Multiple sequence alignment - TraesCS3D01G179200

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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 TraesCS3D01G179200 chr3D 100.000 5215 0 0 1 5215 160889387 160894601 0.000000e+00 9631.0
1 TraesCS3D01G179200 chr3B 94.461 2762 97 33 1876 4617 237633032 237635757 0.000000e+00 4202.0
2 TraesCS3D01G179200 chr3B 89.748 1746 88 43 125 1844 237631231 237632911 0.000000e+00 2148.0
3 TraesCS3D01G179200 chr3B 92.236 322 7 4 4907 5215 237638569 237638885 1.720000e-119 440.0
4 TraesCS3D01G179200 chr3B 96.875 128 4 0 1088 1215 237632282 237632409 1.140000e-51 215.0
5 TraesCS3D01G179200 chr3A 93.943 1849 69 9 2833 4656 189318021 189316191 0.000000e+00 2754.0
6 TraesCS3D01G179200 chr3A 88.032 1738 111 37 125 1844 189320626 189318968 0.000000e+00 1967.0
7 TraesCS3D01G179200 chr3A 94.105 933 38 8 1833 2765 189318940 189318025 0.000000e+00 1402.0
8 TraesCS3D01G179200 chr3A 95.142 247 6 2 4975 5215 189315337 189315091 8.190000e-103 385.0
9 TraesCS3D01G179200 chr3A 95.402 87 1 1 1648 1731 599579482 599579568 9.110000e-28 135.0
10 TraesCS3D01G179200 chr3A 94.643 56 3 0 4846 4901 189315509 189315454 2.590000e-13 87.9
11 TraesCS3D01G179200 chr7D 79.437 462 76 13 2992 3449 426109404 426109850 5.070000e-80 309.0
12 TraesCS3D01G179200 chr7D 94.245 139 7 1 1 139 213380370 213380233 1.470000e-50 211.0
13 TraesCS3D01G179200 chr7D 93.662 142 6 3 1 139 206437581 206437440 5.290000e-50 209.0
14 TraesCS3D01G179200 chr7A 96.970 132 4 0 1 132 324925156 324925025 6.800000e-54 222.0
15 TraesCS3D01G179200 chr5D 96.241 133 5 0 1 133 61715343 61715211 8.790000e-53 219.0
16 TraesCS3D01G179200 chr2D 96.899 129 4 0 1 129 426427926 426427798 3.160000e-52 217.0
17 TraesCS3D01G179200 chr2D 96.899 129 4 0 1 129 560959610 560959482 3.160000e-52 217.0
18 TraesCS3D01G179200 chr2D 89.697 165 13 3 1 165 29162428 29162588 1.900000e-49 207.0
19 TraesCS3D01G179200 chr5B 96.212 132 4 1 1 131 181031939 181031808 1.140000e-51 215.0
20 TraesCS3D01G179200 chr2B 94.891 137 6 1 1 136 39787846 39787710 4.090000e-51 213.0
21 TraesCS3D01G179200 chr2B 85.366 82 11 1 4742 4823 597552980 597553060 3.350000e-12 84.2
22 TraesCS3D01G179200 chr2A 80.435 92 16 2 4732 4822 475811740 475811830 9.370000e-08 69.4


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 TraesCS3D01G179200 chr3D 160889387 160894601 5214 False 9631.00 9631 100.000 1 5215 1 chr3D.!!$F1 5214
1 TraesCS3D01G179200 chr3B 237631231 237638885 7654 False 1751.25 4202 93.330 125 5215 4 chr3B.!!$F1 5090
2 TraesCS3D01G179200 chr3A 189315091 189320626 5535 True 1319.18 2754 93.173 125 5215 5 chr3A.!!$R1 5090

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
968 1007 0.400594 GGAATCGGGGTGGGGAATAG 59.599 60.000 0.00 0.0 0.00 1.73 F
970 1009 1.348036 GAATCGGGGTGGGGAATAGAG 59.652 57.143 0.00 0.0 0.00 2.43 F
2005 2143 0.685097 TTGGTTCCTCCTCGACCAAG 59.315 55.000 3.24 0.0 45.69 3.61 F
2158 2296 0.730494 GTTGTCAAGAATGCTGCCGC 60.730 55.000 0.00 0.0 0.00 6.53 F
2159 2297 0.890542 TTGTCAAGAATGCTGCCGCT 60.891 50.000 0.70 0.0 36.97 5.52 F
3833 3976 1.004745 TCCCTGAAACTGCTCCAATCC 59.995 52.381 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2143 0.169009 GCGGAGACATTTTGGCTGAC 59.831 55.000 0.00 0.0 34.53 3.51 R
2843 2984 1.002033 CTGGAGCGCATAAGAAATGCC 60.002 52.381 11.47 0.0 41.71 4.40 R
3034 3175 0.104671 GTGCCTCTCCTCTCATCAGC 59.895 60.000 0.00 0.0 0.00 4.26 R
3842 3985 0.402121 GTGGGGAGTTGAAGAAGGCT 59.598 55.000 0.00 0.0 0.00 4.58 R
3860 4003 0.544357 TGAGGATCTCCAACGGGTGT 60.544 55.000 0.00 0.0 38.89 4.16 R
4901 7608 0.179108 CCGAGATCACCGTTCCTTCC 60.179 60.000 0.00 0.0 0.00 3.46 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
21 22 4.245845 TCAACAAGTGACTACATACGCA 57.754 40.909 0.00 0.00 0.00 5.24
22 23 4.234574 TCAACAAGTGACTACATACGCAG 58.765 43.478 0.00 0.00 0.00 5.18
23 24 2.607187 ACAAGTGACTACATACGCAGC 58.393 47.619 0.00 0.00 0.00 5.25
24 25 2.029380 ACAAGTGACTACATACGCAGCA 60.029 45.455 0.00 0.00 0.00 4.41
25 26 2.993220 CAAGTGACTACATACGCAGCAA 59.007 45.455 0.00 0.00 0.00 3.91
26 27 3.313012 AGTGACTACATACGCAGCAAA 57.687 42.857 0.00 0.00 0.00 3.68
27 28 3.659786 AGTGACTACATACGCAGCAAAA 58.340 40.909 0.00 0.00 0.00 2.44
28 29 4.253685 AGTGACTACATACGCAGCAAAAT 58.746 39.130 0.00 0.00 0.00 1.82
29 30 4.093408 AGTGACTACATACGCAGCAAAATG 59.907 41.667 0.00 0.00 0.00 2.32
30 31 4.092821 GTGACTACATACGCAGCAAAATGA 59.907 41.667 5.79 0.00 0.00 2.57
31 32 4.329801 TGACTACATACGCAGCAAAATGAG 59.670 41.667 5.79 2.75 0.00 2.90
32 33 4.253685 ACTACATACGCAGCAAAATGAGT 58.746 39.130 5.79 0.00 37.05 3.41
33 34 3.476295 ACATACGCAGCAAAATGAGTG 57.524 42.857 5.79 0.00 34.83 3.51
34 35 3.073678 ACATACGCAGCAAAATGAGTGA 58.926 40.909 5.79 0.00 34.83 3.41
35 36 3.501828 ACATACGCAGCAAAATGAGTGAA 59.498 39.130 5.79 0.00 34.83 3.18
36 37 4.156556 ACATACGCAGCAAAATGAGTGAAT 59.843 37.500 5.79 0.00 34.83 2.57
37 38 3.207474 ACGCAGCAAAATGAGTGAATC 57.793 42.857 0.00 0.00 31.59 2.52
38 39 2.816087 ACGCAGCAAAATGAGTGAATCT 59.184 40.909 0.00 0.00 31.59 2.40
39 40 4.002982 ACGCAGCAAAATGAGTGAATCTA 58.997 39.130 0.00 0.00 31.59 1.98
40 41 4.142816 ACGCAGCAAAATGAGTGAATCTAC 60.143 41.667 0.00 0.00 31.59 2.59
41 42 4.142838 CGCAGCAAAATGAGTGAATCTACA 60.143 41.667 0.00 0.00 0.00 2.74
42 43 5.091431 GCAGCAAAATGAGTGAATCTACAC 58.909 41.667 0.00 0.00 40.60 2.90
85 86 7.962964 ATATTCGTATGTGGTAGTCCATTTG 57.037 36.000 0.00 0.00 46.20 2.32
86 87 5.408880 TTCGTATGTGGTAGTCCATTTGA 57.591 39.130 0.00 0.00 46.20 2.69
87 88 5.408880 TCGTATGTGGTAGTCCATTTGAA 57.591 39.130 0.00 0.00 46.20 2.69
88 89 5.795972 TCGTATGTGGTAGTCCATTTGAAA 58.204 37.500 0.00 0.00 46.20 2.69
89 90 6.411376 TCGTATGTGGTAGTCCATTTGAAAT 58.589 36.000 0.00 0.00 46.20 2.17
90 91 6.537301 TCGTATGTGGTAGTCCATTTGAAATC 59.463 38.462 0.00 0.00 46.20 2.17
91 92 6.315144 CGTATGTGGTAGTCCATTTGAAATCA 59.685 38.462 0.00 0.00 46.20 2.57
92 93 5.957842 TGTGGTAGTCCATTTGAAATCAC 57.042 39.130 0.00 0.00 46.20 3.06
93 94 5.630121 TGTGGTAGTCCATTTGAAATCACT 58.370 37.500 4.85 4.85 46.20 3.41
94 95 6.774673 TGTGGTAGTCCATTTGAAATCACTA 58.225 36.000 3.30 3.30 46.20 2.74
95 96 7.227873 TGTGGTAGTCCATTTGAAATCACTAA 58.772 34.615 7.49 0.00 46.20 2.24
96 97 7.721842 TGTGGTAGTCCATTTGAAATCACTAAA 59.278 33.333 7.49 0.00 46.20 1.85
97 98 8.573035 GTGGTAGTCCATTTGAAATCACTAAAA 58.427 33.333 7.49 0.00 46.20 1.52
98 99 9.137459 TGGTAGTCCATTTGAAATCACTAAAAA 57.863 29.630 7.49 0.00 39.03 1.94
99 100 9.626045 GGTAGTCCATTTGAAATCACTAAAAAG 57.374 33.333 7.49 0.00 0.00 2.27
102 103 8.912988 AGTCCATTTGAAATCACTAAAAAGACA 58.087 29.630 0.00 0.00 0.00 3.41
103 104 9.528018 GTCCATTTGAAATCACTAAAAAGACAA 57.472 29.630 0.00 0.00 0.00 3.18
120 121 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
121 122 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
122 123 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
123 124 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
160 161 7.800155 TGTCACAAAATGAATCTGTGTCTTA 57.200 32.000 1.75 0.00 39.72 2.10
199 207 5.991328 ATTAGTGTCATGATTACCTTGCG 57.009 39.130 0.00 0.00 0.00 4.85
214 222 5.339008 ACCTTGCGATGTTATTACTCTGA 57.661 39.130 0.00 0.00 0.00 3.27
222 230 6.510157 GCGATGTTATTACTCTGATGTGGTTG 60.510 42.308 0.00 0.00 0.00 3.77
236 244 3.917300 TGTGGTTGGGTTAAATCAAGGT 58.083 40.909 0.00 0.00 0.00 3.50
292 300 9.968870 TGTTGTGGTTTTAGTTCAAATTATACC 57.031 29.630 0.00 0.00 0.00 2.73
294 302 8.393671 TGTGGTTTTAGTTCAAATTATACCGT 57.606 30.769 0.00 0.00 0.00 4.83
297 305 8.655092 TGGTTTTAGTTCAAATTATACCGTACG 58.345 33.333 8.69 8.69 0.00 3.67
312 320 4.529446 ACCGTACGTATTTGTTTGCTTTG 58.471 39.130 15.21 0.00 0.00 2.77
313 321 3.359580 CCGTACGTATTTGTTTGCTTTGC 59.640 43.478 15.21 0.00 0.00 3.68
336 344 1.628846 TGTTCTTCTCTGGTTAGGCCC 59.371 52.381 0.00 0.00 36.04 5.80
378 388 5.176592 GTGGTCTATACTTTCACTCCAACC 58.823 45.833 0.00 0.00 0.00 3.77
389 399 5.730296 TTCACTCCAACCTTTTGTTTCAA 57.270 34.783 0.00 0.00 34.00 2.69
390 400 5.930837 TCACTCCAACCTTTTGTTTCAAT 57.069 34.783 0.00 0.00 34.00 2.57
391 401 7.411486 TTCACTCCAACCTTTTGTTTCAATA 57.589 32.000 0.00 0.00 34.00 1.90
394 404 6.868339 CACTCCAACCTTTTGTTTCAATATCC 59.132 38.462 0.00 0.00 34.00 2.59
396 406 7.235399 ACTCCAACCTTTTGTTTCAATATCCAT 59.765 33.333 0.00 0.00 34.00 3.41
398 408 8.527810 TCCAACCTTTTGTTTCAATATCCATAC 58.472 33.333 0.00 0.00 34.00 2.39
399 409 7.763985 CCAACCTTTTGTTTCAATATCCATACC 59.236 37.037 0.00 0.00 34.00 2.73
402 424 7.124147 ACCTTTTGTTTCAATATCCATACCTGG 59.876 37.037 0.00 0.00 44.64 4.45
414 436 4.440808 TCCATACCTGGTAGGAAAAGGAA 58.559 43.478 19.39 0.00 43.61 3.36
415 437 5.043762 TCCATACCTGGTAGGAAAAGGAAT 58.956 41.667 19.39 0.00 43.61 3.01
416 438 5.132144 TCCATACCTGGTAGGAAAAGGAATC 59.868 44.000 19.39 0.00 43.61 2.52
417 439 5.104109 CCATACCTGGTAGGAAAAGGAATCA 60.104 44.000 19.39 0.00 37.67 2.57
418 440 6.410853 CCATACCTGGTAGGAAAAGGAATCAT 60.411 42.308 19.39 0.00 37.67 2.45
419 441 5.117406 ACCTGGTAGGAAAAGGAATCATC 57.883 43.478 0.00 0.00 37.67 2.92
420 442 4.079730 ACCTGGTAGGAAAAGGAATCATCC 60.080 45.833 0.00 0.00 41.43 3.51
504 527 9.871238 AAATTGTACTACAACTATTCATCGAGT 57.129 29.630 3.67 0.00 41.40 4.18
505 528 9.517609 AATTGTACTACAACTATTCATCGAGTC 57.482 33.333 3.67 0.00 41.40 3.36
508 531 8.343366 TGTACTACAACTATTCATCGAGTCATC 58.657 37.037 0.00 0.00 0.00 2.92
509 532 7.334844 ACTACAACTATTCATCGAGTCATCA 57.665 36.000 0.00 0.00 0.00 3.07
510 533 7.946207 ACTACAACTATTCATCGAGTCATCAT 58.054 34.615 0.00 0.00 0.00 2.45
511 534 8.417106 ACTACAACTATTCATCGAGTCATCATT 58.583 33.333 0.00 0.00 0.00 2.57
512 535 7.706281 ACAACTATTCATCGAGTCATCATTC 57.294 36.000 0.00 0.00 0.00 2.67
513 536 7.267857 ACAACTATTCATCGAGTCATCATTCA 58.732 34.615 0.00 0.00 0.00 2.57
514 537 7.930325 ACAACTATTCATCGAGTCATCATTCAT 59.070 33.333 0.00 0.00 0.00 2.57
515 538 8.771766 CAACTATTCATCGAGTCATCATTCATT 58.228 33.333 0.00 0.00 0.00 2.57
516 539 8.531622 ACTATTCATCGAGTCATCATTCATTC 57.468 34.615 0.00 0.00 0.00 2.67
517 540 8.146412 ACTATTCATCGAGTCATCATTCATTCA 58.854 33.333 0.00 0.00 0.00 2.57
518 541 7.981102 ATTCATCGAGTCATCATTCATTCAT 57.019 32.000 0.00 0.00 0.00 2.57
519 542 6.780706 TCATCGAGTCATCATTCATTCATG 57.219 37.500 0.00 0.00 0.00 3.07
520 543 6.285990 TCATCGAGTCATCATTCATTCATGT 58.714 36.000 0.00 0.00 0.00 3.21
521 544 7.436118 TCATCGAGTCATCATTCATTCATGTA 58.564 34.615 0.00 0.00 0.00 2.29
522 545 8.092687 TCATCGAGTCATCATTCATTCATGTAT 58.907 33.333 0.00 0.00 0.00 2.29
523 546 9.362539 CATCGAGTCATCATTCATTCATGTATA 57.637 33.333 0.00 0.00 0.00 1.47
583 614 0.532862 GTGCATCCACGGTAGATGGG 60.533 60.000 16.41 0.00 41.22 4.00
585 616 1.045407 GCATCCACGGTAGATGGGTA 58.955 55.000 16.41 0.00 41.22 3.69
594 627 4.400251 CACGGTAGATGGGTAGAAACAGTA 59.600 45.833 0.00 0.00 0.00 2.74
832 869 1.852309 TGCCTCCATCTCTCTCTCTCT 59.148 52.381 0.00 0.00 0.00 3.10
873 910 1.669265 GCCAACCACGCTATTCCTAAC 59.331 52.381 0.00 0.00 0.00 2.34
874 911 1.931172 CCAACCACGCTATTCCTAACG 59.069 52.381 0.00 0.00 0.00 3.18
875 912 2.417651 CCAACCACGCTATTCCTAACGA 60.418 50.000 0.00 0.00 0.00 3.85
876 913 2.858344 CAACCACGCTATTCCTAACGAG 59.142 50.000 0.00 0.00 0.00 4.18
877 914 2.097825 ACCACGCTATTCCTAACGAGT 58.902 47.619 0.00 0.00 0.00 4.18
878 915 3.282021 ACCACGCTATTCCTAACGAGTA 58.718 45.455 0.00 0.00 0.00 2.59
879 916 3.696051 ACCACGCTATTCCTAACGAGTAA 59.304 43.478 0.00 0.00 0.00 2.24
898 937 2.126580 GACTAACTCGTGCGCCGT 60.127 61.111 16.00 1.03 37.94 5.68
962 1001 2.275418 CCAAGGAATCGGGGTGGG 59.725 66.667 0.00 0.00 0.00 4.61
966 1005 0.924226 AAGGAATCGGGGTGGGGAAT 60.924 55.000 0.00 0.00 0.00 3.01
968 1007 0.400594 GGAATCGGGGTGGGGAATAG 59.599 60.000 0.00 0.00 0.00 1.73
970 1009 1.348036 GAATCGGGGTGGGGAATAGAG 59.652 57.143 0.00 0.00 0.00 2.43
981 1020 2.439880 GGGGAATAGAGGAGGTTTGGAG 59.560 54.545 0.00 0.00 0.00 3.86
984 1023 4.720273 GGGAATAGAGGAGGTTTGGAGTTA 59.280 45.833 0.00 0.00 0.00 2.24
987 1026 3.277416 AGAGGAGGTTTGGAGTTAGGT 57.723 47.619 0.00 0.00 0.00 3.08
992 1031 1.583495 GGTTTGGAGTTAGGTGCGCC 61.583 60.000 8.71 8.71 0.00 6.53
1025 1064 3.435186 GCTGAGGTTTCTGGGCGC 61.435 66.667 0.00 0.00 0.00 6.53
1572 1617 1.720694 CGTCCTTCTCGAGGCTCCTC 61.721 65.000 13.56 5.85 45.87 3.71
1819 1868 4.205587 AGGAATGCAAAGCTAGATTCAGG 58.794 43.478 0.00 0.00 0.00 3.86
1849 1939 3.089284 GGCCTTTACTGTACCTGCAAAT 58.911 45.455 0.00 0.00 0.00 2.32
1906 2044 6.485648 AGTTACACCAGTTACTTCATTGTTCC 59.514 38.462 0.00 0.00 34.17 3.62
1958 2096 5.954757 TGGAGTAGAAAATTTTGGTACCCA 58.045 37.500 8.47 14.13 0.00 4.51
2005 2143 0.685097 TTGGTTCCTCCTCGACCAAG 59.315 55.000 3.24 0.00 45.69 3.61
2156 2294 1.135859 CGAGTTGTCAAGAATGCTGCC 60.136 52.381 0.00 0.00 0.00 4.85
2157 2295 0.877071 AGTTGTCAAGAATGCTGCCG 59.123 50.000 0.00 0.00 0.00 5.69
2158 2296 0.730494 GTTGTCAAGAATGCTGCCGC 60.730 55.000 0.00 0.00 0.00 6.53
2159 2297 0.890542 TTGTCAAGAATGCTGCCGCT 60.891 50.000 0.70 0.00 36.97 5.52
2160 2298 1.136147 GTCAAGAATGCTGCCGCTG 59.864 57.895 0.70 0.00 36.97 5.18
2161 2299 2.202570 CAAGAATGCTGCCGCTGC 60.203 61.111 14.83 14.83 36.97 5.25
2189 2327 3.694926 CAGCAAGGAGGAAGAAGGAAAT 58.305 45.455 0.00 0.00 0.00 2.17
2194 2332 1.286257 GGAGGAAGAAGGAAATGGCCT 59.714 52.381 3.32 0.00 40.93 5.19
2342 2480 2.440409 GCCATTGTGAGTGGTGAGAAT 58.560 47.619 0.00 0.00 39.01 2.40
2450 2588 4.081254 AGACAAGCTGTTGCAGATGATCTA 60.081 41.667 0.00 0.00 42.74 1.98
2465 2603 7.281774 GCAGATGATCTAAATTCTTCAAGGTCA 59.718 37.037 0.00 0.00 33.83 4.02
2534 2672 7.066043 ACAAGATACTTCGTAGTTCAGGTAGAG 59.934 40.741 0.00 0.00 35.78 2.43
2544 2682 1.908643 TCAGGTAGAGCTCCTCCCTA 58.091 55.000 10.93 1.65 32.37 3.53
2560 2698 4.400884 CCTCCCTAATATCTCATGTCTCCG 59.599 50.000 0.00 0.00 0.00 4.63
2561 2699 4.999310 TCCCTAATATCTCATGTCTCCGT 58.001 43.478 0.00 0.00 0.00 4.69
2599 2737 3.411446 TGTTAGTTGATCCTGCCACTTG 58.589 45.455 0.00 0.00 0.00 3.16
2724 2862 7.254852 TGCCGGTATTCAATCATTTTAACTTC 58.745 34.615 1.90 0.00 0.00 3.01
2799 2940 3.948851 TGCGTAAACGTTTGCATTTGTA 58.051 36.364 25.36 8.74 42.22 2.41
2802 2943 5.138788 GCGTAAACGTTTGCATTTGTACTA 58.861 37.500 25.36 0.00 42.22 1.82
2803 2944 5.791480 GCGTAAACGTTTGCATTTGTACTAT 59.209 36.000 25.36 0.00 42.22 2.12
2831 2972 5.129634 TGAAAGGAACAGCTGTCACATTTA 58.870 37.500 25.08 14.17 0.00 1.40
2842 2983 7.826252 ACAGCTGTCACATTTATGTAATCTCTT 59.174 33.333 15.25 0.00 39.39 2.85
2843 2984 8.121086 CAGCTGTCACATTTATGTAATCTCTTG 58.879 37.037 5.25 0.00 39.39 3.02
2932 3073 2.212812 TGTATCACCAAATGCTGCCA 57.787 45.000 0.00 0.00 0.00 4.92
2977 3118 9.349713 AGAAATTATGGTAAATCCGCAGAATTA 57.650 29.630 0.00 0.00 39.52 1.40
3032 3173 4.523943 TGGCTTTGCTTGTGAATCTAATGT 59.476 37.500 0.00 0.00 0.00 2.71
3034 3175 5.346822 GGCTTTGCTTGTGAATCTAATGTTG 59.653 40.000 0.00 0.00 0.00 3.33
3284 3425 2.752903 CCATGCCTTACAAACCAGGTAC 59.247 50.000 0.00 0.00 32.06 3.34
3463 3604 9.027129 CATGGAAAACAATAGATAAGCACATTG 57.973 33.333 0.00 0.00 35.10 2.82
3572 3713 4.481368 TCGTAGTAATTGGTTGATGCCT 57.519 40.909 0.00 0.00 0.00 4.75
3573 3714 4.839121 TCGTAGTAATTGGTTGATGCCTT 58.161 39.130 0.00 0.00 0.00 4.35
3623 3764 4.719026 ACATAGGATCAATGCATGTCCT 57.281 40.909 23.90 23.90 40.45 3.85
3803 3946 1.315690 TCTACTACCTGGGCGATTCG 58.684 55.000 0.62 0.62 0.00 3.34
3833 3976 1.004745 TCCCTGAAACTGCTCCAATCC 59.995 52.381 0.00 0.00 0.00 3.01
3842 3985 2.264480 CTCCAATCCGCCGTGTCA 59.736 61.111 0.00 0.00 0.00 3.58
3860 4003 0.401738 CAGCCTTCTTCAACTCCCCA 59.598 55.000 0.00 0.00 0.00 4.96
4225 4386 5.400870 TGGACTGAGGTGATAGATGATGAT 58.599 41.667 0.00 0.00 0.00 2.45
4439 4607 1.085091 CACCATCAGCAAGCTGTCTC 58.915 55.000 20.34 0.00 43.96 3.36
4440 4608 0.689055 ACCATCAGCAAGCTGTCTCA 59.311 50.000 20.34 2.93 43.96 3.27
4441 4609 1.072806 ACCATCAGCAAGCTGTCTCAA 59.927 47.619 20.34 2.55 43.96 3.02
4442 4610 2.156917 CCATCAGCAAGCTGTCTCAAA 58.843 47.619 20.34 1.84 43.96 2.69
4443 4611 2.161808 CCATCAGCAAGCTGTCTCAAAG 59.838 50.000 20.34 0.00 43.96 2.77
4444 4612 2.627515 TCAGCAAGCTGTCTCAAAGT 57.372 45.000 20.34 0.00 43.96 2.66
4445 4613 3.751479 TCAGCAAGCTGTCTCAAAGTA 57.249 42.857 20.34 0.00 43.96 2.24
4446 4614 4.071961 TCAGCAAGCTGTCTCAAAGTAA 57.928 40.909 20.34 0.00 43.96 2.24
4447 4615 3.809832 TCAGCAAGCTGTCTCAAAGTAAC 59.190 43.478 20.34 0.00 43.96 2.50
4448 4616 3.812053 CAGCAAGCTGTCTCAAAGTAACT 59.188 43.478 13.72 0.00 39.10 2.24
4449 4617 4.061596 AGCAAGCTGTCTCAAAGTAACTC 58.938 43.478 0.00 0.00 0.00 3.01
4450 4618 3.187432 GCAAGCTGTCTCAAAGTAACTCC 59.813 47.826 0.00 0.00 0.00 3.85
4451 4619 4.636249 CAAGCTGTCTCAAAGTAACTCCT 58.364 43.478 0.00 0.00 0.00 3.69
4464 4632 6.360370 AAGTAACTCCTCAAAGTAGCATCA 57.640 37.500 0.00 0.00 0.00 3.07
4473 4641 8.712228 TCCTCAAAGTAGCATCATCTCTTATA 57.288 34.615 0.00 0.00 0.00 0.98
4474 4642 9.319060 TCCTCAAAGTAGCATCATCTCTTATAT 57.681 33.333 0.00 0.00 0.00 0.86
4497 4665 3.063997 CGTTATTGCCTCATGTGGTTCTC 59.936 47.826 15.01 0.00 0.00 2.87
4505 4673 3.119291 CTCATGTGGTTCTCGTCTATGC 58.881 50.000 0.00 0.00 0.00 3.14
4509 4677 2.096980 TGTGGTTCTCGTCTATGCTACG 59.903 50.000 0.00 0.00 41.64 3.51
4510 4678 2.097142 GTGGTTCTCGTCTATGCTACGT 59.903 50.000 0.00 0.00 41.08 3.57
4524 4693 6.972901 TCTATGCTACGTCTCAACAACTTATG 59.027 38.462 0.00 0.00 0.00 1.90
4528 4697 2.987149 ACGTCTCAACAACTTATGAGCG 59.013 45.455 13.76 13.76 42.21 5.03
4557 4728 5.463154 AGAGGTTGAGCTGTAGGAGATAAT 58.537 41.667 0.00 0.00 0.00 1.28
4581 4752 2.289002 CAGACCGATGCTAAAATGGAGC 59.711 50.000 0.00 0.00 40.53 4.70
4640 6673 1.737355 GCAGTTGCCTTGCCAGAACA 61.737 55.000 0.00 0.00 35.54 3.18
4662 6695 2.929531 CTCATGCAGAGTCACGTAGT 57.070 50.000 0.00 0.00 40.09 2.73
4664 6697 3.686128 CTCATGCAGAGTCACGTAGTAC 58.314 50.000 0.00 0.00 38.08 2.73
4665 6698 3.344515 TCATGCAGAGTCACGTAGTACT 58.655 45.455 0.00 0.00 41.61 2.73
4666 6699 3.756963 TCATGCAGAGTCACGTAGTACTT 59.243 43.478 0.00 0.00 41.61 2.24
4667 6700 3.826236 TGCAGAGTCACGTAGTACTTC 57.174 47.619 0.00 0.00 41.61 3.01
4668 6701 2.486982 TGCAGAGTCACGTAGTACTTCC 59.513 50.000 0.00 0.00 41.61 3.46
4669 6702 2.748532 GCAGAGTCACGTAGTACTTCCT 59.251 50.000 0.00 0.00 41.61 3.36
4670 6703 3.181508 GCAGAGTCACGTAGTACTTCCTC 60.182 52.174 0.00 0.00 41.61 3.71
4671 6704 4.255301 CAGAGTCACGTAGTACTTCCTCT 58.745 47.826 0.00 0.47 41.61 3.69
4672 6705 4.696402 CAGAGTCACGTAGTACTTCCTCTT 59.304 45.833 0.00 0.00 41.61 2.85
4673 6706 5.181622 CAGAGTCACGTAGTACTTCCTCTTT 59.818 44.000 0.00 0.00 41.61 2.52
4674 6707 6.370994 CAGAGTCACGTAGTACTTCCTCTTTA 59.629 42.308 0.00 0.00 41.61 1.85
4675 6708 6.939163 AGAGTCACGTAGTACTTCCTCTTTAA 59.061 38.462 0.00 0.00 41.61 1.52
4676 6709 7.446625 AGAGTCACGTAGTACTTCCTCTTTAAA 59.553 37.037 0.00 0.00 41.61 1.52
4677 6710 7.592051 AGTCACGTAGTACTTCCTCTTTAAAG 58.408 38.462 9.04 9.04 41.61 1.85
4678 6711 7.446625 AGTCACGTAGTACTTCCTCTTTAAAGA 59.553 37.037 16.85 16.85 41.61 2.52
4679 6712 8.078596 GTCACGTAGTACTTCCTCTTTAAAGAA 58.921 37.037 18.25 2.52 41.61 2.52
4680 6713 8.632679 TCACGTAGTACTTCCTCTTTAAAGAAA 58.367 33.333 18.25 10.15 41.61 2.52
4681 6714 9.420551 CACGTAGTACTTCCTCTTTAAAGAAAT 57.579 33.333 18.25 5.14 41.61 2.17
4721 6754 9.745880 GAATGTTTAGATCATTAGGAGTCGTTA 57.254 33.333 0.00 0.00 35.94 3.18
4741 6774 8.263269 GTCGTTACGTACTCTACATAGTAGTTC 58.737 40.741 4.24 0.00 32.69 3.01
4742 6775 7.435488 TCGTTACGTACTCTACATAGTAGTTCC 59.565 40.741 4.24 0.00 32.69 3.62
4744 6777 9.103861 GTTACGTACTCTACATAGTAGTTCCTT 57.896 37.037 0.00 0.00 32.69 3.36
4745 6778 9.672673 TTACGTACTCTACATAGTAGTTCCTTT 57.327 33.333 0.00 0.00 32.69 3.11
4746 6779 7.983307 ACGTACTCTACATAGTAGTTCCTTTG 58.017 38.462 4.30 0.00 32.69 2.77
4797 6830 8.923683 GTCATTAAAGTAGTGACCTAAACACTC 58.076 37.037 0.00 0.00 45.58 3.51
4798 6831 8.867097 TCATTAAAGTAGTGACCTAAACACTCT 58.133 33.333 0.00 0.00 45.58 3.24
4799 6832 9.490379 CATTAAAGTAGTGACCTAAACACTCTT 57.510 33.333 0.00 0.00 45.58 2.85
4808 6841 9.628500 AGTGACCTAAACACTCTTAAATTTCTT 57.372 29.630 0.00 0.00 43.84 2.52
4813 6846 9.821662 CCTAAACACTCTTAAATTTCTTTACGG 57.178 33.333 0.00 0.00 0.00 4.02
4816 6849 9.946165 AAACACTCTTAAATTTCTTTACGGAAG 57.054 29.630 0.00 0.00 36.67 3.46
4817 6850 8.095937 ACACTCTTAAATTTCTTTACGGAAGG 57.904 34.615 0.00 0.00 35.98 3.46
4818 6851 7.935210 ACACTCTTAAATTTCTTTACGGAAGGA 59.065 33.333 0.00 0.00 35.98 3.36
4819 6852 8.443937 CACTCTTAAATTTCTTTACGGAAGGAG 58.556 37.037 0.00 0.00 35.98 3.69
4820 6853 8.155510 ACTCTTAAATTTCTTTACGGAAGGAGT 58.844 33.333 0.00 0.00 35.98 3.85
4821 6854 9.649167 CTCTTAAATTTCTTTACGGAAGGAGTA 57.351 33.333 0.00 0.00 35.98 2.59
4889 7596 4.595781 ACTTGACTGTACTTGGGTTGGATA 59.404 41.667 0.00 0.00 0.00 2.59
4894 7601 4.261801 CTGTACTTGGGTTGGATAGTTGG 58.738 47.826 0.00 0.00 0.00 3.77
4896 7603 4.351407 TGTACTTGGGTTGGATAGTTGGAA 59.649 41.667 0.00 0.00 0.00 3.53
4901 7608 3.010138 TGGGTTGGATAGTTGGAAGGAAG 59.990 47.826 0.00 0.00 0.00 3.46
4902 7609 3.621558 GGTTGGATAGTTGGAAGGAAGG 58.378 50.000 0.00 0.00 0.00 3.46
4903 7610 3.265995 GGTTGGATAGTTGGAAGGAAGGA 59.734 47.826 0.00 0.00 0.00 3.36
4904 7611 4.263771 GGTTGGATAGTTGGAAGGAAGGAA 60.264 45.833 0.00 0.00 0.00 3.36
4940 7721 1.555533 GAACGAGGAACATCTCCCCTT 59.444 52.381 0.00 0.00 46.81 3.95
4947 7728 0.121197 AACATCTCCCCTTCCCTCCA 59.879 55.000 0.00 0.00 0.00 3.86
4948 7729 0.327000 ACATCTCCCCTTCCCTCCAG 60.327 60.000 0.00 0.00 0.00 3.86
4949 7730 1.385206 ATCTCCCCTTCCCTCCAGC 60.385 63.158 0.00 0.00 0.00 4.85
4950 7731 1.907470 ATCTCCCCTTCCCTCCAGCT 61.907 60.000 0.00 0.00 0.00 4.24
4973 7766 1.315257 ATGCCAATTCCAGTCGCCAC 61.315 55.000 0.00 0.00 0.00 5.01
5136 7930 7.264947 GGACTTTCTTCTTTTCAAACCATCAA 58.735 34.615 0.00 0.00 0.00 2.57
5159 7953 3.289076 GCGTTTGTTCCTTTCTTTCTCG 58.711 45.455 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.234574 CTGCGTATGTAGTCACTTGTTGA 58.765 43.478 0.00 0.00 0.00 3.18
1 2 3.181530 GCTGCGTATGTAGTCACTTGTTG 60.182 47.826 1.82 0.00 0.00 3.33
2 3 2.993899 GCTGCGTATGTAGTCACTTGTT 59.006 45.455 1.82 0.00 0.00 2.83
3 4 2.029380 TGCTGCGTATGTAGTCACTTGT 60.029 45.455 1.82 0.00 0.00 3.16
4 5 2.606108 TGCTGCGTATGTAGTCACTTG 58.394 47.619 1.82 0.00 0.00 3.16
5 6 3.313012 TTGCTGCGTATGTAGTCACTT 57.687 42.857 1.82 0.00 0.00 3.16
6 7 3.313012 TTTGCTGCGTATGTAGTCACT 57.687 42.857 1.82 0.00 0.00 3.41
7 8 4.092821 TCATTTTGCTGCGTATGTAGTCAC 59.907 41.667 1.82 0.00 0.00 3.67
8 9 4.249661 TCATTTTGCTGCGTATGTAGTCA 58.750 39.130 1.82 0.00 0.00 3.41
9 10 4.330074 ACTCATTTTGCTGCGTATGTAGTC 59.670 41.667 1.82 0.00 0.00 2.59
10 11 4.093408 CACTCATTTTGCTGCGTATGTAGT 59.907 41.667 1.82 2.53 0.00 2.73
11 12 4.329801 TCACTCATTTTGCTGCGTATGTAG 59.670 41.667 0.00 0.00 0.00 2.74
12 13 4.249661 TCACTCATTTTGCTGCGTATGTA 58.750 39.130 0.00 0.00 0.00 2.29
13 14 3.073678 TCACTCATTTTGCTGCGTATGT 58.926 40.909 0.00 0.00 0.00 2.29
14 15 3.745332 TCACTCATTTTGCTGCGTATG 57.255 42.857 0.00 0.00 0.00 2.39
15 16 4.637534 AGATTCACTCATTTTGCTGCGTAT 59.362 37.500 0.00 0.00 0.00 3.06
16 17 4.002982 AGATTCACTCATTTTGCTGCGTA 58.997 39.130 0.00 0.00 0.00 4.42
17 18 2.816087 AGATTCACTCATTTTGCTGCGT 59.184 40.909 0.00 0.00 0.00 5.24
18 19 3.482722 AGATTCACTCATTTTGCTGCG 57.517 42.857 0.00 0.00 0.00 5.18
19 20 5.091431 GTGTAGATTCACTCATTTTGCTGC 58.909 41.667 0.00 0.00 35.68 5.25
20 21 6.492007 AGTGTAGATTCACTCATTTTGCTG 57.508 37.500 0.00 0.00 44.07 4.41
73 74 9.626045 CTTTTTAGTGATTTCAAATGGACTACC 57.374 33.333 0.00 0.00 0.00 3.18
76 77 8.912988 TGTCTTTTTAGTGATTTCAAATGGACT 58.087 29.630 0.00 0.00 0.00 3.85
77 78 9.528018 TTGTCTTTTTAGTGATTTCAAATGGAC 57.472 29.630 0.00 0.00 0.00 4.02
94 95 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
95 96 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
96 97 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
97 98 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
98 99 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
99 100 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
100 101 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
101 102 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
102 103 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
103 104 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
104 105 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
105 106 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
106 107 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
107 108 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
108 109 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
109 110 3.967467 ATTCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
110 111 2.850695 ATTCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
111 112 2.764572 TGAATTCTACTCCCTCCGTTCC 59.235 50.000 7.05 0.00 0.00 3.62
112 113 3.738590 GCTGAATTCTACTCCCTCCGTTC 60.739 52.174 7.05 0.00 0.00 3.95
113 114 2.168728 GCTGAATTCTACTCCCTCCGTT 59.831 50.000 7.05 0.00 0.00 4.44
114 115 1.757699 GCTGAATTCTACTCCCTCCGT 59.242 52.381 7.05 0.00 0.00 4.69
115 116 2.035632 AGCTGAATTCTACTCCCTCCG 58.964 52.381 7.05 0.00 0.00 4.63
116 117 3.198853 ACAAGCTGAATTCTACTCCCTCC 59.801 47.826 7.05 0.00 0.00 4.30
117 118 4.081420 TGACAAGCTGAATTCTACTCCCTC 60.081 45.833 7.05 1.36 0.00 4.30
118 119 3.840666 TGACAAGCTGAATTCTACTCCCT 59.159 43.478 7.05 0.00 0.00 4.20
119 120 3.935828 GTGACAAGCTGAATTCTACTCCC 59.064 47.826 7.05 0.00 0.00 4.30
120 121 4.569943 TGTGACAAGCTGAATTCTACTCC 58.430 43.478 7.05 0.00 0.00 3.85
121 122 6.545504 TTTGTGACAAGCTGAATTCTACTC 57.454 37.500 7.05 0.00 0.00 2.59
122 123 6.942532 TTTTGTGACAAGCTGAATTCTACT 57.057 33.333 7.05 0.95 0.00 2.57
123 124 7.362662 TCATTTTGTGACAAGCTGAATTCTAC 58.637 34.615 7.05 0.00 0.00 2.59
188 196 7.652105 TCAGAGTAATAACATCGCAAGGTAATC 59.348 37.037 0.00 0.00 38.47 1.75
199 207 6.260936 CCCAACCACATCAGAGTAATAACATC 59.739 42.308 0.00 0.00 0.00 3.06
214 222 4.488770 ACCTTGATTTAACCCAACCACAT 58.511 39.130 0.00 0.00 0.00 3.21
269 277 8.393671 ACGGTATAATTTGAACTAAAACCACA 57.606 30.769 0.00 0.00 29.64 4.17
292 300 3.359580 GGCAAAGCAAACAAATACGTACG 59.640 43.478 15.01 15.01 0.00 3.67
294 302 3.003482 ACGGCAAAGCAAACAAATACGTA 59.997 39.130 0.00 0.00 0.00 3.57
297 305 3.120041 ACACGGCAAAGCAAACAAATAC 58.880 40.909 0.00 0.00 0.00 1.89
302 310 0.814457 AGAACACGGCAAAGCAAACA 59.186 45.000 0.00 0.00 0.00 2.83
312 320 2.338500 CTAACCAGAGAAGAACACGGC 58.662 52.381 0.00 0.00 0.00 5.68
313 321 2.931320 GCCTAACCAGAGAAGAACACGG 60.931 54.545 0.00 0.00 0.00 4.94
394 404 6.001449 TGATTCCTTTTCCTACCAGGTATG 57.999 41.667 0.00 0.00 36.53 2.39
396 406 5.132144 GGATGATTCCTTTTCCTACCAGGTA 59.868 44.000 0.00 0.00 39.14 3.08
398 408 4.464947 GGATGATTCCTTTTCCTACCAGG 58.535 47.826 0.00 0.00 39.14 4.45
583 614 3.925299 GGCGTTTCTCCTACTGTTTCTAC 59.075 47.826 0.00 0.00 0.00 2.59
585 616 2.633481 AGGCGTTTCTCCTACTGTTTCT 59.367 45.455 0.00 0.00 30.79 2.52
594 627 4.015872 TGAATTTGTAGGCGTTTCTCCT 57.984 40.909 0.00 0.00 37.72 3.69
787 824 2.657143 CGGAGGAGAGGCCCTATATAC 58.343 57.143 0.00 0.00 36.49 1.47
947 986 0.924226 ATTCCCCACCCCGATTCCTT 60.924 55.000 0.00 0.00 0.00 3.36
959 998 2.205342 CCAAACCTCCTCTATTCCCCA 58.795 52.381 0.00 0.00 0.00 4.96
962 1001 4.846168 AACTCCAAACCTCCTCTATTCC 57.154 45.455 0.00 0.00 0.00 3.01
966 1005 4.094476 CACCTAACTCCAAACCTCCTCTA 58.906 47.826 0.00 0.00 0.00 2.43
968 1007 2.615747 GCACCTAACTCCAAACCTCCTC 60.616 54.545 0.00 0.00 0.00 3.71
970 1009 1.822506 GCACCTAACTCCAAACCTCC 58.177 55.000 0.00 0.00 0.00 4.30
1374 1416 4.115199 GCCTGATCCGCCCACCTT 62.115 66.667 0.00 0.00 0.00 3.50
1819 1868 6.093633 CAGGTACAGTAAAGGCCAAAATAGAC 59.906 42.308 5.01 0.00 0.00 2.59
1926 2064 9.492973 CCAAAATTTTCTACTCCATCAAAATGT 57.507 29.630 0.00 0.00 30.60 2.71
1927 2065 9.492973 ACCAAAATTTTCTACTCCATCAAAATG 57.507 29.630 0.00 0.00 30.60 2.32
1930 2068 8.581578 GGTACCAAAATTTTCTACTCCATCAAA 58.418 33.333 7.15 0.00 0.00 2.69
1931 2069 8.117813 GGTACCAAAATTTTCTACTCCATCAA 57.882 34.615 7.15 0.00 0.00 2.57
1932 2070 7.696992 GGTACCAAAATTTTCTACTCCATCA 57.303 36.000 7.15 0.00 0.00 3.07
1954 2092 5.897250 AGTGTTAGGAAAACTTGAATTGGGT 59.103 36.000 0.00 0.00 0.00 4.51
1958 2096 6.463995 TGCAGTGTTAGGAAAACTTGAATT 57.536 33.333 0.00 0.00 0.00 2.17
2005 2143 0.169009 GCGGAGACATTTTGGCTGAC 59.831 55.000 0.00 0.00 34.53 3.51
2160 2298 3.741476 CTCCTTGCTGCCCAACGC 61.741 66.667 0.00 0.00 38.31 4.84
2161 2299 3.058160 CCTCCTTGCTGCCCAACG 61.058 66.667 0.00 0.00 0.00 4.10
2168 2306 2.867109 TTCCTTCTTCCTCCTTGCTG 57.133 50.000 0.00 0.00 0.00 4.41
2189 2327 1.858739 AAGGGTTTATCGCCAGGCCA 61.859 55.000 5.01 0.00 0.00 5.36
2450 2588 5.003096 AGGGACATGACCTTGAAGAATTT 57.997 39.130 13.95 0.00 33.64 1.82
2465 2603 5.127682 GCAAATAAACCATTCAGAGGGACAT 59.872 40.000 0.00 0.00 0.00 3.06
2534 2672 5.022787 AGACATGAGATATTAGGGAGGAGC 58.977 45.833 0.00 0.00 0.00 4.70
2544 2682 4.160439 ACACACACGGAGACATGAGATATT 59.840 41.667 0.00 0.00 0.00 1.28
2560 2698 4.552166 AACATGCTAAAGACACACACAC 57.448 40.909 0.00 0.00 0.00 3.82
2561 2699 5.364778 ACTAACATGCTAAAGACACACACA 58.635 37.500 0.00 0.00 0.00 3.72
2599 2737 3.120060 AGCAAGTCATGATCGAGCAAAAC 60.120 43.478 7.76 9.11 0.00 2.43
2724 2862 8.201554 TGCATAACTAAATGAAGCTACAGAAG 57.798 34.615 0.00 0.00 0.00 2.85
2799 2940 6.476378 ACAGCTGTTCCTTTCAACATATAGT 58.524 36.000 15.25 0.00 35.70 2.12
2802 2943 5.182001 GTGACAGCTGTTCCTTTCAACATAT 59.818 40.000 22.65 0.00 35.70 1.78
2803 2944 4.515191 GTGACAGCTGTTCCTTTCAACATA 59.485 41.667 22.65 0.00 35.70 2.29
2831 2972 7.521099 CGCATAAGAAATGCCAAGAGATTACAT 60.521 37.037 4.50 0.00 41.71 2.29
2842 2983 1.024271 GGAGCGCATAAGAAATGCCA 58.976 50.000 11.47 0.00 41.71 4.92
2843 2984 1.002033 CTGGAGCGCATAAGAAATGCC 60.002 52.381 11.47 0.00 41.71 4.40
2977 3118 1.556911 AGAGAATGGCCAGTGAATCGT 59.443 47.619 12.17 0.00 0.00 3.73
3032 3173 0.829333 GCCTCTCCTCTCATCAGCAA 59.171 55.000 0.00 0.00 0.00 3.91
3034 3175 0.104671 GTGCCTCTCCTCTCATCAGC 59.895 60.000 0.00 0.00 0.00 4.26
3284 3425 2.430921 GGTCACCAGACACGAGCG 60.431 66.667 0.00 0.00 46.80 5.03
3377 3518 4.613437 ACAAAATGGCTATCATGGACCTT 58.387 39.130 0.00 0.00 35.99 3.50
3463 3604 3.126001 TGGCAGATAATCCAACCGATC 57.874 47.619 0.00 0.00 0.00 3.69
3552 3693 5.560966 AAAGGCATCAACCAATTACTACG 57.439 39.130 0.00 0.00 0.00 3.51
3623 3764 3.838244 AGACTTAAGAGTGTGGTTGCA 57.162 42.857 10.09 0.00 35.88 4.08
3628 3769 8.842358 TTATTGGTTAAGACTTAAGAGTGTGG 57.158 34.615 10.09 0.00 35.88 4.17
3660 3803 7.493971 CAGTGAATTACAGAGAAGGGATTACAG 59.506 40.741 0.00 0.00 0.00 2.74
3833 3976 2.357517 AAGAAGGCTGACACGGCG 60.358 61.111 4.80 4.80 36.46 6.46
3842 3985 0.402121 GTGGGGAGTTGAAGAAGGCT 59.598 55.000 0.00 0.00 0.00 4.58
3860 4003 0.544357 TGAGGATCTCCAACGGGTGT 60.544 55.000 0.00 0.00 38.89 4.16
4203 4355 5.479724 TCATCATCATCTATCACCTCAGTCC 59.520 44.000 0.00 0.00 0.00 3.85
4225 4386 6.183360 ACGAAAGGAACTACGTATCATCATCA 60.183 38.462 0.00 0.00 45.78 3.07
4318 4485 2.467838 CGAGCATTCTGATCACGACAT 58.532 47.619 0.00 0.00 31.10 3.06
4329 4496 1.525535 GGCAGCATCCGAGCATTCT 60.526 57.895 0.00 0.00 36.85 2.40
4439 4607 6.650807 TGATGCTACTTTGAGGAGTTACTTTG 59.349 38.462 0.00 0.00 0.00 2.77
4440 4608 6.769512 TGATGCTACTTTGAGGAGTTACTTT 58.230 36.000 0.00 0.00 0.00 2.66
4441 4609 6.360370 TGATGCTACTTTGAGGAGTTACTT 57.640 37.500 0.00 0.00 0.00 2.24
4442 4610 6.382570 AGATGATGCTACTTTGAGGAGTTACT 59.617 38.462 0.00 0.00 0.00 2.24
4443 4611 6.578023 AGATGATGCTACTTTGAGGAGTTAC 58.422 40.000 0.00 0.00 0.00 2.50
4444 4612 6.609212 AGAGATGATGCTACTTTGAGGAGTTA 59.391 38.462 0.00 0.00 0.00 2.24
4445 4613 5.424895 AGAGATGATGCTACTTTGAGGAGTT 59.575 40.000 0.00 0.00 0.00 3.01
4446 4614 4.961730 AGAGATGATGCTACTTTGAGGAGT 59.038 41.667 0.00 0.00 0.00 3.85
4447 4615 5.534207 AGAGATGATGCTACTTTGAGGAG 57.466 43.478 0.00 0.00 0.00 3.69
4448 4616 5.946942 AAGAGATGATGCTACTTTGAGGA 57.053 39.130 0.00 0.00 0.00 3.71
4449 4617 9.585099 GATATAAGAGATGATGCTACTTTGAGG 57.415 37.037 0.00 0.00 0.00 3.86
4450 4618 9.288124 CGATATAAGAGATGATGCTACTTTGAG 57.712 37.037 0.00 0.00 0.00 3.02
4451 4619 8.797438 ACGATATAAGAGATGATGCTACTTTGA 58.203 33.333 0.00 0.00 0.00 2.69
4464 4632 8.535335 ACATGAGGCAATAACGATATAAGAGAT 58.465 33.333 0.00 0.00 0.00 2.75
4473 4641 3.281727 ACCACATGAGGCAATAACGAT 57.718 42.857 9.34 0.00 0.00 3.73
4474 4642 2.779755 ACCACATGAGGCAATAACGA 57.220 45.000 9.34 0.00 0.00 3.85
4479 4647 1.003580 ACGAGAACCACATGAGGCAAT 59.996 47.619 9.34 0.00 0.00 3.56
4497 4665 3.400505 TGTTGAGACGTAGCATAGACG 57.599 47.619 0.00 0.00 45.75 4.18
4505 4673 4.263209 CGCTCATAAGTTGTTGAGACGTAG 59.737 45.833 17.28 3.93 41.53 3.51
4509 4677 5.591643 TTTCGCTCATAAGTTGTTGAGAC 57.408 39.130 17.28 10.01 41.53 3.36
4510 4678 6.612247 TTTTTCGCTCATAAGTTGTTGAGA 57.388 33.333 17.28 0.00 41.53 3.27
4557 4728 3.450817 TCCATTTTAGCATCGGTCTGAGA 59.549 43.478 0.00 0.00 0.00 3.27
4581 4752 5.238432 TGTGAGCAGTTAATACAACTTGGTG 59.762 40.000 0.00 0.00 0.00 4.17
4692 6725 9.967346 CGACTCCTAATGATCTAAACATTCTTA 57.033 33.333 0.00 0.00 38.61 2.10
4693 6726 8.478877 ACGACTCCTAATGATCTAAACATTCTT 58.521 33.333 0.00 0.00 38.61 2.52
4694 6727 8.012957 ACGACTCCTAATGATCTAAACATTCT 57.987 34.615 0.00 0.00 38.61 2.40
4695 6728 8.649973 AACGACTCCTAATGATCTAAACATTC 57.350 34.615 0.00 0.00 38.61 2.67
4696 6729 9.530633 GTAACGACTCCTAATGATCTAAACATT 57.469 33.333 0.00 0.00 40.40 2.71
4697 6730 7.861372 CGTAACGACTCCTAATGATCTAAACAT 59.139 37.037 0.00 0.00 0.00 2.71
4698 6731 7.148188 ACGTAACGACTCCTAATGATCTAAACA 60.148 37.037 0.00 0.00 0.00 2.83
4699 6732 7.192232 ACGTAACGACTCCTAATGATCTAAAC 58.808 38.462 0.00 0.00 0.00 2.01
4700 6733 7.325660 ACGTAACGACTCCTAATGATCTAAA 57.674 36.000 0.00 0.00 0.00 1.85
4701 6734 6.932356 ACGTAACGACTCCTAATGATCTAA 57.068 37.500 0.00 0.00 0.00 2.10
4702 6735 7.212976 AGTACGTAACGACTCCTAATGATCTA 58.787 38.462 0.00 0.00 0.00 1.98
4703 6736 6.054295 AGTACGTAACGACTCCTAATGATCT 58.946 40.000 0.00 0.00 0.00 2.75
4704 6737 6.202570 AGAGTACGTAACGACTCCTAATGATC 59.797 42.308 11.64 0.00 42.62 2.92
4705 6738 6.054295 AGAGTACGTAACGACTCCTAATGAT 58.946 40.000 11.64 0.00 42.62 2.45
4706 6739 5.423015 AGAGTACGTAACGACTCCTAATGA 58.577 41.667 11.64 0.00 42.62 2.57
4707 6740 5.731599 AGAGTACGTAACGACTCCTAATG 57.268 43.478 11.64 0.00 42.62 1.90
4708 6741 6.341316 TGTAGAGTACGTAACGACTCCTAAT 58.659 40.000 11.64 0.00 42.62 1.73
4709 6742 5.720202 TGTAGAGTACGTAACGACTCCTAA 58.280 41.667 11.64 0.00 42.62 2.69
4710 6743 5.324784 TGTAGAGTACGTAACGACTCCTA 57.675 43.478 11.64 3.08 42.62 2.94
4711 6744 4.193826 TGTAGAGTACGTAACGACTCCT 57.806 45.455 11.64 0.00 42.62 3.69
4712 6745 5.751028 ACTATGTAGAGTACGTAACGACTCC 59.249 44.000 11.64 0.38 42.62 3.85
4713 6746 6.820470 ACTATGTAGAGTACGTAACGACTC 57.180 41.667 7.93 7.93 42.06 3.36
4714 6747 7.484975 ACTACTATGTAGAGTACGTAACGACT 58.515 38.462 11.17 0.00 30.37 4.18
4715 6748 7.687005 ACTACTATGTAGAGTACGTAACGAC 57.313 40.000 11.17 2.28 30.37 4.34
4716 6749 7.435488 GGAACTACTATGTAGAGTACGTAACGA 59.565 40.741 11.17 0.00 30.37 3.85
4717 6750 7.436673 AGGAACTACTATGTAGAGTACGTAACG 59.563 40.741 11.17 0.00 36.02 3.18
4721 6754 7.609532 ACAAAGGAACTACTATGTAGAGTACGT 59.390 37.037 11.17 0.00 38.49 3.57
4772 6805 8.867097 AGAGTGTTTAGGTCACTACTTTAATGA 58.133 33.333 0.00 0.00 44.68 2.57
4773 6806 9.490379 AAGAGTGTTTAGGTCACTACTTTAATG 57.510 33.333 0.00 0.00 44.68 1.90
4782 6815 9.628500 AAGAAATTTAAGAGTGTTTAGGTCACT 57.372 29.630 0.00 0.00 46.86 3.41
4787 6820 9.821662 CCGTAAAGAAATTTAAGAGTGTTTAGG 57.178 33.333 0.00 0.00 0.00 2.69
4790 6823 9.946165 CTTCCGTAAAGAAATTTAAGAGTGTTT 57.054 29.630 0.00 0.00 37.12 2.83
4791 6824 8.565416 CCTTCCGTAAAGAAATTTAAGAGTGTT 58.435 33.333 0.00 0.00 37.12 3.32
4792 6825 7.935210 TCCTTCCGTAAAGAAATTTAAGAGTGT 59.065 33.333 0.00 0.00 37.12 3.55
4793 6826 8.319143 TCCTTCCGTAAAGAAATTTAAGAGTG 57.681 34.615 0.00 0.00 37.12 3.51
4825 6858 6.996509 ACGGGTCAATACTACTACTCAAAAA 58.003 36.000 0.00 0.00 0.00 1.94
4826 6859 6.594788 ACGGGTCAATACTACTACTCAAAA 57.405 37.500 0.00 0.00 0.00 2.44
4827 6860 7.886629 ATACGGGTCAATACTACTACTCAAA 57.113 36.000 0.00 0.00 0.00 2.69
4889 7596 2.224548 CGTTCCTTCCTTCCTTCCAACT 60.225 50.000 0.00 0.00 0.00 3.16
4894 7601 1.346722 TCACCGTTCCTTCCTTCCTTC 59.653 52.381 0.00 0.00 0.00 3.46
4896 7603 1.555533 GATCACCGTTCCTTCCTTCCT 59.444 52.381 0.00 0.00 0.00 3.36
4901 7608 0.179108 CCGAGATCACCGTTCCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
4902 7609 0.815734 TCCGAGATCACCGTTCCTTC 59.184 55.000 0.00 0.00 0.00 3.46
4903 7610 1.067071 GTTCCGAGATCACCGTTCCTT 60.067 52.381 0.00 0.00 0.00 3.36
4904 7611 0.531200 GTTCCGAGATCACCGTTCCT 59.469 55.000 0.00 0.00 0.00 3.36
4940 7721 2.683465 GGCATTGGAGCTGGAGGGA 61.683 63.158 0.00 0.00 34.17 4.20
4947 7728 1.272872 ACTGGAATTGGCATTGGAGCT 60.273 47.619 0.00 0.00 34.17 4.09
4948 7729 1.135721 GACTGGAATTGGCATTGGAGC 59.864 52.381 0.00 0.00 0.00 4.70
4949 7730 1.402968 CGACTGGAATTGGCATTGGAG 59.597 52.381 0.00 0.00 0.00 3.86
4950 7731 1.462616 CGACTGGAATTGGCATTGGA 58.537 50.000 0.00 0.00 0.00 3.53
4973 7766 1.005805 TGTGACCAAATGGGGGATGAG 59.994 52.381 4.17 0.00 42.91 2.90
5136 7930 3.288092 AGAAAGAAAGGAACAAACGCCT 58.712 40.909 0.00 0.00 35.61 5.52


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

AutoCloner maintained by Alex Coulton.