Multiple sequence alignment - TraesCS1A01G261600

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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 TraesCS1A01G261600 chr1A 100.000 3833 0 0 1 3833 456237204 456233372 0.000000e+00 7079.0
1 TraesCS1A01G261600 chr1A 95.000 40 2 0 3485 3524 530163694 530163733 3.200000e-06 63.9
2 TraesCS1A01G261600 chr1D 94.281 2955 100 24 908 3821 355512473 355509547 0.000000e+00 4457.0
3 TraesCS1A01G261600 chr1D 83.264 484 50 11 1 457 355515493 355515014 2.130000e-112 416.0
4 TraesCS1A01G261600 chr1B 94.439 2859 106 11 990 3821 478485725 478482893 0.000000e+00 4349.0
5 TraesCS1A01G261600 chr1B 83.426 899 104 21 1 864 478527453 478526565 0.000000e+00 793.0
6 TraesCS1A01G261600 chr5D 80.165 242 42 5 105 343 496410464 496410702 3.940000e-40 176.0
7 TraesCS1A01G261600 chrUn 84.921 126 16 3 206 330 97189958 97189835 1.450000e-24 124.0
8 TraesCS1A01G261600 chrUn 84.127 126 17 3 206 330 97270312 97270189 6.730000e-23 119.0
9 TraesCS1A01G261600 chrUn 82.540 126 19 3 206 330 285954018 285954141 1.460000e-19 108.0


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 TraesCS1A01G261600 chr1A 456233372 456237204 3832 True 7079.0 7079 100.0000 1 3833 1 chr1A.!!$R1 3832
1 TraesCS1A01G261600 chr1D 355509547 355515493 5946 True 2436.5 4457 88.7725 1 3821 2 chr1D.!!$R1 3820
2 TraesCS1A01G261600 chr1B 478482893 478485725 2832 True 4349.0 4349 94.4390 990 3821 1 chr1B.!!$R1 2831
3 TraesCS1A01G261600 chr1B 478526565 478527453 888 True 793.0 793 83.4260 1 864 1 chr1B.!!$R2 863

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
657 2763 0.246635 TTGACCCTAGCGAACTCTGC 59.753 55.000 0.0 0.0 0.00 4.26 F
1221 3341 0.697079 ACCTCCACCTCTACTCGTCA 59.303 55.000 0.0 0.0 0.00 4.35 F
1569 3689 0.750546 ACGGCTATACTGACGAGGCA 60.751 55.000 0.0 0.0 41.74 4.75 F
1973 4093 1.680314 GAGCAGGGGAGGCTTTTGG 60.680 63.158 0.0 0.0 42.78 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 3581 0.181114 TCCTGGCATCATCCGGAAAG 59.819 55.000 9.01 4.22 34.34 2.62 R
2625 4745 0.610174 CAACAGCCAGCCTCTCACTA 59.390 55.000 0.00 0.00 0.00 2.74 R
2703 4823 1.847506 ATGGCAGTCCCCACAGACA 60.848 57.895 0.00 0.00 39.34 3.41 R
3298 5440 2.403252 ATCTTTCACCAAGCCCTACG 57.597 50.000 0.00 0.00 31.70 3.51 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
58 59 2.608988 AGGTGGACCTGCTGGAGG 60.609 66.667 17.64 14.24 46.55 4.30
81 82 2.202743 GCAGACGGTATGAGCGCA 60.203 61.111 11.47 0.00 43.79 6.09
90 91 0.381089 GTATGAGCGCAGGTACGAGT 59.619 55.000 11.47 0.00 39.88 4.18
92 93 2.881352 GAGCGCAGGTACGAGTGC 60.881 66.667 11.47 12.22 43.01 4.40
93 94 4.436998 AGCGCAGGTACGAGTGCC 62.437 66.667 11.47 1.97 43.53 5.01
168 169 5.656416 TCTCTTCCACCAAACTTCATGTTTT 59.344 36.000 0.00 0.00 45.69 2.43
172 173 5.659463 TCCACCAAACTTCATGTTTTCTTG 58.341 37.500 0.00 0.00 45.69 3.02
174 175 5.291614 CCACCAAACTTCATGTTTTCTTGTG 59.708 40.000 0.00 0.00 45.69 3.33
196 197 4.701651 TGTGTGATGATTTCCTTCCATGTC 59.298 41.667 0.00 0.00 0.00 3.06
204 205 2.311854 CCTTCCATGTCTGGGCCCT 61.312 63.158 25.70 0.00 43.34 5.19
210 211 1.550869 CCATGTCTGGGCCCTTTTTCT 60.551 52.381 25.70 0.00 39.04 2.52
211 212 1.821136 CATGTCTGGGCCCTTTTTCTC 59.179 52.381 25.70 7.01 0.00 2.87
213 214 1.428912 TGTCTGGGCCCTTTTTCTCAT 59.571 47.619 25.70 0.00 0.00 2.90
346 348 8.181573 ACGGTGTGATAAGTGCAAAAATATTAG 58.818 33.333 0.00 0.00 0.00 1.73
349 375 7.435192 GTGTGATAAGTGCAAAAATATTAGCCC 59.565 37.037 0.00 0.00 0.00 5.19
351 377 7.649306 GTGATAAGTGCAAAAATATTAGCCCAG 59.351 37.037 0.00 0.00 0.00 4.45
357 383 5.480073 TGCAAAAATATTAGCCCAGACAACT 59.520 36.000 0.00 0.00 0.00 3.16
360 386 7.378181 CAAAAATATTAGCCCAGACAACTGTT 58.622 34.615 0.00 0.00 42.05 3.16
379 406 3.075005 CGACCCCCACCGATGTCT 61.075 66.667 0.00 0.00 0.00 3.41
380 407 2.656069 CGACCCCCACCGATGTCTT 61.656 63.158 0.00 0.00 0.00 3.01
388 415 1.611673 CCACCGATGTCTTGGAAGCTT 60.612 52.381 0.00 0.00 31.39 3.74
402 429 1.537202 GAAGCTTGGAATGTCGTTGCT 59.463 47.619 2.10 0.00 0.00 3.91
416 443 1.602323 TTGCTGATTCCGGCCGTTT 60.602 52.632 26.12 8.05 44.00 3.60
417 444 1.175983 TTGCTGATTCCGGCCGTTTT 61.176 50.000 26.12 7.63 44.00 2.43
432 459 2.456577 CGTTTTCCCATCCCCTCAATT 58.543 47.619 0.00 0.00 0.00 2.32
447 474 2.877168 CTCAATTGCCTGAGATGGTAGC 59.123 50.000 0.00 0.00 44.82 3.58
516 2622 1.825474 CCAGTCGAGTGACCCAACTAT 59.175 52.381 21.92 0.00 46.74 2.12
519 2625 2.681848 AGTCGAGTGACCCAACTATACG 59.318 50.000 0.00 0.00 46.74 3.06
526 2632 3.109151 TGACCCAACTATACGGAACCAT 58.891 45.455 0.00 0.00 0.00 3.55
527 2633 3.520317 TGACCCAACTATACGGAACCATT 59.480 43.478 0.00 0.00 0.00 3.16
538 2644 1.303091 GGAACCATTGGTCCCGTTCG 61.303 60.000 9.22 0.00 36.34 3.95
540 2646 0.326927 AACCATTGGTCCCGTTCGAT 59.673 50.000 9.22 0.00 33.12 3.59
547 2653 1.511305 GTCCCGTTCGATGCTCTCA 59.489 57.895 0.00 0.00 0.00 3.27
600 2706 2.759973 CACCCTCGGCTCCTGCTA 60.760 66.667 0.00 0.00 39.59 3.49
605 2711 0.755698 CCTCGGCTCCTGCTACCTTA 60.756 60.000 0.00 0.00 39.59 2.69
639 2745 1.375523 GTGGCCCGACGAATGTCTT 60.376 57.895 0.00 0.00 43.21 3.01
655 2761 1.819903 GTCTTGACCCTAGCGAACTCT 59.180 52.381 0.00 0.00 0.00 3.24
657 2763 0.246635 TTGACCCTAGCGAACTCTGC 59.753 55.000 0.00 0.00 0.00 4.26
659 2765 1.340697 TGACCCTAGCGAACTCTGCTA 60.341 52.381 0.00 0.00 43.71 3.49
712 2818 2.283676 TCGCCTCCCGACCTTTCT 60.284 61.111 0.00 0.00 41.89 2.52
722 2828 3.007635 CCCGACCTTTCTATTGTTGGAC 58.992 50.000 0.00 0.00 35.87 4.02
750 2856 7.765360 TCATGTTTCAACTGCTTCTCAATTTTT 59.235 29.630 0.00 0.00 0.00 1.94
805 2916 2.307934 ACAACCATGGTGTGCAAAAC 57.692 45.000 20.60 0.00 0.00 2.43
813 2924 2.297701 TGGTGTGCAAAACTCTTCTCC 58.702 47.619 0.00 0.00 0.00 3.71
829 2945 7.197616 ACTCTTCTCCCTACTACCCTTTAATT 58.802 38.462 0.00 0.00 0.00 1.40
855 2971 9.906660 TGTTTTTACATCAGGTTTTACATCATC 57.093 29.630 0.00 0.00 0.00 2.92
858 2974 8.862325 TTTACATCAGGTTTTACATCATCTGT 57.138 30.769 0.00 0.00 42.13 3.41
860 2976 7.149569 ACATCAGGTTTTACATCATCTGTTG 57.850 36.000 0.00 0.00 39.39 3.33
861 2977 6.151648 ACATCAGGTTTTACATCATCTGTTGG 59.848 38.462 0.00 0.00 39.39 3.77
864 2980 5.707298 CAGGTTTTACATCATCTGTTGGAGT 59.293 40.000 0.00 0.00 39.39 3.85
867 2983 7.390718 AGGTTTTACATCATCTGTTGGAGTTAC 59.609 37.037 0.00 0.00 39.39 2.50
868 2984 7.174253 GGTTTTACATCATCTGTTGGAGTTACA 59.826 37.037 0.00 0.00 39.39 2.41
869 2985 8.730680 GTTTTACATCATCTGTTGGAGTTACAT 58.269 33.333 0.00 0.00 39.39 2.29
870 2986 8.492673 TTTACATCATCTGTTGGAGTTACATC 57.507 34.615 0.00 0.00 39.39 3.06
871 2987 6.305272 ACATCATCTGTTGGAGTTACATCT 57.695 37.500 0.00 0.00 32.90 2.90
873 2989 5.745312 TCATCTGTTGGAGTTACATCTGT 57.255 39.130 0.00 0.00 0.00 3.41
874 2990 6.114187 TCATCTGTTGGAGTTACATCTGTT 57.886 37.500 0.00 0.00 0.00 3.16
875 2991 5.934043 TCATCTGTTGGAGTTACATCTGTTG 59.066 40.000 0.00 0.00 0.00 3.33
876 2992 4.641396 TCTGTTGGAGTTACATCTGTTGG 58.359 43.478 0.00 0.00 0.00 3.77
878 2994 4.641396 TGTTGGAGTTACATCTGTTGGAG 58.359 43.478 0.00 0.00 0.00 3.86
879 2995 4.102524 TGTTGGAGTTACATCTGTTGGAGT 59.897 41.667 0.00 0.00 0.00 3.85
880 2996 4.974645 TGGAGTTACATCTGTTGGAGTT 57.025 40.909 0.00 0.00 0.00 3.01
882 2998 6.620877 TGGAGTTACATCTGTTGGAGTTAT 57.379 37.500 0.00 0.00 0.00 1.89
883 2999 7.016153 TGGAGTTACATCTGTTGGAGTTATT 57.984 36.000 0.00 0.00 0.00 1.40
884 3000 7.103641 TGGAGTTACATCTGTTGGAGTTATTC 58.896 38.462 0.00 0.00 0.00 1.75
886 3002 8.475639 GGAGTTACATCTGTTGGAGTTATTCTA 58.524 37.037 0.00 0.00 0.00 2.10
887 3003 9.871238 GAGTTACATCTGTTGGAGTTATTCTAA 57.129 33.333 0.00 0.00 0.00 2.10
889 3005 9.654663 GTTACATCTGTTGGAGTTATTCTAACT 57.345 33.333 5.68 0.00 44.87 2.24
892 3008 9.036980 ACATCTGTTGGAGTTATTCTAACTACT 57.963 33.333 9.93 0.00 44.87 2.57
901 3017 8.765488 GAGTTATTCTAACTACTCCCTACCTT 57.235 38.462 0.00 0.00 32.74 3.50
903 3019 7.784073 AGTTATTCTAACTACTCCCTACCTTCC 59.216 40.741 0.00 0.00 0.00 3.46
904 3020 5.810456 TTCTAACTACTCCCTACCTTCCT 57.190 43.478 0.00 0.00 0.00 3.36
906 3022 6.915468 TCTAACTACTCCCTACCTTCCTAA 57.085 41.667 0.00 0.00 0.00 2.69
908 3024 3.913509 ACTACTCCCTACCTTCCTAAGC 58.086 50.000 0.00 0.00 0.00 3.09
911 3027 0.720232 TCCCTACCTTCCTAAGCCCA 59.280 55.000 0.00 0.00 0.00 5.36
912 3028 1.297141 TCCCTACCTTCCTAAGCCCAT 59.703 52.381 0.00 0.00 0.00 4.00
925 3042 2.505982 CCCATGTAGGCGGGAGTG 59.494 66.667 0.00 0.00 46.34 3.51
954 3071 3.220447 CCGTTTAGGCCGAACTGAA 57.780 52.632 18.74 0.00 0.00 3.02
955 3072 1.734163 CCGTTTAGGCCGAACTGAAT 58.266 50.000 18.74 0.00 0.00 2.57
960 3077 3.838244 TTAGGCCGAACTGAATAGCAT 57.162 42.857 0.00 0.00 0.00 3.79
987 3105 6.096001 GGAACAAATGAGATACAGCCTTTCAT 59.904 38.462 0.00 0.00 0.00 2.57
988 3106 6.690194 ACAAATGAGATACAGCCTTTCATC 57.310 37.500 0.00 0.00 0.00 2.92
1221 3341 0.697079 ACCTCCACCTCTACTCGTCA 59.303 55.000 0.00 0.00 0.00 4.35
1461 3581 6.645003 TGATCGATATGTACTGTAAATGTGGC 59.355 38.462 0.00 0.00 0.00 5.01
1492 3612 1.619654 TGCCAGGAAGGTGTTTGATG 58.380 50.000 0.00 0.00 40.61 3.07
1501 3621 4.636206 GGAAGGTGTTTGATGGTATGAGTC 59.364 45.833 0.00 0.00 0.00 3.36
1569 3689 0.750546 ACGGCTATACTGACGAGGCA 60.751 55.000 0.00 0.00 41.74 4.75
1675 3795 4.465413 GCGCATTGGAGCTGTTTC 57.535 55.556 0.30 0.00 36.83 2.78
1726 3846 3.921119 ATGACGCATTTGTGTTGTCAT 57.079 38.095 10.49 10.49 43.42 3.06
1863 3983 4.181578 ACATGTACTCCAAATGTAGCGAC 58.818 43.478 0.00 0.00 32.86 5.19
1944 4064 2.424956 GACAATGATTGTTGGAGAGGCC 59.575 50.000 12.62 0.00 45.52 5.19
1973 4093 1.680314 GAGCAGGGGAGGCTTTTGG 60.680 63.158 0.00 0.00 42.78 3.28
2040 4160 5.418840 GGTGACATTTGTTGGGTTGATCTAT 59.581 40.000 0.00 0.00 0.00 1.98
2160 4280 5.682659 TGCTACCTAGATCTTCTTAGTCGT 58.317 41.667 0.00 0.00 0.00 4.34
2214 4334 2.028658 CACTACGATGCCATATGAGCCT 60.029 50.000 3.65 0.00 0.00 4.58
2263 4383 1.837648 CGCATGCAAGAAACACAACA 58.162 45.000 19.57 0.00 0.00 3.33
2484 4604 2.158475 TCTGTTTCATGCTGGGGAAGTT 60.158 45.455 0.00 0.00 0.00 2.66
2625 4745 2.089980 GAGCACCATCTGTTCTTGCAT 58.910 47.619 0.00 0.00 35.57 3.96
2722 4842 1.377725 GTCTGTGGGGACTGCCATG 60.378 63.158 0.00 0.00 35.15 3.66
2723 4843 1.847506 TCTGTGGGGACTGCCATGT 60.848 57.895 0.00 0.00 35.15 3.21
2918 5038 4.582656 ACTTTCCCATGTCTAGAGAGATCG 59.417 45.833 0.00 0.00 33.14 3.69
2977 5097 9.212641 TGAATTGATGTTTCAGTCTTAGAGAAG 57.787 33.333 0.00 0.00 32.27 2.85
3000 5140 2.061509 AAACCGTATATGGGCCAACC 57.938 50.000 11.89 0.00 40.81 3.77
3009 5149 4.662961 GGGCCAACCAACAAGCGC 62.663 66.667 4.39 0.00 39.85 5.92
3028 5168 5.272397 AGCGCGACTAATAGAAACTAGAAC 58.728 41.667 12.10 0.00 0.00 3.01
3032 5172 6.411492 CGCGACTAATAGAAACTAGAACTGTC 59.589 42.308 0.00 0.00 0.00 3.51
3056 5196 7.339466 GTCCATTTGTTGTATCCTATTGTTCCT 59.661 37.037 0.00 0.00 0.00 3.36
3175 5315 7.775397 ACATTTTTGTCAGTGAATTCAAAGG 57.225 32.000 10.35 2.65 32.67 3.11
3176 5316 7.330262 ACATTTTTGTCAGTGAATTCAAAGGT 58.670 30.769 10.35 3.30 32.67 3.50
3177 5317 7.823799 ACATTTTTGTCAGTGAATTCAAAGGTT 59.176 29.630 10.35 0.00 32.67 3.50
3178 5318 9.311916 CATTTTTGTCAGTGAATTCAAAGGTTA 57.688 29.630 10.35 0.00 32.67 2.85
3180 5320 8.870160 TTTTGTCAGTGAATTCAAAGGTTATG 57.130 30.769 10.35 1.44 32.67 1.90
3181 5321 7.581213 TTGTCAGTGAATTCAAAGGTTATGT 57.419 32.000 10.35 0.00 0.00 2.29
3182 5322 7.581213 TGTCAGTGAATTCAAAGGTTATGTT 57.419 32.000 10.35 0.00 0.00 2.71
3183 5323 8.684386 TGTCAGTGAATTCAAAGGTTATGTTA 57.316 30.769 10.35 0.00 0.00 2.41
3184 5324 9.295825 TGTCAGTGAATTCAAAGGTTATGTTAT 57.704 29.630 10.35 0.00 0.00 1.89
3217 5357 6.231951 TCAAAGGTTATGTTGTCGGTGAATA 58.768 36.000 0.00 0.00 0.00 1.75
3283 5425 1.115467 CCCAGCTCTCCGATACTGTT 58.885 55.000 0.00 0.00 0.00 3.16
3414 5557 1.746470 AGAAAAGATAAACCCCGGCG 58.254 50.000 0.00 0.00 0.00 6.46
3426 5569 2.125552 CCGGCGTCTGCATCTTGA 60.126 61.111 6.01 0.00 45.35 3.02
3456 5599 6.472016 ACCCAGCCAAATTTTATTAAGGTTG 58.528 36.000 0.00 0.00 0.00 3.77
3457 5600 6.043822 ACCCAGCCAAATTTTATTAAGGTTGT 59.956 34.615 6.22 0.00 0.00 3.32
3575 5729 1.560505 AACCGGTTGTACGTATCCCT 58.439 50.000 21.56 0.00 0.00 4.20
3601 5755 2.173519 CCATCTTCCATTGGTTGCACT 58.826 47.619 1.86 0.00 0.00 4.40
3606 5760 2.647683 TCCATTGGTTGCACTGTGTA 57.352 45.000 9.86 1.30 0.00 2.90
3616 5770 5.714333 TGGTTGCACTGTGTATTAATCCATT 59.286 36.000 9.86 0.00 0.00 3.16
3645 5799 4.124851 AGTTAGACACAATGGATCCGAC 57.875 45.455 7.39 0.00 0.00 4.79
3647 5801 4.954202 AGTTAGACACAATGGATCCGACTA 59.046 41.667 7.39 0.00 0.00 2.59
3649 5803 2.101582 AGACACAATGGATCCGACTAGC 59.898 50.000 7.39 0.00 0.00 3.42
3658 5818 7.657761 ACAATGGATCCGACTAGCTTATAAAAG 59.342 37.037 7.39 0.00 35.68 2.27
3682 5842 7.112779 AGTTGGAGATGTAGGATTTAAGGTTG 58.887 38.462 0.00 0.00 0.00 3.77
3738 5898 8.776376 TCAAGCTGAACAATTTTTCTTCTTTT 57.224 26.923 5.95 0.00 0.00 2.27
3748 5908 9.056005 ACAATTTTTCTTCTTTTTATGCTTCCC 57.944 29.630 0.00 0.00 0.00 3.97
3754 5914 5.300792 TCTTCTTTTTATGCTTCCCGTTTGT 59.699 36.000 0.00 0.00 0.00 2.83
3796 5957 2.769663 TGTTACTATCACCTTCCCGCAT 59.230 45.455 0.00 0.00 0.00 4.73
3811 5972 0.606401 CGCATGTCCCTCACTTTGGT 60.606 55.000 0.00 0.00 0.00 3.67
3821 5982 4.065789 CCCTCACTTTGGTACTTTGACTC 58.934 47.826 0.00 0.00 0.00 3.36
3822 5983 4.444306 CCCTCACTTTGGTACTTTGACTCA 60.444 45.833 0.00 0.00 0.00 3.41
3823 5984 4.752101 CCTCACTTTGGTACTTTGACTCAG 59.248 45.833 0.00 0.00 0.00 3.35
3824 5985 4.703897 TCACTTTGGTACTTTGACTCAGG 58.296 43.478 0.00 0.00 0.00 3.86
3825 5986 4.163458 TCACTTTGGTACTTTGACTCAGGT 59.837 41.667 0.00 0.00 0.00 4.00
3826 5987 5.364446 TCACTTTGGTACTTTGACTCAGGTA 59.636 40.000 0.00 0.00 0.00 3.08
3827 5988 5.465724 CACTTTGGTACTTTGACTCAGGTAC 59.534 44.000 12.34 12.34 35.27 3.34
3828 5989 5.365895 ACTTTGGTACTTTGACTCAGGTACT 59.634 40.000 16.81 3.03 43.88 2.73
3829 5990 5.464030 TTGGTACTTTGACTCAGGTACTC 57.536 43.478 16.81 11.27 34.60 2.59
3830 5991 3.830755 TGGTACTTTGACTCAGGTACTCC 59.169 47.826 16.81 8.11 34.60 3.85
3831 5992 3.830755 GGTACTTTGACTCAGGTACTCCA 59.169 47.826 16.81 0.00 34.60 3.86
3832 5993 4.082136 GGTACTTTGACTCAGGTACTCCAG 60.082 50.000 16.81 0.00 34.60 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.038033 CCAACTTCTAAGGGGTCAACGA 59.962 50.000 0.00 0.00 0.00 3.85
18 19 2.224450 ACCAACTTCTAAGGGGTCAACG 60.224 50.000 3.33 0.00 34.10 4.10
58 59 3.264897 CATACCGTCTGCCGCTGC 61.265 66.667 0.00 0.00 38.26 5.25
61 62 2.962253 GCTCATACCGTCTGCCGC 60.962 66.667 0.00 0.00 34.38 6.53
81 82 3.812019 CGCTCGGCACTCGTACCT 61.812 66.667 0.00 0.00 40.32 3.08
168 169 4.761739 GGAAGGAAATCATCACACACAAGA 59.238 41.667 0.00 0.00 0.00 3.02
172 173 4.460382 ACATGGAAGGAAATCATCACACAC 59.540 41.667 0.00 0.00 0.00 3.82
174 175 4.946157 AGACATGGAAGGAAATCATCACAC 59.054 41.667 0.00 0.00 0.00 3.82
196 197 2.220653 TCATGAGAAAAAGGGCCCAG 57.779 50.000 27.56 0.00 0.00 4.45
210 211 9.829507 AATCCTTTGTTTAATGTGTTTTCATGA 57.170 25.926 0.00 0.00 0.00 3.07
213 214 9.658799 TGAAATCCTTTGTTTAATGTGTTTTCA 57.341 25.926 0.00 0.00 0.00 2.69
300 302 4.023783 CGTTGTTTAAACCGGATAATCGC 58.976 43.478 9.46 2.14 0.00 4.58
301 303 4.093261 ACCGTTGTTTAAACCGGATAATCG 59.907 41.667 30.47 15.95 43.01 3.34
307 309 1.669779 CACACCGTTGTTTAAACCGGA 59.330 47.619 30.47 11.19 43.01 5.14
346 348 1.891919 TCGCAACAGTTGTCTGGGC 60.892 57.895 14.88 0.00 45.14 5.36
349 375 1.507141 GGGGTCGCAACAGTTGTCTG 61.507 60.000 14.88 5.69 46.18 3.51
351 377 2.258726 GGGGGTCGCAACAGTTGTC 61.259 63.158 14.88 6.42 0.00 3.18
379 406 2.270352 ACGACATTCCAAGCTTCCAA 57.730 45.000 0.00 0.00 0.00 3.53
380 407 1.879380 CAACGACATTCCAAGCTTCCA 59.121 47.619 0.00 0.00 0.00 3.53
388 415 2.083774 GGAATCAGCAACGACATTCCA 58.916 47.619 4.92 0.00 42.70 3.53
402 429 1.676303 GGGAAAACGGCCGGAATCA 60.676 57.895 31.76 0.00 0.00 2.57
416 443 0.032217 GGCAATTGAGGGGATGGGAA 60.032 55.000 10.34 0.00 0.00 3.97
417 444 0.925720 AGGCAATTGAGGGGATGGGA 60.926 55.000 10.34 0.00 0.00 4.37
432 459 1.524002 GCAGCTACCATCTCAGGCA 59.476 57.895 0.00 0.00 0.00 4.75
526 2632 1.079405 GAGCATCGAACGGGACCAA 60.079 57.895 0.00 0.00 0.00 3.67
527 2633 1.945354 GAGAGCATCGAACGGGACCA 61.945 60.000 0.00 0.00 42.67 4.02
538 2644 2.657944 CCGAGCGCTGAGAGCATC 60.658 66.667 18.48 4.43 42.58 3.91
569 2675 4.643387 GGTGCGGCCAACTCCAGT 62.643 66.667 2.24 0.00 37.17 4.00
595 2701 5.329399 AGGATAGGAGTCATAAGGTAGCAG 58.671 45.833 0.00 0.00 0.00 4.24
639 2745 0.612174 AGCAGAGTTCGCTAGGGTCA 60.612 55.000 6.70 0.00 38.15 4.02
655 2761 1.999735 CGAGAACAATTTCGGCTAGCA 59.000 47.619 18.24 0.00 36.78 3.49
712 2818 6.016360 CAGTTGAAACATGAGGTCCAACAATA 60.016 38.462 14.47 0.00 37.08 1.90
722 2828 3.817084 TGAGAAGCAGTTGAAACATGAGG 59.183 43.478 0.00 0.00 0.00 3.86
750 2856 7.172342 ACAGATTATGTAAAAGTGGTGCCTAA 58.828 34.615 0.00 0.00 41.60 2.69
805 2916 7.125963 ACAATTAAAGGGTAGTAGGGAGAAGAG 59.874 40.741 0.00 0.00 0.00 2.85
829 2945 9.906660 GATGATGTAAAACCTGATGTAAAAACA 57.093 29.630 0.00 0.00 0.00 2.83
842 2958 6.575162 AACTCCAACAGATGATGTAAAACC 57.425 37.500 0.00 0.00 43.00 3.27
848 2964 6.111382 CAGATGTAACTCCAACAGATGATGT 58.889 40.000 0.00 0.00 46.97 3.06
849 2965 6.111382 ACAGATGTAACTCCAACAGATGATG 58.889 40.000 0.00 0.00 0.00 3.07
850 2966 6.305272 ACAGATGTAACTCCAACAGATGAT 57.695 37.500 0.00 0.00 0.00 2.45
851 2967 5.745312 ACAGATGTAACTCCAACAGATGA 57.255 39.130 0.00 0.00 0.00 2.92
853 2969 5.013079 TCCAACAGATGTAACTCCAACAGAT 59.987 40.000 0.00 0.00 0.00 2.90
854 2970 4.346709 TCCAACAGATGTAACTCCAACAGA 59.653 41.667 0.00 0.00 0.00 3.41
855 2971 4.641396 TCCAACAGATGTAACTCCAACAG 58.359 43.478 0.00 0.00 0.00 3.16
856 2972 4.102524 ACTCCAACAGATGTAACTCCAACA 59.897 41.667 0.00 0.00 0.00 3.33
857 2973 4.642429 ACTCCAACAGATGTAACTCCAAC 58.358 43.478 0.00 0.00 0.00 3.77
858 2974 4.974645 ACTCCAACAGATGTAACTCCAA 57.025 40.909 0.00 0.00 0.00 3.53
860 2976 7.331791 AGAATAACTCCAACAGATGTAACTCC 58.668 38.462 0.00 0.00 0.00 3.85
861 2977 9.871238 TTAGAATAACTCCAACAGATGTAACTC 57.129 33.333 0.00 0.00 0.00 3.01
867 2983 9.522804 GAGTAGTTAGAATAACTCCAACAGATG 57.477 37.037 5.50 0.00 33.74 2.90
876 2992 8.765488 AAGGTAGGGAGTAGTTAGAATAACTC 57.235 38.462 5.50 0.00 38.08 3.01
878 2994 7.784073 AGGAAGGTAGGGAGTAGTTAGAATAAC 59.216 40.741 0.00 0.00 0.00 1.89
879 2995 7.891328 AGGAAGGTAGGGAGTAGTTAGAATAA 58.109 38.462 0.00 0.00 0.00 1.40
880 2996 7.477345 AGGAAGGTAGGGAGTAGTTAGAATA 57.523 40.000 0.00 0.00 0.00 1.75
882 2998 5.810456 AGGAAGGTAGGGAGTAGTTAGAA 57.190 43.478 0.00 0.00 0.00 2.10
883 2999 6.636798 GCTTAGGAAGGTAGGGAGTAGTTAGA 60.637 46.154 0.00 0.00 0.00 2.10
884 3000 5.535783 GCTTAGGAAGGTAGGGAGTAGTTAG 59.464 48.000 0.00 0.00 0.00 2.34
886 3002 4.288398 GCTTAGGAAGGTAGGGAGTAGTT 58.712 47.826 0.00 0.00 0.00 2.24
887 3003 3.373987 GGCTTAGGAAGGTAGGGAGTAGT 60.374 52.174 0.00 0.00 0.00 2.73
889 3005 2.090887 GGGCTTAGGAAGGTAGGGAGTA 60.091 54.545 0.00 0.00 0.00 2.59
890 3006 1.344189 GGGCTTAGGAAGGTAGGGAGT 60.344 57.143 0.00 0.00 0.00 3.85
891 3007 1.344087 TGGGCTTAGGAAGGTAGGGAG 60.344 57.143 0.00 0.00 0.00 4.30
892 3008 0.720232 TGGGCTTAGGAAGGTAGGGA 59.280 55.000 0.00 0.00 0.00 4.20
894 3010 2.127708 ACATGGGCTTAGGAAGGTAGG 58.872 52.381 0.00 0.00 0.00 3.18
895 3011 3.325135 CCTACATGGGCTTAGGAAGGTAG 59.675 52.174 0.00 0.00 37.64 3.18
896 3012 3.314693 CCTACATGGGCTTAGGAAGGTA 58.685 50.000 0.00 0.00 37.64 3.08
897 3013 2.127708 CCTACATGGGCTTAGGAAGGT 58.872 52.381 0.00 0.00 37.64 3.50
898 3014 2.938956 CCTACATGGGCTTAGGAAGG 57.061 55.000 0.00 0.00 37.64 3.46
911 3027 2.687200 TGCCACTCCCGCCTACAT 60.687 61.111 0.00 0.00 0.00 2.29
912 3028 3.702048 GTGCCACTCCCGCCTACA 61.702 66.667 0.00 0.00 0.00 2.74
951 3068 9.494271 GTATCTCATTTGTTCCTATGCTATTCA 57.506 33.333 0.00 0.00 0.00 2.57
954 3071 7.605691 GCTGTATCTCATTTGTTCCTATGCTAT 59.394 37.037 0.00 0.00 0.00 2.97
955 3072 6.931281 GCTGTATCTCATTTGTTCCTATGCTA 59.069 38.462 0.00 0.00 0.00 3.49
960 3077 5.957771 AGGCTGTATCTCATTTGTTCCTA 57.042 39.130 0.00 0.00 0.00 2.94
1416 3536 3.821033 TCAGAGAAGACTTGACGACATCA 59.179 43.478 0.00 0.00 34.65 3.07
1461 3581 0.181114 TCCTGGCATCATCCGGAAAG 59.819 55.000 9.01 4.22 34.34 2.62
1492 3612 2.633488 GCTGTTCTTGGGACTCATACC 58.367 52.381 0.00 0.00 0.00 2.73
1501 3621 1.594293 ACACGACGCTGTTCTTGGG 60.594 57.895 0.00 0.00 0.00 4.12
1569 3689 4.026300 CTCCGGAAGAGCTCCAGT 57.974 61.111 10.93 0.00 45.74 4.00
1620 3740 5.361285 AGCTCTTACAAATCCTGATACGAGT 59.639 40.000 0.00 0.00 0.00 4.18
1662 3782 4.914983 TCATCTCAAGAAACAGCTCCAAT 58.085 39.130 0.00 0.00 0.00 3.16
1663 3783 4.321718 CTCATCTCAAGAAACAGCTCCAA 58.678 43.478 0.00 0.00 0.00 3.53
1675 3795 0.883814 GCATCCCGCCTCATCTCAAG 60.884 60.000 0.00 0.00 32.94 3.02
1698 3818 6.148645 ACAACACAAATGCGTCATCAATAGTA 59.851 34.615 0.00 0.00 0.00 1.82
1726 3846 2.066340 CAGCCCCACCAGTTACAGA 58.934 57.895 0.00 0.00 0.00 3.41
1863 3983 5.950758 ATACTTCTCTAGCGGAGTGTATG 57.049 43.478 3.78 6.15 42.40 2.39
1944 4064 2.513204 CCTGCTCGACCATGCTGG 60.513 66.667 6.02 6.02 45.02 4.85
1973 4093 5.277538 GCAAGAATCATCCGGTCATAAAGAC 60.278 44.000 0.00 0.00 46.83 3.01
2160 4280 2.092429 AGCTTCTGATAAATGGCCCGAA 60.092 45.455 0.00 0.00 0.00 4.30
2214 4334 1.000521 CCCCCAAGCAGCTTCATCA 60.001 57.895 4.07 0.00 0.00 3.07
2247 4367 3.805422 CAGCATTGTTGTGTTTCTTGCAT 59.195 39.130 0.00 0.00 0.00 3.96
2263 4383 2.559668 CCCTGACACACATTTCAGCATT 59.440 45.455 0.00 0.00 38.36 3.56
2484 4604 5.932619 TTTCTTCTCTCATATCAACCGGA 57.067 39.130 9.46 0.00 0.00 5.14
2625 4745 0.610174 CAACAGCCAGCCTCTCACTA 59.390 55.000 0.00 0.00 0.00 2.74
2703 4823 1.847506 ATGGCAGTCCCCACAGACA 60.848 57.895 0.00 0.00 39.34 3.41
2910 5030 3.984508 TCCATTTCGTACCGATCTCTC 57.015 47.619 0.00 0.00 35.23 3.20
2918 5038 5.638596 AAAAAGGTCATCCATTTCGTACC 57.361 39.130 0.00 0.00 34.15 3.34
2941 5061 8.260270 CTGAAACATCAATTCAGTCATACAGA 57.740 34.615 7.86 0.00 45.53 3.41
2952 5072 9.429359 TCTTCTCTAAGACTGAAACATCAATTC 57.571 33.333 0.00 0.00 36.80 2.17
2974 5094 3.314357 GGCCCATATACGGTTTTGTCTTC 59.686 47.826 0.00 0.00 0.00 2.87
2977 5097 2.645802 TGGCCCATATACGGTTTTGTC 58.354 47.619 0.00 0.00 0.00 3.18
3000 5140 4.091509 AGTTTCTATTAGTCGCGCTTGTTG 59.908 41.667 5.56 0.00 0.00 3.33
3009 5149 7.759465 TGGACAGTTCTAGTTTCTATTAGTCG 58.241 38.462 0.00 0.00 0.00 4.18
3028 5168 7.630242 ACAATAGGATACAACAAATGGACAG 57.370 36.000 0.00 0.00 41.41 3.51
3032 5172 7.645058 AGGAACAATAGGATACAACAAATGG 57.355 36.000 0.00 0.00 41.41 3.16
3056 5196 7.343574 TCTGTTACCAGGATGTACATAAAGCTA 59.656 37.037 8.71 0.00 39.31 3.32
3161 5301 7.910162 CCGATAACATAACCTTTGAATTCACTG 59.090 37.037 7.89 3.81 0.00 3.66
3162 5302 7.610305 ACCGATAACATAACCTTTGAATTCACT 59.390 33.333 7.89 0.00 0.00 3.41
3163 5303 7.696453 CACCGATAACATAACCTTTGAATTCAC 59.304 37.037 7.89 0.00 0.00 3.18
3164 5304 7.608376 TCACCGATAACATAACCTTTGAATTCA 59.392 33.333 3.38 3.38 0.00 2.57
3165 5305 7.981142 TCACCGATAACATAACCTTTGAATTC 58.019 34.615 0.00 0.00 0.00 2.17
3166 5306 7.931578 TCACCGATAACATAACCTTTGAATT 57.068 32.000 0.00 0.00 0.00 2.17
3167 5307 7.931578 TTCACCGATAACATAACCTTTGAAT 57.068 32.000 0.00 0.00 0.00 2.57
3168 5308 7.931578 ATTCACCGATAACATAACCTTTGAA 57.068 32.000 0.00 0.00 0.00 2.69
3169 5309 7.608376 TGAATTCACCGATAACATAACCTTTGA 59.392 33.333 3.38 0.00 0.00 2.69
3170 5310 7.757526 TGAATTCACCGATAACATAACCTTTG 58.242 34.615 3.38 0.00 0.00 2.77
3171 5311 7.931578 TGAATTCACCGATAACATAACCTTT 57.068 32.000 3.38 0.00 0.00 3.11
3172 5312 7.931578 TTGAATTCACCGATAACATAACCTT 57.068 32.000 7.89 0.00 0.00 3.50
3173 5313 7.067008 CCTTTGAATTCACCGATAACATAACCT 59.933 37.037 7.89 0.00 0.00 3.50
3174 5314 7.148137 ACCTTTGAATTCACCGATAACATAACC 60.148 37.037 7.89 0.00 0.00 2.85
3175 5315 7.758495 ACCTTTGAATTCACCGATAACATAAC 58.242 34.615 7.89 0.00 0.00 1.89
3176 5316 7.931578 ACCTTTGAATTCACCGATAACATAA 57.068 32.000 7.89 0.00 0.00 1.90
3177 5317 7.931578 AACCTTTGAATTCACCGATAACATA 57.068 32.000 7.89 0.00 0.00 2.29
3178 5318 6.834168 AACCTTTGAATTCACCGATAACAT 57.166 33.333 7.89 0.00 0.00 2.71
3179 5319 7.392113 ACATAACCTTTGAATTCACCGATAACA 59.608 33.333 7.89 0.00 0.00 2.41
3180 5320 7.758495 ACATAACCTTTGAATTCACCGATAAC 58.242 34.615 7.89 0.00 0.00 1.89
3181 5321 7.931578 ACATAACCTTTGAATTCACCGATAA 57.068 32.000 7.89 0.00 0.00 1.75
3182 5322 7.392113 ACAACATAACCTTTGAATTCACCGATA 59.608 33.333 7.89 0.00 0.00 2.92
3183 5323 6.208599 ACAACATAACCTTTGAATTCACCGAT 59.791 34.615 7.89 0.00 0.00 4.18
3184 5324 5.533154 ACAACATAACCTTTGAATTCACCGA 59.467 36.000 7.89 0.00 0.00 4.69
3243 5385 5.065914 GGGTTGCATAATAGCAGATCAGAA 58.934 41.667 0.00 0.00 46.54 3.02
3283 5425 7.338703 CCAAGCCCTACGAGTAGTATTATATCA 59.661 40.741 9.15 0.00 34.34 2.15
3298 5440 2.403252 ATCTTTCACCAAGCCCTACG 57.597 50.000 0.00 0.00 31.70 3.51
3426 5569 6.625532 AATAAAATTTGGCTGGGTTCATCT 57.374 33.333 0.00 0.00 0.00 2.90
3434 5577 8.311109 ACTACAACCTTAATAAAATTTGGCTGG 58.689 33.333 0.00 0.00 0.00 4.85
3456 5599 5.584253 TCAGAACTGGAGCTTGATACTAC 57.416 43.478 1.93 0.00 0.00 2.73
3457 5600 5.717178 ACTTCAGAACTGGAGCTTGATACTA 59.283 40.000 9.74 0.00 39.86 1.82
3601 5755 8.402798 ACTTTGTGTCAATGGATTAATACACA 57.597 30.769 13.18 13.18 43.81 3.72
3606 5760 9.295825 TGTCTAACTTTGTGTCAATGGATTAAT 57.704 29.630 0.00 0.00 0.00 1.40
3616 5770 5.432645 TCCATTGTGTCTAACTTTGTGTCA 58.567 37.500 0.00 0.00 0.00 3.58
3645 5799 9.482627 CCTACATCTCCAACTTTTATAAGCTAG 57.517 37.037 0.00 0.00 34.60 3.42
3647 5801 8.090788 TCCTACATCTCCAACTTTTATAAGCT 57.909 34.615 0.00 0.00 34.60 3.74
3658 5818 6.884836 ACAACCTTAAATCCTACATCTCCAAC 59.115 38.462 0.00 0.00 0.00 3.77
3730 5890 5.300792 ACAAACGGGAAGCATAAAAAGAAGA 59.699 36.000 0.00 0.00 0.00 2.87
3738 5898 7.976734 CCATTTAATTACAAACGGGAAGCATAA 59.023 33.333 0.00 0.00 0.00 1.90
3745 5905 8.422566 AGTTTTTCCATTTAATTACAAACGGGA 58.577 29.630 0.00 0.00 0.00 5.14
3748 5908 8.491950 CCCAGTTTTTCCATTTAATTACAAACG 58.508 33.333 0.00 0.00 0.00 3.60
3754 5914 9.984190 GTAACACCCAGTTTTTCCATTTAATTA 57.016 29.630 0.00 0.00 41.64 1.40
3796 5957 3.456644 TCAAAGTACCAAAGTGAGGGACA 59.543 43.478 0.00 0.00 42.76 4.02


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

AutoCloner maintained by Alex Coulton.