Multiple sequence alignment - TraesCS6A01G129800

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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 TraesCS6A01G129800 chr6A 100.000 2710 0 0 1 2710 101553187 101555896 0.000000e+00 5005
1 TraesCS6A01G129800 chr6A 86.278 1749 226 13 1 1741 101863802 101865544 0.000000e+00 1888
2 TraesCS6A01G129800 chr6A 85.927 1748 233 9 1 1741 101561079 101562820 0.000000e+00 1853
3 TraesCS6A01G129800 chr6A 90.805 87 8 0 1640 1726 101845403 101845489 1.700000e-22 117
4 TraesCS6A01G129800 chr6D 95.501 2534 73 8 3 2512 84222843 84225359 0.000000e+00 4010
5 TraesCS6A01G129800 chr6D 86.686 1750 223 7 1 1741 84230256 84232004 0.000000e+00 1932
6 TraesCS6A01G129800 chr6D 87.812 1641 194 6 1 1638 84629426 84631063 0.000000e+00 1917
7 TraesCS6A01G129800 chr6D 85.909 1760 216 22 1 1741 84618454 84620200 0.000000e+00 1847
8 TraesCS6A01G129800 chr6D 89.754 244 24 1 2467 2710 84262158 84262400 7.290000e-81 311
9 TraesCS6A01G129800 chr6D 97.273 110 2 1 2602 2710 84225352 84225461 4.610000e-43 185
10 TraesCS6A01G129800 chr6B 86.428 1761 211 21 1 1741 160681549 160683301 0.000000e+00 1903
11 TraesCS6A01G129800 chr6B 87.325 1641 202 5 1 1638 160715384 160717021 0.000000e+00 1873
12 TraesCS6A01G129800 chr6B 85.518 1747 244 6 1 1739 160661606 160663351 0.000000e+00 1816


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 TraesCS6A01G129800 chr6A 101553187 101555896 2709 False 5005.0 5005 100.000 1 2710 1 chr6A.!!$F1 2709
1 TraesCS6A01G129800 chr6A 101863802 101865544 1742 False 1888.0 1888 86.278 1 1741 1 chr6A.!!$F4 1740
2 TraesCS6A01G129800 chr6A 101561079 101562820 1741 False 1853.0 1853 85.927 1 1741 1 chr6A.!!$F2 1740
3 TraesCS6A01G129800 chr6D 84222843 84225461 2618 False 2097.5 4010 96.387 3 2710 2 chr6D.!!$F5 2707
4 TraesCS6A01G129800 chr6D 84230256 84232004 1748 False 1932.0 1932 86.686 1 1741 1 chr6D.!!$F1 1740
5 TraesCS6A01G129800 chr6D 84629426 84631063 1637 False 1917.0 1917 87.812 1 1638 1 chr6D.!!$F4 1637
6 TraesCS6A01G129800 chr6D 84618454 84620200 1746 False 1847.0 1847 85.909 1 1741 1 chr6D.!!$F3 1740
7 TraesCS6A01G129800 chr6B 160681549 160683301 1752 False 1903.0 1903 86.428 1 1741 1 chr6B.!!$F2 1740
8 TraesCS6A01G129800 chr6B 160715384 160717021 1637 False 1873.0 1873 87.325 1 1638 1 chr6B.!!$F3 1637
9 TraesCS6A01G129800 chr6B 160661606 160663351 1745 False 1816.0 1816 85.518 1 1739 1 chr6B.!!$F1 1738

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
42 43 1.059098 TCTGCATCAAGGTGACTGGT 58.941 50.0 0.00 0.0 42.68 4.00 F
1244 1251 0.113190 AAAAGGCCACCAGAGAAGGG 59.887 55.0 5.01 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1524 0.249868 TCCTCCAGTTGTGCTGTTCG 60.250 55.0 0.0 0.0 43.55 3.95 R
2512 2573 0.033504 AGCATGTTCGACAACCTCGT 59.966 50.0 0.0 0.0 43.45 4.18 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
42 43 1.059098 TCTGCATCAAGGTGACTGGT 58.941 50.000 0.00 0.00 42.68 4.00
48 49 4.263462 TGCATCAAGGTGACTGGTATTTCT 60.263 41.667 0.00 0.00 42.68 2.52
182 183 1.405105 TGTGAGCTTTGACAACCAAGC 59.595 47.619 2.67 2.67 35.94 4.01
496 498 4.803329 ATGCTTTCTGGAACTATCCCAT 57.197 40.909 0.00 0.00 45.95 4.00
578 580 1.478916 GCCTAGGTCTCCACTGAAGTC 59.521 57.143 11.31 0.00 0.00 3.01
579 581 2.808919 CCTAGGTCTCCACTGAAGTCA 58.191 52.381 0.00 0.00 0.00 3.41
584 586 3.260380 AGGTCTCCACTGAAGTCATTGAG 59.740 47.826 0.54 0.00 0.00 3.02
708 712 3.135530 GCTGACCTATGGACTCTGGAATT 59.864 47.826 0.00 0.00 0.00 2.17
757 761 6.505272 AGGTCAAGAGTACGAATATTACTGC 58.495 40.000 0.00 0.00 29.58 4.40
760 764 6.140422 GTCAAGAGTACGAATATTACTGCGTC 59.860 42.308 3.48 0.00 38.09 5.19
945 952 5.362430 GGGAATATTGCCACTCAATTGGTTA 59.638 40.000 20.23 0.00 42.48 2.85
1244 1251 0.113190 AAAAGGCCACCAGAGAAGGG 59.887 55.000 5.01 0.00 0.00 3.95
1332 1339 3.718956 CAAGTCCTTTAGATCCCAGGGAT 59.281 47.826 22.40 22.40 46.28 3.85
1348 1355 1.411041 GGATACCTCAGTAACGGCCT 58.589 55.000 0.00 0.00 30.59 5.19
1507 1514 3.036429 GCGGGAGAGGCCAAGATGT 62.036 63.158 5.01 0.00 38.95 3.06
1515 1522 2.570181 GCCAAGATGTGCAGCACC 59.430 61.111 23.06 8.39 32.73 5.01
1517 1524 1.582968 CCAAGATGTGCAGCACCAC 59.417 57.895 23.06 15.78 32.73 4.16
1520 1527 0.534877 AAGATGTGCAGCACCACGAA 60.535 50.000 23.06 3.84 38.55 3.85
1574 1588 1.235281 GGCCGGTGTTTGTTCTCCTC 61.235 60.000 1.90 0.00 0.00 3.71
1606 1628 2.046313 GTTGCTTGAAGAATGCACACG 58.954 47.619 0.00 0.00 36.37 4.49
1710 1747 0.677731 TGTCATGGGTGCAGCTTAGC 60.678 55.000 16.65 0.00 0.00 3.09
1769 1806 1.152440 CAGGTATCTCCTCGCCCCT 60.152 63.158 0.00 0.00 46.24 4.79
1770 1807 0.112606 CAGGTATCTCCTCGCCCCTA 59.887 60.000 0.00 0.00 46.24 3.53
1771 1808 0.858369 AGGTATCTCCTCGCCCCTAA 59.142 55.000 0.00 0.00 44.42 2.69
1772 1809 1.203075 AGGTATCTCCTCGCCCCTAAG 60.203 57.143 0.00 0.00 44.42 2.18
1773 1810 1.480869 GGTATCTCCTCGCCCCTAAGT 60.481 57.143 0.00 0.00 0.00 2.24
1867 1904 0.252197 ACCCTAAAACTGCCGCTAGG 59.748 55.000 0.00 0.00 41.62 3.02
1912 1949 4.473520 GCAGCCGAGCTAAGCCCA 62.474 66.667 3.89 0.00 36.40 5.36
1977 2014 2.569354 GCGATCCCTGCTCCGAGAT 61.569 63.158 0.00 0.00 0.00 2.75
1978 2015 1.288439 CGATCCCTGCTCCGAGATG 59.712 63.158 0.00 0.00 0.00 2.90
2044 2081 3.302347 GACCAGGGAGTGTGGAGCG 62.302 68.421 0.00 0.00 38.57 5.03
2054 2091 3.414700 GTGGAGCGACACAAGGCG 61.415 66.667 8.64 0.00 40.99 5.52
2127 2164 3.428452 CGGCGTAGATGTTTAGTTCTCCA 60.428 47.826 0.00 0.00 0.00 3.86
2131 2168 5.393243 GCGTAGATGTTTAGTTCTCCAGACT 60.393 44.000 0.00 0.00 0.00 3.24
2151 2188 0.962356 AAAGTCTTGCTGGATGCCGG 60.962 55.000 0.00 0.00 42.00 6.13
2196 2233 1.190643 CTGACACCTCTCCCTTCCTC 58.809 60.000 0.00 0.00 0.00 3.71
2202 2239 1.036707 CCTCTCCCTTCCTCGATGTC 58.963 60.000 0.00 0.00 0.00 3.06
2253 2290 2.026734 CAGCTCGACGATGGCGAT 59.973 61.111 0.00 0.00 41.64 4.58
2282 2319 4.165779 GGCATTGTTACTTTGGTGAATCG 58.834 43.478 0.00 0.00 0.00 3.34
2305 2342 5.066593 GTCATTTTGGAGACTTGACCTCTT 58.933 41.667 0.00 0.00 32.47 2.85
2360 2397 4.415332 CGGTAGTGCGGCGTCTGT 62.415 66.667 9.37 0.00 0.00 3.41
2382 2419 0.179067 TGTTGTGTTCGTCTGGGACC 60.179 55.000 0.00 0.00 0.00 4.46
2417 2454 4.292784 GGAGCACTCCTGACTTGC 57.707 61.111 9.54 0.00 46.16 4.01
2505 2566 1.649321 AGACATGCCTTCTCTCACCA 58.351 50.000 0.00 0.00 0.00 4.17
2508 2569 1.088340 CATGCCTTCTCTCACCAGCG 61.088 60.000 0.00 0.00 0.00 5.18
2509 2570 1.548357 ATGCCTTCTCTCACCAGCGT 61.548 55.000 0.00 0.00 0.00 5.07
2510 2571 1.446966 GCCTTCTCTCACCAGCGTC 60.447 63.158 0.00 0.00 0.00 5.19
2511 2572 1.967535 CCTTCTCTCACCAGCGTCA 59.032 57.895 0.00 0.00 0.00 4.35
2512 2573 0.318441 CCTTCTCTCACCAGCGTCAA 59.682 55.000 0.00 0.00 0.00 3.18
2513 2574 1.423395 CTTCTCTCACCAGCGTCAAC 58.577 55.000 0.00 0.00 0.00 3.18
2514 2575 0.318699 TTCTCTCACCAGCGTCAACG 60.319 55.000 0.00 0.00 43.27 4.10
2515 2576 1.170290 TCTCTCACCAGCGTCAACGA 61.170 55.000 6.75 0.00 43.02 3.85
2516 2577 0.730834 CTCTCACCAGCGTCAACGAG 60.731 60.000 6.75 0.00 43.02 4.18
2517 2578 1.734477 CTCACCAGCGTCAACGAGG 60.734 63.158 6.75 9.54 43.02 4.63
2518 2579 2.029073 CACCAGCGTCAACGAGGT 59.971 61.111 6.75 10.17 45.52 3.85
2519 2580 1.594293 CACCAGCGTCAACGAGGTT 60.594 57.895 14.72 2.21 43.36 3.50
2520 2581 1.594293 ACCAGCGTCAACGAGGTTG 60.594 57.895 6.75 2.16 43.36 3.77
2521 2582 1.594293 CCAGCGTCAACGAGGTTGT 60.594 57.895 6.75 0.00 43.23 3.32
2522 2583 1.557443 CCAGCGTCAACGAGGTTGTC 61.557 60.000 6.75 2.57 43.23 3.18
2533 2594 2.601481 GAGGTTGTCGAACATGCTTG 57.399 50.000 0.00 0.00 33.27 4.01
2534 2595 1.873591 GAGGTTGTCGAACATGCTTGT 59.126 47.619 0.00 0.00 37.82 3.16
2535 2596 1.603802 AGGTTGTCGAACATGCTTGTG 59.396 47.619 5.94 0.00 35.83 3.33
2536 2597 1.334960 GGTTGTCGAACATGCTTGTGG 60.335 52.381 5.94 2.15 35.83 4.17
2537 2598 0.310543 TTGTCGAACATGCTTGTGGC 59.689 50.000 5.94 1.30 35.83 5.01
2546 2607 4.030452 GCTTGTGGCAGGCACGAC 62.030 66.667 21.33 9.96 41.35 4.34
2547 2608 3.357079 CTTGTGGCAGGCACGACC 61.357 66.667 21.33 0.00 39.61 4.79
2550 2611 4.760047 GTGGCAGGCACGACCGAT 62.760 66.667 11.99 0.00 46.52 4.18
2551 2612 4.758251 TGGCAGGCACGACCGATG 62.758 66.667 0.00 0.00 46.52 3.84
2554 2615 4.794439 CAGGCACGACCGATGCGA 62.794 66.667 0.00 0.00 46.52 5.10
2555 2616 4.796231 AGGCACGACCGATGCGAC 62.796 66.667 0.00 0.00 46.52 5.19
2557 2618 3.545481 GCACGACCGATGCGACAG 61.545 66.667 0.00 0.00 32.45 3.51
2558 2619 2.178273 CACGACCGATGCGACAGA 59.822 61.111 0.00 0.00 0.00 3.41
2559 2620 1.226688 CACGACCGATGCGACAGAT 60.227 57.895 0.00 0.00 0.00 2.90
2560 2621 0.802222 CACGACCGATGCGACAGATT 60.802 55.000 0.00 0.00 0.00 2.40
2561 2622 0.802222 ACGACCGATGCGACAGATTG 60.802 55.000 0.00 0.00 0.00 2.67
2562 2623 1.482621 CGACCGATGCGACAGATTGG 61.483 60.000 0.00 0.00 0.00 3.16
2563 2624 0.179111 GACCGATGCGACAGATTGGA 60.179 55.000 0.00 0.00 0.00 3.53
2564 2625 0.249120 ACCGATGCGACAGATTGGAA 59.751 50.000 0.00 0.00 0.00 3.53
2565 2626 1.134401 ACCGATGCGACAGATTGGAAT 60.134 47.619 0.00 0.00 0.00 3.01
2566 2627 1.262417 CCGATGCGACAGATTGGAATG 59.738 52.381 0.00 0.00 0.00 2.67
2567 2628 1.333524 CGATGCGACAGATTGGAATGC 60.334 52.381 0.00 0.00 0.00 3.56
2568 2629 1.945394 GATGCGACAGATTGGAATGCT 59.055 47.619 0.00 0.00 0.00 3.79
2569 2630 1.372582 TGCGACAGATTGGAATGCTC 58.627 50.000 0.00 0.00 0.00 4.26
2570 2631 1.065926 TGCGACAGATTGGAATGCTCT 60.066 47.619 0.00 0.00 0.00 4.09
2571 2632 2.012673 GCGACAGATTGGAATGCTCTT 58.987 47.619 0.00 0.00 0.00 2.85
2572 2633 2.421424 GCGACAGATTGGAATGCTCTTT 59.579 45.455 0.00 0.00 0.00 2.52
2573 2634 3.730061 GCGACAGATTGGAATGCTCTTTG 60.730 47.826 0.00 0.00 0.00 2.77
2574 2635 3.686241 CGACAGATTGGAATGCTCTTTGA 59.314 43.478 0.00 0.00 0.00 2.69
2575 2636 4.201792 CGACAGATTGGAATGCTCTTTGAG 60.202 45.833 0.00 0.00 0.00 3.02
2576 2637 4.015084 ACAGATTGGAATGCTCTTTGAGG 58.985 43.478 0.00 0.00 0.00 3.86
2577 2638 4.263639 ACAGATTGGAATGCTCTTTGAGGA 60.264 41.667 0.00 0.00 33.93 3.71
2578 2639 4.888239 CAGATTGGAATGCTCTTTGAGGAT 59.112 41.667 0.00 0.00 42.34 3.24
2579 2640 4.888239 AGATTGGAATGCTCTTTGAGGATG 59.112 41.667 2.51 0.00 39.73 3.51
2580 2641 3.726557 TGGAATGCTCTTTGAGGATGT 57.273 42.857 2.51 0.00 39.73 3.06
2581 2642 4.038271 TGGAATGCTCTTTGAGGATGTT 57.962 40.909 2.51 0.00 39.73 2.71
2582 2643 3.760151 TGGAATGCTCTTTGAGGATGTTG 59.240 43.478 2.51 0.00 39.73 3.33
2583 2644 3.760684 GGAATGCTCTTTGAGGATGTTGT 59.239 43.478 2.51 0.00 39.73 3.32
2584 2645 4.380233 GGAATGCTCTTTGAGGATGTTGTG 60.380 45.833 2.51 0.00 39.73 3.33
2585 2646 2.507484 TGCTCTTTGAGGATGTTGTGG 58.493 47.619 0.00 0.00 0.00 4.17
2586 2647 1.200948 GCTCTTTGAGGATGTTGTGGC 59.799 52.381 0.00 0.00 0.00 5.01
2587 2648 2.787994 CTCTTTGAGGATGTTGTGGCT 58.212 47.619 0.00 0.00 0.00 4.75
2588 2649 3.869912 GCTCTTTGAGGATGTTGTGGCTA 60.870 47.826 0.00 0.00 0.00 3.93
2589 2650 4.326826 CTCTTTGAGGATGTTGTGGCTAA 58.673 43.478 0.00 0.00 0.00 3.09
2590 2651 4.326826 TCTTTGAGGATGTTGTGGCTAAG 58.673 43.478 0.00 0.00 0.00 2.18
2591 2652 3.788227 TTGAGGATGTTGTGGCTAAGT 57.212 42.857 0.00 0.00 0.00 2.24
2592 2653 3.334583 TGAGGATGTTGTGGCTAAGTC 57.665 47.619 0.00 0.00 0.00 3.01
2593 2654 2.637382 TGAGGATGTTGTGGCTAAGTCA 59.363 45.455 0.00 0.00 0.00 3.41
2594 2655 3.072330 TGAGGATGTTGTGGCTAAGTCAA 59.928 43.478 0.00 0.00 0.00 3.18
2595 2656 4.072131 GAGGATGTTGTGGCTAAGTCAAA 58.928 43.478 0.00 0.00 0.00 2.69
2596 2657 4.469657 AGGATGTTGTGGCTAAGTCAAAA 58.530 39.130 0.00 0.00 0.00 2.44
2597 2658 5.079643 AGGATGTTGTGGCTAAGTCAAAAT 58.920 37.500 0.00 0.00 0.00 1.82
2598 2659 5.183904 AGGATGTTGTGGCTAAGTCAAAATC 59.816 40.000 0.00 0.00 35.97 2.17
2599 2660 4.481930 TGTTGTGGCTAAGTCAAAATCG 57.518 40.909 0.00 0.00 0.00 3.34
2600 2661 3.880490 TGTTGTGGCTAAGTCAAAATCGT 59.120 39.130 0.00 0.00 0.00 3.73
2601 2662 4.024387 TGTTGTGGCTAAGTCAAAATCGTC 60.024 41.667 0.00 0.00 0.00 4.20
2602 2663 2.734606 TGTGGCTAAGTCAAAATCGTCG 59.265 45.455 0.00 0.00 0.00 5.12
2603 2664 2.093783 GTGGCTAAGTCAAAATCGTCGG 59.906 50.000 0.00 0.00 0.00 4.79
2619 2680 2.805546 GGGTCATGAGCGCGACTA 59.194 61.111 18.14 0.00 32.57 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.561076 ACCTTGATGCAGATGCCACTA 59.439 47.619 1.72 0.00 41.18 2.74
54 55 5.123502 TCTGGACGTATCTAACAACAGTCTC 59.876 44.000 0.00 0.00 0.00 3.36
182 183 3.107601 TCCTTGACTGGAAGGATACCTG 58.892 50.000 6.38 0.00 45.52 4.00
579 581 6.209986 TCAAAACCATTGATCTGAAGCTCAAT 59.790 34.615 4.03 4.03 40.32 2.57
584 586 5.633830 TCTCAAAACCATTGATCTGAAGC 57.366 39.130 0.00 0.00 0.00 3.86
757 761 1.202348 TGGAGCACACATAGTCAGACG 59.798 52.381 0.00 0.00 0.00 4.18
760 764 3.531934 TGATGGAGCACACATAGTCAG 57.468 47.619 0.00 0.00 0.00 3.51
945 952 5.435686 TGGTATTGCTTGACCTCTGTTAT 57.564 39.130 3.65 0.00 36.62 1.89
1244 1251 4.495422 ACATGTCAATCTCTCGTACAACC 58.505 43.478 0.00 0.00 0.00 3.77
1332 1339 2.029623 GATGAGGCCGTTACTGAGGTA 58.970 52.381 0.00 0.00 0.00 3.08
1348 1355 2.262211 CGTCGTCTGCAATGAAGATGA 58.738 47.619 9.05 9.05 37.36 2.92
1507 1514 3.279116 GCTGTTCGTGGTGCTGCA 61.279 61.111 0.00 0.00 0.00 4.41
1515 1522 0.583438 CTCCAGTTGTGCTGTTCGTG 59.417 55.000 0.00 0.00 43.55 4.35
1517 1524 0.249868 TCCTCCAGTTGTGCTGTTCG 60.250 55.000 0.00 0.00 43.55 3.95
1520 1527 0.532862 CGTTCCTCCAGTTGTGCTGT 60.533 55.000 0.00 0.00 43.55 4.40
1574 1588 5.410067 TCTTCAAGCAACAGAAAAACAAGG 58.590 37.500 0.00 0.00 0.00 3.61
1606 1628 4.608948 AATGATAGCTAGTACCAGCACC 57.391 45.455 15.79 4.63 44.35 5.01
1754 1791 1.998222 ACTTAGGGGCGAGGAGATAC 58.002 55.000 0.00 0.00 0.00 2.24
1769 1806 8.436046 ACCACGTAAACATAACTTCAAACTTA 57.564 30.769 0.00 0.00 0.00 2.24
1770 1807 7.324354 ACCACGTAAACATAACTTCAAACTT 57.676 32.000 0.00 0.00 0.00 2.66
1771 1808 6.930667 ACCACGTAAACATAACTTCAAACT 57.069 33.333 0.00 0.00 0.00 2.66
1772 1809 7.188157 TCAACCACGTAAACATAACTTCAAAC 58.812 34.615 0.00 0.00 0.00 2.93
1773 1810 7.317842 TCAACCACGTAAACATAACTTCAAA 57.682 32.000 0.00 0.00 0.00 2.69
1887 1924 4.925861 GCTCGGCTGCATCCTCCC 62.926 72.222 4.84 0.00 0.00 4.30
1931 1968 1.574428 CACAAGGAAAGGAACGCCG 59.426 57.895 0.00 0.00 39.96 6.46
1977 2014 0.963856 CTGAGCAAGCCAAGCCATCA 60.964 55.000 0.00 0.00 0.00 3.07
1978 2015 1.664321 CCTGAGCAAGCCAAGCCATC 61.664 60.000 0.00 0.00 0.00 3.51
2011 2048 2.743928 GTCTTGGAGCACAGCCGG 60.744 66.667 0.00 0.00 0.00 6.13
2054 2091 4.823276 CAGATCTGGAGCCGACAC 57.177 61.111 15.38 0.00 0.00 3.67
2151 2188 1.334869 CTTGGAAGGTGTTGTCAGCAC 59.665 52.381 11.10 11.10 43.57 4.40
2166 2203 1.971357 GAGGTGTCAGAACTCCTTGGA 59.029 52.381 1.14 0.00 46.80 3.53
2196 2233 1.546029 TCACTGGGAGACAAGACATCG 59.454 52.381 0.00 0.00 0.00 3.84
2202 2239 2.930950 TGGTTTTCACTGGGAGACAAG 58.069 47.619 0.00 0.00 0.00 3.16
2282 2319 4.646572 AGAGGTCAAGTCTCCAAAATGAC 58.353 43.478 0.00 0.00 39.65 3.06
2305 2342 1.227823 CACAAACGTGCTCCCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
2316 2353 2.177580 AGCCACGACACCACAAACG 61.178 57.895 0.00 0.00 0.00 3.60
2344 2381 2.558554 ATCACAGACGCCGCACTACC 62.559 60.000 0.00 0.00 0.00 3.18
2347 2384 2.433145 CATCACAGACGCCGCACT 60.433 61.111 0.00 0.00 0.00 4.40
2360 2397 1.414550 TCCCAGACGAACACAACATCA 59.585 47.619 0.00 0.00 0.00 3.07
2439 2500 3.082619 TCCCAAGAGGACGACCAAT 57.917 52.632 6.71 0.00 40.93 3.16
2505 2566 4.338327 GACAACCTCGTTGACGCT 57.662 55.556 11.29 0.00 45.28 5.07
2508 2569 1.563111 TGTTCGACAACCTCGTTGAC 58.437 50.000 11.29 4.43 45.28 3.18
2509 2570 2.131972 CATGTTCGACAACCTCGTTGA 58.868 47.619 11.29 0.00 45.28 3.18
2511 2572 0.865769 GCATGTTCGACAACCTCGTT 59.134 50.000 0.00 0.00 43.45 3.85
2512 2573 0.033504 AGCATGTTCGACAACCTCGT 59.966 50.000 0.00 0.00 43.45 4.18
2513 2574 1.136252 CAAGCATGTTCGACAACCTCG 60.136 52.381 0.00 0.00 44.44 4.63
2514 2575 1.873591 ACAAGCATGTTCGACAACCTC 59.126 47.619 0.00 0.00 35.91 3.85
2515 2576 1.603802 CACAAGCATGTTCGACAACCT 59.396 47.619 0.00 0.00 37.82 3.50
2516 2577 1.334960 CCACAAGCATGTTCGACAACC 60.335 52.381 0.00 0.00 37.82 3.77
2517 2578 1.925946 GCCACAAGCATGTTCGACAAC 60.926 52.381 0.00 0.00 42.97 3.32
2518 2579 0.310543 GCCACAAGCATGTTCGACAA 59.689 50.000 0.00 0.00 42.97 3.18
2519 2580 1.948508 GCCACAAGCATGTTCGACA 59.051 52.632 0.00 0.00 42.97 4.35
2520 2581 4.847255 GCCACAAGCATGTTCGAC 57.153 55.556 0.00 0.00 42.97 4.20
2529 2590 4.030452 GTCGTGCCTGCCACAAGC 62.030 66.667 0.00 0.00 44.91 4.01
2530 2591 3.357079 GGTCGTGCCTGCCACAAG 61.357 66.667 0.00 0.00 44.91 3.16
2533 2594 4.760047 ATCGGTCGTGCCTGCCAC 62.760 66.667 0.00 0.00 41.15 5.01
2534 2595 4.758251 CATCGGTCGTGCCTGCCA 62.758 66.667 0.00 0.00 34.25 4.92
2537 2598 4.794439 TCGCATCGGTCGTGCCTG 62.794 66.667 10.49 1.77 39.39 4.85
2538 2599 4.796231 GTCGCATCGGTCGTGCCT 62.796 66.667 10.49 0.00 39.39 4.75
2540 2601 3.545481 CTGTCGCATCGGTCGTGC 61.545 66.667 7.49 7.49 39.18 5.34
2541 2602 0.802222 AATCTGTCGCATCGGTCGTG 60.802 55.000 0.00 0.00 0.00 4.35
2542 2603 0.802222 CAATCTGTCGCATCGGTCGT 60.802 55.000 0.00 0.00 0.00 4.34
2543 2604 1.482621 CCAATCTGTCGCATCGGTCG 61.483 60.000 0.00 0.00 0.00 4.79
2544 2605 0.179111 TCCAATCTGTCGCATCGGTC 60.179 55.000 0.00 0.00 0.00 4.79
2545 2606 0.249120 TTCCAATCTGTCGCATCGGT 59.751 50.000 0.00 0.00 0.00 4.69
2546 2607 1.262417 CATTCCAATCTGTCGCATCGG 59.738 52.381 0.00 0.00 0.00 4.18
2547 2608 1.333524 GCATTCCAATCTGTCGCATCG 60.334 52.381 0.00 0.00 0.00 3.84
2548 2609 1.945394 AGCATTCCAATCTGTCGCATC 59.055 47.619 0.00 0.00 0.00 3.91
2549 2610 1.945394 GAGCATTCCAATCTGTCGCAT 59.055 47.619 0.00 0.00 0.00 4.73
2550 2611 1.065926 AGAGCATTCCAATCTGTCGCA 60.066 47.619 0.00 0.00 0.00 5.10
2551 2612 1.661341 AGAGCATTCCAATCTGTCGC 58.339 50.000 0.00 0.00 0.00 5.19
2552 2613 3.686241 TCAAAGAGCATTCCAATCTGTCG 59.314 43.478 0.00 0.00 0.00 4.35
2553 2614 4.096081 CCTCAAAGAGCATTCCAATCTGTC 59.904 45.833 0.00 0.00 0.00 3.51
2554 2615 4.015084 CCTCAAAGAGCATTCCAATCTGT 58.985 43.478 0.00 0.00 0.00 3.41
2555 2616 4.267536 TCCTCAAAGAGCATTCCAATCTG 58.732 43.478 0.00 0.00 0.00 2.90
2556 2617 4.581309 TCCTCAAAGAGCATTCCAATCT 57.419 40.909 0.00 0.00 0.00 2.40
2557 2618 4.643784 ACATCCTCAAAGAGCATTCCAATC 59.356 41.667 0.00 0.00 0.00 2.67
2558 2619 4.607239 ACATCCTCAAAGAGCATTCCAAT 58.393 39.130 0.00 0.00 0.00 3.16
2559 2620 4.038271 ACATCCTCAAAGAGCATTCCAA 57.962 40.909 0.00 0.00 0.00 3.53
2560 2621 3.726557 ACATCCTCAAAGAGCATTCCA 57.273 42.857 0.00 0.00 0.00 3.53
2561 2622 3.760684 ACAACATCCTCAAAGAGCATTCC 59.239 43.478 0.00 0.00 0.00 3.01
2562 2623 4.380233 CCACAACATCCTCAAAGAGCATTC 60.380 45.833 0.00 0.00 0.00 2.67
2563 2624 3.508793 CCACAACATCCTCAAAGAGCATT 59.491 43.478 0.00 0.00 0.00 3.56
2564 2625 3.087031 CCACAACATCCTCAAAGAGCAT 58.913 45.455 0.00 0.00 0.00 3.79
2565 2626 2.507484 CCACAACATCCTCAAAGAGCA 58.493 47.619 0.00 0.00 0.00 4.26
2566 2627 1.200948 GCCACAACATCCTCAAAGAGC 59.799 52.381 0.00 0.00 0.00 4.09
2567 2628 2.787994 AGCCACAACATCCTCAAAGAG 58.212 47.619 0.00 0.00 0.00 2.85
2568 2629 2.957402 AGCCACAACATCCTCAAAGA 57.043 45.000 0.00 0.00 0.00 2.52
2569 2630 4.074970 ACTTAGCCACAACATCCTCAAAG 58.925 43.478 0.00 0.00 0.00 2.77
2570 2631 4.072131 GACTTAGCCACAACATCCTCAAA 58.928 43.478 0.00 0.00 0.00 2.69
2571 2632 3.072330 TGACTTAGCCACAACATCCTCAA 59.928 43.478 0.00 0.00 0.00 3.02
2572 2633 2.637382 TGACTTAGCCACAACATCCTCA 59.363 45.455 0.00 0.00 0.00 3.86
2573 2634 3.334583 TGACTTAGCCACAACATCCTC 57.665 47.619 0.00 0.00 0.00 3.71
2574 2635 3.788227 TTGACTTAGCCACAACATCCT 57.212 42.857 0.00 0.00 0.00 3.24
2575 2636 4.846779 TTTTGACTTAGCCACAACATCC 57.153 40.909 0.00 0.00 0.00 3.51
2576 2637 5.088739 CGATTTTGACTTAGCCACAACATC 58.911 41.667 0.00 0.00 31.56 3.06
2577 2638 4.518970 ACGATTTTGACTTAGCCACAACAT 59.481 37.500 0.00 0.00 0.00 2.71
2578 2639 3.880490 ACGATTTTGACTTAGCCACAACA 59.120 39.130 0.00 0.00 0.00 3.33
2579 2640 4.464112 GACGATTTTGACTTAGCCACAAC 58.536 43.478 0.00 0.00 0.00 3.32
2580 2641 3.185594 CGACGATTTTGACTTAGCCACAA 59.814 43.478 0.00 0.00 0.00 3.33
2581 2642 2.734606 CGACGATTTTGACTTAGCCACA 59.265 45.455 0.00 0.00 0.00 4.17
2582 2643 2.093783 CCGACGATTTTGACTTAGCCAC 59.906 50.000 0.00 0.00 0.00 5.01
2583 2644 2.343101 CCGACGATTTTGACTTAGCCA 58.657 47.619 0.00 0.00 0.00 4.75
2584 2645 1.664151 CCCGACGATTTTGACTTAGCC 59.336 52.381 0.00 0.00 0.00 3.93
2585 2646 2.344025 ACCCGACGATTTTGACTTAGC 58.656 47.619 0.00 0.00 0.00 3.09
2586 2647 3.581755 TGACCCGACGATTTTGACTTAG 58.418 45.455 0.00 0.00 0.00 2.18
2587 2648 3.663995 TGACCCGACGATTTTGACTTA 57.336 42.857 0.00 0.00 0.00 2.24
2588 2649 2.536761 TGACCCGACGATTTTGACTT 57.463 45.000 0.00 0.00 0.00 3.01
2589 2650 2.028476 TCATGACCCGACGATTTTGACT 60.028 45.455 0.00 0.00 0.00 3.41
2590 2651 2.343101 TCATGACCCGACGATTTTGAC 58.657 47.619 0.00 0.00 0.00 3.18
2591 2652 2.616960 CTCATGACCCGACGATTTTGA 58.383 47.619 0.00 0.00 0.00 2.69
2592 2653 1.062587 GCTCATGACCCGACGATTTTG 59.937 52.381 0.00 0.00 0.00 2.44
2593 2654 1.369625 GCTCATGACCCGACGATTTT 58.630 50.000 0.00 0.00 0.00 1.82
2594 2655 0.806102 CGCTCATGACCCGACGATTT 60.806 55.000 0.00 0.00 0.00 2.17
2595 2656 1.226974 CGCTCATGACCCGACGATT 60.227 57.895 0.00 0.00 0.00 3.34
2596 2657 2.413351 CGCTCATGACCCGACGAT 59.587 61.111 0.00 0.00 0.00 3.73
2597 2658 4.492160 GCGCTCATGACCCGACGA 62.492 66.667 13.53 0.00 0.00 4.20
2599 2660 4.492160 TCGCGCTCATGACCCGAC 62.492 66.667 5.56 5.65 0.00 4.79
2600 2661 4.492160 GTCGCGCTCATGACCCGA 62.492 66.667 5.56 8.82 0.00 5.14
2601 2662 2.607668 TTAGTCGCGCTCATGACCCG 62.608 60.000 5.56 6.65 35.71 5.28
2602 2663 0.249489 ATTAGTCGCGCTCATGACCC 60.249 55.000 5.56 0.00 35.71 4.46
2603 2664 0.855349 CATTAGTCGCGCTCATGACC 59.145 55.000 15.20 0.00 35.71 4.02
2619 2680 4.309933 ACGCGACATCATCATACATCATT 58.690 39.130 15.93 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.