Multiple sequence alignment - TraesCS3D01G252000

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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 TraesCS3D01G252000 chr3D 100.000 6289 0 0 1 6289 352792628 352786340 0.000000e+00 11614.0
1 TraesCS3D01G252000 chr3D 91.304 46 4 0 1190 1235 275995106 275995151 5.260000e-06 63.9
2 TraesCS3D01G252000 chr3B 96.593 4168 91 21 489 4628 451846437 451842293 0.000000e+00 6863.0
3 TraesCS3D01G252000 chr3B 94.785 1093 34 10 4625 5699 451842219 451841132 0.000000e+00 1681.0
4 TraesCS3D01G252000 chr3B 92.754 414 19 8 1 411 451846841 451846436 7.020000e-164 588.0
5 TraesCS3D01G252000 chr3B 94.416 197 11 0 6093 6289 451839897 451839701 2.850000e-78 303.0
6 TraesCS3D01G252000 chr3B 92.466 146 8 2 5849 5993 451840622 451840479 8.260000e-49 206.0
7 TraesCS3D01G252000 chr3B 97.872 47 1 0 5768 5814 451840674 451840628 1.450000e-11 82.4
8 TraesCS3D01G252000 chr3B 94.340 53 0 2 6054 6106 451840087 451840038 1.880000e-10 78.7
9 TraesCS3D01G252000 chr3B 89.796 49 5 0 1190 1238 375500105 375500057 5.260000e-06 63.9
10 TraesCS3D01G252000 chr3A 91.087 4712 235 75 9 4628 471364041 471359423 0.000000e+00 6204.0
11 TraesCS3D01G252000 chr3A 91.246 1428 65 23 4659 6032 471359303 471357882 0.000000e+00 1890.0
12 TraesCS3D01G252000 chr3A 94.931 217 10 1 6074 6289 471357781 471357565 7.810000e-89 339.0
13 TraesCS3D01G252000 chr3A 89.796 49 5 0 1190 1238 364198074 364198026 5.260000e-06 63.9
14 TraesCS3D01G252000 chr4B 89.492 1142 91 7 3107 4235 534069399 534070524 0.000000e+00 1417.0
15 TraesCS3D01G252000 chr4B 90.608 181 15 2 3219 3397 190887685 190887505 8.150000e-59 239.0
16 TraesCS3D01G252000 chr5B 90.424 637 43 5 3601 4235 195147441 195146821 0.000000e+00 822.0
17 TraesCS3D01G252000 chr7D 87.072 263 29 3 1692 1954 550989797 550989540 6.170000e-75 292.0
18 TraesCS3D01G252000 chr7B 85.714 266 29 4 1692 1955 595840373 595840115 8.030000e-69 272.0
19 TraesCS3D01G252000 chrUn 89.109 202 20 2 1692 1893 68793296 68793097 3.760000e-62 250.0
20 TraesCS3D01G252000 chr7A 84.091 264 35 5 1692 1954 636909080 636908823 1.350000e-61 248.0
21 TraesCS3D01G252000 chr1A 88.000 200 20 3 1692 1890 25287271 25287467 3.790000e-57 233.0
22 TraesCS3D01G252000 chr2D 87.117 163 20 1 1692 1854 26438601 26438762 3.870000e-42 183.0


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 TraesCS3D01G252000 chr3D 352786340 352792628 6288 True 11614.0 11614 100.000000 1 6289 1 chr3D.!!$R1 6288
1 TraesCS3D01G252000 chr3B 451839701 451846841 7140 True 1400.3 6863 94.746571 1 6289 7 chr3B.!!$R2 6288
2 TraesCS3D01G252000 chr3A 471357565 471364041 6476 True 2811.0 6204 92.421333 9 6289 3 chr3A.!!$R2 6280
3 TraesCS3D01G252000 chr4B 534069399 534070524 1125 False 1417.0 1417 89.492000 3107 4235 1 chr4B.!!$F1 1128
4 TraesCS3D01G252000 chr5B 195146821 195147441 620 True 822.0 822 90.424000 3601 4235 1 chr5B.!!$R1 634

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
72 77 0.676782 GCATAACCGTGGAGCCTTGT 60.677 55.000 0.00 0.0 0.00 3.16 F
1376 1463 0.174845 CTTGGTTCCGGCTATCGTCA 59.825 55.000 0.00 0.0 37.11 4.35 F
1381 1468 1.135199 GTTCCGGCTATCGTCAGTCAA 60.135 52.381 0.00 0.0 37.11 3.18 F
1944 2038 1.599171 CCTCAGCTGCTCTACGAATCG 60.599 57.143 9.47 0.0 0.00 3.34 F
3394 3500 2.575532 CAAGGTCTGAAAGCAGGAACA 58.424 47.619 0.00 0.0 42.53 3.18 F
4128 4247 0.239347 TCGTTCCTCGTTCCTCGTTC 59.761 55.000 0.00 0.0 40.80 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1490 0.471617 AGAGCGGCATATCAAAGGCT 59.528 50.000 1.45 0.0 0.00 4.58 R
2228 2325 1.066143 GGAGGCGACAAGAAGGAATGA 60.066 52.381 0.00 0.0 0.00 2.57 R
3130 3232 2.189594 TTCAACTGACAGCAGGATGG 57.810 50.000 1.25 0.0 46.60 3.51 R
3471 3577 1.202758 TGGAGTGCCAACAACCAGTAG 60.203 52.381 0.00 0.0 42.49 2.57 R
4821 5037 2.053627 GCTTGAAACAATGAGCAACGG 58.946 47.619 0.00 0.0 35.29 4.44 R
5824 6475 0.098728 CGTTGCTAAATGAAGGGCGG 59.901 55.000 0.00 0.0 0.00 6.13 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
72 77 0.676782 GCATAACCGTGGAGCCTTGT 60.677 55.000 0.00 0.00 0.00 3.16
73 78 1.406341 GCATAACCGTGGAGCCTTGTA 60.406 52.381 0.00 0.00 0.00 2.41
74 79 2.550978 CATAACCGTGGAGCCTTGTAG 58.449 52.381 0.00 0.00 0.00 2.74
75 80 1.636148 TAACCGTGGAGCCTTGTAGT 58.364 50.000 0.00 0.00 0.00 2.73
76 81 1.636148 AACCGTGGAGCCTTGTAGTA 58.364 50.000 0.00 0.00 0.00 1.82
77 82 0.893447 ACCGTGGAGCCTTGTAGTAC 59.107 55.000 0.00 0.00 0.00 2.73
119 127 8.836268 ATATTGTGCAAATTAGCCCATAAATG 57.164 30.769 0.00 0.00 0.00 2.32
129 137 1.267806 GCCCATAAATGTGCCGAGATG 59.732 52.381 0.00 0.00 0.00 2.90
242 251 2.435059 GACTGGCGCCTTGTCCTC 60.435 66.667 29.80 14.86 0.00 3.71
327 342 3.044059 CTTAAGCCTGCTGCCGTGC 62.044 63.158 0.00 0.00 42.71 5.34
388 404 1.069636 CAAGAGAAAGCAACTCGGCAC 60.070 52.381 0.00 0.00 39.12 5.01
412 428 5.474876 CACTGGCTTCTAACCTTCTTCATTT 59.525 40.000 0.00 0.00 0.00 2.32
469 507 1.200483 CGACTGTGTTATAGGCGCTG 58.800 55.000 7.64 0.00 40.14 5.18
488 526 1.634973 TGCCATCTCATCCAGTCCAAA 59.365 47.619 0.00 0.00 0.00 3.28
489 527 2.242965 TGCCATCTCATCCAGTCCAAAT 59.757 45.455 0.00 0.00 0.00 2.32
492 531 4.518211 GCCATCTCATCCAGTCCAAATAAG 59.482 45.833 0.00 0.00 0.00 1.73
498 537 5.745227 TCATCCAGTCCAAATAAGGAAGAC 58.255 41.667 0.00 0.00 39.92 3.01
507 546 6.374333 GTCCAAATAAGGAAGACAGTAATGCA 59.626 38.462 0.00 0.00 39.92 3.96
538 585 3.012518 GGTTACGGCAGAGTACAGTAGA 58.987 50.000 0.00 0.00 0.00 2.59
550 601 0.747283 ACAGTAGAGTACCCCGAGCG 60.747 60.000 0.00 0.00 0.00 5.03
574 625 1.152963 CAAAGTATCCGCCAGGGGG 60.153 63.158 16.98 16.98 38.33 5.40
865 942 3.999297 GACGGTCCCTCGAGCTCCT 62.999 68.421 6.99 0.00 34.19 3.69
1249 1335 1.472662 AAGCTGGTACGTGCTCCTGT 61.473 55.000 10.88 0.00 39.59 4.00
1279 1365 3.238108 TCAACTGCTCGGATCTTTCTC 57.762 47.619 0.00 0.00 0.00 2.87
1293 1379 5.510520 GGATCTTTCTCATGCTTCCGAGTAT 60.511 44.000 0.00 0.00 0.00 2.12
1297 1383 4.585955 TCTCATGCTTCCGAGTATTACC 57.414 45.455 0.00 0.00 0.00 2.85
1298 1384 3.958147 TCTCATGCTTCCGAGTATTACCA 59.042 43.478 0.00 0.00 0.00 3.25
1299 1385 4.038042 TCTCATGCTTCCGAGTATTACCAG 59.962 45.833 0.00 0.00 0.00 4.00
1376 1463 0.174845 CTTGGTTCCGGCTATCGTCA 59.825 55.000 0.00 0.00 37.11 4.35
1381 1468 1.135199 GTTCCGGCTATCGTCAGTCAA 60.135 52.381 0.00 0.00 37.11 3.18
1387 1474 2.337583 GCTATCGTCAGTCAAGTTGCA 58.662 47.619 0.00 0.00 0.00 4.08
1491 1578 1.613437 CCTCGTTGGCAGATTTGGTTT 59.387 47.619 0.00 0.00 0.00 3.27
1627 1719 3.808728 TGACAACTAAGTTCAAGCTGCT 58.191 40.909 0.00 0.00 0.00 4.24
1643 1735 3.136077 AGCTGCTGAGTATTGGATGATGT 59.864 43.478 0.00 0.00 0.00 3.06
1644 1736 3.881688 GCTGCTGAGTATTGGATGATGTT 59.118 43.478 0.00 0.00 0.00 2.71
1681 1775 4.092237 TGTGAACGGCAGATACAATAAACG 59.908 41.667 0.00 0.00 0.00 3.60
1944 2038 1.599171 CCTCAGCTGCTCTACGAATCG 60.599 57.143 9.47 0.00 0.00 3.34
1950 2044 2.977169 GCTGCTCTACGAATCGAAGATC 59.023 50.000 10.55 0.00 45.12 2.75
1990 2084 6.069381 AGGAGGAAGTATGGAAGCTTTACATT 60.069 38.462 18.76 6.15 0.00 2.71
2228 2325 6.839124 ACACATACACCAATCATTTGATGT 57.161 33.333 0.00 0.00 42.44 3.06
2443 2541 3.915437 TTTCGCTCCTCATTTTTGTCC 57.085 42.857 0.00 0.00 0.00 4.02
2633 2735 2.817258 TGGGTAGCAATGCAGTGTTTAC 59.183 45.455 16.47 16.84 0.00 2.01
2849 2951 8.849168 TGGCTTAAGTTATTTCCATACATCATG 58.151 33.333 4.02 0.00 0.00 3.07
3159 3261 6.036577 TGCTGTCAGTTGAATGTCATACTA 57.963 37.500 0.93 0.00 0.00 1.82
3177 3279 3.775202 ACTACTTGCTCTGCGTATCTTG 58.225 45.455 0.00 0.00 0.00 3.02
3394 3500 2.575532 CAAGGTCTGAAAGCAGGAACA 58.424 47.619 0.00 0.00 42.53 3.18
3471 3577 7.068348 TGAGGTACTTGGTAGTTATGATGTCTC 59.932 40.741 0.00 0.00 41.55 3.36
3657 3770 0.458669 TCCGTGACCTCTTTATCCGC 59.541 55.000 0.00 0.00 0.00 5.54
3746 3859 9.507329 TTGAATCTATGAGATATTAACTTGCCC 57.493 33.333 0.00 0.00 32.89 5.36
3758 3871 0.919710 ACTTGCCCCCTCCATACTTC 59.080 55.000 0.00 0.00 0.00 3.01
3828 3941 0.521735 GCTTTGAAGGTTACAGGCGG 59.478 55.000 0.00 0.00 0.00 6.13
4117 4236 9.285770 GTAATTGGTTTATTTTGATCGTTCCTC 57.714 33.333 0.00 0.00 0.00 3.71
4118 4237 5.539582 TGGTTTATTTTGATCGTTCCTCG 57.460 39.130 0.00 0.00 41.41 4.63
4119 4238 4.998672 TGGTTTATTTTGATCGTTCCTCGT 59.001 37.500 0.00 0.00 40.80 4.18
4120 4239 5.470777 TGGTTTATTTTGATCGTTCCTCGTT 59.529 36.000 0.00 0.00 40.80 3.85
4121 4240 6.019762 GGTTTATTTTGATCGTTCCTCGTTC 58.980 40.000 0.00 0.00 40.80 3.95
4122 4241 5.789710 TTATTTTGATCGTTCCTCGTTCC 57.210 39.130 0.00 0.00 40.80 3.62
4123 4242 3.396260 TTTTGATCGTTCCTCGTTCCT 57.604 42.857 0.00 0.00 40.80 3.36
4124 4243 2.649331 TTGATCGTTCCTCGTTCCTC 57.351 50.000 0.00 0.00 40.80 3.71
4125 4244 0.450583 TGATCGTTCCTCGTTCCTCG 59.549 55.000 0.00 0.00 40.80 4.63
4126 4245 0.450983 GATCGTTCCTCGTTCCTCGT 59.549 55.000 0.00 0.00 40.80 4.18
4127 4246 0.886563 ATCGTTCCTCGTTCCTCGTT 59.113 50.000 0.00 0.00 40.80 3.85
4128 4247 0.239347 TCGTTCCTCGTTCCTCGTTC 59.761 55.000 0.00 0.00 40.80 3.95
4129 4248 0.240411 CGTTCCTCGTTCCTCGTTCT 59.760 55.000 0.00 0.00 40.80 3.01
4130 4249 1.335689 CGTTCCTCGTTCCTCGTTCTT 60.336 52.381 0.00 0.00 40.80 2.52
4313 4432 5.754782 TCCATTTGTTATGATGTAGGTGCT 58.245 37.500 0.00 0.00 0.00 4.40
4589 4716 6.978080 GTCAAATTTTCTTAGTCAACCTTGCA 59.022 34.615 0.00 0.00 0.00 4.08
4632 4838 3.755378 ACTGGTGCTCTTATTTGCAGAAG 59.245 43.478 0.00 0.00 40.06 2.85
4754 4970 4.341235 TCGTCGAGGACTCCAATCATAATT 59.659 41.667 3.17 0.00 0.00 1.40
4799 5015 6.531594 GGCATCATGATTCATAATCTGCAATG 59.468 38.462 5.16 0.00 37.19 2.82
4808 5024 9.321562 GATTCATAATCTGCAATGTGGAAATTT 57.678 29.630 0.00 0.00 35.02 1.82
4817 5033 6.115446 TGCAATGTGGAAATTTAAAACACCA 58.885 32.000 10.42 8.87 0.00 4.17
4821 5037 9.283420 CAATGTGGAAATTTAAAACACCAAAAC 57.717 29.630 10.61 2.89 0.00 2.43
4823 5039 6.092259 TGTGGAAATTTAAAACACCAAAACCG 59.908 34.615 10.61 0.00 0.00 4.44
5191 5411 4.246458 AGTAGCACTGAGAAAACGATTCC 58.754 43.478 0.00 0.00 0.00 3.01
5192 5412 3.409026 AGCACTGAGAAAACGATTCCT 57.591 42.857 0.00 0.00 0.00 3.36
5611 5852 6.456988 CGTTTCCTGACTATTAATGTGCCTTC 60.457 42.308 0.00 0.00 0.00 3.46
5612 5853 5.692115 TCCTGACTATTAATGTGCCTTCA 57.308 39.130 0.00 0.00 0.00 3.02
5633 5874 0.039527 GGAACAAATGTCGTGTGGCC 60.040 55.000 0.00 0.00 0.00 5.36
5644 5885 4.643463 TGTCGTGTGGCCTTTTAGAAATA 58.357 39.130 3.32 0.00 0.00 1.40
5646 5887 5.708230 TGTCGTGTGGCCTTTTAGAAATATT 59.292 36.000 3.32 0.00 0.00 1.28
5649 5890 7.272731 GTCGTGTGGCCTTTTAGAAATATTTTC 59.727 37.037 3.32 0.00 0.00 2.29
5704 5947 2.200899 GCATGTTTTTGCACTTCGGTT 58.799 42.857 0.00 0.00 42.31 4.44
5759 6409 0.189574 TGGCCTGTTTGGGATGGAAA 59.810 50.000 3.32 0.00 36.00 3.13
5797 6448 4.754372 TGTTGCATGAGTTGAGATGTTC 57.246 40.909 0.00 0.00 0.00 3.18
5820 6471 5.239306 TCTCTTTGGAACTGTTGTATTGCAG 59.761 40.000 0.00 0.00 38.58 4.41
5824 6475 2.488153 GGAACTGTTGTATTGCAGACCC 59.512 50.000 0.00 0.00 36.62 4.46
5847 6499 0.098728 CCTTCATTTAGCAACGCGGG 59.901 55.000 12.47 2.74 0.00 6.13
5891 6544 7.595819 AATTTGGTGGATAAGAACACTGAAA 57.404 32.000 0.00 0.00 37.72 2.69
5928 6581 2.735772 CCCAGGCAGCCGACATAGT 61.736 63.158 5.55 0.00 0.00 2.12
5997 6650 0.323302 TGTCAGGAAACGCATGCCTA 59.677 50.000 13.15 0.00 0.00 3.93
6039 6962 1.454479 CATGGCCAGGGACCACATC 60.454 63.158 13.05 0.00 40.82 3.06
6054 6977 1.683385 CACATCGAGCCTATGTGGAGA 59.317 52.381 13.27 0.00 46.78 3.71
6056 6979 1.271934 CATCGAGCCTATGTGGAGAGG 59.728 57.143 0.00 0.00 38.35 3.69
6134 7275 8.738645 AGGAACTTGTAGATTAATGATGTTCC 57.261 34.615 11.66 11.66 46.42 3.62
6141 7282 4.130118 AGATTAATGATGTTCCGTCAGCC 58.870 43.478 0.00 0.00 32.64 4.85
6243 7384 0.037697 CCGATCGGTTCACTTCACCA 60.038 55.000 26.35 0.00 33.36 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 81 9.726438 GCACAATATTCTCCCAATAATAGTAGT 57.274 33.333 0.00 0.00 0.00 2.73
77 82 9.725019 TGCACAATATTCTCCCAATAATAGTAG 57.275 33.333 0.00 0.00 0.00 2.57
129 137 2.610374 TGAGCGTATACCATTTTTCGCC 59.390 45.455 0.00 0.00 43.73 5.54
242 251 5.282076 GCGTACTTTTTAATGCTTAACCACG 59.718 40.000 0.00 0.00 0.00 4.94
351 367 4.643784 TCTCTTGGTAGGGTCGTTTATCTC 59.356 45.833 0.00 0.00 0.00 2.75
388 404 4.008074 TGAAGAAGGTTAGAAGCCAGTG 57.992 45.455 0.00 0.00 0.00 3.66
438 454 9.362539 CCTATAACACAGTCGTACAACTAATTT 57.637 33.333 0.00 0.00 0.00 1.82
439 455 7.490402 GCCTATAACACAGTCGTACAACTAATT 59.510 37.037 0.00 0.00 0.00 1.40
440 456 6.976925 GCCTATAACACAGTCGTACAACTAAT 59.023 38.462 0.00 0.00 0.00 1.73
441 457 6.324819 GCCTATAACACAGTCGTACAACTAA 58.675 40.000 0.00 0.00 0.00 2.24
443 459 4.673580 CGCCTATAACACAGTCGTACAACT 60.674 45.833 0.00 0.00 0.00 3.16
445 461 3.761657 CGCCTATAACACAGTCGTACAA 58.238 45.455 0.00 0.00 0.00 2.41
446 462 2.478370 GCGCCTATAACACAGTCGTACA 60.478 50.000 0.00 0.00 0.00 2.90
447 463 2.114825 GCGCCTATAACACAGTCGTAC 58.885 52.381 0.00 0.00 0.00 3.67
448 464 2.019249 AGCGCCTATAACACAGTCGTA 58.981 47.619 2.29 0.00 0.00 3.43
449 465 0.815734 AGCGCCTATAACACAGTCGT 59.184 50.000 2.29 0.00 0.00 4.34
450 466 1.200483 CAGCGCCTATAACACAGTCG 58.800 55.000 2.29 0.00 0.00 4.18
451 467 0.931005 GCAGCGCCTATAACACAGTC 59.069 55.000 2.29 0.00 0.00 3.51
453 469 2.311294 GGCAGCGCCTATAACACAG 58.689 57.895 2.29 0.00 46.69 3.66
467 505 0.835276 TGGACTGGATGAGATGGCAG 59.165 55.000 0.00 0.00 0.00 4.85
469 507 2.425143 TTTGGACTGGATGAGATGGC 57.575 50.000 0.00 0.00 0.00 4.40
488 526 8.579850 TTGATTTGCATTACTGTCTTCCTTAT 57.420 30.769 0.00 0.00 0.00 1.73
489 527 7.882791 TCTTGATTTGCATTACTGTCTTCCTTA 59.117 33.333 0.00 0.00 0.00 2.69
492 531 6.404074 CCTCTTGATTTGCATTACTGTCTTCC 60.404 42.308 0.00 0.00 0.00 3.46
498 537 5.649782 AACCCTCTTGATTTGCATTACTG 57.350 39.130 0.00 0.00 0.00 2.74
507 546 2.304761 TCTGCCGTAACCCTCTTGATTT 59.695 45.455 0.00 0.00 0.00 2.17
538 585 1.991121 TGAATATCGCTCGGGGTACT 58.009 50.000 0.00 0.00 0.00 2.73
550 601 4.003648 CCCTGGCGGATACTTTGAATATC 58.996 47.826 0.00 0.00 0.00 1.63
574 625 1.861575 CGCTTTCGCTTTCCCTCTATC 59.138 52.381 0.00 0.00 0.00 2.08
579 630 0.534203 TTGACGCTTTCGCTTTCCCT 60.534 50.000 0.00 0.00 39.84 4.20
835 904 4.361971 ACCGTCGAGGCAGGGAGA 62.362 66.667 0.00 0.00 46.52 3.71
848 925 4.049817 AGGAGCTCGAGGGACCGT 62.050 66.667 15.58 0.00 0.00 4.83
1249 1335 0.518636 GAGCAGTTGAATCGCAGCAA 59.481 50.000 0.00 0.00 0.00 3.91
1279 1365 3.804325 CACTGGTAATACTCGGAAGCATG 59.196 47.826 0.00 0.00 0.00 4.06
1376 1463 1.972872 CAGGAACCTGCAACTTGACT 58.027 50.000 7.95 0.00 37.24 3.41
1401 1488 2.304180 AGAGCGGCATATCAAAGGCTAT 59.696 45.455 1.45 0.00 0.00 2.97
1402 1489 1.694150 AGAGCGGCATATCAAAGGCTA 59.306 47.619 1.45 0.00 0.00 3.93
1403 1490 0.471617 AGAGCGGCATATCAAAGGCT 59.528 50.000 1.45 0.00 0.00 4.58
1404 1491 1.265365 GAAGAGCGGCATATCAAAGGC 59.735 52.381 1.45 0.00 0.00 4.35
1405 1492 2.805099 GAGAAGAGCGGCATATCAAAGG 59.195 50.000 1.45 0.00 0.00 3.11
1407 1494 3.541996 TGAGAAGAGCGGCATATCAAA 57.458 42.857 1.45 0.00 0.00 2.69
1408 1495 3.541996 TTGAGAAGAGCGGCATATCAA 57.458 42.857 1.45 4.67 0.00 2.57
1491 1578 5.085920 AGTCCAAATTGTTCATCCATGGAA 58.914 37.500 20.67 0.00 37.24 3.53
1617 1709 3.701205 TCCAATACTCAGCAGCTTGAA 57.299 42.857 0.00 0.00 0.00 2.69
1644 1736 9.602568 TCTGCCGTTCACATTTTATTACTATAA 57.397 29.630 0.00 0.00 0.00 0.98
1659 1753 4.327898 TCGTTTATTGTATCTGCCGTTCAC 59.672 41.667 0.00 0.00 0.00 3.18
1681 1775 4.817318 ACTGTTTCTCATTCCTCTCCTC 57.183 45.455 0.00 0.00 0.00 3.71
1944 2038 5.882557 TCCTTGCAAAATCCTGTAGATCTTC 59.117 40.000 0.00 0.00 32.47 2.87
1950 2044 3.955471 TCCTCCTTGCAAAATCCTGTAG 58.045 45.455 0.00 0.00 0.00 2.74
1990 2084 6.000840 TCACAGTCCTACAAAATTATGCACA 58.999 36.000 0.00 0.00 0.00 4.57
2228 2325 1.066143 GGAGGCGACAAGAAGGAATGA 60.066 52.381 0.00 0.00 0.00 2.57
3130 3232 2.189594 TTCAACTGACAGCAGGATGG 57.810 50.000 1.25 0.00 46.60 3.51
3159 3261 2.751166 ACAAGATACGCAGAGCAAGT 57.249 45.000 0.00 0.00 0.00 3.16
3394 3500 8.627208 TGATCTTCTCATACTTTTGCTTCTTT 57.373 30.769 0.00 0.00 0.00 2.52
3471 3577 1.202758 TGGAGTGCCAACAACCAGTAG 60.203 52.381 0.00 0.00 42.49 2.57
3657 3770 8.130307 AGAATGAAAACAAAATCAAACCTTCG 57.870 30.769 0.00 0.00 0.00 3.79
3758 3871 3.006110 ACAGAATGCAACAGGTTTCCATG 59.994 43.478 0.00 0.00 42.53 3.66
3828 3941 7.934855 AGGCATTATTCTGATATCAACCATC 57.065 36.000 6.90 0.00 0.00 3.51
4264 4383 7.961326 AAATAAACATGGCTAAGAAGGTCAT 57.039 32.000 0.00 0.00 0.00 3.06
4313 4432 3.256704 ACCACTAATCCTCCCTTCAACA 58.743 45.455 0.00 0.00 0.00 3.33
4589 4716 9.520515 ACCAGTTTATAAGAACAAGTCATGAAT 57.479 29.630 0.00 0.00 31.94 2.57
4632 4838 3.273919 CTTGCACAAAGCTGGAAGTAC 57.726 47.619 0.00 0.00 45.94 2.73
4754 4970 8.811017 TGATGCCCAGATACAAGAAAATAAAAA 58.189 29.630 0.00 0.00 0.00 1.94
4799 5015 6.092396 ACGGTTTTGGTGTTTTAAATTTCCAC 59.908 34.615 0.00 0.00 0.00 4.02
4808 5024 3.192844 TGAGCAACGGTTTTGGTGTTTTA 59.807 39.130 0.00 0.00 0.00 1.52
4817 5033 4.116747 TGAAACAATGAGCAACGGTTTT 57.883 36.364 0.00 0.00 32.32 2.43
4821 5037 2.053627 GCTTGAAACAATGAGCAACGG 58.946 47.619 0.00 0.00 35.29 4.44
4823 5039 4.614946 AGAAGCTTGAAACAATGAGCAAC 58.385 39.130 2.10 0.00 37.59 4.17
5191 5411 2.423926 ACACAGCACACGTAGAAGAG 57.576 50.000 0.00 0.00 0.00 2.85
5192 5412 5.632244 TTATACACAGCACACGTAGAAGA 57.368 39.130 0.00 0.00 0.00 2.87
5424 5646 1.804151 GACTCACAAGCGCCACATAAA 59.196 47.619 2.29 0.00 0.00 1.40
5467 5690 2.669569 CTGGACAAGGTGCACCGG 60.670 66.667 29.68 26.34 42.08 5.28
5568 5791 4.394439 AACGTTACCAGCCAAATTTGTT 57.606 36.364 16.73 2.25 0.00 2.83
5611 5852 2.858260 GCCACACGACATTTGTTCCTTG 60.858 50.000 0.00 0.00 0.00 3.61
5612 5853 1.336755 GCCACACGACATTTGTTCCTT 59.663 47.619 0.00 0.00 0.00 3.36
5619 5860 3.482436 TCTAAAAGGCCACACGACATTT 58.518 40.909 5.01 0.00 0.00 2.32
5667 5908 3.193267 ACATGCACGGCAGACATTAAAAT 59.807 39.130 0.00 0.00 43.65 1.82
5674 5915 0.743688 AAAAACATGCACGGCAGACA 59.256 45.000 0.00 0.00 43.65 3.41
5704 5947 5.186603 TGCATACTTATGGGTTTGCAATCAA 59.813 36.000 0.00 0.00 45.67 2.57
5759 6409 4.940046 TGCAACAACATCAACCACAAAAAT 59.060 33.333 0.00 0.00 0.00 1.82
5797 6448 5.239306 TCTGCAATACAACAGTTCCAAAGAG 59.761 40.000 0.00 0.00 35.37 2.85
5820 6471 1.101635 GCTAAATGAAGGGCGGGGTC 61.102 60.000 0.00 0.00 0.00 4.46
5824 6475 0.098728 CGTTGCTAAATGAAGGGCGG 59.901 55.000 0.00 0.00 0.00 6.13
5847 6499 6.530019 AATTTGGTCAATTAGGACACATCC 57.470 37.500 0.00 0.00 46.69 3.51
5928 6581 3.868369 GCTGTACATGTTCCCTTGCAGTA 60.868 47.826 2.30 0.00 0.00 2.74
6160 7301 1.326951 TGCTAGCATCAGTACCGCCA 61.327 55.000 14.93 0.00 0.00 5.69
6161 7302 0.179084 TTGCTAGCATCAGTACCGCC 60.179 55.000 20.13 0.00 0.00 6.13
6243 7384 1.120530 ACCACCAACGTCAGAACTCT 58.879 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.