Multiple sequence alignment - TraesCS6B01G197300

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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 TraesCS6B01G197300 chr6B 100.000 3290 0 0 1 3290 234558025 234561314 0.000000e+00 6076.0
1 TraesCS6B01G197300 chr6B 81.037 1176 218 5 1083 2257 500894276 500895447 0.000000e+00 931.0
2 TraesCS6B01G197300 chr6B 80.420 143 26 2 3149 3290 508533420 508533279 1.250000e-19 108.0
3 TraesCS6B01G197300 chr6B 100.000 31 0 0 2595 2625 521118951 521118921 1.280000e-04 58.4
4 TraesCS6B01G197300 chr6D 95.765 2574 78 13 13 2572 136130572 136128016 0.000000e+00 4120.0
5 TraesCS6B01G197300 chr6D 80.969 1177 219 5 1082 2257 322572232 322571060 0.000000e+00 928.0
6 TraesCS6B01G197300 chr6D 81.026 1170 217 5 1089 2257 322586924 322585759 0.000000e+00 926.0
7 TraesCS6B01G197300 chr6D 85.085 295 27 12 2697 2988 136127895 136127615 5.370000e-73 285.0
8 TraesCS6B01G197300 chr6D 82.743 226 28 10 3071 3287 136127613 136127390 1.200000e-44 191.0
9 TraesCS6B01G197300 chr6D 79.861 144 28 1 3148 3290 389599252 389599109 1.610000e-18 104.0
10 TraesCS6B01G197300 chr6A 95.315 2604 85 19 1 2588 177263932 177266514 0.000000e+00 4098.0
11 TraesCS6B01G197300 chr6A 81.213 1171 213 7 1089 2257 460006350 460005185 0.000000e+00 937.0
12 TraesCS6B01G197300 chr6A 82.561 453 56 13 2849 3288 177267625 177268067 8.620000e-101 377.0
13 TraesCS6B01G197300 chr6A 81.651 109 20 0 3182 3290 131511342 131511234 1.260000e-14 91.6
14 TraesCS6B01G197300 chr6A 90.476 42 3 1 2589 2629 48909165 48909124 2.000000e-03 54.7
15 TraesCS6B01G197300 chr3A 83.234 1175 192 4 1089 2262 279436871 279435701 0.000000e+00 1074.0
16 TraesCS6B01G197300 chr3D 82.981 1181 196 4 1083 2262 213996935 213998111 0.000000e+00 1062.0
17 TraesCS6B01G197300 chr3D 100.000 32 0 0 2589 2620 595929950 595929919 3.550000e-05 60.2
18 TraesCS6B01G197300 chr3B 82.979 1175 195 4 1089 2262 330800901 330799731 0.000000e+00 1057.0
19 TraesCS6B01G197300 chr1D 82.639 144 24 1 3148 3290 377966556 377966413 3.450000e-25 126.0
20 TraesCS6B01G197300 chr2B 85.981 107 12 3 3185 3290 734683619 734683515 9.650000e-21 111.0
21 TraesCS6B01G197300 chr2B 80.734 109 20 1 3148 3255 796832059 796831951 2.100000e-12 84.2
22 TraesCS6B01G197300 chr2B 92.500 40 3 0 2588 2627 477527188 477527149 1.280000e-04 58.4
23 TraesCS6B01G197300 chr1B 80.556 144 27 1 3148 3290 678869074 678868931 3.470000e-20 110.0
24 TraesCS6B01G197300 chr4D 82.178 101 18 0 3190 3290 42574062 42574162 1.630000e-13 87.9
25 TraesCS6B01G197300 chr5D 94.872 39 2 0 2589 2627 470466585 470466623 9.860000e-06 62.1
26 TraesCS6B01G197300 chr5D 97.222 36 0 1 2589 2624 325461913 325461879 3.550000e-05 60.2
27 TraesCS6B01G197300 chr2A 94.872 39 2 0 2585 2623 629634621 629634659 9.860000e-06 62.1
28 TraesCS6B01G197300 chr2D 100.000 32 0 0 2589 2620 96775328 96775359 3.550000e-05 60.2
29 TraesCS6B01G197300 chr7B 94.595 37 2 0 2589 2625 635699595 635699559 1.280000e-04 58.4


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 TraesCS6B01G197300 chr6B 234558025 234561314 3289 False 6076.0 6076 100.000000 1 3290 1 chr6B.!!$F1 3289
1 TraesCS6B01G197300 chr6B 500894276 500895447 1171 False 931.0 931 81.037000 1083 2257 1 chr6B.!!$F2 1174
2 TraesCS6B01G197300 chr6D 136127390 136130572 3182 True 1532.0 4120 87.864333 13 3287 3 chr6D.!!$R4 3274
3 TraesCS6B01G197300 chr6D 322571060 322572232 1172 True 928.0 928 80.969000 1082 2257 1 chr6D.!!$R1 1175
4 TraesCS6B01G197300 chr6D 322585759 322586924 1165 True 926.0 926 81.026000 1089 2257 1 chr6D.!!$R2 1168
5 TraesCS6B01G197300 chr6A 177263932 177268067 4135 False 2237.5 4098 88.938000 1 3288 2 chr6A.!!$F1 3287
6 TraesCS6B01G197300 chr6A 460005185 460006350 1165 True 937.0 937 81.213000 1089 2257 1 chr6A.!!$R3 1168
7 TraesCS6B01G197300 chr3A 279435701 279436871 1170 True 1074.0 1074 83.234000 1089 2262 1 chr3A.!!$R1 1173
8 TraesCS6B01G197300 chr3D 213996935 213998111 1176 False 1062.0 1062 82.981000 1083 2262 1 chr3D.!!$F1 1179
9 TraesCS6B01G197300 chr3B 330799731 330800901 1170 True 1057.0 1057 82.979000 1089 2262 1 chr3B.!!$R1 1173

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
145 157 0.108041 TAGGGCTTTAGAAACGGCCG 60.108 55.0 26.86 26.86 46.87 6.13 F
320 333 0.535335 GGAGATTGGGTGTACTGCGA 59.465 55.0 0.00 0.00 0.00 5.10 F
1657 1673 1.597742 GTGTCCACACTGTGCTCATT 58.402 50.0 7.90 0.00 43.25 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1673 1.191489 TCTCATCGTGCTGGGTGGAA 61.191 55.0 0.0 0.0 0.0 3.53 R
1882 1898 1.301677 GGTCCTTGCCAGAGAAAGCG 61.302 60.0 0.0 0.0 0.0 4.68 R
2797 3173 0.103937 GCCAGCTCATACTTCGCTCT 59.896 55.0 0.0 0.0 0.0 4.09 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
25 26 2.027653 CCGCCCTTCTTCTTCTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
66 67 2.496111 CTCGTTCCGATCTAGTAGGCT 58.504 52.381 0.00 0.00 34.61 4.58
91 92 4.355543 TCATTTTGCTTCCGTTGCTATC 57.644 40.909 0.00 0.00 0.00 2.08
92 93 4.009675 TCATTTTGCTTCCGTTGCTATCT 58.990 39.130 0.00 0.00 0.00 1.98
93 94 5.182487 TCATTTTGCTTCCGTTGCTATCTA 58.818 37.500 0.00 0.00 0.00 1.98
94 95 5.822519 TCATTTTGCTTCCGTTGCTATCTAT 59.177 36.000 0.00 0.00 0.00 1.98
95 96 5.734855 TTTTGCTTCCGTTGCTATCTATC 57.265 39.130 0.00 0.00 0.00 2.08
100 101 3.284323 TCCGTTGCTATCTATCTTCGC 57.716 47.619 0.00 0.00 0.00 4.70
145 157 0.108041 TAGGGCTTTAGAAACGGCCG 60.108 55.000 26.86 26.86 46.87 6.13
195 208 3.122780 GCGGTGAAATTTGCGCTTATTTT 59.877 39.130 9.73 5.86 0.00 1.82
223 236 6.726490 ACAACTTGTTGTCTAGAGGAAGTA 57.274 37.500 12.73 0.00 0.00 2.24
283 296 1.617533 GGGGATTTCGCCACCCTTTTA 60.618 52.381 8.66 0.00 46.98 1.52
291 304 3.638860 TCGCCACCCTTTTATCTCTCTA 58.361 45.455 0.00 0.00 0.00 2.43
320 333 0.535335 GGAGATTGGGTGTACTGCGA 59.465 55.000 0.00 0.00 0.00 5.10
330 343 2.538449 GGTGTACTGCGACCATTATTCG 59.462 50.000 0.00 0.00 39.56 3.34
372 385 4.918583 GGATTAGCGTTAGTAGTGATGAGC 59.081 45.833 0.00 0.00 0.00 4.26
469 482 3.305131 CGAGCAGTAGTTTGGTCACAGTA 60.305 47.826 6.11 0.00 43.84 2.74
509 525 4.835284 TCACAGTGCAATTGGATAGGTA 57.165 40.909 7.72 0.00 0.00 3.08
558 574 4.141711 GGATTTAGTGCTGGACAGTGGATA 60.142 45.833 1.24 0.00 32.79 2.59
561 577 5.435686 TTAGTGCTGGACAGTGGATAAAT 57.564 39.130 1.24 0.00 32.79 1.40
996 1012 9.291664 CTAAGTTTCTAACCTCTAGAATGTTCG 57.708 37.037 9.86 5.60 34.02 3.95
997 1013 7.463961 AGTTTCTAACCTCTAGAATGTTCGA 57.536 36.000 9.86 7.48 34.02 3.71
999 1015 7.976734 AGTTTCTAACCTCTAGAATGTTCGATG 59.023 37.037 9.86 2.48 34.02 3.84
1000 1016 7.640597 TTCTAACCTCTAGAATGTTCGATGA 57.359 36.000 9.86 4.23 0.00 2.92
1001 1017 7.028926 TCTAACCTCTAGAATGTTCGATGAC 57.971 40.000 9.86 0.00 0.00 3.06
1002 1018 5.661056 AACCTCTAGAATGTTCGATGACA 57.339 39.130 0.00 0.00 0.00 3.58
1003 1019 5.000012 ACCTCTAGAATGTTCGATGACAC 58.000 43.478 0.00 0.00 31.30 3.67
1004 1020 4.142138 ACCTCTAGAATGTTCGATGACACC 60.142 45.833 0.00 0.00 31.30 4.16
1019 1035 6.708502 TCGATGACACCTTTTTGTTCTTATGA 59.291 34.615 0.00 0.00 0.00 2.15
1061 1077 4.278419 ACACTGATCACCTTTTGTTTAGGC 59.722 41.667 0.00 0.00 36.17 3.93
1483 1499 2.306341 ATGCAACTGATGAGACTCCG 57.694 50.000 0.00 0.00 0.00 4.63
1657 1673 1.597742 GTGTCCACACTGTGCTCATT 58.402 50.000 7.90 0.00 43.25 2.57
1882 1898 2.191641 GGAGCTCATGGTGGAGGC 59.808 66.667 17.19 0.00 35.41 4.70
2134 2151 3.502595 CAGGCATGATCATCATCAACCTC 59.497 47.826 4.86 0.00 43.24 3.85
2277 2294 2.659291 CGTGAGCAAACACTTAGCGAAC 60.659 50.000 0.00 0.00 38.47 3.95
2338 2355 6.992664 AATATCTCTATTCACTGCTCCAGT 57.007 37.500 0.00 0.00 46.51 4.00
2409 2427 1.953686 GTGCTTGTATTGTGGGTGTGT 59.046 47.619 0.00 0.00 0.00 3.72
2626 2644 8.603898 TTATGAGACAGAGGGAGTAACATTTA 57.396 34.615 0.00 0.00 0.00 1.40
2628 2646 5.422331 TGAGACAGAGGGAGTAACATTTAGG 59.578 44.000 0.00 0.00 0.00 2.69
2662 2725 3.447950 ACCTAAATGTTACTCCCTCCGT 58.552 45.455 0.00 0.00 0.00 4.69
2663 2726 3.450096 ACCTAAATGTTACTCCCTCCGTC 59.550 47.826 0.00 0.00 0.00 4.79
2664 2727 3.705072 CCTAAATGTTACTCCCTCCGTCT 59.295 47.826 0.00 0.00 0.00 4.18
2665 2728 4.161754 CCTAAATGTTACTCCCTCCGTCTT 59.838 45.833 0.00 0.00 0.00 3.01
2666 2729 5.361857 CCTAAATGTTACTCCCTCCGTCTTA 59.638 44.000 0.00 0.00 0.00 2.10
2667 2730 5.952347 AAATGTTACTCCCTCCGTCTTAT 57.048 39.130 0.00 0.00 0.00 1.73
2669 2732 3.972133 TGTTACTCCCTCCGTCTTATGA 58.028 45.455 0.00 0.00 0.00 2.15
2670 2733 4.543689 TGTTACTCCCTCCGTCTTATGAT 58.456 43.478 0.00 0.00 0.00 2.45
2671 2734 5.698104 TGTTACTCCCTCCGTCTTATGATA 58.302 41.667 0.00 0.00 0.00 2.15
2674 2737 7.946219 TGTTACTCCCTCCGTCTTATGATATAA 59.054 37.037 0.00 0.00 0.00 0.98
2675 2738 8.460428 GTTACTCCCTCCGTCTTATGATATAAG 58.540 40.741 2.85 2.85 0.00 1.73
2676 2739 6.791371 ACTCCCTCCGTCTTATGATATAAGA 58.209 40.000 7.08 7.08 0.00 2.10
2677 2740 6.887545 ACTCCCTCCGTCTTATGATATAAGAG 59.112 42.308 10.62 6.39 34.59 2.85
2679 2742 7.925622 TCCCTCCGTCTTATGATATAAGAGTA 58.074 38.462 10.62 1.33 34.59 2.59
2680 2743 8.558312 TCCCTCCGTCTTATGATATAAGAGTAT 58.442 37.037 10.62 0.00 34.59 2.12
2681 2744 9.848710 CCCTCCGTCTTATGATATAAGAGTATA 57.151 37.037 10.62 0.00 34.59 1.47
2744 2862 5.015515 TGAATACCCTCATGCACATTGAAA 58.984 37.500 0.00 0.00 0.00 2.69
2745 2863 5.657745 TGAATACCCTCATGCACATTGAAAT 59.342 36.000 0.00 0.00 0.00 2.17
2746 2864 3.880047 ACCCTCATGCACATTGAAATG 57.120 42.857 1.45 1.45 42.10 2.32
2758 2881 7.485810 TGCACATTGAAATGATTGAATCCTAG 58.514 34.615 9.94 0.00 39.67 3.02
2773 2896 2.085320 TCCTAGAGCGTTCACTCTCAC 58.915 52.381 1.01 0.00 43.68 3.51
2778 3154 0.240411 AGCGTTCACTCTCACGTACC 59.760 55.000 0.00 0.00 38.70 3.34
2779 3155 1.063951 GCGTTCACTCTCACGTACCG 61.064 60.000 0.00 0.00 38.70 4.02
2780 3156 0.514255 CGTTCACTCTCACGTACCGA 59.486 55.000 0.00 0.00 0.00 4.69
2781 3157 1.069703 CGTTCACTCTCACGTACCGAA 60.070 52.381 0.00 0.00 0.00 4.30
2782 3158 2.314122 GTTCACTCTCACGTACCGAAC 58.686 52.381 0.00 0.00 0.00 3.95
2783 3159 1.888215 TCACTCTCACGTACCGAACT 58.112 50.000 0.00 0.00 0.00 3.01
2784 3160 1.802960 TCACTCTCACGTACCGAACTC 59.197 52.381 0.00 0.00 0.00 3.01
2785 3161 1.805345 CACTCTCACGTACCGAACTCT 59.195 52.381 0.00 0.00 0.00 3.24
2786 3162 2.075338 ACTCTCACGTACCGAACTCTC 58.925 52.381 0.00 0.00 0.00 3.20
2787 3163 2.074576 CTCTCACGTACCGAACTCTCA 58.925 52.381 0.00 0.00 0.00 3.27
2788 3164 1.802960 TCTCACGTACCGAACTCTCAC 59.197 52.381 0.00 0.00 0.00 3.51
2789 3165 0.514255 TCACGTACCGAACTCTCACG 59.486 55.000 0.00 0.00 38.52 4.35
2790 3166 0.236711 CACGTACCGAACTCTCACGT 59.763 55.000 0.00 0.00 45.87 4.49
2791 3167 1.460743 CACGTACCGAACTCTCACGTA 59.539 52.381 0.00 0.00 43.37 3.57
2792 3168 1.461127 ACGTACCGAACTCTCACGTAC 59.539 52.381 0.00 0.00 43.39 3.67
2793 3169 1.728971 CGTACCGAACTCTCACGTACT 59.271 52.381 0.00 0.00 0.00 2.73
2794 3170 2.222685 CGTACCGAACTCTCACGTACTC 60.223 54.545 0.00 0.00 0.00 2.59
2795 3171 2.181954 ACCGAACTCTCACGTACTCT 57.818 50.000 0.00 0.00 0.00 3.24
2796 3172 1.805345 ACCGAACTCTCACGTACTCTG 59.195 52.381 0.00 0.00 0.00 3.35
2797 3173 2.074576 CCGAACTCTCACGTACTCTGA 58.925 52.381 0.00 0.00 0.00 3.27
2805 3181 1.732809 TCACGTACTCTGAGAGCGAAG 59.267 52.381 23.55 17.27 32.04 3.79
2817 3193 0.103937 GAGCGAAGTATGAGCTGGCT 59.896 55.000 0.00 0.00 41.84 4.75
2870 3780 5.384063 ACGAACACATTTTCATATGGCAA 57.616 34.783 2.13 0.00 0.00 4.52
2871 3781 5.777802 ACGAACACATTTTCATATGGCAAA 58.222 33.333 2.13 3.36 0.00 3.68
2878 3788 7.094291 ACACATTTTCATATGGCAAATTTTGGG 60.094 33.333 10.96 2.79 0.00 4.12
2908 3819 9.906660 AGAGCATTTTCATATTTGTTTTCGTTA 57.093 25.926 0.00 0.00 0.00 3.18
3033 3944 4.657436 ATTCTAGAGCGTTAGTTGGGAG 57.343 45.455 0.00 0.00 0.00 4.30
3065 3976 7.305993 GGAAACGTTCATTTGTTTTTAGCTGAG 60.306 37.037 0.00 0.00 38.35 3.35
3069 3980 6.512297 GTTCATTTGTTTTTAGCTGAGGGAA 58.488 36.000 0.00 0.00 0.00 3.97
3106 4017 3.352748 TCCCCCTAGGAGGCGTCA 61.353 66.667 11.48 0.00 40.93 4.35
3107 4018 2.840102 CCCCCTAGGAGGCGTCAG 60.840 72.222 11.48 0.00 38.24 3.51
3108 4019 2.279073 CCCCTAGGAGGCGTCAGA 59.721 66.667 11.48 0.00 32.73 3.27
3109 4020 2.128507 CCCCTAGGAGGCGTCAGAC 61.129 68.421 11.48 0.00 32.73 3.51
3145 4063 2.203139 TGGCTGGTGTTGTCACGG 60.203 61.111 0.00 0.00 44.68 4.94
3146 4064 2.203153 GGCTGGTGTTGTCACGGT 60.203 61.111 0.00 0.00 44.68 4.83
3162 4080 2.501610 GTGGTCCGCCTCATCTCC 59.498 66.667 0.00 0.00 35.27 3.71
3164 4082 3.917760 GGTCCGCCTCATCTCCGG 61.918 72.222 0.00 0.00 43.21 5.14
3171 4099 2.801631 CCTCATCTCCGGTGGCCTC 61.802 68.421 3.32 0.00 0.00 4.70
3178 4106 3.006728 CCGGTGGCCTCAGGGTTA 61.007 66.667 15.43 0.00 34.45 2.85
3182 4110 0.395724 GGTGGCCTCAGGGTTAATGG 60.396 60.000 3.32 0.00 34.45 3.16
3183 4111 0.623723 GTGGCCTCAGGGTTAATGGA 59.376 55.000 3.32 0.00 34.45 3.41
3184 4112 0.623723 TGGCCTCAGGGTTAATGGAC 59.376 55.000 3.32 0.00 34.45 4.02
3188 4117 1.553248 CCTCAGGGTTAATGGACGTGA 59.447 52.381 0.00 0.00 0.00 4.35
3195 4124 3.181454 GGGTTAATGGACGTGATGGATCT 60.181 47.826 0.00 0.00 0.00 2.75
3222 4151 2.041115 GCTGGCGGGAGGACTTTTC 61.041 63.158 0.00 0.00 0.00 2.29
3269 4198 7.432148 TGTTAGGGTTTATATTCTGCTCAGA 57.568 36.000 0.00 0.00 35.27 3.27
3276 4205 4.701663 TTCTGCTCAGAAAGGCGG 57.298 55.556 9.66 0.00 43.79 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.885494 TGAAGAAGAAGAAGAAGAAGAAGAAG 57.115 34.615 0.00 0.00 0.00 2.85
10 11 9.844257 AATGAAGAAGAAGAAGAAGAAGAAGAA 57.156 29.630 0.00 0.00 0.00 2.52
11 12 9.844257 AAATGAAGAAGAAGAAGAAGAAGAAGA 57.156 29.630 0.00 0.00 0.00 2.87
25 26 6.017109 ACGAGCTTAAGCAAAATGAAGAAGAA 60.017 34.615 28.39 0.00 45.16 2.52
66 67 2.741612 CAACGGAAGCAAAATGAAGCA 58.258 42.857 0.00 0.00 0.00 3.91
91 92 1.883275 ACCAGATCGGAGCGAAGATAG 59.117 52.381 10.05 0.00 39.99 2.08
92 93 1.982660 ACCAGATCGGAGCGAAGATA 58.017 50.000 10.05 0.00 39.99 1.98
93 94 1.609555 GTACCAGATCGGAGCGAAGAT 59.390 52.381 10.05 0.00 39.99 2.40
94 95 1.022735 GTACCAGATCGGAGCGAAGA 58.977 55.000 10.05 0.00 39.99 2.87
95 96 0.317103 CGTACCAGATCGGAGCGAAG 60.317 60.000 10.05 0.00 39.99 3.79
100 101 0.179145 AAACGCGTACCAGATCGGAG 60.179 55.000 14.46 3.46 38.63 4.63
145 157 2.586357 GGCGACGGATCAAGAGGC 60.586 66.667 0.00 0.00 0.00 4.70
223 236 3.706373 ACTGCGAACCTGGGCGAT 61.706 61.111 14.14 0.00 0.00 4.58
283 296 7.421147 CCAATCTCCCAAGGATTTTAGAGAGAT 60.421 40.741 0.00 0.00 40.60 2.75
291 304 3.181407 ACACCCAATCTCCCAAGGATTTT 60.181 43.478 0.00 0.00 31.90 1.82
320 333 3.008594 TGGTTCACAGGACGAATAATGGT 59.991 43.478 0.00 0.00 0.00 3.55
372 385 0.602638 TGCGTACAGAACAAGCCCTG 60.603 55.000 0.00 0.00 36.53 4.45
398 411 5.071788 CCAGATAAAAGGACAGGGCACTATA 59.928 44.000 0.00 0.00 0.00 1.31
509 525 3.627577 CCACTATTTCGCAGCATAAAGGT 59.372 43.478 0.00 0.00 0.00 3.50
558 574 3.883830 TGCACTGTGACCAAACAATTT 57.116 38.095 12.86 0.00 0.00 1.82
561 577 3.519579 CAATTGCACTGTGACCAAACAA 58.480 40.909 12.86 5.39 0.00 2.83
990 1006 5.299279 AGAACAAAAAGGTGTCATCGAACAT 59.701 36.000 0.00 0.00 0.00 2.71
995 1011 6.797033 GTCATAAGAACAAAAAGGTGTCATCG 59.203 38.462 0.00 0.00 0.00 3.84
996 1012 7.591426 GTGTCATAAGAACAAAAAGGTGTCATC 59.409 37.037 0.00 0.00 0.00 2.92
997 1013 7.068103 TGTGTCATAAGAACAAAAAGGTGTCAT 59.932 33.333 0.00 0.00 0.00 3.06
999 1015 6.791303 TGTGTCATAAGAACAAAAAGGTGTC 58.209 36.000 0.00 0.00 0.00 3.67
1000 1016 6.767524 TGTGTCATAAGAACAAAAAGGTGT 57.232 33.333 0.00 0.00 0.00 4.16
1001 1017 8.647143 AATTGTGTCATAAGAACAAAAAGGTG 57.353 30.769 0.00 0.00 37.36 4.00
1019 1035 6.992123 TCAGTGTCTCAGAACATAAATTGTGT 59.008 34.615 0.00 0.00 38.99 3.72
1061 1077 3.822735 TCAACTTCAGCCATCTTCTTTGG 59.177 43.478 0.00 0.00 37.31 3.28
1483 1499 1.452833 GCTGAGGGGCATGAACTCC 60.453 63.158 0.00 0.00 0.00 3.85
1657 1673 1.191489 TCTCATCGTGCTGGGTGGAA 61.191 55.000 0.00 0.00 0.00 3.53
1882 1898 1.301677 GGTCCTTGCCAGAGAAAGCG 61.302 60.000 0.00 0.00 0.00 4.68
2134 2151 2.660064 CCCACCCCTCTTGAGGTCG 61.660 68.421 14.77 7.50 32.72 4.79
2257 2274 2.544267 AGTTCGCTAAGTGTTTGCTCAC 59.456 45.455 0.00 0.00 38.46 3.51
2369 2387 4.693283 CACCTCTAAACACAGACACTCAA 58.307 43.478 0.00 0.00 0.00 3.02
2370 2388 3.492656 GCACCTCTAAACACAGACACTCA 60.493 47.826 0.00 0.00 0.00 3.41
2371 2389 3.060602 GCACCTCTAAACACAGACACTC 58.939 50.000 0.00 0.00 0.00 3.51
2409 2427 7.161404 ACATGAGCAGATAAGAACACAAGTAA 58.839 34.615 0.00 0.00 0.00 2.24
2588 2606 9.941325 CCTCTGTCTCATAATATAAGAGCATTT 57.059 33.333 0.00 0.00 0.00 2.32
2589 2607 8.538701 CCCTCTGTCTCATAATATAAGAGCATT 58.461 37.037 0.00 0.00 0.00 3.56
2590 2608 7.898100 TCCCTCTGTCTCATAATATAAGAGCAT 59.102 37.037 0.00 0.00 0.00 3.79
2591 2609 7.241628 TCCCTCTGTCTCATAATATAAGAGCA 58.758 38.462 0.00 0.00 0.00 4.26
2592 2610 7.396055 ACTCCCTCTGTCTCATAATATAAGAGC 59.604 40.741 0.00 0.00 0.00 4.09
2593 2611 8.877864 ACTCCCTCTGTCTCATAATATAAGAG 57.122 38.462 0.00 0.00 0.00 2.85
2596 2614 9.877222 TGTTACTCCCTCTGTCTCATAATATAA 57.123 33.333 0.00 0.00 0.00 0.98
2598 2616 8.964533 ATGTTACTCCCTCTGTCTCATAATAT 57.035 34.615 0.00 0.00 0.00 1.28
2601 2619 7.496346 AAATGTTACTCCCTCTGTCTCATAA 57.504 36.000 0.00 0.00 0.00 1.90
2685 2748 7.970614 GCTTAAAAACCTACTAGTACGCTCTTA 59.029 37.037 0.00 0.00 0.00 2.10
2686 2749 6.810676 GCTTAAAAACCTACTAGTACGCTCTT 59.189 38.462 0.00 0.00 0.00 2.85
2687 2750 6.328714 GCTTAAAAACCTACTAGTACGCTCT 58.671 40.000 0.00 0.00 0.00 4.09
2688 2751 5.518128 GGCTTAAAAACCTACTAGTACGCTC 59.482 44.000 0.00 0.00 0.00 5.03
2689 2752 5.186603 AGGCTTAAAAACCTACTAGTACGCT 59.813 40.000 0.00 0.00 33.38 5.07
2690 2753 5.414360 AGGCTTAAAAACCTACTAGTACGC 58.586 41.667 0.00 0.00 33.38 4.42
2691 2754 6.861144 AGAGGCTTAAAAACCTACTAGTACG 58.139 40.000 0.00 0.00 36.05 3.67
2692 2755 9.747293 CATAGAGGCTTAAAAACCTACTAGTAC 57.253 37.037 0.00 0.00 36.05 2.73
2693 2756 9.705103 TCATAGAGGCTTAAAAACCTACTAGTA 57.295 33.333 1.89 1.89 36.05 1.82
2695 2758 8.697292 ACTCATAGAGGCTTAAAAACCTACTAG 58.303 37.037 0.00 0.00 36.05 2.57
2696 2759 8.475639 CACTCATAGAGGCTTAAAAACCTACTA 58.524 37.037 0.00 0.00 36.05 1.82
2698 2761 7.328737 TCACTCATAGAGGCTTAAAAACCTAC 58.671 38.462 0.00 0.00 36.05 3.18
2699 2762 7.490657 TCACTCATAGAGGCTTAAAAACCTA 57.509 36.000 0.00 0.00 36.05 3.08
2701 2764 7.631717 ATTCACTCATAGAGGCTTAAAAACC 57.368 36.000 0.00 0.00 33.35 3.27
2702 2765 8.613482 GGTATTCACTCATAGAGGCTTAAAAAC 58.387 37.037 0.00 0.00 33.35 2.43
2703 2766 7.773690 GGGTATTCACTCATAGAGGCTTAAAAA 59.226 37.037 0.00 0.00 33.35 1.94
2708 2826 4.561752 AGGGTATTCACTCATAGAGGCTT 58.438 43.478 0.00 0.00 33.35 4.35
2733 2851 6.288941 AGGATTCAATCATTTCAATGTGCA 57.711 33.333 0.00 0.00 37.65 4.57
2744 2862 5.053145 GTGAACGCTCTAGGATTCAATCAT 58.947 41.667 0.00 0.00 33.09 2.45
2745 2863 4.160439 AGTGAACGCTCTAGGATTCAATCA 59.840 41.667 0.00 0.00 33.09 2.57
2746 2864 4.688021 AGTGAACGCTCTAGGATTCAATC 58.312 43.478 0.00 0.00 33.09 2.67
2758 2881 1.604396 GTACGTGAGAGTGAACGCTC 58.396 55.000 7.20 7.20 43.49 5.03
2778 3154 2.994578 TCTCAGAGTACGTGAGAGTTCG 59.005 50.000 20.82 2.97 44.43 3.95
2783 3159 1.067071 TCGCTCTCAGAGTACGTGAGA 60.067 52.381 22.35 22.35 46.57 3.27
2784 3160 1.360820 TCGCTCTCAGAGTACGTGAG 58.639 55.000 17.69 17.69 42.51 3.51
2785 3161 1.732809 CTTCGCTCTCAGAGTACGTGA 59.267 52.381 2.93 1.60 31.39 4.35
2786 3162 1.465387 ACTTCGCTCTCAGAGTACGTG 59.535 52.381 2.93 10.01 31.39 4.49
2787 3163 1.810959 ACTTCGCTCTCAGAGTACGT 58.189 50.000 2.93 0.00 31.39 3.57
2788 3164 3.556365 TCATACTTCGCTCTCAGAGTACG 59.444 47.826 2.93 0.00 31.39 3.67
2789 3165 4.553938 GCTCATACTTCGCTCTCAGAGTAC 60.554 50.000 2.93 0.00 31.39 2.73
2790 3166 3.562141 GCTCATACTTCGCTCTCAGAGTA 59.438 47.826 2.93 0.00 31.39 2.59
2791 3167 2.357637 GCTCATACTTCGCTCTCAGAGT 59.642 50.000 2.93 0.00 31.39 3.24
2792 3168 2.618241 AGCTCATACTTCGCTCTCAGAG 59.382 50.000 0.00 0.00 0.00 3.35
2793 3169 2.357323 CAGCTCATACTTCGCTCTCAGA 59.643 50.000 0.00 0.00 0.00 3.27
2794 3170 2.543445 CCAGCTCATACTTCGCTCTCAG 60.543 54.545 0.00 0.00 0.00 3.35
2795 3171 1.406898 CCAGCTCATACTTCGCTCTCA 59.593 52.381 0.00 0.00 0.00 3.27
2796 3172 1.867698 GCCAGCTCATACTTCGCTCTC 60.868 57.143 0.00 0.00 0.00 3.20
2797 3173 0.103937 GCCAGCTCATACTTCGCTCT 59.896 55.000 0.00 0.00 0.00 4.09
2805 3181 1.651987 TTAACGCAGCCAGCTCATAC 58.348 50.000 0.00 0.00 42.61 2.39
2817 3193 3.478509 TCCTAAGCAAACCTTTAACGCA 58.521 40.909 0.00 0.00 34.95 5.24
2904 3814 1.076332 CTCGCCAAAGGGAGTTAACG 58.924 55.000 0.00 0.00 45.57 3.18
3004 3915 6.086785 ACTAACGCTCTAGAATTACCATCC 57.913 41.667 0.00 0.00 0.00 3.51
3008 3919 5.048507 CCCAACTAACGCTCTAGAATTACC 58.951 45.833 0.00 0.00 0.00 2.85
3033 3944 4.141855 ACAAATGAACGTTTCCGATCAC 57.858 40.909 0.46 0.00 46.55 3.06
3045 3956 6.084326 TCCCTCAGCTAAAAACAAATGAAC 57.916 37.500 0.00 0.00 0.00 3.18
3049 3960 6.916360 TCATTCCCTCAGCTAAAAACAAAT 57.084 33.333 0.00 0.00 0.00 2.32
3050 3961 6.349280 CGATCATTCCCTCAGCTAAAAACAAA 60.349 38.462 0.00 0.00 0.00 2.83
3057 3968 3.432186 CCAACGATCATTCCCTCAGCTAA 60.432 47.826 0.00 0.00 0.00 3.09
3065 3976 2.103263 ACTAGAGCCAACGATCATTCCC 59.897 50.000 0.00 0.00 0.00 3.97
3069 3980 4.021016 GGGATAACTAGAGCCAACGATCAT 60.021 45.833 0.00 0.00 0.00 2.45
3102 4013 1.625616 AATAAGAACGCCGTCTGACG 58.374 50.000 22.49 22.49 42.11 4.35
3103 4014 5.311271 GTTAAAATAAGAACGCCGTCTGAC 58.689 41.667 0.00 0.00 0.00 3.51
3104 4015 4.389687 GGTTAAAATAAGAACGCCGTCTGA 59.610 41.667 0.00 0.00 0.00 3.27
3105 4016 4.390909 AGGTTAAAATAAGAACGCCGTCTG 59.609 41.667 0.00 0.00 0.00 3.51
3106 4017 4.390909 CAGGTTAAAATAAGAACGCCGTCT 59.609 41.667 0.00 0.00 0.00 4.18
3107 4018 4.436451 CCAGGTTAAAATAAGAACGCCGTC 60.436 45.833 0.00 0.00 0.00 4.79
3108 4019 3.437741 CCAGGTTAAAATAAGAACGCCGT 59.562 43.478 0.00 0.00 0.00 5.68
3109 4020 3.729762 GCCAGGTTAAAATAAGAACGCCG 60.730 47.826 0.00 0.00 0.00 6.46
3145 4063 2.501610 GGAGATGAGGCGGACCAC 59.498 66.667 0.00 0.00 39.06 4.16
3146 4064 3.147595 CGGAGATGAGGCGGACCA 61.148 66.667 0.00 0.00 39.06 4.02
3153 4071 2.765807 AGGCCACCGGAGATGAGG 60.766 66.667 9.46 0.54 0.00 3.86
3162 4080 0.748005 CATTAACCCTGAGGCCACCG 60.748 60.000 5.01 0.00 36.11 4.94
3164 4082 0.623723 TCCATTAACCCTGAGGCCAC 59.376 55.000 5.01 0.00 36.11 5.01
3171 4099 2.093181 TCCATCACGTCCATTAACCCTG 60.093 50.000 0.00 0.00 0.00 4.45
3178 4106 1.069204 CCGAGATCCATCACGTCCATT 59.931 52.381 5.80 0.00 38.85 3.16
3182 4110 1.300233 GGCCGAGATCCATCACGTC 60.300 63.158 5.80 0.00 38.85 4.34
3183 4111 1.330655 AAGGCCGAGATCCATCACGT 61.331 55.000 0.00 0.00 38.85 4.49
3184 4112 0.179073 AAAGGCCGAGATCCATCACG 60.179 55.000 0.00 0.00 39.93 4.35
3188 4117 0.465097 CAGCAAAGGCCGAGATCCAT 60.465 55.000 0.00 0.00 42.56 3.41
3222 4151 9.586435 AACAAAACTCAAAGAACCATCTAAAAG 57.414 29.630 0.00 0.00 33.77 2.27


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

AutoCloner maintained by Alex Coulton.