Multiple sequence alignment - TraesCS5D01G252200

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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 TraesCS5D01G252200 chr5D 100.000 3584 0 0 1 3584 357896757 357900340 0.000000e+00 6619.0
1 TraesCS5D01G252200 chr5D 84.699 366 53 3 1540 1904 357898251 357898614 2.630000e-96 363.0
2 TraesCS5D01G252200 chr5D 84.699 366 53 3 1495 1858 357898296 357898660 2.630000e-96 363.0
3 TraesCS5D01G252200 chr5D 81.407 199 34 3 538 734 42979955 42979758 3.700000e-35 159.0
4 TraesCS5D01G252200 chr5A 93.975 3336 135 15 299 3584 458908144 458911463 0.000000e+00 4987.0
5 TraesCS5D01G252200 chr5A 93.399 303 17 2 4 303 458899153 458899455 2.540000e-121 446.0
6 TraesCS5D01G252200 chr5A 83.242 364 48 11 1495 1857 458909430 458909781 4.460000e-84 322.0
7 TraesCS5D01G252200 chr5B 93.867 1875 52 19 1716 3584 422939851 422941668 0.000000e+00 2767.0
8 TraesCS5D01G252200 chr5B 95.464 948 31 6 768 1714 422938451 422939387 0.000000e+00 1502.0
9 TraesCS5D01G252200 chr5B 83.962 742 82 21 1 727 422937607 422938326 0.000000e+00 676.0
10 TraesCS5D01G252200 chr5B 87.500 184 22 1 1675 1857 422939855 422940038 1.010000e-50 211.0
11 TraesCS5D01G252200 chr5B 83.410 217 36 0 1540 1756 422939168 422939384 6.070000e-48 202.0
12 TraesCS5D01G252200 chr5B 86.857 175 23 0 1495 1669 422939213 422939387 2.820000e-46 196.0
13 TraesCS5D01G252200 chr2D 84.656 189 28 1 537 724 586150542 586150730 1.700000e-43 187.0
14 TraesCS5D01G252200 chr2D 82.266 203 35 1 533 734 140934314 140934112 1.320000e-39 174.0
15 TraesCS5D01G252200 chr2D 81.720 186 32 2 543 727 10448908 10448724 1.720000e-33 154.0
16 TraesCS5D01G252200 chr4A 83.158 190 32 0 538 727 552857333 552857144 1.320000e-39 174.0
17 TraesCS5D01G252200 chr7A 81.592 201 32 5 537 736 43250801 43250605 1.030000e-35 161.0
18 TraesCS5D01G252200 chr2B 80.296 203 34 5 537 738 42138969 42139166 8.020000e-32 148.0
19 TraesCS5D01G252200 chr2B 82.840 169 25 4 546 712 500655855 500655689 8.020000e-32 148.0
20 TraesCS5D01G252200 chr6B 78.846 208 40 4 538 742 544636350 544636556 1.740000e-28 137.0
21 TraesCS5D01G252200 chr1A 84.000 75 12 0 278 352 509018325 509018251 4.960000e-09 73.1
22 TraesCS5D01G252200 chr7D 82.051 78 14 0 290 367 366667778 366667701 2.310000e-07 67.6
23 TraesCS5D01G252200 chr7D 76.744 129 24 4 300 425 450271155 450271280 2.310000e-07 67.6
24 TraesCS5D01G252200 chr1D 76.106 113 25 2 308 419 411780350 411780239 1.390000e-04 58.4


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 TraesCS5D01G252200 chr5D 357896757 357900340 3583 False 2448.333333 6619 89.799333 1 3584 3 chr5D.!!$F1 3583
1 TraesCS5D01G252200 chr5A 458908144 458911463 3319 False 2654.500000 4987 88.608500 299 3584 2 chr5A.!!$F2 3285
2 TraesCS5D01G252200 chr5B 422937607 422941668 4061 False 925.666667 2767 88.510000 1 3584 6 chr5B.!!$F1 3583

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
143 144 0.036306 AAAGTGGAAGGGGTGCGTAG 59.964 55.0 0.00 0.0 0.0 3.51 F
180 181 0.036732 AATTCCTCTCAAGTGGCGCA 59.963 50.0 10.83 0.0 0.0 6.09 F
615 629 0.179032 TGGTGCTCGCCTTTTTCTGA 60.179 50.0 0.86 0.0 0.0 3.27 F
1937 2528 0.460311 CCGGTGGAGTCTGGTACATC 59.540 60.0 0.00 0.0 38.2 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 2450 0.946221 CAGCAGACTCGGTTGTGGAC 60.946 60.0 0.00 0.0 0.00 4.02 R
2173 2764 0.252421 AGCTGATCTGACCCCTGTGA 60.252 55.0 3.42 0.0 0.00 3.58 R
2305 2896 0.457853 TCCACTCTCGTGCGCATTAC 60.458 55.0 15.91 0.0 39.86 1.89 R
3206 3797 0.032952 TCAGTTCAAAGACCCGGACG 59.967 55.0 0.73 0.0 0.00 4.79 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
24 25 3.641437 TGTGTTGGTTTTGCATAGCTC 57.359 42.857 0.00 0.00 0.00 4.09
26 27 3.004629 TGTGTTGGTTTTGCATAGCTCTG 59.995 43.478 0.00 0.00 0.00 3.35
28 29 3.253188 TGTTGGTTTTGCATAGCTCTGTC 59.747 43.478 0.00 0.00 0.00 3.51
32 33 4.695455 TGGTTTTGCATAGCTCTGTCTTAC 59.305 41.667 0.00 0.00 0.00 2.34
39 40 4.382040 GCATAGCTCTGTCTTACTGTTCCA 60.382 45.833 0.00 0.00 0.00 3.53
42 43 3.643792 AGCTCTGTCTTACTGTTCCAGTT 59.356 43.478 1.74 0.00 42.59 3.16
43 44 4.833380 AGCTCTGTCTTACTGTTCCAGTTA 59.167 41.667 1.74 0.00 42.59 2.24
44 45 5.047660 AGCTCTGTCTTACTGTTCCAGTTAG 60.048 44.000 1.74 3.29 42.59 2.34
45 46 5.135508 TCTGTCTTACTGTTCCAGTTAGC 57.864 43.478 1.74 1.23 42.59 3.09
79 80 5.163754 GCATGTACCAGTACTTTCATGTTCC 60.164 44.000 18.70 7.10 37.00 3.62
86 87 4.935808 CAGTACTTTCATGTTCCTGTACCC 59.064 45.833 0.00 0.00 33.06 3.69
88 89 6.021030 AGTACTTTCATGTTCCTGTACCCTA 58.979 40.000 0.00 0.00 33.06 3.53
91 92 5.309806 ACTTTCATGTTCCTGTACCCTAAGT 59.690 40.000 0.00 0.00 0.00 2.24
92 93 5.836024 TTCATGTTCCTGTACCCTAAGTT 57.164 39.130 0.00 0.00 0.00 2.66
93 94 5.836024 TCATGTTCCTGTACCCTAAGTTT 57.164 39.130 0.00 0.00 0.00 2.66
94 95 5.556915 TCATGTTCCTGTACCCTAAGTTTG 58.443 41.667 0.00 0.00 0.00 2.93
95 96 5.308497 TCATGTTCCTGTACCCTAAGTTTGA 59.692 40.000 0.00 0.00 0.00 2.69
96 97 5.836024 TGTTCCTGTACCCTAAGTTTGAT 57.164 39.130 0.00 0.00 0.00 2.57
97 98 5.556915 TGTTCCTGTACCCTAAGTTTGATG 58.443 41.667 0.00 0.00 0.00 3.07
98 99 5.308497 TGTTCCTGTACCCTAAGTTTGATGA 59.692 40.000 0.00 0.00 0.00 2.92
99 100 6.183361 TGTTCCTGTACCCTAAGTTTGATGAA 60.183 38.462 0.00 0.00 0.00 2.57
100 101 6.442541 TCCTGTACCCTAAGTTTGATGAAA 57.557 37.500 0.00 0.00 0.00 2.69
110 111 7.040062 CCCTAAGTTTGATGAAATAACACCACA 60.040 37.037 0.00 0.00 0.00 4.17
133 134 8.495949 CACATAGTACAAACAGTAAAGTGGAAG 58.504 37.037 0.00 0.00 33.72 3.46
136 137 3.562182 ACAAACAGTAAAGTGGAAGGGG 58.438 45.455 0.00 0.00 0.00 4.79
137 138 3.053170 ACAAACAGTAAAGTGGAAGGGGT 60.053 43.478 0.00 0.00 0.00 4.95
143 144 0.036306 AAAGTGGAAGGGGTGCGTAG 59.964 55.000 0.00 0.00 0.00 3.51
156 157 4.925576 CGTAGCTACCTGGCGCCG 62.926 72.222 23.90 16.52 37.29 6.46
174 175 1.676014 CCGCGGAAATTCCTCTCAAGT 60.676 52.381 24.07 0.00 33.30 3.16
178 179 1.740025 GGAAATTCCTCTCAAGTGGCG 59.260 52.381 4.46 0.00 32.53 5.69
179 180 1.131315 GAAATTCCTCTCAAGTGGCGC 59.869 52.381 0.00 0.00 0.00 6.53
180 181 0.036732 AATTCCTCTCAAGTGGCGCA 59.963 50.000 10.83 0.00 0.00 6.09
181 182 0.254178 ATTCCTCTCAAGTGGCGCAT 59.746 50.000 10.83 0.00 0.00 4.73
188 189 0.606130 TCAAGTGGCGCATCATGTGT 60.606 50.000 10.83 0.00 0.00 3.72
229 230 6.749923 AAGTTACTACTAGGTTGGAGTACG 57.250 41.667 0.00 0.00 33.17 3.67
243 244 3.579586 TGGAGTACGGGTTAGTTCACATT 59.420 43.478 0.00 0.00 0.00 2.71
249 250 7.562135 AGTACGGGTTAGTTCACATTGATATT 58.438 34.615 0.00 0.00 0.00 1.28
250 251 6.677781 ACGGGTTAGTTCACATTGATATTG 57.322 37.500 0.00 0.00 0.00 1.90
283 284 6.039616 TGTAGTTGGAAGCACAAATTTTGTC 58.960 36.000 11.78 7.51 43.23 3.18
287 288 5.534207 TGGAAGCACAAATTTTGTCTGAT 57.466 34.783 11.78 0.00 43.23 2.90
288 289 5.291178 TGGAAGCACAAATTTTGTCTGATG 58.709 37.500 11.78 2.51 43.23 3.07
295 296 7.223387 AGCACAAATTTTGTCTGATGAAAGTTC 59.777 33.333 11.78 0.00 43.23 3.01
296 297 7.010367 GCACAAATTTTGTCTGATGAAAGTTCA 59.990 33.333 11.78 0.00 43.23 3.18
383 384 7.972832 AATGGTTTGTAATTTAGACTCGTGA 57.027 32.000 0.00 0.00 0.00 4.35
433 434 6.203723 AGACAAATCTAGAAAAGAGCACACAC 59.796 38.462 0.00 0.00 37.74 3.82
435 436 4.521130 ATCTAGAAAAGAGCACACACGA 57.479 40.909 0.00 0.00 37.74 4.35
453 454 1.665679 CGACCAATTTGACATCCCTCG 59.334 52.381 0.00 0.00 0.00 4.63
474 475 1.792367 CGCGTGAATGTGAAACTCTCA 59.208 47.619 0.00 0.00 38.04 3.27
522 523 4.641541 TGCTCCATCATTTGTAATCACCAG 59.358 41.667 0.00 0.00 0.00 4.00
545 559 6.811665 CAGAGTATTTGTGAACGATGGTTAGA 59.188 38.462 0.00 0.00 36.24 2.10
573 587 3.708631 AGTGGTATCTTCAGTCCATCAGG 59.291 47.826 0.00 0.00 32.45 3.86
586 600 3.107601 TCCATCAGGGTTCAAGTCCTAG 58.892 50.000 0.00 0.00 38.11 3.02
606 620 1.237285 ACTTGACATTGGTGCTCGCC 61.237 55.000 0.00 0.00 0.00 5.54
615 629 0.179032 TGGTGCTCGCCTTTTTCTGA 60.179 50.000 0.86 0.00 0.00 3.27
633 647 9.947433 TTTTTCTGAATTTATTTCATGCCATCT 57.053 25.926 0.00 0.00 43.30 2.90
634 648 8.936070 TTTCTGAATTTATTTCATGCCATCTG 57.064 30.769 0.00 0.00 43.30 2.90
654 682 2.390599 CGATGTGCGTTCAGTGGGG 61.391 63.158 0.00 0.00 34.64 4.96
661 689 1.374252 CGTTCAGTGGGGGAAGACG 60.374 63.158 0.00 0.00 0.00 4.18
699 727 6.309737 ACGAAGGTGTTTATAACGACTTCATC 59.690 38.462 17.90 0.00 42.19 2.92
730 759 4.946784 ATAATGTGTCGGCTCAGTTTTC 57.053 40.909 0.00 0.00 0.00 2.29
743 826 4.213482 GCTCAGTTTTCGGAAGTGTTATGT 59.787 41.667 7.02 0.00 0.00 2.29
752 835 3.486108 CGGAAGTGTTATGTATGAGCGTC 59.514 47.826 0.00 0.00 0.00 5.19
891 1004 1.860078 GCTATTATCGCCACGCACC 59.140 57.895 0.00 0.00 0.00 5.01
910 1023 2.080536 CCCAGCTGATCCATCCCCA 61.081 63.158 17.39 0.00 0.00 4.96
925 1038 1.352687 TCCCCACAATTCGACCATCAA 59.647 47.619 0.00 0.00 0.00 2.57
928 1041 2.164219 CCCACAATTCGACCATCAAAGG 59.836 50.000 0.00 0.00 0.00 3.11
929 1042 2.164219 CCACAATTCGACCATCAAAGGG 59.836 50.000 0.00 0.00 0.00 3.95
966 1080 0.745845 CCCAATTCGAGCTCCACCTG 60.746 60.000 8.47 0.86 0.00 4.00
1290 1404 0.682852 TCGTCCATTCCAAGTTCCGT 59.317 50.000 0.00 0.00 0.00 4.69
1722 2313 4.033776 GCTACCCAGCCACAGCCA 62.034 66.667 0.00 0.00 42.37 4.75
1839 2430 3.726517 CCAAGTCCGCTGCAACCG 61.727 66.667 0.00 0.00 0.00 4.44
1874 2465 2.338984 GCGTCCACAACCGAGTCT 59.661 61.111 0.00 0.00 0.00 3.24
1937 2528 0.460311 CCGGTGGAGTCTGGTACATC 59.540 60.000 0.00 0.00 38.20 3.06
1938 2529 1.182667 CGGTGGAGTCTGGTACATCA 58.817 55.000 0.00 0.00 38.20 3.07
2186 2777 1.536418 CCCAGTCACAGGGGTCAGA 60.536 63.158 0.00 0.00 42.90 3.27
2305 2896 2.032071 AACCTTCGCCGGAACCTG 59.968 61.111 5.05 0.00 0.00 4.00
2626 3217 3.311990 TGGCATGATCATAGGTCAGACT 58.688 45.455 8.15 0.00 0.00 3.24
2704 3295 7.458397 TCTGTTGGTTGGATACTACTCATTTT 58.542 34.615 0.00 0.00 42.34 1.82
2706 3297 7.227873 TGTTGGTTGGATACTACTCATTTTCA 58.772 34.615 0.00 0.00 42.34 2.69
2929 3520 4.762251 GGGATTGCTCTTTGTTAACTGAGT 59.238 41.667 18.02 0.00 0.00 3.41
2971 3562 2.420022 GCTGCAATAATCGGACAGTTGT 59.580 45.455 0.00 0.00 0.00 3.32
3018 3609 1.462616 TTGTGCAAGCTGTGTTGTCT 58.537 45.000 0.00 0.00 0.00 3.41
3089 3680 1.341080 CTGGTGAGGGCCAATGTTTT 58.659 50.000 6.18 0.00 38.18 2.43
3156 3747 8.690203 TTGAATACTTTCAGAGGTCAAATGAA 57.310 30.769 0.00 0.00 42.60 2.57
3212 3803 5.824243 GAAGTATTCATGTTATCGTCCGG 57.176 43.478 0.00 0.00 46.62 5.14
3213 3804 4.252971 AGTATTCATGTTATCGTCCGGG 57.747 45.455 0.00 0.00 0.00 5.73
3214 3805 3.640029 AGTATTCATGTTATCGTCCGGGT 59.360 43.478 0.00 0.00 0.00 5.28
3215 3806 2.589798 TTCATGTTATCGTCCGGGTC 57.410 50.000 0.00 0.00 0.00 4.46
3216 3807 1.771565 TCATGTTATCGTCCGGGTCT 58.228 50.000 0.00 0.00 0.00 3.85
3217 3808 2.104967 TCATGTTATCGTCCGGGTCTT 58.895 47.619 0.00 0.00 0.00 3.01
3218 3809 2.498481 TCATGTTATCGTCCGGGTCTTT 59.502 45.455 0.00 0.00 0.00 2.52
3219 3810 2.373540 TGTTATCGTCCGGGTCTTTG 57.626 50.000 0.00 0.00 0.00 2.77
3220 3811 1.894466 TGTTATCGTCCGGGTCTTTGA 59.106 47.619 0.00 0.00 0.00 2.69
3221 3812 2.299582 TGTTATCGTCCGGGTCTTTGAA 59.700 45.455 0.00 0.00 0.00 2.69
3222 3813 2.660189 TATCGTCCGGGTCTTTGAAC 57.340 50.000 0.00 0.00 0.00 3.18
3223 3814 0.974383 ATCGTCCGGGTCTTTGAACT 59.026 50.000 0.00 0.00 0.00 3.01
3224 3815 0.032952 TCGTCCGGGTCTTTGAACTG 59.967 55.000 0.00 0.00 0.00 3.16
3225 3816 0.032952 CGTCCGGGTCTTTGAACTGA 59.967 55.000 0.00 0.00 0.00 3.41
3226 3817 1.539496 CGTCCGGGTCTTTGAACTGAA 60.539 52.381 0.00 0.00 0.00 3.02
3227 3818 2.779506 GTCCGGGTCTTTGAACTGAAT 58.220 47.619 0.00 0.00 0.00 2.57
3268 3881 3.670091 GCTCTGATTCAGTTTCAGCTTGC 60.670 47.826 13.23 2.81 40.35 4.01
3324 3937 6.360618 AGGACTCTGAAAAGAGAATTGTTGT 58.639 36.000 9.65 0.00 39.14 3.32
3386 4000 2.783135 TGTCTCTGAACTGAATTGGGC 58.217 47.619 0.00 0.00 0.00 5.36
3409 4023 2.290960 GGCTGAACTGTACCTGGGATTT 60.291 50.000 0.00 0.00 0.00 2.17
3471 4085 2.651841 AGAGGGCCCTGAAAAGAGAATT 59.348 45.455 34.59 0.00 0.00 2.17
3513 4131 6.430925 TGAATTTGAATCTGACCGTGATTCTT 59.569 34.615 14.76 4.40 45.82 2.52
3554 4172 4.692625 GGCTATATGTATGGTGCTGTCAAG 59.307 45.833 0.00 0.00 0.00 3.02
3562 4180 3.057969 TGGTGCTGTCAAGTATGAAGG 57.942 47.619 0.00 0.00 37.30 3.46
3565 4183 1.340017 TGCTGTCAAGTATGAAGGGGC 60.340 52.381 0.00 0.00 37.30 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.559862 ACATGCAACTTCCTAGCTAACT 57.440 40.909 0.00 0.00 0.00 2.24
42 43 3.772572 TGGTACATGCAACTTCCTAGCTA 59.227 43.478 0.00 0.00 0.00 3.32
43 44 2.571653 TGGTACATGCAACTTCCTAGCT 59.428 45.455 0.00 0.00 0.00 3.32
44 45 2.939103 CTGGTACATGCAACTTCCTAGC 59.061 50.000 0.00 0.00 38.20 3.42
45 46 4.207891 ACTGGTACATGCAACTTCCTAG 57.792 45.455 0.00 0.00 38.20 3.02
79 80 9.226606 TGTTATTTCATCAAACTTAGGGTACAG 57.773 33.333 0.00 0.00 0.00 2.74
88 89 9.077885 ACTATGTGGTGTTATTTCATCAAACTT 57.922 29.630 0.00 0.00 29.89 2.66
91 92 9.508642 TGTACTATGTGGTGTTATTTCATCAAA 57.491 29.630 0.00 0.00 29.89 2.69
92 93 9.508642 TTGTACTATGTGGTGTTATTTCATCAA 57.491 29.630 0.00 0.00 29.89 2.57
93 94 9.508642 TTTGTACTATGTGGTGTTATTTCATCA 57.491 29.630 0.00 0.00 0.00 3.07
94 95 9.769093 GTTTGTACTATGTGGTGTTATTTCATC 57.231 33.333 0.00 0.00 0.00 2.92
95 96 9.290988 TGTTTGTACTATGTGGTGTTATTTCAT 57.709 29.630 0.00 0.00 0.00 2.57
96 97 8.678593 TGTTTGTACTATGTGGTGTTATTTCA 57.321 30.769 0.00 0.00 0.00 2.69
97 98 8.780249 ACTGTTTGTACTATGTGGTGTTATTTC 58.220 33.333 0.00 0.00 0.00 2.17
98 99 8.685838 ACTGTTTGTACTATGTGGTGTTATTT 57.314 30.769 0.00 0.00 0.00 1.40
99 100 9.781633 TTACTGTTTGTACTATGTGGTGTTATT 57.218 29.630 0.00 0.00 0.00 1.40
100 101 9.781633 TTTACTGTTTGTACTATGTGGTGTTAT 57.218 29.630 0.00 0.00 0.00 1.89
110 111 7.166167 CCCTTCCACTTTACTGTTTGTACTAT 58.834 38.462 0.00 0.00 0.00 2.12
112 113 5.374071 CCCTTCCACTTTACTGTTTGTACT 58.626 41.667 0.00 0.00 0.00 2.73
133 134 2.499685 CAGGTAGCTACGCACCCC 59.500 66.667 17.48 2.72 32.82 4.95
136 137 2.582498 CGCCAGGTAGCTACGCAC 60.582 66.667 17.48 4.22 0.00 5.34
153 154 1.024579 TTGAGAGGAATTTCCGCGGC 61.025 55.000 23.51 5.55 41.52 6.53
156 157 1.740025 CCACTTGAGAGGAATTTCCGC 59.260 52.381 10.88 10.88 42.75 5.54
161 162 0.036732 TGCGCCACTTGAGAGGAATT 59.963 50.000 4.18 0.00 0.00 2.17
178 179 4.197498 GGGGCGCACACATGATGC 62.197 66.667 13.89 14.33 39.81 3.91
179 180 2.341875 TTGGGGCGCACACATGATG 61.342 57.895 13.89 0.00 0.00 3.07
180 181 2.035469 TTGGGGCGCACACATGAT 59.965 55.556 13.89 0.00 0.00 2.45
181 182 2.983030 GTTGGGGCGCACACATGA 60.983 61.111 13.89 0.00 0.00 3.07
188 189 1.481901 TTACTACTGGTTGGGGCGCA 61.482 55.000 10.83 0.00 0.00 6.09
215 216 3.359950 ACTAACCCGTACTCCAACCTAG 58.640 50.000 0.00 0.00 0.00 3.02
220 221 2.964464 TGTGAACTAACCCGTACTCCAA 59.036 45.455 0.00 0.00 0.00 3.53
223 224 4.813027 TCAATGTGAACTAACCCGTACTC 58.187 43.478 0.00 0.00 0.00 2.59
229 230 7.773690 ACCTACAATATCAATGTGAACTAACCC 59.226 37.037 0.00 0.00 32.27 4.11
249 250 5.935789 GTGCTTCCAACTACATTAACCTACA 59.064 40.000 0.00 0.00 0.00 2.74
250 251 5.935789 TGTGCTTCCAACTACATTAACCTAC 59.064 40.000 0.00 0.00 0.00 3.18
258 259 6.581712 ACAAAATTTGTGCTTCCAACTACAT 58.418 32.000 10.91 0.00 43.48 2.29
283 284 8.084073 TGAAAGGCTTTTATGAACTTTCATCAG 58.916 33.333 14.66 4.95 46.90 2.90
288 289 8.490355 CATGTTGAAAGGCTTTTATGAACTTTC 58.510 33.333 14.66 0.00 44.33 2.62
295 296 7.318141 AGATCACATGTTGAAAGGCTTTTATG 58.682 34.615 14.66 16.75 37.92 1.90
296 297 7.472334 AGATCACATGTTGAAAGGCTTTTAT 57.528 32.000 14.66 4.31 37.92 1.40
361 362 7.658167 TGAATCACGAGTCTAAATTACAAACCA 59.342 33.333 0.00 0.00 0.00 3.67
433 434 1.665679 CGAGGGATGTCAAATTGGTCG 59.334 52.381 0.00 0.00 0.00 4.79
435 436 1.463674 GCGAGGGATGTCAAATTGGT 58.536 50.000 0.00 0.00 0.00 3.67
453 454 0.512952 AGAGTTTCACATTCACGCGC 59.487 50.000 5.73 0.00 0.00 6.86
474 475 0.745845 GCATCACTTGTCGGGCATCT 60.746 55.000 0.00 0.00 0.00 2.90
522 523 7.201530 CCTTCTAACCATCGTTCACAAATACTC 60.202 40.741 0.00 0.00 33.17 2.59
545 559 3.515901 GGACTGAAGATACCACTGTCCTT 59.484 47.826 0.00 0.00 43.90 3.36
586 600 0.166814 GCGAGCACCAATGTCAAGTC 59.833 55.000 0.00 0.00 0.00 3.01
633 647 2.030412 ACTGAACGCACATCGCCA 59.970 55.556 0.00 0.00 43.23 5.69
634 648 2.476051 CACTGAACGCACATCGCC 59.524 61.111 0.00 0.00 43.23 5.54
689 717 9.912634 ACATTATTTTGAAATTGATGAAGTCGT 57.087 25.926 10.30 0.00 31.15 4.34
699 727 6.585702 TGAGCCGACACATTATTTTGAAATTG 59.414 34.615 0.00 0.00 0.00 2.32
708 736 4.142902 CGAAAACTGAGCCGACACATTATT 60.143 41.667 0.00 0.00 0.00 1.40
711 739 1.531149 CGAAAACTGAGCCGACACATT 59.469 47.619 0.00 0.00 0.00 2.71
717 745 0.391597 ACTTCCGAAAACTGAGCCGA 59.608 50.000 0.00 0.00 0.00 5.54
730 759 3.444916 ACGCTCATACATAACACTTCCG 58.555 45.455 0.00 0.00 0.00 4.30
778 890 7.754924 TCCGAATTTTGCTCATTACTCAAAATC 59.245 33.333 11.12 6.10 44.69 2.17
891 1004 2.838467 GGGGATGGATCAGCTGGGG 61.838 68.421 15.13 0.00 0.00 4.96
910 1023 3.433306 TCCCTTTGATGGTCGAATTGT 57.567 42.857 0.00 0.00 0.00 2.71
966 1080 1.749258 GGGATTGAGGGTTCGGTGC 60.749 63.158 0.00 0.00 0.00 5.01
1290 1404 3.024356 AGGAGGAGGGAGAGCCGA 61.024 66.667 0.00 0.00 33.83 5.54
1722 2313 3.842923 CGGCTCGGCTGTGGAGAT 61.843 66.667 0.00 0.00 33.27 2.75
1859 2450 0.946221 CAGCAGACTCGGTTGTGGAC 60.946 60.000 0.00 0.00 0.00 4.02
1932 2523 1.135939 CGTCGACGCAGGTGATGTA 59.864 57.895 26.59 0.00 0.00 2.29
1937 2528 2.050351 AGAACGTCGACGCAGGTG 60.050 61.111 35.92 11.11 44.43 4.00
1938 2529 2.050351 CAGAACGTCGACGCAGGT 60.050 61.111 35.92 19.64 44.43 4.00
2173 2764 0.252421 AGCTGATCTGACCCCTGTGA 60.252 55.000 3.42 0.00 0.00 3.58
2283 2874 0.601841 GTTCCGGCGAAGGTTCAGAA 60.602 55.000 9.30 0.00 0.00 3.02
2305 2896 0.457853 TCCACTCTCGTGCGCATTAC 60.458 55.000 15.91 0.00 39.86 1.89
2434 3025 2.220586 TGGGCATCACAGGTTCCGA 61.221 57.895 0.00 0.00 0.00 4.55
2475 3066 2.590114 GGGCTGTACAGGTTCCGGT 61.590 63.158 23.95 0.04 0.00 5.28
2626 3217 6.416415 TGAAATTAATAGCCGAACTAACCCA 58.584 36.000 0.00 0.00 33.57 4.51
2704 3295 1.697284 ACTGTCACTCTGTCAGCTGA 58.303 50.000 13.74 13.74 37.09 4.26
2706 3297 3.696045 AGATACTGTCACTCTGTCAGCT 58.304 45.455 0.00 0.00 37.09 4.24
2777 3368 8.196378 ACTCATCAACTAAGAAAAGACTACCT 57.804 34.615 0.00 0.00 0.00 3.08
2929 3520 8.465201 TGCAGCACATTATTTGAATGTACATTA 58.535 29.630 20.83 6.54 38.69 1.90
2971 3562 7.639113 AAACTGGAGAAGAAACACATAACAA 57.361 32.000 0.00 0.00 0.00 2.83
3089 3680 6.331577 TCTAGGTAAGTAGGTACCATGTCA 57.668 41.667 15.94 0.00 45.27 3.58
3156 3747 4.512944 CACTTGCAGTCTCACATAACTTGT 59.487 41.667 0.00 0.00 39.91 3.16
3206 3797 0.032952 TCAGTTCAAAGACCCGGACG 59.967 55.000 0.73 0.00 0.00 4.79
3207 3798 2.249844 TTCAGTTCAAAGACCCGGAC 57.750 50.000 0.73 0.00 0.00 4.79
3208 3799 3.146066 CAATTCAGTTCAAAGACCCGGA 58.854 45.455 0.73 0.00 0.00 5.14
3209 3800 2.228822 CCAATTCAGTTCAAAGACCCGG 59.771 50.000 0.00 0.00 0.00 5.73
3210 3801 2.228822 CCCAATTCAGTTCAAAGACCCG 59.771 50.000 0.00 0.00 0.00 5.28
3211 3802 3.230976 ACCCAATTCAGTTCAAAGACCC 58.769 45.455 0.00 0.00 0.00 4.46
3212 3803 4.937201 AACCCAATTCAGTTCAAAGACC 57.063 40.909 0.00 0.00 0.00 3.85
3213 3804 6.072673 ACGATAACCCAATTCAGTTCAAAGAC 60.073 38.462 0.00 0.00 0.00 3.01
3214 3805 6.001460 ACGATAACCCAATTCAGTTCAAAGA 58.999 36.000 0.00 0.00 0.00 2.52
3215 3806 6.254281 ACGATAACCCAATTCAGTTCAAAG 57.746 37.500 0.00 0.00 0.00 2.77
3216 3807 7.446013 AGTTACGATAACCCAATTCAGTTCAAA 59.554 33.333 0.00 0.00 0.00 2.69
3217 3808 6.938030 AGTTACGATAACCCAATTCAGTTCAA 59.062 34.615 0.00 0.00 0.00 2.69
3218 3809 6.370442 CAGTTACGATAACCCAATTCAGTTCA 59.630 38.462 0.00 0.00 0.00 3.18
3219 3810 6.370718 ACAGTTACGATAACCCAATTCAGTTC 59.629 38.462 0.00 0.00 0.00 3.01
3220 3811 6.235664 ACAGTTACGATAACCCAATTCAGTT 58.764 36.000 0.00 0.00 0.00 3.16
3221 3812 5.801380 ACAGTTACGATAACCCAATTCAGT 58.199 37.500 0.00 0.00 0.00 3.41
3222 3813 6.018994 GCTACAGTTACGATAACCCAATTCAG 60.019 42.308 0.00 0.00 0.00 3.02
3223 3814 5.813672 GCTACAGTTACGATAACCCAATTCA 59.186 40.000 0.00 0.00 0.00 2.57
3224 3815 6.047231 AGCTACAGTTACGATAACCCAATTC 58.953 40.000 0.00 0.00 0.00 2.17
3225 3816 5.985911 AGCTACAGTTACGATAACCCAATT 58.014 37.500 0.00 0.00 0.00 2.32
3226 3817 5.363005 AGAGCTACAGTTACGATAACCCAAT 59.637 40.000 0.00 0.00 0.00 3.16
3227 3818 4.708421 AGAGCTACAGTTACGATAACCCAA 59.292 41.667 0.00 0.00 0.00 4.12
3268 3881 7.171167 AGAGAGAATCATAGTCAAATTGCATCG 59.829 37.037 0.00 0.00 37.82 3.84
3324 3937 6.884295 GCCAACCAATTCATATATAGCCACTA 59.116 38.462 0.00 0.00 0.00 2.74
3386 4000 0.036010 CCCAGGTACAGTTCAGCCAG 60.036 60.000 0.00 0.00 0.00 4.85
3455 4069 4.403752 AGCCAATAATTCTCTTTTCAGGGC 59.596 41.667 0.00 0.00 36.81 5.19
3471 4085 9.585369 TTCAAATTCACCATGATATAGCCAATA 57.415 29.630 0.00 0.00 0.00 1.90
3483 4097 4.156556 ACGGTCAGATTCAAATTCACCATG 59.843 41.667 0.00 0.00 0.00 3.66
3513 4131 3.225104 AGCCAACAATTCTCTTTCAGCA 58.775 40.909 0.00 0.00 0.00 4.41
3554 4172 2.119029 GTTGCCGGCCCCTTCATAC 61.119 63.158 26.77 5.19 0.00 2.39
3562 4180 2.390306 AAAAATGGTGTTGCCGGCCC 62.390 55.000 26.77 18.68 41.21 5.80
3565 4183 3.976339 TCAAAAATGGTGTTGCCGG 57.024 47.368 0.00 0.00 41.21 6.13


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

AutoCloner maintained by Alex Coulton.