381 0.00 0.00 0.00 3.51
5208 5477 9.695526 TTCAAATAATTTGGAACTGAATGAGTG 57.304 29.630 0.00 0.00 40.98 3.51
5271 5540 6.018751 GGTTTTTCTTTCAAGCTTTTAGGCTG 60.019 38.462 0.00 0.00 42.24 4.85
5280 5549 1.017387 CTTTTAGGCTGGGCTTAGCG 58.983 55.000 0.00 0.00 44.60 4.26
5283 5552 1.686325 TTAGGCTGGGCTTAGCGGAG 61.686 60.000 0.00 0.00 44.60 4.63
5289 5558 1.298667 GGGCTTAGCGGAGAAACCA 59.701 57.895 0.00 0.00 38.90 3.67
5331 5600 3.607078 GCTTTTGTGTCTAAGCCGTTGAG 60.607 47.826 0.00 0.00 40.61 3.02
5332 5601 1.508632 TTGTGTCTAAGCCGTTGAGC 58.491 50.000 0.00 0.00 0.00 4.26
5352 5712 2.590092 GGCGGTCCATGCTTAGGT 59.410 61.111 0.00 0.00 0.00 3.08
5362 5722 3.578716 TCCATGCTTAGGTAGGACATAGC 59.421 47.826 0.00 0.00 0.00 2.97
5381 5741 6.795114 ACATAGCGTGTTTTAAAAAGACATCG 59.205 34.615 1.31 5.86 38.01 3.84
5384 5744 4.086664 GCGTGTTTTAAAAAGACATCGAGC 59.913 41.667 1.31 0.18 0.00 5.03
5388 5748 4.759516 TTTAAAAAGACATCGAGCACCC 57.240 40.909 0.00 0.00 0.00 4.61
5391 5751 2.496899 AAAGACATCGAGCACCCATT 57.503 45.000 0.00 0.00 0.00 3.16
5473 5834 6.736110 AGACCAGTAAACAACAGTAGGTAA 57.264 37.500 0.00 0.00 0.00 2.85
5475 5836 6.552350 AGACCAGTAAACAACAGTAGGTAAGA 59.448 38.462 0.00 0.00 0.00 2.10
5496 5857 3.853475 ACGAGGTAAACCCTATTTGACG 58.147 45.455 0.00 0.00 46.51 4.35
5499 5860 4.572909 GAGGTAAACCCTATTTGACGTGT 58.427 43.478 0.00 0.00 46.51 4.49
5539 5900 2.028112 CACATAGGGATACACCGATGGG 60.028 54.545 9.55 2.29 44.80 4.00
5545 5906 2.397413 GATACACCGATGGGCTGGGG 62.397 65.000 0.00 0.00 36.48 4.96
5546 5907 2.907482 ATACACCGATGGGCTGGGGA 62.907 60.000 0.00 0.00 36.48 4.81
5547 5908 4.489771 CACCGATGGGCTGGGGAC 62.490 72.222 0.00 0.00 36.48 4.46
5549 5910 3.727258 CCGATGGGCTGGGGACAA 61.727 66.667 0.00 0.00 42.06 3.18
5550 5911 2.597340 CGATGGGCTGGGGACAAT 59.403 61.111 0.00 0.00 42.06 2.71
5551 5912 1.076777 CGATGGGCTGGGGACAATT 60.077 57.895 0.00 0.00 42.06 2.32
5552 5913 0.182537 CGATGGGCTGGGGACAATTA 59.817 55.000 0.00 0.00 42.06 1.40
5553 5914 1.409521 CGATGGGCTGGGGACAATTAA 60.410 52.381 0.00 0.00 42.06 1.40
5554 5915 2.752829 CGATGGGCTGGGGACAATTAAT 60.753 50.000 0.00 0.00 42.06 1.40
5555 5916 2.157640 TGGGCTGGGGACAATTAATG 57.842 50.000 0.00 0.00 42.06 1.90
5557 5918 2.225496 TGGGCTGGGGACAATTAATGTT 60.225 45.455 0.00 0.00 44.12 2.71
5558 5919 2.837591 GGGCTGGGGACAATTAATGTTT 59.162 45.455 0.00 0.00 44.12 2.83
5559 5920 3.118775 GGGCTGGGGACAATTAATGTTTC 60.119 47.826 0.00 0.00 44.12 2.78
5560 5921 3.428862 GGCTGGGGACAATTAATGTTTCG 60.429 47.826 0.00 0.00 44.12 3.46
5561 5922 3.769536 CTGGGGACAATTAATGTTTCGC 58.230 45.455 0.00 0.00 44.12 4.70
5562 5923 3.426615 TGGGGACAATTAATGTTTCGCT 58.573 40.909 0.00 0.00 44.12 4.93
5563 5924 4.590918 TGGGGACAATTAATGTTTCGCTA 58.409 39.130 0.00 0.00 44.12 4.26
5564 5925 5.010933 TGGGGACAATTAATGTTTCGCTAA 58.989 37.500 0.00 0.00 44.12 3.09
5565 5926 5.654650 TGGGGACAATTAATGTTTCGCTAAT 59.345 36.000 0.00 0.00 44.12 1.73
5566 5927 6.153680 TGGGGACAATTAATGTTTCGCTAATT 59.846 34.615 0.00 0.00 44.12 1.40
5567 5928 7.039270 GGGGACAATTAATGTTTCGCTAATTT 58.961 34.615 0.00 0.00 44.12 1.82
5568 5929 7.547722 GGGGACAATTAATGTTTCGCTAATTTT 59.452 33.333 0.00 0.00 44.12 1.82
5569 5930 8.931775 GGGACAATTAATGTTTCGCTAATTTTT 58.068 29.630 0.00 0.00 44.12 1.94
5613 5974 9.723447 TTTGACTTTTGGTTTTCTTTGTTTTTC 57.277 25.926 0.00 0.00 0.00 2.29
5614 5975 8.438676 TGACTTTTGGTTTTCTTTGTTTTTCA 57.561 26.923 0.00 0.00 0.00 2.69
5615 5976 8.338986 TGACTTTTGGTTTTCTTTGTTTTTCAC 58.661 29.630 0.00 0.00 0.00 3.18
5616 5977 8.445275 ACTTTTGGTTTTCTTTGTTTTTCACT 57.555 26.923 0.00 0.00 0.00 3.41
5617 5978 8.898761 ACTTTTGGTTTTCTTTGTTTTTCACTT 58.101 25.926 0.00 0.00 0.00 3.16
5618 5979 9.381027 CTTTTGGTTTTCTTTGTTTTTCACTTC 57.619 29.630 0.00 0.00 0.00 3.01
5619 5980 8.438676 TTTGGTTTTCTTTGTTTTTCACTTCA 57.561 26.923 0.00 0.00 0.00 3.02
5620 5981 8.438676 TTGGTTTTCTTTGTTTTTCACTTCAA 57.561 26.923 0.00 0.00 0.00 2.69
5621 5982 8.438676 TGGTTTTCTTTGTTTTTCACTTCAAA 57.561 26.923 0.00 0.00 0.00 2.69
5622 5983 8.893727 TGGTTTTCTTTGTTTTTCACTTCAAAA 58.106 25.926 0.00 0.00 31.07 2.44
5623 5984 9.891828 GGTTTTCTTTGTTTTTCACTTCAAAAT 57.108 25.926 0.00 0.00 31.07 1.82
5636 5997 8.885494 TTCACTTCAAAATATTTCCTTTGTGG 57.115 30.769 0.10 0.00 34.74 4.17
5637 5998 6.928492 TCACTTCAAAATATTTCCTTTGTGGC 59.072 34.615 0.10 0.00 34.74 5.01
5638 5999 6.930722 CACTTCAAAATATTTCCTTTGTGGCT 59.069 34.615 0.10 0.00 34.74 4.75
5639 6000 7.442062 CACTTCAAAATATTTCCTTTGTGGCTT 59.558 33.333 0.10 0.00 34.74 4.35
5640 6001 7.992608 ACTTCAAAATATTTCCTTTGTGGCTTT 59.007 29.630 0.10 0.00 34.74 3.51
5641 6002 7.961325 TCAAAATATTTCCTTTGTGGCTTTC 57.039 32.000 0.10 0.00 34.74 2.62
5642 6003 6.934083 TCAAAATATTTCCTTTGTGGCTTTCC 59.066 34.615 0.10 0.00 34.74 3.13
5643 6004 5.420725 AATATTTCCTTTGTGGCTTTCCC 57.579 39.130 0.00 0.00 35.26 3.97
5644 6005 1.036707 TTTCCTTTGTGGCTTTCCCG 58.963 50.000 0.00 0.00 35.87 5.14
5645 6006 0.825840 TTCCTTTGTGGCTTTCCCGG 60.826 55.000 0.00 0.00 35.87 5.73
5646 6007 2.275380 CCTTTGTGGCTTTCCCGGG 61.275 63.158 16.85 16.85 35.87 5.73
5647 6008 2.203567 TTTGTGGCTTTCCCGGGG 60.204 61.111 23.50 6.77 35.87 5.73
5648 6009 2.994643 CTTTGTGGCTTTCCCGGGGT 62.995 60.000 23.50 0.00 35.87 4.95
5649 6010 2.591193 TTTGTGGCTTTCCCGGGGTT 62.591 55.000 23.50 0.00 35.87 4.11
5650 6011 2.203582 GTGGCTTTCCCGGGGTTT 60.204 61.111 23.50 0.00 35.87 3.27
5651 6012 1.835267 GTGGCTTTCCCGGGGTTTT 60.835 57.895 23.50 0.00 35.87 2.43
5652 6013 1.075151 TGGCTTTCCCGGGGTTTTT 60.075 52.632 23.50 0.00 35.87 1.94
5701 6062 7.576861 TTGGGTACTCTTAGTTTTTCTTTGG 57.423 36.000 0.00 0.00 0.00 3.28
5702 6063 6.066032 TGGGTACTCTTAGTTTTTCTTTGGG 58.934 40.000 0.00 0.00 0.00 4.12
5703 6064 6.066690 GGGTACTCTTAGTTTTTCTTTGGGT 58.933 40.000 0.00 0.00 0.00 4.51
5704 6065 6.548622 GGGTACTCTTAGTTTTTCTTTGGGTT 59.451 38.462 0.00 0.00 0.00 4.11
5705 6066 7.069085 GGGTACTCTTAGTTTTTCTTTGGGTTT 59.931 37.037 0.00 0.00 0.00 3.27
5706 6067 8.472413 GGTACTCTTAGTTTTTCTTTGGGTTTT 58.528 33.333 0.00 0.00 0.00 2.43
5707 6068 9.512435 GTACTCTTAGTTTTTCTTTGGGTTTTC 57.488 33.333 0.00 0.00 0.00 2.29
5708 6069 8.362464 ACTCTTAGTTTTTCTTTGGGTTTTCT 57.638 30.769 0.00 0.00 0.00 2.52
5709 6070 8.812972 ACTCTTAGTTTTTCTTTGGGTTTTCTT 58.187 29.630 0.00 0.00 0.00 2.52
5710 6071 9.653287 CTCTTAGTTTTTCTTTGGGTTTTCTTT 57.347 29.630 0.00 0.00 0.00 2.52
5721 6082 9.594936 TCTTTGGGTTTTCTTTTATTCTATGGA 57.405 29.630 0.00 0.00 0.00 3.41
5722 6083 9.860898 CTTTGGGTTTTCTTTTATTCTATGGAG 57.139 33.333 0.00 0.00 0.00 3.86
5723 6084 8.950007 TTGGGTTTTCTTTTATTCTATGGAGT 57.050 30.769 0.00 0.00 0.00 3.85
5724 6085 8.950007 TGGGTTTTCTTTTATTCTATGGAGTT 57.050 30.769 0.00 0.00 0.00 3.01
5725 6086 9.374711 TGGGTTTTCTTTTATTCTATGGAGTTT 57.625 29.630 0.00 0.00 0.00 2.66
5741 6102 9.639601 CTATGGAGTTTTCCTTTATTTGTTTCC 57.360 33.333 0.00 0.00 44.36 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.105466 GCTTTGGCTCGCTCTGGAG 61.105 63.158 0.00 0.00 37.11 3.86
31 32 2.046892 GCTTTGGCTCGCTCTGGA 60.047 61.111 0.00 0.00 35.22 3.86
32 33 3.130160 GGCTTTGGCTCGCTCTGG 61.130 66.667 0.00 0.00 38.73 3.86
33 34 2.359107 TGGCTTTGGCTCGCTCTG 60.359 61.111 0.00 0.00 38.73 3.35
34 35 2.046507 CTGGCTTTGGCTCGCTCT 60.047 61.111 0.00 0.00 38.73 4.09
35 36 3.130160 CCTGGCTTTGGCTCGCTC 61.130 66.667 0.00 0.00 38.73 5.03
42 43 1.821332 GATCCGAGCCTGGCTTTGG 60.821 63.158 26.42 26.42 39.88 3.28
43 44 0.677731 TTGATCCGAGCCTGGCTTTG 60.678 55.000 24.26 17.87 39.88 2.77
44 45 0.393537 CTTGATCCGAGCCTGGCTTT 60.394 55.000 24.26 8.35 39.88 3.51
45 46 1.222936 CTTGATCCGAGCCTGGCTT 59.777 57.895 24.26 6.46 39.88 4.35
46 47 2.906458 CTTGATCCGAGCCTGGCT 59.094 61.111 23.64 23.64 43.88 4.75
47 48 2.899339 GCTTGATCCGAGCCTGGC 60.899 66.667 11.65 11.65 35.00 4.85
48 49 1.227497 GAGCTTGATCCGAGCCTGG 60.227 63.158 12.94 0.00 41.50 4.45
49 50 1.591059 CGAGCTTGATCCGAGCCTG 60.591 63.158 12.94 4.38 41.50 4.85
50 51 2.790791 CCGAGCTTGATCCGAGCCT 61.791 63.158 12.94 3.24 41.50 4.58
51 52 2.279784 CCGAGCTTGATCCGAGCC 60.280 66.667 12.94 5.86 41.50 4.70
52 53 2.964389 GCCGAGCTTGATCCGAGC 60.964 66.667 1.22 9.51 40.93 5.03
53 54 1.299773 GAGCCGAGCTTGATCCGAG 60.300 63.158 1.22 0.00 39.88 4.63
54 55 2.808315 GAGCCGAGCTTGATCCGA 59.192 61.111 1.22 0.00 39.88 4.55
55 56 2.656651 CGAGCCGAGCTTGATCCG 60.657 66.667 1.22 0.00 42.27 4.18
56 57 2.279784 CCGAGCCGAGCTTGATCC 60.280 66.667 13.01 0.00 42.27 3.36
57 58 2.964389 GCCGAGCCGAGCTTGATC 60.964 66.667 13.01 0.00 42.27 2.92
58 59 3.438017 GAGCCGAGCCGAGCTTGAT 62.438 63.158 13.01 1.90 42.27 2.57
59 60 4.135153 GAGCCGAGCCGAGCTTGA 62.135 66.667 13.01 0.00 42.27 3.02
69 70 4.838486 GACACGAGCCGAGCCGAG 62.838 72.222 11.42 7.65 0.00 4.63
72 73 4.803426 CTGGACACGAGCCGAGCC 62.803 72.222 1.50 1.42 0.00 4.70
74 75 4.803426 GGCTGGACACGAGCCGAG 62.803 72.222 8.81 0.00 46.47 4.63
78 79 2.184579 GTAGGGCTGGACACGAGC 59.815 66.667 0.00 0.00 35.57 5.03
79 80 0.681564 AGAGTAGGGCTGGACACGAG 60.682 60.000 0.00 0.00 0.00 4.18
80 81 0.965866 CAGAGTAGGGCTGGACACGA 60.966 60.000 0.00 0.00 0.00 4.35
81 82 1.513158 CAGAGTAGGGCTGGACACG 59.487 63.158 0.00 0.00 0.00 4.49
91 92 3.854669 CAGCGCCCCCAGAGTAGG 61.855 72.222 2.29 0.00 0.00 3.18
92 93 3.077556 ACAGCGCCCCCAGAGTAG 61.078 66.667 2.29 0.00 0.00 2.57
93 94 3.390521 CACAGCGCCCCCAGAGTA 61.391 66.667 2.29 0.00 0.00 2.59
196 197 1.712977 GAAGAAGCAGGCGCATGAGG 61.713 60.000 28.37 0.00 42.27 3.86
211 212 2.556189 GCGATGCAGATCTAGGAGAAGA 59.444 50.000 0.00 0.00 0.00 2.87
214 215 1.202989 AGGCGATGCAGATCTAGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
228 229 3.083997 GAGACCCACCCAGGCGAT 61.084 66.667 0.00 0.00 35.39 4.58
231 232 2.352805 CAAGAGACCCACCCAGGC 59.647 66.667 0.00 0.00 35.39 4.85
261 267 2.811101 CTGAGCTACCGGCAGGAG 59.189 66.667 10.86 3.90 44.79 3.69
274 416 3.439476 CACAGAGCCAGAATTTTCCTGAG 59.561 47.826 0.00 0.00 33.65 3.35
275 417 3.181440 ACACAGAGCCAGAATTTTCCTGA 60.181 43.478 0.00 0.00 33.65 3.86
290 432 6.433766 GGACAATTTCTGAAGAAACACAGAG 58.566 40.000 7.62 0.00 45.55 3.35
467 609 0.935196 GGGCGTATTTAAGCAGACGG 59.065 55.000 0.00 0.00 35.87 4.79
481 623 4.029809 CCGGGAGAAAAGGGGCGT 62.030 66.667 0.00 0.00 0.00 5.68
487 629 2.272471 GAGGGGCCGGGAGAAAAG 59.728 66.667 2.18 0.00 0.00 2.27
501 643 9.284968 TCTTTTAACCTTTATCTTTGTCAGAGG 57.715 33.333 0.00 0.00 33.87 3.69
554 696 6.630443 GCAAGAAATGAGCATACAGAATAACG 59.370 38.462 0.00 0.00 0.00 3.18
616 758 2.200373 TGCTGCCTAAAGGAAGTTCC 57.800 50.000 14.54 14.54 43.19 3.62
618 760 2.297315 GCTTTGCTGCCTAAAGGAAGTT 59.703 45.455 12.58 0.00 43.19 2.66
645 787 2.888414 GAGAGGACTGCTAGTGGGATAC 59.112 54.545 0.00 0.00 0.00 2.24
828 970 5.278758 CGAGAAAGGGTGGATAAGAGATCTC 60.279 48.000 15.29 15.29 0.00 2.75
859 1001 9.965902 ACAGGTTTAAGAGATCTCACATTATTT 57.034 29.630 24.39 10.44 0.00 1.40
860 1002 9.388506 CACAGGTTTAAGAGATCTCACATTATT 57.611 33.333 24.39 11.13 0.00 1.40
861 1003 7.497249 GCACAGGTTTAAGAGATCTCACATTAT 59.503 37.037 24.39 0.00 0.00 1.28
862 1004 6.818644 GCACAGGTTTAAGAGATCTCACATTA 59.181 38.462 24.39 11.53 0.00 1.90
879 1021 2.956333 GGGTCTAAACTTTGCACAGGTT 59.044 45.455 8.45 8.45 0.00 3.50
932 1074 9.090692 CTGAAAAATAAATACAAATGAGCAGGG 57.909 33.333 0.00 0.00 0.00 4.45
1003 1145 5.510671 CAAACTTGTACGTGAGAAGCAAAT 58.489 37.500 0.00 0.00 31.46 2.32
1015 1157 4.150980 TCCAATCGTTAGCAAACTTGTACG 59.849 41.667 0.00 0.00 33.15 3.67
1128 1270 6.566197 AAACTGAGTCAAGCATAAAAGGAG 57.434 37.500 0.00 0.00 0.00 3.69
1144 1286 6.019318 CCAATGACTTGCAAAAGAAAACTGAG 60.019 38.462 0.00 0.00 0.00 3.35
1213 1370 1.608590 CCACAAGTCGGCACAAATCTT 59.391 47.619 0.00 0.00 0.00 2.40
1214 1371 1.238439 CCACAAGTCGGCACAAATCT 58.762 50.000 0.00 0.00 0.00 2.40
1352 1533 2.559668 ACGGTACAAGGAAATGTCGAGA 59.440 45.455 0.00 0.00 34.75 4.04
1354 1535 3.319755 GAACGGTACAAGGAAATGTCGA 58.680 45.455 0.00 0.00 34.75 4.20
1371 1561 2.472488 GCAAAAGCAACTTGATGGAACG 59.528 45.455 0.00 0.00 0.00 3.95
1393 1583 5.641209 GTCATGATCAGCAAAGTAGTTGAGT 59.359 40.000 0.00 0.00 39.87 3.41
1738 1929 6.697641 ACTAAAAGGAAGTATGGACAGGAA 57.302 37.500 0.00 0.00 0.00 3.36
2170 2361 4.427096 TCAAACGAACTCTTGCAAACAA 57.573 36.364 0.00 0.00 0.00 2.83
2288 2487 6.758416 CAGAGAACATGTAGCTAACAGCATAA 59.242 38.462 0.00 0.00 45.56 1.90
2295 2495 6.311690 GGAAGTTCAGAGAACATGTAGCTAAC 59.688 42.308 11.92 2.15 0.00 2.34
2303 2503 4.550076 AGGAGGAAGTTCAGAGAACATG 57.450 45.455 11.92 0.00 0.00 3.21
2349 2549 4.989279 ACAATTGTTATGTCCTGATGCC 57.011 40.909 4.92 0.00 0.00 4.40
2696 2904 1.128692 GAGGATTTCGACCGTTGCAAG 59.871 52.381 0.00 0.00 0.00 4.01
2823 3031 5.419542 TGTTTAGCAGATCGAAGCTGTAAT 58.580 37.500 17.37 8.65 41.97 1.89
2824 3032 4.816392 TGTTTAGCAGATCGAAGCTGTAA 58.184 39.130 17.37 12.17 41.97 2.41
2825 3033 4.450082 TGTTTAGCAGATCGAAGCTGTA 57.550 40.909 17.37 8.10 41.97 2.74
2921 3129 1.888512 GATTGTTGGGTGTGCATGACT 59.111 47.619 0.00 0.00 0.00 3.41
3048 3274 4.781775 TGGGTTACTTTGAACAGGAGAA 57.218 40.909 0.00 0.00 0.00 2.87
3155 3381 1.071814 GTGCTTACCGTCCCCACAA 59.928 57.895 0.00 0.00 0.00 3.33
3315 3541 3.378427 GTGGATCACTATTTGCCTGTTCC 59.622 47.826 0.00 0.00 0.00 3.62
3339 3565 1.002011 GCCCCTCCCTTCAACTGAC 60.002 63.158 0.00 0.00 0.00 3.51
3357 3583 6.624352 TCAAGGACAGATTCTGAAAACAAG 57.376 37.500 20.33 4.29 35.18 3.16
3474 3700 3.394940 TGGTGTACCCTGGTAATTCACAA 59.605 43.478 14.09 4.10 31.14 3.33
3522 3748 1.607148 GGTGGTACTTGTTCCTTGCAC 59.393 52.381 0.00 0.00 0.00 4.57
3560 3786 7.564793 TGGTACATTTTCAGATGTATAGCTGT 58.435 34.615 4.59 0.00 42.59 4.40
3593 3819 3.763897 GGACACTGGTATTGCCTTTGATT 59.236 43.478 0.00 0.00 38.35 2.57
3690 3916 8.782339 TTTTCTTTATAACCTTTACTCCCTCG 57.218 34.615 0.00 0.00 0.00 4.63
3855 4081 7.497249 CAGCTCAGTAATTTTCCAGCTATAAGT 59.503 37.037 0.00 0.00 35.44 2.24
3865 4091 7.857885 GCACAATATACAGCTCAGTAATTTTCC 59.142 37.037 0.00 0.00 0.00 3.13
4035 4261 8.860780 AATCTAAGAAGAAATGCTGAAGTTCT 57.139 30.769 4.17 0.00 44.88 3.01
4044 4270 7.163001 ACAGGGAAAATCTAAGAAGAAATGC 57.837 36.000 0.00 0.00 34.73 3.56
4311 4537 0.037046 CAAATTTCTGCACTGGGGCC 60.037 55.000 0.00 0.00 0.00 5.80
4347 4573 6.092122 CGTTCCTCACATAGCATCTGTTAAAA 59.908 38.462 0.00 0.00 0.00 1.52
4403 4629 2.280592 GTCAGTCCAAACCCGCGT 60.281 61.111 4.92 0.00 0.00 6.01
4451 4677 2.645838 ATCGTGCCATTATCTTGCCT 57.354 45.000 0.00 0.00 0.00 4.75
4519 4745 5.784578 AATGATAAAATAACGAAGCCCCC 57.215 39.130 0.00 0.00 0.00 5.40
4755 5007 6.150332 TCCCCAGTATGATCTTCTCCAAATA 58.850 40.000 0.00 0.00 39.69 1.40
4773 5025 0.036010 CTGCAGTTGGTACTCCCCAG 60.036 60.000 5.25 0.00 35.49 4.45
4790 5042 2.733552 CGGTCAACACTCTGAATGTCTG 59.266 50.000 0.00 0.00 0.00 3.51
4813 5065 1.468565 CCTGGCAATCAACATCAAGCG 60.469 52.381 0.00 0.00 0.00 4.68
4829 5081 4.826183 ACTAGTAGTCCTATTAACGCCTGG 59.174 45.833 0.00 0.00 0.00 4.45
4845 5097 6.205076 ACATCCGCTACATCTTACACTAGTAG 59.795 42.308 0.00 0.00 36.22 2.57
4918 5180 9.364989 TGTACAAACAATTCAAAAAGAGAAAGG 57.635 29.630 0.00 0.00 30.91 3.11
4924 5186 9.921637 AGAACTTGTACAAACAATTCAAAAAGA 57.078 25.926 10.03 0.00 44.43 2.52
4934 5196 9.175312 TGGTTACATAAGAACTTGTACAAACAA 57.825 29.630 10.03 0.00 43.32 2.83
4936 5198 8.833493 ACTGGTTACATAAGAACTTGTACAAAC 58.167 33.333 10.03 4.58 0.00 2.93
4975 5238 8.168681 ACGTTTCAATTACAAACAAGAAACAG 57.831 30.769 13.93 9.81 42.81 3.16
5000 5269 7.011576 ACAACAGATAACGTACATTCACACAAA 59.988 33.333 0.00 0.00 0.00 2.83
5087 5356 4.757149 ACCTGACATAGAAAACAAGCAGAC 59.243 41.667 0.00 0.00 0.00 3.51
5094 5363 7.936847 ACTTTGTGATACCTGACATAGAAAACA 59.063 33.333 0.00 0.00 0.00 2.83
5095 5364 8.230486 CACTTTGTGATACCTGACATAGAAAAC 58.770 37.037 0.00 0.00 35.23 2.43
5123 5392 7.823745 AATAATTTGAAACAGAGTGAGTGGT 57.176 32.000 0.00 0.00 0.00 4.16
5151 5420 4.998672 CCCGTTCAGTTCCATACTAAAACA 59.001 41.667 0.00 0.00 34.56 2.83
5171 5440 6.320164 TCCAAATTATTTGAAGGATGTACCCG 59.680 38.462 18.13 0.00 43.26 5.28
5173 5442 8.749354 AGTTCCAAATTATTTGAAGGATGTACC 58.251 33.333 18.13 0.00 43.26 3.34
5181 5450 9.918630 ACTCATTCAGTTCCAAATTATTTGAAG 57.081 29.630 18.13 3.75 35.66 3.02
5271 5540 0.322187 TTGGTTTCTCCGCTAAGCCC 60.322 55.000 0.00 0.00 39.52 5.19
5280 5549 1.239347 GAGCCACACTTGGTTTCTCC 58.761 55.000 0.00 0.00 45.98 3.71
5283 5552 1.949257 CCGAGCCACACTTGGTTTC 59.051 57.895 0.00 0.00 45.98 2.78
5332 5601 4.169696 TAAGCATGGACCGCCCGG 62.170 66.667 4.96 4.96 42.03 5.73
5336 5696 0.249911 CCTACCTAAGCATGGACCGC 60.250 60.000 0.00 0.00 0.00 5.68
5348 5708 6.528537 TTAAAACACGCTATGTCCTACCTA 57.471 37.500 0.00 0.00 42.31 3.08
5352 5712 7.441760 TGTCTTTTTAAAACACGCTATGTCCTA 59.558 33.333 0.00 0.00 42.31 2.94
5360 5720 5.412526 TCGATGTCTTTTTAAAACACGCT 57.587 34.783 0.00 0.00 0.00 5.07
5362 5722 5.113529 GTGCTCGATGTCTTTTTAAAACACG 59.886 40.000 0.00 4.20 0.00 4.49
5381 5741 4.016444 TCCACTAAATCAAATGGGTGCTC 58.984 43.478 0.00 0.00 32.73 4.26
5421 5782 6.255020 GCTACCGAAAAGATTACGATTTCAGA 59.745 38.462 0.00 0.00 33.68 3.27
5430 5791 5.752472 GGTCTTAGGCTACCGAAAAGATTAC 59.248 44.000 0.00 0.00 29.59 1.89
5496 5857 3.536158 TTTGCTCGCTATTTGACACAC 57.464 42.857 0.00 0.00 0.00 3.82
5499 5860 3.750652 TGTGATTTGCTCGCTATTTGACA 59.249 39.130 0.00 0.00 35.31 3.58
5510 5871 4.757149 GGTGTATCCCTATGTGATTTGCTC 59.243 45.833 0.00 0.00 0.00 4.26
5539 5900 3.769536 CGAAACATTAATTGTCCCCAGC 58.230 45.455 0.00 0.00 37.68 4.85
5587 5948 9.723447 GAAAAACAAAGAAAACCAAAAGTCAAA 57.277 25.926 0.00 0.00 0.00 2.69
5588 5949 8.893727 TGAAAAACAAAGAAAACCAAAAGTCAA 58.106 25.926 0.00 0.00 0.00 3.18
5589 5950 8.338986 GTGAAAAACAAAGAAAACCAAAAGTCA 58.661 29.630 0.00 0.00 0.00 3.41
5590 5951 8.556194 AGTGAAAAACAAAGAAAACCAAAAGTC 58.444 29.630 0.00 0.00 0.00 3.01
5591 5952 8.445275 AGTGAAAAACAAAGAAAACCAAAAGT 57.555 26.923 0.00 0.00 0.00 2.66
5592 5953 9.381027 GAAGTGAAAAACAAAGAAAACCAAAAG 57.619 29.630 0.00 0.00 0.00 2.27
5593 5954 8.893727 TGAAGTGAAAAACAAAGAAAACCAAAA 58.106 25.926 0.00 0.00 0.00 2.44
5594 5955 8.438676 TGAAGTGAAAAACAAAGAAAACCAAA 57.561 26.923 0.00 0.00 0.00 3.28
5595 5956 8.438676 TTGAAGTGAAAAACAAAGAAAACCAA 57.561 26.923 0.00 0.00 0.00 3.67
5596 5957 8.438676 TTTGAAGTGAAAAACAAAGAAAACCA 57.561 26.923 0.00 0.00 0.00 3.67
5597 5958 9.891828 ATTTTGAAGTGAAAAACAAAGAAAACC 57.108 25.926 0.00 0.00 34.54 3.27
5610 5971 9.323985 CCACAAAGGAAATATTTTGAAGTGAAA 57.676 29.630 16.48 0.00 41.22 2.69
5611 5972 7.440856 GCCACAAAGGAAATATTTTGAAGTGAA 59.559 33.333 16.48 0.00 41.22 3.18
5612 5973 6.928492 GCCACAAAGGAAATATTTTGAAGTGA 59.072 34.615 16.48 0.00 41.22 3.41
5613 5974 6.930722 AGCCACAAAGGAAATATTTTGAAGTG 59.069 34.615 1.43 8.07 41.22 3.16
5614 5975 7.066307 AGCCACAAAGGAAATATTTTGAAGT 57.934 32.000 1.43 0.00 41.22 3.01
5615 5976 7.967890 AAGCCACAAAGGAAATATTTTGAAG 57.032 32.000 1.43 0.00 41.22 3.02
5616 5977 7.443879 GGAAAGCCACAAAGGAAATATTTTGAA 59.556 33.333 1.43 0.00 41.22 2.69
5617 5978 6.934083 GGAAAGCCACAAAGGAAATATTTTGA 59.066 34.615 1.43 0.00 41.22 2.69
5618 5979 6.149308 GGGAAAGCCACAAAGGAAATATTTTG 59.851 38.462 1.43 0.00 41.22 2.44
5619 5980 6.237901 GGGAAAGCCACAAAGGAAATATTTT 58.762 36.000 1.43 0.00 41.22 1.82
5620 5981 5.568624 CGGGAAAGCCACAAAGGAAATATTT 60.569 40.000 0.00 0.00 41.22 1.40
5621 5982 4.081697 CGGGAAAGCCACAAAGGAAATATT 60.082 41.667 0.00 0.00 41.22 1.28
5622 5983 3.447229 CGGGAAAGCCACAAAGGAAATAT 59.553 43.478 0.00 0.00 41.22 1.28
5623 5984 2.823154 CGGGAAAGCCACAAAGGAAATA 59.177 45.455 0.00 0.00 41.22 1.40
5624 5985 1.618343 CGGGAAAGCCACAAAGGAAAT 59.382 47.619 0.00 0.00 41.22 2.17
5625 5986 1.036707 CGGGAAAGCCACAAAGGAAA 58.963 50.000 0.00 0.00 41.22 3.13
5626 5987 0.825840 CCGGGAAAGCCACAAAGGAA 60.826 55.000 0.00 0.00 41.22 3.36
5627 5988 1.228429 CCGGGAAAGCCACAAAGGA 60.228 57.895 0.00 0.00 41.22 3.36
5628 5989 2.275380 CCCGGGAAAGCCACAAAGG 61.275 63.158 18.48 0.00 41.84 3.11
5629 5990 2.275380 CCCCGGGAAAGCCACAAAG 61.275 63.158 26.32 0.00 35.15 2.77
5630 5991 2.203567 CCCCGGGAAAGCCACAAA 60.204 61.111 26.32 0.00 35.15 2.83
5631 5992 2.591193 AAACCCCGGGAAAGCCACAA 62.591 55.000 26.32 0.00 35.15 3.33
5632 5993 2.591193 AAAACCCCGGGAAAGCCACA 62.591 55.000 26.32 0.00 35.15 4.17
5633 5994 1.404479 AAAAACCCCGGGAAAGCCAC 61.404 55.000 26.32 0.00 35.15 5.01
5634 5995 1.075151 AAAAACCCCGGGAAAGCCA 60.075 52.632 26.32 0.00 35.15 4.75
5635 5996 3.879844 AAAAACCCCGGGAAAGCC 58.120 55.556 26.32 0.00 0.00 4.35
5675 6036 8.638873 CCAAAGAAAAACTAAGAGTACCCAAAT 58.361 33.333 0.00 0.00 0.00 2.32
5676 6037 7.068962 CCCAAAGAAAAACTAAGAGTACCCAAA 59.931 37.037 0.00 0.00 0.00 3.28
5677 6038 6.548251 CCCAAAGAAAAACTAAGAGTACCCAA 59.452 38.462 0.00 0.00 0.00 4.12
5678 6039 6.066032 CCCAAAGAAAAACTAAGAGTACCCA 58.934 40.000 0.00 0.00 0.00 4.51
5679 6040 6.066690 ACCCAAAGAAAAACTAAGAGTACCC 58.933 40.000 0.00 0.00 0.00 3.69
5680 6041 7.578310 AACCCAAAGAAAAACTAAGAGTACC 57.422 36.000 0.00 0.00 0.00 3.34
5681 6042 9.512435 GAAAACCCAAAGAAAAACTAAGAGTAC 57.488 33.333 0.00 0.00 0.00 2.73
5682 6043 9.470399 AGAAAACCCAAAGAAAAACTAAGAGTA 57.530 29.630 0.00 0.00 0.00 2.59
5683 6044 8.362464 AGAAAACCCAAAGAAAAACTAAGAGT 57.638 30.769 0.00 0.00 0.00 3.24
5684 6045 9.653287 AAAGAAAACCCAAAGAAAAACTAAGAG 57.347 29.630 0.00 0.00 0.00 2.85
5695 6056 9.594936 TCCATAGAATAAAAGAAAACCCAAAGA 57.405 29.630 0.00 0.00 0.00 2.52
5696 6057 9.860898 CTCCATAGAATAAAAGAAAACCCAAAG 57.139 33.333 0.00 0.00 0.00 2.77
5697 6058 9.374711 ACTCCATAGAATAAAAGAAAACCCAAA 57.625 29.630 0.00 0.00 0.00 3.28
5698 6059 8.950007 ACTCCATAGAATAAAAGAAAACCCAA 57.050 30.769 0.00 0.00 0.00 4.12
5699 6060 8.950007 AACTCCATAGAATAAAAGAAAACCCA 57.050 30.769 0.00 0.00 0.00 4.51
5715 6076 9.639601 GGAAACAAATAAAGGAAAACTCCATAG 57.360 33.333 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.