Multiple sequence alignment - TraesCS2A01G044000

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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 TraesCS2A01G044000 chr2A 100.000 4429 0 0 1 4429 17506250 17501822 0.000000e+00 8179
1 TraesCS2A01G044000 chr2A 89.925 3315 309 10 1129 4429 17551523 17548220 0.000000e+00 4248
2 TraesCS2A01G044000 chr2A 88.113 3306 362 16 1142 4429 17536179 17532887 0.000000e+00 3899
3 TraesCS2A01G044000 chr2A 90.527 2069 191 5 2363 4429 17475731 17473666 0.000000e+00 2730
4 TraesCS2A01G044000 chr2A 81.911 3317 483 70 1129 4391 17415161 17411908 0.000000e+00 2693
5 TraesCS2A01G044000 chr2A 81.118 3326 522 67 1146 4406 17543552 17540268 0.000000e+00 2566
6 TraesCS2A01G044000 chr2A 91.117 1621 140 2 2812 4429 17599024 17597405 0.000000e+00 2193
7 TraesCS2A01G044000 chr2A 84.581 1589 208 13 1129 2698 17427339 17425769 0.000000e+00 1543
8 TraesCS2A01G044000 chr2A 84.958 718 41 31 1 681 17554032 17553345 0.000000e+00 665
9 TraesCS2A01G044000 chr2A 81.776 867 89 33 52 882 17416249 17415416 0.000000e+00 662
10 TraesCS2A01G044000 chr2A 85.097 463 35 15 3 450 17428396 17427953 4.070000e-120 442
11 TraesCS2A01G044000 chr2A 81.548 504 52 15 450 919 17536942 17536446 1.160000e-100 377
12 TraesCS2A01G044000 chr2A 83.421 380 45 9 56 431 17538218 17537853 1.970000e-88 337
13 TraesCS2A01G044000 chr2A 86.538 312 32 7 300 608 17596063 17595759 7.100000e-88 335
14 TraesCS2A01G044000 chr2A 80.430 419 31 24 675 1070 17552115 17551725 5.640000e-69 272
15 TraesCS2A01G044000 chr2A 77.113 485 42 31 611 1072 17544147 17543709 2.680000e-52 217
16 TraesCS2A01G044000 chr2A 83.012 259 14 8 681 909 17427945 17427687 1.610000e-49 207
17 TraesCS2A01G044000 chr2A 85.890 163 23 0 922 1084 17415418 17415256 1.640000e-39 174
18 TraesCS2A01G044000 chr2B 89.566 3316 320 15 1129 4429 27546808 27543504 0.000000e+00 4183
19 TraesCS2A01G044000 chr2B 85.642 1588 195 18 1129 2698 27620479 27618907 0.000000e+00 1639
20 TraesCS2A01G044000 chr2B 89.478 1283 127 6 3097 4374 27617256 27615977 0.000000e+00 1615
21 TraesCS2A01G044000 chr2B 85.003 1587 210 16 1129 2697 27584249 27582673 0.000000e+00 1587
22 TraesCS2A01G044000 chr2B 87.538 1308 157 6 2812 4117 27582528 27581225 0.000000e+00 1507
23 TraesCS2A01G044000 chr2B 82.968 593 61 22 31 608 27621560 27620993 2.380000e-137 499
24 TraesCS2A01G044000 chr2B 90.141 355 30 3 241 592 27548489 27548137 1.450000e-124 457
25 TraesCS2A01G044000 chr2B 82.571 459 25 23 639 1070 27547446 27547016 1.960000e-93 353
26 TraesCS2A01G044000 chr2B 86.391 169 20 3 923 1089 27620736 27620569 9.790000e-42 182
27 TraesCS2A01G044000 chr2B 92.632 95 7 0 788 882 27584598 27584504 2.150000e-28 137
28 TraesCS2A01G044000 chr2D 85.714 3269 417 30 1134 4370 15474247 15470997 0.000000e+00 3404
29 TraesCS2A01G044000 chr2D 88.355 2121 236 4 2265 4377 15507414 15505297 0.000000e+00 2538
30 TraesCS2A01G044000 chr2D 86.334 1361 156 18 1129 2472 15460211 15458864 0.000000e+00 1456
31 TraesCS2A01G044000 chr2D 89.130 184 12 3 16 195 15495489 15495310 5.770000e-54 222
32 TraesCS2A01G044000 chr2D 93.617 141 8 1 3 142 15466539 15466399 4.490000e-50 209
33 TraesCS2A01G044000 chr2D 86.577 149 20 0 924 1072 15460458 15460310 9.860000e-37 165
34 TraesCS2A01G044000 chr2D 85.366 123 15 1 926 1045 15474531 15474409 1.670000e-24 124
35 TraesCS2A01G044000 chr6B 85.841 113 9 6 449 560 29920070 29920176 3.620000e-21 113


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 TraesCS2A01G044000 chr2A 17501822 17506250 4428 True 8179.000000 8179 100.000000 1 4429 1 chr2A.!!$R2 4428
1 TraesCS2A01G044000 chr2A 17473666 17475731 2065 True 2730.000000 2730 90.527000 2363 4429 1 chr2A.!!$R1 2066
2 TraesCS2A01G044000 chr2A 17548220 17554032 5812 True 1728.333333 4248 85.104333 1 4429 3 chr2A.!!$R6 4428
3 TraesCS2A01G044000 chr2A 17532887 17544147 11260 True 1479.200000 3899 82.262600 56 4429 5 chr2A.!!$R5 4373
4 TraesCS2A01G044000 chr2A 17595759 17599024 3265 True 1264.000000 2193 88.827500 300 4429 2 chr2A.!!$R7 4129
5 TraesCS2A01G044000 chr2A 17411908 17416249 4341 True 1176.333333 2693 83.192333 52 4391 3 chr2A.!!$R3 4339
6 TraesCS2A01G044000 chr2A 17425769 17428396 2627 True 730.666667 1543 84.230000 3 2698 3 chr2A.!!$R4 2695
7 TraesCS2A01G044000 chr2B 27543504 27548489 4985 True 1664.333333 4183 87.426000 241 4429 3 chr2B.!!$R1 4188
8 TraesCS2A01G044000 chr2B 27581225 27584598 3373 True 1077.000000 1587 88.391000 788 4117 3 chr2B.!!$R2 3329
9 TraesCS2A01G044000 chr2B 27615977 27621560 5583 True 983.750000 1639 86.119750 31 4374 4 chr2B.!!$R3 4343
10 TraesCS2A01G044000 chr2D 15505297 15507414 2117 True 2538.000000 2538 88.355000 2265 4377 1 chr2D.!!$R3 2112
11 TraesCS2A01G044000 chr2D 15470997 15474531 3534 True 1764.000000 3404 85.540000 926 4370 2 chr2D.!!$R5 3444
12 TraesCS2A01G044000 chr2D 15458864 15460458 1594 True 810.500000 1456 86.455500 924 2472 2 chr2D.!!$R4 1548

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
912 9674 0.035317 TCGTTTGACATGGAGCTGCT 59.965 50.0 6.82 0.00 0.00 4.24 F
913 9675 0.167470 CGTTTGACATGGAGCTGCTG 59.833 55.0 7.01 4.98 0.00 4.41 F
914 9676 0.524862 GTTTGACATGGAGCTGCTGG 59.475 55.0 7.01 0.58 0.00 4.85 F
2035 11107 0.729116 CTGGTTGCTATGGACTTGCG 59.271 55.0 0.00 0.00 0.00 4.85 F
2503 11579 0.873054 GATGATGAGCATCCAAGCCG 59.127 55.0 0.00 0.00 46.23 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 11163 0.399454 CCAATCTCCCATGCCGATCT 59.601 55.000 0.00 0.0 0.00 2.75 R
2096 11168 1.069668 GAATTGCCAATCTCCCATGCC 59.930 52.381 0.00 0.0 0.00 4.40 R
2160 11232 1.222766 GCTGCAGCCTCATCAGATCG 61.223 60.000 28.76 0.0 34.31 3.69 R
3007 12119 0.464013 GCAGTCCAGCAGCATGAGAT 60.464 55.000 0.00 0.0 39.69 2.75 R
3760 14106 0.779997 AGTTGGGGAGTGGCAAAGAT 59.220 50.000 0.00 0.0 0.00 2.40 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
56 61 1.419387 AGGCTTGACTTGAGTGAGCTT 59.581 47.619 12.85 5.81 35.43 3.74
57 62 1.534595 GGCTTGACTTGAGTGAGCTTG 59.465 52.381 12.85 0.00 35.43 4.01
58 63 1.069364 GCTTGACTTGAGTGAGCTTGC 60.069 52.381 0.00 0.00 33.54 4.01
59 64 1.534595 CTTGACTTGAGTGAGCTTGCC 59.465 52.381 0.00 0.00 0.00 4.52
105 5980 2.719739 CCTCAACATGGAAGCAGACAT 58.280 47.619 0.00 0.00 0.00 3.06
106 5981 3.877559 CCTCAACATGGAAGCAGACATA 58.122 45.455 0.00 0.00 0.00 2.29
107 5982 3.624861 CCTCAACATGGAAGCAGACATAC 59.375 47.826 0.00 0.00 0.00 2.39
108 5983 4.256110 CTCAACATGGAAGCAGACATACA 58.744 43.478 0.00 0.00 0.00 2.29
195 6070 0.321034 GGTACCTGGTCCGGTTTGAC 60.321 60.000 0.63 0.00 38.49 3.18
245 6154 4.287720 GCAAGTTACAGCTGTGGTAAAAC 58.712 43.478 29.57 22.91 32.94 2.43
250 6159 5.411669 AGTTACAGCTGTGGTAAAACTATGC 59.588 40.000 29.57 2.97 32.94 3.14
288 6200 7.437793 AATTTTTGGCATGAAAATGGTGTAG 57.562 32.000 9.89 0.00 36.94 2.74
289 6201 4.533919 TTTGGCATGAAAATGGTGTAGG 57.466 40.909 0.00 0.00 0.00 3.18
522 7350 5.628130 AGAATCTAATGATGGATGTGGTGG 58.372 41.667 0.00 0.00 32.44 4.61
533 7361 1.803453 ATGTGGTGGGTGGGAAGCAT 61.803 55.000 0.00 0.00 0.00 3.79
560 7388 8.401709 GGAATTCACAGCTTTTATTTAGAGAGG 58.598 37.037 7.93 0.00 0.00 3.69
581 7409 3.489416 GGTAAAGCACAAAGAAAAAGCGG 59.511 43.478 0.00 0.00 0.00 5.52
591 7639 0.945743 GAAAAAGCGGGCAAAGCAGG 60.946 55.000 0.00 0.00 37.01 4.85
603 7651 0.895100 AAAGCAGGCGCAAGGAATGA 60.895 50.000 10.83 0.00 42.27 2.57
618 7668 6.665465 CAAGGAATGACAGCATATGTGTATG 58.335 40.000 4.29 1.67 44.17 2.39
717 9431 2.485814 GTCTCCATGCAACTTCCAGTTC 59.514 50.000 0.00 0.00 36.03 3.01
733 9447 2.065799 AGTTCCCTTGTCCACCTCATT 58.934 47.619 0.00 0.00 0.00 2.57
742 9459 5.300286 CCTTGTCCACCTCATTGATTTATCC 59.700 44.000 0.00 0.00 0.00 2.59
885 9647 5.010282 TGTAGGAAAGGAAGGAATTTGCTC 58.990 41.667 0.00 0.00 36.31 4.26
904 9666 0.179192 CCCGCACATCGTTTGACATG 60.179 55.000 0.00 0.00 36.19 3.21
905 9667 0.179192 CCGCACATCGTTTGACATGG 60.179 55.000 0.00 0.00 36.19 3.66
906 9668 0.795698 CGCACATCGTTTGACATGGA 59.204 50.000 0.00 0.00 0.00 3.41
907 9669 1.201954 CGCACATCGTTTGACATGGAG 60.202 52.381 0.00 0.00 0.00 3.86
908 9670 1.466360 GCACATCGTTTGACATGGAGC 60.466 52.381 0.00 0.00 0.00 4.70
909 9671 2.079158 CACATCGTTTGACATGGAGCT 58.921 47.619 0.00 0.00 0.00 4.09
910 9672 2.079158 ACATCGTTTGACATGGAGCTG 58.921 47.619 0.00 0.00 0.00 4.24
911 9673 1.089920 ATCGTTTGACATGGAGCTGC 58.910 50.000 0.00 0.00 0.00 5.25
912 9674 0.035317 TCGTTTGACATGGAGCTGCT 59.965 50.000 6.82 0.00 0.00 4.24
913 9675 0.167470 CGTTTGACATGGAGCTGCTG 59.833 55.000 7.01 4.98 0.00 4.41
914 9676 0.524862 GTTTGACATGGAGCTGCTGG 59.475 55.000 7.01 0.58 0.00 4.85
915 9677 1.246056 TTTGACATGGAGCTGCTGGC 61.246 55.000 7.01 5.17 42.19 4.85
916 9678 2.827642 GACATGGAGCTGCTGGCC 60.828 66.667 7.01 3.19 43.05 5.36
917 9679 3.336568 ACATGGAGCTGCTGGCCT 61.337 61.111 7.01 0.00 43.05 5.19
918 9680 2.044252 CATGGAGCTGCTGGCCTT 60.044 61.111 7.01 0.00 43.05 4.35
919 9681 2.119655 CATGGAGCTGCTGGCCTTC 61.120 63.158 7.01 0.00 43.05 3.46
920 9682 2.307162 ATGGAGCTGCTGGCCTTCT 61.307 57.895 7.01 0.00 43.05 2.85
921 9683 1.860944 ATGGAGCTGCTGGCCTTCTT 61.861 55.000 7.01 0.00 43.05 2.52
922 9684 1.303970 GGAGCTGCTGGCCTTCTTT 60.304 57.895 7.01 0.00 43.05 2.52
974 9739 4.955925 AGCGAGAACTAGATCATATCCG 57.044 45.455 0.00 0.00 0.00 4.18
1024 9790 1.833630 CTCCAGAGGTAATCCAGCACA 59.166 52.381 0.00 0.00 35.89 4.57
1072 9870 2.673368 GCAGATTTGTGTCCTACTTCGG 59.327 50.000 0.00 0.00 0.00 4.30
1080 9913 2.381725 GTCCTACTTCGGACCTTTGG 57.618 55.000 0.00 0.00 46.19 3.28
1083 9916 1.829222 CCTACTTCGGACCTTTGGCTA 59.171 52.381 0.00 0.00 0.00 3.93
1106 9939 9.896263 GCTATTTAGTGGTAGTATAGTCAAGAC 57.104 37.037 0.00 0.00 0.00 3.01
1113 10075 7.889073 AGTGGTAGTATAGTCAAGACTCAAGAA 59.111 37.037 5.91 0.00 42.54 2.52
1114 10076 8.688151 GTGGTAGTATAGTCAAGACTCAAGAAT 58.312 37.037 5.91 0.00 42.54 2.40
1119 10081 8.918116 AGTATAGTCAAGACTCAAGAATATGCA 58.082 33.333 5.91 0.00 42.54 3.96
1120 10082 8.973378 GTATAGTCAAGACTCAAGAATATGCAC 58.027 37.037 5.91 0.00 42.54 4.57
1121 10083 5.181748 AGTCAAGACTCAAGAATATGCACC 58.818 41.667 0.00 0.00 36.92 5.01
1122 10084 4.937620 GTCAAGACTCAAGAATATGCACCA 59.062 41.667 0.00 0.00 0.00 4.17
1123 10085 4.937620 TCAAGACTCAAGAATATGCACCAC 59.062 41.667 0.00 0.00 0.00 4.16
1300 10348 9.874205 CCTCATTTGGTGTTATTATTGTTGAAT 57.126 29.630 0.00 0.00 0.00 2.57
1322 10370 6.949117 ATACTGCAGAAGATAAGGATCCAT 57.051 37.500 23.35 4.17 31.81 3.41
1327 10375 4.023365 GCAGAAGATAAGGATCCATGCAAC 60.023 45.833 15.82 0.10 36.24 4.17
1332 10380 4.336433 AGATAAGGATCCATGCAACAAACG 59.664 41.667 15.82 0.00 31.81 3.60
1408 10456 3.895232 TGTGATCTACTTCAAGGGCTC 57.105 47.619 0.00 0.00 0.00 4.70
1409 10457 3.173151 TGTGATCTACTTCAAGGGCTCA 58.827 45.455 0.00 0.00 0.00 4.26
1658 10706 3.843027 CCAGAGGGGTGATAGCAGATATT 59.157 47.826 0.00 0.00 0.00 1.28
1664 10712 8.347591 AGAGGGGTGATAGCAGATATTAGAATA 58.652 37.037 0.00 0.00 0.00 1.75
1752 10800 4.766373 ACATTGATTTGTATGAGTGTGGCA 59.234 37.500 0.00 0.00 0.00 4.92
1818 10866 1.369091 CGGGAGGTTTCGGAGCAATG 61.369 60.000 0.00 0.00 0.00 2.82
1935 11007 0.886563 ACTGCATGAAGAGGCTTTGC 59.113 50.000 8.02 0.00 0.00 3.68
1959 11031 2.275380 GCCAAGTGCACGGGGATTT 61.275 57.895 27.38 7.41 40.77 2.17
2001 11073 3.118482 CCACAAGATAGTCATGGAGTGCT 60.118 47.826 0.00 0.00 31.69 4.40
2010 11082 5.220710 AGTCATGGAGTGCTTCATATACC 57.779 43.478 0.00 0.00 0.00 2.73
2011 11083 4.655649 AGTCATGGAGTGCTTCATATACCA 59.344 41.667 0.00 0.00 0.00 3.25
2034 11106 1.470098 CACTGGTTGCTATGGACTTGC 59.530 52.381 0.00 0.00 0.00 4.01
2035 11107 0.729116 CTGGTTGCTATGGACTTGCG 59.271 55.000 0.00 0.00 0.00 4.85
2085 11157 5.371176 TGTGATGGTATTATAGAGGGCCAAA 59.629 40.000 6.18 0.00 0.00 3.28
2091 11163 7.817440 TGGTATTATAGAGGGCCAAAACAATA 58.183 34.615 6.18 1.00 0.00 1.90
2092 11164 7.942341 TGGTATTATAGAGGGCCAAAACAATAG 59.058 37.037 6.18 0.00 0.00 1.73
2096 11168 3.545703 AGAGGGCCAAAACAATAGATCG 58.454 45.455 6.18 0.00 0.00 3.69
2121 11193 2.577563 TGGGAGATTGGCAATTCTCTGA 59.422 45.455 25.12 15.98 0.00 3.27
2141 11213 4.717877 TGAAGAGAAACATGAGCTTGGAA 58.282 39.130 0.00 0.00 0.00 3.53
2149 11221 4.996788 ACATGAGCTTGGAATTGGATTC 57.003 40.909 0.00 0.00 38.55 2.52
2150 11222 4.346730 ACATGAGCTTGGAATTGGATTCA 58.653 39.130 0.00 0.00 41.03 2.57
2151 11223 4.960469 ACATGAGCTTGGAATTGGATTCAT 59.040 37.500 0.00 0.00 41.03 2.57
2160 11232 8.078596 GCTTGGAATTGGATTCATCTGTTATAC 58.921 37.037 3.39 0.00 41.03 1.47
2313 11388 6.305272 TCTTCCTTTCTGCAGATGAACTAT 57.695 37.500 19.04 0.00 0.00 2.12
2503 11579 0.873054 GATGATGAGCATCCAAGCCG 59.127 55.000 0.00 0.00 46.23 5.52
2666 11742 0.878416 TAAGTGATTTGTGTGGCGGC 59.122 50.000 0.00 0.00 0.00 6.53
2734 11813 4.556233 TGTATGGAGAACGAAGACACAAG 58.444 43.478 0.00 0.00 0.00 3.16
2835 11947 4.668576 TTGCTTGAGTCATTTAGCTTCG 57.331 40.909 14.70 0.00 34.77 3.79
2853 11965 1.330521 TCGTCAACAAAGCTGCAACTC 59.669 47.619 1.02 0.00 0.00 3.01
2904 12016 3.561725 GGGTTGTTCTCAGTTGAAGAGTG 59.438 47.826 0.00 0.00 34.73 3.51
2915 12027 5.010112 TCAGTTGAAGAGTGTACTTCTCAGG 59.990 44.000 16.53 0.00 44.34 3.86
2929 12041 2.077803 TCTCAGGGGAAATTTGGGGAA 58.922 47.619 0.00 0.00 0.00 3.97
2958 12070 2.525629 TGGACCTCTCGGGCACAA 60.526 61.111 0.00 0.00 41.63 3.33
3007 12119 1.210478 GGAAGCTCCATACCTCAAGCA 59.790 52.381 0.00 0.00 36.28 3.91
3092 12204 2.461695 TGGGTTTTGGAGAAGTTGCAA 58.538 42.857 0.00 0.00 35.10 4.08
3243 13571 5.787953 TGCATCTTTTGACTTCAATTGGA 57.212 34.783 5.42 0.00 35.55 3.53
3383 13714 1.166531 GCCGTGAAGTTGCTCAAGGT 61.167 55.000 7.33 0.00 44.22 3.50
3458 13798 2.923121 AGAAGAACTGCAAGCTGTCAA 58.077 42.857 5.05 0.00 37.60 3.18
3562 13905 4.224594 TGCAAGATGAAGAGAAGATGGAGT 59.775 41.667 0.00 0.00 0.00 3.85
3606 13952 3.128242 ACAACACTCGGAGGATTAGTACG 59.872 47.826 10.23 0.00 0.00 3.67
3703 14049 1.766494 CATTCCATGCCCACAAGCTA 58.234 50.000 0.00 0.00 0.00 3.32
3708 14054 1.409241 CCATGCCCACAAGCTACAGAT 60.409 52.381 0.00 0.00 0.00 2.90
3755 14101 0.548510 GAGAGGTGCCCCAAGCTATT 59.451 55.000 0.00 0.00 44.23 1.73
3760 14106 1.768870 GGTGCCCCAAGCTATTCTCTA 59.231 52.381 0.00 0.00 44.23 2.43
3863 14209 2.353704 CGTGCTACATCTGGAACTGGAA 60.354 50.000 0.00 0.00 0.00 3.53
4005 14351 1.326852 GAGACGCTCGAGATCGTGTAA 59.673 52.381 20.41 0.00 39.22 2.41
4383 14732 1.282157 AGGTGAGCTATGTTTGGTCCC 59.718 52.381 0.00 0.00 0.00 4.46
4414 14763 9.085645 TCCTTTCATCAGTAACTTACTTAGTGA 57.914 33.333 0.00 2.15 45.14 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 63 1.468520 CATTACTTTGCCACGTCAGGG 59.531 52.381 0.00 0.00 0.00 4.45
59 64 2.416547 CTCATTACTTTGCCACGTCAGG 59.583 50.000 0.00 0.00 0.00 3.86
105 5980 2.217745 TGGTGCGGACCCACATGTA 61.218 57.895 24.47 0.00 42.34 2.29
106 5981 3.565214 TGGTGCGGACCCACATGT 61.565 61.111 24.47 0.00 42.34 3.21
151 6026 3.791887 CGTTGTAAAATTCAAACCGCACA 59.208 39.130 0.00 0.00 0.00 4.57
154 6029 3.116700 CGTCGTTGTAAAATTCAAACCGC 59.883 43.478 0.00 0.00 0.00 5.68
203 6078 3.735240 TGCGCTGCAGATTTTTGTAAAAG 59.265 39.130 20.43 0.00 33.32 2.27
204 6079 3.711086 TGCGCTGCAGATTTTTGTAAAA 58.289 36.364 20.43 0.00 33.32 1.52
205 6080 3.361794 TGCGCTGCAGATTTTTGTAAA 57.638 38.095 20.43 0.00 33.32 2.01
209 6084 1.774639 ACTTGCGCTGCAGATTTTTG 58.225 45.000 20.43 4.72 40.61 2.44
210 6085 2.514205 AACTTGCGCTGCAGATTTTT 57.486 40.000 20.43 0.00 40.61 1.94
211 6086 2.293122 TGTAACTTGCGCTGCAGATTTT 59.707 40.909 20.43 3.38 40.61 1.82
222 6125 1.790755 TACCACAGCTGTAACTTGCG 58.209 50.000 21.20 4.97 0.00 4.85
245 6154 2.937469 TTGCATTTTGGACCGCATAG 57.063 45.000 0.00 0.00 33.71 2.23
334 6251 2.069273 CTTTTGGCCACTGAGACTACG 58.931 52.381 3.88 0.00 0.00 3.51
491 7315 7.558807 ACATCCATCATTAGATTCTTTGCTTGA 59.441 33.333 0.00 0.00 30.20 3.02
522 7350 1.478105 GTGAATTCCATGCTTCCCACC 59.522 52.381 2.27 0.00 0.00 4.61
533 7361 8.862325 TCTCTAAATAAAAGCTGTGAATTCCA 57.138 30.769 2.27 0.00 0.00 3.53
560 7388 3.489416 CCCGCTTTTTCTTTGTGCTTTAC 59.511 43.478 0.00 0.00 0.00 2.01
581 7409 4.729856 CCTTGCGCCTGCTTTGCC 62.730 66.667 4.18 0.00 43.34 4.52
591 7639 1.016627 TATGCTGTCATTCCTTGCGC 58.983 50.000 0.00 0.00 34.22 6.09
673 8151 1.737838 TGCCTTGCGTAGAAGGAATG 58.262 50.000 12.54 0.00 44.87 2.67
717 9431 2.814805 ATCAATGAGGTGGACAAGGG 57.185 50.000 0.00 0.00 0.00 3.95
885 9647 0.179192 CATGTCAAACGATGTGCGGG 60.179 55.000 0.00 0.00 46.49 6.13
904 9666 0.897401 AAAAGAAGGCCAGCAGCTCC 60.897 55.000 5.01 0.00 43.05 4.70
905 9667 0.964700 AAAAAGAAGGCCAGCAGCTC 59.035 50.000 5.01 0.00 43.05 4.09
906 9668 3.138214 AAAAAGAAGGCCAGCAGCT 57.862 47.368 5.01 0.00 43.05 4.24
921 9683 1.601903 CCAGCAGCTACACGTCAAAAA 59.398 47.619 0.00 0.00 0.00 1.94
922 9684 1.225855 CCAGCAGCTACACGTCAAAA 58.774 50.000 0.00 0.00 0.00 2.44
929 9691 1.301677 GACAAGGCCAGCAGCTACAC 61.302 60.000 5.01 0.00 43.05 2.90
932 9694 2.265739 CGACAAGGCCAGCAGCTA 59.734 61.111 5.01 0.00 43.05 3.32
974 9739 7.869937 TGATGAATCAGACCGATCTTATTCTTC 59.130 37.037 17.05 17.05 42.48 2.87
1020 9786 2.225019 CACTGAAGATCAAGGTGTGTGC 59.775 50.000 0.00 0.00 0.00 4.57
1024 9790 6.094603 GCATTAATCACTGAAGATCAAGGTGT 59.905 38.462 0.00 0.00 0.00 4.16
1072 9870 5.742063 ACTACCACTAAATAGCCAAAGGTC 58.258 41.667 0.00 0.00 0.00 3.85
1074 9872 8.648693 ACTATACTACCACTAAATAGCCAAAGG 58.351 37.037 0.00 0.00 0.00 3.11
1075 9873 9.694137 GACTATACTACCACTAAATAGCCAAAG 57.306 37.037 0.00 0.00 0.00 2.77
1080 9913 9.896263 GTCTTGACTATACTACCACTAAATAGC 57.104 37.037 0.00 0.00 0.00 2.97
1083 9916 9.696572 TGAGTCTTGACTATACTACCACTAAAT 57.303 33.333 3.00 0.00 0.00 1.40
1108 9941 9.071276 AGGATAATTAAGTGGTGCATATTCTTG 57.929 33.333 0.00 0.00 0.00 3.02
1113 10075 7.749666 AGTGAGGATAATTAAGTGGTGCATAT 58.250 34.615 0.00 0.00 0.00 1.78
1114 10076 7.136822 AGTGAGGATAATTAAGTGGTGCATA 57.863 36.000 0.00 0.00 0.00 3.14
1116 10078 5.428253 GAGTGAGGATAATTAAGTGGTGCA 58.572 41.667 0.00 0.00 0.00 4.57
1117 10079 4.508124 CGAGTGAGGATAATTAAGTGGTGC 59.492 45.833 0.00 0.00 0.00 5.01
1118 10080 4.508124 GCGAGTGAGGATAATTAAGTGGTG 59.492 45.833 0.00 0.00 0.00 4.17
1119 10081 4.161565 TGCGAGTGAGGATAATTAAGTGGT 59.838 41.667 0.00 0.00 0.00 4.16
1120 10082 4.693283 TGCGAGTGAGGATAATTAAGTGG 58.307 43.478 0.00 0.00 0.00 4.00
1121 10083 5.755375 ACATGCGAGTGAGGATAATTAAGTG 59.245 40.000 0.00 0.00 0.00 3.16
1122 10084 5.918608 ACATGCGAGTGAGGATAATTAAGT 58.081 37.500 0.00 0.00 0.00 2.24
1123 10085 6.851222 AACATGCGAGTGAGGATAATTAAG 57.149 37.500 0.00 0.00 0.00 1.85
1214 10238 7.810658 ACAAGGCGCATCATAATTATAAGAAG 58.189 34.615 10.83 0.00 0.00 2.85
1300 10348 5.512060 GCATGGATCCTTATCTTCTGCAGTA 60.512 44.000 14.67 2.58 34.14 2.74
1322 10370 0.041400 CAGCATCGACGTTTGTTGCA 60.041 50.000 20.09 0.00 35.11 4.08
1327 10375 1.510623 GCTGCAGCATCGACGTTTG 60.511 57.895 33.36 0.00 41.59 2.93
1347 10395 5.395768 CCTCCAAAACACCGATTATCTCTCT 60.396 44.000 0.00 0.00 0.00 3.10
1358 10406 2.161609 GCTTGTATCCTCCAAAACACCG 59.838 50.000 0.00 0.00 0.00 4.94
1408 10456 2.692041 GAGGATGCTCCCAATCCTTTTG 59.308 50.000 2.14 0.00 44.27 2.44
1409 10457 2.312741 TGAGGATGCTCCCAATCCTTTT 59.687 45.455 12.15 0.00 44.27 2.27
1428 10476 3.523157 TGGGCTACCAGATTGAGAATTGA 59.477 43.478 0.00 0.00 43.37 2.57
1510 10558 2.416747 CTCTCATGCTTTTCCACACGA 58.583 47.619 0.00 0.00 0.00 4.35
1752 10800 9.614792 GTTACTCAAAAGTGATATTACTGGGAT 57.385 33.333 0.16 0.00 36.92 3.85
1784 10832 2.034066 CCGTGCCAGGTCCACAAT 59.966 61.111 0.00 0.00 32.85 2.71
1818 10866 6.156429 TCCTTTTCCCCTTCTTCTAGTATGAC 59.844 42.308 0.00 0.00 0.00 3.06
1959 11031 2.614481 GGTTTATGTTGTCCGGCTGAGA 60.614 50.000 0.00 0.00 0.00 3.27
2019 11091 0.727398 GTCCGCAAGTCCATAGCAAC 59.273 55.000 0.00 0.00 0.00 4.17
2034 11106 1.518325 TAGTTTGGTGCATGTGTCCG 58.482 50.000 0.00 0.00 0.00 4.79
2035 11107 3.367292 CCAATAGTTTGGTGCATGTGTCC 60.367 47.826 0.00 0.00 46.27 4.02
2076 11148 2.618709 CCGATCTATTGTTTTGGCCCTC 59.381 50.000 0.00 0.00 0.00 4.30
2085 11157 2.705658 TCTCCCATGCCGATCTATTGTT 59.294 45.455 0.00 0.00 0.00 2.83
2091 11163 0.399454 CCAATCTCCCATGCCGATCT 59.601 55.000 0.00 0.00 0.00 2.75
2092 11164 1.239968 GCCAATCTCCCATGCCGATC 61.240 60.000 0.00 0.00 0.00 3.69
2096 11168 1.069668 GAATTGCCAATCTCCCATGCC 59.930 52.381 0.00 0.00 0.00 4.40
2121 11193 5.047519 CCAATTCCAAGCTCATGTTTCTCTT 60.048 40.000 0.00 0.00 0.00 2.85
2141 11213 8.588472 TCAGATCGTATAACAGATGAATCCAAT 58.412 33.333 0.00 0.00 0.00 3.16
2149 11221 5.804473 GCCTCATCAGATCGTATAACAGATG 59.196 44.000 0.00 0.00 34.30 2.90
2150 11222 5.714333 AGCCTCATCAGATCGTATAACAGAT 59.286 40.000 0.00 0.00 0.00 2.90
2151 11223 5.048434 CAGCCTCATCAGATCGTATAACAGA 60.048 44.000 0.00 0.00 0.00 3.41
2160 11232 1.222766 GCTGCAGCCTCATCAGATCG 61.223 60.000 28.76 0.00 34.31 3.69
2313 11388 8.309656 TGGCAATATTGATGTTGTATTTGTTGA 58.690 29.630 19.73 0.00 32.34 3.18
2503 11579 5.183713 TGGAAACATGACATGTCTTCATTCC 59.816 40.000 27.56 27.56 44.07 3.01
2666 11742 3.963428 AGTACTACAAGGCTTGGTCTG 57.037 47.619 29.26 17.79 34.12 3.51
2734 11813 2.790433 TGGGGAACTGTGCTTGATTAC 58.210 47.619 0.00 0.00 0.00 1.89
2835 11947 1.678101 AGGAGTTGCAGCTTTGTTGAC 59.322 47.619 3.97 0.00 0.00 3.18
2853 11965 4.382901 GGAGATGCTAGATATCTTGGCAGG 60.383 50.000 25.92 0.00 37.10 4.85
2904 12016 4.017126 CCCAAATTTCCCCTGAGAAGTAC 58.983 47.826 0.00 0.00 0.00 2.73
2915 12027 1.203250 TCCAGGTTCCCCAAATTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
2929 12041 2.284995 GGTCCAGCTCCTCCAGGT 60.285 66.667 0.00 0.00 36.34 4.00
2958 12070 2.241176 TGAGGTCAAGGGTTTTCACTGT 59.759 45.455 0.00 0.00 31.71 3.55
3007 12119 0.464013 GCAGTCCAGCAGCATGAGAT 60.464 55.000 0.00 0.00 39.69 2.75
3092 12204 1.742761 CAGATTGGACGGTGCTGATT 58.257 50.000 0.31 0.00 0.00 2.57
3187 13515 3.909732 CCTAATGGTGAAGCCCCAAATA 58.090 45.455 0.00 0.00 35.14 1.40
3383 13714 2.763710 TGCTGCTGGCTCCCGATA 60.764 61.111 0.00 0.00 42.39 2.92
3562 13905 1.262417 TGTTCCTGTAGCGATCCACA 58.738 50.000 0.00 0.00 0.00 4.17
3606 13952 1.168714 CAGGGGCTAAAGCAACACTC 58.831 55.000 4.07 0.00 44.36 3.51
3701 14047 1.153289 AGCCAGCGCCAATCTGTAG 60.153 57.895 2.29 0.00 34.57 2.74
3703 14049 2.437359 GAGCCAGCGCCAATCTGT 60.437 61.111 2.29 0.00 34.57 3.41
3708 14054 2.638354 CCATTTGAGCCAGCGCCAA 61.638 57.895 2.29 0.00 34.57 4.52
3755 14101 2.119495 GGGGAGTGGCAAAGATAGAGA 58.881 52.381 0.00 0.00 0.00 3.10
3760 14106 0.779997 AGTTGGGGAGTGGCAAAGAT 59.220 50.000 0.00 0.00 0.00 2.40
3863 14209 5.249780 TCCACTTGGTTGGTATGTTGTAT 57.750 39.130 0.00 0.00 37.93 2.29
4005 14351 3.843027 AGACTTCCTTCAGATCACCACAT 59.157 43.478 0.00 0.00 0.00 3.21
4295 14641 0.830648 TGGTTCATAGAGCGAAGGGG 59.169 55.000 0.00 0.00 0.00 4.79
4383 14732 7.607250 AGTAAGTTACTGATGAAAGGAGACAG 58.393 38.462 14.82 0.00 37.69 3.51


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

AutoCloner maintained by Alex Coulton.