Multiple sequence alignment - TraesCS6D01G315200

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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 TraesCS6D01G315200 chr6D 100.000 3522 0 0 1 3522 423674186 423677707 0.000000e+00 6505.0
1 TraesCS6D01G315200 chr6D 98.113 53 1 0 3434 3486 3456728 3456780 3.740000e-15 93.5
2 TraesCS6D01G315200 chr6A 90.414 2441 109 51 550 2927 568016515 568014137 0.000000e+00 3096.0
3 TraesCS6D01G315200 chr6A 88.256 281 29 4 1 278 568017165 568016886 2.030000e-87 333.0
4 TraesCS6D01G315200 chr6A 91.525 177 9 3 3220 3392 568013703 568013529 4.540000e-59 239.0
5 TraesCS6D01G315200 chr6B 86.814 1949 116 49 1548 3434 638935287 638933418 0.000000e+00 2045.0
6 TraesCS6D01G315200 chr6B 92.657 858 48 14 608 1456 638936221 638935370 0.000000e+00 1221.0
7 TraesCS6D01G315200 chr6B 100.000 48 0 0 3439 3486 204169084 204169037 4.840000e-14 89.8
8 TraesCS6D01G315200 chr5A 86.061 165 23 0 1286 1450 462145411 462145575 1.000000e-40 178.0
9 TraesCS6D01G315200 chr5D 85.802 162 23 0 1286 1447 361606671 361606832 4.670000e-39 172.0
10 TraesCS6D01G315200 chr5D 98.113 53 1 0 3434 3486 525599569 525599517 3.740000e-15 93.5
11 TraesCS6D01G315200 chr5B 85.802 162 23 0 1286 1447 427239014 427239175 4.670000e-39 172.0
12 TraesCS6D01G315200 chr5B 93.651 63 3 1 3424 3486 57968005 57967944 3.740000e-15 93.5
13 TraesCS6D01G315200 chr5B 94.915 59 1 2 3429 3486 696575540 696575483 1.350000e-14 91.6
14 TraesCS6D01G315200 chr2A 91.753 97 6 1 196 290 599780170 599780266 2.210000e-27 134.0
15 TraesCS6D01G315200 chr4A 98.113 53 0 1 3438 3489 46423218 46423166 1.350000e-14 91.6
16 TraesCS6D01G315200 chr1D 94.915 59 1 2 3428 3486 354529331 354529387 1.350000e-14 91.6
17 TraesCS6D01G315200 chr2B 94.828 58 2 1 3429 3486 245689651 245689595 4.840000e-14 89.8
18 TraesCS6D01G315200 chr2B 90.909 66 4 2 3421 3486 97013769 97013832 1.740000e-13 87.9


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 TraesCS6D01G315200 chr6D 423674186 423677707 3521 False 6505.000000 6505 100.0000 1 3522 1 chr6D.!!$F2 3521
1 TraesCS6D01G315200 chr6A 568013529 568017165 3636 True 1222.666667 3096 90.0650 1 3392 3 chr6A.!!$R1 3391
2 TraesCS6D01G315200 chr6B 638933418 638936221 2803 True 1633.000000 2045 89.7355 608 3434 2 chr6B.!!$R2 2826

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
410 423 0.099968 TTCGAAGGCATCTACGACGG 59.900 55.0 0.00 0.0 34.59 4.79 F
957 1098 0.109086 CACATCTCTCTTCCGCGTGT 60.109 55.0 4.92 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2251 0.042581 TAGCATGGGGAGTCTGTGGA 59.957 55.0 0.0 0.0 0.0 4.02 R
2929 3242 0.238289 ATGAAAAGACAACTGCCGCG 59.762 50.0 0.0 0.0 0.0 6.46 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 3.451665 AACCTGTGTAGCGGACGT 58.548 55.556 0.00 0.00 0.00 4.34
21 22 1.028330 CCTGTGTAGCGGACGTCCTA 61.028 60.000 30.92 15.79 0.00 2.94
29 30 2.768492 CGGACGTCCTAACTCCCCG 61.768 68.421 30.92 12.45 0.00 5.73
31 32 1.382692 GGACGTCCTAACTCCCCGAG 61.383 65.000 27.64 0.00 35.52 4.63
35 36 1.077212 TCCTAACTCCCCGAGACCG 60.077 63.158 0.00 0.00 33.32 4.79
39 40 2.843912 TAACTCCCCGAGACCGACCC 62.844 65.000 0.00 0.00 38.22 4.46
41 42 4.437587 TCCCCGAGACCGACCCTC 62.438 72.222 0.00 0.00 38.22 4.30
62 64 2.165845 CGATTTGGAGTCGTCCTAAGGT 59.834 50.000 0.00 0.00 44.30 3.50
67 69 4.996788 TGGAGTCGTCCTAAGGTATTTC 57.003 45.455 0.00 0.00 44.30 2.17
69 71 3.629398 GGAGTCGTCCTAAGGTATTTCGA 59.371 47.826 0.00 0.00 40.17 3.71
71 73 4.991472 AGTCGTCCTAAGGTATTTCGAAC 58.009 43.478 0.00 0.00 0.00 3.95
74 76 3.788163 CGTCCTAAGGTATTTCGAACGTC 59.212 47.826 0.00 0.00 0.00 4.34
76 78 3.111098 CCTAAGGTATTTCGAACGTCCG 58.889 50.000 0.00 0.00 0.00 4.79
87 89 1.667756 CGAACGTCCGAACCAATCTGA 60.668 52.381 0.00 0.00 0.00 3.27
88 90 2.618053 GAACGTCCGAACCAATCTGAT 58.382 47.619 0.00 0.00 0.00 2.90
102 104 5.032863 CCAATCTGATCGAAAACAAGATGC 58.967 41.667 0.00 0.00 0.00 3.91
107 109 3.496507 TGATCGAAAACAAGATGCGTTCA 59.503 39.130 0.00 0.00 0.00 3.18
145 147 4.536364 AAGCATACGAACCATTCAATCG 57.464 40.909 0.00 0.00 42.05 3.34
148 150 4.816385 AGCATACGAACCATTCAATCGAAT 59.184 37.500 1.03 0.00 42.81 3.34
149 151 5.050091 AGCATACGAACCATTCAATCGAATC 60.050 40.000 1.03 0.00 39.96 2.52
151 153 4.600012 ACGAACCATTCAATCGAATCAC 57.400 40.909 1.03 0.00 39.96 3.06
170 172 4.069304 TCACAAAGGGACGATTTGGTAAG 58.931 43.478 0.00 0.00 41.05 2.34
175 177 1.347221 GACGATTTGGTAAGGCGCG 59.653 57.895 0.00 0.00 0.00 6.86
194 196 2.159435 GCGTTAACCATGCGGATTCTTT 60.159 45.455 0.00 0.00 35.59 2.52
201 204 3.320541 ACCATGCGGATTCTTTTGTTGAA 59.679 39.130 0.00 0.00 35.59 2.69
220 223 6.603201 TGTTGAAGTCCAAAATTCAAGTCTCT 59.397 34.615 1.71 0.00 43.90 3.10
227 230 6.484977 GTCCAAAATTCAAGTCTCTTGTCTCT 59.515 38.462 8.93 0.00 0.00 3.10
260 263 9.353999 GCTTTCTCACAAACGGATTAAAAATAT 57.646 29.630 0.00 0.00 0.00 1.28
297 300 3.798794 TGGATAAACCATGGGCTCG 57.201 52.632 18.09 0.00 44.64 5.03
298 301 1.208706 TGGATAAACCATGGGCTCGA 58.791 50.000 18.09 1.34 44.64 4.04
299 302 1.562008 TGGATAAACCATGGGCTCGAA 59.438 47.619 18.09 0.00 44.64 3.71
310 313 4.258543 CATGGGCTCGAAAAGTTAGGTTA 58.741 43.478 0.00 0.00 0.00 2.85
322 325 4.553330 AGTTAGGTTACATGTGGTGGAG 57.447 45.455 9.11 0.00 0.00 3.86
333 336 2.462301 TGGTGGAGCCAACTCATCA 58.538 52.632 6.08 0.00 45.94 3.07
335 338 0.615331 GGTGGAGCCAACTCATCAGA 59.385 55.000 0.00 0.00 45.42 3.27
365 368 2.914695 TACACTTAGCGTTGGTGGTT 57.085 45.000 10.63 0.00 35.53 3.67
366 369 1.305201 ACACTTAGCGTTGGTGGTTG 58.695 50.000 10.63 0.00 35.53 3.77
373 376 0.858583 GCGTTGGTGGTTGCATTTTC 59.141 50.000 0.00 0.00 0.00 2.29
375 378 2.126467 CGTTGGTGGTTGCATTTTCTG 58.874 47.619 0.00 0.00 0.00 3.02
410 423 0.099968 TTCGAAGGCATCTACGACGG 59.900 55.000 0.00 0.00 34.59 4.79
427 440 1.204704 ACGGCTTCGTCAATCTCATGA 59.795 47.619 0.00 0.00 44.73 3.07
428 441 1.590238 CGGCTTCGTCAATCTCATGAC 59.410 52.381 0.00 0.00 44.96 3.06
435 448 1.394917 GTCAATCTCATGACGGTGTGC 59.605 52.381 0.00 0.00 40.23 4.57
448 463 4.314440 TGTGCCGGCTCAGTGTCC 62.314 66.667 29.70 5.56 0.00 4.02
465 480 1.030488 TCCCTGAGACGCTCGTAAGG 61.030 60.000 9.85 9.85 32.35 2.69
474 489 1.210478 ACGCTCGTAAGGGGTAGAGTA 59.790 52.381 0.00 0.00 39.68 2.59
490 509 3.517602 AGAGTATGTGCGCGTTTATTCA 58.482 40.909 8.43 0.00 0.00 2.57
492 511 4.025730 AGAGTATGTGCGCGTTTATTCATG 60.026 41.667 8.43 0.00 0.00 3.07
499 518 2.032799 GCGCGTTTATTCATGGGAATGA 59.967 45.455 8.43 0.00 43.47 2.57
500 519 3.849645 GCGCGTTTATTCATGGGAATGAG 60.850 47.826 8.43 0.00 43.47 2.90
515 534 2.028420 ATGAGTGCATGTGCGTATGT 57.972 45.000 0.00 0.00 45.83 2.29
516 535 2.663826 TGAGTGCATGTGCGTATGTA 57.336 45.000 0.00 0.00 45.83 2.29
518 537 2.865551 TGAGTGCATGTGCGTATGTATG 59.134 45.455 0.00 0.00 45.83 2.39
519 538 3.123050 GAGTGCATGTGCGTATGTATGA 58.877 45.455 0.00 0.00 45.83 2.15
520 539 3.126073 AGTGCATGTGCGTATGTATGAG 58.874 45.455 0.00 0.00 45.83 2.90
532 551 2.933495 TGTATGAGTGCGTCTGTACC 57.067 50.000 0.00 0.00 0.00 3.34
538 557 1.993370 GAGTGCGTCTGTACCATGTTC 59.007 52.381 0.00 0.00 0.00 3.18
628 759 2.158813 AGCCGGTCTTCAAAAGAACAGA 60.159 45.455 1.90 0.00 45.67 3.41
629 760 2.031944 GCCGGTCTTCAAAAGAACAGAC 60.032 50.000 1.90 0.00 45.67 3.51
737 869 2.138320 GTCCCGTCATCTATGCACATG 58.862 52.381 0.00 0.00 0.00 3.21
753 885 3.181499 GCACATGCATCCTCTTTTCTCTG 60.181 47.826 0.00 0.00 41.59 3.35
759 891 4.183101 GCATCCTCTTTTCTCTGTCTCTG 58.817 47.826 0.00 0.00 0.00 3.35
762 902 2.605030 CTCTTTTCTCTGTCTCTGCCG 58.395 52.381 0.00 0.00 0.00 5.69
763 903 1.964223 TCTTTTCTCTGTCTCTGCCGT 59.036 47.619 0.00 0.00 0.00 5.68
899 1040 6.378280 GGTATAAATTATTCTGGCCATGGAGG 59.622 42.308 18.40 4.19 41.84 4.30
938 1079 4.784177 AGAGGTAGAAGCTAGGTAGTGAC 58.216 47.826 0.00 0.00 0.00 3.67
957 1098 0.109086 CACATCTCTCTTCCGCGTGT 60.109 55.000 4.92 0.00 0.00 4.49
958 1099 0.109086 ACATCTCTCTTCCGCGTGTG 60.109 55.000 4.92 0.00 0.00 3.82
979 1120 3.444916 GCATCTGCATCTTGGTCAATTG 58.555 45.455 0.00 0.00 41.59 2.32
985 1126 3.321396 TGCATCTTGGTCAATTGCTTGAA 59.679 39.130 0.00 0.00 42.85 2.69
1083 1234 3.851128 GTAGGAGGAGGCGGTGGC 61.851 72.222 0.00 0.00 38.90 5.01
1140 1291 0.400213 TGGAGTTGGACGGAAGCAAT 59.600 50.000 0.00 0.00 0.00 3.56
1238 1410 4.087892 CGGCAGTGACCCTGGAGG 62.088 72.222 0.00 0.00 41.81 4.30
1496 1696 7.797121 ATTTGGATGTAATTTTCAGGGAGTT 57.203 32.000 0.00 0.00 0.00 3.01
1588 1788 1.528076 ATCCATAATTGGCGGCGCA 60.528 52.632 34.36 15.19 43.29 6.09
1942 2157 4.899239 CTGAGGATCGTGGCGGGC 62.899 72.222 0.00 0.00 38.61 6.13
2033 2248 0.801067 CAGCCTCAAGGTACGTACGC 60.801 60.000 16.72 14.93 37.57 4.42
2035 2250 1.074872 GCCTCAAGGTACGTACGCAC 61.075 60.000 16.72 13.27 37.57 5.34
2036 2251 0.524862 CCTCAAGGTACGTACGCACT 59.475 55.000 16.72 8.19 0.00 4.40
2056 2280 0.179000 CCACAGACTCCCCATGCTAC 59.821 60.000 0.00 0.00 0.00 3.58
2242 2468 0.687757 TTGACGCTAGATGAGGGGCT 60.688 55.000 0.00 0.00 46.57 5.19
2243 2469 1.365633 GACGCTAGATGAGGGGCTG 59.634 63.158 0.00 0.00 43.01 4.85
2244 2470 2.030262 CGCTAGATGAGGGGCTGC 59.970 66.667 0.00 0.00 34.46 5.25
2245 2471 2.800541 CGCTAGATGAGGGGCTGCA 61.801 63.158 0.50 0.00 34.46 4.41
2246 2472 1.227793 GCTAGATGAGGGGCTGCAC 60.228 63.158 0.50 0.00 0.00 4.57
2247 2473 1.449353 CTAGATGAGGGGCTGCACC 59.551 63.158 14.54 14.54 37.93 5.01
2248 2474 1.003442 TAGATGAGGGGCTGCACCT 59.997 57.895 26.36 26.36 42.18 4.00
2249 2475 1.340399 TAGATGAGGGGCTGCACCTG 61.340 60.000 31.46 0.00 38.79 4.00
2250 2476 4.437587 ATGAGGGGCTGCACCTGC 62.438 66.667 31.46 19.69 38.79 4.85
2271 2497 0.966875 TGCATGGATTGACTGCCACC 60.967 55.000 0.00 0.00 36.92 4.61
2288 2514 1.959226 CCGTGTTTGCTGCCGTAGT 60.959 57.895 0.00 0.00 0.00 2.73
2290 2516 1.082104 GTGTTTGCTGCCGTAGTGC 60.082 57.895 0.00 0.00 0.00 4.40
2292 2518 1.966451 GTTTGCTGCCGTAGTGCCT 60.966 57.895 0.00 0.00 0.00 4.75
2293 2519 1.965930 TTTGCTGCCGTAGTGCCTG 60.966 57.895 0.00 0.00 0.00 4.85
2296 2522 2.816958 CTGCCGTAGTGCCTGCAG 60.817 66.667 6.78 6.78 44.43 4.41
2324 2563 2.286833 ACGTCCATTTCTTTGTGTCGTG 59.713 45.455 0.00 0.00 0.00 4.35
2336 2576 2.703416 TGTGTCGTGGACTCGTAGTAT 58.297 47.619 0.00 0.00 33.15 2.12
2354 2594 8.978539 TCGTAGTATGTAGCAAATGAATTCATC 58.021 33.333 20.95 9.22 35.10 2.92
2366 2606 7.972277 GCAAATGAATTCATCTGAAAAGCTCTA 59.028 33.333 23.05 0.00 37.61 2.43
2526 2775 1.334243 GCAGAGCTGTACGTAGGTAGG 59.666 57.143 0.00 0.00 0.00 3.18
2530 2781 2.547634 GAGCTGTACGTAGGTAGGTAGC 59.452 54.545 14.04 14.04 34.23 3.58
2531 2782 1.606189 GCTGTACGTAGGTAGGTAGCC 59.394 57.143 0.00 0.00 30.78 3.93
2561 2813 3.897325 TGTAACAGTTCACGAGCTACTG 58.103 45.455 11.25 11.25 43.72 2.74
2590 2842 7.493743 TTACGAGTAGTAAGCAAGATCTAGG 57.506 40.000 0.00 0.00 40.15 3.02
2627 2879 0.747283 AGGCACTGCAGCTTGATAGC 60.747 55.000 15.27 6.57 43.11 2.97
2777 3039 2.203126 CCGAATGCAGGGAGCCTC 60.203 66.667 0.00 0.00 44.83 4.70
2778 3040 2.739996 CCGAATGCAGGGAGCCTCT 61.740 63.158 0.00 0.00 44.83 3.69
2779 3041 1.222936 CGAATGCAGGGAGCCTCTT 59.777 57.895 0.00 0.00 44.83 2.85
2780 3042 1.094073 CGAATGCAGGGAGCCTCTTG 61.094 60.000 0.00 0.00 44.83 3.02
2781 3043 0.750911 GAATGCAGGGAGCCTCTTGG 60.751 60.000 0.00 0.00 44.83 3.61
2849 3114 5.828299 TGCATGTACAATTAAGGCTTACC 57.172 39.130 6.43 0.00 0.00 2.85
2932 3245 6.486657 TTACTTTTTACTGATCGTATCGCG 57.513 37.500 0.00 0.00 43.01 5.87
2933 3246 3.795101 ACTTTTTACTGATCGTATCGCGG 59.205 43.478 6.13 0.00 41.72 6.46
2934 3247 1.762419 TTTACTGATCGTATCGCGGC 58.238 50.000 6.13 0.00 41.72 6.53
2935 3248 0.664224 TTACTGATCGTATCGCGGCA 59.336 50.000 6.13 0.00 41.72 5.69
2936 3249 0.237498 TACTGATCGTATCGCGGCAG 59.763 55.000 6.13 5.55 43.60 4.85
2937 3250 1.008424 CTGATCGTATCGCGGCAGT 60.008 57.895 6.13 0.00 41.72 4.40
2938 3251 0.595053 CTGATCGTATCGCGGCAGTT 60.595 55.000 6.13 0.00 41.72 3.16
2939 3252 0.869880 TGATCGTATCGCGGCAGTTG 60.870 55.000 6.13 0.00 41.72 3.16
2940 3253 0.870307 GATCGTATCGCGGCAGTTGT 60.870 55.000 6.13 0.00 41.72 3.32
2941 3254 0.870307 ATCGTATCGCGGCAGTTGTC 60.870 55.000 6.13 0.00 41.72 3.18
2942 3255 1.516386 CGTATCGCGGCAGTTGTCT 60.516 57.895 6.13 0.00 36.85 3.41
2943 3256 1.076533 CGTATCGCGGCAGTTGTCTT 61.077 55.000 6.13 0.00 36.85 3.01
2944 3257 1.076332 GTATCGCGGCAGTTGTCTTT 58.924 50.000 6.13 0.00 0.00 2.52
2945 3258 1.463444 GTATCGCGGCAGTTGTCTTTT 59.537 47.619 6.13 0.00 0.00 2.27
2946 3259 0.517316 ATCGCGGCAGTTGTCTTTTC 59.483 50.000 6.13 0.00 0.00 2.29
2947 3260 0.812014 TCGCGGCAGTTGTCTTTTCA 60.812 50.000 6.13 0.00 0.00 2.69
2948 3261 0.238289 CGCGGCAGTTGTCTTTTCAT 59.762 50.000 0.00 0.00 0.00 2.57
2949 3262 1.334960 CGCGGCAGTTGTCTTTTCATT 60.335 47.619 0.00 0.00 0.00 2.57
2950 3263 2.053627 GCGGCAGTTGTCTTTTCATTG 58.946 47.619 0.00 0.00 0.00 2.82
2951 3264 2.543653 GCGGCAGTTGTCTTTTCATTGT 60.544 45.455 0.00 0.00 0.00 2.71
2952 3265 3.304391 GCGGCAGTTGTCTTTTCATTGTA 60.304 43.478 0.00 0.00 0.00 2.41
2953 3266 4.219033 CGGCAGTTGTCTTTTCATTGTAC 58.781 43.478 0.00 0.00 0.00 2.90
2954 3267 4.024048 CGGCAGTTGTCTTTTCATTGTACT 60.024 41.667 0.00 0.00 0.00 2.73
2955 3268 5.452777 GGCAGTTGTCTTTTCATTGTACTC 58.547 41.667 0.00 0.00 0.00 2.59
2956 3269 5.239525 GGCAGTTGTCTTTTCATTGTACTCT 59.760 40.000 0.00 0.00 0.00 3.24
2957 3270 6.426937 GGCAGTTGTCTTTTCATTGTACTCTA 59.573 38.462 0.00 0.00 0.00 2.43
2958 3271 7.360438 GGCAGTTGTCTTTTCATTGTACTCTAG 60.360 40.741 0.00 0.00 0.00 2.43
2959 3272 7.513968 CAGTTGTCTTTTCATTGTACTCTAGC 58.486 38.462 0.00 0.00 0.00 3.42
2960 3273 7.386299 CAGTTGTCTTTTCATTGTACTCTAGCT 59.614 37.037 0.00 0.00 0.00 3.32
2961 3274 8.585881 AGTTGTCTTTTCATTGTACTCTAGCTA 58.414 33.333 0.00 0.00 0.00 3.32
2962 3275 8.648968 GTTGTCTTTTCATTGTACTCTAGCTAC 58.351 37.037 0.00 0.00 0.00 3.58
2963 3276 7.892609 TGTCTTTTCATTGTACTCTAGCTACA 58.107 34.615 0.00 0.00 0.00 2.74
2969 3282 9.555727 TTTCATTGTACTCTAGCTACAGTTTTT 57.444 29.630 6.99 0.00 0.00 1.94
2970 3283 8.534333 TCATTGTACTCTAGCTACAGTTTTTG 57.466 34.615 6.99 1.92 0.00 2.44
2977 3290 8.764524 ACTCTAGCTACAGTTTTTGTTGATAG 57.235 34.615 0.00 7.40 46.13 2.08
3029 3347 9.019764 GGGATAAAATAACACATTTGACAATCG 57.980 33.333 0.00 0.00 0.00 3.34
3040 3358 7.148771 ACACATTTGACAATCGCATATTTTGTG 60.149 33.333 0.00 0.00 33.92 3.33
3067 3385 5.192176 AAACAAATGTTGCCAAAGTTGGAT 58.808 33.333 14.38 0.00 43.71 3.41
3069 3387 6.152492 AAACAAATGTTGCCAAAGTTGGATTT 59.848 30.769 14.38 7.75 43.71 2.17
3119 3441 7.555965 AGCCAACCAATTAGTATCCAATTTTC 58.444 34.615 0.00 0.00 0.00 2.29
3120 3442 7.400052 AGCCAACCAATTAGTATCCAATTTTCT 59.600 33.333 0.00 0.00 0.00 2.52
3121 3443 8.691797 GCCAACCAATTAGTATCCAATTTTCTA 58.308 33.333 0.00 0.00 0.00 2.10
3274 3788 8.980143 TTTGAAAAAGTCCAGTTTTACTTCTG 57.020 30.769 0.00 0.00 34.91 3.02
3378 3906 1.531423 CTAAGTAGCCGGCGGATAGA 58.469 55.000 33.44 14.96 0.00 1.98
3385 3913 0.605860 GCCGGCGGATAGACTCTCTA 60.606 60.000 33.44 0.00 32.87 2.43
3403 3931 8.343168 ACTCTCTATATATAGGTCACTTGCAC 57.657 38.462 17.81 0.00 0.00 4.57
3405 3933 6.940867 TCTCTATATATAGGTCACTTGCACGT 59.059 38.462 17.81 0.00 0.00 4.49
3437 3965 3.863142 CTTGCAAAGGGGAGAAATGAG 57.137 47.619 0.00 0.00 41.27 2.90
3438 3966 2.978156 TGCAAAGGGGAGAAATGAGT 57.022 45.000 0.00 0.00 0.00 3.41
3439 3967 3.243359 TGCAAAGGGGAGAAATGAGTT 57.757 42.857 0.00 0.00 0.00 3.01
3440 3968 3.575805 TGCAAAGGGGAGAAATGAGTTT 58.424 40.909 0.00 0.00 0.00 2.66
3441 3969 3.966665 TGCAAAGGGGAGAAATGAGTTTT 59.033 39.130 0.00 0.00 0.00 2.43
3442 3970 4.408596 TGCAAAGGGGAGAAATGAGTTTTT 59.591 37.500 0.00 0.00 0.00 1.94
3465 3993 4.586306 TTTAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
3466 3994 1.299939 AGAAAAGGAGGATGACCCCC 58.700 55.000 0.00 0.00 36.73 5.40
3467 3995 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
3468 3996 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
3474 4002 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
3480 4008 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
3481 4009 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
3482 4010 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
3485 4013 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
3486 4014 2.586245 CCTCTGCATCTGGGCGAA 59.414 61.111 0.00 0.00 36.28 4.70
3487 4015 1.078214 CCTCTGCATCTGGGCGAAA 60.078 57.895 0.00 0.00 36.28 3.46
3488 4016 1.094073 CCTCTGCATCTGGGCGAAAG 61.094 60.000 0.00 0.00 36.28 2.62
3489 4017 1.078214 TCTGCATCTGGGCGAAAGG 60.078 57.895 0.00 0.00 36.28 3.11
3490 4018 2.045045 TGCATCTGGGCGAAAGGG 60.045 61.111 0.00 0.00 36.28 3.95
3491 4019 2.830370 GCATCTGGGCGAAAGGGG 60.830 66.667 0.00 0.00 0.00 4.79
3492 4020 2.998097 CATCTGGGCGAAAGGGGA 59.002 61.111 0.00 0.00 0.00 4.81
3493 4021 1.153086 CATCTGGGCGAAAGGGGAG 60.153 63.158 0.00 0.00 0.00 4.30
3494 4022 1.306997 ATCTGGGCGAAAGGGGAGA 60.307 57.895 0.00 0.00 0.00 3.71
3495 4023 0.914417 ATCTGGGCGAAAGGGGAGAA 60.914 55.000 0.00 0.00 0.00 2.87
3496 4024 1.131303 TCTGGGCGAAAGGGGAGAAA 61.131 55.000 0.00 0.00 0.00 2.52
3497 4025 0.678048 CTGGGCGAAAGGGGAGAAAG 60.678 60.000 0.00 0.00 0.00 2.62
3498 4026 1.378646 GGGCGAAAGGGGAGAAAGG 60.379 63.158 0.00 0.00 0.00 3.11
3499 4027 1.683441 GGCGAAAGGGGAGAAAGGA 59.317 57.895 0.00 0.00 0.00 3.36
3500 4028 0.393132 GGCGAAAGGGGAGAAAGGAG 60.393 60.000 0.00 0.00 0.00 3.69
3501 4029 0.325272 GCGAAAGGGGAGAAAGGAGT 59.675 55.000 0.00 0.00 0.00 3.85
3502 4030 1.553704 GCGAAAGGGGAGAAAGGAGTA 59.446 52.381 0.00 0.00 0.00 2.59
3503 4031 2.027469 GCGAAAGGGGAGAAAGGAGTAA 60.027 50.000 0.00 0.00 0.00 2.24
3504 4032 3.558533 GCGAAAGGGGAGAAAGGAGTAAA 60.559 47.826 0.00 0.00 0.00 2.01
3505 4033 4.648651 CGAAAGGGGAGAAAGGAGTAAAA 58.351 43.478 0.00 0.00 0.00 1.52
3506 4034 4.695928 CGAAAGGGGAGAAAGGAGTAAAAG 59.304 45.833 0.00 0.00 0.00 2.27
3507 4035 4.659529 AAGGGGAGAAAGGAGTAAAAGG 57.340 45.455 0.00 0.00 0.00 3.11
3508 4036 3.610260 AGGGGAGAAAGGAGTAAAAGGT 58.390 45.455 0.00 0.00 0.00 3.50
3509 4037 4.771338 AGGGGAGAAAGGAGTAAAAGGTA 58.229 43.478 0.00 0.00 0.00 3.08
3510 4038 5.167921 AGGGGAGAAAGGAGTAAAAGGTAA 58.832 41.667 0.00 0.00 0.00 2.85
3511 4039 5.613973 AGGGGAGAAAGGAGTAAAAGGTAAA 59.386 40.000 0.00 0.00 0.00 2.01
3512 4040 6.103649 AGGGGAGAAAGGAGTAAAAGGTAAAA 59.896 38.462 0.00 0.00 0.00 1.52
3513 4041 6.779049 GGGGAGAAAGGAGTAAAAGGTAAAAA 59.221 38.462 0.00 0.00 0.00 1.94
3514 4042 7.453752 GGGGAGAAAGGAGTAAAAGGTAAAAAT 59.546 37.037 0.00 0.00 0.00 1.82
3515 4043 9.524496 GGGAGAAAGGAGTAAAAGGTAAAAATA 57.476 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.089920 GAGTTAGGACGTCCGCTACA 58.910 55.000 28.26 10.07 42.08 2.74
11 12 2.768492 CGGGGAGTTAGGACGTCCG 61.768 68.421 28.26 10.56 42.08 4.79
17 18 1.077212 CGGTCTCGGGGAGTTAGGA 60.077 63.158 0.00 0.00 0.00 2.94
21 22 2.679287 GGTCGGTCTCGGGGAGTT 60.679 66.667 0.00 0.00 36.95 3.01
29 30 0.179108 CCAAATCGAGGGTCGGTCTC 60.179 60.000 0.00 0.00 40.88 3.36
31 32 0.179108 CTCCAAATCGAGGGTCGGTC 60.179 60.000 0.00 0.00 40.88 4.79
35 36 0.531200 ACGACTCCAAATCGAGGGTC 59.469 55.000 0.78 0.00 42.25 4.46
39 40 3.489398 CCTTAGGACGACTCCAAATCGAG 60.489 52.174 0.00 0.00 42.25 4.04
41 42 2.165845 ACCTTAGGACGACTCCAAATCG 59.834 50.000 4.77 0.00 45.17 3.34
67 69 0.713883 CAGATTGGTTCGGACGTTCG 59.286 55.000 10.83 10.83 0.00 3.95
69 71 2.618053 GATCAGATTGGTTCGGACGTT 58.382 47.619 0.00 0.00 31.05 3.99
71 73 1.200483 CGATCAGATTGGTTCGGACG 58.800 55.000 0.00 0.00 31.05 4.79
74 76 3.435327 TGTTTTCGATCAGATTGGTTCGG 59.565 43.478 0.00 0.00 32.67 4.30
76 78 6.241207 TCTTGTTTTCGATCAGATTGGTTC 57.759 37.500 0.00 0.00 0.00 3.62
87 89 4.481930 TTGAACGCATCTTGTTTTCGAT 57.518 36.364 0.00 0.00 0.00 3.59
88 90 3.953874 TTGAACGCATCTTGTTTTCGA 57.046 38.095 0.00 0.00 0.00 3.71
102 104 8.591312 TGCTTTTTAAGTCTTGAATTTTGAACG 58.409 29.630 0.00 0.00 0.00 3.95
107 109 9.959749 TCGTATGCTTTTTAAGTCTTGAATTTT 57.040 25.926 0.00 0.00 0.00 1.82
145 147 3.506067 ACCAAATCGTCCCTTTGTGATTC 59.494 43.478 0.00 0.00 32.83 2.52
148 150 2.649531 ACCAAATCGTCCCTTTGTGA 57.350 45.000 0.00 0.00 32.83 3.58
149 151 3.190535 CCTTACCAAATCGTCCCTTTGTG 59.809 47.826 0.00 0.00 32.83 3.33
151 153 2.163613 GCCTTACCAAATCGTCCCTTTG 59.836 50.000 0.00 0.00 34.17 2.77
175 177 4.805219 ACAAAAGAATCCGCATGGTTAAC 58.195 39.130 0.00 0.00 36.30 2.01
194 196 7.122650 AGAGACTTGAATTTTGGACTTCAACAA 59.877 33.333 0.00 0.00 36.67 2.83
201 204 6.360618 AGACAAGAGACTTGAATTTTGGACT 58.639 36.000 16.65 0.00 0.00 3.85
220 223 5.589855 TGTGAGAAAGCATGAAAAGAGACAA 59.410 36.000 0.00 0.00 0.00 3.18
227 230 4.097135 TCCGTTTGTGAGAAAGCATGAAAA 59.903 37.500 0.00 0.00 0.00 2.29
280 283 2.341846 TTCGAGCCCATGGTTTATCC 57.658 50.000 11.73 0.00 0.00 2.59
281 284 3.694566 ACTTTTCGAGCCCATGGTTTATC 59.305 43.478 11.73 1.94 0.00 1.75
282 285 3.697166 ACTTTTCGAGCCCATGGTTTAT 58.303 40.909 11.73 0.00 0.00 1.40
283 286 3.149005 ACTTTTCGAGCCCATGGTTTA 57.851 42.857 11.73 0.00 0.00 2.01
284 287 1.995376 ACTTTTCGAGCCCATGGTTT 58.005 45.000 11.73 0.00 0.00 3.27
285 288 1.995376 AACTTTTCGAGCCCATGGTT 58.005 45.000 11.73 0.00 0.00 3.67
286 289 2.618045 CCTAACTTTTCGAGCCCATGGT 60.618 50.000 11.73 0.00 0.00 3.55
287 290 2.017049 CCTAACTTTTCGAGCCCATGG 58.983 52.381 4.14 4.14 0.00 3.66
288 291 2.711542 ACCTAACTTTTCGAGCCCATG 58.288 47.619 0.00 0.00 0.00 3.66
289 292 3.434940 AACCTAACTTTTCGAGCCCAT 57.565 42.857 0.00 0.00 0.00 4.00
290 293 2.943036 AACCTAACTTTTCGAGCCCA 57.057 45.000 0.00 0.00 0.00 5.36
291 294 3.667360 TGTAACCTAACTTTTCGAGCCC 58.333 45.455 0.00 0.00 0.00 5.19
292 295 4.694037 ACATGTAACCTAACTTTTCGAGCC 59.306 41.667 0.00 0.00 0.00 4.70
293 296 5.390567 CCACATGTAACCTAACTTTTCGAGC 60.391 44.000 0.00 0.00 0.00 5.03
294 297 5.699458 ACCACATGTAACCTAACTTTTCGAG 59.301 40.000 0.00 0.00 0.00 4.04
295 298 5.467399 CACCACATGTAACCTAACTTTTCGA 59.533 40.000 0.00 0.00 0.00 3.71
296 299 5.334569 CCACCACATGTAACCTAACTTTTCG 60.335 44.000 0.00 0.00 0.00 3.46
297 300 5.766174 TCCACCACATGTAACCTAACTTTTC 59.234 40.000 0.00 0.00 0.00 2.29
298 301 5.697067 TCCACCACATGTAACCTAACTTTT 58.303 37.500 0.00 0.00 0.00 2.27
299 302 5.313280 TCCACCACATGTAACCTAACTTT 57.687 39.130 0.00 0.00 0.00 2.66
328 331 6.596309 AGTGTATGACTTGAACTCTGATGA 57.404 37.500 0.00 0.00 0.00 2.92
333 336 5.047943 ACGCTAAGTGTATGACTTGAACTCT 60.048 40.000 0.00 0.00 45.05 3.24
335 338 5.135508 ACGCTAAGTGTATGACTTGAACT 57.864 39.130 0.00 0.00 45.05 3.01
348 351 0.040425 GCAACCACCAACGCTAAGTG 60.040 55.000 0.00 0.00 0.00 3.16
375 378 5.582550 CCTTCGAAGGCCTGAAATAAATTC 58.417 41.667 30.28 0.00 39.76 2.17
415 428 1.394917 GCACACCGTCATGAGATTGAC 59.605 52.381 0.00 0.00 42.10 3.18
430 443 3.044305 GACACTGAGCCGGCACAC 61.044 66.667 31.54 19.58 0.00 3.82
445 458 0.099082 CTTACGAGCGTCTCAGGGAC 59.901 60.000 0.00 0.00 41.28 4.46
448 463 1.433879 CCCTTACGAGCGTCTCAGG 59.566 63.158 0.00 4.01 0.00 3.86
454 469 0.034670 ACTCTACCCCTTACGAGCGT 60.035 55.000 0.00 0.00 0.00 5.07
460 475 2.545322 GCGCACATACTCTACCCCTTAC 60.545 54.545 0.30 0.00 0.00 2.34
465 480 0.179119 AACGCGCACATACTCTACCC 60.179 55.000 5.73 0.00 0.00 3.69
474 489 1.065401 CCCATGAATAAACGCGCACAT 59.935 47.619 5.73 0.00 0.00 3.21
490 509 1.108776 GCACATGCACTCATTCCCAT 58.891 50.000 0.00 0.00 41.59 4.00
492 511 1.308069 ACGCACATGCACTCATTCCC 61.308 55.000 4.49 0.00 42.21 3.97
499 518 3.126073 CTCATACATACGCACATGCACT 58.874 45.455 4.49 0.00 42.21 4.40
500 519 2.866156 ACTCATACATACGCACATGCAC 59.134 45.455 4.49 0.00 42.21 4.57
564 693 6.695278 CGTACCGGGTAGTAAATTTTCGAATA 59.305 38.462 7.25 0.00 0.00 1.75
568 697 3.000222 GCGTACCGGGTAGTAAATTTTCG 60.000 47.826 7.25 5.47 0.00 3.46
737 869 4.183101 CAGAGACAGAGAAAAGAGGATGC 58.817 47.826 0.00 0.00 0.00 3.91
753 885 2.401766 CCATGGCAACGGCAGAGAC 61.402 63.158 0.00 0.00 42.43 3.36
808 948 3.433615 GCGGTGTGATTAGGCTATGATTC 59.566 47.826 0.00 0.00 0.00 2.52
871 1012 5.570205 TGGCCAGAATAATTTATACCCGA 57.430 39.130 0.00 0.00 0.00 5.14
899 1040 1.070445 CTCGGTCCATGGCTCCATC 59.930 63.158 20.41 0.00 33.90 3.51
920 1061 5.591067 AGATGTGTCACTACCTAGCTTCTAC 59.409 44.000 4.27 0.00 0.00 2.59
938 1079 0.109086 ACACGCGGAAGAGAGATGTG 60.109 55.000 12.47 0.00 33.96 3.21
958 1099 3.444916 CAATTGACCAAGATGCAGATGC 58.555 45.455 0.00 0.00 42.50 3.91
979 1120 2.174349 CGCTCGGCTTGTTCAAGC 59.826 61.111 23.97 23.97 44.76 4.01
985 1126 2.885644 CATACGCGCTCGGCTTGT 60.886 61.111 5.73 0.00 40.44 3.16
1059 1210 0.395862 CGCCTCCTCCTACTCCTTCA 60.396 60.000 0.00 0.00 0.00 3.02
1083 1234 3.448340 CCATTCCCGCCCCAAACG 61.448 66.667 0.00 0.00 0.00 3.60
1281 1453 3.080121 CGCTTCCTCCTCCCTGCT 61.080 66.667 0.00 0.00 0.00 4.24
1709 1909 2.028385 GCGGGAAGGTGAAGAAGTCTAA 60.028 50.000 0.00 0.00 0.00 2.10
2033 2248 0.251354 CATGGGGAGTCTGTGGAGTG 59.749 60.000 0.00 0.00 0.00 3.51
2035 2250 1.222936 GCATGGGGAGTCTGTGGAG 59.777 63.158 0.00 0.00 0.00 3.86
2036 2251 0.042581 TAGCATGGGGAGTCTGTGGA 59.957 55.000 0.00 0.00 0.00 4.02
2056 2280 2.674796 AAGAAACGGCTACAGCTAGG 57.325 50.000 0.54 0.00 41.70 3.02
2243 2469 0.529773 CAATCCATGCATGCAGGTGC 60.530 55.000 28.58 5.31 45.25 5.01
2244 2470 1.107945 TCAATCCATGCATGCAGGTG 58.892 50.000 28.58 20.91 0.00 4.00
2245 2471 1.108776 GTCAATCCATGCATGCAGGT 58.891 50.000 28.58 10.57 0.00 4.00
2246 2472 1.067060 CAGTCAATCCATGCATGCAGG 59.933 52.381 26.69 25.77 0.00 4.85
2247 2473 1.536072 GCAGTCAATCCATGCATGCAG 60.536 52.381 26.69 16.97 38.98 4.41
2248 2474 0.458260 GCAGTCAATCCATGCATGCA 59.542 50.000 25.04 25.04 38.98 3.96
2249 2475 0.249322 GGCAGTCAATCCATGCATGC 60.249 55.000 21.69 11.82 41.78 4.06
2250 2476 1.107945 TGGCAGTCAATCCATGCATG 58.892 50.000 20.19 20.19 41.78 4.06
2251 2477 1.108776 GTGGCAGTCAATCCATGCAT 58.891 50.000 0.00 0.00 41.78 3.96
2271 2497 1.204062 CACTACGGCAGCAAACACG 59.796 57.895 0.00 0.00 0.00 4.49
2288 2514 2.125552 CGTTCGATCCTGCAGGCA 60.126 61.111 28.91 17.08 34.44 4.75
2290 2516 1.519455 GGACGTTCGATCCTGCAGG 60.519 63.158 27.87 27.87 33.03 4.85
2292 2518 0.249120 AATGGACGTTCGATCCTGCA 59.751 50.000 5.20 0.00 37.13 4.41
2293 2519 1.327764 GAAATGGACGTTCGATCCTGC 59.672 52.381 5.20 0.00 37.13 4.85
2294 2520 2.893637 AGAAATGGACGTTCGATCCTG 58.106 47.619 5.20 0.00 37.13 3.86
2295 2521 3.611766 AAGAAATGGACGTTCGATCCT 57.388 42.857 5.20 0.00 37.13 3.24
2296 2522 3.435671 ACAAAGAAATGGACGTTCGATCC 59.564 43.478 0.00 0.00 36.70 3.36
2324 2563 5.828747 TCATTTGCTACATACTACGAGTCC 58.171 41.667 0.00 0.00 0.00 3.85
2336 2576 7.543172 GCTTTTCAGATGAATTCATTTGCTACA 59.457 33.333 26.44 12.25 38.08 2.74
2354 2594 5.240891 TCAACCAGACATAGAGCTTTTCAG 58.759 41.667 0.00 0.00 0.00 3.02
2359 2599 5.366460 CATCATCAACCAGACATAGAGCTT 58.634 41.667 0.00 0.00 0.00 3.74
2360 2600 4.743045 GCATCATCAACCAGACATAGAGCT 60.743 45.833 0.00 0.00 0.00 4.09
2366 2606 2.812836 TGGCATCATCAACCAGACAT 57.187 45.000 0.00 0.00 0.00 3.06
2392 2632 4.329545 TCTTCCACCTGCGGCCAC 62.330 66.667 2.24 0.00 0.00 5.01
2530 2781 2.824936 TGAACTGTTACATGCCAATGGG 59.175 45.455 0.00 0.00 38.19 4.00
2531 2782 3.670359 CGTGAACTGTTACATGCCAATGG 60.670 47.826 0.00 0.00 38.19 3.16
2561 2813 8.077386 AGATCTTGCTTACTACTCGTAATTAGC 58.923 37.037 0.00 0.00 37.45 3.09
2572 2824 8.347035 CAAGTACTCCTAGATCTTGCTTACTAC 58.653 40.741 0.00 0.00 31.19 2.73
2590 2842 2.622436 CCTACAAGGCTGCAAGTACTC 58.378 52.381 0.50 0.00 35.30 2.59
2660 2920 5.414765 CGTAGGACATGCATAGGTACATAGA 59.585 44.000 0.00 0.00 0.00 1.98
2762 3022 0.750911 CCAAGAGGCTCCCTGCATTC 60.751 60.000 11.71 0.00 45.15 2.67
2764 3024 1.919600 GACCAAGAGGCTCCCTGCAT 61.920 60.000 11.71 0.19 45.15 3.96
2768 3030 1.204113 CCAAGACCAAGAGGCTCCCT 61.204 60.000 11.71 0.00 39.06 4.20
2771 3033 0.687354 TGTCCAAGACCAAGAGGCTC 59.313 55.000 6.34 6.34 39.06 4.70
2772 3034 1.366319 ATGTCCAAGACCAAGAGGCT 58.634 50.000 0.00 0.00 39.06 4.58
2773 3035 3.567478 ATATGTCCAAGACCAAGAGGC 57.433 47.619 0.00 0.00 39.06 4.70
2775 3037 5.520288 CGTACAATATGTCCAAGACCAAGAG 59.480 44.000 0.00 0.00 0.00 2.85
2776 3038 5.416083 CGTACAATATGTCCAAGACCAAGA 58.584 41.667 0.00 0.00 0.00 3.02
2777 3039 4.570772 CCGTACAATATGTCCAAGACCAAG 59.429 45.833 0.00 0.00 0.00 3.61
2778 3040 4.020039 ACCGTACAATATGTCCAAGACCAA 60.020 41.667 0.00 0.00 0.00 3.67
2779 3041 3.516300 ACCGTACAATATGTCCAAGACCA 59.484 43.478 0.00 0.00 0.00 4.02
2780 3042 4.133013 ACCGTACAATATGTCCAAGACC 57.867 45.455 0.00 0.00 0.00 3.85
2781 3043 5.063060 GTCAACCGTACAATATGTCCAAGAC 59.937 44.000 0.00 0.00 0.00 3.01
2849 3114 4.506654 CCTTCGATTATTGGTACCGAACAG 59.493 45.833 5.77 0.00 35.71 3.16
2925 3238 1.076332 AAAGACAACTGCCGCGATAC 58.924 50.000 8.23 0.00 0.00 2.24
2926 3239 1.730064 GAAAAGACAACTGCCGCGATA 59.270 47.619 8.23 0.00 0.00 2.92
2927 3240 0.517316 GAAAAGACAACTGCCGCGAT 59.483 50.000 8.23 0.00 0.00 4.58
2928 3241 0.812014 TGAAAAGACAACTGCCGCGA 60.812 50.000 8.23 0.00 0.00 5.87
2929 3242 0.238289 ATGAAAAGACAACTGCCGCG 59.762 50.000 0.00 0.00 0.00 6.46
2930 3243 2.053627 CAATGAAAAGACAACTGCCGC 58.946 47.619 0.00 0.00 0.00 6.53
2931 3244 3.354089 ACAATGAAAAGACAACTGCCG 57.646 42.857 0.00 0.00 0.00 5.69
2932 3245 5.239525 AGAGTACAATGAAAAGACAACTGCC 59.760 40.000 0.00 0.00 0.00 4.85
2933 3246 6.305693 AGAGTACAATGAAAAGACAACTGC 57.694 37.500 0.00 0.00 0.00 4.40
2934 3247 7.386299 AGCTAGAGTACAATGAAAAGACAACTG 59.614 37.037 0.00 0.00 0.00 3.16
2935 3248 7.445945 AGCTAGAGTACAATGAAAAGACAACT 58.554 34.615 0.00 0.00 0.00 3.16
2936 3249 7.659652 AGCTAGAGTACAATGAAAAGACAAC 57.340 36.000 0.00 0.00 0.00 3.32
2937 3250 8.364894 TGTAGCTAGAGTACAATGAAAAGACAA 58.635 33.333 0.00 0.00 0.00 3.18
2938 3251 7.892609 TGTAGCTAGAGTACAATGAAAAGACA 58.107 34.615 0.00 0.00 0.00 3.41
2939 3252 8.030106 ACTGTAGCTAGAGTACAATGAAAAGAC 58.970 37.037 21.23 0.00 30.04 3.01
2940 3253 8.123639 ACTGTAGCTAGAGTACAATGAAAAGA 57.876 34.615 21.23 0.00 30.04 2.52
2941 3254 8.764524 AACTGTAGCTAGAGTACAATGAAAAG 57.235 34.615 22.64 0.00 30.04 2.27
2942 3255 9.555727 AAAACTGTAGCTAGAGTACAATGAAAA 57.444 29.630 22.64 0.00 30.04 2.29
2943 3256 9.555727 AAAAACTGTAGCTAGAGTACAATGAAA 57.444 29.630 22.64 0.00 30.04 2.69
2944 3257 8.988934 CAAAAACTGTAGCTAGAGTACAATGAA 58.011 33.333 22.64 0.00 30.04 2.57
2945 3258 8.148351 ACAAAAACTGTAGCTAGAGTACAATGA 58.852 33.333 22.64 0.00 36.10 2.57
2946 3259 8.311650 ACAAAAACTGTAGCTAGAGTACAATG 57.688 34.615 22.64 19.32 36.10 2.82
2947 3260 8.774586 CAACAAAAACTGTAGCTAGAGTACAAT 58.225 33.333 22.64 5.60 37.23 2.71
2948 3261 7.982919 TCAACAAAAACTGTAGCTAGAGTACAA 59.017 33.333 22.64 2.22 37.23 2.41
2949 3262 7.494211 TCAACAAAAACTGTAGCTAGAGTACA 58.506 34.615 22.64 5.01 37.23 2.90
2950 3263 7.941795 TCAACAAAAACTGTAGCTAGAGTAC 57.058 36.000 22.64 0.00 37.23 2.73
2951 3264 9.856488 CTATCAACAAAAACTGTAGCTAGAGTA 57.144 33.333 22.64 6.19 37.23 2.59
2952 3265 8.368668 ACTATCAACAAAAACTGTAGCTAGAGT 58.631 33.333 17.40 17.40 37.23 3.24
2953 3266 8.764524 ACTATCAACAAAAACTGTAGCTAGAG 57.235 34.615 16.00 16.00 37.23 2.43
2957 3270 9.502091 TGATAACTATCAACAAAAACTGTAGCT 57.498 29.630 0.00 0.00 39.58 3.32
2958 3271 9.760660 CTGATAACTATCAACAAAAACTGTAGC 57.239 33.333 1.30 0.00 41.72 3.58
3006 3324 8.978564 TGCGATTGTCAAATGTGTTATTTTAT 57.021 26.923 0.00 0.00 0.00 1.40
3021 3339 7.936950 TTTTTCACAAAATATGCGATTGTCA 57.063 28.000 0.00 0.00 35.22 3.58
3106 3428 7.775053 TTGGCAACTTAGAAAATTGGATACT 57.225 32.000 0.00 0.00 35.02 2.12
3155 3510 5.878116 ACCAATTGTAGCTCGTTTTATGCTA 59.122 36.000 4.43 0.00 38.15 3.49
3156 3511 4.700213 ACCAATTGTAGCTCGTTTTATGCT 59.300 37.500 4.43 0.00 40.43 3.79
3161 3516 9.968870 TTTATTTAACCAATTGTAGCTCGTTTT 57.031 25.926 4.43 0.00 0.00 2.43
3195 3550 9.945904 AAACCAACTAGGACAAAACAATAAAAA 57.054 25.926 0.00 0.00 41.22 1.94
3197 3552 8.198778 GGAAACCAACTAGGACAAAACAATAAA 58.801 33.333 0.00 0.00 41.22 1.40
3198 3553 7.342284 TGGAAACCAACTAGGACAAAACAATAA 59.658 33.333 0.00 0.00 41.22 1.40
3199 3554 6.834451 TGGAAACCAACTAGGACAAAACAATA 59.166 34.615 0.00 0.00 41.22 1.90
3200 3555 5.659079 TGGAAACCAACTAGGACAAAACAAT 59.341 36.000 0.00 0.00 41.22 2.71
3201 3556 5.017490 TGGAAACCAACTAGGACAAAACAA 58.983 37.500 0.00 0.00 41.22 2.83
3202 3557 4.399934 GTGGAAACCAACTAGGACAAAACA 59.600 41.667 0.00 0.00 41.22 2.83
3203 3558 4.643334 AGTGGAAACCAACTAGGACAAAAC 59.357 41.667 0.00 0.00 41.22 2.43
3208 3563 4.886496 AGTAGTGGAAACCAACTAGGAC 57.114 45.455 0.00 0.00 41.22 3.85
3250 3764 8.117813 ACAGAAGTAAAACTGGACTTTTTCAA 57.882 30.769 0.00 0.00 36.04 2.69
3251 3765 7.696992 ACAGAAGTAAAACTGGACTTTTTCA 57.303 32.000 0.00 0.00 36.04 2.69
3252 3766 8.459635 AGAACAGAAGTAAAACTGGACTTTTTC 58.540 33.333 0.00 0.00 36.04 2.29
3256 3770 6.415573 ACAGAACAGAAGTAAAACTGGACTT 58.584 36.000 0.00 0.00 38.60 3.01
3257 3771 5.990668 ACAGAACAGAAGTAAAACTGGACT 58.009 37.500 0.00 0.00 38.30 3.85
3258 3772 6.679327 AACAGAACAGAAGTAAAACTGGAC 57.321 37.500 0.00 0.00 38.30 4.02
3274 3788 2.228822 CCATAGCACCACCAAACAGAAC 59.771 50.000 0.00 0.00 0.00 3.01
3378 3906 7.119992 CGTGCAAGTGACCTATATATAGAGAGT 59.880 40.741 19.51 9.95 32.05 3.24
3385 3913 4.262463 CCCACGTGCAAGTGACCTATATAT 60.262 45.833 30.69 0.00 44.43 0.86
3442 3970 5.330233 GGGGTCATCCTCCTTTTCTAAAAA 58.670 41.667 0.00 0.00 35.33 1.94
3443 3971 4.930696 GGGGTCATCCTCCTTTTCTAAAA 58.069 43.478 0.00 0.00 35.33 1.52
3444 3972 4.586306 GGGGTCATCCTCCTTTTCTAAA 57.414 45.455 0.00 0.00 35.33 1.85
3457 3985 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
3463 3991 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3464 3992 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
3465 3993 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
3468 3996 3.687321 TTCGCCCAGATGCAGAGGC 62.687 63.158 8.59 8.59 42.18 4.70
3469 3997 1.078214 TTTCGCCCAGATGCAGAGG 60.078 57.895 0.00 0.00 0.00 3.69
3470 3998 1.094073 CCTTTCGCCCAGATGCAGAG 61.094 60.000 0.00 0.00 0.00 3.35
3471 3999 1.078214 CCTTTCGCCCAGATGCAGA 60.078 57.895 0.00 0.00 0.00 4.26
3472 4000 2.117156 CCCTTTCGCCCAGATGCAG 61.117 63.158 0.00 0.00 0.00 4.41
3473 4001 2.045045 CCCTTTCGCCCAGATGCA 60.045 61.111 0.00 0.00 0.00 3.96
3474 4002 2.830370 CCCCTTTCGCCCAGATGC 60.830 66.667 0.00 0.00 0.00 3.91
3475 4003 1.153086 CTCCCCTTTCGCCCAGATG 60.153 63.158 0.00 0.00 0.00 2.90
3476 4004 0.914417 TTCTCCCCTTTCGCCCAGAT 60.914 55.000 0.00 0.00 0.00 2.90
3477 4005 1.131303 TTTCTCCCCTTTCGCCCAGA 61.131 55.000 0.00 0.00 0.00 3.86
3478 4006 0.678048 CTTTCTCCCCTTTCGCCCAG 60.678 60.000 0.00 0.00 0.00 4.45
3479 4007 1.378762 CTTTCTCCCCTTTCGCCCA 59.621 57.895 0.00 0.00 0.00 5.36
3480 4008 1.378646 CCTTTCTCCCCTTTCGCCC 60.379 63.158 0.00 0.00 0.00 6.13
3481 4009 0.393132 CTCCTTTCTCCCCTTTCGCC 60.393 60.000 0.00 0.00 0.00 5.54
3482 4010 0.325272 ACTCCTTTCTCCCCTTTCGC 59.675 55.000 0.00 0.00 0.00 4.70
3483 4011 3.975168 TTACTCCTTTCTCCCCTTTCG 57.025 47.619 0.00 0.00 0.00 3.46
3484 4012 5.010933 CCTTTTACTCCTTTCTCCCCTTTC 58.989 45.833 0.00 0.00 0.00 2.62
3485 4013 4.419200 ACCTTTTACTCCTTTCTCCCCTTT 59.581 41.667 0.00 0.00 0.00 3.11
3486 4014 3.988186 ACCTTTTACTCCTTTCTCCCCTT 59.012 43.478 0.00 0.00 0.00 3.95
3487 4015 3.610260 ACCTTTTACTCCTTTCTCCCCT 58.390 45.455 0.00 0.00 0.00 4.79
3488 4016 5.509832 TTACCTTTTACTCCTTTCTCCCC 57.490 43.478 0.00 0.00 0.00 4.81
3489 4017 7.828508 TTTTTACCTTTTACTCCTTTCTCCC 57.171 36.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.