Multiple sequence alignment - TraesCS3D01G372500

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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 TraesCS3D01G372500 chr3D 100.000 4401 0 0 1 4401 485356856 485361256 0.000000e+00 8128.0
1 TraesCS3D01G372500 chr3B 92.717 3323 159 50 472 3752 648102510 648105791 0.000000e+00 4719.0
2 TraesCS3D01G372500 chr3B 87.413 286 26 4 4119 4401 648106836 648107114 1.970000e-83 320.0
3 TraesCS3D01G372500 chr3B 96.154 52 2 0 3752 3803 648105747 648105798 7.840000e-13 86.1
4 TraesCS3D01G372500 chr3A 91.251 1886 130 17 1892 3752 628303212 628305087 0.000000e+00 2536.0
5 TraesCS3D01G372500 chr3A 91.997 1437 87 16 478 1897 628301610 628303035 0.000000e+00 1991.0
6 TraesCS3D01G372500 chr3A 90.705 312 23 1 1 312 628301314 628301619 1.140000e-110 411.0
7 TraesCS3D01G372500 chr3A 86.538 364 33 7 3752 4110 628305043 628305395 1.920000e-103 387.0
8 TraesCS3D01G372500 chr3A 89.105 257 11 5 4162 4401 628306557 628306813 1.990000e-78 303.0
9 TraesCS3D01G372500 chr1D 83.884 484 60 14 1016 1491 366223408 366223881 3.120000e-121 446.0
10 TraesCS3D01G372500 chr1D 76.000 450 92 13 2955 3395 366224962 366225404 7.410000e-53 219.0
11 TraesCS3D01G372500 chr1A 83.096 491 61 18 1016 1493 465524785 465524304 1.130000e-115 427.0
12 TraesCS3D01G372500 chr1A 86.813 91 12 0 2961 3051 465523236 465523146 7.790000e-18 102.0
13 TraesCS3D01G372500 chr1B 83.704 405 46 17 1095 1495 491266349 491265961 9.000000e-97 364.0
14 TraesCS3D01G372500 chr7D 93.939 165 8 1 314 476 523432066 523432230 9.450000e-62 248.0
15 TraesCS3D01G372500 chr5A 91.463 164 13 1 314 476 615163661 615163498 1.590000e-54 224.0
16 TraesCS3D01G372500 chr5A 94.444 36 1 1 625 659 42272052 42272017 2.000000e-03 54.7
17 TraesCS3D01G372500 chr4A 89.820 167 17 0 314 480 489060320 489060486 9.590000e-52 215.0
18 TraesCS3D01G372500 chr4A 83.929 168 26 1 310 476 559898343 559898510 4.560000e-35 159.0
19 TraesCS3D01G372500 chr4B 87.730 163 12 1 314 476 452716846 452716692 2.700000e-42 183.0
20 TraesCS3D01G372500 chr5B 85.366 164 23 1 314 476 415053569 415053732 7.570000e-38 169.0
21 TraesCS3D01G372500 chr2B 84.568 162 25 0 314 475 421374817 421374656 1.270000e-35 161.0
22 TraesCS3D01G372500 chr2B 91.667 48 4 0 612 659 435690563 435690516 2.840000e-07 67.6
23 TraesCS3D01G372500 chr2D 80.588 170 27 3 307 476 38195015 38194852 4.620000e-25 126.0
24 TraesCS3D01G372500 chr6D 94.737 38 2 0 435 472 63734697 63734734 4.750000e-05 60.2
25 TraesCS3D01G372500 chrUn 94.444 36 1 1 625 659 255357032 255357067 2.000000e-03 54.7


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 TraesCS3D01G372500 chr3D 485356856 485361256 4400 False 8128.000000 8128 100.000000 1 4401 1 chr3D.!!$F1 4400
1 TraesCS3D01G372500 chr3B 648102510 648107114 4604 False 1708.366667 4719 92.094667 472 4401 3 chr3B.!!$F1 3929
2 TraesCS3D01G372500 chr3A 628301314 628306813 5499 False 1125.600000 2536 89.919200 1 4401 5 chr3A.!!$F1 4400
3 TraesCS3D01G372500 chr1D 366223408 366225404 1996 False 332.500000 446 79.942000 1016 3395 2 chr1D.!!$F1 2379
4 TraesCS3D01G372500 chr1A 465523146 465524785 1639 True 264.500000 427 84.954500 1016 3051 2 chr1A.!!$R1 2035

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
226 227 0.104120 TGGAGATATCGCAACGGGTG 59.896 55.0 8.79 0.0 0.00 4.61 F
1362 1430 0.106708 TCGTCAGCAACCTCAAGCTT 59.893 50.0 0.00 0.0 39.50 3.74 F
1562 1989 2.028523 CGTGAGATTTAGCTCTTGCGTG 59.971 50.0 0.00 0.0 45.42 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2984 1.202976 ACAAACCTTGCAGCTCAGGAT 60.203 47.619 16.13 3.60 0.00 3.24 R
2515 3429 0.176219 AAGCAAAAGCAGCACAGCAA 59.824 45.000 0.00 0.00 36.85 3.91 R
3454 4405 0.868602 CTGTATACGTTCCGCCGGTG 60.869 60.000 8.42 8.42 0.00 4.94 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
45 46 0.942410 CGCGGGTTGTTCTTTCTCGA 60.942 55.000 0.00 0.00 0.00 4.04
46 47 0.790814 GCGGGTTGTTCTTTCTCGAG 59.209 55.000 5.93 5.93 0.00 4.04
49 50 2.545113 CGGGTTGTTCTTTCTCGAGTCA 60.545 50.000 13.13 0.00 0.00 3.41
59 60 2.073252 TCTCGAGTCAGGTATGGCAT 57.927 50.000 13.13 4.88 31.62 4.40
77 78 2.233271 CATGAAGTGCTTTCCTGGTGT 58.767 47.619 0.00 0.00 34.77 4.16
78 79 2.435372 TGAAGTGCTTTCCTGGTGTT 57.565 45.000 0.00 0.00 34.77 3.32
118 119 0.321919 TGCCTGGTGATGTGCTTCTC 60.322 55.000 0.00 0.00 0.00 2.87
134 135 0.832135 TCTCTGAGTGGTGGGTGTCC 60.832 60.000 4.32 0.00 0.00 4.02
136 137 0.399949 TCTGAGTGGTGGGTGTCCTT 60.400 55.000 0.00 0.00 0.00 3.36
176 177 2.247437 GCACCGCCAAGATCGATCC 61.247 63.158 21.66 5.59 0.00 3.36
207 208 1.002134 CTCACGGCCTGGTCCATTT 60.002 57.895 0.00 0.00 0.00 2.32
208 209 1.303236 TCACGGCCTGGTCCATTTG 60.303 57.895 0.00 2.45 0.00 2.32
222 223 3.059597 GTCCATTTGGAGATATCGCAACG 60.060 47.826 8.79 0.00 46.49 4.10
223 224 2.224079 CCATTTGGAGATATCGCAACGG 59.776 50.000 8.79 0.00 37.39 4.44
224 225 1.948104 TTTGGAGATATCGCAACGGG 58.052 50.000 8.79 0.00 0.00 5.28
225 226 0.828022 TTGGAGATATCGCAACGGGT 59.172 50.000 8.79 0.00 0.00 5.28
226 227 0.104120 TGGAGATATCGCAACGGGTG 59.896 55.000 8.79 0.00 0.00 4.61
244 245 3.257561 CATCTTCGACGGGCAGCG 61.258 66.667 0.00 0.00 0.00 5.18
245 246 4.514577 ATCTTCGACGGGCAGCGG 62.515 66.667 0.00 0.00 0.00 5.52
263 264 3.441290 CCCTCCGTCTCGCGTCTT 61.441 66.667 5.77 0.00 39.32 3.01
269 270 2.710971 CGTCTCGCGTCTTGTGCAG 61.711 63.158 5.77 0.00 35.54 4.41
310 311 0.811616 CTATGAGCCAAGGCCGACAC 60.812 60.000 7.62 0.00 43.17 3.67
311 312 2.252072 TATGAGCCAAGGCCGACACC 62.252 60.000 7.62 0.00 43.17 4.16
326 327 2.847234 ACCCGTGGTGGAGCTTCA 60.847 61.111 0.00 0.00 42.00 3.02
327 328 2.358737 CCCGTGGTGGAGCTTCAC 60.359 66.667 17.52 17.52 42.00 3.18
335 336 2.730550 GTGGAGCTTCACCCAAATTG 57.269 50.000 14.82 0.00 33.69 2.32
336 337 0.968405 TGGAGCTTCACCCAAATTGC 59.032 50.000 0.00 0.00 0.00 3.56
337 338 1.260544 GGAGCTTCACCCAAATTGCT 58.739 50.000 0.00 0.00 0.00 3.91
338 339 1.067354 GGAGCTTCACCCAAATTGCTG 60.067 52.381 0.00 0.00 0.00 4.41
339 340 0.971386 AGCTTCACCCAAATTGCTGG 59.029 50.000 0.00 0.00 36.10 4.85
345 346 4.455906 CCAAATTGCTGGGCGGGC 62.456 66.667 0.00 0.00 32.32 6.13
346 347 4.455906 CAAATTGCTGGGCGGGCC 62.456 66.667 14.65 14.65 0.00 5.80
384 385 7.611213 CGAAGGAAATTACTACTGGAATGTT 57.389 36.000 0.00 0.00 0.00 2.71
385 386 8.712285 CGAAGGAAATTACTACTGGAATGTTA 57.288 34.615 0.00 0.00 0.00 2.41
386 387 9.326413 CGAAGGAAATTACTACTGGAATGTTAT 57.674 33.333 0.00 0.00 0.00 1.89
389 390 9.628500 AGGAAATTACTACTGGAATGTTATTCC 57.372 33.333 12.53 12.53 39.03 3.01
390 391 9.403583 GGAAATTACTACTGGAATGTTATTCCA 57.596 33.333 19.11 19.11 45.61 3.53
393 394 8.924511 ATTACTACTGGAATGTTATTCCATGG 57.075 34.615 20.17 4.97 46.47 3.66
394 395 5.133221 ACTACTGGAATGTTATTCCATGGC 58.867 41.667 20.17 0.00 46.47 4.40
395 396 3.299503 ACTGGAATGTTATTCCATGGCC 58.700 45.455 20.17 0.00 46.47 5.36
396 397 3.052642 ACTGGAATGTTATTCCATGGCCT 60.053 43.478 20.17 0.00 46.47 5.19
397 398 4.167892 ACTGGAATGTTATTCCATGGCCTA 59.832 41.667 20.17 0.00 46.47 3.93
398 399 5.136068 TGGAATGTTATTCCATGGCCTAA 57.864 39.130 17.01 4.29 43.17 2.69
399 400 5.714863 TGGAATGTTATTCCATGGCCTAAT 58.285 37.500 17.01 4.53 43.17 1.73
400 401 6.857848 TGGAATGTTATTCCATGGCCTAATA 58.142 36.000 17.01 3.45 43.17 0.98
401 402 6.947733 TGGAATGTTATTCCATGGCCTAATAG 59.052 38.462 17.01 0.00 43.17 1.73
402 403 6.948309 GGAATGTTATTCCATGGCCTAATAGT 59.052 38.462 6.96 4.83 38.45 2.12
403 404 8.107095 GGAATGTTATTCCATGGCCTAATAGTA 58.893 37.037 6.96 0.42 38.45 1.82
404 405 9.167311 GAATGTTATTCCATGGCCTAATAGTAG 57.833 37.037 6.96 0.00 0.00 2.57
428 429 6.621737 GTGTACATCACAGAAATTTGCATG 57.378 37.500 0.00 0.00 45.51 4.06
429 430 6.151691 GTGTACATCACAGAAATTTGCATGT 58.848 36.000 0.00 0.00 45.51 3.21
430 431 6.088483 GTGTACATCACAGAAATTTGCATGTG 59.912 38.462 16.29 16.29 45.51 3.21
431 432 5.204409 ACATCACAGAAATTTGCATGTGT 57.796 34.783 19.43 0.00 42.80 3.72
432 433 5.603596 ACATCACAGAAATTTGCATGTGTT 58.396 33.333 19.43 12.87 42.80 3.32
433 434 5.464057 ACATCACAGAAATTTGCATGTGTTG 59.536 36.000 22.34 22.34 43.78 3.33
434 435 4.370049 TCACAGAAATTTGCATGTGTTGG 58.630 39.130 19.43 3.60 42.80 3.77
435 436 3.495377 CACAGAAATTTGCATGTGTTGGG 59.505 43.478 15.00 0.00 38.54 4.12
436 437 2.481185 CAGAAATTTGCATGTGTTGGGC 59.519 45.455 0.00 0.00 0.00 5.36
437 438 1.460359 GAAATTTGCATGTGTTGGGCG 59.540 47.619 0.00 0.00 0.00 6.13
438 439 0.320596 AATTTGCATGTGTTGGGCGG 60.321 50.000 0.00 0.00 0.00 6.13
439 440 2.169937 ATTTGCATGTGTTGGGCGGG 62.170 55.000 0.00 0.00 0.00 6.13
558 559 1.002011 GAGCAACCCTGGTCTTCCC 60.002 63.158 0.00 0.00 44.97 3.97
562 563 1.229400 AACCCTGGTCTTCCCGCTA 60.229 57.895 0.00 0.00 35.15 4.26
563 564 1.551019 AACCCTGGTCTTCCCGCTAC 61.551 60.000 0.00 0.00 35.15 3.58
570 571 1.405121 GGTCTTCCCGCTACGTTCATT 60.405 52.381 0.00 0.00 0.00 2.57
573 574 1.393539 CTTCCCGCTACGTTCATTGTG 59.606 52.381 0.00 0.00 0.00 3.33
577 578 1.319374 CCGCTACGTTCATTGTGTACG 59.681 52.381 0.00 7.42 44.80 3.67
580 581 2.471749 GCTACGTTCATTGTGTACGCAC 60.472 50.000 9.03 0.00 43.43 5.34
586 587 2.984562 TCATTGTGTACGCACCATCAT 58.015 42.857 9.03 0.00 44.65 2.45
588 589 2.177394 TTGTGTACGCACCATCATGT 57.823 45.000 9.03 0.00 44.65 3.21
589 590 3.320673 TTGTGTACGCACCATCATGTA 57.679 42.857 9.03 0.00 44.65 2.29
592 593 4.364860 TGTGTACGCACCATCATGTATAC 58.635 43.478 4.65 0.00 44.65 1.47
593 594 4.098807 TGTGTACGCACCATCATGTATACT 59.901 41.667 4.65 0.00 44.65 2.12
594 595 4.680110 GTGTACGCACCATCATGTATACTC 59.320 45.833 4.17 0.00 39.61 2.59
595 596 4.339814 TGTACGCACCATCATGTATACTCA 59.660 41.667 4.17 0.00 0.00 3.41
596 597 3.717707 ACGCACCATCATGTATACTCAC 58.282 45.455 4.17 0.00 0.00 3.51
597 598 3.384789 ACGCACCATCATGTATACTCACT 59.615 43.478 4.17 0.00 0.00 3.41
599 600 4.697514 GCACCATCATGTATACTCACTGT 58.302 43.478 4.17 0.00 0.00 3.55
606 627 8.703336 CCATCATGTATACTCACTGTATTTTCG 58.297 37.037 4.17 0.00 41.64 3.46
619 640 7.606456 TCACTGTATTTTCGCTTTCCTTCTAAT 59.394 33.333 0.00 0.00 0.00 1.73
622 643 9.922305 CTGTATTTTCGCTTTCCTTCTAATAAG 57.078 33.333 0.00 0.00 0.00 1.73
624 645 9.106070 GTATTTTCGCTTTCCTTCTAATAAGGA 57.894 33.333 2.34 2.34 44.23 3.36
721 743 2.544685 CCGTGTCTTCTGCTTATCCTG 58.455 52.381 0.00 0.00 0.00 3.86
907 930 2.531685 CTCACCTCCCCAACCCCA 60.532 66.667 0.00 0.00 0.00 4.96
932 955 4.335584 CGAGGGCGCGAGATCTCC 62.336 72.222 17.13 8.89 0.00 3.71
1035 1064 2.202932 GACACGATCCCGCTGCAT 60.203 61.111 0.00 0.00 39.95 3.96
1362 1430 0.106708 TCGTCAGCAACCTCAAGCTT 59.893 50.000 0.00 0.00 39.50 3.74
1562 1989 2.028523 CGTGAGATTTAGCTCTTGCGTG 59.971 50.000 0.00 0.00 45.42 5.34
1804 2495 6.699575 AGTGCTGTATCCAATTAATTCCAC 57.300 37.500 0.00 0.00 0.00 4.02
1870 2562 4.501400 GCACTTATTCTGCTGTGGGTTTTT 60.501 41.667 0.00 0.00 0.00 1.94
1951 2841 6.922957 GCACTATGTTCTTGGTTCAAAATTGA 59.077 34.615 0.00 0.00 34.92 2.57
1958 2848 7.826252 TGTTCTTGGTTCAAAATTGATTTGGAA 59.174 29.630 2.82 2.82 46.85 3.53
2013 2903 3.110705 ACTAGTGGTGAATGATGAGCCT 58.889 45.455 0.00 0.00 0.00 4.58
2062 2955 9.045745 ACCATTGGTCCAATTTTTATGTTCTAT 57.954 29.630 14.80 0.00 31.05 1.98
2184 3085 2.699251 TGGTATAGTCATACTGCGCG 57.301 50.000 0.00 0.00 37.70 6.86
2219 3121 6.282199 GTTCTCTTAGAACCTGTGGATGTA 57.718 41.667 8.32 0.00 46.68 2.29
2224 3126 7.785028 TCTCTTAGAACCTGTGGATGTATATGT 59.215 37.037 0.00 0.00 0.00 2.29
2251 3163 4.635765 TCCGAATGCTTCTAAGATTGGTTG 59.364 41.667 0.00 0.00 0.00 3.77
2371 3285 4.622260 AAGTGCCCTTGTGCAAAATATT 57.378 36.364 0.00 0.00 44.11 1.28
2515 3429 7.550551 TCGTCAATATTTTCTCTTGCAGAAGAT 59.449 33.333 1.42 0.00 42.37 2.40
2617 3532 7.359181 GCAGAAAGTATGCCAAAACACAATTAC 60.359 37.037 0.00 0.00 37.73 1.89
2653 3568 8.649973 TGTTTTTACCATGTTCAAATGTAACC 57.350 30.769 0.00 0.00 0.00 2.85
2686 3601 5.443230 TGTCATGGAATGTTGTGGGTATA 57.557 39.130 0.00 0.00 46.80 1.47
2688 3603 4.275936 GTCATGGAATGTTGTGGGTATAGC 59.724 45.833 0.00 0.00 46.80 2.97
2716 3631 8.995027 TTACATTATATGGAAGAAAGCATGGT 57.005 30.769 0.00 0.00 33.60 3.55
2780 3695 9.413048 GAACATTATAGCTACAGACTTATGGAC 57.587 37.037 0.00 0.00 0.00 4.02
2811 3750 9.962759 CACTTTTGAACTTTTTCTGATTTTGAG 57.037 29.630 0.00 0.00 32.36 3.02
2821 3760 9.339492 CTTTTTCTGATTTTGAGTTCTCTATGC 57.661 33.333 1.53 0.00 0.00 3.14
2844 3783 6.714356 TGCTGGCATATTAGCATTGTTATGTA 59.286 34.615 0.00 0.00 44.36 2.29
2864 3803 3.850122 AATTTTCTTCTAGCGGCCAAC 57.150 42.857 2.24 0.00 0.00 3.77
2871 3810 3.702548 TCTTCTAGCGGCCAACATACTTA 59.297 43.478 2.24 0.00 0.00 2.24
2876 3815 3.074412 AGCGGCCAACATACTTATATGC 58.926 45.455 2.24 0.00 41.83 3.14
2877 3816 2.811431 GCGGCCAACATACTTATATGCA 59.189 45.455 2.24 0.00 41.83 3.96
2879 3818 4.437390 GCGGCCAACATACTTATATGCATC 60.437 45.833 0.19 0.00 41.83 3.91
2891 3830 9.751542 ATACTTATATGCATCGCTTATAGTTCC 57.248 33.333 0.19 0.00 34.35 3.62
2896 3835 2.300437 GCATCGCTTATAGTTCCCCTCT 59.700 50.000 0.00 0.00 0.00 3.69
2935 3874 5.104982 ACAAATTTGTCTTTGCTTCCTTCCA 60.105 36.000 18.13 0.00 39.26 3.53
2937 3876 6.916360 AATTTGTCTTTGCTTCCTTCCATA 57.084 33.333 0.00 0.00 0.00 2.74
2950 3889 6.455360 TTCCTTCCATACAAAATGCTGATC 57.545 37.500 0.00 0.00 0.00 2.92
2952 3891 6.899089 TCCTTCCATACAAAATGCTGATCTA 58.101 36.000 0.00 0.00 0.00 1.98
2959 3898 8.671921 CCATACAAAATGCTGATCTATATGTCC 58.328 37.037 0.00 0.00 0.00 4.02
2993 3932 2.736721 GTCTGAAGTATTTGCTGTCGCA 59.263 45.455 0.00 0.00 46.24 5.10
3069 4015 2.665008 AAGCGCTGCCTCTCACACAA 62.665 55.000 12.58 0.00 0.00 3.33
3071 4017 1.864862 CGCTGCCTCTCACACAAAG 59.135 57.895 0.00 0.00 0.00 2.77
3088 4039 4.606071 GCACACTTGCTCGATCCT 57.394 55.556 0.00 0.00 46.17 3.24
3091 4042 2.555199 GCACACTTGCTCGATCCTAAT 58.445 47.619 0.00 0.00 46.17 1.73
3115 4066 7.624360 TTATACCTGCTGTGGAATTTTGTAG 57.376 36.000 0.00 0.00 0.00 2.74
3133 4084 7.977789 TTTGTAGTGATTTATTGCTGTCTCA 57.022 32.000 0.00 0.00 0.00 3.27
3208 4159 2.584835 TGTTTCCTCTGGATGTTGGG 57.415 50.000 0.00 0.00 0.00 4.12
3214 4165 2.276309 CTCTGGATGTTGGGGCCCTC 62.276 65.000 25.93 17.17 0.00 4.30
3440 4391 9.764870 CAATGTAGTAACATCTGAAATGTTGAG 57.235 33.333 12.42 0.00 45.79 3.02
3454 4405 1.611491 TGTTGAGATTTTCCCCGTTGC 59.389 47.619 0.00 0.00 0.00 4.17
3555 4506 3.001414 CCTTCACATGAGCAAGAGACAG 58.999 50.000 0.00 0.00 0.00 3.51
3579 4530 9.696917 CAGAAGGCTGTAAAATTAGTTGAAAAT 57.303 29.630 0.00 0.00 37.37 1.82
3616 4567 4.202524 TGGTCTACTGTTGTAAAGGGCATT 60.203 41.667 0.00 0.00 0.00 3.56
3642 4593 2.095415 GCTTTGGACCACGTAATTGACC 60.095 50.000 0.00 0.00 0.00 4.02
3643 4594 2.932855 TTGGACCACGTAATTGACCA 57.067 45.000 0.00 0.00 0.00 4.02
3752 4703 2.905415 ATTCATCTGGTTGCCCTTGA 57.095 45.000 0.00 0.00 0.00 3.02
3755 4706 2.956132 TCATCTGGTTGCCCTTGAAAA 58.044 42.857 0.00 0.00 0.00 2.29
3756 4707 3.303938 TCATCTGGTTGCCCTTGAAAAA 58.696 40.909 0.00 0.00 0.00 1.94
3758 4709 5.083122 TCATCTGGTTGCCCTTGAAAAATA 58.917 37.500 0.00 0.00 0.00 1.40
3760 4711 6.213195 TCATCTGGTTGCCCTTGAAAAATATT 59.787 34.615 0.00 0.00 0.00 1.28
3762 4713 5.046663 TCTGGTTGCCCTTGAAAAATATTCC 60.047 40.000 0.00 0.00 0.00 3.01
3764 4715 5.072329 TGGTTGCCCTTGAAAAATATTCCAA 59.928 36.000 0.00 0.00 0.00 3.53
3765 4716 5.643348 GGTTGCCCTTGAAAAATATTCCAAG 59.357 40.000 13.77 13.77 36.64 3.61
3770 4721 6.726258 CCTTGAAAAATATTCCAAGGCAAC 57.274 37.500 21.22 0.00 45.98 4.17
3787 4738 4.781934 GGCAACTAGGTAATTCATCTGGT 58.218 43.478 0.00 0.00 0.00 4.00
3789 4740 5.066505 GGCAACTAGGTAATTCATCTGGTTG 59.933 44.000 18.54 18.54 46.02 3.77
3792 4743 3.018423 AGGTAATTCATCTGGTTGCCC 57.982 47.619 0.00 0.00 0.00 5.36
3793 4744 2.582636 AGGTAATTCATCTGGTTGCCCT 59.417 45.455 0.00 0.00 0.00 5.19
3794 4745 3.011708 AGGTAATTCATCTGGTTGCCCTT 59.988 43.478 0.00 0.00 0.00 3.95
3795 4746 3.131046 GGTAATTCATCTGGTTGCCCTTG 59.869 47.826 0.00 0.00 0.00 3.61
3796 4747 1.856629 ATTCATCTGGTTGCCCTTGG 58.143 50.000 0.00 0.00 0.00 3.61
3797 4748 0.776810 TTCATCTGGTTGCCCTTGGA 59.223 50.000 0.00 0.00 0.00 3.53
3799 4750 1.108776 CATCTGGTTGCCCTTGGATG 58.891 55.000 0.00 0.00 31.83 3.51
3800 4751 0.706433 ATCTGGTTGCCCTTGGATGT 59.294 50.000 0.00 0.00 0.00 3.06
3801 4752 1.367346 TCTGGTTGCCCTTGGATGTA 58.633 50.000 0.00 0.00 0.00 2.29
3802 4753 1.004277 TCTGGTTGCCCTTGGATGTAC 59.996 52.381 0.00 0.00 0.00 2.90
3811 4837 3.503748 GCCCTTGGATGTACATAATCTGC 59.496 47.826 8.71 4.32 0.00 4.26
3845 4871 3.886505 TGCCCGTTCTTATTGTGAAACTT 59.113 39.130 0.00 0.00 38.04 2.66
3846 4872 4.023536 TGCCCGTTCTTATTGTGAAACTTC 60.024 41.667 0.00 0.00 38.04 3.01
3849 4875 6.072893 GCCCGTTCTTATTGTGAAACTTCTTA 60.073 38.462 0.00 0.00 38.04 2.10
3856 4884 7.604164 TCTTATTGTGAAACTTCTTAGCCTCAG 59.396 37.037 0.00 0.00 38.04 3.35
3921 4952 1.678101 AGGCTGTTTGTGACTGAAAGC 59.322 47.619 0.00 0.00 37.60 3.51
3949 5008 3.187637 TGTGTCTGCTTTTATTGCGTACC 59.812 43.478 0.00 0.00 0.00 3.34
3968 5027 3.858247 ACCGGTATTGTCTAACTTCTGC 58.142 45.455 4.49 0.00 0.00 4.26
3986 5045 3.517500 TCTGCCATATCTGTGTTGTGGTA 59.482 43.478 0.00 0.00 32.56 3.25
4041 5127 1.374758 GCTGTGTCCTAGCGTTGCT 60.375 57.895 0.00 0.00 43.41 3.91
4054 5140 1.453155 CGTTGCTCACCAGCCTTATT 58.547 50.000 0.00 0.00 46.26 1.40
4055 5141 2.627945 CGTTGCTCACCAGCCTTATTA 58.372 47.619 0.00 0.00 46.26 0.98
4091 5177 1.892474 CGGATTTGGTTCCATGTGGTT 59.108 47.619 0.00 0.00 35.34 3.67
4110 5196 1.031571 TGCGAGGAAATCATGTGCCC 61.032 55.000 0.00 0.00 0.00 5.36
4111 5197 0.749454 GCGAGGAAATCATGTGCCCT 60.749 55.000 0.00 0.00 0.00 5.19
4112 5198 1.475034 GCGAGGAAATCATGTGCCCTA 60.475 52.381 0.00 0.00 0.00 3.53
4113 5199 2.487934 CGAGGAAATCATGTGCCCTAG 58.512 52.381 0.00 0.00 0.00 3.02
4114 5200 2.808202 CGAGGAAATCATGTGCCCTAGG 60.808 54.545 0.06 0.06 0.00 3.02
4116 5202 2.852449 AGGAAATCATGTGCCCTAGGAA 59.148 45.455 11.48 0.00 0.00 3.36
4117 5203 3.269381 AGGAAATCATGTGCCCTAGGAAA 59.731 43.478 11.48 0.00 0.00 3.13
4120 5805 2.507407 TCATGTGCCCTAGGAAAACC 57.493 50.000 11.48 0.00 0.00 3.27
4132 5817 1.431845 GAAAACCGCATAAGCCGGG 59.568 57.895 2.18 0.00 38.29 5.73
4153 5838 1.094073 CACACTGCATCTGCCCTAGC 61.094 60.000 0.00 0.00 41.18 3.42
4203 6406 2.007608 GATACCGGCACTTTCTGAACC 58.992 52.381 0.00 0.00 0.00 3.62
4269 6472 2.032681 ACAGAGCGGTCTTTGCCC 59.967 61.111 15.83 0.00 0.00 5.36
4290 6493 4.141459 CCCCTCTAGTAGAAACCCAAATCC 60.141 50.000 0.64 0.00 0.00 3.01
4355 6575 3.059800 GCAATCCGAATAAGGCGTTCTAC 60.060 47.826 0.00 0.00 0.00 2.59
4357 6577 3.431922 TCCGAATAAGGCGTTCTACAG 57.568 47.619 0.00 0.00 0.00 2.74
4359 6579 1.517276 CGAATAAGGCGTTCTACAGCG 59.483 52.381 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.790814 CTCGAGAAAGAACAACCCGC 59.209 55.000 6.58 0.00 0.00 6.13
28 29 2.059541 GACTCGAGAAAGAACAACCCG 58.940 52.381 21.68 0.00 0.00 5.28
30 31 3.060602 CCTGACTCGAGAAAGAACAACC 58.939 50.000 21.68 0.00 0.00 3.77
45 46 3.272574 CACTTCATGCCATACCTGACT 57.727 47.619 0.00 0.00 0.00 3.41
59 60 2.023673 CAACACCAGGAAAGCACTTCA 58.976 47.619 0.00 0.00 35.55 3.02
77 78 1.374125 CAGTGTCGGCGTGGATCAA 60.374 57.895 6.85 0.00 0.00 2.57
78 79 2.261361 CAGTGTCGGCGTGGATCA 59.739 61.111 6.85 0.00 0.00 2.92
103 104 1.973515 ACTCAGAGAAGCACATCACCA 59.026 47.619 3.79 0.00 0.00 4.17
118 119 0.035458 GAAGGACACCCACCACTCAG 59.965 60.000 0.00 0.00 33.88 3.35
134 135 3.207669 GGGGCATGCGAGCAGAAG 61.208 66.667 12.44 0.00 35.83 2.85
156 157 1.766143 GATCGATCTTGGCGGTGCAC 61.766 60.000 18.29 8.80 0.00 4.57
176 177 2.586418 CGTGAGCATGATGACGGAG 58.414 57.895 15.33 0.00 0.00 4.63
207 208 0.104120 CACCCGTTGCGATATCTCCA 59.896 55.000 0.34 0.00 0.00 3.86
208 209 1.222115 GCACCCGTTGCGATATCTCC 61.222 60.000 0.34 0.00 42.79 3.71
222 223 2.511600 CCCGTCGAAGATGCACCC 60.512 66.667 0.00 0.00 43.31 4.61
223 224 3.195698 GCCCGTCGAAGATGCACC 61.196 66.667 0.00 0.00 43.31 5.01
224 225 2.434185 TGCCCGTCGAAGATGCAC 60.434 61.111 10.42 0.00 43.31 4.57
225 226 2.125552 CTGCCCGTCGAAGATGCA 60.126 61.111 12.97 12.97 43.31 3.96
226 227 3.567797 GCTGCCCGTCGAAGATGC 61.568 66.667 0.00 2.92 43.31 3.91
227 228 3.257561 CGCTGCCCGTCGAAGATG 61.258 66.667 0.00 0.00 44.47 2.90
259 260 2.435805 TCCTGGATATCCTGCACAAGAC 59.564 50.000 22.35 0.00 36.82 3.01
263 264 0.752658 CGTCCTGGATATCCTGCACA 59.247 55.000 22.35 6.25 36.82 4.57
269 270 0.318762 GTGCCTCGTCCTGGATATCC 59.681 60.000 15.39 15.39 0.00 2.59
310 311 2.358737 GTGAAGCTCCACCACGGG 60.359 66.667 0.00 0.00 34.36 5.28
316 317 1.337167 GCAATTTGGGTGAAGCTCCAC 60.337 52.381 0.00 0.00 36.37 4.02
317 318 0.968405 GCAATTTGGGTGAAGCTCCA 59.032 50.000 0.00 0.00 0.00 3.86
318 319 1.067354 CAGCAATTTGGGTGAAGCTCC 60.067 52.381 0.00 0.00 38.52 4.70
319 320 1.067354 CCAGCAATTTGGGTGAAGCTC 60.067 52.381 0.00 0.00 38.52 4.09
320 321 0.971386 CCAGCAATTTGGGTGAAGCT 59.029 50.000 0.00 0.00 38.52 3.74
321 322 3.520187 CCAGCAATTTGGGTGAAGC 57.480 52.632 0.00 0.00 38.52 3.86
328 329 4.455906 GCCCGCCCAGCAATTTGG 62.456 66.667 0.00 0.00 38.00 3.28
329 330 4.455906 GGCCCGCCCAGCAATTTG 62.456 66.667 0.00 0.00 0.00 2.32
352 353 1.134367 GTAATTTCCTTCGGCTTGGCC 59.866 52.381 0.00 0.00 46.75 5.36
353 354 2.092323 AGTAATTTCCTTCGGCTTGGC 58.908 47.619 0.00 0.00 0.00 4.52
354 355 4.332819 CAGTAGTAATTTCCTTCGGCTTGG 59.667 45.833 0.00 0.00 0.00 3.61
355 356 4.332819 CCAGTAGTAATTTCCTTCGGCTTG 59.667 45.833 0.00 0.00 0.00 4.01
356 357 4.224370 TCCAGTAGTAATTTCCTTCGGCTT 59.776 41.667 0.00 0.00 0.00 4.35
357 358 3.773119 TCCAGTAGTAATTTCCTTCGGCT 59.227 43.478 0.00 0.00 0.00 5.52
358 359 4.133013 TCCAGTAGTAATTTCCTTCGGC 57.867 45.455 0.00 0.00 0.00 5.54
359 360 6.113411 ACATTCCAGTAGTAATTTCCTTCGG 58.887 40.000 0.00 0.00 0.00 4.30
360 361 7.611213 AACATTCCAGTAGTAATTTCCTTCG 57.389 36.000 0.00 0.00 0.00 3.79
363 364 9.628500 GGAATAACATTCCAGTAGTAATTTCCT 57.372 33.333 12.12 0.00 38.45 3.36
364 365 9.403583 TGGAATAACATTCCAGTAGTAATTTCC 57.596 33.333 15.08 0.00 43.17 3.13
377 378 6.948309 ACTATTAGGCCATGGAATAACATTCC 59.052 38.462 18.40 10.42 39.03 3.01
378 379 9.167311 CTACTATTAGGCCATGGAATAACATTC 57.833 37.037 18.40 0.00 0.00 2.67
379 380 8.109634 CCTACTATTAGGCCATGGAATAACATT 58.890 37.037 18.40 0.00 38.72 2.71
380 381 7.633789 CCTACTATTAGGCCATGGAATAACAT 58.366 38.462 18.40 0.00 38.72 2.71
381 382 7.016153 CCTACTATTAGGCCATGGAATAACA 57.984 40.000 18.40 1.36 38.72 2.41
406 407 6.151004 CACATGCAAATTTCTGTGATGTACA 58.849 36.000 9.74 0.00 41.11 2.90
407 408 6.151691 ACACATGCAAATTTCTGTGATGTAC 58.848 36.000 19.77 0.00 41.11 2.90
408 409 6.330004 ACACATGCAAATTTCTGTGATGTA 57.670 33.333 19.77 0.00 41.11 2.29
409 410 5.204409 ACACATGCAAATTTCTGTGATGT 57.796 34.783 19.77 9.91 41.11 3.06
410 411 5.107259 CCAACACATGCAAATTTCTGTGATG 60.107 40.000 19.77 17.39 41.11 3.07
411 412 4.992319 CCAACACATGCAAATTTCTGTGAT 59.008 37.500 19.77 7.68 41.11 3.06
412 413 4.370049 CCAACACATGCAAATTTCTGTGA 58.630 39.130 19.77 0.00 41.11 3.58
413 414 3.495377 CCCAACACATGCAAATTTCTGTG 59.505 43.478 13.02 13.02 43.54 3.66
414 415 3.731089 CCCAACACATGCAAATTTCTGT 58.269 40.909 0.00 0.00 0.00 3.41
415 416 2.481185 GCCCAACACATGCAAATTTCTG 59.519 45.455 0.00 0.00 0.00 3.02
416 417 2.769893 GCCCAACACATGCAAATTTCT 58.230 42.857 0.00 0.00 0.00 2.52
417 418 1.460359 CGCCCAACACATGCAAATTTC 59.540 47.619 0.00 0.00 0.00 2.17
418 419 1.510776 CGCCCAACACATGCAAATTT 58.489 45.000 0.00 0.00 0.00 1.82
419 420 0.320596 CCGCCCAACACATGCAAATT 60.321 50.000 0.00 0.00 0.00 1.82
420 421 1.292860 CCGCCCAACACATGCAAAT 59.707 52.632 0.00 0.00 0.00 2.32
421 422 2.733301 CCGCCCAACACATGCAAA 59.267 55.556 0.00 0.00 0.00 3.68
422 423 3.301554 CCCGCCCAACACATGCAA 61.302 61.111 0.00 0.00 0.00 4.08
472 473 1.586028 CTTTGATGTTGGCCGGTGG 59.414 57.895 1.90 0.00 0.00 4.61
473 474 1.586028 CCTTTGATGTTGGCCGGTG 59.414 57.895 1.90 0.00 0.00 4.94
474 475 1.606313 CCCTTTGATGTTGGCCGGT 60.606 57.895 1.90 0.00 0.00 5.28
475 476 0.684153 ATCCCTTTGATGTTGGCCGG 60.684 55.000 0.00 0.00 30.54 6.13
476 477 0.457035 CATCCCTTTGATGTTGGCCG 59.543 55.000 0.00 0.00 44.91 6.13
485 486 2.649312 AGGTGGTTGATCATCCCTTTGA 59.351 45.455 18.25 0.00 0.00 2.69
503 504 2.029560 GGAAACTACGTCTTCGGAAGGT 60.030 50.000 17.19 10.70 41.85 3.50
523 524 1.826385 CTCAGCCCCAACTTACAAGG 58.174 55.000 0.00 0.00 0.00 3.61
558 559 1.266211 GCGTACACAATGAACGTAGCG 60.266 52.381 0.00 0.00 38.81 4.26
573 574 4.680110 GTGAGTATACATGATGGTGCGTAC 59.320 45.833 5.50 0.00 0.00 3.67
577 578 4.697514 ACAGTGAGTATACATGATGGTGC 58.302 43.478 5.50 0.00 0.00 5.01
580 581 8.703336 CGAAAATACAGTGAGTATACATGATGG 58.297 37.037 5.50 0.00 42.56 3.51
586 587 7.277098 GGAAAGCGAAAATACAGTGAGTATACA 59.723 37.037 5.50 0.00 42.56 2.29
588 589 7.553334 AGGAAAGCGAAAATACAGTGAGTATA 58.447 34.615 0.00 0.00 42.56 1.47
589 590 6.407202 AGGAAAGCGAAAATACAGTGAGTAT 58.593 36.000 0.00 0.00 45.27 2.12
592 593 5.409826 AGAAGGAAAGCGAAAATACAGTGAG 59.590 40.000 0.00 0.00 0.00 3.51
593 594 5.305585 AGAAGGAAAGCGAAAATACAGTGA 58.694 37.500 0.00 0.00 0.00 3.41
594 595 5.613358 AGAAGGAAAGCGAAAATACAGTG 57.387 39.130 0.00 0.00 0.00 3.66
595 596 7.923414 ATTAGAAGGAAAGCGAAAATACAGT 57.077 32.000 0.00 0.00 0.00 3.55
596 597 9.922305 CTTATTAGAAGGAAAGCGAAAATACAG 57.078 33.333 0.00 0.00 0.00 2.74
597 598 8.889717 CCTTATTAGAAGGAAAGCGAAAATACA 58.110 33.333 0.00 0.00 39.81 2.29
619 640 6.567701 CGCAAAGCTTATGTGTCTTTTCCTTA 60.568 38.462 0.00 0.00 0.00 2.69
622 643 3.914364 CGCAAAGCTTATGTGTCTTTTCC 59.086 43.478 0.00 0.00 0.00 3.13
624 645 4.568152 ACGCAAAGCTTATGTGTCTTTT 57.432 36.364 16.82 1.44 36.89 2.27
663 685 3.179443 TGGTATCATCGAGCAACCTTC 57.821 47.619 9.55 0.00 0.00 3.46
677 699 3.944015 AGAGCTGAACTGCATTTGGTATC 59.056 43.478 0.00 0.00 34.99 2.24
678 700 3.693085 CAGAGCTGAACTGCATTTGGTAT 59.307 43.478 0.00 0.00 34.99 2.73
680 702 1.884579 CAGAGCTGAACTGCATTTGGT 59.115 47.619 0.00 0.00 34.99 3.67
703 725 2.675348 GTGCAGGATAAGCAGAAGACAC 59.325 50.000 0.00 0.00 43.63 3.67
721 743 0.308376 GGACGGTCTAGATCGAGTGC 59.692 60.000 31.19 11.94 38.51 4.40
1362 1430 2.522367 GGGGTTGGGGAAGACGACA 61.522 63.158 0.00 0.00 0.00 4.35
1562 1989 6.920758 AGATATCATGAAGTCGAGCACTAAAC 59.079 38.462 5.32 0.00 32.30 2.01
1633 2250 5.734855 ACTAACCATGAATCGCAACATAC 57.265 39.130 0.00 0.00 0.00 2.39
1635 2252 5.428253 AGTACTAACCATGAATCGCAACAT 58.572 37.500 0.00 0.00 0.00 2.71
1636 2253 4.827692 AGTACTAACCATGAATCGCAACA 58.172 39.130 0.00 0.00 0.00 3.33
1637 2254 5.447279 CCAAGTACTAACCATGAATCGCAAC 60.447 44.000 0.00 0.00 0.00 4.17
1638 2255 4.634004 CCAAGTACTAACCATGAATCGCAA 59.366 41.667 0.00 0.00 0.00 4.85
1639 2256 4.081365 TCCAAGTACTAACCATGAATCGCA 60.081 41.667 0.00 0.00 0.00 5.10
1849 2541 5.010012 CAGAAAAACCCACAGCAGAATAAGT 59.990 40.000 0.00 0.00 0.00 2.24
1870 2562 2.877097 TGAGCTAAAATGGGCACAGA 57.123 45.000 0.00 0.00 0.00 3.41
2062 2955 7.990886 GTCCACAACTGGTCCATTAGATAATTA 59.009 37.037 0.00 0.00 38.90 1.40
2091 2984 1.202976 ACAAACCTTGCAGCTCAGGAT 60.203 47.619 16.13 3.60 0.00 3.24
2251 3163 3.181491 ACACCACATTGTTGCACAGTAAC 60.181 43.478 0.00 0.00 0.00 2.50
2444 3358 7.367285 GTGTCAATGCCATAAAACTTTACTGA 58.633 34.615 0.00 0.00 0.00 3.41
2452 3366 4.947388 TCCTAGGTGTCAATGCCATAAAAC 59.053 41.667 9.08 0.00 0.00 2.43
2515 3429 0.176219 AAGCAAAAGCAGCACAGCAA 59.824 45.000 0.00 0.00 36.85 3.91
2617 3532 5.010012 ACATGGTAAAAACAGCAGAGAAAGG 59.990 40.000 0.00 0.00 0.00 3.11
2670 3585 3.188159 TCGCTATACCCACAACATTCC 57.812 47.619 0.00 0.00 0.00 3.01
2686 3601 7.661437 TGCTTTCTTCCATATAATGTAATCGCT 59.339 33.333 0.00 0.00 0.00 4.93
2688 3603 9.764870 CATGCTTTCTTCCATATAATGTAATCG 57.235 33.333 0.00 0.00 0.00 3.34
2811 3750 5.240891 TGCTAATATGCCAGCATAGAGAAC 58.759 41.667 20.47 10.21 42.68 3.01
2844 3783 3.153919 TGTTGGCCGCTAGAAGAAAATT 58.846 40.909 0.00 0.00 0.00 1.82
2854 3793 4.250464 GCATATAAGTATGTTGGCCGCTA 58.750 43.478 0.00 0.00 39.90 4.26
2857 3796 4.201714 CGATGCATATAAGTATGTTGGCCG 60.202 45.833 0.00 0.00 39.90 6.13
2871 3810 4.471386 AGGGGAACTATAAGCGATGCATAT 59.529 41.667 0.00 0.00 0.00 1.78
2876 3815 4.282195 AGAAGAGGGGAACTATAAGCGATG 59.718 45.833 0.00 0.00 0.00 3.84
2877 3816 4.484912 AGAAGAGGGGAACTATAAGCGAT 58.515 43.478 0.00 0.00 0.00 4.58
2879 3818 3.892588 AGAGAAGAGGGGAACTATAAGCG 59.107 47.826 0.00 0.00 0.00 4.68
2888 3827 5.906772 AAACTACAAAGAGAAGAGGGGAA 57.093 39.130 0.00 0.00 0.00 3.97
2890 3829 6.110411 TGTAAACTACAAAGAGAAGAGGGG 57.890 41.667 0.00 0.00 35.38 4.79
2915 3854 5.774690 TGTATGGAAGGAAGCAAAGACAAAT 59.225 36.000 0.00 0.00 0.00 2.32
2919 3858 5.705609 TTTGTATGGAAGGAAGCAAAGAC 57.294 39.130 0.00 0.00 0.00 3.01
2926 3865 5.902613 TCAGCATTTTGTATGGAAGGAAG 57.097 39.130 0.00 0.00 0.00 3.46
2937 3876 8.627403 CAAAGGACATATAGATCAGCATTTTGT 58.373 33.333 0.00 0.00 0.00 2.83
2950 3889 8.873830 CAGACTACAAACACAAAGGACATATAG 58.126 37.037 0.00 0.00 0.00 1.31
2952 3891 7.450074 TCAGACTACAAACACAAAGGACATAT 58.550 34.615 0.00 0.00 0.00 1.78
2959 3898 9.438291 CAAATACTTCAGACTACAAACACAAAG 57.562 33.333 0.00 0.00 0.00 2.77
3029 3968 5.643777 GCTTACCAGAAGCAGAACATTTAGA 59.356 40.000 4.45 0.00 42.56 2.10
3082 4033 5.047306 TCCACAGCAGGTATAATTAGGATCG 60.047 44.000 0.00 0.00 0.00 3.69
3088 4039 8.588290 ACAAAATTCCACAGCAGGTATAATTA 57.412 30.769 0.00 0.00 0.00 1.40
3091 4042 7.120579 CACTACAAAATTCCACAGCAGGTATAA 59.879 37.037 0.00 0.00 0.00 0.98
3115 4066 4.154737 TGCAGTGAGACAGCAATAAATCAC 59.845 41.667 0.00 0.00 37.68 3.06
3133 4084 3.574074 GATGTGCCCACCCTGCAGT 62.574 63.158 13.81 0.00 39.87 4.40
3208 4159 1.217244 CAGCAAGCAAATGAGGGCC 59.783 57.895 0.00 0.00 0.00 5.80
3214 4165 3.374220 TTGTCCTTCAGCAAGCAAATG 57.626 42.857 0.00 0.00 0.00 2.32
3440 4391 1.211709 CGGTGCAACGGGGAAAATC 59.788 57.895 18.51 0.00 38.12 2.17
3454 4405 0.868602 CTGTATACGTTCCGCCGGTG 60.869 60.000 8.42 8.42 0.00 4.94
3659 4610 9.053840 CATCATATATCAGCAGTTGAAGAAGTT 57.946 33.333 0.00 0.00 39.77 2.66
3752 4703 8.658840 TTACCTAGTTGCCTTGGAATATTTTT 57.341 30.769 0.00 0.00 37.09 1.94
3755 4706 8.058847 TGAATTACCTAGTTGCCTTGGAATATT 58.941 33.333 0.00 0.00 37.09 1.28
3756 4707 7.582719 TGAATTACCTAGTTGCCTTGGAATAT 58.417 34.615 0.00 0.00 37.09 1.28
3758 4709 5.826643 TGAATTACCTAGTTGCCTTGGAAT 58.173 37.500 0.00 0.00 37.09 3.01
3760 4711 4.919774 TGAATTACCTAGTTGCCTTGGA 57.080 40.909 0.00 0.00 37.09 3.53
3762 4713 5.297776 CCAGATGAATTACCTAGTTGCCTTG 59.702 44.000 0.00 0.00 0.00 3.61
3764 4715 4.475016 ACCAGATGAATTACCTAGTTGCCT 59.525 41.667 0.00 0.00 0.00 4.75
3765 4716 4.781934 ACCAGATGAATTACCTAGTTGCC 58.218 43.478 0.00 0.00 0.00 4.52
3766 4717 6.124088 CAACCAGATGAATTACCTAGTTGC 57.876 41.667 0.00 0.00 0.00 4.17
3768 4719 5.193679 GGCAACCAGATGAATTACCTAGTT 58.806 41.667 0.00 0.00 0.00 2.24
3769 4720 4.781934 GGCAACCAGATGAATTACCTAGT 58.218 43.478 0.00 0.00 0.00 2.57
3786 4737 5.009010 CAGATTATGTACATCCAAGGGCAAC 59.991 44.000 12.68 0.00 0.00 4.17
3787 4738 5.132502 CAGATTATGTACATCCAAGGGCAA 58.867 41.667 12.68 0.00 0.00 4.52
3789 4740 3.503748 GCAGATTATGTACATCCAAGGGC 59.496 47.826 12.68 7.06 0.00 5.19
3792 4743 7.663081 ACCATAAGCAGATTATGTACATCCAAG 59.337 37.037 12.68 1.45 46.38 3.61
3793 4744 7.445096 CACCATAAGCAGATTATGTACATCCAA 59.555 37.037 12.68 2.22 46.38 3.53
3794 4745 6.936335 CACCATAAGCAGATTATGTACATCCA 59.064 38.462 12.68 0.38 46.38 3.41
3795 4746 7.161404 TCACCATAAGCAGATTATGTACATCC 58.839 38.462 12.68 3.24 46.38 3.51
3796 4747 8.783833 ATCACCATAAGCAGATTATGTACATC 57.216 34.615 12.68 0.00 46.38 3.06
3799 4750 8.607459 GCATATCACCATAAGCAGATTATGTAC 58.393 37.037 15.65 0.00 46.38 2.90
3800 4751 7.770433 GGCATATCACCATAAGCAGATTATGTA 59.230 37.037 15.65 3.91 46.38 2.29
3801 4752 6.600822 GGCATATCACCATAAGCAGATTATGT 59.399 38.462 15.65 3.43 46.38 2.29
3811 4837 4.008074 AGAACGGGCATATCACCATAAG 57.992 45.455 0.00 0.00 0.00 1.73
3856 4884 4.590850 AATCTTTCAGTCCCAAACAAGC 57.409 40.909 0.00 0.00 0.00 4.01
3901 4932 1.678101 GCTTTCAGTCACAAACAGCCT 59.322 47.619 0.00 0.00 0.00 4.58
3921 4952 5.331756 CGCAATAAAAGCAGACACAACAAAG 60.332 40.000 0.00 0.00 0.00 2.77
3949 5008 3.857052 TGGCAGAAGTTAGACAATACCG 58.143 45.455 0.00 0.00 0.00 4.02
3968 5027 3.565482 GCCATACCACAACACAGATATGG 59.435 47.826 4.10 4.10 41.28 2.74
3986 5045 9.632638 ATCACTAACTACAATAGAAAATGCCAT 57.367 29.630 0.00 0.00 0.00 4.40
4041 5127 4.562767 TCCTGGTATAATAAGGCTGGTGA 58.437 43.478 0.00 0.00 0.00 4.02
4054 5140 2.189676 TCCGTTTTGGCTCCTGGTATA 58.810 47.619 0.00 0.00 37.80 1.47
4055 5141 0.988832 TCCGTTTTGGCTCCTGGTAT 59.011 50.000 0.00 0.00 37.80 2.73
4082 5168 1.133025 GATTTCCTCGCAACCACATGG 59.867 52.381 0.00 0.00 42.17 3.66
4091 5177 1.031571 GGGCACATGATTTCCTCGCA 61.032 55.000 0.00 0.00 0.00 5.10
4110 5196 1.597663 CGGCTTATGCGGTTTTCCTAG 59.402 52.381 0.54 0.00 40.82 3.02
4111 5197 1.658994 CGGCTTATGCGGTTTTCCTA 58.341 50.000 0.54 0.00 40.82 2.94
4112 5198 1.029947 CCGGCTTATGCGGTTTTCCT 61.030 55.000 7.28 0.00 40.82 3.36
4113 5199 1.431845 CCGGCTTATGCGGTTTTCC 59.568 57.895 7.28 0.00 40.82 3.13
4114 5200 1.431845 CCCGGCTTATGCGGTTTTC 59.568 57.895 0.00 0.00 40.82 2.29
4116 5202 3.138128 GCCCGGCTTATGCGGTTT 61.138 61.111 0.71 0.00 40.82 3.27
4132 5817 2.541547 TAGGGCAGATGCAGTGTGGC 62.542 60.000 7.19 9.95 44.79 5.01
4153 5838 9.838339 AGTTCATGAGATTTTACCTAGGTTATG 57.162 33.333 22.11 11.52 0.00 1.90
4155 5840 7.769044 GCAGTTCATGAGATTTTACCTAGGTTA 59.231 37.037 22.11 8.46 0.00 2.85
4157 5842 6.116126 GCAGTTCATGAGATTTTACCTAGGT 58.884 40.000 20.57 20.57 0.00 3.08
4160 5845 6.946340 TCTGCAGTTCATGAGATTTTACCTA 58.054 36.000 14.67 0.00 0.00 3.08
4203 6406 3.405831 TGCCTTGTTCAGTTCATCAGAG 58.594 45.455 0.00 0.00 0.00 3.35
4269 6472 4.141459 GGGGATTTGGGTTTCTACTAGAGG 60.141 50.000 0.00 0.00 0.00 3.69
4290 6493 5.118286 GCTTTGTTCATGGGATTAATTGGG 58.882 41.667 0.00 0.00 0.00 4.12
4357 6577 1.724582 AATAAACCGAGCCCATGCGC 61.725 55.000 0.00 0.00 44.33 6.09
4359 6579 1.476488 ACAAATAAACCGAGCCCATGC 59.524 47.619 0.00 0.00 37.95 4.06


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

AutoCloner maintained by Alex Coulton.