Multiple sequence alignment - TraesCS3A01G171800

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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 TraesCS3A01G171800 chr3A 100.000 2525 0 0 1 2525 186706977 186709501 0.000000e+00 4663.0
1 TraesCS3A01G171800 chr3A 99.830 589 1 0 1937 2525 457934604 457934016 0.000000e+00 1083.0
2 TraesCS3A01G171800 chr3A 98.673 603 6 1 1925 2525 7331376 7330774 0.000000e+00 1068.0
3 TraesCS3A01G171800 chr3A 81.429 140 19 7 4 140 599980186 599980051 9.550000e-20 108.0
4 TraesCS3A01G171800 chr3B 88.123 1987 163 36 1 1937 237097115 237099078 0.000000e+00 2294.0
5 TraesCS3A01G171800 chr3B 78.505 107 21 2 56 161 521113974 521114079 4.510000e-08 69.4
6 TraesCS3A01G171800 chr3D 97.788 1311 24 2 632 1937 160524507 160525817 0.000000e+00 2255.0
7 TraesCS3A01G171800 chr3D 76.552 145 25 8 355 494 471101369 471101509 1.250000e-08 71.3
8 TraesCS3A01G171800 chr4A 99.831 591 1 0 1935 2525 607376176 607376766 0.000000e+00 1086.0
9 TraesCS3A01G171800 chr7A 99.830 589 1 0 1937 2525 84756782 84756194 0.000000e+00 1083.0
10 TraesCS3A01G171800 chr7A 99.661 590 2 0 1936 2525 332823277 332823866 0.000000e+00 1079.0
11 TraesCS3A01G171800 chr7A 79.755 163 27 6 3 163 576864353 576864195 2.050000e-21 113.0
12 TraesCS3A01G171800 chr7A 79.755 163 28 5 3 163 658203551 658203710 2.050000e-21 113.0
13 TraesCS3A01G171800 chr7B 99.661 590 2 0 1936 2525 412900894 412900305 0.000000e+00 1079.0
14 TraesCS3A01G171800 chr7B 81.818 143 19 6 1 140 672818016 672818154 2.050000e-21 113.0
15 TraesCS3A01G171800 chr2A 99.661 590 2 0 1936 2525 125629644 125630233 0.000000e+00 1079.0
16 TraesCS3A01G171800 chr2A 99.660 589 2 0 1937 2525 608903984 608903396 0.000000e+00 1077.0
17 TraesCS3A01G171800 chr6A 99.660 589 2 0 1937 2525 454430026 454429438 0.000000e+00 1077.0
18 TraesCS3A01G171800 chr6A 87.912 91 10 1 3 93 56068911 56068822 3.440000e-19 106.0
19 TraesCS3A01G171800 chr7D 82.775 209 23 8 339 540 556323354 556323556 9.280000e-40 174.0
20 TraesCS3A01G171800 chr2D 78.448 232 37 9 1 232 11510845 11511063 3.390000e-29 139.0
21 TraesCS3A01G171800 chr2D 79.130 115 15 6 1 113 524331969 524331862 1.250000e-08 71.3
22 TraesCS3A01G171800 chr2B 79.365 189 20 16 341 520 104801626 104801448 5.710000e-22 115.0
23 TraesCS3A01G171800 chr2B 82.653 98 15 2 6 102 108501647 108501551 4.480000e-13 86.1
24 TraesCS3A01G171800 chr6B 76.415 212 48 2 1 211 716616226 716616016 2.050000e-21 113.0
25 TraesCS3A01G171800 chr6D 78.481 158 26 8 339 495 449180129 449180279 2.070000e-16 97.1
26 TraesCS3A01G171800 chr1D 74.790 238 49 8 3 232 294215228 294214994 2.070000e-16 97.1
27 TraesCS3A01G171800 chr5A 92.500 40 3 0 355 394 317983767 317983806 9.760000e-05 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 TraesCS3A01G171800 chr3A 186706977 186709501 2524 False 4663 4663 100.000 1 2525 1 chr3A.!!$F1 2524
1 TraesCS3A01G171800 chr3A 457934016 457934604 588 True 1083 1083 99.830 1937 2525 1 chr3A.!!$R2 588
2 TraesCS3A01G171800 chr3A 7330774 7331376 602 True 1068 1068 98.673 1925 2525 1 chr3A.!!$R1 600
3 TraesCS3A01G171800 chr3B 237097115 237099078 1963 False 2294 2294 88.123 1 1937 1 chr3B.!!$F1 1936
4 TraesCS3A01G171800 chr3D 160524507 160525817 1310 False 2255 2255 97.788 632 1937 1 chr3D.!!$F1 1305
5 TraesCS3A01G171800 chr4A 607376176 607376766 590 False 1086 1086 99.831 1935 2525 1 chr4A.!!$F1 590
6 TraesCS3A01G171800 chr7A 84756194 84756782 588 True 1083 1083 99.830 1937 2525 1 chr7A.!!$R1 588
7 TraesCS3A01G171800 chr7A 332823277 332823866 589 False 1079 1079 99.661 1936 2525 1 chr7A.!!$F1 589
8 TraesCS3A01G171800 chr7B 412900305 412900894 589 True 1079 1079 99.661 1936 2525 1 chr7B.!!$R1 589
9 TraesCS3A01G171800 chr2A 125629644 125630233 589 False 1079 1079 99.661 1936 2525 1 chr2A.!!$F1 589
10 TraesCS3A01G171800 chr2A 608903396 608903984 588 True 1077 1077 99.660 1937 2525 1 chr2A.!!$R1 588
11 TraesCS3A01G171800 chr6A 454429438 454430026 588 True 1077 1077 99.660 1937 2525 1 chr6A.!!$R2 588

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
612 636 0.036858 GAACCACCTCCTCAGCTGAC 60.037 60.0 13.74 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1588 0.032678 GCGTGTCCGATCCATGAGAT 59.967 55.0 0.0 0.0 38.17 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
28 29 1.372683 CACCTCCACACACCCTCTG 59.627 63.158 0.00 0.00 0.00 3.35
33 34 1.836166 CTCCACACACCCTCTGATGAT 59.164 52.381 0.00 0.00 0.00 2.45
35 36 1.376543 CACACACCCTCTGATGATGC 58.623 55.000 0.00 0.00 0.00 3.91
54 55 1.723542 GCTAGACGCATCATCGGAATG 59.276 52.381 0.00 0.00 38.92 2.67
59 60 2.270986 GCATCATCGGAATGGGGGC 61.271 63.158 0.00 0.00 33.42 5.80
63 64 1.302832 CATCGGAATGGGGGCTAGC 60.303 63.158 6.04 6.04 0.00 3.42
67 68 2.517919 GAATGGGGGCTAGCCAGG 59.482 66.667 34.09 0.00 37.98 4.45
73 74 2.001269 GGGGCTAGCCAGGGAGAAA 61.001 63.158 34.09 0.00 37.98 2.52
74 75 1.356494 GGGGCTAGCCAGGGAGAAAT 61.356 60.000 34.09 0.00 37.98 2.17
84 85 5.143369 AGCCAGGGAGAAATTTATTCCATC 58.857 41.667 12.70 1.24 32.50 3.51
90 91 7.776969 CAGGGAGAAATTTATTCCATCTTCAGA 59.223 37.037 12.70 0.00 32.50 3.27
91 92 7.997803 AGGGAGAAATTTATTCCATCTTCAGAG 59.002 37.037 12.70 0.00 32.50 3.35
93 94 9.054922 GGAGAAATTTATTCCATCTTCAGAGAG 57.945 37.037 13.67 0.00 34.85 3.20
96 97 2.906691 ATTCCATCTTCAGAGAGCCG 57.093 50.000 0.00 0.00 34.85 5.52
97 98 1.561643 TTCCATCTTCAGAGAGCCGT 58.438 50.000 0.00 0.00 34.85 5.68
100 101 1.411977 CCATCTTCAGAGAGCCGTCAT 59.588 52.381 0.00 0.00 34.85 3.06
106 107 2.055042 AGAGAGCCGTCATCGCCTT 61.055 57.895 0.00 0.00 35.54 4.35
117 118 3.067106 GTCATCGCCTTGTCTTCTCAAA 58.933 45.455 0.00 0.00 0.00 2.69
118 119 3.686726 GTCATCGCCTTGTCTTCTCAAAT 59.313 43.478 0.00 0.00 0.00 2.32
127 128 5.641209 CCTTGTCTTCTCAAATAGGACACAG 59.359 44.000 0.00 0.00 36.78 3.66
144 145 5.940470 GGACACAGATCCTAAACAAACTCAT 59.060 40.000 0.00 0.00 35.68 2.90
178 179 0.909610 ACGGAGCAAGATTCCTCCCA 60.910 55.000 0.00 0.00 43.78 4.37
181 182 0.915364 GAGCAAGATTCCTCCCACCT 59.085 55.000 0.00 0.00 0.00 4.00
185 186 1.064166 CAAGATTCCTCCCACCTGCAT 60.064 52.381 0.00 0.00 0.00 3.96
195 196 3.675790 ACCTGCATGGGCCATGGT 61.676 61.111 39.54 29.40 41.64 3.55
196 197 2.836360 CCTGCATGGGCCATGGTC 60.836 66.667 39.54 27.31 41.64 4.02
231 232 4.547367 CCCGGGGCCATCGAAGAC 62.547 72.222 14.71 0.00 42.51 3.01
232 233 3.781307 CCGGGGCCATCGAAGACA 61.781 66.667 17.64 0.00 42.51 3.41
233 234 2.505982 CGGGGCCATCGAAGACAT 59.494 61.111 4.39 0.00 42.51 3.06
235 236 2.189499 GGGGCCATCGAAGACATGC 61.189 63.158 4.39 0.00 42.51 4.06
236 237 2.537560 GGGCCATCGAAGACATGCG 61.538 63.158 4.39 0.00 42.51 4.73
237 238 1.521457 GGCCATCGAAGACATGCGA 60.521 57.895 0.00 0.00 42.51 5.10
238 239 1.638467 GCCATCGAAGACATGCGAC 59.362 57.895 0.00 0.00 42.51 5.19
241 242 1.153842 ATCGAAGACATGCGACGCA 60.154 52.632 26.68 26.68 42.51 5.24
242 243 0.528466 ATCGAAGACATGCGACGCAT 60.528 50.000 28.84 28.84 45.57 4.73
250 251 4.758251 TGCGACGCATGTGGGAGG 62.758 66.667 20.50 0.00 31.71 4.30
260 261 4.832608 GTGGGAGGCGGCCGTAAG 62.833 72.222 28.70 0.00 0.00 2.34
280 298 4.917906 AGCCTTTTCTTGTAGATGAGGT 57.082 40.909 0.00 0.00 32.43 3.85
284 302 5.551233 CCTTTTCTTGTAGATGAGGTGACA 58.449 41.667 0.00 0.00 0.00 3.58
285 303 5.641209 CCTTTTCTTGTAGATGAGGTGACAG 59.359 44.000 0.00 0.00 0.00 3.51
302 320 4.570663 GCTACGTGAGGCGGCGAT 62.571 66.667 12.98 0.00 46.52 4.58
304 322 1.357690 CTACGTGAGGCGGCGATTA 59.642 57.895 12.98 0.00 46.52 1.75
308 326 1.004277 CGTGAGGCGGCGATTATCTC 61.004 60.000 12.98 9.21 36.85 2.75
320 339 3.579709 CGATTATCTCGCTGGCATAAGT 58.420 45.455 0.00 0.00 41.14 2.24
327 346 2.885266 CTCGCTGGCATAAGTAGGTCTA 59.115 50.000 0.00 0.00 0.00 2.59
339 358 4.167652 AGTAGGTCTAGCTGGACGTATT 57.832 45.455 28.04 23.07 38.34 1.89
341 360 2.736347 AGGTCTAGCTGGACGTATTGT 58.264 47.619 21.97 1.50 37.12 2.71
342 361 3.097614 AGGTCTAGCTGGACGTATTGTT 58.902 45.455 21.97 0.94 37.12 2.83
343 362 3.130693 AGGTCTAGCTGGACGTATTGTTC 59.869 47.826 21.97 7.12 37.12 3.18
344 363 3.130693 GGTCTAGCTGGACGTATTGTTCT 59.869 47.826 22.19 0.00 37.12 3.01
345 364 4.337555 GGTCTAGCTGGACGTATTGTTCTA 59.662 45.833 22.19 0.00 37.12 2.10
346 365 5.009811 GGTCTAGCTGGACGTATTGTTCTAT 59.990 44.000 22.19 0.00 37.12 1.98
347 366 5.915758 GTCTAGCTGGACGTATTGTTCTATG 59.084 44.000 14.93 0.00 0.00 2.23
348 367 5.826208 TCTAGCTGGACGTATTGTTCTATGA 59.174 40.000 0.00 0.00 0.00 2.15
385 404 5.833131 AGAGGATGGCAGTTTTAAAGTTCAA 59.167 36.000 0.00 0.00 0.00 2.69
387 406 5.362430 AGGATGGCAGTTTTAAAGTTCAACA 59.638 36.000 0.00 0.00 0.00 3.33
397 417 9.986833 AGTTTTAAAGTTCAACATTGCAATTTC 57.013 25.926 9.83 0.00 0.00 2.17
406 426 9.372541 GTTCAACATTGCAATTTCATTTTGTAG 57.627 29.630 9.83 0.00 0.00 2.74
409 429 9.719279 CAACATTGCAATTTCATTTTGTAGTTT 57.281 25.926 9.83 0.00 0.00 2.66
415 435 9.900710 TGCAATTTCATTTTGTAGTTTATACGT 57.099 25.926 0.00 0.00 0.00 3.57
483 504 8.525290 AGATGGCAGTTTTTATAAAGTAGCAT 57.475 30.769 12.73 0.00 0.00 3.79
534 556 4.016444 GGCAATTAGGGTCTTGTTGATGA 58.984 43.478 0.00 0.00 0.00 2.92
541 563 7.681939 TTAGGGTCTTGTTGATGACATTTAC 57.318 36.000 0.00 0.00 38.26 2.01
543 565 6.068010 AGGGTCTTGTTGATGACATTTACAA 58.932 36.000 12.79 12.79 38.26 2.41
566 588 5.995565 AAAAGTTAAATGGACCTAAGCCC 57.004 39.130 0.00 0.00 0.00 5.19
567 589 4.668138 AAGTTAAATGGACCTAAGCCCA 57.332 40.909 0.00 0.00 36.79 5.36
568 590 4.881157 AGTTAAATGGACCTAAGCCCAT 57.119 40.909 0.00 0.00 44.52 4.00
570 592 4.229582 AGTTAAATGGACCTAAGCCCATGA 59.770 41.667 0.00 0.00 41.98 3.07
571 593 3.979501 AAATGGACCTAAGCCCATGAT 57.020 42.857 0.00 0.00 41.98 2.45
572 594 6.102615 AGTTAAATGGACCTAAGCCCATGATA 59.897 38.462 0.00 0.00 41.98 2.15
573 595 5.605540 AAATGGACCTAAGCCCATGATAT 57.394 39.130 0.00 0.00 41.98 1.63
577 601 4.536090 TGGACCTAAGCCCATGATATTAGG 59.464 45.833 19.82 19.82 46.43 2.69
580 604 5.170198 ACCTAAGCCCATGATATTAGGGAA 58.830 41.667 22.84 0.00 45.66 3.97
584 608 4.251169 AGCCCATGATATTAGGGAAGGAA 58.749 43.478 11.14 0.00 45.80 3.36
585 609 4.860278 AGCCCATGATATTAGGGAAGGAAT 59.140 41.667 11.14 0.00 45.80 3.01
589 613 6.660949 CCCATGATATTAGGGAAGGAATGAAC 59.339 42.308 0.00 0.00 45.80 3.18
604 628 1.371558 GAACAGCGAACCACCTCCT 59.628 57.895 0.00 0.00 0.00 3.69
606 630 1.407656 AACAGCGAACCACCTCCTCA 61.408 55.000 0.00 0.00 0.00 3.86
607 631 1.079543 CAGCGAACCACCTCCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
608 632 2.435059 GCGAACCACCTCCTCAGC 60.435 66.667 0.00 0.00 0.00 4.26
609 633 2.948720 GCGAACCACCTCCTCAGCT 61.949 63.158 0.00 0.00 0.00 4.24
610 634 1.079543 CGAACCACCTCCTCAGCTG 60.080 63.158 7.63 7.63 0.00 4.24
612 636 0.036858 GAACCACCTCCTCAGCTGAC 60.037 60.000 13.74 0.00 0.00 3.51
614 638 0.546267 ACCACCTCCTCAGCTGACAT 60.546 55.000 13.74 0.00 0.00 3.06
615 639 0.107800 CCACCTCCTCAGCTGACATG 60.108 60.000 13.74 3.03 0.00 3.21
616 640 0.743701 CACCTCCTCAGCTGACATGC 60.744 60.000 13.74 0.00 0.00 4.06
617 641 1.153208 CCTCCTCAGCTGACATGCC 60.153 63.158 13.74 0.00 0.00 4.40
618 642 1.153208 CTCCTCAGCTGACATGCCC 60.153 63.158 13.74 0.00 0.00 5.36
619 643 2.124403 CCTCAGCTGACATGCCCC 60.124 66.667 13.74 0.00 0.00 5.80
621 645 1.340399 CCTCAGCTGACATGCCCCTA 61.340 60.000 13.74 0.00 0.00 3.53
624 648 2.369860 CTCAGCTGACATGCCCCTATTA 59.630 50.000 13.74 0.00 0.00 0.98
625 649 2.369860 TCAGCTGACATGCCCCTATTAG 59.630 50.000 13.74 0.00 0.00 1.73
626 650 1.072965 AGCTGACATGCCCCTATTAGC 59.927 52.381 0.00 0.00 0.00 3.09
627 651 1.072965 GCTGACATGCCCCTATTAGCT 59.927 52.381 0.00 0.00 0.00 3.32
629 653 3.406764 CTGACATGCCCCTATTAGCTTC 58.593 50.000 0.00 0.00 0.00 3.86
653 680 8.439993 TCCAAAAAGTAATTAAAAGGCAAACC 57.560 30.769 0.00 0.00 0.00 3.27
1545 1588 9.987726 ATCTAATCTCATATAGGTCACATCTCA 57.012 33.333 0.00 0.00 0.00 3.27
1682 1732 8.827177 TTTATGTTCGTCTCATCTTGTTTACT 57.173 30.769 0.00 0.00 0.00 2.24
1758 1808 5.064707 TGTTTCTAAATTCTGATACCGCTGC 59.935 40.000 0.00 0.00 0.00 5.25
1774 1824 3.486708 CCGCTGCTATTTTCGTGCATTTA 60.487 43.478 0.00 0.00 36.07 1.40
1820 1871 2.158460 GGATAAAAGGGGCCACATAGCT 60.158 50.000 8.31 0.00 0.00 3.32
1875 1926 3.260740 CAACAAAATGCAACACCACACT 58.739 40.909 0.00 0.00 0.00 3.55
1888 1940 5.818678 ACACCACACTATTTTCCTAGACA 57.181 39.130 0.00 0.00 0.00 3.41
1911 1963 1.959710 TGCATCACCCCACCTAACTA 58.040 50.000 0.00 0.00 0.00 2.24
2406 2460 4.279671 GGGACACACATTCCACACAATAAA 59.720 41.667 0.00 0.00 34.45 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.288091 CGTCTAGCATCATCAGAGGGTG 60.288 54.545 0.00 0.00 36.85 4.61
21 22 1.959985 CGTCTAGCATCATCAGAGGGT 59.040 52.381 0.00 0.00 39.80 4.34
35 36 2.332104 CCATTCCGATGATGCGTCTAG 58.668 52.381 7.58 0.00 35.16 2.43
47 48 3.168528 GGCTAGCCCCCATTCCGA 61.169 66.667 24.19 0.00 0.00 4.55
48 49 3.482232 CTGGCTAGCCCCCATTCCG 62.482 68.421 30.81 5.30 34.56 4.30
54 55 4.499116 TCTCCCTGGCTAGCCCCC 62.499 72.222 30.81 6.92 34.56 5.40
59 60 5.694995 TGGAATAAATTTCTCCCTGGCTAG 58.305 41.667 13.92 0.00 0.00 3.42
63 64 6.835488 TGAAGATGGAATAAATTTCTCCCTGG 59.165 38.462 13.92 0.00 0.00 4.45
67 68 8.970859 TCTCTGAAGATGGAATAAATTTCTCC 57.029 34.615 10.89 10.89 0.00 3.71
73 74 5.163258 ACGGCTCTCTGAAGATGGAATAAAT 60.163 40.000 0.00 0.00 0.00 1.40
74 75 4.162320 ACGGCTCTCTGAAGATGGAATAAA 59.838 41.667 0.00 0.00 0.00 1.40
84 85 0.869454 GCGATGACGGCTCTCTGAAG 60.869 60.000 0.00 0.00 40.15 3.02
96 97 2.370281 TGAGAAGACAAGGCGATGAC 57.630 50.000 0.26 0.00 0.00 3.06
97 98 3.401033 TTTGAGAAGACAAGGCGATGA 57.599 42.857 0.26 0.00 0.00 2.92
100 101 3.513912 TCCTATTTGAGAAGACAAGGCGA 59.486 43.478 0.00 0.00 0.00 5.54
106 107 6.351371 GGATCTGTGTCCTATTTGAGAAGACA 60.351 42.308 0.00 0.00 35.32 3.41
118 119 6.269077 TGAGTTTGTTTAGGATCTGTGTCCTA 59.731 38.462 7.25 7.25 46.70 2.94
150 151 7.696992 AGGAATCTTGCTCCGTTTTTAAATA 57.303 32.000 0.00 0.00 38.08 1.40
153 154 5.622770 GAGGAATCTTGCTCCGTTTTTAA 57.377 39.130 0.34 0.00 39.43 1.52
162 163 0.915364 AGGTGGGAGGAATCTTGCTC 59.085 55.000 3.10 3.10 43.91 4.26
170 171 3.089838 CCATGCAGGTGGGAGGAA 58.910 61.111 0.00 0.00 35.55 3.36
178 179 3.667217 GACCATGGCCCATGCAGGT 62.667 63.158 18.67 11.12 40.20 4.00
181 182 3.670319 TGGACCATGGCCCATGCA 61.670 61.111 17.04 8.27 40.20 3.96
216 217 1.889105 CATGTCTTCGATGGCCCCG 60.889 63.158 0.00 3.90 0.00 5.73
217 218 2.189499 GCATGTCTTCGATGGCCCC 61.189 63.158 0.00 0.00 0.00 5.80
233 234 4.758251 CCTCCCACATGCGTCGCA 62.758 66.667 24.05 24.05 44.86 5.10
243 244 4.832608 CTTACGGCCGCCTCCCAC 62.833 72.222 28.58 0.00 0.00 4.61
253 254 3.332034 TCTACAAGAAAAGGCTTACGGC 58.668 45.455 0.00 0.00 40.90 5.68
254 255 5.175859 TCATCTACAAGAAAAGGCTTACGG 58.824 41.667 0.00 0.00 0.00 4.02
255 256 5.292101 CCTCATCTACAAGAAAAGGCTTACG 59.708 44.000 0.00 0.00 0.00 3.18
256 257 6.092807 CACCTCATCTACAAGAAAAGGCTTAC 59.907 42.308 0.00 0.00 34.89 2.34
257 258 6.013725 TCACCTCATCTACAAGAAAAGGCTTA 60.014 38.462 0.00 0.00 34.89 3.09
258 259 5.006386 CACCTCATCTACAAGAAAAGGCTT 58.994 41.667 0.00 0.00 34.89 4.35
260 261 4.393371 GTCACCTCATCTACAAGAAAAGGC 59.607 45.833 7.51 0.00 34.89 4.35
261 262 5.551233 TGTCACCTCATCTACAAGAAAAGG 58.449 41.667 6.47 6.47 36.56 3.11
262 263 5.121454 GCTGTCACCTCATCTACAAGAAAAG 59.879 44.000 0.00 0.00 0.00 2.27
271 289 2.683362 CACGTAGCTGTCACCTCATCTA 59.317 50.000 0.00 0.00 0.00 1.98
280 298 2.566529 CGCCTCACGTAGCTGTCA 59.433 61.111 0.00 0.00 36.87 3.58
285 303 2.672908 TAATCGCCGCCTCACGTAGC 62.673 60.000 0.00 0.00 41.42 3.58
301 319 4.528596 ACCTACTTATGCCAGCGAGATAAT 59.471 41.667 0.00 0.00 0.00 1.28
302 320 3.895656 ACCTACTTATGCCAGCGAGATAA 59.104 43.478 0.00 0.00 0.00 1.75
304 322 2.297597 GACCTACTTATGCCAGCGAGAT 59.702 50.000 0.00 0.00 0.00 2.75
308 326 2.608261 GCTAGACCTACTTATGCCAGCG 60.608 54.545 0.00 0.00 0.00 5.18
316 335 3.641434 ACGTCCAGCTAGACCTACTTA 57.359 47.619 6.71 0.00 32.91 2.24
317 336 2.510928 ACGTCCAGCTAGACCTACTT 57.489 50.000 6.71 0.00 32.91 2.24
320 339 3.894759 ACAATACGTCCAGCTAGACCTA 58.105 45.455 6.71 0.27 32.91 3.08
327 346 4.159693 TGTCATAGAACAATACGTCCAGCT 59.840 41.667 0.00 0.00 0.00 4.24
344 363 8.535335 GCCATCCTCTAGATAAAGAATGTCATA 58.465 37.037 0.00 0.00 32.37 2.15
345 364 7.016957 TGCCATCCTCTAGATAAAGAATGTCAT 59.983 37.037 0.00 0.00 32.37 3.06
346 365 6.327365 TGCCATCCTCTAGATAAAGAATGTCA 59.673 38.462 0.00 0.00 32.37 3.58
347 366 6.763355 TGCCATCCTCTAGATAAAGAATGTC 58.237 40.000 0.00 0.00 32.37 3.06
348 367 6.328672 ACTGCCATCCTCTAGATAAAGAATGT 59.671 38.462 0.00 0.00 32.37 2.71
455 476 8.338986 GCTACTTTATAAAAACTGCCATCTCTC 58.661 37.037 0.00 0.00 0.00 3.20
463 484 8.964420 TGAACATGCTACTTTATAAAAACTGC 57.036 30.769 0.00 2.98 0.00 4.40
511 532 3.517296 TCAACAAGACCCTAATTGCCA 57.483 42.857 0.00 0.00 0.00 4.92
543 565 5.841783 TGGGCTTAGGTCCATTTAACTTTTT 59.158 36.000 0.00 0.00 43.05 1.94
563 585 4.657814 TTCCTTCCCTAATATCATGGGC 57.342 45.455 0.00 0.00 40.69 5.36
565 587 7.233632 TGTTCATTCCTTCCCTAATATCATGG 58.766 38.462 0.00 0.00 0.00 3.66
566 588 7.094463 GCTGTTCATTCCTTCCCTAATATCATG 60.094 40.741 0.00 0.00 0.00 3.07
567 589 6.944862 GCTGTTCATTCCTTCCCTAATATCAT 59.055 38.462 0.00 0.00 0.00 2.45
568 590 6.299141 GCTGTTCATTCCTTCCCTAATATCA 58.701 40.000 0.00 0.00 0.00 2.15
570 592 5.071788 TCGCTGTTCATTCCTTCCCTAATAT 59.928 40.000 0.00 0.00 0.00 1.28
571 593 4.407621 TCGCTGTTCATTCCTTCCCTAATA 59.592 41.667 0.00 0.00 0.00 0.98
572 594 3.199946 TCGCTGTTCATTCCTTCCCTAAT 59.800 43.478 0.00 0.00 0.00 1.73
573 595 2.569853 TCGCTGTTCATTCCTTCCCTAA 59.430 45.455 0.00 0.00 0.00 2.69
577 601 1.468914 GGTTCGCTGTTCATTCCTTCC 59.531 52.381 0.00 0.00 0.00 3.46
580 604 1.523758 GTGGTTCGCTGTTCATTCCT 58.476 50.000 0.00 0.00 0.00 3.36
584 608 0.321653 GGAGGTGGTTCGCTGTTCAT 60.322 55.000 0.00 0.00 0.00 2.57
585 609 1.070786 GGAGGTGGTTCGCTGTTCA 59.929 57.895 0.00 0.00 0.00 3.18
589 613 1.079543 CTGAGGAGGTGGTTCGCTG 60.080 63.158 0.00 0.00 0.00 5.18
604 628 1.216064 AATAGGGGCATGTCAGCTGA 58.784 50.000 13.74 13.74 34.17 4.26
606 630 1.072965 GCTAATAGGGGCATGTCAGCT 59.927 52.381 0.00 0.00 34.17 4.24
607 631 1.072965 AGCTAATAGGGGCATGTCAGC 59.927 52.381 0.00 0.00 0.00 4.26
608 632 3.406764 GAAGCTAATAGGGGCATGTCAG 58.593 50.000 0.00 0.00 0.00 3.51
609 633 2.106511 GGAAGCTAATAGGGGCATGTCA 59.893 50.000 0.00 0.00 0.00 3.58
610 634 2.106511 TGGAAGCTAATAGGGGCATGTC 59.893 50.000 0.00 0.00 0.00 3.06
612 636 2.957402 TGGAAGCTAATAGGGGCATG 57.043 50.000 0.00 0.00 0.00 4.06
614 638 3.748645 TTTTGGAAGCTAATAGGGGCA 57.251 42.857 0.00 0.00 0.00 5.36
615 639 4.023980 ACTTTTTGGAAGCTAATAGGGGC 58.976 43.478 0.00 0.00 0.00 5.80
616 640 7.898014 ATTACTTTTTGGAAGCTAATAGGGG 57.102 36.000 0.00 0.00 0.00 4.79
624 648 7.505258 TGCCTTTTAATTACTTTTTGGAAGCT 58.495 30.769 0.00 0.00 0.00 3.74
625 649 7.722795 TGCCTTTTAATTACTTTTTGGAAGC 57.277 32.000 0.00 0.00 0.00 3.86
626 650 9.929722 GTTTGCCTTTTAATTACTTTTTGGAAG 57.070 29.630 0.00 0.00 0.00 3.46
627 651 8.894731 GGTTTGCCTTTTAATTACTTTTTGGAA 58.105 29.630 0.00 0.00 0.00 3.53
629 653 7.348956 CGGTTTGCCTTTTAATTACTTTTTGG 58.651 34.615 0.00 0.00 0.00 3.28
693 720 3.158676 GACGCTGGGAATAGTAGGATCT 58.841 50.000 0.00 0.00 0.00 2.75
696 723 1.063492 TGGACGCTGGGAATAGTAGGA 60.063 52.381 0.00 0.00 0.00 2.94
697 724 1.068741 GTGGACGCTGGGAATAGTAGG 59.931 57.143 0.00 0.00 0.00 3.18
698 725 1.068741 GGTGGACGCTGGGAATAGTAG 59.931 57.143 0.00 0.00 0.00 2.57
757 786 1.129811 CTTTAATGTGGCCCGTTCGTC 59.870 52.381 0.00 0.00 0.00 4.20
1483 1526 2.402305 GCGGCAGTTCTCAGATATCTG 58.598 52.381 24.32 24.32 45.08 2.90
1545 1588 0.032678 GCGTGTCCGATCCATGAGAT 59.967 55.000 0.00 0.00 38.17 2.75
1682 1732 4.282449 CCGGGTAATATACACATCTCACCA 59.718 45.833 0.00 0.00 30.72 4.17
1758 1808 9.520204 AAAAGATCCATAAATGCACGAAAATAG 57.480 29.630 0.00 0.00 0.00 1.73
1862 1913 3.561143 AGGAAAATAGTGTGGTGTTGCA 58.439 40.909 0.00 0.00 0.00 4.08
1875 1926 6.712095 GGTGATGCATCATGTCTAGGAAAATA 59.288 38.462 30.89 0.22 39.30 1.40
1888 1940 1.521764 TAGGTGGGGTGATGCATCAT 58.478 50.000 30.89 16.22 39.30 2.45
1911 1963 6.620877 TGTCTAGGATGTAGGTTGTTCATT 57.379 37.500 0.00 0.00 0.00 2.57
2406 2460 6.762702 TCAAGTATCAACATCATTGCATGT 57.237 33.333 0.00 0.00 38.74 3.21


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

AutoCloner maintained by Alex Coulton.