Multiple sequence alignment - TraesCS3B01G199000

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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 TraesCS3B01G199000 chr3B 100.000 4883 0 0 1 4883 226786232 226791114 0.000000e+00 9018.0
1 TraesCS3B01G199000 chr3B 96.416 279 10 0 2577 2855 751272101 751272379 1.240000e-125 460.0
2 TraesCS3B01G199000 chr3D 93.125 2502 86 32 132 2582 154182949 154180483 0.000000e+00 3589.0
3 TraesCS3B01G199000 chr3D 96.479 1136 32 6 2862 3994 154180485 154179355 0.000000e+00 1869.0
4 TraesCS3B01G199000 chr3D 88.984 935 39 31 3987 4883 154178542 154177634 0.000000e+00 1098.0
5 TraesCS3B01G199000 chr3D 99.065 107 1 0 13 119 154183883 154183777 4.990000e-45 193.0
6 TraesCS3B01G199000 chr3A 91.886 2502 108 34 136 2582 172967021 172964560 0.000000e+00 3408.0
7 TraesCS3B01G199000 chr3A 92.208 2092 81 37 2859 4883 172964565 172962489 0.000000e+00 2885.0
8 TraesCS3B01G199000 chr3A 100.000 114 0 0 1 114 172967129 172967016 1.380000e-50 211.0
9 TraesCS3B01G199000 chr7A 98.188 276 4 1 2584 2858 250690806 250691081 9.510000e-132 481.0
10 TraesCS3B01G199000 chr6A 97.122 278 8 0 2580 2857 277269244 277268967 2.060000e-128 470.0
11 TraesCS3B01G199000 chr6A 89.041 73 6 2 3013 3084 560032829 560032758 6.730000e-14 89.8
12 TraesCS3B01G199000 chr1B 97.122 278 8 0 2580 2857 537462898 537462621 2.060000e-128 470.0
13 TraesCS3B01G199000 chr1B 97.426 272 7 0 2584 2855 29393000 29393271 9.570000e-127 464.0
14 TraesCS3B01G199000 chr2A 97.426 272 7 0 2584 2855 715824829 715824558 9.570000e-127 464.0
15 TraesCS3B01G199000 chr2A 97.059 272 8 0 2584 2855 634890771 634890500 4.450000e-125 459.0
16 TraesCS3B01G199000 chrUn 97.059 272 8 0 2584 2855 83678630 83678901 4.450000e-125 459.0
17 TraesCS3B01G199000 chr4B 96.085 281 11 0 2577 2857 553345069 553345349 4.450000e-125 459.0
18 TraesCS3B01G199000 chr6D 91.781 73 4 2 3013 3084 415027746 415027675 3.110000e-17 100.0
19 TraesCS3B01G199000 chr6B 90.411 73 5 2 3013 3084 625779386 625779315 1.450000e-15 95.3


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 TraesCS3B01G199000 chr3B 226786232 226791114 4882 False 9018.00 9018 100.00000 1 4883 1 chr3B.!!$F1 4882
1 TraesCS3B01G199000 chr3D 154177634 154183883 6249 True 1687.25 3589 94.41325 13 4883 4 chr3D.!!$R1 4870
2 TraesCS3B01G199000 chr3A 172962489 172967129 4640 True 2168.00 3408 94.69800 1 4883 3 chr3A.!!$R1 4882

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
119 120 3.190953 ACCAGCTCGTTTCTGACTAGTAC 59.809 47.826 0.00 0.00 33.54 2.73 F
1341 2218 0.613260 CGGAGGACCACAAGGATCAA 59.387 55.000 0.00 0.00 38.69 2.57 F
2452 3350 0.808453 CCTTACCGTACGTGCATGGG 60.808 60.000 15.21 4.47 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 2471 0.250295 TTCCTGCCGTTCCTGTCTTG 60.250 55.000 0.0 0.0 0.0 3.02 R
2882 3780 1.532868 CACCTTTGACCAAGAAGCGAG 59.467 52.381 0.0 0.0 33.8 5.03 R
4363 6103 0.108186 CATGCAGAGCTTCCCGTACA 60.108 55.000 0.0 0.0 0.0 2.90 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
119 120 3.190953 ACCAGCTCGTTTCTGACTAGTAC 59.809 47.826 0.00 0.00 33.54 2.73
121 122 4.634883 CCAGCTCGTTTCTGACTAGTACTA 59.365 45.833 1.89 1.89 33.54 1.82
122 123 5.220700 CCAGCTCGTTTCTGACTAGTACTAG 60.221 48.000 25.30 25.30 39.04 2.57
126 127 6.534793 GCTCGTTTCTGACTAGTACTAGTAGT 59.465 42.308 30.80 15.35 45.63 2.73
127 128 7.704472 GCTCGTTTCTGACTAGTACTAGTAGTA 59.296 40.741 30.80 19.99 45.63 1.82
130 946 9.364989 CGTTTCTGACTAGTACTAGTAGTAGTT 57.635 37.037 35.04 24.67 46.61 2.24
291 1114 6.277918 CAAAAGAGAATTGCTCAACAAACC 57.722 37.500 0.00 0.00 46.45 3.27
339 1174 4.217550 GCACAACAAACCCATACACATAGT 59.782 41.667 0.00 0.00 0.00 2.12
340 1175 5.413213 GCACAACAAACCCATACACATAGTA 59.587 40.000 0.00 0.00 37.06 1.82
341 1176 6.403200 GCACAACAAACCCATACACATAGTAG 60.403 42.308 0.00 0.00 35.85 2.57
342 1177 6.653320 CACAACAAACCCATACACATAGTAGT 59.347 38.462 0.00 0.00 35.85 2.73
483 1319 5.694458 CCTGGTAGCAAATGTTGGTTAAAAC 59.306 40.000 0.00 0.00 42.20 2.43
504 1340 5.169992 ACGCTACCCCTAGTAAACATTTT 57.830 39.130 0.00 0.00 0.00 1.82
509 1345 6.262496 GCTACCCCTAGTAAACATTTTCCATC 59.738 42.308 0.00 0.00 0.00 3.51
520 1357 9.134734 GTAAACATTTTCCATCTTGCGAAAATA 57.865 29.630 7.28 0.00 43.45 1.40
533 1370 5.781452 TGCGAAAATATGCGTGTTACTTA 57.219 34.783 0.00 0.00 0.00 2.24
536 1373 7.560700 TGCGAAAATATGCGTGTTACTTATAG 58.439 34.615 0.00 0.00 0.00 1.31
1040 1917 2.522193 CCCTCTCCCCTCGGCTAC 60.522 72.222 0.00 0.00 0.00 3.58
1063 1940 1.178276 GGCGTCTCTCTCTTCTCCAA 58.822 55.000 0.00 0.00 0.00 3.53
1305 2182 1.222936 CATGAAGAAGAGCCGGGCT 59.777 57.895 24.13 24.13 43.88 5.19
1341 2218 0.613260 CGGAGGACCACAAGGATCAA 59.387 55.000 0.00 0.00 38.69 2.57
1399 2276 1.539388 TCACCATTAACGTACGTCCGT 59.461 47.619 23.05 8.99 44.23 4.69
1429 2306 4.655963 TCTTCACCCATTCTTCTTCCTTG 58.344 43.478 0.00 0.00 0.00 3.61
1447 2324 4.280677 TCCTTGTTAAATGGCAAGACTTGG 59.719 41.667 16.80 0.00 43.29 3.61
1455 2332 3.741476 CAAGACTTGGCAGCCGGC 61.741 66.667 21.89 21.89 43.74 6.13
1476 2356 6.017109 CCGGCACTGCTTGTTTTTCTATATAT 60.017 38.462 0.00 0.00 0.00 0.86
1477 2357 7.172532 CCGGCACTGCTTGTTTTTCTATATATA 59.827 37.037 0.00 0.00 0.00 0.86
1478 2358 8.721478 CGGCACTGCTTGTTTTTCTATATATAT 58.279 33.333 0.00 0.00 0.00 0.86
1657 2543 4.590850 TGATCTGTCCATACAATCTCGG 57.409 45.455 0.00 0.00 34.49 4.63
1707 2593 4.489771 GGTGGATCTGGCCGGTGG 62.490 72.222 12.43 0.00 0.00 4.61
1941 2827 5.435820 CCCACGAGGTACTATTCTTACTC 57.564 47.826 0.00 0.00 41.55 2.59
1990 2878 5.705609 TGACTTGGCCAAGAAATTTACTC 57.294 39.130 44.50 29.92 40.79 2.59
2158 3046 4.029186 CGGTCGTCGTCCAACGGA 62.029 66.667 9.20 0.00 42.81 4.69
2353 3244 2.464459 CGAAGCCCCGATTGTGAGC 61.464 63.158 0.00 0.00 0.00 4.26
2363 3254 1.129998 CGATTGTGAGCCTGCTTCTTG 59.870 52.381 0.00 0.00 0.00 3.02
2380 3271 7.365741 TGCTTCTTGTTCTTCTTGATCATTTC 58.634 34.615 0.00 0.00 0.00 2.17
2452 3350 0.808453 CCTTACCGTACGTGCATGGG 60.808 60.000 15.21 4.47 0.00 4.00
2535 3433 4.564116 CCACGCGCCTACTACCGG 62.564 72.222 5.73 0.00 0.00 5.28
2582 3480 2.380084 CGCAAGCAGGTACTCCTAAA 57.620 50.000 0.00 0.00 43.07 1.85
2583 3481 2.271800 CGCAAGCAGGTACTCCTAAAG 58.728 52.381 0.00 0.00 43.07 1.85
2584 3482 2.633488 GCAAGCAGGTACTCCTAAAGG 58.367 52.381 0.00 0.00 43.07 3.11
2585 3483 2.633488 CAAGCAGGTACTCCTAAAGGC 58.367 52.381 0.00 0.00 43.07 4.35
2586 3484 1.952621 AGCAGGTACTCCTAAAGGCA 58.047 50.000 0.00 0.00 43.07 4.75
2587 3485 2.482494 AGCAGGTACTCCTAAAGGCAT 58.518 47.619 0.00 0.00 43.07 4.40
2588 3486 2.171448 AGCAGGTACTCCTAAAGGCATG 59.829 50.000 0.00 0.00 43.07 4.06
2589 3487 2.092914 GCAGGTACTCCTAAAGGCATGT 60.093 50.000 0.00 0.00 43.07 3.21
2590 3488 3.134081 GCAGGTACTCCTAAAGGCATGTA 59.866 47.826 0.00 0.00 43.07 2.29
2591 3489 4.694339 CAGGTACTCCTAAAGGCATGTAC 58.306 47.826 13.51 13.51 43.07 2.90
2592 3490 4.161565 CAGGTACTCCTAAAGGCATGTACA 59.838 45.833 18.93 0.00 43.07 2.90
2593 3491 4.781087 AGGTACTCCTAAAGGCATGTACAA 59.219 41.667 18.93 0.00 43.12 2.41
2594 3492 5.428783 AGGTACTCCTAAAGGCATGTACAAT 59.571 40.000 18.93 10.46 43.12 2.71
2595 3493 5.527582 GGTACTCCTAAAGGCATGTACAATG 59.472 44.000 18.93 0.12 37.58 2.82
2596 3494 4.526970 ACTCCTAAAGGCATGTACAATGG 58.473 43.478 0.00 0.00 34.44 3.16
2597 3495 4.018415 ACTCCTAAAGGCATGTACAATGGT 60.018 41.667 0.00 0.00 34.44 3.55
2598 3496 4.929479 TCCTAAAGGCATGTACAATGGTT 58.071 39.130 0.00 0.00 34.44 3.67
2599 3497 5.329399 TCCTAAAGGCATGTACAATGGTTT 58.671 37.500 0.00 0.93 34.44 3.27
2600 3498 5.777732 TCCTAAAGGCATGTACAATGGTTTT 59.222 36.000 0.00 0.69 34.44 2.43
2601 3499 6.948886 TCCTAAAGGCATGTACAATGGTTTTA 59.051 34.615 0.00 1.82 34.44 1.52
2602 3500 7.617723 TCCTAAAGGCATGTACAATGGTTTTAT 59.382 33.333 0.00 0.00 34.44 1.40
2603 3501 7.920682 CCTAAAGGCATGTACAATGGTTTTATC 59.079 37.037 0.00 0.00 0.00 1.75
2604 3502 7.480760 AAAGGCATGTACAATGGTTTTATCT 57.519 32.000 0.00 0.00 0.00 1.98
2605 3503 7.480760 AAGGCATGTACAATGGTTTTATCTT 57.519 32.000 0.00 0.00 0.00 2.40
2606 3504 8.588290 AAGGCATGTACAATGGTTTTATCTTA 57.412 30.769 0.00 0.00 0.00 2.10
2607 3505 8.225603 AGGCATGTACAATGGTTTTATCTTAG 57.774 34.615 0.00 0.00 0.00 2.18
2608 3506 6.918022 GGCATGTACAATGGTTTTATCTTAGC 59.082 38.462 0.00 0.00 0.00 3.09
2609 3507 7.416213 GGCATGTACAATGGTTTTATCTTAGCA 60.416 37.037 0.00 0.00 0.00 3.49
2610 3508 7.973388 GCATGTACAATGGTTTTATCTTAGCAA 59.027 33.333 0.00 0.00 0.00 3.91
2613 3511 7.973388 TGTACAATGGTTTTATCTTAGCAATGC 59.027 33.333 0.00 0.00 0.00 3.56
2614 3512 6.340522 ACAATGGTTTTATCTTAGCAATGCC 58.659 36.000 0.00 0.00 0.00 4.40
2615 3513 6.070881 ACAATGGTTTTATCTTAGCAATGCCA 60.071 34.615 0.00 0.00 0.00 4.92
2616 3514 6.736110 ATGGTTTTATCTTAGCAATGCCAT 57.264 33.333 0.00 0.00 0.00 4.40
2617 3515 5.904941 TGGTTTTATCTTAGCAATGCCATG 58.095 37.500 0.00 0.00 0.00 3.66
2618 3516 5.421693 TGGTTTTATCTTAGCAATGCCATGT 59.578 36.000 0.00 0.00 0.00 3.21
2619 3517 6.605194 TGGTTTTATCTTAGCAATGCCATGTA 59.395 34.615 0.00 0.00 0.00 2.29
2620 3518 7.141363 GGTTTTATCTTAGCAATGCCATGTAG 58.859 38.462 0.00 0.00 0.00 2.74
2621 3519 6.882610 TTTATCTTAGCAATGCCATGTAGG 57.117 37.500 0.00 0.00 41.84 3.18
2622 3520 4.712051 ATCTTAGCAATGCCATGTAGGA 57.288 40.909 0.00 0.00 41.22 2.94
2623 3521 4.712051 TCTTAGCAATGCCATGTAGGAT 57.288 40.909 0.00 0.00 41.22 3.24
2624 3522 5.823861 TCTTAGCAATGCCATGTAGGATA 57.176 39.130 0.00 0.00 41.22 2.59
2625 3523 5.798132 TCTTAGCAATGCCATGTAGGATAG 58.202 41.667 0.00 0.00 41.22 2.08
2626 3524 5.543790 TCTTAGCAATGCCATGTAGGATAGA 59.456 40.000 0.00 0.00 41.22 1.98
2627 3525 4.923516 AGCAATGCCATGTAGGATAGAT 57.076 40.909 0.00 0.00 41.22 1.98
2628 3526 4.586884 AGCAATGCCATGTAGGATAGATG 58.413 43.478 0.00 0.00 41.60 2.90
2629 3527 4.287845 AGCAATGCCATGTAGGATAGATGA 59.712 41.667 0.00 0.00 44.42 2.92
2630 3528 5.045066 AGCAATGCCATGTAGGATAGATGAT 60.045 40.000 0.00 0.00 44.42 2.45
2631 3529 5.066117 GCAATGCCATGTAGGATAGATGATG 59.934 44.000 0.00 0.00 44.42 3.07
2632 3530 6.412214 CAATGCCATGTAGGATAGATGATGA 58.588 40.000 0.00 0.00 44.42 2.92
2633 3531 5.672421 TGCCATGTAGGATAGATGATGAG 57.328 43.478 0.00 0.00 44.42 2.90
2634 3532 4.468868 TGCCATGTAGGATAGATGATGAGG 59.531 45.833 0.00 0.00 44.42 3.86
2635 3533 4.469227 GCCATGTAGGATAGATGATGAGGT 59.531 45.833 0.00 0.00 44.42 3.85
2636 3534 5.626347 GCCATGTAGGATAGATGATGAGGTG 60.626 48.000 0.00 0.00 44.42 4.00
2637 3535 5.105023 CCATGTAGGATAGATGATGAGGTGG 60.105 48.000 0.00 0.00 44.42 4.61
2638 3536 5.339423 TGTAGGATAGATGATGAGGTGGA 57.661 43.478 0.00 0.00 0.00 4.02
2639 3537 5.328565 TGTAGGATAGATGATGAGGTGGAG 58.671 45.833 0.00 0.00 0.00 3.86
2640 3538 3.788933 AGGATAGATGATGAGGTGGAGG 58.211 50.000 0.00 0.00 0.00 4.30
2641 3539 3.404081 AGGATAGATGATGAGGTGGAGGA 59.596 47.826 0.00 0.00 0.00 3.71
2642 3540 4.140591 AGGATAGATGATGAGGTGGAGGAA 60.141 45.833 0.00 0.00 0.00 3.36
2643 3541 4.594920 GGATAGATGATGAGGTGGAGGAAA 59.405 45.833 0.00 0.00 0.00 3.13
2644 3542 5.279910 GGATAGATGATGAGGTGGAGGAAAG 60.280 48.000 0.00 0.00 0.00 2.62
2645 3543 3.729108 AGATGATGAGGTGGAGGAAAGA 58.271 45.455 0.00 0.00 0.00 2.52
2646 3544 3.710677 AGATGATGAGGTGGAGGAAAGAG 59.289 47.826 0.00 0.00 0.00 2.85
2647 3545 3.190383 TGATGAGGTGGAGGAAAGAGA 57.810 47.619 0.00 0.00 0.00 3.10
2648 3546 3.520696 TGATGAGGTGGAGGAAAGAGAA 58.479 45.455 0.00 0.00 0.00 2.87
2649 3547 3.261897 TGATGAGGTGGAGGAAAGAGAAC 59.738 47.826 0.00 0.00 0.00 3.01
2650 3548 2.977808 TGAGGTGGAGGAAAGAGAACT 58.022 47.619 0.00 0.00 0.00 3.01
2651 3549 2.900546 TGAGGTGGAGGAAAGAGAACTC 59.099 50.000 0.00 0.00 0.00 3.01
2652 3550 2.900546 GAGGTGGAGGAAAGAGAACTCA 59.099 50.000 4.64 0.00 32.98 3.41
2653 3551 3.517500 GAGGTGGAGGAAAGAGAACTCAT 59.482 47.826 4.64 0.00 32.98 2.90
2654 3552 4.689062 AGGTGGAGGAAAGAGAACTCATA 58.311 43.478 4.64 0.00 32.98 2.15
2655 3553 5.094387 AGGTGGAGGAAAGAGAACTCATAA 58.906 41.667 4.64 0.00 32.98 1.90
2656 3554 5.188751 AGGTGGAGGAAAGAGAACTCATAAG 59.811 44.000 4.64 0.00 32.98 1.73
2657 3555 5.187967 GGTGGAGGAAAGAGAACTCATAAGA 59.812 44.000 4.64 0.00 32.98 2.10
2658 3556 6.295916 GGTGGAGGAAAGAGAACTCATAAGAA 60.296 42.308 4.64 0.00 32.98 2.52
2659 3557 7.334858 GTGGAGGAAAGAGAACTCATAAGAAT 58.665 38.462 4.64 0.00 32.98 2.40
2660 3558 8.478877 GTGGAGGAAAGAGAACTCATAAGAATA 58.521 37.037 4.64 0.00 32.98 1.75
2661 3559 8.700051 TGGAGGAAAGAGAACTCATAAGAATAG 58.300 37.037 4.64 0.00 32.98 1.73
2662 3560 8.919145 GGAGGAAAGAGAACTCATAAGAATAGA 58.081 37.037 4.64 0.00 32.98 1.98
2663 3561 9.744468 GAGGAAAGAGAACTCATAAGAATAGAC 57.256 37.037 4.64 0.00 0.00 2.59
2664 3562 9.487442 AGGAAAGAGAACTCATAAGAATAGACT 57.513 33.333 4.64 0.00 0.00 3.24
2669 3567 9.474313 AGAGAACTCATAAGAATAGACTTGTCT 57.526 33.333 8.41 8.41 0.00 3.41
2674 3572 9.474313 ACTCATAAGAATAGACTTGTCTTCTCT 57.526 33.333 8.66 8.19 33.70 3.10
2698 3596 9.090103 TCTTATTTAAGAGAAGACAAGAGGTGA 57.910 33.333 0.00 0.00 37.40 4.02
2699 3597 9.883142 CTTATTTAAGAGAAGACAAGAGGTGAT 57.117 33.333 0.00 0.00 35.33 3.06
2700 3598 9.877178 TTATTTAAGAGAAGACAAGAGGTGATC 57.123 33.333 0.00 0.00 0.00 2.92
2701 3599 7.546250 TTTAAGAGAAGACAAGAGGTGATCT 57.454 36.000 0.00 0.00 41.27 2.75
2702 3600 5.659440 AAGAGAAGACAAGAGGTGATCTC 57.341 43.478 0.00 0.00 37.23 2.75
2716 3614 6.491714 AGGTGATCTCTTAGCACAATATGT 57.508 37.500 0.00 0.00 46.59 2.29
2717 3615 6.520272 AGGTGATCTCTTAGCACAATATGTC 58.480 40.000 0.00 0.00 46.59 3.06
2718 3616 6.326064 AGGTGATCTCTTAGCACAATATGTCT 59.674 38.462 0.00 0.00 46.59 3.41
2719 3617 6.644592 GGTGATCTCTTAGCACAATATGTCTC 59.355 42.308 0.00 0.00 46.59 3.36
2720 3618 7.205992 GTGATCTCTTAGCACAATATGTCTCA 58.794 38.462 0.00 0.00 44.13 3.27
2721 3619 7.168972 GTGATCTCTTAGCACAATATGTCTCAC 59.831 40.741 0.00 0.00 44.13 3.51
2722 3620 5.907207 TCTCTTAGCACAATATGTCTCACC 58.093 41.667 0.00 0.00 0.00 4.02
2723 3621 5.422012 TCTCTTAGCACAATATGTCTCACCA 59.578 40.000 0.00 0.00 0.00 4.17
2724 3622 5.419542 TCTTAGCACAATATGTCTCACCAC 58.580 41.667 0.00 0.00 0.00 4.16
2725 3623 3.701205 AGCACAATATGTCTCACCACA 57.299 42.857 0.00 0.00 0.00 4.17
2726 3624 4.019792 AGCACAATATGTCTCACCACAA 57.980 40.909 0.00 0.00 0.00 3.33
2727 3625 4.592942 AGCACAATATGTCTCACCACAAT 58.407 39.130 0.00 0.00 0.00 2.71
2728 3626 5.012239 AGCACAATATGTCTCACCACAATT 58.988 37.500 0.00 0.00 0.00 2.32
2729 3627 5.477984 AGCACAATATGTCTCACCACAATTT 59.522 36.000 0.00 0.00 0.00 1.82
2730 3628 6.015180 AGCACAATATGTCTCACCACAATTTT 60.015 34.615 0.00 0.00 0.00 1.82
2731 3629 7.176515 AGCACAATATGTCTCACCACAATTTTA 59.823 33.333 0.00 0.00 0.00 1.52
2732 3630 7.485913 GCACAATATGTCTCACCACAATTTTAG 59.514 37.037 0.00 0.00 0.00 1.85
2733 3631 7.970061 CACAATATGTCTCACCACAATTTTAGG 59.030 37.037 0.00 0.00 0.00 2.69
2734 3632 7.888021 ACAATATGTCTCACCACAATTTTAGGA 59.112 33.333 0.00 0.00 0.00 2.94
2735 3633 8.739039 CAATATGTCTCACCACAATTTTAGGAA 58.261 33.333 0.00 0.00 0.00 3.36
2736 3634 9.479549 AATATGTCTCACCACAATTTTAGGAAT 57.520 29.630 0.00 0.00 0.00 3.01
2737 3635 7.781324 ATGTCTCACCACAATTTTAGGAATT 57.219 32.000 0.00 0.00 0.00 2.17
2738 3636 8.877864 ATGTCTCACCACAATTTTAGGAATTA 57.122 30.769 0.00 0.00 0.00 1.40
2739 3637 8.106247 TGTCTCACCACAATTTTAGGAATTAC 57.894 34.615 0.00 0.00 0.00 1.89
2740 3638 7.942341 TGTCTCACCACAATTTTAGGAATTACT 59.058 33.333 0.00 0.00 0.00 2.24
2741 3639 9.444600 GTCTCACCACAATTTTAGGAATTACTA 57.555 33.333 0.00 0.00 0.00 1.82
2742 3640 9.667107 TCTCACCACAATTTTAGGAATTACTAG 57.333 33.333 0.00 0.00 0.00 2.57
2743 3641 9.449719 CTCACCACAATTTTAGGAATTACTAGT 57.550 33.333 0.00 0.00 0.00 2.57
2744 3642 9.802039 TCACCACAATTTTAGGAATTACTAGTT 57.198 29.630 0.00 0.00 0.00 2.24
2771 3669 7.246171 TGAAGATAAGGCTAAGATATGACCC 57.754 40.000 0.00 0.00 0.00 4.46
2772 3670 6.787458 TGAAGATAAGGCTAAGATATGACCCA 59.213 38.462 0.00 0.00 0.00 4.51
2773 3671 7.459125 TGAAGATAAGGCTAAGATATGACCCAT 59.541 37.037 0.00 0.00 0.00 4.00
2774 3672 7.821134 AGATAAGGCTAAGATATGACCCATT 57.179 36.000 0.00 0.00 0.00 3.16
2775 3673 7.628234 AGATAAGGCTAAGATATGACCCATTG 58.372 38.462 0.00 0.00 0.00 2.82
2776 3674 5.653255 AAGGCTAAGATATGACCCATTGT 57.347 39.130 0.00 0.00 0.00 2.71
2777 3675 6.763715 AAGGCTAAGATATGACCCATTGTA 57.236 37.500 0.00 0.00 0.00 2.41
2778 3676 6.365970 AGGCTAAGATATGACCCATTGTAG 57.634 41.667 0.00 0.00 0.00 2.74
2779 3677 6.084738 AGGCTAAGATATGACCCATTGTAGA 58.915 40.000 0.00 0.00 0.00 2.59
2780 3678 6.014156 AGGCTAAGATATGACCCATTGTAGAC 60.014 42.308 0.00 0.00 0.00 2.59
2781 3679 6.239600 GGCTAAGATATGACCCATTGTAGACA 60.240 42.308 0.00 0.00 0.00 3.41
2782 3680 7.217200 GCTAAGATATGACCCATTGTAGACAA 58.783 38.462 0.00 0.00 40.51 3.18
2783 3681 7.715249 GCTAAGATATGACCCATTGTAGACAAA 59.285 37.037 0.00 0.00 39.55 2.83
2784 3682 9.613428 CTAAGATATGACCCATTGTAGACAAAA 57.387 33.333 0.00 0.00 39.55 2.44
2785 3683 8.877864 AAGATATGACCCATTGTAGACAAAAA 57.122 30.769 0.00 0.00 39.55 1.94
2810 3708 9.807649 AAAATTTACCATCTCTAAATCACATGC 57.192 29.630 0.00 0.00 0.00 4.06
2811 3709 8.523915 AATTTACCATCTCTAAATCACATGCA 57.476 30.769 0.00 0.00 0.00 3.96
2812 3710 7.936496 TTTACCATCTCTAAATCACATGCAA 57.064 32.000 0.00 0.00 0.00 4.08
2813 3711 7.558161 TTACCATCTCTAAATCACATGCAAG 57.442 36.000 0.00 0.00 0.00 4.01
2814 3712 5.748402 ACCATCTCTAAATCACATGCAAGA 58.252 37.500 0.00 0.00 0.00 3.02
2815 3713 5.587844 ACCATCTCTAAATCACATGCAAGAC 59.412 40.000 0.00 0.00 0.00 3.01
2816 3714 5.821470 CCATCTCTAAATCACATGCAAGACT 59.179 40.000 0.00 0.00 0.00 3.24
2817 3715 6.318144 CCATCTCTAAATCACATGCAAGACTT 59.682 38.462 0.00 0.00 0.00 3.01
2818 3716 7.496920 CCATCTCTAAATCACATGCAAGACTTA 59.503 37.037 0.00 0.00 0.00 2.24
2819 3717 8.886719 CATCTCTAAATCACATGCAAGACTTAA 58.113 33.333 0.00 0.00 0.00 1.85
2820 3718 8.846943 TCTCTAAATCACATGCAAGACTTAAA 57.153 30.769 0.00 0.00 0.00 1.52
2821 3719 9.283768 TCTCTAAATCACATGCAAGACTTAAAA 57.716 29.630 0.00 0.00 0.00 1.52
2827 3725 9.846248 AATCACATGCAAGACTTAAAATAAGAC 57.154 29.630 0.00 0.00 0.00 3.01
2828 3726 8.621532 TCACATGCAAGACTTAAAATAAGACT 57.378 30.769 0.00 0.83 0.00 3.24
2829 3727 9.719355 TCACATGCAAGACTTAAAATAAGACTA 57.281 29.630 0.00 0.00 0.00 2.59
2850 3748 9.770097 AGACTATCTTATCAACCATTGTACATG 57.230 33.333 0.00 0.00 0.00 3.21
2851 3749 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
2852 3750 6.639632 ATCTTATCAACCATTGTACATGCC 57.360 37.500 0.00 0.00 0.00 4.40
2853 3751 4.887071 TCTTATCAACCATTGTACATGCCC 59.113 41.667 0.00 0.00 0.00 5.36
2854 3752 2.897271 TCAACCATTGTACATGCCCT 57.103 45.000 0.00 0.00 0.00 5.19
2855 3753 4.518278 ATCAACCATTGTACATGCCCTA 57.482 40.909 0.00 0.00 0.00 3.53
2856 3754 4.308526 TCAACCATTGTACATGCCCTAA 57.691 40.909 0.00 0.00 0.00 2.69
2857 3755 4.269183 TCAACCATTGTACATGCCCTAAG 58.731 43.478 0.00 0.00 0.00 2.18
2870 3768 6.200114 ACATGCCCTAAGTCCTAACTAACTA 58.800 40.000 0.00 0.00 33.48 2.24
3482 4380 4.340246 CTGCCAGGCCAGCTGTCA 62.340 66.667 13.81 0.00 0.00 3.58
3611 4509 0.934436 GCAACGCGAACAACAGCAAT 60.934 50.000 15.93 0.00 0.00 3.56
3614 4512 3.233578 CAACGCGAACAACAGCAATAAT 58.766 40.909 15.93 0.00 0.00 1.28
3683 4581 0.178068 ACAACACCAACAGCGAGACT 59.822 50.000 0.00 0.00 0.00 3.24
3695 4593 0.737715 GCGAGACTCAATGAACGGCT 60.738 55.000 2.82 0.00 0.00 5.52
3697 4595 1.656095 CGAGACTCAATGAACGGCTTC 59.344 52.381 2.82 0.00 0.00 3.86
3722 4621 5.050490 TCAAGTTCGGAAAGAGTTGAGAAG 58.950 41.667 0.00 0.00 32.20 2.85
3989 5716 5.939764 AATAATGGCGCCTCAGAGATATA 57.060 39.130 29.70 2.45 0.00 0.86
4033 5761 4.832823 AGAAATGTGGGGGTAAAGAACAAG 59.167 41.667 0.00 0.00 0.00 3.16
4040 5768 2.160205 GGGTAAAGAACAAGGACAGCC 58.840 52.381 0.00 0.00 0.00 4.85
4078 5806 4.273005 ACGTGTTTGTTCACATCTTGAC 57.727 40.909 0.00 0.00 38.12 3.18
4106 5834 2.127528 ACCCCCTCTCCCCTTTCC 59.872 66.667 0.00 0.00 0.00 3.13
4155 5885 4.082571 CCTTCTTCTCGTTGGCATTTTCAT 60.083 41.667 0.00 0.00 0.00 2.57
4291 6022 3.081804 GTCAGTTCGTCCCCATTTGAAT 58.918 45.455 0.00 0.00 0.00 2.57
4305 6041 6.441274 CCCATTTGAATAGTACATCACATGC 58.559 40.000 13.00 0.00 34.13 4.06
4308 6044 7.646526 CCATTTGAATAGTACATCACATGCTTG 59.353 37.037 13.00 0.00 34.13 4.01
4318 6054 0.245266 CACATGCTTGATGCCTGCAA 59.755 50.000 6.60 0.00 40.29 4.08
4373 6113 6.007936 TGAAATTTGAACATGTACGGGAAG 57.992 37.500 0.00 0.00 0.00 3.46
4374 6114 4.434713 AATTTGAACATGTACGGGAAGC 57.565 40.909 0.00 0.00 0.00 3.86
4375 6115 2.851263 TTGAACATGTACGGGAAGCT 57.149 45.000 0.00 0.00 0.00 3.74
4376 6116 2.380084 TGAACATGTACGGGAAGCTC 57.620 50.000 0.00 0.00 0.00 4.09
4409 6181 0.172352 CTCCAAGGACTCGCAGTCTC 59.828 60.000 13.59 6.51 44.46 3.36
4525 6311 2.569354 GCACGGGGAAAATGTGGCA 61.569 57.895 0.00 0.00 34.24 4.92
4527 6313 1.906333 ACGGGGAAAATGTGGCACC 60.906 57.895 16.26 0.00 0.00 5.01
4645 6437 1.531739 GAGGCATGGGGCGTTTTCAA 61.532 55.000 0.00 0.00 46.16 2.69
4670 6463 4.047059 CCGCGGCGGTATCGGTAT 62.047 66.667 32.14 0.00 42.73 2.73
4861 6654 1.735198 CGCTTGCGGTCGGACTTTA 60.735 57.895 8.23 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 7.828717 GGTCAGGTCTAGACTAAAACTACTACT 59.171 40.741 21.88 3.68 36.29 2.57
122 123 7.828717 AGGTCAGGTCTAGACTAAAACTACTAC 59.171 40.741 21.88 9.01 36.29 2.73
126 127 5.418209 GCAGGTCAGGTCTAGACTAAAACTA 59.582 44.000 21.88 0.00 36.29 2.24
127 128 4.221041 GCAGGTCAGGTCTAGACTAAAACT 59.779 45.833 21.88 12.21 36.29 2.66
130 946 4.017808 GAGCAGGTCAGGTCTAGACTAAA 58.982 47.826 21.88 5.31 36.29 1.85
136 952 0.681564 ACGGAGCAGGTCAGGTCTAG 60.682 60.000 4.72 0.00 36.33 2.43
291 1114 3.872459 ATATGGGGCCTCTTCTCTTTG 57.128 47.619 3.07 0.00 0.00 2.77
363 1198 3.452755 TCGATGACTCGCCATTTGTAT 57.547 42.857 0.00 0.00 44.65 2.29
449 1285 2.735772 GCTACCAGGCCAGCTGCTA 61.736 63.158 8.66 0.00 40.92 3.49
483 1319 4.573607 GGAAAATGTTTACTAGGGGTAGCG 59.426 45.833 0.00 0.00 0.00 4.26
509 1345 4.647964 AGTAACACGCATATTTTCGCAAG 58.352 39.130 0.00 0.00 0.00 4.01
520 1357 3.552273 CGGCTCCTATAAGTAACACGCAT 60.552 47.826 0.00 0.00 0.00 4.73
657 1515 2.559922 AATTTATGGGCGGGGCGACA 62.560 55.000 0.00 0.00 36.10 4.35
1040 1917 1.134175 GAGAAGAGAGAGACGCCTTGG 59.866 57.143 0.00 0.00 0.00 3.61
1063 1940 0.835941 ATGCAAATCGAGAGCCTCCT 59.164 50.000 0.00 0.00 0.00 3.69
1104 1981 4.465446 CCTCCTCCTCCTCCGCCA 62.465 72.222 0.00 0.00 0.00 5.69
1191 2068 2.134287 GTCCGCCTCCATGCTCCTA 61.134 63.158 0.00 0.00 0.00 2.94
1399 2276 0.400213 AATGGGTGAAGAAGCGGTGA 59.600 50.000 0.00 0.00 0.00 4.02
1429 2306 3.578688 CTGCCAAGTCTTGCCATTTAAC 58.421 45.455 7.09 0.00 0.00 2.01
1452 2329 3.559238 ATAGAAAAACAAGCAGTGCCG 57.441 42.857 12.58 5.99 0.00 5.69
1478 2358 8.830580 GGTAAGTATTAGATCGCCGTACATATA 58.169 37.037 0.00 0.00 0.00 0.86
1479 2359 7.555554 AGGTAAGTATTAGATCGCCGTACATAT 59.444 37.037 0.00 0.00 0.00 1.78
1480 2360 6.881065 AGGTAAGTATTAGATCGCCGTACATA 59.119 38.462 0.00 0.00 0.00 2.29
1481 2361 5.709164 AGGTAAGTATTAGATCGCCGTACAT 59.291 40.000 0.00 0.00 0.00 2.29
1482 2362 5.065914 AGGTAAGTATTAGATCGCCGTACA 58.934 41.667 0.00 0.00 0.00 2.90
1483 2363 5.619625 AGGTAAGTATTAGATCGCCGTAC 57.380 43.478 0.00 0.00 0.00 3.67
1591 2471 0.250295 TTCCTGCCGTTCCTGTCTTG 60.250 55.000 0.00 0.00 0.00 3.02
1593 2473 1.371558 GTTCCTGCCGTTCCTGTCT 59.628 57.895 0.00 0.00 0.00 3.41
1657 2543 1.838943 GACAACGCTAATCGACGAGAC 59.161 52.381 3.01 0.00 41.67 3.36
1707 2593 5.803967 AGTTAATACCGATCGAGTCAAACAC 59.196 40.000 18.66 3.59 0.00 3.32
1760 2646 2.021068 GCTCAGCTCGGCCTGTATCA 62.021 60.000 0.00 0.00 34.47 2.15
1941 2827 4.083565 GTGATCCCTAGCTAGGTTAGAGG 58.916 52.174 33.00 19.33 42.03 3.69
1990 2878 7.713764 AAAACGGAAAAAGAGGAATTGATTG 57.286 32.000 0.00 0.00 0.00 2.67
2107 2995 1.213013 CTCCGTGGACGAGTTGGAG 59.787 63.158 0.00 0.00 43.02 3.86
2158 3046 2.657237 CGCTCAGGGTCCTCGTTT 59.343 61.111 0.00 0.00 0.00 3.60
2266 3157 3.842925 TTGCTGGTCGTGGCCCTTC 62.843 63.158 0.00 0.00 0.00 3.46
2329 3220 3.165160 AATCGGGGCTTCGGATCGG 62.165 63.158 0.00 0.00 34.84 4.18
2353 3244 4.758674 TGATCAAGAAGAACAAGAAGCAGG 59.241 41.667 0.00 0.00 0.00 4.85
2406 3297 4.504461 GCACGATTCATACACAAGGACTAG 59.496 45.833 0.00 0.00 0.00 2.57
2576 3474 4.584638 ACCATTGTACATGCCTTTAGGA 57.415 40.909 0.00 0.00 37.39 2.94
2577 3475 5.659440 AAACCATTGTACATGCCTTTAGG 57.341 39.130 0.00 0.00 38.53 2.69
2578 3476 8.686334 AGATAAAACCATTGTACATGCCTTTAG 58.314 33.333 0.00 0.00 0.00 1.85
2579 3477 8.588290 AGATAAAACCATTGTACATGCCTTTA 57.412 30.769 0.00 4.96 0.00 1.85
2580 3478 7.480760 AGATAAAACCATTGTACATGCCTTT 57.519 32.000 0.00 3.15 0.00 3.11
2581 3479 7.480760 AAGATAAAACCATTGTACATGCCTT 57.519 32.000 0.00 0.00 0.00 4.35
2582 3480 7.201821 GCTAAGATAAAACCATTGTACATGCCT 60.202 37.037 0.00 0.00 0.00 4.75
2583 3481 6.918022 GCTAAGATAAAACCATTGTACATGCC 59.082 38.462 0.00 0.00 0.00 4.40
2584 3482 7.479980 TGCTAAGATAAAACCATTGTACATGC 58.520 34.615 0.00 0.00 0.00 4.06
2587 3485 7.973388 GCATTGCTAAGATAAAACCATTGTACA 59.027 33.333 0.16 0.00 0.00 2.90
2588 3486 7.435192 GGCATTGCTAAGATAAAACCATTGTAC 59.565 37.037 8.82 0.00 0.00 2.90
2589 3487 7.123397 TGGCATTGCTAAGATAAAACCATTGTA 59.877 33.333 8.82 0.00 0.00 2.41
2590 3488 6.070881 TGGCATTGCTAAGATAAAACCATTGT 60.071 34.615 8.82 0.00 0.00 2.71
2591 3489 6.339730 TGGCATTGCTAAGATAAAACCATTG 58.660 36.000 8.82 0.00 0.00 2.82
2592 3490 6.543430 TGGCATTGCTAAGATAAAACCATT 57.457 33.333 8.82 0.00 0.00 3.16
2593 3491 6.098695 ACATGGCATTGCTAAGATAAAACCAT 59.901 34.615 8.82 0.00 34.60 3.55
2594 3492 5.421693 ACATGGCATTGCTAAGATAAAACCA 59.578 36.000 8.82 0.00 0.00 3.67
2595 3493 5.906073 ACATGGCATTGCTAAGATAAAACC 58.094 37.500 8.82 0.00 0.00 3.27
2596 3494 7.013274 TCCTACATGGCATTGCTAAGATAAAAC 59.987 37.037 8.82 0.00 35.26 2.43
2597 3495 7.059788 TCCTACATGGCATTGCTAAGATAAAA 58.940 34.615 8.82 0.00 35.26 1.52
2598 3496 6.600388 TCCTACATGGCATTGCTAAGATAAA 58.400 36.000 8.82 0.00 35.26 1.40
2599 3497 6.186420 TCCTACATGGCATTGCTAAGATAA 57.814 37.500 8.82 0.00 35.26 1.75
2600 3498 5.823861 TCCTACATGGCATTGCTAAGATA 57.176 39.130 8.82 0.00 35.26 1.98
2601 3499 4.712051 TCCTACATGGCATTGCTAAGAT 57.288 40.909 8.82 0.00 35.26 2.40
2602 3500 4.712051 ATCCTACATGGCATTGCTAAGA 57.288 40.909 8.82 0.00 35.26 2.10
2603 3501 5.798132 TCTATCCTACATGGCATTGCTAAG 58.202 41.667 8.82 1.77 35.26 2.18
2604 3502 5.823861 TCTATCCTACATGGCATTGCTAA 57.176 39.130 8.82 0.00 35.26 3.09
2605 3503 5.484998 TCATCTATCCTACATGGCATTGCTA 59.515 40.000 8.82 2.16 35.26 3.49
2606 3504 4.287845 TCATCTATCCTACATGGCATTGCT 59.712 41.667 8.82 0.00 35.26 3.91
2607 3505 4.582869 TCATCTATCCTACATGGCATTGC 58.417 43.478 0.00 0.00 35.26 3.56
2608 3506 6.412214 TCATCATCTATCCTACATGGCATTG 58.588 40.000 0.00 0.00 35.26 2.82
2609 3507 6.352823 CCTCATCATCTATCCTACATGGCATT 60.353 42.308 0.00 0.00 35.26 3.56
2610 3508 5.130643 CCTCATCATCTATCCTACATGGCAT 59.869 44.000 0.00 0.00 35.26 4.40
2611 3509 4.468868 CCTCATCATCTATCCTACATGGCA 59.531 45.833 0.00 0.00 35.26 4.92
2612 3510 4.469227 ACCTCATCATCTATCCTACATGGC 59.531 45.833 0.00 0.00 35.26 4.40
2613 3511 5.105023 CCACCTCATCATCTATCCTACATGG 60.105 48.000 0.00 0.00 37.10 3.66
2614 3512 5.718607 TCCACCTCATCATCTATCCTACATG 59.281 44.000 0.00 0.00 0.00 3.21
2615 3513 5.908590 TCCACCTCATCATCTATCCTACAT 58.091 41.667 0.00 0.00 0.00 2.29
2616 3514 5.328565 CTCCACCTCATCATCTATCCTACA 58.671 45.833 0.00 0.00 0.00 2.74
2617 3515 4.709397 CCTCCACCTCATCATCTATCCTAC 59.291 50.000 0.00 0.00 0.00 3.18
2618 3516 4.608028 TCCTCCACCTCATCATCTATCCTA 59.392 45.833 0.00 0.00 0.00 2.94
2619 3517 3.404081 TCCTCCACCTCATCATCTATCCT 59.596 47.826 0.00 0.00 0.00 3.24
2620 3518 3.784178 TCCTCCACCTCATCATCTATCC 58.216 50.000 0.00 0.00 0.00 2.59
2621 3519 5.541868 TCTTTCCTCCACCTCATCATCTATC 59.458 44.000 0.00 0.00 0.00 2.08
2622 3520 5.471424 TCTTTCCTCCACCTCATCATCTAT 58.529 41.667 0.00 0.00 0.00 1.98
2623 3521 4.883759 TCTTTCCTCCACCTCATCATCTA 58.116 43.478 0.00 0.00 0.00 1.98
2624 3522 3.710677 CTCTTTCCTCCACCTCATCATCT 59.289 47.826 0.00 0.00 0.00 2.90
2625 3523 3.708631 TCTCTTTCCTCCACCTCATCATC 59.291 47.826 0.00 0.00 0.00 2.92
2626 3524 3.729108 TCTCTTTCCTCCACCTCATCAT 58.271 45.455 0.00 0.00 0.00 2.45
2627 3525 3.190383 TCTCTTTCCTCCACCTCATCA 57.810 47.619 0.00 0.00 0.00 3.07
2628 3526 3.517500 AGTTCTCTTTCCTCCACCTCATC 59.482 47.826 0.00 0.00 0.00 2.92
2629 3527 3.517500 GAGTTCTCTTTCCTCCACCTCAT 59.482 47.826 0.00 0.00 0.00 2.90
2630 3528 2.900546 GAGTTCTCTTTCCTCCACCTCA 59.099 50.000 0.00 0.00 0.00 3.86
2631 3529 2.900546 TGAGTTCTCTTTCCTCCACCTC 59.099 50.000 1.53 0.00 0.00 3.85
2632 3530 2.977808 TGAGTTCTCTTTCCTCCACCT 58.022 47.619 1.53 0.00 0.00 4.00
2633 3531 3.990959 ATGAGTTCTCTTTCCTCCACC 57.009 47.619 1.53 0.00 0.00 4.61
2634 3532 6.287589 TCTTATGAGTTCTCTTTCCTCCAC 57.712 41.667 1.53 0.00 0.00 4.02
2635 3533 6.935240 TTCTTATGAGTTCTCTTTCCTCCA 57.065 37.500 1.53 0.00 0.00 3.86
2636 3534 8.919145 TCTATTCTTATGAGTTCTCTTTCCTCC 58.081 37.037 1.53 0.00 0.00 4.30
2637 3535 9.744468 GTCTATTCTTATGAGTTCTCTTTCCTC 57.256 37.037 1.53 0.00 0.00 3.71
2638 3536 9.487442 AGTCTATTCTTATGAGTTCTCTTTCCT 57.513 33.333 1.53 0.00 0.00 3.36
2643 3541 9.474313 AGACAAGTCTATTCTTATGAGTTCTCT 57.526 33.333 0.00 0.00 38.35 3.10
2648 3546 9.474313 AGAGAAGACAAGTCTATTCTTATGAGT 57.526 33.333 2.72 0.00 39.39 3.41
2672 3570 9.090103 TCACCTCTTGTCTTCTCTTAAATAAGA 57.910 33.333 3.08 3.08 39.82 2.10
2673 3571 9.883142 ATCACCTCTTGTCTTCTCTTAAATAAG 57.117 33.333 0.00 0.00 34.65 1.73
2674 3572 9.877178 GATCACCTCTTGTCTTCTCTTAAATAA 57.123 33.333 0.00 0.00 0.00 1.40
2675 3573 9.261035 AGATCACCTCTTGTCTTCTCTTAAATA 57.739 33.333 0.00 0.00 0.00 1.40
2676 3574 8.144862 AGATCACCTCTTGTCTTCTCTTAAAT 57.855 34.615 0.00 0.00 0.00 1.40
2677 3575 7.546250 AGATCACCTCTTGTCTTCTCTTAAA 57.454 36.000 0.00 0.00 0.00 1.52
2678 3576 7.164230 GAGATCACCTCTTGTCTTCTCTTAA 57.836 40.000 0.00 0.00 38.86 1.85
2679 3577 6.767524 GAGATCACCTCTTGTCTTCTCTTA 57.232 41.667 0.00 0.00 38.86 2.10
2680 3578 5.659440 GAGATCACCTCTTGTCTTCTCTT 57.341 43.478 0.00 0.00 38.86 2.85
2692 3590 6.520272 ACATATTGTGCTAAGAGATCACCTC 58.480 40.000 0.00 0.00 42.28 3.85
2693 3591 6.326064 AGACATATTGTGCTAAGAGATCACCT 59.674 38.462 0.00 0.00 0.00 4.00
2694 3592 6.520272 AGACATATTGTGCTAAGAGATCACC 58.480 40.000 0.00 0.00 0.00 4.02
2695 3593 7.168972 GTGAGACATATTGTGCTAAGAGATCAC 59.831 40.741 0.00 0.00 0.00 3.06
2696 3594 7.205992 GTGAGACATATTGTGCTAAGAGATCA 58.794 38.462 0.00 0.00 0.00 2.92
2697 3595 6.644592 GGTGAGACATATTGTGCTAAGAGATC 59.355 42.308 0.00 0.00 0.00 2.75
2698 3596 6.098838 TGGTGAGACATATTGTGCTAAGAGAT 59.901 38.462 0.00 0.00 0.00 2.75
2699 3597 5.422012 TGGTGAGACATATTGTGCTAAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
2700 3598 5.521735 GTGGTGAGACATATTGTGCTAAGAG 59.478 44.000 0.00 0.00 0.00 2.85
2701 3599 5.046663 TGTGGTGAGACATATTGTGCTAAGA 60.047 40.000 0.00 0.00 0.00 2.10
2702 3600 5.178061 TGTGGTGAGACATATTGTGCTAAG 58.822 41.667 0.00 0.00 0.00 2.18
2703 3601 5.159273 TGTGGTGAGACATATTGTGCTAA 57.841 39.130 0.00 0.00 0.00 3.09
2704 3602 4.817318 TGTGGTGAGACATATTGTGCTA 57.183 40.909 0.00 0.00 0.00 3.49
2705 3603 3.701205 TGTGGTGAGACATATTGTGCT 57.299 42.857 0.00 0.00 0.00 4.40
2706 3604 4.970662 ATTGTGGTGAGACATATTGTGC 57.029 40.909 0.00 0.00 0.00 4.57
2707 3605 7.970061 CCTAAAATTGTGGTGAGACATATTGTG 59.030 37.037 0.00 0.00 0.00 3.33
2708 3606 7.888021 TCCTAAAATTGTGGTGAGACATATTGT 59.112 33.333 0.00 0.00 0.00 2.71
2709 3607 8.279970 TCCTAAAATTGTGGTGAGACATATTG 57.720 34.615 0.00 0.00 0.00 1.90
2710 3608 8.877864 TTCCTAAAATTGTGGTGAGACATATT 57.122 30.769 0.00 0.00 0.00 1.28
2711 3609 9.479549 AATTCCTAAAATTGTGGTGAGACATAT 57.520 29.630 0.00 0.00 0.00 1.78
2712 3610 8.877864 AATTCCTAAAATTGTGGTGAGACATA 57.122 30.769 0.00 0.00 0.00 2.29
2713 3611 7.781324 AATTCCTAAAATTGTGGTGAGACAT 57.219 32.000 0.00 0.00 0.00 3.06
2714 3612 7.942341 AGTAATTCCTAAAATTGTGGTGAGACA 59.058 33.333 0.00 0.00 0.00 3.41
2715 3613 8.336801 AGTAATTCCTAAAATTGTGGTGAGAC 57.663 34.615 0.00 0.00 0.00 3.36
2716 3614 9.667107 CTAGTAATTCCTAAAATTGTGGTGAGA 57.333 33.333 0.00 0.00 0.00 3.27
2717 3615 9.449719 ACTAGTAATTCCTAAAATTGTGGTGAG 57.550 33.333 0.00 0.00 0.00 3.51
2718 3616 9.802039 AACTAGTAATTCCTAAAATTGTGGTGA 57.198 29.630 0.00 0.00 0.00 4.02
2745 3643 8.325046 GGGTCATATCTTAGCCTTATCTTCAAT 58.675 37.037 0.00 0.00 0.00 2.57
2746 3644 7.292356 TGGGTCATATCTTAGCCTTATCTTCAA 59.708 37.037 0.00 0.00 34.30 2.69
2747 3645 6.787458 TGGGTCATATCTTAGCCTTATCTTCA 59.213 38.462 0.00 0.00 34.30 3.02
2748 3646 7.246171 TGGGTCATATCTTAGCCTTATCTTC 57.754 40.000 0.00 0.00 34.30 2.87
2749 3647 7.821134 ATGGGTCATATCTTAGCCTTATCTT 57.179 36.000 0.00 0.00 34.30 2.40
2750 3648 7.238514 ACAATGGGTCATATCTTAGCCTTATCT 59.761 37.037 0.00 0.00 34.30 1.98
2751 3649 7.398024 ACAATGGGTCATATCTTAGCCTTATC 58.602 38.462 0.00 0.00 34.30 1.75
2752 3650 7.335127 ACAATGGGTCATATCTTAGCCTTAT 57.665 36.000 0.00 0.00 34.30 1.73
2753 3651 6.763715 ACAATGGGTCATATCTTAGCCTTA 57.236 37.500 0.00 0.00 34.30 2.69
2754 3652 5.653255 ACAATGGGTCATATCTTAGCCTT 57.347 39.130 0.00 0.00 34.30 4.35
2755 3653 6.014156 GTCTACAATGGGTCATATCTTAGCCT 60.014 42.308 0.00 0.00 34.30 4.58
2756 3654 6.166982 GTCTACAATGGGTCATATCTTAGCC 58.833 44.000 0.00 0.00 0.00 3.93
2757 3655 6.759272 TGTCTACAATGGGTCATATCTTAGC 58.241 40.000 0.00 0.00 0.00 3.09
2758 3656 9.613428 TTTTGTCTACAATGGGTCATATCTTAG 57.387 33.333 0.00 0.00 35.55 2.18
2759 3657 9.967451 TTTTTGTCTACAATGGGTCATATCTTA 57.033 29.630 0.00 0.00 35.55 2.10
2760 3658 8.877864 TTTTTGTCTACAATGGGTCATATCTT 57.122 30.769 0.00 0.00 35.55 2.40
2784 3682 9.807649 GCATGTGATTTAGAGATGGTAAATTTT 57.192 29.630 0.00 0.00 31.58 1.82
2785 3683 8.970020 TGCATGTGATTTAGAGATGGTAAATTT 58.030 29.630 0.00 0.00 31.58 1.82
2786 3684 8.523915 TGCATGTGATTTAGAGATGGTAAATT 57.476 30.769 0.00 0.00 31.58 1.82
2787 3685 8.523915 TTGCATGTGATTTAGAGATGGTAAAT 57.476 30.769 0.00 0.00 33.65 1.40
2788 3686 7.828717 TCTTGCATGTGATTTAGAGATGGTAAA 59.171 33.333 0.00 0.00 0.00 2.01
2789 3687 7.280876 GTCTTGCATGTGATTTAGAGATGGTAA 59.719 37.037 0.00 0.00 0.00 2.85
2790 3688 6.763135 GTCTTGCATGTGATTTAGAGATGGTA 59.237 38.462 0.00 0.00 0.00 3.25
2791 3689 5.587844 GTCTTGCATGTGATTTAGAGATGGT 59.412 40.000 0.00 0.00 0.00 3.55
2792 3690 5.821470 AGTCTTGCATGTGATTTAGAGATGG 59.179 40.000 0.00 0.00 0.00 3.51
2793 3691 6.922247 AGTCTTGCATGTGATTTAGAGATG 57.078 37.500 0.00 0.00 0.00 2.90
2794 3692 9.453572 TTTAAGTCTTGCATGTGATTTAGAGAT 57.546 29.630 0.00 0.00 0.00 2.75
2795 3693 8.846943 TTTAAGTCTTGCATGTGATTTAGAGA 57.153 30.769 0.00 0.00 0.00 3.10
2801 3699 9.846248 GTCTTATTTTAAGTCTTGCATGTGATT 57.154 29.630 0.00 0.00 0.00 2.57
2802 3700 9.236006 AGTCTTATTTTAAGTCTTGCATGTGAT 57.764 29.630 0.00 0.00 0.00 3.06
2803 3701 8.621532 AGTCTTATTTTAAGTCTTGCATGTGA 57.378 30.769 0.00 0.00 0.00 3.58
2824 3722 9.770097 CATGTACAATGGTTGATAAGATAGTCT 57.230 33.333 0.00 0.00 0.00 3.24
2825 3723 8.499162 GCATGTACAATGGTTGATAAGATAGTC 58.501 37.037 0.00 0.00 0.00 2.59
2826 3724 7.445402 GGCATGTACAATGGTTGATAAGATAGT 59.555 37.037 0.00 0.00 0.00 2.12
2827 3725 7.094634 GGGCATGTACAATGGTTGATAAGATAG 60.095 40.741 0.00 0.00 0.00 2.08
2828 3726 6.714810 GGGCATGTACAATGGTTGATAAGATA 59.285 38.462 0.00 0.00 0.00 1.98
2829 3727 5.536161 GGGCATGTACAATGGTTGATAAGAT 59.464 40.000 0.00 0.00 0.00 2.40
2830 3728 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
2831 3729 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
2832 3730 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
2833 3731 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
2834 3732 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
2835 3733 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
2836 3734 4.016444 ACTTAGGGCATGTACAATGGTTG 58.984 43.478 0.00 0.00 0.00 3.77
2837 3735 4.270008 GACTTAGGGCATGTACAATGGTT 58.730 43.478 0.00 0.00 0.00 3.67
2838 3736 3.371595 GGACTTAGGGCATGTACAATGGT 60.372 47.826 0.00 0.00 0.00 3.55
2839 3737 3.117888 AGGACTTAGGGCATGTACAATGG 60.118 47.826 0.00 0.00 0.00 3.16
2840 3738 4.156455 AGGACTTAGGGCATGTACAATG 57.844 45.455 0.00 0.12 0.00 2.82
2841 3739 5.428783 AGTTAGGACTTAGGGCATGTACAAT 59.571 40.000 0.00 0.00 29.87 2.71
2842 3740 4.781087 AGTTAGGACTTAGGGCATGTACAA 59.219 41.667 0.00 0.00 29.87 2.41
2843 3741 4.359105 AGTTAGGACTTAGGGCATGTACA 58.641 43.478 0.00 0.00 29.87 2.90
2844 3742 6.097981 AGTTAGTTAGGACTTAGGGCATGTAC 59.902 42.308 0.00 0.00 37.33 2.90
2845 3743 6.200114 AGTTAGTTAGGACTTAGGGCATGTA 58.800 40.000 0.00 0.00 37.33 2.29
2846 3744 5.030820 AGTTAGTTAGGACTTAGGGCATGT 58.969 41.667 0.00 0.00 37.33 3.21
2847 3745 5.615925 AGTTAGTTAGGACTTAGGGCATG 57.384 43.478 0.00 0.00 37.33 4.06
2848 3746 5.304871 GCTAGTTAGTTAGGACTTAGGGCAT 59.695 44.000 0.00 0.00 37.33 4.40
2849 3747 4.648307 GCTAGTTAGTTAGGACTTAGGGCA 59.352 45.833 0.00 0.00 37.33 5.36
2850 3748 4.039004 GGCTAGTTAGTTAGGACTTAGGGC 59.961 50.000 0.00 0.00 37.33 5.19
2851 3749 5.068855 GTGGCTAGTTAGTTAGGACTTAGGG 59.931 48.000 0.00 0.00 37.33 3.53
2852 3750 5.221009 CGTGGCTAGTTAGTTAGGACTTAGG 60.221 48.000 0.00 0.00 37.33 2.69
2853 3751 5.587844 TCGTGGCTAGTTAGTTAGGACTTAG 59.412 44.000 0.00 0.00 37.33 2.18
2854 3752 5.355350 GTCGTGGCTAGTTAGTTAGGACTTA 59.645 44.000 0.00 0.00 37.33 2.24
2855 3753 4.157472 GTCGTGGCTAGTTAGTTAGGACTT 59.843 45.833 0.00 0.00 37.33 3.01
2856 3754 3.693578 GTCGTGGCTAGTTAGTTAGGACT 59.306 47.826 0.00 0.00 39.97 3.85
2857 3755 3.693578 AGTCGTGGCTAGTTAGTTAGGAC 59.306 47.826 0.00 0.00 32.11 3.85
2882 3780 1.532868 CACCTTTGACCAAGAAGCGAG 59.467 52.381 0.00 0.00 33.80 5.03
3545 4443 4.286320 ATCGACGAGATGGCCGCC 62.286 66.667 1.04 1.04 38.36 6.13
3611 4509 6.760298 TCACGTTGTTGTTACTGGTGTTATTA 59.240 34.615 0.00 0.00 0.00 0.98
3614 4512 4.329528 GTCACGTTGTTGTTACTGGTGTTA 59.670 41.667 0.00 0.00 0.00 2.41
3695 4593 3.447918 ACTCTTTCCGAACTTGACGAA 57.552 42.857 0.00 0.00 0.00 3.85
3697 4595 3.120792 TCAACTCTTTCCGAACTTGACG 58.879 45.455 0.00 0.00 0.00 4.35
3722 4621 2.216898 CTTGCAACCTAGCTATCTGGC 58.783 52.381 0.00 0.00 34.99 4.85
3822 4724 8.199449 ACGAAAGAAAAAGGGTGATCGTATATA 58.801 33.333 0.00 0.00 40.11 0.86
3870 4772 8.244113 GGGAAGGAATGAACTAATACAACTTTG 58.756 37.037 0.00 0.00 0.00 2.77
3871 4773 7.396339 GGGGAAGGAATGAACTAATACAACTTT 59.604 37.037 0.00 0.00 0.00 2.66
3872 4774 6.890268 GGGGAAGGAATGAACTAATACAACTT 59.110 38.462 0.00 0.00 0.00 2.66
3873 4775 6.217693 AGGGGAAGGAATGAACTAATACAACT 59.782 38.462 0.00 0.00 0.00 3.16
3954 4861 7.871853 AGGCGCCATTATTTTACTTATTACTG 58.128 34.615 31.54 0.00 0.00 2.74
3976 4883 7.719193 TGACTAGCATAGATATATCTCTGAGGC 59.281 40.741 24.82 18.17 42.77 4.70
4033 5761 2.109181 GCATCCGGTAGGCTGTCC 59.891 66.667 0.00 0.00 36.10 4.02
4040 5768 1.880675 ACGTAGATGAGCATCCGGTAG 59.119 52.381 0.00 0.00 38.58 3.18
4106 5834 0.321122 AAGCCAAGACAAGAGAGCCG 60.321 55.000 0.00 0.00 0.00 5.52
4155 5885 2.047274 GCTGGGCAGCGACTTGTA 60.047 61.111 0.00 0.00 45.29 2.41
4216 5946 1.888436 CGGCCTGCTGACTTGGTCTA 61.888 60.000 0.00 0.00 33.15 2.59
4305 6041 3.096541 CAACGTTGCAGGCATCAAG 57.903 52.632 16.51 0.00 0.00 3.02
4352 6092 4.522789 AGCTTCCCGTACATGTTCAAATTT 59.477 37.500 2.30 0.00 0.00 1.82
4363 6103 0.108186 CATGCAGAGCTTCCCGTACA 60.108 55.000 0.00 0.00 0.00 2.90
4374 6114 1.153208 GAGTGCTCCCCATGCAGAG 60.153 63.158 5.98 5.98 41.41 3.35
4375 6115 2.673200 GGAGTGCTCCCCATGCAGA 61.673 63.158 6.98 0.00 43.94 4.26
4376 6116 2.124403 GGAGTGCTCCCCATGCAG 60.124 66.667 6.98 0.00 43.94 4.41
4409 6181 1.981256 AACCCACACCAGCTTAACTG 58.019 50.000 0.00 0.00 46.77 3.16
4476 6262 0.681243 GCACCATGAGTTTCCCTCCC 60.681 60.000 0.00 0.00 39.65 4.30
4527 6313 1.477558 CCATGATTTCTCCCCTTCCGG 60.478 57.143 0.00 0.00 0.00 5.14
4583 6375 1.280746 GACGACGACGAGACACCAA 59.719 57.895 15.32 0.00 42.66 3.67
4584 6376 2.941333 GACGACGACGAGACACCA 59.059 61.111 15.32 0.00 42.66 4.17
4670 6463 2.623094 TACGTAATCGCCTCCCCCGA 62.623 60.000 0.00 0.00 41.18 5.14
4861 6654 3.711059 ATCTCGTAGACCCCGCCGT 62.711 63.158 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.