Multiple sequence alignment - TraesCS7D01G434800

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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 TraesCS7D01G434800 chr7D 100.000 2597 0 0 1 2597 554373117 554370521 0.000000e+00 4796.0
1 TraesCS7D01G434800 chr7D 84.937 239 30 6 1397 1631 554486140 554485904 1.200000e-58 237.0
2 TraesCS7D01G434800 chr7D 82.427 239 36 5 1397 1631 554420800 554420564 1.220000e-48 204.0
3 TraesCS7D01G434800 chr7D 81.679 262 33 11 1427 1682 554474164 554473912 1.220000e-48 204.0
4 TraesCS7D01G434800 chr7D 83.784 185 27 3 1100 1281 554353783 554353599 3.440000e-39 172.0
5 TraesCS7D01G434800 chr7D 83.243 185 28 3 1100 1281 588667685 588667501 1.600000e-37 167.0
6 TraesCS7D01G434800 chr7D 73.947 380 75 18 1158 1531 554183741 554183380 5.830000e-27 132.0
7 TraesCS7D01G434800 chr7D 100.000 54 0 0 1740 1793 554371325 554371272 1.640000e-17 100.0
8 TraesCS7D01G434800 chr7D 100.000 54 0 0 1793 1846 554371378 554371325 1.640000e-17 100.0
9 TraesCS7D01G434800 chr7D 88.732 71 5 2 651 720 554467921 554467853 1.660000e-12 84.2
10 TraesCS7D01G434800 chr7D 87.324 71 6 2 651 720 554512846 554512778 7.710000e-11 78.7
11 TraesCS7D01G434800 chr7D 87.324 71 6 2 651 720 554519118 554519050 7.710000e-11 78.7
12 TraesCS7D01G434800 chr7B 93.381 982 44 8 717 1683 600459046 600460021 0.000000e+00 1434.0
13 TraesCS7D01G434800 chr7B 89.145 737 52 9 1793 2504 31806402 31805669 0.000000e+00 893.0
14 TraesCS7D01G434800 chr7B 84.364 550 68 11 102 641 600458448 600458989 8.230000e-145 523.0
15 TraesCS7D01G434800 chr7B 88.831 385 36 6 2215 2597 150557127 150557506 1.410000e-127 466.0
16 TraesCS7D01G434800 chr7B 83.587 329 32 12 1904 2224 150551366 150551680 3.270000e-74 289.0
17 TraesCS7D01G434800 chr7B 81.379 290 38 9 1397 1682 600364586 600364863 3.360000e-54 222.0
18 TraesCS7D01G434800 chr7B 83.333 240 32 8 1397 1631 600351618 600351854 5.630000e-52 215.0
19 TraesCS7D01G434800 chr7B 83.333 240 32 8 1397 1631 600389938 600390174 5.630000e-52 215.0
20 TraesCS7D01G434800 chr7B 80.690 290 40 9 1397 1682 600311959 600312236 7.280000e-51 211.0
21 TraesCS7D01G434800 chr7B 83.422 187 28 3 1098 1281 663258231 663258417 1.240000e-38 171.0
22 TraesCS7D01G434800 chr7B 93.137 102 5 1 1689 1788 31806455 31806354 5.790000e-32 148.0
23 TraesCS7D01G434800 chr7B 88.679 106 10 2 15 118 138389554 138389449 7.540000e-26 128.0
24 TraesCS7D01G434800 chr7A 91.658 947 56 13 754 1684 639777479 639778418 0.000000e+00 1290.0
25 TraesCS7D01G434800 chr7A 84.026 457 35 14 321 758 639774404 639774841 3.110000e-109 405.0
26 TraesCS7D01G434800 chr7A 84.375 352 35 9 1 335 639774033 639774381 6.930000e-86 327.0
27 TraesCS7D01G434800 chr7A 85.915 71 7 2 651 720 639596477 639596545 3.580000e-09 73.1
28 TraesCS7D01G434800 chr5D 90.571 700 48 9 1904 2597 448811915 448812602 0.000000e+00 911.0
29 TraesCS7D01G434800 chr5D 88.462 104 10 2 1687 1788 448811794 448811897 9.760000e-25 124.0
30 TraesCS7D01G434800 chr5D 93.878 49 3 0 1793 1841 448811849 448811897 9.970000e-10 75.0
31 TraesCS7D01G434800 chr1B 87.319 828 66 12 1783 2597 174089235 174090036 0.000000e+00 911.0
32 TraesCS7D01G434800 chr1B 83.784 814 91 22 1794 2597 343365865 343366647 0.000000e+00 734.0
33 TraesCS7D01G434800 chr1B 88.889 54 2 2 1686 1735 197856769 197856716 2.160000e-06 63.9
34 TraesCS7D01G434800 chr4D 87.500 704 69 11 1904 2597 314077770 314077076 0.000000e+00 795.0
35 TraesCS7D01G434800 chr2B 84.491 806 83 24 1795 2590 79520690 79521463 0.000000e+00 758.0
36 TraesCS7D01G434800 chr6B 85.917 703 81 12 1904 2597 24343366 24342673 0.000000e+00 734.0
37 TraesCS7D01G434800 chr6B 85.775 703 82 12 1904 2597 24260145 24259452 0.000000e+00 728.0
38 TraesCS7D01G434800 chr3D 94.000 50 1 2 1685 1732 604838356 604838405 9.970000e-10 75.0
39 TraesCS7D01G434800 chr1D 92.157 51 2 2 1687 1735 46385698 46385648 1.290000e-08 71.3
40 TraesCS7D01G434800 chr1D 90.000 50 3 1 1689 1736 390688638 390688589 2.160000e-06 63.9


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 TraesCS7D01G434800 chr7D 554370521 554373117 2596 True 1665.333333 4796 100.000000 1 2597 3 chr7D.!!$R10 2596
1 TraesCS7D01G434800 chr7B 600458448 600460021 1573 False 978.500000 1434 88.872500 102 1683 2 chr7B.!!$F8 1581
2 TraesCS7D01G434800 chr7B 31805669 31806455 786 True 520.500000 893 91.141000 1689 2504 2 chr7B.!!$R2 815
3 TraesCS7D01G434800 chr7A 639774033 639778418 4385 False 674.000000 1290 86.686333 1 1684 3 chr7A.!!$F2 1683
4 TraesCS7D01G434800 chr5D 448811794 448812602 808 False 370.000000 911 90.970333 1687 2597 3 chr5D.!!$F1 910
5 TraesCS7D01G434800 chr1B 174089235 174090036 801 False 911.000000 911 87.319000 1783 2597 1 chr1B.!!$F1 814
6 TraesCS7D01G434800 chr1B 343365865 343366647 782 False 734.000000 734 83.784000 1794 2597 1 chr1B.!!$F2 803
7 TraesCS7D01G434800 chr4D 314077076 314077770 694 True 795.000000 795 87.500000 1904 2597 1 chr4D.!!$R1 693
8 TraesCS7D01G434800 chr2B 79520690 79521463 773 False 758.000000 758 84.491000 1795 2590 1 chr2B.!!$F1 795
9 TraesCS7D01G434800 chr6B 24342673 24343366 693 True 734.000000 734 85.917000 1904 2597 1 chr6B.!!$R2 693
10 TraesCS7D01G434800 chr6B 24259452 24260145 693 True 728.000000 728 85.775000 1904 2597 1 chr6B.!!$R1 693

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
535 604 0.469917 CCATGGCAAGTAGACCGGAT 59.53 55.0 9.46 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 4709 0.035458 AGTGACTAGTTGGTGCTGCC 59.965 55.0 0.0 0.0 37.9 4.85 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
27 28 4.299155 CACATACGCCCTTACTAGACATG 58.701 47.826 0.00 0.00 0.00 3.21
28 29 3.958798 ACATACGCCCTTACTAGACATGT 59.041 43.478 0.00 0.00 0.00 3.21
37 38 5.414765 CCCTTACTAGACATGTTTTTGGTCC 59.585 44.000 0.00 0.00 31.99 4.46
38 39 5.121768 CCTTACTAGACATGTTTTTGGTCCG 59.878 44.000 0.00 0.00 31.99 4.79
86 87 2.249309 ACCCTCCGGACTTATCTTGT 57.751 50.000 0.00 0.00 0.00 3.16
115 116 8.784994 TCCTATGAACAATAACGTTTAAGCAAA 58.215 29.630 5.91 0.00 0.00 3.68
144 160 4.039004 TGTTTAGCAACGTTACCACCTCTA 59.961 41.667 0.00 0.00 35.40 2.43
212 230 1.829222 GGATGACCGGTTTGACTCCTA 59.171 52.381 9.42 0.00 0.00 2.94
221 239 3.056749 CGGTTTGACTCCTAGTGCTTACT 60.057 47.826 0.00 0.00 0.00 2.24
227 245 3.367321 ACTCCTAGTGCTTACTCTTCCC 58.633 50.000 0.00 0.00 0.00 3.97
232 250 0.542333 GTGCTTACTCTTCCCCTCCC 59.458 60.000 0.00 0.00 0.00 4.30
236 254 2.894864 GCTTACTCTTCCCCTCCCTCTT 60.895 54.545 0.00 0.00 0.00 2.85
336 354 1.120795 CATGAGGGGAGGAGAGGAGC 61.121 65.000 0.00 0.00 0.00 4.70
337 355 1.303423 ATGAGGGGAGGAGAGGAGCT 61.303 60.000 0.00 0.00 0.00 4.09
338 356 1.457455 GAGGGGAGGAGAGGAGCTG 60.457 68.421 0.00 0.00 0.00 4.24
339 357 2.236959 GAGGGGAGGAGAGGAGCTGT 62.237 65.000 0.00 0.00 0.00 4.40
341 359 1.309688 GGGAGGAGAGGAGCTGTCT 59.690 63.158 0.00 0.00 0.00 3.41
342 360 0.755327 GGGAGGAGAGGAGCTGTCTC 60.755 65.000 12.53 12.53 39.92 3.36
350 368 2.680352 GAGCTGTCTCCGGGGTCA 60.680 66.667 0.00 0.00 33.19 4.02
351 369 2.681778 AGCTGTCTCCGGGGTCAG 60.682 66.667 22.57 22.57 0.00 3.51
353 371 3.077556 CTGTCTCCGGGGTCAGGG 61.078 72.222 19.65 0.00 0.00 4.45
355 373 3.075641 GTCTCCGGGGTCAGGGTC 61.076 72.222 0.00 0.00 0.00 4.46
356 374 3.596799 TCTCCGGGGTCAGGGTCA 61.597 66.667 0.00 0.00 0.00 4.02
358 376 4.715130 TCCGGGGTCAGGGTCAGG 62.715 72.222 0.00 0.00 0.00 3.86
362 380 4.416738 GGGTCAGGGTCAGGCAGC 62.417 72.222 0.00 0.00 0.00 5.25
363 381 4.767255 GGTCAGGGTCAGGCAGCG 62.767 72.222 0.00 0.00 0.00 5.18
380 436 2.833582 GCGAGGATCTCACCCCGA 60.834 66.667 0.00 0.00 0.00 5.14
408 464 1.001393 GCTGGGGAAACGGGATGAA 60.001 57.895 0.00 0.00 0.00 2.57
423 479 3.371059 GGGATGAAGGAGAGGGAGAAAAC 60.371 52.174 0.00 0.00 0.00 2.43
466 522 8.617290 TTTAAGAGAACTAACAGTTGAATCCC 57.383 34.615 0.00 0.00 38.80 3.85
480 536 1.315257 AATCCCGCTTGTCATGTGGC 61.315 55.000 11.89 0.00 34.02 5.01
494 563 5.018809 GTCATGTGGCCCAATATAATCCAT 58.981 41.667 0.00 0.00 0.00 3.41
495 564 5.481473 GTCATGTGGCCCAATATAATCCATT 59.519 40.000 0.00 0.00 0.00 3.16
496 565 6.014327 GTCATGTGGCCCAATATAATCCATTT 60.014 38.462 0.00 0.00 0.00 2.32
497 566 5.804944 TGTGGCCCAATATAATCCATTTG 57.195 39.130 0.00 0.00 0.00 2.32
498 567 5.462240 TGTGGCCCAATATAATCCATTTGA 58.538 37.500 0.00 0.00 0.00 2.69
499 568 5.304101 TGTGGCCCAATATAATCCATTTGAC 59.696 40.000 0.00 0.00 0.00 3.18
500 569 5.539955 GTGGCCCAATATAATCCATTTGACT 59.460 40.000 0.00 0.00 0.00 3.41
501 570 6.041979 GTGGCCCAATATAATCCATTTGACTT 59.958 38.462 0.00 0.00 0.00 3.01
502 571 6.614906 TGGCCCAATATAATCCATTTGACTTT 59.385 34.615 0.00 0.00 0.00 2.66
503 572 7.127032 TGGCCCAATATAATCCATTTGACTTTT 59.873 33.333 0.00 0.00 0.00 2.27
504 573 7.442062 GGCCCAATATAATCCATTTGACTTTTG 59.558 37.037 0.00 0.00 0.00 2.44
505 574 7.986889 GCCCAATATAATCCATTTGACTTTTGT 59.013 33.333 0.00 0.00 0.00 2.83
521 590 5.175859 ACTTTTGTACTACGTCATCCATGG 58.824 41.667 4.97 4.97 0.00 3.66
532 601 1.138859 TCATCCATGGCAAGTAGACCG 59.861 52.381 6.96 0.00 0.00 4.79
534 603 0.616395 TCCATGGCAAGTAGACCGGA 60.616 55.000 9.46 0.00 0.00 5.14
535 604 0.469917 CCATGGCAAGTAGACCGGAT 59.530 55.000 9.46 0.00 0.00 4.18
552 621 3.765511 CCGGATATGTTAGAATCGGGGTA 59.234 47.826 0.00 0.00 38.36 3.69
566 635 7.823665 AGAATCGGGGTAAAATTTGACTTAAC 58.176 34.615 5.64 0.00 0.00 2.01
568 637 5.383476 TCGGGGTAAAATTTGACTTAACCA 58.617 37.500 5.64 0.00 36.71 3.67
647 716 4.812626 AGTTCTTTGTGACGAATTACCGTT 59.187 37.500 0.00 0.00 43.49 4.44
648 717 5.295045 AGTTCTTTGTGACGAATTACCGTTT 59.705 36.000 0.00 0.00 43.49 3.60
649 718 5.738118 TCTTTGTGACGAATTACCGTTTT 57.262 34.783 0.00 0.00 43.49 2.43
650 719 6.841443 TCTTTGTGACGAATTACCGTTTTA 57.159 33.333 0.00 0.00 43.49 1.52
651 720 6.879962 TCTTTGTGACGAATTACCGTTTTAG 58.120 36.000 0.00 0.00 43.49 1.85
653 722 6.601741 TTGTGACGAATTACCGTTTTAGTT 57.398 33.333 0.00 0.00 43.49 2.24
654 723 6.214205 TGTGACGAATTACCGTTTTAGTTC 57.786 37.500 0.00 0.00 43.49 3.01
659 746 8.180267 TGACGAATTACCGTTTTAGTTCAAAAA 58.820 29.630 0.00 0.00 43.49 1.94
681 768 3.053831 ACCGGATCGACAAACTCAAAT 57.946 42.857 9.46 0.00 0.00 2.32
694 781 9.478019 CGACAAACTCAAATTCACATCTTATAC 57.522 33.333 0.00 0.00 0.00 1.47
703 790 6.834959 ATTCACATCTTATACGCAGAACAG 57.165 37.500 0.00 0.00 0.00 3.16
748 835 0.528924 TCTGTGTACCCGATTCCGTG 59.471 55.000 0.00 0.00 0.00 4.94
839 3576 7.014615 CCCAAAATTCCATACTAAGGATTCCTG 59.985 40.741 5.84 0.00 34.56 3.86
847 3584 0.830648 TAAGGATTCCTGCCCGACTG 59.169 55.000 5.84 0.00 32.13 3.51
886 3623 4.389374 AGTCCCCGTTCAATATAAGCATG 58.611 43.478 0.00 0.00 0.00 4.06
964 3701 2.099263 GAGCAGCATAGGAGACACGTAA 59.901 50.000 0.00 0.00 0.00 3.18
1011 3748 4.112433 TCGAGCATGGCCATGGCA 62.112 61.111 39.72 23.14 44.11 4.92
1012 3749 3.142162 CGAGCATGGCCATGGCAA 61.142 61.111 39.72 28.74 42.43 4.52
1138 3875 2.739671 TCTTCCTCGTCGACGCGA 60.740 61.111 32.19 25.05 39.60 5.87
1245 3982 3.108289 CACGTGGAGCTGCAGACG 61.108 66.667 20.43 20.38 37.82 4.18
1404 4153 0.391597 TCACAAACACGGAGGAGGAC 59.608 55.000 0.00 0.00 0.00 3.85
1606 4364 9.752961 TCGGATTGATAAAGTAATCGTGAATTA 57.247 29.630 0.00 0.00 34.83 1.40
1626 4384 5.601583 TTAATCTATGGGTGAACTGCGTA 57.398 39.130 0.00 0.00 0.00 4.42
1627 4385 2.953466 TCTATGGGTGAACTGCGTAC 57.047 50.000 0.00 0.00 0.00 3.67
1628 4386 1.133598 TCTATGGGTGAACTGCGTACG 59.866 52.381 11.84 11.84 0.00 3.67
1629 4387 0.889994 TATGGGTGAACTGCGTACGT 59.110 50.000 17.90 0.00 0.00 3.57
1656 4418 8.655970 CGTCACTCATACTGTATTTGATTTGAA 58.344 33.333 0.00 0.00 0.00 2.69
1657 4419 9.979270 GTCACTCATACTGTATTTGATTTGAAG 57.021 33.333 0.00 0.00 0.00 3.02
1678 4440 5.614923 AGAGATGTATCCGTGACTAATCG 57.385 43.478 0.00 0.00 0.00 3.34
1684 4446 6.193514 TGTATCCGTGACTAATCGTTGTAA 57.806 37.500 0.00 0.00 0.00 2.41
1685 4447 6.619744 TGTATCCGTGACTAATCGTTGTAAA 58.380 36.000 0.00 0.00 0.00 2.01
1746 4510 2.260434 GTCCGCTCTGTGCCGTAA 59.740 61.111 0.00 0.00 38.78 3.18
1778 4542 7.371936 CCTATTGTCAACCGTCCAAAATTTAA 58.628 34.615 0.00 0.00 0.00 1.52
1787 4551 2.027561 GTCCAAAATTTAACCCCTGCCC 60.028 50.000 0.00 0.00 0.00 5.36
1788 4552 2.158081 TCCAAAATTTAACCCCTGCCCT 60.158 45.455 0.00 0.00 0.00 5.19
1789 4553 2.236146 CCAAAATTTAACCCCTGCCCTC 59.764 50.000 0.00 0.00 0.00 4.30
1790 4554 1.847328 AAATTTAACCCCTGCCCTCG 58.153 50.000 0.00 0.00 0.00 4.63
1791 4555 0.996583 AATTTAACCCCTGCCCTCGA 59.003 50.000 0.00 0.00 0.00 4.04
1792 4556 1.222567 ATTTAACCCCTGCCCTCGAT 58.777 50.000 0.00 0.00 0.00 3.59
1799 4563 2.499205 CTGCCCTCGATGCCGTAA 59.501 61.111 4.80 0.00 37.05 3.18
1831 4595 7.371936 CCTATTGTCAACCGTCCAAAATTTAA 58.628 34.615 0.00 0.00 0.00 1.52
1841 4605 2.158081 TCCAAAATTTAACCCCTGCCCT 60.158 45.455 0.00 0.00 0.00 5.19
1849 4613 0.694444 AACCCCTGCCCTCGATATGT 60.694 55.000 0.00 0.00 0.00 2.29
1877 4641 3.859411 TTCTCCACAAAACCAACACAC 57.141 42.857 0.00 0.00 0.00 3.82
1902 4666 4.907034 CTCGCACGCGACGCCTAT 62.907 66.667 15.93 0.00 44.01 2.57
1928 4705 1.516386 CACGCGACGCCTATCTTGT 60.516 57.895 15.93 0.87 0.00 3.16
2046 4829 3.160585 CCCCAGCTGTTCCAGTGA 58.839 61.111 13.81 0.00 33.43 3.41
2118 4901 3.976942 CAGCAAAACAAATCTCTGGTTCG 59.023 43.478 0.00 0.00 0.00 3.95
2135 4918 4.130118 GGTTCGAGCAATAACATGGATCT 58.870 43.478 0.53 0.00 0.00 2.75
2173 4966 2.079170 TTGGATGGTGGCAAAAGACA 57.921 45.000 0.00 0.00 0.00 3.41
2290 5086 6.543831 GGACAGTGGTAGCAAAAATCATAGAT 59.456 38.462 0.00 0.00 0.00 1.98
2444 5245 2.268920 GCCGGTTCCAGCATCTCA 59.731 61.111 1.90 0.00 0.00 3.27
2445 5246 1.153086 GCCGGTTCCAGCATCTCAT 60.153 57.895 1.90 0.00 0.00 2.90
2446 5247 1.162800 GCCGGTTCCAGCATCTCATC 61.163 60.000 1.90 0.00 0.00 2.92
2459 5262 1.101635 TCTCATCTGCCCGTCGTAGG 61.102 60.000 0.00 0.00 0.00 3.18
2517 5320 2.331132 GCAGCAGCCACACCTCTTC 61.331 63.158 0.00 0.00 33.58 2.87
2580 5383 3.884774 TTCCAACACCGCCTGGCT 61.885 61.111 17.92 0.00 39.70 4.75
2590 5393 2.282745 GCCTGGCTTGGAGCTTGT 60.283 61.111 12.43 0.00 41.99 3.16
2593 5396 0.036732 CCTGGCTTGGAGCTTGTACA 59.963 55.000 0.00 0.00 41.99 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.142687 CCAAAAACATGTCTAGTAAGGGCG 60.143 45.833 0.00 0.00 0.00 6.13
12 13 4.765339 ACCAAAAACATGTCTAGTAAGGGC 59.235 41.667 0.00 0.00 0.00 5.19
13 14 5.414765 GGACCAAAAACATGTCTAGTAAGGG 59.585 44.000 0.00 0.00 0.00 3.95
27 28 1.183030 CCTTCCCCCGGACCAAAAAC 61.183 60.000 0.73 0.00 0.00 2.43
28 29 1.154221 CCTTCCCCCGGACCAAAAA 59.846 57.895 0.73 0.00 0.00 1.94
37 38 4.547367 GATGGCGACCTTCCCCCG 62.547 72.222 0.00 0.00 0.00 5.73
38 39 1.128188 ATAGATGGCGACCTTCCCCC 61.128 60.000 7.74 0.00 0.00 5.40
70 71 4.833390 AGGAAAACAAGATAAGTCCGGAG 58.167 43.478 3.06 0.00 0.00 4.63
86 87 9.615295 GCTTAAACGTTATTGTTCATAGGAAAA 57.385 29.630 0.00 0.00 34.13 2.29
115 116 4.395542 TGGTAACGTTGCTAAACACACTTT 59.604 37.500 16.07 0.00 42.51 2.66
212 230 1.574263 GGAGGGGAAGAGTAAGCACT 58.426 55.000 0.00 0.00 37.87 4.40
221 239 0.547712 CACCAAGAGGGAGGGGAAGA 60.548 60.000 0.00 0.00 41.15 2.87
227 245 1.415659 CTAGATGCACCAAGAGGGAGG 59.584 57.143 0.00 0.00 41.15 4.30
232 250 0.531532 CCGGCTAGATGCACCAAGAG 60.532 60.000 0.00 0.00 45.15 2.85
236 254 2.584064 CACCGGCTAGATGCACCA 59.416 61.111 0.00 0.00 45.15 4.17
286 304 2.600173 CAACCCCATGCACCGGTT 60.600 61.111 2.97 7.87 40.55 4.44
287 305 4.676951 CCAACCCCATGCACCGGT 62.677 66.667 0.00 0.00 0.00 5.28
336 354 3.077556 CCCTGACCCCGGAGACAG 61.078 72.222 0.73 5.55 0.00 3.51
337 355 3.899545 GACCCTGACCCCGGAGACA 62.900 68.421 0.73 0.00 0.00 3.41
338 356 3.075641 GACCCTGACCCCGGAGAC 61.076 72.222 0.73 0.00 0.00 3.36
339 357 3.596799 TGACCCTGACCCCGGAGA 61.597 66.667 0.73 0.00 0.00 3.71
341 359 4.715130 CCTGACCCTGACCCCGGA 62.715 72.222 0.73 0.00 0.00 5.14
346 364 4.767255 CGCTGCCTGACCCTGACC 62.767 72.222 0.00 0.00 0.00 4.02
353 371 4.521062 ATCCTCGCGCTGCCTGAC 62.521 66.667 5.56 0.00 0.00 3.51
355 373 4.218578 AGATCCTCGCGCTGCCTG 62.219 66.667 5.56 0.00 0.00 4.85
356 374 3.910490 GAGATCCTCGCGCTGCCT 61.910 66.667 5.56 0.00 0.00 4.75
358 376 2.959071 GTGAGATCCTCGCGCTGC 60.959 66.667 5.56 0.00 31.28 5.25
359 377 2.279120 GGTGAGATCCTCGCGCTG 60.279 66.667 5.56 0.00 41.37 5.18
360 378 3.532155 GGGTGAGATCCTCGCGCT 61.532 66.667 5.56 0.00 45.93 5.92
362 380 4.271816 CGGGGTGAGATCCTCGCG 62.272 72.222 0.00 0.00 44.58 5.87
408 464 7.366011 CCACATTATTAGTTTTCTCCCTCTCCT 60.366 40.741 0.00 0.00 0.00 3.69
466 522 1.597797 ATTGGGCCACATGACAAGCG 61.598 55.000 5.23 0.00 0.00 4.68
508 577 3.028130 TCTACTTGCCATGGATGACGTA 58.972 45.455 18.40 7.68 0.00 3.57
521 590 5.449107 TCTAACATATCCGGTCTACTTGC 57.551 43.478 0.00 0.00 0.00 4.01
532 601 8.631480 AATTTTACCCCGATTCTAACATATCC 57.369 34.615 0.00 0.00 0.00 2.59
534 603 9.635404 TCAAATTTTACCCCGATTCTAACATAT 57.365 29.630 0.00 0.00 0.00 1.78
535 604 8.895737 GTCAAATTTTACCCCGATTCTAACATA 58.104 33.333 0.00 0.00 0.00 2.29
568 637 5.220951 CGTCTAGATCACTGCAGTAATGACT 60.221 44.000 21.20 15.88 35.80 3.41
607 676 7.070821 ACAAAGAACTACTCCCTCTGTAAAGAA 59.929 37.037 0.00 0.00 0.00 2.52
608 677 6.553852 ACAAAGAACTACTCCCTCTGTAAAGA 59.446 38.462 0.00 0.00 0.00 2.52
659 746 2.536761 TGAGTTTGTCGATCCGGTTT 57.463 45.000 0.00 0.00 0.00 3.27
669 756 9.478019 CGTATAAGATGTGAATTTGAGTTTGTC 57.522 33.333 0.00 0.00 0.00 3.18
681 768 5.961272 TCTGTTCTGCGTATAAGATGTGAA 58.039 37.500 0.00 0.00 0.00 3.18
694 781 5.273170 TCATTTTGTTCTTTCTGTTCTGCG 58.727 37.500 0.00 0.00 0.00 5.18
703 790 5.727434 AGGCCATGATCATTTTGTTCTTTC 58.273 37.500 5.16 0.00 0.00 2.62
748 835 2.354203 CGGGGATGAATCCTTAGCTAGC 60.354 54.545 6.62 6.62 46.35 3.42
847 3584 0.312416 ACTCGCCGATACTGATCTGC 59.688 55.000 0.00 0.00 38.54 4.26
886 3623 4.443266 ACGCAGGCGCTTCCTCTC 62.443 66.667 14.32 0.00 45.52 3.20
946 3683 3.784701 ACTTACGTGTCTCCTATGCTG 57.215 47.619 0.00 0.00 0.00 4.41
951 3688 3.881688 GGCTGATACTTACGTGTCTCCTA 59.118 47.826 0.00 0.00 33.00 2.94
964 3701 2.894126 CTCTAATCGGGTGGCTGATACT 59.106 50.000 0.00 0.00 0.00 2.12
1098 3835 1.663379 CCGTGACGTAGATGGGCTCA 61.663 60.000 3.64 0.00 0.00 4.26
1245 3982 4.451150 TCGTCCAGCATCACCGGC 62.451 66.667 0.00 0.00 0.00 6.13
1324 4061 0.317938 GCGTCGTCTTCAGTGTCTGT 60.318 55.000 0.00 0.00 32.61 3.41
1355 4098 0.388520 CTCGAACATGACGACTGCCA 60.389 55.000 13.48 0.00 35.88 4.92
1404 4153 3.989698 ATCCTTGTCGTCGGCAGCG 62.990 63.158 0.00 0.00 0.00 5.18
1531 4289 7.118971 CACCAGAATTCCTAAGAATGCTATAGC 59.881 40.741 18.18 18.18 45.31 2.97
1606 4364 3.737047 CGTACGCAGTTCACCCATAGATT 60.737 47.826 0.52 0.00 37.78 2.40
1626 4384 4.959596 AATACAGTATGAGTGACGACGT 57.040 40.909 0.00 0.00 39.69 4.34
1627 4385 5.329493 TCAAATACAGTATGAGTGACGACG 58.671 41.667 0.00 0.00 39.69 5.12
1628 4386 7.757097 AATCAAATACAGTATGAGTGACGAC 57.243 36.000 0.00 0.00 39.69 4.34
1629 4387 8.032451 TCAAATCAAATACAGTATGAGTGACGA 58.968 33.333 0.00 0.00 39.69 4.20
1656 4418 5.064558 ACGATTAGTCACGGATACATCTCT 58.935 41.667 0.00 0.00 0.00 3.10
1657 4419 5.359716 ACGATTAGTCACGGATACATCTC 57.640 43.478 0.00 0.00 0.00 2.75
1678 4440 3.187842 CCCAGTACTCGCCTTTTTACAAC 59.812 47.826 0.00 0.00 0.00 3.32
1684 4446 1.375523 CGCCCAGTACTCGCCTTTT 60.376 57.895 0.00 0.00 0.00 2.27
1685 4447 2.264794 CGCCCAGTACTCGCCTTT 59.735 61.111 0.00 0.00 0.00 3.11
1717 4479 3.292159 GCGGACCGGCCAAGTTTT 61.292 61.111 17.22 0.00 35.94 2.43
1746 4510 4.443034 GGACGGTTGACAATAGGCTAATCT 60.443 45.833 0.00 0.00 0.00 2.40
1787 4551 2.029828 AGGCTAATCTTACGGCATCGAG 60.030 50.000 0.00 0.00 40.11 4.04
1788 4552 1.961394 AGGCTAATCTTACGGCATCGA 59.039 47.619 0.00 0.00 40.11 3.59
1789 4553 2.440539 AGGCTAATCTTACGGCATCG 57.559 50.000 0.00 0.00 43.02 3.84
1790 4554 5.238583 ACAATAGGCTAATCTTACGGCATC 58.761 41.667 0.00 0.00 0.00 3.91
1791 4555 5.221641 TGACAATAGGCTAATCTTACGGCAT 60.222 40.000 0.00 0.00 0.00 4.40
1792 4556 4.100344 TGACAATAGGCTAATCTTACGGCA 59.900 41.667 0.00 0.00 0.00 5.69
1799 4563 4.443034 GGACGGTTGACAATAGGCTAATCT 60.443 45.833 0.00 0.00 0.00 2.40
1831 4595 0.190069 TACATATCGAGGGCAGGGGT 59.810 55.000 0.00 0.00 0.00 4.95
1849 4613 4.963373 TGGTTTTGTGGAGAAAGACGATA 58.037 39.130 0.00 0.00 0.00 2.92
1896 4660 2.655364 CGTGCGACAGGATAGGCG 60.655 66.667 0.00 0.00 0.00 5.52
1897 4661 2.962253 GCGTGCGACAGGATAGGC 60.962 66.667 0.00 0.00 0.00 3.93
1898 4662 2.655364 CGCGTGCGACAGGATAGG 60.655 66.667 8.89 0.00 42.83 2.57
1899 4663 2.407616 TCGCGTGCGACAGGATAG 59.592 61.111 13.62 0.00 44.01 2.08
1923 4700 2.280797 GGTGCTGCCACGACAAGA 60.281 61.111 0.00 0.00 43.00 3.02
1932 4709 0.035458 AGTGACTAGTTGGTGCTGCC 59.965 55.000 0.00 0.00 37.90 4.85
2046 4829 1.334869 CTTCTTCCAAAGCGCAACTGT 59.665 47.619 11.47 0.00 0.00 3.55
2118 4901 3.216800 TGCCAGATCCATGTTATTGCTC 58.783 45.455 0.00 0.00 0.00 4.26
2247 5041 7.147312 CACTGTCCTTTTGATTTTTGCTATCA 58.853 34.615 0.00 0.00 0.00 2.15
2249 5043 6.041979 ACCACTGTCCTTTTGATTTTTGCTAT 59.958 34.615 0.00 0.00 0.00 2.97
2290 5086 4.458989 CAGCTCTAATTTTTGCTACCACCA 59.541 41.667 0.00 0.00 34.10 4.17
2364 5160 6.872920 ACTGTTCTTTTGTTTTGCTGGAATA 58.127 32.000 0.00 0.00 0.00 1.75
2403 5204 1.972198 CGGGAGCTACAACCAGTGA 59.028 57.895 0.00 0.00 0.00 3.41
2444 5245 0.968901 TTGTCCTACGACGGGCAGAT 60.969 55.000 0.00 0.00 40.28 2.90
2445 5246 1.604308 TTGTCCTACGACGGGCAGA 60.604 57.895 0.00 0.00 40.28 4.26
2446 5247 1.445582 GTTGTCCTACGACGGGCAG 60.446 63.158 0.00 0.00 40.28 4.85
2517 5320 4.201851 CCGTTGTCATCTAAAGCTGGAATG 60.202 45.833 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.