Multiple sequence alignment - TraesCS2D01G040500

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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 TraesCS2D01G040500 chr2D 100.000 3419 0 0 1 3419 14745345 14748763 0.000000e+00 6314.0
1 TraesCS2D01G040500 chr2D 83.990 1624 217 27 727 2341 14729219 14730808 0.000000e+00 1519.0
2 TraesCS2D01G040500 chr2A 90.105 3436 231 39 1 3407 16830738 16834093 0.000000e+00 4361.0
3 TraesCS2D01G040500 chr2A 90.448 1696 100 23 1 1693 16825324 16826960 0.000000e+00 2178.0
4 TraesCS2D01G040500 chr2A 83.391 1734 208 45 727 2423 16820879 16822569 0.000000e+00 1533.0
5 TraesCS2D01G040500 chr2A 84.785 769 96 11 1351 2113 16837604 16836851 0.000000e+00 752.0
6 TraesCS2D01G040500 chr2A 84.874 476 57 8 731 1205 16838376 16837915 1.860000e-127 466.0
7 TraesCS2D01G040500 chr2A 76.510 149 33 2 2457 2604 338519162 338519015 2.830000e-11 80.5
8 TraesCS2D01G040500 chr2B 91.998 2587 177 18 1 2575 26508175 26510743 0.000000e+00 3603.0
9 TraesCS2D01G040500 chr2B 92.866 1696 96 13 1 1693 26502531 26504204 0.000000e+00 2438.0
10 TraesCS2D01G040500 chr2B 83.540 1610 204 35 746 2339 26493839 26495403 0.000000e+00 1448.0
11 TraesCS2D01G040500 chr2B 94.659 880 44 1 1696 2575 26521445 26522321 0.000000e+00 1362.0
12 TraesCS2D01G040500 chr2B 82.442 991 149 19 1352 2334 26526892 26525919 0.000000e+00 843.0
13 TraesCS2D01G040500 chr2B 89.662 474 25 8 2948 3416 26523012 26523466 1.770000e-162 582.0
14 TraesCS2D01G040500 chr2B 89.241 474 26 8 2948 3416 26511431 26511884 1.380000e-158 569.0
15 TraesCS2D01G040500 chr2B 80.775 671 118 8 1650 2313 13797653 13798319 6.540000e-142 514.0
16 TraesCS2D01G040500 chr2B 84.472 483 58 9 725 1205 26527581 26527114 8.640000e-126 460.0
17 TraesCS2D01G040500 chr2B 87.363 364 30 6 2586 2946 26510783 26511133 1.480000e-108 403.0
18 TraesCS2D01G040500 chr2B 87.017 362 31 7 2588 2946 26522367 26522715 8.890000e-106 394.0
19 TraesCS2D01G040500 chr6B 81.449 345 58 6 1379 1720 662501851 662501510 9.340000e-71 278.0
20 TraesCS2D01G040500 chr7A 84.074 270 37 6 141 404 323434122 323434391 4.380000e-64 255.0
21 TraesCS2D01G040500 chr7D 82.331 266 42 5 140 401 587390307 587390043 3.430000e-55 226.0
22 TraesCS2D01G040500 chr7D 76.510 149 33 2 2457 2604 379063124 379062977 2.830000e-11 80.5
23 TraesCS2D01G040500 chr5D 81.139 281 47 6 126 402 560037857 560038135 1.600000e-53 220.0
24 TraesCS2D01G040500 chr7B 80.870 115 22 0 2457 2571 374487012 374486898 1.310000e-14 91.6


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 TraesCS2D01G040500 chr2D 14745345 14748763 3418 False 6314.000000 6314 100.000000 1 3419 1 chr2D.!!$F2 3418
1 TraesCS2D01G040500 chr2D 14729219 14730808 1589 False 1519.000000 1519 83.990000 727 2341 1 chr2D.!!$F1 1614
2 TraesCS2D01G040500 chr2A 16820879 16834093 13214 False 2690.666667 4361 87.981333 1 3407 3 chr2A.!!$F1 3406
3 TraesCS2D01G040500 chr2A 16836851 16838376 1525 True 609.000000 752 84.829500 731 2113 2 chr2A.!!$R2 1382
4 TraesCS2D01G040500 chr2B 26502531 26511884 9353 False 1753.250000 3603 90.367000 1 3416 4 chr2B.!!$F3 3415
5 TraesCS2D01G040500 chr2B 26493839 26495403 1564 False 1448.000000 1448 83.540000 746 2339 1 chr2B.!!$F2 1593
6 TraesCS2D01G040500 chr2B 26521445 26523466 2021 False 779.333333 1362 90.446000 1696 3416 3 chr2B.!!$F4 1720
7 TraesCS2D01G040500 chr2B 26525919 26527581 1662 True 651.500000 843 83.457000 725 2334 2 chr2B.!!$R1 1609
8 TraesCS2D01G040500 chr2B 13797653 13798319 666 False 514.000000 514 80.775000 1650 2313 1 chr2B.!!$F1 663

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
188 4636 0.759346 GGGTGTCACACAAGTCCTCT 59.241 55.0 10.85 0.0 35.86 3.69 F
1284 16861 0.030908 CTGCTACTGCTACCGCTACC 59.969 60.0 0.00 0.0 40.48 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 17103 0.034059 CTGCTGACGTTGTCCTCCTT 59.966 55.0 0.0 0.0 0.0 3.36 R
2746 18588 0.588252 CGGAAGCAGACCACAACAAG 59.412 55.0 0.0 0.0 0.0 3.16 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
38 4484 7.701539 ATCAGCATCTACAACACCAAATTAA 57.298 32.000 0.00 0.00 0.00 1.40
161 4607 2.770164 ATGCACAGTAGGTCCTTGAC 57.230 50.000 0.00 0.00 0.00 3.18
171 4619 1.425448 AGGTCCTTGACTTTTCAGGGG 59.575 52.381 3.23 0.00 46.83 4.79
179 4627 1.947456 GACTTTTCAGGGGTGTCACAC 59.053 52.381 0.00 0.00 0.00 3.82
188 4636 0.759346 GGGTGTCACACAAGTCCTCT 59.241 55.000 10.85 0.00 35.86 3.69
195 4643 5.864474 GTGTCACACAAGTCCTCTAACTATG 59.136 44.000 2.00 0.00 34.08 2.23
216 4664 9.159254 ACTATGAAAATCATCATACAGGTCCTA 57.841 33.333 0.00 0.00 40.44 2.94
286 4734 9.865484 GAACTACTTTAGTGTTGAACTGATTTC 57.135 33.333 0.00 0.00 40.26 2.17
335 4783 7.491372 CACTTCAAGGATTTGGATGATGATTTG 59.509 37.037 0.00 0.00 34.97 2.32
374 4822 1.227468 GACGCCCCCGAAATAGTCC 60.227 63.158 0.00 0.00 38.29 3.85
405 4853 7.716998 ACCTATATGCACTCCACTCTAAAAATG 59.283 37.037 0.00 0.00 0.00 2.32
459 10356 5.965334 CGGGTATTTCGAAGTCAAATCATTG 59.035 40.000 0.00 0.00 37.92 2.82
506 10403 7.321772 ACGATGACGATATCTTAATTGAACG 57.678 36.000 0.34 0.00 42.66 3.95
550 10447 7.849804 TTTCTTTGTAGACTGAGCCATAATC 57.150 36.000 0.00 0.00 0.00 1.75
554 10451 5.939764 TGTAGACTGAGCCATAATCACTT 57.060 39.130 0.00 0.00 0.00 3.16
556 10453 6.108687 TGTAGACTGAGCCATAATCACTTTG 58.891 40.000 0.00 0.00 0.00 2.77
557 10454 3.944015 AGACTGAGCCATAATCACTTTGC 59.056 43.478 0.00 0.00 0.00 3.68
559 10456 3.944015 ACTGAGCCATAATCACTTTGCTC 59.056 43.478 0.00 0.00 44.11 4.26
562 10459 5.744171 TGAGCCATAATCACTTTGCTCTTA 58.256 37.500 10.26 0.00 44.16 2.10
563 10460 6.179756 TGAGCCATAATCACTTTGCTCTTAA 58.820 36.000 10.26 0.00 44.16 1.85
564 10461 6.317140 TGAGCCATAATCACTTTGCTCTTAAG 59.683 38.462 10.26 0.00 44.16 1.85
565 10462 6.418101 AGCCATAATCACTTTGCTCTTAAGA 58.582 36.000 4.81 4.81 0.00 2.10
566 10463 7.059156 AGCCATAATCACTTTGCTCTTAAGAT 58.941 34.615 5.44 0.00 0.00 2.40
648 10551 9.678260 GGGATAAGATGCTTATCTTTATGTCAT 57.322 33.333 20.40 0.00 40.91 3.06
655 10559 5.465390 TGCTTATCTTTATGTCATGGTACGC 59.535 40.000 0.00 0.00 0.00 4.42
824 16377 7.519032 TTTTGTTATGGTACTTGCTAGCTTT 57.481 32.000 17.23 2.34 0.00 3.51
827 16380 1.821216 TGGTACTTGCTAGCTTTGCC 58.179 50.000 17.23 12.78 0.00 4.52
851 16404 4.093743 TGAGCATCACTTACCAAGTAGGA 58.906 43.478 0.00 0.00 42.56 2.94
852 16405 4.081642 TGAGCATCACTTACCAAGTAGGAC 60.082 45.833 0.00 0.00 42.56 3.85
853 16406 3.119101 AGCATCACTTACCAAGTAGGACG 60.119 47.826 0.00 0.00 40.46 4.79
854 16407 3.368116 GCATCACTTACCAAGTAGGACGT 60.368 47.826 0.00 0.00 40.46 4.34
1131 16684 3.461061 CAGCACATCCATCTATGTCGTT 58.539 45.455 0.00 0.00 38.01 3.85
1158 16711 1.488393 GCTTGCCTTGTCCTCTCCTAT 59.512 52.381 0.00 0.00 0.00 2.57
1161 16714 1.127343 GCCTTGTCCTCTCCTATGCT 58.873 55.000 0.00 0.00 0.00 3.79
1241 16803 1.207089 CCTTGATCCTGCTACGGTTGA 59.793 52.381 0.00 0.00 0.00 3.18
1264 16841 3.011369 TCCTGCTCCTTCTACTCCTGTTA 59.989 47.826 0.00 0.00 0.00 2.41
1270 16847 5.188988 TCCTTCTACTCCTGTTACTGCTA 57.811 43.478 0.00 0.00 0.00 3.49
1278 16855 2.758979 TCCTGTTACTGCTACTGCTACC 59.241 50.000 0.00 0.00 40.48 3.18
1282 16859 2.336945 TACTGCTACTGCTACCGCTA 57.663 50.000 0.00 0.00 40.48 4.26
1284 16861 0.030908 CTGCTACTGCTACCGCTACC 59.969 60.000 0.00 0.00 40.48 3.18
1285 16862 0.681887 TGCTACTGCTACCGCTACCA 60.682 55.000 0.00 0.00 40.48 3.25
1288 16865 1.065701 CTACTGCTACCGCTACCACTG 59.934 57.143 0.00 0.00 36.97 3.66
1307 17052 1.616091 GCTCCTGCTCCTGCTCTTCT 61.616 60.000 0.00 0.00 40.48 2.85
1319 17103 3.360867 CTGCTCTTCTTGTAGGAGGAGA 58.639 50.000 7.21 0.00 44.51 3.71
1332 17116 1.258676 GAGGAGAAGGAGGACAACGT 58.741 55.000 0.00 0.00 0.00 3.99
1337 17121 0.033504 GAAGGAGGACAACGTCAGCA 59.966 55.000 0.00 0.00 33.68 4.41
1412 17199 1.714794 CTAATCGCCATCTTAGCCGG 58.285 55.000 0.00 0.00 0.00 6.13
1473 17260 1.522355 CTGGCAAGCGGACGATGAT 60.522 57.895 0.00 0.00 0.00 2.45
1615 17402 1.134340 TGAACCGCAAGTTGTACAGGT 60.134 47.619 4.48 6.68 39.40 4.00
1616 17403 1.944709 GAACCGCAAGTTGTACAGGTT 59.055 47.619 19.47 19.47 43.72 3.50
1620 17407 1.687563 GCAAGTTGTACAGGTTGGGT 58.312 50.000 16.71 0.00 0.00 4.51
1623 17410 3.824443 GCAAGTTGTACAGGTTGGGTATT 59.176 43.478 16.71 0.00 0.00 1.89
1653 17440 3.434319 CTCCACGTGTGCATGGCC 61.434 66.667 15.65 0.00 35.81 5.36
1689 17476 1.078497 CATGGGTGCCTACGCTTCA 60.078 57.895 0.00 0.00 40.18 3.02
1798 17585 1.289109 CTGGTACTTCCGCAACCACG 61.289 60.000 0.00 0.00 38.36 4.94
1799 17586 2.674084 GGTACTTCCGCAACCACGC 61.674 63.158 0.00 0.00 33.28 5.34
2091 17890 0.174617 TCGTTGCCATCGTCATGCTA 59.825 50.000 0.00 0.00 0.00 3.49
2494 18299 8.850007 ATCCTAAGTCAAACTTCTTTAGGTTC 57.150 34.615 8.08 0.00 39.51 3.62
2497 18302 7.603024 CCTAAGTCAAACTTCTTTAGGTTCGAT 59.397 37.037 0.00 0.00 39.51 3.59
2510 18315 3.677190 AGGTTCGATCGAGTCTATAGGG 58.323 50.000 18.54 0.00 0.00 3.53
2536 18341 3.690628 TGTACCGACATCTACAACATCGA 59.309 43.478 0.00 0.00 34.77 3.59
2537 18342 3.861276 ACCGACATCTACAACATCGAA 57.139 42.857 0.00 0.00 34.77 3.71
2656 18494 9.936759 ACTTAAGAAAGTTTGACCAAATTTTGA 57.063 25.926 16.87 4.08 43.60 2.69
2658 18496 7.609760 AAGAAAGTTTGACCAAATTTTGACC 57.390 32.000 16.87 6.61 39.33 4.02
2710 18551 5.997843 ACCGAGGTAGTATTTGCCTAAAAT 58.002 37.500 0.00 0.00 42.62 1.82
2746 18588 2.846193 TGTGGTGGAGCTTTTGTAGTC 58.154 47.619 0.00 0.00 0.00 2.59
2761 18604 2.434336 TGTAGTCTTGTTGTGGTCTGCT 59.566 45.455 0.00 0.00 0.00 4.24
2770 18613 1.045407 TGTGGTCTGCTTCCGTTACT 58.955 50.000 0.00 0.00 0.00 2.24
2776 18619 3.391049 GTCTGCTTCCGTTACTGTCTTT 58.609 45.455 0.00 0.00 0.00 2.52
2869 18715 1.613925 CATCCGTATCATCGTCACCCT 59.386 52.381 0.00 0.00 0.00 4.34
2870 18716 2.643995 TCCGTATCATCGTCACCCTA 57.356 50.000 0.00 0.00 0.00 3.53
2896 18742 1.660104 GCACGCTTAATTGCCAAATGG 59.340 47.619 0.00 0.00 38.53 3.16
2918 18764 1.568504 TGAATCCAGACCGGCTTACT 58.431 50.000 0.00 0.00 33.14 2.24
3123 19266 5.524281 GTGTAGGCACTTCTCCTTAATAAGC 59.476 44.000 0.00 0.00 42.13 3.09
3203 19346 5.906285 GCAGCATGATCTTTAGATTTCGTTC 59.094 40.000 0.00 0.00 39.69 3.95
3205 19348 7.343691 CAGCATGATCTTTAGATTTCGTTCTC 58.656 38.462 0.00 0.00 39.69 2.87
3223 19366 0.817654 TCAGAGGACTATGCACACGG 59.182 55.000 0.00 0.00 0.00 4.94
3224 19367 0.817654 CAGAGGACTATGCACACGGA 59.182 55.000 0.00 0.00 0.00 4.69
3267 19411 4.876701 GGCGTGGCCTGATATGAA 57.123 55.556 3.32 0.00 46.69 2.57
3268 19412 3.329300 GGCGTGGCCTGATATGAAT 57.671 52.632 3.32 0.00 46.69 2.57
3269 19413 0.877071 GGCGTGGCCTGATATGAATG 59.123 55.000 3.32 0.00 46.69 2.67
3270 19414 0.239347 GCGTGGCCTGATATGAATGC 59.761 55.000 3.32 0.00 0.00 3.56
3278 19422 4.142447 GGCCTGATATGAATGCATGTGATC 60.142 45.833 0.00 2.14 35.94 2.92
3293 19437 0.697658 TGATCATGGCCTTGTGACCA 59.302 50.000 17.54 7.35 41.06 4.02
3326 19470 2.220653 ACCATCCAAACCATGTCCTG 57.779 50.000 0.00 0.00 0.00 3.86
3334 19478 2.479566 AACCATGTCCTGTGTAGCAG 57.520 50.000 0.00 0.00 44.63 4.24
3335 19479 0.036010 ACCATGTCCTGTGTAGCAGC 60.036 55.000 0.00 0.00 43.71 5.25
3338 19482 2.158914 CCATGTCCTGTGTAGCAGCATA 60.159 50.000 0.00 0.00 43.71 3.14
3339 19483 3.495629 CCATGTCCTGTGTAGCAGCATAT 60.496 47.826 0.00 0.00 43.71 1.78
3340 19484 3.183793 TGTCCTGTGTAGCAGCATATG 57.816 47.619 0.00 0.00 43.71 1.78
3341 19485 2.765699 TGTCCTGTGTAGCAGCATATGA 59.234 45.455 6.97 0.00 43.71 2.15
3342 19486 3.197549 TGTCCTGTGTAGCAGCATATGAA 59.802 43.478 6.97 0.00 43.71 2.57
3343 19487 4.191544 GTCCTGTGTAGCAGCATATGAAA 58.808 43.478 6.97 0.00 43.71 2.69
3344 19488 4.635765 GTCCTGTGTAGCAGCATATGAAAA 59.364 41.667 6.97 0.00 43.71 2.29
3345 19489 4.635765 TCCTGTGTAGCAGCATATGAAAAC 59.364 41.667 6.97 0.00 43.71 2.43
3346 19490 4.395854 CCTGTGTAGCAGCATATGAAAACA 59.604 41.667 6.97 0.07 43.71 2.83
3347 19491 5.106197 CCTGTGTAGCAGCATATGAAAACAA 60.106 40.000 6.97 0.00 43.71 2.83
3348 19492 5.698832 TGTGTAGCAGCATATGAAAACAAC 58.301 37.500 6.97 0.00 0.00 3.32
3349 19493 5.095490 GTGTAGCAGCATATGAAAACAACC 58.905 41.667 6.97 0.00 0.00 3.77
3353 19497 5.609423 AGCAGCATATGAAAACAACCAAAA 58.391 33.333 6.97 0.00 0.00 2.44
3370 19514 8.761689 ACAACCAAAATGGCTAGATTTCATAAT 58.238 29.630 0.00 0.00 42.67 1.28
3380 19524 7.765360 TGGCTAGATTTCATAATTTGCCAAAAG 59.235 33.333 0.00 0.00 38.96 2.27
3401 19549 7.944729 AAAGCAGACCATTACTATGAATTGT 57.055 32.000 0.00 0.00 33.37 2.71
3411 19559 2.874701 ACTATGAATTGTGGCTCGCATC 59.125 45.455 0.00 0.00 0.00 3.91
3416 19564 2.557059 ATTGTGGCTCGCATCGACGA 62.557 55.000 0.00 0.00 40.36 4.20
3417 19565 3.248171 GTGGCTCGCATCGACGAC 61.248 66.667 0.00 0.00 37.09 4.34
3418 19566 3.743636 TGGCTCGCATCGACGACA 61.744 61.111 0.00 0.00 37.09 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.521906 TGTAGATGCTGATAGGTTCTGTC 57.478 43.478 0.00 0.00 0.00 3.51
161 4607 2.051334 TGTGTGACACCCCTGAAAAG 57.949 50.000 13.85 0.00 32.73 2.27
170 4618 3.069729 AGTTAGAGGACTTGTGTGACACC 59.930 47.826 13.85 0.00 32.73 4.16
171 4619 4.323553 AGTTAGAGGACTTGTGTGACAC 57.676 45.455 9.14 9.14 34.56 3.67
179 4627 9.605275 TGATGATTTTCATAGTTAGAGGACTTG 57.395 33.333 0.00 0.00 37.20 3.16
188 4636 9.778741 GGACCTGTATGATGATTTTCATAGTTA 57.221 33.333 0.00 0.00 38.83 2.24
195 4643 9.178758 ACTTTTAGGACCTGTATGATGATTTTC 57.821 33.333 3.53 0.00 0.00 2.29
242 4690 7.862675 AGTAGTTCAAGGACCTATATTTTGCT 58.137 34.615 0.00 0.00 0.00 3.91
286 4734 2.231478 AGTAAGTGTGTCATCCAGTCCG 59.769 50.000 0.00 0.00 0.00 4.79
374 4822 2.037772 GTGGAGTGCATATAGGTCCCTG 59.962 54.545 0.00 0.00 0.00 4.45
435 4883 5.734855 ATGATTTGACTTCGAAATACCCG 57.265 39.130 0.00 0.00 0.00 5.28
483 10380 6.362551 ACCGTTCAATTAAGATATCGTCATCG 59.637 38.462 0.00 0.00 38.55 3.84
517 10414 8.239998 GCTCAGTCTACAAAGAAATTGCTATTT 58.760 33.333 5.79 5.79 43.13 1.40
522 10419 4.216257 TGGCTCAGTCTACAAAGAAATTGC 59.784 41.667 0.00 0.00 43.13 3.56
550 10447 7.272948 GCAAAATCAGATCTTAAGAGCAAAGTG 59.727 37.037 21.97 11.68 31.88 3.16
554 10451 8.454106 GTTAGCAAAATCAGATCTTAAGAGCAA 58.546 33.333 21.97 10.45 31.88 3.91
556 10453 8.207521 AGTTAGCAAAATCAGATCTTAAGAGC 57.792 34.615 12.88 12.88 0.00 4.09
557 10454 9.598517 AGAGTTAGCAAAATCAGATCTTAAGAG 57.401 33.333 11.53 0.00 32.11 2.85
562 10459 9.377312 GACTTAGAGTTAGCAAAATCAGATCTT 57.623 33.333 0.00 0.00 32.11 2.40
563 10460 8.535335 TGACTTAGAGTTAGCAAAATCAGATCT 58.465 33.333 0.00 0.00 32.11 2.75
564 10461 8.599774 GTGACTTAGAGTTAGCAAAATCAGATC 58.400 37.037 0.00 0.00 32.11 2.75
565 10462 8.097038 TGTGACTTAGAGTTAGCAAAATCAGAT 58.903 33.333 0.00 0.00 32.11 2.90
566 10463 7.441836 TGTGACTTAGAGTTAGCAAAATCAGA 58.558 34.615 0.00 0.00 32.11 3.27
648 10551 0.812549 TCTATCAACTGCGCGTACCA 59.187 50.000 8.43 0.00 0.00 3.25
655 10559 9.935682 ATGTATTGTATTTTTCTATCAACTGCG 57.064 29.630 0.00 0.00 0.00 5.18
827 16380 7.345168 TCCTACTTGGTAAGTGATGCTCACG 62.345 48.000 4.56 0.00 43.54 4.35
847 16400 1.285667 TGGTGGATCCAGTACGTCCTA 59.714 52.381 16.81 0.00 41.93 2.94
888 16441 1.808945 CCGATCTTATGGCCATTCAGC 59.191 52.381 26.37 9.94 0.00 4.26
912 16465 1.081641 CGTCGTTCGTAGCACTGGT 60.082 57.895 0.00 0.00 34.52 4.00
1131 16684 4.892965 ACAAGGCAAGCCACCGCA 62.893 61.111 14.40 0.00 38.92 5.69
1158 16711 1.299089 CGCGATATGGACGACAGCA 60.299 57.895 0.00 0.00 0.00 4.41
1161 16714 1.002142 CCTAACGCGATATGGACGACA 60.002 52.381 15.93 0.00 0.00 4.35
1221 16783 1.207089 TCAACCGTAGCAGGATCAAGG 59.793 52.381 0.00 0.00 34.73 3.61
1241 16803 2.023501 ACAGGAGTAGAAGGAGCAGGAT 60.024 50.000 0.00 0.00 0.00 3.24
1278 16855 2.510238 GCAGGAGCAGTGGTAGCG 60.510 66.667 0.00 0.00 41.58 4.26
1282 16859 2.203907 AGGAGCAGGAGCAGTGGT 60.204 61.111 0.00 0.00 45.49 4.16
1284 16861 2.436292 GCAGGAGCAGGAGCAGTG 60.436 66.667 0.00 0.00 45.49 3.66
1285 16862 2.607134 AGCAGGAGCAGGAGCAGT 60.607 61.111 0.00 0.00 45.49 4.40
1288 16865 1.153389 GAAGAGCAGGAGCAGGAGC 60.153 63.158 0.00 0.00 45.49 4.70
1307 17052 2.382305 TGTCCTCCTTCTCCTCCTACAA 59.618 50.000 0.00 0.00 0.00 2.41
1319 17103 0.034059 CTGCTGACGTTGTCCTCCTT 59.966 55.000 0.00 0.00 0.00 3.36
1345 17132 2.328099 GCTCCTTGCTTCGTGGTGG 61.328 63.158 0.00 0.00 38.95 4.61
1412 17199 0.393944 GGCTTGGTAGGTAAGTGCCC 60.394 60.000 0.00 0.00 33.45 5.36
1446 17233 4.684134 GCTTGCCAGAAGCCCCCA 62.684 66.667 0.00 0.00 42.71 4.96
1449 17236 4.722700 TCCGCTTGCCAGAAGCCC 62.723 66.667 1.99 0.00 42.71 5.19
1473 17260 2.740826 GCGCGGTGTCCAAGCTTA 60.741 61.111 8.83 0.00 0.00 3.09
1615 17402 3.744941 CGTAGCACCGAATACCCAA 57.255 52.632 0.00 0.00 0.00 4.12
1665 17452 4.175337 TAGGCACCCATGAGCGCC 62.175 66.667 2.29 0.00 45.23 6.53
1820 17616 3.371898 TGCTCGTCGTCGTCTTATTCTTA 59.628 43.478 1.33 0.00 38.33 2.10
2043 17842 3.325870 CATGAACGAAGTGGAGTTGCTA 58.674 45.455 0.00 0.00 45.00 3.49
2091 17890 2.037136 GCTCAGCGTCAATGGCAGT 61.037 57.895 0.00 0.00 0.00 4.40
2226 18028 1.003839 CTTGGTACTTCCTGCCGCA 60.004 57.895 0.00 0.00 37.07 5.69
2428 18233 9.707957 AAACTGAAATGGAATGGGTAATACATA 57.292 29.630 0.00 0.00 0.00 2.29
2429 18234 8.608185 AAACTGAAATGGAATGGGTAATACAT 57.392 30.769 0.00 0.00 0.00 2.29
2430 18235 9.535170 TTAAACTGAAATGGAATGGGTAATACA 57.465 29.630 0.00 0.00 0.00 2.29
2440 18245 9.588096 ACCTAGAACTTTAAACTGAAATGGAAT 57.412 29.630 0.00 0.00 0.00 3.01
2488 18293 4.529769 TCCCTATAGACTCGATCGAACCTA 59.470 45.833 19.92 20.63 0.00 3.08
2494 18299 5.630661 ACATTTCCCTATAGACTCGATCG 57.369 43.478 9.36 9.36 0.00 3.69
2497 18302 4.758674 CGGTACATTTCCCTATAGACTCGA 59.241 45.833 0.00 0.00 0.00 4.04
2510 18315 6.291637 CGATGTTGTAGATGTCGGTACATTTC 60.292 42.308 0.00 0.00 46.49 2.17
2650 18488 9.753674 TGAAAGTGATTTATCCTAGGTCAAAAT 57.246 29.630 9.08 12.55 0.00 1.82
2651 18489 9.581289 TTGAAAGTGATTTATCCTAGGTCAAAA 57.419 29.630 9.08 8.35 0.00 2.44
2652 18490 9.753674 ATTGAAAGTGATTTATCCTAGGTCAAA 57.246 29.630 9.08 10.47 0.00 2.69
2674 18512 6.057321 ACTACCTCGGTTCCAAAATATTGA 57.943 37.500 0.00 0.00 38.94 2.57
2736 18578 5.730568 GCAGACCACAACAAGACTACAAAAG 60.731 44.000 0.00 0.00 0.00 2.27
2738 18580 3.625764 GCAGACCACAACAAGACTACAAA 59.374 43.478 0.00 0.00 0.00 2.83
2746 18588 0.588252 CGGAAGCAGACCACAACAAG 59.412 55.000 0.00 0.00 0.00 3.16
2761 18604 7.201670 GGAAAAGAAGAAAAGACAGTAACGGAA 60.202 37.037 0.00 0.00 0.00 4.30
2770 18613 8.940397 ATAGGAATGGAAAAGAAGAAAAGACA 57.060 30.769 0.00 0.00 0.00 3.41
2850 18696 1.996798 AGGGTGACGATGATACGGAT 58.003 50.000 0.00 0.00 37.61 4.18
2851 18697 2.643995 TAGGGTGACGATGATACGGA 57.356 50.000 0.00 0.00 37.61 4.69
2852 18698 3.754850 TGTATAGGGTGACGATGATACGG 59.245 47.826 0.00 0.00 37.61 4.02
2853 18699 5.332707 CATGTATAGGGTGACGATGATACG 58.667 45.833 0.00 0.00 39.31 3.06
2869 18715 3.879892 TGGCAATTAAGCGTGCATGTATA 59.120 39.130 7.93 0.00 42.74 1.47
2870 18716 2.687425 TGGCAATTAAGCGTGCATGTAT 59.313 40.909 7.93 0.00 42.74 2.29
2896 18742 2.044123 AAGCCGGTCTGGATTCAATC 57.956 50.000 1.90 0.00 45.17 2.67
2918 18764 7.148205 GGTTACAGTTTGGTTCTTGTTAACTCA 60.148 37.037 7.22 0.00 0.00 3.41
3123 19266 4.956075 AGTTGGTTATTGCCTTATTGGGAG 59.044 41.667 0.00 0.00 37.50 4.30
3203 19346 1.202348 CCGTGTGCATAGTCCTCTGAG 60.202 57.143 0.00 0.00 0.00 3.35
3205 19348 0.817654 TCCGTGTGCATAGTCCTCTG 59.182 55.000 0.00 0.00 0.00 3.35
3293 19437 8.381636 TGGTTTGGATGGTTTTTGAAATATCAT 58.618 29.630 0.00 0.00 34.96 2.45
3326 19470 5.095490 GGTTGTTTTCATATGCTGCTACAC 58.905 41.667 0.00 0.00 0.00 2.90
3334 19478 5.412286 AGCCATTTTGGTTGTTTTCATATGC 59.588 36.000 0.00 0.00 40.46 3.14
3335 19479 8.034215 TCTAGCCATTTTGGTTGTTTTCATATG 58.966 33.333 0.00 0.00 40.46 1.78
3338 19482 6.418057 TCTAGCCATTTTGGTTGTTTTCAT 57.582 33.333 0.00 0.00 40.46 2.57
3339 19483 5.860941 TCTAGCCATTTTGGTTGTTTTCA 57.139 34.783 0.00 0.00 40.46 2.69
3340 19484 7.440856 TGAAATCTAGCCATTTTGGTTGTTTTC 59.559 33.333 0.00 2.72 40.46 2.29
3341 19485 7.278875 TGAAATCTAGCCATTTTGGTTGTTTT 58.721 30.769 0.00 0.00 40.46 2.43
3342 19486 6.825610 TGAAATCTAGCCATTTTGGTTGTTT 58.174 32.000 0.00 0.00 40.46 2.83
3343 19487 6.418057 TGAAATCTAGCCATTTTGGTTGTT 57.582 33.333 0.00 0.00 40.46 2.83
3344 19488 6.610075 ATGAAATCTAGCCATTTTGGTTGT 57.390 33.333 0.00 0.00 40.46 3.32
3345 19489 9.603921 AATTATGAAATCTAGCCATTTTGGTTG 57.396 29.630 0.00 0.00 40.46 3.77
3347 19491 9.603921 CAAATTATGAAATCTAGCCATTTTGGT 57.396 29.630 0.00 0.00 40.46 3.67
3348 19492 8.553696 GCAAATTATGAAATCTAGCCATTTTGG 58.446 33.333 0.00 0.00 41.55 3.28
3349 19493 8.553696 GGCAAATTATGAAATCTAGCCATTTTG 58.446 33.333 0.00 0.00 36.73 2.44
3353 19497 6.982160 TGGCAAATTATGAAATCTAGCCAT 57.018 33.333 0.00 0.00 39.37 4.40
3370 19514 8.662584 TCATAGTAATGGTCTGCTTTTGGCAAA 61.663 37.037 8.93 8.93 40.96 3.68
3380 19524 5.506317 GCCACAATTCATAGTAATGGTCTGC 60.506 44.000 0.00 0.00 33.61 4.26
3401 19549 3.743636 TGTCGTCGATGCGAGCCA 61.744 61.111 0.00 0.00 41.85 4.75


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

AutoCloner maintained by Alex Coulton.