Multiple sequence alignment - TraesCS7D01G055900

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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 TraesCS7D01G055900 chr7D 100.000 3320 0 0 1 3320 29836587 29833268 0.000000e+00 6131
1 TraesCS7D01G055900 chr7A 90.572 3341 210 40 1 3313 30095557 30092294 0.000000e+00 4327
2 TraesCS7D01G055900 chr7A 96.721 61 2 0 2879 2939 30092760 30092700 5.860000e-18 102
3 TraesCS7D01G055900 chr4A 89.063 3374 226 54 1 3313 699883099 699886390 0.000000e+00 4054


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 TraesCS7D01G055900 chr7D 29833268 29836587 3319 True 6131.0 6131 100.0000 1 3320 1 chr7D.!!$R1 3319
1 TraesCS7D01G055900 chr7A 30092294 30095557 3263 True 2214.5 4327 93.6465 1 3313 2 chr7A.!!$R1 3312
2 TraesCS7D01G055900 chr4A 699883099 699886390 3291 False 4054.0 4054 89.0630 1 3313 1 chr4A.!!$F1 3312

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
622 641 0.03601 GTGTGTCAGCTATGGGCAGT 60.036 55.0 0.0 0.0 44.79 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2709 1.633432 TGGAACTGGGAATCAATCGGT 59.367 47.619 0.0 0.0 0.0 4.69 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
85 102 3.222855 CCCAAGTTGCAACGCCCA 61.223 61.111 23.21 0.00 0.00 5.36
86 103 2.027460 CCAAGTTGCAACGCCCAC 59.973 61.111 23.21 0.00 0.00 4.61
87 104 2.780094 CCAAGTTGCAACGCCCACA 61.780 57.895 23.21 0.00 0.00 4.17
88 105 1.588667 CAAGTTGCAACGCCCACAC 60.589 57.895 23.21 0.00 0.00 3.82
89 106 2.781158 AAGTTGCAACGCCCACACC 61.781 57.895 23.21 0.00 0.00 4.16
90 107 4.279043 GTTGCAACGCCCACACCC 62.279 66.667 14.90 0.00 0.00 4.61
335 352 4.125695 ACCGTCGGTAGAAGCGCC 62.126 66.667 17.19 0.00 39.21 6.53
371 388 3.112709 GGTGAAGCGTCCTCGTGC 61.113 66.667 0.00 0.00 39.49 5.34
403 420 2.258591 CCCGATGATCGCGTAGGG 59.741 66.667 9.74 1.44 39.23 3.53
448 465 1.482748 GGACGGGTGGGTTCCAGTTA 61.483 60.000 0.00 0.00 36.15 2.24
475 492 2.621998 CACCGGTTGTAGATACTCCGAT 59.378 50.000 2.97 7.95 42.25 4.18
497 514 1.002533 CCCCCTCGGTTCCTCCTTA 59.997 63.158 0.00 0.00 0.00 2.69
527 544 4.552365 ATGGTGCCCGCGGATCTG 62.552 66.667 30.73 11.36 0.00 2.90
542 559 1.457303 GATCTGCAACATCCGCGTATC 59.543 52.381 4.92 0.00 0.00 2.24
582 600 1.970640 AGGAAATGGGGTGTTGCTTTC 59.029 47.619 0.00 0.00 0.00 2.62
587 605 1.908299 GGGGTGTTGCTTTCCTGGG 60.908 63.158 0.00 0.00 0.00 4.45
593 612 0.827507 GTTGCTTTCCTGGGGCAGAA 60.828 55.000 9.10 0.00 37.28 3.02
621 640 0.745845 GGTGTGTCAGCTATGGGCAG 60.746 60.000 0.00 0.00 44.79 4.85
622 641 0.036010 GTGTGTCAGCTATGGGCAGT 60.036 55.000 0.00 0.00 44.79 4.40
623 642 1.207089 GTGTGTCAGCTATGGGCAGTA 59.793 52.381 0.00 0.00 44.79 2.74
624 643 2.118679 TGTGTCAGCTATGGGCAGTAT 58.881 47.619 0.00 0.00 44.79 2.12
625 644 2.158914 TGTGTCAGCTATGGGCAGTATG 60.159 50.000 0.00 0.00 44.79 2.39
626 645 2.118679 TGTCAGCTATGGGCAGTATGT 58.881 47.619 0.00 0.00 44.79 2.29
627 646 2.103094 TGTCAGCTATGGGCAGTATGTC 59.897 50.000 0.00 0.00 44.79 3.06
636 658 2.199291 GGCAGTATGTCAATTGCTGC 57.801 50.000 20.38 20.38 43.01 5.25
656 678 3.943381 TGCTAGCTCTGATCAATTTGTGG 59.057 43.478 17.23 0.00 0.00 4.17
657 679 3.314635 GCTAGCTCTGATCAATTTGTGGG 59.685 47.826 7.70 0.00 0.00 4.61
658 680 3.446442 AGCTCTGATCAATTTGTGGGT 57.554 42.857 0.00 0.00 0.00 4.51
659 681 3.087031 AGCTCTGATCAATTTGTGGGTG 58.913 45.455 0.00 0.00 0.00 4.61
660 682 2.821969 GCTCTGATCAATTTGTGGGTGT 59.178 45.455 0.00 0.00 0.00 4.16
661 683 3.256631 GCTCTGATCAATTTGTGGGTGTT 59.743 43.478 0.00 0.00 0.00 3.32
662 684 4.616835 GCTCTGATCAATTTGTGGGTGTTC 60.617 45.833 0.00 0.00 0.00 3.18
663 685 4.728772 TCTGATCAATTTGTGGGTGTTCT 58.271 39.130 0.00 0.00 0.00 3.01
664 686 4.761739 TCTGATCAATTTGTGGGTGTTCTC 59.238 41.667 0.00 0.00 0.00 2.87
665 687 3.501828 TGATCAATTTGTGGGTGTTCTCG 59.498 43.478 0.00 0.00 0.00 4.04
666 688 2.226330 TCAATTTGTGGGTGTTCTCGG 58.774 47.619 0.00 0.00 0.00 4.63
667 689 1.953686 CAATTTGTGGGTGTTCTCGGT 59.046 47.619 0.00 0.00 0.00 4.69
682 716 1.200716 CTCGGTAGTGTTCTGGCGTTA 59.799 52.381 0.00 0.00 0.00 3.18
684 718 1.343506 GGTAGTGTTCTGGCGTTACG 58.656 55.000 0.00 0.00 0.00 3.18
720 767 2.380410 CCCTGAAGCGGACGAAACG 61.380 63.158 0.00 0.00 0.00 3.60
731 778 4.738740 AGCGGACGAAACGATCTAAATAAG 59.261 41.667 0.00 0.00 0.00 1.73
740 787 6.436843 AACGATCTAAATAAGGCAAGGTTG 57.563 37.500 0.00 0.00 0.00 3.77
761 813 1.403249 CGTAGTTAACCGGGTGTCTGG 60.403 57.143 0.00 0.00 45.02 3.86
795 847 5.659048 AAATCGGATTAAGATTCAGACGC 57.341 39.130 3.22 0.00 37.34 5.19
798 850 2.543031 CGGATTAAGATTCAGACGCCGA 60.543 50.000 0.00 0.00 38.57 5.54
800 852 3.243434 GGATTAAGATTCAGACGCCGAGA 60.243 47.826 0.00 0.00 0.00 4.04
804 856 1.135257 AGATTCAGACGCCGAGAAGTG 60.135 52.381 0.00 0.00 0.00 3.16
809 861 0.597637 AGACGCCGAGAAGTGTGTTG 60.598 55.000 0.00 0.00 0.00 3.33
813 865 1.594518 CGCCGAGAAGTGTGTTGTTTG 60.595 52.381 0.00 0.00 0.00 2.93
823 875 6.589907 AGAAGTGTGTTGTTTGTTTCCATTTC 59.410 34.615 0.00 0.00 0.00 2.17
828 880 6.148480 TGTGTTGTTTGTTTCCATTTCTTTGG 59.852 34.615 0.00 0.00 38.18 3.28
832 884 7.751768 TGTTTGTTTCCATTTCTTTGGTTTT 57.248 28.000 0.00 0.00 38.01 2.43
837 889 7.569240 TGTTTCCATTTCTTTGGTTTTGGTAT 58.431 30.769 0.00 0.00 38.01 2.73
838 890 8.049721 TGTTTCCATTTCTTTGGTTTTGGTATT 58.950 29.630 0.00 0.00 38.01 1.89
901 957 3.311106 GTGGTCGAAACAACTGATCGTA 58.689 45.455 0.00 0.00 37.79 3.43
936 992 1.531602 GCAGGCTTGTGGGGTTTCT 60.532 57.895 0.00 0.00 0.00 2.52
970 1026 3.254629 TGGAAGATTGCTGCCACTC 57.745 52.632 0.00 0.00 45.39 3.51
991 1047 7.674348 CCACTCATCTCCAGGGTATACTTTATA 59.326 40.741 2.25 0.00 0.00 0.98
993 1049 8.679725 ACTCATCTCCAGGGTATACTTTATAGA 58.320 37.037 2.25 2.10 0.00 1.98
998 1054 8.453681 TCTCCAGGGTATACTTTATAGATCACA 58.546 37.037 2.25 0.00 0.00 3.58
1017 1073 0.615331 ACATGGAGACGGTTGATGCT 59.385 50.000 0.00 0.00 0.00 3.79
1073 1129 2.834689 CGATGTCCGTGTTTGCTTTAC 58.165 47.619 0.00 0.00 0.00 2.01
1086 1142 1.743995 CTTTACAAGGACCGGCGGG 60.744 63.158 31.78 14.51 40.11 6.13
1135 1191 2.436292 ACTCGTCCGTCCTCTCCG 60.436 66.667 0.00 0.00 0.00 4.63
1136 1192 3.878519 CTCGTCCGTCCTCTCCGC 61.879 72.222 0.00 0.00 0.00 5.54
1179 1238 2.042831 GCTGGGTCAAAGCGATGCT 61.043 57.895 0.00 0.00 42.56 3.79
1198 1257 2.418197 GCTCGTTCTGGTGGTAGCAATA 60.418 50.000 0.00 0.00 0.00 1.90
1199 1258 3.857052 CTCGTTCTGGTGGTAGCAATAA 58.143 45.455 0.00 0.00 0.00 1.40
1200 1259 3.592059 TCGTTCTGGTGGTAGCAATAAC 58.408 45.455 0.00 0.00 0.00 1.89
1210 1269 5.095490 GTGGTAGCAATAACAACTGCATTC 58.905 41.667 0.00 0.00 41.17 2.67
1362 1421 3.127203 TCTCTCTCAAATCCGAGTTCGTC 59.873 47.826 0.48 0.00 37.74 4.20
1383 1442 3.379650 CGAAACCTGCATCGGGTAT 57.620 52.632 0.00 0.00 43.15 2.73
1672 1731 4.162320 TGGATGAAGATGTAAGGTCTGTCC 59.838 45.833 0.00 0.00 0.00 4.02
1692 1751 2.887152 CCTGAGGGAAGGTTTGACAAAG 59.113 50.000 0.00 0.00 32.17 2.77
1704 1763 4.380444 GGTTTGACAAAGCTGTTCTCAACA 60.380 41.667 20.20 0.00 39.52 3.33
1809 1868 3.950397 TGACATTGACTGGATAACCACC 58.050 45.455 0.00 0.00 41.77 4.61
1816 1875 1.975680 ACTGGATAACCACCGTCTTGT 59.024 47.619 0.00 0.00 41.77 3.16
1918 1977 3.671740 AGTATAGCTCAGGTCTGTGGA 57.328 47.619 0.00 0.00 0.00 4.02
1929 1988 1.603172 GGTCTGTGGACTGTGAAGACG 60.603 57.143 0.00 0.00 41.82 4.18
2005 2064 1.639722 TCTCCCGTCAACATCCAGAA 58.360 50.000 0.00 0.00 0.00 3.02
2180 2239 2.431057 GTGACCAGTCGGATATCCTGTT 59.569 50.000 19.61 0.00 35.59 3.16
2325 2384 3.209410 CCCTATCAGCTTGTAAGGCTTG 58.791 50.000 10.69 0.00 38.03 4.01
2391 2473 8.311109 GGTTATACCAACCAAATTCTCATTGTT 58.689 33.333 1.30 0.00 38.42 2.83
2476 2564 5.599732 TGCAGTATGTTCTTGTTGCAAATT 58.400 33.333 0.00 0.00 38.47 1.82
2624 2714 2.500504 GGTTAAGAGTTCCTGGACCGAT 59.499 50.000 0.00 0.00 0.00 4.18
2628 2718 2.472029 AGAGTTCCTGGACCGATTGAT 58.528 47.619 0.00 0.00 0.00 2.57
2674 2764 2.136026 ACCTTTTGTTCCTGAGGACCT 58.864 47.619 0.00 0.00 33.47 3.85
2675 2765 2.514160 ACCTTTTGTTCCTGAGGACCTT 59.486 45.455 0.00 0.00 33.47 3.50
2719 2809 2.574006 TGTTCTCTGGCATGCTTTCT 57.426 45.000 18.92 0.00 0.00 2.52
2720 2810 2.867624 TGTTCTCTGGCATGCTTTCTT 58.132 42.857 18.92 0.00 0.00 2.52
2740 2830 2.122768 TGGTTCCATGGCCAAAAACTT 58.877 42.857 10.96 0.00 0.00 2.66
2741 2831 2.103941 TGGTTCCATGGCCAAAAACTTC 59.896 45.455 10.96 3.78 0.00 3.01
2746 2836 2.634453 CCATGGCCAAAAACTTCCTCTT 59.366 45.455 10.96 0.00 0.00 2.85
2753 2843 6.155393 TGGCCAAAAACTTCCTCTTAAGAAAA 59.845 34.615 0.61 3.50 0.00 2.29
2756 2846 7.979537 GCCAAAAACTTCCTCTTAAGAAAAAGA 59.020 33.333 23.49 10.32 34.39 2.52
2766 2856 7.751768 CTCTTAAGAAAAAGAGGTTGATGGT 57.248 36.000 6.63 0.00 45.80 3.55
2776 2866 4.218312 AGAGGTTGATGGTTTGCTTCTTT 58.782 39.130 0.00 0.00 0.00 2.52
2795 2885 5.596845 TCTTTCAGGTTATGTTGCCAAAAC 58.403 37.500 0.00 0.00 0.00 2.43
2797 2887 5.606348 TTCAGGTTATGTTGCCAAAACTT 57.394 34.783 0.00 0.00 0.00 2.66
2824 2914 1.630878 CCTGTTTACTCCCTCTGCCTT 59.369 52.381 0.00 0.00 0.00 4.35
2923 3014 5.721876 TTGACACGAACGTCTTACATTTT 57.278 34.783 0.00 0.00 36.82 1.82
2938 3029 1.466167 CATTTTGCGACAGAGGGAGTG 59.534 52.381 0.00 0.00 0.00 3.51
3051 3142 9.542462 CATGGTATATATTAACAATCCCTACCG 57.458 37.037 0.00 0.00 30.94 4.02
3163 3255 5.599732 TCAAGTTTGTGCTTTGCAATATGT 58.400 33.333 0.00 0.00 41.47 2.29
3175 3267 2.942376 TGCAATATGTGTTAAGAGGCCG 59.058 45.455 0.00 0.00 0.00 6.13
3184 3278 0.248289 TTAAGAGGCCGGGAAAGTCG 59.752 55.000 2.18 0.00 0.00 4.18
3285 3379 2.230508 TGTCTTCACTAAACCGCTCGAT 59.769 45.455 0.00 0.00 0.00 3.59
3291 3385 2.664568 CACTAAACCGCTCGATTCGAAA 59.335 45.455 10.38 0.00 34.74 3.46
3313 3408 2.815503 ACAACACTAAATTACGGGCCAC 59.184 45.455 4.39 0.00 0.00 5.01
3314 3409 3.078837 CAACACTAAATTACGGGCCACT 58.921 45.455 4.39 0.00 0.00 4.00
3315 3410 2.706890 ACACTAAATTACGGGCCACTG 58.293 47.619 4.39 0.00 0.00 3.66
3316 3411 1.400494 CACTAAATTACGGGCCACTGC 59.600 52.381 4.39 0.00 0.00 4.40
3317 3412 1.003812 ACTAAATTACGGGCCACTGCA 59.996 47.619 4.39 0.00 40.13 4.41
3318 3413 2.297701 CTAAATTACGGGCCACTGCAT 58.702 47.619 4.39 0.00 40.13 3.96
3319 3414 1.102978 AAATTACGGGCCACTGCATC 58.897 50.000 4.39 0.00 40.13 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 110 4.881381 TGGGGATGGGGATGGGGG 62.881 72.222 0.00 0.00 0.00 5.40
94 111 3.511610 GTGGGGATGGGGATGGGG 61.512 72.222 0.00 0.00 0.00 4.96
95 112 3.511610 GGTGGGGATGGGGATGGG 61.512 72.222 0.00 0.00 0.00 4.00
96 113 3.889692 CGGTGGGGATGGGGATGG 61.890 72.222 0.00 0.00 0.00 3.51
97 114 3.889692 CCGGTGGGGATGGGGATG 61.890 72.222 0.00 0.00 38.47 3.51
325 342 1.227176 CCCTAACCGGCGCTTCTAC 60.227 63.158 7.64 0.00 0.00 2.59
335 352 4.867599 GCGCGTCCTCCCTAACCG 62.868 72.222 8.43 0.00 0.00 4.44
391 408 3.214123 CCGACCCCTACGCGATCA 61.214 66.667 15.93 0.00 0.00 2.92
398 415 1.017701 CGAGCAAAACCGACCCCTAC 61.018 60.000 0.00 0.00 0.00 3.18
403 420 2.664436 CGACCGAGCAAAACCGACC 61.664 63.158 0.00 0.00 0.00 4.79
432 449 0.321298 CTGTAACTGGAACCCACCCG 60.321 60.000 0.00 0.00 0.00 5.28
435 452 1.418637 TGGTCTGTAACTGGAACCCAC 59.581 52.381 0.00 0.00 0.00 4.61
448 465 1.640917 ATCTACAACCGGTGGTCTGT 58.359 50.000 20.58 16.62 33.12 3.41
487 504 1.934525 GCGCTAAAGCTAAGGAGGAAC 59.065 52.381 0.00 0.00 39.32 3.62
497 514 2.174334 CACCATGTGCGCTAAAGCT 58.826 52.632 9.73 0.00 39.32 3.74
527 544 0.859232 AATCGATACGCGGATGTTGC 59.141 50.000 9.57 0.00 41.33 4.17
542 559 1.674322 ACACCTGGGCCGAAAATCG 60.674 57.895 0.00 0.00 40.07 3.34
582 600 2.673523 CCTCTGTTCTGCCCCAGG 59.326 66.667 0.00 0.00 31.51 4.45
587 605 1.673665 CACCTGCCTCTGTTCTGCC 60.674 63.158 0.00 0.00 0.00 4.85
593 612 1.750930 CTGACACACCTGCCTCTGT 59.249 57.895 0.00 0.00 0.00 3.41
621 640 4.025061 CAGAGCTAGCAGCAATTGACATAC 60.025 45.833 18.83 0.00 45.56 2.39
622 641 4.124970 CAGAGCTAGCAGCAATTGACATA 58.875 43.478 18.83 0.00 45.56 2.29
623 642 2.943690 CAGAGCTAGCAGCAATTGACAT 59.056 45.455 18.83 0.00 45.56 3.06
624 643 2.027837 TCAGAGCTAGCAGCAATTGACA 60.028 45.455 18.83 0.00 45.56 3.58
625 644 2.625737 TCAGAGCTAGCAGCAATTGAC 58.374 47.619 18.83 0.30 45.56 3.18
626 645 3.118519 TGATCAGAGCTAGCAGCAATTGA 60.119 43.478 18.83 10.79 45.56 2.57
627 646 3.203716 TGATCAGAGCTAGCAGCAATTG 58.796 45.455 18.83 0.00 45.56 2.32
628 647 3.555527 TGATCAGAGCTAGCAGCAATT 57.444 42.857 18.83 0.00 45.56 2.32
631 650 3.555527 AATTGATCAGAGCTAGCAGCA 57.444 42.857 18.83 1.46 45.56 4.41
632 651 3.626670 ACAAATTGATCAGAGCTAGCAGC 59.373 43.478 18.83 8.57 42.84 5.25
636 658 4.334759 CACCCACAAATTGATCAGAGCTAG 59.665 45.833 0.00 0.00 0.00 3.42
656 678 2.609737 CCAGAACACTACCGAGAACACC 60.610 54.545 0.00 0.00 0.00 4.16
657 679 2.673833 CCAGAACACTACCGAGAACAC 58.326 52.381 0.00 0.00 0.00 3.32
658 680 1.000506 GCCAGAACACTACCGAGAACA 59.999 52.381 0.00 0.00 0.00 3.18
659 681 1.711206 GCCAGAACACTACCGAGAAC 58.289 55.000 0.00 0.00 0.00 3.01
660 682 0.242825 CGCCAGAACACTACCGAGAA 59.757 55.000 0.00 0.00 0.00 2.87
661 683 0.892358 ACGCCAGAACACTACCGAGA 60.892 55.000 0.00 0.00 0.00 4.04
662 684 0.038526 AACGCCAGAACACTACCGAG 60.039 55.000 0.00 0.00 0.00 4.63
663 685 1.068333 GTAACGCCAGAACACTACCGA 60.068 52.381 0.00 0.00 0.00 4.69
664 686 1.343506 GTAACGCCAGAACACTACCG 58.656 55.000 0.00 0.00 0.00 4.02
665 687 1.343506 CGTAACGCCAGAACACTACC 58.656 55.000 0.00 0.00 0.00 3.18
666 688 1.336240 ACCGTAACGCCAGAACACTAC 60.336 52.381 0.00 0.00 0.00 2.73
667 689 0.961019 ACCGTAACGCCAGAACACTA 59.039 50.000 0.00 0.00 0.00 2.74
684 718 1.134699 GGGGTACTAACTAACGGCACC 60.135 57.143 0.00 0.00 0.00 5.01
740 787 0.244721 AGACACCCGGTTAACTACGC 59.755 55.000 5.42 0.00 0.00 4.42
741 788 1.403249 CCAGACACCCGGTTAACTACG 60.403 57.143 5.42 1.33 0.00 3.51
742 789 1.895131 TCCAGACACCCGGTTAACTAC 59.105 52.381 5.42 0.00 0.00 2.73
783 835 1.546476 ACTTCTCGGCGTCTGAATCTT 59.454 47.619 6.85 0.00 0.00 2.40
790 842 0.597637 CAACACACTTCTCGGCGTCT 60.598 55.000 6.85 0.00 0.00 4.18
795 847 3.757745 AACAAACAACACACTTCTCGG 57.242 42.857 0.00 0.00 0.00 4.63
813 865 8.445275 AATACCAAAACCAAAGAAATGGAAAC 57.555 30.769 0.00 0.00 43.54 2.78
823 875 9.801873 CCTATGACATTAATACCAAAACCAAAG 57.198 33.333 0.00 0.00 0.00 2.77
838 890 9.502091 GTGCTGGTTATAAATCCTATGACATTA 57.498 33.333 0.00 0.00 0.00 1.90
845 897 8.275040 AACAGAAGTGCTGGTTATAAATCCTAT 58.725 33.333 2.37 0.00 43.69 2.57
901 957 3.998341 GCCTGCACAAACATCATGAAAAT 59.002 39.130 0.00 0.00 0.00 1.82
936 992 3.703556 TCTTCCACCTTCATTTGCAACAA 59.296 39.130 0.00 0.00 0.00 2.83
970 1026 9.480861 TGATCTATAAAGTATACCCTGGAGATG 57.519 37.037 10.35 0.00 0.00 2.90
991 1047 1.561643 ACCGTCTCCATGTGTGATCT 58.438 50.000 0.00 0.00 0.00 2.75
993 1049 1.623311 TCAACCGTCTCCATGTGTGAT 59.377 47.619 0.00 0.00 0.00 3.06
998 1054 0.615331 AGCATCAACCGTCTCCATGT 59.385 50.000 0.00 0.00 0.00 3.21
1017 1073 5.048782 GTCAGCAAACTTGTATCCATCAACA 60.049 40.000 0.00 0.00 0.00 3.33
1135 1191 0.378610 GCGAAATACTTGCTCCTGGC 59.621 55.000 0.00 0.00 42.22 4.85
1136 1192 0.652592 CGCGAAATACTTGCTCCTGG 59.347 55.000 0.00 0.00 0.00 4.45
1179 1238 3.007074 TGTTATTGCTACCACCAGAACGA 59.993 43.478 0.00 0.00 0.00 3.85
1198 1257 3.996150 CTGGACTTGAATGCAGTTGTT 57.004 42.857 0.00 0.00 33.62 2.83
1210 1269 2.046892 CCTCGGGCACTGGACTTG 60.047 66.667 0.00 0.00 33.92 3.16
1340 1399 3.082548 ACGAACTCGGATTTGAGAGAGA 58.917 45.455 3.88 0.00 44.95 3.10
1380 1439 4.133078 CCCAGGAAGCAGATTCAAGATAC 58.867 47.826 0.00 0.00 39.91 2.24
1383 1442 2.026822 GTCCCAGGAAGCAGATTCAAGA 60.027 50.000 0.00 0.00 39.91 3.02
1672 1731 2.294512 GCTTTGTCAAACCTTCCCTCAG 59.705 50.000 0.00 0.00 0.00 3.35
1692 1751 3.743396 CAGTCCTAAGTGTTGAGAACAGC 59.257 47.826 0.00 0.00 43.10 4.40
1698 1757 3.306364 CCAGTCCAGTCCTAAGTGTTGAG 60.306 52.174 0.00 0.00 0.00 3.02
1704 1763 3.270960 AGAGATCCAGTCCAGTCCTAAGT 59.729 47.826 0.00 0.00 0.00 2.24
1809 1868 3.742882 TCAGCTCAATCTTTGACAAGACG 59.257 43.478 0.00 0.00 42.05 4.18
1816 1875 4.568956 TCGTTCATCAGCTCAATCTTTGA 58.431 39.130 0.00 0.00 38.17 2.69
1918 1977 5.899120 TCTATAAGCTTCGTCTTCACAGT 57.101 39.130 0.00 0.00 0.00 3.55
1929 1988 6.536941 CCTTTCCAGTCACTTCTATAAGCTTC 59.463 42.308 0.00 0.00 36.05 3.86
2005 2064 2.079158 CCATGTCTTCACAAGATGCGT 58.921 47.619 0.00 0.00 40.18 5.24
2180 2239 3.254629 GCTTTCTGCATCCAGTCCA 57.745 52.632 0.00 0.00 42.31 4.02
2232 2291 2.095919 GCGGTAACACCACATCTCAAAC 60.096 50.000 0.00 0.00 38.47 2.93
2325 2384 9.341899 CTTACAGTCTACAATTAAAACAATGGC 57.658 33.333 0.00 0.00 0.00 4.40
2359 2418 3.547054 TTGGTTGGTATAACCGGCTAG 57.453 47.619 0.00 0.00 42.58 3.42
2391 2473 3.295093 ACATCCACAACAACAACATCCA 58.705 40.909 0.00 0.00 0.00 3.41
2581 2670 7.982761 ACCTGGTTTACAATGTAATACGAAA 57.017 32.000 6.67 0.00 0.00 3.46
2587 2676 9.582648 AACTCTTAACCTGGTTTACAATGTAAT 57.417 29.630 18.58 0.00 0.00 1.89
2619 2709 1.633432 TGGAACTGGGAATCAATCGGT 59.367 47.619 0.00 0.00 0.00 4.69
2624 2714 2.490718 CCTGGTTGGAACTGGGAATCAA 60.491 50.000 0.00 0.00 38.35 2.57
2628 2718 0.476771 GACCTGGTTGGAACTGGGAA 59.523 55.000 0.00 0.00 39.71 3.97
2674 2764 5.191727 TCCTTCAGGATCCATGCTTAAAA 57.808 39.130 15.82 0.00 39.78 1.52
2675 2765 4.860802 TCCTTCAGGATCCATGCTTAAA 57.139 40.909 15.82 0.00 39.78 1.52
2719 2809 2.122768 AGTTTTTGGCCATGGAACCAA 58.877 42.857 18.40 17.71 44.11 3.67
2720 2810 1.799933 AGTTTTTGGCCATGGAACCA 58.200 45.000 18.40 11.92 0.00 3.67
2746 2836 6.323739 AGCAAACCATCAACCTCTTTTTCTTA 59.676 34.615 0.00 0.00 0.00 2.10
2753 2843 3.837355 AGAAGCAAACCATCAACCTCTT 58.163 40.909 0.00 0.00 0.00 2.85
2756 2846 3.960102 TGAAAGAAGCAAACCATCAACCT 59.040 39.130 0.00 0.00 0.00 3.50
2757 2847 4.301628 CTGAAAGAAGCAAACCATCAACC 58.698 43.478 0.00 0.00 34.07 3.77
2758 2848 4.202151 ACCTGAAAGAAGCAAACCATCAAC 60.202 41.667 0.00 0.00 34.07 3.18
2759 2849 3.960102 ACCTGAAAGAAGCAAACCATCAA 59.040 39.130 0.00 0.00 34.07 2.57
2760 2850 3.565307 ACCTGAAAGAAGCAAACCATCA 58.435 40.909 0.00 0.00 34.07 3.07
2761 2851 4.590850 AACCTGAAAGAAGCAAACCATC 57.409 40.909 0.00 0.00 34.07 3.51
2762 2852 5.539955 ACATAACCTGAAAGAAGCAAACCAT 59.460 36.000 0.00 0.00 34.07 3.55
2763 2853 4.892934 ACATAACCTGAAAGAAGCAAACCA 59.107 37.500 0.00 0.00 34.07 3.67
2764 2854 5.453567 ACATAACCTGAAAGAAGCAAACC 57.546 39.130 0.00 0.00 34.07 3.27
2765 2855 5.175673 GCAACATAACCTGAAAGAAGCAAAC 59.824 40.000 0.00 0.00 34.07 2.93
2766 2856 5.288804 GCAACATAACCTGAAAGAAGCAAA 58.711 37.500 0.00 0.00 34.07 3.68
2795 2885 2.814336 GGGAGTAAACAGGAGCAACAAG 59.186 50.000 0.00 0.00 0.00 3.16
2797 2887 2.038557 GAGGGAGTAAACAGGAGCAACA 59.961 50.000 0.00 0.00 0.00 3.33
2902 2993 4.551217 GCAAAATGTAAGACGTTCGTGTCA 60.551 41.667 1.74 0.00 41.41 3.58
2903 2994 3.898361 GCAAAATGTAAGACGTTCGTGTC 59.102 43.478 1.74 0.00 39.21 3.67
2904 2995 3.602946 CGCAAAATGTAAGACGTTCGTGT 60.603 43.478 1.74 0.00 0.00 4.49
2905 2996 2.894000 CGCAAAATGTAAGACGTTCGTG 59.106 45.455 1.74 0.00 0.00 4.35
2923 3014 0.541063 TTACCACTCCCTCTGTCGCA 60.541 55.000 0.00 0.00 0.00 5.10
2938 3029 4.036852 GGAACATCAGGCTATTTGCTTACC 59.963 45.833 0.00 0.00 42.39 2.85
2960 3051 2.775911 TGCAAGATCAGGACAGAAGG 57.224 50.000 0.00 0.00 0.00 3.46
3044 3135 9.191995 GCATTTTGATTATTTTATTCGGTAGGG 57.808 33.333 0.00 0.00 0.00 3.53
3163 3255 1.002773 GACTTTCCCGGCCTCTTAACA 59.997 52.381 0.00 0.00 0.00 2.41
3175 3267 4.695928 AGAATGCTAAAGAACGACTTTCCC 59.304 41.667 13.37 8.29 44.36 3.97
3184 3278 6.487689 AGCTGTACAAGAATGCTAAAGAAC 57.512 37.500 4.85 0.00 31.71 3.01
3285 3379 6.428799 CCCGTAATTTAGTGTTGTTTTCGAA 58.571 36.000 0.00 0.00 0.00 3.71
3291 3385 3.253921 GTGGCCCGTAATTTAGTGTTGTT 59.746 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.