Multiple sequence alignment - TraesCS2D01G131600

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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 TraesCS2D01G131600 chr2D 100.000 4424 0 0 1 4424 76754973 76750550 0.000000e+00 8170.0
1 TraesCS2D01G131600 chr2B 92.767 3954 229 22 219 4148 117994955 117991035 0.000000e+00 5664.0
2 TraesCS2D01G131600 chr2B 89.956 229 14 5 1 221 117995275 117995048 2.010000e-73 287.0
3 TraesCS2D01G131600 chr2B 80.000 80 14 2 1193 1271 729766806 729766884 1.720000e-04 58.4
4 TraesCS2D01G131600 chr2A 92.216 2595 152 25 1856 4418 77239867 77237291 0.000000e+00 3627.0
5 TraesCS2D01G131600 chr2A 90.622 1866 142 10 1 1843 77241820 77239965 0.000000e+00 2446.0
6 TraesCS2D01G131600 chr7A 77.764 2424 497 30 1000 3405 625535238 625532839 0.000000e+00 1452.0
7 TraesCS2D01G131600 chr7A 77.768 2366 473 37 1061 3405 625631943 625629610 0.000000e+00 1406.0
8 TraesCS2D01G131600 chr7A 85.417 240 27 7 4181 4418 665428293 665428526 4.420000e-60 243.0
9 TraesCS2D01G131600 chr6B 77.234 2372 481 50 1061 3405 694667730 694665391 0.000000e+00 1334.0
10 TraesCS2D01G131600 chr6B 85.124 242 31 4 4181 4420 46393468 46393230 4.420000e-60 243.0
11 TraesCS2D01G131600 chr6B 88.660 194 18 3 4228 4420 703398994 703399184 2.660000e-57 233.0
12 TraesCS2D01G131600 chr7D 76.202 2391 490 55 1067 3422 556719533 556717187 0.000000e+00 1190.0
13 TraesCS2D01G131600 chr7D 79.025 1621 317 20 1798 3405 543639597 543637987 0.000000e+00 1088.0
14 TraesCS2D01G131600 chr7D 87.137 241 27 3 4181 4420 575442197 575442434 2.030000e-68 270.0
15 TraesCS2D01G131600 chr7B 77.549 1648 345 17 1787 3420 604100038 604098402 0.000000e+00 970.0
16 TraesCS2D01G131600 chr7B 77.264 1601 339 18 1839 3424 584029084 584030674 0.000000e+00 917.0
17 TraesCS2D01G131600 chr7B 85.477 241 29 5 4181 4420 636984631 636984866 3.420000e-61 246.0
18 TraesCS2D01G131600 chrUn 78.125 1536 317 13 1879 3403 365696599 365695072 0.000000e+00 957.0
19 TraesCS2D01G131600 chrUn 89.474 247 20 3 4181 4422 324024263 324024508 1.550000e-79 307.0
20 TraesCS2D01G131600 chr3D 87.029 239 29 2 4182 4420 416497467 416497231 7.290000e-68 268.0
21 TraesCS2D01G131600 chr4A 82.716 243 35 6 4181 4420 584660622 584660860 4.480000e-50 209.0


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 TraesCS2D01G131600 chr2D 76750550 76754973 4423 True 8170.0 8170 100.0000 1 4424 1 chr2D.!!$R1 4423
1 TraesCS2D01G131600 chr2B 117991035 117995275 4240 True 2975.5 5664 91.3615 1 4148 2 chr2B.!!$R1 4147
2 TraesCS2D01G131600 chr2A 77237291 77241820 4529 True 3036.5 3627 91.4190 1 4418 2 chr2A.!!$R1 4417
3 TraesCS2D01G131600 chr7A 625532839 625535238 2399 True 1452.0 1452 77.7640 1000 3405 1 chr7A.!!$R1 2405
4 TraesCS2D01G131600 chr7A 625629610 625631943 2333 True 1406.0 1406 77.7680 1061 3405 1 chr7A.!!$R2 2344
5 TraesCS2D01G131600 chr6B 694665391 694667730 2339 True 1334.0 1334 77.2340 1061 3405 1 chr6B.!!$R2 2344
6 TraesCS2D01G131600 chr7D 556717187 556719533 2346 True 1190.0 1190 76.2020 1067 3422 1 chr7D.!!$R2 2355
7 TraesCS2D01G131600 chr7D 543637987 543639597 1610 True 1088.0 1088 79.0250 1798 3405 1 chr7D.!!$R1 1607
8 TraesCS2D01G131600 chr7B 604098402 604100038 1636 True 970.0 970 77.5490 1787 3420 1 chr7B.!!$R1 1633
9 TraesCS2D01G131600 chr7B 584029084 584030674 1590 False 917.0 917 77.2640 1839 3424 1 chr7B.!!$F1 1585
10 TraesCS2D01G131600 chrUn 365695072 365696599 1527 True 957.0 957 78.1250 1879 3403 1 chrUn.!!$R1 1524

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
834 948 0.242555 CACATTTTTACCGCGCCCTT 59.757 50.0 0.0 0.0 0.0 3.95 F
1287 1411 0.249953 TCAAAAACACCGCCTCGCTA 60.250 50.0 0.0 0.0 0.0 4.26 F
1486 1610 0.535102 CCACCCCACAGACACACTTC 60.535 60.0 0.0 0.0 0.0 3.01 F
1703 1827 0.674534 GTGTCGGCTCCAGGGTATAG 59.325 60.0 0.0 0.0 0.0 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2098 0.746659 ACACTGAGCTTTTGGTTGGC 59.253 50.000 0.0 0.0 0.00 4.52 R
2988 3228 0.247736 CTCTGGCTGTGGTCAGTACC 59.752 60.000 0.0 0.0 44.74 3.34 R
3246 3486 3.374988 TGCAAGCTAATTCAACCTCATCG 59.625 43.478 0.0 0.0 0.00 3.84 R
3609 3863 3.791973 ACTTTCAGCTCTACCTCATCG 57.208 47.619 0.0 0.0 0.00 3.84 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 5.669447 ACTGGATCAATCCCTGAGTCTATTT 59.331 40.000 6.57 0.00 46.59 1.40
79 80 7.063544 AGGTGACTTTAAAGATCGAGATTTTCG 59.936 37.037 21.92 0.00 45.32 3.46
131 142 6.930722 CCAATAAAGGACAATTGCAAAGAAGT 59.069 34.615 1.71 0.00 32.79 3.01
140 151 7.112984 GGACAATTGCAAAGAAGTAAGTAAACG 59.887 37.037 1.71 0.00 0.00 3.60
288 394 9.632807 GTTTGTTAATTGGCATGAATTAGTGTA 57.367 29.630 0.00 0.00 31.13 2.90
394 500 3.744660 GGTTATCTACCAAGCATCTGGG 58.255 50.000 4.72 0.00 46.92 4.45
507 617 7.485913 GCTACATACAACCAATTTGAATGACAG 59.514 37.037 0.00 0.36 38.73 3.51
728 839 0.400594 ACCCCGAAGTTTCTTCCCTG 59.599 55.000 4.28 0.00 0.00 4.45
769 883 1.692519 ACGGCAAGACTAGACCACTTT 59.307 47.619 0.00 0.00 0.00 2.66
773 887 4.753107 CGGCAAGACTAGACCACTTTAAAA 59.247 41.667 0.00 0.00 0.00 1.52
830 944 0.519961 AGACCACATTTTTACCGCGC 59.480 50.000 0.00 0.00 0.00 6.86
831 945 0.455464 GACCACATTTTTACCGCGCC 60.455 55.000 0.00 0.00 0.00 6.53
832 946 1.153920 CCACATTTTTACCGCGCCC 60.154 57.895 0.00 0.00 0.00 6.13
834 948 0.242555 CACATTTTTACCGCGCCCTT 59.757 50.000 0.00 0.00 0.00 3.95
856 972 1.533625 GTGCAAGGCAGTTGGTCATA 58.466 50.000 0.00 0.00 40.08 2.15
857 973 2.094675 GTGCAAGGCAGTTGGTCATAT 58.905 47.619 0.00 0.00 40.08 1.78
858 974 2.098117 GTGCAAGGCAGTTGGTCATATC 59.902 50.000 0.00 0.00 40.08 1.63
860 976 2.945440 GCAAGGCAGTTGGTCATATCCA 60.945 50.000 0.70 0.00 36.56 3.41
861 977 2.684881 CAAGGCAGTTGGTCATATCCAC 59.315 50.000 0.00 0.00 37.20 4.02
862 978 1.212935 AGGCAGTTGGTCATATCCACC 59.787 52.381 0.00 0.00 37.20 4.61
863 979 1.064758 GGCAGTTGGTCATATCCACCA 60.065 52.381 0.00 0.00 42.48 4.17
909 1033 1.869767 CTGCTTGACTTCACCACAGAC 59.130 52.381 0.00 0.00 0.00 3.51
923 1047 3.244078 ACCACAGACGCTTACAGATTTGA 60.244 43.478 0.00 0.00 0.00 2.69
940 1064 7.093333 ACAGATTTGATATATATGACCGCTCCA 60.093 37.037 0.00 0.00 0.00 3.86
944 1068 4.402474 TGATATATATGACCGCTCCACAGG 59.598 45.833 0.00 0.00 0.00 4.00
984 1108 2.473378 CAGTGCAAAGCTCGCTCG 59.527 61.111 9.28 0.42 0.00 5.03
1166 1290 3.883830 TGGCTTCTTTGAAACAAGCAA 57.116 38.095 17.41 5.67 43.70 3.91
1229 1353 0.850100 TGGTTCAACACAGTCCCCAT 59.150 50.000 0.00 0.00 0.00 4.00
1287 1411 0.249953 TCAAAAACACCGCCTCGCTA 60.250 50.000 0.00 0.00 0.00 4.26
1297 1421 1.073216 CGCCTCGCTACAACTCACAG 61.073 60.000 0.00 0.00 0.00 3.66
1373 1497 0.817634 TCCACCCAAGCAAACGTCAG 60.818 55.000 0.00 0.00 0.00 3.51
1376 1500 1.608590 CACCCAAGCAAACGTCAGAAT 59.391 47.619 0.00 0.00 0.00 2.40
1479 1603 1.029681 GTTTTGACCACCCCACAGAC 58.970 55.000 0.00 0.00 0.00 3.51
1486 1610 0.535102 CCACCCCACAGACACACTTC 60.535 60.000 0.00 0.00 0.00 3.01
1525 1649 2.419574 GGATTAGACAAGCTAACCGGCA 60.420 50.000 0.00 0.00 41.64 5.69
1624 1748 2.555757 GGTGCAGATCAGTTCTTGCTTT 59.444 45.455 0.00 0.00 32.80 3.51
1638 1762 1.080434 GCTTTCACGGCTCGACTCT 60.080 57.895 1.50 0.00 0.00 3.24
1703 1827 0.674534 GTGTCGGCTCCAGGGTATAG 59.325 60.000 0.00 0.00 0.00 1.31
1777 1901 7.671302 AGAGAAGTATGTTGTTGAGAGCTTAA 58.329 34.615 0.00 0.00 0.00 1.85
1791 1927 5.067413 TGAGAGCTTAACCGACGAGAATATT 59.933 40.000 0.00 0.00 0.00 1.28
1806 1942 7.015289 ACGAGAATATTGTTTTTCGTCATGTG 58.985 34.615 0.00 0.00 36.68 3.21
1877 2098 4.384056 CAAGACTGGATATTGGCCTACAG 58.616 47.826 3.32 1.58 0.00 2.74
1910 2131 1.202348 TCAGTGTGATGTCTACGCAGG 59.798 52.381 0.00 0.00 0.00 4.85
2100 2321 3.431725 CGGTTCGCCTCTTTGCCC 61.432 66.667 0.00 0.00 34.30 5.36
2123 2344 3.181461 TGTGTTAGGTTGCCCAAAAATGG 60.181 43.478 0.00 0.00 0.00 3.16
2175 2396 0.958091 AGTGCGCACAAATTTGCCTA 59.042 45.000 39.21 0.00 39.53 3.93
2290 2511 6.012658 GTGGCACAACAAAGAATTCAGATA 57.987 37.500 13.86 0.00 44.16 1.98
2452 2685 6.605119 TGGAGAAACAAAAGGAAGAGATCTT 58.395 36.000 0.00 0.00 39.23 2.40
2549 2788 5.588845 ACATTTCACAGATAAATTGGGGGA 58.411 37.500 0.00 0.00 0.00 4.81
2832 3072 2.896039 ACCAGGTATCAGATAGCCCTC 58.104 52.381 14.84 0.00 33.87 4.30
2877 3117 1.109609 TGCATGAGAGCTGTCGAGAT 58.890 50.000 6.36 0.00 34.99 2.75
2940 3180 7.539712 TCTCGATGCTTTATTTGTTCCTAAG 57.460 36.000 0.00 0.00 0.00 2.18
2943 3183 7.332557 TCGATGCTTTATTTGTTCCTAAGGTA 58.667 34.615 0.00 0.00 0.00 3.08
2988 3228 3.359695 TTGGGAAGGGATTTTAGTCGG 57.640 47.619 0.00 0.00 0.00 4.79
3246 3486 4.978083 ATTGCAAGGTGATGTCAATCTC 57.022 40.909 4.94 0.00 33.61 2.75
3451 3691 7.653713 CACACTTGAGTAACTAGAGATGTTGTT 59.346 37.037 0.00 0.00 0.00 2.83
3463 3703 5.687780 AGAGATGTTGTTATGATCATGCCA 58.312 37.500 18.72 11.25 0.00 4.92
3514 3754 9.983804 GTTTTACTTATCCTACAAATGTAGTGC 57.016 33.333 16.97 0.00 44.88 4.40
3536 3776 5.983118 TGCACTTATCATGGTCGTATAGTTG 59.017 40.000 0.00 0.00 0.00 3.16
3558 3798 6.117911 TGTATCCATGTATTTCAAGTTGCG 57.882 37.500 0.00 0.00 0.00 4.85
3580 3823 5.444218 GCGTGTAACAGCTTCAATGTACTAC 60.444 44.000 0.00 0.00 35.74 2.73
3609 3863 5.163343 TGCAGTTCTCCAATATAGTGGTACC 60.163 44.000 18.26 4.43 39.88 3.34
3614 3868 5.637127 TCTCCAATATAGTGGTACCGATGA 58.363 41.667 18.26 4.98 39.88 2.92
3631 3885 4.261405 CCGATGAGGTAGAGCTGAAAGTAG 60.261 50.000 0.00 0.00 32.84 2.57
3640 3895 7.398904 AGGTAGAGCTGAAAGTAGATCTCTTTT 59.601 37.037 16.33 11.13 42.06 2.27
3723 3978 0.244721 TGAGATGTCGCTGGTGACTG 59.755 55.000 14.12 0.00 39.64 3.51
3888 4149 3.333414 GCGTTGTGCAGCAGAAGA 58.667 55.556 4.95 0.00 45.45 2.87
4083 4347 5.791336 AAAGTTTTCTTAAAGCCCTCTGG 57.209 39.130 0.00 0.00 39.48 3.86
4094 4358 1.628846 AGCCCTCTGGTTTGTACGAAT 59.371 47.619 0.00 0.00 0.00 3.34
4101 4365 6.338146 CCTCTGGTTTGTACGAATAGATTCA 58.662 40.000 11.17 0.33 36.61 2.57
4132 4396 7.288852 CCTATGTAGGATAGGGATCGATCATTT 59.711 40.741 25.93 13.14 46.63 2.32
4133 4397 6.286240 TGTAGGATAGGGATCGATCATTTG 57.714 41.667 25.93 0.00 32.28 2.32
4148 4413 8.537049 TCGATCATTTGCATTCAAAGAAAAAT 57.463 26.923 0.00 0.00 44.47 1.82
4187 4453 1.067060 GAGTCTGGTTGTTTTGCACCC 59.933 52.381 0.00 0.00 0.00 4.61
4205 4485 2.582436 CCCGCTACACCCACGATT 59.418 61.111 0.00 0.00 0.00 3.34
4218 4498 5.048991 ACACCCACGATTAAAAACTTAGCAG 60.049 40.000 0.00 0.00 0.00 4.24
4225 4505 9.180678 CACGATTAAAAACTTAGCAGAACAAAT 57.819 29.630 0.00 0.00 0.00 2.32
4285 4565 7.216494 AGCAAATGTTTTAGGTGCTTACAAAT 58.784 30.769 0.00 0.00 42.77 2.32
4288 4568 9.862585 CAAATGTTTTAGGTGCTTACAAATTTC 57.137 29.630 0.00 0.00 0.00 2.17
4290 4570 9.830975 AATGTTTTAGGTGCTTACAAATTTCTT 57.169 25.926 0.00 0.00 0.00 2.52
4294 4574 4.631131 AGGTGCTTACAAATTTCTTTGGC 58.369 39.130 3.42 0.00 44.97 4.52
4306 4586 5.750352 ATTTCTTTGGCCAAATGACATCT 57.250 34.783 30.46 9.69 0.00 2.90
4313 4593 2.092753 GGCCAAATGACATCTGAGGAGA 60.093 50.000 0.00 0.00 0.00 3.71
4315 4595 4.205587 GCCAAATGACATCTGAGGAGATT 58.794 43.478 0.00 0.00 36.75 2.40
4317 4597 5.450137 GCCAAATGACATCTGAGGAGATTTG 60.450 44.000 16.50 16.50 36.75 2.32
4319 4599 6.825213 CCAAATGACATCTGAGGAGATTTGTA 59.175 38.462 19.27 0.00 36.75 2.41
4320 4600 7.201679 CCAAATGACATCTGAGGAGATTTGTAC 60.202 40.741 19.27 0.00 36.75 2.90
4418 4698 9.603298 CATATGGAGATCGTTCAATGTTATTTG 57.397 33.333 0.00 0.00 0.00 2.32
4419 4699 6.435430 TGGAGATCGTTCAATGTTATTTGG 57.565 37.500 0.00 0.00 0.00 3.28
4420 4700 5.943416 TGGAGATCGTTCAATGTTATTTGGT 59.057 36.000 0.00 0.00 0.00 3.67
4421 4701 6.128035 TGGAGATCGTTCAATGTTATTTGGTG 60.128 38.462 0.00 0.00 0.00 4.17
4422 4702 6.128007 GGAGATCGTTCAATGTTATTTGGTGT 60.128 38.462 0.00 0.00 0.00 4.16
4423 4703 6.842163 AGATCGTTCAATGTTATTTGGTGTC 58.158 36.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.720769 AAATCTCGATCTTTAAAGTCACCTTTA 57.279 29.630 14.74 0.00 41.18 1.85
79 80 4.454504 CACACCCTTATAGACAAACCACAC 59.545 45.833 0.00 0.00 0.00 3.82
131 142 5.349817 TCACGGAAACAACAACGTTTACTTA 59.650 36.000 0.00 0.00 39.17 2.24
140 151 2.420722 TCTTGGTCACGGAAACAACAAC 59.579 45.455 0.00 0.00 0.00 3.32
189 200 6.818281 TGTAATAACTTGGCTAGTGGGTAT 57.182 37.500 1.53 0.00 37.12 2.73
255 361 7.459795 TCATGCCAATTAACAAACATACTGA 57.540 32.000 0.00 0.00 0.00 3.41
288 394 4.592778 ACCCAAAATAATGCACAAACTCCT 59.407 37.500 0.00 0.00 0.00 3.69
384 490 1.274703 ACGGATCCACCCAGATGCTT 61.275 55.000 13.41 0.00 32.81 3.91
394 500 2.795175 ATGATCACGTACGGATCCAC 57.205 50.000 28.37 15.27 40.32 4.02
589 699 3.014304 ACATCTCAGCAGCCAATCAAT 57.986 42.857 0.00 0.00 0.00 2.57
728 839 2.625790 TGGAATGGTTGGTGCAAAGTAC 59.374 45.455 0.00 0.00 0.00 2.73
832 946 1.364901 CAACTGCCTTGCACCCAAG 59.635 57.895 0.00 0.00 46.38 3.61
834 948 2.521465 CCAACTGCCTTGCACCCA 60.521 61.111 0.00 0.00 33.79 4.51
856 972 0.895530 AATCGTGTCGAGTGGTGGAT 59.104 50.000 0.00 0.00 39.91 3.41
857 973 1.536940 TAATCGTGTCGAGTGGTGGA 58.463 50.000 2.51 0.00 39.91 4.02
858 974 2.579207 ATAATCGTGTCGAGTGGTGG 57.421 50.000 2.51 0.00 39.91 4.61
860 976 5.571784 TTAGAATAATCGTGTCGAGTGGT 57.428 39.130 2.51 0.00 39.91 4.16
861 977 6.439599 AGATTAGAATAATCGTGTCGAGTGG 58.560 40.000 2.51 0.00 39.91 4.00
862 978 8.283992 AGTAGATTAGAATAATCGTGTCGAGTG 58.716 37.037 2.51 0.00 39.91 3.51
863 979 8.380743 AGTAGATTAGAATAATCGTGTCGAGT 57.619 34.615 4.36 0.00 39.91 4.18
909 1033 8.746751 CGGTCATATATATCAAATCTGTAAGCG 58.253 37.037 0.00 0.00 0.00 4.68
923 1047 3.706594 CCCTGTGGAGCGGTCATATATAT 59.293 47.826 17.59 0.00 0.00 0.86
940 1064 1.059006 GGGATGGATGCTCTCCCTGT 61.059 60.000 15.23 0.00 44.49 4.00
944 1068 0.689623 ATTCGGGATGGATGCTCTCC 59.310 55.000 0.00 0.00 45.19 3.71
984 1108 1.307097 GCATGATGAACAGAGGGAGC 58.693 55.000 0.00 0.00 0.00 4.70
1166 1290 0.329596 GCTCTGGGAGGATTTGGTGT 59.670 55.000 0.00 0.00 0.00 4.16
1287 1411 0.032678 CGCTGGAGACTGTGAGTTGT 59.967 55.000 0.00 0.00 41.78 3.32
1297 1421 2.109126 GGTTGCCATCGCTGGAGAC 61.109 63.158 10.06 6.22 46.37 3.36
1479 1603 1.079127 CGCCCCTGGTAGAAGTGTG 60.079 63.158 0.00 0.00 0.00 3.82
1486 1610 1.450312 CAAGCTTCGCCCCTGGTAG 60.450 63.158 0.00 0.00 0.00 3.18
1509 1633 0.613260 TCATGCCGGTTAGCTTGTCT 59.387 50.000 1.90 0.00 38.63 3.41
1525 1649 1.369625 GAAACCAGACGGCGATTCAT 58.630 50.000 16.62 0.00 34.57 2.57
1624 1748 0.965866 ATGGAAGAGTCGAGCCGTGA 60.966 55.000 0.00 0.00 0.00 4.35
1638 1762 3.554934 GCTGGACCAATATGACATGGAA 58.445 45.455 0.00 0.00 39.12 3.53
1777 1901 4.687483 ACGAAAAACAATATTCTCGTCGGT 59.313 37.500 0.00 0.00 34.68 4.69
1791 1927 4.916831 GCATCAATCACATGACGAAAAACA 59.083 37.500 0.00 0.00 30.82 2.83
1806 1942 1.964552 CCTGACCAGAGGCATCAATC 58.035 55.000 0.00 0.00 0.00 2.67
1877 2098 0.746659 ACACTGAGCTTTTGGTTGGC 59.253 50.000 0.00 0.00 0.00 4.52
2084 2305 2.034221 AGGGCAAAGAGGCGAACC 59.966 61.111 0.00 0.00 45.36 3.62
2123 2344 2.164422 GTGGCAATCCCTACTTTTCTGC 59.836 50.000 0.00 0.00 0.00 4.26
2152 2373 1.190763 GCAAATTTGTGCGCACTCTTG 59.809 47.619 37.59 30.59 34.21 3.02
2290 2511 4.704965 AGGCGAAAGTAAAGTGTTTCTCT 58.295 39.130 0.00 0.00 31.61 3.10
2452 2685 9.184523 CCCATTACTACCATAAATTTTGTGAGA 57.815 33.333 7.38 0.00 0.00 3.27
2549 2788 5.258051 TGAACACAGAACCAAAACTACCTT 58.742 37.500 0.00 0.00 0.00 3.50
2832 3072 1.202428 GCTAACCCTCTAGCAACTCCG 60.202 57.143 0.00 0.00 43.25 4.63
2877 3117 9.002600 GGCTTGATATCACAATGTATGATGTAA 57.997 33.333 4.48 0.00 37.38 2.41
2940 3180 1.683385 GCCATCCCAAAATCTGCTACC 59.317 52.381 0.00 0.00 0.00 3.18
2943 3183 1.941377 TTGCCATCCCAAAATCTGCT 58.059 45.000 0.00 0.00 0.00 4.24
2988 3228 0.247736 CTCTGGCTGTGGTCAGTACC 59.752 60.000 0.00 0.00 44.74 3.34
3246 3486 3.374988 TGCAAGCTAATTCAACCTCATCG 59.625 43.478 0.00 0.00 0.00 3.84
3436 3676 7.443575 GGCATGATCATAACAACATCTCTAGTT 59.556 37.037 8.15 0.00 0.00 2.24
3451 3691 9.571816 TTTAACATAGACATTGGCATGATCATA 57.428 29.630 8.15 0.00 34.11 2.15
3514 3754 9.343103 GATACAACTATACGACCATGATAAGTG 57.657 37.037 0.00 0.00 0.00 3.16
3536 3776 5.965334 CACGCAACTTGAAATACATGGATAC 59.035 40.000 0.00 0.00 0.00 2.24
3558 3798 8.928270 ATAGTAGTACATTGAAGCTGTTACAC 57.072 34.615 2.52 0.00 0.00 2.90
3580 3823 7.095910 CCACTATATTGGAGAACTGCAGATAG 58.904 42.308 23.35 15.12 39.24 2.08
3609 3863 3.791973 ACTTTCAGCTCTACCTCATCG 57.208 47.619 0.00 0.00 0.00 3.84
3614 3868 6.013554 AGAGATCTACTTTCAGCTCTACCT 57.986 41.667 0.00 0.00 31.49 3.08
3723 3978 3.055385 TGGAGGAGCTACACCATTTACAC 60.055 47.826 11.62 0.00 0.00 2.90
3795 4052 3.794717 CATTGGAGGAGAGTCTGACATG 58.205 50.000 10.88 0.00 0.00 3.21
3888 4149 4.640771 TTCAGTAGGTTCAGATTTGCCT 57.359 40.909 0.00 0.00 35.28 4.75
4069 4333 3.435671 CGTACAAACCAGAGGGCTTTAAG 59.564 47.826 0.00 0.00 37.90 1.85
4072 4336 1.418637 TCGTACAAACCAGAGGGCTTT 59.581 47.619 0.00 0.00 37.90 3.51
4120 4384 5.824429 TCTTTGAATGCAAATGATCGATCC 58.176 37.500 22.31 7.27 42.66 3.36
4121 4385 7.745022 TTTCTTTGAATGCAAATGATCGATC 57.255 32.000 18.72 18.72 42.66 3.69
4132 4396 8.934825 GGCTAATGTAATTTTTCTTTGAATGCA 58.065 29.630 0.00 0.00 37.87 3.96
4133 4397 9.154847 AGGCTAATGTAATTTTTCTTTGAATGC 57.845 29.630 0.00 0.00 37.87 3.56
4187 4453 1.678598 TAATCGTGGGTGTAGCGGGG 61.679 60.000 0.00 0.00 0.00 5.73
4234 4514 5.947228 AATCGAATCTGCAAAGTTTCAGA 57.053 34.783 15.49 15.49 42.72 3.27
4235 4515 7.466805 TCATAATCGAATCTGCAAAGTTTCAG 58.533 34.615 0.00 8.09 0.00 3.02
4236 4516 7.376435 TCATAATCGAATCTGCAAAGTTTCA 57.624 32.000 0.00 0.00 0.00 2.69
4237 4517 6.413235 GCTCATAATCGAATCTGCAAAGTTTC 59.587 38.462 0.00 0.00 0.00 2.78
4238 4518 6.127925 TGCTCATAATCGAATCTGCAAAGTTT 60.128 34.615 0.00 0.00 0.00 2.66
4239 4519 5.355071 TGCTCATAATCGAATCTGCAAAGTT 59.645 36.000 0.00 0.00 0.00 2.66
4240 4520 4.877823 TGCTCATAATCGAATCTGCAAAGT 59.122 37.500 0.00 0.00 0.00 2.66
4241 4521 5.413969 TGCTCATAATCGAATCTGCAAAG 57.586 39.130 0.00 0.00 0.00 2.77
4253 4533 7.260603 AGCACCTAAAACATTTGCTCATAATC 58.739 34.615 0.00 0.00 39.32 1.75
4285 4565 4.588106 TCAGATGTCATTTGGCCAAAGAAA 59.412 37.500 32.85 24.23 33.32 2.52
4288 4568 3.119245 CCTCAGATGTCATTTGGCCAAAG 60.119 47.826 32.85 24.06 33.32 2.77
4290 4570 2.041485 TCCTCAGATGTCATTTGGCCAA 59.959 45.455 16.05 16.05 0.00 4.52
4294 4574 5.651139 ACAAATCTCCTCAGATGTCATTTGG 59.349 40.000 3.68 0.00 38.55 3.28
4343 4623 9.622004 CTGCATCCATGTTTCAGATTTTATATC 57.378 33.333 0.00 0.00 0.00 1.63
4360 4640 2.753452 CAAACTCTTGCTCTGCATCCAT 59.247 45.455 0.00 0.00 38.76 3.41


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

AutoCloner maintained by Alex Coulton.