Multiple sequence alignment - TraesCS6A01G185800

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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 TraesCS6A01G185800 chr6A 100.000 3602 0 0 1 3602 218799132 218802733 0.000000e+00 6652.0
1 TraesCS6A01G185800 chr6A 85.905 823 97 10 1985 2806 218813325 218814129 0.000000e+00 859.0
2 TraesCS6A01G185800 chr6A 95.760 283 10 1 306 586 218906802 218906520 4.240000e-124 455.0
3 TraesCS6A01G185800 chr6A 93.478 184 11 1 1 183 218907125 218906942 4.580000e-69 272.0
4 TraesCS6A01G185800 chr6A 100.000 40 0 0 3071 3110 218800902 218800863 1.390000e-09 75.0
5 TraesCS6A01G185800 chr6A 100.000 40 0 0 1732 1771 218802241 218802202 1.390000e-09 75.0
6 TraesCS6A01G185800 chr6A 97.561 41 1 0 265 305 218906861 218906821 1.790000e-08 71.3
7 TraesCS6A01G185800 chr6B 94.828 2494 110 10 265 2754 290213078 290215556 0.000000e+00 3873.0
8 TraesCS6A01G185800 chr6B 93.919 1365 64 6 265 1626 290233905 290232557 0.000000e+00 2043.0
9 TraesCS6A01G185800 chr6B 91.465 785 57 3 2292 3075 290226828 290226053 0.000000e+00 1070.0
10 TraesCS6A01G185800 chr6B 88.428 795 79 5 1985 2779 290224723 290223942 0.000000e+00 946.0
11 TraesCS6A01G185800 chr6B 94.321 405 23 0 1899 2303 290230396 290229992 3.950000e-174 621.0
12 TraesCS6A01G185800 chr6B 85.745 463 54 7 3151 3602 290225806 290225345 2.520000e-131 479.0
13 TraesCS6A01G185800 chr6B 91.630 227 18 1 2740 2965 290218632 290218858 2.700000e-81 313.0
14 TraesCS6A01G185800 chr6B 93.443 183 9 3 1 183 290234165 290233986 5.930000e-68 268.0
15 TraesCS6A01G185800 chr6B 92.896 183 10 3 1 183 290212818 290212997 2.760000e-66 263.0
16 TraesCS6A01G185800 chr6B 94.872 156 8 0 1752 1907 290230718 290230563 9.990000e-61 244.0
17 TraesCS6A01G185800 chr6B 91.304 161 10 4 1 158 290187086 290187245 2.180000e-52 217.0
18 TraesCS6A01G185800 chr6D 93.964 2568 125 9 417 2975 159713884 159716430 0.000000e+00 3856.0
19 TraesCS6A01G185800 chr6D 96.159 1640 47 4 721 2352 159792774 159791143 0.000000e+00 2665.0
20 TraesCS6A01G185800 chr6D 94.433 467 21 4 265 729 159797073 159796610 0.000000e+00 713.0
21 TraesCS6A01G185800 chr6D 94.444 450 21 3 3154 3602 159716713 159717159 0.000000e+00 689.0
22 TraesCS6A01G185800 chr6D 94.222 450 24 2 3154 3602 159790086 159789638 0.000000e+00 686.0
23 TraesCS6A01G185800 chr6D 86.529 631 68 5 2170 2800 159779763 159780376 0.000000e+00 678.0
24 TraesCS6A01G185800 chr6D 91.852 405 30 2 2670 3074 159790737 159790336 2.430000e-156 562.0
25 TraesCS6A01G185800 chr6D 97.126 174 4 1 1 173 159712200 159712373 3.520000e-75 292.0
26 TraesCS6A01G185800 chr6D 88.889 216 14 4 162 377 159713678 159713883 1.280000e-64 257.0
27 TraesCS6A01G185800 chr6D 89.674 184 18 1 1985 2168 159717765 159717947 2.160000e-57 233.0
28 TraesCS6A01G185800 chr6D 95.833 48 2 0 136 183 159797201 159797154 1.070000e-10 78.7
29 TraesCS6A01G185800 chr6D 100.000 40 0 0 3071 3110 159791724 159791763 1.390000e-09 75.0
30 TraesCS6A01G185800 chr6D 95.000 40 2 0 3071 3110 159715227 159715188 3.000000e-06 63.9
31 TraesCS6A01G185800 chrUn 93.982 1213 70 2 1862 3074 244767578 244766369 0.000000e+00 1832.0
32 TraesCS6A01G185800 chrUn 93.899 1213 72 1 1862 3074 244756833 244755623 0.000000e+00 1829.0
33 TraesCS6A01G185800 chrUn 92.909 832 25 9 417 1239 244758751 244757945 0.000000e+00 1179.0
34 TraesCS6A01G185800 chrUn 86.618 822 92 6 1985 2806 244765063 244764260 0.000000e+00 893.0
35 TraesCS6A01G185800 chrUn 94.222 450 24 2 3154 3602 244766119 244765671 0.000000e+00 686.0
36 TraesCS6A01G185800 chrUn 95.745 188 7 1 3154 3340 244755373 244755186 5.840000e-78 302.0
37 TraesCS6A01G185800 chrUn 97.701 174 3 1 1 173 244760562 244760389 7.560000e-77 298.0
38 TraesCS6A01G185800 chrUn 88.372 215 15 4 162 376 244758957 244758753 2.150000e-62 250.0


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 TraesCS6A01G185800 chr6A 218799132 218802733 3601 False 6652.000000 6652 100.000000 1 3602 1 chr6A.!!$F1 3601
1 TraesCS6A01G185800 chr6A 218813325 218814129 804 False 859.000000 859 85.905000 1985 2806 1 chr6A.!!$F2 821
2 TraesCS6A01G185800 chr6A 218906520 218907125 605 True 266.100000 455 95.599667 1 586 3 chr6A.!!$R2 585
3 TraesCS6A01G185800 chr6B 290212818 290218858 6040 False 1483.000000 3873 93.118000 1 2965 3 chr6B.!!$F2 2964
4 TraesCS6A01G185800 chr6B 290223942 290234165 10223 True 810.142857 2043 91.741857 1 3602 7 chr6B.!!$R1 3601
5 TraesCS6A01G185800 chr6D 159712200 159717947 5747 False 1065.400000 3856 92.819400 1 3602 5 chr6D.!!$F3 3601
6 TraesCS6A01G185800 chr6D 159789638 159797201 7563 True 940.940000 2665 94.499800 136 3602 5 chr6D.!!$R2 3466
7 TraesCS6A01G185800 chr6D 159779763 159780376 613 False 678.000000 678 86.529000 2170 2800 1 chr6D.!!$F1 630
8 TraesCS6A01G185800 chrUn 244755186 244767578 12392 True 908.625000 1832 92.931000 1 3602 8 chrUn.!!$R1 3601

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
561 9113 0.171231 GAATTGGGCTGGCGAGTTTC 59.829 55.0 0.00 0.0 0.00 2.78 F
988 13396 0.731514 CAAATCAGCGCCACTGCAAG 60.732 55.0 2.29 0.0 46.76 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 16337 0.834612 TCCTTGGTGAACACGAACCT 59.165 50.0 0.0 0.0 37.36 3.50 R
2878 23527 0.035739 GCCCCTCCAACTAAACGTCA 59.964 55.0 0.0 0.0 0.00 4.35 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
95 7116 7.857389 CACATGAACCAGGAATATTTGTATTCG 59.143 37.037 0.00 0.00 37.33 3.34
214 8716 1.999735 CGTCATGTCAACCAAGCGTAT 59.000 47.619 0.00 0.00 0.00 3.06
216 8718 2.095853 GTCATGTCAACCAAGCGTATGG 59.904 50.000 7.02 7.02 46.38 2.74
227 8729 3.004524 CCAAGCGTATGGGTAGTAGAGAC 59.995 52.174 1.10 0.00 36.79 3.36
228 8730 3.572632 AGCGTATGGGTAGTAGAGACA 57.427 47.619 0.00 0.00 0.00 3.41
229 8731 4.101645 AGCGTATGGGTAGTAGAGACAT 57.898 45.455 0.00 0.00 0.00 3.06
230 8732 4.471548 AGCGTATGGGTAGTAGAGACATT 58.528 43.478 0.00 0.00 0.00 2.71
231 8733 4.894114 AGCGTATGGGTAGTAGAGACATTT 59.106 41.667 0.00 0.00 0.00 2.32
232 8734 5.363005 AGCGTATGGGTAGTAGAGACATTTT 59.637 40.000 0.00 0.00 0.00 1.82
233 8735 5.462398 GCGTATGGGTAGTAGAGACATTTTG 59.538 44.000 0.00 0.00 0.00 2.44
234 8736 6.570692 CGTATGGGTAGTAGAGACATTTTGT 58.429 40.000 0.00 0.00 0.00 2.83
235 8737 7.039882 CGTATGGGTAGTAGAGACATTTTGTT 58.960 38.462 0.00 0.00 0.00 2.83
236 8738 7.010183 CGTATGGGTAGTAGAGACATTTTGTTG 59.990 40.741 0.00 0.00 0.00 3.33
237 8739 6.182507 TGGGTAGTAGAGACATTTTGTTGT 57.817 37.500 0.00 0.00 0.00 3.32
238 8740 6.597562 TGGGTAGTAGAGACATTTTGTTGTT 58.402 36.000 0.00 0.00 0.00 2.83
239 8741 7.737869 TGGGTAGTAGAGACATTTTGTTGTTA 58.262 34.615 0.00 0.00 0.00 2.41
240 8742 8.380099 TGGGTAGTAGAGACATTTTGTTGTTAT 58.620 33.333 0.00 0.00 0.00 1.89
241 8743 9.227777 GGGTAGTAGAGACATTTTGTTGTTATT 57.772 33.333 0.00 0.00 0.00 1.40
297 8826 9.828852 TTGTTAAATAATACGTCGAAGCAAATT 57.171 25.926 0.00 0.00 0.00 1.82
432 8979 2.983192 TGTGACCCCTCAGAAATTACCA 59.017 45.455 0.00 0.00 0.00 3.25
561 9113 0.171231 GAATTGGGCTGGCGAGTTTC 59.829 55.000 0.00 0.00 0.00 2.78
598 9151 6.350103 TGATAAAATTATACGTGTCCAGCCA 58.650 36.000 0.00 0.00 0.00 4.75
757 13156 6.566141 GCTTTCGGCACCCTTAATTATTTTA 58.434 36.000 0.00 0.00 41.35 1.52
986 13394 2.628696 CCAAATCAGCGCCACTGCA 61.629 57.895 2.29 0.00 46.76 4.41
987 13395 1.286570 CAAATCAGCGCCACTGCAA 59.713 52.632 2.29 0.00 46.76 4.08
988 13396 0.731514 CAAATCAGCGCCACTGCAAG 60.732 55.000 2.29 0.00 46.76 4.01
1377 13785 2.437716 CTTGGGCGCGGTTACCAT 60.438 61.111 8.83 0.00 33.63 3.55
1404 13812 2.256461 GTGTCCGCGGACTACGTT 59.744 61.111 46.72 0.00 46.52 3.99
1410 13818 3.530104 GCGGACTACGTTGACGCG 61.530 66.667 21.12 3.53 46.52 6.01
1437 13845 2.029073 CAGCTGTGGGTCGACGTT 59.971 61.111 9.92 0.00 0.00 3.99
1503 13911 2.353803 GGACTATCTGCAACTCACCGTT 60.354 50.000 0.00 0.00 35.88 4.44
1530 13938 1.381928 CGCTCTCCAATGCTGGCATT 61.382 55.000 14.14 14.14 46.35 3.56
1668 14076 2.440599 GCATTGGGTGGACTGGGT 59.559 61.111 0.00 0.00 0.00 4.51
1797 15918 2.354199 GGAGCTGCTCATTTCTAAGCAC 59.646 50.000 28.95 5.29 43.30 4.40
1856 15977 1.278238 CAGCTTAACCGGACGCTAAG 58.722 55.000 9.46 10.42 0.00 2.18
1904 16200 2.128035 CTCCGAAGCCGATATCAACAC 58.872 52.381 3.12 0.00 38.22 3.32
1913 16209 1.926510 CGATATCAACACGCTTGCTGA 59.073 47.619 3.12 0.00 32.39 4.26
2016 16312 5.778241 TGTCAACCAGAAACTAGAGATGGTA 59.222 40.000 11.98 0.00 43.36 3.25
2041 16337 1.900016 CAGCTGAGCTTTGTGCCCA 60.900 57.895 8.42 0.00 44.23 5.36
2083 16379 2.295349 GTGACGTACTTCCAGTTCCTCA 59.705 50.000 0.00 0.00 0.00 3.86
2091 16387 1.180456 TCCAGTTCCTCAACCGCGTA 61.180 55.000 4.92 0.00 32.22 4.42
2104 16400 3.807538 GCGTACGCGTGGAGGAGA 61.808 66.667 26.17 0.00 40.81 3.71
2191 16487 0.240145 ACGCATTCTCGACTTCGACA 59.760 50.000 0.00 0.00 44.22 4.35
2319 19790 0.108329 CCACTGGCGAGGACGTATTT 60.108 55.000 0.00 0.00 41.98 1.40
2361 19832 3.505808 GGCTCTATCTGCCGATGAC 57.494 57.895 0.20 0.00 41.03 3.06
2370 19842 1.729470 CTGCCGATGACCTAGAGCGT 61.729 60.000 0.00 0.00 0.00 5.07
2392 19864 1.938585 ACAGAGGGAGAACCAATCGA 58.061 50.000 0.00 0.00 43.89 3.59
2500 19972 0.610232 GGCCAAGTGGAGCAACATCT 60.610 55.000 0.00 0.00 37.39 2.90
2505 19977 3.607741 CAAGTGGAGCAACATCTCTCAT 58.392 45.455 0.00 0.00 33.70 2.90
2738 20296 9.142014 TGTTTCCAGAATTTTGAAAATAGGAGA 57.858 29.630 14.67 10.49 30.47 3.71
2941 23591 5.105997 CCAATGTCTTCATCTTGTTCCCTTC 60.106 44.000 0.00 0.00 32.56 3.46
2988 23638 7.142021 GCTCAATTACTCGTGATAGATCTTCA 58.858 38.462 0.00 1.90 0.00 3.02
3012 23662 3.874383 TGGATCTCCAAACCTTCACAA 57.126 42.857 0.00 0.00 44.35 3.33
3013 23663 4.387026 TGGATCTCCAAACCTTCACAAT 57.613 40.909 0.00 0.00 44.35 2.71
3014 23664 5.512942 TGGATCTCCAAACCTTCACAATA 57.487 39.130 0.00 0.00 44.35 1.90
3043 23693 3.627395 TGGCGATCCACAATTACTCTT 57.373 42.857 0.00 0.00 37.47 2.85
3085 23735 1.875963 CCATCTGGTGAACGCAACC 59.124 57.895 0.00 0.00 0.00 3.77
3086 23736 0.888736 CCATCTGGTGAACGCAACCA 60.889 55.000 4.58 4.58 0.00 3.67
3087 23737 0.238289 CATCTGGTGAACGCAACCAC 59.762 55.000 0.58 0.00 0.00 4.16
3088 23738 0.179032 ATCTGGTGAACGCAACCACA 60.179 50.000 0.58 0.00 35.13 4.17
3089 23739 0.179032 TCTGGTGAACGCAACCACAT 60.179 50.000 0.58 0.00 35.13 3.21
3090 23740 0.238289 CTGGTGAACGCAACCACATC 59.762 55.000 0.58 0.00 35.13 3.06
3091 23741 1.169661 TGGTGAACGCAACCACATCC 61.170 55.000 0.58 0.00 35.13 3.51
3097 23747 0.108804 ACGCAACCACATCCGAGTAG 60.109 55.000 0.00 0.00 0.00 2.57
3098 23748 0.806102 CGCAACCACATCCGAGTAGG 60.806 60.000 0.00 0.00 42.97 3.18
3099 23749 1.090052 GCAACCACATCCGAGTAGGC 61.090 60.000 0.00 0.00 40.77 3.93
3101 23751 0.981183 AACCACATCCGAGTAGGCAA 59.019 50.000 0.00 0.00 40.77 4.52
3102 23752 0.537188 ACCACATCCGAGTAGGCAAG 59.463 55.000 0.00 0.00 40.77 4.01
3103 23753 0.537188 CCACATCCGAGTAGGCAAGT 59.463 55.000 0.00 0.00 40.77 3.16
3104 23754 1.471676 CCACATCCGAGTAGGCAAGTC 60.472 57.143 0.00 0.00 40.77 3.01
3108 23758 4.787999 CGAGTAGGCAAGTCGGAC 57.212 61.111 0.00 0.00 45.51 4.79
3109 23759 1.139095 CGAGTAGGCAAGTCGGACC 59.861 63.158 4.14 0.00 45.51 4.46
3110 23760 1.592400 CGAGTAGGCAAGTCGGACCA 61.592 60.000 4.14 0.00 45.51 4.02
3113 23763 0.034337 GTAGGCAAGTCGGACCAACA 59.966 55.000 4.14 0.00 0.00 3.33
3115 23765 0.606401 AGGCAAGTCGGACCAACATG 60.606 55.000 4.14 0.00 0.00 3.21
3116 23766 0.889186 GGCAAGTCGGACCAACATGT 60.889 55.000 4.14 0.00 0.00 3.21
3132 23782 3.495331 ACATGTGGTTGCATTTACCAGA 58.505 40.909 9.03 8.60 45.86 3.86
3133 23783 3.507233 ACATGTGGTTGCATTTACCAGAG 59.493 43.478 9.03 5.15 45.86 3.35
3134 23784 3.500448 TGTGGTTGCATTTACCAGAGA 57.500 42.857 9.03 0.00 45.86 3.10
3135 23785 3.146066 TGTGGTTGCATTTACCAGAGAC 58.854 45.455 9.03 0.00 45.86 3.36
3138 23788 3.181434 TGGTTGCATTTACCAGAGACCTT 60.181 43.478 4.57 0.00 40.65 3.50
3139 23789 3.440522 GGTTGCATTTACCAGAGACCTTC 59.559 47.826 0.98 0.00 35.67 3.46
3142 23792 3.072330 TGCATTTACCAGAGACCTTCACA 59.928 43.478 0.00 0.00 0.00 3.58
3143 23793 4.263462 TGCATTTACCAGAGACCTTCACAT 60.263 41.667 0.00 0.00 0.00 3.21
3144 23794 4.095483 GCATTTACCAGAGACCTTCACATG 59.905 45.833 0.00 0.00 0.00 3.21
3146 23796 2.847327 ACCAGAGACCTTCACATGTG 57.153 50.000 20.18 20.18 0.00 3.21
3147 23797 1.349026 ACCAGAGACCTTCACATGTGG 59.651 52.381 25.16 12.41 0.00 4.17
3148 23798 1.349026 CCAGAGACCTTCACATGTGGT 59.651 52.381 25.16 15.74 36.70 4.16
3150 23800 2.810274 CAGAGACCTTCACATGTGGTTG 59.190 50.000 25.16 15.30 33.74 3.77
3151 23801 1.537202 GAGACCTTCACATGTGGTTGC 59.463 52.381 25.16 11.39 33.74 4.17
3152 23802 0.238289 GACCTTCACATGTGGTTGCG 59.762 55.000 25.16 11.05 33.74 4.85
3162 23985 2.203280 TGGTTGCGTCCCACCAAG 60.203 61.111 0.00 0.00 0.00 3.61
3181 24004 2.787994 AGATGTTGTTGCTAGCTTGCT 58.212 42.857 20.64 0.00 0.00 3.91
3185 24008 2.886523 TGTTGTTGCTAGCTTGCTCAAT 59.113 40.909 23.39 0.00 33.43 2.57
3292 24116 2.356695 TCCAATTCTGAAGATGCATGCG 59.643 45.455 14.09 0.00 0.00 4.73
3401 24225 1.738099 GAAGCTCGACATGCGGTGT 60.738 57.895 9.16 0.00 45.83 4.16
3411 24235 0.378257 CATGCGGTGTAGGTGCAATC 59.622 55.000 0.00 0.00 42.65 2.67
3430 24254 3.361281 TCTGGTCAGTATACTCGTGGT 57.639 47.619 1.26 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 8716 6.182507 ACAACAAAATGTCTCTACTACCCA 57.817 37.500 0.00 0.00 0.00 4.51
244 8746 8.449397 CAAAATCAAAATGTCACCTCACAAAAA 58.551 29.630 0.00 0.00 0.00 1.94
245 8747 7.605691 ACAAAATCAAAATGTCACCTCACAAAA 59.394 29.630 0.00 0.00 0.00 2.44
246 8748 7.102346 ACAAAATCAAAATGTCACCTCACAAA 58.898 30.769 0.00 0.00 0.00 2.83
247 8749 6.638610 ACAAAATCAAAATGTCACCTCACAA 58.361 32.000 0.00 0.00 0.00 3.33
248 8750 6.219417 ACAAAATCAAAATGTCACCTCACA 57.781 33.333 0.00 0.00 0.00 3.58
249 8751 6.534793 ACAACAAAATCAAAATGTCACCTCAC 59.465 34.615 0.00 0.00 0.00 3.51
250 8752 6.638610 ACAACAAAATCAAAATGTCACCTCA 58.361 32.000 0.00 0.00 0.00 3.86
251 8753 7.538303 AACAACAAAATCAAAATGTCACCTC 57.462 32.000 0.00 0.00 0.00 3.85
252 8754 9.442047 TTTAACAACAAAATCAAAATGTCACCT 57.558 25.926 0.00 0.00 0.00 4.00
297 8826 6.854496 AACTAACACTCAATTTCTAACGCA 57.146 33.333 0.00 0.00 0.00 5.24
367 8914 5.690865 TGGACTTGGAGAACACTAATTTGT 58.309 37.500 0.00 0.00 0.00 2.83
415 8962 4.946160 TTGATGGTAATTTCTGAGGGGT 57.054 40.909 0.00 0.00 0.00 4.95
545 9097 1.600636 CAGAAACTCGCCAGCCCAA 60.601 57.895 0.00 0.00 0.00 4.12
598 9151 2.503356 AGATTTGACTCGGAGCTCCATT 59.497 45.455 31.67 15.28 35.14 3.16
757 13156 8.934023 TTTTGAATGTATTGACTTTAGAGGGT 57.066 30.769 0.00 0.00 0.00 4.34
986 13394 0.534877 TGCCATGTCGTTGCAGACTT 60.535 50.000 7.52 0.00 41.47 3.01
987 13395 0.534877 TTGCCATGTCGTTGCAGACT 60.535 50.000 7.52 0.00 41.47 3.24
988 13396 0.110056 CTTGCCATGTCGTTGCAGAC 60.110 55.000 0.00 0.00 41.30 3.51
989 13397 0.250252 TCTTGCCATGTCGTTGCAGA 60.250 50.000 0.00 0.00 36.21 4.26
990 13398 0.592637 TTCTTGCCATGTCGTTGCAG 59.407 50.000 0.00 0.00 36.21 4.41
991 13399 0.310543 GTTCTTGCCATGTCGTTGCA 59.689 50.000 0.00 0.00 0.00 4.08
992 13400 0.593128 AGTTCTTGCCATGTCGTTGC 59.407 50.000 0.00 0.00 0.00 4.17
993 13401 1.136252 CGAGTTCTTGCCATGTCGTTG 60.136 52.381 0.00 0.00 0.00 4.10
1355 13763 3.910914 TAACCGCGCCCAAGCATGT 62.911 57.895 0.00 0.00 39.83 3.21
1372 13780 1.635844 GACACGTTGATGCGATGGTA 58.364 50.000 0.00 0.00 35.59 3.25
1377 13785 3.109547 GCGGACACGTTGATGCGA 61.110 61.111 8.96 0.00 43.45 5.10
1437 13845 3.610791 CTTCAGCGTCGCACGGAGA 62.611 63.158 21.09 6.14 42.82 3.71
1797 15918 5.894673 TAGTCAAAACTTGCTTCGCTAGCG 61.895 45.833 30.91 30.91 43.85 4.26
1809 15930 3.751698 GGCCTTCGACATAGTCAAAACTT 59.248 43.478 0.00 0.00 36.92 2.66
1810 15931 3.244422 TGGCCTTCGACATAGTCAAAACT 60.244 43.478 3.32 0.00 39.66 2.66
1815 15936 1.899814 ACTTGGCCTTCGACATAGTCA 59.100 47.619 3.32 0.00 32.09 3.41
1856 15977 1.603739 GTTGACTTGGGGCCCTCAC 60.604 63.158 25.93 12.90 0.00 3.51
1913 16209 2.418910 CCAGTCTCGGATGCGAGGT 61.419 63.158 32.27 19.39 36.71 3.85
2041 16337 0.834612 TCCTTGGTGAACACGAACCT 59.165 50.000 0.00 0.00 37.36 3.50
2091 16387 2.597805 ACAGTCTCCTCCACGCGT 60.598 61.111 5.58 5.58 0.00 6.01
2104 16400 3.616721 AGCCGACCGAAGCACAGT 61.617 61.111 0.00 0.00 0.00 3.55
2191 16487 2.980233 GCCTTTGAGCACGCCAGT 60.980 61.111 0.00 0.00 0.00 4.00
2319 19790 1.000060 CGAAGAAGTCCCACCGTGTAA 60.000 52.381 0.00 0.00 0.00 2.41
2361 19832 1.141254 TCCCTCTGTAGACGCTCTAGG 59.859 57.143 0.00 0.00 28.01 3.02
2370 19842 3.024547 CGATTGGTTCTCCCTCTGTAGA 58.975 50.000 0.00 0.00 0.00 2.59
2392 19864 2.289195 CCTTGTCACAAAATGCCAGCAT 60.289 45.455 0.00 0.00 38.46 3.79
2500 19972 5.635278 TCATATTTGGCCTTGAGATGAGA 57.365 39.130 3.32 0.00 0.00 3.27
2505 19977 3.181429 GGGGATCATATTTGGCCTTGAGA 60.181 47.826 3.32 0.00 0.00 3.27
2615 20087 4.156455 TCTAATGGAGGAAATGTCAGCC 57.844 45.455 0.00 0.00 0.00 4.85
2773 23422 3.621715 AGTGTGGAGACGTCTTTTGAAAC 59.378 43.478 21.08 13.16 0.00 2.78
2779 23428 4.755123 CCAAATAAGTGTGGAGACGTCTTT 59.245 41.667 21.08 11.23 37.03 2.52
2837 23486 5.879223 TGAACAGGTGCAACAAATTTGAAAT 59.121 32.000 24.64 7.53 39.98 2.17
2878 23527 0.035739 GCCCCTCCAACTAAACGTCA 59.964 55.000 0.00 0.00 0.00 4.35
2879 23528 0.323957 AGCCCCTCCAACTAAACGTC 59.676 55.000 0.00 0.00 0.00 4.34
2926 23575 5.576563 TTTACCTGAAGGGAACAAGATGA 57.423 39.130 0.56 0.00 37.86 2.92
2929 23578 5.768164 GTGATTTTACCTGAAGGGAACAAGA 59.232 40.000 0.56 0.00 37.86 3.02
2941 23591 4.189231 CCCGGTCTAAGTGATTTTACCTG 58.811 47.826 0.00 0.00 0.00 4.00
3008 23658 5.036737 GGATCGCCAAAGAACAATATTGTG 58.963 41.667 21.46 9.14 41.31 3.33
3043 23693 6.371548 GGTTACATGTTAGTTCAGAGCATTCA 59.628 38.462 2.30 0.00 0.00 2.57
3075 23725 0.948623 CTCGGATGTGGTTGCGTTCA 60.949 55.000 0.00 0.00 0.00 3.18
3076 23726 0.949105 ACTCGGATGTGGTTGCGTTC 60.949 55.000 0.00 0.00 0.00 3.95
3077 23727 0.319083 TACTCGGATGTGGTTGCGTT 59.681 50.000 0.00 0.00 0.00 4.84
3079 23729 0.806102 CCTACTCGGATGTGGTTGCG 60.806 60.000 0.00 0.00 33.16 4.85
3080 23730 1.090052 GCCTACTCGGATGTGGTTGC 61.090 60.000 0.00 0.00 33.16 4.17
3081 23731 0.249120 TGCCTACTCGGATGTGGTTG 59.751 55.000 0.00 0.00 33.16 3.77
3082 23732 0.981183 TTGCCTACTCGGATGTGGTT 59.019 50.000 0.00 0.00 33.16 3.67
3083 23733 0.537188 CTTGCCTACTCGGATGTGGT 59.463 55.000 0.00 0.00 33.16 4.16
3084 23734 0.537188 ACTTGCCTACTCGGATGTGG 59.463 55.000 0.00 0.00 33.16 4.17
3085 23735 1.799181 CGACTTGCCTACTCGGATGTG 60.799 57.143 0.00 0.00 33.16 3.21
3086 23736 0.456221 CGACTTGCCTACTCGGATGT 59.544 55.000 0.00 0.00 33.16 3.06
3087 23737 3.258225 CGACTTGCCTACTCGGATG 57.742 57.895 0.00 0.00 33.16 3.51
3090 23740 1.139095 GTCCGACTTGCCTACTCGG 59.861 63.158 0.00 0.00 46.95 4.63
3091 23741 1.139095 GGTCCGACTTGCCTACTCG 59.861 63.158 0.00 0.00 0.00 4.18
3097 23747 0.889186 ACATGTTGGTCCGACTTGCC 60.889 55.000 20.32 0.00 0.00 4.52
3098 23748 0.238289 CACATGTTGGTCCGACTTGC 59.762 55.000 20.32 0.00 0.00 4.01
3099 23749 0.874390 CCACATGTTGGTCCGACTTG 59.126 55.000 19.24 19.24 41.10 3.16
3110 23760 3.894427 TCTGGTAAATGCAACCACATGTT 59.106 39.130 4.57 0.00 42.10 2.71
3113 23763 3.758554 GTCTCTGGTAAATGCAACCACAT 59.241 43.478 4.57 0.00 42.10 3.21
3115 23765 2.488153 GGTCTCTGGTAAATGCAACCAC 59.512 50.000 4.57 0.00 42.10 4.16
3116 23766 2.375174 AGGTCTCTGGTAAATGCAACCA 59.625 45.455 8.44 8.44 44.75 3.67
3118 23768 4.072131 TGAAGGTCTCTGGTAAATGCAAC 58.928 43.478 0.00 0.00 0.00 4.17
3119 23769 4.072131 GTGAAGGTCTCTGGTAAATGCAA 58.928 43.478 0.00 0.00 0.00 4.08
3120 23770 3.072330 TGTGAAGGTCTCTGGTAAATGCA 59.928 43.478 0.00 0.00 0.00 3.96
3122 23772 5.122869 CACATGTGAAGGTCTCTGGTAAATG 59.877 44.000 21.64 0.00 0.00 2.32
3123 23773 5.248640 CACATGTGAAGGTCTCTGGTAAAT 58.751 41.667 21.64 0.00 0.00 1.40
3125 23775 3.007940 CCACATGTGAAGGTCTCTGGTAA 59.992 47.826 27.46 0.00 0.00 2.85
3127 23777 1.349026 CCACATGTGAAGGTCTCTGGT 59.651 52.381 27.46 0.00 0.00 4.00
3129 23779 2.810274 CAACCACATGTGAAGGTCTCTG 59.190 50.000 27.46 8.32 33.74 3.35
3130 23780 2.811873 GCAACCACATGTGAAGGTCTCT 60.812 50.000 27.46 0.00 33.74 3.10
3132 23782 1.609208 GCAACCACATGTGAAGGTCT 58.391 50.000 27.46 5.26 33.74 3.85
3133 23783 0.238289 CGCAACCACATGTGAAGGTC 59.762 55.000 27.46 10.55 33.74 3.85
3134 23784 0.465460 ACGCAACCACATGTGAAGGT 60.465 50.000 27.46 13.96 37.20 3.50
3135 23785 0.238289 GACGCAACCACATGTGAAGG 59.762 55.000 27.46 13.25 34.89 3.46
3138 23788 1.599518 GGGACGCAACCACATGTGA 60.600 57.895 27.46 0.00 34.89 3.58
3139 23789 1.896183 TGGGACGCAACCACATGTG 60.896 57.895 19.31 19.31 36.87 3.21
3146 23796 1.303317 ATCTTGGTGGGACGCAACC 60.303 57.895 4.94 4.84 43.02 3.77
3147 23797 0.889186 ACATCTTGGTGGGACGCAAC 60.889 55.000 0.00 0.00 43.02 4.17
3148 23798 0.179004 AACATCTTGGTGGGACGCAA 60.179 50.000 0.00 0.00 43.02 4.85
3150 23800 0.889186 ACAACATCTTGGTGGGACGC 60.889 55.000 0.00 0.00 39.97 5.19
3151 23801 1.266718 CAACAACATCTTGGTGGGACG 59.733 52.381 0.00 0.00 39.97 4.79
3152 23802 1.000274 GCAACAACATCTTGGTGGGAC 60.000 52.381 0.71 0.00 44.27 4.46
3162 23985 2.485426 TGAGCAAGCTAGCAACAACATC 59.515 45.455 18.83 5.96 36.85 3.06
3181 24004 7.733969 TGAGAATTCAAATTTCCAACCATTGA 58.266 30.769 8.44 0.00 0.00 2.57
3185 24008 8.977267 AAATTGAGAATTCAAATTTCCAACCA 57.023 26.923 18.78 0.00 45.82 3.67
3292 24116 3.144506 CACATCCTGGATAGTGGATTGC 58.855 50.000 21.56 0.00 40.76 3.56
3344 24168 2.839486 TCTTCGTCTGTGGCAGAATT 57.161 45.000 0.00 0.00 42.46 2.17
3371 24195 3.863407 GAGCTTCCTCGGTTGGATT 57.137 52.632 0.00 0.00 35.83 3.01
3401 24225 5.208890 AGTATACTGACCAGATTGCACCTA 58.791 41.667 4.10 0.00 0.00 3.08
3411 24235 3.014623 TCACCACGAGTATACTGACCAG 58.985 50.000 10.90 0.00 0.00 4.00
3430 24254 5.338381 GGTCTACTCATGTGGATTCCTTTCA 60.338 44.000 3.95 1.68 36.13 2.69
3479 24307 0.605589 CTCCTCCGATCATAGGTGCC 59.394 60.000 9.56 0.00 34.30 5.01
3575 24407 5.003804 GCTACAGTTTTGGAGGATTTCTCA 58.996 41.667 0.00 0.00 44.19 3.27


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

AutoCloner maintained by Alex Coulton.