Multiple sequence alignment - TraesCS3B01G295900

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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 TraesCS3B01G295900 chr3B 100.000 3171 0 0 1 3171 474316868 474320038 0.000000e+00 5856
1 TraesCS3B01G295900 chr3B 87.137 482 53 4 54 533 541629925 541629451 3.600000e-149 538
2 TraesCS3B01G295900 chr2D 95.842 1371 55 2 1803 3171 302185203 302186573 0.000000e+00 2215
3 TraesCS3B01G295900 chr2D 95.770 1371 56 2 1803 3171 118692410 118693780 0.000000e+00 2209
4 TraesCS3B01G295900 chr2D 79.134 762 131 15 214 962 607647921 607647175 4.720000e-138 501
5 TraesCS3B01G295900 chr6D 95.842 1371 54 3 1803 3171 160616883 160618252 0.000000e+00 2213
6 TraesCS3B01G295900 chr6D 95.697 1371 57 2 1803 3171 397450427 397449057 0.000000e+00 2204
7 TraesCS3B01G295900 chr6D 95.697 1371 57 2 1803 3171 397512503 397511133 0.000000e+00 2204
8 TraesCS3B01G295900 chr6D 87.992 483 51 4 54 534 459193280 459192803 5.940000e-157 564
9 TraesCS3B01G295900 chr3D 95.703 1373 55 4 1803 3171 65338969 65337597 0.000000e+00 2206
10 TraesCS3B01G295900 chr4D 95.697 1371 56 3 1803 3171 350725624 350724255 0.000000e+00 2202
11 TraesCS3B01G295900 chr4D 95.693 1370 57 2 1803 3170 489287014 489285645 0.000000e+00 2202
12 TraesCS3B01G295900 chrUn 95.624 1371 58 2 1803 3171 19290286 19288916 0.000000e+00 2198
13 TraesCS3B01G295900 chrUn 94.776 134 7 0 1 134 63865254 63865387 3.210000e-50 209
14 TraesCS3B01G295900 chr2B 82.206 1596 254 21 214 1798 740735491 740733915 0.000000e+00 1347
15 TraesCS3B01G295900 chr2B 86.528 913 121 1 836 1746 236318119 236319031 0.000000e+00 1003
16 TraesCS3B01G295900 chr2B 84.968 632 88 6 159 786 236317478 236318106 4.460000e-178 634
17 TraesCS3B01G295900 chr2B 87.552 482 51 4 54 533 368015694 368016168 1.660000e-152 549
18 TraesCS3B01G295900 chr2B 86.515 482 56 4 54 533 655296602 655297076 3.620000e-144 521
19 TraesCS3B01G295900 chr6B 86.140 974 130 5 836 1807 357050706 357049736 0.000000e+00 1046
20 TraesCS3B01G295900 chr6B 85.524 974 136 5 836 1807 600992020 600992990 0.000000e+00 1013
21 TraesCS3B01G295900 chr6B 92.698 493 22 1 1315 1807 324593725 324594203 0.000000e+00 699
22 TraesCS3B01G295900 chr6B 86.190 630 83 4 159 786 357051346 357050719 0.000000e+00 678
23 TraesCS3B01G295900 chr6B 85.397 630 89 3 159 786 600991379 600992007 0.000000e+00 651
24 TraesCS3B01G295900 chr2A 81.306 1118 178 20 216 1321 739278629 739277531 0.000000e+00 878
25 TraesCS3B01G295900 chr3A 92.661 327 24 0 1481 1807 337350931 337351257 3.700000e-129 472
26 TraesCS3B01G295900 chr3A 92.339 248 16 3 1 246 337350687 337350933 1.810000e-92 350
27 TraesCS3B01G295900 chr1B 87.332 371 38 3 54 422 679337560 679337197 1.760000e-112 416
28 TraesCS3B01G295900 chr5D 90.047 211 19 1 54 262 484743402 484743192 4.030000e-69 272
29 TraesCS3B01G295900 chr6A 93.137 102 7 0 1 102 182191741 182191842 1.970000e-32 150
30 TraesCS3B01G295900 chr7D 98.305 59 1 0 16 74 514755053 514755111 1.560000e-18 104


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 TraesCS3B01G295900 chr3B 474316868 474320038 3170 False 5856.0 5856 100.0000 1 3171 1 chr3B.!!$F1 3170
1 TraesCS3B01G295900 chr2D 302185203 302186573 1370 False 2215.0 2215 95.8420 1803 3171 1 chr2D.!!$F2 1368
2 TraesCS3B01G295900 chr2D 118692410 118693780 1370 False 2209.0 2209 95.7700 1803 3171 1 chr2D.!!$F1 1368
3 TraesCS3B01G295900 chr2D 607647175 607647921 746 True 501.0 501 79.1340 214 962 1 chr2D.!!$R1 748
4 TraesCS3B01G295900 chr6D 160616883 160618252 1369 False 2213.0 2213 95.8420 1803 3171 1 chr6D.!!$F1 1368
5 TraesCS3B01G295900 chr6D 397449057 397450427 1370 True 2204.0 2204 95.6970 1803 3171 1 chr6D.!!$R1 1368
6 TraesCS3B01G295900 chr6D 397511133 397512503 1370 True 2204.0 2204 95.6970 1803 3171 1 chr6D.!!$R2 1368
7 TraesCS3B01G295900 chr3D 65337597 65338969 1372 True 2206.0 2206 95.7030 1803 3171 1 chr3D.!!$R1 1368
8 TraesCS3B01G295900 chr4D 350724255 350725624 1369 True 2202.0 2202 95.6970 1803 3171 1 chr4D.!!$R1 1368
9 TraesCS3B01G295900 chr4D 489285645 489287014 1369 True 2202.0 2202 95.6930 1803 3170 1 chr4D.!!$R2 1367
10 TraesCS3B01G295900 chrUn 19288916 19290286 1370 True 2198.0 2198 95.6240 1803 3171 1 chrUn.!!$R1 1368
11 TraesCS3B01G295900 chr2B 740733915 740735491 1576 True 1347.0 1347 82.2060 214 1798 1 chr2B.!!$R1 1584
12 TraesCS3B01G295900 chr2B 236317478 236319031 1553 False 818.5 1003 85.7480 159 1746 2 chr2B.!!$F3 1587
13 TraesCS3B01G295900 chr6B 357049736 357051346 1610 True 862.0 1046 86.1650 159 1807 2 chr6B.!!$R1 1648
14 TraesCS3B01G295900 chr6B 600991379 600992990 1611 False 832.0 1013 85.4605 159 1807 2 chr6B.!!$F2 1648
15 TraesCS3B01G295900 chr2A 739277531 739278629 1098 True 878.0 878 81.3060 216 1321 1 chr2A.!!$R1 1105
16 TraesCS3B01G295900 chr3A 337350687 337351257 570 False 411.0 472 92.5000 1 1807 2 chr3A.!!$F1 1806

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
129 131 0.393077 AACGCTCAAGCTACTGGTGT 59.607 50.0 0.00 0.00 39.32 4.16 F
951 969 0.820226 TTGAGTGGCATCTCGAGAGG 59.180 55.0 22.26 22.26 37.28 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1141 0.597072 CGAACCCGCTCTATACCCTC 59.403 60.0 0.00 0.0 0.00 4.3 R
2853 2879 0.966920 ACAGTACCTTACGCTGCAGT 59.033 50.0 16.64 0.0 33.87 4.4 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
77 79 0.988832 CCCTGTTGTGGTTAGCCCTA 59.011 55.000 0.00 0.00 0.00 3.53
78 80 1.339727 CCCTGTTGTGGTTAGCCCTAC 60.340 57.143 0.00 0.00 0.00 3.18
83 85 4.475345 TGTTGTGGTTAGCCCTACAAATT 58.525 39.130 3.52 0.00 36.58 1.82
90 92 7.040271 TGTGGTTAGCCCTACAAATTTTAACTC 60.040 37.037 0.00 3.15 0.00 3.01
97 99 5.476945 CCCTACAAATTTTAACTCAGCTGGT 59.523 40.000 15.13 7.99 0.00 4.00
123 125 3.307242 CCAACATCTAACGCTCAAGCTAC 59.693 47.826 0.00 0.00 39.32 3.58
124 126 4.177026 CAACATCTAACGCTCAAGCTACT 58.823 43.478 0.00 0.00 39.32 2.57
125 127 3.775202 ACATCTAACGCTCAAGCTACTG 58.225 45.455 0.00 0.00 39.32 2.74
129 131 0.393077 AACGCTCAAGCTACTGGTGT 59.607 50.000 0.00 0.00 39.32 4.16
205 207 8.713708 TTGTATGGGAAGGTAATTTTGAGAAA 57.286 30.769 0.00 0.00 0.00 2.52
271 273 7.500892 TGTCATAAACTTCTTACTGCAAAAGGA 59.499 33.333 8.24 0.00 0.00 3.36
289 291 1.609208 GAACCAGTGGCACTTCACAT 58.391 50.000 19.43 2.48 39.93 3.21
293 295 1.955778 CCAGTGGCACTTCACATTTGA 59.044 47.619 19.43 0.00 39.93 2.69
359 361 4.536065 GCCAAAGCAACAAAAATTAAGGC 58.464 39.130 0.00 0.00 39.53 4.35
361 363 5.560760 GCCAAAGCAACAAAAATTAAGGCTC 60.561 40.000 0.00 0.00 39.53 4.70
362 364 5.526846 CCAAAGCAACAAAAATTAAGGCTCA 59.473 36.000 0.00 0.00 0.00 4.26
374 379 7.775053 AAATTAAGGCTCACAAAGGTTGATA 57.225 32.000 0.00 0.00 0.00 2.15
379 385 4.016444 GGCTCACAAAGGTTGATAATGGA 58.984 43.478 0.00 0.00 0.00 3.41
399 405 6.036577 TGGAAAAGCCAATTTGGAGAATAC 57.963 37.500 19.76 3.62 45.87 1.89
401 407 6.951198 TGGAAAAGCCAATTTGGAGAATACTA 59.049 34.615 19.76 1.08 45.87 1.82
403 409 8.478066 GGAAAAGCCAATTTGGAGAATACTATT 58.522 33.333 19.76 0.72 40.96 1.73
445 451 5.125097 CAGGAAAGAGCTTGCACTAATGATT 59.875 40.000 0.00 0.00 0.00 2.57
475 481 4.332683 TGAGTACCCTCTGTCTATGGTT 57.667 45.455 0.00 0.00 38.61 3.67
491 497 6.540914 GTCTATGGTTGATCATTCGGGTTTTA 59.459 38.462 0.00 0.00 0.00 1.52
523 529 9.522804 TTTTGTTCTACATTACAACCAATGTTC 57.477 29.630 6.77 0.00 44.75 3.18
525 531 7.870826 TGTTCTACATTACAACCAATGTTCAG 58.129 34.615 6.77 0.77 44.75 3.02
535 541 5.123820 ACAACCAATGTTCAGAATGGTATCG 59.876 40.000 7.26 3.21 45.15 2.92
589 595 5.290493 TGTATGCAACCGAGAAGGATAAT 57.710 39.130 0.00 0.00 45.00 1.28
598 604 6.494666 ACCGAGAAGGATAATATGGTGAAA 57.505 37.500 0.00 0.00 45.00 2.69
653 659 2.368548 ACTACAGACATGTGGACTGCAA 59.631 45.455 1.15 0.00 40.16 4.08
793 808 7.513371 AAAATGCATGTTCATTTCACCATTT 57.487 28.000 0.00 4.04 43.56 2.32
794 809 7.513371 AAATGCATGTTCATTTCACCATTTT 57.487 28.000 0.00 0.00 41.35 1.82
796 811 8.618702 AATGCATGTTCATTTCACCATTTTTA 57.381 26.923 0.00 0.00 33.18 1.52
806 821 9.958180 TCATTTCACCATTTTTAGTCTGAGATA 57.042 29.630 0.00 0.00 0.00 1.98
810 825 9.739276 TTCACCATTTTTAGTCTGAGATATTGT 57.261 29.630 0.00 0.00 0.00 2.71
862 880 7.656412 TCTGAAATGTTTGCTTTGCTTATGTA 58.344 30.769 0.00 0.00 0.00 2.29
863 881 7.594758 TCTGAAATGTTTGCTTTGCTTATGTAC 59.405 33.333 0.00 0.00 0.00 2.90
865 883 7.381948 TGAAATGTTTGCTTTGCTTATGTACTG 59.618 33.333 0.00 0.00 0.00 2.74
875 893 5.446143 TGCTTATGTACTGGGTTTGTTTG 57.554 39.130 0.00 0.00 0.00 2.93
920 938 2.030091 CAGTCATATGTCAAGCACTGCG 59.970 50.000 1.90 0.00 0.00 5.18
921 939 1.009078 TCATATGTCAAGCACTGCGC 58.991 50.000 0.00 0.00 42.91 6.09
951 969 0.820226 TTGAGTGGCATCTCGAGAGG 59.180 55.000 22.26 22.26 37.28 3.69
975 993 2.343484 TATCGACGGTGACTCTGGAT 57.657 50.000 0.00 0.00 0.00 3.41
1030 1048 2.439409 TGCCAGACATGTTGGATTCTG 58.561 47.619 23.18 14.46 37.96 3.02
1049 1067 8.820831 GGATTCTGATTCTCTTATATTGGAGGA 58.179 37.037 0.21 0.00 0.00 3.71
1123 1141 3.586174 AGATGGTATGGATGTCATGGAGG 59.414 47.826 0.00 0.00 37.30 4.30
1154 1172 1.355971 CGGGTTCGTGATAGTGTTGG 58.644 55.000 0.00 0.00 0.00 3.77
1157 1175 3.606687 GGGTTCGTGATAGTGTTGGATT 58.393 45.455 0.00 0.00 0.00 3.01
1166 1184 5.473504 GTGATAGTGTTGGATTTTGGTCTGT 59.526 40.000 0.00 0.00 0.00 3.41
1173 1191 4.715534 TGGATTTTGGTCTGTTACTCCA 57.284 40.909 0.00 0.00 0.00 3.86
1193 1211 4.221262 TCCAAAGAGGCATGAGAAATTTGG 59.779 41.667 17.13 17.13 44.11 3.28
1229 1247 8.709646 ACGAACTCTAAACATTGAATACAAGAC 58.290 33.333 0.00 0.00 39.46 3.01
1237 1255 6.331369 ACATTGAATACAAGACAAGGTTGG 57.669 37.500 0.00 0.00 39.46 3.77
1238 1256 4.846779 TTGAATACAAGACAAGGTTGGC 57.153 40.909 0.00 0.00 36.08 4.52
1254 1272 4.892934 AGGTTGGCTCTTGATTGTAAAACA 59.107 37.500 0.00 0.00 0.00 2.83
1266 1284 8.741101 TTGATTGTAAAACAAGATGGAATTCG 57.259 30.769 0.00 0.00 41.94 3.34
1274 1292 4.504858 ACAAGATGGAATTCGACCTACAC 58.495 43.478 0.00 0.00 0.00 2.90
1283 1301 5.353123 GGAATTCGACCTACACAATGCTAAA 59.647 40.000 0.00 0.00 0.00 1.85
1325 1345 9.476202 CATAGAGGTTTTTGAAAAACTAAAGGG 57.524 33.333 26.68 13.15 45.40 3.95
1327 1347 7.913789 AGAGGTTTTTGAAAAACTAAAGGGTT 58.086 30.769 26.68 8.13 45.40 4.11
1431 1451 4.025040 TGATGTCACAGAGGCATTTTCT 57.975 40.909 0.00 0.00 44.12 2.52
1456 1476 5.973565 GGCACTAAATATGTCACTGCAAATC 59.026 40.000 0.00 0.00 0.00 2.17
1458 1478 7.012327 GGCACTAAATATGTCACTGCAAATCTA 59.988 37.037 0.00 0.00 0.00 1.98
1508 1530 3.974719 TGGCAATACAGAAATGGGCTAA 58.025 40.909 0.00 0.00 0.00 3.09
1513 1535 6.940298 GGCAATACAGAAATGGGCTAATAGTA 59.060 38.462 0.00 0.00 0.00 1.82
1514 1536 7.094762 GGCAATACAGAAATGGGCTAATAGTAC 60.095 40.741 0.00 0.00 0.00 2.73
1544 1566 2.507484 TGTGCAAAAGATGTCTGAGGG 58.493 47.619 0.00 0.00 0.00 4.30
1602 1624 1.395954 CATGGTCTGATGTCTGTTGCG 59.604 52.381 0.00 0.00 0.00 4.85
1614 1636 2.033662 GTCTGTTGCGACTGTTCTTGAC 60.034 50.000 5.50 0.00 0.00 3.18
1725 1747 6.351286 GGAACTTAATGGCTGATTTGTTGGAT 60.351 38.462 0.00 0.00 0.00 3.41
1726 1748 7.147915 GGAACTTAATGGCTGATTTGTTGGATA 60.148 37.037 0.00 0.00 0.00 2.59
1727 1749 7.902920 ACTTAATGGCTGATTTGTTGGATAT 57.097 32.000 0.00 0.00 0.00 1.63
1753 1775 1.410517 GAGAAGATGATGAGGCCACGA 59.589 52.381 5.01 0.00 0.00 4.35
1762 1784 1.262417 TGAGGCCACGACTACATCAA 58.738 50.000 5.01 0.00 0.00 2.57
1775 1797 5.351465 CGACTACATCAAAGGTTGTTAGCAT 59.649 40.000 0.00 0.00 0.00 3.79
1781 1803 2.557924 CAAAGGTTGTTAGCATGGCTGA 59.442 45.455 0.07 0.00 40.10 4.26
1948 1971 6.426937 GGTTATATTGGTCGCACATATCTTGT 59.573 38.462 0.00 0.00 39.91 3.16
1983 2006 6.088016 TGCATTGCTTCTACTTTGTTGAAT 57.912 33.333 10.49 0.00 28.57 2.57
1986 2009 6.421801 GCATTGCTTCTACTTTGTTGAATTGT 59.578 34.615 0.16 0.00 28.57 2.71
2105 2128 8.394971 TCAAATGTTGTTCTTGTGTATCAGAT 57.605 30.769 0.00 0.00 0.00 2.90
2193 2216 6.426587 AGTGGCACCTGATAAATCAAATAGT 58.573 36.000 15.27 0.00 36.18 2.12
2261 2284 3.655777 ACTCTAGCAGACTCTAGCCCTAT 59.344 47.826 0.00 0.00 36.77 2.57
2395 2420 5.472137 GCAAAGAGTACACCAAATCCAGTTA 59.528 40.000 0.00 0.00 0.00 2.24
2446 2471 2.762327 CCAATTGCAGCAAATAGGACCT 59.238 45.455 12.97 0.00 0.00 3.85
2511 2536 1.001378 GTCAGGAACTTTGTGCGCATT 60.001 47.619 15.91 2.15 34.60 3.56
2512 2537 2.225491 GTCAGGAACTTTGTGCGCATTA 59.775 45.455 15.91 2.58 34.60 1.90
2710 2735 2.644992 CAAGGGTTGGTTGCGCTC 59.355 61.111 9.73 1.18 0.00 5.03
2734 2760 6.712095 TCTTCAAGCACTGTTGATGAAGTATT 59.288 34.615 18.19 0.00 42.78 1.89
2761 2787 1.509644 CTTGAGGCAAGCGCACTTCA 61.510 55.000 11.47 8.06 41.24 3.02
2777 2803 3.698040 CACTTCAATGGCAAGCCTCTAAT 59.302 43.478 12.96 0.00 36.94 1.73
2818 2844 3.827876 TCCGGTGCTACATTTATCCGATA 59.172 43.478 0.00 0.00 40.29 2.92
2853 2879 4.594123 TCTTGTTACACATTGGTCTCGA 57.406 40.909 0.00 0.00 0.00 4.04
2943 2969 5.597806 ACGTCTCACTTGTATGAAAACTGA 58.402 37.500 0.00 0.00 0.00 3.41
2994 3020 3.731216 CCACAGAATCTCGCAACTATACG 59.269 47.826 0.00 0.00 0.00 3.06
3034 3060 2.094130 GTGAGTACCTCTTGCCCTGTAC 60.094 54.545 0.00 0.00 35.04 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 5.473931 AGAAGCTATTGGTCTATACATGCG 58.526 41.667 0.00 0.00 0.00 4.73
41 43 1.213926 AGGGCCTTGAGAAGCTATTGG 59.786 52.381 0.00 0.00 0.00 3.16
77 79 5.048013 GGCTACCAGCTGAGTTAAAATTTGT 60.048 40.000 17.39 1.95 41.99 2.83
78 80 5.402398 GGCTACCAGCTGAGTTAAAATTTG 58.598 41.667 17.39 0.00 41.99 2.32
83 85 1.982226 TGGGCTACCAGCTGAGTTAAA 59.018 47.619 17.39 0.00 43.37 1.52
97 99 1.828595 TGAGCGTTAGATGTTGGGCTA 59.171 47.619 0.00 0.00 0.00 3.93
123 125 1.300971 CGATGCTCCCACAACACCAG 61.301 60.000 0.00 0.00 0.00 4.00
124 126 1.302431 CGATGCTCCCACAACACCA 60.302 57.895 0.00 0.00 0.00 4.17
125 127 2.690778 GCGATGCTCCCACAACACC 61.691 63.158 0.00 0.00 0.00 4.16
129 131 1.675310 CCTTGCGATGCTCCCACAA 60.675 57.895 0.00 0.00 0.00 3.33
205 207 7.989170 GCCTTCCATTCTCCATCAATTAATTTT 59.011 33.333 0.00 0.00 0.00 1.82
211 213 3.958798 CAGCCTTCCATTCTCCATCAATT 59.041 43.478 0.00 0.00 0.00 2.32
271 273 2.071778 AATGTGAAGTGCCACTGGTT 57.928 45.000 0.00 0.00 37.89 3.67
289 291 4.613925 AGAGCTCATGTGACTCTTCAAA 57.386 40.909 17.77 0.00 37.50 2.69
334 336 3.295585 AATTTTTGTTGCTTTGGCCCT 57.704 38.095 0.00 0.00 37.74 5.19
359 361 6.587608 GCTTTTCCATTATCAACCTTTGTGAG 59.412 38.462 0.00 0.00 0.00 3.51
361 363 5.639082 GGCTTTTCCATTATCAACCTTTGTG 59.361 40.000 0.00 0.00 34.01 3.33
362 364 5.306678 TGGCTTTTCCATTATCAACCTTTGT 59.693 36.000 0.00 0.00 40.72 2.83
374 379 5.565455 TTCTCCAAATTGGCTTTTCCATT 57.435 34.783 7.24 0.00 46.04 3.16
445 451 3.646162 ACAGAGGGTACTCATGAACACAA 59.354 43.478 2.73 0.00 46.44 3.33
475 481 7.475137 AAATTTCCTAAAACCCGAATGATCA 57.525 32.000 0.00 0.00 0.00 2.92
491 497 8.919145 TGGTTGTAATGTAGAACAAAATTTCCT 58.081 29.630 0.00 0.00 37.35 3.36
553 559 6.818142 CGGTTGCATACATATCCAGAATATCA 59.182 38.462 0.00 0.00 0.00 2.15
564 570 4.955811 TCCTTCTCGGTTGCATACATAT 57.044 40.909 0.00 0.00 0.00 1.78
575 581 6.494666 TTTCACCATATTATCCTTCTCGGT 57.505 37.500 0.00 0.00 0.00 4.69
607 613 5.759506 TGGCAACTCGATTTTTGAAGTTA 57.240 34.783 5.90 0.00 37.61 2.24
653 659 6.176183 CCATGTAACCTCTCTTCTGATGTTT 58.824 40.000 0.00 0.00 0.00 2.83
727 741 8.802267 TGAAAAAGAATGGGTATTTACCTCAAG 58.198 33.333 6.71 0.00 45.72 3.02
738 752 8.713708 TGTAAGGATTTGAAAAAGAATGGGTA 57.286 30.769 0.00 0.00 0.00 3.69
740 754 8.900983 TTTGTAAGGATTTGAAAAAGAATGGG 57.099 30.769 0.00 0.00 0.00 4.00
769 784 7.513371 AAATGGTGAAATGAACATGCATTTT 57.487 28.000 11.19 0.00 45.63 1.82
776 791 8.859090 TCAGACTAAAAATGGTGAAATGAACAT 58.141 29.630 0.00 0.00 0.00 2.71
824 839 9.962759 GCAAACATTTCAGATTGATAATTTGAC 57.037 29.630 0.00 0.00 32.43 3.18
825 840 9.932207 AGCAAACATTTCAGATTGATAATTTGA 57.068 25.926 0.00 0.00 30.97 2.69
829 844 8.662141 GCAAAGCAAACATTTCAGATTGATAAT 58.338 29.630 0.00 0.00 0.00 1.28
862 880 0.534873 GGCACACAAACAAACCCAGT 59.465 50.000 0.00 0.00 0.00 4.00
863 881 0.823460 AGGCACACAAACAAACCCAG 59.177 50.000 0.00 0.00 0.00 4.45
865 883 1.650825 CAAGGCACACAAACAAACCC 58.349 50.000 0.00 0.00 0.00 4.11
920 938 0.951040 CCACTCAACAAGGGACTCGC 60.951 60.000 0.00 0.00 38.49 5.03
921 939 0.951040 GCCACTCAACAAGGGACTCG 60.951 60.000 0.00 0.00 38.49 4.18
951 969 3.304123 CCAGAGTCACCGTCGATATCTTC 60.304 52.174 0.34 0.00 0.00 2.87
975 993 6.934056 AGCTTTATCATTTGGTGTGCAATTA 58.066 32.000 0.00 0.00 0.00 1.40
1067 1085 1.167851 AAGTATGTGTGCAGCGCAAT 58.832 45.000 11.04 9.22 41.47 3.56
1071 1089 4.968626 TCAAATTAAGTATGTGTGCAGCG 58.031 39.130 0.00 0.00 0.00 5.18
1123 1141 0.597072 CGAACCCGCTCTATACCCTC 59.403 60.000 0.00 0.00 0.00 4.30
1157 1175 4.714632 CCTCTTTGGAGTAACAGACCAAA 58.285 43.478 0.00 0.00 46.76 3.28
1166 1184 4.908601 TTCTCATGCCTCTTTGGAGTAA 57.091 40.909 0.00 0.00 37.86 2.24
1173 1191 6.423776 TTTCCAAATTTCTCATGCCTCTTT 57.576 33.333 0.00 0.00 0.00 2.52
1193 1211 5.516090 TGTTTAGAGTTCGTGCCATTTTTC 58.484 37.500 0.00 0.00 0.00 2.29
1229 1247 5.452078 TTTACAATCAAGAGCCAACCTTG 57.548 39.130 0.00 0.00 41.63 3.61
1237 1255 6.913170 TCCATCTTGTTTTACAATCAAGAGC 58.087 36.000 12.97 0.00 46.47 4.09
1238 1256 9.918630 AATTCCATCTTGTTTTACAATCAAGAG 57.081 29.630 12.97 7.43 46.47 2.85
1254 1272 4.819105 TGTGTAGGTCGAATTCCATCTT 57.181 40.909 0.00 0.00 0.00 2.40
1283 1301 9.632638 AAACCTCTATGTATTCTAATGCAATGT 57.367 29.630 0.00 0.00 34.72 2.71
1299 1319 9.476202 CCCTTTAGTTTTTCAAAAACCTCTATG 57.524 33.333 20.00 6.88 0.00 2.23
1306 1326 8.312896 TCACAACCCTTTAGTTTTTCAAAAAC 57.687 30.769 16.67 16.67 0.00 2.43
1325 1345 9.118236 GACAGCAACTAAATAATTTCTCACAAC 57.882 33.333 0.00 0.00 0.00 3.32
1327 1347 7.446931 TGGACAGCAACTAAATAATTTCTCACA 59.553 33.333 0.00 0.00 0.00 3.58
1372 1392 5.392057 GCCTATCACAAAGTTCCTTAGCAAC 60.392 44.000 0.00 0.00 0.00 4.17
1403 1423 4.847198 TGCCTCTGTGACATCATACAAAT 58.153 39.130 0.00 0.00 0.00 2.32
1407 1427 5.587844 AGAAAATGCCTCTGTGACATCATAC 59.412 40.000 0.00 0.00 0.00 2.39
1419 1439 3.439857 TTAGTGCCAGAAAATGCCTCT 57.560 42.857 0.00 0.00 0.00 3.69
1431 1451 3.949132 TGCAGTGACATATTTAGTGCCA 58.051 40.909 0.00 0.00 39.42 4.92
1458 1478 8.980596 TGAATGCCACATATTTTAGGAAAGAAT 58.019 29.630 0.00 0.00 0.00 2.40
1508 1530 9.890629 TCTTTTGCACAATCTCATTAGTACTAT 57.109 29.630 2.79 0.00 0.00 2.12
1513 1535 7.392673 AGACATCTTTTGCACAATCTCATTAGT 59.607 33.333 0.00 0.00 0.00 2.24
1514 1536 7.696872 CAGACATCTTTTGCACAATCTCATTAG 59.303 37.037 0.00 0.00 0.00 1.73
1602 1624 2.640316 ACCTTGGGTCAAGAACAGTC 57.360 50.000 9.01 0.00 43.42 3.51
1614 1636 5.413833 CAGCATATGAAGCTTATACCTTGGG 59.586 44.000 6.97 0.00 41.14 4.12
1725 1747 7.013750 GTGGCCTCATCATCTTCTCGATATATA 59.986 40.741 3.32 0.00 0.00 0.86
1726 1748 5.896106 TGGCCTCATCATCTTCTCGATATAT 59.104 40.000 3.32 0.00 0.00 0.86
1727 1749 5.126222 GTGGCCTCATCATCTTCTCGATATA 59.874 44.000 3.32 0.00 0.00 0.86
1753 1775 5.415701 CCATGCTAACAACCTTTGATGTAGT 59.584 40.000 0.00 0.00 0.00 2.73
1762 1784 2.584835 TCAGCCATGCTAACAACCTT 57.415 45.000 0.00 0.00 36.40 3.50
1841 1863 3.928754 TCCACTAGGGAGCTACATTGAT 58.071 45.455 0.00 0.00 42.15 2.57
1875 1898 5.790096 TGATGGGTGAATAAGATAGGGCATA 59.210 40.000 0.00 0.00 0.00 3.14
1983 2006 7.601130 ACGATGTGTAAACTAAGCTAATGACAA 59.399 33.333 0.00 0.00 0.00 3.18
1986 2009 7.094631 ACACGATGTGTAAACTAAGCTAATGA 58.905 34.615 0.00 0.00 45.56 2.57
2022 2045 3.535561 ACTGAAAATGGATAGGCAGACG 58.464 45.455 0.00 0.00 0.00 4.18
2024 2047 5.692115 TGTACTGAAAATGGATAGGCAGA 57.308 39.130 0.00 0.00 0.00 4.26
2105 2128 1.142060 TCGCCCTCTTCCTTTTGAACA 59.858 47.619 0.00 0.00 0.00 3.18
2166 2189 4.835284 TGATTTATCAGGTGCCACTACA 57.165 40.909 0.00 0.00 32.11 2.74
2193 2216 6.765989 GTGATATTGCAACTACACCTAATGGA 59.234 38.462 0.00 0.00 37.04 3.41
2261 2284 4.009675 GGCATCAGAAATGACCAGTGTAA 58.990 43.478 0.00 0.00 0.00 2.41
2326 2351 2.099141 GCTGGTGCTATGTCAACTGA 57.901 50.000 0.00 0.00 36.03 3.41
2395 2420 2.890945 CTGGTTCGAAAAGGGATTTGGT 59.109 45.455 0.00 0.00 0.00 3.67
2710 2735 4.825546 ACTTCATCAACAGTGCTTGAAG 57.174 40.909 16.91 16.91 43.37 3.02
2761 2787 3.281727 TTCGATTAGAGGCTTGCCATT 57.718 42.857 14.54 3.94 0.00 3.16
2777 2803 4.927425 CCGGAGACTTTACTGAAATTTCGA 59.073 41.667 13.34 2.46 0.00 3.71
2818 2844 7.907214 GTGTAACAAGATTATTCCAGTCACT 57.093 36.000 0.00 0.00 36.32 3.41
2853 2879 0.966920 ACAGTACCTTACGCTGCAGT 59.033 50.000 16.64 0.00 33.87 4.40
2943 2969 7.282675 CCTTGAGAATGAATGTTCTTCTGCTAT 59.717 37.037 10.22 0.00 38.51 2.97
2994 3020 0.388134 CAAGAGCAATGCAGTGTGCC 60.388 55.000 16.47 5.33 44.23 5.01
3034 3060 8.475331 AACAACTATGAAAGTAAGTATGGTCG 57.525 34.615 0.00 0.00 37.50 4.79


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

AutoCloner maintained by Alex Coulton.