Multiple sequence alignment - TraesCS4B01G090700

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 TraesCS4B01G090700 chr4B 100.000 5387 0 0 1 5387 93292395 93287009 0.000000e+00 9949.0
1 TraesCS4B01G090700 chr4D 94.187 4559 109 47 793 5303 62880695 62876245 0.000000e+00 6807.0
2 TraesCS4B01G090700 chr4D 89.001 691 51 11 1 682 62881444 62880770 0.000000e+00 832.0
3 TraesCS4B01G090700 chr4D 86.497 785 59 19 34 794 62883399 62882638 0.000000e+00 819.0
4 TraesCS4B01G090700 chr4D 93.939 66 1 1 730 795 62880776 62880714 4.440000e-16 97.1
5 TraesCS4B01G090700 chr4A 92.863 3895 130 55 742 4558 533444374 533448198 0.000000e+00 5517.0
6 TraesCS4B01G090700 chr4A 93.590 468 17 7 4780 5243 533448197 533448655 0.000000e+00 686.0
7 TraesCS4B01G090700 chr4A 86.751 634 40 19 132 759 533443734 533444329 0.000000e+00 665.0
8 TraesCS4B01G090700 chr3A 96.875 96 1 2 5292 5387 744439301 744439208 5.580000e-35 159.0
9 TraesCS4B01G090700 chr3A 97.778 90 1 1 5298 5387 311128372 311128284 2.600000e-33 154.0
10 TraesCS4B01G090700 chr3A 95.833 96 3 1 5293 5387 568149499 568149594 2.600000e-33 154.0
11 TraesCS4B01G090700 chr7B 96.842 95 1 2 5294 5387 152466573 152466666 2.010000e-34 158.0
12 TraesCS4B01G090700 chr7B 96.842 95 2 1 5293 5387 608203064 608203157 2.010000e-34 158.0
13 TraesCS4B01G090700 chr7B 95.050 101 2 3 5289 5387 446162692 446162593 7.220000e-34 156.0
14 TraesCS4B01G090700 chr5B 96.842 95 1 2 5294 5387 1751353 1751260 2.010000e-34 158.0
15 TraesCS4B01G090700 chr1B 95.098 102 2 3 5288 5387 381609766 381609866 2.010000e-34 158.0
16 TraesCS4B01G090700 chr1B 95.789 95 4 0 5293 5387 26851039 26850945 2.600000e-33 154.0
17 TraesCS4B01G090700 chr6A 84.713 157 11 10 1845 1989 249149063 249149218 1.560000e-30 145.0


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 TraesCS4B01G090700 chr4B 93287009 93292395 5386 True 9949.000000 9949 100.000 1 5387 1 chr4B.!!$R1 5386
1 TraesCS4B01G090700 chr4D 62876245 62883399 7154 True 2138.775000 6807 90.906 1 5303 4 chr4D.!!$R1 5302
2 TraesCS4B01G090700 chr4A 533443734 533448655 4921 False 2289.333333 5517 91.068 132 5243 3 chr4A.!!$F1 5111

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
36 37 0.039617 AGATCATGAGACGCGCTAGC 60.040 55.000 5.73 4.06 40.74 3.42 F
37 38 0.318191 GATCATGAGACGCGCTAGCA 60.318 55.000 16.45 0.00 45.49 3.49 F
1621 3701 0.974383 AGTCGTCCGGGAATTTCTGT 59.026 50.000 0.00 0.00 0.00 3.41 F
2422 4594 1.198408 ACACGCTGAACTGCAATGATG 59.802 47.619 10.24 0.00 0.00 3.07 F
2611 4784 0.402504 TTAACGGCCATGAAGGTGGT 59.597 50.000 2.24 0.00 41.47 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 3191 0.109689 GCTAGATCCGATCGGGTTCG 60.110 60.000 32.79 18.73 39.17 3.95 R
1871 3984 1.001378 CCGTTGGGCTCTTCTTTGTTG 60.001 52.381 0.00 0.00 0.00 3.33 R
2536 4709 1.213537 GCCATGCAGCAAATGTCGT 59.786 52.632 0.00 0.00 0.00 4.34 R
3964 6138 0.739462 CGACGCACTTGCCTTGGATA 60.739 55.000 0.00 0.00 37.91 2.59 R
4486 6663 1.203287 GAAGATTTTGGTGGCCAGAGC 59.797 52.381 5.11 0.00 33.81 4.09 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.988379 TTGCACCTGACAAACAAGATC 57.012 42.857 0.00 0.00 0.00 2.75
22 23 2.929641 TGCACCTGACAAACAAGATCA 58.070 42.857 0.00 0.00 0.00 2.92
23 24 3.489355 TGCACCTGACAAACAAGATCAT 58.511 40.909 0.00 0.00 0.00 2.45
24 25 3.253921 TGCACCTGACAAACAAGATCATG 59.746 43.478 0.00 0.00 0.00 3.07
25 26 3.503363 GCACCTGACAAACAAGATCATGA 59.497 43.478 4.68 0.00 0.00 3.07
26 27 4.379186 GCACCTGACAAACAAGATCATGAG 60.379 45.833 4.68 0.00 0.00 2.90
27 28 4.999311 CACCTGACAAACAAGATCATGAGA 59.001 41.667 4.68 0.00 0.00 3.27
28 29 4.999950 ACCTGACAAACAAGATCATGAGAC 59.000 41.667 4.68 0.00 0.00 3.36
29 30 4.092529 CCTGACAAACAAGATCATGAGACG 59.907 45.833 4.68 0.00 0.00 4.18
30 31 3.433274 TGACAAACAAGATCATGAGACGC 59.567 43.478 4.68 0.00 0.00 5.19
31 32 2.413112 ACAAACAAGATCATGAGACGCG 59.587 45.455 3.53 3.53 0.00 6.01
32 33 1.002366 AACAAGATCATGAGACGCGC 58.998 50.000 5.73 0.00 0.00 6.86
33 34 0.174389 ACAAGATCATGAGACGCGCT 59.826 50.000 5.73 3.91 0.00 5.92
34 35 1.405463 ACAAGATCATGAGACGCGCTA 59.595 47.619 5.73 0.00 0.00 4.26
35 36 2.049959 CAAGATCATGAGACGCGCTAG 58.950 52.381 5.73 0.00 0.00 3.42
36 37 0.039617 AGATCATGAGACGCGCTAGC 60.040 55.000 5.73 4.06 40.74 3.42
37 38 0.318191 GATCATGAGACGCGCTAGCA 60.318 55.000 16.45 0.00 45.49 3.49
43 44 1.135228 TGAGACGCGCTAGCAACAATA 60.135 47.619 16.45 0.00 45.49 1.90
44 45 1.255600 GAGACGCGCTAGCAACAATAC 59.744 52.381 16.45 0.00 45.49 1.89
47 48 1.659098 ACGCGCTAGCAACAATACTTC 59.341 47.619 16.45 0.00 45.49 3.01
51 52 2.737359 CGCTAGCAACAATACTTCCGGA 60.737 50.000 16.45 0.00 0.00 5.14
58 59 3.594603 ACAATACTTCCGGAGTGAGTG 57.405 47.619 16.05 11.42 39.48 3.51
85 86 2.720915 ACTACTACGACTGGGAAGGTC 58.279 52.381 0.00 0.00 0.00 3.85
104 105 4.803613 AGGTCGTTTTTGAGCAATGTTTTC 59.196 37.500 0.00 0.00 38.81 2.29
105 106 4.564769 GGTCGTTTTTGAGCAATGTTTTCA 59.435 37.500 0.00 0.00 36.41 2.69
109 110 6.019156 TCGTTTTTGAGCAATGTTTTCATTCC 60.019 34.615 0.00 0.00 46.18 3.01
133 134 5.149273 GCTAATGAAATGTATCATGTGCCG 58.851 41.667 0.00 0.00 39.90 5.69
183 2165 5.814764 TTCTCTTACTATGTGGACGAGTC 57.185 43.478 0.00 0.00 0.00 3.36
206 2188 5.046159 TCACCGGGTTGTCTAGTCAATAAAT 60.046 40.000 6.32 0.00 0.00 1.40
272 2254 2.945447 AACATTTGCACCCATCATCG 57.055 45.000 0.00 0.00 0.00 3.84
288 2270 2.831526 TCATCGAGGACATCAAGTTCCA 59.168 45.455 0.00 0.00 0.00 3.53
330 2312 5.063438 CCAAACATGAAGTGGTAGTATGTCG 59.937 44.000 0.00 0.00 31.30 4.35
353 2335 1.807142 GAGAGGCCAACTTTGTAGCAC 59.193 52.381 5.01 0.00 0.00 4.40
384 2366 7.335924 ACTTGCGAAAATTGGTAGTATGTGTAT 59.664 33.333 0.00 0.00 0.00 2.29
392 2374 9.474313 AAATTGGTAGTATGTGTATGGTGAATT 57.526 29.630 0.00 0.00 0.00 2.17
428 2412 4.164981 ACACTGATGTACCTCCCAAAGTA 58.835 43.478 0.00 0.00 37.26 2.24
430 2414 5.250774 ACACTGATGTACCTCCCAAAGTAAT 59.749 40.000 0.00 0.00 37.26 1.89
455 2439 2.037901 TCTGCTTTGGGTGATTTGCAA 58.962 42.857 0.00 0.00 0.00 4.08
460 2444 2.926778 TTGGGTGATTTGCAAAAGGG 57.073 45.000 17.19 0.00 0.00 3.95
518 2505 3.314307 TGATGACGACCTTCCCTAGAT 57.686 47.619 0.00 0.00 0.00 1.98
519 2506 4.448720 TGATGACGACCTTCCCTAGATA 57.551 45.455 0.00 0.00 0.00 1.98
597 2587 3.625764 AGTTTAGCGTTGCTGTCAAAGAA 59.374 39.130 0.70 0.00 40.10 2.52
618 2608 4.235079 AGACAACCAAATATAGGCAGCA 57.765 40.909 0.00 0.00 0.00 4.41
654 2644 7.595819 ACCAAAATCTGATCTACCAAACAAA 57.404 32.000 0.00 0.00 0.00 2.83
655 2645 8.017418 ACCAAAATCTGATCTACCAAACAAAA 57.983 30.769 0.00 0.00 0.00 2.44
672 2662 9.379811 CCAAACAAAAATATTCCAAATTCAACG 57.620 29.630 0.00 0.00 0.00 4.10
680 2670 9.744468 AAATATTCCAAATTCAACGGCTATTAC 57.256 29.630 0.00 0.00 0.00 1.89
687 2677 7.807907 CCAAATTCAACGGCTATTACCATATTC 59.192 37.037 0.00 0.00 0.00 1.75
694 2684 3.119245 GGCTATTACCATATTCGGCGAGA 60.119 47.826 10.46 2.37 0.00 4.04
695 2685 3.858238 GCTATTACCATATTCGGCGAGAC 59.142 47.826 10.46 0.00 0.00 3.36
697 2687 3.637998 TTACCATATTCGGCGAGACTC 57.362 47.619 10.46 0.00 0.00 3.36
703 2693 1.376543 ATTCGGCGAGACTCGTCTTA 58.623 50.000 25.51 14.23 43.21 2.10
704 2694 1.376543 TTCGGCGAGACTCGTCTTAT 58.623 50.000 25.51 0.00 43.21 1.73
705 2695 2.229675 TCGGCGAGACTCGTCTTATA 57.770 50.000 25.51 7.17 43.21 0.98
721 2711 6.759827 TCGTCTTATACCAAAACCAATAGAGC 59.240 38.462 0.00 0.00 0.00 4.09
832 2903 3.831911 TCCAGAAAATTCCCGCTTCAATT 59.168 39.130 0.00 0.00 0.00 2.32
875 2946 3.470567 CGCAGACGTGTTCGCTCC 61.471 66.667 0.00 0.00 41.18 4.70
917 2989 1.552578 GGGCAAAACCGTAATTCCCT 58.447 50.000 0.00 0.00 40.62 4.20
919 2991 2.164338 GGCAAAACCGTAATTCCCTGA 58.836 47.619 0.00 0.00 0.00 3.86
920 2992 2.559231 GGCAAAACCGTAATTCCCTGAA 59.441 45.455 0.00 0.00 0.00 3.02
922 2994 4.501743 GGCAAAACCGTAATTCCCTGAAAA 60.502 41.667 0.00 0.00 0.00 2.29
1012 3091 3.264052 CACCCACCCACCCATCCA 61.264 66.667 0.00 0.00 0.00 3.41
1039 3118 8.834465 CCATGATCTGAAAATTTACGAATCTCT 58.166 33.333 0.00 0.00 0.00 3.10
1111 3191 2.288948 ACCGCCGGTTTAAAATTTTCCC 60.289 45.455 1.02 5.52 27.29 3.97
1351 3431 3.637273 GTGCGGGGGTTCCTGTCT 61.637 66.667 0.00 0.00 41.53 3.41
1600 3680 1.477700 TGTTATTTCAGCATGCCCAGC 59.522 47.619 15.66 0.00 34.76 4.85
1619 3699 1.136500 GCTAGTCGTCCGGGAATTTCT 59.864 52.381 0.00 0.00 0.00 2.52
1620 3700 2.810650 CTAGTCGTCCGGGAATTTCTG 58.189 52.381 0.00 0.00 0.00 3.02
1621 3701 0.974383 AGTCGTCCGGGAATTTCTGT 59.026 50.000 0.00 0.00 0.00 3.41
1622 3702 1.346722 AGTCGTCCGGGAATTTCTGTT 59.653 47.619 0.00 0.00 0.00 3.16
1623 3703 2.148768 GTCGTCCGGGAATTTCTGTTT 58.851 47.619 0.00 0.00 0.00 2.83
1624 3704 2.551032 GTCGTCCGGGAATTTCTGTTTT 59.449 45.455 0.00 0.00 0.00 2.43
1625 3705 3.004002 GTCGTCCGGGAATTTCTGTTTTT 59.996 43.478 0.00 0.00 0.00 1.94
1692 3803 4.590647 TCAGCTATAGATTTCTCTGGGGTG 59.409 45.833 3.21 0.00 32.66 4.61
1705 3816 3.780850 CTCTGGGGTGGGTAAAGAGTATT 59.219 47.826 0.00 0.00 31.67 1.89
1714 3825 5.045797 GTGGGTAAAGAGTATTGGAGTTCCT 60.046 44.000 0.00 0.00 36.82 3.36
1715 3826 6.155737 GTGGGTAAAGAGTATTGGAGTTCCTA 59.844 42.308 0.00 0.00 36.82 2.94
1716 3827 6.383147 TGGGTAAAGAGTATTGGAGTTCCTAG 59.617 42.308 0.00 0.00 36.82 3.02
1717 3828 6.610425 GGGTAAAGAGTATTGGAGTTCCTAGA 59.390 42.308 0.00 0.00 36.82 2.43
1718 3829 7.290481 GGGTAAAGAGTATTGGAGTTCCTAGAT 59.710 40.741 0.00 0.00 36.82 1.98
1773 3884 4.762765 TGTAAAATCCGTGTAAAGGCATGT 59.237 37.500 0.00 0.00 34.48 3.21
1997 4122 1.471684 GAACAGAGGCTGGCAAATGAG 59.528 52.381 3.38 0.00 35.51 2.90
2019 4144 3.517500 GCAGCCTATTCCTAATAGCCTCT 59.482 47.826 1.83 0.00 39.61 3.69
2020 4145 4.622695 GCAGCCTATTCCTAATAGCCTCTG 60.623 50.000 1.83 8.40 39.61 3.35
2021 4146 4.774726 CAGCCTATTCCTAATAGCCTCTGA 59.225 45.833 11.88 0.00 39.61 3.27
2022 4147 5.424895 CAGCCTATTCCTAATAGCCTCTGAT 59.575 44.000 11.88 0.00 39.61 2.90
2023 4148 6.609212 CAGCCTATTCCTAATAGCCTCTGATA 59.391 42.308 11.88 0.00 39.61 2.15
2024 4149 6.838612 AGCCTATTCCTAATAGCCTCTGATAG 59.161 42.308 1.83 0.00 39.61 2.08
2084 4214 3.864243 TGTTATACGTTTGCTCGGGAAT 58.136 40.909 0.00 0.00 34.94 3.01
2100 4230 3.443681 CGGGAATTTAAAGCCACATCTGT 59.556 43.478 10.89 0.00 0.00 3.41
2121 4266 6.875726 TCTGTTGACAAATAGATGACCTTGAG 59.124 38.462 0.00 0.00 29.42 3.02
2127 4272 8.154203 TGACAAATAGATGACCTTGAGTTACAA 58.846 33.333 0.00 0.00 36.97 2.41
2275 4420 1.686052 GTTGTGGCCTGATGGTTCAAA 59.314 47.619 3.32 0.00 35.27 2.69
2277 4422 3.448093 TGTGGCCTGATGGTTCAAATA 57.552 42.857 3.32 0.00 35.27 1.40
2361 4533 7.776107 TCACTCCAAACAAATGTGACAATAAA 58.224 30.769 0.00 0.00 33.45 1.40
2362 4534 8.253810 TCACTCCAAACAAATGTGACAATAAAA 58.746 29.630 0.00 0.00 33.45 1.52
2363 4535 8.877779 CACTCCAAACAAATGTGACAATAAAAA 58.122 29.630 0.00 0.00 0.00 1.94
2364 4536 8.878769 ACTCCAAACAAATGTGACAATAAAAAC 58.121 29.630 0.00 0.00 0.00 2.43
2365 4537 7.899974 TCCAAACAAATGTGACAATAAAAACG 58.100 30.769 0.00 0.00 0.00 3.60
2366 4538 7.010552 TCCAAACAAATGTGACAATAAAAACGG 59.989 33.333 0.00 0.00 0.00 4.44
2367 4539 7.201565 CCAAACAAATGTGACAATAAAAACGGT 60.202 33.333 0.00 0.00 0.00 4.83
2368 4540 7.835634 AACAAATGTGACAATAAAAACGGTT 57.164 28.000 0.00 0.00 0.00 4.44
2369 4541 7.227992 ACAAATGTGACAATAAAAACGGTTG 57.772 32.000 0.00 0.00 0.00 3.77
2370 4542 5.898630 AATGTGACAATAAAAACGGTTGC 57.101 34.783 0.00 0.00 0.00 4.17
2371 4543 4.371855 TGTGACAATAAAAACGGTTGCA 57.628 36.364 0.00 0.00 0.00 4.08
2372 4544 4.744570 TGTGACAATAAAAACGGTTGCAA 58.255 34.783 0.00 0.00 0.00 4.08
2415 4587 6.362283 ACAAATAAAATTACACGCTGAACTGC 59.638 34.615 0.00 0.00 0.00 4.40
2416 4588 3.980646 AAAATTACACGCTGAACTGCA 57.019 38.095 4.76 0.00 0.00 4.41
2417 4589 3.980646 AAATTACACGCTGAACTGCAA 57.019 38.095 4.76 0.00 0.00 4.08
2418 4590 4.503741 AAATTACACGCTGAACTGCAAT 57.496 36.364 4.76 0.00 0.00 3.56
2419 4591 2.967459 TTACACGCTGAACTGCAATG 57.033 45.000 4.76 4.54 0.00 2.82
2420 4592 2.162319 TACACGCTGAACTGCAATGA 57.838 45.000 10.24 0.00 0.00 2.57
2421 4593 1.527034 ACACGCTGAACTGCAATGAT 58.473 45.000 10.24 0.00 0.00 2.45
2422 4594 1.198408 ACACGCTGAACTGCAATGATG 59.802 47.619 10.24 0.00 0.00 3.07
2423 4595 1.198408 CACGCTGAACTGCAATGATGT 59.802 47.619 4.76 0.00 0.00 3.06
2424 4596 1.466167 ACGCTGAACTGCAATGATGTC 59.534 47.619 4.76 0.00 0.00 3.06
2425 4597 1.736126 CGCTGAACTGCAATGATGTCT 59.264 47.619 4.76 0.00 0.00 3.41
2426 4598 2.161012 CGCTGAACTGCAATGATGTCTT 59.839 45.455 4.76 0.00 0.00 3.01
2427 4599 3.727079 CGCTGAACTGCAATGATGTCTTC 60.727 47.826 4.76 0.00 0.00 2.87
2428 4600 3.189910 GCTGAACTGCAATGATGTCTTCA 59.810 43.478 0.00 0.00 39.12 3.02
2429 4601 4.672024 GCTGAACTGCAATGATGTCTTCAG 60.672 45.833 0.00 0.00 37.89 3.02
2430 4602 4.644498 TGAACTGCAATGATGTCTTCAGA 58.356 39.130 0.00 0.00 37.89 3.27
2431 4603 5.250982 TGAACTGCAATGATGTCTTCAGAT 58.749 37.500 0.00 0.00 37.89 2.90
2432 4604 6.408869 TGAACTGCAATGATGTCTTCAGATA 58.591 36.000 0.00 0.00 37.89 1.98
2433 4605 7.052248 TGAACTGCAATGATGTCTTCAGATAT 58.948 34.615 0.00 0.00 37.89 1.63
2434 4606 6.862711 ACTGCAATGATGTCTTCAGATATG 57.137 37.500 0.00 0.00 37.89 1.78
2435 4607 6.589135 ACTGCAATGATGTCTTCAGATATGA 58.411 36.000 0.00 0.00 37.89 2.15
2436 4608 6.482641 ACTGCAATGATGTCTTCAGATATGAC 59.517 38.462 0.00 0.00 37.89 3.06
2437 4609 6.350906 TGCAATGATGTCTTCAGATATGACA 58.649 36.000 0.00 0.00 43.93 3.58
2438 4610 6.824704 TGCAATGATGTCTTCAGATATGACAA 59.175 34.615 0.00 0.00 43.28 3.18
2536 4709 3.654321 ACTATGCCCAGATTGATGATCCA 59.346 43.478 0.00 0.00 35.21 3.41
2539 4712 1.202687 GCCCAGATTGATGATCCACGA 60.203 52.381 0.00 0.00 35.21 4.35
2611 4784 0.402504 TTAACGGCCATGAAGGTGGT 59.597 50.000 2.24 0.00 41.47 4.16
2712 4885 8.761575 AGGCAAATTTACACATTTATGTTGAG 57.238 30.769 0.00 0.00 39.39 3.02
2751 4925 6.650390 CCTTTCTGTAATTTGTTGGGAAATGG 59.350 38.462 0.00 0.00 0.00 3.16
2807 4981 3.136443 AGGTTTCAGTGTTGGATGTCTCA 59.864 43.478 0.00 0.00 0.00 3.27
2975 5149 3.322254 TGTCACTCTCTCACTTCTTTCCC 59.678 47.826 0.00 0.00 0.00 3.97
3057 5231 1.599047 CGCCCTCTCACCACATTCT 59.401 57.895 0.00 0.00 0.00 2.40
3229 5403 1.871080 CTGAAAGTTCTCCGTGCTGT 58.129 50.000 0.00 0.00 0.00 4.40
3494 5668 2.391616 TACTCATTGCAGGCTCACAG 57.608 50.000 0.00 0.00 0.00 3.66
3571 5745 4.800993 CGTGACATCAAGTTCCTCTATGAC 59.199 45.833 0.00 0.00 0.00 3.06
3597 5771 2.092429 TCCTCAACCCTCATACAATGCC 60.092 50.000 0.00 0.00 0.00 4.40
3634 5808 7.207383 CAGAACATATTCATGAACATGCCAAT 58.793 34.615 23.45 9.88 38.65 3.16
3799 5973 5.298989 TCCCAGCAGAACTTTTAACACTA 57.701 39.130 0.00 0.00 0.00 2.74
3800 5974 5.686753 TCCCAGCAGAACTTTTAACACTAA 58.313 37.500 0.00 0.00 0.00 2.24
3840 6014 2.435069 CTGATCTGAAGATGGAGGCTGT 59.565 50.000 0.00 0.00 34.37 4.40
3964 6138 1.202818 GGAGCAAAAGGGACTGTCAGT 60.203 52.381 4.81 4.81 40.86 3.41
3979 6153 1.740025 GTCAGTATCCAAGGCAAGTGC 59.260 52.381 0.00 0.00 41.14 4.40
3982 6156 0.727398 GTATCCAAGGCAAGTGCGTC 59.273 55.000 0.00 0.00 43.26 5.19
4031 6205 1.415200 GATGGAGAGGGGTGTAGACC 58.585 60.000 0.00 0.00 42.27 3.85
4423 6600 5.300792 GGGTTCACAAATGAGGAAACTTACA 59.699 40.000 7.27 0.00 44.43 2.41
4486 6663 2.423185 TGGTTCAGTGACTTGCTTTGTG 59.577 45.455 0.00 0.00 0.00 3.33
4529 6706 7.225784 TCTAAATGGCACTGAAAAATAAGCA 57.774 32.000 0.00 0.00 0.00 3.91
4553 6730 9.529325 GCAGAAACTGTTTTAAAACCTAAGATT 57.471 29.630 24.55 16.75 38.11 2.40
4609 6787 6.343716 AGACAGCATGAATGAGTATCTAGG 57.656 41.667 0.00 0.00 39.69 3.02
4646 6824 6.256757 ACTGAAGATCTAGAACGCTTTTATGC 59.743 38.462 0.00 0.00 0.00 3.14
4653 6831 7.435068 TCTAGAACGCTTTTATGCTTTCTTT 57.565 32.000 12.14 0.00 45.18 2.52
4654 6832 7.871853 TCTAGAACGCTTTTATGCTTTCTTTT 58.128 30.769 12.14 0.00 45.18 2.27
4656 6834 6.503524 AGAACGCTTTTATGCTTTCTTTTCA 58.496 32.000 3.04 0.00 45.18 2.69
4688 6866 7.129425 AGAAATACCTCAGATGAACCTCTACT 58.871 38.462 0.00 0.00 0.00 2.57
4766 6945 5.049405 ACAATACTGCAGTTACAAGTTCAGC 60.049 40.000 27.06 0.00 0.00 4.26
4767 6946 2.917933 ACTGCAGTTACAAGTTCAGCA 58.082 42.857 15.25 0.00 0.00 4.41
4780 6959 7.928307 ACAAGTTCAGCAGTAATGAATATGT 57.072 32.000 0.00 0.00 38.81 2.29
5004 7189 6.881065 ACAAAGAATAGTGAAAGAGCATGCTA 59.119 34.615 22.74 0.44 0.00 3.49
5034 7219 1.824230 TCCAAGTTGCAGCAACACTTT 59.176 42.857 34.38 20.34 45.66 2.66
5085 7270 2.509964 GGTGGATACTGGGGACAATTCT 59.490 50.000 0.00 0.00 42.06 2.40
5096 7281 8.980481 ACTGGGGACAATTCTTAAATATACAG 57.020 34.615 0.00 0.00 42.06 2.74
5197 7382 6.699642 GCTAAGCTCCACTTATTAGAGTTCTG 59.300 42.308 0.00 0.00 40.11 3.02
5235 7422 0.396060 TATGATGGGCGTGCATAGCA 59.604 50.000 16.99 0.00 35.60 3.49
5329 7516 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
5330 7517 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
5331 7518 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
5332 7519 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
5333 7520 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
5339 7526 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
5340 7527 0.179084 GTGCATGTAGCTCCCGCTTA 60.179 55.000 0.00 0.00 46.47 3.09
5341 7528 0.179084 TGCATGTAGCTCCCGCTTAC 60.179 55.000 0.00 0.00 46.47 2.34
5342 7529 1.215655 GCATGTAGCTCCCGCTTACG 61.216 60.000 0.00 0.00 46.47 3.18
5343 7530 1.067582 ATGTAGCTCCCGCTTACGC 59.932 57.895 0.00 0.00 46.47 4.42
5344 7531 1.672854 ATGTAGCTCCCGCTTACGCA 61.673 55.000 0.00 0.00 46.47 5.24
5345 7532 1.589196 GTAGCTCCCGCTTACGCAG 60.589 63.158 0.00 0.00 46.47 5.18
5346 7533 2.782222 TAGCTCCCGCTTACGCAGG 61.782 63.158 0.00 0.00 46.47 4.85
5348 7535 3.771160 CTCCCGCTTACGCAGGGT 61.771 66.667 16.64 0.00 44.78 4.34
5349 7536 3.718210 CTCCCGCTTACGCAGGGTC 62.718 68.421 16.64 0.00 44.78 4.46
5350 7537 4.832608 CCCGCTTACGCAGGGTCC 62.833 72.222 11.33 0.00 41.79 4.46
5351 7538 4.077184 CCGCTTACGCAGGGTCCA 62.077 66.667 0.00 0.00 38.22 4.02
5352 7539 2.509336 CGCTTACGCAGGGTCCAG 60.509 66.667 0.00 0.00 35.30 3.86
5353 7540 2.125106 GCTTACGCAGGGTCCAGG 60.125 66.667 0.00 0.00 35.78 4.45
5354 7541 2.584608 CTTACGCAGGGTCCAGGG 59.415 66.667 0.00 0.00 0.00 4.45
5355 7542 1.987855 CTTACGCAGGGTCCAGGGA 60.988 63.158 0.00 0.00 0.00 4.20
5356 7543 1.536907 TTACGCAGGGTCCAGGGAA 60.537 57.895 0.00 0.00 0.00 3.97
5357 7544 1.550130 TTACGCAGGGTCCAGGGAAG 61.550 60.000 0.00 0.00 0.00 3.46
5358 7545 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
5359 7546 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
5360 7547 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
5361 7548 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
5362 7549 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
5363 7550 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
5364 7551 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
5365 7552 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
5366 7553 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
5367 7554 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
5368 7555 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
5369 7556 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
5370 7557 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
5371 7558 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
5372 7559 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
5373 7560 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
5374 7561 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
5375 7562 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
5385 7572 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
5386 7573 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.286353 TGATCTTGTTTGTCAGGTGCAA 58.714 40.909 0.00 0.00 0.00 4.08
2 3 2.929641 TGATCTTGTTTGTCAGGTGCA 58.070 42.857 0.00 0.00 0.00 4.57
3 4 3.503363 TCATGATCTTGTTTGTCAGGTGC 59.497 43.478 8.33 0.00 0.00 5.01
4 5 4.999311 TCTCATGATCTTGTTTGTCAGGTG 59.001 41.667 8.33 0.00 0.00 4.00
5 6 4.999950 GTCTCATGATCTTGTTTGTCAGGT 59.000 41.667 8.33 0.00 0.00 4.00
6 7 4.092529 CGTCTCATGATCTTGTTTGTCAGG 59.907 45.833 8.33 0.00 0.00 3.86
7 8 4.435253 GCGTCTCATGATCTTGTTTGTCAG 60.435 45.833 8.33 0.00 0.00 3.51
8 9 3.433274 GCGTCTCATGATCTTGTTTGTCA 59.567 43.478 8.33 0.00 0.00 3.58
9 10 3.482598 CGCGTCTCATGATCTTGTTTGTC 60.483 47.826 8.33 0.00 0.00 3.18
10 11 2.413112 CGCGTCTCATGATCTTGTTTGT 59.587 45.455 8.33 0.00 0.00 2.83
11 12 2.785681 GCGCGTCTCATGATCTTGTTTG 60.786 50.000 8.43 1.82 0.00 2.93
12 13 1.394917 GCGCGTCTCATGATCTTGTTT 59.605 47.619 8.43 0.00 0.00 2.83
13 14 1.002366 GCGCGTCTCATGATCTTGTT 58.998 50.000 8.43 0.00 0.00 2.83
14 15 0.174389 AGCGCGTCTCATGATCTTGT 59.826 50.000 8.43 0.00 0.00 3.16
15 16 2.049959 CTAGCGCGTCTCATGATCTTG 58.950 52.381 8.43 2.18 0.00 3.02
16 17 1.601663 GCTAGCGCGTCTCATGATCTT 60.602 52.381 8.43 0.00 0.00 2.40
17 18 0.039617 GCTAGCGCGTCTCATGATCT 60.040 55.000 8.43 0.00 0.00 2.75
18 19 0.318191 TGCTAGCGCGTCTCATGATC 60.318 55.000 10.77 0.00 39.65 2.92
19 20 0.103026 TTGCTAGCGCGTCTCATGAT 59.897 50.000 10.77 0.00 39.65 2.45
20 21 0.802222 GTTGCTAGCGCGTCTCATGA 60.802 55.000 10.77 0.00 39.65 3.07
21 22 1.078201 TGTTGCTAGCGCGTCTCATG 61.078 55.000 10.77 1.41 39.65 3.07
22 23 0.389817 TTGTTGCTAGCGCGTCTCAT 60.390 50.000 10.77 0.00 39.65 2.90
23 24 0.389817 ATTGTTGCTAGCGCGTCTCA 60.390 50.000 10.77 0.00 39.65 3.27
24 25 1.255600 GTATTGTTGCTAGCGCGTCTC 59.744 52.381 10.77 0.00 39.65 3.36
25 26 1.135083 AGTATTGTTGCTAGCGCGTCT 60.135 47.619 10.77 8.22 39.65 4.18
26 27 1.278238 AGTATTGTTGCTAGCGCGTC 58.722 50.000 10.77 0.00 39.65 5.19
27 28 1.659098 GAAGTATTGTTGCTAGCGCGT 59.341 47.619 10.77 0.00 39.65 6.01
28 29 1.004927 GGAAGTATTGTTGCTAGCGCG 60.005 52.381 10.77 0.00 39.65 6.86
29 30 1.004927 CGGAAGTATTGTTGCTAGCGC 60.005 52.381 10.77 0.00 0.00 5.92
30 31 1.593006 CCGGAAGTATTGTTGCTAGCG 59.407 52.381 10.77 0.00 0.00 4.26
31 32 2.866762 CTCCGGAAGTATTGTTGCTAGC 59.133 50.000 8.10 8.10 0.00 3.42
32 33 3.865745 CACTCCGGAAGTATTGTTGCTAG 59.134 47.826 5.23 0.00 36.07 3.42
33 34 3.512329 TCACTCCGGAAGTATTGTTGCTA 59.488 43.478 5.23 0.00 36.07 3.49
34 35 2.301870 TCACTCCGGAAGTATTGTTGCT 59.698 45.455 5.23 0.00 36.07 3.91
35 36 2.673368 CTCACTCCGGAAGTATTGTTGC 59.327 50.000 5.23 0.00 36.07 4.17
36 37 3.679980 CACTCACTCCGGAAGTATTGTTG 59.320 47.826 5.23 0.00 36.07 3.33
37 38 3.306780 CCACTCACTCCGGAAGTATTGTT 60.307 47.826 5.23 0.00 36.07 2.83
43 44 1.186267 GGTCCACTCACTCCGGAAGT 61.186 60.000 5.23 2.95 39.44 3.01
44 45 1.592223 GGTCCACTCACTCCGGAAG 59.408 63.158 5.23 2.16 0.00 3.46
47 48 2.214216 TTGGGTCCACTCACTCCGG 61.214 63.158 0.00 0.00 0.00 5.14
51 52 2.400467 AGTAGTTGGGTCCACTCACT 57.600 50.000 0.00 0.00 0.00 3.41
58 59 1.475682 CCAGTCGTAGTAGTTGGGTCC 59.524 57.143 0.00 0.00 0.00 4.46
85 86 6.128729 GGAATGAAAACATTGCTCAAAAACG 58.871 36.000 0.00 0.00 31.45 3.60
104 105 7.536281 CACATGATACATTTCATTAGCGGAATG 59.464 37.037 0.00 7.79 45.57 2.67
105 106 7.587629 CACATGATACATTTCATTAGCGGAAT 58.412 34.615 0.00 0.00 34.09 3.01
109 110 5.149273 GGCACATGATACATTTCATTAGCG 58.851 41.667 0.00 0.00 35.61 4.26
117 118 5.294306 CACTAGTTCGGCACATGATACATTT 59.706 40.000 0.00 0.00 0.00 2.32
122 123 4.937201 ATCACTAGTTCGGCACATGATA 57.063 40.909 0.00 0.00 0.00 2.15
172 173 3.299977 CCCGGTGACTCGTCCACA 61.300 66.667 0.00 0.00 36.31 4.17
183 2165 2.762535 ATTGACTAGACAACCCGGTG 57.237 50.000 9.81 0.00 32.50 4.94
206 2188 8.759641 CAAAAACATAATCACATTTTCCACGAA 58.240 29.630 0.00 0.00 0.00 3.85
272 2254 1.743996 GGCTGGAACTTGATGTCCTC 58.256 55.000 0.00 0.00 0.00 3.71
288 2270 1.202879 TGGAGAACCACATTTTCGGCT 60.203 47.619 0.00 0.00 41.77 5.52
330 2312 2.226674 GCTACAAAGTTGGCCTCTCAAC 59.773 50.000 3.32 0.00 45.22 3.18
353 2335 2.726633 ACCAATTTTCGCAAGTTCACG 58.273 42.857 0.00 0.00 39.48 4.35
384 2366 6.653320 GTGTTCCAAGACACTATAATTCACCA 59.347 38.462 1.17 0.00 44.99 4.17
428 2412 2.318908 TCACCCAAAGCAGAAGCAATT 58.681 42.857 0.00 0.00 45.49 2.32
430 2414 1.999648 ATCACCCAAAGCAGAAGCAA 58.000 45.000 0.00 0.00 45.49 3.91
488 2475 6.086871 GGAAGGTCGTCATCATTTTCTTTTC 58.913 40.000 0.00 0.00 0.00 2.29
493 2480 3.610911 AGGGAAGGTCGTCATCATTTTC 58.389 45.455 0.00 0.00 0.00 2.29
597 2587 4.235079 TGCTGCCTATATTTGGTTGTCT 57.765 40.909 0.00 0.00 0.00 3.41
618 2608 9.147732 AGATCAGATTTTGGTAAGGTTTCTTTT 57.852 29.630 0.00 0.00 34.59 2.27
654 2644 9.744468 GTAATAGCCGTTGAATTTGGAATATTT 57.256 29.630 0.00 0.00 0.00 1.40
655 2645 8.357402 GGTAATAGCCGTTGAATTTGGAATATT 58.643 33.333 0.00 0.00 0.00 1.28
672 2662 3.119245 TCTCGCCGAATATGGTAATAGCC 60.119 47.826 0.00 0.00 0.00 3.93
680 2670 0.311165 ACGAGTCTCGCCGAATATGG 59.689 55.000 22.00 0.00 45.12 2.74
687 2677 1.070041 GGTATAAGACGAGTCTCGCCG 60.070 57.143 22.00 0.00 45.12 6.46
694 2684 7.844009 TCTATTGGTTTTGGTATAAGACGAGT 58.156 34.615 0.00 0.00 0.00 4.18
695 2685 7.042658 GCTCTATTGGTTTTGGTATAAGACGAG 60.043 40.741 0.00 0.00 0.00 4.18
697 2687 6.018180 GGCTCTATTGGTTTTGGTATAAGACG 60.018 42.308 0.00 0.00 0.00 4.18
703 2693 3.201266 TCGGGCTCTATTGGTTTTGGTAT 59.799 43.478 0.00 0.00 0.00 2.73
704 2694 2.572556 TCGGGCTCTATTGGTTTTGGTA 59.427 45.455 0.00 0.00 0.00 3.25
705 2695 1.353022 TCGGGCTCTATTGGTTTTGGT 59.647 47.619 0.00 0.00 0.00 3.67
721 2711 2.165167 TGAGCGGGTAATAGTATCGGG 58.835 52.381 0.00 0.00 0.00 5.14
832 2903 1.211949 CGGGAAAAGAGGGGCTGATTA 59.788 52.381 0.00 0.00 0.00 1.75
900 2971 3.926821 TTCAGGGAATTACGGTTTTGC 57.073 42.857 0.00 0.00 0.00 3.68
917 2989 3.207778 CTGTAGGTCGGTTTGGTTTTCA 58.792 45.455 0.00 0.00 0.00 2.69
919 2991 2.578786 CCTGTAGGTCGGTTTGGTTTT 58.421 47.619 0.00 0.00 0.00 2.43
920 2992 1.816572 GCCTGTAGGTCGGTTTGGTTT 60.817 52.381 0.00 0.00 37.57 3.27
922 2994 1.373812 GCCTGTAGGTCGGTTTGGT 59.626 57.895 0.00 0.00 37.57 3.67
1012 3091 8.511604 AGATTCGTAAATTTTCAGATCATGGT 57.488 30.769 0.00 0.00 0.00 3.55
1111 3191 0.109689 GCTAGATCCGATCGGGTTCG 60.110 60.000 32.79 18.73 39.17 3.95
1473 3553 1.114627 CTCCTCGACCACATCCATGA 58.885 55.000 0.00 0.00 0.00 3.07
1600 3680 2.165845 ACAGAAATTCCCGGACGACTAG 59.834 50.000 0.73 0.00 0.00 2.57
1622 3702 7.126573 ACCAGAAATTCCCACCTTTAAGAAAAA 59.873 33.333 0.00 0.00 0.00 1.94
1623 3703 6.613679 ACCAGAAATTCCCACCTTTAAGAAAA 59.386 34.615 0.00 0.00 0.00 2.29
1624 3704 6.140377 ACCAGAAATTCCCACCTTTAAGAAA 58.860 36.000 0.00 0.00 0.00 2.52
1625 3705 5.711698 ACCAGAAATTCCCACCTTTAAGAA 58.288 37.500 0.00 0.00 0.00 2.52
1626 3706 5.333566 ACCAGAAATTCCCACCTTTAAGA 57.666 39.130 0.00 0.00 0.00 2.10
1627 3707 6.419484 AAACCAGAAATTCCCACCTTTAAG 57.581 37.500 0.00 0.00 0.00 1.85
1628 3708 6.157123 ACAAAACCAGAAATTCCCACCTTTAA 59.843 34.615 0.00 0.00 0.00 1.52
1629 3709 5.663556 ACAAAACCAGAAATTCCCACCTTTA 59.336 36.000 0.00 0.00 0.00 1.85
1630 3710 4.473196 ACAAAACCAGAAATTCCCACCTTT 59.527 37.500 0.00 0.00 0.00 3.11
1631 3711 4.037222 ACAAAACCAGAAATTCCCACCTT 58.963 39.130 0.00 0.00 0.00 3.50
1632 3712 3.653164 ACAAAACCAGAAATTCCCACCT 58.347 40.909 0.00 0.00 0.00 4.00
1633 3713 5.738619 ATACAAAACCAGAAATTCCCACC 57.261 39.130 0.00 0.00 0.00 4.61
1634 3714 8.630037 CCTATATACAAAACCAGAAATTCCCAC 58.370 37.037 0.00 0.00 0.00 4.61
1635 3715 8.340757 ACCTATATACAAAACCAGAAATTCCCA 58.659 33.333 0.00 0.00 0.00 4.37
1636 3716 8.630037 CACCTATATACAAAACCAGAAATTCCC 58.370 37.037 0.00 0.00 0.00 3.97
1637 3717 9.185680 ACACCTATATACAAAACCAGAAATTCC 57.814 33.333 0.00 0.00 0.00 3.01
1641 3721 9.357161 ACAAACACCTATATACAAAACCAGAAA 57.643 29.630 0.00 0.00 0.00 2.52
1642 3722 8.788806 CACAAACACCTATATACAAAACCAGAA 58.211 33.333 0.00 0.00 0.00 3.02
1643 3723 7.940137 ACACAAACACCTATATACAAAACCAGA 59.060 33.333 0.00 0.00 0.00 3.86
1644 3724 8.106247 ACACAAACACCTATATACAAAACCAG 57.894 34.615 0.00 0.00 0.00 4.00
1692 3803 5.695424 AGGAACTCCAATACTCTTTACCC 57.305 43.478 0.00 0.00 38.89 3.69
1705 3816 7.496346 ACACAAATCTAATCTAGGAACTCCA 57.504 36.000 0.00 0.00 41.75 3.86
1773 3884 6.260050 GGGTAGTCAAATCTAATTCATGCGAA 59.740 38.462 0.00 0.00 35.05 4.70
1869 3982 2.287009 CGTTGGGCTCTTCTTTGTTGAC 60.287 50.000 0.00 0.00 0.00 3.18
1870 3983 1.946768 CGTTGGGCTCTTCTTTGTTGA 59.053 47.619 0.00 0.00 0.00 3.18
1871 3984 1.001378 CCGTTGGGCTCTTCTTTGTTG 60.001 52.381 0.00 0.00 0.00 3.33
1872 3985 1.133915 TCCGTTGGGCTCTTCTTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
2056 4186 6.029607 CCGAGCAAACGTATAACAAGTAGTA 58.970 40.000 0.00 0.00 0.00 1.82
2057 4187 4.860907 CCGAGCAAACGTATAACAAGTAGT 59.139 41.667 0.00 0.00 0.00 2.73
2058 4188 4.266976 CCCGAGCAAACGTATAACAAGTAG 59.733 45.833 0.00 0.00 0.00 2.57
2059 4189 4.082300 TCCCGAGCAAACGTATAACAAGTA 60.082 41.667 0.00 0.00 0.00 2.24
2060 4190 2.997986 CCCGAGCAAACGTATAACAAGT 59.002 45.455 0.00 0.00 0.00 3.16
2061 4191 3.255725 TCCCGAGCAAACGTATAACAAG 58.744 45.455 0.00 0.00 0.00 3.16
2062 4192 3.316071 TCCCGAGCAAACGTATAACAA 57.684 42.857 0.00 0.00 0.00 2.83
2063 4193 3.316071 TTCCCGAGCAAACGTATAACA 57.684 42.857 0.00 0.00 0.00 2.41
2064 4194 4.870221 AATTCCCGAGCAAACGTATAAC 57.130 40.909 0.00 0.00 0.00 1.89
2065 4195 6.981762 TTAAATTCCCGAGCAAACGTATAA 57.018 33.333 0.00 0.00 0.00 0.98
2066 4196 6.457257 GCTTTAAATTCCCGAGCAAACGTATA 60.457 38.462 0.00 0.00 33.68 1.47
2067 4197 5.675323 GCTTTAAATTCCCGAGCAAACGTAT 60.675 40.000 0.00 0.00 33.68 3.06
2068 4198 4.378666 GCTTTAAATTCCCGAGCAAACGTA 60.379 41.667 0.00 0.00 33.68 3.57
2069 4199 3.610821 GCTTTAAATTCCCGAGCAAACGT 60.611 43.478 0.00 0.00 33.68 3.99
2070 4200 2.914838 GCTTTAAATTCCCGAGCAAACG 59.085 45.455 0.00 0.00 33.68 3.60
2071 4201 3.250744 GGCTTTAAATTCCCGAGCAAAC 58.749 45.455 0.00 0.00 35.12 2.93
2072 4202 2.894126 TGGCTTTAAATTCCCGAGCAAA 59.106 40.909 0.00 0.00 35.12 3.68
2076 4206 3.947834 AGATGTGGCTTTAAATTCCCGAG 59.052 43.478 4.71 0.00 0.00 4.63
2084 4214 5.843673 TTGTCAACAGATGTGGCTTTAAA 57.156 34.783 0.00 0.00 0.00 1.52
2100 4230 8.154203 TGTAACTCAAGGTCATCTATTTGTCAA 58.846 33.333 0.00 0.00 0.00 3.18
2113 4243 3.498777 GCTCCAAGTTGTAACTCAAGGTC 59.501 47.826 1.45 0.00 38.57 3.85
2115 4245 2.814336 GGCTCCAAGTTGTAACTCAAGG 59.186 50.000 1.45 1.88 38.57 3.61
2116 4246 3.476552 TGGCTCCAAGTTGTAACTCAAG 58.523 45.455 1.45 0.00 38.57 3.02
2121 4266 5.195001 TCAATTTGGCTCCAAGTTGTAAC 57.805 39.130 25.79 0.00 46.60 2.50
2127 4272 3.499338 TGACATCAATTTGGCTCCAAGT 58.501 40.909 1.26 0.00 37.24 3.16
2275 4420 5.476945 GGTGAACCAACCTTGTCTCAAATAT 59.523 40.000 0.00 0.00 37.24 1.28
2277 4422 3.636764 GGTGAACCAACCTTGTCTCAAAT 59.363 43.478 0.00 0.00 37.24 2.32
2326 4475 6.403866 TTTGTTTGGAGTGATATTGTTGCT 57.596 33.333 0.00 0.00 0.00 3.91
2341 4490 7.122550 CCGTTTTTATTGTCACATTTGTTTGG 58.877 34.615 0.00 0.00 0.00 3.28
2370 4542 3.313249 TGTCATCAGAAGTTGCAGTGTTG 59.687 43.478 0.00 0.00 0.00 3.33
2371 4543 3.544684 TGTCATCAGAAGTTGCAGTGTT 58.455 40.909 0.00 0.00 0.00 3.32
2372 4544 3.198409 TGTCATCAGAAGTTGCAGTGT 57.802 42.857 0.00 0.00 0.00 3.55
2435 4607 9.754382 GCACCTGATCATTGATTAAATAATTGT 57.246 29.630 8.34 0.00 0.00 2.71
2436 4608 9.199982 GGCACCTGATCATTGATTAAATAATTG 57.800 33.333 8.34 0.00 0.00 2.32
2536 4709 1.213537 GCCATGCAGCAAATGTCGT 59.786 52.632 0.00 0.00 0.00 4.34
2611 4784 1.661463 ATCCTGTCAAGAGGCTGGAA 58.339 50.000 0.00 0.00 36.54 3.53
2731 4904 7.227049 AGTACCATTTCCCAACAAATTACAG 57.773 36.000 0.00 0.00 0.00 2.74
2807 4981 5.296035 CCGGTAGTCAACTTCAAACTTCTTT 59.704 40.000 0.00 0.00 0.00 2.52
3057 5231 5.105187 CCAAGACATAGAGGAACAGATCACA 60.105 44.000 0.00 0.00 0.00 3.58
3229 5403 2.257207 GCATAGCCACCCACCTATCTA 58.743 52.381 0.00 0.00 0.00 1.98
3494 5668 4.789012 TCTTTGGTGGCAAGATTTCATC 57.211 40.909 0.00 0.00 0.00 2.92
3538 5712 2.920724 TGATGTCACGGAAAAGGTGA 57.079 45.000 0.00 0.00 41.82 4.02
3571 5745 2.016393 TATGAGGGTTGAGGAGCGCG 62.016 60.000 0.00 0.00 0.00 6.86
3597 5771 8.509690 CATGAATATGTTCTGGCTTATAAGGTG 58.490 37.037 14.28 0.00 35.33 4.00
3634 5808 3.432186 CCAAAAGGACCATCGCAGATCTA 60.432 47.826 0.00 0.00 45.12 1.98
3808 5982 2.680312 TCAGATCAGCAACAGTAGCC 57.320 50.000 0.00 0.00 0.00 3.93
3840 6014 8.593679 TCAAGTAGATACTTTGGAATGTTCTCA 58.406 33.333 2.47 0.00 43.57 3.27
3964 6138 0.739462 CGACGCACTTGCCTTGGATA 60.739 55.000 0.00 0.00 37.91 2.59
4031 6205 6.587226 CCACATGAACAATTAACTGTCCATTG 59.413 38.462 0.00 9.29 34.60 2.82
4423 6600 8.462016 GGAATATCACACTAAAACTTCATGCTT 58.538 33.333 0.00 0.00 0.00 3.91
4486 6663 1.203287 GAAGATTTTGGTGGCCAGAGC 59.797 52.381 5.11 0.00 33.81 4.09
4653 6831 9.573166 TCATCTGAGGTATTTCTTCTTTTTGAA 57.427 29.630 0.00 0.00 0.00 2.69
4654 6832 9.573166 TTCATCTGAGGTATTTCTTCTTTTTGA 57.427 29.630 0.00 0.00 0.00 2.69
4656 6834 8.797438 GGTTCATCTGAGGTATTTCTTCTTTTT 58.203 33.333 0.00 0.00 0.00 1.94
4688 6866 7.852550 TTTCCATATTGCATTTGGGATCATA 57.147 32.000 9.46 0.00 32.92 2.15
4766 6945 9.442033 CTGTGCAAACATACATATTCATTACTG 57.558 33.333 0.00 0.00 0.00 2.74
4767 6946 9.177608 ACTGTGCAAACATACATATTCATTACT 57.822 29.630 0.00 0.00 0.00 2.24
4780 6959 8.105097 ACAATGTATACAACTGTGCAAACATA 57.895 30.769 18.33 0.00 0.00 2.29
4980 7165 6.192234 AGCATGCTCTTTCACTATTCTTTG 57.808 37.500 16.30 0.00 0.00 2.77
4984 7169 5.043903 TCGTAGCATGCTCTTTCACTATTC 58.956 41.667 26.57 0.00 0.00 1.75
5004 7189 2.028130 TGCAACTTGGAATTTGGTCGT 58.972 42.857 0.00 0.00 0.00 4.34
5034 7219 7.938140 ATTTTGCTTGTTGTTAGGCTATAGA 57.062 32.000 3.21 0.00 0.00 1.98
5235 7422 1.464198 AGGCTTCCCTTGGACTGGT 60.464 57.895 0.00 0.00 38.74 4.00
5306 7493 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
5307 7494 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
5308 7495 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
5309 7496 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
5310 7497 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
5311 7498 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
5312 7499 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
5313 7500 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
5314 7501 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
5315 7502 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
5337 7524 1.550130 TTCCCTGGACCCTGCGTAAG 61.550 60.000 0.00 0.00 43.44 2.34
5338 7525 1.536907 TTCCCTGGACCCTGCGTAA 60.537 57.895 0.00 0.00 0.00 3.18
5339 7526 1.987855 CTTCCCTGGACCCTGCGTA 60.988 63.158 0.00 0.00 0.00 4.42
5340 7527 3.322466 CTTCCCTGGACCCTGCGT 61.322 66.667 0.00 0.00 0.00 5.24
5341 7528 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
5342 7529 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
5343 7530 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
5344 7531 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
5345 7532 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
5346 7533 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
5347 7534 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
5348 7535 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
5349 7536 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
5350 7537 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
5351 7538 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
5352 7539 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
5353 7540 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
5354 7541 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
5355 7542 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
5356 7543 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
5357 7544 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
5358 7545 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
5359 7546 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
5364 7551 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
5365 7552 3.714391 GCGTACTATAGACCCAAAGTGG 58.286 50.000 6.78 0.00 37.25 4.00


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

AutoCloner maintained by Alex Coulton.