Multiple sequence alignment - TraesCS5B01G150000

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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 TraesCS5B01G150000 chr5B 100.000 3158 0 0 1 3158 278011793 278014950 0.000000e+00 5832.0
1 TraesCS5B01G150000 chr5D 94.379 2544 79 16 1 2508 244624100 244626615 0.000000e+00 3847.0
2 TraesCS5B01G150000 chr5D 91.223 319 25 2 2510 2828 337582907 337582592 6.260000e-117 431.0
3 TraesCS5B01G150000 chr5D 91.250 320 18 4 2842 3158 244626646 244626958 8.090000e-116 427.0
4 TraesCS5B01G150000 chr5D 93.204 103 4 1 73 175 250069618 250069717 7.060000e-32 148.0
5 TraesCS5B01G150000 chr5A 96.054 1419 44 5 722 2140 328807103 328808509 0.000000e+00 2300.0
6 TraesCS5B01G150000 chr5A 97.588 622 9 3 1 620 328804633 328805250 0.000000e+00 1061.0
7 TraesCS5B01G150000 chr5A 89.572 374 18 5 2141 2508 328808674 328809032 3.710000e-124 455.0
8 TraesCS5B01G150000 chr5A 92.171 281 14 3 2883 3158 328809081 328809358 1.060000e-104 390.0
9 TraesCS5B01G150000 chr5A 91.346 104 8 1 68 170 698639622 698639725 1.180000e-29 141.0
10 TraesCS5B01G150000 chr3B 79.940 663 105 18 895 1546 597547158 597546513 2.220000e-126 462.0
11 TraesCS5B01G150000 chr3B 90.549 328 26 4 2509 2835 89057092 89056769 2.250000e-116 429.0
12 TraesCS5B01G150000 chr3B 90.654 321 27 2 2509 2829 646823584 646823267 1.050000e-114 424.0
13 TraesCS5B01G150000 chr3B 82.443 131 21 2 1966 2095 597545972 597545843 2.570000e-21 113.0
14 TraesCS5B01G150000 chr3D 79.789 663 106 18 895 1546 454747753 454747108 1.030000e-124 457.0
15 TraesCS5B01G150000 chr3D 90.244 328 28 3 2504 2831 165375497 165375174 2.910000e-115 425.0
16 TraesCS5B01G150000 chr3D 81.679 131 22 2 1966 2095 454746563 454746434 1.200000e-19 108.0
17 TraesCS5B01G150000 chr3A 79.758 662 108 17 895 1546 596796029 596795384 1.030000e-124 457.0
18 TraesCS5B01G150000 chr3A 82.443 131 21 2 1966 2095 596794837 596794708 2.570000e-21 113.0
19 TraesCS5B01G150000 chr7A 92.212 321 22 2 2509 2829 433430215 433429898 4.800000e-123 451.0
20 TraesCS5B01G150000 chr2B 91.358 324 24 3 2506 2829 284487429 284487110 1.040000e-119 440.0
21 TraesCS5B01G150000 chr1B 91.277 321 22 5 2509 2828 357540239 357540554 1.740000e-117 433.0
22 TraesCS5B01G150000 chr4D 90.625 320 27 2 2509 2828 34816572 34816256 3.770000e-114 422.0
23 TraesCS5B01G150000 chr4D 78.700 277 53 4 1666 1939 334117409 334117682 2.500000e-41 180.0
24 TraesCS5B01G150000 chr7B 90.154 325 28 3 2506 2829 270897404 270897083 1.350000e-113 420.0
25 TraesCS5B01G150000 chr4A 78.909 275 56 2 1666 1939 139546501 139546228 5.380000e-43 185.0
26 TraesCS5B01G150000 chr6A 96.591 88 3 0 86 173 610350314 610350227 2.540000e-31 147.0
27 TraesCS5B01G150000 chr2D 95.556 90 4 0 81 170 331544237 331544148 9.130000e-31 145.0
28 TraesCS5B01G150000 chr2D 92.929 99 6 1 83 180 15192879 15192977 3.280000e-30 143.0
29 TraesCS5B01G150000 chr6D 92.079 101 6 2 86 186 59623259 59623161 1.180000e-29 141.0
30 TraesCS5B01G150000 chr6D 75.897 195 43 3 1002 1194 452497322 452497514 2.590000e-16 97.1
31 TraesCS5B01G150000 chr1A 87.826 115 11 2 72 186 427520594 427520483 7.110000e-27 132.0


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 TraesCS5B01G150000 chr5B 278011793 278014950 3157 False 5832.0 5832 100.00000 1 3158 1 chr5B.!!$F1 3157
1 TraesCS5B01G150000 chr5D 244624100 244626958 2858 False 2137.0 3847 92.81450 1 3158 2 chr5D.!!$F2 3157
2 TraesCS5B01G150000 chr5A 328804633 328809358 4725 False 1051.5 2300 93.84625 1 3158 4 chr5A.!!$F2 3157
3 TraesCS5B01G150000 chr3B 597545843 597547158 1315 True 287.5 462 81.19150 895 2095 2 chr3B.!!$R3 1200
4 TraesCS5B01G150000 chr3D 454746434 454747753 1319 True 282.5 457 80.73400 895 2095 2 chr3D.!!$R2 1200
5 TraesCS5B01G150000 chr3A 596794708 596796029 1321 True 285.0 457 81.10050 895 2095 2 chr3A.!!$R1 1200

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
435 438 1.619654 TTTGTGGCTTGACCCATCTG 58.380 50.000 0.0 0.0 37.2 2.90 F
1102 2859 1.078426 CCTCATTGGTGGGTCGTCC 60.078 63.158 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 3452 0.172578 CACCGCCATCTTCGACTACA 59.827 55.0 0.00 0.00 0.0 2.74 R
2650 4723 0.256752 TCTAGTGGCCAAGCATGCAT 59.743 50.0 21.98 4.57 0.0 3.96 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
39 40 6.265304 AGAGGTGAGTAGAATAGAAGGGTTT 58.735 40.000 0.00 0.00 0.00 3.27
55 56 3.660669 AGGGTTTGATGGGAACTAGGAAA 59.339 43.478 0.00 0.00 0.00 3.13
435 438 1.619654 TTTGTGGCTTGACCCATCTG 58.380 50.000 0.00 0.00 37.20 2.90
463 466 2.290260 TGTGGAGCCTGGAGTTATGTTG 60.290 50.000 0.00 0.00 0.00 3.33
550 553 5.234543 GCTTATTGTACAGCTAGCCAAGTAC 59.765 44.000 24.59 24.59 37.82 2.73
551 554 6.540438 TTATTGTACAGCTAGCCAAGTACT 57.460 37.500 28.14 18.63 38.09 2.73
552 555 7.649533 TTATTGTACAGCTAGCCAAGTACTA 57.350 36.000 28.14 24.30 38.09 1.82
575 578 3.728385 AGCCAGGTAGATCTTTTTGCT 57.272 42.857 0.00 0.40 0.00 3.91
629 658 2.618709 GTGGCTGGTGGTAAATGATAGC 59.381 50.000 0.00 0.00 0.00 2.97
647 895 9.838339 AATGATAGCTGTACTTTATTTAGCACT 57.162 29.630 0.00 0.00 36.87 4.40
670 918 9.088512 CACTACTAAGATTGATTTCAGTGTACC 57.911 37.037 0.00 0.00 0.00 3.34
764 2521 9.424319 TCTGACTGAAAAGTATCTGAATTACAC 57.576 33.333 0.00 0.00 0.00 2.90
1102 2859 1.078426 CCTCATTGGTGGGTCGTCC 60.078 63.158 0.00 0.00 0.00 4.79
1315 3072 2.816958 CGGCTCACATTCTGCGCT 60.817 61.111 9.73 0.00 0.00 5.92
1360 3117 3.384532 GCGGGGAAGTCGGTGGTA 61.385 66.667 0.00 0.00 0.00 3.25
1753 3540 2.832201 GCGAGGTAGTACCGGCCT 60.832 66.667 21.23 0.00 44.90 5.19
1846 3633 0.822164 GCTTAAGGTAGGAGGCGTCA 59.178 55.000 8.91 0.00 0.00 4.35
2025 3925 2.815308 GGTGATGGCGTCGGAGAT 59.185 61.111 1.67 0.00 40.67 2.75
2164 4228 7.858498 AGGAGTACTATCTATCTAGCTCTTCC 58.142 42.308 0.00 0.00 0.00 3.46
2242 4307 4.079970 TCATATAGGAGGAAGGCGTACTG 58.920 47.826 0.00 0.00 0.00 2.74
2279 4344 4.588528 ACAGCTGAAAATGCTAAAAGGGAA 59.411 37.500 23.35 0.00 38.92 3.97
2280 4345 5.070313 ACAGCTGAAAATGCTAAAAGGGAAA 59.930 36.000 23.35 0.00 38.92 3.13
2281 4346 5.990996 CAGCTGAAAATGCTAAAAGGGAAAA 59.009 36.000 8.42 0.00 38.92 2.29
2282 4347 6.146673 CAGCTGAAAATGCTAAAAGGGAAAAG 59.853 38.462 8.42 0.00 38.92 2.27
2283 4348 6.041979 AGCTGAAAATGCTAAAAGGGAAAAGA 59.958 34.615 0.00 0.00 39.21 2.52
2321 4388 2.086869 AGCATGCTGTACCACATGTTC 58.913 47.619 21.98 9.52 44.43 3.18
2333 4401 4.406456 ACCACATGTTCTTTTAGGCATGA 58.594 39.130 9.89 0.00 40.61 3.07
2339 4407 5.794687 TGTTCTTTTAGGCATGATGTACG 57.205 39.130 0.00 0.00 0.00 3.67
2358 4427 6.167685 TGTACGACATGTTAGCCTATTGTTT 58.832 36.000 0.00 0.00 0.00 2.83
2387 4456 1.606668 CCACACACGCAACAACCTAAT 59.393 47.619 0.00 0.00 0.00 1.73
2417 4486 8.262227 ACAGCCAAATCATGAAATAAATGACAT 58.738 29.630 0.00 0.00 36.89 3.06
2457 4530 8.798859 ATGCAATTAGAGACTCTGTTTATTGT 57.201 30.769 15.55 3.10 0.00 2.71
2480 4553 4.982295 TGAATCTATGCAATTACGGACTCG 59.018 41.667 0.00 0.00 43.02 4.18
2493 4566 1.374252 GACTCGCGCTTTCAGGGAA 60.374 57.895 5.56 0.00 0.00 3.97
2512 4585 3.942115 GGAACCCTTCTTGAATGCTACTC 59.058 47.826 0.00 0.00 0.00 2.59
2514 4587 2.239907 ACCCTTCTTGAATGCTACTCCC 59.760 50.000 0.00 0.00 0.00 4.30
2516 4589 3.432890 CCCTTCTTGAATGCTACTCCCTC 60.433 52.174 0.00 0.00 0.00 4.30
2517 4590 3.432890 CCTTCTTGAATGCTACTCCCTCC 60.433 52.174 0.00 0.00 0.00 4.30
2519 4592 3.454858 TCTTGAATGCTACTCCCTCCTT 58.545 45.455 0.00 0.00 0.00 3.36
2520 4593 3.846588 TCTTGAATGCTACTCCCTCCTTT 59.153 43.478 0.00 0.00 0.00 3.11
2521 4594 4.289672 TCTTGAATGCTACTCCCTCCTTTT 59.710 41.667 0.00 0.00 0.00 2.27
2522 4595 4.222124 TGAATGCTACTCCCTCCTTTTC 57.778 45.455 0.00 0.00 0.00 2.29
2523 4596 2.990066 ATGCTACTCCCTCCTTTTCG 57.010 50.000 0.00 0.00 0.00 3.46
2524 4597 0.902531 TGCTACTCCCTCCTTTTCGG 59.097 55.000 0.00 0.00 0.00 4.30
2525 4598 0.903236 GCTACTCCCTCCTTTTCGGT 59.097 55.000 0.00 0.00 0.00 4.69
2526 4599 1.278413 GCTACTCCCTCCTTTTCGGTT 59.722 52.381 0.00 0.00 0.00 4.44
2527 4600 2.290134 GCTACTCCCTCCTTTTCGGTTT 60.290 50.000 0.00 0.00 0.00 3.27
2528 4601 3.055602 GCTACTCCCTCCTTTTCGGTTTA 60.056 47.826 0.00 0.00 0.00 2.01
2529 4602 4.383880 GCTACTCCCTCCTTTTCGGTTTAT 60.384 45.833 0.00 0.00 0.00 1.40
2530 4603 5.163374 GCTACTCCCTCCTTTTCGGTTTATA 60.163 44.000 0.00 0.00 0.00 0.98
2531 4604 5.354842 ACTCCCTCCTTTTCGGTTTATAG 57.645 43.478 0.00 0.00 0.00 1.31
2532 4605 4.163649 ACTCCCTCCTTTTCGGTTTATAGG 59.836 45.833 0.00 0.00 0.00 2.57
2533 4606 3.457012 TCCCTCCTTTTCGGTTTATAGGG 59.543 47.826 0.00 0.00 41.33 3.53
2534 4607 3.201487 CCCTCCTTTTCGGTTTATAGGGT 59.799 47.826 0.00 0.00 37.23 4.34
2535 4608 4.324797 CCCTCCTTTTCGGTTTATAGGGTT 60.325 45.833 0.00 0.00 37.23 4.11
2536 4609 4.880120 CCTCCTTTTCGGTTTATAGGGTTC 59.120 45.833 0.00 0.00 0.00 3.62
2537 4610 5.493809 CTCCTTTTCGGTTTATAGGGTTCA 58.506 41.667 0.00 0.00 0.00 3.18
2538 4611 5.878627 TCCTTTTCGGTTTATAGGGTTCAA 58.121 37.500 0.00 0.00 0.00 2.69
2539 4612 6.305411 TCCTTTTCGGTTTATAGGGTTCAAA 58.695 36.000 0.00 0.00 0.00 2.69
2540 4613 6.949463 TCCTTTTCGGTTTATAGGGTTCAAAT 59.051 34.615 0.00 0.00 0.00 2.32
2541 4614 7.121611 TCCTTTTCGGTTTATAGGGTTCAAATC 59.878 37.037 0.00 0.00 0.00 2.17
2542 4615 7.122204 CCTTTTCGGTTTATAGGGTTCAAATCT 59.878 37.037 0.00 0.00 0.00 2.40
2543 4616 8.411991 TTTTCGGTTTATAGGGTTCAAATCTT 57.588 30.769 0.00 0.00 0.00 2.40
2544 4617 9.517868 TTTTCGGTTTATAGGGTTCAAATCTTA 57.482 29.630 0.00 0.00 0.00 2.10
2545 4618 9.517868 TTTCGGTTTATAGGGTTCAAATCTTAA 57.482 29.630 0.00 0.00 0.00 1.85
2546 4619 9.517868 TTCGGTTTATAGGGTTCAAATCTTAAA 57.482 29.630 0.00 0.00 0.00 1.52
2547 4620 9.689501 TCGGTTTATAGGGTTCAAATCTTAAAT 57.310 29.630 0.00 0.00 0.00 1.40
2548 4621 9.946165 CGGTTTATAGGGTTCAAATCTTAAATC 57.054 33.333 0.00 0.00 0.00 2.17
2555 4628 8.884124 AGGGTTCAAATCTTAAATCTCATCAA 57.116 30.769 0.00 0.00 0.00 2.57
2556 4629 8.743714 AGGGTTCAAATCTTAAATCTCATCAAC 58.256 33.333 0.00 0.00 0.00 3.18
2557 4630 7.976175 GGGTTCAAATCTTAAATCTCATCAACC 59.024 37.037 0.00 0.00 0.00 3.77
2558 4631 8.522830 GGTTCAAATCTTAAATCTCATCAACCA 58.477 33.333 0.00 0.00 0.00 3.67
2559 4632 9.912634 GTTCAAATCTTAAATCTCATCAACCAA 57.087 29.630 0.00 0.00 0.00 3.67
2561 4634 9.519191 TCAAATCTTAAATCTCATCAACCAAGA 57.481 29.630 0.00 0.00 0.00 3.02
2570 4643 9.865321 AAATCTCATCAACCAAGATATTTTGTG 57.135 29.630 5.36 0.00 0.00 3.33
2571 4644 8.812513 ATCTCATCAACCAAGATATTTTGTGA 57.187 30.769 5.36 4.02 0.00 3.58
2572 4645 8.272545 TCTCATCAACCAAGATATTTTGTGAG 57.727 34.615 13.28 13.28 33.33 3.51
2573 4646 7.884877 TCTCATCAACCAAGATATTTTGTGAGT 59.115 33.333 16.51 3.32 33.54 3.41
2574 4647 7.819644 TCATCAACCAAGATATTTTGTGAGTG 58.180 34.615 5.36 4.83 0.00 3.51
2575 4648 6.573664 TCAACCAAGATATTTTGTGAGTGG 57.426 37.500 5.36 0.00 0.00 4.00
2576 4649 6.303054 TCAACCAAGATATTTTGTGAGTGGA 58.697 36.000 5.36 0.00 0.00 4.02
2577 4650 6.430925 TCAACCAAGATATTTTGTGAGTGGAG 59.569 38.462 5.36 0.00 0.00 3.86
2578 4651 5.256474 ACCAAGATATTTTGTGAGTGGAGG 58.744 41.667 5.36 0.00 0.00 4.30
2579 4652 5.014123 ACCAAGATATTTTGTGAGTGGAGGA 59.986 40.000 5.36 0.00 0.00 3.71
2580 4653 5.945784 CCAAGATATTTTGTGAGTGGAGGAA 59.054 40.000 5.36 0.00 0.00 3.36
2581 4654 6.604795 CCAAGATATTTTGTGAGTGGAGGAAT 59.395 38.462 5.36 0.00 0.00 3.01
2582 4655 7.415989 CCAAGATATTTTGTGAGTGGAGGAATG 60.416 40.741 5.36 0.00 0.00 2.67
2583 4656 6.725364 AGATATTTTGTGAGTGGAGGAATGT 58.275 36.000 0.00 0.00 0.00 2.71
2584 4657 7.861629 AGATATTTTGTGAGTGGAGGAATGTA 58.138 34.615 0.00 0.00 0.00 2.29
2585 4658 8.497745 AGATATTTTGTGAGTGGAGGAATGTAT 58.502 33.333 0.00 0.00 0.00 2.29
2586 4659 8.682936 ATATTTTGTGAGTGGAGGAATGTATC 57.317 34.615 0.00 0.00 0.00 2.24
2587 4660 5.762179 TTTGTGAGTGGAGGAATGTATCT 57.238 39.130 0.00 0.00 0.00 1.98
2588 4661 5.344743 TTGTGAGTGGAGGAATGTATCTC 57.655 43.478 0.00 0.00 0.00 2.75
2589 4662 4.352893 TGTGAGTGGAGGAATGTATCTCA 58.647 43.478 0.00 0.00 0.00 3.27
2590 4663 4.964897 TGTGAGTGGAGGAATGTATCTCAT 59.035 41.667 0.00 0.00 38.57 2.90
2591 4664 6.136155 TGTGAGTGGAGGAATGTATCTCATA 58.864 40.000 0.00 0.00 35.48 2.15
2592 4665 6.784473 TGTGAGTGGAGGAATGTATCTCATAT 59.216 38.462 0.00 0.00 35.48 1.78
2593 4666 7.290948 TGTGAGTGGAGGAATGTATCTCATATT 59.709 37.037 0.00 0.00 35.48 1.28
2594 4667 8.153550 GTGAGTGGAGGAATGTATCTCATATTT 58.846 37.037 0.00 0.00 35.48 1.40
2595 4668 8.717717 TGAGTGGAGGAATGTATCTCATATTTT 58.282 33.333 0.00 0.00 35.48 1.82
2622 4695 9.391006 ACTACAAAACTACTCAAATTCAACTCA 57.609 29.630 0.00 0.00 0.00 3.41
2625 4698 7.649306 ACAAAACTACTCAAATTCAACTCATGC 59.351 33.333 0.00 0.00 0.00 4.06
2626 4699 6.882610 AACTACTCAAATTCAACTCATGCA 57.117 33.333 0.00 0.00 0.00 3.96
2627 4700 7.458409 AACTACTCAAATTCAACTCATGCAT 57.542 32.000 0.00 0.00 0.00 3.96
2628 4701 7.458409 ACTACTCAAATTCAACTCATGCATT 57.542 32.000 0.00 0.00 0.00 3.56
2629 4702 8.565896 ACTACTCAAATTCAACTCATGCATTA 57.434 30.769 0.00 0.00 0.00 1.90
2630 4703 9.013229 ACTACTCAAATTCAACTCATGCATTAA 57.987 29.630 0.00 0.00 0.00 1.40
2633 4706 9.715121 ACTCAAATTCAACTCATGCATTAATTT 57.285 25.926 0.00 0.74 0.00 1.82
2649 4722 8.655092 TGCATTAATTTAAGTTAATTGCAGTGC 58.345 29.630 21.97 18.06 35.58 4.40
2650 4723 8.655092 GCATTAATTTAAGTTAATTGCAGTGCA 58.345 29.630 15.37 15.37 33.24 4.57
2666 4739 3.294750 CATGCATGCTTGGCCACT 58.705 55.556 22.49 0.00 0.00 4.00
2667 4740 2.495809 CATGCATGCTTGGCCACTA 58.504 52.632 22.49 0.00 0.00 2.74
2668 4741 0.384309 CATGCATGCTTGGCCACTAG 59.616 55.000 22.49 1.27 0.00 2.57
2669 4742 0.256752 ATGCATGCTTGGCCACTAGA 59.743 50.000 20.33 0.00 0.00 2.43
2670 4743 0.256752 TGCATGCTTGGCCACTAGAT 59.743 50.000 20.33 0.00 0.00 1.98
2671 4744 0.666913 GCATGCTTGGCCACTAGATG 59.333 55.000 3.88 6.90 0.00 2.90
2672 4745 1.748244 GCATGCTTGGCCACTAGATGA 60.748 52.381 3.88 0.00 0.00 2.92
2673 4746 2.219458 CATGCTTGGCCACTAGATGAG 58.781 52.381 3.88 0.00 0.00 2.90
2674 4747 1.279496 TGCTTGGCCACTAGATGAGT 58.721 50.000 3.88 0.00 39.82 3.41
2675 4748 2.466846 TGCTTGGCCACTAGATGAGTA 58.533 47.619 3.88 0.00 35.64 2.59
2676 4749 2.432146 TGCTTGGCCACTAGATGAGTAG 59.568 50.000 3.88 0.00 35.64 2.57
2677 4750 2.695666 GCTTGGCCACTAGATGAGTAGA 59.304 50.000 3.88 0.00 35.64 2.59
2678 4751 3.133003 GCTTGGCCACTAGATGAGTAGAA 59.867 47.826 3.88 0.00 35.64 2.10
2679 4752 4.383118 GCTTGGCCACTAGATGAGTAGAAA 60.383 45.833 3.88 0.00 35.64 2.52
2680 4753 4.737855 TGGCCACTAGATGAGTAGAAAC 57.262 45.455 0.00 0.00 35.64 2.78
2681 4754 4.093743 TGGCCACTAGATGAGTAGAAACA 58.906 43.478 0.00 0.00 35.64 2.83
2682 4755 4.716784 TGGCCACTAGATGAGTAGAAACAT 59.283 41.667 0.00 0.00 35.64 2.71
2683 4756 5.189736 TGGCCACTAGATGAGTAGAAACATT 59.810 40.000 0.00 0.00 35.64 2.71
2684 4757 6.382859 TGGCCACTAGATGAGTAGAAACATTA 59.617 38.462 0.00 0.00 35.64 1.90
2685 4758 6.702282 GGCCACTAGATGAGTAGAAACATTAC 59.298 42.308 0.00 0.00 35.64 1.89
2686 4759 7.265673 GCCACTAGATGAGTAGAAACATTACA 58.734 38.462 0.00 0.00 35.64 2.41
2687 4760 7.928706 GCCACTAGATGAGTAGAAACATTACAT 59.071 37.037 0.00 0.00 35.64 2.29
2688 4761 9.254133 CCACTAGATGAGTAGAAACATTACATG 57.746 37.037 0.00 0.00 35.64 3.21
2689 4762 8.759641 CACTAGATGAGTAGAAACATTACATGC 58.240 37.037 0.00 0.00 35.64 4.06
2690 4763 8.478066 ACTAGATGAGTAGAAACATTACATGCA 58.522 33.333 0.00 0.00 36.27 3.96
2691 4764 9.486497 CTAGATGAGTAGAAACATTACATGCAT 57.514 33.333 0.00 0.00 0.00 3.96
2692 4765 8.743085 AGATGAGTAGAAACATTACATGCATT 57.257 30.769 0.00 0.00 0.00 3.56
2693 4766 9.836864 AGATGAGTAGAAACATTACATGCATTA 57.163 29.630 0.00 0.00 0.00 1.90
2695 4768 9.618890 ATGAGTAGAAACATTACATGCATTAGT 57.381 29.630 0.00 0.00 0.00 2.24
2696 4769 8.882736 TGAGTAGAAACATTACATGCATTAGTG 58.117 33.333 0.00 3.43 0.00 2.74
2697 4770 8.792830 AGTAGAAACATTACATGCATTAGTGT 57.207 30.769 0.00 4.05 0.00 3.55
2698 4771 8.668353 AGTAGAAACATTACATGCATTAGTGTG 58.332 33.333 13.60 9.01 0.00 3.82
2699 4772 7.452880 AGAAACATTACATGCATTAGTGTGT 57.547 32.000 13.60 10.29 0.00 3.72
2700 4773 7.885297 AGAAACATTACATGCATTAGTGTGTT 58.115 30.769 13.60 13.17 32.83 3.32
2701 4774 8.023128 AGAAACATTACATGCATTAGTGTGTTC 58.977 33.333 16.16 16.63 31.37 3.18
2702 4775 6.194796 ACATTACATGCATTAGTGTGTTCC 57.805 37.500 0.00 0.00 0.00 3.62
2703 4776 5.945784 ACATTACATGCATTAGTGTGTTCCT 59.054 36.000 0.00 0.00 0.00 3.36
2704 4777 6.434028 ACATTACATGCATTAGTGTGTTCCTT 59.566 34.615 0.00 0.00 0.00 3.36
2705 4778 6.892658 TTACATGCATTAGTGTGTTCCTTT 57.107 33.333 0.00 0.00 0.00 3.11
2706 4779 5.789643 ACATGCATTAGTGTGTTCCTTTT 57.210 34.783 0.00 0.00 0.00 2.27
2707 4780 6.160576 ACATGCATTAGTGTGTTCCTTTTT 57.839 33.333 0.00 0.00 0.00 1.94
2708 4781 7.283625 ACATGCATTAGTGTGTTCCTTTTTA 57.716 32.000 0.00 0.00 0.00 1.52
2709 4782 7.721402 ACATGCATTAGTGTGTTCCTTTTTAA 58.279 30.769 0.00 0.00 0.00 1.52
2710 4783 8.367156 ACATGCATTAGTGTGTTCCTTTTTAAT 58.633 29.630 0.00 0.00 0.00 1.40
2711 4784 9.206870 CATGCATTAGTGTGTTCCTTTTTAATT 57.793 29.630 0.00 0.00 0.00 1.40
2712 4785 8.810652 TGCATTAGTGTGTTCCTTTTTAATTC 57.189 30.769 0.00 0.00 0.00 2.17
2713 4786 8.637986 TGCATTAGTGTGTTCCTTTTTAATTCT 58.362 29.630 0.00 0.00 0.00 2.40
2714 4787 9.476202 GCATTAGTGTGTTCCTTTTTAATTCTT 57.524 29.630 0.00 0.00 0.00 2.52
2716 4789 8.865590 TTAGTGTGTTCCTTTTTAATTCTTGC 57.134 30.769 0.00 0.00 0.00 4.01
2717 4790 6.872920 AGTGTGTTCCTTTTTAATTCTTGCA 58.127 32.000 0.00 0.00 0.00 4.08
2718 4791 7.500141 AGTGTGTTCCTTTTTAATTCTTGCAT 58.500 30.769 0.00 0.00 0.00 3.96
2719 4792 7.439056 AGTGTGTTCCTTTTTAATTCTTGCATG 59.561 33.333 0.00 0.00 0.00 4.06
2720 4793 6.202570 TGTGTTCCTTTTTAATTCTTGCATGC 59.797 34.615 11.82 11.82 0.00 4.06
2721 4794 6.202570 GTGTTCCTTTTTAATTCTTGCATGCA 59.797 34.615 18.46 18.46 0.00 3.96
2722 4795 6.765036 TGTTCCTTTTTAATTCTTGCATGCAA 59.235 30.769 30.12 30.12 0.00 4.08
2723 4796 7.281774 TGTTCCTTTTTAATTCTTGCATGCAAA 59.718 29.630 31.37 19.79 35.33 3.68
2724 4797 7.798596 TCCTTTTTAATTCTTGCATGCAAAA 57.201 28.000 31.37 25.81 35.33 2.44
2725 4798 8.218338 TCCTTTTTAATTCTTGCATGCAAAAA 57.782 26.923 31.37 26.21 35.33 1.94
2726 4799 8.848182 TCCTTTTTAATTCTTGCATGCAAAAAT 58.152 25.926 31.37 27.20 35.33 1.82
2727 4800 9.465985 CCTTTTTAATTCTTGCATGCAAAAATT 57.534 25.926 34.73 34.73 39.19 1.82
2733 4806 8.455598 AATTCTTGCATGCAAAAATTTAATGC 57.544 26.923 30.14 17.54 34.17 3.56
2744 4817 9.070149 TGCAAAAATTTAATGCACTTCAAAAAC 57.930 25.926 21.26 0.00 44.52 2.43
2745 4818 9.288124 GCAAAAATTTAATGCACTTCAAAAACT 57.712 25.926 18.82 0.00 39.81 2.66
2755 4828 9.598517 AATGCACTTCAAAAACTAAAAATGAGA 57.401 25.926 0.00 0.00 0.00 3.27
2756 4829 9.768662 ATGCACTTCAAAAACTAAAAATGAGAT 57.231 25.926 0.00 0.00 0.00 2.75
2757 4830 9.033481 TGCACTTCAAAAACTAAAAATGAGATG 57.967 29.630 0.00 0.00 0.00 2.90
2758 4831 9.248291 GCACTTCAAAAACTAAAAATGAGATGA 57.752 29.630 0.00 0.00 0.00 2.92
2766 4839 9.852091 AAAACTAAAAATGAGATGAAGATGAGC 57.148 29.630 0.00 0.00 0.00 4.26
2767 4840 7.565323 ACTAAAAATGAGATGAAGATGAGCC 57.435 36.000 0.00 0.00 0.00 4.70
2768 4841 7.114754 ACTAAAAATGAGATGAAGATGAGCCA 58.885 34.615 0.00 0.00 0.00 4.75
2769 4842 7.778853 ACTAAAAATGAGATGAAGATGAGCCAT 59.221 33.333 0.00 0.00 0.00 4.40
2770 4843 7.419711 AAAAATGAGATGAAGATGAGCCATT 57.580 32.000 0.00 0.00 0.00 3.16
2771 4844 7.419711 AAAATGAGATGAAGATGAGCCATTT 57.580 32.000 0.00 0.00 35.34 2.32
2772 4845 8.529424 AAAATGAGATGAAGATGAGCCATTTA 57.471 30.769 0.00 0.00 33.50 1.40
2773 4846 8.529424 AAATGAGATGAAGATGAGCCATTTAA 57.471 30.769 0.00 0.00 33.05 1.52
2774 4847 8.529424 AATGAGATGAAGATGAGCCATTTAAA 57.471 30.769 0.00 0.00 0.00 1.52
2775 4848 8.707796 ATGAGATGAAGATGAGCCATTTAAAT 57.292 30.769 0.00 0.00 0.00 1.40
2776 4849 8.529424 TGAGATGAAGATGAGCCATTTAAATT 57.471 30.769 0.00 0.00 0.00 1.82
2777 4850 8.410912 TGAGATGAAGATGAGCCATTTAAATTG 58.589 33.333 0.00 0.00 0.00 2.32
2778 4851 8.529424 AGATGAAGATGAGCCATTTAAATTGA 57.471 30.769 3.53 0.00 0.00 2.57
2779 4852 8.974238 AGATGAAGATGAGCCATTTAAATTGAA 58.026 29.630 3.53 0.00 0.00 2.69
2780 4853 9.590451 GATGAAGATGAGCCATTTAAATTGAAA 57.410 29.630 3.53 0.00 0.00 2.69
2781 4854 9.947433 ATGAAGATGAGCCATTTAAATTGAAAA 57.053 25.926 3.53 0.00 0.00 2.29
2782 4855 9.775854 TGAAGATGAGCCATTTAAATTGAAAAA 57.224 25.926 3.53 0.00 0.00 1.94
2815 4888 9.816787 AAGTTGAAATAAACCCTATAAACCAGA 57.183 29.630 0.00 0.00 0.00 3.86
2816 4889 9.816787 AGTTGAAATAAACCCTATAAACCAGAA 57.183 29.630 0.00 0.00 0.00 3.02
2819 4892 9.250246 TGAAATAAACCCTATAAACCAGAAAGG 57.750 33.333 0.00 0.00 45.67 3.11
2820 4893 9.470399 GAAATAAACCCTATAAACCAGAAAGGA 57.530 33.333 0.00 0.00 41.22 3.36
2821 4894 9.475620 AAATAAACCCTATAAACCAGAAAGGAG 57.524 33.333 0.00 0.00 41.22 3.69
2822 4895 5.452341 AACCCTATAAACCAGAAAGGAGG 57.548 43.478 0.00 0.00 41.22 4.30
2823 4896 4.439253 CCCTATAAACCAGAAAGGAGGG 57.561 50.000 0.00 0.00 39.46 4.30
2824 4897 4.045022 CCCTATAAACCAGAAAGGAGGGA 58.955 47.826 0.00 0.00 45.41 4.20
2825 4898 4.103311 CCCTATAAACCAGAAAGGAGGGAG 59.897 50.000 0.00 0.00 45.41 4.30
2831 4904 6.910259 AAACCAGAAAGGAGGGAGTATTAT 57.090 37.500 0.00 0.00 41.22 1.28
2837 4911 7.420680 CCAGAAAGGAGGGAGTATTATGTTGAT 60.421 40.741 0.00 0.00 41.22 2.57
2838 4912 7.659390 CAGAAAGGAGGGAGTATTATGTTGATC 59.341 40.741 0.00 0.00 0.00 2.92
3014 5093 8.908786 TTGAGGAAATAATGTATAAGAGCCTG 57.091 34.615 0.00 0.00 0.00 4.85
3015 5094 8.262601 TGAGGAAATAATGTATAAGAGCCTGA 57.737 34.615 0.00 0.00 0.00 3.86
3056 5135 6.754193 ACATTTTCATGATGATGCATGCATA 58.246 32.000 32.27 17.85 44.08 3.14
3104 5183 2.700722 AAGCTAGCTAGAAAGGTGCC 57.299 50.000 25.15 3.82 34.60 5.01
3137 5216 6.749923 ATTTCTTAAGGCTGAAGCAAGTAG 57.250 37.500 6.75 0.00 44.36 2.57
3138 5217 4.891992 TCTTAAGGCTGAAGCAAGTAGT 57.108 40.909 6.75 0.00 44.36 2.73
3139 5218 4.569943 TCTTAAGGCTGAAGCAAGTAGTG 58.430 43.478 6.75 0.00 44.36 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.886609 TCACAATTTTCCTAGTTCCCATCA 58.113 37.500 0.00 0.00 0.00 3.07
55 56 8.553696 GTCAAGAAAGAAATTTGCATCACAATT 58.446 29.630 0.00 0.00 38.31 2.32
159 160 4.410228 CCATCAAGAAAGATACTCCCTCCA 59.590 45.833 0.00 0.00 0.00 3.86
435 438 1.673665 CCAGGCTCCACAGACTTGC 60.674 63.158 0.00 0.00 34.70 4.01
463 466 1.672356 ACAGGGCACGACTGCATTC 60.672 57.895 0.11 0.00 46.28 2.67
550 553 5.755861 GCAAAAAGATCTACCTGGCTACTAG 59.244 44.000 0.00 0.00 0.00 2.57
551 554 5.425539 AGCAAAAAGATCTACCTGGCTACTA 59.574 40.000 0.00 0.00 0.00 1.82
552 555 4.226168 AGCAAAAAGATCTACCTGGCTACT 59.774 41.667 0.00 0.00 0.00 2.57
575 578 1.348064 AGGAGAAATGGTGTCGGTCA 58.652 50.000 0.00 0.00 0.00 4.02
642 890 7.390027 ACACTGAAATCAATCTTAGTAGTGCT 58.610 34.615 0.00 0.00 37.19 4.40
645 893 8.812972 TGGTACACTGAAATCAATCTTAGTAGT 58.187 33.333 0.00 0.00 0.00 2.73
670 918 2.104281 TCCTGCATCATGAGATCCAGTG 59.896 50.000 0.09 0.00 38.19 3.66
787 2544 5.352016 TGCCGCGTTCTAGTTATTTACATTT 59.648 36.000 4.92 0.00 0.00 2.32
871 2628 7.387397 TGCTGAAGAAATCAAAGTTGTTGTTTT 59.613 29.630 0.00 0.00 37.67 2.43
872 2629 6.873076 TGCTGAAGAAATCAAAGTTGTTGTTT 59.127 30.769 0.00 0.00 37.67 2.83
873 2630 6.397272 TGCTGAAGAAATCAAAGTTGTTGTT 58.603 32.000 0.00 0.00 37.67 2.83
874 2631 5.964758 TGCTGAAGAAATCAAAGTTGTTGT 58.035 33.333 0.00 0.00 37.67 3.32
875 2632 6.890663 TTGCTGAAGAAATCAAAGTTGTTG 57.109 33.333 0.00 0.00 37.67 3.33
876 2633 8.392612 CAATTTGCTGAAGAAATCAAAGTTGTT 58.607 29.630 0.00 0.00 37.67 2.83
877 2634 7.011669 CCAATTTGCTGAAGAAATCAAAGTTGT 59.988 33.333 0.00 0.00 37.67 3.32
878 2635 7.349711 CCAATTTGCTGAAGAAATCAAAGTTG 58.650 34.615 0.00 0.00 37.67 3.16
879 2636 6.017687 GCCAATTTGCTGAAGAAATCAAAGTT 60.018 34.615 0.00 0.00 37.67 2.66
932 2689 0.313672 GATGGAGTAGGAGAGCTGCG 59.686 60.000 0.00 0.00 0.00 5.18
1102 2859 0.738389 ACACCGCAAAGTTCAACCTG 59.262 50.000 0.00 0.00 0.00 4.00
1315 3072 0.318360 CGGTGCAGTTCGACTACACA 60.318 55.000 15.57 1.40 42.77 3.72
1390 3147 1.135094 CCATCCTCCAGGCACACTAT 58.865 55.000 0.00 0.00 34.44 2.12
1660 3429 0.179137 CCATCTTCGACTACAGCGCA 60.179 55.000 11.47 0.00 0.00 6.09
1665 3452 0.172578 CACCGCCATCTTCGACTACA 59.827 55.000 0.00 0.00 0.00 2.74
1753 3540 1.227823 CACTTTCGACCAGCCACCA 60.228 57.895 0.00 0.00 0.00 4.17
1756 3543 1.300620 CGTCACTTTCGACCAGCCA 60.301 57.895 0.00 0.00 31.91 4.75
1831 3618 2.711922 CGCTGACGCCTCCTACCTT 61.712 63.158 0.00 0.00 0.00 3.50
2025 3925 4.641645 CCGGTGCAGCTCCCAACA 62.642 66.667 14.92 0.00 0.00 3.33
2242 4307 3.273434 TCAGCTGTTCAATATGTGGAGC 58.727 45.455 14.67 0.00 0.00 4.70
2321 4388 5.294306 ACATGTCGTACATCATGCCTAAAAG 59.706 40.000 20.14 2.94 43.34 2.27
2333 4401 5.914033 ACAATAGGCTAACATGTCGTACAT 58.086 37.500 0.00 0.00 39.91 2.29
2339 4407 7.088589 ACATGAAACAATAGGCTAACATGTC 57.911 36.000 0.00 7.50 41.66 3.06
2358 4427 2.356913 CGTGTGTGGCCGACATGA 60.357 61.111 18.10 4.18 36.78 3.07
2457 4530 4.982295 CGAGTCCGTAATTGCATAGATTCA 59.018 41.667 0.00 0.00 0.00 2.57
2480 4553 1.587043 GAAGGGTTCCCTGAAAGCGC 61.587 60.000 11.50 0.00 36.42 5.92
2493 4566 2.239907 GGGAGTAGCATTCAAGAAGGGT 59.760 50.000 4.57 4.57 36.72 4.34
2495 4568 3.432890 GGAGGGAGTAGCATTCAAGAAGG 60.433 52.174 0.00 0.00 0.00 3.46
2508 4581 5.364735 CCTATAAACCGAAAAGGAGGGAGTA 59.635 44.000 0.00 0.00 45.00 2.59
2510 4583 4.444449 CCCTATAAACCGAAAAGGAGGGAG 60.444 50.000 0.00 0.00 46.86 4.30
2512 4585 3.816994 CCCTATAAACCGAAAAGGAGGG 58.183 50.000 0.00 0.00 45.00 4.30
2514 4587 5.493809 TGAACCCTATAAACCGAAAAGGAG 58.506 41.667 0.00 0.00 45.00 3.69
2517 4590 8.051901 AGATTTGAACCCTATAAACCGAAAAG 57.948 34.615 0.00 0.00 0.00 2.27
2519 4592 9.517868 TTAAGATTTGAACCCTATAAACCGAAA 57.482 29.630 0.00 0.00 0.00 3.46
2520 4593 9.517868 TTTAAGATTTGAACCCTATAAACCGAA 57.482 29.630 0.00 0.00 0.00 4.30
2521 4594 9.689501 ATTTAAGATTTGAACCCTATAAACCGA 57.310 29.630 0.00 0.00 0.00 4.69
2522 4595 9.946165 GATTTAAGATTTGAACCCTATAAACCG 57.054 33.333 0.00 0.00 0.00 4.44
2529 4602 9.973661 TTGATGAGATTTAAGATTTGAACCCTA 57.026 29.630 0.00 0.00 0.00 3.53
2530 4603 8.743714 GTTGATGAGATTTAAGATTTGAACCCT 58.256 33.333 0.00 0.00 0.00 4.34
2531 4604 7.976175 GGTTGATGAGATTTAAGATTTGAACCC 59.024 37.037 0.00 0.00 0.00 4.11
2532 4605 8.522830 TGGTTGATGAGATTTAAGATTTGAACC 58.477 33.333 0.00 0.00 0.00 3.62
2533 4606 9.912634 TTGGTTGATGAGATTTAAGATTTGAAC 57.087 29.630 0.00 0.00 0.00 3.18
2535 4608 9.519191 TCTTGGTTGATGAGATTTAAGATTTGA 57.481 29.630 0.00 0.00 0.00 2.69
2544 4617 9.865321 CACAAAATATCTTGGTTGATGAGATTT 57.135 29.630 0.00 0.00 33.37 2.17
2545 4618 9.246670 TCACAAAATATCTTGGTTGATGAGATT 57.753 29.630 0.00 0.00 32.68 2.40
2546 4619 8.812513 TCACAAAATATCTTGGTTGATGAGAT 57.187 30.769 0.00 0.00 34.67 2.75
2547 4620 7.884877 ACTCACAAAATATCTTGGTTGATGAGA 59.115 33.333 11.33 0.00 35.30 3.27
2548 4621 7.966753 CACTCACAAAATATCTTGGTTGATGAG 59.033 37.037 5.30 5.30 36.41 2.90
2549 4622 7.094248 CCACTCACAAAATATCTTGGTTGATGA 60.094 37.037 0.00 0.00 0.00 2.92
2550 4623 7.031372 CCACTCACAAAATATCTTGGTTGATG 58.969 38.462 0.00 0.00 0.00 3.07
2551 4624 6.947733 TCCACTCACAAAATATCTTGGTTGAT 59.052 34.615 0.00 0.00 0.00 2.57
2552 4625 6.303054 TCCACTCACAAAATATCTTGGTTGA 58.697 36.000 0.00 0.00 0.00 3.18
2553 4626 6.349611 CCTCCACTCACAAAATATCTTGGTTG 60.350 42.308 0.00 0.00 0.00 3.77
2554 4627 5.711976 CCTCCACTCACAAAATATCTTGGTT 59.288 40.000 0.00 0.00 0.00 3.67
2555 4628 5.014123 TCCTCCACTCACAAAATATCTTGGT 59.986 40.000 0.00 0.00 0.00 3.67
2556 4629 5.500234 TCCTCCACTCACAAAATATCTTGG 58.500 41.667 0.00 0.00 0.00 3.61
2557 4630 7.121759 ACATTCCTCCACTCACAAAATATCTTG 59.878 37.037 0.00 0.00 0.00 3.02
2558 4631 7.177878 ACATTCCTCCACTCACAAAATATCTT 58.822 34.615 0.00 0.00 0.00 2.40
2559 4632 6.725364 ACATTCCTCCACTCACAAAATATCT 58.275 36.000 0.00 0.00 0.00 1.98
2560 4633 8.682936 ATACATTCCTCCACTCACAAAATATC 57.317 34.615 0.00 0.00 0.00 1.63
2561 4634 8.497745 AGATACATTCCTCCACTCACAAAATAT 58.502 33.333 0.00 0.00 0.00 1.28
2562 4635 7.861629 AGATACATTCCTCCACTCACAAAATA 58.138 34.615 0.00 0.00 0.00 1.40
2563 4636 6.725364 AGATACATTCCTCCACTCACAAAAT 58.275 36.000 0.00 0.00 0.00 1.82
2564 4637 6.126863 AGATACATTCCTCCACTCACAAAA 57.873 37.500 0.00 0.00 0.00 2.44
2565 4638 5.248248 TGAGATACATTCCTCCACTCACAAA 59.752 40.000 0.00 0.00 0.00 2.83
2566 4639 4.777366 TGAGATACATTCCTCCACTCACAA 59.223 41.667 0.00 0.00 0.00 3.33
2567 4640 4.352893 TGAGATACATTCCTCCACTCACA 58.647 43.478 0.00 0.00 0.00 3.58
2568 4641 5.543507 ATGAGATACATTCCTCCACTCAC 57.456 43.478 0.00 0.00 35.45 3.51
2569 4642 7.862274 AATATGAGATACATTCCTCCACTCA 57.138 36.000 0.00 0.00 40.07 3.41
2596 4669 9.391006 TGAGTTGAATTTGAGTAGTTTTGTAGT 57.609 29.630 0.00 0.00 0.00 2.73
2599 4672 7.649306 GCATGAGTTGAATTTGAGTAGTTTTGT 59.351 33.333 0.00 0.00 0.00 2.83
2600 4673 7.648908 TGCATGAGTTGAATTTGAGTAGTTTTG 59.351 33.333 0.00 0.00 0.00 2.44
2601 4674 7.715657 TGCATGAGTTGAATTTGAGTAGTTTT 58.284 30.769 0.00 0.00 0.00 2.43
2602 4675 7.275888 TGCATGAGTTGAATTTGAGTAGTTT 57.724 32.000 0.00 0.00 0.00 2.66
2603 4676 6.882610 TGCATGAGTTGAATTTGAGTAGTT 57.117 33.333 0.00 0.00 0.00 2.24
2604 4677 7.458409 AATGCATGAGTTGAATTTGAGTAGT 57.542 32.000 0.00 0.00 28.14 2.73
2607 4680 9.715121 AAATTAATGCATGAGTTGAATTTGAGT 57.285 25.926 0.00 0.00 35.12 3.41
2623 4696 8.655092 GCACTGCAATTAACTTAAATTAATGCA 58.345 29.630 17.40 17.40 36.86 3.96
2624 4697 8.655092 TGCACTGCAATTAACTTAAATTAATGC 58.345 29.630 0.00 8.92 35.42 3.56
2649 4722 0.384309 CTAGTGGCCAAGCATGCATG 59.616 55.000 22.70 22.70 0.00 4.06
2650 4723 0.256752 TCTAGTGGCCAAGCATGCAT 59.743 50.000 21.98 4.57 0.00 3.96
2651 4724 0.256752 ATCTAGTGGCCAAGCATGCA 59.743 50.000 21.98 0.00 0.00 3.96
2652 4725 0.666913 CATCTAGTGGCCAAGCATGC 59.333 55.000 7.24 10.51 0.00 4.06
2653 4726 2.219458 CTCATCTAGTGGCCAAGCATG 58.781 52.381 7.24 7.98 0.00 4.06
2654 4727 1.842562 ACTCATCTAGTGGCCAAGCAT 59.157 47.619 7.24 0.00 36.93 3.79
2655 4728 1.279496 ACTCATCTAGTGGCCAAGCA 58.721 50.000 7.24 0.00 36.93 3.91
2656 4729 2.695666 TCTACTCATCTAGTGGCCAAGC 59.304 50.000 7.24 0.00 39.39 4.01
2657 4730 5.112686 GTTTCTACTCATCTAGTGGCCAAG 58.887 45.833 7.24 1.33 39.39 3.61
2658 4731 4.530553 TGTTTCTACTCATCTAGTGGCCAA 59.469 41.667 7.24 0.00 39.39 4.52
2659 4732 4.093743 TGTTTCTACTCATCTAGTGGCCA 58.906 43.478 0.00 0.00 39.39 5.36
2660 4733 4.737855 TGTTTCTACTCATCTAGTGGCC 57.262 45.455 0.00 0.00 39.39 5.36
2661 4734 7.265673 TGTAATGTTTCTACTCATCTAGTGGC 58.734 38.462 0.00 0.00 39.39 5.01
2662 4735 9.254133 CATGTAATGTTTCTACTCATCTAGTGG 57.746 37.037 0.00 0.00 40.20 4.00
2681 4754 7.466746 AAAGGAACACACTAATGCATGTAAT 57.533 32.000 0.00 0.00 0.00 1.89
2682 4755 6.892658 AAAGGAACACACTAATGCATGTAA 57.107 33.333 0.00 0.00 0.00 2.41
2683 4756 6.892658 AAAAGGAACACACTAATGCATGTA 57.107 33.333 0.00 0.00 0.00 2.29
2684 4757 5.789643 AAAAGGAACACACTAATGCATGT 57.210 34.783 0.00 0.00 0.00 3.21
2685 4758 8.761575 ATTAAAAAGGAACACACTAATGCATG 57.238 30.769 0.00 0.00 0.00 4.06
2686 4759 9.423061 GAATTAAAAAGGAACACACTAATGCAT 57.577 29.630 0.00 0.00 0.00 3.96
2687 4760 8.637986 AGAATTAAAAAGGAACACACTAATGCA 58.362 29.630 0.00 0.00 0.00 3.96
2688 4761 9.476202 AAGAATTAAAAAGGAACACACTAATGC 57.524 29.630 0.00 0.00 0.00 3.56
2690 4763 9.476202 GCAAGAATTAAAAAGGAACACACTAAT 57.524 29.630 0.00 0.00 0.00 1.73
2691 4764 8.470805 TGCAAGAATTAAAAAGGAACACACTAA 58.529 29.630 0.00 0.00 0.00 2.24
2692 4765 8.001881 TGCAAGAATTAAAAAGGAACACACTA 57.998 30.769 0.00 0.00 0.00 2.74
2693 4766 6.872920 TGCAAGAATTAAAAAGGAACACACT 58.127 32.000 0.00 0.00 0.00 3.55
2694 4767 7.566709 CATGCAAGAATTAAAAAGGAACACAC 58.433 34.615 0.00 0.00 0.00 3.82
2695 4768 6.202570 GCATGCAAGAATTAAAAAGGAACACA 59.797 34.615 14.21 0.00 0.00 3.72
2696 4769 6.202570 TGCATGCAAGAATTAAAAAGGAACAC 59.797 34.615 20.30 0.00 0.00 3.32
2697 4770 6.286758 TGCATGCAAGAATTAAAAAGGAACA 58.713 32.000 20.30 0.00 0.00 3.18
2698 4771 6.783892 TGCATGCAAGAATTAAAAAGGAAC 57.216 33.333 20.30 0.00 0.00 3.62
2699 4772 7.798596 TTTGCATGCAAGAATTAAAAAGGAA 57.201 28.000 30.25 10.13 37.24 3.36
2700 4773 7.798596 TTTTGCATGCAAGAATTAAAAAGGA 57.201 28.000 30.25 10.57 37.24 3.36
2701 4774 9.465985 AATTTTTGCATGCAAGAATTAAAAAGG 57.534 25.926 39.53 0.00 43.88 3.11
2707 4780 9.557338 GCATTAAATTTTTGCATGCAAGAATTA 57.443 25.926 39.94 31.72 44.47 1.40
2708 4781 8.082852 TGCATTAAATTTTTGCATGCAAGAATT 58.917 25.926 37.18 37.18 46.00 2.17
2709 4782 7.539366 GTGCATTAAATTTTTGCATGCAAGAAT 59.461 29.630 32.40 32.40 46.90 2.40
2710 4783 6.856938 GTGCATTAAATTTTTGCATGCAAGAA 59.143 30.769 31.20 31.20 46.90 2.52
2711 4784 6.205076 AGTGCATTAAATTTTTGCATGCAAGA 59.795 30.769 30.25 24.77 46.90 3.02
2712 4785 6.375377 AGTGCATTAAATTTTTGCATGCAAG 58.625 32.000 30.25 17.64 46.90 4.01
2713 4786 6.315091 AGTGCATTAAATTTTTGCATGCAA 57.685 29.167 28.80 28.80 46.90 4.08
2714 4787 5.943706 AGTGCATTAAATTTTTGCATGCA 57.056 30.435 18.46 18.46 46.90 3.96
2715 4788 6.372185 TGAAGTGCATTAAATTTTTGCATGC 58.628 32.000 23.21 11.82 46.90 4.06
2716 4789 8.783999 TTTGAAGTGCATTAAATTTTTGCATG 57.216 26.923 23.21 11.29 46.90 4.06
2717 4790 9.798994 TTTTTGAAGTGCATTAAATTTTTGCAT 57.201 22.222 23.21 13.48 46.90 3.96
2718 4791 9.070149 GTTTTTGAAGTGCATTAAATTTTTGCA 57.930 25.926 19.00 19.00 43.63 4.08
2719 4792 9.288124 AGTTTTTGAAGTGCATTAAATTTTTGC 57.712 25.926 15.27 15.27 36.91 3.68
2729 4802 9.598517 TCTCATTTTTAGTTTTTGAAGTGCATT 57.401 25.926 0.00 0.00 0.00 3.56
2730 4803 9.768662 ATCTCATTTTTAGTTTTTGAAGTGCAT 57.231 25.926 0.00 0.00 0.00 3.96
2731 4804 9.033481 CATCTCATTTTTAGTTTTTGAAGTGCA 57.967 29.630 0.00 0.00 0.00 4.57
2732 4805 9.248291 TCATCTCATTTTTAGTTTTTGAAGTGC 57.752 29.630 0.00 0.00 0.00 4.40
2740 4813 9.852091 GCTCATCTTCATCTCATTTTTAGTTTT 57.148 29.630 0.00 0.00 0.00 2.43
2741 4814 8.465201 GGCTCATCTTCATCTCATTTTTAGTTT 58.535 33.333 0.00 0.00 0.00 2.66
2742 4815 7.613022 TGGCTCATCTTCATCTCATTTTTAGTT 59.387 33.333 0.00 0.00 0.00 2.24
2743 4816 7.114754 TGGCTCATCTTCATCTCATTTTTAGT 58.885 34.615 0.00 0.00 0.00 2.24
2744 4817 7.563888 TGGCTCATCTTCATCTCATTTTTAG 57.436 36.000 0.00 0.00 0.00 1.85
2745 4818 8.529424 AATGGCTCATCTTCATCTCATTTTTA 57.471 30.769 0.00 0.00 0.00 1.52
2746 4819 7.419711 AATGGCTCATCTTCATCTCATTTTT 57.580 32.000 0.00 0.00 0.00 1.94
2747 4820 7.419711 AAATGGCTCATCTTCATCTCATTTT 57.580 32.000 0.00 0.00 31.98 1.82
2748 4821 8.529424 TTAAATGGCTCATCTTCATCTCATTT 57.471 30.769 0.00 0.00 37.37 2.32
2749 4822 8.529424 TTTAAATGGCTCATCTTCATCTCATT 57.471 30.769 0.00 0.00 0.00 2.57
2750 4823 8.707796 ATTTAAATGGCTCATCTTCATCTCAT 57.292 30.769 0.00 0.00 0.00 2.90
2751 4824 8.410912 CAATTTAAATGGCTCATCTTCATCTCA 58.589 33.333 0.39 0.00 0.00 3.27
2752 4825 8.627403 TCAATTTAAATGGCTCATCTTCATCTC 58.373 33.333 0.39 0.00 0.00 2.75
2753 4826 8.529424 TCAATTTAAATGGCTCATCTTCATCT 57.471 30.769 0.39 0.00 0.00 2.90
2754 4827 9.590451 TTTCAATTTAAATGGCTCATCTTCATC 57.410 29.630 0.39 0.00 0.00 2.92
2755 4828 9.947433 TTTTCAATTTAAATGGCTCATCTTCAT 57.053 25.926 0.39 0.00 0.00 2.57
2756 4829 9.775854 TTTTTCAATTTAAATGGCTCATCTTCA 57.224 25.926 0.39 0.00 0.00 3.02
2789 4862 9.816787 TCTGGTTTATAGGGTTTATTTCAACTT 57.183 29.630 0.00 0.00 0.00 2.66
2790 4863 9.816787 TTCTGGTTTATAGGGTTTATTTCAACT 57.183 29.630 0.00 0.00 0.00 3.16
2793 4866 9.250246 CCTTTCTGGTTTATAGGGTTTATTTCA 57.750 33.333 0.00 0.00 0.00 2.69
2794 4867 9.470399 TCCTTTCTGGTTTATAGGGTTTATTTC 57.530 33.333 0.00 0.00 37.07 2.17
2795 4868 9.475620 CTCCTTTCTGGTTTATAGGGTTTATTT 57.524 33.333 0.00 0.00 37.07 1.40
2796 4869 8.059461 CCTCCTTTCTGGTTTATAGGGTTTATT 58.941 37.037 0.00 0.00 37.07 1.40
2797 4870 7.367459 CCCTCCTTTCTGGTTTATAGGGTTTAT 60.367 40.741 0.00 0.00 39.14 1.40
2798 4871 6.069264 CCCTCCTTTCTGGTTTATAGGGTTTA 60.069 42.308 0.00 0.00 39.14 2.01
2799 4872 5.281558 CCCTCCTTTCTGGTTTATAGGGTTT 60.282 44.000 0.00 0.00 39.14 3.27
2800 4873 4.229812 CCCTCCTTTCTGGTTTATAGGGTT 59.770 45.833 0.00 0.00 39.14 4.11
2801 4874 3.786450 CCCTCCTTTCTGGTTTATAGGGT 59.214 47.826 0.00 0.00 39.14 4.34
2802 4875 4.045022 TCCCTCCTTTCTGGTTTATAGGG 58.955 47.826 0.00 0.00 43.08 3.53
2803 4876 4.722279 ACTCCCTCCTTTCTGGTTTATAGG 59.278 45.833 0.00 0.00 37.07 2.57
2804 4877 5.959583 ACTCCCTCCTTTCTGGTTTATAG 57.040 43.478 0.00 0.00 37.07 1.31
2805 4878 9.684702 ATAATACTCCCTCCTTTCTGGTTTATA 57.315 33.333 0.00 0.00 37.07 0.98
2806 4879 6.910259 AATACTCCCTCCTTTCTGGTTTAT 57.090 37.500 0.00 0.00 37.07 1.40
2807 4880 7.404980 ACATAATACTCCCTCCTTTCTGGTTTA 59.595 37.037 0.00 0.00 37.07 2.01
2808 4881 6.217693 ACATAATACTCCCTCCTTTCTGGTTT 59.782 38.462 0.00 0.00 37.07 3.27
2809 4882 5.731678 ACATAATACTCCCTCCTTTCTGGTT 59.268 40.000 0.00 0.00 37.07 3.67
2810 4883 5.289510 ACATAATACTCCCTCCTTTCTGGT 58.710 41.667 0.00 0.00 37.07 4.00
2811 4884 5.896073 ACATAATACTCCCTCCTTTCTGG 57.104 43.478 0.00 0.00 37.10 3.86
2812 4885 6.889198 TCAACATAATACTCCCTCCTTTCTG 58.111 40.000 0.00 0.00 0.00 3.02
2813 4886 7.348274 TGATCAACATAATACTCCCTCCTTTCT 59.652 37.037 0.00 0.00 0.00 2.52
2814 4887 7.509546 TGATCAACATAATACTCCCTCCTTTC 58.490 38.462 0.00 0.00 0.00 2.62
2815 4888 7.451731 TGATCAACATAATACTCCCTCCTTT 57.548 36.000 0.00 0.00 0.00 3.11
2816 4889 7.639062 ATGATCAACATAATACTCCCTCCTT 57.361 36.000 0.00 0.00 37.46 3.36
2817 4890 8.742125 TTATGATCAACATAATACTCCCTCCT 57.258 34.615 0.00 0.00 43.73 3.69
2818 4891 9.965902 ATTTATGATCAACATAATACTCCCTCC 57.034 33.333 0.00 0.00 46.52 4.30
2831 4904 8.108551 TGTTGTCATGTCATTTATGATCAACA 57.891 30.769 19.68 19.68 43.72 3.33
2897 4971 5.815222 CGGGTTTGAAAGAAAAATCTTTGGT 59.185 36.000 8.44 0.00 39.74 3.67
3011 5090 1.833630 TCCATGTCTAGTTGGCTCAGG 59.166 52.381 0.00 0.00 32.80 3.86
3014 5093 3.334583 TGTTCCATGTCTAGTTGGCTC 57.665 47.619 0.00 2.42 32.80 4.70
3015 5094 4.307032 AATGTTCCATGTCTAGTTGGCT 57.693 40.909 0.00 0.00 32.80 4.75
3104 5183 8.498054 TTCAGCCTTAAGAAATTCAGATACTG 57.502 34.615 3.36 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.