Multiple sequence alignment - TraesCS2B01G194000

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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 TraesCS2B01G194000 chr2B 100.000 2222 0 0 1 2222 170972801 170970580 0.000000e+00 4104.0
1 TraesCS2B01G194000 chr2B 100.000 179 0 0 2374 2552 170970428 170970250 5.260000e-87 331.0
2 TraesCS2B01G194000 chr2B 99.329 149 1 0 2073 2221 170970428 170970280 1.160000e-68 270.0
3 TraesCS2B01G194000 chr2B 99.329 149 1 0 2374 2522 170970729 170970581 1.160000e-68 270.0
4 TraesCS2B01G194000 chr2A 92.408 922 50 12 654 1568 120776777 120775869 0.000000e+00 1297.0
5 TraesCS2B01G194000 chr2A 93.285 551 11 6 1634 2158 579853504 579852954 0.000000e+00 789.0
6 TraesCS2B01G194000 chr2D 90.639 908 58 15 674 1568 118895530 118894637 0.000000e+00 1181.0
7 TraesCS2B01G194000 chr2D 88.519 601 59 8 21 616 308977753 308978348 0.000000e+00 719.0
8 TraesCS2B01G194000 chr2D 88.552 594 62 5 21 612 603205701 603206290 0.000000e+00 715.0
9 TraesCS2B01G194000 chr1B 99.492 590 3 0 1633 2222 323250021 323249432 0.000000e+00 1074.0
10 TraesCS2B01G194000 chr1B 98.876 178 2 0 2374 2551 323249581 323249404 4.100000e-83 318.0
11 TraesCS2B01G194000 chr1B 94.152 171 10 0 2051 2221 48757246 48757416 7.000000e-66 261.0
12 TraesCS2B01G194000 chr1B 92.655 177 13 0 2374 2550 48757268 48757444 3.260000e-64 255.0
13 TraesCS2B01G194000 chr5B 98.644 590 7 1 1633 2222 509507025 509506437 0.000000e+00 1044.0
14 TraesCS2B01G194000 chr5B 98.387 372 5 1 1631 2001 278461678 278461307 0.000000e+00 652.0
15 TraesCS2B01G194000 chr5B 97.207 179 5 0 2374 2552 509506586 509506408 1.150000e-78 303.0
16 TraesCS2B01G194000 chr1A 98.305 472 7 1 1634 2105 583921877 583921407 0.000000e+00 826.0
17 TraesCS2B01G194000 chr4D 91.002 589 47 5 32 616 19401505 19400919 0.000000e+00 789.0
18 TraesCS2B01G194000 chr4D 88.704 602 64 3 18 616 105141472 105140872 0.000000e+00 732.0
19 TraesCS2B01G194000 chr7D 90.232 604 52 6 18 616 574072090 574071489 0.000000e+00 782.0
20 TraesCS2B01G194000 chr7D 89.037 602 57 6 21 616 379845270 379844672 0.000000e+00 737.0
21 TraesCS2B01G194000 chr6D 89.333 600 58 5 21 616 386326137 386326734 0.000000e+00 749.0
22 TraesCS2B01G194000 chrUn 98.571 420 6 0 1803 2222 475390770 475391189 0.000000e+00 743.0
23 TraesCS2B01G194000 chrUn 97.207 179 5 0 2374 2552 449028801 449028623 1.150000e-78 303.0
24 TraesCS2B01G194000 chrUn 97.207 179 5 0 2374 2552 475391040 475391218 1.150000e-78 303.0
25 TraesCS2B01G194000 chrUn 98.675 151 2 0 2072 2222 449028802 449028652 4.190000e-68 268.0
26 TraesCS2B01G194000 chr3D 89.167 600 58 6 21 616 20755160 20754564 0.000000e+00 741.0
27 TraesCS2B01G194000 chr3D 76.101 318 45 22 1925 2221 569199286 569199593 1.230000e-28 137.0
28 TraesCS2B01G194000 chr6B 88.226 603 63 6 19 616 491951713 491952312 0.000000e+00 713.0
29 TraesCS2B01G194000 chr6B 98.343 362 5 1 1634 1994 184166558 184166197 3.580000e-178 634.0
30 TraesCS2B01G194000 chr7B 98.638 367 4 1 1632 1998 339668187 339667822 0.000000e+00 649.0
31 TraesCS2B01G194000 chr7B 98.171 164 3 0 2389 2552 339667316 339667153 1.160000e-73 287.0
32 TraesCS2B01G194000 chr7B 99.259 135 1 0 2088 2222 339667316 339667182 7.050000e-61 244.0
33 TraesCS2B01G194000 chr6A 98.873 355 4 0 1633 1987 104111044 104110690 3.580000e-178 634.0
34 TraesCS2B01G194000 chr6A 96.711 152 5 0 2401 2552 104110292 104110141 1.170000e-63 254.0
35 TraesCS2B01G194000 chr6A 97.561 123 3 0 2100 2222 104110292 104110170 7.150000e-51 211.0
36 TraesCS2B01G194000 chr3B 98.522 203 3 0 2020 2222 663521244 663521446 2.410000e-95 359.0
37 TraesCS2B01G194000 chr3B 97.207 179 5 0 2374 2552 663521297 663521475 1.150000e-78 303.0
38 TraesCS2B01G194000 chr3B 100.000 29 0 0 4 32 498059718 498059746 1.000000e-03 54.7


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 TraesCS2B01G194000 chr2B 170970250 170972801 2551 True 1243.750000 4104 99.664500 1 2552 4 chr2B.!!$R1 2551
1 TraesCS2B01G194000 chr2A 120775869 120776777 908 True 1297.000000 1297 92.408000 654 1568 1 chr2A.!!$R1 914
2 TraesCS2B01G194000 chr2A 579852954 579853504 550 True 789.000000 789 93.285000 1634 2158 1 chr2A.!!$R2 524
3 TraesCS2B01G194000 chr2D 118894637 118895530 893 True 1181.000000 1181 90.639000 674 1568 1 chr2D.!!$R1 894
4 TraesCS2B01G194000 chr2D 308977753 308978348 595 False 719.000000 719 88.519000 21 616 1 chr2D.!!$F1 595
5 TraesCS2B01G194000 chr2D 603205701 603206290 589 False 715.000000 715 88.552000 21 612 1 chr2D.!!$F2 591
6 TraesCS2B01G194000 chr1B 323249404 323250021 617 True 696.000000 1074 99.184000 1633 2551 2 chr1B.!!$R1 918
7 TraesCS2B01G194000 chr5B 509506408 509507025 617 True 673.500000 1044 97.925500 1633 2552 2 chr5B.!!$R2 919
8 TraesCS2B01G194000 chr4D 19400919 19401505 586 True 789.000000 789 91.002000 32 616 1 chr4D.!!$R1 584
9 TraesCS2B01G194000 chr4D 105140872 105141472 600 True 732.000000 732 88.704000 18 616 1 chr4D.!!$R2 598
10 TraesCS2B01G194000 chr7D 574071489 574072090 601 True 782.000000 782 90.232000 18 616 1 chr7D.!!$R2 598
11 TraesCS2B01G194000 chr7D 379844672 379845270 598 True 737.000000 737 89.037000 21 616 1 chr7D.!!$R1 595
12 TraesCS2B01G194000 chr6D 386326137 386326734 597 False 749.000000 749 89.333000 21 616 1 chr6D.!!$F1 595
13 TraesCS2B01G194000 chr3D 20754564 20755160 596 True 741.000000 741 89.167000 21 616 1 chr3D.!!$R1 595
14 TraesCS2B01G194000 chr6B 491951713 491952312 599 False 713.000000 713 88.226000 19 616 1 chr6B.!!$F1 597
15 TraesCS2B01G194000 chr7B 339667153 339668187 1034 True 393.333333 649 98.689333 1632 2552 3 chr7B.!!$R1 920
16 TraesCS2B01G194000 chr6A 104110141 104111044 903 True 366.333333 634 97.715000 1633 2552 3 chr6A.!!$R1 919

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
633 644 0.248949 GTCTAATGGACTCCGCCGAC 60.249 60.0 0.0 0.0 41.46 4.79 F
648 659 0.320073 CCGACGAGTTTGCCAAGGTA 60.320 55.0 0.0 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1518 0.966920 ATCCTGAACACGACCGTCTT 59.033 50.000 0.0 0.0 0.0 3.01 R
1576 1605 1.001406 GGATAGATGGAGAGCAACCCG 59.999 57.143 0.0 0.0 0.0 5.28 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
136 137 2.126071 CGTCCGCTGTTCGTCCAT 60.126 61.111 0.00 0.00 36.19 3.41
282 285 1.002134 CCAACATCAACCCTCGCCT 60.002 57.895 0.00 0.00 0.00 5.52
495 506 3.147595 CGGCCAGATCCTCACCGA 61.148 66.667 2.24 0.00 46.71 4.69
528 539 4.096003 CCGGCCCACTTGTCGGAT 62.096 66.667 0.00 0.00 44.69 4.18
555 566 2.423898 GGCAGCTAGCTGGTCCGTA 61.424 63.158 38.52 0.00 43.77 4.02
604 615 4.946266 TTCGTCGACGCCCGCAAA 62.946 61.111 32.19 17.52 39.60 3.68
613 624 3.959975 GCCCGCAAACTGTTCGCA 61.960 61.111 4.17 0.00 0.00 5.10
631 642 4.732106 GTCTAATGGACTCCGCCG 57.268 61.111 0.00 0.00 41.46 6.46
632 643 2.112898 GTCTAATGGACTCCGCCGA 58.887 57.895 0.00 0.00 41.46 5.54
633 644 0.248949 GTCTAATGGACTCCGCCGAC 60.249 60.000 0.00 0.00 41.46 4.79
634 645 1.299165 CTAATGGACTCCGCCGACG 60.299 63.158 0.00 0.00 39.67 5.12
635 646 1.721664 CTAATGGACTCCGCCGACGA 61.722 60.000 0.00 0.00 43.93 4.20
636 647 1.721664 TAATGGACTCCGCCGACGAG 61.722 60.000 0.00 0.00 43.93 4.18
638 649 3.745803 GGACTCCGCCGACGAGTT 61.746 66.667 0.00 0.00 43.93 3.01
639 650 2.257676 GACTCCGCCGACGAGTTT 59.742 61.111 0.00 0.00 43.93 2.66
640 651 2.049433 ACTCCGCCGACGAGTTTG 60.049 61.111 0.00 0.00 43.93 2.93
641 652 3.479269 CTCCGCCGACGAGTTTGC 61.479 66.667 0.00 0.00 43.93 3.68
644 655 3.342627 CGCCGACGAGTTTGCCAA 61.343 61.111 0.00 0.00 43.93 4.52
645 656 2.556287 GCCGACGAGTTTGCCAAG 59.444 61.111 0.00 0.00 0.00 3.61
646 657 2.966309 GCCGACGAGTTTGCCAAGG 61.966 63.158 0.00 0.00 0.00 3.61
647 658 1.597027 CCGACGAGTTTGCCAAGGT 60.597 57.895 0.00 0.00 0.00 3.50
648 659 0.320073 CCGACGAGTTTGCCAAGGTA 60.320 55.000 0.00 0.00 0.00 3.08
649 660 0.788391 CGACGAGTTTGCCAAGGTAC 59.212 55.000 0.00 0.00 0.00 3.34
650 661 1.870580 CGACGAGTTTGCCAAGGTACA 60.871 52.381 0.00 0.00 0.00 2.90
651 662 2.215196 GACGAGTTTGCCAAGGTACAA 58.785 47.619 0.00 0.00 0.00 2.41
652 663 2.218603 ACGAGTTTGCCAAGGTACAAG 58.781 47.619 0.00 0.00 0.00 3.16
663 674 1.280457 AGGTACAAGGCCCTCTTCTG 58.720 55.000 0.00 0.00 32.41 3.02
678 689 1.617018 TTCTGGGAGATGGGACGCAG 61.617 60.000 0.00 0.00 44.54 5.18
681 692 2.764128 GGAGATGGGACGCAGGGA 60.764 66.667 0.00 0.00 0.00 4.20
682 693 2.143419 GGAGATGGGACGCAGGGAT 61.143 63.158 0.00 0.00 0.00 3.85
733 745 2.032634 CCGGCGCTACAAAGAAGCA 61.033 57.895 7.64 0.00 40.08 3.91
751 763 3.964909 AGCAAATCTTCACGGACAAAAC 58.035 40.909 0.00 0.00 0.00 2.43
765 777 1.238439 CAAAACACATCGAGCTGGGT 58.762 50.000 0.00 0.00 33.04 4.51
832 844 2.654912 GCCACTCGAACGACAACGG 61.655 63.158 0.00 0.00 44.46 4.44
840 852 4.903010 ACGACAACGGGCGCAACT 62.903 61.111 10.83 0.00 44.46 3.16
869 881 4.389992 CCACGCAGTATATATTTGCTCTGG 59.610 45.833 15.78 15.09 41.61 3.86
999 1025 2.103042 GCTTGTTGCGCCGAGAGAT 61.103 57.895 4.18 0.00 0.00 2.75
1012 1038 2.830923 CCGAGAGATATGGCCTTCTCAT 59.169 50.000 23.84 13.89 40.69 2.90
1054 1080 4.671590 TCGCCCTCGTCCTGTCCA 62.672 66.667 0.00 0.00 36.96 4.02
1058 1084 2.283966 CCTCGTCCTGTCCACCCT 60.284 66.667 0.00 0.00 0.00 4.34
1194 1223 3.670377 GGCAACACCACCTTCGGC 61.670 66.667 0.00 0.00 38.86 5.54
1227 1256 4.854784 GACGATGAGCTCCGCGCA 62.855 66.667 20.84 0.00 43.16 6.09
1255 1284 2.675423 CTGGGTCCGACCTCGTCA 60.675 66.667 17.27 5.86 38.64 4.35
1316 1345 2.184579 GAGCTACCTGTCCACCGC 59.815 66.667 0.00 0.00 0.00 5.68
1320 1349 2.524640 TACCTGTCCACCGCCACA 60.525 61.111 0.00 0.00 0.00 4.17
1512 1541 0.100682 CGGTCGTGTTCAGGATCGAT 59.899 55.000 18.95 0.00 39.04 3.59
1552 1581 1.400530 CCCCGGCCACTACTTCTAGG 61.401 65.000 2.24 0.00 0.00 3.02
1553 1582 1.442148 CCGGCCACTACTTCTAGGC 59.558 63.158 2.24 0.00 46.28 3.93
1564 1593 6.369065 CCACTACTTCTAGGCAAAAAGTACTG 59.631 42.308 0.00 0.00 35.08 2.74
1568 1597 6.174049 ACTTCTAGGCAAAAAGTACTGGATC 58.826 40.000 0.00 0.00 31.68 3.36
1569 1598 5.099042 TCTAGGCAAAAAGTACTGGATCC 57.901 43.478 4.20 4.20 0.00 3.36
1570 1599 2.711542 AGGCAAAAAGTACTGGATCCG 58.288 47.619 7.39 4.62 0.00 4.18
1571 1600 2.304761 AGGCAAAAAGTACTGGATCCGA 59.695 45.455 7.39 0.00 0.00 4.55
1572 1601 3.054361 AGGCAAAAAGTACTGGATCCGAT 60.054 43.478 7.39 0.00 0.00 4.18
1573 1602 3.312697 GGCAAAAAGTACTGGATCCGATC 59.687 47.826 7.39 0.00 0.00 3.69
1574 1603 3.001330 GCAAAAAGTACTGGATCCGATCG 59.999 47.826 8.51 8.51 0.00 3.69
1575 1604 4.181578 CAAAAAGTACTGGATCCGATCGT 58.818 43.478 15.09 4.25 0.00 3.73
1576 1605 3.712091 AAAGTACTGGATCCGATCGTC 57.288 47.619 15.09 5.74 0.00 4.20
1577 1606 1.227639 AGTACTGGATCCGATCGTCG 58.772 55.000 15.09 0.00 40.07 5.12
1586 1615 2.490217 CGATCGTCGGGTTGCTCT 59.510 61.111 7.03 0.00 36.00 4.09
1587 1616 1.586564 CGATCGTCGGGTTGCTCTC 60.587 63.158 7.03 0.00 36.00 3.20
1588 1617 1.227002 GATCGTCGGGTTGCTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
1589 1618 1.945354 GATCGTCGGGTTGCTCTCCA 61.945 60.000 0.00 0.00 0.00 3.86
1590 1619 1.330655 ATCGTCGGGTTGCTCTCCAT 61.331 55.000 0.00 0.00 0.00 3.41
1591 1620 1.519455 CGTCGGGTTGCTCTCCATC 60.519 63.158 0.00 0.00 0.00 3.51
1592 1621 1.901085 GTCGGGTTGCTCTCCATCT 59.099 57.895 0.00 0.00 0.00 2.90
1593 1622 1.112113 GTCGGGTTGCTCTCCATCTA 58.888 55.000 0.00 0.00 0.00 1.98
1594 1623 1.689273 GTCGGGTTGCTCTCCATCTAT 59.311 52.381 0.00 0.00 0.00 1.98
1595 1624 1.964223 TCGGGTTGCTCTCCATCTATC 59.036 52.381 0.00 0.00 0.00 2.08
1596 1625 1.001406 CGGGTTGCTCTCCATCTATCC 59.999 57.143 0.00 0.00 0.00 2.59
1597 1626 1.001406 GGGTTGCTCTCCATCTATCCG 59.999 57.143 0.00 0.00 0.00 4.18
1598 1627 1.964223 GGTTGCTCTCCATCTATCCGA 59.036 52.381 0.00 0.00 0.00 4.55
1599 1628 2.564947 GGTTGCTCTCCATCTATCCGAT 59.435 50.000 0.00 0.00 0.00 4.18
1600 1629 3.367910 GGTTGCTCTCCATCTATCCGATC 60.368 52.174 0.00 0.00 0.00 3.69
1601 1630 3.448093 TGCTCTCCATCTATCCGATCT 57.552 47.619 0.00 0.00 0.00 2.75
1602 1631 3.772387 TGCTCTCCATCTATCCGATCTT 58.228 45.455 0.00 0.00 0.00 2.40
1603 1632 3.761218 TGCTCTCCATCTATCCGATCTTC 59.239 47.826 0.00 0.00 0.00 2.87
1604 1633 4.016444 GCTCTCCATCTATCCGATCTTCT 58.984 47.826 0.00 0.00 0.00 2.85
1605 1634 4.096382 GCTCTCCATCTATCCGATCTTCTC 59.904 50.000 0.00 0.00 0.00 2.87
1904 1936 1.305129 CCATGCAATCCCACACCCA 60.305 57.895 0.00 0.00 0.00 4.51
2213 2661 3.479269 CTGTTCGCTTCGCCCGAC 61.479 66.667 0.00 0.00 34.01 4.79
2220 2668 2.356553 CTTCGCCCGACGGTCAAA 60.357 61.111 13.94 2.64 43.89 2.69
2221 2669 2.662527 TTCGCCCGACGGTCAAAC 60.663 61.111 13.94 0.00 43.89 2.93
2434 2882 4.838486 CGTCGCTGTCGGCTCCTC 62.838 72.222 1.37 0.00 38.35 3.71
2435 2883 4.838486 GTCGCTGTCGGCTCCTCG 62.838 72.222 1.37 0.00 37.34 4.63
2439 2887 4.504916 CTGTCGGCTCCTCGGCTG 62.505 72.222 0.00 0.00 39.72 4.85
2453 2901 4.266070 GCTGCCATGCCGATGCTG 62.266 66.667 0.00 0.00 38.71 4.41
2454 2902 4.266070 CTGCCATGCCGATGCTGC 62.266 66.667 0.00 0.00 38.71 5.25
2457 2905 3.896133 CCATGCCGATGCTGCCAC 61.896 66.667 0.00 0.00 38.71 5.01
2458 2906 3.896133 CATGCCGATGCTGCCACC 61.896 66.667 0.00 0.00 38.71 4.61
2522 2970 1.740296 CTTCGCCCGACGGTCAAAT 60.740 57.895 13.94 0.00 43.89 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
79 80 2.123683 TTGGGCCGCCTTTTGTGA 60.124 55.556 9.86 0.00 0.00 3.58
101 102 3.025743 CGCGTCCGTTTGTGTCGA 61.026 61.111 0.00 0.00 0.00 4.20
127 128 1.952102 TAGGTCGCCCATGGACGAAC 61.952 60.000 28.85 28.85 46.19 3.95
136 137 1.306654 ACCAGGAATAGGTCGCCCA 60.307 57.895 0.00 0.00 32.90 5.36
270 273 3.706373 GAGGCAGGCGAGGGTTGA 61.706 66.667 0.00 0.00 0.00 3.18
282 285 2.670592 TCGACGACGAAGGAGGCA 60.671 61.111 7.68 0.00 45.74 4.75
306 309 2.126110 CGCCGACAAAAATGGGCC 60.126 61.111 0.00 0.00 40.18 5.80
536 547 2.856039 TACGGACCAGCTAGCTGCCT 62.856 60.000 34.82 23.11 44.23 4.75
614 625 0.248949 GTCGGCGGAGTCCATTAGAC 60.249 60.000 10.49 8.91 46.71 2.59
615 626 1.721664 CGTCGGCGGAGTCCATTAGA 61.722 60.000 10.49 0.00 0.00 2.10
616 627 1.299165 CGTCGGCGGAGTCCATTAG 60.299 63.158 10.49 0.00 0.00 1.73
617 628 1.721664 CTCGTCGGCGGAGTCCATTA 61.722 60.000 10.62 0.00 38.89 1.90
618 629 3.064987 CTCGTCGGCGGAGTCCATT 62.065 63.158 10.62 0.00 38.89 3.16
619 630 3.518998 CTCGTCGGCGGAGTCCAT 61.519 66.667 10.62 0.00 38.89 3.41
621 632 3.278592 AAACTCGTCGGCGGAGTCC 62.279 63.158 17.09 0.00 38.89 3.85
622 633 2.087009 CAAACTCGTCGGCGGAGTC 61.087 63.158 17.09 1.55 38.89 3.36
623 634 2.049433 CAAACTCGTCGGCGGAGT 60.049 61.111 10.62 12.16 38.89 3.85
624 635 3.479269 GCAAACTCGTCGGCGGAG 61.479 66.667 10.62 9.49 38.89 4.63
627 638 3.295228 CTTGGCAAACTCGTCGGCG 62.295 63.158 1.15 1.15 39.92 6.46
628 639 2.556287 CTTGGCAAACTCGTCGGC 59.444 61.111 0.00 0.00 0.00 5.54
629 640 0.320073 TACCTTGGCAAACTCGTCGG 60.320 55.000 0.00 0.00 0.00 4.79
630 641 0.788391 GTACCTTGGCAAACTCGTCG 59.212 55.000 0.00 0.00 0.00 5.12
631 642 1.873698 TGTACCTTGGCAAACTCGTC 58.126 50.000 0.00 0.00 0.00 4.20
632 643 2.218603 CTTGTACCTTGGCAAACTCGT 58.781 47.619 0.00 0.00 0.00 4.18
633 644 1.535462 CCTTGTACCTTGGCAAACTCG 59.465 52.381 0.00 0.00 0.00 4.18
634 645 1.269723 GCCTTGTACCTTGGCAAACTC 59.730 52.381 13.69 0.00 45.46 3.01
635 646 1.328279 GCCTTGTACCTTGGCAAACT 58.672 50.000 13.69 0.00 45.46 2.66
636 647 3.886044 GCCTTGTACCTTGGCAAAC 57.114 52.632 13.69 0.00 45.46 2.93
640 651 1.378646 GAGGGCCTTGTACCTTGGC 60.379 63.158 7.89 11.08 45.42 4.52
641 652 0.698818 AAGAGGGCCTTGTACCTTGG 59.301 55.000 7.89 0.00 37.18 3.61
642 653 1.630878 AGAAGAGGGCCTTGTACCTTG 59.369 52.381 7.89 0.00 37.18 3.61
643 654 1.630878 CAGAAGAGGGCCTTGTACCTT 59.369 52.381 7.89 5.70 37.18 3.50
644 655 1.280457 CAGAAGAGGGCCTTGTACCT 58.720 55.000 7.89 0.00 40.54 3.08
645 656 0.253327 CCAGAAGAGGGCCTTGTACC 59.747 60.000 7.89 0.00 34.68 3.34
646 657 0.253327 CCCAGAAGAGGGCCTTGTAC 59.747 60.000 7.89 0.00 43.10 2.90
647 658 2.696864 CCCAGAAGAGGGCCTTGTA 58.303 57.895 7.89 0.00 43.10 2.41
648 659 3.500635 CCCAGAAGAGGGCCTTGT 58.499 61.111 7.89 0.00 43.10 3.16
663 674 3.866582 CCCTGCGTCCCATCTCCC 61.867 72.222 0.00 0.00 0.00 4.30
714 726 2.033194 GCTTCTTTGTAGCGCCGGT 61.033 57.895 2.29 0.00 0.00 5.28
733 745 4.974368 TGTGTTTTGTCCGTGAAGATTT 57.026 36.364 0.00 0.00 0.00 2.17
751 763 0.531532 GATCCACCCAGCTCGATGTG 60.532 60.000 0.00 0.00 0.00 3.21
783 795 4.379936 GACATATGTCACGTACGTACGGC 61.380 52.174 41.07 31.38 43.31 5.68
827 839 4.025401 GTGGAGTTGCGCCCGTTG 62.025 66.667 4.18 0.00 0.00 4.10
840 852 2.385135 TATATACTGCGTGGGGTGGA 57.615 50.000 0.00 0.00 0.00 4.02
886 898 1.980765 AGAGAGTTGAGATGGGTGCAA 59.019 47.619 0.00 0.00 0.00 4.08
992 1018 3.427368 CGATGAGAAGGCCATATCTCTCG 60.427 52.174 24.78 24.00 42.07 4.04
994 1020 3.505386 ACGATGAGAAGGCCATATCTCT 58.495 45.455 24.78 15.13 42.07 3.10
999 1025 1.399714 ACGACGATGAGAAGGCCATA 58.600 50.000 5.01 0.00 0.00 2.74
1035 1061 3.371063 GACAGGACGAGGGCGACA 61.371 66.667 0.00 0.00 41.64 4.35
1255 1284 0.998145 AAGAAGCCCTGGAATCTGCT 59.002 50.000 0.00 0.00 35.08 4.24
1320 1349 4.657824 CCGGCGGTGAACACGAGT 62.658 66.667 19.97 0.00 0.00 4.18
1428 1457 2.597903 GCCATCCTGAACTCCCCC 59.402 66.667 0.00 0.00 0.00 5.40
1458 1487 1.375908 GCTGACGACCTTCATGGCA 60.376 57.895 0.00 0.00 40.22 4.92
1460 1489 2.456119 GCGCTGACGACCTTCATGG 61.456 63.158 0.00 0.00 43.93 3.66
1489 1518 0.966920 ATCCTGAACACGACCGTCTT 59.033 50.000 0.00 0.00 0.00 3.01
1512 1541 2.343758 GGCAGGAGCACGAACAGA 59.656 61.111 0.00 0.00 44.61 3.41
1552 1581 3.001330 CGATCGGATCCAGTACTTTTTGC 59.999 47.826 13.41 0.00 0.00 3.68
1553 1582 4.181578 ACGATCGGATCCAGTACTTTTTG 58.818 43.478 20.98 0.00 0.00 2.44
1554 1583 4.430908 GACGATCGGATCCAGTACTTTTT 58.569 43.478 20.98 0.00 0.00 1.94
1569 1598 1.586564 GAGAGCAACCCGACGATCG 60.587 63.158 14.88 14.88 40.07 3.69
1570 1599 1.227002 GGAGAGCAACCCGACGATC 60.227 63.158 0.00 0.00 0.00 3.69
1571 1600 1.330655 ATGGAGAGCAACCCGACGAT 61.331 55.000 0.00 0.00 0.00 3.73
1572 1601 1.945354 GATGGAGAGCAACCCGACGA 61.945 60.000 0.00 0.00 0.00 4.20
1573 1602 1.519455 GATGGAGAGCAACCCGACG 60.519 63.158 0.00 0.00 0.00 5.12
1574 1603 1.112113 TAGATGGAGAGCAACCCGAC 58.888 55.000 0.00 0.00 0.00 4.79
1575 1604 1.964223 GATAGATGGAGAGCAACCCGA 59.036 52.381 0.00 0.00 0.00 5.14
1576 1605 1.001406 GGATAGATGGAGAGCAACCCG 59.999 57.143 0.00 0.00 0.00 5.28
1577 1606 1.001406 CGGATAGATGGAGAGCAACCC 59.999 57.143 0.00 0.00 0.00 4.11
1578 1607 1.964223 TCGGATAGATGGAGAGCAACC 59.036 52.381 0.00 0.00 0.00 3.77
1579 1608 3.509575 AGATCGGATAGATGGAGAGCAAC 59.490 47.826 0.00 0.00 40.26 4.17
1580 1609 3.772387 AGATCGGATAGATGGAGAGCAA 58.228 45.455 0.00 0.00 40.26 3.91
1581 1610 3.448093 AGATCGGATAGATGGAGAGCA 57.552 47.619 0.00 0.00 40.26 4.26
1582 1611 4.016444 AGAAGATCGGATAGATGGAGAGC 58.984 47.826 0.00 0.00 40.26 4.09
1583 1612 5.818136 GAGAAGATCGGATAGATGGAGAG 57.182 47.826 0.00 0.00 40.26 3.20
1614 1643 8.723311 CGGAAGTGTAAATGGTTTATGTAAGAA 58.277 33.333 0.00 0.00 0.00 2.52
1615 1644 7.148373 GCGGAAGTGTAAATGGTTTATGTAAGA 60.148 37.037 0.00 0.00 0.00 2.10
1616 1645 6.964934 GCGGAAGTGTAAATGGTTTATGTAAG 59.035 38.462 0.00 0.00 0.00 2.34
1617 1646 6.655848 AGCGGAAGTGTAAATGGTTTATGTAA 59.344 34.615 0.00 0.00 0.00 2.41
1618 1647 6.174760 AGCGGAAGTGTAAATGGTTTATGTA 58.825 36.000 0.00 0.00 0.00 2.29
1619 1648 5.007682 AGCGGAAGTGTAAATGGTTTATGT 58.992 37.500 0.00 0.00 0.00 2.29
1620 1649 5.560966 AGCGGAAGTGTAAATGGTTTATG 57.439 39.130 0.00 0.00 0.00 1.90
1621 1650 5.163794 CGAAGCGGAAGTGTAAATGGTTTAT 60.164 40.000 0.00 0.00 0.00 1.40
1622 1651 4.152759 CGAAGCGGAAGTGTAAATGGTTTA 59.847 41.667 0.00 0.00 0.00 2.01
1623 1652 3.058501 CGAAGCGGAAGTGTAAATGGTTT 60.059 43.478 0.00 0.00 0.00 3.27
1624 1653 2.482721 CGAAGCGGAAGTGTAAATGGTT 59.517 45.455 0.00 0.00 0.00 3.67
1625 1654 2.073816 CGAAGCGGAAGTGTAAATGGT 58.926 47.619 0.00 0.00 0.00 3.55
1626 1655 2.806288 CGAAGCGGAAGTGTAAATGG 57.194 50.000 0.00 0.00 0.00 3.16
1889 1921 1.378382 CGATGGGTGTGGGATTGCA 60.378 57.895 0.00 0.00 0.00 4.08
2422 2870 4.504916 CAGCCGAGGAGCCGACAG 62.505 72.222 0.00 0.00 0.00 3.51
2436 2884 4.266070 CAGCATCGGCATGGCAGC 62.266 66.667 20.37 18.52 44.61 5.25
2437 2885 4.266070 GCAGCATCGGCATGGCAG 62.266 66.667 20.37 12.01 44.61 4.85
2440 2888 3.896133 GTGGCAGCATCGGCATGG 61.896 66.667 0.00 0.00 44.06 3.66
2441 2889 3.896133 GGTGGCAGCATCGGCATG 61.896 66.667 12.58 0.00 44.06 4.06
2504 2952 1.740296 ATTTGACCGTCGGGCGAAG 60.740 57.895 24.04 0.00 37.55 3.79
2505 2953 2.030401 CATTTGACCGTCGGGCGAA 61.030 57.895 22.29 22.29 44.77 4.70
2506 2954 2.433491 CATTTGACCGTCGGGCGA 60.433 61.111 17.28 10.25 44.77 5.54
2507 2955 4.160635 GCATTTGACCGTCGGGCG 62.161 66.667 17.28 0.02 40.95 6.13


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

AutoCloner maintained by Alex Coulton.