Multiple sequence alignment - TraesCS1A01G221700

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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 TraesCS1A01G221700 chr1A 100.000 3138 0 0 1 3138 391234596 391237733 0.000000e+00 5795
1 TraesCS1A01G221700 chr1D 87.684 1900 86 51 620 2440 311256748 311258578 0.000000e+00 2076
2 TraesCS1A01G221700 chr1D 88.114 631 32 21 2 627 311256044 311256636 0.000000e+00 710
3 TraesCS1A01G221700 chr1B 89.773 1144 43 26 620 1720 420993838 420994950 0.000000e+00 1397
4 TraesCS1A01G221700 chr1B 86.326 724 58 23 1730 2440 420994993 420995688 0.000000e+00 750
5 TraesCS1A01G221700 chr1B 85.856 403 29 18 227 627 420993315 420993691 1.360000e-108 403
6 TraesCS1A01G221700 chr1B 84.615 234 25 8 1 228 420992637 420992865 4.070000e-54 222
7 TraesCS1A01G221700 chr3A 96.232 690 24 2 2450 3138 712464624 712465312 0.000000e+00 1129
8 TraesCS1A01G221700 chr3A 94.262 122 7 0 1085 1206 101958811 101958690 1.490000e-43 187
9 TraesCS1A01G221700 chr5B 96.755 678 19 1 2461 3138 409449173 409448499 0.000000e+00 1127
10 TraesCS1A01G221700 chr7B 95.507 690 29 2 2450 3138 597601657 597600969 0.000000e+00 1101
11 TraesCS1A01G221700 chr3B 95.044 686 32 2 2453 3138 660988307 660987624 0.000000e+00 1077
12 TraesCS1A01G221700 chr3B 96.429 504 14 2 2639 3138 810784020 810784523 0.000000e+00 828
13 TraesCS1A01G221700 chr4D 83.140 688 111 5 2453 3138 490593190 490592506 9.560000e-175 623
14 TraesCS1A01G221700 chr4D 82.394 284 39 8 1063 1345 497915949 497915676 1.450000e-58 237
15 TraesCS1A01G221700 chr4A 82.779 691 113 6 2451 3138 137954591 137953904 2.070000e-171 612
16 TraesCS1A01G221700 chr4A 93.333 105 7 0 1442 1546 36622875 36622771 4.190000e-34 156
17 TraesCS1A01G221700 chr4A 92.079 101 4 2 1083 1182 36623006 36622909 4.220000e-29 139
18 TraesCS1A01G221700 chr4A 81.065 169 18 7 2273 2441 145036292 145036138 4.250000e-24 122
19 TraesCS1A01G221700 chr2D 81.979 677 120 2 2461 3136 52505028 52505703 9.760000e-160 573
20 TraesCS1A01G221700 chr2A 81.684 677 122 2 2461 3136 672508050 672508725 2.110000e-156 562
21 TraesCS1A01G221700 chr2A 89.575 259 20 6 1023 1281 104770702 104770451 3.900000e-84 322
22 TraesCS1A01G221700 chr6A 95.902 122 5 0 1085 1206 20336243 20336122 6.860000e-47 198
23 TraesCS1A01G221700 chr6B 93.333 105 2 3 1079 1182 25967268 25967168 1.950000e-32 150
24 TraesCS1A01G221700 chr5A 93.590 78 4 1 1079 1156 64659020 64658944 7.110000e-22 115


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 TraesCS1A01G221700 chr1A 391234596 391237733 3137 False 5795 5795 100.0000 1 3138 1 chr1A.!!$F1 3137
1 TraesCS1A01G221700 chr1D 311256044 311258578 2534 False 1393 2076 87.8990 2 2440 2 chr1D.!!$F1 2438
2 TraesCS1A01G221700 chr1B 420992637 420995688 3051 False 693 1397 86.6425 1 2440 4 chr1B.!!$F1 2439
3 TraesCS1A01G221700 chr3A 712464624 712465312 688 False 1129 1129 96.2320 2450 3138 1 chr3A.!!$F1 688
4 TraesCS1A01G221700 chr5B 409448499 409449173 674 True 1127 1127 96.7550 2461 3138 1 chr5B.!!$R1 677
5 TraesCS1A01G221700 chr7B 597600969 597601657 688 True 1101 1101 95.5070 2450 3138 1 chr7B.!!$R1 688
6 TraesCS1A01G221700 chr3B 660987624 660988307 683 True 1077 1077 95.0440 2453 3138 1 chr3B.!!$R1 685
7 TraesCS1A01G221700 chr3B 810784020 810784523 503 False 828 828 96.4290 2639 3138 1 chr3B.!!$F1 499
8 TraesCS1A01G221700 chr4D 490592506 490593190 684 True 623 623 83.1400 2453 3138 1 chr4D.!!$R1 685
9 TraesCS1A01G221700 chr4A 137953904 137954591 687 True 612 612 82.7790 2451 3138 1 chr4A.!!$R1 687
10 TraesCS1A01G221700 chr2D 52505028 52505703 675 False 573 573 81.9790 2461 3136 1 chr2D.!!$F1 675
11 TraesCS1A01G221700 chr2A 672508050 672508725 675 False 562 562 81.6840 2461 3136 1 chr2A.!!$F1 675

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
221 226 0.959553 ATACGACAGATACCGGCAGG 59.040 55.0 0.0 0.0 45.13 4.85 F
1385 2055 0.320697 CGGTTTCCTTCCTTCTCGGT 59.679 55.0 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2461 0.250166 GCCGGCGGGATAGTATTGTT 60.250 55.0 29.48 0.0 34.06 2.83 R
2254 2974 0.034863 TAAGCACCGTTCCCAATCCC 60.035 55.0 0.00 0.0 0.00 3.85 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
46 47 3.121030 ACAAGACGCATCGCCAGC 61.121 61.111 0.00 0.00 0.00 4.85
71 72 9.346725 GCTCCATCAGTTTTTCTTTTGTTATAG 57.653 33.333 0.00 0.00 0.00 1.31
130 135 1.556911 GCTCCATCTCCAACTCCAAGA 59.443 52.381 0.00 0.00 0.00 3.02
175 180 2.014857 GCCGGATTAAGAAACCTCACC 58.985 52.381 5.05 0.00 0.00 4.02
184 189 2.322658 AGAAACCTCACCACTAACGGA 58.677 47.619 0.00 0.00 0.00 4.69
221 226 0.959553 ATACGACAGATACCGGCAGG 59.040 55.000 0.00 0.00 45.13 4.85
492 949 1.818674 CCGGCCTGCTTTAATCACTTT 59.181 47.619 0.00 0.00 0.00 2.66
495 952 2.232208 GGCCTGCTTTAATCACTTTGCT 59.768 45.455 0.00 0.00 0.00 3.91
499 956 6.101997 GCCTGCTTTAATCACTTTGCTATTT 58.898 36.000 0.00 0.00 0.00 1.40
543 1001 5.701290 CCCGAAGAAGAGAAAAACTGTACAT 59.299 40.000 0.00 0.00 0.00 2.29
570 1028 6.655425 TGAATTCCCACATTGAAACATACGTA 59.345 34.615 2.27 0.00 0.00 3.57
572 1030 5.155278 TCCCACATTGAAACATACGTACT 57.845 39.130 0.00 0.00 0.00 2.73
574 1032 6.101332 TCCCACATTGAAACATACGTACTAC 58.899 40.000 0.00 0.00 0.00 2.73
658 1270 2.355115 GGTGGGAATCGTGGCCTT 59.645 61.111 3.32 0.00 0.00 4.35
735 1350 2.122769 TCCGTCAGGGTGGGTCAA 60.123 61.111 0.00 0.00 38.33 3.18
864 1479 1.349357 GCCTCCATCTATCCACTTCCC 59.651 57.143 0.00 0.00 0.00 3.97
904 1522 1.905843 CAATCCGGCCAACCAACCA 60.906 57.895 2.24 0.00 34.57 3.67
905 1523 1.152440 AATCCGGCCAACCAACCAA 60.152 52.632 2.24 0.00 34.57 3.67
906 1524 1.468506 AATCCGGCCAACCAACCAAC 61.469 55.000 2.24 0.00 34.57 3.77
907 1525 3.611674 CCGGCCAACCAACCAACC 61.612 66.667 2.24 0.00 34.57 3.77
927 1571 3.842923 ACTGCCCGATCAGCTCCG 61.843 66.667 6.31 0.00 37.59 4.63
930 1574 3.532155 GCCCGATCAGCTCCGTCT 61.532 66.667 0.00 0.00 0.00 4.18
1263 1915 4.776322 CCGGCCATGCTCGACCAA 62.776 66.667 2.24 0.00 0.00 3.67
1377 2047 0.536460 TGCAACCTCGGTTTCCTTCC 60.536 55.000 0.00 0.00 36.00 3.46
1379 2049 1.818131 GCAACCTCGGTTTCCTTCCTT 60.818 52.381 0.00 0.00 36.00 3.36
1380 2050 2.152016 CAACCTCGGTTTCCTTCCTTC 58.848 52.381 0.00 0.00 36.00 3.46
1381 2051 1.730851 ACCTCGGTTTCCTTCCTTCT 58.269 50.000 0.00 0.00 0.00 2.85
1382 2052 1.624312 ACCTCGGTTTCCTTCCTTCTC 59.376 52.381 0.00 0.00 0.00 2.87
1385 2055 0.320697 CGGTTTCCTTCCTTCTCGGT 59.679 55.000 0.00 0.00 0.00 4.69
1392 2062 2.837371 CTTCCTTCTCGGTCACGGCC 62.837 65.000 0.00 0.00 41.39 6.13
1766 2470 5.654317 TTGCGTGACGAAAAACAATACTA 57.346 34.783 10.10 0.00 0.00 1.82
1768 2472 5.849858 TGCGTGACGAAAAACAATACTATC 58.150 37.500 10.10 0.00 0.00 2.08
1770 2474 5.725864 GCGTGACGAAAAACAATACTATCCC 60.726 44.000 10.10 0.00 0.00 3.85
1771 2475 5.499652 CGTGACGAAAAACAATACTATCCCG 60.500 44.000 0.00 0.00 0.00 5.14
1773 2477 3.624410 ACGAAAAACAATACTATCCCGCC 59.376 43.478 0.00 0.00 0.00 6.13
1774 2478 3.302870 CGAAAAACAATACTATCCCGCCG 60.303 47.826 0.00 0.00 0.00 6.46
1775 2479 2.249844 AAACAATACTATCCCGCCGG 57.750 50.000 0.00 0.00 0.00 6.13
1808 2514 2.151202 GGCGTGATTCCTGAGAACAAA 58.849 47.619 0.00 0.00 33.97 2.83
1829 2535 3.753787 AGGCATTATTAGGCTGGGC 57.246 52.632 0.00 0.00 40.72 5.36
1837 2543 1.972660 ATTAGGCTGGGCTGTCGTCC 61.973 60.000 6.93 0.00 34.70 4.79
1881 2590 3.242248 GTCGAGGAACCAAATACGATTCG 59.758 47.826 4.14 4.14 32.78 3.34
1929 2638 3.796717 GCCGATATGTTTAAGCCAAAAGC 59.203 43.478 0.00 0.00 44.25 3.51
1953 2662 7.661847 AGCAGTGCTTTTCTACTTACTAACAAT 59.338 33.333 13.14 0.00 33.89 2.71
2015 2729 0.600255 CACCGGACGAGAAAAGCAGT 60.600 55.000 9.46 0.00 0.00 4.40
2037 2757 8.384365 GCAGTGAGCTTTTACTTTCTTATACTC 58.616 37.037 0.00 0.00 41.15 2.59
2205 2925 6.174049 AGTAGGTGGAGATAGTTTTTCTTGC 58.826 40.000 0.00 0.00 0.00 4.01
2221 2941 6.843069 TTTCTTGCTAGCCAAAATTTTGTC 57.157 33.333 25.25 15.89 36.45 3.18
2254 2974 4.815308 TGCAAAAATTGTGAGGTCCATTTG 59.185 37.500 0.00 0.00 0.00 2.32
2255 2975 4.213906 GCAAAAATTGTGAGGTCCATTTGG 59.786 41.667 0.00 0.00 0.00 3.28
2256 2976 4.622260 AAAATTGTGAGGTCCATTTGGG 57.378 40.909 0.00 0.00 35.41 4.12
2257 2977 3.541242 AATTGTGAGGTCCATTTGGGA 57.459 42.857 0.00 0.00 45.89 4.37
2273 2993 0.034863 GGGATTGGGAACGGTGCTTA 60.035 55.000 0.00 0.00 0.00 3.09
2274 2994 1.092348 GGATTGGGAACGGTGCTTAC 58.908 55.000 0.00 0.00 0.00 2.34
2283 3003 3.124636 GGAACGGTGCTTACATGTAAGTG 59.875 47.826 34.74 26.15 43.28 3.16
2284 3004 3.671008 ACGGTGCTTACATGTAAGTGA 57.329 42.857 34.74 23.85 43.28 3.41
2285 3005 3.997762 ACGGTGCTTACATGTAAGTGAA 58.002 40.909 34.74 23.01 43.28 3.18
2305 3025 6.832384 AGTGAAGGAGATACTGTAAATACGGA 59.168 38.462 6.41 0.00 36.44 4.69
2307 3027 7.434602 GTGAAGGAGATACTGTAAATACGGAAC 59.565 40.741 6.41 0.00 36.44 3.62
2308 3028 7.123098 TGAAGGAGATACTGTAAATACGGAACA 59.877 37.037 6.41 0.00 36.44 3.18
2342 3063 3.997064 CTCAGTTCGGCCTCCTGCG 62.997 68.421 0.00 0.00 42.61 5.18
2419 3140 2.751259 TGTGCTCATTCTCATGCTTTCC 59.249 45.455 0.00 0.00 0.00 3.13
2427 3148 2.430465 TCTCATGCTTTCCTGCAGTTC 58.570 47.619 13.81 0.00 46.71 3.01
2428 3149 2.156917 CTCATGCTTTCCTGCAGTTCA 58.843 47.619 13.81 3.17 46.71 3.18
2431 3152 2.346766 TGCTTTCCTGCAGTTCAAGA 57.653 45.000 13.81 0.00 38.12 3.02
2435 3156 3.067320 GCTTTCCTGCAGTTCAAGACTTT 59.933 43.478 13.81 0.00 36.10 2.66
2440 3161 5.300752 TCCTGCAGTTCAAGACTTTCTTAG 58.699 41.667 13.81 0.00 33.78 2.18
2441 3162 5.070446 TCCTGCAGTTCAAGACTTTCTTAGA 59.930 40.000 13.81 0.00 33.78 2.10
2442 3163 5.936956 CCTGCAGTTCAAGACTTTCTTAGAT 59.063 40.000 13.81 0.00 33.78 1.98
2443 3164 7.039011 TCCTGCAGTTCAAGACTTTCTTAGATA 60.039 37.037 13.81 0.00 33.78 1.98
2444 3165 7.277539 CCTGCAGTTCAAGACTTTCTTAGATAG 59.722 40.741 13.81 0.00 33.78 2.08
2445 3166 7.671302 TGCAGTTCAAGACTTTCTTAGATAGT 58.329 34.615 5.06 5.06 33.78 2.12
2446 3167 8.150945 TGCAGTTCAAGACTTTCTTAGATAGTT 58.849 33.333 6.77 0.00 33.78 2.24
2447 3168 8.994170 GCAGTTCAAGACTTTCTTAGATAGTTT 58.006 33.333 6.77 0.00 33.78 2.66
2452 3173 9.698309 TCAAGACTTTCTTAGATAGTTTCTGTG 57.302 33.333 6.77 0.00 33.78 3.66
2453 3174 8.439286 CAAGACTTTCTTAGATAGTTTCTGTGC 58.561 37.037 6.77 0.00 33.78 4.57
2454 3175 7.100409 AGACTTTCTTAGATAGTTTCTGTGCC 58.900 38.462 6.77 0.00 35.79 5.01
2455 3176 7.010339 ACTTTCTTAGATAGTTTCTGTGCCT 57.990 36.000 0.00 0.00 35.79 4.75
2456 3177 8.135382 ACTTTCTTAGATAGTTTCTGTGCCTA 57.865 34.615 0.00 0.00 35.79 3.93
2457 3178 8.763601 ACTTTCTTAGATAGTTTCTGTGCCTAT 58.236 33.333 0.00 0.00 35.79 2.57
2458 3179 9.255304 CTTTCTTAGATAGTTTCTGTGCCTATC 57.745 37.037 0.00 0.00 38.10 2.08
2459 3180 8.540507 TTCTTAGATAGTTTCTGTGCCTATCT 57.459 34.615 11.78 11.78 45.68 1.98
2575 3296 4.516698 TGGAAGTTCTTGAAGCAAGTGATC 59.483 41.667 2.25 0.00 41.66 2.92
2651 3372 6.586344 ACATCGGTGAGATATTCTGTCAAAT 58.414 36.000 0.65 0.00 37.52 2.32
2705 3426 2.281484 GTGGTCTTCGGCAAGGCA 60.281 61.111 4.22 0.00 35.75 4.75
2794 3515 6.136155 TGTGTCTTCTGGTGATATATCTCCA 58.864 40.000 26.98 26.98 45.27 3.86
2872 3593 3.323243 CATGCTTTTCTTTGAGGCAAGG 58.677 45.455 0.00 0.00 36.49 3.61
3103 3831 4.682021 AGGGAGATTCCAAAACCTTCAT 57.318 40.909 0.00 0.00 38.64 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.957680 TGTGGACGTCCTTTGTGTACTA 59.042 45.455 33.39 8.02 36.82 1.82
71 72 7.158021 GGGATTGCTGCTGAGGATATATATAC 58.842 42.308 0.00 0.00 0.00 1.47
73 74 5.668991 TGGGATTGCTGCTGAGGATATATAT 59.331 40.000 0.00 0.00 0.00 0.86
74 75 5.032170 TGGGATTGCTGCTGAGGATATATA 58.968 41.667 0.00 0.00 0.00 0.86
75 76 3.848377 TGGGATTGCTGCTGAGGATATAT 59.152 43.478 0.00 0.00 0.00 0.86
76 77 3.250617 TGGGATTGCTGCTGAGGATATA 58.749 45.455 0.00 0.00 0.00 0.86
78 79 1.510492 TGGGATTGCTGCTGAGGATA 58.490 50.000 0.00 0.00 0.00 2.59
79 80 0.627451 TTGGGATTGCTGCTGAGGAT 59.373 50.000 0.00 0.00 0.00 3.24
80 81 0.405198 TTTGGGATTGCTGCTGAGGA 59.595 50.000 0.00 0.00 0.00 3.71
81 82 0.529378 GTTTGGGATTGCTGCTGAGG 59.471 55.000 0.00 0.00 0.00 3.86
82 83 0.169672 CGTTTGGGATTGCTGCTGAG 59.830 55.000 0.00 0.00 0.00 3.35
83 84 1.865788 GCGTTTGGGATTGCTGCTGA 61.866 55.000 0.00 0.00 0.00 4.26
84 85 1.444895 GCGTTTGGGATTGCTGCTG 60.445 57.895 0.00 0.00 0.00 4.41
85 86 2.964978 GCGTTTGGGATTGCTGCT 59.035 55.556 0.00 0.00 0.00 4.24
88 89 2.332654 GGTCGCGTTTGGGATTGCT 61.333 57.895 5.77 0.00 39.47 3.91
89 90 2.178273 GGTCGCGTTTGGGATTGC 59.822 61.111 5.77 0.00 39.47 3.56
91 92 2.360726 GGGGTCGCGTTTGGGATT 60.361 61.111 5.77 0.00 39.47 3.01
92 93 4.770874 CGGGGTCGCGTTTGGGAT 62.771 66.667 5.77 0.00 39.47 3.85
175 180 2.602257 TCTGATGCCATCCGTTAGTG 57.398 50.000 1.49 0.00 0.00 2.74
184 189 3.429960 CGTATCCGATGATCTGATGCCAT 60.430 47.826 9.26 0.00 35.63 4.40
221 226 1.142097 GCCCAACTAGCTCTCCGAC 59.858 63.158 0.00 0.00 0.00 4.79
370 827 2.997315 CAGAGGCCGGGACAGACA 60.997 66.667 0.92 0.00 0.00 3.41
371 828 3.775654 CCAGAGGCCGGGACAGAC 61.776 72.222 0.92 0.00 0.00 3.51
372 829 3.317436 ATCCAGAGGCCGGGACAGA 62.317 63.158 14.89 1.19 39.44 3.41
373 830 2.765807 ATCCAGAGGCCGGGACAG 60.766 66.667 14.89 0.00 39.44 3.51
499 956 7.867305 TCGGGCATTATTACTATCACAAAAA 57.133 32.000 0.00 0.00 0.00 1.94
504 961 7.152645 TCTTCTTCGGGCATTATTACTATCAC 58.847 38.462 0.00 0.00 0.00 3.06
505 962 7.232737 TCTCTTCTTCGGGCATTATTACTATCA 59.767 37.037 0.00 0.00 0.00 2.15
506 963 7.603651 TCTCTTCTTCGGGCATTATTACTATC 58.396 38.462 0.00 0.00 0.00 2.08
508 965 6.971726 TCTCTTCTTCGGGCATTATTACTA 57.028 37.500 0.00 0.00 0.00 1.82
509 966 5.871396 TCTCTTCTTCGGGCATTATTACT 57.129 39.130 0.00 0.00 0.00 2.24
510 967 6.920569 TTTCTCTTCTTCGGGCATTATTAC 57.079 37.500 0.00 0.00 0.00 1.89
511 968 7.610305 AGTTTTTCTCTTCTTCGGGCATTATTA 59.390 33.333 0.00 0.00 0.00 0.98
512 969 6.434340 AGTTTTTCTCTTCTTCGGGCATTATT 59.566 34.615 0.00 0.00 0.00 1.40
572 1030 3.120338 CGACCCTTTCTTGTACGTACGTA 60.120 47.826 23.60 23.60 0.00 3.57
574 1032 2.245096 CGACCCTTTCTTGTACGTACG 58.755 52.381 20.18 15.01 0.00 3.67
575 1033 3.288809 ACGACCCTTTCTTGTACGTAC 57.711 47.619 18.90 18.90 0.00 3.67
576 1034 4.323417 TCTACGACCCTTTCTTGTACGTA 58.677 43.478 0.00 0.00 34.52 3.57
578 1036 3.438087 TCTCTACGACCCTTTCTTGTACG 59.562 47.826 0.00 0.00 0.00 3.67
580 1038 5.591877 GGTATCTCTACGACCCTTTCTTGTA 59.408 44.000 0.00 0.00 0.00 2.41
715 1330 2.603776 ACCCACCCTGACGGACTC 60.604 66.667 0.00 0.00 34.64 3.36
716 1331 2.603776 GACCCACCCTGACGGACT 60.604 66.667 0.00 0.00 34.64 3.85
735 1350 1.134521 TGGTGACTTGCGAGTTGAGTT 60.135 47.619 8.34 0.00 35.88 3.01
836 1451 2.109517 ATAGATGGAGGCAGCTGCGG 62.110 60.000 31.19 0.00 43.26 5.69
904 1522 2.933287 TGATCGGGCAGTGGGGTT 60.933 61.111 0.00 0.00 0.00 4.11
905 1523 3.402681 CTGATCGGGCAGTGGGGT 61.403 66.667 0.00 0.00 0.00 4.95
906 1524 4.864334 GCTGATCGGGCAGTGGGG 62.864 72.222 3.14 0.00 38.17 4.96
907 1525 3.746949 GAGCTGATCGGGCAGTGGG 62.747 68.421 3.14 0.00 38.17 4.61
927 1571 2.505557 CGTCGGGTTGCGGTAGAC 60.506 66.667 0.00 0.00 0.00 2.59
1392 2062 0.600255 AAACTCAACCGGTCAGCTCG 60.600 55.000 8.04 0.00 0.00 5.03
1588 2258 1.336632 ACAGGGAGAGCAGGAGCATC 61.337 60.000 0.00 0.00 45.49 3.91
1757 2461 0.250166 GCCGGCGGGATAGTATTGTT 60.250 55.000 29.48 0.00 34.06 2.83
1759 2463 1.736645 CGCCGGCGGGATAGTATTG 60.737 63.158 40.50 8.19 34.06 1.90
1808 2514 1.145738 CCCAGCCTAATAATGCCTGGT 59.854 52.381 0.00 0.00 0.00 4.00
1829 2535 3.147294 CGAAAGCACGGACGACAG 58.853 61.111 0.00 0.00 0.00 3.51
1929 2638 8.988934 TCATTGTTAGTAAGTAGAAAAGCACTG 58.011 33.333 0.00 0.00 0.00 3.66
1953 2662 6.316140 CCGATCCATTTGTTTAGATGACTTCA 59.684 38.462 0.00 0.00 0.00 3.02
1965 2679 1.737793 GAAGCGTCCGATCCATTTGTT 59.262 47.619 0.00 0.00 0.00 2.83
1967 2681 1.328680 CAGAAGCGTCCGATCCATTTG 59.671 52.381 0.00 0.00 0.00 2.32
2015 2729 9.216117 GGTTGAGTATAAGAAAGTAAAAGCTCA 57.784 33.333 0.00 0.00 0.00 4.26
2025 2739 7.044181 TCAGATGCTGGTTGAGTATAAGAAAG 58.956 38.462 0.00 0.00 31.51 2.62
2182 2902 6.174049 AGCAAGAAAAACTATCTCCACCTAC 58.826 40.000 0.00 0.00 0.00 3.18
2221 2941 9.206870 ACCTCACAATTTTTGCATAATAACTTG 57.793 29.630 0.00 0.00 0.00 3.16
2254 2974 0.034863 TAAGCACCGTTCCCAATCCC 60.035 55.000 0.00 0.00 0.00 3.85
2255 2975 1.092348 GTAAGCACCGTTCCCAATCC 58.908 55.000 0.00 0.00 0.00 3.01
2256 2976 1.816074 TGTAAGCACCGTTCCCAATC 58.184 50.000 0.00 0.00 0.00 2.67
2257 2977 2.091541 CATGTAAGCACCGTTCCCAAT 58.908 47.619 0.00 0.00 0.00 3.16
2258 2978 1.202830 ACATGTAAGCACCGTTCCCAA 60.203 47.619 0.00 0.00 0.00 4.12
2273 2993 6.859112 ACAGTATCTCCTTCACTTACATGT 57.141 37.500 2.69 2.69 0.00 3.21
2274 2994 9.823647 ATTTACAGTATCTCCTTCACTTACATG 57.176 33.333 0.00 0.00 0.00 3.21
2283 3003 7.486647 TGTTCCGTATTTACAGTATCTCCTTC 58.513 38.462 0.00 0.00 0.00 3.46
2284 3004 7.414222 TGTTCCGTATTTACAGTATCTCCTT 57.586 36.000 0.00 0.00 0.00 3.36
2285 3005 7.414222 TTGTTCCGTATTTACAGTATCTCCT 57.586 36.000 0.00 0.00 0.00 3.69
2302 3022 0.655733 AAGCACGACTGTTTGTTCCG 59.344 50.000 0.00 0.00 0.00 4.30
2305 3025 2.544267 GAGCTAAGCACGACTGTTTGTT 59.456 45.455 0.00 0.00 0.00 2.83
2307 3027 2.135139 TGAGCTAAGCACGACTGTTTG 58.865 47.619 0.00 0.00 0.00 2.93
2308 3028 2.224066 ACTGAGCTAAGCACGACTGTTT 60.224 45.455 0.00 0.00 0.00 2.83
2419 3140 7.816995 ACTATCTAAGAAAGTCTTGAACTGCAG 59.183 37.037 13.48 13.48 37.29 4.41
2427 3148 8.439286 GCACAGAAACTATCTAAGAAAGTCTTG 58.561 37.037 0.70 0.00 37.29 3.02
2428 3149 7.604545 GGCACAGAAACTATCTAAGAAAGTCTT 59.395 37.037 0.00 0.00 40.35 3.01
2431 3152 7.010339 AGGCACAGAAACTATCTAAGAAAGT 57.990 36.000 0.00 0.00 36.32 2.66
2440 3161 7.045126 ACACTAGATAGGCACAGAAACTATC 57.955 40.000 0.00 0.00 42.00 2.08
2441 3162 8.713708 ATACACTAGATAGGCACAGAAACTAT 57.286 34.615 0.00 0.00 0.00 2.12
2442 3163 8.534954 AATACACTAGATAGGCACAGAAACTA 57.465 34.615 0.00 0.00 0.00 2.24
2443 3164 7.124298 TGAATACACTAGATAGGCACAGAAACT 59.876 37.037 0.00 0.00 0.00 2.66
2444 3165 7.222999 GTGAATACACTAGATAGGCACAGAAAC 59.777 40.741 0.00 0.00 42.99 2.78
2445 3166 7.265673 GTGAATACACTAGATAGGCACAGAAA 58.734 38.462 0.00 0.00 42.99 2.52
2446 3167 6.183360 GGTGAATACACTAGATAGGCACAGAA 60.183 42.308 0.00 0.00 45.32 3.02
2447 3168 5.302059 GGTGAATACACTAGATAGGCACAGA 59.698 44.000 0.00 0.00 45.32 3.41
2448 3169 5.069119 TGGTGAATACACTAGATAGGCACAG 59.931 44.000 0.00 0.00 45.32 3.66
2449 3170 4.959839 TGGTGAATACACTAGATAGGCACA 59.040 41.667 0.00 0.00 45.32 4.57
2450 3171 5.531122 TGGTGAATACACTAGATAGGCAC 57.469 43.478 0.00 1.79 45.32 5.01
2451 3172 8.435931 AATATGGTGAATACACTAGATAGGCA 57.564 34.615 0.00 0.00 45.32 4.75
2483 3204 7.093333 ACAGAAACTTTTTGTTGGATCCTTCTT 60.093 33.333 14.23 0.00 39.13 2.52
2651 3372 6.901615 TGAATCTAAGAGGGTCCCATTAAA 57.098 37.500 11.55 0.00 0.00 1.52
2705 3426 4.027782 ACAAGAAGGGGGATAGAGGATT 57.972 45.455 0.00 0.00 0.00 3.01
2794 3515 4.319177 GTGCTCTTCTACACACCTTGATT 58.681 43.478 0.00 0.00 36.77 2.57
3103 3831 5.365403 CCAAACGCTTGGTTAAACTCATA 57.635 39.130 9.51 0.00 46.25 2.15


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

AutoCloner maintained by Alex Coulton.