Multiple sequence alignment - TraesCS4B01G202300

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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 TraesCS4B01G202300 chr4B 100.000 3735 0 0 1 3735 433179933 433176199 0.000000e+00 6898
1 TraesCS4B01G202300 chr4D 95.575 2915 77 24 4 2888 349913339 349910447 0.000000e+00 4621
2 TraesCS4B01G202300 chr4D 86.800 250 26 4 2870 3118 349910436 349910193 4.750000e-69 272
3 TraesCS4B01G202300 chr4A 94.243 2901 104 27 6 2873 114789808 114792678 0.000000e+00 4373
4 TraesCS4B01G202300 chr4A 85.279 591 81 6 3041 3626 578106736 578106147 4.130000e-169 604
5 TraesCS4B01G202300 chr5B 84.480 567 82 6 3064 3626 375795862 375796426 4.210000e-154 555
6 TraesCS4B01G202300 chr5D 83.701 589 90 6 3042 3625 295079756 295080343 5.450000e-153 551
7 TraesCS4B01G202300 chr3B 84.035 570 78 12 3064 3625 410612496 410613060 1.530000e-148 536
8 TraesCS4B01G202300 chr7A 82.594 586 90 7 3042 3622 143185298 143185876 1.200000e-139 507
9 TraesCS4B01G202300 chr2D 82.777 569 90 8 3064 3626 474995226 474994660 5.570000e-138 501
10 TraesCS4B01G202300 chr2D 82.601 569 91 8 3064 3626 474989553 474988987 2.590000e-136 496
11 TraesCS4B01G202300 chr1D 81.976 577 93 9 3045 3614 413945159 413944587 2.610000e-131 479
12 TraesCS4B01G202300 chr1B 82.024 573 90 9 3064 3626 604833251 604833820 3.380000e-130 475


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 TraesCS4B01G202300 chr4B 433176199 433179933 3734 True 6898.0 6898 100.0000 1 3735 1 chr4B.!!$R1 3734
1 TraesCS4B01G202300 chr4D 349910193 349913339 3146 True 2446.5 4621 91.1875 4 3118 2 chr4D.!!$R1 3114
2 TraesCS4B01G202300 chr4A 114789808 114792678 2870 False 4373.0 4373 94.2430 6 2873 1 chr4A.!!$F1 2867
3 TraesCS4B01G202300 chr4A 578106147 578106736 589 True 604.0 604 85.2790 3041 3626 1 chr4A.!!$R1 585
4 TraesCS4B01G202300 chr5B 375795862 375796426 564 False 555.0 555 84.4800 3064 3626 1 chr5B.!!$F1 562
5 TraesCS4B01G202300 chr5D 295079756 295080343 587 False 551.0 551 83.7010 3042 3625 1 chr5D.!!$F1 583
6 TraesCS4B01G202300 chr3B 410612496 410613060 564 False 536.0 536 84.0350 3064 3625 1 chr3B.!!$F1 561
7 TraesCS4B01G202300 chr7A 143185298 143185876 578 False 507.0 507 82.5940 3042 3622 1 chr7A.!!$F1 580
8 TraesCS4B01G202300 chr2D 474994660 474995226 566 True 501.0 501 82.7770 3064 3626 1 chr2D.!!$R2 562
9 TraesCS4B01G202300 chr2D 474988987 474989553 566 True 496.0 496 82.6010 3064 3626 1 chr2D.!!$R1 562
10 TraesCS4B01G202300 chr1D 413944587 413945159 572 True 479.0 479 81.9760 3045 3614 1 chr1D.!!$R1 569
11 TraesCS4B01G202300 chr1B 604833251 604833820 569 False 475.0 475 82.0240 3064 3626 1 chr1B.!!$F1 562

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
865 900 0.034477 GGGCGAAAAGGAATGGAGGA 60.034 55.0 0.0 0.0 0.0 3.71 F
1462 1521 0.108585 GTGCAGAGGTGGTGAAGGAA 59.891 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2226 0.687920 TGGTGGAGTTGATGGCGTTA 59.312 50.0 0.0 0.0 0.0 3.18 R
3412 3520 0.034756 CATCGTTGGAGGGTGTGTGA 59.965 55.0 0.0 0.0 0.0 3.58 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
74 78 7.420002 CAATTGCAGATTTTCTAATCGATCCA 58.580 34.615 0.00 0.00 43.99 3.41
77 81 4.754114 GCAGATTTTCTAATCGATCCAGCT 59.246 41.667 0.00 0.00 43.99 4.24
89 93 1.412343 GATCCAGCTCTTGTCTCCTCC 59.588 57.143 0.00 0.00 0.00 4.30
121 125 0.665670 CGTATCATCCGCTCTGCCTG 60.666 60.000 0.00 0.00 0.00 4.85
196 205 1.226974 CTCCTCACGCCGGTATGTG 60.227 63.158 14.89 14.89 37.44 3.21
237 246 3.630148 GCACGTCCGCCGATCATG 61.630 66.667 0.00 0.00 40.70 3.07
256 265 1.378382 TCATGTGTGCCCCAATCCG 60.378 57.895 0.00 0.00 0.00 4.18
262 276 3.498071 TGCCCCAATCCGATCCCC 61.498 66.667 0.00 0.00 0.00 4.81
263 277 4.643387 GCCCCAATCCGATCCCCG 62.643 72.222 0.00 0.00 38.18 5.73
264 278 3.168528 CCCCAATCCGATCCCCGT 61.169 66.667 0.00 0.00 36.31 5.28
265 279 2.752807 CCCCAATCCGATCCCCGTT 61.753 63.158 0.00 0.00 36.31 4.44
316 330 6.495872 AGGGGTTCTACTATATTGTAATGCGA 59.504 38.462 0.00 0.00 0.00 5.10
406 420 2.474359 CGCTCATCGCCTCTTCTTTATG 59.526 50.000 0.00 0.00 34.21 1.90
409 423 2.170397 TCATCGCCTCTTCTTTATGGCA 59.830 45.455 0.00 0.00 45.13 4.92
418 432 5.047802 CCTCTTCTTTATGGCAAAAGCTTGA 60.048 40.000 0.00 11.01 36.58 3.02
531 545 3.182182 GGCATTGCGATCTTCCTTTTTC 58.818 45.455 1.91 0.00 0.00 2.29
532 546 3.119352 GGCATTGCGATCTTCCTTTTTCT 60.119 43.478 1.91 0.00 0.00 2.52
533 547 4.101235 GCATTGCGATCTTCCTTTTTCTC 58.899 43.478 0.00 0.00 0.00 2.87
534 548 4.142513 GCATTGCGATCTTCCTTTTTCTCT 60.143 41.667 0.00 0.00 0.00 3.10
535 549 5.065218 GCATTGCGATCTTCCTTTTTCTCTA 59.935 40.000 0.00 0.00 0.00 2.43
536 550 6.713520 CATTGCGATCTTCCTTTTTCTCTAG 58.286 40.000 0.00 0.00 0.00 2.43
537 551 5.661056 TGCGATCTTCCTTTTTCTCTAGA 57.339 39.130 0.00 0.00 0.00 2.43
545 559 8.343168 TCTTCCTTTTTCTCTAGACTGTAGAG 57.657 38.462 4.17 4.17 41.72 2.43
616 630 8.355913 TGTGTATGTGAGCAAATTAAATTGACA 58.644 29.630 7.46 3.48 31.84 3.58
617 631 9.190858 GTGTATGTGAGCAAATTAAATTGACAA 57.809 29.630 7.46 0.00 31.84 3.18
707 724 6.707440 TTGGTTCATACTTGCTTTTCTTCA 57.293 33.333 0.00 0.00 0.00 3.02
720 737 4.024048 GCTTTTCTTCACCATCGACTTTCA 60.024 41.667 0.00 0.00 0.00 2.69
724 741 3.926527 TCTTCACCATCGACTTTCATTCG 59.073 43.478 0.00 0.00 37.85 3.34
747 764 5.241662 GTGTCTATCTCTTTTGCTGTTCCT 58.758 41.667 0.00 0.00 0.00 3.36
749 766 6.205658 GTGTCTATCTCTTTTGCTGTTCCTTT 59.794 38.462 0.00 0.00 0.00 3.11
750 767 6.772716 TGTCTATCTCTTTTGCTGTTCCTTTT 59.227 34.615 0.00 0.00 0.00 2.27
759 787 4.835284 TGCTGTTCCTTTTTCCCTTTTT 57.165 36.364 0.00 0.00 0.00 1.94
760 788 4.765273 TGCTGTTCCTTTTTCCCTTTTTC 58.235 39.130 0.00 0.00 0.00 2.29
765 793 7.255977 GCTGTTCCTTTTTCCCTTTTTCTAGAT 60.256 37.037 0.00 0.00 0.00 1.98
813 848 2.224209 GGTGGGAATGATAGGGTACGTG 60.224 54.545 0.00 0.00 0.00 4.49
822 857 4.761975 TGATAGGGTACGTGATTTGGAAC 58.238 43.478 0.00 0.00 0.00 3.62
838 873 4.715534 TGGAACTTGGTAGGTGAATTCA 57.284 40.909 3.38 3.38 0.00 2.57
865 900 0.034477 GGGCGAAAAGGAATGGAGGA 60.034 55.000 0.00 0.00 0.00 3.71
890 929 0.807667 ACGACGAATGGCTGCTGATC 60.808 55.000 0.00 0.00 0.00 2.92
905 947 2.748605 CTGATCGTGTTATGGCCTCTC 58.251 52.381 3.32 0.00 0.00 3.20
913 955 2.435805 TGTTATGGCCTCTCATGGACTC 59.564 50.000 3.32 0.00 35.73 3.36
916 958 2.550277 TGGCCTCTCATGGACTCTTA 57.450 50.000 3.32 0.00 35.73 2.10
1239 1285 4.778143 GGCTACGTGGCCCTGGTG 62.778 72.222 30.99 0.00 45.92 4.17
1370 1416 2.170187 TCTACGTCTAGTCCCCTCTCAC 59.830 54.545 0.00 0.00 0.00 3.51
1393 1445 3.756677 CACTCTCACACGCACGCG 61.757 66.667 10.36 10.36 46.03 6.01
1462 1521 0.108585 GTGCAGAGGTGGTGAAGGAA 59.891 55.000 0.00 0.00 0.00 3.36
1762 1821 1.870055 GCACCAACCTCGACCTCGTA 61.870 60.000 0.00 0.00 40.80 3.43
2167 2226 0.909610 TCCACGAGGAAGGGCTGAAT 60.910 55.000 0.00 0.00 42.23 2.57
2265 2324 2.050168 GTACGTGGACGCGGACAA 60.050 61.111 15.09 0.00 44.49 3.18
2506 2565 1.154599 GCTGTCGTTCGTCGTCGTA 60.155 57.895 1.33 0.00 40.80 3.43
2686 2745 2.283676 TCGGGGTCTGGACTGTCC 60.284 66.667 19.96 19.96 36.96 4.02
2742 2801 3.656559 TGTACGCCATCTGATCATGATG 58.343 45.455 14.30 19.85 40.51 3.07
2758 2817 2.456287 GATGATCCCCACGCCCTAGC 62.456 65.000 0.00 0.00 0.00 3.42
2778 2837 3.374058 AGCGCAACATTGATTACACTACC 59.626 43.478 11.47 0.00 0.00 3.18
2853 2912 5.105106 TGACATTTTTATCCGGTAGCTCAGA 60.105 40.000 0.00 0.00 0.00 3.27
2854 2913 5.741011 ACATTTTTATCCGGTAGCTCAGAA 58.259 37.500 0.00 0.00 0.00 3.02
2912 3001 4.759693 ACCGTTTGCTGAATGTTGATTAGA 59.240 37.500 0.00 0.00 0.00 2.10
2922 3011 3.773418 TGTTGATTAGAACGGGGAACA 57.227 42.857 0.00 0.00 0.00 3.18
2926 3015 2.907696 TGATTAGAACGGGGAACAGGAA 59.092 45.455 0.00 0.00 0.00 3.36
2928 3017 2.314071 TAGAACGGGGAACAGGAAGA 57.686 50.000 0.00 0.00 0.00 2.87
2950 3039 2.159226 AGTACAGTAGCAAGGATGTCGC 60.159 50.000 0.00 0.00 0.00 5.19
2955 3044 0.108186 TAGCAAGGATGTCGCCAGTG 60.108 55.000 0.00 0.00 0.00 3.66
3160 3254 3.491639 CGACGACAATAAACACTGGAACA 59.508 43.478 0.00 0.00 0.00 3.18
3192 3286 3.842923 CGCTGTCATCGCCCCTCT 61.843 66.667 0.00 0.00 0.00 3.69
3226 3326 4.202326 CCGGGCAAACCTTATGTAGTAGAT 60.202 45.833 0.00 0.00 36.97 1.98
3236 3336 9.710818 AACCTTATGTAGTAGATAGTCAGGAAA 57.289 33.333 9.46 0.00 0.00 3.13
3299 3401 3.120338 GCAACCATCGTCGATGAAGAAAA 60.120 43.478 31.82 0.00 42.09 2.29
3341 3449 4.457466 AGTCTGTAAACACCCAAACGAAT 58.543 39.130 0.00 0.00 0.00 3.34
3401 3509 0.962489 GATCCCACGAGATCCGACAT 59.038 55.000 10.05 0.00 41.76 3.06
3402 3510 0.676184 ATCCCACGAGATCCGACATG 59.324 55.000 10.05 0.00 41.76 3.21
3418 3526 2.948979 GACATGGACAAACCTTCACACA 59.051 45.455 0.00 0.00 39.86 3.72
3440 3548 0.872021 CTCCAACGATGCTAGACGCC 60.872 60.000 0.00 0.00 38.05 5.68
3441 3549 1.141881 CCAACGATGCTAGACGCCT 59.858 57.895 0.00 0.00 38.05 5.52
3442 3550 0.460284 CCAACGATGCTAGACGCCTT 60.460 55.000 0.00 0.00 38.05 4.35
3524 3633 2.672996 CCCCAACCAAGACGCTGG 60.673 66.667 0.00 0.00 42.68 4.85
3550 3659 4.664688 AACAAGAATGAGAATGGGGTCT 57.335 40.909 0.00 0.00 0.00 3.85
3578 3687 2.670148 GCGGGGAGGTGAGGTCATT 61.670 63.158 0.00 0.00 0.00 2.57
3581 3690 1.265454 GGGGAGGTGAGGTCATTCGT 61.265 60.000 0.00 0.00 0.00 3.85
3632 3741 4.460683 CGGACCGGCGGGAAATGA 62.461 66.667 31.78 0.00 36.97 2.57
3633 3742 2.045731 GGACCGGCGGGAAATGAA 60.046 61.111 31.78 0.00 36.97 2.57
3634 3743 1.453197 GGACCGGCGGGAAATGAAT 60.453 57.895 31.78 5.90 36.97 2.57
3635 3744 0.179040 GGACCGGCGGGAAATGAATA 60.179 55.000 31.78 0.00 36.97 1.75
3636 3745 1.226746 GACCGGCGGGAAATGAATAG 58.773 55.000 31.78 0.00 36.97 1.73
3637 3746 0.834612 ACCGGCGGGAAATGAATAGA 59.165 50.000 31.78 0.00 36.97 1.98
3638 3747 1.226746 CCGGCGGGAAATGAATAGAC 58.773 55.000 20.56 0.00 34.06 2.59
3639 3748 1.202651 CCGGCGGGAAATGAATAGACT 60.203 52.381 20.56 0.00 34.06 3.24
3640 3749 2.561569 CGGCGGGAAATGAATAGACTT 58.438 47.619 0.00 0.00 0.00 3.01
3641 3750 2.943033 CGGCGGGAAATGAATAGACTTT 59.057 45.455 0.00 0.00 0.00 2.66
3642 3751 3.377172 CGGCGGGAAATGAATAGACTTTT 59.623 43.478 0.00 0.00 0.00 2.27
3643 3752 4.672409 GGCGGGAAATGAATAGACTTTTG 58.328 43.478 0.00 0.00 0.00 2.44
3644 3753 4.398044 GGCGGGAAATGAATAGACTTTTGA 59.602 41.667 0.00 0.00 0.00 2.69
3645 3754 5.332707 GCGGGAAATGAATAGACTTTTGAC 58.667 41.667 0.00 0.00 0.00 3.18
3646 3755 5.123979 GCGGGAAATGAATAGACTTTTGACT 59.876 40.000 0.00 0.00 0.00 3.41
3647 3756 6.315393 GCGGGAAATGAATAGACTTTTGACTA 59.685 38.462 0.00 0.00 0.00 2.59
3648 3757 7.012421 GCGGGAAATGAATAGACTTTTGACTAT 59.988 37.037 0.00 0.00 38.63 2.12
3649 3758 9.542462 CGGGAAATGAATAGACTTTTGACTATA 57.458 33.333 0.00 0.00 36.64 1.31
3657 3766 9.425577 GAATAGACTTTTGACTATATGGGTAGC 57.574 37.037 0.00 0.00 36.64 3.58
3658 3767 8.728596 ATAGACTTTTGACTATATGGGTAGCT 57.271 34.615 0.00 0.00 36.07 3.32
3659 3768 6.821388 AGACTTTTGACTATATGGGTAGCTG 58.179 40.000 0.00 0.00 0.00 4.24
3660 3769 6.611642 AGACTTTTGACTATATGGGTAGCTGA 59.388 38.462 0.00 0.00 0.00 4.26
3661 3770 7.125811 AGACTTTTGACTATATGGGTAGCTGAA 59.874 37.037 0.00 0.00 0.00 3.02
3662 3771 7.806180 ACTTTTGACTATATGGGTAGCTGAAT 58.194 34.615 0.00 0.00 0.00 2.57
3663 3772 8.275040 ACTTTTGACTATATGGGTAGCTGAATT 58.725 33.333 0.00 0.00 0.00 2.17
3664 3773 9.125026 CTTTTGACTATATGGGTAGCTGAATTT 57.875 33.333 0.00 0.00 0.00 1.82
3665 3774 9.474313 TTTTGACTATATGGGTAGCTGAATTTT 57.526 29.630 0.00 0.00 0.00 1.82
3666 3775 8.450578 TTGACTATATGGGTAGCTGAATTTTG 57.549 34.615 0.00 0.00 0.00 2.44
3667 3776 7.573710 TGACTATATGGGTAGCTGAATTTTGT 58.426 34.615 0.00 0.00 0.00 2.83
3668 3777 8.710239 TGACTATATGGGTAGCTGAATTTTGTA 58.290 33.333 0.00 0.00 0.00 2.41
3669 3778 9.726438 GACTATATGGGTAGCTGAATTTTGTAT 57.274 33.333 0.00 0.00 0.00 2.29
3719 3828 9.376075 TGAAAATTGCTTTTTATTGACTTGTCA 57.624 25.926 0.00 0.00 37.65 3.58
3722 3831 8.891671 AATTGCTTTTTATTGACTTGTCATGT 57.108 26.923 4.18 0.19 0.00 3.21
3723 3832 9.979578 AATTGCTTTTTATTGACTTGTCATGTA 57.020 25.926 4.18 0.00 0.00 2.29
3724 3833 9.630098 ATTGCTTTTTATTGACTTGTCATGTAG 57.370 29.630 4.18 0.00 0.00 2.74
3725 3834 7.083858 TGCTTTTTATTGACTTGTCATGTAGC 58.916 34.615 4.18 8.42 0.00 3.58
3726 3835 7.083858 GCTTTTTATTGACTTGTCATGTAGCA 58.916 34.615 4.18 0.00 0.00 3.49
3727 3836 7.756722 GCTTTTTATTGACTTGTCATGTAGCAT 59.243 33.333 4.18 0.00 0.00 3.79
3728 3837 9.282247 CTTTTTATTGACTTGTCATGTAGCATC 57.718 33.333 4.18 0.00 0.00 3.91
3729 3838 6.588348 TTATTGACTTGTCATGTAGCATCG 57.412 37.500 4.18 0.00 0.00 3.84
3730 3839 3.866883 TGACTTGTCATGTAGCATCGA 57.133 42.857 0.00 0.00 0.00 3.59
3731 3840 3.774066 TGACTTGTCATGTAGCATCGAG 58.226 45.455 0.00 0.00 0.00 4.04
3732 3841 3.119291 GACTTGTCATGTAGCATCGAGG 58.881 50.000 0.00 0.00 0.00 4.63
3733 3842 2.159043 ACTTGTCATGTAGCATCGAGGG 60.159 50.000 0.00 0.00 0.00 4.30
3734 3843 1.775385 TGTCATGTAGCATCGAGGGA 58.225 50.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.763073 TGGAATCATGTTTTTGTGTGCAA 58.237 34.783 0.00 0.00 0.00 4.08
1 2 4.397481 TGGAATCATGTTTTTGTGTGCA 57.603 36.364 0.00 0.00 0.00 4.57
2 3 5.927954 AATGGAATCATGTTTTTGTGTGC 57.072 34.783 0.00 0.00 33.18 4.57
3 4 6.482641 TGGAAATGGAATCATGTTTTTGTGTG 59.517 34.615 0.00 0.00 33.18 3.82
4 5 6.590068 TGGAAATGGAATCATGTTTTTGTGT 58.410 32.000 0.00 0.00 33.18 3.72
5 6 7.361371 CCATGGAAATGGAATCATGTTTTTGTG 60.361 37.037 5.56 0.00 44.39 3.33
7 8 6.403855 GCCATGGAAATGGAATCATGTTTTTG 60.404 38.462 18.40 0.00 44.39 2.44
8 9 5.648960 GCCATGGAAATGGAATCATGTTTTT 59.351 36.000 18.40 0.00 44.39 1.94
9 10 5.045432 AGCCATGGAAATGGAATCATGTTTT 60.045 36.000 18.40 0.00 44.39 2.43
10 11 4.472108 AGCCATGGAAATGGAATCATGTTT 59.528 37.500 18.40 0.00 44.39 2.83
13 14 3.802329 GCAGCCATGGAAATGGAATCATG 60.802 47.826 18.40 0.00 44.39 3.07
74 78 0.617249 CTGGGGAGGAGACAAGAGCT 60.617 60.000 0.00 0.00 0.00 4.09
77 81 0.616111 GAGCTGGGGAGGAGACAAGA 60.616 60.000 0.00 0.00 0.00 3.02
89 93 1.403814 TGATACGAAGGAGAGCTGGG 58.596 55.000 0.00 0.00 0.00 4.45
121 125 2.581409 CCGATCCGCACGTACCAC 60.581 66.667 0.00 0.00 0.00 4.16
181 190 0.719465 GAAACACATACCGGCGTGAG 59.281 55.000 22.06 12.97 36.91 3.51
196 205 2.338785 GCTGGCAGGAGCAGGAAAC 61.339 63.158 17.64 0.00 44.61 2.78
231 240 1.027357 GGGGCACACATGACATGATC 58.973 55.000 22.19 7.30 34.30 2.92
232 241 0.332293 TGGGGCACACATGACATGAT 59.668 50.000 22.19 6.78 34.30 2.45
233 242 0.112025 TTGGGGCACACATGACATGA 59.888 50.000 22.19 0.00 34.30 3.07
235 244 1.477553 GATTGGGGCACACATGACAT 58.522 50.000 0.00 0.00 34.30 3.06
236 245 0.611618 GGATTGGGGCACACATGACA 60.612 55.000 0.00 0.00 34.30 3.58
237 246 1.656818 CGGATTGGGGCACACATGAC 61.657 60.000 0.00 0.00 0.00 3.06
256 265 3.776656 CACGAACGAACGGGGATC 58.223 61.111 0.14 0.00 37.61 3.36
262 276 3.467119 CGAGCCCACGAACGAACG 61.467 66.667 0.14 0.00 39.31 3.95
263 277 3.774702 GCGAGCCCACGAACGAAC 61.775 66.667 0.14 0.00 35.09 3.95
409 423 2.298163 CTGATTGCCACCTCAAGCTTTT 59.702 45.455 0.00 0.00 33.84 2.27
418 432 2.360350 CGCCACTGATTGCCACCT 60.360 61.111 0.00 0.00 0.00 4.00
487 501 1.786937 TGCCCATTCTCTCTCTCTCC 58.213 55.000 0.00 0.00 0.00 3.71
488 502 4.128643 CAAATGCCCATTCTCTCTCTCTC 58.871 47.826 0.00 0.00 0.00 3.20
531 545 4.973168 AGGCATCTCTCTACAGTCTAGAG 58.027 47.826 0.00 5.93 41.72 2.43
532 546 5.605069 ACTAGGCATCTCTCTACAGTCTAGA 59.395 44.000 6.40 0.00 0.00 2.43
533 547 5.865085 ACTAGGCATCTCTCTACAGTCTAG 58.135 45.833 0.00 0.00 0.00 2.43
534 548 5.897851 ACTAGGCATCTCTCTACAGTCTA 57.102 43.478 0.00 0.00 0.00 2.59
535 549 4.788925 ACTAGGCATCTCTCTACAGTCT 57.211 45.455 0.00 0.00 0.00 3.24
536 550 5.358442 TCAAACTAGGCATCTCTCTACAGTC 59.642 44.000 0.00 0.00 0.00 3.51
537 551 5.265191 TCAAACTAGGCATCTCTCTACAGT 58.735 41.667 0.00 0.00 0.00 3.55
545 559 6.024049 CGTTGAAAATCAAACTAGGCATCTC 58.976 40.000 0.00 0.00 38.22 2.75
616 630 2.936032 GAGTGCCCTCCCCACCTT 60.936 66.667 0.00 0.00 33.75 3.50
720 737 5.482908 ACAGCAAAAGAGATAGACACGAAT 58.517 37.500 0.00 0.00 0.00 3.34
724 741 5.241662 AGGAACAGCAAAAGAGATAGACAC 58.758 41.667 0.00 0.00 0.00 3.67
813 848 6.208599 TGAATTCACCTACCAAGTTCCAAATC 59.791 38.462 3.38 0.00 0.00 2.17
822 857 2.422597 TGCGTGAATTCACCTACCAAG 58.577 47.619 28.40 15.79 43.66 3.61
865 900 1.086696 CAGCCATTCGTCGTCCATTT 58.913 50.000 0.00 0.00 0.00 2.32
890 929 1.138859 TCCATGAGAGGCCATAACACG 59.861 52.381 5.01 0.00 0.00 4.49
905 947 3.067320 TGAGACGAGCATAAGAGTCCATG 59.933 47.826 0.00 0.00 34.41 3.66
913 955 3.867493 TGCAAGAATGAGACGAGCATAAG 59.133 43.478 0.00 0.00 0.00 1.73
916 958 2.277969 CTGCAAGAATGAGACGAGCAT 58.722 47.619 0.00 0.00 34.07 3.79
1029 1075 3.490759 ATCTTCTTGCGCCGCGTG 61.491 61.111 15.34 5.49 0.00 5.34
1035 1081 0.179179 GCTTGGTCATCTTCTTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
1370 1416 1.214062 GCGTGTGAGAGTGAGAGGG 59.786 63.158 0.00 0.00 0.00 4.30
1393 1445 3.264897 ATGAAGATGGCGCGCGAC 61.265 61.111 37.18 34.98 0.00 5.19
1396 1448 0.376852 TAAACATGAAGATGGCGCGC 59.623 50.000 25.94 25.94 33.39 6.86
1786 1845 2.347490 GGGAGGTTGAGCAGCGAA 59.653 61.111 0.00 0.00 0.00 4.70
2125 2184 1.825090 TGTTGATGCGCTTCTGGATT 58.175 45.000 22.11 0.00 0.00 3.01
2167 2226 0.687920 TGGTGGAGTTGATGGCGTTA 59.312 50.000 0.00 0.00 0.00 3.18
2308 2367 2.575921 AGATGATGAAGGGGGTCTGA 57.424 50.000 0.00 0.00 0.00 3.27
2686 2745 3.733960 TCGACCCACTCGTGCTCG 61.734 66.667 0.81 0.81 43.45 5.03
2758 2817 4.629634 TCAGGTAGTGTAATCAATGTTGCG 59.370 41.667 0.00 0.00 0.00 4.85
2778 2837 3.795101 GGTCATCGTACGTGGTAAATCAG 59.205 47.826 16.05 0.00 0.00 2.90
2853 2912 8.743085 AATGATCACTAGTAATGCACAATCTT 57.257 30.769 0.00 0.00 0.00 2.40
2854 2913 8.743085 AAATGATCACTAGTAATGCACAATCT 57.257 30.769 0.00 0.00 0.00 2.40
2912 3001 1.137697 ACTTCTTCCTGTTCCCCGTT 58.862 50.000 0.00 0.00 0.00 4.44
2922 3011 4.417437 TCCTTGCTACTGTACTTCTTCCT 58.583 43.478 0.00 0.00 0.00 3.36
2926 3015 4.142359 CGACATCCTTGCTACTGTACTTCT 60.142 45.833 0.00 0.00 0.00 2.85
2928 3017 3.676324 GCGACATCCTTGCTACTGTACTT 60.676 47.826 0.00 0.00 0.00 2.24
3056 3145 8.857098 CCATGATTGAAGATGAATAGGTCAATT 58.143 33.333 0.00 0.00 40.50 2.32
3057 3146 7.039923 GCCATGATTGAAGATGAATAGGTCAAT 60.040 37.037 0.00 0.00 40.50 2.57
3060 3149 5.766670 TGCCATGATTGAAGATGAATAGGTC 59.233 40.000 0.00 0.00 0.00 3.85
3062 3151 5.768662 ACTGCCATGATTGAAGATGAATAGG 59.231 40.000 0.00 0.00 0.00 2.57
3134 3228 3.060363 CCAGTGTTTATTGTCGTCGCTAC 59.940 47.826 0.00 0.00 0.00 3.58
3145 3239 3.482436 TCGGCTTGTTCCAGTGTTTATT 58.518 40.909 0.00 0.00 0.00 1.40
3147 3241 2.623878 TCGGCTTGTTCCAGTGTTTA 57.376 45.000 0.00 0.00 0.00 2.01
3178 3272 1.000359 TGAGAGAGGGGCGATGACA 60.000 57.895 0.00 0.00 0.00 3.58
3226 3326 3.678056 AGCACGACAATTTCCTGACTA 57.322 42.857 0.00 0.00 0.00 2.59
3236 3336 1.077716 GGGGCCTTAGCACGACAAT 60.078 57.895 0.84 0.00 46.55 2.71
3320 3422 4.823790 ATTCGTTTGGGTGTTTACAGAC 57.176 40.909 0.00 0.00 0.00 3.51
3321 3423 4.756135 GGTATTCGTTTGGGTGTTTACAGA 59.244 41.667 0.00 0.00 0.00 3.41
3382 3490 0.962489 ATGTCGGATCTCGTGGGATC 59.038 55.000 0.89 0.89 40.78 3.36
3401 3509 1.683629 GGGTGTGTGAAGGTTTGTCCA 60.684 52.381 0.00 0.00 39.02 4.02
3402 3510 1.029681 GGGTGTGTGAAGGTTTGTCC 58.970 55.000 0.00 0.00 0.00 4.02
3412 3520 0.034756 CATCGTTGGAGGGTGTGTGA 59.965 55.000 0.00 0.00 0.00 3.58
3418 3526 0.824759 GTCTAGCATCGTTGGAGGGT 59.175 55.000 0.00 0.00 38.38 4.34
3440 3548 2.211250 TCTATCCCCGTCCCGATAAG 57.789 55.000 0.00 0.00 0.00 1.73
3441 3549 2.242043 GTTCTATCCCCGTCCCGATAA 58.758 52.381 0.00 0.00 0.00 1.75
3442 3550 1.883638 CGTTCTATCCCCGTCCCGATA 60.884 57.143 0.00 0.00 0.00 2.92
3524 3633 6.360618 ACCCCATTCTCATTCTTGTTAGATC 58.639 40.000 0.00 0.00 0.00 2.75
3566 3675 2.233305 AGGTACGAATGACCTCACCT 57.767 50.000 0.00 0.00 44.33 4.00
3576 3685 1.971357 CTAGGCCATGGAGGTACGAAT 59.029 52.381 18.40 0.00 40.61 3.34
3578 3687 0.554305 TCTAGGCCATGGAGGTACGA 59.446 55.000 18.40 0.05 40.61 3.43
3631 3740 9.425577 GCTACCCATATAGTCAAAAGTCTATTC 57.574 37.037 0.00 0.00 0.00 1.75
3632 3741 9.160412 AGCTACCCATATAGTCAAAAGTCTATT 57.840 33.333 0.00 0.00 0.00 1.73
3633 3742 8.589338 CAGCTACCCATATAGTCAAAAGTCTAT 58.411 37.037 0.00 0.00 0.00 1.98
3634 3743 7.783119 TCAGCTACCCATATAGTCAAAAGTCTA 59.217 37.037 0.00 0.00 0.00 2.59
3635 3744 6.611642 TCAGCTACCCATATAGTCAAAAGTCT 59.388 38.462 0.00 0.00 0.00 3.24
3636 3745 6.817184 TCAGCTACCCATATAGTCAAAAGTC 58.183 40.000 0.00 0.00 0.00 3.01
3637 3746 6.808321 TCAGCTACCCATATAGTCAAAAGT 57.192 37.500 0.00 0.00 0.00 2.66
3638 3747 8.682936 AATTCAGCTACCCATATAGTCAAAAG 57.317 34.615 0.00 0.00 0.00 2.27
3639 3748 9.474313 AAAATTCAGCTACCCATATAGTCAAAA 57.526 29.630 0.00 0.00 0.00 2.44
3640 3749 8.902806 CAAAATTCAGCTACCCATATAGTCAAA 58.097 33.333 0.00 0.00 0.00 2.69
3641 3750 8.052748 ACAAAATTCAGCTACCCATATAGTCAA 58.947 33.333 0.00 0.00 0.00 3.18
3642 3751 7.573710 ACAAAATTCAGCTACCCATATAGTCA 58.426 34.615 0.00 0.00 0.00 3.41
3643 3752 9.726438 ATACAAAATTCAGCTACCCATATAGTC 57.274 33.333 0.00 0.00 0.00 2.59
3693 3802 9.376075 TGACAAGTCAATAAAAAGCAATTTTCA 57.624 25.926 0.00 0.00 38.21 2.69
3696 3805 9.328845 ACATGACAAGTCAATAAAAAGCAATTT 57.671 25.926 7.02 0.00 43.58 1.82
3697 3806 8.891671 ACATGACAAGTCAATAAAAAGCAATT 57.108 26.923 7.02 0.00 43.58 2.32
3698 3807 9.630098 CTACATGACAAGTCAATAAAAAGCAAT 57.370 29.630 7.02 0.00 43.58 3.56
3699 3808 7.594758 GCTACATGACAAGTCAATAAAAAGCAA 59.405 33.333 7.02 0.00 43.58 3.91
3700 3809 7.083858 GCTACATGACAAGTCAATAAAAAGCA 58.916 34.615 7.02 0.00 43.58 3.91
3701 3810 7.083858 TGCTACATGACAAGTCAATAAAAAGC 58.916 34.615 7.02 10.48 43.58 3.51
3702 3811 9.282247 GATGCTACATGACAAGTCAATAAAAAG 57.718 33.333 7.02 1.54 43.58 2.27
3703 3812 7.962373 CGATGCTACATGACAAGTCAATAAAAA 59.038 33.333 7.02 0.00 43.58 1.94
3704 3813 7.333174 TCGATGCTACATGACAAGTCAATAAAA 59.667 33.333 7.02 0.00 43.58 1.52
3705 3814 6.816140 TCGATGCTACATGACAAGTCAATAAA 59.184 34.615 7.02 0.00 43.58 1.40
3706 3815 6.337356 TCGATGCTACATGACAAGTCAATAA 58.663 36.000 7.02 0.00 43.58 1.40
3707 3816 5.901552 TCGATGCTACATGACAAGTCAATA 58.098 37.500 7.02 2.71 43.58 1.90
3708 3817 4.758688 TCGATGCTACATGACAAGTCAAT 58.241 39.130 7.02 1.63 43.58 2.57
3709 3818 4.176271 CTCGATGCTACATGACAAGTCAA 58.824 43.478 7.02 0.00 43.58 3.18
3710 3819 3.429410 CCTCGATGCTACATGACAAGTCA 60.429 47.826 5.24 5.24 44.59 3.41
3711 3820 3.119291 CCTCGATGCTACATGACAAGTC 58.881 50.000 0.00 0.00 0.00 3.01
3712 3821 2.159043 CCCTCGATGCTACATGACAAGT 60.159 50.000 0.00 0.00 0.00 3.16
3713 3822 2.101415 TCCCTCGATGCTACATGACAAG 59.899 50.000 0.00 0.00 0.00 3.16
3714 3823 2.107366 TCCCTCGATGCTACATGACAA 58.893 47.619 0.00 0.00 0.00 3.18
3715 3824 1.775385 TCCCTCGATGCTACATGACA 58.225 50.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.