Multiple sequence alignment - TraesCS2D01G326300

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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 TraesCS2D01G326300 chr2D 100.000 3970 0 0 1 3970 419784650 419780681 0.000000e+00 7332.0
1 TraesCS2D01G326300 chr2B 94.388 3172 110 25 817 3970 492148480 492145359 0.000000e+00 4809.0
2 TraesCS2D01G326300 chr2B 91.029 680 29 19 1 679 492149459 492148811 0.000000e+00 889.0
3 TraesCS2D01G326300 chr2B 95.833 48 2 0 694 741 492148825 492148778 1.180000e-10 78.7
4 TraesCS2D01G326300 chr2A 93.551 2636 96 30 723 3329 570192644 570195234 0.000000e+00 3858.0
5 TraesCS2D01G326300 chr2A 90.361 664 34 11 3316 3970 570195262 570195904 0.000000e+00 845.0
6 TraesCS2D01G326300 chr2A 89.655 551 33 12 1 549 570191937 570192465 0.000000e+00 680.0
7 TraesCS2D01G326300 chr3B 76.514 545 72 30 1 536 21405304 21405801 3.060000e-61 246.0
8 TraesCS2D01G326300 chr7D 89.583 192 20 0 1058 1249 531553840 531554031 1.100000e-60 244.0
9 TraesCS2D01G326300 chr7A 84.524 252 33 5 1001 1249 611969535 611969783 1.100000e-60 244.0
10 TraesCS2D01G326300 chr7A 83.539 243 34 5 997 1236 611776746 611776985 5.160000e-54 222.0
11 TraesCS2D01G326300 chr3A 89.595 173 18 0 139 311 22147920 22147748 1.860000e-53 220.0
12 TraesCS2D01G326300 chr3A 82.890 263 25 14 1 263 22229084 22228842 6.680000e-53 219.0
13 TraesCS2D01G326300 chr5D 86.802 197 25 1 1053 1249 318059886 318060081 6.680000e-53 219.0
14 TraesCS2D01G326300 chr5A 86.802 197 25 1 1053 1249 412913483 412913678 6.680000e-53 219.0
15 TraesCS2D01G326300 chr3D 98.291 117 2 0 147 263 14449377 14449493 5.200000e-49 206.0


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 TraesCS2D01G326300 chr2D 419780681 419784650 3969 True 7332.000000 7332 100.000 1 3970 1 chr2D.!!$R1 3969
1 TraesCS2D01G326300 chr2B 492145359 492149459 4100 True 1925.566667 4809 93.750 1 3970 3 chr2B.!!$R1 3969
2 TraesCS2D01G326300 chr2A 570191937 570195904 3967 False 1794.333333 3858 91.189 1 3970 3 chr2A.!!$F1 3969

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
741 805 0.107456 CTGACAGCTCGGCCCATTAT 59.893 55.0 0.0 0.0 0.0 1.28 F
1263 1557 0.757512 GGTAACTTCCGATCCCTCCC 59.242 60.0 0.0 0.0 0.0 4.30 F
1845 2141 0.456824 ACACACGCATCGCTGTCTAG 60.457 55.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1891 0.836606 TGACACCAGGAGCAAGAACA 59.163 50.000 0.0 0.0 0.00 3.18 R
2223 2523 0.877649 CTGGGACGGCAATGATCTCG 60.878 60.000 0.0 0.0 0.00 4.04 R
3673 4063 1.750930 CACTCCTCGATGGGGGATG 59.249 63.158 0.0 0.0 41.89 3.51 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
32 33 2.435805 GGCATGGACTGAAGATGGACTA 59.564 50.000 0.00 0.00 0.00 2.59
118 119 2.028112 TGTCGCTTAGGCACAATTCTCT 60.028 45.455 0.00 0.00 38.60 3.10
119 120 3.003480 GTCGCTTAGGCACAATTCTCTT 58.997 45.455 0.00 0.00 38.60 2.85
120 121 4.181578 GTCGCTTAGGCACAATTCTCTTA 58.818 43.478 0.00 0.00 38.60 2.10
122 123 5.050490 TCGCTTAGGCACAATTCTCTTATC 58.950 41.667 0.00 0.00 38.60 1.75
123 124 4.084849 CGCTTAGGCACAATTCTCTTATCG 60.085 45.833 0.00 0.00 38.60 2.92
126 127 3.462021 AGGCACAATTCTCTTATCGCTC 58.538 45.455 0.00 0.00 0.00 5.03
127 128 3.133721 AGGCACAATTCTCTTATCGCTCT 59.866 43.478 0.00 0.00 0.00 4.09
128 129 3.492756 GGCACAATTCTCTTATCGCTCTC 59.507 47.826 0.00 0.00 0.00 3.20
129 130 3.181377 GCACAATTCTCTTATCGCTCTCG 59.819 47.826 0.00 0.00 0.00 4.04
130 131 3.181377 CACAATTCTCTTATCGCTCTCGC 59.819 47.826 0.00 0.00 35.26 5.03
145 146 1.506718 TCGCGAGAGTGCTAACTGG 59.493 57.895 3.71 0.00 42.50 4.00
150 151 2.464865 CGAGAGTGCTAACTGGTATGC 58.535 52.381 0.00 0.00 36.52 3.14
188 189 0.191064 TCCAGTTCCACCCAGAGAGT 59.809 55.000 0.00 0.00 0.00 3.24
278 279 1.110518 CCTCCGAGGGGAAGTAGAGC 61.111 65.000 6.53 0.00 43.27 4.09
329 330 8.815565 AAGTAGAGACTATTGTTGAGAGATCA 57.184 34.615 0.00 0.00 33.58 2.92
330 331 8.450578 AGTAGAGACTATTGTTGAGAGATCAG 57.549 38.462 0.00 0.00 32.65 2.90
331 332 8.271458 AGTAGAGACTATTGTTGAGAGATCAGA 58.729 37.037 0.00 0.00 32.65 3.27
332 333 9.066892 GTAGAGACTATTGTTGAGAGATCAGAT 57.933 37.037 0.00 0.00 0.00 2.90
333 334 8.169977 AGAGACTATTGTTGAGAGATCAGATC 57.830 38.462 1.64 1.64 0.00 2.75
334 335 7.779326 AGAGACTATTGTTGAGAGATCAGATCA 59.221 37.037 13.14 0.00 0.00 2.92
335 336 7.944061 AGACTATTGTTGAGAGATCAGATCAG 58.056 38.462 13.14 0.00 0.00 2.90
336 337 7.014518 AGACTATTGTTGAGAGATCAGATCAGG 59.985 40.741 13.14 0.00 0.00 3.86
337 338 3.815856 TGTTGAGAGATCAGATCAGGC 57.184 47.619 13.14 1.92 0.00 4.85
363 364 0.756815 GCAGGATGGGGCCTAAAAGG 60.757 60.000 0.84 0.00 36.22 3.11
382 383 3.683802 AGGCAAACAGATTCAGAGGAAG 58.316 45.455 0.00 0.00 36.25 3.46
416 418 2.489938 AGAGCTTTCCGTTGCCATTA 57.510 45.000 0.00 0.00 0.00 1.90
471 473 5.050490 CGAGATCCCGTATGAACTTCATTT 58.950 41.667 9.57 0.00 38.26 2.32
535 537 3.349022 TCGGTGGAAACTGAAGTTGTTT 58.651 40.909 0.00 0.00 39.92 2.83
578 580 1.614903 CCTTCTGGCACAATGCTTCAA 59.385 47.619 0.13 0.00 44.28 2.69
594 597 5.185454 TGCTTCAAACTTCAGAGTTCAGAA 58.815 37.500 0.00 1.00 45.18 3.02
641 644 3.444034 GGTTTATGCCTTTCCCAACTCTC 59.556 47.826 0.00 0.00 0.00 3.20
649 713 4.141937 GCCTTTCCCAACTCTCTTTTTGTT 60.142 41.667 0.00 0.00 0.00 2.83
652 716 6.535150 CCTTTCCCAACTCTCTTTTTGTTTTC 59.465 38.462 0.00 0.00 0.00 2.29
653 717 5.243426 TCCCAACTCTCTTTTTGTTTTCG 57.757 39.130 0.00 0.00 0.00 3.46
654 718 4.944930 TCCCAACTCTCTTTTTGTTTTCGA 59.055 37.500 0.00 0.00 0.00 3.71
655 719 5.065988 TCCCAACTCTCTTTTTGTTTTCGAG 59.934 40.000 0.00 0.00 0.00 4.04
659 723 7.540745 CCAACTCTCTTTTTGTTTTCGAGAAAA 59.459 33.333 6.89 6.89 37.90 2.29
660 724 8.578769 CAACTCTCTTTTTGTTTTCGAGAAAAG 58.421 33.333 10.85 2.57 40.53 2.27
662 726 6.033966 TCTCTTTTTGTTTTCGAGAAAAGCC 58.966 36.000 10.85 2.40 40.53 4.35
665 729 6.871492 TCTTTTTGTTTTCGAGAAAAGCCTTT 59.129 30.769 10.85 0.00 40.53 3.11
676 740 4.657013 AGAAAAGCCTTTCCAACTCCTAG 58.343 43.478 4.13 0.00 41.72 3.02
681 745 3.157881 GCCTTTCCAACTCCTAGCTTTT 58.842 45.455 0.00 0.00 0.00 2.27
710 774 5.721960 TGAGAAGTTCCAACTCCTAGCTAAT 59.278 40.000 0.00 0.00 38.57 1.73
741 805 0.107456 CTGACAGCTCGGCCCATTAT 59.893 55.000 0.00 0.00 0.00 1.28
789 853 1.673665 CAAGAGCCCAGACCACAGC 60.674 63.158 0.00 0.00 0.00 4.40
937 1231 1.481056 CCGTTCCCTTCCACCTGTCT 61.481 60.000 0.00 0.00 0.00 3.41
1263 1557 0.757512 GGTAACTTCCGATCCCTCCC 59.242 60.000 0.00 0.00 0.00 4.30
1333 1628 5.179045 ACCGAGGTTACAATACAGATACG 57.821 43.478 0.00 0.00 0.00 3.06
1381 1676 4.277174 TGACGACTTAACGGGTAACTAACA 59.723 41.667 0.00 0.00 37.61 2.41
1382 1677 4.798574 ACGACTTAACGGGTAACTAACAG 58.201 43.478 0.00 0.00 37.61 3.16
1383 1678 4.518970 ACGACTTAACGGGTAACTAACAGA 59.481 41.667 0.00 0.00 37.61 3.41
1384 1679 5.091431 CGACTTAACGGGTAACTAACAGAG 58.909 45.833 0.00 0.00 0.00 3.35
1465 1760 1.679032 GCACTCTGCCCCTTCGTTTAT 60.679 52.381 0.00 0.00 37.42 1.40
1481 1776 7.096558 CCTTCGTTTATCGCAGTTCTTACTATC 60.097 40.741 0.00 0.00 39.67 2.08
1610 1905 2.417933 CGAGAATTGTTCTTGCTCCTGG 59.582 50.000 0.00 0.00 40.87 4.45
1724 2020 9.836864 TGTTGTATGTTATGAAGCTAGATCAAT 57.163 29.630 0.00 0.00 0.00 2.57
1737 2033 8.659925 AAGCTAGATCAATTTAGTCATGACTG 57.340 34.615 33.76 19.79 42.52 3.51
1807 2103 1.014044 TCGTGAACGCCTGCTCATTC 61.014 55.000 0.00 0.00 39.60 2.67
1834 2130 0.663867 GATTGCATTGCACACACGCA 60.664 50.000 11.66 0.00 38.71 5.24
1845 2141 0.456824 ACACACGCATCGCTGTCTAG 60.457 55.000 0.00 0.00 0.00 2.43
1856 2152 0.798771 GCTGTCTAGCCGTCTGTTCG 60.799 60.000 0.00 0.00 44.33 3.95
1917 2214 4.452825 TGTCGACCACAAAACTTATTGGA 58.547 39.130 14.12 0.00 34.56 3.53
2141 2441 6.334989 TGCATGATTGTGAATTTTCTGATCC 58.665 36.000 0.00 0.00 0.00 3.36
2223 2523 1.412343 GAGATGAAGAGGGAGCAGGAC 59.588 57.143 0.00 0.00 0.00 3.85
2275 2575 6.721318 ACATGGACATAACTGGATAACAAGT 58.279 36.000 0.00 0.00 0.00 3.16
2297 2598 0.035056 CCAGATTCCCCCAGTGTGTC 60.035 60.000 0.00 0.00 0.00 3.67
2313 2614 1.532868 GTGTCTGTAACTTGCAGCCTG 59.467 52.381 2.14 0.00 34.21 4.85
2411 2717 2.281761 CCGCATGAGTATGGCCCC 60.282 66.667 0.00 0.00 34.79 5.80
2541 2878 6.472016 TGAAAATGTAGATACTGCCACAGAA 58.528 36.000 0.78 0.00 35.18 3.02
2566 2903 8.764524 ACTGTCAAGACTGAAAATGTAGATAC 57.235 34.615 13.06 0.00 31.88 2.24
2572 2909 8.651588 CAAGACTGAAAATGTAGATACTGACAC 58.348 37.037 0.00 0.00 0.00 3.67
2576 2913 8.031864 ACTGAAAATGTAGATACTGACACAGAG 58.968 37.037 5.76 0.00 35.18 3.35
2577 2914 7.896811 TGAAAATGTAGATACTGACACAGAGT 58.103 34.615 5.76 0.00 35.18 3.24
2581 2918 6.255596 TGTAGATACTGACACAGAGTTGTC 57.744 41.667 5.76 0.00 45.34 3.18
2600 2937 3.925913 TGTCAAGAAAACAAAGCAACTGC 59.074 39.130 0.00 0.00 42.49 4.40
2717 3054 1.830477 CCTAGAAGAGCCTTGCAGAGT 59.170 52.381 0.00 0.00 0.00 3.24
2750 3087 3.971150 AGCGCTATCTTATATCATCGGC 58.029 45.455 8.99 0.00 0.00 5.54
2822 3159 3.369787 CCATGCTCACATCAGTTGGAGTA 60.370 47.826 0.00 0.00 32.87 2.59
2912 3249 4.216687 AGCGCTGTCCAGACTACTATTATC 59.783 45.833 10.39 0.00 0.00 1.75
3052 3389 7.765360 AGATGTGAATTTGCTTCTTTGAACAAA 59.235 29.630 0.17 0.17 36.53 2.83
3217 3556 5.658468 TGTAAGCTGAACTGAGATGAGATG 58.342 41.667 0.00 0.00 0.00 2.90
3218 3557 4.822685 AAGCTGAACTGAGATGAGATGT 57.177 40.909 0.00 0.00 0.00 3.06
3219 3558 4.389890 AGCTGAACTGAGATGAGATGTC 57.610 45.455 0.00 0.00 0.00 3.06
3220 3559 3.768215 AGCTGAACTGAGATGAGATGTCA 59.232 43.478 0.00 0.00 37.02 3.58
3221 3560 4.222366 AGCTGAACTGAGATGAGATGTCAA 59.778 41.667 0.00 0.00 35.88 3.18
3222 3561 4.567558 GCTGAACTGAGATGAGATGTCAAG 59.432 45.833 0.00 0.00 35.88 3.02
3223 3562 5.722263 CTGAACTGAGATGAGATGTCAAGT 58.278 41.667 0.00 0.00 35.88 3.16
3328 3709 5.368523 TGGGACTCTATGGGTAAACTTATGG 59.631 44.000 0.00 0.00 0.00 2.74
3470 3859 2.292521 ACTATCAACCCAGCCTGAGAGA 60.293 50.000 0.00 0.00 35.06 3.10
3471 3860 1.202330 ATCAACCCAGCCTGAGAGAG 58.798 55.000 0.00 0.00 0.00 3.20
3783 4175 3.053842 AGACCGATGGTTCTCTACTGGTA 60.054 47.826 0.00 0.00 35.25 3.25
3906 4298 1.135024 CCAAAATCTGGCACCATTCCG 60.135 52.381 0.00 0.00 38.76 4.30
3907 4299 1.135024 CAAAATCTGGCACCATTCCGG 60.135 52.381 0.00 0.00 42.50 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 0.524392 CCAGTTAGCACTCTCGCGAG 60.524 60.000 30.03 30.03 43.10 5.03
127 128 1.241990 ACCAGTTAGCACTCTCGCGA 61.242 55.000 9.26 9.26 36.85 5.87
128 129 0.450583 TACCAGTTAGCACTCTCGCG 59.549 55.000 0.00 0.00 36.85 5.87
129 130 2.464865 CATACCAGTTAGCACTCTCGC 58.535 52.381 0.00 0.00 0.00 5.03
130 131 2.099921 AGCATACCAGTTAGCACTCTCG 59.900 50.000 0.00 0.00 0.00 4.04
131 132 3.118956 ACAGCATACCAGTTAGCACTCTC 60.119 47.826 0.00 0.00 0.00 3.20
132 133 2.834549 ACAGCATACCAGTTAGCACTCT 59.165 45.455 0.00 0.00 0.00 3.24
133 134 3.252974 ACAGCATACCAGTTAGCACTC 57.747 47.619 0.00 0.00 0.00 3.51
134 135 4.223032 AGTTACAGCATACCAGTTAGCACT 59.777 41.667 0.00 0.00 0.00 4.40
135 136 4.504858 AGTTACAGCATACCAGTTAGCAC 58.495 43.478 0.00 0.00 0.00 4.40
136 137 4.466370 AGAGTTACAGCATACCAGTTAGCA 59.534 41.667 0.00 0.00 0.00 3.49
137 138 5.012328 AGAGTTACAGCATACCAGTTAGC 57.988 43.478 0.00 0.00 0.00 3.09
140 141 4.286032 TGGAAGAGTTACAGCATACCAGTT 59.714 41.667 0.00 0.00 0.00 3.16
145 146 3.432326 CCCCTGGAAGAGTTACAGCATAC 60.432 52.174 0.00 0.00 34.07 2.39
150 151 1.555533 GACCCCCTGGAAGAGTTACAG 59.444 57.143 0.00 0.00 34.07 2.74
188 189 1.891933 TGCCTTCAGGGGTGATGATA 58.108 50.000 0.00 0.00 35.18 2.15
278 279 2.110901 ACTGCTCTGCTTCCTGAATG 57.889 50.000 0.00 0.00 0.00 2.67
329 330 3.013327 TGCCTGCCTGCCTGATCT 61.013 61.111 0.00 0.00 0.00 2.75
330 331 2.516460 CTGCCTGCCTGCCTGATC 60.516 66.667 0.00 0.00 0.00 2.92
331 332 4.124943 CCTGCCTGCCTGCCTGAT 62.125 66.667 0.00 0.00 0.00 2.90
333 334 4.124943 ATCCTGCCTGCCTGCCTG 62.125 66.667 0.00 0.00 0.00 4.85
334 335 4.124943 CATCCTGCCTGCCTGCCT 62.125 66.667 0.00 0.00 0.00 4.75
337 338 4.517934 CCCCATCCTGCCTGCCTG 62.518 72.222 0.00 0.00 0.00 4.85
363 364 2.751806 CCCTTCCTCTGAATCTGTTTGC 59.248 50.000 0.00 0.00 0.00 3.68
367 368 5.131809 CCTTATTCCCTTCCTCTGAATCTGT 59.868 44.000 0.00 0.00 31.55 3.41
382 383 5.105310 GGAAAGCTCTTTTTCCCTTATTCCC 60.105 44.000 3.83 0.00 46.78 3.97
471 473 1.729517 CACGACGCACATAATTGACCA 59.270 47.619 0.00 0.00 0.00 4.02
559 561 3.054878 GTTTGAAGCATTGTGCCAGAAG 58.945 45.455 0.00 0.00 46.52 2.85
570 572 5.371526 TCTGAACTCTGAAGTTTGAAGCAT 58.628 37.500 0.00 0.00 45.80 3.79
594 597 5.122396 GGAACAGAGAACAAATAGCGAACAT 59.878 40.000 0.00 0.00 0.00 2.71
641 644 6.647212 AAGGCTTTTCTCGAAAACAAAAAG 57.353 33.333 0.00 0.00 40.18 2.27
649 713 3.951680 AGTTGGAAAGGCTTTTCTCGAAA 59.048 39.130 18.72 2.47 41.92 3.46
652 716 2.226674 GGAGTTGGAAAGGCTTTTCTCG 59.773 50.000 18.72 0.00 41.92 4.04
653 717 3.491342 AGGAGTTGGAAAGGCTTTTCTC 58.509 45.455 18.72 18.36 41.92 2.87
654 718 3.602205 AGGAGTTGGAAAGGCTTTTCT 57.398 42.857 18.72 12.27 41.92 2.52
655 719 3.191581 GCTAGGAGTTGGAAAGGCTTTTC 59.808 47.826 14.66 13.03 41.59 2.29
659 723 1.662686 AGCTAGGAGTTGGAAAGGCT 58.337 50.000 0.00 0.00 0.00 4.58
660 724 2.498644 AAGCTAGGAGTTGGAAAGGC 57.501 50.000 0.00 0.00 0.00 4.35
683 747 5.063880 GCTAGGAGTTGGAACTTCTCAAAA 58.936 41.667 3.46 0.00 40.97 2.44
684 748 4.348168 AGCTAGGAGTTGGAACTTCTCAAA 59.652 41.667 3.46 0.00 40.97 2.69
685 749 3.904339 AGCTAGGAGTTGGAACTTCTCAA 59.096 43.478 3.46 0.00 40.97 3.02
686 750 3.511477 AGCTAGGAGTTGGAACTTCTCA 58.489 45.455 3.46 0.00 40.97 3.27
688 752 6.898521 ACTATTAGCTAGGAGTTGGAACTTCT 59.101 38.462 5.65 5.65 46.48 2.85
689 753 6.981559 CACTATTAGCTAGGAGTTGGAACTTC 59.018 42.308 6.84 0.00 39.88 3.01
690 754 6.127026 CCACTATTAGCTAGGAGTTGGAACTT 60.127 42.308 6.84 0.00 39.88 2.66
691 755 5.364157 CCACTATTAGCTAGGAGTTGGAACT 59.636 44.000 6.84 0.00 43.16 3.01
692 756 5.363005 TCCACTATTAGCTAGGAGTTGGAAC 59.637 44.000 16.85 0.00 30.09 3.62
693 757 5.363005 GTCCACTATTAGCTAGGAGTTGGAA 59.637 44.000 18.82 9.26 33.18 3.53
694 758 4.894114 GTCCACTATTAGCTAGGAGTTGGA 59.106 45.833 16.03 16.03 30.37 3.53
695 759 4.039366 GGTCCACTATTAGCTAGGAGTTGG 59.961 50.000 6.84 10.88 0.00 3.77
696 760 4.261656 CGGTCCACTATTAGCTAGGAGTTG 60.262 50.000 6.84 4.87 0.00 3.16
697 761 3.890147 CGGTCCACTATTAGCTAGGAGTT 59.110 47.826 6.84 0.00 0.00 3.01
698 762 3.137913 TCGGTCCACTATTAGCTAGGAGT 59.862 47.826 0.00 1.85 0.00 3.85
699 763 3.502979 GTCGGTCCACTATTAGCTAGGAG 59.497 52.174 0.00 1.25 0.00 3.69
700 764 3.484407 GTCGGTCCACTATTAGCTAGGA 58.516 50.000 0.00 0.00 0.00 2.94
710 774 1.248785 GCTGTCAGGTCGGTCCACTA 61.249 60.000 1.14 0.00 39.02 2.74
741 805 1.094785 GCCTTCGCTCATTGGCTTAA 58.905 50.000 0.00 0.00 41.92 1.85
937 1231 2.568612 CGACAAGCGAGAGAGGCA 59.431 61.111 0.00 0.00 44.57 4.75
1179 1473 4.194720 GCGGTGAGGACGAGCGAT 62.195 66.667 0.00 0.00 36.43 4.58
1263 1557 1.074752 GAGAAGCAAAGCAGAGGACG 58.925 55.000 0.00 0.00 0.00 4.79
1333 1628 1.778591 CGCGTGTTGACAAAACAATCC 59.221 47.619 9.17 0.00 32.36 3.01
1371 1666 7.629130 CGATCTGTACTACTCTGTTAGTTACC 58.371 42.308 0.00 0.00 39.80 2.85
1381 1676 0.582482 CGCGCGATCTGTACTACTCT 59.418 55.000 28.94 0.00 0.00 3.24
1382 1677 0.304098 ACGCGCGATCTGTACTACTC 59.696 55.000 39.36 0.00 0.00 2.59
1383 1678 1.526041 CTACGCGCGATCTGTACTACT 59.474 52.381 39.36 12.01 0.00 2.57
1384 1679 1.260033 ACTACGCGCGATCTGTACTAC 59.740 52.381 39.36 0.00 0.00 2.73
1465 1760 1.667212 TCGCGATAGTAAGAACTGCGA 59.333 47.619 3.71 1.96 46.29 5.10
1481 1776 1.885560 TCTCCCTAATCTCTCTCGCG 58.114 55.000 0.00 0.00 0.00 5.87
1571 1866 5.114785 TCTCGCTTGCTAGCTTAATCTAG 57.885 43.478 17.23 8.68 45.51 2.43
1596 1891 0.836606 TGACACCAGGAGCAAGAACA 59.163 50.000 0.00 0.00 0.00 3.18
1610 1905 7.667043 TTACAGTTGGACATAATTCTGACAC 57.333 36.000 0.00 0.00 0.00 3.67
1737 2033 1.750206 TGTGCCATGGTGAATACATGC 59.250 47.619 14.67 0.00 43.29 4.06
1741 2037 2.128771 ACCTGTGCCATGGTGAATAC 57.871 50.000 14.67 6.00 34.90 1.89
1765 2061 5.112220 TGTAACAAAGCAAGATTCAGCAG 57.888 39.130 4.31 0.00 0.00 4.24
1845 2141 2.091744 GCTAAAGTAACGAACAGACGGC 59.908 50.000 0.00 0.00 37.61 5.68
1856 2152 4.515567 AGTTGCAGTTGAGGCTAAAGTAAC 59.484 41.667 0.00 0.00 0.00 2.50
1917 2214 6.156949 TGTCTATCTCATGGGCTAACTTTTCT 59.843 38.462 0.00 0.00 0.00 2.52
2223 2523 0.877649 CTGGGACGGCAATGATCTCG 60.878 60.000 0.00 0.00 0.00 4.04
2275 2575 1.633432 CACACTGGGGGAATCTGGTAA 59.367 52.381 0.00 0.00 0.00 2.85
2297 2598 1.160137 GGTCAGGCTGCAAGTTACAG 58.840 55.000 10.34 0.00 38.22 2.74
2313 2614 4.823790 ACAAGTCAAAATACCAACGGTC 57.176 40.909 0.00 0.00 37.09 4.79
2533 2870 1.869767 CAGTCTTGACAGTTCTGTGGC 59.130 52.381 10.29 0.00 0.00 5.01
2541 2878 8.589338 AGTATCTACATTTTCAGTCTTGACAGT 58.411 33.333 3.49 0.00 31.71 3.55
2572 2909 5.401550 TGCTTTGTTTTCTTGACAACTCTG 58.598 37.500 2.10 0.00 36.79 3.35
2576 2913 5.668621 GCAGTTGCTTTGTTTTCTTGACAAC 60.669 40.000 0.00 0.00 36.79 3.32
2577 2914 4.388469 GCAGTTGCTTTGTTTTCTTGACAA 59.612 37.500 0.00 0.00 38.21 3.18
2581 2918 4.152045 TGTTGCAGTTGCTTTGTTTTCTTG 59.848 37.500 5.62 0.00 42.66 3.02
2588 2925 5.174395 TGTTAATTGTTGCAGTTGCTTTGT 58.826 33.333 5.62 0.00 42.66 2.83
2600 2937 6.527722 ACGCAATATGCTCTTGTTAATTGTTG 59.472 34.615 0.43 0.00 42.25 3.33
2717 3054 7.962964 ATAAGATAGCGCTATTGTTAAAGCA 57.037 32.000 29.53 11.97 38.70 3.91
2912 3249 2.253452 GCAGAAGCAACAGCACCG 59.747 61.111 0.00 0.00 41.58 4.94
3217 3556 5.685841 TGCGCTAATTTCACTTTACTTGAC 58.314 37.500 9.73 0.00 0.00 3.18
3218 3557 5.933187 TGCGCTAATTTCACTTTACTTGA 57.067 34.783 9.73 0.00 0.00 3.02
3219 3558 6.984740 TTTGCGCTAATTTCACTTTACTTG 57.015 33.333 9.73 0.00 0.00 3.16
3220 3559 7.200455 ACTTTTGCGCTAATTTCACTTTACTT 58.800 30.769 9.73 0.00 0.00 2.24
3221 3560 6.735130 ACTTTTGCGCTAATTTCACTTTACT 58.265 32.000 9.73 0.00 0.00 2.24
3222 3561 6.087687 GGACTTTTGCGCTAATTTCACTTTAC 59.912 38.462 9.73 0.00 0.00 2.01
3223 3562 6.146898 GGACTTTTGCGCTAATTTCACTTTA 58.853 36.000 9.73 0.00 0.00 1.85
3328 3709 6.867293 CCTAGTTGTGGTAGAACAGTAACTTC 59.133 42.308 0.00 0.00 33.60 3.01
3411 3798 9.725019 AAATCATCGTAAGGCATATTCTATGAA 57.275 29.630 0.00 0.00 38.47 2.57
3531 3920 1.808945 CTGAGACGCCTTGAGCAATTT 59.191 47.619 0.00 0.00 44.04 1.82
3673 4063 1.750930 CACTCCTCGATGGGGGATG 59.249 63.158 0.00 0.00 41.89 3.51
3906 4298 2.358898 TGAAGAGCTGAAAAGTGCAACC 59.641 45.455 0.00 0.00 37.80 3.77
3907 4299 3.313526 TCTGAAGAGCTGAAAAGTGCAAC 59.686 43.478 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.