Multiple sequence alignment - TraesCS1A01G107600

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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 TraesCS1A01G107600 chr1A 100.000 4784 0 0 1 4784 105907285 105902502 0.000000e+00 8835.0
1 TraesCS1A01G107600 chr1A 99.482 193 0 1 2389 2580 534541847 534541655 2.740000e-92 350.0
2 TraesCS1A01G107600 chr1A 85.470 117 5 10 2011 2121 105905165 105905275 1.410000e-20 111.0
3 TraesCS1A01G107600 chr1A 97.619 42 0 1 2026 2067 415637354 415637314 2.390000e-08 71.3
4 TraesCS1A01G107600 chr1A 97.436 39 0 1 2073 2110 415637316 415637354 1.110000e-06 65.8
5 TraesCS1A01G107600 chr1D 96.341 2241 55 12 1 2229 106954443 106956668 0.000000e+00 3659.0
6 TraesCS1A01G107600 chr1D 94.128 2231 97 15 2576 4784 106957871 106960089 0.000000e+00 3363.0
7 TraesCS1A01G107600 chr1D 94.595 111 4 2 2225 2333 106957742 106957852 2.290000e-38 171.0
8 TraesCS1A01G107600 chr1D 86.275 102 6 6 2011 2110 106956559 106956464 2.360000e-18 104.0
9 TraesCS1A01G107600 chr1D 97.500 40 0 1 2028 2067 326158694 326158656 3.090000e-07 67.6
10 TraesCS1A01G107600 chr1D 97.297 37 0 1 2352 2388 106957853 106957888 1.440000e-05 62.1
11 TraesCS1A01G107600 chr1D 97.297 37 0 1 2073 2108 326158658 326158694 1.440000e-05 62.1
12 TraesCS1A01G107600 chr1B 91.914 2226 110 31 2576 4774 159915861 159913679 0.000000e+00 3049.0
13 TraesCS1A01G107600 chr1B 97.079 1164 33 1 896 2059 159917283 159916121 0.000000e+00 1960.0
14 TraesCS1A01G107600 chr1B 97.351 906 13 4 1 897 159918345 159917442 0.000000e+00 1530.0
15 TraesCS1A01G107600 chr1B 92.829 251 8 4 2087 2333 159916125 159915881 5.890000e-94 355.0
16 TraesCS1A01G107600 chr1B 93.258 89 1 4 2026 2110 481710715 481710802 5.030000e-25 126.0
17 TraesCS1A01G107600 chr1B 89.000 100 4 6 2018 2111 481710812 481710714 3.030000e-22 117.0
18 TraesCS1A01G107600 chr1B 95.122 41 2 0 2348 2388 159915884 159915844 1.110000e-06 65.8
19 TraesCS1A01G107600 chr3A 96.818 220 6 1 2372 2591 359345748 359345966 2.720000e-97 366.0
20 TraesCS1A01G107600 chr3A 100.000 190 0 0 2386 2575 437863750 437863561 7.620000e-93 351.0
21 TraesCS1A01G107600 chr3A 84.685 111 14 3 4542 4651 156232088 156231980 1.820000e-19 108.0
22 TraesCS1A01G107600 chr3A 87.234 94 7 5 2024 2114 434000981 434000890 8.470000e-18 102.0
23 TraesCS1A01G107600 chr4A 100.000 192 0 0 2389 2580 31161982 31161791 5.890000e-94 355.0
24 TraesCS1A01G107600 chr2A 98.990 198 1 1 2389 2586 775435555 775435359 2.120000e-93 353.0
25 TraesCS1A01G107600 chr2A 84.483 116 17 1 4546 4660 25042412 25042527 3.910000e-21 113.0
26 TraesCS1A01G107600 chr2B 100.000 190 0 0 2387 2576 197148792 197148603 7.620000e-93 351.0
27 TraesCS1A01G107600 chr5B 96.279 215 4 4 2378 2589 527606175 527605962 2.740000e-92 350.0
28 TraesCS1A01G107600 chr5A 99.479 192 1 0 2385 2576 485382281 485382090 2.740000e-92 350.0
29 TraesCS1A01G107600 chr5A 87.000 100 13 0 4550 4649 547820771 547820672 3.910000e-21 113.0
30 TraesCS1A01G107600 chr5A 89.888 89 7 2 2023 2110 692175876 692175963 3.910000e-21 113.0
31 TraesCS1A01G107600 chr5A 85.047 107 15 1 4550 4655 584069252 584069146 1.820000e-19 108.0
32 TraesCS1A01G107600 chr7A 98.477 197 3 0 2377 2573 433079869 433079673 9.850000e-92 348.0
33 TraesCS1A01G107600 chr7A 88.764 89 8 2 2023 2110 721706001 721706088 1.820000e-19 108.0
34 TraesCS1A01G107600 chr3D 89.691 97 10 0 4550 4646 574442778 574442682 1.810000e-24 124.0
35 TraesCS1A01G107600 chr3D 82.979 94 6 7 2024 2114 301440314 301440400 5.130000e-10 76.8
36 TraesCS1A01G107600 chr5D 86.087 115 14 2 4534 4648 530428441 530428329 6.500000e-24 122.0
37 TraesCS1A01G107600 chr5D 91.250 80 5 2 2032 2110 184043722 184043800 1.820000e-19 108.0
38 TraesCS1A01G107600 chr5D 88.750 80 7 2 2026 2104 184043800 184043722 3.940000e-16 97.1
39 TraesCS1A01G107600 chr6D 86.667 105 14 0 4545 4649 345760567 345760463 3.030000e-22 117.0
40 TraesCS1A01G107600 chr6D 100.000 29 0 0 2079 2107 242995716 242995744 2.000000e-03 54.7
41 TraesCS1A01G107600 chr6D 100.000 29 0 0 2029 2057 242995744 242995716 2.000000e-03 54.7
42 TraesCS1A01G107600 chr6A 87.755 98 12 0 4550 4647 442400369 442400466 1.090000e-21 115.0
43 TraesCS1A01G107600 chr4D 88.636 88 8 2 2024 2110 36590518 36590432 6.550000e-19 106.0


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 TraesCS1A01G107600 chr1A 105902502 105907285 4783 True 8835.000 8835 100.00000 1 4784 1 chr1A.!!$R1 4783
1 TraesCS1A01G107600 chr1D 106954443 106960089 5646 False 1813.775 3659 95.59025 1 4784 4 chr1D.!!$F2 4783
2 TraesCS1A01G107600 chr1B 159913679 159918345 4666 True 1391.960 3049 94.85900 1 4774 5 chr1B.!!$R2 4773

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
932 1105 2.127251 GCAGCTGCAACTTGTTTAACC 58.873 47.619 33.36 0.00 41.59 2.85 F
2344 3606 0.115745 ACCTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 0.00 3.53 F
2425 3687 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 3681 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.00 0.00 44.78 4.85 R
3780 5045 0.320374 CGCACTACTTGGTCCCTCAA 59.680 55.0 0.00 0.00 0.00 3.02 R
4275 5542 1.038681 TGATCACATGCCATGGCCAC 61.039 55.0 33.44 16.03 41.09 5.01 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
68 69 9.965824 TTTGTTTCATTTCAAGTTTCTATCCTC 57.034 29.630 0.00 0.00 0.00 3.71
665 678 4.033009 TGTGGTATCTGAGGACATGTCAT 58.967 43.478 26.47 20.88 0.00 3.06
812 825 4.950475 TCAGATCCGTGTGACTCTAATCTT 59.050 41.667 0.00 0.00 0.00 2.40
932 1105 2.127251 GCAGCTGCAACTTGTTTAACC 58.873 47.619 33.36 0.00 41.59 2.85
1032 1205 6.014840 GGCATCATTATCACAATTCCCAGATT 60.015 38.462 0.00 0.00 0.00 2.40
1151 1327 8.628116 CCAGTTTTGGTGAACTCATTTAGTTGC 61.628 40.741 0.00 0.00 42.95 4.17
1301 1477 4.118410 GTCAGTCTTATGGTCAGCAGATG 58.882 47.826 0.00 0.00 0.00 2.90
1391 1567 5.818136 ATGCACCATACAATACTCAACAC 57.182 39.130 0.00 0.00 0.00 3.32
1412 1588 2.540101 CGTGCCTTCTTTAAGCTATCCG 59.460 50.000 0.00 0.00 0.00 4.18
1413 1589 3.737047 CGTGCCTTCTTTAAGCTATCCGA 60.737 47.826 0.00 0.00 0.00 4.55
1414 1590 4.189231 GTGCCTTCTTTAAGCTATCCGAA 58.811 43.478 0.00 0.00 0.00 4.30
1566 1742 6.338146 TCCAATAATCAGTTCTCTGGTTACG 58.662 40.000 3.55 0.00 46.01 3.18
1598 1774 3.228453 TCCTGTTCCTACTCGTGAAACT 58.772 45.455 0.00 0.00 31.75 2.66
1799 1978 7.207454 TCCAAATGCAAATGCTCCTTTTGGA 62.207 40.000 24.51 24.51 44.19 3.53
1924 2103 9.399797 TGCTTCTAATCTGATGTGTTTTCATAT 57.600 29.630 0.00 0.00 34.41 1.78
1953 2132 7.903145 TCTACTTCTGCTAAGATTTGGTACAA 58.097 34.615 6.41 0.00 36.19 2.41
2019 2198 7.418337 TGGACAGAATAGCTCTTTGTATACA 57.582 36.000 0.08 0.08 29.07 2.29
2020 2199 8.023021 TGGACAGAATAGCTCTTTGTATACAT 57.977 34.615 6.36 0.00 29.07 2.29
2128 2308 9.802039 AGGGAGTAACATTTACAAAAATAGACA 57.198 29.630 0.00 0.00 33.45 3.41
2284 3546 1.797635 GCTCAGTTCTCAGACTTGTGC 59.202 52.381 0.00 0.00 0.00 4.57
2326 3588 7.048512 AGCATAGGACTTTCACCAGTTAATAC 58.951 38.462 0.00 0.00 0.00 1.89
2329 3591 8.701895 CATAGGACTTTCACCAGTTAATACCTA 58.298 37.037 0.00 0.00 0.00 3.08
2330 3592 6.944096 AGGACTTTCACCAGTTAATACCTAC 58.056 40.000 0.00 0.00 0.00 3.18
2331 3593 6.729569 AGGACTTTCACCAGTTAATACCTACT 59.270 38.462 0.00 0.00 0.00 2.57
2332 3594 7.040494 GGACTTTCACCAGTTAATACCTACTC 58.960 42.308 0.00 0.00 0.00 2.59
2333 3595 6.944096 ACTTTCACCAGTTAATACCTACTCC 58.056 40.000 0.00 0.00 0.00 3.85
2334 3596 5.945144 TTCACCAGTTAATACCTACTCCC 57.055 43.478 0.00 0.00 0.00 4.30
2335 3597 5.216665 TCACCAGTTAATACCTACTCCCT 57.783 43.478 0.00 0.00 0.00 4.20
2336 3598 5.206587 TCACCAGTTAATACCTACTCCCTC 58.793 45.833 0.00 0.00 0.00 4.30
2337 3599 4.344390 CACCAGTTAATACCTACTCCCTCC 59.656 50.000 0.00 0.00 0.00 4.30
2338 3600 3.573110 CCAGTTAATACCTACTCCCTCCG 59.427 52.174 0.00 0.00 0.00 4.63
2339 3601 4.213513 CAGTTAATACCTACTCCCTCCGT 58.786 47.826 0.00 0.00 0.00 4.69
2340 3602 4.648307 CAGTTAATACCTACTCCCTCCGTT 59.352 45.833 0.00 0.00 0.00 4.44
2341 3603 4.892345 AGTTAATACCTACTCCCTCCGTTC 59.108 45.833 0.00 0.00 0.00 3.95
2342 3604 2.378378 ATACCTACTCCCTCCGTTCC 57.622 55.000 0.00 0.00 0.00 3.62
2343 3605 1.002069 TACCTACTCCCTCCGTTCCA 58.998 55.000 0.00 0.00 0.00 3.53
2344 3606 0.115745 ACCTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 0.00 3.53
2345 3607 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
2346 3608 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
2350 3612 2.092049 ACTCCCTCCGTTCCAAAAACTT 60.092 45.455 0.00 0.00 0.00 2.66
2382 3644 7.978975 CAGTTTAATTGTAATATGGGTTGGTGG 59.021 37.037 0.00 0.00 0.00 4.61
2383 3645 7.676468 AGTTTAATTGTAATATGGGTTGGTGGT 59.324 33.333 0.00 0.00 0.00 4.16
2384 3646 8.968969 GTTTAATTGTAATATGGGTTGGTGGTA 58.031 33.333 0.00 0.00 0.00 3.25
2385 3647 9.716556 TTTAATTGTAATATGGGTTGGTGGTAT 57.283 29.630 0.00 0.00 0.00 2.73
2386 3648 7.833285 AATTGTAATATGGGTTGGTGGTATC 57.167 36.000 0.00 0.00 0.00 2.24
2387 3649 5.313280 TGTAATATGGGTTGGTGGTATCC 57.687 43.478 0.00 0.00 0.00 2.59
2388 3650 3.502123 AATATGGGTTGGTGGTATCCG 57.498 47.619 0.00 0.00 0.00 4.18
2389 3651 2.177811 TATGGGTTGGTGGTATCCGA 57.822 50.000 0.00 0.00 0.00 4.55
2390 3652 1.291109 ATGGGTTGGTGGTATCCGAA 58.709 50.000 0.00 0.00 0.00 4.30
2391 3653 0.616371 TGGGTTGGTGGTATCCGAAG 59.384 55.000 0.00 0.00 0.00 3.79
2412 3674 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2413 3675 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2414 3676 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2415 3677 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2416 3678 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2417 3679 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2418 3680 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2423 3685 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2424 3686 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2425 3687 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2426 3688 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2427 3689 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2428 3690 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2429 3691 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2430 3692 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2431 3693 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2432 3694 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2433 3695 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2434 3696 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2435 3697 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2436 3698 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2437 3699 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2452 3714 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2453 3715 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2454 3716 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2455 3717 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2456 3718 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2457 3719 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2458 3720 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2459 3721 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2460 3722 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2461 3723 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
2475 3737 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2476 3738 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2477 3739 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2478 3740 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2479 3741 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2480 3742 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2481 3743 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2482 3744 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2483 3745 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2484 3746 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2485 3747 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2486 3748 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2487 3749 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2488 3750 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2489 3751 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2490 3752 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2491 3753 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2492 3754 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2493 3755 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2494 3756 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2495 3757 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2496 3758 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2497 3759 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2498 3760 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2499 3761 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2500 3762 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2501 3763 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2502 3764 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2503 3765 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2504 3766 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2505 3767 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2506 3768 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2507 3769 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2508 3770 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2509 3771 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2510 3772 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2511 3773 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2512 3774 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2517 3779 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2518 3780 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2519 3781 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2520 3782 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2521 3783 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2522 3784 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2523 3785 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2524 3786 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2525 3787 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2526 3788 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2527 3789 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2528 3790 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2529 3791 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2530 3792 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2531 3793 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2532 3794 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2533 3795 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2534 3796 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2535 3797 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2536 3798 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2561 3823 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2562 3824 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2563 3825 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2564 3826 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2565 3827 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2566 3828 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2567 3829 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2568 3830 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2569 3831 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2570 3832 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
2645 3908 8.804912 AGATTGTCATCAAAGAAGCTAAGAAT 57.195 30.769 0.00 0.00 37.11 2.40
2773 4038 2.040178 ACTTCCTGGTTCTTCTGACGT 58.960 47.619 0.00 0.00 0.00 4.34
2819 4084 3.511934 ACACTCCTAGACCAGTTCATCAC 59.488 47.826 0.00 0.00 0.00 3.06
2913 4178 2.158943 GCTAACCCTCGCTATCAACCTT 60.159 50.000 0.00 0.00 0.00 3.50
2919 4184 2.103094 CCTCGCTATCAACCTTCCATGA 59.897 50.000 0.00 0.00 0.00 3.07
2939 4204 1.219213 ACCAGCTATCCTCCTGCTACT 59.781 52.381 0.00 0.00 35.05 2.57
3002 4267 2.363683 GCTGCATCTTTTAGACAGCCT 58.636 47.619 1.93 0.00 46.21 4.58
3033 4298 2.023791 TCTGTAGGGCATGGTGGTAGTA 60.024 50.000 0.00 0.00 0.00 1.82
3357 4622 1.709147 CCGCCTACAGCTGCATCAAC 61.709 60.000 15.27 0.00 40.39 3.18
3558 4823 4.901197 TTTGCCTGGTAAGATGACACTA 57.099 40.909 0.00 0.00 0.00 2.74
3567 4832 6.192044 TGGTAAGATGACACTACTATGTGGA 58.808 40.000 0.00 0.00 41.84 4.02
3586 4851 6.339730 TGTGGAATCATAATTGCCAACAATC 58.660 36.000 0.00 0.00 45.90 2.67
3588 4853 7.043565 GTGGAATCATAATTGCCAACAATCTT 58.956 34.615 0.00 0.00 45.90 2.40
3780 5045 1.285641 CGCCGCAAATGAAACCACT 59.714 52.632 0.00 0.00 0.00 4.00
3816 5081 0.465460 GCGCCCCTCCACATTTATCA 60.465 55.000 0.00 0.00 0.00 2.15
3853 5118 5.059161 TCAGTTATATCTGCTCATTGTGCC 58.941 41.667 8.14 0.00 35.63 5.01
3996 5261 3.648545 AGCCTCTGATCCCCAGTAATTAC 59.351 47.826 7.57 7.57 43.38 1.89
4022 5289 1.470098 CGCAAGATGTCCCTCCTTTTG 59.530 52.381 0.00 0.00 43.02 2.44
4031 5298 0.593128 CCCTCCTTTTGCTGTTGACG 59.407 55.000 0.00 0.00 0.00 4.35
4033 5300 1.264288 CCTCCTTTTGCTGTTGACGTC 59.736 52.381 9.11 9.11 0.00 4.34
4099 5366 4.399395 CCTGCCAGCTTCGCCTCA 62.399 66.667 0.17 0.00 0.00 3.86
4201 5468 2.428925 GCCTTGCATGGGTGATGGG 61.429 63.158 19.47 0.00 31.99 4.00
4239 5506 2.750237 GATGGTTGGGTCCGGTGC 60.750 66.667 0.00 0.00 0.00 5.01
4275 5542 1.238439 GTGGTGAACTCATGTGGTGG 58.762 55.000 0.00 0.00 0.00 4.61
4337 5605 2.223595 ACGTGAGAGCCGTGAGATAATG 60.224 50.000 0.00 0.00 37.12 1.90
4423 5703 0.527817 GCAGTCGTTATGTCCCCTCG 60.528 60.000 0.00 0.00 0.00 4.63
4447 5727 9.439461 TCGGGGATTCATCTCAATAATATATCT 57.561 33.333 0.00 0.00 0.00 1.98
4482 5763 6.502138 AGATCCCAACCCTTCATTTTGAATA 58.498 36.000 0.00 0.00 35.59 1.75
4490 5771 6.949715 ACCCTTCATTTTGAATATTGCACAT 58.050 32.000 0.00 0.00 35.59 3.21
4531 5814 1.168714 GAATCCTGCACGCTTTTCCT 58.831 50.000 0.00 0.00 0.00 3.36
4535 5818 0.734889 CCTGCACGCTTTTCCTATGG 59.265 55.000 0.00 0.00 0.00 2.74
4539 5822 2.290387 TGCACGCTTTTCCTATGGGTTA 60.290 45.455 0.00 0.00 0.00 2.85
4558 5844 8.808240 TGGGTTAATTACATTATACTCCCTCT 57.192 34.615 0.00 0.00 0.00 3.69
4587 5873 9.349713 TCCAAAATAAGTGTCTCAACTTTGTAT 57.650 29.630 0.00 0.00 40.77 2.29
4625 5911 8.589629 CAAAATTACATTAAGCTTGATGCACTC 58.410 33.333 26.25 0.00 45.94 3.51
4633 5919 4.978083 AGCTTGATGCACTCATTTTAGG 57.022 40.909 0.00 0.00 45.94 2.69
4637 5923 5.735354 GCTTGATGCACTCATTTTAGGATGG 60.735 44.000 0.00 0.00 42.31 3.51
4639 5925 5.508567 TGATGCACTCATTTTAGGATGGAA 58.491 37.500 0.00 0.00 31.96 3.53
4640 5926 5.591472 TGATGCACTCATTTTAGGATGGAAG 59.409 40.000 0.00 0.00 31.96 3.46
4642 5928 4.018506 TGCACTCATTTTAGGATGGAAGGA 60.019 41.667 0.00 0.00 0.00 3.36
4644 5930 5.749462 CACTCATTTTAGGATGGAAGGAGT 58.251 41.667 0.00 0.00 42.89 3.85
4645 5931 6.632672 GCACTCATTTTAGGATGGAAGGAGTA 60.633 42.308 2.86 0.00 40.98 2.59
4647 5933 7.995488 CACTCATTTTAGGATGGAAGGAGTATT 59.005 37.037 2.86 0.00 40.98 1.89
4648 5934 9.225682 ACTCATTTTAGGATGGAAGGAGTATTA 57.774 33.333 1.38 0.00 41.08 0.98
4722 6008 1.486310 TCGAGGGTATGCATGCTTTCT 59.514 47.619 20.33 10.75 0.00 2.52
4739 6025 5.238432 TGCTTTCTGTCATGTTTCGTATGTT 59.762 36.000 0.00 0.00 0.00 2.71
4749 6035 5.219226 TGTTTCGTATGTTGTTTGTTCGT 57.781 34.783 0.00 0.00 0.00 3.85
4774 6062 5.114780 TGCATTTACCCGTAGCGTAAATTA 58.885 37.500 3.77 0.00 41.43 1.40
4775 6063 5.583854 TGCATTTACCCGTAGCGTAAATTAA 59.416 36.000 3.77 0.00 41.43 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.499232 AGTGCAGTCAGTTAAAGTGATAACTTT 59.501 33.333 12.92 12.92 42.06 2.66
68 69 7.408756 TTCAAAGATAATGAAAGATGGTGGG 57.591 36.000 0.00 0.00 34.04 4.61
283 286 9.185192 CTGGTTAAAACAATCTGAAGTTTCATC 57.815 33.333 10.65 4.38 36.98 2.92
406 417 5.537295 TCAGTTAAGGTACAGTTACTGCTCA 59.463 40.000 12.80 0.00 34.37 4.26
619 632 9.168451 ACATGTCATCCTTATACTAGTCGATAG 57.832 37.037 0.00 0.00 37.53 2.08
625 638 8.958060 ATACCACATGTCATCCTTATACTAGT 57.042 34.615 0.00 0.00 0.00 2.57
812 825 4.527038 CAGACCTTAGAACTGTGGGAAGTA 59.473 45.833 0.00 0.00 0.00 2.24
932 1105 5.244785 TGAGGCACAGTATTAGTACTTCG 57.755 43.478 0.00 0.00 39.12 3.79
1032 1205 4.178540 GGTTCGTACGATCCATTCTTGAA 58.821 43.478 31.20 7.08 34.89 2.69
1125 1301 6.391227 ACTAAATGAGTTCACCAAAACTGG 57.609 37.500 0.00 0.00 39.55 4.00
1301 1477 2.941583 AAGGTTCCAGGGGCTCCC 60.942 66.667 0.00 0.00 45.90 4.30
1391 1567 2.540101 CGGATAGCTTAAAGAAGGCACG 59.460 50.000 0.00 0.00 32.84 5.34
1412 1588 9.589111 GGAATAAAACTATCCTCCGATCTATTC 57.411 37.037 0.00 0.00 0.00 1.75
1413 1589 9.327731 AGGAATAAAACTATCCTCCGATCTATT 57.672 33.333 0.00 0.00 39.36 1.73
1414 1590 8.754080 CAGGAATAAAACTATCCTCCGATCTAT 58.246 37.037 0.00 0.00 41.63 1.98
1421 1597 6.464607 GGACTCCAGGAATAAAACTATCCTCC 60.465 46.154 0.00 0.00 41.63 4.30
1566 1742 0.681243 GGAACAGGATTCAGGGGCAC 60.681 60.000 0.00 0.00 0.00 5.01
1598 1774 3.838565 TGAACTTATTTGTGGAGGGCAA 58.161 40.909 0.00 0.00 0.00 4.52
1799 1978 1.301716 CCGCTGTACTGGTGCACTT 60.302 57.895 17.98 4.07 0.00 3.16
1800 1979 2.343758 CCGCTGTACTGGTGCACT 59.656 61.111 17.98 0.00 0.00 4.40
1801 1980 2.725203 TTCCCGCTGTACTGGTGCAC 62.725 60.000 8.80 8.80 0.00 4.57
1924 2103 7.224297 ACCAAATCTTAGCAGAAGTAGAACAA 58.776 34.615 0.00 0.00 30.76 2.83
1953 2132 4.513406 TTCACCTGACTACCCAAAAGTT 57.487 40.909 0.00 0.00 0.00 2.66
2128 2308 0.325272 GAAGGCTTTTCCTCCCTCGT 59.675 55.000 0.00 0.00 46.94 4.18
2284 3546 5.760253 CCTATGCTTGAAACTAGTGGTATGG 59.240 44.000 0.00 0.00 0.00 2.74
2326 3588 1.272807 TTTGGAACGGAGGGAGTAGG 58.727 55.000 0.00 0.00 0.00 3.18
2329 3591 1.493446 AGTTTTTGGAACGGAGGGAGT 59.507 47.619 0.00 0.00 0.00 3.85
2330 3592 2.271944 AGTTTTTGGAACGGAGGGAG 57.728 50.000 0.00 0.00 0.00 4.30
2331 3593 2.740506 AAGTTTTTGGAACGGAGGGA 57.259 45.000 0.00 0.00 0.00 4.20
2332 3594 5.462530 AATAAAGTTTTTGGAACGGAGGG 57.537 39.130 0.00 0.00 0.00 4.30
2333 3595 5.010213 TGGAATAAAGTTTTTGGAACGGAGG 59.990 40.000 0.00 0.00 0.00 4.30
2334 3596 6.079424 TGGAATAAAGTTTTTGGAACGGAG 57.921 37.500 0.00 0.00 0.00 4.63
2335 3597 5.595133 ACTGGAATAAAGTTTTTGGAACGGA 59.405 36.000 0.00 0.00 0.00 4.69
2336 3598 5.838529 ACTGGAATAAAGTTTTTGGAACGG 58.161 37.500 0.00 0.00 0.00 4.44
2337 3599 7.764695 AAACTGGAATAAAGTTTTTGGAACG 57.235 32.000 0.00 0.00 43.60 3.95
2382 3644 4.297207 AGGCTCCCCTTCGGATAC 57.703 61.111 0.00 0.00 41.00 2.24
2394 3656 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2395 3657 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2396 3658 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2397 3659 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2398 3660 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2399 3661 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2400 3662 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2401 3663 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2405 3667 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2406 3668 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2407 3669 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2408 3670 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2409 3671 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2410 3672 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2411 3673 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2412 3674 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2413 3675 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2414 3676 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2415 3677 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2416 3678 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2417 3679 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2418 3680 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2419 3681 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2420 3682 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2432 3694 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2433 3695 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2434 3696 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2435 3697 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2436 3698 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2437 3699 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2438 3700 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2439 3701 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2440 3702 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2441 3703 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2442 3704 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2443 3705 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2444 3706 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2445 3707 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2446 3708 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2447 3709 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2448 3710 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2449 3711 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2450 3712 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2451 3713 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2452 3714 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2453 3715 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2465 3727 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2466 3728 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2467 3729 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2468 3730 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2469 3731 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2470 3732 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2471 3733 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2472 3734 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2473 3735 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2474 3736 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2475 3737 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2476 3738 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2477 3739 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2478 3740 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2479 3741 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2480 3742 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2481 3743 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2482 3744 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2483 3745 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2484 3746 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2485 3747 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2486 3748 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2487 3749 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2488 3750 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2489 3751 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2490 3752 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2491 3753 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2501 3763 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2502 3764 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2503 3765 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2504 3766 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2505 3767 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2506 3768 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2507 3769 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2508 3770 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2509 3771 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2510 3772 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2511 3773 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2512 3774 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2513 3775 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2514 3776 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2515 3777 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2516 3778 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2517 3779 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2518 3780 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2519 3781 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2531 3793 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2534 3796 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2535 3797 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2536 3798 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2537 3799 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2543 3805 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2544 3806 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2545 3807 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2546 3808 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2547 3809 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2659 3924 0.620556 GCTTCCATCTGTCCCTGGAA 59.379 55.000 0.00 4.14 46.63 3.53
2819 4084 1.202290 GGATAATTGTGGCCAGCGTTG 60.202 52.381 5.11 0.00 0.00 4.10
2913 4178 1.221523 AGGAGGATAGCTGGTCATGGA 59.778 52.381 0.00 0.00 0.00 3.41
2919 4184 1.219213 AGTAGCAGGAGGATAGCTGGT 59.781 52.381 0.00 0.00 39.30 4.00
3002 4267 1.035932 GCCCTACAGAGACGTGCCTA 61.036 60.000 0.00 0.00 0.00 3.93
3033 4298 3.012959 TCCCTCATCCTTCTACTCCTTGT 59.987 47.826 0.00 0.00 0.00 3.16
3193 4458 5.758296 TCATAAAACGCTTCAAAGAGAGTGT 59.242 36.000 0.31 0.00 29.85 3.55
3240 4505 6.609876 AGGATCTAATGCTTCTCTAGACTCA 58.390 40.000 0.00 0.00 0.00 3.41
3243 4508 6.490040 AGTGAGGATCTAATGCTTCTCTAGAC 59.510 42.308 0.00 0.00 34.92 2.59
3558 4823 6.606796 TGTTGGCAATTATGATTCCACATAGT 59.393 34.615 1.92 0.00 34.80 2.12
3586 4851 3.149196 ACCAGGAATACAGTGCAACAAG 58.851 45.455 0.00 0.00 41.43 3.16
3588 4853 2.949177 ACCAGGAATACAGTGCAACA 57.051 45.000 0.00 0.00 41.43 3.33
3780 5045 0.320374 CGCACTACTTGGTCCCTCAA 59.680 55.000 0.00 0.00 0.00 3.02
3853 5118 1.225855 TTACACAGCCAACTTGAGCG 58.774 50.000 0.00 0.00 0.00 5.03
3902 5167 5.275881 GCACGATGTTTTGAGTTCACAAAAG 60.276 40.000 0.00 0.00 45.90 2.27
3965 5230 3.075134 GGGGATCAGAGGCTTTGGATAAT 59.925 47.826 5.08 0.00 0.00 1.28
3996 5261 1.067821 GAGGGACATCTTGCGAGTAGG 59.932 57.143 0.00 0.00 0.00 3.18
4014 5279 2.213499 AGACGTCAACAGCAAAAGGAG 58.787 47.619 19.50 0.00 0.00 3.69
4016 5281 1.070577 CGAGACGTCAACAGCAAAAGG 60.071 52.381 19.50 0.00 0.00 3.11
4017 5282 1.858458 TCGAGACGTCAACAGCAAAAG 59.142 47.619 19.50 0.00 0.00 2.27
4022 5289 1.452399 GAAACTCGAGACGTCAACAGC 59.548 52.381 21.68 0.44 0.00 4.40
4031 5298 6.096036 TCAATCATGAGAAGAAACTCGAGAC 58.904 40.000 21.68 9.99 39.49 3.36
4099 5366 2.108278 AACCGTCCCGTTTGCTAGCT 62.108 55.000 17.23 0.00 0.00 3.32
4161 5428 4.802563 GCATGAAGAAATTAGAAGCAAGCC 59.197 41.667 0.00 0.00 0.00 4.35
4201 5468 2.032681 GTCAGGAGGGTGGTGCAC 59.967 66.667 8.80 8.80 0.00 4.57
4275 5542 1.038681 TGATCACATGCCATGGCCAC 61.039 55.000 33.44 16.03 41.09 5.01
4337 5605 2.167861 CGAAGCTGTAAGGCGAGCC 61.168 63.158 5.89 5.89 35.69 4.70
4396 5673 3.131396 GACATAACGACTGCTTATGGGG 58.869 50.000 7.36 0.00 36.35 4.96
4423 5703 9.703892 CGAGATATATTATTGAGATGAATCCCC 57.296 37.037 0.00 0.00 0.00 4.81
4447 5727 1.743958 GTTGGGATCTCGTCTTCTCGA 59.256 52.381 0.00 0.00 38.19 4.04
4509 5792 2.094545 GGAAAAGCGTGCAGGATTCAAT 60.095 45.455 10.66 0.34 0.00 2.57
4517 5800 0.734889 CCCATAGGAAAAGCGTGCAG 59.265 55.000 0.00 0.00 33.47 4.41
4539 5822 8.331931 TGGAACAGAGGGAGTATAATGTAATT 57.668 34.615 0.00 0.00 41.28 1.40
4558 5844 7.639113 AAGTTGAGACACTTATTTTGGAACA 57.361 32.000 0.00 0.00 35.10 3.18
4561 5847 7.639113 ACAAAGTTGAGACACTTATTTTGGA 57.361 32.000 0.00 0.00 35.87 3.53
4606 5892 5.909621 AATGAGTGCATCAAGCTTAATGT 57.090 34.783 11.29 0.00 45.94 2.71
4607 5893 7.434307 CCTAAAATGAGTGCATCAAGCTTAATG 59.566 37.037 5.11 5.11 45.94 1.90
4609 5895 6.658816 TCCTAAAATGAGTGCATCAAGCTTAA 59.341 34.615 0.00 0.00 45.94 1.85
4619 5905 4.018506 TCCTTCCATCCTAAAATGAGTGCA 60.019 41.667 0.00 0.00 0.00 4.57
4625 5911 9.853177 AGTTAATACTCCTTCCATCCTAAAATG 57.147 33.333 0.00 0.00 0.00 2.32
4653 5939 6.582264 GCGAACAGACAGAGTAAGTTTTAAG 58.418 40.000 0.00 0.00 0.00 1.85
4654 5940 5.174398 CGCGAACAGACAGAGTAAGTTTTAA 59.826 40.000 0.00 0.00 0.00 1.52
4667 5953 0.249531 TTAGCAACCGCGAACAGACA 60.250 50.000 8.23 0.00 45.49 3.41
4722 6008 6.125327 ACAAACAACATACGAAACATGACA 57.875 33.333 0.00 0.00 0.00 3.58
4739 6025 3.003897 GGGTAAATGCAGACGAACAAACA 59.996 43.478 0.00 0.00 0.00 2.83
4749 6035 0.533491 ACGCTACGGGTAAATGCAGA 59.467 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.