Multiple sequence alignment - TraesCS6D01G224700

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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 TraesCS6D01G224700 chr6D 100.000 3608 0 0 1 3608 316563235 316566842 0.000000e+00 6663.0
1 TraesCS6D01G224700 chr6B 94.441 3238 123 27 100 3322 507796846 507793651 0.000000e+00 4929.0
2 TraesCS6D01G224700 chr6A 95.234 2287 59 14 637 2895 454546008 454548272 0.000000e+00 3574.0
3 TraesCS6D01G224700 chr6A 94.015 518 27 2 92 609 454545498 454546011 0.000000e+00 782.0
4 TraesCS6D01G224700 chr6A 89.677 465 34 8 2892 3352 454548347 454548801 6.720000e-162 580.0
5 TraesCS6D01G224700 chr3D 96.970 33 1 0 1734 1766 351287637 351287669 5.030000e-04 56.5


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 TraesCS6D01G224700 chr6D 316563235 316566842 3607 False 6663.000000 6663 100.000000 1 3608 1 chr6D.!!$F1 3607
1 TraesCS6D01G224700 chr6B 507793651 507796846 3195 True 4929.000000 4929 94.441000 100 3322 1 chr6B.!!$R1 3222
2 TraesCS6D01G224700 chr6A 454545498 454548801 3303 False 1645.333333 3574 92.975333 92 3352 3 chr6A.!!$F1 3260

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
23 24 0.981183 TGGTTCGCTGGTTATCCTGT 59.019 50.000 0.00 0.0 35.49 4.00 F
882 901 1.063567 CCTCTCCCGCTATATAGCCCT 60.064 57.143 25.48 0.0 46.34 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 1941 2.669133 CGCCACCTTGGGATCCTCA 61.669 63.158 12.58 5.20 38.19 3.86 R
2775 2806 0.586802 GTGGTCAAAACACTCGAGCC 59.413 55.000 13.61 3.25 35.98 4.70 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 4.497291 TTTATGGTTCGCTGGTTATCCT 57.503 40.909 0.00 0.00 34.23 3.24
22 23 2.332063 ATGGTTCGCTGGTTATCCTG 57.668 50.000 0.00 0.00 36.04 3.86
23 24 0.981183 TGGTTCGCTGGTTATCCTGT 59.019 50.000 0.00 0.00 35.49 4.00
24 25 1.349688 TGGTTCGCTGGTTATCCTGTT 59.650 47.619 0.00 0.00 35.49 3.16
25 26 1.737793 GGTTCGCTGGTTATCCTGTTG 59.262 52.381 0.00 0.00 35.49 3.33
26 27 2.614481 GGTTCGCTGGTTATCCTGTTGA 60.614 50.000 0.00 0.00 35.49 3.18
27 28 3.270877 GTTCGCTGGTTATCCTGTTGAT 58.729 45.455 0.00 0.00 37.49 2.57
28 29 2.905075 TCGCTGGTTATCCTGTTGATG 58.095 47.619 0.00 0.00 34.76 3.07
29 30 2.236146 TCGCTGGTTATCCTGTTGATGT 59.764 45.455 0.00 0.00 34.76 3.06
30 31 3.449377 TCGCTGGTTATCCTGTTGATGTA 59.551 43.478 0.00 0.00 34.76 2.29
31 32 4.081365 TCGCTGGTTATCCTGTTGATGTAA 60.081 41.667 0.00 0.00 34.76 2.41
32 33 4.034048 CGCTGGTTATCCTGTTGATGTAAC 59.966 45.833 0.00 0.00 39.80 2.50
33 34 4.335594 GCTGGTTATCCTGTTGATGTAACC 59.664 45.833 5.82 5.82 40.39 2.85
34 35 5.496556 CTGGTTATCCTGTTGATGTAACCA 58.503 41.667 12.96 12.96 44.39 3.67
35 36 6.073447 TGGTTATCCTGTTGATGTAACCAT 57.927 37.500 10.34 0.00 42.90 3.55
36 37 5.885352 TGGTTATCCTGTTGATGTAACCATG 59.115 40.000 10.34 0.00 42.90 3.66
37 38 5.221048 GGTTATCCTGTTGATGTAACCATGC 60.221 44.000 7.52 0.00 40.00 4.06
38 39 3.719268 TCCTGTTGATGTAACCATGCT 57.281 42.857 0.00 0.00 38.55 3.79
39 40 3.346315 TCCTGTTGATGTAACCATGCTG 58.654 45.455 0.00 0.00 38.55 4.41
40 41 3.084039 CCTGTTGATGTAACCATGCTGT 58.916 45.455 0.00 0.00 38.55 4.40
41 42 4.019771 TCCTGTTGATGTAACCATGCTGTA 60.020 41.667 0.00 0.00 38.55 2.74
42 43 4.699735 CCTGTTGATGTAACCATGCTGTAA 59.300 41.667 0.00 0.00 38.55 2.41
43 44 5.391950 CCTGTTGATGTAACCATGCTGTAAC 60.392 44.000 0.00 0.00 38.55 2.50
44 45 5.312895 TGTTGATGTAACCATGCTGTAACT 58.687 37.500 0.00 0.00 38.55 2.24
45 46 5.181056 TGTTGATGTAACCATGCTGTAACTG 59.819 40.000 0.00 0.00 38.55 3.16
46 47 5.159273 TGATGTAACCATGCTGTAACTGA 57.841 39.130 0.00 0.00 0.00 3.41
47 48 5.555966 TGATGTAACCATGCTGTAACTGAA 58.444 37.500 0.00 0.00 0.00 3.02
48 49 5.643348 TGATGTAACCATGCTGTAACTGAAG 59.357 40.000 0.00 0.00 0.00 3.02
49 50 5.222079 TGTAACCATGCTGTAACTGAAGA 57.778 39.130 0.00 0.00 0.00 2.87
50 51 5.804639 TGTAACCATGCTGTAACTGAAGAT 58.195 37.500 0.00 0.00 0.00 2.40
51 52 6.237901 TGTAACCATGCTGTAACTGAAGATT 58.762 36.000 0.00 0.00 0.00 2.40
52 53 7.390823 TGTAACCATGCTGTAACTGAAGATTA 58.609 34.615 0.00 0.00 0.00 1.75
53 54 6.743575 AACCATGCTGTAACTGAAGATTAC 57.256 37.500 0.00 0.00 33.85 1.89
54 55 4.870426 ACCATGCTGTAACTGAAGATTACG 59.130 41.667 0.00 0.00 35.65 3.18
55 56 4.260375 CCATGCTGTAACTGAAGATTACGC 60.260 45.833 0.00 0.00 35.65 4.42
56 57 3.259064 TGCTGTAACTGAAGATTACGCC 58.741 45.455 0.00 0.00 35.65 5.68
57 58 2.281762 GCTGTAACTGAAGATTACGCCG 59.718 50.000 0.00 0.00 35.65 6.46
58 59 3.508762 CTGTAACTGAAGATTACGCCGT 58.491 45.455 0.00 0.00 35.65 5.68
59 60 3.247442 TGTAACTGAAGATTACGCCGTG 58.753 45.455 0.00 0.00 35.65 4.94
60 61 2.450609 AACTGAAGATTACGCCGTGT 57.549 45.000 0.00 0.00 0.00 4.49
61 62 1.992170 ACTGAAGATTACGCCGTGTC 58.008 50.000 0.00 0.00 0.00 3.67
62 63 1.544691 ACTGAAGATTACGCCGTGTCT 59.455 47.619 0.00 0.00 0.00 3.41
63 64 2.029290 ACTGAAGATTACGCCGTGTCTT 60.029 45.455 16.23 16.23 33.87 3.01
64 65 3.192001 ACTGAAGATTACGCCGTGTCTTA 59.808 43.478 16.24 7.48 31.51 2.10
65 66 4.171005 CTGAAGATTACGCCGTGTCTTAA 58.829 43.478 16.24 10.49 31.51 1.85
66 67 4.751060 TGAAGATTACGCCGTGTCTTAAT 58.249 39.130 16.24 1.33 31.51 1.40
67 68 4.565166 TGAAGATTACGCCGTGTCTTAATG 59.435 41.667 16.24 0.00 31.51 1.90
68 69 3.454375 AGATTACGCCGTGTCTTAATGG 58.546 45.455 0.00 0.00 0.00 3.16
69 70 3.131577 AGATTACGCCGTGTCTTAATGGA 59.868 43.478 0.00 0.00 0.00 3.41
70 71 3.316071 TTACGCCGTGTCTTAATGGAA 57.684 42.857 0.00 0.00 0.00 3.53
71 72 2.396590 ACGCCGTGTCTTAATGGAAT 57.603 45.000 0.00 0.00 0.00 3.01
72 73 3.530265 ACGCCGTGTCTTAATGGAATA 57.470 42.857 0.00 0.00 0.00 1.75
73 74 3.192466 ACGCCGTGTCTTAATGGAATAC 58.808 45.455 0.00 0.00 0.00 1.89
74 75 2.542595 CGCCGTGTCTTAATGGAATACC 59.457 50.000 0.00 0.00 0.00 2.73
75 76 2.542595 GCCGTGTCTTAATGGAATACCG 59.457 50.000 0.00 0.00 39.42 4.02
76 77 3.128349 CCGTGTCTTAATGGAATACCGG 58.872 50.000 0.00 0.00 39.42 5.28
77 78 3.431207 CCGTGTCTTAATGGAATACCGGT 60.431 47.826 13.98 13.98 39.42 5.28
78 79 3.554324 CGTGTCTTAATGGAATACCGGTG 59.446 47.826 19.93 0.00 39.42 4.94
79 80 4.510571 GTGTCTTAATGGAATACCGGTGT 58.489 43.478 19.93 8.05 39.42 4.16
80 81 4.939439 GTGTCTTAATGGAATACCGGTGTT 59.061 41.667 19.93 18.55 39.42 3.32
81 82 5.064325 GTGTCTTAATGGAATACCGGTGTTC 59.936 44.000 30.02 30.02 39.42 3.18
82 83 4.573607 GTCTTAATGGAATACCGGTGTTCC 59.426 45.833 41.16 41.16 46.91 3.62
89 90 5.900865 GGAATACCGGTGTTCCATTTAAA 57.099 39.130 42.04 12.58 46.27 1.52
90 91 6.270156 GGAATACCGGTGTTCCATTTAAAA 57.730 37.500 42.04 12.37 46.27 1.52
91 92 6.689554 GGAATACCGGTGTTCCATTTAAAAA 58.310 36.000 42.04 11.93 46.27 1.94
172 173 4.771356 CCGACGCGACATGGACGT 62.771 66.667 15.93 9.28 43.83 4.34
239 244 8.680001 AGGTTTGACTAACGAATTAACAAAACT 58.320 29.630 0.00 0.00 38.46 2.66
268 273 1.202114 CCCGTACTACGTACCAAAGCA 59.798 52.381 7.79 0.00 40.58 3.91
287 292 2.028883 GCATTGTCGCGGACTAGTTAAC 59.971 50.000 6.13 0.00 33.15 2.01
289 294 3.367992 TTGTCGCGGACTAGTTAACAA 57.632 42.857 6.13 2.85 33.15 2.83
364 369 2.310233 CCGGTGTCAGTGTGAAGCG 61.310 63.158 0.00 6.95 32.50 4.68
479 484 2.432628 GTCTCGGTCAAGCCACGG 60.433 66.667 0.00 0.00 36.97 4.94
525 530 1.271876 GGTTAACTACGCACGCCTAC 58.728 55.000 5.42 0.00 0.00 3.18
547 552 4.756135 ACTCGCCATTAGACTAGTACTAGC 59.244 45.833 26.54 19.29 36.66 3.42
562 569 1.201998 ACTAGCACGTACATCGACACG 60.202 52.381 12.83 12.83 42.86 4.49
640 647 1.595993 ATAGACTATCCCGCGCGCAT 61.596 55.000 32.61 20.40 0.00 4.73
805 816 4.030452 GACCAACCACTGCGCTGC 62.030 66.667 14.80 0.00 0.00 5.25
882 901 1.063567 CCTCTCCCGCTATATAGCCCT 60.064 57.143 25.48 0.00 46.34 5.19
1350 1374 2.745884 TTCTTCGTGCCCATGCCG 60.746 61.111 0.00 0.00 36.33 5.69
1935 1959 2.190578 GAGGATCCCAAGGTGGCG 59.809 66.667 8.55 0.00 35.79 5.69
1972 1996 2.573609 CTACAAGACGGCCGGGGAAG 62.574 65.000 31.76 17.14 0.00 3.46
2226 2250 1.374252 CAAGGTCAACGTCCTCCGG 60.374 63.158 0.00 0.00 42.24 5.14
2696 2721 3.802685 GTCGGTTCCAGGAAAATATCTCG 59.197 47.826 2.45 0.49 0.00 4.04
2775 2806 4.318333 CGTGACATAATTGATCAGGCGAAG 60.318 45.833 0.00 0.00 0.00 3.79
2872 2912 4.410400 CCGGTTCCCTCCCTGCAC 62.410 72.222 0.00 0.00 0.00 4.57
2877 2917 0.907230 GTTCCCTCCCTGCACTCTCT 60.907 60.000 0.00 0.00 0.00 3.10
2933 3051 5.402630 AGGGTAGAATTTTTCAACCCATGT 58.597 37.500 11.22 0.00 38.35 3.21
2934 3052 6.557568 AGGGTAGAATTTTTCAACCCATGTA 58.442 36.000 11.22 0.00 38.35 2.29
2935 3053 6.436218 AGGGTAGAATTTTTCAACCCATGTAC 59.564 38.462 11.22 0.00 38.35 2.90
2976 3094 8.873830 ACTTTTTACTATCAACATCAGTCATCG 58.126 33.333 0.00 0.00 0.00 3.84
2983 3101 3.932710 TCAACATCAGTCATCGGCTTAAC 59.067 43.478 0.00 0.00 0.00 2.01
2993 3111 4.156008 GTCATCGGCTTAACCACAATTCTT 59.844 41.667 0.00 0.00 39.03 2.52
3025 3143 9.217278 CTTATGAATGATTCTGATCCCTGTAAG 57.783 37.037 6.73 0.00 0.00 2.34
3037 3155 9.837681 TCTGATCCCTGTAAGATTATTATACCA 57.162 33.333 0.00 0.00 34.07 3.25
3038 3156 9.877178 CTGATCCCTGTAAGATTATTATACCAC 57.123 37.037 0.00 0.00 34.07 4.16
3039 3157 9.615660 TGATCCCTGTAAGATTATTATACCACT 57.384 33.333 0.00 0.00 34.07 4.00
3085 3206 3.462982 TGTTAGTGATTGCAACACTCGT 58.537 40.909 26.94 13.92 45.58 4.18
3126 3247 2.959030 AGAGCGGCCTTTTTCTTTTCTT 59.041 40.909 0.00 0.00 0.00 2.52
3131 3252 3.802139 CGGCCTTTTTCTTTTCTTTGGTC 59.198 43.478 0.00 0.00 0.00 4.02
3164 3285 6.657966 CCGAACCTCCCTTTTTAGTCTTTTAT 59.342 38.462 0.00 0.00 0.00 1.40
3200 3324 8.152898 TCTAGGGTAGTTTTTCAGTACTTTTCC 58.847 37.037 0.00 0.00 32.40 3.13
3209 3333 3.724374 TCAGTACTTTTCCCGTGTCTTG 58.276 45.455 0.00 0.00 0.00 3.02
3213 3337 5.238650 CAGTACTTTTCCCGTGTCTTGAAAT 59.761 40.000 0.00 0.00 0.00 2.17
3243 3367 5.241403 TCAGTGGTACAGAAATCAACCAT 57.759 39.130 0.00 0.00 43.53 3.55
3245 3369 4.396166 CAGTGGTACAGAAATCAACCATCC 59.604 45.833 0.00 0.00 43.53 3.51
3330 3454 4.735985 CATCGGAGCATGAATGACAAAAA 58.264 39.130 0.00 0.00 0.00 1.94
3331 3455 4.424061 TCGGAGCATGAATGACAAAAAG 57.576 40.909 0.00 0.00 0.00 2.27
3332 3456 4.071423 TCGGAGCATGAATGACAAAAAGA 58.929 39.130 0.00 0.00 0.00 2.52
3333 3457 4.518590 TCGGAGCATGAATGACAAAAAGAA 59.481 37.500 0.00 0.00 0.00 2.52
3341 3465 5.115480 TGAATGACAAAAAGAAAAGTGGCC 58.885 37.500 0.00 0.00 0.00 5.36
3342 3466 5.104982 TGAATGACAAAAAGAAAAGTGGCCT 60.105 36.000 3.32 0.00 0.00 5.19
3352 3476 5.514500 AGAAAAGTGGCCTCTATGGTTAA 57.486 39.130 7.96 0.00 38.35 2.01
3353 3477 5.887754 AGAAAAGTGGCCTCTATGGTTAAA 58.112 37.500 7.96 0.00 38.35 1.52
3354 3478 5.710567 AGAAAAGTGGCCTCTATGGTTAAAC 59.289 40.000 7.96 0.00 38.35 2.01
3355 3479 4.929146 AAGTGGCCTCTATGGTTAAACT 57.071 40.909 7.96 0.00 38.35 2.66
3356 3480 6.382919 AAAGTGGCCTCTATGGTTAAACTA 57.617 37.500 7.96 0.00 38.35 2.24
3357 3481 5.615925 AGTGGCCTCTATGGTTAAACTAG 57.384 43.478 5.27 0.00 38.35 2.57
3358 3482 5.278061 AGTGGCCTCTATGGTTAAACTAGA 58.722 41.667 5.27 0.00 38.35 2.43
3359 3483 5.724854 AGTGGCCTCTATGGTTAAACTAGAA 59.275 40.000 5.27 0.00 38.35 2.10
3360 3484 6.214819 AGTGGCCTCTATGGTTAAACTAGAAA 59.785 38.462 5.27 0.00 38.35 2.52
3361 3485 6.882678 GTGGCCTCTATGGTTAAACTAGAAAA 59.117 38.462 3.32 0.00 38.35 2.29
3362 3486 7.556635 GTGGCCTCTATGGTTAAACTAGAAAAT 59.443 37.037 3.32 0.00 38.35 1.82
3363 3487 8.113462 TGGCCTCTATGGTTAAACTAGAAAATT 58.887 33.333 3.32 0.00 38.35 1.82
3364 3488 8.406297 GGCCTCTATGGTTAAACTAGAAAATTG 58.594 37.037 0.00 0.00 38.35 2.32
3365 3489 7.915923 GCCTCTATGGTTAAACTAGAAAATTGC 59.084 37.037 0.00 0.00 38.35 3.56
3366 3490 9.178758 CCTCTATGGTTAAACTAGAAAATTGCT 57.821 33.333 0.00 0.00 0.00 3.91
3367 3491 9.994432 CTCTATGGTTAAACTAGAAAATTGCTG 57.006 33.333 0.00 0.00 0.00 4.41
3368 3492 9.733556 TCTATGGTTAAACTAGAAAATTGCTGA 57.266 29.630 0.00 0.00 0.00 4.26
3369 3493 9.774742 CTATGGTTAAACTAGAAAATTGCTGAC 57.225 33.333 0.00 0.00 0.00 3.51
3370 3494 6.664515 TGGTTAAACTAGAAAATTGCTGACG 58.335 36.000 0.00 0.00 0.00 4.35
3371 3495 6.483974 TGGTTAAACTAGAAAATTGCTGACGA 59.516 34.615 0.00 0.00 0.00 4.20
3372 3496 7.012515 TGGTTAAACTAGAAAATTGCTGACGAA 59.987 33.333 0.00 0.00 0.00 3.85
3373 3497 7.534239 GGTTAAACTAGAAAATTGCTGACGAAG 59.466 37.037 0.00 0.00 0.00 3.79
3374 3498 6.861065 AAACTAGAAAATTGCTGACGAAGA 57.139 33.333 0.00 0.00 0.00 2.87
3375 3499 6.473397 AACTAGAAAATTGCTGACGAAGAG 57.527 37.500 0.00 0.00 0.00 2.85
3376 3500 5.784177 ACTAGAAAATTGCTGACGAAGAGA 58.216 37.500 0.00 0.00 0.00 3.10
3377 3501 6.402222 ACTAGAAAATTGCTGACGAAGAGAT 58.598 36.000 0.00 0.00 0.00 2.75
3378 3502 5.542616 AGAAAATTGCTGACGAAGAGATG 57.457 39.130 0.00 0.00 0.00 2.90
3379 3503 5.240891 AGAAAATTGCTGACGAAGAGATGA 58.759 37.500 0.00 0.00 0.00 2.92
3380 3504 4.935885 AAATTGCTGACGAAGAGATGAC 57.064 40.909 0.00 0.00 0.00 3.06
3381 3505 3.599730 ATTGCTGACGAAGAGATGACA 57.400 42.857 0.00 0.00 0.00 3.58
3382 3506 2.643933 TGCTGACGAAGAGATGACAG 57.356 50.000 0.00 0.00 0.00 3.51
3383 3507 1.889170 TGCTGACGAAGAGATGACAGT 59.111 47.619 0.00 0.00 0.00 3.55
3384 3508 3.081804 TGCTGACGAAGAGATGACAGTA 58.918 45.455 0.00 0.00 0.00 2.74
3385 3509 3.696548 TGCTGACGAAGAGATGACAGTAT 59.303 43.478 0.00 0.00 0.00 2.12
3386 3510 4.041049 GCTGACGAAGAGATGACAGTATG 58.959 47.826 0.00 0.00 46.00 2.39
3387 3511 4.201960 GCTGACGAAGAGATGACAGTATGA 60.202 45.833 0.00 0.00 39.69 2.15
3388 3512 5.236655 TGACGAAGAGATGACAGTATGAC 57.763 43.478 0.00 0.00 39.69 3.06
3389 3513 4.700213 TGACGAAGAGATGACAGTATGACA 59.300 41.667 0.00 0.00 46.13 3.58
3390 3514 4.987832 ACGAAGAGATGACAGTATGACAC 58.012 43.478 0.00 0.00 44.67 3.67
3391 3515 4.702612 ACGAAGAGATGACAGTATGACACT 59.297 41.667 0.00 0.00 44.67 3.55
3403 3527 5.407407 AGTATGACACTGACGGAATTCTT 57.593 39.130 5.23 0.00 35.62 2.52
3404 3528 5.794894 AGTATGACACTGACGGAATTCTTT 58.205 37.500 5.23 0.00 35.62 2.52
3405 3529 6.931838 AGTATGACACTGACGGAATTCTTTA 58.068 36.000 5.23 0.00 35.62 1.85
3406 3530 7.383687 AGTATGACACTGACGGAATTCTTTAA 58.616 34.615 5.23 0.00 35.62 1.52
3407 3531 7.876068 AGTATGACACTGACGGAATTCTTTAAA 59.124 33.333 5.23 0.00 35.62 1.52
3408 3532 6.928979 TGACACTGACGGAATTCTTTAAAA 57.071 33.333 5.23 0.00 0.00 1.52
3409 3533 7.323049 TGACACTGACGGAATTCTTTAAAAA 57.677 32.000 5.23 0.00 0.00 1.94
3435 3559 9.462606 AAAATGGAAACCTCGAAAGTATATTCT 57.537 29.630 0.00 0.00 0.00 2.40
3437 3561 9.765795 AATGGAAACCTCGAAAGTATATTCTAG 57.234 33.333 0.00 0.00 0.00 2.43
3438 3562 8.302515 TGGAAACCTCGAAAGTATATTCTAGT 57.697 34.615 0.00 0.00 0.00 2.57
3439 3563 8.755977 TGGAAACCTCGAAAGTATATTCTAGTT 58.244 33.333 0.00 0.00 0.00 2.24
3440 3564 9.597170 GGAAACCTCGAAAGTATATTCTAGTTT 57.403 33.333 0.00 0.00 31.76 2.66
3443 3567 8.853469 ACCTCGAAAGTATATTCTAGTTTTCG 57.147 34.615 9.99 9.99 44.68 3.46
3461 3585 8.859517 AGTTTTCGAAAATTCCATTTTTACGA 57.140 26.923 24.93 0.00 42.15 3.43
3462 3586 8.748582 AGTTTTCGAAAATTCCATTTTTACGAC 58.251 29.630 24.93 8.15 42.15 4.34
3463 3587 7.626144 TTTCGAAAATTCCATTTTTACGACC 57.374 32.000 8.44 0.00 42.15 4.79
3464 3588 5.701855 TCGAAAATTCCATTTTTACGACCC 58.298 37.500 0.00 0.00 42.15 4.46
3465 3589 5.474189 TCGAAAATTCCATTTTTACGACCCT 59.526 36.000 0.00 0.00 42.15 4.34
3466 3590 5.571357 CGAAAATTCCATTTTTACGACCCTG 59.429 40.000 0.00 0.00 42.15 4.45
3467 3591 6.413783 AAAATTCCATTTTTACGACCCTGT 57.586 33.333 0.00 0.00 39.28 4.00
3468 3592 5.638596 AATTCCATTTTTACGACCCTGTC 57.361 39.130 0.00 0.00 0.00 3.51
3477 3601 3.932289 GACCCTGTCGTTGTCGTG 58.068 61.111 0.00 0.00 38.33 4.35
3478 3602 1.066918 GACCCTGTCGTTGTCGTGT 59.933 57.895 0.00 0.00 38.33 4.49
3479 3603 0.529119 GACCCTGTCGTTGTCGTGTT 60.529 55.000 0.00 0.00 38.33 3.32
3480 3604 0.808453 ACCCTGTCGTTGTCGTGTTG 60.808 55.000 0.00 0.00 38.33 3.33
3481 3605 0.528901 CCCTGTCGTTGTCGTGTTGA 60.529 55.000 0.00 0.00 38.33 3.18
3482 3606 1.282817 CCTGTCGTTGTCGTGTTGAA 58.717 50.000 0.00 0.00 38.33 2.69
3483 3607 1.864711 CCTGTCGTTGTCGTGTTGAAT 59.135 47.619 0.00 0.00 38.33 2.57
3484 3608 2.348498 CCTGTCGTTGTCGTGTTGAATG 60.348 50.000 0.00 0.00 38.33 2.67
3485 3609 2.538037 CTGTCGTTGTCGTGTTGAATGA 59.462 45.455 0.00 0.00 38.33 2.57
3486 3610 2.930682 TGTCGTTGTCGTGTTGAATGAA 59.069 40.909 0.00 0.00 38.33 2.57
3487 3611 3.000825 TGTCGTTGTCGTGTTGAATGAAG 59.999 43.478 0.00 0.00 38.33 3.02
3488 3612 3.244345 GTCGTTGTCGTGTTGAATGAAGA 59.756 43.478 0.00 0.00 38.33 2.87
3489 3613 4.055360 TCGTTGTCGTGTTGAATGAAGAT 58.945 39.130 0.00 0.00 38.33 2.40
3490 3614 4.149922 TCGTTGTCGTGTTGAATGAAGATC 59.850 41.667 0.00 0.00 38.33 2.75
3491 3615 4.084589 CGTTGTCGTGTTGAATGAAGATCA 60.085 41.667 0.00 0.00 0.00 2.92
3492 3616 4.990543 TGTCGTGTTGAATGAAGATCAC 57.009 40.909 0.00 0.00 0.00 3.06
3493 3617 3.745975 TGTCGTGTTGAATGAAGATCACC 59.254 43.478 0.00 0.00 0.00 4.02
3494 3618 3.997021 GTCGTGTTGAATGAAGATCACCT 59.003 43.478 0.00 0.00 0.00 4.00
3495 3619 4.092091 GTCGTGTTGAATGAAGATCACCTC 59.908 45.833 0.00 0.00 0.00 3.85
3496 3620 4.021104 TCGTGTTGAATGAAGATCACCTCT 60.021 41.667 0.00 0.00 34.96 3.69
3504 3628 2.100605 AAGATCACCTCTTCGTTGCC 57.899 50.000 0.00 0.00 40.26 4.52
3505 3629 0.108615 AGATCACCTCTTCGTTGCCG 60.109 55.000 0.00 0.00 0.00 5.69
3506 3630 1.696832 GATCACCTCTTCGTTGCCGC 61.697 60.000 0.00 0.00 0.00 6.53
3507 3631 2.449031 ATCACCTCTTCGTTGCCGCA 62.449 55.000 0.00 0.00 0.00 5.69
3508 3632 2.034879 CACCTCTTCGTTGCCGCAT 61.035 57.895 0.00 0.00 0.00 4.73
3509 3633 2.034879 ACCTCTTCGTTGCCGCATG 61.035 57.895 0.00 0.00 0.00 4.06
3510 3634 2.753966 CCTCTTCGTTGCCGCATGG 61.754 63.158 0.00 0.00 38.77 3.66
3520 3644 4.845580 CCGCATGGCCGAAGAGCT 62.846 66.667 0.00 0.00 0.00 4.09
3521 3645 3.267860 CGCATGGCCGAAGAGCTC 61.268 66.667 5.27 5.27 0.00 4.09
3522 3646 2.188994 GCATGGCCGAAGAGCTCT 59.811 61.111 11.45 11.45 0.00 4.09
3523 3647 1.451028 GCATGGCCGAAGAGCTCTT 60.451 57.895 28.83 28.83 39.23 2.85
3524 3648 1.028868 GCATGGCCGAAGAGCTCTTT 61.029 55.000 29.02 13.69 36.11 2.52
3525 3649 1.012841 CATGGCCGAAGAGCTCTTTC 58.987 55.000 29.02 19.80 36.11 2.62
3526 3650 0.107459 ATGGCCGAAGAGCTCTTTCC 60.107 55.000 29.02 26.39 36.11 3.13
3527 3651 1.296715 GGCCGAAGAGCTCTTTCCA 59.703 57.895 29.02 0.00 36.11 3.53
3528 3652 0.107459 GGCCGAAGAGCTCTTTCCAT 60.107 55.000 29.02 7.58 36.11 3.41
3529 3653 1.012841 GCCGAAGAGCTCTTTCCATG 58.987 55.000 29.02 16.30 36.11 3.66
3530 3654 1.661341 CCGAAGAGCTCTTTCCATGG 58.339 55.000 29.02 20.28 36.11 3.66
3531 3655 1.012841 CGAAGAGCTCTTTCCATGGC 58.987 55.000 29.02 13.81 36.11 4.40
3532 3656 1.387539 GAAGAGCTCTTTCCATGGCC 58.612 55.000 29.02 10.78 36.11 5.36
3533 3657 0.393537 AAGAGCTCTTTCCATGGCCG 60.394 55.000 23.49 0.00 30.82 6.13
3534 3658 2.439156 AGCTCTTTCCATGGCCGC 60.439 61.111 6.96 4.70 0.00 6.53
3535 3659 3.521796 GCTCTTTCCATGGCCGCC 61.522 66.667 6.96 1.04 0.00 6.13
3536 3660 2.273449 CTCTTTCCATGGCCGCCT 59.727 61.111 11.61 0.00 0.00 5.52
3537 3661 2.045045 TCTTTCCATGGCCGCCTG 60.045 61.111 11.61 6.43 0.00 4.85
3538 3662 3.142838 CTTTCCATGGCCGCCTGG 61.143 66.667 17.40 17.40 38.77 4.45
3539 3663 4.757355 TTTCCATGGCCGCCTGGG 62.757 66.667 21.10 17.12 39.58 4.45
3550 3674 4.400961 GCCTGGGCGAAGAGTGCT 62.401 66.667 0.00 0.00 0.00 4.40
3551 3675 2.125350 CCTGGGCGAAGAGTGCTC 60.125 66.667 0.00 0.00 0.00 4.26
3552 3676 2.654079 CCTGGGCGAAGAGTGCTCT 61.654 63.158 0.00 0.00 42.75 4.09
3559 3683 2.665603 AAGAGTGCTCTTCGGGCC 59.334 61.111 8.51 0.00 46.13 5.80
3560 3684 3.302347 AAGAGTGCTCTTCGGGCCG 62.302 63.158 22.51 22.51 46.13 6.13
3561 3685 3.760035 GAGTGCTCTTCGGGCCGA 61.760 66.667 27.46 27.46 0.00 5.54
3562 3686 3.991536 GAGTGCTCTTCGGGCCGAC 62.992 68.421 31.23 18.05 34.89 4.79
3576 3700 4.065281 CGACGGGGCCGAAGAGTT 62.065 66.667 0.00 0.00 42.83 3.01
3577 3701 2.703798 CGACGGGGCCGAAGAGTTA 61.704 63.158 0.00 0.00 42.83 2.24
3578 3702 1.153686 GACGGGGCCGAAGAGTTAC 60.154 63.158 0.00 0.00 42.83 2.50
3579 3703 1.602327 GACGGGGCCGAAGAGTTACT 61.602 60.000 0.00 0.00 42.83 2.24
3580 3704 1.141234 CGGGGCCGAAGAGTTACTC 59.859 63.158 3.85 3.85 42.83 2.59
3581 3705 1.321074 CGGGGCCGAAGAGTTACTCT 61.321 60.000 9.37 9.37 43.37 3.24
3592 3716 4.258702 AGAGTTACTCTTCGTTGCATGT 57.741 40.909 9.37 0.00 37.60 3.21
3593 3717 3.990469 AGAGTTACTCTTCGTTGCATGTG 59.010 43.478 9.37 0.00 37.60 3.21
3594 3718 2.480419 AGTTACTCTTCGTTGCATGTGC 59.520 45.455 0.00 0.00 42.50 4.57
3595 3719 1.067693 TACTCTTCGTTGCATGTGCG 58.932 50.000 0.01 0.00 45.83 5.34
3596 3720 1.133253 CTCTTCGTTGCATGTGCGG 59.867 57.895 0.01 0.00 45.83 5.69
3597 3721 1.291184 CTCTTCGTTGCATGTGCGGA 61.291 55.000 0.01 0.00 45.83 5.54
3598 3722 1.154413 CTTCGTTGCATGTGCGGAC 60.154 57.895 0.00 0.00 45.83 4.79
3599 3723 2.816692 CTTCGTTGCATGTGCGGACG 62.817 60.000 20.42 20.42 46.90 4.79
3601 3725 2.942879 GTTGCATGTGCGGACGAA 59.057 55.556 1.60 0.00 45.83 3.85
3602 3726 1.281353 GTTGCATGTGCGGACGAAA 59.719 52.632 1.60 0.00 45.83 3.46
3603 3727 0.317436 GTTGCATGTGCGGACGAAAA 60.317 50.000 1.60 0.00 45.83 2.29
3604 3728 0.040514 TTGCATGTGCGGACGAAAAG 60.041 50.000 1.60 0.00 45.83 2.27
3605 3729 1.163420 TGCATGTGCGGACGAAAAGT 61.163 50.000 1.60 0.00 45.83 2.66
3606 3730 0.040425 GCATGTGCGGACGAAAAGTT 60.040 50.000 1.60 0.00 0.00 2.66
3607 3731 1.950472 CATGTGCGGACGAAAAGTTC 58.050 50.000 1.60 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.196193 CAGGATAACCAGCGAACCATAAA 58.804 43.478 0.00 0.00 38.94 1.40
1 2 3.199071 ACAGGATAACCAGCGAACCATAA 59.801 43.478 0.00 0.00 38.94 1.90
2 3 2.769663 ACAGGATAACCAGCGAACCATA 59.230 45.455 0.00 0.00 38.94 2.74
4 5 0.981183 ACAGGATAACCAGCGAACCA 59.019 50.000 0.00 0.00 38.94 3.67
5 6 1.737793 CAACAGGATAACCAGCGAACC 59.262 52.381 0.00 0.00 38.94 3.62
6 7 2.695359 TCAACAGGATAACCAGCGAAC 58.305 47.619 0.00 0.00 38.94 3.95
7 8 3.270027 CATCAACAGGATAACCAGCGAA 58.730 45.455 0.00 0.00 38.94 4.70
8 9 2.236146 ACATCAACAGGATAACCAGCGA 59.764 45.455 0.00 0.00 38.94 4.93
9 10 2.632377 ACATCAACAGGATAACCAGCG 58.368 47.619 0.00 0.00 38.94 5.18
10 11 4.335594 GGTTACATCAACAGGATAACCAGC 59.664 45.833 6.60 0.00 41.39 4.85
11 12 5.496556 TGGTTACATCAACAGGATAACCAG 58.503 41.667 9.53 0.00 44.26 4.00
12 13 5.506730 TGGTTACATCAACAGGATAACCA 57.493 39.130 9.53 9.53 45.74 3.67
13 14 5.221048 GCATGGTTACATCAACAGGATAACC 60.221 44.000 4.82 4.82 41.81 2.85
14 15 5.590259 AGCATGGTTACATCAACAGGATAAC 59.410 40.000 0.00 0.00 39.04 1.89
15 16 5.589855 CAGCATGGTTACATCAACAGGATAA 59.410 40.000 0.00 0.00 39.04 1.75
16 17 5.125356 CAGCATGGTTACATCAACAGGATA 58.875 41.667 0.00 0.00 39.04 2.59
17 18 3.949754 CAGCATGGTTACATCAACAGGAT 59.050 43.478 0.00 0.00 39.04 3.24
18 19 3.244875 ACAGCATGGTTACATCAACAGGA 60.245 43.478 0.00 0.00 43.62 3.86
19 20 3.084039 ACAGCATGGTTACATCAACAGG 58.916 45.455 0.00 0.00 43.62 4.00
20 21 5.412594 AGTTACAGCATGGTTACATCAACAG 59.587 40.000 0.00 0.00 43.62 3.16
21 22 5.181056 CAGTTACAGCATGGTTACATCAACA 59.819 40.000 0.00 0.00 43.62 3.33
22 23 5.411361 TCAGTTACAGCATGGTTACATCAAC 59.589 40.000 0.00 0.00 43.62 3.18
23 24 5.555966 TCAGTTACAGCATGGTTACATCAA 58.444 37.500 0.00 0.00 43.62 2.57
24 25 5.159273 TCAGTTACAGCATGGTTACATCA 57.841 39.130 0.00 0.00 43.62 3.07
25 26 5.874810 TCTTCAGTTACAGCATGGTTACATC 59.125 40.000 0.00 0.00 43.62 3.06
26 27 5.804639 TCTTCAGTTACAGCATGGTTACAT 58.195 37.500 0.00 0.00 43.62 2.29
27 28 5.222079 TCTTCAGTTACAGCATGGTTACA 57.778 39.130 0.00 0.00 43.62 2.41
28 29 6.743575 AATCTTCAGTTACAGCATGGTTAC 57.256 37.500 0.00 0.00 43.62 2.50
29 30 6.533723 CGTAATCTTCAGTTACAGCATGGTTA 59.466 38.462 0.00 0.00 43.62 2.85
30 31 5.351465 CGTAATCTTCAGTTACAGCATGGTT 59.649 40.000 0.00 0.00 43.62 3.67
31 32 4.870426 CGTAATCTTCAGTTACAGCATGGT 59.130 41.667 0.00 0.00 43.62 3.55
32 33 4.260375 GCGTAATCTTCAGTTACAGCATGG 60.260 45.833 0.00 0.00 43.62 3.66
33 34 4.260375 GGCGTAATCTTCAGTTACAGCATG 60.260 45.833 0.00 0.00 46.00 4.06
34 35 3.871594 GGCGTAATCTTCAGTTACAGCAT 59.128 43.478 11.66 0.00 35.41 3.79
35 36 3.259064 GGCGTAATCTTCAGTTACAGCA 58.741 45.455 11.66 0.00 35.41 4.41
36 37 2.281762 CGGCGTAATCTTCAGTTACAGC 59.718 50.000 0.00 0.00 32.83 4.40
37 38 3.303495 CACGGCGTAATCTTCAGTTACAG 59.697 47.826 14.22 0.00 32.83 2.74
38 39 3.247442 CACGGCGTAATCTTCAGTTACA 58.753 45.455 14.22 0.00 32.83 2.41
39 40 3.248266 ACACGGCGTAATCTTCAGTTAC 58.752 45.455 14.22 0.00 0.00 2.50
40 41 3.192001 AGACACGGCGTAATCTTCAGTTA 59.808 43.478 14.22 0.00 0.00 2.24
41 42 2.029290 AGACACGGCGTAATCTTCAGTT 60.029 45.455 14.22 0.00 0.00 3.16
42 43 1.544691 AGACACGGCGTAATCTTCAGT 59.455 47.619 14.22 3.10 0.00 3.41
43 44 2.279582 AGACACGGCGTAATCTTCAG 57.720 50.000 14.22 0.00 0.00 3.02
44 45 2.736144 AAGACACGGCGTAATCTTCA 57.264 45.000 24.85 0.00 0.00 3.02
45 46 4.025979 CCATTAAGACACGGCGTAATCTTC 60.026 45.833 30.44 15.92 33.53 2.87
46 47 3.869246 CCATTAAGACACGGCGTAATCTT 59.131 43.478 29.79 29.79 35.60 2.40
47 48 3.131577 TCCATTAAGACACGGCGTAATCT 59.868 43.478 14.22 16.27 0.00 2.40
48 49 3.450578 TCCATTAAGACACGGCGTAATC 58.549 45.455 14.22 14.00 0.00 1.75
49 50 3.530265 TCCATTAAGACACGGCGTAAT 57.470 42.857 14.22 5.57 0.00 1.89
50 51 3.316071 TTCCATTAAGACACGGCGTAA 57.684 42.857 14.22 2.78 0.00 3.18
51 52 3.530265 ATTCCATTAAGACACGGCGTA 57.470 42.857 14.22 0.00 0.00 4.42
52 53 2.396590 ATTCCATTAAGACACGGCGT 57.603 45.000 6.77 6.77 0.00 5.68
53 54 2.542595 GGTATTCCATTAAGACACGGCG 59.457 50.000 4.80 4.80 30.58 6.46
54 55 2.542595 CGGTATTCCATTAAGACACGGC 59.457 50.000 0.00 0.00 30.58 5.68
55 56 3.128349 CCGGTATTCCATTAAGACACGG 58.872 50.000 0.00 0.00 37.05 4.94
56 57 3.554324 CACCGGTATTCCATTAAGACACG 59.446 47.826 6.87 0.00 30.58 4.49
57 58 4.510571 ACACCGGTATTCCATTAAGACAC 58.489 43.478 6.87 0.00 30.58 3.67
58 59 4.829872 ACACCGGTATTCCATTAAGACA 57.170 40.909 6.87 0.00 30.58 3.41
59 60 4.573607 GGAACACCGGTATTCCATTAAGAC 59.426 45.833 34.69 8.94 43.40 3.01
60 61 4.773013 GGAACACCGGTATTCCATTAAGA 58.227 43.478 34.69 0.00 43.40 2.10
202 207 5.739161 CGTTAGTCAAACCTACCGTGTATAC 59.261 44.000 0.00 0.00 34.33 1.47
256 261 0.515564 GCGACAATGCTTTGGTACGT 59.484 50.000 15.92 0.00 37.15 3.57
268 273 3.581024 TGTTAACTAGTCCGCGACAAT 57.419 42.857 8.23 0.00 34.60 2.71
287 292 1.227999 ACTGTTGACCGCGGATGTTG 61.228 55.000 35.90 18.54 0.00 3.33
289 294 1.667830 CACTGTTGACCGCGGATGT 60.668 57.895 35.90 10.08 0.00 3.06
364 369 2.747855 CTTGGTCCAGCGGCTTCC 60.748 66.667 0.00 4.18 0.00 3.46
385 390 1.002624 TCCCTCGCATGTGGTTTCC 60.003 57.895 6.39 0.00 0.00 3.13
479 484 3.138128 CCGGCGGGGTTGGATTTC 61.138 66.667 20.56 0.00 0.00 2.17
525 530 4.755629 TGCTAGTACTAGTCTAATGGCGAG 59.244 45.833 26.76 4.19 35.65 5.03
547 552 0.800683 ATGCCGTGTCGATGTACGTG 60.801 55.000 15.34 9.83 43.13 4.49
615 622 2.475852 GCGCGGGATAGTCTATTCTACG 60.476 54.545 8.83 8.26 0.00 3.51
684 691 2.695759 CCGCGCACAGAGAGAGACT 61.696 63.158 8.75 0.00 0.00 3.24
786 797 1.968017 CAGCGCAGTGGTTGGTCAT 60.968 57.895 11.47 0.00 0.00 3.06
808 819 5.982890 AATTATTAATTGATGAGCGGGGG 57.017 39.130 0.83 0.00 0.00 5.40
882 901 3.454587 GACACACCACGTCTGGGCA 62.455 63.158 0.00 0.00 42.74 5.36
969 993 8.926374 TCCTCCGTCAACAATAGGTTATAATTA 58.074 33.333 0.00 0.00 37.72 1.40
1068 1092 3.282745 CTGCGTAGAGGCGTGGTGT 62.283 63.158 0.00 0.00 35.06 4.16
1917 1941 2.669133 CGCCACCTTGGGATCCTCA 61.669 63.158 12.58 5.20 38.19 3.86
2696 2721 4.727235 ACGAAAACGAGAAGATGGAAAC 57.273 40.909 0.00 0.00 0.00 2.78
2705 2730 2.540516 TGCATCGAAACGAAAACGAGAA 59.459 40.909 0.00 0.00 39.99 2.87
2707 2732 2.570468 TGCATCGAAACGAAAACGAG 57.430 45.000 0.00 0.00 39.99 4.18
2775 2806 0.586802 GTGGTCAAAACACTCGAGCC 59.413 55.000 13.61 3.25 35.98 4.70
2779 2810 3.691049 ACATTGTGGTCAAAACACTCG 57.309 42.857 0.00 0.00 39.52 4.18
2877 2917 5.183228 GGAATGGAATCGGTCTCTGTTTTA 58.817 41.667 0.00 0.00 0.00 1.52
2933 3051 9.677567 AGTAAAAAGTCGACGTTAATGTTAGTA 57.322 29.630 17.05 0.00 0.00 1.82
2934 3052 8.579682 AGTAAAAAGTCGACGTTAATGTTAGT 57.420 30.769 17.05 11.37 0.00 2.24
3035 3153 7.385752 TGAATTGTTAACCGTAAGAAGTAGTGG 59.614 37.037 2.48 0.00 43.02 4.00
3036 3154 8.301730 TGAATTGTTAACCGTAAGAAGTAGTG 57.698 34.615 2.48 0.00 43.02 2.74
3037 3155 9.498176 AATGAATTGTTAACCGTAAGAAGTAGT 57.502 29.630 2.48 0.00 43.02 2.73
3069 3190 2.157668 CCACTACGAGTGTTGCAATCAC 59.842 50.000 18.57 18.57 44.50 3.06
3085 3206 4.157246 TCTAGCTTTGGTGACTTCCACTA 58.843 43.478 0.00 0.00 45.03 2.74
3099 3220 1.813178 GAAAAAGGCCGCTCTAGCTTT 59.187 47.619 0.00 0.00 39.32 3.51
3131 3252 2.047560 GGAGGTTCGGGGTTGTCG 60.048 66.667 0.00 0.00 0.00 4.35
3164 3285 4.408904 AACTACCCTAGACTGGTGGTAA 57.591 45.455 6.17 0.00 45.63 2.85
3200 3324 7.535258 CACTGAAGATTTTATTTCAAGACACGG 59.465 37.037 0.00 0.00 33.30 4.94
3213 3337 9.567776 TTGATTTCTGTACCACTGAAGATTTTA 57.432 29.630 0.00 0.00 37.36 1.52
3258 3382 9.239551 ACACTGAGTGATAGTACAGTTTATACA 57.760 33.333 20.97 0.00 40.84 2.29
3266 3390 7.814587 TGAAAATGACACTGAGTGATAGTACAG 59.185 37.037 20.97 0.00 36.96 2.74
3269 3393 6.813649 GCTGAAAATGACACTGAGTGATAGTA 59.186 38.462 20.97 0.75 36.96 1.82
3278 3402 9.624697 GTATTAATTTGCTGAAAATGACACTGA 57.375 29.630 0.00 0.00 38.52 3.41
3330 3454 5.514500 TTAACCATAGAGGCCACTTTTCT 57.486 39.130 8.39 1.80 43.14 2.52
3331 3455 5.710567 AGTTTAACCATAGAGGCCACTTTTC 59.289 40.000 8.39 0.00 43.14 2.29
3332 3456 5.641155 AGTTTAACCATAGAGGCCACTTTT 58.359 37.500 8.39 0.00 43.14 2.27
3333 3457 5.256806 AGTTTAACCATAGAGGCCACTTT 57.743 39.130 8.39 0.00 43.14 2.66
3341 3465 9.994432 CAGCAATTTTCTAGTTTAACCATAGAG 57.006 33.333 0.00 0.00 0.00 2.43
3342 3466 9.733556 TCAGCAATTTTCTAGTTTAACCATAGA 57.266 29.630 0.00 0.00 0.00 1.98
3352 3476 6.223852 TCTCTTCGTCAGCAATTTTCTAGTT 58.776 36.000 0.00 0.00 0.00 2.24
3353 3477 5.784177 TCTCTTCGTCAGCAATTTTCTAGT 58.216 37.500 0.00 0.00 0.00 2.57
3354 3478 6.533012 TCATCTCTTCGTCAGCAATTTTCTAG 59.467 38.462 0.00 0.00 0.00 2.43
3355 3479 6.311445 GTCATCTCTTCGTCAGCAATTTTCTA 59.689 38.462 0.00 0.00 0.00 2.10
3356 3480 5.121454 GTCATCTCTTCGTCAGCAATTTTCT 59.879 40.000 0.00 0.00 0.00 2.52
3357 3481 5.106948 TGTCATCTCTTCGTCAGCAATTTTC 60.107 40.000 0.00 0.00 0.00 2.29
3358 3482 4.756642 TGTCATCTCTTCGTCAGCAATTTT 59.243 37.500 0.00 0.00 0.00 1.82
3359 3483 4.318332 TGTCATCTCTTCGTCAGCAATTT 58.682 39.130 0.00 0.00 0.00 1.82
3360 3484 3.930336 TGTCATCTCTTCGTCAGCAATT 58.070 40.909 0.00 0.00 0.00 2.32
3361 3485 3.056250 ACTGTCATCTCTTCGTCAGCAAT 60.056 43.478 0.00 0.00 0.00 3.56
3362 3486 2.297315 ACTGTCATCTCTTCGTCAGCAA 59.703 45.455 0.00 0.00 0.00 3.91
3363 3487 1.889170 ACTGTCATCTCTTCGTCAGCA 59.111 47.619 0.00 0.00 0.00 4.41
3364 3488 2.645730 ACTGTCATCTCTTCGTCAGC 57.354 50.000 0.00 0.00 0.00 4.26
3365 3489 5.163713 TGTCATACTGTCATCTCTTCGTCAG 60.164 44.000 0.00 0.00 0.00 3.51
3366 3490 4.700213 TGTCATACTGTCATCTCTTCGTCA 59.300 41.667 0.00 0.00 0.00 4.35
3367 3491 5.031578 GTGTCATACTGTCATCTCTTCGTC 58.968 45.833 0.00 0.00 0.00 4.20
3368 3492 4.702612 AGTGTCATACTGTCATCTCTTCGT 59.297 41.667 0.00 0.00 38.49 3.85
3369 3493 5.242069 AGTGTCATACTGTCATCTCTTCG 57.758 43.478 0.00 0.00 38.49 3.79
3381 3505 5.407407 AAGAATTCCGTCAGTGTCATACT 57.593 39.130 0.65 0.00 41.36 2.12
3382 3506 7.591006 TTAAAGAATTCCGTCAGTGTCATAC 57.409 36.000 0.65 0.00 0.00 2.39
3383 3507 8.610248 TTTTAAAGAATTCCGTCAGTGTCATA 57.390 30.769 0.65 0.00 0.00 2.15
3384 3508 7.504924 TTTTAAAGAATTCCGTCAGTGTCAT 57.495 32.000 0.65 0.00 0.00 3.06
3385 3509 6.928979 TTTTAAAGAATTCCGTCAGTGTCA 57.071 33.333 0.65 0.00 0.00 3.58
3409 3533 9.462606 AGAATATACTTTCGAGGTTTCCATTTT 57.537 29.630 0.00 0.00 0.00 1.82
3411 3535 9.765795 CTAGAATATACTTTCGAGGTTTCCATT 57.234 33.333 0.00 0.00 0.00 3.16
3412 3536 8.925338 ACTAGAATATACTTTCGAGGTTTCCAT 58.075 33.333 0.00 0.00 33.98 3.41
3413 3537 8.302515 ACTAGAATATACTTTCGAGGTTTCCA 57.697 34.615 0.00 0.00 33.98 3.53
3414 3538 9.597170 AAACTAGAATATACTTTCGAGGTTTCC 57.403 33.333 0.00 0.00 35.54 3.13
3417 3541 9.298774 CGAAAACTAGAATATACTTTCGAGGTT 57.701 33.333 8.61 0.00 44.74 3.50
3418 3542 8.680903 TCGAAAACTAGAATATACTTTCGAGGT 58.319 33.333 12.00 0.00 45.22 3.85
3446 3570 5.638596 GACAGGGTCGTAAAAATGGAATT 57.361 39.130 0.00 0.00 38.98 2.17
3460 3584 0.529119 AACACGACAACGACAGGGTC 60.529 55.000 0.00 0.00 42.66 4.46
3461 3585 0.808453 CAACACGACAACGACAGGGT 60.808 55.000 0.00 0.00 42.66 4.34
3462 3586 0.528901 TCAACACGACAACGACAGGG 60.529 55.000 0.00 0.00 42.66 4.45
3463 3587 1.282817 TTCAACACGACAACGACAGG 58.717 50.000 0.00 0.00 42.66 4.00
3464 3588 2.538037 TCATTCAACACGACAACGACAG 59.462 45.455 0.00 0.00 42.66 3.51
3465 3589 2.541556 TCATTCAACACGACAACGACA 58.458 42.857 0.00 0.00 42.66 4.35
3466 3590 3.244345 TCTTCATTCAACACGACAACGAC 59.756 43.478 0.00 0.00 42.66 4.34
3467 3591 3.449632 TCTTCATTCAACACGACAACGA 58.550 40.909 0.00 0.00 42.66 3.85
3468 3592 3.852471 TCTTCATTCAACACGACAACG 57.148 42.857 0.00 0.00 45.75 4.10
3469 3593 5.140177 GTGATCTTCATTCAACACGACAAC 58.860 41.667 0.00 0.00 0.00 3.32
3470 3594 4.213270 GGTGATCTTCATTCAACACGACAA 59.787 41.667 0.00 0.00 30.96 3.18
3471 3595 3.745975 GGTGATCTTCATTCAACACGACA 59.254 43.478 0.00 0.00 30.96 4.35
3472 3596 3.997021 AGGTGATCTTCATTCAACACGAC 59.003 43.478 0.00 0.00 33.09 4.34
3473 3597 4.021104 AGAGGTGATCTTCATTCAACACGA 60.021 41.667 0.00 0.00 32.99 4.35
3474 3598 4.248859 AGAGGTGATCTTCATTCAACACG 58.751 43.478 0.00 0.00 32.99 4.49
3486 3610 3.842869 GGCAACGAAGAGGTGATCT 57.157 52.632 0.00 0.00 40.93 2.75
3503 3627 4.845580 AGCTCTTCGGCCATGCGG 62.846 66.667 2.24 0.00 0.00 5.69
3504 3628 3.267860 GAGCTCTTCGGCCATGCG 61.268 66.667 6.43 0.00 0.00 4.73
3505 3629 1.028868 AAAGAGCTCTTCGGCCATGC 61.029 55.000 28.58 0.00 34.61 4.06
3506 3630 1.012841 GAAAGAGCTCTTCGGCCATG 58.987 55.000 28.58 0.00 34.61 3.66
3507 3631 0.107459 GGAAAGAGCTCTTCGGCCAT 60.107 55.000 28.58 12.57 34.61 4.40
3508 3632 1.296715 GGAAAGAGCTCTTCGGCCA 59.703 57.895 28.58 0.00 34.61 5.36
3509 3633 0.107459 ATGGAAAGAGCTCTTCGGCC 60.107 55.000 28.58 26.38 34.61 6.13
3510 3634 1.012841 CATGGAAAGAGCTCTTCGGC 58.987 55.000 28.58 19.55 34.61 5.54
3511 3635 1.661341 CCATGGAAAGAGCTCTTCGG 58.339 55.000 28.58 18.78 34.61 4.30
3512 3636 1.012841 GCCATGGAAAGAGCTCTTCG 58.987 55.000 28.58 14.37 34.61 3.79
3513 3637 1.387539 GGCCATGGAAAGAGCTCTTC 58.612 55.000 28.58 20.19 34.61 2.87
3514 3638 0.393537 CGGCCATGGAAAGAGCTCTT 60.394 55.000 23.49 23.49 37.91 2.85
3515 3639 1.222936 CGGCCATGGAAAGAGCTCT 59.777 57.895 18.40 11.45 0.00 4.09
3516 3640 2.476320 GCGGCCATGGAAAGAGCTC 61.476 63.158 18.40 5.27 0.00 4.09
3517 3641 2.439156 GCGGCCATGGAAAGAGCT 60.439 61.111 18.40 0.00 0.00 4.09
3518 3642 3.521796 GGCGGCCATGGAAAGAGC 61.522 66.667 18.40 12.05 0.00 4.09
3519 3643 2.117156 CAGGCGGCCATGGAAAGAG 61.117 63.158 23.09 1.79 0.00 2.85
3520 3644 2.045045 CAGGCGGCCATGGAAAGA 60.045 61.111 23.09 0.00 0.00 2.52
3521 3645 3.142838 CCAGGCGGCCATGGAAAG 61.143 66.667 24.57 6.55 39.02 2.62
3522 3646 4.757355 CCCAGGCGGCCATGGAAA 62.757 66.667 28.23 0.00 39.02 3.13
3533 3657 4.400961 AGCACTCTTCGCCCAGGC 62.401 66.667 0.00 0.00 37.85 4.85
3534 3658 2.125350 GAGCACTCTTCGCCCAGG 60.125 66.667 0.00 0.00 0.00 4.45
3535 3659 1.294780 AAGAGCACTCTTCGCCCAG 59.705 57.895 7.10 0.00 46.13 4.45
3536 3660 3.471620 AAGAGCACTCTTCGCCCA 58.528 55.556 7.10 0.00 46.13 5.36
3543 3667 3.764466 CGGCCCGAAGAGCACTCT 61.764 66.667 0.00 0.00 42.75 3.24
3544 3668 3.760035 TCGGCCCGAAGAGCACTC 61.760 66.667 1.70 0.00 26.75 3.51
3545 3669 4.070552 GTCGGCCCGAAGAGCACT 62.071 66.667 7.77 0.00 37.72 4.40
3559 3683 2.703798 TAACTCTTCGGCCCCGTCG 61.704 63.158 6.61 0.00 40.74 5.12
3560 3684 1.153686 GTAACTCTTCGGCCCCGTC 60.154 63.158 6.61 0.00 40.74 4.79
3561 3685 1.602327 GAGTAACTCTTCGGCCCCGT 61.602 60.000 6.61 0.00 40.74 5.28
3562 3686 1.141234 GAGTAACTCTTCGGCCCCG 59.859 63.158 0.00 0.00 41.35 5.73
3563 3687 0.903236 AAGAGTAACTCTTCGGCCCC 59.097 55.000 0.00 0.00 46.42 5.80
3570 3694 7.033589 GCACATGCAACGAAGAGTAACTCTT 62.034 44.000 0.00 0.00 45.78 2.85
3571 3695 3.990469 CACATGCAACGAAGAGTAACTCT 59.010 43.478 0.00 0.00 43.37 3.24
3572 3696 3.423645 GCACATGCAACGAAGAGTAACTC 60.424 47.826 0.00 0.00 41.59 3.01
3573 3697 2.480419 GCACATGCAACGAAGAGTAACT 59.520 45.455 0.00 0.00 41.59 2.24
3574 3698 2.721797 CGCACATGCAACGAAGAGTAAC 60.722 50.000 4.49 0.00 42.21 2.50
3575 3699 1.459209 CGCACATGCAACGAAGAGTAA 59.541 47.619 4.49 0.00 42.21 2.24
3576 3700 1.067693 CGCACATGCAACGAAGAGTA 58.932 50.000 4.49 0.00 42.21 2.59
3577 3701 1.568612 CCGCACATGCAACGAAGAGT 61.569 55.000 4.49 0.00 42.21 3.24
3578 3702 1.133253 CCGCACATGCAACGAAGAG 59.867 57.895 4.49 0.00 42.21 2.85
3579 3703 1.301322 TCCGCACATGCAACGAAGA 60.301 52.632 4.49 0.00 42.21 2.87
3580 3704 1.154413 GTCCGCACATGCAACGAAG 60.154 57.895 4.49 0.00 42.21 3.79
3581 3705 2.942879 GTCCGCACATGCAACGAA 59.057 55.556 4.49 0.00 42.21 3.85
3582 3706 3.410516 CGTCCGCACATGCAACGA 61.411 61.111 18.73 2.77 46.26 3.85
3583 3707 2.436997 TTTCGTCCGCACATGCAACG 62.437 55.000 17.87 17.87 45.37 4.10
3584 3708 0.317436 TTTTCGTCCGCACATGCAAC 60.317 50.000 4.49 0.76 42.21 4.17
3585 3709 0.040514 CTTTTCGTCCGCACATGCAA 60.041 50.000 4.49 0.00 42.21 4.08
3586 3710 1.163420 ACTTTTCGTCCGCACATGCA 61.163 50.000 4.49 0.00 42.21 3.96
3587 3711 0.040425 AACTTTTCGTCCGCACATGC 60.040 50.000 0.00 0.00 37.78 4.06
3588 3712 1.950472 GAACTTTTCGTCCGCACATG 58.050 50.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.