Multiple sequence alignment - TraesCS2D01G368100

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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 TraesCS2D01G368100 chr2D 100.000 5854 0 0 1 5854 472479472 472473619 0.000000e+00 10811.0
1 TraesCS2D01G368100 chr2D 97.826 46 1 0 2 47 378758758 378758803 4.860000e-11 80.5
2 TraesCS2D01G368100 chr2D 95.918 49 2 0 1 49 378759724 378759772 4.860000e-11 80.5
3 TraesCS2D01G368100 chr2A 97.122 5212 97 22 651 5854 613999779 613994613 0.000000e+00 8745.0
4 TraesCS2D01G368100 chr2B 96.223 2277 45 9 3584 5854 551643177 551640936 0.000000e+00 3690.0
5 TraesCS2D01G368100 chr2B 96.608 2034 49 12 696 2719 551646371 551644348 0.000000e+00 3356.0
6 TraesCS2D01G368100 chr2B 98.780 820 10 0 2781 3600 551644357 551643538 0.000000e+00 1459.0
7 TraesCS2D01G368100 chr2B 85.197 608 72 14 27 620 21865674 21866277 5.020000e-170 608.0
8 TraesCS2D01G368100 chr7D 85.857 601 73 9 27 618 616425649 616425052 3.850000e-176 628.0
9 TraesCS2D01G368100 chr7D 91.781 73 4 1 4944 5014 454933786 454933714 3.730000e-17 100.0
10 TraesCS2D01G368100 chr1D 85.476 599 74 11 27 618 489533624 489533032 3.880000e-171 612.0
11 TraesCS2D01G368100 chr7A 85.333 600 71 14 28 619 79230325 79229735 6.490000e-169 604.0
12 TraesCS2D01G368100 chr7A 84.577 603 82 10 27 621 205182530 205181931 6.530000e-164 588.0
13 TraesCS2D01G368100 chr7A 81.001 679 79 32 4637 5287 726602281 726601625 1.470000e-135 494.0
14 TraesCS2D01G368100 chr3D 86.111 576 63 14 51 617 580344549 580345116 6.490000e-169 604.0
15 TraesCS2D01G368100 chr3D 83.258 442 56 14 4944 5375 60518696 60519129 1.980000e-104 390.0
16 TraesCS2D01G368100 chrUn 85.142 599 73 12 27 615 47655224 47654632 3.020000e-167 599.0
17 TraesCS2D01G368100 chr4D 85.260 597 70 17 32 618 434096329 434095741 3.020000e-167 599.0
18 TraesCS2D01G368100 chr1B 84.950 598 70 17 27 618 474441649 474442232 6.530000e-164 588.0
19 TraesCS2D01G368100 chr3B 83.408 446 56 13 4944 5379 357686975 357686538 1.180000e-106 398.0
20 TraesCS2D01G368100 chr3B 80.779 411 67 10 4445 4851 449841328 449841730 1.580000e-80 311.0
21 TraesCS2D01G368100 chr5D 82.039 412 63 9 4445 4852 208539713 208539309 2.020000e-89 340.0
22 TraesCS2D01G368100 chr5D 88.732 71 8 0 5217 5287 484657360 484657290 2.910000e-13 87.9
23 TraesCS2D01G368100 chr5B 81.728 405 62 10 4452 4852 31287531 31287927 1.570000e-85 327.0
24 TraesCS2D01G368100 chr3A 80.415 434 72 10 4445 4873 57910746 57911171 9.470000e-83 318.0
25 TraesCS2D01G368100 chr3A 80.230 435 73 11 4445 4873 745552497 745552924 1.220000e-81 315.0
26 TraesCS2D01G368100 chr5A 80.583 412 69 9 4445 4852 3456764 3456360 2.050000e-79 307.0
27 TraesCS2D01G368100 chr7B 76.812 345 29 21 1 342 586654830 586655126 4.730000e-31 147.0
28 TraesCS2D01G368100 chr7B 88.732 71 8 0 5217 5287 102760785 102760715 2.910000e-13 87.9
29 TraesCS2D01G368100 chr6B 88.732 71 8 0 5217 5287 623362621 623362551 2.910000e-13 87.9
30 TraesCS2D01G368100 chr4A 96.000 50 2 0 1 50 737498729 737498680 1.350000e-11 82.4


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 TraesCS2D01G368100 chr2D 472473619 472479472 5853 True 10811 10811 100.000000 1 5854 1 chr2D.!!$R1 5853
1 TraesCS2D01G368100 chr2A 613994613 613999779 5166 True 8745 8745 97.122000 651 5854 1 chr2A.!!$R1 5203
2 TraesCS2D01G368100 chr2B 551640936 551646371 5435 True 2835 3690 97.203667 696 5854 3 chr2B.!!$R1 5158
3 TraesCS2D01G368100 chr2B 21865674 21866277 603 False 608 608 85.197000 27 620 1 chr2B.!!$F1 593
4 TraesCS2D01G368100 chr7D 616425052 616425649 597 True 628 628 85.857000 27 618 1 chr7D.!!$R2 591
5 TraesCS2D01G368100 chr1D 489533032 489533624 592 True 612 612 85.476000 27 618 1 chr1D.!!$R1 591
6 TraesCS2D01G368100 chr7A 79229735 79230325 590 True 604 604 85.333000 28 619 1 chr7A.!!$R1 591
7 TraesCS2D01G368100 chr7A 205181931 205182530 599 True 588 588 84.577000 27 621 1 chr7A.!!$R2 594
8 TraesCS2D01G368100 chr7A 726601625 726602281 656 True 494 494 81.001000 4637 5287 1 chr7A.!!$R3 650
9 TraesCS2D01G368100 chr3D 580344549 580345116 567 False 604 604 86.111000 51 617 1 chr3D.!!$F2 566
10 TraesCS2D01G368100 chrUn 47654632 47655224 592 True 599 599 85.142000 27 615 1 chrUn.!!$R1 588
11 TraesCS2D01G368100 chr4D 434095741 434096329 588 True 599 599 85.260000 32 618 1 chr4D.!!$R1 586
12 TraesCS2D01G368100 chr1B 474441649 474442232 583 False 588 588 84.950000 27 618 1 chr1B.!!$F1 591

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
22 23 0.250124 TTTTTCTTCCGCGAGAGGCA 60.250 50.000 8.23 0.00 43.84 4.75 F
93 94 0.586802 GTGTTTTCACGAGAGGCACC 59.413 55.000 0.00 0.00 41.13 5.01 F
571 604 1.742761 CCACTTGTCGCAATCTGGAT 58.257 50.000 9.14 0.00 0.00 3.41 F
1139 1183 1.076995 GTTTTAGCCCCCGGAGCAT 60.077 57.895 17.33 6.46 0.00 3.79 F
1596 1646 2.953466 ATGGCGCGGATATTACGTAT 57.047 45.000 8.83 0.00 0.00 3.06 F
2764 2815 0.176219 ATGCATGGCCATTCGGTTTG 59.824 50.000 17.92 5.56 33.28 2.93 F
3316 3367 3.278574 TGCCAGTTATCAGTATTGTGCC 58.721 45.455 0.00 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1094 1137 0.036671 CTACGGTCCCAACTCCCAAC 60.037 60.000 0.00 0.0 0.00 3.77 R
1098 1141 0.248565 GTTCCTACGGTCCCAACTCC 59.751 60.000 0.00 0.0 0.00 3.85 R
1385 1435 3.122937 GCATCTTGCAACTAAGAACCG 57.877 47.619 0.00 0.0 44.26 4.44 R
2313 2364 3.381272 TGACAGAAAAAGCCTTTGGACAG 59.619 43.478 0.00 0.0 0.00 3.51 R
3380 3431 2.278026 CCATTTGGCGCTTAGGAAAC 57.722 50.000 7.64 0.0 0.00 2.78 R
4036 4465 1.407979 GAAGGGCAATGCATCTCCAAG 59.592 52.381 7.79 0.0 0.00 3.61 R
5178 5636 0.455410 GTTCAGCAAACCACAGCACA 59.545 50.000 0.00 0.0 31.20 4.57 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 2.540145 TTTTTCTTCCGCGAGAGGC 58.460 52.632 8.23 0.00 38.69 4.70
22 23 0.250124 TTTTTCTTCCGCGAGAGGCA 60.250 50.000 8.23 0.00 43.84 4.75
23 24 0.949105 TTTTCTTCCGCGAGAGGCAC 60.949 55.000 8.23 0.00 43.84 5.01
24 25 3.626680 TTCTTCCGCGAGAGGCACG 62.627 63.158 8.23 0.00 43.84 5.34
30 31 2.556287 GCGAGAGGCACGGTTTTG 59.444 61.111 0.00 0.00 42.87 2.44
93 94 0.586802 GTGTTTTCACGAGAGGCACC 59.413 55.000 0.00 0.00 41.13 5.01
196 205 5.241749 GCATAGTTGTGCTTTCGCGAGAA 62.242 47.826 9.59 6.24 44.03 2.87
221 235 2.434359 CGTGCCTCCTCGGAAACC 60.434 66.667 0.00 0.00 33.16 3.27
571 604 1.742761 CCACTTGTCGCAATCTGGAT 58.257 50.000 9.14 0.00 0.00 3.41
589 623 2.648059 GATGGTGGGAGTGATCTTTGG 58.352 52.381 0.00 0.00 0.00 3.28
621 655 6.931838 ACTCATTAACTAGTGATTTCGACCA 58.068 36.000 0.00 0.00 0.00 4.02
622 656 7.383687 ACTCATTAACTAGTGATTTCGACCAA 58.616 34.615 0.00 0.00 0.00 3.67
623 657 7.331193 ACTCATTAACTAGTGATTTCGACCAAC 59.669 37.037 0.00 0.00 0.00 3.77
624 658 6.592607 TCATTAACTAGTGATTTCGACCAACC 59.407 38.462 0.00 0.00 0.00 3.77
625 659 4.618920 AACTAGTGATTTCGACCAACCT 57.381 40.909 0.00 0.00 0.00 3.50
626 660 4.618920 ACTAGTGATTTCGACCAACCTT 57.381 40.909 0.00 0.00 0.00 3.50
627 661 4.315803 ACTAGTGATTTCGACCAACCTTG 58.684 43.478 0.00 0.00 0.00 3.61
628 662 1.880027 AGTGATTTCGACCAACCTTGC 59.120 47.619 0.00 0.00 0.00 4.01
629 663 1.880027 GTGATTTCGACCAACCTTGCT 59.120 47.619 0.00 0.00 0.00 3.91
630 664 3.071479 GTGATTTCGACCAACCTTGCTA 58.929 45.455 0.00 0.00 0.00 3.49
631 665 3.689649 GTGATTTCGACCAACCTTGCTAT 59.310 43.478 0.00 0.00 0.00 2.97
632 666 3.689161 TGATTTCGACCAACCTTGCTATG 59.311 43.478 0.00 0.00 0.00 2.23
633 667 3.410631 TTTCGACCAACCTTGCTATGA 57.589 42.857 0.00 0.00 0.00 2.15
634 668 3.627395 TTCGACCAACCTTGCTATGAT 57.373 42.857 0.00 0.00 0.00 2.45
635 669 3.179443 TCGACCAACCTTGCTATGATC 57.821 47.619 0.00 0.00 0.00 2.92
636 670 1.860950 CGACCAACCTTGCTATGATCG 59.139 52.381 0.00 0.00 0.00 3.69
637 671 2.738643 CGACCAACCTTGCTATGATCGT 60.739 50.000 0.00 0.00 0.00 3.73
638 672 3.490249 CGACCAACCTTGCTATGATCGTA 60.490 47.826 0.00 0.00 0.00 3.43
639 673 4.632153 GACCAACCTTGCTATGATCGTAT 58.368 43.478 0.00 0.00 0.00 3.06
640 674 4.380531 ACCAACCTTGCTATGATCGTATG 58.619 43.478 0.00 0.00 0.00 2.39
641 675 4.100963 ACCAACCTTGCTATGATCGTATGA 59.899 41.667 0.00 0.00 0.00 2.15
642 676 4.687948 CCAACCTTGCTATGATCGTATGAG 59.312 45.833 0.00 0.00 0.00 2.90
643 677 5.292765 CAACCTTGCTATGATCGTATGAGT 58.707 41.667 0.00 0.00 0.00 3.41
644 678 5.537300 ACCTTGCTATGATCGTATGAGTT 57.463 39.130 0.00 0.00 0.00 3.01
645 679 5.292765 ACCTTGCTATGATCGTATGAGTTG 58.707 41.667 0.00 0.00 0.00 3.16
646 680 5.069119 ACCTTGCTATGATCGTATGAGTTGA 59.931 40.000 0.00 0.00 0.00 3.18
647 681 6.162079 CCTTGCTATGATCGTATGAGTTGAT 58.838 40.000 0.00 0.00 0.00 2.57
648 682 6.648310 CCTTGCTATGATCGTATGAGTTGATT 59.352 38.462 0.00 0.00 0.00 2.57
649 683 7.814587 CCTTGCTATGATCGTATGAGTTGATTA 59.185 37.037 0.00 0.00 0.00 1.75
650 684 9.196552 CTTGCTATGATCGTATGAGTTGATTAA 57.803 33.333 0.00 0.00 0.00 1.40
651 685 8.520835 TGCTATGATCGTATGAGTTGATTAAC 57.479 34.615 0.00 0.00 37.06 2.01
652 686 7.598869 TGCTATGATCGTATGAGTTGATTAACC 59.401 37.037 0.00 0.00 37.52 2.85
653 687 7.598869 GCTATGATCGTATGAGTTGATTAACCA 59.401 37.037 0.00 0.00 37.52 3.67
654 688 7.953158 ATGATCGTATGAGTTGATTAACCAG 57.047 36.000 0.00 0.00 37.52 4.00
730 765 7.220683 CACAAAAGCTTTATTTATGATCACCGG 59.779 37.037 13.10 0.00 0.00 5.28
1094 1137 3.561213 CAGCAGCGTCCGCATGAG 61.561 66.667 14.70 0.00 44.88 2.90
1095 1138 4.074526 AGCAGCGTCCGCATGAGT 62.075 61.111 14.70 0.00 44.88 3.41
1096 1139 3.121030 GCAGCGTCCGCATGAGTT 61.121 61.111 14.70 0.00 44.88 3.01
1097 1140 2.780643 CAGCGTCCGCATGAGTTG 59.219 61.111 14.70 0.00 44.88 3.16
1098 1141 2.434884 AGCGTCCGCATGAGTTGG 60.435 61.111 14.70 0.00 44.88 3.77
1139 1183 1.076995 GTTTTAGCCCCCGGAGCAT 60.077 57.895 17.33 6.46 0.00 3.79
1300 1348 4.825085 CCCCAGAGATCTCTTGTAGTCTAC 59.175 50.000 22.95 2.81 37.98 2.59
1385 1435 8.256611 TGATGAACTGATTTAGCTCTTTGTAC 57.743 34.615 0.00 0.00 0.00 2.90
1399 1449 4.695396 TCTTTGTACGGTTCTTAGTTGCA 58.305 39.130 0.00 0.00 0.00 4.08
1400 1450 5.117584 TCTTTGTACGGTTCTTAGTTGCAA 58.882 37.500 0.00 0.00 0.00 4.08
1596 1646 2.953466 ATGGCGCGGATATTACGTAT 57.047 45.000 8.83 0.00 0.00 3.06
1638 1688 5.583061 TCATAAGTTTGTGAACTGTCAACGT 59.417 36.000 0.00 0.00 45.18 3.99
1720 1770 5.226396 GTGACTGCCACATCTCATAGTATC 58.774 45.833 0.00 0.00 45.03 2.24
1919 1970 4.290985 TGTTCCCCATGTTCTCCAGATTTA 59.709 41.667 0.00 0.00 0.00 1.40
2198 2249 6.152831 AGGGTGCTAACTAAATTGTTTGATCC 59.847 38.462 0.00 0.00 0.00 3.36
2313 2364 4.574013 GCTGCTATAGATATCAACATGGGC 59.426 45.833 3.21 5.50 0.00 5.36
2412 2463 7.986085 ACATGCCTATATGGTCTTATTTGTC 57.014 36.000 0.00 0.00 38.35 3.18
2426 2477 8.884726 GGTCTTATTTGTCCTCTTACTTTCATC 58.115 37.037 0.00 0.00 0.00 2.92
2725 2776 3.683365 AACACCCAAGATTGCAAATCC 57.317 42.857 1.71 0.00 0.00 3.01
2764 2815 0.176219 ATGCATGGCCATTCGGTTTG 59.824 50.000 17.92 5.56 33.28 2.93
2777 2828 6.201997 GCCATTCGGTTTGTTAGAATTTTGTT 59.798 34.615 0.00 0.00 32.87 2.83
2926 2977 8.192110 TGGGTTTAGTTTTCACAGTAATCAAAC 58.808 33.333 0.00 0.00 0.00 2.93
3316 3367 3.278574 TGCCAGTTATCAGTATTGTGCC 58.721 45.455 0.00 0.00 0.00 5.01
3331 3382 5.757099 ATTGTGCCTACTTTACACCTAGT 57.243 39.130 0.00 0.00 33.30 2.57
3380 3431 9.983804 TTTGATTGCGATAGTAGTACTATATCG 57.016 33.333 28.10 28.10 46.86 2.92
3722 4151 5.077564 AGTACCTTGGGAGGATTTCAAAAC 58.922 41.667 0.00 0.00 46.74 2.43
3958 4387 5.068591 GGAAAGGTGTGATAAAGTGTGGTTT 59.931 40.000 0.00 0.00 0.00 3.27
4156 4585 4.681244 TGCAAGATGCCATTTTTCATAGGC 60.681 41.667 0.00 0.00 44.23 3.93
4322 4751 6.668283 TCTTGAAGGAACCTAGTACATTAGCT 59.332 38.462 0.00 0.00 0.00 3.32
4554 4983 6.429385 AGAAAACTAAGGATCAAACTGCAGAG 59.571 38.462 23.35 9.98 0.00 3.35
5122 5580 2.885135 ATGCATTGGAGTGAAGTGGA 57.115 45.000 0.00 0.00 0.00 4.02
5172 5630 2.256174 GCTAATTGTACGAGCGTGTCA 58.744 47.619 5.69 2.54 0.00 3.58
5178 5636 0.317603 GTACGAGCGTGTCAGTGTGT 60.318 55.000 5.69 0.00 0.00 3.72
5249 5708 7.324178 AGAGTATGAAGGTGTTGTTAGCTAAG 58.676 38.462 6.38 0.00 0.00 2.18
5252 5711 5.546621 TGAAGGTGTTGTTAGCTAAGACT 57.453 39.130 6.38 0.00 0.00 3.24
5310 5769 4.201871 TGTCCAAGTTGCAACTTCGTAAAG 60.202 41.667 35.97 24.60 45.65 1.85
5509 5969 0.322008 CTGAAGTCCTGTTGGCTCCC 60.322 60.000 0.00 0.00 0.00 4.30
5590 6050 0.774908 TTGGATCCCTCGGTTGGTTT 59.225 50.000 9.90 0.00 0.00 3.27
5591 6051 0.774908 TGGATCCCTCGGTTGGTTTT 59.225 50.000 9.90 0.00 0.00 2.43
5592 6052 1.173913 GGATCCCTCGGTTGGTTTTG 58.826 55.000 0.00 0.00 0.00 2.44
5593 6053 1.546998 GGATCCCTCGGTTGGTTTTGT 60.547 52.381 0.00 0.00 0.00 2.83
5594 6054 2.235891 GATCCCTCGGTTGGTTTTGTT 58.764 47.619 0.00 0.00 0.00 2.83
5730 6190 4.445453 TCAACTGAGGATTCATGGATTCG 58.555 43.478 0.00 0.00 31.68 3.34
5755 6215 0.180642 TCGTGGGGTACAGTTTTGCA 59.819 50.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.374252 GTGCCTCTCGCGGAAGAAA 60.374 57.895 6.13 0.00 42.08 2.52
7 8 4.116328 CGTGCCTCTCGCGGAAGA 62.116 66.667 6.13 0.90 44.36 2.87
13 14 2.556287 CAAAACCGTGCCTCTCGC 59.444 61.111 0.00 0.00 38.31 5.03
14 15 1.507141 AAGCAAAACCGTGCCTCTCG 61.507 55.000 0.00 0.00 46.14 4.04
15 16 0.238553 GAAGCAAAACCGTGCCTCTC 59.761 55.000 0.00 0.00 46.14 3.20
16 17 1.172812 GGAAGCAAAACCGTGCCTCT 61.173 55.000 0.00 0.00 46.14 3.69
17 18 1.285950 GGAAGCAAAACCGTGCCTC 59.714 57.895 0.00 0.00 46.14 4.70
18 19 2.551912 CGGAAGCAAAACCGTGCCT 61.552 57.895 0.00 0.00 46.14 4.75
19 20 2.050442 CGGAAGCAAAACCGTGCC 60.050 61.111 0.00 0.00 46.14 5.01
24 25 1.443802 CCTCTCTCGGAAGCAAAACC 58.556 55.000 0.00 0.00 0.00 3.27
25 26 0.799393 GCCTCTCTCGGAAGCAAAAC 59.201 55.000 0.00 0.00 32.03 2.43
30 31 2.202676 CGTGCCTCTCTCGGAAGC 60.203 66.667 0.00 0.00 32.35 3.86
37 38 0.179018 AAGCAAAACCGTGCCTCTCT 60.179 50.000 0.00 0.00 46.14 3.10
77 78 1.959226 GCGGTGCCTCTCGTGAAAA 60.959 57.895 0.00 0.00 0.00 2.29
93 94 2.736995 TTTTCGAGAGGCACGGCG 60.737 61.111 4.80 4.80 0.00 6.46
239 259 5.178438 CCTCTCACGGAAGAAAAAGAAGAAG 59.822 44.000 0.00 0.00 0.00 2.85
240 260 5.057149 CCTCTCACGGAAGAAAAAGAAGAA 58.943 41.667 0.00 0.00 0.00 2.52
241 261 4.632153 CCTCTCACGGAAGAAAAAGAAGA 58.368 43.478 0.00 0.00 0.00 2.87
242 262 3.187432 GCCTCTCACGGAAGAAAAAGAAG 59.813 47.826 0.00 0.00 0.00 2.85
245 265 2.224314 GTGCCTCTCACGGAAGAAAAAG 59.776 50.000 0.00 0.00 35.76 2.27
273 294 4.116328 CGTGCCTCTCGCGGAAGA 62.116 66.667 6.13 0.90 44.36 2.87
376 400 8.697507 ATCCCATATTGATAGGTTTGAAGAAC 57.302 34.615 0.00 0.00 0.00 3.01
377 401 8.727149 AGATCCCATATTGATAGGTTTGAAGAA 58.273 33.333 0.00 0.00 0.00 2.52
378 402 8.280258 AGATCCCATATTGATAGGTTTGAAGA 57.720 34.615 0.00 0.00 0.00 2.87
419 446 1.064505 CACCGTTAGATTCCTCGCGTA 59.935 52.381 5.77 0.00 0.00 4.42
571 604 1.741028 TCCAAAGATCACTCCCACCA 58.259 50.000 0.00 0.00 0.00 4.17
621 655 5.537300 ACTCATACGATCATAGCAAGGTT 57.463 39.130 0.00 0.00 0.00 3.50
622 656 5.069119 TCAACTCATACGATCATAGCAAGGT 59.931 40.000 0.00 0.00 0.00 3.50
623 657 5.532557 TCAACTCATACGATCATAGCAAGG 58.467 41.667 0.00 0.00 0.00 3.61
624 658 7.649370 AATCAACTCATACGATCATAGCAAG 57.351 36.000 0.00 0.00 0.00 4.01
625 659 8.978539 GTTAATCAACTCATACGATCATAGCAA 58.021 33.333 0.00 0.00 0.00 3.91
626 660 7.598869 GGTTAATCAACTCATACGATCATAGCA 59.401 37.037 0.00 0.00 34.88 3.49
627 661 7.598869 TGGTTAATCAACTCATACGATCATAGC 59.401 37.037 0.00 0.00 34.88 2.97
628 662 9.133627 CTGGTTAATCAACTCATACGATCATAG 57.866 37.037 0.00 0.00 34.88 2.23
629 663 8.856103 TCTGGTTAATCAACTCATACGATCATA 58.144 33.333 0.00 0.00 34.88 2.15
630 664 7.726216 TCTGGTTAATCAACTCATACGATCAT 58.274 34.615 0.00 0.00 34.88 2.45
631 665 7.107639 TCTGGTTAATCAACTCATACGATCA 57.892 36.000 0.00 0.00 34.88 2.92
632 666 8.594881 AATCTGGTTAATCAACTCATACGATC 57.405 34.615 0.00 0.00 34.88 3.69
633 667 8.964476 AAATCTGGTTAATCAACTCATACGAT 57.036 30.769 0.00 0.00 34.88 3.73
634 668 8.786826 AAAATCTGGTTAATCAACTCATACGA 57.213 30.769 0.00 0.00 34.88 3.43
730 765 0.827507 TTCTTGCTTGGGTTGGGCTC 60.828 55.000 0.00 0.00 0.00 4.70
741 776 2.371658 AAGCCCAACTCTTCTTGCTT 57.628 45.000 0.00 0.00 34.45 3.91
1092 1135 1.003718 CGGTCCCAACTCCCAACTC 60.004 63.158 0.00 0.00 0.00 3.01
1093 1136 0.472352 TACGGTCCCAACTCCCAACT 60.472 55.000 0.00 0.00 0.00 3.16
1094 1137 0.036671 CTACGGTCCCAACTCCCAAC 60.037 60.000 0.00 0.00 0.00 3.77
1095 1138 1.196104 CCTACGGTCCCAACTCCCAA 61.196 60.000 0.00 0.00 0.00 4.12
1096 1139 1.611261 CCTACGGTCCCAACTCCCA 60.611 63.158 0.00 0.00 0.00 4.37
1097 1140 0.906282 TTCCTACGGTCCCAACTCCC 60.906 60.000 0.00 0.00 0.00 4.30
1098 1141 0.248565 GTTCCTACGGTCCCAACTCC 59.751 60.000 0.00 0.00 0.00 3.85
1139 1183 1.213296 GCTTGAATCTAGGACCCCCA 58.787 55.000 0.00 0.00 33.88 4.96
1191 1235 1.664321 GCTACTCGATGACCCCGTGT 61.664 60.000 0.00 0.00 37.48 4.49
1238 1286 2.822255 TAGCAACGGGGCAATCGC 60.822 61.111 3.39 0.00 35.83 4.58
1280 1328 5.361427 TCCGTAGACTACAAGAGATCTCTG 58.639 45.833 25.78 20.06 40.36 3.35
1385 1435 3.122937 GCATCTTGCAACTAAGAACCG 57.877 47.619 0.00 0.00 44.26 4.44
1399 1449 6.239232 GCATTTATTCAGGAATCCAGCATCTT 60.239 38.462 0.61 0.00 32.50 2.40
1400 1450 5.243283 GCATTTATTCAGGAATCCAGCATCT 59.757 40.000 0.61 0.00 32.50 2.90
1520 1570 5.510179 CCCTGCAAAAATCACTGACAGAATT 60.510 40.000 10.08 5.79 0.00 2.17
1720 1770 9.477484 AACATTATTGGAGTAAAGCTATCTACG 57.523 33.333 0.00 0.00 0.00 3.51
2198 2249 7.751047 ATTCAAAGCTTTGATCAAATCATCG 57.249 32.000 35.66 10.23 45.65 3.84
2313 2364 3.381272 TGACAGAAAAAGCCTTTGGACAG 59.619 43.478 0.00 0.00 0.00 3.51
2412 2463 6.301169 AGTACAAGGGATGAAAGTAAGAGG 57.699 41.667 0.00 0.00 0.00 3.69
2426 2477 8.958119 TGAATAAGCATAGTAAAGTACAAGGG 57.042 34.615 0.00 0.00 0.00 3.95
2764 2815 9.535878 TCAATTTGGGTACAACAAAATTCTAAC 57.464 29.630 15.86 0.00 40.74 2.34
2777 2828 8.795842 ATTTAAGTCGTATCAATTTGGGTACA 57.204 30.769 0.00 0.00 0.00 2.90
2926 2977 5.929697 ATATGCACCACGTCATATTTCAG 57.070 39.130 0.00 0.00 33.45 3.02
3331 3382 9.748708 CAAAGTACATGGAGATTTTTCTTTTGA 57.251 29.630 0.00 0.00 0.00 2.69
3380 3431 2.278026 CCATTTGGCGCTTAGGAAAC 57.722 50.000 7.64 0.00 0.00 2.78
3958 4387 2.492088 ACTTACGCTACATCTGCTGACA 59.508 45.455 0.00 0.00 0.00 3.58
4036 4465 1.407979 GAAGGGCAATGCATCTCCAAG 59.592 52.381 7.79 0.00 0.00 3.61
4156 4585 1.518056 ATCCAGCGGCACACACAAAG 61.518 55.000 1.45 0.00 0.00 2.77
4322 4751 6.263168 GCCTCTTAAGCTAAATATTCCAGCAA 59.737 38.462 18.94 8.67 37.78 3.91
4554 4983 5.850614 TGACTCCTTCCTAAACAGTGTTAC 58.149 41.667 9.37 0.00 0.00 2.50
5122 5580 7.455058 TGTAACTTACAATCATGTACTGGGTT 58.545 34.615 0.00 0.00 41.64 4.11
5150 5608 1.990563 ACACGCTCGTACAATTAGCAC 59.009 47.619 0.00 0.00 35.98 4.40
5172 5630 0.810648 CAAACCACAGCACACACACT 59.189 50.000 0.00 0.00 0.00 3.55
5178 5636 0.455410 GTTCAGCAAACCACAGCACA 59.545 50.000 0.00 0.00 31.20 4.57
5310 5769 1.333619 TGCTGTCTTTTCCGAAGCAAC 59.666 47.619 0.00 0.00 40.72 4.17
5590 6050 7.229707 TCTCCGGAGAAAACATTCATAAAACAA 59.770 33.333 31.91 1.52 33.91 2.83
5591 6051 6.712998 TCTCCGGAGAAAACATTCATAAAACA 59.287 34.615 31.91 1.88 33.91 2.83
5592 6052 7.141100 TCTCCGGAGAAAACATTCATAAAAC 57.859 36.000 31.91 0.00 33.91 2.43
5593 6053 7.829211 AGATCTCCGGAGAAAACATTCATAAAA 59.171 33.333 36.58 9.55 41.36 1.52
5594 6054 7.338710 AGATCTCCGGAGAAAACATTCATAAA 58.661 34.615 36.58 10.25 41.36 1.40
5730 6190 5.454520 CAAAACTGTACCCCACGAAATAAC 58.545 41.667 0.00 0.00 0.00 1.89
5784 6247 3.751175 TCAGTCTAAATCAACGGCCTTTG 59.249 43.478 15.65 15.65 0.00 2.77


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

AutoCloner maintained by Alex Coulton.