Multiple sequence alignment - TraesCS1A01G220500

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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 TraesCS1A01G220500 chr1A 100.000 4926 0 0 1704 6629 389798912 389803837 0.000000e+00 9097.0
1 TraesCS1A01G220500 chr1A 100.000 1458 0 0 1 1458 389797209 389798666 0.000000e+00 2693.0
2 TraesCS1A01G220500 chr1A 96.879 865 25 2 3 865 71082797 71081933 0.000000e+00 1447.0
3 TraesCS1A01G220500 chr1A 86.049 853 84 19 1782 2616 389768169 389769004 0.000000e+00 883.0
4 TraesCS1A01G220500 chr1A 91.297 563 48 1 4166 4728 389769788 389770349 0.000000e+00 767.0
5 TraesCS1A01G220500 chr1A 88.000 500 29 13 959 1458 389767544 389768012 4.490000e-156 562.0
6 TraesCS1A01G220500 chr1A 90.756 357 31 1 4933 5289 389770466 389770820 6.020000e-130 475.0
7 TraesCS1A01G220500 chr1A 88.714 381 40 2 6250 6629 516557181 516557559 4.680000e-126 462.0
8 TraesCS1A01G220500 chr1A 80.781 640 71 21 5504 6121 389770946 389771555 2.820000e-123 453.0
9 TraesCS1A01G220500 chr1A 84.356 326 37 4 3581 3895 389769412 389769734 2.320000e-79 307.0
10 TraesCS1A01G220500 chr1A 88.446 251 20 6 5316 5558 389770808 389771057 1.810000e-75 294.0
11 TraesCS1A01G220500 chr1A 90.374 187 13 5 2691 2876 389769107 389769289 2.390000e-59 241.0
12 TraesCS1A01G220500 chr1A 93.827 81 5 0 4816 4896 389770378 389770458 9.030000e-24 122.0
13 TraesCS1A01G220500 chr1A 96.364 55 2 0 5559 5613 389802657 389802711 2.550000e-14 91.6
14 TraesCS1A01G220500 chr3A 98.945 4931 33 8 1704 6629 128585657 128580741 0.000000e+00 8800.0
15 TraesCS1A01G220500 chr3A 99.113 564 5 0 895 1458 128586774 128586211 0.000000e+00 1014.0
16 TraesCS1A01G220500 chr3A 84.705 948 90 28 1704 2616 128719755 128718828 0.000000e+00 896.0
17 TraesCS1A01G220500 chr3A 91.652 563 46 1 4166 4728 128718043 128717482 0.000000e+00 778.0
18 TraesCS1A01G220500 chr3A 87.600 500 31 13 959 1458 128720287 128719819 9.720000e-153 551.0
19 TraesCS1A01G220500 chr3A 90.476 357 32 1 4933 5289 128717365 128717011 2.800000e-128 470.0
20 TraesCS1A01G220500 chr3A 80.312 640 74 22 5504 6121 128716885 128716276 2.840000e-118 436.0
21 TraesCS1A01G220500 chr3A 85.276 326 34 4 3581 3895 128718419 128718097 2.310000e-84 324.0
22 TraesCS1A01G220500 chr3A 88.235 238 19 6 5322 5551 128717017 128716781 6.550000e-70 276.0
23 TraesCS1A01G220500 chr3A 90.909 187 13 4 2691 2876 128718725 128718542 1.430000e-61 248.0
24 TraesCS1A01G220500 chr3A 100.000 91 0 0 4749 4839 741209477 741209567 1.140000e-37 169.0
25 TraesCS1A01G220500 chr3A 93.827 81 5 0 4816 4896 128717453 128717373 9.030000e-24 122.0
26 TraesCS1A01G220500 chr3A 96.364 55 2 0 5449 5503 128581807 128581753 2.550000e-14 91.6
27 TraesCS1A01G220500 chr3A 88.679 53 6 0 5449 5501 128716828 128716776 1.540000e-06 65.8
28 TraesCS1A01G220500 chr1D 95.552 4317 137 28 1730 6011 309917386 309921682 0.000000e+00 6857.0
29 TraesCS1A01G220500 chr1D 85.564 949 81 30 1704 2616 309852711 309853639 0.000000e+00 942.0
30 TraesCS1A01G220500 chr1D 92.945 567 26 5 895 1458 309916738 309917293 0.000000e+00 813.0
31 TraesCS1A01G220500 chr1D 91.312 564 49 0 4166 4729 309854454 309855017 0.000000e+00 771.0
32 TraesCS1A01G220500 chr1D 86.525 564 34 15 895 1458 309852126 309852647 3.450000e-162 582.0
33 TraesCS1A01G220500 chr1D 90.083 242 14 7 6011 6250 309921741 309921974 8.350000e-79 305.0
34 TraesCS1A01G220500 chr1D 83.636 330 36 5 3581 3895 309854081 309854407 1.810000e-75 294.0
35 TraesCS1A01G220500 chr1D 90.000 220 22 0 4933 5152 309855134 309855353 1.090000e-72 285.0
36 TraesCS1A01G220500 chr1D 87.550 249 24 4 5316 5558 309901369 309901616 1.410000e-71 281.0
37 TraesCS1A01G220500 chr1D 78.947 475 55 18 5504 5963 309901505 309901949 1.410000e-71 281.0
38 TraesCS1A01G220500 chr1D 91.979 187 10 5 2691 2876 309853742 309853924 2.370000e-64 257.0
39 TraesCS1A01G220500 chr1D 90.141 142 12 1 5148 5289 309901242 309901381 4.080000e-42 183.0
40 TraesCS1A01G220500 chr1D 93.902 82 5 0 4816 4897 309855046 309855127 2.510000e-24 124.0
41 TraesCS1A01G220500 chr1B 95.331 1949 65 10 3573 5502 419948442 419950383 0.000000e+00 3072.0
42 TraesCS1A01G220500 chr1B 94.136 1893 53 20 1704 3582 419941323 419943171 0.000000e+00 2828.0
43 TraesCS1A01G220500 chr1B 85.329 1779 156 32 3581 5289 419770768 419772511 0.000000e+00 1742.0
44 TraesCS1A01G220500 chr1B 84.615 949 87 30 1704 2616 419769498 419770423 0.000000e+00 889.0
45 TraesCS1A01G220500 chr1B 92.769 567 28 5 895 1458 419940704 419941260 0.000000e+00 808.0
46 TraesCS1A01G220500 chr1B 88.246 553 30 14 911 1458 419768912 419769434 4.360000e-176 628.0
47 TraesCS1A01G220500 chr1B 87.004 277 27 6 43 316 359192913 359193183 3.000000e-78 303.0
48 TraesCS1A01G220500 chr1B 86.508 252 24 7 5316 5558 419772499 419772749 1.100000e-67 268.0
49 TraesCS1A01G220500 chr1B 89.444 180 14 4 2691 2869 419770525 419770700 8.650000e-54 222.0
50 TraesCS1A01G220500 chr1B 90.210 143 12 2 5504 5644 419772638 419772780 1.140000e-42 185.0
51 TraesCS1A01G220500 chr7A 88.996 827 73 14 51 864 1911779 1912600 0.000000e+00 1007.0
52 TraesCS1A01G220500 chr7A 85.978 271 34 3 2967 3235 546012058 546012326 3.030000e-73 287.0
53 TraesCS1A01G220500 chr7A 100.000 29 0 0 864 892 176245153 176245181 3.000000e-03 54.7
54 TraesCS1A01G220500 chr7A 100.000 28 0 0 5831 5858 640450119 640450146 1.200000e-02 52.8
55 TraesCS1A01G220500 chr4A 93.668 379 24 0 6251 6629 616607023 616606645 9.650000e-158 568.0
56 TraesCS1A01G220500 chr4A 85.821 536 58 11 3046 3579 406758913 406759432 2.700000e-153 553.0
57 TraesCS1A01G220500 chr6A 92.388 381 28 1 6250 6629 79324491 79324111 5.850000e-150 542.0
58 TraesCS1A01G220500 chr6A 90.186 377 35 2 6251 6627 558111275 558110901 2.150000e-134 490.0
59 TraesCS1A01G220500 chr3B 90.000 420 41 1 440 858 15804279 15804698 5.850000e-150 542.0
60 TraesCS1A01G220500 chr3B 85.652 230 16 9 5 217 15803232 15803461 6.690000e-55 226.0
61 TraesCS1A01G220500 chr3B 76.282 156 20 11 5718 5858 235856381 235856228 4.290000e-07 67.6
62 TraesCS1A01G220500 chr3B 94.444 36 1 1 864 899 738195245 738195211 3.000000e-03 54.7
63 TraesCS1A01G220500 chr6D 86.282 503 44 12 51 549 448621907 448622388 2.120000e-144 523.0
64 TraesCS1A01G220500 chr6D 91.304 46 4 0 5700 5745 294088185 294088230 5.550000e-06 63.9
65 TraesCS1A01G220500 chr5B 90.501 379 33 3 6250 6627 526266618 526266994 1.280000e-136 497.0
66 TraesCS1A01G220500 chr5B 90.000 380 36 2 6250 6629 526247216 526247593 2.150000e-134 490.0
67 TraesCS1A01G220500 chr5B 93.023 43 3 0 5703 5745 54700619 54700577 5.550000e-06 63.9
68 TraesCS1A01G220500 chr2B 90.263 380 35 2 6251 6629 795990798 795990420 4.620000e-136 496.0
69 TraesCS1A01G220500 chr2B 93.333 195 13 0 3386 3580 61334727 61334533 8.410000e-74 289.0
70 TraesCS1A01G220500 chr2B 91.892 111 7 2 51 159 38023375 38023485 3.200000e-33 154.0
71 TraesCS1A01G220500 chr3D 90.617 373 34 1 6257 6629 18791437 18791808 1.660000e-135 494.0
72 TraesCS1A01G220500 chr3D 91.795 195 16 0 3386 3580 566242884 566242690 8.470000e-69 272.0
73 TraesCS1A01G220500 chr6B 82.432 444 58 18 2963 3400 87325837 87326266 2.920000e-98 370.0
74 TraesCS1A01G220500 chr6B 91.457 199 15 1 3386 3582 87326289 87326487 8.470000e-69 272.0
75 TraesCS1A01G220500 chr2D 83.548 389 54 6 2966 3347 36119095 36119480 8.180000e-94 355.0
76 TraesCS1A01G220500 chr2D 84.682 346 46 3 3018 3361 110963149 110962809 8.230000e-89 339.0
77 TraesCS1A01G220500 chr2D 84.279 229 32 3 3009 3235 3303622 3303848 3.110000e-53 220.0
78 TraesCS1A01G220500 chr5D 94.359 195 11 0 3386 3580 9226937 9227131 3.890000e-77 300.0
79 TraesCS1A01G220500 chr5D 93.023 43 3 0 5703 5745 51683337 51683295 5.550000e-06 63.9
80 TraesCS1A01G220500 chr4D 86.347 271 33 3 2967 3235 229900769 229901037 6.500000e-75 292.0
81 TraesCS1A01G220500 chrUn 90.769 195 17 1 3386 3579 17288781 17288975 6.590000e-65 259.0
82 TraesCS1A01G220500 chr5A 93.478 46 3 0 5700 5745 100651460 100651415 1.190000e-07 69.4
83 TraesCS1A01G220500 chr7B 74.479 192 31 13 5770 5945 526134013 526133824 4.290000e-07 67.6
84 TraesCS1A01G220500 chr7D 96.875 32 1 0 864 895 162762015 162762046 3.000000e-03 54.7


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 TraesCS1A01G220500 chr1A 389797209 389803837 6628 False 3960.533333 9097 98.788000 1 6629 3 chr1A.!!$F3 6628
1 TraesCS1A01G220500 chr1A 71081933 71082797 864 True 1447.000000 1447 96.879000 3 865 1 chr1A.!!$R1 862
2 TraesCS1A01G220500 chr1A 389767544 389771555 4011 False 456.000000 883 88.209556 959 6121 9 chr1A.!!$F2 5162
3 TraesCS1A01G220500 chr3A 128580741 128585657 4916 True 4445.800000 8800 97.654500 1704 6629 2 chr3A.!!$R2 4925
4 TraesCS1A01G220500 chr3A 128586211 128586774 563 True 1014.000000 1014 99.113000 895 1458 1 chr3A.!!$R1 563
5 TraesCS1A01G220500 chr3A 128716276 128720287 4011 True 416.680000 896 88.167100 959 6121 10 chr3A.!!$R3 5162
6 TraesCS1A01G220500 chr1D 309916738 309921974 5236 False 2658.333333 6857 92.860000 895 6250 3 chr1D.!!$F3 5355
7 TraesCS1A01G220500 chr1D 309852126 309855353 3227 False 465.000000 942 88.988286 895 5152 7 chr1D.!!$F1 4257
8 TraesCS1A01G220500 chr1D 309901242 309901949 707 False 248.333333 281 85.546000 5148 5963 3 chr1D.!!$F2 815
9 TraesCS1A01G220500 chr1B 419948442 419950383 1941 False 3072.000000 3072 95.331000 3573 5502 1 chr1B.!!$F2 1929
10 TraesCS1A01G220500 chr1B 419940704 419943171 2467 False 1818.000000 2828 93.452500 895 3582 2 chr1B.!!$F4 2687
11 TraesCS1A01G220500 chr1B 419768912 419772780 3868 False 655.666667 1742 87.392000 911 5644 6 chr1B.!!$F3 4733
12 TraesCS1A01G220500 chr7A 1911779 1912600 821 False 1007.000000 1007 88.996000 51 864 1 chr7A.!!$F1 813
13 TraesCS1A01G220500 chr4A 406758913 406759432 519 False 553.000000 553 85.821000 3046 3579 1 chr4A.!!$F1 533
14 TraesCS1A01G220500 chr3B 15803232 15804698 1466 False 384.000000 542 87.826000 5 858 2 chr3B.!!$F1 853
15 TraesCS1A01G220500 chr6B 87325837 87326487 650 False 321.000000 370 86.944500 2963 3582 2 chr6B.!!$F1 619

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
541 589 0.037447 TGCCGTTGGTGATGAATCCA 59.963 50.000 0.0 0.0 0.0 3.41 F
883 931 0.173255 GCCACATGGTTGCCACATAC 59.827 55.000 0.0 0.0 35.8 2.39 F
884 932 1.543607 CCACATGGTTGCCACATACA 58.456 50.000 0.0 0.0 35.8 2.29 F
885 933 2.101783 CCACATGGTTGCCACATACAT 58.898 47.619 0.0 0.0 35.8 2.29 F
5535 6329 1.615883 CTATGATAGAGTGCTGCCCGT 59.384 52.381 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2751 4.497291 AAACTGTCTCAACTGGTACCAA 57.503 40.909 17.11 0.0 0.00 3.67 R
4246 5007 7.251321 AGTGGTTCAGAAGTATCTCAGAATT 57.749 36.000 0.00 0.0 32.03 2.17 R
5535 6329 8.880244 GGTCTCCACATATATATTATATGCCCA 58.120 37.037 12.33 0.0 35.88 5.36 R
5551 6402 6.382087 TCATAGGTAGTAATGGTCTCCACAT 58.618 40.000 0.00 0.0 35.80 3.21 R
6410 7333 0.627986 AGGAGCATGGGAGGGAAAAG 59.372 55.000 0.00 0.0 0.00 2.27 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
137 154 2.318908 TGTTGGAGCCTTTTGCAATCT 58.681 42.857 0.00 0.00 44.83 2.40
206 226 1.605710 CCAAGCTTCAGACAACACTGG 59.394 52.381 0.00 0.00 38.31 4.00
209 229 3.498774 AGCTTCAGACAACACTGGATT 57.501 42.857 0.00 0.00 38.31 3.01
217 264 6.353323 TCAGACAACACTGGATTTTACAAGA 58.647 36.000 0.00 0.00 38.31 3.02
393 441 2.181021 CTCGCCGCCGTACTTCTT 59.819 61.111 0.00 0.00 35.54 2.52
413 461 4.095036 TCTTCTATGTCACTACGTGCTCTG 59.905 45.833 0.00 0.00 32.98 3.35
417 465 0.039074 GTCACTACGTGCTCTGCTGT 60.039 55.000 0.00 0.00 32.98 4.40
467 515 5.291178 CAGAATCAACAACAAATCAAGCCA 58.709 37.500 0.00 0.00 0.00 4.75
501 549 1.199624 GGAGCAAAACAAGCACAACG 58.800 50.000 0.00 0.00 0.00 4.10
503 551 0.179113 AGCAAAACAAGCACAACGGG 60.179 50.000 0.00 0.00 0.00 5.28
529 577 1.448540 CAGTCCTAGGCTGCCGTTG 60.449 63.158 13.96 7.31 0.00 4.10
541 589 0.037447 TGCCGTTGGTGATGAATCCA 59.963 50.000 0.00 0.00 0.00 3.41
642 690 4.373116 TCGGCGTTGAGACCCAGC 62.373 66.667 6.85 0.00 0.00 4.85
797 845 2.059786 CCTTGCGGGCCAAATCCAT 61.060 57.895 4.39 0.00 31.94 3.41
849 897 2.286127 GAAGACGAGCGAAGGGGAGG 62.286 65.000 0.00 0.00 0.00 4.30
865 913 1.560860 GAGGAATAGCCACGCGATGC 61.561 60.000 15.93 15.35 40.02 3.91
866 914 2.607892 GGAATAGCCACGCGATGCC 61.608 63.158 15.93 0.00 32.48 4.40
867 915 1.887242 GAATAGCCACGCGATGCCA 60.887 57.895 15.93 3.79 0.00 4.92
868 916 2.105960 GAATAGCCACGCGATGCCAC 62.106 60.000 15.93 2.97 0.00 5.01
869 917 2.867793 AATAGCCACGCGATGCCACA 62.868 55.000 15.93 3.40 0.00 4.17
870 918 2.665008 ATAGCCACGCGATGCCACAT 62.665 55.000 15.93 5.69 0.00 3.21
871 919 4.541482 GCCACGCGATGCCACATG 62.541 66.667 15.93 0.00 0.00 3.21
872 920 3.879682 CCACGCGATGCCACATGG 61.880 66.667 15.93 2.73 38.53 3.66
873 921 3.126879 CACGCGATGCCACATGGT 61.127 61.111 15.93 0.00 37.57 3.55
874 922 2.359850 ACGCGATGCCACATGGTT 60.360 55.556 15.93 0.00 37.57 3.67
875 923 2.100797 CGCGATGCCACATGGTTG 59.899 61.111 0.00 0.00 37.57 3.77
876 924 2.202650 GCGATGCCACATGGTTGC 60.203 61.111 0.00 0.00 37.57 4.17
877 925 2.491152 CGATGCCACATGGTTGCC 59.509 61.111 0.00 0.00 37.57 4.52
878 926 2.341875 CGATGCCACATGGTTGCCA 61.342 57.895 0.00 0.00 38.19 4.92
879 927 1.216178 GATGCCACATGGTTGCCAC 59.784 57.895 0.00 0.00 35.80 5.01
880 928 1.533513 ATGCCACATGGTTGCCACA 60.534 52.632 0.00 0.00 35.80 4.17
881 929 0.905809 ATGCCACATGGTTGCCACAT 60.906 50.000 0.00 0.00 35.80 3.21
882 930 0.251519 TGCCACATGGTTGCCACATA 60.252 50.000 0.00 0.00 35.80 2.29
883 931 0.173255 GCCACATGGTTGCCACATAC 59.827 55.000 0.00 0.00 35.80 2.39
884 932 1.543607 CCACATGGTTGCCACATACA 58.456 50.000 0.00 0.00 35.80 2.29
885 933 2.101783 CCACATGGTTGCCACATACAT 58.898 47.619 0.00 0.00 35.80 2.29
886 934 3.286353 CCACATGGTTGCCACATACATA 58.714 45.455 0.00 0.00 35.80 2.29
887 935 3.890756 CCACATGGTTGCCACATACATAT 59.109 43.478 0.00 0.00 35.80 1.78
888 936 4.341806 CCACATGGTTGCCACATACATATT 59.658 41.667 0.00 0.00 35.80 1.28
889 937 5.163426 CCACATGGTTGCCACATACATATTT 60.163 40.000 0.00 0.00 35.80 1.40
890 938 5.978919 CACATGGTTGCCACATACATATTTC 59.021 40.000 0.00 0.00 35.80 2.17
891 939 4.891627 TGGTTGCCACATACATATTTCG 57.108 40.909 0.00 0.00 0.00 3.46
892 940 4.518249 TGGTTGCCACATACATATTTCGA 58.482 39.130 0.00 0.00 0.00 3.71
893 941 5.129634 TGGTTGCCACATACATATTTCGAT 58.870 37.500 0.00 0.00 0.00 3.59
2182 2634 5.189928 TCAGCACTAAAGGTGTTTCTTTCA 58.810 37.500 0.00 0.00 46.86 2.69
2299 2751 3.306472 TGGTGTTGCCTCCTTTTTACT 57.694 42.857 0.00 0.00 38.35 2.24
5528 6322 7.394923 AGACCATTACTACCTATGATAGAGTGC 59.605 40.741 0.00 0.00 0.00 4.40
5535 6329 1.615883 CTATGATAGAGTGCTGCCCGT 59.384 52.381 0.00 0.00 0.00 5.28
5677 6529 1.913778 ATGCATTGCCTGTGTTCTCA 58.086 45.000 6.12 0.00 0.00 3.27
6121 7044 1.150081 GGAGATGGGGTGATGCAGG 59.850 63.158 0.00 0.00 0.00 4.85
6122 7045 1.348008 GGAGATGGGGTGATGCAGGA 61.348 60.000 0.00 0.00 0.00 3.86
6334 7257 1.004277 TGTCCAATCAGTTAGGCCCAC 59.996 52.381 0.00 0.00 0.00 4.61
6335 7258 1.282157 GTCCAATCAGTTAGGCCCACT 59.718 52.381 0.00 0.00 0.00 4.00
6343 7266 3.329520 TCAGTTAGGCCCACTATTGTGTT 59.670 43.478 0.00 0.00 42.34 3.32
6427 7350 1.467920 CACTTTTCCCTCCCATGCTC 58.532 55.000 0.00 0.00 0.00 4.26
6441 7364 1.741706 CATGCTCCTGTTTAGTGGCAG 59.258 52.381 0.00 0.00 34.62 4.85
6626 7549 1.615392 AGAATGTGCCTGAACTTTGCC 59.385 47.619 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 154 4.327898 GGTTCAGTTATTTGCACGACGATA 59.672 41.667 0.00 0.00 0.00 2.92
206 226 4.479619 CTGCTGCAACCTCTTGTAAAATC 58.520 43.478 3.02 0.00 0.00 2.17
209 229 2.229792 CCTGCTGCAACCTCTTGTAAA 58.770 47.619 3.02 0.00 0.00 2.01
217 264 2.856000 ACCTCCCTGCTGCAACCT 60.856 61.111 3.02 0.00 0.00 3.50
467 515 1.228306 CTCCCTAGGACGGCGAGAT 60.228 63.158 16.62 0.01 0.00 2.75
501 549 1.051556 CCTAGGACTGGAAGCTCCCC 61.052 65.000 1.05 0.00 37.60 4.81
503 551 0.689412 AGCCTAGGACTGGAAGCTCC 60.689 60.000 14.75 0.00 37.60 4.70
529 577 3.484407 CCATCTCCTTGGATTCATCACC 58.516 50.000 0.00 0.00 39.25 4.02
541 589 1.367848 AGAACTCCCTCCCATCTCCTT 59.632 52.381 0.00 0.00 0.00 3.36
597 645 1.587054 CCTCTCGTCGCACCTCTTT 59.413 57.895 0.00 0.00 0.00 2.52
666 714 0.531532 ACATCTATGTGCGCCTGCTC 60.532 55.000 4.18 0.00 43.34 4.26
669 717 1.215244 CTGACATCTATGTGCGCCTG 58.785 55.000 4.18 0.00 41.95 4.85
797 845 2.225091 ACCACATGAATCTTCCTTGCCA 60.225 45.455 0.00 0.00 0.00 4.92
805 853 1.167851 CGCACCACCACATGAATCTT 58.832 50.000 0.00 0.00 0.00 2.40
865 913 1.543607 TGTATGTGGCAACCATGTGG 58.456 50.000 0.00 0.00 35.28 4.17
866 914 5.518848 AATATGTATGTGGCAACCATGTG 57.481 39.130 1.16 0.00 35.28 3.21
867 915 5.221028 CGAAATATGTATGTGGCAACCATGT 60.221 40.000 1.16 0.00 35.28 3.21
868 916 5.008514 TCGAAATATGTATGTGGCAACCATG 59.991 40.000 1.16 0.00 35.28 3.66
869 917 5.129634 TCGAAATATGTATGTGGCAACCAT 58.870 37.500 0.00 0.00 35.28 3.55
870 918 4.518249 TCGAAATATGTATGTGGCAACCA 58.482 39.130 0.00 0.00 0.00 3.67
871 919 5.689383 ATCGAAATATGTATGTGGCAACC 57.311 39.130 0.00 0.00 0.00 3.77
872 920 7.635423 TGTTATCGAAATATGTATGTGGCAAC 58.365 34.615 0.00 0.00 0.00 4.17
873 921 7.793927 TGTTATCGAAATATGTATGTGGCAA 57.206 32.000 0.00 0.00 0.00 4.52
874 922 7.793927 TTGTTATCGAAATATGTATGTGGCA 57.206 32.000 0.00 0.00 0.00 4.92
875 923 9.509855 TTTTTGTTATCGAAATATGTATGTGGC 57.490 29.630 0.00 0.00 0.00 5.01
878 926 9.730420 GCCTTTTTGTTATCGAAATATGTATGT 57.270 29.630 0.00 0.00 0.00 2.29
879 927 9.729023 TGCCTTTTTGTTATCGAAATATGTATG 57.271 29.630 0.00 0.00 0.00 2.39
882 930 8.921670 GTTTGCCTTTTTGTTATCGAAATATGT 58.078 29.630 0.00 0.00 0.00 2.29
883 931 8.101510 CGTTTGCCTTTTTGTTATCGAAATATG 58.898 33.333 0.00 0.00 0.00 1.78
884 932 7.810759 ACGTTTGCCTTTTTGTTATCGAAATAT 59.189 29.630 0.00 0.00 0.00 1.28
885 933 7.113684 CACGTTTGCCTTTTTGTTATCGAAATA 59.886 33.333 0.00 0.00 0.00 1.40
886 934 5.980715 ACGTTTGCCTTTTTGTTATCGAAAT 59.019 32.000 0.00 0.00 0.00 2.17
887 935 5.230306 CACGTTTGCCTTTTTGTTATCGAAA 59.770 36.000 0.00 0.00 0.00 3.46
888 936 4.735822 CACGTTTGCCTTTTTGTTATCGAA 59.264 37.500 0.00 0.00 0.00 3.71
889 937 4.035324 TCACGTTTGCCTTTTTGTTATCGA 59.965 37.500 0.00 0.00 0.00 3.59
890 938 4.145756 GTCACGTTTGCCTTTTTGTTATCG 59.854 41.667 0.00 0.00 0.00 2.92
891 939 4.443063 GGTCACGTTTGCCTTTTTGTTATC 59.557 41.667 0.00 0.00 0.00 1.75
892 940 4.098807 AGGTCACGTTTGCCTTTTTGTTAT 59.901 37.500 0.00 0.00 0.00 1.89
893 941 3.444388 AGGTCACGTTTGCCTTTTTGTTA 59.556 39.130 0.00 0.00 0.00 2.41
2299 2751 4.497291 AAACTGTCTCAACTGGTACCAA 57.503 40.909 17.11 0.00 0.00 3.67
4246 5007 7.251321 AGTGGTTCAGAAGTATCTCAGAATT 57.749 36.000 0.00 0.00 32.03 2.17
5535 6329 8.880244 GGTCTCCACATATATATTATATGCCCA 58.120 37.037 12.33 0.00 35.88 5.36
5551 6402 6.382087 TCATAGGTAGTAATGGTCTCCACAT 58.618 40.000 0.00 0.00 35.80 3.21
6121 7044 0.734889 CGTCAATTCACCATGCCCTC 59.265 55.000 0.00 0.00 0.00 4.30
6122 7045 0.327924 TCGTCAATTCACCATGCCCT 59.672 50.000 0.00 0.00 0.00 5.19
6191 7114 3.556999 TCTAAGTCCATCCTCTTCTCCG 58.443 50.000 0.00 0.00 0.00 4.63
6334 7257 3.016031 TGGTGCATGGCTAACACAATAG 58.984 45.455 8.50 0.00 36.00 1.73
6335 7258 3.016031 CTGGTGCATGGCTAACACAATA 58.984 45.455 8.50 0.00 36.00 1.90
6343 7266 2.045045 GTGGCTGGTGCATGGCTA 60.045 61.111 10.95 2.36 41.91 3.93
6410 7333 0.627986 AGGAGCATGGGAGGGAAAAG 59.372 55.000 0.00 0.00 0.00 2.27
6441 7364 5.128919 CCAGATATAATTATGAGGCTGGCC 58.871 45.833 17.26 3.00 35.74 5.36
6576 7499 6.927294 AGTCCGATAAAGCCTTCATAAAAG 57.073 37.500 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.