Multiple sequence alignment - TraesCS6B01G054800

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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 TraesCS6B01G054800 chr6B 100.000 3716 0 0 1 3716 35513854 35517569 0.000000e+00 6863.0
1 TraesCS6B01G054800 chr6B 82.031 128 17 5 455 577 406833295 406833169 1.830000e-18 104.0
2 TraesCS6B01G054800 chr6D 91.553 2048 101 22 574 2572 20589396 20591420 0.000000e+00 2758.0
3 TraesCS6B01G054800 chr6D 91.421 373 29 3 1 373 37103814 37103445 3.310000e-140 508.0
4 TraesCS6B01G054800 chr6D 98.718 156 2 0 421 576 37103444 37103289 1.020000e-70 278.0
5 TraesCS6B01G054800 chr6D 82.203 118 18 3 461 575 173896580 173896463 8.490000e-17 99.0
6 TraesCS6B01G054800 chr6A 92.445 1681 74 23 930 2572 20508385 20510050 0.000000e+00 2351.0
7 TraesCS6B01G054800 chr1B 95.602 1137 49 1 2581 3716 394910889 394912025 0.000000e+00 1821.0
8 TraesCS6B01G054800 chr1B 90.548 1132 106 1 2586 3716 678558887 678560018 0.000000e+00 1496.0
9 TraesCS6B01G054800 chr1B 89.122 763 71 7 1505 2255 156838469 156837707 0.000000e+00 939.0
10 TraesCS6B01G054800 chr1B 88.263 213 25 0 1017 1229 156838992 156838780 4.760000e-64 255.0
11 TraesCS6B01G054800 chr3B 95.499 1133 49 2 2585 3716 810145912 810144781 0.000000e+00 1808.0
12 TraesCS6B01G054800 chr2B 92.247 1135 86 2 2584 3716 534241074 534239940 0.000000e+00 1607.0
13 TraesCS6B01G054800 chr7A 91.777 1131 91 2 2586 3714 644860152 644859022 0.000000e+00 1572.0
14 TraesCS6B01G054800 chr7A 81.111 270 39 7 94 362 43787846 43788104 4.860000e-49 206.0
15 TraesCS6B01G054800 chr7A 81.111 270 39 6 94 362 43797074 43797332 4.860000e-49 206.0
16 TraesCS6B01G054800 chr7A 81.181 271 37 6 94 362 43850360 43850618 4.860000e-49 206.0
17 TraesCS6B01G054800 chr7A 80.741 270 40 6 94 362 43815444 43815702 2.260000e-47 200.0
18 TraesCS6B01G054800 chr5B 92.764 995 69 2 2725 3716 703080669 703081663 0.000000e+00 1435.0
19 TraesCS6B01G054800 chr5B 91.854 577 40 5 1 575 576875129 576875700 0.000000e+00 798.0
20 TraesCS6B01G054800 chr2D 86.252 1142 152 5 2577 3716 71232844 71231706 0.000000e+00 1234.0
21 TraesCS6B01G054800 chr2D 77.205 1145 247 13 2576 3714 155124921 155123785 0.000000e+00 656.0
22 TraesCS6B01G054800 chr2D 85.083 181 25 2 1 181 9119928 9120106 2.280000e-42 183.0
23 TraesCS6B01G054800 chr4B 94.904 726 35 2 2581 3304 621970509 621971234 0.000000e+00 1134.0
24 TraesCS6B01G054800 chr1A 85.200 973 98 23 1296 2255 91174941 91175880 0.000000e+00 957.0
25 TraesCS6B01G054800 chr1A 88.312 231 26 1 1022 1252 91174610 91174839 3.660000e-70 276.0
26 TraesCS6B01G054800 chr1A 83.178 107 15 3 472 575 251688041 251687935 1.100000e-15 95.3
27 TraesCS6B01G054800 chr1D 89.605 760 67 2 1505 2252 95936112 95936871 0.000000e+00 955.0
28 TraesCS6B01G054800 chr1D 86.831 243 28 2 1014 1252 95935602 95935844 6.120000e-68 268.0
29 TraesCS6B01G054800 chr1D 88.696 115 11 2 1295 1408 95935935 95936048 5.000000e-29 139.0
30 TraesCS6B01G054800 chrUn 94.783 575 29 1 1 575 76412859 76413432 0.000000e+00 894.0
31 TraesCS6B01G054800 chr5A 92.014 576 41 4 1 575 590059765 590060336 0.000000e+00 804.0
32 TraesCS6B01G054800 chr5D 91.652 575 44 3 1 575 469428258 469428828 0.000000e+00 793.0
33 TraesCS6B01G054800 chr7B 80.916 131 21 2 449 575 21564161 21564291 2.360000e-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 TraesCS6B01G054800 chr6B 35513854 35517569 3715 False 6863.0 6863 100.000000 1 3716 1 chr6B.!!$F1 3715
1 TraesCS6B01G054800 chr6D 20589396 20591420 2024 False 2758.0 2758 91.553000 574 2572 1 chr6D.!!$F1 1998
2 TraesCS6B01G054800 chr6D 37103289 37103814 525 True 393.0 508 95.069500 1 576 2 chr6D.!!$R2 575
3 TraesCS6B01G054800 chr6A 20508385 20510050 1665 False 2351.0 2351 92.445000 930 2572 1 chr6A.!!$F1 1642
4 TraesCS6B01G054800 chr1B 394910889 394912025 1136 False 1821.0 1821 95.602000 2581 3716 1 chr1B.!!$F1 1135
5 TraesCS6B01G054800 chr1B 678558887 678560018 1131 False 1496.0 1496 90.548000 2586 3716 1 chr1B.!!$F2 1130
6 TraesCS6B01G054800 chr1B 156837707 156838992 1285 True 597.0 939 88.692500 1017 2255 2 chr1B.!!$R1 1238
7 TraesCS6B01G054800 chr3B 810144781 810145912 1131 True 1808.0 1808 95.499000 2585 3716 1 chr3B.!!$R1 1131
8 TraesCS6B01G054800 chr2B 534239940 534241074 1134 True 1607.0 1607 92.247000 2584 3716 1 chr2B.!!$R1 1132
9 TraesCS6B01G054800 chr7A 644859022 644860152 1130 True 1572.0 1572 91.777000 2586 3714 1 chr7A.!!$R1 1128
10 TraesCS6B01G054800 chr5B 703080669 703081663 994 False 1435.0 1435 92.764000 2725 3716 1 chr5B.!!$F2 991
11 TraesCS6B01G054800 chr5B 576875129 576875700 571 False 798.0 798 91.854000 1 575 1 chr5B.!!$F1 574
12 TraesCS6B01G054800 chr2D 71231706 71232844 1138 True 1234.0 1234 86.252000 2577 3716 1 chr2D.!!$R1 1139
13 TraesCS6B01G054800 chr2D 155123785 155124921 1136 True 656.0 656 77.205000 2576 3714 1 chr2D.!!$R2 1138
14 TraesCS6B01G054800 chr4B 621970509 621971234 725 False 1134.0 1134 94.904000 2581 3304 1 chr4B.!!$F1 723
15 TraesCS6B01G054800 chr1A 91174610 91175880 1270 False 616.5 957 86.756000 1022 2255 2 chr1A.!!$F1 1233
16 TraesCS6B01G054800 chr1D 95935602 95936871 1269 False 454.0 955 88.377333 1014 2252 3 chr1D.!!$F1 1238
17 TraesCS6B01G054800 chrUn 76412859 76413432 573 False 894.0 894 94.783000 1 575 1 chrUn.!!$F1 574
18 TraesCS6B01G054800 chr5A 590059765 590060336 571 False 804.0 804 92.014000 1 575 1 chr5A.!!$F1 574
19 TraesCS6B01G054800 chr5D 469428258 469428828 570 False 793.0 793 91.652000 1 575 1 chr5D.!!$F1 574

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
261 263 0.107703 TCTCGCCCATGTGACATTCC 60.108 55.0 0.00 0.0 0.0 3.01 F
1041 1055 0.100682 GAAGCTAGGCATGTCGACGA 59.899 55.0 11.62 0.0 0.0 4.20 F
1629 1747 0.824182 CCTCTTCGCCGTCCTCCTAT 60.824 60.0 0.00 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1513 0.110373 AAAGCAAACGACGAATCCGC 60.110 50.0 0.0 0.0 39.95 5.54 R
2574 2744 0.680618 TTGGGCAACAGCTTGAATGG 59.319 50.0 0.0 0.0 39.74 3.16 R
2722 2892 2.214376 TGGGGTAGCACATTTTCCAG 57.786 50.0 0.0 0.0 0.00 3.86 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
85 87 7.462571 AAAAAGCTAGACCCACGAATATTTT 57.537 32.000 0.00 0.00 0.00 1.82
87 89 8.570068 AAAAGCTAGACCCACGAATATTTTTA 57.430 30.769 0.00 0.00 0.00 1.52
261 263 0.107703 TCTCGCCCATGTGACATTCC 60.108 55.000 0.00 0.00 0.00 3.01
368 372 9.533253 AATTTTTATTCCAAGAACTTGTGACAG 57.467 29.630 12.54 0.00 38.85 3.51
377 381 6.538742 CCAAGAACTTGTGACAGACTAAAGAA 59.461 38.462 12.54 0.00 38.85 2.52
416 420 3.449737 GGGGGCCACTTAAAGATAAAACC 59.550 47.826 4.16 0.00 0.00 3.27
494 499 7.261829 ACATCACATTTGGTTCAAATTTTGG 57.738 32.000 9.18 0.00 40.60 3.28
590 595 6.751514 TGCTAGTTGTCACAAAGAGAAAAA 57.248 33.333 0.00 0.00 30.49 1.94
633 638 9.801873 TTTGTCACAAAAAGATAAGGAGAAAAG 57.198 29.630 0.00 0.00 0.00 2.27
637 642 7.942341 TCACAAAAAGATAAGGAGAAAAGGCTA 59.058 33.333 0.00 0.00 0.00 3.93
641 646 9.451002 AAAAAGATAAGGAGAAAAGGCTACTAC 57.549 33.333 0.00 0.00 0.00 2.73
645 650 8.066247 AGATAAGGAGAAAAGGCTACTACCTAA 58.934 37.037 0.00 0.00 39.93 2.69
652 657 6.554228 AGAAAAGGCTACTACCTAATACTCCC 59.446 42.308 0.00 0.00 39.93 4.30
660 665 6.039415 ACTACCTAATACTCCCTCCATTCA 57.961 41.667 0.00 0.00 0.00 2.57
703 709 3.598019 TTGGCTGAGATTCCAAATTGC 57.402 42.857 0.00 0.00 39.22 3.56
707 713 3.508762 GCTGAGATTCCAAATTGCAGTG 58.491 45.455 0.00 0.00 0.00 3.66
740 746 2.288091 CCACATGCATGTTTGGACGAAA 60.288 45.455 29.48 0.00 39.39 3.46
744 750 2.293170 TGCATGTTTGGACGAAACTGA 58.707 42.857 13.32 0.00 43.90 3.41
751 757 1.052124 TGGACGAAACTGACCCTGGT 61.052 55.000 0.00 0.00 0.00 4.00
767 773 4.265078 ACCCTGGTTTAGAATCTCCTCTCT 60.265 45.833 0.00 0.00 0.00 3.10
816 826 2.100916 GAGGCTGCTTTCGTCCATACTA 59.899 50.000 0.00 0.00 0.00 1.82
826 836 5.607939 TTCGTCCATACTACAACATCCAT 57.392 39.130 0.00 0.00 0.00 3.41
846 856 4.099727 CCATGTCATGCATTGGTATTGGAA 59.900 41.667 7.35 0.00 35.19 3.53
872 882 4.767409 AGAATGTATGCGCACTATAGAGGA 59.233 41.667 14.90 0.00 0.00 3.71
873 883 5.243954 AGAATGTATGCGCACTATAGAGGAA 59.756 40.000 14.90 0.00 0.00 3.36
874 884 4.505313 TGTATGCGCACTATAGAGGAAG 57.495 45.455 14.90 0.00 0.00 3.46
875 885 3.255888 TGTATGCGCACTATAGAGGAAGG 59.744 47.826 14.90 0.00 0.00 3.46
876 886 1.040646 TGCGCACTATAGAGGAAGGG 58.959 55.000 5.66 0.96 0.00 3.95
879 889 1.271102 CGCACTATAGAGGAAGGGAGC 59.729 57.143 6.78 0.00 0.00 4.70
885 895 5.242838 CACTATAGAGGAAGGGAGCACTTAG 59.757 48.000 6.78 0.00 0.00 2.18
891 901 5.309806 AGAGGAAGGGAGCACTTAGTTTAAA 59.690 40.000 0.00 0.00 0.00 1.52
964 975 0.527565 CATTCCCGGTTGAGCTTTGG 59.472 55.000 0.00 0.00 0.00 3.28
999 1013 6.183359 GCGTACTCAGTGAAAAGTGAATACTC 60.183 42.308 0.00 0.00 35.69 2.59
1012 1026 5.209202 AGTGAATACTCGTCGATCAGTCGA 61.209 45.833 0.00 0.00 43.31 4.20
1013 1027 6.477355 AGTGAATACTCGTCGATCAGTCGAT 61.477 44.000 3.72 0.00 45.52 3.59
1014 1028 8.194011 AGTGAATACTCGTCGATCAGTCGATC 62.194 46.154 3.72 0.00 45.52 3.69
1041 1055 0.100682 GAAGCTAGGCATGTCGACGA 59.899 55.000 11.62 0.00 0.00 4.20
1062 1076 1.429930 TGCAGGGAAGAAGGTGTACA 58.570 50.000 0.00 0.00 0.00 2.90
1220 1238 4.339530 GCCATCCTCCTTGAAAGGTAATTC 59.660 45.833 8.91 0.00 46.54 2.17
1266 1285 7.770897 AGTTACTTGATCTGGATGTAATTCACC 59.229 37.037 0.00 0.00 0.00 4.02
1268 1287 5.882557 ACTTGATCTGGATGTAATTCACCAC 59.117 40.000 0.00 0.00 0.00 4.16
1297 1391 8.539856 AAATTAGGTCATCCCCCTTAATATCT 57.460 34.615 0.00 0.00 33.35 1.98
1309 1403 8.383175 TCCCCCTTAATATCTATGAATGTCAAC 58.617 37.037 0.00 0.00 0.00 3.18
1329 1423 1.197721 CGATTTTGCAGGAGAAACGCT 59.802 47.619 0.00 0.00 0.00 5.07
1383 1477 7.896811 AGATATTCATGTATGCTTTACTCGGA 58.103 34.615 0.00 0.00 0.00 4.55
1417 1512 2.487762 CACGACACCATTAACATTGCCT 59.512 45.455 0.00 0.00 0.00 4.75
1418 1513 2.487762 ACGACACCATTAACATTGCCTG 59.512 45.455 0.00 0.00 0.00 4.85
1419 1514 2.731968 CGACACCATTAACATTGCCTGC 60.732 50.000 0.00 0.00 0.00 4.85
1434 1530 1.225745 CTGCGGATTCGTCGTTTGC 60.226 57.895 0.00 0.00 38.89 3.68
1480 1587 8.191446 GGAAGTGATCATATATACATGCGTACT 58.809 37.037 0.00 0.00 0.00 2.73
1483 1590 7.489435 AGTGATCATATATACATGCGTACTTGC 59.511 37.037 0.00 0.00 0.00 4.01
1629 1747 0.824182 CCTCTTCGCCGTCCTCCTAT 60.824 60.000 0.00 0.00 0.00 2.57
1633 1751 4.008330 CTCTTCGCCGTCCTCCTATATTA 58.992 47.826 0.00 0.00 0.00 0.98
1806 1960 1.406903 GAAGCAAGGGGATTGGATGG 58.593 55.000 0.00 0.00 39.47 3.51
1932 2086 3.437795 AATGCCTGCTCAGCACGC 61.438 61.111 13.23 13.23 44.40 5.34
2075 2232 0.835971 TGTCCTTCTACCTGCAGGCA 60.836 55.000 33.06 20.12 39.32 4.75
2228 2385 4.814294 GTCGCCGGGCTGTACAGG 62.814 72.222 23.95 9.68 0.00 4.00
2275 2435 2.742116 AACAGTCACCACCGCCACT 61.742 57.895 0.00 0.00 0.00 4.00
2315 2475 1.010935 CATCAGCAGCGTCTGACGTT 61.011 55.000 28.38 21.75 44.88 3.99
2415 2575 3.614399 GCTTCACAGGTGTAGCTGT 57.386 52.632 19.66 10.67 46.25 4.40
2573 2743 8.524870 TTAACGAACATCTAGTAACAAACTCC 57.475 34.615 0.00 0.00 39.80 3.85
2574 2744 5.476614 ACGAACATCTAGTAACAAACTCCC 58.523 41.667 0.00 0.00 39.80 4.30
2579 2749 6.415573 ACATCTAGTAACAAACTCCCCATTC 58.584 40.000 0.00 0.00 39.80 2.67
2582 2752 6.472887 TCTAGTAACAAACTCCCCATTCAAG 58.527 40.000 0.00 0.00 39.80 3.02
2722 2892 4.552166 AAGAATGCATTGGTATACGTGC 57.448 40.909 18.59 15.51 38.05 5.34
2979 3150 2.571202 TGGGATATATCTGGCGCATTGA 59.429 45.455 10.83 3.94 0.00 2.57
3121 3292 2.496297 ACAGGAACATGGGATGAGGAT 58.504 47.619 0.00 0.00 0.00 3.24
3168 3339 6.055588 CGGTGGATGTTCAAAGGATATTACT 58.944 40.000 0.00 0.00 0.00 2.24
3193 3364 7.685481 TGATTCCAGTCAACACTAATTCCTTA 58.315 34.615 0.00 0.00 0.00 2.69
3344 3517 4.287585 TCCGGAGATTTGGAGGAAACTTTA 59.712 41.667 0.00 0.00 44.43 1.85
3392 3565 0.532115 ATCTTTTGTTGGCGGGCATC 59.468 50.000 4.64 5.27 0.00 3.91
3698 3876 2.866923 TGGTATCTCTGGTGGATCCA 57.133 50.000 11.44 11.44 45.01 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 7.990886 TCAATAAAAATATTCGTGGGTCTAGCT 59.009 33.333 0.00 0.00 0.00 3.32
71 73 7.889873 TCCATCAATAAAAATATTCGTGGGT 57.110 32.000 0.00 0.00 0.00 4.51
87 89 8.148437 ACTCATTCTATGCTCTATCCATCAAT 57.852 34.615 0.00 0.00 0.00 2.57
215 217 5.710513 TCTTTAATTCATGTGTGCAAGCT 57.289 34.783 0.00 0.00 0.00 3.74
222 224 7.041780 GGCGAGATACATCTTTAATTCATGTGT 60.042 37.037 0.00 0.00 37.25 3.72
261 263 6.762187 TGGCCATCACAAATTTATGCTAAATG 59.238 34.615 0.00 0.00 0.00 2.32
363 367 3.402628 GGCACCTTCTTTAGTCTGTCA 57.597 47.619 0.00 0.00 0.00 3.58
393 397 4.090819 GTTTTATCTTTAAGTGGCCCCCA 58.909 43.478 0.00 0.00 0.00 4.96
416 420 7.672983 TGGTTTTCTCTTAGCTAGAAACATG 57.327 36.000 9.23 0.00 41.43 3.21
583 588 7.737972 AGTTAGCCTTTTCTCTCTTTTTCTC 57.262 36.000 0.00 0.00 0.00 2.87
590 595 5.760743 GTGACAAAGTTAGCCTTTTCTCTCT 59.239 40.000 0.00 0.00 41.51 3.10
633 638 4.202652 TGGAGGGAGTATTAGGTAGTAGCC 60.203 50.000 0.00 0.00 0.00 3.93
637 642 6.039415 TGAATGGAGGGAGTATTAGGTAGT 57.961 41.667 0.00 0.00 0.00 2.73
641 646 6.694445 ATTCTGAATGGAGGGAGTATTAGG 57.306 41.667 1.31 0.00 0.00 2.69
645 650 5.983333 ACAATTCTGAATGGAGGGAGTAT 57.017 39.130 11.67 0.00 0.00 2.12
652 657 3.935203 ACGCACTACAATTCTGAATGGAG 59.065 43.478 11.67 10.22 33.52 3.86
690 696 1.403249 GCGCACTGCAATTTGGAATCT 60.403 47.619 0.30 0.00 45.45 2.40
703 709 2.807895 GGCTGCAAATGCGCACTG 60.808 61.111 14.90 15.16 45.83 3.66
707 713 2.125832 ATGTGGCTGCAAATGCGC 60.126 55.556 0.00 0.00 45.83 6.09
729 735 1.602377 CAGGGTCAGTTTCGTCCAAAC 59.398 52.381 0.00 0.00 44.38 2.93
740 746 3.519913 GGAGATTCTAAACCAGGGTCAGT 59.480 47.826 0.00 0.00 0.00 3.41
744 750 4.034410 GAGAGGAGATTCTAAACCAGGGT 58.966 47.826 0.00 0.00 0.00 4.34
751 757 6.999272 ACGCACTATAGAGAGGAGATTCTAAA 59.001 38.462 6.78 0.00 30.33 1.85
767 773 1.954382 CAGCCTGTCCTACGCACTATA 59.046 52.381 0.00 0.00 0.00 1.31
816 826 3.118920 CCAATGCATGACATGGATGTTGT 60.119 43.478 21.48 4.76 40.66 3.32
826 836 4.343231 AGTTCCAATACCAATGCATGACA 58.657 39.130 0.00 0.00 0.00 3.58
846 856 6.127869 CCTCTATAGTGCGCATACATTCTAGT 60.128 42.308 15.91 2.51 0.00 2.57
872 882 6.303839 TCATGTTTAAACTAAGTGCTCCCTT 58.696 36.000 18.72 0.00 0.00 3.95
873 883 5.876357 TCATGTTTAAACTAAGTGCTCCCT 58.124 37.500 18.72 0.00 0.00 4.20
874 884 5.392057 GCTCATGTTTAAACTAAGTGCTCCC 60.392 44.000 18.72 0.00 0.00 4.30
875 885 5.181245 TGCTCATGTTTAAACTAAGTGCTCC 59.819 40.000 18.72 2.68 0.00 4.70
876 886 6.241207 TGCTCATGTTTAAACTAAGTGCTC 57.759 37.500 18.72 8.18 0.00 4.26
964 975 8.638685 TTTTCACTGAGTACGCCTTATATAAC 57.361 34.615 0.00 0.00 0.00 1.89
1012 1026 0.830023 GCCTAGCTTCTCCTCCCGAT 60.830 60.000 0.00 0.00 0.00 4.18
1013 1027 1.455959 GCCTAGCTTCTCCTCCCGA 60.456 63.158 0.00 0.00 0.00 5.14
1014 1028 1.118356 ATGCCTAGCTTCTCCTCCCG 61.118 60.000 0.00 0.00 0.00 5.14
1015 1029 0.396060 CATGCCTAGCTTCTCCTCCC 59.604 60.000 0.00 0.00 0.00 4.30
1020 1034 1.846541 GTCGACATGCCTAGCTTCTC 58.153 55.000 11.55 0.00 0.00 2.87
1041 1055 2.375174 TGTACACCTTCTTCCCTGCATT 59.625 45.455 0.00 0.00 0.00 3.56
1062 1076 2.426738 CCCGTATCACCATTGCAACAAT 59.573 45.455 0.00 0.00 0.00 2.71
1252 1271 9.184523 CTAATTTTAGGTGGTGAATTACATCCA 57.815 33.333 0.00 0.00 0.00 3.41
1253 1272 8.630037 CCTAATTTTAGGTGGTGAATTACATCC 58.370 37.037 8.02 0.00 44.26 3.51
1279 1343 8.552296 ACATTCATAGATATTAAGGGGGATGAC 58.448 37.037 0.00 0.00 0.00 3.06
1281 1345 8.551440 TGACATTCATAGATATTAAGGGGGATG 58.449 37.037 0.00 0.00 0.00 3.51
1286 1350 9.658799 ATCGTTGACATTCATAGATATTAAGGG 57.341 33.333 0.00 0.00 0.00 3.95
1297 1391 5.414144 TCCTGCAAAATCGTTGACATTCATA 59.586 36.000 0.00 0.00 0.00 2.15
1309 1403 1.197721 AGCGTTTCTCCTGCAAAATCG 59.802 47.619 0.00 0.00 0.00 3.34
1383 1477 3.762288 TGGTGTCGTGCTCTTACTCTTAT 59.238 43.478 0.00 0.00 0.00 1.73
1417 1512 1.225376 AAGCAAACGACGAATCCGCA 61.225 50.000 0.00 0.00 39.95 5.69
1418 1513 0.110373 AAAGCAAACGACGAATCCGC 60.110 50.000 0.00 0.00 39.95 5.54
1419 1514 1.969256 CAAAAGCAAACGACGAATCCG 59.031 47.619 0.00 0.00 42.50 4.18
1434 1530 7.272084 CACTTCCTCGATCAATTTAAGCAAAAG 59.728 37.037 0.00 0.00 0.00 2.27
1480 1587 5.506686 TGCAATACTTGTTACTGTTGCAA 57.493 34.783 7.98 0.00 45.95 4.08
1483 1590 4.903585 CGTGTGCAATACTTGTTACTGTTG 59.096 41.667 0.00 0.00 0.00 3.33
1629 1747 3.728845 GGAGCTTGATGGCTTCGTAATA 58.271 45.455 0.00 0.00 43.20 0.98
1633 1751 4.625800 GGAGCTTGATGGCTTCGT 57.374 55.556 0.00 0.00 43.20 3.85
1806 1960 0.674895 AGCATCAGGAACGTGCCTTC 60.675 55.000 14.25 2.36 39.62 3.46
1932 2086 4.087892 CAGGGCGAGGGACTGTGG 62.088 72.222 0.00 0.00 41.55 4.17
2075 2232 2.107750 CGCCTCTCGATGCACCAT 59.892 61.111 0.00 0.00 41.67 3.55
2255 2412 2.110213 GGCGGTGGTGACTGTTGA 59.890 61.111 0.00 0.00 0.00 3.18
2275 2435 1.828660 GGAGCTAGTCTAGGCGGCA 60.829 63.158 13.08 0.00 0.00 5.69
2279 2439 1.272212 GATGCAGGAGCTAGTCTAGGC 59.728 57.143 8.97 3.90 42.74 3.93
2285 2445 2.600439 TGCTGATGCAGGAGCTAGT 58.400 52.632 17.92 0.00 45.31 2.57
2309 2469 2.225491 GCAGCATCCTTGTTTAACGTCA 59.775 45.455 0.00 0.00 0.00 4.35
2311 2471 2.226330 TGCAGCATCCTTGTTTAACGT 58.774 42.857 0.00 0.00 0.00 3.99
2315 2475 4.286297 ACTACTGCAGCATCCTTGTTTA 57.714 40.909 15.27 0.00 0.00 2.01
2370 2530 7.118496 TCTTGATATTCTTCTCCTCCAACTC 57.882 40.000 0.00 0.00 0.00 3.01
2415 2575 3.446161 CGGTAAGAGAACCCTGTATGTCA 59.554 47.826 0.00 0.00 36.03 3.58
2418 2578 2.483188 GCCGGTAAGAGAACCCTGTATG 60.483 54.545 1.90 0.00 36.03 2.39
2572 2742 1.593265 GGCAACAGCTTGAATGGGG 59.407 57.895 0.00 0.00 0.00 4.96
2573 2743 1.186917 TGGGCAACAGCTTGAATGGG 61.187 55.000 0.00 0.00 39.74 4.00
2574 2744 0.680618 TTGGGCAACAGCTTGAATGG 59.319 50.000 0.00 0.00 39.74 3.16
2579 2749 3.131155 TGCTTGGGCAACAGCTTG 58.869 55.556 3.83 0.00 46.36 4.01
2722 2892 2.214376 TGGGGTAGCACATTTTCCAG 57.786 50.000 0.00 0.00 0.00 3.86
2979 3150 6.169094 CAAATGTTGACACTCTCTCCAGTAT 58.831 40.000 0.00 0.00 0.00 2.12
3032 3203 4.142315 CCGACTTGAGATTACCTTTCGGTA 60.142 45.833 0.00 0.00 43.29 4.02
3121 3292 7.674348 ACCGGATTAAAGGTAGATCTGATGATA 59.326 37.037 9.46 0.00 39.30 2.15
3135 3306 3.616219 TGAACATCCACCGGATTAAAGG 58.384 45.455 9.46 0.00 39.79 3.11
3168 3339 6.126863 AGGAATTAGTGTTGACTGGAATCA 57.873 37.500 0.00 0.00 33.21 2.57
3344 3517 4.884668 TTACGTGGGATCTTGAGTTTCT 57.115 40.909 0.00 0.00 0.00 2.52
3392 3565 6.127730 GGATTTTAGGGGGATAATTACATGCG 60.128 42.308 0.00 0.00 0.00 4.73
3398 3571 8.107095 CGAGAATGGATTTTAGGGGGATAATTA 58.893 37.037 0.00 0.00 0.00 1.40
3649 3824 5.278414 CCACTGCAATGACTTGTTTGACATA 60.278 40.000 0.00 0.00 34.69 2.29


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

AutoCloner maintained by Alex Coulton.