Multiple sequence alignment - TraesCS5A01G165000

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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 TraesCS5A01G165000 chr5A 100.000 3752 0 0 1 3752 353608392 353604641 0.000000e+00 6929.0
1 TraesCS5A01G165000 chr5D 96.458 2710 62 12 497 3178 267074387 267077090 0.000000e+00 4442.0
2 TraesCS5A01G165000 chr5D 94.958 476 15 5 3281 3752 267077083 267077553 0.000000e+00 737.0
3 TraesCS5A01G165000 chr5D 88.072 503 56 4 2 500 267072643 267073145 8.970000e-166 593.0
4 TraesCS5A01G165000 chr5D 94.828 58 3 0 3223 3280 257502231 257502288 1.440000e-14 91.6
5 TraesCS5A01G165000 chr5B 97.736 2474 50 2 708 3175 301195972 301198445 0.000000e+00 4253.0
6 TraesCS5A01G165000 chr5B 95.388 477 13 3 3281 3752 301198441 301198913 0.000000e+00 750.0
7 TraesCS5A01G165000 chr5B 86.207 609 52 11 2 593 301194115 301194708 6.840000e-177 630.0
8 TraesCS5A01G165000 chr5B 100.000 51 0 0 3230 3280 291786956 291787006 1.110000e-15 95.3
9 TraesCS5A01G165000 chr5B 81.481 81 15 0 501 581 429408129 429408049 2.420000e-07 67.6
10 TraesCS5A01G165000 chr1A 88.068 176 20 1 85 259 485567325 485567500 1.370000e-49 207.0
11 TraesCS5A01G165000 chr4D 74.385 488 87 28 11 464 509440316 509439833 1.390000e-39 174.0
12 TraesCS5A01G165000 chr3B 95.588 68 3 0 163 230 257525484 257525417 3.960000e-20 110.0
13 TraesCS5A01G165000 chr6A 96.667 60 2 0 3223 3282 596426563 596426622 2.380000e-17 100.0
14 TraesCS5A01G165000 chr6D 100.000 53 0 0 3230 3282 450832067 450832119 8.580000e-17 99.0
15 TraesCS5A01G165000 chr7D 100.000 51 0 0 3230 3280 617790642 617790592 1.110000e-15 95.3
16 TraesCS5A01G165000 chr7A 98.182 55 0 1 3230 3283 428822275 428822329 1.110000e-15 95.3
17 TraesCS5A01G165000 chr3D 98.148 54 1 0 3230 3283 26165745 26165692 1.110000e-15 95.3
18 TraesCS5A01G165000 chr2D 100.000 51 0 0 3230 3280 215831917 215831967 1.110000e-15 95.3
19 TraesCS5A01G165000 chr2A 100.000 51 0 0 3230 3280 17316434 17316384 1.110000e-15 95.3


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 TraesCS5A01G165000 chr5A 353604641 353608392 3751 True 6929.000000 6929 100.000000 1 3752 1 chr5A.!!$R1 3751
1 TraesCS5A01G165000 chr5D 267072643 267077553 4910 False 1924.000000 4442 93.162667 2 3752 3 chr5D.!!$F2 3750
2 TraesCS5A01G165000 chr5B 301194115 301198913 4798 False 1877.666667 4253 93.110333 2 3752 3 chr5B.!!$F2 3750

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
44 46 0.032403 ACGGTTCGGTTGATGAACGA 59.968 50.000 0.00 0.00 45.19 3.85 F
626 3044 0.667993 AGATGCAACCAAACACCGTG 59.332 50.000 0.00 0.00 0.00 4.94 F
627 3045 0.939106 GATGCAACCAAACACCGTGC 60.939 55.000 0.00 0.00 0.00 5.34 F
629 3047 1.140804 GCAACCAAACACCGTGCTT 59.859 52.632 0.00 0.00 0.00 3.91 F
630 3048 1.145162 GCAACCAAACACCGTGCTTG 61.145 55.000 7.56 7.56 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 4405 1.805261 CTGAGCGCACATCGTCGATG 61.805 60.000 29.12 29.12 44.71 3.84 R
2051 4503 1.067060 CGATCGACCACAGGCAGATAA 59.933 52.381 10.26 0.00 0.00 1.75 R
2053 4505 1.439228 CGATCGACCACAGGCAGAT 59.561 57.895 10.26 0.00 0.00 2.90 R
2187 4639 2.105128 GCGAGCACGTGGATAGCT 59.895 61.111 18.88 7.45 42.17 3.32 R
2800 5252 7.805071 AGAAAACAAATTAGAAGCATCACGAAG 59.195 33.333 0.00 0.00 0.00 3.79 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
34 36 3.308705 GGAGGGTGACGGTTCGGT 61.309 66.667 0.00 0.00 0.00 4.69
44 46 0.032403 ACGGTTCGGTTGATGAACGA 59.968 50.000 0.00 0.00 45.19 3.85
148 155 2.352805 CCCTGACACCCAGAAGGC 59.647 66.667 0.00 0.00 45.78 4.35
237 244 2.353579 GTGAACGTCTAGGAGAGCTCTC 59.646 54.545 31.89 31.89 42.14 3.20
281 291 7.148523 GGTTTAGTTTAAGACTGTCGTATTGGG 60.149 40.741 4.34 0.00 39.48 4.12
370 380 2.814336 GCCTGCTAGCATATTGGTAACC 59.186 50.000 19.72 0.00 29.14 2.85
389 399 1.002624 GCACCATCTTCACGGGGAA 60.003 57.895 0.00 0.00 0.00 3.97
404 421 2.546373 CGGGGAAGTTACTCGACAACAA 60.546 50.000 0.00 0.00 0.00 2.83
427 444 2.389998 GTTGCATGTAACCAAACACCG 58.610 47.619 15.06 0.00 30.75 4.94
480 498 1.751924 CCAACTTTCGTTTCACCCCAA 59.248 47.619 0.00 0.00 0.00 4.12
482 500 2.685897 CAACTTTCGTTTCACCCCAAGA 59.314 45.455 0.00 0.00 0.00 3.02
486 504 4.202430 ACTTTCGTTTCACCCCAAGATAGT 60.202 41.667 0.00 0.00 0.00 2.12
489 507 2.027561 CGTTTCACCCCAAGATAGTGGA 60.028 50.000 0.00 0.00 41.65 4.02
522 1785 6.183360 ACAACCAAACAAAGTGCAGATATTGA 60.183 34.615 7.46 0.00 0.00 2.57
625 3043 1.398692 AAGATGCAACCAAACACCGT 58.601 45.000 0.00 0.00 0.00 4.83
626 3044 0.667993 AGATGCAACCAAACACCGTG 59.332 50.000 0.00 0.00 0.00 4.94
627 3045 0.939106 GATGCAACCAAACACCGTGC 60.939 55.000 0.00 0.00 0.00 5.34
628 3046 1.391157 ATGCAACCAAACACCGTGCT 61.391 50.000 0.00 0.00 0.00 4.40
629 3047 1.140804 GCAACCAAACACCGTGCTT 59.859 52.632 0.00 0.00 0.00 3.91
630 3048 1.145162 GCAACCAAACACCGTGCTTG 61.145 55.000 7.56 7.56 0.00 4.01
640 3058 1.200716 CACCGTGCTTGCATTTCTGAT 59.799 47.619 0.00 0.00 0.00 2.90
658 3076 3.738982 TGATGAGACAACGAAACACCAT 58.261 40.909 0.00 0.00 0.00 3.55
672 3090 1.274167 ACACCATGCTTGCATTTCTGG 59.726 47.619 5.24 8.24 0.00 3.86
673 3091 1.274167 CACCATGCTTGCATTTCTGGT 59.726 47.619 11.48 11.48 37.47 4.00
693 3111 3.291585 GTGAGAAACAACACGATGCAAG 58.708 45.455 0.00 0.00 0.00 4.01
697 3115 4.601019 AGAAACAACACGATGCAAGAAAG 58.399 39.130 0.00 0.00 0.00 2.62
698 3116 4.096382 AGAAACAACACGATGCAAGAAAGT 59.904 37.500 0.00 0.00 0.00 2.66
699 3117 5.295787 AGAAACAACACGATGCAAGAAAGTA 59.704 36.000 0.00 0.00 0.00 2.24
700 3118 5.689383 AACAACACGATGCAAGAAAGTAT 57.311 34.783 0.00 0.00 0.00 2.12
704 3122 4.827692 ACACGATGCAAGAAAGTATACCA 58.172 39.130 0.00 0.00 0.00 3.25
744 3185 3.499737 GCGTGTCCGGAATGGCAG 61.500 66.667 5.23 0.00 37.80 4.85
955 3401 2.689034 CCTCGCTTTCCCCTCCCT 60.689 66.667 0.00 0.00 0.00 4.20
1767 4219 3.345808 TTGCGCGTGCTTGACTCC 61.346 61.111 23.16 0.00 43.34 3.85
1905 4357 2.583441 CCGTCCTGGCTCTGGTTCA 61.583 63.158 0.00 0.00 0.00 3.18
1953 4405 4.125703 CAGCTATCAAGAATGTGGTCTCC 58.874 47.826 0.00 0.00 0.00 3.71
2019 4471 4.278170 CCAGTTCTGGTTGATTTACTTGCA 59.722 41.667 10.40 0.00 0.00 4.08
2020 4472 5.047802 CCAGTTCTGGTTGATTTACTTGCAT 60.048 40.000 10.40 0.00 0.00 3.96
2187 4639 5.220873 CGATCTTCAGAATTCTGTCCTACGA 60.221 44.000 29.80 16.61 44.12 3.43
2800 5252 7.445707 GGTTGATATTTACCTTCATCTCCCTTC 59.554 40.741 1.09 0.00 0.00 3.46
2842 5294 6.545504 TGTTTTCTTTGTCTATCACTGAGC 57.454 37.500 0.00 0.00 0.00 4.26
3006 5458 1.633945 GGTTGGTGGGATGGTCTAGTT 59.366 52.381 0.00 0.00 0.00 2.24
3044 5496 3.535561 GGCTACAATGCTCATACTGTGT 58.464 45.455 0.00 0.00 0.00 3.72
3113 5565 6.254281 ACTAAATGCTCACATGGTTTGTAC 57.746 37.500 0.00 0.00 36.57 2.90
3117 5569 2.154462 GCTCACATGGTTTGTACTGCT 58.846 47.619 0.00 0.00 36.57 4.24
3135 5587 0.242825 CTGTTGCCCTGTCATTGCTG 59.757 55.000 0.00 0.00 0.00 4.41
3178 5630 1.228228 TGGCCATTCCATGAGGAGC 59.772 57.895 0.00 0.00 46.74 4.70
3179 5631 1.228228 GGCCATTCCATGAGGAGCA 59.772 57.895 0.00 0.00 46.74 4.26
3180 5632 0.396139 GGCCATTCCATGAGGAGCAA 60.396 55.000 0.00 0.00 46.74 3.91
3181 5633 1.700955 GCCATTCCATGAGGAGCAAT 58.299 50.000 0.00 0.00 46.74 3.56
3182 5634 1.340248 GCCATTCCATGAGGAGCAATG 59.660 52.381 0.00 0.00 46.74 2.82
3183 5635 2.662866 CCATTCCATGAGGAGCAATGT 58.337 47.619 0.00 0.00 46.74 2.71
3184 5636 3.028850 CCATTCCATGAGGAGCAATGTT 58.971 45.455 0.00 0.00 46.74 2.71
3185 5637 3.449737 CCATTCCATGAGGAGCAATGTTT 59.550 43.478 0.00 0.00 46.74 2.83
3186 5638 4.081309 CCATTCCATGAGGAGCAATGTTTT 60.081 41.667 0.00 0.00 46.74 2.43
3187 5639 5.484715 CATTCCATGAGGAGCAATGTTTTT 58.515 37.500 0.00 0.00 46.74 1.94
3188 5640 6.351202 CCATTCCATGAGGAGCAATGTTTTTA 60.351 38.462 0.00 0.00 46.74 1.52
3189 5641 6.662865 TTCCATGAGGAGCAATGTTTTTAA 57.337 33.333 0.00 0.00 46.74 1.52
3190 5642 6.271488 TCCATGAGGAGCAATGTTTTTAAG 57.729 37.500 0.00 0.00 39.61 1.85
3191 5643 5.185635 TCCATGAGGAGCAATGTTTTTAAGG 59.814 40.000 0.00 0.00 39.61 2.69
3192 5644 4.519540 TGAGGAGCAATGTTTTTAAGGC 57.480 40.909 0.00 0.00 0.00 4.35
3193 5645 3.057596 TGAGGAGCAATGTTTTTAAGGCG 60.058 43.478 0.00 0.00 0.00 5.52
3194 5646 2.231235 AGGAGCAATGTTTTTAAGGCGG 59.769 45.455 0.00 0.00 0.00 6.13
3195 5647 2.029380 GGAGCAATGTTTTTAAGGCGGT 60.029 45.455 0.00 0.00 0.00 5.68
3196 5648 3.191791 GGAGCAATGTTTTTAAGGCGGTA 59.808 43.478 0.00 0.00 0.00 4.02
3197 5649 4.321378 GGAGCAATGTTTTTAAGGCGGTAA 60.321 41.667 0.00 0.00 0.00 2.85
3198 5650 4.805219 AGCAATGTTTTTAAGGCGGTAAG 58.195 39.130 0.00 0.00 0.00 2.34
3199 5651 3.924073 GCAATGTTTTTAAGGCGGTAAGG 59.076 43.478 0.00 0.00 0.00 2.69
3207 5659 2.349755 GGCGGTAAGGCAACCTGA 59.650 61.111 7.36 0.00 45.92 3.86
3208 5660 1.302993 GGCGGTAAGGCAACCTGAA 60.303 57.895 7.36 0.00 45.92 3.02
3209 5661 0.679960 GGCGGTAAGGCAACCTGAAT 60.680 55.000 7.36 0.00 45.92 2.57
3210 5662 0.733150 GCGGTAAGGCAACCTGAATC 59.267 55.000 7.36 0.00 37.39 2.52
3211 5663 1.006832 CGGTAAGGCAACCTGAATCG 58.993 55.000 7.36 0.00 37.39 3.34
3212 5664 1.404986 CGGTAAGGCAACCTGAATCGA 60.405 52.381 7.36 0.00 37.39 3.59
3213 5665 2.280628 GGTAAGGCAACCTGAATCGAG 58.719 52.381 2.05 0.00 36.53 4.04
3214 5666 1.666189 GTAAGGCAACCTGAATCGAGC 59.334 52.381 0.00 0.00 32.13 5.03
3215 5667 0.036732 AAGGCAACCTGAATCGAGCA 59.963 50.000 0.00 0.00 32.13 4.26
3216 5668 0.674895 AGGCAACCTGAATCGAGCAC 60.675 55.000 0.00 0.00 29.57 4.40
3217 5669 1.648467 GGCAACCTGAATCGAGCACC 61.648 60.000 0.00 0.00 0.00 5.01
3218 5670 0.955428 GCAACCTGAATCGAGCACCA 60.955 55.000 0.00 0.00 0.00 4.17
3219 5671 0.798776 CAACCTGAATCGAGCACCAC 59.201 55.000 0.00 0.00 0.00 4.16
3220 5672 0.321653 AACCTGAATCGAGCACCACC 60.322 55.000 0.00 0.00 0.00 4.61
3221 5673 1.450312 CCTGAATCGAGCACCACCC 60.450 63.158 0.00 0.00 0.00 4.61
3222 5674 1.811266 CTGAATCGAGCACCACCCG 60.811 63.158 0.00 0.00 0.00 5.28
3223 5675 3.195698 GAATCGAGCACCACCCGC 61.196 66.667 0.00 0.00 0.00 6.13
3224 5676 4.778143 AATCGAGCACCACCCGCC 62.778 66.667 0.00 0.00 0.00 6.13
3228 5680 4.162690 GAGCACCACCCGCCCTAG 62.163 72.222 0.00 0.00 0.00 3.02
3231 5683 4.473520 CACCACCCGCCCTAGCAG 62.474 72.222 0.00 0.00 39.83 4.24
3241 5693 3.151906 CCTAGCAGGGCGCCTTAT 58.848 61.111 28.56 13.68 44.04 1.73
3242 5694 1.004440 CCTAGCAGGGCGCCTTATC 60.004 63.158 28.56 14.14 44.04 1.75
3243 5695 1.373497 CTAGCAGGGCGCCTTATCG 60.373 63.158 28.56 8.38 44.04 2.92
3261 5713 4.208632 CCTAAGCGTCCAAGGCAG 57.791 61.111 0.00 0.00 0.00 4.85
3262 5714 1.450312 CCTAAGCGTCCAAGGCAGG 60.450 63.158 0.00 0.00 0.00 4.85
3263 5715 1.596934 CTAAGCGTCCAAGGCAGGA 59.403 57.895 0.00 0.00 34.64 3.86
3277 5729 2.785713 GCAGGACGCCTTAAAAACAA 57.214 45.000 0.00 0.00 32.94 2.83
3278 5730 3.297830 GCAGGACGCCTTAAAAACAAT 57.702 42.857 0.00 0.00 32.94 2.71
3279 5731 2.986479 GCAGGACGCCTTAAAAACAATG 59.014 45.455 0.00 0.00 32.94 2.82
3303 5755 0.954452 GGAGTTTGGCCAGAGTGTTG 59.046 55.000 8.65 0.00 0.00 3.33
3304 5756 0.954452 GAGTTTGGCCAGAGTGTTGG 59.046 55.000 8.65 0.00 41.35 3.77
3305 5757 0.258774 AGTTTGGCCAGAGTGTTGGT 59.741 50.000 5.11 0.00 40.49 3.67
3306 5758 1.111277 GTTTGGCCAGAGTGTTGGTT 58.889 50.000 5.11 0.00 40.49 3.67
3435 5887 4.099266 CCTTTGGACAGTGGAAACATCAAA 59.901 41.667 0.00 0.00 46.14 2.69
3497 5949 4.587684 AGTGAGACGGAAGAGGAAAGTAAA 59.412 41.667 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.212490 CCATGCGCAATCGGTGTTT 59.788 52.632 17.11 0.00 35.95 2.83
8 9 1.750399 GTCACCCTCCATGCGCAAT 60.750 57.895 17.11 0.00 0.00 3.56
34 36 3.009033 AGGATGACCCTTTCGTTCATCAA 59.991 43.478 11.75 0.00 44.85 2.57
102 109 5.237815 CAACTTGAAGGTGACTATGTAGCA 58.762 41.667 3.67 0.00 42.68 3.49
103 110 4.093556 GCAACTTGAAGGTGACTATGTAGC 59.906 45.833 15.54 0.00 42.68 3.58
237 244 1.136695 ACCAACCAACATGCACAACAG 59.863 47.619 0.00 0.00 0.00 3.16
295 305 5.472137 AGCATGGTACGACACTTAAACAAAT 59.528 36.000 0.00 0.00 0.00 2.32
370 380 2.796483 TTCCCCGTGAAGATGGTGCG 62.796 60.000 0.00 0.00 0.00 5.34
385 395 2.479275 GCTTGTTGTCGAGTAACTTCCC 59.521 50.000 12.19 0.00 0.00 3.97
389 399 2.503920 ACGCTTGTTGTCGAGTAACT 57.496 45.000 12.19 0.00 0.00 2.24
404 421 1.678627 TGTTTGGTTACATGCAACGCT 59.321 42.857 2.74 0.00 0.00 5.07
427 444 3.307339 TTACGCGAAAACACAAGACAC 57.693 42.857 15.93 0.00 0.00 3.67
480 498 6.686484 TGGTTGTATGCATATCCACTATCT 57.314 37.500 10.16 0.00 0.00 1.98
482 500 7.059788 TGTTTGGTTGTATGCATATCCACTAT 58.940 34.615 20.21 0.00 0.00 2.12
486 504 6.210385 ACTTTGTTTGGTTGTATGCATATCCA 59.790 34.615 10.16 15.18 0.00 3.41
489 507 5.868801 GCACTTTGTTTGGTTGTATGCATAT 59.131 36.000 10.16 0.00 0.00 1.78
552 1815 2.535012 TTGCATGTGTGTCTCGGTTA 57.465 45.000 0.00 0.00 0.00 2.85
625 3043 3.414269 TGTCTCATCAGAAATGCAAGCA 58.586 40.909 0.00 0.00 0.00 3.91
626 3044 4.164294 GTTGTCTCATCAGAAATGCAAGC 58.836 43.478 0.00 0.00 0.00 4.01
627 3045 4.152938 TCGTTGTCTCATCAGAAATGCAAG 59.847 41.667 0.00 0.00 0.00 4.01
628 3046 4.064388 TCGTTGTCTCATCAGAAATGCAA 58.936 39.130 0.00 0.00 0.00 4.08
629 3047 3.663025 TCGTTGTCTCATCAGAAATGCA 58.337 40.909 0.00 0.00 0.00 3.96
630 3048 4.668576 TTCGTTGTCTCATCAGAAATGC 57.331 40.909 0.00 0.00 0.00 3.56
640 3058 1.601903 GCATGGTGTTTCGTTGTCTCA 59.398 47.619 0.00 0.00 0.00 3.27
658 3076 2.275134 TCTCACCAGAAATGCAAGCA 57.725 45.000 0.00 0.00 0.00 3.91
672 3090 3.002246 TCTTGCATCGTGTTGTTTCTCAC 59.998 43.478 0.00 0.00 0.00 3.51
673 3091 3.202097 TCTTGCATCGTGTTGTTTCTCA 58.798 40.909 0.00 0.00 0.00 3.27
955 3401 2.039624 GGGGAGTGGAGCAGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
1953 4405 1.805261 CTGAGCGCACATCGTCGATG 61.805 60.000 29.12 29.12 44.71 3.84
2051 4503 1.067060 CGATCGACCACAGGCAGATAA 59.933 52.381 10.26 0.00 0.00 1.75
2053 4505 1.439228 CGATCGACCACAGGCAGAT 59.561 57.895 10.26 0.00 0.00 2.90
2187 4639 2.105128 GCGAGCACGTGGATAGCT 59.895 61.111 18.88 7.45 42.17 3.32
2800 5252 7.805071 AGAAAACAAATTAGAAGCATCACGAAG 59.195 33.333 0.00 0.00 0.00 3.79
2887 5339 2.414481 GCAGCATGTAGTCAGTGAACAG 59.586 50.000 0.00 0.00 39.31 3.16
3006 5458 1.604308 CCCAATGCTCCTGTGCACA 60.604 57.895 20.37 20.37 46.33 4.57
3044 5496 4.425180 TCACCAAACAGTTGTTAGCCTA 57.575 40.909 0.00 0.00 37.25 3.93
3113 5565 0.242825 CAATGACAGGGCAACAGCAG 59.757 55.000 0.00 0.00 39.74 4.24
3117 5569 1.180456 CCAGCAATGACAGGGCAACA 61.180 55.000 4.21 0.00 39.74 3.33
3170 5622 4.380867 CGCCTTAAAAACATTGCTCCTCAT 60.381 41.667 0.00 0.00 0.00 2.90
3171 5623 3.057596 CGCCTTAAAAACATTGCTCCTCA 60.058 43.478 0.00 0.00 0.00 3.86
3172 5624 3.501950 CGCCTTAAAAACATTGCTCCTC 58.498 45.455 0.00 0.00 0.00 3.71
3173 5625 2.231235 CCGCCTTAAAAACATTGCTCCT 59.769 45.455 0.00 0.00 0.00 3.69
3174 5626 2.029380 ACCGCCTTAAAAACATTGCTCC 60.029 45.455 0.00 0.00 0.00 4.70
3175 5627 3.297830 ACCGCCTTAAAAACATTGCTC 57.702 42.857 0.00 0.00 0.00 4.26
3176 5628 4.321675 CCTTACCGCCTTAAAAACATTGCT 60.322 41.667 0.00 0.00 0.00 3.91
3177 5629 3.924073 CCTTACCGCCTTAAAAACATTGC 59.076 43.478 0.00 0.00 0.00 3.56
3178 5630 3.924073 GCCTTACCGCCTTAAAAACATTG 59.076 43.478 0.00 0.00 0.00 2.82
3179 5631 3.574826 TGCCTTACCGCCTTAAAAACATT 59.425 39.130 0.00 0.00 0.00 2.71
3180 5632 3.158676 TGCCTTACCGCCTTAAAAACAT 58.841 40.909 0.00 0.00 0.00 2.71
3181 5633 2.584236 TGCCTTACCGCCTTAAAAACA 58.416 42.857 0.00 0.00 0.00 2.83
3182 5634 3.311106 GTTGCCTTACCGCCTTAAAAAC 58.689 45.455 0.00 0.00 0.00 2.43
3183 5635 2.296752 GGTTGCCTTACCGCCTTAAAAA 59.703 45.455 0.00 0.00 0.00 1.94
3184 5636 1.887854 GGTTGCCTTACCGCCTTAAAA 59.112 47.619 0.00 0.00 0.00 1.52
3185 5637 1.074244 AGGTTGCCTTACCGCCTTAAA 59.926 47.619 0.00 0.00 43.21 1.52
3186 5638 0.694196 AGGTTGCCTTACCGCCTTAA 59.306 50.000 0.00 0.00 43.21 1.85
3187 5639 0.035820 CAGGTTGCCTTACCGCCTTA 60.036 55.000 0.00 0.00 43.21 2.69
3188 5640 1.303317 CAGGTTGCCTTACCGCCTT 60.303 57.895 0.00 0.00 43.21 4.35
3189 5641 1.774894 TTCAGGTTGCCTTACCGCCT 61.775 55.000 0.00 0.00 43.21 5.52
3190 5642 0.679960 ATTCAGGTTGCCTTACCGCC 60.680 55.000 0.00 0.00 43.21 6.13
3191 5643 0.733150 GATTCAGGTTGCCTTACCGC 59.267 55.000 0.00 0.00 43.21 5.68
3192 5644 1.006832 CGATTCAGGTTGCCTTACCG 58.993 55.000 0.00 0.00 43.21 4.02
3193 5645 2.280628 CTCGATTCAGGTTGCCTTACC 58.719 52.381 0.00 0.00 38.53 2.85
3194 5646 1.666189 GCTCGATTCAGGTTGCCTTAC 59.334 52.381 0.00 0.00 0.00 2.34
3195 5647 1.277842 TGCTCGATTCAGGTTGCCTTA 59.722 47.619 0.00 0.00 0.00 2.69
3196 5648 0.036732 TGCTCGATTCAGGTTGCCTT 59.963 50.000 0.00 0.00 0.00 4.35
3197 5649 0.674895 GTGCTCGATTCAGGTTGCCT 60.675 55.000 0.00 0.00 0.00 4.75
3198 5650 1.648467 GGTGCTCGATTCAGGTTGCC 61.648 60.000 0.00 0.00 0.00 4.52
3199 5651 0.955428 TGGTGCTCGATTCAGGTTGC 60.955 55.000 0.00 0.00 0.00 4.17
3200 5652 0.798776 GTGGTGCTCGATTCAGGTTG 59.201 55.000 0.00 0.00 0.00 3.77
3201 5653 0.321653 GGTGGTGCTCGATTCAGGTT 60.322 55.000 0.00 0.00 0.00 3.50
3202 5654 1.296715 GGTGGTGCTCGATTCAGGT 59.703 57.895 0.00 0.00 0.00 4.00
3203 5655 1.450312 GGGTGGTGCTCGATTCAGG 60.450 63.158 0.00 0.00 0.00 3.86
3204 5656 1.811266 CGGGTGGTGCTCGATTCAG 60.811 63.158 0.00 0.00 45.67 3.02
3205 5657 2.264480 CGGGTGGTGCTCGATTCA 59.736 61.111 0.00 0.00 45.67 2.57
3206 5658 3.195698 GCGGGTGGTGCTCGATTC 61.196 66.667 0.00 0.00 45.67 2.52
3207 5659 4.778143 GGCGGGTGGTGCTCGATT 62.778 66.667 0.00 0.00 45.67 3.34
3211 5663 4.162690 CTAGGGCGGGTGGTGCTC 62.163 72.222 0.00 0.00 0.00 4.26
3214 5666 4.473520 CTGCTAGGGCGGGTGGTG 62.474 72.222 0.00 0.00 40.90 4.17
3224 5676 1.004440 GATAAGGCGCCCTGCTAGG 60.004 63.158 26.15 0.00 45.43 3.02
3225 5677 1.373497 CGATAAGGCGCCCTGCTAG 60.373 63.158 26.15 6.94 45.43 3.42
3226 5678 2.734591 CGATAAGGCGCCCTGCTA 59.265 61.111 26.15 10.35 45.43 3.49
3244 5696 1.450312 CCTGCCTTGGACGCTTAGG 60.450 63.158 0.00 0.00 0.00 2.69
3245 5697 0.741221 GTCCTGCCTTGGACGCTTAG 60.741 60.000 5.14 0.00 45.69 2.18
3246 5698 1.295423 GTCCTGCCTTGGACGCTTA 59.705 57.895 5.14 0.00 45.69 3.09
3247 5699 2.032681 GTCCTGCCTTGGACGCTT 59.967 61.111 5.14 0.00 45.69 4.68
3258 5710 2.785713 TTGTTTTTAAGGCGTCCTGC 57.214 45.000 0.00 0.00 45.38 4.85
3259 5711 4.497473 TCATTGTTTTTAAGGCGTCCTG 57.503 40.909 0.00 0.00 32.13 3.86
3260 5712 4.764823 TCATCATTGTTTTTAAGGCGTCCT 59.235 37.500 0.00 0.00 33.87 3.85
3261 5713 5.054390 TCATCATTGTTTTTAAGGCGTCC 57.946 39.130 0.00 0.00 0.00 4.79
3262 5714 5.095490 CCTCATCATTGTTTTTAAGGCGTC 58.905 41.667 0.00 0.00 0.00 5.19
3263 5715 4.764823 TCCTCATCATTGTTTTTAAGGCGT 59.235 37.500 0.00 0.00 0.00 5.68
3264 5716 5.106157 ACTCCTCATCATTGTTTTTAAGGCG 60.106 40.000 0.00 0.00 0.00 5.52
3265 5717 6.272822 ACTCCTCATCATTGTTTTTAAGGC 57.727 37.500 0.00 0.00 0.00 4.35
3266 5718 7.599998 CCAAACTCCTCATCATTGTTTTTAAGG 59.400 37.037 0.00 0.00 0.00 2.69
3267 5719 7.116805 GCCAAACTCCTCATCATTGTTTTTAAG 59.883 37.037 0.00 0.00 0.00 1.85
3268 5720 6.928492 GCCAAACTCCTCATCATTGTTTTTAA 59.072 34.615 0.00 0.00 0.00 1.52
3269 5721 6.454795 GCCAAACTCCTCATCATTGTTTTTA 58.545 36.000 0.00 0.00 0.00 1.52
3270 5722 5.299949 GCCAAACTCCTCATCATTGTTTTT 58.700 37.500 0.00 0.00 0.00 1.94
3271 5723 4.262592 GGCCAAACTCCTCATCATTGTTTT 60.263 41.667 0.00 0.00 0.00 2.43
3272 5724 3.259123 GGCCAAACTCCTCATCATTGTTT 59.741 43.478 0.00 0.00 0.00 2.83
3273 5725 2.827921 GGCCAAACTCCTCATCATTGTT 59.172 45.455 0.00 0.00 0.00 2.83
3274 5726 2.225091 TGGCCAAACTCCTCATCATTGT 60.225 45.455 0.61 0.00 0.00 2.71
3275 5727 2.426024 CTGGCCAAACTCCTCATCATTG 59.574 50.000 7.01 0.00 0.00 2.82
3276 5728 2.309755 TCTGGCCAAACTCCTCATCATT 59.690 45.455 7.01 0.00 0.00 2.57
3277 5729 1.918262 TCTGGCCAAACTCCTCATCAT 59.082 47.619 7.01 0.00 0.00 2.45
3278 5730 1.280133 CTCTGGCCAAACTCCTCATCA 59.720 52.381 7.01 0.00 0.00 3.07
3279 5731 1.280421 ACTCTGGCCAAACTCCTCATC 59.720 52.381 7.01 0.00 0.00 2.92
3303 5755 5.360591 CCTGTCCTACAATGAGTATGAACC 58.639 45.833 0.00 0.00 30.61 3.62
3304 5756 5.360591 CCCTGTCCTACAATGAGTATGAAC 58.639 45.833 0.00 0.00 30.61 3.18
3305 5757 4.141711 GCCCTGTCCTACAATGAGTATGAA 60.142 45.833 0.00 0.00 30.61 2.57
3306 5758 3.388024 GCCCTGTCCTACAATGAGTATGA 59.612 47.826 0.00 0.00 30.93 2.15
3365 5817 8.603898 TGTTAATTTCCACTATCTCTACCTGA 57.396 34.615 0.00 0.00 0.00 3.86
3435 5887 6.352516 CCTCAATGCACTTCTCTTTACCTAT 58.647 40.000 0.00 0.00 0.00 2.57
3575 6032 4.111916 CAACACAAAACTTTTCCGCATCT 58.888 39.130 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.