Multiple sequence alignment - TraesCS1A01G372900

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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 TraesCS1A01G372900 chr1A 100.000 3554 0 0 1 3554 549300452 549304005 0.000000e+00 6564
1 TraesCS1A01G372900 chr1D 91.542 2483 131 30 1 2437 455758854 455761303 0.000000e+00 3349
2 TraesCS1A01G372900 chr1D 92.563 1116 53 15 2446 3553 455761498 455762591 0.000000e+00 1574
3 TraesCS1A01G372900 chr1B 92.237 1752 82 19 1 1714 626096619 626098354 0.000000e+00 2433
4 TraesCS1A01G372900 chr1B 89.507 1601 101 37 1712 3291 626098397 626099951 0.000000e+00 1964
5 TraesCS1A01G372900 chr1B 88.550 262 9 4 3293 3554 626100036 626100276 7.460000e-77 298


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 TraesCS1A01G372900 chr1A 549300452 549304005 3553 False 6564.0 6564 100.0000 1 3554 1 chr1A.!!$F1 3553
1 TraesCS1A01G372900 chr1D 455758854 455762591 3737 False 2461.5 3349 92.0525 1 3553 2 chr1D.!!$F1 3552
2 TraesCS1A01G372900 chr1B 626096619 626100276 3657 False 1565.0 2433 90.0980 1 3554 3 chr1B.!!$F1 3553

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
553 583 3.321682 TCAACCATGCCTTTTCTTGGAAG 59.678 43.478 0.00 0.0 35.79 3.46 F
1202 1254 0.178068 GCATAGAAACTGCGGAGGGA 59.822 55.000 9.36 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1471 0.526211 TTCGCACTCGCTGTACAGAT 59.474 50.0 27.08 5.34 35.3 2.90 R
2801 3125 0.034670 GTTGCATGCTCCCTCTCCTT 60.035 55.0 20.33 0.00 0.0 3.36 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
61 62 6.972901 GGTTCTTACAACTTCTGAAAAAGTGG 59.027 38.462 0.00 0.00 39.40 4.00
70 71 7.222000 ACTTCTGAAAAAGTGGTTTGTTACA 57.778 32.000 0.00 0.00 38.06 2.41
75 76 8.740906 TCTGAAAAAGTGGTTTGTTACATGTTA 58.259 29.630 2.30 0.00 0.00 2.41
97 98 7.563556 TGTTATCCACACATTAGACTCCAGATA 59.436 37.037 0.00 0.00 0.00 1.98
205 207 6.630444 TCACGATACCAACTACTCCTATTC 57.370 41.667 0.00 0.00 0.00 1.75
291 294 8.074370 GGGTTTTGTTACAGTAAGAATTGTCTC 58.926 37.037 3.83 0.00 30.70 3.36
292 295 8.837389 GGTTTTGTTACAGTAAGAATTGTCTCT 58.163 33.333 3.83 0.00 30.70 3.10
363 366 9.447040 CAATCTTGTGACAAAGCATATTCTATG 57.553 33.333 0.00 0.00 0.00 2.23
467 470 3.466836 CTTTTCTTGGAAGGGCAAAACC 58.533 45.455 0.00 0.00 37.93 3.27
500 503 8.736751 TTGTTAAGAAAAGACAAAGTGTGTTC 57.263 30.769 0.00 0.00 41.96 3.18
501 504 8.106247 TGTTAAGAAAAGACAAAGTGTGTTCT 57.894 30.769 0.00 0.00 41.96 3.01
503 506 9.704098 GTTAAGAAAAGACAAAGTGTGTTCTAG 57.296 33.333 0.80 0.00 41.96 2.43
504 507 9.661563 TTAAGAAAAGACAAAGTGTGTTCTAGA 57.338 29.630 0.80 0.00 41.96 2.43
553 583 3.321682 TCAACCATGCCTTTTCTTGGAAG 59.678 43.478 0.00 0.00 35.79 3.46
570 600 4.285863 TGGAAGGACAAGAATGGTTGTTT 58.714 39.130 0.00 0.00 40.83 2.83
575 605 4.342092 AGGACAAGAATGGTTGTTTCCTTG 59.658 41.667 0.00 0.00 40.83 3.61
596 626 9.720769 TCCTTGAGAAAAGAAAACGTCTTATAT 57.279 29.630 0.00 0.00 46.36 0.86
663 704 6.999705 AATAATGCTCCTCTGAGAATCTCT 57.000 37.500 11.92 0.00 35.67 3.10
668 709 6.805016 TGCTCCTCTGAGAATCTCTTATTT 57.195 37.500 11.92 0.00 41.42 1.40
789 836 6.998074 TGCACACTTAGCCTAGCATTATAAAT 59.002 34.615 0.00 0.00 0.00 1.40
1075 1127 1.376942 CAGCTCCAGTGAAGGCCAG 60.377 63.158 5.01 0.00 0.00 4.85
1180 1232 3.135530 GCTGACCAAGATAACCAGAGGAT 59.864 47.826 0.00 0.00 0.00 3.24
1202 1254 0.178068 GCATAGAAACTGCGGAGGGA 59.822 55.000 9.36 0.00 0.00 4.20
1203 1255 1.808133 GCATAGAAACTGCGGAGGGAG 60.808 57.143 9.36 0.00 37.67 4.30
1204 1256 1.757118 CATAGAAACTGCGGAGGGAGA 59.243 52.381 9.36 0.00 35.29 3.71
1269 1321 0.895559 CCCTTTTCGCCAAGCCTCTT 60.896 55.000 0.00 0.00 0.00 2.85
1281 1333 1.972872 AGCCTCTTCACAAACAGGTG 58.027 50.000 0.00 0.00 40.16 4.00
1300 1352 2.670414 GTGAGTTGAAGAGAATCCTGCG 59.330 50.000 0.00 0.00 33.66 5.18
1318 1370 2.053627 GCGGAACAAGCTGTTGAATTG 58.946 47.619 6.31 0.00 41.28 2.32
1319 1371 2.287547 GCGGAACAAGCTGTTGAATTGA 60.288 45.455 6.31 0.00 41.28 2.57
1320 1372 3.612479 GCGGAACAAGCTGTTGAATTGAT 60.612 43.478 6.31 0.00 41.28 2.57
1321 1373 4.161333 CGGAACAAGCTGTTGAATTGATC 58.839 43.478 6.31 0.00 41.28 2.92
1322 1374 4.161333 GGAACAAGCTGTTGAATTGATCG 58.839 43.478 6.31 0.00 41.28 3.69
1323 1375 3.837213 ACAAGCTGTTGAATTGATCGG 57.163 42.857 0.00 0.00 37.10 4.18
1324 1376 3.149196 ACAAGCTGTTGAATTGATCGGT 58.851 40.909 0.00 0.00 37.10 4.69
1325 1377 3.569701 ACAAGCTGTTGAATTGATCGGTT 59.430 39.130 0.00 0.00 37.10 4.44
1326 1378 4.037923 ACAAGCTGTTGAATTGATCGGTTT 59.962 37.500 0.00 0.00 37.10 3.27
1349 1401 1.625508 GGTTCCCATCCCAGTAGGTCT 60.626 57.143 0.00 0.00 36.75 3.85
1383 1435 2.001812 ATGTGCTCGTAGCTTCTGTG 57.998 50.000 0.00 0.00 42.97 3.66
1384 1436 0.673985 TGTGCTCGTAGCTTCTGTGT 59.326 50.000 0.00 0.00 42.97 3.72
1393 1445 5.220381 TCGTAGCTTCTGTGTCTGTAAAAG 58.780 41.667 0.00 0.00 0.00 2.27
1414 1466 5.674052 AGTCTTTGTATGCTGATGAGTCT 57.326 39.130 0.00 0.00 0.00 3.24
1419 1471 8.721478 GTCTTTGTATGCTGATGAGTCTTTTTA 58.279 33.333 0.00 0.00 0.00 1.52
1506 1558 3.642901 TCGATAGCGAGGTCTTTGC 57.357 52.632 0.00 0.00 42.51 3.68
1571 1623 2.834549 TGATGAGGAAGGTTCAGAGGAC 59.165 50.000 0.00 0.00 0.00 3.85
1625 1677 0.397941 TGAGGCTGTCCAAGGAACAG 59.602 55.000 0.00 11.78 33.74 3.16
1763 1864 6.398095 TCATTCGGCATATATACAGGAACAG 58.602 40.000 0.00 0.00 0.00 3.16
1926 2033 4.564769 CAGAAGAGCGAGGAAATCTAACAC 59.435 45.833 0.00 0.00 0.00 3.32
2108 2215 2.383245 CTGTCTGGGTTCAGCACGGT 62.383 60.000 0.00 0.00 40.69 4.83
2151 2258 4.572571 GCCACCACCCGTTCCACA 62.573 66.667 0.00 0.00 0.00 4.17
2169 2279 2.202756 GTCTCCGCCGTGTCATCC 60.203 66.667 0.00 0.00 0.00 3.51
2234 2344 2.690653 TTTGGCCCCTTCACCGTCAG 62.691 60.000 0.00 0.00 0.00 3.51
2282 2392 1.374125 CCTCGGCGACATTGTGACA 60.374 57.895 4.99 0.00 0.00 3.58
2341 2462 9.250624 GCCTAAGTTATGTAAATAGTCTGTCAG 57.749 37.037 0.00 0.00 0.00 3.51
2432 2564 9.533253 GTTTAGCCAGTTTTATAACGGTAGATA 57.467 33.333 0.00 0.00 39.31 1.98
2444 2762 4.162096 ACGGTAGATAAGCTCGCTTATG 57.838 45.455 24.31 14.00 45.88 1.90
2485 2803 1.021968 ACGTGGCTGACTTTGGAAAC 58.978 50.000 0.00 0.00 0.00 2.78
2501 2819 5.860941 TGGAAACTTGATTTGGCTTTGTA 57.139 34.783 0.00 0.00 0.00 2.41
2502 2820 6.227298 TGGAAACTTGATTTGGCTTTGTAA 57.773 33.333 0.00 0.00 0.00 2.41
2505 2823 7.772757 TGGAAACTTGATTTGGCTTTGTAAAAT 59.227 29.630 0.00 0.00 0.00 1.82
2532 2856 6.990341 TGATCAATGATGTGGTTTGTAGAG 57.010 37.500 0.00 0.00 0.00 2.43
2568 2892 6.204495 GGCAATTGTCAGGAGATCTCTAATTC 59.796 42.308 21.81 5.30 0.00 2.17
2631 2955 5.768164 CCTGGTTAAACATTAACTGTGACCT 59.232 40.000 11.51 0.00 38.39 3.85
2643 2967 2.899900 ACTGTGACCTAATGACTCTGCA 59.100 45.455 0.00 0.00 0.00 4.41
2657 2981 1.476891 CTCTGCATGCTGGCTGAAAAT 59.523 47.619 22.54 0.00 40.52 1.82
2658 2982 2.686405 CTCTGCATGCTGGCTGAAAATA 59.314 45.455 22.54 1.23 40.52 1.40
2720 3044 3.319137 TTGAGGCTGTATCACTGTCAC 57.681 47.619 0.00 0.00 0.00 3.67
2800 3124 2.159043 TGATTGCCGGCAAAAAGAAACA 60.159 40.909 42.74 27.51 39.55 2.83
2801 3125 2.386661 TTGCCGGCAAAAAGAAACAA 57.613 40.000 38.61 13.20 32.44 2.83
2802 3126 2.386661 TGCCGGCAAAAAGAAACAAA 57.613 40.000 30.74 0.00 0.00 2.83
2803 3127 2.275318 TGCCGGCAAAAAGAAACAAAG 58.725 42.857 30.74 0.00 0.00 2.77
2871 3195 5.440610 ACTGATGTATGGAATTCTGGGTTC 58.559 41.667 5.23 0.00 0.00 3.62
2872 3196 4.792068 TGATGTATGGAATTCTGGGTTCC 58.208 43.478 5.23 0.00 44.32 3.62
2873 3197 3.662759 TGTATGGAATTCTGGGTTCCC 57.337 47.619 5.23 0.12 43.60 3.97
2874 3198 2.092646 TGTATGGAATTCTGGGTTCCCG 60.093 50.000 5.23 0.00 43.60 5.14
2941 3272 6.073058 TGTCACCTAAGTGTACACTACGTTAG 60.073 42.308 28.13 22.88 44.83 2.34
2988 3319 6.056236 GGGATATAGTTTGGACTTTGGACTC 58.944 44.000 0.00 0.00 37.33 3.36
3010 3341 3.181454 CGGAATATGCAGAGGGTTAGGTT 60.181 47.826 0.00 0.00 0.00 3.50
3016 3347 4.717279 TGCAGAGGGTTAGGTTTTTAGT 57.283 40.909 0.00 0.00 0.00 2.24
3019 3350 5.067954 GCAGAGGGTTAGGTTTTTAGTTCA 58.932 41.667 0.00 0.00 0.00 3.18
3053 3384 6.299805 AGTCAGGACTATTAATCAAGTGCA 57.700 37.500 11.18 0.00 40.43 4.57
3055 3386 6.070538 AGTCAGGACTATTAATCAAGTGCACT 60.071 38.462 15.25 15.25 40.43 4.40
3107 3438 2.497675 TGTTGGCTAGACAGGAGATCAC 59.502 50.000 0.00 0.00 0.00 3.06
3196 3527 2.568090 GCCATGGCCAACTTGTCG 59.432 61.111 27.24 0.00 34.56 4.35
3251 3583 0.471617 GCACCCATAGTCATGCTCCT 59.528 55.000 0.00 0.00 35.16 3.69
3252 3584 1.694150 GCACCCATAGTCATGCTCCTA 59.306 52.381 0.00 0.00 35.16 2.94
3255 3587 1.905215 CCCATAGTCATGCTCCTAGGG 59.095 57.143 9.46 0.44 35.42 3.53
3256 3588 2.614259 CCATAGTCATGCTCCTAGGGT 58.386 52.381 9.46 0.00 31.97 4.34
3257 3589 3.502303 CCCATAGTCATGCTCCTAGGGTA 60.502 52.174 9.46 0.00 34.16 3.69
3258 3590 4.357325 CCATAGTCATGCTCCTAGGGTAT 58.643 47.826 9.46 1.91 31.97 2.73
3266 3598 3.353557 TGCTCCTAGGGTATGTATAGCG 58.646 50.000 9.46 0.00 0.00 4.26
3274 3606 6.096987 CCTAGGGTATGTATAGCGATGTTGAT 59.903 42.308 0.00 0.00 0.00 2.57
3306 3721 6.239232 GGTTAACATACACGTATCATCTCCCT 60.239 42.308 8.10 0.00 0.00 4.20
3384 3799 6.625362 TGCATCTTTTGTAACACACTTTTCA 58.375 32.000 0.00 0.00 0.00 2.69
3441 3856 2.432628 GCACGTCGAGACAAGGGG 60.433 66.667 0.00 0.00 0.00 4.79
3463 3878 2.139118 GAGACACAGGAAGTTGACAGC 58.861 52.381 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.424703 AGCAAGTCCAATTGTGTAGCAT 58.575 40.909 4.43 0.00 32.56 3.79
61 62 9.554724 CTAATGTGTGGATAACATGTAACAAAC 57.445 33.333 0.00 2.24 41.97 2.93
70 71 6.384015 TCTGGAGTCTAATGTGTGGATAACAT 59.616 38.462 0.00 0.00 41.97 2.71
75 76 6.139671 ACTATCTGGAGTCTAATGTGTGGAT 58.860 40.000 0.00 0.00 0.00 3.41
97 98 6.317140 CACAAATAAGTAGCCATGATGTGACT 59.683 38.462 0.00 0.00 38.25 3.41
205 207 2.031163 GCTACGGCTGCCTATGGG 59.969 66.667 17.92 2.80 35.22 4.00
261 263 8.508875 CAATTCTTACTGTAACAAAACCCGTAT 58.491 33.333 0.00 0.00 0.00 3.06
363 366 9.875675 TCAATAATTGTGCTTTGCAAAAATAAC 57.124 25.926 13.84 9.33 39.34 1.89
370 373 7.725818 TTTGATCAATAATTGTGCTTTGCAA 57.274 28.000 9.40 0.00 41.47 4.08
427 430 1.511850 GGCATGGTTGAAAGCCAAAC 58.488 50.000 0.00 0.00 46.26 2.93
553 583 4.340950 TCAAGGAAACAACCATTCTTGTCC 59.659 41.667 0.00 0.00 33.03 4.02
570 600 9.720769 ATATAAGACGTTTTCTTTTCTCAAGGA 57.279 29.630 0.00 0.00 42.37 3.36
596 626 5.500234 CATTTCTCCCACACATTAGGAAGA 58.500 41.667 0.00 0.00 0.00 2.87
761 808 3.904800 TGCTAGGCTAAGTGTGCAATA 57.095 42.857 3.21 0.00 0.00 1.90
857 904 7.556275 ACACGTTTGGATTGGATTGTTATCTAT 59.444 33.333 0.00 0.00 0.00 1.98
916 965 4.526970 AGCAAGTAATCATCGGGTTTGAT 58.473 39.130 0.00 0.00 35.35 2.57
922 971 4.261322 CCAATCAAGCAAGTAATCATCGGG 60.261 45.833 0.00 0.00 0.00 5.14
983 1032 1.407989 GGAGTGATGAGGCAAAGAGGG 60.408 57.143 0.00 0.00 0.00 4.30
1152 1204 4.326826 TGGTTATCTTGGTCAGCTCTTTG 58.673 43.478 0.00 0.00 0.00 2.77
1180 1232 2.158957 CCCTCCGCAGTTTCTATGCTTA 60.159 50.000 0.00 0.00 41.61 3.09
1202 1254 2.423892 TGCTTCGTCGCTATCTTCTTCT 59.576 45.455 0.00 0.00 0.00 2.85
1203 1255 2.798680 TGCTTCGTCGCTATCTTCTTC 58.201 47.619 0.00 0.00 0.00 2.87
1204 1256 2.941453 TGCTTCGTCGCTATCTTCTT 57.059 45.000 0.00 0.00 0.00 2.52
1269 1321 4.081142 TCTCTTCAACTCACCTGTTTGTGA 60.081 41.667 0.00 0.00 42.75 3.58
1300 1352 4.161333 CGATCAATTCAACAGCTTGTTCC 58.839 43.478 0.00 0.00 38.77 3.62
1324 1376 5.211631 CCTACTGGGATGGGAACCGAAAA 62.212 52.174 0.00 0.00 46.83 2.29
1325 1377 3.750500 CCTACTGGGATGGGAACCGAAA 61.751 54.545 0.00 0.00 46.83 3.46
1326 1378 2.245405 CCTACTGGGATGGGAACCGAA 61.245 57.143 0.00 0.00 46.83 4.30
1383 1435 7.421530 TCAGCATACAAAGACTTTTACAGAC 57.578 36.000 0.00 0.00 0.00 3.51
1384 1436 7.877612 TCATCAGCATACAAAGACTTTTACAGA 59.122 33.333 0.00 0.00 0.00 3.41
1393 1445 6.734104 AAAGACTCATCAGCATACAAAGAC 57.266 37.500 0.00 0.00 0.00 3.01
1414 1466 3.366724 CGCACTCGCTGTACAGATAAAAA 59.633 43.478 27.08 3.43 35.30 1.94
1419 1471 0.526211 TTCGCACTCGCTGTACAGAT 59.474 50.000 27.08 5.34 35.30 2.90
1506 1558 3.748660 TATGCATGGACGGCGGTGG 62.749 63.158 13.24 0.00 0.00 4.61
1571 1623 2.350522 CTTCCACCTCCATTGTCTTCG 58.649 52.381 0.00 0.00 0.00 3.79
1625 1677 2.479901 GCTACCCTCTAGAAACGCAGAC 60.480 54.545 0.00 0.00 0.00 3.51
1763 1864 1.464997 CGGTTGGCTAAACAGCTCTTC 59.535 52.381 0.00 0.00 40.86 2.87
1799 1900 2.328099 CCAGACCTCAACTTGGCGC 61.328 63.158 0.00 0.00 0.00 6.53
1926 2033 3.063997 GCTTCGTCCTGTGATAAACATGG 59.936 47.826 0.00 0.00 38.39 3.66
2119 2226 1.450134 TGGCGTCACATGATGAGCC 60.450 57.895 19.49 19.49 45.05 4.70
2151 2258 2.711922 GGATGACACGGCGGAGACT 61.712 63.158 13.24 0.00 0.00 3.24
2185 2295 1.170290 CCGGGAAACAAGGTGGACAC 61.170 60.000 0.00 0.00 0.00 3.67
2341 2462 7.210174 TCCTTTCTATGTATGTACATCACTGC 58.790 38.462 12.68 0.00 45.11 4.40
2432 2564 1.831736 ACACCTACCATAAGCGAGCTT 59.168 47.619 15.05 15.05 39.83 3.74
2444 2762 5.007332 CGTAATAGCAAATTCCACACCTACC 59.993 44.000 0.00 0.00 0.00 3.18
2514 2838 4.985538 ACACCTCTACAAACCACATCATT 58.014 39.130 0.00 0.00 0.00 2.57
2528 2852 1.951209 TTGCCAGGATGACACCTCTA 58.049 50.000 0.00 0.00 39.69 2.43
2532 2856 1.474077 GACAATTGCCAGGATGACACC 59.526 52.381 5.05 0.00 39.69 4.16
2568 2892 2.813754 CTGTGACTGGTACACAAATGGG 59.186 50.000 0.00 0.00 45.49 4.00
2631 2955 1.211212 AGCCAGCATGCAGAGTCATTA 59.789 47.619 21.98 0.00 31.97 1.90
2643 2967 5.664294 TCATTGTTATTTTCAGCCAGCAT 57.336 34.783 0.00 0.00 0.00 3.79
2657 2981 6.264832 GTCCGCATCATCAATTTCATTGTTA 58.735 36.000 0.00 0.00 41.02 2.41
2658 2982 5.104374 GTCCGCATCATCAATTTCATTGTT 58.896 37.500 0.00 0.00 41.02 2.83
2671 2995 0.035152 TTTGCAGAGGTCCGCATCAT 60.035 50.000 0.00 0.00 38.10 2.45
2800 3124 0.700564 TTGCATGCTCCCTCTCCTTT 59.299 50.000 20.33 0.00 0.00 3.11
2801 3125 0.034670 GTTGCATGCTCCCTCTCCTT 60.035 55.000 20.33 0.00 0.00 3.36
2802 3126 1.606531 GTTGCATGCTCCCTCTCCT 59.393 57.895 20.33 0.00 0.00 3.69
2803 3127 1.817099 CGTTGCATGCTCCCTCTCC 60.817 63.158 20.33 0.00 0.00 3.71
2972 3303 2.249844 TCCGAGTCCAAAGTCCAAAC 57.750 50.000 0.00 0.00 0.00 2.93
2973 3304 3.502123 ATTCCGAGTCCAAAGTCCAAA 57.498 42.857 0.00 0.00 0.00 3.28
2975 3306 3.681594 GCATATTCCGAGTCCAAAGTCCA 60.682 47.826 0.00 0.00 0.00 4.02
2977 3308 3.531538 TGCATATTCCGAGTCCAAAGTC 58.468 45.455 0.00 0.00 0.00 3.01
2978 3309 3.197766 TCTGCATATTCCGAGTCCAAAGT 59.802 43.478 0.00 0.00 0.00 2.66
2979 3310 3.797039 TCTGCATATTCCGAGTCCAAAG 58.203 45.455 0.00 0.00 0.00 2.77
2988 3319 2.368875 ACCTAACCCTCTGCATATTCCG 59.631 50.000 0.00 0.00 0.00 4.30
3029 3360 7.124298 AGTGCACTTGATTAATAGTCCTGACTA 59.876 37.037 15.25 9.31 46.68 2.59
3031 3362 6.036517 CAGTGCACTTGATTAATAGTCCTGAC 59.963 42.308 18.94 0.00 0.00 3.51
3036 3367 5.500931 GCGACAGTGCACTTGATTAATAGTC 60.501 44.000 18.94 16.29 34.15 2.59
3044 3375 4.777384 TGCGACAGTGCACTTGAT 57.223 50.000 18.94 5.57 40.62 2.57
3053 3384 0.537143 TCTTTTGGCCATGCGACAGT 60.537 50.000 6.09 0.00 0.00 3.55
3055 3386 0.250684 TCTCTTTTGGCCATGCGACA 60.251 50.000 6.09 0.00 0.00 4.35
3107 3438 3.861797 CCCGGACCATCCCCTTCG 61.862 72.222 0.73 0.00 31.13 3.79
3127 3458 0.749454 CCAGATACCCTTGGCACAGC 60.749 60.000 0.00 0.00 42.39 4.40
3196 3527 8.516811 AACTAAATCACATAATACGGATCGAC 57.483 34.615 0.00 0.00 0.00 4.20
3251 3583 8.762481 ATATCAACATCGCTATACATACCCTA 57.238 34.615 0.00 0.00 0.00 3.53
3252 3584 7.661536 ATATCAACATCGCTATACATACCCT 57.338 36.000 0.00 0.00 0.00 4.34
3257 3589 9.890629 ACCAAATATATCAACATCGCTATACAT 57.109 29.630 0.00 0.00 0.00 2.29
3258 3590 9.719355 AACCAAATATATCAACATCGCTATACA 57.281 29.630 0.00 0.00 0.00 2.29
3398 3813 7.541091 CGTAATCGCCAAGCTTATCTTATCTTA 59.459 37.037 0.00 0.00 32.74 2.10
3399 3814 6.366332 CGTAATCGCCAAGCTTATCTTATCTT 59.634 38.462 0.00 0.00 32.74 2.40
3400 3815 5.864474 CGTAATCGCCAAGCTTATCTTATCT 59.136 40.000 0.00 0.00 32.74 1.98
3401 3816 6.083925 CGTAATCGCCAAGCTTATCTTATC 57.916 41.667 0.00 0.00 32.74 1.75
3441 3856 3.648009 CTGTCAACTTCCTGTGTCTCTC 58.352 50.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.