Multiple sequence alignment - TraesCS4B01G137600

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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 TraesCS4B01G137600 chr4B 100.000 5701 0 0 1 5701 181431242 181436942 0.000000e+00 10528.0
1 TraesCS4B01G137600 chr4B 84.091 88 10 4 4827 4912 646926403 646926488 1.320000e-11 82.4
2 TraesCS4B01G137600 chr4A 95.240 2689 73 21 3038 5701 454600455 454603113 0.000000e+00 4205.0
3 TraesCS4B01G137600 chr4A 89.660 1557 80 38 652 2187 454592745 454594241 0.000000e+00 1908.0
4 TraesCS4B01G137600 chr4A 92.326 860 37 10 2181 3033 454599653 454600490 0.000000e+00 1195.0
5 TraesCS4B01G137600 chr4D 93.053 2116 83 37 945 3033 119228777 119230855 0.000000e+00 3035.0
6 TraesCS4B01G137600 chr4D 95.143 1894 70 18 3027 4911 119230810 119232690 0.000000e+00 2968.0
7 TraesCS4B01G137600 chr4D 91.581 677 41 5 5039 5701 119232862 119233536 0.000000e+00 920.0
8 TraesCS4B01G137600 chr4D 90.439 387 18 6 604 983 119228391 119228765 5.130000e-135 492.0
9 TraesCS4B01G137600 chr4D 82.960 446 42 12 116 543 119227482 119227911 6.980000e-99 372.0
10 TraesCS4B01G137600 chr4D 100.000 30 0 0 4713 4742 263708595 263708624 7.980000e-04 56.5
11 TraesCS4B01G137600 chr3A 85.552 353 33 10 4376 4715 146597216 146596869 2.530000e-93 353.0
12 TraesCS4B01G137600 chr5B 80.000 370 58 12 3976 4341 276948734 276948377 5.670000e-65 259.0
13 TraesCS4B01G137600 chr5A 80.115 347 56 8 3998 4341 328002948 328002612 4.410000e-61 246.0
14 TraesCS4B01G137600 chrUn 88.293 205 19 4 4515 4718 112546229 112546029 2.050000e-59 241.0
15 TraesCS4B01G137600 chrUn 96.970 33 1 0 4713 4745 69931952 69931920 7.980000e-04 56.5
16 TraesCS4B01G137600 chrUn 96.970 33 1 0 4713 4745 95362203 95362171 7.980000e-04 56.5
17 TraesCS4B01G137600 chr1A 88.293 205 19 5 4515 4718 279838941 279838741 2.050000e-59 241.0
18 TraesCS4B01G137600 chr1A 100.000 28 0 0 2253 2280 305368237 305368264 1.000000e-02 52.8
19 TraesCS4B01G137600 chr6B 87.204 211 22 4 4509 4718 78227535 78227741 9.550000e-58 235.0
20 TraesCS4B01G137600 chr5D 75.357 280 54 11 4406 4682 243827954 243827687 2.790000e-23 121.0
21 TraesCS4B01G137600 chr5D 83.333 90 10 5 4826 4912 374663803 374663716 1.700000e-10 78.7
22 TraesCS4B01G137600 chr7D 84.091 88 12 2 4826 4912 92824190 92824276 3.660000e-12 84.2
23 TraesCS4B01G137600 chr2B 84.091 88 10 4 4827 4912 609079757 609079672 1.320000e-11 82.4
24 TraesCS4B01G137600 chr2B 97.500 40 1 0 4873 4912 682134500 682134461 1.020000e-07 69.4
25 TraesCS4B01G137600 chr1B 97.500 40 1 0 4873 4912 363615651 363615612 1.020000e-07 69.4
26 TraesCS4B01G137600 chr7A 95.349 43 1 1 4871 4912 261819471 261819513 3.690000e-07 67.6
27 TraesCS4B01G137600 chr1D 91.667 48 2 1 2253 2300 326159387 326159342 1.330000e-06 65.8
28 TraesCS4B01G137600 chr1D 96.970 33 1 0 4713 4745 178846416 178846384 7.980000e-04 56.5
29 TraesCS4B01G137600 chr2A 94.737 38 2 0 2253 2290 74782100 74782063 6.170000e-05 60.2
30 TraesCS4B01G137600 chr6D 96.970 33 1 0 4713 4745 42691255 42691223 7.980000e-04 56.5
31 TraesCS4B01G137600 chr6D 96.970 33 1 0 4713 4745 345417680 345417648 7.980000e-04 56.5
32 TraesCS4B01G137600 chr6D 96.970 33 1 0 4713 4745 373381748 373381716 7.980000e-04 56.5
33 TraesCS4B01G137600 chr3D 96.970 33 1 0 4713 4745 72887660 72887628 7.980000e-04 56.5
34 TraesCS4B01G137600 chr3D 92.105 38 3 0 2253 2290 582626027 582625990 3.000000e-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 TraesCS4B01G137600 chr4B 181431242 181436942 5700 False 10528.0 10528 100.0000 1 5701 1 chr4B.!!$F1 5700
1 TraesCS4B01G137600 chr4A 454599653 454603113 3460 False 2700.0 4205 93.7830 2181 5701 2 chr4A.!!$F2 3520
2 TraesCS4B01G137600 chr4A 454592745 454594241 1496 False 1908.0 1908 89.6600 652 2187 1 chr4A.!!$F1 1535
3 TraesCS4B01G137600 chr4D 119227482 119233536 6054 False 1557.4 3035 90.6352 116 5701 5 chr4D.!!$F2 5585

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
386 398 0.095935 CTGTCAAATTGAGCTCCGCG 59.904 55.000 12.15 0.00 0.00 6.46 F
1033 1528 0.390472 GAAGTGCTTCAGGGGAGACG 60.390 60.000 7.03 0.00 39.31 4.18 F
2466 2989 0.321298 TTGTCCTTAGAAGGTGCGCC 60.321 55.000 8.71 8.71 46.54 6.53 F
2470 2993 0.804933 CCTTAGAAGGTGCGCCGTAC 60.805 60.000 11.42 6.48 41.41 3.67 F
3207 3738 1.001378 GGCGTGCAGTTTGTCTTGAAT 60.001 47.619 0.00 0.00 0.00 2.57 F
4295 4832 0.329596 GGGCAGGACCAGTTTGATCT 59.670 55.000 0.00 0.00 42.05 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2861 2.672714 TCAACAATTCGTCCTCAGTCG 58.327 47.619 0.00 0.0 0.00 4.18 R
2696 3222 0.320508 GTGTTCTCGGTGGGGTTCTC 60.321 60.000 0.00 0.0 0.00 2.87 R
3889 4426 3.146066 TGTTGTGTTCCAGACTATTGGC 58.854 45.455 0.00 0.0 38.16 4.52 R
4185 4722 3.325870 TGTCATCTTAAGTTCTGGTGCG 58.674 45.455 1.63 0.0 0.00 5.34 R
4471 5009 1.148273 AAACTCTGGGCGCTTGTCA 59.852 52.632 7.64 0.0 0.00 3.58 R
5332 6042 1.466025 AACCAGGACCTTGCGACGTA 61.466 55.000 0.00 0.0 0.00 3.57 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
22 23 4.215109 TGCTAGGGAATAATTTGGAAGGC 58.785 43.478 0.00 0.00 0.00 4.35
23 24 3.574396 GCTAGGGAATAATTTGGAAGGCC 59.426 47.826 0.00 0.00 0.00 5.19
24 25 4.692777 GCTAGGGAATAATTTGGAAGGCCT 60.693 45.833 0.00 0.00 34.31 5.19
25 26 3.646534 AGGGAATAATTTGGAAGGCCTG 58.353 45.455 5.69 0.00 34.31 4.85
26 27 3.012844 AGGGAATAATTTGGAAGGCCTGT 59.987 43.478 5.69 0.00 34.31 4.00
27 28 4.231890 AGGGAATAATTTGGAAGGCCTGTA 59.768 41.667 5.69 0.00 34.31 2.74
28 29 5.103086 AGGGAATAATTTGGAAGGCCTGTAT 60.103 40.000 5.69 0.00 34.31 2.29
29 30 5.602561 GGGAATAATTTGGAAGGCCTGTATT 59.397 40.000 5.69 4.70 34.31 1.89
30 31 6.099701 GGGAATAATTTGGAAGGCCTGTATTT 59.900 38.462 5.69 0.00 34.31 1.40
31 32 7.289084 GGGAATAATTTGGAAGGCCTGTATTTA 59.711 37.037 5.69 0.57 34.31 1.40
32 33 8.700973 GGAATAATTTGGAAGGCCTGTATTTAA 58.299 33.333 5.69 0.00 34.31 1.52
35 36 6.731292 ATTTGGAAGGCCTGTATTTAATCC 57.269 37.500 5.69 7.58 34.31 3.01
36 37 4.178956 TGGAAGGCCTGTATTTAATCCC 57.821 45.455 5.69 0.00 34.31 3.85
37 38 3.117284 TGGAAGGCCTGTATTTAATCCCC 60.117 47.826 5.69 0.00 34.31 4.81
38 39 3.140332 GGAAGGCCTGTATTTAATCCCCT 59.860 47.826 5.69 0.00 0.00 4.79
39 40 4.399219 GAAGGCCTGTATTTAATCCCCTC 58.601 47.826 5.69 0.00 0.00 4.30
40 41 3.403322 AGGCCTGTATTTAATCCCCTCA 58.597 45.455 3.11 0.00 0.00 3.86
41 42 3.791545 AGGCCTGTATTTAATCCCCTCAA 59.208 43.478 3.11 0.00 0.00 3.02
42 43 3.889538 GGCCTGTATTTAATCCCCTCAAC 59.110 47.826 0.00 0.00 0.00 3.18
43 44 4.532834 GCCTGTATTTAATCCCCTCAACA 58.467 43.478 0.00 0.00 0.00 3.33
44 45 5.140454 GCCTGTATTTAATCCCCTCAACAT 58.860 41.667 0.00 0.00 0.00 2.71
45 46 5.598417 GCCTGTATTTAATCCCCTCAACATT 59.402 40.000 0.00 0.00 0.00 2.71
46 47 6.775629 GCCTGTATTTAATCCCCTCAACATTA 59.224 38.462 0.00 0.00 0.00 1.90
47 48 7.255486 GCCTGTATTTAATCCCCTCAACATTAC 60.255 40.741 0.00 0.00 0.00 1.89
48 49 7.777910 CCTGTATTTAATCCCCTCAACATTACA 59.222 37.037 0.00 0.00 0.00 2.41
49 50 9.354673 CTGTATTTAATCCCCTCAACATTACAT 57.645 33.333 0.00 0.00 0.00 2.29
50 51 9.349713 TGTATTTAATCCCCTCAACATTACATC 57.650 33.333 0.00 0.00 0.00 3.06
51 52 6.935741 TTTAATCCCCTCAACATTACATCG 57.064 37.500 0.00 0.00 0.00 3.84
52 53 4.771114 AATCCCCTCAACATTACATCGA 57.229 40.909 0.00 0.00 0.00 3.59
53 54 4.982241 ATCCCCTCAACATTACATCGAT 57.018 40.909 0.00 0.00 0.00 3.59
54 55 4.071961 TCCCCTCAACATTACATCGATG 57.928 45.455 23.68 23.68 0.00 3.84
55 56 3.454447 TCCCCTCAACATTACATCGATGT 59.546 43.478 31.93 31.93 44.48 3.06
56 57 4.080582 TCCCCTCAACATTACATCGATGTT 60.081 41.667 34.06 16.37 45.80 2.71
57 58 4.640201 CCCCTCAACATTACATCGATGTTT 59.360 41.667 34.06 20.13 43.23 2.83
58 59 5.820423 CCCCTCAACATTACATCGATGTTTA 59.180 40.000 34.06 22.69 43.23 2.01
59 60 6.317642 CCCCTCAACATTACATCGATGTTTAA 59.682 38.462 34.06 23.62 43.23 1.52
60 61 7.186804 CCCTCAACATTACATCGATGTTTAAC 58.813 38.462 34.06 0.00 43.23 2.01
61 62 7.065803 CCCTCAACATTACATCGATGTTTAACT 59.934 37.037 34.06 14.94 43.23 2.24
62 63 8.450964 CCTCAACATTACATCGATGTTTAACTT 58.549 33.333 34.06 16.77 43.23 2.66
173 174 8.524487 AGCGGTTATTAGATAAAGAGGTGATAG 58.476 37.037 0.00 0.00 0.00 2.08
178 179 2.900546 AGATAAAGAGGTGATAGGCGGG 59.099 50.000 0.00 0.00 0.00 6.13
192 193 2.665165 AGGCGGGAAATAATTCATGCA 58.335 42.857 8.06 0.00 38.34 3.96
198 199 5.051816 CGGGAAATAATTCATGCAAATGCT 58.948 37.500 6.97 0.00 38.44 3.79
199 200 5.050634 CGGGAAATAATTCATGCAAATGCTG 60.051 40.000 6.97 3.14 38.44 4.41
205 206 2.647529 TCATGCAAATGCTGAGCTTG 57.352 45.000 5.83 3.85 42.66 4.01
222 223 4.740902 AGCTTGGTTTATTTTGAGGACCT 58.259 39.130 0.00 0.00 0.00 3.85
258 259 2.103771 CGGACCTGAGTTGGATCATGAT 59.896 50.000 8.25 8.25 0.00 2.45
259 260 3.432749 CGGACCTGAGTTGGATCATGATT 60.433 47.826 10.14 0.00 0.00 2.57
260 261 4.133078 GGACCTGAGTTGGATCATGATTC 58.867 47.826 10.14 8.56 0.00 2.52
261 262 4.384537 GGACCTGAGTTGGATCATGATTCA 60.385 45.833 12.97 12.97 0.00 2.57
262 263 5.374921 GACCTGAGTTGGATCATGATTCAT 58.625 41.667 17.58 3.52 0.00 2.57
263 264 5.131067 ACCTGAGTTGGATCATGATTCATG 58.869 41.667 17.58 18.71 42.60 3.07
289 290 0.610232 AAGTGAACCTGCCATGCCTC 60.610 55.000 0.00 0.00 0.00 4.70
298 299 1.471684 CTGCCATGCCTCTCAAAACTC 59.528 52.381 0.00 0.00 0.00 3.01
299 300 0.449388 GCCATGCCTCTCAAAACTCG 59.551 55.000 0.00 0.00 0.00 4.18
303 304 3.120060 CCATGCCTCTCAAAACTCGAAAG 60.120 47.826 0.00 0.00 0.00 2.62
305 306 1.136224 GCCTCTCAAAACTCGAAAGCG 60.136 52.381 0.00 0.00 39.35 4.68
308 309 3.061429 CCTCTCAAAACTCGAAAGCGATC 59.939 47.826 0.00 0.00 46.80 3.69
311 312 2.798283 TCAAAACTCGAAAGCGATCGTT 59.202 40.909 17.81 8.05 46.80 3.85
328 329 3.277715 TCGTTGCTGATGATTTGGCATA 58.722 40.909 0.00 0.00 34.59 3.14
333 334 5.294734 TGCTGATGATTTGGCATACTCTA 57.705 39.130 0.00 0.00 0.00 2.43
367 379 7.565450 AAGACAATTTTTGCTTTTGTTTTGC 57.435 28.000 0.00 0.00 33.92 3.68
386 398 0.095935 CTGTCAAATTGAGCTCCGCG 59.904 55.000 12.15 0.00 0.00 6.46
392 404 0.753262 AATTGAGCTCCGCGTATCCT 59.247 50.000 12.15 0.00 0.00 3.24
402 414 1.670811 CCGCGTATCCTGATTTGCTTT 59.329 47.619 4.92 0.00 0.00 3.51
406 418 4.201773 CGCGTATCCTGATTTGCTTTACAA 60.202 41.667 0.00 0.00 36.13 2.41
412 424 9.076596 GTATCCTGATTTGCTTTACAATTCAAC 57.923 33.333 5.00 0.00 44.06 3.18
428 440 8.006298 ACAATTCAACTTTATTGTTCTGGTCA 57.994 30.769 0.00 0.00 40.97 4.02
430 442 6.385649 TTCAACTTTATTGTTCTGGTCACC 57.614 37.500 0.00 0.00 0.00 4.02
432 444 2.812011 ACTTTATTGTTCTGGTCACCGC 59.188 45.455 0.00 0.00 0.00 5.68
437 449 1.021202 TGTTCTGGTCACCGCAAAAG 58.979 50.000 0.00 0.00 0.00 2.27
440 452 2.045561 TCTGGTCACCGCAAAAGAAA 57.954 45.000 0.00 0.00 0.00 2.52
441 453 2.370349 TCTGGTCACCGCAAAAGAAAA 58.630 42.857 0.00 0.00 0.00 2.29
442 454 2.357637 TCTGGTCACCGCAAAAGAAAAG 59.642 45.455 0.00 0.00 0.00 2.27
443 455 2.357637 CTGGTCACCGCAAAAGAAAAGA 59.642 45.455 0.00 0.00 0.00 2.52
444 456 2.755655 TGGTCACCGCAAAAGAAAAGAA 59.244 40.909 0.00 0.00 0.00 2.52
445 457 3.193691 TGGTCACCGCAAAAGAAAAGAAA 59.806 39.130 0.00 0.00 0.00 2.52
446 458 4.177783 GGTCACCGCAAAAGAAAAGAAAA 58.822 39.130 0.00 0.00 0.00 2.29
447 459 4.627900 GGTCACCGCAAAAGAAAAGAAAAA 59.372 37.500 0.00 0.00 0.00 1.94
481 493 2.290960 GGGTCCAAGGTGTAGAAGCATT 60.291 50.000 0.00 0.00 0.00 3.56
484 496 4.265073 GTCCAAGGTGTAGAAGCATTGAT 58.735 43.478 0.00 0.00 0.00 2.57
493 509 6.071952 GGTGTAGAAGCATTGATGGAAAAGAA 60.072 38.462 0.00 0.00 0.00 2.52
507 523 4.098654 TGGAAAAGAAGGCGAAAAACATCA 59.901 37.500 0.00 0.00 0.00 3.07
510 526 6.202762 GGAAAAGAAGGCGAAAAACATCAAAT 59.797 34.615 0.00 0.00 0.00 2.32
513 529 6.529463 AGAAGGCGAAAAACATCAAATTTG 57.471 33.333 12.15 12.15 0.00 2.32
514 530 6.279882 AGAAGGCGAAAAACATCAAATTTGA 58.720 32.000 22.52 22.52 42.14 2.69
516 532 8.087750 AGAAGGCGAAAAACATCAAATTTGATA 58.912 29.630 28.61 7.64 45.62 2.15
517 533 8.600449 AAGGCGAAAAACATCAAATTTGATAA 57.400 26.923 28.61 6.92 45.62 1.75
518 534 8.776376 AGGCGAAAAACATCAAATTTGATAAT 57.224 26.923 28.61 18.86 45.62 1.28
520 536 9.476761 GGCGAAAAACATCAAATTTGATAATTC 57.523 29.630 28.61 24.65 45.62 2.17
543 562 4.635765 CCAAATCCTCTAAAATCGTGAGCA 59.364 41.667 0.00 0.00 0.00 4.26
544 563 5.123820 CCAAATCCTCTAAAATCGTGAGCAA 59.876 40.000 0.00 0.00 0.00 3.91
545 564 6.253746 CAAATCCTCTAAAATCGTGAGCAAG 58.746 40.000 0.00 0.00 0.00 4.01
550 569 5.179368 CCTCTAAAATCGTGAGCAAGAACAA 59.821 40.000 0.00 0.00 0.00 2.83
551 570 6.293407 CCTCTAAAATCGTGAGCAAGAACAAA 60.293 38.462 0.00 0.00 0.00 2.83
552 571 6.427150 TCTAAAATCGTGAGCAAGAACAAAC 58.573 36.000 0.00 0.00 0.00 2.93
554 573 4.836125 AATCGTGAGCAAGAACAAACAT 57.164 36.364 0.00 0.00 0.00 2.71
556 575 2.290367 TCGTGAGCAAGAACAAACATGG 59.710 45.455 0.00 0.00 0.00 3.66
557 576 2.290367 CGTGAGCAAGAACAAACATGGA 59.710 45.455 0.00 0.00 0.00 3.41
558 577 3.607775 CGTGAGCAAGAACAAACATGGAG 60.608 47.826 0.00 0.00 0.00 3.86
560 579 4.036734 GTGAGCAAGAACAAACATGGAGAA 59.963 41.667 0.00 0.00 0.00 2.87
561 580 4.644234 TGAGCAAGAACAAACATGGAGAAA 59.356 37.500 0.00 0.00 0.00 2.52
564 583 6.218746 AGCAAGAACAAACATGGAGAAATTC 58.781 36.000 0.00 0.00 0.00 2.17
565 584 5.406477 GCAAGAACAAACATGGAGAAATTCC 59.594 40.000 0.00 0.00 46.98 3.01
583 900 2.750815 CGTCTGACGGAATGGAACC 58.249 57.895 21.78 0.00 38.08 3.62
589 906 3.568007 TCTGACGGAATGGAACCTTTTTG 59.432 43.478 0.00 0.00 0.00 2.44
590 907 3.556999 TGACGGAATGGAACCTTTTTGA 58.443 40.909 0.00 0.00 0.00 2.69
607 924 8.722480 CCTTTTTGAGGGAATATTTGGAAATC 57.278 34.615 0.00 0.00 42.26 2.17
608 925 8.542926 CCTTTTTGAGGGAATATTTGGAAATCT 58.457 33.333 0.00 0.00 42.26 2.40
657 1096 8.726870 AATTTTGATAATTTCTTCAGCATGGG 57.273 30.769 0.00 0.00 36.16 4.00
666 1105 6.514012 TTTCTTCAGCATGGGGAATATCTA 57.486 37.500 0.00 0.00 36.16 1.98
675 1114 6.556116 AGCATGGGGAATATCTAAAAAGCAAT 59.444 34.615 0.00 0.00 0.00 3.56
882 1323 6.146347 CACTCTTTTCCTTCCTTTACTCTTCG 59.854 42.308 0.00 0.00 0.00 3.79
903 1350 1.620819 CTACGCTCCATGGGCTAGAAT 59.379 52.381 13.02 0.00 0.00 2.40
904 1351 0.394565 ACGCTCCATGGGCTAGAATC 59.605 55.000 13.02 0.00 0.00 2.52
905 1352 0.683973 CGCTCCATGGGCTAGAATCT 59.316 55.000 13.02 0.00 0.00 2.40
906 1353 1.337635 CGCTCCATGGGCTAGAATCTC 60.338 57.143 13.02 0.00 0.00 2.75
907 1354 1.977129 GCTCCATGGGCTAGAATCTCT 59.023 52.381 13.02 0.00 0.00 3.10
908 1355 2.028203 GCTCCATGGGCTAGAATCTCTC 60.028 54.545 13.02 0.00 0.00 3.20
933 1380 2.937149 CTCTCTGCCATCATCACACTTG 59.063 50.000 0.00 0.00 0.00 3.16
937 1384 3.014623 CTGCCATCATCACACTTGACAT 58.985 45.455 0.00 0.00 33.38 3.06
940 1387 4.281435 TGCCATCATCACACTTGACATTTT 59.719 37.500 0.00 0.00 33.38 1.82
941 1388 4.624024 GCCATCATCACACTTGACATTTTG 59.376 41.667 0.00 0.00 33.38 2.44
1033 1528 0.390472 GAAGTGCTTCAGGGGAGACG 60.390 60.000 7.03 0.00 39.31 4.18
1034 1529 0.832135 AAGTGCTTCAGGGGAGACGA 60.832 55.000 0.00 0.00 0.00 4.20
1035 1530 1.079750 GTGCTTCAGGGGAGACGAC 60.080 63.158 0.00 0.00 0.00 4.34
1036 1531 2.182030 GCTTCAGGGGAGACGACG 59.818 66.667 0.00 0.00 0.00 5.12
1037 1532 2.341101 GCTTCAGGGGAGACGACGA 61.341 63.158 0.00 0.00 0.00 4.20
1038 1533 1.874345 GCTTCAGGGGAGACGACGAA 61.874 60.000 0.00 0.00 0.00 3.85
1067 1562 1.213926 AGACCACTACCCCTACTACCG 59.786 57.143 0.00 0.00 0.00 4.02
1178 1679 2.461110 GCGCGTCCATGGTAACTGG 61.461 63.158 12.58 0.00 34.93 4.00
1201 1703 1.605058 CCTACCCACCACTCTCCGTG 61.605 65.000 0.00 0.00 43.41 4.94
1250 1752 5.186021 TGTCAAGTCAGATTAAGTCTCCCTC 59.814 44.000 0.00 0.00 34.00 4.30
1257 1759 1.183549 TTAAGTCTCCCTCGCCACTC 58.816 55.000 0.00 0.00 0.00 3.51
1273 1776 4.142447 CGCCACTCAAGTACAGTACTATGT 60.142 45.833 13.87 9.85 38.26 2.29
1274 1777 5.103000 GCCACTCAAGTACAGTACTATGTG 58.897 45.833 21.69 21.69 38.26 3.21
1275 1778 5.336531 GCCACTCAAGTACAGTACTATGTGT 60.337 44.000 24.08 20.41 38.26 3.72
1276 1779 6.688578 CCACTCAAGTACAGTACTATGTGTT 58.311 40.000 24.08 7.05 38.26 3.32
1277 1780 7.152645 CCACTCAAGTACAGTACTATGTGTTT 58.847 38.462 24.08 6.51 38.26 2.83
1278 1781 7.328737 CCACTCAAGTACAGTACTATGTGTTTC 59.671 40.741 24.08 0.00 38.26 2.78
1279 1782 7.865889 CACTCAAGTACAGTACTATGTGTTTCA 59.134 37.037 13.87 0.00 38.26 2.69
1280 1783 8.082852 ACTCAAGTACAGTACTATGTGTTTCAG 58.917 37.037 13.87 5.09 38.26 3.02
1281 1784 6.866770 TCAAGTACAGTACTATGTGTTTCAGC 59.133 38.462 13.87 0.00 38.26 4.26
1282 1785 6.591750 AGTACAGTACTATGTGTTTCAGCT 57.408 37.500 11.84 0.00 37.23 4.24
1283 1786 6.994221 AGTACAGTACTATGTGTTTCAGCTT 58.006 36.000 11.84 0.00 37.23 3.74
1284 1787 7.442656 AGTACAGTACTATGTGTTTCAGCTTT 58.557 34.615 11.84 0.00 37.23 3.51
1285 1788 6.787085 ACAGTACTATGTGTTTCAGCTTTC 57.213 37.500 0.00 0.00 30.46 2.62
1286 1789 6.288294 ACAGTACTATGTGTTTCAGCTTTCA 58.712 36.000 0.00 0.00 30.46 2.69
1287 1790 6.425114 ACAGTACTATGTGTTTCAGCTTTCAG 59.575 38.462 0.00 0.00 30.46 3.02
1288 1791 4.756084 ACTATGTGTTTCAGCTTTCAGC 57.244 40.909 0.00 0.00 42.84 4.26
1311 1814 6.903419 GCTTTCAGCTTGAACTTTACTGTAT 58.097 36.000 0.00 0.00 35.89 2.29
1366 1869 6.159293 TGCAGATTCATAACGATGAGGATAC 58.841 40.000 0.00 0.00 43.03 2.24
1531 2051 9.956720 CTAGAATCAAAGGTTAAAGCCATAATG 57.043 33.333 0.00 0.00 0.00 1.90
1723 2245 7.303634 ACACATACGACAAGTTTAATCATCC 57.696 36.000 0.00 0.00 0.00 3.51
1739 2261 6.872585 AATCATCCCTTTTGCTCCAATTTA 57.127 33.333 0.00 0.00 0.00 1.40
1780 2302 2.287970 ACGCGACATGTGTGAAGACTAA 60.288 45.455 15.93 0.00 40.56 2.24
1900 2422 5.297029 GGCCCTCACACTTGATAGTATTTTC 59.703 44.000 0.00 0.00 31.96 2.29
2103 2626 3.856900 AGGACCTACCAAATGCCTTTTT 58.143 40.909 0.00 0.00 42.04 1.94
2109 2632 5.221441 ACCTACCAAATGCCTTTTTGACTTC 60.221 40.000 5.68 0.00 38.58 3.01
2116 2639 6.959639 AATGCCTTTTTGACTTCTCTTACA 57.040 33.333 0.00 0.00 0.00 2.41
2121 2644 9.077885 TGCCTTTTTGACTTCTCTTACAAATAT 57.922 29.630 0.00 0.00 33.38 1.28
2134 2657 9.837681 TCTCTTACAAATATAGGGTGATCCATA 57.162 33.333 0.00 0.00 38.24 2.74
2244 2767 6.702723 CAGTTTTCAGCATTGAGAAATCCAAA 59.297 34.615 5.81 0.00 34.10 3.28
2327 2850 7.067008 CCCTTTATATGGGTGTAGTTTTGTGAG 59.933 40.741 3.77 0.00 39.82 3.51
2332 2855 8.732746 ATATGGGTGTAGTTTTGTGAGATTAC 57.267 34.615 0.00 0.00 0.00 1.89
2388 2911 5.888982 TGATTAGATAAGTGGAAGGGGAC 57.111 43.478 0.00 0.00 0.00 4.46
2463 2986 5.548406 TCTTACTTTGTCCTTAGAAGGTGC 58.452 41.667 8.17 3.95 46.54 5.01
2466 2989 0.321298 TTGTCCTTAGAAGGTGCGCC 60.321 55.000 8.71 8.71 46.54 6.53
2467 2990 1.810030 GTCCTTAGAAGGTGCGCCG 60.810 63.158 11.42 0.00 46.54 6.46
2469 2992 0.966875 TCCTTAGAAGGTGCGCCGTA 60.967 55.000 11.42 1.05 46.54 4.02
2470 2993 0.804933 CCTTAGAAGGTGCGCCGTAC 60.805 60.000 11.42 6.48 41.41 3.67
2568 3094 5.599242 GGAGAGCAAGAAGGGTAGTAGTAAT 59.401 44.000 0.00 0.00 0.00 1.89
2765 3291 1.840635 GCCCTAAACTGGATCCAGAGT 59.159 52.381 41.91 30.25 46.30 3.24
2827 3353 2.698855 ACATAGTTCAGGCGAGCATT 57.301 45.000 0.00 0.00 0.00 3.56
2992 3522 2.162681 CCAGGAAACCCACTGATGTTC 58.837 52.381 0.00 0.00 36.86 3.18
3016 3546 7.817641 TCGCATTAATATTTGGTTGTTACACA 58.182 30.769 0.00 0.00 0.00 3.72
3034 3564 9.476202 TGTTACACATGACTATATATGTTCAGC 57.524 33.333 0.00 0.00 35.46 4.26
3035 3565 9.476202 GTTACACATGACTATATATGTTCAGCA 57.524 33.333 0.00 0.00 35.46 4.41
3207 3738 1.001378 GGCGTGCAGTTTGTCTTGAAT 60.001 47.619 0.00 0.00 0.00 2.57
3411 3942 2.851071 CGATCCGAGGGAGTCTGGC 61.851 68.421 0.00 0.00 34.05 4.85
3700 4234 8.559536 TGTTTGAACTAAGACACATTCTGAATC 58.440 33.333 0.00 0.00 33.46 2.52
3789 4324 6.673154 AAACAGCACGGATACCTATTTTAC 57.327 37.500 0.00 0.00 0.00 2.01
3793 4328 6.097270 ACAGCACGGATACCTATTTTACTACA 59.903 38.462 0.00 0.00 0.00 2.74
3875 4412 7.831691 TTAAAACCTTCCTGTGATCATTCAA 57.168 32.000 0.00 0.00 32.48 2.69
3889 4426 3.979948 TCATTCAATTGGCACTTGTGTG 58.020 40.909 15.94 14.84 46.37 3.82
3952 4489 2.600792 GGCGCTTGCTTTGATCTAATCG 60.601 50.000 7.64 0.00 39.13 3.34
3973 4510 1.082169 TGAACGCGCATTCACTTGC 60.082 52.632 15.87 0.00 39.29 4.01
4185 4722 6.834168 TCATGAGTTAAAAGGGGAATTGAC 57.166 37.500 0.00 0.00 0.00 3.18
4194 4731 0.608035 GGGGAATTGACGCACCAGAA 60.608 55.000 0.00 0.00 0.00 3.02
4212 4749 7.275183 CACCAGAACTTAAGATGACATATGGA 58.725 38.462 10.09 0.00 0.00 3.41
4295 4832 0.329596 GGGCAGGACCAGTTTGATCT 59.670 55.000 0.00 0.00 42.05 2.75
4299 4836 3.135530 GGCAGGACCAGTTTGATCTCTAT 59.864 47.826 0.00 0.00 38.86 1.98
4352 4890 3.030291 TCCAGGTGAAACAAGCACAAAT 58.970 40.909 0.00 0.00 39.98 2.32
4471 5009 2.548057 CGCATGGCATTTTACGACCTAT 59.452 45.455 0.00 0.00 0.00 2.57
4742 5284 3.116300 CCATGTCTCGAACTAATGGTCG 58.884 50.000 7.56 0.00 0.00 4.79
4780 5322 4.837093 TTGGTAACTAGGGTGGATCTTG 57.163 45.455 0.00 0.00 37.61 3.02
4966 5655 4.081752 TCTCTTTGCTGCTTTCACCAAAAA 60.082 37.500 0.00 0.00 30.09 1.94
4977 5666 6.097554 TGCTTTCACCAAAAAGTCCAAATAGA 59.902 34.615 0.00 0.00 38.30 1.98
5035 5725 5.009510 TGCATTAACAATAATCCGGTGATGG 59.990 40.000 0.00 0.00 29.08 3.51
5037 5727 1.593196 ACAATAATCCGGTGATGGCG 58.407 50.000 0.00 0.00 0.00 5.69
5262 5958 4.398044 ACATTAAACATTCCAAGGCTACCG 59.602 41.667 0.00 0.00 0.00 4.02
5332 6042 5.210430 TCCTGCCATATCCACAAAATGATT 58.790 37.500 0.00 0.00 0.00 2.57
5334 6044 6.265196 TCCTGCCATATCCACAAAATGATTAC 59.735 38.462 0.00 0.00 0.00 1.89
5338 6048 6.362686 CCATATCCACAAAATGATTACGTCG 58.637 40.000 0.00 0.00 0.00 5.12
5538 6248 1.673168 GCGCCATTCCAGAATCTCTT 58.327 50.000 0.00 0.00 0.00 2.85
5567 6277 3.128938 TCCTGTTCTACGCTTCTAGCTTC 59.871 47.826 0.00 0.00 39.60 3.86
5580 6290 5.514204 GCTTCTAGCTTCGTTATTACGTTGA 59.486 40.000 3.97 0.00 42.40 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.215109 GCCTTCCAAATTATTCCCTAGCA 58.785 43.478 0.00 0.00 0.00 3.49
1 2 3.574396 GGCCTTCCAAATTATTCCCTAGC 59.426 47.826 0.00 0.00 0.00 3.42
2 3 4.829492 CAGGCCTTCCAAATTATTCCCTAG 59.171 45.833 0.00 0.00 33.74 3.02
3 4 4.231890 ACAGGCCTTCCAAATTATTCCCTA 59.768 41.667 0.00 0.00 33.74 3.53
4 5 3.012844 ACAGGCCTTCCAAATTATTCCCT 59.987 43.478 0.00 0.00 33.74 4.20
5 6 3.374764 ACAGGCCTTCCAAATTATTCCC 58.625 45.455 0.00 0.00 33.74 3.97
6 7 6.731292 AATACAGGCCTTCCAAATTATTCC 57.269 37.500 0.00 0.00 33.74 3.01
9 10 8.870116 GGATTAAATACAGGCCTTCCAAATTAT 58.130 33.333 0.00 0.00 33.74 1.28
10 11 7.289084 GGGATTAAATACAGGCCTTCCAAATTA 59.711 37.037 15.97 3.87 33.74 1.40
11 12 6.099701 GGGATTAAATACAGGCCTTCCAAATT 59.900 38.462 15.97 4.09 33.74 1.82
12 13 5.602561 GGGATTAAATACAGGCCTTCCAAAT 59.397 40.000 15.97 6.40 33.74 2.32
13 14 4.959839 GGGATTAAATACAGGCCTTCCAAA 59.040 41.667 15.97 2.01 33.74 3.28
14 15 4.542697 GGGATTAAATACAGGCCTTCCAA 58.457 43.478 15.97 0.70 33.74 3.53
15 16 3.117284 GGGGATTAAATACAGGCCTTCCA 60.117 47.826 15.97 0.00 33.74 3.53
16 17 3.140332 AGGGGATTAAATACAGGCCTTCC 59.860 47.826 0.00 4.60 0.00 3.46
17 18 4.141251 TGAGGGGATTAAATACAGGCCTTC 60.141 45.833 0.00 0.00 0.00 3.46
18 19 3.791545 TGAGGGGATTAAATACAGGCCTT 59.208 43.478 0.00 0.00 0.00 4.35
19 20 3.403322 TGAGGGGATTAAATACAGGCCT 58.597 45.455 0.00 0.00 0.00 5.19
20 21 3.876309 TGAGGGGATTAAATACAGGCC 57.124 47.619 0.00 0.00 0.00 5.19
21 22 4.532834 TGTTGAGGGGATTAAATACAGGC 58.467 43.478 0.00 0.00 0.00 4.85
22 23 7.777910 TGTAATGTTGAGGGGATTAAATACAGG 59.222 37.037 0.00 0.00 0.00 4.00
23 24 8.746052 TGTAATGTTGAGGGGATTAAATACAG 57.254 34.615 0.00 0.00 0.00 2.74
24 25 9.349713 GATGTAATGTTGAGGGGATTAAATACA 57.650 33.333 0.00 0.00 0.00 2.29
25 26 8.504005 CGATGTAATGTTGAGGGGATTAAATAC 58.496 37.037 0.00 0.00 0.00 1.89
26 27 8.433599 TCGATGTAATGTTGAGGGGATTAAATA 58.566 33.333 0.00 0.00 0.00 1.40
27 28 7.287061 TCGATGTAATGTTGAGGGGATTAAAT 58.713 34.615 0.00 0.00 0.00 1.40
28 29 6.654959 TCGATGTAATGTTGAGGGGATTAAA 58.345 36.000 0.00 0.00 0.00 1.52
29 30 6.241882 TCGATGTAATGTTGAGGGGATTAA 57.758 37.500 0.00 0.00 0.00 1.40
30 31 5.880164 TCGATGTAATGTTGAGGGGATTA 57.120 39.130 0.00 0.00 0.00 1.75
31 32 4.771114 TCGATGTAATGTTGAGGGGATT 57.229 40.909 0.00 0.00 0.00 3.01
32 33 4.103153 ACATCGATGTAATGTTGAGGGGAT 59.897 41.667 29.05 0.00 39.68 3.85
33 34 3.454447 ACATCGATGTAATGTTGAGGGGA 59.546 43.478 29.05 0.00 39.68 4.81
34 35 3.808728 ACATCGATGTAATGTTGAGGGG 58.191 45.455 29.05 0.00 39.68 4.79
35 36 5.818136 AAACATCGATGTAATGTTGAGGG 57.182 39.130 30.16 0.03 44.44 4.30
36 37 7.974675 AGTTAAACATCGATGTAATGTTGAGG 58.025 34.615 30.16 0.24 44.44 3.86
149 150 7.760340 GCCTATCACCTCTTTATCTAATAACCG 59.240 40.741 0.00 0.00 0.00 4.44
152 153 7.093465 CCCGCCTATCACCTCTTTATCTAATAA 60.093 40.741 0.00 0.00 0.00 1.40
161 162 1.580059 TTCCCGCCTATCACCTCTTT 58.420 50.000 0.00 0.00 0.00 2.52
173 174 3.451141 TTGCATGAATTATTTCCCGCC 57.549 42.857 0.00 0.00 30.74 6.13
178 179 6.479001 AGCTCAGCATTTGCATGAATTATTTC 59.521 34.615 0.00 0.00 45.16 2.17
192 193 6.523840 TCAAAATAAACCAAGCTCAGCATTT 58.476 32.000 0.00 0.00 0.00 2.32
198 199 4.522789 GGTCCTCAAAATAAACCAAGCTCA 59.477 41.667 0.00 0.00 0.00 4.26
199 200 4.767409 AGGTCCTCAAAATAAACCAAGCTC 59.233 41.667 0.00 0.00 32.25 4.09
237 238 1.482182 TCATGATCCAACTCAGGTCCG 59.518 52.381 0.00 0.00 0.00 4.79
240 241 4.849813 TGAATCATGATCCAACTCAGGT 57.150 40.909 9.06 0.00 0.00 4.00
258 259 4.136796 CAGGTTCACTTCCTTGTCATGAA 58.863 43.478 0.00 0.00 32.37 2.57
259 260 3.743521 CAGGTTCACTTCCTTGTCATGA 58.256 45.455 0.00 0.00 32.37 3.07
260 261 2.227388 GCAGGTTCACTTCCTTGTCATG 59.773 50.000 0.00 0.00 32.37 3.07
261 262 2.508526 GCAGGTTCACTTCCTTGTCAT 58.491 47.619 0.00 0.00 32.37 3.06
262 263 1.476833 GGCAGGTTCACTTCCTTGTCA 60.477 52.381 0.00 0.00 32.37 3.58
263 264 1.239347 GGCAGGTTCACTTCCTTGTC 58.761 55.000 0.00 0.00 32.37 3.18
264 265 0.550914 TGGCAGGTTCACTTCCTTGT 59.449 50.000 0.00 0.00 33.17 3.16
265 266 1.542915 CATGGCAGGTTCACTTCCTTG 59.457 52.381 0.00 0.00 33.17 3.61
298 299 0.647410 ATCAGCAACGATCGCTTTCG 59.353 50.000 16.60 1.24 44.56 3.46
299 300 1.660607 TCATCAGCAACGATCGCTTTC 59.339 47.619 16.60 3.61 37.72 2.62
303 304 2.369600 CAAATCATCAGCAACGATCGC 58.630 47.619 16.60 0.00 0.00 4.58
305 306 2.097954 TGCCAAATCATCAGCAACGATC 59.902 45.455 0.00 0.00 30.97 3.69
308 309 2.572191 ATGCCAAATCATCAGCAACG 57.428 45.000 0.00 0.00 38.99 4.10
311 312 4.160642 AGAGTATGCCAAATCATCAGCA 57.839 40.909 0.00 0.00 40.00 4.41
333 334 8.518430 AAGCAAAAATTGTCTTTTGGGTAAAT 57.482 26.923 9.99 0.00 43.49 1.40
352 364 5.679734 TTTGACAGCAAAACAAAAGCAAA 57.320 30.435 0.00 0.00 40.82 3.68
386 398 9.076596 GTTGAATTGTAAAGCAAATCAGGATAC 57.923 33.333 0.00 0.00 44.77 2.24
402 414 9.126151 TGACCAGAACAATAAAGTTGAATTGTA 57.874 29.630 14.13 0.00 43.66 2.41
406 418 6.293955 CGGTGACCAGAACAATAAAGTTGAAT 60.294 38.462 1.11 0.00 0.00 2.57
412 424 2.811431 TGCGGTGACCAGAACAATAAAG 59.189 45.455 1.11 0.00 0.00 1.85
424 436 3.430333 TTCTTTTCTTTTGCGGTGACC 57.570 42.857 0.00 0.00 0.00 4.02
444 456 6.320926 CCTTGGACCCAAAACAATGAATTTTT 59.679 34.615 2.84 0.00 35.33 1.94
445 457 5.827267 CCTTGGACCCAAAACAATGAATTTT 59.173 36.000 2.84 0.00 35.33 1.82
446 458 5.104151 ACCTTGGACCCAAAACAATGAATTT 60.104 36.000 2.84 0.00 35.33 1.82
447 459 4.411869 ACCTTGGACCCAAAACAATGAATT 59.588 37.500 2.84 0.00 35.33 2.17
448 460 3.973305 ACCTTGGACCCAAAACAATGAAT 59.027 39.130 2.84 0.00 35.33 2.57
481 493 4.098654 TGTTTTTCGCCTTCTTTTCCATCA 59.901 37.500 0.00 0.00 0.00 3.07
484 496 4.098654 TGATGTTTTTCGCCTTCTTTTCCA 59.901 37.500 0.00 0.00 0.00 3.53
493 509 8.776376 ATTATCAAATTTGATGTTTTTCGCCT 57.224 26.923 33.94 13.90 46.68 5.52
513 529 9.884465 CACGATTTTAGAGGATTTGGAATTATC 57.116 33.333 0.00 0.00 0.00 1.75
514 530 9.627123 TCACGATTTTAGAGGATTTGGAATTAT 57.373 29.630 0.00 0.00 0.00 1.28
515 531 9.109393 CTCACGATTTTAGAGGATTTGGAATTA 57.891 33.333 0.00 0.00 0.00 1.40
516 532 7.415653 GCTCACGATTTTAGAGGATTTGGAATT 60.416 37.037 0.00 0.00 0.00 2.17
517 533 6.038714 GCTCACGATTTTAGAGGATTTGGAAT 59.961 38.462 0.00 0.00 0.00 3.01
518 534 5.354234 GCTCACGATTTTAGAGGATTTGGAA 59.646 40.000 0.00 0.00 0.00 3.53
520 536 4.635765 TGCTCACGATTTTAGAGGATTTGG 59.364 41.667 0.00 0.00 0.00 3.28
535 554 2.290367 CCATGTTTGTTCTTGCTCACGA 59.710 45.455 0.00 0.00 0.00 4.35
543 562 5.301805 ACGGAATTTCTCCATGTTTGTTCTT 59.698 36.000 0.00 0.00 45.74 2.52
544 563 4.827284 ACGGAATTTCTCCATGTTTGTTCT 59.173 37.500 0.00 0.00 45.74 3.01
545 564 5.048713 AGACGGAATTTCTCCATGTTTGTTC 60.049 40.000 0.00 0.00 45.74 3.18
550 569 4.003648 GTCAGACGGAATTTCTCCATGTT 58.996 43.478 0.00 0.00 45.74 2.71
551 570 3.600388 GTCAGACGGAATTTCTCCATGT 58.400 45.455 0.00 0.00 45.74 3.21
552 571 2.604914 CGTCAGACGGAATTTCTCCATG 59.395 50.000 15.64 0.00 45.74 3.66
554 573 2.363788 CGTCAGACGGAATTTCTCCA 57.636 50.000 15.64 0.00 45.74 3.86
565 584 0.246635 AGGTTCCATTCCGTCAGACG 59.753 55.000 16.50 16.50 42.11 4.18
566 585 2.474410 AAGGTTCCATTCCGTCAGAC 57.526 50.000 0.00 0.00 0.00 3.51
568 587 3.568007 TCAAAAAGGTTCCATTCCGTCAG 59.432 43.478 0.00 0.00 0.00 3.51
569 588 3.556999 TCAAAAAGGTTCCATTCCGTCA 58.443 40.909 0.00 0.00 0.00 4.35
570 589 3.057526 CCTCAAAAAGGTTCCATTCCGTC 60.058 47.826 0.00 0.00 40.67 4.79
583 900 9.948964 AAGATTTCCAAATATTCCCTCAAAAAG 57.051 29.630 0.00 0.00 0.00 2.27
589 906 5.221521 GCCCAAGATTTCCAAATATTCCCTC 60.222 44.000 0.00 0.00 28.13 4.30
590 907 4.655649 GCCCAAGATTTCCAAATATTCCCT 59.344 41.667 0.00 0.00 28.13 4.20
601 918 3.633986 CCAAGTCATAGCCCAAGATTTCC 59.366 47.826 0.00 0.00 0.00 3.13
602 919 3.067320 GCCAAGTCATAGCCCAAGATTTC 59.933 47.826 0.00 0.00 0.00 2.17
607 924 1.838112 TTGCCAAGTCATAGCCCAAG 58.162 50.000 0.00 0.00 0.00 3.61
608 925 2.300956 TTTGCCAAGTCATAGCCCAA 57.699 45.000 0.00 0.00 0.00 4.12
638 1077 6.661304 ATTCCCCATGCTGAAGAAATTATC 57.339 37.500 0.00 0.00 0.00 1.75
641 1080 6.379579 AGATATTCCCCATGCTGAAGAAATT 58.620 36.000 0.00 0.00 0.00 1.82
657 1096 7.435192 CCGGTTTCATTGCTTTTTAGATATTCC 59.565 37.037 0.00 0.00 0.00 3.01
666 1105 4.500716 CCAGTACCGGTTTCATTGCTTTTT 60.501 41.667 15.04 0.00 0.00 1.94
737 1176 2.832129 ACCTTCGTTCAGAGAGCCAATA 59.168 45.455 0.00 0.00 0.00 1.90
738 1177 1.625818 ACCTTCGTTCAGAGAGCCAAT 59.374 47.619 0.00 0.00 0.00 3.16
739 1178 1.000955 GACCTTCGTTCAGAGAGCCAA 59.999 52.381 0.00 0.00 0.00 4.52
740 1179 0.603569 GACCTTCGTTCAGAGAGCCA 59.396 55.000 0.00 0.00 0.00 4.75
903 1350 2.509131 TGATGGCAGAGAGAGAGAGAGA 59.491 50.000 0.00 0.00 0.00 3.10
904 1351 2.934887 TGATGGCAGAGAGAGAGAGAG 58.065 52.381 0.00 0.00 0.00 3.20
905 1352 3.117587 TGATGATGGCAGAGAGAGAGAGA 60.118 47.826 0.00 0.00 0.00 3.10
906 1353 3.005050 GTGATGATGGCAGAGAGAGAGAG 59.995 52.174 0.00 0.00 0.00 3.20
907 1354 2.957680 GTGATGATGGCAGAGAGAGAGA 59.042 50.000 0.00 0.00 0.00 3.10
908 1355 2.694109 TGTGATGATGGCAGAGAGAGAG 59.306 50.000 0.00 0.00 0.00 3.20
933 1380 7.571059 GCTTCTCTTCTCTCTTGTCAAAATGTC 60.571 40.741 0.00 0.00 0.00 3.06
937 1384 5.674525 TGCTTCTCTTCTCTCTTGTCAAAA 58.325 37.500 0.00 0.00 0.00 2.44
940 1387 3.305950 GCTGCTTCTCTTCTCTCTTGTCA 60.306 47.826 0.00 0.00 0.00 3.58
941 1388 3.253230 GCTGCTTCTCTTCTCTCTTGTC 58.747 50.000 0.00 0.00 0.00 3.18
976 1423 1.592948 TCCTCCTCCTCCGTCTTCTA 58.407 55.000 0.00 0.00 0.00 2.10
983 1430 0.683973 CATGGATTCCTCCTCCTCCG 59.316 60.000 3.95 0.00 42.59 4.63
1033 1528 4.245845 AGTGGTCTTCTTCTTCTTCGTC 57.754 45.455 0.00 0.00 0.00 4.20
1034 1529 4.022155 GGTAGTGGTCTTCTTCTTCTTCGT 60.022 45.833 0.00 0.00 0.00 3.85
1035 1530 4.487019 GGTAGTGGTCTTCTTCTTCTTCG 58.513 47.826 0.00 0.00 0.00 3.79
1036 1531 4.322877 GGGGTAGTGGTCTTCTTCTTCTTC 60.323 50.000 0.00 0.00 0.00 2.87
1037 1532 3.583526 GGGGTAGTGGTCTTCTTCTTCTT 59.416 47.826 0.00 0.00 0.00 2.52
1038 1533 3.174779 GGGGTAGTGGTCTTCTTCTTCT 58.825 50.000 0.00 0.00 0.00 2.85
1178 1679 0.903236 GAGAGTGGTGGGTAGGGTTC 59.097 60.000 0.00 0.00 0.00 3.62
1201 1703 4.092383 GGCATTTGCATGAACAAGATGAAC 59.908 41.667 4.74 0.00 44.36 3.18
1250 1752 4.142447 ACATAGTACTGTACTTGAGTGGCG 60.142 45.833 24.09 8.00 40.14 5.69
1257 1759 6.868864 AGCTGAAACACATAGTACTGTACTTG 59.131 38.462 24.09 21.22 40.14 3.16
1288 1791 9.813080 GTAATACAGTAAAGTTCAAGCTGAAAG 57.187 33.333 0.00 0.00 38.22 2.62
1305 1808 7.148188 CCATTGCATGAAGACTTGTAATACAGT 60.148 37.037 0.00 0.00 35.82 3.55
1308 1811 7.088589 ACCATTGCATGAAGACTTGTAATAC 57.911 36.000 0.00 0.00 35.82 1.89
1311 1814 5.048782 GTGACCATTGCATGAAGACTTGTAA 60.049 40.000 0.00 0.00 32.65 2.41
1366 1869 6.357198 CACGCCAATGAAAAGAAAAGAAATG 58.643 36.000 0.00 0.00 0.00 2.32
1427 1930 8.295288 TCGTACTAGAAAACTAGACAGAAAAGG 58.705 37.037 10.60 0.00 0.00 3.11
1428 1931 9.843334 ATCGTACTAGAAAACTAGACAGAAAAG 57.157 33.333 10.60 0.00 0.00 2.27
1431 1934 9.622004 CAAATCGTACTAGAAAACTAGACAGAA 57.378 33.333 10.60 0.00 0.00 3.02
1433 1936 9.622004 TTCAAATCGTACTAGAAAACTAGACAG 57.378 33.333 10.60 2.66 0.00 3.51
1531 2051 4.600692 AAACCACATAGAAAAGGTTGCC 57.399 40.909 0.00 0.00 43.17 4.52
1700 2222 6.538742 AGGGATGATTAAACTTGTCGTATGTG 59.461 38.462 0.00 0.00 0.00 3.21
1723 2245 3.934579 GTGGCATAAATTGGAGCAAAAGG 59.065 43.478 0.00 0.00 0.00 3.11
1739 2261 3.440173 CGTCATAGGAAAACAAGTGGCAT 59.560 43.478 0.00 0.00 0.00 4.40
1914 2436 6.953101 TGGACAAGAGGTATAAGCAAATGTA 58.047 36.000 0.00 0.00 0.00 2.29
1922 2444 5.776173 ACTCGATGGACAAGAGGTATAAG 57.224 43.478 11.13 0.00 36.40 1.73
2103 2626 8.603898 TCACCCTATATTTGTAAGAGAAGTCA 57.396 34.615 0.00 0.00 0.00 3.41
2109 2632 9.877178 GTATGGATCACCCTATATTTGTAAGAG 57.123 37.037 0.00 0.00 35.38 2.85
2121 2644 6.046286 TGTGTAGATAGGTATGGATCACCCTA 59.954 42.308 0.00 0.00 36.67 3.53
2122 2645 5.162870 TGTGTAGATAGGTATGGATCACCCT 60.163 44.000 0.00 0.00 36.67 4.34
2123 2646 5.084519 TGTGTAGATAGGTATGGATCACCC 58.915 45.833 0.00 0.00 36.67 4.61
2134 2657 9.330063 CATTACAAATCACATGTGTAGATAGGT 57.670 33.333 24.63 16.02 32.27 3.08
2277 2800 6.126449 GGGAAAATAAGTCACTCCCTCCTATT 60.126 42.308 0.00 0.00 42.25 1.73
2338 2861 2.672714 TCAACAATTCGTCCTCAGTCG 58.327 47.619 0.00 0.00 0.00 4.18
2388 2911 6.607735 AAAGGACAAAATGAAGTTTGCATG 57.392 33.333 3.32 0.00 41.33 4.06
2456 2979 4.424566 TCCGTACGGCGCACCTTC 62.425 66.667 29.64 0.00 39.71 3.46
2463 2986 1.800315 CAGTGTTCTCCGTACGGCG 60.800 63.158 29.64 23.94 40.95 6.46
2466 2989 2.410785 TTGACAGTGTTCTCCGTACG 57.589 50.000 8.69 8.69 0.00 3.67
2467 2990 5.345202 CACTTATTGACAGTGTTCTCCGTAC 59.655 44.000 0.00 0.00 37.47 3.67
2469 2992 4.038763 TCACTTATTGACAGTGTTCTCCGT 59.961 41.667 0.00 0.00 42.12 4.69
2470 2993 4.556233 TCACTTATTGACAGTGTTCTCCG 58.444 43.478 0.00 0.00 42.12 4.63
2471 2994 7.324178 ACTATCACTTATTGACAGTGTTCTCC 58.676 38.462 0.00 0.00 40.68 3.71
2498 3024 7.888021 TCCTTATTCTAATTCTTCTTTGTGGCA 59.112 33.333 0.00 0.00 0.00 4.92
2616 3142 8.216423 AGATTGCATTAGTTCTATTCAGTGGAT 58.784 33.333 0.00 0.00 0.00 3.41
2696 3222 0.320508 GTGTTCTCGGTGGGGTTCTC 60.321 60.000 0.00 0.00 0.00 2.87
2765 3291 4.098914 ACAAGTTACCTCCAAATCAGCA 57.901 40.909 0.00 0.00 0.00 4.41
2827 3353 5.989168 CCGTATTAGTCAGTGCATTATTCCA 59.011 40.000 0.00 0.00 0.00 3.53
3052 3582 9.755804 CTGAGTTGAACATATATAGTCATGTGT 57.244 33.333 0.00 0.00 35.59 3.72
3053 3583 9.755804 ACTGAGTTGAACATATATAGTCATGTG 57.244 33.333 0.00 0.00 35.59 3.21
3054 3584 9.973450 GACTGAGTTGAACATATATAGTCATGT 57.027 33.333 0.00 0.00 36.96 3.21
3055 3585 9.416794 GGACTGAGTTGAACATATATAGTCATG 57.583 37.037 0.00 0.00 35.08 3.07
3056 3586 9.373450 AGGACTGAGTTGAACATATATAGTCAT 57.627 33.333 0.00 0.00 35.08 3.06
3057 3587 8.768501 AGGACTGAGTTGAACATATATAGTCA 57.231 34.615 0.00 2.38 35.08 3.41
3058 3588 8.301002 GGAGGACTGAGTTGAACATATATAGTC 58.699 40.741 0.00 0.00 33.22 2.59
3059 3589 7.785028 TGGAGGACTGAGTTGAACATATATAGT 59.215 37.037 0.00 0.00 0.00 2.12
3060 3590 8.183104 TGGAGGACTGAGTTGAACATATATAG 57.817 38.462 0.00 0.00 0.00 1.31
3061 3591 8.004801 TCTGGAGGACTGAGTTGAACATATATA 58.995 37.037 0.00 0.00 0.00 0.86
3102 3632 6.837568 AGTTGTAGAATTCGAGGATACCCTTA 59.162 38.462 0.00 0.00 44.53 2.69
3103 3633 5.661759 AGTTGTAGAATTCGAGGATACCCTT 59.338 40.000 0.00 0.00 44.53 3.95
3117 3648 3.197983 TGGGATGGGGAAGTTGTAGAAT 58.802 45.455 0.00 0.00 0.00 2.40
3207 3738 1.621317 TCACATCTGACCGGCAAAGTA 59.379 47.619 0.00 0.00 0.00 2.24
3291 3822 6.595716 GTGACCTGTGAGAATACTTTTATGCT 59.404 38.462 0.00 0.00 0.00 3.79
3624 4157 9.401058 CTTTTGGAATCCAGTATAAGTGAATCT 57.599 33.333 0.86 0.00 33.81 2.40
3673 4207 7.857734 TCAGAATGTGTCTTAGTTCAAACAA 57.142 32.000 0.00 0.00 37.40 2.83
3674 4208 7.857734 TTCAGAATGTGTCTTAGTTCAAACA 57.142 32.000 0.00 0.00 37.40 2.83
3675 4209 8.017946 GGATTCAGAATGTGTCTTAGTTCAAAC 58.982 37.037 0.00 0.00 37.40 2.93
3700 4234 6.710744 AGTACTAGTTTGAATGGACAAAGTGG 59.289 38.462 0.00 0.00 42.84 4.00
3806 4342 5.845985 TCTTCTTATTTTCAGTGACTGCG 57.154 39.130 7.93 0.00 0.00 5.18
3852 4389 8.306038 CAATTGAATGATCACAGGAAGGTTTTA 58.694 33.333 0.00 0.00 34.61 1.52
3868 4405 3.979948 CACACAAGTGCCAATTGAATGA 58.020 40.909 12.36 0.00 39.21 2.57
3889 4426 3.146066 TGTTGTGTTCCAGACTATTGGC 58.854 45.455 0.00 0.00 38.16 4.52
3973 4510 5.349543 GCTTTCATGCCATTCCAAAGTAAAG 59.650 40.000 0.00 0.00 0.00 1.85
4036 4573 4.277476 AGGATCTCTTCGTCTGAACAGAT 58.723 43.478 7.77 0.00 41.00 2.90
4185 4722 3.325870 TGTCATCTTAAGTTCTGGTGCG 58.674 45.455 1.63 0.00 0.00 5.34
4194 4731 9.566432 GATTCCTTTCCATATGTCATCTTAAGT 57.434 33.333 1.63 0.00 0.00 2.24
4295 4832 5.988287 TGCAATAGACATCACCAACATAGA 58.012 37.500 0.00 0.00 0.00 1.98
4299 4836 4.158209 CCATTGCAATAGACATCACCAACA 59.842 41.667 12.53 0.00 0.00 3.33
4352 4890 6.559810 CAATTAAATTGGTCGAAGGCATGTA 58.440 36.000 0.00 0.00 36.63 2.29
4471 5009 1.148273 AAACTCTGGGCGCTTGTCA 59.852 52.632 7.64 0.00 0.00 3.58
4742 5284 6.938596 AGTTACCAAACTATACACACCTTTCC 59.061 38.462 0.00 0.00 44.26 3.13
4966 5655 6.100279 TGGCACTGATAGATTCTATTTGGACT 59.900 38.462 7.61 0.00 0.00 3.85
4977 5666 5.999044 AGTCATTCTTGGCACTGATAGATT 58.001 37.500 0.00 0.00 0.00 2.40
5035 5725 2.827555 CATGTCTCTTCGTTTTGACGC 58.172 47.619 0.00 0.00 32.64 5.19
5037 5727 3.878086 TGCATGTCTCTTCGTTTTGAC 57.122 42.857 0.00 0.00 0.00 3.18
5262 5958 2.917971 CTCTTCGACCACAGAACGAATC 59.082 50.000 0.00 0.00 43.22 2.52
5332 6042 1.466025 AACCAGGACCTTGCGACGTA 61.466 55.000 0.00 0.00 0.00 3.57
5334 6044 1.597027 AAACCAGGACCTTGCGACG 60.597 57.895 0.00 0.00 0.00 5.12
5338 6048 1.806247 GCAAACAAACCAGGACCTTGC 60.806 52.381 0.00 0.00 0.00 4.01
5538 6248 2.978824 GTAGAACAGGAGCCGCCA 59.021 61.111 0.00 0.00 40.02 5.69


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

AutoCloner maintained by Alex Coulton.