Multiple sequence alignment - TraesCS4D01G040400

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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 TraesCS4D01G040400 chr4D 100.000 3872 0 0 1 3872 18780062 18783933 0.000000e+00 7151.0
1 TraesCS4D01G040400 chr4D 79.333 150 29 2 1929 2077 30005079 30005227 1.900000e-18 104.0
2 TraesCS4D01G040400 chr4A 91.497 3940 194 79 1 3867 582480597 582476726 0.000000e+00 5289.0
3 TraesCS4D01G040400 chr4A 84.438 1041 136 13 1888 2923 729477055 729476036 0.000000e+00 1002.0
4 TraesCS4D01G040400 chr4A 80.851 141 25 2 1938 2077 573172934 573172795 4.090000e-20 110.0
5 TraesCS4D01G040400 chr4B 91.653 2947 104 53 488 3372 30860880 30863746 0.000000e+00 3949.0
6 TraesCS4D01G040400 chr4B 93.103 464 20 3 2034 2497 389754555 389755006 0.000000e+00 669.0
7 TraesCS4D01G040400 chr4B 87.625 299 15 9 3487 3775 30863762 30864048 1.040000e-85 327.0
8 TraesCS4D01G040400 chr4B 94.811 212 7 2 2462 2672 389755009 389755217 1.040000e-85 327.0
9 TraesCS4D01G040400 chr4B 78.571 154 30 3 1925 2077 42776335 42776184 8.850000e-17 99.0
10 TraesCS4D01G040400 chr4B 91.429 70 6 0 325 394 30860789 30860858 3.180000e-16 97.1
11 TraesCS4D01G040400 chr5A 93.906 640 23 5 2034 2672 363860115 363859491 0.000000e+00 952.0
12 TraesCS4D01G040400 chr7B 93.750 464 17 3 2034 2497 60629189 60629640 0.000000e+00 686.0
13 TraesCS4D01G040400 chr7B 94.811 212 7 2 2462 2672 60629643 60629851 1.040000e-85 327.0
14 TraesCS4D01G040400 chr1B 93.750 464 17 3 2034 2497 605938407 605937956 0.000000e+00 686.0
15 TraesCS4D01G040400 chr1B 95.631 206 5 2 2468 2672 605937947 605937745 1.040000e-85 327.0
16 TraesCS4D01G040400 chr6B 92.111 431 22 3 2067 2497 623993608 623994026 7.160000e-167 597.0
17 TraesCS4D01G040400 chr6B 92.925 212 11 2 2462 2672 623994029 623994237 4.860000e-79 305.0
18 TraesCS4D01G040400 chr7D 85.832 487 49 10 2436 2922 9093038 9093504 2.080000e-137 499.0
19 TraesCS4D01G040400 chr7D 80.357 168 10 10 1590 1756 9092893 9093038 5.290000e-19 106.0
20 TraesCS4D01G040400 chr7A 90.580 276 23 1 1151 1426 563212858 563212586 2.840000e-96 363.0
21 TraesCS4D01G040400 chr7A 86.297 343 26 11 1425 1767 562904760 562904439 1.710000e-93 353.0
22 TraesCS4D01G040400 chr3A 81.863 204 36 1 1925 2127 434950942 434950739 1.850000e-38 171.0


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 TraesCS4D01G040400 chr4D 18780062 18783933 3871 False 7151.0 7151 100.000000 1 3872 1 chr4D.!!$F1 3871
1 TraesCS4D01G040400 chr4A 582476726 582480597 3871 True 5289.0 5289 91.497000 1 3867 1 chr4A.!!$R2 3866
2 TraesCS4D01G040400 chr4A 729476036 729477055 1019 True 1002.0 1002 84.438000 1888 2923 1 chr4A.!!$R3 1035
3 TraesCS4D01G040400 chr4B 30860789 30864048 3259 False 1457.7 3949 90.235667 325 3775 3 chr4B.!!$F1 3450
4 TraesCS4D01G040400 chr4B 389754555 389755217 662 False 498.0 669 93.957000 2034 2672 2 chr4B.!!$F2 638
5 TraesCS4D01G040400 chr5A 363859491 363860115 624 True 952.0 952 93.906000 2034 2672 1 chr5A.!!$R1 638
6 TraesCS4D01G040400 chr7B 60629189 60629851 662 False 506.5 686 94.280500 2034 2672 2 chr7B.!!$F1 638
7 TraesCS4D01G040400 chr1B 605937745 605938407 662 True 506.5 686 94.690500 2034 2672 2 chr1B.!!$R1 638
8 TraesCS4D01G040400 chr6B 623993608 623994237 629 False 451.0 597 92.518000 2067 2672 2 chr6B.!!$F1 605
9 TraesCS4D01G040400 chr7D 9092893 9093504 611 False 302.5 499 83.094500 1590 2922 2 chr7D.!!$F1 1332

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
965 1033 0.100325 CTTCGCGCAATTATTGGCCA 59.900 50.000 8.75 0.0 0.0 5.36 F
1959 2058 1.153628 CCCCTACCTCAAGTTCGCG 60.154 63.158 0.00 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2531 0.605319 GGAATGTGCCGGAGTTGTGA 60.605 55.0 5.05 0.0 0.0 3.58 R
3423 3618 0.395862 TCCCCAAGCCAAACGTTCAA 60.396 50.0 0.00 0.0 0.0 2.69 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
24 25 7.437793 GAATTCTCCTCCAATCATGAAGATC 57.562 40.000 0.00 0.00 35.39 2.75
26 27 3.323115 TCTCCTCCAATCATGAAGATCGG 59.677 47.826 0.00 0.00 35.39 4.18
30 31 2.092484 TCCAATCATGAAGATCGGCCAA 60.092 45.455 2.24 0.00 35.39 4.52
79 80 3.981416 CGTGTGTCGCATTAGCTATGTAT 59.019 43.478 0.00 0.00 39.10 2.29
88 89 5.406477 CGCATTAGCTATGTATGTGTCATGT 59.594 40.000 8.63 0.00 39.10 3.21
103 104 5.596268 TGTCATGTGAGACAAAATCGAAG 57.404 39.130 0.00 0.00 44.92 3.79
104 105 4.452114 TGTCATGTGAGACAAAATCGAAGG 59.548 41.667 0.00 0.00 44.92 3.46
105 106 4.452455 GTCATGTGAGACAAAATCGAAGGT 59.548 41.667 0.00 0.00 38.40 3.50
107 108 5.869344 TCATGTGAGACAAAATCGAAGGTAG 59.131 40.000 0.00 0.00 0.00 3.18
108 109 4.566004 TGTGAGACAAAATCGAAGGTAGG 58.434 43.478 0.00 0.00 0.00 3.18
109 110 4.282449 TGTGAGACAAAATCGAAGGTAGGA 59.718 41.667 0.00 0.00 0.00 2.94
125 129 4.827284 AGGTAGGAGAAATGTTGGTTGTTG 59.173 41.667 0.00 0.00 0.00 3.33
130 134 5.366477 AGGAGAAATGTTGGTTGTTGGATTT 59.634 36.000 0.00 0.00 0.00 2.17
132 136 6.232581 AGAAATGTTGGTTGTTGGATTTGA 57.767 33.333 0.00 0.00 0.00 2.69
139 143 3.443329 TGGTTGTTGGATTTGATCATCGG 59.557 43.478 0.00 0.00 0.00 4.18
160 164 4.443621 GGTAGACAAGTTAGGGCATCTTC 58.556 47.826 0.00 0.00 0.00 2.87
189 193 8.260270 TCACATGATTCTAGAAACACATGAAG 57.740 34.615 32.51 26.89 35.97 3.02
191 195 9.154847 CACATGATTCTAGAAACACATGAAGTA 57.845 33.333 32.51 10.18 35.97 2.24
206 210 7.042523 ACACATGAAGTAAAAAGATTGCAAAGC 60.043 33.333 1.71 0.00 0.00 3.51
209 213 9.362539 CATGAAGTAAAAAGATTGCAAAGCTAT 57.637 29.630 1.71 0.00 45.10 2.97
241 245 2.815478 TCATGCACGGTTTTTGGTTTC 58.185 42.857 0.00 0.00 0.00 2.78
261 265 0.318275 GTTGCATCGCCGGAAAAACA 60.318 50.000 5.05 0.00 0.00 2.83
267 271 1.540267 TCGCCGGAAAAACATGGATT 58.460 45.000 5.05 0.00 0.00 3.01
268 272 1.201181 TCGCCGGAAAAACATGGATTG 59.799 47.619 5.05 0.00 0.00 2.67
284 288 8.661352 ACATGGATTGTTTTTAGGAGTTTTTG 57.339 30.769 0.00 0.00 33.74 2.44
291 295 7.654022 TGTTTTTAGGAGTTTTTGAGTGGAT 57.346 32.000 0.00 0.00 0.00 3.41
292 296 7.488322 TGTTTTTAGGAGTTTTTGAGTGGATG 58.512 34.615 0.00 0.00 0.00 3.51
298 302 5.045286 AGGAGTTTTTGAGTGGATGCTAGAT 60.045 40.000 0.00 0.00 0.00 1.98
300 304 6.183360 GGAGTTTTTGAGTGGATGCTAGATTC 60.183 42.308 0.00 0.00 0.00 2.52
302 306 5.441718 TTTTGAGTGGATGCTAGATTCCT 57.558 39.130 11.41 0.00 32.95 3.36
304 308 6.560003 TTTGAGTGGATGCTAGATTCCTTA 57.440 37.500 11.41 0.00 32.95 2.69
352 356 4.509970 TGGTAAATATTCGTGCTGGATTCG 59.490 41.667 0.00 0.00 0.00 3.34
370 374 5.233689 GGATTCGATCCTACAAACTAAACGG 59.766 44.000 6.63 0.00 46.19 4.44
371 375 4.789012 TCGATCCTACAAACTAAACGGT 57.211 40.909 0.00 0.00 0.00 4.83
374 378 4.925054 CGATCCTACAAACTAAACGGTCAA 59.075 41.667 0.00 0.00 0.00 3.18
377 381 5.613329 TCCTACAAACTAAACGGTCAACAT 58.387 37.500 0.00 0.00 0.00 2.71
442 448 1.533625 GCCCTCAACAGTGCAATACA 58.466 50.000 0.00 0.00 0.00 2.29
458 464 5.009911 TGCAATACACAGATGCTTCAAAGTT 59.990 36.000 2.07 0.00 40.66 2.66
482 489 6.705747 TTGGAATCCATTTTGCCATGAGCG 62.706 45.833 1.39 0.00 37.64 5.03
531 538 2.283532 AGCGCACAGAGAGGGAGT 60.284 61.111 11.47 0.00 0.00 3.85
532 539 2.183046 GCGCACAGAGAGGGAGTC 59.817 66.667 0.30 0.00 0.00 3.36
721 748 3.702048 GCCAGCGACCCACCACTA 61.702 66.667 0.00 0.00 0.00 2.74
821 881 4.792648 GCTGCTCTGCTCGCTCGT 62.793 66.667 0.00 0.00 0.00 4.18
822 882 2.126149 CTGCTCTGCTCGCTCGTT 60.126 61.111 0.00 0.00 0.00 3.85
823 883 2.126307 TGCTCTGCTCGCTCGTTC 60.126 61.111 0.00 0.00 0.00 3.95
824 884 2.180518 GCTCTGCTCGCTCGTTCT 59.819 61.111 0.00 0.00 0.00 3.01
829 889 2.103340 GCTCGCTCGTTCTCCTCC 59.897 66.667 0.00 0.00 0.00 4.30
830 890 2.802106 CTCGCTCGTTCTCCTCCC 59.198 66.667 0.00 0.00 0.00 4.30
831 891 2.035155 TCGCTCGTTCTCCTCCCA 59.965 61.111 0.00 0.00 0.00 4.37
832 892 1.999071 CTCGCTCGTTCTCCTCCCAG 61.999 65.000 0.00 0.00 0.00 4.45
833 893 2.344203 CGCTCGTTCTCCTCCCAGT 61.344 63.158 0.00 0.00 0.00 4.00
834 894 1.878656 CGCTCGTTCTCCTCCCAGTT 61.879 60.000 0.00 0.00 0.00 3.16
853 913 2.237965 CCCACCCCAACCATCTCCA 61.238 63.158 0.00 0.00 0.00 3.86
875 935 2.243736 TCTCCTCCTTCTTCCTCCTCTC 59.756 54.545 0.00 0.00 0.00 3.20
876 936 1.289530 TCCTCCTTCTTCCTCCTCTCC 59.710 57.143 0.00 0.00 0.00 3.71
878 938 1.007721 CTCCTTCTTCCTCCTCTCCCA 59.992 57.143 0.00 0.00 0.00 4.37
949 1017 0.387750 CCGAGGCAAGCAAAAGCTTC 60.388 55.000 0.00 0.00 33.98 3.86
965 1033 0.100325 CTTCGCGCAATTATTGGCCA 59.900 50.000 8.75 0.00 0.00 5.36
1146 1236 2.813908 CTCGGGTACAAGGTGCGC 60.814 66.667 0.00 0.00 0.00 6.09
1293 1383 1.295423 CTACAACCCCACCGACCTG 59.705 63.158 0.00 0.00 0.00 4.00
1438 1531 2.045242 CCTCCGTCGACTCCTCCA 60.045 66.667 14.70 0.00 0.00 3.86
1445 1538 1.683707 TCGACTCCTCCAGCAGCAT 60.684 57.895 0.00 0.00 0.00 3.79
1563 1659 3.268965 GAGCAGCACCTCGTCGTCA 62.269 63.158 0.00 0.00 0.00 4.35
1566 1662 1.517257 CAGCACCTCGTCGTCATCC 60.517 63.158 0.00 0.00 0.00 3.51
1578 1674 1.777030 CGTCATCCTCCTCCTCGTCG 61.777 65.000 0.00 0.00 0.00 5.12
1959 2058 1.153628 CCCCTACCTCAAGTTCGCG 60.154 63.158 0.00 0.00 0.00 5.87
2926 3066 1.271001 TGAGCATGGAGGACAACACAG 60.271 52.381 0.00 0.00 0.00 3.66
3008 3151 5.873712 AGAAGCTAAATGTCATGTCAGTGAG 59.126 40.000 0.00 0.93 0.00 3.51
3040 3183 4.843101 GACCGGCTACGATCGATC 57.157 61.111 24.34 15.68 44.60 3.69
3065 3208 3.308705 GGGTGGTTCCGTCCGTCT 61.309 66.667 0.00 0.00 37.00 4.18
3082 3225 0.904865 TCTGGCGTGAAGAGGTGGAT 60.905 55.000 0.00 0.00 0.00 3.41
3109 3257 4.988716 ACTCCGAGCCGACCACCA 62.989 66.667 0.00 0.00 0.00 4.17
3110 3258 4.436998 CTCCGAGCCGACCACCAC 62.437 72.222 0.00 0.00 0.00 4.16
3191 3357 3.390311 CCCGTAAAACTCCTAAGCCCTAT 59.610 47.826 0.00 0.00 0.00 2.57
3194 3360 6.239800 CCCGTAAAACTCCTAAGCCCTATTAT 60.240 42.308 0.00 0.00 0.00 1.28
3245 3416 6.699575 ATTGCTATGTGTAATTCCTCCAAC 57.300 37.500 0.00 0.00 0.00 3.77
3265 3436 5.221028 CCAACCGCTCATATCAAAATAAGCA 60.221 40.000 0.00 0.00 0.00 3.91
3372 3567 4.455533 TCTGTTCTGTTATGTTCATGGTGC 59.544 41.667 0.00 0.00 0.00 5.01
3383 3578 0.036671 TCATGGTGCTCACTGCTCTG 60.037 55.000 0.00 0.00 43.37 3.35
3397 3592 3.054582 ACTGCTCTGATGAACATGATGGT 60.055 43.478 0.00 0.00 0.00 3.55
3398 3593 3.275999 TGCTCTGATGAACATGATGGTG 58.724 45.455 0.00 0.00 0.00 4.17
3399 3594 2.033049 GCTCTGATGAACATGATGGTGC 59.967 50.000 0.00 0.00 0.00 5.01
3400 3595 2.617308 CTCTGATGAACATGATGGTGCC 59.383 50.000 0.00 0.00 0.00 5.01
3401 3596 2.240414 TCTGATGAACATGATGGTGCCT 59.760 45.455 0.00 0.00 0.00 4.75
3402 3597 2.617308 CTGATGAACATGATGGTGCCTC 59.383 50.000 0.00 0.00 0.00 4.70
3403 3598 1.952296 GATGAACATGATGGTGCCTCC 59.048 52.381 0.00 0.00 0.00 4.30
3423 3618 2.496111 CAATGGTGGCTTTGCAATTGT 58.504 42.857 7.40 0.00 0.00 2.71
3427 3622 2.093288 TGGTGGCTTTGCAATTGTTGAA 60.093 40.909 7.40 0.00 0.00 2.69
3431 3626 2.607180 GGCTTTGCAATTGTTGAACGTT 59.393 40.909 0.00 0.00 0.00 3.99
3434 3629 4.576678 CTTTGCAATTGTTGAACGTTTGG 58.423 39.130 0.46 0.00 0.00 3.28
3453 3648 1.228552 CTTGGGGACTTGGTGGTGG 60.229 63.158 0.00 0.00 0.00 4.61
3454 3649 2.006805 CTTGGGGACTTGGTGGTGGT 62.007 60.000 0.00 0.00 0.00 4.16
3455 3650 2.115266 GGGGACTTGGTGGTGGTG 59.885 66.667 0.00 0.00 0.00 4.17
3463 3658 2.091640 TTGGTGGTGGTGCATGGGAT 62.092 55.000 0.00 0.00 0.00 3.85
3492 3687 4.343814 TCACATCACGGATTAGATTAGCCA 59.656 41.667 0.00 0.00 0.00 4.75
3594 3789 0.249398 CTCGTGTAGTTTCCCCTGGG 59.751 60.000 5.50 5.50 0.00 4.45
3600 3795 4.696805 GTTTCCCCTGGGGTGCCC 62.697 72.222 30.69 13.76 44.74 5.36
3672 3868 1.272490 CCTGCACGTTAGTTGGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
3767 3976 2.051345 GTTTCTGCACAACGGCCG 60.051 61.111 26.86 26.86 0.00 6.13
3786 3995 2.741985 CCGTCTGAATGCCGCACA 60.742 61.111 0.00 0.00 0.00 4.57
3791 4000 2.361483 TGAATGCCGCACAGCCAT 60.361 55.556 0.00 0.00 0.00 4.40
3803 4012 2.479049 GCACAGCCATAGCAATCAGTTG 60.479 50.000 0.00 0.00 43.56 3.16
3804 4013 2.098607 CACAGCCATAGCAATCAGTTGG 59.901 50.000 0.00 0.00 43.56 3.77
3812 4021 5.533528 CCATAGCAATCAGTTGGATGATCAA 59.466 40.000 0.00 0.00 39.00 2.57
3816 4025 4.679662 CAATCAGTTGGATGATCAAAGCC 58.320 43.478 0.00 2.38 39.00 4.35
3817 4026 3.438216 TCAGTTGGATGATCAAAGCCA 57.562 42.857 0.00 5.31 0.00 4.75
3818 4027 3.765381 TCAGTTGGATGATCAAAGCCAA 58.235 40.909 18.60 18.60 38.02 4.52
3820 4029 4.219070 TCAGTTGGATGATCAAAGCCAAAG 59.781 41.667 22.12 18.43 41.61 2.77
3821 4030 3.056322 AGTTGGATGATCAAAGCCAAAGC 60.056 43.478 22.12 14.44 41.61 3.51
3854 4063 3.791539 CACTGCTGATCGGTGCTC 58.208 61.111 2.89 0.00 44.30 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.597404 CGATCTTCATGATTGGAGGAGA 57.403 45.455 0.00 0.00 35.14 3.71
21 22 4.800554 CCATAGGGTTGGCCGATC 57.199 61.111 0.00 0.00 34.97 3.69
30 31 3.809013 CGGGGCAAGCCATAGGGT 61.809 66.667 13.87 0.00 37.98 4.34
43 44 1.137479 ACACACGGTTATGATACGGGG 59.863 52.381 0.00 0.00 34.87 5.73
79 80 4.376146 TCGATTTTGTCTCACATGACACA 58.624 39.130 0.00 0.00 45.32 3.72
88 89 4.770531 TCTCCTACCTTCGATTTTGTCTCA 59.229 41.667 0.00 0.00 0.00 3.27
100 101 5.070685 ACAACCAACATTTCTCCTACCTTC 58.929 41.667 0.00 0.00 0.00 3.46
101 102 5.061721 ACAACCAACATTTCTCCTACCTT 57.938 39.130 0.00 0.00 0.00 3.50
102 103 4.724279 ACAACCAACATTTCTCCTACCT 57.276 40.909 0.00 0.00 0.00 3.08
103 104 4.022329 CCAACAACCAACATTTCTCCTACC 60.022 45.833 0.00 0.00 0.00 3.18
104 105 4.825085 TCCAACAACCAACATTTCTCCTAC 59.175 41.667 0.00 0.00 0.00 3.18
105 106 5.055265 TCCAACAACCAACATTTCTCCTA 57.945 39.130 0.00 0.00 0.00 2.94
107 108 4.871933 ATCCAACAACCAACATTTCTCC 57.128 40.909 0.00 0.00 0.00 3.71
108 109 6.279882 TCAAATCCAACAACCAACATTTCTC 58.720 36.000 0.00 0.00 0.00 2.87
109 110 6.232581 TCAAATCCAACAACCAACATTTCT 57.767 33.333 0.00 0.00 0.00 2.52
125 129 5.360591 ACTTGTCTACCGATGATCAAATCC 58.639 41.667 0.00 0.00 0.00 3.01
130 134 4.341235 CCCTAACTTGTCTACCGATGATCA 59.659 45.833 0.00 0.00 0.00 2.92
132 136 3.069729 GCCCTAACTTGTCTACCGATGAT 59.930 47.826 0.00 0.00 0.00 2.45
139 143 4.113354 CGAAGATGCCCTAACTTGTCTAC 58.887 47.826 0.00 0.00 0.00 2.59
160 164 7.294676 TGTGTTTCTAGAATCATGTGAATCG 57.705 36.000 17.11 0.00 0.00 3.34
189 193 5.291858 GGGCATAGCTTTGCAATCTTTTTAC 59.708 40.000 27.00 8.44 44.59 2.01
191 195 4.256110 GGGCATAGCTTTGCAATCTTTTT 58.744 39.130 27.00 0.00 44.59 1.94
206 210 4.304110 GTGCATGATTCAAATGGGCATAG 58.696 43.478 0.00 0.00 31.92 2.23
209 213 1.135053 CGTGCATGATTCAAATGGGCA 60.135 47.619 0.00 0.00 0.00 5.36
241 245 1.081774 TTTTTCCGGCGATGCAACG 60.082 52.632 12.54 12.54 0.00 4.10
261 265 8.704668 ACTCAAAAACTCCTAAAAACAATCCAT 58.295 29.630 0.00 0.00 0.00 3.41
267 271 7.488322 CATCCACTCAAAAACTCCTAAAAACA 58.512 34.615 0.00 0.00 0.00 2.83
268 272 6.420903 GCATCCACTCAAAAACTCCTAAAAAC 59.579 38.462 0.00 0.00 0.00 2.43
273 277 4.640771 AGCATCCACTCAAAAACTCCTA 57.359 40.909 0.00 0.00 0.00 2.94
275 279 4.579869 TCTAGCATCCACTCAAAAACTCC 58.420 43.478 0.00 0.00 0.00 3.85
279 283 5.819991 AGGAATCTAGCATCCACTCAAAAA 58.180 37.500 13.97 0.00 38.23 1.94
284 288 5.247110 TCCATAAGGAATCTAGCATCCACTC 59.753 44.000 13.97 0.00 42.23 3.51
304 308 9.826574 CAAGGATTCATTTTGTATTCATTCCAT 57.173 29.630 0.00 0.00 0.00 3.41
317 321 9.801873 CACGAATATTTACCAAGGATTCATTTT 57.198 29.630 0.00 0.00 0.00 1.82
352 356 5.697633 TGTTGACCGTTTAGTTTGTAGGATC 59.302 40.000 0.00 0.00 0.00 3.36
402 408 2.093235 CCTCTTTGAATCGAAGGAGCCT 60.093 50.000 10.14 0.00 0.00 4.58
403 409 2.284190 CCTCTTTGAATCGAAGGAGCC 58.716 52.381 10.14 0.00 0.00 4.70
404 410 1.668237 GCCTCTTTGAATCGAAGGAGC 59.332 52.381 10.14 9.38 0.00 4.70
442 448 5.596836 TTCCAAAACTTTGAAGCATCTGT 57.403 34.783 3.72 0.00 40.55 3.41
443 449 5.636543 GGATTCCAAAACTTTGAAGCATCTG 59.363 40.000 3.72 0.00 40.55 2.90
444 450 5.305128 TGGATTCCAAAACTTTGAAGCATCT 59.695 36.000 1.94 0.00 40.55 2.90
445 451 5.540911 TGGATTCCAAAACTTTGAAGCATC 58.459 37.500 1.94 0.00 40.55 3.91
446 452 5.549742 TGGATTCCAAAACTTTGAAGCAT 57.450 34.783 1.94 0.00 40.55 3.79
447 453 5.549742 ATGGATTCCAAAACTTTGAAGCA 57.450 34.783 9.98 0.00 40.55 3.91
448 454 6.866010 AAATGGATTCCAAAACTTTGAAGC 57.134 33.333 9.98 0.35 40.55 3.86
458 464 4.834534 CTCATGGCAAAATGGATTCCAAA 58.165 39.130 9.98 0.00 36.95 3.28
482 489 2.039405 CCTCTCTGTGGCTTGCAGC 61.039 63.158 0.11 0.11 41.46 5.25
521 528 0.462403 GCTACGTCGACTCCCTCTCT 60.462 60.000 14.70 0.00 0.00 3.10
531 538 3.138798 GGGGCTCTGCTACGTCGA 61.139 66.667 0.00 0.00 0.00 4.20
532 539 2.685387 GATGGGGCTCTGCTACGTCG 62.685 65.000 0.00 0.00 0.00 5.12
573 600 1.509548 CCACCCCAGAAATCCCCACT 61.510 60.000 0.00 0.00 0.00 4.00
575 602 1.467190 ACCACCCCAGAAATCCCCA 60.467 57.895 0.00 0.00 0.00 4.96
821 881 0.840722 GGTGGGAACTGGGAGGAGAA 60.841 60.000 0.00 0.00 0.00 2.87
822 882 1.229529 GGTGGGAACTGGGAGGAGA 60.230 63.158 0.00 0.00 0.00 3.71
823 883 2.301738 GGGTGGGAACTGGGAGGAG 61.302 68.421 0.00 0.00 0.00 3.69
824 884 2.204090 GGGTGGGAACTGGGAGGA 60.204 66.667 0.00 0.00 0.00 3.71
829 889 2.092904 ATGGTTGGGGTGGGAACTGG 62.093 60.000 0.00 0.00 0.00 4.00
830 890 0.611896 GATGGTTGGGGTGGGAACTG 60.612 60.000 0.00 0.00 0.00 3.16
831 891 0.776080 AGATGGTTGGGGTGGGAACT 60.776 55.000 0.00 0.00 0.00 3.01
832 892 0.323451 GAGATGGTTGGGGTGGGAAC 60.323 60.000 0.00 0.00 0.00 3.62
833 893 1.506028 GGAGATGGTTGGGGTGGGAA 61.506 60.000 0.00 0.00 0.00 3.97
834 894 1.928567 GGAGATGGTTGGGGTGGGA 60.929 63.158 0.00 0.00 0.00 4.37
853 913 2.865165 AGAGGAGGAAGAAGGAGGAGAT 59.135 50.000 0.00 0.00 0.00 2.75
949 1017 0.317269 CTCTGGCCAATAATTGCGCG 60.317 55.000 7.01 0.00 0.00 6.86
965 1033 3.844211 ACCTCGCCTCTCTATCTATCTCT 59.156 47.826 0.00 0.00 0.00 3.10
995 1063 1.270358 GGTACTCCCGCTTCATGATCC 60.270 57.143 0.00 0.00 0.00 3.36
1008 1089 3.834799 CCGGCGTCCTGGTACTCC 61.835 72.222 6.01 0.00 0.00 3.85
1188 1278 1.303074 CATCCCCATGGCCATCTCG 60.303 63.158 17.61 4.68 0.00 4.04
1293 1383 1.153997 GCTCTCGACCCAAGACGAC 60.154 63.158 0.00 0.00 35.29 4.34
1296 1386 1.086634 GCATGCTCTCGACCCAAGAC 61.087 60.000 11.37 0.00 0.00 3.01
1299 1389 1.078918 CAGCATGCTCTCGACCCAA 60.079 57.895 19.68 0.00 0.00 4.12
1397 1490 3.030882 GATCGAAGTAGCCGCCGC 61.031 66.667 0.00 0.00 0.00 6.53
1398 1491 1.370657 GAGATCGAAGTAGCCGCCG 60.371 63.158 0.00 0.00 0.00 6.46
1404 1497 0.824182 AGGGCGGGAGATCGAAGTAG 60.824 60.000 0.00 0.00 0.00 2.57
1563 1659 0.179040 GAGACGACGAGGAGGAGGAT 60.179 60.000 0.00 0.00 0.00 3.24
1566 1662 1.149361 CGAGAGACGACGAGGAGGAG 61.149 65.000 0.00 0.00 45.77 3.69
1959 2058 2.904866 TGGTTGGCGGTGAAGTGC 60.905 61.111 0.00 0.00 0.00 4.40
2058 2157 3.394836 GCGAGGGCCTGGAGAAGT 61.395 66.667 20.75 0.00 0.00 3.01
2427 2531 0.605319 GGAATGTGCCGGAGTTGTGA 60.605 55.000 5.05 0.00 0.00 3.58
2778 2918 2.821437 TCCTTCTCCTCCACCTTGTAG 58.179 52.381 0.00 0.00 0.00 2.74
2864 3004 3.701604 AACTCGCGAGATCACGGCC 62.702 63.158 40.58 0.00 40.84 6.13
2872 3012 1.850640 GCGTTCAAAACTCGCGAGA 59.149 52.632 40.58 17.22 40.51 4.04
2873 3013 4.399840 GCGTTCAAAACTCGCGAG 57.600 55.556 33.45 33.45 40.51 5.03
2972 3112 7.716998 TGACATTTAGCTTCTTCTTCTTCAAGT 59.283 33.333 0.00 0.00 0.00 3.16
3039 3182 3.384532 GAACCACCCGTAGCCCGA 61.385 66.667 0.00 0.00 39.56 5.14
3040 3183 4.462280 GGAACCACCCGTAGCCCG 62.462 72.222 0.00 0.00 0.00 6.13
3065 3208 1.296392 CATCCACCTCTTCACGCCA 59.704 57.895 0.00 0.00 0.00 5.69
3082 3225 2.974489 GCTCGGAGTTCGTCGTCCA 61.974 63.158 6.90 0.00 40.32 4.02
3109 3257 4.504340 GGGATTACATTACTACATGCCGGT 60.504 45.833 1.90 0.00 0.00 5.28
3110 3258 4.000988 GGGATTACATTACTACATGCCGG 58.999 47.826 0.00 0.00 0.00 6.13
3111 3259 4.894784 AGGGATTACATTACTACATGCCG 58.105 43.478 0.00 0.00 30.94 5.69
3245 3416 4.457810 CGTGCTTATTTTGATATGAGCGG 58.542 43.478 0.00 0.00 39.31 5.52
3265 3436 1.004200 CTAACAAAGTCCGGCCCGT 60.004 57.895 0.85 0.00 0.00 5.28
3372 3567 3.858247 TCATGTTCATCAGAGCAGTGAG 58.142 45.455 0.00 0.00 38.42 3.51
3383 3578 1.952296 GGAGGCACCATCATGTTCATC 59.048 52.381 0.00 0.00 38.79 2.92
3403 3598 2.496111 ACAATTGCAAAGCCACCATTG 58.504 42.857 1.71 3.24 0.00 2.82
3404 3599 2.879646 CAACAATTGCAAAGCCACCATT 59.120 40.909 1.71 0.00 0.00 3.16
3405 3600 2.104451 TCAACAATTGCAAAGCCACCAT 59.896 40.909 1.71 0.00 0.00 3.55
3406 3601 1.483827 TCAACAATTGCAAAGCCACCA 59.516 42.857 1.71 0.00 0.00 4.17
3407 3602 2.237393 TCAACAATTGCAAAGCCACC 57.763 45.000 1.71 0.00 0.00 4.61
3408 3603 2.033832 CGTTCAACAATTGCAAAGCCAC 60.034 45.455 1.71 0.00 0.00 5.01
3409 3604 2.200067 CGTTCAACAATTGCAAAGCCA 58.800 42.857 1.71 0.00 0.00 4.75
3410 3605 2.200899 ACGTTCAACAATTGCAAAGCC 58.799 42.857 1.71 0.00 0.00 4.35
3411 3606 3.923827 AACGTTCAACAATTGCAAAGC 57.076 38.095 1.71 0.00 0.00 3.51
3423 3618 0.395862 TCCCCAAGCCAAACGTTCAA 60.396 50.000 0.00 0.00 0.00 2.69
3427 3622 1.106944 CAAGTCCCCAAGCCAAACGT 61.107 55.000 0.00 0.00 0.00 3.99
3431 3626 1.152567 CACCAAGTCCCCAAGCCAA 60.153 57.895 0.00 0.00 0.00 4.52
3434 3629 1.903404 CACCACCAAGTCCCCAAGC 60.903 63.158 0.00 0.00 0.00 4.01
3453 3648 2.646930 TGTGAATCTCATCCCATGCAC 58.353 47.619 0.00 0.00 0.00 4.57
3454 3649 3.117813 TGATGTGAATCTCATCCCATGCA 60.118 43.478 18.91 0.00 40.38 3.96
3455 3650 3.252701 GTGATGTGAATCTCATCCCATGC 59.747 47.826 18.91 4.76 40.38 4.06
3463 3658 5.852282 TCTAATCCGTGATGTGAATCTCA 57.148 39.130 0.00 0.00 0.00 3.27
3496 3691 1.069636 CAAGCTCTCAAAGACGGCAAC 60.070 52.381 0.00 0.00 0.00 4.17
3562 3757 5.209818 ACTACACGAGATCTTTCCAACAA 57.790 39.130 0.00 0.00 0.00 2.83
3600 3795 4.248842 TGACCACACACCCAGCCG 62.249 66.667 0.00 0.00 0.00 5.52
3786 3995 3.117776 TCATCCAACTGATTGCTATGGCT 60.118 43.478 1.68 0.00 39.59 4.75
3791 4000 5.066893 GCTTTGATCATCCAACTGATTGCTA 59.933 40.000 0.00 0.00 36.01 3.49
3816 4025 0.809241 TTGGTGCGGCAAAAGCTTTG 60.809 50.000 13.54 8.26 35.28 2.77
3817 4026 0.809636 GTTGGTGCGGCAAAAGCTTT 60.810 50.000 5.69 5.69 35.28 3.51
3818 4027 1.227234 GTTGGTGCGGCAAAAGCTT 60.227 52.632 3.23 0.00 35.28 3.74
3820 4029 2.661537 GGTTGGTGCGGCAAAAGC 60.662 61.111 3.23 8.65 0.00 3.51
3821 4030 1.591327 GTGGTTGGTGCGGCAAAAG 60.591 57.895 3.23 0.00 0.00 2.27
3822 4031 2.055042 AGTGGTTGGTGCGGCAAAA 61.055 52.632 3.23 0.00 0.00 2.44
3824 4033 3.215568 CAGTGGTTGGTGCGGCAA 61.216 61.111 3.23 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.