Multiple sequence alignment - TraesCS4D01G210300

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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 TraesCS4D01G210300 chr4D 100.000 3695 0 0 1 3695 361977785 361981479 0.000000e+00 6824.0
1 TraesCS4D01G210300 chr4D 78.000 300 58 8 3400 3695 85642201 85641906 8.150000e-42 182.0
2 TraesCS4D01G210300 chr4B 92.576 2613 96 25 205 2778 447364336 447366889 0.000000e+00 3661.0
3 TraesCS4D01G210300 chr4B 94.332 494 27 1 2798 3291 447366876 447367368 0.000000e+00 756.0
4 TraesCS4D01G210300 chr4B 92.402 408 28 3 3287 3693 447371342 447371747 2.470000e-161 579.0
5 TraesCS4D01G210300 chr4A 96.052 1697 44 8 1102 2778 103333141 103331448 0.000000e+00 2741.0
6 TraesCS4D01G210300 chr4A 88.424 717 58 6 3004 3695 103324016 103323300 0.000000e+00 841.0
7 TraesCS4D01G210300 chr4A 93.525 417 13 5 697 1105 103333590 103333180 3.160000e-170 608.0
8 TraesCS4D01G210300 chr4A 83.810 420 46 14 19 432 103334870 103334467 2.690000e-101 379.0
9 TraesCS4D01G210300 chr4A 98.462 195 2 1 449 643 103333782 103333589 3.530000e-90 342.0
10 TraesCS4D01G210300 chr4A 82.051 429 37 20 2884 3288 424387368 424386956 2.750000e-86 329.0
11 TraesCS4D01G210300 chr4A 88.333 180 21 0 2602 2781 424387670 424387491 2.230000e-52 217.0
12 TraesCS4D01G210300 chr6B 90.215 419 23 7 433 851 546430117 546430517 7.030000e-147 531.0
13 TraesCS4D01G210300 chr7B 87.805 369 43 2 3326 3692 74831900 74831532 7.330000e-117 431.0
14 TraesCS4D01G210300 chr5A 84.314 459 48 16 2884 3325 28845969 28846420 9.480000e-116 427.0
15 TraesCS4D01G210300 chr5A 87.791 172 20 1 2602 2773 28845667 28845837 2.250000e-47 200.0
16 TraesCS4D01G210300 chr5A 76.282 312 66 8 3367 3674 33155564 33155257 3.820000e-35 159.0
17 TraesCS4D01G210300 chr7A 85.326 368 52 2 3326 3692 120140840 120140474 2.690000e-101 379.0
18 TraesCS4D01G210300 chr7A 82.297 418 49 13 2878 3290 700417699 700418096 4.570000e-89 339.0
19 TraesCS4D01G210300 chr2D 84.239 368 56 2 3327 3692 420747572 420747205 1.260000e-94 357.0
20 TraesCS4D01G210300 chr2D 94.000 50 3 0 1164 1213 546807565 546807516 3.960000e-10 76.8
21 TraesCS4D01G210300 chrUn 83.127 403 45 11 2891 3288 83451524 83451140 2.730000e-91 346.0
22 TraesCS4D01G210300 chr6A 81.182 457 57 19 2878 3325 178249890 178250326 1.270000e-89 340.0
23 TraesCS4D01G210300 chr6A 83.721 172 14 2 2602 2773 178249606 178249763 2.300000e-32 150.0
24 TraesCS4D01G210300 chr1B 83.200 375 59 2 3325 3695 174295690 174296064 1.270000e-89 340.0
25 TraesCS4D01G210300 chr2A 81.693 437 44 16 2919 3325 723581231 723581661 7.650000e-87 331.0
26 TraesCS4D01G210300 chr2A 81.744 367 66 1 3327 3692 566475961 566475595 4.640000e-79 305.0
27 TraesCS4D01G210300 chr2A 94.000 50 3 0 1164 1213 689760401 689760450 3.960000e-10 76.8
28 TraesCS4D01G210300 chr3A 81.384 419 56 14 2878 3288 520408722 520409126 4.600000e-84 322.0
29 TraesCS4D01G210300 chr2B 74.888 223 34 13 1293 1495 653446685 653446465 8.500000e-12 82.4


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 TraesCS4D01G210300 chr4D 361977785 361981479 3694 False 6824.000000 6824 100.000000 1 3695 1 chr4D.!!$F1 3694
1 TraesCS4D01G210300 chr4B 447364336 447371747 7411 False 1665.333333 3661 93.103333 205 3693 3 chr4B.!!$F1 3488
2 TraesCS4D01G210300 chr4A 103331448 103334870 3422 True 1017.500000 2741 92.962250 19 2778 4 chr4A.!!$R2 2759
3 TraesCS4D01G210300 chr4A 103323300 103324016 716 True 841.000000 841 88.424000 3004 3695 1 chr4A.!!$R1 691
4 TraesCS4D01G210300 chr4A 424386956 424387670 714 True 273.000000 329 85.192000 2602 3288 2 chr4A.!!$R3 686
5 TraesCS4D01G210300 chr5A 28845667 28846420 753 False 313.500000 427 86.052500 2602 3325 2 chr5A.!!$F1 723
6 TraesCS4D01G210300 chr6A 178249606 178250326 720 False 245.000000 340 82.451500 2602 3325 2 chr6A.!!$F1 723

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
64 65 0.032515 TCCCCTCTATGTGAAGCCGA 60.033 55.000 0.0 0.0 0.00 5.54 F
855 1548 0.039764 TCCTCCATCCACAGACGAGT 59.960 55.000 0.0 0.0 0.00 4.18 F
964 1657 1.137479 TCCGGGTTTATCATCCGTCAC 59.863 52.381 0.0 0.0 41.98 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1759 1.063806 GCTGTACGCTGTTGACTGAG 58.936 55.000 2.99 0.0 35.14 3.35 R
2188 2931 1.275856 CTCAGCTTCTCCTTCACTGCT 59.724 52.381 0.00 0.0 0.00 4.24 R
2789 3553 2.091098 AACCCAAGTTTAACACCCCC 57.909 50.000 0.00 0.0 29.61 5.40 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 2.700773 GGAGTTTGACATGGCGGGC 61.701 63.158 0.00 0.00 0.00 6.13
27 28 4.776647 GTTTGACATGGCGGGCGC 62.777 66.667 0.00 0.00 41.06 6.53
55 56 1.577736 CCCCATAGCTCCCCTCTATG 58.422 60.000 0.00 3.68 41.72 2.23
62 63 0.107643 GCTCCCCTCTATGTGAAGCC 59.892 60.000 0.00 0.00 0.00 4.35
64 65 0.032515 TCCCCTCTATGTGAAGCCGA 60.033 55.000 0.00 0.00 0.00 5.54
69 70 1.135915 CTCTATGTGAAGCCGAGCTGT 59.864 52.381 0.00 0.00 39.62 4.40
70 71 1.134995 TCTATGTGAAGCCGAGCTGTG 60.135 52.381 0.00 0.00 39.62 3.66
77 78 2.597510 GCCGAGCTGTGGGGTTTT 60.598 61.111 0.00 0.00 0.00 2.43
78 79 2.919494 GCCGAGCTGTGGGGTTTTG 61.919 63.158 0.00 0.00 0.00 2.44
79 80 1.228124 CCGAGCTGTGGGGTTTTGA 60.228 57.895 0.00 0.00 0.00 2.69
90 91 2.701951 TGGGGTTTTGAACGTCTAGAGT 59.298 45.455 0.00 0.00 0.00 3.24
97 98 1.163554 GAACGTCTAGAGTGGTCCGT 58.836 55.000 0.00 0.00 0.00 4.69
106 107 1.003233 AGAGTGGTCCGTCCCAATTTC 59.997 52.381 0.00 0.00 35.92 2.17
110 111 1.074727 TGGTCCGTCCCAATTTCATGT 59.925 47.619 0.00 0.00 34.77 3.21
111 112 2.167662 GGTCCGTCCCAATTTCATGTT 58.832 47.619 0.00 0.00 0.00 2.71
112 113 2.560981 GGTCCGTCCCAATTTCATGTTT 59.439 45.455 0.00 0.00 0.00 2.83
113 114 3.759618 GGTCCGTCCCAATTTCATGTTTA 59.240 43.478 0.00 0.00 0.00 2.01
115 116 5.449999 GGTCCGTCCCAATTTCATGTTTATC 60.450 44.000 0.00 0.00 0.00 1.75
119 120 5.516339 CGTCCCAATTTCATGTTTATCTTGC 59.484 40.000 0.00 0.00 0.00 4.01
126 127 8.461222 CAATTTCATGTTTATCTTGCAGACCTA 58.539 33.333 0.00 0.00 0.00 3.08
144 145 2.299297 CCTAGAAGTGTCCGGACTGTTT 59.701 50.000 33.39 23.52 0.00 2.83
146 147 1.760613 AGAAGTGTCCGGACTGTTTGA 59.239 47.619 33.39 11.17 0.00 2.69
147 148 2.368875 AGAAGTGTCCGGACTGTTTGAT 59.631 45.455 33.39 13.67 0.00 2.57
148 149 2.457366 AGTGTCCGGACTGTTTGATC 57.543 50.000 33.39 13.79 0.00 2.92
149 150 1.002087 AGTGTCCGGACTGTTTGATCC 59.998 52.381 33.39 5.25 0.00 3.36
150 151 1.052617 TGTCCGGACTGTTTGATCCA 58.947 50.000 33.39 8.08 34.35 3.41
151 152 1.001974 TGTCCGGACTGTTTGATCCAG 59.998 52.381 33.39 0.00 34.35 3.86
152 153 1.275291 GTCCGGACTGTTTGATCCAGA 59.725 52.381 27.64 0.00 34.35 3.86
153 154 1.275291 TCCGGACTGTTTGATCCAGAC 59.725 52.381 0.00 0.00 34.35 3.51
158 163 4.378770 CGGACTGTTTGATCCAGACATTTG 60.379 45.833 4.68 0.00 34.35 2.32
161 166 4.279169 ACTGTTTGATCCAGACATTTGTGG 59.721 41.667 4.68 0.00 34.04 4.17
174 179 5.007332 AGACATTTGTGGTCGTTTTAGTGAC 59.993 40.000 0.00 0.00 40.20 3.67
189 195 1.106285 GTGACCCATTTGGAGATGCC 58.894 55.000 0.00 0.00 37.39 4.40
198 204 5.139727 CCATTTGGAGATGCCCTAACATAA 58.860 41.667 0.00 0.00 37.39 1.90
199 205 5.010012 CCATTTGGAGATGCCCTAACATAAC 59.990 44.000 0.00 0.00 37.39 1.89
200 206 4.853468 TTGGAGATGCCCTAACATAACA 57.147 40.909 0.00 0.00 34.97 2.41
201 207 5.387113 TTGGAGATGCCCTAACATAACAT 57.613 39.130 0.00 0.00 34.97 2.71
202 208 6.508030 TTGGAGATGCCCTAACATAACATA 57.492 37.500 0.00 0.00 34.97 2.29
203 209 6.114187 TGGAGATGCCCTAACATAACATAG 57.886 41.667 0.00 0.00 34.97 2.23
206 212 5.555017 AGATGCCCTAACATAACATAGCAG 58.445 41.667 0.00 0.00 31.70 4.24
210 216 5.600898 TGCCCTAACATAACATAGCAGTCTA 59.399 40.000 0.00 0.00 0.00 2.59
212 218 6.239345 GCCCTAACATAACATAGCAGTCTAGT 60.239 42.308 0.00 0.00 0.00 2.57
218 224 4.624336 AACATAGCAGTCTAGTCACTCG 57.376 45.455 0.00 0.00 0.00 4.18
264 270 5.006746 GGCAGGTTACTATCAAATCGTTGAG 59.993 44.000 0.00 0.00 46.75 3.02
325 331 2.933492 GCACTTACCGTGGCAGTGATTA 60.933 50.000 18.49 0.00 43.97 1.75
354 360 2.505866 CGTTTAGCGTTCCAGCAATTC 58.494 47.619 0.00 0.00 40.15 2.17
360 366 3.642705 AGCGTTCCAGCAATTCTTTTTC 58.357 40.909 0.00 0.00 40.15 2.29
368 375 6.748132 TCCAGCAATTCTTTTTCCAAACTAG 58.252 36.000 0.00 0.00 0.00 2.57
411 418 0.245539 TACAGAAGGCGTACCACAGC 59.754 55.000 0.00 0.00 39.06 4.40
454 480 1.132262 CATACAACCACATGCGGGAAC 59.868 52.381 10.76 0.00 0.00 3.62
679 1372 2.128771 ATGTAGTGACATGCCCCAAC 57.871 50.000 0.00 0.00 44.90 3.77
771 1464 1.400846 GCGTGGACGACTTCTCATCTA 59.599 52.381 2.73 0.00 43.02 1.98
772 1465 2.033550 GCGTGGACGACTTCTCATCTAT 59.966 50.000 2.73 0.00 43.02 1.98
773 1466 3.850374 GCGTGGACGACTTCTCATCTATC 60.850 52.174 2.73 0.00 43.02 2.08
774 1467 3.562141 CGTGGACGACTTCTCATCTATCT 59.438 47.826 0.00 0.00 43.02 1.98
816 1509 2.477375 CTGCCGACTGCGTTTAGTTAAA 59.523 45.455 0.00 0.00 45.60 1.52
817 1510 2.221517 TGCCGACTGCGTTTAGTTAAAC 59.778 45.455 4.98 4.98 45.60 2.01
855 1548 0.039764 TCCTCCATCCACAGACGAGT 59.960 55.000 0.00 0.00 0.00 4.18
963 1656 1.411246 CTCCGGGTTTATCATCCGTCA 59.589 52.381 0.00 0.00 41.98 4.35
964 1657 1.137479 TCCGGGTTTATCATCCGTCAC 59.863 52.381 0.00 0.00 41.98 3.67
965 1658 1.205657 CGGGTTTATCATCCGTCACG 58.794 55.000 0.00 0.00 39.04 4.35
1007 1700 1.458445 GCTTCGAACGTTCCTGTAACC 59.542 52.381 22.07 1.50 34.33 2.85
1014 1707 4.312443 GAACGTTCCTGTAACCATTCTGA 58.688 43.478 17.68 0.00 34.33 3.27
1093 1794 2.090658 CGTACAGCTACAGTTTGCTTCG 59.909 50.000 0.00 2.12 37.44 3.79
1978 2721 2.341846 TCTTCCGGCAAAAAGACACT 57.658 45.000 0.00 0.00 0.00 3.55
2188 2931 4.805231 CCCGTGACCATACGCGCA 62.805 66.667 5.73 0.00 42.44 6.09
2549 3292 4.082841 TGCGCAGTTCATCATGTGTAAATT 60.083 37.500 5.66 0.00 0.00 1.82
2887 3651 7.095857 GGAGTTTGAGACATTGCTAGATATTCG 60.096 40.741 0.00 0.00 0.00 3.34
2910 3729 5.858049 CGTTAGAAGCTGCATCATTGAAAAA 59.142 36.000 7.68 0.00 0.00 1.94
2967 3791 3.270027 TGCCATAACTTTGGATCAGTCG 58.730 45.455 0.00 0.00 39.25 4.18
2974 3798 8.575720 CCATAACTTTGGATCAGTCGTGTAGAC 61.576 44.444 0.00 0.00 43.68 2.59
2986 3810 1.448308 CGTGTAGACGCGCAATCTATG 59.552 52.381 18.41 10.03 43.06 2.23
2995 3819 5.642491 AGACGCGCAATCTATGTAGACTATA 59.358 40.000 5.73 0.00 34.72 1.31
3071 3896 4.894114 ACAAAGTAGGCGTACATAGGAGAT 59.106 41.667 18.13 0.00 0.00 2.75
3109 3934 6.377146 ACATGAGTATAAGCACCGGAAAATTT 59.623 34.615 9.46 0.00 0.00 1.82
3222 4071 2.987413 TTTCACGACCAATGTGATGC 57.013 45.000 0.00 0.00 45.10 3.91
3330 8157 0.831711 GGAACAACCAGCACCCCATT 60.832 55.000 0.00 0.00 38.79 3.16
3361 8188 1.202698 CCTCGGGTGGATCTCAATTCC 60.203 57.143 0.00 0.00 0.00 3.01
3381 8208 6.693315 TTCCGAAAAGATCTTGTCAAAGTT 57.307 33.333 22.68 6.26 34.78 2.66
3382 8209 6.693315 TCCGAAAAGATCTTGTCAAAGTTT 57.307 33.333 22.68 5.57 34.78 2.66
3383 8210 6.494842 TCCGAAAAGATCTTGTCAAAGTTTG 58.505 36.000 22.68 9.44 34.78 2.93
3480 8308 2.197577 GCGATTCTCCTCTAGTTGTGC 58.802 52.381 0.00 0.00 0.00 4.57
3488 8316 1.351017 CCTCTAGTTGTGCCCTTTCCA 59.649 52.381 0.00 0.00 0.00 3.53
3603 8431 3.753272 TGAAGAGTTTAATGACTGGCAGC 59.247 43.478 15.89 8.22 0.00 5.25
3609 8437 3.603158 TTAATGACTGGCAGCGTCTTA 57.397 42.857 15.89 4.96 32.70 2.10
3613 8441 1.001974 TGACTGGCAGCGTCTTATTGT 59.998 47.619 15.89 0.00 32.70 2.71
3631 8459 1.066858 TGTCTGCATTCCCGTTCTCTC 60.067 52.381 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.095059 GCCATGTCAAACTCCATCACAC 60.095 50.000 0.00 0.00 0.00 3.82
1 2 2.161855 GCCATGTCAAACTCCATCACA 58.838 47.619 0.00 0.00 0.00 3.58
2 3 1.131126 CGCCATGTCAAACTCCATCAC 59.869 52.381 0.00 0.00 0.00 3.06
3 4 1.452110 CGCCATGTCAAACTCCATCA 58.548 50.000 0.00 0.00 0.00 3.07
4 5 0.734889 CCGCCATGTCAAACTCCATC 59.265 55.000 0.00 0.00 0.00 3.51
5 6 0.680921 CCCGCCATGTCAAACTCCAT 60.681 55.000 0.00 0.00 0.00 3.41
6 7 1.303236 CCCGCCATGTCAAACTCCA 60.303 57.895 0.00 0.00 0.00 3.86
7 8 2.700773 GCCCGCCATGTCAAACTCC 61.701 63.158 0.00 0.00 0.00 3.85
8 9 2.877691 GCCCGCCATGTCAAACTC 59.122 61.111 0.00 0.00 0.00 3.01
9 10 3.055719 CGCCCGCCATGTCAAACT 61.056 61.111 0.00 0.00 0.00 2.66
10 11 4.776647 GCGCCCGCCATGTCAAAC 62.777 66.667 0.00 0.00 34.56 2.93
25 26 3.093835 TATGGGGGAACAGGGGCG 61.094 66.667 0.00 0.00 0.00 6.13
27 28 1.697754 AGCTATGGGGGAACAGGGG 60.698 63.158 0.00 0.00 0.00 4.79
32 33 1.386057 AGGGGAGCTATGGGGGAAC 60.386 63.158 0.00 0.00 0.00 3.62
33 34 1.073706 GAGGGGAGCTATGGGGGAA 60.074 63.158 0.00 0.00 0.00 3.97
39 40 3.306641 GCTTCACATAGAGGGGAGCTATG 60.307 52.174 0.00 0.00 46.67 2.23
41 42 2.320781 GCTTCACATAGAGGGGAGCTA 58.679 52.381 0.00 0.00 0.00 3.32
55 56 2.743928 CCCACAGCTCGGCTTCAC 60.744 66.667 0.00 0.00 36.40 3.18
62 63 0.310854 GTTCAAAACCCCACAGCTCG 59.689 55.000 0.00 0.00 0.00 5.03
64 65 0.395173 ACGTTCAAAACCCCACAGCT 60.395 50.000 0.00 0.00 0.00 4.24
69 70 2.701951 ACTCTAGACGTTCAAAACCCCA 59.298 45.455 0.00 0.00 0.00 4.96
70 71 3.064931 CACTCTAGACGTTCAAAACCCC 58.935 50.000 0.00 0.00 0.00 4.95
77 78 1.162698 CGGACCACTCTAGACGTTCA 58.837 55.000 0.00 0.00 0.00 3.18
78 79 1.130186 GACGGACCACTCTAGACGTTC 59.870 57.143 5.44 0.00 34.43 3.95
79 80 1.163554 GACGGACCACTCTAGACGTT 58.836 55.000 5.44 0.00 34.43 3.99
90 91 1.074727 ACATGAAATTGGGACGGACCA 59.925 47.619 0.00 0.00 41.20 4.02
97 98 6.436847 TCTGCAAGATAAACATGAAATTGGGA 59.563 34.615 0.00 0.00 38.67 4.37
115 116 2.672478 CGGACACTTCTAGGTCTGCAAG 60.672 54.545 0.00 0.00 34.00 4.01
119 120 1.473278 GTCCGGACACTTCTAGGTCTG 59.527 57.143 29.75 0.00 39.56 3.51
126 127 1.760613 TCAAACAGTCCGGACACTTCT 59.239 47.619 35.00 12.66 0.00 2.85
144 145 2.038426 ACGACCACAAATGTCTGGATCA 59.962 45.455 0.00 0.00 0.00 2.92
146 147 2.859165 ACGACCACAAATGTCTGGAT 57.141 45.000 0.00 0.00 0.00 3.41
147 148 2.631160 AACGACCACAAATGTCTGGA 57.369 45.000 0.00 0.00 0.00 3.86
148 149 3.708563 AAAACGACCACAAATGTCTGG 57.291 42.857 0.00 0.00 0.00 3.86
149 150 5.007234 TCACTAAAACGACCACAAATGTCTG 59.993 40.000 0.00 0.00 0.00 3.51
150 151 5.007332 GTCACTAAAACGACCACAAATGTCT 59.993 40.000 0.00 0.00 0.00 3.41
151 152 5.202640 GTCACTAAAACGACCACAAATGTC 58.797 41.667 0.00 0.00 0.00 3.06
152 153 5.164606 GTCACTAAAACGACCACAAATGT 57.835 39.130 0.00 0.00 0.00 2.71
161 166 3.816523 TCCAAATGGGTCACTAAAACGAC 59.183 43.478 0.00 0.00 38.11 4.34
174 179 2.310538 GTTAGGGCATCTCCAAATGGG 58.689 52.381 0.00 0.00 36.21 4.00
178 183 5.186256 TGTTATGTTAGGGCATCTCCAAA 57.814 39.130 0.00 0.00 36.21 3.28
189 195 7.863375 GTGACTAGACTGCTATGTTATGTTAGG 59.137 40.741 0.00 0.00 0.00 2.69
198 204 3.375610 CACGAGTGACTAGACTGCTATGT 59.624 47.826 0.00 0.00 0.00 2.29
199 205 3.790456 GCACGAGTGACTAGACTGCTATG 60.790 52.174 7.50 0.00 0.00 2.23
200 206 2.356382 GCACGAGTGACTAGACTGCTAT 59.644 50.000 7.50 0.00 0.00 2.97
201 207 1.738350 GCACGAGTGACTAGACTGCTA 59.262 52.381 7.50 0.00 0.00 3.49
202 208 0.523966 GCACGAGTGACTAGACTGCT 59.476 55.000 7.50 0.00 0.00 4.24
203 209 0.456995 GGCACGAGTGACTAGACTGC 60.457 60.000 7.50 0.00 35.21 4.40
218 224 3.587923 TGTTACCTACACAATACGGCAC 58.412 45.455 0.00 0.00 0.00 5.01
264 270 1.198759 TTACCACCAGGAGGGCTCAC 61.199 60.000 7.97 0.00 42.05 3.51
354 360 8.175716 CGGCTAATAACTCTAGTTTGGAAAAAG 58.824 37.037 0.00 0.00 39.31 2.27
360 366 6.145338 TCTCGGCTAATAACTCTAGTTTGG 57.855 41.667 0.00 0.00 39.31 3.28
368 375 5.575995 ACGTCTTTTTCTCGGCTAATAACTC 59.424 40.000 0.00 0.00 0.00 3.01
454 480 3.470888 CCTCGGTGGCCTAGGTGG 61.471 72.222 11.31 0.00 32.50 4.61
676 1369 4.641645 TGGAGGCGCCACCAGTTG 62.642 66.667 37.76 0.00 43.33 3.16
816 1509 1.412453 TTAGGGGAAGGTGCGTGTGT 61.412 55.000 0.00 0.00 0.00 3.72
817 1510 0.035439 ATTAGGGGAAGGTGCGTGTG 60.035 55.000 0.00 0.00 0.00 3.82
855 1548 3.258372 AGAAGACGAAGGAAGCATGTGTA 59.742 43.478 0.00 0.00 0.00 2.90
1014 1707 7.123547 GCCTGCAAGTAGTTATAGGAGAGATAT 59.876 40.741 13.54 0.00 0.00 1.63
1054 1753 1.287730 CGCTGTTGACTGAGTGAGGC 61.288 60.000 0.00 0.00 0.00 4.70
1060 1759 1.063806 GCTGTACGCTGTTGACTGAG 58.936 55.000 2.99 0.00 35.14 3.35
1093 1794 2.547855 GGCCATGACCAAACCAAAGAAC 60.548 50.000 0.00 0.00 0.00 3.01
1699 2442 2.110967 CAACCTGAGCTCGCCCATG 61.111 63.158 9.64 0.63 0.00 3.66
1978 2721 1.803289 CTCTGACGATGTCGAGGCA 59.197 57.895 9.67 3.76 43.02 4.75
2188 2931 1.275856 CTCAGCTTCTCCTTCACTGCT 59.724 52.381 0.00 0.00 0.00 4.24
2728 3491 2.111384 CTCCCACCACTGCACTACTAT 58.889 52.381 0.00 0.00 0.00 2.12
2789 3553 2.091098 AACCCAAGTTTAACACCCCC 57.909 50.000 0.00 0.00 29.61 5.40
2790 3554 5.611128 TTAAAACCCAAGTTTAACACCCC 57.389 39.130 0.00 0.00 45.54 4.95
2791 3555 7.769507 TCAAATTAAAACCCAAGTTTAACACCC 59.230 33.333 0.00 0.00 45.54 4.61
2792 3556 8.719560 TCAAATTAAAACCCAAGTTTAACACC 57.280 30.769 0.00 0.00 45.54 4.16
2822 3586 6.016527 TCACGTGTGAGACATAAAGTAGAACT 60.017 38.462 16.51 0.00 34.14 3.01
2887 3651 6.183360 GCTTTTTCAATGATGCAGCTTCTAAC 60.183 38.462 2.53 0.00 0.00 2.34
2910 3729 3.932822 TGTTATCATGTGTACGTTGGCT 58.067 40.909 0.00 0.00 0.00 4.75
2967 3791 2.460918 ACATAGATTGCGCGTCTACAC 58.539 47.619 20.34 1.34 31.47 2.90
2974 3798 6.315551 ACTTATAGTCTACATAGATTGCGCG 58.684 40.000 0.00 0.00 34.39 6.86
2995 3819 7.224753 CGAATACTGTGTTATGCTCCATTACTT 59.775 37.037 0.00 0.00 0.00 2.24
3002 3827 6.877855 CATAACGAATACTGTGTTATGCTCC 58.122 40.000 12.75 0.00 44.66 4.70
3109 3934 5.129485 CCTCATCTCCTACAAGGAAAAGCTA 59.871 44.000 0.00 0.00 45.28 3.32
3222 4071 0.950836 TGGCACAAATGACCGTGAAG 59.049 50.000 0.00 0.00 35.02 3.02
3330 8157 1.533625 CACCCGAGGATGAAGCAAAA 58.466 50.000 0.00 0.00 0.00 2.44
3361 8188 6.414987 GGACAAACTTTGACAAGATCTTTTCG 59.585 38.462 15.13 3.78 33.72 3.46
3381 8208 2.570415 TGGGATTAAACAGCGGACAA 57.430 45.000 0.00 0.00 0.00 3.18
3382 8209 2.290641 ACATGGGATTAAACAGCGGACA 60.291 45.455 0.00 0.00 0.00 4.02
3383 8210 2.354821 GACATGGGATTAAACAGCGGAC 59.645 50.000 0.00 0.00 0.00 4.79
3568 8396 7.546250 TTAAACTCTTCAGGAGACAGAGAAT 57.454 36.000 2.46 0.00 44.45 2.40
3603 8431 2.285220 CGGGAATGCAGACAATAAGACG 59.715 50.000 0.00 0.00 0.00 4.18
3609 8437 2.026822 AGAGAACGGGAATGCAGACAAT 60.027 45.455 0.00 0.00 0.00 2.71
3613 8441 0.173481 CGAGAGAACGGGAATGCAGA 59.827 55.000 0.00 0.00 0.00 4.26
3631 8459 3.438615 ATCGAGTCCTCCCCCTCCG 62.439 68.421 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.