Multiple sequence alignment - TraesCS5A01G194900

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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 TraesCS5A01G194900 chr5A 100.000 3937 0 0 1 3937 398277220 398281156 0.000000e+00 7271
1 TraesCS5A01G194900 chr5D 94.897 3018 120 18 939 3937 301110436 301113438 0.000000e+00 4689
2 TraesCS5A01G194900 chr5D 76.292 329 45 18 358 674 301109840 301110147 1.140000e-30 145
3 TraesCS5A01G194900 chr5B 90.996 3332 156 60 1 3275 344307095 344310339 0.000000e+00 4359
4 TraesCS5A01G194900 chr5B 91.331 646 42 11 3301 3935 344310325 344310967 0.000000e+00 870


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 TraesCS5A01G194900 chr5A 398277220 398281156 3936 False 7271.0 7271 100.0000 1 3937 1 chr5A.!!$F1 3936
1 TraesCS5A01G194900 chr5D 301109840 301113438 3598 False 2417.0 4689 85.5945 358 3937 2 chr5D.!!$F1 3579
2 TraesCS5A01G194900 chr5B 344307095 344310967 3872 False 2614.5 4359 91.1635 1 3935 2 chr5B.!!$F1 3934

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
995 1097 0.179205 GCAGCTTCTTGACATGCGAC 60.179 55.0 0.00 0.0 0.0 5.19 F
1800 1902 0.394565 AAGAGTCGCAGCCTCAACTT 59.605 50.0 1.98 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1985 0.653636 CCCATGCGCATCATTTTTGC 59.346 50.0 22.51 0.0 36.74 3.68 R
3545 3662 0.036732 CCTGCAACCCTACTGCTTGA 59.963 55.0 0.00 0.0 40.59 3.02 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
101 102 1.786937 TCCCCTTGCTTTGCTTTCAA 58.213 45.000 0.00 0.00 0.00 2.69
114 115 1.740025 GCTTTCAAGTCATTCTCCGGG 59.260 52.381 0.00 0.00 0.00 5.73
117 118 1.452108 CAAGTCATTCTCCGGGGGC 60.452 63.158 0.00 0.00 0.00 5.80
145 146 1.797388 GACAAGCAACGCAACGCAAC 61.797 55.000 0.00 0.00 0.00 4.17
149 150 2.946597 CAACGCAACGCAACGCAA 60.947 55.556 0.00 0.00 0.00 4.85
151 152 4.605967 ACGCAACGCAACGCAAGG 62.606 61.111 0.00 0.00 46.39 3.61
153 154 3.959975 GCAACGCAACGCAAGGGA 61.960 61.111 0.00 0.00 46.39 4.20
154 155 2.051345 CAACGCAACGCAAGGGAC 60.051 61.111 0.00 0.00 46.39 4.46
155 156 3.645975 AACGCAACGCAAGGGACG 61.646 61.111 0.00 0.00 46.39 4.79
158 159 3.959975 GCAACGCAAGGGACGCAA 61.960 61.111 0.00 0.00 46.39 4.85
159 160 2.252260 CAACGCAAGGGACGCAAG 59.748 61.111 0.00 0.00 46.39 4.01
160 161 2.110213 AACGCAAGGGACGCAAGA 59.890 55.556 0.00 0.00 46.39 3.02
161 162 1.961277 AACGCAAGGGACGCAAGAG 60.961 57.895 0.00 0.00 46.39 2.85
162 163 2.048222 CGCAAGGGACGCAAGAGA 60.048 61.111 0.00 0.00 43.62 3.10
163 164 2.097038 CGCAAGGGACGCAAGAGAG 61.097 63.158 0.00 0.00 43.62 3.20
164 165 1.293498 GCAAGGGACGCAAGAGAGA 59.707 57.895 0.00 0.00 43.62 3.10
165 166 0.739112 GCAAGGGACGCAAGAGAGAG 60.739 60.000 0.00 0.00 43.62 3.20
166 167 0.605589 CAAGGGACGCAAGAGAGAGT 59.394 55.000 0.00 0.00 43.62 3.24
188 189 2.851102 CGATCCCATCCCCTGCCT 60.851 66.667 0.00 0.00 0.00 4.75
236 237 4.388577 CCCCCTTCTCCATTTATTAGGG 57.611 50.000 0.00 0.00 41.63 3.53
238 239 3.767711 CCCTTCTCCATTTATTAGGGGC 58.232 50.000 0.00 0.00 38.92 5.80
239 240 3.140144 CCCTTCTCCATTTATTAGGGGCA 59.860 47.826 0.00 0.00 38.92 5.36
240 241 4.401925 CCTTCTCCATTTATTAGGGGCAG 58.598 47.826 0.00 0.00 0.00 4.85
241 242 4.401925 CTTCTCCATTTATTAGGGGCAGG 58.598 47.826 0.00 0.00 0.00 4.85
242 243 3.403322 TCTCCATTTATTAGGGGCAGGT 58.597 45.455 0.00 0.00 0.00 4.00
243 244 3.791545 TCTCCATTTATTAGGGGCAGGTT 59.208 43.478 0.00 0.00 0.00 3.50
244 245 4.141251 TCTCCATTTATTAGGGGCAGGTTC 60.141 45.833 0.00 0.00 0.00 3.62
249 250 2.808906 ATTAGGGGCAGGTTCACTTC 57.191 50.000 0.00 0.00 0.00 3.01
261 262 2.996621 GGTTCACTTCTTGATCCACTCG 59.003 50.000 0.00 0.00 41.99 4.18
269 270 1.821753 CTTGATCCACTCGTCTCACCT 59.178 52.381 0.00 0.00 0.00 4.00
270 271 2.801077 TGATCCACTCGTCTCACCTA 57.199 50.000 0.00 0.00 0.00 3.08
271 272 3.081710 TGATCCACTCGTCTCACCTAA 57.918 47.619 0.00 0.00 0.00 2.69
272 273 3.632333 TGATCCACTCGTCTCACCTAAT 58.368 45.455 0.00 0.00 0.00 1.73
273 274 4.788679 TGATCCACTCGTCTCACCTAATA 58.211 43.478 0.00 0.00 0.00 0.98
274 275 4.822350 TGATCCACTCGTCTCACCTAATAG 59.178 45.833 0.00 0.00 0.00 1.73
328 329 3.191539 CCTCTTCGCCGCTCAAGC 61.192 66.667 0.00 0.00 37.78 4.01
339 341 2.747855 CTCAAGCTTCCGGCACCC 60.748 66.667 0.00 0.00 44.79 4.61
355 357 0.250513 ACCCGGCTCAGAATCTTCAC 59.749 55.000 0.00 0.00 0.00 3.18
356 358 0.539051 CCCGGCTCAGAATCTTCACT 59.461 55.000 0.00 0.00 0.00 3.41
393 415 0.250234 CTTGCCGATCCAGGTCAAGA 59.750 55.000 13.50 0.00 42.52 3.02
408 430 1.351017 TCAAGAACCCTCGCCTGAAAT 59.649 47.619 0.00 0.00 0.00 2.17
417 439 2.989166 CCTCGCCTGAAATTTTTCTTGC 59.011 45.455 4.80 6.10 38.02 4.01
420 449 2.989166 CGCCTGAAATTTTTCTTGCTCC 59.011 45.455 4.80 0.00 38.02 4.70
428 457 6.148150 TGAAATTTTTCTTGCTCCATGATTGC 59.852 34.615 0.00 0.00 38.02 3.56
433 462 1.068588 CTTGCTCCATGATTGCCCATG 59.931 52.381 0.00 0.00 42.58 3.66
474 503 1.348696 GGAGTCGAGGTTTGGGGTTAA 59.651 52.381 0.00 0.00 0.00 2.01
475 504 2.224597 GGAGTCGAGGTTTGGGGTTAAA 60.225 50.000 0.00 0.00 0.00 1.52
476 505 3.072211 GAGTCGAGGTTTGGGGTTAAAG 58.928 50.000 0.00 0.00 0.00 1.85
477 506 2.440627 AGTCGAGGTTTGGGGTTAAAGT 59.559 45.455 0.00 0.00 0.00 2.66
478 507 3.117776 AGTCGAGGTTTGGGGTTAAAGTT 60.118 43.478 0.00 0.00 0.00 2.66
479 508 4.102996 AGTCGAGGTTTGGGGTTAAAGTTA 59.897 41.667 0.00 0.00 0.00 2.24
488 517 7.988599 GGTTTGGGGTTAAAGTTAAAAAGATGT 59.011 33.333 0.00 0.00 0.00 3.06
552 581 1.765314 TCCTCTGCTTCCTTGATAGGC 59.235 52.381 0.00 0.00 41.69 3.93
604 636 8.425577 ACTCGCGTAATCTTTTACTACTACTA 57.574 34.615 5.77 0.00 36.37 1.82
605 637 9.050601 ACTCGCGTAATCTTTTACTACTACTAT 57.949 33.333 5.77 0.00 36.37 2.12
630 662 5.881923 ACTTACCTTCCAAAGTCACACTA 57.118 39.130 0.00 0.00 30.08 2.74
648 680 4.142227 ACACTACCACTGGAATTAGTAGCG 60.142 45.833 0.71 0.00 34.99 4.26
728 782 1.699634 TGGGGAAGCAGCATAGGATAC 59.300 52.381 0.00 0.00 0.00 2.24
738 792 5.420421 AGCAGCATAGGATACATGGTACTAG 59.580 44.000 0.00 0.00 41.41 2.57
780 843 3.687125 TGTCCTACTCCTATATCTGGCG 58.313 50.000 0.00 0.00 0.00 5.69
783 846 3.018149 CCTACTCCTATATCTGGCGTCC 58.982 54.545 0.00 0.00 0.00 4.79
829 893 1.953686 CACTGGGGACGTTTGTGAATT 59.046 47.619 0.00 0.00 0.00 2.17
846 910 9.979578 TTTGTGAATTGTTTACATCATAAGCTT 57.020 25.926 3.48 3.48 0.00 3.74
850 914 9.013229 TGAATTGTTTACATCATAAGCTTGAGT 57.987 29.630 9.86 2.96 0.00 3.41
885 950 5.621197 TTCGGGAATGTTTGTGAGTTATG 57.379 39.130 0.00 0.00 0.00 1.90
886 951 3.438781 TCGGGAATGTTTGTGAGTTATGC 59.561 43.478 0.00 0.00 0.00 3.14
887 952 3.190327 CGGGAATGTTTGTGAGTTATGCA 59.810 43.478 0.00 0.00 0.00 3.96
888 953 4.142403 CGGGAATGTTTGTGAGTTATGCAT 60.142 41.667 3.79 3.79 0.00 3.96
889 954 5.104374 GGGAATGTTTGTGAGTTATGCATG 58.896 41.667 10.16 0.00 0.00 4.06
890 955 5.336690 GGGAATGTTTGTGAGTTATGCATGT 60.337 40.000 10.16 0.00 0.00 3.21
892 957 7.312154 GGAATGTTTGTGAGTTATGCATGTTA 58.688 34.615 10.16 0.00 0.00 2.41
898 995 9.708222 GTTTGTGAGTTATGCATGTTATAGAAG 57.292 33.333 10.16 0.00 0.00 2.85
905 1002 8.686334 AGTTATGCATGTTATAGAAGGTTTTGG 58.314 33.333 10.16 0.00 0.00 3.28
910 1007 6.974622 GCATGTTATAGAAGGTTTTGGTGATG 59.025 38.462 0.00 0.00 0.00 3.07
913 1010 7.398829 TGTTATAGAAGGTTTTGGTGATGCTA 58.601 34.615 0.00 0.00 0.00 3.49
917 1019 6.272822 AGAAGGTTTTGGTGATGCTATTTC 57.727 37.500 0.00 0.00 0.00 2.17
919 1021 3.443681 AGGTTTTGGTGATGCTATTTCCG 59.556 43.478 0.00 0.00 0.00 4.30
924 1026 3.879998 TGGTGATGCTATTTCCGCTTTA 58.120 40.909 0.00 0.00 0.00 1.85
925 1027 4.460263 TGGTGATGCTATTTCCGCTTTAT 58.540 39.130 0.00 0.00 0.00 1.40
926 1028 4.275689 TGGTGATGCTATTTCCGCTTTATG 59.724 41.667 0.00 0.00 0.00 1.90
927 1029 4.222114 GTGATGCTATTTCCGCTTTATGC 58.778 43.478 0.00 0.00 38.57 3.14
964 1066 4.284378 GCTAATGCTGATGGTCAACTTC 57.716 45.455 0.00 0.00 36.03 3.01
995 1097 0.179205 GCAGCTTCTTGACATGCGAC 60.179 55.000 0.00 0.00 0.00 5.19
1209 1311 1.407299 CCGATGAACTCCAATCAGCCA 60.407 52.381 0.00 0.00 29.58 4.75
1269 1371 1.662044 CCACAAGGTGCTTTCTGGC 59.338 57.895 0.00 0.00 31.34 4.85
1272 1374 0.886490 ACAAGGTGCTTTCTGGCGAG 60.886 55.000 0.00 0.00 34.52 5.03
1329 1431 0.759346 AAGTGGACAGTTTCTCGCCT 59.241 50.000 0.00 0.00 0.00 5.52
1338 1440 2.490115 CAGTTTCTCGCCTGTCTCTACT 59.510 50.000 0.00 0.00 0.00 2.57
1386 1488 4.020617 TGCCCTTCTGAGCCACCG 62.021 66.667 0.00 0.00 0.00 4.94
1393 1495 1.191489 TTCTGAGCCACCGTGGATGA 61.191 55.000 22.37 8.46 35.51 2.92
1767 1869 2.423947 GGATGGCTGTGGGAATTCATCT 60.424 50.000 7.93 0.00 33.59 2.90
1800 1902 0.394565 AAGAGTCGCAGCCTCAACTT 59.605 50.000 1.98 0.00 0.00 2.66
1981 2085 2.584791 CTTTGTAGATTTGCACGCCAC 58.415 47.619 0.00 0.00 0.00 5.01
1997 2101 2.658224 CGCCACACGTACTTTCTTTTCG 60.658 50.000 0.00 0.00 36.87 3.46
2038 2142 8.732746 TTCACTACAAGGAATCTTTTATAGCC 57.267 34.615 0.00 0.00 0.00 3.93
2048 2152 8.112183 AGGAATCTTTTATAGCCCCATTATCTG 58.888 37.037 0.00 0.00 0.00 2.90
2058 2162 6.083487 AGCCCCATTATCTGCATATTACAT 57.917 37.500 0.00 0.00 0.00 2.29
2098 2202 6.478512 TGAAATTAAAGGAACAGGCTGTTT 57.521 33.333 31.60 19.17 41.28 2.83
2100 2204 8.012957 TGAAATTAAAGGAACAGGCTGTTTAA 57.987 30.769 31.60 24.54 41.28 1.52
2153 2257 1.261619 CTGTCAGTCCTTTGTGCGTTC 59.738 52.381 0.00 0.00 0.00 3.95
2258 2362 0.824182 TGCACCCGGGTAAAAGTTGG 60.824 55.000 29.72 12.88 0.00 3.77
2322 2426 6.211184 TGATGTCCATTTTATGCCTCTTTTGT 59.789 34.615 0.00 0.00 0.00 2.83
2323 2427 7.395772 TGATGTCCATTTTATGCCTCTTTTGTA 59.604 33.333 0.00 0.00 0.00 2.41
2324 2428 7.156876 TGTCCATTTTATGCCTCTTTTGTAG 57.843 36.000 0.00 0.00 0.00 2.74
2622 2727 2.656560 AGACCATGTCGTCAAGCTAC 57.343 50.000 5.12 0.00 37.67 3.58
2765 2870 0.833287 CCTGGACGGTGATGAAGGAT 59.167 55.000 0.00 0.00 0.00 3.24
2774 2879 2.570135 GTGATGAAGGATGAGAAGGCC 58.430 52.381 0.00 0.00 0.00 5.19
2991 3099 3.008704 GGTGGTAGGTAAAGAAAGCTCCA 59.991 47.826 0.00 0.00 0.00 3.86
3046 3154 6.373005 TGATGGAATTCTTAGAACCACTCA 57.627 37.500 6.48 8.62 33.38 3.41
3076 3184 2.104451 AGCCTTGCTGGTGATATCTCTG 59.896 50.000 3.98 2.36 37.57 3.35
3222 3334 0.474184 CCTGAGTGGTGGTGGAACTT 59.526 55.000 0.00 0.00 36.74 2.66
3377 3489 2.354303 CGACTACATGTAAACCTGGGCA 60.354 50.000 7.06 0.00 0.00 5.36
3379 3491 2.017049 CTACATGTAAACCTGGGCAGC 58.983 52.381 7.06 0.00 0.00 5.25
3447 3559 2.543777 TACTCAGCTTGGTGTTGACC 57.456 50.000 0.00 0.00 43.48 4.02
3474 3588 3.553904 AGCACAATTTGGTGGCAATTTT 58.446 36.364 0.78 0.00 39.19 1.82
3512 3629 9.590088 GTTCTTGTTGATAGTTTAAAGTTACCG 57.410 33.333 0.00 0.00 0.00 4.02
3517 3634 8.362639 TGTTGATAGTTTAAAGTTACCGAGAGT 58.637 33.333 0.00 0.00 0.00 3.24
3535 3652 9.720769 ACCGAGAGTTATTTTAATCTCAGAAAA 57.279 29.630 0.00 0.00 38.46 2.29
3546 3663 9.965824 TTTTAATCTCAGAAAACAAAGTCCATC 57.034 29.630 0.00 0.00 0.00 3.51
3548 3665 7.587037 AATCTCAGAAAACAAAGTCCATCAA 57.413 32.000 0.00 0.00 0.00 2.57
3549 3666 6.624352 TCTCAGAAAACAAAGTCCATCAAG 57.376 37.500 0.00 0.00 0.00 3.02
3550 3667 5.009010 TCTCAGAAAACAAAGTCCATCAAGC 59.991 40.000 0.00 0.00 0.00 4.01
3551 3668 4.644234 TCAGAAAACAAAGTCCATCAAGCA 59.356 37.500 0.00 0.00 0.00 3.91
3552 3669 4.980434 CAGAAAACAAAGTCCATCAAGCAG 59.020 41.667 0.00 0.00 0.00 4.24
3553 3670 4.646492 AGAAAACAAAGTCCATCAAGCAGT 59.354 37.500 0.00 0.00 0.00 4.40
3556 3673 3.679389 ACAAAGTCCATCAAGCAGTAGG 58.321 45.455 0.00 0.00 0.00 3.18
3568 3685 0.674895 GCAGTAGGGTTGCAGGAGTG 60.675 60.000 0.00 0.00 41.17 3.51
3569 3686 0.976641 CAGTAGGGTTGCAGGAGTGA 59.023 55.000 0.00 0.00 0.00 3.41
3584 3705 5.336849 GCAGGAGTGACTCTTTCTAGCTAAA 60.337 44.000 12.92 0.00 0.00 1.85
3586 3707 7.327214 CAGGAGTGACTCTTTCTAGCTAAATT 58.673 38.462 12.92 0.00 0.00 1.82
3592 3713 9.818796 GTGACTCTTTCTAGCTAAATTCAAAAG 57.181 33.333 0.00 0.00 0.00 2.27
3603 3724 7.837505 AGCTAAATTCAAAAGTTAAAACGTGC 58.162 30.769 0.00 0.00 0.00 5.34
3604 3725 7.489757 AGCTAAATTCAAAAGTTAAAACGTGCA 59.510 29.630 0.00 0.00 0.00 4.57
3618 3739 4.836125 AACGTGCAAAACAGATTGAGAT 57.164 36.364 0.00 0.00 31.84 2.75
3621 3742 3.671433 CGTGCAAAACAGATTGAGATGGG 60.671 47.826 0.00 0.00 31.84 4.00
3629 3750 5.698741 ACAGATTGAGATGGGTTGTATCA 57.301 39.130 0.00 0.00 0.00 2.15
3633 3754 7.121759 ACAGATTGAGATGGGTTGTATCAAAAG 59.878 37.037 0.00 0.00 33.91 2.27
3639 3760 3.420893 TGGGTTGTATCAAAAGCTCCAG 58.579 45.455 0.00 0.00 0.00 3.86
3640 3761 2.755103 GGGTTGTATCAAAAGCTCCAGG 59.245 50.000 0.00 0.00 0.00 4.45
3651 3773 7.623999 TCAAAAGCTCCAGGAGAATATCTAT 57.376 36.000 21.89 0.00 0.00 1.98
3799 3927 0.662970 GCAAACGGAAATTGCGCAGA 60.663 50.000 11.31 1.94 43.14 4.26
3800 3928 1.330306 CAAACGGAAATTGCGCAGAG 58.670 50.000 11.31 2.22 33.30 3.35
3812 3940 2.741930 CGCAGAGACGCTTCATCAA 58.258 52.632 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.423015 ACAATCAGACGCAAAGACAGATAT 58.577 37.500 0.00 0.00 0.00 1.63
101 102 2.285368 TGCCCCCGGAGAATGACT 60.285 61.111 0.73 0.00 0.00 3.41
114 115 2.331132 GCTTGTCTGTCTGCTGCCC 61.331 63.158 0.00 0.00 0.00 5.36
117 118 0.234106 CGTTGCTTGTCTGTCTGCTG 59.766 55.000 0.00 0.00 0.00 4.41
123 124 1.351707 CGTTGCGTTGCTTGTCTGT 59.648 52.632 0.00 0.00 0.00 3.41
145 146 2.048222 TCTCTTGCGTCCCTTGCG 60.048 61.111 0.00 0.00 34.24 4.85
147 148 0.605589 ACTCTCTCTTGCGTCCCTTG 59.394 55.000 0.00 0.00 0.00 3.61
149 150 1.882989 GCACTCTCTCTTGCGTCCCT 61.883 60.000 0.00 0.00 0.00 4.20
150 151 1.446966 GCACTCTCTCTTGCGTCCC 60.447 63.158 0.00 0.00 0.00 4.46
151 152 0.457681 GAGCACTCTCTCTTGCGTCC 60.458 60.000 0.00 0.00 43.87 4.79
152 153 0.457681 GGAGCACTCTCTCTTGCGTC 60.458 60.000 0.00 0.00 43.87 5.19
153 154 1.589113 GGAGCACTCTCTCTTGCGT 59.411 57.895 0.00 0.00 43.87 5.24
154 155 1.515952 CGGAGCACTCTCTCTTGCG 60.516 63.158 0.00 0.00 43.87 4.85
155 156 0.459489 ATCGGAGCACTCTCTCTTGC 59.541 55.000 0.00 0.00 39.31 4.01
156 157 1.066908 GGATCGGAGCACTCTCTCTTG 59.933 57.143 0.00 0.00 39.31 3.02
157 158 1.398692 GGATCGGAGCACTCTCTCTT 58.601 55.000 0.00 0.00 39.31 2.85
158 159 0.467290 GGGATCGGAGCACTCTCTCT 60.467 60.000 0.00 0.00 39.31 3.10
159 160 0.753479 TGGGATCGGAGCACTCTCTC 60.753 60.000 0.00 0.00 39.31 3.20
160 161 0.105760 ATGGGATCGGAGCACTCTCT 60.106 55.000 0.00 0.00 39.31 3.10
161 162 0.316841 GATGGGATCGGAGCACTCTC 59.683 60.000 0.00 0.00 38.62 3.20
162 163 1.118356 GGATGGGATCGGAGCACTCT 61.118 60.000 0.00 0.00 0.00 3.24
163 164 1.369321 GGATGGGATCGGAGCACTC 59.631 63.158 0.00 0.00 0.00 3.51
164 165 2.143419 GGGATGGGATCGGAGCACT 61.143 63.158 0.00 0.00 0.00 4.40
165 166 2.427753 GGGATGGGATCGGAGCAC 59.572 66.667 0.00 0.00 0.00 4.40
166 167 2.849162 GGGGATGGGATCGGAGCA 60.849 66.667 0.00 0.00 0.00 4.26
195 196 2.103340 GAAGAGCTCGCGGAGACC 59.897 66.667 6.13 0.00 0.00 3.85
196 197 1.063488 GAGAAGAGCTCGCGGAGAC 59.937 63.158 6.13 0.00 33.17 3.36
197 198 2.115911 GGAGAAGAGCTCGCGGAGA 61.116 63.158 6.13 0.00 44.91 3.71
198 199 2.411290 GGAGAAGAGCTCGCGGAG 59.589 66.667 6.13 3.47 44.91 4.63
199 200 3.141488 GGGAGAAGAGCTCGCGGA 61.141 66.667 6.13 0.00 45.10 5.54
236 237 2.087646 GGATCAAGAAGTGAACCTGCC 58.912 52.381 0.00 0.00 44.08 4.85
237 238 2.485814 GTGGATCAAGAAGTGAACCTGC 59.514 50.000 0.00 0.00 46.84 4.85
238 239 3.999663 GAGTGGATCAAGAAGTGAACCTG 59.000 47.826 0.00 0.00 46.84 4.00
239 240 3.306364 CGAGTGGATCAAGAAGTGAACCT 60.306 47.826 0.00 0.00 46.84 3.50
240 241 2.996621 CGAGTGGATCAAGAAGTGAACC 59.003 50.000 0.00 0.00 46.89 3.62
241 242 3.654414 ACGAGTGGATCAAGAAGTGAAC 58.346 45.455 0.00 0.00 40.50 3.18
242 243 3.574396 AGACGAGTGGATCAAGAAGTGAA 59.426 43.478 0.00 0.00 40.50 3.18
243 244 3.157881 AGACGAGTGGATCAAGAAGTGA 58.842 45.455 0.00 0.00 41.67 3.41
244 245 3.057245 TGAGACGAGTGGATCAAGAAGTG 60.057 47.826 0.00 0.00 0.00 3.16
249 250 1.821753 AGGTGAGACGAGTGGATCAAG 59.178 52.381 0.00 0.00 0.00 3.02
261 262 5.990996 ACGAGCTAGTACTATTAGGTGAGAC 59.009 44.000 2.33 0.00 0.00 3.36
269 270 4.248859 CCGGCTACGAGCTAGTACTATTA 58.751 47.826 2.33 0.00 44.60 0.98
270 271 3.072944 CCGGCTACGAGCTAGTACTATT 58.927 50.000 2.33 0.00 44.60 1.73
271 272 2.697654 CCGGCTACGAGCTAGTACTAT 58.302 52.381 2.33 0.00 44.60 2.12
272 273 1.875576 GCCGGCTACGAGCTAGTACTA 60.876 57.143 22.15 1.89 44.60 1.82
273 274 1.165284 GCCGGCTACGAGCTAGTACT 61.165 60.000 22.15 0.00 44.60 2.73
274 275 1.282265 GCCGGCTACGAGCTAGTAC 59.718 63.158 22.15 1.03 44.60 2.73
297 298 2.279784 GAGGAAGGCGCTGATCCG 60.280 66.667 7.64 0.00 38.31 4.18
306 307 4.459089 AGCGGCGAAGAGGAAGGC 62.459 66.667 12.98 0.00 0.00 4.35
307 308 2.202810 GAGCGGCGAAGAGGAAGG 60.203 66.667 12.98 0.00 0.00 3.46
333 334 2.514824 GATTCTGAGCCGGGTGCC 60.515 66.667 12.94 0.00 42.71 5.01
336 338 0.250513 GTGAAGATTCTGAGCCGGGT 59.749 55.000 5.45 5.45 0.00 5.28
339 341 1.923204 CGAAGTGAAGATTCTGAGCCG 59.077 52.381 0.00 0.00 0.00 5.52
393 415 3.230976 AGAAAAATTTCAGGCGAGGGTT 58.769 40.909 8.47 0.00 39.61 4.11
408 430 3.306919 GGGCAATCATGGAGCAAGAAAAA 60.307 43.478 0.00 0.00 0.00 1.94
434 463 0.870393 ATCGAATGATGGCATGACGC 59.130 50.000 3.81 0.00 36.11 5.19
435 464 2.589338 CATCGAATGATGGCATGACG 57.411 50.000 3.81 5.32 46.76 4.35
474 503 7.504924 TCGGATTGACACATCTTTTTAACTT 57.495 32.000 0.00 0.00 0.00 2.66
475 504 6.348540 GCTCGGATTGACACATCTTTTTAACT 60.349 38.462 0.00 0.00 0.00 2.24
476 505 5.795441 GCTCGGATTGACACATCTTTTTAAC 59.205 40.000 0.00 0.00 0.00 2.01
477 506 5.705441 AGCTCGGATTGACACATCTTTTTAA 59.295 36.000 0.00 0.00 0.00 1.52
478 507 5.122239 CAGCTCGGATTGACACATCTTTTTA 59.878 40.000 0.00 0.00 0.00 1.52
479 508 4.074970 AGCTCGGATTGACACATCTTTTT 58.925 39.130 0.00 0.00 0.00 1.94
488 517 0.036388 GGGAACAGCTCGGATTGACA 60.036 55.000 0.00 0.00 0.00 3.58
520 549 1.162800 GCAGAGGAATCATGGCGACC 61.163 60.000 0.00 0.00 0.00 4.79
604 636 8.147244 AGTGTGACTTTGGAAGGTAAGTATAT 57.853 34.615 0.00 0.00 34.88 0.86
605 637 7.549147 AGTGTGACTTTGGAAGGTAAGTATA 57.451 36.000 0.00 0.00 34.88 1.47
606 638 6.435292 AGTGTGACTTTGGAAGGTAAGTAT 57.565 37.500 0.00 0.00 34.88 2.12
612 644 2.775384 TGGTAGTGTGACTTTGGAAGGT 59.225 45.455 0.00 0.00 0.00 3.50
624 656 5.109903 GCTACTAATTCCAGTGGTAGTGTG 58.890 45.833 17.25 12.14 34.25 3.82
625 657 4.142227 CGCTACTAATTCCAGTGGTAGTGT 60.142 45.833 17.25 10.49 36.70 3.55
630 662 2.159282 CGTCGCTACTAATTCCAGTGGT 60.159 50.000 9.54 0.00 30.23 4.16
648 680 2.157085 CGCCAAGAAGAAAGTAACCGTC 59.843 50.000 0.00 0.00 0.00 4.79
728 782 7.145985 ACGCTGTAAATGATACTAGTACCATG 58.854 38.462 10.66 0.00 0.00 3.66
738 792 5.316488 CAGTGCTACGCTGTAAATGATAC 57.684 43.478 0.00 0.00 37.23 2.24
763 826 3.687125 TGGACGCCAGATATAGGAGTAG 58.313 50.000 3.53 0.00 39.36 2.57
764 827 3.801307 TGGACGCCAGATATAGGAGTA 57.199 47.619 3.53 0.00 39.36 2.59
765 828 2.677542 TGGACGCCAGATATAGGAGT 57.322 50.000 3.21 3.21 42.07 3.85
766 829 4.543590 ATTTGGACGCCAGATATAGGAG 57.456 45.455 1.01 0.00 33.81 3.69
767 830 4.974645 AATTTGGACGCCAGATATAGGA 57.025 40.909 3.06 0.00 33.81 2.94
768 831 7.687941 AATTAATTTGGACGCCAGATATAGG 57.312 36.000 0.00 0.00 33.81 2.57
783 846 5.851177 ACTGCTTCGTGTCGAAATTAATTTG 59.149 36.000 17.98 10.28 45.23 2.32
846 910 8.629158 CATTCCCGAAATTATTGGATAAACTCA 58.371 33.333 0.00 0.00 0.00 3.41
850 914 9.593134 CAAACATTCCCGAAATTATTGGATAAA 57.407 29.630 0.00 0.00 0.00 1.40
852 916 8.194104 CACAAACATTCCCGAAATTATTGGATA 58.806 33.333 0.00 0.00 30.12 2.59
865 930 3.190327 TGCATAACTCACAAACATTCCCG 59.810 43.478 0.00 0.00 0.00 5.14
885 950 6.509418 TCACCAAAACCTTCTATAACATGC 57.491 37.500 0.00 0.00 0.00 4.06
886 951 6.974622 GCATCACCAAAACCTTCTATAACATG 59.025 38.462 0.00 0.00 0.00 3.21
887 952 6.891908 AGCATCACCAAAACCTTCTATAACAT 59.108 34.615 0.00 0.00 0.00 2.71
888 953 6.245408 AGCATCACCAAAACCTTCTATAACA 58.755 36.000 0.00 0.00 0.00 2.41
889 954 6.759497 AGCATCACCAAAACCTTCTATAAC 57.241 37.500 0.00 0.00 0.00 1.89
890 955 9.474313 AAATAGCATCACCAAAACCTTCTATAA 57.526 29.630 0.00 0.00 0.00 0.98
892 957 7.068716 GGAAATAGCATCACCAAAACCTTCTAT 59.931 37.037 0.00 0.00 0.00 1.98
898 995 3.769536 CGGAAATAGCATCACCAAAACC 58.230 45.455 0.00 0.00 0.00 3.27
905 1002 4.222114 GCATAAAGCGGAAATAGCATCAC 58.778 43.478 0.00 0.00 37.01 3.06
919 1021 2.900122 ACACACATGTCGCATAAAGC 57.100 45.000 0.00 0.00 31.55 3.51
924 1026 1.935873 GCTCATACACACATGTCGCAT 59.064 47.619 0.00 0.00 40.48 4.73
925 1027 1.066929 AGCTCATACACACATGTCGCA 60.067 47.619 0.00 0.00 40.48 5.10
926 1028 1.645034 AGCTCATACACACATGTCGC 58.355 50.000 0.00 0.00 40.48 5.19
927 1029 4.318333 GCATTAGCTCATACACACATGTCG 60.318 45.833 0.00 0.00 37.80 4.35
928 1030 5.088141 GCATTAGCTCATACACACATGTC 57.912 43.478 0.00 0.00 37.80 3.06
980 1082 2.407090 TCAGTGTCGCATGTCAAGAAG 58.593 47.619 0.00 0.00 0.00 2.85
981 1083 2.524569 TCAGTGTCGCATGTCAAGAA 57.475 45.000 0.00 0.00 0.00 2.52
1041 1143 2.749621 CTCCTGAAATAAGCAGCGGTTT 59.250 45.455 0.00 0.00 32.06 3.27
1209 1311 3.950395 GCTGAAGAAACCAGGCATCTATT 59.050 43.478 0.00 0.00 32.51 1.73
1269 1371 2.225019 GCCCATGTAATTCAGATGCTCG 59.775 50.000 0.00 0.00 0.00 5.03
1272 1374 1.267806 CCGCCCATGTAATTCAGATGC 59.732 52.381 0.00 0.00 0.00 3.91
1329 1431 4.324267 TGATGTCGTCAAGAGTAGAGACA 58.676 43.478 0.00 0.00 41.85 3.41
1338 1440 2.785713 TCGTGTTGATGTCGTCAAGA 57.214 45.000 7.76 4.11 46.99 3.02
1386 1488 1.369625 AAGCCGTCGAAATCATCCAC 58.630 50.000 0.00 0.00 0.00 4.02
1393 1495 3.438781 TGCTTCATAAAAGCCGTCGAAAT 59.561 39.130 7.26 0.00 42.36 2.17
1548 1650 3.752222 CCATCTCATAGCATGCCTTCTTC 59.248 47.826 15.66 0.00 0.00 2.87
1767 1869 4.038763 TGCGACTCTTTACCAGAAGAAGAA 59.961 41.667 0.00 0.00 35.38 2.52
1800 1902 2.879826 CTGCACATCATAGTGTCGTGA 58.120 47.619 0.00 0.00 41.52 4.35
1883 1985 0.653636 CCCATGCGCATCATTTTTGC 59.346 50.000 22.51 0.00 36.74 3.68
1981 2085 9.801714 ACATAATAAACGAAAAGAAAGTACGTG 57.198 29.630 0.00 0.00 37.28 4.49
2038 2142 7.148018 GGTTGGATGTAATATGCAGATAATGGG 60.148 40.741 0.00 0.00 0.00 4.00
2048 2152 6.879458 CCTAACTAGGGTTGGATGTAATATGC 59.121 42.308 0.00 0.00 39.86 3.14
2100 2204 9.983024 ACTACATATATACAGACTGGAGCTAAT 57.017 33.333 7.51 0.00 0.00 1.73
2153 2257 6.103997 ACTGGCTTGCAATTTTGATTATGAG 58.896 36.000 0.00 0.00 0.00 2.90
2223 2327 4.158764 CGGGTGCATTTACCTTTTATCCAA 59.841 41.667 0.00 0.00 40.66 3.53
2234 2338 2.821378 ACTTTTACCCGGGTGCATTTAC 59.179 45.455 36.97 0.00 0.00 2.01
2281 2385 2.583143 CATCAGTGGACATGATGCCAT 58.417 47.619 10.84 0.53 45.35 4.40
2622 2727 2.383527 GCGAGGCCTGACGAAACAG 61.384 63.158 12.00 0.00 37.61 3.16
2774 2879 4.521062 CGCTCCCCTTCTGGCTCG 62.521 72.222 0.00 0.00 0.00 5.03
2991 3099 5.211973 TCCTACTCCACAAAGCAGATATCT 58.788 41.667 0.00 0.00 0.00 1.98
3046 3154 2.762327 CACCAGCAAGGCTTCCAAATAT 59.238 45.455 0.00 0.00 43.14 1.28
3097 3209 9.592196 ACTAAAACCCTTCCTATATATACACGA 57.408 33.333 0.00 0.00 0.00 4.35
3222 3334 3.493129 CCGTTCAAGTCGACTGATTTTGA 59.507 43.478 20.85 15.64 32.28 2.69
3292 3404 9.502091 AGAAGACAACAAAGTTACATATGCTTA 57.498 29.630 1.58 0.00 0.00 3.09
3377 3489 4.576330 AGAACCAAGTTATAGGCTTGCT 57.424 40.909 11.44 4.05 41.27 3.91
3379 3491 6.575162 ACAAAGAACCAAGTTATAGGCTTG 57.425 37.500 0.00 10.44 42.00 4.01
3447 3559 2.746269 CCACCAAATTGTGCTCAGTTG 58.254 47.619 0.00 2.93 34.85 3.16
3535 3652 3.560025 CCCTACTGCTTGATGGACTTTGT 60.560 47.826 0.00 0.00 0.00 2.83
3540 3657 2.359900 CAACCCTACTGCTTGATGGAC 58.640 52.381 0.00 0.00 0.00 4.02
3542 3659 1.098050 GCAACCCTACTGCTTGATGG 58.902 55.000 0.00 0.00 36.84 3.51
3543 3660 1.741706 CTGCAACCCTACTGCTTGATG 59.258 52.381 0.00 0.00 40.59 3.07
3544 3661 1.340405 CCTGCAACCCTACTGCTTGAT 60.340 52.381 0.00 0.00 40.59 2.57
3545 3662 0.036732 CCTGCAACCCTACTGCTTGA 59.963 55.000 0.00 0.00 40.59 3.02
3546 3663 0.036732 TCCTGCAACCCTACTGCTTG 59.963 55.000 0.00 0.00 40.59 4.01
3548 3665 0.838122 ACTCCTGCAACCCTACTGCT 60.838 55.000 0.00 0.00 40.59 4.24
3549 3666 0.674895 CACTCCTGCAACCCTACTGC 60.675 60.000 0.00 0.00 40.35 4.40
3550 3667 0.976641 TCACTCCTGCAACCCTACTG 59.023 55.000 0.00 0.00 0.00 2.74
3551 3668 0.977395 GTCACTCCTGCAACCCTACT 59.023 55.000 0.00 0.00 0.00 2.57
3552 3669 0.977395 AGTCACTCCTGCAACCCTAC 59.023 55.000 0.00 0.00 0.00 3.18
3553 3670 1.203187 AGAGTCACTCCTGCAACCCTA 60.203 52.381 0.00 0.00 0.00 3.53
3556 3673 2.147150 GAAAGAGTCACTCCTGCAACC 58.853 52.381 0.00 0.00 0.00 3.77
3584 3705 7.797819 TGTTTTGCACGTTTTAACTTTTGAAT 58.202 26.923 0.00 0.00 0.00 2.57
3586 3707 6.641314 TCTGTTTTGCACGTTTTAACTTTTGA 59.359 30.769 0.00 0.00 0.00 2.69
3592 3713 6.470877 TCTCAATCTGTTTTGCACGTTTTAAC 59.529 34.615 0.00 0.00 0.00 2.01
3597 3718 4.539870 CATCTCAATCTGTTTTGCACGTT 58.460 39.130 0.00 0.00 0.00 3.99
3599 3720 3.495193 CCATCTCAATCTGTTTTGCACG 58.505 45.455 0.00 0.00 0.00 5.34
3600 3721 3.256631 ACCCATCTCAATCTGTTTTGCAC 59.743 43.478 0.00 0.00 0.00 4.57
3603 3724 5.458041 ACAACCCATCTCAATCTGTTTTG 57.542 39.130 0.00 0.00 0.00 2.44
3604 3725 6.947733 TGATACAACCCATCTCAATCTGTTTT 59.052 34.615 0.00 0.00 0.00 2.43
3618 3739 3.420893 CTGGAGCTTTTGATACAACCCA 58.579 45.455 0.00 0.00 0.00 4.51
3621 3742 4.579869 TCTCCTGGAGCTTTTGATACAAC 58.420 43.478 19.08 0.00 0.00 3.32
3629 3750 8.938883 TGTTATAGATATTCTCCTGGAGCTTTT 58.061 33.333 19.08 3.94 0.00 2.27
3633 3754 7.179338 TCCTTGTTATAGATATTCTCCTGGAGC 59.821 40.741 19.08 4.53 0.00 4.70
3799 3927 1.670087 CCGAGTGTTGATGAAGCGTCT 60.670 52.381 0.31 0.00 0.00 4.18
3800 3928 0.716108 CCGAGTGTTGATGAAGCGTC 59.284 55.000 0.00 0.00 0.00 5.19
3839 3967 3.944233 GCGTTTCGTTGCCGTGGT 61.944 61.111 0.00 0.00 35.01 4.16


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

AutoCloner maintained by Alex Coulton.