Multiple sequence alignment - TraesCS1D01G167400

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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 TraesCS1D01G167400 chr1D 100.000 4130 0 0 1 4130 238471686 238467557 0.000000e+00 7627.0
1 TraesCS1D01G167400 chr1B 91.733 2262 119 34 248 2480 335732000 335734222 0.000000e+00 3079.0
2 TraesCS1D01G167400 chr1B 92.852 1273 60 13 2864 4130 335734617 335735864 0.000000e+00 1818.0
3 TraesCS1D01G167400 chr1B 92.727 385 23 4 2495 2874 335734207 335734591 6.030000e-153 551.0
4 TraesCS1D01G167400 chr1B 80.252 238 21 15 9 226 335731775 335732006 5.530000e-34 156.0
5 TraesCS1D01G167400 chr1B 83.750 80 7 4 3929 4005 335735714 335735790 2.060000e-08 71.3
6 TraesCS1D01G167400 chr1A 90.715 1454 78 24 2701 4127 302198821 302197398 0.000000e+00 1884.0
7 TraesCS1D01G167400 chr1A 87.033 1658 109 44 786 2375 302200858 302199239 0.000000e+00 1773.0
8 TraesCS1D01G167400 chr1A 88.670 812 33 21 5 793 302201682 302200907 0.000000e+00 935.0
9 TraesCS1D01G167400 chr1A 82.432 296 23 10 2374 2667 302199179 302198911 8.930000e-57 231.0


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 TraesCS1D01G167400 chr1D 238467557 238471686 4129 True 7627.00 7627 100.0000 1 4130 1 chr1D.!!$R1 4129
1 TraesCS1D01G167400 chr1B 335731775 335735864 4089 False 1135.06 3079 88.2628 9 4130 5 chr1B.!!$F1 4121
2 TraesCS1D01G167400 chr1A 302197398 302201682 4284 True 1205.75 1884 87.2125 5 4127 4 chr1A.!!$R1 4122

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
226 256 0.108585 ATGCCACGGTGGTATCCATC 59.891 55.000 26.86 10.03 38.53 3.51 F
228 258 0.249911 GCCACGGTGGTATCCATCTC 60.250 60.000 26.86 4.56 40.46 2.75 F
953 1059 0.516877 TTCAGCCGCTTGATCAAACG 59.483 50.000 21.40 21.40 0.00 3.60 F
1527 1665 0.101759 CTGCTTGGGGAATGCGAATG 59.898 55.000 0.00 0.00 0.00 2.67 F
2255 2450 1.062587 CCAAGCAAGAGAATTACCGCG 59.937 52.381 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1450 0.465705 GCAGGGGATGAAGATGACGA 59.534 55.000 0.00 0.00 0.00 4.20 R
1330 1451 0.533755 GGCAGGGGATGAAGATGACG 60.534 60.000 0.00 0.00 0.00 4.35 R
2082 2247 1.203523 CAGGTGTGCTCTGAGTACCTC 59.796 57.143 20.74 14.13 39.63 3.85 R
2963 3328 1.144057 GAATCGGATCCGGTGCTGT 59.856 57.895 32.79 12.09 40.25 4.40 R
3653 4033 0.251341 AGCCGGAACTTCCTTGCATT 60.251 50.000 5.05 0.62 35.30 3.56 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
35 36 9.736023 TTTTCTCTCTTTTTCTCTTTATTGTGC 57.264 29.630 0.00 0.00 0.00 4.57
41 42 5.508200 TTTTCTCTTTATTGTGCGGTGTT 57.492 34.783 0.00 0.00 0.00 3.32
42 43 4.481930 TTCTCTTTATTGTGCGGTGTTG 57.518 40.909 0.00 0.00 0.00 3.33
57 68 3.064134 CGGTGTTGTGTTGTGTTGTATCA 59.936 43.478 0.00 0.00 0.00 2.15
74 85 2.561478 TCACTGGTTGTAAGGGCTTC 57.439 50.000 0.00 0.00 0.00 3.86
75 86 1.156736 CACTGGTTGTAAGGGCTTCG 58.843 55.000 0.00 0.00 0.00 3.79
79 90 3.000727 CTGGTTGTAAGGGCTTCGTTAG 58.999 50.000 0.00 0.00 0.00 2.34
155 170 4.363999 CGAGGACGAAATAGATCAAGCTT 58.636 43.478 0.00 0.00 42.66 3.74
219 249 1.068921 GCAAAAATGCCACGGTGGT 59.931 52.632 26.86 6.75 40.46 4.16
220 250 0.315568 GCAAAAATGCCACGGTGGTA 59.684 50.000 26.86 23.74 40.46 3.25
221 251 1.067213 GCAAAAATGCCACGGTGGTAT 60.067 47.619 26.86 24.89 45.01 2.73
222 252 2.874849 CAAAAATGCCACGGTGGTATC 58.125 47.619 27.44 12.93 42.18 2.24
223 253 1.470051 AAAATGCCACGGTGGTATCC 58.530 50.000 27.44 12.59 42.18 2.59
224 254 0.329931 AAATGCCACGGTGGTATCCA 59.670 50.000 27.44 17.50 42.18 3.41
225 255 0.550914 AATGCCACGGTGGTATCCAT 59.449 50.000 27.44 18.83 42.18 3.41
226 256 0.108585 ATGCCACGGTGGTATCCATC 59.891 55.000 26.86 10.03 38.53 3.51
227 257 0.980754 TGCCACGGTGGTATCCATCT 60.981 55.000 26.86 0.00 40.46 2.90
228 258 0.249911 GCCACGGTGGTATCCATCTC 60.250 60.000 26.86 4.56 40.46 2.75
229 259 1.119684 CCACGGTGGTATCCATCTCA 58.880 55.000 19.15 0.00 35.28 3.27
230 260 1.694150 CCACGGTGGTATCCATCTCAT 59.306 52.381 19.15 0.00 35.28 2.90
231 261 2.897326 CCACGGTGGTATCCATCTCATA 59.103 50.000 19.15 0.00 35.28 2.15
232 262 3.515502 CCACGGTGGTATCCATCTCATAT 59.484 47.826 19.15 0.00 35.28 1.78
233 263 4.020218 CCACGGTGGTATCCATCTCATATT 60.020 45.833 19.15 0.00 35.28 1.28
234 264 5.513094 CCACGGTGGTATCCATCTCATATTT 60.513 44.000 19.15 0.00 35.28 1.40
235 265 5.997746 CACGGTGGTATCCATCTCATATTTT 59.002 40.000 0.00 0.00 35.28 1.82
236 266 6.486657 CACGGTGGTATCCATCTCATATTTTT 59.513 38.462 0.00 0.00 35.28 1.94
370 401 3.792956 CGGTATCATGTGAAGCAATTTGC 59.207 43.478 13.55 13.55 45.46 3.68
460 491 1.126846 GTCAAATGCTCGTCGTCCAAG 59.873 52.381 0.00 0.00 0.00 3.61
463 494 0.537188 AATGCTCGTCGTCCAAGGAT 59.463 50.000 0.00 0.00 0.00 3.24
553 596 1.624813 CATCCCAACCAAACCAAGCAT 59.375 47.619 0.00 0.00 0.00 3.79
600 648 2.030562 CCCCGTGTCACTGTCACC 59.969 66.667 0.65 0.00 32.86 4.02
654 702 3.208383 CGCCAGCCACACACACAA 61.208 61.111 0.00 0.00 0.00 3.33
783 832 1.068741 CTCTGTACACCGGATAAGGCC 59.931 57.143 9.46 0.00 33.69 5.19
835 940 4.047822 CCGAGCATCACTTCATTACTCTC 58.952 47.826 0.00 0.00 33.17 3.20
878 984 0.972983 CCTCCTCGCTTCCTTCCTCA 60.973 60.000 0.00 0.00 0.00 3.86
953 1059 0.516877 TTCAGCCGCTTGATCAAACG 59.483 50.000 21.40 21.40 0.00 3.60
1088 1208 1.809547 GCAAGTGCCTCCTCTTCTTTC 59.190 52.381 0.00 0.00 34.31 2.62
1152 1272 4.838486 CGCGGGCGACTGACTCTC 62.838 72.222 7.38 0.00 42.83 3.20
1153 1273 3.749064 GCGGGCGACTGACTCTCA 61.749 66.667 0.00 0.00 39.98 3.27
1327 1448 1.067776 GGACAGTTCGACGAGGTCATT 60.068 52.381 20.52 0.00 32.09 2.57
1328 1449 1.986378 GACAGTTCGACGAGGTCATTG 59.014 52.381 16.56 5.26 32.09 2.82
1329 1450 1.340248 ACAGTTCGACGAGGTCATTGT 59.660 47.619 0.00 0.00 32.09 2.71
1330 1451 1.986378 CAGTTCGACGAGGTCATTGTC 59.014 52.381 0.00 0.00 38.76 3.18
1347 1468 1.482182 TGTCGTCATCTTCATCCCCTG 59.518 52.381 0.00 0.00 0.00 4.45
1376 1511 2.096762 CCTCGTTTTCCCGTACGTTTTC 60.097 50.000 15.21 0.00 38.79 2.29
1459 1597 3.016474 GCGCGTGAGTTGCTCTTCC 62.016 63.158 8.43 0.00 0.00 3.46
1527 1665 0.101759 CTGCTTGGGGAATGCGAATG 59.898 55.000 0.00 0.00 0.00 2.67
1628 1787 3.557054 GCCCACTTGATCAGTTCACTGTA 60.557 47.826 6.84 0.00 44.12 2.74
1660 1819 3.130340 CACTTGTGTTAAACCAGCAACCT 59.870 43.478 0.00 0.00 0.00 3.50
1708 1867 1.525923 CTCCCTCTGGCATGGACAG 59.474 63.158 8.07 0.00 40.64 3.51
2023 2188 8.144478 TCTGCTAGTACTGCTATTTTCCTAATG 58.856 37.037 5.39 0.00 0.00 1.90
2029 2194 8.322091 AGTACTGCTATTTTCCTAATGACTGTT 58.678 33.333 0.00 0.00 0.00 3.16
2036 2201 9.653287 CTATTTTCCTAATGACTGTTACTGTCA 57.347 33.333 23.29 23.29 44.01 3.58
2082 2247 2.507102 ACGTCGCGGCATTCTCAG 60.507 61.111 12.89 0.00 0.00 3.35
2157 2352 5.997129 TCTAACATGAAGTTTGCTCACATGA 59.003 36.000 0.00 0.00 41.64 3.07
2175 2370 3.526931 TGAAGGATAGACCGAAGCTTG 57.473 47.619 2.10 0.00 44.74 4.01
2206 2401 7.488322 TCAGAAATAAACCAAACAACTTCCTG 58.512 34.615 0.00 0.00 0.00 3.86
2222 2417 4.020218 ACTTCCTGAACATTCTCGGAATGA 60.020 41.667 24.37 8.89 37.09 2.57
2255 2450 1.062587 CCAAGCAAGAGAATTACCGCG 59.937 52.381 0.00 0.00 0.00 6.46
2267 2462 1.452953 TTACCGCGGCATCGAGATCT 61.453 55.000 28.58 3.48 38.46 2.75
2268 2463 1.853114 TACCGCGGCATCGAGATCTC 61.853 60.000 28.58 13.05 38.46 2.75
2284 2479 4.816984 TCGGAGACCTCGGGCTCC 62.817 72.222 25.30 25.30 40.26 4.70
2431 2687 8.267894 ACTACTTTACTGGAATGCATCTTACAT 58.732 33.333 0.00 0.00 0.00 2.29
2432 2688 7.944729 ACTTTACTGGAATGCATCTTACATT 57.055 32.000 0.00 0.00 40.37 2.71
2436 2692 5.503927 ACTGGAATGCATCTTACATTGTCT 58.496 37.500 0.00 0.00 37.85 3.41
2457 2713 8.591114 TGTCTAGTTACAAGCCTTATCTTACT 57.409 34.615 0.00 0.00 0.00 2.24
2458 2714 9.032624 TGTCTAGTTACAAGCCTTATCTTACTT 57.967 33.333 0.00 0.00 0.00 2.24
2463 2719 9.433153 AGTTACAAGCCTTATCTTACTTACAAC 57.567 33.333 0.00 0.00 0.00 3.32
2464 2720 9.211485 GTTACAAGCCTTATCTTACTTACAACA 57.789 33.333 0.00 0.00 0.00 3.33
2465 2721 9.953565 TTACAAGCCTTATCTTACTTACAACAT 57.046 29.630 0.00 0.00 0.00 2.71
2466 2722 8.268850 ACAAGCCTTATCTTACTTACAACATG 57.731 34.615 0.00 0.00 0.00 3.21
2467 2723 7.883311 ACAAGCCTTATCTTACTTACAACATGT 59.117 33.333 0.00 0.00 0.00 3.21
2468 2724 8.391106 CAAGCCTTATCTTACTTACAACATGTC 58.609 37.037 0.00 0.00 0.00 3.06
2469 2725 7.852263 AGCCTTATCTTACTTACAACATGTCT 58.148 34.615 0.00 0.00 0.00 3.41
2470 2726 8.322091 AGCCTTATCTTACTTACAACATGTCTT 58.678 33.333 0.00 0.00 0.00 3.01
2471 2727 9.595823 GCCTTATCTTACTTACAACATGTCTTA 57.404 33.333 0.00 0.00 0.00 2.10
2503 2759 3.907894 TTTTGCGGTGGATGTCTTAAC 57.092 42.857 0.00 0.00 0.00 2.01
2558 2826 8.293699 AGAACTTCACCTTTTAAATTCAGTGT 57.706 30.769 0.00 0.00 0.00 3.55
2601 2870 2.741228 GCAGAAGCGTCAAGAGGATCAT 60.741 50.000 1.61 0.00 37.82 2.45
2697 2966 2.304180 AGTGGTTCCTTCCATGTCTCAG 59.696 50.000 0.00 0.00 39.81 3.35
2796 3122 1.160137 CAAAGTAGAGTGCAGGTGGC 58.840 55.000 0.00 0.00 45.13 5.01
2854 3183 4.418392 CACATTGCTCTTTTATGTGCCTC 58.582 43.478 0.00 0.00 41.64 4.70
2860 3189 5.994250 TGCTCTTTTATGTGCCTCTCTAAT 58.006 37.500 0.00 0.00 0.00 1.73
2867 3232 2.910199 TGTGCCTCTCTAATCATGTGC 58.090 47.619 0.00 0.00 0.00 4.57
2870 3235 2.693074 TGCCTCTCTAATCATGTGCGTA 59.307 45.455 0.00 0.00 0.00 4.42
2889 3254 4.500887 GCGTATGTTCTCTTGCATAGGGTA 60.501 45.833 0.00 0.00 35.34 3.69
2963 3328 0.179234 TGTTCTGACGGCAGGAACAA 59.821 50.000 24.69 9.44 42.53 2.83
3120 3488 3.704061 AGAAGGAAGTCAGATACTCCAGC 59.296 47.826 0.00 0.00 37.50 4.85
3121 3489 3.107402 AGGAAGTCAGATACTCCAGCA 57.893 47.619 0.00 0.00 37.50 4.41
3122 3490 3.030291 AGGAAGTCAGATACTCCAGCAG 58.970 50.000 0.00 0.00 37.50 4.24
3135 3503 0.035725 CCAGCAGCACCTGAATCTCA 60.036 55.000 5.32 0.00 34.77 3.27
3136 3504 1.408405 CCAGCAGCACCTGAATCTCAT 60.408 52.381 5.32 0.00 34.77 2.90
3163 3533 2.069273 GACCATGGTTCAGAAGACACG 58.931 52.381 20.85 0.00 0.00 4.49
3247 3617 7.764443 TGTTCATAGGTTGCAAGTAAGACTATC 59.236 37.037 0.00 0.00 0.00 2.08
3282 3652 0.524862 AAGCCTGCTTGCTGAATTCG 59.475 50.000 3.09 0.00 41.80 3.34
3291 3661 4.093408 TGCTTGCTGAATTCGTTCATAGTC 59.907 41.667 0.04 0.00 0.00 2.59
3300 3670 4.322080 TTCGTTCATAGTCTGGCATAGG 57.678 45.455 0.00 0.00 0.00 2.57
3501 3879 7.660208 CCAATCCTAACAACTACAGTAAGTGTT 59.340 37.037 11.48 11.48 40.94 3.32
3524 3902 3.127425 ACTCTGACCTAAAACACAGCC 57.873 47.619 0.00 0.00 0.00 4.85
3536 3914 1.059098 ACACAGCCACTCCTGAATCA 58.941 50.000 0.00 0.00 36.67 2.57
3547 3927 4.574013 CACTCCTGAATCAGCTTAACCATC 59.426 45.833 4.40 0.00 0.00 3.51
3548 3928 4.225942 ACTCCTGAATCAGCTTAACCATCA 59.774 41.667 4.40 0.00 0.00 3.07
3554 3934 3.120321 TCAGCTTAACCATCACGTTGT 57.880 42.857 0.00 0.00 0.00 3.32
3570 3950 2.921121 CGTTGTTGCTACGCTAAGATCA 59.079 45.455 0.00 0.00 31.73 2.92
3571 3951 3.000674 CGTTGTTGCTACGCTAAGATCAG 60.001 47.826 0.00 0.00 31.73 2.90
3572 3952 3.165058 TGTTGCTACGCTAAGATCAGG 57.835 47.619 0.00 0.00 0.00 3.86
3573 3953 2.159099 TGTTGCTACGCTAAGATCAGGG 60.159 50.000 0.00 0.00 34.78 4.45
3574 3954 1.040646 TGCTACGCTAAGATCAGGGG 58.959 55.000 0.00 0.00 32.99 4.79
3575 3955 1.329256 GCTACGCTAAGATCAGGGGA 58.671 55.000 0.00 0.00 32.99 4.81
3576 3956 1.000052 GCTACGCTAAGATCAGGGGAC 60.000 57.143 0.00 0.00 32.99 4.46
3712 4095 1.001641 GAGACATGGGGCAGCAGTT 60.002 57.895 0.00 0.00 0.00 3.16
3715 4098 0.682209 GACATGGGGCAGCAGTTGAT 60.682 55.000 0.00 0.00 0.00 2.57
3936 4319 0.935831 CGCCTCGTTGACGTTGTACA 60.936 55.000 3.25 0.00 40.80 2.90
3986 4375 1.078848 GCTGTCCTCCTCGTTGCAT 60.079 57.895 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.539436 AGAGAAAAAGAGAGAAAAACACAACC 58.461 34.615 0.00 0.00 0.00 3.77
2 3 8.972262 AAGAGAAAAAGAGAGAAAAACACAAC 57.028 30.769 0.00 0.00 0.00 3.32
35 36 3.064134 TGATACAACACAACACAACACCG 59.936 43.478 0.00 0.00 0.00 4.94
41 42 3.879998 ACCAGTGATACAACACAACACA 58.120 40.909 0.00 0.00 42.45 3.72
42 43 4.095782 ACAACCAGTGATACAACACAACAC 59.904 41.667 0.00 0.00 42.45 3.32
57 68 0.763035 ACGAAGCCCTTACAACCAGT 59.237 50.000 0.00 0.00 0.00 4.00
74 85 1.465187 GCGCCTGGCTTTAAACTAACG 60.465 52.381 17.92 0.00 39.11 3.18
75 86 2.257974 GCGCCTGGCTTTAAACTAAC 57.742 50.000 17.92 0.00 39.11 2.34
119 134 1.404391 GTCCTCGCTCGTTCATTCCTA 59.596 52.381 0.00 0.00 0.00 2.94
125 140 0.242825 ATTTCGTCCTCGCTCGTTCA 59.757 50.000 0.00 0.00 36.96 3.18
155 170 0.847373 TTGCTAGACCCAACCCAACA 59.153 50.000 0.00 0.00 0.00 3.33
235 265 9.874205 GAAATGACATGGATATTTCCTTTCAAA 57.126 29.630 15.20 0.00 43.07 2.69
236 266 9.258629 AGAAATGACATGGATATTTCCTTTCAA 57.741 29.630 19.31 0.00 43.07 2.69
237 267 8.827832 AGAAATGACATGGATATTTCCTTTCA 57.172 30.769 19.31 4.10 43.07 2.69
238 268 9.525409 CAAGAAATGACATGGATATTTCCTTTC 57.475 33.333 19.31 11.74 43.07 2.62
239 269 8.480501 CCAAGAAATGACATGGATATTTCCTTT 58.519 33.333 19.31 11.05 43.07 3.11
240 270 7.620888 ACCAAGAAATGACATGGATATTTCCTT 59.379 33.333 19.31 13.53 43.07 3.36
241 271 7.128077 ACCAAGAAATGACATGGATATTTCCT 58.872 34.615 19.31 10.32 43.07 3.36
242 272 7.352079 ACCAAGAAATGACATGGATATTTCC 57.648 36.000 19.31 0.00 40.12 3.13
246 276 8.863086 CCATAAACCAAGAAATGACATGGATAT 58.137 33.333 0.00 0.00 36.75 1.63
460 491 4.626081 CCGGCCGGGTGATCATCC 62.626 72.222 37.42 15.65 0.00 3.51
553 596 1.742831 GCACTGTGTTTCTTGTGTGGA 59.257 47.619 9.86 0.00 33.44 4.02
600 648 2.154798 TTTCCGTGGCTCGAGTGAGG 62.155 60.000 15.13 12.44 42.79 3.86
653 701 0.182775 GCCCCTGATTGATACCGGTT 59.817 55.000 15.04 0.00 0.00 4.44
654 702 0.694444 AGCCCCTGATTGATACCGGT 60.694 55.000 13.98 13.98 0.00 5.28
708 757 1.202348 TGATGTCATCGTCGCTTCACT 59.798 47.619 8.29 0.00 32.69 3.41
783 832 1.456518 TGCAGGGGATCTCTCTCGG 60.457 63.158 0.00 0.00 0.00 4.63
815 920 5.016051 TGGAGAGTAATGAAGTGATGCTC 57.984 43.478 0.00 0.00 0.00 4.26
835 940 1.266175 GAAGCTGGCGATGAATGATGG 59.734 52.381 0.00 0.00 0.00 3.51
878 984 3.160679 AGCAGCTTGGGTTTTCTATGT 57.839 42.857 0.00 0.00 0.00 2.29
1088 1208 1.221840 CCATGGTGAACGGGAGAGG 59.778 63.158 2.57 0.00 0.00 3.69
1152 1272 1.082821 CAACGACACGCACACCATG 60.083 57.895 0.00 0.00 0.00 3.66
1153 1273 2.892334 GCAACGACACGCACACCAT 61.892 57.895 0.00 0.00 0.00 3.55
1327 1448 1.482182 CAGGGGATGAAGATGACGACA 59.518 52.381 0.00 0.00 0.00 4.35
1328 1449 1.808133 GCAGGGGATGAAGATGACGAC 60.808 57.143 0.00 0.00 0.00 4.34
1329 1450 0.465705 GCAGGGGATGAAGATGACGA 59.534 55.000 0.00 0.00 0.00 4.20
1330 1451 0.533755 GGCAGGGGATGAAGATGACG 60.534 60.000 0.00 0.00 0.00 4.35
1331 1452 0.842635 AGGCAGGGGATGAAGATGAC 59.157 55.000 0.00 0.00 0.00 3.06
1347 1468 2.563427 GAAAACGAGGCAGCAGGC 59.437 61.111 0.00 0.00 43.74 4.85
1357 1478 1.864082 GGAAAACGTACGGGAAAACGA 59.136 47.619 21.06 0.00 41.55 3.85
1376 1511 1.784062 CGAAGCAAAGCTCGTCAGG 59.216 57.895 0.00 0.00 38.25 3.86
1459 1597 6.969828 AGCGATTAAACTAGGACAAAAGAG 57.030 37.500 0.00 0.00 0.00 2.85
1527 1665 1.737838 TGTGCCAGTTGATCGATTCC 58.262 50.000 0.00 0.00 0.00 3.01
1628 1787 2.717639 AACACAAGTGGAGCTCAAGT 57.282 45.000 17.19 3.81 34.19 3.16
1660 1819 4.686091 CAGCGAGCGGATGAGATAATTAAA 59.314 41.667 0.00 0.00 32.47 1.52
1708 1867 2.515996 TTACAGGTAGGCAGCACGGC 62.516 60.000 0.00 0.00 41.61 5.68
1827 1992 1.719780 CACAACTACGACCGCTTTCTC 59.280 52.381 0.00 0.00 0.00 2.87
2023 2188 5.874810 TCCTGCATTAATGACAGTAACAGTC 59.125 40.000 25.07 6.70 33.25 3.51
2029 2194 6.408092 CCCTACTTCCTGCATTAATGACAGTA 60.408 42.308 25.07 17.64 33.25 2.74
2036 2201 4.526438 AAGCCCTACTTCCTGCATTAAT 57.474 40.909 0.00 0.00 30.77 1.40
2066 2231 2.202610 TCTGAGAATGCCGCGACG 60.203 61.111 8.23 0.00 0.00 5.12
2082 2247 1.203523 CAGGTGTGCTCTGAGTACCTC 59.796 57.143 20.74 14.13 39.63 3.85
2092 2257 2.393271 AGCTAATCACAGGTGTGCTC 57.607 50.000 5.17 0.00 45.25 4.26
2098 2263 5.536161 ACATTTGTCAAAGCTAATCACAGGT 59.464 36.000 4.03 0.00 0.00 4.00
2099 2264 6.017400 ACATTTGTCAAAGCTAATCACAGG 57.983 37.500 4.03 0.00 0.00 4.00
2144 2339 4.333926 GGTCTATCCTTCATGTGAGCAAAC 59.666 45.833 0.00 0.00 0.00 2.93
2157 2352 2.678190 GCACAAGCTTCGGTCTATCCTT 60.678 50.000 0.00 0.00 37.91 3.36
2175 2370 3.552604 TTGGTTTATTTCTGAGCGCAC 57.447 42.857 11.47 3.13 0.00 5.34
2206 2401 4.331168 CCTGAACTCATTCCGAGAATGTTC 59.669 45.833 19.48 17.23 45.45 3.18
2267 2462 4.816984 GGAGCCCGAGGTCTCCGA 62.817 72.222 3.23 0.00 40.49 4.55
2268 2463 4.824515 AGGAGCCCGAGGTCTCCG 62.825 72.222 12.91 0.00 44.67 4.63
2273 2468 1.306141 TTGATGAGGAGCCCGAGGT 60.306 57.895 0.00 0.00 0.00 3.85
2431 2687 9.032624 AGTAAGATAAGGCTTGTAACTAGACAA 57.967 33.333 10.69 0.00 36.98 3.18
2432 2688 8.591114 AGTAAGATAAGGCTTGTAACTAGACA 57.409 34.615 10.69 0.00 0.00 3.41
2482 2738 3.632604 TGTTAAGACATCCACCGCAAAAA 59.367 39.130 0.00 0.00 0.00 1.94
2483 2739 3.215151 TGTTAAGACATCCACCGCAAAA 58.785 40.909 0.00 0.00 0.00 2.44
2484 2740 2.852449 TGTTAAGACATCCACCGCAAA 58.148 42.857 0.00 0.00 0.00 3.68
2485 2741 2.552599 TGTTAAGACATCCACCGCAA 57.447 45.000 0.00 0.00 0.00 4.85
2486 2742 2.552599 TTGTTAAGACATCCACCGCA 57.447 45.000 0.00 0.00 35.29 5.69
2487 2743 4.083003 TGAAATTGTTAAGACATCCACCGC 60.083 41.667 0.00 0.00 35.29 5.68
2488 2744 5.621197 TGAAATTGTTAAGACATCCACCG 57.379 39.130 0.00 0.00 35.29 4.94
2489 2745 6.981722 AGTTGAAATTGTTAAGACATCCACC 58.018 36.000 0.00 0.00 35.29 4.61
2490 2746 7.875971 AGAGTTGAAATTGTTAAGACATCCAC 58.124 34.615 0.00 0.00 35.29 4.02
2491 2747 9.567776 TTAGAGTTGAAATTGTTAAGACATCCA 57.432 29.630 0.00 0.00 35.29 3.41
2548 2816 8.225603 AGTAAGTGAAACATGACACTGAATTT 57.774 30.769 19.07 10.19 44.94 1.82
2558 2826 9.665719 TCTGCATAATTAGTAAGTGAAACATGA 57.334 29.630 0.00 0.00 41.43 3.07
2601 2870 3.692101 CCCATCCACTTGTTGCGTTTATA 59.308 43.478 0.00 0.00 0.00 0.98
2667 2936 3.230976 GGAAGGAACCACTGTGGATTTT 58.769 45.455 32.30 16.74 40.96 1.82
2697 2966 5.572896 CACAAGTTCAGTTCAGGTTTTGTTC 59.427 40.000 0.00 0.00 0.00 3.18
2796 3122 3.603532 TGCTGAGAATTTAGGAGTGCAG 58.396 45.455 0.00 0.00 0.00 4.41
2854 3183 6.212235 AGAGAACATACGCACATGATTAGAG 58.788 40.000 0.00 0.00 0.00 2.43
2860 3189 2.672874 GCAAGAGAACATACGCACATGA 59.327 45.455 0.00 0.00 0.00 3.07
2867 3232 4.060038 ACCCTATGCAAGAGAACATACG 57.940 45.455 0.00 0.00 0.00 3.06
2870 3235 3.181465 CCGTACCCTATGCAAGAGAACAT 60.181 47.826 0.00 0.00 0.00 2.71
2963 3328 1.144057 GAATCGGATCCGGTGCTGT 59.856 57.895 32.79 12.09 40.25 4.40
3120 3488 4.700700 TGACATATGAGATTCAGGTGCTG 58.299 43.478 10.38 0.00 0.00 4.41
3121 3489 4.652881 TCTGACATATGAGATTCAGGTGCT 59.347 41.667 10.38 0.00 36.84 4.40
3122 3490 4.749099 GTCTGACATATGAGATTCAGGTGC 59.251 45.833 10.38 3.35 36.84 5.01
3135 3503 5.426509 TCTTCTGAACCATGGTCTGACATAT 59.573 40.000 20.07 0.00 0.00 1.78
3136 3504 4.777366 TCTTCTGAACCATGGTCTGACATA 59.223 41.667 20.07 6.58 0.00 2.29
3163 3533 4.947388 AGTCTACTGGTCAGATCAGAACTC 59.053 45.833 18.19 5.35 36.22 3.01
3247 3617 2.636893 AGGCTTCATAGTATCCAGCTGG 59.363 50.000 27.87 27.87 0.00 4.85
3282 3652 4.130118 CCAACCTATGCCAGACTATGAAC 58.870 47.826 0.00 0.00 0.00 3.18
3291 3661 6.533730 TCTCATATAAACCAACCTATGCCAG 58.466 40.000 0.00 0.00 0.00 4.85
3300 3670 7.367285 TGTTGCTGTTTCTCATATAAACCAAC 58.633 34.615 11.15 11.15 38.31 3.77
3443 3821 7.443575 GGGTACACGAGTGACTCTATTATTCTA 59.556 40.741 11.26 0.00 0.00 2.10
3451 3829 2.816087 GTTGGGTACACGAGTGACTCTA 59.184 50.000 11.26 0.00 0.00 2.43
3462 3840 1.310216 GGATTGGGCGTTGGGTACAC 61.310 60.000 0.00 0.00 0.00 2.90
3501 3879 5.061179 GGCTGTGTTTTAGGTCAGAGTTTA 58.939 41.667 0.00 0.00 0.00 2.01
3524 3902 3.942829 TGGTTAAGCTGATTCAGGAGTG 58.057 45.455 15.28 0.00 31.21 3.51
3536 3914 2.031157 GCAACAACGTGATGGTTAAGCT 60.031 45.455 6.19 0.00 0.00 3.74
3571 3951 1.132500 CCACTGATCTTAGGGTCCCC 58.868 60.000 3.51 0.00 0.00 4.81
3572 3952 1.763545 GACCACTGATCTTAGGGTCCC 59.236 57.143 0.00 0.00 41.67 4.46
3573 3953 2.467880 TGACCACTGATCTTAGGGTCC 58.532 52.381 17.68 6.50 45.81 4.46
3574 3954 4.020128 ACTTTGACCACTGATCTTAGGGTC 60.020 45.833 15.16 15.16 46.40 4.46
3575 3955 3.910627 ACTTTGACCACTGATCTTAGGGT 59.089 43.478 0.00 0.00 33.78 4.34
3576 3956 4.559862 ACTTTGACCACTGATCTTAGGG 57.440 45.455 0.00 0.00 0.00 3.53
3577 3957 5.422331 TCCTACTTTGACCACTGATCTTAGG 59.578 44.000 0.00 0.00 0.00 2.69
3578 3958 6.378564 TCTCCTACTTTGACCACTGATCTTAG 59.621 42.308 0.00 0.00 0.00 2.18
3579 3959 6.253758 TCTCCTACTTTGACCACTGATCTTA 58.746 40.000 0.00 0.00 0.00 2.10
3580 3960 5.087323 TCTCCTACTTTGACCACTGATCTT 58.913 41.667 0.00 0.00 0.00 2.40
3581 3961 4.678256 TCTCCTACTTTGACCACTGATCT 58.322 43.478 0.00 0.00 0.00 2.75
3582 3962 4.142049 CCTCTCCTACTTTGACCACTGATC 60.142 50.000 0.00 0.00 0.00 2.92
3583 3963 3.772025 CCTCTCCTACTTTGACCACTGAT 59.228 47.826 0.00 0.00 0.00 2.90
3584 3964 3.165875 CCTCTCCTACTTTGACCACTGA 58.834 50.000 0.00 0.00 0.00 3.41
3585 3965 3.165875 TCCTCTCCTACTTTGACCACTG 58.834 50.000 0.00 0.00 0.00 3.66
3653 4033 0.251341 AGCCGGAACTTCCTTGCATT 60.251 50.000 5.05 0.62 35.30 3.56
3712 4095 0.749049 CAGCGAGGAGATGGACATCA 59.251 55.000 14.16 0.00 40.22 3.07
3986 4375 2.753043 GACCTCCCGCTGGTCGTA 60.753 66.667 0.00 0.00 43.55 3.43


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

AutoCloner maintained by Alex Coulton.