Multiple sequence alignment - TraesCS4D01G161100

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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 TraesCS4D01G161100 chr4D 100.000 2509 0 0 1 2509 241050460 241047952 0.000000e+00 4634.0
1 TraesCS4D01G161100 chr4D 95.921 1716 62 5 797 2509 123508493 123506783 0.000000e+00 2774.0
2 TraesCS4D01G161100 chr4D 95.746 1716 65 5 797 2509 123655192 123653482 0.000000e+00 2758.0
3 TraesCS4D01G161100 chr4D 95.632 1717 65 7 797 2509 123737989 123736279 0.000000e+00 2747.0
4 TraesCS4D01G161100 chr4D 94.521 73 4 0 663 735 241148547 241148619 2.040000e-21 113.0
5 TraesCS4D01G161100 chr4D 100.000 42 0 0 664 705 123669637 123669678 7.440000e-11 78.7
6 TraesCS4D01G161100 chr4D 100.000 42 0 0 664 705 483688878 483688837 7.440000e-11 78.7
7 TraesCS4D01G161100 chrUn 97.376 1715 42 3 798 2509 221548767 221547053 0.000000e+00 2915.0
8 TraesCS4D01G161100 chrUn 97.318 1715 43 3 798 2509 186191765 186190051 0.000000e+00 2909.0
9 TraesCS4D01G161100 chrUn 97.246 581 14 1 1 581 326341660 326342238 0.000000e+00 983.0
10 TraesCS4D01G161100 chrUn 97.074 581 15 1 1 581 189392374 189391796 0.000000e+00 977.0
11 TraesCS4D01G161100 chr7B 97.145 1716 45 4 798 2509 743005713 743007428 0.000000e+00 2894.0
12 TraesCS4D01G161100 chr7B 97.074 581 15 1 1 581 743086034 743085456 0.000000e+00 977.0
13 TraesCS4D01G161100 chr7A 96.968 1715 46 4 798 2509 120880100 120881811 0.000000e+00 2874.0
14 TraesCS4D01G161100 chr3A 96.037 1716 62 5 798 2509 51915811 51917524 0.000000e+00 2787.0
15 TraesCS4D01G161100 chr6A 95.683 1714 70 4 798 2509 79143328 79145039 0.000000e+00 2752.0
16 TraesCS4D01G161100 chr6A 97.074 581 15 1 1 581 608894122 608894700 0.000000e+00 977.0
17 TraesCS4D01G161100 chr5A 97.418 581 13 1 1 581 16603084 16603662 0.000000e+00 989.0
18 TraesCS4D01G161100 chr1D 97.418 581 13 1 1 581 141321765 141322343 0.000000e+00 989.0
19 TraesCS4D01G161100 chr1D 100.000 42 0 0 664 705 351085620 351085661 7.440000e-11 78.7
20 TraesCS4D01G161100 chr7D 97.251 582 13 2 1 581 626698655 626699234 0.000000e+00 983.0
21 TraesCS4D01G161100 chr6B 97.246 581 14 1 1 581 394511188 394510610 0.000000e+00 983.0
22 TraesCS4D01G161100 chr6B 100.000 42 0 0 664 705 264846401 264846442 7.440000e-11 78.7
23 TraesCS4D01G161100 chr2A 97.246 581 14 1 1 581 618280121 618280699 0.000000e+00 983.0
24 TraesCS4D01G161100 chr3D 100.000 42 0 0 664 705 154779839 154779798 7.440000e-11 78.7
25 TraesCS4D01G161100 chr3D 100.000 42 0 0 664 705 523884623 523884582 7.440000e-11 78.7
26 TraesCS4D01G161100 chr1B 100.000 42 0 0 664 705 135077658 135077699 7.440000e-11 78.7
27 TraesCS4D01G161100 chr1B 100.000 42 0 0 664 705 550740583 550740542 7.440000e-11 78.7


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 TraesCS4D01G161100 chr4D 241047952 241050460 2508 True 4634 4634 100.000 1 2509 1 chr4D.!!$R4 2508
1 TraesCS4D01G161100 chr4D 123506783 123508493 1710 True 2774 2774 95.921 797 2509 1 chr4D.!!$R1 1712
2 TraesCS4D01G161100 chr4D 123653482 123655192 1710 True 2758 2758 95.746 797 2509 1 chr4D.!!$R2 1712
3 TraesCS4D01G161100 chr4D 123736279 123737989 1710 True 2747 2747 95.632 797 2509 1 chr4D.!!$R3 1712
4 TraesCS4D01G161100 chrUn 221547053 221548767 1714 True 2915 2915 97.376 798 2509 1 chrUn.!!$R3 1711
5 TraesCS4D01G161100 chrUn 186190051 186191765 1714 True 2909 2909 97.318 798 2509 1 chrUn.!!$R1 1711
6 TraesCS4D01G161100 chrUn 326341660 326342238 578 False 983 983 97.246 1 581 1 chrUn.!!$F1 580
7 TraesCS4D01G161100 chrUn 189391796 189392374 578 True 977 977 97.074 1 581 1 chrUn.!!$R2 580
8 TraesCS4D01G161100 chr7B 743005713 743007428 1715 False 2894 2894 97.145 798 2509 1 chr7B.!!$F1 1711
9 TraesCS4D01G161100 chr7B 743085456 743086034 578 True 977 977 97.074 1 581 1 chr7B.!!$R1 580
10 TraesCS4D01G161100 chr7A 120880100 120881811 1711 False 2874 2874 96.968 798 2509 1 chr7A.!!$F1 1711
11 TraesCS4D01G161100 chr3A 51915811 51917524 1713 False 2787 2787 96.037 798 2509 1 chr3A.!!$F1 1711
12 TraesCS4D01G161100 chr6A 79143328 79145039 1711 False 2752 2752 95.683 798 2509 1 chr6A.!!$F1 1711
13 TraesCS4D01G161100 chr6A 608894122 608894700 578 False 977 977 97.074 1 581 1 chr6A.!!$F2 580
14 TraesCS4D01G161100 chr5A 16603084 16603662 578 False 989 989 97.418 1 581 1 chr5A.!!$F1 580
15 TraesCS4D01G161100 chr1D 141321765 141322343 578 False 989 989 97.418 1 581 1 chr1D.!!$F1 580
16 TraesCS4D01G161100 chr7D 626698655 626699234 579 False 983 983 97.251 1 581 1 chr7D.!!$F1 580
17 TraesCS4D01G161100 chr6B 394510610 394511188 578 True 983 983 97.246 1 581 1 chr6B.!!$R1 580
18 TraesCS4D01G161100 chr2A 618280121 618280699 578 False 983 983 97.246 1 581 1 chr2A.!!$F1 580

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
693 695 0.036388 CGGAGGAAGCAGGCTTACAA 60.036 55.0 17.91 0.0 39.29 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1649 1.46852 CACCAAGAATTTGATCGCCGT 59.531 47.619 0.0 0.0 36.36 5.68 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
121 122 4.919774 TCCTACCTGCTAATGGTTGAAA 57.080 40.909 0.00 0.00 38.88 2.69
432 433 9.639601 TGAAATACGTATATCTTCTTGGCTATG 57.360 33.333 8.83 0.00 0.00 2.23
479 480 6.403878 TCAACCTATAAGCAGACCTTTGTAC 58.596 40.000 0.00 0.00 34.95 2.90
485 486 0.865769 GCAGACCTTTGTACACACCG 59.134 55.000 0.00 0.00 0.00 4.94
510 511 7.410513 CGTTGTAACTGAACTAGCTATTCACAC 60.411 40.741 11.99 10.89 32.67 3.82
524 525 8.256356 AGCTATTCACACAGAAAGGTCTATAT 57.744 34.615 0.00 0.00 40.22 0.86
550 551 1.122227 TATACCAACTACGCACCCCC 58.878 55.000 0.00 0.00 0.00 5.40
577 579 4.166246 ACTTCTTTTTCCTTCTCCCGTT 57.834 40.909 0.00 0.00 0.00 4.44
581 583 4.134563 TCTTTTTCCTTCTCCCGTTCTTG 58.865 43.478 0.00 0.00 0.00 3.02
582 584 3.570912 TTTTCCTTCTCCCGTTCTTGT 57.429 42.857 0.00 0.00 0.00 3.16
583 585 2.543777 TTCCTTCTCCCGTTCTTGTG 57.456 50.000 0.00 0.00 0.00 3.33
584 586 1.712056 TCCTTCTCCCGTTCTTGTGA 58.288 50.000 0.00 0.00 0.00 3.58
585 587 2.257207 TCCTTCTCCCGTTCTTGTGAT 58.743 47.619 0.00 0.00 0.00 3.06
586 588 3.437213 TCCTTCTCCCGTTCTTGTGATA 58.563 45.455 0.00 0.00 0.00 2.15
587 589 4.030913 TCCTTCTCCCGTTCTTGTGATAT 58.969 43.478 0.00 0.00 0.00 1.63
588 590 5.205821 TCCTTCTCCCGTTCTTGTGATATA 58.794 41.667 0.00 0.00 0.00 0.86
589 591 5.659525 TCCTTCTCCCGTTCTTGTGATATAA 59.340 40.000 0.00 0.00 0.00 0.98
590 592 6.155565 TCCTTCTCCCGTTCTTGTGATATAAA 59.844 38.462 0.00 0.00 0.00 1.40
591 593 6.821665 CCTTCTCCCGTTCTTGTGATATAAAA 59.178 38.462 0.00 0.00 0.00 1.52
592 594 7.499232 CCTTCTCCCGTTCTTGTGATATAAAAT 59.501 37.037 0.00 0.00 0.00 1.82
593 595 9.542462 CTTCTCCCGTTCTTGTGATATAAAATA 57.458 33.333 0.00 0.00 0.00 1.40
594 596 9.893634 TTCTCCCGTTCTTGTGATATAAAATAA 57.106 29.630 0.00 0.00 0.00 1.40
597 599 9.839817 TCCCGTTCTTGTGATATAAAATAATGA 57.160 29.630 0.00 0.00 0.00 2.57
674 676 9.482627 AGAGTTAGAAAATATCAACCGATCATC 57.517 33.333 0.00 0.00 32.73 2.92
675 677 8.299262 AGTTAGAAAATATCAACCGATCATCG 57.701 34.615 0.00 0.00 40.07 3.84
685 687 3.191903 CGATCATCGGAGGAAGCAG 57.808 57.895 0.00 0.00 36.00 4.24
686 688 0.319383 CGATCATCGGAGGAAGCAGG 60.319 60.000 0.00 0.00 36.00 4.85
687 689 0.602372 GATCATCGGAGGAAGCAGGC 60.602 60.000 0.00 0.00 0.00 4.85
688 690 1.053264 ATCATCGGAGGAAGCAGGCT 61.053 55.000 0.00 0.00 0.00 4.58
689 691 1.222936 CATCGGAGGAAGCAGGCTT 59.777 57.895 6.17 6.17 39.23 4.35
690 692 0.465705 CATCGGAGGAAGCAGGCTTA 59.534 55.000 6.49 0.00 36.26 3.09
691 693 0.466124 ATCGGAGGAAGCAGGCTTAC 59.534 55.000 8.20 8.20 37.15 2.34
692 694 0.902984 TCGGAGGAAGCAGGCTTACA 60.903 55.000 17.91 0.00 39.29 2.41
693 695 0.036388 CGGAGGAAGCAGGCTTACAA 60.036 55.000 17.91 0.00 39.29 2.41
694 696 1.743996 GGAGGAAGCAGGCTTACAAG 58.256 55.000 17.91 0.00 39.29 3.16
695 697 1.279271 GGAGGAAGCAGGCTTACAAGA 59.721 52.381 17.91 0.00 39.29 3.02
696 698 2.290323 GGAGGAAGCAGGCTTACAAGAA 60.290 50.000 17.91 0.00 39.29 2.52
697 699 3.412386 GAGGAAGCAGGCTTACAAGAAA 58.588 45.455 17.91 0.00 39.29 2.52
698 700 3.149981 AGGAAGCAGGCTTACAAGAAAC 58.850 45.455 17.91 0.00 39.29 2.78
699 701 3.149981 GGAAGCAGGCTTACAAGAAACT 58.850 45.455 11.31 0.00 36.89 2.66
700 702 3.057946 GGAAGCAGGCTTACAAGAAACTG 60.058 47.826 11.31 0.00 36.89 3.16
701 703 3.492102 AGCAGGCTTACAAGAAACTGA 57.508 42.857 10.83 0.00 0.00 3.41
702 704 4.026356 AGCAGGCTTACAAGAAACTGAT 57.974 40.909 10.83 4.28 0.00 2.90
703 705 3.755378 AGCAGGCTTACAAGAAACTGATG 59.245 43.478 10.83 0.00 0.00 3.07
704 706 3.119708 GCAGGCTTACAAGAAACTGATGG 60.120 47.826 10.83 0.00 0.00 3.51
705 707 4.326826 CAGGCTTACAAGAAACTGATGGA 58.673 43.478 0.00 0.00 0.00 3.41
706 708 4.946157 CAGGCTTACAAGAAACTGATGGAT 59.054 41.667 0.00 0.00 0.00 3.41
707 709 5.416952 CAGGCTTACAAGAAACTGATGGATT 59.583 40.000 0.00 0.00 0.00 3.01
708 710 6.012745 AGGCTTACAAGAAACTGATGGATTT 58.987 36.000 0.00 0.00 0.00 2.17
709 711 6.151817 AGGCTTACAAGAAACTGATGGATTTC 59.848 38.462 0.00 0.00 35.46 2.17
710 712 6.151817 GGCTTACAAGAAACTGATGGATTTCT 59.848 38.462 0.00 0.00 45.03 2.52
711 713 7.247019 GCTTACAAGAAACTGATGGATTTCTC 58.753 38.462 0.05 0.00 42.89 2.87
712 714 7.120432 GCTTACAAGAAACTGATGGATTTCTCT 59.880 37.037 0.05 0.00 42.89 3.10
713 715 8.553459 TTACAAGAAACTGATGGATTTCTCTC 57.447 34.615 0.05 0.00 42.89 3.20
714 716 6.777782 ACAAGAAACTGATGGATTTCTCTCT 58.222 36.000 0.05 0.00 42.89 3.10
715 717 7.230027 ACAAGAAACTGATGGATTTCTCTCTT 58.770 34.615 0.05 0.00 42.89 2.85
716 718 8.378565 ACAAGAAACTGATGGATTTCTCTCTTA 58.621 33.333 0.05 0.00 42.89 2.10
717 719 9.393512 CAAGAAACTGATGGATTTCTCTCTTAT 57.606 33.333 0.05 0.00 42.89 1.73
718 720 9.972106 AAGAAACTGATGGATTTCTCTCTTATT 57.028 29.630 0.05 0.00 42.89 1.40
719 721 9.612066 AGAAACTGATGGATTTCTCTCTTATTC 57.388 33.333 0.00 0.00 40.36 1.75
720 722 9.612066 GAAACTGATGGATTTCTCTCTTATTCT 57.388 33.333 0.00 0.00 33.00 2.40
762 764 7.787725 AACGAGAGAATTAATATGTGGTTCC 57.212 36.000 0.00 0.00 0.00 3.62
763 765 7.125792 ACGAGAGAATTAATATGTGGTTCCT 57.874 36.000 0.00 0.00 0.00 3.36
764 766 7.210873 ACGAGAGAATTAATATGTGGTTCCTC 58.789 38.462 0.00 0.00 0.00 3.71
765 767 7.070074 ACGAGAGAATTAATATGTGGTTCCTCT 59.930 37.037 0.00 0.00 0.00 3.69
766 768 8.577296 CGAGAGAATTAATATGTGGTTCCTCTA 58.423 37.037 0.00 0.00 0.00 2.43
779 781 8.418597 TGTGGTTCCTCTATATCTTGTATACC 57.581 38.462 0.00 0.00 0.00 2.73
780 782 8.008332 TGTGGTTCCTCTATATCTTGTATACCA 58.992 37.037 0.00 0.00 0.00 3.25
781 783 8.524487 GTGGTTCCTCTATATCTTGTATACCAG 58.476 40.741 0.00 0.00 32.01 4.00
782 784 8.232412 TGGTTCCTCTATATCTTGTATACCAGT 58.768 37.037 0.00 0.00 0.00 4.00
783 785 9.750783 GGTTCCTCTATATCTTGTATACCAGTA 57.249 37.037 0.00 0.00 0.00 2.74
896 898 1.410882 GAGCCTTTACGAGCAGGATCT 59.589 52.381 8.80 0.00 41.61 2.75
1064 1066 4.087907 AGAATAGGGCCTTATCTACCGAC 58.912 47.826 13.45 0.00 0.00 4.79
1089 1091 1.207089 CCCTACTTGGTCGATGAAGCA 59.793 52.381 6.35 0.00 0.00 3.91
1114 1116 6.781014 ACTTCGTTCCTATCTGGACCATATTA 59.219 38.462 0.00 0.00 46.14 0.98
1144 1146 6.122277 ACTGATTCTTTCACTGTTCTCCAAA 58.878 36.000 0.00 0.00 0.00 3.28
1145 1147 6.603201 ACTGATTCTTTCACTGTTCTCCAAAA 59.397 34.615 0.00 0.00 0.00 2.44
1161 1163 9.877178 GTTCTCCAAAAGTCTTATCAAGATCTA 57.123 33.333 0.00 0.00 40.18 1.98
1274 1276 1.210722 GGAAGTGGAACAGAGGATCCC 59.789 57.143 8.55 0.00 41.80 3.85
1363 1366 6.628185 TGTTTAAGTCGGAGGATCTTAGAAC 58.372 40.000 0.00 0.00 33.73 3.01
1426 1437 0.405585 CTTTTCTCTTCCAGCCCCCA 59.594 55.000 0.00 0.00 0.00 4.96
1479 1490 1.702957 CCCGGCCCCTATTTGATAAGA 59.297 52.381 0.00 0.00 0.00 2.10
1527 1538 4.734398 TGACAAATATGGTTTGATGGCC 57.266 40.909 0.00 0.00 33.83 5.36
1546 1557 3.200165 GGCCCTTCTCTACTAACCACAAT 59.800 47.826 0.00 0.00 0.00 2.71
1635 1646 4.641396 CTGATTCGTATGGAATTAGCCCA 58.359 43.478 0.00 0.00 45.33 5.36
1638 1649 3.916359 TCGTATGGAATTAGCCCAACA 57.084 42.857 0.00 0.00 37.22 3.33
1739 1751 1.067142 GGTTATGCCGGCGATGATAGA 60.067 52.381 23.90 0.49 0.00 1.98
1768 1780 6.896021 TTGGTAATTGGTTTGTTCCGATTA 57.104 33.333 0.00 0.00 40.72 1.75
1909 1921 1.340568 GGACAGTCTATCCGCCCTTAC 59.659 57.143 0.00 0.00 0.00 2.34
1973 1985 8.619546 AGCAATTTTTAGTCTTCATCTATCAGC 58.380 33.333 0.00 0.00 0.00 4.26
2033 2045 1.078709 ATCTTCAACATGCGTGGACG 58.921 50.000 11.36 0.00 43.27 4.79
2121 2133 3.880047 TTATCACTTCCGGTACTGGTG 57.120 47.619 20.40 15.93 0.00 4.17
2225 2239 4.218312 ACCAGCATCTCTTTTGGTTCTTT 58.782 39.130 0.00 0.00 40.94 2.52
2455 2469 3.117398 ACCATGATCATAGTTGTGCCCAT 60.117 43.478 8.15 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 1.489560 AACTAGAGGCCGCCAAGGTT 61.490 55.000 13.15 8.07 43.70 3.50
167 168 7.653647 ACCATTTGTTTAAGCTTATTCGTTCA 58.346 30.769 7.08 0.00 0.00 3.18
432 433 5.538849 AAAAGCCTGTAGAGATAGCCTAC 57.461 43.478 0.00 0.00 37.57 3.18
479 480 3.183775 GCTAGTTCAGTTACAACGGTGTG 59.816 47.826 18.38 0.00 38.82 3.82
485 486 7.384115 TGTGTGAATAGCTAGTTCAGTTACAAC 59.616 37.037 14.85 9.55 36.35 3.32
524 525 4.261155 GGTGCGTAGTTGGTATATGTACGA 60.261 45.833 4.49 0.00 39.00 3.43
550 551 6.535508 CGGGAGAAGGAAAAAGAAGTATACAG 59.464 42.308 5.50 0.00 0.00 2.74
648 650 9.482627 GATGATCGGTTGATATTTTCTAACTCT 57.517 33.333 0.00 0.00 34.09 3.24
649 651 8.428536 CGATGATCGGTTGATATTTTCTAACTC 58.571 37.037 7.00 0.00 36.00 3.01
650 652 8.299262 CGATGATCGGTTGATATTTTCTAACT 57.701 34.615 7.00 0.00 36.00 2.24
667 669 0.319383 CCTGCTTCCTCCGATGATCG 60.319 60.000 8.05 8.05 40.07 3.69
668 670 0.602372 GCCTGCTTCCTCCGATGATC 60.602 60.000 0.00 0.00 0.00 2.92
669 671 1.053264 AGCCTGCTTCCTCCGATGAT 61.053 55.000 0.00 0.00 0.00 2.45
670 672 1.267574 AAGCCTGCTTCCTCCGATGA 61.268 55.000 0.00 0.00 0.00 2.92
671 673 0.465705 TAAGCCTGCTTCCTCCGATG 59.534 55.000 7.81 0.00 37.47 3.84
672 674 0.466124 GTAAGCCTGCTTCCTCCGAT 59.534 55.000 7.81 0.00 37.47 4.18
673 675 0.902984 TGTAAGCCTGCTTCCTCCGA 60.903 55.000 7.81 0.00 37.47 4.55
674 676 0.036388 TTGTAAGCCTGCTTCCTCCG 60.036 55.000 7.81 0.00 37.47 4.63
675 677 1.279271 TCTTGTAAGCCTGCTTCCTCC 59.721 52.381 7.81 0.00 37.47 4.30
676 678 2.770164 TCTTGTAAGCCTGCTTCCTC 57.230 50.000 7.81 1.73 37.47 3.71
677 679 3.149981 GTTTCTTGTAAGCCTGCTTCCT 58.850 45.455 7.81 0.00 37.47 3.36
678 680 3.057946 CAGTTTCTTGTAAGCCTGCTTCC 60.058 47.826 7.81 0.00 37.47 3.46
679 681 3.815401 TCAGTTTCTTGTAAGCCTGCTTC 59.185 43.478 7.81 1.48 37.47 3.86
680 682 3.820557 TCAGTTTCTTGTAAGCCTGCTT 58.179 40.909 9.63 9.63 39.83 3.91
681 683 3.492102 TCAGTTTCTTGTAAGCCTGCT 57.508 42.857 0.00 0.00 0.00 4.24
682 684 3.119708 CCATCAGTTTCTTGTAAGCCTGC 60.120 47.826 0.00 0.00 0.00 4.85
683 685 4.326826 TCCATCAGTTTCTTGTAAGCCTG 58.673 43.478 0.00 0.00 0.00 4.85
684 686 4.640771 TCCATCAGTTTCTTGTAAGCCT 57.359 40.909 0.00 0.00 0.00 4.58
685 687 5.904362 AATCCATCAGTTTCTTGTAAGCC 57.096 39.130 0.00 0.00 0.00 4.35
686 688 7.120432 AGAGAAATCCATCAGTTTCTTGTAAGC 59.880 37.037 2.35 0.00 42.87 3.09
687 689 8.558973 AGAGAAATCCATCAGTTTCTTGTAAG 57.441 34.615 2.35 0.00 42.87 2.34
688 690 8.378565 AGAGAGAAATCCATCAGTTTCTTGTAA 58.621 33.333 2.35 0.00 42.87 2.41
689 691 7.911651 AGAGAGAAATCCATCAGTTTCTTGTA 58.088 34.615 2.35 0.00 42.87 2.41
690 692 6.777782 AGAGAGAAATCCATCAGTTTCTTGT 58.222 36.000 2.35 0.00 42.87 3.16
691 693 7.684937 AAGAGAGAAATCCATCAGTTTCTTG 57.315 36.000 2.35 0.00 42.87 3.02
692 694 9.972106 AATAAGAGAGAAATCCATCAGTTTCTT 57.028 29.630 2.35 0.00 42.87 2.52
693 695 9.612066 GAATAAGAGAGAAATCCATCAGTTTCT 57.388 33.333 0.41 0.41 44.82 2.52
694 696 9.612066 AGAATAAGAGAGAAATCCATCAGTTTC 57.388 33.333 0.00 0.00 35.18 2.78
736 738 9.321562 GGAACCACATATTAATTCTCTCGTTAA 57.678 33.333 0.00 0.00 0.00 2.01
737 739 8.701895 AGGAACCACATATTAATTCTCTCGTTA 58.298 33.333 0.00 0.00 0.00 3.18
738 740 7.565680 AGGAACCACATATTAATTCTCTCGTT 58.434 34.615 0.00 0.00 0.00 3.85
739 741 7.070074 AGAGGAACCACATATTAATTCTCTCGT 59.930 37.037 0.00 0.00 0.00 4.18
740 742 7.437748 AGAGGAACCACATATTAATTCTCTCG 58.562 38.462 0.00 0.00 0.00 4.04
753 755 9.036980 GGTATACAAGATATAGAGGAACCACAT 57.963 37.037 5.01 0.00 0.00 3.21
754 756 8.008332 TGGTATACAAGATATAGAGGAACCACA 58.992 37.037 5.01 0.00 0.00 4.17
755 757 8.418597 TGGTATACAAGATATAGAGGAACCAC 57.581 38.462 5.01 0.00 0.00 4.16
756 758 8.232412 ACTGGTATACAAGATATAGAGGAACCA 58.768 37.037 14.49 0.00 0.00 3.67
757 759 8.653036 ACTGGTATACAAGATATAGAGGAACC 57.347 38.462 14.49 0.00 0.00 3.62
775 777 9.628500 GGAGGAAAAGTTATTGATTACTGGTAT 57.372 33.333 0.00 0.00 0.00 2.73
776 778 8.832735 AGGAGGAAAAGTTATTGATTACTGGTA 58.167 33.333 0.00 0.00 0.00 3.25
777 779 7.699878 AGGAGGAAAAGTTATTGATTACTGGT 58.300 34.615 0.00 0.00 0.00 4.00
778 780 8.581253 AAGGAGGAAAAGTTATTGATTACTGG 57.419 34.615 0.00 0.00 0.00 4.00
779 781 9.231297 TGAAGGAGGAAAAGTTATTGATTACTG 57.769 33.333 0.00 0.00 0.00 2.74
780 782 9.981460 ATGAAGGAGGAAAAGTTATTGATTACT 57.019 29.630 0.00 0.00 0.00 2.24
791 793 9.674068 GAAGAGTAATAATGAAGGAGGAAAAGT 57.326 33.333 0.00 0.00 0.00 2.66
792 794 9.114952 GGAAGAGTAATAATGAAGGAGGAAAAG 57.885 37.037 0.00 0.00 0.00 2.27
793 795 8.836735 AGGAAGAGTAATAATGAAGGAGGAAAA 58.163 33.333 0.00 0.00 0.00 2.29
794 796 8.393959 AGGAAGAGTAATAATGAAGGAGGAAA 57.606 34.615 0.00 0.00 0.00 3.13
795 797 7.071321 GGAGGAAGAGTAATAATGAAGGAGGAA 59.929 40.741 0.00 0.00 0.00 3.36
896 898 4.006989 CTGAATGAACGTAACCCATCCAA 58.993 43.478 0.00 0.00 0.00 3.53
923 925 4.137543 CAGAGGGGTATTGTGATTAAGCC 58.862 47.826 0.00 0.00 0.00 4.35
1020 1022 4.511617 TTGATAAAGCGCCACAAATTCA 57.488 36.364 2.29 0.00 0.00 2.57
1064 1066 1.392710 ATCGACCAAGTAGGGCTCGG 61.393 60.000 0.00 0.00 46.64 4.63
1114 1116 3.627577 ACAGTGAAAGAATCAGTTGCGTT 59.372 39.130 0.00 0.00 39.78 4.84
1144 1146 6.366340 TCTCCCGTAGATCTTGATAAGACTT 58.634 40.000 0.00 0.00 41.01 3.01
1145 1147 5.942961 TCTCCCGTAGATCTTGATAAGACT 58.057 41.667 0.00 0.00 41.01 3.24
1161 1163 0.266152 ATCCTCCCTCATTCTCCCGT 59.734 55.000 0.00 0.00 0.00 5.28
1281 1283 1.203038 TGCTTGCTCTTGGGGATTTCA 60.203 47.619 0.00 0.00 0.00 2.69
1527 1538 9.265901 CAATATCATTGTGGTTAGTAGAGAAGG 57.734 37.037 0.00 0.00 0.00 3.46
1546 1557 8.733092 AGATGAAATAGAGAGTCCCAATATCA 57.267 34.615 0.00 0.00 0.00 2.15
1635 1646 2.095263 CCAAGAATTTGATCGCCGTGTT 60.095 45.455 0.00 0.00 36.36 3.32
1638 1649 1.468520 CACCAAGAATTTGATCGCCGT 59.531 47.619 0.00 0.00 36.36 5.68
1739 1751 6.472016 GGAACAAACCAATTACCAAATCCAT 58.528 36.000 0.00 0.00 0.00 3.41
1768 1780 2.158711 CCATGTCAGGTGCACCTATCAT 60.159 50.000 37.27 33.89 46.65 2.45
1909 1921 2.872245 CAGAATGGCTGGTAATACCACG 59.128 50.000 8.27 6.31 44.79 4.94
2033 2045 7.118390 GTGGTAATCTATGCATAGTCATTCCAC 59.882 40.741 29.65 29.65 30.10 4.02
2121 2133 6.285224 GGTTAATAACATTGTAATTGCCCCC 58.715 40.000 5.45 0.00 0.00 5.40
2225 2239 5.467738 AGAATATACACCTCTGGATGACCA 58.532 41.667 0.00 0.00 44.76 4.02
2287 2301 6.790232 AGATTGGTTTTCTTGAAAAGGTCA 57.210 33.333 8.57 5.83 46.24 4.02
2306 2320 3.261897 CCATGCCTAGATACCCGAAGATT 59.738 47.826 0.00 0.00 0.00 2.40
2307 2321 2.834549 CCATGCCTAGATACCCGAAGAT 59.165 50.000 0.00 0.00 0.00 2.40
2455 2469 9.109393 CGATCCAACTAAAGATTTTGATTCCTA 57.891 33.333 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.