Multiple sequence alignment - TraesCS3D01G422500

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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 TraesCS3D01G422500 chr3D 100.000 2815 0 0 1 2815 535143555 535146369 0.000000e+00 5199
1 TraesCS3D01G422500 chr3D 96.791 374 10 2 2444 2815 328949817 328949444 8.560000e-175 623
2 TraesCS3D01G422500 chr6D 96.939 2254 39 8 1 2231 61814019 61811773 0.000000e+00 3753
3 TraesCS3D01G422500 chr6D 98.513 1345 20 0 212 1556 65307821 65309165 0.000000e+00 2374
4 TraesCS3D01G422500 chr6D 95.468 684 13 5 1552 2217 65317487 65318170 0.000000e+00 1075
5 TraesCS3D01G422500 chr6D 97.051 373 10 1 2444 2815 357407433 357407061 6.620000e-176 627
6 TraesCS3D01G422500 chr6D 96.791 374 10 2 2444 2815 305118842 305119215 8.560000e-175 623
7 TraesCS3D01G422500 chr6D 96.783 373 11 1 2444 2815 220462650 220462278 3.080000e-174 621
8 TraesCS3D01G422500 chr6D 99.190 247 2 0 2208 2454 61811725 61811479 1.990000e-121 446
9 TraesCS3D01G422500 chr6D 99.174 242 2 0 2208 2449 65318234 65318475 1.200000e-118 436
10 TraesCS3D01G422500 chr2D 95.477 2233 83 2 3 2217 226333160 226335392 0.000000e+00 3548
11 TraesCS3D01G422500 chr2D 87.135 2503 241 57 3 2453 621361718 621364191 0.000000e+00 2763
12 TraesCS3D01G422500 chr2D 97.059 374 9 2 2444 2815 150936747 150937120 1.840000e-176 628
13 TraesCS3D01G422500 chr2D 97.059 374 9 2 2444 2815 384188208 384188581 1.840000e-176 628
14 TraesCS3D01G422500 chr2D 96.791 374 10 2 2444 2815 354563059 354563432 8.560000e-175 623
15 TraesCS3D01G422500 chr2D 96.016 251 8 1 2205 2453 226335453 226335703 9.390000e-110 407
16 TraesCS3D01G422500 chr5B 95.948 2147 74 12 1 2143 567869108 567866971 0.000000e+00 3470
17 TraesCS3D01G422500 chr5B 84.909 497 44 22 1975 2449 567867038 567866551 9.130000e-130 473
18 TraesCS3D01G422500 chr5B 87.067 433 31 16 2040 2449 41904163 41903733 1.530000e-127 466
19 TraesCS3D01G422500 chr5B 94.355 248 12 2 2206 2452 542676890 542677136 2.050000e-101 379
20 TraesCS3D01G422500 chr5B 87.000 300 26 12 1848 2143 41904443 41904153 2.700000e-85 326
21 TraesCS3D01G422500 chr3B 95.573 2146 67 13 1 2142 8785066 8787187 0.000000e+00 3411
22 TraesCS3D01G422500 chr3B 95.305 2151 66 12 1 2148 106957258 106955140 0.000000e+00 3380
23 TraesCS3D01G422500 chr3B 94.694 245 12 1 2205 2449 8788161 8788404 2.050000e-101 379
24 TraesCS3D01G422500 chr3B 94.309 246 13 1 2208 2453 106954983 106954739 2.650000e-100 375
25 TraesCS3D01G422500 chr7A 87.179 2457 251 43 3 2416 683510164 683507729 0.000000e+00 2734
26 TraesCS3D01G422500 chr7A 89.403 2010 181 20 3 1988 683625670 683627671 0.000000e+00 2503
27 TraesCS3D01G422500 chr1B 90.413 1888 160 14 3 1875 7321294 7319413 0.000000e+00 2464
28 TraesCS3D01G422500 chr4A 87.845 1160 93 25 3 1123 649887674 649888824 0.000000e+00 1317
29 TraesCS3D01G422500 chr4B 92.396 697 44 5 4 693 38607826 38608520 0.000000e+00 985
30 TraesCS3D01G422500 chr5D 97.548 367 8 1 2450 2815 406837811 406838177 6.620000e-176 627
31 TraesCS3D01G422500 chr5D 96.708 243 6 1 2208 2448 43162447 43162205 1.210000e-108 403
32 TraesCS3D01G422500 chr7D 96.791 374 10 2 2444 2815 369349396 369349023 8.560000e-175 623
33 TraesCS3D01G422500 chr4D 91.740 339 26 1 1536 1872 26202517 26202855 1.180000e-128 470


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 TraesCS3D01G422500 chr3D 535143555 535146369 2814 False 5199.0 5199 100.0000 1 2815 1 chr3D.!!$F1 2814
1 TraesCS3D01G422500 chr6D 65307821 65309165 1344 False 2374.0 2374 98.5130 212 1556 1 chr6D.!!$F1 1344
2 TraesCS3D01G422500 chr6D 61811479 61814019 2540 True 2099.5 3753 98.0645 1 2454 2 chr6D.!!$R3 2453
3 TraesCS3D01G422500 chr6D 65317487 65318475 988 False 755.5 1075 97.3210 1552 2449 2 chr6D.!!$F3 897
4 TraesCS3D01G422500 chr2D 621361718 621364191 2473 False 2763.0 2763 87.1350 3 2453 1 chr2D.!!$F4 2450
5 TraesCS3D01G422500 chr2D 226333160 226335703 2543 False 1977.5 3548 95.7465 3 2453 2 chr2D.!!$F5 2450
6 TraesCS3D01G422500 chr5B 567866551 567869108 2557 True 1971.5 3470 90.4285 1 2449 2 chr5B.!!$R2 2448
7 TraesCS3D01G422500 chr5B 41903733 41904443 710 True 396.0 466 87.0335 1848 2449 2 chr5B.!!$R1 601
8 TraesCS3D01G422500 chr3B 8785066 8788404 3338 False 1895.0 3411 95.1335 1 2449 2 chr3B.!!$F1 2448
9 TraesCS3D01G422500 chr3B 106954739 106957258 2519 True 1877.5 3380 94.8070 1 2453 2 chr3B.!!$R1 2452
10 TraesCS3D01G422500 chr7A 683507729 683510164 2435 True 2734.0 2734 87.1790 3 2416 1 chr7A.!!$R1 2413
11 TraesCS3D01G422500 chr7A 683625670 683627671 2001 False 2503.0 2503 89.4030 3 1988 1 chr7A.!!$F1 1985
12 TraesCS3D01G422500 chr1B 7319413 7321294 1881 True 2464.0 2464 90.4130 3 1875 1 chr1B.!!$R1 1872
13 TraesCS3D01G422500 chr4A 649887674 649888824 1150 False 1317.0 1317 87.8450 3 1123 1 chr4A.!!$F1 1120
14 TraesCS3D01G422500 chr4B 38607826 38608520 694 False 985.0 985 92.3960 4 693 1 chr4B.!!$F1 689

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
40 41 2.098280 CGACTCCATGAGAACTGATCGT 59.902 50.000 0.00 0.0 33.32 3.73 F
1488 1542 1.133025 GTGCAGCGCAACCAATAGAAT 59.867 47.619 11.47 0.0 41.47 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1668 1.435256 ACCTTGGGCAGTTCTAGTGT 58.565 50.0 0.0 0.0 0.00 3.55 R
2714 3872 0.977395 AGCCCGAACTAGCTCAAACT 59.023 50.0 0.0 0.0 32.71 2.66 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
40 41 2.098280 CGACTCCATGAGAACTGATCGT 59.902 50.000 0.00 0.00 33.32 3.73
213 214 4.293494 TCTAGCTCCATTCAGATCCACTT 58.707 43.478 0.00 0.00 0.00 3.16
616 624 7.721286 ACTCAATAAGAAGTGTTCAAGTCAG 57.279 36.000 0.00 0.00 0.00 3.51
731 739 6.600427 ACATGTGATTTAGCAAGATGATGTCA 59.400 34.615 0.00 0.00 0.00 3.58
732 740 7.121611 ACATGTGATTTAGCAAGATGATGTCAA 59.878 33.333 0.00 0.00 0.00 3.18
1114 1161 8.044060 TGCTATAAAGGCAATACATGATAAGC 57.956 34.615 0.00 0.00 36.71 3.09
1488 1542 1.133025 GTGCAGCGCAACCAATAGAAT 59.867 47.619 11.47 0.00 41.47 2.40
1548 1602 1.606668 CAAAAAGGCAGCGAACAGGTA 59.393 47.619 0.00 0.00 0.00 3.08
1614 1668 7.333323 TCAAGATGCTATGAAATCACTTGAGA 58.667 34.615 0.00 0.00 37.92 3.27
1636 1690 3.244457 ACACTAGAACTGCCCAAGGTTAC 60.244 47.826 0.00 0.00 0.00 2.50
1637 1691 3.008049 CACTAGAACTGCCCAAGGTTACT 59.992 47.826 0.00 0.00 0.00 2.24
1638 1692 2.861147 AGAACTGCCCAAGGTTACTC 57.139 50.000 0.00 0.00 0.00 2.59
2054 2221 2.939103 GGACAAGTGCTGCTGTATAAGG 59.061 50.000 0.00 0.00 0.00 2.69
2157 2419 6.961554 GTGCTGCTGTATAAGTTATGTTGTTC 59.038 38.462 5.61 0.00 0.00 3.18
2176 2441 8.507249 TGTTGTTCTAAAATTGTTGTTTTTGGG 58.493 29.630 0.00 0.00 33.62 4.12
2416 3574 1.287217 ATTGGGGCCAATTCAATGCA 58.713 45.000 4.39 0.00 43.32 3.96
2454 3612 2.159114 ACATCCAAACAAAGCGCAAGTT 60.159 40.909 11.47 8.35 41.68 2.66
2455 3613 3.067461 ACATCCAAACAAAGCGCAAGTTA 59.933 39.130 11.47 0.00 41.68 2.24
2456 3614 3.784701 TCCAAACAAAGCGCAAGTTAA 57.215 38.095 11.47 0.00 41.68 2.01
2457 3615 4.314740 TCCAAACAAAGCGCAAGTTAAT 57.685 36.364 11.47 0.00 41.68 1.40
2458 3616 5.440234 TCCAAACAAAGCGCAAGTTAATA 57.560 34.783 11.47 0.00 41.68 0.98
2459 3617 6.019779 TCCAAACAAAGCGCAAGTTAATAT 57.980 33.333 11.47 0.00 41.68 1.28
2460 3618 6.451393 TCCAAACAAAGCGCAAGTTAATATT 58.549 32.000 11.47 0.00 41.68 1.28
2461 3619 7.594714 TCCAAACAAAGCGCAAGTTAATATTA 58.405 30.769 11.47 0.00 41.68 0.98
2462 3620 7.753132 TCCAAACAAAGCGCAAGTTAATATTAG 59.247 33.333 11.47 0.00 41.68 1.73
2463 3621 7.753132 CCAAACAAAGCGCAAGTTAATATTAGA 59.247 33.333 11.47 0.00 41.68 2.10
2464 3622 9.123709 CAAACAAAGCGCAAGTTAATATTAGAA 57.876 29.630 11.47 0.00 41.68 2.10
2465 3623 8.895932 AACAAAGCGCAAGTTAATATTAGAAG 57.104 30.769 11.47 0.00 41.68 2.85
2466 3624 6.967199 ACAAAGCGCAAGTTAATATTAGAAGC 59.033 34.615 11.47 0.00 41.68 3.86
2467 3625 6.927294 AAGCGCAAGTTAATATTAGAAGCT 57.073 33.333 11.47 0.90 41.68 3.74
2468 3626 8.335356 CAAAGCGCAAGTTAATATTAGAAGCTA 58.665 33.333 11.47 0.00 41.68 3.32
2469 3627 8.433421 AAGCGCAAGTTAATATTAGAAGCTAA 57.567 30.769 11.47 0.00 41.68 3.09
2470 3628 8.608844 AGCGCAAGTTAATATTAGAAGCTAAT 57.391 30.769 11.47 5.19 41.68 1.73
2471 3629 9.706691 AGCGCAAGTTAATATTAGAAGCTAATA 57.293 29.630 11.47 8.78 41.68 0.98
2490 3648 7.997107 CTAATAAGCAATTGCACAATGATGT 57.003 32.000 30.89 5.18 45.16 3.06
2492 3650 7.997107 AATAAGCAATTGCACAATGATGTAG 57.003 32.000 30.89 0.00 45.16 2.74
2493 3651 5.395682 AAGCAATTGCACAATGATGTAGT 57.604 34.783 30.89 3.64 45.16 2.73
2494 3652 6.513806 AAGCAATTGCACAATGATGTAGTA 57.486 33.333 30.89 0.00 45.16 1.82
2495 3653 5.883661 AGCAATTGCACAATGATGTAGTAC 58.116 37.500 30.89 0.00 45.16 2.73
2496 3654 5.415389 AGCAATTGCACAATGATGTAGTACA 59.585 36.000 30.89 5.24 45.16 2.90
2497 3655 6.072008 AGCAATTGCACAATGATGTAGTACAA 60.072 34.615 30.89 0.00 45.16 2.41
2498 3656 6.033831 GCAATTGCACAATGATGTAGTACAAC 59.966 38.462 25.36 5.27 37.82 3.32
2499 3657 6.816134 ATTGCACAATGATGTAGTACAACA 57.184 33.333 14.75 14.75 37.82 3.33
2500 3658 5.605564 TGCACAATGATGTAGTACAACAC 57.394 39.130 14.70 6.91 37.82 3.32
2501 3659 5.304778 TGCACAATGATGTAGTACAACACT 58.695 37.500 14.70 2.00 37.82 3.55
2502 3660 5.408299 TGCACAATGATGTAGTACAACACTC 59.592 40.000 14.70 5.19 37.82 3.51
2503 3661 5.639506 GCACAATGATGTAGTACAACACTCT 59.360 40.000 14.70 1.45 37.82 3.24
2504 3662 6.147821 GCACAATGATGTAGTACAACACTCTT 59.852 38.462 14.70 4.11 37.82 2.85
2505 3663 7.307989 GCACAATGATGTAGTACAACACTCTTT 60.308 37.037 14.70 6.25 37.82 2.52
2506 3664 8.559536 CACAATGATGTAGTACAACACTCTTTT 58.440 33.333 14.70 3.45 37.82 2.27
2507 3665 9.772973 ACAATGATGTAGTACAACACTCTTTTA 57.227 29.630 14.70 0.00 38.24 1.52
2536 3694 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2538 3696 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2539 3697 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2540 3698 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2541 3699 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2542 3700 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2543 3701 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2544 3702 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2545 3703 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2546 3704 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2547 3705 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2548 3706 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2549 3707 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
2550 3708 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2551 3709 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2552 3710 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2553 3711 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2554 3712 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2555 3713 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2556 3714 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2557 3715 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2558 3716 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2559 3717 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2563 3721 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2564 3722 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2581 3739 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2582 3740 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2583 3741 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2584 3742 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2585 3743 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2586 3744 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2587 3745 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
2588 3746 6.854091 ATATTTAGGAACGGAGGGAGTATC 57.146 41.667 0.00 0.00 0.00 2.24
2589 3747 3.967467 TTAGGAACGGAGGGAGTATCT 57.033 47.619 0.00 0.00 33.73 1.98
2590 3748 2.850695 AGGAACGGAGGGAGTATCTT 57.149 50.000 0.00 0.00 33.73 2.40
2591 3749 3.967467 AGGAACGGAGGGAGTATCTTA 57.033 47.619 0.00 0.00 33.73 2.10
2592 3750 4.472690 AGGAACGGAGGGAGTATCTTAT 57.527 45.455 0.00 0.00 33.73 1.73
2593 3751 5.595814 AGGAACGGAGGGAGTATCTTATA 57.404 43.478 0.00 0.00 33.73 0.98
2594 3752 5.961897 AGGAACGGAGGGAGTATCTTATAA 58.038 41.667 0.00 0.00 33.73 0.98
2595 3753 5.774184 AGGAACGGAGGGAGTATCTTATAAC 59.226 44.000 0.00 0.00 33.73 1.89
2596 3754 5.537674 GGAACGGAGGGAGTATCTTATAACA 59.462 44.000 0.00 0.00 33.73 2.41
2597 3755 6.210984 GGAACGGAGGGAGTATCTTATAACAT 59.789 42.308 0.00 0.00 33.73 2.71
2598 3756 6.837471 ACGGAGGGAGTATCTTATAACATC 57.163 41.667 0.00 0.00 33.73 3.06
2599 3757 5.715753 ACGGAGGGAGTATCTTATAACATCC 59.284 44.000 0.00 0.00 33.73 3.51
2600 3758 5.715279 CGGAGGGAGTATCTTATAACATCCA 59.285 44.000 0.00 0.00 33.73 3.41
2601 3759 6.210784 CGGAGGGAGTATCTTATAACATCCAA 59.789 42.308 0.00 0.00 33.73 3.53
2602 3760 7.093289 CGGAGGGAGTATCTTATAACATCCAAT 60.093 40.741 0.00 0.00 33.73 3.16
2603 3761 9.268282 GGAGGGAGTATCTTATAACATCCAATA 57.732 37.037 0.00 0.00 33.73 1.90
2648 3806 5.387113 ACATCTTATGTTATGGGCTGGAA 57.613 39.130 0.00 0.00 41.63 3.53
2649 3807 5.380043 ACATCTTATGTTATGGGCTGGAAG 58.620 41.667 0.00 0.00 41.63 3.46
2650 3808 4.437682 TCTTATGTTATGGGCTGGAAGG 57.562 45.455 0.00 0.00 0.00 3.46
2651 3809 4.044308 TCTTATGTTATGGGCTGGAAGGA 58.956 43.478 0.00 0.00 0.00 3.36
2652 3810 4.103153 TCTTATGTTATGGGCTGGAAGGAG 59.897 45.833 0.00 0.00 0.00 3.69
2653 3811 1.668826 TGTTATGGGCTGGAAGGAGT 58.331 50.000 0.00 0.00 0.00 3.85
2654 3812 1.992557 TGTTATGGGCTGGAAGGAGTT 59.007 47.619 0.00 0.00 0.00 3.01
2655 3813 2.378547 TGTTATGGGCTGGAAGGAGTTT 59.621 45.455 0.00 0.00 0.00 2.66
2656 3814 3.589735 TGTTATGGGCTGGAAGGAGTTTA 59.410 43.478 0.00 0.00 0.00 2.01
2657 3815 4.200092 GTTATGGGCTGGAAGGAGTTTAG 58.800 47.826 0.00 0.00 0.00 1.85
2658 3816 1.742308 TGGGCTGGAAGGAGTTTAGT 58.258 50.000 0.00 0.00 0.00 2.24
2659 3817 1.351017 TGGGCTGGAAGGAGTTTAGTG 59.649 52.381 0.00 0.00 0.00 2.74
2660 3818 1.454201 GGCTGGAAGGAGTTTAGTGC 58.546 55.000 0.00 0.00 0.00 4.40
2661 3819 1.271379 GGCTGGAAGGAGTTTAGTGCA 60.271 52.381 0.00 0.00 0.00 4.57
2662 3820 2.619074 GGCTGGAAGGAGTTTAGTGCAT 60.619 50.000 0.00 0.00 0.00 3.96
2663 3821 3.084786 GCTGGAAGGAGTTTAGTGCATT 58.915 45.455 0.00 0.00 0.00 3.56
2664 3822 3.127721 GCTGGAAGGAGTTTAGTGCATTC 59.872 47.826 0.00 0.00 0.00 2.67
2665 3823 4.583871 CTGGAAGGAGTTTAGTGCATTCT 58.416 43.478 0.00 0.00 0.00 2.40
2666 3824 4.985538 TGGAAGGAGTTTAGTGCATTCTT 58.014 39.130 0.00 0.00 0.00 2.52
2667 3825 6.121776 TGGAAGGAGTTTAGTGCATTCTTA 57.878 37.500 0.00 0.00 0.00 2.10
2668 3826 5.938125 TGGAAGGAGTTTAGTGCATTCTTAC 59.062 40.000 0.00 0.00 0.00 2.34
2669 3827 5.938125 GGAAGGAGTTTAGTGCATTCTTACA 59.062 40.000 0.00 0.00 0.00 2.41
2670 3828 6.430000 GGAAGGAGTTTAGTGCATTCTTACAA 59.570 38.462 0.00 0.00 0.00 2.41
2671 3829 7.040686 GGAAGGAGTTTAGTGCATTCTTACAAA 60.041 37.037 0.00 0.00 0.00 2.83
2672 3830 8.409358 AAGGAGTTTAGTGCATTCTTACAAAT 57.591 30.769 0.00 0.00 0.00 2.32
2673 3831 8.409358 AGGAGTTTAGTGCATTCTTACAAATT 57.591 30.769 0.00 0.00 0.00 1.82
2674 3832 9.515226 AGGAGTTTAGTGCATTCTTACAAATTA 57.485 29.630 0.00 0.00 0.00 1.40
2677 3835 9.988350 AGTTTAGTGCATTCTTACAAATTATCG 57.012 29.630 0.00 0.00 0.00 2.92
2678 3836 9.221775 GTTTAGTGCATTCTTACAAATTATCGG 57.778 33.333 0.00 0.00 0.00 4.18
2679 3837 5.821204 AGTGCATTCTTACAAATTATCGGC 58.179 37.500 0.00 0.00 0.00 5.54
2680 3838 5.590259 AGTGCATTCTTACAAATTATCGGCT 59.410 36.000 0.00 0.00 0.00 5.52
2681 3839 6.765989 AGTGCATTCTTACAAATTATCGGCTA 59.234 34.615 0.00 0.00 0.00 3.93
2682 3840 7.282224 AGTGCATTCTTACAAATTATCGGCTAA 59.718 33.333 0.00 0.00 0.00 3.09
2683 3841 8.076178 GTGCATTCTTACAAATTATCGGCTAAT 58.924 33.333 0.00 0.00 0.00 1.73
2684 3842 8.629158 TGCATTCTTACAAATTATCGGCTAATT 58.371 29.630 0.00 0.00 40.93 1.40
2690 3848 9.382244 CTTACAAATTATCGGCTAATTAACTGC 57.618 33.333 0.00 0.00 38.76 4.40
2691 3849 7.568199 ACAAATTATCGGCTAATTAACTGCT 57.432 32.000 0.00 0.00 38.76 4.24
2692 3850 7.417612 ACAAATTATCGGCTAATTAACTGCTG 58.582 34.615 0.00 0.00 38.76 4.41
2693 3851 5.613358 ATTATCGGCTAATTAACTGCTGC 57.387 39.130 0.00 0.00 33.50 5.25
2694 3852 2.691409 TCGGCTAATTAACTGCTGCT 57.309 45.000 0.00 0.00 33.50 4.24
2695 3853 2.279741 TCGGCTAATTAACTGCTGCTG 58.720 47.619 4.89 4.89 33.50 4.41
2696 3854 2.009774 CGGCTAATTAACTGCTGCTGT 58.990 47.619 6.33 6.33 0.00 4.40
2697 3855 3.118920 TCGGCTAATTAACTGCTGCTGTA 60.119 43.478 12.66 0.00 33.50 2.74
2698 3856 3.809832 CGGCTAATTAACTGCTGCTGTAT 59.190 43.478 12.66 1.06 0.00 2.29
2699 3857 4.084328 CGGCTAATTAACTGCTGCTGTATC 60.084 45.833 12.66 0.00 0.00 2.24
2700 3858 4.214332 GGCTAATTAACTGCTGCTGTATCC 59.786 45.833 12.66 0.00 0.00 2.59
2701 3859 4.816385 GCTAATTAACTGCTGCTGTATCCA 59.184 41.667 12.66 0.00 0.00 3.41
2702 3860 5.471456 GCTAATTAACTGCTGCTGTATCCAT 59.529 40.000 12.66 0.00 0.00 3.41
2703 3861 5.762825 AATTAACTGCTGCTGTATCCATG 57.237 39.130 12.66 0.00 0.00 3.66
2704 3862 2.048444 AACTGCTGCTGTATCCATGG 57.952 50.000 12.66 4.97 0.00 3.66
2705 3863 0.182061 ACTGCTGCTGTATCCATGGG 59.818 55.000 13.02 0.00 0.00 4.00
2706 3864 0.182061 CTGCTGCTGTATCCATGGGT 59.818 55.000 13.02 7.52 0.00 4.51
2707 3865 0.625316 TGCTGCTGTATCCATGGGTT 59.375 50.000 13.02 2.34 0.00 4.11
2708 3866 1.843206 TGCTGCTGTATCCATGGGTTA 59.157 47.619 13.02 1.26 0.00 2.85
2709 3867 2.222027 GCTGCTGTATCCATGGGTTAC 58.778 52.381 13.02 14.37 0.00 2.50
2710 3868 2.421388 GCTGCTGTATCCATGGGTTACA 60.421 50.000 20.50 20.50 36.07 2.41
2716 3874 6.235231 CTGTATCCATGGGTTACAGTTAGT 57.765 41.667 29.34 0.00 44.53 2.24
2717 3875 6.630203 TGTATCCATGGGTTACAGTTAGTT 57.370 37.500 18.85 0.00 34.25 2.24
2718 3876 7.023171 TGTATCCATGGGTTACAGTTAGTTT 57.977 36.000 18.85 0.00 34.25 2.66
2719 3877 6.882140 TGTATCCATGGGTTACAGTTAGTTTG 59.118 38.462 18.85 0.00 34.25 2.93
2720 3878 5.570205 TCCATGGGTTACAGTTAGTTTGA 57.430 39.130 13.02 0.00 0.00 2.69
2721 3879 5.556915 TCCATGGGTTACAGTTAGTTTGAG 58.443 41.667 13.02 0.00 0.00 3.02
2722 3880 4.156008 CCATGGGTTACAGTTAGTTTGAGC 59.844 45.833 2.85 0.00 0.00 4.26
2723 3881 4.699925 TGGGTTACAGTTAGTTTGAGCT 57.300 40.909 0.00 0.00 0.00 4.09
2724 3882 5.811796 TGGGTTACAGTTAGTTTGAGCTA 57.188 39.130 0.00 0.00 0.00 3.32
2725 3883 5.790593 TGGGTTACAGTTAGTTTGAGCTAG 58.209 41.667 0.00 0.00 0.00 3.42
2726 3884 5.306160 TGGGTTACAGTTAGTTTGAGCTAGT 59.694 40.000 0.00 0.00 0.00 2.57
2727 3885 6.183361 TGGGTTACAGTTAGTTTGAGCTAGTT 60.183 38.462 0.00 0.00 0.00 2.24
2728 3886 6.368243 GGGTTACAGTTAGTTTGAGCTAGTTC 59.632 42.308 0.00 0.00 0.00 3.01
2729 3887 6.089150 GGTTACAGTTAGTTTGAGCTAGTTCG 59.911 42.308 1.89 0.00 0.00 3.95
2730 3888 4.557205 ACAGTTAGTTTGAGCTAGTTCGG 58.443 43.478 1.89 0.00 0.00 4.30
2731 3889 3.927142 CAGTTAGTTTGAGCTAGTTCGGG 59.073 47.826 1.89 0.00 0.00 5.14
2732 3890 2.667473 TAGTTTGAGCTAGTTCGGGC 57.333 50.000 1.89 0.00 0.00 6.13
2733 3891 0.977395 AGTTTGAGCTAGTTCGGGCT 59.023 50.000 1.89 0.00 41.88 5.19
2740 3898 3.460857 AGCTAGTTCGGGCTCAAATAG 57.539 47.619 0.00 0.00 32.98 1.73
2765 3923 8.598041 AGCCCTAAAGTATATCTAAACATGAGG 58.402 37.037 0.00 0.00 0.00 3.86
2766 3924 7.824779 GCCCTAAAGTATATCTAAACATGAGGG 59.175 40.741 0.00 0.00 40.36 4.30
2767 3925 7.824779 CCCTAAAGTATATCTAAACATGAGGGC 59.175 40.741 0.00 0.00 31.56 5.19
2768 3926 8.598041 CCTAAAGTATATCTAAACATGAGGGCT 58.402 37.037 0.00 0.00 0.00 5.19
2771 3929 8.728596 AAGTATATCTAAACATGAGGGCTAGT 57.271 34.615 0.00 0.00 0.00 2.57
2772 3930 8.728596 AGTATATCTAAACATGAGGGCTAGTT 57.271 34.615 0.00 0.00 0.00 2.24
2773 3931 9.160412 AGTATATCTAAACATGAGGGCTAGTTT 57.840 33.333 0.00 0.00 37.82 2.66
2774 3932 9.209175 GTATATCTAAACATGAGGGCTAGTTTG 57.791 37.037 0.00 0.00 35.90 2.93
2775 3933 5.755409 TCTAAACATGAGGGCTAGTTTGA 57.245 39.130 0.00 0.00 35.90 2.69
2776 3934 5.734720 TCTAAACATGAGGGCTAGTTTGAG 58.265 41.667 0.00 0.00 35.90 3.02
2777 3935 2.409948 ACATGAGGGCTAGTTTGAGC 57.590 50.000 0.00 0.00 42.05 4.26
2778 3936 1.912043 ACATGAGGGCTAGTTTGAGCT 59.088 47.619 0.00 0.00 42.43 4.09
2779 3937 3.107601 ACATGAGGGCTAGTTTGAGCTA 58.892 45.455 0.00 0.00 42.43 3.32
2780 3938 3.133721 ACATGAGGGCTAGTTTGAGCTAG 59.866 47.826 0.00 0.00 42.43 3.42
2781 3939 2.821437 TGAGGGCTAGTTTGAGCTAGT 58.179 47.619 4.22 0.00 42.43 2.57
2782 3940 3.173965 TGAGGGCTAGTTTGAGCTAGTT 58.826 45.455 4.22 0.00 42.43 2.24
2783 3941 3.055819 TGAGGGCTAGTTTGAGCTAGTTG 60.056 47.826 4.22 0.00 42.43 3.16
2784 3942 2.010497 GGGCTAGTTTGAGCTAGTTGC 58.990 52.381 4.22 0.00 42.43 4.17
2785 3943 2.615493 GGGCTAGTTTGAGCTAGTTGCA 60.615 50.000 0.00 0.00 45.94 4.08
2786 3944 3.274288 GGCTAGTTTGAGCTAGTTGCAT 58.726 45.455 0.00 0.00 45.94 3.96
2787 3945 3.311048 GGCTAGTTTGAGCTAGTTGCATC 59.689 47.826 0.00 0.00 45.94 3.91
2788 3946 4.187694 GCTAGTTTGAGCTAGTTGCATCT 58.812 43.478 2.28 2.28 45.94 2.90
2789 3947 5.352284 GCTAGTTTGAGCTAGTTGCATCTA 58.648 41.667 4.48 4.48 45.94 1.98
2790 3948 5.988561 GCTAGTTTGAGCTAGTTGCATCTAT 59.011 40.000 4.98 0.00 45.94 1.98
2791 3949 7.148641 GCTAGTTTGAGCTAGTTGCATCTATA 58.851 38.462 4.98 0.00 45.94 1.31
2792 3950 7.653713 GCTAGTTTGAGCTAGTTGCATCTATAA 59.346 37.037 4.98 0.00 45.94 0.98
2793 3951 9.703892 CTAGTTTGAGCTAGTTGCATCTATAAT 57.296 33.333 4.98 0.00 45.94 1.28
2794 3952 8.600449 AGTTTGAGCTAGTTGCATCTATAATC 57.400 34.615 4.98 4.99 45.94 1.75
2795 3953 7.659390 AGTTTGAGCTAGTTGCATCTATAATCC 59.341 37.037 4.98 0.00 45.94 3.01
2796 3954 6.670695 TGAGCTAGTTGCATCTATAATCCA 57.329 37.500 4.98 0.00 45.94 3.41
2797 3955 6.459066 TGAGCTAGTTGCATCTATAATCCAC 58.541 40.000 4.98 0.00 45.94 4.02
2798 3956 5.799213 AGCTAGTTGCATCTATAATCCACC 58.201 41.667 4.98 0.00 45.94 4.61
2799 3957 4.938226 GCTAGTTGCATCTATAATCCACCC 59.062 45.833 4.98 0.00 42.31 4.61
2800 3958 5.513094 GCTAGTTGCATCTATAATCCACCCA 60.513 44.000 4.98 0.00 42.31 4.51
2801 3959 5.387113 AGTTGCATCTATAATCCACCCAA 57.613 39.130 0.00 0.00 0.00 4.12
2802 3960 5.765510 AGTTGCATCTATAATCCACCCAAA 58.234 37.500 0.00 0.00 0.00 3.28
2803 3961 6.194235 AGTTGCATCTATAATCCACCCAAAA 58.806 36.000 0.00 0.00 0.00 2.44
2804 3962 6.667414 AGTTGCATCTATAATCCACCCAAAAA 59.333 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.069318 TGAGGTACAACAAATGCATCTTGA 58.931 37.500 20.96 3.82 0.00 3.02
75 76 6.721704 AAGAGAACAAAAAGCCAAGAGAAT 57.278 33.333 0.00 0.00 0.00 2.40
616 624 3.129287 CCTGAAGTTGGTCCATGCATTAC 59.871 47.826 0.00 0.00 0.00 1.89
731 739 5.711976 ACATCTAGCTACCACAAAAGCAATT 59.288 36.000 0.00 0.00 41.32 2.32
732 740 5.256474 ACATCTAGCTACCACAAAAGCAAT 58.744 37.500 0.00 0.00 41.32 3.56
1488 1542 4.201891 GGCTTCGACGACTACTTCATCTAA 60.202 45.833 0.00 0.00 0.00 2.10
1614 1668 1.435256 ACCTTGGGCAGTTCTAGTGT 58.565 50.000 0.00 0.00 0.00 3.55
1636 1690 3.054508 AGCAAGGATTTCAAGAGGAGGAG 60.055 47.826 0.00 0.00 0.00 3.69
1637 1691 2.915604 AGCAAGGATTTCAAGAGGAGGA 59.084 45.455 0.00 0.00 0.00 3.71
1638 1692 3.015327 CAGCAAGGATTTCAAGAGGAGG 58.985 50.000 0.00 0.00 0.00 4.30
1969 2041 6.599244 AGCAGCACTTATAAATCAGCACTTAA 59.401 34.615 0.00 0.00 0.00 1.85
2054 2221 1.798735 CAGCACATGTACAGCAGCC 59.201 57.895 9.10 0.00 0.00 4.85
2157 2419 9.018716 GCAATTTCCCAAAAACAACAATTTTAG 57.981 29.630 0.00 0.00 31.50 1.85
2416 3574 4.154942 GGATGTTGATATTCAGGGCCATT 58.845 43.478 6.18 0.00 0.00 3.16
2464 3622 7.632028 ACATCATTGTGCAATTGCTTATTAGCT 60.632 33.333 29.37 7.23 40.49 3.32
2465 3623 6.477688 ACATCATTGTGCAATTGCTTATTAGC 59.522 34.615 29.37 11.94 40.36 3.09
2466 3624 7.997107 ACATCATTGTGCAATTGCTTATTAG 57.003 32.000 29.37 15.45 42.66 1.73
2467 3625 8.685427 ACTACATCATTGTGCAATTGCTTATTA 58.315 29.630 29.37 12.64 42.66 0.98
2468 3626 7.549839 ACTACATCATTGTGCAATTGCTTATT 58.450 30.769 29.37 12.66 42.66 1.40
2469 3627 7.104043 ACTACATCATTGTGCAATTGCTTAT 57.896 32.000 29.37 17.01 42.66 1.73
2470 3628 6.513806 ACTACATCATTGTGCAATTGCTTA 57.486 33.333 29.37 16.27 42.66 3.09
2471 3629 5.395682 ACTACATCATTGTGCAATTGCTT 57.604 34.783 29.37 10.45 42.66 3.91
2472 3630 5.415389 TGTACTACATCATTGTGCAATTGCT 59.585 36.000 29.37 8.06 42.66 3.91
2473 3631 5.639757 TGTACTACATCATTGTGCAATTGC 58.360 37.500 23.69 23.69 36.53 3.56
2474 3632 7.060979 GTGTTGTACTACATCATTGTGCAATTG 59.939 37.037 13.21 0.00 39.80 2.32
2475 3633 7.040478 AGTGTTGTACTACATCATTGTGCAATT 60.040 33.333 13.21 0.00 39.80 2.32
2476 3634 6.430925 AGTGTTGTACTACATCATTGTGCAAT 59.569 34.615 13.21 0.00 39.80 3.56
2477 3635 5.762711 AGTGTTGTACTACATCATTGTGCAA 59.237 36.000 13.21 0.00 38.04 4.08
2478 3636 5.304778 AGTGTTGTACTACATCATTGTGCA 58.695 37.500 13.21 0.00 38.04 4.57
2479 3637 5.639506 AGAGTGTTGTACTACATCATTGTGC 59.360 40.000 13.21 0.00 40.53 4.57
2480 3638 7.658179 AAGAGTGTTGTACTACATCATTGTG 57.342 36.000 13.21 0.00 40.53 3.33
2481 3639 8.677148 AAAAGAGTGTTGTACTACATCATTGT 57.323 30.769 13.21 1.83 40.53 2.71
2510 3668 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2512 3670 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2513 3671 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2514 3672 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2515 3673 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2516 3674 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2517 3675 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2518 3676 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2519 3677 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2520 3678 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2521 3679 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2537 3695 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2538 3696 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2555 3713 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2556 3714 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2557 3715 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2558 3716 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2559 3717 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2560 3718 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2561 3719 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2562 3720 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2563 3721 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2564 3722 7.017531 AGATACTCCCTCCGTTCCTAAATATT 58.982 38.462 0.00 0.00 0.00 1.28
2565 3723 6.563163 AGATACTCCCTCCGTTCCTAAATAT 58.437 40.000 0.00 0.00 0.00 1.28
2566 3724 5.961897 AGATACTCCCTCCGTTCCTAAATA 58.038 41.667 0.00 0.00 0.00 1.40
2567 3725 4.817286 AGATACTCCCTCCGTTCCTAAAT 58.183 43.478 0.00 0.00 0.00 1.40
2568 3726 4.261411 AGATACTCCCTCCGTTCCTAAA 57.739 45.455 0.00 0.00 0.00 1.85
2569 3727 3.967467 AGATACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
2570 3728 3.967467 AAGATACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
2571 3729 2.850695 AAGATACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
2572 3730 5.537674 TGTTATAAGATACTCCCTCCGTTCC 59.462 44.000 0.00 0.00 0.00 3.62
2573 3731 6.645790 TGTTATAAGATACTCCCTCCGTTC 57.354 41.667 0.00 0.00 0.00 3.95
2574 3732 6.210984 GGATGTTATAAGATACTCCCTCCGTT 59.789 42.308 0.00 0.00 0.00 4.44
2575 3733 5.715753 GGATGTTATAAGATACTCCCTCCGT 59.284 44.000 0.00 0.00 0.00 4.69
2576 3734 5.715279 TGGATGTTATAAGATACTCCCTCCG 59.285 44.000 6.40 0.00 0.00 4.63
2577 3735 7.554959 TTGGATGTTATAAGATACTCCCTCC 57.445 40.000 6.40 0.00 0.00 4.30
2627 3785 4.763793 CCTTCCAGCCCATAACATAAGATG 59.236 45.833 0.00 0.00 0.00 2.90
2628 3786 4.665009 TCCTTCCAGCCCATAACATAAGAT 59.335 41.667 0.00 0.00 0.00 2.40
2629 3787 4.044308 TCCTTCCAGCCCATAACATAAGA 58.956 43.478 0.00 0.00 0.00 2.10
2630 3788 4.141390 ACTCCTTCCAGCCCATAACATAAG 60.141 45.833 0.00 0.00 0.00 1.73
2631 3789 3.785887 ACTCCTTCCAGCCCATAACATAA 59.214 43.478 0.00 0.00 0.00 1.90
2632 3790 3.393687 ACTCCTTCCAGCCCATAACATA 58.606 45.455 0.00 0.00 0.00 2.29
2633 3791 2.208872 ACTCCTTCCAGCCCATAACAT 58.791 47.619 0.00 0.00 0.00 2.71
2634 3792 1.668826 ACTCCTTCCAGCCCATAACA 58.331 50.000 0.00 0.00 0.00 2.41
2635 3793 2.808906 AACTCCTTCCAGCCCATAAC 57.191 50.000 0.00 0.00 0.00 1.89
2636 3794 3.850173 ACTAAACTCCTTCCAGCCCATAA 59.150 43.478 0.00 0.00 0.00 1.90
2637 3795 3.199946 CACTAAACTCCTTCCAGCCCATA 59.800 47.826 0.00 0.00 0.00 2.74
2638 3796 2.025887 CACTAAACTCCTTCCAGCCCAT 60.026 50.000 0.00 0.00 0.00 4.00
2639 3797 1.351017 CACTAAACTCCTTCCAGCCCA 59.649 52.381 0.00 0.00 0.00 5.36
2640 3798 1.950954 GCACTAAACTCCTTCCAGCCC 60.951 57.143 0.00 0.00 0.00 5.19
2641 3799 1.271379 TGCACTAAACTCCTTCCAGCC 60.271 52.381 0.00 0.00 0.00 4.85
2642 3800 2.185004 TGCACTAAACTCCTTCCAGC 57.815 50.000 0.00 0.00 0.00 4.85
2643 3801 4.583871 AGAATGCACTAAACTCCTTCCAG 58.416 43.478 0.00 0.00 0.00 3.86
2644 3802 4.640771 AGAATGCACTAAACTCCTTCCA 57.359 40.909 0.00 0.00 0.00 3.53
2645 3803 5.938125 TGTAAGAATGCACTAAACTCCTTCC 59.062 40.000 0.00 0.00 0.00 3.46
2646 3804 7.435068 TTGTAAGAATGCACTAAACTCCTTC 57.565 36.000 0.00 0.00 0.00 3.46
2647 3805 7.817418 TTTGTAAGAATGCACTAAACTCCTT 57.183 32.000 0.00 0.00 0.00 3.36
2648 3806 8.409358 AATTTGTAAGAATGCACTAAACTCCT 57.591 30.769 0.00 0.00 0.00 3.69
2651 3809 9.988350 CGATAATTTGTAAGAATGCACTAAACT 57.012 29.630 0.00 0.00 0.00 2.66
2652 3810 9.221775 CCGATAATTTGTAAGAATGCACTAAAC 57.778 33.333 0.00 0.00 0.00 2.01
2653 3811 7.913297 GCCGATAATTTGTAAGAATGCACTAAA 59.087 33.333 0.00 0.00 0.00 1.85
2654 3812 7.282224 AGCCGATAATTTGTAAGAATGCACTAA 59.718 33.333 0.00 0.00 0.00 2.24
2655 3813 6.765989 AGCCGATAATTTGTAAGAATGCACTA 59.234 34.615 0.00 0.00 0.00 2.74
2656 3814 5.590259 AGCCGATAATTTGTAAGAATGCACT 59.410 36.000 0.00 0.00 0.00 4.40
2657 3815 5.821204 AGCCGATAATTTGTAAGAATGCAC 58.179 37.500 0.00 0.00 0.00 4.57
2658 3816 7.561021 TTAGCCGATAATTTGTAAGAATGCA 57.439 32.000 0.00 0.00 0.00 3.96
2664 3822 9.382244 GCAGTTAATTAGCCGATAATTTGTAAG 57.618 33.333 6.93 0.00 40.48 2.34
2665 3823 9.116067 AGCAGTTAATTAGCCGATAATTTGTAA 57.884 29.630 6.93 0.00 40.48 2.41
2666 3824 8.556194 CAGCAGTTAATTAGCCGATAATTTGTA 58.444 33.333 6.93 0.00 40.48 2.41
2667 3825 7.417612 CAGCAGTTAATTAGCCGATAATTTGT 58.582 34.615 6.93 0.00 40.48 2.83
2668 3826 6.360681 GCAGCAGTTAATTAGCCGATAATTTG 59.639 38.462 6.93 1.82 40.48 2.32
2669 3827 6.263168 AGCAGCAGTTAATTAGCCGATAATTT 59.737 34.615 6.93 0.00 40.48 1.82
2670 3828 5.765182 AGCAGCAGTTAATTAGCCGATAATT 59.235 36.000 6.84 6.84 44.51 1.40
2671 3829 5.180117 CAGCAGCAGTTAATTAGCCGATAAT 59.820 40.000 0.00 0.00 35.51 1.28
2672 3830 4.511454 CAGCAGCAGTTAATTAGCCGATAA 59.489 41.667 0.00 0.00 0.00 1.75
2673 3831 4.058124 CAGCAGCAGTTAATTAGCCGATA 58.942 43.478 0.00 0.00 0.00 2.92
2674 3832 2.874701 CAGCAGCAGTTAATTAGCCGAT 59.125 45.455 0.00 0.00 0.00 4.18
2675 3833 2.279741 CAGCAGCAGTTAATTAGCCGA 58.720 47.619 0.00 0.00 0.00 5.54
2676 3834 2.009774 ACAGCAGCAGTTAATTAGCCG 58.990 47.619 0.00 0.00 0.00 5.52
2677 3835 4.214332 GGATACAGCAGCAGTTAATTAGCC 59.786 45.833 0.00 0.00 0.00 3.93
2678 3836 4.816385 TGGATACAGCAGCAGTTAATTAGC 59.184 41.667 0.00 0.00 46.17 3.09
2695 3853 7.107542 TCAAACTAACTGTAACCCATGGATAC 58.892 38.462 15.22 16.07 32.59 2.24
2696 3854 7.260387 TCAAACTAACTGTAACCCATGGATA 57.740 36.000 15.22 2.90 0.00 2.59
2697 3855 6.134535 TCAAACTAACTGTAACCCATGGAT 57.865 37.500 15.22 4.04 0.00 3.41
2698 3856 5.556915 CTCAAACTAACTGTAACCCATGGA 58.443 41.667 15.22 0.00 0.00 3.41
2699 3857 4.156008 GCTCAAACTAACTGTAACCCATGG 59.844 45.833 4.14 4.14 0.00 3.66
2700 3858 5.003804 AGCTCAAACTAACTGTAACCCATG 58.996 41.667 0.00 0.00 0.00 3.66
2701 3859 5.242795 AGCTCAAACTAACTGTAACCCAT 57.757 39.130 0.00 0.00 0.00 4.00
2702 3860 4.699925 AGCTCAAACTAACTGTAACCCA 57.300 40.909 0.00 0.00 0.00 4.51
2703 3861 5.791666 ACTAGCTCAAACTAACTGTAACCC 58.208 41.667 0.00 0.00 0.00 4.11
2704 3862 6.089150 CGAACTAGCTCAAACTAACTGTAACC 59.911 42.308 0.00 0.00 0.00 2.85
2705 3863 6.089150 CCGAACTAGCTCAAACTAACTGTAAC 59.911 42.308 0.00 0.00 0.00 2.50
2706 3864 6.154445 CCGAACTAGCTCAAACTAACTGTAA 58.846 40.000 0.00 0.00 0.00 2.41
2707 3865 5.336213 CCCGAACTAGCTCAAACTAACTGTA 60.336 44.000 0.00 0.00 0.00 2.74
2708 3866 4.557205 CCGAACTAGCTCAAACTAACTGT 58.443 43.478 0.00 0.00 0.00 3.55
2709 3867 3.927142 CCCGAACTAGCTCAAACTAACTG 59.073 47.826 0.00 0.00 0.00 3.16
2710 3868 3.616802 GCCCGAACTAGCTCAAACTAACT 60.617 47.826 0.00 0.00 0.00 2.24
2711 3869 2.671888 GCCCGAACTAGCTCAAACTAAC 59.328 50.000 0.00 0.00 0.00 2.34
2712 3870 2.565834 AGCCCGAACTAGCTCAAACTAA 59.434 45.455 0.00 0.00 32.71 2.24
2713 3871 2.176889 AGCCCGAACTAGCTCAAACTA 58.823 47.619 0.00 0.00 32.71 2.24
2714 3872 0.977395 AGCCCGAACTAGCTCAAACT 59.023 50.000 0.00 0.00 32.71 2.66
2715 3873 3.534721 AGCCCGAACTAGCTCAAAC 57.465 52.632 0.00 0.00 32.71 2.93
2720 3878 2.483889 GCTATTTGAGCCCGAACTAGCT 60.484 50.000 0.00 0.00 46.41 3.32
2721 3879 1.867865 GCTATTTGAGCCCGAACTAGC 59.132 52.381 0.00 0.00 46.41 3.42
2739 3897 8.598041 CCTCATGTTTAGATATACTTTAGGGCT 58.402 37.037 0.00 0.00 0.00 5.19
2740 3898 7.824779 CCCTCATGTTTAGATATACTTTAGGGC 59.175 40.741 0.00 0.00 0.00 5.19
2741 3899 7.824779 GCCCTCATGTTTAGATATACTTTAGGG 59.175 40.741 0.00 0.00 0.00 3.53
2742 3900 8.598041 AGCCCTCATGTTTAGATATACTTTAGG 58.402 37.037 0.00 0.00 0.00 2.69
2745 3903 9.160412 ACTAGCCCTCATGTTTAGATATACTTT 57.840 33.333 0.00 0.00 0.00 2.66
2746 3904 8.728596 ACTAGCCCTCATGTTTAGATATACTT 57.271 34.615 0.00 0.00 0.00 2.24
2747 3905 8.728596 AACTAGCCCTCATGTTTAGATATACT 57.271 34.615 0.00 0.00 0.00 2.12
2748 3906 9.209175 CAAACTAGCCCTCATGTTTAGATATAC 57.791 37.037 0.00 0.00 32.29 1.47
2749 3907 9.154632 TCAAACTAGCCCTCATGTTTAGATATA 57.845 33.333 0.00 0.00 32.29 0.86
2750 3908 8.034313 TCAAACTAGCCCTCATGTTTAGATAT 57.966 34.615 0.00 0.00 32.29 1.63
2751 3909 7.432148 TCAAACTAGCCCTCATGTTTAGATA 57.568 36.000 0.00 0.00 32.29 1.98
2752 3910 6.313519 TCAAACTAGCCCTCATGTTTAGAT 57.686 37.500 0.00 0.00 32.29 1.98
2753 3911 5.734720 CTCAAACTAGCCCTCATGTTTAGA 58.265 41.667 0.00 0.00 32.29 2.10
2754 3912 4.333926 GCTCAAACTAGCCCTCATGTTTAG 59.666 45.833 0.00 0.00 36.45 1.85
2755 3913 4.019321 AGCTCAAACTAGCCCTCATGTTTA 60.019 41.667 0.00 0.00 43.86 2.01
2756 3914 3.084786 GCTCAAACTAGCCCTCATGTTT 58.915 45.455 0.00 0.00 36.45 2.83
2757 3915 2.307098 AGCTCAAACTAGCCCTCATGTT 59.693 45.455 0.00 0.00 43.86 2.71
2758 3916 1.912043 AGCTCAAACTAGCCCTCATGT 59.088 47.619 0.00 0.00 43.86 3.21
2759 3917 2.706339 AGCTCAAACTAGCCCTCATG 57.294 50.000 0.00 0.00 43.86 3.07
2760 3918 3.379452 ACTAGCTCAAACTAGCCCTCAT 58.621 45.455 0.00 0.00 42.91 2.90
2761 3919 2.821437 ACTAGCTCAAACTAGCCCTCA 58.179 47.619 0.00 0.00 42.91 3.86
2762 3920 3.526534 CAACTAGCTCAAACTAGCCCTC 58.473 50.000 0.00 0.00 42.91 4.30
2763 3921 2.355209 GCAACTAGCTCAAACTAGCCCT 60.355 50.000 0.00 0.00 42.91 5.19
2764 3922 2.010497 GCAACTAGCTCAAACTAGCCC 58.990 52.381 0.00 0.00 42.91 5.19
2765 3923 2.699954 TGCAACTAGCTCAAACTAGCC 58.300 47.619 0.00 0.00 42.91 3.93
2766 3924 4.187694 AGATGCAACTAGCTCAAACTAGC 58.812 43.478 0.00 0.00 42.91 3.42
2767 3925 9.703892 ATTATAGATGCAACTAGCTCAAACTAG 57.296 33.333 9.72 0.00 45.94 2.57
2768 3926 9.698309 GATTATAGATGCAACTAGCTCAAACTA 57.302 33.333 9.72 0.00 45.94 2.24
2769 3927 7.659390 GGATTATAGATGCAACTAGCTCAAACT 59.341 37.037 9.72 0.00 45.94 2.66
2770 3928 7.442364 TGGATTATAGATGCAACTAGCTCAAAC 59.558 37.037 9.72 1.07 45.94 2.93
2771 3929 7.442364 GTGGATTATAGATGCAACTAGCTCAAA 59.558 37.037 9.72 0.27 45.94 2.69
2772 3930 6.931281 GTGGATTATAGATGCAACTAGCTCAA 59.069 38.462 9.72 2.13 45.94 3.02
2773 3931 6.459066 GTGGATTATAGATGCAACTAGCTCA 58.541 40.000 9.72 1.64 45.94 4.26
2774 3932 5.872070 GGTGGATTATAGATGCAACTAGCTC 59.128 44.000 9.72 5.94 45.94 4.09
2775 3933 5.280215 GGGTGGATTATAGATGCAACTAGCT 60.280 44.000 9.72 0.00 45.94 3.32
2776 3934 4.938226 GGGTGGATTATAGATGCAACTAGC 59.062 45.833 9.72 0.00 45.96 3.42
2777 3935 6.114187 TGGGTGGATTATAGATGCAACTAG 57.886 41.667 9.72 0.00 0.00 2.57
2778 3936 6.508030 TTGGGTGGATTATAGATGCAACTA 57.492 37.500 6.13 6.13 0.00 2.24
2779 3937 5.387113 TTGGGTGGATTATAGATGCAACT 57.613 39.130 0.86 0.86 0.00 3.16
2780 3938 6.463995 TTTTGGGTGGATTATAGATGCAAC 57.536 37.500 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.