Multiple sequence alignment - TraesCS7A01G188900

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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 TraesCS7A01G188900 chr7A 100.000 3192 0 0 1 3192 145460887 145464078 0.000000e+00 5895.0
1 TraesCS7A01G188900 chr7A 90.476 84 5 3 2593 2676 581879575 581879495 1.210000e-19 108.0
2 TraesCS7A01G188900 chr7B 92.324 1876 75 30 721 2570 107562886 107564718 0.000000e+00 2603.0
3 TraesCS7A01G188900 chr7B 80.892 471 50 15 2759 3190 107602585 107603054 5.100000e-88 335.0
4 TraesCS7A01G188900 chr7B 81.277 235 23 9 2469 2686 539863299 539863069 1.520000e-38 171.0
5 TraesCS7A01G188900 chr7B 79.268 164 11 6 2593 2733 107564839 107565002 3.390000e-15 93.5
6 TraesCS7A01G188900 chr7D 92.403 1856 74 35 595 2443 144148404 144146609 0.000000e+00 2584.0
7 TraesCS7A01G188900 chr7D 92.181 972 52 14 1479 2443 144145607 144144653 0.000000e+00 1352.0
8 TraesCS7A01G188900 chr7D 92.078 972 51 17 1479 2443 144146584 144145632 0.000000e+00 1345.0
9 TraesCS7A01G188900 chr7D 85.297 891 50 28 1834 2696 144144239 144143402 0.000000e+00 845.0
10 TraesCS7A01G188900 chr7D 97.849 372 8 0 1479 1850 144144628 144144257 0.000000e+00 643.0
11 TraesCS7A01G188900 chr7D 80.739 514 73 12 34 523 143739157 143739668 8.360000e-101 377.0
12 TraesCS7A01G188900 chr7D 82.197 264 40 5 7 269 619803309 619803052 1.490000e-53 220.0
13 TraesCS7A01G188900 chr6B 80.387 362 61 9 54 410 452829248 452829604 1.890000e-67 267.0
14 TraesCS7A01G188900 chr6B 78.994 338 60 8 54 387 452941666 452941996 1.490000e-53 220.0
15 TraesCS7A01G188900 chr6B 78.519 270 43 14 115 375 272010298 272010035 2.550000e-36 163.0
16 TraesCS7A01G188900 chr6B 77.517 298 44 14 2853 3133 662088388 662088679 1.190000e-34 158.0
17 TraesCS7A01G188900 chr2B 87.124 233 19 6 2461 2687 604992787 604992560 1.470000e-63 254.0
18 TraesCS7A01G188900 chr2B 79.352 247 26 11 2461 2686 22785683 22785441 1.980000e-32 150.0
19 TraesCS7A01G188900 chr1A 80.294 340 60 7 10 345 527695807 527695471 1.900000e-62 250.0
20 TraesCS7A01G188900 chr1A 76.471 340 64 14 102 428 310866114 310866450 1.520000e-38 171.0
21 TraesCS7A01G188900 chr1A 77.600 250 16 11 2466 2676 589823402 589823650 7.240000e-22 115.0
22 TraesCS7A01G188900 chr4D 80.165 242 42 6 115 352 399642709 399642470 3.270000e-40 176.0
23 TraesCS7A01G188900 chr4D 79.231 260 27 14 2956 3190 43611761 43611504 4.260000e-34 156.0
24 TraesCS7A01G188900 chr4D 93.333 45 3 0 1310 1354 320212577 320212533 2.050000e-07 67.6
25 TraesCS7A01G188900 chr2A 82.251 231 15 9 2461 2666 657517532 657517303 3.270000e-40 176.0
26 TraesCS7A01G188900 chr2A 85.517 145 10 9 2990 3130 124403431 124403568 1.190000e-29 141.0
27 TraesCS7A01G188900 chr6A 78.682 258 47 8 12 265 1722027 1722280 7.080000e-37 165.0
28 TraesCS7A01G188900 chr5D 88.095 126 11 4 2988 3110 478211370 478211494 2.570000e-31 147.0
29 TraesCS7A01G188900 chr5D 81.122 196 22 12 2947 3133 44603753 44603564 3.320000e-30 143.0
30 TraesCS7A01G188900 chr5D 88.235 51 6 0 3140 3190 30564740 30564690 9.560000e-06 62.1
31 TraesCS7A01G188900 chr2D 85.315 143 11 9 2995 3130 166561917 166561778 4.290000e-29 139.0
32 TraesCS7A01G188900 chr4B 83.448 145 15 8 2989 3129 420107288 420107149 3.340000e-25 126.0
33 TraesCS7A01G188900 chr4B 91.667 48 4 0 1307 1354 400397577 400397624 2.050000e-07 67.6
34 TraesCS7A01G188900 chr4B 94.286 35 2 0 3155 3189 391140307 391140341 2.000000e-03 54.7
35 TraesCS7A01G188900 chr4A 76.371 237 34 15 2896 3120 734436736 734436510 1.210000e-19 108.0
36 TraesCS7A01G188900 chr4A 91.667 48 4 0 1307 1354 152650442 152650489 2.050000e-07 67.6
37 TraesCS7A01G188900 chr4A 100.000 34 0 0 3157 3190 2266539 2266506 2.660000e-06 63.9
38 TraesCS7A01G188900 chr5A 84.615 65 9 1 3127 3190 523030678 523030614 2.660000e-06 63.9
39 TraesCS7A01G188900 chr1D 85.246 61 9 0 3130 3190 54903218 54903278 2.660000e-06 63.9
40 TraesCS7A01G188900 chr5B 88.000 50 6 0 3140 3189 706723422 706723471 3.440000e-05 60.2


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 TraesCS7A01G188900 chr7A 145460887 145464078 3191 False 5895.00 5895 100.0000 1 3192 1 chr7A.!!$F1 3191
1 TraesCS7A01G188900 chr7B 107562886 107565002 2116 False 1348.25 2603 85.7960 721 2733 2 chr7B.!!$F2 2012
2 TraesCS7A01G188900 chr7D 144143402 144148404 5002 True 1353.80 2584 91.9616 595 2696 5 chr7D.!!$R2 2101
3 TraesCS7A01G188900 chr7D 143739157 143739668 511 False 377.00 377 80.7390 34 523 1 chr7D.!!$F1 489

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
99 100 0.029577 TGAGGGGCCCATACACCATA 60.030 55.0 27.72 0.0 0.00 2.74 F
545 570 0.179078 TTGTACGGCAACACGGTTCT 60.179 50.0 0.00 0.0 38.39 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1462 0.527817 ATGATCGAACCGGAGCGTTC 60.528 55.0 9.46 15.65 39.03 3.95 R
2217 5219 0.239879 AAGCGTACGCATTTTGGTGG 59.760 50.0 38.58 0.00 44.88 4.61 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
19 20 3.443045 CATGCCGCTCACCCCAAC 61.443 66.667 0.00 0.00 0.00 3.77
20 21 3.965258 ATGCCGCTCACCCCAACA 61.965 61.111 0.00 0.00 0.00 3.33
21 22 3.505790 ATGCCGCTCACCCCAACAA 62.506 57.895 0.00 0.00 0.00 2.83
22 23 2.676471 GCCGCTCACCCCAACAAT 60.676 61.111 0.00 0.00 0.00 2.71
23 24 2.700773 GCCGCTCACCCCAACAATC 61.701 63.158 0.00 0.00 0.00 2.67
24 25 1.303236 CCGCTCACCCCAACAATCA 60.303 57.895 0.00 0.00 0.00 2.57
25 26 1.308069 CCGCTCACCCCAACAATCAG 61.308 60.000 0.00 0.00 0.00 2.90
26 27 1.885871 GCTCACCCCAACAATCAGC 59.114 57.895 0.00 0.00 0.00 4.26
27 28 1.598701 GCTCACCCCAACAATCAGCC 61.599 60.000 0.00 0.00 0.00 4.85
28 29 0.967380 CTCACCCCAACAATCAGCCC 60.967 60.000 0.00 0.00 0.00 5.19
29 30 2.035626 ACCCCAACAATCAGCCCG 59.964 61.111 0.00 0.00 0.00 6.13
30 31 3.451894 CCCCAACAATCAGCCCGC 61.452 66.667 0.00 0.00 0.00 6.13
31 32 2.676121 CCCAACAATCAGCCCGCA 60.676 61.111 0.00 0.00 0.00 5.69
32 33 2.703798 CCCAACAATCAGCCCGCAG 61.704 63.158 0.00 0.00 0.00 5.18
51 52 3.842820 CAGTCTGTACTGTGACATCAGG 58.157 50.000 13.60 0.00 46.76 3.86
54 55 2.232208 TCTGTACTGTGACATCAGGCAG 59.768 50.000 16.29 16.29 40.37 4.85
72 73 0.610687 AGAGCTTTCGGGAGGAACTG 59.389 55.000 0.00 0.00 41.55 3.16
80 81 2.637383 GGGAGGAACTGACGACGCT 61.637 63.158 0.00 0.00 41.55 5.07
83 84 0.455295 GAGGAACTGACGACGCTGAG 60.455 60.000 0.00 0.00 41.55 3.35
84 85 1.444553 GGAACTGACGACGCTGAGG 60.445 63.158 0.00 0.00 0.00 3.86
85 86 1.444553 GAACTGACGACGCTGAGGG 60.445 63.158 0.00 0.00 0.00 4.30
86 87 2.820767 GAACTGACGACGCTGAGGGG 62.821 65.000 0.51 0.00 0.00 4.79
93 94 3.462199 GACGCTGAGGGGCCCATAC 62.462 68.421 27.72 16.09 0.00 2.39
99 100 0.029577 TGAGGGGCCCATACACCATA 60.030 55.000 27.72 0.00 0.00 2.74
105 106 1.427368 GGCCCATACACCATAATCCCA 59.573 52.381 0.00 0.00 0.00 4.37
134 135 6.280643 GTGATTAGTGTGTATATGCCAGTGA 58.719 40.000 0.00 0.00 0.00 3.41
153 154 6.350864 CCAGTGACAGTCTCAGATCAAATACT 60.351 42.308 1.31 0.00 0.00 2.12
161 162 9.381033 CAGTCTCAGATCAAATACTCAAATCTT 57.619 33.333 0.00 0.00 0.00 2.40
165 166 9.770503 CTCAGATCAAATACTCAAATCTTGTTG 57.229 33.333 0.00 0.00 0.00 3.33
178 179 7.866729 TCAAATCTTGTTGAGCGTGTTATTAA 58.133 30.769 0.00 0.00 32.56 1.40
198 199 9.893634 TTATTAAGAAATAACCTTGGACATCGA 57.106 29.630 0.00 0.00 33.56 3.59
199 200 7.605410 TTAAGAAATAACCTTGGACATCGAC 57.395 36.000 0.00 0.00 0.00 4.20
224 225 1.614824 CCAGGCCCACTTCTCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
236 237 4.080243 CACTTCTCTCCTAGGTGGTCTCTA 60.080 50.000 9.08 0.00 37.07 2.43
252 253 0.606604 TCTACCTGCCTTGTCGTTCC 59.393 55.000 0.00 0.00 0.00 3.62
258 259 3.411351 CCTTGTCGTTCCGCCACG 61.411 66.667 0.00 0.00 41.78 4.94
271 272 1.006825 CGCCACGTTGAATCACTCGA 61.007 55.000 12.46 0.00 0.00 4.04
303 304 1.864251 ACCCAGGCCTATCACTACCTA 59.136 52.381 3.98 0.00 0.00 3.08
327 328 4.689612 TGGTACCATCTATTCCTTCAGC 57.310 45.455 11.60 0.00 0.00 4.26
328 329 3.391296 TGGTACCATCTATTCCTTCAGCC 59.609 47.826 11.60 0.00 0.00 4.85
330 331 2.781667 ACCATCTATTCCTTCAGCCCT 58.218 47.619 0.00 0.00 0.00 5.19
331 332 3.126453 ACCATCTATTCCTTCAGCCCTT 58.874 45.455 0.00 0.00 0.00 3.95
340 341 2.028385 TCCTTCAGCCCTTAGTTCGAAC 60.028 50.000 20.71 20.71 0.00 3.95
346 347 5.741011 TCAGCCCTTAGTTCGAACATTATT 58.259 37.500 28.78 11.34 0.00 1.40
390 391 5.830799 AGTATATCTGTGATCATTGGCCA 57.169 39.130 0.00 0.00 0.00 5.36
394 395 3.438216 TCTGTGATCATTGGCCAAAGA 57.562 42.857 24.51 24.51 0.00 2.52
397 398 3.084039 TGTGATCATTGGCCAAAGAGAC 58.916 45.455 25.94 23.03 0.00 3.36
400 401 1.909700 TCATTGGCCAAAGAGACCAC 58.090 50.000 24.71 0.00 31.83 4.16
401 402 0.523072 CATTGGCCAAAGAGACCACG 59.477 55.000 24.71 0.00 31.83 4.94
404 405 2.032681 GCCAAAGAGACCACGGCT 59.967 61.111 0.00 0.00 39.73 5.52
411 412 3.914426 AAGAGACCACGGCTCAATAAT 57.086 42.857 0.00 0.00 34.85 1.28
412 413 3.185246 AGAGACCACGGCTCAATAATG 57.815 47.619 0.00 0.00 34.85 1.90
419 420 3.565482 CCACGGCTCAATAATGTAGCAAT 59.435 43.478 0.00 0.00 38.01 3.56
421 422 3.003689 ACGGCTCAATAATGTAGCAATGC 59.996 43.478 0.00 0.00 38.01 3.56
428 429 4.981806 ATAATGTAGCAATGCAAACGGT 57.018 36.364 8.35 0.08 0.00 4.83
429 430 2.634982 ATGTAGCAATGCAAACGGTG 57.365 45.000 8.35 0.00 0.00 4.94
431 432 1.535028 TGTAGCAATGCAAACGGTGAG 59.465 47.619 8.35 0.00 0.00 3.51
432 433 1.804151 GTAGCAATGCAAACGGTGAGA 59.196 47.619 8.35 0.00 0.00 3.27
433 434 0.593128 AGCAATGCAAACGGTGAGAC 59.407 50.000 8.35 0.00 0.00 3.36
445 470 1.813178 CGGTGAGACTCTAGCAGACAA 59.187 52.381 3.68 0.00 0.00 3.18
449 474 4.459685 GGTGAGACTCTAGCAGACAACTAA 59.540 45.833 3.68 0.00 0.00 2.24
469 494 6.475207 ACTAACATTTATTTACTTCGCAGCG 58.525 36.000 9.06 9.06 0.00 5.18
495 520 4.759782 CACGGGTGATTCAAGATAGTTCT 58.240 43.478 0.00 0.00 0.00 3.01
496 521 5.681437 GCACGGGTGATTCAAGATAGTTCTA 60.681 44.000 2.38 0.00 0.00 2.10
497 522 6.338146 CACGGGTGATTCAAGATAGTTCTAA 58.662 40.000 0.00 0.00 0.00 2.10
541 566 3.920144 TTTTTGTACGGCAACACGG 57.080 47.368 0.00 0.00 36.72 4.94
542 567 1.093159 TTTTTGTACGGCAACACGGT 58.907 45.000 0.00 0.00 36.72 4.83
543 568 1.093159 TTTTGTACGGCAACACGGTT 58.907 45.000 0.00 0.00 36.72 4.44
544 569 0.656785 TTTGTACGGCAACACGGTTC 59.343 50.000 0.00 0.00 36.72 3.62
545 570 0.179078 TTGTACGGCAACACGGTTCT 60.179 50.000 0.00 0.00 38.39 3.01
546 571 0.672889 TGTACGGCAACACGGTTCTA 59.327 50.000 0.00 0.00 38.39 2.10
547 572 1.068281 TGTACGGCAACACGGTTCTAA 59.932 47.619 0.00 0.00 38.39 2.10
548 573 2.288948 TGTACGGCAACACGGTTCTAAT 60.289 45.455 0.00 0.00 38.39 1.73
549 574 1.886886 ACGGCAACACGGTTCTAATT 58.113 45.000 0.00 0.00 38.39 1.40
550 575 1.802365 ACGGCAACACGGTTCTAATTC 59.198 47.619 0.00 0.00 38.39 2.17
551 576 2.073816 CGGCAACACGGTTCTAATTCT 58.926 47.619 0.00 0.00 0.00 2.40
552 577 3.255725 CGGCAACACGGTTCTAATTCTA 58.744 45.455 0.00 0.00 0.00 2.10
553 578 3.061697 CGGCAACACGGTTCTAATTCTAC 59.938 47.826 0.00 0.00 0.00 2.59
554 579 4.251268 GGCAACACGGTTCTAATTCTACT 58.749 43.478 0.00 0.00 0.00 2.57
555 580 4.694037 GGCAACACGGTTCTAATTCTACTT 59.306 41.667 0.00 0.00 0.00 2.24
556 581 5.180680 GGCAACACGGTTCTAATTCTACTTT 59.819 40.000 0.00 0.00 0.00 2.66
557 582 6.293790 GGCAACACGGTTCTAATTCTACTTTT 60.294 38.462 0.00 0.00 0.00 2.27
558 583 6.577427 GCAACACGGTTCTAATTCTACTTTTG 59.423 38.462 0.00 0.00 0.00 2.44
559 584 6.237313 ACACGGTTCTAATTCTACTTTTGC 57.763 37.500 0.00 0.00 0.00 3.68
560 585 5.761234 ACACGGTTCTAATTCTACTTTTGCA 59.239 36.000 0.00 0.00 0.00 4.08
561 586 6.261381 ACACGGTTCTAATTCTACTTTTGCAA 59.739 34.615 0.00 0.00 0.00 4.08
562 587 6.577427 CACGGTTCTAATTCTACTTTTGCAAC 59.423 38.462 0.00 0.00 0.00 4.17
563 588 5.788531 CGGTTCTAATTCTACTTTTGCAACG 59.211 40.000 0.00 0.00 0.00 4.10
564 589 5.567915 GGTTCTAATTCTACTTTTGCAACGC 59.432 40.000 0.00 0.00 0.00 4.84
565 590 5.933187 TCTAATTCTACTTTTGCAACGCA 57.067 34.783 0.00 0.00 36.47 5.24
566 591 5.685841 TCTAATTCTACTTTTGCAACGCAC 58.314 37.500 0.00 0.00 38.71 5.34
567 592 3.980646 ATTCTACTTTTGCAACGCACA 57.019 38.095 0.00 0.00 38.71 4.57
568 593 3.766676 TTCTACTTTTGCAACGCACAA 57.233 38.095 0.00 0.00 38.71 3.33
570 595 2.032799 TCTACTTTTGCAACGCACAAGG 59.967 45.455 16.64 5.89 46.58 3.61
571 596 0.814457 ACTTTTGCAACGCACAAGGA 59.186 45.000 16.64 0.00 46.58 3.36
572 597 1.202290 ACTTTTGCAACGCACAAGGAG 60.202 47.619 16.64 2.58 46.58 3.69
573 598 1.065401 CTTTTGCAACGCACAAGGAGA 59.935 47.619 0.00 0.00 41.06 3.71
574 599 1.317613 TTTGCAACGCACAAGGAGAT 58.682 45.000 0.00 0.00 38.71 2.75
575 600 0.592637 TTGCAACGCACAAGGAGATG 59.407 50.000 0.00 0.00 38.71 2.90
576 601 0.534877 TGCAACGCACAAGGAGATGT 60.535 50.000 0.00 0.00 31.71 3.06
582 607 3.639099 CACAAGGAGATGTGCTGGT 57.361 52.632 0.00 0.00 43.67 4.00
583 608 1.446907 CACAAGGAGATGTGCTGGTC 58.553 55.000 0.00 0.00 43.67 4.02
584 609 1.002888 CACAAGGAGATGTGCTGGTCT 59.997 52.381 0.00 0.00 43.67 3.85
585 610 1.277557 ACAAGGAGATGTGCTGGTCTC 59.722 52.381 0.00 4.80 40.06 3.36
586 611 1.554160 CAAGGAGATGTGCTGGTCTCT 59.446 52.381 10.94 0.00 40.50 3.10
587 612 2.762887 CAAGGAGATGTGCTGGTCTCTA 59.237 50.000 10.94 0.00 40.50 2.43
588 613 3.107402 AGGAGATGTGCTGGTCTCTAA 57.893 47.619 10.94 0.00 40.50 2.10
589 614 2.763448 AGGAGATGTGCTGGTCTCTAAC 59.237 50.000 10.94 0.00 40.50 2.34
590 615 2.497675 GGAGATGTGCTGGTCTCTAACA 59.502 50.000 10.94 0.00 40.50 2.41
591 616 3.055819 GGAGATGTGCTGGTCTCTAACAA 60.056 47.826 10.94 0.00 40.50 2.83
592 617 4.383552 GGAGATGTGCTGGTCTCTAACAAT 60.384 45.833 10.94 0.00 40.50 2.71
593 618 4.511527 AGATGTGCTGGTCTCTAACAATG 58.488 43.478 0.00 0.00 0.00 2.82
635 660 1.191535 TGGATCGGACGGTTGAAGAT 58.808 50.000 0.00 0.00 0.00 2.40
641 666 2.424601 TCGGACGGTTGAAGATCGTAAT 59.575 45.455 0.00 0.00 37.25 1.89
645 670 6.017192 TCGGACGGTTGAAGATCGTAATATAA 60.017 38.462 0.00 0.00 37.25 0.98
655 680 9.529325 TGAAGATCGTAATATAAGTCACCTTTG 57.471 33.333 0.00 0.00 31.89 2.77
675 700 2.360726 GGTCGGGAAAATGGCGGT 60.361 61.111 0.00 0.00 0.00 5.68
677 702 0.677414 GGTCGGGAAAATGGCGGTTA 60.677 55.000 0.00 0.00 0.00 2.85
825 850 1.202188 GCTTGCCACCGAATTAAGCTC 60.202 52.381 0.00 0.00 40.29 4.09
845 870 0.960861 GCTGAAAAGTTCCCCTCCCG 60.961 60.000 0.00 0.00 0.00 5.14
961 990 5.105310 TCAACCAGGACTTGATTAGTAGAGC 60.105 44.000 0.00 0.00 37.17 4.09
982 1011 2.970974 GAGGCCTGAACAAGCACGC 61.971 63.158 12.00 0.00 0.00 5.34
999 1028 2.643644 GCGCTCGCAGATCATCGAC 61.644 63.158 9.59 3.39 41.49 4.20
1404 1433 2.731976 CACTTCACCAACTTCTCGTAGC 59.268 50.000 0.00 0.00 0.00 3.58
1405 1434 2.628657 ACTTCACCAACTTCTCGTAGCT 59.371 45.455 0.00 0.00 0.00 3.32
1407 1436 4.082679 ACTTCACCAACTTCTCGTAGCTAG 60.083 45.833 0.00 0.00 0.00 3.42
1408 1437 3.682696 TCACCAACTTCTCGTAGCTAGA 58.317 45.455 0.00 0.00 0.00 2.43
1409 1438 3.439476 TCACCAACTTCTCGTAGCTAGAC 59.561 47.826 0.00 0.00 0.00 2.59
1410 1439 3.190744 CACCAACTTCTCGTAGCTAGACA 59.809 47.826 0.00 0.00 0.00 3.41
1430 1459 5.010516 AGACAGCATGGTAGTATCATGAGAC 59.989 44.000 24.68 12.62 43.25 3.36
1432 1461 5.306419 ACAGCATGGTAGTATCATGAGACAT 59.694 40.000 24.68 9.85 43.25 3.06
1433 1462 5.638234 CAGCATGGTAGTATCATGAGACATG 59.362 44.000 24.68 16.33 43.25 3.21
1434 1463 5.541484 AGCATGGTAGTATCATGAGACATGA 59.459 40.000 24.68 15.14 43.25 3.07
1455 2460 0.661780 CGCTCCGGTTCGATCATCTC 60.662 60.000 11.58 0.00 0.00 2.75
1457 2462 1.000283 GCTCCGGTTCGATCATCTCAT 60.000 52.381 0.00 0.00 0.00 2.90
1458 2463 2.924454 GCTCCGGTTCGATCATCTCATC 60.924 54.545 0.00 0.00 0.00 2.92
1459 2464 2.556189 CTCCGGTTCGATCATCTCATCT 59.444 50.000 0.00 0.00 0.00 2.90
1460 2465 2.294512 TCCGGTTCGATCATCTCATCTG 59.705 50.000 0.00 0.00 0.00 2.90
1461 2466 2.294512 CCGGTTCGATCATCTCATCTGA 59.705 50.000 0.00 0.00 0.00 3.27
1462 2467 3.304257 CGGTTCGATCATCTCATCTGAC 58.696 50.000 0.00 0.00 0.00 3.51
1463 2468 3.004210 CGGTTCGATCATCTCATCTGACT 59.996 47.826 0.00 0.00 0.00 3.41
1471 2476 2.907458 TCTCATCTGACTGAGACCCA 57.093 50.000 12.65 0.00 45.13 4.51
1477 2482 2.512515 GACTGAGACCCATGGCGC 60.513 66.667 6.09 0.00 0.00 6.53
1933 4935 2.029964 GCCACGTTCCAGTTCGGA 59.970 61.111 0.00 0.00 44.40 4.55
1969 4971 1.592669 CCAGGACATCATCGACCGC 60.593 63.158 0.00 0.00 0.00 5.68
2150 5152 3.243892 CGCTCGAGACGCTCAAGC 61.244 66.667 18.75 9.01 37.78 4.01
2202 5204 3.795041 CAGCTAGCCTGCCTGCCT 61.795 66.667 12.13 0.00 34.21 4.75
2203 5205 3.795041 AGCTAGCCTGCCTGCCTG 61.795 66.667 12.13 0.00 0.00 4.85
2205 5207 4.871910 CTAGCCTGCCTGCCTGCC 62.872 72.222 0.00 0.00 0.00 4.85
2238 5240 0.165079 ACCAAAATGCGTACGCTTCG 59.835 50.000 36.99 20.26 42.51 3.79
2255 5257 4.564116 GACATGCATGGGCGCTGC 62.564 66.667 29.41 12.75 45.35 5.25
2282 5284 6.961554 GCTGTGTGTTGTCTTAATTATACTGC 59.038 38.462 0.00 0.00 0.00 4.40
2283 5285 7.056002 TGTGTGTTGTCTTAATTATACTGCG 57.944 36.000 0.00 0.00 0.00 5.18
2284 5286 6.091577 TGTGTGTTGTCTTAATTATACTGCGG 59.908 38.462 0.00 0.00 0.00 5.69
2305 5307 3.365969 GGGTGCTTCGATTGTAACCAAAG 60.366 47.826 6.30 0.00 33.44 2.77
2315 5317 6.984474 TCGATTGTAACCAAAGTAGGATGATC 59.016 38.462 0.00 0.00 33.44 2.92
2317 5319 5.925506 TGTAACCAAAGTAGGATGATCGA 57.074 39.130 0.00 0.00 0.00 3.59
2318 5320 6.288941 TGTAACCAAAGTAGGATGATCGAA 57.711 37.500 0.00 0.00 0.00 3.71
2319 5321 6.703319 TGTAACCAAAGTAGGATGATCGAAA 58.297 36.000 0.00 0.00 0.00 3.46
2320 5322 7.162761 TGTAACCAAAGTAGGATGATCGAAAA 58.837 34.615 0.00 0.00 0.00 2.29
2321 5323 7.827236 TGTAACCAAAGTAGGATGATCGAAAAT 59.173 33.333 0.00 0.00 0.00 1.82
2322 5324 7.703058 AACCAAAGTAGGATGATCGAAAATT 57.297 32.000 0.00 0.00 0.00 1.82
2323 5325 7.321745 ACCAAAGTAGGATGATCGAAAATTC 57.678 36.000 0.00 0.00 0.00 2.17
2324 5326 7.112779 ACCAAAGTAGGATGATCGAAAATTCT 58.887 34.615 0.00 0.00 0.00 2.40
2325 5327 8.265055 ACCAAAGTAGGATGATCGAAAATTCTA 58.735 33.333 0.00 0.00 0.00 2.10
2326 5328 8.768955 CCAAAGTAGGATGATCGAAAATTCTAG 58.231 37.037 0.00 0.00 0.00 2.43
2327 5329 8.768955 CAAAGTAGGATGATCGAAAATTCTAGG 58.231 37.037 0.00 0.00 0.00 3.02
2328 5330 7.841282 AGTAGGATGATCGAAAATTCTAGGA 57.159 36.000 0.00 0.00 0.00 2.94
2329 5331 8.429237 AGTAGGATGATCGAAAATTCTAGGAT 57.571 34.615 0.00 0.00 0.00 3.24
2330 5332 8.310382 AGTAGGATGATCGAAAATTCTAGGATG 58.690 37.037 0.00 0.00 0.00 3.51
2331 5333 7.308450 AGGATGATCGAAAATTCTAGGATGA 57.692 36.000 0.00 0.00 0.00 2.92
2433 5441 5.314718 ACCAGGATCATGCATCTATCAAA 57.685 39.130 16.59 0.00 0.00 2.69
2437 5445 6.316640 CCAGGATCATGCATCTATCAAATCTC 59.683 42.308 16.59 2.98 0.00 2.75
2443 5451 6.935208 TCATGCATCTATCAAATCTCAAGAGG 59.065 38.462 0.00 0.00 0.00 3.69
2466 5474 5.123344 GGCCACTATTAAGACGTTGATGTTT 59.877 40.000 0.00 0.00 0.00 2.83
2467 5475 6.314400 GGCCACTATTAAGACGTTGATGTTTA 59.686 38.462 0.00 0.00 0.00 2.01
2473 5481 4.985044 AAGACGTTGATGTTTAAGACGG 57.015 40.909 0.00 0.00 37.99 4.79
2486 5494 7.972832 TGTTTAAGACGGTGATGTTCTATTT 57.027 32.000 0.00 0.00 0.00 1.40
2510 5518 7.236674 TGCATGTGAAATTTCAAGTTCAAAG 57.763 32.000 22.07 13.03 43.48 2.77
2524 5536 6.938030 TCAAGTTCAAAGACGGTACCATTTAT 59.062 34.615 13.54 0.00 0.00 1.40
2533 5546 4.894784 ACGGTACCATTTATGAGCTATGG 58.105 43.478 13.54 10.38 43.55 2.74
2553 5573 5.314718 TGGAATCAGCCATGAATAGTGAT 57.685 39.130 0.00 0.00 39.39 3.06
2593 5697 5.721876 TTCATTGCTGCTTTTGTCTTTTG 57.278 34.783 0.00 0.00 0.00 2.44
2594 5698 4.121317 TCATTGCTGCTTTTGTCTTTTGG 58.879 39.130 0.00 0.00 0.00 3.28
2595 5699 3.608316 TTGCTGCTTTTGTCTTTTGGT 57.392 38.095 0.00 0.00 0.00 3.67
2601 5721 5.050837 GCTGCTTTTGTCTTTTGGTAATGTG 60.051 40.000 0.00 0.00 0.00 3.21
2651 5778 9.227490 CTAATAGAACATCACACTCTTAAGACG 57.773 37.037 0.00 0.91 0.00 4.18
2688 5818 8.293114 TGAGATTTTATTTTTGAAACTTCGCC 57.707 30.769 0.00 0.00 0.00 5.54
2708 5851 2.036256 AAGGGTGCTGATGTGCCC 59.964 61.111 0.00 0.00 41.36 5.36
2746 5889 9.920946 AGGAGACTAGGAAAATATATGCAAAAA 57.079 29.630 0.00 0.00 40.61 1.94
2929 6072 9.834628 AAACGTGTATAGAAAAATGTTACCATG 57.165 29.630 0.00 0.00 0.00 3.66
2930 6073 8.556213 ACGTGTATAGAAAAATGTTACCATGT 57.444 30.769 0.00 0.00 0.00 3.21
2931 6074 9.656040 ACGTGTATAGAAAAATGTTACCATGTA 57.344 29.630 0.00 0.00 0.00 2.29
3037 6180 9.594478 AAAGGATTTGAAAAATTCTAAACGTGT 57.406 25.926 0.00 0.00 36.60 4.49
3053 6196 9.866936 TCTAAACGTGTATACAAAAATGTTGAC 57.133 29.630 7.25 0.00 0.00 3.18
3054 6197 7.917720 AAACGTGTATACAAAAATGTTGACC 57.082 32.000 7.25 0.00 0.00 4.02
3055 6198 6.621316 ACGTGTATACAAAAATGTTGACCA 57.379 33.333 7.25 0.00 0.00 4.02
3056 6199 7.209471 ACGTGTATACAAAAATGTTGACCAT 57.791 32.000 7.25 0.00 34.36 3.55
3057 6200 7.081349 ACGTGTATACAAAAATGTTGACCATG 58.919 34.615 7.25 0.00 32.82 3.66
3058 6201 7.081349 CGTGTATACAAAAATGTTGACCATGT 58.919 34.615 7.25 0.00 32.82 3.21
3059 6202 8.231161 CGTGTATACAAAAATGTTGACCATGTA 58.769 33.333 7.25 0.00 32.82 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.443045 GTTGGGGTGAGCGGCATG 61.443 66.667 1.45 0.00 0.00 4.06
3 4 2.786512 ATTGTTGGGGTGAGCGGCAT 62.787 55.000 1.45 0.00 0.00 4.40
4 5 3.505790 ATTGTTGGGGTGAGCGGCA 62.506 57.895 1.45 0.00 0.00 5.69
5 6 2.676471 ATTGTTGGGGTGAGCGGC 60.676 61.111 0.00 0.00 0.00 6.53
6 7 1.303236 TGATTGTTGGGGTGAGCGG 60.303 57.895 0.00 0.00 0.00 5.52
7 8 1.926511 GCTGATTGTTGGGGTGAGCG 61.927 60.000 0.00 0.00 0.00 5.03
8 9 1.598701 GGCTGATTGTTGGGGTGAGC 61.599 60.000 0.00 0.00 0.00 4.26
9 10 0.967380 GGGCTGATTGTTGGGGTGAG 60.967 60.000 0.00 0.00 0.00 3.51
10 11 1.076549 GGGCTGATTGTTGGGGTGA 59.923 57.895 0.00 0.00 0.00 4.02
11 12 2.342650 CGGGCTGATTGTTGGGGTG 61.343 63.158 0.00 0.00 0.00 4.61
12 13 2.035626 CGGGCTGATTGTTGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
13 14 3.451894 GCGGGCTGATTGTTGGGG 61.452 66.667 0.00 0.00 0.00 4.96
14 15 2.676121 TGCGGGCTGATTGTTGGG 60.676 61.111 0.00 0.00 0.00 4.12
15 16 1.926511 GACTGCGGGCTGATTGTTGG 61.927 60.000 0.00 0.00 0.00 3.77
16 17 0.957395 AGACTGCGGGCTGATTGTTG 60.957 55.000 0.00 0.00 0.00 3.33
17 18 0.957395 CAGACTGCGGGCTGATTGTT 60.957 55.000 25.19 0.00 34.06 2.83
18 19 1.376424 CAGACTGCGGGCTGATTGT 60.376 57.895 25.19 0.00 34.06 2.71
19 20 0.108186 TACAGACTGCGGGCTGATTG 60.108 55.000 35.32 9.89 36.07 2.67
20 21 0.108138 GTACAGACTGCGGGCTGATT 60.108 55.000 35.32 16.24 36.07 2.57
21 22 0.972983 AGTACAGACTGCGGGCTGAT 60.973 55.000 35.32 20.38 33.41 2.90
22 23 1.606601 AGTACAGACTGCGGGCTGA 60.607 57.895 35.32 15.59 33.41 4.26
23 24 1.446792 CAGTACAGACTGCGGGCTG 60.447 63.158 27.48 27.48 46.41 4.85
24 25 2.973899 CAGTACAGACTGCGGGCT 59.026 61.111 0.00 0.00 46.41 5.19
31 32 2.232452 GCCTGATGTCACAGTACAGACT 59.768 50.000 9.94 1.71 36.30 3.24
32 33 2.029020 TGCCTGATGTCACAGTACAGAC 60.029 50.000 9.94 0.80 36.30 3.51
45 46 1.094073 CCCGAAAGCTCTGCCTGATG 61.094 60.000 0.00 0.00 0.00 3.07
49 50 2.664081 CCTCCCGAAAGCTCTGCCT 61.664 63.158 0.00 0.00 0.00 4.75
51 52 1.021920 GTTCCTCCCGAAAGCTCTGC 61.022 60.000 0.00 0.00 30.39 4.26
54 55 0.608640 TCAGTTCCTCCCGAAAGCTC 59.391 55.000 0.00 0.00 30.39 4.09
80 81 0.029577 TATGGTGTATGGGCCCCTCA 60.030 55.000 22.27 13.09 0.00 3.86
83 84 1.272480 GGATTATGGTGTATGGGCCCC 60.272 57.143 22.27 3.99 0.00 5.80
84 85 1.272480 GGGATTATGGTGTATGGGCCC 60.272 57.143 17.59 17.59 0.00 5.80
85 86 1.427368 TGGGATTATGGTGTATGGGCC 59.573 52.381 0.00 0.00 0.00 5.80
86 87 2.514803 GTGGGATTATGGTGTATGGGC 58.485 52.381 0.00 0.00 0.00 5.36
105 106 4.502604 GCATATACACACTAATCACCCCGT 60.503 45.833 0.00 0.00 0.00 5.28
134 135 8.538701 AGATTTGAGTATTTGATCTGAGACTGT 58.461 33.333 0.00 0.00 0.00 3.55
153 154 5.940192 ATAACACGCTCAACAAGATTTGA 57.060 34.783 0.00 0.00 34.30 2.69
178 179 4.019681 TGGTCGATGTCCAAGGTTATTTCT 60.020 41.667 0.00 0.00 31.50 2.52
187 188 1.450312 GCCCTGGTCGATGTCCAAG 60.450 63.158 0.00 0.00 34.35 3.61
188 189 2.668632 GCCCTGGTCGATGTCCAA 59.331 61.111 0.00 0.00 34.35 3.53
189 190 3.399181 GGCCCTGGTCGATGTCCA 61.399 66.667 0.00 0.00 0.00 4.02
216 217 3.202595 GGTAGAGACCACCTAGGAGAGAA 59.797 52.174 17.98 0.00 46.12 2.87
252 253 1.006825 TCGAGTGATTCAACGTGGCG 61.007 55.000 12.05 0.00 0.00 5.69
258 259 1.996191 GACAGCCTCGAGTGATTCAAC 59.004 52.381 12.31 0.00 0.00 3.18
271 272 3.322466 CTGGGTTCCCGACAGCCT 61.322 66.667 3.27 0.00 32.59 4.58
309 310 3.941629 AGGGCTGAAGGAATAGATGGTA 58.058 45.455 0.00 0.00 0.00 3.25
311 312 3.872459 AAGGGCTGAAGGAATAGATGG 57.128 47.619 0.00 0.00 0.00 3.51
314 315 4.099573 CGAACTAAGGGCTGAAGGAATAGA 59.900 45.833 0.00 0.00 0.00 1.98
319 320 1.933021 TCGAACTAAGGGCTGAAGGA 58.067 50.000 0.00 0.00 0.00 3.36
372 373 5.104402 TCTCTTTGGCCAATGATCACAGATA 60.104 40.000 28.60 13.21 0.00 1.98
377 378 2.424956 GGTCTCTTTGGCCAATGATCAC 59.575 50.000 28.60 25.41 40.97 3.06
387 388 2.032681 AGCCGTGGTCTCTTTGGC 59.967 61.111 0.00 0.00 46.07 4.52
390 391 3.695830 TTATTGAGCCGTGGTCTCTTT 57.304 42.857 10.32 3.13 0.00 2.52
394 395 3.741388 GCTACATTATTGAGCCGTGGTCT 60.741 47.826 5.03 0.00 0.00 3.85
397 398 2.560504 TGCTACATTATTGAGCCGTGG 58.439 47.619 0.00 0.00 35.24 4.94
400 401 3.003585 TGCATTGCTACATTATTGAGCCG 59.996 43.478 10.49 0.00 35.24 5.52
401 402 4.572985 TGCATTGCTACATTATTGAGCC 57.427 40.909 10.49 0.00 35.24 4.70
404 405 5.105957 ACCGTTTGCATTGCTACATTATTGA 60.106 36.000 10.49 0.00 0.00 2.57
411 412 1.535028 CTCACCGTTTGCATTGCTACA 59.465 47.619 10.49 0.00 0.00 2.74
412 413 1.804151 TCTCACCGTTTGCATTGCTAC 59.196 47.619 10.49 7.23 0.00 3.58
419 420 1.336887 GCTAGAGTCTCACCGTTTGCA 60.337 52.381 0.00 0.00 0.00 4.08
421 422 2.229062 TCTGCTAGAGTCTCACCGTTTG 59.771 50.000 0.00 0.00 0.00 2.93
428 429 5.070685 TGTTAGTTGTCTGCTAGAGTCTCA 58.929 41.667 0.00 0.00 0.00 3.27
429 430 5.630661 TGTTAGTTGTCTGCTAGAGTCTC 57.369 43.478 0.00 0.00 0.00 3.36
431 432 8.934507 ATAAATGTTAGTTGTCTGCTAGAGTC 57.065 34.615 0.00 0.00 0.00 3.36
432 433 9.726438 AAATAAATGTTAGTTGTCTGCTAGAGT 57.274 29.630 0.00 0.00 0.00 3.24
445 470 6.311935 TCGCTGCGAAGTAAATAAATGTTAGT 59.688 34.615 23.88 0.00 31.06 2.24
449 474 5.539582 TTCGCTGCGAAGTAAATAAATGT 57.460 34.783 31.14 0.00 41.05 2.71
469 494 1.808411 TCTTGAATCACCCGTGCTTC 58.192 50.000 4.80 4.80 36.55 3.86
475 500 8.438676 AAATTAGAACTATCTTGAATCACCCG 57.561 34.615 0.00 0.00 37.10 5.28
523 548 1.093159 ACCGTGTTGCCGTACAAAAA 58.907 45.000 0.00 0.00 40.82 1.94
524 549 1.063764 GAACCGTGTTGCCGTACAAAA 59.936 47.619 0.00 0.00 40.82 2.44
525 550 0.656785 GAACCGTGTTGCCGTACAAA 59.343 50.000 0.00 0.00 40.82 2.83
526 551 0.179078 AGAACCGTGTTGCCGTACAA 60.179 50.000 0.00 0.00 35.33 2.41
527 552 0.672889 TAGAACCGTGTTGCCGTACA 59.327 50.000 0.00 0.00 0.00 2.90
528 553 1.782044 TTAGAACCGTGTTGCCGTAC 58.218 50.000 0.00 0.00 0.00 3.67
529 554 2.747396 ATTAGAACCGTGTTGCCGTA 57.253 45.000 0.00 0.00 0.00 4.02
530 555 1.802365 GAATTAGAACCGTGTTGCCGT 59.198 47.619 0.00 0.00 0.00 5.68
531 556 2.073816 AGAATTAGAACCGTGTTGCCG 58.926 47.619 0.00 0.00 0.00 5.69
532 557 4.251268 AGTAGAATTAGAACCGTGTTGCC 58.749 43.478 0.00 0.00 0.00 4.52
533 558 5.857822 AAGTAGAATTAGAACCGTGTTGC 57.142 39.130 0.00 0.00 0.00 4.17
534 559 6.577427 GCAAAAGTAGAATTAGAACCGTGTTG 59.423 38.462 0.00 0.00 0.00 3.33
535 560 6.261381 TGCAAAAGTAGAATTAGAACCGTGTT 59.739 34.615 0.00 0.00 0.00 3.32
536 561 5.761234 TGCAAAAGTAGAATTAGAACCGTGT 59.239 36.000 0.00 0.00 0.00 4.49
537 562 6.236017 TGCAAAAGTAGAATTAGAACCGTG 57.764 37.500 0.00 0.00 0.00 4.94
538 563 6.565247 CGTTGCAAAAGTAGAATTAGAACCGT 60.565 38.462 0.00 0.00 0.00 4.83
539 564 5.788531 CGTTGCAAAAGTAGAATTAGAACCG 59.211 40.000 0.00 0.00 0.00 4.44
540 565 5.567915 GCGTTGCAAAAGTAGAATTAGAACC 59.432 40.000 0.00 0.00 0.00 3.62
541 566 6.086371 GTGCGTTGCAAAAGTAGAATTAGAAC 59.914 38.462 0.00 0.00 41.47 3.01
542 567 6.140110 GTGCGTTGCAAAAGTAGAATTAGAA 58.860 36.000 0.00 0.00 41.47 2.10
543 568 5.237561 TGTGCGTTGCAAAAGTAGAATTAGA 59.762 36.000 0.00 0.00 41.47 2.10
544 569 5.448438 TGTGCGTTGCAAAAGTAGAATTAG 58.552 37.500 0.00 0.00 41.47 1.73
545 570 5.425577 TGTGCGTTGCAAAAGTAGAATTA 57.574 34.783 0.00 0.00 41.47 1.40
546 571 4.300189 TGTGCGTTGCAAAAGTAGAATT 57.700 36.364 0.00 0.00 41.47 2.17
547 572 3.980646 TGTGCGTTGCAAAAGTAGAAT 57.019 38.095 0.00 0.00 41.47 2.40
548 573 3.690422 CTTGTGCGTTGCAAAAGTAGAA 58.310 40.909 12.50 2.24 45.69 2.10
549 574 3.332761 CTTGTGCGTTGCAAAAGTAGA 57.667 42.857 12.50 0.00 45.69 2.59
554 579 1.098869 TCTCCTTGTGCGTTGCAAAA 58.901 45.000 0.00 0.00 41.47 2.44
555 580 1.001487 CATCTCCTTGTGCGTTGCAAA 60.001 47.619 0.00 0.00 41.47 3.68
556 581 0.592637 CATCTCCTTGTGCGTTGCAA 59.407 50.000 0.00 0.00 41.47 4.08
557 582 0.534877 ACATCTCCTTGTGCGTTGCA 60.535 50.000 0.00 0.00 35.60 4.08
558 583 0.110056 CACATCTCCTTGTGCGTTGC 60.110 55.000 0.00 0.00 40.45 4.17
565 590 1.277557 GAGACCAGCACATCTCCTTGT 59.722 52.381 0.82 0.00 36.18 3.16
566 591 1.554160 AGAGACCAGCACATCTCCTTG 59.446 52.381 7.33 0.00 42.04 3.61
567 592 1.949799 AGAGACCAGCACATCTCCTT 58.050 50.000 7.33 0.00 42.04 3.36
568 593 2.763448 GTTAGAGACCAGCACATCTCCT 59.237 50.000 7.33 0.00 42.04 3.69
569 594 2.497675 TGTTAGAGACCAGCACATCTCC 59.502 50.000 7.33 0.00 42.04 3.71
570 595 3.876274 TGTTAGAGACCAGCACATCTC 57.124 47.619 3.58 3.58 41.50 2.75
571 596 4.019860 ACATTGTTAGAGACCAGCACATCT 60.020 41.667 0.00 0.00 0.00 2.90
572 597 4.256920 ACATTGTTAGAGACCAGCACATC 58.743 43.478 0.00 0.00 0.00 3.06
573 598 4.292186 ACATTGTTAGAGACCAGCACAT 57.708 40.909 0.00 0.00 0.00 3.21
574 599 3.769739 ACATTGTTAGAGACCAGCACA 57.230 42.857 0.00 0.00 0.00 4.57
575 600 5.178797 ACATACATTGTTAGAGACCAGCAC 58.821 41.667 0.00 0.00 33.74 4.40
576 601 5.420725 ACATACATTGTTAGAGACCAGCA 57.579 39.130 0.00 0.00 33.74 4.41
577 602 5.986135 CCTACATACATTGTTAGAGACCAGC 59.014 44.000 0.00 0.00 39.87 4.85
578 603 7.068839 ACTCCTACATACATTGTTAGAGACCAG 59.931 40.741 0.00 0.00 37.98 4.00
579 604 6.895756 ACTCCTACATACATTGTTAGAGACCA 59.104 38.462 0.00 0.00 37.98 4.02
580 605 7.349412 ACTCCTACATACATTGTTAGAGACC 57.651 40.000 0.00 0.00 37.98 3.85
581 606 9.654663 AAAACTCCTACATACATTGTTAGAGAC 57.345 33.333 0.00 0.00 37.98 3.36
610 635 1.024579 AACCGTCCGATCCATGCAAC 61.025 55.000 0.00 0.00 0.00 4.17
611 636 1.024046 CAACCGTCCGATCCATGCAA 61.024 55.000 0.00 0.00 0.00 4.08
655 680 2.746803 CGCCATTTTCCCGACCGTC 61.747 63.158 0.00 0.00 0.00 4.79
675 700 4.819630 AGCCGTCTGAAAACACAGAAATAA 59.180 37.500 0.00 0.00 46.34 1.40
677 702 3.003689 CAGCCGTCTGAAAACACAGAAAT 59.996 43.478 0.00 0.00 46.34 2.17
825 850 0.960861 GGGAGGGGAACTTTTCAGCG 60.961 60.000 0.00 0.00 0.00 5.18
961 990 0.595095 GTGCTTGTTCAGGCCTCTTG 59.405 55.000 0.00 0.00 0.00 3.02
982 1011 0.662672 ATGTCGATGATCTGCGAGCG 60.663 55.000 10.07 0.00 37.18 5.03
989 1018 2.501316 TCACAACCCATGTCGATGATCT 59.499 45.455 0.00 0.00 41.46 2.75
999 1028 1.021390 GCGTCCTCTCACAACCCATG 61.021 60.000 0.00 0.00 0.00 3.66
1404 1433 6.432472 TCTCATGATACTACCATGCTGTCTAG 59.568 42.308 0.00 0.00 40.74 2.43
1405 1434 6.207614 GTCTCATGATACTACCATGCTGTCTA 59.792 42.308 4.07 0.00 40.74 2.59
1407 1436 5.221322 TGTCTCATGATACTACCATGCTGTC 60.221 44.000 11.98 0.00 40.74 3.51
1408 1437 4.651045 TGTCTCATGATACTACCATGCTGT 59.349 41.667 11.98 0.00 40.74 4.40
1409 1438 5.205759 TGTCTCATGATACTACCATGCTG 57.794 43.478 11.98 0.00 40.74 4.41
1410 1439 5.541484 TCATGTCTCATGATACTACCATGCT 59.459 40.000 11.98 0.00 40.74 3.79
1412 1441 6.364435 CGTTCATGTCTCATGATACTACCATG 59.636 42.308 11.98 7.64 41.93 3.66
1413 1442 6.450545 CGTTCATGTCTCATGATACTACCAT 58.549 40.000 11.98 0.00 0.00 3.55
1414 1443 5.736207 GCGTTCATGTCTCATGATACTACCA 60.736 44.000 11.98 0.00 0.00 3.25
1415 1444 4.681942 GCGTTCATGTCTCATGATACTACC 59.318 45.833 11.98 1.32 0.00 3.18
1416 1445 5.524284 AGCGTTCATGTCTCATGATACTAC 58.476 41.667 11.98 7.46 0.00 2.73
1417 1446 5.278512 GGAGCGTTCATGTCTCATGATACTA 60.279 44.000 11.98 0.45 0.00 1.82
1418 1447 4.500545 GGAGCGTTCATGTCTCATGATACT 60.501 45.833 11.98 10.04 0.00 2.12
1430 1459 0.806102 ATCGAACCGGAGCGTTCATG 60.806 55.000 9.46 0.00 41.89 3.07
1432 1461 1.153901 GATCGAACCGGAGCGTTCA 60.154 57.895 9.46 0.00 41.89 3.18
1433 1462 0.527817 ATGATCGAACCGGAGCGTTC 60.528 55.000 9.46 15.65 39.03 3.95
1434 1463 0.527817 GATGATCGAACCGGAGCGTT 60.528 55.000 9.46 6.20 0.00 4.84
1455 2460 1.474677 GCCATGGGTCTCAGTCAGATG 60.475 57.143 15.13 0.00 32.08 2.90
1457 2462 1.607801 CGCCATGGGTCTCAGTCAGA 61.608 60.000 15.13 0.00 0.00 3.27
1458 2463 1.153489 CGCCATGGGTCTCAGTCAG 60.153 63.158 15.13 0.00 0.00 3.51
1459 2464 2.981302 CGCCATGGGTCTCAGTCA 59.019 61.111 15.13 0.00 0.00 3.41
1460 2465 2.512515 GCGCCATGGGTCTCAGTC 60.513 66.667 15.13 0.00 0.00 3.51
1461 2466 2.673200 ATGCGCCATGGGTCTCAGT 61.673 57.895 15.13 0.00 0.00 3.41
1462 2467 2.184830 CATGCGCCATGGGTCTCAG 61.185 63.158 15.13 0.00 38.11 3.35
1463 2468 2.124612 CATGCGCCATGGGTCTCA 60.125 61.111 15.13 0.00 38.11 3.27
1969 4971 1.819632 GAAGCCGTGCATGTAGGGG 60.820 63.158 21.75 10.08 0.00 4.79
2217 5219 0.239879 AAGCGTACGCATTTTGGTGG 59.760 50.000 38.58 0.00 44.88 4.61
2238 5240 4.564116 GCAGCGCCCATGCATGTC 62.564 66.667 24.58 14.74 43.31 3.06
2255 5257 8.171196 CAGTATAATTAAGACAACACACAGCAG 58.829 37.037 0.00 0.00 0.00 4.24
2256 5258 7.360861 GCAGTATAATTAAGACAACACACAGCA 60.361 37.037 0.00 0.00 0.00 4.41
2258 5260 7.173419 CGCAGTATAATTAAGACAACACACAG 58.827 38.462 0.00 0.00 0.00 3.66
2282 5284 0.725117 GGTTACAATCGAAGCACCCG 59.275 55.000 0.00 0.00 0.00 5.28
2283 5285 1.816074 TGGTTACAATCGAAGCACCC 58.184 50.000 0.00 0.00 29.71 4.61
2284 5286 3.252458 ACTTTGGTTACAATCGAAGCACC 59.748 43.478 2.65 0.00 34.48 5.01
2305 5307 8.307483 TCATCCTAGAATTTTCGATCATCCTAC 58.693 37.037 0.00 0.00 0.00 3.18
2340 5342 5.329191 TGCATCTATTCTCCATCCCATTT 57.671 39.130 0.00 0.00 0.00 2.32
2391 5397 4.956075 TGGTATGCTGTTCTCTCATACTCA 59.044 41.667 10.28 5.59 41.18 3.41
2396 5402 3.378512 TCCTGGTATGCTGTTCTCTCAT 58.621 45.455 0.00 0.00 0.00 2.90
2410 5416 6.438186 TTTGATAGATGCATGATCCTGGTA 57.562 37.500 2.46 0.00 0.00 3.25
2411 5417 4.987963 TTGATAGATGCATGATCCTGGT 57.012 40.909 2.46 0.00 0.00 4.00
2433 5441 5.221342 CGTCTTAATAGTGGCCTCTTGAGAT 60.221 44.000 13.50 0.00 27.31 2.75
2437 5445 4.124851 ACGTCTTAATAGTGGCCTCTTG 57.875 45.455 13.50 0.00 0.00 3.02
2443 5451 5.796350 AACATCAACGTCTTAATAGTGGC 57.204 39.130 0.00 0.00 0.00 5.01
2466 5474 5.483811 TGCAAATAGAACATCACCGTCTTA 58.516 37.500 0.00 0.00 0.00 2.10
2467 5475 4.323417 TGCAAATAGAACATCACCGTCTT 58.677 39.130 0.00 0.00 0.00 3.01
2473 5481 8.470040 AATTTCACATGCAAATAGAACATCAC 57.530 30.769 0.00 0.00 0.00 3.06
2486 5494 7.010367 GTCTTTGAACTTGAAATTTCACATGCA 59.990 33.333 20.35 12.99 36.83 3.96
2510 5518 4.929808 CCATAGCTCATAAATGGTACCGTC 59.070 45.833 7.19 0.00 36.26 4.79
2524 5536 2.707257 TCATGGCTGATTCCATAGCTCA 59.293 45.455 0.00 0.00 44.63 4.26
2533 5546 6.630444 AACATCACTATTCATGGCTGATTC 57.370 37.500 0.00 0.00 0.00 2.52
2548 5568 7.931407 TGAATAGTGTCAACAGTAAACATCACT 59.069 33.333 2.01 0.00 35.61 3.41
2553 5573 7.228507 AGCAATGAATAGTGTCAACAGTAAACA 59.771 33.333 2.01 6.05 35.61 2.83
2593 5697 8.432110 AAATTTCCAAGTTCAAACACATTACC 57.568 30.769 0.00 0.00 0.00 2.85
2594 5698 9.092876 TGAAATTTCCAAGTTCAAACACATTAC 57.907 29.630 15.48 0.00 41.84 1.89
2595 5699 9.092876 GTGAAATTTCCAAGTTCAAACACATTA 57.907 29.630 15.48 0.00 45.59 1.90
2601 5721 8.871686 AGTATGTGAAATTTCCAAGTTCAAAC 57.128 30.769 15.48 4.42 45.59 2.93
2672 5799 4.501400 CCCTTCAGGCGAAGTTTCAAAAAT 60.501 41.667 14.71 0.00 46.19 1.82
2688 5818 1.310933 GGCACATCAGCACCCTTCAG 61.311 60.000 0.00 0.00 35.83 3.02
2708 5851 5.492895 TCCTAGTCTCCTAGATGAATAGCG 58.507 45.833 11.37 7.29 42.90 4.26
3011 6154 9.594478 ACACGTTTAGAATTTTTCAAATCCTTT 57.406 25.926 0.00 0.00 0.00 3.11
3027 6170 9.866936 GTCAACATTTTTGTATACACGTTTAGA 57.133 29.630 4.68 0.00 0.00 2.10
3028 6171 9.109533 GGTCAACATTTTTGTATACACGTTTAG 57.890 33.333 4.68 0.00 0.00 1.85
3029 6172 8.618677 TGGTCAACATTTTTGTATACACGTTTA 58.381 29.630 4.68 0.00 0.00 2.01
3030 6173 7.481642 TGGTCAACATTTTTGTATACACGTTT 58.518 30.769 4.68 0.00 0.00 3.60
3031 6174 7.028926 TGGTCAACATTTTTGTATACACGTT 57.971 32.000 4.68 1.99 0.00 3.99
3032 6175 6.621316 TGGTCAACATTTTTGTATACACGT 57.379 33.333 4.68 0.00 0.00 4.49
3033 6176 7.081349 ACATGGTCAACATTTTTGTATACACG 58.919 34.615 4.68 0.00 37.84 4.49


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

AutoCloner maintained by Alex Coulton.