Multiple sequence alignment - TraesCS2B01G135200

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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 TraesCS2B01G135200 chr2B 100.000 2948 0 0 1 2948 101544048 101541101 0.000000e+00 5445.0
1 TraesCS2B01G135200 chr2B 99.560 455 2 0 2494 2948 101529218 101528764 0.000000e+00 830.0
2 TraesCS2B01G135200 chr2B 77.546 864 112 44 699 1510 103845846 103845013 2.080000e-121 446.0
3 TraesCS2B01G135200 chr2B 77.187 846 121 39 708 1510 103901138 103900322 7.550000e-116 427.0
4 TraesCS2B01G135200 chr2B 76.266 1007 115 66 584 1512 104052989 104052029 3.510000e-114 422.0
5 TraesCS2B01G135200 chr2B 76.705 880 125 43 678 1510 103956347 103955501 1.630000e-112 416.0
6 TraesCS2B01G135200 chr2B 75.877 713 96 36 853 1510 104005871 104005180 7.990000e-76 294.0
7 TraesCS2B01G135200 chr2B 77.580 562 71 28 853 1382 104019277 104018739 3.720000e-74 289.0
8 TraesCS2B01G135200 chr2B 75.543 691 102 36 856 1508 103869959 103869298 8.050000e-71 278.0
9 TraesCS2B01G135200 chr2B 85.075 67 9 1 1416 1481 104018724 104018658 1.900000e-07 67.6
10 TraesCS2B01G135200 chr2A 88.568 1627 122 36 552 2133 65954251 65952644 0.000000e+00 1916.0
11 TraesCS2B01G135200 chr2A 91.398 1395 81 20 567 1937 66004748 66003369 0.000000e+00 1875.0
12 TraesCS2B01G135200 chr2A 87.479 591 48 6 2089 2674 65952640 65952071 0.000000e+00 658.0
13 TraesCS2B01G135200 chr2A 88.679 530 25 9 3 531 66005349 66004854 5.400000e-172 614.0
14 TraesCS2B01G135200 chr2A 78.161 696 103 28 849 1508 66909569 66908887 5.920000e-107 398.0
15 TraesCS2B01G135200 chr2A 78.211 693 93 28 848 1510 66915225 66914561 9.910000e-105 390.0
16 TraesCS2B01G135200 chr2A 80.608 526 28 20 1 518 65954845 65954386 3.640000e-89 339.0
17 TraesCS2B01G135200 chr2A 100.000 29 0 0 530 558 66004772 66004744 1.000000e-03 54.7
18 TraesCS2B01G135200 chr2D 89.027 1531 98 29 1 1503 69029425 69027937 0.000000e+00 1832.0
19 TraesCS2B01G135200 chr2D 91.655 731 56 2 2223 2948 69027178 69026448 0.000000e+00 1007.0
20 TraesCS2B01G135200 chr2D 89.906 426 34 4 1568 1987 69027935 69027513 9.300000e-150 540.0
21 TraesCS2B01G135200 chr2D 77.036 884 133 40 666 1508 67447829 67448683 7.500000e-121 444.0
22 TraesCS2B01G135200 chr2D 76.862 886 113 47 678 1508 67445153 67446001 1.630000e-112 416.0
23 TraesCS2B01G135200 chr2D 76.371 711 95 36 848 1510 67442688 67443373 6.130000e-82 315.0
24 TraesCS2B01G135200 chr2D 93.827 81 5 0 8 88 68811617 68811697 3.990000e-24 122.0
25 TraesCS2B01G135200 chr2D 89.583 96 3 1 2008 2096 69027524 69027429 6.680000e-22 115.0
26 TraesCS2B01G135200 chr2D 92.593 81 2 1 248 328 68855648 68855724 2.400000e-21 113.0
27 TraesCS2B01G135200 chr2D 74.183 306 60 13 1071 1373 68905035 68904746 3.110000e-20 110.0
28 TraesCS2B01G135200 chr2D 89.655 58 6 0 1724 1781 67454641 67454698 1.130000e-09 75.0
29 TraesCS2B01G135200 chr4A 78.613 173 28 6 60 231 631905000 631904836 4.020000e-19 106.0


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 TraesCS2B01G135200 chr2B 101541101 101544048 2947 True 5445.000000 5445 100.000000 1 2948 1 chr2B.!!$R2 2947
1 TraesCS2B01G135200 chr2B 103845013 103845846 833 True 446.000000 446 77.546000 699 1510 1 chr2B.!!$R3 811
2 TraesCS2B01G135200 chr2B 103900322 103901138 816 True 427.000000 427 77.187000 708 1510 1 chr2B.!!$R5 802
3 TraesCS2B01G135200 chr2B 104052029 104052989 960 True 422.000000 422 76.266000 584 1512 1 chr2B.!!$R8 928
4 TraesCS2B01G135200 chr2B 103955501 103956347 846 True 416.000000 416 76.705000 678 1510 1 chr2B.!!$R6 832
5 TraesCS2B01G135200 chr2B 104005180 104005871 691 True 294.000000 294 75.877000 853 1510 1 chr2B.!!$R7 657
6 TraesCS2B01G135200 chr2B 103869298 103869959 661 True 278.000000 278 75.543000 856 1508 1 chr2B.!!$R4 652
7 TraesCS2B01G135200 chr2A 65952071 65954845 2774 True 971.000000 1916 85.551667 1 2674 3 chr2A.!!$R3 2673
8 TraesCS2B01G135200 chr2A 66003369 66005349 1980 True 847.900000 1875 93.359000 3 1937 3 chr2A.!!$R4 1934
9 TraesCS2B01G135200 chr2A 66908887 66909569 682 True 398.000000 398 78.161000 849 1508 1 chr2A.!!$R1 659
10 TraesCS2B01G135200 chr2A 66914561 66915225 664 True 390.000000 390 78.211000 848 1510 1 chr2A.!!$R2 662
11 TraesCS2B01G135200 chr2D 69026448 69029425 2977 True 873.500000 1832 90.042750 1 2948 4 chr2D.!!$R2 2947
12 TraesCS2B01G135200 chr2D 67442688 67448683 5995 False 391.666667 444 76.756333 666 1510 3 chr2D.!!$F4 844

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
154 158 1.045407 GGGTATGGGCGTCATGTCTA 58.955 55.000 0.00 0.00 37.30 2.59 F
843 5370 1.399440 CAAGCTATCTGTTGCGCACAT 59.601 47.619 11.12 2.18 33.76 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 5606 0.248289 GGGAAACTACGTGGCTAGCA 59.752 55.0 18.24 0.0 0.0 3.49 R
2676 7501 0.103937 GAGTTCCGGGATCAGCTCTG 59.896 60.0 0.00 0.0 0.0 3.35 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
154 158 1.045407 GGGTATGGGCGTCATGTCTA 58.955 55.000 0.00 0.00 37.30 2.59
207 216 4.639755 TCCCTGTAAATATCGTGACGTACA 59.360 41.667 4.40 5.08 0.00 2.90
208 217 5.125257 TCCCTGTAAATATCGTGACGTACAA 59.875 40.000 4.40 0.00 0.00 2.41
345 354 7.716799 ATATTACCTTGTTTTTGGCATGAGA 57.283 32.000 0.00 0.00 0.00 3.27
346 355 5.860941 TTACCTTGTTTTTGGCATGAGAA 57.139 34.783 0.00 0.00 0.00 2.87
348 357 3.181466 ACCTTGTTTTTGGCATGAGAACC 60.181 43.478 0.00 0.00 0.00 3.62
349 358 3.070015 CCTTGTTTTTGGCATGAGAACCT 59.930 43.478 0.00 0.00 0.00 3.50
350 359 4.443315 CCTTGTTTTTGGCATGAGAACCTT 60.443 41.667 0.00 0.00 0.00 3.50
357 366 4.057406 TGGCATGAGAACCTTGTTTTTG 57.943 40.909 0.00 0.00 0.00 2.44
358 367 3.181467 TGGCATGAGAACCTTGTTTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
501 511 8.921670 GCGTTTAAATTCACAAGGTTAATCAAT 58.078 29.630 0.00 0.00 0.00 2.57
671 870 2.637872 TCCACTCTTCCAGTAGTTTGGG 59.362 50.000 0.00 0.00 38.81 4.12
726 2521 7.281040 AGAACAATCTTTCATCAGAAGCAAA 57.719 32.000 0.00 0.00 34.71 3.68
738 2533 7.615403 TCATCAGAAGCAAACTATAACAGTCT 58.385 34.615 0.00 0.00 36.04 3.24
739 2534 8.097038 TCATCAGAAGCAAACTATAACAGTCTT 58.903 33.333 0.00 0.00 36.04 3.01
740 2535 9.371136 CATCAGAAGCAAACTATAACAGTCTTA 57.629 33.333 0.00 0.00 36.04 2.10
741 2536 9.944376 ATCAGAAGCAAACTATAACAGTCTTAA 57.056 29.630 0.00 0.00 36.04 1.85
843 5370 1.399440 CAAGCTATCTGTTGCGCACAT 59.601 47.619 11.12 2.18 33.76 3.21
844 5371 1.742761 AGCTATCTGTTGCGCACATT 58.257 45.000 11.12 5.32 33.76 2.71
845 5372 1.667724 AGCTATCTGTTGCGCACATTC 59.332 47.619 11.12 1.38 33.76 2.67
846 5373 1.667724 GCTATCTGTTGCGCACATTCT 59.332 47.619 11.12 0.00 33.76 2.40
951 5489 3.324099 CTCGTACGTCGCTGGCAGT 62.324 63.158 17.16 0.00 39.67 4.40
1012 5593 1.959226 CGCAACAAGCCCGTACAGT 60.959 57.895 0.00 0.00 41.38 3.55
1023 5604 1.670674 CCCGTACAGTAAAGCTCGCAA 60.671 52.381 0.00 0.00 0.00 4.85
1024 5605 1.389106 CCGTACAGTAAAGCTCGCAAC 59.611 52.381 0.00 0.00 0.00 4.17
1025 5606 2.325761 CGTACAGTAAAGCTCGCAACT 58.674 47.619 0.00 0.00 0.00 3.16
1145 5759 0.531974 ATGTCAACGTGTTCAGCCGT 60.532 50.000 0.00 0.00 39.32 5.68
1187 5801 4.452733 GTCTTCGGCGACCCTGGG 62.453 72.222 10.16 12.28 0.00 4.45
1379 6017 2.100631 GGTGTTCATCCCTGTCGCG 61.101 63.158 0.00 0.00 0.00 5.87
1539 6192 1.150536 GAAGGGTTGTGCTGGGACA 59.849 57.895 0.00 0.00 0.00 4.02
1713 6366 0.794605 GTCGCCAGCGCAGAAAAATC 60.795 55.000 11.47 0.00 39.59 2.17
1826 6479 2.268920 GACAGGGCCGCTCATGAA 59.731 61.111 0.00 0.00 0.00 2.57
1831 6484 3.654020 GGCCGCTCATGAATCCGC 61.654 66.667 0.00 0.00 0.00 5.54
1832 6485 2.896854 GCCGCTCATGAATCCGCA 60.897 61.111 0.00 0.00 0.00 5.69
1840 6493 2.874086 CTCATGAATCCGCATACAAGCA 59.126 45.455 0.00 0.00 0.00 3.91
1896 6549 6.730447 TGAAAACTTCCCATATTCATCAGGA 58.270 36.000 0.00 0.00 0.00 3.86
1897 6550 7.356680 TGAAAACTTCCCATATTCATCAGGAT 58.643 34.615 0.00 0.00 0.00 3.24
1977 6640 1.216444 GAGATGCACACGCTCCAGA 59.784 57.895 0.00 0.00 39.64 3.86
1981 6644 0.531532 ATGCACACGCTCCAGATAGC 60.532 55.000 0.00 0.00 39.64 2.97
1982 6645 1.142748 GCACACGCTCCAGATAGCT 59.857 57.895 0.00 0.00 40.49 3.32
1983 6646 0.460987 GCACACGCTCCAGATAGCTT 60.461 55.000 0.00 0.00 40.49 3.74
1984 6647 1.284657 CACACGCTCCAGATAGCTTG 58.715 55.000 0.00 0.00 44.79 4.01
1985 6648 0.176680 ACACGCTCCAGATAGCTTGG 59.823 55.000 0.00 0.00 43.86 3.61
1986 6649 0.176680 CACGCTCCAGATAGCTTGGT 59.823 55.000 2.88 0.00 40.49 3.67
1987 6650 0.176680 ACGCTCCAGATAGCTTGGTG 59.823 55.000 2.88 2.08 40.49 4.17
1988 6651 0.461548 CGCTCCAGATAGCTTGGTGA 59.538 55.000 8.79 0.00 40.49 4.02
1989 6652 1.069823 CGCTCCAGATAGCTTGGTGAT 59.930 52.381 8.79 0.00 40.49 3.06
1990 6653 2.484417 CGCTCCAGATAGCTTGGTGATT 60.484 50.000 8.79 0.00 40.49 2.57
1991 6654 3.137533 GCTCCAGATAGCTTGGTGATTC 58.862 50.000 8.79 0.00 39.50 2.52
1992 6655 3.181456 GCTCCAGATAGCTTGGTGATTCT 60.181 47.826 8.79 0.00 39.50 2.40
1993 6656 4.630111 CTCCAGATAGCTTGGTGATTCTC 58.370 47.826 2.88 0.00 0.00 2.87
1994 6657 4.033009 TCCAGATAGCTTGGTGATTCTCA 58.967 43.478 2.88 0.00 0.00 3.27
1995 6658 4.471025 TCCAGATAGCTTGGTGATTCTCAA 59.529 41.667 2.88 0.00 0.00 3.02
1996 6659 5.045651 TCCAGATAGCTTGGTGATTCTCAAA 60.046 40.000 2.88 0.00 0.00 2.69
1997 6660 5.649395 CCAGATAGCTTGGTGATTCTCAAAA 59.351 40.000 0.00 0.00 0.00 2.44
1998 6661 6.151648 CCAGATAGCTTGGTGATTCTCAAAAA 59.848 38.462 0.00 0.00 0.00 1.94
2128 6907 4.938226 CCTTCTCCTGTGAGTGATTAAACC 59.062 45.833 0.00 0.00 39.75 3.27
2133 6912 6.013379 TCTCCTGTGAGTGATTAAACCTCAAT 60.013 38.462 5.79 0.00 39.75 2.57
2134 6913 6.173339 TCCTGTGAGTGATTAAACCTCAATC 58.827 40.000 5.79 2.83 37.01 2.67
2216 6995 3.254060 GAAGCGAAGTGTTAGAGCATCA 58.746 45.455 0.00 0.00 37.82 3.07
2241 7061 5.144100 TCCACAACAATGTTTATTGGAGGT 58.856 37.500 13.84 0.00 46.33 3.85
2306 7131 2.603110 TCGAACTCAAGATGCATAACGC 59.397 45.455 0.00 0.00 42.89 4.84
2307 7132 2.285834 CGAACTCAAGATGCATAACGCC 60.286 50.000 0.00 0.00 41.33 5.68
2392 7217 1.813513 AAGGAGAACAATGGTGAGCG 58.186 50.000 0.00 0.00 0.00 5.03
2394 7219 1.899814 AGGAGAACAATGGTGAGCGTA 59.100 47.619 0.00 0.00 0.00 4.42
2413 7238 3.003689 CGTAATCGTACCCGGATGTACTT 59.996 47.826 16.05 9.08 39.14 2.24
2444 7269 1.133450 TCGATGGCTACTCTAAGGCCT 60.133 52.381 0.00 0.00 45.45 5.19
2450 7275 2.436173 GGCTACTCTAAGGCCTGACAAT 59.564 50.000 5.69 0.00 42.31 2.71
2454 7279 3.084786 ACTCTAAGGCCTGACAATTTGC 58.915 45.455 5.69 0.00 0.00 3.68
2459 7284 1.761784 AGGCCTGACAATTTGCACAAA 59.238 42.857 3.11 0.00 34.46 2.83
2546 7371 2.382882 TGGAACACTTGTGCATTCCAA 58.617 42.857 17.76 1.72 45.90 3.53
2579 7404 2.613026 ATATTCACGGGATTGCGACA 57.387 45.000 0.00 0.00 0.00 4.35
2591 7416 1.686355 TTGCGACAATCAAAGGGTGT 58.314 45.000 0.00 0.00 0.00 4.16
2599 7424 0.591170 ATCAAAGGGTGTCAAACGCG 59.409 50.000 3.53 3.53 46.08 6.01
2633 7458 2.450476 GGGAGGTTGCAAGAACATGAT 58.550 47.619 0.00 0.00 0.00 2.45
2641 7466 6.014840 AGGTTGCAAGAACATGATTTGAAGAT 60.015 34.615 0.00 0.00 0.00 2.40
2692 7517 1.340399 ATGCAGAGCTGATCCCGGAA 61.340 55.000 0.73 0.00 0.00 4.30
2694 7519 1.965754 GCAGAGCTGATCCCGGAACT 61.966 60.000 0.73 0.00 0.00 3.01
2698 7523 0.467384 AGCTGATCCCGGAACTCATG 59.533 55.000 0.73 0.00 0.00 3.07
2712 7537 3.807538 CATGGACGTGGCAGCAGC 61.808 66.667 0.00 0.00 41.10 5.25
2734 7559 4.522789 GCCAAAGAAGAGGTGGAAACAATA 59.477 41.667 0.00 0.00 46.06 1.90
2776 7601 4.214545 CCATAGCGAGTCAGGTTAGTCTAG 59.785 50.000 0.00 0.00 0.00 2.43
2780 7605 3.439476 GCGAGTCAGGTTAGTCTAGAACA 59.561 47.826 0.00 0.00 0.00 3.18
2782 7607 5.632959 CGAGTCAGGTTAGTCTAGAACAAG 58.367 45.833 0.00 0.00 0.00 3.16
2824 7649 3.598299 TCGTGTTGAGATGATCATGCAA 58.402 40.909 14.30 13.94 37.89 4.08
2845 7670 2.362369 GCAGCCAGGCTAGAGGACA 61.362 63.158 15.64 0.00 36.40 4.02
2878 7703 1.278127 CCGAGGTGTTATTGACCTGGT 59.722 52.381 0.00 0.00 44.28 4.00
2880 7705 3.430374 CCGAGGTGTTATTGACCTGGTAG 60.430 52.174 0.00 0.00 44.28 3.18
2894 7719 2.233922 CCTGGTAGGTGAAGTAGTGGTG 59.766 54.545 0.00 0.00 0.00 4.17
2897 7722 2.612221 GGTAGGTGAAGTAGTGGTGTGC 60.612 54.545 0.00 0.00 0.00 4.57
2940 7765 3.449528 TCATCGATGAGGAAGAGCTTG 57.550 47.619 23.99 0.00 32.11 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.629051 ACTATAGCACCGAAACTTGCC 58.371 47.619 0.00 0.00 39.75 4.52
154 158 4.054359 AGATCAGCGGGATATCCTAACT 57.946 45.455 21.18 12.81 36.00 2.24
253 262 6.898041 TGAATAATCAAACTCAAAGACACCG 58.102 36.000 0.00 0.00 30.99 4.94
331 340 4.058721 ACAAGGTTCTCATGCCAAAAAC 57.941 40.909 0.00 0.00 0.00 2.43
332 341 4.751767 AACAAGGTTCTCATGCCAAAAA 57.248 36.364 0.00 0.00 0.00 1.94
333 342 4.751767 AAACAAGGTTCTCATGCCAAAA 57.248 36.364 0.00 0.00 0.00 2.44
334 343 4.751767 AAAACAAGGTTCTCATGCCAAA 57.248 36.364 0.00 0.00 0.00 3.28
335 344 4.440880 CAAAAACAAGGTTCTCATGCCAA 58.559 39.130 0.00 0.00 0.00 4.52
336 345 3.181467 CCAAAAACAAGGTTCTCATGCCA 60.181 43.478 0.00 0.00 0.00 4.92
337 346 3.392882 CCAAAAACAAGGTTCTCATGCC 58.607 45.455 0.00 0.00 0.00 4.40
338 347 2.802247 GCCAAAAACAAGGTTCTCATGC 59.198 45.455 0.00 0.00 0.00 4.06
339 348 4.057406 TGCCAAAAACAAGGTTCTCATG 57.943 40.909 0.00 0.00 0.00 3.07
340 349 4.344679 TCATGCCAAAAACAAGGTTCTCAT 59.655 37.500 0.00 0.00 0.00 2.90
341 350 3.703556 TCATGCCAAAAACAAGGTTCTCA 59.296 39.130 0.00 0.00 0.00 3.27
342 351 4.301628 CTCATGCCAAAAACAAGGTTCTC 58.698 43.478 0.00 0.00 0.00 2.87
343 352 3.070015 CCTCATGCCAAAAACAAGGTTCT 59.930 43.478 0.00 0.00 0.00 3.01
344 353 3.069443 TCCTCATGCCAAAAACAAGGTTC 59.931 43.478 0.00 0.00 0.00 3.62
345 354 3.037549 TCCTCATGCCAAAAACAAGGTT 58.962 40.909 0.00 0.00 0.00 3.50
346 355 2.629617 CTCCTCATGCCAAAAACAAGGT 59.370 45.455 0.00 0.00 0.00 3.50
348 357 5.183713 TCATACTCCTCATGCCAAAAACAAG 59.816 40.000 0.00 0.00 0.00 3.16
349 358 5.076182 TCATACTCCTCATGCCAAAAACAA 58.924 37.500 0.00 0.00 0.00 2.83
350 359 4.661222 TCATACTCCTCATGCCAAAAACA 58.339 39.130 0.00 0.00 0.00 2.83
565 761 1.278699 GCCCAATTGCCCATGAAGAAA 59.721 47.619 0.00 0.00 0.00 2.52
671 870 6.785488 TCCACTGATGCGACATATAATTTC 57.215 37.500 0.00 0.00 0.00 2.17
762 2563 5.171339 TCTTCTAGAACACCTACGGTACT 57.829 43.478 0.00 0.00 32.11 2.73
763 2564 5.356470 ACATCTTCTAGAACACCTACGGTAC 59.644 44.000 0.00 0.00 32.11 3.34
764 2565 5.503927 ACATCTTCTAGAACACCTACGGTA 58.496 41.667 0.00 0.00 32.11 4.02
843 5370 6.581712 CCAAGGGAAATTTCAACAGAAAGAA 58.418 36.000 19.49 0.00 34.96 2.52
844 5371 5.453198 GCCAAGGGAAATTTCAACAGAAAGA 60.453 40.000 19.49 0.00 34.96 2.52
845 5372 4.751600 GCCAAGGGAAATTTCAACAGAAAG 59.248 41.667 19.49 2.19 34.96 2.62
846 5373 4.163078 TGCCAAGGGAAATTTCAACAGAAA 59.837 37.500 19.49 0.00 35.86 2.52
999 5580 2.000447 GAGCTTTACTGTACGGGCTTG 59.000 52.381 6.65 0.00 0.00 4.01
1023 5604 1.067071 GGAAACTACGTGGCTAGCAGT 60.067 52.381 18.24 15.14 0.00 4.40
1024 5605 1.641577 GGAAACTACGTGGCTAGCAG 58.358 55.000 18.24 7.28 0.00 4.24
1025 5606 0.248289 GGGAAACTACGTGGCTAGCA 59.752 55.000 18.24 0.00 0.00 3.49
1145 5759 1.411246 GTGATGGCGTACACCTCCATA 59.589 52.381 0.85 0.00 40.43 2.74
1519 6172 3.365265 CCCAGCACAACCCTTCGC 61.365 66.667 0.00 0.00 0.00 4.70
1547 6200 3.379445 AGCTCGTACCCCACCACG 61.379 66.667 0.00 0.00 39.48 4.94
1580 6233 1.868997 GACGTACGTCGGAGGACAA 59.131 57.895 30.48 0.00 43.61 3.18
1813 6466 2.974698 CGGATTCATGAGCGGCCC 60.975 66.667 0.00 0.00 0.00 5.80
1817 6470 1.501169 TGTATGCGGATTCATGAGCG 58.499 50.000 0.00 0.00 0.00 5.03
1826 6479 1.089481 CCGTGTGCTTGTATGCGGAT 61.089 55.000 0.00 0.00 41.45 4.18
1831 6484 2.784596 CGGCCGTGTGCTTGTATG 59.215 61.111 19.50 0.00 40.92 2.39
1832 6485 3.124921 GCGGCCGTGTGCTTGTAT 61.125 61.111 28.70 0.00 40.92 2.29
1971 6634 4.100653 TGAGAATCACCAAGCTATCTGGAG 59.899 45.833 9.96 2.02 42.56 3.86
1995 6658 9.131791 TGTACCAAGCTATCTTTCTTTCTTTTT 57.868 29.630 0.00 0.00 0.00 1.94
1996 6659 8.691661 TGTACCAAGCTATCTTTCTTTCTTTT 57.308 30.769 0.00 0.00 0.00 2.27
1997 6660 8.870075 ATGTACCAAGCTATCTTTCTTTCTTT 57.130 30.769 0.00 0.00 0.00 2.52
1998 6661 8.870075 AATGTACCAAGCTATCTTTCTTTCTT 57.130 30.769 0.00 0.00 0.00 2.52
1999 6662 7.554476 GGAATGTACCAAGCTATCTTTCTTTCT 59.446 37.037 0.00 0.00 0.00 2.52
2000 6663 7.466050 CGGAATGTACCAAGCTATCTTTCTTTC 60.466 40.741 0.00 0.00 0.00 2.62
2001 6664 6.316390 CGGAATGTACCAAGCTATCTTTCTTT 59.684 38.462 0.00 0.00 0.00 2.52
2002 6665 5.817816 CGGAATGTACCAAGCTATCTTTCTT 59.182 40.000 0.00 0.00 0.00 2.52
2003 6666 5.104900 ACGGAATGTACCAAGCTATCTTTCT 60.105 40.000 0.00 0.00 0.00 2.52
2004 6667 5.116882 ACGGAATGTACCAAGCTATCTTTC 58.883 41.667 0.00 0.00 0.00 2.62
2005 6668 5.099042 ACGGAATGTACCAAGCTATCTTT 57.901 39.130 0.00 0.00 0.00 2.52
2006 6669 4.161565 TGACGGAATGTACCAAGCTATCTT 59.838 41.667 0.00 0.00 0.00 2.40
2007 6670 3.704566 TGACGGAATGTACCAAGCTATCT 59.295 43.478 0.00 0.00 0.00 1.98
2146 6925 4.304110 CATGCTGCTCTTGTCAATTTGTT 58.696 39.130 0.00 0.00 0.00 2.83
2216 6995 6.269769 ACCTCCAATAAACATTGTTGTGGATT 59.730 34.615 21.19 13.35 35.83 3.01
2241 7061 1.336125 TGCATTGCATCACAAACGTCA 59.664 42.857 7.38 0.00 42.86 4.35
2273 7093 1.201647 TGAGTTCGATCCGTTGACCTC 59.798 52.381 0.00 0.00 0.00 3.85
2319 7144 1.586564 CTCTTCCGCGGTGATCGAC 60.587 63.158 27.15 0.00 42.43 4.20
2323 7148 0.105039 GGATTCTCTTCCGCGGTGAT 59.895 55.000 27.15 9.90 0.00 3.06
2392 7217 4.574599 AAGTACATCCGGGTACGATTAC 57.425 45.455 13.32 0.00 46.40 1.89
2394 7219 5.351458 GTTTAAGTACATCCGGGTACGATT 58.649 41.667 13.32 7.65 46.40 3.34
2413 7238 1.471119 AGCCATCGACTCGAGGTTTA 58.529 50.000 18.41 0.00 39.91 2.01
2444 7269 4.756642 TGGTTTGTTTTGTGCAAATTGTCA 59.243 33.333 0.00 0.00 38.00 3.58
2450 7275 6.988580 TCATGATATGGTTTGTTTTGTGCAAA 59.011 30.769 0.00 0.00 33.96 3.68
2454 7279 6.808212 GGTCTCATGATATGGTTTGTTTTGTG 59.192 38.462 0.00 0.00 0.00 3.33
2459 7284 5.819991 AGTGGTCTCATGATATGGTTTGTT 58.180 37.500 0.00 0.00 0.00 2.83
2546 7371 8.343168 TCCCGTGAATATTTGTTTGTTATTCT 57.657 30.769 0.00 0.00 34.75 2.40
2579 7404 1.001815 CGCGTTTGACACCCTTTGATT 60.002 47.619 0.00 0.00 0.00 2.57
2591 7416 2.589442 AGGTTTCGGCGCGTTTGA 60.589 55.556 8.43 0.00 0.00 2.69
2599 7424 1.377333 CTCCCCAAGAGGTTTCGGC 60.377 63.158 0.00 0.00 39.13 5.54
2633 7458 7.989416 ACCGATTAACAACCTTATCTTCAAA 57.011 32.000 0.00 0.00 0.00 2.69
2676 7501 0.103937 GAGTTCCGGGATCAGCTCTG 59.896 60.000 0.00 0.00 0.00 3.35
2677 7502 0.324738 TGAGTTCCGGGATCAGCTCT 60.325 55.000 0.00 0.00 0.00 4.09
2692 7517 2.046892 GCTGCCACGTCCATGAGT 60.047 61.111 0.00 0.00 0.00 3.41
2694 7519 2.046988 CTGCTGCCACGTCCATGA 60.047 61.111 0.00 0.00 0.00 3.07
2712 7537 6.127619 GGATATTGTTTCCACCTCTTCTTTGG 60.128 42.308 0.00 0.00 33.21 3.28
2757 7582 3.630892 TCTAGACTAACCTGACTCGCT 57.369 47.619 0.00 0.00 0.00 4.93
2776 7601 7.550906 AGCTGAACTTCCTATCATAACTTGTTC 59.449 37.037 0.00 0.00 33.94 3.18
2824 7649 3.465403 CTCTAGCCTGGCTGCGGT 61.465 66.667 30.83 7.06 40.10 5.68
2845 7670 2.625823 CCTCGGTTGCGCCAATGTT 61.626 57.895 4.18 0.00 36.97 2.71
2878 7703 2.036733 GTGCACACCACTACTTCACCTA 59.963 50.000 13.17 0.00 41.35 3.08
2880 7705 1.226746 GTGCACACCACTACTTCACC 58.773 55.000 13.17 0.00 41.35 4.02
2894 7719 2.622942 TGGTTCTCAAATTGAGGTGCAC 59.377 45.455 21.35 8.80 44.39 4.57
2897 7722 6.430925 TGAAGTATGGTTCTCAAATTGAGGTG 59.569 38.462 21.35 0.00 44.39 4.00


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

AutoCloner maintained by Alex Coulton.