Multiple sequence alignment - TraesCS7A01G490900

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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 TraesCS7A01G490900 chr7A 100.000 2417 0 0 1 2417 680243599 680246015 0.000000e+00 4464.0
1 TraesCS7A01G490900 chr7A 87.482 711 72 14 746 1450 689252003 689252702 0.000000e+00 804.0
2 TraesCS7A01G490900 chr7A 76.415 212 36 12 1758 1958 680325698 680325906 4.250000e-18 102.0
3 TraesCS7A01G490900 chr7B 90.526 1446 104 14 1 1432 661468170 661469596 0.000000e+00 1881.0
4 TraesCS7A01G490900 chr7B 89.238 827 72 14 634 1453 661998651 661999467 0.000000e+00 1018.0
5 TraesCS7A01G490900 chr7B 92.210 706 47 5 747 1450 662311722 662311023 0.000000e+00 992.0
6 TraesCS7A01G490900 chr7B 88.972 798 68 20 660 1453 661716355 661717136 0.000000e+00 968.0
7 TraesCS7A01G490900 chr7B 89.717 671 60 9 750 1417 662010201 662009537 0.000000e+00 848.0
8 TraesCS7A01G490900 chr7B 87.945 730 69 15 732 1450 674194077 674194798 0.000000e+00 843.0
9 TraesCS7A01G490900 chr7B 96.344 465 13 3 1955 2417 662000584 662001046 0.000000e+00 761.0
10 TraesCS7A01G490900 chr7B 83.333 276 28 10 2144 2417 661914145 661914404 3.110000e-59 239.0
11 TraesCS7A01G490900 chr7B 80.205 293 43 5 1451 1728 661717173 661717465 3.150000e-49 206.0
12 TraesCS7A01G490900 chr7B 79.208 202 31 6 1758 1948 662311102 662310901 1.950000e-26 130.0
13 TraesCS7A01G490900 chr7B 83.459 133 17 4 1759 1886 662466085 662466217 4.220000e-23 119.0
14 TraesCS7A01G490900 chr7B 78.173 197 26 11 1758 1953 674194719 674194899 2.540000e-20 110.0
15 TraesCS7A01G490900 chr7B 81.148 122 18 4 1758 1876 661717056 661717175 2.560000e-15 93.5
16 TraesCS7A01G490900 chr7B 81.452 124 14 8 1758 1876 661999387 661999506 2.560000e-15 93.5
17 TraesCS7A01G490900 chr7B 85.870 92 4 7 1977 2068 662310743 662310661 3.310000e-14 89.8
18 TraesCS7A01G490900 chr7D 91.011 890 44 18 561 1432 588252604 588253475 0.000000e+00 1168.0
19 TraesCS7A01G490900 chr7D 90.401 823 58 13 634 1450 588472122 588471315 0.000000e+00 1062.0
20 TraesCS7A01G490900 chr7D 91.396 709 52 8 748 1453 588409061 588409763 0.000000e+00 963.0
21 TraesCS7A01G490900 chr7D 84.532 556 67 12 7 550 588251990 588252538 1.270000e-147 532.0
22 TraesCS7A01G490900 chr7D 92.342 222 16 1 1551 1771 588410260 588410481 5.020000e-82 315.0
23 TraesCS7A01G490900 chr7D 89.831 118 4 2 1451 1560 588409800 588409917 6.960000e-31 145.0
24 TraesCS7A01G490900 chr7D 89.412 85 9 0 2249 2333 574855272 574855188 9.140000e-20 108.0
25 TraesCS7A01G490900 chr7D 82.787 122 17 3 1758 1876 588409682 588409802 3.290000e-19 106.0
26 TraesCS7A01G490900 chr7D 80.000 135 20 6 1758 1886 588539373 588539506 2.560000e-15 93.5
27 TraesCS7A01G490900 chr3D 89.625 694 49 10 747 1437 455037640 455036967 0.000000e+00 861.0
28 TraesCS7A01G490900 chr5A 94.366 71 1 2 2081 2149 630347675 630347606 3.290000e-19 106.0
29 TraesCS7A01G490900 chr4B 81.955 133 16 5 1758 1883 625595032 625595163 3.290000e-19 106.0
30 TraesCS7A01G490900 chr2A 94.366 71 1 2 2081 2149 335838395 335838326 3.290000e-19 106.0
31 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 93409864 93409933 1.530000e-17 100.0
32 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 216518835 216518904 1.530000e-17 100.0
33 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 216522223 216522292 1.530000e-17 100.0
34 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 346596727 346596796 1.530000e-17 100.0
35 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 372771886 372771955 1.530000e-17 100.0
36 TraesCS7A01G490900 chrUn 92.958 71 2 2 2081 2149 396205593 396205662 1.530000e-17 100.0


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 TraesCS7A01G490900 chr7A 680243599 680246015 2416 False 4464.000000 4464 100.000000 1 2417 1 chr7A.!!$F1 2416
1 TraesCS7A01G490900 chr7A 689252003 689252702 699 False 804.000000 804 87.482000 746 1450 1 chr7A.!!$F3 704
2 TraesCS7A01G490900 chr7B 661468170 661469596 1426 False 1881.000000 1881 90.526000 1 1432 1 chr7B.!!$F1 1431
3 TraesCS7A01G490900 chr7B 662009537 662010201 664 True 848.000000 848 89.717000 750 1417 1 chr7B.!!$R1 667
4 TraesCS7A01G490900 chr7B 661998651 662001046 2395 False 624.166667 1018 89.011333 634 2417 3 chr7B.!!$F5 1783
5 TraesCS7A01G490900 chr7B 674194077 674194899 822 False 476.500000 843 83.059000 732 1953 2 chr7B.!!$F6 1221
6 TraesCS7A01G490900 chr7B 661716355 661717465 1110 False 422.500000 968 83.441667 660 1876 3 chr7B.!!$F4 1216
7 TraesCS7A01G490900 chr7B 662310661 662311722 1061 True 403.933333 992 85.762667 747 2068 3 chr7B.!!$R2 1321
8 TraesCS7A01G490900 chr7D 588471315 588472122 807 True 1062.000000 1062 90.401000 634 1450 1 chr7D.!!$R2 816
9 TraesCS7A01G490900 chr7D 588251990 588253475 1485 False 850.000000 1168 87.771500 7 1432 2 chr7D.!!$F2 1425
10 TraesCS7A01G490900 chr7D 588409061 588410481 1420 False 382.250000 963 89.089000 748 1876 4 chr7D.!!$F3 1128
11 TraesCS7A01G490900 chr3D 455036967 455037640 673 True 861.000000 861 89.625000 747 1437 1 chr3D.!!$R1 690

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
882 979 0.038744 CACCAATCAGAGCCCACCTT 59.961 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2432 0.944311 CGGAGGTGAACTTGGTGACG 60.944 60.0 0.0 0.0 0.0 4.35 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 1.517242 CTTTGAGGCGACTTTGCTCT 58.483 50.000 0.00 0.00 44.43 4.09
22 23 1.196354 CTTTGAGGCGACTTTGCTCTG 59.804 52.381 0.00 0.00 44.43 3.35
23 24 0.392706 TTGAGGCGACTTTGCTCTGA 59.607 50.000 0.00 0.00 44.43 3.27
27 28 0.107945 GGCGACTTTGCTCTGAGGAT 60.108 55.000 6.83 0.00 34.52 3.24
86 87 2.340337 TGATGTCACAACGCTCATGAG 58.660 47.619 18.84 18.84 0.00 2.90
91 92 1.069978 TCACAACGCTCATGAGGAACA 59.930 47.619 23.89 0.00 0.00 3.18
92 93 1.195448 CACAACGCTCATGAGGAACAC 59.805 52.381 23.89 6.06 0.00 3.32
173 174 0.245266 TTCTAGCGCCGAATCACACA 59.755 50.000 2.29 0.00 0.00 3.72
178 179 0.725784 GCGCCGAATCACACAAGTTG 60.726 55.000 0.00 0.00 0.00 3.16
220 221 2.094182 ACGTGGCGATGAAAGTGACTAT 60.094 45.455 0.00 0.00 0.00 2.12
221 222 2.930040 CGTGGCGATGAAAGTGACTATT 59.070 45.455 0.00 0.00 0.00 1.73
246 247 2.962421 GTTGTGGGGATTTTGTCCTTCA 59.038 45.455 0.00 0.00 46.91 3.02
260 270 3.704061 TGTCCTTCATCGATGTACCATCA 59.296 43.478 24.09 14.32 0.00 3.07
268 278 3.977427 TCGATGTACCATCATTTCCTCG 58.023 45.455 5.19 0.00 0.00 4.63
274 284 1.812571 ACCATCATTTCCTCGTGCAAC 59.187 47.619 0.00 0.00 0.00 4.17
293 303 1.674962 ACGGTATGAGACTCGTAAGGC 59.325 52.381 5.96 0.00 34.50 4.35
294 304 1.333881 CGGTATGAGACTCGTAAGGCG 60.334 57.143 5.96 0.00 43.01 5.52
295 305 1.001597 GGTATGAGACTCGTAAGGCGG 60.002 57.143 5.96 0.00 41.72 6.13
296 306 1.674962 GTATGAGACTCGTAAGGCGGT 59.325 52.381 5.96 0.00 41.72 5.68
297 307 0.456221 ATGAGACTCGTAAGGCGGTG 59.544 55.000 0.00 0.00 41.72 4.94
298 308 0.892358 TGAGACTCGTAAGGCGGTGT 60.892 55.000 0.00 0.00 41.72 4.16
299 309 0.456312 GAGACTCGTAAGGCGGTGTG 60.456 60.000 0.00 0.00 41.72 3.82
300 310 1.177256 AGACTCGTAAGGCGGTGTGT 61.177 55.000 0.00 0.00 41.72 3.72
301 311 0.523072 GACTCGTAAGGCGGTGTGTA 59.477 55.000 0.00 0.00 41.72 2.90
302 312 0.961019 ACTCGTAAGGCGGTGTGTAA 59.039 50.000 0.00 0.00 41.72 2.41
303 313 1.068055 ACTCGTAAGGCGGTGTGTAAG 60.068 52.381 0.00 0.00 41.72 2.34
304 314 1.200716 CTCGTAAGGCGGTGTGTAAGA 59.799 52.381 0.00 0.00 41.72 2.10
349 370 3.134127 GCATTGGCGGTGTCCCTC 61.134 66.667 0.00 0.00 0.00 4.30
372 393 0.986527 ATGATGGCATAGGCGGATCA 59.013 50.000 13.15 13.15 41.21 2.92
375 396 0.986527 ATGGCATAGGCGGATCATCA 59.013 50.000 0.00 0.00 42.47 3.07
455 477 1.006102 CCAAGCACGACGACTTCCT 60.006 57.895 0.00 0.00 0.00 3.36
502 524 2.874701 GACAAAGCATATGAGCGATGGT 59.125 45.455 6.97 0.00 40.15 3.55
525 547 1.370900 CAGCGCACCAGCAAGTTTC 60.371 57.895 11.47 0.00 42.27 2.78
550 572 0.900182 TCGAGGTCATGAGGCTGTGT 60.900 55.000 0.00 0.00 0.00 3.72
558 635 6.259893 AGGTCATGAGGCTGTGTATATCTAT 58.740 40.000 0.00 0.00 0.00 1.98
559 636 6.154192 AGGTCATGAGGCTGTGTATATCTATG 59.846 42.308 0.00 0.00 0.00 2.23
565 642 3.056821 GGCTGTGTATATCTATGGTCGCA 60.057 47.826 0.00 0.00 0.00 5.10
625 709 3.963428 ATACGAAGTCCTGAGCTGTTT 57.037 42.857 0.00 0.00 43.93 2.83
696 789 1.214175 TGGAGAAAGCCCAGTTGACAA 59.786 47.619 0.00 0.00 0.00 3.18
729 822 4.344865 TGGGGCGAAACCAGGCTC 62.345 66.667 0.00 0.00 42.05 4.70
882 979 0.038744 CACCAATCAGAGCCCACCTT 59.961 55.000 0.00 0.00 0.00 3.50
895 992 2.610873 CCCACCTTCCTCCTCCTATAC 58.389 57.143 0.00 0.00 0.00 1.47
948 1048 3.732849 CCTCCCACCTTCCCAGCC 61.733 72.222 0.00 0.00 0.00 4.85
955 1058 1.341080 CACCTTCCCAGCCAAAACAT 58.659 50.000 0.00 0.00 0.00 2.71
1129 1249 3.368948 CGAGAAGAAGGGGAAGAAGAAGG 60.369 52.174 0.00 0.00 0.00 3.46
1320 1440 1.676968 CACCATCACGTCCAGGGAA 59.323 57.895 1.78 0.00 34.87 3.97
1332 1452 1.081174 TCCAGGGAAATCCAGACCTCT 59.919 52.381 1.22 0.00 38.24 3.69
1398 1518 2.430367 GGAACCAAGGCCGTCACT 59.570 61.111 0.00 0.00 0.00 3.41
1484 1645 9.685276 TTCATTATCTTGTGAAATAGTGATGGT 57.315 29.630 0.00 0.00 31.85 3.55
1518 1687 1.204941 GTCTCGTGGCTCTGTACCATT 59.795 52.381 0.00 0.00 39.95 3.16
1529 1698 5.582665 GGCTCTGTACCATTTTCAGTTCTAG 59.417 44.000 0.00 0.00 0.00 2.43
1544 1713 3.584848 AGTTCTAGTCCCTGTTGCTTCAT 59.415 43.478 0.00 0.00 0.00 2.57
1566 1735 6.369890 TCATTTGACAGAGTTCTTGCTATGAC 59.630 38.462 0.00 0.00 32.56 3.06
1686 2340 6.449448 GAGACGTTTCTCTGTTTCGTTTAT 57.551 37.500 0.00 0.00 44.54 1.40
1718 2372 6.821388 AGTTTTCAACTGTCTGTCTATGAGT 58.179 36.000 0.00 0.00 41.01 3.41
1761 2415 4.251268 AGGCTGACTAAATTAACACGTCC 58.749 43.478 0.00 0.00 0.00 4.79
1800 2454 0.535102 CACCAAGTTCACCTCCGCTT 60.535 55.000 0.00 0.00 0.00 4.68
1815 2469 0.815615 CGCTTAGATGGCCTGTTCCC 60.816 60.000 3.32 0.00 0.00 3.97
1816 2470 0.548510 GCTTAGATGGCCTGTTCCCT 59.451 55.000 3.32 0.00 0.00 4.20
1817 2471 1.768870 GCTTAGATGGCCTGTTCCCTA 59.231 52.381 3.32 0.00 0.00 3.53
1820 2474 1.051812 AGATGGCCTGTTCCCTATCG 58.948 55.000 3.32 0.00 0.00 2.92
1832 2486 1.062428 TCCCTATCGTCCTGGTGGATT 60.062 52.381 7.37 0.00 45.29 3.01
1833 2487 1.070758 CCCTATCGTCCTGGTGGATTG 59.929 57.143 7.37 6.08 45.29 2.67
1834 2488 1.762957 CCTATCGTCCTGGTGGATTGT 59.237 52.381 7.37 0.00 45.29 2.71
1857 2511 2.996621 GTTGCTCTGTAGGTAGCTGTTG 59.003 50.000 4.27 0.00 39.53 3.33
1858 2512 1.550524 TGCTCTGTAGGTAGCTGTTGG 59.449 52.381 4.27 0.00 39.53 3.77
1859 2513 1.550976 GCTCTGTAGGTAGCTGTTGGT 59.449 52.381 4.27 0.00 35.80 3.67
1860 2514 2.758979 GCTCTGTAGGTAGCTGTTGGTA 59.241 50.000 4.27 0.00 35.80 3.25
1861 2515 3.429135 GCTCTGTAGGTAGCTGTTGGTAC 60.429 52.174 4.27 0.00 44.00 3.34
1868 2522 3.328382 GTAGCTGTTGGTACCATGTCA 57.672 47.619 17.17 14.07 40.24 3.58
1869 2523 3.873910 GTAGCTGTTGGTACCATGTCAT 58.126 45.455 17.17 5.07 40.24 3.06
1870 2524 2.991250 AGCTGTTGGTACCATGTCATC 58.009 47.619 17.17 11.00 0.00 2.92
1871 2525 2.573462 AGCTGTTGGTACCATGTCATCT 59.427 45.455 17.17 12.95 0.00 2.90
1872 2526 3.009473 AGCTGTTGGTACCATGTCATCTT 59.991 43.478 17.17 2.34 0.00 2.40
1873 2527 3.127548 GCTGTTGGTACCATGTCATCTTG 59.872 47.826 17.17 5.38 0.00 3.02
1874 2528 4.326826 CTGTTGGTACCATGTCATCTTGT 58.673 43.478 17.17 0.00 0.00 3.16
1875 2529 5.487433 CTGTTGGTACCATGTCATCTTGTA 58.513 41.667 17.17 0.00 0.00 2.41
1876 2530 5.242434 TGTTGGTACCATGTCATCTTGTAC 58.758 41.667 17.17 6.71 0.00 2.90
1877 2531 4.481368 TGGTACCATGTCATCTTGTACC 57.519 45.455 11.60 19.76 36.74 3.34
1878 2532 4.101114 TGGTACCATGTCATCTTGTACCT 58.899 43.478 23.51 0.00 37.02 3.08
1879 2533 4.534500 TGGTACCATGTCATCTTGTACCTT 59.466 41.667 23.51 0.00 37.02 3.50
1880 2534 4.876107 GGTACCATGTCATCTTGTACCTTG 59.124 45.833 19.51 0.00 34.28 3.61
1881 2535 4.640771 ACCATGTCATCTTGTACCTTGT 57.359 40.909 0.00 0.00 0.00 3.16
1882 2536 4.326826 ACCATGTCATCTTGTACCTTGTG 58.673 43.478 0.00 0.00 0.00 3.33
1883 2537 4.202461 ACCATGTCATCTTGTACCTTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
1884 2538 4.154737 CCATGTCATCTTGTACCTTGTGTG 59.845 45.833 0.00 0.00 0.00 3.82
1885 2539 3.738982 TGTCATCTTGTACCTTGTGTGG 58.261 45.455 0.00 0.00 0.00 4.17
1886 2540 3.074412 GTCATCTTGTACCTTGTGTGGG 58.926 50.000 0.00 0.00 0.00 4.61
1887 2541 2.976185 TCATCTTGTACCTTGTGTGGGA 59.024 45.455 0.00 0.00 0.00 4.37
1888 2542 3.392947 TCATCTTGTACCTTGTGTGGGAA 59.607 43.478 0.00 0.00 0.00 3.97
1889 2543 3.202829 TCTTGTACCTTGTGTGGGAAC 57.797 47.619 0.00 0.00 0.00 3.62
1890 2544 2.506231 TCTTGTACCTTGTGTGGGAACA 59.494 45.455 0.00 0.00 38.70 3.18
1901 2555 3.968045 TGGGAACACACAACACACT 57.032 47.368 0.00 0.00 33.40 3.55
1902 2556 1.458398 TGGGAACACACAACACACTG 58.542 50.000 0.00 0.00 33.40 3.66
1903 2557 1.271652 TGGGAACACACAACACACTGT 60.272 47.619 0.00 0.00 33.40 3.55
1904 2558 1.816224 GGGAACACACAACACACTGTT 59.184 47.619 0.00 0.00 42.08 3.16
1910 2564 3.119531 ACACACAACACACTGTTTCATGG 60.120 43.478 0.00 0.00 38.77 3.66
1919 2573 3.244353 ACACTGTTTCATGGTCTGGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
1932 2586 3.833732 TCTGGAGAGACAGTAACAGTGT 58.166 45.455 0.00 0.00 39.48 3.55
1952 2606 7.879677 ACAGTGTTGATTTATTCAGTCTCATGA 59.120 33.333 0.00 0.00 35.27 3.07
1976 2872 1.212935 AGCACCCTGTTTCAGTCAACT 59.787 47.619 0.00 0.00 0.00 3.16
2040 2936 4.284490 TCCTCCTAATTAGGCTATGCTGTG 59.716 45.833 24.52 6.65 43.31 3.66
2079 2975 8.043113 AGAATGTAGTTAGATGTTCAGAATGCA 58.957 33.333 0.00 0.00 34.76 3.96
2101 2997 2.554142 TCATGACATGAGTGATTCGGC 58.446 47.619 14.24 0.00 33.59 5.54
2116 3012 2.806945 TCGGCAGATTTGGATTCCTT 57.193 45.000 3.95 0.00 0.00 3.36
2132 3028 8.757307 TGGATTCCTTTCCTATATATCCACTT 57.243 34.615 3.95 0.00 36.17 3.16
2133 3029 8.605947 TGGATTCCTTTCCTATATATCCACTTG 58.394 37.037 3.95 0.00 36.17 3.16
2166 3063 4.235079 TCATCCTGTAATTTGTGGGGAG 57.765 45.455 0.00 0.00 0.00 4.30
2185 3082 4.400567 GGGAGAAAATGTTTGAGGATCTGG 59.599 45.833 0.00 0.00 34.92 3.86
2217 3114 2.297701 ACGGTGTTGCTTTGATCTGTT 58.702 42.857 0.00 0.00 0.00 3.16
2224 3121 3.581024 TGCTTTGATCTGTTTCATGCC 57.419 42.857 0.00 0.00 0.00 4.40
2343 3240 3.578716 ACTGTAGCTACTGTGGTGACAAT 59.421 43.478 29.10 7.15 46.06 2.71
2374 3271 7.308830 GCCATAGTTCATATGTTCAGGAAATCC 60.309 40.741 1.90 0.00 39.84 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.037882 CTCAGAGCAAAGTCGCCTCA 60.038 55.000 0.00 0.00 0.00 3.86
21 22 1.384989 GGGCGTCGAGAGAATCCTCA 61.385 60.000 0.00 0.00 45.01 3.86
22 23 1.104577 AGGGCGTCGAGAGAATCCTC 61.105 60.000 0.00 0.00 45.01 3.71
23 24 0.684805 AAGGGCGTCGAGAGAATCCT 60.685 55.000 0.00 0.00 45.01 3.24
27 28 1.183030 TGGAAAGGGCGTCGAGAGAA 61.183 55.000 0.00 0.00 45.01 2.87
75 76 0.670546 CGGTGTTCCTCATGAGCGTT 60.671 55.000 17.76 0.00 0.00 4.84
82 83 3.403038 CTTCAAAGTCGGTGTTCCTCAT 58.597 45.455 0.00 0.00 0.00 2.90
86 87 1.202722 TCCCTTCAAAGTCGGTGTTCC 60.203 52.381 0.00 0.00 0.00 3.62
91 92 1.358152 TGGATCCCTTCAAAGTCGGT 58.642 50.000 9.90 0.00 0.00 4.69
92 93 2.717639 ATGGATCCCTTCAAAGTCGG 57.282 50.000 9.90 0.00 0.00 4.79
125 126 2.357760 GGAAGCGGCGTTGTACCA 60.358 61.111 9.37 0.00 0.00 3.25
173 174 3.428862 CCGCTTGAAGGAACAAACAACTT 60.429 43.478 0.00 0.00 0.00 2.66
178 179 1.333791 CGACCGCTTGAAGGAACAAAC 60.334 52.381 0.00 0.00 0.00 2.93
220 221 3.181474 GGACAAAATCCCCACAACGAAAA 60.181 43.478 0.00 0.00 42.46 2.29
221 222 2.362717 GGACAAAATCCCCACAACGAAA 59.637 45.455 0.00 0.00 42.46 3.46
260 270 2.006888 CATACCGTTGCACGAGGAAAT 58.993 47.619 9.75 0.77 46.05 2.17
268 278 1.269166 CGAGTCTCATACCGTTGCAC 58.731 55.000 0.00 0.00 0.00 4.57
274 284 2.402640 GCCTTACGAGTCTCATACCG 57.597 55.000 0.00 0.00 0.00 4.02
293 303 1.263217 GCAAACACCTCTTACACACCG 59.737 52.381 0.00 0.00 0.00 4.94
294 304 1.607148 GGCAAACACCTCTTACACACC 59.393 52.381 0.00 0.00 0.00 4.16
295 305 2.290641 CAGGCAAACACCTCTTACACAC 59.709 50.000 0.00 0.00 38.26 3.82
296 306 2.571212 CAGGCAAACACCTCTTACACA 58.429 47.619 0.00 0.00 38.26 3.72
297 307 1.880027 CCAGGCAAACACCTCTTACAC 59.120 52.381 0.00 0.00 38.26 2.90
298 308 1.771854 TCCAGGCAAACACCTCTTACA 59.228 47.619 0.00 0.00 38.26 2.41
299 309 2.427506 CTCCAGGCAAACACCTCTTAC 58.572 52.381 0.00 0.00 38.26 2.34
300 310 1.351017 CCTCCAGGCAAACACCTCTTA 59.649 52.381 0.00 0.00 38.26 2.10
301 311 0.111253 CCTCCAGGCAAACACCTCTT 59.889 55.000 0.00 0.00 38.26 2.85
302 312 1.763770 CCTCCAGGCAAACACCTCT 59.236 57.895 0.00 0.00 38.26 3.69
303 313 4.404691 CCTCCAGGCAAACACCTC 57.595 61.111 0.00 0.00 38.26 3.85
347 368 1.436600 GCCTATGCCATCATCACGAG 58.563 55.000 0.00 0.00 34.22 4.18
349 370 1.293963 CCGCCTATGCCATCATCACG 61.294 60.000 0.00 0.00 34.22 4.35
372 393 2.487934 CCTGATTCCGCGAAGAATGAT 58.512 47.619 8.23 0.00 36.60 2.45
375 396 2.695314 GCCTGATTCCGCGAAGAAT 58.305 52.632 8.23 9.28 39.19 2.40
455 477 4.758251 CAGCCATCCACGCGGACA 62.758 66.667 12.47 0.00 46.79 4.02
508 530 2.896801 CGAAACTTGCTGGTGCGCT 61.897 57.895 9.73 0.00 43.34 5.92
525 547 0.031314 CCTCATGACCTCGACATCCG 59.969 60.000 0.00 0.00 40.25 4.18
599 683 3.639094 AGCTCAGGACTTCGTATATTGCT 59.361 43.478 0.00 0.00 0.00 3.91
600 684 3.738282 CAGCTCAGGACTTCGTATATTGC 59.262 47.826 0.00 0.00 0.00 3.56
601 685 4.938080 ACAGCTCAGGACTTCGTATATTG 58.062 43.478 0.00 0.00 0.00 1.90
602 686 5.599999 AACAGCTCAGGACTTCGTATATT 57.400 39.130 0.00 0.00 0.00 1.28
604 688 6.519679 TTAAACAGCTCAGGACTTCGTATA 57.480 37.500 0.00 0.00 0.00 1.47
625 709 4.922692 CCATCGACATTTTGCTTTGCTTTA 59.077 37.500 0.00 0.00 0.00 1.85
696 789 2.725450 CACGCGCGCATGTGTTTT 60.725 55.556 32.58 3.21 0.00 2.43
729 822 4.426313 GAAAGGTGGGCGGGGAGG 62.426 72.222 0.00 0.00 0.00 4.30
882 979 2.309162 CGGAGGATGTATAGGAGGAGGA 59.691 54.545 0.00 0.00 0.00 3.71
948 1048 2.414559 GGAGATGTGCGGTGATGTTTTG 60.415 50.000 0.00 0.00 0.00 2.44
955 1058 3.770040 CGGGGAGATGTGCGGTGA 61.770 66.667 0.00 0.00 0.00 4.02
1129 1249 1.016653 GTCTCCACGCTCTTCTTGGC 61.017 60.000 0.00 0.00 34.33 4.52
1383 1503 0.763035 ACTTAGTGACGGCCTTGGTT 59.237 50.000 0.00 0.00 0.00 3.67
1398 1518 5.198965 ACTATCTAAGCGGAGGTGAACTTA 58.801 41.667 0.00 0.00 39.47 2.24
1479 1640 4.260170 AGACAGATCAAAGAAGCACCATC 58.740 43.478 0.00 0.00 0.00 3.51
1484 1645 3.320626 CACGAGACAGATCAAAGAAGCA 58.679 45.455 0.00 0.00 0.00 3.91
1518 1687 3.391296 AGCAACAGGGACTAGAACTGAAA 59.609 43.478 16.08 0.00 36.02 2.69
1529 1698 2.622942 TGTCAAATGAAGCAACAGGGAC 59.377 45.455 0.00 0.00 0.00 4.46
1544 1713 4.997395 GGTCATAGCAAGAACTCTGTCAAA 59.003 41.667 0.00 0.00 0.00 2.69
1566 1735 5.278463 CCAAGATAAACTCACACAAACAGGG 60.278 44.000 0.00 0.00 0.00 4.45
1635 2289 6.579666 AGTTGAGTGTCATTGTATGCAAAT 57.420 33.333 0.00 0.00 38.21 2.32
1654 2308 3.511856 GAGAAACGTCTCTGCAAGTTG 57.488 47.619 0.00 0.00 45.99 3.16
1708 2362 1.204704 CGGCCACAAGACTCATAGACA 59.795 52.381 2.24 0.00 0.00 3.41
1711 2365 1.148157 CGCGGCCACAAGACTCATAG 61.148 60.000 2.24 0.00 0.00 2.23
1734 2388 3.203716 GTTAATTTAGTCAGCCTCCCCG 58.796 50.000 0.00 0.00 0.00 5.73
1778 2432 0.944311 CGGAGGTGAACTTGGTGACG 60.944 60.000 0.00 0.00 0.00 4.35
1800 2454 2.248248 CGATAGGGAACAGGCCATCTA 58.752 52.381 5.01 0.00 0.00 1.98
1832 2486 2.632996 AGCTACCTACAGAGCAACAACA 59.367 45.455 0.00 0.00 41.36 3.33
1833 2487 2.996621 CAGCTACCTACAGAGCAACAAC 59.003 50.000 0.00 0.00 41.36 3.32
1834 2488 2.632996 ACAGCTACCTACAGAGCAACAA 59.367 45.455 0.00 0.00 41.36 2.83
1857 2511 4.755266 AGGTACAAGATGACATGGTACC 57.245 45.455 21.88 21.88 36.53 3.34
1858 2512 5.351465 CACAAGGTACAAGATGACATGGTAC 59.649 44.000 0.00 3.16 0.00 3.34
1859 2513 5.012664 ACACAAGGTACAAGATGACATGGTA 59.987 40.000 0.00 0.00 0.00 3.25
1860 2514 4.202461 ACACAAGGTACAAGATGACATGGT 60.202 41.667 0.00 0.00 0.00 3.55
1861 2515 4.154737 CACACAAGGTACAAGATGACATGG 59.845 45.833 0.00 0.00 0.00 3.66
1862 2516 4.154737 CCACACAAGGTACAAGATGACATG 59.845 45.833 0.00 0.00 0.00 3.21
1863 2517 4.326826 CCACACAAGGTACAAGATGACAT 58.673 43.478 0.00 0.00 0.00 3.06
1864 2518 3.495983 CCCACACAAGGTACAAGATGACA 60.496 47.826 0.00 0.00 0.00 3.58
1865 2519 3.074412 CCCACACAAGGTACAAGATGAC 58.926 50.000 0.00 0.00 0.00 3.06
1866 2520 2.976185 TCCCACACAAGGTACAAGATGA 59.024 45.455 0.00 0.00 0.00 2.92
1867 2521 3.417069 TCCCACACAAGGTACAAGATG 57.583 47.619 0.00 0.00 0.00 2.90
1868 2522 3.137544 TGTTCCCACACAAGGTACAAGAT 59.862 43.478 0.00 0.00 0.00 2.40
1869 2523 2.506231 TGTTCCCACACAAGGTACAAGA 59.494 45.455 0.00 0.00 0.00 3.02
1870 2524 2.925724 TGTTCCCACACAAGGTACAAG 58.074 47.619 0.00 0.00 0.00 3.16
1882 2536 1.132262 CAGTGTGTTGTGTGTTCCCAC 59.868 52.381 0.00 0.00 42.19 4.61
1883 2537 1.271652 ACAGTGTGTTGTGTGTTCCCA 60.272 47.619 0.00 0.00 0.00 4.37
1884 2538 1.459450 ACAGTGTGTTGTGTGTTCCC 58.541 50.000 0.00 0.00 0.00 3.97
1885 2539 3.057876 TGAAACAGTGTGTTGTGTGTTCC 60.058 43.478 0.00 0.00 40.14 3.62
1886 2540 4.153958 TGAAACAGTGTGTTGTGTGTTC 57.846 40.909 0.00 0.00 40.14 3.18
1887 2541 4.484236 CATGAAACAGTGTGTTGTGTGTT 58.516 39.130 0.00 0.00 40.14 3.32
1888 2542 3.119531 CCATGAAACAGTGTGTTGTGTGT 60.120 43.478 0.00 0.00 40.14 3.72
1889 2543 3.119531 ACCATGAAACAGTGTGTTGTGTG 60.120 43.478 0.00 0.00 40.14 3.82
1890 2544 3.088532 ACCATGAAACAGTGTGTTGTGT 58.911 40.909 0.00 0.00 40.14 3.72
1891 2545 3.378112 AGACCATGAAACAGTGTGTTGTG 59.622 43.478 0.00 0.00 40.14 3.33
1892 2546 3.378112 CAGACCATGAAACAGTGTGTTGT 59.622 43.478 0.00 0.00 40.14 3.32
1893 2547 3.243168 CCAGACCATGAAACAGTGTGTTG 60.243 47.826 0.00 0.00 40.14 3.33
1894 2548 2.951642 CCAGACCATGAAACAGTGTGTT 59.048 45.455 0.00 0.00 43.41 3.32
1895 2549 2.172505 TCCAGACCATGAAACAGTGTGT 59.827 45.455 0.00 0.00 0.00 3.72
1896 2550 2.810274 CTCCAGACCATGAAACAGTGTG 59.190 50.000 0.00 0.00 0.00 3.82
1897 2551 2.705658 TCTCCAGACCATGAAACAGTGT 59.294 45.455 0.00 0.00 0.00 3.55
1898 2552 3.007290 TCTCTCCAGACCATGAAACAGTG 59.993 47.826 0.00 0.00 0.00 3.66
1899 2553 3.007398 GTCTCTCCAGACCATGAAACAGT 59.993 47.826 0.00 0.00 43.14 3.55
1900 2554 3.594134 GTCTCTCCAGACCATGAAACAG 58.406 50.000 0.00 0.00 43.14 3.16
1901 2555 3.685139 GTCTCTCCAGACCATGAAACA 57.315 47.619 0.00 0.00 43.14 2.83
1919 2573 8.774586 ACTGAATAAATCAACACTGTTACTGTC 58.225 33.333 0.00 0.00 37.67 3.51
1932 2586 8.618677 GCTGAATCATGAGACTGAATAAATCAA 58.381 33.333 0.09 0.00 37.67 2.57
1952 2606 2.158623 TGACTGAAACAGGGTGCTGAAT 60.159 45.455 0.00 0.00 35.51 2.57
1976 2872 3.252458 TCTGAAGAAATCGACACTCGTCA 59.748 43.478 8.04 8.04 42.74 4.35
2040 2936 2.777832 ACATTCTGAGAAGACAGGGC 57.222 50.000 0.00 0.00 38.31 5.19
2079 2975 3.562973 GCCGAATCACTCATGTCATGATT 59.437 43.478 15.84 16.45 43.93 2.57
2132 3028 4.908601 ACAGGATGATGAAGTACCAACA 57.091 40.909 0.00 0.00 39.69 3.33
2133 3029 7.865706 AATTACAGGATGATGAAGTACCAAC 57.134 36.000 0.00 0.00 39.69 3.77
2166 3063 5.256474 TCCTCCAGATCCTCAAACATTTTC 58.744 41.667 0.00 0.00 0.00 2.29
2185 3082 4.251268 AGCAACACCGTTACTATTTCCTC 58.749 43.478 0.00 0.00 0.00 3.71
2217 3114 5.195185 TGAGCATGATAAGAAAGGCATGAA 58.805 37.500 0.00 0.00 40.29 2.57
2224 3121 9.118300 AGGTAAAGATTGAGCATGATAAGAAAG 57.882 33.333 0.00 0.00 0.00 2.62
2288 3185 7.534239 CACTTTTACTAAAGAATCGCTTGTTCC 59.466 37.037 4.77 0.00 42.78 3.62
2374 3271 3.531982 GACAATTGAACTGTTCGTCGTG 58.468 45.455 13.59 12.24 0.00 4.35


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

AutoCloner maintained by Alex Coulton.