Multiple sequence alignment - TraesCS1A01G083300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G083300 chr1A 100.000 3972 0 0 1 3972 67466265 67470236 0.000000e+00 7336.0
1 TraesCS1A01G083300 chr1D 93.897 2507 111 23 1 2476 68884359 68886854 0.000000e+00 3744.0
2 TraesCS1A01G083300 chr1D 92.429 634 40 6 3339 3972 68887447 68888072 0.000000e+00 898.0
3 TraesCS1A01G083300 chr1D 94.223 502 13 8 2696 3187 68886890 68887385 0.000000e+00 752.0
4 TraesCS1A01G083300 chr1D 83.582 67 10 1 2568 2634 426753746 426753811 1.190000e-05 62.1
5 TraesCS1A01G083300 chr1B 93.105 2509 120 32 1 2476 110125056 110127544 0.000000e+00 3626.0
6 TraesCS1A01G083300 chr1B 90.251 1313 82 19 2667 3967 110127561 110128839 0.000000e+00 1674.0
7 TraesCS1A01G083300 chr1B 100.000 34 0 0 1191 1224 110126314 110126347 3.310000e-06 63.9
8 TraesCS1A01G083300 chr2D 86.616 523 44 9 1356 1874 476041907 476041407 4.480000e-154 555.0
9 TraesCS1A01G083300 chr5B 85.824 522 52 8 1352 1872 249370338 249370838 5.840000e-148 534.0
10 TraesCS1A01G083300 chr5B 79.812 213 34 7 3762 3972 112533449 112533654 3.200000e-31 147.0
11 TraesCS1A01G083300 chr5B 93.069 101 6 1 3661 3761 263474170 263474071 3.200000e-31 147.0
12 TraesCS1A01G083300 chr2B 84.110 365 48 7 1514 1874 556849993 556849635 1.060000e-90 344.0
13 TraesCS1A01G083300 chr2B 93.069 101 6 1 3661 3761 205849699 205849600 3.200000e-31 147.0
14 TraesCS1A01G083300 chr2B 91.262 103 8 1 3662 3764 593665430 593665329 5.350000e-29 139.0
15 TraesCS1A01G083300 chr2A 95.050 101 4 1 3662 3762 543987252 543987153 1.480000e-34 158.0
16 TraesCS1A01G083300 chr5D 92.233 103 6 2 3662 3764 215138744 215138644 1.150000e-30 145.0
17 TraesCS1A01G083300 chr5A 92.157 102 7 1 3662 3763 374656556 374656456 4.140000e-30 143.0
18 TraesCS1A01G083300 chr7A 92.000 100 7 1 3662 3761 567017383 567017285 5.350000e-29 139.0
19 TraesCS1A01G083300 chr3D 86.301 73 10 0 2789 2861 157345613 157345541 3.290000e-11 80.5
20 TraesCS1A01G083300 chr7D 95.000 40 2 0 2608 2647 271755973 271755934 3.310000e-06 63.9
21 TraesCS1A01G083300 chr3B 82.192 73 13 0 2789 2861 228505991 228505919 3.310000e-06 63.9
22 TraesCS1A01G083300 chrUn 100.000 28 0 0 3512 3539 299357638 299357611 7.000000e-03 52.8
23 TraesCS1A01G083300 chr3A 100.000 28 0 0 3512 3539 11126005 11125978 7.000000e-03 52.8
24 TraesCS1A01G083300 chr3A 100.000 28 0 0 3512 3539 11134656 11134629 7.000000e-03 52.8
25 TraesCS1A01G083300 chr3A 100.000 28 0 0 3512 3539 11141528 11141501 7.000000e-03 52.8


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 TraesCS1A01G083300 chr1A 67466265 67470236 3971 False 7336.000000 7336 100.000000 1 3972 1 chr1A.!!$F1 3971
1 TraesCS1A01G083300 chr1D 68884359 68888072 3713 False 1798.000000 3744 93.516333 1 3972 3 chr1D.!!$F2 3971
2 TraesCS1A01G083300 chr1B 110125056 110128839 3783 False 1787.966667 3626 94.452000 1 3967 3 chr1B.!!$F1 3966
3 TraesCS1A01G083300 chr2D 476041407 476041907 500 True 555.000000 555 86.616000 1356 1874 1 chr2D.!!$R1 518
4 TraesCS1A01G083300 chr5B 249370338 249370838 500 False 534.000000 534 85.824000 1352 1872 1 chr5B.!!$F2 520

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
467 472 0.397564 TGACTGCTCACTGGCAATGA 59.602 50.000 0.00 0.0 41.94 2.57 F
1060 1085 0.459237 CACCTGCTCTACCGCTCTTG 60.459 60.000 0.00 0.0 0.00 3.02 F
1168 1194 0.529773 TTGTCGGCGATGATAGTGGC 60.530 55.000 14.79 0.0 0.00 5.01 F
2482 2536 1.228552 CCTGGTGGGTGGGTTGAAG 60.229 63.158 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2465 2519 0.405585 ATCTTCAACCCACCCACCAG 59.594 55.000 0.00 0.0 0.00 4.00 R
2714 2768 0.179202 TCGCGCATGCACATTTACAC 60.179 50.000 19.57 0.0 42.97 2.90 R
2715 2769 0.731994 ATCGCGCATGCACATTTACA 59.268 45.000 19.57 0.0 42.97 2.41 R
3553 3621 1.069090 GTTCAGACCGCACAGTCCA 59.931 57.895 0.00 0.0 37.49 4.02 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
172 173 2.655685 GCGGCTCGATCGTCCTTC 60.656 66.667 15.94 8.36 0.00 3.46
174 175 2.482333 CGGCTCGATCGTCCTTCCT 61.482 63.158 15.94 0.00 0.00 3.36
306 311 1.059942 CTCGCCGGTTGAATTTTTGC 58.940 50.000 1.90 0.00 0.00 3.68
427 432 1.802880 GCGGTGATCACGTGATAAGCT 60.803 52.381 32.14 14.84 32.50 3.74
430 435 4.109766 CGGTGATCACGTGATAAGCTTTA 58.890 43.478 32.14 8.88 32.50 1.85
431 436 4.207224 CGGTGATCACGTGATAAGCTTTAG 59.793 45.833 32.14 18.81 32.50 1.85
458 463 3.141398 TCACTTGGAATTGACTGCTCAC 58.859 45.455 0.00 0.00 0.00 3.51
459 464 3.144506 CACTTGGAATTGACTGCTCACT 58.855 45.455 0.00 0.00 0.00 3.41
461 466 2.189594 TGGAATTGACTGCTCACTGG 57.810 50.000 0.00 0.00 0.00 4.00
462 467 0.807496 GGAATTGACTGCTCACTGGC 59.193 55.000 0.00 0.00 0.00 4.85
463 468 1.527034 GAATTGACTGCTCACTGGCA 58.473 50.000 0.00 0.00 40.15 4.92
465 470 2.211250 ATTGACTGCTCACTGGCAAT 57.789 45.000 0.00 0.00 45.34 3.56
466 471 1.241165 TTGACTGCTCACTGGCAATG 58.759 50.000 0.00 0.00 41.94 2.82
467 472 0.397564 TGACTGCTCACTGGCAATGA 59.602 50.000 0.00 0.00 41.94 2.57
468 473 1.202794 TGACTGCTCACTGGCAATGAA 60.203 47.619 0.00 0.00 41.94 2.57
469 474 2.089980 GACTGCTCACTGGCAATGAAT 58.910 47.619 0.00 0.00 41.94 2.57
472 477 2.230508 CTGCTCACTGGCAATGAATTGT 59.769 45.455 0.00 0.00 41.94 2.71
473 478 2.029739 TGCTCACTGGCAATGAATTGTG 60.030 45.455 0.00 0.00 39.43 3.33
474 479 2.229543 GCTCACTGGCAATGAATTGTGA 59.770 45.455 0.00 1.72 39.88 3.58
475 480 3.119245 GCTCACTGGCAATGAATTGTGAT 60.119 43.478 0.00 0.00 39.88 3.06
476 481 4.619863 GCTCACTGGCAATGAATTGTGATT 60.620 41.667 0.00 0.00 39.88 2.57
477 482 5.063180 TCACTGGCAATGAATTGTGATTC 57.937 39.130 0.00 0.00 41.67 2.52
519 524 9.874205 ATAATTCATGAATTTGACGAAATTGGT 57.126 25.926 32.57 10.98 41.06 3.67
522 527 4.313277 TGAATTTGACGAAATTGGTGCA 57.687 36.364 0.00 0.00 41.06 4.57
551 556 4.917415 GCACAAAAGCATTTCAAGATACGT 59.083 37.500 0.00 0.00 37.28 3.57
571 576 2.791383 TCAAGCGGAACCAAAATGTG 57.209 45.000 0.00 0.00 0.00 3.21
605 618 1.342174 CAAATGTCAGGCAAGCACCTT 59.658 47.619 0.00 0.00 38.26 3.50
625 638 0.679960 TCTCGCGGGAGACATGAAGA 60.680 55.000 26.55 3.93 44.28 2.87
633 646 2.303022 GGGAGACATGAAGAGTGGAACA 59.697 50.000 0.00 0.00 41.43 3.18
655 668 3.460103 TGAGTTTCCACGTCAACCTAAC 58.540 45.455 0.00 0.00 0.00 2.34
656 669 2.473984 GAGTTTCCACGTCAACCTAACG 59.526 50.000 0.00 0.00 45.37 3.18
701 719 3.096852 CCCCTGGGAAAATTTCAGGTAC 58.903 50.000 16.20 0.00 44.78 3.34
702 720 3.501385 CCCCTGGGAAAATTTCAGGTACA 60.501 47.826 16.20 0.00 44.78 2.90
704 722 3.190535 CCTGGGAAAATTTCAGGTACACG 59.809 47.826 13.73 0.00 42.17 4.49
706 724 4.658063 TGGGAAAATTTCAGGTACACGAT 58.342 39.130 8.09 0.00 0.00 3.73
707 725 5.074115 TGGGAAAATTTCAGGTACACGATT 58.926 37.500 8.09 0.00 0.00 3.34
776 799 5.574830 GCTAGCAATCTCCATGACTTATACG 59.425 44.000 10.63 0.00 0.00 3.06
790 813 3.068307 ACTTATACGGACACTGCCTGATC 59.932 47.826 0.00 0.00 0.00 2.92
882 907 0.524604 TCCGACGTCATACATGCACG 60.525 55.000 17.16 0.00 37.35 5.34
1011 1036 2.173519 CCAACAACTCATGCTTCCCAT 58.826 47.619 0.00 0.00 33.39 4.00
1019 1044 1.288633 TCATGCTTCCCATCCAACCAT 59.711 47.619 0.00 0.00 29.71 3.55
1060 1085 0.459237 CACCTGCTCTACCGCTCTTG 60.459 60.000 0.00 0.00 0.00 3.02
1168 1194 0.529773 TTGTCGGCGATGATAGTGGC 60.530 55.000 14.79 0.00 0.00 5.01
1371 1397 4.337060 CGTGCAGGACCGACGTCA 62.337 66.667 17.16 0.00 41.13 4.35
1449 1480 1.893801 GGTGGAGGAGACGAAGAAGAA 59.106 52.381 0.00 0.00 0.00 2.52
1971 2010 2.159198 CCAGCACCTGCATTAATTCCAC 60.159 50.000 0.00 0.00 45.16 4.02
2047 2094 4.634133 GGCACACCGACGACGACA 62.634 66.667 9.28 0.00 42.66 4.35
2097 2144 1.662044 CTGGTCAAAAGCAGGGCAC 59.338 57.895 0.00 0.00 45.33 5.01
2196 2243 8.011290 ACTCTAGGTGATTAGTGGTACCAATAT 58.989 37.037 21.90 12.79 35.66 1.28
2197 2244 9.529823 CTCTAGGTGATTAGTGGTACCAATATA 57.470 37.037 21.90 13.32 35.66 0.86
2312 2359 4.680237 CACCCTTCGCCACGCTCA 62.680 66.667 0.00 0.00 0.00 4.26
2334 2381 3.781770 CTCCAGTCGCGATCAGCCC 62.782 68.421 14.06 0.00 44.76 5.19
2341 2388 4.593864 GCGATCAGCCCGTCTCCC 62.594 72.222 0.00 0.00 40.81 4.30
2345 2392 4.779733 TCAGCCCGTCTCCCTCCC 62.780 72.222 0.00 0.00 0.00 4.30
2360 2407 2.251818 CCTCCCCGTACTCATCATCAT 58.748 52.381 0.00 0.00 0.00 2.45
2410 2464 8.749026 AGTTAATTAGTAGTGCTAGACTGCTA 57.251 34.615 12.62 12.62 45.07 3.49
2423 2477 4.808414 AGACTGCTAGTATGTCTTTGCA 57.192 40.909 8.06 0.00 37.76 4.08
2436 2490 7.978982 GTATGTCTTTGCATACTGTTTGATCT 58.021 34.615 2.29 0.00 44.57 2.75
2453 2507 6.861065 TTGATCTTAATTAATCTGGGTCGC 57.139 37.500 0.00 0.00 0.00 5.19
2454 2508 5.305585 TGATCTTAATTAATCTGGGTCGCC 58.694 41.667 0.00 0.00 0.00 5.54
2455 2509 4.764050 TCTTAATTAATCTGGGTCGCCA 57.236 40.909 0.00 0.00 0.00 5.69
2456 2510 4.703897 TCTTAATTAATCTGGGTCGCCAG 58.296 43.478 2.85 2.85 39.01 4.85
2465 2519 2.124695 GGTCGCCAGAACCATCCC 60.125 66.667 0.00 0.00 0.00 3.85
2466 2520 2.670148 GGTCGCCAGAACCATCCCT 61.670 63.158 0.00 0.00 0.00 4.20
2467 2521 1.450312 GTCGCCAGAACCATCCCTG 60.450 63.158 0.00 0.00 0.00 4.45
2482 2536 1.228552 CCTGGTGGGTGGGTTGAAG 60.229 63.158 0.00 0.00 0.00 3.02
2483 2537 1.715019 CCTGGTGGGTGGGTTGAAGA 61.715 60.000 0.00 0.00 0.00 2.87
2485 2539 1.633432 CTGGTGGGTGGGTTGAAGATA 59.367 52.381 0.00 0.00 0.00 1.98
2488 2542 4.051478 TGGTGGGTGGGTTGAAGATATAT 58.949 43.478 0.00 0.00 0.00 0.86
2489 2543 4.480537 TGGTGGGTGGGTTGAAGATATATT 59.519 41.667 0.00 0.00 0.00 1.28
2490 2544 5.043732 TGGTGGGTGGGTTGAAGATATATTT 60.044 40.000 0.00 0.00 0.00 1.40
2491 2545 5.897250 GGTGGGTGGGTTGAAGATATATTTT 59.103 40.000 0.00 0.00 0.00 1.82
2492 2546 6.382859 GGTGGGTGGGTTGAAGATATATTTTT 59.617 38.462 0.00 0.00 0.00 1.94
2493 2547 7.264947 GTGGGTGGGTTGAAGATATATTTTTG 58.735 38.462 0.00 0.00 0.00 2.44
2494 2548 7.123547 GTGGGTGGGTTGAAGATATATTTTTGA 59.876 37.037 0.00 0.00 0.00 2.69
2495 2549 7.676043 TGGGTGGGTTGAAGATATATTTTTGAA 59.324 33.333 0.00 0.00 0.00 2.69
2496 2550 8.197439 GGGTGGGTTGAAGATATATTTTTGAAG 58.803 37.037 0.00 0.00 0.00 3.02
2497 2551 8.966868 GGTGGGTTGAAGATATATTTTTGAAGA 58.033 33.333 0.00 0.00 0.00 2.87
2518 2572 8.175069 TGAAGAACATCAAATAAACGTAGATGC 58.825 33.333 0.00 0.00 39.64 3.91
2519 2573 7.609760 AGAACATCAAATAAACGTAGATGCA 57.390 32.000 0.00 0.00 39.64 3.96
2520 2574 7.464358 AGAACATCAAATAAACGTAGATGCAC 58.536 34.615 0.00 0.00 39.64 4.57
2521 2575 6.119144 ACATCAAATAAACGTAGATGCACC 57.881 37.500 0.00 0.00 39.64 5.01
2522 2576 5.065988 ACATCAAATAAACGTAGATGCACCC 59.934 40.000 0.00 0.00 39.64 4.61
2523 2577 4.580868 TCAAATAAACGTAGATGCACCCA 58.419 39.130 0.00 0.00 0.00 4.51
2524 2578 5.189928 TCAAATAAACGTAGATGCACCCAT 58.810 37.500 0.00 0.00 0.00 4.00
2525 2579 5.065859 TCAAATAAACGTAGATGCACCCATG 59.934 40.000 0.00 0.00 0.00 3.66
2526 2580 2.489938 AAACGTAGATGCACCCATGT 57.510 45.000 0.00 0.00 0.00 3.21
2527 2581 3.620427 AAACGTAGATGCACCCATGTA 57.380 42.857 0.00 0.00 0.00 2.29
2528 2582 3.838244 AACGTAGATGCACCCATGTAT 57.162 42.857 0.00 0.00 30.93 2.29
2529 2583 3.111853 ACGTAGATGCACCCATGTATG 57.888 47.619 0.00 0.00 39.11 2.39
2530 2584 1.800586 CGTAGATGCACCCATGTATGC 59.199 52.381 10.69 10.69 42.40 3.14
2538 2592 4.494350 GCACCCATGTATGCAAGATTAG 57.506 45.455 12.31 0.00 41.65 1.73
2539 2593 3.304928 GCACCCATGTATGCAAGATTAGC 60.305 47.826 12.31 0.00 41.65 3.09
2540 2594 3.058708 CACCCATGTATGCAAGATTAGCG 60.059 47.826 0.00 0.00 33.85 4.26
2541 2595 3.141398 CCCATGTATGCAAGATTAGCGT 58.859 45.455 0.00 0.00 35.08 5.07
2542 2596 3.058708 CCCATGTATGCAAGATTAGCGTG 60.059 47.826 0.00 0.00 32.61 5.34
2543 2597 3.809279 CCATGTATGCAAGATTAGCGTGA 59.191 43.478 0.00 0.00 32.61 4.35
2544 2598 4.319046 CCATGTATGCAAGATTAGCGTGAC 60.319 45.833 0.00 0.00 32.61 3.67
2545 2599 4.123497 TGTATGCAAGATTAGCGTGACT 57.877 40.909 0.00 0.00 32.61 3.41
2546 2600 4.503910 TGTATGCAAGATTAGCGTGACTT 58.496 39.130 0.00 0.00 32.61 3.01
2547 2601 4.566759 TGTATGCAAGATTAGCGTGACTTC 59.433 41.667 0.00 0.00 32.61 3.01
2548 2602 2.346803 TGCAAGATTAGCGTGACTTCC 58.653 47.619 0.00 0.00 33.85 3.46
2549 2603 2.028112 TGCAAGATTAGCGTGACTTCCT 60.028 45.455 0.00 0.00 33.85 3.36
2550 2604 3.003480 GCAAGATTAGCGTGACTTCCTT 58.997 45.455 0.00 0.00 0.00 3.36
2551 2605 4.181578 GCAAGATTAGCGTGACTTCCTTA 58.818 43.478 0.00 0.00 0.00 2.69
2552 2606 4.268884 GCAAGATTAGCGTGACTTCCTTAG 59.731 45.833 0.00 0.00 0.00 2.18
2553 2607 5.651530 CAAGATTAGCGTGACTTCCTTAGA 58.348 41.667 0.00 0.00 0.00 2.10
2554 2608 6.276847 CAAGATTAGCGTGACTTCCTTAGAT 58.723 40.000 0.00 0.00 0.00 1.98
2555 2609 5.837437 AGATTAGCGTGACTTCCTTAGATG 58.163 41.667 0.00 0.00 0.00 2.90
2556 2610 2.301577 AGCGTGACTTCCTTAGATGC 57.698 50.000 0.00 0.00 0.00 3.91
2557 2611 1.550524 AGCGTGACTTCCTTAGATGCA 59.449 47.619 0.00 0.00 0.00 3.96
2558 2612 1.661112 GCGTGACTTCCTTAGATGCAC 59.339 52.381 0.00 0.00 0.00 4.57
2559 2613 2.675317 GCGTGACTTCCTTAGATGCACT 60.675 50.000 0.00 0.00 0.00 4.40
2560 2614 3.182967 CGTGACTTCCTTAGATGCACTC 58.817 50.000 0.00 0.00 0.00 3.51
2561 2615 3.367395 CGTGACTTCCTTAGATGCACTCA 60.367 47.826 0.00 0.00 0.00 3.41
2562 2616 4.679106 CGTGACTTCCTTAGATGCACTCAT 60.679 45.833 0.00 0.00 35.17 2.90
2563 2617 5.450550 CGTGACTTCCTTAGATGCACTCATA 60.451 44.000 0.00 0.00 31.96 2.15
2564 2618 6.520272 GTGACTTCCTTAGATGCACTCATAT 58.480 40.000 0.00 0.00 31.96 1.78
2565 2619 7.522236 CGTGACTTCCTTAGATGCACTCATATA 60.522 40.741 0.00 0.00 31.96 0.86
2566 2620 7.596995 GTGACTTCCTTAGATGCACTCATATAC 59.403 40.741 0.00 0.00 31.96 1.47
2567 2621 7.287696 TGACTTCCTTAGATGCACTCATATACA 59.712 37.037 0.00 0.00 31.96 2.29
2568 2622 8.023021 ACTTCCTTAGATGCACTCATATACAA 57.977 34.615 0.00 0.00 31.96 2.41
2569 2623 8.654997 ACTTCCTTAGATGCACTCATATACAAT 58.345 33.333 0.00 0.00 31.96 2.71
2571 2625 9.929180 TTCCTTAGATGCACTCATATACAATAC 57.071 33.333 0.00 0.00 31.96 1.89
2572 2626 9.314133 TCCTTAGATGCACTCATATACAATACT 57.686 33.333 0.00 0.00 31.96 2.12
2573 2627 9.579768 CCTTAGATGCACTCATATACAATACTC 57.420 37.037 0.00 0.00 31.96 2.59
2574 2628 9.579768 CTTAGATGCACTCATATACAATACTCC 57.420 37.037 0.00 0.00 31.96 3.85
2575 2629 6.940739 AGATGCACTCATATACAATACTCCC 58.059 40.000 0.00 0.00 31.96 4.30
2576 2630 6.728164 AGATGCACTCATATACAATACTCCCT 59.272 38.462 0.00 0.00 31.96 4.20
2577 2631 6.346477 TGCACTCATATACAATACTCCCTC 57.654 41.667 0.00 0.00 0.00 4.30
2578 2632 5.838521 TGCACTCATATACAATACTCCCTCA 59.161 40.000 0.00 0.00 0.00 3.86
2579 2633 6.326323 TGCACTCATATACAATACTCCCTCAA 59.674 38.462 0.00 0.00 0.00 3.02
2580 2634 7.016563 TGCACTCATATACAATACTCCCTCAAT 59.983 37.037 0.00 0.00 0.00 2.57
2581 2635 7.547370 GCACTCATATACAATACTCCCTCAATC 59.453 40.741 0.00 0.00 0.00 2.67
2582 2636 8.037758 CACTCATATACAATACTCCCTCAATCC 58.962 40.741 0.00 0.00 0.00 3.01
2583 2637 7.181125 ACTCATATACAATACTCCCTCAATCCC 59.819 40.741 0.00 0.00 0.00 3.85
2584 2638 7.022496 TCATATACAATACTCCCTCAATCCCA 58.978 38.462 0.00 0.00 0.00 4.37
2585 2639 5.832539 ATACAATACTCCCTCAATCCCAG 57.167 43.478 0.00 0.00 0.00 4.45
2586 2640 3.736094 ACAATACTCCCTCAATCCCAGA 58.264 45.455 0.00 0.00 0.00 3.86
2587 2641 4.310740 ACAATACTCCCTCAATCCCAGAT 58.689 43.478 0.00 0.00 0.00 2.90
2588 2642 4.728860 ACAATACTCCCTCAATCCCAGATT 59.271 41.667 0.00 0.00 0.00 2.40
2589 2643 5.911178 ACAATACTCCCTCAATCCCAGATTA 59.089 40.000 0.00 0.00 0.00 1.75
2590 2644 6.564152 ACAATACTCCCTCAATCCCAGATTAT 59.436 38.462 0.00 0.00 0.00 1.28
2591 2645 7.074237 ACAATACTCCCTCAATCCCAGATTATT 59.926 37.037 0.00 0.00 0.00 1.40
2592 2646 7.654287 ATACTCCCTCAATCCCAGATTATTT 57.346 36.000 0.00 0.00 0.00 1.40
2593 2647 5.699143 ACTCCCTCAATCCCAGATTATTTG 58.301 41.667 0.00 0.00 0.00 2.32
2594 2648 5.194537 ACTCCCTCAATCCCAGATTATTTGT 59.805 40.000 0.00 0.00 0.00 2.83
2595 2649 6.091076 TCCCTCAATCCCAGATTATTTGTT 57.909 37.500 0.00 0.00 0.00 2.83
2596 2650 5.893255 TCCCTCAATCCCAGATTATTTGTTG 59.107 40.000 0.00 0.00 0.00 3.33
2597 2651 5.452356 CCCTCAATCCCAGATTATTTGTTGC 60.452 44.000 0.00 0.00 0.00 4.17
2598 2652 5.247507 TCAATCCCAGATTATTTGTTGCG 57.752 39.130 0.00 0.00 0.00 4.85
2599 2653 4.097741 TCAATCCCAGATTATTTGTTGCGG 59.902 41.667 0.00 0.00 0.00 5.69
2600 2654 3.358111 TCCCAGATTATTTGTTGCGGA 57.642 42.857 0.00 0.00 0.00 5.54
2601 2655 3.691575 TCCCAGATTATTTGTTGCGGAA 58.308 40.909 0.00 0.00 0.00 4.30
2602 2656 4.082845 TCCCAGATTATTTGTTGCGGAAA 58.917 39.130 0.00 0.00 0.00 3.13
2603 2657 4.709397 TCCCAGATTATTTGTTGCGGAAAT 59.291 37.500 0.00 0.00 0.00 2.17
2604 2658 4.805192 CCCAGATTATTTGTTGCGGAAATG 59.195 41.667 0.00 0.00 0.00 2.32
2605 2659 4.805192 CCAGATTATTTGTTGCGGAAATGG 59.195 41.667 0.00 0.00 0.00 3.16
2606 2660 5.394005 CCAGATTATTTGTTGCGGAAATGGA 60.394 40.000 0.00 0.00 0.00 3.41
2607 2661 6.275335 CAGATTATTTGTTGCGGAAATGGAT 58.725 36.000 0.00 0.00 0.00 3.41
2608 2662 7.424803 CAGATTATTTGTTGCGGAAATGGATA 58.575 34.615 0.00 0.00 0.00 2.59
2609 2663 7.592533 CAGATTATTTGTTGCGGAAATGGATAG 59.407 37.037 0.00 0.00 0.00 2.08
2610 2664 7.502226 AGATTATTTGTTGCGGAAATGGATAGA 59.498 33.333 0.00 0.00 0.00 1.98
2611 2665 5.913137 ATTTGTTGCGGAAATGGATAGAA 57.087 34.783 0.00 0.00 0.00 2.10
2612 2666 5.713792 TTTGTTGCGGAAATGGATAGAAA 57.286 34.783 0.00 0.00 0.00 2.52
2613 2667 5.913137 TTGTTGCGGAAATGGATAGAAAT 57.087 34.783 0.00 0.00 0.00 2.17
2614 2668 5.913137 TGTTGCGGAAATGGATAGAAATT 57.087 34.783 0.00 0.00 0.00 1.82
2615 2669 5.649557 TGTTGCGGAAATGGATAGAAATTG 58.350 37.500 0.00 0.00 0.00 2.32
2616 2670 5.417266 TGTTGCGGAAATGGATAGAAATTGA 59.583 36.000 0.00 0.00 0.00 2.57
2617 2671 6.096705 TGTTGCGGAAATGGATAGAAATTGAT 59.903 34.615 0.00 0.00 0.00 2.57
2618 2672 6.075762 TGCGGAAATGGATAGAAATTGATG 57.924 37.500 0.00 0.00 0.00 3.07
2619 2673 5.593909 TGCGGAAATGGATAGAAATTGATGT 59.406 36.000 0.00 0.00 0.00 3.06
2620 2674 6.770303 TGCGGAAATGGATAGAAATTGATGTA 59.230 34.615 0.00 0.00 0.00 2.29
2621 2675 7.448161 TGCGGAAATGGATAGAAATTGATGTAT 59.552 33.333 0.00 0.00 0.00 2.29
2622 2676 8.299570 GCGGAAATGGATAGAAATTGATGTATT 58.700 33.333 0.00 0.00 0.00 1.89
2659 2713 6.764877 ATGTCGAGCTATAAAATTACCACG 57.235 37.500 0.00 0.00 0.00 4.94
2660 2714 5.893687 TGTCGAGCTATAAAATTACCACGA 58.106 37.500 0.00 0.00 0.00 4.35
2661 2715 5.745294 TGTCGAGCTATAAAATTACCACGAC 59.255 40.000 0.00 0.00 43.82 4.34
2662 2716 5.975939 GTCGAGCTATAAAATTACCACGACT 59.024 40.000 0.00 0.00 41.55 4.18
2663 2717 6.474751 GTCGAGCTATAAAATTACCACGACTT 59.525 38.462 0.00 0.00 41.55 3.01
2664 2718 7.009907 GTCGAGCTATAAAATTACCACGACTTT 59.990 37.037 0.00 0.00 41.55 2.66
2665 2719 7.221452 TCGAGCTATAAAATTACCACGACTTTC 59.779 37.037 0.00 0.00 0.00 2.62
2674 2728 5.796424 TTACCACGACTTTCCTAGAGTTT 57.204 39.130 0.00 0.00 0.00 2.66
2705 2759 5.869753 TCTACTCACGGTTACTCTTACAC 57.130 43.478 0.00 0.00 0.00 2.90
2714 2768 4.167268 GGTTACTCTTACACGAGCTTCAG 58.833 47.826 0.00 0.00 34.35 3.02
2715 2769 4.321082 GGTTACTCTTACACGAGCTTCAGT 60.321 45.833 0.00 0.00 34.35 3.41
2780 2837 0.776810 TGTGATTTTGCCAGGGGAGA 59.223 50.000 0.00 0.00 0.00 3.71
2885 2942 1.116308 TCGATTCCTACGGGCATGAA 58.884 50.000 0.00 0.00 0.00 2.57
2886 2943 1.202486 TCGATTCCTACGGGCATGAAC 60.202 52.381 0.00 0.00 0.00 3.18
2889 2946 0.251916 TTCCTACGGGCATGAACAGG 59.748 55.000 0.00 0.00 0.00 4.00
2890 2947 1.819632 CCTACGGGCATGAACAGGC 60.820 63.158 0.00 2.78 37.39 4.85
2891 2948 1.078497 CTACGGGCATGAACAGGCA 60.078 57.895 13.09 0.00 40.32 4.75
2899 2960 1.241165 CATGAACAGGCAGCAAGTGA 58.759 50.000 0.00 0.00 0.00 3.41
2913 2974 5.277250 GCAGCAAGTGAATAAGCTAAGCTAG 60.277 44.000 0.00 0.00 38.25 3.42
2918 2979 6.339587 AGTGAATAAGCTAAGCTAGGCTAG 57.660 41.667 17.33 17.33 38.25 3.42
2945 3010 5.615708 CATCTACATGCTTGAATACATCGC 58.384 41.667 6.60 0.00 0.00 4.58
3097 3164 8.125728 TCATGTATGTGTGTATCAATGTTACG 57.874 34.615 0.00 0.00 0.00 3.18
3101 3168 5.463499 TGTGTGTATCAATGTTACGATGC 57.537 39.130 0.00 0.00 0.00 3.91
3296 3364 3.799432 TGGTATTTTACACACAGCCCT 57.201 42.857 0.00 0.00 0.00 5.19
3316 3384 6.182507 CCCTTAGGCCTAACATGTAATACA 57.817 41.667 21.68 0.00 0.00 2.29
3317 3385 6.597562 CCCTTAGGCCTAACATGTAATACAA 58.402 40.000 21.68 0.00 0.00 2.41
3318 3386 7.057894 CCCTTAGGCCTAACATGTAATACAAA 58.942 38.462 21.68 0.00 0.00 2.83
3319 3387 7.558444 CCCTTAGGCCTAACATGTAATACAAAA 59.442 37.037 21.68 0.00 0.00 2.44
3320 3388 8.403236 CCTTAGGCCTAACATGTAATACAAAAC 58.597 37.037 21.68 0.00 0.00 2.43
3321 3389 6.769134 AGGCCTAACATGTAATACAAAACC 57.231 37.500 1.29 0.00 0.00 3.27
3322 3390 6.249951 AGGCCTAACATGTAATACAAAACCA 58.750 36.000 1.29 0.00 0.00 3.67
3323 3391 6.895204 AGGCCTAACATGTAATACAAAACCAT 59.105 34.615 1.29 0.00 0.00 3.55
3356 3424 4.981806 TTTCCACTTCCTTTTGTCAGTG 57.018 40.909 0.00 0.00 37.07 3.66
3530 3598 5.769835 TCTAAGGGCATCTTCAAAATGGAT 58.230 37.500 0.00 0.00 36.93 3.41
3553 3621 1.901464 AAACTGCCCGCATCCGTTT 60.901 52.632 0.00 0.00 0.00 3.60
3567 3635 1.594293 CGTTTGGACTGTGCGGTCT 60.594 57.895 10.54 0.00 36.55 3.85
3569 3637 0.531974 GTTTGGACTGTGCGGTCTGA 60.532 55.000 10.54 0.00 36.55 3.27
3631 3699 1.623311 TGCATCACCCTTTCTCTTCGA 59.377 47.619 0.00 0.00 0.00 3.71
3639 3707 4.393371 CACCCTTTCTCTTCGAAGAAATCC 59.607 45.833 26.87 0.00 45.90 3.01
3788 3856 4.330250 CATAGGGAGCACATGAATTAGGG 58.670 47.826 0.00 0.00 0.00 3.53
3798 3866 3.769300 ACATGAATTAGGGTTTTGCCTCC 59.231 43.478 0.00 0.00 37.43 4.30
3812 3880 2.642254 CCTCCCGCGGTGACTTACA 61.642 63.158 26.12 0.00 0.00 2.41
3819 3887 1.976045 CGCGGTGACTTACAAAATTGC 59.024 47.619 0.00 0.00 0.00 3.56
3823 3891 3.243234 CGGTGACTTACAAAATTGCACCA 60.243 43.478 15.46 0.00 43.28 4.17
3887 3955 7.823799 GGATGAATATTGGTTTTGGTGAAATGT 59.176 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.187946 GAGGATGACTGGTGGCGG 59.812 66.667 0.00 0.00 0.00 6.13
306 311 7.789202 TCTGGATAAGATAGATCAAAGGGAG 57.211 40.000 0.00 0.00 0.00 4.30
448 453 0.397564 TCATTGCCAGTGAGCAGTCA 59.602 50.000 6.43 0.00 45.13 3.41
450 455 2.211250 ATTCATTGCCAGTGAGCAGT 57.789 45.000 6.43 1.95 45.13 4.40
466 471 9.897744 TCAGTTGATTTTACTGAATCACAATTC 57.102 29.630 3.39 0.00 46.54 2.17
519 524 2.090400 TGCTTTTGTGCAAAACTGCA 57.910 40.000 15.55 15.55 43.22 4.41
522 527 5.642919 TCTTGAAATGCTTTTGTGCAAAACT 59.357 32.000 1.76 0.00 46.61 2.66
551 556 2.690497 TCACATTTTGGTTCCGCTTGAA 59.310 40.909 0.00 0.00 0.00 2.69
571 576 4.774124 TGACATTTGATCCCTCACATCTC 58.226 43.478 0.00 0.00 0.00 2.75
605 618 0.173481 CTTCATGTCTCCCGCGAGAA 59.827 55.000 8.23 0.00 46.74 2.87
625 638 2.158813 ACGTGGAAACTCATGTTCCACT 60.159 45.455 29.55 19.91 43.71 4.00
633 646 2.930826 AGGTTGACGTGGAAACTCAT 57.069 45.000 0.00 0.00 0.00 2.90
655 668 3.057806 AGGTCCCGCTTAAATTTTCAACG 60.058 43.478 0.00 0.00 0.00 4.10
656 669 4.234574 CAGGTCCCGCTTAAATTTTCAAC 58.765 43.478 0.00 0.00 0.00 3.18
657 670 3.257127 CCAGGTCCCGCTTAAATTTTCAA 59.743 43.478 0.00 0.00 0.00 2.69
662 675 0.683179 GGCCAGGTCCCGCTTAAATT 60.683 55.000 0.00 0.00 0.00 1.82
664 677 2.353573 GGCCAGGTCCCGCTTAAA 59.646 61.111 0.00 0.00 0.00 1.52
665 678 3.723922 GGGCCAGGTCCCGCTTAA 61.724 66.667 4.39 0.00 36.38 1.85
776 799 0.036732 TGTTGGATCAGGCAGTGTCC 59.963 55.000 0.00 0.00 0.00 4.02
790 813 5.180117 GCATATATCAGCAGTAACCTGTTGG 59.820 44.000 6.70 0.00 46.49 3.77
882 907 5.012148 ACTTCCTACAGTACATGATATGGGC 59.988 44.000 0.00 0.00 33.60 5.36
1028 1053 1.915614 GCAGGTGAGTGACAATGCCG 61.916 60.000 0.00 0.00 37.45 5.69
1168 1194 3.720193 ACCTCGTCACCGTCGTCG 61.720 66.667 0.00 0.00 35.01 5.12
1252 1278 1.049289 ATACCCGCCTCCTCAACTCC 61.049 60.000 0.00 0.00 0.00 3.85
1315 1341 1.056660 GTCTCCTTGACAAGACCCCA 58.943 55.000 16.99 0.00 44.73 4.96
1449 1480 2.049433 CGTTGTCGCTCCCGAAGT 60.049 61.111 0.00 0.00 46.34 3.01
1651 1682 2.660802 CCCACCACGACTACCACC 59.339 66.667 0.00 0.00 0.00 4.61
1657 1688 2.847234 TGCTTCCCCACCACGACT 60.847 61.111 0.00 0.00 0.00 4.18
1816 1851 3.080647 GGAGAGGCCGTAACATTGG 57.919 57.895 0.00 0.00 0.00 3.16
1971 2010 1.032794 TATCTGCAGCTAGTGACCCG 58.967 55.000 9.47 0.00 0.00 5.28
2047 2094 2.188994 GGGCGAGCAGAGATGCTT 59.811 61.111 3.97 0.00 46.36 3.91
2077 2124 1.108727 TGCCCTGCTTTTGACCAGTG 61.109 55.000 0.00 0.00 0.00 3.66
2080 2127 1.832167 GGTGCCCTGCTTTTGACCA 60.832 57.895 0.00 0.00 0.00 4.02
2097 2144 2.988010 TTCATTGATGGAGTCGAGGG 57.012 50.000 0.00 0.00 0.00 4.30
2196 2243 1.972795 ACGGTTGGCCAGACTTAGTTA 59.027 47.619 5.11 0.00 34.09 2.24
2197 2244 0.763035 ACGGTTGGCCAGACTTAGTT 59.237 50.000 5.11 0.00 34.09 2.24
2312 2359 3.532155 GATCGCGACTGGAGGCCT 61.532 66.667 12.93 3.86 0.00 5.19
2317 2364 3.838271 GGGCTGATCGCGACTGGA 61.838 66.667 12.93 0.00 40.44 3.86
2334 2381 1.823041 GAGTACGGGGAGGGAGACG 60.823 68.421 0.00 0.00 0.00 4.18
2341 2388 5.655488 GATTATGATGATGAGTACGGGGAG 58.345 45.833 0.00 0.00 0.00 4.30
2345 2392 5.573282 GGAACGATTATGATGATGAGTACGG 59.427 44.000 0.00 0.00 0.00 4.02
2346 2393 6.088217 GTGGAACGATTATGATGATGAGTACG 59.912 42.308 0.00 0.00 0.00 3.67
2448 2502 2.124695 GGGATGGTTCTGGCGACC 60.125 66.667 0.00 0.00 37.69 4.79
2465 2519 0.405585 ATCTTCAACCCACCCACCAG 59.594 55.000 0.00 0.00 0.00 4.00
2466 2520 1.748732 TATCTTCAACCCACCCACCA 58.251 50.000 0.00 0.00 0.00 4.17
2467 2521 4.724279 ATATATCTTCAACCCACCCACC 57.276 45.455 0.00 0.00 0.00 4.61
2469 2523 7.185565 TCAAAAATATATCTTCAACCCACCCA 58.814 34.615 0.00 0.00 0.00 4.51
2470 2524 7.654022 TCAAAAATATATCTTCAACCCACCC 57.346 36.000 0.00 0.00 0.00 4.61
2492 2546 8.175069 GCATCTACGTTTATTTGATGTTCTTCA 58.825 33.333 0.00 0.00 37.44 3.02
2493 2547 8.175069 TGCATCTACGTTTATTTGATGTTCTTC 58.825 33.333 0.00 0.00 37.44 2.87
2494 2548 7.962918 GTGCATCTACGTTTATTTGATGTTCTT 59.037 33.333 0.00 0.00 37.44 2.52
2495 2549 7.414098 GGTGCATCTACGTTTATTTGATGTTCT 60.414 37.037 0.00 0.00 37.44 3.01
2496 2550 6.687105 GGTGCATCTACGTTTATTTGATGTTC 59.313 38.462 0.00 0.00 37.44 3.18
2497 2551 6.404293 GGGTGCATCTACGTTTATTTGATGTT 60.404 38.462 0.00 0.00 37.44 2.71
2498 2552 5.065988 GGGTGCATCTACGTTTATTTGATGT 59.934 40.000 0.00 0.00 37.44 3.06
2499 2553 5.065859 TGGGTGCATCTACGTTTATTTGATG 59.934 40.000 0.00 0.44 37.96 3.07
2500 2554 5.189928 TGGGTGCATCTACGTTTATTTGAT 58.810 37.500 0.00 0.00 0.00 2.57
2501 2555 4.580868 TGGGTGCATCTACGTTTATTTGA 58.419 39.130 0.00 0.00 0.00 2.69
2502 2556 4.955925 TGGGTGCATCTACGTTTATTTG 57.044 40.909 0.00 0.00 0.00 2.32
2503 2557 4.947388 ACATGGGTGCATCTACGTTTATTT 59.053 37.500 0.00 0.00 0.00 1.40
2504 2558 4.523083 ACATGGGTGCATCTACGTTTATT 58.477 39.130 0.00 0.00 0.00 1.40
2505 2559 4.150897 ACATGGGTGCATCTACGTTTAT 57.849 40.909 0.00 0.00 0.00 1.40
2506 2560 3.620427 ACATGGGTGCATCTACGTTTA 57.380 42.857 0.00 0.00 0.00 2.01
2507 2561 2.489938 ACATGGGTGCATCTACGTTT 57.510 45.000 0.00 0.00 0.00 3.60
2508 2562 3.466836 CATACATGGGTGCATCTACGTT 58.533 45.455 0.00 0.00 0.00 3.99
2509 2563 2.806745 GCATACATGGGTGCATCTACGT 60.807 50.000 16.72 0.00 40.94 3.57
2510 2564 1.800586 GCATACATGGGTGCATCTACG 59.199 52.381 16.72 0.00 40.94 3.51
2511 2565 2.849942 TGCATACATGGGTGCATCTAC 58.150 47.619 19.40 0.00 45.60 2.59
2517 2571 3.304928 GCTAATCTTGCATACATGGGTGC 60.305 47.826 15.27 15.27 41.61 5.01
2518 2572 3.058708 CGCTAATCTTGCATACATGGGTG 60.059 47.826 0.00 0.00 0.00 4.61
2519 2573 3.141398 CGCTAATCTTGCATACATGGGT 58.859 45.455 0.00 0.00 0.00 4.51
2520 2574 3.058708 CACGCTAATCTTGCATACATGGG 60.059 47.826 0.00 0.00 0.00 4.00
2521 2575 3.809279 TCACGCTAATCTTGCATACATGG 59.191 43.478 0.00 0.00 0.00 3.66
2522 2576 4.509230 AGTCACGCTAATCTTGCATACATG 59.491 41.667 0.00 0.00 0.00 3.21
2523 2577 4.697514 AGTCACGCTAATCTTGCATACAT 58.302 39.130 0.00 0.00 0.00 2.29
2524 2578 4.123497 AGTCACGCTAATCTTGCATACA 57.877 40.909 0.00 0.00 0.00 2.29
2525 2579 4.025647 GGAAGTCACGCTAATCTTGCATAC 60.026 45.833 0.00 0.00 0.00 2.39
2526 2580 4.119862 GGAAGTCACGCTAATCTTGCATA 58.880 43.478 0.00 0.00 0.00 3.14
2527 2581 2.939103 GGAAGTCACGCTAATCTTGCAT 59.061 45.455 0.00 0.00 0.00 3.96
2528 2582 2.028112 AGGAAGTCACGCTAATCTTGCA 60.028 45.455 0.00 0.00 32.25 4.08
2529 2583 2.622436 AGGAAGTCACGCTAATCTTGC 58.378 47.619 0.00 0.00 0.00 4.01
2530 2584 5.651530 TCTAAGGAAGTCACGCTAATCTTG 58.348 41.667 0.00 0.00 0.00 3.02
2531 2585 5.916661 TCTAAGGAAGTCACGCTAATCTT 57.083 39.130 0.00 0.00 0.00 2.40
2532 2586 5.737635 GCATCTAAGGAAGTCACGCTAATCT 60.738 44.000 0.00 0.00 0.00 2.40
2533 2587 4.446051 GCATCTAAGGAAGTCACGCTAATC 59.554 45.833 0.00 0.00 0.00 1.75
2534 2588 4.141937 TGCATCTAAGGAAGTCACGCTAAT 60.142 41.667 0.00 0.00 0.00 1.73
2535 2589 3.194755 TGCATCTAAGGAAGTCACGCTAA 59.805 43.478 0.00 0.00 0.00 3.09
2536 2590 2.758423 TGCATCTAAGGAAGTCACGCTA 59.242 45.455 0.00 0.00 0.00 4.26
2537 2591 1.550524 TGCATCTAAGGAAGTCACGCT 59.449 47.619 0.00 0.00 0.00 5.07
2538 2592 1.661112 GTGCATCTAAGGAAGTCACGC 59.339 52.381 0.00 0.00 0.00 5.34
2539 2593 3.182967 GAGTGCATCTAAGGAAGTCACG 58.817 50.000 0.00 0.00 0.00 4.35
2540 2594 4.193826 TGAGTGCATCTAAGGAAGTCAC 57.806 45.455 0.00 0.00 0.00 3.67
2541 2595 6.737720 ATATGAGTGCATCTAAGGAAGTCA 57.262 37.500 0.00 0.00 35.94 3.41
2542 2596 7.661968 TGTATATGAGTGCATCTAAGGAAGTC 58.338 38.462 0.00 0.00 35.94 3.01
2543 2597 7.603180 TGTATATGAGTGCATCTAAGGAAGT 57.397 36.000 0.00 0.00 35.94 3.01
2545 2599 9.929180 GTATTGTATATGAGTGCATCTAAGGAA 57.071 33.333 0.00 0.00 35.94 3.36
2546 2600 9.314133 AGTATTGTATATGAGTGCATCTAAGGA 57.686 33.333 0.00 0.00 35.94 3.36
2547 2601 9.579768 GAGTATTGTATATGAGTGCATCTAAGG 57.420 37.037 0.00 0.00 35.94 2.69
2548 2602 9.579768 GGAGTATTGTATATGAGTGCATCTAAG 57.420 37.037 0.00 0.00 35.94 2.18
2549 2603 8.531982 GGGAGTATTGTATATGAGTGCATCTAA 58.468 37.037 0.00 0.00 35.94 2.10
2550 2604 7.895962 AGGGAGTATTGTATATGAGTGCATCTA 59.104 37.037 0.00 0.00 35.94 1.98
2551 2605 6.728164 AGGGAGTATTGTATATGAGTGCATCT 59.272 38.462 0.00 0.00 35.94 2.90
2552 2606 6.940739 AGGGAGTATTGTATATGAGTGCATC 58.059 40.000 0.00 0.00 35.94 3.91
2553 2607 6.498303 TGAGGGAGTATTGTATATGAGTGCAT 59.502 38.462 0.00 0.00 38.54 3.96
2554 2608 5.838521 TGAGGGAGTATTGTATATGAGTGCA 59.161 40.000 0.00 0.00 0.00 4.57
2555 2609 6.346477 TGAGGGAGTATTGTATATGAGTGC 57.654 41.667 0.00 0.00 0.00 4.40
2556 2610 8.037758 GGATTGAGGGAGTATTGTATATGAGTG 58.962 40.741 0.00 0.00 0.00 3.51
2557 2611 7.181125 GGGATTGAGGGAGTATTGTATATGAGT 59.819 40.741 0.00 0.00 0.00 3.41
2558 2612 7.180946 TGGGATTGAGGGAGTATTGTATATGAG 59.819 40.741 0.00 0.00 0.00 2.90
2559 2613 7.022496 TGGGATTGAGGGAGTATTGTATATGA 58.978 38.462 0.00 0.00 0.00 2.15
2560 2614 7.180946 TCTGGGATTGAGGGAGTATTGTATATG 59.819 40.741 0.00 0.00 0.00 1.78
2561 2615 7.256399 TCTGGGATTGAGGGAGTATTGTATAT 58.744 38.462 0.00 0.00 0.00 0.86
2562 2616 6.630131 TCTGGGATTGAGGGAGTATTGTATA 58.370 40.000 0.00 0.00 0.00 1.47
2563 2617 5.476983 TCTGGGATTGAGGGAGTATTGTAT 58.523 41.667 0.00 0.00 0.00 2.29
2564 2618 4.890988 TCTGGGATTGAGGGAGTATTGTA 58.109 43.478 0.00 0.00 0.00 2.41
2565 2619 3.736094 TCTGGGATTGAGGGAGTATTGT 58.264 45.455 0.00 0.00 0.00 2.71
2566 2620 4.989875 ATCTGGGATTGAGGGAGTATTG 57.010 45.455 0.00 0.00 0.00 1.90
2567 2621 7.654287 AATAATCTGGGATTGAGGGAGTATT 57.346 36.000 3.37 0.00 0.00 1.89
2568 2622 7.074237 ACAAATAATCTGGGATTGAGGGAGTAT 59.926 37.037 3.37 0.00 0.00 2.12
2569 2623 6.389869 ACAAATAATCTGGGATTGAGGGAGTA 59.610 38.462 3.37 0.00 0.00 2.59
2570 2624 5.194537 ACAAATAATCTGGGATTGAGGGAGT 59.805 40.000 3.37 0.00 0.00 3.85
2571 2625 5.699143 ACAAATAATCTGGGATTGAGGGAG 58.301 41.667 3.37 0.00 0.00 4.30
2572 2626 5.732331 ACAAATAATCTGGGATTGAGGGA 57.268 39.130 3.37 0.00 0.00 4.20
2573 2627 5.452356 GCAACAAATAATCTGGGATTGAGGG 60.452 44.000 3.37 0.00 0.00 4.30
2574 2628 5.594926 GCAACAAATAATCTGGGATTGAGG 58.405 41.667 3.37 0.00 0.00 3.86
2575 2629 5.276270 CGCAACAAATAATCTGGGATTGAG 58.724 41.667 3.37 0.00 0.00 3.02
2576 2630 4.097741 CCGCAACAAATAATCTGGGATTGA 59.902 41.667 3.37 0.00 0.00 2.57
2577 2631 4.097741 TCCGCAACAAATAATCTGGGATTG 59.902 41.667 3.37 0.00 0.00 2.67
2578 2632 4.277476 TCCGCAACAAATAATCTGGGATT 58.723 39.130 0.00 0.00 0.00 3.01
2579 2633 3.897239 TCCGCAACAAATAATCTGGGAT 58.103 40.909 0.00 0.00 0.00 3.85
2580 2634 3.358111 TCCGCAACAAATAATCTGGGA 57.642 42.857 0.00 0.00 0.00 4.37
2581 2635 4.448537 TTTCCGCAACAAATAATCTGGG 57.551 40.909 0.00 0.00 0.00 4.45
2582 2636 4.805192 CCATTTCCGCAACAAATAATCTGG 59.195 41.667 0.00 0.00 0.00 3.86
2583 2637 5.649557 TCCATTTCCGCAACAAATAATCTG 58.350 37.500 0.00 0.00 0.00 2.90
2584 2638 5.913137 TCCATTTCCGCAACAAATAATCT 57.087 34.783 0.00 0.00 0.00 2.40
2585 2639 7.648142 TCTATCCATTTCCGCAACAAATAATC 58.352 34.615 0.00 0.00 0.00 1.75
2586 2640 7.581213 TCTATCCATTTCCGCAACAAATAAT 57.419 32.000 0.00 0.00 0.00 1.28
2587 2641 7.397892 TTCTATCCATTTCCGCAACAAATAA 57.602 32.000 0.00 0.00 0.00 1.40
2588 2642 7.397892 TTTCTATCCATTTCCGCAACAAATA 57.602 32.000 0.00 0.00 0.00 1.40
2589 2643 5.913137 TTCTATCCATTTCCGCAACAAAT 57.087 34.783 0.00 0.00 0.00 2.32
2590 2644 5.713792 TTTCTATCCATTTCCGCAACAAA 57.286 34.783 0.00 0.00 0.00 2.83
2591 2645 5.913137 ATTTCTATCCATTTCCGCAACAA 57.087 34.783 0.00 0.00 0.00 2.83
2592 2646 5.417266 TCAATTTCTATCCATTTCCGCAACA 59.583 36.000 0.00 0.00 0.00 3.33
2593 2647 5.890334 TCAATTTCTATCCATTTCCGCAAC 58.110 37.500 0.00 0.00 0.00 4.17
2594 2648 6.096705 ACATCAATTTCTATCCATTTCCGCAA 59.903 34.615 0.00 0.00 0.00 4.85
2595 2649 5.593909 ACATCAATTTCTATCCATTTCCGCA 59.406 36.000 0.00 0.00 0.00 5.69
2596 2650 6.076981 ACATCAATTTCTATCCATTTCCGC 57.923 37.500 0.00 0.00 0.00 5.54
2633 2687 8.922676 CGTGGTAATTTTATAGCTCGACATATT 58.077 33.333 0.00 0.00 40.62 1.28
2634 2688 8.301720 TCGTGGTAATTTTATAGCTCGACATAT 58.698 33.333 0.00 0.00 41.45 1.78
2635 2689 7.650890 TCGTGGTAATTTTATAGCTCGACATA 58.349 34.615 0.00 0.00 41.45 2.29
2636 2690 6.509656 TCGTGGTAATTTTATAGCTCGACAT 58.490 36.000 0.00 0.00 41.45 3.06
2637 2691 5.893687 TCGTGGTAATTTTATAGCTCGACA 58.106 37.500 0.00 0.00 41.45 4.35
2639 2693 6.140303 AGTCGTGGTAATTTTATAGCTCGA 57.860 37.500 0.00 6.59 42.98 4.04
2640 2694 6.823678 AAGTCGTGGTAATTTTATAGCTCG 57.176 37.500 0.00 0.00 39.95 5.03
2641 2695 7.494952 AGGAAAGTCGTGGTAATTTTATAGCTC 59.505 37.037 0.00 0.00 0.00 4.09
2642 2696 7.336396 AGGAAAGTCGTGGTAATTTTATAGCT 58.664 34.615 0.00 0.00 0.00 3.32
2643 2697 7.549615 AGGAAAGTCGTGGTAATTTTATAGC 57.450 36.000 0.00 0.00 0.00 2.97
2646 2700 8.537858 ACTCTAGGAAAGTCGTGGTAATTTTAT 58.462 33.333 0.00 0.00 0.00 1.40
2647 2701 7.899973 ACTCTAGGAAAGTCGTGGTAATTTTA 58.100 34.615 0.00 0.00 0.00 1.52
2648 2702 6.766429 ACTCTAGGAAAGTCGTGGTAATTTT 58.234 36.000 0.00 0.00 0.00 1.82
2649 2703 6.356186 ACTCTAGGAAAGTCGTGGTAATTT 57.644 37.500 0.00 0.00 0.00 1.82
2650 2704 5.997384 ACTCTAGGAAAGTCGTGGTAATT 57.003 39.130 0.00 0.00 0.00 1.40
2651 2705 5.997384 AACTCTAGGAAAGTCGTGGTAAT 57.003 39.130 0.00 0.00 0.00 1.89
2652 2706 5.796424 AAACTCTAGGAAAGTCGTGGTAA 57.204 39.130 0.00 0.00 0.00 2.85
2653 2707 7.472334 AATAAACTCTAGGAAAGTCGTGGTA 57.528 36.000 0.00 0.00 0.00 3.25
2654 2708 5.997384 ATAAACTCTAGGAAAGTCGTGGT 57.003 39.130 0.00 0.00 0.00 4.16
2689 2743 2.095364 AGCTCGTGTAAGAGTAACCGTG 60.095 50.000 0.00 0.00 40.26 4.94
2692 2746 4.167268 CTGAAGCTCGTGTAAGAGTAACC 58.833 47.826 0.00 0.00 40.26 2.85
2698 2752 4.841443 TTACACTGAAGCTCGTGTAAGA 57.159 40.909 22.18 9.95 46.06 2.10
2705 2759 2.480037 TGCACATTTACACTGAAGCTCG 59.520 45.455 0.00 0.00 0.00 5.03
2714 2768 0.179202 TCGCGCATGCACATTTACAC 60.179 50.000 19.57 0.00 42.97 2.90
2715 2769 0.731994 ATCGCGCATGCACATTTACA 59.268 45.000 19.57 0.00 42.97 2.41
2780 2837 1.295423 CCTTCACGTCCACCGGATT 59.705 57.895 9.46 0.00 42.24 3.01
2885 2942 1.815003 GCTTATTCACTTGCTGCCTGT 59.185 47.619 0.00 0.00 0.00 4.00
2886 2943 2.089980 AGCTTATTCACTTGCTGCCTG 58.910 47.619 0.00 0.00 34.19 4.85
2889 2946 3.376546 AGCTTAGCTTATTCACTTGCTGC 59.623 43.478 0.00 0.00 33.89 5.25
2890 2947 5.236047 CCTAGCTTAGCTTATTCACTTGCTG 59.764 44.000 13.44 0.00 40.44 4.41
2891 2948 5.363939 CCTAGCTTAGCTTATTCACTTGCT 58.636 41.667 13.44 0.00 40.44 3.91
2922 2983 5.390251 GGCGATGTATTCAAGCATGTAGATG 60.390 44.000 0.00 0.00 34.59 2.90
2933 2998 2.963548 TACACGGGCGATGTATTCAA 57.036 45.000 0.00 0.00 0.00 2.69
2945 3010 4.314961 TGCTGCTTCATATATTACACGGG 58.685 43.478 0.00 0.00 0.00 5.28
3101 3168 3.735746 ACGTCGTGATATATGCACACATG 59.264 43.478 0.00 0.00 37.04 3.21
3199 3266 4.290093 TCTGGTCCATACAACTAGCATCT 58.710 43.478 0.00 0.00 0.00 2.90
3272 3339 4.705023 GGGCTGTGTGTAAAATACCATCTT 59.295 41.667 0.00 0.00 0.00 2.40
3296 3364 7.889073 TGGTTTTGTATTACATGTTAGGCCTAA 59.111 33.333 21.68 21.68 0.00 2.69
3316 3384 5.163045 TGGAAATAAGGGGCAAAATGGTTTT 60.163 36.000 0.00 0.00 0.00 2.43
3317 3385 4.352298 TGGAAATAAGGGGCAAAATGGTTT 59.648 37.500 0.00 0.00 0.00 3.27
3318 3386 3.913163 TGGAAATAAGGGGCAAAATGGTT 59.087 39.130 0.00 0.00 0.00 3.67
3319 3387 3.263170 GTGGAAATAAGGGGCAAAATGGT 59.737 43.478 0.00 0.00 0.00 3.55
3320 3388 3.519107 AGTGGAAATAAGGGGCAAAATGG 59.481 43.478 0.00 0.00 0.00 3.16
3321 3389 4.824479 AGTGGAAATAAGGGGCAAAATG 57.176 40.909 0.00 0.00 0.00 2.32
3322 3390 4.225042 GGAAGTGGAAATAAGGGGCAAAAT 59.775 41.667 0.00 0.00 0.00 1.82
3323 3391 3.580895 GGAAGTGGAAATAAGGGGCAAAA 59.419 43.478 0.00 0.00 0.00 2.44
3419 3487 7.507616 TCCAGCTAGTTTTCCCTTTTAAAATGA 59.492 33.333 0.09 0.00 0.00 2.57
3425 3493 5.185056 GCATTCCAGCTAGTTTTCCCTTTTA 59.815 40.000 0.00 0.00 0.00 1.52
3431 3499 1.751351 GGGCATTCCAGCTAGTTTTCC 59.249 52.381 0.00 0.00 35.00 3.13
3530 3598 1.377202 GATGCGGGCAGTTTGAGGA 60.377 57.895 0.00 0.00 0.00 3.71
3553 3621 1.069090 GTTCAGACCGCACAGTCCA 59.931 57.895 0.00 0.00 37.49 4.02
3595 3663 7.177568 AGGGTGATGCAGTATAGTAACAGATAG 59.822 40.741 0.00 0.00 0.00 2.08
3612 3680 2.386661 TCGAAGAGAAAGGGTGATGC 57.613 50.000 0.00 0.00 0.00 3.91
3631 3699 6.006449 ACTTGTGATAGCTGTTGGATTTCTT 58.994 36.000 0.00 0.00 0.00 2.52
3639 3707 4.452114 TGTTGCTACTTGTGATAGCTGTTG 59.548 41.667 0.00 0.00 44.52 3.33
3682 3750 3.077359 CAAGAACAAGGGGAGTGATGAC 58.923 50.000 0.00 0.00 0.00 3.06
3788 3856 4.038080 CACCGCGGGAGGCAAAAC 62.038 66.667 31.76 0.00 43.84 2.43
3798 3866 2.580589 CAATTTTGTAAGTCACCGCGG 58.419 47.619 26.86 26.86 0.00 6.46
3801 3869 3.243234 TGGTGCAATTTTGTAAGTCACCG 60.243 43.478 10.45 0.00 43.84 4.94
3802 3870 4.298332 CTGGTGCAATTTTGTAAGTCACC 58.702 43.478 8.99 8.99 41.93 4.02
3819 3887 3.812053 GAGCCTATAATCACTTGCTGGTG 59.188 47.826 0.00 3.78 38.44 4.17
3823 3891 4.712476 CTTGGAGCCTATAATCACTTGCT 58.288 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.