Multiple sequence alignment - TraesCS5D01G382000

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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 TraesCS5D01G382000 chr5D 100.000 2450 0 0 1 2450 451956600 451954151 0.000000e+00 4525.0
1 TraesCS5D01G382000 chr5D 84.157 890 52 30 662 1470 451971033 451970152 0.000000e+00 780.0
2 TraesCS5D01G382000 chr5D 79.426 209 25 14 1774 1967 451969929 451969724 5.500000e-27 132.0
3 TraesCS5D01G382000 chr5A 87.566 1142 51 37 929 2013 570784986 570783879 0.000000e+00 1238.0
4 TraesCS5D01G382000 chr5A 84.898 927 56 32 662 1533 570789410 570788513 0.000000e+00 859.0
5 TraesCS5D01G382000 chr5A 83.973 730 66 29 910 1606 570792023 570791312 0.000000e+00 652.0
6 TraesCS5D01G382000 chr5A 78.905 493 79 11 37 527 299588938 299589407 6.580000e-81 311.0
7 TraesCS5D01G382000 chr5A 88.350 103 10 1 2263 2363 570783509 570783407 3.310000e-24 122.0
8 TraesCS5D01G382000 chr5B 82.334 1268 99 51 662 1847 551799766 551798542 0.000000e+00 985.0
9 TraesCS5D01G382000 chr5B 85.082 972 73 35 662 1584 551740729 551739781 0.000000e+00 926.0
10 TraesCS5D01G382000 chr5B 83.915 945 76 39 941 1847 551764889 551763983 0.000000e+00 833.0
11 TraesCS5D01G382000 chr5B 92.824 432 23 4 2024 2448 551684756 551684326 9.620000e-174 619.0
12 TraesCS5D01G382000 chr5B 89.977 439 20 7 1439 1872 551685175 551684756 1.660000e-151 545.0
13 TraesCS5D01G382000 chr5B 85.337 416 58 1 37 452 311547810 311547398 6.260000e-116 427.0
14 TraesCS5D01G382000 chr5B 87.153 288 21 5 669 945 551767687 551767405 1.830000e-81 313.0
15 TraesCS5D01G382000 chr5B 82.895 76 7 4 1872 1947 551739365 551739296 2.030000e-06 63.9
16 TraesCS5D01G382000 chr5B 82.895 76 7 1 1872 1947 551798467 551798398 2.030000e-06 63.9
17 TraesCS5D01G382000 chr2D 88.038 418 47 3 37 452 112538251 112538667 2.190000e-135 492.0
18 TraesCS5D01G382000 chr2D 85.714 420 52 7 37 452 209113249 209113664 1.040000e-118 436.0
19 TraesCS5D01G382000 chr2B 87.050 417 52 2 37 452 162860272 162860687 1.030000e-128 470.0
20 TraesCS5D01G382000 chr2B 81.217 575 73 13 39 578 95792898 95792324 4.840000e-117 431.0
21 TraesCS5D01G382000 chr1D 87.019 416 54 0 37 452 10419681 10419266 1.030000e-128 470.0
22 TraesCS5D01G382000 chr1D 85.714 126 10 4 452 569 491415845 491415970 2.560000e-25 126.0
23 TraesCS5D01G382000 chr4D 85.817 416 58 1 37 452 495615530 495615944 8.040000e-120 440.0
24 TraesCS5D01G382000 chr4D 87.241 290 19 8 1724 2013 128996798 128996527 5.090000e-82 315.0
25 TraesCS5D01G382000 chr4D 85.561 187 11 9 1827 2013 99237363 99237193 5.380000e-42 182.0
26 TraesCS5D01G382000 chr4D 93.506 77 5 0 451 527 80083230 80083154 5.540000e-22 115.0
27 TraesCS5D01G382000 chr3A 85.442 419 56 3 37 452 693124977 693124561 4.840000e-117 431.0
28 TraesCS5D01G382000 chr1B 85.472 413 60 0 39 451 57805584 57805172 4.840000e-117 431.0
29 TraesCS5D01G382000 chr6D 88.621 290 15 8 1724 2013 75524877 75525148 1.090000e-88 337.0
30 TraesCS5D01G382000 chr6D 86.096 187 11 6 1827 2013 75531422 75531593 1.160000e-43 187.0
31 TraesCS5D01G382000 chr6D 98.077 52 1 0 1772 1823 124235705 124235654 9.330000e-15 91.6
32 TraesCS5D01G382000 chr3D 92.000 200 10 3 1724 1923 431277685 431277878 2.400000e-70 276.0
33 TraesCS5D01G382000 chr3D 95.652 69 3 0 1945 2013 431277996 431278064 7.160000e-21 111.0
34 TraesCS5D01G382000 chr4A 93.069 101 6 1 1724 1823 594591841 594591941 1.960000e-31 147.0
35 TraesCS5D01G382000 chr7B 91.463 82 7 0 451 532 6175308 6175227 1.990000e-21 113.0
36 TraesCS5D01G382000 chr7D 91.463 82 4 3 451 532 117781037 117780959 2.580000e-20 110.0
37 TraesCS5D01G382000 chr7D 92.308 78 5 1 450 527 578841229 578841305 2.580000e-20 110.0
38 TraesCS5D01G382000 chr7D 92.208 77 5 1 451 527 579046891 579046966 9.260000e-20 108.0
39 TraesCS5D01G382000 chr4B 92.308 78 5 1 451 527 596781653 596781576 2.580000e-20 110.0
40 TraesCS5D01G382000 chr2A 92.208 77 6 0 451 527 226459594 226459518 2.580000e-20 110.0
41 TraesCS5D01G382000 chr3B 97.368 38 1 0 3 40 400306812 400306775 5.650000e-07 65.8


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 TraesCS5D01G382000 chr5D 451954151 451956600 2449 True 4525.00 4525 100.00000 1 2450 1 chr5D.!!$R1 2449
1 TraesCS5D01G382000 chr5D 451969724 451971033 1309 True 456.00 780 81.79150 662 1967 2 chr5D.!!$R2 1305
2 TraesCS5D01G382000 chr5A 570783407 570792023 8616 True 717.75 1238 86.19675 662 2363 4 chr5A.!!$R1 1701
3 TraesCS5D01G382000 chr5B 551684326 551685175 849 True 582.00 619 91.40050 1439 2448 2 chr5B.!!$R2 1009
4 TraesCS5D01G382000 chr5B 551763983 551767687 3704 True 573.00 833 85.53400 669 1847 2 chr5B.!!$R4 1178
5 TraesCS5D01G382000 chr5B 551798398 551799766 1368 True 524.45 985 82.61450 662 1947 2 chr5B.!!$R5 1285
6 TraesCS5D01G382000 chr5B 551739296 551740729 1433 True 494.95 926 83.98850 662 1947 2 chr5B.!!$R3 1285
7 TraesCS5D01G382000 chr2B 95792324 95792898 574 True 431.00 431 81.21700 39 578 1 chr2B.!!$R1 539

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
193 194 0.032017 ATGTTCTCCCCGCCTAGTCT 60.032 55.0 0.0 0.0 0.0 3.24 F
459 487 0.322816 TGATTGAGGGGCTTCAGTGC 60.323 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1156 5712 0.239082 TACGTCATGAGCGTGTCGTT 59.761 50.0 24.18 7.25 42.22 3.85 R
1936 10892 0.537188 AGGGGATGTGCTACGAACAG 59.463 55.0 0.00 0.00 0.00 3.16 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
21 22 3.140814 GGCCGGATTTGCCCAGTC 61.141 66.667 5.05 0.00 43.33 3.51
22 23 3.140814 GCCGGATTTGCCCAGTCC 61.141 66.667 5.05 0.00 0.00 3.85
31 32 2.349755 GCCCAGTCCGGCTGTAAA 59.650 61.111 19.93 0.00 46.10 2.01
32 33 1.077716 GCCCAGTCCGGCTGTAAAT 60.078 57.895 19.93 0.00 46.10 1.40
34 35 1.376609 CCCAGTCCGGCTGTAAATGC 61.377 60.000 19.93 0.00 43.55 3.56
35 36 0.392998 CCAGTCCGGCTGTAAATGCT 60.393 55.000 19.93 0.00 43.55 3.79
43 44 2.420129 CGGCTGTAAATGCTCTTAGGGT 60.420 50.000 0.00 0.00 0.00 4.34
50 51 2.196742 ATGCTCTTAGGGTCATGGGA 57.803 50.000 0.00 0.00 0.00 4.37
102 103 2.039879 AGGGCTCCGTTTTTAGATGTGT 59.960 45.455 0.00 0.00 0.00 3.72
109 110 6.539649 TCCGTTTTTAGATGTGTCTTCAAG 57.460 37.500 0.00 0.00 35.87 3.02
175 176 3.244700 CGGCTCCCTGAAGATGGAATAAT 60.245 47.826 0.00 0.00 0.00 1.28
177 178 4.446889 GGCTCCCTGAAGATGGAATAATGT 60.447 45.833 0.00 0.00 0.00 2.71
193 194 0.032017 ATGTTCTCCCCGCCTAGTCT 60.032 55.000 0.00 0.00 0.00 3.24
199 200 2.356780 CCCCGCCTAGTCTCCGTTT 61.357 63.158 0.00 0.00 0.00 3.60
205 206 1.404391 GCCTAGTCTCCGTTTCGATGA 59.596 52.381 0.00 0.00 0.00 2.92
221 222 2.320367 GATGATGCGTCTACCATCGTC 58.680 52.381 7.58 13.33 44.04 4.20
228 229 1.000521 TCTACCATCGTCGGTGGGT 60.001 57.895 27.65 17.00 40.39 4.51
236 237 2.747686 GTCGGTGGGTGTGTGGAT 59.252 61.111 0.00 0.00 0.00 3.41
264 265 2.514824 GGCGGATCTGTCCTTGGC 60.515 66.667 2.89 0.00 42.73 4.52
282 283 0.811616 GCGGATTTGCTCGGATCTGT 60.812 55.000 0.42 0.00 32.45 3.41
284 285 1.594862 CGGATTTGCTCGGATCTGTTC 59.405 52.381 0.42 0.00 0.00 3.18
287 288 1.710013 TTTGCTCGGATCTGTTCGTC 58.290 50.000 0.42 0.00 0.00 4.20
305 306 0.722469 TCGTTCGTCTACGTTCGTGC 60.722 55.000 8.14 0.00 42.01 5.34
308 309 1.717645 GTTCGTCTACGTTCGTGCATT 59.282 47.619 8.14 0.00 40.80 3.56
313 314 3.181534 CGTCTACGTTCGTGCATTTTCAT 60.182 43.478 8.14 0.00 34.11 2.57
317 318 4.475763 ACGTTCGTGCATTTTCATGTTA 57.524 36.364 0.00 0.00 32.28 2.41
345 346 4.533225 TTCGATCTACGCTACTCTTCAC 57.467 45.455 0.00 0.00 42.26 3.18
347 348 2.348685 CGATCTACGCTACTCTTCACCG 60.349 54.545 0.00 0.00 34.51 4.94
380 381 1.264749 TTCTGGTGCGCTGGTCCTAT 61.265 55.000 9.73 0.00 0.00 2.57
385 386 3.480133 GCGCTGGTCCTATGGGGT 61.480 66.667 0.00 0.00 36.25 4.95
394 395 2.116238 GTCCTATGGGGTCTTAGCACA 58.884 52.381 0.00 0.00 31.46 4.57
397 398 2.238646 CCTATGGGGTCTTAGCACAACA 59.761 50.000 0.00 0.00 30.29 3.33
403 404 3.477530 GGGTCTTAGCACAACAACTTCT 58.522 45.455 0.00 0.00 0.00 2.85
404 405 3.883489 GGGTCTTAGCACAACAACTTCTT 59.117 43.478 0.00 0.00 0.00 2.52
426 427 7.553334 TCTTGACTGTCTACTACAACAAGTTT 58.447 34.615 9.51 0.00 44.28 2.66
428 429 9.309516 CTTGACTGTCTACTACAACAAGTTTTA 57.690 33.333 9.51 0.00 41.93 1.52
451 452 2.190578 CTCCGGTGATTGAGGGGC 59.809 66.667 0.00 0.00 0.00 5.80
459 487 0.322816 TGATTGAGGGGCTTCAGTGC 60.323 55.000 0.00 0.00 0.00 4.40
489 517 1.105167 CGCCAGGTGGTCTACGGATA 61.105 60.000 0.00 0.00 37.57 2.59
533 568 1.063764 GTTGTTCGTTGTACCGCCAAA 59.936 47.619 0.00 0.00 0.00 3.28
540 575 4.001652 TCGTTGTACCGCCAAAATGAATA 58.998 39.130 0.00 0.00 0.00 1.75
544 579 6.199393 GTTGTACCGCCAAAATGAATAGATC 58.801 40.000 0.00 0.00 0.00 2.75
546 581 2.878406 ACCGCCAAAATGAATAGATCGG 59.122 45.455 0.00 0.00 40.09 4.18
548 583 3.753272 CCGCCAAAATGAATAGATCGGAT 59.247 43.478 0.00 0.00 36.77 4.18
588 624 9.777297 AAAAACTAATGTGAATAGCCATGTTTT 57.223 25.926 0.00 0.00 36.07 2.43
589 625 9.777297 AAAACTAATGTGAATAGCCATGTTTTT 57.223 25.926 0.00 0.00 32.36 1.94
619 655 7.505585 TGATAGAATAAAAAGTTATGGCTGGGG 59.494 37.037 0.00 0.00 30.04 4.96
620 656 5.589831 AGAATAAAAAGTTATGGCTGGGGT 58.410 37.500 0.00 0.00 30.04 4.95
621 657 6.022958 AGAATAAAAAGTTATGGCTGGGGTT 58.977 36.000 0.00 0.00 30.04 4.11
622 658 6.500400 AGAATAAAAAGTTATGGCTGGGGTTT 59.500 34.615 0.00 0.00 30.04 3.27
623 659 7.676468 AGAATAAAAAGTTATGGCTGGGGTTTA 59.324 33.333 0.00 0.00 30.04 2.01
624 660 7.800300 ATAAAAAGTTATGGCTGGGGTTTAA 57.200 32.000 0.00 0.00 0.00 1.52
625 661 5.738619 AAAAGTTATGGCTGGGGTTTAAG 57.261 39.130 0.00 0.00 0.00 1.85
626 662 4.668138 AAGTTATGGCTGGGGTTTAAGA 57.332 40.909 0.00 0.00 0.00 2.10
627 663 4.668138 AGTTATGGCTGGGGTTTAAGAA 57.332 40.909 0.00 0.00 0.00 2.52
628 664 5.005628 AGTTATGGCTGGGGTTTAAGAAA 57.994 39.130 0.00 0.00 0.00 2.52
629 665 5.399113 AGTTATGGCTGGGGTTTAAGAAAA 58.601 37.500 0.00 0.00 0.00 2.29
630 666 6.022958 AGTTATGGCTGGGGTTTAAGAAAAT 58.977 36.000 0.00 0.00 0.00 1.82
631 667 7.186268 AGTTATGGCTGGGGTTTAAGAAAATA 58.814 34.615 0.00 0.00 0.00 1.40
632 668 5.932619 ATGGCTGGGGTTTAAGAAAATAC 57.067 39.130 0.00 0.00 0.00 1.89
633 669 4.742012 TGGCTGGGGTTTAAGAAAATACA 58.258 39.130 0.00 0.00 0.00 2.29
634 670 5.148502 TGGCTGGGGTTTAAGAAAATACAA 58.851 37.500 0.00 0.00 0.00 2.41
636 672 6.099845 TGGCTGGGGTTTAAGAAAATACAAAA 59.900 34.615 0.00 0.00 0.00 2.44
638 674 7.214381 GCTGGGGTTTAAGAAAATACAAAAGT 58.786 34.615 0.00 0.00 0.00 2.66
639 675 7.384115 GCTGGGGTTTAAGAAAATACAAAAGTC 59.616 37.037 0.00 0.00 0.00 3.01
641 677 8.417884 TGGGGTTTAAGAAAATACAAAAGTCAG 58.582 33.333 0.00 0.00 0.00 3.51
642 678 7.384115 GGGGTTTAAGAAAATACAAAAGTCAGC 59.616 37.037 0.00 0.00 0.00 4.26
643 679 8.141909 GGGTTTAAGAAAATACAAAAGTCAGCT 58.858 33.333 0.00 0.00 0.00 4.24
644 680 8.968242 GGTTTAAGAAAATACAAAAGTCAGCTG 58.032 33.333 7.63 7.63 0.00 4.24
645 681 9.730420 GTTTAAGAAAATACAAAAGTCAGCTGA 57.270 29.630 13.74 13.74 0.00 4.26
646 682 9.950680 TTTAAGAAAATACAAAAGTCAGCTGAG 57.049 29.630 18.89 7.58 0.00 3.35
647 683 6.566197 AGAAAATACAAAAGTCAGCTGAGG 57.434 37.500 18.89 7.17 0.00 3.86
648 684 5.474876 AGAAAATACAAAAGTCAGCTGAGGG 59.525 40.000 18.89 7.53 0.00 4.30
649 685 4.640771 AATACAAAAGTCAGCTGAGGGA 57.359 40.909 18.89 1.43 0.00 4.20
654 690 2.262423 AAGTCAGCTGAGGGACAAAC 57.738 50.000 18.89 2.90 36.50 2.93
655 691 1.131638 AGTCAGCTGAGGGACAAACA 58.868 50.000 18.89 0.00 36.50 2.83
656 692 1.071385 AGTCAGCTGAGGGACAAACAG 59.929 52.381 18.89 0.00 36.50 3.16
705 2666 7.937294 CAGCGACGTTGTTTTTCATTTTATTAC 59.063 33.333 4.37 0.00 0.00 1.89
719 2680 4.563140 TTTATTACGAGAGGCAAAGGGT 57.437 40.909 0.00 0.00 0.00 4.34
733 2694 4.139038 GCAAAGGGTTACAAGTTACAGGA 58.861 43.478 0.00 0.00 0.00 3.86
734 2695 4.581409 GCAAAGGGTTACAAGTTACAGGAA 59.419 41.667 0.00 0.00 0.00 3.36
737 2698 7.685884 GCAAAGGGTTACAAGTTACAGGAAAAT 60.686 37.037 0.00 0.00 0.00 1.82
967 5495 2.217038 AAAGGCTGGACTGGAGCGA 61.217 57.895 0.00 0.00 37.32 4.93
984 5512 0.583438 CGATAGTTCGCTGGCATTGG 59.417 55.000 0.00 0.00 38.75 3.16
1012 5559 4.530857 GGAGCATGGACCCGGACG 62.531 72.222 0.73 0.00 0.00 4.79
1026 5573 4.719369 GACGTCGCGCTCCACCTT 62.719 66.667 5.56 0.00 0.00 3.50
1069 5616 2.951745 CGGTGCTCATCGTCGCTC 60.952 66.667 0.00 0.00 0.00 5.03
1078 5625 2.883468 ATCGTCGCTCTAGCCGTCG 61.883 63.158 12.94 12.94 37.91 5.12
1248 5834 4.019312 TGCGCCATCTGCCTGTCA 62.019 61.111 4.18 0.00 36.24 3.58
1531 10296 4.233635 GCAGAGGATGCGCGCTTG 62.234 66.667 33.29 19.60 46.99 4.01
1532 10297 4.233635 CAGAGGATGCGCGCTTGC 62.234 66.667 33.29 29.96 0.00 4.01
1549 10321 2.821366 CACATGCGAGGGAGGCAC 60.821 66.667 0.00 0.00 44.23 5.01
1688 10558 0.249657 GGCATCGGACAAGAGGCTAG 60.250 60.000 3.73 0.00 45.93 3.42
1689 10559 0.461961 GCATCGGACAAGAGGCTAGT 59.538 55.000 0.00 0.00 43.66 2.57
1690 10560 1.681793 GCATCGGACAAGAGGCTAGTA 59.318 52.381 0.00 0.00 43.66 1.82
1748 10641 6.092396 TGCCATTGCAATAAATTACAAGCAAG 59.908 34.615 12.53 0.00 46.66 4.01
1768 10665 6.650807 AGCAAGTTTAATTGAAGTGATCGAGA 59.349 34.615 0.00 0.00 31.55 4.04
1769 10666 6.958193 GCAAGTTTAATTGAAGTGATCGAGAG 59.042 38.462 0.00 0.00 31.55 3.20
1852 10774 4.657824 CGTCGACTGCCAACCGGT 62.658 66.667 14.70 0.00 35.17 5.28
1859 10784 1.670811 GACTGCCAACCGGTTATCATG 59.329 52.381 21.79 8.02 31.71 3.07
1935 10891 3.067106 ACTTTGACATGTTCTAGCCACG 58.933 45.455 0.00 0.00 0.00 4.94
1936 10892 1.438651 TTGACATGTTCTAGCCACGC 58.561 50.000 0.00 0.00 0.00 5.34
1942 10898 0.666274 TGTTCTAGCCACGCTGTTCG 60.666 55.000 0.00 0.00 40.10 3.95
1969 10925 5.417580 GCACATCCCCTTGTATTTTAACTCA 59.582 40.000 0.00 0.00 0.00 3.41
2013 10969 1.279840 GCGTGGACTTTGACACAGC 59.720 57.895 0.00 0.00 37.45 4.40
2014 10970 1.941812 CGTGGACTTTGACACAGCC 59.058 57.895 0.00 0.00 37.45 4.85
2015 10971 0.532862 CGTGGACTTTGACACAGCCT 60.533 55.000 0.00 0.00 37.45 4.58
2019 11183 1.269257 GGACTTTGACACAGCCTTTGC 60.269 52.381 0.00 0.00 37.95 3.68
2088 11256 5.047519 TCCTTCCCTTGTACTTTAACTCTCG 60.048 44.000 0.00 0.00 0.00 4.04
2098 11266 5.796424 ACTTTAACTCTCGAAACCACCTA 57.204 39.130 0.00 0.00 0.00 3.08
2104 11272 4.300189 CTCTCGAAACCACCTATGAGAG 57.700 50.000 3.00 3.00 42.22 3.20
2160 11329 1.139853 GGCACATAGTCCTTCCTCCAG 59.860 57.143 0.00 0.00 0.00 3.86
2209 11378 5.034797 GCACAAACTACTCCTTTCAAACAC 58.965 41.667 0.00 0.00 0.00 3.32
2231 11400 8.076714 ACACGATTAAGATAACATAGTGCATG 57.923 34.615 0.00 0.00 40.78 4.06
2247 11416 5.946298 AGTGCATGATTGTTCATAACACTG 58.054 37.500 16.67 0.00 46.61 3.66
2309 11478 8.813951 ACTACCACTTAATTAAGCTCAAGTACT 58.186 33.333 22.45 0.00 36.79 2.73
2321 11490 3.066203 GCTCAAGTACTGCTCTACTCCTC 59.934 52.174 0.00 0.00 0.00 3.71
2368 11539 1.153756 CCCACTGAAGCCCAACCTT 59.846 57.895 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.140814 GGACTGGGCAAATCCGGC 61.141 66.667 0.00 0.00 36.66 6.13
18 19 0.905357 AGAGCATTTACAGCCGGACT 59.095 50.000 5.05 0.00 0.00 3.85
19 20 1.739067 AAGAGCATTTACAGCCGGAC 58.261 50.000 5.05 0.00 0.00 4.79
20 21 2.158957 CCTAAGAGCATTTACAGCCGGA 60.159 50.000 5.05 0.00 0.00 5.14
21 22 2.213499 CCTAAGAGCATTTACAGCCGG 58.787 52.381 0.00 0.00 0.00 6.13
22 23 2.213499 CCCTAAGAGCATTTACAGCCG 58.787 52.381 0.00 0.00 0.00 5.52
24 25 3.873910 TGACCCTAAGAGCATTTACAGC 58.126 45.455 0.00 0.00 0.00 4.40
25 26 4.818546 CCATGACCCTAAGAGCATTTACAG 59.181 45.833 0.00 0.00 0.00 2.74
28 29 4.044308 TCCCATGACCCTAAGAGCATTTA 58.956 43.478 0.00 0.00 0.00 1.40
30 31 2.441001 CTCCCATGACCCTAAGAGCATT 59.559 50.000 0.00 0.00 0.00 3.56
31 32 2.053244 CTCCCATGACCCTAAGAGCAT 58.947 52.381 0.00 0.00 0.00 3.79
32 33 1.500474 CTCCCATGACCCTAAGAGCA 58.500 55.000 0.00 0.00 0.00 4.26
34 35 0.390860 CGCTCCCATGACCCTAAGAG 59.609 60.000 0.00 0.00 0.00 2.85
35 36 0.325296 ACGCTCCCATGACCCTAAGA 60.325 55.000 0.00 0.00 0.00 2.10
77 78 0.326927 CTAAAAACGGAGCCCTCCCA 59.673 55.000 8.68 0.00 46.96 4.37
102 103 6.605594 ACACAAACCCTAACAAATCTTGAAGA 59.394 34.615 0.00 0.00 0.00 2.87
109 110 6.002082 AGTAGGACACAAACCCTAACAAATC 58.998 40.000 0.00 0.00 36.84 2.17
150 151 3.854669 ATCTTCAGGGAGCCGCCG 61.855 66.667 0.00 0.00 37.63 6.46
175 176 0.683504 GAGACTAGGCGGGGAGAACA 60.684 60.000 0.00 0.00 0.00 3.18
177 178 1.076192 GGAGACTAGGCGGGGAGAA 60.076 63.158 0.00 0.00 0.00 2.87
193 194 0.172578 AGACGCATCATCGAAACGGA 59.827 50.000 0.00 0.00 0.00 4.69
199 200 2.706555 GATGGTAGACGCATCATCGA 57.293 50.000 0.00 0.00 0.00 3.59
205 206 1.359117 CCGACGATGGTAGACGCAT 59.641 57.895 0.00 0.00 0.00 4.73
221 222 1.095228 GCATATCCACACACCCACCG 61.095 60.000 0.00 0.00 0.00 4.94
228 229 0.752658 CGGAGAGGCATATCCACACA 59.247 55.000 13.13 0.00 36.55 3.72
264 265 1.594862 GAACAGATCCGAGCAAATCCG 59.405 52.381 0.00 0.00 0.00 4.18
335 336 2.901042 GCCCCCGGTGAAGAGTAG 59.099 66.667 0.00 0.00 0.00 2.57
347 348 2.203437 AGAACAACAACCGCCCCC 60.203 61.111 0.00 0.00 0.00 5.40
358 359 1.891919 GACCAGCGCACCAGAACAA 60.892 57.895 11.47 0.00 0.00 2.83
380 381 1.493022 AGTTGTTGTGCTAAGACCCCA 59.507 47.619 0.00 0.00 0.00 4.96
385 386 5.294306 CAGTCAAGAAGTTGTTGTGCTAAGA 59.706 40.000 12.07 0.00 34.98 2.10
394 395 7.108841 TGTAGTAGACAGTCAAGAAGTTGTT 57.891 36.000 2.66 0.00 32.64 2.83
397 398 7.108841 TGTTGTAGTAGACAGTCAAGAAGTT 57.891 36.000 2.66 0.00 39.88 2.66
403 404 9.090692 GTAAAACTTGTTGTAGTAGACAGTCAA 57.909 33.333 2.66 0.00 39.88 3.18
404 405 7.707893 GGTAAAACTTGTTGTAGTAGACAGTCA 59.292 37.037 2.66 0.00 39.88 3.41
443 444 0.538057 CAAGCACTGAAGCCCCTCAA 60.538 55.000 0.00 0.00 34.23 3.02
451 452 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
459 487 0.732880 CACCTGGCGACGACTACAAG 60.733 60.000 0.65 0.00 0.00 3.16
511 539 0.869730 GGCGGTACAACGAACAACAT 59.130 50.000 0.00 0.00 35.47 2.71
513 541 0.656785 TTGGCGGTACAACGAACAAC 59.343 50.000 0.00 0.00 35.47 3.32
514 542 1.376543 TTTGGCGGTACAACGAACAA 58.623 45.000 0.00 0.00 35.47 2.83
527 555 4.214119 ACATCCGATCTATTCATTTTGGCG 59.786 41.667 0.00 0.00 0.00 5.69
592 628 8.912988 CCCAGCCATAACTTTTTATTCTATCAA 58.087 33.333 0.00 0.00 0.00 2.57
593 629 7.505585 CCCCAGCCATAACTTTTTATTCTATCA 59.494 37.037 0.00 0.00 0.00 2.15
595 631 7.362234 ACCCCAGCCATAACTTTTTATTCTAT 58.638 34.615 0.00 0.00 0.00 1.98
596 632 6.737608 ACCCCAGCCATAACTTTTTATTCTA 58.262 36.000 0.00 0.00 0.00 2.10
597 633 5.589831 ACCCCAGCCATAACTTTTTATTCT 58.410 37.500 0.00 0.00 0.00 2.40
598 634 5.932619 ACCCCAGCCATAACTTTTTATTC 57.067 39.130 0.00 0.00 0.00 1.75
599 635 6.696042 AAACCCCAGCCATAACTTTTTATT 57.304 33.333 0.00 0.00 0.00 1.40
600 636 7.676468 TCTTAAACCCCAGCCATAACTTTTTAT 59.324 33.333 0.00 0.00 0.00 1.40
601 637 7.011382 TCTTAAACCCCAGCCATAACTTTTTA 58.989 34.615 0.00 0.00 0.00 1.52
602 638 5.841783 TCTTAAACCCCAGCCATAACTTTTT 59.158 36.000 0.00 0.00 0.00 1.94
603 639 5.399113 TCTTAAACCCCAGCCATAACTTTT 58.601 37.500 0.00 0.00 0.00 2.27
604 640 5.005628 TCTTAAACCCCAGCCATAACTTT 57.994 39.130 0.00 0.00 0.00 2.66
605 641 4.668138 TCTTAAACCCCAGCCATAACTT 57.332 40.909 0.00 0.00 0.00 2.66
606 642 4.668138 TTCTTAAACCCCAGCCATAACT 57.332 40.909 0.00 0.00 0.00 2.24
608 644 6.954684 TGTATTTTCTTAAACCCCAGCCATAA 59.045 34.615 0.00 0.00 0.00 1.90
609 645 6.494952 TGTATTTTCTTAAACCCCAGCCATA 58.505 36.000 0.00 0.00 0.00 2.74
610 646 5.337788 TGTATTTTCTTAAACCCCAGCCAT 58.662 37.500 0.00 0.00 0.00 4.40
611 647 4.742012 TGTATTTTCTTAAACCCCAGCCA 58.258 39.130 0.00 0.00 0.00 4.75
612 648 5.731957 TTGTATTTTCTTAAACCCCAGCC 57.268 39.130 0.00 0.00 0.00 4.85
614 650 8.417884 TGACTTTTGTATTTTCTTAAACCCCAG 58.582 33.333 0.00 0.00 0.00 4.45
615 651 8.307582 TGACTTTTGTATTTTCTTAAACCCCA 57.692 30.769 0.00 0.00 0.00 4.96
616 652 7.384115 GCTGACTTTTGTATTTTCTTAAACCCC 59.616 37.037 0.00 0.00 0.00 4.95
619 655 9.730420 TCAGCTGACTTTTGTATTTTCTTAAAC 57.270 29.630 13.74 0.00 0.00 2.01
620 656 9.950680 CTCAGCTGACTTTTGTATTTTCTTAAA 57.049 29.630 13.74 0.00 0.00 1.52
621 657 8.567948 CCTCAGCTGACTTTTGTATTTTCTTAA 58.432 33.333 13.74 0.00 0.00 1.85
622 658 7.174946 CCCTCAGCTGACTTTTGTATTTTCTTA 59.825 37.037 13.74 0.00 0.00 2.10
623 659 6.015940 CCCTCAGCTGACTTTTGTATTTTCTT 60.016 38.462 13.74 0.00 0.00 2.52
624 660 5.474876 CCCTCAGCTGACTTTTGTATTTTCT 59.525 40.000 13.74 0.00 0.00 2.52
625 661 5.473504 TCCCTCAGCTGACTTTTGTATTTTC 59.526 40.000 13.74 0.00 0.00 2.29
626 662 5.241728 GTCCCTCAGCTGACTTTTGTATTTT 59.758 40.000 13.74 0.00 0.00 1.82
627 663 4.762251 GTCCCTCAGCTGACTTTTGTATTT 59.238 41.667 13.74 0.00 0.00 1.40
628 664 4.202461 TGTCCCTCAGCTGACTTTTGTATT 60.202 41.667 13.74 0.00 32.67 1.89
629 665 3.327757 TGTCCCTCAGCTGACTTTTGTAT 59.672 43.478 13.74 0.00 32.67 2.29
630 666 2.703536 TGTCCCTCAGCTGACTTTTGTA 59.296 45.455 13.74 0.00 32.67 2.41
631 667 1.490490 TGTCCCTCAGCTGACTTTTGT 59.510 47.619 13.74 0.00 32.67 2.83
632 668 2.260844 TGTCCCTCAGCTGACTTTTG 57.739 50.000 13.74 2.19 32.67 2.44
633 669 2.952310 GTTTGTCCCTCAGCTGACTTTT 59.048 45.455 13.74 0.00 32.67 2.27
634 670 2.092429 TGTTTGTCCCTCAGCTGACTTT 60.092 45.455 13.74 0.00 32.67 2.66
636 672 1.071385 CTGTTTGTCCCTCAGCTGACT 59.929 52.381 13.74 0.00 32.67 3.41
638 674 1.131638 ACTGTTTGTCCCTCAGCTGA 58.868 50.000 17.19 17.19 33.12 4.26
639 675 1.972872 AACTGTTTGTCCCTCAGCTG 58.027 50.000 7.63 7.63 33.12 4.24
641 677 2.226674 GCTAAACTGTTTGTCCCTCAGC 59.773 50.000 15.69 10.49 33.12 4.26
642 678 3.499918 CAGCTAAACTGTTTGTCCCTCAG 59.500 47.826 15.69 4.55 41.86 3.35
643 679 3.476552 CAGCTAAACTGTTTGTCCCTCA 58.523 45.455 15.69 0.00 41.86 3.86
655 691 8.335532 TGTCTTGCATTTATTACAGCTAAACT 57.664 30.769 0.00 0.00 0.00 2.66
656 692 8.606727 CTGTCTTGCATTTATTACAGCTAAAC 57.393 34.615 0.00 0.00 0.00 2.01
666 2619 2.742053 ACGTCGCTGTCTTGCATTTATT 59.258 40.909 0.00 0.00 0.00 1.40
667 2620 2.346803 ACGTCGCTGTCTTGCATTTAT 58.653 42.857 0.00 0.00 0.00 1.40
674 2627 2.452006 AAAACAACGTCGCTGTCTTG 57.548 45.000 1.08 0.00 0.00 3.02
705 2666 2.076863 CTTGTAACCCTTTGCCTCTCG 58.923 52.381 0.00 0.00 0.00 4.04
750 2711 9.647797 TCTCAATTCCTTTGAAAATGATGAATG 57.352 29.630 0.00 0.00 43.64 2.67
752 2713 9.081204 TCTCTCAATTCCTTTGAAAATGATGAA 57.919 29.630 0.00 0.00 43.64 2.57
753 2714 8.640063 TCTCTCAATTCCTTTGAAAATGATGA 57.360 30.769 0.00 0.00 43.64 2.92
754 2715 9.355215 CTTCTCTCAATTCCTTTGAAAATGATG 57.645 33.333 0.00 0.00 43.64 3.07
771 2732 8.915057 ATTCAATTGTCTTCTTCTTCTCTCAA 57.085 30.769 5.13 0.00 0.00 3.02
772 2740 8.915057 AATTCAATTGTCTTCTTCTTCTCTCA 57.085 30.769 5.13 0.00 0.00 3.27
802 2774 1.873863 GGCACTACTCCGGTTTTGC 59.126 57.895 0.00 4.53 33.74 3.68
967 5495 0.394216 TGCCAATGCCAGCGAACTAT 60.394 50.000 0.00 0.00 36.33 2.12
984 5512 1.143183 CATGCTCCTTGGCCAATGC 59.857 57.895 20.85 22.30 0.00 3.56
1012 5559 2.564553 ATCTGAAGGTGGAGCGCGAC 62.565 60.000 12.10 1.97 0.00 5.19
1156 5712 0.239082 TACGTCATGAGCGTGTCGTT 59.761 50.000 24.18 7.25 42.22 3.85
1248 5834 4.790962 TCGCCCTCGCCGTACTCT 62.791 66.667 0.00 0.00 35.26 3.24
1531 10296 4.783621 TGCCTCCCTCGCATGTGC 62.784 66.667 0.00 0.00 37.78 4.57
1532 10297 2.821366 GTGCCTCCCTCGCATGTG 60.821 66.667 0.00 0.00 38.76 3.21
1533 10298 4.101448 GGTGCCTCCCTCGCATGT 62.101 66.667 0.00 0.00 38.76 3.21
1534 10299 3.746949 GAGGTGCCTCCCTCGCATG 62.747 68.421 6.98 0.00 41.58 4.06
1535 10300 3.474570 GAGGTGCCTCCCTCGCAT 61.475 66.667 6.98 0.00 41.58 4.73
1540 10305 0.613012 GCAAATTGAGGTGCCTCCCT 60.613 55.000 14.97 0.37 42.09 4.20
1541 10306 0.899717 TGCAAATTGAGGTGCCTCCC 60.900 55.000 14.97 0.00 42.09 4.30
1549 10321 3.592059 CATTTCCACCTGCAAATTGAGG 58.408 45.455 0.00 3.65 35.26 3.86
1688 10558 2.987149 CGTGTGTGAGATGGTGTTCTAC 59.013 50.000 0.00 0.00 0.00 2.59
1689 10559 2.609491 GCGTGTGTGAGATGGTGTTCTA 60.609 50.000 0.00 0.00 0.00 2.10
1690 10560 1.873903 GCGTGTGTGAGATGGTGTTCT 60.874 52.381 0.00 0.00 0.00 3.01
1748 10641 7.596749 TTCCTCTCGATCACTTCAATTAAAC 57.403 36.000 0.00 0.00 0.00 2.01
1777 10674 1.262683 GCTCGCTATTGGCATCAACTC 59.737 52.381 0.00 0.00 41.91 3.01
1859 10784 6.983307 TGCTCAGCTTAGATAGAAGTTGATTC 59.017 38.462 0.00 1.21 43.16 2.52
1935 10891 1.090052 GGGGATGTGCTACGAACAGC 61.090 60.000 0.00 0.00 42.15 4.40
1936 10892 0.537188 AGGGGATGTGCTACGAACAG 59.463 55.000 0.00 0.00 0.00 3.16
1942 10898 6.602009 AGTTAAAATACAAGGGGATGTGCTAC 59.398 38.462 0.00 0.00 34.75 3.58
2088 11256 6.594547 GGAGTTAAACTCTCATAGGTGGTTTC 59.405 42.308 0.00 0.00 44.46 2.78
2209 11378 9.750882 CAATCATGCACTATGTTATCTTAATCG 57.249 33.333 0.00 0.00 38.01 3.34
2265 11434 6.001460 TGGTAGTTCAGGTTAATTTGAGTGG 58.999 40.000 0.00 0.00 0.00 4.00
2309 11478 1.600638 TCCGACGAGGAGTAGAGCA 59.399 57.895 0.00 0.00 45.98 4.26
2321 11490 3.659089 AACGCAATCCCCTCCGACG 62.659 63.158 0.00 0.00 0.00 5.12
2353 11522 4.929807 CCAAGGTTGGGCTTCAGT 57.070 55.556 0.27 0.00 44.70 3.41


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

AutoCloner maintained by Alex Coulton.