Multiple sequence alignment - TraesCS6D01G334300

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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 TraesCS6D01G334300 chr6D 100.000 3146 0 0 1 3146 436420170 436423315 0.000000e+00 5810
1 TraesCS6D01G334300 chr6D 89.870 1461 92 21 749 2179 436638072 436639506 0.000000e+00 1827
2 TraesCS6D01G334300 chr6D 84.576 590 50 18 752 1321 436474437 436473869 5.930000e-152 547
3 TraesCS6D01G334300 chr6D 84.880 291 38 5 361 650 69292945 69292660 3.970000e-74 289
4 TraesCS6D01G334300 chr6D 86.154 260 35 1 16 275 454889488 454889230 2.390000e-71 279
5 TraesCS6D01G334300 chr6D 85.769 260 36 1 16 275 454923043 454922785 1.110000e-69 274
6 TraesCS6D01G334300 chr6A 92.097 2518 109 41 1 2480 584592653 584595118 0.000000e+00 3465
7 TraesCS6D01G334300 chr6A 88.843 1461 120 19 742 2179 584695528 584694088 0.000000e+00 1755
8 TraesCS6D01G334300 chr6A 86.790 1620 129 32 750 2316 584757957 584759544 0.000000e+00 1727
9 TraesCS6D01G334300 chr6A 87.263 950 77 18 1400 2316 584717354 584716416 0.000000e+00 1044
10 TraesCS6D01G334300 chr6A 83.588 524 45 14 750 1253 584717867 584717365 1.330000e-123 453
11 TraesCS6D01G334300 chr6B 89.941 1521 84 24 752 2243 659808739 659810219 0.000000e+00 1897
12 TraesCS6D01G334300 chr6B 91.864 676 47 6 2477 3146 337834197 337834870 0.000000e+00 937
13 TraesCS6D01G334300 chr6B 90.962 686 50 7 2469 3146 628692192 628692873 0.000000e+00 913
14 TraesCS6D01G334300 chr6B 91.579 665 48 7 2480 3137 691614444 691615107 0.000000e+00 911
15 TraesCS6D01G334300 chr6B 90.388 541 49 3 1642 2179 659653863 659653323 0.000000e+00 708
16 TraesCS6D01G334300 chr3B 89.501 1524 106 21 749 2248 663573495 663574988 0.000000e+00 1879
17 TraesCS6D01G334300 chr3B 91.716 676 49 5 2478 3146 754854631 754853956 0.000000e+00 931
18 TraesCS6D01G334300 chr3D 89.253 1526 101 21 747 2248 502158160 502159646 0.000000e+00 1851
19 TraesCS6D01G334300 chr3D 86.873 259 30 4 15 273 79555352 79555098 1.430000e-73 287
20 TraesCS6D01G334300 chr1D 92.456 676 44 5 2477 3146 209092212 209092886 0.000000e+00 959
21 TraesCS6D01G334300 chr1D 83.556 450 48 15 2001 2441 414876457 414876889 6.320000e-107 398
22 TraesCS6D01G334300 chr1D 85.467 289 38 3 362 650 318585626 318585910 6.600000e-77 298
23 TraesCS6D01G334300 chrUn 91.864 676 48 5 2478 3146 310310852 310310177 0.000000e+00 937
24 TraesCS6D01G334300 chrUn 91.864 676 48 5 2478 3146 315279527 315280202 0.000000e+00 937
25 TraesCS6D01G334300 chr5B 91.150 678 51 8 2477 3146 211475667 211476343 0.000000e+00 911
26 TraesCS6D01G334300 chr5B 91.111 675 54 5 2478 3146 673044138 673043464 0.000000e+00 909
27 TraesCS6D01G334300 chr1A 82.927 451 56 17 2001 2441 511606776 511607215 1.370000e-103 387
28 TraesCS6D01G334300 chr1A 85.714 259 32 5 15 272 544607506 544607252 5.170000e-68 268
29 TraesCS6D01G334300 chr5D 85.911 291 34 7 361 650 535008277 535008561 1.420000e-78 303
30 TraesCS6D01G334300 chr5D 85.263 285 34 8 372 653 479382974 479382695 1.430000e-73 287
31 TraesCS6D01G334300 chr2A 85.374 294 39 4 358 650 729555248 729554958 5.100000e-78 302
32 TraesCS6D01G334300 chr2A 84.536 291 41 4 361 650 743571926 743571639 5.140000e-73 285
33 TraesCS6D01G334300 chr2A 86.260 262 28 7 17 273 755670374 755670632 8.590000e-71 278
34 TraesCS6D01G334300 chr5A 85.223 291 40 3 360 650 458978774 458979061 2.370000e-76 296
35 TraesCS6D01G334300 chr5A 86.822 258 32 2 15 272 538101219 538101474 1.430000e-73 287
36 TraesCS6D01G334300 chr5A 85.433 254 36 1 15 268 276110969 276110717 2.410000e-66 263
37 TraesCS6D01G334300 chr4D 84.694 294 41 4 361 653 108913778 108913488 1.100000e-74 291
38 TraesCS6D01G334300 chr2D 85.263 285 33 5 367 650 106145778 106145502 5.140000e-73 285
39 TraesCS6D01G334300 chr7D 86.166 253 32 3 16 268 562925765 562925516 1.440000e-68 270


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 TraesCS6D01G334300 chr6D 436420170 436423315 3145 False 5810.0 5810 100.0000 1 3146 1 chr6D.!!$F1 3145
1 TraesCS6D01G334300 chr6D 436638072 436639506 1434 False 1827.0 1827 89.8700 749 2179 1 chr6D.!!$F2 1430
2 TraesCS6D01G334300 chr6D 436473869 436474437 568 True 547.0 547 84.5760 752 1321 1 chr6D.!!$R2 569
3 TraesCS6D01G334300 chr6A 584592653 584595118 2465 False 3465.0 3465 92.0970 1 2480 1 chr6A.!!$F1 2479
4 TraesCS6D01G334300 chr6A 584694088 584695528 1440 True 1755.0 1755 88.8430 742 2179 1 chr6A.!!$R1 1437
5 TraesCS6D01G334300 chr6A 584757957 584759544 1587 False 1727.0 1727 86.7900 750 2316 1 chr6A.!!$F2 1566
6 TraesCS6D01G334300 chr6A 584716416 584717867 1451 True 748.5 1044 85.4255 750 2316 2 chr6A.!!$R2 1566
7 TraesCS6D01G334300 chr6B 659808739 659810219 1480 False 1897.0 1897 89.9410 752 2243 1 chr6B.!!$F3 1491
8 TraesCS6D01G334300 chr6B 337834197 337834870 673 False 937.0 937 91.8640 2477 3146 1 chr6B.!!$F1 669
9 TraesCS6D01G334300 chr6B 628692192 628692873 681 False 913.0 913 90.9620 2469 3146 1 chr6B.!!$F2 677
10 TraesCS6D01G334300 chr6B 691614444 691615107 663 False 911.0 911 91.5790 2480 3137 1 chr6B.!!$F4 657
11 TraesCS6D01G334300 chr6B 659653323 659653863 540 True 708.0 708 90.3880 1642 2179 1 chr6B.!!$R1 537
12 TraesCS6D01G334300 chr3B 663573495 663574988 1493 False 1879.0 1879 89.5010 749 2248 1 chr3B.!!$F1 1499
13 TraesCS6D01G334300 chr3B 754853956 754854631 675 True 931.0 931 91.7160 2478 3146 1 chr3B.!!$R1 668
14 TraesCS6D01G334300 chr3D 502158160 502159646 1486 False 1851.0 1851 89.2530 747 2248 1 chr3D.!!$F1 1501
15 TraesCS6D01G334300 chr1D 209092212 209092886 674 False 959.0 959 92.4560 2477 3146 1 chr1D.!!$F1 669
16 TraesCS6D01G334300 chrUn 310310177 310310852 675 True 937.0 937 91.8640 2478 3146 1 chrUn.!!$R1 668
17 TraesCS6D01G334300 chrUn 315279527 315280202 675 False 937.0 937 91.8640 2478 3146 1 chrUn.!!$F1 668
18 TraesCS6D01G334300 chr5B 211475667 211476343 676 False 911.0 911 91.1500 2477 3146 1 chr5B.!!$F1 669
19 TraesCS6D01G334300 chr5B 673043464 673044138 674 True 909.0 909 91.1110 2478 3146 1 chr5B.!!$R1 668

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
775 797 0.028242 CGATCTGAACTCGGAGTCGG 59.972 60.0 11.71 10.03 34.27 4.79 F
827 865 0.178918 CTATCACCCTCCCTCCCTCC 60.179 65.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2004 0.252881 AGGAGAGTCTGGATGGCCAA 60.253 55.0 10.96 0.0 45.41 4.52 R
2740 2861 1.083806 CGGCGCATCAAGCTAAGTCA 61.084 55.0 10.83 0.0 42.61 3.41 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
41 42 1.143073 AGGGTTCAAGTCCTGGTGTTC 59.857 52.381 0.00 0.00 31.11 3.18
42 43 1.133915 GGGTTCAAGTCCTGGTGTTCA 60.134 52.381 0.00 0.00 0.00 3.18
48 49 6.381801 GTTCAAGTCCTGGTGTTCATATTTG 58.618 40.000 0.00 0.00 0.00 2.32
94 95 2.154854 CGATATGCGTTCAGTGGGAT 57.845 50.000 0.00 0.00 34.64 3.85
99 100 0.037326 TGCGTTCAGTGGGATGAGAC 60.037 55.000 0.00 0.00 0.00 3.36
126 127 1.272131 CGACTACGAGGCGTCTACG 59.728 63.158 4.69 0.00 42.99 3.51
161 162 1.714794 CCGAAGATGATATGTCGGCC 58.285 55.000 0.00 0.00 45.74 6.13
170 171 1.271102 GATATGTCGGCCCAGTCTCTC 59.729 57.143 0.00 0.00 0.00 3.20
172 173 3.827898 GTCGGCCCAGTCTCTCGG 61.828 72.222 0.00 0.00 0.00 4.63
195 196 3.140519 AGGTACTCATAGGAGGTAGGGTG 59.859 52.174 9.55 0.00 45.81 4.61
199 200 0.389391 CATAGGAGGTAGGGTGTGCG 59.611 60.000 0.00 0.00 0.00 5.34
217 218 2.556622 TGCGTGTGTGAGTTCATAGAGA 59.443 45.455 0.00 0.00 0.00 3.10
257 258 1.162698 TGAGCGCTTACGTCTGTACT 58.837 50.000 13.26 0.00 42.83 2.73
272 274 6.759827 ACGTCTGTACTGTGTTACAAAGAAAT 59.240 34.615 9.83 0.00 0.00 2.17
277 279 9.864034 CTGTACTGTGTTACAAAGAAATGTAAG 57.136 33.333 9.83 0.00 44.15 2.34
278 280 8.339714 TGTACTGTGTTACAAAGAAATGTAAGC 58.660 33.333 9.83 0.00 44.15 3.09
282 284 7.639039 TGTGTTACAAAGAAATGTAAGCTGAG 58.361 34.615 0.44 0.00 44.15 3.35
364 366 1.380650 ACACCGGGCTGTGGTTTTT 60.381 52.632 6.32 0.00 40.62 1.94
365 367 1.362355 CACCGGGCTGTGGTTTTTC 59.638 57.895 6.32 0.00 37.72 2.29
369 371 1.957877 CCGGGCTGTGGTTTTTCTTTA 59.042 47.619 0.00 0.00 0.00 1.85
374 379 4.569162 GGGCTGTGGTTTTTCTTTAAACAC 59.431 41.667 0.00 0.00 39.27 3.32
379 384 7.008901 GCTGTGGTTTTTCTTTAAACACAGTAC 59.991 37.037 25.63 12.82 41.96 2.73
381 386 8.024285 TGTGGTTTTTCTTTAAACACAGTACAG 58.976 33.333 2.58 0.00 39.27 2.74
383 388 8.238631 TGGTTTTTCTTTAAACACAGTACAGAC 58.761 33.333 0.00 0.00 39.27 3.51
390 395 0.600255 ACACAGTACAGACGCAAGCC 60.600 55.000 0.00 0.00 45.62 4.35
393 398 1.071605 CAGTACAGACGCAAGCCTTC 58.928 55.000 0.00 0.00 45.62 3.46
411 433 3.121279 CCTTCATACATACGCGCATACAC 59.879 47.826 5.73 0.00 0.00 2.90
415 437 1.556564 ACATACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
433 455 1.815421 CCCCTATGAGCGCACACAC 60.815 63.158 10.42 0.00 0.00 3.82
434 456 2.167219 CCCTATGAGCGCACACACG 61.167 63.158 10.42 1.23 0.00 4.49
435 457 1.153842 CCTATGAGCGCACACACGA 60.154 57.895 10.42 0.00 34.06 4.35
438 460 0.319125 TATGAGCGCACACACGAACA 60.319 50.000 10.42 0.00 34.06 3.18
439 461 1.157257 ATGAGCGCACACACGAACAA 61.157 50.000 10.42 0.00 34.06 2.83
440 462 1.367665 GAGCGCACACACGAACAAC 60.368 57.895 11.47 0.00 34.06 3.32
457 479 5.526506 AACAACGTACCCCTATGAGTATC 57.473 43.478 0.00 0.00 0.00 2.24
460 482 5.301298 ACAACGTACCCCTATGAGTATCTTC 59.699 44.000 0.00 0.00 34.92 2.87
473 495 6.184580 TGAGTATCTTCGAAAGACTGAGTC 57.815 41.667 3.98 3.98 41.01 3.36
511 533 5.730550 AGATTTACAAAGTCATCGTAGGCA 58.269 37.500 0.00 0.00 0.00 4.75
530 552 0.109412 ACCTCATCGTCGACGGAAAC 60.109 55.000 35.05 0.00 40.29 2.78
548 570 1.325355 ACGTCTCCTCCGACTGAAAA 58.675 50.000 0.00 0.00 0.00 2.29
554 576 3.012518 CTCCTCCGACTGAAAATGCATT 58.987 45.455 5.99 5.99 0.00 3.56
558 580 2.159430 TCCGACTGAAAATGCATTGTCG 59.841 45.455 29.10 29.10 44.32 4.35
560 582 3.410850 CGACTGAAAATGCATTGTCGAG 58.589 45.455 30.90 24.93 46.58 4.04
563 585 5.437289 ACTGAAAATGCATTGTCGAGAAA 57.563 34.783 24.15 9.94 0.00 2.52
564 586 5.830912 ACTGAAAATGCATTGTCGAGAAAA 58.169 33.333 24.15 9.39 0.00 2.29
565 587 6.449698 ACTGAAAATGCATTGTCGAGAAAAT 58.550 32.000 24.15 8.80 0.00 1.82
566 588 6.583806 ACTGAAAATGCATTGTCGAGAAAATC 59.416 34.615 24.15 4.75 0.00 2.17
609 631 3.002791 TGCGAACATCAGGACTTGAATC 58.997 45.455 0.00 0.00 39.77 2.52
618 640 1.685148 GGACTTGAATCCTGATGGGC 58.315 55.000 0.00 0.00 35.68 5.36
619 641 1.213926 GGACTTGAATCCTGATGGGCT 59.786 52.381 0.00 0.00 35.68 5.19
620 642 2.439507 GGACTTGAATCCTGATGGGCTA 59.560 50.000 0.00 0.00 35.68 3.93
621 643 3.495806 GGACTTGAATCCTGATGGGCTAG 60.496 52.174 0.00 0.00 35.68 3.42
624 646 2.775418 TGAATCCTGATGGGCTAGGAA 58.225 47.619 0.00 0.00 45.59 3.36
625 647 3.330198 TGAATCCTGATGGGCTAGGAAT 58.670 45.455 0.00 0.00 45.59 3.01
626 648 4.502415 TGAATCCTGATGGGCTAGGAATA 58.498 43.478 0.00 0.00 45.59 1.75
627 649 4.287067 TGAATCCTGATGGGCTAGGAATAC 59.713 45.833 0.00 0.00 45.59 1.89
629 651 2.090210 TCCTGATGGGCTAGGAATACCA 60.090 50.000 0.00 0.00 40.03 3.25
630 652 2.039084 CCTGATGGGCTAGGAATACCAC 59.961 54.545 0.00 0.00 38.94 4.16
631 653 2.975489 CTGATGGGCTAGGAATACCACT 59.025 50.000 0.00 0.00 38.94 4.00
632 654 2.705658 TGATGGGCTAGGAATACCACTG 59.294 50.000 0.00 0.00 38.94 3.66
633 655 2.263895 TGGGCTAGGAATACCACTGT 57.736 50.000 0.00 0.00 38.94 3.55
634 656 2.557869 TGGGCTAGGAATACCACTGTT 58.442 47.619 0.00 0.00 38.94 3.16
645 667 5.104485 GGAATACCACTGTTCCTCTAACCAT 60.104 44.000 0.00 0.00 40.55 3.55
646 668 3.983044 ACCACTGTTCCTCTAACCATC 57.017 47.619 0.00 0.00 37.27 3.51
647 669 2.572104 ACCACTGTTCCTCTAACCATCC 59.428 50.000 0.00 0.00 37.27 3.51
648 670 2.571653 CCACTGTTCCTCTAACCATCCA 59.428 50.000 0.00 0.00 37.27 3.41
649 671 3.009033 CCACTGTTCCTCTAACCATCCAA 59.991 47.826 0.00 0.00 37.27 3.53
650 672 4.506625 CCACTGTTCCTCTAACCATCCAAA 60.507 45.833 0.00 0.00 37.27 3.28
651 673 5.256474 CACTGTTCCTCTAACCATCCAAAT 58.744 41.667 0.00 0.00 37.27 2.32
652 674 6.414732 CACTGTTCCTCTAACCATCCAAATA 58.585 40.000 0.00 0.00 37.27 1.40
653 675 7.056635 CACTGTTCCTCTAACCATCCAAATAT 58.943 38.462 0.00 0.00 37.27 1.28
654 676 7.227512 CACTGTTCCTCTAACCATCCAAATATC 59.772 40.741 0.00 0.00 37.27 1.63
655 677 6.601332 TGTTCCTCTAACCATCCAAATATCC 58.399 40.000 0.00 0.00 37.27 2.59
656 678 6.159575 TGTTCCTCTAACCATCCAAATATCCA 59.840 38.462 0.00 0.00 37.27 3.41
657 679 6.840090 TCCTCTAACCATCCAAATATCCAA 57.160 37.500 0.00 0.00 0.00 3.53
658 680 6.601332 TCCTCTAACCATCCAAATATCCAAC 58.399 40.000 0.00 0.00 0.00 3.77
659 681 5.770162 CCTCTAACCATCCAAATATCCAACC 59.230 44.000 0.00 0.00 0.00 3.77
660 682 6.334378 TCTAACCATCCAAATATCCAACCA 57.666 37.500 0.00 0.00 0.00 3.67
661 683 6.126409 TCTAACCATCCAAATATCCAACCAC 58.874 40.000 0.00 0.00 0.00 4.16
662 684 4.329638 ACCATCCAAATATCCAACCACA 57.670 40.909 0.00 0.00 0.00 4.17
663 685 4.682563 ACCATCCAAATATCCAACCACAA 58.317 39.130 0.00 0.00 0.00 3.33
664 686 5.090139 ACCATCCAAATATCCAACCACAAA 58.910 37.500 0.00 0.00 0.00 2.83
665 687 5.725822 ACCATCCAAATATCCAACCACAAAT 59.274 36.000 0.00 0.00 0.00 2.32
666 688 6.215227 ACCATCCAAATATCCAACCACAAATT 59.785 34.615 0.00 0.00 0.00 1.82
775 797 0.028242 CGATCTGAACTCGGAGTCGG 59.972 60.000 11.71 10.03 34.27 4.79
820 858 6.070938 ACGTTATAAATAGCTATCACCCTCCC 60.071 42.308 6.72 0.00 0.00 4.30
821 859 6.154706 CGTTATAAATAGCTATCACCCTCCCT 59.845 42.308 6.72 0.00 0.00 4.20
822 860 7.557724 GTTATAAATAGCTATCACCCTCCCTC 58.442 42.308 6.72 0.00 0.00 4.30
823 861 2.632763 ATAGCTATCACCCTCCCTCC 57.367 55.000 0.00 0.00 0.00 4.30
824 862 0.487772 TAGCTATCACCCTCCCTCCC 59.512 60.000 0.00 0.00 0.00 4.30
825 863 1.237458 GCTATCACCCTCCCTCCCT 59.763 63.158 0.00 0.00 0.00 4.20
826 864 0.834261 GCTATCACCCTCCCTCCCTC 60.834 65.000 0.00 0.00 0.00 4.30
827 865 0.178918 CTATCACCCTCCCTCCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
1030 1104 1.852648 GGAAAAAGCGGCAAAAGCG 59.147 52.632 1.45 0.00 40.04 4.68
1524 1604 3.710722 AGGAAGCACAGCTCCGGG 61.711 66.667 0.00 0.00 38.25 5.73
1614 1694 0.313043 TCGACTTTGACCTCGTCCAC 59.687 55.000 0.00 0.00 0.00 4.02
1827 1907 4.980805 GACACGAGGGCGGCACAA 62.981 66.667 12.47 0.00 43.17 3.33
1924 2004 2.357034 AGGTCGCGCATGAACGTT 60.357 55.556 8.75 0.00 34.88 3.99
1946 2026 1.828768 CCATCCAGACTCTCCTGCC 59.171 63.158 0.00 0.00 32.97 4.85
2187 2273 8.660295 TTATTGTTCTTCTACTAGGAACTGGA 57.340 34.615 9.34 0.00 40.33 3.86
2189 2275 7.554959 TTGTTCTTCTACTAGGAACTGGATT 57.445 36.000 9.34 0.00 40.33 3.01
2190 2276 7.171630 TGTTCTTCTACTAGGAACTGGATTC 57.828 40.000 9.34 0.00 40.33 2.52
2337 2450 7.751047 TTTCGAAAGATAAACCTAGTGATCG 57.249 36.000 6.47 0.00 41.60 3.69
2429 2542 5.663106 TCAGTCCATAAGAAACATCTAGCCT 59.337 40.000 0.00 0.00 0.00 4.58
2549 2666 9.898152 GCCTCTAGCTTAATATAAGAATGGATT 57.102 33.333 0.00 0.00 38.99 3.01
2740 2861 5.191722 TGGTGTCCCTTATTCTGAATAAGCT 59.808 40.000 31.13 5.37 45.73 3.74
2817 2938 1.080025 GACCTCAAAGACCCGACCG 60.080 63.158 0.00 0.00 0.00 4.79
3066 3197 9.823098 TTTGTTGAAATTCACAAACATTTCTTG 57.177 25.926 14.84 0.00 39.29 3.02
3088 3219 9.906660 TCTTGAAAGCATGAACGTTTTATAAAT 57.093 25.926 0.46 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 4.692371 CGCATATCGTCGAAAATTCTGA 57.308 40.909 0.00 0.00 0.00 3.27
107 108 1.142185 CGTAGACGCCTCGTAGTCGA 61.142 60.000 0.00 0.00 41.37 4.20
121 122 4.672542 CGGATTTTACGAAGTCACCGTAGA 60.673 45.833 0.00 0.00 43.93 2.59
125 126 2.598589 TCGGATTTTACGAAGTCACCG 58.401 47.619 0.00 0.00 43.93 4.94
147 148 1.620819 AGACTGGGCCGACATATCATC 59.379 52.381 0.00 0.00 0.00 2.92
155 156 3.827898 CCGAGAGACTGGGCCGAC 61.828 72.222 0.00 0.00 0.00 4.79
161 162 1.065345 TGAGTACCTCCGAGAGACTGG 60.065 57.143 6.84 0.00 0.00 4.00
170 171 2.660670 ACCTCCTATGAGTACCTCCG 57.339 55.000 0.00 0.00 36.86 4.63
172 173 3.398629 ACCCTACCTCCTATGAGTACCTC 59.601 52.174 0.00 0.00 36.86 3.85
195 196 2.663602 CTCTATGAACTCACACACGCAC 59.336 50.000 0.00 0.00 0.00 5.34
217 218 7.218963 CGCTCATATATACGCGCATATAATCAT 59.781 37.037 20.00 5.09 39.11 2.45
247 248 5.252969 TCTTTGTAACACAGTACAGACGT 57.747 39.130 0.00 0.00 35.47 4.34
248 249 6.578020 TTTCTTTGTAACACAGTACAGACG 57.422 37.500 0.00 0.00 35.47 4.18
257 258 7.255104 CCTCAGCTTACATTTCTTTGTAACACA 60.255 37.037 0.00 0.00 37.20 3.72
277 279 0.528017 GCCAACCTAAAAGCCTCAGC 59.472 55.000 0.00 0.00 40.32 4.26
278 280 2.206576 AGCCAACCTAAAAGCCTCAG 57.793 50.000 0.00 0.00 0.00 3.35
282 284 9.309516 GTAAAATAATAAGCCAACCTAAAAGCC 57.690 33.333 0.00 0.00 0.00 4.35
325 327 4.196971 GTCCATAGCAATTTCCGTTAGGT 58.803 43.478 0.00 0.00 39.05 3.08
364 366 4.684877 TGCGTCTGTACTGTGTTTAAAGA 58.315 39.130 0.00 0.00 0.00 2.52
365 367 5.398176 TTGCGTCTGTACTGTGTTTAAAG 57.602 39.130 0.00 0.00 0.00 1.85
369 371 1.597663 GCTTGCGTCTGTACTGTGTTT 59.402 47.619 0.00 0.00 0.00 2.83
374 379 1.071605 GAAGGCTTGCGTCTGTACTG 58.928 55.000 3.46 0.00 0.00 2.74
379 384 1.725641 TGTATGAAGGCTTGCGTCTG 58.274 50.000 3.46 0.00 0.00 3.51
381 386 2.218759 CGTATGTATGAAGGCTTGCGTC 59.781 50.000 3.46 0.00 0.00 5.19
383 388 1.070577 GCGTATGTATGAAGGCTTGCG 60.071 52.381 3.46 0.00 0.00 4.85
390 395 3.981416 AGTGTATGCGCGTATGTATGAAG 59.019 43.478 20.45 0.00 0.00 3.02
393 398 3.119628 GTGAGTGTATGCGCGTATGTATG 59.880 47.826 20.45 0.00 0.00 2.39
411 433 1.227380 GTGCGCTCATAGGGGTGAG 60.227 63.158 9.73 0.00 46.59 3.51
415 437 1.815421 GTGTGTGCGCTCATAGGGG 60.815 63.158 16.02 0.00 0.00 4.79
433 455 2.165030 ACTCATAGGGGTACGTTGTTCG 59.835 50.000 0.00 0.00 46.00 3.95
434 456 3.881937 ACTCATAGGGGTACGTTGTTC 57.118 47.619 0.00 0.00 0.00 3.18
435 457 5.206587 AGATACTCATAGGGGTACGTTGTT 58.793 41.667 0.00 0.00 0.00 2.83
438 460 4.518211 CGAAGATACTCATAGGGGTACGTT 59.482 45.833 0.00 0.00 0.00 3.99
439 461 4.070716 CGAAGATACTCATAGGGGTACGT 58.929 47.826 0.00 0.00 0.00 3.57
440 462 4.321718 TCGAAGATACTCATAGGGGTACG 58.678 47.826 0.00 0.00 0.00 3.67
441 463 6.489361 TCTTTCGAAGATACTCATAGGGGTAC 59.511 42.308 0.00 0.00 35.04 3.34
443 465 5.302313 GTCTTTCGAAGATACTCATAGGGGT 59.698 44.000 0.00 0.00 40.18 4.95
444 466 5.536916 AGTCTTTCGAAGATACTCATAGGGG 59.463 44.000 0.00 0.00 40.18 4.79
445 467 6.263392 TCAGTCTTTCGAAGATACTCATAGGG 59.737 42.308 0.00 0.00 40.18 3.53
446 468 7.012894 ACTCAGTCTTTCGAAGATACTCATAGG 59.987 40.741 0.00 0.00 40.18 2.57
457 479 1.335964 TGCCGACTCAGTCTTTCGAAG 60.336 52.381 2.61 0.00 34.62 3.79
460 482 2.561733 TATGCCGACTCAGTCTTTCG 57.438 50.000 2.61 0.00 0.00 3.46
504 526 1.298413 CGACGATGAGGTGCCTACG 60.298 63.158 0.00 9.22 0.00 3.51
509 531 2.537792 TTCCGTCGACGATGAGGTGC 62.538 60.000 37.65 0.00 43.02 5.01
511 533 0.109412 GTTTCCGTCGACGATGAGGT 60.109 55.000 37.65 0.00 43.02 3.85
530 552 2.263077 CATTTTCAGTCGGAGGAGACG 58.737 52.381 0.00 0.00 45.26 4.18
540 562 4.668576 TCTCGACAATGCATTTTCAGTC 57.331 40.909 21.99 18.14 0.00 3.51
548 570 6.757897 TTAAGGATTTTCTCGACAATGCAT 57.242 33.333 0.00 0.00 0.00 3.96
554 576 9.456147 TGGATTTATTTAAGGATTTTCTCGACA 57.544 29.630 0.00 0.00 0.00 4.35
578 600 5.516339 GTCCTGATGTTCGCATTATTTTTGG 59.484 40.000 0.00 0.00 38.08 3.28
581 603 6.150976 TCAAGTCCTGATGTTCGCATTATTTT 59.849 34.615 0.00 0.00 38.08 1.82
609 631 2.039084 GTGGTATTCCTAGCCCATCAGG 59.961 54.545 0.00 0.00 34.73 3.86
612 634 2.706190 ACAGTGGTATTCCTAGCCCATC 59.294 50.000 0.00 0.00 34.23 3.51
613 635 2.776665 ACAGTGGTATTCCTAGCCCAT 58.223 47.619 0.00 0.00 34.23 4.00
616 638 3.195471 GGAACAGTGGTATTCCTAGCC 57.805 52.381 4.18 0.00 41.13 3.93
621 643 4.224370 TGGTTAGAGGAACAGTGGTATTCC 59.776 45.833 3.34 3.34 44.14 3.01
624 646 4.409247 GGATGGTTAGAGGAACAGTGGTAT 59.591 45.833 0.00 0.00 40.09 2.73
625 647 3.773119 GGATGGTTAGAGGAACAGTGGTA 59.227 47.826 0.00 0.00 40.09 3.25
626 648 2.572104 GGATGGTTAGAGGAACAGTGGT 59.428 50.000 0.00 0.00 40.09 4.16
627 649 2.571653 TGGATGGTTAGAGGAACAGTGG 59.428 50.000 0.00 0.00 40.09 4.00
629 651 4.993705 TTTGGATGGTTAGAGGAACAGT 57.006 40.909 0.00 0.00 40.09 3.55
630 652 6.712547 GGATATTTGGATGGTTAGAGGAACAG 59.287 42.308 0.00 0.00 40.09 3.16
631 653 6.159575 TGGATATTTGGATGGTTAGAGGAACA 59.840 38.462 0.00 0.00 40.09 3.18
632 654 6.601332 TGGATATTTGGATGGTTAGAGGAAC 58.399 40.000 0.00 0.00 37.31 3.62
633 655 6.840090 TGGATATTTGGATGGTTAGAGGAA 57.160 37.500 0.00 0.00 0.00 3.36
634 656 6.410388 GGTTGGATATTTGGATGGTTAGAGGA 60.410 42.308 0.00 0.00 0.00 3.71
659 681 1.394697 GTGTCGCGAACCAATTTGTG 58.605 50.000 12.06 0.00 0.00 3.33
660 682 0.309612 GGTGTCGCGAACCAATTTGT 59.690 50.000 25.60 0.00 37.65 2.83
661 683 0.724453 CGGTGTCGCGAACCAATTTG 60.724 55.000 27.92 14.96 37.57 2.32
662 684 1.572447 CGGTGTCGCGAACCAATTT 59.428 52.632 27.92 0.00 37.57 1.82
663 685 2.322081 CCGGTGTCGCGAACCAATT 61.322 57.895 27.92 0.00 37.57 2.32
664 686 2.740826 CCGGTGTCGCGAACCAAT 60.741 61.111 27.92 0.00 37.57 3.16
665 687 4.973055 CCCGGTGTCGCGAACCAA 62.973 66.667 27.92 9.01 37.57 3.67
820 858 2.058595 AATGGACGGACGGAGGGAG 61.059 63.158 0.00 0.00 0.00 4.30
821 859 2.038329 AATGGACGGACGGAGGGA 59.962 61.111 0.00 0.00 0.00 4.20
822 860 1.686325 ATCAATGGACGGACGGAGGG 61.686 60.000 0.00 0.00 0.00 4.30
823 861 0.249489 GATCAATGGACGGACGGAGG 60.249 60.000 0.00 0.00 0.00 4.30
824 862 0.249489 GGATCAATGGACGGACGGAG 60.249 60.000 0.00 0.00 0.00 4.63
825 863 0.973496 TGGATCAATGGACGGACGGA 60.973 55.000 0.00 0.00 0.00 4.69
826 864 0.106708 ATGGATCAATGGACGGACGG 59.893 55.000 0.00 0.00 0.00 4.79
827 865 1.502231 GATGGATCAATGGACGGACG 58.498 55.000 0.00 0.00 0.00 4.79
1824 1904 0.676782 GCAATGCCGGTACCTCTTGT 60.677 55.000 10.90 0.00 0.00 3.16
1827 1907 1.221840 CTGCAATGCCGGTACCTCT 59.778 57.895 10.90 0.00 0.00 3.69
1924 2004 0.252881 AGGAGAGTCTGGATGGCCAA 60.253 55.000 10.96 0.00 45.41 4.52
1946 2026 1.959226 CGGAACCAAGTGTCCGTGG 60.959 63.158 3.96 0.00 44.80 4.94
2152 2236 4.837972 AGAAGAACAATAAGCAGAGACCC 58.162 43.478 0.00 0.00 0.00 4.46
2155 2239 7.834681 TCCTAGTAGAAGAACAATAAGCAGAGA 59.165 37.037 0.00 0.00 0.00 3.10
2298 2411 3.328382 TCGAAAATACCACCTCCACAG 57.672 47.619 0.00 0.00 0.00 3.66
2509 2626 9.845740 TTAAGCTAGAGGCATGTAATTTTATCA 57.154 29.630 0.00 0.00 44.79 2.15
2685 2806 1.089920 CAGTGGTAGCTTCCATGCAC 58.910 55.000 15.81 2.47 39.81 4.57
2740 2861 1.083806 CGGCGCATCAAGCTAAGTCA 61.084 55.000 10.83 0.00 42.61 3.41
2817 2938 1.167851 TTGAGTGGCTAGCAACATGC 58.832 50.000 24.16 12.98 45.46 4.06
2955 3079 2.794350 GGAAAATTGTTCACGTTGCCAG 59.206 45.455 0.00 0.00 0.00 4.85
3034 3165 8.545229 TGTTTGTGAATTTCAACAAATGTTCT 57.455 26.923 20.07 0.00 35.83 3.01


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

AutoCloner maintained by Alex Coulton.