Multiple sequence alignment - TraesCS5D01G097100

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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 TraesCS5D01G097100 chr5D 100.000 5982 0 0 1 5982 107586558 107580577 0.000000e+00 11047.0
1 TraesCS5D01G097100 chr5B 96.744 4546 97 27 844 5376 116896630 116892123 0.000000e+00 7528.0
2 TraesCS5D01G097100 chr5B 91.332 623 39 8 5368 5981 116892086 116891470 0.000000e+00 837.0
3 TraesCS5D01G097100 chr5B 98.507 134 2 0 1769 1902 713095787 713095654 2.790000e-58 237.0
4 TraesCS5D01G097100 chr5A 94.252 3375 139 25 1 3331 110383797 110380434 0.000000e+00 5107.0
5 TraesCS5D01G097100 chr5A 94.041 2064 75 20 3324 5376 110380010 110377984 0.000000e+00 3086.0
6 TraesCS5D01G097100 chr5A 93.893 393 20 3 5590 5981 110377864 110377475 1.860000e-164 590.0
7 TraesCS5D01G097100 chr5A 93.069 101 6 1 5436 5535 110377960 110377860 4.830000e-31 147.0
8 TraesCS5D01G097100 chr3B 76.850 527 111 10 1 522 762340786 762341306 2.730000e-73 287.0
9 TraesCS5D01G097100 chr3B 77.903 267 56 3 22 287 429328182 429328446 4.800000e-36 163.0
10 TraesCS5D01G097100 chr4D 76.493 519 111 10 9 522 440047917 440047405 7.640000e-69 272.0
11 TraesCS5D01G097100 chr4D 77.778 459 86 13 22 469 378791739 378791286 9.880000e-68 268.0
12 TraesCS5D01G097100 chr4D 76.424 509 91 22 3857 4346 128191463 128190965 1.290000e-61 248.0
13 TraesCS5D01G097100 chr4D 99.254 134 1 0 1769 1902 123688984 123688851 5.990000e-60 243.0
14 TraesCS5D01G097100 chr4D 93.269 104 7 0 1085 1188 128193493 128193390 2.890000e-33 154.0
15 TraesCS5D01G097100 chr4B 76.424 509 91 20 3857 4346 192114122 192113624 1.290000e-61 248.0
16 TraesCS5D01G097100 chr4B 93.269 104 7 0 1085 1188 192116153 192116050 2.890000e-33 154.0
17 TraesCS5D01G097100 chr4B 78.715 249 35 15 22 261 44501575 44501336 3.730000e-32 150.0
18 TraesCS5D01G097100 chrUn 98.507 134 2 0 1769 1902 233525245 233525378 2.790000e-58 237.0
19 TraesCS5D01G097100 chrUn 98.507 134 2 0 1769 1902 257944135 257944002 2.790000e-58 237.0
20 TraesCS5D01G097100 chr1D 98.507 134 2 0 1769 1902 212428891 212428758 2.790000e-58 237.0
21 TraesCS5D01G097100 chr1B 98.507 134 2 0 1769 1902 49784901 49785034 2.790000e-58 237.0
22 TraesCS5D01G097100 chr1B 98.507 134 2 0 1769 1902 583550331 583550198 2.790000e-58 237.0
23 TraesCS5D01G097100 chr4A 80.189 318 48 11 4035 4346 439009216 439009524 2.170000e-54 224.0
24 TraesCS5D01G097100 chr4A 92.308 104 8 0 1085 1188 439006969 439007072 1.340000e-31 148.0
25 TraesCS5D01G097100 chr2B 74.460 509 113 16 22 522 144153795 144154294 2.830000e-48 204.0
26 TraesCS5D01G097100 chr2A 78.947 114 21 3 171 283 566441778 566441667 2.310000e-09 75.0
27 TraesCS5D01G097100 chr3D 83.117 77 12 1 211 286 121796624 121796700 1.080000e-07 69.4


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 TraesCS5D01G097100 chr5D 107580577 107586558 5981 True 11047.0 11047 100.00000 1 5982 1 chr5D.!!$R1 5981
1 TraesCS5D01G097100 chr5B 116891470 116896630 5160 True 4182.5 7528 94.03800 844 5981 2 chr5B.!!$R2 5137
2 TraesCS5D01G097100 chr5A 110377475 110383797 6322 True 2232.5 5107 93.81375 1 5981 4 chr5A.!!$R1 5980
3 TraesCS5D01G097100 chr3B 762340786 762341306 520 False 287.0 287 76.85000 1 522 1 chr3B.!!$F2 521
4 TraesCS5D01G097100 chr4D 440047405 440047917 512 True 272.0 272 76.49300 9 522 1 chr4D.!!$R3 513
5 TraesCS5D01G097100 chr4D 128190965 128193493 2528 True 201.0 248 84.84650 1085 4346 2 chr4D.!!$R4 3261
6 TraesCS5D01G097100 chr4B 192113624 192116153 2529 True 201.0 248 84.84650 1085 4346 2 chr4B.!!$R2 3261

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
58 59 0.108041 AACGACAAACCACGGTGTCT 60.108 50.000 7.45 0.00 41.65 3.41 F
1562 1596 0.839946 ACCAGAGCTGTGGACTTTGT 59.160 50.000 34.84 9.84 40.44 2.83 F
1655 1691 1.075374 CCCTCAGGGTTTCATTGACCA 59.925 52.381 0.00 0.00 38.25 4.02 F
1998 2035 5.047802 CACCTGAATTTATGTCAAGGTGCTT 60.048 40.000 6.71 0.00 37.42 3.91 F
2547 2590 0.881118 GCCAATTTGTCAAGGAGCGA 59.119 50.000 0.00 0.00 0.00 4.93 F
2983 3032 2.355010 AAGAAGTTCTTGGCTGCTGT 57.645 45.000 17.35 0.00 34.98 4.40 F
4637 5170 4.531732 AGAAATGAAGACCTCAGCTTCTCT 59.468 41.667 0.00 0.00 41.71 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1842 0.034198 GAGCCGAAGATTCTAGGGGC 59.966 60.000 12.30 12.30 40.80 5.80 R
2378 2421 4.074627 TCCGTTGATTGTGTGACCTTAA 57.925 40.909 0.00 0.00 0.00 1.85 R
2547 2590 7.620094 AGATGTGTAACTACCTCAACTCCTAAT 59.380 37.037 0.00 0.00 38.04 1.73 R
3778 4297 7.306399 CCATGTTAATCCAAATACGACGTAGAC 60.306 40.741 13.87 2.24 0.00 2.59 R
4491 5024 1.697432 TGGTAGTTTGGACCACCTCTG 59.303 52.381 0.00 0.00 42.15 3.35 R
4831 5364 2.430248 ATCATGCTTCAGCCATGACA 57.570 45.000 12.97 0.00 39.48 3.58 R
5478 6065 1.673665 CACTGCAGTCCCCAAGAGC 60.674 63.158 18.64 0.00 0.00 4.09 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
58 59 0.108041 AACGACAAACCACGGTGTCT 60.108 50.000 7.45 0.00 41.65 3.41
140 141 1.613925 TCCGACAACTTCTGACTGAGG 59.386 52.381 0.00 0.00 0.00 3.86
170 171 1.741706 CCTTGACTGCTGCCATAGTTG 59.258 52.381 0.00 0.00 0.00 3.16
216 237 3.454812 AGTTTACATGGCCTCTAATCCGT 59.545 43.478 3.32 0.00 0.00 4.69
219 240 5.617528 TTACATGGCCTCTAATCCGTTTA 57.382 39.130 3.32 0.00 0.00 2.01
220 241 4.073293 ACATGGCCTCTAATCCGTTTAG 57.927 45.455 3.32 0.00 38.98 1.85
231 253 2.534019 CCGTTTAGCATCGCCGCAT 61.534 57.895 0.00 0.00 0.00 4.73
277 299 7.026631 TCATTTTGTTCGAGAAAATGTGTCT 57.973 32.000 27.17 6.22 45.19 3.41
299 321 1.358152 TGGTCAGATCCGGGTTCTTT 58.642 50.000 0.00 0.00 0.00 2.52
324 346 4.565236 TGTGCCATCAACACATCAGTATGA 60.565 41.667 0.00 0.00 42.77 2.15
343 365 8.347771 CAGTATGATGACATTATGACAAAAGGG 58.652 37.037 0.00 0.00 39.69 3.95
363 385 1.527311 GCTTTCGTCGCAACTCTTCTT 59.473 47.619 0.00 0.00 0.00 2.52
379 401 2.144482 TCTTCGAGTTTCGGTCCAAC 57.856 50.000 0.00 0.00 40.88 3.77
394 416 4.117685 GGTCCAACTTATGCTTACTACCG 58.882 47.826 0.00 0.00 0.00 4.02
471 498 6.178607 TGTATATGAATGTCATCACCTGCT 57.821 37.500 0.00 0.00 38.26 4.24
488 515 5.008415 CACCTGCTGATCCTTGTTATGATTC 59.992 44.000 0.00 0.00 0.00 2.52
500 527 7.282224 TCCTTGTTATGATTCGGTTAGGATTTG 59.718 37.037 0.00 0.00 0.00 2.32
546 573 8.782339 ACCCTATATTATGTTAACGTAATGGC 57.218 34.615 30.54 0.00 38.23 4.40
599 626 8.294341 TCTCAATTGTTTACTCTTAGACGTTG 57.706 34.615 5.13 0.00 0.00 4.10
600 627 7.924412 TCTCAATTGTTTACTCTTAGACGTTGT 59.076 33.333 5.13 0.00 0.00 3.32
601 628 9.188588 CTCAATTGTTTACTCTTAGACGTTGTA 57.811 33.333 5.13 0.00 0.00 2.41
654 682 4.877823 TGGTTCTATGCTTCATGTGACATC 59.122 41.667 0.00 0.00 0.00 3.06
662 690 3.311871 GCTTCATGTGACATCCTCATCAC 59.688 47.826 0.00 0.00 44.56 3.06
681 709 4.126437 TCACATTGTATCGTTAGGCCATG 58.874 43.478 5.01 0.00 0.00 3.66
688 716 8.779303 CATTGTATCGTTAGGCCATGTATTTTA 58.221 33.333 5.01 0.00 0.00 1.52
690 718 8.911918 TGTATCGTTAGGCCATGTATTTTAAT 57.088 30.769 5.01 0.00 0.00 1.40
713 741 8.611654 AATGTGTTGTTTTACGTATTACTCCT 57.388 30.769 0.00 0.00 0.00 3.69
714 742 9.709495 AATGTGTTGTTTTACGTATTACTCCTA 57.291 29.630 0.00 0.00 0.00 2.94
752 780 6.349300 AGTGATGTGAAAGTCTAGTTTGTGT 58.651 36.000 0.00 0.00 0.00 3.72
855 887 4.768968 AGTCATTGCAAGTTAGCTCCAAAT 59.231 37.500 4.94 0.00 34.99 2.32
956 988 3.025924 TGGAGCAGCCAGTGAAAAG 57.974 52.632 0.00 0.00 43.33 2.27
1034 1066 1.234615 CCAGTGCTACAAACCACCGG 61.235 60.000 0.00 0.00 32.48 5.28
1192 1224 4.147449 TCTCCGCGCAGGTGATGG 62.147 66.667 8.75 0.00 41.99 3.51
1562 1596 0.839946 ACCAGAGCTGTGGACTTTGT 59.160 50.000 34.84 9.84 40.44 2.83
1606 1640 2.196502 GGGGTTTCACCGGTGGTT 59.803 61.111 33.40 0.00 39.83 3.67
1655 1691 1.075374 CCCTCAGGGTTTCATTGACCA 59.925 52.381 0.00 0.00 38.25 4.02
1754 1791 7.433708 TCAAGTATGTTGTTTGTTCATCGAT 57.566 32.000 0.00 0.00 0.00 3.59
1936 1973 8.935844 CAATTAGTTTTTAGCTGGGATTTTTCC 58.064 33.333 0.00 0.00 0.00 3.13
1998 2035 5.047802 CACCTGAATTTATGTCAAGGTGCTT 60.048 40.000 6.71 0.00 37.42 3.91
2053 2093 9.736023 GATTTAACTTCTAACCAGCAATATTGG 57.264 33.333 17.02 3.97 41.60 3.16
2088 2128 9.695526 TCAGCATTATATTTATTTTGATGGTGC 57.304 29.630 7.51 0.00 39.81 5.01
2378 2421 9.936759 TTTCTGAAATTTGTAACTTGTTCCTTT 57.063 25.926 0.00 0.00 0.00 3.11
2547 2590 0.881118 GCCAATTTGTCAAGGAGCGA 59.119 50.000 0.00 0.00 0.00 4.93
2983 3032 2.355010 AAGAAGTTCTTGGCTGCTGT 57.645 45.000 17.35 0.00 34.98 4.40
3778 4297 6.537301 TGTATTTTGAAATGGAGGTAGTAGCG 59.463 38.462 0.00 0.00 0.00 4.26
4031 4551 7.397221 TGTTAATCAGGATGGATGACATATCC 58.603 38.462 8.64 8.64 40.72 2.59
4189 4722 5.684626 GCTTTGCTCTGCATATTATGTTCAC 59.315 40.000 5.60 0.00 38.76 3.18
4464 4997 4.594920 TGGTGCCAGGAATCCAAATTAAAA 59.405 37.500 0.61 0.00 0.00 1.52
4637 5170 4.531732 AGAAATGAAGACCTCAGCTTCTCT 59.468 41.667 0.00 0.00 41.71 3.10
4856 5389 0.302890 GGCTGAAGCATGATTCGTCG 59.697 55.000 18.17 10.43 44.36 5.12
4892 5426 5.808030 CGGTGTTTAAGTTGTGTCCATTTTT 59.192 36.000 0.00 0.00 0.00 1.94
5022 5557 2.229792 TCTTGCTTTGCGGTTCTGATT 58.770 42.857 0.00 0.00 0.00 2.57
5033 5568 0.811281 GTTCTGATTCCTTTGGGCCG 59.189 55.000 0.00 0.00 0.00 6.13
5059 5594 5.819379 GGCACAATGAGATCAAGATAAGTCA 59.181 40.000 0.00 0.00 0.00 3.41
5070 5605 1.134788 AGATAAGTCAACCCGGCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
5084 5619 1.086696 GCTTCGCCAGATTTACAGCA 58.913 50.000 0.00 0.00 0.00 4.41
5140 5675 0.108424 GCGGCTTGTGATGTCTCTCT 60.108 55.000 0.00 0.00 0.00 3.10
5252 5792 9.607285 GATGACTTAAAATGTTTGATTGTACGT 57.393 29.630 0.00 0.00 0.00 3.57
5338 5878 4.328440 GCACTCTGCTACATTAACTGTGAG 59.672 45.833 0.00 0.00 40.96 3.51
5346 5886 4.447138 ACATTAACTGTGAGGGTTTGGA 57.553 40.909 0.00 0.00 36.48 3.53
5376 5916 1.066143 AGTAGCGCACCTTGCAATACT 60.066 47.619 11.47 1.80 45.36 2.12
5377 5917 2.167693 AGTAGCGCACCTTGCAATACTA 59.832 45.455 11.47 0.00 45.36 1.82
5378 5918 1.369625 AGCGCACCTTGCAATACTAC 58.630 50.000 11.47 0.00 45.36 2.73
5379 5919 1.083489 GCGCACCTTGCAATACTACA 58.917 50.000 0.30 0.00 45.36 2.74
5380 5920 1.202031 GCGCACCTTGCAATACTACAC 60.202 52.381 0.30 0.00 45.36 2.90
5382 5922 2.094258 CGCACCTTGCAATACTACACTG 59.906 50.000 0.00 0.00 45.36 3.66
5401 5984 6.109359 ACACTGTATAGTTTTGCAGAGGATC 58.891 40.000 0.00 0.00 34.07 3.36
5427 6010 6.976088 TGAACCCACTGTAAAATATGTTGTG 58.024 36.000 0.00 0.00 0.00 3.33
5459 6046 6.665992 TGACACTCTTATCCACAAACTAGT 57.334 37.500 0.00 0.00 0.00 2.57
5478 6065 8.873215 AACTAGTATACAAAATGTCGGAGATG 57.127 34.615 5.50 0.00 40.67 2.90
5488 6075 1.001631 TCGGAGATGCTCTTGGGGA 59.998 57.895 0.00 0.00 0.00 4.81
5565 6155 4.204012 TGTGTAACATGGCTAATAAGGGC 58.796 43.478 0.00 0.00 45.67 5.19
5581 6171 1.078426 GGCAGATACAACCGCACCT 60.078 57.895 0.00 0.00 0.00 4.00
5584 6174 1.943968 GCAGATACAACCGCACCTTCA 60.944 52.381 0.00 0.00 0.00 3.02
5592 6182 2.106683 CCGCACCTTCAATCGGGTC 61.107 63.158 0.00 0.00 38.35 4.46
5649 6239 3.517296 TTGGTTGTGGCCTCATTAAGA 57.483 42.857 8.61 0.00 0.00 2.10
5690 6280 5.772825 AGTTGTGTTGTGATGTGCTTATT 57.227 34.783 0.00 0.00 0.00 1.40
5694 6284 5.527951 TGTGTTGTGATGTGCTTATTTTCC 58.472 37.500 0.00 0.00 0.00 3.13
5933 6526 2.427453 TGGGAGCAGAGAGAACGATAAC 59.573 50.000 0.00 0.00 0.00 1.89
5935 6528 3.068873 GGGAGCAGAGAGAACGATAACAT 59.931 47.826 0.00 0.00 0.00 2.71
5960 6553 3.073946 TGGTAGAAGAAAGAAAGTGGGGG 59.926 47.826 0.00 0.00 0.00 5.40
5981 6574 3.561503 GCGTAAGAAAATTTTCGCACCT 58.438 40.909 22.41 11.49 43.44 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.703001 AACCAGGTTATCACTGAGGTG 57.297 47.619 1.71 0.00 44.23 4.00
20 21 3.698250 TGGACGACCAAGAAACCAG 57.302 52.632 3.49 0.00 43.91 4.00
58 59 1.953231 CTGCCTCATCACTGGAGCGA 61.953 60.000 0.00 0.00 0.00 4.93
140 141 3.201290 CAGCAGTCAAGGGATGATGTAC 58.799 50.000 0.00 0.00 40.97 2.90
189 210 3.629142 AGAGGCCATGTAAACTGTACC 57.371 47.619 5.01 0.00 0.00 3.34
216 237 1.090728 TTTCATGCGGCGATGCTAAA 58.909 45.000 12.98 6.59 35.36 1.85
219 240 2.039974 TGTTTCATGCGGCGATGCT 61.040 52.632 12.98 0.00 35.36 3.79
220 241 1.869132 GTGTTTCATGCGGCGATGC 60.869 57.895 12.98 0.00 0.00 3.91
277 299 0.902531 GAACCCGGATCTGACCAAGA 59.097 55.000 0.73 0.00 39.94 3.02
324 346 6.610075 AAAGCCCTTTTGTCATAATGTCAT 57.390 33.333 0.00 0.00 0.00 3.06
343 365 1.140816 AGAAGAGTTGCGACGAAAGC 58.859 50.000 0.00 0.00 0.00 3.51
363 385 3.581755 CATAAGTTGGACCGAAACTCGA 58.418 45.455 0.00 0.00 43.74 4.04
379 401 3.625938 GTCCGTCGGTAGTAAGCATAAG 58.374 50.000 11.88 0.00 0.00 1.73
394 416 1.557443 CCTCAACTTGTGCGTCCGTC 61.557 60.000 0.00 0.00 0.00 4.79
471 498 6.099125 TCCTAACCGAATCATAACAAGGATCA 59.901 38.462 0.00 0.00 0.00 2.92
488 515 3.545703 AGATCAAGGCAAATCCTAACCG 58.454 45.455 0.00 0.00 46.94 4.44
596 623 2.125793 GGCCCGACCGAGTACAAC 60.126 66.667 0.00 0.00 0.00 3.32
597 624 2.283388 AGGCCCGACCGAGTACAA 60.283 61.111 0.00 0.00 46.52 2.41
599 626 3.885521 CGAGGCCCGACCGAGTAC 61.886 72.222 0.00 0.00 46.52 2.73
600 627 4.100084 TCGAGGCCCGACCGAGTA 62.100 66.667 11.66 0.00 46.52 2.59
618 646 6.219473 AGCATAGAACCAATCTAACATCTCG 58.781 40.000 0.00 0.00 43.73 4.04
654 682 4.449068 GCCTAACGATACAATGTGATGAGG 59.551 45.833 0.00 0.00 0.00 3.86
662 690 6.801539 AATACATGGCCTAACGATACAATG 57.198 37.500 3.32 0.00 0.00 2.82
688 716 8.611654 AGGAGTAATACGTAAAACAACACATT 57.388 30.769 0.00 0.00 0.00 2.71
728 756 6.349300 ACACAAACTAGACTTTCACATCACT 58.651 36.000 0.00 0.00 0.00 3.41
729 757 6.604735 ACACAAACTAGACTTTCACATCAC 57.395 37.500 0.00 0.00 0.00 3.06
730 758 7.042992 CGTTACACAAACTAGACTTTCACATCA 60.043 37.037 0.00 0.00 35.81 3.07
748 776 2.841215 CTTTCTTGGGACCGTTACACA 58.159 47.619 0.00 0.00 0.00 3.72
752 780 1.880646 GCTGCTTTCTTGGGACCGTTA 60.881 52.381 0.00 0.00 0.00 3.18
1034 1066 0.108945 GTAGGTGGACGCTGTGGTAC 60.109 60.000 0.00 0.00 0.00 3.34
1192 1224 1.760480 GAGGAGACAGAGAGGGGGC 60.760 68.421 0.00 0.00 0.00 5.80
1336 1369 1.082117 AAATTCTAGCACGACGCCCG 61.082 55.000 0.00 0.00 44.04 6.13
1446 1479 2.844072 TTTCGGCCGATCGCACATCA 62.844 55.000 31.56 7.62 40.31 3.07
1562 1596 1.582610 GGATTTTCCCGTCAGCGCAA 61.583 55.000 11.47 0.00 36.67 4.85
1655 1691 9.682465 GATCTAATAAGGGGTGTTACTTTTCTT 57.318 33.333 0.00 0.00 0.00 2.52
1754 1791 3.223435 TGGTTCCGAAGCCATTAAAACA 58.777 40.909 7.83 0.00 0.00 2.83
1805 1842 0.034198 GAGCCGAAGATTCTAGGGGC 59.966 60.000 12.30 12.30 40.80 5.80
1936 1973 5.120399 TGGACCTATTACAATTTACAGGCG 58.880 41.667 0.00 0.00 0.00 5.52
1998 2035 3.263261 TGTTGACAGTACAAACTTCGCA 58.737 40.909 0.00 0.00 31.97 5.10
2086 2126 3.459227 TGACAGGAATTCTATGATGGGCA 59.541 43.478 15.27 0.68 0.00 5.36
2087 2127 4.090761 TGACAGGAATTCTATGATGGGC 57.909 45.455 15.27 0.00 0.00 5.36
2088 2128 5.013913 AGGATGACAGGAATTCTATGATGGG 59.986 44.000 15.27 0.00 0.00 4.00
2378 2421 4.074627 TCCGTTGATTGTGTGACCTTAA 57.925 40.909 0.00 0.00 0.00 1.85
2547 2590 7.620094 AGATGTGTAACTACCTCAACTCCTAAT 59.380 37.037 0.00 0.00 38.04 1.73
3724 4242 7.823745 ACATGAGTTTGTCCTAAGTCAAATT 57.176 32.000 0.00 0.00 39.99 1.82
3725 4243 7.502226 TGAACATGAGTTTGTCCTAAGTCAAAT 59.498 33.333 0.00 0.00 39.99 2.32
3778 4297 7.306399 CCATGTTAATCCAAATACGACGTAGAC 60.306 40.741 13.87 2.24 0.00 2.59
3993 4513 7.875327 TCCTGATTAACATTAAAACCTAGCC 57.125 36.000 0.00 0.00 0.00 3.93
4031 4551 1.755179 AATCTCCAACCTGGCAATCG 58.245 50.000 0.00 0.00 37.47 3.34
4189 4722 9.170734 TCAGAATGATATTCAGAACAGAAAAGG 57.829 33.333 4.56 0.00 42.56 3.11
4464 4997 1.708341 AAATGTTCACCCTTGCAGCT 58.292 45.000 0.00 0.00 0.00 4.24
4491 5024 1.697432 TGGTAGTTTGGACCACCTCTG 59.303 52.381 0.00 0.00 42.15 3.35
4613 5146 5.012975 AGAGAAGCTGAGGTCTTCATTTCTT 59.987 40.000 10.98 4.53 41.68 2.52
4637 5170 9.739276 AAATGGAAGATATGAGTTCTGTGTTAA 57.261 29.630 0.00 0.00 0.00 2.01
4763 5296 3.068165 CCATAGACCTGCAGTGAATCGTA 59.932 47.826 13.81 0.00 0.00 3.43
4831 5364 2.430248 ATCATGCTTCAGCCATGACA 57.570 45.000 12.97 0.00 39.48 3.58
4856 5389 7.041848 ACAACTTAAACACCGGAACTATACAAC 60.042 37.037 9.46 0.00 0.00 3.32
5022 5557 4.344865 GTGCCTCGGCCCAAAGGA 62.345 66.667 15.90 0.00 41.09 3.36
5033 5568 6.054295 ACTTATCTTGATCTCATTGTGCCTC 58.946 40.000 0.00 0.00 0.00 4.70
5070 5605 4.568956 ACCAAAAATGCTGTAAATCTGGC 58.431 39.130 0.00 0.00 0.00 4.85
5084 5619 3.736740 GCGGACACAACAGAACCAAAAAT 60.737 43.478 0.00 0.00 0.00 1.82
5140 5675 1.708993 AAGCCTGAAGCCACAGTCCA 61.709 55.000 6.93 0.00 45.47 4.02
5281 5821 6.423862 TGTCTTTTAAGTTTGACCGAATTCG 58.576 36.000 20.92 20.92 39.44 3.34
5338 5878 1.272147 ACTGCAGAGGATTCCAAACCC 60.272 52.381 23.35 0.00 0.00 4.11
5346 5886 1.900351 TGCGCTACTGCAGAGGATT 59.100 52.632 23.35 0.00 40.62 3.01
5376 5916 6.599356 TCCTCTGCAAAACTATACAGTGTA 57.401 37.500 5.24 5.24 34.36 2.90
5377 5917 5.483685 TCCTCTGCAAAACTATACAGTGT 57.516 39.130 0.00 0.00 34.36 3.55
5378 5918 6.344500 AGATCCTCTGCAAAACTATACAGTG 58.656 40.000 0.00 0.00 34.36 3.66
5379 5919 6.552445 AGATCCTCTGCAAAACTATACAGT 57.448 37.500 0.00 0.00 36.19 3.55
5380 5920 7.044181 TCAAGATCCTCTGCAAAACTATACAG 58.956 38.462 0.00 0.00 0.00 2.74
5382 5922 7.201652 GGTTCAAGATCCTCTGCAAAACTATAC 60.202 40.741 0.00 0.00 0.00 1.47
5395 5978 4.553330 TTACAGTGGGTTCAAGATCCTC 57.447 45.455 0.00 0.00 0.00 3.71
5401 5984 7.594758 CACAACATATTTTACAGTGGGTTCAAG 59.405 37.037 0.00 0.00 0.00 3.02
5427 6010 3.756963 GGATAAGAGTGTCAAACCAACCC 59.243 47.826 0.00 0.00 0.00 4.11
5478 6065 1.673665 CACTGCAGTCCCCAAGAGC 60.674 63.158 18.64 0.00 0.00 4.09
5541 6131 6.001460 GCCCTTATTAGCCATGTTACACATA 58.999 40.000 0.00 0.00 36.53 2.29
5545 6135 4.165180 TCTGCCCTTATTAGCCATGTTACA 59.835 41.667 0.00 0.00 0.00 2.41
5565 6155 2.093306 TGAAGGTGCGGTTGTATCTG 57.907 50.000 0.00 0.00 0.00 2.90
5649 6239 7.068226 ACACAACTTAGCAACCAGAAACTAAAT 59.932 33.333 0.00 0.00 0.00 1.40
5719 6309 3.037549 TGGACTCACTTTTGCCCATTTT 58.962 40.909 0.00 0.00 0.00 1.82
5933 6526 6.294176 CCCACTTTCTTTCTTCTACCAACATG 60.294 42.308 0.00 0.00 0.00 3.21
5935 6528 5.130350 CCCACTTTCTTTCTTCTACCAACA 58.870 41.667 0.00 0.00 0.00 3.33
5960 6553 3.561503 AGGTGCGAAAATTTTCTTACGC 58.438 40.909 24.53 22.77 44.95 4.42


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

AutoCloner maintained by Alex Coulton.