Multiple sequence alignment - TraesCS3A01G462800

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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 TraesCS3A01G462800 chr3A 100.000 2249 0 0 1 2249 697619186 697621434 0.000000e+00 4154
1 TraesCS3A01G462800 chr3A 85.714 343 43 6 845 1183 697632391 697632731 7.640000e-95 357
2 TraesCS3A01G462800 chr3A 85.673 342 42 4 845 1183 697685883 697686220 9.880000e-94 353
3 TraesCS3A01G462800 chr3A 78.689 427 47 13 133 544 697675209 697675606 6.200000e-61 244
4 TraesCS3A01G462800 chr3A 87.560 209 22 2 1180 1385 697683388 697683595 2.890000e-59 239
5 TraesCS3A01G462800 chr3A 88.710 186 16 2 1959 2139 353624600 353624415 2.910000e-54 222
6 TraesCS3A01G462800 chr3A 100.000 85 0 0 50 134 660055876 660055960 8.320000e-35 158
7 TraesCS3A01G462800 chr3A 96.774 93 2 1 45 137 727583900 727583991 1.080000e-33 154
8 TraesCS3A01G462800 chr3D 93.436 1493 72 16 133 1606 562505926 562507411 0.000000e+00 2191
9 TraesCS3A01G462800 chr3D 83.333 432 46 12 133 544 562539997 562540422 2.110000e-100 375
10 TraesCS3A01G462800 chr3D 86.510 341 43 3 845 1183 562517736 562518075 2.730000e-99 372
11 TraesCS3A01G462800 chr3D 85.673 342 42 4 845 1183 562582019 562582356 9.880000e-94 353
12 TraesCS3A01G462800 chr3D 77.833 600 99 24 1388 1966 554795302 554795888 7.690000e-90 340
13 TraesCS3A01G462800 chr3D 77.627 590 99 24 1391 1958 49564297 49563719 5.990000e-86 327
14 TraesCS3A01G462800 chr3B 94.135 1023 52 7 350 1365 749727812 749728833 0.000000e+00 1550
15 TraesCS3A01G462800 chr3B 90.988 1032 54 12 1236 2249 749728834 749729844 0.000000e+00 1354
16 TraesCS3A01G462800 chr3B 87.135 342 40 4 845 1183 749986231 749986571 3.500000e-103 385
17 TraesCS3A01G462800 chr3B 82.944 428 53 10 133 544 749861585 749862008 3.530000e-98 368
18 TraesCS3A01G462800 chr3B 83.862 347 51 5 845 1188 749863954 749864298 2.150000e-85 326
19 TraesCS3A01G462800 chr3B 90.654 214 15 1 1180 1388 749986634 749986847 1.700000e-71 279
20 TraesCS3A01G462800 chr3B 89.806 206 11 2 133 328 749727521 749727726 2.870000e-64 255
21 TraesCS3A01G462800 chr3B 85.714 203 20 6 1946 2139 774394197 774394399 2.930000e-49 206
22 TraesCS3A01G462800 chr3B 93.333 90 6 0 2160 2249 749983693 749983782 1.400000e-27 134
23 TraesCS3A01G462800 chr7A 79.132 599 94 19 1389 1966 721930023 721930611 3.500000e-103 385
24 TraesCS3A01G462800 chr7A 86.631 187 19 3 1960 2140 253535964 253535778 3.790000e-48 202
25 TraesCS3A01G462800 chr6A 78.584 579 95 22 1388 1947 9195482 9194914 2.750000e-94 355
26 TraesCS3A01G462800 chr4A 77.425 598 102 23 1376 1952 622473990 622474575 2.150000e-85 326
27 TraesCS3A01G462800 chr4A 95.789 95 2 2 41 135 413301318 413301410 3.870000e-33 152
28 TraesCS3A01G462800 chr2B 77.196 592 107 20 1386 1959 431915590 431916171 1.000000e-83 320
29 TraesCS3A01G462800 chr1A 75.606 578 114 18 1388 1947 532830163 532829595 6.160000e-66 261
30 TraesCS3A01G462800 chr1A 88.649 185 16 2 1960 2139 589247001 589247185 1.050000e-53 220
31 TraesCS3A01G462800 chr2A 89.617 183 14 2 1962 2139 611937185 611937003 6.250000e-56 228
32 TraesCS3A01G462800 chr2A 95.745 94 4 0 50 143 750532392 750532485 3.870000e-33 152
33 TraesCS3A01G462800 chr1D 88.136 177 16 2 1961 2132 439346811 439346987 2.930000e-49 206
34 TraesCS3A01G462800 chr1D 93.939 99 4 2 50 147 415055221 415055124 5.000000e-32 148
35 TraesCS3A01G462800 chr2D 88.439 173 15 2 1974 2141 491950015 491950187 1.050000e-48 204
36 TraesCS3A01G462800 chrUn 86.631 187 17 4 1963 2143 379839253 379839437 1.360000e-47 200
37 TraesCS3A01G462800 chr6D 98.889 90 1 0 45 134 15372641 15372552 6.430000e-36 161
38 TraesCS3A01G462800 chr7B 96.842 95 2 1 41 134 622831029 622831123 8.320000e-35 158
39 TraesCS3A01G462800 chr7B 95.745 94 4 0 42 135 427291862 427291955 3.870000e-33 152
40 TraesCS3A01G462800 chr6B 97.753 89 2 0 50 138 718478685 718478773 1.080000e-33 154


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 TraesCS3A01G462800 chr3A 697619186 697621434 2248 False 4154 4154 100.0000 1 2249 1 chr3A.!!$F2 2248
1 TraesCS3A01G462800 chr3A 697683388 697686220 2832 False 296 353 86.6165 845 1385 2 chr3A.!!$F6 540
2 TraesCS3A01G462800 chr3D 562505926 562507411 1485 False 2191 2191 93.4360 133 1606 1 chr3D.!!$F2 1473
3 TraesCS3A01G462800 chr3D 554795302 554795888 586 False 340 340 77.8330 1388 1966 1 chr3D.!!$F1 578
4 TraesCS3A01G462800 chr3D 49563719 49564297 578 True 327 327 77.6270 1391 1958 1 chr3D.!!$R1 567
5 TraesCS3A01G462800 chr3B 749727521 749729844 2323 False 1053 1550 91.6430 133 2249 3 chr3B.!!$F2 2116
6 TraesCS3A01G462800 chr3B 749861585 749864298 2713 False 347 368 83.4030 133 1188 2 chr3B.!!$F3 1055
7 TraesCS3A01G462800 chr3B 749983693 749986847 3154 False 266 385 90.3740 845 2249 3 chr3B.!!$F4 1404
8 TraesCS3A01G462800 chr7A 721930023 721930611 588 False 385 385 79.1320 1389 1966 1 chr7A.!!$F1 577
9 TraesCS3A01G462800 chr6A 9194914 9195482 568 True 355 355 78.5840 1388 1947 1 chr6A.!!$R1 559
10 TraesCS3A01G462800 chr4A 622473990 622474575 585 False 326 326 77.4250 1376 1952 1 chr4A.!!$F2 576
11 TraesCS3A01G462800 chr2B 431915590 431916171 581 False 320 320 77.1960 1386 1959 1 chr2B.!!$F1 573
12 TraesCS3A01G462800 chr1A 532829595 532830163 568 True 261 261 75.6060 1388 1947 1 chr1A.!!$R1 559

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
957 3234 0.178975 ATCGACCACAAAGCCCCAAA 60.179 50.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 4520 1.599797 CCAAAGCGGTCGGACCTTT 60.6 57.895 23.86 15.61 35.66 3.11 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
21 22 3.449918 TCCACCCATCATCACTAGTTCA 58.550 45.455 0.00 0.00 0.00 3.18
22 23 3.197766 TCCACCCATCATCACTAGTTCAC 59.802 47.826 0.00 0.00 0.00 3.18
23 24 3.198635 CCACCCATCATCACTAGTTCACT 59.801 47.826 0.00 0.00 0.00 3.41
24 25 4.405680 CCACCCATCATCACTAGTTCACTA 59.594 45.833 0.00 0.00 0.00 2.74
26 27 5.127845 CACCCATCATCACTAGTTCACTACT 59.872 44.000 0.00 0.00 41.04 2.57
27 28 5.721960 ACCCATCATCACTAGTTCACTACTT 59.278 40.000 0.00 0.00 38.33 2.24
29 30 6.127338 CCCATCATCACTAGTTCACTACTTCA 60.127 42.308 0.00 0.00 38.33 3.02
30 31 6.977502 CCATCATCACTAGTTCACTACTTCAG 59.022 42.308 0.00 0.00 38.33 3.02
31 32 7.363355 CCATCATCACTAGTTCACTACTTCAGT 60.363 40.741 0.00 0.00 38.33 3.41
33 34 7.594714 TCATCACTAGTTCACTACTTCAGTTC 58.405 38.462 0.00 0.00 38.33 3.01
34 35 7.448777 TCATCACTAGTTCACTACTTCAGTTCT 59.551 37.037 0.00 0.00 38.33 3.01
35 36 8.731605 CATCACTAGTTCACTACTTCAGTTCTA 58.268 37.037 0.00 0.00 38.33 2.10
36 37 8.687292 TCACTAGTTCACTACTTCAGTTCTAA 57.313 34.615 0.00 0.00 38.33 2.10
37 38 8.784994 TCACTAGTTCACTACTTCAGTTCTAAG 58.215 37.037 0.00 0.00 38.33 2.18
38 39 8.024285 CACTAGTTCACTACTTCAGTTCTAAGG 58.976 40.741 0.00 0.00 38.33 2.69
40 41 6.075984 AGTTCACTACTTCAGTTCTAAGGGA 58.924 40.000 0.00 0.00 34.26 4.20
41 42 6.553852 AGTTCACTACTTCAGTTCTAAGGGAA 59.446 38.462 0.00 0.00 34.26 3.97
42 43 6.989155 TCACTACTTCAGTTCTAAGGGAAA 57.011 37.500 0.00 0.00 34.26 3.13
43 44 7.369551 TCACTACTTCAGTTCTAAGGGAAAA 57.630 36.000 0.00 0.00 34.26 2.29
44 45 7.974504 TCACTACTTCAGTTCTAAGGGAAAAT 58.025 34.615 0.00 0.00 34.26 1.82
45 46 8.437575 TCACTACTTCAGTTCTAAGGGAAAATT 58.562 33.333 0.00 0.00 34.26 1.82
46 47 9.067986 CACTACTTCAGTTCTAAGGGAAAATTT 57.932 33.333 0.00 0.00 34.26 1.82
47 48 9.067986 ACTACTTCAGTTCTAAGGGAAAATTTG 57.932 33.333 0.00 0.00 35.51 2.32
48 49 9.284968 CTACTTCAGTTCTAAGGGAAAATTTGA 57.715 33.333 0.00 0.00 35.51 2.69
49 50 8.712228 ACTTCAGTTCTAAGGGAAAATTTGAT 57.288 30.769 0.00 0.00 35.51 2.57
50 51 9.807921 ACTTCAGTTCTAAGGGAAAATTTGATA 57.192 29.630 0.00 0.00 35.51 2.15
52 53 9.807921 TTCAGTTCTAAGGGAAAATTTGATACT 57.192 29.630 0.00 0.00 35.51 2.12
53 54 9.449719 TCAGTTCTAAGGGAAAATTTGATACTC 57.550 33.333 0.00 0.00 35.51 2.59
55 56 7.834681 AGTTCTAAGGGAAAATTTGATACTCCC 59.165 37.037 14.68 14.68 45.35 4.30
60 61 5.510430 GGGAAAATTTGATACTCCCTCTGT 58.490 41.667 15.08 0.00 42.25 3.41
61 62 6.659824 GGGAAAATTTGATACTCCCTCTGTA 58.340 40.000 15.08 0.00 42.25 2.74
62 63 7.116736 GGGAAAATTTGATACTCCCTCTGTAA 58.883 38.462 15.08 0.00 42.25 2.41
63 64 7.614192 GGGAAAATTTGATACTCCCTCTGTAAA 59.386 37.037 15.08 0.00 42.25 2.01
64 65 9.190317 GGAAAATTTGATACTCCCTCTGTAAAT 57.810 33.333 0.00 0.00 0.00 1.40
125 126 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
126 127 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
127 128 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
128 129 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
130 131 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
131 132 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
174 176 0.685458 ATCCCAATGGCAGCCAGAAC 60.685 55.000 21.51 0.00 36.75 3.01
177 179 0.245539 CCAATGGCAGCCAGAACAAG 59.754 55.000 21.51 5.50 36.75 3.16
223 226 4.042809 ACTCCACAACAATGGTATTCCTCA 59.957 41.667 0.00 0.00 40.95 3.86
236 241 5.129650 TGGTATTCCTCATCACGGACAAATA 59.870 40.000 0.00 0.00 34.23 1.40
274 288 9.844257 AAATTAGAGTGCTAGCTTATCAGAAAT 57.156 29.630 17.23 9.19 0.00 2.17
307 321 6.983984 TCATCAACTGAAGCATTGATTTGAA 58.016 32.000 0.00 0.00 41.69 2.69
448 535 4.868268 ACACTCCTGACCATAGCTAACTA 58.132 43.478 0.00 0.00 0.00 2.24
479 566 2.030451 GCTCCCTCACAAAAGCAAAGAG 60.030 50.000 0.00 0.00 34.86 2.85
957 3234 0.178975 ATCGACCACAAAGCCCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
1026 3303 3.241530 AGGGTGACGAAGCTGGCA 61.242 61.111 0.00 0.00 0.00 4.92
1053 3330 1.292223 CGTGGTGGTGATCTTCGGT 59.708 57.895 0.00 0.00 0.00 4.69
1079 3356 0.895100 AACCGCTTCATGTGCCATGT 60.895 50.000 12.89 1.77 0.00 3.21
1128 3407 1.891919 GAGCTGGACGGTGCACAAA 60.892 57.895 20.43 0.00 0.00 2.83
1331 3806 2.133553 CGAGCCAAGCTAGTGATCATG 58.866 52.381 0.00 0.00 39.88 3.07
1337 3812 3.806521 CCAAGCTAGTGATCATGTAGTGC 59.193 47.826 0.00 0.00 0.00 4.40
1381 3870 8.031277 AGTTTTGGAAAGCTCATCAAACATATC 58.969 33.333 13.34 0.00 0.00 1.63
1425 3914 4.921547 AGTGGAAACTTTTCGCTTTTCTC 58.078 39.130 0.00 0.00 38.06 2.87
1427 3916 3.375922 TGGAAACTTTTCGCTTTTCTCGT 59.624 39.130 0.00 0.00 38.06 4.18
1617 4116 7.597288 TTACTATGAGACTATGGCTGCTTTA 57.403 36.000 0.00 0.00 0.00 1.85
1658 4157 0.943673 CACAATGACACGGTGAGCAA 59.056 50.000 16.29 0.00 34.52 3.91
1670 4169 1.205417 GGTGAGCAAAATGACCCATGG 59.795 52.381 4.14 4.14 0.00 3.66
1716 4219 2.643801 CGTAGTCTAGACCCTCCCCTAT 59.356 54.545 19.38 0.00 0.00 2.57
1765 4268 7.820578 ACTATACTGAGTCGCTAACCTAATT 57.179 36.000 0.00 0.00 0.00 1.40
1907 4417 2.662527 TCGGTGTTCGTTTCCGGC 60.663 61.111 0.00 0.00 43.75 6.13
1952 4462 4.412843 ACCGGGGTTTCTGTATTCATTTT 58.587 39.130 6.32 0.00 0.00 1.82
1960 4470 9.974980 GGGTTTCTGTATTCATTTTCACTTTAA 57.025 29.630 0.00 0.00 0.00 1.52
1992 4502 3.116531 GGTGCACGTAACTCCCGC 61.117 66.667 11.45 0.00 0.00 6.13
1996 4506 1.373748 GCACGTAACTCCCGCTTGA 60.374 57.895 0.00 0.00 0.00 3.02
2010 4520 4.649705 TTGAGCAGGGTCCGGGGA 62.650 66.667 0.00 0.00 0.00 4.81
2036 4546 1.405797 CCGACCGCTTTGGGTGTATAA 60.406 52.381 0.00 0.00 44.64 0.98
2039 4549 4.312443 CGACCGCTTTGGGTGTATAATAT 58.688 43.478 0.00 0.00 44.64 1.28
2051 4561 5.316987 GGTGTATAATATGCAGCCTTTCCT 58.683 41.667 8.96 0.00 37.40 3.36
2054 4564 7.094762 GGTGTATAATATGCAGCCTTTCCTTAC 60.095 40.741 8.96 0.00 37.40 2.34
2082 4592 5.820947 TCTGTAAGAGGTTGTTTCCAGAAAC 59.179 40.000 14.88 14.88 43.98 2.78
2109 4619 1.955778 CCTCATGGTCACAAAGCAACA 59.044 47.619 0.00 0.00 39.21 3.33
2157 4667 4.523943 CCTTCATTCATTTCCACTTCCACA 59.476 41.667 0.00 0.00 0.00 4.17
2186 4696 2.165437 TCTTTCAGTTTTGCCGCTTGTT 59.835 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.478206 AGTGAACTAGTGATGATGGGTG 57.522 45.455 0.00 0.00 0.00 4.61
3 4 5.273208 AGTAGTGAACTAGTGATGATGGGT 58.727 41.667 0.00 0.00 36.36 4.51
4 5 5.860941 AGTAGTGAACTAGTGATGATGGG 57.139 43.478 0.00 0.00 36.36 4.00
5 6 6.867550 TGAAGTAGTGAACTAGTGATGATGG 58.132 40.000 0.00 0.00 37.50 3.51
6 7 7.542890 ACTGAAGTAGTGAACTAGTGATGATG 58.457 38.462 0.00 0.00 37.50 3.07
8 9 7.448777 AGAACTGAAGTAGTGAACTAGTGATGA 59.551 37.037 0.00 0.00 40.26 2.92
10 11 7.768807 AGAACTGAAGTAGTGAACTAGTGAT 57.231 36.000 0.00 0.00 40.26 3.06
12 13 8.024285 CCTTAGAACTGAAGTAGTGAACTAGTG 58.976 40.741 0.00 0.00 40.26 2.74
13 14 7.177041 CCCTTAGAACTGAAGTAGTGAACTAGT 59.823 40.741 0.00 0.00 40.26 2.57
14 15 7.393796 TCCCTTAGAACTGAAGTAGTGAACTAG 59.606 40.741 0.00 0.00 40.26 2.57
15 16 7.236529 TCCCTTAGAACTGAAGTAGTGAACTA 58.763 38.462 0.00 0.00 40.26 2.24
16 17 6.075984 TCCCTTAGAACTGAAGTAGTGAACT 58.924 40.000 0.00 0.00 40.26 3.01
17 18 6.342338 TCCCTTAGAACTGAAGTAGTGAAC 57.658 41.667 0.00 0.00 40.26 3.18
18 19 6.989155 TTCCCTTAGAACTGAAGTAGTGAA 57.011 37.500 0.00 0.00 40.26 3.18
19 20 6.989155 TTTCCCTTAGAACTGAAGTAGTGA 57.011 37.500 0.00 0.00 40.26 3.41
20 21 8.622948 AATTTTCCCTTAGAACTGAAGTAGTG 57.377 34.615 0.00 0.00 40.26 2.74
21 22 9.067986 CAAATTTTCCCTTAGAACTGAAGTAGT 57.932 33.333 0.00 0.00 42.89 2.73
22 23 9.284968 TCAAATTTTCCCTTAGAACTGAAGTAG 57.715 33.333 0.00 0.00 32.95 2.57
23 24 9.807921 ATCAAATTTTCCCTTAGAACTGAAGTA 57.192 29.630 0.00 0.00 32.95 2.24
24 25 8.712228 ATCAAATTTTCCCTTAGAACTGAAGT 57.288 30.769 0.00 0.00 32.95 3.01
26 27 9.807921 AGTATCAAATTTTCCCTTAGAACTGAA 57.192 29.630 0.00 0.00 32.95 3.02
27 28 9.449719 GAGTATCAAATTTTCCCTTAGAACTGA 57.550 33.333 0.00 0.00 31.04 3.41
29 30 7.834681 GGGAGTATCAAATTTTCCCTTAGAACT 59.165 37.037 15.08 3.57 43.39 3.01
30 31 7.997482 GGGAGTATCAAATTTTCCCTTAGAAC 58.003 38.462 15.08 0.00 43.39 3.01
37 38 5.510430 ACAGAGGGAGTATCAAATTTTCCC 58.490 41.667 14.68 14.68 46.41 3.97
38 39 8.575649 TTTACAGAGGGAGTATCAAATTTTCC 57.424 34.615 0.00 0.00 36.25 3.13
100 101 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
102 103 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
103 104 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
105 106 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
106 107 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
107 108 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
108 109 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
109 110 9.512588 TCTACTCCCTCCGTAAACTAATATAAG 57.487 37.037 0.00 0.00 0.00 1.73
112 113 7.093858 GCATCTACTCCCTCCGTAAACTAATAT 60.094 40.741 0.00 0.00 0.00 1.28
114 115 5.010820 GCATCTACTCCCTCCGTAAACTAAT 59.989 44.000 0.00 0.00 0.00 1.73
115 116 4.340381 GCATCTACTCCCTCCGTAAACTAA 59.660 45.833 0.00 0.00 0.00 2.24
117 118 2.694109 GCATCTACTCCCTCCGTAAACT 59.306 50.000 0.00 0.00 0.00 2.66
119 120 2.037144 GGCATCTACTCCCTCCGTAAA 58.963 52.381 0.00 0.00 0.00 2.01
120 121 1.063492 TGGCATCTACTCCCTCCGTAA 60.063 52.381 0.00 0.00 0.00 3.18
121 122 0.554305 TGGCATCTACTCCCTCCGTA 59.446 55.000 0.00 0.00 0.00 4.02
122 123 0.105453 ATGGCATCTACTCCCTCCGT 60.105 55.000 0.00 0.00 0.00 4.69
124 125 3.511477 TCTAATGGCATCTACTCCCTCC 58.489 50.000 0.00 0.00 0.00 4.30
125 126 4.774726 TCATCTAATGGCATCTACTCCCTC 59.225 45.833 0.00 0.00 0.00 4.30
126 127 4.756564 TCATCTAATGGCATCTACTCCCT 58.243 43.478 0.00 0.00 0.00 4.20
127 128 5.012561 ACTTCATCTAATGGCATCTACTCCC 59.987 44.000 0.00 0.00 0.00 4.30
128 129 6.107901 ACTTCATCTAATGGCATCTACTCC 57.892 41.667 0.00 0.00 0.00 3.85
174 176 2.342910 GCACCAAGCATCACTTCTTG 57.657 50.000 0.00 0.00 44.79 3.02
274 288 8.403236 CAATGCTTCAGTTGATGATTAATCAGA 58.597 33.333 21.97 10.76 46.01 3.27
409 496 8.928448 TCAGGAGTGTAGCTAATCTTTGATATT 58.072 33.333 0.00 0.00 0.00 1.28
425 512 4.868268 AGTTAGCTATGGTCAGGAGTGTA 58.132 43.478 0.00 0.00 0.00 2.90
448 535 4.574674 TTGTGAGGGAGCAAAGTGATAT 57.425 40.909 0.00 0.00 0.00 1.63
479 566 4.106029 TGAATTCTAGCACCTCGTGTAC 57.894 45.455 7.05 0.00 35.75 2.90
643 814 5.046304 TCAAGACAGGCAGAAGTTTAGCTAT 60.046 40.000 0.00 0.00 0.00 2.97
758 961 0.396435 CTTTTGGGAGGGGCCAAAAC 59.604 55.000 4.39 0.00 39.34 2.43
957 3234 2.558359 GCTGGCTGTAGGATGTTGTTTT 59.442 45.455 0.00 0.00 0.00 2.43
1004 3281 1.837051 AGCTTCGTCACCCTGTCCA 60.837 57.895 0.00 0.00 0.00 4.02
1037 3314 0.034756 CACACCGAAGATCACCACCA 59.965 55.000 0.00 0.00 0.00 4.17
1128 3407 2.845345 CCAGGGGTCCTTTGCCAGT 61.845 63.158 0.00 0.00 0.00 4.00
1331 3806 2.856032 CTGCACTGCACGCACTAC 59.144 61.111 0.00 0.00 35.08 2.73
1337 3812 0.926155 CTATGTAGCTGCACTGCACG 59.074 55.000 6.66 0.00 44.32 5.34
1381 3870 4.013728 TCCATTTTCATCCCTAACCGTTG 58.986 43.478 0.00 0.00 0.00 4.10
1425 3914 5.038033 TCTTTCCATTTTCGTTTTTCCACG 58.962 37.500 0.00 0.00 41.78 4.94
1427 3916 7.907214 TTTTCTTTCCATTTTCGTTTTTCCA 57.093 28.000 0.00 0.00 0.00 3.53
1445 3934 9.517868 TGCAAATTTCCATTTCCATATTTTCTT 57.482 25.926 0.00 0.00 29.41 2.52
1617 4116 1.261480 TTGTTTGGTGGTTGTGCTGT 58.739 45.000 0.00 0.00 0.00 4.40
1658 4157 1.311059 GGCCTCCCATGGGTCATTT 59.689 57.895 30.28 0.00 36.47 2.32
1670 4169 1.749258 GTCGTGGAATTGGGCCTCC 60.749 63.158 4.53 3.86 0.00 4.30
1804 4307 7.014230 ACCATAGAAAAACACAAGCACAGTAAT 59.986 33.333 0.00 0.00 0.00 1.89
1808 4311 5.186996 ACCATAGAAAAACACAAGCACAG 57.813 39.130 0.00 0.00 0.00 3.66
1907 4417 8.820933 CGGTAATGAATATGGAAGCATATACTG 58.179 37.037 0.00 0.00 0.00 2.74
1961 4471 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
1992 4502 4.101448 CCCCGGACCCTGCTCAAG 62.101 72.222 0.73 0.00 0.00 3.02
1996 4506 3.330720 CTTTCCCCGGACCCTGCT 61.331 66.667 0.73 0.00 0.00 4.24
2010 4520 1.599797 CCAAAGCGGTCGGACCTTT 60.600 57.895 23.86 15.61 35.66 3.11
2019 4529 3.818773 GCATATTATACACCCAAAGCGGT 59.181 43.478 0.00 0.00 36.18 5.68
2036 4546 6.040166 CAGAAATGTAAGGAAAGGCTGCATAT 59.960 38.462 0.50 0.00 0.00 1.78
2039 4549 3.507233 CAGAAATGTAAGGAAAGGCTGCA 59.493 43.478 0.50 0.00 0.00 4.41
2049 4559 7.745620 AACAACCTCTTACAGAAATGTAAGG 57.254 36.000 21.68 13.68 46.67 2.69
2051 4561 7.776030 TGGAAACAACCTCTTACAGAAATGTAA 59.224 33.333 1.31 1.31 37.44 2.41
2054 4564 6.486657 TCTGGAAACAACCTCTTACAGAAATG 59.513 38.462 0.00 0.00 42.06 2.32
2069 4579 8.850028 ATGAGGTCATGGGTTTCTGGAAACAA 62.850 42.308 22.31 13.26 42.36 2.83
2157 4667 4.083110 CGGCAAAACTGAAAGATCATGACT 60.083 41.667 0.00 0.00 37.43 3.41


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

AutoCloner maintained by Alex Coulton.