Multiple sequence alignment - TraesCS3A01G533100

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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 TraesCS3A01G533100 chr3A 100.000 4525 0 0 1 4525 745896952 745901476 0.000000e+00 8357
1 TraesCS3A01G533100 chr3B 92.431 3567 167 40 9 3534 818440541 818444045 0.000000e+00 4996
2 TraesCS3A01G533100 chr3B 87.740 416 42 5 4089 4499 818444675 818445086 1.140000e-130 477
3 TraesCS3A01G533100 chr3B 91.538 130 10 1 3775 3903 818444344 818444473 1.290000e-40 178
4 TraesCS3A01G533100 chr3D 91.724 1752 119 12 1221 2966 611112322 611114053 0.000000e+00 2409
5 TraesCS3A01G533100 chr3D 94.178 979 39 10 3536 4499 611114779 611115754 0.000000e+00 1476
6 TraesCS3A01G533100 chr3D 88.121 1027 85 29 196 1202 611110742 611111751 0.000000e+00 1186
7 TraesCS3A01G533100 chr3D 95.932 590 24 0 2945 3534 611114098 611114687 0.000000e+00 957
8 TraesCS3A01G533100 chr7A 82.399 1017 154 15 2521 3532 734687107 734686111 0.000000e+00 863
9 TraesCS3A01G533100 chr2D 82.417 1018 152 18 2521 3532 2047990 2048986 0.000000e+00 863
10 TraesCS3A01G533100 chr7D 81.281 1015 169 11 2521 3532 632859041 632860037 0.000000e+00 802
11 TraesCS3A01G533100 chr5B 75.294 935 204 19 2572 3500 625117745 625118658 5.410000e-114 422
12 TraesCS3A01G533100 chr5B 75.214 936 203 20 2572 3500 623171964 623172877 2.520000e-112 416
13 TraesCS3A01G533100 chr5B 75.214 936 203 21 2572 3500 626842931 626843844 2.520000e-112 416
14 TraesCS3A01G533100 chr5B 75.187 935 205 19 2572 3500 628697294 628698207 2.520000e-112 416
15 TraesCS3A01G533100 chr5B 75.267 938 199 25 2572 3500 629897921 629898834 2.520000e-112 416
16 TraesCS3A01G533100 chr5B 75.085 887 186 24 2620 3498 633176192 633175333 9.190000e-102 381
17 TraesCS3A01G533100 chr5A 75.133 941 207 19 2575 3509 625733452 625732533 2.520000e-112 416
18 TraesCS3A01G533100 chr6D 75.118 848 182 22 2667 3497 44338 43503 1.990000e-98 370


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 TraesCS3A01G533100 chr3A 745896952 745901476 4524 False 8357.000000 8357 100.000000 1 4525 1 chr3A.!!$F1 4524
1 TraesCS3A01G533100 chr3B 818440541 818445086 4545 False 1883.666667 4996 90.569667 9 4499 3 chr3B.!!$F1 4490
2 TraesCS3A01G533100 chr3D 611110742 611115754 5012 False 1507.000000 2409 92.488750 196 4499 4 chr3D.!!$F1 4303
3 TraesCS3A01G533100 chr7A 734686111 734687107 996 True 863.000000 863 82.399000 2521 3532 1 chr7A.!!$R1 1011
4 TraesCS3A01G533100 chr2D 2047990 2048986 996 False 863.000000 863 82.417000 2521 3532 1 chr2D.!!$F1 1011
5 TraesCS3A01G533100 chr7D 632859041 632860037 996 False 802.000000 802 81.281000 2521 3532 1 chr7D.!!$F1 1011
6 TraesCS3A01G533100 chr5B 625117745 625118658 913 False 422.000000 422 75.294000 2572 3500 1 chr5B.!!$F2 928
7 TraesCS3A01G533100 chr5B 623171964 623172877 913 False 416.000000 416 75.214000 2572 3500 1 chr5B.!!$F1 928
8 TraesCS3A01G533100 chr5B 626842931 626843844 913 False 416.000000 416 75.214000 2572 3500 1 chr5B.!!$F3 928
9 TraesCS3A01G533100 chr5B 628697294 628698207 913 False 416.000000 416 75.187000 2572 3500 1 chr5B.!!$F4 928
10 TraesCS3A01G533100 chr5B 629897921 629898834 913 False 416.000000 416 75.267000 2572 3500 1 chr5B.!!$F5 928
11 TraesCS3A01G533100 chr5B 633175333 633176192 859 True 381.000000 381 75.085000 2620 3498 1 chr5B.!!$R1 878
12 TraesCS3A01G533100 chr5A 625732533 625733452 919 True 416.000000 416 75.133000 2575 3509 1 chr5A.!!$R1 934
13 TraesCS3A01G533100 chr6D 43503 44338 835 True 370.000000 370 75.118000 2667 3497 1 chr6D.!!$R1 830

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
198 199 0.318762 GGCATATGGACGGACTCTCC 59.681 60.0 4.56 0.00 0.00 3.71 F
2092 2717 0.032403 ACAACTTTGCGTGCATGCAT 59.968 45.0 32.76 16.81 45.78 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2752 0.034477 CAAGGGTACAAATCCGGCCT 60.034 55.000 0.0 0.0 0.0 5.19 R
3528 4228 1.691434 CACCTCCCCTGCTTCTATCTC 59.309 57.143 0.0 0.0 0.0 2.75 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
25 26 2.196245 GCCCCCGATTCTTCATGCC 61.196 63.158 0.00 0.00 0.00 4.40
33 34 3.243873 CCGATTCTTCATGCCAGCTAGTA 60.244 47.826 0.00 0.00 0.00 1.82
41 42 3.004839 TCATGCCAGCTAGTAACGATCTC 59.995 47.826 0.00 0.00 0.00 2.75
57 58 0.843309 TCTCTTCCAGCCCAACACAA 59.157 50.000 0.00 0.00 0.00 3.33
93 94 2.354821 GGCATTAGTTTGCTCTAACGGG 59.645 50.000 0.00 0.00 42.38 5.28
95 96 3.270877 CATTAGTTTGCTCTAACGGGCT 58.729 45.455 0.00 0.00 33.56 5.19
104 105 0.906775 TCTAACGGGCTAGGTTTGGG 59.093 55.000 0.00 0.00 0.00 4.12
110 111 0.893727 GGGCTAGGTTTGGGTGTGTG 60.894 60.000 0.00 0.00 0.00 3.82
130 131 2.824936 TGTTTGCCGATCATGGACAAAT 59.175 40.909 0.00 0.00 37.36 2.32
133 134 1.134753 TGCCGATCATGGACAAATTGC 59.865 47.619 0.00 0.00 0.00 3.56
162 163 9.941325 GAGTATCCATCTAGTTTCATGATTGAT 57.059 33.333 0.00 0.00 0.00 2.57
163 164 9.722184 AGTATCCATCTAGTTTCATGATTGATG 57.278 33.333 10.47 10.47 0.00 3.07
164 165 6.872628 TCCATCTAGTTTCATGATTGATGC 57.127 37.500 11.47 0.00 31.32 3.91
165 166 6.358991 TCCATCTAGTTTCATGATTGATGCA 58.641 36.000 11.47 0.00 31.32 3.96
166 167 6.261603 TCCATCTAGTTTCATGATTGATGCAC 59.738 38.462 11.47 0.00 31.32 4.57
167 168 5.723492 TCTAGTTTCATGATTGATGCACG 57.277 39.130 0.00 0.00 31.32 5.34
168 169 5.418676 TCTAGTTTCATGATTGATGCACGA 58.581 37.500 0.00 0.00 31.32 4.35
169 170 4.611310 AGTTTCATGATTGATGCACGAG 57.389 40.909 0.00 0.00 31.32 4.18
170 171 4.256110 AGTTTCATGATTGATGCACGAGA 58.744 39.130 0.00 0.00 31.32 4.04
198 199 0.318762 GGCATATGGACGGACTCTCC 59.681 60.000 4.56 0.00 0.00 3.71
221 222 9.491675 CTCCAATCTCGAGTATAGTACTTTCTA 57.508 37.037 13.13 0.00 39.59 2.10
304 310 1.432024 ACAGTGTCCAGTAGGGGTACT 59.568 52.381 0.00 0.00 37.22 2.73
843 860 2.009774 GACCATCATCCGTGTGAAAGG 58.990 52.381 7.26 7.26 35.02 3.11
848 865 1.879380 TCATCCGTGTGAAAGGCTTTG 59.121 47.619 18.79 2.02 0.00 2.77
905 948 5.222213 ACTCCATGGAAGAATTCTCCAACTT 60.222 40.000 22.39 10.07 46.56 2.66
967 1010 5.585844 ACAAAACACATAGCATCATCATCGA 59.414 36.000 0.00 0.00 0.00 3.59
1030 1079 2.284478 TGCTGCTGCTCCTCCTCT 60.284 61.111 17.00 0.00 40.48 3.69
1033 1082 1.449956 CTGCTGCTCCTCCTCTTGC 60.450 63.158 0.00 0.00 0.00 4.01
1038 1087 2.186384 CTCCTCCTCTTGCCTGCG 59.814 66.667 0.00 0.00 0.00 5.18
1098 1147 4.201679 CCGGCACCGATCACGCTA 62.202 66.667 11.42 0.00 42.83 4.26
1137 1186 2.825836 GGCCAAGTGAGCATCCCG 60.826 66.667 0.00 0.00 0.00 5.14
1264 1865 1.527380 TGGACGCAAACCAGAACCC 60.527 57.895 0.00 0.00 33.22 4.11
1309 1910 0.321122 CATCCCCGAGCCAGATAAGC 60.321 60.000 0.00 0.00 0.00 3.09
1372 1973 1.341156 CCTGGTGGAGGGGAAGCTAG 61.341 65.000 0.00 0.00 38.36 3.42
1380 1981 0.916358 AGGGGAAGCTAGTGGTGCAT 60.916 55.000 0.00 0.00 0.00 3.96
1557 2158 1.671850 CCAAGTTGTGAGGCGTACGAT 60.672 52.381 21.65 6.25 0.00 3.73
1576 2177 3.844741 GAGTCTACCTCCCCGAGC 58.155 66.667 0.00 0.00 33.79 5.03
1581 2182 3.506059 CTACCTCCCCGAGCGCATG 62.506 68.421 11.47 0.00 0.00 4.06
1851 2467 2.021068 ATCCATGTCCGCGACCTCAG 62.021 60.000 8.23 0.00 0.00 3.35
1863 2479 1.835927 GACCTCAGCAACCAGAGCCT 61.836 60.000 0.00 0.00 0.00 4.58
1872 2488 2.373502 GCAACCAGAGCCTAAGGGATAT 59.626 50.000 0.00 0.00 33.58 1.63
1890 2506 4.374702 GCGTGCACCAGCGACAAG 62.375 66.667 12.15 0.00 46.23 3.16
1893 2509 1.595382 GTGCACCAGCGACAAGAGT 60.595 57.895 5.22 0.00 46.23 3.24
1895 2511 0.038251 TGCACCAGCGACAAGAGTAG 60.038 55.000 0.00 0.00 46.23 2.57
1965 2581 1.739196 GGACGGGTACGAAGGCAAC 60.739 63.158 0.00 0.00 44.60 4.17
1998 2614 0.598065 CTGCTGGTTGCCAAGGTAAC 59.402 55.000 11.08 11.08 42.00 2.50
2003 2621 4.982269 GCTGGTTGCCAAGGTAACATACC 61.982 52.174 19.35 5.75 41.41 2.73
2021 2639 2.450476 ACCAGACCTTGCATCAATTCC 58.550 47.619 0.00 0.00 0.00 3.01
2060 2678 8.839310 AGTATCTGTGGCATTAATTCATCTAC 57.161 34.615 0.00 0.00 0.00 2.59
2085 2710 9.997482 ACCTATTTATATTAACAACTTTGCGTG 57.003 29.630 0.00 0.00 0.00 5.34
2086 2711 8.953990 CCTATTTATATTAACAACTTTGCGTGC 58.046 33.333 0.00 0.00 0.00 5.34
2092 2717 0.032403 ACAACTTTGCGTGCATGCAT 59.968 45.000 32.76 16.81 45.78 3.96
2127 2752 5.952526 TGTAGACATTAACGAGTGTGAGA 57.047 39.130 0.00 0.00 0.00 3.27
2132 2757 0.242825 TTAACGAGTGTGAGAGGCCG 59.757 55.000 0.00 0.00 0.00 6.13
2136 2761 1.901085 GAGTGTGAGAGGCCGGATT 59.099 57.895 5.05 0.00 0.00 3.01
2150 2775 0.808755 CGGATTTGTACCCTTGCCAC 59.191 55.000 0.00 0.00 0.00 5.01
2169 2794 0.877071 CGGGATATGCCAGAACATGC 59.123 55.000 14.28 0.00 38.95 4.06
2349 2983 6.601741 TGATTTGGCAAATTTGTTTGACTC 57.398 33.333 25.02 10.76 40.53 3.36
2372 3006 8.314751 ACTCTCTTTATATATTGCGGCATAGTT 58.685 33.333 2.28 0.00 0.00 2.24
2399 3033 7.942341 TGATCCATGTTTTTACTAACTGACCTT 59.058 33.333 0.00 0.00 0.00 3.50
2400 3034 9.444600 GATCCATGTTTTTACTAACTGACCTTA 57.555 33.333 0.00 0.00 0.00 2.69
2432 3066 8.340443 CGATCTGTTTGTTGATCACATAATCAT 58.660 33.333 0.00 0.00 39.06 2.45
2448 3082 8.514594 CACATAATCATAAAGGTTCACTTGTGT 58.485 33.333 0.46 0.00 39.96 3.72
2509 3143 6.174760 AGGTATATAACGTGGTTTCTTTGCA 58.825 36.000 0.00 0.00 0.00 4.08
2510 3144 6.826741 AGGTATATAACGTGGTTTCTTTGCAT 59.173 34.615 0.00 0.00 0.00 3.96
2511 3145 7.338449 AGGTATATAACGTGGTTTCTTTGCATT 59.662 33.333 0.00 0.00 0.00 3.56
2512 3146 7.431084 GGTATATAACGTGGTTTCTTTGCATTG 59.569 37.037 0.00 0.00 0.00 2.82
2513 3147 1.851658 ACGTGGTTTCTTTGCATTGC 58.148 45.000 0.46 0.46 0.00 3.56
2519 3153 1.344114 GTTTCTTTGCATTGCTCCCCA 59.656 47.619 10.49 0.00 0.00 4.96
2569 3203 2.298729 TCATAGCACTTTTGGGGTTTGC 59.701 45.455 0.00 0.00 33.38 3.68
2637 3271 2.779742 AAATGGCGGCCCTGCACTAA 62.780 55.000 17.97 0.00 36.28 2.24
2640 3274 2.700773 GGCGGCCCTGCACTAAAAG 61.701 63.158 8.12 0.00 36.28 2.27
2955 3589 3.124466 TGACACTCTTCACAACAACAACG 59.876 43.478 0.00 0.00 0.00 4.10
3105 3805 7.293073 ACCAGCAAATATACTCTTGGATGATT 58.707 34.615 0.00 0.00 0.00 2.57
3285 3985 8.828688 AGTTGTACTATTGGAACTTGTAAGTC 57.171 34.615 0.00 0.00 38.57 3.01
3408 4108 3.832490 TCAAGAACCGAGAGATTTGGAGA 59.168 43.478 0.00 0.00 34.08 3.71
3517 4217 5.395546 GCCTTCTCACATTGAAGAGATCTCT 60.396 44.000 19.92 19.92 42.37 3.10
3570 4365 8.269966 AGGTGTGCCTTTGTTTTAAGAAAACTG 61.270 37.037 14.12 6.34 45.62 3.16
3585 4380 3.773860 AAACTGTGTGAACGCATTTGA 57.226 38.095 0.00 0.00 35.63 2.69
3602 4397 6.558909 GCATTTGAAAGATCTGGGAGTAAAG 58.441 40.000 0.00 0.00 0.00 1.85
3622 4417 2.630580 AGGCGTTTTTATGGCAAGGAAA 59.369 40.909 0.00 0.00 0.00 3.13
3623 4418 3.260632 AGGCGTTTTTATGGCAAGGAAAT 59.739 39.130 0.00 0.00 0.00 2.17
3696 4495 4.284829 TGGTCACTGCTGATTGTTGATA 57.715 40.909 0.00 0.00 0.00 2.15
3717 4516 0.861837 GCTTGAATATCCGACAGCCG 59.138 55.000 0.00 0.00 38.18 5.52
3780 4591 7.442969 TCTCGTTACTAGCCTTTTCAATGAAAA 59.557 33.333 18.68 18.68 38.90 2.29
3782 4593 8.234546 TCGTTACTAGCCTTTTCAATGAAAATC 58.765 33.333 19.84 14.66 40.14 2.17
4052 4907 2.988839 GCAACCAGCAGATCCCCCT 61.989 63.158 0.00 0.00 44.79 4.79
4078 4933 0.380378 TCCTTTTGAGCACGCACAAC 59.620 50.000 1.19 0.00 0.00 3.32
4081 4936 2.010582 TTTTGAGCACGCACAACCCC 62.011 55.000 1.19 0.00 0.00 4.95
4130 4986 0.840617 TGTGGACCCAGTTGTAAGCA 59.159 50.000 0.00 0.00 0.00 3.91
4142 4998 6.040878 CCAGTTGTAAGCAGGTGTATAGTAC 58.959 44.000 0.00 0.00 0.00 2.73
4245 5101 3.506810 TGAAGCTTTTGTTTTGGTGTCG 58.493 40.909 0.00 0.00 0.00 4.35
4366 5226 1.834896 TCAGGAGCCAGCGGTTATAAA 59.165 47.619 0.00 0.00 0.00 1.40
4388 5248 7.962964 AAAGTGAACTTTTATCGATGAGTCA 57.037 32.000 8.54 0.00 43.07 3.41
4392 5252 7.819415 AGTGAACTTTTATCGATGAGTCAATCA 59.181 33.333 8.54 7.48 43.70 2.57
4458 5318 8.053776 TGTTGGTATCTAGGTTAGATAGAGGA 57.946 38.462 6.15 0.00 45.62 3.71
4480 5340 7.489160 AGGAAAGGTTTGAATTTGAACTGTAC 58.511 34.615 5.28 0.00 0.00 2.90
4500 5360 3.226884 CGAGTGACGGGTTCCAATT 57.773 52.632 0.00 0.00 38.46 2.32
4501 5361 1.519408 CGAGTGACGGGTTCCAATTT 58.481 50.000 0.00 0.00 38.46 1.82
4502 5362 1.877443 CGAGTGACGGGTTCCAATTTT 59.123 47.619 0.00 0.00 38.46 1.82
4503 5363 2.350388 CGAGTGACGGGTTCCAATTTTG 60.350 50.000 0.00 0.00 38.46 2.44
4504 5364 2.882137 GAGTGACGGGTTCCAATTTTGA 59.118 45.455 0.00 0.00 0.00 2.69
4505 5365 3.292460 AGTGACGGGTTCCAATTTTGAA 58.708 40.909 0.00 0.00 0.00 2.69
4506 5366 3.702045 AGTGACGGGTTCCAATTTTGAAA 59.298 39.130 0.00 0.00 0.00 2.69
4507 5367 4.160626 AGTGACGGGTTCCAATTTTGAAAA 59.839 37.500 0.00 0.00 0.00 2.29
4508 5368 4.870991 GTGACGGGTTCCAATTTTGAAAAA 59.129 37.500 0.00 0.00 0.00 1.94
4509 5369 5.525745 GTGACGGGTTCCAATTTTGAAAAAT 59.474 36.000 0.00 0.00 40.15 1.82
4510 5370 6.702282 GTGACGGGTTCCAATTTTGAAAAATA 59.298 34.615 1.61 0.00 37.62 1.40
4511 5371 6.702282 TGACGGGTTCCAATTTTGAAAAATAC 59.298 34.615 1.61 0.00 37.62 1.89
4512 5372 6.822442 ACGGGTTCCAATTTTGAAAAATACT 58.178 32.000 1.61 0.00 37.62 2.12
4513 5373 7.276658 ACGGGTTCCAATTTTGAAAAATACTT 58.723 30.769 1.61 0.00 37.62 2.24
4514 5374 7.225734 ACGGGTTCCAATTTTGAAAAATACTTG 59.774 33.333 1.61 0.00 37.62 3.16
4515 5375 7.307692 CGGGTTCCAATTTTGAAAAATACTTGG 60.308 37.037 12.33 12.33 37.62 3.61
4516 5376 7.717436 GGGTTCCAATTTTGAAAAATACTTGGA 59.283 33.333 15.66 15.66 40.26 3.53
4517 5377 9.114952 GGTTCCAATTTTGAAAAATACTTGGAA 57.885 29.630 22.52 22.52 44.26 3.53
4519 5379 8.376889 TCCAATTTTGAAAAATACTTGGAAGC 57.623 30.769 16.75 0.00 39.62 3.86
4520 5380 8.210265 TCCAATTTTGAAAAATACTTGGAAGCT 58.790 29.630 16.75 0.00 39.62 3.74
4521 5381 8.839343 CCAATTTTGAAAAATACTTGGAAGCTT 58.161 29.630 12.97 0.00 37.58 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.616628 AAGAATCGGGGGCAGGAGT 60.617 57.895 0.00 0.00 0.00 3.85
3 4 0.988145 ATGAAGAATCGGGGGCAGGA 60.988 55.000 0.00 0.00 0.00 3.86
6 7 1.453745 GCATGAAGAATCGGGGGCA 60.454 57.895 0.00 0.00 0.00 5.36
7 8 2.196245 GGCATGAAGAATCGGGGGC 61.196 63.158 0.00 0.00 0.00 5.80
8 9 0.820891 CTGGCATGAAGAATCGGGGG 60.821 60.000 0.00 0.00 0.00 5.40
9 10 1.450531 GCTGGCATGAAGAATCGGGG 61.451 60.000 0.00 0.00 0.00 5.73
10 11 0.465097 AGCTGGCATGAAGAATCGGG 60.465 55.000 0.00 0.00 0.00 5.14
11 12 2.141517 CTAGCTGGCATGAAGAATCGG 58.858 52.381 0.00 0.00 0.00 4.18
12 13 2.831333 ACTAGCTGGCATGAAGAATCG 58.169 47.619 0.00 0.00 0.00 3.34
13 14 4.210120 CGTTACTAGCTGGCATGAAGAATC 59.790 45.833 0.00 0.00 0.00 2.52
14 15 4.122776 CGTTACTAGCTGGCATGAAGAAT 58.877 43.478 0.00 0.00 0.00 2.40
25 26 4.791411 GCTGGAAGAGATCGTTACTAGCTG 60.791 50.000 0.00 0.00 34.07 4.24
33 34 0.984230 TTGGGCTGGAAGAGATCGTT 59.016 50.000 0.00 0.00 34.07 3.85
41 42 3.132925 CAAAATTGTGTTGGGCTGGAAG 58.867 45.455 0.00 0.00 0.00 3.46
57 58 7.472334 AACTAATGCCTCAGAATCACAAAAT 57.528 32.000 0.00 0.00 0.00 1.82
93 94 1.687563 AACACACACCCAAACCTAGC 58.312 50.000 0.00 0.00 0.00 3.42
95 96 1.751924 GCAAACACACACCCAAACCTA 59.248 47.619 0.00 0.00 0.00 3.08
104 105 1.401409 CCATGATCGGCAAACACACAC 60.401 52.381 0.00 0.00 0.00 3.82
110 111 3.508744 ATTTGTCCATGATCGGCAAAC 57.491 42.857 2.87 0.00 35.97 2.93
130 131 5.425217 TGAAACTAGATGGATACTCCTGCAA 59.575 40.000 0.00 0.00 37.46 4.08
133 134 7.295322 TCATGAAACTAGATGGATACTCCTG 57.705 40.000 0.00 0.00 37.46 3.86
143 144 6.018507 TCGTGCATCAATCATGAAACTAGATG 60.019 38.462 0.00 10.09 39.49 2.90
161 162 2.093500 TGCCTAACTTCATCTCGTGCAT 60.093 45.455 0.00 0.00 0.00 3.96
162 163 1.275010 TGCCTAACTTCATCTCGTGCA 59.725 47.619 0.00 0.00 0.00 4.57
163 164 2.010145 TGCCTAACTTCATCTCGTGC 57.990 50.000 0.00 0.00 0.00 5.34
164 165 4.687948 CCATATGCCTAACTTCATCTCGTG 59.312 45.833 0.00 0.00 0.00 4.35
165 166 4.588951 TCCATATGCCTAACTTCATCTCGT 59.411 41.667 0.00 0.00 0.00 4.18
166 167 4.926238 GTCCATATGCCTAACTTCATCTCG 59.074 45.833 0.00 0.00 0.00 4.04
167 168 4.926238 CGTCCATATGCCTAACTTCATCTC 59.074 45.833 0.00 0.00 0.00 2.75
168 169 4.262635 CCGTCCATATGCCTAACTTCATCT 60.263 45.833 0.00 0.00 0.00 2.90
169 170 3.997021 CCGTCCATATGCCTAACTTCATC 59.003 47.826 0.00 0.00 0.00 2.92
170 171 3.646162 TCCGTCCATATGCCTAACTTCAT 59.354 43.478 0.00 0.00 0.00 2.57
272 273 8.097038 CCTACTGGACACTGTATTATATGCAAT 58.903 37.037 0.00 0.00 34.57 3.56
290 296 4.501433 TGGTTAAAAGTACCCCTACTGGA 58.499 43.478 0.00 0.00 33.14 3.86
304 310 5.652994 ACTTTGTTGAGCACTGGTTAAAA 57.347 34.783 0.00 0.00 0.00 1.52
349 355 3.233684 GGTCTTCACCTAAGTCTTCCG 57.766 52.381 0.00 0.00 40.00 4.30
361 367 5.803020 ATCGAATGCTTTTAGGTCTTCAC 57.197 39.130 0.00 0.00 0.00 3.18
499 506 8.886369 ACCCAAGTGTGCCAATACTAATATATA 58.114 33.333 0.00 0.00 0.00 0.86
507 514 2.158534 TGAACCCAAGTGTGCCAATACT 60.159 45.455 0.00 0.00 0.00 2.12
612 620 8.348983 GCTTTTGCTAAACGTGATACTATCTA 57.651 34.615 0.00 0.00 43.35 1.98
934 977 8.286800 TGATGCTATGTGTTTTGTTACAGTTAC 58.713 33.333 0.00 0.00 0.00 2.50
935 978 8.384607 TGATGCTATGTGTTTTGTTACAGTTA 57.615 30.769 0.00 0.00 0.00 2.24
937 980 6.875948 TGATGCTATGTGTTTTGTTACAGT 57.124 33.333 0.00 0.00 0.00 3.55
938 981 7.529158 TGATGATGCTATGTGTTTTGTTACAG 58.471 34.615 0.00 0.00 0.00 2.74
939 982 7.446001 TGATGATGCTATGTGTTTTGTTACA 57.554 32.000 0.00 0.00 0.00 2.41
940 983 7.374228 CGATGATGATGCTATGTGTTTTGTTAC 59.626 37.037 0.00 0.00 0.00 2.50
941 984 7.279758 TCGATGATGATGCTATGTGTTTTGTTA 59.720 33.333 0.00 0.00 0.00 2.41
942 985 6.093909 TCGATGATGATGCTATGTGTTTTGTT 59.906 34.615 0.00 0.00 0.00 2.83
943 986 5.585844 TCGATGATGATGCTATGTGTTTTGT 59.414 36.000 0.00 0.00 0.00 2.83
944 987 5.905733 GTCGATGATGATGCTATGTGTTTTG 59.094 40.000 0.00 0.00 0.00 2.44
945 988 5.585844 TGTCGATGATGATGCTATGTGTTTT 59.414 36.000 0.00 0.00 0.00 2.43
967 1010 4.037222 TGGTGGTGATATATGGTGTCTGT 58.963 43.478 0.00 0.00 0.00 3.41
1033 1082 0.677731 ACCACCATGATTGTCGCAGG 60.678 55.000 0.00 0.00 0.00 4.85
1038 1087 0.611618 TGGCCACCACCATGATTGTC 60.612 55.000 0.00 0.00 33.75 3.18
1264 1865 5.452077 GGCTGGTGGAGTAGTAGATTACTTG 60.452 48.000 0.00 0.00 40.14 3.16
1309 1910 3.046390 GCGACGAGGATGAGTTGATAAG 58.954 50.000 0.00 0.00 0.00 1.73
1372 1973 3.747976 GAACGGGGCATGCACCAC 61.748 66.667 37.05 23.40 40.17 4.16
1380 1981 2.992689 TCGTAGCTGAACGGGGCA 60.993 61.111 9.06 0.00 43.05 5.36
1423 2024 0.870307 ATAGTCATCGTTGTCGCCGC 60.870 55.000 0.00 0.00 36.96 6.53
1430 2031 3.303329 CGGGAATTGCATAGTCATCGTTG 60.303 47.826 0.00 0.00 0.00 4.10
1539 2140 1.671850 CCATCGTACGCCTCACAACTT 60.672 52.381 11.24 0.00 0.00 2.66
1573 2174 2.391821 CGTCGTGTTCATGCGCTC 59.608 61.111 9.73 0.00 0.00 5.03
1576 2177 4.483683 CGCCGTCGTGTTCATGCG 62.484 66.667 0.00 0.00 35.81 4.73
1641 2242 1.205179 ACGTTGAAAAAGCCCGGTTTT 59.795 42.857 0.00 0.00 0.00 2.43
1668 2269 6.833041 TCTGTAGTACTCCCTCTCAAGATAG 58.167 44.000 0.00 0.00 0.00 2.08
1801 2417 0.952497 ACGAAGTCTAGCACGACGGA 60.952 55.000 0.00 0.00 29.74 4.69
1851 2467 0.548510 ATCCCTTAGGCTCTGGTTGC 59.451 55.000 0.00 0.00 0.00 4.17
1863 2479 0.833949 TGGTGCACGCATATCCCTTA 59.166 50.000 11.45 0.00 0.00 2.69
1890 2506 1.201880 GGGACTTCGACACACCTACTC 59.798 57.143 0.00 0.00 0.00 2.59
1893 2509 0.113776 AGGGGACTTCGACACACCTA 59.886 55.000 4.90 0.00 37.44 3.08
1895 2511 3.468063 AGGGGACTTCGACACACC 58.532 61.111 0.00 0.00 37.44 4.16
1998 2614 4.037208 GGAATTGATGCAAGGTCTGGTATG 59.963 45.833 0.00 0.00 0.00 2.39
2003 2621 3.760151 TGAAGGAATTGATGCAAGGTCTG 59.240 43.478 0.00 0.00 0.00 3.51
2021 2639 6.072175 GCCACAGATACTCCTACTAGATGAAG 60.072 46.154 0.00 0.00 0.00 3.02
2060 2678 8.953990 GCACGCAAAGTTGTTAATATAAATAGG 58.046 33.333 0.00 0.00 0.00 2.57
2092 2717 7.479980 GTTAATGTCTACAAATAAGGCATGCA 58.520 34.615 21.36 0.00 38.32 3.96
2095 2720 7.769044 ACTCGTTAATGTCTACAAATAAGGCAT 59.231 33.333 0.00 0.00 40.95 4.40
2101 2726 8.517056 TCTCACACTCGTTAATGTCTACAAATA 58.483 33.333 0.00 0.00 0.00 1.40
2102 2727 7.375834 TCTCACACTCGTTAATGTCTACAAAT 58.624 34.615 0.00 0.00 0.00 2.32
2127 2752 0.034477 CAAGGGTACAAATCCGGCCT 60.034 55.000 0.00 0.00 0.00 5.19
2132 2757 0.808755 CGTGGCAAGGGTACAAATCC 59.191 55.000 0.00 0.00 0.00 3.01
2136 2761 2.432563 CCCGTGGCAAGGGTACAA 59.567 61.111 28.01 0.00 43.89 2.41
2150 2775 0.877071 GCATGTTCTGGCATATCCCG 59.123 55.000 0.00 0.00 0.00 5.14
2169 2794 3.379372 CAGGTGCATTTGTATCCTCCTTG 59.621 47.826 0.00 0.00 0.00 3.61
2268 2893 6.944290 GGTTGAGGGTAATTAAGTTGGTTACT 59.056 38.462 10.27 0.00 39.32 2.24
2349 2983 8.935844 TCAAACTATGCCGCAATATATAAAGAG 58.064 33.333 0.00 0.00 0.00 2.85
2372 3006 7.942341 AGGTCAGTTAGTAAAAACATGGATCAA 59.058 33.333 0.00 0.00 0.00 2.57
2400 3034 9.716531 ATGTGATCAACAAACAGATCGATATAT 57.283 29.630 0.00 0.00 43.61 0.86
2509 3143 3.851976 TGCACCTATATATGGGGAGCAAT 59.148 43.478 25.04 2.34 39.34 3.56
2510 3144 3.255831 TGCACCTATATATGGGGAGCAA 58.744 45.455 25.04 14.36 39.34 3.91
2511 3145 2.914536 TGCACCTATATATGGGGAGCA 58.085 47.619 24.09 24.09 39.73 4.26
2512 3146 3.610911 GTTGCACCTATATATGGGGAGC 58.389 50.000 18.49 19.74 35.31 4.70
2513 3147 3.369471 CGGTTGCACCTATATATGGGGAG 60.369 52.174 18.49 11.67 35.66 4.30
2519 3153 1.066430 CCGCCGGTTGCACCTATATAT 60.066 52.381 1.90 0.00 41.33 0.86
2569 3203 1.134461 TCTCTCTACGGAGAAGGACGG 60.134 57.143 0.00 0.00 46.50 4.79
2955 3589 2.052157 CACCTTCTTCTTGTCGTCGTC 58.948 52.381 0.00 0.00 0.00 4.20
3020 3720 3.070476 TGCATGTAAGCAAGACCATCA 57.930 42.857 0.00 0.00 42.46 3.07
3285 3985 3.071023 TCCAAATATGTAGCCTTCCTCCG 59.929 47.826 0.00 0.00 0.00 4.63
3381 4081 6.490040 TCCAAATCTCTCGGTTCTTGAAATTT 59.510 34.615 0.00 0.00 0.00 1.82
3387 4087 4.193826 TCTCCAAATCTCTCGGTTCTTG 57.806 45.455 0.00 0.00 0.00 3.02
3408 4108 6.318900 GCAACCCTTGTAATGCTACTAAGAAT 59.681 38.462 0.00 0.00 35.93 2.40
3517 4217 6.096987 CCCTGCTTCTATCTCTAACTACACAA 59.903 42.308 0.00 0.00 0.00 3.33
3528 4228 1.691434 CACCTCCCCTGCTTCTATCTC 59.309 57.143 0.00 0.00 0.00 2.75
3534 4234 2.360475 GCACACCTCCCCTGCTTC 60.360 66.667 0.00 0.00 0.00 3.86
3557 4352 5.700846 TGCGTTCACACAGTTTTCTTAAAA 58.299 33.333 0.00 0.00 0.00 1.52
3559 4354 4.948608 TGCGTTCACACAGTTTTCTTAA 57.051 36.364 0.00 0.00 0.00 1.85
3570 4365 4.614284 CAGATCTTTCAAATGCGTTCACAC 59.386 41.667 0.00 0.00 0.00 3.82
3573 4368 3.191162 CCCAGATCTTTCAAATGCGTTCA 59.809 43.478 0.00 0.00 0.00 3.18
3574 4369 3.440173 TCCCAGATCTTTCAAATGCGTTC 59.560 43.478 0.00 0.00 0.00 3.95
3575 4370 3.420893 TCCCAGATCTTTCAAATGCGTT 58.579 40.909 0.00 0.00 0.00 4.84
3576 4371 3.012518 CTCCCAGATCTTTCAAATGCGT 58.987 45.455 0.00 0.00 0.00 5.24
3577 4372 3.012518 ACTCCCAGATCTTTCAAATGCG 58.987 45.455 0.00 0.00 0.00 4.73
3585 4380 2.572104 ACGCCTTTACTCCCAGATCTTT 59.428 45.455 0.00 0.00 0.00 2.52
3602 4397 2.734276 TTCCTTGCCATAAAAACGCC 57.266 45.000 0.00 0.00 0.00 5.68
3696 4495 2.565841 GGCTGTCGGATATTCAAGCTT 58.434 47.619 0.00 0.00 0.00 3.74
3749 4548 6.331061 TGAAAAGGCTAGTAACGAGAAGATC 58.669 40.000 0.00 0.00 0.00 2.75
4052 4907 2.926838 GCGTGCTCAAAAGGAAAACAAA 59.073 40.909 0.00 0.00 0.00 2.83
4130 4986 9.601810 TGGATATGATTTCTGTACTATACACCT 57.398 33.333 0.00 0.00 34.46 4.00
4142 4998 3.567164 GTGGCTGGTGGATATGATTTCTG 59.433 47.826 0.00 0.00 0.00 3.02
4366 5226 7.819415 TGATTGACTCATCGATAAAAGTTCACT 59.181 33.333 0.00 0.00 0.00 3.41
4384 5244 8.543774 AGTACCTCTTTTATCACATGATTGACT 58.456 33.333 0.00 0.00 36.05 3.41
4458 5318 6.750039 CGTGTACAGTTCAAATTCAAACCTTT 59.250 34.615 0.00 0.00 0.00 3.11
4480 5340 0.320421 ATTGGAACCCGTCACTCGTG 60.320 55.000 0.00 0.00 37.94 4.35
4491 5351 8.669946 TCCAAGTATTTTTCAAAATTGGAACC 57.330 30.769 11.64 0.00 39.62 3.62
4494 5354 8.210265 AGCTTCCAAGTATTTTTCAAAATTGGA 58.790 29.630 10.42 10.42 40.26 3.53


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

AutoCloner maintained by Alex Coulton.