Multiple sequence alignment - TraesCS1B01G419700

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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 TraesCS1B01G419700 chr1B 100.000 3567 0 0 1 3567 643057891 643061457 0.000000e+00 6588.0
1 TraesCS1B01G419700 chr1B 100.000 565 0 0 3773 4337 643061663 643062227 0.000000e+00 1044.0
2 TraesCS1B01G419700 chr1B 87.709 179 19 3 712 888 325812723 325812546 5.690000e-49 206.0
3 TraesCS1B01G419700 chr1D 96.502 3230 87 12 347 3567 466102150 466105362 0.000000e+00 5315.0
4 TraesCS1B01G419700 chr1D 90.244 574 46 6 3773 4337 466105413 466105985 0.000000e+00 741.0
5 TraesCS1B01G419700 chr1D 92.754 207 7 1 29 235 466101648 466101846 4.240000e-75 292.0
6 TraesCS1B01G419700 chr5D 79.854 2328 343 71 997 3295 1882018 1884248 0.000000e+00 1585.0
7 TraesCS1B01G419700 chr5D 90.361 166 15 1 727 891 412100096 412100261 2.630000e-52 217.0
8 TraesCS1B01G419700 chr5D 78.922 204 25 11 127 315 1881491 1881691 5.890000e-24 122.0
9 TraesCS1B01G419700 chr2B 82.931 1201 175 18 984 2166 28149841 28151029 0.000000e+00 1055.0
10 TraesCS1B01G419700 chr2B 80.387 775 126 12 2300 3073 28151148 28151897 2.260000e-157 566.0
11 TraesCS1B01G419700 chr2B 85.055 542 77 4 3799 4336 67211687 67211146 2.280000e-152 549.0
12 TraesCS1B01G419700 chr2B 89.222 167 16 2 728 892 361574993 361574827 1.580000e-49 207.0
13 TraesCS1B01G419700 chr2B 71.406 633 164 11 2318 2940 8354944 8355569 2.700000e-32 150.0
14 TraesCS1B01G419700 chr5A 80.702 1197 187 30 1918 3073 853162 854355 0.000000e+00 891.0
15 TraesCS1B01G419700 chr2D 85.847 537 72 4 3804 4336 641491314 641490778 6.290000e-158 568.0
16 TraesCS1B01G419700 chr2D 89.412 170 16 2 722 890 87407359 87407527 3.400000e-51 213.0
17 TraesCS1B01G419700 chr7D 85.083 543 77 4 3799 4337 523396615 523397157 6.340000e-153 551.0
18 TraesCS1B01G419700 chr4A 84.843 541 79 3 3800 4337 739526695 739527235 3.820000e-150 542.0
19 TraesCS1B01G419700 chrUn 84.346 543 76 7 3798 4333 399759815 399760355 1.380000e-144 523.0
20 TraesCS1B01G419700 chrUn 84.220 545 75 9 3797 4333 308232005 308232546 1.790000e-143 520.0
21 TraesCS1B01G419700 chrUn 71.136 634 164 13 2318 2940 224599647 224600272 5.850000e-29 139.0
22 TraesCS1B01G419700 chrUn 71.136 634 164 13 2318 2940 251471608 251472233 5.850000e-29 139.0
23 TraesCS1B01G419700 chrUn 70.998 631 164 13 2321 2940 365643962 365643340 2.720000e-27 134.0
24 TraesCS1B01G419700 chrUn 70.681 631 166 13 2318 2937 212988899 212989521 5.890000e-24 122.0
25 TraesCS1B01G419700 chr6B 84.486 535 77 5 3804 4333 502012131 502012664 1.380000e-144 523.0
26 TraesCS1B01G419700 chr7B 84.358 537 77 5 3803 4333 735987061 735986526 1.790000e-143 520.0
27 TraesCS1B01G419700 chr5B 81.867 557 64 20 1311 1842 759920 760464 6.660000e-118 435.0
28 TraesCS1B01G419700 chr5B 83.200 250 27 2 1927 2161 762486 762735 9.450000e-52 215.0
29 TraesCS1B01G419700 chr3D 90.184 163 15 1 728 889 553037752 553037914 1.220000e-50 211.0
30 TraesCS1B01G419700 chr3D 90.123 162 15 1 728 888 87926000 87926161 4.390000e-50 209.0
31 TraesCS1B01G419700 chr3D 88.824 170 17 2 722 890 459077435 459077267 1.580000e-49 207.0
32 TraesCS1B01G419700 chr2A 88.304 171 18 2 727 896 78849620 78849789 2.040000e-48 204.0
33 TraesCS1B01G419700 chr6D 72.464 345 76 15 1808 2144 29468905 29468572 4.620000e-15 93.5
34 TraesCS1B01G419700 chr6D 100.000 30 0 0 1 30 444880616 444880645 6.060000e-04 56.5
35 TraesCS1B01G419700 chr3B 100.000 30 0 0 1 30 440515242 440515271 6.060000e-04 56.5


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 TraesCS1B01G419700 chr1B 643057891 643062227 4336 False 3816.0 6588 100.000000 1 4337 2 chr1B.!!$F1 4336
1 TraesCS1B01G419700 chr1D 466101648 466105985 4337 False 2116.0 5315 93.166667 29 4337 3 chr1D.!!$F1 4308
2 TraesCS1B01G419700 chr5D 1881491 1884248 2757 False 853.5 1585 79.388000 127 3295 2 chr5D.!!$F2 3168
3 TraesCS1B01G419700 chr2B 28149841 28151897 2056 False 810.5 1055 81.659000 984 3073 2 chr2B.!!$F2 2089
4 TraesCS1B01G419700 chr2B 67211146 67211687 541 True 549.0 549 85.055000 3799 4336 1 chr2B.!!$R1 537
5 TraesCS1B01G419700 chr5A 853162 854355 1193 False 891.0 891 80.702000 1918 3073 1 chr5A.!!$F1 1155
6 TraesCS1B01G419700 chr2D 641490778 641491314 536 True 568.0 568 85.847000 3804 4336 1 chr2D.!!$R1 532
7 TraesCS1B01G419700 chr7D 523396615 523397157 542 False 551.0 551 85.083000 3799 4337 1 chr7D.!!$F1 538
8 TraesCS1B01G419700 chr4A 739526695 739527235 540 False 542.0 542 84.843000 3800 4337 1 chr4A.!!$F1 537
9 TraesCS1B01G419700 chrUn 399759815 399760355 540 False 523.0 523 84.346000 3798 4333 1 chrUn.!!$F5 535
10 TraesCS1B01G419700 chrUn 308232005 308232546 541 False 520.0 520 84.220000 3797 4333 1 chrUn.!!$F4 536
11 TraesCS1B01G419700 chr6B 502012131 502012664 533 False 523.0 523 84.486000 3804 4333 1 chr6B.!!$F1 529
12 TraesCS1B01G419700 chr7B 735986526 735987061 535 True 520.0 520 84.358000 3803 4333 1 chr7B.!!$R1 530
13 TraesCS1B01G419700 chr5B 759920 762735 2815 False 325.0 435 82.533500 1311 2161 2 chr5B.!!$F1 850

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
21 22 0.449388 GCTTGTGCCTGTACTGATGC 59.551 55.000 0.60 0.00 0.00 3.91 F
24 25 0.975887 TGTGCCTGTACTGATGCTCA 59.024 50.000 0.60 2.09 0.00 4.26 F
124 125 1.198713 ACAGCCTCTCCACATGGTAG 58.801 55.000 0.00 0.00 36.34 3.18 F
446 654 1.461897 GACACGTTTCCACCATAACCG 59.538 52.381 0.00 0.00 0.00 4.44 F
1985 4192 1.336755 GGCCCATAACTTATTGCCACG 59.663 52.381 11.75 0.00 38.73 4.94 F
2682 4942 1.303561 GGCATCCCTGTGCACAAGA 60.304 57.895 21.98 20.03 46.81 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1400 0.772124 AGAGGAGGGGCAGGAACAAA 60.772 55.000 0.00 0.0 0.00 2.83 R
1772 2018 0.836606 TGTCCTGTCAGCTTGGTTGA 59.163 50.000 0.00 0.0 0.00 3.18 R
1985 4192 1.237285 ACCATCTTGGAGCAACACGC 61.237 55.000 0.00 0.0 40.96 5.34 R
2334 4590 2.359850 GCAATGTCCCGCACCTCA 60.360 61.111 0.00 0.0 0.00 3.86 R
2921 5190 1.454663 GCTTCCTTCTGGATGGCCC 60.455 63.158 0.00 0.0 42.81 5.80 R
4019 6307 0.037590 TTTGGTGCGCTGGTCCTATT 59.962 50.000 9.73 0.0 0.00 1.73 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
17 18 2.863153 GCGCTTGTGCCTGTACTG 59.137 61.111 0.00 0.00 35.36 2.74
18 19 1.667830 GCGCTTGTGCCTGTACTGA 60.668 57.895 0.00 0.00 35.36 3.41
19 20 1.021390 GCGCTTGTGCCTGTACTGAT 61.021 55.000 0.00 0.00 35.36 2.90
20 21 0.723414 CGCTTGTGCCTGTACTGATG 59.277 55.000 0.60 0.00 35.36 3.07
21 22 0.449388 GCTTGTGCCTGTACTGATGC 59.551 55.000 0.60 0.00 0.00 3.91
22 23 1.947678 GCTTGTGCCTGTACTGATGCT 60.948 52.381 0.60 0.00 0.00 3.79
23 24 2.005451 CTTGTGCCTGTACTGATGCTC 58.995 52.381 0.60 0.00 0.00 4.26
24 25 0.975887 TGTGCCTGTACTGATGCTCA 59.024 50.000 0.60 2.09 0.00 4.26
25 26 1.347378 TGTGCCTGTACTGATGCTCAA 59.653 47.619 0.60 0.00 0.00 3.02
26 27 2.224499 TGTGCCTGTACTGATGCTCAAA 60.224 45.455 0.60 0.00 0.00 2.69
27 28 2.813754 GTGCCTGTACTGATGCTCAAAA 59.186 45.455 0.60 0.00 0.00 2.44
81 82 1.916697 GCTTCAGCCGTTTCCAGCTC 61.917 60.000 0.00 0.00 37.18 4.09
99 100 3.011032 AGCTCAAAAATCCAGGACCTCAT 59.989 43.478 0.00 0.00 0.00 2.90
104 105 7.690301 GCTCAAAAATCCAGGACCTCATATCTA 60.690 40.741 0.00 0.00 0.00 1.98
124 125 1.198713 ACAGCCTCTCCACATGGTAG 58.801 55.000 0.00 0.00 36.34 3.18
177 178 5.374071 CCAGGTGATGGTAACCTTATTACC 58.626 45.833 8.61 8.61 46.14 2.85
178 179 5.132144 CCAGGTGATGGTAACCTTATTACCT 59.868 44.000 15.09 0.99 46.14 3.08
179 180 6.353602 CCAGGTGATGGTAACCTTATTACCTT 60.354 42.308 15.09 9.88 46.14 3.50
298 320 2.677914 AGGGAACAAAGGAAAAGTGGG 58.322 47.619 0.00 0.00 0.00 4.61
302 324 4.442893 GGGAACAAAGGAAAAGTGGGAAAG 60.443 45.833 0.00 0.00 0.00 2.62
307 329 5.840693 ACAAAGGAAAAGTGGGAAAGATGAT 59.159 36.000 0.00 0.00 0.00 2.45
315 337 3.205282 AGTGGGAAAGATGATAAAGGGGG 59.795 47.826 0.00 0.00 0.00 5.40
333 355 3.664869 GGGGGAGAGAGAAGGGAAT 57.335 57.895 0.00 0.00 0.00 3.01
334 356 2.797285 GGGGGAGAGAGAAGGGAATA 57.203 55.000 0.00 0.00 0.00 1.75
335 357 2.615391 GGGGGAGAGAGAAGGGAATAG 58.385 57.143 0.00 0.00 0.00 1.73
336 358 2.615391 GGGGAGAGAGAAGGGAATAGG 58.385 57.143 0.00 0.00 0.00 2.57
337 359 2.180308 GGGGAGAGAGAAGGGAATAGGA 59.820 54.545 0.00 0.00 0.00 2.94
338 360 3.236047 GGGAGAGAGAAGGGAATAGGAC 58.764 54.545 0.00 0.00 0.00 3.85
339 361 3.374318 GGGAGAGAGAAGGGAATAGGACA 60.374 52.174 0.00 0.00 0.00 4.02
340 362 4.488770 GGAGAGAGAAGGGAATAGGACAT 58.511 47.826 0.00 0.00 0.00 3.06
341 363 4.283212 GGAGAGAGAAGGGAATAGGACATG 59.717 50.000 0.00 0.00 0.00 3.21
342 364 4.889780 AGAGAGAAGGGAATAGGACATGT 58.110 43.478 0.00 0.00 0.00 3.21
343 365 6.031964 AGAGAGAAGGGAATAGGACATGTA 57.968 41.667 0.00 0.00 0.00 2.29
344 366 5.836358 AGAGAGAAGGGAATAGGACATGTAC 59.164 44.000 0.00 0.00 0.00 2.90
345 367 5.782925 AGAGAAGGGAATAGGACATGTACT 58.217 41.667 16.54 16.54 0.00 2.73
420 628 3.875727 CGCTAGACTGCCAGTAGTACTAA 59.124 47.826 3.61 0.00 0.00 2.24
442 650 5.155278 ACATAAGACACGTTTCCACCATA 57.845 39.130 0.00 0.00 0.00 2.74
445 653 2.774687 AGACACGTTTCCACCATAACC 58.225 47.619 0.00 0.00 0.00 2.85
446 654 1.461897 GACACGTTTCCACCATAACCG 59.538 52.381 0.00 0.00 0.00 4.44
591 799 9.892130 ACTCCTAAACTAAATCTAATCTTGGTG 57.108 33.333 0.00 0.00 0.00 4.17
653 861 6.595716 GGAAAGTGCAACAATCTAGTATGAGT 59.404 38.462 0.00 0.00 41.43 3.41
720 928 4.164822 ACTTGTGATTGCAGCATAACAC 57.835 40.909 15.62 15.62 0.00 3.32
748 956 4.401837 GGTACTCTCTCCGTTCCTAAACAT 59.598 45.833 0.00 0.00 34.93 2.71
785 993 9.570468 AGAGGTTTCAATATAGACTACATACGA 57.430 33.333 0.00 0.00 0.00 3.43
889 1098 6.819947 ATATTTAAGAACGGGGGAAGTACT 57.180 37.500 0.00 0.00 0.00 2.73
921 1130 5.390613 ACTGTACGTATTCTTTTTGCATGC 58.609 37.500 11.82 11.82 0.00 4.06
922 1131 5.181245 ACTGTACGTATTCTTTTTGCATGCT 59.819 36.000 20.33 0.00 0.00 3.79
923 1132 6.007936 TGTACGTATTCTTTTTGCATGCTT 57.992 33.333 20.33 0.00 0.00 3.91
924 1133 5.855925 TGTACGTATTCTTTTTGCATGCTTG 59.144 36.000 20.33 4.57 0.00 4.01
976 1185 6.854778 TGTGTTGATGTTGGAATATGACATG 58.145 36.000 0.00 0.00 34.38 3.21
984 1193 5.048852 TGTTGGAATATGACATGTGTGTGTG 60.049 40.000 1.15 0.00 39.09 3.82
988 1197 6.883756 TGGAATATGACATGTGTGTGTGTATT 59.116 34.615 1.15 0.00 39.09 1.89
1004 1213 5.183140 GTGTGTATTTTAAGCAGACCATGGT 59.817 40.000 19.89 19.89 42.89 3.55
1032 1241 2.714259 TTGCACCGCTAAAGCAACT 58.286 47.368 2.44 0.00 42.71 3.16
1191 1400 2.242043 CTCTTCCTTGGTGCCAACATT 58.758 47.619 0.00 0.00 0.00 2.71
1245 1457 2.478292 ACCATCGGTAATGAAGACCCT 58.522 47.619 0.00 0.00 37.59 4.34
1340 1552 2.906389 TGATGTGGGCTAGTCTTGTTCT 59.094 45.455 0.00 0.00 0.00 3.01
1365 1577 3.660111 GCCGTCAACACCACTGCC 61.660 66.667 0.00 0.00 0.00 4.85
1511 1732 7.053498 ACAATGCAAAAATGGTCCTTAAAAGT 58.947 30.769 0.00 0.00 0.00 2.66
1543 1770 6.109359 CCTGAAGACGTATTGATCCTTCTTT 58.891 40.000 0.00 0.00 35.53 2.52
1729 1975 3.069729 AGTTACAGGAGAGGACACAACAC 59.930 47.826 0.00 0.00 0.00 3.32
1882 4081 5.537674 AGGTCTTCAATGAAGCAGTTGAAAT 59.462 36.000 17.58 0.00 42.01 2.17
1929 4128 4.938080 TCAAGCTCCTAAGATGTCGATTC 58.062 43.478 0.00 0.00 0.00 2.52
1957 4156 5.363868 AGCCATACAATTGCTGAGACTAGTA 59.636 40.000 5.05 0.00 33.23 1.82
1985 4192 1.336755 GGCCCATAACTTATTGCCACG 59.663 52.381 11.75 0.00 38.73 4.94
2191 4405 3.616219 ACTTTTGCGAATGTGGGCTATA 58.384 40.909 4.48 0.00 0.00 1.31
2202 4416 2.054799 GTGGGCTATACTTCATGGGGA 58.945 52.381 0.00 0.00 0.00 4.81
2257 4510 7.809665 TCACTGTCAAATGTATTGTGATTCTG 58.190 34.615 0.00 0.00 0.00 3.02
2508 4765 4.098894 AGCATTGGGAGGACAAAATGAAT 58.901 39.130 0.00 0.00 32.86 2.57
2539 4796 3.675126 TATTTGCGCTCCACCCAAGCT 62.675 52.381 9.73 0.00 37.62 3.74
2682 4942 1.303561 GGCATCCCTGTGCACAAGA 60.304 57.895 21.98 20.03 46.81 3.02
2726 4989 2.060383 CCCTCTCGGCATCCAGTGA 61.060 63.158 0.00 0.00 0.00 3.41
2799 5068 2.808906 TGGAAGAGAGATCGGAGTCA 57.191 50.000 0.00 0.00 0.00 3.41
2926 5195 0.036732 CAAGAGCTTGTACAGGGCCA 59.963 55.000 6.18 0.00 35.92 5.36
2958 5227 1.605202 GCCAAACATGCAATCGTGGTT 60.605 47.619 10.47 0.00 39.59 3.67
2998 5270 1.611673 CGTTGAATCCTGAAGGGCTGT 60.612 52.381 0.00 0.00 35.41 4.40
3087 5362 2.796651 CTGCTCAAGAATGGCGCC 59.203 61.111 22.73 22.73 0.00 6.53
3335 5610 4.441079 GCCTAACGCTCCTAGTGATGTTTA 60.441 45.833 0.00 0.00 0.00 2.01
3349 5625 9.233232 CTAGTGATGTTTAACTTTGGTTTGAAC 57.767 33.333 0.00 0.00 36.92 3.18
3353 5629 8.307483 TGATGTTTAACTTTGGTTTGAACTCAA 58.693 29.630 0.00 0.00 36.92 3.02
3424 5701 8.430801 AGTGCTAGCTATTCTAAGAAACATTG 57.569 34.615 17.23 0.00 0.00 2.82
3520 5803 9.681062 CCTTAGTGTAATATTTCTCTTTTCCCA 57.319 33.333 0.00 0.00 0.00 4.37
3531 5814 3.381272 TCTCTTTTCCCAAGTGCAAGTTG 59.619 43.478 0.00 0.00 46.76 3.16
3550 5833 9.852091 GCAAGTTGAGAAGATATTTTGATCTTT 57.148 29.630 7.16 0.00 44.46 2.52
3802 6087 6.734104 ACATTTGTGCTACTCTTCAATCTC 57.266 37.500 0.00 0.00 0.00 2.75
3847 6135 6.872628 TCTATTCATCTTCAATCATGGCAC 57.127 37.500 0.00 0.00 0.00 5.01
3850 6138 8.380867 TCTATTCATCTTCAATCATGGCACTAT 58.619 33.333 0.00 0.00 0.00 2.12
3853 6141 8.929260 TTCATCTTCAATCATGGCACTATAAT 57.071 30.769 0.00 0.00 0.00 1.28
3863 6151 5.999600 TCATGGCACTATAATGAACATCAGG 59.000 40.000 0.00 0.00 0.00 3.86
3899 6187 2.866923 TCCAGATCCATAGACCACCA 57.133 50.000 0.00 0.00 0.00 4.17
3901 6189 3.668821 TCCAGATCCATAGACCACCAAT 58.331 45.455 0.00 0.00 0.00 3.16
3996 6284 6.036735 GCACAACTTGTTTTAGTAGACAGTCA 59.963 38.462 2.66 0.00 0.00 3.41
3997 6285 7.413657 GCACAACTTGTTTTAGTAGACAGTCAA 60.414 37.037 2.66 0.00 0.00 3.18
4019 6307 1.302192 GTCGTTGTGCTAAGGCCCA 60.302 57.895 0.00 0.00 37.74 5.36
4079 6368 7.376336 CGATGAAGAATAACGTAGATCGAAAGT 59.624 37.037 0.00 0.00 42.86 2.66
4108 6397 7.067859 CCAATCCAAAGACACATGAACATAGAT 59.932 37.037 0.00 0.00 0.00 1.98
4125 6414 3.996921 AGATGAACAACAGCCAGATCT 57.003 42.857 0.00 0.00 35.25 2.75
4129 6418 2.369860 TGAACAACAGCCAGATCTGAGT 59.630 45.455 24.62 15.65 37.51 3.41
4137 6426 4.411540 ACAGCCAGATCTGAGTAAATCCAT 59.588 41.667 24.62 0.00 37.51 3.41
4203 6496 0.104487 TTAGACGCACCACCGAAACA 59.896 50.000 0.00 0.00 0.00 2.83
4221 6514 0.692419 CAGGTGCTAGGTGGGGAGAT 60.692 60.000 0.00 0.00 0.00 2.75
4243 6536 5.157940 TCTTTGTTCCATCTTCAGAGAGG 57.842 43.478 0.00 0.00 34.85 3.69
4289 6582 4.795962 GCAGGACACAAACCCTAACAAATG 60.796 45.833 0.00 0.00 0.00 2.32
4310 6603 2.728318 GTCAAAGGAACGACTAACGACC 59.272 50.000 0.00 0.00 45.77 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.021390 ATCAGTACAGGCACAAGCGC 61.021 55.000 0.00 0.00 43.41 5.92
2 3 0.449388 GCATCAGTACAGGCACAAGC 59.551 55.000 0.00 0.00 41.10 4.01
3 4 2.005451 GAGCATCAGTACAGGCACAAG 58.995 52.381 0.00 0.00 33.17 3.16
5 6 0.975887 TGAGCATCAGTACAGGCACA 59.024 50.000 0.00 0.00 42.56 4.57
6 7 3.840831 TGAGCATCAGTACAGGCAC 57.159 52.632 0.00 0.00 42.56 5.01
25 26 6.418057 TTCAACATGGCTAAGGTGATTTTT 57.582 33.333 0.00 0.00 0.00 1.94
26 27 6.610075 ATTCAACATGGCTAAGGTGATTTT 57.390 33.333 0.00 0.00 0.00 1.82
27 28 6.400568 CAATTCAACATGGCTAAGGTGATTT 58.599 36.000 0.00 0.00 0.00 2.17
81 82 7.775093 TGTTAGATATGAGGTCCTGGATTTTTG 59.225 37.037 0.00 0.00 0.00 2.44
99 100 3.643320 CCATGTGGAGAGGCTGTTAGATA 59.357 47.826 0.00 0.00 37.39 1.98
104 105 1.556911 CTACCATGTGGAGAGGCTGTT 59.443 52.381 5.96 0.00 38.94 3.16
124 125 9.964303 CTTGGACTATACATAGCATGATCTATC 57.036 37.037 0.00 0.00 33.68 2.08
172 173 9.959721 ACACATCTTTCATGTACTTAAGGTAAT 57.040 29.630 7.53 0.00 31.56 1.89
179 180 9.996554 CCCATATACACATCTTTCATGTACTTA 57.003 33.333 0.00 0.00 31.88 2.24
241 257 6.341316 TCTGGATGCTAGACATGTTCTTTAC 58.659 40.000 0.00 0.00 39.84 2.01
253 275 3.334910 TCCTTGGATCTGGATGCTAGA 57.665 47.619 12.94 0.00 34.93 2.43
315 337 2.615391 CTATTCCCTTCTCTCTCCCCC 58.385 57.143 0.00 0.00 0.00 5.40
316 338 2.180308 TCCTATTCCCTTCTCTCTCCCC 59.820 54.545 0.00 0.00 0.00 4.81
317 339 3.236047 GTCCTATTCCCTTCTCTCTCCC 58.764 54.545 0.00 0.00 0.00 4.30
318 340 3.917300 TGTCCTATTCCCTTCTCTCTCC 58.083 50.000 0.00 0.00 0.00 3.71
321 343 5.836358 AGTACATGTCCTATTCCCTTCTCTC 59.164 44.000 0.00 0.00 0.00 3.20
323 345 7.598759 TTAGTACATGTCCTATTCCCTTCTC 57.401 40.000 0.00 0.00 0.00 2.87
324 346 8.568617 AATTAGTACATGTCCTATTCCCTTCT 57.431 34.615 0.00 0.00 0.00 2.85
327 349 9.845214 AGATAATTAGTACATGTCCTATTCCCT 57.155 33.333 0.00 0.00 0.00 4.20
334 356 9.632638 ATGCAAAAGATAATTAGTACATGTCCT 57.367 29.630 0.00 0.00 0.00 3.85
335 357 9.669353 CATGCAAAAGATAATTAGTACATGTCC 57.331 33.333 0.00 0.00 0.00 4.02
336 358 9.669353 CCATGCAAAAGATAATTAGTACATGTC 57.331 33.333 0.00 0.00 31.53 3.06
337 359 9.189156 ACCATGCAAAAGATAATTAGTACATGT 57.811 29.630 2.69 2.69 31.53 3.21
342 364 9.349713 CCCTTACCATGCAAAAGATAATTAGTA 57.650 33.333 0.00 0.00 0.00 1.82
343 365 7.839200 ACCCTTACCATGCAAAAGATAATTAGT 59.161 33.333 0.00 0.00 0.00 2.24
344 366 8.137437 CACCCTTACCATGCAAAAGATAATTAG 58.863 37.037 0.00 0.00 0.00 1.73
345 367 7.417342 GCACCCTTACCATGCAAAAGATAATTA 60.417 37.037 0.00 0.00 39.23 1.40
420 628 3.478857 TGGTGGAAACGTGTCTTATGT 57.521 42.857 5.55 0.00 0.00 2.29
442 650 1.079127 ATGCGTGCTAAGAGCGGTT 60.079 52.632 0.00 0.00 46.26 4.44
445 653 2.322422 GCATGCGTGCTAAGAGCG 59.678 61.111 23.72 0.00 46.26 5.03
506 714 0.963225 TGGAGACGTCAATTCGGACA 59.037 50.000 19.50 1.64 37.66 4.02
591 799 8.691797 AGAGAGAGAAATAGAGATTGTTGTACC 58.308 37.037 0.00 0.00 0.00 3.34
653 861 4.756642 AGAAGAACATCACGAGCAAATCAA 59.243 37.500 0.00 0.00 0.00 2.57
720 928 2.159085 GGAACGGAGAGAGTACCAATGG 60.159 54.545 0.00 0.00 0.00 3.16
856 1065 8.963725 CCCCCGTTCTTAAATATAAGTCTTTTT 58.036 33.333 0.00 0.00 39.65 1.94
889 1098 9.762933 AAAAAGAATACGTACAGTACTACCAAA 57.237 29.630 9.10 0.00 38.29 3.28
921 1130 1.959747 CTGAGAAACACGCATGCAAG 58.040 50.000 19.57 11.70 0.00 4.01
922 1131 0.040157 GCTGAGAAACACGCATGCAA 60.040 50.000 19.57 0.00 0.00 4.08
923 1132 1.165284 TGCTGAGAAACACGCATGCA 61.165 50.000 19.57 0.00 33.40 3.96
924 1133 0.040157 TTGCTGAGAAACACGCATGC 60.040 50.000 7.91 7.91 34.56 4.06
925 1134 1.265095 AGTTGCTGAGAAACACGCATG 59.735 47.619 6.03 0.00 34.56 4.06
926 1135 1.597742 AGTTGCTGAGAAACACGCAT 58.402 45.000 6.03 0.00 34.56 4.73
927 1136 1.378531 AAGTTGCTGAGAAACACGCA 58.621 45.000 6.03 0.00 33.43 5.24
928 1137 2.475200 AAAGTTGCTGAGAAACACGC 57.525 45.000 6.03 0.00 0.00 5.34
929 1138 5.156804 AGTTAAAGTTGCTGAGAAACACG 57.843 39.130 6.03 0.00 0.00 4.49
976 1185 5.008217 TGGTCTGCTTAAAATACACACACAC 59.992 40.000 0.00 0.00 0.00 3.82
984 1193 5.163652 GGTGACCATGGTCTGCTTAAAATAC 60.164 44.000 37.92 25.21 44.80 1.89
988 1197 2.790433 GGTGACCATGGTCTGCTTAAA 58.210 47.619 37.92 18.81 44.80 1.52
1004 1213 2.622011 GCGGTGCAATTTCCGGTGA 61.622 57.895 14.50 0.00 45.85 4.02
1031 1240 7.036996 TCTATGTGCTTAGAGAAGTCATCAG 57.963 40.000 0.00 0.00 34.11 2.90
1032 1241 7.432059 CATCTATGTGCTTAGAGAAGTCATCA 58.568 38.462 0.00 0.00 34.11 3.07
1191 1400 0.772124 AGAGGAGGGGCAGGAACAAA 60.772 55.000 0.00 0.00 0.00 2.83
1245 1457 6.154203 AGATCAGATGAATAAAGAGCGACA 57.846 37.500 0.00 0.00 0.00 4.35
1340 1552 1.514678 GGTGTTGACGGCAGCAATCA 61.515 55.000 10.25 0.00 36.98 2.57
1365 1577 2.604914 GTCATCATCACCAGCAACTACG 59.395 50.000 0.00 0.00 0.00 3.51
1486 1704 7.012232 CACTTTTAAGGACCATTTTTGCATTGT 59.988 33.333 0.00 0.00 0.00 2.71
1511 1732 4.680237 CGTCTTCAGGCGCCACCA 62.680 66.667 31.54 8.82 43.14 4.17
1543 1770 3.304391 GCAACAATAAGAGCAAACGGTGA 60.304 43.478 0.00 0.00 0.00 4.02
1729 1975 1.561643 TGAGGCTCCTTCTGTACCAG 58.438 55.000 12.86 0.00 0.00 4.00
1772 2018 0.836606 TGTCCTGTCAGCTTGGTTGA 59.163 50.000 0.00 0.00 0.00 3.18
1882 4081 9.123709 GAACAACGCAAATGAGAAACATAAATA 57.876 29.630 0.00 0.00 38.38 1.40
1893 4092 2.975851 GAGCTTGAACAACGCAAATGAG 59.024 45.455 0.00 0.00 0.00 2.90
1957 4156 5.244626 GCAATAAGTTATGGGCCTTGATGAT 59.755 40.000 4.53 0.00 0.00 2.45
1985 4192 1.237285 ACCATCTTGGAGCAACACGC 61.237 55.000 0.00 0.00 40.96 5.34
2202 4416 3.957508 TGGTCATTCCATGTCCATGAT 57.042 42.857 8.82 0.00 42.22 2.45
2241 4455 6.066690 CCAGATCCCAGAATCACAATACATT 58.933 40.000 0.00 0.00 0.00 2.71
2257 4510 8.218488 AGTACTTCCATATTTTAACCAGATCCC 58.782 37.037 0.00 0.00 0.00 3.85
2334 4590 2.359850 GCAATGTCCCGCACCTCA 60.360 61.111 0.00 0.00 0.00 3.86
2539 4796 1.620819 GAGAAGAGCCACTGGAGTTGA 59.379 52.381 0.00 0.00 0.00 3.18
2682 4942 0.686441 TGCCGGCCTGTAGATGTAGT 60.686 55.000 26.77 0.00 0.00 2.73
2779 5042 2.755655 GTGACTCCGATCTCTCTTCCAA 59.244 50.000 0.00 0.00 0.00 3.53
2799 5068 4.008933 GCAGACTCGGGCTGGTGT 62.009 66.667 8.57 0.00 34.00 4.16
2921 5190 1.454663 GCTTCCTTCTGGATGGCCC 60.455 63.158 0.00 0.00 42.81 5.80
2926 5195 2.978156 TGTTTGGCTTCCTTCTGGAT 57.022 45.000 0.00 0.00 42.81 3.41
3087 5362 1.518133 CAGCTTCTTCCCGAGCTCG 60.518 63.158 29.06 29.06 35.17 5.03
3240 5515 3.023119 TGCCCAAATGAGCGTTATCAAT 58.977 40.909 0.00 0.00 31.76 2.57
3241 5516 2.441410 TGCCCAAATGAGCGTTATCAA 58.559 42.857 0.00 0.00 31.76 2.57
3369 5646 5.047872 CACCACACCAATCAAGATCAATCAA 60.048 40.000 0.00 0.00 0.00 2.57
3511 5794 3.360867 TCAACTTGCACTTGGGAAAAGA 58.639 40.909 3.94 0.00 0.00 2.52
3520 5803 8.169977 TCAAAATATCTTCTCAACTTGCACTT 57.830 30.769 0.00 0.00 0.00 3.16
3899 6187 3.990092 TCAGTGCTTGTAGTCGTCAATT 58.010 40.909 0.00 0.00 0.00 2.32
3901 6189 3.446310 TTCAGTGCTTGTAGTCGTCAA 57.554 42.857 0.00 0.00 0.00 3.18
3996 6284 2.034179 GGCCTTAGCACAACGACTTTTT 59.966 45.455 0.00 0.00 42.56 1.94
3997 6285 1.607148 GGCCTTAGCACAACGACTTTT 59.393 47.619 0.00 0.00 42.56 2.27
4019 6307 0.037590 TTTGGTGCGCTGGTCCTATT 59.962 50.000 9.73 0.00 0.00 1.73
4079 6368 6.244654 TGTTCATGTGTCTTTGGATTGGATA 58.755 36.000 0.00 0.00 0.00 2.59
4108 6397 2.369860 ACTCAGATCTGGCTGTTGTTCA 59.630 45.455 22.42 0.00 37.20 3.18
4137 6426 3.002042 GTGTTCGACGAATCTATCCTCGA 59.998 47.826 14.27 0.00 41.66 4.04
4155 6444 2.203153 GGCGTGTGGAGGTGTGTT 60.203 61.111 0.00 0.00 0.00 3.32
4203 6496 0.399233 GATCTCCCCACCTAGCACCT 60.399 60.000 0.00 0.00 0.00 4.00
4253 6546 1.980765 TGTCCTGCTCAGAAAGGTGAT 59.019 47.619 0.00 0.00 34.94 3.06
4256 6549 1.131638 TGTGTCCTGCTCAGAAAGGT 58.868 50.000 0.00 0.00 34.94 3.50
4289 6582 2.728318 GGTCGTTAGTCGTTCCTTTGAC 59.272 50.000 0.00 0.00 40.80 3.18


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

AutoCloner maintained by Alex Coulton.