Multiple sequence alignment - TraesCS3D01G457700

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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 TraesCS3D01G457700 chr3D 100.000 3994 0 0 1 3994 563420317 563416324 0.000000e+00 7376.0
1 TraesCS3D01G457700 chr3D 89.902 713 62 7 1 705 98564790 98565500 0.000000e+00 909.0
2 TraesCS3D01G457700 chr3D 77.544 285 50 9 1923 2206 563418563 563418292 4.130000e-35 159.0
3 TraesCS3D01G457700 chr3A 95.205 1439 60 2 768 2206 698004424 698002995 0.000000e+00 2266.0
4 TraesCS3D01G457700 chr3A 90.811 1665 116 18 1924 3578 698003097 698001460 0.000000e+00 2193.0
5 TraesCS3D01G457700 chr3A 89.394 198 21 0 1924 2121 698003007 698002810 2.380000e-62 250.0
6 TraesCS3D01G457700 chr3A 92.453 106 8 0 1926 2031 698002915 698002810 6.910000e-33 152.0
7 TraesCS3D01G457700 chr3A 90.291 103 10 0 2104 2206 698003277 698003175 6.960000e-28 135.0
8 TraesCS3D01G457700 chr3B 94.548 1394 57 4 814 2201 750786691 750785311 0.000000e+00 2135.0
9 TraesCS3D01G457700 chr3B 92.548 1315 76 3 1924 3238 750785318 750784026 0.000000e+00 1866.0
10 TraesCS3D01G457700 chr3B 88.860 781 69 7 3230 3994 750783055 750782277 0.000000e+00 944.0
11 TraesCS3D01G457700 chr3B 90.345 290 28 0 1917 2206 750785505 750785216 8.100000e-102 381.0
12 TraesCS3D01G457700 chr3B 89.753 283 29 0 1924 2206 750785408 750785126 2.930000e-96 363.0
13 TraesCS3D01G457700 chr3B 81.250 416 63 11 3590 3994 244973710 244974121 4.980000e-84 322.0
14 TraesCS3D01G457700 chr3B 88.384 198 23 0 1924 2121 750785228 750785031 5.160000e-59 239.0
15 TraesCS3D01G457700 chr3B 92.453 106 8 0 2101 2206 750785591 750785486 6.910000e-33 152.0
16 TraesCS3D01G457700 chr4D 91.061 716 56 5 5 713 440031967 440031253 0.000000e+00 961.0
17 TraesCS3D01G457700 chr4D 84.211 57 7 2 3745 3799 50161723 50161779 2.000000e-03 54.7
18 TraesCS3D01G457700 chr7B 90.403 719 60 5 1 712 729126764 729127480 0.000000e+00 937.0
19 TraesCS3D01G457700 chr7B 90.056 714 62 5 6 712 729067976 729068687 0.000000e+00 917.0
20 TraesCS3D01G457700 chr7B 89.847 719 62 7 1 712 729194460 729195174 0.000000e+00 913.0
21 TraesCS3D01G457700 chr1D 90.510 706 59 4 7 704 4432671 4431966 0.000000e+00 926.0
22 TraesCS3D01G457700 chr1D 82.184 174 24 3 3624 3791 140058191 140058019 4.160000e-30 143.0
23 TraesCS3D01G457700 chr5A 89.733 711 63 6 4 705 41459862 41460571 0.000000e+00 900.0
24 TraesCS3D01G457700 chr1A 89.650 715 52 8 7 708 20251132 20250427 0.000000e+00 891.0
25 TraesCS3D01G457700 chr1A 82.184 174 24 3 3624 3791 150796187 150796359 4.160000e-30 143.0
26 TraesCS3D01G457700 chr1B 89.185 712 70 3 1 705 625061653 625062364 0.000000e+00 881.0
27 TraesCS3D01G457700 chr1B 81.818 154 22 2 3627 3775 198481438 198481590 1.510000e-24 124.0
28 TraesCS3D01G457700 chr4A 78.804 184 30 5 3622 3799 10233209 10233029 9.070000e-22 115.0
29 TraesCS3D01G457700 chr5D 78.981 157 20 7 3624 3769 563728359 563728513 1.180000e-15 95.3


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 TraesCS3D01G457700 chr3D 563416324 563420317 3993 True 3767.500000 7376 88.772000 1 3994 2 chr3D.!!$R1 3993
1 TraesCS3D01G457700 chr3D 98564790 98565500 710 False 909.000000 909 89.902000 1 705 1 chr3D.!!$F1 704
2 TraesCS3D01G457700 chr3A 698001460 698004424 2964 True 999.200000 2266 91.630800 768 3578 5 chr3A.!!$R1 2810
3 TraesCS3D01G457700 chr3B 750782277 750786691 4414 True 868.571429 2135 90.984429 814 3994 7 chr3B.!!$R1 3180
4 TraesCS3D01G457700 chr4D 440031253 440031967 714 True 961.000000 961 91.061000 5 713 1 chr4D.!!$R1 708
5 TraesCS3D01G457700 chr7B 729126764 729127480 716 False 937.000000 937 90.403000 1 712 1 chr7B.!!$F2 711
6 TraesCS3D01G457700 chr7B 729067976 729068687 711 False 917.000000 917 90.056000 6 712 1 chr7B.!!$F1 706
7 TraesCS3D01G457700 chr7B 729194460 729195174 714 False 913.000000 913 89.847000 1 712 1 chr7B.!!$F3 711
8 TraesCS3D01G457700 chr1D 4431966 4432671 705 True 926.000000 926 90.510000 7 704 1 chr1D.!!$R1 697
9 TraesCS3D01G457700 chr5A 41459862 41460571 709 False 900.000000 900 89.733000 4 705 1 chr5A.!!$F1 701
10 TraesCS3D01G457700 chr1A 20250427 20251132 705 True 891.000000 891 89.650000 7 708 1 chr1A.!!$R1 701
11 TraesCS3D01G457700 chr1B 625061653 625062364 711 False 881.000000 881 89.185000 1 705 1 chr1B.!!$F2 704

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
757 779 0.532573 GCCGATCACTTGTCCAGAGA 59.467 55.000 0.00 0.0 0.00 3.10 F
1643 1665 0.029567 GAGGATGACGCTAGTGTCGG 59.970 60.000 26.76 0.0 41.87 4.79 F
1731 1753 1.000163 GATGCTCCGGCGATAGAGAAA 60.000 52.381 9.30 0.0 42.25 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1694 0.326238 TCCTCCATGGTGACTACCCC 60.326 60.0 15.47 0.0 46.96 4.95 R
2859 3161 0.326264 GCCTCCTTCACATCAGTGGT 59.674 55.0 0.00 0.0 45.91 4.16 R
3650 4948 0.470341 GATCTAGGTCCTTGCCACCC 59.530 60.0 0.00 0.0 33.96 4.61 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
38 41 0.809385 CGATCACGTGTGTACCTCCT 59.191 55.000 16.51 0.00 34.56 3.69
48 51 3.442977 GTGTGTACCTCCTAGAATGACGT 59.557 47.826 0.00 0.00 0.00 4.34
50 53 3.693085 GTGTACCTCCTAGAATGACGTCA 59.307 47.826 22.48 22.48 0.00 4.35
59 64 1.697432 AGAATGACGTCACCAAGGGAA 59.303 47.619 22.71 0.00 0.00 3.97
131 138 1.618345 CCAGAGGTAGCAGAGAGTGGT 60.618 57.143 0.00 0.00 40.92 4.16
228 242 3.437049 CCGAAAGTTTTCACCCAGATCTC 59.563 47.826 0.00 0.00 37.01 2.75
337 351 2.885861 GAGACTCGCCGTCACCAT 59.114 61.111 7.31 0.00 45.32 3.55
356 370 4.007644 CCTGACAGGCAGCCACGA 62.008 66.667 15.80 0.00 43.50 4.35
387 401 1.490490 GCACCACCCAGATCCAATCTA 59.510 52.381 0.00 0.00 37.58 1.98
432 446 3.989698 CTGTCTAGGCGGCACCACG 62.990 68.421 13.08 0.00 43.14 4.94
500 514 2.048597 TTCGAAGCACCGCGTCAT 60.049 55.556 4.92 0.00 36.90 3.06
508 522 4.778143 ACCGCGTCATCAAGCCCC 62.778 66.667 4.92 0.00 0.00 5.80
531 545 1.810151 GAAAATGACTAAGCCGCCACA 59.190 47.619 0.00 0.00 0.00 4.17
547 561 1.074566 CCACAAGGAAGAAGGGAAGCT 59.925 52.381 0.00 0.00 36.89 3.74
721 743 2.899339 GCCGAGGGCTCATCTTGC 60.899 66.667 0.00 0.00 46.69 4.01
722 744 2.586245 CCGAGGGCTCATCTTGCA 59.414 61.111 0.00 0.00 0.00 4.08
723 745 1.078214 CCGAGGGCTCATCTTGCAA 60.078 57.895 0.00 0.00 0.00 4.08
724 746 1.094073 CCGAGGGCTCATCTTGCAAG 61.094 60.000 20.81 20.81 0.00 4.01
725 747 1.712977 CGAGGGCTCATCTTGCAAGC 61.713 60.000 21.99 10.33 35.27 4.01
729 751 3.642901 GCTCATCTTGCAAGCCATG 57.357 52.632 21.99 19.57 0.00 3.66
749 771 4.505217 GTGCGCGCCGATCACTTG 62.505 66.667 30.77 0.00 0.00 3.16
751 773 4.210304 GCGCGCCGATCACTTGTC 62.210 66.667 23.24 0.00 0.00 3.18
752 774 3.554692 CGCGCCGATCACTTGTCC 61.555 66.667 0.00 0.00 0.00 4.02
753 775 2.434185 GCGCCGATCACTTGTCCA 60.434 61.111 0.00 0.00 0.00 4.02
754 776 2.456119 GCGCCGATCACTTGTCCAG 61.456 63.158 0.00 0.00 0.00 3.86
755 777 1.215382 CGCCGATCACTTGTCCAGA 59.785 57.895 0.00 0.00 0.00 3.86
756 778 0.803768 CGCCGATCACTTGTCCAGAG 60.804 60.000 0.00 0.00 0.00 3.35
757 779 0.532573 GCCGATCACTTGTCCAGAGA 59.467 55.000 0.00 0.00 0.00 3.10
758 780 1.737363 GCCGATCACTTGTCCAGAGAC 60.737 57.143 0.00 0.00 43.83 3.36
759 781 1.468224 CCGATCACTTGTCCAGAGACG 60.468 57.143 0.00 0.00 46.74 4.18
760 782 1.468224 CGATCACTTGTCCAGAGACGG 60.468 57.143 0.00 0.00 46.74 4.79
761 783 1.546476 GATCACTTGTCCAGAGACGGT 59.454 52.381 0.00 0.00 46.74 4.83
762 784 2.281539 TCACTTGTCCAGAGACGGTA 57.718 50.000 0.00 0.00 46.74 4.02
763 785 2.803956 TCACTTGTCCAGAGACGGTAT 58.196 47.619 0.00 0.00 46.74 2.73
764 786 2.492088 TCACTTGTCCAGAGACGGTATG 59.508 50.000 0.00 0.00 46.74 2.39
765 787 1.825474 ACTTGTCCAGAGACGGTATGG 59.175 52.381 1.15 1.15 46.74 2.74
766 788 2.100197 CTTGTCCAGAGACGGTATGGA 58.900 52.381 5.38 5.38 46.74 3.41
801 823 2.356313 CAGCAACGACGGTGAGCT 60.356 61.111 18.96 4.13 38.44 4.09
823 845 5.723295 CTGCAACCTGGCTATTAAAAACAT 58.277 37.500 0.00 0.00 34.04 2.71
886 908 1.075979 CCCTAATTTTGCAACGCCGC 61.076 55.000 0.00 0.00 0.00 6.53
1177 1199 3.775654 CGGCGAAGGAGAAGGCCT 61.776 66.667 0.00 0.00 43.38 5.19
1297 1319 1.203364 AGAAAGAGGGGGAGAGCAAGA 60.203 52.381 0.00 0.00 0.00 3.02
1326 1348 3.591254 GAAGGGAGCAGTCGCCGTT 62.591 63.158 0.00 0.00 41.74 4.44
1440 1462 2.813908 GACGGTGTGGCATCGACC 60.814 66.667 8.84 8.58 40.81 4.79
1554 1576 1.338136 GGGGCGAAGATCAGGAAGGA 61.338 60.000 0.00 0.00 0.00 3.36
1581 1603 0.457853 CCGAGGCGATTGAAGACGAA 60.458 55.000 0.00 0.00 0.00 3.85
1634 1656 0.460284 ATCAACGTGGAGGATGACGC 60.460 55.000 0.00 0.00 39.22 5.19
1643 1665 0.029567 GAGGATGACGCTAGTGTCGG 59.970 60.000 26.76 0.00 41.87 4.79
1645 1667 1.433879 GATGACGCTAGTGTCGGCT 59.566 57.895 26.76 16.32 41.87 5.52
1694 1716 1.202698 GGTAGTCACCATGGAGGATGC 60.203 57.143 21.47 6.43 45.04 3.91
1731 1753 1.000163 GATGCTCCGGCGATAGAGAAA 60.000 52.381 9.30 0.00 42.25 2.52
2202 2500 4.358841 TTGGTGGATGCCCCGGTG 62.359 66.667 0.00 0.00 37.93 4.94
2214 2512 1.304052 CCCGGTGGCCAAAGATGAA 60.304 57.895 7.24 0.00 0.00 2.57
2224 2522 4.037446 TGGCCAAAGATGAACAAAGTGTAC 59.963 41.667 0.61 0.00 0.00 2.90
2228 2526 5.299279 CCAAAGATGAACAAAGTGTACCTGT 59.701 40.000 0.00 0.00 0.00 4.00
2246 2544 4.431131 CGCCTTGGTGGATGCCCT 62.431 66.667 0.00 0.00 38.35 5.19
2250 2548 1.077265 CTTGGTGGATGCCCTGGTT 59.923 57.895 0.00 0.00 0.00 3.67
2377 2675 1.070786 GAGGTCGAAACTGCCACCA 59.929 57.895 0.00 0.00 0.00 4.17
2379 2677 1.070786 GGTCGAAACTGCCACCAGA 59.929 57.895 0.00 0.00 41.77 3.86
2383 2681 1.598130 GAAACTGCCACCAGAGCGT 60.598 57.895 0.00 0.00 41.77 5.07
2554 2852 1.021390 CAAAGAGGCCGCAGTCGAAT 61.021 55.000 9.88 0.00 38.10 3.34
2563 2861 2.754472 CCGCAGTCGAATCCAATGATA 58.246 47.619 0.00 0.00 38.10 2.15
2590 2888 1.071699 AGCAAACTAAGGAGGCAACGA 59.928 47.619 0.00 0.00 46.39 3.85
2715 3017 3.885901 CCTTGAGAGACGATGATGGTAGA 59.114 47.826 0.00 0.00 0.00 2.59
2718 3020 6.207614 CCTTGAGAGACGATGATGGTAGATTA 59.792 42.308 0.00 0.00 0.00 1.75
2722 3024 8.300286 TGAGAGACGATGATGGTAGATTAAATC 58.700 37.037 0.00 0.00 0.00 2.17
2773 3075 6.425721 CACATTTGCATGTTCAGGATTTCTTT 59.574 34.615 0.00 0.00 41.16 2.52
2774 3076 6.425721 ACATTTGCATGTTCAGGATTTCTTTG 59.574 34.615 0.00 0.00 41.16 2.77
2775 3077 5.534207 TTGCATGTTCAGGATTTCTTTGT 57.466 34.783 0.00 0.00 0.00 2.83
2776 3078 5.534207 TGCATGTTCAGGATTTCTTTGTT 57.466 34.783 0.00 0.00 0.00 2.83
2777 3079 5.916318 TGCATGTTCAGGATTTCTTTGTTT 58.084 33.333 0.00 0.00 0.00 2.83
2778 3080 6.347696 TGCATGTTCAGGATTTCTTTGTTTT 58.652 32.000 0.00 0.00 0.00 2.43
2779 3081 6.822676 TGCATGTTCAGGATTTCTTTGTTTTT 59.177 30.769 0.00 0.00 0.00 1.94
2851 3153 1.832719 TTTGCAGGGGAATCGGACGA 61.833 55.000 0.00 0.00 0.00 4.20
2913 3215 0.847373 GGAAAAGGGAGGGGAGGATC 59.153 60.000 0.00 0.00 0.00 3.36
3053 3355 1.076332 GGTGCGTGTATGAACCACTC 58.924 55.000 0.00 0.00 37.52 3.51
3152 3457 6.172966 CGCATTCGTAGAAACAAATTATGC 57.827 37.500 0.00 0.00 45.90 3.14
3190 3495 5.282055 TGGCTAGATCTACATCCAACAAG 57.718 43.478 0.00 0.00 0.00 3.16
3345 4630 3.745803 GCCCGTTCGTCGAGGAGT 61.746 66.667 7.98 0.00 42.86 3.85
3386 4671 2.047560 TCGTCACTCGAGCGGAGA 60.048 61.111 13.61 4.71 46.23 3.71
3451 4747 1.305201 GTTGTTGGCCGAAGTTCTCA 58.695 50.000 0.00 0.00 0.00 3.27
3457 4753 1.301716 GCCGAAGTTCTCAGCCACA 60.302 57.895 0.56 0.00 0.00 4.17
3476 4772 1.703014 ATGGGCAGTGAGGCATCGAT 61.703 55.000 0.00 0.00 46.44 3.59
3495 4791 0.605319 TGCAAGAGGTTTGTAGCCCG 60.605 55.000 0.00 0.00 0.00 6.13
3579 4877 1.452108 CTTCCCCACCGAATCCAGC 60.452 63.158 0.00 0.00 0.00 4.85
3605 4903 2.558359 CAAAGTTAGAGGGCTTGGGTTG 59.442 50.000 0.00 0.00 0.00 3.77
3608 4906 1.154430 TTAGAGGGCTTGGGTTGGTT 58.846 50.000 0.00 0.00 0.00 3.67
3609 4907 2.040679 GTTAGAGGGCTTGGGTTGGTTA 59.959 50.000 0.00 0.00 0.00 2.85
3650 4948 0.106149 GGGGAATAGTAGTGCCACGG 59.894 60.000 10.46 0.00 0.00 4.94
3674 4972 1.052617 GCAAGGACCTAGATCCCCTC 58.947 60.000 0.00 0.00 39.91 4.30
3676 4974 0.935194 AAGGACCTAGATCCCCTCGT 59.065 55.000 0.00 0.00 39.91 4.18
3677 4975 0.479378 AGGACCTAGATCCCCTCGTC 59.521 60.000 0.00 0.00 39.91 4.20
3679 4977 0.479378 GACCTAGATCCCCTCGTCCT 59.521 60.000 0.00 0.00 0.00 3.85
3691 4989 1.152735 TCGTCCTAGGGCTAGCCTG 60.153 63.158 32.18 21.21 36.10 4.85
3719 5017 1.591703 GGAGACACGAGTGCCATGA 59.408 57.895 2.76 0.00 0.00 3.07
3728 5026 3.246936 CACGAGTGCCATGATATGAACAG 59.753 47.826 0.00 0.00 0.00 3.16
3752 5050 5.105146 GGATATGTTAGGCTGGGAGTCTATG 60.105 48.000 0.00 0.00 31.68 2.23
3755 5053 2.088104 TAGGCTGGGAGTCTATGGTG 57.912 55.000 0.00 0.00 29.80 4.17
3769 5067 5.046807 AGTCTATGGTGTGGGTAAAGTGTAC 60.047 44.000 0.00 0.00 0.00 2.90
3771 5069 3.928005 TGGTGTGGGTAAAGTGTACAA 57.072 42.857 0.00 0.00 0.00 2.41
3775 5073 4.201657 GTGTGGGTAAAGTGTACAACCTT 58.798 43.478 12.95 3.97 32.38 3.50
3776 5074 4.274214 GTGTGGGTAAAGTGTACAACCTTC 59.726 45.833 12.95 7.92 32.38 3.46
3780 5078 5.067954 GGGTAAAGTGTACAACCTTCACAT 58.932 41.667 12.95 0.00 34.94 3.21
3781 5079 6.183361 TGGGTAAAGTGTACAACCTTCACATA 60.183 38.462 12.95 0.00 34.94 2.29
3784 5084 6.861065 AAAGTGTACAACCTTCACATAGTG 57.139 37.500 0.00 0.00 34.94 2.74
3804 5104 4.992951 AGTGTGTGTTAAACCTATCGGAAC 59.007 41.667 0.00 0.00 0.00 3.62
3838 5138 2.643551 GTCATGGACAACATTCGGGAT 58.356 47.619 0.00 0.00 37.84 3.85
3851 5151 2.994186 TCGGGATTAAGCCACTAACC 57.006 50.000 12.67 0.00 0.00 2.85
3856 5156 3.542648 GGATTAAGCCACTAACCTGTCC 58.457 50.000 4.48 0.00 0.00 4.02
3859 5159 5.104652 GGATTAAGCCACTAACCTGTCCTTA 60.105 44.000 4.48 0.00 0.00 2.69
3953 5254 0.687920 TGTGTGGCCACTTCGGATTA 59.312 50.000 34.75 10.93 42.34 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 1.092348 TACACACGTGATCGAGGGAG 58.908 55.000 25.01 2.73 40.62 4.30
38 41 2.531771 TCCCTTGGTGACGTCATTCTA 58.468 47.619 23.12 12.74 0.00 2.10
48 51 1.124780 TGTCGTTCTTCCCTTGGTGA 58.875 50.000 0.00 0.00 0.00 4.02
50 53 0.108019 GGTGTCGTTCTTCCCTTGGT 59.892 55.000 0.00 0.00 0.00 3.67
59 64 2.049063 GCGCTCTGGTGTCGTTCT 60.049 61.111 0.00 0.00 0.00 3.01
113 120 1.638589 AGACCACTCTCTGCTACCTCT 59.361 52.381 0.00 0.00 0.00 3.69
131 138 0.756294 TGCCGTGGAGAAGTTCAAGA 59.244 50.000 5.50 0.00 0.00 3.02
228 242 2.633488 GGGAGTTGGATTCCTTCGAAG 58.367 52.381 18.51 18.51 35.01 3.79
265 279 2.203337 TGTGCTCAACCTGGTGGC 60.203 61.111 0.00 6.43 36.63 5.01
366 380 0.753111 GATTGGATCTGGGTGGTGCC 60.753 60.000 0.00 0.00 0.00 5.01
491 505 4.778143 GGGGCTTGATGACGCGGT 62.778 66.667 12.47 0.00 0.00 5.68
508 522 0.377203 GCGGCTTAGTCATTTTCGGG 59.623 55.000 0.00 0.00 0.00 5.14
512 526 1.904287 TGTGGCGGCTTAGTCATTTT 58.096 45.000 11.43 0.00 0.00 1.82
515 529 0.392998 CCTTGTGGCGGCTTAGTCAT 60.393 55.000 11.43 0.00 0.00 3.06
531 545 0.322008 CGCAGCTTCCCTTCTTCCTT 60.322 55.000 0.00 0.00 0.00 3.36
576 590 2.599578 CAAAGCCCAGGCAGTGCT 60.600 61.111 16.11 0.00 44.88 4.40
732 754 4.505217 CAAGTGATCGGCGCGCAC 62.505 66.667 34.42 21.81 0.00 5.34
734 756 4.210304 GACAAGTGATCGGCGCGC 62.210 66.667 25.94 25.94 0.00 6.86
735 757 3.554692 GGACAAGTGATCGGCGCG 61.555 66.667 0.00 0.00 0.00 6.86
736 758 2.434185 TGGACAAGTGATCGGCGC 60.434 61.111 0.00 0.00 0.00 6.53
737 759 0.803768 CTCTGGACAAGTGATCGGCG 60.804 60.000 0.00 0.00 0.00 6.46
738 760 0.532573 TCTCTGGACAAGTGATCGGC 59.467 55.000 0.00 0.00 0.00 5.54
739 761 1.468224 CGTCTCTGGACAAGTGATCGG 60.468 57.143 0.00 0.00 42.21 4.18
740 762 1.468224 CCGTCTCTGGACAAGTGATCG 60.468 57.143 0.00 0.00 42.21 3.69
741 763 1.546476 ACCGTCTCTGGACAAGTGATC 59.454 52.381 0.00 0.00 42.21 2.92
742 764 1.633774 ACCGTCTCTGGACAAGTGAT 58.366 50.000 0.00 0.00 42.21 3.06
743 765 2.281539 TACCGTCTCTGGACAAGTGA 57.718 50.000 0.00 0.00 42.21 3.41
744 766 2.417379 CCATACCGTCTCTGGACAAGTG 60.417 54.545 0.00 0.00 42.21 3.16
745 767 1.825474 CCATACCGTCTCTGGACAAGT 59.175 52.381 0.00 0.00 42.21 3.16
746 768 2.100197 TCCATACCGTCTCTGGACAAG 58.900 52.381 0.00 0.00 42.21 3.16
747 769 2.225382 TCCATACCGTCTCTGGACAA 57.775 50.000 0.00 0.00 42.21 3.18
748 770 3.991972 TCCATACCGTCTCTGGACA 57.008 52.632 0.00 0.00 42.21 4.02
750 772 2.100197 CTTGTCCATACCGTCTCTGGA 58.900 52.381 0.00 0.00 36.73 3.86
751 773 1.825474 ACTTGTCCATACCGTCTCTGG 59.175 52.381 0.00 0.00 0.00 3.86
752 774 2.231478 ACACTTGTCCATACCGTCTCTG 59.769 50.000 0.00 0.00 0.00 3.35
753 775 2.526432 ACACTTGTCCATACCGTCTCT 58.474 47.619 0.00 0.00 0.00 3.10
754 776 3.314541 AACACTTGTCCATACCGTCTC 57.685 47.619 0.00 0.00 0.00 3.36
755 777 4.082354 GTCTAACACTTGTCCATACCGTCT 60.082 45.833 0.00 0.00 0.00 4.18
756 778 4.082354 AGTCTAACACTTGTCCATACCGTC 60.082 45.833 0.00 0.00 26.56 4.79
757 779 3.830755 AGTCTAACACTTGTCCATACCGT 59.169 43.478 0.00 0.00 26.56 4.83
758 780 4.421948 GAGTCTAACACTTGTCCATACCG 58.578 47.826 0.00 0.00 34.41 4.02
759 781 4.157289 TCGAGTCTAACACTTGTCCATACC 59.843 45.833 0.00 0.00 37.72 2.73
760 782 5.306532 TCGAGTCTAACACTTGTCCATAC 57.693 43.478 0.00 0.00 37.72 2.39
761 783 5.242171 TGTTCGAGTCTAACACTTGTCCATA 59.758 40.000 6.15 0.00 37.72 2.74
762 784 4.038763 TGTTCGAGTCTAACACTTGTCCAT 59.961 41.667 6.15 0.00 37.72 3.41
763 785 3.382227 TGTTCGAGTCTAACACTTGTCCA 59.618 43.478 6.15 0.00 37.72 4.02
764 786 3.973657 TGTTCGAGTCTAACACTTGTCC 58.026 45.455 6.15 0.00 37.72 4.02
765 787 3.425858 GCTGTTCGAGTCTAACACTTGTC 59.574 47.826 6.15 0.00 37.72 3.18
766 788 3.181479 TGCTGTTCGAGTCTAACACTTGT 60.181 43.478 6.15 0.00 37.72 3.16
801 823 5.736951 ATGTTTTTAATAGCCAGGTTGCA 57.263 34.783 0.00 0.00 0.00 4.08
823 845 0.893270 GCTGTGGCATGGTTGGTGTA 60.893 55.000 0.00 0.00 38.54 2.90
1297 1319 0.903236 GCTCCCTTCTTACCGTCCTT 59.097 55.000 0.00 0.00 0.00 3.36
1326 1348 2.203669 TTCCCCTTGTCGTCGGGA 60.204 61.111 0.00 0.00 44.37 5.14
1440 1462 1.936880 GACGATGACGCTCTCGCTG 60.937 63.158 0.00 0.00 43.96 5.18
1542 1564 1.418334 CCGACCATCCTTCCTGATCT 58.582 55.000 0.00 0.00 0.00 2.75
1546 1568 2.190578 GGCCGACCATCCTTCCTG 59.809 66.667 0.00 0.00 35.26 3.86
1665 1687 3.079478 GTGACTACCCCCGTCCCC 61.079 72.222 0.00 0.00 0.00 4.81
1666 1688 3.079478 GGTGACTACCCCCGTCCC 61.079 72.222 0.00 0.00 41.36 4.46
1667 1689 1.688187 ATGGTGACTACCCCCGTCC 60.688 63.158 0.00 0.00 46.96 4.79
1668 1690 1.520666 CATGGTGACTACCCCCGTC 59.479 63.158 0.00 0.00 46.96 4.79
1669 1691 1.993391 CCATGGTGACTACCCCCGT 60.993 63.158 2.57 0.00 46.96 5.28
1670 1692 1.686325 CTCCATGGTGACTACCCCCG 61.686 65.000 12.58 0.00 46.96 5.73
1671 1693 1.345715 CCTCCATGGTGACTACCCCC 61.346 65.000 15.47 0.00 46.96 5.40
1672 1694 0.326238 TCCTCCATGGTGACTACCCC 60.326 60.000 15.47 0.00 46.96 4.95
1673 1695 1.417890 CATCCTCCATGGTGACTACCC 59.582 57.143 15.47 0.00 46.96 3.69
1694 1716 0.979665 ATCGGCTGGGATGATACTGG 59.020 55.000 0.00 0.00 0.00 4.00
1731 1753 1.266175 ACGAACGTGTCAATCTCGTCT 59.734 47.619 3.52 0.00 43.80 4.18
2161 2459 2.412421 GCAGTTTCACTTTCCTGCTG 57.588 50.000 0.00 0.00 45.25 4.41
2196 2494 1.304052 TTCATCTTTGGCCACCGGG 60.304 57.895 3.88 0.00 37.18 5.73
2202 2500 3.733443 ACACTTTGTTCATCTTTGGCC 57.267 42.857 0.00 0.00 0.00 5.36
2208 2506 4.307432 CGACAGGTACACTTTGTTCATCT 58.693 43.478 0.00 0.00 0.00 2.90
2214 2512 0.756903 AGGCGACAGGTACACTTTGT 59.243 50.000 0.00 0.00 0.00 2.83
2224 2522 1.746615 CATCCACCAAGGCGACAGG 60.747 63.158 0.00 0.00 37.29 4.00
2228 2526 4.424711 GGGCATCCACCAAGGCGA 62.425 66.667 0.00 0.00 37.29 5.54
2246 2544 1.607178 CCATCTGCCTTGGCAACCA 60.607 57.895 15.63 3.18 0.00 3.67
2250 2548 0.609957 CACTTCCATCTGCCTTGGCA 60.610 55.000 14.10 14.10 34.06 4.92
2363 2661 1.301716 GCTCTGGTGGCAGTTTCGA 60.302 57.895 0.00 0.00 0.00 3.71
2521 2819 2.028930 CCTCTTTGACGACAGTAGGCTT 60.029 50.000 0.00 0.00 0.00 4.35
2554 2852 3.904800 TTGCTCGGTCTTATCATTGGA 57.095 42.857 0.00 0.00 0.00 3.53
2563 2861 2.028020 CCTCCTTAGTTTGCTCGGTCTT 60.028 50.000 0.00 0.00 0.00 3.01
2590 2888 2.361357 CACCTCCTCCTCCGTCGT 60.361 66.667 0.00 0.00 0.00 4.34
2663 2961 0.471780 TGTCTCCTCCTGTTCTGGCA 60.472 55.000 0.00 0.00 0.00 4.92
2694 2992 5.703978 ATCTACCATCATCGTCTCTCAAG 57.296 43.478 0.00 0.00 0.00 3.02
2715 3017 7.886629 TGGCTAGCAAATGAAGAGATTTAAT 57.113 32.000 18.24 0.00 0.00 1.40
2718 3020 5.655532 ACATGGCTAGCAAATGAAGAGATTT 59.344 36.000 27.28 7.61 0.00 2.17
2722 3024 3.943381 TGACATGGCTAGCAAATGAAGAG 59.057 43.478 27.28 8.74 0.00 2.85
2859 3161 0.326264 GCCTCCTTCACATCAGTGGT 59.674 55.000 0.00 0.00 45.91 4.16
2913 3215 1.153939 CTTCCTCGACGGTCAGCTG 60.154 63.158 7.63 7.63 0.00 4.24
3053 3355 4.999950 AGGAAGAGAGCAAACTGTACATTG 59.000 41.667 0.00 0.00 0.00 2.82
3152 3457 1.081509 CCAAACATTCCCGCGTGTG 60.082 57.895 4.92 0.18 0.00 3.82
3190 3495 6.073003 GCATGTGATGGTACCTAGCTTAATTC 60.073 42.308 14.36 0.00 0.00 2.17
3272 4557 2.617215 GAGGGGGTTGGGGATGGT 60.617 66.667 0.00 0.00 0.00 3.55
3276 4561 2.609610 CGAAGAGGGGGTTGGGGA 60.610 66.667 0.00 0.00 0.00 4.81
3328 4613 3.745803 ACTCCTCGACGAACGGGC 61.746 66.667 0.00 0.00 41.71 6.13
3332 4617 1.733399 GGCACACTCCTCGACGAAC 60.733 63.158 0.00 0.00 0.00 3.95
3334 4619 3.733960 CGGCACACTCCTCGACGA 61.734 66.667 0.00 0.00 0.00 4.20
3336 4621 3.681835 ACCGGCACACTCCTCGAC 61.682 66.667 0.00 0.00 0.00 4.20
3457 4753 1.703014 ATCGATGCCTCACTGCCCAT 61.703 55.000 0.00 0.00 0.00 4.00
3476 4772 0.605319 CGGGCTACAAACCTCTTGCA 60.605 55.000 0.00 0.00 0.00 4.08
3579 4877 3.077359 CAAGCCCTCTAACTTTGGACAG 58.923 50.000 0.00 0.00 0.00 3.51
3605 4903 6.039941 TCAGGAATCTTTCGAGATCTCTAACC 59.960 42.308 20.26 12.09 0.00 2.85
3608 4906 5.767665 CCTCAGGAATCTTTCGAGATCTCTA 59.232 44.000 20.26 7.03 0.00 2.43
3609 4907 4.584325 CCTCAGGAATCTTTCGAGATCTCT 59.416 45.833 20.26 0.00 0.00 3.10
3650 4948 0.470341 GATCTAGGTCCTTGCCACCC 59.530 60.000 0.00 0.00 33.96 4.61
3674 4972 2.862223 GCAGGCTAGCCCTAGGACG 61.862 68.421 30.42 10.93 44.09 4.79
3676 4974 2.521950 CGCAGGCTAGCCCTAGGA 60.522 66.667 30.42 0.00 44.09 2.94
3677 4975 3.620785 CCGCAGGCTAGCCCTAGG 61.621 72.222 30.42 24.58 46.14 3.02
3691 4989 4.131088 GTGTCTCCGACCTCCCGC 62.131 72.222 0.00 0.00 0.00 6.13
3709 5007 4.077300 TCCTGTTCATATCATGGCACTC 57.923 45.455 0.00 0.00 0.00 3.51
3719 5017 6.296662 CCCAGCCTAACATATCCTGTTCATAT 60.297 42.308 0.00 0.00 44.99 1.78
3728 5026 3.243724 AGACTCCCAGCCTAACATATCC 58.756 50.000 0.00 0.00 0.00 2.59
3739 5037 0.179000 CCACACCATAGACTCCCAGC 59.821 60.000 0.00 0.00 0.00 4.85
3752 5050 2.880268 GGTTGTACACTTTACCCACACC 59.120 50.000 0.00 0.00 0.00 4.16
3755 5053 4.274214 GTGAAGGTTGTACACTTTACCCAC 59.726 45.833 10.26 8.76 29.84 4.61
3809 5109 2.879462 GTCCATGACCGTCGACGC 60.879 66.667 31.73 19.56 38.18 5.19
3814 5114 1.393539 CGAATGTTGTCCATGACCGTC 59.606 52.381 0.00 0.00 32.82 4.79
3838 5138 5.308759 AGTTAAGGACAGGTTAGTGGCTTAA 59.691 40.000 0.00 0.00 0.00 1.85
3884 5184 6.095432 TGTTGCTTAACATTAAACCATGCT 57.905 33.333 0.00 0.00 0.00 3.79
3885 5185 6.966435 ATGTTGCTTAACATTAAACCATGC 57.034 33.333 0.11 0.00 40.22 4.06
3919 5220 5.479724 TGGCCACACATTTCATCTTAAATCA 59.520 36.000 0.00 0.00 0.00 2.57
3937 5238 2.325583 TCATAATCCGAAGTGGCCAC 57.674 50.000 29.22 29.22 37.80 5.01
3940 5241 6.619801 AAAGTTATCATAATCCGAAGTGGC 57.380 37.500 0.00 0.00 37.80 5.01


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

AutoCloner maintained by Alex Coulton.