Multiple sequence alignment - TraesCS2D01G317600

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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 TraesCS2D01G317600 chr2D 100.000 5674 0 0 1717 7390 407207573 407201900 0.000000e+00 10479.0
1 TraesCS2D01G317600 chr2D 100.000 1465 0 0 1 1465 407209289 407207825 0.000000e+00 2706.0
2 TraesCS2D01G317600 chr2D 98.134 268 2 1 99 366 407207841 407208105 1.450000e-126 464.0
3 TraesCS2D01G317600 chr2D 98.134 268 2 1 1185 1449 407208924 407209191 1.450000e-126 464.0
4 TraesCS2D01G317600 chr2D 80.812 271 24 11 453 721 634261630 634261386 3.520000e-43 187.0
5 TraesCS2D01G317600 chr4D 99.280 5277 31 5 1717 6991 329014017 329019288 0.000000e+00 9527.0
6 TraesCS2D01G317600 chr4D 98.759 403 3 2 6989 7390 329019328 329019729 0.000000e+00 715.0
7 TraesCS2D01G317600 chr4D 98.904 365 2 1 98 462 329013994 329013632 0.000000e+00 651.0
8 TraesCS2D01G317600 chr4D 98.820 339 2 2 843 1181 329010336 329010672 2.950000e-168 603.0
9 TraesCS2D01G317600 chr4D 97.826 276 4 2 1185 1459 329013728 329014002 6.710000e-130 475.0
10 TraesCS2D01G317600 chr4D 98.134 268 5 0 455 722 329011075 329010808 1.120000e-127 468.0
11 TraesCS2D01G317600 chr4D 99.153 118 1 0 724 841 329010348 329010231 5.810000e-51 213.0
12 TraesCS2D01G317600 chr4B 93.641 2988 118 24 1741 4669 408960424 408963398 0.000000e+00 4399.0
13 TraesCS2D01G317600 chr4B 91.659 2218 76 46 4803 6990 408963647 408965785 0.000000e+00 2970.0
14 TraesCS2D01G317600 chr4B 97.270 403 11 0 320 722 408960122 408959720 0.000000e+00 684.0
15 TraesCS2D01G317600 chr4B 93.275 342 12 4 843 1181 408959244 408959577 1.850000e-135 494.0
16 TraesCS2D01G317600 chr4B 83.929 392 34 18 7003 7390 408968226 408968592 1.530000e-91 348.0
17 TraesCS2D01G317600 chr4B 94.702 151 7 1 177 326 408960306 408960156 4.460000e-57 233.0
18 TraesCS2D01G317600 chr4B 94.040 151 8 1 1225 1374 408960156 408960306 2.070000e-55 228.0
19 TraesCS2D01G317600 chr4B 93.443 122 4 2 724 841 408959256 408959135 2.120000e-40 178.0
20 TraesCS2D01G317600 chr4B 93.750 96 2 1 1 92 94946991 94947086 2.780000e-29 141.0
21 TraesCS2D01G317600 chr4B 95.745 47 2 0 1185 1231 408960076 408960122 7.950000e-10 76.8
22 TraesCS2D01G317600 chr4A 95.574 1717 32 7 3052 4740 141111930 141110230 0.000000e+00 2710.0
23 TraesCS2D01G317600 chr4A 91.029 1594 60 29 4738 6306 141109995 141108460 0.000000e+00 2074.0
24 TraesCS2D01G317600 chr4A 89.543 1138 46 30 1945 3055 141113091 141112000 0.000000e+00 1375.0
25 TraesCS2D01G317600 chr4A 91.655 719 26 15 6298 6990 141108425 141107715 0.000000e+00 965.0
26 TraesCS2D01G317600 chr4A 85.323 402 16 12 7010 7390 141107564 141107185 7.000000e-100 375.0
27 TraesCS2D01G317600 chr4A 91.176 136 11 1 320 455 671960146 671960012 4.550000e-42 183.0
28 TraesCS2D01G317600 chr4A 90.476 126 6 5 722 841 141118174 141118299 2.130000e-35 161.0
29 TraesCS2D01G317600 chr4A 94.048 84 5 0 639 722 671959677 671959594 2.160000e-25 128.0
30 TraesCS2D01G317600 chr4A 91.489 47 3 1 1185 1231 671960101 671960146 6.190000e-06 63.9
31 TraesCS2D01G317600 chr1B 96.825 1638 22 6 3126 4740 135935677 135934047 0.000000e+00 2710.0
32 TraesCS2D01G317600 chr1B 97.372 1408 25 4 1748 3144 135937273 135935867 0.000000e+00 2385.0
33 TraesCS2D01G317600 chr1B 94.035 1140 39 13 4739 5874 135933812 135932698 0.000000e+00 1701.0
34 TraesCS2D01G317600 chr1B 96.542 347 8 4 5971 6313 135932701 135932355 8.320000e-159 571.0
35 TraesCS2D01G317600 chr1B 94.690 339 7 3 843 1181 135938647 135938320 3.950000e-142 516.0
36 TraesCS2D01G317600 chr1B 98.897 272 1 2 7120 7390 135932359 135932089 1.110000e-132 484.0
37 TraesCS2D01G317600 chr1B 98.188 276 5 0 167 442 135937704 135937979 4.010000e-132 483.0
38 TraesCS2D01G317600 chr1B 98.500 200 3 0 1185 1384 135937903 135937704 3.280000e-93 353.0
39 TraesCS2D01G317600 chr1B 97.340 188 5 0 481 668 135937978 135938165 3.330000e-83 320.0
40 TraesCS2D01G317600 chr1B 84.229 279 23 9 453 722 29581496 29581230 1.230000e-62 252.0
41 TraesCS2D01G317600 chr1B 87.838 74 1 1 724 797 135938635 135938700 6.150000e-11 80.5
42 TraesCS2D01G317600 chr1B 100.000 43 0 0 799 841 135938758 135938716 6.150000e-11 80.5
43 TraesCS2D01G317600 chr7B 94.212 933 47 2 2187 3113 412539789 412540720 0.000000e+00 1417.0
44 TraesCS2D01G317600 chr7B 93.569 933 53 2 2187 3113 658771411 658772342 0.000000e+00 1384.0
45 TraesCS2D01G317600 chr7B 93.462 933 54 2 2187 3113 658519445 658520376 0.000000e+00 1378.0
46 TraesCS2D01G317600 chr7B 93.462 933 54 2 2187 3113 658644960 658645891 0.000000e+00 1378.0
47 TraesCS2D01G317600 chr7B 79.121 273 42 12 453 722 595525488 595525748 2.740000e-39 174.0
48 TraesCS2D01G317600 chrUn 93.140 933 56 3 2187 3113 228136413 228135483 0.000000e+00 1362.0
49 TraesCS2D01G317600 chrUn 93.496 861 54 2 2253 3113 404788125 404788983 0.000000e+00 1279.0
50 TraesCS2D01G317600 chr5B 82.686 283 30 11 453 722 595292003 595291727 4.460000e-57 233.0
51 TraesCS2D01G317600 chr1A 81.091 275 31 16 453 722 518050765 518050507 4.520000e-47 200.0
52 TraesCS2D01G317600 chr1A 80.000 275 34 16 453 722 586704516 586704774 4.550000e-42 183.0
53 TraesCS2D01G317600 chr1A 96.774 93 2 1 1 92 382098794 382098886 3.570000e-33 154.0
54 TraesCS2D01G317600 chr1A 92.708 96 2 2 1 92 462342288 462342382 4.650000e-27 134.0
55 TraesCS2D01G317600 chr2A 91.912 136 10 1 320 455 591660635 591660501 9.790000e-44 189.0
56 TraesCS2D01G317600 chr2A 96.429 84 3 0 639 722 591660166 591660083 1.000000e-28 139.0
57 TraesCS2D01G317600 chr2A 91.489 47 3 1 1185 1231 591660590 591660635 6.190000e-06 63.9
58 TraesCS2D01G317600 chr3B 91.176 136 11 1 320 455 730552923 730552789 4.550000e-42 183.0
59 TraesCS2D01G317600 chr3B 91.489 47 3 1 1185 1231 730552878 730552923 6.190000e-06 63.9
60 TraesCS2D01G317600 chr3D 80.443 271 23 13 453 721 202477964 202477722 5.890000e-41 180.0
61 TraesCS2D01G317600 chr5A 90.441 136 12 1 320 455 549015505 549015639 2.120000e-40 178.0
62 TraesCS2D01G317600 chr5A 96.429 84 3 0 639 722 549015974 549016057 1.000000e-28 139.0
63 TraesCS2D01G317600 chr5A 91.489 47 3 1 1185 1231 549015550 549015505 6.190000e-06 63.9
64 TraesCS2D01G317600 chr3A 79.412 272 35 16 453 719 54339294 54339549 9.860000e-39 172.0
65 TraesCS2D01G317600 chr3A 78.909 275 37 16 453 722 54360354 54360096 4.590000e-37 167.0
66 TraesCS2D01G317600 chr3A 78.676 272 37 16 453 719 54365790 54366045 2.130000e-35 161.0
67 TraesCS2D01G317600 chr5D 98.913 92 1 0 1 92 182936555 182936646 1.650000e-36 165.0
68 TraesCS2D01G317600 chr5D 92.708 96 3 1 1 92 47010092 47010187 1.290000e-27 135.0
69 TraesCS2D01G317600 chr2B 92.727 110 8 0 612 721 436539386 436539495 7.670000e-35 159.0
70 TraesCS2D01G317600 chr6B 94.681 94 3 2 1 92 673015488 673015581 2.150000e-30 145.0
71 TraesCS2D01G317600 chr6D 92.708 96 3 1 1 92 143473338 143473433 1.290000e-27 135.0
72 TraesCS2D01G317600 chr6D 92.708 96 3 1 1 92 208576792 208576697 1.290000e-27 135.0
73 TraesCS2D01G317600 chr1D 92.708 96 3 1 1 92 327011873 327011968 1.290000e-27 135.0
74 TraesCS2D01G317600 chr7D 100.000 38 0 0 1142 1179 546258523 546258486 3.700000e-08 71.3


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 TraesCS2D01G317600 chr2D 407201900 407209289 7389 True 6592.5000 10479 100.000000 1 7390 2 chr2D.!!$R2 7389
1 TraesCS2D01G317600 chr2D 407207841 407209191 1350 False 464.0000 464 98.134000 99 1449 2 chr2D.!!$F1 1350
2 TraesCS2D01G317600 chr4D 329010336 329019729 9393 False 2830.0000 9527 98.671250 843 7390 4 chr4D.!!$F1 6547
3 TraesCS2D01G317600 chr4D 329010231 329013994 3763 True 444.0000 651 98.730333 98 841 3 chr4D.!!$R1 743
4 TraesCS2D01G317600 chr4B 408959244 408968592 9348 False 1419.3000 4399 92.048167 843 7390 6 chr4B.!!$F2 6547
5 TraesCS2D01G317600 chr4B 408959135 408960306 1171 True 365.0000 684 95.138333 177 841 3 chr4B.!!$R1 664
6 TraesCS2D01G317600 chr4A 141107185 141113091 5906 True 1499.8000 2710 90.624800 1945 7390 5 chr4A.!!$R1 5445
7 TraesCS2D01G317600 chr1B 135932089 135938758 6669 True 1100.0625 2710 97.107625 799 7390 8 chr1B.!!$R2 6591
8 TraesCS2D01G317600 chr1B 135937704 135938700 996 False 294.5000 483 94.455333 167 797 3 chr1B.!!$F1 630
9 TraesCS2D01G317600 chr7B 412539789 412540720 931 False 1417.0000 1417 94.212000 2187 3113 1 chr7B.!!$F1 926
10 TraesCS2D01G317600 chr7B 658771411 658772342 931 False 1384.0000 1384 93.569000 2187 3113 1 chr7B.!!$F5 926
11 TraesCS2D01G317600 chr7B 658519445 658520376 931 False 1378.0000 1378 93.462000 2187 3113 1 chr7B.!!$F3 926
12 TraesCS2D01G317600 chr7B 658644960 658645891 931 False 1378.0000 1378 93.462000 2187 3113 1 chr7B.!!$F4 926
13 TraesCS2D01G317600 chrUn 228135483 228136413 930 True 1362.0000 1362 93.140000 2187 3113 1 chrUn.!!$R1 926
14 TraesCS2D01G317600 chrUn 404788125 404788983 858 False 1279.0000 1279 93.496000 2253 3113 1 chrUn.!!$F1 860

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
83 84 1.107114 TTGGCAAGAAAACGAAGGCA 58.893 45.000 0.00 0.00 0.00 4.75 F
84 85 1.107114 TGGCAAGAAAACGAAGGCAA 58.893 45.000 0.00 0.00 0.00 4.52 F
85 86 1.202359 TGGCAAGAAAACGAAGGCAAC 60.202 47.619 0.00 0.00 0.00 4.17 F
722 3328 2.201732 ACACTGCAGTAGTTTGTGTCG 58.798 47.619 21.20 5.45 37.29 4.35 F
3022 9746 6.717289 ACTGTGCCTAATAAGTTTGGTATGA 58.283 36.000 0.00 0.00 33.44 2.15 F
3344 10353 3.134804 ACTGCTGAGACTAAGTTTGGTGT 59.865 43.478 0.00 0.00 0.00 4.16 F
4622 11668 4.458989 TGCTATGAATTTCAGGTTGGTCAC 59.541 41.667 5.21 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 4350 1.070275 AACCGGAGTTGTCGTTCCC 59.930 57.895 9.46 0.00 33.97 3.97 R
1345 7655 4.524318 CGCCCCCGACATAACGCT 62.524 66.667 0.00 0.00 36.29 5.07 R
2410 9126 6.569179 ACACAAACACCTCACATTAATACC 57.431 37.500 0.00 0.00 0.00 2.73 R
3037 9761 6.448006 AGCTAATTACTACGTAATGCAGGAG 58.552 40.000 0.00 0.00 38.52 3.69 R
4254 11276 1.945394 GGTTGTCAGCATCAGCCTATG 59.055 52.381 0.00 0.00 43.56 2.23 R
4789 12072 2.993937 TCGGACACAAGGAAAAACAGT 58.006 42.857 0.00 0.00 0.00 3.55 R
6699 14110 1.355210 CACTGCTCGCCAAACGTTT 59.645 52.632 7.96 7.96 44.19 3.60 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
36 37 8.816640 AAAATTAATGTGTGCTAAGTTTCCTG 57.183 30.769 0.00 0.00 0.00 3.86
37 38 7.524717 AATTAATGTGTGCTAAGTTTCCTGT 57.475 32.000 0.00 0.00 0.00 4.00
38 39 6.952773 TTAATGTGTGCTAAGTTTCCTGTT 57.047 33.333 0.00 0.00 0.00 3.16
39 40 8.630054 ATTAATGTGTGCTAAGTTTCCTGTTA 57.370 30.769 0.00 0.00 0.00 2.41
40 41 8.630054 TTAATGTGTGCTAAGTTTCCTGTTAT 57.370 30.769 0.00 0.00 0.00 1.89
41 42 7.524717 AATGTGTGCTAAGTTTCCTGTTATT 57.475 32.000 0.00 0.00 0.00 1.40
42 43 6.952773 TGTGTGCTAAGTTTCCTGTTATTT 57.047 33.333 0.00 0.00 0.00 1.40
43 44 6.734137 TGTGTGCTAAGTTTCCTGTTATTTG 58.266 36.000 0.00 0.00 0.00 2.32
44 45 6.320164 TGTGTGCTAAGTTTCCTGTTATTTGT 59.680 34.615 0.00 0.00 0.00 2.83
45 46 7.499563 TGTGTGCTAAGTTTCCTGTTATTTGTA 59.500 33.333 0.00 0.00 0.00 2.41
46 47 8.512138 GTGTGCTAAGTTTCCTGTTATTTGTAT 58.488 33.333 0.00 0.00 0.00 2.29
47 48 9.073475 TGTGCTAAGTTTCCTGTTATTTGTATT 57.927 29.630 0.00 0.00 0.00 1.89
48 49 9.341899 GTGCTAAGTTTCCTGTTATTTGTATTG 57.658 33.333 0.00 0.00 0.00 1.90
49 50 9.073475 TGCTAAGTTTCCTGTTATTTGTATTGT 57.927 29.630 0.00 0.00 0.00 2.71
50 51 9.556030 GCTAAGTTTCCTGTTATTTGTATTGTC 57.444 33.333 0.00 0.00 0.00 3.18
58 59 9.559732 TCCTGTTATTTGTATTGTCATAGATGG 57.440 33.333 0.00 0.00 0.00 3.51
59 60 9.559732 CCTGTTATTTGTATTGTCATAGATGGA 57.440 33.333 0.00 0.00 0.00 3.41
67 68 8.625786 TGTATTGTCATAGATGGATGAATTGG 57.374 34.615 0.00 0.00 37.58 3.16
68 69 6.585695 ATTGTCATAGATGGATGAATTGGC 57.414 37.500 0.00 0.00 37.58 4.52
69 70 5.051409 TGTCATAGATGGATGAATTGGCA 57.949 39.130 0.00 0.00 37.58 4.92
70 71 5.447757 TGTCATAGATGGATGAATTGGCAA 58.552 37.500 0.68 0.68 37.58 4.52
71 72 5.533528 TGTCATAGATGGATGAATTGGCAAG 59.466 40.000 5.96 0.00 37.58 4.01
72 73 5.766670 GTCATAGATGGATGAATTGGCAAGA 59.233 40.000 5.96 0.00 37.58 3.02
73 74 6.263842 GTCATAGATGGATGAATTGGCAAGAA 59.736 38.462 5.96 0.00 37.58 2.52
74 75 6.834969 TCATAGATGGATGAATTGGCAAGAAA 59.165 34.615 5.96 0.00 32.84 2.52
75 76 7.342541 TCATAGATGGATGAATTGGCAAGAAAA 59.657 33.333 5.96 0.00 32.84 2.29
76 77 5.727434 AGATGGATGAATTGGCAAGAAAAC 58.273 37.500 5.96 0.00 0.00 2.43
77 78 3.911868 TGGATGAATTGGCAAGAAAACG 58.088 40.909 5.96 0.00 0.00 3.60
78 79 3.571828 TGGATGAATTGGCAAGAAAACGA 59.428 39.130 5.96 0.00 0.00 3.85
79 80 4.038522 TGGATGAATTGGCAAGAAAACGAA 59.961 37.500 5.96 0.00 0.00 3.85
80 81 4.622740 GGATGAATTGGCAAGAAAACGAAG 59.377 41.667 5.96 0.00 0.00 3.79
81 82 3.976169 TGAATTGGCAAGAAAACGAAGG 58.024 40.909 5.96 0.00 0.00 3.46
82 83 2.438868 ATTGGCAAGAAAACGAAGGC 57.561 45.000 5.96 0.00 0.00 4.35
83 84 1.107114 TTGGCAAGAAAACGAAGGCA 58.893 45.000 0.00 0.00 0.00 4.75
84 85 1.107114 TGGCAAGAAAACGAAGGCAA 58.893 45.000 0.00 0.00 0.00 4.52
85 86 1.202359 TGGCAAGAAAACGAAGGCAAC 60.202 47.619 0.00 0.00 0.00 4.17
722 3328 2.201732 ACACTGCAGTAGTTTGTGTCG 58.798 47.619 21.20 5.45 37.29 4.35
2596 9313 8.907222 TTTCCGGAACTTGTACTAGTTAAATT 57.093 30.769 18.64 0.80 38.43 1.82
3022 9746 6.717289 ACTGTGCCTAATAAGTTTGGTATGA 58.283 36.000 0.00 0.00 33.44 2.15
3037 9761 9.712305 AGTTTGGTATGATATTAGTGCTACATC 57.288 33.333 0.00 0.00 0.00 3.06
3344 10353 3.134804 ACTGCTGAGACTAAGTTTGGTGT 59.865 43.478 0.00 0.00 0.00 4.16
3427 10444 4.563580 GGCCATCTTCTGTCAGTCAAACTA 60.564 45.833 0.00 0.00 0.00 2.24
3958 10978 7.716612 AGGAAAAGGTAACAATGTTTGAAGAG 58.283 34.615 3.17 0.00 41.41 2.85
4254 11276 7.119262 ACCACTGTTTATTCACTGCTATGTTAC 59.881 37.037 0.00 0.00 0.00 2.50
4410 11432 6.303839 TGCCTGTTCAGGAAAATAGTAGTTT 58.696 36.000 21.32 0.00 0.00 2.66
4622 11668 4.458989 TGCTATGAATTTCAGGTTGGTCAC 59.541 41.667 5.21 0.00 0.00 3.67
4789 12072 6.553953 TTGTGCCTATAAGTTATGACCAGA 57.446 37.500 5.61 0.00 0.00 3.86
5112 12399 4.709397 ACTTTGGTGTGAGAAATGAACCAA 59.291 37.500 1.55 1.55 46.43 3.67
5623 12916 8.752005 TTGGATTCTAAAGCTATGCTAATTGT 57.248 30.769 0.00 0.00 38.25 2.71
5941 13250 5.183904 GTCTACCTTGCATTTCAACCTGAAT 59.816 40.000 0.00 0.00 36.11 2.57
5966 13276 2.139118 GCGTTCCAAGCCAGATAGATC 58.861 52.381 0.00 0.00 0.00 2.75
6125 13437 5.688823 TCAGTGTGCATCTTTATTTCGTTG 58.311 37.500 0.00 0.00 0.00 4.10
6210 13525 3.698289 TCTGGTCTATCTCGTTGGTCTT 58.302 45.455 0.00 0.00 0.00 3.01
6699 14110 1.481363 TGCCGATTCCCGTGTAATGTA 59.519 47.619 0.00 0.00 36.31 2.29
6700 14111 2.093606 TGCCGATTCCCGTGTAATGTAA 60.094 45.455 0.00 0.00 36.31 2.41
6940 14363 6.193761 GCCGCTTACGCTTACAATAATAAAA 58.806 36.000 0.00 0.00 38.22 1.52
7007 14495 1.541233 GCCAGAGATCCACCGTAATGG 60.541 57.143 0.00 0.00 46.41 3.16
7244 17136 4.673403 GTGATGTCACGTGGCTGA 57.327 55.556 22.43 1.39 37.10 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.260002 CAGGAAACTTAGCACACATTAATTTTT 57.740 29.630 0.00 0.00 40.21 1.94
11 12 8.421002 ACAGGAAACTTAGCACACATTAATTTT 58.579 29.630 0.00 0.00 40.21 1.82
12 13 7.951591 ACAGGAAACTTAGCACACATTAATTT 58.048 30.769 0.00 0.00 40.21 1.82
13 14 7.524717 ACAGGAAACTTAGCACACATTAATT 57.475 32.000 0.00 0.00 40.21 1.40
14 15 7.524717 AACAGGAAACTTAGCACACATTAAT 57.475 32.000 0.00 0.00 40.21 1.40
15 16 6.952773 AACAGGAAACTTAGCACACATTAA 57.047 33.333 0.00 0.00 40.21 1.40
16 17 8.630054 AATAACAGGAAACTTAGCACACATTA 57.370 30.769 0.00 0.00 40.21 1.90
17 18 7.524717 AATAACAGGAAACTTAGCACACATT 57.475 32.000 0.00 0.00 40.21 2.71
18 19 7.014230 ACAAATAACAGGAAACTTAGCACACAT 59.986 33.333 0.00 0.00 40.21 3.21
19 20 6.320164 ACAAATAACAGGAAACTTAGCACACA 59.680 34.615 0.00 0.00 40.21 3.72
20 21 6.735130 ACAAATAACAGGAAACTTAGCACAC 58.265 36.000 0.00 0.00 40.21 3.82
21 22 6.952773 ACAAATAACAGGAAACTTAGCACA 57.047 33.333 0.00 0.00 40.21 4.57
22 23 9.341899 CAATACAAATAACAGGAAACTTAGCAC 57.658 33.333 0.00 0.00 40.21 4.40
23 24 9.073475 ACAATACAAATAACAGGAAACTTAGCA 57.927 29.630 0.00 0.00 40.21 3.49
24 25 9.556030 GACAATACAAATAACAGGAAACTTAGC 57.444 33.333 0.00 0.00 40.21 3.09
32 33 9.559732 CCATCTATGACAATACAAATAACAGGA 57.440 33.333 0.00 0.00 0.00 3.86
33 34 9.559732 TCCATCTATGACAATACAAATAACAGG 57.440 33.333 0.00 0.00 0.00 4.00
41 42 9.070179 CCAATTCATCCATCTATGACAATACAA 57.930 33.333 0.00 0.00 35.63 2.41
42 43 7.175467 GCCAATTCATCCATCTATGACAATACA 59.825 37.037 0.00 0.00 35.63 2.29
43 44 7.175467 TGCCAATTCATCCATCTATGACAATAC 59.825 37.037 0.00 0.00 35.63 1.89
44 45 7.232910 TGCCAATTCATCCATCTATGACAATA 58.767 34.615 0.00 0.00 35.63 1.90
45 46 6.072649 TGCCAATTCATCCATCTATGACAAT 58.927 36.000 0.00 0.00 35.63 2.71
46 47 5.447757 TGCCAATTCATCCATCTATGACAA 58.552 37.500 0.00 0.00 35.63 3.18
47 48 5.051409 TGCCAATTCATCCATCTATGACA 57.949 39.130 0.00 0.00 35.63 3.58
48 49 5.766670 TCTTGCCAATTCATCCATCTATGAC 59.233 40.000 0.00 0.00 35.63 3.06
49 50 5.944135 TCTTGCCAATTCATCCATCTATGA 58.056 37.500 0.00 0.00 34.07 2.15
50 51 6.644248 TTCTTGCCAATTCATCCATCTATG 57.356 37.500 0.00 0.00 0.00 2.23
51 52 7.495055 GTTTTCTTGCCAATTCATCCATCTAT 58.505 34.615 0.00 0.00 0.00 1.98
52 53 6.404623 CGTTTTCTTGCCAATTCATCCATCTA 60.405 38.462 0.00 0.00 0.00 1.98
53 54 5.622914 CGTTTTCTTGCCAATTCATCCATCT 60.623 40.000 0.00 0.00 0.00 2.90
54 55 4.563976 CGTTTTCTTGCCAATTCATCCATC 59.436 41.667 0.00 0.00 0.00 3.51
55 56 4.220382 TCGTTTTCTTGCCAATTCATCCAT 59.780 37.500 0.00 0.00 0.00 3.41
56 57 3.571828 TCGTTTTCTTGCCAATTCATCCA 59.428 39.130 0.00 0.00 0.00 3.41
57 58 4.173036 TCGTTTTCTTGCCAATTCATCC 57.827 40.909 0.00 0.00 0.00 3.51
58 59 4.622740 CCTTCGTTTTCTTGCCAATTCATC 59.377 41.667 0.00 0.00 0.00 2.92
59 60 4.559153 CCTTCGTTTTCTTGCCAATTCAT 58.441 39.130 0.00 0.00 0.00 2.57
60 61 3.798548 GCCTTCGTTTTCTTGCCAATTCA 60.799 43.478 0.00 0.00 0.00 2.57
61 62 2.731451 GCCTTCGTTTTCTTGCCAATTC 59.269 45.455 0.00 0.00 0.00 2.17
62 63 2.102252 TGCCTTCGTTTTCTTGCCAATT 59.898 40.909 0.00 0.00 0.00 2.32
63 64 1.686052 TGCCTTCGTTTTCTTGCCAAT 59.314 42.857 0.00 0.00 0.00 3.16
64 65 1.107114 TGCCTTCGTTTTCTTGCCAA 58.893 45.000 0.00 0.00 0.00 4.52
65 66 1.107114 TTGCCTTCGTTTTCTTGCCA 58.893 45.000 0.00 0.00 0.00 4.92
66 67 1.067060 AGTTGCCTTCGTTTTCTTGCC 59.933 47.619 0.00 0.00 0.00 4.52
67 68 2.492019 AGTTGCCTTCGTTTTCTTGC 57.508 45.000 0.00 0.00 0.00 4.01
68 69 5.402270 CCAATTAGTTGCCTTCGTTTTCTTG 59.598 40.000 0.00 0.00 33.90 3.02
69 70 5.528870 CCAATTAGTTGCCTTCGTTTTCTT 58.471 37.500 0.00 0.00 33.90 2.52
70 71 4.558697 GCCAATTAGTTGCCTTCGTTTTCT 60.559 41.667 0.00 0.00 33.90 2.52
71 72 3.673338 GCCAATTAGTTGCCTTCGTTTTC 59.327 43.478 0.00 0.00 33.90 2.29
72 73 3.068873 TGCCAATTAGTTGCCTTCGTTTT 59.931 39.130 0.00 0.00 33.90 2.43
73 74 2.625790 TGCCAATTAGTTGCCTTCGTTT 59.374 40.909 0.00 0.00 33.90 3.60
74 75 2.235016 TGCCAATTAGTTGCCTTCGTT 58.765 42.857 0.00 0.00 33.90 3.85
75 76 1.904287 TGCCAATTAGTTGCCTTCGT 58.096 45.000 0.00 0.00 33.90 3.85
76 77 2.487762 TCTTGCCAATTAGTTGCCTTCG 59.512 45.455 0.00 0.00 33.90 3.79
77 78 4.237724 GTTCTTGCCAATTAGTTGCCTTC 58.762 43.478 0.00 0.00 33.90 3.46
78 79 3.006859 GGTTCTTGCCAATTAGTTGCCTT 59.993 43.478 0.00 0.00 33.90 4.35
79 80 2.562738 GGTTCTTGCCAATTAGTTGCCT 59.437 45.455 0.00 0.00 33.90 4.75
80 81 2.353704 GGGTTCTTGCCAATTAGTTGCC 60.354 50.000 0.00 0.00 33.90 4.52
81 82 2.671070 CGGGTTCTTGCCAATTAGTTGC 60.671 50.000 0.00 0.00 33.90 4.17
82 83 2.556622 ACGGGTTCTTGCCAATTAGTTG 59.443 45.455 0.00 0.00 35.05 3.16
83 84 2.556622 CACGGGTTCTTGCCAATTAGTT 59.443 45.455 0.00 0.00 0.00 2.24
84 85 2.159382 CACGGGTTCTTGCCAATTAGT 58.841 47.619 0.00 0.00 0.00 2.24
85 86 2.159382 ACACGGGTTCTTGCCAATTAG 58.841 47.619 0.00 0.00 0.00 1.73
86 87 2.156098 GACACGGGTTCTTGCCAATTA 58.844 47.619 0.00 0.00 0.00 1.40
87 88 0.958822 GACACGGGTTCTTGCCAATT 59.041 50.000 0.00 0.00 0.00 2.32
88 89 0.179004 TGACACGGGTTCTTGCCAAT 60.179 50.000 0.00 0.00 0.00 3.16
89 90 1.098712 GTGACACGGGTTCTTGCCAA 61.099 55.000 0.00 0.00 0.00 4.52
90 91 1.525077 GTGACACGGGTTCTTGCCA 60.525 57.895 0.00 0.00 0.00 4.92
91 92 2.258726 GGTGACACGGGTTCTTGCC 61.259 63.158 0.00 0.00 0.00 4.52
92 93 2.258726 GGGTGACACGGGTTCTTGC 61.259 63.158 0.00 0.00 0.00 4.01
93 94 1.599797 GGGGTGACACGGGTTCTTG 60.600 63.158 0.00 0.00 0.00 3.02
94 95 2.826003 GGGGGTGACACGGGTTCTT 61.826 63.158 0.00 0.00 0.00 2.52
95 96 3.246880 GGGGGTGACACGGGTTCT 61.247 66.667 0.00 0.00 0.00 3.01
96 97 4.692475 CGGGGGTGACACGGGTTC 62.692 72.222 0.00 0.00 0.00 3.62
574 3180 6.710744 AGAAAAGTGTACATAAAGACACAGGG 59.289 38.462 0.00 0.00 46.83 4.45
722 3328 1.134367 GTTTCGCTATTTCTTGCCCCC 59.866 52.381 0.00 0.00 0.00 5.40
841 3928 3.107447 CGGCGGGGCAAGAAATAC 58.893 61.111 0.00 0.00 0.00 1.89
877 4039 3.787001 GGAACTCGAGCCAGGGGG 61.787 72.222 13.61 0.00 37.18 5.40
1181 4350 1.070275 AACCGGAGTTGTCGTTCCC 59.930 57.895 9.46 0.00 33.97 3.97
1345 7655 4.524318 CGCCCCCGACATAACGCT 62.524 66.667 0.00 0.00 36.29 5.07
2410 9126 6.569179 ACACAAACACCTCACATTAATACC 57.431 37.500 0.00 0.00 0.00 2.73
3022 9746 6.617782 ATGCAGGAGATGTAGCACTAATAT 57.382 37.500 0.00 0.00 40.14 1.28
3037 9761 6.448006 AGCTAATTACTACGTAATGCAGGAG 58.552 40.000 0.00 0.00 38.52 3.69
3069 9866 6.457528 GCTGGACATAAGCACATTTTCTCTAC 60.458 42.308 0.00 0.00 40.52 2.59
3427 10444 9.686683 GGAATATGGCCATCTATTAACATAACT 57.313 33.333 24.80 0.00 0.00 2.24
4254 11276 1.945394 GGTTGTCAGCATCAGCCTATG 59.055 52.381 0.00 0.00 43.56 2.23
4410 11432 5.647658 AGCCTGAACGATTGAAACAATATCA 59.352 36.000 0.00 0.00 0.00 2.15
4622 11668 6.313658 GCAAATATTTTTGGCCCTAGACAAAG 59.686 38.462 0.00 0.00 42.09 2.77
4789 12072 2.993937 TCGGACACAAGGAAAAACAGT 58.006 42.857 0.00 0.00 0.00 3.55
5112 12399 3.228188 TGTTGCCCAATCAAGAGAGTT 57.772 42.857 0.00 0.00 0.00 3.01
5623 12916 7.117523 GCATACAGCAAACAAAATGGTGATTAA 59.882 33.333 12.10 0.00 46.44 1.40
6125 13437 9.400638 CACATAAAGAGACGAAGAATCCTATAC 57.599 37.037 0.00 0.00 0.00 1.47
6210 13525 7.015289 CGAAAATGCAAGAAGTCTCGAATAAA 58.985 34.615 0.00 0.00 0.00 1.40
6699 14110 1.355210 CACTGCTCGCCAAACGTTT 59.645 52.632 7.96 7.96 44.19 3.60
6700 14111 2.542907 CCACTGCTCGCCAAACGTT 61.543 57.895 0.00 0.00 44.19 3.99
7007 14495 1.686052 AGACCAGCAGATCCGATCTTC 59.314 52.381 8.26 4.01 37.58 2.87
7039 16910 3.863142 GTACTGTACCATCCGTCTGTT 57.137 47.619 6.70 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.