Multiple sequence alignment - TraesCS5A01G212900

Loading Multiple Alignment...

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 TraesCS5A01G212900 chr5A 100.000 4889 0 0 1 4889 428147460 428152348 0.000000e+00 9029.0
1 TraesCS5A01G212900 chr5A 93.458 321 21 0 4569 4889 184259210 184259530 1.230000e-130 477.0
2 TraesCS5A01G212900 chr5A 93.478 322 20 1 4569 4889 563313666 563313345 1.230000e-130 477.0
3 TraesCS5A01G212900 chr5A 92.923 325 22 1 4565 4889 616635846 616635523 5.730000e-129 472.0
4 TraesCS5A01G212900 chr5D 94.597 4590 168 32 6 4569 328440327 328435792 0.000000e+00 7029.0
5 TraesCS5A01G212900 chr5D 93.051 331 21 2 4560 4889 292644568 292644239 2.650000e-132 483.0
6 TraesCS5A01G212900 chr5B 91.385 4318 231 46 205 4459 381721026 381716787 0.000000e+00 5782.0
7 TraesCS5A01G212900 chr5B 87.879 66 7 1 4505 4569 498885976 498886041 5.250000e-10 76.8
8 TraesCS5A01G212900 chr5B 88.525 61 7 0 4508 4568 98836189 98836129 1.890000e-09 75.0
9 TraesCS5A01G212900 chr4A 97.188 320 7 2 4570 4889 139718057 139717740 1.550000e-149 540.0
10 TraesCS5A01G212900 chr4A 83.562 73 10 2 4507 4577 27642118 27642046 3.160000e-07 67.6
11 TraesCS5A01G212900 chr6D 95.625 320 13 1 4570 4889 5732337 5732019 3.380000e-141 512.0
12 TraesCS5A01G212900 chr6D 83.983 462 69 4 1 457 337846817 337847278 5.810000e-119 438.0
13 TraesCS5A01G212900 chr6D 81.898 453 76 4 1 447 389587497 389587045 1.280000e-100 377.0
14 TraesCS5A01G212900 chr2D 95.016 321 15 1 4570 4889 531751246 531751566 2.030000e-138 503.0
15 TraesCS5A01G212900 chr2D 93.789 322 19 1 4569 4889 640367311 640367632 2.650000e-132 483.0
16 TraesCS5A01G212900 chr3D 93.750 320 19 1 4569 4888 182184714 182185032 3.420000e-131 479.0
17 TraesCS5A01G212900 chr3A 83.120 468 73 5 1 463 16154490 16154024 5.850000e-114 422.0
18 TraesCS5A01G212900 chr3A 80.879 455 82 4 13 463 191540309 191539856 2.160000e-93 353.0
19 TraesCS5A01G212900 chr3A 91.935 62 5 0 4506 4567 26139755 26139816 2.420000e-13 87.9
20 TraesCS5A01G212900 chr6B 81.529 471 81 5 1 466 482469871 482469402 2.760000e-102 383.0
21 TraesCS5A01G212900 chr3B 81.400 457 76 8 12 461 749037274 749036820 1.000000e-96 364.0
22 TraesCS5A01G212900 chr3B 90.323 62 6 0 4508 4569 501386933 501386872 1.130000e-11 82.4
23 TraesCS5A01G212900 chr3B 86.364 66 8 1 4508 4573 416577746 416577682 2.440000e-08 71.3
24 TraesCS5A01G212900 chr7D 81.144 472 67 15 5 463 509561187 509561649 4.650000e-95 359.0
25 TraesCS5A01G212900 chr1D 80.477 461 84 4 3 457 347407901 347408361 1.010000e-91 348.0
26 TraesCS5A01G212900 chr1D 96.552 58 2 0 4512 4569 463470932 463470875 4.030000e-16 97.1
27 TraesCS5A01G212900 chr1D 85.135 74 9 2 4506 4577 33623043 33622970 1.890000e-09 75.0


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 TraesCS5A01G212900 chr5A 428147460 428152348 4888 False 9029 9029 100.000 1 4889 1 chr5A.!!$F2 4888
1 TraesCS5A01G212900 chr5D 328435792 328440327 4535 True 7029 7029 94.597 6 4569 1 chr5D.!!$R2 4563
2 TraesCS5A01G212900 chr5B 381716787 381721026 4239 True 5782 5782 91.385 205 4459 1 chr5B.!!$R2 4254

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
95 99 0.034380 ATCCTCCTCGAGTTCGTCCA 60.034 55.000 12.31 0.0 40.80 4.02 F
244 250 0.179145 ACGATAACGACTTCAGGCGG 60.179 55.000 7.07 0.0 42.66 6.13 F
916 944 0.242017 CAGCAAAACCCTAGCAGCAC 59.758 55.000 0.00 0.0 0.00 4.40 F
974 1002 1.007618 GTAGCACGTAGATCCCGCC 60.008 63.158 2.55 0.0 0.00 6.13 F
1957 1995 1.272536 GGACCTCGATATGGGAGCCTA 60.273 57.143 0.00 0.0 0.00 3.93 F
3609 3668 1.227853 GGCTGTTCCTGTTGTCGGT 60.228 57.895 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 1959 1.069358 GGTCCCTTATGCTCTCTTCCG 59.931 57.143 0.00 0.0 0.00 4.30 R
1933 1971 2.822006 GCTCCCATATCGAGGTCCCTTA 60.822 54.545 0.00 0.0 0.00 2.69 R
2598 2640 0.253327 GAGGACCCCTGGTGTGATTC 59.747 60.000 0.00 0.0 35.25 2.52 R
2697 2739 3.599343 TGTGACATCCTTGCAGTCATAC 58.401 45.455 8.74 0.0 43.35 2.39 R
3623 3682 1.559368 CCTTTGCCCATGGATTGACA 58.441 50.000 15.22 0.0 0.00 3.58 R
4571 4651 0.596082 CGGTCTCCGTTTGGCATTTT 59.404 50.000 0.00 0.0 42.73 1.82 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
53 57 1.521681 GATGGCGGCGCTACTTCTT 60.522 57.895 32.30 10.36 0.00 2.52
54 58 1.078426 ATGGCGGCGCTACTTCTTT 60.078 52.632 32.30 6.37 0.00 2.52
60 64 2.159037 GCGGCGCTACTTCTTTAAGTTT 59.841 45.455 26.86 0.00 43.60 2.66
66 70 5.620011 GCGCTACTTCTTTAAGTTTGTGTTC 59.380 40.000 0.00 0.00 43.60 3.18
91 95 1.601903 CTCTGATCCTCCTCGAGTTCG 59.398 57.143 12.31 0.00 41.45 3.95
95 99 0.034380 ATCCTCCTCGAGTTCGTCCA 60.034 55.000 12.31 0.00 40.80 4.02
97 101 0.818296 CCTCCTCGAGTTCGTCCATT 59.182 55.000 12.31 0.00 40.80 3.16
140 144 2.543238 CGGCGTAGGTTCCTATTGTCTC 60.543 54.545 0.00 0.00 0.00 3.36
186 190 4.635223 TCTCATCTTATGGCGAGATTTGG 58.365 43.478 0.00 0.00 31.66 3.28
187 191 3.141398 TCATCTTATGGCGAGATTTGGC 58.859 45.455 0.00 0.00 31.66 4.52
193 197 1.447838 GGCGAGATTTGGCGTCAGA 60.448 57.895 0.00 0.00 31.48 3.27
203 207 0.390340 TGGCGTCAGATGCTTCAGAC 60.390 55.000 14.44 13.24 35.62 3.51
222 226 1.586028 CCATGCAAGGGTTCAACGG 59.414 57.895 0.00 0.00 29.31 4.44
239 243 3.317608 GGCGACGATAACGACTTCA 57.682 52.632 0.00 0.00 42.66 3.02
244 250 0.179145 ACGATAACGACTTCAGGCGG 60.179 55.000 7.07 0.00 42.66 6.13
308 314 4.394712 AAGGTCAAGCCGGCTCCG 62.395 66.667 32.93 24.15 43.70 4.63
328 334 0.600057 GTAGGGGAACGACGACAACT 59.400 55.000 0.00 0.51 0.00 3.16
329 335 1.812571 GTAGGGGAACGACGACAACTA 59.187 52.381 0.00 0.00 0.00 2.24
377 384 5.556915 CAGTAGTGATTGTTTGGGGTCTTA 58.443 41.667 0.00 0.00 0.00 2.10
384 391 6.434340 GTGATTGTTTGGGGTCTTAGAATCTT 59.566 38.462 0.00 0.00 0.00 2.40
427 434 9.443323 TGTTTTAGATGCTTTGTACTTATGCTA 57.557 29.630 0.00 0.00 0.00 3.49
498 505 8.697507 AAAACCTGAATCTATTTGTCACTTCT 57.302 30.769 0.00 0.00 0.00 2.85
499 506 9.793259 AAAACCTGAATCTATTTGTCACTTCTA 57.207 29.630 0.00 0.00 0.00 2.10
519 526 8.472413 ACTTCTACTAGTGTTTTGTACTGACAA 58.528 33.333 5.39 0.00 43.94 3.18
588 595 1.677637 GCGGAGGGGGAGTACTTCTG 61.678 65.000 0.01 0.00 0.00 3.02
635 650 1.008538 CAACAAACAGAGCCACGGC 60.009 57.895 0.00 0.00 42.33 5.68
656 671 2.029020 CCAACTCGAGTCAGTCAATCCA 60.029 50.000 20.33 0.00 0.00 3.41
668 683 4.652131 AATCCAACGGCCCGCACA 62.652 61.111 1.23 0.00 0.00 4.57
688 703 2.507102 CTGACGGCAGTACGCAGG 60.507 66.667 11.12 6.61 45.17 4.85
689 704 3.989698 CTGACGGCAGTACGCAGGG 62.990 68.421 11.12 4.74 45.17 4.45
690 705 4.814294 GACGGCAGTACGCAGGGG 62.814 72.222 12.45 0.00 45.17 4.79
735 750 3.112709 GTCTTGCTGGCCGTCGTC 61.113 66.667 0.00 0.00 0.00 4.20
736 751 3.303135 TCTTGCTGGCCGTCGTCT 61.303 61.111 0.00 0.00 0.00 4.18
737 752 2.811317 CTTGCTGGCCGTCGTCTC 60.811 66.667 0.00 0.00 0.00 3.36
738 753 4.717629 TTGCTGGCCGTCGTCTCG 62.718 66.667 0.00 0.00 0.00 4.04
827 843 4.104183 CCGCCTCCCGCCCTTTTA 62.104 66.667 0.00 0.00 35.03 1.52
860 876 4.954118 AGGTCCGGCTCACCACCA 62.954 66.667 12.97 0.00 34.96 4.17
861 877 4.699522 GGTCCGGCTCACCACCAC 62.700 72.222 5.94 0.00 33.13 4.16
862 878 4.699522 GTCCGGCTCACCACCACC 62.700 72.222 0.00 0.00 34.57 4.61
916 944 0.242017 CAGCAAAACCCTAGCAGCAC 59.758 55.000 0.00 0.00 0.00 4.40
972 1000 4.916412 CGTAGCACGTAGATCCCG 57.084 61.111 0.00 1.17 36.74 5.14
973 1001 1.370172 CGTAGCACGTAGATCCCGC 60.370 63.158 2.55 0.00 36.74 6.13
974 1002 1.007618 GTAGCACGTAGATCCCGCC 60.008 63.158 2.55 0.00 0.00 6.13
975 1003 2.198287 TAGCACGTAGATCCCGCCC 61.198 63.158 2.55 0.00 0.00 6.13
1521 1549 3.633094 GACGCTCTTCCTCGCTGCA 62.633 63.158 0.00 0.00 0.00 4.41
1551 1579 2.037367 CTCGGGGTCCAGGTGAGA 59.963 66.667 0.00 0.00 0.00 3.27
1567 1595 2.159234 GTGAGACATTTCAGCTGCACTC 59.841 50.000 9.47 10.88 0.00 3.51
1572 1600 2.290768 ACATTTCAGCTGCACTCTCCAT 60.291 45.455 9.47 0.00 0.00 3.41
1591 1619 6.886459 TCTCCATCAGCTTGCTTAATTTTACT 59.114 34.615 0.00 0.00 0.00 2.24
1592 1620 6.855836 TCCATCAGCTTGCTTAATTTTACTG 58.144 36.000 0.00 0.00 0.00 2.74
1598 1626 6.917477 CAGCTTGCTTAATTTTACTGTCACAA 59.083 34.615 0.00 0.00 0.00 3.33
1620 1648 8.131100 CACAAGTTTTGACAAGATTGTATGACT 58.869 33.333 11.89 0.00 42.43 3.41
1629 1657 8.147704 TGACAAGATTGTATGACTAGTCACAAA 58.852 33.333 27.41 20.30 41.25 2.83
1646 1681 8.927675 AGTCACAAATTGGTATAGTTAAACCA 57.072 30.769 0.00 0.00 43.99 3.67
1683 1720 6.441093 TGAATTAATGACTCACATTGGCTC 57.559 37.500 0.00 0.00 46.93 4.70
1697 1734 5.877012 CACATTGGCTCTAGAATAACACTGT 59.123 40.000 0.00 0.00 0.00 3.55
1718 1755 2.540383 TCCTGTCCACTCATGCTTAGT 58.460 47.619 0.00 0.00 0.00 2.24
1733 1770 8.718102 TCATGCTTAGTCTGTAAAGGAATTAC 57.282 34.615 0.00 0.00 43.52 1.89
1755 1792 9.814899 ATTACAGTGATGTCATTTTGTTTCAAA 57.185 25.926 0.00 0.00 0.00 2.69
1760 1797 9.520204 AGTGATGTCATTTTGTTTCAAACTTAG 57.480 29.630 1.10 0.00 0.00 2.18
1763 1800 9.185192 GATGTCATTTTGTTTCAAACTTAGAGG 57.815 33.333 1.10 0.00 0.00 3.69
1787 1825 7.016268 AGGAAGTTGAACTAGGATGTTCTTACA 59.984 37.037 0.00 0.00 44.63 2.41
1794 1832 8.692710 TGAACTAGGATGTTCTTACATATCGTT 58.307 33.333 8.52 0.00 44.90 3.85
1814 1852 5.006941 TCGTTTGGCTGTAACTTTTACAGTC 59.993 40.000 19.29 19.29 46.92 3.51
1836 1874 4.219070 TCTGGTGCATTTTCTTCCAATGAG 59.781 41.667 0.00 0.00 34.05 2.90
1900 1938 3.498774 AGATACTGGCCATTGATGTCC 57.501 47.619 5.51 0.00 0.00 4.02
1909 1947 2.229792 CCATTGATGTCCCCATTACCG 58.770 52.381 0.00 0.00 0.00 4.02
1921 1959 4.468510 TCCCCATTACCGTCATATGGATAC 59.531 45.833 2.13 0.00 41.05 2.24
1933 1971 5.019470 TCATATGGATACGGAAGAGAGCAT 58.981 41.667 2.13 0.00 42.51 3.79
1957 1995 1.272536 GGACCTCGATATGGGAGCCTA 60.273 57.143 0.00 0.00 0.00 3.93
2269 2307 6.527023 CGTATTTGCGACCACCTATCTTATAG 59.473 42.308 0.00 0.00 0.00 1.31
2286 2328 8.742125 ATCTTATAGATCATTAAGTCCCACCA 57.258 34.615 12.00 0.00 25.75 4.17
2318 2360 9.896645 GTATGTTGGATGATCCTATGTTATGAT 57.103 33.333 13.44 0.00 37.46 2.45
2697 2739 2.568956 TCCCTTCTGGACACTTCATCTG 59.431 50.000 0.00 0.00 38.61 2.90
2769 2811 2.671963 GGGGCTCCAAACACCGAC 60.672 66.667 0.00 0.00 0.00 4.79
2825 2867 4.633565 GGTTTACTTGATTCCTGAGCTCTG 59.366 45.833 16.19 14.67 0.00 3.35
2882 2924 6.168270 ACTGGATAACAATCTAGCCTCTTC 57.832 41.667 0.00 0.00 33.11 2.87
2946 2988 8.792633 TCCATGTTATCTTGGTTTCTTAACTTG 58.207 33.333 5.81 0.00 39.16 3.16
3297 3356 6.543831 AGTGAATTACTCTGAAATGTATGGGC 59.456 38.462 0.00 0.00 33.17 5.36
3531 3590 4.777463 ACATAACCCTAGAAAATGTCCGG 58.223 43.478 0.00 0.00 0.00 5.14
3537 3596 2.290705 CCTAGAAAATGTCCGGGTTGGT 60.291 50.000 0.00 0.00 39.52 3.67
3609 3668 1.227853 GGCTGTTCCTGTTGTCGGT 60.228 57.895 0.00 0.00 0.00 4.69
3623 3682 7.287005 TCCTGTTGTCGGTAACATCTCTTATAT 59.713 37.037 5.98 0.00 39.60 0.86
3720 3779 3.924114 TTCCATGATATGTCGGTTGGT 57.076 42.857 0.00 0.00 0.00 3.67
3894 3953 2.059541 GACTACAGTTTCTGACACGGC 58.940 52.381 3.70 0.00 35.18 5.68
3917 3976 5.159209 CGGTTCGTCTCACTGTACTATTTT 58.841 41.667 0.00 0.00 0.00 1.82
3947 4007 2.072298 CAGTGGTCAGCTTAGTCTTGC 58.928 52.381 0.00 0.00 0.00 4.01
3965 4025 2.710377 TGCTTTACTGCATACACAGGG 58.290 47.619 0.00 0.00 42.21 4.45
3996 4056 2.976882 TGTAGCTGTTTACACCTCCCTT 59.023 45.455 0.00 0.00 0.00 3.95
4055 4115 9.971922 TTGTCTATACTGTGTCATAGAATGATG 57.028 33.333 3.27 0.00 42.04 3.07
4187 4255 3.717707 TCACTCTGTCAAAAGGTCTTCG 58.282 45.455 0.00 0.00 0.00 3.79
4239 4307 3.208747 ACACCTTGTCCCTTGTGTAAG 57.791 47.619 0.00 0.00 39.98 2.34
4331 4399 6.817765 TCTCTTTGGCTTTCGAATTACATT 57.182 33.333 0.00 0.00 0.00 2.71
4340 4408 7.708752 TGGCTTTCGAATTACATTTGAAAAAGT 59.291 29.630 0.00 0.00 46.47 2.66
4347 4415 7.759433 CGAATTACATTTGAAAAAGTAGGGCAT 59.241 33.333 0.00 0.00 0.00 4.40
4468 4548 6.694411 CAGTTGACTGAGAAAGGTTTGAAATG 59.306 38.462 5.19 0.00 46.59 2.32
4521 4601 4.741928 TCAGCAGTATATACTCCCTCCA 57.258 45.455 12.62 0.00 33.46 3.86
4536 4616 7.947782 ACTCCCTCCATTCCTAAATATAACA 57.052 36.000 0.00 0.00 0.00 2.41
4569 4649 7.491696 AGAGATTTTAACAAGGACTACATACGC 59.508 37.037 0.00 0.00 0.00 4.42
4570 4650 5.766702 TTTTAACAAGGACTACATACGCG 57.233 39.130 3.53 3.53 0.00 6.01
4571 4651 4.700268 TTAACAAGGACTACATACGCGA 57.300 40.909 15.93 0.00 0.00 5.87
4572 4652 3.581024 AACAAGGACTACATACGCGAA 57.419 42.857 15.93 0.00 0.00 4.70
4573 4653 3.581024 ACAAGGACTACATACGCGAAA 57.419 42.857 15.93 0.00 0.00 3.46
4574 4654 3.916761 ACAAGGACTACATACGCGAAAA 58.083 40.909 15.93 0.00 0.00 2.29
4575 4655 4.501071 ACAAGGACTACATACGCGAAAAT 58.499 39.130 15.93 0.00 0.00 1.82
4576 4656 4.328983 ACAAGGACTACATACGCGAAAATG 59.671 41.667 15.93 15.74 0.00 2.32
4577 4657 2.864343 AGGACTACATACGCGAAAATGC 59.136 45.455 15.93 0.80 0.00 3.56
4578 4658 2.033151 GGACTACATACGCGAAAATGCC 60.033 50.000 15.93 6.33 0.00 4.40
4579 4659 2.605818 GACTACATACGCGAAAATGCCA 59.394 45.455 15.93 4.57 0.00 4.92
4580 4660 3.004171 ACTACATACGCGAAAATGCCAA 58.996 40.909 15.93 2.54 0.00 4.52
4581 4661 2.999507 ACATACGCGAAAATGCCAAA 57.000 40.000 15.93 0.00 0.00 3.28
4582 4662 2.591133 ACATACGCGAAAATGCCAAAC 58.409 42.857 15.93 0.00 0.00 2.93
4583 4663 1.577134 CATACGCGAAAATGCCAAACG 59.423 47.619 15.93 0.00 0.00 3.60
4584 4664 0.110147 TACGCGAAAATGCCAAACGG 60.110 50.000 15.93 0.00 0.00 4.44
4585 4665 1.081774 CGCGAAAATGCCAAACGGA 60.082 52.632 0.00 0.00 0.00 4.69
4586 4666 1.065031 CGCGAAAATGCCAAACGGAG 61.065 55.000 0.00 0.00 0.00 4.63
4587 4667 0.239879 GCGAAAATGCCAAACGGAGA 59.760 50.000 0.00 0.00 0.00 3.71
4588 4668 1.963747 CGAAAATGCCAAACGGAGAC 58.036 50.000 0.00 0.00 0.00 3.36
4589 4669 1.401018 CGAAAATGCCAAACGGAGACC 60.401 52.381 0.00 0.00 0.00 3.85
4601 4681 3.941081 GAGACCGAGCTCCATGGA 58.059 61.111 15.27 15.27 0.00 3.41
4602 4682 1.739049 GAGACCGAGCTCCATGGAG 59.261 63.158 33.73 33.73 44.56 3.86
4603 4683 1.743321 GAGACCGAGCTCCATGGAGG 61.743 65.000 36.92 26.01 42.19 4.30
4604 4684 3.453070 GACCGAGCTCCATGGAGGC 62.453 68.421 36.92 28.76 42.19 4.70
4605 4685 4.247380 CCGAGCTCCATGGAGGCC 62.247 72.222 36.92 23.97 42.19 5.19
4606 4686 3.160047 CGAGCTCCATGGAGGCCT 61.160 66.667 36.92 27.78 42.19 5.19
4607 4687 2.739996 CGAGCTCCATGGAGGCCTT 61.740 63.158 36.92 17.72 42.19 4.35
4608 4688 1.611965 GAGCTCCATGGAGGCCTTT 59.388 57.895 36.92 17.10 42.19 3.11
4609 4689 0.839946 GAGCTCCATGGAGGCCTTTA 59.160 55.000 36.92 4.58 42.19 1.85
4610 4690 1.423161 GAGCTCCATGGAGGCCTTTAT 59.577 52.381 36.92 16.48 42.19 1.40
4611 4691 1.855599 AGCTCCATGGAGGCCTTTATT 59.144 47.619 36.92 13.75 42.19 1.40
4612 4692 2.245806 AGCTCCATGGAGGCCTTTATTT 59.754 45.455 36.92 13.14 42.19 1.40
4613 4693 2.363359 GCTCCATGGAGGCCTTTATTTG 59.637 50.000 36.92 13.51 42.19 2.32
4614 4694 3.902218 CTCCATGGAGGCCTTTATTTGA 58.098 45.455 31.14 3.17 38.51 2.69
4615 4695 4.280819 CTCCATGGAGGCCTTTATTTGAA 58.719 43.478 31.14 0.00 38.51 2.69
4616 4696 4.682563 TCCATGGAGGCCTTTATTTGAAA 58.317 39.130 11.44 0.00 37.29 2.69
4617 4697 5.090139 TCCATGGAGGCCTTTATTTGAAAA 58.910 37.500 11.44 0.00 37.29 2.29
4618 4698 5.046663 TCCATGGAGGCCTTTATTTGAAAAC 60.047 40.000 11.44 0.00 37.29 2.43
4619 4699 5.046376 CCATGGAGGCCTTTATTTGAAAACT 60.046 40.000 6.77 0.00 0.00 2.66
4620 4700 6.466812 CATGGAGGCCTTTATTTGAAAACTT 58.533 36.000 6.77 0.00 0.00 2.66
4621 4701 6.493189 TGGAGGCCTTTATTTGAAAACTTT 57.507 33.333 6.77 0.00 0.00 2.66
4622 4702 7.604657 TGGAGGCCTTTATTTGAAAACTTTA 57.395 32.000 6.77 0.00 0.00 1.85
4623 4703 8.024145 TGGAGGCCTTTATTTGAAAACTTTAA 57.976 30.769 6.77 0.00 0.00 1.52
4624 4704 8.487028 TGGAGGCCTTTATTTGAAAACTTTAAA 58.513 29.630 6.77 0.00 0.00 1.52
4625 4705 9.332502 GGAGGCCTTTATTTGAAAACTTTAAAA 57.667 29.630 6.77 0.00 0.00 1.52
4698 4778 7.872993 ACCTAGATACATAATGTACATGTGTGC 59.127 37.037 25.77 19.80 35.42 4.57
4699 4779 7.872483 CCTAGATACATAATGTACATGTGTGCA 59.128 37.037 25.77 14.40 44.32 4.57
4700 4780 9.260002 CTAGATACATAATGTACATGTGTGCAA 57.740 33.333 25.77 13.89 43.49 4.08
4701 4781 8.504812 AGATACATAATGTACATGTGTGCAAA 57.495 30.769 25.77 13.64 43.49 3.68
4702 4782 9.123902 AGATACATAATGTACATGTGTGCAAAT 57.876 29.630 25.77 16.51 43.49 2.32
4703 4783 9.734620 GATACATAATGTACATGTGTGCAAATT 57.265 29.630 25.77 6.78 43.49 1.82
4705 4785 8.830201 ACATAATGTACATGTGTGCAAATTTT 57.170 26.923 20.33 1.42 43.49 1.82
4706 4786 8.924691 ACATAATGTACATGTGTGCAAATTTTC 58.075 29.630 20.33 0.00 43.49 2.29
4707 4787 8.923683 CATAATGTACATGTGTGCAAATTTTCA 58.076 29.630 9.63 0.00 43.49 2.69
4708 4788 7.410800 AATGTACATGTGTGCAAATTTTCAG 57.589 32.000 9.63 0.00 43.49 3.02
4709 4789 5.288015 TGTACATGTGTGCAAATTTTCAGG 58.712 37.500 9.11 0.00 37.70 3.86
4710 4790 3.132925 ACATGTGTGCAAATTTTCAGGC 58.867 40.909 0.00 0.00 0.00 4.85
4711 4791 3.181463 ACATGTGTGCAAATTTTCAGGCT 60.181 39.130 0.00 0.00 0.00 4.58
4712 4792 2.823984 TGTGTGCAAATTTTCAGGCTG 58.176 42.857 8.58 8.58 0.00 4.85
4713 4793 2.429971 TGTGTGCAAATTTTCAGGCTGA 59.570 40.909 14.43 14.43 0.00 4.26
4714 4794 3.118847 TGTGTGCAAATTTTCAGGCTGAA 60.119 39.130 25.38 25.38 34.03 3.02
4715 4795 3.870419 GTGTGCAAATTTTCAGGCTGAAA 59.130 39.130 32.85 32.85 43.84 2.69
4716 4796 4.512571 GTGTGCAAATTTTCAGGCTGAAAT 59.487 37.500 35.58 23.10 44.75 2.17
4717 4797 5.695816 GTGTGCAAATTTTCAGGCTGAAATA 59.304 36.000 35.58 26.76 44.75 1.40
4718 4798 5.695816 TGTGCAAATTTTCAGGCTGAAATAC 59.304 36.000 35.58 25.90 44.75 1.89
4719 4799 5.695816 GTGCAAATTTTCAGGCTGAAATACA 59.304 36.000 35.58 25.89 44.75 2.29
4720 4800 6.369615 GTGCAAATTTTCAGGCTGAAATACAT 59.630 34.615 35.58 25.56 44.75 2.29
4721 4801 6.935771 TGCAAATTTTCAGGCTGAAATACATT 59.064 30.769 35.58 28.76 44.75 2.71
4722 4802 8.093307 TGCAAATTTTCAGGCTGAAATACATTA 58.907 29.630 35.58 23.35 44.75 1.90
4723 4803 8.934825 GCAAATTTTCAGGCTGAAATACATTAA 58.065 29.630 35.58 22.72 44.75 1.40
4728 4808 9.995003 TTTTCAGGCTGAAATACATTAAAATGT 57.005 25.926 35.58 12.61 44.75 2.71
4729 4809 8.984891 TTCAGGCTGAAATACATTAAAATGTG 57.015 30.769 26.78 2.27 40.45 3.21
4730 4810 8.801299 TTCAGGCTGAAATACATTAAAATGTGA 58.199 29.630 26.78 0.00 40.45 3.58
4761 4841 5.876651 AAAAAGACAAATCTGGAGCCTTT 57.123 34.783 0.00 0.00 34.48 3.11
4762 4842 5.876651 AAAAGACAAATCTGGAGCCTTTT 57.123 34.783 0.00 0.00 34.48 2.27
4763 4843 6.976934 AAAAGACAAATCTGGAGCCTTTTA 57.023 33.333 0.00 0.00 34.48 1.52
4764 4844 6.581171 AAAGACAAATCTGGAGCCTTTTAG 57.419 37.500 0.00 0.00 34.48 1.85
4765 4845 4.013050 AGACAAATCTGGAGCCTTTTAGC 58.987 43.478 0.00 0.00 32.29 3.09
4766 4846 3.758554 GACAAATCTGGAGCCTTTTAGCA 59.241 43.478 0.00 0.00 34.23 3.49
4767 4847 4.347607 ACAAATCTGGAGCCTTTTAGCAT 58.652 39.130 0.00 0.00 34.23 3.79
4768 4848 5.509498 ACAAATCTGGAGCCTTTTAGCATA 58.491 37.500 0.00 0.00 34.23 3.14
4769 4849 6.131961 ACAAATCTGGAGCCTTTTAGCATAT 58.868 36.000 0.00 0.00 34.23 1.78
4770 4850 6.040166 ACAAATCTGGAGCCTTTTAGCATATG 59.960 38.462 0.00 0.00 34.23 1.78
4771 4851 4.778213 TCTGGAGCCTTTTAGCATATGT 57.222 40.909 4.29 0.00 34.23 2.29
4772 4852 5.887214 TCTGGAGCCTTTTAGCATATGTA 57.113 39.130 4.29 0.00 34.23 2.29
4773 4853 5.611374 TCTGGAGCCTTTTAGCATATGTAC 58.389 41.667 4.29 0.00 34.23 2.90
4774 4854 5.366768 TCTGGAGCCTTTTAGCATATGTACT 59.633 40.000 4.29 0.00 34.23 2.73
4775 4855 5.368145 TGGAGCCTTTTAGCATATGTACTG 58.632 41.667 4.29 0.00 34.23 2.74
4776 4856 5.104527 TGGAGCCTTTTAGCATATGTACTGT 60.105 40.000 4.29 0.00 34.23 3.55
4777 4857 5.823045 GGAGCCTTTTAGCATATGTACTGTT 59.177 40.000 4.29 0.00 34.23 3.16
4778 4858 6.017852 GGAGCCTTTTAGCATATGTACTGTTC 60.018 42.308 4.29 0.00 34.23 3.18
4779 4859 6.414732 AGCCTTTTAGCATATGTACTGTTCA 58.585 36.000 4.29 0.00 34.23 3.18
4780 4860 7.056635 AGCCTTTTAGCATATGTACTGTTCAT 58.943 34.615 4.29 5.26 34.23 2.57
4781 4861 7.227512 AGCCTTTTAGCATATGTACTGTTCATC 59.772 37.037 4.29 0.00 34.23 2.92
4782 4862 7.227512 GCCTTTTAGCATATGTACTGTTCATCT 59.772 37.037 4.29 0.00 0.00 2.90
4783 4863 9.764363 CCTTTTAGCATATGTACTGTTCATCTA 57.236 33.333 4.29 0.00 0.00 1.98
4794 4874 9.770097 ATGTACTGTTCATCTATAAAGTCCATG 57.230 33.333 0.00 0.00 0.00 3.66
4795 4875 8.977412 TGTACTGTTCATCTATAAAGTCCATGA 58.023 33.333 0.00 0.00 0.00 3.07
4796 4876 9.988815 GTACTGTTCATCTATAAAGTCCATGAT 57.011 33.333 0.00 0.00 0.00 2.45
4798 4878 9.911788 ACTGTTCATCTATAAAGTCCATGATTT 57.088 29.630 0.00 0.00 0.00 2.17
4801 4881 9.956720 GTTCATCTATAAAGTCCATGATTTTGG 57.043 33.333 0.00 0.00 38.18 3.28
4802 4882 9.699410 TTCATCTATAAAGTCCATGATTTTGGT 57.301 29.630 0.00 0.00 38.01 3.67
4803 4883 9.699410 TCATCTATAAAGTCCATGATTTTGGTT 57.301 29.630 0.00 0.00 38.01 3.67
4839 4919 6.855763 TTGCAATTCAAGGTATTTCATCCT 57.144 33.333 0.00 0.00 35.34 3.24
4840 4920 6.211587 TGCAATTCAAGGTATTTCATCCTG 57.788 37.500 0.00 0.00 33.97 3.86
4841 4921 5.951148 TGCAATTCAAGGTATTTCATCCTGA 59.049 36.000 0.00 0.00 33.97 3.86
4842 4922 6.436847 TGCAATTCAAGGTATTTCATCCTGAA 59.563 34.615 0.00 0.00 34.03 3.02
4854 4934 6.477053 TTTCATCCTGAAATTTTCCACACA 57.523 33.333 6.68 0.00 41.02 3.72
4855 4935 6.669125 TTCATCCTGAAATTTTCCACACAT 57.331 33.333 6.68 0.00 32.71 3.21
4856 4936 7.773489 TTCATCCTGAAATTTTCCACACATA 57.227 32.000 6.68 0.00 32.71 2.29
4857 4937 7.156876 TCATCCTGAAATTTTCCACACATAC 57.843 36.000 6.68 0.00 0.00 2.39
4858 4938 6.718912 TCATCCTGAAATTTTCCACACATACA 59.281 34.615 6.68 0.00 0.00 2.29
4859 4939 6.325919 TCCTGAAATTTTCCACACATACAC 57.674 37.500 6.68 0.00 0.00 2.90
4860 4940 6.068010 TCCTGAAATTTTCCACACATACACT 58.932 36.000 6.68 0.00 0.00 3.55
4861 4941 6.549364 TCCTGAAATTTTCCACACATACACTT 59.451 34.615 6.68 0.00 0.00 3.16
4862 4942 7.069331 TCCTGAAATTTTCCACACATACACTTT 59.931 33.333 6.68 0.00 0.00 2.66
4863 4943 8.356657 CCTGAAATTTTCCACACATACACTTTA 58.643 33.333 6.68 0.00 0.00 1.85
4864 4944 9.180678 CTGAAATTTTCCACACATACACTTTAC 57.819 33.333 6.68 0.00 0.00 2.01
4865 4945 8.687242 TGAAATTTTCCACACATACACTTTACA 58.313 29.630 6.68 0.00 0.00 2.41
4866 4946 9.691362 GAAATTTTCCACACATACACTTTACAT 57.309 29.630 0.00 0.00 0.00 2.29
4867 4947 9.691362 AAATTTTCCACACATACACTTTACATC 57.309 29.630 0.00 0.00 0.00 3.06
4868 4948 6.811253 TTTCCACACATACACTTTACATCC 57.189 37.500 0.00 0.00 0.00 3.51
4869 4949 5.755409 TCCACACATACACTTTACATCCT 57.245 39.130 0.00 0.00 0.00 3.24
4870 4950 6.121776 TCCACACATACACTTTACATCCTT 57.878 37.500 0.00 0.00 0.00 3.36
4871 4951 5.937540 TCCACACATACACTTTACATCCTTG 59.062 40.000 0.00 0.00 0.00 3.61
4872 4952 5.391950 CCACACATACACTTTACATCCTTGC 60.392 44.000 0.00 0.00 0.00 4.01
4873 4953 5.181056 CACACATACACTTTACATCCTTGCA 59.819 40.000 0.00 0.00 0.00 4.08
4874 4954 5.945784 ACACATACACTTTACATCCTTGCAT 59.054 36.000 0.00 0.00 0.00 3.96
4875 4955 7.065683 CACACATACACTTTACATCCTTGCATA 59.934 37.037 0.00 0.00 0.00 3.14
4876 4956 7.065803 ACACATACACTTTACATCCTTGCATAC 59.934 37.037 0.00 0.00 0.00 2.39
4877 4957 7.065683 CACATACACTTTACATCCTTGCATACA 59.934 37.037 0.00 0.00 0.00 2.29
4878 4958 7.775093 ACATACACTTTACATCCTTGCATACAT 59.225 33.333 0.00 0.00 0.00 2.29
4879 4959 6.441093 ACACTTTACATCCTTGCATACATG 57.559 37.500 0.00 0.00 0.00 3.21
4880 4960 5.945784 ACACTTTACATCCTTGCATACATGT 59.054 36.000 2.69 2.69 33.95 3.21
4881 4961 6.127925 ACACTTTACATCCTTGCATACATGTG 60.128 38.462 9.11 0.00 31.83 3.21
4882 4962 5.945784 ACTTTACATCCTTGCATACATGTGT 59.054 36.000 9.11 0.00 31.83 3.72
4883 4963 7.065683 CACTTTACATCCTTGCATACATGTGTA 59.934 37.037 9.11 0.00 31.83 2.90
4884 4964 7.775093 ACTTTACATCCTTGCATACATGTGTAT 59.225 33.333 9.11 0.00 41.58 2.29
4885 4965 8.518430 TTTACATCCTTGCATACATGTGTATT 57.482 30.769 9.11 0.00 39.06 1.89
4886 4966 8.518430 TTACATCCTTGCATACATGTGTATTT 57.482 30.769 9.11 0.00 39.06 1.40
4887 4967 7.408756 ACATCCTTGCATACATGTGTATTTT 57.591 32.000 9.11 0.00 39.06 1.82
4888 4968 7.839907 ACATCCTTGCATACATGTGTATTTTT 58.160 30.769 9.11 0.00 39.06 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 57 3.882888 CAGAGCCTGGAACACAAACTTAA 59.117 43.478 0.00 0.00 0.00 1.85
54 58 3.135712 TCAGAGCCTGGAACACAAACTTA 59.864 43.478 0.00 0.00 31.51 2.24
60 64 0.615331 GGATCAGAGCCTGGAACACA 59.385 55.000 0.00 0.00 31.51 3.72
66 70 1.462731 CGAGGAGGATCAGAGCCTGG 61.463 65.000 13.41 0.00 35.44 4.45
95 99 5.099042 AGCTCCGTTTACTACATCCAAAT 57.901 39.130 0.00 0.00 0.00 2.32
97 101 3.118884 GGAGCTCCGTTTACTACATCCAA 60.119 47.826 19.06 0.00 0.00 3.53
121 125 4.388378 AAGAGACAATAGGAACCTACGC 57.612 45.455 2.47 0.00 0.00 4.42
140 144 1.668419 CTAATCTCACCGCCCCAAAG 58.332 55.000 0.00 0.00 0.00 2.77
193 197 1.471119 CTTGCATGGGTCTGAAGCAT 58.529 50.000 0.00 0.00 34.87 3.79
222 226 1.189403 CCTGAAGTCGTTATCGTCGC 58.811 55.000 0.00 0.00 38.33 5.19
229 233 1.290955 CCACCGCCTGAAGTCGTTA 59.709 57.895 0.00 0.00 0.00 3.18
250 256 0.244450 TTCGTACACGTGCCCCTAAG 59.756 55.000 17.22 2.94 40.80 2.18
308 314 0.389037 GTTGTCGTCGTTCCCCTACC 60.389 60.000 0.00 0.00 0.00 3.18
317 323 1.439365 GACGCGTAGTTGTCGTCGT 60.439 57.895 13.97 0.00 42.18 4.34
345 351 4.185467 ACAATCACTACTGCTGTCAGAG 57.815 45.455 3.32 1.03 42.95 3.35
352 358 2.108250 ACCCCAAACAATCACTACTGCT 59.892 45.455 0.00 0.00 0.00 4.24
406 413 7.500992 AGCTTAGCATAAGTACAAAGCATCTA 58.499 34.615 7.07 0.00 41.31 1.98
452 459 7.389884 GGTTTTAGACTACCTCTTTTCCGAAAT 59.610 37.037 0.00 0.00 0.00 2.17
499 506 8.857098 TCTATCTTGTCAGTACAAAACACTAGT 58.143 33.333 0.00 0.00 44.79 2.57
519 526 6.951198 ACATCCGGTCTATTCTTCATCTATCT 59.049 38.462 0.00 0.00 0.00 1.98
555 562 1.923227 CTCCGCTTCCCCTTTTTCGC 61.923 60.000 0.00 0.00 0.00 4.70
564 571 3.691297 TACTCCCCCTCCGCTTCCC 62.691 68.421 0.00 0.00 0.00 3.97
635 650 2.029020 TGGATTGACTGACTCGAGTTGG 60.029 50.000 21.08 17.04 0.00 3.77
656 671 4.988598 CAGACTGTGCGGGCCGTT 62.989 66.667 28.82 6.83 0.00 4.44
668 683 2.201436 CTGCGTACTGCCGTCAGACT 62.201 60.000 0.00 0.00 45.60 3.24
670 685 2.566529 CTGCGTACTGCCGTCAGA 59.433 61.111 0.00 0.00 45.60 3.27
734 749 1.975407 GGGAGGAACCACGACGAGA 60.975 63.158 0.00 0.00 41.20 4.04
735 750 2.572284 GGGAGGAACCACGACGAG 59.428 66.667 0.00 0.00 41.20 4.18
736 751 2.993264 GGGGAGGAACCACGACGA 60.993 66.667 0.00 0.00 41.20 4.20
737 752 4.078516 GGGGGAGGAACCACGACG 62.079 72.222 0.00 0.00 44.45 5.12
738 753 2.522367 TTGGGGGAGGAACCACGAC 61.522 63.158 0.00 0.00 44.45 4.34
827 843 1.275573 GACCTCGGGAGCACTAGTTTT 59.724 52.381 0.00 0.00 0.00 2.43
889 911 1.912763 GGGTTTTGCTGCCCATGGA 60.913 57.895 15.22 0.00 44.23 3.41
1311 1339 3.402681 ACCCACTGGCCCATCGAG 61.403 66.667 0.00 0.00 33.59 4.04
1387 1415 3.723348 GAAGGCCGCCGTGTTGAC 61.723 66.667 1.24 0.00 0.00 3.18
1521 1549 3.222855 CCGAGGATCTCAGCGCCT 61.223 66.667 2.29 0.00 33.97 5.52
1551 1579 1.072806 TGGAGAGTGCAGCTGAAATGT 59.927 47.619 20.43 4.05 0.00 2.71
1567 1595 6.971184 CAGTAAAATTAAGCAAGCTGATGGAG 59.029 38.462 0.00 0.00 0.00 3.86
1572 1600 6.262049 TGTGACAGTAAAATTAAGCAAGCTGA 59.738 34.615 0.00 0.00 0.00 4.26
1592 1620 8.128582 TCATACAATCTTGTCAAAACTTGTGAC 58.871 33.333 5.25 5.25 44.67 3.67
1598 1626 9.209175 GACTAGTCATACAATCTTGTCAAAACT 57.791 33.333 18.20 3.03 42.35 2.66
1610 1638 9.905713 ATACCAATTTGTGACTAGTCATACAAT 57.094 29.630 27.54 20.66 42.18 2.71
1658 1695 7.341256 AGAGCCAATGTGAGTCATTAATTCAAT 59.659 33.333 0.00 0.00 43.93 2.57
1659 1696 6.660521 AGAGCCAATGTGAGTCATTAATTCAA 59.339 34.615 0.00 0.00 43.93 2.69
1679 1716 5.112686 CAGGAACAGTGTTATTCTAGAGCC 58.887 45.833 8.88 2.48 0.00 4.70
1680 1717 5.725362 ACAGGAACAGTGTTATTCTAGAGC 58.275 41.667 8.88 0.00 0.00 4.09
1683 1720 5.869888 GTGGACAGGAACAGTGTTATTCTAG 59.130 44.000 8.88 5.33 0.00 2.43
1697 1734 2.906389 ACTAAGCATGAGTGGACAGGAA 59.094 45.455 0.00 0.00 0.00 3.36
1733 1770 7.760131 AGTTTGAAACAAAATGACATCACTG 57.240 32.000 11.02 0.00 0.00 3.66
1735 1772 9.515020 TCTAAGTTTGAAACAAAATGACATCAC 57.485 29.630 11.02 0.00 0.00 3.06
1787 1825 7.389607 ACTGTAAAAGTTACAGCCAAACGATAT 59.610 33.333 22.16 2.64 46.46 1.63
1794 1832 4.819630 CCAGACTGTAAAAGTTACAGCCAA 59.180 41.667 22.16 0.00 46.46 4.52
1814 1852 4.021719 ACTCATTGGAAGAAAATGCACCAG 60.022 41.667 0.00 0.00 35.43 4.00
1836 1874 3.848019 CGCAATAAGCTGTCAATGTTGAC 59.152 43.478 16.82 16.82 46.38 3.18
1900 1938 4.430007 CGTATCCATATGACGGTAATGGG 58.570 47.826 3.65 4.79 40.53 4.00
1909 1947 4.218635 TGCTCTCTTCCGTATCCATATGAC 59.781 45.833 3.65 0.00 0.00 3.06
1921 1959 1.069358 GGTCCCTTATGCTCTCTTCCG 59.931 57.143 0.00 0.00 0.00 4.30
1933 1971 2.822006 GCTCCCATATCGAGGTCCCTTA 60.822 54.545 0.00 0.00 0.00 2.69
1957 1995 4.536090 TCCTTCAGGTCTTGACCATGTATT 59.464 41.667 20.36 0.00 34.94 1.89
2010 2048 5.893726 CGTTAAAATGCAACAAAAGGAAACG 59.106 36.000 0.00 0.00 0.00 3.60
2073 2111 7.039784 AGCATTGAAATGGACTAAGCAAGTAAA 60.040 33.333 5.25 0.00 36.30 2.01
2229 2267 8.117988 GTCGCAAATACGGATACTTCATTTTAA 58.882 33.333 0.00 0.00 0.00 1.52
2244 2282 3.093717 AGATAGGTGGTCGCAAATACG 57.906 47.619 0.00 0.00 0.00 3.06
2269 2307 5.888161 ACTTTCATGGTGGGACTTAATGATC 59.112 40.000 0.00 0.00 0.00 2.92
2286 2328 8.443176 ACATAGGATCATCCAACATACTTTCAT 58.557 33.333 6.42 0.00 39.61 2.57
2353 2395 8.006298 TCTTCACATGAATAACCAACAAAACT 57.994 30.769 0.00 0.00 33.01 2.66
2598 2640 0.253327 GAGGACCCCTGGTGTGATTC 59.747 60.000 0.00 0.00 35.25 2.52
2697 2739 3.599343 TGTGACATCCTTGCAGTCATAC 58.401 45.455 8.74 0.00 43.35 2.39
2769 2811 4.319177 GAAAATGACCTGGATCTATCCCG 58.681 47.826 0.00 0.12 46.59 5.14
3297 3356 7.381408 TGATCTGACAAACTTTGACTAGTAACG 59.619 37.037 8.55 0.00 0.00 3.18
3531 3590 3.800506 CGGTCTTTATCACGATACCAACC 59.199 47.826 0.00 1.20 0.00 3.77
3537 3596 7.384932 TCGTTATAGTCGGTCTTTATCACGATA 59.615 37.037 0.00 0.00 37.69 2.92
3609 3668 9.948964 CCATGGATTGACATATAAGAGATGTTA 57.051 33.333 5.56 0.00 37.65 2.41
3623 3682 1.559368 CCTTTGCCCATGGATTGACA 58.441 50.000 15.22 0.00 0.00 3.58
3720 3779 5.804639 ACATGGTGCTTCTTGTCAAGTATA 58.195 37.500 12.30 0.00 0.00 1.47
3894 3953 4.352600 AATAGTACAGTGAGACGAACCG 57.647 45.455 0.00 0.00 0.00 4.44
3917 3976 2.245028 AGCTGACCACTGGATACTCCTA 59.755 50.000 0.71 0.00 37.46 2.94
3932 3991 4.143009 GCAGTAAAGCAAGACTAAGCTGAC 60.143 45.833 3.35 5.43 41.70 3.51
3947 4007 6.515272 AAATTCCCTGTGTATGCAGTAAAG 57.485 37.500 0.00 0.00 34.84 1.85
3965 4025 7.837505 GGTGTAAACAGCTACAAACAAAATTC 58.162 34.615 5.09 0.00 40.88 2.17
3996 4056 4.020928 TCCTTAAATACACGCCTGAGACAA 60.021 41.667 0.00 0.00 0.00 3.18
4055 4115 4.866486 GGGATGAAATGTGAAAACAGATGC 59.134 41.667 0.00 0.00 0.00 3.91
4162 4230 6.570571 CGAAGACCTTTTGACAGAGTGAGATA 60.571 42.308 0.00 0.00 0.00 1.98
4187 4255 5.808540 TGTATGGCTGTACTGACGTTATTTC 59.191 40.000 5.55 0.00 0.00 2.17
4239 4307 7.550906 AGACTAGCAGAATAAGATTTGTTCCAC 59.449 37.037 0.00 0.00 31.92 4.02
4356 4426 2.664916 GCATGCTGCGAAAGAAAGAAA 58.335 42.857 11.37 0.00 31.71 2.52
4357 4427 2.336554 GCATGCTGCGAAAGAAAGAA 57.663 45.000 11.37 0.00 31.71 2.52
4486 4566 2.286872 CTGCTGATCCCTGACATGAAC 58.713 52.381 0.00 0.00 0.00 3.18
4488 4568 1.576577 ACTGCTGATCCCTGACATGA 58.423 50.000 0.00 0.00 0.00 3.07
4551 4631 4.700268 TTCGCGTATGTAGTCCTTGTTA 57.300 40.909 5.77 0.00 0.00 2.41
4554 4634 4.782195 GCATTTTCGCGTATGTAGTCCTTG 60.782 45.833 5.77 0.00 0.00 3.61
4562 4642 2.591133 GTTTGGCATTTTCGCGTATGT 58.409 42.857 5.77 0.00 0.00 2.29
4569 4649 1.401018 GGTCTCCGTTTGGCATTTTCG 60.401 52.381 0.00 0.00 34.14 3.46
4570 4650 1.401018 CGGTCTCCGTTTGGCATTTTC 60.401 52.381 0.00 0.00 42.73 2.29
4571 4651 0.596082 CGGTCTCCGTTTGGCATTTT 59.404 50.000 0.00 0.00 42.73 1.82
4572 4652 2.253513 CGGTCTCCGTTTGGCATTT 58.746 52.632 0.00 0.00 42.73 2.32
4573 4653 3.981308 CGGTCTCCGTTTGGCATT 58.019 55.556 0.00 0.00 42.73 3.56
4584 4664 1.739049 CTCCATGGAGCTCGGTCTC 59.261 63.158 28.45 0.00 35.31 3.36
4585 4665 1.760086 CCTCCATGGAGCTCGGTCT 60.760 63.158 32.97 0.00 40.69 3.85
4586 4666 2.818132 CCTCCATGGAGCTCGGTC 59.182 66.667 32.97 0.00 40.69 4.79
4587 4667 3.474570 GCCTCCATGGAGCTCGGT 61.475 66.667 32.97 0.00 40.69 4.69
4588 4668 4.247380 GGCCTCCATGGAGCTCGG 62.247 72.222 32.97 22.55 40.69 4.63
4589 4669 2.262774 AAAGGCCTCCATGGAGCTCG 62.263 60.000 32.97 21.57 40.69 5.03
4590 4670 0.839946 TAAAGGCCTCCATGGAGCTC 59.160 55.000 32.97 25.21 40.69 4.09
4591 4671 1.527457 ATAAAGGCCTCCATGGAGCT 58.473 50.000 32.97 23.24 40.69 4.09
4592 4672 2.363359 CAAATAAAGGCCTCCATGGAGC 59.637 50.000 32.97 26.44 40.69 4.70
4593 4673 3.902218 TCAAATAAAGGCCTCCATGGAG 58.098 45.455 31.69 31.69 41.63 3.86
4594 4674 4.329638 TTCAAATAAAGGCCTCCATGGA 57.670 40.909 15.27 15.27 38.35 3.41
4595 4675 5.046376 AGTTTTCAAATAAAGGCCTCCATGG 60.046 40.000 5.23 4.97 39.35 3.66
4596 4676 6.041423 AGTTTTCAAATAAAGGCCTCCATG 57.959 37.500 5.23 1.29 0.00 3.66
4597 4677 6.686484 AAGTTTTCAAATAAAGGCCTCCAT 57.314 33.333 5.23 0.00 0.00 3.41
4598 4678 6.493189 AAAGTTTTCAAATAAAGGCCTCCA 57.507 33.333 5.23 0.00 0.00 3.86
4599 4679 8.896320 TTTAAAGTTTTCAAATAAAGGCCTCC 57.104 30.769 5.23 0.00 0.00 4.30
4672 4752 7.872993 GCACACATGTACATTATGTATCTAGGT 59.127 37.037 17.98 4.03 36.67 3.08
4673 4753 7.872483 TGCACACATGTACATTATGTATCTAGG 59.128 37.037 17.98 9.14 36.67 3.02
4674 4754 8.816640 TGCACACATGTACATTATGTATCTAG 57.183 34.615 17.98 9.67 36.67 2.43
4675 4755 9.606631 TTTGCACACATGTACATTATGTATCTA 57.393 29.630 17.98 9.97 36.67 1.98
4676 4756 8.504812 TTTGCACACATGTACATTATGTATCT 57.495 30.769 17.98 0.00 36.67 1.98
4677 4757 9.734620 AATTTGCACACATGTACATTATGTATC 57.265 29.630 17.98 14.10 36.67 2.24
4679 4759 9.920133 AAAATTTGCACACATGTACATTATGTA 57.080 25.926 17.98 0.29 36.67 2.29
4680 4760 8.830201 AAAATTTGCACACATGTACATTATGT 57.170 26.923 14.24 14.24 39.23 2.29
4681 4761 8.923683 TGAAAATTTGCACACATGTACATTATG 58.076 29.630 5.37 10.25 0.00 1.90
4682 4762 9.142515 CTGAAAATTTGCACACATGTACATTAT 57.857 29.630 5.37 0.00 0.00 1.28
4683 4763 7.598118 CCTGAAAATTTGCACACATGTACATTA 59.402 33.333 5.37 0.00 0.00 1.90
4684 4764 6.424509 CCTGAAAATTTGCACACATGTACATT 59.575 34.615 5.37 0.00 0.00 2.71
4685 4765 5.927689 CCTGAAAATTTGCACACATGTACAT 59.072 36.000 1.41 1.41 0.00 2.29
4686 4766 5.288015 CCTGAAAATTTGCACACATGTACA 58.712 37.500 0.00 0.00 0.00 2.90
4687 4767 4.150451 GCCTGAAAATTTGCACACATGTAC 59.850 41.667 0.00 0.00 0.00 2.90
4688 4768 4.039004 AGCCTGAAAATTTGCACACATGTA 59.961 37.500 0.00 0.00 0.00 2.29
4689 4769 3.132925 GCCTGAAAATTTGCACACATGT 58.867 40.909 0.00 0.00 0.00 3.21
4690 4770 3.185594 CAGCCTGAAAATTTGCACACATG 59.814 43.478 0.00 0.00 0.00 3.21
4691 4771 3.069872 TCAGCCTGAAAATTTGCACACAT 59.930 39.130 0.00 0.00 0.00 3.21
4692 4772 2.429971 TCAGCCTGAAAATTTGCACACA 59.570 40.909 0.00 0.00 0.00 3.72
4693 4773 3.096489 TCAGCCTGAAAATTTGCACAC 57.904 42.857 0.00 0.00 0.00 3.82
4694 4774 3.815856 TTCAGCCTGAAAATTTGCACA 57.184 38.095 4.27 0.00 32.71 4.57
4703 4783 9.421806 CACATTTTAATGTATTTCAGCCTGAAA 57.578 29.630 21.26 21.26 46.75 2.69
4739 4819 5.876651 AAAGGCTCCAGATTTGTCTTTTT 57.123 34.783 0.00 0.00 0.00 1.94
4740 4820 5.876651 AAAAGGCTCCAGATTTGTCTTTT 57.123 34.783 0.00 0.00 0.00 2.27
4741 4821 5.047731 GCTAAAAGGCTCCAGATTTGTCTTT 60.048 40.000 0.00 0.00 0.00 2.52
4742 4822 4.460731 GCTAAAAGGCTCCAGATTTGTCTT 59.539 41.667 0.00 0.00 0.00 3.01
4743 4823 4.013050 GCTAAAAGGCTCCAGATTTGTCT 58.987 43.478 0.00 0.00 0.00 3.41
4744 4824 3.758554 TGCTAAAAGGCTCCAGATTTGTC 59.241 43.478 0.00 0.00 0.00 3.18
4745 4825 3.766545 TGCTAAAAGGCTCCAGATTTGT 58.233 40.909 0.00 0.00 0.00 2.83
4746 4826 4.996788 ATGCTAAAAGGCTCCAGATTTG 57.003 40.909 0.00 0.00 0.00 2.32
4747 4827 6.131961 ACATATGCTAAAAGGCTCCAGATTT 58.868 36.000 1.58 0.00 0.00 2.17
4748 4828 5.699143 ACATATGCTAAAAGGCTCCAGATT 58.301 37.500 1.58 0.00 0.00 2.40
4749 4829 5.316158 ACATATGCTAAAAGGCTCCAGAT 57.684 39.130 1.58 0.00 0.00 2.90
4750 4830 4.778213 ACATATGCTAAAAGGCTCCAGA 57.222 40.909 1.58 0.00 0.00 3.86
4751 4831 5.468072 CAGTACATATGCTAAAAGGCTCCAG 59.532 44.000 1.58 0.00 0.00 3.86
4752 4832 5.104527 ACAGTACATATGCTAAAAGGCTCCA 60.105 40.000 1.58 0.00 0.00 3.86
4753 4833 5.368989 ACAGTACATATGCTAAAAGGCTCC 58.631 41.667 1.58 0.00 0.00 4.70
4754 4834 6.538742 TGAACAGTACATATGCTAAAAGGCTC 59.461 38.462 1.58 0.00 0.00 4.70
4755 4835 6.414732 TGAACAGTACATATGCTAAAAGGCT 58.585 36.000 1.58 0.00 0.00 4.58
4756 4836 6.677781 TGAACAGTACATATGCTAAAAGGC 57.322 37.500 1.58 0.00 0.00 4.35
4757 4837 8.668510 AGATGAACAGTACATATGCTAAAAGG 57.331 34.615 1.58 0.00 0.00 3.11
4768 4848 9.770097 CATGGACTTTATAGATGAACAGTACAT 57.230 33.333 0.00 0.00 36.43 2.29
4769 4849 8.977412 TCATGGACTTTATAGATGAACAGTACA 58.023 33.333 0.00 0.00 29.71 2.90
4770 4850 9.988815 ATCATGGACTTTATAGATGAACAGTAC 57.011 33.333 0.00 0.00 0.00 2.73
4772 4852 9.911788 AAATCATGGACTTTATAGATGAACAGT 57.088 29.630 0.00 0.00 0.00 3.55
4775 4855 9.956720 CCAAAATCATGGACTTTATAGATGAAC 57.043 33.333 0.00 0.00 43.54 3.18
4776 4856 9.699410 ACCAAAATCATGGACTTTATAGATGAA 57.301 29.630 0.00 0.00 43.54 2.57
4777 4857 9.699410 AACCAAAATCATGGACTTTATAGATGA 57.301 29.630 0.00 0.00 43.54 2.92
4804 4884 6.586868 CTTGAATTGCAAGCTGTACAAAAA 57.413 33.333 4.94 0.00 46.67 1.94
4814 4894 8.579705 CAGGATGAAATACCTTGAATTGCAAGC 61.580 40.741 4.94 0.00 45.98 4.01
4815 4895 6.755141 CAGGATGAAATACCTTGAATTGCAAG 59.245 38.462 4.94 0.00 46.53 4.01
4816 4896 6.436847 TCAGGATGAAATACCTTGAATTGCAA 59.563 34.615 0.00 0.00 45.97 4.08
4817 4897 5.951148 TCAGGATGAAATACCTTGAATTGCA 59.049 36.000 0.00 0.00 45.97 4.08
4818 4898 6.455360 TCAGGATGAAATACCTTGAATTGC 57.545 37.500 0.00 0.00 45.97 3.56
4834 4914 6.808212 GTGTATGTGTGGAAAATTTCAGGATG 59.192 38.462 8.09 0.00 37.54 3.51
4835 4915 6.721208 AGTGTATGTGTGGAAAATTTCAGGAT 59.279 34.615 8.09 0.00 0.00 3.24
4836 4916 6.068010 AGTGTATGTGTGGAAAATTTCAGGA 58.932 36.000 8.09 0.00 0.00 3.86
4837 4917 6.331369 AGTGTATGTGTGGAAAATTTCAGG 57.669 37.500 8.09 0.00 0.00 3.86
4838 4918 9.180678 GTAAAGTGTATGTGTGGAAAATTTCAG 57.819 33.333 8.09 0.00 0.00 3.02
4839 4919 8.687242 TGTAAAGTGTATGTGTGGAAAATTTCA 58.313 29.630 8.09 0.00 0.00 2.69
4840 4920 9.691362 ATGTAAAGTGTATGTGTGGAAAATTTC 57.309 29.630 0.00 0.00 0.00 2.17
4841 4921 9.691362 GATGTAAAGTGTATGTGTGGAAAATTT 57.309 29.630 0.00 0.00 0.00 1.82
4842 4922 8.303876 GGATGTAAAGTGTATGTGTGGAAAATT 58.696 33.333 0.00 0.00 0.00 1.82
4843 4923 7.669722 AGGATGTAAAGTGTATGTGTGGAAAAT 59.330 33.333 0.00 0.00 0.00 1.82
4844 4924 7.001674 AGGATGTAAAGTGTATGTGTGGAAAA 58.998 34.615 0.00 0.00 0.00 2.29
4845 4925 6.539173 AGGATGTAAAGTGTATGTGTGGAAA 58.461 36.000 0.00 0.00 0.00 3.13
4846 4926 6.121776 AGGATGTAAAGTGTATGTGTGGAA 57.878 37.500 0.00 0.00 0.00 3.53
4847 4927 5.755409 AGGATGTAAAGTGTATGTGTGGA 57.245 39.130 0.00 0.00 0.00 4.02
4848 4928 5.391950 GCAAGGATGTAAAGTGTATGTGTGG 60.392 44.000 0.00 0.00 0.00 4.17
4849 4929 5.181056 TGCAAGGATGTAAAGTGTATGTGTG 59.819 40.000 0.00 0.00 0.00 3.82
4850 4930 5.312895 TGCAAGGATGTAAAGTGTATGTGT 58.687 37.500 0.00 0.00 0.00 3.72
4851 4931 5.878332 TGCAAGGATGTAAAGTGTATGTG 57.122 39.130 0.00 0.00 0.00 3.21
4852 4932 7.109501 TGTATGCAAGGATGTAAAGTGTATGT 58.890 34.615 0.00 0.00 0.00 2.29
4853 4933 7.552458 TGTATGCAAGGATGTAAAGTGTATG 57.448 36.000 0.00 0.00 0.00 2.39
4854 4934 7.775093 ACATGTATGCAAGGATGTAAAGTGTAT 59.225 33.333 0.00 0.00 0.00 2.29
4855 4935 7.065683 CACATGTATGCAAGGATGTAAAGTGTA 59.934 37.037 0.00 0.00 0.00 2.90
4856 4936 5.945784 ACATGTATGCAAGGATGTAAAGTGT 59.054 36.000 0.00 0.00 0.00 3.55
4857 4937 6.127925 ACACATGTATGCAAGGATGTAAAGTG 60.128 38.462 0.00 0.00 0.00 3.16
4858 4938 5.945784 ACACATGTATGCAAGGATGTAAAGT 59.054 36.000 0.00 1.15 0.00 2.66
4859 4939 6.441093 ACACATGTATGCAAGGATGTAAAG 57.559 37.500 0.00 0.66 0.00 1.85
4860 4940 8.518430 AATACACATGTATGCAAGGATGTAAA 57.482 30.769 0.00 1.34 40.78 2.01
4861 4941 8.518430 AAATACACATGTATGCAAGGATGTAA 57.482 30.769 0.00 1.61 40.78 2.41
4862 4942 8.518430 AAAATACACATGTATGCAAGGATGTA 57.482 30.769 0.00 4.93 40.78 2.29
4863 4943 7.408756 AAAATACACATGTATGCAAGGATGT 57.591 32.000 0.00 0.00 40.78 3.06


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

AutoCloner maintained by Alex Coulton.