Multiple sequence alignment - TraesCS3D01G540700

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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 TraesCS3D01G540700 chr3D 100.000 2777 0 0 1 2777 612262729 612265505 0.000000e+00 5129.0
1 TraesCS3D01G540700 chr3D 92.029 138 10 1 2277 2413 8368057 8367920 2.820000e-45 193.0
2 TraesCS3D01G540700 chr3D 80.085 236 43 4 1010 1243 555532100 555532333 3.680000e-39 172.0
3 TraesCS3D01G540700 chr3B 92.628 1248 53 12 830 2055 826919837 826918607 0.000000e+00 1759.0
4 TraesCS3D01G540700 chr3B 91.104 326 24 2 346 670 826747042 826746721 1.180000e-118 436.0
5 TraesCS3D01G540700 chr3B 88.920 361 21 11 1 346 826747496 826747140 7.110000e-116 427.0
6 TraesCS3D01G540700 chr3B 91.558 308 25 1 2471 2777 826911119 826910812 9.190000e-115 424.0
7 TraesCS3D01G540700 chr3B 89.224 232 14 7 2041 2270 826911326 826911104 2.110000e-71 279.0
8 TraesCS3D01G540700 chr3B 81.951 205 35 2 1040 1243 738716934 738717137 3.680000e-39 172.0
9 TraesCS3D01G540700 chr3B 95.699 93 4 0 2685 2777 826746724 826746632 1.720000e-32 150.0
10 TraesCS3D01G540700 chr3B 89.815 108 9 1 40 147 826920105 826920000 1.340000e-28 137.0
11 TraesCS3D01G540700 chr3A 91.809 1111 63 8 697 1801 746900416 746901504 0.000000e+00 1522.0
12 TraesCS3D01G540700 chr3A 88.425 527 37 13 1907 2413 746901495 746902017 5.080000e-172 614.0
13 TraesCS3D01G540700 chr3A 92.623 366 27 0 2412 2777 746901957 746902322 6.810000e-146 527.0
14 TraesCS3D01G540700 chr3A 92.795 347 24 1 1 347 746899601 746899946 4.130000e-138 501.0
15 TraesCS3D01G540700 chr3A 91.765 340 19 3 348 687 746900044 746900374 5.420000e-127 464.0
16 TraesCS3D01G540700 chr3A 77.558 557 104 11 1014 1570 607234406 607233871 1.610000e-82 316.0
17 TraesCS3D01G540700 chr3A 77.419 558 106 10 1014 1570 607146283 607145745 5.770000e-82 315.0
18 TraesCS3D01G540700 chr3A 91.367 139 10 2 2276 2412 697499211 697499349 3.650000e-44 189.0
19 TraesCS3D01G540700 chr3A 78.723 235 47 3 1010 1243 692677625 692677857 1.330000e-33 154.0
20 TraesCS3D01G540700 chr6B 88.326 711 68 8 1015 1719 643131466 643132167 0.000000e+00 839.0
21 TraesCS3D01G540700 chr6B 89.604 606 52 4 1015 1619 642989561 642990156 0.000000e+00 760.0
22 TraesCS3D01G540700 chr6D 86.991 761 70 15 1015 1766 427170926 427171666 0.000000e+00 830.0
23 TraesCS3D01G540700 chr6A 85.963 748 73 19 1015 1758 571881425 571882144 0.000000e+00 771.0
24 TraesCS3D01G540700 chr5D 92.199 141 10 1 2277 2416 375170784 375170924 6.070000e-47 198.0
25 TraesCS3D01G540700 chr5D 92.647 136 9 1 2277 2411 51198242 51198377 7.850000e-46 195.0
26 TraesCS3D01G540700 chr5D 92.537 134 9 1 2277 2409 519276155 519276022 1.020000e-44 191.0
27 TraesCS3D01G540700 chr7B 92.086 139 9 2 2276 2413 162843804 162843941 7.850000e-46 195.0
28 TraesCS3D01G540700 chr7B 91.367 139 10 2 2277 2413 681684987 681685125 3.650000e-44 189.0
29 TraesCS3D01G540700 chr1D 92.593 135 9 1 2276 2409 364722137 364722271 2.820000e-45 193.0
30 TraesCS3D01G540700 chr7D 91.971 137 10 1 2277 2412 560703201 560703065 1.020000e-44 191.0
31 TraesCS3D01G540700 chr7A 94.340 53 3 0 2412 2464 503045294 503045346 6.370000e-12 82.4
32 TraesCS3D01G540700 chr1A 91.379 58 5 0 2412 2469 584688703 584688646 2.290000e-11 80.5
33 TraesCS3D01G540700 chr2A 89.655 58 6 0 2412 2469 666840672 666840615 1.070000e-09 75.0
34 TraesCS3D01G540700 chr5A 91.667 48 4 0 2424 2471 309773704 309773657 1.780000e-07 67.6
35 TraesCS3D01G540700 chr4B 93.182 44 3 0 2426 2469 606747874 606747831 6.420000e-07 65.8


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 TraesCS3D01G540700 chr3D 612262729 612265505 2776 False 5129.000000 5129 100.000000 1 2777 1 chr3D.!!$F2 2776
1 TraesCS3D01G540700 chr3B 826918607 826920105 1498 True 948.000000 1759 91.221500 40 2055 2 chr3B.!!$R3 2015
2 TraesCS3D01G540700 chr3B 826910812 826911326 514 True 351.500000 424 90.391000 2041 2777 2 chr3B.!!$R2 736
3 TraesCS3D01G540700 chr3B 826746632 826747496 864 True 337.666667 436 91.907667 1 2777 3 chr3B.!!$R1 2776
4 TraesCS3D01G540700 chr3A 746899601 746902322 2721 False 725.600000 1522 91.483400 1 2777 5 chr3A.!!$F3 2776
5 TraesCS3D01G540700 chr3A 607233871 607234406 535 True 316.000000 316 77.558000 1014 1570 1 chr3A.!!$R2 556
6 TraesCS3D01G540700 chr3A 607145745 607146283 538 True 315.000000 315 77.419000 1014 1570 1 chr3A.!!$R1 556
7 TraesCS3D01G540700 chr6B 643131466 643132167 701 False 839.000000 839 88.326000 1015 1719 1 chr6B.!!$F2 704
8 TraesCS3D01G540700 chr6B 642989561 642990156 595 False 760.000000 760 89.604000 1015 1619 1 chr6B.!!$F1 604
9 TraesCS3D01G540700 chr6D 427170926 427171666 740 False 830.000000 830 86.991000 1015 1766 1 chr6D.!!$F1 751
10 TraesCS3D01G540700 chr6A 571881425 571882144 719 False 771.000000 771 85.963000 1015 1758 1 chr6A.!!$F1 743

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
635 750 0.249398 ATACCCGTCACAACTCAGCC 59.751 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 2648 0.032403 TCAGTACGAACCAACCCGTG 59.968 55.0 0.0 0.0 39.54 4.94 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
33 34 6.236409 TCGATAGTCGATAGGAATTACCACT 58.764 40.000 0.00 0.00 44.82 4.00
48 49 9.349713 GGAATTACCACTCCATTGATGTTAATA 57.650 33.333 0.00 0.00 38.79 0.98
133 149 6.431234 ACTCATCACACCCTTGAACTTTATTC 59.569 38.462 0.00 0.00 0.00 1.75
138 154 5.530915 CACACCCTTGAACTTTATTCTCACA 59.469 40.000 0.00 0.00 0.00 3.58
262 278 7.865820 TCCATCAAAGTCTTTCTAGATTGGAT 58.134 34.615 0.00 0.00 31.86 3.41
279 295 4.736126 TGGATACATGACAACTCATCGT 57.264 40.909 0.00 0.00 46.17 3.73
289 305 2.750166 ACAACTCATCGTCATCGTCTCT 59.250 45.455 0.00 0.00 38.33 3.10
328 344 3.628008 TGCCATGAGCTCATCTGAAAAT 58.372 40.909 26.44 0.67 44.23 1.82
433 547 7.061441 ACAAAGATTACAGTTACGTACACATCG 59.939 37.037 0.00 0.00 0.00 3.84
438 552 4.002982 ACAGTTACGTACACATCGTAGGA 58.997 43.478 0.00 0.00 43.01 2.94
463 577 2.033049 GCATTGGCATCACTCATCTCAC 59.967 50.000 0.00 0.00 40.72 3.51
538 652 6.591062 GTCACACGTATTCCAGGTTACAAATA 59.409 38.462 0.00 0.00 0.00 1.40
543 657 8.670135 CACGTATTCCAGGTTACAAATATTTCA 58.330 33.333 0.00 0.00 0.00 2.69
634 749 1.067142 TCATACCCGTCACAACTCAGC 60.067 52.381 0.00 0.00 0.00 4.26
635 750 0.249398 ATACCCGTCACAACTCAGCC 59.751 55.000 0.00 0.00 0.00 4.85
636 751 1.116536 TACCCGTCACAACTCAGCCA 61.117 55.000 0.00 0.00 0.00 4.75
637 752 1.669115 CCCGTCACAACTCAGCCAG 60.669 63.158 0.00 0.00 0.00 4.85
687 802 1.431243 AGAGACCTGAGGTGAGGAACT 59.569 52.381 9.89 0.00 37.50 3.01
688 803 1.548269 GAGACCTGAGGTGAGGAACTG 59.452 57.143 9.89 0.00 34.85 3.16
690 805 1.971357 GACCTGAGGTGAGGAACTGAA 59.029 52.381 9.89 0.00 34.85 3.02
691 806 2.368875 GACCTGAGGTGAGGAACTGAAA 59.631 50.000 9.89 0.00 34.85 2.69
693 808 3.395941 ACCTGAGGTGAGGAACTGAAAAT 59.604 43.478 1.77 0.00 41.55 1.82
694 809 4.597507 ACCTGAGGTGAGGAACTGAAAATA 59.402 41.667 1.77 0.00 41.55 1.40
747 896 8.764287 CATTACCTCCAAGATTTTTGTCAAAAC 58.236 33.333 10.29 0.77 34.63 2.43
752 901 5.982516 TCCAAGATTTTTGTCAAAACATCGG 59.017 36.000 10.29 12.47 34.63 4.18
795 944 4.671831 TGGAAATAATGAACCCTGCTCAA 58.328 39.130 0.00 0.00 0.00 3.02
805 954 2.863809 ACCCTGCTCAAATCTTTTCGT 58.136 42.857 0.00 0.00 0.00 3.85
835 984 0.540923 ACTCATGGGCAGAGAAGAGC 59.459 55.000 0.00 0.00 36.91 4.09
859 1008 2.298411 AAAATTGCATCGCCCATGAC 57.702 45.000 0.00 0.00 33.80 3.06
887 1036 5.504853 TGTCATGTACAGGGCAATTCATTA 58.495 37.500 13.14 0.00 33.01 1.90
888 1037 6.128486 TGTCATGTACAGGGCAATTCATTAT 58.872 36.000 13.14 0.00 33.01 1.28
889 1038 6.039605 TGTCATGTACAGGGCAATTCATTATG 59.960 38.462 13.14 0.00 33.01 1.90
890 1039 6.262944 GTCATGTACAGGGCAATTCATTATGA 59.737 38.462 7.34 0.00 0.00 2.15
891 1040 6.487668 TCATGTACAGGGCAATTCATTATGAG 59.512 38.462 7.81 0.00 0.00 2.90
892 1041 5.132502 TGTACAGGGCAATTCATTATGAGG 58.867 41.667 0.00 0.00 0.00 3.86
893 1042 3.569491 ACAGGGCAATTCATTATGAGGG 58.431 45.455 0.00 0.00 0.00 4.30
895 1044 2.519691 AGGGCAATTCATTATGAGGGGT 59.480 45.455 0.00 0.00 0.00 4.95
940 1089 3.639561 TCTCCGCTGCTATATAAACACCA 59.360 43.478 0.00 0.00 0.00 4.17
953 1106 7.834881 ATATAAACACCAATCCTCGAGTAGA 57.165 36.000 12.31 2.45 0.00 2.59
983 1140 3.695060 CACATACCTACCTCGTCTCAGTT 59.305 47.826 0.00 0.00 0.00 3.16
987 1144 4.298103 ACCTACCTCGTCTCAGTTTCTA 57.702 45.455 0.00 0.00 0.00 2.10
988 1145 4.263435 ACCTACCTCGTCTCAGTTTCTAG 58.737 47.826 0.00 0.00 0.00 2.43
989 1146 4.019501 ACCTACCTCGTCTCAGTTTCTAGA 60.020 45.833 0.00 0.00 0.00 2.43
1007 1170 1.284198 AGAAGTCTCTGGCATGGCAAT 59.716 47.619 23.47 5.33 0.00 3.56
1233 1396 1.517832 CTCCGTCGAGGCCATCTTT 59.482 57.895 5.01 0.00 40.77 2.52
1557 1720 3.461773 GTGCTCCAGGAGGCGCTA 61.462 66.667 18.83 0.00 45.91 4.26
1749 1918 0.692756 TCGCCCCAGGAATGGACATA 60.693 55.000 0.00 0.00 0.00 2.29
1773 1942 1.342672 AACACGGCGGATTCCCCTAT 61.343 55.000 13.24 0.00 0.00 2.57
1800 1969 7.092979 TGAGGAAGTGAGAAGAAGATGAATGAT 60.093 37.037 0.00 0.00 0.00 2.45
1839 2008 0.250513 AGTCCATCCGTTCTTCCAGC 59.749 55.000 0.00 0.00 0.00 4.85
1840 2009 0.036388 GTCCATCCGTTCTTCCAGCA 60.036 55.000 0.00 0.00 0.00 4.41
1921 2090 2.483106 GCCGTTGATGATGATCCATCTG 59.517 50.000 11.69 4.12 42.49 2.90
1922 2091 2.483106 CCGTTGATGATGATCCATCTGC 59.517 50.000 11.69 5.45 42.49 4.26
1964 2137 6.325919 TGCAATCTTGTTTTCCTATTTCGT 57.674 33.333 0.00 0.00 0.00 3.85
1980 2153 8.344098 TCCTATTTCGTTTTTATTGTCGTTGTT 58.656 29.630 0.00 0.00 0.00 2.83
2056 2234 9.305925 GAGATTAATGAAATAAAAGCCCTTGTG 57.694 33.333 0.00 0.00 0.00 3.33
2071 2249 4.688021 CCCTTGTGTACTTATCTCTGCTC 58.312 47.826 0.00 0.00 0.00 4.26
2072 2250 4.355437 CCTTGTGTACTTATCTCTGCTCG 58.645 47.826 0.00 0.00 0.00 5.03
2073 2251 4.096532 CCTTGTGTACTTATCTCTGCTCGA 59.903 45.833 0.00 0.00 0.00 4.04
2074 2252 5.221145 CCTTGTGTACTTATCTCTGCTCGAT 60.221 44.000 0.00 0.00 0.00 3.59
2075 2253 5.425577 TGTGTACTTATCTCTGCTCGATC 57.574 43.478 0.00 0.00 0.00 3.69
2177 2357 7.440198 TGTAAGATTTGCACAATGAAAATGGA 58.560 30.769 0.00 0.00 0.00 3.41
2233 2413 2.347452 CACGTGTTATGTTCATCCCGAC 59.653 50.000 7.58 0.00 0.00 4.79
2301 2494 2.027745 TCTCCTCCACTGAAAGCACATC 60.028 50.000 0.00 0.00 37.60 3.06
2302 2495 1.081892 CCTCCACTGAAAGCACATCG 58.918 55.000 0.00 0.00 37.60 3.84
2306 2499 1.005037 ACTGAAAGCACATCGCCGA 60.005 52.632 0.00 0.00 44.04 5.54
2319 2512 5.504994 GCACATCGCCGAAAATCCTAAAATA 60.505 40.000 0.00 0.00 32.94 1.40
2326 2519 7.913297 TCGCCGAAAATCCTAAAATAAATTCAG 59.087 33.333 0.00 0.00 0.00 3.02
2341 2534 5.779529 AAATTCAGGAATAATGCGAGCAT 57.220 34.783 4.52 4.52 38.46 3.79
2343 2536 3.473923 TCAGGAATAATGCGAGCATCA 57.526 42.857 11.26 0.00 35.31 3.07
2354 2547 1.363744 CGAGCATCAGGACTTGAACC 58.636 55.000 0.00 0.00 39.77 3.62
2361 2554 2.770164 CAGGACTTGAACCCTGGTAG 57.230 55.000 0.00 0.00 44.68 3.18
2365 2558 2.185387 GACTTGAACCCTGGTAGGCTA 58.815 52.381 0.00 0.00 32.73 3.93
2366 2559 2.168728 GACTTGAACCCTGGTAGGCTAG 59.831 54.545 0.00 0.00 32.73 3.42
2376 2569 3.100671 CTGGTAGGCTAGGGATATCACC 58.899 54.545 0.00 1.67 0.00 4.02
2413 2606 2.414750 CCACAGGTTGGTTCACACC 58.585 57.895 0.00 0.00 44.56 4.16
2414 2607 1.106944 CCACAGGTTGGTTCACACCC 61.107 60.000 0.00 0.00 43.49 4.61
2415 2608 0.106719 CACAGGTTGGTTCACACCCT 60.107 55.000 0.00 0.00 43.78 4.34
2417 2610 2.627771 AGGTTGGTTCACACCCTGA 58.372 52.632 0.00 0.00 41.00 3.86
2418 2611 1.149101 AGGTTGGTTCACACCCTGAT 58.851 50.000 0.00 0.00 41.00 2.90
2419 2612 2.344592 AGGTTGGTTCACACCCTGATA 58.655 47.619 0.00 0.00 41.00 2.15
2420 2613 2.305927 AGGTTGGTTCACACCCTGATAG 59.694 50.000 0.00 0.00 41.00 2.08
2421 2614 2.618045 GGTTGGTTCACACCCTGATAGG 60.618 54.545 0.00 0.00 43.49 2.57
2422 2615 0.618458 TGGTTCACACCCTGATAGGC 59.382 55.000 0.00 0.00 43.49 3.93
2423 2616 0.912486 GGTTCACACCCTGATAGGCT 59.088 55.000 0.00 0.00 37.03 4.58
2424 2617 1.407437 GGTTCACACCCTGATAGGCTG 60.407 57.143 0.00 0.00 37.03 4.85
2425 2618 0.911769 TTCACACCCTGATAGGCTGG 59.088 55.000 0.00 0.00 32.73 4.85
2433 2626 2.837947 CCTGATAGGCTGGGGATATCA 58.162 52.381 4.83 0.00 35.29 2.15
2434 2627 2.503356 CCTGATAGGCTGGGGATATCAC 59.497 54.545 4.83 0.00 33.51 3.06
2435 2628 3.448934 CTGATAGGCTGGGGATATCACT 58.551 50.000 4.65 0.00 33.51 3.41
2436 2629 3.176411 TGATAGGCTGGGGATATCACTG 58.824 50.000 4.65 2.41 32.41 3.66
2437 2630 2.795291 TAGGCTGGGGATATCACTGT 57.205 50.000 4.65 0.00 0.00 3.55
2438 2631 1.428869 AGGCTGGGGATATCACTGTC 58.571 55.000 4.65 2.79 0.00 3.51
2439 2632 0.398318 GGCTGGGGATATCACTGTCC 59.602 60.000 4.65 0.00 32.06 4.02
2447 2640 4.715713 GGGATATCACTGTCCCTTTAACC 58.284 47.826 4.83 0.00 46.69 2.85
2448 2641 4.165372 GGGATATCACTGTCCCTTTAACCA 59.835 45.833 4.83 0.00 46.69 3.67
2449 2642 5.163088 GGGATATCACTGTCCCTTTAACCAT 60.163 44.000 4.83 0.00 46.69 3.55
2450 2643 5.998363 GGATATCACTGTCCCTTTAACCATC 59.002 44.000 4.83 0.00 0.00 3.51
2451 2644 3.713826 TCACTGTCCCTTTAACCATCC 57.286 47.619 0.00 0.00 0.00 3.51
2452 2645 2.983192 TCACTGTCCCTTTAACCATCCA 59.017 45.455 0.00 0.00 0.00 3.41
2453 2646 3.396276 TCACTGTCCCTTTAACCATCCAA 59.604 43.478 0.00 0.00 0.00 3.53
2454 2647 3.506067 CACTGTCCCTTTAACCATCCAAC 59.494 47.826 0.00 0.00 0.00 3.77
2455 2648 3.089284 CTGTCCCTTTAACCATCCAACC 58.911 50.000 0.00 0.00 0.00 3.77
2456 2649 2.447429 TGTCCCTTTAACCATCCAACCA 59.553 45.455 0.00 0.00 0.00 3.67
2457 2650 2.823747 GTCCCTTTAACCATCCAACCAC 59.176 50.000 0.00 0.00 0.00 4.16
2458 2651 1.816224 CCCTTTAACCATCCAACCACG 59.184 52.381 0.00 0.00 0.00 4.94
2459 2652 1.816224 CCTTTAACCATCCAACCACGG 59.184 52.381 0.00 0.00 0.00 4.94
2460 2653 1.816224 CTTTAACCATCCAACCACGGG 59.184 52.381 0.00 0.00 0.00 5.28
2461 2654 0.772384 TTAACCATCCAACCACGGGT 59.228 50.000 0.00 0.00 37.65 5.28
2555 2748 0.323087 ATTGAAGGTACGGCCCCAAC 60.323 55.000 0.00 0.00 38.26 3.77
2558 2751 2.847435 GAAGGTACGGCCCCAACGAG 62.847 65.000 0.00 0.00 38.26 4.18
2569 2762 2.422479 GCCCCAACGAGATAAAAAGGTC 59.578 50.000 0.00 0.00 0.00 3.85
2649 2843 9.435688 AAAAATAGATAACAAAAAGTGATGCCC 57.564 29.630 0.00 0.00 0.00 5.36
2651 2845 3.443681 AGATAACAAAAAGTGATGCCCCG 59.556 43.478 0.00 0.00 0.00 5.73
2710 2904 1.788229 TGTCATCAAGGCCCTCGATA 58.212 50.000 0.00 0.00 0.00 2.92
2728 2922 3.253188 CGATAAACATAATGGCCAGTGGG 59.747 47.826 17.71 10.23 37.18 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.011533 CCCTGCATAGCTAGATTTCTAGTGT 59.988 44.000 14.43 6.65 45.85 3.55
70 86 0.753111 GGTGCATGAATCTCACCCCC 60.753 60.000 7.92 0.00 43.27 5.40
155 171 5.581126 TTGCCATTAATCCACTAGCAAAG 57.419 39.130 0.00 0.00 35.95 2.77
279 295 4.833390 TGTCAGAAGAGTAGAGACGATGA 58.167 43.478 0.00 0.00 32.08 2.92
284 300 4.076394 ACACCTGTCAGAAGAGTAGAGAC 58.924 47.826 0.00 0.00 0.00 3.36
289 305 2.037251 GGCAACACCTGTCAGAAGAGTA 59.963 50.000 0.00 0.00 34.51 2.59
463 577 4.688511 AGTAGCTAGAGAGACAAACACG 57.311 45.455 0.00 0.00 0.00 4.49
634 749 3.307242 GCTACTGAATTAAGACACGCTGG 59.693 47.826 0.00 0.00 0.00 4.85
635 750 3.926527 TGCTACTGAATTAAGACACGCTG 59.073 43.478 0.00 0.00 0.00 5.18
636 751 4.188247 TGCTACTGAATTAAGACACGCT 57.812 40.909 0.00 0.00 0.00 5.07
637 752 4.725169 GCTTGCTACTGAATTAAGACACGC 60.725 45.833 0.00 0.00 0.00 5.34
714 861 9.757227 CAAAAATCTTGGAGGTAATGTTTGTAA 57.243 29.630 0.00 0.00 0.00 2.41
715 862 8.919145 ACAAAAATCTTGGAGGTAATGTTTGTA 58.081 29.630 1.65 0.00 34.63 2.41
721 868 8.764287 GTTTTGACAAAAATCTTGGAGGTAATG 58.236 33.333 14.75 0.00 37.59 1.90
738 885 5.521906 TGGAATTTCCGATGTTTTGACAA 57.478 34.783 10.79 0.00 40.17 3.18
747 896 6.389091 TGAAGTTTTGATGGAATTTCCGATG 58.611 36.000 10.79 0.00 40.17 3.84
795 944 0.110823 GTCACGCGCACGAAAAGATT 60.111 50.000 5.73 0.00 43.93 2.40
805 954 2.316867 CCATGAGTTGTCACGCGCA 61.317 57.895 5.73 0.00 34.75 6.09
835 984 3.077229 TGGGCGATGCAATTTTTATCG 57.923 42.857 9.99 9.99 44.65 2.92
859 1008 2.355197 TGCCCTGTACATGACAAATCG 58.645 47.619 0.00 0.00 37.70 3.34
862 1011 4.148079 TGAATTGCCCTGTACATGACAAA 58.852 39.130 0.00 0.00 37.70 2.83
887 1036 0.259938 GGAGGAATTGCACCCCTCAT 59.740 55.000 22.36 1.46 46.28 2.90
888 1037 0.846427 AGGAGGAATTGCACCCCTCA 60.846 55.000 22.36 0.00 46.28 3.86
889 1038 0.106967 GAGGAGGAATTGCACCCCTC 60.107 60.000 16.07 16.07 44.32 4.30
890 1039 1.915078 CGAGGAGGAATTGCACCCCT 61.915 60.000 9.76 7.45 33.20 4.79
891 1040 1.452108 CGAGGAGGAATTGCACCCC 60.452 63.158 9.76 0.00 0.00 4.95
892 1041 0.744771 GACGAGGAGGAATTGCACCC 60.745 60.000 9.76 5.16 0.00 4.61
893 1042 0.250513 AGACGAGGAGGAATTGCACC 59.749 55.000 5.25 5.25 0.00 5.01
895 1044 1.623311 TCAAGACGAGGAGGAATTGCA 59.377 47.619 0.00 0.00 0.00 4.08
940 1089 2.691011 GTCTGGCTTCTACTCGAGGATT 59.309 50.000 18.41 0.00 0.00 3.01
953 1106 2.766828 GAGGTAGGTATGTGTCTGGCTT 59.233 50.000 0.00 0.00 0.00 4.35
983 1140 2.169352 GCCATGCCAGAGACTTCTAGAA 59.831 50.000 4.81 4.81 30.73 2.10
987 1144 0.694771 TTGCCATGCCAGAGACTTCT 59.305 50.000 0.00 0.00 0.00 2.85
988 1145 1.404391 CATTGCCATGCCAGAGACTTC 59.596 52.381 0.00 0.00 0.00 3.01
989 1146 1.471119 CATTGCCATGCCAGAGACTT 58.529 50.000 0.00 0.00 0.00 3.01
1032 1195 4.802051 TTCTGCCGCCCCATGCTC 62.802 66.667 0.00 0.00 38.05 4.26
1231 1394 2.031465 GGGGACGAAGCGGTCAAA 59.969 61.111 7.68 0.00 38.70 2.69
1233 1396 3.379445 GAGGGGACGAAGCGGTCA 61.379 66.667 7.68 0.00 38.70 4.02
1749 1918 2.281484 AATCCGCCGTGTTGCACT 60.281 55.556 0.00 0.00 31.34 4.40
1773 1942 6.425210 TTCATCTTCTTCTCACTTCCTCAA 57.575 37.500 0.00 0.00 0.00 3.02
1784 1953 8.260099 TGACTGGATATCATTCATCTTCTTCT 57.740 34.615 4.83 0.00 31.33 2.85
1800 1969 0.586802 CGCGACTCGATGACTGGATA 59.413 55.000 0.00 0.00 41.67 2.59
1868 2037 6.048732 TGCATATAACCAAAGACTCACTGA 57.951 37.500 0.00 0.00 0.00 3.41
1955 2124 8.496872 AACAACGACAATAAAAACGAAATAGG 57.503 30.769 0.00 0.00 0.00 2.57
1958 2127 7.632897 GCAAAACAACGACAATAAAAACGAAAT 59.367 29.630 0.00 0.00 0.00 2.17
1980 2153 4.551388 GACCCAATATGTTTCGTTGCAAA 58.449 39.130 0.00 0.00 0.00 3.68
1989 2167 6.496565 TCACAATTGAAGGACCCAATATGTTT 59.503 34.615 13.59 0.00 33.51 2.83
2056 2234 3.058846 TGCGATCGAGCAGAGATAAGTAC 60.059 47.826 21.57 0.00 42.92 2.73
2233 2413 5.235186 CAGTTTTGTGTAGACTGTCCAGAAG 59.765 44.000 3.76 0.00 36.81 2.85
2301 2494 7.167468 CCTGAATTTATTTTAGGATTTTCGGCG 59.833 37.037 0.00 0.00 30.53 6.46
2302 2495 8.194769 TCCTGAATTTATTTTAGGATTTTCGGC 58.805 33.333 0.00 0.00 32.24 5.54
2319 2512 5.300034 TGATGCTCGCATTATTCCTGAATTT 59.700 36.000 5.79 0.00 36.70 1.82
2326 2519 2.481952 GTCCTGATGCTCGCATTATTCC 59.518 50.000 5.79 0.00 36.70 3.01
2343 2536 1.657804 CCTACCAGGGTTCAAGTCCT 58.342 55.000 0.00 0.00 0.00 3.85
2354 2547 3.100671 GTGATATCCCTAGCCTACCAGG 58.899 54.545 0.00 0.00 38.80 4.45
2358 2551 2.754002 GACGGTGATATCCCTAGCCTAC 59.246 54.545 0.00 0.00 0.00 3.18
2360 2553 1.550409 GGACGGTGATATCCCTAGCCT 60.550 57.143 0.00 0.00 0.00 4.58
2361 2554 0.896226 GGACGGTGATATCCCTAGCC 59.104 60.000 0.00 0.03 0.00 3.93
2368 2561 3.228453 TGGTTAGAGGGACGGTGATATC 58.772 50.000 0.00 0.00 0.00 1.63
2372 2565 1.481871 GATGGTTAGAGGGACGGTGA 58.518 55.000 0.00 0.00 0.00 4.02
2376 2569 1.134491 GGTTGGATGGTTAGAGGGACG 60.134 57.143 0.00 0.00 0.00 4.79
2412 2605 2.122768 GATATCCCCAGCCTATCAGGG 58.877 57.143 0.00 0.00 40.98 4.45
2413 2606 2.503356 GTGATATCCCCAGCCTATCAGG 59.497 54.545 0.00 0.00 38.80 3.86
2414 2607 3.197333 CAGTGATATCCCCAGCCTATCAG 59.803 52.174 0.00 0.00 33.70 2.90
2415 2608 3.176411 CAGTGATATCCCCAGCCTATCA 58.824 50.000 0.00 0.00 31.25 2.15
2416 2609 3.177228 ACAGTGATATCCCCAGCCTATC 58.823 50.000 0.00 0.00 0.00 2.08
2417 2610 3.177228 GACAGTGATATCCCCAGCCTAT 58.823 50.000 0.00 0.00 0.00 2.57
2418 2611 2.609747 GACAGTGATATCCCCAGCCTA 58.390 52.381 0.00 0.00 0.00 3.93
2419 2612 1.428869 GACAGTGATATCCCCAGCCT 58.571 55.000 0.00 0.00 0.00 4.58
2420 2613 0.398318 GGACAGTGATATCCCCAGCC 59.602 60.000 0.00 0.00 0.00 4.85
2421 2614 0.398318 GGGACAGTGATATCCCCAGC 59.602 60.000 6.08 0.00 37.04 4.85
2422 2615 2.109229 AGGGACAGTGATATCCCCAG 57.891 55.000 12.60 0.00 43.27 4.45
2423 2616 2.587060 AAGGGACAGTGATATCCCCA 57.413 50.000 12.60 0.00 43.27 4.96
2424 2617 4.445879 GGTTAAAGGGACAGTGATATCCCC 60.446 50.000 12.60 5.99 43.27 4.81
2425 2618 4.165372 TGGTTAAAGGGACAGTGATATCCC 59.835 45.833 8.92 8.92 42.59 3.85
2426 2619 5.367945 TGGTTAAAGGGACAGTGATATCC 57.632 43.478 0.00 0.00 0.00 2.59
2427 2620 5.998363 GGATGGTTAAAGGGACAGTGATATC 59.002 44.000 0.00 0.00 0.00 1.63
2428 2621 5.431731 TGGATGGTTAAAGGGACAGTGATAT 59.568 40.000 0.00 0.00 0.00 1.63
2429 2622 4.785914 TGGATGGTTAAAGGGACAGTGATA 59.214 41.667 0.00 0.00 0.00 2.15
2430 2623 3.591527 TGGATGGTTAAAGGGACAGTGAT 59.408 43.478 0.00 0.00 0.00 3.06
2431 2624 2.983192 TGGATGGTTAAAGGGACAGTGA 59.017 45.455 0.00 0.00 0.00 3.41
2432 2625 3.433306 TGGATGGTTAAAGGGACAGTG 57.567 47.619 0.00 0.00 0.00 3.66
2433 2626 3.499745 GGTTGGATGGTTAAAGGGACAGT 60.500 47.826 0.00 0.00 0.00 3.55
2434 2627 3.089284 GGTTGGATGGTTAAAGGGACAG 58.911 50.000 0.00 0.00 0.00 3.51
2435 2628 2.447429 TGGTTGGATGGTTAAAGGGACA 59.553 45.455 0.00 0.00 0.00 4.02
2436 2629 2.823747 GTGGTTGGATGGTTAAAGGGAC 59.176 50.000 0.00 0.00 0.00 4.46
2437 2630 2.553466 CGTGGTTGGATGGTTAAAGGGA 60.553 50.000 0.00 0.00 0.00 4.20
2438 2631 1.816224 CGTGGTTGGATGGTTAAAGGG 59.184 52.381 0.00 0.00 0.00 3.95
2439 2632 1.816224 CCGTGGTTGGATGGTTAAAGG 59.184 52.381 0.00 0.00 0.00 3.11
2440 2633 1.816224 CCCGTGGTTGGATGGTTAAAG 59.184 52.381 0.00 0.00 0.00 1.85
2441 2634 1.145325 ACCCGTGGTTGGATGGTTAAA 59.855 47.619 0.00 0.00 27.29 1.52
2442 2635 0.772384 ACCCGTGGTTGGATGGTTAA 59.228 50.000 0.00 0.00 27.29 2.01
2443 2636 0.772384 AACCCGTGGTTGGATGGTTA 59.228 50.000 7.42 0.00 45.07 2.85
2444 2637 1.539665 AACCCGTGGTTGGATGGTT 59.460 52.632 7.42 0.00 45.07 3.67
2445 2638 3.257133 AACCCGTGGTTGGATGGT 58.743 55.556 7.42 0.00 45.07 3.55
2455 2648 0.032403 TCAGTACGAACCAACCCGTG 59.968 55.000 0.00 0.00 39.54 4.94
2456 2649 0.316204 CTCAGTACGAACCAACCCGT 59.684 55.000 0.00 0.00 42.15 5.28
2457 2650 1.012486 GCTCAGTACGAACCAACCCG 61.012 60.000 0.00 0.00 0.00 5.28
2458 2651 0.034337 TGCTCAGTACGAACCAACCC 59.966 55.000 0.00 0.00 0.00 4.11
2459 2652 1.873698 TTGCTCAGTACGAACCAACC 58.126 50.000 0.00 0.00 0.00 3.77
2460 2653 2.870411 AGTTTGCTCAGTACGAACCAAC 59.130 45.455 0.00 0.00 32.71 3.77
2461 2654 3.188159 AGTTTGCTCAGTACGAACCAA 57.812 42.857 0.00 0.00 32.71 3.67
2462 2655 2.902705 AGTTTGCTCAGTACGAACCA 57.097 45.000 0.00 0.00 32.71 3.67
2463 2656 3.910648 ACTAGTTTGCTCAGTACGAACC 58.089 45.455 0.00 0.00 32.71 3.62
2464 2657 4.980434 TCAACTAGTTTGCTCAGTACGAAC 59.020 41.667 5.07 0.00 34.88 3.95
2465 2658 5.190992 TCAACTAGTTTGCTCAGTACGAA 57.809 39.130 5.07 0.00 34.88 3.85
2466 2659 4.841443 TCAACTAGTTTGCTCAGTACGA 57.159 40.909 5.07 0.00 34.88 3.43
2467 2660 6.469595 GTCTATCAACTAGTTTGCTCAGTACG 59.530 42.308 5.07 0.00 34.88 3.67
2468 2661 7.273815 GTGTCTATCAACTAGTTTGCTCAGTAC 59.726 40.741 5.07 0.00 34.88 2.73
2469 2662 7.039993 TGTGTCTATCAACTAGTTTGCTCAGTA 60.040 37.037 5.07 0.00 34.88 2.74
2555 2748 4.575885 TGTCCCTTGACCTTTTTATCTCG 58.424 43.478 0.00 0.00 41.01 4.04
2558 2751 5.239963 TCGTTTGTCCCTTGACCTTTTTATC 59.760 40.000 0.00 0.00 41.01 1.75
2569 2762 1.001378 CTTGGCTTCGTTTGTCCCTTG 60.001 52.381 0.00 0.00 0.00 3.61
2640 2834 1.973281 CTGCAAACGGGGCATCACT 60.973 57.895 0.00 0.00 41.06 3.41
2649 2843 3.896648 ACTTGACATTACTGCAAACGG 57.103 42.857 0.00 0.00 0.00 4.44
2651 2845 8.289618 TGAGATTAACTTGACATTACTGCAAAC 58.710 33.333 0.00 0.00 0.00 2.93
2710 2904 2.917713 TCCCACTGGCCATTATGTTT 57.082 45.000 5.51 0.00 0.00 2.83
2728 2922 2.229792 TCCTCAACACACTGCCATTTC 58.770 47.619 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.