Multiple sequence alignment - TraesCS2D01G069700

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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 TraesCS2D01G069700 chr2D 100.000 3518 0 0 1 3518 29190096 29186579 0.000000e+00 6497.0
1 TraesCS2D01G069700 chr2D 90.081 615 50 6 2741 3349 601714734 601714125 0.000000e+00 787.0
2 TraesCS2D01G069700 chr2D 95.858 169 7 0 3347 3515 608438808 608438976 1.240000e-69 274.0
3 TraesCS2D01G069700 chr2D 88.889 90 9 1 2444 2533 29171700 29171612 3.710000e-20 110.0
4 TraesCS2D01G069700 chr2D 100.000 28 0 0 2736 2763 536177528 536177555 6.000000e-03 52.8
5 TraesCS2D01G069700 chr2B 88.270 2745 196 64 1 2662 47416095 47418796 0.000000e+00 3169.0
6 TraesCS2D01G069700 chr2B 73.357 563 121 19 1079 1625 135089970 135089421 7.760000e-42 182.0
7 TraesCS2D01G069700 chr2B 78.723 141 19 9 2120 2254 13220571 13220706 2.250000e-12 84.2
8 TraesCS2D01G069700 chr2B 100.000 29 0 0 2735 2763 152706667 152706639 2.000000e-03 54.7
9 TraesCS2D01G069700 chr2A 91.208 2070 116 23 629 2662 31202805 31200766 0.000000e+00 2754.0
10 TraesCS2D01G069700 chr2A 87.179 156 19 1 2378 2533 31146902 31146748 3.610000e-40 176.0
11 TraesCS2D01G069700 chr6B 88.206 602 59 8 2756 3349 712181300 712181897 0.000000e+00 708.0
12 TraesCS2D01G069700 chr6B 95.930 172 7 0 3347 3518 712182456 712182627 2.670000e-71 279.0
13 TraesCS2D01G069700 chr6B 100.000 28 0 0 2736 2763 551980900 551980927 6.000000e-03 52.8
14 TraesCS2D01G069700 chr5D 87.356 609 64 10 2751 3349 103993688 103993083 0.000000e+00 686.0
15 TraesCS2D01G069700 chr5D 95.349 172 8 0 3347 3518 417610238 417610409 1.240000e-69 274.0
16 TraesCS2D01G069700 chr3A 87.065 603 64 11 2759 3353 594035401 594035997 0.000000e+00 669.0
17 TraesCS2D01G069700 chr3A 86.591 619 67 12 2739 3353 697755707 697756313 0.000000e+00 669.0
18 TraesCS2D01G069700 chr3A 85.920 625 65 11 2738 3353 30229305 30228695 0.000000e+00 645.0
19 TraesCS2D01G069700 chr1A 87.081 596 61 10 2765 3346 379502674 379503267 0.000000e+00 660.0
20 TraesCS2D01G069700 chr1A 95.349 172 8 0 3347 3518 372466179 372466008 1.240000e-69 274.0
21 TraesCS2D01G069700 chr7B 87.778 540 58 8 2813 3348 603997219 603997754 2.980000e-175 625.0
22 TraesCS2D01G069700 chr7B 95.376 173 7 1 3347 3518 586758684 586758856 1.240000e-69 274.0
23 TraesCS2D01G069700 chr7B 100.000 31 0 0 2738 2768 586959738 586959768 1.360000e-04 58.4
24 TraesCS2D01G069700 chr6D 84.375 608 76 13 2756 3349 345291471 345292073 2.350000e-161 579.0
25 TraesCS2D01G069700 chr6D 95.349 172 8 0 3347 3518 223933605 223933434 1.240000e-69 274.0
26 TraesCS2D01G069700 chr6D 79.327 208 26 7 2732 2925 106957832 106957628 2.850000e-26 130.0
27 TraesCS2D01G069700 chr3B 80.414 531 73 22 2842 3349 762851271 762851793 3.320000e-100 375.0
28 TraesCS2D01G069700 chr3B 95.349 172 8 0 3347 3518 683349174 683349345 1.240000e-69 274.0
29 TraesCS2D01G069700 chr4B 79.121 546 67 32 2842 3349 5837714 5838250 2.020000e-87 333.0
30 TraesCS2D01G069700 chr4D 95.349 172 8 0 3347 3518 3505860 3505689 1.240000e-69 274.0
31 TraesCS2D01G069700 chr4A 95.349 172 8 0 3347 3518 729323792 729323621 1.240000e-69 274.0
32 TraesCS2D01G069700 chr7D 79.703 202 27 10 141 337 72841530 72841722 2.200000e-27 134.0
33 TraesCS2D01G069700 chr5B 100.000 28 0 0 2736 2763 585472211 585472184 6.000000e-03 52.8
34 TraesCS2D01G069700 chr3D 100.000 28 0 0 2735 2762 84888537 84888564 6.000000e-03 52.8


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 TraesCS2D01G069700 chr2D 29186579 29190096 3517 True 6497.0 6497 100.000 1 3518 1 chr2D.!!$R2 3517
1 TraesCS2D01G069700 chr2D 601714125 601714734 609 True 787.0 787 90.081 2741 3349 1 chr2D.!!$R3 608
2 TraesCS2D01G069700 chr2B 47416095 47418796 2701 False 3169.0 3169 88.270 1 2662 1 chr2B.!!$F2 2661
3 TraesCS2D01G069700 chr2A 31200766 31202805 2039 True 2754.0 2754 91.208 629 2662 1 chr2A.!!$R2 2033
4 TraesCS2D01G069700 chr6B 712181300 712182627 1327 False 493.5 708 92.068 2756 3518 2 chr6B.!!$F2 762
5 TraesCS2D01G069700 chr5D 103993083 103993688 605 True 686.0 686 87.356 2751 3349 1 chr5D.!!$R1 598
6 TraesCS2D01G069700 chr3A 594035401 594035997 596 False 669.0 669 87.065 2759 3353 1 chr3A.!!$F1 594
7 TraesCS2D01G069700 chr3A 697755707 697756313 606 False 669.0 669 86.591 2739 3353 1 chr3A.!!$F2 614
8 TraesCS2D01G069700 chr3A 30228695 30229305 610 True 645.0 645 85.920 2738 3353 1 chr3A.!!$R1 615
9 TraesCS2D01G069700 chr1A 379502674 379503267 593 False 660.0 660 87.081 2765 3346 1 chr1A.!!$F1 581
10 TraesCS2D01G069700 chr7B 603997219 603997754 535 False 625.0 625 87.778 2813 3348 1 chr7B.!!$F3 535
11 TraesCS2D01G069700 chr6D 345291471 345292073 602 False 579.0 579 84.375 2756 3349 1 chr6D.!!$F1 593
12 TraesCS2D01G069700 chr3B 762851271 762851793 522 False 375.0 375 80.414 2842 3349 1 chr3B.!!$F2 507
13 TraesCS2D01G069700 chr4B 5837714 5838250 536 False 333.0 333 79.121 2842 3349 1 chr4B.!!$F1 507

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
675 721 0.03601 ATGTGTCTAGCTGGTGTGCC 60.036 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 2762 0.249953 TTGCGGACCGTGTGTAATGT 60.25 50.0 16.73 0.0 0.0 2.71 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
157 161 9.634163 ACAAGAATAATTTTCGGTATTCCAAAC 57.366 29.630 0.00 0.00 37.41 2.93
309 317 2.728817 GGGACCGTATCGCTCCTG 59.271 66.667 4.00 0.00 37.30 3.86
310 318 2.125961 GGGACCGTATCGCTCCTGT 61.126 63.158 4.00 0.00 37.30 4.00
313 321 2.331805 CCGTATCGCTCCTGTCGG 59.668 66.667 0.00 0.00 0.00 4.79
314 322 2.331805 CGTATCGCTCCTGTCGGG 59.668 66.667 0.00 0.00 0.00 5.14
355 366 6.461788 CCCAACCGTTCAAGGATTTAAAAGAA 60.462 38.462 0.00 0.00 34.73 2.52
358 369 7.342769 ACCGTTCAAGGATTTAAAAGAAAGT 57.657 32.000 0.00 0.00 34.73 2.66
463 477 9.393512 AGTTCATGGATTTGAAAACAAAAATCA 57.606 25.926 9.58 0.00 42.18 2.57
464 478 9.437045 GTTCATGGATTTGAAAACAAAAATCAC 57.563 29.630 9.58 1.87 42.18 3.06
465 479 7.849496 TCATGGATTTGAAAACAAAAATCACG 58.151 30.769 9.58 0.00 42.18 4.35
466 480 6.595772 TGGATTTGAAAACAAAAATCACGG 57.404 33.333 9.58 0.00 42.18 4.94
467 481 6.341316 TGGATTTGAAAACAAAAATCACGGA 58.659 32.000 9.58 0.00 42.18 4.69
468 482 6.989169 TGGATTTGAAAACAAAAATCACGGAT 59.011 30.769 9.58 0.00 42.18 4.18
469 483 7.497249 TGGATTTGAAAACAAAAATCACGGATT 59.503 29.630 9.58 0.00 42.18 3.01
470 484 8.341903 GGATTTGAAAACAAAAATCACGGATTT 58.658 29.630 9.58 6.17 43.07 2.17
471 485 9.157259 GATTTGAAAACAAAAATCACGGATTTG 57.843 29.630 11.14 6.05 40.77 2.32
472 486 7.834068 TTGAAAACAAAAATCACGGATTTGA 57.166 28.000 11.14 0.00 40.77 2.69
473 487 7.834068 TGAAAACAAAAATCACGGATTTGAA 57.166 28.000 11.14 0.00 40.77 2.69
474 488 8.256611 TGAAAACAAAAATCACGGATTTGAAA 57.743 26.923 11.14 0.00 40.77 2.69
596 642 6.149474 ACAAAAACCAAACAGAGATATCTCCG 59.851 38.462 25.88 19.72 43.88 4.63
604 650 8.577296 CCAAACAGAGATATCTCCGTAGATTTA 58.423 37.037 25.88 0.00 43.88 1.40
614 660 4.337274 TCTCCGTAGATTTAGTTCGCATCA 59.663 41.667 0.00 0.00 0.00 3.07
618 664 6.016527 TCCGTAGATTTAGTTCGCATCATACT 60.017 38.462 0.00 0.00 0.00 2.12
662 708 5.837437 AGATATCTCCTTCGTTGATGTGTC 58.163 41.667 0.00 0.00 0.00 3.67
666 712 3.119459 TCTCCTTCGTTGATGTGTCTAGC 60.119 47.826 0.00 0.00 0.00 3.42
667 713 2.826128 TCCTTCGTTGATGTGTCTAGCT 59.174 45.455 0.00 0.00 0.00 3.32
675 721 0.036010 ATGTGTCTAGCTGGTGTGCC 60.036 55.000 0.00 0.00 0.00 5.01
676 722 1.376037 GTGTCTAGCTGGTGTGCCC 60.376 63.158 0.00 0.00 0.00 5.36
677 723 1.841103 TGTCTAGCTGGTGTGCCCA 60.841 57.895 0.00 0.00 42.51 5.36
678 724 1.374947 GTCTAGCTGGTGTGCCCAA 59.625 57.895 0.00 0.00 44.65 4.12
679 725 0.674895 GTCTAGCTGGTGTGCCCAAG 60.675 60.000 0.00 0.00 44.65 3.61
680 726 2.034066 TAGCTGGTGTGCCCAAGC 59.966 61.111 0.00 0.00 44.65 4.01
705 751 4.008539 GCAGGAGTGCGAAGAAAATAAG 57.991 45.455 0.00 0.00 40.71 1.73
715 761 7.021196 GTGCGAAGAAAATAAGATAGTTTGCA 58.979 34.615 0.00 0.00 0.00 4.08
772 819 9.944376 ACTCTGTAGTTAATGCTTTCATTCTTA 57.056 29.630 0.00 0.00 41.68 2.10
831 878 0.252881 ATTCCCTCCAGCTCCACAGA 60.253 55.000 0.00 0.00 0.00 3.41
868 915 9.533253 CAATTTGACTAATTCCACTTGAACTTT 57.467 29.630 0.00 0.00 34.19 2.66
910 961 2.783284 CGCATCAACAACTTTCACACAC 59.217 45.455 0.00 0.00 0.00 3.82
916 967 2.802719 ACAACTTTCACACACCCAACT 58.197 42.857 0.00 0.00 0.00 3.16
941 992 0.685660 AAGTCTCCGTTGTTCCTCCC 59.314 55.000 0.00 0.00 0.00 4.30
950 1001 2.515854 GTTGTTCCTCCCTTTTCCTCC 58.484 52.381 0.00 0.00 0.00 4.30
951 1002 0.690762 TGTTCCTCCCTTTTCCTCCG 59.309 55.000 0.00 0.00 0.00 4.63
1104 1179 4.111016 CCGTGCGTCGTCCTGCTA 62.111 66.667 0.00 0.00 37.94 3.49
1822 1897 1.597854 CGGTCAAGCAGCTCCAACA 60.598 57.895 0.00 0.00 0.00 3.33
2004 2079 1.750018 CATGCCAAGCCATGACGGA 60.750 57.895 0.00 0.00 44.12 4.69
2181 2256 1.302511 GGGGTTCATGTCGCACTGT 60.303 57.895 0.00 0.00 0.00 3.55
2193 2268 1.600916 GCACTGTGGGTGGAACTCC 60.601 63.158 10.21 0.00 45.44 3.85
2284 2359 2.725312 GCCATCCTGACGGAGCTGA 61.725 63.158 0.00 0.00 44.06 4.26
2388 2463 0.550147 TGGAAGGGGAGAAGGGAAGG 60.550 60.000 0.00 0.00 0.00 3.46
2423 2498 3.710722 CAGGCGGCTTCAGGAGGT 61.711 66.667 9.66 0.00 0.00 3.85
2569 2669 5.559148 ATCCATGATACTCTGTTTCCTCC 57.441 43.478 0.00 0.00 0.00 4.30
2574 2674 3.245984 TGATACTCTGTTTCCTCCCTCCA 60.246 47.826 0.00 0.00 0.00 3.86
2624 2724 6.262601 CACGGTAATTGTTTGAAGAGTTGTT 58.737 36.000 0.00 0.00 0.00 2.83
2641 2741 7.616313 AGAGTTGTTCTGATTTTAGTCCTAGG 58.384 38.462 0.82 0.82 33.93 3.02
2650 2750 7.769044 TCTGATTTTAGTCCTAGGTAAACATGC 59.231 37.037 9.08 0.00 0.00 4.06
2652 2752 7.552687 TGATTTTAGTCCTAGGTAAACATGCTG 59.447 37.037 9.08 0.00 0.00 4.41
2653 2753 6.368779 TTTAGTCCTAGGTAAACATGCTGT 57.631 37.500 9.08 0.00 0.00 4.40
2669 2769 7.686438 ACATGCTGTTTAGATCAACATTACA 57.314 32.000 0.00 0.00 36.08 2.41
2670 2770 7.530010 ACATGCTGTTTAGATCAACATTACAC 58.470 34.615 0.00 0.00 36.08 2.90
2671 2771 7.174772 ACATGCTGTTTAGATCAACATTACACA 59.825 33.333 0.00 0.00 36.08 3.72
2672 2772 6.898041 TGCTGTTTAGATCAACATTACACAC 58.102 36.000 0.00 0.00 36.08 3.82
2673 2773 6.015504 GCTGTTTAGATCAACATTACACACG 58.984 40.000 0.00 0.00 36.08 4.49
2674 2774 6.474819 TGTTTAGATCAACATTACACACGG 57.525 37.500 0.00 0.00 31.48 4.94
2675 2775 5.992829 TGTTTAGATCAACATTACACACGGT 59.007 36.000 0.00 0.00 31.48 4.83
2676 2776 6.146510 TGTTTAGATCAACATTACACACGGTC 59.853 38.462 0.00 0.00 31.48 4.79
2677 2777 3.596214 AGATCAACATTACACACGGTCC 58.404 45.455 0.00 0.00 0.00 4.46
2678 2778 1.785768 TCAACATTACACACGGTCCG 58.214 50.000 10.48 10.48 0.00 4.79
2679 2779 0.165079 CAACATTACACACGGTCCGC 59.835 55.000 12.28 0.00 0.00 5.54
2680 2780 0.249953 AACATTACACACGGTCCGCA 60.250 50.000 12.28 0.00 0.00 5.69
2681 2781 0.249953 ACATTACACACGGTCCGCAA 60.250 50.000 12.28 0.00 0.00 4.85
2682 2782 0.442310 CATTACACACGGTCCGCAAG 59.558 55.000 12.28 4.17 0.00 4.01
2683 2783 1.296056 ATTACACACGGTCCGCAAGC 61.296 55.000 12.28 0.00 0.00 4.01
2696 2796 3.725459 CAAGCGTGCGTGATGGCA 61.725 61.111 1.33 0.00 41.45 4.92
2702 2802 3.635191 TGCGTGATGGCACCCTCA 61.635 61.111 0.00 0.00 42.09 3.86
2703 2803 2.359850 GCGTGATGGCACCCTCAA 60.360 61.111 0.00 0.00 42.09 3.02
2704 2804 1.750399 GCGTGATGGCACCCTCAAT 60.750 57.895 0.00 0.00 42.09 2.57
2705 2805 1.718757 GCGTGATGGCACCCTCAATC 61.719 60.000 0.00 0.00 42.09 2.67
2706 2806 1.431488 CGTGATGGCACCCTCAATCG 61.431 60.000 0.00 0.00 42.09 3.34
2707 2807 0.392998 GTGATGGCACCCTCAATCGT 60.393 55.000 0.00 0.00 39.14 3.73
2708 2808 0.107703 TGATGGCACCCTCAATCGTC 60.108 55.000 0.00 0.00 0.00 4.20
2709 2809 0.107703 GATGGCACCCTCAATCGTCA 60.108 55.000 0.00 0.00 0.00 4.35
2710 2810 0.327924 ATGGCACCCTCAATCGTCAA 59.672 50.000 0.00 0.00 0.00 3.18
2711 2811 0.605319 TGGCACCCTCAATCGTCAAC 60.605 55.000 0.00 0.00 0.00 3.18
2712 2812 1.305930 GGCACCCTCAATCGTCAACC 61.306 60.000 0.00 0.00 0.00 3.77
2713 2813 1.305930 GCACCCTCAATCGTCAACCC 61.306 60.000 0.00 0.00 0.00 4.11
2714 2814 0.036164 CACCCTCAATCGTCAACCCA 59.964 55.000 0.00 0.00 0.00 4.51
2715 2815 0.991920 ACCCTCAATCGTCAACCCAT 59.008 50.000 0.00 0.00 0.00 4.00
2716 2816 1.340017 ACCCTCAATCGTCAACCCATG 60.340 52.381 0.00 0.00 0.00 3.66
2717 2817 0.734889 CCTCAATCGTCAACCCATGC 59.265 55.000 0.00 0.00 0.00 4.06
2718 2818 1.452110 CTCAATCGTCAACCCATGCA 58.548 50.000 0.00 0.00 0.00 3.96
2719 2819 1.811965 CTCAATCGTCAACCCATGCAA 59.188 47.619 0.00 0.00 0.00 4.08
2720 2820 1.811965 TCAATCGTCAACCCATGCAAG 59.188 47.619 0.00 0.00 0.00 4.01
2721 2821 0.527565 AATCGTCAACCCATGCAAGC 59.472 50.000 0.00 0.00 0.00 4.01
2722 2822 0.608856 ATCGTCAACCCATGCAAGCA 60.609 50.000 0.00 0.00 0.00 3.91
2723 2823 1.081242 CGTCAACCCATGCAAGCAC 60.081 57.895 0.00 0.00 0.00 4.40
2724 2824 1.794151 CGTCAACCCATGCAAGCACA 61.794 55.000 0.00 0.00 0.00 4.57
2725 2825 0.604578 GTCAACCCATGCAAGCACAT 59.395 50.000 0.00 0.00 0.00 3.21
2726 2826 1.001181 GTCAACCCATGCAAGCACATT 59.999 47.619 0.00 0.00 0.00 2.71
2727 2827 1.001068 TCAACCCATGCAAGCACATTG 59.999 47.619 0.00 0.37 42.20 2.82
2728 2828 1.050204 AACCCATGCAAGCACATTGT 58.950 45.000 0.00 0.00 41.29 2.71
2729 2829 1.050204 ACCCATGCAAGCACATTGTT 58.950 45.000 0.00 0.00 41.29 2.83
2730 2830 1.417145 ACCCATGCAAGCACATTGTTT 59.583 42.857 0.00 0.00 41.29 2.83
2731 2831 2.158784 ACCCATGCAAGCACATTGTTTT 60.159 40.909 0.00 0.00 41.29 2.43
2732 2832 2.224549 CCCATGCAAGCACATTGTTTTG 59.775 45.455 0.00 6.48 41.29 2.44
2733 2833 3.132160 CCATGCAAGCACATTGTTTTGA 58.868 40.909 12.62 2.25 41.29 2.69
2734 2834 3.185594 CCATGCAAGCACATTGTTTTGAG 59.814 43.478 12.62 4.35 41.29 3.02
2735 2835 3.523606 TGCAAGCACATTGTTTTGAGT 57.476 38.095 12.62 0.00 41.29 3.41
2736 2836 3.859443 TGCAAGCACATTGTTTTGAGTT 58.141 36.364 12.62 0.00 41.29 3.01
2762 2864 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
2809 2913 2.970324 AAGTTTTGCGCGGCGAGA 60.970 55.556 28.54 10.51 0.00 4.04
3097 3243 2.042639 GGCCATTCCATGCCCACT 60.043 61.111 0.00 0.00 41.97 4.00
3184 3332 3.562232 AAAACGGGCCACCCTCGA 61.562 61.111 4.39 0.00 42.67 4.04
3228 3378 2.224402 GGATGTCCCAAGAGCTCATACC 60.224 54.545 17.77 2.40 34.14 2.73
3339 3490 3.042682 TGATCCCAAAATCTAGCCGGTA 58.957 45.455 1.90 0.00 0.00 4.02
3371 4083 3.106827 TGGTCATCAACTAGATCAGCCA 58.893 45.455 0.00 0.00 33.72 4.75
3387 4099 1.070758 AGCCAGAATACCGTATGCCAG 59.929 52.381 0.00 0.00 0.00 4.85
3402 4114 1.714899 GCCAGCATACGCAAATCGGT 61.715 55.000 0.00 0.00 43.86 4.69
3457 4169 2.491621 GCGGCATTCCTCCTTTGC 59.508 61.111 0.00 0.00 35.64 3.68
3494 4206 1.673033 GGCTCGCTAGTTTCTCTGCAA 60.673 52.381 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 135 9.634163 GTTTGGAATACCGAAAATTATTCTTGT 57.366 29.630 0.00 0.00 40.78 3.16
298 306 2.027751 GCCCGACAGGAGCGATAC 59.972 66.667 0.00 0.00 41.02 2.24
336 347 8.850454 TGAACTTTCTTTTAAATCCTTGAACG 57.150 30.769 0.00 0.00 0.00 3.95
447 461 8.256611 TCAAATCCGTGATTTTTGTTTTCAAA 57.743 26.923 8.56 0.00 46.39 2.69
450 464 9.548208 TTTTTCAAATCCGTGATTTTTGTTTTC 57.452 25.926 8.56 0.00 39.82 2.29
487 501 8.286800 TCTTAAACCTGTGTATTTTCACATTCG 58.713 33.333 0.09 0.00 45.38 3.34
561 601 3.320673 TTGGTTTTTGTTTGTCCGCTT 57.679 38.095 0.00 0.00 0.00 4.68
562 602 2.997303 GTTTGGTTTTTGTTTGTCCGCT 59.003 40.909 0.00 0.00 0.00 5.52
563 603 2.737252 TGTTTGGTTTTTGTTTGTCCGC 59.263 40.909 0.00 0.00 0.00 5.54
564 604 4.238514 TCTGTTTGGTTTTTGTTTGTCCG 58.761 39.130 0.00 0.00 0.00 4.79
596 642 8.804688 AAGAGTATGATGCGAACTAAATCTAC 57.195 34.615 0.00 0.00 0.00 2.59
604 650 9.900710 CTAGTAATAAAGAGTATGATGCGAACT 57.099 33.333 0.00 0.00 0.00 3.01
626 672 7.582633 CGAAGGAGATATCTCTACATCCCTAGT 60.583 44.444 27.65 5.67 42.48 2.57
627 673 6.765989 CGAAGGAGATATCTCTACATCCCTAG 59.234 46.154 27.65 12.00 42.48 3.02
675 721 1.288127 GCACTCCTGCTTTGCTTGG 59.712 57.895 0.00 0.00 40.63 3.61
676 722 1.081641 CGCACTCCTGCTTTGCTTG 60.082 57.895 0.00 0.00 41.77 4.01
677 723 0.819259 TTCGCACTCCTGCTTTGCTT 60.819 50.000 0.00 0.00 41.77 3.91
678 724 1.227943 TTCGCACTCCTGCTTTGCT 60.228 52.632 0.00 0.00 41.77 3.91
679 725 1.208614 CTTCGCACTCCTGCTTTGC 59.791 57.895 0.00 0.00 41.77 3.68
680 726 1.229428 TTCTTCGCACTCCTGCTTTG 58.771 50.000 0.00 0.00 41.77 2.77
681 727 1.967319 TTTCTTCGCACTCCTGCTTT 58.033 45.000 0.00 0.00 41.77 3.51
688 734 7.426743 GCAAACTATCTTATTTTCTTCGCACTC 59.573 37.037 0.00 0.00 0.00 3.51
705 751 1.065126 AGCTGGGGTCTGCAAACTATC 60.065 52.381 0.00 0.00 39.84 2.08
715 761 2.114616 CTCAACTCATAGCTGGGGTCT 58.885 52.381 0.00 0.00 0.00 3.85
764 811 4.051237 CGATGGCAGACGAATAAGAATGA 58.949 43.478 10.54 0.00 0.00 2.57
798 845 3.555168 GGAGGGAATACTTACCATGCTCG 60.555 52.174 0.00 0.00 0.00 5.03
801 848 3.744660 CTGGAGGGAATACTTACCATGC 58.255 50.000 0.00 0.00 0.00 4.06
802 849 3.392616 AGCTGGAGGGAATACTTACCATG 59.607 47.826 0.00 0.00 0.00 3.66
803 850 3.648545 GAGCTGGAGGGAATACTTACCAT 59.351 47.826 0.00 0.00 0.00 3.55
805 852 2.369203 GGAGCTGGAGGGAATACTTACC 59.631 54.545 0.00 0.00 0.00 2.85
806 853 3.039011 TGGAGCTGGAGGGAATACTTAC 58.961 50.000 0.00 0.00 0.00 2.34
807 854 3.039011 GTGGAGCTGGAGGGAATACTTA 58.961 50.000 0.00 0.00 0.00 2.24
808 855 1.840635 GTGGAGCTGGAGGGAATACTT 59.159 52.381 0.00 0.00 0.00 2.24
910 961 1.001378 CGGAGACTTTTTGCAGTTGGG 60.001 52.381 0.00 0.00 0.00 4.12
916 967 2.098443 GGAACAACGGAGACTTTTTGCA 59.902 45.455 0.00 0.00 0.00 4.08
941 992 0.250727 TTGGTGGCTCGGAGGAAAAG 60.251 55.000 7.20 0.00 0.00 2.27
950 1001 1.812571 ACAGCTAATTTTGGTGGCTCG 59.187 47.619 13.18 0.00 37.25 5.03
951 1002 2.672195 GCACAGCTAATTTTGGTGGCTC 60.672 50.000 13.18 0.73 37.25 4.70
983 1051 3.566523 GCCATGATAGTCACTAGCGTAC 58.433 50.000 0.00 0.00 0.00 3.67
987 1055 1.937108 GCCGCCATGATAGTCACTAGC 60.937 57.143 0.00 0.00 0.00 3.42
992 1060 2.421314 CCGCCGCCATGATAGTCA 59.579 61.111 0.00 0.00 0.00 3.41
1090 1165 4.129737 GGCTAGCAGGACGACGCA 62.130 66.667 18.24 0.00 0.00 5.24
1116 1191 2.517919 GGGATGAGGTGGCCCATC 59.482 66.667 10.37 10.37 41.64 3.51
1699 1774 0.318441 TCCTCGAAGCTGTTGACCAG 59.682 55.000 0.00 0.00 44.53 4.00
1822 1897 1.374758 CCAGCTCGTCGGCTTCTTT 60.375 57.895 5.60 0.00 41.00 2.52
2004 2079 1.681486 CCCCCAAGGCGTTGTTGTTT 61.681 55.000 17.23 0.00 30.95 2.83
2220 2295 2.592861 GGCCAGGTGATCATCGGC 60.593 66.667 24.75 24.75 42.21 5.54
2569 2669 4.286297 TCCACAAAACAGAGTATGGAGG 57.714 45.455 0.00 0.00 32.50 4.30
2574 2674 7.596494 CATGTTCATTCCACAAAACAGAGTAT 58.404 34.615 0.00 0.00 35.30 2.12
2624 2724 7.769044 GCATGTTTACCTAGGACTAAAATCAGA 59.231 37.037 17.98 0.00 0.00 3.27
2650 2750 6.147164 ACCGTGTGTAATGTTGATCTAAACAG 59.853 38.462 5.06 0.00 42.99 3.16
2652 2752 6.401796 GGACCGTGTGTAATGTTGATCTAAAC 60.402 42.308 0.00 0.00 0.00 2.01
2653 2753 5.640357 GGACCGTGTGTAATGTTGATCTAAA 59.360 40.000 0.00 0.00 0.00 1.85
2662 2762 0.249953 TTGCGGACCGTGTGTAATGT 60.250 50.000 16.73 0.00 0.00 2.71
2663 2763 0.442310 CTTGCGGACCGTGTGTAATG 59.558 55.000 16.73 0.00 0.00 1.90
2664 2764 1.296056 GCTTGCGGACCGTGTGTAAT 61.296 55.000 16.73 0.00 0.00 1.89
2665 2765 1.957186 GCTTGCGGACCGTGTGTAA 60.957 57.895 16.73 2.99 0.00 2.41
2666 2766 2.356553 GCTTGCGGACCGTGTGTA 60.357 61.111 16.73 0.00 0.00 2.90
2679 2779 3.725459 TGCCATCACGCACGCTTG 61.725 61.111 0.00 0.00 32.62 4.01
2687 2787 1.431488 CGATTGAGGGTGCCATCACG 61.431 60.000 4.96 3.55 44.03 4.35
2688 2788 0.392998 ACGATTGAGGGTGCCATCAC 60.393 55.000 4.96 0.00 42.40 3.06
2689 2789 0.107703 GACGATTGAGGGTGCCATCA 60.108 55.000 1.02 1.02 0.00 3.07
2690 2790 0.107703 TGACGATTGAGGGTGCCATC 60.108 55.000 0.00 0.00 0.00 3.51
2691 2791 0.327924 TTGACGATTGAGGGTGCCAT 59.672 50.000 0.00 0.00 0.00 4.40
2692 2792 0.605319 GTTGACGATTGAGGGTGCCA 60.605 55.000 0.00 0.00 0.00 4.92
2693 2793 1.305930 GGTTGACGATTGAGGGTGCC 61.306 60.000 0.00 0.00 0.00 5.01
2694 2794 1.305930 GGGTTGACGATTGAGGGTGC 61.306 60.000 0.00 0.00 0.00 5.01
2695 2795 0.036164 TGGGTTGACGATTGAGGGTG 59.964 55.000 0.00 0.00 0.00 4.61
2696 2796 0.991920 ATGGGTTGACGATTGAGGGT 59.008 50.000 0.00 0.00 0.00 4.34
2697 2797 1.382522 CATGGGTTGACGATTGAGGG 58.617 55.000 0.00 0.00 0.00 4.30
2698 2798 0.734889 GCATGGGTTGACGATTGAGG 59.265 55.000 0.00 0.00 0.00 3.86
2699 2799 1.452110 TGCATGGGTTGACGATTGAG 58.548 50.000 0.00 0.00 0.00 3.02
2700 2800 1.811965 CTTGCATGGGTTGACGATTGA 59.188 47.619 0.00 0.00 0.00 2.57
2701 2801 1.733389 GCTTGCATGGGTTGACGATTG 60.733 52.381 1.34 0.00 0.00 2.67
2702 2802 0.527565 GCTTGCATGGGTTGACGATT 59.472 50.000 1.34 0.00 0.00 3.34
2703 2803 0.608856 TGCTTGCATGGGTTGACGAT 60.609 50.000 1.34 0.00 0.00 3.73
2704 2804 1.228094 TGCTTGCATGGGTTGACGA 60.228 52.632 1.34 0.00 0.00 4.20
2705 2805 1.081242 GTGCTTGCATGGGTTGACG 60.081 57.895 0.00 0.00 0.00 4.35
2706 2806 0.604578 ATGTGCTTGCATGGGTTGAC 59.395 50.000 0.00 0.00 0.00 3.18
2707 2807 1.001068 CAATGTGCTTGCATGGGTTGA 59.999 47.619 0.00 0.00 0.00 3.18
2708 2808 1.270412 ACAATGTGCTTGCATGGGTTG 60.270 47.619 0.00 4.98 38.50 3.77
2709 2809 1.050204 ACAATGTGCTTGCATGGGTT 58.950 45.000 0.00 0.00 38.50 4.11
2710 2810 1.050204 AACAATGTGCTTGCATGGGT 58.950 45.000 0.00 0.00 38.50 4.51
2711 2811 2.172851 AAACAATGTGCTTGCATGGG 57.827 45.000 0.00 0.00 38.50 4.00
2712 2812 3.132160 TCAAAACAATGTGCTTGCATGG 58.868 40.909 0.00 0.00 38.50 3.66
2713 2813 3.805422 ACTCAAAACAATGTGCTTGCATG 59.195 39.130 0.00 0.00 38.50 4.06
2714 2814 4.062677 ACTCAAAACAATGTGCTTGCAT 57.937 36.364 0.00 0.00 38.50 3.96
2715 2815 3.523606 ACTCAAAACAATGTGCTTGCA 57.476 38.095 4.20 0.00 38.50 4.08
2716 2816 4.114794 AGAACTCAAAACAATGTGCTTGC 58.885 39.130 4.20 0.00 38.50 4.01
2717 2817 7.195646 TCTTAGAACTCAAAACAATGTGCTTG 58.804 34.615 2.96 2.96 40.90 4.01
2718 2818 7.333528 TCTTAGAACTCAAAACAATGTGCTT 57.666 32.000 0.00 0.00 0.00 3.91
2719 2819 6.514048 GCTCTTAGAACTCAAAACAATGTGCT 60.514 38.462 0.00 0.00 0.00 4.40
2720 2820 5.626955 GCTCTTAGAACTCAAAACAATGTGC 59.373 40.000 0.00 0.00 0.00 4.57
2721 2821 6.728200 TGCTCTTAGAACTCAAAACAATGTG 58.272 36.000 0.00 0.00 0.00 3.21
2722 2822 6.942532 TGCTCTTAGAACTCAAAACAATGT 57.057 33.333 0.00 0.00 0.00 2.71
2723 2823 7.814642 AGATGCTCTTAGAACTCAAAACAATG 58.185 34.615 0.00 0.00 0.00 2.82
2724 2824 7.120432 GGAGATGCTCTTAGAACTCAAAACAAT 59.880 37.037 0.00 0.00 0.00 2.71
2725 2825 6.428159 GGAGATGCTCTTAGAACTCAAAACAA 59.572 38.462 0.00 0.00 0.00 2.83
2726 2826 5.934625 GGAGATGCTCTTAGAACTCAAAACA 59.065 40.000 0.00 0.00 0.00 2.83
2727 2827 5.934625 TGGAGATGCTCTTAGAACTCAAAAC 59.065 40.000 0.00 0.00 0.00 2.43
2728 2828 6.114187 TGGAGATGCTCTTAGAACTCAAAA 57.886 37.500 0.00 0.00 0.00 2.44
2729 2829 5.745312 TGGAGATGCTCTTAGAACTCAAA 57.255 39.130 0.00 0.00 0.00 2.69
2730 2830 5.012046 TGTTGGAGATGCTCTTAGAACTCAA 59.988 40.000 0.00 0.00 0.00 3.02
2731 2831 4.528206 TGTTGGAGATGCTCTTAGAACTCA 59.472 41.667 0.00 0.00 0.00 3.41
2732 2832 5.078411 TGTTGGAGATGCTCTTAGAACTC 57.922 43.478 0.00 0.00 0.00 3.01
2733 2833 4.622695 GCTGTTGGAGATGCTCTTAGAACT 60.623 45.833 0.00 0.00 0.00 3.01
2734 2834 3.620821 GCTGTTGGAGATGCTCTTAGAAC 59.379 47.826 0.00 0.00 0.00 3.01
2735 2835 3.369892 GGCTGTTGGAGATGCTCTTAGAA 60.370 47.826 0.00 0.00 0.00 2.10
2736 2836 2.169352 GGCTGTTGGAGATGCTCTTAGA 59.831 50.000 0.00 0.00 0.00 2.10
2890 2996 3.750652 TGCATATGTTGTTTCTGCGAGAA 59.249 39.130 4.29 0.00 35.63 2.87
2898 3005 5.527951 TGTTTGGAGTGCATATGTTGTTTC 58.472 37.500 4.29 0.00 0.00 2.78
3097 3243 5.770919 TCAGAAGGATCTCATCAAGGAGTA 58.229 41.667 0.00 0.00 36.30 2.59
3145 3292 2.281539 TGCCTCCTATCATGCCATTG 57.718 50.000 0.00 0.00 0.00 2.82
3203 3353 1.280421 GAGCTCTTGGGACATCCTGTT 59.720 52.381 6.43 0.00 39.30 3.16
3228 3378 4.098044 TGGCCAAGATTTAGACTACTCTCG 59.902 45.833 0.61 0.00 0.00 4.04
3339 3490 3.389329 AGTTGATGACCACTTGTGAGAGT 59.611 43.478 1.89 0.00 0.00 3.24
3371 4083 3.926616 GTATGCTGGCATACGGTATTCT 58.073 45.455 23.81 0.00 45.90 2.40
3387 4099 1.129624 TGACAACCGATTTGCGTATGC 59.870 47.619 0.00 0.00 39.01 3.14
3392 4104 4.838959 GGTGACAACCGATTTGCG 57.161 55.556 0.00 0.00 39.01 4.85
3494 4206 2.034879 CCGAGTTGTTCAGGCGCAT 61.035 57.895 10.83 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.