Multiple sequence alignment - TraesCS6A01G274100

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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 TraesCS6A01G274100 chr6A 100.000 2540 0 0 1 2540 500504159 500506698 0.000000e+00 4691
1 TraesCS6A01G274100 chr6A 88.506 87 9 1 2412 2498 4415713 4415628 1.240000e-18 104
2 TraesCS6A01G274100 chr6D 91.796 2389 87 37 1 2331 358975520 358977857 0.000000e+00 3225
3 TraesCS6A01G274100 chr6B 91.053 2470 84 42 1 2400 540589582 540591984 0.000000e+00 3210
4 TraesCS6A01G274100 chr6B 91.719 1582 74 23 851 2400 560198793 560197237 0.000000e+00 2143
5 TraesCS6A01G274100 chr6B 94.649 598 14 6 1 589 560199435 560198847 0.000000e+00 911
6 TraesCS6A01G274100 chr6B 100.000 53 0 0 784 836 560198834 560198782 5.780000e-17 99
7 TraesCS6A01G274100 chr1D 91.954 87 6 1 2412 2498 402722724 402722639 1.230000e-23 121
8 TraesCS6A01G274100 chr1D 90.698 86 7 1 2413 2498 58438871 58438787 2.070000e-21 113
9 TraesCS6A01G274100 chr5B 90.805 87 7 1 2413 2499 375770588 375770503 5.740000e-22 115
10 TraesCS6A01G274100 chr2B 89.412 85 8 1 2413 2497 7854976 7855059 3.460000e-19 106
11 TraesCS6A01G274100 chr2B 85.714 98 12 2 2409 2505 607246140 607246236 4.470000e-18 102
12 TraesCS6A01G274100 chr2D 88.506 87 9 1 2412 2498 538943422 538943507 1.240000e-18 104
13 TraesCS6A01G274100 chr2D 87.356 87 9 2 2413 2498 99658208 99658123 5.780000e-17 99
14 TraesCS6A01G274100 chr4A 87.640 89 9 2 2413 2501 732377055 732377141 4.470000e-18 102


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 TraesCS6A01G274100 chr6A 500504159 500506698 2539 False 4691 4691 100.000 1 2540 1 chr6A.!!$F1 2539
1 TraesCS6A01G274100 chr6D 358975520 358977857 2337 False 3225 3225 91.796 1 2331 1 chr6D.!!$F1 2330
2 TraesCS6A01G274100 chr6B 540589582 540591984 2402 False 3210 3210 91.053 1 2400 1 chr6B.!!$F1 2399
3 TraesCS6A01G274100 chr6B 560197237 560199435 2198 True 1051 2143 95.456 1 2400 3 chr6B.!!$R1 2399

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
597 656 0.457509 CAGCACAGTAGAGCGTGAGG 60.458 60.0 0.0 0.0 36.39 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2528 0.255318 ACGAGACGGAGGGAGTACAT 59.745 55.0 0.0 0.0 0.0 2.29 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
21 22 1.134699 CAGGCTGGCGTAATCTGAAGA 60.135 52.381 6.61 0.00 0.00 2.87
110 111 0.877649 CCATCCGTCGAGCATTCCTG 60.878 60.000 0.00 0.00 0.00 3.86
199 206 1.135315 CGTTGCTACGTACCTAGGCAA 60.135 52.381 9.30 13.34 42.72 4.52
319 328 2.189594 AACCAAACCCTACGCCTAAC 57.810 50.000 0.00 0.00 0.00 2.34
341 350 2.766313 TGTCACCTCACGGAATTTGAG 58.234 47.619 0.00 0.00 40.30 3.02
483 494 1.524002 CGATGTGATGTCCCTGCCT 59.476 57.895 0.00 0.00 0.00 4.75
484 495 0.812811 CGATGTGATGTCCCTGCCTG 60.813 60.000 0.00 0.00 0.00 4.85
485 496 1.077212 ATGTGATGTCCCTGCCTGC 60.077 57.895 0.00 0.00 0.00 4.85
486 497 1.569030 ATGTGATGTCCCTGCCTGCT 61.569 55.000 0.00 0.00 0.00 4.24
487 498 1.451028 GTGATGTCCCTGCCTGCTC 60.451 63.158 0.00 0.00 0.00 4.26
488 499 2.191641 GATGTCCCTGCCTGCTCC 59.808 66.667 0.00 0.00 0.00 4.70
489 500 2.285969 ATGTCCCTGCCTGCTCCT 60.286 61.111 0.00 0.00 0.00 3.69
490 501 2.605854 GATGTCCCTGCCTGCTCCTG 62.606 65.000 0.00 0.00 0.00 3.86
491 502 4.792804 GTCCCTGCCTGCTCCTGC 62.793 72.222 0.00 0.00 40.20 4.85
493 504 4.486503 CCCTGCCTGCTCCTGCTC 62.487 72.222 0.00 0.00 40.48 4.26
494 505 4.834453 CCTGCCTGCTCCTGCTCG 62.834 72.222 0.00 0.00 40.48 5.03
503 524 4.447989 TCCTGCTCGCTGCTGCTC 62.448 66.667 14.03 3.53 43.37 4.26
538 559 2.623535 TGCTTTGATCCAATGCAATGC 58.376 42.857 14.94 0.00 46.30 3.56
539 560 2.028020 TGCTTTGATCCAATGCAATGCA 60.028 40.909 11.44 11.44 46.30 3.96
540 561 3.004171 GCTTTGATCCAATGCAATGCAA 58.996 40.909 13.45 0.00 43.62 4.08
583 630 3.285215 AGCAGCACAGCACAGCAC 61.285 61.111 0.00 0.00 36.85 4.40
584 631 3.588906 GCAGCACAGCACAGCACA 61.589 61.111 0.00 0.00 0.00 4.57
585 632 2.637589 CAGCACAGCACAGCACAG 59.362 61.111 0.00 0.00 0.00 3.66
586 633 2.184830 CAGCACAGCACAGCACAGT 61.185 57.895 0.00 0.00 0.00 3.55
597 656 0.457509 CAGCACAGTAGAGCGTGAGG 60.458 60.000 0.00 0.00 36.39 3.86
839 917 2.901813 CCTCTGCCTCTGCCTCTG 59.098 66.667 0.00 0.00 36.33 3.35
840 918 2.187424 CTCTGCCTCTGCCTCTGC 59.813 66.667 0.00 0.00 36.33 4.26
841 919 3.388703 CTCTGCCTCTGCCTCTGCC 62.389 68.421 0.00 0.00 36.33 4.85
842 920 4.486503 CTGCCTCTGCCTCTGCCC 62.487 72.222 0.00 0.00 36.33 5.36
851 929 4.247380 CCTCTGCCCCGCTCCATC 62.247 72.222 0.00 0.00 0.00 3.51
852 930 3.160047 CTCTGCCCCGCTCCATCT 61.160 66.667 0.00 0.00 0.00 2.90
853 931 3.457625 CTCTGCCCCGCTCCATCTG 62.458 68.421 0.00 0.00 0.00 2.90
857 935 4.247380 CCCCGCTCCATCTGCCTC 62.247 72.222 0.00 0.00 0.00 4.70
858 936 3.160047 CCCGCTCCATCTGCCTCT 61.160 66.667 0.00 0.00 0.00 3.69
1131 1209 2.010582 GCGTCATCTCCTTCCTCGCT 62.011 60.000 0.00 0.00 39.26 4.93
1215 1293 0.898789 ACCAGCACTACTACGGCACT 60.899 55.000 0.00 0.00 0.00 4.40
1219 1297 2.094906 CAGCACTACTACGGCACTAACA 60.095 50.000 0.00 0.00 0.00 2.41
1224 1302 0.038892 ACTACGGCACTAACACGGTG 60.039 55.000 6.58 6.58 37.70 4.94
1287 1365 4.845580 AAGCCCATGCCGAGCTCG 62.846 66.667 29.06 29.06 38.69 5.03
1416 1494 2.981909 CAGCAGCACCACCACCAG 60.982 66.667 0.00 0.00 0.00 4.00
1553 1631 4.701765 GGTTCATGATCATCACAGTAGCT 58.298 43.478 4.86 0.00 0.00 3.32
1561 1639 6.711277 TGATCATCACAGTAGCTTTTAGGTT 58.289 36.000 0.00 0.00 0.00 3.50
1562 1640 6.818644 TGATCATCACAGTAGCTTTTAGGTTC 59.181 38.462 0.00 0.00 0.00 3.62
1563 1641 6.109156 TCATCACAGTAGCTTTTAGGTTCA 57.891 37.500 0.00 0.00 0.00 3.18
1653 1732 1.347097 CCATCGGCGATCATAGCGTG 61.347 60.000 21.25 7.70 35.00 5.34
1799 1879 1.136147 GGCTGCACGAAAGCATCAG 59.864 57.895 0.50 0.00 44.68 2.90
1865 1945 1.517257 GATGACTGGACACTCGGCG 60.517 63.158 0.00 0.00 0.00 6.46
1922 2002 0.593773 CCCTGCAACGAAAAACACCG 60.594 55.000 0.00 0.00 0.00 4.94
1923 2003 0.378962 CCTGCAACGAAAAACACCGA 59.621 50.000 0.00 0.00 0.00 4.69
1957 2037 1.664302 GCGGAAGTTCTGCTTTGCTTC 60.664 52.381 26.28 0.00 45.06 3.86
1982 2062 4.098349 CCCACAAGAATGGACCACAATATG 59.902 45.833 0.00 0.00 43.02 1.78
2059 2150 6.983307 TCAGAAGAAGAATCTAAGCTGCATAC 59.017 38.462 1.02 0.00 33.77 2.39
2063 2154 7.928307 AGAAGAATCTAAGCTGCATACAAAA 57.072 32.000 1.02 0.00 32.88 2.44
2064 2155 8.517062 AGAAGAATCTAAGCTGCATACAAAAT 57.483 30.769 1.02 0.00 32.88 1.82
2065 2156 9.618890 AGAAGAATCTAAGCTGCATACAAAATA 57.381 29.630 1.02 0.00 32.88 1.40
2149 2262 6.327279 CATCATAAGGATGCATTCACACAT 57.673 37.500 7.96 0.00 46.35 3.21
2208 2324 2.109425 AGATAAAACCCTCACACGCC 57.891 50.000 0.00 0.00 0.00 5.68
2264 2383 4.970662 ATTCGCATTTGTCACAGCTATT 57.029 36.364 0.00 0.00 0.00 1.73
2267 2386 3.871006 TCGCATTTGTCACAGCTATTAGG 59.129 43.478 0.00 0.00 0.00 2.69
2333 2452 7.171678 AGACTTCACCATTTCTCGAAACTAAAG 59.828 37.037 0.00 0.00 32.51 1.85
2400 2519 5.178797 AGGTGTTGCAGAGATGTAATGTAC 58.821 41.667 0.00 0.00 0.00 2.90
2401 2520 5.046304 AGGTGTTGCAGAGATGTAATGTACT 60.046 40.000 0.00 0.00 0.00 2.73
2402 2521 6.154534 AGGTGTTGCAGAGATGTAATGTACTA 59.845 38.462 0.00 0.00 0.00 1.82
2403 2522 6.477033 GGTGTTGCAGAGATGTAATGTACTAG 59.523 42.308 0.00 0.00 0.00 2.57
2404 2523 7.258441 GTGTTGCAGAGATGTAATGTACTAGA 58.742 38.462 0.00 0.00 0.00 2.43
2405 2524 7.923344 GTGTTGCAGAGATGTAATGTACTAGAT 59.077 37.037 0.00 0.00 0.00 1.98
2406 2525 7.922811 TGTTGCAGAGATGTAATGTACTAGATG 59.077 37.037 0.00 0.00 0.00 2.90
2407 2526 7.588497 TGCAGAGATGTAATGTACTAGATGT 57.412 36.000 0.00 0.00 0.00 3.06
2408 2527 8.691661 TGCAGAGATGTAATGTACTAGATGTA 57.308 34.615 0.00 0.00 0.00 2.29
2409 2528 9.131791 TGCAGAGATGTAATGTACTAGATGTAA 57.868 33.333 0.00 0.00 32.25 2.41
2420 2539 8.638629 ATGTACTAGATGTAATGTACTCCCTC 57.361 38.462 0.00 0.00 36.98 4.30
2421 2540 7.002879 TGTACTAGATGTAATGTACTCCCTCC 58.997 42.308 0.00 0.00 36.98 4.30
2422 2541 5.071370 ACTAGATGTAATGTACTCCCTCCG 58.929 45.833 0.00 0.00 0.00 4.63
2423 2542 3.912248 AGATGTAATGTACTCCCTCCGT 58.088 45.455 0.00 0.00 0.00 4.69
2424 2543 3.890147 AGATGTAATGTACTCCCTCCGTC 59.110 47.826 0.00 0.00 0.00 4.79
2425 2544 3.377253 TGTAATGTACTCCCTCCGTCT 57.623 47.619 0.00 0.00 0.00 4.18
2426 2545 3.285484 TGTAATGTACTCCCTCCGTCTC 58.715 50.000 0.00 0.00 0.00 3.36
2427 2546 1.390565 AATGTACTCCCTCCGTCTCG 58.609 55.000 0.00 0.00 0.00 4.04
2428 2547 0.255318 ATGTACTCCCTCCGTCTCGT 59.745 55.000 0.00 0.00 0.00 4.18
2429 2548 0.904649 TGTACTCCCTCCGTCTCGTA 59.095 55.000 0.00 0.00 0.00 3.43
2430 2549 1.278985 TGTACTCCCTCCGTCTCGTAA 59.721 52.381 0.00 0.00 0.00 3.18
2431 2550 2.092753 TGTACTCCCTCCGTCTCGTAAT 60.093 50.000 0.00 0.00 0.00 1.89
2432 2551 1.390565 ACTCCCTCCGTCTCGTAATG 58.609 55.000 0.00 0.00 0.00 1.90
2433 2552 1.340795 ACTCCCTCCGTCTCGTAATGT 60.341 52.381 0.00 0.00 0.00 2.71
2434 2553 2.092753 ACTCCCTCCGTCTCGTAATGTA 60.093 50.000 0.00 0.00 0.00 2.29
2435 2554 2.947652 CTCCCTCCGTCTCGTAATGTAA 59.052 50.000 0.00 0.00 0.00 2.41
2436 2555 3.355378 TCCCTCCGTCTCGTAATGTAAA 58.645 45.455 0.00 0.00 0.00 2.01
2437 2556 3.763360 TCCCTCCGTCTCGTAATGTAAAA 59.237 43.478 0.00 0.00 0.00 1.52
2438 2557 4.220382 TCCCTCCGTCTCGTAATGTAAAAA 59.780 41.667 0.00 0.00 0.00 1.94
2439 2558 4.328169 CCCTCCGTCTCGTAATGTAAAAAC 59.672 45.833 0.00 0.00 0.00 2.43
2440 2559 4.030977 CCTCCGTCTCGTAATGTAAAAACG 59.969 45.833 0.00 0.00 37.96 3.60
2441 2560 4.545610 TCCGTCTCGTAATGTAAAAACGT 58.454 39.130 0.00 0.00 37.83 3.99
2442 2561 4.981674 TCCGTCTCGTAATGTAAAAACGTT 59.018 37.500 0.00 0.00 37.83 3.99
2443 2562 5.461737 TCCGTCTCGTAATGTAAAAACGTTT 59.538 36.000 7.96 7.96 37.83 3.60
2444 2563 6.019156 TCCGTCTCGTAATGTAAAAACGTTTT 60.019 34.615 20.26 20.26 37.83 2.43
2445 2564 6.628461 CCGTCTCGTAATGTAAAAACGTTTTT 59.372 34.615 33.94 33.94 42.51 1.94
2471 2590 9.990360 TTGACACTACACTAGATTCAATAAACA 57.010 29.630 0.00 0.00 30.64 2.83
2491 2610 9.698309 ATAAACATCTTACATTATGAGACGGAG 57.302 33.333 0.00 0.00 0.00 4.63
2492 2611 6.090483 ACATCTTACATTATGAGACGGAGG 57.910 41.667 0.00 0.00 0.00 4.30
2493 2612 5.011125 ACATCTTACATTATGAGACGGAGGG 59.989 44.000 0.00 0.00 0.00 4.30
2494 2613 4.800023 TCTTACATTATGAGACGGAGGGA 58.200 43.478 0.00 0.00 0.00 4.20
2495 2614 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
2496 2615 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
2497 2616 4.180377 ACATTATGAGACGGAGGGAGTA 57.820 45.455 0.00 0.00 0.00 2.59
2498 2617 4.742012 ACATTATGAGACGGAGGGAGTAT 58.258 43.478 0.00 0.00 0.00 2.12
2499 2618 4.524714 ACATTATGAGACGGAGGGAGTATG 59.475 45.833 0.00 0.00 0.00 2.39
2500 2619 4.448720 TTATGAGACGGAGGGAGTATGA 57.551 45.455 0.00 0.00 0.00 2.15
2501 2620 2.054232 TGAGACGGAGGGAGTATGAC 57.946 55.000 0.00 0.00 0.00 3.06
2502 2621 1.283905 TGAGACGGAGGGAGTATGACA 59.716 52.381 0.00 0.00 0.00 3.58
2503 2622 1.950909 GAGACGGAGGGAGTATGACAG 59.049 57.143 0.00 0.00 0.00 3.51
2504 2623 1.564818 AGACGGAGGGAGTATGACAGA 59.435 52.381 0.00 0.00 0.00 3.41
2505 2624 2.025226 AGACGGAGGGAGTATGACAGAA 60.025 50.000 0.00 0.00 0.00 3.02
2506 2625 2.959707 GACGGAGGGAGTATGACAGAAT 59.040 50.000 0.00 0.00 0.00 2.40
2507 2626 3.375699 ACGGAGGGAGTATGACAGAATT 58.624 45.455 0.00 0.00 0.00 2.17
2508 2627 4.543689 ACGGAGGGAGTATGACAGAATTA 58.456 43.478 0.00 0.00 0.00 1.40
2509 2628 4.341520 ACGGAGGGAGTATGACAGAATTAC 59.658 45.833 0.00 0.00 0.00 1.89
2510 2629 4.556898 CGGAGGGAGTATGACAGAATTACG 60.557 50.000 0.00 0.00 0.00 3.18
2511 2630 4.341520 GGAGGGAGTATGACAGAATTACGT 59.658 45.833 0.00 0.00 0.00 3.57
2512 2631 5.507650 GGAGGGAGTATGACAGAATTACGTC 60.508 48.000 0.00 0.72 0.00 4.34
2513 2632 4.341520 AGGGAGTATGACAGAATTACGTCC 59.658 45.833 0.00 0.00 0.00 4.79
2514 2633 4.501058 GGGAGTATGACAGAATTACGTCCC 60.501 50.000 0.00 0.00 33.47 4.46
2515 2634 4.098960 GGAGTATGACAGAATTACGTCCCA 59.901 45.833 0.00 0.00 0.00 4.37
2516 2635 5.221461 GGAGTATGACAGAATTACGTCCCAT 60.221 44.000 0.00 0.00 0.00 4.00
2517 2636 5.844004 AGTATGACAGAATTACGTCCCATC 58.156 41.667 0.00 0.00 0.00 3.51
2518 2637 4.753516 ATGACAGAATTACGTCCCATCA 57.246 40.909 0.00 0.00 0.00 3.07
2519 2638 4.753516 TGACAGAATTACGTCCCATCAT 57.246 40.909 0.00 0.00 0.00 2.45
2520 2639 5.862678 TGACAGAATTACGTCCCATCATA 57.137 39.130 0.00 0.00 0.00 2.15
2521 2640 6.228616 TGACAGAATTACGTCCCATCATAA 57.771 37.500 0.00 0.00 0.00 1.90
2522 2641 6.645306 TGACAGAATTACGTCCCATCATAAA 58.355 36.000 0.00 0.00 0.00 1.40
2523 2642 7.279615 TGACAGAATTACGTCCCATCATAAAT 58.720 34.615 0.00 0.00 0.00 1.40
2524 2643 8.425703 TGACAGAATTACGTCCCATCATAAATA 58.574 33.333 0.00 0.00 0.00 1.40
2525 2644 9.436957 GACAGAATTACGTCCCATCATAAATAT 57.563 33.333 0.00 0.00 0.00 1.28
2532 2651 7.979786 ACGTCCCATCATAAATATATCTCCT 57.020 36.000 0.00 0.00 0.00 3.69
2534 2653 9.488762 ACGTCCCATCATAAATATATCTCCTAA 57.511 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.475280 TGAACGGCGTAATGTAGAGCT 59.525 47.619 15.20 0.00 0.00 4.09
110 111 3.918220 CGAGAAGCATGCGTCGCC 61.918 66.667 26.02 20.24 0.00 5.54
199 206 3.377172 GCGTGTAGGAGGCACAATAATTT 59.623 43.478 0.00 0.00 36.71 1.82
341 350 4.030306 CGATCTAAAACGCCTCGCATATAC 59.970 45.833 0.00 0.00 0.00 1.47
438 449 2.672195 GCTTCTTTGATTGCTTTCCCCG 60.672 50.000 0.00 0.00 0.00 5.73
503 524 3.188786 GCAACCGTAGCAGCGAGG 61.189 66.667 1.45 2.80 0.00 4.63
536 557 2.266554 CTTTTGCTTTTGGACGTTGCA 58.733 42.857 0.00 0.00 0.00 4.08
537 558 1.005032 GCTTTTGCTTTTGGACGTTGC 60.005 47.619 0.00 0.00 43.35 4.17
538 559 2.996691 GCTTTTGCTTTTGGACGTTG 57.003 45.000 0.00 0.00 43.35 4.10
583 630 2.103143 CGCCCTCACGCTCTACTG 59.897 66.667 0.00 0.00 0.00 2.74
584 631 2.045242 TCGCCCTCACGCTCTACT 60.045 61.111 0.00 0.00 0.00 2.57
585 632 2.409651 CTCGCCCTCACGCTCTAC 59.590 66.667 0.00 0.00 0.00 2.59
586 633 2.829003 CCTCGCCCTCACGCTCTA 60.829 66.667 0.00 0.00 0.00 2.43
610 669 1.374758 GGCACAACGTCTCCCTCAG 60.375 63.158 0.00 0.00 0.00 3.35
611 670 2.137528 TGGCACAACGTCTCCCTCA 61.138 57.895 0.00 0.00 31.92 3.86
674 751 1.594862 GAGATCTTTGAACGCATCGGG 59.405 52.381 0.00 0.00 0.00 5.14
729 806 4.672801 GCCCATCTTTTCACTCATTCGTTC 60.673 45.833 0.00 0.00 0.00 3.95
730 807 3.191371 GCCCATCTTTTCACTCATTCGTT 59.809 43.478 0.00 0.00 0.00 3.85
731 808 2.749621 GCCCATCTTTTCACTCATTCGT 59.250 45.455 0.00 0.00 0.00 3.85
732 809 2.223112 CGCCCATCTTTTCACTCATTCG 60.223 50.000 0.00 0.00 0.00 3.34
840 918 4.247380 GAGGCAGATGGAGCGGGG 62.247 72.222 0.00 0.00 0.00 5.73
841 919 3.160047 AGAGGCAGATGGAGCGGG 61.160 66.667 0.00 0.00 0.00 6.13
842 920 2.108566 CAGAGGCAGATGGAGCGG 59.891 66.667 0.00 0.00 0.00 5.52
843 921 2.588314 GCAGAGGCAGATGGAGCG 60.588 66.667 0.00 0.00 40.72 5.03
844 922 2.203181 GGCAGAGGCAGATGGAGC 60.203 66.667 0.00 0.00 43.71 4.70
845 923 2.509916 GGGCAGAGGCAGATGGAG 59.490 66.667 0.00 0.00 43.71 3.86
846 924 3.092511 GGGGCAGAGGCAGATGGA 61.093 66.667 0.00 0.00 43.71 3.41
847 925 4.559063 CGGGGCAGAGGCAGATGG 62.559 72.222 0.00 0.00 43.71 3.51
854 932 4.247380 GATGGAGCGGGGCAGAGG 62.247 72.222 0.00 0.00 0.00 3.69
855 933 1.475169 TATGATGGAGCGGGGCAGAG 61.475 60.000 0.00 0.00 0.00 3.35
856 934 1.053835 TTATGATGGAGCGGGGCAGA 61.054 55.000 0.00 0.00 0.00 4.26
857 935 0.179020 TTTATGATGGAGCGGGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
858 936 0.257328 TTTTATGATGGAGCGGGGCA 59.743 50.000 0.00 0.00 0.00 5.36
957 1035 1.226547 GCCTCTCGTGCTCTCGAAG 60.227 63.158 0.00 0.00 39.34 3.79
1098 1176 4.988598 ACGCCCAGCACGGTGAAG 62.989 66.667 13.29 2.70 36.85 3.02
1594 1673 3.710209 AAATGCCTAGCAGACACTCTT 57.290 42.857 0.00 0.00 43.65 2.85
1595 1674 3.772025 AGTAAATGCCTAGCAGACACTCT 59.228 43.478 0.00 0.00 43.65 3.24
1653 1732 5.050295 CCCAAAACTAGAGTGAAGAACGAAC 60.050 44.000 0.00 0.00 0.00 3.95
1799 1879 2.494918 CAGGACCCCATCGACGAC 59.505 66.667 0.00 0.00 0.00 4.34
1922 2002 1.787012 TCCGCTTGAACTAAACGGTC 58.213 50.000 0.00 0.00 44.17 4.79
1923 2003 2.140717 CTTCCGCTTGAACTAAACGGT 58.859 47.619 0.00 0.00 44.17 4.83
1943 2023 1.032014 TGGGTGAAGCAAAGCAGAAC 58.968 50.000 0.00 0.00 0.00 3.01
1957 2037 1.247567 GTGGTCCATTCTTGTGGGTG 58.752 55.000 0.00 0.00 39.80 4.61
2002 2086 1.078709 CACTGAACTATGCCGTGTGG 58.921 55.000 0.00 0.00 38.77 4.17
2208 2324 8.049721 ACCTAATCTTGTCTTTCCAGAATAAGG 58.950 37.037 0.00 0.00 31.11 2.69
2264 2383 2.419021 GCTACGTTTGCACCCATACCTA 60.419 50.000 0.00 0.00 0.00 3.08
2267 2386 1.444836 TGCTACGTTTGCACCCATAC 58.555 50.000 11.10 0.00 35.31 2.39
2378 2497 5.178797 AGTACATTACATCTCTGCAACACC 58.821 41.667 0.00 0.00 0.00 4.16
2400 2519 5.071370 ACGGAGGGAGTACATTACATCTAG 58.929 45.833 0.00 0.00 0.00 2.43
2401 2520 5.057843 ACGGAGGGAGTACATTACATCTA 57.942 43.478 0.00 0.00 0.00 1.98
2402 2521 3.890147 GACGGAGGGAGTACATTACATCT 59.110 47.826 0.00 0.00 0.00 2.90
2403 2522 3.890147 AGACGGAGGGAGTACATTACATC 59.110 47.826 0.00 0.00 0.00 3.06
2404 2523 3.890147 GAGACGGAGGGAGTACATTACAT 59.110 47.826 0.00 0.00 0.00 2.29
2405 2524 3.285484 GAGACGGAGGGAGTACATTACA 58.715 50.000 0.00 0.00 0.00 2.41
2406 2525 2.290093 CGAGACGGAGGGAGTACATTAC 59.710 54.545 0.00 0.00 0.00 1.89
2407 2526 2.092753 ACGAGACGGAGGGAGTACATTA 60.093 50.000 0.00 0.00 0.00 1.90
2408 2527 1.340795 ACGAGACGGAGGGAGTACATT 60.341 52.381 0.00 0.00 0.00 2.71
2409 2528 0.255318 ACGAGACGGAGGGAGTACAT 59.745 55.000 0.00 0.00 0.00 2.29
2410 2529 0.904649 TACGAGACGGAGGGAGTACA 59.095 55.000 0.00 0.00 0.00 2.90
2411 2530 2.029838 TTACGAGACGGAGGGAGTAC 57.970 55.000 0.00 0.00 0.00 2.73
2412 2531 2.092753 ACATTACGAGACGGAGGGAGTA 60.093 50.000 0.00 0.00 0.00 2.59
2413 2532 1.340795 ACATTACGAGACGGAGGGAGT 60.341 52.381 0.00 0.00 0.00 3.85
2414 2533 1.390565 ACATTACGAGACGGAGGGAG 58.609 55.000 0.00 0.00 0.00 4.30
2415 2534 2.715749 TACATTACGAGACGGAGGGA 57.284 50.000 0.00 0.00 0.00 4.20
2416 2535 3.788333 TTTACATTACGAGACGGAGGG 57.212 47.619 0.00 0.00 0.00 4.30
2417 2536 4.030977 CGTTTTTACATTACGAGACGGAGG 59.969 45.833 0.00 0.00 37.47 4.30
2418 2537 4.618489 ACGTTTTTACATTACGAGACGGAG 59.382 41.667 0.00 0.00 38.56 4.63
2419 2538 4.545610 ACGTTTTTACATTACGAGACGGA 58.454 39.130 0.00 0.00 38.56 4.69
2420 2539 4.891277 ACGTTTTTACATTACGAGACGG 57.109 40.909 0.00 0.00 38.56 4.79
2421 2540 7.579425 AAAAACGTTTTTACATTACGAGACG 57.421 32.000 31.82 0.00 38.50 4.18
2445 2564 9.990360 TGTTTATTGAATCTAGTGTAGTGTCAA 57.010 29.630 0.00 0.00 35.64 3.18
2465 2584 9.698309 CTCCGTCTCATAATGTAAGATGTTTAT 57.302 33.333 0.00 0.00 0.00 1.40
2466 2585 8.141909 CCTCCGTCTCATAATGTAAGATGTTTA 58.858 37.037 0.00 0.00 0.00 2.01
2467 2586 6.986817 CCTCCGTCTCATAATGTAAGATGTTT 59.013 38.462 0.00 0.00 0.00 2.83
2468 2587 6.463049 CCCTCCGTCTCATAATGTAAGATGTT 60.463 42.308 0.00 0.00 0.00 2.71
2469 2588 5.011125 CCCTCCGTCTCATAATGTAAGATGT 59.989 44.000 0.00 0.00 0.00 3.06
2470 2589 5.243954 TCCCTCCGTCTCATAATGTAAGATG 59.756 44.000 0.00 0.00 0.00 2.90
2471 2590 5.394738 TCCCTCCGTCTCATAATGTAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
2472 2591 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
2473 2592 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
2474 2593 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
2475 2594 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
2476 2595 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
2477 2596 4.767409 TCATACTCCCTCCGTCTCATAATG 59.233 45.833 0.00 0.00 0.00 1.90
2478 2597 4.767928 GTCATACTCCCTCCGTCTCATAAT 59.232 45.833 0.00 0.00 0.00 1.28
2479 2598 4.142790 GTCATACTCCCTCCGTCTCATAA 58.857 47.826 0.00 0.00 0.00 1.90
2480 2599 3.137728 TGTCATACTCCCTCCGTCTCATA 59.862 47.826 0.00 0.00 0.00 2.15
2481 2600 2.091830 TGTCATACTCCCTCCGTCTCAT 60.092 50.000 0.00 0.00 0.00 2.90
2482 2601 1.283905 TGTCATACTCCCTCCGTCTCA 59.716 52.381 0.00 0.00 0.00 3.27
2483 2602 1.950909 CTGTCATACTCCCTCCGTCTC 59.049 57.143 0.00 0.00 0.00 3.36
2484 2603 1.564818 TCTGTCATACTCCCTCCGTCT 59.435 52.381 0.00 0.00 0.00 4.18
2485 2604 2.054232 TCTGTCATACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
2486 2605 2.526888 TTCTGTCATACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
2487 2606 4.556898 CGTAATTCTGTCATACTCCCTCCG 60.557 50.000 0.00 0.00 0.00 4.63
2488 2607 4.341520 ACGTAATTCTGTCATACTCCCTCC 59.658 45.833 0.00 0.00 0.00 4.30
2489 2608 5.507650 GGACGTAATTCTGTCATACTCCCTC 60.508 48.000 10.95 0.00 36.83 4.30
2490 2609 4.341520 GGACGTAATTCTGTCATACTCCCT 59.658 45.833 10.95 0.00 36.83 4.20
2491 2610 4.501058 GGGACGTAATTCTGTCATACTCCC 60.501 50.000 10.95 0.00 36.83 4.30
2492 2611 4.098960 TGGGACGTAATTCTGTCATACTCC 59.901 45.833 10.95 4.59 36.83 3.85
2493 2612 5.258456 TGGGACGTAATTCTGTCATACTC 57.742 43.478 10.95 0.00 36.83 2.59
2494 2613 5.362717 TGATGGGACGTAATTCTGTCATACT 59.637 40.000 10.95 0.00 36.83 2.12
2495 2614 5.597806 TGATGGGACGTAATTCTGTCATAC 58.402 41.667 10.95 3.31 36.83 2.39
2496 2615 5.862678 TGATGGGACGTAATTCTGTCATA 57.137 39.130 10.95 1.75 36.83 2.15
2497 2616 4.753516 TGATGGGACGTAATTCTGTCAT 57.246 40.909 10.95 0.00 36.83 3.06
2498 2617 4.753516 ATGATGGGACGTAATTCTGTCA 57.246 40.909 10.95 0.00 36.83 3.58
2499 2618 7.730364 ATTTATGATGGGACGTAATTCTGTC 57.270 36.000 0.00 2.21 0.00 3.51
2506 2625 9.488762 AGGAGATATATTTATGATGGGACGTAA 57.511 33.333 0.00 0.00 0.00 3.18
2508 2627 7.979786 AGGAGATATATTTATGATGGGACGT 57.020 36.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.