Multiple sequence alignment - TraesCS7A01G228500

Loading Multiple Alignment...

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 TraesCS7A01G228500 chr7A 100.000 2574 0 0 654 3227 198940717 198943290 0.000000e+00 4754.0
1 TraesCS7A01G228500 chr7A 100.000 318 0 0 1 318 198940064 198940381 3.590000e-164 588.0
2 TraesCS7A01G228500 chr7A 95.161 62 3 0 2819 2880 599805373 599805434 7.370000e-17 99.0
3 TraesCS7A01G228500 chr7A 100.000 31 0 0 2788 2818 250603476 250603446 1.250000e-04 58.4
4 TraesCS7A01G228500 chr7D 95.178 2136 87 7 654 2789 190079507 190081626 0.000000e+00 3360.0
5 TraesCS7A01G228500 chr7D 97.977 346 6 1 2883 3227 190081656 190082001 1.660000e-167 599.0
6 TraesCS7A01G228500 chr7D 92.095 253 6 5 66 318 190078733 190078971 8.570000e-91 344.0
7 TraesCS7A01G228500 chr7B 94.014 2155 111 8 654 2806 334770748 334772886 0.000000e+00 3249.0
8 TraesCS7A01G228500 chr7B 89.565 345 35 1 2883 3227 334772979 334773322 1.370000e-118 436.0
9 TraesCS7A01G228500 chr7B 91.822 269 7 5 64 318 334769809 334770076 8.510000e-96 361.0
10 TraesCS7A01G228500 chr7B 97.059 34 1 0 2785 2818 371732285 371732252 1.250000e-04 58.4
11 TraesCS7A01G228500 chr4D 96.774 62 2 0 2819 2880 494875975 494875914 1.580000e-18 104.0
12 TraesCS7A01G228500 chr1D 96.774 62 2 0 2819 2880 478187898 478187959 1.580000e-18 104.0
13 TraesCS7A01G228500 chr1D 95.161 62 3 0 2819 2880 344594178 344594117 7.370000e-17 99.0
14 TraesCS7A01G228500 chr4B 95.161 62 3 0 2819 2880 564869531 564869470 7.370000e-17 99.0
15 TraesCS7A01G228500 chr4B 95.161 62 3 0 2819 2880 571617712 571617773 7.370000e-17 99.0
16 TraesCS7A01G228500 chr3D 95.161 62 3 0 2819 2880 82748048 82747987 7.370000e-17 99.0
17 TraesCS7A01G228500 chr1A 95.161 62 3 0 2819 2880 498452731 498452670 7.370000e-17 99.0
18 TraesCS7A01G228500 chr6B 93.651 63 4 0 2819 2881 21137192 21137254 9.530000e-16 95.3
19 TraesCS7A01G228500 chrUn 100.000 31 0 0 2788 2818 321243139 321243169 1.250000e-04 58.4
20 TraesCS7A01G228500 chrUn 100.000 31 0 0 2788 2818 322420849 322420819 1.250000e-04 58.4
21 TraesCS7A01G228500 chr4A 94.595 37 2 0 2781 2817 632148849 632148885 1.250000e-04 58.4
22 TraesCS7A01G228500 chr3B 97.059 34 1 0 2785 2818 763232054 763232087 1.250000e-04 58.4
23 TraesCS7A01G228500 chr2D 100.000 31 0 0 2788 2818 342103750 342103720 1.250000e-04 58.4
24 TraesCS7A01G228500 chr1B 97.059 34 1 0 2784 2817 59468599 59468566 1.250000e-04 58.4
25 TraesCS7A01G228500 chr1B 97.059 34 1 0 2782 2815 198648790 198648757 1.250000e-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 TraesCS7A01G228500 chr7A 198940064 198943290 3226 False 2671.000000 4754 100.000000 1 3227 2 chr7A.!!$F2 3226
1 TraesCS7A01G228500 chr7D 190078733 190082001 3268 False 1434.333333 3360 95.083333 66 3227 3 chr7D.!!$F1 3161
2 TraesCS7A01G228500 chr7B 334769809 334773322 3513 False 1348.666667 3249 91.800333 64 3227 3 chr7B.!!$F1 3163

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
107 120 0.108992 TGTAAACCCTAGTGCGAGCG 60.109 55.0 0.0 0.0 0.0 5.03 F
1173 1537 0.038166 ATGGATTGTTGGTCTGCGGT 59.962 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 1770 0.321210 TGCTACCATTGTGTCCCACG 60.321 55.0 0.0 0.0 37.14 4.94 R
2858 3223 0.036875 CCCTCCGTCCAGAAAAGCTT 59.963 55.0 0.0 0.0 0.00 3.74 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
28 29 8.915036 TGAAATAGAAGGACTACAGAATAGACC 58.085 37.037 0.00 0.00 33.62 3.85
29 30 9.138596 GAAATAGAAGGACTACAGAATAGACCT 57.861 37.037 0.00 0.00 40.46 3.85
30 31 9.495382 AAATAGAAGGACTACAGAATAGACCTT 57.505 33.333 14.75 14.75 46.72 3.50
31 32 9.495382 AATAGAAGGACTACAGAATAGACCTTT 57.505 33.333 15.59 10.08 45.07 3.11
32 33 7.800300 AGAAGGACTACAGAATAGACCTTTT 57.200 36.000 15.59 9.64 45.07 2.27
33 34 8.208575 AGAAGGACTACAGAATAGACCTTTTT 57.791 34.615 15.59 7.71 45.07 1.94
72 73 6.057627 AGACAATACTAGGTGTATCGTTCG 57.942 41.667 0.00 0.00 40.69 3.95
75 76 2.846039 ACTAGGTGTATCGTTCGCTG 57.154 50.000 0.00 0.00 0.00 5.18
105 118 1.134788 CCCTGTAAACCCTAGTGCGAG 60.135 57.143 0.00 0.00 0.00 5.03
106 119 1.641577 CTGTAAACCCTAGTGCGAGC 58.358 55.000 0.00 0.00 0.00 5.03
107 120 0.108992 TGTAAACCCTAGTGCGAGCG 60.109 55.000 0.00 0.00 0.00 5.03
108 121 0.171903 GTAAACCCTAGTGCGAGCGA 59.828 55.000 0.00 0.00 0.00 4.93
109 122 0.454600 TAAACCCTAGTGCGAGCGAG 59.545 55.000 0.00 0.00 0.00 5.03
270 298 2.951101 AACCCACCCTTCTACGCCG 61.951 63.158 0.00 0.00 0.00 6.46
271 299 4.832608 CCCACCCTTCTACGCCGC 62.833 72.222 0.00 0.00 0.00 6.53
272 300 4.832608 CCACCCTTCTACGCCGCC 62.833 72.222 0.00 0.00 0.00 6.13
774 1138 4.821589 CACTCCCTCCGCCGCTTC 62.822 72.222 0.00 0.00 0.00 3.86
854 1218 1.698116 TGGTCCCAAGGAACCACCA 60.698 57.895 0.00 0.00 38.96 4.17
880 1244 1.365699 TCTTGAAATCGCCTTACGCC 58.634 50.000 0.00 0.00 43.23 5.68
1017 1381 3.738745 GATGGTGGTGGATGGGGCC 62.739 68.421 0.00 0.00 0.00 5.80
1173 1537 0.038166 ATGGATTGTTGGTCTGCGGT 59.962 50.000 0.00 0.00 0.00 5.68
1179 1543 2.606519 TTGGTCTGCGGTAGGGCT 60.607 61.111 0.00 0.00 0.00 5.19
1222 1586 1.219213 GGAGAATGGAGAGGGAGGAGA 59.781 57.143 0.00 0.00 0.00 3.71
1323 1687 5.765182 GGTGACTGAAGAAATGAGGAAGAAA 59.235 40.000 0.00 0.00 0.00 2.52
1380 1744 1.021202 TCACTGGGTTTTGCAAGTCG 58.979 50.000 0.00 0.00 0.00 4.18
1389 1753 0.472471 TTTGCAAGTCGGGAGAGGTT 59.528 50.000 0.00 0.00 41.26 3.50
1507 1871 3.138283 TGGGAAGATGATTAAGGCCGAAT 59.862 43.478 5.69 5.69 0.00 3.34
1516 1880 8.352942 AGATGATTAAGGCCGAATTGTTATTTC 58.647 33.333 7.29 0.00 0.00 2.17
1684 2048 9.929180 TTACTTATAGCATATTGATCAGTGGAC 57.071 33.333 0.13 0.00 0.00 4.02
1700 2064 1.278985 TGGACTGTGCAATGTAGGGAG 59.721 52.381 0.00 0.00 0.00 4.30
1755 2119 4.626081 GGTCGTGGCTGTGCACCT 62.626 66.667 15.69 0.00 0.00 4.00
1788 2152 5.006386 GCTTATACTTCCATGATCAAGGGG 58.994 45.833 16.67 10.63 0.00 4.79
1815 2179 1.771255 GCTTCTGGGATGGTAGATGGT 59.229 52.381 0.00 0.00 0.00 3.55
1860 2224 1.304381 GGCAAGGGGTGATGCTGAA 60.304 57.895 0.00 0.00 0.00 3.02
1863 2227 0.038744 CAAGGGGTGATGCTGAACCT 59.961 55.000 2.93 0.00 36.64 3.50
1903 2267 2.226962 ATTGCTTGATGGGTTGCTCT 57.773 45.000 0.00 0.00 0.00 4.09
1907 2271 0.038744 CTTGATGGGTTGCTCTGGGT 59.961 55.000 0.00 0.00 0.00 4.51
1912 2276 1.059584 TGGGTTGCTCTGGGTGAAGA 61.060 55.000 0.00 0.00 0.00 2.87
1980 2344 2.319844 TGTGATCCAGACACAGTGACT 58.680 47.619 7.81 3.10 42.20 3.41
1989 2353 3.059884 AGACACAGTGACTTGCAATACG 58.940 45.455 7.81 0.00 0.00 3.06
2020 2384 1.352352 AGATTGAGGTTGGACAGGGTG 59.648 52.381 0.00 0.00 0.00 4.61
2234 2598 5.948758 AGATTTGGAGGTTCTGAGGATTTTC 59.051 40.000 0.00 0.00 0.00 2.29
2236 2600 4.559862 TGGAGGTTCTGAGGATTTTCTC 57.440 45.455 0.00 0.00 0.00 2.87
2238 2602 4.223923 TGGAGGTTCTGAGGATTTTCTCTC 59.776 45.833 0.00 0.00 34.98 3.20
2239 2603 4.469586 GGAGGTTCTGAGGATTTTCTCTCT 59.530 45.833 0.00 0.00 34.98 3.10
2240 2604 5.395214 GGAGGTTCTGAGGATTTTCTCTCTC 60.395 48.000 0.00 0.00 34.98 3.20
2241 2605 5.341169 AGGTTCTGAGGATTTTCTCTCTCT 58.659 41.667 0.00 0.00 34.98 3.10
2242 2606 5.422012 AGGTTCTGAGGATTTTCTCTCTCTC 59.578 44.000 0.00 0.00 34.98 3.20
2243 2607 5.422012 GGTTCTGAGGATTTTCTCTCTCTCT 59.578 44.000 0.00 0.00 34.98 3.10
2272 2636 9.678260 GATTTCTTGATAATACCATAGGAGCAT 57.322 33.333 0.00 0.00 0.00 3.79
2414 2778 9.346725 GCTTGTTTTTGAGAATTATCTAACCTG 57.653 33.333 1.19 1.77 35.54 4.00
2419 2783 5.201713 TGAGAATTATCTAACCTGCTCGG 57.798 43.478 1.19 0.00 35.54 4.63
2447 2811 1.134098 TCTGCATGCCCTTAAGCCTAC 60.134 52.381 16.68 0.00 0.00 3.18
2449 2813 1.312815 GCATGCCCTTAAGCCTACAG 58.687 55.000 6.36 0.00 0.00 2.74
2491 2855 2.436417 GTGATGCTTTTGCCAGACCTA 58.564 47.619 0.00 0.00 46.87 3.08
2517 2881 4.707448 TGAGTATCACTTGTCCTTCCTCTC 59.293 45.833 0.00 0.00 42.56 3.20
2521 2885 0.980423 ACTTGTCCTTCCTCTCCTGC 59.020 55.000 0.00 0.00 0.00 4.85
2533 2897 1.194781 TCTCCTGCTGTCCTTGACCC 61.195 60.000 0.00 0.00 0.00 4.46
2536 2900 0.393537 CCTGCTGTCCTTGACCCATC 60.394 60.000 0.00 0.00 0.00 3.51
2559 2923 5.127845 TCTGTTTCTGACTCTGTGTCTCTTT 59.872 40.000 10.76 0.00 45.54 2.52
2560 2924 5.352284 TGTTTCTGACTCTGTGTCTCTTTC 58.648 41.667 10.76 1.40 45.54 2.62
2569 2933 5.710099 ACTCTGTGTCTCTTTCTCCTAGAAG 59.290 44.000 0.00 0.00 35.37 2.85
2573 2937 5.475220 TGTGTCTCTTTCTCCTAGAAGTGAG 59.525 44.000 11.94 11.94 37.66 3.51
2620 2984 9.998106 ACCATACTATATTGTTATGACTTGTCC 57.002 33.333 0.00 0.00 0.00 4.02
2626 2990 9.469807 CTATATTGTTATGACTTGTCCTGAGTC 57.530 37.037 0.00 0.00 42.98 3.36
2631 2995 4.647564 ATGACTTGTCCTGAGTCCAAAT 57.352 40.909 2.20 0.00 42.20 2.32
2678 3043 9.941325 TGTTTATTGTTAAATGATTGCCTTGAT 57.059 25.926 0.00 0.00 30.34 2.57
2708 3073 6.798959 GCTCTACAAATGCTGAACTAGTTTTG 59.201 38.462 10.02 11.21 37.51 2.44
2764 3129 7.497249 AGTGCTTTCACCATATTAGAATCTGTC 59.503 37.037 0.00 0.00 44.16 3.51
2797 3162 2.177233 TCCTCTACCACATACTCCCTCC 59.823 54.545 0.00 0.00 0.00 4.30
2800 3165 1.955080 CTACCACATACTCCCTCCGTC 59.045 57.143 0.00 0.00 0.00 4.79
2801 3166 0.335361 ACCACATACTCCCTCCGTCT 59.665 55.000 0.00 0.00 0.00 4.18
2802 3167 0.747255 CCACATACTCCCTCCGTCTG 59.253 60.000 0.00 0.00 0.00 3.51
2803 3168 1.685180 CCACATACTCCCTCCGTCTGA 60.685 57.143 0.00 0.00 0.00 3.27
2807 3172 3.581332 ACATACTCCCTCCGTCTGAAAAA 59.419 43.478 0.00 0.00 0.00 1.94
2827 3192 6.635030 AAAAACTTGTCCCTTTAGTGCTAG 57.365 37.500 0.00 0.00 0.00 3.42
2829 3194 5.763876 AACTTGTCCCTTTAGTGCTAGAT 57.236 39.130 0.00 0.00 0.00 1.98
2830 3195 6.869206 AACTTGTCCCTTTAGTGCTAGATA 57.131 37.500 0.00 0.00 0.00 1.98
2831 3196 6.223351 ACTTGTCCCTTTAGTGCTAGATAC 57.777 41.667 0.00 0.00 0.00 2.24
2832 3197 5.720041 ACTTGTCCCTTTAGTGCTAGATACA 59.280 40.000 0.00 0.00 0.00 2.29
2833 3198 6.384305 ACTTGTCCCTTTAGTGCTAGATACAT 59.616 38.462 0.00 0.00 0.00 2.29
2834 3199 6.406692 TGTCCCTTTAGTGCTAGATACATC 57.593 41.667 0.00 0.00 0.00 3.06
2835 3200 5.304614 TGTCCCTTTAGTGCTAGATACATCC 59.695 44.000 0.00 0.00 0.00 3.51
2836 3201 5.304614 GTCCCTTTAGTGCTAGATACATCCA 59.695 44.000 0.00 0.00 0.00 3.41
2837 3202 6.014156 GTCCCTTTAGTGCTAGATACATCCAT 60.014 42.308 0.00 0.00 0.00 3.41
2839 3204 7.072454 TCCCTTTAGTGCTAGATACATCCATTT 59.928 37.037 0.00 0.00 0.00 2.32
2840 3205 7.173907 CCCTTTAGTGCTAGATACATCCATTTG 59.826 40.741 0.00 0.00 0.00 2.32
2842 3207 8.893219 TTTAGTGCTAGATACATCCATTTGAG 57.107 34.615 0.00 0.00 0.00 3.02
2844 3209 7.129457 AGTGCTAGATACATCCATTTGAGAA 57.871 36.000 0.00 0.00 0.00 2.87
2845 3210 7.568349 AGTGCTAGATACATCCATTTGAGAAA 58.432 34.615 0.00 0.00 0.00 2.52
2847 3212 7.280876 GTGCTAGATACATCCATTTGAGAAACA 59.719 37.037 0.00 0.00 0.00 2.83
2848 3213 7.828717 TGCTAGATACATCCATTTGAGAAACAA 59.171 33.333 0.00 0.00 36.65 2.83
2849 3214 8.341173 GCTAGATACATCCATTTGAGAAACAAG 58.659 37.037 0.00 0.00 39.77 3.16
2850 3215 7.093322 AGATACATCCATTTGAGAAACAAGC 57.907 36.000 0.00 0.00 39.77 4.01
2851 3216 6.888632 AGATACATCCATTTGAGAAACAAGCT 59.111 34.615 0.00 0.00 39.77 3.74
2853 3218 5.535333 ACATCCATTTGAGAAACAAGCTTG 58.465 37.500 24.84 24.84 39.77 4.01
2854 3219 5.302568 ACATCCATTTGAGAAACAAGCTTGA 59.697 36.000 32.50 8.10 39.77 3.02
2855 3220 5.443185 TCCATTTGAGAAACAAGCTTGAG 57.557 39.130 32.50 7.94 39.77 3.02
2856 3221 5.132502 TCCATTTGAGAAACAAGCTTGAGA 58.867 37.500 32.50 4.85 39.77 3.27
2857 3222 5.009010 TCCATTTGAGAAACAAGCTTGAGAC 59.991 40.000 32.50 20.14 39.77 3.36
2858 3223 5.221106 CCATTTGAGAAACAAGCTTGAGACA 60.221 40.000 32.50 19.34 39.77 3.41
2859 3224 5.895636 TTTGAGAAACAAGCTTGAGACAA 57.104 34.783 32.50 23.06 39.77 3.18
2860 3225 5.490139 TTGAGAAACAAGCTTGAGACAAG 57.510 39.130 32.50 4.70 34.20 3.16
2861 3226 3.313526 TGAGAAACAAGCTTGAGACAAGC 59.686 43.478 32.50 23.31 43.31 4.01
2869 3234 3.279853 GCTTGAGACAAGCTTTTCTGG 57.720 47.619 19.57 10.28 40.01 3.86
2880 3245 0.391793 CTTTTCTGGACGGAGGGAGC 60.392 60.000 0.00 0.00 0.00 4.70
2881 3246 1.838073 TTTTCTGGACGGAGGGAGCC 61.838 60.000 0.00 0.00 0.00 4.70
3147 3538 5.920193 TCTGAAGAATTTATTTGGGCAGG 57.080 39.130 0.00 0.00 0.00 4.85
3168 3559 4.889995 AGGGCTCTTAAATATTTCTGGCAC 59.110 41.667 3.39 6.72 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.915036 GGTCTATTCTGTAGTCCTTCTATTTCA 58.085 37.037 0.00 0.00 0.00 2.69
3 4 9.138596 AGGTCTATTCTGTAGTCCTTCTATTTC 57.861 37.037 0.00 0.00 30.76 2.17
4 5 9.495382 AAGGTCTATTCTGTAGTCCTTCTATTT 57.505 33.333 7.49 0.00 38.19 1.40
5 6 9.495382 AAAGGTCTATTCTGTAGTCCTTCTATT 57.505 33.333 11.95 0.00 40.45 1.73
6 7 9.495382 AAAAGGTCTATTCTGTAGTCCTTCTAT 57.505 33.333 11.95 2.93 40.45 1.98
7 8 8.896722 AAAAGGTCTATTCTGTAGTCCTTCTA 57.103 34.615 11.95 0.00 40.45 2.10
8 9 7.800300 AAAAGGTCTATTCTGTAGTCCTTCT 57.200 36.000 11.95 0.00 40.45 2.85
37 38 9.344772 CACCTAGTATTGTCTATTCTGTAGACT 57.655 37.037 14.25 1.03 43.15 3.24
38 39 9.122779 ACACCTAGTATTGTCTATTCTGTAGAC 57.877 37.037 7.99 7.99 43.06 2.59
42 43 8.784994 CGATACACCTAGTATTGTCTATTCTGT 58.215 37.037 0.00 0.00 43.39 3.41
52 53 4.675565 CAGCGAACGATACACCTAGTATTG 59.324 45.833 0.00 0.00 46.09 1.90
53 54 4.337555 ACAGCGAACGATACACCTAGTATT 59.662 41.667 0.00 0.00 43.39 1.89
54 55 3.881688 ACAGCGAACGATACACCTAGTAT 59.118 43.478 0.00 0.00 45.98 2.12
55 56 3.273434 ACAGCGAACGATACACCTAGTA 58.727 45.455 0.00 0.00 37.06 1.82
56 57 2.089980 ACAGCGAACGATACACCTAGT 58.910 47.619 0.00 0.00 0.00 2.57
57 58 2.846039 ACAGCGAACGATACACCTAG 57.154 50.000 0.00 0.00 0.00 3.02
58 59 2.032550 GCTACAGCGAACGATACACCTA 59.967 50.000 0.00 0.00 0.00 3.08
59 60 1.202268 GCTACAGCGAACGATACACCT 60.202 52.381 0.00 0.00 0.00 4.00
60 61 1.197910 GCTACAGCGAACGATACACC 58.802 55.000 0.00 0.00 0.00 4.16
61 62 1.904144 TGCTACAGCGAACGATACAC 58.096 50.000 0.00 0.00 45.83 2.90
62 63 2.640346 TTGCTACAGCGAACGATACA 57.360 45.000 0.00 0.00 45.83 2.29
72 73 2.762535 TACAGGGAGTTTGCTACAGC 57.237 50.000 0.00 0.00 42.50 4.40
75 76 3.079578 GGGTTTACAGGGAGTTTGCTAC 58.920 50.000 0.00 0.00 0.00 3.58
107 120 3.894547 TTCGGCAAACCCTCGCCTC 62.895 63.158 0.00 0.00 46.62 4.70
108 121 2.764637 ATTTCGGCAAACCCTCGCCT 62.765 55.000 0.00 0.00 46.62 5.52
109 122 2.340328 ATTTCGGCAAACCCTCGCC 61.340 57.895 0.00 0.00 45.28 5.54
246 259 0.843343 TAGAAGGGTGGGTTGGGGAC 60.843 60.000 0.00 0.00 0.00 4.46
254 267 4.832608 GCGGCGTAGAAGGGTGGG 62.833 72.222 9.37 0.00 0.00 4.61
284 312 4.043100 TCGGAGTGGGAGAGGCGA 62.043 66.667 0.00 0.00 0.00 5.54
288 316 0.323908 AAGGAGTCGGAGTGGGAGAG 60.324 60.000 0.00 0.00 0.00 3.20
854 1218 4.414337 AAGGCGATTTCAAGATAGAGCT 57.586 40.909 0.00 0.00 0.00 4.09
880 1244 1.205655 TGGAATGCTCTCGTGGAGAAG 59.794 52.381 11.15 0.00 44.45 2.85
914 1278 4.141597 TGGAATATGTGAACTTATCCGGCA 60.142 41.667 0.00 0.00 0.00 5.69
1179 1543 3.334891 ACCCCCATTGCGGCACTA 61.335 61.111 0.05 0.00 0.00 2.74
1222 1586 1.442769 GTCATCACAGTTGGCGTCAT 58.557 50.000 0.00 0.00 0.00 3.06
1380 1744 1.349357 GATGCCCTATCAACCTCTCCC 59.651 57.143 0.00 0.00 35.78 4.30
1389 1753 0.541392 ACGCTGTTGATGCCCTATCA 59.459 50.000 0.00 0.00 43.92 2.15
1406 1770 0.321210 TGCTACCATTGTGTCCCACG 60.321 55.000 0.00 0.00 37.14 4.94
1507 1871 6.071952 GCCTCAACCATCTCTTGAAATAACAA 60.072 38.462 0.00 0.00 0.00 2.83
1516 1880 4.021719 ACATTTTGCCTCAACCATCTCTTG 60.022 41.667 0.00 0.00 0.00 3.02
1600 1964 2.768527 CCCAGATAGAAAGAGCCTGTGA 59.231 50.000 0.00 0.00 0.00 3.58
1684 2048 3.548745 TGATCTCCCTACATTGCACAG 57.451 47.619 0.00 0.00 0.00 3.66
1700 2064 5.411977 CAGACCATCATAGCATCCTTTGATC 59.588 44.000 0.00 0.00 37.57 2.92
1755 2119 9.797642 ATCATGGAAGTATAAGCAATTGTATCA 57.202 29.630 7.40 0.00 0.00 2.15
1788 2152 0.883833 CCATCCCAGAAGCACACAAC 59.116 55.000 0.00 0.00 0.00 3.32
1907 2271 1.125093 TGCCCGAGGAAGGTTCTTCA 61.125 55.000 9.48 0.00 33.35 3.02
1912 2276 1.000896 CCATTGCCCGAGGAAGGTT 60.001 57.895 0.00 0.00 0.00 3.50
1989 2353 1.339151 ACCTCAATCTCCCGCAAGAAC 60.339 52.381 0.00 0.00 43.02 3.01
2020 2384 3.035363 CCTCTAAGAACTCCCTCCCTTC 58.965 54.545 0.00 0.00 0.00 3.46
2095 2459 0.322456 TTAGCCAGCATCACCACCAC 60.322 55.000 0.00 0.00 0.00 4.16
2098 2462 2.691409 TACTTAGCCAGCATCACCAC 57.309 50.000 0.00 0.00 0.00 4.16
2272 2636 6.374333 AGTTCAGAAAAACTCAAGCAAGTGTA 59.626 34.615 0.00 0.00 34.37 2.90
2397 2761 4.501571 GCCGAGCAGGTTAGATAATTCTCA 60.502 45.833 0.17 0.00 43.70 3.27
2405 2769 1.403687 GGGAGCCGAGCAGGTTAGAT 61.404 60.000 0.17 0.00 43.70 1.98
2406 2770 2.058595 GGGAGCCGAGCAGGTTAGA 61.059 63.158 0.17 0.00 43.70 2.10
2408 2772 0.105658 ATAGGGAGCCGAGCAGGTTA 60.106 55.000 0.17 0.00 43.70 2.85
2414 2778 1.825281 ATGCAGATAGGGAGCCGAGC 61.825 60.000 0.00 0.00 0.00 5.03
2419 2783 1.303155 GGGCATGCAGATAGGGAGC 60.303 63.158 21.36 0.00 0.00 4.70
2463 2827 2.493278 GGCAAAAGCATCACCATACAGT 59.507 45.455 0.00 0.00 0.00 3.55
2466 2830 2.754552 TCTGGCAAAAGCATCACCATAC 59.245 45.455 0.00 0.00 0.00 2.39
2491 2855 7.072562 AGAGGAAGGACAAGTGATACTCATAT 58.927 38.462 0.00 0.00 0.00 1.78
2513 2877 0.248843 GGTCAAGGACAGCAGGAGAG 59.751 60.000 0.00 0.00 33.68 3.20
2517 2881 0.393537 GATGGGTCAAGGACAGCAGG 60.394 60.000 0.00 0.00 33.68 4.85
2521 2885 2.867109 AACAGATGGGTCAAGGACAG 57.133 50.000 0.00 0.00 33.68 3.51
2559 2923 1.394532 ACCCCCTCACTTCTAGGAGA 58.605 55.000 4.59 0.00 36.08 3.71
2560 2924 1.834263 CAACCCCCTCACTTCTAGGAG 59.166 57.143 0.00 0.00 36.08 3.69
2569 2933 1.809567 CTTGCAAGCAACCCCCTCAC 61.810 60.000 14.65 0.00 0.00 3.51
2573 2937 0.180171 AAAACTTGCAAGCAACCCCC 59.820 50.000 26.27 0.00 0.00 5.40
2647 3012 9.971744 GGCAATCATTTAACAATAAACATTGAC 57.028 29.630 13.69 9.82 37.11 3.18
2660 3025 7.141363 AGCGAATATCAAGGCAATCATTTAAC 58.859 34.615 0.00 0.00 0.00 2.01
2678 3043 5.419542 AGTTCAGCATTTGTAGAGCGAATA 58.580 37.500 0.00 0.00 30.27 1.75
2764 3129 4.892345 TGTGGTAGAGGATTGATGAGAGAG 59.108 45.833 0.00 0.00 0.00 3.20
2807 3172 5.763876 ATCTAGCACTAAAGGGACAAGTT 57.236 39.130 0.00 0.00 0.00 2.66
2809 3174 6.222038 TGTATCTAGCACTAAAGGGACAAG 57.778 41.667 0.00 0.00 0.00 3.16
2810 3175 6.183360 GGATGTATCTAGCACTAAAGGGACAA 60.183 42.308 0.00 0.00 0.00 3.18
2811 3176 5.304614 GGATGTATCTAGCACTAAAGGGACA 59.695 44.000 0.00 0.00 0.00 4.02
2813 3178 5.464069 TGGATGTATCTAGCACTAAAGGGA 58.536 41.667 0.00 0.00 0.00 4.20
2814 3179 5.808366 TGGATGTATCTAGCACTAAAGGG 57.192 43.478 0.00 0.00 0.00 3.95
2816 3181 8.893219 TCAAATGGATGTATCTAGCACTAAAG 57.107 34.615 0.00 0.00 0.00 1.85
2822 3187 7.337938 TGTTTCTCAAATGGATGTATCTAGCA 58.662 34.615 0.00 0.00 0.00 3.49
2823 3188 7.792374 TGTTTCTCAAATGGATGTATCTAGC 57.208 36.000 0.00 0.00 0.00 3.42
2825 3190 8.049117 AGCTTGTTTCTCAAATGGATGTATCTA 58.951 33.333 0.00 0.00 35.48 1.98
2826 3191 6.888632 AGCTTGTTTCTCAAATGGATGTATCT 59.111 34.615 0.00 0.00 35.48 1.98
2827 3192 7.093322 AGCTTGTTTCTCAAATGGATGTATC 57.907 36.000 0.00 0.00 35.48 2.24
2829 3194 6.489700 TCAAGCTTGTTTCTCAAATGGATGTA 59.510 34.615 25.19 0.00 35.48 2.29
2830 3195 5.302568 TCAAGCTTGTTTCTCAAATGGATGT 59.697 36.000 25.19 0.00 35.48 3.06
2831 3196 5.775686 TCAAGCTTGTTTCTCAAATGGATG 58.224 37.500 25.19 0.00 35.48 3.51
2832 3197 5.771666 TCTCAAGCTTGTTTCTCAAATGGAT 59.228 36.000 25.19 0.00 35.48 3.41
2833 3198 5.009010 GTCTCAAGCTTGTTTCTCAAATGGA 59.991 40.000 25.19 1.02 35.48 3.41
2834 3199 5.218139 GTCTCAAGCTTGTTTCTCAAATGG 58.782 41.667 25.19 0.00 35.48 3.16
2835 3200 5.824429 TGTCTCAAGCTTGTTTCTCAAATG 58.176 37.500 25.19 0.00 35.48 2.32
2836 3201 6.455360 TTGTCTCAAGCTTGTTTCTCAAAT 57.545 33.333 25.19 0.00 35.48 2.32
2837 3202 5.677091 GCTTGTCTCAAGCTTGTTTCTCAAA 60.677 40.000 25.19 11.13 40.01 2.69
2839 3204 3.313526 GCTTGTCTCAAGCTTGTTTCTCA 59.686 43.478 25.19 15.00 40.01 3.27
2840 3205 3.882982 GCTTGTCTCAAGCTTGTTTCTC 58.117 45.455 25.19 12.90 40.01 2.87
2849 3214 2.880890 TCCAGAAAAGCTTGTCTCAAGC 59.119 45.455 16.65 21.90 43.31 4.01
2850 3215 3.059325 CGTCCAGAAAAGCTTGTCTCAAG 60.059 47.826 16.65 8.62 0.00 3.02
2851 3216 2.872245 CGTCCAGAAAAGCTTGTCTCAA 59.128 45.455 16.65 4.84 0.00 3.02
2853 3218 1.801178 CCGTCCAGAAAAGCTTGTCTC 59.199 52.381 16.65 5.03 0.00 3.36
2854 3219 1.416401 TCCGTCCAGAAAAGCTTGTCT 59.584 47.619 13.74 13.74 0.00 3.41
2855 3220 1.801178 CTCCGTCCAGAAAAGCTTGTC 59.199 52.381 8.73 8.73 0.00 3.18
2856 3221 1.543429 CCTCCGTCCAGAAAAGCTTGT 60.543 52.381 0.00 0.00 0.00 3.16
2857 3222 1.160137 CCTCCGTCCAGAAAAGCTTG 58.840 55.000 0.00 0.00 0.00 4.01
2858 3223 0.036875 CCCTCCGTCCAGAAAAGCTT 59.963 55.000 0.00 0.00 0.00 3.74
2859 3224 0.836400 TCCCTCCGTCCAGAAAAGCT 60.836 55.000 0.00 0.00 0.00 3.74
2860 3225 0.391793 CTCCCTCCGTCCAGAAAAGC 60.392 60.000 0.00 0.00 0.00 3.51
2861 3226 0.391793 GCTCCCTCCGTCCAGAAAAG 60.392 60.000 0.00 0.00 0.00 2.27
2862 3227 1.677552 GCTCCCTCCGTCCAGAAAA 59.322 57.895 0.00 0.00 0.00 2.29
2868 3233 1.554583 AAAGAAGGCTCCCTCCGTCC 61.555 60.000 0.00 0.00 35.59 4.79
2869 3234 0.108089 GAAAGAAGGCTCCCTCCGTC 60.108 60.000 0.00 0.00 35.28 4.79
2880 3245 3.765511 TGATGCATCCAAAGGAAAGAAGG 59.234 43.478 23.67 0.00 34.34 3.46
2881 3246 5.395682 TTGATGCATCCAAAGGAAAGAAG 57.604 39.130 23.67 0.00 34.34 2.85
3085 3476 9.349713 ACTGAATCCACACTTCAAAATAGTAAA 57.650 29.630 0.00 0.00 32.53 2.01
3147 3538 6.319911 AGAAGTGCCAGAAATATTTAAGAGCC 59.680 38.462 0.00 0.00 0.00 4.70
3168 3559 5.399858 CCAAATGAAGCATCAACAGAGAAG 58.600 41.667 0.00 0.00 39.49 2.85


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

AutoCloner maintained by Alex Coulton.