Multiple sequence alignment - TraesCS7D01G387200

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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 TraesCS7D01G387200 chr7D 100.000 4159 0 0 1 4159 501098611 501094453 0.000000e+00 7681
1 TraesCS7D01G387200 chr7D 91.852 135 8 3 503 635 53506219 53506086 7.100000e-43 185
2 TraesCS7D01G387200 chr7B 94.622 3570 130 31 637 4159 530382231 530378677 0.000000e+00 5472
3 TraesCS7D01G387200 chr7B 90.514 506 36 7 18 515 530382737 530382236 0.000000e+00 658
4 TraesCS7D01G387200 chr7B 91.729 133 8 2 507 638 456489733 456489863 9.180000e-42 182
5 TraesCS7D01G387200 chr7A 92.046 3583 192 41 634 4159 567586138 567582592 0.000000e+00 4951
6 TraesCS7D01G387200 chr7A 87.843 510 46 13 18 522 567586632 567586134 5.990000e-163 584
7 TraesCS7D01G387200 chr2B 93.333 660 37 5 3296 3952 38033567 38032912 0.000000e+00 968
8 TraesCS7D01G387200 chr2B 93.651 126 4 4 514 637 594838172 594838049 7.100000e-43 185
9 TraesCS7D01G387200 chr3D 95.161 124 5 1 521 643 341502523 341502400 1.180000e-45 195
10 TraesCS7D01G387200 chr4A 94.444 126 4 3 512 635 571587194 571587070 1.530000e-44 191
11 TraesCS7D01G387200 chr6D 93.701 127 7 1 514 639 287026020 287025894 5.490000e-44 189
12 TraesCS7D01G387200 chr6B 93.701 127 6 2 521 645 438623339 438623465 5.490000e-44 189
13 TraesCS7D01G387200 chr6B 92.366 131 7 3 517 645 656170439 656170568 2.550000e-42 183
14 TraesCS7D01G387200 chr1A 90.972 144 7 5 501 640 385891774 385891915 5.490000e-44 189


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 TraesCS7D01G387200 chr7D 501094453 501098611 4158 True 7681.0 7681 100.0000 1 4159 1 chr7D.!!$R2 4158
1 TraesCS7D01G387200 chr7B 530378677 530382737 4060 True 3065.0 5472 92.5680 18 4159 2 chr7B.!!$R1 4141
2 TraesCS7D01G387200 chr7A 567582592 567586632 4040 True 2767.5 4951 89.9445 18 4159 2 chr7A.!!$R1 4141
3 TraesCS7D01G387200 chr2B 38032912 38033567 655 True 968.0 968 93.3330 3296 3952 1 chr2B.!!$R1 656

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
539 551 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
542 554 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
1269 1308 0.622136 TGCTCACAGAGGCATCCATT 59.378 50.0 0.00 0.0 33.23 3.16 F
1764 1825 0.927029 AATGGAAACCCTAGCTCCCC 59.073 55.0 0.00 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1813 1.528341 TTCAGAGGGGGAGCTAGGGT 61.528 60.000 0.0 0.0 0.00 4.34 R
1914 1975 4.647611 AGTTCAATAACCACCGTCAATCA 58.352 39.130 0.0 0.0 36.15 2.57 R
2627 2689 4.644103 AGGAATGCCAAGATTTGAATCG 57.356 40.909 0.0 0.0 37.27 3.34 R
3423 3488 0.918799 TGTCTGGGGTGGGCACATAT 60.919 55.000 0.0 0.0 0.00 1.78 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
128 136 0.387565 GATCCCGGAGAGACTTCTGC 59.612 60.000 0.73 0.00 38.32 4.26
143 151 0.685097 TCTGCTGGAAAGGTAACGCT 59.315 50.000 0.00 0.00 46.39 5.07
158 166 4.277672 GGTAACGCTCTTTTCTCCCTTTTT 59.722 41.667 0.00 0.00 0.00 1.94
161 169 3.149981 CGCTCTTTTCTCCCTTTTTCCT 58.850 45.455 0.00 0.00 0.00 3.36
169 177 1.000274 CTCCCTTTTTCCTTTGCCGTG 60.000 52.381 0.00 0.00 0.00 4.94
192 200 3.073650 AGTTCTTGGTCAGGATTCTTGCT 59.926 43.478 0.00 0.00 0.00 3.91
195 203 1.538047 TGGTCAGGATTCTTGCTTGC 58.462 50.000 0.00 0.00 0.00 4.01
230 238 3.890756 TGCATCTGTTCTTGTTGTGGATT 59.109 39.130 0.00 0.00 0.00 3.01
285 293 1.901833 AGTGGAAAATGGGATGTTGCC 59.098 47.619 0.00 0.00 0.00 4.52
319 327 3.197549 TGCTGGATGTATGTGCTAGTTGA 59.802 43.478 0.00 0.00 0.00 3.18
351 359 9.234384 GACTGCATTTCTTTGATTATGAAGATG 57.766 33.333 0.00 0.00 32.40 2.90
371 383 9.261180 GAAGATGGAATAATCGAATCTTGTGTA 57.739 33.333 10.22 0.00 38.63 2.90
374 386 9.208022 GATGGAATAATCGAATCTTGTGTATGA 57.792 33.333 0.00 0.00 0.00 2.15
375 387 8.956533 TGGAATAATCGAATCTTGTGTATGAA 57.043 30.769 0.00 0.00 0.00 2.57
376 388 9.389755 TGGAATAATCGAATCTTGTGTATGAAA 57.610 29.630 0.00 0.00 0.00 2.69
397 409 2.034999 GGGCCGGATTGTGTTGGA 59.965 61.111 5.05 0.00 0.00 3.53
398 410 2.046285 GGGCCGGATTGTGTTGGAG 61.046 63.158 5.05 0.00 0.00 3.86
404 416 3.306019 GCCGGATTGTGTTGGAGAAAAAT 60.306 43.478 5.05 0.00 0.00 1.82
494 506 3.008375 GCCTCATCTGCAGGATACCATTA 59.992 47.826 15.13 0.00 31.91 1.90
530 542 5.848833 ACTGTTATTACTTACTCCCTCCG 57.151 43.478 0.00 0.00 0.00 4.63
531 543 5.267587 ACTGTTATTACTTACTCCCTCCGT 58.732 41.667 0.00 0.00 0.00 4.69
532 544 5.359292 ACTGTTATTACTTACTCCCTCCGTC 59.641 44.000 0.00 0.00 0.00 4.79
533 545 4.646492 TGTTATTACTTACTCCCTCCGTCC 59.354 45.833 0.00 0.00 0.00 4.79
534 546 1.755179 TTACTTACTCCCTCCGTCCG 58.245 55.000 0.00 0.00 0.00 4.79
535 547 0.107017 TACTTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
536 548 1.077212 CTTACTCCCTCCGTCCGGA 60.077 63.158 0.00 0.00 42.90 5.14
537 549 0.682209 CTTACTCCCTCCGTCCGGAA 60.682 60.000 5.23 0.00 44.66 4.30
538 550 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
539 551 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
540 552 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
541 553 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
542 554 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
543 555 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
544 556 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
545 557 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
546 558 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
547 559 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
548 560 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
549 561 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
550 562 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
551 563 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
552 564 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
553 565 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
554 566 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
555 567 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
556 568 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
557 569 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
558 570 6.598064 CGGAAATACTTGTCCTAGAAATGGTT 59.402 38.462 0.00 0.00 0.00 3.67
559 571 7.414098 CGGAAATACTTGTCCTAGAAATGGTTG 60.414 40.741 0.00 0.00 0.00 3.77
560 572 7.393515 GGAAATACTTGTCCTAGAAATGGTTGT 59.606 37.037 0.00 0.00 0.00 3.32
561 573 9.444600 GAAATACTTGTCCTAGAAATGGTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
562 574 9.975218 AAATACTTGTCCTAGAAATGGTTGTAT 57.025 29.630 0.00 0.00 0.00 2.29
563 575 9.614792 AATACTTGTCCTAGAAATGGTTGTATC 57.385 33.333 0.00 0.00 0.00 2.24
564 576 7.259088 ACTTGTCCTAGAAATGGTTGTATCT 57.741 36.000 0.00 0.00 0.00 1.98
565 577 8.375493 ACTTGTCCTAGAAATGGTTGTATCTA 57.625 34.615 0.00 0.00 0.00 1.98
566 578 8.478877 ACTTGTCCTAGAAATGGTTGTATCTAG 58.521 37.037 0.00 0.00 40.55 2.43
567 579 8.603898 TTGTCCTAGAAATGGTTGTATCTAGA 57.396 34.615 9.60 0.00 42.48 2.43
568 580 8.008513 TGTCCTAGAAATGGTTGTATCTAGAC 57.991 38.462 9.60 7.06 42.48 2.59
569 581 7.839705 TGTCCTAGAAATGGTTGTATCTAGACT 59.160 37.037 9.60 0.00 42.48 3.24
570 582 8.697292 GTCCTAGAAATGGTTGTATCTAGACTT 58.303 37.037 9.60 0.00 42.48 3.01
571 583 9.931698 TCCTAGAAATGGTTGTATCTAGACTTA 57.068 33.333 9.60 0.00 42.48 2.24
611 623 8.682936 ACATTCATGTTATCCATTTCTAGGAC 57.317 34.615 0.00 0.00 37.90 3.85
612 624 8.274322 ACATTCATGTTATCCATTTCTAGGACA 58.726 33.333 0.00 0.00 37.90 4.02
613 625 9.123902 CATTCATGTTATCCATTTCTAGGACAA 57.876 33.333 0.00 0.00 38.13 3.18
614 626 8.737168 TTCATGTTATCCATTTCTAGGACAAG 57.263 34.615 0.00 0.00 38.13 3.16
615 627 7.861629 TCATGTTATCCATTTCTAGGACAAGT 58.138 34.615 0.00 0.00 38.13 3.16
616 628 8.988060 TCATGTTATCCATTTCTAGGACAAGTA 58.012 33.333 0.00 0.00 38.13 2.24
617 629 9.784531 CATGTTATCCATTTCTAGGACAAGTAT 57.215 33.333 0.00 0.00 38.13 2.12
621 633 9.847224 TTATCCATTTCTAGGACAAGTATTTCC 57.153 33.333 0.00 0.00 38.13 3.13
622 634 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
623 635 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
624 636 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
625 637 5.593679 TTCTAGGACAAGTATTTCCGGAG 57.406 43.478 3.34 0.00 36.95 4.63
651 663 4.654262 GGGAGTATTAGTGAATCCTGGTCA 59.346 45.833 0.00 0.00 0.00 4.02
654 666 7.283329 GGAGTATTAGTGAATCCTGGTCATTT 58.717 38.462 0.00 0.00 0.00 2.32
697 717 4.579340 TGGTTCCGTAATTGTTTGTTGCTA 59.421 37.500 0.00 0.00 0.00 3.49
710 730 5.709631 TGTTTGTTGCTATAGGATGCTTTGA 59.290 36.000 1.04 0.00 0.00 2.69
712 732 6.381481 TTGTTGCTATAGGATGCTTTGATG 57.619 37.500 1.04 0.00 0.00 3.07
772 792 8.400947 TGAATGCTAGCTATCAAAATTGTCTTC 58.599 33.333 17.23 0.00 0.00 2.87
776 796 8.454106 TGCTAGCTATCAAAATTGTCTTCTTTC 58.546 33.333 17.23 0.00 0.00 2.62
851 889 8.674263 AATACACAAGAGATGGAGATCAAATC 57.326 34.615 0.00 0.00 0.00 2.17
928 966 6.569228 GAAAACACAAAGCTACTGGTTTTC 57.431 37.500 22.36 22.36 43.51 2.29
967 1005 6.739100 GTCTATTGAGCTATATCGTTGACTCG 59.261 42.308 0.00 0.00 0.00 4.18
994 1032 5.073691 TCCTTTCCTTTCAGGAGAGTGAAAT 59.926 40.000 9.01 0.00 46.73 2.17
1068 1107 4.084849 CGCAATGAAATACGAGATGAGACC 60.085 45.833 0.00 0.00 0.00 3.85
1069 1108 4.084849 GCAATGAAATACGAGATGAGACCG 60.085 45.833 0.00 0.00 0.00 4.79
1269 1308 0.622136 TGCTCACAGAGGCATCCATT 59.378 50.000 0.00 0.00 33.23 3.16
1392 1431 4.393680 TCTGTGGTTATAAACAACATCGGC 59.606 41.667 4.38 0.00 44.00 5.54
1452 1491 7.563188 TCATCTAAGCTCAATACTTCTCCTTCT 59.437 37.037 0.00 0.00 0.00 2.85
1459 1498 6.312672 GCTCAATACTTCTCCTTCTTGTTCTC 59.687 42.308 0.00 0.00 0.00 2.87
1487 1526 7.431084 GTGTTACTTTCGAACATTTTGTGATGT 59.569 33.333 0.00 0.00 41.83 3.06
1489 1528 9.103048 GTTACTTTCGAACATTTTGTGATGTAG 57.897 33.333 0.00 0.00 39.25 2.74
1503 1542 7.701539 TTGTGATGTAGCTTAAATTCACCAT 57.298 32.000 0.00 0.00 34.11 3.55
1537 1576 2.481441 TGGATAATCCAGTGCTCCACT 58.519 47.619 0.00 0.00 46.51 4.00
1539 1578 3.388024 TGGATAATCCAGTGCTCCACTAC 59.612 47.826 0.00 0.00 43.43 2.73
1601 1640 1.653151 GGCCTATGTTTGGAGACGAC 58.347 55.000 0.00 0.00 0.00 4.34
1666 1709 4.107622 GCATGTGTTTATTGCTTAGCTGG 58.892 43.478 5.60 0.00 33.61 4.85
1686 1730 2.034685 GGTTGACTTGGGTTTCTTCAGC 59.965 50.000 0.00 0.00 0.00 4.26
1698 1742 5.241728 GGGTTTCTTCAGCACATTACTTTCT 59.758 40.000 0.00 0.00 0.00 2.52
1752 1813 7.716799 AGTACTATCAAATGGCAAATGGAAA 57.283 32.000 0.00 0.00 0.00 3.13
1764 1825 0.927029 AATGGAAACCCTAGCTCCCC 59.073 55.000 0.00 0.00 0.00 4.81
1834 1895 1.795286 GACCAGTTCGAACTTGAGCTG 59.205 52.381 29.92 18.26 44.11 4.24
1846 1907 4.899352 ACTTGAGCTGGTTAGAAGTCAT 57.101 40.909 0.00 0.00 0.00 3.06
1964 2025 7.602753 TGATAGGTGATGTATTATCTGGAACG 58.397 38.462 0.00 0.00 0.00 3.95
2306 2367 2.029110 TGTAGCAATGCCCAAGCTTTTC 60.029 45.455 0.00 0.00 39.68 2.29
2439 2500 6.403866 TTCTTGCCATTGTTCAGTTATGTT 57.596 33.333 0.00 0.00 0.00 2.71
2441 2502 4.517952 TGCCATTGTTCAGTTATGTTGG 57.482 40.909 0.00 0.00 0.00 3.77
2453 2514 9.959749 GTTCAGTTATGTTGGTTCTAAATGAAA 57.040 29.630 6.13 0.00 39.59 2.69
2455 2516 9.349713 TCAGTTATGTTGGTTCTAAATGAAAGT 57.650 29.630 0.00 0.00 36.30 2.66
2627 2689 1.063174 GATGATGTGCTCGCCAACTTC 59.937 52.381 0.00 0.00 0.00 3.01
3017 3082 9.887406 CCTGTATTAACACATAAACTCGTTTTT 57.113 29.630 0.00 0.00 34.23 1.94
3422 3487 3.057876 TGTTCTTTTGTTGGCGCGAATAT 60.058 39.130 12.10 0.00 0.00 1.28
3423 3488 4.154375 TGTTCTTTTGTTGGCGCGAATATA 59.846 37.500 12.10 0.00 0.00 0.86
3591 3659 5.560722 TGTTACCATCCTTCACTTCTGAA 57.439 39.130 0.00 0.00 35.04 3.02
3593 3661 5.763204 TGTTACCATCCTTCACTTCTGAAAC 59.237 40.000 0.00 0.00 35.92 2.78
3702 3771 3.461061 CCGTCTACATCCTAGTCGTACA 58.539 50.000 0.00 0.00 0.00 2.90
3704 3773 4.366586 CGTCTACATCCTAGTCGTACAGA 58.633 47.826 0.00 0.00 0.00 3.41
3705 3774 4.807834 CGTCTACATCCTAGTCGTACAGAA 59.192 45.833 0.00 0.00 0.00 3.02
3706 3775 5.292834 CGTCTACATCCTAGTCGTACAGAAA 59.707 44.000 0.00 0.00 0.00 2.52
3868 3950 6.882610 TCATTCTATATTGTCAATGGGTGC 57.117 37.500 8.39 0.00 0.00 5.01
3870 3952 6.487668 TCATTCTATATTGTCAATGGGTGCTG 59.512 38.462 8.39 0.57 0.00 4.41
3890 3972 5.701290 TGCTGGAAGTAGAACTAAAAAGAGC 59.299 40.000 0.00 0.00 35.30 4.09
3894 3976 8.418597 TGGAAGTAGAACTAAAAAGAGCTAGA 57.581 34.615 0.00 0.00 0.00 2.43
3934 4017 0.385390 AGTGGTTTTTGCCTTCTGCG 59.615 50.000 0.00 0.00 45.60 5.18
3935 4018 0.102300 GTGGTTTTTGCCTTCTGCGT 59.898 50.000 0.00 0.00 45.60 5.24
3938 4021 1.202359 GGTTTTTGCCTTCTGCGTTGA 60.202 47.619 0.00 0.00 45.60 3.18
4137 4233 5.529289 TGTCAGGATTCTTAGTATCCAGGT 58.471 41.667 17.96 0.00 43.33 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1 2 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2 3 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
3 4 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
4 5 3.244044 GCCTCTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
5 6 2.703007 GCCTCTCTCTCTCTCTCTCTCT 59.297 54.545 0.00 0.00 0.00 3.10
6 7 2.546795 CGCCTCTCTCTCTCTCTCTCTC 60.547 59.091 0.00 0.00 0.00 3.20
7 8 1.414181 CGCCTCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
8 9 1.541233 CCGCCTCTCTCTCTCTCTCTC 60.541 61.905 0.00 0.00 0.00 3.20
9 10 0.469917 CCGCCTCTCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
10 11 1.166531 GCCGCCTCTCTCTCTCTCTC 61.167 65.000 0.00 0.00 0.00 3.20
11 12 1.152963 GCCGCCTCTCTCTCTCTCT 60.153 63.158 0.00 0.00 0.00 3.10
12 13 2.193536 GGCCGCCTCTCTCTCTCTC 61.194 68.421 0.71 0.00 0.00 3.20
13 14 2.123897 GGCCGCCTCTCTCTCTCT 60.124 66.667 0.71 0.00 0.00 3.10
14 15 3.223589 GGGCCGCCTCTCTCTCTC 61.224 72.222 9.86 0.00 0.00 3.20
15 16 3.731766 GAGGGCCGCCTCTCTCTCT 62.732 68.421 9.86 0.00 34.30 3.10
16 17 3.223589 GAGGGCCGCCTCTCTCTC 61.224 72.222 9.86 3.02 34.30 3.20
39 40 0.179045 ACTTGTGGACTGTGGTCTGC 60.179 55.000 0.00 0.00 41.82 4.26
40 41 2.158900 AGAACTTGTGGACTGTGGTCTG 60.159 50.000 0.00 0.00 41.82 3.51
41 42 2.119495 AGAACTTGTGGACTGTGGTCT 58.881 47.619 0.00 0.00 41.82 3.85
42 43 2.622064 AGAACTTGTGGACTGTGGTC 57.378 50.000 0.00 0.00 41.43 4.02
43 44 2.505819 AGAAGAACTTGTGGACTGTGGT 59.494 45.455 0.00 0.00 0.00 4.16
128 136 4.065789 AGAAAAGAGCGTTACCTTTCCAG 58.934 43.478 0.00 0.00 32.01 3.86
143 151 4.100963 GGCAAAGGAAAAAGGGAGAAAAGA 59.899 41.667 0.00 0.00 0.00 2.52
158 166 1.593196 CAAGAACTCACGGCAAAGGA 58.407 50.000 0.00 0.00 0.00 3.36
161 169 1.305201 GACCAAGAACTCACGGCAAA 58.695 50.000 0.00 0.00 0.00 3.68
169 177 3.438434 GCAAGAATCCTGACCAAGAACTC 59.562 47.826 0.00 0.00 0.00 3.01
192 200 2.495155 TGCAGCTTTCTCCATAGCAA 57.505 45.000 0.00 0.00 39.85 3.91
195 203 3.806380 ACAGATGCAGCTTTCTCCATAG 58.194 45.455 0.00 0.00 0.00 2.23
230 238 4.949238 CCACAGAACCCATTATCATCACAA 59.051 41.667 0.00 0.00 0.00 3.33
285 293 3.679389 ACATCCAGCAACTGTCCTAAAG 58.321 45.455 0.00 0.00 0.00 1.85
351 359 9.869844 CTTTCATACACAAGATTCGATTATTCC 57.130 33.333 0.00 0.00 0.00 3.01
364 376 1.737793 GGCCCGACTTTCATACACAAG 59.262 52.381 0.00 0.00 0.00 3.16
371 383 0.748005 CAATCCGGCCCGACTTTCAT 60.748 55.000 3.71 0.00 0.00 2.57
374 386 1.674322 CACAATCCGGCCCGACTTT 60.674 57.895 3.71 0.00 0.00 2.66
375 387 2.046314 CACAATCCGGCCCGACTT 60.046 61.111 3.71 0.00 0.00 3.01
376 388 2.890766 AACACAATCCGGCCCGACT 61.891 57.895 3.71 0.00 0.00 4.18
397 409 9.875691 AAGTCAACTGAAGCTTTTTATTTTTCT 57.124 25.926 0.00 0.00 0.00 2.52
404 416 7.328249 CACAACAAAGTCAACTGAAGCTTTTTA 59.672 33.333 0.00 0.00 0.00 1.52
509 521 5.221204 GGACGGAGGGAGTAAGTAATAACAG 60.221 48.000 0.00 0.00 0.00 3.16
515 527 1.683011 CCGGACGGAGGGAGTAAGTAA 60.683 57.143 4.40 0.00 37.50 2.24
517 529 1.379576 CCGGACGGAGGGAGTAAGT 60.380 63.158 4.40 0.00 37.50 2.24
520 532 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
521 533 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
522 534 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
523 535 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
524 536 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
525 537 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
526 538 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
527 539 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
528 540 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
529 541 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
530 542 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
531 543 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
532 544 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
533 545 6.113411 ACCATTTCTAGGACAAGTATTTCCG 58.887 40.000 0.00 0.00 36.95 4.30
534 546 7.393515 ACAACCATTTCTAGGACAAGTATTTCC 59.606 37.037 0.00 0.00 0.00 3.13
535 547 8.336801 ACAACCATTTCTAGGACAAGTATTTC 57.663 34.615 0.00 0.00 0.00 2.17
536 548 9.975218 ATACAACCATTTCTAGGACAAGTATTT 57.025 29.630 0.00 0.00 0.00 1.40
537 549 9.614792 GATACAACCATTTCTAGGACAAGTATT 57.385 33.333 0.00 0.00 0.00 1.89
538 550 8.993424 AGATACAACCATTTCTAGGACAAGTAT 58.007 33.333 0.00 0.00 0.00 2.12
539 551 8.375493 AGATACAACCATTTCTAGGACAAGTA 57.625 34.615 0.00 0.00 0.00 2.24
540 552 7.259088 AGATACAACCATTTCTAGGACAAGT 57.741 36.000 0.00 0.00 0.00 3.16
541 553 8.696374 TCTAGATACAACCATTTCTAGGACAAG 58.304 37.037 6.10 0.00 38.67 3.16
542 554 8.475639 GTCTAGATACAACCATTTCTAGGACAA 58.524 37.037 0.00 0.00 38.67 3.18
543 555 7.839705 AGTCTAGATACAACCATTTCTAGGACA 59.160 37.037 0.00 0.00 38.67 4.02
544 556 8.240267 AGTCTAGATACAACCATTTCTAGGAC 57.760 38.462 0.00 0.00 38.67 3.85
545 557 8.840200 AAGTCTAGATACAACCATTTCTAGGA 57.160 34.615 0.00 0.00 38.67 2.94
585 597 9.778741 GTCCTAGAAATGGATAACATGAATGTA 57.221 33.333 0.00 0.00 40.44 2.29
586 598 8.274322 TGTCCTAGAAATGGATAACATGAATGT 58.726 33.333 0.00 0.00 40.44 2.71
587 599 8.681486 TGTCCTAGAAATGGATAACATGAATG 57.319 34.615 0.00 0.00 40.44 2.67
588 600 9.347240 CTTGTCCTAGAAATGGATAACATGAAT 57.653 33.333 0.00 0.00 40.44 2.57
589 601 8.328758 ACTTGTCCTAGAAATGGATAACATGAA 58.671 33.333 0.00 0.00 40.44 2.57
590 602 7.861629 ACTTGTCCTAGAAATGGATAACATGA 58.138 34.615 0.00 0.00 40.44 3.07
591 603 9.784531 ATACTTGTCCTAGAAATGGATAACATG 57.215 33.333 0.00 0.00 40.44 3.21
595 607 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
596 608 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
597 609 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
598 610 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
599 611 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
600 612 6.346096 TCCGGAAATACTTGTCCTAGAAATG 58.654 40.000 0.00 0.00 0.00 2.32
601 613 6.408206 CCTCCGGAAATACTTGTCCTAGAAAT 60.408 42.308 5.23 0.00 0.00 2.17
602 614 5.105064 CCTCCGGAAATACTTGTCCTAGAAA 60.105 44.000 5.23 0.00 0.00 2.52
603 615 4.404715 CCTCCGGAAATACTTGTCCTAGAA 59.595 45.833 5.23 0.00 0.00 2.10
604 616 3.958798 CCTCCGGAAATACTTGTCCTAGA 59.041 47.826 5.23 0.00 0.00 2.43
605 617 3.958798 TCCTCCGGAAATACTTGTCCTAG 59.041 47.826 5.23 0.00 0.00 3.02
606 618 3.958798 CTCCTCCGGAAATACTTGTCCTA 59.041 47.826 5.23 0.00 0.00 2.94
607 619 2.766828 CTCCTCCGGAAATACTTGTCCT 59.233 50.000 5.23 0.00 0.00 3.85
608 620 2.158943 CCTCCTCCGGAAATACTTGTCC 60.159 54.545 5.23 0.00 0.00 4.02
609 621 2.158943 CCCTCCTCCGGAAATACTTGTC 60.159 54.545 5.23 0.00 0.00 3.18
610 622 1.838077 CCCTCCTCCGGAAATACTTGT 59.162 52.381 5.23 0.00 0.00 3.16
611 623 2.103263 CTCCCTCCTCCGGAAATACTTG 59.897 54.545 5.23 0.00 0.00 3.16
612 624 2.292984 ACTCCCTCCTCCGGAAATACTT 60.293 50.000 5.23 0.00 0.00 2.24
613 625 1.291335 ACTCCCTCCTCCGGAAATACT 59.709 52.381 5.23 0.00 0.00 2.12
614 626 1.790818 ACTCCCTCCTCCGGAAATAC 58.209 55.000 5.23 0.00 0.00 1.89
615 627 3.917324 ATACTCCCTCCTCCGGAAATA 57.083 47.619 5.23 0.00 0.00 1.40
616 628 2.797285 ATACTCCCTCCTCCGGAAAT 57.203 50.000 5.23 0.00 0.00 2.17
617 629 2.563039 AATACTCCCTCCTCCGGAAA 57.437 50.000 5.23 0.00 0.00 3.13
618 630 2.517127 ACTAATACTCCCTCCTCCGGAA 59.483 50.000 5.23 0.00 0.00 4.30
619 631 2.141911 ACTAATACTCCCTCCTCCGGA 58.858 52.381 2.93 2.93 0.00 5.14
620 632 2.158505 TCACTAATACTCCCTCCTCCGG 60.159 54.545 0.00 0.00 0.00 5.14
621 633 3.225177 TCACTAATACTCCCTCCTCCG 57.775 52.381 0.00 0.00 0.00 4.63
622 634 4.528987 GGATTCACTAATACTCCCTCCTCC 59.471 50.000 0.00 0.00 0.00 4.30
623 635 5.245075 CAGGATTCACTAATACTCCCTCCTC 59.755 48.000 0.00 0.00 33.69 3.71
624 636 5.151454 CAGGATTCACTAATACTCCCTCCT 58.849 45.833 0.00 0.00 33.69 3.69
625 637 4.284746 CCAGGATTCACTAATACTCCCTCC 59.715 50.000 0.00 0.00 33.69 4.30
626 638 4.902448 ACCAGGATTCACTAATACTCCCTC 59.098 45.833 0.00 0.00 33.69 4.30
627 639 4.897051 ACCAGGATTCACTAATACTCCCT 58.103 43.478 0.00 0.00 33.69 4.20
628 640 4.654262 TGACCAGGATTCACTAATACTCCC 59.346 45.833 0.00 0.00 33.69 4.30
629 641 5.871396 TGACCAGGATTCACTAATACTCC 57.129 43.478 0.00 0.00 33.69 3.85
630 642 9.832445 TTAAATGACCAGGATTCACTAATACTC 57.168 33.333 0.00 0.00 33.69 2.59
651 663 7.786464 ACCAAAGGGCTAGATGATGAATTAAAT 59.214 33.333 0.00 0.00 37.90 1.40
654 666 6.266131 ACCAAAGGGCTAGATGATGAATTA 57.734 37.500 0.00 0.00 37.90 1.40
697 717 8.093307 CAGAGTATACACATCAAAGCATCCTAT 58.907 37.037 5.50 0.00 0.00 2.57
710 730 9.854668 AGTCATAGTAGTTCAGAGTATACACAT 57.145 33.333 5.50 0.00 0.00 3.21
772 792 6.618379 GCCTTGTTTAATGCAAATTCCGAAAG 60.618 38.462 0.00 0.00 0.00 2.62
776 796 3.993081 TGCCTTGTTTAATGCAAATTCCG 59.007 39.130 0.00 0.00 35.03 4.30
887 925 8.520351 TGTGTTTTCTCTCGATACTTCTTATGA 58.480 33.333 0.00 0.00 0.00 2.15
928 966 8.136057 AGCTCAATAGACTATTTGATTTGACG 57.864 34.615 4.91 0.00 0.00 4.35
950 988 4.762765 AGGATTCGAGTCAACGATATAGCT 59.237 41.667 10.32 0.00 41.82 3.32
994 1032 3.616219 CATTCCCGACACCCATTTTCTA 58.384 45.455 0.00 0.00 0.00 2.10
1269 1308 2.635714 CTGCACCTGATAAGCATGTCA 58.364 47.619 0.00 0.00 37.68 3.58
1452 1491 5.870433 TGTTCGAAAGTAACACAGAGAACAA 59.130 36.000 0.00 0.00 42.14 2.83
1459 1498 6.964370 TCACAAAATGTTCGAAAGTAACACAG 59.036 34.615 0.00 0.00 39.51 3.66
1487 1526 4.947388 GTCCCACATGGTGAATTTAAGCTA 59.053 41.667 0.00 0.00 35.23 3.32
1489 1528 3.763897 AGTCCCACATGGTGAATTTAAGC 59.236 43.478 0.00 0.00 35.23 3.09
1503 1542 5.192722 TGGATTATCCATAACAAGTCCCACA 59.807 40.000 10.29 0.00 42.67 4.17
1528 1567 7.224949 GGATTAAAAGATACTGTAGTGGAGCAC 59.775 40.741 0.00 0.00 34.10 4.40
1565 1604 1.589716 GCCCTGAAGTGTGCCATCAC 61.590 60.000 0.00 0.00 43.40 3.06
1567 1606 2.048603 GGCCCTGAAGTGTGCCATC 61.049 63.158 0.00 0.00 43.46 3.51
1601 1640 7.545362 AGAACATCTTGGAATTATTCGTGAG 57.455 36.000 0.00 0.00 0.00 3.51
1648 1689 5.048713 AGTCAACCAGCTAAGCAATAAACAC 60.049 40.000 0.00 0.00 0.00 3.32
1666 1709 2.687935 TGCTGAAGAAACCCAAGTCAAC 59.312 45.455 0.00 0.00 0.00 3.18
1752 1813 1.528341 TTCAGAGGGGGAGCTAGGGT 61.528 60.000 0.00 0.00 0.00 4.34
1764 1825 9.282247 CAAAATGACGAATTATTTCTTCAGAGG 57.718 33.333 10.92 0.78 41.66 3.69
1914 1975 4.647611 AGTTCAATAACCACCGTCAATCA 58.352 39.130 0.00 0.00 36.15 2.57
2306 2367 8.428063 ACAGAACTAAGATCATCTATTTCTGGG 58.572 37.037 23.95 10.57 39.07 4.45
2453 2514 8.450578 TGTGAACTGTAGAATCATGAAAAACT 57.549 30.769 0.00 0.00 0.00 2.66
2455 2516 7.013178 TGCTGTGAACTGTAGAATCATGAAAAA 59.987 33.333 0.00 0.00 0.00 1.94
2468 2530 5.062528 TCATTGTCAATGCTGTGAACTGTA 58.937 37.500 19.02 0.00 38.77 2.74
2627 2689 4.644103 AGGAATGCCAAGATTTGAATCG 57.356 40.909 0.00 0.00 37.27 3.34
3017 3082 5.544441 TTCCATAAGGATCCCTTGGAAAA 57.456 39.130 26.67 13.64 43.49 2.29
3311 3376 4.051661 ACCATCCAATTCTTCCATGTGT 57.948 40.909 0.00 0.00 0.00 3.72
3409 3474 3.485216 GGCACATATATATTCGCGCCAAC 60.485 47.826 0.00 0.00 38.20 3.77
3422 3487 1.136828 GTCTGGGGTGGGCACATATA 58.863 55.000 0.00 0.00 0.00 0.86
3423 3488 0.918799 TGTCTGGGGTGGGCACATAT 60.919 55.000 0.00 0.00 0.00 1.78
3539 3607 7.576098 GCCACTTTATTTTTATTCGGAACCTCA 60.576 37.037 0.00 0.00 0.00 3.86
3591 3659 5.235186 GCATGTATCGAATCTACAGCTTGTT 59.765 40.000 3.93 0.00 32.91 2.83
3593 3661 4.987285 AGCATGTATCGAATCTACAGCTTG 59.013 41.667 12.10 4.93 33.63 4.01
3757 3839 6.625960 GCCTTTCTGAATTTCACTTCCCATAC 60.626 42.308 0.00 0.00 0.00 2.39
3868 3950 8.524487 TCTAGCTCTTTTTAGTTCTACTTCCAG 58.476 37.037 0.00 0.00 0.00 3.86
3870 3952 9.708092 TTTCTAGCTCTTTTTAGTTCTACTTCC 57.292 33.333 0.00 0.00 0.00 3.46
3934 4017 0.322546 CTAGGTGCCCCTTGGTCAAC 60.323 60.000 0.00 0.00 42.66 3.18
3935 4018 2.074967 CTAGGTGCCCCTTGGTCAA 58.925 57.895 0.00 0.00 42.66 3.18
3938 4021 2.204151 AGCTAGGTGCCCCTTGGT 60.204 61.111 0.00 0.00 42.66 3.67
4099 4195 6.773976 ATCCTGACAAAAGAAAAACACTCA 57.226 33.333 0.00 0.00 0.00 3.41
4137 4233 4.284829 TGTCATTGTACTCATTGGCTGA 57.715 40.909 0.00 0.00 32.78 4.26


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

AutoCloner maintained by Alex Coulton.