Multiple sequence alignment - TraesCS5A01G198300

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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 TraesCS5A01G198300 chr5A 100.000 2237 0 0 1 2237 402658878 402656642 0.000000e+00 4132.0
1 TraesCS5A01G198300 chr5B 89.303 2281 170 30 1 2237 354716388 354714138 0.000000e+00 2793.0
2 TraesCS5A01G198300 chr5D 89.644 2192 161 38 1 2153 309402936 309400772 0.000000e+00 2730.0
3 TraesCS5A01G198300 chr5D 75.862 174 35 5 396 564 483708019 483707848 5.120000e-12 82.4
4 TraesCS5A01G198300 chr4D 81.452 124 21 2 400 522 399221962 399221840 1.410000e-17 100.0
5 TraesCS5A01G198300 chr6D 93.878 49 3 0 394 442 316488721 316488673 8.570000e-10 75.0
6 TraesCS5A01G198300 chr1D 90.566 53 4 1 394 445 78132804 78132856 3.990000e-08 69.4
7 TraesCS5A01G198300 chr7A 97.436 39 1 0 394 432 728715337 728715299 1.430000e-07 67.6
8 TraesCS5A01G198300 chr7A 97.436 39 1 0 394 432 728841093 728841055 1.430000e-07 67.6
9 TraesCS5A01G198300 chr7A 75.610 123 26 3 394 515 402193583 402193702 8.630000e-05 58.4
10 TraesCS5A01G198300 chr6A 73.810 168 39 4 394 558 579419452 579419617 6.670000e-06 62.1
11 TraesCS5A01G198300 chr4A 78.125 96 18 2 428 523 598048144 598048236 8.630000e-05 58.4


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 TraesCS5A01G198300 chr5A 402656642 402658878 2236 True 4132 4132 100.000 1 2237 1 chr5A.!!$R1 2236
1 TraesCS5A01G198300 chr5B 354714138 354716388 2250 True 2793 2793 89.303 1 2237 1 chr5B.!!$R1 2236
2 TraesCS5A01G198300 chr5D 309400772 309402936 2164 True 2730 2730 89.644 1 2153 1 chr5D.!!$R1 2152

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
30 31 0.462759 GACGGGAGCTGGGATGAAAG 60.463 60.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1489 0.249699 TATGAATCGGCCGCGAACAT 60.25 50.0 23.51 22.72 0.0 2.71 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
21 22 2.125350 GAGGCTTGACGGGAGCTG 60.125 66.667 0.00 0.00 40.01 4.24
30 31 0.462759 GACGGGAGCTGGGATGAAAG 60.463 60.000 0.00 0.00 0.00 2.62
31 32 1.821332 CGGGAGCTGGGATGAAAGC 60.821 63.158 0.00 0.00 39.82 3.51
58 60 2.378547 AGGGTTTTATTGGTCAGGCTCA 59.621 45.455 0.00 0.00 0.00 4.26
61 63 3.429410 GGTTTTATTGGTCAGGCTCATGC 60.429 47.826 0.00 0.00 38.76 4.06
68 70 1.340017 GGTCAGGCTCATGCTTTGGTA 60.340 52.381 0.00 0.00 39.59 3.25
69 71 1.740025 GTCAGGCTCATGCTTTGGTAC 59.260 52.381 0.00 0.00 39.59 3.34
71 73 2.161855 CAGGCTCATGCTTTGGTACAA 58.838 47.619 0.00 0.00 41.28 2.41
74 76 2.754552 GGCTCATGCTTTGGTACAATCA 59.245 45.455 0.00 0.00 41.28 2.57
106 108 3.016736 AGCGTTGGGAATATTTGGAGTG 58.983 45.455 0.00 0.00 0.00 3.51
117 119 6.150140 GGAATATTTGGAGTGGAGATATGTGC 59.850 42.308 0.00 0.00 0.00 4.57
126 128 4.716784 AGTGGAGATATGTGCTTTGTCCTA 59.283 41.667 0.00 0.00 0.00 2.94
134 139 0.676466 TGCTTTGTCCTACCATGCCG 60.676 55.000 0.00 0.00 0.00 5.69
152 157 3.195661 GCCGACGTCCTTAATGAAGATT 58.804 45.455 10.58 0.00 34.25 2.40
170 175 6.596888 TGAAGATTGAGAGATTAAAGGTGCTG 59.403 38.462 0.00 0.00 0.00 4.41
188 193 3.802139 TGCTGAAACTACAAGTTCTCGTG 59.198 43.478 0.00 0.00 37.47 4.35
259 264 1.026584 TGGTTCGTGTCTTGTCTCGA 58.973 50.000 0.00 0.00 0.00 4.04
273 278 6.697892 GTCTTGTCTCGATGAACCCTTATAAG 59.302 42.308 5.43 5.43 0.00 1.73
345 350 9.710900 GAAAAAGTTATTGAATCCCTGTGAATT 57.289 29.630 0.00 0.00 0.00 2.17
372 378 7.972832 TTTGATATCTTCCACTTTAACACGT 57.027 32.000 3.98 0.00 0.00 4.49
386 392 3.399440 AACACGTTACAAACCCGGATA 57.601 42.857 0.73 0.00 0.00 2.59
390 396 1.655099 CGTTACAAACCCGGATACACG 59.345 52.381 0.73 0.00 0.00 4.49
424 430 2.022129 GTCACCACAGACGCCTTCG 61.022 63.158 0.00 0.00 42.43 3.79
442 448 2.384382 TCGTAGTCGACAAAAACGTCC 58.616 47.619 19.50 0.00 41.35 4.79
456 462 3.547054 AACGTCCCTTCACAGTAAACA 57.453 42.857 0.00 0.00 0.00 2.83
464 470 5.888724 TCCCTTCACAGTAAACAAACATCAA 59.111 36.000 0.00 0.00 0.00 2.57
467 473 7.032580 CCTTCACAGTAAACAAACATCAACAA 58.967 34.615 0.00 0.00 0.00 2.83
470 476 8.459521 TCACAGTAAACAAACATCAACAAAAG 57.540 30.769 0.00 0.00 0.00 2.27
474 480 7.010091 CAGTAAACAAACATCAACAAAAGGTCC 59.990 37.037 0.00 0.00 0.00 4.46
477 483 4.202010 ACAAACATCAACAAAAGGTCCGAG 60.202 41.667 0.00 0.00 0.00 4.63
537 557 2.239907 GGACTTTTCCTGATGGGCTAGT 59.760 50.000 0.00 0.00 39.13 2.57
538 558 3.308473 GGACTTTTCCTGATGGGCTAGTT 60.308 47.826 0.00 0.00 39.13 2.24
539 559 3.942115 GACTTTTCCTGATGGGCTAGTTC 59.058 47.826 0.00 0.00 34.39 3.01
540 560 3.282885 CTTTTCCTGATGGGCTAGTTCC 58.717 50.000 0.00 0.00 34.39 3.62
541 561 2.270434 TTCCTGATGGGCTAGTTCCT 57.730 50.000 5.97 0.00 34.39 3.36
542 562 2.270434 TCCTGATGGGCTAGTTCCTT 57.730 50.000 5.97 0.42 34.39 3.36
543 563 2.119495 TCCTGATGGGCTAGTTCCTTC 58.881 52.381 10.89 10.89 34.39 3.46
544 564 1.839994 CCTGATGGGCTAGTTCCTTCA 59.160 52.381 16.20 16.20 37.08 3.02
545 565 2.420687 CCTGATGGGCTAGTTCCTTCAC 60.421 54.545 14.37 0.00 35.49 3.18
546 566 2.237143 CTGATGGGCTAGTTCCTTCACA 59.763 50.000 14.37 0.00 35.49 3.58
547 567 2.642311 TGATGGGCTAGTTCCTTCACAA 59.358 45.455 14.37 0.00 34.73 3.33
548 568 2.859165 TGGGCTAGTTCCTTCACAAG 57.141 50.000 5.97 0.00 0.00 3.16
569 589 7.651704 CACAAGGAACCAAACCATTTAAACTAG 59.348 37.037 0.00 0.00 0.00 2.57
574 594 6.796705 ACCAAACCATTTAAACTAGACTCG 57.203 37.500 0.00 0.00 0.00 4.18
621 662 1.583054 AGAAGGTTCTGAACACACGC 58.417 50.000 21.01 4.47 35.89 5.34
791 833 2.171940 CAGCTCACGCGCACTTTC 59.828 61.111 5.73 0.00 42.32 2.62
800 842 2.351774 CGCACTTTCACGCGCAAA 60.352 55.556 5.73 4.64 45.57 3.68
810 852 2.739287 CGCGCAAACCCCTCGTTA 60.739 61.111 8.75 0.00 33.05 3.18
828 870 3.607542 CGTTAAAACGTTCGCTCCCAAAT 60.608 43.478 0.00 0.00 46.63 2.32
831 873 1.296056 AACGTTCGCTCCCAAATCGG 61.296 55.000 0.00 0.00 0.00 4.18
832 874 2.791927 GTTCGCTCCCAAATCGGC 59.208 61.111 0.00 0.00 0.00 5.54
878 926 2.366167 CCAGCTCTCCCTCCCTCA 59.634 66.667 0.00 0.00 0.00 3.86
931 980 2.954756 CTACGCCTACACGTACCGCG 62.955 65.000 14.45 14.45 46.19 6.46
981 1030 4.679662 AGCTAGCACATTTCATTGATTGC 58.320 39.130 18.83 0.00 31.29 3.56
1006 1055 1.595382 GATCCGTTCGGCATGGAGG 60.595 63.158 6.35 0.00 44.45 4.30
1237 1286 1.293818 GGCGATTCCCCTAGCTAGC 59.706 63.158 15.74 6.62 0.00 3.42
1242 1291 0.104725 ATTCCCCTAGCTAGCTGGCT 60.105 55.000 28.46 28.46 45.29 4.75
1243 1292 1.050988 TTCCCCTAGCTAGCTGGCTG 61.051 60.000 32.45 21.32 43.01 4.85
1252 1301 2.254737 CTAGCTGGCTGCCTCTGCTT 62.255 60.000 28.30 17.56 44.23 3.91
1253 1302 2.532465 TAGCTGGCTGCCTCTGCTTG 62.532 60.000 28.30 10.41 44.23 4.01
1263 1312 1.089920 CCTCTGCTTGTGTGGTATGC 58.910 55.000 0.00 0.00 0.00 3.14
1300 1349 5.522097 TGCATATATCGCACGTATAAATGGG 59.478 40.000 5.94 0.00 33.55 4.00
1301 1350 5.751509 GCATATATCGCACGTATAAATGGGA 59.248 40.000 6.68 6.68 41.40 4.37
1425 1474 7.119116 GGAGTTTTGTTTTGTTTTTCTGTCCAT 59.881 33.333 0.00 0.00 0.00 3.41
1466 1515 2.662791 CGCGGCCGATTCATATTCTTTG 60.663 50.000 33.48 0.00 36.29 2.77
1520 1569 8.745837 CAATCTTGCGGTGTTATGATAAAAATC 58.254 33.333 0.00 0.00 0.00 2.17
1521 1570 7.384439 TCTTGCGGTGTTATGATAAAAATCA 57.616 32.000 0.00 0.00 34.73 2.57
1558 1609 5.818678 TTTGTCGCACCTATATAATCCCT 57.181 39.130 0.00 0.00 0.00 4.20
1563 1614 8.598202 TGTCGCACCTATATAATCCCTTTATA 57.402 34.615 0.00 0.00 37.22 0.98
1566 1617 9.038072 TCGCACCTATATAATCCCTTTATAACA 57.962 33.333 0.00 0.00 36.57 2.41
1567 1618 9.832445 CGCACCTATATAATCCCTTTATAACAT 57.168 33.333 0.00 0.00 36.57 2.71
1589 1640 3.772025 TCCCTTTGTGGCAAAGAAAGAAA 59.228 39.130 19.50 2.58 40.73 2.52
1590 1641 4.408596 TCCCTTTGTGGCAAAGAAAGAAAT 59.591 37.500 19.50 0.00 40.73 2.17
1592 1643 5.696270 CCCTTTGTGGCAAAGAAAGAAATAC 59.304 40.000 19.50 0.00 40.73 1.89
1594 1645 6.200854 CCTTTGTGGCAAAGAAAGAAATACAC 59.799 38.462 19.50 0.00 40.73 2.90
1596 1647 5.830912 TGTGGCAAAGAAAGAAATACACAG 58.169 37.500 0.00 0.00 33.09 3.66
1602 1654 8.726988 GGCAAAGAAAGAAATACACAGTACATA 58.273 33.333 0.00 0.00 0.00 2.29
1632 1684 6.441093 CACAGTATGCATTGTTAACTGGAT 57.559 37.500 23.71 7.08 42.53 3.41
1636 1688 9.845740 ACAGTATGCATTGTTAACTGGATATAA 57.154 29.630 23.71 0.00 42.53 0.98
1641 1693 9.632638 ATGCATTGTTAACTGGATATAAGAGTT 57.367 29.630 7.22 0.00 34.36 3.01
1677 1732 4.808414 TCGATTTTCACCACTCTCAGAT 57.192 40.909 0.00 0.00 0.00 2.90
1685 1740 1.118838 CCACTCTCAGATCCTGTCCC 58.881 60.000 0.00 0.00 32.61 4.46
1691 1746 4.158786 CTCTCAGATCCTGTCCCATATGT 58.841 47.826 1.24 0.00 32.61 2.29
1704 1759 6.903516 TGTCCCATATGTCTCATCTTTGATT 58.096 36.000 1.24 0.00 0.00 2.57
1715 1770 9.820725 TGTCTCATCTTTGATTTCAAAACAAAT 57.179 25.926 6.07 0.00 44.24 2.32
1754 1838 8.577048 TGAGCAGTAGACAGTAGTACTTTAAT 57.423 34.615 0.00 0.00 0.00 1.40
1985 2069 6.594159 TGACTAGTCTGCTTAAATTAGTTGGC 59.406 38.462 23.01 0.00 0.00 4.52
1987 2071 3.689649 AGTCTGCTTAAATTAGTTGGCCG 59.310 43.478 0.00 0.00 0.00 6.13
2147 2231 5.836347 AGAAGACAAAAGCTTTGATGGAAC 58.164 37.500 13.54 4.96 0.00 3.62
2164 2248 2.952310 GGAACATGATGCTTTAGGGTCC 59.048 50.000 0.00 0.00 0.00 4.46
2165 2249 2.332063 ACATGATGCTTTAGGGTCCG 57.668 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.454663 GGCTTTCATCCCAGCTCCC 60.455 63.158 0.00 0.00 36.20 4.30
21 22 0.179006 CCCTAGCAGGCTTTCATCCC 60.179 60.000 0.00 0.00 32.73 3.85
30 31 2.688446 GACCAATAAAACCCTAGCAGGC 59.312 50.000 0.00 0.00 32.73 4.85
31 32 3.947834 CTGACCAATAAAACCCTAGCAGG 59.052 47.826 0.00 0.00 34.30 4.85
43 44 3.370840 AAGCATGAGCCTGACCAATAA 57.629 42.857 0.00 0.00 43.56 1.40
58 60 5.047164 TGCTCAATTGATTGTACCAAAGCAT 60.047 36.000 8.96 0.00 36.13 3.79
61 63 6.258230 TCTGCTCAATTGATTGTACCAAAG 57.742 37.500 8.96 0.00 38.84 2.77
68 70 2.816087 ACGCTTCTGCTCAATTGATTGT 59.184 40.909 8.96 0.00 38.84 2.71
69 71 3.482722 ACGCTTCTGCTCAATTGATTG 57.517 42.857 8.96 0.00 39.10 2.67
71 73 2.163010 CCAACGCTTCTGCTCAATTGAT 59.837 45.455 8.96 0.00 36.97 2.57
74 76 0.883833 CCCAACGCTTCTGCTCAATT 59.116 50.000 0.00 0.00 36.97 2.32
106 108 4.141711 TGGTAGGACAAAGCACATATCTCC 60.142 45.833 0.00 0.00 0.00 3.71
117 119 1.369625 GTCGGCATGGTAGGACAAAG 58.630 55.000 0.00 0.00 0.00 2.77
126 128 0.539986 ATTAAGGACGTCGGCATGGT 59.460 50.000 9.92 0.00 0.00 3.55
134 139 6.565234 TCTCTCAATCTTCATTAAGGACGTC 58.435 40.000 7.13 7.13 33.22 4.34
152 157 5.869579 AGTTTCAGCACCTTTAATCTCTCA 58.130 37.500 0.00 0.00 0.00 3.27
164 169 3.184581 CGAGAACTTGTAGTTTCAGCACC 59.815 47.826 0.00 0.00 38.80 5.01
170 175 6.388278 ACCTATCACGAGAACTTGTAGTTTC 58.612 40.000 0.00 0.00 38.80 2.78
188 193 7.028361 GCCATAACACGATTCTACTACCTATC 58.972 42.308 0.00 0.00 0.00 2.08
244 249 2.351447 GGTTCATCGAGACAAGACACGA 60.351 50.000 0.00 0.00 37.30 4.35
247 252 2.248248 AGGGTTCATCGAGACAAGACA 58.752 47.619 0.00 0.00 0.00 3.41
346 351 8.842280 ACGTGTTAAAGTGGAAGATATCAAAAA 58.158 29.630 5.32 0.00 0.00 1.94
347 352 8.385898 ACGTGTTAAAGTGGAAGATATCAAAA 57.614 30.769 5.32 0.00 0.00 2.44
348 353 7.972832 ACGTGTTAAAGTGGAAGATATCAAA 57.027 32.000 5.32 0.00 0.00 2.69
352 357 8.836268 TTGTAACGTGTTAAAGTGGAAGATAT 57.164 30.769 0.00 0.00 0.00 1.63
360 365 4.273274 CGGGTTTGTAACGTGTTAAAGTG 58.727 43.478 0.00 0.00 0.00 3.16
361 366 3.312146 CCGGGTTTGTAACGTGTTAAAGT 59.688 43.478 0.00 0.00 0.00 2.66
362 367 3.559242 TCCGGGTTTGTAACGTGTTAAAG 59.441 43.478 0.00 0.00 0.00 1.85
372 378 1.001746 TGCGTGTATCCGGGTTTGTAA 59.998 47.619 0.00 0.00 0.00 2.41
386 392 0.313987 TTCGTCACTCTCATGCGTGT 59.686 50.000 5.68 0.00 31.45 4.49
390 396 2.354109 TGACTTCGTCACTCTCATGC 57.646 50.000 0.00 0.00 37.67 4.06
424 430 2.747436 AGGGACGTTTTTGTCGACTAC 58.253 47.619 17.92 8.60 39.83 2.73
433 439 4.701171 TGTTTACTGTGAAGGGACGTTTTT 59.299 37.500 0.00 0.00 0.00 1.94
442 448 6.559810 TGTTGATGTTTGTTTACTGTGAAGG 58.440 36.000 0.00 0.00 0.00 3.46
456 462 3.951680 ACTCGGACCTTTTGTTGATGTTT 59.048 39.130 0.00 0.00 0.00 2.83
464 470 6.059484 TCTGAATTTAACTCGGACCTTTTGT 58.941 36.000 0.00 0.00 0.00 2.83
467 473 7.576861 TTTTCTGAATTTAACTCGGACCTTT 57.423 32.000 0.00 0.00 0.00 3.11
470 476 6.308041 GCATTTTTCTGAATTTAACTCGGACC 59.692 38.462 0.00 0.00 0.00 4.46
474 480 7.096106 TGCTTGCATTTTTCTGAATTTAACTCG 60.096 33.333 0.00 0.00 0.00 4.18
477 483 7.071414 GGTGCTTGCATTTTTCTGAATTTAAC 58.929 34.615 0.00 0.00 0.00 2.01
540 560 4.670896 AATGGTTTGGTTCCTTGTGAAG 57.329 40.909 0.00 0.00 32.37 3.02
541 561 6.546428 TTAAATGGTTTGGTTCCTTGTGAA 57.454 33.333 0.00 0.00 0.00 3.18
542 562 6.155393 AGTTTAAATGGTTTGGTTCCTTGTGA 59.845 34.615 0.00 0.00 0.00 3.58
543 563 6.345298 AGTTTAAATGGTTTGGTTCCTTGTG 58.655 36.000 0.00 0.00 0.00 3.33
544 564 6.553953 AGTTTAAATGGTTTGGTTCCTTGT 57.446 33.333 0.00 0.00 0.00 3.16
545 565 7.865889 GTCTAGTTTAAATGGTTTGGTTCCTTG 59.134 37.037 0.00 0.00 0.00 3.61
546 566 7.783119 AGTCTAGTTTAAATGGTTTGGTTCCTT 59.217 33.333 0.00 0.00 0.00 3.36
547 567 7.295340 AGTCTAGTTTAAATGGTTTGGTTCCT 58.705 34.615 0.00 0.00 0.00 3.36
548 568 7.520451 AGTCTAGTTTAAATGGTTTGGTTCC 57.480 36.000 0.00 0.00 0.00 3.62
549 569 7.295930 CGAGTCTAGTTTAAATGGTTTGGTTC 58.704 38.462 0.00 0.00 0.00 3.62
621 662 1.630244 CTGCCCTTCGCTTTGTCTCG 61.630 60.000 0.00 0.00 38.78 4.04
784 826 2.292916 GGTTTGCGCGTGAAAGTGC 61.293 57.895 8.43 0.00 46.83 4.40
810 852 1.069500 CGATTTGGGAGCGAACGTTTT 60.069 47.619 0.46 0.00 0.00 2.43
817 859 4.483243 GGGCCGATTTGGGAGCGA 62.483 66.667 0.00 0.00 38.63 4.93
832 874 2.299967 AAATAGGGGAGGGGGAGGGG 62.300 65.000 0.00 0.00 0.00 4.79
981 1030 2.202932 CCGAACGGATCAGCAGGG 60.203 66.667 7.53 0.00 37.50 4.45
1006 1055 3.151022 CCTCCTCCTCCTGGCGAC 61.151 72.222 0.00 0.00 0.00 5.19
1217 1266 0.318762 CTAGCTAGGGGAATCGCCAC 59.681 60.000 18.78 7.45 41.99 5.01
1224 1273 1.050988 CAGCCAGCTAGCTAGGGGAA 61.051 60.000 25.21 0.00 42.61 3.97
1237 1286 2.033757 ACAAGCAGAGGCAGCCAG 59.966 61.111 15.80 4.00 44.61 4.85
1242 1291 0.692476 ATACCACACAAGCAGAGGCA 59.308 50.000 0.00 0.00 44.61 4.75
1243 1292 1.089920 CATACCACACAAGCAGAGGC 58.910 55.000 0.00 0.00 41.61 4.70
1297 1346 8.482943 CCATAATCGTTCAATATATACCTCCCA 58.517 37.037 0.00 0.00 0.00 4.37
1300 1349 9.886132 AACCCATAATCGTTCAATATATACCTC 57.114 33.333 0.00 0.00 0.00 3.85
1301 1350 9.667107 CAACCCATAATCGTTCAATATATACCT 57.333 33.333 0.00 0.00 0.00 3.08
1401 1450 7.977789 ATGGACAGAAAAACAAAACAAAACT 57.022 28.000 0.00 0.00 0.00 2.66
1406 1455 9.883142 AGAAATAATGGACAGAAAAACAAAACA 57.117 25.926 0.00 0.00 0.00 2.83
1425 1474 6.908284 GCCGCGAACATTATTACAAGAAATAA 59.092 34.615 8.23 0.00 36.15 1.40
1439 1488 1.095228 ATGAATCGGCCGCGAACATT 61.095 50.000 23.51 15.06 0.00 2.71
1440 1489 0.249699 TATGAATCGGCCGCGAACAT 60.250 50.000 23.51 22.72 0.00 2.71
1441 1490 0.249699 ATATGAATCGGCCGCGAACA 60.250 50.000 23.51 17.61 0.00 3.18
1442 1491 0.865769 AATATGAATCGGCCGCGAAC 59.134 50.000 23.51 12.21 0.00 3.95
1466 1515 6.291112 CGACGATCACAAGTACATGAATACAC 60.291 42.308 4.87 0.00 0.00 2.90
1480 1529 3.306973 GCAAGATTGATCGACGATCACAA 59.693 43.478 34.02 23.50 46.87 3.33
1520 1569 8.372521 GGTGCGACAAAACTTATATTTTTCATG 58.627 33.333 0.00 0.00 29.17 3.07
1521 1570 8.303876 AGGTGCGACAAAACTTATATTTTTCAT 58.696 29.630 0.00 0.00 29.17 2.57
1531 1582 7.658575 GGGATTATATAGGTGCGACAAAACTTA 59.341 37.037 0.00 0.00 0.00 2.24
1537 1588 5.818678 AAGGGATTATATAGGTGCGACAA 57.181 39.130 0.00 0.00 0.00 3.18
1558 1609 6.495181 TCTTTGCCACAAAGGGATGTTATAAA 59.505 34.615 17.44 0.00 37.68 1.40
1563 1614 2.676748 TCTTTGCCACAAAGGGATGTT 58.323 42.857 17.44 0.00 37.68 2.71
1566 1617 3.575805 TCTTTCTTTGCCACAAAGGGAT 58.424 40.909 17.44 0.00 37.68 3.85
1567 1618 3.025322 TCTTTCTTTGCCACAAAGGGA 57.975 42.857 17.44 11.55 38.09 4.20
1575 1626 6.544197 TGTACTGTGTATTTCTTTCTTTGCCA 59.456 34.615 0.00 0.00 0.00 4.92
1589 1640 6.724893 TGTGCATACCTATGTACTGTGTAT 57.275 37.500 12.85 0.00 45.62 2.29
1590 1641 6.144078 CTGTGCATACCTATGTACTGTGTA 57.856 41.667 12.85 0.00 45.62 2.90
1636 1688 8.480643 AATCGATCGAAAACAAGATAAACTCT 57.519 30.769 23.50 0.00 34.96 3.24
1641 1693 7.960738 GGTGAAAATCGATCGAAAACAAGATAA 59.039 33.333 23.50 0.00 0.00 1.75
1643 1695 6.072728 TGGTGAAAATCGATCGAAAACAAGAT 60.073 34.615 23.50 0.00 0.00 2.40
1645 1697 5.339611 GTGGTGAAAATCGATCGAAAACAAG 59.660 40.000 23.50 0.00 0.00 3.16
1647 1699 4.513692 AGTGGTGAAAATCGATCGAAAACA 59.486 37.500 23.50 16.15 0.00 2.83
1648 1700 5.030874 AGTGGTGAAAATCGATCGAAAAC 57.969 39.130 23.50 14.74 0.00 2.43
1653 1708 3.511699 TGAGAGTGGTGAAAATCGATCG 58.488 45.455 9.36 9.36 0.00 3.69
1677 1732 8.575628 ATCAAAGATGAGACATATGGGACAGGA 61.576 40.741 7.80 0.00 40.17 3.86
1704 1759 3.882888 AGCCGTCTGAGATTTGTTTTGAA 59.117 39.130 0.00 0.00 0.00 2.69
1985 2069 8.782144 CCTTCTTATTAGGAGTAGTAACTACGG 58.218 40.741 0.00 0.00 41.96 4.02
1987 2071 8.575589 GCCCTTCTTATTAGGAGTAGTAACTAC 58.424 40.741 0.00 0.00 35.56 2.73
2147 2231 2.332063 ACGGACCCTAAAGCATCATG 57.668 50.000 0.00 0.00 0.00 3.07
2153 2237 4.216902 ACAAACAAATACGGACCCTAAAGC 59.783 41.667 0.00 0.00 0.00 3.51
2157 2241 4.519730 CCAAACAAACAAATACGGACCCTA 59.480 41.667 0.00 0.00 0.00 3.53
2164 2248 7.284518 ACTTTGAACCAAACAAACAAATACG 57.715 32.000 0.00 0.00 34.30 3.06


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

AutoCloner maintained by Alex Coulton.