Multiple sequence alignment - TraesCS4A01G011100

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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 TraesCS4A01G011100 chr4A 100.000 6217 0 0 1 6217 6340840 6347056 0.000000e+00 11481.0
1 TraesCS4A01G011100 chr4A 84.541 621 74 6 1792 2411 6277810 6278409 4.150000e-166 595.0
2 TraesCS4A01G011100 chr4A 83.858 508 61 11 1050 1547 6067521 6068017 1.220000e-126 464.0
3 TraesCS4A01G011100 chr4A 89.474 266 24 4 2238 2500 6489958 6490222 3.590000e-87 333.0
4 TraesCS4A01G011100 chr4A 86.400 250 33 1 1546 1795 6105716 6105964 7.940000e-69 272.0
5 TraesCS4A01G011100 chr4A 86.321 212 22 6 2457 2664 6278413 6278621 2.260000e-54 224.0
6 TraesCS4A01G011100 chr4A 89.286 140 13 1 5700 5837 583713350 583713489 2.300000e-39 174.0
7 TraesCS4A01G011100 chr4B 96.183 4139 88 26 1 4104 578677895 578673792 0.000000e+00 6704.0
8 TraesCS4A01G011100 chr4B 93.047 2143 54 21 4104 6214 578673620 578671541 0.000000e+00 3044.0
9 TraesCS4A01G011100 chr4B 85.375 841 102 12 1726 2558 578361447 578360620 0.000000e+00 852.0
10 TraesCS4A01G011100 chr4B 85.256 841 103 12 1726 2558 578445718 578444891 0.000000e+00 846.0
11 TraesCS4A01G011100 chr4B 85.137 841 104 12 1726 2558 578491251 578490424 0.000000e+00 841.0
12 TraesCS4A01G011100 chr4B 87.550 498 50 7 1049 1537 579094188 579093694 3.250000e-157 566.0
13 TraesCS4A01G011100 chr4B 87.627 493 50 7 1050 1534 579092856 579092367 4.210000e-156 562.0
14 TraesCS4A01G011100 chr4B 85.163 492 50 13 1049 1532 579091526 579091050 3.370000e-132 483.0
15 TraesCS4A01G011100 chr4D 96.146 3140 89 18 972 4104 463341359 463338245 0.000000e+00 5099.0
16 TraesCS4A01G011100 chr4D 95.231 2139 54 16 4104 6214 463338073 463335955 0.000000e+00 3341.0
17 TraesCS4A01G011100 chr4D 83.833 600 61 23 370 961 508283425 508283996 7.090000e-149 538.0
18 TraesCS4A01G011100 chr4D 90.123 162 14 2 2934 3095 462546931 462547090 6.320000e-50 209.0
19 TraesCS4A01G011100 chr4D 90.476 84 5 2 214 296 463383850 463383769 2.370000e-19 108.0
20 TraesCS4A01G011100 chr7B 81.431 517 52 19 452 961 610786984 610786505 3.520000e-102 383.0
21 TraesCS4A01G011100 chr7B 92.308 169 12 1 794 961 612893387 612893555 8.050000e-59 239.0
22 TraesCS4A01G011100 chr7B 82.437 279 26 10 1 278 725602954 725602698 8.110000e-54 222.0
23 TraesCS4A01G011100 chr7B 82.437 279 26 10 1 278 725638693 725638437 8.110000e-54 222.0
24 TraesCS4A01G011100 chr7B 89.412 85 9 0 5894 5978 166469629 166469545 2.370000e-19 108.0
25 TraesCS4A01G011100 chr7B 89.286 84 9 0 5895 5978 669030678 669030595 8.520000e-19 106.0
26 TraesCS4A01G011100 chr7B 90.698 43 4 0 5965 6007 679797185 679797227 2.420000e-04 58.4
27 TraesCS4A01G011100 chr7D 85.260 346 35 7 617 961 615595830 615596160 5.970000e-90 342.0
28 TraesCS4A01G011100 chr7D 90.000 140 12 1 5700 5837 508611003 508611142 4.950000e-41 180.0
29 TraesCS4A01G011100 chr7D 89.706 136 12 1 5704 5837 397991625 397991490 8.290000e-39 172.0
30 TraesCS4A01G011100 chr2D 88.265 196 20 3 2281 2474 373675402 373675208 1.350000e-56 231.0
31 TraesCS4A01G011100 chr2D 89.209 139 12 2 5700 5835 524963778 524963640 2.980000e-38 171.0
32 TraesCS4A01G011100 chr2D 84.884 86 12 1 5963 6048 239718168 239718084 1.110000e-12 86.1
33 TraesCS4A01G011100 chr2D 97.727 44 1 0 5975 6018 239718288 239718245 6.680000e-10 76.8
34 TraesCS4A01G011100 chr2B 86.730 211 25 3 2262 2470 443156331 443156122 1.350000e-56 231.0
35 TraesCS4A01G011100 chr2B 78.058 278 28 15 1 277 384328521 384328766 1.810000e-30 145.0
36 TraesCS4A01G011100 chr2B 89.286 56 5 1 5963 6018 283176083 283176029 1.120000e-07 69.4
37 TraesCS4A01G011100 chr2B 95.238 42 2 0 5977 6018 283176201 283176160 4.020000e-07 67.6
38 TraesCS4A01G011100 chrUn 82.437 279 26 10 1 278 353853633 353853377 8.110000e-54 222.0
39 TraesCS4A01G011100 chrUn 82.437 279 26 10 1 278 380048359 380048103 8.110000e-54 222.0
40 TraesCS4A01G011100 chr3A 90.714 140 10 2 5700 5837 726769106 726768968 3.830000e-42 183.0
41 TraesCS4A01G011100 chr3A 90.588 85 8 0 5894 5978 45876802 45876886 5.090000e-21 113.0
42 TraesCS4A01G011100 chr3A 90.566 53 5 0 909 961 94177625 94177573 3.110000e-08 71.3
43 TraesCS4A01G011100 chr3D 89.286 140 13 1 5700 5837 128214029 128214168 2.300000e-39 174.0
44 TraesCS4A01G011100 chr3B 88.194 144 15 1 5696 5837 552226425 552226568 2.980000e-38 171.0
45 TraesCS4A01G011100 chr3B 92.941 85 6 0 5894 5978 429211853 429211769 2.350000e-24 124.0
46 TraesCS4A01G011100 chr3B 94.937 79 3 1 201 278 171824103 171824181 8.460000e-24 122.0
47 TraesCS4A01G011100 chr5D 79.211 279 22 13 1 278 422467024 422467267 1.790000e-35 161.0
48 TraesCS4A01G011100 chr1A 82.468 154 14 7 126 278 552347236 552347095 8.460000e-24 122.0
49 TraesCS4A01G011100 chr6B 91.765 85 7 0 5894 5978 672423621 672423537 1.090000e-22 119.0
50 TraesCS4A01G011100 chr6B 88.235 85 10 0 5894 5978 144974397 144974481 1.100000e-17 102.0
51 TraesCS4A01G011100 chr6D 89.412 85 9 0 5894 5978 408308541 408308457 2.370000e-19 108.0
52 TraesCS4A01G011100 chr5A 85.047 107 10 4 314 418 600610456 600610354 3.070000e-18 104.0
53 TraesCS4A01G011100 chr2A 84.884 86 12 1 5963 6048 235326362 235326446 1.110000e-12 86.1
54 TraesCS4A01G011100 chr7A 92.453 53 4 0 909 961 665769277 665769225 6.680000e-10 76.8
55 TraesCS4A01G011100 chr5B 83.750 80 10 3 5963 6041 641921248 641921171 8.640000e-09 73.1


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 TraesCS4A01G011100 chr4A 6340840 6347056 6216 False 11481.0 11481 100.0000 1 6217 1 chr4A.!!$F3 6216
1 TraesCS4A01G011100 chr4A 6277810 6278621 811 False 409.5 595 85.4310 1792 2664 2 chr4A.!!$F6 872
2 TraesCS4A01G011100 chr4B 578671541 578677895 6354 True 4874.0 6704 94.6150 1 6214 2 chr4B.!!$R4 6213
3 TraesCS4A01G011100 chr4B 578360620 578361447 827 True 852.0 852 85.3750 1726 2558 1 chr4B.!!$R1 832
4 TraesCS4A01G011100 chr4B 578444891 578445718 827 True 846.0 846 85.2560 1726 2558 1 chr4B.!!$R2 832
5 TraesCS4A01G011100 chr4B 578490424 578491251 827 True 841.0 841 85.1370 1726 2558 1 chr4B.!!$R3 832
6 TraesCS4A01G011100 chr4B 579091050 579094188 3138 True 537.0 566 86.7800 1049 1537 3 chr4B.!!$R5 488
7 TraesCS4A01G011100 chr4D 463335955 463341359 5404 True 4220.0 5099 95.6885 972 6214 2 chr4D.!!$R2 5242
8 TraesCS4A01G011100 chr4D 508283425 508283996 571 False 538.0 538 83.8330 370 961 1 chr4D.!!$F2 591

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
719 749 1.407437 GGGGACAGCATTCGAGATGTT 60.407 52.381 0.00 0.00 38.41 2.71 F
2105 3684 0.468585 TCCAATGGCATGCCCTGATC 60.469 55.000 33.44 8.41 34.56 2.92 F
3245 4887 1.138069 TCGTTGGAGTCTTCTTGCACA 59.862 47.619 0.00 0.00 0.00 4.57 F
4086 5729 0.891373 GCTGTGCAGAGAGGTAGTCA 59.109 55.000 16.28 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 4028 1.066502 GGTTGGTTGCAACTGTTTGGT 60.067 47.619 27.64 0.0 35.54 3.67 R
4086 5729 1.141881 CTCCGCTATGTCTTGGCGT 59.858 57.895 13.98 0.0 46.23 5.68 R
5032 6848 0.685097 GTACCTTGTGTCCAGCTCCA 59.315 55.000 0.00 0.0 0.00 3.86 R
5453 7272 0.394625 GGTCTCCTCACGCTAGGACT 60.395 60.000 2.27 0.0 40.86 3.85 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
203 204 2.544267 AGTTACAAGCGAGCAAACTGAC 59.456 45.455 0.00 0.00 0.00 3.51
227 228 5.395214 CCAATTTAAGGTACCCAAATGCCTC 60.395 44.000 18.21 0.00 32.81 4.70
228 229 4.390129 TTTAAGGTACCCAAATGCCTCA 57.610 40.909 8.74 0.00 32.81 3.86
229 230 2.990740 AAGGTACCCAAATGCCTCAA 57.009 45.000 8.74 0.00 32.81 3.02
230 231 3.473113 AAGGTACCCAAATGCCTCAAT 57.527 42.857 8.74 0.00 32.81 2.57
231 232 3.473113 AGGTACCCAAATGCCTCAATT 57.527 42.857 8.74 0.00 26.15 2.32
232 233 3.790126 AGGTACCCAAATGCCTCAATTT 58.210 40.909 8.74 0.00 26.15 1.82
233 234 3.769300 AGGTACCCAAATGCCTCAATTTC 59.231 43.478 8.74 0.00 26.15 2.17
234 235 3.513515 GGTACCCAAATGCCTCAATTTCA 59.486 43.478 0.00 0.00 0.00 2.69
248 249 5.335976 CCTCAATTTCAGACTTAGGGTTTGC 60.336 44.000 0.00 0.00 31.08 3.68
280 281 4.133820 CCAGTTTCCTGTACATGAACACA 58.866 43.478 12.47 0.00 36.95 3.72
284 285 6.426633 CAGTTTCCTGTACATGAACACATACA 59.573 38.462 12.47 0.00 33.80 2.29
285 286 7.119699 CAGTTTCCTGTACATGAACACATACAT 59.880 37.037 12.47 0.00 33.80 2.29
286 287 8.318412 AGTTTCCTGTACATGAACACATACATA 58.682 33.333 12.47 0.00 0.00 2.29
288 289 9.679661 TTTCCTGTACATGAACACATACATAAT 57.320 29.630 12.47 0.00 0.00 1.28
289 290 9.679661 TTCCTGTACATGAACACATACATAATT 57.320 29.630 9.25 0.00 0.00 1.40
290 291 9.325198 TCCTGTACATGAACACATACATAATTC 57.675 33.333 0.00 0.00 0.00 2.17
291 292 9.330063 CCTGTACATGAACACATACATAATTCT 57.670 33.333 0.00 0.00 0.00 2.40
295 296 7.475015 ACATGAACACATACATAATTCTGCAC 58.525 34.615 0.00 0.00 0.00 4.57
296 297 7.337689 ACATGAACACATACATAATTCTGCACT 59.662 33.333 0.00 0.00 0.00 4.40
297 298 7.075674 TGAACACATACATAATTCTGCACTG 57.924 36.000 0.00 0.00 0.00 3.66
298 299 6.878389 TGAACACATACATAATTCTGCACTGA 59.122 34.615 0.00 0.00 0.00 3.41
299 300 7.553760 TGAACACATACATAATTCTGCACTGAT 59.446 33.333 0.00 0.00 0.00 2.90
300 301 8.962884 AACACATACATAATTCTGCACTGATA 57.037 30.769 0.00 0.00 0.00 2.15
362 387 8.641541 ACAAAGAAATATGTCATTGTCAACCTT 58.358 29.630 10.12 0.00 35.16 3.50
394 419 6.595772 AAAGAATTTATCAGCTCTAGTGCG 57.404 37.500 10.93 6.70 35.86 5.34
440 465 9.467990 CAAATGAATTTGCAAAATTAGACATCG 57.532 29.630 17.19 7.09 40.42 3.84
470 496 8.802267 TCCTTTGGCCTATAATTTATACAATGC 58.198 33.333 3.32 0.00 0.00 3.56
597 627 7.254932 GTAACCTTTTACCAAATGCAAATGCAA 60.255 33.333 12.67 0.00 41.96 4.08
719 749 1.407437 GGGGACAGCATTCGAGATGTT 60.407 52.381 0.00 0.00 38.41 2.71
962 1001 2.094752 CCATGGTCCCGTTCAACATTTC 60.095 50.000 2.57 0.00 0.00 2.17
1217 2611 5.741510 TCTGTTTTTGTGCATGAGTTTAACG 59.258 36.000 0.00 0.00 0.00 3.18
1480 2875 2.040145 TGGATGTCAATCTGAAGCCACA 59.960 45.455 0.00 0.00 32.95 4.17
1581 3060 4.396166 ACATTGGCAGTGTAAGTAATGAGC 59.604 41.667 14.46 0.00 31.79 4.26
1671 3150 1.772063 GACGGACGTGCAAGTTGCTT 61.772 55.000 27.17 12.54 45.31 3.91
2071 3650 6.040278 TCAACAGGTAAAAATCTGCAACATGA 59.960 34.615 0.00 0.00 34.57 3.07
2105 3684 0.468585 TCCAATGGCATGCCCTGATC 60.469 55.000 33.44 8.41 34.56 2.92
2135 3714 3.697424 TGCAGAATGGCGGCAATT 58.303 50.000 18.31 11.09 44.72 2.32
2540 4182 3.244353 CCCGCCAATAGAAGATCAGACAT 60.244 47.826 0.00 0.00 0.00 3.06
2575 4217 5.172687 AGTTTTCTTTTGCCTTCCCAAAA 57.827 34.783 0.00 0.00 41.07 2.44
2587 4229 2.576832 CCCAAAAGGGTGCCTGCAG 61.577 63.158 6.78 6.78 32.13 4.41
2817 4459 4.162690 GGATCCGCCAACCTCGCT 62.163 66.667 0.00 0.00 36.34 4.93
3011 4653 6.526566 ACTTAGTAAAAGAAACACAGCTCG 57.473 37.500 0.00 0.00 0.00 5.03
3205 4847 8.778358 CCTTTATTCACTGCTTCTATCAATACC 58.222 37.037 0.00 0.00 0.00 2.73
3245 4887 1.138069 TCGTTGGAGTCTTCTTGCACA 59.862 47.619 0.00 0.00 0.00 4.57
3822 5464 5.295950 TGATGAAAATTTGTGGCGTTTGAT 58.704 33.333 0.00 0.00 0.00 2.57
3901 5543 3.322254 TGTCGGTTTACAATGGGCAATTT 59.678 39.130 0.00 0.00 0.00 1.82
4086 5729 0.891373 GCTGTGCAGAGAGGTAGTCA 59.109 55.000 16.28 0.00 0.00 3.41
4170 5985 1.737793 GGGTAAATGCCGAGAGTGTTG 59.262 52.381 0.00 0.00 0.00 3.33
4291 6106 2.290960 GGTGGAGGAGGCTAAACATTGT 60.291 50.000 0.00 0.00 0.00 2.71
4472 6287 1.412387 GAGCGCCTCAAAGCTTTTTG 58.588 50.000 9.53 5.11 44.69 2.44
4575 6390 3.222287 AGAGGAGCTTAGCCCTCTG 57.778 57.895 29.94 0.00 46.56 3.35
4679 6494 1.841302 GACACAGACCAGCCCATCCA 61.841 60.000 0.00 0.00 0.00 3.41
4762 6577 5.012046 AGTGAATGATGGACACTGTAACAGA 59.988 40.000 0.00 0.00 42.18 3.41
4774 6589 2.215196 TGTAACAGAACAAAGACGGGC 58.785 47.619 0.00 0.00 0.00 6.13
4798 6613 6.538742 GCCGATTAGTACCATAATGCATGTAT 59.461 38.462 0.00 0.00 32.21 2.29
5032 6848 4.430441 ACCTGAACTTCTACTGGATCCTT 58.570 43.478 14.23 2.24 0.00 3.36
5145 6961 6.866010 TGCGTCAATGCAAATCTTCTATAT 57.134 33.333 0.00 0.00 43.02 0.86
5168 6984 2.579201 CCTGTCGACAAGCCCGAT 59.421 61.111 20.49 0.00 38.38 4.18
5372 7188 2.505819 CCCTATATAGTGTGGGATGGGC 59.494 54.545 8.92 0.00 42.11 5.36
5373 7189 3.454858 CCTATATAGTGTGGGATGGGCT 58.545 50.000 8.92 0.00 0.00 5.19
5374 7190 4.574172 CCCTATATAGTGTGGGATGGGCTA 60.574 50.000 8.92 0.00 42.11 3.93
5376 7192 4.910458 ATATAGTGTGGGATGGGCTAAC 57.090 45.455 0.00 0.00 0.00 2.34
5377 7193 2.263895 TAGTGTGGGATGGGCTAACT 57.736 50.000 0.00 0.00 0.00 2.24
5378 7194 1.372501 AGTGTGGGATGGGCTAACTT 58.627 50.000 0.00 0.00 0.00 2.66
5450 7269 2.492088 GTGACAAGGTTATTTGGCCCTC 59.508 50.000 0.00 0.00 35.11 4.30
5451 7270 2.100197 GACAAGGTTATTTGGCCCTCC 58.900 52.381 0.00 0.00 29.48 4.30
5452 7271 1.716503 ACAAGGTTATTTGGCCCTCCT 59.283 47.619 0.00 0.00 32.32 3.69
5453 7272 2.923629 ACAAGGTTATTTGGCCCTCCTA 59.076 45.455 0.00 0.00 32.32 2.94
5454 7273 3.053619 ACAAGGTTATTTGGCCCTCCTAG 60.054 47.826 0.00 0.00 32.32 3.02
5455 7274 2.859951 AGGTTATTTGGCCCTCCTAGT 58.140 47.619 0.00 0.00 0.00 2.57
5496 7315 0.531657 TGCTTTGCTGCTGTTGTGTT 59.468 45.000 0.00 0.00 0.00 3.32
5638 7457 2.793232 GGAGTCACGTGTCTTGTGTTAC 59.207 50.000 16.33 3.56 38.48 2.50
5735 7567 9.445878 AGAGATTTCAATACGGACTATATACGA 57.554 33.333 0.00 0.00 0.00 3.43
5785 7617 5.888105 AGATTCACTCATTTTGCTGTATGC 58.112 37.500 0.00 0.00 43.25 3.14
5937 7771 2.728839 ACATTAATTGTGCGTTTTGCCG 59.271 40.909 0.00 0.00 45.60 5.69
6007 7851 4.455070 TTGCTATCACCTAGAGCCTAGA 57.545 45.455 9.94 0.00 41.98 2.43
6033 7877 0.321210 TAAGTGCTTGCTTAGGCGCA 60.321 50.000 10.83 0.00 42.25 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 0.584396 TCGCTTGTAACTTGTTGCCG 59.416 50.000 0.00 0.00 0.00 5.69
227 228 5.712152 AGCAAACCCTAAGTCTGAAATTG 57.288 39.130 0.00 0.00 0.00 2.32
228 229 6.731292 AAAGCAAACCCTAAGTCTGAAATT 57.269 33.333 0.00 0.00 0.00 1.82
229 230 6.731292 AAAAGCAAACCCTAAGTCTGAAAT 57.269 33.333 0.00 0.00 0.00 2.17
230 231 6.538945 AAAAAGCAAACCCTAAGTCTGAAA 57.461 33.333 0.00 0.00 0.00 2.69
261 262 6.795098 TGTATGTGTTCATGTACAGGAAAC 57.205 37.500 23.28 20.94 32.61 2.78
390 415 3.485877 GGCTGACAATGACTTTATCGCAC 60.486 47.826 0.00 0.00 0.00 5.34
394 419 6.500684 TTTGAGGCTGACAATGACTTTATC 57.499 37.500 0.00 0.00 0.00 1.75
499 525 3.179443 TCTATTCCTTGCATGGTCGAC 57.821 47.619 17.54 7.13 0.00 4.20
509 535 3.758023 TGTGCATGTGGTTCTATTCCTTG 59.242 43.478 0.00 0.00 0.00 3.61
597 627 5.667626 TGGAGTAGGGAGATTAAATTCAGCT 59.332 40.000 0.00 0.00 0.00 4.24
672 702 8.795786 TGCACAAAATAGAAAATACTGTTCAC 57.204 30.769 0.00 0.00 0.00 3.18
719 749 7.492020 GGCAATAAAATAGTGATGTTGCATTGA 59.508 33.333 11.01 0.00 41.47 2.57
1114 2508 5.652014 GGACCCAACATGATGTAAAGATTGA 59.348 40.000 0.00 0.00 0.00 2.57
1217 2611 3.381045 GCCTCTGCAACAAAAACTTACC 58.619 45.455 0.00 0.00 37.47 2.85
1281 2675 1.718757 GCCATGGCTTTACTGGCGAG 61.719 60.000 29.98 0.00 45.35 5.03
1480 2875 2.661866 GCAGCCACGTCGAGTTGT 60.662 61.111 0.00 0.00 0.00 3.32
1581 3060 3.129287 GGTAAGTCCTGCATTCCAACATG 59.871 47.826 0.00 0.00 0.00 3.21
1613 3092 1.496001 TCCTCCACGTAGCTATACCCA 59.504 52.381 0.00 0.00 0.00 4.51
1667 3146 1.078918 CTCGGTGGCATCAGAAGCA 60.079 57.895 0.00 0.00 0.00 3.91
1671 3150 2.725312 GGAGCTCGGTGGCATCAGA 61.725 63.158 7.83 0.00 34.17 3.27
1775 3255 1.943340 GCCACGGAGATTCCAATCTTC 59.057 52.381 3.31 0.60 45.39 2.87
2014 3593 2.329678 CTTCGTCGCTCAGCCTCGAT 62.330 60.000 10.85 0.00 37.06 3.59
2071 3650 4.330250 CCATTGGAGATCGAGGCAAATAT 58.670 43.478 0.00 0.00 0.00 1.28
2105 3684 4.802039 GCCATTCTGCAAACAACATATCAG 59.198 41.667 0.00 0.00 0.00 2.90
2135 3714 3.535561 GGCTGCTATCTGCTCTTTTACA 58.464 45.455 0.00 0.00 43.37 2.41
2392 4028 1.066502 GGTTGGTTGCAACTGTTTGGT 60.067 47.619 27.64 0.00 35.54 3.67
2540 4182 6.237969 GCAAAAGAAAACTAACATTGGCGAAA 60.238 34.615 0.00 0.00 0.00 3.46
2575 4217 1.225704 GAATAGCTGCAGGCACCCT 59.774 57.895 17.12 5.92 44.79 4.34
2587 4229 6.529220 AGATGATTGGTTACCTCAGAATAGC 58.471 40.000 2.07 0.00 0.00 2.97
3011 4653 1.375523 CCGTTCTGGCCTACACCAC 60.376 63.158 3.32 0.00 35.33 4.16
3129 4771 1.200020 GGTCCAAGGATGTTGCTTTCG 59.800 52.381 0.00 0.00 0.00 3.46
3205 4847 5.103000 ACGAGGATCTGAAAGTTGTTATCG 58.897 41.667 0.00 0.00 33.76 2.92
3245 4887 4.231890 TCCTCTATTTATTTTGGGCCTGGT 59.768 41.667 4.53 0.00 0.00 4.00
3637 5279 9.699410 ATTTGAGTAAGATGATATTTTGGGTGA 57.301 29.630 0.00 0.00 0.00 4.02
3665 5307 8.651588 CAGTTTAATCAGATATCAGATTACGGC 58.348 37.037 23.04 17.12 35.16 5.68
3822 5464 8.898761 CCTAACCAAGTAAACATGCATAACATA 58.101 33.333 0.00 0.00 36.64 2.29
3901 5543 3.983344 CGATTGTCGAGCATATCACATCA 59.017 43.478 0.00 0.00 43.74 3.07
4030 5672 1.664321 CTCTGCCTTGAAGCCCATGC 61.664 60.000 0.00 0.00 37.95 4.06
4086 5729 1.141881 CTCCGCTATGTCTTGGCGT 59.858 57.895 13.98 0.00 46.23 5.68
4170 5985 4.660938 AAGGCCACCCTGGTTCGC 62.661 66.667 5.01 0.00 41.90 4.70
4275 6090 6.969993 TTGTTTTACAATGTTTAGCCTCCT 57.030 33.333 0.00 0.00 32.34 3.69
4465 6280 1.419381 TTCCAACTCCCCCAAAAAGC 58.581 50.000 0.00 0.00 0.00 3.51
4472 6287 1.133606 TGTCAGTTTTCCAACTCCCCC 60.134 52.381 0.00 0.00 41.69 5.40
4574 6389 4.082081 CAGCTTCAAATATCAAACAGGGCA 60.082 41.667 0.00 0.00 0.00 5.36
4575 6390 4.082026 ACAGCTTCAAATATCAAACAGGGC 60.082 41.667 0.00 0.00 0.00 5.19
4762 6577 1.002773 ACTAATCGGCCCGTCTTTGTT 59.997 47.619 1.63 0.00 0.00 2.83
4774 6589 7.549134 ACATACATGCATTATGGTACTAATCGG 59.451 37.037 22.03 2.30 41.25 4.18
5032 6848 0.685097 GTACCTTGTGTCCAGCTCCA 59.315 55.000 0.00 0.00 0.00 3.86
5089 6905 6.128172 GCTTCAGTTTGCACATAAGATGTACT 60.128 38.462 0.00 0.00 42.70 2.73
5145 6961 1.292223 GCTTGTCGACAGGCACCTA 59.708 57.895 38.27 14.81 46.60 3.08
5168 6984 4.334552 TGCTGATCATCCTTAAAGCAACA 58.665 39.130 0.00 0.00 37.69 3.33
5175 6991 3.181462 ACGATGCTGCTGATCATCCTTAA 60.181 43.478 0.00 0.00 36.60 1.85
5372 7188 4.081752 AGTCACATCTCAGGCTCAAGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
5373 7189 3.834813 AGTCACATCTCAGGCTCAAGTTA 59.165 43.478 0.00 0.00 0.00 2.24
5374 7190 2.636893 AGTCACATCTCAGGCTCAAGTT 59.363 45.455 0.00 0.00 0.00 2.66
5376 7192 2.496871 AGAGTCACATCTCAGGCTCAAG 59.503 50.000 0.00 0.00 36.97 3.02
5377 7193 2.495270 GAGAGTCACATCTCAGGCTCAA 59.505 50.000 0.00 0.00 44.32 3.02
5378 7194 2.098614 GAGAGTCACATCTCAGGCTCA 58.901 52.381 0.00 0.00 44.32 4.26
5450 7269 1.141254 TCTCCTCACGCTAGGACTAGG 59.859 57.143 8.33 1.85 40.86 3.02
5451 7270 2.215196 GTCTCCTCACGCTAGGACTAG 58.785 57.143 2.27 1.98 40.86 2.57
5452 7271 1.134159 GGTCTCCTCACGCTAGGACTA 60.134 57.143 2.27 0.00 40.86 2.59
5453 7272 0.394625 GGTCTCCTCACGCTAGGACT 60.395 60.000 2.27 0.00 40.86 3.85
5454 7273 0.394625 AGGTCTCCTCACGCTAGGAC 60.395 60.000 2.27 0.00 40.86 3.85
5455 7274 2.000164 AGGTCTCCTCACGCTAGGA 59.000 57.895 6.22 6.22 43.58 2.94
5496 7315 4.223255 ACATGCAACCAATCAAATGGATCA 59.777 37.500 0.00 0.00 43.54 2.92
5638 7457 4.398319 ACGATAATCCAAATAGGGCCTTG 58.602 43.478 13.45 3.49 38.24 3.61
5688 7509 6.158695 TCTCTAAAAAGGCTTGGATGGAGTAT 59.841 38.462 0.00 0.00 0.00 2.12
5689 7510 5.487488 TCTCTAAAAAGGCTTGGATGGAGTA 59.513 40.000 0.00 0.00 0.00 2.59
5690 7511 4.289672 TCTCTAAAAAGGCTTGGATGGAGT 59.710 41.667 0.00 0.00 0.00 3.85
5691 7512 4.848357 TCTCTAAAAAGGCTTGGATGGAG 58.152 43.478 0.00 7.31 0.00 3.86
5697 7529 7.698130 CGTATTGAAATCTCTAAAAAGGCTTGG 59.302 37.037 0.00 0.00 0.00 3.61
5785 7617 7.284034 ACCTTTTAGAGATTCCAATATGCACTG 59.716 37.037 0.00 0.00 0.00 3.66
5829 7663 1.511768 GCTGAGACGTGTACTCCCC 59.488 63.158 0.00 0.00 33.95 4.81


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

AutoCloner maintained by Alex Coulton.