Multiple sequence alignment - TraesCS6D01G302800

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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 TraesCS6D01G302800 chr6D 100.000 2713 0 0 1 2713 411766072 411768784 0.000000e+00 5011
1 TraesCS6D01G302800 chr6D 86.116 569 37 18 852 1410 411725812 411726348 2.340000e-160 575
2 TraesCS6D01G302800 chr6D 80.357 112 11 5 698 803 411725687 411725793 1.040000e-09 75
3 TraesCS6D01G302800 chr6A 85.639 2472 218 76 300 2702 556676052 556678455 0.000000e+00 2471
4 TraesCS6D01G302800 chr6A 87.368 570 30 17 852 1409 556669408 556669947 1.380000e-172 616
5 TraesCS6D01G302800 chr6A 78.451 891 117 31 1537 2403 99974470 99973631 1.860000e-141 512
6 TraesCS6D01G302800 chr6A 82.059 340 22 12 1 304 556675604 556675940 1.250000e-63 254
7 TraesCS6D01G302800 chr6B 85.874 1791 127 53 1 1715 619482884 619484624 0.000000e+00 1790
8 TraesCS6D01G302800 chr6B 84.655 971 100 27 1717 2662 619492676 619493622 0.000000e+00 922
9 TraesCS6D01G302800 chr6B 85.191 628 40 23 852 1452 619404493 619405094 1.800000e-166 595
10 TraesCS6D01G302800 chr5D 87.412 707 65 12 1717 2413 358668156 358668848 0.000000e+00 791
11 TraesCS6D01G302800 chr3A 83.824 340 43 9 1095 1430 541225952 541226283 2.030000e-81 313
12 TraesCS6D01G302800 chr3B 81.765 340 49 9 1095 1430 536429377 536429047 3.440000e-69 272
13 TraesCS6D01G302800 chr7D 86.512 215 17 4 2140 2354 32581201 32581403 2.720000e-55 226
14 TraesCS6D01G302800 chr2D 81.081 259 25 11 1802 2060 178526749 178526983 4.610000e-43 185
15 TraesCS6D01G302800 chr2D 80.216 278 28 14 1802 2076 178694514 178694767 1.660000e-42 183
16 TraesCS6D01G302800 chr3D 87.162 148 17 2 1096 1242 410518622 410518476 1.670000e-37 167
17 TraesCS6D01G302800 chr2B 80.247 243 23 9 1818 2060 235902336 235902553 2.800000e-35 159
18 TraesCS6D01G302800 chr2B 88.636 132 11 2 1929 2060 235899758 235899885 1.010000e-34 158
19 TraesCS6D01G302800 chr2A 78.277 267 26 13 1811 2074 193578279 193578516 2.820000e-30 143


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 TraesCS6D01G302800 chr6D 411766072 411768784 2712 False 5011.0 5011 100.0000 1 2713 1 chr6D.!!$F1 2712
1 TraesCS6D01G302800 chr6D 411725687 411726348 661 False 325.0 575 83.2365 698 1410 2 chr6D.!!$F2 712
2 TraesCS6D01G302800 chr6A 556675604 556678455 2851 False 1362.5 2471 83.8490 1 2702 2 chr6A.!!$F2 2701
3 TraesCS6D01G302800 chr6A 556669408 556669947 539 False 616.0 616 87.3680 852 1409 1 chr6A.!!$F1 557
4 TraesCS6D01G302800 chr6A 99973631 99974470 839 True 512.0 512 78.4510 1537 2403 1 chr6A.!!$R1 866
5 TraesCS6D01G302800 chr6B 619482884 619484624 1740 False 1790.0 1790 85.8740 1 1715 1 chr6B.!!$F2 1714
6 TraesCS6D01G302800 chr6B 619492676 619493622 946 False 922.0 922 84.6550 1717 2662 1 chr6B.!!$F3 945
7 TraesCS6D01G302800 chr6B 619404493 619405094 601 False 595.0 595 85.1910 852 1452 1 chr6B.!!$F1 600
8 TraesCS6D01G302800 chr5D 358668156 358668848 692 False 791.0 791 87.4120 1717 2413 1 chr5D.!!$F1 696

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
283 319 0.242825 CTTGCGGGACTGTCTTCGTA 59.757 55.0 18.98 14.55 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2163 0.749649 ATGATCTCCTCGGACACTGC 59.25 55.0 0.0 0.0 0.0 4.4 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
73 79 2.641439 TTTTGCTTGTGCGGGCAAGG 62.641 55.000 14.44 0.00 46.75 3.61
129 135 3.650950 AAGGCGGCACATGGGAGT 61.651 61.111 13.08 0.00 0.00 3.85
167 181 1.072505 GAAGGTTCCCGTGGCAGAA 59.927 57.895 0.00 0.00 0.00 3.02
184 198 0.535335 GAACCACAGTAGCATCCGGA 59.465 55.000 6.61 6.61 0.00 5.14
221 235 7.481642 CGAGATAGCAATCCCGTATAACTAAT 58.518 38.462 0.00 0.00 29.50 1.73
222 236 7.974501 CGAGATAGCAATCCCGTATAACTAATT 59.025 37.037 0.00 0.00 29.50 1.40
259 295 6.868622 ACACATATTCTAGAAAGAGACGCTT 58.131 36.000 9.71 0.00 38.88 4.68
282 318 1.006102 CTTGCGGGACTGTCTTCGT 60.006 57.895 18.98 0.00 0.00 3.85
283 319 0.242825 CTTGCGGGACTGTCTTCGTA 59.757 55.000 18.98 14.55 0.00 3.43
331 483 1.540580 GCGTACAGGGAAGATTAGCCC 60.541 57.143 0.00 0.00 45.04 5.19
336 488 1.496429 CAGGGAAGATTAGCCCCATGT 59.504 52.381 0.00 0.00 45.89 3.21
370 526 3.240134 AAGATATGGGCGCGGCGAT 62.240 57.895 30.86 30.86 0.00 4.58
400 557 4.966965 TTTTCGAAGCTTTACCAACACA 57.033 36.364 0.00 0.00 0.00 3.72
479 645 1.484240 AGAGTGCAGTGCTCCCTAATC 59.516 52.381 17.60 4.14 33.69 1.75
552 722 6.867519 TTCTTGGACAAGTGTAGATGGATA 57.132 37.500 11.44 0.00 39.38 2.59
574 744 4.226113 AGATAAGTCGTTATCCGTCTGC 57.774 45.455 2.97 0.00 44.02 4.26
590 760 1.618343 TCTGCCTCGAGAATCACAACA 59.382 47.619 15.71 0.00 33.17 3.33
599 769 2.476619 GAGAATCACAACACCACGTCAG 59.523 50.000 0.00 0.00 33.17 3.51
608 782 1.542030 ACACCACGTCAGTCATCTCTC 59.458 52.381 0.00 0.00 0.00 3.20
621 795 2.537714 ATCTCTCTCCCCCAAGCCGT 62.538 60.000 0.00 0.00 0.00 5.68
657 831 2.546321 CTTCACACGAGTGCACGC 59.454 61.111 12.01 11.45 45.49 5.34
658 832 2.202810 TTCACACGAGTGCACGCA 60.203 55.556 20.77 0.00 45.49 5.24
659 833 2.416372 CTTCACACGAGTGCACGCAC 62.416 60.000 20.77 14.28 45.49 5.34
681 859 3.943691 CACGTCCCCCGGGTCAAA 61.944 66.667 21.85 0.00 42.24 2.69
693 871 2.288152 CCGGGTCAAAGTCAAACCATTG 60.288 50.000 0.00 0.00 37.92 2.82
728 906 4.634133 TGACACGACGACGCCACC 62.634 66.667 7.30 0.00 43.96 4.61
833 1034 1.866853 CTCCTTCCCGGCAAAGCAAC 61.867 60.000 0.00 0.00 0.00 4.17
834 1035 2.255252 CTTCCCGGCAAAGCAACG 59.745 61.111 0.00 0.00 0.00 4.10
835 1036 3.896863 CTTCCCGGCAAAGCAACGC 62.897 63.158 0.00 0.00 0.00 4.84
841 1042 4.940593 GCAAAGCAACGCGGCCAA 62.941 61.111 12.47 0.00 0.00 4.52
842 1043 2.049248 CAAAGCAACGCGGCCAAT 60.049 55.556 12.47 0.00 0.00 3.16
843 1044 2.088178 CAAAGCAACGCGGCCAATC 61.088 57.895 12.47 0.00 0.00 2.67
844 1045 2.560119 AAAGCAACGCGGCCAATCA 61.560 52.632 12.47 0.00 0.00 2.57
845 1046 2.476534 AAAGCAACGCGGCCAATCAG 62.477 55.000 12.47 0.00 0.00 2.90
846 1047 4.481112 GCAACGCGGCCAATCAGG 62.481 66.667 12.47 0.00 41.84 3.86
867 1078 1.820481 CCCACGAAACCCACAACGT 60.820 57.895 0.00 0.00 39.53 3.99
913 1125 4.561606 ACGACCGAGAGAAAAATAATCACG 59.438 41.667 0.00 0.00 0.00 4.35
1019 1239 3.499737 CACCGCCGAAGCATCCAC 61.500 66.667 0.00 0.00 39.83 4.02
1055 1290 1.632409 ACCTCATCATCTGCCACAAGT 59.368 47.619 0.00 0.00 0.00 3.16
1060 1310 3.943381 TCATCATCTGCCACAAGTGATTC 59.057 43.478 0.94 0.00 0.00 2.52
1068 1318 0.734889 CACAAGTGATTCGCCATCCC 59.265 55.000 0.00 0.00 0.00 3.85
1334 1591 3.735029 GGCACCGACGACGACTCT 61.735 66.667 9.28 0.00 42.66 3.24
1337 1594 2.033755 CACCGACGACGACTCTCCT 61.034 63.158 9.28 0.00 42.66 3.69
1339 1596 0.888285 ACCGACGACGACTCTCCTTT 60.888 55.000 9.28 0.00 42.66 3.11
1350 1619 0.737715 CTCTCCTTTGCCTTCGTCGG 60.738 60.000 0.00 0.00 0.00 4.79
1416 1688 3.123620 CAGCTTGGAGTCAGCGGC 61.124 66.667 0.00 0.00 0.00 6.53
1419 1691 2.435586 CTTGGAGTCAGCGGCTGG 60.436 66.667 28.18 11.17 31.51 4.85
1431 1703 0.320421 GCGGCTGGTTAGTTCTGACA 60.320 55.000 0.00 0.00 0.00 3.58
1435 1707 2.486548 GGCTGGTTAGTTCTGACACCAA 60.487 50.000 0.00 0.00 0.00 3.67
1459 1737 3.147629 GGGTAGATACTAGCGAGCTTGA 58.852 50.000 12.99 0.00 0.00 3.02
1463 1741 6.095720 GGGTAGATACTAGCGAGCTTGATAAT 59.904 42.308 12.99 0.00 0.00 1.28
1464 1742 7.363094 GGGTAGATACTAGCGAGCTTGATAATT 60.363 40.741 12.99 0.00 0.00 1.40
1465 1743 7.698970 GGTAGATACTAGCGAGCTTGATAATTC 59.301 40.741 12.99 0.19 0.00 2.17
1466 1744 7.461182 AGATACTAGCGAGCTTGATAATTCT 57.539 36.000 12.99 2.56 0.00 2.40
1467 1745 7.312154 AGATACTAGCGAGCTTGATAATTCTG 58.688 38.462 12.99 0.00 0.00 3.02
1516 1794 4.024725 CGTGGTTTGACCGTTTGAGATTTA 60.025 41.667 0.00 0.00 42.58 1.40
1559 1837 5.633830 AACTCAGCATGTAAATCAGGTTG 57.366 39.130 0.00 0.00 39.65 3.77
1574 1852 1.605451 GTTGGGTGGGGCCTTGTAC 60.605 63.158 0.84 0.00 37.43 2.90
1620 1898 8.786898 TCGGGATGATGAATTATTTGATTCTTC 58.213 33.333 6.57 6.57 39.12 2.87
1639 1917 7.715265 TTCTTCACAGTTTGTCTTCTGTATC 57.285 36.000 0.00 0.00 42.05 2.24
1641 1919 7.445121 TCTTCACAGTTTGTCTTCTGTATCAT 58.555 34.615 0.00 0.00 42.05 2.45
1648 1926 7.800380 CAGTTTGTCTTCTGTATCATTTGTGAC 59.200 37.037 0.00 0.00 0.00 3.67
1667 1945 5.163353 TGTGACTGTGGATTGTTCAGTTCTA 60.163 40.000 0.00 0.00 41.58 2.10
1796 2101 1.480545 AGGGTTTTGCAACAGACCAAC 59.519 47.619 21.02 12.61 34.15 3.77
1799 2104 2.165437 GGTTTTGCAACAGACCAACAGA 59.835 45.455 16.83 0.00 34.15 3.41
1808 2113 2.578021 ACAGACCAACAGAATAGGCCAT 59.422 45.455 5.01 0.00 0.00 4.40
1854 2163 9.062524 TGGAATATAGTTTTATTGATCGGGTTG 57.937 33.333 0.00 0.00 0.00 3.77
1925 2236 7.033791 AGTATGTAATCGGTCACTTGTACTTG 58.966 38.462 0.00 0.00 0.00 3.16
2042 2353 4.760204 TGAATAGGAGCAAGCATCATCATG 59.240 41.667 0.00 0.00 0.00 3.07
2082 2396 4.019174 ACCATAAAGGGACAAATGCAGAG 58.981 43.478 0.00 0.00 43.89 3.35
2086 2400 1.542492 AGGGACAAATGCAGAGCTTG 58.458 50.000 0.00 0.00 0.00 4.01
2089 2403 1.135460 GGACAAATGCAGAGCTTGAGC 60.135 52.381 0.00 0.00 42.49 4.26
2135 2453 7.833682 TGAATAGTGGGCATTTTCTGAAGATTA 59.166 33.333 0.00 0.00 0.00 1.75
2166 2484 1.211457 AGATGGGAGCCATGACAGAAC 59.789 52.381 0.00 0.00 45.26 3.01
2205 2527 5.914074 CAGATGATATCAGAGTCGTTGTGAG 59.086 44.000 11.78 0.00 31.90 3.51
2239 2565 7.320384 ACTCAAATTTCCCCTTCAAATTGAT 57.680 32.000 0.00 0.00 34.39 2.57
2240 2566 7.163441 ACTCAAATTTCCCCTTCAAATTGATG 58.837 34.615 0.00 0.00 34.39 3.07
2241 2567 7.016465 ACTCAAATTTCCCCTTCAAATTGATGA 59.984 33.333 10.03 0.43 34.39 2.92
2252 2578 6.647334 TTCAAATTGATGAAGTGCCTAACA 57.353 33.333 0.00 0.00 34.50 2.41
2282 2608 9.065871 GCTAAAATTTGCTGACTTACACTTATG 57.934 33.333 0.00 0.00 0.00 1.90
2318 2644 2.161609 CACGGCCTGTGGAACTTTATTC 59.838 50.000 16.84 0.00 45.21 1.75
2337 2663 9.743057 CTTTATTCACATCCACAAAGTAAAACA 57.257 29.630 0.00 0.00 0.00 2.83
2347 2673 4.905866 CACAAAGTAAAACATGACTCTGCG 59.094 41.667 0.00 0.00 0.00 5.18
2348 2674 4.024048 ACAAAGTAAAACATGACTCTGCGG 60.024 41.667 0.00 0.00 0.00 5.69
2354 2680 2.376808 ACATGACTCTGCGGAAGAAG 57.623 50.000 0.00 0.00 38.49 2.85
2355 2681 1.066573 ACATGACTCTGCGGAAGAAGG 60.067 52.381 0.00 0.00 37.37 3.46
2357 2683 0.891373 TGACTCTGCGGAAGAAGGAG 59.109 55.000 0.00 0.00 37.37 3.69
2359 2685 1.754226 GACTCTGCGGAAGAAGGAGAT 59.246 52.381 0.00 0.00 37.37 2.75
2360 2686 1.480137 ACTCTGCGGAAGAAGGAGATG 59.520 52.381 0.00 0.00 37.37 2.90
2373 2700 6.174720 AGAAGGAGATGTGTTGTTTAGTCA 57.825 37.500 0.00 0.00 0.00 3.41
2405 2732 0.250858 TGACCCTGCACATTCCACAG 60.251 55.000 0.00 0.00 0.00 3.66
2413 2740 3.220940 TGCACATTCCACAGTGATTGAA 58.779 40.909 0.62 0.00 37.97 2.69
2426 2753 8.212317 CACAGTGATTGAATGTTGTGGATATA 57.788 34.615 0.00 0.00 33.98 0.86
2427 2754 8.843262 CACAGTGATTGAATGTTGTGGATATAT 58.157 33.333 0.00 0.00 33.98 0.86
2430 2757 9.507329 AGTGATTGAATGTTGTGGATATATACC 57.493 33.333 0.00 0.00 0.00 2.73
2431 2758 9.283768 GTGATTGAATGTTGTGGATATATACCA 57.716 33.333 0.00 0.00 34.84 3.25
2432 2759 9.859152 TGATTGAATGTTGTGGATATATACCAA 57.141 29.630 5.72 1.42 39.22 3.67
2436 2763 8.575589 TGAATGTTGTGGATATATACCAAATGC 58.424 33.333 5.72 0.00 39.22 3.56
2437 2764 8.710749 AATGTTGTGGATATATACCAAATGCT 57.289 30.769 5.72 0.00 39.22 3.79
2438 2765 9.806448 AATGTTGTGGATATATACCAAATGCTA 57.194 29.630 5.72 0.00 39.22 3.49
2439 2766 9.979897 ATGTTGTGGATATATACCAAATGCTAT 57.020 29.630 5.72 0.00 39.22 2.97
2440 2767 9.448438 TGTTGTGGATATATACCAAATGCTATC 57.552 33.333 5.72 0.00 39.22 2.08
2441 2768 9.448438 GTTGTGGATATATACCAAATGCTATCA 57.552 33.333 5.72 0.00 39.22 2.15
2451 2778 8.954834 ATACCAAATGCTATCAATAATCCCAA 57.045 30.769 0.00 0.00 0.00 4.12
2453 2780 8.954834 ACCAAATGCTATCAATAATCCCAATA 57.045 30.769 0.00 0.00 0.00 1.90
2454 2781 9.551339 ACCAAATGCTATCAATAATCCCAATAT 57.449 29.630 0.00 0.00 0.00 1.28
2483 2810 9.354673 AGAATCATGAAATTTTATGGATACGGT 57.645 29.630 19.47 1.95 42.51 4.83
2525 2857 2.171003 CAGACCAACCCTGGAAATTCC 58.829 52.381 4.79 4.79 46.92 3.01
2590 2922 3.736224 CCAGCTGGCCATCCTGGT 61.736 66.667 30.74 14.79 40.92 4.00
2604 2936 3.746045 TCCTGGTAAGAACACACTGAC 57.254 47.619 0.00 0.00 0.00 3.51
2605 2937 3.305720 TCCTGGTAAGAACACACTGACT 58.694 45.455 0.00 0.00 0.00 3.41
2606 2938 4.476297 TCCTGGTAAGAACACACTGACTA 58.524 43.478 0.00 0.00 0.00 2.59
2607 2939 4.897076 TCCTGGTAAGAACACACTGACTAA 59.103 41.667 0.00 0.00 0.00 2.24
2617 2949 1.694150 ACACTGACTAAAGCCTCAGCA 59.306 47.619 0.00 0.00 43.56 4.41
2636 2968 2.580962 CATCTGATCCGAGGACTGAGA 58.419 52.381 0.00 0.00 0.00 3.27
2649 2981 5.521735 CGAGGACTGAGATAAATGGTTGAAG 59.478 44.000 0.00 0.00 0.00 3.02
2652 2984 6.214412 AGGACTGAGATAAATGGTTGAAGACT 59.786 38.462 0.00 0.00 0.00 3.24
2654 2986 7.492994 GGACTGAGATAAATGGTTGAAGACTAC 59.507 40.741 0.00 0.00 0.00 2.73
2658 2990 5.812642 AGATAAATGGTTGAAGACTACAGCG 59.187 40.000 0.00 0.00 0.00 5.18
2662 2994 2.299013 TGGTTGAAGACTACAGCGACAT 59.701 45.455 0.00 0.00 0.00 3.06
2663 2995 2.668457 GGTTGAAGACTACAGCGACATG 59.332 50.000 0.00 0.00 0.00 3.21
2665 2997 3.934457 TGAAGACTACAGCGACATGAA 57.066 42.857 0.00 0.00 0.00 2.57
2667 2999 4.176271 TGAAGACTACAGCGACATGAATG 58.824 43.478 0.00 0.00 0.00 2.67
2676 3008 4.542662 AGCGACATGAATGCTGATTTAC 57.457 40.909 0.00 0.00 37.62 2.01
2677 3009 4.194640 AGCGACATGAATGCTGATTTACT 58.805 39.130 0.00 0.00 37.62 2.24
2678 3010 5.359756 AGCGACATGAATGCTGATTTACTA 58.640 37.500 0.00 0.00 37.62 1.82
2679 3011 5.464722 AGCGACATGAATGCTGATTTACTAG 59.535 40.000 0.00 0.00 37.62 2.57
2697 3030 5.674933 ACTAGTAAAAACAGAGCAGCAAC 57.325 39.130 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 181 0.981183 TTTCCGGATGCTACTGTGGT 59.019 50.000 4.15 0.00 0.00 4.16
184 198 0.039074 CTATCTCGCCTCGCCGATTT 60.039 55.000 0.00 0.00 36.54 2.17
221 235 5.943416 AGAATATGTGTTTTGACCATCGGAA 59.057 36.000 0.00 0.00 0.00 4.30
222 236 5.496556 AGAATATGTGTTTTGACCATCGGA 58.503 37.500 0.00 0.00 0.00 4.55
259 295 1.045407 AGACAGTCCCGCAAGTTGTA 58.955 50.000 4.48 0.00 0.00 2.41
282 318 7.578310 ATTAGTAGTTTGAGTGCCTCGTATA 57.422 36.000 0.00 0.00 32.35 1.47
283 319 5.909621 TTAGTAGTTTGAGTGCCTCGTAT 57.090 39.130 0.00 0.00 32.35 3.06
305 457 1.108776 TCTTCCCTGTACGCGCTAAT 58.891 50.000 5.73 0.00 0.00 1.73
331 483 1.468520 CGGTTTGACCAGCTAACATGG 59.531 52.381 0.00 0.00 43.87 3.66
336 488 3.695830 ATCTTCGGTTTGACCAGCTAA 57.304 42.857 0.00 0.00 38.47 3.09
370 526 6.431543 TGGTAAAGCTTCGAAAAATGACCATA 59.568 34.615 13.86 0.00 0.00 2.74
440 602 5.178623 CACTCTACGTGCCAGTTCAAATTTA 59.821 40.000 0.00 0.00 36.72 1.40
441 603 4.024048 CACTCTACGTGCCAGTTCAAATTT 60.024 41.667 0.00 0.00 36.72 1.82
444 606 2.479837 CACTCTACGTGCCAGTTCAAA 58.520 47.619 0.00 0.00 36.72 2.69
466 628 1.478510 CAGACGTGATTAGGGAGCACT 59.521 52.381 0.00 0.00 42.43 4.40
467 629 1.204941 ACAGACGTGATTAGGGAGCAC 59.795 52.381 0.00 0.00 41.21 4.40
468 630 1.204704 CACAGACGTGATTAGGGAGCA 59.795 52.381 0.00 0.00 46.80 4.26
469 631 1.204941 ACACAGACGTGATTAGGGAGC 59.795 52.381 0.00 0.00 46.80 4.70
470 632 2.231478 ACACACAGACGTGATTAGGGAG 59.769 50.000 0.00 0.00 46.80 4.30
479 645 5.552043 GTGGTTTCCAACACACAGACGTG 62.552 52.174 0.00 0.00 41.64 4.49
552 722 4.499357 GGCAGACGGATAACGACTTATCTT 60.499 45.833 5.93 0.00 44.81 2.40
569 739 1.996191 GTTGTGATTCTCGAGGCAGAC 59.004 52.381 13.56 5.67 0.00 3.51
574 744 2.069273 GTGGTGTTGTGATTCTCGAGG 58.931 52.381 13.56 0.00 0.00 4.63
590 760 2.088423 GAGAGAGATGACTGACGTGGT 58.912 52.381 0.00 0.00 0.00 4.16
599 769 0.467804 GCTTGGGGGAGAGAGATGAC 59.532 60.000 0.00 0.00 0.00 3.06
608 782 3.628646 CTTGGACGGCTTGGGGGAG 62.629 68.421 0.00 0.00 0.00 4.30
621 795 4.225042 TGAAGGCTGCTAAGATTACTTGGA 59.775 41.667 0.00 0.00 36.86 3.53
676 854 2.796593 GCTGCAATGGTTTGACTTTGAC 59.203 45.455 0.00 0.00 34.60 3.18
677 855 2.543445 CGCTGCAATGGTTTGACTTTGA 60.543 45.455 0.00 0.00 34.60 2.69
678 856 1.788308 CGCTGCAATGGTTTGACTTTG 59.212 47.619 0.00 0.00 34.60 2.77
679 857 1.269726 CCGCTGCAATGGTTTGACTTT 60.270 47.619 0.00 0.00 34.60 2.66
680 858 0.314935 CCGCTGCAATGGTTTGACTT 59.685 50.000 0.00 0.00 34.60 3.01
681 859 1.959085 CCGCTGCAATGGTTTGACT 59.041 52.632 0.00 0.00 34.60 3.41
693 871 3.615536 AACATCTTTGCGCCGCTGC 62.616 57.895 11.67 1.30 0.00 5.25
838 1039 4.776322 TCGTGGGCGCCTGATTGG 62.776 66.667 28.56 10.12 38.14 3.16
839 1040 2.331893 TTTCGTGGGCGCCTGATTG 61.332 57.895 28.56 12.20 38.14 2.67
840 1041 2.033448 TTTCGTGGGCGCCTGATT 59.967 55.556 28.56 0.00 38.14 2.57
841 1042 2.746277 GTTTCGTGGGCGCCTGAT 60.746 61.111 28.56 0.00 38.14 2.90
847 1048 2.902846 TTGTGGGTTTCGTGGGCG 60.903 61.111 0.00 0.00 39.92 6.13
848 1049 2.725641 GTTGTGGGTTTCGTGGGC 59.274 61.111 0.00 0.00 0.00 5.36
849 1050 1.378124 AACGTTGTGGGTTTCGTGGG 61.378 55.000 0.00 0.00 36.65 4.61
850 1051 0.452585 AAACGTTGTGGGTTTCGTGG 59.547 50.000 0.00 0.00 36.65 4.94
867 1078 1.587613 GCAAACGCAAGCGGTGAAA 60.588 52.632 19.30 0.00 40.27 2.69
1012 1232 2.205074 CTCTTGTGTATCGGTGGATGC 58.795 52.381 0.00 0.00 36.00 3.91
1019 1239 0.456221 AGGTCGCTCTTGTGTATCGG 59.544 55.000 0.00 0.00 0.00 4.18
1055 1290 0.623194 TCAAAGGGGATGGCGAATCA 59.377 50.000 0.00 0.00 36.98 2.57
1060 1310 0.740737 GTCAATCAAAGGGGATGGCG 59.259 55.000 0.00 0.00 0.00 5.69
1068 1318 2.679837 CGGTGGATCAGTCAATCAAAGG 59.320 50.000 0.00 0.00 0.00 3.11
1350 1619 2.717809 GCGACGACCACGAAGAAGC 61.718 63.158 0.00 0.00 42.66 3.86
1416 1688 4.216257 CCATTTGGTGTCAGAACTAACCAG 59.784 45.833 0.00 0.00 43.31 4.00
1419 1691 4.766404 CCCATTTGGTGTCAGAACTAAC 57.234 45.455 0.00 0.00 0.00 2.34
1435 1707 3.768878 AGCTCGCTAGTATCTACCCATT 58.231 45.455 0.00 0.00 0.00 3.16
1444 1716 6.987386 ACAGAATTATCAAGCTCGCTAGTAT 58.013 36.000 0.00 0.00 0.00 2.12
1459 1737 6.176183 CCAGGACAGTTCAGAACAGAATTAT 58.824 40.000 15.85 0.00 0.00 1.28
1463 1741 2.104792 CCCAGGACAGTTCAGAACAGAA 59.895 50.000 15.85 0.00 0.00 3.02
1464 1742 1.694150 CCCAGGACAGTTCAGAACAGA 59.306 52.381 15.85 0.00 0.00 3.41
1465 1743 1.417890 ACCCAGGACAGTTCAGAACAG 59.582 52.381 15.85 10.03 0.00 3.16
1466 1744 1.507140 ACCCAGGACAGTTCAGAACA 58.493 50.000 15.85 0.00 0.00 3.18
1467 1745 2.618709 CAAACCCAGGACAGTTCAGAAC 59.381 50.000 5.00 5.00 0.00 3.01
1535 1813 6.449698 CAACCTGATTTACATGCTGAGTTTT 58.550 36.000 0.00 0.00 0.00 2.43
1536 1814 5.047802 CCAACCTGATTTACATGCTGAGTTT 60.048 40.000 0.00 0.00 0.00 2.66
1537 1815 4.460382 CCAACCTGATTTACATGCTGAGTT 59.540 41.667 0.00 0.00 0.00 3.01
1538 1816 4.012374 CCAACCTGATTTACATGCTGAGT 58.988 43.478 0.00 0.00 0.00 3.41
1539 1817 3.379372 CCCAACCTGATTTACATGCTGAG 59.621 47.826 0.00 0.00 0.00 3.35
1540 1818 3.245229 ACCCAACCTGATTTACATGCTGA 60.245 43.478 0.00 0.00 0.00 4.26
1541 1819 3.091545 ACCCAACCTGATTTACATGCTG 58.908 45.455 0.00 0.00 0.00 4.41
1542 1820 3.091545 CACCCAACCTGATTTACATGCT 58.908 45.455 0.00 0.00 0.00 3.79
1543 1821 2.166254 CCACCCAACCTGATTTACATGC 59.834 50.000 0.00 0.00 0.00 4.06
1559 1837 0.850784 ATATGTACAAGGCCCCACCC 59.149 55.000 0.00 0.00 40.58 4.61
1574 1852 7.650890 TCCCGATTCAAATCAATGAACATATG 58.349 34.615 0.00 0.00 41.78 1.78
1620 1898 7.588854 CACAAATGATACAGAAGACAAACTGTG 59.411 37.037 0.00 0.00 45.20 3.66
1639 1917 5.185668 TGAACAATCCACAGTCACAAATG 57.814 39.130 0.00 0.00 0.00 2.32
1641 1919 4.269183 ACTGAACAATCCACAGTCACAAA 58.731 39.130 0.00 0.00 40.19 2.83
1648 1926 5.541845 TCTGTAGAACTGAACAATCCACAG 58.458 41.667 0.00 0.00 37.62 3.66
1777 2082 1.205893 TGTTGGTCTGTTGCAAAACCC 59.794 47.619 18.99 10.37 0.00 4.11
1778 2083 2.165437 TCTGTTGGTCTGTTGCAAAACC 59.835 45.455 16.29 16.29 0.00 3.27
1779 2084 3.502191 TCTGTTGGTCTGTTGCAAAAC 57.498 42.857 0.00 1.10 0.00 2.43
1796 2101 2.104451 ACAGCAGAGATGGCCTATTCTG 59.896 50.000 19.98 19.98 39.94 3.02
1799 2104 4.989875 AATACAGCAGAGATGGCCTATT 57.010 40.909 3.32 0.00 0.00 1.73
1808 2113 3.386078 CCAGCTCCTTAATACAGCAGAGA 59.614 47.826 0.00 0.00 35.46 3.10
1854 2163 0.749649 ATGATCTCCTCGGACACTGC 59.250 55.000 0.00 0.00 0.00 4.40
1911 2222 4.002906 TGATCCACAAGTACAAGTGACC 57.997 45.455 16.47 7.66 37.97 4.02
1925 2236 5.994668 GGATGAGGTTAGAGAAATGATCCAC 59.005 44.000 0.00 0.00 0.00 4.02
2025 2336 2.847441 TCTCATGATGATGCTTGCTCC 58.153 47.619 0.00 0.00 0.00 4.70
2061 2375 3.181483 GCTCTGCATTTGTCCCTTTATGG 60.181 47.826 0.00 0.00 0.00 2.74
2082 2396 4.475944 ACGTCATATTTGTTTGCTCAAGC 58.524 39.130 0.00 0.00 42.50 4.01
2086 2400 6.021596 CAGGTAACGTCATATTTGTTTGCTC 58.978 40.000 0.00 0.00 46.39 4.26
2089 2403 9.702726 CTATTCAGGTAACGTCATATTTGTTTG 57.297 33.333 0.00 0.00 46.39 2.93
2135 2453 1.065564 GCTCCCATCTGTCTCTGCTTT 60.066 52.381 0.00 0.00 0.00 3.51
2205 2527 4.556233 GGGAAATTTGAGTACTTGTTGGC 58.444 43.478 0.00 0.00 0.00 4.52
2210 2532 6.648879 TTGAAGGGGAAATTTGAGTACTTG 57.351 37.500 0.00 0.00 0.00 3.16
2246 2572 6.363357 GTCAGCAAATTTTAGCTTGTGTTAGG 59.637 38.462 0.00 0.00 39.50 2.69
2251 2577 6.917477 TGTAAGTCAGCAAATTTTAGCTTGTG 59.083 34.615 0.00 0.00 39.50 3.33
2252 2578 6.918022 GTGTAAGTCAGCAAATTTTAGCTTGT 59.082 34.615 0.00 0.00 39.50 3.16
2259 2585 9.463443 GAACATAAGTGTAAGTCAGCAAATTTT 57.537 29.630 0.00 0.00 37.67 1.82
2282 2608 1.235724 CCGTGGTGAAAAGAGGGAAC 58.764 55.000 0.00 0.00 0.00 3.62
2318 2644 6.738114 AGTCATGTTTTACTTTGTGGATGTG 58.262 36.000 0.00 0.00 0.00 3.21
2337 2663 1.480137 CTCCTTCTTCCGCAGAGTCAT 59.520 52.381 0.00 0.00 31.12 3.06
2347 2673 5.998363 ACTAAACAACACATCTCCTTCTTCC 59.002 40.000 0.00 0.00 0.00 3.46
2348 2674 6.706270 TGACTAAACAACACATCTCCTTCTTC 59.294 38.462 0.00 0.00 0.00 2.87
2354 2680 6.650807 TGATTCTGACTAAACAACACATCTCC 59.349 38.462 0.00 0.00 0.00 3.71
2355 2681 7.658179 TGATTCTGACTAAACAACACATCTC 57.342 36.000 0.00 0.00 0.00 2.75
2388 2715 0.538057 CACTGTGGAATGTGCAGGGT 60.538 55.000 0.00 0.00 34.79 4.34
2389 2716 0.250858 TCACTGTGGAATGTGCAGGG 60.251 55.000 8.11 0.00 35.15 4.45
2405 2732 9.283768 TGGTATATATCCACAACATTCAATCAC 57.716 33.333 0.00 0.00 0.00 3.06
2413 2740 9.979897 ATAGCATTTGGTATATATCCACAACAT 57.020 29.630 0.58 0.00 37.01 2.71
2426 2753 8.954834 TTGGGATTATTGATAGCATTTGGTAT 57.045 30.769 2.08 2.08 40.97 2.73
2427 2754 8.954834 ATTGGGATTATTGATAGCATTTGGTA 57.045 30.769 0.00 0.00 0.00 3.25
2428 2755 7.860649 ATTGGGATTATTGATAGCATTTGGT 57.139 32.000 0.00 0.00 0.00 3.67
2471 2798 9.785982 TGAAATGATTTCATACCGTATCCATAA 57.214 29.630 16.04 0.00 44.21 1.90
2525 2857 1.422531 AGCTGGAGAAGATAGCAGGG 58.577 55.000 0.00 0.00 39.84 4.45
2552 2884 1.476085 TGCCGGAAATGCATTTACCTG 59.524 47.619 25.36 21.42 32.85 4.00
2590 2922 5.069914 TGAGGCTTTAGTCAGTGTGTTCTTA 59.930 40.000 0.00 0.00 0.00 2.10
2604 2936 3.401182 GGATCAGATGCTGAGGCTTTAG 58.599 50.000 3.36 0.00 44.08 1.85
2605 2937 2.224137 CGGATCAGATGCTGAGGCTTTA 60.224 50.000 0.00 0.00 44.08 1.85
2606 2938 1.474677 CGGATCAGATGCTGAGGCTTT 60.475 52.381 0.00 0.00 44.08 3.51
2607 2939 0.106335 CGGATCAGATGCTGAGGCTT 59.894 55.000 0.00 0.00 44.08 4.35
2617 2949 3.524095 ATCTCAGTCCTCGGATCAGAT 57.476 47.619 0.00 0.00 0.00 2.90
2636 2968 5.581085 GTCGCTGTAGTCTTCAACCATTTAT 59.419 40.000 0.00 0.00 0.00 1.40
2649 2981 2.283617 CAGCATTCATGTCGCTGTAGTC 59.716 50.000 19.09 0.00 46.36 2.59
2665 2997 8.669243 GCTCTGTTTTTACTAGTAAATCAGCAT 58.331 33.333 30.75 3.03 37.33 3.79
2667 2999 8.029642 TGCTCTGTTTTTACTAGTAAATCAGC 57.970 34.615 30.75 26.69 37.33 4.26
2670 3002 8.029642 TGCTGCTCTGTTTTTACTAGTAAATC 57.970 34.615 24.89 20.36 35.27 2.17
2671 3003 7.979444 TGCTGCTCTGTTTTTACTAGTAAAT 57.021 32.000 24.89 0.00 35.27 1.40
2672 3004 7.517734 CGTTGCTGCTCTGTTTTTACTAGTAAA 60.518 37.037 21.52 21.52 33.63 2.01
2674 3006 5.404366 CGTTGCTGCTCTGTTTTTACTAGTA 59.596 40.000 0.00 0.00 0.00 1.82
2675 3007 4.211374 CGTTGCTGCTCTGTTTTTACTAGT 59.789 41.667 0.00 0.00 0.00 2.57
2676 3008 4.702392 CGTTGCTGCTCTGTTTTTACTAG 58.298 43.478 0.00 0.00 0.00 2.57
2677 3009 3.059188 GCGTTGCTGCTCTGTTTTTACTA 60.059 43.478 0.00 0.00 0.00 1.82
2678 3010 2.287009 GCGTTGCTGCTCTGTTTTTACT 60.287 45.455 0.00 0.00 0.00 2.24
2679 3011 2.044135 GCGTTGCTGCTCTGTTTTTAC 58.956 47.619 0.00 0.00 0.00 2.01
2684 3017 1.097547 AACTGCGTTGCTGCTCTGTT 61.098 50.000 0.00 1.91 35.36 3.16


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

AutoCloner maintained by Alex Coulton.