Multiple sequence alignment - TraesCS2B01G555200

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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 TraesCS2B01G555200 chr2B 100.000 3806 0 0 1 3806 750000922 750004727 0.000000e+00 7029.0
1 TraesCS2B01G555200 chr2D 92.877 2120 91 24 737 2843 615591305 615593377 0.000000e+00 3024.0
2 TraesCS2B01G555200 chr2D 86.381 771 59 23 1 744 615590481 615591232 0.000000e+00 800.0
3 TraesCS2B01G555200 chr2D 92.351 353 21 4 3452 3804 615611900 615612246 7.340000e-137 497.0
4 TraesCS2B01G555200 chr2D 89.720 214 19 3 3120 3330 615611704 615611917 1.740000e-68 270.0
5 TraesCS2B01G555200 chr2D 88.660 194 14 5 2936 3123 615611113 615611304 2.960000e-56 230.0
6 TraesCS2B01G555200 chr2D 83.962 106 11 5 3453 3555 458161372 458161474 3.130000e-16 97.1
7 TraesCS2B01G555200 chr2A 90.215 2279 128 49 752 2973 745655312 745657552 0.000000e+00 2885.0
8 TraesCS2B01G555200 chr2A 84.530 627 59 16 2602 3192 745659446 745660070 1.520000e-163 586.0
9 TraesCS2B01G555200 chr2A 80.179 782 77 37 1 748 745654486 745655223 7.290000e-142 514.0
10 TraesCS2B01G555200 chr6B 88.626 211 18 2 1213 1423 703169316 703169112 6.310000e-63 252.0
11 TraesCS2B01G555200 chr6B 86.631 187 21 4 3120 3304 487136353 487136169 1.790000e-48 204.0
12 TraesCS2B01G555200 chr6B 93.023 43 2 1 3328 3369 47929037 47929079 1.140000e-05 62.1
13 TraesCS2B01G555200 chr6D 87.204 211 21 2 1213 1423 461418920 461418716 6.360000e-58 235.0
14 TraesCS2B01G555200 chr6D 82.381 210 35 2 3111 3320 472495705 472495912 8.400000e-42 182.0
15 TraesCS2B01G555200 chr6D 100.000 34 0 0 3518 3551 437774849 437774816 3.170000e-06 63.9
16 TraesCS2B01G555200 chr6A 87.204 211 21 2 1213 1423 608093955 608093751 6.360000e-58 235.0
17 TraesCS2B01G555200 chr7A 85.567 194 23 5 3113 3304 204737060 204736870 8.340000e-47 198.0
18 TraesCS2B01G555200 chr7A 86.022 186 22 4 3121 3304 230300984 230301167 3.000000e-46 196.0
19 TraesCS2B01G555200 chr7A 85.792 183 22 4 3124 3304 649424797 649424977 1.400000e-44 191.0
20 TraesCS2B01G555200 chr7A 83.069 189 28 4 3118 3304 221262265 221262451 6.540000e-38 169.0
21 TraesCS2B01G555200 chr5A 85.263 190 22 6 3118 3304 270372872 270373058 1.400000e-44 191.0
22 TraesCS2B01G555200 chr4B 82.870 216 34 3 3117 3330 471307833 471308047 1.400000e-44 191.0
23 TraesCS2B01G555200 chr4B 97.368 38 1 0 3332 3369 614068703 614068740 8.830000e-07 65.8
24 TraesCS2B01G555200 chr4D 79.798 99 18 2 3466 3563 190480208 190480111 1.900000e-08 71.3
25 TraesCS2B01G555200 chr1B 97.561 41 0 1 3330 3369 161379113 161379153 6.820000e-08 69.4
26 TraesCS2B01G555200 chr1A 95.000 40 1 1 3331 3369 6172054 6172093 1.140000e-05 62.1


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 TraesCS2B01G555200 chr2B 750000922 750004727 3805 False 7029.000000 7029 100.000000 1 3806 1 chr2B.!!$F1 3805
1 TraesCS2B01G555200 chr2D 615590481 615593377 2896 False 1912.000000 3024 89.629000 1 2843 2 chr2D.!!$F2 2842
2 TraesCS2B01G555200 chr2D 615611113 615612246 1133 False 332.333333 497 90.243667 2936 3804 3 chr2D.!!$F3 868
3 TraesCS2B01G555200 chr2A 745654486 745660070 5584 False 1328.333333 2885 84.974667 1 3192 3 chr2A.!!$F1 3191

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
44 52 0.320374 TCAGTCGGCGAGTGGAATTT 59.680 50.0 36.15 3.5 34.12 1.82 F
1509 1676 0.179000 CGGGCTTCAGGCAAGATACT 59.821 55.0 2.41 0.0 44.01 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1710 0.321919 GCCACCAGAGAGCAATGTGA 60.322 55.0 0.00 0.0 0.0 3.58 R
3427 6330 0.654683 GCAGGCGCTAAATGACTGAG 59.345 55.0 7.64 0.0 34.3 3.35 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
44 52 0.320374 TCAGTCGGCGAGTGGAATTT 59.680 50.000 36.15 3.50 34.12 1.82
96 109 3.726517 CTGCCGCCGGTCAAGTTG 61.727 66.667 4.45 0.00 0.00 3.16
174 198 0.472898 CCCTTATCCGTCCCTTTCCC 59.527 60.000 0.00 0.00 0.00 3.97
194 218 3.979497 CTCCAACCCCCACCCCAC 61.979 72.222 0.00 0.00 0.00 4.61
236 264 2.746269 GCTACAAGTAACACGGACACA 58.254 47.619 0.00 0.00 0.00 3.72
292 324 2.698797 ACTTCTTCTTCGTCCACCTTCA 59.301 45.455 0.00 0.00 0.00 3.02
301 333 1.872773 GTCCACCTTCATCTCCCTCT 58.127 55.000 0.00 0.00 0.00 3.69
304 336 2.038659 CCACCTTCATCTCCCTCTCTC 58.961 57.143 0.00 0.00 0.00 3.20
331 363 2.841160 GCCGGTCACCACAACCAAC 61.841 63.158 1.90 0.00 36.53 3.77
341 373 2.362375 CAACCAACCCCCATCCCG 60.362 66.667 0.00 0.00 0.00 5.14
343 375 3.218386 AACCAACCCCCATCCCGTG 62.218 63.158 0.00 0.00 0.00 4.94
352 384 2.749044 CATCCCGTGCTTGCTGCT 60.749 61.111 0.00 0.00 43.37 4.24
374 406 1.526917 CCCCGTTGGATCATCAGCC 60.527 63.158 0.00 0.00 35.39 4.85
375 407 1.889105 CCCGTTGGATCATCAGCCG 60.889 63.158 0.00 0.00 0.00 5.52
449 485 1.377202 TGCTCCGGCAACCTGATTC 60.377 57.895 0.00 0.00 46.36 2.52
450 486 2.115291 GCTCCGGCAACCTGATTCC 61.115 63.158 0.00 0.00 38.54 3.01
452 488 3.508840 CCGGCAACCTGATTCCGC 61.509 66.667 0.00 0.00 40.49 5.54
479 518 4.101430 AGCTTTGGTTTGATTTGACATGGT 59.899 37.500 0.00 0.00 0.00 3.55
481 520 5.350504 TTTGGTTTGATTTGACATGGTGT 57.649 34.783 0.00 0.00 0.00 4.16
563 610 1.136110 GTAGTTGCTCTGCTCTCCTCC 59.864 57.143 0.00 0.00 0.00 4.30
591 642 0.716591 TGCTAGGAGGAAGGGAGGAA 59.283 55.000 0.00 0.00 0.00 3.36
595 646 2.980699 AGGAGGAAGGGAGGAAATCT 57.019 50.000 0.00 0.00 0.00 2.40
596 647 2.770447 AGGAGGAAGGGAGGAAATCTC 58.230 52.381 0.00 0.00 41.71 2.75
597 648 2.320675 AGGAGGAAGGGAGGAAATCTCT 59.679 50.000 0.00 0.00 42.18 3.10
628 679 1.113517 ACGGTACACTGCTCCACTGT 61.114 55.000 0.00 0.00 0.00 3.55
639 690 2.290260 TGCTCCACTGTTCAATCCGATT 60.290 45.455 0.00 0.00 0.00 3.34
649 700 2.528125 TCAATCCGATTTGCAATTGCG 58.472 42.857 24.58 10.34 45.83 4.85
650 701 2.094803 TCAATCCGATTTGCAATTGCGT 60.095 40.909 24.58 13.60 45.83 5.24
651 702 1.912001 ATCCGATTTGCAATTGCGTG 58.088 45.000 24.58 12.08 45.83 5.34
652 703 0.595588 TCCGATTTGCAATTGCGTGT 59.404 45.000 24.58 12.88 45.83 4.49
653 704 0.709467 CCGATTTGCAATTGCGTGTG 59.291 50.000 24.58 13.08 45.83 3.82
668 723 2.870435 GCGTGTGTCTGAACCTACCAAT 60.870 50.000 0.00 0.00 0.00 3.16
670 725 3.554129 CGTGTGTCTGAACCTACCAATCA 60.554 47.826 0.00 0.00 0.00 2.57
674 729 5.247337 TGTGTCTGAACCTACCAATCATACA 59.753 40.000 0.00 0.00 30.65 2.29
682 737 8.158132 TGAACCTACCAATCATACAAACAGTAA 58.842 33.333 0.00 0.00 36.05 2.24
685 740 8.107095 ACCTACCAATCATACAAACAGTAACAT 58.893 33.333 0.00 0.00 36.05 2.71
719 777 2.536365 TCATTCACCGCGTACAGAATC 58.464 47.619 4.92 0.00 0.00 2.52
759 902 4.766088 CCCGCTCGCTTTGCTTGC 62.766 66.667 0.00 0.00 0.00 4.01
791 935 0.322726 CCACCATGTGATGTGCCTCA 60.323 55.000 0.00 0.00 35.23 3.86
798 942 1.195115 GTGATGTGCCTCACCCTCTA 58.805 55.000 0.90 0.00 39.72 2.43
800 944 0.466124 GATGTGCCTCACCCTCTACC 59.534 60.000 0.00 0.00 32.73 3.18
818 962 0.662970 CCGCTCTGCTTCTAGATCGC 60.663 60.000 7.41 7.41 35.60 4.58
831 975 6.183360 GCTTCTAGATCGCGCAACAATATAAT 60.183 38.462 8.75 0.00 0.00 1.28
832 976 7.009265 GCTTCTAGATCGCGCAACAATATAATA 59.991 37.037 8.75 0.00 0.00 0.98
833 977 7.736031 TCTAGATCGCGCAACAATATAATAC 57.264 36.000 8.75 0.00 0.00 1.89
863 1010 5.278957 GCTTGATGGTGTTTGTTGGAGTAAT 60.279 40.000 0.00 0.00 0.00 1.89
864 1011 6.072175 GCTTGATGGTGTTTGTTGGAGTAATA 60.072 38.462 0.00 0.00 0.00 0.98
865 1012 7.523052 GCTTGATGGTGTTTGTTGGAGTAATAA 60.523 37.037 0.00 0.00 0.00 1.40
878 1025 5.007682 TGGAGTAATAAACCTTGACTTGGC 58.992 41.667 0.00 0.00 0.00 4.52
918 1065 7.122204 GCCACTTTACCATTCTTTACTACCAAT 59.878 37.037 0.00 0.00 0.00 3.16
919 1066 9.675464 CCACTTTACCATTCTTTACTACCAATA 57.325 33.333 0.00 0.00 0.00 1.90
922 1069 9.675464 CTTTACCATTCTTTACTACCAATACCA 57.325 33.333 0.00 0.00 0.00 3.25
1140 1307 1.977544 AGAGACCACTTCGACCCCG 60.978 63.158 0.00 0.00 37.07 5.73
1141 1308 2.203596 AGACCACTTCGACCCCGT 60.204 61.111 0.00 0.00 37.05 5.28
1251 1418 2.511600 CCATCAACGCCTCCGACC 60.512 66.667 0.00 0.00 38.29 4.79
1509 1676 0.179000 CGGGCTTCAGGCAAGATACT 59.821 55.000 2.41 0.00 44.01 2.12
1510 1677 1.673168 GGGCTTCAGGCAAGATACTG 58.327 55.000 2.41 0.00 44.01 2.74
1511 1678 1.020437 GGCTTCAGGCAAGATACTGC 58.980 55.000 0.00 0.00 44.01 4.40
1512 1679 1.679944 GGCTTCAGGCAAGATACTGCA 60.680 52.381 0.00 0.00 44.52 4.41
1513 1680 2.295885 GCTTCAGGCAAGATACTGCAT 58.704 47.619 0.00 0.00 44.52 3.96
1514 1681 3.470709 GCTTCAGGCAAGATACTGCATA 58.529 45.455 0.00 0.00 44.52 3.14
1515 1682 3.249559 GCTTCAGGCAAGATACTGCATAC 59.750 47.826 0.00 0.00 44.52 2.39
1516 1683 4.445453 CTTCAGGCAAGATACTGCATACA 58.555 43.478 0.00 0.00 44.52 2.29
1517 1684 4.510711 CTTCAGGCAAGATACTGCATACAG 59.489 45.833 0.00 0.00 44.52 2.74
1518 1685 5.683249 CTTCAGGCAAGATACTGCATACAGA 60.683 44.000 0.00 0.00 44.52 3.41
1519 1686 6.963348 CTTCAGGCAAGATACTGCATACAGAT 60.963 42.308 0.00 0.00 44.52 2.90
1542 1710 9.338968 AGATATATACTCCACCAACCACATATT 57.661 33.333 0.00 0.00 0.00 1.28
1554 1722 5.449588 CCAACCACATATTCACATTGCTCTC 60.450 44.000 0.00 0.00 0.00 3.20
1555 1723 5.108187 ACCACATATTCACATTGCTCTCT 57.892 39.130 0.00 0.00 0.00 3.10
1570 1738 3.655810 CTCTGGTGGCTCTGTCGGC 62.656 68.421 0.00 0.00 0.00 5.54
1887 2055 4.891992 TTCCAGGTACTTCTTCTTCTGG 57.108 45.455 0.00 0.00 42.10 3.86
1911 2079 4.562143 GCTTGGATTGAAGCCTGAAACATT 60.562 41.667 0.00 0.00 42.23 2.71
1923 2091 6.527423 AGCCTGAAACATTTGAATGAATTGT 58.473 32.000 10.48 0.00 39.67 2.71
1948 2116 3.448660 TGAAGATCGATCTGCAGGAAGAA 59.551 43.478 28.96 7.56 37.55 2.52
1964 2132 7.014134 TGCAGGAAGAAATGAACTGAATTTGTA 59.986 33.333 0.00 0.00 0.00 2.41
2046 2214 2.664851 TGGAACGCCAAGCTGTCG 60.665 61.111 0.00 0.00 42.49 4.35
2118 2286 3.751175 CCACAGCGGTAAGAAAATGAAGA 59.249 43.478 0.00 0.00 0.00 2.87
2132 2300 7.663827 AGAAAATGAAGATTGTGCATTCAGAA 58.336 30.769 5.94 0.00 36.47 3.02
2143 2311 5.737860 TGTGCATTCAGAATCAGATACACT 58.262 37.500 0.00 0.00 0.00 3.55
2153 2321 9.154847 TCAGAATCAGATACACTATGTTTTGTG 57.845 33.333 0.00 0.00 39.80 3.33
2195 2364 3.188048 ACAGGTCAGAAGTACGTACGAAG 59.812 47.826 24.41 11.25 0.00 3.79
2433 2602 2.099652 CTCCGACACCAACAGGCTGA 62.100 60.000 23.66 0.00 0.00 4.26
2704 2891 0.321564 TTTCATGGTCAGTGGCGAGG 60.322 55.000 0.00 0.00 0.00 4.63
2714 2901 3.003173 TGGCGAGGTGGAAGAGGG 61.003 66.667 0.00 0.00 0.00 4.30
2742 2929 1.680860 CCCTCATGTGCTGATGCTGAA 60.681 52.381 0.00 0.00 40.48 3.02
2748 2935 0.656785 GTGCTGATGCTGAAGCTAGC 59.343 55.000 6.62 6.62 43.95 3.42
2754 2941 4.083908 GCTGATGCTGAAGCTAGCTTAATC 60.084 45.833 29.39 25.17 44.01 1.75
2805 5271 7.988028 GGATCCTAATTAATCCTAGTATGGCAC 59.012 40.741 3.84 0.00 38.74 5.01
2812 5278 7.849322 TTAATCCTAGTATGGCACTATGTGA 57.151 36.000 1.52 0.00 39.06 3.58
2816 5282 5.302059 TCCTAGTATGGCACTATGTGAGTTC 59.698 44.000 1.52 0.00 39.06 3.01
2820 5286 1.343142 TGGCACTATGTGAGTTCGTGT 59.657 47.619 1.52 0.00 35.64 4.49
2824 5290 3.120991 GCACTATGTGAGTTCGTGTTGTC 60.121 47.826 1.52 0.00 35.64 3.18
2825 5291 4.048504 CACTATGTGAGTTCGTGTTGTCA 58.951 43.478 0.00 0.00 35.64 3.58
2827 5293 4.923871 ACTATGTGAGTTCGTGTTGTCATC 59.076 41.667 0.00 0.00 33.13 2.92
2828 5294 3.452755 TGTGAGTTCGTGTTGTCATCT 57.547 42.857 0.00 0.00 0.00 2.90
2861 5351 7.516452 TCCAATTGTGTGTGGATATGATATGA 58.484 34.615 4.43 0.00 39.04 2.15
2890 5380 7.862274 AGAGTATCATTAGGTGGATGAATCA 57.138 36.000 0.00 0.00 37.11 2.57
2900 5390 5.874093 AGGTGGATGAATCAGTGATTATCC 58.126 41.667 27.18 27.18 35.41 2.59
2950 5440 2.930109 TCTCAGCCTCCTAGTTTCCT 57.070 50.000 0.00 0.00 0.00 3.36
2973 5464 8.313292 TCCTTTTTGCTGTAAAATTGAGCATAT 58.687 29.630 4.52 0.00 42.17 1.78
2974 5465 9.585099 CCTTTTTGCTGTAAAATTGAGCATATA 57.415 29.630 4.52 0.00 42.17 0.86
2993 5484 8.049117 AGCATATATCTCTTTGTTCTTTCACCA 58.951 33.333 0.00 0.00 0.00 4.17
3026 5517 7.652909 CAGCAGTGTCATTTTAAGATTGGAAAA 59.347 33.333 0.00 0.00 0.00 2.29
3047 5538 8.647226 GGAAAATTGGAATACTTGTTTCATTCG 58.353 33.333 0.00 0.00 30.89 3.34
3110 5606 4.080129 CCTCTCCATGGATCAAAAGGAAGA 60.080 45.833 16.63 3.82 0.00 2.87
3126 6025 7.707467 AAAGGAAGAAGATATTTAGGGCCTA 57.293 36.000 9.81 9.81 0.00 3.93
3138 6037 9.077885 GATATTTAGGGCCTATTTGATTCACAA 57.922 33.333 15.37 1.57 36.65 3.33
3146 6045 7.449704 GGGCCTATTTGATTCACAAGATTCTAT 59.550 37.037 0.84 0.00 39.77 1.98
3160 6060 9.104965 CACAAGATTCTATAAACGTGGGAATAA 57.895 33.333 0.00 0.00 0.00 1.40
3168 6068 9.467258 TCTATAAACGTGGGAATAAGATAAACG 57.533 33.333 0.00 0.00 35.78 3.60
3171 6071 9.768662 ATAAACGTGGGAATAAGATAAACGTAT 57.231 29.630 0.00 0.00 41.44 3.06
3176 6076 9.414295 CGTGGGAATAAGATAAACGTATGATTA 57.586 33.333 0.00 0.00 0.00 1.75
3199 6101 9.760077 ATTAAAATTTCATGCTCATCTCAATCC 57.240 29.630 0.00 0.00 0.00 3.01
3225 6127 5.280654 AGGATTTTGCTGTGTTTGATTGT 57.719 34.783 0.00 0.00 0.00 2.71
3232 6134 9.926158 ATTTTGCTGTGTTTGATTGTATCATAA 57.074 25.926 0.00 0.00 39.39 1.90
3296 6199 8.198109 GCTAGAAATCCAATGAGAAGTAGTACA 58.802 37.037 2.52 0.00 0.00 2.90
3317 6220 9.965902 AGTACAAAGAAATAATCAGGAGAACAT 57.034 29.630 0.00 0.00 0.00 2.71
3320 6223 9.525826 ACAAAGAAATAATCAGGAGAACATTCT 57.474 29.630 0.00 0.00 41.00 2.40
3324 6227 9.829507 AGAAATAATCAGGAGAACATTCTACAG 57.170 33.333 6.62 0.00 40.75 2.74
3325 6228 8.443953 AAATAATCAGGAGAACATTCTACAGC 57.556 34.615 6.62 0.00 40.75 4.40
3326 6229 5.426689 AATCAGGAGAACATTCTACAGCA 57.573 39.130 6.62 0.00 40.75 4.41
3327 6230 5.627182 ATCAGGAGAACATTCTACAGCAT 57.373 39.130 6.62 0.00 40.75 3.79
3328 6231 5.426689 TCAGGAGAACATTCTACAGCATT 57.573 39.130 6.62 0.00 40.75 3.56
3329 6232 5.423015 TCAGGAGAACATTCTACAGCATTC 58.577 41.667 6.62 0.00 40.75 2.67
3330 6233 5.188555 TCAGGAGAACATTCTACAGCATTCT 59.811 40.000 6.62 0.00 40.75 2.40
3331 6234 5.879223 CAGGAGAACATTCTACAGCATTCTT 59.121 40.000 6.62 0.00 40.75 2.52
3332 6235 6.373774 CAGGAGAACATTCTACAGCATTCTTT 59.626 38.462 6.62 0.00 40.75 2.52
3333 6236 6.944862 AGGAGAACATTCTACAGCATTCTTTT 59.055 34.615 6.62 0.00 40.75 2.27
3334 6237 7.449704 AGGAGAACATTCTACAGCATTCTTTTT 59.550 33.333 6.62 0.00 40.75 1.94
3354 6257 4.320608 TTTTTGAACCATGCAGGAGAAC 57.679 40.909 0.00 0.00 41.22 3.01
3355 6258 2.957402 TTGAACCATGCAGGAGAACT 57.043 45.000 0.00 0.00 41.22 3.01
3365 6268 2.174363 CAGGAGAACTGCATGTGACA 57.826 50.000 0.00 0.00 40.97 3.58
3366 6269 2.497138 CAGGAGAACTGCATGTGACAA 58.503 47.619 0.00 0.00 40.97 3.18
3367 6270 3.079578 CAGGAGAACTGCATGTGACAAT 58.920 45.455 0.00 0.00 40.97 2.71
3368 6271 4.256110 CAGGAGAACTGCATGTGACAATA 58.744 43.478 0.00 0.00 40.97 1.90
3369 6272 4.331992 CAGGAGAACTGCATGTGACAATAG 59.668 45.833 0.00 0.00 40.97 1.73
3370 6273 4.019860 AGGAGAACTGCATGTGACAATAGT 60.020 41.667 0.00 0.00 0.00 2.12
3371 6274 5.187772 AGGAGAACTGCATGTGACAATAGTA 59.812 40.000 0.00 0.00 0.00 1.82
3372 6275 5.292101 GGAGAACTGCATGTGACAATAGTAC 59.708 44.000 0.00 0.00 0.00 2.73
3373 6276 5.793817 AGAACTGCATGTGACAATAGTACA 58.206 37.500 0.00 0.00 0.00 2.90
3374 6277 6.230472 AGAACTGCATGTGACAATAGTACAA 58.770 36.000 0.00 0.00 0.00 2.41
3375 6278 6.710295 AGAACTGCATGTGACAATAGTACAAA 59.290 34.615 0.00 0.00 0.00 2.83
3376 6279 6.875948 ACTGCATGTGACAATAGTACAAAA 57.124 33.333 0.00 0.00 0.00 2.44
3377 6280 6.668323 ACTGCATGTGACAATAGTACAAAAC 58.332 36.000 0.00 0.00 0.00 2.43
3378 6281 5.684850 TGCATGTGACAATAGTACAAAACG 58.315 37.500 0.00 0.00 0.00 3.60
3379 6282 5.467063 TGCATGTGACAATAGTACAAAACGA 59.533 36.000 0.00 0.00 0.00 3.85
3380 6283 5.788531 GCATGTGACAATAGTACAAAACGAC 59.211 40.000 0.00 0.00 0.00 4.34
3381 6284 5.910637 TGTGACAATAGTACAAAACGACC 57.089 39.130 0.00 0.00 0.00 4.79
3382 6285 4.751098 TGTGACAATAGTACAAAACGACCC 59.249 41.667 0.00 0.00 0.00 4.46
3383 6286 4.751098 GTGACAATAGTACAAAACGACCCA 59.249 41.667 0.00 0.00 0.00 4.51
3384 6287 5.236911 GTGACAATAGTACAAAACGACCCAA 59.763 40.000 0.00 0.00 0.00 4.12
3385 6288 5.236911 TGACAATAGTACAAAACGACCCAAC 59.763 40.000 0.00 0.00 0.00 3.77
3386 6289 5.124645 ACAATAGTACAAAACGACCCAACA 58.875 37.500 0.00 0.00 0.00 3.33
3387 6290 5.589452 ACAATAGTACAAAACGACCCAACAA 59.411 36.000 0.00 0.00 0.00 2.83
3388 6291 5.678132 ATAGTACAAAACGACCCAACAAC 57.322 39.130 0.00 0.00 0.00 3.32
3389 6292 3.345414 AGTACAAAACGACCCAACAACA 58.655 40.909 0.00 0.00 0.00 3.33
3390 6293 3.757493 AGTACAAAACGACCCAACAACAA 59.243 39.130 0.00 0.00 0.00 2.83
3391 6294 3.662247 ACAAAACGACCCAACAACAAA 57.338 38.095 0.00 0.00 0.00 2.83
3392 6295 3.991367 ACAAAACGACCCAACAACAAAA 58.009 36.364 0.00 0.00 0.00 2.44
3393 6296 4.377897 ACAAAACGACCCAACAACAAAAA 58.622 34.783 0.00 0.00 0.00 1.94
3394 6297 4.449405 ACAAAACGACCCAACAACAAAAAG 59.551 37.500 0.00 0.00 0.00 2.27
3395 6298 2.951457 ACGACCCAACAACAAAAAGG 57.049 45.000 0.00 0.00 0.00 3.11
3396 6299 1.134936 ACGACCCAACAACAAAAAGGC 60.135 47.619 0.00 0.00 0.00 4.35
3397 6300 1.134965 CGACCCAACAACAAAAAGGCA 60.135 47.619 0.00 0.00 0.00 4.75
3398 6301 2.675317 CGACCCAACAACAAAAAGGCAA 60.675 45.455 0.00 0.00 0.00 4.52
3399 6302 3.339141 GACCCAACAACAAAAAGGCAAA 58.661 40.909 0.00 0.00 0.00 3.68
3400 6303 3.753797 GACCCAACAACAAAAAGGCAAAA 59.246 39.130 0.00 0.00 0.00 2.44
3401 6304 4.145052 ACCCAACAACAAAAAGGCAAAAA 58.855 34.783 0.00 0.00 0.00 1.94
3430 6333 9.753674 AAATAAATAAGGAGAACAATGACCTCA 57.246 29.630 8.32 0.00 31.89 3.86
3431 6334 8.970859 ATAAATAAGGAGAACAATGACCTCAG 57.029 34.615 8.32 0.00 31.89 3.35
3432 6335 6.380079 AATAAGGAGAACAATGACCTCAGT 57.620 37.500 8.32 0.00 31.89 3.41
3433 6336 3.971245 AGGAGAACAATGACCTCAGTC 57.029 47.619 8.32 0.00 43.83 3.51
3443 6346 1.291132 GACCTCAGTCATTTAGCGCC 58.709 55.000 2.29 0.00 42.99 6.53
3444 6347 0.905357 ACCTCAGTCATTTAGCGCCT 59.095 50.000 2.29 0.00 0.00 5.52
3445 6348 1.293924 CCTCAGTCATTTAGCGCCTG 58.706 55.000 2.29 1.91 0.00 4.85
3446 6349 0.654683 CTCAGTCATTTAGCGCCTGC 59.345 55.000 2.29 0.00 43.24 4.85
3498 6401 6.718912 TCATGAATCAAACAACCAATGTAGGA 59.281 34.615 0.00 0.00 42.99 2.94
3508 6411 8.943594 AACAACCAATGTAGGAAAAATACCTA 57.056 30.769 0.00 0.00 42.99 3.08
3509 6412 8.943594 ACAACCAATGTAGGAAAAATACCTAA 57.056 30.769 0.00 0.00 41.63 2.69
3510 6413 9.020731 ACAACCAATGTAGGAAAAATACCTAAG 57.979 33.333 0.00 0.00 41.63 2.18
3615 6518 8.879427 ATATTAAACCTTTGTGCTAAGGACTT 57.121 30.769 16.88 12.02 46.28 3.01
3723 6626 6.571925 CGGTGTAAACTATAGATTCTAGCCCC 60.572 46.154 6.78 0.00 0.00 5.80
3724 6627 6.295745 GGTGTAAACTATAGATTCTAGCCCCC 60.296 46.154 6.78 0.00 0.00 5.40
3762 6665 6.494835 TGCTACTATGAGGAATTGCTCTCATA 59.505 38.462 25.01 19.58 45.61 2.15
3763 6666 7.179872 TGCTACTATGAGGAATTGCTCTCATAT 59.820 37.037 25.01 13.95 45.93 1.78
3764 6667 8.040132 GCTACTATGAGGAATTGCTCTCATATT 58.960 37.037 25.01 17.63 45.93 1.28
3765 6668 9.585099 CTACTATGAGGAATTGCTCTCATATTC 57.415 37.037 25.01 0.46 45.93 1.75
3778 6681 7.748677 TGCTCTCATATTCTTATGGGAAATGA 58.251 34.615 0.00 0.00 43.23 2.57
3779 6682 7.881751 TGCTCTCATATTCTTATGGGAAATGAG 59.118 37.037 16.69 16.69 43.23 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.425359 CCGACTGAATACAAGCAAGCAAG 60.425 47.826 0.00 0.00 0.00 4.01
44 52 6.314400 GCCAACTAGTCAACATAAACCGAATA 59.686 38.462 0.00 0.00 0.00 1.75
85 98 2.285083 TGACTTGTTCAACTTGACCGG 58.715 47.619 0.00 0.00 0.00 5.28
86 99 2.936498 ACTGACTTGTTCAACTTGACCG 59.064 45.455 0.00 0.00 32.21 4.79
96 109 2.033662 GCTGTTGACGACTGACTTGTTC 60.034 50.000 3.99 0.00 0.00 3.18
193 217 0.633835 TGAGGATCTAGGGGAGGGGT 60.634 60.000 0.00 0.00 34.92 4.95
194 218 0.568192 TTGAGGATCTAGGGGAGGGG 59.432 60.000 0.00 0.00 34.92 4.79
195 219 2.050918 GTTTGAGGATCTAGGGGAGGG 58.949 57.143 0.00 0.00 34.92 4.30
196 220 1.689273 CGTTTGAGGATCTAGGGGAGG 59.311 57.143 0.00 0.00 34.92 4.30
197 221 1.069358 GCGTTTGAGGATCTAGGGGAG 59.931 57.143 0.00 0.00 34.92 4.30
198 222 1.120530 GCGTTTGAGGATCTAGGGGA 58.879 55.000 0.00 0.00 34.92 4.81
199 223 1.123928 AGCGTTTGAGGATCTAGGGG 58.876 55.000 0.00 0.00 34.92 4.79
200 224 2.693591 TGTAGCGTTTGAGGATCTAGGG 59.306 50.000 0.00 0.00 34.92 3.53
201 225 4.142138 ACTTGTAGCGTTTGAGGATCTAGG 60.142 45.833 0.00 0.00 34.92 3.02
292 324 2.939298 CGGGGGAGAGAGGGAGAT 59.061 66.667 0.00 0.00 0.00 2.75
323 355 2.858655 GGGATGGGGGTTGGTTGT 59.141 61.111 0.00 0.00 0.00 3.32
343 375 3.741476 CGGGGTGAAGCAGCAAGC 61.741 66.667 0.00 0.00 46.19 4.01
352 384 0.988063 TGATGATCCAACGGGGTGAA 59.012 50.000 0.00 0.00 38.11 3.18
403 435 5.587043 TCAACCAAGTAATCAACGAAGTGTT 59.413 36.000 0.00 0.00 45.00 3.32
405 437 5.666969 TCAACCAAGTAATCAACGAAGTG 57.333 39.130 0.00 0.00 45.00 3.16
408 440 6.567701 GCAAGATCAACCAAGTAATCAACGAA 60.568 38.462 0.00 0.00 0.00 3.85
410 442 5.088739 GCAAGATCAACCAAGTAATCAACG 58.911 41.667 0.00 0.00 0.00 4.10
414 450 4.034510 CGGAGCAAGATCAACCAAGTAATC 59.965 45.833 0.00 0.00 0.00 1.75
419 455 1.089920 CCGGAGCAAGATCAACCAAG 58.910 55.000 0.00 0.00 0.00 3.61
449 485 1.172180 TCAAACCAAAGCTGGAGCGG 61.172 55.000 0.00 0.00 46.92 5.52
450 486 0.883833 ATCAAACCAAAGCTGGAGCG 59.116 50.000 0.00 0.00 46.92 5.03
452 488 4.202141 TGTCAAATCAAACCAAAGCTGGAG 60.202 41.667 0.00 0.00 46.92 3.86
479 518 2.158813 GGTTCACTTTCACTCCCTCACA 60.159 50.000 0.00 0.00 0.00 3.58
481 520 1.420138 GGGTTCACTTTCACTCCCTCA 59.580 52.381 0.00 0.00 32.89 3.86
546 593 1.153667 CGGAGGAGAGCAGAGCAAC 60.154 63.158 0.00 0.00 0.00 4.17
563 610 1.107114 TCCTCCTAGCAGAAGAAGCG 58.893 55.000 0.00 0.00 37.01 4.68
628 679 2.922387 CGCAATTGCAAATCGGATTGAA 59.078 40.909 28.77 0.00 42.21 2.69
639 690 1.020437 TCAGACACACGCAATTGCAA 58.980 45.000 28.77 0.00 42.21 4.08
649 700 4.002906 TGATTGGTAGGTTCAGACACAC 57.997 45.455 0.00 0.00 0.00 3.82
650 701 4.908601 ATGATTGGTAGGTTCAGACACA 57.091 40.909 0.00 0.00 0.00 3.72
651 702 5.730550 TGTATGATTGGTAGGTTCAGACAC 58.269 41.667 0.00 0.00 36.86 3.67
652 703 6.367374 TTGTATGATTGGTAGGTTCAGACA 57.633 37.500 0.00 0.00 39.17 3.41
653 704 6.653320 TGTTTGTATGATTGGTAGGTTCAGAC 59.347 38.462 0.00 0.00 33.39 3.51
694 749 2.535984 CTGTACGCGGTGAATGAATCTC 59.464 50.000 12.47 0.00 0.00 2.75
695 750 2.165641 TCTGTACGCGGTGAATGAATCT 59.834 45.455 12.47 0.00 0.00 2.40
719 777 4.790766 GCAAGGAAGCCAAATGTATCATCG 60.791 45.833 0.00 0.00 0.00 3.84
759 902 3.064408 CACATGGTGGATGAAGATGAACG 59.936 47.826 0.00 0.00 35.80 3.95
791 935 1.305381 AAGCAGAGCGGTAGAGGGT 60.305 57.895 0.00 0.00 0.00 4.34
818 962 7.170828 TCAAGCAGGTAGTATTATATTGTTGCG 59.829 37.037 0.00 0.00 33.39 4.85
831 975 4.202419 ACAAACACCATCAAGCAGGTAGTA 60.202 41.667 0.00 0.00 36.07 1.82
832 976 3.149196 CAAACACCATCAAGCAGGTAGT 58.851 45.455 0.00 0.00 36.07 2.73
833 977 3.149196 ACAAACACCATCAAGCAGGTAG 58.851 45.455 0.00 0.00 36.07 3.18
863 1010 0.109723 AGGCGCCAAGTCAAGGTTTA 59.890 50.000 31.54 0.00 0.00 2.01
864 1011 1.152756 AGGCGCCAAGTCAAGGTTT 60.153 52.632 31.54 0.00 0.00 3.27
865 1012 1.898574 CAGGCGCCAAGTCAAGGTT 60.899 57.895 31.54 0.00 0.00 3.50
918 1065 3.605634 CTGGTGGACGATGAATTTGGTA 58.394 45.455 0.00 0.00 0.00 3.25
919 1066 2.436417 CTGGTGGACGATGAATTTGGT 58.564 47.619 0.00 0.00 0.00 3.67
920 1067 1.133025 GCTGGTGGACGATGAATTTGG 59.867 52.381 0.00 0.00 0.00 3.28
922 1069 2.496899 AGCTGGTGGACGATGAATTT 57.503 45.000 0.00 0.00 0.00 1.82
924 1071 2.026822 AGAAAGCTGGTGGACGATGAAT 60.027 45.455 0.00 0.00 0.00 2.57
1115 1282 0.605589 CGAAGTGGTCTCTGCCTTCT 59.394 55.000 0.00 0.00 32.93 2.85
1122 1289 1.977544 CGGGGTCGAAGTGGTCTCT 60.978 63.158 0.00 0.00 39.00 3.10
1251 1418 2.279120 GATGGAGTCGGCGCTCAG 60.279 66.667 24.88 0.00 37.24 3.35
1509 1676 7.310423 GGTTGGTGGAGTATATATCTGTATGCA 60.310 40.741 0.00 0.00 0.00 3.96
1510 1677 7.042335 GGTTGGTGGAGTATATATCTGTATGC 58.958 42.308 0.00 0.00 0.00 3.14
1511 1678 8.035394 GTGGTTGGTGGAGTATATATCTGTATG 58.965 40.741 0.00 0.00 0.00 2.39
1512 1679 7.733047 TGTGGTTGGTGGAGTATATATCTGTAT 59.267 37.037 0.00 0.00 0.00 2.29
1513 1680 7.070629 TGTGGTTGGTGGAGTATATATCTGTA 58.929 38.462 0.00 0.00 0.00 2.74
1514 1681 5.903010 TGTGGTTGGTGGAGTATATATCTGT 59.097 40.000 0.00 0.00 0.00 3.41
1515 1682 6.419484 TGTGGTTGGTGGAGTATATATCTG 57.581 41.667 0.00 0.00 0.00 2.90
1516 1683 8.917414 ATATGTGGTTGGTGGAGTATATATCT 57.083 34.615 0.00 0.00 0.00 1.98
1517 1684 9.601217 GAATATGTGGTTGGTGGAGTATATATC 57.399 37.037 0.00 0.00 0.00 1.63
1518 1685 9.111519 TGAATATGTGGTTGGTGGAGTATATAT 57.888 33.333 0.00 0.00 0.00 0.86
1519 1686 8.372459 GTGAATATGTGGTTGGTGGAGTATATA 58.628 37.037 0.00 0.00 0.00 0.86
1542 1710 0.321919 GCCACCAGAGAGCAATGTGA 60.322 55.000 0.00 0.00 0.00 3.58
1570 1738 8.542132 CATCAAATTCGCCATTAATTTTACTGG 58.458 33.333 3.09 3.09 35.00 4.00
1790 1958 2.586079 CGCATAGGCCACGACAGG 60.586 66.667 5.01 0.00 36.38 4.00
1911 2079 8.722480 ATCGATCTTCAGTACAATTCATTCAA 57.278 30.769 0.00 0.00 0.00 2.69
1923 2091 3.555966 TCCTGCAGATCGATCTTCAGTA 58.444 45.455 36.46 27.05 43.61 2.74
1948 2116 9.528018 AACGAAATGTTACAAATTCAGTTCATT 57.472 25.926 12.45 6.65 39.61 2.57
1964 2132 7.542130 GGAAAATTATCTGAGCAACGAAATGTT 59.458 33.333 0.00 0.00 43.09 2.71
1970 2138 3.621268 CCGGAAAATTATCTGAGCAACGA 59.379 43.478 0.00 0.00 0.00 3.85
2046 2214 1.227674 CCTAGCCATGCCGAAGTCC 60.228 63.158 0.00 0.00 0.00 3.85
2088 2256 2.758770 TTACCGCTGTGGAGACGTGC 62.759 60.000 15.34 0.00 42.00 5.34
2118 2286 6.827251 AGTGTATCTGATTCTGAATGCACAAT 59.173 34.615 7.78 1.49 0.00 2.71
2132 2300 8.267183 TCATCCACAAAACATAGTGTATCTGAT 58.733 33.333 0.00 0.00 33.99 2.90
2433 2602 3.461773 CGGGTCCACGATCAGCCT 61.462 66.667 0.00 0.00 35.47 4.58
2465 2634 1.359848 CCACCGACTTGATGCTGTAC 58.640 55.000 0.00 0.00 0.00 2.90
2665 2852 1.381851 CCTTTCTTGCCCTCCTGCT 59.618 57.895 0.00 0.00 0.00 4.24
2704 2891 1.000771 GGCCCTTTCCCTCTTCCAC 60.001 63.158 0.00 0.00 0.00 4.02
2714 2901 2.054453 GCACATGAGGGGCCCTTTC 61.054 63.158 29.49 19.96 31.76 2.62
2742 2929 4.410228 TCAATCACCTGGATTAAGCTAGCT 59.590 41.667 12.68 12.68 44.41 3.32
2754 2941 7.408756 TGGAAAAATCTAATCAATCACCTGG 57.591 36.000 0.00 0.00 0.00 4.45
2800 5266 1.343142 ACACGAACTCACATAGTGCCA 59.657 47.619 0.00 0.00 38.88 4.92
2805 5271 5.164233 AGATGACAACACGAACTCACATAG 58.836 41.667 0.00 0.00 0.00 2.23
2812 5278 3.804325 CACTCAAGATGACAACACGAACT 59.196 43.478 0.00 0.00 0.00 3.01
2816 5282 3.369147 GGATCACTCAAGATGACAACACG 59.631 47.826 0.00 0.00 0.00 4.49
2820 5286 6.005823 ACAATTGGATCACTCAAGATGACAA 58.994 36.000 10.83 0.00 0.00 3.18
2824 5290 5.182570 ACACACAATTGGATCACTCAAGATG 59.817 40.000 10.83 0.00 0.00 2.90
2825 5291 5.182570 CACACACAATTGGATCACTCAAGAT 59.817 40.000 10.83 0.00 0.00 2.40
2827 5293 4.320714 CCACACACAATTGGATCACTCAAG 60.321 45.833 10.83 0.00 34.46 3.02
2828 5294 3.569277 CCACACACAATTGGATCACTCAA 59.431 43.478 10.83 0.00 34.46 3.02
2867 5357 7.601886 CACTGATTCATCCACCTAATGATACTC 59.398 40.741 0.00 0.00 33.36 2.59
2869 5359 7.445121 TCACTGATTCATCCACCTAATGATAC 58.555 38.462 0.00 0.00 33.36 2.24
2873 5363 8.859236 ATAATCACTGATTCATCCACCTAATG 57.141 34.615 7.57 0.00 33.95 1.90
2881 5371 6.528321 TGACAGGATAATCACTGATTCATCC 58.472 40.000 19.99 19.99 38.09 3.51
2890 5380 5.363562 TGATGCTTGACAGGATAATCACT 57.636 39.130 0.00 0.00 29.51 3.41
2919 5409 5.880901 AGGAGGCTGAGATTGTTTTTCTAA 58.119 37.500 0.00 0.00 0.00 2.10
2920 5410 5.505181 AGGAGGCTGAGATTGTTTTTCTA 57.495 39.130 0.00 0.00 0.00 2.10
2923 5413 5.248380 ACTAGGAGGCTGAGATTGTTTTT 57.752 39.130 0.00 0.00 0.00 1.94
2924 5414 4.917906 ACTAGGAGGCTGAGATTGTTTT 57.082 40.909 0.00 0.00 0.00 2.43
2928 5418 3.454082 AGGAAACTAGGAGGCTGAGATTG 59.546 47.826 0.00 0.00 40.61 2.67
2931 5421 2.930109 AGGAAACTAGGAGGCTGAGA 57.070 50.000 0.00 0.00 40.61 3.27
2940 5430 8.764287 CAATTTTACAGCAAAAAGGAAACTAGG 58.236 33.333 0.00 0.00 42.68 3.02
2973 5464 8.405531 CAAAAGTGGTGAAAGAACAAAGAGATA 58.594 33.333 0.00 0.00 0.00 1.98
2974 5465 7.260603 CAAAAGTGGTGAAAGAACAAAGAGAT 58.739 34.615 0.00 0.00 0.00 2.75
2993 5484 3.806625 AAATGACACTGCTGCAAAAGT 57.193 38.095 3.02 2.19 0.00 2.66
3026 5517 9.787532 CATAACGAATGAAACAAGTATTCCAAT 57.212 29.630 0.00 0.00 37.86 3.16
3047 5538 6.163135 ACCTTGCATCCTAGTAGTCATAAC 57.837 41.667 0.00 0.00 0.00 1.89
3110 5606 9.301897 GTGAATCAAATAGGCCCTAAATATCTT 57.698 33.333 0.00 0.00 0.00 2.40
3146 6045 9.033481 CATACGTTTATCTTATTCCCACGTTTA 57.967 33.333 0.00 0.00 39.84 2.01
3176 6076 7.419711 AGGATTGAGATGAGCATGAAATTTT 57.580 32.000 0.00 0.00 0.00 1.82
3199 6101 8.246180 ACAATCAAACACAGCAAAATCCTATAG 58.754 33.333 0.00 0.00 0.00 1.31
3333 6236 3.960102 AGTTCTCCTGCATGGTTCAAAAA 59.040 39.130 0.00 0.00 37.07 1.94
3334 6237 3.318839 CAGTTCTCCTGCATGGTTCAAAA 59.681 43.478 0.00 0.00 33.59 2.44
3335 6238 2.886523 CAGTTCTCCTGCATGGTTCAAA 59.113 45.455 0.00 0.00 33.59 2.69
3336 6239 2.507484 CAGTTCTCCTGCATGGTTCAA 58.493 47.619 0.00 0.00 33.59 2.69
3337 6240 2.189594 CAGTTCTCCTGCATGGTTCA 57.810 50.000 0.00 0.00 33.59 3.18
3346 6249 2.174363 TGTCACATGCAGTTCTCCTG 57.826 50.000 0.00 0.00 44.53 3.86
3347 6250 2.936919 TTGTCACATGCAGTTCTCCT 57.063 45.000 0.00 0.00 0.00 3.69
3348 6251 4.256920 ACTATTGTCACATGCAGTTCTCC 58.743 43.478 0.00 0.00 0.00 3.71
3349 6252 5.869344 TGTACTATTGTCACATGCAGTTCTC 59.131 40.000 0.00 0.00 0.00 2.87
3350 6253 5.793817 TGTACTATTGTCACATGCAGTTCT 58.206 37.500 0.00 0.00 0.00 3.01
3351 6254 6.480524 TTGTACTATTGTCACATGCAGTTC 57.519 37.500 0.00 0.00 0.00 3.01
3352 6255 6.875948 TTTGTACTATTGTCACATGCAGTT 57.124 33.333 0.00 0.00 0.00 3.16
3353 6256 6.565811 CGTTTTGTACTATTGTCACATGCAGT 60.566 38.462 0.00 0.00 0.00 4.40
3354 6257 5.790003 CGTTTTGTACTATTGTCACATGCAG 59.210 40.000 0.00 0.00 0.00 4.41
3355 6258 5.467063 TCGTTTTGTACTATTGTCACATGCA 59.533 36.000 0.00 0.00 0.00 3.96
3356 6259 5.788531 GTCGTTTTGTACTATTGTCACATGC 59.211 40.000 0.00 0.00 0.00 4.06
3357 6260 6.304126 GGTCGTTTTGTACTATTGTCACATG 58.696 40.000 0.00 0.00 0.00 3.21
3358 6261 5.410439 GGGTCGTTTTGTACTATTGTCACAT 59.590 40.000 0.00 0.00 0.00 3.21
3359 6262 4.751098 GGGTCGTTTTGTACTATTGTCACA 59.249 41.667 0.00 0.00 0.00 3.58
3360 6263 4.751098 TGGGTCGTTTTGTACTATTGTCAC 59.249 41.667 0.00 0.00 0.00 3.67
3361 6264 4.958509 TGGGTCGTTTTGTACTATTGTCA 58.041 39.130 0.00 0.00 0.00 3.58
3362 6265 5.236911 TGTTGGGTCGTTTTGTACTATTGTC 59.763 40.000 0.00 0.00 0.00 3.18
3363 6266 5.124645 TGTTGGGTCGTTTTGTACTATTGT 58.875 37.500 0.00 0.00 0.00 2.71
3364 6267 5.676532 TGTTGGGTCGTTTTGTACTATTG 57.323 39.130 0.00 0.00 0.00 1.90
3365 6268 5.589452 TGTTGTTGGGTCGTTTTGTACTATT 59.411 36.000 0.00 0.00 0.00 1.73
3366 6269 5.124645 TGTTGTTGGGTCGTTTTGTACTAT 58.875 37.500 0.00 0.00 0.00 2.12
3367 6270 4.511527 TGTTGTTGGGTCGTTTTGTACTA 58.488 39.130 0.00 0.00 0.00 1.82
3368 6271 3.345414 TGTTGTTGGGTCGTTTTGTACT 58.655 40.909 0.00 0.00 0.00 2.73
3369 6272 3.761311 TGTTGTTGGGTCGTTTTGTAC 57.239 42.857 0.00 0.00 0.00 2.90
3370 6273 4.778534 TTTGTTGTTGGGTCGTTTTGTA 57.221 36.364 0.00 0.00 0.00 2.41
3371 6274 3.662247 TTTGTTGTTGGGTCGTTTTGT 57.338 38.095 0.00 0.00 0.00 2.83
3372 6275 4.143009 CCTTTTTGTTGTTGGGTCGTTTTG 60.143 41.667 0.00 0.00 0.00 2.44
3373 6276 3.997681 CCTTTTTGTTGTTGGGTCGTTTT 59.002 39.130 0.00 0.00 0.00 2.43
3374 6277 3.591023 CCTTTTTGTTGTTGGGTCGTTT 58.409 40.909 0.00 0.00 0.00 3.60
3375 6278 2.675603 GCCTTTTTGTTGTTGGGTCGTT 60.676 45.455 0.00 0.00 0.00 3.85
3376 6279 1.134936 GCCTTTTTGTTGTTGGGTCGT 60.135 47.619 0.00 0.00 0.00 4.34
3377 6280 1.134965 TGCCTTTTTGTTGTTGGGTCG 60.135 47.619 0.00 0.00 0.00 4.79
3378 6281 2.682155 TGCCTTTTTGTTGTTGGGTC 57.318 45.000 0.00 0.00 0.00 4.46
3379 6282 3.425162 TTTGCCTTTTTGTTGTTGGGT 57.575 38.095 0.00 0.00 0.00 4.51
3380 6283 4.773323 TTTTTGCCTTTTTGTTGTTGGG 57.227 36.364 0.00 0.00 0.00 4.12
3404 6307 9.753674 TGAGGTCATTGTTCTCCTTATTTATTT 57.246 29.630 6.57 0.00 0.00 1.40
3405 6308 9.401058 CTGAGGTCATTGTTCTCCTTATTTATT 57.599 33.333 6.57 0.00 0.00 1.40
3406 6309 8.552296 ACTGAGGTCATTGTTCTCCTTATTTAT 58.448 33.333 6.57 0.00 0.00 1.40
3407 6310 7.918076 ACTGAGGTCATTGTTCTCCTTATTTA 58.082 34.615 6.57 0.00 0.00 1.40
3408 6311 6.784031 ACTGAGGTCATTGTTCTCCTTATTT 58.216 36.000 6.57 0.00 0.00 1.40
3409 6312 6.013379 TGACTGAGGTCATTGTTCTCCTTATT 60.013 38.462 0.00 0.00 46.19 1.40
3410 6313 5.485353 TGACTGAGGTCATTGTTCTCCTTAT 59.515 40.000 0.00 0.00 46.19 1.73
3411 6314 4.838423 TGACTGAGGTCATTGTTCTCCTTA 59.162 41.667 0.00 0.00 46.19 2.69
3412 6315 3.648067 TGACTGAGGTCATTGTTCTCCTT 59.352 43.478 0.00 0.00 46.19 3.36
3413 6316 3.242867 TGACTGAGGTCATTGTTCTCCT 58.757 45.455 0.00 0.00 46.19 3.69
3414 6317 3.685139 TGACTGAGGTCATTGTTCTCC 57.315 47.619 0.00 0.00 46.19 3.71
3424 6327 1.134670 AGGCGCTAAATGACTGAGGTC 60.135 52.381 7.64 0.00 42.42 3.85
3425 6328 0.905357 AGGCGCTAAATGACTGAGGT 59.095 50.000 7.64 0.00 0.00 3.85
3426 6329 1.293924 CAGGCGCTAAATGACTGAGG 58.706 55.000 7.64 0.00 0.00 3.86
3427 6330 0.654683 GCAGGCGCTAAATGACTGAG 59.345 55.000 7.64 0.00 34.30 3.35
3428 6331 2.767536 GCAGGCGCTAAATGACTGA 58.232 52.632 7.64 0.00 34.30 3.41
3433 6336 9.480433 AGAATGTTCTAAAGCAGGCGCTAAATG 62.480 40.741 7.64 2.52 41.38 2.32
3434 6337 7.575265 AGAATGTTCTAAAGCAGGCGCTAAAT 61.575 38.462 7.64 0.00 41.38 1.40
3435 6338 6.317676 AGAATGTTCTAAAGCAGGCGCTAAA 61.318 40.000 7.64 0.00 41.38 1.85
3436 6339 4.863115 AGAATGTTCTAAAGCAGGCGCTAA 60.863 41.667 7.64 0.00 41.38 3.09
3437 6340 3.369471 AGAATGTTCTAAAGCAGGCGCTA 60.369 43.478 7.64 0.00 41.38 4.26
3438 6341 2.616510 AGAATGTTCTAAAGCAGGCGCT 60.617 45.455 7.64 0.00 43.16 5.92
3439 6342 1.740025 AGAATGTTCTAAAGCAGGCGC 59.260 47.619 0.00 0.00 35.34 6.53
3440 6343 3.932710 TGTAGAATGTTCTAAAGCAGGCG 59.067 43.478 4.16 0.00 41.12 5.52
3441 6344 5.181245 TGTTGTAGAATGTTCTAAAGCAGGC 59.819 40.000 4.16 0.00 41.12 4.85
3442 6345 6.801539 TGTTGTAGAATGTTCTAAAGCAGG 57.198 37.500 4.16 0.00 41.12 4.85
3443 6346 8.506437 TGAATGTTGTAGAATGTTCTAAAGCAG 58.494 33.333 12.86 0.00 40.19 4.24
3444 6347 8.389779 TGAATGTTGTAGAATGTTCTAAAGCA 57.610 30.769 10.62 10.62 40.81 3.91
3445 6348 9.846248 AATGAATGTTGTAGAATGTTCTAAAGC 57.154 29.630 4.16 2.55 41.12 3.51
3449 6352 9.942850 TGAGAATGAATGTTGTAGAATGTTCTA 57.057 29.630 0.00 0.00 38.70 2.10
3450 6353 8.853077 TGAGAATGAATGTTGTAGAATGTTCT 57.147 30.769 0.45 0.45 41.24 3.01
3555 6458 0.394352 CAGTCCGCAATAAGGGCCTT 60.394 55.000 24.44 24.44 32.84 4.35
3568 6471 0.962356 AAGGCTCCAAATGCAGTCCG 60.962 55.000 0.00 0.00 0.00 4.79
3582 6485 8.134202 AGCACAAAGGTTTAATATAAAAGGCT 57.866 30.769 0.00 0.00 0.00 4.58
3612 6515 9.461312 TTTTATTATGTAAGGCATCTCACAAGT 57.539 29.630 0.00 0.00 38.94 3.16
3615 6518 8.352201 GCATTTTATTATGTAAGGCATCTCACA 58.648 33.333 0.00 0.00 38.94 3.58
3652 6555 7.337150 AGTATTGCATCGTGTGAAAAATTTG 57.663 32.000 0.00 0.00 0.00 2.32
3654 6557 7.945033 AAAGTATTGCATCGTGTGAAAAATT 57.055 28.000 0.00 0.00 0.00 1.82
3681 6584 7.867305 TTACACCGCTATTTTGGATCAAATA 57.133 32.000 0.00 0.00 33.19 1.40
3698 6601 6.388278 GGGCTAGAATCTATAGTTTACACCG 58.612 44.000 0.00 0.00 0.00 4.94
3723 6626 0.244721 GTAGCAAGGCTGGCAAAAGG 59.755 55.000 17.80 0.00 40.10 3.11
3724 6627 1.251251 AGTAGCAAGGCTGGCAAAAG 58.749 50.000 17.80 0.00 40.10 2.27


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

AutoCloner maintained by Alex Coulton.