Multiple sequence alignment - TraesCS1D01G328800

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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 TraesCS1D01G328800 chr1D 100.000 2809 0 0 1 2809 420371510 420374318 0.000000e+00 5188.0
1 TraesCS1D01G328800 chr1D 84.979 486 58 10 1407 1882 7013910 7013430 1.960000e-131 479.0
2 TraesCS1D01G328800 chr1D 82.410 415 52 13 904 1313 7014353 7013955 2.680000e-90 342.0
3 TraesCS1D01G328800 chr1D 78.704 108 13 8 2496 2598 25776606 25776504 2.340000e-06 63.9
4 TraesCS1D01G328800 chr1B 87.173 2370 167 67 469 2805 567985386 567987651 0.000000e+00 2566.0
5 TraesCS1D01G328800 chr1B 88.602 465 48 3 833 1294 567443628 567444090 6.790000e-156 560.0
6 TraesCS1D01G328800 chr1B 89.920 377 26 4 1399 1765 567465823 567466197 2.530000e-130 475.0
7 TraesCS1D01G328800 chr1B 89.458 332 22 5 511 840 567424316 567424636 9.370000e-110 407.0
8 TraesCS1D01G328800 chr1B 85.890 326 23 2 1 304 567414506 567414830 2.700000e-85 326.0
9 TraesCS1D01G328800 chr1B 89.520 229 12 5 298 514 567416541 567416769 2.130000e-71 279.0
10 TraesCS1D01G328800 chr1B 80.357 112 15 5 2496 2603 41392163 41392055 8.340000e-11 78.7
11 TraesCS1D01G328800 chr1A 87.552 1197 74 23 177 1327 516731496 516732663 0.000000e+00 1315.0
12 TraesCS1D01G328800 chr1A 92.743 565 23 9 1365 1924 516732662 516733213 0.000000e+00 800.0
13 TraesCS1D01G328800 chr1A 83.916 429 42 16 2175 2596 516733373 516733781 4.390000e-103 385.0
14 TraesCS1D01G328800 chr1A 81.034 116 16 4 2491 2603 27128221 27128109 1.390000e-13 87.9
15 TraesCS1D01G328800 chr7D 88.776 392 44 0 1411 1802 163215248 163214857 5.440000e-132 481.0
16 TraesCS1D01G328800 chr7D 84.848 297 45 0 1001 1297 163251263 163250967 1.640000e-77 300.0
17 TraesCS1D01G328800 chr7B 88.060 402 47 1 1402 1802 125243900 125243499 2.530000e-130 475.0
18 TraesCS1D01G328800 chr7B 88.060 402 47 1 1402 1802 125313076 125312675 2.530000e-130 475.0
19 TraesCS1D01G328800 chr7B 87.811 402 48 1 1402 1802 125221111 125220710 1.180000e-128 470.0
20 TraesCS1D01G328800 chr7B 87.811 402 48 1 1402 1802 125280264 125279863 1.180000e-128 470.0
21 TraesCS1D01G328800 chr7B 86.869 297 39 0 1001 1297 125356010 125355714 1.610000e-87 333.0
22 TraesCS1D01G328800 chr7B 86.532 297 40 0 1001 1297 125363228 125362932 7.500000e-86 327.0
23 TraesCS1D01G328800 chr7B 86.047 301 42 0 997 1297 125244252 125243952 9.700000e-85 324.0
24 TraesCS1D01G328800 chr7A 87.345 403 49 2 1402 1802 164393683 164393281 7.090000e-126 460.0
25 TraesCS1D01G328800 chr6B 82.692 416 55 11 904 1313 11470544 11470140 1.240000e-93 353.0
26 TraesCS1D01G328800 chr3A 88.889 54 5 1 2689 2742 568621527 568621475 6.490000e-07 65.8


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 TraesCS1D01G328800 chr1D 420371510 420374318 2808 False 5188.000000 5188 100.000000 1 2809 1 chr1D.!!$F1 2808
1 TraesCS1D01G328800 chr1D 7013430 7014353 923 True 410.500000 479 83.694500 904 1882 2 chr1D.!!$R2 978
2 TraesCS1D01G328800 chr1B 567985386 567987651 2265 False 2566.000000 2566 87.173000 469 2805 1 chr1B.!!$F4 2336
3 TraesCS1D01G328800 chr1B 567414506 567416769 2263 False 302.500000 326 87.705000 1 514 2 chr1B.!!$F5 513
4 TraesCS1D01G328800 chr1A 516731496 516733781 2285 False 833.333333 1315 88.070333 177 2596 3 chr1A.!!$F1 2419
5 TraesCS1D01G328800 chr7B 125243499 125244252 753 True 399.500000 475 87.053500 997 1802 2 chr7B.!!$R6 805

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
870 2629 0.249398 TCCGGCAAGTCCTCTTTAGC 59.751 55.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 4416 0.482446 AACTTGGCATGGTTCCCTCA 59.518 50.0 5.31 0.0 0.0 3.86 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
57 58 1.249407 GATAGACCCGTGGCTAGGAG 58.751 60.000 0.00 0.00 0.00 3.69
69 70 3.511934 GTGGCTAGGAGAAGTCTTCAAGA 59.488 47.826 14.97 0.00 0.00 3.02
73 74 5.815222 GGCTAGGAGAAGTCTTCAAGAATTC 59.185 44.000 18.01 18.01 46.32 2.17
92 93 8.169977 AGAATTCTTTTTAGATGTTGTGCAGA 57.830 30.769 0.88 0.00 0.00 4.26
104 105 3.186409 TGTTGTGCAGACGAATTAGAAGC 59.814 43.478 0.00 0.00 0.00 3.86
111 112 3.436704 CAGACGAATTAGAAGCTTTGGCA 59.563 43.478 0.00 0.00 41.70 4.92
129 130 2.749865 AATGATCAACGTGGCGGCG 61.750 57.895 0.51 0.51 37.94 6.46
145 146 1.677576 CGGCGTAGTATTGTAGGGTCA 59.322 52.381 0.00 0.00 0.00 4.02
254 279 7.235812 AGTTATGATGAATAGGTAGGGAGGAAC 59.764 40.741 0.00 0.00 0.00 3.62
426 2180 6.869388 TGCGTTACACTACTTAATCAATGACA 59.131 34.615 0.00 0.00 0.00 3.58
436 2190 7.596749 ACTTAATCAATGACAAGTTAGTCCG 57.403 36.000 6.32 0.00 37.73 4.79
551 2306 2.467566 TAACTCCAAGGCTCGGAAAC 57.532 50.000 0.00 0.00 30.33 2.78
609 2364 7.862873 ACATCGTCACTCACAACATATATACAG 59.137 37.037 0.00 0.00 0.00 2.74
623 2379 6.992715 ACATATATACAGAAAACAGCTCCACC 59.007 38.462 0.00 0.00 0.00 4.61
629 2385 2.028930 AGAAAACAGCTCCACCTAGTCG 60.029 50.000 0.00 0.00 0.00 4.18
712 2468 6.154706 CCAATCTTACCTTGTAGGAGTACACT 59.845 42.308 0.00 0.00 38.95 3.55
713 2469 7.341256 CCAATCTTACCTTGTAGGAGTACACTA 59.659 40.741 0.00 0.00 38.95 2.74
789 2548 2.291411 ACTTAGTCCGCCAAGTCCTCTA 60.291 50.000 0.00 0.00 28.88 2.43
870 2629 0.249398 TCCGGCAAGTCCTCTTTAGC 59.751 55.000 0.00 0.00 0.00 3.09
893 2655 7.593825 AGCGGCATCAGGAAAATATTATTTAC 58.406 34.615 1.45 0.10 0.00 2.01
991 2762 0.986992 ACGTGTAGAATAACGCACGC 59.013 50.000 14.48 0.00 46.94 5.34
1141 2915 2.098680 CGGTGAGACTCGACGAGC 59.901 66.667 24.38 16.47 32.04 5.03
1197 2971 2.670592 GGCGCCCGGTACAGTTTT 60.671 61.111 18.11 0.00 0.00 2.43
1239 3013 1.671742 GGTGCTCTCCTCCGACAAA 59.328 57.895 0.00 0.00 0.00 2.83
1330 3107 9.804758 ATTACTACTTCTACTTAACATGTGCTC 57.195 33.333 0.00 0.00 0.00 4.26
1331 3108 7.228314 ACTACTTCTACTTAACATGTGCTCA 57.772 36.000 0.00 0.00 0.00 4.26
1332 3109 7.091443 ACTACTTCTACTTAACATGTGCTCAC 58.909 38.462 0.00 0.00 0.00 3.51
1333 3110 6.102897 ACTTCTACTTAACATGTGCTCACT 57.897 37.500 0.00 0.00 0.00 3.41
1334 3111 6.159988 ACTTCTACTTAACATGTGCTCACTC 58.840 40.000 0.00 0.00 0.00 3.51
1335 3112 5.073311 TCTACTTAACATGTGCTCACTCC 57.927 43.478 0.00 0.00 0.00 3.85
1336 3113 2.688507 ACTTAACATGTGCTCACTCCG 58.311 47.619 0.00 0.00 0.00 4.63
1337 3114 2.037251 ACTTAACATGTGCTCACTCCGT 59.963 45.455 0.00 0.00 0.00 4.69
1338 3115 2.363788 TAACATGTGCTCACTCCGTC 57.636 50.000 0.00 0.00 0.00 4.79
1339 3116 0.320771 AACATGTGCTCACTCCGTCC 60.321 55.000 0.00 0.00 0.00 4.79
1340 3117 1.448540 CATGTGCTCACTCCGTCCC 60.449 63.158 1.47 0.00 0.00 4.46
1341 3118 1.913262 ATGTGCTCACTCCGTCCCA 60.913 57.895 1.47 0.00 0.00 4.37
1342 3119 1.267574 ATGTGCTCACTCCGTCCCAT 61.268 55.000 1.47 0.00 0.00 4.00
1343 3120 0.613572 TGTGCTCACTCCGTCCCATA 60.614 55.000 1.47 0.00 0.00 2.74
1344 3121 0.753262 GTGCTCACTCCGTCCCATAT 59.247 55.000 0.00 0.00 0.00 1.78
1345 3122 1.139058 GTGCTCACTCCGTCCCATATT 59.861 52.381 0.00 0.00 0.00 1.28
1346 3123 2.364324 GTGCTCACTCCGTCCCATATTA 59.636 50.000 0.00 0.00 0.00 0.98
1347 3124 3.006967 GTGCTCACTCCGTCCCATATTAT 59.993 47.826 0.00 0.00 0.00 1.28
1348 3125 4.219944 GTGCTCACTCCGTCCCATATTATA 59.780 45.833 0.00 0.00 0.00 0.98
1349 3126 5.023452 TGCTCACTCCGTCCCATATTATAT 58.977 41.667 0.00 0.00 0.00 0.86
1350 3127 5.483937 TGCTCACTCCGTCCCATATTATATT 59.516 40.000 0.00 0.00 0.00 1.28
1351 3128 6.666113 TGCTCACTCCGTCCCATATTATATTA 59.334 38.462 0.00 0.00 0.00 0.98
1352 3129 7.344612 TGCTCACTCCGTCCCATATTATATTAT 59.655 37.037 0.00 0.00 0.00 1.28
1353 3130 7.653713 GCTCACTCCGTCCCATATTATATTATG 59.346 40.741 7.41 7.41 0.00 1.90
1354 3131 8.018537 TCACTCCGTCCCATATTATATTATGG 57.981 38.462 20.13 20.13 45.57 2.74
1404 3198 7.565323 AATCAGAGATCTTATTGGTTGCTTC 57.435 36.000 0.00 0.00 0.00 3.86
1442 3239 2.577700 CAGGGATACGACTACAGCTCT 58.422 52.381 0.00 0.00 37.60 4.09
1661 3458 3.292936 AAGGCGTCGACGGTGACT 61.293 61.111 36.13 15.69 40.23 3.41
1816 3614 4.214971 CCTCAAGAAAGAGTGACACATTGG 59.785 45.833 8.59 0.00 33.75 3.16
1818 3616 5.192927 TCAAGAAAGAGTGACACATTGGTT 58.807 37.500 8.59 0.00 0.00 3.67
1819 3617 5.296780 TCAAGAAAGAGTGACACATTGGTTC 59.703 40.000 8.59 4.23 0.00 3.62
1820 3618 3.809832 AGAAAGAGTGACACATTGGTTCG 59.190 43.478 8.59 0.00 0.00 3.95
1821 3619 3.469008 AAGAGTGACACATTGGTTCGA 57.531 42.857 8.59 0.00 0.00 3.71
1845 3643 7.361201 CGATCAGATTTTATGGCCGATTACATT 60.361 37.037 0.00 0.00 0.00 2.71
1950 3790 9.887629 GTACTAGTACATATGAGGCTGAGTATA 57.112 37.037 25.02 0.00 36.15 1.47
2009 3857 8.746052 TTAATGTCCCGATGATGTTTTAGATT 57.254 30.769 0.00 0.00 0.00 2.40
2010 3858 9.839817 TTAATGTCCCGATGATGTTTTAGATTA 57.160 29.630 0.00 0.00 0.00 1.75
2013 3861 7.735917 TGTCCCGATGATGTTTTAGATTAGAT 58.264 34.615 0.00 0.00 0.00 1.98
2015 3863 7.657761 GTCCCGATGATGTTTTAGATTAGATGT 59.342 37.037 0.00 0.00 0.00 3.06
2017 3865 7.657354 CCCGATGATGTTTTAGATTAGATGTGA 59.343 37.037 0.00 0.00 0.00 3.58
2051 3899 4.171005 GCTACAGAATGCGTACACAGTTA 58.829 43.478 0.00 0.00 42.53 2.24
2057 3905 2.448926 TGCGTACACAGTTAGCATGT 57.551 45.000 0.00 0.00 32.43 3.21
2148 3996 7.561021 AACCAAATTTTAACAAATCACACCC 57.439 32.000 0.00 0.00 30.80 4.61
2150 3998 5.333721 CCAAATTTTAACAAATCACACCCGC 60.334 40.000 0.00 0.00 30.80 6.13
2151 3999 4.592485 ATTTTAACAAATCACACCCGCA 57.408 36.364 0.00 0.00 0.00 5.69
2152 4000 3.634568 TTTAACAAATCACACCCGCAG 57.365 42.857 0.00 0.00 0.00 5.18
2153 4001 0.878416 TAACAAATCACACCCGCAGC 59.122 50.000 0.00 0.00 0.00 5.25
2155 4003 1.106351 ACAAATCACACCCGCAGCAA 61.106 50.000 0.00 0.00 0.00 3.91
2157 4005 0.968405 AAATCACACCCGCAGCAAAT 59.032 45.000 0.00 0.00 0.00 2.32
2159 4007 1.832883 ATCACACCCGCAGCAAATAA 58.167 45.000 0.00 0.00 0.00 1.40
2163 4011 3.759086 TCACACCCGCAGCAAATAAAATA 59.241 39.130 0.00 0.00 0.00 1.40
2169 4017 6.636850 CACCCGCAGCAAATAAAATATTCTAC 59.363 38.462 0.00 0.00 0.00 2.59
2170 4018 6.546034 ACCCGCAGCAAATAAAATATTCTACT 59.454 34.615 0.00 0.00 0.00 2.57
2171 4019 6.857964 CCCGCAGCAAATAAAATATTCTACTG 59.142 38.462 0.00 0.00 0.00 2.74
2173 4021 7.587757 CCGCAGCAAATAAAATATTCTACTGAC 59.412 37.037 0.00 0.00 0.00 3.51
2183 4031 7.840342 AAATATTCTACTGACTCTGTGCTTG 57.160 36.000 0.00 0.00 0.00 4.01
2191 4039 5.858381 ACTGACTCTGTGCTTGATTAGAAA 58.142 37.500 0.00 0.00 0.00 2.52
2229 4077 7.324935 TGTCTGAAGTCAAACAGTGTAAAGTA 58.675 34.615 0.00 0.00 35.84 2.24
2397 4247 7.432838 TGATGATGCATGTGAAAACAATATTCG 59.567 33.333 2.46 0.00 0.00 3.34
2419 4269 4.204370 CGTCACAGTACGCATACATAGTTG 59.796 45.833 0.00 0.00 35.87 3.16
2666 4518 5.844301 ATCACAAACATTTTTGAATCGGC 57.156 34.783 11.21 0.00 44.38 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.684805 AGACTTCTCCTAGCCACGGG 60.685 60.000 0.00 0.00 0.00 5.28
69 70 6.857964 CGTCTGCACAACATCTAAAAAGAATT 59.142 34.615 0.00 0.00 0.00 2.17
73 74 5.342806 TCGTCTGCACAACATCTAAAAAG 57.657 39.130 0.00 0.00 0.00 2.27
85 86 3.319137 AGCTTCTAATTCGTCTGCACA 57.681 42.857 0.00 0.00 0.00 4.57
86 87 4.398247 CAAAGCTTCTAATTCGTCTGCAC 58.602 43.478 0.00 0.00 0.00 4.57
87 88 3.436704 CCAAAGCTTCTAATTCGTCTGCA 59.563 43.478 0.00 0.00 0.00 4.41
92 93 4.458989 TCATTGCCAAAGCTTCTAATTCGT 59.541 37.500 0.00 0.00 40.80 3.85
104 105 2.598589 CCACGTTGATCATTGCCAAAG 58.401 47.619 0.00 0.00 0.00 2.77
111 112 2.749865 CGCCGCCACGTTGATCATT 61.750 57.895 0.00 0.00 0.00 2.57
129 130 5.105064 ACCACATGTGACCCTACAATACTAC 60.105 44.000 27.46 0.00 33.69 2.73
145 146 4.039730 GCTCTATCACCATCTACCACATGT 59.960 45.833 0.00 0.00 0.00 3.21
254 279 0.543277 TCTACAGCAGGGCAATCCAG 59.457 55.000 0.00 0.00 38.24 3.86
309 334 6.852664 ACTAAGTGAAGTTTGTTTTCCACTG 58.147 36.000 0.00 0.00 0.00 3.66
426 2180 5.046591 TGAGATGATTTGTCCGGACTAACTT 60.047 40.000 33.39 18.95 0.00 2.66
436 2190 3.755378 AGTTGCACTGAGATGATTTGTCC 59.245 43.478 0.00 0.00 0.00 4.02
489 2244 4.278669 TCGCCAATGCCAAAAGTAAACTTA 59.721 37.500 0.00 0.00 34.61 2.24
551 2306 2.661537 TGCTCCGTTGTGTGCTCG 60.662 61.111 0.00 0.00 0.00 5.03
609 2364 2.029290 TCGACTAGGTGGAGCTGTTTTC 60.029 50.000 0.00 0.00 0.00 2.29
623 2379 2.693591 TGTTAGGCCTGGATTCGACTAG 59.306 50.000 17.99 0.00 0.00 2.57
629 2385 4.864704 TTGTTTTGTTAGGCCTGGATTC 57.135 40.909 17.99 1.43 0.00 2.52
666 2422 1.135523 GCTCCGCTGCTTTGCTAAC 59.864 57.895 0.00 0.00 0.00 2.34
712 2468 2.615447 CCGTCCACTTCAGTACGCTATA 59.385 50.000 0.00 0.00 34.13 1.31
713 2469 1.404391 CCGTCCACTTCAGTACGCTAT 59.596 52.381 0.00 0.00 34.13 2.97
752 2511 8.988934 GCGGACTAAGTGATCATCATTAATTAA 58.011 33.333 0.00 0.00 0.00 1.40
753 2512 7.602644 GGCGGACTAAGTGATCATCATTAATTA 59.397 37.037 0.00 0.00 0.00 1.40
754 2513 6.428159 GGCGGACTAAGTGATCATCATTAATT 59.572 38.462 0.00 0.00 0.00 1.40
755 2514 5.934625 GGCGGACTAAGTGATCATCATTAAT 59.065 40.000 0.00 0.00 0.00 1.40
756 2515 5.163353 TGGCGGACTAAGTGATCATCATTAA 60.163 40.000 0.00 0.00 0.00 1.40
757 2516 4.343814 TGGCGGACTAAGTGATCATCATTA 59.656 41.667 0.00 0.00 0.00 1.90
761 2520 2.890808 TGGCGGACTAAGTGATCATC 57.109 50.000 0.00 0.00 0.00 2.92
769 2528 1.187087 AGAGGACTTGGCGGACTAAG 58.813 55.000 0.00 0.00 0.00 2.18
870 2629 6.523201 GCGTAAATAATATTTTCCTGATGCCG 59.477 38.462 3.36 0.00 0.00 5.69
893 2655 5.120830 GGAATATATAGTGTTCCTGCAAGCG 59.879 44.000 6.41 0.00 42.91 4.68
991 2762 0.250424 TGAGGAGCCATGTGTGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
1083 2857 3.611674 GTGGTTTTGGGTGCCCGG 61.612 66.667 0.00 0.00 39.42 5.73
1131 2905 1.729838 GAAGTTGCGCTCGTCGAGT 60.730 57.895 22.61 1.45 41.67 4.18
1141 2915 4.093952 CTGCAGGGCGAAGTTGCG 62.094 66.667 5.57 0.00 40.62 4.85
1263 3037 2.419851 CCTGATCTCAGTTCTTGGGCTC 60.420 54.545 6.46 0.00 42.27 4.70
1327 3104 7.653713 CATAATATAATATGGGACGGAGTGAGC 59.346 40.741 0.44 0.00 33.10 4.26
1328 3105 8.144478 CCATAATATAATATGGGACGGAGTGAG 58.856 40.741 16.39 0.00 45.73 3.51
1329 3106 8.018537 CCATAATATAATATGGGACGGAGTGA 57.981 38.462 16.39 0.00 45.73 3.41
1346 3123 8.319146 CCCAAATACTACTTCGTCCCATAATAT 58.681 37.037 0.00 0.00 0.00 1.28
1347 3124 7.290714 ACCCAAATACTACTTCGTCCCATAATA 59.709 37.037 0.00 0.00 0.00 0.98
1348 3125 6.100714 ACCCAAATACTACTTCGTCCCATAAT 59.899 38.462 0.00 0.00 0.00 1.28
1349 3126 5.426185 ACCCAAATACTACTTCGTCCCATAA 59.574 40.000 0.00 0.00 0.00 1.90
1350 3127 4.964262 ACCCAAATACTACTTCGTCCCATA 59.036 41.667 0.00 0.00 0.00 2.74
1351 3128 3.778629 ACCCAAATACTACTTCGTCCCAT 59.221 43.478 0.00 0.00 0.00 4.00
1352 3129 3.175594 ACCCAAATACTACTTCGTCCCA 58.824 45.455 0.00 0.00 0.00 4.37
1353 3130 3.900966 ACCCAAATACTACTTCGTCCC 57.099 47.619 0.00 0.00 0.00 4.46
1404 3198 3.494048 CCCTGCAGGTAGAAGAATAGCAG 60.494 52.174 30.63 6.74 45.44 4.24
1442 3239 2.124529 TCAAACTGCCACACGCCA 60.125 55.556 0.00 0.00 36.24 5.69
1564 3361 2.103736 GGTCGTAGTACCGCAGCC 59.896 66.667 0.00 0.00 0.00 4.85
1661 3458 1.011968 GCTTGCCGTCGATGTACACA 61.012 55.000 0.00 0.00 0.00 3.72
1816 3614 3.807622 TCGGCCATAAAATCTGATCGAAC 59.192 43.478 2.24 0.00 0.00 3.95
1818 3616 3.744238 TCGGCCATAAAATCTGATCGA 57.256 42.857 2.24 0.00 0.00 3.59
1819 3617 5.408299 TGTAATCGGCCATAAAATCTGATCG 59.592 40.000 2.24 0.00 0.00 3.69
1820 3618 6.801539 TGTAATCGGCCATAAAATCTGATC 57.198 37.500 2.24 0.00 0.00 2.92
1821 3619 7.765695 AATGTAATCGGCCATAAAATCTGAT 57.234 32.000 2.24 0.00 0.00 2.90
1876 3690 6.213397 ACACAGCCACTATGATATATAAGGCA 59.787 38.462 0.00 0.00 43.13 4.75
1883 3697 9.271828 CAAACAATACACAGCCACTATGATATA 57.728 33.333 0.00 0.00 0.00 0.86
1884 3698 7.775093 ACAAACAATACACAGCCACTATGATAT 59.225 33.333 0.00 0.00 0.00 1.63
2010 3858 9.764363 TCTGTAGCGAATATTATTTTCACATCT 57.236 29.630 0.00 0.00 0.00 2.90
2030 3878 4.265556 GCTAACTGTGTACGCATTCTGTAG 59.734 45.833 10.02 4.82 0.00 2.74
2131 3979 3.797184 GCTGCGGGTGTGATTTGTTAAAA 60.797 43.478 0.00 0.00 0.00 1.52
2134 3982 0.878416 GCTGCGGGTGTGATTTGTTA 59.122 50.000 0.00 0.00 0.00 2.41
2140 3988 1.832883 TTATTTGCTGCGGGTGTGAT 58.167 45.000 0.00 0.00 0.00 3.06
2142 3990 2.430546 TTTTATTTGCTGCGGGTGTG 57.569 45.000 0.00 0.00 0.00 3.82
2143 3991 5.127031 AGAATATTTTATTTGCTGCGGGTGT 59.873 36.000 0.00 0.00 0.00 4.16
2147 3995 7.587757 GTCAGTAGAATATTTTATTTGCTGCGG 59.412 37.037 0.00 0.00 0.00 5.69
2148 3996 8.338259 AGTCAGTAGAATATTTTATTTGCTGCG 58.662 33.333 0.00 0.00 0.00 5.18
2157 4005 9.371136 CAAGCACAGAGTCAGTAGAATATTTTA 57.629 33.333 0.00 0.00 0.00 1.52
2159 4007 7.615403 TCAAGCACAGAGTCAGTAGAATATTT 58.385 34.615 0.00 0.00 0.00 1.40
2163 4011 5.674052 ATCAAGCACAGAGTCAGTAGAAT 57.326 39.130 0.00 0.00 0.00 2.40
2169 4017 5.163874 GCTTTCTAATCAAGCACAGAGTCAG 60.164 44.000 0.00 0.00 45.19 3.51
2170 4018 4.692625 GCTTTCTAATCAAGCACAGAGTCA 59.307 41.667 0.00 0.00 45.19 3.41
2171 4019 4.201666 CGCTTTCTAATCAAGCACAGAGTC 60.202 45.833 5.56 0.00 46.01 3.36
2173 4021 3.681897 ACGCTTTCTAATCAAGCACAGAG 59.318 43.478 5.56 0.00 46.01 3.35
2182 4030 8.946085 AGACAAAATTCATACGCTTTCTAATCA 58.054 29.630 0.00 0.00 0.00 2.57
2183 4031 9.214953 CAGACAAAATTCATACGCTTTCTAATC 57.785 33.333 0.00 0.00 0.00 1.75
2191 4039 5.700832 TGACTTCAGACAAAATTCATACGCT 59.299 36.000 0.00 0.00 0.00 5.07
2332 4182 5.486735 TGCATCAAGGATTTGGTTGAAAT 57.513 34.783 0.00 0.00 36.31 2.17
2367 4217 4.281435 TGTTTTCACATGCATCATCAGGTT 59.719 37.500 0.00 0.00 0.00 3.50
2397 4247 4.026804 GCAACTATGTATGCGTACTGTGAC 60.027 45.833 16.78 6.11 32.17 3.67
2419 4269 7.707104 ACTAAGTATACATCTGCAAAAATGGC 58.293 34.615 5.50 0.00 0.00 4.40
2466 4318 5.333875 GGACTATTTCCGCGGAACAATATTC 60.334 44.000 38.87 31.04 33.46 1.75
2564 4416 0.482446 AACTTGGCATGGTTCCCTCA 59.518 50.000 5.31 0.00 0.00 3.86
2640 4492 9.081997 GCCGATTCAAAAATGTTTGTGATATAA 57.918 29.630 8.22 0.00 43.90 0.98
2649 4501 4.363999 TGTTCGCCGATTCAAAAATGTTT 58.636 34.783 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.