Multiple sequence alignment - TraesCS5D01G407000

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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 TraesCS5D01G407000 chr5D 100.000 2639 0 0 1 2639 472398412 472401050 0.000000e+00 4874.0
1 TraesCS5D01G407000 chr5B 88.381 2255 174 36 1 2208 578814423 578816636 0.000000e+00 2632.0
2 TraesCS5D01G407000 chr5B 84.857 1017 105 20 709 1683 579003104 579004113 0.000000e+00 979.0
3 TraesCS5D01G407000 chr5B 91.463 328 28 0 2291 2618 578816641 578816968 4.010000e-123 451.0
4 TraesCS5D01G407000 chr5B 81.628 430 64 12 2034 2457 579007815 579008235 2.520000e-90 342.0
5 TraesCS5D01G407000 chr5B 79.475 419 84 2 1305 1722 579150042 579150459 1.990000e-76 296.0
6 TraesCS5D01G407000 chr5A 89.443 1042 93 7 685 1710 591673240 591674280 0.000000e+00 1299.0
7 TraesCS5D01G407000 chr5A 84.593 701 56 31 1 661 591672483 591673171 0.000000e+00 649.0
8 TraesCS5D01G407000 chr5A 80.935 535 84 14 2034 2554 591675575 591676105 8.790000e-110 407.0
9 TraesCS5D01G407000 chr5A 77.647 340 62 11 1356 1691 671198718 671199047 7.450000e-46 195.0
10 TraesCS5D01G407000 chr5A 79.275 193 33 5 1533 1722 591868594 591868782 7.670000e-26 128.0
11 TraesCS5D01G407000 chr5A 79.096 177 29 6 2034 2208 632364324 632364494 5.970000e-22 115.0
12 TraesCS5D01G407000 chr4D 75.610 574 118 19 1126 1691 489751225 489751784 5.600000e-67 265.0
13 TraesCS5D01G407000 chr4D 79.570 186 36 2 2042 2226 471425840 471425656 5.930000e-27 132.0
14 TraesCS5D01G407000 chr4B 75.436 574 119 21 1126 1691 628709645 628710204 2.610000e-65 259.0
15 TraesCS5D01G407000 chr3B 78.109 201 36 7 2042 2239 787440578 787440773 1.280000e-23 121.0
16 TraesCS5D01G407000 chr2B 77.540 187 37 5 2051 2235 2080970 2081153 9.990000e-20 108.0
17 TraesCS5D01G407000 chr2B 76.720 189 37 5 2042 2230 597886350 597886531 6.010000e-17 99.0
18 TraesCS5D01G407000 chr6B 76.410 195 43 3 2042 2235 717633365 717633557 4.650000e-18 102.0
19 TraesCS5D01G407000 chr6D 80.303 132 24 2 2076 2207 429826943 429826814 6.010000e-17 99.0
20 TraesCS5D01G407000 chr2A 91.489 47 0 2 2359 2401 14817959 14817913 7.890000e-06 62.1
21 TraesCS5D01G407000 chr4A 100.000 28 0 0 2371 2398 669168363 669168390 5.000000e-03 52.8
22 TraesCS5D01G407000 chr1B 100.000 28 0 0 2371 2398 197750330 197750357 5.000000e-03 52.8


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 TraesCS5D01G407000 chr5D 472398412 472401050 2638 False 4874.0 4874 100.000000 1 2639 1 chr5D.!!$F1 2638
1 TraesCS5D01G407000 chr5B 578814423 578816968 2545 False 1541.5 2632 89.922000 1 2618 2 chr5B.!!$F2 2617
2 TraesCS5D01G407000 chr5B 579003104 579008235 5131 False 660.5 979 83.242500 709 2457 2 chr5B.!!$F3 1748
3 TraesCS5D01G407000 chr5A 591672483 591676105 3622 False 785.0 1299 84.990333 1 2554 3 chr5A.!!$F4 2553
4 TraesCS5D01G407000 chr4D 489751225 489751784 559 False 265.0 265 75.610000 1126 1691 1 chr4D.!!$F1 565
5 TraesCS5D01G407000 chr4B 628709645 628710204 559 False 259.0 259 75.436000 1126 1691 1 chr4B.!!$F1 565

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
883 984 0.103208 CCGGAAACTCGAGGAGGATG 59.897 60.0 18.41 1.66 33.35 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 6237 0.462789 ACGGGCCCTATTGTTAGTCG 59.537 55.0 22.43 3.91 0.0 4.18 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
30 31 0.246910 TGCGCCGGTCTATGTAAACA 59.753 50.000 4.18 0.00 0.00 2.83
69 79 8.565896 TTACTAGTAGTAACATTTCCGTCAGA 57.434 34.615 17.12 0.00 35.89 3.27
116 126 3.425359 GCGACATTTGACCTGATCTTGTG 60.425 47.826 0.00 0.00 0.00 3.33
117 127 3.425359 CGACATTTGACCTGATCTTGTGC 60.425 47.826 0.00 0.00 0.00 4.57
162 172 0.433492 CGTACGTACACTGCACTTGC 59.567 55.000 24.50 0.00 42.50 4.01
253 272 4.084287 TCGTTCTATACACTCCACTTGGT 58.916 43.478 0.00 0.00 36.34 3.67
261 280 9.429109 TCTATACACTCCACTTGGTTAATATGA 57.571 33.333 0.00 0.00 36.34 2.15
288 313 4.866508 TGGTCTGTTAGACAGTTACTGG 57.133 45.455 17.21 0.00 46.79 4.00
383 408 7.944061 TCCCGATAATAACGAGTAGATTTTCA 58.056 34.615 0.00 0.00 0.00 2.69
392 417 5.779922 ACGAGTAGATTTTCAGCAACTACA 58.220 37.500 0.00 0.00 36.78 2.74
393 418 5.634020 ACGAGTAGATTTTCAGCAACTACAC 59.366 40.000 0.00 0.00 36.78 2.90
408 433 5.228012 GCAACTACACGTAAACGGAGTATAC 59.772 44.000 7.50 0.00 45.00 1.47
417 442 7.009448 CACGTAAACGGAGTATACATAAGCAAA 59.991 37.037 5.50 0.00 45.00 3.68
418 443 7.221452 ACGTAAACGGAGTATACATAAGCAAAG 59.779 37.037 5.50 0.00 45.00 2.77
422 447 7.916914 ACGGAGTATACATAAGCAAAGTTTT 57.083 32.000 5.50 0.00 41.94 2.43
423 448 7.971455 ACGGAGTATACATAAGCAAAGTTTTC 58.029 34.615 5.50 0.00 41.94 2.29
424 449 7.117454 CGGAGTATACATAAGCAAAGTTTTCG 58.883 38.462 5.50 0.00 0.00 3.46
425 450 7.201496 CGGAGTATACATAAGCAAAGTTTTCGT 60.201 37.037 5.50 0.00 0.00 3.85
434 459 4.993905 AGCAAAGTTTTCGTAGCAACTTT 58.006 34.783 4.90 4.90 45.26 2.66
439 464 5.344207 AGTTTTCGTAGCAACTTTAGCAG 57.656 39.130 0.00 0.00 28.37 4.24
450 475 4.383948 GCAACTTTAGCAGAATCAAAGCAC 59.616 41.667 0.00 0.00 33.50 4.40
452 477 5.368256 ACTTTAGCAGAATCAAAGCACTG 57.632 39.130 0.00 0.00 33.50 3.66
474 501 5.865085 TGAAGCTCAGTAGTACAACCAAAT 58.135 37.500 2.52 0.00 0.00 2.32
475 502 5.700832 TGAAGCTCAGTAGTACAACCAAATG 59.299 40.000 2.52 0.00 0.00 2.32
483 510 6.372659 CAGTAGTACAACCAAATGAAGCTCAT 59.627 38.462 2.52 0.00 39.09 2.90
670 717 1.866483 ATGATCCAGCCAGCCAACCA 61.866 55.000 0.00 0.00 0.00 3.67
707 808 1.761784 AGCCTGATGATCTCTCCACAC 59.238 52.381 0.00 0.00 0.00 3.82
787 888 2.484203 GCGCTTACGTCCTCGAGT 59.516 61.111 12.31 0.00 42.83 4.18
814 915 2.423446 CGATGGGCAGGACCTAGC 59.577 66.667 0.00 0.02 39.10 3.42
874 975 2.033194 GGCCTCAACCGGAAACTCG 61.033 63.158 9.46 0.00 0.00 4.18
875 976 1.005394 GCCTCAACCGGAAACTCGA 60.005 57.895 9.46 0.00 0.00 4.04
882 983 0.324460 ACCGGAAACTCGAGGAGGAT 60.324 55.000 18.41 0.00 33.35 3.24
883 984 0.103208 CCGGAAACTCGAGGAGGATG 59.897 60.000 18.41 1.66 33.35 3.51
884 985 0.818296 CGGAAACTCGAGGAGGATGT 59.182 55.000 18.41 0.00 33.35 3.06
886 987 1.134670 GGAAACTCGAGGAGGATGTGG 60.135 57.143 18.41 0.00 33.35 4.17
887 988 1.550976 GAAACTCGAGGAGGATGTGGT 59.449 52.381 18.41 0.00 33.35 4.16
891 1007 2.091830 ACTCGAGGAGGATGTGGTCATA 60.092 50.000 18.41 0.00 33.35 2.15
900 1016 3.912528 AGGATGTGGTCATATATGGTGCT 59.087 43.478 12.78 1.34 34.06 4.40
1008 1133 2.025887 GTGGGAGGTGGTGATGAAAGAT 60.026 50.000 0.00 0.00 0.00 2.40
1058 1183 3.206150 ACAAACTGAAGAATGACACGCT 58.794 40.909 0.00 0.00 0.00 5.07
1102 1227 0.600255 CGACGGACTTATGGATGGCC 60.600 60.000 0.00 0.00 0.00 5.36
1143 1268 4.148825 GTCTGGCTCGTCGGGCAT 62.149 66.667 20.58 0.00 40.86 4.40
1196 1321 1.530771 GGCACATGATGGAGAGGCT 59.469 57.895 0.00 0.00 0.00 4.58
1221 1346 0.410663 TGAACCTCCCGACCTTCCTA 59.589 55.000 0.00 0.00 0.00 2.94
1227 1352 2.706190 CCTCCCGACCTTCCTATTCAAT 59.294 50.000 0.00 0.00 0.00 2.57
1289 1414 1.300620 CGCAGGACGTGGTCAAGAA 60.301 57.895 0.00 0.00 36.87 2.52
1315 1440 3.381045 CTGCACTTCACGAGTTACTTCA 58.619 45.455 0.00 0.00 36.10 3.02
1342 1467 2.661866 GTGCGGCAACAGTCTCGT 60.662 61.111 3.23 0.00 0.00 4.18
1351 1476 0.107897 AACAGTCTCGTGTTGCCACA 60.108 50.000 0.00 0.00 41.93 4.17
1376 1501 1.427020 GCATGGAGAAGCTGTTCGC 59.573 57.895 0.00 0.00 37.79 4.70
1386 1511 2.358737 CTGTTCGCCCGGCTTTCT 60.359 61.111 8.05 0.00 0.00 2.52
1503 1640 1.027357 CCTGTGTTGCAAGCAAGTCT 58.973 50.000 7.88 0.00 36.52 3.24
1637 1776 3.390521 CGGGCTCCAGCAGTGGTA 61.391 66.667 0.03 0.00 45.28 3.25
1750 4846 1.598924 GCAAGCTGTCAAGTGCAGTTC 60.599 52.381 3.08 0.00 36.97 3.01
1835 4931 9.953565 ACCAATTTAGCTATAGTGAGTTGTAAA 57.046 29.630 12.37 0.00 0.00 2.01
1861 5274 5.450592 TGTGCTAGAACAATTGCAAATGA 57.549 34.783 21.10 0.00 37.17 2.57
1949 5362 0.733150 GCGTTGGTTTGATAGAGGCC 59.267 55.000 0.00 0.00 0.00 5.19
1951 5364 1.674817 CGTTGGTTTGATAGAGGCCGT 60.675 52.381 0.00 0.00 0.00 5.68
1956 5369 1.632018 TTTGATAGAGGCCGTGGGGG 61.632 60.000 0.00 0.00 39.58 5.40
1998 5529 5.413213 CCATCCAACAATTGCAAATGACAAT 59.587 36.000 21.10 6.14 39.38 2.71
2090 5736 2.034812 CCTGTAGACTATGAAGGCGTCC 59.965 54.545 0.00 0.00 35.06 4.79
2136 5782 3.687125 TGATGTACCGACTCAGTCTCTT 58.313 45.455 2.61 0.00 0.00 2.85
2141 5787 1.074084 ACCGACTCAGTCTCTTGGAGA 59.926 52.381 2.61 0.00 36.22 3.71
2149 5795 3.384146 TCAGTCTCTTGGAGATGCTCATC 59.616 47.826 1.75 1.75 40.98 2.92
2154 5800 1.347050 CTTGGAGATGCTCATCGGGAT 59.653 52.381 4.41 0.00 42.48 3.85
2216 5872 5.047872 TGTTTGTTGTATGAGCATCTGCATT 60.048 36.000 4.79 0.00 45.16 3.56
2231 5887 8.562892 AGCATCTGCATTTGTACTATGATAAAC 58.437 33.333 4.79 0.00 45.16 2.01
2281 5937 4.877378 AACTACACAATAGACCCGACAA 57.123 40.909 0.00 0.00 0.00 3.18
2285 5941 3.135994 ACACAATAGACCCGACAACAAC 58.864 45.455 0.00 0.00 0.00 3.32
2289 5945 4.825085 ACAATAGACCCGACAACAACAATT 59.175 37.500 0.00 0.00 0.00 2.32
2350 6006 8.606830 ACTTCTCCAATCCTAAAATTAGTGTCT 58.393 33.333 0.00 0.00 0.00 3.41
2388 6044 3.030873 TGCTTATTTTGGGATGGAGGG 57.969 47.619 0.00 0.00 0.00 4.30
2502 6162 7.989741 ACTTTATAGAGATTTGAGTGGATGTGG 59.010 37.037 0.00 0.00 0.00 4.17
2538 6198 7.372451 TCCTTAGAAATTCCAATGTTACACG 57.628 36.000 0.00 0.00 0.00 4.49
2539 6199 6.373216 TCCTTAGAAATTCCAATGTTACACGG 59.627 38.462 0.00 0.00 0.00 4.94
2544 6204 3.328382 TTCCAATGTTACACGGGAGAG 57.672 47.619 0.00 0.00 0.00 3.20
2557 6217 4.184629 CACGGGAGAGTTTCTTAGGATTG 58.815 47.826 0.00 0.00 0.00 2.67
2577 6237 9.620259 AGGATTGATGTAAGTCCTCTAAAAATC 57.380 33.333 0.00 0.00 36.36 2.17
2578 6238 8.552034 GGATTGATGTAAGTCCTCTAAAAATCG 58.448 37.037 0.00 0.00 0.00 3.34
2581 6241 7.837863 TGATGTAAGTCCTCTAAAAATCGACT 58.162 34.615 0.00 0.00 35.34 4.18
2590 6250 9.032420 GTCCTCTAAAAATCGACTAACAATAGG 57.968 37.037 0.00 0.00 33.15 2.57
2599 6259 1.153329 TAACAATAGGGCCCGTGCG 60.153 57.895 18.44 9.60 38.85 5.34
2601 6261 2.437716 CAATAGGGCCCGTGCGTT 60.438 61.111 18.44 5.19 38.85 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.179094 TTTACATAGACCGGCGCAGG 60.179 55.000 25.72 25.72 37.30 4.85
14 15 3.124636 CACTGTTGTTTACATAGACCGGC 59.875 47.826 0.00 0.00 35.85 6.13
48 54 7.177216 TCCTTTCTGACGGAAATGTTACTACTA 59.823 37.037 9.87 0.00 42.25 1.82
49 55 6.014840 TCCTTTCTGACGGAAATGTTACTACT 60.015 38.462 9.87 0.00 42.25 2.57
50 56 6.161381 TCCTTTCTGACGGAAATGTTACTAC 58.839 40.000 9.87 0.00 42.25 2.73
116 126 1.993370 ACGTACTTGCTCTTCGAATGC 59.007 47.619 14.04 14.04 0.00 3.56
117 127 3.237660 CGTACGTACTTGCTCTTCGAATG 59.762 47.826 22.55 0.00 0.00 2.67
272 297 4.591498 ACATGACCCAGTAACTGTCTAACA 59.409 41.667 0.00 0.00 0.00 2.41
273 298 5.148651 ACATGACCCAGTAACTGTCTAAC 57.851 43.478 0.00 0.00 0.00 2.34
274 299 5.818678 AACATGACCCAGTAACTGTCTAA 57.181 39.130 0.00 0.00 0.00 2.10
275 300 6.014647 ACTAACATGACCCAGTAACTGTCTA 58.985 40.000 0.00 0.00 0.00 2.59
276 301 4.838986 ACTAACATGACCCAGTAACTGTCT 59.161 41.667 0.00 0.00 0.00 3.41
277 302 4.929808 CACTAACATGACCCAGTAACTGTC 59.070 45.833 0.00 0.00 0.00 3.51
278 303 4.591498 TCACTAACATGACCCAGTAACTGT 59.409 41.667 0.00 0.00 0.00 3.55
383 408 2.035066 ACTCCGTTTACGTGTAGTTGCT 59.965 45.455 0.00 0.00 37.74 3.91
392 417 6.135290 TGCTTATGTATACTCCGTTTACGT 57.865 37.500 4.17 0.00 37.74 3.57
393 418 7.221452 ACTTTGCTTATGTATACTCCGTTTACG 59.779 37.037 4.17 0.00 39.44 3.18
408 433 6.142817 AGTTGCTACGAAAACTTTGCTTATG 58.857 36.000 0.00 0.00 32.75 1.90
417 442 5.054477 TCTGCTAAAGTTGCTACGAAAACT 58.946 37.500 0.00 0.00 38.25 2.66
418 443 5.338614 TCTGCTAAAGTTGCTACGAAAAC 57.661 39.130 0.00 0.00 0.00 2.43
422 447 4.816392 TGATTCTGCTAAAGTTGCTACGA 58.184 39.130 0.00 0.00 0.00 3.43
423 448 5.530519 TTGATTCTGCTAAAGTTGCTACG 57.469 39.130 0.00 0.00 0.00 3.51
424 449 5.797434 GCTTTGATTCTGCTAAAGTTGCTAC 59.203 40.000 0.00 0.00 34.69 3.58
425 450 5.473162 TGCTTTGATTCTGCTAAAGTTGCTA 59.527 36.000 0.00 0.00 34.69 3.49
434 459 3.438087 GCTTCAGTGCTTTGATTCTGCTA 59.562 43.478 0.00 0.00 0.00 3.49
439 464 4.080969 CTGAGCTTCAGTGCTTTGATTC 57.919 45.455 0.00 0.00 44.17 2.52
452 477 5.932303 TCATTTGGTTGTACTACTGAGCTTC 59.068 40.000 7.38 0.00 0.00 3.86
474 501 3.421919 TGATCCACAACATGAGCTTCA 57.578 42.857 0.00 0.00 0.00 3.02
475 502 4.514441 CCTATGATCCACAACATGAGCTTC 59.486 45.833 0.00 0.00 0.00 3.86
483 510 5.453339 GCTAAGCTACCTATGATCCACAACA 60.453 44.000 0.00 0.00 0.00 3.33
583 630 0.456824 TGCTTCAGCTCATCGACGTC 60.457 55.000 5.18 5.18 42.66 4.34
670 717 6.924913 TCAGGCTATGCAGATACTAAATCT 57.075 37.500 0.00 0.00 0.00 2.40
707 808 1.299541 GCCCCTGTGACATTGATACG 58.700 55.000 0.00 0.00 0.00 3.06
750 851 1.926511 CTTTGACCATGCAGGCGACC 61.927 60.000 0.00 0.00 43.14 4.79
787 888 4.819761 GCCCATCGCTCTGTCGCA 62.820 66.667 0.00 0.00 0.00 5.10
845 946 0.875059 GTTGAGGCCGAAGTGAAAGG 59.125 55.000 0.00 0.00 0.00 3.11
856 957 2.033194 CGAGTTTCCGGTTGAGGCC 61.033 63.158 0.00 0.00 0.00 5.19
866 967 1.134670 CCACATCCTCCTCGAGTTTCC 60.135 57.143 12.31 0.00 0.00 3.13
874 975 4.780021 ACCATATATGACCACATCCTCCTC 59.220 45.833 14.54 0.00 37.87 3.71
875 976 4.533707 CACCATATATGACCACATCCTCCT 59.466 45.833 14.54 0.00 37.87 3.69
882 983 6.127730 CGTAGATAGCACCATATATGACCACA 60.128 42.308 14.54 0.00 0.00 4.17
883 984 6.095021 TCGTAGATAGCACCATATATGACCAC 59.905 42.308 14.54 1.13 0.00 4.16
884 985 6.184789 TCGTAGATAGCACCATATATGACCA 58.815 40.000 14.54 0.00 0.00 4.02
886 987 6.183360 TGCTCGTAGATAGCACCATATATGAC 60.183 42.308 14.54 3.55 44.78 3.06
887 988 5.885912 TGCTCGTAGATAGCACCATATATGA 59.114 40.000 14.54 0.00 44.78 2.15
943 1068 0.456221 CTGAAGGCGACGACATACCT 59.544 55.000 2.19 0.00 0.00 3.08
984 1109 0.909610 TCATCACCACCTCCCACTCC 60.910 60.000 0.00 0.00 0.00 3.85
992 1117 4.407296 GGTAGAGATCTTTCATCACCACCT 59.593 45.833 0.00 0.00 0.00 4.00
1030 1155 7.195646 GTGTCATTCTTCAGTTTGTTGATCAA 58.804 34.615 3.38 3.38 0.00 2.57
1058 1183 2.181777 CGCACGCTAGCTTGGAGA 59.818 61.111 21.37 0.00 0.00 3.71
1088 1213 2.213499 CGACTTGGCCATCCATAAGTC 58.787 52.381 19.04 19.04 42.66 3.01
1102 1227 1.519455 CGCTTCCTAGGCCGACTTG 60.519 63.158 2.96 0.00 0.00 3.16
1143 1268 3.390521 AGTGATGCGCCGAGGGAA 61.391 61.111 4.18 0.00 0.00 3.97
1180 1305 0.835276 TCCAGCCTCTCCATCATGTG 59.165 55.000 0.00 0.00 0.00 3.21
1196 1321 2.119611 TCGGGAGGTTCAGCTCCA 59.880 61.111 23.32 4.43 41.34 3.86
1221 1346 2.114670 CACCTGCGGCGGATTGAAT 61.115 57.895 11.13 0.00 0.00 2.57
1283 1408 1.134128 TGAAGTGCAGGTGCTTCTTGA 60.134 47.619 13.92 6.62 41.05 3.02
1289 1414 1.301244 CTCGTGAAGTGCAGGTGCT 60.301 57.895 3.18 0.00 42.66 4.40
1351 1476 2.906458 CTTCTCCATGCGCTCCCT 59.094 61.111 9.73 0.00 0.00 4.20
1376 1501 2.124151 CCCATGGAGAAAGCCGGG 60.124 66.667 15.22 0.00 0.00 5.73
1386 1511 1.224315 CAGATTCGGCACCCATGGA 59.776 57.895 15.22 0.00 0.00 3.41
1471 1596 1.002134 CACAGGGAAAGCGGTCCAT 60.002 57.895 10.45 0.75 39.70 3.41
1637 1776 0.741221 GAGCTCGCCATTCGGTTTCT 60.741 55.000 0.00 0.00 39.05 2.52
1750 4846 4.404507 ACAAGAAAACGTTCCGATGATG 57.595 40.909 0.00 0.00 33.92 3.07
1806 4902 7.705325 ACAACTCACTATAGCTAAATTGGTACG 59.295 37.037 0.00 0.00 0.00 3.67
1835 4931 7.441760 TCATTTGCAATTGTTCTAGCACAAATT 59.558 29.630 11.98 4.93 40.07 1.82
1836 4932 6.930164 TCATTTGCAATTGTTCTAGCACAAAT 59.070 30.769 11.98 0.80 40.07 2.32
1932 5345 1.737793 CACGGCCTCTATCAAACCAAC 59.262 52.381 0.00 0.00 0.00 3.77
1949 5362 4.752879 CGGTACAGCACCCCCACG 62.753 72.222 0.00 0.00 45.52 4.94
1951 5364 1.493854 AAATCGGTACAGCACCCCCA 61.494 55.000 0.00 0.00 45.52 4.96
1956 5369 2.147958 TGGACAAAATCGGTACAGCAC 58.852 47.619 0.00 0.00 0.00 4.40
2136 5782 2.309136 TATCCCGATGAGCATCTCCA 57.691 50.000 8.66 0.00 35.72 3.86
2141 5787 1.980765 ACACCATATCCCGATGAGCAT 59.019 47.619 0.00 0.00 0.00 3.79
2149 5795 1.270094 ACGTATGCACACCATATCCCG 60.270 52.381 0.00 0.00 38.60 5.14
2185 5831 6.625873 TGCTCATACAACAAACACATACAA 57.374 33.333 0.00 0.00 0.00 2.41
2278 5934 1.299773 CCGCGCCAATTGTTGTTGT 60.300 52.632 0.00 0.00 0.00 3.32
2281 5937 4.698651 CGCCGCGCCAATTGTTGT 62.699 61.111 0.00 0.00 0.00 3.32
2350 6006 7.667043 ATAAGCAACTTTGTACGAAATCAGA 57.333 32.000 0.00 0.00 0.00 3.27
2502 6162 7.818930 TGGAATTTCTAAGGATTGTTTTGCATC 59.181 33.333 0.00 0.00 0.00 3.91
2538 6198 5.995446 ACATCAATCCTAAGAAACTCTCCC 58.005 41.667 0.00 0.00 0.00 4.30
2539 6199 8.261522 ACTTACATCAATCCTAAGAAACTCTCC 58.738 37.037 0.00 0.00 0.00 3.71
2544 6204 8.261522 AGAGGACTTACATCAATCCTAAGAAAC 58.738 37.037 0.00 0.00 41.79 2.78
2557 6217 9.798994 TTAGTCGATTTTTAGAGGACTTACATC 57.201 33.333 0.00 0.00 38.74 3.06
2577 6237 0.462789 ACGGGCCCTATTGTTAGTCG 59.537 55.000 22.43 3.91 0.00 4.18
2578 6238 1.949465 CACGGGCCCTATTGTTAGTC 58.051 55.000 22.43 0.00 0.00 2.59
2581 6241 1.153329 CGCACGGGCCCTATTGTTA 60.153 57.895 22.43 0.00 36.38 2.41


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

AutoCloner maintained by Alex Coulton.