Multiple sequence alignment - TraesCS3B01G092800

Loading Multiple Alignment...

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 TraesCS3B01G092800 chr3B 100.000 2245 0 0 1 2245 61897836 61895592 0.000000e+00 4146.0
1 TraesCS3B01G092800 chr3B 100.000 133 0 0 2639 2771 61895198 61895066 2.130000e-61 246.0
2 TraesCS3B01G092800 chr3D 93.624 1631 87 9 297 1922 39033529 39031911 0.000000e+00 2420.0
3 TraesCS3B01G092800 chr3D 91.692 325 22 3 1925 2245 39031865 39031542 1.960000e-121 446.0
4 TraesCS3B01G092800 chr3D 78.437 691 124 13 952 1639 39120675 39120007 7.090000e-116 427.0
5 TraesCS3B01G092800 chr3D 100.000 130 0 0 167 296 39038652 39038523 9.920000e-60 241.0
6 TraesCS3B01G092800 chr3D 96.078 51 2 0 2713 2763 39031509 39031459 1.770000e-12 84.2
7 TraesCS3B01G092800 chr3D 96.078 51 1 1 122 171 39038715 39038665 6.360000e-12 82.4
8 TraesCS3B01G092800 chr3A 92.886 1504 99 4 167 1670 50383954 50382459 0.000000e+00 2178.0
9 TraesCS3B01G092800 chr3A 89.922 258 16 5 1925 2174 50382207 50381952 9.570000e-85 324.0
10 TraesCS3B01G092800 chr3A 92.268 194 15 0 1701 1894 50382461 50382268 2.720000e-70 276.0
11 TraesCS3B01G092800 chr3A 88.596 114 7 5 31 144 50384497 50384390 1.730000e-27 134.0
12 TraesCS3B01G092800 chr3A 97.778 45 1 0 1834 1878 50382248 50382204 8.230000e-11 78.7
13 TraesCS3B01G092800 chr5A 81.385 693 96 14 952 1639 459003911 459003247 4.060000e-148 534.0
14 TraesCS3B01G092800 chr5B 81.358 692 93 20 952 1639 423366369 423365710 5.250000e-147 531.0
15 TraesCS3B01G092800 chr7A 79.798 693 104 19 952 1639 105778276 105777615 3.230000e-129 472.0
16 TraesCS3B01G092800 chr7A 79.221 693 107 25 952 1639 105767428 105766768 5.440000e-122 448.0
17 TraesCS3B01G092800 chr7A 78.425 584 98 23 1649 2218 146026476 146027045 3.390000e-94 355.0
18 TraesCS3B01G092800 chr7A 80.303 462 78 7 947 1408 736465810 736466258 1.230000e-88 337.0
19 TraesCS3B01G092800 chr7B 79.335 692 109 23 952 1639 59180498 59179837 3.250000e-124 455.0
20 TraesCS3B01G092800 chr7B 76.079 556 109 16 1649 2196 114940179 114940718 4.550000e-68 268.0
21 TraesCS3B01G092800 chr7B 78.431 306 45 14 1833 2124 59179271 59178973 2.190000e-41 180.0
22 TraesCS3B01G092800 chr7D 79.161 691 112 19 952 1639 101799042 101798381 1.510000e-122 449.0
23 TraesCS3B01G092800 chr7D 77.345 693 130 15 952 1639 143975785 143975115 4.330000e-103 385.0
24 TraesCS3B01G092800 chr7D 75.916 573 109 20 1649 2210 152948614 152949168 1.640000e-67 267.0
25 TraesCS3B01G092800 chr7D 79.062 320 57 6 1934 2245 143950196 143949879 7.780000e-51 211.0


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 TraesCS3B01G092800 chr3B 61895066 61897836 2770 True 2196.00 4146 100.000 1 2771 2 chr3B.!!$R1 2770
1 TraesCS3B01G092800 chr3D 39031459 39033529 2070 True 983.40 2420 93.798 297 2763 3 chr3D.!!$R2 2466
2 TraesCS3B01G092800 chr3D 39120007 39120675 668 True 427.00 427 78.437 952 1639 1 chr3D.!!$R1 687
3 TraesCS3B01G092800 chr3A 50381952 50384497 2545 True 598.14 2178 92.290 31 2174 5 chr3A.!!$R1 2143
4 TraesCS3B01G092800 chr5A 459003247 459003911 664 True 534.00 534 81.385 952 1639 1 chr5A.!!$R1 687
5 TraesCS3B01G092800 chr5B 423365710 423366369 659 True 531.00 531 81.358 952 1639 1 chr5B.!!$R1 687
6 TraesCS3B01G092800 chr7A 105777615 105778276 661 True 472.00 472 79.798 952 1639 1 chr7A.!!$R2 687
7 TraesCS3B01G092800 chr7A 105766768 105767428 660 True 448.00 448 79.221 952 1639 1 chr7A.!!$R1 687
8 TraesCS3B01G092800 chr7A 146026476 146027045 569 False 355.00 355 78.425 1649 2218 1 chr7A.!!$F1 569
9 TraesCS3B01G092800 chr7B 59178973 59180498 1525 True 317.50 455 78.883 952 2124 2 chr7B.!!$R1 1172
10 TraesCS3B01G092800 chr7B 114940179 114940718 539 False 268.00 268 76.079 1649 2196 1 chr7B.!!$F1 547
11 TraesCS3B01G092800 chr7D 101798381 101799042 661 True 449.00 449 79.161 952 1639 1 chr7D.!!$R1 687
12 TraesCS3B01G092800 chr7D 143975115 143975785 670 True 385.00 385 77.345 952 1639 1 chr7D.!!$R3 687
13 TraesCS3B01G092800 chr7D 152948614 152949168 554 False 267.00 267 75.916 1649 2210 1 chr7D.!!$F1 561

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
903 1317 0.107214 TTTAAGCGCCTCCCCTGATG 60.107 55.0 2.29 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 3547 0.166597 CGATGTGTGTGCATGTGGTC 59.833 55.0 0.0 0.0 0.0 4.02 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
28 29 9.569167 TGAAGAAAATAGAGAAGTACGTATGTG 57.431 33.333 0.00 0.00 0.00 3.21
29 30 7.988904 AGAAAATAGAGAAGTACGTATGTGC 57.011 36.000 0.00 0.00 0.00 4.57
46 47 3.392431 CATGAAGAGCGTGCCTCG 58.608 61.111 0.00 0.00 45.54 4.63
47 48 1.153765 CATGAAGAGCGTGCCTCGA 60.154 57.895 2.66 0.00 45.54 4.04
48 49 0.737367 CATGAAGAGCGTGCCTCGAA 60.737 55.000 2.66 0.00 45.54 3.71
49 50 0.459237 ATGAAGAGCGTGCCTCGAAG 60.459 55.000 2.66 0.00 45.54 3.79
50 51 2.433318 AAGAGCGTGCCTCGAAGC 60.433 61.111 0.00 0.00 45.54 3.86
56 57 2.158959 CGTGCCTCGAAGCTTACCG 61.159 63.158 7.65 0.00 42.86 4.02
60 61 1.141234 CCTCGAAGCTTACCGGTCC 59.859 63.158 12.40 0.00 0.00 4.46
63 64 2.510918 GAAGCTTACCGGTCCCGC 60.511 66.667 12.40 12.85 38.24 6.13
81 82 1.283793 CGCATGCATTCGGGGATTC 59.716 57.895 19.57 0.00 0.00 2.52
85 86 0.184451 ATGCATTCGGGGATTCAGCT 59.816 50.000 0.00 0.00 0.00 4.24
144 541 1.077645 CCAATGGCGCCATCGTTTTG 61.078 55.000 40.38 32.22 35.31 2.44
171 568 8.591940 TGGGAGATAGAGATTAATCATCTTGTG 58.408 37.037 17.56 0.00 42.92 3.33
172 569 8.592809 GGGAGATAGAGATTAATCATCTTGTGT 58.407 37.037 17.56 8.15 42.92 3.72
225 639 0.179100 CTGGATGTAGCTGACACCCG 60.179 60.000 0.00 0.00 46.46 5.28
229 643 1.068588 GATGTAGCTGACACCCGCATA 59.931 52.381 0.00 0.00 42.17 3.14
239 653 2.202878 CCCGCATACACCACCTCG 60.203 66.667 0.00 0.00 0.00 4.63
263 677 3.632145 GCCCGACATGGTGAATTATCTTT 59.368 43.478 0.00 0.00 35.15 2.52
274 688 7.715657 TGGTGAATTATCTTTCCATGTATTGC 58.284 34.615 0.00 0.00 0.00 3.56
295 709 6.591750 TGCTAGATTAGGCTAACTATGGAC 57.408 41.667 9.55 0.00 0.00 4.02
326 740 2.121832 ATCCAGTGACCGGGGACA 59.878 61.111 6.32 0.00 32.60 4.02
361 775 3.633235 TCGTTTTGCGTAAACATGCATT 58.367 36.364 0.00 0.00 45.20 3.56
503 917 2.604046 AGAACAATAGCAGGGCTACG 57.396 50.000 0.00 0.00 44.24 3.51
588 1002 1.658409 GCGGCAACAGCAACAGAAC 60.658 57.895 0.00 0.00 36.37 3.01
589 1003 1.726865 CGGCAACAGCAACAGAACA 59.273 52.632 0.00 0.00 0.00 3.18
590 1004 0.311790 CGGCAACAGCAACAGAACAT 59.688 50.000 0.00 0.00 0.00 2.71
591 1005 1.774639 GGCAACAGCAACAGAACATG 58.225 50.000 0.00 0.00 0.00 3.21
609 1023 1.675552 TGCATGTAGATCGGACGAGA 58.324 50.000 0.00 0.00 0.00 4.04
721 1135 0.251832 AGAGACCCGTCACCTGTCAT 60.252 55.000 0.00 0.00 0.00 3.06
722 1136 0.173708 GAGACCCGTCACCTGTCATC 59.826 60.000 0.00 0.00 0.00 2.92
753 1167 1.383523 GCCCTGACAATAGGACAAGC 58.616 55.000 0.00 0.00 40.42 4.01
754 1168 1.340017 GCCCTGACAATAGGACAAGCA 60.340 52.381 0.00 0.00 40.42 3.91
828 1242 5.356426 AGGAACACAATTAAACAAAGGCAC 58.644 37.500 0.00 0.00 0.00 5.01
873 1287 2.358737 GCCTTGCCAGTACACGCT 60.359 61.111 0.00 0.00 0.00 5.07
900 1314 1.543429 CCTATTTAAGCGCCTCCCCTG 60.543 57.143 2.29 0.00 0.00 4.45
903 1317 0.107214 TTTAAGCGCCTCCCCTGATG 60.107 55.000 2.29 0.00 0.00 3.07
923 1337 9.160496 CCTGATGTATCTAGCTCATTAAATTCC 57.840 37.037 0.00 0.00 0.00 3.01
1001 1425 2.428171 AGTTCAGCAGCAACAACAACAT 59.572 40.909 0.00 0.00 0.00 2.71
1173 1597 0.628668 AGGCCAAGATGGGGGAGAAT 60.629 55.000 5.01 0.00 38.19 2.40
1275 1699 1.073548 GGCCACGGGTAAGGACAAA 59.926 57.895 0.00 0.00 31.39 2.83
1454 1878 1.594194 ATCGCAAATGCCGCTTCCAA 61.594 50.000 0.00 0.00 37.91 3.53
1467 1891 2.993899 CGCTTCCAATAACGTGTCTTCT 59.006 45.455 0.00 0.00 0.00 2.85
1592 2022 7.503521 TTTGCACTGATTCAGTTTATGTACA 57.496 32.000 16.64 0.00 42.59 2.90
1683 2524 3.308705 GAGGACGTTGGGACCGGT 61.309 66.667 6.92 6.92 0.00 5.28
1750 2591 2.481854 AGATCTTGTCGATGAGCATGC 58.518 47.619 10.51 10.51 30.84 4.06
1757 2598 0.249031 TCGATGAGCATGCGTACAGG 60.249 55.000 13.01 10.18 0.00 4.00
1777 2618 2.026636 GGTGGGGCATGTTGAAGTACTA 60.027 50.000 0.00 0.00 0.00 1.82
1813 2654 8.892723 TGATCCAAGAAAACATATATGTGTGTC 58.107 33.333 18.94 15.11 41.61 3.67
1897 2742 4.626042 TGCACCGCATTTTATTTTTCAGT 58.374 34.783 0.00 0.00 31.71 3.41
1917 2803 3.817647 AGTGTGATTCCAAGAGAGTTTGC 59.182 43.478 0.00 0.00 0.00 3.68
1923 2809 0.455633 CCAAGAGAGTTTGCATGCGC 60.456 55.000 14.09 0.00 39.24 6.09
1930 2816 2.984718 TTTGCATGCGCTGGCTCA 60.985 55.556 21.16 8.35 40.82 4.26
1932 2818 2.274232 TTTGCATGCGCTGGCTCATC 62.274 55.000 21.16 0.69 40.82 2.92
1967 2856 5.364778 TCTTGTGCTAGTGTTGTGTGTATT 58.635 37.500 0.00 0.00 0.00 1.89
1995 2884 2.752354 GGCTTGTACATGCACCACATAA 59.248 45.455 28.60 0.00 36.64 1.90
2069 2968 9.415008 ACACCATGCATGTTTTAAACCTATATA 57.585 29.630 24.58 0.00 0.00 0.86
2106 3013 7.697352 TTGTTAAATTGTGAATGCTTGACTG 57.303 32.000 0.00 0.00 0.00 3.51
2111 3018 3.564235 TGTGAATGCTTGACTGAATGC 57.436 42.857 0.00 0.00 0.00 3.56
2211 3118 5.249622 TCCATCCACCACATAAACTCTTACA 59.750 40.000 0.00 0.00 0.00 2.41
2218 3125 7.277981 CCACCACATAAACTCTTACATACACTC 59.722 40.741 0.00 0.00 0.00 3.51
2658 3565 1.527034 AGACCACATGCACACACATC 58.473 50.000 0.00 0.00 0.00 3.06
2659 3566 0.166597 GACCACATGCACACACATCG 59.833 55.000 0.00 0.00 0.00 3.84
2660 3567 0.534877 ACCACATGCACACACATCGT 60.535 50.000 0.00 0.00 0.00 3.73
2661 3568 1.270571 ACCACATGCACACACATCGTA 60.271 47.619 0.00 0.00 0.00 3.43
2662 3569 2.009051 CCACATGCACACACATCGTAT 58.991 47.619 0.00 0.00 0.00 3.06
2663 3570 2.419673 CCACATGCACACACATCGTATT 59.580 45.455 0.00 0.00 0.00 1.89
2664 3571 3.485711 CCACATGCACACACATCGTATTC 60.486 47.826 0.00 0.00 0.00 1.75
2665 3572 2.677836 ACATGCACACACATCGTATTCC 59.322 45.455 0.00 0.00 0.00 3.01
2666 3573 2.760634 TGCACACACATCGTATTCCT 57.239 45.000 0.00 0.00 0.00 3.36
2667 3574 3.878160 TGCACACACATCGTATTCCTA 57.122 42.857 0.00 0.00 0.00 2.94
2668 3575 4.400529 TGCACACACATCGTATTCCTAT 57.599 40.909 0.00 0.00 0.00 2.57
2669 3576 4.119136 TGCACACACATCGTATTCCTATG 58.881 43.478 0.00 0.00 0.00 2.23
2670 3577 4.142049 TGCACACACATCGTATTCCTATGA 60.142 41.667 0.00 0.00 0.00 2.15
2671 3578 4.445718 GCACACACATCGTATTCCTATGAG 59.554 45.833 0.00 0.00 0.00 2.90
2672 3579 5.736207 GCACACACATCGTATTCCTATGAGA 60.736 44.000 0.00 0.00 0.00 3.27
2673 3580 6.273071 CACACACATCGTATTCCTATGAGAA 58.727 40.000 0.00 0.00 0.00 2.87
2674 3581 6.199154 CACACACATCGTATTCCTATGAGAAC 59.801 42.308 0.00 0.00 0.00 3.01
2675 3582 5.692204 CACACATCGTATTCCTATGAGAACC 59.308 44.000 0.00 0.00 0.00 3.62
2676 3583 5.598830 ACACATCGTATTCCTATGAGAACCT 59.401 40.000 0.00 0.00 0.00 3.50
2677 3584 6.153067 CACATCGTATTCCTATGAGAACCTC 58.847 44.000 0.00 0.00 0.00 3.85
2678 3585 5.244178 ACATCGTATTCCTATGAGAACCTCC 59.756 44.000 0.00 0.00 0.00 4.30
2679 3586 3.819337 TCGTATTCCTATGAGAACCTCCG 59.181 47.826 0.00 0.00 0.00 4.63
2680 3587 3.819337 CGTATTCCTATGAGAACCTCCGA 59.181 47.826 0.00 0.00 0.00 4.55
2681 3588 4.459685 CGTATTCCTATGAGAACCTCCGAT 59.540 45.833 0.00 0.00 0.00 4.18
2682 3589 5.646793 CGTATTCCTATGAGAACCTCCGATA 59.353 44.000 0.00 0.00 0.00 2.92
2683 3590 6.150641 CGTATTCCTATGAGAACCTCCGATAA 59.849 42.308 0.00 0.00 0.00 1.75
2684 3591 7.148052 CGTATTCCTATGAGAACCTCCGATAAT 60.148 40.741 0.00 0.00 0.00 1.28
2685 3592 6.996180 TTCCTATGAGAACCTCCGATAATT 57.004 37.500 0.00 0.00 0.00 1.40
2686 3593 6.996180 TCCTATGAGAACCTCCGATAATTT 57.004 37.500 0.00 0.00 0.00 1.82
2687 3594 6.759272 TCCTATGAGAACCTCCGATAATTTG 58.241 40.000 0.00 0.00 0.00 2.32
2688 3595 6.553476 TCCTATGAGAACCTCCGATAATTTGA 59.447 38.462 0.00 0.00 0.00 2.69
2689 3596 6.870965 CCTATGAGAACCTCCGATAATTTGAG 59.129 42.308 0.00 0.00 0.00 3.02
2690 3597 4.442706 TGAGAACCTCCGATAATTTGAGC 58.557 43.478 0.00 0.00 0.00 4.26
2691 3598 3.809905 AGAACCTCCGATAATTTGAGCC 58.190 45.455 0.00 0.00 0.00 4.70
2692 3599 2.240493 ACCTCCGATAATTTGAGCCG 57.760 50.000 0.00 0.00 0.00 5.52
2693 3600 1.760613 ACCTCCGATAATTTGAGCCGA 59.239 47.619 0.00 0.00 0.00 5.54
2694 3601 2.135933 CCTCCGATAATTTGAGCCGAC 58.864 52.381 0.00 0.00 0.00 4.79
2695 3602 2.483013 CCTCCGATAATTTGAGCCGACA 60.483 50.000 0.00 0.00 0.00 4.35
2696 3603 3.194861 CTCCGATAATTTGAGCCGACAA 58.805 45.455 0.00 0.00 0.00 3.18
2697 3604 3.194861 TCCGATAATTTGAGCCGACAAG 58.805 45.455 0.00 0.00 0.00 3.16
2698 3605 3.118920 TCCGATAATTTGAGCCGACAAGA 60.119 43.478 0.00 0.00 0.00 3.02
2699 3606 3.809832 CCGATAATTTGAGCCGACAAGAT 59.190 43.478 0.00 0.00 0.00 2.40
2700 3607 4.319046 CCGATAATTTGAGCCGACAAGATG 60.319 45.833 0.00 0.00 0.00 2.90
2701 3608 2.927553 AATTTGAGCCGACAAGATGC 57.072 45.000 0.00 0.00 0.00 3.91
2702 3609 0.729116 ATTTGAGCCGACAAGATGCG 59.271 50.000 0.00 0.00 0.00 4.73
2703 3610 0.320334 TTTGAGCCGACAAGATGCGA 60.320 50.000 0.00 0.00 0.00 5.10
2704 3611 0.320334 TTGAGCCGACAAGATGCGAA 60.320 50.000 0.00 0.00 0.00 4.70
2705 3612 1.014044 TGAGCCGACAAGATGCGAAC 61.014 55.000 0.00 0.00 0.00 3.95
2706 3613 1.696832 GAGCCGACAAGATGCGAACC 61.697 60.000 0.00 0.00 0.00 3.62
2707 3614 2.750888 GCCGACAAGATGCGAACCC 61.751 63.158 0.00 0.00 0.00 4.11
2708 3615 1.375396 CCGACAAGATGCGAACCCA 60.375 57.895 0.00 0.00 0.00 4.51
2709 3616 1.635663 CCGACAAGATGCGAACCCAC 61.636 60.000 0.00 0.00 0.00 4.61
2710 3617 1.635663 CGACAAGATGCGAACCCACC 61.636 60.000 0.00 0.00 0.00 4.61
2711 3618 0.321653 GACAAGATGCGAACCCACCT 60.322 55.000 0.00 0.00 0.00 4.00
2712 3619 0.981183 ACAAGATGCGAACCCACCTA 59.019 50.000 0.00 0.00 0.00 3.08
2713 3620 1.559682 ACAAGATGCGAACCCACCTAT 59.440 47.619 0.00 0.00 0.00 2.57
2770 3677 8.603242 ATGTATACTTTCTTAATTAGGTGCCG 57.397 34.615 4.17 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.569167 CACATACGTACTTCTCTATTTTCTTCA 57.431 33.333 0.00 0.00 0.00 3.02
3 4 8.533153 GCACATACGTACTTCTCTATTTTCTTC 58.467 37.037 0.00 0.00 0.00 2.87
4 5 8.033038 TGCACATACGTACTTCTCTATTTTCTT 58.967 33.333 0.00 0.00 0.00 2.52
5 6 7.544622 TGCACATACGTACTTCTCTATTTTCT 58.455 34.615 0.00 0.00 0.00 2.52
6 7 7.751047 TGCACATACGTACTTCTCTATTTTC 57.249 36.000 0.00 0.00 0.00 2.29
7 8 7.979537 TCATGCACATACGTACTTCTCTATTTT 59.020 33.333 0.00 0.00 0.00 1.82
8 9 7.489160 TCATGCACATACGTACTTCTCTATTT 58.511 34.615 0.00 0.00 0.00 1.40
9 10 7.039313 TCATGCACATACGTACTTCTCTATT 57.961 36.000 0.00 0.00 0.00 1.73
10 11 6.635030 TCATGCACATACGTACTTCTCTAT 57.365 37.500 0.00 0.00 0.00 1.98
11 12 6.317893 TCTTCATGCACATACGTACTTCTCTA 59.682 38.462 0.00 0.00 0.00 2.43
12 13 4.983671 TCATGCACATACGTACTTCTCT 57.016 40.909 0.00 0.00 0.00 3.10
13 14 5.340803 TCTTCATGCACATACGTACTTCTC 58.659 41.667 0.00 0.00 0.00 2.87
14 15 5.324784 TCTTCATGCACATACGTACTTCT 57.675 39.130 0.00 0.00 0.00 2.85
15 16 4.026475 GCTCTTCATGCACATACGTACTTC 60.026 45.833 0.00 0.00 0.00 3.01
16 17 3.865745 GCTCTTCATGCACATACGTACTT 59.134 43.478 0.00 0.00 0.00 2.24
17 18 3.448686 GCTCTTCATGCACATACGTACT 58.551 45.455 0.00 0.00 0.00 2.73
18 19 2.216488 CGCTCTTCATGCACATACGTAC 59.784 50.000 0.00 0.00 0.00 3.67
19 20 2.159296 ACGCTCTTCATGCACATACGTA 60.159 45.455 0.00 0.00 0.00 3.57
20 21 1.280982 CGCTCTTCATGCACATACGT 58.719 50.000 0.00 0.00 0.00 3.57
21 22 1.005662 CACGCTCTTCATGCACATACG 60.006 52.381 0.00 0.00 0.00 3.06
22 23 1.267732 GCACGCTCTTCATGCACATAC 60.268 52.381 0.00 0.00 39.23 2.39
23 24 1.009078 GCACGCTCTTCATGCACATA 58.991 50.000 0.00 0.00 39.23 2.29
24 25 1.651240 GGCACGCTCTTCATGCACAT 61.651 55.000 0.00 0.00 41.27 3.21
25 26 2.327343 GGCACGCTCTTCATGCACA 61.327 57.895 0.00 0.00 41.27 4.57
26 27 1.975363 GAGGCACGCTCTTCATGCAC 61.975 60.000 0.00 0.00 41.27 4.57
27 28 1.742880 GAGGCACGCTCTTCATGCA 60.743 57.895 0.00 0.00 41.27 3.96
28 29 2.806856 CGAGGCACGCTCTTCATGC 61.807 63.158 0.00 0.00 38.68 4.06
29 30 0.737367 TTCGAGGCACGCTCTTCATG 60.737 55.000 0.00 0.00 42.26 3.07
42 43 1.141234 GGACCGGTAAGCTTCGAGG 59.859 63.158 7.34 7.37 0.00 4.63
43 44 1.141234 GGGACCGGTAAGCTTCGAG 59.859 63.158 7.34 0.00 0.00 4.04
44 45 2.703798 CGGGACCGGTAAGCTTCGA 61.704 63.158 7.34 0.00 35.56 3.71
45 46 2.202703 CGGGACCGGTAAGCTTCG 60.203 66.667 7.34 0.40 35.56 3.79
46 47 2.510918 GCGGGACCGGTAAGCTTC 60.511 66.667 7.34 0.00 40.19 3.86
47 48 4.446413 CGCGGGACCGGTAAGCTT 62.446 66.667 21.07 3.48 40.19 3.74
50 51 4.524318 ATGCGCGGGACCGGTAAG 62.524 66.667 7.34 2.51 40.19 2.34
56 57 4.256090 GAATGCATGCGCGGGACC 62.256 66.667 14.09 0.00 42.97 4.46
63 64 1.283793 GAATCCCCGAATGCATGCG 59.716 57.895 20.74 20.74 0.00 4.73
144 541 8.592809 ACAAGATGATTAATCTCTATCTCCCAC 58.407 37.037 16.24 0.00 45.37 4.61
196 610 1.645034 CTACATCCAGGAGCACGTTG 58.355 55.000 0.00 0.00 0.00 4.10
204 618 1.195115 GGTGTCAGCTACATCCAGGA 58.805 55.000 0.00 0.00 41.10 3.86
225 639 3.564027 GCGCGAGGTGGTGTATGC 61.564 66.667 12.10 0.00 0.00 3.14
239 653 1.092921 TAATTCACCATGTCGGGCGC 61.093 55.000 0.00 0.00 40.22 6.53
263 677 7.235606 AGTTAGCCTAATCTAGCAATACATGGA 59.764 37.037 0.00 0.00 0.00 3.41
274 688 9.429359 CAATTGTCCATAGTTAGCCTAATCTAG 57.571 37.037 0.00 0.00 0.00 2.43
326 740 7.401484 ACGCAAAACGATTTATGTTTTCAAT 57.599 28.000 1.18 0.00 45.11 2.57
452 866 6.993786 TGGCGTTTAATTGAGATGTATCAA 57.006 33.333 0.00 0.00 43.04 2.57
568 982 4.347453 CTGTTGCTGTTGCCGCCC 62.347 66.667 0.00 0.00 38.71 6.13
588 1002 2.030805 TCTCGTCCGATCTACATGCATG 60.031 50.000 25.09 25.09 0.00 4.06
589 1003 2.230660 TCTCGTCCGATCTACATGCAT 58.769 47.619 0.00 0.00 0.00 3.96
590 1004 1.675552 TCTCGTCCGATCTACATGCA 58.324 50.000 0.00 0.00 0.00 3.96
591 1005 2.605823 CCTTCTCGTCCGATCTACATGC 60.606 54.545 0.00 0.00 0.00 4.06
609 1023 1.988406 GCGGTCCTCTACCCACCTT 60.988 63.158 0.00 0.00 46.62 3.50
753 1167 3.381045 TCGTCTTTACAACTGTGCTCTG 58.619 45.455 0.00 0.00 0.00 3.35
754 1168 3.553096 CCTCGTCTTTACAACTGTGCTCT 60.553 47.826 0.00 0.00 0.00 4.09
828 1242 4.143263 GCCAAAGAAGCATCGACATTTTTG 60.143 41.667 0.00 0.00 0.00 2.44
873 1287 4.189231 GAGGCGCTTAAATAGGAGTGAAA 58.811 43.478 7.64 0.00 0.00 2.69
891 1305 1.552792 GCTAGATACATCAGGGGAGGC 59.447 57.143 0.00 0.00 0.00 4.70
903 1317 9.732130 ATGGAAGGAATTTAATGAGCTAGATAC 57.268 33.333 0.00 0.00 0.00 2.24
923 1337 3.457234 TCGCTGTATGCAACTATGGAAG 58.543 45.455 0.00 0.00 43.06 3.46
1001 1425 1.550130 CCCCGGTGGAAGCTCTAACA 61.550 60.000 0.00 0.00 35.39 2.41
1152 1576 1.076485 CTCCCCCATCTTGGCCTTG 60.076 63.158 3.32 0.00 35.79 3.61
1173 1597 3.644265 TCTGGCAGTAAAAGTACCACTCA 59.356 43.478 15.27 0.00 0.00 3.41
1275 1699 2.936993 GCAATGTGGGTTGACGATCTCT 60.937 50.000 0.00 0.00 0.00 3.10
1311 1735 2.165030 CACCAATGTCTTCTTCATGCCC 59.835 50.000 0.00 0.00 0.00 5.36
1515 1945 0.874607 GTATGGACGGACGACCATGC 60.875 60.000 29.30 25.76 46.67 4.06
1591 2021 4.096382 GCAAACCACATACTCCTACCAATG 59.904 45.833 0.00 0.00 0.00 2.82
1592 2022 4.263727 TGCAAACCACATACTCCTACCAAT 60.264 41.667 0.00 0.00 0.00 3.16
1645 2486 2.183478 TGTGACACCATGGATGACAC 57.817 50.000 26.55 26.55 41.28 3.67
1683 2524 1.227823 CTGGTCGTTGTTGCCAGGA 60.228 57.895 0.00 0.00 44.36 3.86
1686 2527 2.203280 CCCTGGTCGTTGTTGCCA 60.203 61.111 0.00 0.00 0.00 4.92
1750 2591 1.002624 AACATGCCCCACCTGTACG 60.003 57.895 0.00 0.00 0.00 3.67
1757 2598 2.200373 AGTACTTCAACATGCCCCAC 57.800 50.000 0.00 0.00 0.00 4.61
1807 2648 7.645340 GGATGATTAATTAATGCACAGACACAC 59.355 37.037 15.39 4.18 0.00 3.82
1813 2654 8.789762 TCTGATGGATGATTAATTAATGCACAG 58.210 33.333 15.39 12.55 0.00 3.66
1897 2742 3.819368 TGCAAACTCTCTTGGAATCACA 58.181 40.909 0.00 0.00 0.00 3.58
1917 2803 2.543802 CCAGATGAGCCAGCGCATG 61.544 63.158 13.73 4.88 36.63 4.06
1923 2809 2.119655 GGCAAGCCAGATGAGCCAG 61.120 63.158 6.14 0.00 44.59 4.85
1930 2816 0.990374 ACAAGAGAGGCAAGCCAGAT 59.010 50.000 14.40 0.00 38.92 2.90
1932 2818 1.584380 GCACAAGAGAGGCAAGCCAG 61.584 60.000 14.40 0.00 38.92 4.85
1967 2856 2.675844 GTGCATGTACAAGCCGATACAA 59.324 45.455 19.55 0.00 35.05 2.41
1995 2884 7.155328 GCAAATGTAGCTAGATATACACCAGT 58.845 38.462 3.44 0.00 34.88 4.00
2006 2895 7.921786 AGTTTACAATGCAAATGTAGCTAGA 57.078 32.000 13.43 0.00 34.92 2.43
2092 2991 3.564235 TGCATTCAGTCAAGCATTCAC 57.436 42.857 0.00 0.00 31.05 3.18
2099 2998 5.723492 TCACGATAATGCATTCAGTCAAG 57.277 39.130 16.86 8.11 0.00 3.02
2106 3013 9.449550 TGTAATCAAATTCACGATAATGCATTC 57.550 29.630 16.86 1.10 0.00 2.67
2638 3545 1.881973 GATGTGTGTGCATGTGGTCTT 59.118 47.619 0.00 0.00 0.00 3.01
2639 3546 1.527034 GATGTGTGTGCATGTGGTCT 58.473 50.000 0.00 0.00 0.00 3.85
2640 3547 0.166597 CGATGTGTGTGCATGTGGTC 59.833 55.000 0.00 0.00 0.00 4.02
2641 3548 0.534877 ACGATGTGTGTGCATGTGGT 60.535 50.000 0.00 0.00 0.00 4.16
2642 3549 1.437625 TACGATGTGTGTGCATGTGG 58.562 50.000 0.00 0.00 0.00 4.17
2647 3554 2.760634 AGGAATACGATGTGTGTGCA 57.239 45.000 0.00 0.00 0.00 4.57
2648 3555 4.368315 TCATAGGAATACGATGTGTGTGC 58.632 43.478 0.00 0.00 0.00 4.57
2658 3565 3.819337 TCGGAGGTTCTCATAGGAATACG 59.181 47.826 0.00 0.00 31.08 3.06
2659 3566 5.986501 ATCGGAGGTTCTCATAGGAATAC 57.013 43.478 0.00 0.00 31.08 1.89
2660 3567 8.666129 AATTATCGGAGGTTCTCATAGGAATA 57.334 34.615 0.00 0.00 31.08 1.75
2661 3568 7.560796 AATTATCGGAGGTTCTCATAGGAAT 57.439 36.000 0.00 0.00 31.08 3.01
2662 3569 6.996180 AATTATCGGAGGTTCTCATAGGAA 57.004 37.500 0.00 0.00 31.08 3.36
2663 3570 6.553476 TCAAATTATCGGAGGTTCTCATAGGA 59.447 38.462 0.00 0.00 31.08 2.94
2664 3571 6.759272 TCAAATTATCGGAGGTTCTCATAGG 58.241 40.000 0.00 0.00 31.08 2.57
2665 3572 6.367422 GCTCAAATTATCGGAGGTTCTCATAG 59.633 42.308 0.00 0.00 31.08 2.23
2666 3573 6.223852 GCTCAAATTATCGGAGGTTCTCATA 58.776 40.000 0.00 0.00 31.08 2.15
2667 3574 5.059833 GCTCAAATTATCGGAGGTTCTCAT 58.940 41.667 0.00 0.00 31.08 2.90
2668 3575 4.442706 GCTCAAATTATCGGAGGTTCTCA 58.557 43.478 0.00 0.00 31.08 3.27
2669 3576 3.810386 GGCTCAAATTATCGGAGGTTCTC 59.190 47.826 0.00 0.00 0.00 2.87
2670 3577 3.741388 CGGCTCAAATTATCGGAGGTTCT 60.741 47.826 0.00 0.00 0.00 3.01
2671 3578 2.544267 CGGCTCAAATTATCGGAGGTTC 59.456 50.000 0.00 0.00 0.00 3.62
2672 3579 2.169769 TCGGCTCAAATTATCGGAGGTT 59.830 45.455 0.00 0.00 0.00 3.50
2673 3580 1.760613 TCGGCTCAAATTATCGGAGGT 59.239 47.619 0.00 0.00 0.00 3.85
2674 3581 2.135933 GTCGGCTCAAATTATCGGAGG 58.864 52.381 0.00 0.00 0.00 4.30
2675 3582 2.821546 TGTCGGCTCAAATTATCGGAG 58.178 47.619 0.00 0.00 0.00 4.63
2676 3583 2.971660 TGTCGGCTCAAATTATCGGA 57.028 45.000 0.00 0.00 0.00 4.55
2677 3584 3.194861 TCTTGTCGGCTCAAATTATCGG 58.805 45.455 0.00 0.00 0.00 4.18
2678 3585 4.766007 CATCTTGTCGGCTCAAATTATCG 58.234 43.478 0.00 0.00 0.00 2.92
2679 3586 4.531332 GCATCTTGTCGGCTCAAATTATC 58.469 43.478 0.00 0.00 0.00 1.75
2680 3587 3.002656 CGCATCTTGTCGGCTCAAATTAT 59.997 43.478 0.00 0.00 0.00 1.28
2681 3588 2.351418 CGCATCTTGTCGGCTCAAATTA 59.649 45.455 0.00 0.00 0.00 1.40
2682 3589 1.131126 CGCATCTTGTCGGCTCAAATT 59.869 47.619 0.00 0.00 0.00 1.82
2683 3590 0.729116 CGCATCTTGTCGGCTCAAAT 59.271 50.000 0.00 0.00 0.00 2.32
2684 3591 0.320334 TCGCATCTTGTCGGCTCAAA 60.320 50.000 0.00 0.00 0.00 2.69
2685 3592 0.320334 TTCGCATCTTGTCGGCTCAA 60.320 50.000 0.00 0.00 0.00 3.02
2686 3593 1.014044 GTTCGCATCTTGTCGGCTCA 61.014 55.000 0.00 0.00 0.00 4.26
2687 3594 1.696832 GGTTCGCATCTTGTCGGCTC 61.697 60.000 0.00 0.00 0.00 4.70
2688 3595 1.741770 GGTTCGCATCTTGTCGGCT 60.742 57.895 0.00 0.00 0.00 5.52
2689 3596 2.750888 GGGTTCGCATCTTGTCGGC 61.751 63.158 0.00 0.00 0.00 5.54
2690 3597 1.375396 TGGGTTCGCATCTTGTCGG 60.375 57.895 0.00 0.00 0.00 4.79
2691 3598 1.635663 GGTGGGTTCGCATCTTGTCG 61.636 60.000 0.00 0.00 0.00 4.35
2692 3599 0.321653 AGGTGGGTTCGCATCTTGTC 60.322 55.000 0.00 0.00 0.00 3.18
2693 3600 0.981183 TAGGTGGGTTCGCATCTTGT 59.019 50.000 7.87 0.00 0.00 3.16
2694 3601 1.942657 CATAGGTGGGTTCGCATCTTG 59.057 52.381 7.87 3.81 0.00 3.02
2695 3602 1.559682 ACATAGGTGGGTTCGCATCTT 59.440 47.619 7.87 0.00 0.00 2.40
2696 3603 1.204146 ACATAGGTGGGTTCGCATCT 58.796 50.000 7.70 7.70 0.00 2.90
2697 3604 2.902705 TACATAGGTGGGTTCGCATC 57.097 50.000 0.00 0.00 0.00 3.91
2698 3605 2.504175 ACTTACATAGGTGGGTTCGCAT 59.496 45.455 0.00 0.00 0.00 4.73
2699 3606 1.903860 ACTTACATAGGTGGGTTCGCA 59.096 47.619 0.00 0.00 0.00 5.10
2700 3607 2.093869 TCACTTACATAGGTGGGTTCGC 60.094 50.000 1.77 0.00 34.46 4.70
2701 3608 3.880047 TCACTTACATAGGTGGGTTCG 57.120 47.619 1.77 0.00 34.46 3.95
2702 3609 5.353394 TCATCACTTACATAGGTGGGTTC 57.647 43.478 1.77 0.00 34.46 3.62
2703 3610 5.772393 TTCATCACTTACATAGGTGGGTT 57.228 39.130 1.77 0.00 34.46 4.11
2704 3611 5.772393 TTTCATCACTTACATAGGTGGGT 57.228 39.130 1.77 0.00 34.46 4.51
2705 3612 8.156820 TGATATTTCATCACTTACATAGGTGGG 58.843 37.037 1.77 0.00 34.46 4.61
2706 3613 9.730705 ATGATATTTCATCACTTACATAGGTGG 57.269 33.333 1.77 0.00 38.18 4.61


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

AutoCloner maintained by Alex Coulton.