Multiple sequence alignment - TraesCS1D01G217300

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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 TraesCS1D01G217300 chr1D 100.000 3593 0 0 1 3593 302823167 302819575 0.000000e+00 6636.0
1 TraesCS1D01G217300 chr1A 93.585 3180 163 16 427 3593 377432826 377429675 0.000000e+00 4704.0
2 TraesCS1D01G217300 chr1A 90.487 452 21 13 1 448 377444227 377443794 8.650000e-161 577.0
3 TraesCS1D01G217300 chr1A 86.928 153 12 5 308 460 362624122 362623978 7.980000e-37 165.0
4 TraesCS1D01G217300 chr1B 94.585 2955 111 19 659 3593 409632948 409630023 0.000000e+00 4525.0
5 TraesCS1D01G217300 chr1B 86.957 138 7 3 87 215 409633348 409633213 1.040000e-30 145.0
6 TraesCS1D01G217300 chr7D 93.333 135 8 1 326 460 34756885 34757018 7.870000e-47 198.0
7 TraesCS1D01G217300 chr6A 91.216 148 10 3 326 472 411770386 411770241 7.870000e-47 198.0
8 TraesCS1D01G217300 chr5D 88.344 163 11 4 299 461 528717431 528717277 4.740000e-44 189.0
9 TraesCS1D01G217300 chr5B 88.344 163 11 3 299 461 665744622 665744468 4.740000e-44 189.0
10 TraesCS1D01G217300 chr5B 90.647 139 12 1 328 466 636609437 636609300 2.200000e-42 183.0
11 TraesCS1D01G217300 chr5A 88.344 163 11 4 299 461 656872438 656872284 4.740000e-44 189.0
12 TraesCS1D01G217300 chr4B 91.111 135 11 1 326 460 146469349 146469216 7.920000e-42 182.0
13 TraesCS1D01G217300 chr3D 87.500 152 12 5 308 459 76231138 76230994 6.170000e-38 169.0
14 TraesCS1D01G217300 chr3D 94.231 52 3 0 18 69 54385988 54385937 2.970000e-11 80.5
15 TraesCS1D01G217300 chr3D 91.071 56 3 2 597 652 615100020 615100073 1.380000e-09 75.0
16 TraesCS1D01G217300 chr3B 85.938 128 12 5 58 182 84736510 84736386 8.090000e-27 132.0
17 TraesCS1D01G217300 chr3B 94.444 54 1 2 609 662 27199183 27199132 8.270000e-12 82.4
18 TraesCS1D01G217300 chr3B 94.444 54 1 2 609 662 74292869 74292818 8.270000e-12 82.4
19 TraesCS1D01G217300 chr3B 95.652 46 2 0 18 63 84737008 84736963 1.380000e-09 75.0
20 TraesCS1D01G217300 chr7B 97.872 47 1 0 608 654 304527178 304527224 8.270000e-12 82.4
21 TraesCS1D01G217300 chr2A 92.857 56 4 0 599 654 750625026 750624971 8.270000e-12 82.4
22 TraesCS1D01G217300 chr7A 90.164 61 5 1 595 654 230567507 230567567 1.070000e-10 78.7
23 TraesCS1D01G217300 chr6D 92.593 54 3 1 601 654 3257055 3257003 3.850000e-10 76.8
24 TraesCS1D01G217300 chr4A 91.071 56 5 0 599 654 11585487 11585432 3.850000e-10 76.8
25 TraesCS1D01G217300 chr3A 93.750 48 2 1 17 63 65350435 65350388 1.790000e-08 71.3


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 TraesCS1D01G217300 chr1D 302819575 302823167 3592 True 6636 6636 100.000 1 3593 1 chr1D.!!$R1 3592
1 TraesCS1D01G217300 chr1A 377429675 377432826 3151 True 4704 4704 93.585 427 3593 1 chr1A.!!$R2 3166
2 TraesCS1D01G217300 chr1B 409630023 409633348 3325 True 2335 4525 90.771 87 3593 2 chr1B.!!$R1 3506

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
75 76 0.824109 CTGCAAGAGGGGTCGACATA 59.176 55.0 18.91 0.0 34.07 2.29 F
1542 1598 0.179124 GCTTGGTGCTCTACTCCGAG 60.179 60.0 0.00 0.0 43.67 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 1659 1.078918 CCATGAGACCAGCGCAAGA 60.079 57.895 11.47 0.0 43.02 3.02 R
2764 2821 0.532862 CCGCGCTTGTTCAGGGATAT 60.533 55.000 5.56 0.0 37.67 1.63 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
37 38 7.088589 GCTCAAGCTGGAATTAATTTACAGA 57.911 36.000 25.64 12.19 38.21 3.41
38 39 7.538575 GCTCAAGCTGGAATTAATTTACAGAA 58.461 34.615 25.64 13.27 38.21 3.02
39 40 7.486232 GCTCAAGCTGGAATTAATTTACAGAAC 59.514 37.037 25.64 15.09 38.21 3.01
40 41 7.826690 TCAAGCTGGAATTAATTTACAGAACC 58.173 34.615 25.64 12.87 31.12 3.62
41 42 6.436843 AGCTGGAATTAATTTACAGAACCG 57.563 37.500 25.64 10.43 31.12 4.44
42 43 5.944007 AGCTGGAATTAATTTACAGAACCGT 59.056 36.000 25.64 10.20 31.12 4.83
43 44 6.433093 AGCTGGAATTAATTTACAGAACCGTT 59.567 34.615 25.64 9.63 31.12 4.44
44 45 7.039993 AGCTGGAATTAATTTACAGAACCGTTT 60.040 33.333 25.64 8.52 31.12 3.60
45 46 8.238631 GCTGGAATTAATTTACAGAACCGTTTA 58.761 33.333 25.64 0.25 31.12 2.01
46 47 9.769093 CTGGAATTAATTTACAGAACCGTTTAG 57.231 33.333 20.57 1.37 31.12 1.85
47 48 8.238631 TGGAATTAATTTACAGAACCGTTTAGC 58.761 33.333 1.43 0.00 0.00 3.09
48 49 8.456471 GGAATTAATTTACAGAACCGTTTAGCT 58.544 33.333 1.43 0.00 0.00 3.32
49 50 9.836076 GAATTAATTTACAGAACCGTTTAGCTT 57.164 29.630 1.43 0.00 0.00 3.74
50 51 9.620660 AATTAATTTACAGAACCGTTTAGCTTG 57.379 29.630 0.00 0.00 0.00 4.01
51 52 6.628919 AATTTACAGAACCGTTTAGCTTGT 57.371 33.333 0.00 0.00 0.00 3.16
52 53 7.733402 AATTTACAGAACCGTTTAGCTTGTA 57.267 32.000 0.00 0.00 0.00 2.41
53 54 7.733402 ATTTACAGAACCGTTTAGCTTGTAA 57.267 32.000 0.00 0.00 0.00 2.41
54 55 7.551035 TTTACAGAACCGTTTAGCTTGTAAA 57.449 32.000 9.43 9.43 0.00 2.01
55 56 5.413969 ACAGAACCGTTTAGCTTGTAAAC 57.586 39.130 0.00 0.00 34.91 2.01
56 57 4.274214 ACAGAACCGTTTAGCTTGTAAACC 59.726 41.667 0.00 0.00 34.81 3.27
57 58 4.514066 CAGAACCGTTTAGCTTGTAAACCT 59.486 41.667 0.00 0.00 34.81 3.50
58 59 4.514066 AGAACCGTTTAGCTTGTAAACCTG 59.486 41.667 0.00 0.00 34.81 4.00
59 60 2.551032 ACCGTTTAGCTTGTAAACCTGC 59.449 45.455 0.00 0.00 34.81 4.85
60 61 2.550606 CCGTTTAGCTTGTAAACCTGCA 59.449 45.455 0.00 0.00 34.81 4.41
61 62 3.003897 CCGTTTAGCTTGTAAACCTGCAA 59.996 43.478 0.00 0.00 34.81 4.08
62 63 4.219033 CGTTTAGCTTGTAAACCTGCAAG 58.781 43.478 0.00 0.00 45.26 4.01
63 64 4.024387 CGTTTAGCTTGTAAACCTGCAAGA 60.024 41.667 7.08 0.00 45.30 3.02
64 65 5.452777 GTTTAGCTTGTAAACCTGCAAGAG 58.547 41.667 7.08 0.00 45.30 2.85
65 66 2.508526 AGCTTGTAAACCTGCAAGAGG 58.491 47.619 7.08 0.00 45.30 3.69
72 73 2.266055 CCTGCAAGAGGGGTCGAC 59.734 66.667 7.13 7.13 38.36 4.20
73 74 2.583441 CCTGCAAGAGGGGTCGACA 61.583 63.158 18.91 0.00 38.36 4.35
74 75 1.599047 CTGCAAGAGGGGTCGACAT 59.401 57.895 18.91 1.93 34.07 3.06
75 76 0.824109 CTGCAAGAGGGGTCGACATA 59.176 55.000 18.91 0.00 34.07 2.29
76 77 1.414181 CTGCAAGAGGGGTCGACATAT 59.586 52.381 18.91 1.10 34.07 1.78
77 78 1.837439 TGCAAGAGGGGTCGACATATT 59.163 47.619 18.91 3.31 0.00 1.28
78 79 2.213499 GCAAGAGGGGTCGACATATTG 58.787 52.381 18.91 15.98 0.00 1.90
79 80 2.838736 CAAGAGGGGTCGACATATTGG 58.161 52.381 18.91 0.00 0.00 3.16
80 81 1.424638 AGAGGGGTCGACATATTGGG 58.575 55.000 18.91 0.00 0.00 4.12
81 82 1.062428 AGAGGGGTCGACATATTGGGA 60.062 52.381 18.91 0.00 0.00 4.37
82 83 1.766496 GAGGGGTCGACATATTGGGAA 59.234 52.381 18.91 0.00 0.00 3.97
83 84 1.768870 AGGGGTCGACATATTGGGAAG 59.231 52.381 18.91 0.00 0.00 3.46
84 85 1.489230 GGGGTCGACATATTGGGAAGT 59.511 52.381 18.91 0.00 0.00 3.01
85 86 2.701951 GGGGTCGACATATTGGGAAGTA 59.298 50.000 18.91 0.00 0.00 2.24
95 96 5.594317 ACATATTGGGAAGTAGCAATGTTCC 59.406 40.000 0.00 0.00 39.31 3.62
100 101 2.673368 GGAAGTAGCAATGTTCCGTCTG 59.327 50.000 0.00 0.00 30.84 3.51
101 102 3.326747 GAAGTAGCAATGTTCCGTCTGT 58.673 45.455 0.00 0.00 0.00 3.41
102 103 4.491676 GAAGTAGCAATGTTCCGTCTGTA 58.508 43.478 0.00 0.00 0.00 2.74
103 104 4.111375 AGTAGCAATGTTCCGTCTGTAG 57.889 45.455 0.00 0.00 0.00 2.74
104 105 2.386661 AGCAATGTTCCGTCTGTAGG 57.613 50.000 0.00 0.00 0.00 3.18
173 178 4.079980 TCTGCTGCAACTTAAAGTGGTA 57.920 40.909 3.02 0.00 0.00 3.25
183 188 6.238925 GCAACTTAAAGTGGTATGGTGAAAGT 60.239 38.462 0.00 0.00 0.00 2.66
190 195 2.158534 TGGTATGGTGAAAGTGCCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
244 289 5.833131 TGCTTATTTGACCCTTTTGTTCTCT 59.167 36.000 0.00 0.00 0.00 3.10
248 293 5.576447 TTTGACCCTTTTGTTCTCTGTTC 57.424 39.130 0.00 0.00 0.00 3.18
277 324 3.387374 ACTATCAGTCCTGGAGATTGCAG 59.613 47.826 0.00 0.00 35.43 4.41
286 333 2.417933 CTGGAGATTGCAGGTTTCGAAG 59.582 50.000 0.00 0.00 31.71 3.79
292 341 5.281727 AGATTGCAGGTTTCGAAGTTTTTC 58.718 37.500 0.00 0.00 0.00 2.29
318 367 6.377327 GAGAAAAACTCACTCCATTCACAA 57.623 37.500 0.00 0.00 44.36 3.33
319 368 6.773976 AGAAAAACTCACTCCATTCACAAA 57.226 33.333 0.00 0.00 0.00 2.83
320 369 7.352079 AGAAAAACTCACTCCATTCACAAAT 57.648 32.000 0.00 0.00 0.00 2.32
321 370 8.463930 AGAAAAACTCACTCCATTCACAAATA 57.536 30.769 0.00 0.00 0.00 1.40
322 371 8.352942 AGAAAAACTCACTCCATTCACAAATAC 58.647 33.333 0.00 0.00 0.00 1.89
323 372 7.823745 AAAACTCACTCCATTCACAAATACT 57.176 32.000 0.00 0.00 0.00 2.12
324 373 6.808008 AACTCACTCCATTCACAAATACTG 57.192 37.500 0.00 0.00 0.00 2.74
325 374 5.869579 ACTCACTCCATTCACAAATACTGT 58.130 37.500 0.00 0.00 39.56 3.55
326 375 7.004555 ACTCACTCCATTCACAAATACTGTA 57.995 36.000 0.00 0.00 36.10 2.74
327 376 7.624549 ACTCACTCCATTCACAAATACTGTAT 58.375 34.615 0.00 0.00 36.10 2.29
328 377 8.758829 ACTCACTCCATTCACAAATACTGTATA 58.241 33.333 0.00 0.00 36.10 1.47
329 378 9.599866 CTCACTCCATTCACAAATACTGTATAA 57.400 33.333 0.00 0.00 36.10 0.98
330 379 9.599866 TCACTCCATTCACAAATACTGTATAAG 57.400 33.333 0.00 0.00 36.10 1.73
331 380 9.599866 CACTCCATTCACAAATACTGTATAAGA 57.400 33.333 0.00 0.00 36.10 2.10
376 425 9.832445 ATGAATTACATACGGACTAAAATGAGT 57.168 29.630 0.00 0.00 37.46 3.41
377 426 9.093970 TGAATTACATACGGACTAAAATGAGTG 57.906 33.333 0.00 0.00 0.00 3.51
378 427 9.309516 GAATTACATACGGACTAAAATGAGTGA 57.690 33.333 0.00 0.00 0.00 3.41
379 428 9.661563 AATTACATACGGACTAAAATGAGTGAA 57.338 29.630 0.00 0.00 0.00 3.18
380 429 6.963049 ACATACGGACTAAAATGAGTGAAC 57.037 37.500 0.00 0.00 0.00 3.18
381 430 6.460781 ACATACGGACTAAAATGAGTGAACA 58.539 36.000 0.00 0.00 0.00 3.18
382 431 6.932400 ACATACGGACTAAAATGAGTGAACAA 59.068 34.615 0.00 0.00 0.00 2.83
383 432 7.442969 ACATACGGACTAAAATGAGTGAACAAA 59.557 33.333 0.00 0.00 0.00 2.83
384 433 6.056428 ACGGACTAAAATGAGTGAACAAAC 57.944 37.500 0.00 0.00 0.00 2.93
385 434 5.587043 ACGGACTAAAATGAGTGAACAAACA 59.413 36.000 0.00 0.00 0.00 2.83
386 435 5.907391 CGGACTAAAATGAGTGAACAAACAC 59.093 40.000 0.00 0.00 40.60 3.32
387 436 6.457663 CGGACTAAAATGAGTGAACAAACACA 60.458 38.462 0.00 0.00 42.45 3.72
388 437 6.691388 GGACTAAAATGAGTGAACAAACACAC 59.309 38.462 0.00 0.00 42.45 3.82
389 438 6.560711 ACTAAAATGAGTGAACAAACACACC 58.439 36.000 0.00 0.00 42.45 4.16
390 439 5.398603 AAAATGAGTGAACAAACACACCA 57.601 34.783 0.00 0.00 42.45 4.17
391 440 5.398603 AAATGAGTGAACAAACACACCAA 57.601 34.783 0.00 0.00 42.45 3.67
392 441 5.398603 AATGAGTGAACAAACACACCAAA 57.601 34.783 0.00 0.00 42.45 3.28
393 442 4.855715 TGAGTGAACAAACACACCAAAA 57.144 36.364 0.00 0.00 42.45 2.44
394 443 5.398603 TGAGTGAACAAACACACCAAAAT 57.601 34.783 0.00 0.00 42.45 1.82
395 444 5.167121 TGAGTGAACAAACACACCAAAATG 58.833 37.500 0.00 0.00 42.45 2.32
396 445 5.146010 AGTGAACAAACACACCAAAATGT 57.854 34.783 0.00 0.00 42.45 2.71
411 460 9.653287 ACACCAAAATGTGTCTATATATATCCG 57.347 33.333 0.00 0.00 46.15 4.18
412 461 9.869757 CACCAAAATGTGTCTATATATATCCGA 57.130 33.333 0.00 0.00 0.00 4.55
471 520 4.094476 TGGAGGGAGTATTTCTTTCGACT 58.906 43.478 0.00 0.00 0.00 4.18
516 565 8.937634 AATTCAAATTATTGAGTGAGAATGGC 57.062 30.769 0.00 0.00 45.82 4.40
540 589 5.118286 CAAATTGTGCTGGGTTTCTCTTTT 58.882 37.500 0.00 0.00 0.00 2.27
560 609 9.665264 CTCTTTTATAAAGTTCTTTCGTTTGCT 57.335 29.630 0.87 0.00 0.00 3.91
562 611 9.233232 CTTTTATAAAGTTCTTTCGTTTGCTGT 57.767 29.630 0.87 0.00 0.00 4.40
569 618 5.992217 AGTTCTTTCGTTTGCTGTAGAGAAT 59.008 36.000 0.00 0.00 0.00 2.40
577 626 6.757010 TCGTTTGCTGTAGAGAATAAATCCTC 59.243 38.462 0.00 0.00 0.00 3.71
613 664 5.049886 ACCGTTTTGAAAAATCTCGTACTCC 60.050 40.000 0.00 0.00 0.00 3.85
622 673 1.915141 TCTCGTACTCCCTCCGTTTT 58.085 50.000 0.00 0.00 0.00 2.43
631 682 6.591448 CGTACTCCCTCCGTTTTAAAATAAGT 59.409 38.462 3.52 3.73 0.00 2.24
633 684 6.301486 ACTCCCTCCGTTTTAAAATAAGTGT 58.699 36.000 3.52 0.01 0.00 3.55
634 685 6.429078 ACTCCCTCCGTTTTAAAATAAGTGTC 59.571 38.462 3.52 0.00 0.00 3.67
655 706 8.038944 AGTGTCTCAACTTTGTACTAACTTTGA 58.961 33.333 0.00 2.39 0.00 2.69
690 741 1.133823 TGGTCAACACTCAACTGGCAT 60.134 47.619 0.00 0.00 0.00 4.40
738 789 4.844998 TTCAGATGGAACGCAAATCAAA 57.155 36.364 0.00 0.00 0.00 2.69
813 864 2.959071 GATGCTCGTCGCTCCTGC 60.959 66.667 0.00 0.00 40.11 4.85
1542 1598 0.179124 GCTTGGTGCTCTACTCCGAG 60.179 60.000 0.00 0.00 43.67 4.63
1574 1630 1.066071 GTCTCCTTCCCTTGGCTACAC 60.066 57.143 0.00 0.00 0.00 2.90
1593 1649 1.215382 CGATCACACCTTCTCGGCA 59.785 57.895 0.00 0.00 35.61 5.69
1603 1659 1.821061 CTTCTCGGCACTCCTGGTGT 61.821 60.000 0.00 0.00 46.86 4.16
1777 1833 3.406764 GAGATGCCTGTGAAAGACTTGT 58.593 45.455 0.00 0.00 0.00 3.16
1791 1847 1.129251 GACTTGTGCATGTGGACATCG 59.871 52.381 8.17 5.73 45.59 3.84
2386 2442 5.014123 ACCAAGAGATACAGGATTGTTCCAA 59.986 40.000 0.00 0.00 45.30 3.53
2442 2498 1.721487 CCGTTCATCCCGTTCATGC 59.279 57.895 0.00 0.00 0.00 4.06
2474 2530 5.624159 AGTTGAATGGATCAGAAGTTCACA 58.376 37.500 5.50 0.00 39.77 3.58
2529 2585 2.182014 GTTGGGAAATGCGCGATAAAC 58.818 47.619 12.10 0.00 0.00 2.01
2565 2621 2.751166 TGAGTAAAGCAGAGGAGCAC 57.249 50.000 0.00 0.00 36.85 4.40
2623 2679 5.120674 GCTTGCTCTTCAAAGTTTGTTTTGT 59.879 36.000 15.08 0.00 38.77 2.83
2645 2701 3.245984 TGAGGTTATCTCCCTTGACTCCA 60.246 47.826 0.00 0.00 41.76 3.86
2655 2711 2.821969 CCCTTGACTCCAATGTTGAAGG 59.178 50.000 0.00 0.00 33.34 3.46
2657 2713 4.338879 CCTTGACTCCAATGTTGAAGGAT 58.661 43.478 0.00 0.00 34.45 3.24
2694 2751 9.561069 ACAGATTACTTGTGATAAGAACTTTGT 57.439 29.630 0.00 0.00 0.00 2.83
2697 2754 9.813080 GATTACTTGTGATAAGAACTTTGTCAC 57.187 33.333 17.54 17.54 37.43 3.67
2698 2755 8.725405 TTACTTGTGATAAGAACTTTGTCACA 57.275 30.769 20.52 20.52 41.15 3.58
2703 2760 6.479990 TGTGATAAGAACTTTGTCACAGTGAG 59.520 38.462 20.52 0.00 39.63 3.51
2739 2796 3.819368 TGCACAGGAGACATTCTTTTGA 58.181 40.909 0.00 0.00 0.00 2.69
2754 2811 4.950050 TCTTTTGAGAACAGAGACTGGAC 58.050 43.478 0.00 0.00 35.51 4.02
2756 2813 4.327982 TTTGAGAACAGAGACTGGACAG 57.672 45.455 0.00 0.00 35.51 3.51
2761 2818 0.760567 ACAGAGACTGGACAGGTGCA 60.761 55.000 4.14 0.00 35.51 4.57
2762 2819 0.612229 CAGAGACTGGACAGGTGCAT 59.388 55.000 4.14 0.00 0.00 3.96
2763 2820 0.901124 AGAGACTGGACAGGTGCATC 59.099 55.000 4.14 0.00 0.00 3.91
2764 2821 0.610174 GAGACTGGACAGGTGCATCA 59.390 55.000 0.00 0.00 0.00 3.07
2765 2822 1.209019 GAGACTGGACAGGTGCATCAT 59.791 52.381 0.00 0.00 0.00 2.45
2779 2836 3.004106 GTGCATCATATCCCTGAACAAGC 59.996 47.826 0.00 0.00 0.00 4.01
2781 2838 1.953559 TCATATCCCTGAACAAGCGC 58.046 50.000 0.00 0.00 0.00 5.92
2783 2840 0.532862 ATATCCCTGAACAAGCGCGG 60.533 55.000 8.83 0.00 0.00 6.46
2785 2842 1.895020 ATCCCTGAACAAGCGCGGTA 61.895 55.000 12.91 0.00 0.00 4.02
2788 2845 1.647346 CCTGAACAAGCGCGGTATAA 58.353 50.000 12.91 0.00 0.00 0.98
2791 2848 2.413796 CTGAACAAGCGCGGTATAACAA 59.586 45.455 12.91 0.00 0.00 2.83
2793 2850 3.437395 TGAACAAGCGCGGTATAACAATT 59.563 39.130 12.91 0.00 0.00 2.32
2827 2884 2.358737 GTGGTGAAGGGACCTGCG 60.359 66.667 0.00 0.00 36.88 5.18
2836 2893 4.489771 GGACCTGCGGACATGGGG 62.490 72.222 0.00 0.00 0.00 4.96
2874 2932 3.554337 GCGTAACTGAAGGAAGAGGAACA 60.554 47.826 0.00 0.00 0.00 3.18
2929 2987 4.814234 TGGCATACCAAGTAAATAGCGAAG 59.186 41.667 0.00 0.00 45.37 3.79
2933 2991 6.258068 GCATACCAAGTAAATAGCGAAGAAGT 59.742 38.462 0.00 0.00 0.00 3.01
2996 3054 1.203038 ACATGCCAATGGACACAGGAA 60.203 47.619 2.05 0.00 38.19 3.36
2997 3055 1.475280 CATGCCAATGGACACAGGAAG 59.525 52.381 2.05 0.00 0.00 3.46
3039 3108 1.901591 TTTCTGCTGGCCTTCTTGAG 58.098 50.000 3.32 0.00 0.00 3.02
3041 3110 1.283347 TCTGCTGGCCTTCTTGAGAT 58.717 50.000 3.32 0.00 0.00 2.75
3043 3112 1.743958 CTGCTGGCCTTCTTGAGATTG 59.256 52.381 3.32 0.00 0.00 2.67
3044 3113 0.455005 GCTGGCCTTCTTGAGATTGC 59.545 55.000 3.32 0.00 0.00 3.56
3045 3114 1.954258 GCTGGCCTTCTTGAGATTGCT 60.954 52.381 3.32 0.00 0.00 3.91
3046 3115 1.743958 CTGGCCTTCTTGAGATTGCTG 59.256 52.381 3.32 0.00 0.00 4.41
3047 3116 0.455005 GGCCTTCTTGAGATTGCTGC 59.545 55.000 0.00 0.00 0.00 5.25
3048 3117 1.171308 GCCTTCTTGAGATTGCTGCA 58.829 50.000 0.00 0.00 0.00 4.41
3049 3118 1.749634 GCCTTCTTGAGATTGCTGCAT 59.250 47.619 1.84 0.00 0.00 3.96
3050 3119 2.165845 GCCTTCTTGAGATTGCTGCATT 59.834 45.455 1.84 0.00 0.00 3.56
3051 3120 3.734293 GCCTTCTTGAGATTGCTGCATTC 60.734 47.826 14.85 14.85 0.00 2.67
3052 3121 3.442625 CCTTCTTGAGATTGCTGCATTCA 59.557 43.478 22.15 14.95 0.00 2.57
3053 3122 4.413087 CTTCTTGAGATTGCTGCATTCAC 58.587 43.478 22.15 17.47 0.00 3.18
3054 3123 3.682696 TCTTGAGATTGCTGCATTCACT 58.317 40.909 22.15 11.33 0.00 3.41
3055 3124 4.077108 TCTTGAGATTGCTGCATTCACTT 58.923 39.130 22.15 6.02 0.00 3.16
3056 3125 3.842732 TGAGATTGCTGCATTCACTTG 57.157 42.857 22.15 0.00 0.00 3.16
3057 3126 3.414269 TGAGATTGCTGCATTCACTTGA 58.586 40.909 22.15 0.00 0.00 3.02
3058 3127 3.822167 TGAGATTGCTGCATTCACTTGAA 59.178 39.130 22.15 0.00 38.56 2.69
3059 3128 4.278919 TGAGATTGCTGCATTCACTTGAAA 59.721 37.500 22.15 0.00 37.61 2.69
3060 3129 5.204409 AGATTGCTGCATTCACTTGAAAA 57.796 34.783 22.15 0.00 37.61 2.29
3061 3130 5.603596 AGATTGCTGCATTCACTTGAAAAA 58.396 33.333 22.15 0.00 37.61 1.94
3125 3194 5.192927 TCTGTGTCCAGTTTCAGAAAATGT 58.807 37.500 19.32 0.00 39.82 2.71
3166 3236 5.280654 ACAGCAAGGAAATGTGATTTTGT 57.719 34.783 0.00 0.00 31.47 2.83
3284 3354 5.163804 TGGTGCATAAATCGTGTATGTTGTC 60.164 40.000 0.00 0.00 32.51 3.18
3292 3362 3.904571 TCGTGTATGTTGTCTGTGTACC 58.095 45.455 0.00 0.00 0.00 3.34
3299 3369 2.616376 TGTTGTCTGTGTACCAACATGC 59.384 45.455 9.66 0.00 42.41 4.06
3312 3382 2.574322 CAACATGCGTGACAAAGCTAC 58.426 47.619 14.17 0.00 0.00 3.58
3346 3417 5.596845 TGGATGTTGTTTTCTTTTGCTACC 58.403 37.500 0.00 0.00 0.00 3.18
3505 3583 1.952990 ACGCCATCATGTTCAACAACA 59.047 42.857 0.00 0.00 46.71 3.33
3550 3628 8.885693 AAGCAGATAAAATTCCCTAGAAAAGT 57.114 30.769 0.00 0.00 35.09 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.088589 TCTGTAAATTAATTCCAGCTTGAGC 57.911 36.000 17.09 0.00 42.49 4.26
14 15 7.970614 GGTTCTGTAAATTAATTCCAGCTTGAG 59.029 37.037 17.09 2.29 0.00 3.02
15 16 7.361713 CGGTTCTGTAAATTAATTCCAGCTTGA 60.362 37.037 17.09 0.00 0.00 3.02
16 17 6.747280 CGGTTCTGTAAATTAATTCCAGCTTG 59.253 38.462 17.09 7.97 0.00 4.01
17 18 6.433093 ACGGTTCTGTAAATTAATTCCAGCTT 59.567 34.615 17.09 0.00 0.00 3.74
18 19 5.944007 ACGGTTCTGTAAATTAATTCCAGCT 59.056 36.000 17.09 0.29 0.00 4.24
19 20 6.190954 ACGGTTCTGTAAATTAATTCCAGC 57.809 37.500 17.09 8.69 0.00 4.85
20 21 9.769093 CTAAACGGTTCTGTAAATTAATTCCAG 57.231 33.333 16.29 16.29 0.00 3.86
21 22 8.238631 GCTAAACGGTTCTGTAAATTAATTCCA 58.761 33.333 0.10 1.16 0.00 3.53
22 23 8.456471 AGCTAAACGGTTCTGTAAATTAATTCC 58.544 33.333 0.10 0.00 0.00 3.01
23 24 9.836076 AAGCTAAACGGTTCTGTAAATTAATTC 57.164 29.630 0.10 0.00 0.00 2.17
24 25 9.620660 CAAGCTAAACGGTTCTGTAAATTAATT 57.379 29.630 0.00 0.00 0.00 1.40
25 26 8.789762 ACAAGCTAAACGGTTCTGTAAATTAAT 58.210 29.630 0.00 0.00 0.00 1.40
26 27 8.156994 ACAAGCTAAACGGTTCTGTAAATTAA 57.843 30.769 0.00 0.00 0.00 1.40
27 28 7.733402 ACAAGCTAAACGGTTCTGTAAATTA 57.267 32.000 0.00 0.00 0.00 1.40
28 29 6.628919 ACAAGCTAAACGGTTCTGTAAATT 57.371 33.333 0.00 0.00 0.00 1.82
29 30 7.733402 TTACAAGCTAAACGGTTCTGTAAAT 57.267 32.000 0.00 0.00 0.00 1.40
30 31 7.408910 GTTTACAAGCTAAACGGTTCTGTAAA 58.591 34.615 14.08 14.08 33.15 2.01
31 32 6.018016 GGTTTACAAGCTAAACGGTTCTGTAA 60.018 38.462 0.00 0.00 38.06 2.41
32 33 5.466393 GGTTTACAAGCTAAACGGTTCTGTA 59.534 40.000 0.00 0.00 38.06 2.74
33 34 4.274214 GGTTTACAAGCTAAACGGTTCTGT 59.726 41.667 0.00 0.00 38.06 3.41
34 35 4.514066 AGGTTTACAAGCTAAACGGTTCTG 59.486 41.667 0.00 0.00 38.06 3.02
35 36 4.514066 CAGGTTTACAAGCTAAACGGTTCT 59.486 41.667 0.00 0.00 38.06 3.01
36 37 4.779987 CAGGTTTACAAGCTAAACGGTTC 58.220 43.478 0.00 0.00 38.06 3.62
37 38 3.004002 GCAGGTTTACAAGCTAAACGGTT 59.996 43.478 4.86 0.00 38.06 4.44
38 39 2.551032 GCAGGTTTACAAGCTAAACGGT 59.449 45.455 4.86 0.00 38.06 4.83
39 40 2.550606 TGCAGGTTTACAAGCTAAACGG 59.449 45.455 4.86 1.93 38.06 4.44
40 41 3.889196 TGCAGGTTTACAAGCTAAACG 57.111 42.857 4.86 0.00 38.06 3.60
41 42 5.432885 TCTTGCAGGTTTACAAGCTAAAC 57.567 39.130 2.51 2.51 42.41 2.01
42 43 4.518970 CCTCTTGCAGGTTTACAAGCTAAA 59.481 41.667 0.00 0.00 42.41 1.85
43 44 4.072131 CCTCTTGCAGGTTTACAAGCTAA 58.928 43.478 0.00 0.00 42.41 3.09
44 45 3.559171 CCCTCTTGCAGGTTTACAAGCTA 60.559 47.826 0.00 0.00 42.41 3.32
45 46 2.508526 CCTCTTGCAGGTTTACAAGCT 58.491 47.619 0.00 0.00 42.41 3.74
46 47 1.541588 CCCTCTTGCAGGTTTACAAGC 59.458 52.381 0.00 0.00 42.41 4.01
47 48 2.162681 CCCCTCTTGCAGGTTTACAAG 58.837 52.381 0.00 0.00 41.51 3.16
48 49 1.497286 ACCCCTCTTGCAGGTTTACAA 59.503 47.619 0.00 0.00 41.51 2.41
49 50 1.073284 GACCCCTCTTGCAGGTTTACA 59.927 52.381 0.00 0.00 41.51 2.41
50 51 1.822506 GACCCCTCTTGCAGGTTTAC 58.177 55.000 0.00 0.00 41.51 2.01
51 52 0.323629 CGACCCCTCTTGCAGGTTTA 59.676 55.000 0.00 0.00 41.51 2.01
52 53 1.073199 CGACCCCTCTTGCAGGTTT 59.927 57.895 0.00 0.00 41.51 3.27
53 54 1.841556 TCGACCCCTCTTGCAGGTT 60.842 57.895 0.00 0.00 41.51 3.50
54 55 2.203788 TCGACCCCTCTTGCAGGT 60.204 61.111 0.00 0.00 41.51 4.00
55 56 1.903877 ATGTCGACCCCTCTTGCAGG 61.904 60.000 14.12 0.00 43.01 4.85
56 57 0.824109 TATGTCGACCCCTCTTGCAG 59.176 55.000 14.12 0.00 0.00 4.41
57 58 1.496060 ATATGTCGACCCCTCTTGCA 58.504 50.000 14.12 0.00 0.00 4.08
58 59 2.213499 CAATATGTCGACCCCTCTTGC 58.787 52.381 14.12 0.00 0.00 4.01
59 60 2.485479 CCCAATATGTCGACCCCTCTTG 60.485 54.545 14.12 9.34 0.00 3.02
60 61 1.768870 CCCAATATGTCGACCCCTCTT 59.231 52.381 14.12 0.00 0.00 2.85
61 62 1.062428 TCCCAATATGTCGACCCCTCT 60.062 52.381 14.12 0.00 0.00 3.69
62 63 1.420430 TCCCAATATGTCGACCCCTC 58.580 55.000 14.12 0.00 0.00 4.30
63 64 1.768870 CTTCCCAATATGTCGACCCCT 59.231 52.381 14.12 0.03 0.00 4.79
64 65 1.489230 ACTTCCCAATATGTCGACCCC 59.511 52.381 14.12 0.00 0.00 4.95
65 66 3.802675 GCTACTTCCCAATATGTCGACCC 60.803 52.174 14.12 0.00 0.00 4.46
66 67 3.181469 TGCTACTTCCCAATATGTCGACC 60.181 47.826 14.12 0.00 0.00 4.79
67 68 4.054780 TGCTACTTCCCAATATGTCGAC 57.945 45.455 9.11 9.11 0.00 4.20
68 69 4.746535 TTGCTACTTCCCAATATGTCGA 57.253 40.909 0.00 0.00 0.00 4.20
69 70 4.816385 ACATTGCTACTTCCCAATATGTCG 59.184 41.667 0.00 0.00 30.96 4.35
70 71 6.238759 GGAACATTGCTACTTCCCAATATGTC 60.239 42.308 0.00 0.00 30.96 3.06
71 72 5.594317 GGAACATTGCTACTTCCCAATATGT 59.406 40.000 0.00 0.00 30.96 2.29
72 73 5.277974 CGGAACATTGCTACTTCCCAATATG 60.278 44.000 2.18 0.00 31.26 1.78
73 74 4.821805 CGGAACATTGCTACTTCCCAATAT 59.178 41.667 2.18 0.00 31.26 1.28
74 75 4.196193 CGGAACATTGCTACTTCCCAATA 58.804 43.478 2.18 0.00 31.26 1.90
75 76 3.016736 CGGAACATTGCTACTTCCCAAT 58.983 45.455 2.18 0.00 31.26 3.16
76 77 2.224670 ACGGAACATTGCTACTTCCCAA 60.225 45.455 0.00 0.00 31.26 4.12
77 78 1.349688 ACGGAACATTGCTACTTCCCA 59.650 47.619 0.00 0.00 31.26 4.37
78 79 2.007608 GACGGAACATTGCTACTTCCC 58.992 52.381 0.00 0.00 31.26 3.97
79 80 2.673368 CAGACGGAACATTGCTACTTCC 59.327 50.000 0.00 0.00 0.00 3.46
80 81 3.326747 ACAGACGGAACATTGCTACTTC 58.673 45.455 0.00 0.00 0.00 3.01
81 82 3.402628 ACAGACGGAACATTGCTACTT 57.597 42.857 0.00 0.00 0.00 2.24
82 83 3.119101 CCTACAGACGGAACATTGCTACT 60.119 47.826 0.00 0.00 0.00 2.57
83 84 3.187700 CCTACAGACGGAACATTGCTAC 58.812 50.000 0.00 0.00 0.00 3.58
84 85 2.829720 ACCTACAGACGGAACATTGCTA 59.170 45.455 0.00 0.00 0.00 3.49
85 86 1.623811 ACCTACAGACGGAACATTGCT 59.376 47.619 0.00 0.00 0.00 3.91
95 96 3.861276 TTGACCATACACCTACAGACG 57.139 47.619 0.00 0.00 0.00 4.18
100 101 8.788325 AATAAAGACTTTGACCATACACCTAC 57.212 34.615 10.80 0.00 0.00 3.18
101 102 9.444600 GAAATAAAGACTTTGACCATACACCTA 57.555 33.333 10.80 0.00 0.00 3.08
102 103 8.164070 AGAAATAAAGACTTTGACCATACACCT 58.836 33.333 10.80 0.00 0.00 4.00
103 104 8.237267 CAGAAATAAAGACTTTGACCATACACC 58.763 37.037 10.80 0.00 0.00 4.16
104 105 8.237267 CCAGAAATAAAGACTTTGACCATACAC 58.763 37.037 10.80 0.00 0.00 2.90
153 158 4.379813 CCATACCACTTTAAGTTGCAGCAG 60.380 45.833 2.55 0.00 0.00 4.24
183 188 4.042311 TCCAGTAACTATTTCCACAAGGCA 59.958 41.667 0.00 0.00 33.74 4.75
224 269 7.060421 AGAACAGAGAACAAAAGGGTCAAATA 58.940 34.615 0.00 0.00 0.00 1.40
225 270 5.893824 AGAACAGAGAACAAAAGGGTCAAAT 59.106 36.000 0.00 0.00 0.00 2.32
244 289 7.123383 TCCAGGACTGATAGTTACATAGAACA 58.877 38.462 0.00 0.00 0.00 3.18
248 293 8.303156 CAATCTCCAGGACTGATAGTTACATAG 58.697 40.741 0.00 0.00 0.00 2.23
301 350 6.299141 ACAGTATTTGTGAATGGAGTGAGTT 58.701 36.000 0.00 0.00 38.99 3.01
302 351 5.869579 ACAGTATTTGTGAATGGAGTGAGT 58.130 37.500 0.00 0.00 38.99 3.41
303 352 9.599866 TTATACAGTATTTGTGAATGGAGTGAG 57.400 33.333 0.00 0.00 41.10 3.51
304 353 9.599866 CTTATACAGTATTTGTGAATGGAGTGA 57.400 33.333 0.00 0.00 41.10 3.41
305 354 9.599866 TCTTATACAGTATTTGTGAATGGAGTG 57.400 33.333 0.00 0.00 41.10 3.51
350 399 9.832445 ACTCATTTTAGTCCGTATGTAATTCAT 57.168 29.630 0.00 0.00 40.25 2.57
351 400 9.093970 CACTCATTTTAGTCCGTATGTAATTCA 57.906 33.333 0.00 0.00 0.00 2.57
352 401 9.309516 TCACTCATTTTAGTCCGTATGTAATTC 57.690 33.333 0.00 0.00 0.00 2.17
353 402 9.661563 TTCACTCATTTTAGTCCGTATGTAATT 57.338 29.630 0.00 0.00 0.00 1.40
354 403 9.095065 GTTCACTCATTTTAGTCCGTATGTAAT 57.905 33.333 0.00 0.00 0.00 1.89
355 404 8.089597 TGTTCACTCATTTTAGTCCGTATGTAA 58.910 33.333 0.00 0.00 0.00 2.41
356 405 7.604549 TGTTCACTCATTTTAGTCCGTATGTA 58.395 34.615 0.00 0.00 0.00 2.29
357 406 6.460781 TGTTCACTCATTTTAGTCCGTATGT 58.539 36.000 0.00 0.00 0.00 2.29
358 407 6.961359 TGTTCACTCATTTTAGTCCGTATG 57.039 37.500 0.00 0.00 0.00 2.39
359 408 7.442969 TGTTTGTTCACTCATTTTAGTCCGTAT 59.557 33.333 0.00 0.00 0.00 3.06
360 409 6.762187 TGTTTGTTCACTCATTTTAGTCCGTA 59.238 34.615 0.00 0.00 0.00 4.02
361 410 5.587043 TGTTTGTTCACTCATTTTAGTCCGT 59.413 36.000 0.00 0.00 0.00 4.69
362 411 5.907391 GTGTTTGTTCACTCATTTTAGTCCG 59.093 40.000 0.00 0.00 35.68 4.79
363 412 6.691388 GTGTGTTTGTTCACTCATTTTAGTCC 59.309 38.462 0.00 0.00 38.90 3.85
364 413 6.691388 GGTGTGTTTGTTCACTCATTTTAGTC 59.309 38.462 0.00 0.00 38.90 2.59
365 414 6.151985 TGGTGTGTTTGTTCACTCATTTTAGT 59.848 34.615 0.00 0.00 38.90 2.24
366 415 6.559810 TGGTGTGTTTGTTCACTCATTTTAG 58.440 36.000 0.00 0.00 38.90 1.85
367 416 6.516739 TGGTGTGTTTGTTCACTCATTTTA 57.483 33.333 0.00 0.00 38.90 1.52
368 417 5.398603 TGGTGTGTTTGTTCACTCATTTT 57.601 34.783 0.00 0.00 38.90 1.82
369 418 5.398603 TTGGTGTGTTTGTTCACTCATTT 57.601 34.783 0.00 0.00 38.90 2.32
370 419 5.398603 TTTGGTGTGTTTGTTCACTCATT 57.601 34.783 0.00 0.00 38.90 2.57
371 420 5.398603 TTTTGGTGTGTTTGTTCACTCAT 57.601 34.783 0.00 0.00 38.90 2.90
372 421 4.855715 TTTTGGTGTGTTTGTTCACTCA 57.144 36.364 0.00 0.00 38.90 3.41
373 422 5.062058 CACATTTTGGTGTGTTTGTTCACTC 59.938 40.000 0.00 0.00 43.43 3.51
374 423 4.928615 CACATTTTGGTGTGTTTGTTCACT 59.071 37.500 0.00 0.00 43.43 3.41
375 424 5.202046 CACATTTTGGTGTGTTTGTTCAC 57.798 39.130 0.00 0.00 43.43 3.18
386 435 9.869757 TCGGATATATATAGACACATTTTGGTG 57.130 33.333 0.00 0.00 44.35 4.17
427 476 9.388506 CTCCATTCACAAATACTAAGATGTTCT 57.611 33.333 0.00 0.00 0.00 3.01
428 477 8.616076 CCTCCATTCACAAATACTAAGATGTTC 58.384 37.037 0.00 0.00 0.00 3.18
429 478 7.557719 CCCTCCATTCACAAATACTAAGATGTT 59.442 37.037 0.00 0.00 0.00 2.71
430 479 7.056635 CCCTCCATTCACAAATACTAAGATGT 58.943 38.462 0.00 0.00 0.00 3.06
431 480 7.282585 TCCCTCCATTCACAAATACTAAGATG 58.717 38.462 0.00 0.00 0.00 2.90
432 481 7.127955 ACTCCCTCCATTCACAAATACTAAGAT 59.872 37.037 0.00 0.00 0.00 2.40
433 482 6.443849 ACTCCCTCCATTCACAAATACTAAGA 59.556 38.462 0.00 0.00 0.00 2.10
434 483 6.653989 ACTCCCTCCATTCACAAATACTAAG 58.346 40.000 0.00 0.00 0.00 2.18
435 484 6.636454 ACTCCCTCCATTCACAAATACTAA 57.364 37.500 0.00 0.00 0.00 2.24
436 485 7.931015 ATACTCCCTCCATTCACAAATACTA 57.069 36.000 0.00 0.00 0.00 1.82
437 486 6.831664 ATACTCCCTCCATTCACAAATACT 57.168 37.500 0.00 0.00 0.00 2.12
438 487 7.775561 AGAAATACTCCCTCCATTCACAAATAC 59.224 37.037 0.00 0.00 0.00 1.89
492 541 7.124599 TGGCCATTCTCACTCAATAATTTGAAT 59.875 33.333 0.00 0.00 41.22 2.57
516 565 2.629617 AGAGAAACCCAGCACAATTTGG 59.370 45.455 0.78 0.00 0.00 3.28
540 589 8.821147 TCTACAGCAAACGAAAGAACTTTATA 57.179 30.769 0.00 0.00 32.11 0.98
553 602 6.535150 TGAGGATTTATTCTCTACAGCAAACG 59.465 38.462 0.03 0.00 0.00 3.60
596 647 3.119245 CGGAGGGAGTACGAGATTTTTCA 60.119 47.826 0.00 0.00 0.00 2.69
613 664 7.429636 TGAGACACTTATTTTAAAACGGAGG 57.570 36.000 1.97 0.00 0.00 4.30
631 682 8.780846 TTCAAAGTTAGTACAAAGTTGAGACA 57.219 30.769 0.00 0.00 0.00 3.41
690 741 2.777692 ACCAGTTTCTCTTTCACCCAGA 59.222 45.455 0.00 0.00 0.00 3.86
738 789 5.499139 ACAATTTGAACACACGATGAGTT 57.501 34.783 2.79 0.00 33.97 3.01
813 864 2.160417 GGCCACGAGAGAAAAATGTGAG 59.840 50.000 0.00 0.00 32.39 3.51
858 911 1.032794 TGGTCGATCCAGATCCGAAG 58.967 55.000 0.00 0.00 41.93 3.79
905 958 1.824852 GGGCCGTCCAATTCAAAATCT 59.175 47.619 0.00 0.00 35.00 2.40
1068 1124 4.357947 GCCGAGACGCTGTGGTGA 62.358 66.667 0.00 0.00 0.00 4.02
1110 1166 3.791586 GAGAGGGTGGGCAGGAGC 61.792 72.222 0.00 0.00 41.10 4.70
1500 1556 3.864686 CGCATTTCTCCACCGCCG 61.865 66.667 0.00 0.00 0.00 6.46
1593 1649 2.031163 GCGCAAGACACCAGGAGT 59.969 61.111 0.30 0.00 43.02 3.85
1603 1659 1.078918 CCATGAGACCAGCGCAAGA 60.079 57.895 11.47 0.00 43.02 3.02
1605 1661 1.375908 GTCCATGAGACCAGCGCAA 60.376 57.895 11.47 0.00 39.84 4.85
1777 1833 3.541996 AACTATCGATGTCCACATGCA 57.458 42.857 8.54 0.00 36.57 3.96
2233 2289 6.406370 TCATCTGAACAAACAATCCTATCGT 58.594 36.000 0.00 0.00 0.00 3.73
2386 2442 5.707298 CCACACAAACATAATGGTCTTCTCT 59.293 40.000 0.00 0.00 0.00 3.10
2442 2498 6.276091 TCTGATCCATTCAACTACTTCATCG 58.724 40.000 0.00 0.00 32.78 3.84
2474 2530 3.821033 AGCTTGTTTGCTAGAACCGAATT 59.179 39.130 0.00 0.00 42.10 2.17
2529 2585 2.289072 ACTCATCAACTCTGTGTTCCCG 60.289 50.000 0.00 0.00 36.63 5.14
2532 2588 5.466728 TGCTTTACTCATCAACTCTGTGTTC 59.533 40.000 0.00 0.00 36.63 3.18
2536 2592 5.474578 TCTGCTTTACTCATCAACTCTGT 57.525 39.130 0.00 0.00 0.00 3.41
2579 2635 5.064441 AGCACTCATTTATTTTGGACTGC 57.936 39.130 0.00 0.00 0.00 4.40
2623 2679 3.245984 TGGAGTCAAGGGAGATAACCTCA 60.246 47.826 0.00 0.00 43.76 3.86
2645 2701 2.097825 GCCTGAGCATCCTTCAACATT 58.902 47.619 0.00 0.00 39.53 2.71
2671 2727 9.813080 GTGACAAAGTTCTTATCACAAGTAATC 57.187 33.333 17.43 0.00 39.57 1.75
2697 2754 4.595116 CAAAGAACAAACAGCTCTCACTG 58.405 43.478 0.00 0.00 43.59 3.66
2698 2755 3.065925 GCAAAGAACAAACAGCTCTCACT 59.934 43.478 0.00 0.00 0.00 3.41
2703 2760 3.111098 CTGTGCAAAGAACAAACAGCTC 58.889 45.455 0.00 0.00 32.61 4.09
2739 2796 1.967066 CACCTGTCCAGTCTCTGTTCT 59.033 52.381 0.00 0.00 0.00 3.01
2756 2813 3.213206 TGTTCAGGGATATGATGCACC 57.787 47.619 0.00 0.00 0.00 5.01
2761 2818 2.498167 GCGCTTGTTCAGGGATATGAT 58.502 47.619 0.00 0.00 37.67 2.45
2762 2819 1.806247 CGCGCTTGTTCAGGGATATGA 60.806 52.381 5.56 0.00 37.67 2.15
2763 2820 0.583438 CGCGCTTGTTCAGGGATATG 59.417 55.000 5.56 0.00 37.67 1.78
2764 2821 0.532862 CCGCGCTTGTTCAGGGATAT 60.533 55.000 5.56 0.00 37.67 1.63
2765 2822 1.153449 CCGCGCTTGTTCAGGGATA 60.153 57.895 5.56 0.00 37.67 2.59
2779 2836 3.600717 TGATGCAATTGTTATACCGCG 57.399 42.857 7.40 0.00 0.00 6.46
2781 2838 9.897744 ATTCTTTATGATGCAATTGTTATACCG 57.102 29.630 7.40 0.00 0.00 4.02
2785 2842 8.632679 ACCGATTCTTTATGATGCAATTGTTAT 58.367 29.630 7.40 2.19 0.00 1.89
2788 2845 6.267817 CACCGATTCTTTATGATGCAATTGT 58.732 36.000 7.40 0.00 0.00 2.71
2791 2848 4.889409 ACCACCGATTCTTTATGATGCAAT 59.111 37.500 0.00 0.00 0.00 3.56
2793 2850 3.627123 CACCACCGATTCTTTATGATGCA 59.373 43.478 0.00 0.00 0.00 3.96
2827 2884 1.379044 CAGCAGAACCCCCATGTCC 60.379 63.158 0.00 0.00 0.00 4.02
2853 2910 4.022242 TCTGTTCCTCTTCCTTCAGTTACG 60.022 45.833 0.00 0.00 0.00 3.18
2858 2915 7.123355 AGAATATCTGTTCCTCTTCCTTCAG 57.877 40.000 0.00 0.00 0.00 3.02
2922 2980 6.801539 ATTTGTGAAATCACTTCTTCGCTA 57.198 33.333 14.15 0.00 46.55 4.26
2949 3007 5.743026 TGACAAAGCGATGTTTACTTGAA 57.257 34.783 0.00 0.00 32.57 2.69
2955 3013 4.513318 TGTGACATGACAAAGCGATGTTTA 59.487 37.500 0.00 0.00 32.57 2.01
2997 3055 2.035530 AGTAATGCTGAGCTTCCTGC 57.964 50.000 5.83 0.00 43.29 4.85
3039 3108 5.910637 TTTTTCAAGTGAATGCAGCAATC 57.089 34.783 0.00 0.00 33.54 2.67
3041 3110 5.585445 ACAATTTTTCAAGTGAATGCAGCAA 59.415 32.000 0.00 0.00 32.13 3.91
3043 3112 5.662211 ACAATTTTTCAAGTGAATGCAGC 57.338 34.783 0.00 0.00 32.13 5.25
3044 3113 6.925165 ACCTACAATTTTTCAAGTGAATGCAG 59.075 34.615 0.00 0.00 32.13 4.41
3045 3114 6.815089 ACCTACAATTTTTCAAGTGAATGCA 58.185 32.000 0.00 0.00 32.13 3.96
3046 3115 7.865385 TGTACCTACAATTTTTCAAGTGAATGC 59.135 33.333 0.00 0.00 32.13 3.56
3047 3116 9.743057 TTGTACCTACAATTTTTCAAGTGAATG 57.257 29.630 0.00 0.00 40.93 2.67
3061 3130 9.561069 GGATGATGAACTATTTGTACCTACAAT 57.439 33.333 0.00 0.00 44.72 2.71
3077 3146 7.677454 TGCAGATACAATATGGATGATGAAC 57.323 36.000 0.00 0.00 0.00 3.18
3125 3194 6.169800 TGCTGTAATGCAAGTATCTGTACAA 58.830 36.000 0.00 0.00 40.29 2.41
3166 3236 4.968259 ACACAACTACATGCTAACCTGAA 58.032 39.130 0.00 0.00 0.00 3.02
3284 3354 1.194547 GTCACGCATGTTGGTACACAG 59.805 52.381 0.00 0.00 39.29 3.66
3292 3362 2.224079 AGTAGCTTTGTCACGCATGTTG 59.776 45.455 0.00 0.00 0.00 3.33
3299 3369 4.688879 TGTTTATGGAGTAGCTTTGTCACG 59.311 41.667 0.00 0.00 0.00 4.35
3346 3417 7.806487 GCATATGAAATGAATGTATCACCTGTG 59.194 37.037 6.97 0.00 41.93 3.66
3550 3628 6.642540 CGCAATTCTCAGCATACATAGTTAGA 59.357 38.462 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.