Multiple sequence alignment - TraesCS2D01G396100

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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 TraesCS2D01G396100 chr2D 100.000 3434 0 0 1 3434 507217715 507214282 0.000000e+00 6342.0
1 TraesCS2D01G396100 chr2D 75.277 991 212 29 1401 2373 507259182 507260157 3.150000e-120 442.0
2 TraesCS2D01G396100 chr2D 82.090 402 58 7 2985 3380 141994621 141994228 7.100000e-87 331.0
3 TraesCS2D01G396100 chr2A 93.851 2472 106 18 172 2608 651823296 651820836 0.000000e+00 3681.0
4 TraesCS2D01G396100 chr2A 75.851 940 193 30 1401 2320 651916171 651917096 6.760000e-122 448.0
5 TraesCS2D01G396100 chr2A 95.385 130 3 2 2607 2736 651820806 651820680 1.620000e-48 204.0
6 TraesCS2D01G396100 chr2A 90.000 80 5 3 2736 2812 651820515 651820436 2.180000e-17 100.0
7 TraesCS2D01G396100 chr2B 93.555 2467 115 25 182 2610 595371048 595368588 0.000000e+00 3635.0
8 TraesCS2D01G396100 chr2B 88.734 719 63 11 2607 3323 595368549 595367847 0.000000e+00 863.0
9 TraesCS2D01G396100 chr2B 74.669 983 214 29 1401 2364 595578428 595579394 1.480000e-108 403.0
10 TraesCS2D01G396100 chr2B 84.328 134 11 5 1 131 595371417 595371291 4.650000e-24 122.0
11 TraesCS2D01G396100 chr6A 84.462 502 66 9 2941 3434 25765259 25765756 5.150000e-133 484.0
12 TraesCS2D01G396100 chr4A 82.174 460 67 11 2938 3384 164709982 164710439 6.950000e-102 381.0
13 TraesCS2D01G396100 chr7D 81.366 483 71 13 2941 3418 124874033 124874501 3.240000e-100 375.0
14 TraesCS2D01G396100 chr3D 83.171 410 59 9 2961 3363 336869970 336869564 1.950000e-97 366.0
15 TraesCS2D01G396100 chr4B 79.843 511 84 12 2937 3434 359681650 359682154 4.220000e-94 355.0
16 TraesCS2D01G396100 chr5B 82.555 407 63 8 2962 3363 136017897 136017494 5.450000e-93 351.0
17 TraesCS2D01G396100 chr6B 83.038 395 56 11 2992 3380 391098578 391098189 7.050000e-92 348.0
18 TraesCS2D01G396100 chr3B 84.722 72 7 4 62 131 783090838 783090907 6.150000e-08 69.4


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 TraesCS2D01G396100 chr2D 507214282 507217715 3433 True 6342.000000 6342 100.000000 1 3434 1 chr2D.!!$R2 3433
1 TraesCS2D01G396100 chr2D 507259182 507260157 975 False 442.000000 442 75.277000 1401 2373 1 chr2D.!!$F1 972
2 TraesCS2D01G396100 chr2A 651820436 651823296 2860 True 1328.333333 3681 93.078667 172 2812 3 chr2A.!!$R1 2640
3 TraesCS2D01G396100 chr2A 651916171 651917096 925 False 448.000000 448 75.851000 1401 2320 1 chr2A.!!$F1 919
4 TraesCS2D01G396100 chr2B 595367847 595371417 3570 True 1540.000000 3635 88.872333 1 3323 3 chr2B.!!$R1 3322
5 TraesCS2D01G396100 chr2B 595578428 595579394 966 False 403.000000 403 74.669000 1401 2364 1 chr2B.!!$F1 963
6 TraesCS2D01G396100 chr4B 359681650 359682154 504 False 355.000000 355 79.843000 2937 3434 1 chr4B.!!$F1 497

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
865 1098 0.042581 ATTTCCCAATCCCCACACCC 59.957 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 3005 0.179084 GATCGGATCGAGGTGCCAAA 60.179 55.0 1.62 0.0 39.91 3.28 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
56 58 6.819284 ACTGCCAATTGAGAAAATGAGAAAA 58.181 32.000 7.12 0.00 0.00 2.29
57 59 7.274447 ACTGCCAATTGAGAAAATGAGAAAAA 58.726 30.769 7.12 0.00 0.00 1.94
59 61 7.499292 TGCCAATTGAGAAAATGAGAAAAAGA 58.501 30.769 7.12 0.00 0.00 2.52
68 72 9.971922 GAGAAAATGAGAAAAAGAGGATTTTCA 57.028 29.630 13.20 0.00 46.75 2.69
120 124 6.230472 ACACAAAAGATTCATAAAAAGGCCC 58.770 36.000 0.00 0.00 0.00 5.80
121 125 5.348451 CACAAAAGATTCATAAAAAGGCCCG 59.652 40.000 0.00 0.00 0.00 6.13
122 126 4.736126 AAAGATTCATAAAAAGGCCCGG 57.264 40.909 0.00 0.00 0.00 5.73
123 127 3.382083 AGATTCATAAAAAGGCCCGGT 57.618 42.857 0.00 0.00 0.00 5.28
124 128 3.708451 AGATTCATAAAAAGGCCCGGTT 58.292 40.909 0.00 0.00 0.00 4.44
125 129 4.862371 AGATTCATAAAAAGGCCCGGTTA 58.138 39.130 0.00 0.00 0.00 2.85
126 130 4.887655 AGATTCATAAAAAGGCCCGGTTAG 59.112 41.667 0.00 0.00 0.00 2.34
133 137 2.043349 GGCCCGGTTAGCCCAATT 60.043 61.111 8.93 0.00 45.16 2.32
134 138 1.684391 GGCCCGGTTAGCCCAATTT 60.684 57.895 8.93 0.00 45.16 1.82
135 139 1.672854 GGCCCGGTTAGCCCAATTTC 61.673 60.000 8.93 0.00 45.16 2.17
136 140 0.683179 GCCCGGTTAGCCCAATTTCT 60.683 55.000 0.00 0.00 0.00 2.52
137 141 1.409101 GCCCGGTTAGCCCAATTTCTA 60.409 52.381 0.00 0.00 0.00 2.10
138 142 2.294979 CCCGGTTAGCCCAATTTCTAC 58.705 52.381 0.00 0.00 0.00 2.59
139 143 2.294979 CCGGTTAGCCCAATTTCTACC 58.705 52.381 0.00 0.00 0.00 3.18
140 144 2.294979 CGGTTAGCCCAATTTCTACCC 58.705 52.381 0.00 0.00 0.00 3.69
141 145 2.356330 CGGTTAGCCCAATTTCTACCCA 60.356 50.000 0.00 0.00 0.00 4.51
142 146 3.687264 CGGTTAGCCCAATTTCTACCCAT 60.687 47.826 0.00 0.00 0.00 4.00
143 147 4.286707 GGTTAGCCCAATTTCTACCCATT 58.713 43.478 0.00 0.00 0.00 3.16
146 150 6.362248 GTTAGCCCAATTTCTACCCATTCTA 58.638 40.000 0.00 0.00 0.00 2.10
147 151 4.793201 AGCCCAATTTCTACCCATTCTAC 58.207 43.478 0.00 0.00 0.00 2.59
148 152 4.229582 AGCCCAATTTCTACCCATTCTACA 59.770 41.667 0.00 0.00 0.00 2.74
149 153 4.338400 GCCCAATTTCTACCCATTCTACAC 59.662 45.833 0.00 0.00 0.00 2.90
150 154 5.505780 CCCAATTTCTACCCATTCTACACA 58.494 41.667 0.00 0.00 0.00 3.72
151 155 6.129179 CCCAATTTCTACCCATTCTACACAT 58.871 40.000 0.00 0.00 0.00 3.21
153 157 7.201821 CCCAATTTCTACCCATTCTACACATTC 60.202 40.741 0.00 0.00 0.00 2.67
154 158 7.339212 CCAATTTCTACCCATTCTACACATTCA 59.661 37.037 0.00 0.00 0.00 2.57
155 159 8.906867 CAATTTCTACCCATTCTACACATTCAT 58.093 33.333 0.00 0.00 0.00 2.57
160 164 9.613428 TCTACCCATTCTACACATTCATAAAAG 57.387 33.333 0.00 0.00 0.00 2.27
161 165 7.645058 ACCCATTCTACACATTCATAAAAGG 57.355 36.000 0.00 0.00 0.00 3.11
162 166 6.096846 ACCCATTCTACACATTCATAAAAGGC 59.903 38.462 0.00 0.00 0.00 4.35
165 169 7.284034 CCATTCTACACATTCATAAAAGGCTCT 59.716 37.037 0.00 0.00 0.00 4.09
166 170 7.849804 TTCTACACATTCATAAAAGGCTCTC 57.150 36.000 0.00 0.00 0.00 3.20
167 171 7.187824 TCTACACATTCATAAAAGGCTCTCT 57.812 36.000 0.00 0.00 0.00 3.10
168 172 7.268586 TCTACACATTCATAAAAGGCTCTCTC 58.731 38.462 0.00 0.00 0.00 3.20
169 173 5.809001 ACACATTCATAAAAGGCTCTCTCA 58.191 37.500 0.00 0.00 0.00 3.27
171 175 5.879223 CACATTCATAAAAGGCTCTCTCAGT 59.121 40.000 0.00 0.00 0.00 3.41
173 177 4.744795 TCATAAAAGGCTCTCTCAGTCC 57.255 45.455 0.00 0.00 0.00 3.85
176 180 5.190528 TCATAAAAGGCTCTCTCAGTCCATT 59.809 40.000 0.00 0.00 0.00 3.16
180 375 2.699846 AGGCTCTCTCAGTCCATTGATC 59.300 50.000 0.00 0.00 0.00 2.92
187 382 3.524789 TCTCAGTCCATTGATCCACCAAT 59.475 43.478 0.00 0.00 37.24 3.16
218 413 2.452505 TCACTGATCCATACACGACCA 58.547 47.619 0.00 0.00 0.00 4.02
219 414 2.829120 TCACTGATCCATACACGACCAA 59.171 45.455 0.00 0.00 0.00 3.67
278 473 0.543174 GACCTCCAGTCCTCCACACT 60.543 60.000 0.00 0.00 39.84 3.55
286 481 1.228894 TCCTCCACACTCCTCGCTT 60.229 57.895 0.00 0.00 0.00 4.68
296 491 0.323629 CTCCTCGCTTGGTAAACCCA 59.676 55.000 0.00 0.00 43.27 4.51
301 496 1.065709 TCGCTTGGTAAACCCATCTCC 60.066 52.381 0.00 0.00 44.74 3.71
312 526 0.468214 CCCATCTCCTAGTCGCTCCA 60.468 60.000 0.00 0.00 0.00 3.86
337 551 0.610785 CGGCAACACCCCACCTAAAT 60.611 55.000 0.00 0.00 33.26 1.40
421 635 1.272212 GCCAACCCGACATGTTTTCAT 59.728 47.619 0.00 0.00 41.78 2.57
438 652 2.725312 ATGGACTGCTCGCGGTGAT 61.725 57.895 6.13 0.00 35.39 3.06
471 685 3.942130 GGTTCAGAAAACCCAATGAGG 57.058 47.619 0.00 0.00 34.26 3.86
472 686 3.496331 GGTTCAGAAAACCCAATGAGGA 58.504 45.455 0.00 0.00 41.22 3.71
480 694 2.843909 ACCCAATGAGGATAGGGGAT 57.156 50.000 1.34 0.00 45.83 3.85
522 736 2.990479 GTTGACGGAGGCAGGGAT 59.010 61.111 0.00 0.00 0.00 3.85
526 740 4.741239 ACGGAGGCAGGGATGGGT 62.741 66.667 0.00 0.00 0.00 4.51
537 751 0.394938 GGGATGGGTTTGCGGTTTTT 59.605 50.000 0.00 0.00 0.00 1.94
602 826 0.537188 GCCATCTTGAGACGGAAGGA 59.463 55.000 0.00 0.00 26.45 3.36
603 827 1.472376 GCCATCTTGAGACGGAAGGAG 60.472 57.143 0.00 0.00 26.45 3.69
658 889 4.444306 CGCCAGATAACATTTCCCTAGGAA 60.444 45.833 11.48 0.00 40.27 3.36
702 933 1.142097 GCCGGAGTCTACCTGAAGC 59.858 63.158 5.05 0.00 0.00 3.86
848 1081 0.250038 CATCTCCATCCGTCCGCATT 60.250 55.000 0.00 0.00 0.00 3.56
862 1095 0.969917 CGCATTTCCCAATCCCCACA 60.970 55.000 0.00 0.00 0.00 4.17
865 1098 0.042581 ATTTCCCAATCCCCACACCC 59.957 55.000 0.00 0.00 0.00 4.61
992 1235 4.354943 CCTCCTCCCCACCCAGGT 62.355 72.222 0.00 0.00 34.66 4.00
1140 1383 4.033776 CCGCCCTCCAAGCTTCCA 62.034 66.667 0.00 0.00 0.00 3.53
1169 1412 2.815647 CGCAACCTCCTCTTCCGC 60.816 66.667 0.00 0.00 0.00 5.54
1246 1489 4.051167 TCTACGACCTCCCCGCCA 62.051 66.667 0.00 0.00 0.00 5.69
1284 1527 0.527600 TCGCCATGTGTGATACGCTC 60.528 55.000 0.00 0.00 0.00 5.03
2206 2455 2.028203 TGGTCTGTCTTCATTGATCGCA 60.028 45.455 0.00 0.00 0.00 5.10
2271 2520 2.063979 CATCCCAGAGGCACGGGTA 61.064 63.158 10.45 0.00 43.57 3.69
2558 2807 3.883489 AGCCTTACTTTTGACTGTGGTTC 59.117 43.478 0.00 0.00 0.00 3.62
2640 2931 3.696548 TGTACATTGGAGTTTGCAACACA 59.303 39.130 0.00 0.00 28.29 3.72
2714 3005 5.361571 TGCATCAAATGGAGTATGAAATGCT 59.638 36.000 0.00 0.00 43.99 3.79
2791 3247 1.123077 TCCGAGTACTCCTACGGCTA 58.877 55.000 17.23 0.00 44.19 3.93
2796 3252 0.585838 GTACTCCTACGGCTACTCGC 59.414 60.000 0.00 0.00 38.13 5.03
2830 3286 5.927281 TGATACTATCTTTATACCGGGGC 57.073 43.478 6.32 0.00 0.00 5.80
2834 3290 1.412453 ATCTTTATACCGGGGCCGCA 61.412 55.000 21.08 0.00 38.24 5.69
2883 3339 8.164058 TCAAATGATATGTGTCACAAGTTTGA 57.836 30.769 10.28 16.54 31.69 2.69
2906 3362 3.872511 TGAATCAACATGGTCCAATGC 57.127 42.857 0.00 0.00 0.00 3.56
2908 3364 2.537633 ATCAACATGGTCCAATGCCT 57.462 45.000 0.00 0.00 0.00 4.75
2909 3365 2.307496 TCAACATGGTCCAATGCCTT 57.693 45.000 0.00 0.00 0.00 4.35
2912 3368 2.299582 CAACATGGTCCAATGCCTTCAA 59.700 45.455 0.00 0.00 0.00 2.69
2913 3369 2.823959 ACATGGTCCAATGCCTTCAAT 58.176 42.857 0.00 0.00 0.00 2.57
2914 3370 3.979911 ACATGGTCCAATGCCTTCAATA 58.020 40.909 0.00 0.00 0.00 1.90
2917 3373 4.248174 TGGTCCAATGCCTTCAATATCA 57.752 40.909 0.00 0.00 0.00 2.15
2918 3374 4.806892 TGGTCCAATGCCTTCAATATCAT 58.193 39.130 0.00 0.00 0.00 2.45
2919 3375 5.210430 TGGTCCAATGCCTTCAATATCATT 58.790 37.500 0.00 0.00 0.00 2.57
2920 3376 5.302568 TGGTCCAATGCCTTCAATATCATTC 59.697 40.000 0.00 0.00 0.00 2.67
2921 3377 5.537674 GGTCCAATGCCTTCAATATCATTCT 59.462 40.000 0.00 0.00 0.00 2.40
2922 3378 6.041296 GGTCCAATGCCTTCAATATCATTCTT 59.959 38.462 0.00 0.00 0.00 2.52
2923 3379 7.418254 GGTCCAATGCCTTCAATATCATTCTTT 60.418 37.037 0.00 0.00 0.00 2.52
2924 3380 7.983484 GTCCAATGCCTTCAATATCATTCTTTT 59.017 33.333 0.00 0.00 0.00 2.27
2925 3381 8.542080 TCCAATGCCTTCAATATCATTCTTTTT 58.458 29.630 0.00 0.00 0.00 1.94
2954 3410 7.147828 TGCGGGGTTTAATATCATTCATTTTGA 60.148 33.333 0.00 0.00 0.00 2.69
2988 3444 3.220507 TGGCATCAGCGAAATCTTTTG 57.779 42.857 0.00 0.00 43.41 2.44
3068 3524 6.918022 CCGTTTTAATCATTAAATCTGCCTCC 59.082 38.462 3.35 0.00 35.26 4.30
3085 3541 2.484264 CCTCCACGTGATCTTCAAAACC 59.516 50.000 19.30 0.00 0.00 3.27
3335 3802 6.701400 GGTAATTGTTGGTAATTCATCATGGC 59.299 38.462 0.00 0.00 32.79 4.40
3346 3813 9.034544 GGTAATTCATCATGGCAAATTTAGTTC 57.965 33.333 0.00 0.00 0.00 3.01
3357 3824 7.944061 TGGCAAATTTAGTTCATAGATCATGG 58.056 34.615 0.00 0.00 35.16 3.66
3358 3825 6.865205 GGCAAATTTAGTTCATAGATCATGGC 59.135 38.462 0.00 0.00 35.16 4.40
3364 3831 7.750229 TTAGTTCATAGATCATGGCAATTCC 57.250 36.000 0.00 0.00 35.16 3.01
3380 3848 4.883585 GCAATTCCAGTATCTTGACCATGA 59.116 41.667 0.00 0.00 0.00 3.07
3381 3849 5.357878 GCAATTCCAGTATCTTGACCATGAA 59.642 40.000 0.00 0.00 0.00 2.57
3384 3852 8.306038 CAATTCCAGTATCTTGACCATGAAAAA 58.694 33.333 0.00 0.00 0.00 1.94
3387 3855 9.699410 TTCCAGTATCTTGACCATGAAAAATAT 57.301 29.630 0.00 0.00 0.00 1.28
3422 3890 4.909001 ACCATGGCAAATTTTAGTGCATT 58.091 34.783 13.04 0.00 42.74 3.56
3430 3898 8.039538 TGGCAAATTTTAGTGCATTTATCATGA 58.960 29.630 0.00 0.00 42.74 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 33 6.409524 TTCTCATTTTCTCAATTGGCAGTT 57.590 33.333 5.42 0.00 0.00 3.16
32 34 6.409524 TTTCTCATTTTCTCAATTGGCAGT 57.590 33.333 5.42 0.00 0.00 4.40
79 83 9.539825 TCTTTTGTGTTTAAAATGCACATACAT 57.460 25.926 10.01 0.00 41.86 2.29
80 84 8.932945 TCTTTTGTGTTTAAAATGCACATACA 57.067 26.923 10.01 0.00 41.86 2.29
117 121 0.683179 AGAAATTGGGCTAACCGGGC 60.683 55.000 6.32 0.00 44.64 6.13
120 124 2.294979 GGGTAGAAATTGGGCTAACCG 58.705 52.381 0.00 0.00 44.64 4.44
121 125 3.375647 TGGGTAGAAATTGGGCTAACC 57.624 47.619 9.34 9.34 43.34 2.85
122 126 5.201243 AGAATGGGTAGAAATTGGGCTAAC 58.799 41.667 0.00 0.00 0.00 2.34
123 127 5.466127 AGAATGGGTAGAAATTGGGCTAA 57.534 39.130 0.00 0.00 0.00 3.09
124 128 5.430417 TGTAGAATGGGTAGAAATTGGGCTA 59.570 40.000 0.00 0.00 0.00 3.93
125 129 4.229582 TGTAGAATGGGTAGAAATTGGGCT 59.770 41.667 0.00 0.00 0.00 5.19
126 130 4.338400 GTGTAGAATGGGTAGAAATTGGGC 59.662 45.833 0.00 0.00 0.00 5.36
129 133 8.279970 TGAATGTGTAGAATGGGTAGAAATTG 57.720 34.615 0.00 0.00 0.00 2.32
132 136 9.967451 TTTATGAATGTGTAGAATGGGTAGAAA 57.033 29.630 0.00 0.00 0.00 2.52
133 137 9.967451 TTTTATGAATGTGTAGAATGGGTAGAA 57.033 29.630 0.00 0.00 0.00 2.10
134 138 9.613428 CTTTTATGAATGTGTAGAATGGGTAGA 57.387 33.333 0.00 0.00 0.00 2.59
135 139 8.840321 CCTTTTATGAATGTGTAGAATGGGTAG 58.160 37.037 0.00 0.00 0.00 3.18
136 140 7.284489 GCCTTTTATGAATGTGTAGAATGGGTA 59.716 37.037 0.00 0.00 0.00 3.69
137 141 6.096846 GCCTTTTATGAATGTGTAGAATGGGT 59.903 38.462 0.00 0.00 0.00 4.51
138 142 6.322201 AGCCTTTTATGAATGTGTAGAATGGG 59.678 38.462 0.00 0.00 0.00 4.00
139 143 7.284034 AGAGCCTTTTATGAATGTGTAGAATGG 59.716 37.037 0.00 0.00 0.00 3.16
140 144 8.218338 AGAGCCTTTTATGAATGTGTAGAATG 57.782 34.615 0.00 0.00 0.00 2.67
141 145 8.270744 AGAGAGCCTTTTATGAATGTGTAGAAT 58.729 33.333 0.00 0.00 0.00 2.40
142 146 7.624549 AGAGAGCCTTTTATGAATGTGTAGAA 58.375 34.615 0.00 0.00 0.00 2.10
143 147 7.093333 TGAGAGAGCCTTTTATGAATGTGTAGA 60.093 37.037 0.00 0.00 0.00 2.59
146 150 5.809001 TGAGAGAGCCTTTTATGAATGTGT 58.191 37.500 0.00 0.00 0.00 3.72
147 151 5.879223 ACTGAGAGAGCCTTTTATGAATGTG 59.121 40.000 0.00 0.00 0.00 3.21
148 152 6.059787 ACTGAGAGAGCCTTTTATGAATGT 57.940 37.500 0.00 0.00 0.00 2.71
149 153 5.526846 GGACTGAGAGAGCCTTTTATGAATG 59.473 44.000 0.00 0.00 0.00 2.67
150 154 5.190528 TGGACTGAGAGAGCCTTTTATGAAT 59.809 40.000 0.00 0.00 0.00 2.57
151 155 4.532126 TGGACTGAGAGAGCCTTTTATGAA 59.468 41.667 0.00 0.00 0.00 2.57
153 157 4.478206 TGGACTGAGAGAGCCTTTTATG 57.522 45.455 0.00 0.00 0.00 1.90
154 158 5.190528 TCAATGGACTGAGAGAGCCTTTTAT 59.809 40.000 0.00 0.00 0.00 1.40
155 159 4.532126 TCAATGGACTGAGAGAGCCTTTTA 59.468 41.667 0.00 0.00 0.00 1.52
157 161 2.909006 TCAATGGACTGAGAGAGCCTTT 59.091 45.455 0.00 0.00 0.00 3.11
160 164 2.224257 GGATCAATGGACTGAGAGAGCC 60.224 54.545 0.00 0.00 0.00 4.70
161 165 2.433604 TGGATCAATGGACTGAGAGAGC 59.566 50.000 0.00 0.00 0.00 4.09
162 166 3.181467 GGTGGATCAATGGACTGAGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
165 169 2.550175 TGGTGGATCAATGGACTGAGA 58.450 47.619 0.00 0.00 0.00 3.27
166 170 3.354948 TTGGTGGATCAATGGACTGAG 57.645 47.619 0.00 0.00 0.00 3.35
167 171 4.320546 AATTGGTGGATCAATGGACTGA 57.679 40.909 0.00 0.00 37.42 3.41
168 172 4.708421 AGAAATTGGTGGATCAATGGACTG 59.292 41.667 0.00 0.00 37.42 3.51
169 173 4.939255 AGAAATTGGTGGATCAATGGACT 58.061 39.130 0.00 0.00 37.42 3.85
171 175 5.200483 GGTAGAAATTGGTGGATCAATGGA 58.800 41.667 0.00 0.00 37.42 3.41
173 177 4.955450 TGGGTAGAAATTGGTGGATCAATG 59.045 41.667 0.00 0.00 37.42 2.82
176 180 4.879295 ATGGGTAGAAATTGGTGGATCA 57.121 40.909 0.00 0.00 0.00 2.92
180 375 4.158394 CAGTGAATGGGTAGAAATTGGTGG 59.842 45.833 0.00 0.00 0.00 4.61
187 382 5.715439 ATGGATCAGTGAATGGGTAGAAA 57.285 39.130 0.00 0.00 0.00 2.52
243 438 1.586154 GGTCGTGTGATTTGGGGCTG 61.586 60.000 0.00 0.00 0.00 4.85
296 491 0.106469 TGCTGGAGCGACTAGGAGAT 60.106 55.000 0.00 0.00 45.83 2.75
301 496 1.515088 CGTGTGCTGGAGCGACTAG 60.515 63.158 0.00 0.00 45.83 2.57
323 537 3.920841 AGGTTTAGATTTAGGTGGGGTGT 59.079 43.478 0.00 0.00 0.00 4.16
327 541 5.367060 AGCTCTAGGTTTAGATTTAGGTGGG 59.633 44.000 0.00 0.00 35.43 4.61
337 551 5.187967 CAGGAGGAAAAGCTCTAGGTTTAGA 59.812 44.000 7.52 0.00 43.95 2.10
421 635 3.381983 ATCACCGCGAGCAGTCCA 61.382 61.111 8.23 0.00 0.00 4.02
422 636 2.887568 CATCACCGCGAGCAGTCC 60.888 66.667 8.23 0.00 0.00 3.85
465 679 1.376649 GCCCATCCCCTATCCTCATT 58.623 55.000 0.00 0.00 0.00 2.57
467 681 0.029163 TTGCCCATCCCCTATCCTCA 60.029 55.000 0.00 0.00 0.00 3.86
469 683 1.619298 TTTTGCCCATCCCCTATCCT 58.381 50.000 0.00 0.00 0.00 3.24
537 751 1.830408 CCAAACCTGTCCCCGCAAA 60.830 57.895 0.00 0.00 0.00 3.68
541 755 3.801068 TTGCCCAAACCTGTCCCCG 62.801 63.158 0.00 0.00 0.00 5.73
578 802 0.321564 CCGTCTCAAGATGGCAACCA 60.322 55.000 5.35 0.00 43.52 3.67
602 826 1.963172 GGAACCCAGTGAACGTTTCT 58.037 50.000 0.46 1.38 0.00 2.52
633 862 3.199880 AGGGAAATGTTATCTGGCGAG 57.800 47.619 0.00 0.00 0.00 5.03
739 972 2.288458 TGCTTTCGGTTAAGGTTGTTCG 59.712 45.455 0.00 0.00 0.00 3.95
848 1081 2.553330 GGGGTGTGGGGATTGGGAA 61.553 63.158 0.00 0.00 0.00 3.97
862 1095 2.363361 CAGTACGGGGAGAGGGGT 59.637 66.667 0.00 0.00 0.00 4.95
865 1098 4.208686 GCGCAGTACGGGGAGAGG 62.209 72.222 14.08 0.00 43.93 3.69
992 1235 4.743125 TCCCGGCCATGGTGGGTA 62.743 66.667 31.52 20.74 43.75 3.69
1057 1300 0.033504 GCGCCGAGGAGGATTGATAA 59.966 55.000 0.00 0.00 45.00 1.75
1246 1489 3.451141 GAGCAGATCCTCGTTGAAGAT 57.549 47.619 0.00 0.00 0.00 2.40
2265 2514 2.423898 CCTCATCTGCCGTACCCGT 61.424 63.158 0.00 0.00 0.00 5.28
2271 2520 3.842923 CGCTCCCTCATCTGCCGT 61.843 66.667 0.00 0.00 0.00 5.68
2443 2692 0.679505 TGACAGTTTGGTCCTCTCCG 59.320 55.000 0.00 0.00 36.97 4.63
2558 2807 7.993821 CAGTATCGCTGTAATTCCCATATAG 57.006 40.000 0.00 0.00 40.27 1.31
2640 2931 1.985473 TTGATGCAGCCTGTCAAACT 58.015 45.000 0.00 0.00 0.00 2.66
2714 3005 0.179084 GATCGGATCGAGGTGCCAAA 60.179 55.000 1.62 0.00 39.91 3.28
2830 3286 1.033746 ATCAGGCCAAATCACTGCGG 61.034 55.000 5.01 0.00 32.42 5.69
2854 3310 9.814899 AACTTGTGACACATATCATTTGAAAAA 57.185 25.926 9.55 0.00 0.00 1.94
2855 3311 9.814899 AAACTTGTGACACATATCATTTGAAAA 57.185 25.926 9.55 0.00 0.00 2.29
2857 3313 8.628280 TCAAACTTGTGACACATATCATTTGAA 58.372 29.630 19.82 10.90 31.40 2.69
2858 3314 8.075574 GTCAAACTTGTGACACATATCATTTGA 58.924 33.333 9.55 15.98 46.00 2.69
2883 3339 4.382254 GCATTGGACCATGTTGATTCATGT 60.382 41.667 0.00 0.00 42.29 3.21
2890 3346 2.170166 GAAGGCATTGGACCATGTTGA 58.830 47.619 0.00 0.00 0.00 3.18
2922 3378 6.783708 ATGATATTAAACCCCGCAGAAAAA 57.216 33.333 0.00 0.00 0.00 1.94
2923 3379 6.378564 TGAATGATATTAAACCCCGCAGAAAA 59.621 34.615 0.00 0.00 0.00 2.29
2924 3380 5.888724 TGAATGATATTAAACCCCGCAGAAA 59.111 36.000 0.00 0.00 0.00 2.52
2925 3381 5.441500 TGAATGATATTAAACCCCGCAGAA 58.558 37.500 0.00 0.00 0.00 3.02
2926 3382 5.042463 TGAATGATATTAAACCCCGCAGA 57.958 39.130 0.00 0.00 0.00 4.26
2927 3383 5.964958 ATGAATGATATTAAACCCCGCAG 57.035 39.130 0.00 0.00 0.00 5.18
2928 3384 6.723298 AAATGAATGATATTAAACCCCGCA 57.277 33.333 0.00 0.00 0.00 5.69
2929 3385 7.169140 GTCAAAATGAATGATATTAAACCCCGC 59.831 37.037 0.00 0.00 0.00 6.13
2930 3386 8.194104 TGTCAAAATGAATGATATTAAACCCCG 58.806 33.333 0.00 0.00 0.00 5.73
2954 3410 5.106436 CGCTGATGCCATATGTTTGATATGT 60.106 40.000 1.24 0.00 35.36 2.29
2966 3422 4.202040 CCAAAAGATTTCGCTGATGCCATA 60.202 41.667 0.00 0.00 35.36 2.74
2970 3426 3.492421 TCCAAAAGATTTCGCTGATGC 57.508 42.857 0.00 0.00 0.00 3.91
3064 3520 2.484264 GGTTTTGAAGATCACGTGGAGG 59.516 50.000 17.00 0.00 0.00 4.30
3068 3524 6.508563 CGAGATATGGTTTTGAAGATCACGTG 60.509 42.308 9.94 9.94 0.00 4.49
3121 3579 4.605640 AACATCATGACAACTTTTGGGG 57.394 40.909 0.00 0.00 34.12 4.96
3122 3580 6.083098 TGTAACATCATGACAACTTTTGGG 57.917 37.500 0.00 0.00 34.12 4.12
3247 3713 9.566432 AAACTTGTCATGGCCAATTAATAAAAA 57.434 25.926 10.96 0.00 0.00 1.94
3266 3732 5.764192 TGCCGTGGTTAATTACTAAACTTGT 59.236 36.000 0.00 0.00 0.00 3.16
3317 3784 7.614124 AAATTTGCCATGATGAATTACCAAC 57.386 32.000 0.00 0.00 0.00 3.77
3320 3787 8.947055 AACTAAATTTGCCATGATGAATTACC 57.053 30.769 0.00 0.00 0.00 2.85
3335 3802 9.976511 ATTGCCATGATCTATGAACTAAATTTG 57.023 29.630 0.00 0.00 39.21 2.32
3357 3824 4.883585 TCATGGTCAAGATACTGGAATTGC 59.116 41.667 0.00 0.00 0.00 3.56
3358 3825 7.395190 TTTCATGGTCAAGATACTGGAATTG 57.605 36.000 0.00 0.00 0.00 2.32
3393 3861 7.118971 GCACTAAAATTTGCCATGGTTCATAAA 59.881 33.333 14.67 7.97 32.21 1.40
3394 3862 6.593382 GCACTAAAATTTGCCATGGTTCATAA 59.407 34.615 14.67 1.30 32.21 1.90
3406 3874 8.871862 TGTCATGATAAATGCACTAAAATTTGC 58.128 29.630 0.00 0.00 39.33 3.68


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

AutoCloner maintained by Alex Coulton.