Multiple sequence alignment - TraesCS3D01G436700

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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 TraesCS3D01G436700 chr3D 100.000 2641 0 0 1 2641 548536384 548533744 0.000000e+00 4878
1 TraesCS3D01G436700 chr3D 86.247 778 86 11 6 768 300117604 300116833 0.000000e+00 824
2 TraesCS3D01G436700 chr3D 86.544 706 80 10 3 698 572429418 572430118 0.000000e+00 763
3 TraesCS3D01G436700 chr3D 84.184 784 105 9 2 768 190271471 190270690 0.000000e+00 743
4 TraesCS3D01G436700 chr3B 82.148 1322 92 59 771 2012 726471112 726469855 0.000000e+00 1002
5 TraesCS3D01G436700 chr3B 82.808 698 56 27 771 1443 726748249 726747591 1.370000e-157 566
6 TraesCS3D01G436700 chr3B 83.775 604 83 11 1886 2480 726740012 726739415 2.300000e-155 558
7 TraesCS3D01G436700 chr3B 92.391 92 2 2 883 974 727132912 727132826 2.760000e-25 126
8 TraesCS3D01G436700 chr3B 86.792 106 9 3 1576 1681 726745191 726745091 2.150000e-21 113
9 TraesCS3D01G436700 chr3A 89.571 652 35 9 806 1444 686128350 686127719 0.000000e+00 797
10 TraesCS3D01G436700 chr3A 83.679 772 105 15 3 758 222881 222115 0.000000e+00 708
11 TraesCS3D01G436700 chr3A 93.077 130 8 1 1537 1665 686127663 686127534 3.470000e-44 189
12 TraesCS3D01G436700 chr5B 85.931 725 94 5 3 720 605528405 605529128 0.000000e+00 767
13 TraesCS3D01G436700 chr2D 84.439 784 106 8 1 768 326361269 326362052 0.000000e+00 758
14 TraesCS3D01G436700 chr2D 84.527 782 104 8 1 768 524047129 524047907 0.000000e+00 758
15 TraesCS3D01G436700 chr2D 79.407 573 107 11 2033 2597 354988195 354988764 6.850000e-106 394
16 TraesCS3D01G436700 chr4B 83.290 766 111 9 1 751 623982568 623983331 0.000000e+00 689
17 TraesCS3D01G436700 chr7D 82.776 778 111 14 1 768 181341813 181342577 0.000000e+00 673
18 TraesCS3D01G436700 chr7D 78.361 610 116 11 2046 2641 99187683 99187076 5.330000e-102 381
19 TraesCS3D01G436700 chr6D 80.439 547 93 10 2106 2640 2900554 2900010 3.170000e-109 405
20 TraesCS3D01G436700 chr2A 78.205 624 116 16 2033 2640 474808078 474808697 5.330000e-102 381
21 TraesCS3D01G436700 chr2B 78.746 574 109 12 2033 2597 422511792 422512361 3.210000e-99 372
22 TraesCS3D01G436700 chr1D 78.153 563 116 6 2041 2597 347407746 347408307 4.180000e-93 351
23 TraesCS3D01G436700 chr4A 79.012 486 90 12 2033 2510 691156982 691156501 3.280000e-84 322
24 TraesCS3D01G436700 chr4D 76.260 615 125 13 2033 2633 8151997 8152604 9.180000e-80 307


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 TraesCS3D01G436700 chr3D 548533744 548536384 2640 True 4878.0 4878 100.000 1 2641 1 chr3D.!!$R3 2640
1 TraesCS3D01G436700 chr3D 300116833 300117604 771 True 824.0 824 86.247 6 768 1 chr3D.!!$R2 762
2 TraesCS3D01G436700 chr3D 572429418 572430118 700 False 763.0 763 86.544 3 698 1 chr3D.!!$F1 695
3 TraesCS3D01G436700 chr3D 190270690 190271471 781 True 743.0 743 84.184 2 768 1 chr3D.!!$R1 766
4 TraesCS3D01G436700 chr3B 726469855 726471112 1257 True 1002.0 1002 82.148 771 2012 1 chr3B.!!$R1 1241
5 TraesCS3D01G436700 chr3B 726739415 726740012 597 True 558.0 558 83.775 1886 2480 1 chr3B.!!$R2 594
6 TraesCS3D01G436700 chr3B 726745091 726748249 3158 True 339.5 566 84.800 771 1681 2 chr3B.!!$R4 910
7 TraesCS3D01G436700 chr3A 222115 222881 766 True 708.0 708 83.679 3 758 1 chr3A.!!$R1 755
8 TraesCS3D01G436700 chr3A 686127534 686128350 816 True 493.0 797 91.324 806 1665 2 chr3A.!!$R2 859
9 TraesCS3D01G436700 chr5B 605528405 605529128 723 False 767.0 767 85.931 3 720 1 chr5B.!!$F1 717
10 TraesCS3D01G436700 chr2D 326361269 326362052 783 False 758.0 758 84.439 1 768 1 chr2D.!!$F1 767
11 TraesCS3D01G436700 chr2D 524047129 524047907 778 False 758.0 758 84.527 1 768 1 chr2D.!!$F3 767
12 TraesCS3D01G436700 chr2D 354988195 354988764 569 False 394.0 394 79.407 2033 2597 1 chr2D.!!$F2 564
13 TraesCS3D01G436700 chr4B 623982568 623983331 763 False 689.0 689 83.290 1 751 1 chr4B.!!$F1 750
14 TraesCS3D01G436700 chr7D 181341813 181342577 764 False 673.0 673 82.776 1 768 1 chr7D.!!$F1 767
15 TraesCS3D01G436700 chr7D 99187076 99187683 607 True 381.0 381 78.361 2046 2641 1 chr7D.!!$R1 595
16 TraesCS3D01G436700 chr6D 2900010 2900554 544 True 405.0 405 80.439 2106 2640 1 chr6D.!!$R1 534
17 TraesCS3D01G436700 chr2A 474808078 474808697 619 False 381.0 381 78.205 2033 2640 1 chr2A.!!$F1 607
18 TraesCS3D01G436700 chr2B 422511792 422512361 569 False 372.0 372 78.746 2033 2597 1 chr2B.!!$F1 564
19 TraesCS3D01G436700 chr1D 347407746 347408307 561 False 351.0 351 78.153 2041 2597 1 chr1D.!!$F1 556
20 TraesCS3D01G436700 chr4D 8151997 8152604 607 False 307.0 307 76.260 2033 2633 1 chr4D.!!$F1 600

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
768 801 0.531532 CAGGCTGCCGTAGAAGATGG 60.532 60.0 13.96 0.0 37.27 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 4901 0.522495 GCGCGCCGTTATCATTGTTT 60.522 50.0 23.24 0.0 0.0 2.83 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
19 20 4.856801 GGCACGGGCATGGACGAT 62.857 66.667 13.89 0.00 43.71 3.73
51 52 2.683933 CCCCTCCAGTGCCTACGT 60.684 66.667 0.00 0.00 0.00 3.57
125 145 3.889044 GCGCGGAGGAGATCGACA 61.889 66.667 8.83 0.00 0.00 4.35
279 299 3.374367 GTGCCCGGTTTCTTCTTTATCTC 59.626 47.826 0.00 0.00 0.00 2.75
305 325 2.515398 CTGGCTTGGGTGTCCACA 59.485 61.111 0.00 0.00 43.94 4.17
310 330 0.890996 GCTTGGGTGTCCACAGAAGG 60.891 60.000 0.00 0.00 43.94 3.46
389 409 4.018141 TCGAATATAGGGAAGATACGGGGA 60.018 45.833 0.00 0.00 0.00 4.81
525 547 8.626576 CATACGTGCACATAGTTTTAAGTTTTG 58.373 33.333 18.64 0.00 0.00 2.44
529 551 7.514435 CGTGCACATAGTTTTAAGTTTTGGTTG 60.514 37.037 18.64 0.00 0.00 3.77
575 598 4.030134 TGCGTTTGGTTTGTACGAAATT 57.970 36.364 0.00 0.00 35.01 1.82
598 621 5.172205 TCGTCATGTTTGTATGAAATCCGA 58.828 37.500 0.00 0.00 38.69 4.55
654 677 3.824414 ATTTCGTCCGATTGGTTTGAC 57.176 42.857 0.00 0.00 36.30 3.18
667 690 6.090088 CGATTGGTTTGACTTGTTGTGAAAAA 59.910 34.615 0.00 0.00 33.83 1.94
690 713 1.153628 GCGTCTAGCGTTGGATGGT 60.154 57.895 6.95 0.00 43.66 3.55
728 751 3.647771 ACGGAGTGGCCCCTTTCC 61.648 66.667 0.00 0.61 42.51 3.13
729 752 4.426313 CGGAGTGGCCCCTTTCCC 62.426 72.222 0.00 0.00 0.00 3.97
760 793 4.165926 TTTTTGCAGGCTGCCGTA 57.834 50.000 34.58 18.32 44.23 4.02
768 801 0.531532 CAGGCTGCCGTAGAAGATGG 60.532 60.000 13.96 0.00 37.27 3.51
792 827 1.559682 AGACCAACGGCCATATCAACT 59.440 47.619 2.24 0.00 0.00 3.16
796 831 2.951642 CCAACGGCCATATCAACTTGAT 59.048 45.455 2.24 9.26 40.72 2.57
909 944 2.145536 CTGTTGCTCACACATACTGCA 58.854 47.619 0.00 0.00 0.00 4.41
1077 1124 3.304996 CGAGACAAGACAAGAAGCAGAGA 60.305 47.826 0.00 0.00 0.00 3.10
1078 1125 3.987220 GAGACAAGACAAGAAGCAGAGAC 59.013 47.826 0.00 0.00 0.00 3.36
1321 1383 2.125512 GTCGCATCGTGCCTCCTT 60.126 61.111 4.73 0.00 41.12 3.36
1337 1399 1.148310 CCTTGACTGCTACAACACGG 58.852 55.000 0.00 0.00 0.00 4.94
1382 1444 0.462047 CTACCTCGGATGCACCAACC 60.462 60.000 0.00 0.00 38.90 3.77
1459 1533 0.032678 CATCCGGCTAGCGATGAACT 59.967 55.000 21.49 0.00 38.53 3.01
1463 1537 2.486982 TCCGGCTAGCGATGAACTATAC 59.513 50.000 9.00 0.00 0.00 1.47
1466 1540 3.854240 CGGCTAGCGATGAACTATACATG 59.146 47.826 9.00 0.00 0.00 3.21
1474 1548 4.558697 CGATGAACTATACATGGCCTCGAA 60.559 45.833 3.32 0.00 0.00 3.71
1475 1549 4.746535 TGAACTATACATGGCCTCGAAA 57.253 40.909 3.32 0.00 0.00 3.46
1492 1566 6.183360 GCCTCGAAATGTATGACATCATATGG 60.183 42.308 2.13 0.00 37.97 2.74
1493 1567 7.099120 CCTCGAAATGTATGACATCATATGGA 58.901 38.462 2.13 0.00 37.97 3.41
1518 3572 3.563088 CGCATACGCACCGCATGT 61.563 61.111 0.00 0.00 38.40 3.21
1524 3582 3.483574 GCATACGCACCGCATGTATAATC 60.484 47.826 0.00 0.00 33.69 1.75
1526 3584 0.438445 CGCACCGCATGTATAATCCG 59.562 55.000 0.00 0.00 0.00 4.18
1575 3660 5.048643 ACCCTCTCACGTATGAATAAGATCG 60.049 44.000 0.00 0.00 33.30 3.69
1581 3941 7.012610 TCTCACGTATGAATAAGATCGGTTGTA 59.987 37.037 0.00 0.00 33.30 2.41
1603 3965 2.883386 AGTACTTCGTTTCAGTCGACCT 59.117 45.455 13.01 0.00 37.05 3.85
1662 4035 8.304596 GGTGAATATACACAGCTTGCTACTATA 58.695 37.037 0.00 0.00 41.88 1.31
1694 4067 7.360946 GCTTACATAATAATGATTCCGTCCCAC 60.361 40.741 0.00 0.00 36.54 4.61
1702 4075 1.550976 GATTCCGTCCCACTCTCTGTT 59.449 52.381 0.00 0.00 0.00 3.16
1704 4077 2.297698 TCCGTCCCACTCTCTGTTTA 57.702 50.000 0.00 0.00 0.00 2.01
1717 4090 7.155328 CACTCTCTGTTTATGTGGTTCTAACT 58.845 38.462 0.00 0.00 0.00 2.24
1718 4091 7.657761 CACTCTCTGTTTATGTGGTTCTAACTT 59.342 37.037 0.00 0.00 0.00 2.66
1719 4092 7.873505 ACTCTCTGTTTATGTGGTTCTAACTTC 59.126 37.037 0.00 0.00 0.00 3.01
1720 4093 7.732025 TCTCTGTTTATGTGGTTCTAACTTCA 58.268 34.615 0.00 0.00 0.00 3.02
1721 4094 8.208224 TCTCTGTTTATGTGGTTCTAACTTCAA 58.792 33.333 0.00 0.00 0.00 2.69
1722 4095 8.740123 TCTGTTTATGTGGTTCTAACTTCAAA 57.260 30.769 0.00 0.00 0.00 2.69
1723 4096 9.349713 TCTGTTTATGTGGTTCTAACTTCAAAT 57.650 29.630 0.00 0.00 0.00 2.32
1728 4101 9.575868 TTATGTGGTTCTAACTTCAAATAACCA 57.424 29.630 0.00 0.00 42.94 3.67
1729 4102 7.504924 TGTGGTTCTAACTTCAAATAACCAG 57.495 36.000 5.04 0.00 45.04 4.00
1730 4103 7.284074 TGTGGTTCTAACTTCAAATAACCAGA 58.716 34.615 5.04 1.67 45.04 3.86
1731 4104 7.942341 TGTGGTTCTAACTTCAAATAACCAGAT 59.058 33.333 5.04 0.00 45.04 2.90
1732 4105 9.444600 GTGGTTCTAACTTCAAATAACCAGATA 57.555 33.333 5.04 0.00 45.04 1.98
1763 4136 4.624336 ACAGCGAGAGAATGTAGTACTG 57.376 45.455 5.39 0.00 31.89 2.74
1768 4141 3.303461 CGAGAGAATGTAGTACTGCCTCG 60.303 52.174 17.11 17.11 35.74 4.63
1769 4142 2.952978 AGAGAATGTAGTACTGCCTCGG 59.047 50.000 5.39 0.00 0.00 4.63
1773 4146 1.913778 TGTAGTACTGCCTCGGTTCA 58.086 50.000 5.39 0.00 0.00 3.18
1774 4147 2.241160 TGTAGTACTGCCTCGGTTCAA 58.759 47.619 5.39 0.00 0.00 2.69
1783 4157 6.190954 ACTGCCTCGGTTCAAAAATATAAC 57.809 37.500 0.00 0.00 0.00 1.89
1789 4163 7.544217 GCCTCGGTTCAAAAATATAACATGTTT 59.456 33.333 17.78 7.40 0.00 2.83
1858 4234 8.095792 TGCATTTGTTAATTCATTTCAGTCCAT 58.904 29.630 0.00 0.00 0.00 3.41
2017 4397 8.402798 TCATCACTTTTTCTTTGCCATTAGTA 57.597 30.769 0.00 0.00 0.00 1.82
2024 4404 8.532977 TTTTTCTTTGCCATTAGTATTTGAGC 57.467 30.769 0.00 0.00 0.00 4.26
2040 4420 1.964223 TGAGCGACCAACTTTCTCTCT 59.036 47.619 0.00 0.00 0.00 3.10
2043 4423 3.394719 AGCGACCAACTTTCTCTCTTTC 58.605 45.455 0.00 0.00 0.00 2.62
2083 4467 5.106118 GGCTAGAGCAAACTTTCCCTTTTAG 60.106 44.000 3.54 0.00 44.36 1.85
2090 4474 6.551227 AGCAAACTTTCCCTTTTAGACTTCAT 59.449 34.615 0.00 0.00 0.00 2.57
2122 4509 2.688477 TGAATTTGCCTCCCCTTTGTT 58.312 42.857 0.00 0.00 0.00 2.83
2134 4521 1.164041 CCTTTGTTTGTCGCTCCGGT 61.164 55.000 0.00 0.00 0.00 5.28
2154 4542 2.925170 CCTATGGCGGGGAGGAGG 60.925 72.222 0.00 0.00 31.45 4.30
2208 4598 9.159364 GTTTAGGTTATGATTTTTAGTCCTCGT 57.841 33.333 0.00 0.00 0.00 4.18
2211 4601 8.075761 AGGTTATGATTTTTAGTCCTCGTAGT 57.924 34.615 0.00 0.00 0.00 2.73
2222 4612 1.805945 CTCGTAGTTGTGGCGCTCC 60.806 63.158 7.64 0.00 0.00 4.70
2234 4624 4.457496 CGCTCCGGCAGATGGTGT 62.457 66.667 0.00 0.00 38.60 4.16
2247 4637 2.300152 AGATGGTGTCGCTTCTTCTTCA 59.700 45.455 0.00 0.00 0.00 3.02
2249 4639 2.912771 TGGTGTCGCTTCTTCTTCAAA 58.087 42.857 0.00 0.00 0.00 2.69
2300 4691 5.333339 CGAGTTTGTCTGTTTGGATGTAGTG 60.333 44.000 0.00 0.00 0.00 2.74
2332 4723 2.941064 CGGTGTAGATTCCTGTCGTCTA 59.059 50.000 0.00 0.00 0.00 2.59
2371 4762 0.387239 GGTTTCTTGTCATGTGGCGC 60.387 55.000 0.00 0.00 0.00 6.53
2385 4776 2.202349 GCGCGATTTGGTGTCAGC 60.202 61.111 12.10 0.00 0.00 4.26
2394 4785 0.535780 TTGGTGTCAGCTGCTTCAGG 60.536 55.000 9.47 0.00 31.21 3.86
2421 4812 1.523515 CAATGGTTCAACGACGACGAA 59.476 47.619 15.32 0.26 42.66 3.85
2512 4905 2.652095 CGGCTCCGGTAGGGAAACA 61.652 63.158 0.00 0.00 46.61 2.83
2513 4906 1.681076 GGCTCCGGTAGGGAAACAA 59.319 57.895 0.00 0.00 46.61 2.83
2527 4920 0.522495 AAACAATGATAACGGCGCGC 60.522 50.000 25.94 25.94 0.00 6.86
2542 4935 4.513519 CGCCAACGCCTCATTCTA 57.486 55.556 0.00 0.00 0.00 2.10
2582 4976 2.361119 CGGTGGTCTCGGAATCTTGATA 59.639 50.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.854666 TCTTTCTCTGTCTGCATGCTAC 58.145 45.455 20.33 16.95 0.00 3.58
199 219 0.618981 CCTTCCTGGGACCCAAGTAC 59.381 60.000 15.87 0.00 30.80 2.73
279 299 2.034687 CCAAGCCAGGGTGGTCTG 59.965 66.667 0.00 0.00 40.46 3.51
366 386 4.018141 TCCCCGTATCTTCCCTATATTCGA 60.018 45.833 0.00 0.00 0.00 3.71
369 389 6.328592 TCTTTCCCCGTATCTTCCCTATATT 58.671 40.000 0.00 0.00 0.00 1.28
371 391 5.343833 TCTTTCCCCGTATCTTCCCTATA 57.656 43.478 0.00 0.00 0.00 1.31
406 426 2.046507 GCCAGACTGCCAGGAGTG 60.047 66.667 0.00 0.00 0.00 3.51
424 444 2.818274 GCGGCGGATCCTTTCGTT 60.818 61.111 9.78 0.00 0.00 3.85
575 598 5.172205 TCGGATTTCATACAAACATGACGA 58.828 37.500 0.00 0.00 34.69 4.20
598 621 2.223340 GCGGATTTCATGCAAACTCGAT 60.223 45.455 0.00 0.00 0.00 3.59
675 698 0.392461 GGCAACCATCCAACGCTAGA 60.392 55.000 0.00 0.00 0.00 2.43
716 739 1.380380 CATCAGGGAAAGGGGCCAC 60.380 63.158 4.39 0.00 0.00 5.01
728 751 2.961424 AAAAACCTCCCGCATCAGG 58.039 52.632 0.00 0.00 35.69 3.86
760 793 2.093447 CCGTTGGTCTAAGCCATCTTCT 60.093 50.000 0.00 0.00 38.48 2.85
768 801 2.143925 GATATGGCCGTTGGTCTAAGC 58.856 52.381 0.77 0.00 0.00 3.09
769 802 3.469008 TGATATGGCCGTTGGTCTAAG 57.531 47.619 0.77 0.00 0.00 2.18
792 827 9.202273 GTATTATTTTCAAAACTGTGCCATCAA 57.798 29.630 0.00 0.00 0.00 2.57
868 903 0.106419 AACCGGCCCTTTTCTTGTCA 60.106 50.000 0.00 0.00 0.00 3.58
925 960 2.281761 CCGTGGAGCAAGCAAGGT 60.282 61.111 0.00 0.00 0.00 3.50
1006 1048 1.003839 TGCTGGGTTCGATCGCTTT 60.004 52.632 11.09 0.00 0.00 3.51
1007 1049 1.741770 GTGCTGGGTTCGATCGCTT 60.742 57.895 11.09 0.00 0.00 4.68
1008 1050 2.125512 GTGCTGGGTTCGATCGCT 60.126 61.111 11.09 0.00 0.00 4.93
1213 1266 1.145598 AGCAGTCATCTCATGGCCG 59.854 57.895 0.00 0.00 34.84 6.13
1217 1270 1.158484 CCGGCAGCAGTCATCTCATG 61.158 60.000 0.00 0.00 0.00 3.07
1321 1383 1.301401 GGCCGTGTTGTAGCAGTCA 60.301 57.895 0.00 0.00 0.00 3.41
1337 1399 4.489771 CATGGTCCCTCCGGTGGC 62.490 72.222 17.44 4.32 39.52 5.01
1459 1533 6.163476 GTCATACATTTCGAGGCCATGTATA 58.837 40.000 19.77 9.95 40.57 1.47
1463 1537 3.205338 TGTCATACATTTCGAGGCCATG 58.795 45.455 5.01 1.17 0.00 3.66
1466 1540 3.466836 TGATGTCATACATTTCGAGGCC 58.533 45.455 0.00 0.00 39.27 5.19
1475 1549 9.881649 GTTGATACTCCATATGATGTCATACAT 57.118 33.333 3.65 0.00 42.43 2.29
1518 3572 0.102663 TGCGCGGTGAACGGATTATA 59.897 50.000 8.83 0.00 44.51 0.98
1524 3582 3.645157 GAATGTGCGCGGTGAACGG 62.645 63.158 8.83 0.00 44.51 4.44
1526 3584 2.175811 GGAATGTGCGCGGTGAAC 59.824 61.111 8.83 0.00 0.00 3.18
1575 3660 5.108103 CGACTGAAACGAAGTACTTACAACC 60.108 44.000 8.42 0.00 45.00 3.77
1581 3941 3.317430 AGGTCGACTGAAACGAAGTACTT 59.683 43.478 16.46 8.13 45.00 2.24
1603 3965 1.209383 GCTCGTGTCTAGTCGCACA 59.791 57.895 12.55 0.00 35.51 4.57
1665 4038 9.378551 GGACGGAATCATTATTATGTAAGCATA 57.621 33.333 0.00 0.00 36.58 3.14
1666 4039 7.336931 GGGACGGAATCATTATTATGTAAGCAT 59.663 37.037 0.00 0.00 39.03 3.79
1667 4040 6.653320 GGGACGGAATCATTATTATGTAAGCA 59.347 38.462 0.00 0.00 33.34 3.91
1668 4041 6.653320 TGGGACGGAATCATTATTATGTAAGC 59.347 38.462 0.00 0.00 33.34 3.09
1687 4060 3.254060 CACATAAACAGAGAGTGGGACG 58.746 50.000 0.00 0.00 0.00 4.79
1688 4061 3.600388 CCACATAAACAGAGAGTGGGAC 58.400 50.000 0.00 0.00 44.55 4.46
1694 4067 7.872993 TGAAGTTAGAACCACATAAACAGAGAG 59.127 37.037 0.00 0.00 0.00 3.20
1702 4075 9.575868 TGGTTATTTGAAGTTAGAACCACATAA 57.424 29.630 0.24 0.00 40.97 1.90
1704 4077 7.942341 TCTGGTTATTTGAAGTTAGAACCACAT 59.058 33.333 0.24 0.00 40.97 3.21
1720 4093 9.236006 GCTGTTCCATCATATATCTGGTTATTT 57.764 33.333 9.62 0.00 0.00 1.40
1721 4094 7.550551 CGCTGTTCCATCATATATCTGGTTATT 59.449 37.037 9.62 0.00 0.00 1.40
1722 4095 7.044181 CGCTGTTCCATCATATATCTGGTTAT 58.956 38.462 9.62 0.00 0.00 1.89
1723 4096 6.210584 TCGCTGTTCCATCATATATCTGGTTA 59.789 38.462 9.62 0.22 0.00 2.85
1724 4097 5.012046 TCGCTGTTCCATCATATATCTGGTT 59.988 40.000 9.62 0.00 0.00 3.67
1725 4098 4.528206 TCGCTGTTCCATCATATATCTGGT 59.472 41.667 9.62 0.00 0.00 4.00
1726 4099 5.077134 TCGCTGTTCCATCATATATCTGG 57.923 43.478 4.95 4.95 0.00 3.86
1727 4100 5.958955 TCTCGCTGTTCCATCATATATCTG 58.041 41.667 0.00 0.00 0.00 2.90
1728 4101 5.948758 TCTCTCGCTGTTCCATCATATATCT 59.051 40.000 0.00 0.00 0.00 1.98
1729 4102 6.201226 TCTCTCGCTGTTCCATCATATATC 57.799 41.667 0.00 0.00 0.00 1.63
1730 4103 6.596309 TTCTCTCGCTGTTCCATCATATAT 57.404 37.500 0.00 0.00 0.00 0.86
1731 4104 6.015095 ACATTCTCTCGCTGTTCCATCATATA 60.015 38.462 0.00 0.00 0.00 0.86
1732 4105 4.944619 TTCTCTCGCTGTTCCATCATAT 57.055 40.909 0.00 0.00 0.00 1.78
1733 4106 4.100035 ACATTCTCTCGCTGTTCCATCATA 59.900 41.667 0.00 0.00 0.00 2.15
1734 4107 3.118482 ACATTCTCTCGCTGTTCCATCAT 60.118 43.478 0.00 0.00 0.00 2.45
1735 4108 2.234661 ACATTCTCTCGCTGTTCCATCA 59.765 45.455 0.00 0.00 0.00 3.07
1736 4109 2.898705 ACATTCTCTCGCTGTTCCATC 58.101 47.619 0.00 0.00 0.00 3.51
1737 4110 3.449018 ACTACATTCTCTCGCTGTTCCAT 59.551 43.478 0.00 0.00 0.00 3.41
1738 4111 2.826128 ACTACATTCTCTCGCTGTTCCA 59.174 45.455 0.00 0.00 0.00 3.53
1739 4112 3.512033 ACTACATTCTCTCGCTGTTCC 57.488 47.619 0.00 0.00 0.00 3.62
1743 4116 3.367607 GCAGTACTACATTCTCTCGCTG 58.632 50.000 0.00 0.00 0.00 5.18
1751 4124 3.119245 TGAACCGAGGCAGTACTACATTC 60.119 47.826 0.00 0.00 0.00 2.67
1756 4129 4.339872 TTTTTGAACCGAGGCAGTACTA 57.660 40.909 0.00 0.00 0.00 1.82
1763 4136 6.560711 ACATGTTATATTTTTGAACCGAGGC 58.439 36.000 0.00 0.00 0.00 4.70
1832 4208 7.440198 TGGACTGAAATGAATTAACAAATGCA 58.560 30.769 0.00 0.00 0.00 3.96
1865 4241 9.403583 ACAAATATAAGACGGTGTGGATATTTT 57.596 29.630 12.17 5.84 30.71 1.82
1866 4242 8.836413 CACAAATATAAGACGGTGTGGATATTT 58.164 33.333 10.30 10.30 34.19 1.40
1874 4250 4.628333 CCGTTCACAAATATAAGACGGTGT 59.372 41.667 4.03 0.00 34.05 4.16
1879 4255 9.230932 GTACTACTCCGTTCACAAATATAAGAC 57.769 37.037 0.00 0.00 0.00 3.01
2017 4397 3.744660 AGAGAAAGTTGGTCGCTCAAAT 58.255 40.909 0.00 0.00 0.00 2.32
2024 4404 3.067833 GGGAAAGAGAGAAAGTTGGTCG 58.932 50.000 0.00 0.00 0.00 4.79
2083 4467 4.046938 TCATAGACTCGCCAATGAAGTC 57.953 45.455 0.00 0.00 0.00 3.01
2090 4474 2.682856 GGCAAATTCATAGACTCGCCAA 59.317 45.455 0.00 0.00 38.20 4.52
2140 4527 2.527875 GATCCTCCTCCCCGCCAT 60.528 66.667 0.00 0.00 0.00 4.40
2154 4542 2.444895 AGAGGAGGCACCGGGATC 60.445 66.667 6.32 0.00 44.74 3.36
2208 4598 4.752879 GCCGGAGCGCCACAACTA 62.753 66.667 5.05 0.00 0.00 2.24
2222 4612 2.434884 AAGCGACACCATCTGCCG 60.435 61.111 0.00 0.00 0.00 5.69
2232 4622 5.296780 AGACAAATTTGAAGAAGAAGCGACA 59.703 36.000 24.64 0.00 0.00 4.35
2234 4624 6.377327 AAGACAAATTTGAAGAAGAAGCGA 57.623 33.333 24.64 0.00 0.00 4.93
2332 4723 1.838073 CTAACCTCACCGCCCCAAGT 61.838 60.000 0.00 0.00 0.00 3.16
2371 4762 0.877071 AAGCAGCTGACACCAAATCG 59.123 50.000 20.43 0.00 0.00 3.34
2385 4776 2.617308 CCATTGCATAGACCTGAAGCAG 59.383 50.000 0.00 0.00 36.47 4.24
2394 4785 3.483574 CGTCGTTGAACCATTGCATAGAC 60.484 47.826 0.00 0.00 0.00 2.59
2466 4859 1.573829 TTTTCGATGACAGCACCGGC 61.574 55.000 0.00 0.00 41.61 6.13
2469 4862 1.464997 GACCTTTTCGATGACAGCACC 59.535 52.381 0.00 0.00 0.00 5.01
2471 4864 2.542020 TGACCTTTTCGATGACAGCA 57.458 45.000 0.00 0.00 0.00 4.41
2483 4876 2.034221 GGAGCCGGCTTGACCTTT 59.966 61.111 33.34 5.00 35.61 3.11
2508 4901 0.522495 GCGCGCCGTTATCATTGTTT 60.522 50.000 23.24 0.00 0.00 2.83
2510 4903 2.707039 GCGCGCCGTTATCATTGT 59.293 55.556 23.24 0.00 0.00 2.71
2512 4905 2.109739 TTGGCGCGCCGTTATCATT 61.110 52.632 41.73 0.00 39.42 2.57
2513 4906 2.512745 TTGGCGCGCCGTTATCAT 60.513 55.556 41.73 0.00 39.42 2.45
2527 4920 1.154205 CCGCTAGAATGAGGCGTTGG 61.154 60.000 0.00 0.00 46.23 3.77
2533 4926 1.293924 CTGTTGCCGCTAGAATGAGG 58.706 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.