Multiple sequence alignment - TraesCS1D01G330700

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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 TraesCS1D01G330700 chr1D 100.000 7207 0 0 1 7207 421029953 421022747 0.000000e+00 13309.0
1 TraesCS1D01G330700 chr1A 93.338 4143 122 43 3155 7207 517403430 517399352 0.000000e+00 5980.0
2 TraesCS1D01G330700 chr1A 91.769 1385 62 16 1581 2920 517404904 517403527 0.000000e+00 1879.0
3 TraesCS1D01G330700 chr1A 87.213 610 44 14 1114 1692 517405372 517404766 0.000000e+00 664.0
4 TraesCS1D01G330700 chr1A 92.093 430 24 5 1634 2063 232827723 232828142 1.340000e-166 597.0
5 TraesCS1D01G330700 chr1A 85.805 472 39 15 983 1447 232827240 232827690 6.540000e-130 475.0
6 TraesCS1D01G330700 chr1A 84.456 386 40 14 220 596 517407201 517406827 5.310000e-96 363.0
7 TraesCS1D01G330700 chr1A 90.987 233 14 6 713 939 517406169 517405938 2.530000e-79 307.0
8 TraesCS1D01G330700 chr1A 87.958 191 15 4 1 191 517407379 517407197 1.220000e-52 219.0
9 TraesCS1D01G330700 chr1A 96.117 103 3 1 2962 3063 517403529 517403427 4.470000e-37 167.0
10 TraesCS1D01G330700 chr1B 88.973 1977 121 37 5036 6978 570027009 570025096 0.000000e+00 2353.0
11 TraesCS1D01G330700 chr1B 91.903 1519 71 17 1581 3063 570030161 570028659 0.000000e+00 2076.0
12 TraesCS1D01G330700 chr1B 95.862 1160 36 4 3155 4309 570028662 570027510 0.000000e+00 1866.0
13 TraesCS1D01G330700 chr1B 91.458 679 38 10 806 1478 570030875 570030211 0.000000e+00 915.0
14 TraesCS1D01G330700 chr1B 89.213 445 44 4 4399 4841 570027467 570027025 2.940000e-153 553.0
15 TraesCS1D01G330700 chr1B 83.390 584 70 10 1 582 570032216 570031658 3.850000e-142 516.0
16 TraesCS1D01G330700 chr1B 85.593 118 5 3 7101 7207 570024811 570024695 5.910000e-21 113.0
17 TraesCS1D01G330700 chr3A 91.860 430 25 4 1634 2063 71337764 71338183 6.230000e-165 592.0
18 TraesCS1D01G330700 chr3A 84.107 560 55 19 906 1447 71337188 71337731 1.790000e-140 510.0
19 TraesCS1D01G330700 chr6B 84.148 593 46 27 890 1468 76914310 76914868 1.380000e-146 531.0
20 TraesCS1D01G330700 chr5A 87.474 479 29 20 901 1367 11366206 11366665 2.300000e-144 523.0
21 TraesCS1D01G330700 chr5D 87.212 391 45 2 3219 3606 342681 343069 2.390000e-119 440.0
22 TraesCS1D01G330700 chr5D 84.286 70 11 0 609 678 30957886 30957817 1.300000e-07 69.4
23 TraesCS1D01G330700 chr2D 84.985 333 39 7 6103 6429 628940991 628940664 1.940000e-85 327.0
24 TraesCS1D01G330700 chr2D 97.143 105 2 1 3062 3166 574067006 574067109 7.430000e-40 176.0
25 TraesCS1D01G330700 chr2D 100.000 35 0 0 6043 6077 628941031 628940997 1.680000e-06 65.8
26 TraesCS1D01G330700 chr4D 100.000 99 0 0 3061 3159 94883331 94883429 4.440000e-42 183.0
27 TraesCS1D01G330700 chr2A 96.364 110 4 0 3050 3159 619208140 619208031 1.600000e-41 182.0
28 TraesCS1D01G330700 chr2A 94.495 109 4 1 3062 3170 39712157 39712051 4.470000e-37 167.0
29 TraesCS1D01G330700 chr7B 96.296 108 3 1 3052 3159 421056862 421056968 7.430000e-40 176.0
30 TraesCS1D01G330700 chr7B 93.277 119 4 2 3053 3168 220430981 220431098 9.610000e-39 172.0
31 TraesCS1D01G330700 chr7A 96.262 107 4 0 3056 3162 330338608 330338714 7.430000e-40 176.0
32 TraesCS1D01G330700 chr5B 93.103 116 6 2 3062 3176 91884434 91884548 1.240000e-37 169.0
33 TraesCS1D01G330700 chrUn 94.495 109 4 1 3062 3170 12894094 12893988 4.470000e-37 167.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G330700 chr1D 421022747 421029953 7206 True 13309.000000 13309 100.000000 1 7207 1 chr1D.!!$R1 7206
1 TraesCS1D01G330700 chr1A 517399352 517407379 8027 True 1368.428571 5980 90.262571 1 7207 7 chr1A.!!$R1 7206
2 TraesCS1D01G330700 chr1A 232827240 232828142 902 False 536.000000 597 88.949000 983 2063 2 chr1A.!!$F1 1080
3 TraesCS1D01G330700 chr1B 570024695 570032216 7521 True 1198.857143 2353 89.484571 1 7207 7 chr1B.!!$R1 7206
4 TraesCS1D01G330700 chr3A 71337188 71338183 995 False 551.000000 592 87.983500 906 2063 2 chr3A.!!$F1 1157
5 TraesCS1D01G330700 chr6B 76914310 76914868 558 False 531.000000 531 84.148000 890 1468 1 chr6B.!!$F1 578

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
348 355 0.321653 ACGTTGATTCCCAGCTCCAC 60.322 55.000 0.00 0.0 0.0 4.02 F
357 364 1.153086 CCAGCTCCACCACTATGCC 60.153 63.158 0.00 0.0 0.0 4.40 F
1370 2843 0.036765 CAAATCGTCGGAAGGTGGGA 60.037 55.000 0.00 0.0 0.0 4.37 F
2470 3976 1.152589 TGTGATGGGCCTGCAACAA 60.153 52.632 4.53 0.0 0.0 2.83 F
3076 4609 1.431633 TGAAGTACTCCCTCTGTCCCA 59.568 52.381 0.00 0.0 0.0 4.37 F
4672 6219 0.534412 ATCAGCAAGTCCCGTCTCAG 59.466 55.000 0.00 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 2843 1.002134 CGGAACCAGGACAGGCAAT 60.002 57.895 0.00 0.00 0.00 3.56 R
1499 2979 1.146263 CAGACGGGTATTCTGGGCC 59.854 63.158 0.00 0.00 37.44 5.80 R
3141 4674 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12 R
4010 5547 2.011548 GCTTGATACGGTGCCATGTCA 61.012 52.381 0.00 0.00 0.00 3.58 R
5060 6613 2.989840 CAACGGTGAGCTCACTTTCTAG 59.010 50.000 38.17 25.36 45.73 2.43 R
6370 7961 0.615331 ACATTCTCATGGCCTGTCGT 59.385 50.000 3.32 0.00 34.27 4.34 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
30 31 2.892425 CCGGAGCCAATCGAGTGC 60.892 66.667 7.49 3.23 0.00 4.40
71 73 5.799827 AGCTCCTATAATTGAGTCACTCC 57.200 43.478 1.24 0.00 0.00 3.85
72 74 4.279671 AGCTCCTATAATTGAGTCACTCCG 59.720 45.833 1.24 0.00 0.00 4.63
74 76 5.221263 GCTCCTATAATTGAGTCACTCCGAA 60.221 44.000 1.24 0.00 0.00 4.30
152 154 2.669569 GGCAACGAGCTGGCAAGA 60.670 61.111 0.00 0.00 44.79 3.02
204 206 5.007234 GTGCGCATATATGTCCTTGTGTTTA 59.993 40.000 15.91 0.00 0.00 2.01
206 208 6.931840 TGCGCATATATGTCCTTGTGTTTATA 59.068 34.615 5.66 0.00 0.00 0.98
209 211 8.648097 CGCATATATGTCCTTGTGTTTATACTC 58.352 37.037 14.14 0.00 0.00 2.59
221 223 7.319052 TGTGTTTATACTCTTAACCTCCCAA 57.681 36.000 0.00 0.00 0.00 4.12
236 239 7.446106 AACCTCCCAAAATTTAGGAAAAACT 57.554 32.000 11.00 0.00 33.16 2.66
237 240 6.826668 ACCTCCCAAAATTTAGGAAAAACTG 58.173 36.000 11.00 0.08 33.16 3.16
240 243 5.131142 TCCCAAAATTTAGGAAAAACTGCCA 59.869 36.000 7.29 0.00 0.00 4.92
263 266 7.153985 CCATTGAACCATGACACTTATTTTGT 58.846 34.615 0.00 0.00 0.00 2.83
266 269 9.691362 ATTGAACCATGACACTTATTTTGTAAC 57.309 29.630 0.00 0.00 0.00 2.50
346 353 1.534729 AAACGTTGATTCCCAGCTCC 58.465 50.000 0.00 0.00 0.00 4.70
347 354 0.400213 AACGTTGATTCCCAGCTCCA 59.600 50.000 0.00 0.00 0.00 3.86
348 355 0.321653 ACGTTGATTCCCAGCTCCAC 60.322 55.000 0.00 0.00 0.00 4.02
357 364 1.153086 CCAGCTCCACCACTATGCC 60.153 63.158 0.00 0.00 0.00 4.40
377 384 3.532542 CCCTAACTCCGTTGGATCTTTC 58.467 50.000 0.00 0.00 0.00 2.62
378 385 3.055385 CCCTAACTCCGTTGGATCTTTCA 60.055 47.826 0.00 0.00 0.00 2.69
384 391 5.130350 ACTCCGTTGGATCTTTCAAAGAAA 58.870 37.500 3.35 0.00 41.63 2.52
386 393 5.130350 TCCGTTGGATCTTTCAAAGAAAGT 58.870 37.500 16.45 6.78 41.63 2.66
400 407 8.915871 TTCAAAGAAAGTGACAAAGATTTCAG 57.084 30.769 0.00 0.00 34.77 3.02
401 408 8.279970 TCAAAGAAAGTGACAAAGATTTCAGA 57.720 30.769 0.00 0.00 34.77 3.27
416 423 6.125029 AGATTTCAGACCATCCCACTTTATG 58.875 40.000 0.00 0.00 0.00 1.90
420 427 4.080356 TCAGACCATCCCACTTTATGAAGG 60.080 45.833 1.95 0.00 37.19 3.46
426 433 5.366768 CCATCCCACTTTATGAAGGTCTAGA 59.633 44.000 1.95 0.00 37.19 2.43
427 434 6.463614 CCATCCCACTTTATGAAGGTCTAGAG 60.464 46.154 1.95 0.00 37.19 2.43
436 443 4.021102 TGAAGGTCTAGAGGGCAAAAAG 57.979 45.455 0.00 0.00 0.00 2.27
441 448 4.080638 AGGTCTAGAGGGCAAAAAGATGAG 60.081 45.833 0.00 0.00 0.00 2.90
444 451 5.352846 GTCTAGAGGGCAAAAAGATGAGAAC 59.647 44.000 0.00 0.00 0.00 3.01
457 464 5.039480 AGATGAGAACACAAAAGCGATTG 57.961 39.130 0.00 3.37 36.37 2.67
471 478 7.591426 ACAAAAGCGATTGAAGTTTGAATAGAC 59.409 33.333 10.86 0.00 34.16 2.59
473 480 4.330074 AGCGATTGAAGTTTGAATAGACGG 59.670 41.667 0.00 0.00 0.00 4.79
480 487 4.124851 AGTTTGAATAGACGGTAGCCTG 57.875 45.455 0.00 0.00 0.00 4.85
502 509 3.295800 CGAGGCGGAACTAACCCT 58.704 61.111 0.00 0.00 0.00 4.34
503 510 1.153628 CGAGGCGGAACTAACCCTG 60.154 63.158 0.00 0.00 0.00 4.45
504 511 1.221021 GAGGCGGAACTAACCCTGG 59.779 63.158 0.00 0.00 0.00 4.45
528 535 7.842743 TGGTAGAACCTAACCTATACATCTTGT 59.157 37.037 0.00 0.00 39.58 3.16
561 569 2.036731 TCGAGAGAGGGGCGGAAA 59.963 61.111 0.00 0.00 34.84 3.13
579 784 4.159506 CGGAAAAGAGAGAATGAGAGAGGT 59.840 45.833 0.00 0.00 0.00 3.85
596 801 6.794534 AGAGAGGTGAAAATGAAAACCCTAT 58.205 36.000 0.00 0.00 32.85 2.57
623 1132 3.953712 TTTGATACTTCCTCTGTCGCA 57.046 42.857 0.00 0.00 0.00 5.10
624 1133 4.471904 TTTGATACTTCCTCTGTCGCAT 57.528 40.909 0.00 0.00 0.00 4.73
728 1474 3.268013 ACGAAAAGATTTTGAGCCACG 57.732 42.857 0.00 0.00 0.00 4.94
745 1491 3.057526 GCCACGGCTAAAGAAGAACAAAT 60.058 43.478 0.00 0.00 38.26 2.32
757 1505 4.761739 AGAAGAACAAATGATTTCGAGCCA 59.238 37.500 0.00 0.00 0.00 4.75
770 1518 1.968493 TCGAGCCACTCCACTTTACTT 59.032 47.619 0.00 0.00 0.00 2.24
772 1520 2.338500 GAGCCACTCCACTTTACTTCG 58.662 52.381 0.00 0.00 0.00 3.79
774 1522 2.028930 AGCCACTCCACTTTACTTCGAG 60.029 50.000 0.00 0.00 0.00 4.04
835 1861 3.741476 AGGACGCGACGGTGGTAC 61.741 66.667 15.93 0.00 0.00 3.34
1279 2749 1.202817 GGTCGGTTTTGTTGTGGTTGT 59.797 47.619 0.00 0.00 0.00 3.32
1315 2786 3.088532 TGACTGTGTTGTTTTCTTGGCT 58.911 40.909 0.00 0.00 0.00 4.75
1370 2843 0.036765 CAAATCGTCGGAAGGTGGGA 60.037 55.000 0.00 0.00 0.00 4.37
1375 2848 1.749258 GTCGGAAGGTGGGATTGCC 60.749 63.158 0.00 0.00 0.00 4.52
1383 2856 1.379044 GTGGGATTGCCTGTCCTGG 60.379 63.158 0.00 0.00 36.00 4.45
1390 2863 2.047179 GCCTGTCCTGGTTCCGTC 60.047 66.667 0.00 0.00 0.00 4.79
1401 2877 2.211806 TGGTTCCGTCCGTAAAGTTTG 58.788 47.619 0.00 0.00 0.00 2.93
1437 2917 1.607628 CAGAATTCAGGCAGGCATAGC 59.392 52.381 8.44 0.00 0.00 2.97
1487 2967 1.339134 CACGCGTCGGTGTATTTCG 59.661 57.895 9.86 0.00 34.49 3.46
1496 2976 1.795872 CGGTGTATTTCGCTTCACACA 59.204 47.619 6.10 0.00 42.40 3.72
1497 2977 2.159841 CGGTGTATTTCGCTTCACACAG 60.160 50.000 6.10 0.00 42.40 3.66
1498 2978 2.412847 GGTGTATTTCGCTTCACACAGC 60.413 50.000 6.10 0.00 42.40 4.40
1579 3059 6.017440 CCATTTTGTTCCGAGTTCTGAAGTTA 60.017 38.462 0.00 0.00 0.00 2.24
1585 3065 6.070995 TGTTCCGAGTTCTGAAGTTATACCAT 60.071 38.462 0.00 0.00 0.00 3.55
1586 3066 6.540438 TCCGAGTTCTGAAGTTATACCATT 57.460 37.500 0.00 0.00 0.00 3.16
1587 3067 6.942976 TCCGAGTTCTGAAGTTATACCATTT 58.057 36.000 0.00 0.00 0.00 2.32
1588 3068 7.391620 TCCGAGTTCTGAAGTTATACCATTTT 58.608 34.615 0.00 0.00 0.00 1.82
1589 3069 7.333423 TCCGAGTTCTGAAGTTATACCATTTTG 59.667 37.037 0.00 0.00 0.00 2.44
1590 3070 7.119262 CCGAGTTCTGAAGTTATACCATTTTGT 59.881 37.037 0.00 0.00 0.00 2.83
1591 3071 8.504005 CGAGTTCTGAAGTTATACCATTTTGTT 58.496 33.333 0.00 0.00 0.00 2.83
1592 3072 9.827411 GAGTTCTGAAGTTATACCATTTTGTTC 57.173 33.333 0.00 0.00 0.00 3.18
1593 3073 9.574516 AGTTCTGAAGTTATACCATTTTGTTCT 57.425 29.630 0.00 0.00 0.00 3.01
1594 3074 9.612620 GTTCTGAAGTTATACCATTTTGTTCTG 57.387 33.333 0.00 0.00 0.00 3.02
1595 3075 9.567776 TTCTGAAGTTATACCATTTTGTTCTGA 57.432 29.630 0.00 0.00 0.00 3.27
1596 3076 9.219603 TCTGAAGTTATACCATTTTGTTCTGAG 57.780 33.333 0.00 0.00 0.00 3.35
1597 3077 8.918202 TGAAGTTATACCATTTTGTTCTGAGT 57.082 30.769 0.00 0.00 0.00 3.41
1598 3078 9.349713 TGAAGTTATACCATTTTGTTCTGAGTT 57.650 29.630 0.00 0.00 0.00 3.01
1599 3079 9.827411 GAAGTTATACCATTTTGTTCTGAGTTC 57.173 33.333 0.00 0.00 0.00 3.01
1600 3080 9.574516 AAGTTATACCATTTTGTTCTGAGTTCT 57.425 29.630 0.00 0.00 0.00 3.01
1601 3081 9.003658 AGTTATACCATTTTGTTCTGAGTTCTG 57.996 33.333 0.00 0.00 0.00 3.02
1602 3082 8.999431 GTTATACCATTTTGTTCTGAGTTCTGA 58.001 33.333 0.00 0.00 0.00 3.27
1603 3083 9.567776 TTATACCATTTTGTTCTGAGTTCTGAA 57.432 29.630 0.00 0.00 0.00 3.02
1604 3084 6.382869 ACCATTTTGTTCTGAGTTCTGAAG 57.617 37.500 2.21 0.00 35.07 3.02
1605 3085 5.888161 ACCATTTTGTTCTGAGTTCTGAAGT 59.112 36.000 0.00 0.00 35.07 3.01
1606 3086 6.378280 ACCATTTTGTTCTGAGTTCTGAAGTT 59.622 34.615 0.00 0.00 35.07 2.66
1607 3087 7.093771 ACCATTTTGTTCTGAGTTCTGAAGTTT 60.094 33.333 0.00 0.00 35.07 2.66
1608 3088 8.405531 CCATTTTGTTCTGAGTTCTGAAGTTTA 58.594 33.333 0.00 0.00 35.07 2.01
1609 3089 9.956720 CATTTTGTTCTGAGTTCTGAAGTTTAT 57.043 29.630 0.00 0.00 35.07 1.40
1612 3092 8.603242 TTGTTCTGAGTTCTGAAGTTTATACC 57.397 34.615 0.00 0.00 35.07 2.73
1613 3093 7.732025 TGTTCTGAGTTCTGAAGTTTATACCA 58.268 34.615 0.00 0.00 35.07 3.25
1653 3133 6.210078 TGAATTTGTACCATTTTGTTCCGAC 58.790 36.000 0.00 0.00 0.00 4.79
1668 3148 2.515854 TCCGACTTCTGAAGCTGTACT 58.484 47.619 17.00 0.00 0.00 2.73
1694 3174 3.194861 TGTTCCGAGTTCTGAAGTTGTG 58.805 45.455 10.75 3.99 0.00 3.33
1891 3371 1.277273 TCAGGTCTGCATTCTGTCTGG 59.723 52.381 9.78 0.00 0.00 3.86
2050 3530 9.071276 ACAGTACTCATTTCTCATTTTCATTGT 57.929 29.630 0.00 0.00 0.00 2.71
2218 3700 5.481473 ACTCAAACACCAGATGGCATATTTT 59.519 36.000 0.00 0.00 39.32 1.82
2220 3702 7.178274 ACTCAAACACCAGATGGCATATTTTAA 59.822 33.333 0.00 0.00 39.32 1.52
2221 3703 7.319646 TCAAACACCAGATGGCATATTTTAAC 58.680 34.615 0.00 0.00 39.32 2.01
2222 3704 6.849085 AACACCAGATGGCATATTTTAACA 57.151 33.333 0.00 0.00 39.32 2.41
2229 3732 9.814899 CCAGATGGCATATTTTAACATTTAACA 57.185 29.630 0.00 0.00 0.00 2.41
2329 3832 6.161381 GTCTCGAGTTACCCAGAAAACATTA 58.839 40.000 13.13 0.00 0.00 1.90
2334 3837 8.347035 TCGAGTTACCCAGAAAACATTAAAAAG 58.653 33.333 0.00 0.00 0.00 2.27
2358 3861 8.324163 AGCCTGAAACAAAACATACTAAGTAG 57.676 34.615 0.00 0.00 0.00 2.57
2421 3927 5.617252 CAGAAAGGAGTAAAACCACACCTA 58.383 41.667 0.00 0.00 38.40 3.08
2469 3975 1.902918 GTGTGATGGGCCTGCAACA 60.903 57.895 4.53 1.14 0.00 3.33
2470 3976 1.152589 TGTGATGGGCCTGCAACAA 60.153 52.632 4.53 0.00 0.00 2.83
2496 4010 3.544684 ACTCAATGCTGTGTCTTGTTCA 58.455 40.909 0.00 0.00 0.00 3.18
2503 4017 4.136051 TGCTGTGTCTTGTTCATGATTGA 58.864 39.130 0.00 0.00 0.00 2.57
2544 4058 2.168521 GGCCTCTCTAGTTGCATGTGTA 59.831 50.000 0.00 0.00 0.00 2.90
2590 4121 2.056815 TTGCCAGTGCTTGCAACCA 61.057 52.632 6.60 0.00 42.19 3.67
2716 4247 9.507329 TCTAGCAATTAATGGTTCCATTATCTC 57.493 33.333 20.46 12.29 40.93 2.75
2908 4441 5.217978 ACAAGTGGATTACGTTTGGAGTA 57.782 39.130 0.00 0.00 0.00 2.59
2989 4522 2.537401 GTACCATACACTCGGCTTGAC 58.463 52.381 0.00 0.00 0.00 3.18
3073 4606 9.886132 TTATTTTTATGAAGTACTCCCTCTGTC 57.114 33.333 0.00 0.00 0.00 3.51
3074 4607 5.934402 TTTATGAAGTACTCCCTCTGTCC 57.066 43.478 0.00 0.00 0.00 4.02
3075 4608 2.233305 TGAAGTACTCCCTCTGTCCC 57.767 55.000 0.00 0.00 0.00 4.46
3076 4609 1.431633 TGAAGTACTCCCTCTGTCCCA 59.568 52.381 0.00 0.00 0.00 4.37
3077 4610 2.158219 TGAAGTACTCCCTCTGTCCCAA 60.158 50.000 0.00 0.00 0.00 4.12
3078 4611 2.715763 AGTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
3079 4612 2.986050 AGTACTCCCTCTGTCCCAAAA 58.014 47.619 0.00 0.00 0.00 2.44
3080 4613 3.532102 AGTACTCCCTCTGTCCCAAAAT 58.468 45.455 0.00 0.00 0.00 1.82
3081 4614 4.695606 AGTACTCCCTCTGTCCCAAAATA 58.304 43.478 0.00 0.00 0.00 1.40
3082 4615 5.098663 AGTACTCCCTCTGTCCCAAAATAA 58.901 41.667 0.00 0.00 0.00 1.40
3083 4616 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
3084 4617 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
3085 4618 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
3086 4619 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
3087 4620 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
3088 4621 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
3089 4622 5.316987 CCTCTGTCCCAAAATAAGTGTCTT 58.683 41.667 0.00 0.00 0.00 3.01
3090 4623 6.472887 CCTCTGTCCCAAAATAAGTGTCTTA 58.527 40.000 0.00 0.00 0.00 2.10
3091 4624 6.940298 CCTCTGTCCCAAAATAAGTGTCTTAA 59.060 38.462 0.00 0.00 0.00 1.85
3092 4625 7.094762 CCTCTGTCCCAAAATAAGTGTCTTAAC 60.095 40.741 0.00 0.00 0.00 2.01
3093 4626 7.514721 TCTGTCCCAAAATAAGTGTCTTAACT 58.485 34.615 0.00 0.00 0.00 2.24
3094 4627 7.996644 TCTGTCCCAAAATAAGTGTCTTAACTT 59.003 33.333 0.00 0.00 42.89 2.66
3095 4628 8.528044 TGTCCCAAAATAAGTGTCTTAACTTT 57.472 30.769 0.00 0.00 40.77 2.66
3096 4629 8.410141 TGTCCCAAAATAAGTGTCTTAACTTTG 58.590 33.333 14.00 14.00 40.77 2.77
3097 4630 8.410912 GTCCCAAAATAAGTGTCTTAACTTTGT 58.589 33.333 16.72 0.00 40.77 2.83
3098 4631 9.629878 TCCCAAAATAAGTGTCTTAACTTTGTA 57.370 29.630 16.72 8.94 40.77 2.41
3099 4632 9.673454 CCCAAAATAAGTGTCTTAACTTTGTAC 57.327 33.333 16.72 0.00 40.77 2.90
3105 4638 9.857957 ATAAGTGTCTTAACTTTGTACTAGCTC 57.142 33.333 0.00 0.00 40.77 4.09
3106 4639 7.527568 AGTGTCTTAACTTTGTACTAGCTCT 57.472 36.000 0.00 0.00 0.00 4.09
3107 4640 8.632906 AGTGTCTTAACTTTGTACTAGCTCTA 57.367 34.615 0.00 0.00 0.00 2.43
3108 4641 8.732531 AGTGTCTTAACTTTGTACTAGCTCTAG 58.267 37.037 0.00 2.55 39.04 2.43
3110 4643 9.730705 TGTCTTAACTTTGTACTAGCTCTAGTA 57.269 33.333 11.59 11.59 43.98 1.82
3134 4667 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
3135 4668 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
3136 4669 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
3137 4670 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
3138 4671 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
3139 4672 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
3140 4673 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
3141 4674 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
3142 4675 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
3143 4676 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
3144 4677 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
3145 4678 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
3146 4679 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
3147 4680 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
3148 4681 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
3149 4682 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
3150 4683 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
3151 4684 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3152 4685 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3153 4686 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3154 4687 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3155 4688 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3156 4689 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3157 4690 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3188 4721 6.767524 ATGAACTTGTGAAAAGTGGTTACA 57.232 33.333 0.00 0.00 0.00 2.41
3222 4755 4.394920 TGTCTTTTCTGTTCACACACCTTC 59.605 41.667 0.00 0.00 0.00 3.46
3275 4808 3.748048 CACTCGATGACACCAGAAATTGT 59.252 43.478 0.00 0.00 0.00 2.71
3396 4929 5.388654 ACATCAAAATGGACTTCTGGAACT 58.611 37.500 0.00 0.00 37.19 3.01
3413 4946 5.061179 TGGAACTAGTGTTAAGTTTGAGGC 58.939 41.667 0.00 0.00 37.31 4.70
3423 4956 3.334583 AAGTTTGAGGCGAGCATCTAA 57.665 42.857 11.05 6.89 0.00 2.10
4010 5547 2.282887 GGCGGTTCCATTGTGGGT 60.283 61.111 0.00 0.00 38.32 4.51
4233 5770 7.369551 TCCAAGAACCAGAAGTAACTAGAAA 57.630 36.000 0.00 0.00 0.00 2.52
4238 5775 6.369065 AGAACCAGAAGTAACTAGAAATTGCG 59.631 38.462 0.00 0.00 0.00 4.85
4300 5837 8.948631 AGATGTGTACATATTTACTTGGACTG 57.051 34.615 6.55 0.00 36.57 3.51
4381 5927 4.906618 TCTCTTTTACCCATTGTGGTCTC 58.093 43.478 0.73 0.00 39.91 3.36
4460 6006 4.989277 TGCATGCAAGAGGAATATACCAT 58.011 39.130 20.30 0.00 0.00 3.55
4496 6042 4.100035 ACTGCGATGAGGAATTCATAGTCA 59.900 41.667 7.93 4.80 46.51 3.41
4671 6218 0.976641 AATCAGCAAGTCCCGTCTCA 59.023 50.000 0.00 0.00 0.00 3.27
4672 6219 0.534412 ATCAGCAAGTCCCGTCTCAG 59.466 55.000 0.00 0.00 0.00 3.35
4903 6456 3.887621 TGCTGGATAGAGTTACACACC 57.112 47.619 0.00 0.00 0.00 4.16
4965 6518 3.904339 ACCACTCATGACTGGAACTACTT 59.096 43.478 23.51 1.49 0.00 2.24
5060 6613 5.501156 AGAATTGTCCTGGGATTGTTCTAC 58.499 41.667 0.00 0.00 0.00 2.59
5071 6624 6.936279 TGGGATTGTTCTACTAGAAAGTGAG 58.064 40.000 0.00 0.00 35.75 3.51
5096 6649 1.944024 CCGTTGGTGCTGTCACTTAAA 59.056 47.619 0.00 0.00 42.72 1.52
5109 6662 6.073167 GCTGTCACTTAAAGTTTTCCCTAGAC 60.073 42.308 0.00 0.00 0.00 2.59
5110 6663 7.133133 TGTCACTTAAAGTTTTCCCTAGACT 57.867 36.000 0.00 0.00 0.00 3.24
5111 6664 8.253867 TGTCACTTAAAGTTTTCCCTAGACTA 57.746 34.615 0.00 0.00 0.00 2.59
5112 6665 8.365647 TGTCACTTAAAGTTTTCCCTAGACTAG 58.634 37.037 2.18 2.18 0.00 2.57
5113 6666 8.583296 GTCACTTAAAGTTTTCCCTAGACTAGA 58.417 37.037 11.27 0.00 0.00 2.43
5114 6667 8.804204 TCACTTAAAGTTTTCCCTAGACTAGAG 58.196 37.037 11.27 0.00 0.00 2.43
5171 6724 5.767665 TGGAAATCCATACCGGTTGATATTG 59.232 40.000 15.04 0.00 42.01 1.90
5273 6829 5.046304 TCTCGAAGGTTCTCTTTTCATGGAT 60.046 40.000 0.00 0.00 35.50 3.41
5279 6835 1.745087 TCTCTTTTCATGGATTGCGGC 59.255 47.619 0.00 0.00 0.00 6.53
5488 7046 7.790782 TCATAAAGTAAAAATGAGGGGCTTT 57.209 32.000 0.00 0.00 0.00 3.51
5507 7065 4.085517 GCTTTATTTACAGTCGCTCGCTAG 60.086 45.833 0.00 0.00 0.00 3.42
5566 7124 1.109323 AAAGCAAGCACGCCTTCCTT 61.109 50.000 0.00 0.00 32.91 3.36
5842 7408 4.405680 AGCATACTGTACCATAGAGCACAA 59.594 41.667 0.00 0.00 0.00 3.33
5858 7424 5.239525 AGAGCACAAATTGGACAAGAGTTAC 59.760 40.000 0.00 0.00 0.00 2.50
6003 7577 6.986817 AGTATTTCCTTGACCATACTCATTCG 59.013 38.462 0.00 0.00 28.10 3.34
6006 7580 3.517901 TCCTTGACCATACTCATTCGGTT 59.482 43.478 0.00 0.00 0.00 4.44
6015 7589 0.445436 CTCATTCGGTTCTGCTGTGC 59.555 55.000 0.00 0.00 0.00 4.57
6016 7590 0.250252 TCATTCGGTTCTGCTGTGCA 60.250 50.000 0.00 0.00 36.92 4.57
6211 7802 1.871408 CGGTGCTGGCTCATAGATCAC 60.871 57.143 0.00 0.00 0.00 3.06
6241 7832 7.366847 ACATACCTGACATAGCATAGAGTTT 57.633 36.000 0.00 0.00 0.00 2.66
6279 7870 1.004918 ACCTCTCCGCAGTTTTCCG 60.005 57.895 0.00 0.00 0.00 4.30
6363 7954 4.083271 GGTTGTTGTTATCTTCTGCTGGAC 60.083 45.833 0.00 0.00 0.00 4.02
6371 7962 4.361253 TCTGCTGGACGCTGAAAC 57.639 55.556 0.00 0.00 42.63 2.78
6508 8101 1.489481 TCCATCGGAGATGCTCAAGT 58.511 50.000 4.60 0.00 45.12 3.16
6512 8105 2.662006 TCGGAGATGCTCAAGTTGAG 57.338 50.000 25.68 25.68 46.90 3.02
6586 8183 4.347000 TGTACAGTTTTAGGAGGAGCTGTT 59.653 41.667 0.00 0.00 38.09 3.16
6607 8204 1.137872 TGATTTGCCGCCACAGTTTTT 59.862 42.857 0.00 0.00 0.00 1.94
6673 8273 1.233019 GGATGCGCTGATGTTGCTAT 58.767 50.000 9.73 0.00 0.00 2.97
6731 8331 1.893808 CTTCACCGGTGCACTGCTT 60.894 57.895 30.25 6.16 0.00 3.91
6780 8380 3.621715 ACGATTGTCCTATTTTTCCGAGC 59.378 43.478 0.00 0.00 0.00 5.03
6855 8455 1.571460 CTTCGCTTCACTGCCACAC 59.429 57.895 0.00 0.00 0.00 3.82
6863 8463 0.751277 TCACTGCCACACAAACTGGG 60.751 55.000 0.00 0.00 0.00 4.45
6908 8508 6.767456 ACCCTGAATTTTGAAAATGCATACA 58.233 32.000 11.51 0.00 0.00 2.29
6929 8538 1.264557 CATCGTAGCGAGGTAGGTCAG 59.735 57.143 0.00 0.00 39.91 3.51
6930 8539 0.463295 TCGTAGCGAGGTAGGTCAGG 60.463 60.000 0.00 0.00 0.00 3.86
6931 8540 0.747283 CGTAGCGAGGTAGGTCAGGT 60.747 60.000 0.00 0.00 0.00 4.00
6932 8541 0.739561 GTAGCGAGGTAGGTCAGGTG 59.260 60.000 0.00 0.00 0.00 4.00
6933 8542 0.395311 TAGCGAGGTAGGTCAGGTGG 60.395 60.000 0.00 0.00 0.00 4.61
6934 8543 1.681327 GCGAGGTAGGTCAGGTGGA 60.681 63.158 0.00 0.00 0.00 4.02
6935 8544 1.946475 GCGAGGTAGGTCAGGTGGAC 61.946 65.000 0.00 0.00 46.20 4.02
6962 8571 2.762535 ATTATACGGGGCAATCGAGG 57.237 50.000 0.00 0.00 0.00 4.63
6978 8587 1.364626 GAGGCTGAAGATGGTGCACG 61.365 60.000 11.45 0.00 0.00 5.34
6979 8588 2.401766 GGCTGAAGATGGTGCACGG 61.402 63.158 11.45 0.00 0.00 4.94
6980 8589 3.044059 GCTGAAGATGGTGCACGGC 62.044 63.158 11.45 2.25 0.00 5.68
6981 8590 1.376424 CTGAAGATGGTGCACGGCT 60.376 57.895 11.45 4.80 0.00 5.52
6982 8591 0.108186 CTGAAGATGGTGCACGGCTA 60.108 55.000 11.45 0.00 0.00 3.93
6983 8592 0.391130 TGAAGATGGTGCACGGCTAC 60.391 55.000 11.45 0.00 0.00 3.58
7001 8678 1.176527 ACGGCCAATGTTTCCTGATG 58.823 50.000 2.24 0.00 0.00 3.07
7018 8695 6.546484 TCCTGATGGTCTTCTTTTCTGAAAT 58.454 36.000 3.31 0.00 34.23 2.17
7092 8791 4.572795 GCTTCTACTGCCTCTTAATTCCAC 59.427 45.833 0.00 0.00 0.00 4.02
7102 8801 4.440802 CCTCTTAATTCCACGAGTCCTGAG 60.441 50.000 0.00 0.00 0.00 3.35
7111 8894 0.387202 CGAGTCCTGAGCGATTGGAT 59.613 55.000 0.00 0.00 32.03 3.41
7148 8931 5.106436 CCAAACCCGAATCTTTTGTAGGTAC 60.106 44.000 0.00 0.00 0.00 3.34
7150 8933 5.231702 ACCCGAATCTTTTGTAGGTACAA 57.768 39.130 0.00 0.00 43.80 2.41
7175 8969 5.858381 ACACAGCTTAATTTCTCAGTCTGA 58.142 37.500 1.78 1.78 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.514577 ACTCGATTGGCTCCGGCG 62.515 66.667 0.00 0.00 39.81 6.46
30 31 2.416431 GCTAGCTTGCCATGAAACTTGG 60.416 50.000 9.15 0.00 37.31 3.61
71 73 0.813610 TGTGGCTCCAACACTGTTCG 60.814 55.000 0.00 0.00 39.52 3.95
72 74 1.388547 TTGTGGCTCCAACACTGTTC 58.611 50.000 0.00 0.00 39.52 3.18
74 76 1.102978 GTTTGTGGCTCCAACACTGT 58.897 50.000 0.00 0.00 39.52 3.55
152 154 5.143369 GGGATTATGAAGGAAATCTTGGCT 58.857 41.667 0.00 0.00 35.50 4.75
166 168 1.308047 GCGCACATGTGGGATTATGA 58.692 50.000 38.26 0.00 45.10 2.15
204 206 8.842764 TCCTAAATTTTGGGAGGTTAAGAGTAT 58.157 33.333 17.07 0.00 35.14 2.12
206 208 7.098845 TCCTAAATTTTGGGAGGTTAAGAGT 57.901 36.000 17.07 0.00 35.14 3.24
209 211 9.268268 GTTTTTCCTAAATTTTGGGAGGTTAAG 57.732 33.333 17.07 0.00 41.63 1.85
221 223 7.228507 GGTTCAATGGCAGTTTTTCCTAAATTT 59.771 33.333 0.00 0.00 0.00 1.82
236 239 2.291209 AGTGTCATGGTTCAATGGCA 57.709 45.000 0.00 0.00 39.78 4.92
237 240 4.989279 ATAAGTGTCATGGTTCAATGGC 57.011 40.909 0.00 0.00 32.60 4.40
240 243 9.691362 GTTACAAAATAAGTGTCATGGTTCAAT 57.309 29.630 0.00 0.00 0.00 2.57
306 313 1.347707 AGAGGCCAAATGAGTCGAACA 59.652 47.619 5.01 0.00 0.00 3.18
310 317 2.348666 CGTTTAGAGGCCAAATGAGTCG 59.651 50.000 5.01 0.00 0.00 4.18
346 353 1.202533 CGGAGTTAGGGCATAGTGGTG 60.203 57.143 0.00 0.00 0.00 4.17
347 354 1.120530 CGGAGTTAGGGCATAGTGGT 58.879 55.000 0.00 0.00 0.00 4.16
348 355 1.120530 ACGGAGTTAGGGCATAGTGG 58.879 55.000 0.00 0.00 37.78 4.00
357 364 7.018782 TCTTTGAAAGATCCAACGGAGTTAGG 61.019 42.308 3.02 0.00 40.24 2.69
377 384 7.433425 GGTCTGAAATCTTTGTCACTTTCTTTG 59.567 37.037 0.00 0.00 0.00 2.77
378 385 7.122650 TGGTCTGAAATCTTTGTCACTTTCTTT 59.877 33.333 0.00 0.00 0.00 2.52
384 391 5.006386 GGATGGTCTGAAATCTTTGTCACT 58.994 41.667 2.68 0.00 0.00 3.41
386 393 4.202556 TGGGATGGTCTGAAATCTTTGTCA 60.203 41.667 2.68 0.00 0.00 3.58
400 407 4.200092 GACCTTCATAAAGTGGGATGGTC 58.800 47.826 9.30 9.30 43.85 4.02
401 408 3.852578 AGACCTTCATAAAGTGGGATGGT 59.147 43.478 0.00 0.00 40.53 3.55
416 423 4.287766 TCTTTTTGCCCTCTAGACCTTC 57.712 45.455 0.00 0.00 0.00 3.46
420 427 5.091261 TCTCATCTTTTTGCCCTCTAGAC 57.909 43.478 0.00 0.00 0.00 2.59
426 433 3.565307 TGTGTTCTCATCTTTTTGCCCT 58.435 40.909 0.00 0.00 0.00 5.19
427 434 4.320608 TTGTGTTCTCATCTTTTTGCCC 57.679 40.909 0.00 0.00 0.00 5.36
436 443 5.034554 TCAATCGCTTTTGTGTTCTCATC 57.965 39.130 0.00 0.00 0.00 2.92
441 448 5.514914 TCAAACTTCAATCGCTTTTGTGTTC 59.485 36.000 0.00 0.00 0.00 3.18
444 451 5.947503 TTCAAACTTCAATCGCTTTTGTG 57.052 34.783 0.00 0.00 0.00 3.33
457 464 4.567159 CAGGCTACCGTCTATTCAAACTTC 59.433 45.833 0.00 0.00 0.00 3.01
502 509 7.842743 ACAAGATGTATAGGTTAGGTTCTACCA 59.157 37.037 0.00 0.00 41.95 3.25
503 510 8.142551 CACAAGATGTATAGGTTAGGTTCTACC 58.857 40.741 0.00 0.00 38.99 3.18
504 511 8.910944 TCACAAGATGTATAGGTTAGGTTCTAC 58.089 37.037 0.00 0.00 0.00 2.59
528 535 2.305052 TCTCGAGAGTCTACCCAAGTCA 59.695 50.000 12.08 0.00 0.00 3.41
561 569 6.678568 TTTTCACCTCTCTCATTCTCTCTT 57.321 37.500 0.00 0.00 0.00 2.85
596 801 9.042008 GCGACAGAGGAAGTATCAAATATTTTA 57.958 33.333 0.00 0.00 0.00 1.52
612 1121 6.521162 TGCTTTTATATTATGCGACAGAGGA 58.479 36.000 0.00 0.00 0.00 3.71
617 1126 9.794685 TCAAAAATGCTTTTATATTATGCGACA 57.205 25.926 0.00 0.00 32.85 4.35
706 1315 4.148891 CGTGGCTCAAAATCTTTTCGTAC 58.851 43.478 0.00 0.00 0.00 3.67
728 1474 7.305474 TCGAAATCATTTGTTCTTCTTTAGCC 58.695 34.615 0.00 0.00 0.00 3.93
740 1486 2.749621 GGAGTGGCTCGAAATCATTTGT 59.250 45.455 0.00 0.00 0.00 2.83
741 1487 2.749076 TGGAGTGGCTCGAAATCATTTG 59.251 45.455 0.00 0.00 0.00 2.32
745 1491 0.976641 AGTGGAGTGGCTCGAAATCA 59.023 50.000 0.00 0.00 0.00 2.57
757 1505 1.275573 GGGCTCGAAGTAAAGTGGAGT 59.724 52.381 0.00 0.00 0.00 3.85
835 1861 2.513897 GGATTGCTTCGGTCGGGG 60.514 66.667 0.00 0.00 0.00 5.73
944 2001 4.899239 CATGCGGCGGAGGAGGTC 62.899 72.222 7.44 0.00 0.00 3.85
1279 2749 1.067295 AGTCAGCAATCCAAGGTCCA 58.933 50.000 0.00 0.00 0.00 4.02
1315 2786 1.956477 GGAGCTGCTGAAAAGGAACAA 59.044 47.619 7.01 0.00 0.00 2.83
1370 2843 1.002134 CGGAACCAGGACAGGCAAT 60.002 57.895 0.00 0.00 0.00 3.56
1375 2848 1.246056 TACGGACGGAACCAGGACAG 61.246 60.000 0.00 0.00 0.00 3.51
1383 2856 2.609002 ACACAAACTTTACGGACGGAAC 59.391 45.455 0.00 0.00 0.00 3.62
1390 2863 5.182380 ACCCATATGAACACAAACTTTACGG 59.818 40.000 3.65 0.00 0.00 4.02
1401 2877 5.647658 TGAATTCTGTGACCCATATGAACAC 59.352 40.000 3.65 11.24 0.00 3.32
1437 2917 2.202388 CGCGCACAAATCAGCCAG 60.202 61.111 8.75 0.00 0.00 4.85
1496 2976 3.861797 CGGGTATTCTGGGCCGCT 61.862 66.667 0.00 0.00 0.00 5.52
1497 2977 4.171103 ACGGGTATTCTGGGCCGC 62.171 66.667 0.00 0.00 0.00 6.53
1498 2978 2.108362 GACGGGTATTCTGGGCCG 59.892 66.667 0.00 0.00 0.00 6.13
1499 2979 1.146263 CAGACGGGTATTCTGGGCC 59.854 63.158 0.00 0.00 37.44 5.80
1500 2980 4.857251 CAGACGGGTATTCTGGGC 57.143 61.111 0.00 0.00 37.44 5.36
1579 3059 7.721399 ACTTCAGAACTCAGAACAAAATGGTAT 59.279 33.333 0.00 0.00 0.00 2.73
1586 3066 9.052759 GGTATAAACTTCAGAACTCAGAACAAA 57.947 33.333 0.00 0.00 0.00 2.83
1587 3067 8.208224 TGGTATAAACTTCAGAACTCAGAACAA 58.792 33.333 0.00 0.00 0.00 2.83
1588 3068 7.732025 TGGTATAAACTTCAGAACTCAGAACA 58.268 34.615 0.00 0.00 0.00 3.18
1589 3069 8.779354 ATGGTATAAACTTCAGAACTCAGAAC 57.221 34.615 0.00 0.00 0.00 3.01
1590 3070 9.793259 AAATGGTATAAACTTCAGAACTCAGAA 57.207 29.630 0.00 0.00 0.00 3.02
1591 3071 9.793259 AAAATGGTATAAACTTCAGAACTCAGA 57.207 29.630 0.00 0.00 0.00 3.27
1592 3072 9.831737 CAAAATGGTATAAACTTCAGAACTCAG 57.168 33.333 0.00 0.00 0.00 3.35
1593 3073 9.349713 ACAAAATGGTATAAACTTCAGAACTCA 57.650 29.630 0.00 0.00 0.00 3.41
1598 3078 9.567776 TCAGAACAAAATGGTATAAACTTCAGA 57.432 29.630 0.00 0.00 0.00 3.27
1610 3090 9.048446 CAAATTCAGAAATCAGAACAAAATGGT 57.952 29.630 0.00 0.00 0.00 3.55
1611 3091 9.048446 ACAAATTCAGAAATCAGAACAAAATGG 57.952 29.630 0.00 0.00 0.00 3.16
1653 3133 7.522374 GGAACAAAATAGTACAGCTTCAGAAG 58.478 38.462 5.72 5.72 0.00 2.85
1668 3148 6.540914 ACAACTTCAGAACTCGGAACAAAATA 59.459 34.615 0.00 0.00 0.00 1.40
1694 3174 4.305989 TCACAACTCAGAACAAAATGGC 57.694 40.909 0.00 0.00 0.00 4.40
1891 3371 6.969473 GCTCAATTAAGAAGCCAAGATACAAC 59.031 38.462 0.00 0.00 0.00 3.32
2050 3530 7.378966 CAGAGAACACCACAGACTTAGAATAA 58.621 38.462 0.00 0.00 0.00 1.40
2059 3539 1.202580 AGTGCAGAGAACACCACAGAC 60.203 52.381 0.00 0.00 38.87 3.51
2320 3823 9.833182 TTTTGTTTCAGGCTTTTTAATGTTTTC 57.167 25.926 0.00 0.00 0.00 2.29
2329 3832 9.313118 CTTAGTATGTTTTGTTTCAGGCTTTTT 57.687 29.630 0.00 0.00 0.00 1.94
2334 3837 8.319143 TCTACTTAGTATGTTTTGTTTCAGGC 57.681 34.615 0.00 0.00 0.00 4.85
2358 3861 4.883083 TCTCAGATACTGGTGTGTTGTTC 58.117 43.478 0.00 0.00 31.51 3.18
2363 3866 6.437477 TGTCTAAATCTCAGATACTGGTGTGT 59.563 38.462 0.00 0.00 31.51 3.72
2421 3927 1.202734 AGTGAGAATGTGTGCTGCAGT 60.203 47.619 16.64 0.00 0.00 4.40
2469 3975 7.042797 ACAAGACACAGCATTGAGTATTTTT 57.957 32.000 0.00 0.00 28.91 1.94
2470 3976 6.639632 ACAAGACACAGCATTGAGTATTTT 57.360 33.333 0.00 0.00 28.91 1.82
2503 4017 8.230306 AGAGGCCTAATAATTGATTCTCCATTT 58.770 33.333 4.42 0.00 0.00 2.32
2590 4121 3.400054 GGGCGGCTACCTCAGGTT 61.400 66.667 0.00 0.00 37.09 3.50
2716 4247 2.031157 GGTCACCAAACCAATCAACTCG 60.031 50.000 0.00 0.00 39.27 4.18
3022 4555 2.749076 CCCGATCAACTTGCATGAAAGA 59.251 45.455 20.85 0.00 0.00 2.52
3063 4596 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
3064 4597 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
3065 4598 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
3066 4599 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
3067 4600 7.661847 AGTTAAGACACTTATTTTGGGACAGAG 59.338 37.037 0.00 0.00 42.39 3.35
3068 4601 7.514721 AGTTAAGACACTTATTTTGGGACAGA 58.485 34.615 0.00 0.00 42.39 3.41
3069 4602 7.745620 AGTTAAGACACTTATTTTGGGACAG 57.254 36.000 0.00 0.00 42.39 3.51
3070 4603 8.410141 CAAAGTTAAGACACTTATTTTGGGACA 58.590 33.333 0.92 0.00 35.87 4.02
3071 4604 8.410912 ACAAAGTTAAGACACTTATTTTGGGAC 58.589 33.333 19.96 6.58 35.87 4.46
3072 4605 8.528044 ACAAAGTTAAGACACTTATTTTGGGA 57.472 30.769 19.96 0.00 35.87 4.37
3073 4606 9.673454 GTACAAAGTTAAGACACTTATTTTGGG 57.327 33.333 19.96 8.06 35.87 4.12
3079 4612 9.857957 GAGCTAGTACAAAGTTAAGACACTTAT 57.142 33.333 0.00 0.00 35.87 1.73
3080 4613 9.075678 AGAGCTAGTACAAAGTTAAGACACTTA 57.924 33.333 0.00 0.00 35.87 2.24
3081 4614 7.953752 AGAGCTAGTACAAAGTTAAGACACTT 58.046 34.615 0.00 0.00 38.74 3.16
3082 4615 7.527568 AGAGCTAGTACAAAGTTAAGACACT 57.472 36.000 0.00 0.00 0.00 3.55
3083 4616 8.513774 ACTAGAGCTAGTACAAAGTTAAGACAC 58.486 37.037 8.35 0.00 43.98 3.67
3084 4617 8.632906 ACTAGAGCTAGTACAAAGTTAAGACA 57.367 34.615 8.35 0.00 43.98 3.41
3109 4642 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
3110 4643 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
3111 4644 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
3112 4645 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
3113 4646 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
3114 4647 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
3115 4648 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
3116 4649 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
3117 4650 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
3118 4651 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
3119 4652 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
3120 4653 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
3121 4654 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
3122 4655 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
3123 4656 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
3124 4657 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
3125 4658 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
3126 4659 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
3127 4660 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
3128 4661 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
3129 4662 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
3130 4663 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3131 4664 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3132 4665 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3133 4666 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3134 4667 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3135 4668 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3136 4669 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3137 4670 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3138 4671 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3139 4672 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
3140 4673 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
3141 4674 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3142 4675 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
3143 4676 1.962100 CTTACATACTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
3144 4677 2.664015 ACTTACATACTCCCTCCGTCC 58.336 52.381 0.00 0.00 0.00 4.79
3145 4678 5.068636 TCATACTTACATACTCCCTCCGTC 58.931 45.833 0.00 0.00 0.00 4.79
3146 4679 5.057843 TCATACTTACATACTCCCTCCGT 57.942 43.478 0.00 0.00 0.00 4.69
3147 4680 5.535406 AGTTCATACTTACATACTCCCTCCG 59.465 44.000 0.00 0.00 0.00 4.63
3148 4681 6.980416 AGTTCATACTTACATACTCCCTCC 57.020 41.667 0.00 0.00 0.00 4.30
3149 4682 7.707035 CACAAGTTCATACTTACATACTCCCTC 59.293 40.741 0.00 0.00 42.67 4.30
3150 4683 7.399191 TCACAAGTTCATACTTACATACTCCCT 59.601 37.037 0.00 0.00 42.67 4.20
3151 4684 7.553334 TCACAAGTTCATACTTACATACTCCC 58.447 38.462 0.00 0.00 42.67 4.30
3152 4685 8.997621 TTCACAAGTTCATACTTACATACTCC 57.002 34.615 0.00 0.00 42.67 3.85
3157 4690 8.567948 CCACTTTTCACAAGTTCATACTTACAT 58.432 33.333 0.00 0.00 42.67 2.29
3188 4721 6.318648 TGAACAGAAAAGACAGCATACAACTT 59.681 34.615 0.00 0.00 0.00 2.66
3222 4755 0.381801 AACCAGCACGCAAACAAGAG 59.618 50.000 0.00 0.00 0.00 2.85
3275 4808 2.569354 GCCGGAAAACCATGCACCA 61.569 57.895 5.05 0.00 0.00 4.17
3396 4929 3.243941 TGCTCGCCTCAAACTTAACACTA 60.244 43.478 0.00 0.00 0.00 2.74
3413 4946 5.295292 ACAACTGGATTTGATTAGATGCTCG 59.705 40.000 0.00 0.00 0.00 5.03
3423 4956 5.471556 TGATGCAAACAACTGGATTTGAT 57.528 34.783 0.00 0.00 37.91 2.57
4010 5547 2.011548 GCTTGATACGGTGCCATGTCA 61.012 52.381 0.00 0.00 0.00 3.58
4233 5770 3.257873 TCCATTTCATGTTTGGACGCAAT 59.742 39.130 9.11 0.00 34.65 3.56
4381 5927 9.888878 CATATATGCAACAGGAGAAAATGTAAG 57.111 33.333 0.00 0.00 0.00 2.34
4460 6006 3.132111 TCATCGCAGTCCTTTGCAGTATA 59.868 43.478 0.00 0.00 44.28 1.47
4496 6042 7.783119 ACTTTCAACCCTAAAACTGTATCCTTT 59.217 33.333 0.00 0.00 0.00 3.11
5060 6613 2.989840 CAACGGTGAGCTCACTTTCTAG 59.010 50.000 38.17 25.36 45.73 2.43
5096 6649 5.013258 ACACCTCTAGTCTAGGGAAAACT 57.987 43.478 8.46 0.00 38.54 2.66
5109 6662 9.817809 TGCTTTAATAGTCAAATACACCTCTAG 57.182 33.333 0.00 0.00 0.00 2.43
5111 6664 9.331282 GATGCTTTAATAGTCAAATACACCTCT 57.669 33.333 0.00 0.00 0.00 3.69
5112 6665 8.560374 GGATGCTTTAATAGTCAAATACACCTC 58.440 37.037 0.00 0.00 0.00 3.85
5113 6666 8.275040 AGGATGCTTTAATAGTCAAATACACCT 58.725 33.333 0.00 0.00 0.00 4.00
5114 6667 8.451908 AGGATGCTTTAATAGTCAAATACACC 57.548 34.615 0.00 0.00 0.00 4.16
5171 6724 5.557866 ACAAGACTACCACAAGATAAACCC 58.442 41.667 0.00 0.00 0.00 4.11
5273 6829 2.092968 AGATCCTAAATCACTGCCGCAA 60.093 45.455 0.00 0.00 0.00 4.85
5279 6835 4.047822 GACGAGCAGATCCTAAATCACTG 58.952 47.826 0.00 0.00 0.00 3.66
5488 7046 3.624410 TGACTAGCGAGCGACTGTAAATA 59.376 43.478 0.00 0.00 0.00 1.40
5507 7065 5.356882 TGCACAAATTTAGTGTAGCTGAC 57.643 39.130 16.72 0.00 39.17 3.51
5842 7408 7.304497 ACTCTACTGTAACTCTTGTCCAATT 57.696 36.000 0.00 0.00 0.00 2.32
5858 7424 5.413309 AAGGATGTTTGAGGACTCTACTG 57.587 43.478 0.56 0.00 0.00 2.74
6003 7577 2.825205 ACAAAAATGCACAGCAGAACC 58.175 42.857 0.00 0.00 43.65 3.62
6006 7580 3.797451 TGAACAAAAATGCACAGCAGA 57.203 38.095 0.00 0.00 43.65 4.26
6015 7589 7.065204 TGCCATCATGATCATTGAACAAAAATG 59.935 33.333 5.16 5.48 36.54 2.32
6016 7590 7.106890 TGCCATCATGATCATTGAACAAAAAT 58.893 30.769 5.16 0.00 0.00 1.82
6211 7802 4.769688 TGCTATGTCAGGTATGTTCTTGG 58.230 43.478 0.00 0.00 0.00 3.61
6241 7832 1.302366 GATCGCATGTCATGGCTTGA 58.698 50.000 16.70 0.00 0.00 3.02
6279 7870 2.877691 GCCGAGGCATGTTGGAAC 59.122 61.111 9.58 0.00 41.49 3.62
6363 7954 2.034879 ATGGCCTGTCGTTTCAGCG 61.035 57.895 3.32 0.00 34.47 5.18
6370 7961 0.615331 ACATTCTCATGGCCTGTCGT 59.385 50.000 3.32 0.00 34.27 4.34
6371 7962 1.012086 CACATTCTCATGGCCTGTCG 58.988 55.000 3.32 0.00 34.27 4.35
6570 8167 5.278957 GCAAATCAAACAGCTCCTCCTAAAA 60.279 40.000 0.00 0.00 0.00 1.52
6571 8168 4.218417 GCAAATCAAACAGCTCCTCCTAAA 59.782 41.667 0.00 0.00 0.00 1.85
6586 8183 0.749649 AAACTGTGGCGGCAAATCAA 59.250 45.000 15.50 0.00 0.00 2.57
6607 8204 3.483411 CGATGATCGCGACAACATTGAAA 60.483 43.478 23.66 0.00 31.14 2.69
6609 8206 1.587946 CGATGATCGCGACAACATTGA 59.412 47.619 23.66 1.18 31.14 2.57
6622 8222 3.251004 GGCAGGTCAAATTACCGATGATC 59.749 47.826 0.00 0.00 44.77 2.92
6673 8273 5.037383 TGGTTGGTGAAATGTACTGTGTA 57.963 39.130 0.00 0.00 0.00 2.90
6731 8331 1.671054 CTCTTTCCCTTTCGGCGCA 60.671 57.895 10.83 0.00 0.00 6.09
6780 8380 0.803768 CTTCTGTGGACGGCGATCAG 60.804 60.000 16.62 15.32 0.00 2.90
6863 8463 2.297033 TCAGCAAATTGGAAACTGGAGC 59.703 45.455 0.00 0.00 0.00 4.70
6908 8508 1.307097 GACCTACCTCGCTACGATGT 58.693 55.000 3.55 3.55 38.21 3.06
6930 8539 2.867975 CCGTATAATTTCGGTGGTCCAC 59.132 50.000 14.13 14.13 41.58 4.02
6931 8540 2.158928 CCCGTATAATTTCGGTGGTCCA 60.159 50.000 12.79 0.00 44.51 4.02
6932 8541 2.486918 CCCGTATAATTTCGGTGGTCC 58.513 52.381 12.79 0.00 44.51 4.46
6933 8542 2.486918 CCCCGTATAATTTCGGTGGTC 58.513 52.381 12.79 0.00 44.51 4.02
6934 8543 1.475571 GCCCCGTATAATTTCGGTGGT 60.476 52.381 12.79 0.00 44.51 4.16
6935 8544 1.232119 GCCCCGTATAATTTCGGTGG 58.768 55.000 12.79 13.31 44.51 4.61
6936 8545 1.956297 TGCCCCGTATAATTTCGGTG 58.044 50.000 12.79 5.51 44.51 4.94
6937 8546 2.713863 TTGCCCCGTATAATTTCGGT 57.286 45.000 12.79 0.00 44.51 4.69
6962 8571 3.044059 GCCGTGCACCATCTTCAGC 62.044 63.158 12.15 0.00 0.00 4.26
6979 8588 0.451783 CAGGAAACATTGGCCGTAGC 59.548 55.000 0.00 0.00 38.76 3.58
6980 8589 2.107950 TCAGGAAACATTGGCCGTAG 57.892 50.000 0.00 0.00 0.00 3.51
6981 8590 2.364632 CATCAGGAAACATTGGCCGTA 58.635 47.619 0.00 0.00 0.00 4.02
6982 8591 1.176527 CATCAGGAAACATTGGCCGT 58.823 50.000 0.00 0.00 0.00 5.68
6983 8592 0.457035 CCATCAGGAAACATTGGCCG 59.543 55.000 0.00 0.00 36.89 6.13
6984 8593 1.478105 GACCATCAGGAAACATTGGCC 59.522 52.381 0.00 0.00 38.69 5.36
6996 8673 8.975439 CAAAATTTCAGAAAAGAAGACCATCAG 58.025 33.333 0.00 0.00 0.00 2.90
7001 8678 7.492524 AGGTCAAAATTTCAGAAAAGAAGACC 58.507 34.615 21.69 21.69 36.85 3.85
7018 8695 6.214191 TCTGTGTAAATTGCAAGGTCAAAA 57.786 33.333 4.94 0.00 0.00 2.44
7066 8755 5.986741 GGAATTAAGAGGCAGTAGAAGCTAC 59.013 44.000 0.00 0.00 0.00 3.58
7078 8767 2.168728 AGGACTCGTGGAATTAAGAGGC 59.831 50.000 0.00 0.00 38.00 4.70
7092 8791 0.387202 ATCCAATCGCTCAGGACTCG 59.613 55.000 0.00 0.00 33.57 4.18
7111 8894 0.605319 GGTTTGGTCATGCGACTGGA 60.605 55.000 0.00 0.00 42.21 3.86
7148 8931 7.377928 CAGACTGAGAAATTAAGCTGTGTTTTG 59.622 37.037 0.00 0.00 0.00 2.44
7150 8933 6.767902 TCAGACTGAGAAATTAAGCTGTGTTT 59.232 34.615 0.00 0.00 0.00 2.83
7155 8949 6.800892 GCTTTTCAGACTGAGAAATTAAGCTG 59.199 38.462 9.49 0.00 35.26 4.24
7156 8950 6.488006 TGCTTTTCAGACTGAGAAATTAAGCT 59.512 34.615 21.38 0.00 37.30 3.74
7175 8969 1.239347 GAAGAGAAGGCGGTGCTTTT 58.761 50.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.