Multiple sequence alignment - TraesCS4A01G068400

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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 TraesCS4A01G068400 chr4A 100.000 3626 0 0 1 3626 66908705 66912330 0.000000e+00 6697.0
1 TraesCS4A01G068400 chr4B 91.240 2774 110 46 1 2688 472132248 472134974 0.000000e+00 3653.0
2 TraesCS4A01G068400 chr4B 89.253 763 60 11 2861 3615 472135307 472136055 0.000000e+00 935.0
3 TraesCS4A01G068400 chr4B 96.377 138 4 1 2684 2821 472135016 472135152 3.640000e-55 226.0
4 TraesCS4A01G068400 chr4D 95.917 1984 58 11 714 2687 385510588 385512558 0.000000e+00 3193.0
5 TraesCS4A01G068400 chr4D 89.977 868 55 18 2684 3547 385512598 385513437 0.000000e+00 1092.0
6 TraesCS4A01G068400 chr4D 87.834 748 18 24 1 717 385509854 385510559 0.000000e+00 809.0
7 TraesCS4A01G068400 chr4D 72.840 486 103 25 1366 1838 147079798 147080267 4.880000e-29 139.0
8 TraesCS4A01G068400 chr1A 78.164 1209 202 52 1348 2528 573242674 573243848 0.000000e+00 713.0
9 TraesCS4A01G068400 chr1D 77.843 1187 207 49 1367 2528 477189301 477190456 0.000000e+00 684.0
10 TraesCS4A01G068400 chr1D 75.773 1197 239 43 1348 2523 474375365 474376531 1.140000e-154 556.0
11 TraesCS4A01G068400 chr7A 76.686 1201 230 40 1348 2526 545934574 545935746 3.980000e-174 621.0
12 TraesCS4A01G068400 chr7A 75.189 661 131 28 1870 2518 167904018 167903379 7.670000e-72 281.0
13 TraesCS4A01G068400 chr7B 76.303 1190 238 38 1348 2518 470836764 470835600 2.410000e-166 595.0
14 TraesCS4A01G068400 chr7B 75.417 659 123 33 1870 2513 130746660 130746026 2.130000e-72 283.0
15 TraesCS4A01G068400 chr7B 81.333 150 20 5 3470 3617 610738589 610738732 8.230000e-22 115.0
16 TraesCS4A01G068400 chr1B 76.340 1175 233 40 1367 2523 659723969 659725116 4.030000e-164 588.0
17 TraesCS4A01G068400 chr7D 75.730 1199 245 38 1348 2526 451187598 451186426 8.790000e-156 560.0
18 TraesCS4A01G068400 chr6A 74.148 851 183 31 1675 2511 525030561 525029734 5.840000e-83 318.0
19 TraesCS4A01G068400 chr6A 76.981 265 48 11 1579 1838 40217847 40218103 4.880000e-29 139.0
20 TraesCS4A01G068400 chr6D 73.796 851 186 32 1675 2511 383227681 383226854 5.880000e-78 302.0
21 TraesCS4A01G068400 chr6D 76.981 265 48 10 1579 1838 36222562 36222818 4.880000e-29 139.0
22 TraesCS4A01G068400 chr6B 77.358 265 47 10 1579 1838 75915784 75916040 1.050000e-30 145.0
23 TraesCS4A01G068400 chr3D 95.122 41 2 0 3574 3614 382803969 382804009 8.400000e-07 65.8


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 TraesCS4A01G068400 chr4A 66908705 66912330 3625 False 6697.000000 6697 100.000000 1 3626 1 chr4A.!!$F1 3625
1 TraesCS4A01G068400 chr4B 472132248 472136055 3807 False 1604.666667 3653 92.290000 1 3615 3 chr4B.!!$F1 3614
2 TraesCS4A01G068400 chr4D 385509854 385513437 3583 False 1698.000000 3193 91.242667 1 3547 3 chr4D.!!$F2 3546
3 TraesCS4A01G068400 chr1A 573242674 573243848 1174 False 713.000000 713 78.164000 1348 2528 1 chr1A.!!$F1 1180
4 TraesCS4A01G068400 chr1D 477189301 477190456 1155 False 684.000000 684 77.843000 1367 2528 1 chr1D.!!$F2 1161
5 TraesCS4A01G068400 chr1D 474375365 474376531 1166 False 556.000000 556 75.773000 1348 2523 1 chr1D.!!$F1 1175
6 TraesCS4A01G068400 chr7A 545934574 545935746 1172 False 621.000000 621 76.686000 1348 2526 1 chr7A.!!$F1 1178
7 TraesCS4A01G068400 chr7A 167903379 167904018 639 True 281.000000 281 75.189000 1870 2518 1 chr7A.!!$R1 648
8 TraesCS4A01G068400 chr7B 470835600 470836764 1164 True 595.000000 595 76.303000 1348 2518 1 chr7B.!!$R2 1170
9 TraesCS4A01G068400 chr7B 130746026 130746660 634 True 283.000000 283 75.417000 1870 2513 1 chr7B.!!$R1 643
10 TraesCS4A01G068400 chr1B 659723969 659725116 1147 False 588.000000 588 76.340000 1367 2523 1 chr1B.!!$F1 1156
11 TraesCS4A01G068400 chr7D 451186426 451187598 1172 True 560.000000 560 75.730000 1348 2526 1 chr7D.!!$R1 1178
12 TraesCS4A01G068400 chr6A 525029734 525030561 827 True 318.000000 318 74.148000 1675 2511 1 chr6A.!!$R1 836
13 TraesCS4A01G068400 chr6D 383226854 383227681 827 True 302.000000 302 73.796000 1675 2511 1 chr6D.!!$R1 836

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
858 955 0.310854 GAGGCCACAAGTTTGTTCCG 59.689 55.0 5.01 0.0 39.91 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2857 3155 0.034616 GCCGGAGCAGCAATCTATCT 59.965 55.0 5.05 0.0 39.53 1.98 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
118 130 3.670377 GCCCAACCAACACGAGCC 61.670 66.667 0.00 0.00 0.00 4.70
124 136 1.264288 CAACCAACACGAGCCTCTTTC 59.736 52.381 0.00 0.00 0.00 2.62
137 149 4.445545 CTTTCCTTCGCGGCGCAC 62.446 66.667 32.61 3.11 0.00 5.34
152 164 1.007849 GCACGCGGATGTGGTTTTT 60.008 52.632 12.47 0.00 40.26 1.94
225 237 2.099431 CGAGCAGAGAGGCAACAGC 61.099 63.158 0.00 0.00 41.41 4.40
278 302 3.257561 CCGTTGGATCGCTCGCTG 61.258 66.667 0.00 0.00 0.00 5.18
279 303 3.257561 CGTTGGATCGCTCGCTGG 61.258 66.667 0.00 0.00 0.00 4.85
448 488 1.351153 CCGTCTCTTTCTTTCTCCGC 58.649 55.000 0.00 0.00 0.00 5.54
528 578 3.068064 TCCATGAGCACCGCGAGA 61.068 61.111 8.23 0.00 0.00 4.04
555 605 6.849305 GTCGTAACAGTAACACTTTTGGATTG 59.151 38.462 0.00 0.00 0.00 2.67
586 636 1.307097 GGTCGATACGTACAGCTCCT 58.693 55.000 0.00 0.00 0.00 3.69
587 637 1.263752 GGTCGATACGTACAGCTCCTC 59.736 57.143 0.00 0.00 0.00 3.71
588 638 1.263752 GTCGATACGTACAGCTCCTCC 59.736 57.143 0.00 0.00 0.00 4.30
589 639 1.140452 TCGATACGTACAGCTCCTCCT 59.860 52.381 0.00 0.00 0.00 3.69
590 640 1.264557 CGATACGTACAGCTCCTCCTG 59.735 57.143 0.00 0.00 38.78 3.86
591 641 2.299521 GATACGTACAGCTCCTCCTGT 58.700 52.381 0.00 0.23 46.98 4.00
592 642 3.474600 GATACGTACAGCTCCTCCTGTA 58.525 50.000 0.00 0.00 43.86 2.74
606 656 1.726853 CCTGTACAGGTAGCAAGTGC 58.273 55.000 30.57 0.00 43.61 4.40
627 677 2.401351 GTCGTCACTTGGAGTTGTACC 58.599 52.381 0.00 0.00 0.00 3.34
698 757 4.778143 GTGCAGGTACAGGCCGGG 62.778 72.222 8.08 1.20 0.00 5.73
717 780 1.069378 GCTGTAGTCGTGGCACGTAC 61.069 60.000 35.65 29.76 43.14 3.67
720 783 2.150390 TGTAGTCGTGGCACGTACTAA 58.850 47.619 33.03 25.10 43.14 2.24
732 829 0.846387 CGTACTAAGCGCGCGTTTTG 60.846 55.000 35.40 32.97 0.00 2.44
858 955 0.310854 GAGGCCACAAGTTTGTTCCG 59.689 55.000 5.01 0.00 39.91 4.30
938 1035 3.423154 CCAACTCACGCTTCCGGC 61.423 66.667 0.00 0.00 39.22 6.13
973 1070 1.238439 CAACTCACACCAAAGGCGAT 58.762 50.000 0.00 0.00 0.00 4.58
974 1071 1.197721 CAACTCACACCAAAGGCGATC 59.802 52.381 0.00 0.00 0.00 3.69
975 1072 0.670546 ACTCACACCAAAGGCGATCG 60.671 55.000 11.69 11.69 0.00 3.69
976 1073 0.389817 CTCACACCAAAGGCGATCGA 60.390 55.000 21.57 0.00 0.00 3.59
978 1075 0.948623 CACACCAAAGGCGATCGACA 60.949 55.000 25.47 0.00 0.00 4.35
979 1076 0.949105 ACACCAAAGGCGATCGACAC 60.949 55.000 25.47 10.26 0.00 3.67
1059 1164 3.680786 CTCACGGCGGAGGTGACA 61.681 66.667 13.24 0.00 39.36 3.58
1140 1245 0.601046 TCATCATCAAGATCCGGCGC 60.601 55.000 0.00 0.00 33.72 6.53
1227 1332 2.722201 CCTCACGTCCTACCTGCCC 61.722 68.421 0.00 0.00 0.00 5.36
1849 1975 4.278513 TCCAGGCCAACCCCAACG 62.279 66.667 5.01 0.00 36.11 4.10
2271 2397 3.006728 ATCCCCAACTTCCGGCGA 61.007 61.111 9.30 0.00 0.00 5.54
2626 2773 1.218316 CCCAAGGCCTACGTCTGAC 59.782 63.158 5.16 0.00 0.00 3.51
2630 2777 1.674441 CAAGGCCTACGTCTGACGATA 59.326 52.381 33.99 20.58 46.05 2.92
2631 2778 1.307097 AGGCCTACGTCTGACGATAC 58.693 55.000 33.99 19.49 46.05 2.24
2632 2779 1.019673 GGCCTACGTCTGACGATACA 58.980 55.000 33.99 15.60 46.05 2.29
2634 2781 2.034305 GGCCTACGTCTGACGATACATT 59.966 50.000 33.99 14.74 46.05 2.71
2635 2782 3.251729 GGCCTACGTCTGACGATACATTA 59.748 47.826 33.99 15.07 46.05 1.90
2636 2783 4.217497 GCCTACGTCTGACGATACATTAC 58.783 47.826 33.99 12.26 46.05 1.89
2637 2784 4.024218 GCCTACGTCTGACGATACATTACT 60.024 45.833 33.99 12.62 46.05 2.24
2638 2785 5.178252 GCCTACGTCTGACGATACATTACTA 59.822 44.000 33.99 13.07 46.05 1.82
2639 2786 6.588552 CCTACGTCTGACGATACATTACTAC 58.411 44.000 33.99 0.00 46.05 2.73
2640 2787 5.075670 ACGTCTGACGATACATTACTACG 57.924 43.478 33.99 5.75 46.05 3.51
2641 2788 3.898946 CGTCTGACGATACATTACTACGC 59.101 47.826 24.86 0.00 46.05 4.42
2648 2795 2.682256 TACATTACTACGCCGCCGCC 62.682 60.000 0.00 0.00 38.22 6.13
2796 2989 8.373048 ACTTCAAGTGTGAATTATAAACGACA 57.627 30.769 0.00 0.00 42.85 4.35
2821 3014 8.433126 CAAATATATACGACGAGGTTTCATTCC 58.567 37.037 0.00 0.00 0.00 3.01
2825 3018 1.087501 GACGAGGTTTCATTCCAGCC 58.912 55.000 0.00 0.00 0.00 4.85
2839 3137 6.781943 TCATTCCAGCCATGATTGTATGATA 58.218 36.000 0.00 0.00 0.00 2.15
2846 3144 7.012421 CCAGCCATGATTGTATGATATGATCTG 59.988 40.741 0.00 0.00 0.00 2.90
2847 3145 7.553044 CAGCCATGATTGTATGATATGATCTGT 59.447 37.037 0.00 0.00 0.00 3.41
2849 3147 8.396390 GCCATGATTGTATGATATGATCTGTTC 58.604 37.037 0.00 0.00 0.00 3.18
2851 3149 9.668497 CATGATTGTATGATATGATCTGTTCCT 57.332 33.333 0.00 0.00 0.00 3.36
2852 3150 9.668497 ATGATTGTATGATATGATCTGTTCCTG 57.332 33.333 0.00 0.00 0.00 3.86
2853 3151 8.098912 TGATTGTATGATATGATCTGTTCCTGG 58.901 37.037 0.00 0.00 0.00 4.45
2854 3152 7.616528 TTGTATGATATGATCTGTTCCTGGA 57.383 36.000 0.00 0.00 0.00 3.86
2855 3153 7.803487 TGTATGATATGATCTGTTCCTGGAT 57.197 36.000 0.00 0.00 0.00 3.41
2856 3154 8.211030 TGTATGATATGATCTGTTCCTGGATT 57.789 34.615 0.00 0.00 0.00 3.01
2857 3155 9.325248 TGTATGATATGATCTGTTCCTGGATTA 57.675 33.333 0.00 0.00 0.00 1.75
2858 3156 9.814899 GTATGATATGATCTGTTCCTGGATTAG 57.185 37.037 0.00 0.00 0.00 1.73
2912 3220 3.069074 CGTCCGTAACGTATGGATTGA 57.931 47.619 6.61 0.00 45.10 2.57
2921 3229 1.217882 GTATGGATTGAGTTCGCGGG 58.782 55.000 6.13 0.00 0.00 6.13
2952 3260 2.190161 GAACCTTCCAAAACGTTGTGC 58.810 47.619 13.26 0.00 32.40 4.57
2958 3266 2.103340 AAAACGTTGTGCCACGGC 59.897 55.556 0.00 0.00 44.82 5.68
2991 3299 1.592400 GCTAACGGCCTTGGTTTCCC 61.592 60.000 0.00 0.00 34.27 3.97
3016 3324 2.565834 CCCTCGGTTCAGTTTCTTCCTA 59.434 50.000 0.00 0.00 0.00 2.94
3017 3325 3.586892 CCTCGGTTCAGTTTCTTCCTAC 58.413 50.000 0.00 0.00 0.00 3.18
3098 3410 2.248280 TGCTCATTGGTGTAACGTGT 57.752 45.000 0.00 0.00 38.12 4.49
3104 3419 5.465532 TCATTGGTGTAACGTGTAAGGTA 57.534 39.130 0.00 0.00 38.12 3.08
3105 3420 5.472148 TCATTGGTGTAACGTGTAAGGTAG 58.528 41.667 0.00 0.00 38.12 3.18
3106 3421 4.935352 TTGGTGTAACGTGTAAGGTAGT 57.065 40.909 0.00 0.00 38.12 2.73
3107 3422 6.208402 TCATTGGTGTAACGTGTAAGGTAGTA 59.792 38.462 0.00 0.00 38.12 1.82
3108 3423 6.588719 TTGGTGTAACGTGTAAGGTAGTAT 57.411 37.500 0.00 0.00 38.12 2.12
3109 3424 7.695480 TTGGTGTAACGTGTAAGGTAGTATA 57.305 36.000 0.00 0.00 38.12 1.47
3110 3425 7.320443 TGGTGTAACGTGTAAGGTAGTATAG 57.680 40.000 0.00 0.00 38.12 1.31
3111 3426 6.183360 TGGTGTAACGTGTAAGGTAGTATAGC 60.183 42.308 0.00 0.00 38.12 2.97
3129 3444 7.724287 AGTATAGCATATGATGATGAGCGATT 58.276 34.615 6.97 0.00 0.00 3.34
3159 3474 2.728839 CTGTTTGAGCACGACTTCTCTC 59.271 50.000 0.00 0.00 0.00 3.20
3176 3491 2.203567 CTGGCCCCCGTGGAAAAA 60.204 61.111 0.00 0.00 35.39 1.94
3177 3492 1.609210 CTGGCCCCCGTGGAAAAAT 60.609 57.895 0.00 0.00 35.39 1.82
3178 3493 0.323908 CTGGCCCCCGTGGAAAAATA 60.324 55.000 0.00 0.00 35.39 1.40
3179 3494 0.323908 TGGCCCCCGTGGAAAAATAG 60.324 55.000 0.00 0.00 35.39 1.73
3180 3495 1.672854 GGCCCCCGTGGAAAAATAGC 61.673 60.000 0.00 0.00 35.39 2.97
3270 3585 1.126846 GCAGTTGAAGGTCGTTCATCG 59.873 52.381 8.70 6.39 44.89 3.84
3353 3668 5.582269 TGACTTTCTGCATTCATAGCTGTAC 59.418 40.000 0.00 0.00 33.36 2.90
3384 3701 1.412387 AAACTCGAAAGCGTACGGTC 58.588 50.000 21.59 8.28 38.98 4.79
3406 3723 5.821995 GTCTACTCCTACTCTGATTTACGGT 59.178 44.000 0.00 0.00 0.00 4.83
3408 3725 7.661027 GTCTACTCCTACTCTGATTTACGGTAT 59.339 40.741 0.00 0.00 0.00 2.73
3412 3729 7.980099 ACTCCTACTCTGATTTACGGTATTTTG 59.020 37.037 0.00 0.00 0.00 2.44
3413 3730 7.844009 TCCTACTCTGATTTACGGTATTTTGT 58.156 34.615 0.00 0.00 0.00 2.83
3477 3796 1.603802 CACGATGGTGCAAAGAACACT 59.396 47.619 0.00 0.00 37.35 3.55
3479 3798 2.806244 ACGATGGTGCAAAGAACACTAC 59.194 45.455 0.00 0.00 38.14 2.73
3522 3841 5.368145 CATGTATGTACACCACCTAGCAAT 58.632 41.667 0.00 0.00 39.30 3.56
3524 3843 4.468153 TGTATGTACACCACCTAGCAATGA 59.532 41.667 0.00 0.00 0.00 2.57
3530 3849 3.519510 ACACCACCTAGCAATGAGTACAT 59.480 43.478 0.00 0.00 38.50 2.29
3555 3874 2.591715 AGCAAGCCAAAGACGCGT 60.592 55.556 13.85 13.85 0.00 6.01
3557 3876 2.170985 CAAGCCAAAGACGCGTCG 59.829 61.111 31.56 19.27 34.09 5.12
3558 3877 2.028484 AAGCCAAAGACGCGTCGA 59.972 55.556 31.56 0.00 34.09 4.20
3579 3898 4.687948 CGATGTCATCGCTCATTCCTTATT 59.312 41.667 21.42 0.00 46.55 1.40
3580 3899 5.389202 CGATGTCATCGCTCATTCCTTATTG 60.389 44.000 21.42 0.00 46.55 1.90
3581 3900 4.129380 TGTCATCGCTCATTCCTTATTGG 58.871 43.478 0.00 0.00 37.10 3.16
3594 3913 1.743394 CTTATTGGAGCCGGACAAACC 59.257 52.381 5.05 0.18 0.00 3.27
3602 3921 0.458260 GCCGGACAAACCTTGTTGTT 59.542 50.000 5.05 0.00 45.52 2.83
3615 3934 3.736252 CCTTGTTGTTGTAGACAGTCGAG 59.264 47.826 0.00 0.00 39.94 4.04
3616 3935 4.499188 CCTTGTTGTTGTAGACAGTCGAGA 60.499 45.833 0.00 0.00 39.94 4.04
3617 3936 3.961182 TGTTGTTGTAGACAGTCGAGAC 58.039 45.455 0.00 0.00 39.94 3.36
3618 3937 2.963498 TGTTGTAGACAGTCGAGACG 57.037 50.000 0.00 0.00 36.20 4.18
3619 3938 2.216046 TGTTGTAGACAGTCGAGACGT 58.784 47.619 0.00 0.00 36.20 4.34
3620 3939 2.032290 TGTTGTAGACAGTCGAGACGTG 60.032 50.000 0.00 4.12 36.20 4.49
3621 3940 0.516001 TGTAGACAGTCGAGACGTGC 59.484 55.000 0.00 0.00 36.20 5.34
3622 3941 0.516001 GTAGACAGTCGAGACGTGCA 59.484 55.000 0.00 0.00 36.20 4.57
3623 3942 0.516001 TAGACAGTCGAGACGTGCAC 59.484 55.000 6.82 6.82 36.20 4.57
3624 3943 1.008881 GACAGTCGAGACGTGCACA 60.009 57.895 18.64 0.00 36.20 4.57
3625 3944 0.999228 GACAGTCGAGACGTGCACAG 60.999 60.000 18.64 12.16 36.20 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 130 3.854459 GCGCCGCGAAGGAAAGAG 61.854 66.667 18.91 0.00 45.00 2.85
137 149 6.692232 TTTAATTTAAAAACCACATCCGCG 57.308 33.333 0.00 0.00 0.00 6.46
152 164 9.802039 TGACCTAGCTTTCTCCTTTTTAATTTA 57.198 29.630 0.00 0.00 0.00 1.40
213 225 3.482783 GACGCGCTGTTGCCTCTC 61.483 66.667 5.73 0.00 35.36 3.20
471 521 3.991536 GAAGAGGCGTCCGTCAGGC 62.992 68.421 2.06 0.00 37.47 4.85
521 571 1.862147 CTGTTACGACGTCTCGCGG 60.862 63.158 14.70 0.00 44.33 6.46
528 578 4.268405 CCAAAAGTGTTACTGTTACGACGT 59.732 41.667 5.52 5.52 0.00 4.34
555 605 3.294943 CGTATCGACCACGTCTAATTCC 58.705 50.000 12.06 0.00 40.69 3.01
586 636 1.275291 GCACTTGCTACCTGTACAGGA 59.725 52.381 41.87 25.85 43.89 3.86
587 637 1.726853 GCACTTGCTACCTGTACAGG 58.273 55.000 35.54 35.54 45.36 4.00
588 638 1.336887 ACGCACTTGCTACCTGTACAG 60.337 52.381 16.34 16.34 39.32 2.74
589 639 0.677288 ACGCACTTGCTACCTGTACA 59.323 50.000 0.00 0.00 39.32 2.90
590 640 1.347320 GACGCACTTGCTACCTGTAC 58.653 55.000 0.00 0.00 39.32 2.90
591 641 0.109458 CGACGCACTTGCTACCTGTA 60.109 55.000 0.00 0.00 39.32 2.74
592 642 1.372997 CGACGCACTTGCTACCTGT 60.373 57.895 0.00 0.00 39.32 4.00
593 643 1.344942 GACGACGCACTTGCTACCTG 61.345 60.000 0.00 0.00 39.32 4.00
594 644 1.080705 GACGACGCACTTGCTACCT 60.081 57.895 0.00 0.00 39.32 3.08
595 645 1.372499 TGACGACGCACTTGCTACC 60.372 57.895 0.00 0.00 39.32 3.18
596 646 0.663568 AGTGACGACGCACTTGCTAC 60.664 55.000 15.94 0.00 46.42 3.58
597 647 1.658114 AGTGACGACGCACTTGCTA 59.342 52.632 15.94 0.00 46.42 3.49
598 648 2.417516 AGTGACGACGCACTTGCT 59.582 55.556 15.94 0.00 46.42 3.91
603 653 0.874607 AACTCCAAGTGACGACGCAC 60.875 55.000 12.53 12.53 39.05 5.34
604 654 0.874175 CAACTCCAAGTGACGACGCA 60.874 55.000 0.62 0.00 0.00 5.24
605 655 0.874607 ACAACTCCAAGTGACGACGC 60.875 55.000 0.00 0.00 0.00 5.19
606 656 2.049228 GTACAACTCCAAGTGACGACG 58.951 52.381 0.00 0.00 0.00 5.12
644 703 5.962433 TCTTCTGATGAAAACTACCCGTAG 58.038 41.667 0.22 0.22 39.04 3.51
677 736 2.045926 GCCTGTACCTGCACCCAG 60.046 66.667 0.00 0.00 38.85 4.45
698 757 1.069378 GTACGTGCCACGACTACAGC 61.069 60.000 25.94 1.82 46.05 4.40
717 780 2.869702 GGCAAAACGCGCGCTTAG 60.870 61.111 32.58 18.88 43.84 2.18
797 894 0.463116 CTTATAGGCGCCCAAACCGT 60.463 55.000 26.15 4.77 0.00 4.83
973 1070 1.949015 GAGACGTACTCGCGTGTCGA 61.949 60.000 27.03 9.28 45.79 4.20
974 1071 1.577117 GAGACGTACTCGCGTGTCG 60.577 63.158 18.12 20.69 45.79 4.35
975 1072 4.339565 GAGACGTACTCGCGTGTC 57.660 61.111 18.12 12.63 45.79 3.67
982 1079 2.224549 CCATGGATCTCGAGACGTACTC 59.775 54.545 19.30 10.92 41.79 2.59
983 1080 2.158798 TCCATGGATCTCGAGACGTACT 60.159 50.000 19.30 0.06 0.00 2.73
1115 1220 2.742589 CGGATCTTGATGATGATGCTGG 59.257 50.000 0.00 0.00 35.14 4.85
1116 1221 2.742589 CCGGATCTTGATGATGATGCTG 59.257 50.000 0.00 0.00 35.14 4.41
1117 1222 2.874861 GCCGGATCTTGATGATGATGCT 60.875 50.000 5.05 0.00 35.14 3.79
1344 1449 3.760537 CTTGAAGTAGTAGACGGTGAGC 58.239 50.000 0.00 0.00 0.00 4.26
1860 1986 1.444553 GTTCTCGGTGCTGAGGACG 60.445 63.158 8.04 0.00 34.89 4.79
2616 2763 6.287679 CGTAGTAATGTATCGTCAGACGTAG 58.712 44.000 22.16 0.00 43.14 3.51
2626 2773 1.334054 GGCGGCGTAGTAATGTATCG 58.666 55.000 9.37 0.00 0.00 2.92
2630 2777 2.584143 GCGGCGGCGTAGTAATGT 60.584 61.111 32.35 0.00 0.00 2.71
2631 2778 3.335534 GGCGGCGGCGTAGTAATG 61.336 66.667 32.35 2.19 41.24 1.90
2632 2779 4.936823 CGGCGGCGGCGTAGTAAT 62.937 66.667 41.70 0.00 46.33 1.89
2648 2795 0.388520 TCTTCGTGTGGAGTCATGCG 60.389 55.000 0.00 0.00 0.00 4.73
2658 2805 8.446273 AGAAAAGAATCATGTAATCTTCGTGTG 58.554 33.333 9.64 0.00 32.45 3.82
2727 2920 1.153289 CTCGCCCATGGAACCTGAG 60.153 63.158 15.22 8.65 0.00 3.35
2753 2946 7.328493 ACTTGAAGTACAAAAGCTGAAAACAAC 59.672 33.333 0.00 0.00 38.08 3.32
2796 2989 8.145767 TGGAATGAAACCTCGTCGTATATATTT 58.854 33.333 0.00 0.00 0.00 1.40
2821 3014 7.553044 ACAGATCATATCATACAATCATGGCTG 59.447 37.037 0.00 0.00 0.00 4.85
2825 3018 9.668497 AGGAACAGATCATATCATACAATCATG 57.332 33.333 0.00 0.00 0.00 3.07
2839 3137 8.914213 ATCTATCTAATCCAGGAACAGATCAT 57.086 34.615 16.15 9.43 0.00 2.45
2846 3144 5.411053 GCAGCAATCTATCTAATCCAGGAAC 59.589 44.000 0.00 0.00 0.00 3.62
2847 3145 5.309020 AGCAGCAATCTATCTAATCCAGGAA 59.691 40.000 0.00 0.00 0.00 3.36
2849 3147 5.163281 AGCAGCAATCTATCTAATCCAGG 57.837 43.478 0.00 0.00 0.00 4.45
2851 3149 4.322273 CGGAGCAGCAATCTATCTAATCCA 60.322 45.833 0.00 0.00 0.00 3.41
2852 3150 4.180057 CGGAGCAGCAATCTATCTAATCC 58.820 47.826 0.00 0.00 0.00 3.01
2853 3151 4.180057 CCGGAGCAGCAATCTATCTAATC 58.820 47.826 0.00 0.00 0.00 1.75
2854 3152 3.618507 GCCGGAGCAGCAATCTATCTAAT 60.619 47.826 5.05 0.00 39.53 1.73
2855 3153 2.289072 GCCGGAGCAGCAATCTATCTAA 60.289 50.000 5.05 0.00 39.53 2.10
2856 3154 1.273606 GCCGGAGCAGCAATCTATCTA 59.726 52.381 5.05 0.00 39.53 1.98
2857 3155 0.034616 GCCGGAGCAGCAATCTATCT 59.965 55.000 5.05 0.00 39.53 1.98
2858 3156 1.287730 CGCCGGAGCAGCAATCTATC 61.288 60.000 5.05 0.00 39.83 2.08
2921 3229 1.578206 GGAAGGTTCAAGTGGCGAGC 61.578 60.000 0.00 0.00 0.00 5.03
2926 3234 2.425668 ACGTTTTGGAAGGTTCAAGTGG 59.574 45.455 0.00 0.00 30.13 4.00
2930 3238 3.839293 CACAACGTTTTGGAAGGTTCAA 58.161 40.909 6.54 0.00 40.71 2.69
2934 3242 0.458260 GGCACAACGTTTTGGAAGGT 59.542 50.000 15.71 0.00 37.00 3.50
2952 3260 1.216710 GACCAGAAGAGAGCCGTGG 59.783 63.158 0.00 0.00 0.00 4.94
2958 3266 1.202200 CGTTAGCCGACCAGAAGAGAG 60.202 57.143 0.00 0.00 39.56 3.20
2991 3299 0.955919 GAAACTGAACCGAGGGCCAG 60.956 60.000 6.18 0.00 34.41 4.85
3016 3324 0.969149 TGGTCAGCTCGTTCAGATGT 59.031 50.000 0.00 0.00 39.74 3.06
3017 3325 1.354040 GTGGTCAGCTCGTTCAGATG 58.646 55.000 0.00 0.00 40.18 2.90
3053 3361 3.704381 CGAGACTCTTCCTCGGTTG 57.296 57.895 0.03 0.00 46.85 3.77
3104 3419 6.705863 TCGCTCATCATCATATGCTATACT 57.294 37.500 0.00 0.00 0.00 2.12
3105 3420 7.943413 AATCGCTCATCATCATATGCTATAC 57.057 36.000 0.00 0.00 0.00 1.47
3106 3421 8.854117 AGTAATCGCTCATCATCATATGCTATA 58.146 33.333 0.00 0.00 0.00 1.31
3107 3422 7.724287 AGTAATCGCTCATCATCATATGCTAT 58.276 34.615 0.00 0.00 0.00 2.97
3108 3423 7.105241 AGTAATCGCTCATCATCATATGCTA 57.895 36.000 0.00 0.00 0.00 3.49
3109 3424 5.975282 AGTAATCGCTCATCATCATATGCT 58.025 37.500 0.00 0.00 0.00 3.79
3110 3425 6.456584 CCAAGTAATCGCTCATCATCATATGC 60.457 42.308 0.00 0.00 0.00 3.14
3111 3426 6.036844 CCCAAGTAATCGCTCATCATCATATG 59.963 42.308 0.00 0.00 0.00 1.78
3129 3444 2.805295 CGTGCTCAAACAGACCCAAGTA 60.805 50.000 0.00 0.00 0.00 2.24
3159 3474 0.323908 TATTTTTCCACGGGGGCCAG 60.324 55.000 2.42 0.22 36.21 4.85
3176 3491 1.344953 TGCCCCGAACTGGATGCTAT 61.345 55.000 0.00 0.00 42.00 2.97
3177 3492 1.344953 ATGCCCCGAACTGGATGCTA 61.345 55.000 0.00 0.00 42.00 3.49
3178 3493 2.683465 ATGCCCCGAACTGGATGCT 61.683 57.895 0.00 0.00 42.00 3.79
3179 3494 2.124151 ATGCCCCGAACTGGATGC 60.124 61.111 0.00 0.00 42.00 3.91
3180 3495 2.484062 GCATGCCCCGAACTGGATG 61.484 63.158 6.36 0.00 42.00 3.51
3353 3668 4.792125 GAGTTTTCGACCGTTGCG 57.208 55.556 0.00 0.00 0.00 4.85
3384 3701 7.982761 ATACCGTAAATCAGAGTAGGAGTAG 57.017 40.000 0.00 0.00 0.00 2.57
3416 3733 9.986833 GTTTGCAAACTTTTGACAAAGATAATT 57.013 25.926 30.49 0.00 41.97 1.40
3418 3735 8.770438 AGTTTGCAAACTTTTGACAAAGATAA 57.230 26.923 33.85 0.00 46.52 1.75
3422 3741 8.655092 TGAATAGTTTGCAAACTTTTGACAAAG 58.345 29.630 40.87 0.00 46.52 2.77
3441 3760 8.721478 GCACCATCGTGATATTTTATGAATAGT 58.279 33.333 0.00 0.00 43.14 2.12
3450 3769 5.895636 TCTTTGCACCATCGTGATATTTT 57.104 34.783 0.00 0.00 43.14 1.82
3462 3781 3.616219 ACTTGTAGTGTTCTTTGCACCA 58.384 40.909 0.00 0.00 37.56 4.17
3499 3818 4.400529 TGCTAGGTGGTGTACATACATG 57.599 45.455 0.00 0.00 38.63 3.21
3502 3821 5.018539 TCATTGCTAGGTGGTGTACATAC 57.981 43.478 0.00 1.52 0.00 2.39
3509 3828 3.610040 TGTACTCATTGCTAGGTGGTG 57.390 47.619 0.00 0.00 0.00 4.17
3511 3830 2.874701 GCATGTACTCATTGCTAGGTGG 59.125 50.000 0.00 0.00 31.15 4.61
3522 3841 3.677148 GCTTGCTCTAGTGCATGTACTCA 60.677 47.826 20.38 9.22 42.96 3.41
3524 3843 2.419297 GGCTTGCTCTAGTGCATGTACT 60.419 50.000 24.79 20.58 42.96 2.73
3530 3849 1.072173 TCTTTGGCTTGCTCTAGTGCA 59.928 47.619 15.24 15.24 41.65 4.57
3557 3876 5.106791 CCAATAAGGAATGAGCGATGACATC 60.107 44.000 5.28 5.28 41.22 3.06
3558 3877 4.758674 CCAATAAGGAATGAGCGATGACAT 59.241 41.667 0.00 0.00 41.22 3.06
3573 3892 1.743394 GTTTGTCCGGCTCCAATAAGG 59.257 52.381 0.00 0.00 39.47 2.69
3579 3898 1.228124 CAAGGTTTGTCCGGCTCCA 60.228 57.895 0.00 0.00 41.99 3.86
3580 3899 0.822121 AACAAGGTTTGTCCGGCTCC 60.822 55.000 0.00 0.00 44.59 4.70
3581 3900 0.310854 CAACAAGGTTTGTCCGGCTC 59.689 55.000 0.00 0.00 44.59 4.70
3584 3903 1.474879 ACAACAACAAGGTTTGTCCGG 59.525 47.619 0.00 0.00 44.59 5.14
3594 3913 4.441415 GTCTCGACTGTCTACAACAACAAG 59.559 45.833 6.21 0.00 37.45 3.16
3602 3921 0.516001 GCACGTCTCGACTGTCTACA 59.484 55.000 6.21 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.