Multiple sequence alignment - TraesCS5A01G179700

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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 TraesCS5A01G179700 chr5A 100.000 4036 0 0 1 4036 377937811 377941846 0.000000e+00 7454.0
1 TraesCS5A01G179700 chr5D 93.498 1215 40 12 2838 4030 285680290 285681487 0.000000e+00 1770.0
2 TraesCS5A01G179700 chr5D 88.965 1314 65 32 1171 2407 285678158 285679468 0.000000e+00 1550.0
3 TraesCS5A01G179700 chr5D 93.233 1064 27 19 132 1187 285677110 285678136 0.000000e+00 1524.0
4 TraesCS5A01G179700 chr5D 96.512 344 12 0 2393 2736 285679508 285679851 1.630000e-158 569.0
5 TraesCS5A01G179700 chr5D 91.743 109 1 3 2735 2839 285679920 285680024 1.170000e-30 145.0
6 TraesCS5A01G179700 chr5B 91.549 1065 52 15 1710 2736 323882681 323883745 0.000000e+00 1434.0
7 TraesCS5A01G179700 chr5B 91.324 1095 26 18 117 1187 323880677 323881726 0.000000e+00 1432.0
8 TraesCS5A01G179700 chr5B 91.908 1001 40 19 2736 3722 323883827 323884800 0.000000e+00 1362.0
9 TraesCS5A01G179700 chr5B 94.220 346 15 2 1171 1516 323881748 323882088 1.290000e-144 523.0
10 TraesCS5A01G179700 chr5B 90.909 308 11 9 3724 4030 323885066 323885357 8.130000e-107 398.0
11 TraesCS5A01G179700 chr5B 93.785 177 11 0 1509 1685 323882166 323882342 2.390000e-67 267.0
12 TraesCS5A01G179700 chr5B 89.855 69 2 1 47 115 323880575 323880638 2.580000e-12 84.2
13 TraesCS5A01G179700 chr2A 94.479 163 9 0 3738 3900 417102883 417102721 6.700000e-63 252.0


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 TraesCS5A01G179700 chr5A 377937811 377941846 4035 False 7454.000000 7454 100.000000 1 4036 1 chr5A.!!$F1 4035
1 TraesCS5A01G179700 chr5D 285677110 285681487 4377 False 1111.600000 1770 92.790200 132 4030 5 chr5D.!!$F1 3898
2 TraesCS5A01G179700 chr5B 323880575 323885357 4782 False 785.742857 1434 91.935714 47 4030 7 chr5B.!!$F1 3983

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
420 466 0.104855 CCCCGAAGAATCTGCGATGA 59.895 55.0 13.05 0.0 33.75 2.92 F
2004 2543 0.812549 AAACGCCGTTCACCAACTTT 59.187 45.0 1.60 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2627 0.674895 GGCCACTCGTCTGCATCTTT 60.675 55.0 0.0 0.0 0.00 2.52 R
3369 4458 0.805614 ACCAGATCGAGAGACACACG 59.194 55.0 0.0 0.0 46.97 4.49 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
25 26 7.810658 CCTAATTATGTGCGAAATATGAAGCT 58.189 34.615 0.00 0.00 0.00 3.74
26 27 8.935844 CCTAATTATGTGCGAAATATGAAGCTA 58.064 33.333 0.00 0.00 0.00 3.32
30 31 9.658799 ATTATGTGCGAAATATGAAGCTATACT 57.341 29.630 0.00 0.00 0.00 2.12
31 32 6.769608 TGTGCGAAATATGAAGCTATACTG 57.230 37.500 0.00 0.00 0.00 2.74
32 33 5.177511 TGTGCGAAATATGAAGCTATACTGC 59.822 40.000 0.00 0.00 0.00 4.40
33 34 4.690748 TGCGAAATATGAAGCTATACTGCC 59.309 41.667 0.00 0.00 0.00 4.85
34 35 4.932200 GCGAAATATGAAGCTATACTGCCT 59.068 41.667 0.00 0.00 0.00 4.75
35 36 6.100004 GCGAAATATGAAGCTATACTGCCTA 58.900 40.000 0.00 0.00 0.00 3.93
36 37 6.590292 GCGAAATATGAAGCTATACTGCCTAA 59.410 38.462 0.00 0.00 0.00 2.69
37 38 7.201478 GCGAAATATGAAGCTATACTGCCTAAG 60.201 40.741 0.00 0.00 0.00 2.18
38 39 7.201478 CGAAATATGAAGCTATACTGCCTAAGC 60.201 40.741 0.00 0.00 40.48 3.09
40 41 4.060038 TGAAGCTATACTGCCTAAGCAC 57.940 45.455 0.00 0.00 46.52 4.40
41 42 3.181465 TGAAGCTATACTGCCTAAGCACC 60.181 47.826 0.00 0.00 46.52 5.01
42 43 2.398588 AGCTATACTGCCTAAGCACCA 58.601 47.619 0.00 0.00 46.52 4.17
43 44 2.771943 AGCTATACTGCCTAAGCACCAA 59.228 45.455 0.00 0.00 46.52 3.67
44 45 3.199946 AGCTATACTGCCTAAGCACCAAA 59.800 43.478 0.00 0.00 46.52 3.28
45 46 4.137543 GCTATACTGCCTAAGCACCAAAT 58.862 43.478 0.00 0.00 46.52 2.32
81 82 2.040278 TGGAGGTAGCAAAACAGAGCAT 59.960 45.455 0.00 0.00 0.00 3.79
86 87 2.363788 AGCAAAACAGAGCATGCATG 57.636 45.000 22.70 22.70 41.18 4.06
87 88 1.616865 AGCAAAACAGAGCATGCATGT 59.383 42.857 26.79 20.52 41.18 3.21
88 89 2.821378 AGCAAAACAGAGCATGCATGTA 59.179 40.909 26.79 0.00 41.18 2.29
89 90 3.119602 AGCAAAACAGAGCATGCATGTAG 60.120 43.478 26.79 18.10 41.18 2.74
90 91 3.366679 GCAAAACAGAGCATGCATGTAGT 60.367 43.478 26.79 16.79 38.63 2.73
107 108 6.505272 CATGTAGTGTAGGACTAACTAAGCC 58.495 44.000 0.00 0.00 38.96 4.35
115 116 6.723052 TGTAGGACTAACTAAGCCAGTTACTT 59.277 38.462 4.77 0.00 45.93 2.24
117 118 5.778750 AGGACTAACTAAGCCAGTTACTTGA 59.221 40.000 4.77 0.00 45.93 3.02
118 119 6.440965 AGGACTAACTAAGCCAGTTACTTGAT 59.559 38.462 4.77 0.00 45.93 2.57
119 120 6.757478 GGACTAACTAAGCCAGTTACTTGATC 59.243 42.308 4.77 0.00 45.93 2.92
120 121 7.241042 ACTAACTAAGCCAGTTACTTGATCA 57.759 36.000 4.77 0.00 45.93 2.92
121 122 7.097834 ACTAACTAAGCCAGTTACTTGATCAC 58.902 38.462 0.00 0.00 45.93 3.06
122 123 5.746990 ACTAAGCCAGTTACTTGATCACT 57.253 39.130 0.00 0.00 31.59 3.41
123 124 6.852420 ACTAAGCCAGTTACTTGATCACTA 57.148 37.500 0.00 0.00 31.59 2.74
124 125 6.631962 ACTAAGCCAGTTACTTGATCACTAC 58.368 40.000 0.00 0.00 31.59 2.73
128 166 4.433615 CCAGTTACTTGATCACTACGCAT 58.566 43.478 0.00 0.00 0.00 4.73
224 262 5.895636 ATGTCGTGAATATGCCAAAAAGA 57.104 34.783 0.00 0.00 0.00 2.52
323 369 2.271497 CCTCAAGCCAGGAGCCAG 59.729 66.667 0.00 0.00 45.47 4.85
420 466 0.104855 CCCCGAAGAATCTGCGATGA 59.895 55.000 13.05 0.00 33.75 2.92
435 485 2.906182 GATGAGATGTGCCGCGACCA 62.906 60.000 8.23 0.33 0.00 4.02
437 487 3.649277 GAGATGTGCCGCGACCACT 62.649 63.158 23.55 13.34 34.38 4.00
592 642 4.734652 AACCCATGGTTGGTAGCG 57.265 55.556 11.73 0.00 45.07 4.26
927 989 1.849692 TGCCTAAGCCATCCACCATTA 59.150 47.619 0.00 0.00 38.69 1.90
968 1030 3.059044 GCACATCGTAGTGTTCGTGTTAG 59.941 47.826 10.67 0.00 41.52 2.34
969 1031 4.469552 CACATCGTAGTGTTCGTGTTAGA 58.530 43.478 2.54 0.00 34.83 2.10
984 1046 4.804139 CGTGTTAGAGAGAGAGAGAGAGAC 59.196 50.000 0.00 0.00 0.00 3.36
1072 1138 6.934056 AGTTAGGAAATAACAATGCATGCAA 58.066 32.000 26.68 8.17 45.34 4.08
1137 1203 1.140312 TCAGCTGGGACTTGGTTTCT 58.860 50.000 15.13 0.00 0.00 2.52
1215 1319 4.853468 TGGTTCTAGCATATGGGTGAAA 57.147 40.909 4.56 0.00 0.00 2.69
1216 1320 4.780815 TGGTTCTAGCATATGGGTGAAAG 58.219 43.478 4.56 0.00 0.00 2.62
1217 1321 3.565902 GGTTCTAGCATATGGGTGAAAGC 59.434 47.826 4.56 0.00 0.00 3.51
1218 1322 4.455606 GTTCTAGCATATGGGTGAAAGCT 58.544 43.478 4.56 0.00 36.20 3.74
1370 1498 7.713750 ACTTTCAAGTTAGTTAAAGGCTTTCC 58.286 34.615 17.13 8.55 35.21 3.13
1406 1534 3.551846 CGATATTGGGTTAGCTTGGGTT 58.448 45.455 0.00 0.00 0.00 4.11
1489 1627 3.314913 TCGGCTTGCACATATTTATGGTG 59.685 43.478 2.85 0.00 38.00 4.17
1601 1825 5.831997 AGTTGTTATTTGTTTCCTGCAGAC 58.168 37.500 17.39 6.14 0.00 3.51
1623 1847 3.515502 CCTCATCAACTAGTTCAGGTCCA 59.484 47.826 4.77 0.00 0.00 4.02
1681 1905 2.233271 AGAAGAACGTCACCGAGGTAA 58.767 47.619 0.00 0.00 37.88 2.85
1685 1909 4.789012 AGAACGTCACCGAGGTAATAAA 57.211 40.909 0.00 0.00 37.88 1.40
1686 1910 5.334724 AGAACGTCACCGAGGTAATAAAT 57.665 39.130 0.00 0.00 37.88 1.40
1687 1911 5.727434 AGAACGTCACCGAGGTAATAAATT 58.273 37.500 0.00 0.00 37.88 1.82
1693 2223 6.019318 CGTCACCGAGGTAATAAATTTGTAGG 60.019 42.308 0.00 0.00 35.63 3.18
1744 2282 8.589335 TTTTGACAGTGACATCTCTTTAGTAC 57.411 34.615 0.00 0.00 0.00 2.73
1811 2349 6.166984 TCTCATTTCATCTAACCAGCTAGG 57.833 41.667 0.00 0.00 45.67 3.02
2004 2543 0.812549 AAACGCCGTTCACCAACTTT 59.187 45.000 1.60 0.00 0.00 2.66
2032 2571 3.256631 CCTCACCCAAGGTTCATTTCAAG 59.743 47.826 0.00 0.00 31.02 3.02
2034 2573 2.629617 CACCCAAGGTTCATTTCAAGCT 59.370 45.455 0.00 0.00 35.59 3.74
2082 2625 5.789643 AACAGATGTAGCACAAATTGGTT 57.210 34.783 0.00 0.00 37.13 3.67
2084 2627 6.892658 ACAGATGTAGCACAAATTGGTTAA 57.107 33.333 0.00 0.00 37.13 2.01
2087 2630 7.867403 ACAGATGTAGCACAAATTGGTTAAAAG 59.133 33.333 0.00 0.00 37.13 2.27
2096 2639 5.920273 ACAAATTGGTTAAAAGATGCAGACG 59.080 36.000 0.00 0.00 0.00 4.18
2101 2644 3.125316 GGTTAAAAGATGCAGACGAGTGG 59.875 47.826 0.00 0.00 0.00 4.00
2255 2802 6.157904 CACATTCACTTTGCCATAACAATGA 58.842 36.000 0.00 0.00 0.00 2.57
2256 2803 6.814644 CACATTCACTTTGCCATAACAATGAT 59.185 34.615 0.00 0.00 0.00 2.45
2326 2878 7.395190 ACAGATTGCAAGCAAGATAAATACA 57.605 32.000 18.24 0.00 39.47 2.29
2362 2914 4.504461 CGGAGATTTGAGGACAAGTTATCG 59.496 45.833 0.00 0.00 37.32 2.92
2463 3096 1.142748 GGTGATGGAGGAGCGTGAG 59.857 63.158 0.00 0.00 0.00 3.51
2621 3254 8.344831 TGAGCAAACTTATCATTAATCAATCGG 58.655 33.333 0.00 0.00 0.00 4.18
2646 3279 6.238953 GCTAATAAGTGGGTCACTCGATCTAA 60.239 42.308 0.75 0.00 44.62 2.10
2657 3294 4.395231 TCACTCGATCTAACACTAGGTGTG 59.605 45.833 4.02 0.00 46.79 3.82
2869 3940 5.044919 AGGAACAAAGATGGACATACATGGA 60.045 40.000 0.00 0.00 0.00 3.41
2870 3941 5.652014 GGAACAAAGATGGACATACATGGAA 59.348 40.000 0.00 0.00 0.00 3.53
2871 3942 6.322201 GGAACAAAGATGGACATACATGGAAT 59.678 38.462 0.00 0.00 0.00 3.01
2872 3943 7.502226 GGAACAAAGATGGACATACATGGAATA 59.498 37.037 0.00 0.00 0.00 1.75
2873 3944 9.071276 GAACAAAGATGGACATACATGGAATAT 57.929 33.333 0.00 0.00 0.00 1.28
2874 3945 8.400184 ACAAAGATGGACATACATGGAATATG 57.600 34.615 0.00 0.00 36.32 1.78
2875 3946 7.449395 ACAAAGATGGACATACATGGAATATGG 59.551 37.037 0.00 0.00 34.83 2.74
2876 3947 5.503927 AGATGGACATACATGGAATATGGC 58.496 41.667 0.00 0.00 37.33 4.40
3079 4153 2.489329 CCGTACGTGAAGGGAAGAACTA 59.511 50.000 15.21 0.00 0.00 2.24
3081 4155 4.381292 CCGTACGTGAAGGGAAGAACTATT 60.381 45.833 15.21 0.00 0.00 1.73
3085 4159 6.313744 ACGTGAAGGGAAGAACTATTTTTG 57.686 37.500 0.00 0.00 0.00 2.44
3086 4160 5.154222 CGTGAAGGGAAGAACTATTTTTGC 58.846 41.667 0.00 0.00 0.00 3.68
3180 4264 5.038683 TCGTACGTAGTGCCAATATTCAAG 58.961 41.667 16.05 0.00 45.73 3.02
3282 4367 6.275335 TGATTTCTCTTGCTTTGTTCCTTTG 58.725 36.000 0.00 0.00 0.00 2.77
3290 4375 4.367450 TGCTTTGTTCCTTTGAATTTCGG 58.633 39.130 0.00 0.00 31.98 4.30
3369 4458 1.083489 TGCATGCTGGCTTTACGTAC 58.917 50.000 20.33 0.00 34.04 3.67
3390 4479 1.542030 GTGTGTCTCTCGATCTGGTGT 59.458 52.381 0.00 0.00 0.00 4.16
3393 4482 1.067565 TGTCTCTCGATCTGGTGTTGC 60.068 52.381 0.00 0.00 0.00 4.17
3413 4502 3.312421 TGCTAATGATAAAAGCTCCGCAC 59.688 43.478 0.00 0.00 37.16 5.34
3476 4568 0.397941 CCAGGAGCAGTGAAGAACCA 59.602 55.000 0.00 0.00 0.00 3.67
3477 4569 1.004044 CCAGGAGCAGTGAAGAACCAT 59.996 52.381 0.00 0.00 0.00 3.55
3478 4570 2.082231 CAGGAGCAGTGAAGAACCATG 58.918 52.381 0.00 0.00 0.00 3.66
3479 4571 1.701847 AGGAGCAGTGAAGAACCATGT 59.298 47.619 0.00 0.00 0.00 3.21
3513 4605 3.002656 CCTCGTTTGATATCCATGTGTGC 59.997 47.826 0.00 0.00 0.00 4.57
3639 4735 1.033746 CAACCCAGGCATGCTCGATT 61.034 55.000 18.92 3.36 0.00 3.34
3715 4811 8.221766 GGGATTTTCTTTCTATCGTTTATAGCG 58.778 37.037 0.00 0.00 37.98 4.26
3740 5100 2.873170 TTGTATTTCGTGCTTGCTCG 57.127 45.000 10.28 10.28 0.00 5.03
3901 5266 4.553330 ACTAATAGTAATGCCCGGATGG 57.447 45.455 0.73 0.00 37.09 3.51
3902 5267 8.939630 TCTAACTAATAGTAATGCCCGGATGGG 61.940 44.444 0.73 0.00 44.47 4.00
4026 5391 4.385825 TCCAAAATGTATGTATCCGAGGC 58.614 43.478 0.00 0.00 0.00 4.70
4030 5395 4.955811 AATGTATGTATCCGAGGCTTGA 57.044 40.909 2.43 0.00 0.00 3.02
4031 5396 3.728076 TGTATGTATCCGAGGCTTGAC 57.272 47.619 2.43 0.00 0.00 3.18
4032 5397 3.028130 TGTATGTATCCGAGGCTTGACA 58.972 45.455 2.43 0.00 0.00 3.58
4033 5398 3.449377 TGTATGTATCCGAGGCTTGACAA 59.551 43.478 2.43 0.00 0.00 3.18
4034 5399 2.380084 TGTATCCGAGGCTTGACAAC 57.620 50.000 2.43 0.00 0.00 3.32
4035 5400 1.278238 GTATCCGAGGCTTGACAACG 58.722 55.000 2.43 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.810658 AGCTTCATATTTCGCACATAATTAGG 58.189 34.615 0.00 0.00 0.00 2.69
4 5 9.658799 AGTATAGCTTCATATTTCGCACATAAT 57.341 29.630 0.00 0.00 0.00 1.28
5 6 8.925700 CAGTATAGCTTCATATTTCGCACATAA 58.074 33.333 0.00 0.00 0.00 1.90
6 7 7.063426 GCAGTATAGCTTCATATTTCGCACATA 59.937 37.037 0.00 0.00 0.00 2.29
7 8 6.128445 GCAGTATAGCTTCATATTTCGCACAT 60.128 38.462 0.00 0.00 0.00 3.21
8 9 5.177511 GCAGTATAGCTTCATATTTCGCACA 59.822 40.000 0.00 0.00 0.00 4.57
9 10 5.389935 GGCAGTATAGCTTCATATTTCGCAC 60.390 44.000 0.00 0.00 34.17 5.34
10 11 4.690748 GGCAGTATAGCTTCATATTTCGCA 59.309 41.667 0.00 0.00 34.17 5.10
11 12 4.932200 AGGCAGTATAGCTTCATATTTCGC 59.068 41.667 0.00 0.00 34.17 4.70
12 13 7.201478 GCTTAGGCAGTATAGCTTCATATTTCG 60.201 40.741 0.00 0.00 38.54 3.46
13 14 7.604164 TGCTTAGGCAGTATAGCTTCATATTTC 59.396 37.037 0.00 0.00 44.28 2.17
14 15 7.453393 TGCTTAGGCAGTATAGCTTCATATTT 58.547 34.615 0.00 0.00 44.28 1.40
15 16 7.009179 TGCTTAGGCAGTATAGCTTCATATT 57.991 36.000 0.00 0.00 44.28 1.28
16 17 6.611613 TGCTTAGGCAGTATAGCTTCATAT 57.388 37.500 0.00 0.00 44.28 1.78
18 19 4.963318 TGCTTAGGCAGTATAGCTTCAT 57.037 40.909 0.00 0.00 44.28 2.57
31 32 3.761752 TGGTTCTAATTTGGTGCTTAGGC 59.238 43.478 0.00 0.00 39.26 3.93
32 33 4.142381 GCTGGTTCTAATTTGGTGCTTAGG 60.142 45.833 0.00 0.00 0.00 2.69
33 34 4.702131 AGCTGGTTCTAATTTGGTGCTTAG 59.298 41.667 0.00 0.00 0.00 2.18
34 35 4.662278 AGCTGGTTCTAATTTGGTGCTTA 58.338 39.130 0.00 0.00 0.00 3.09
35 36 3.500343 AGCTGGTTCTAATTTGGTGCTT 58.500 40.909 0.00 0.00 0.00 3.91
36 37 3.160679 AGCTGGTTCTAATTTGGTGCT 57.839 42.857 0.00 0.00 0.00 4.40
37 38 3.181496 GCTAGCTGGTTCTAATTTGGTGC 60.181 47.826 7.70 0.00 0.00 5.01
38 39 4.095483 CAGCTAGCTGGTTCTAATTTGGTG 59.905 45.833 33.06 5.98 40.17 4.17
39 40 4.265073 CAGCTAGCTGGTTCTAATTTGGT 58.735 43.478 33.06 0.00 40.17 3.67
40 41 4.889832 CAGCTAGCTGGTTCTAATTTGG 57.110 45.455 33.06 6.16 40.17 3.28
81 82 6.405508 GCTTAGTTAGTCCTACACTACATGCA 60.406 42.308 0.00 0.00 37.32 3.96
86 87 5.651576 ACTGGCTTAGTTAGTCCTACACTAC 59.348 44.000 0.00 0.00 37.32 2.73
87 88 5.824421 ACTGGCTTAGTTAGTCCTACACTA 58.176 41.667 0.00 0.00 35.67 2.74
88 89 4.675038 ACTGGCTTAGTTAGTCCTACACT 58.325 43.478 0.00 0.00 35.67 3.55
107 108 6.266323 ACTATGCGTAGTGATCAAGTAACTG 58.734 40.000 17.85 0.00 39.66 3.16
128 166 0.461870 CCTGCGGCACAGCATTACTA 60.462 55.000 0.00 0.00 46.97 1.82
224 262 3.693807 AGCCATGATTGTTGTGTCTCAT 58.306 40.909 0.00 0.00 0.00 2.90
323 369 1.821216 TGCTAGCTTGCCAGGTTAAC 58.179 50.000 17.57 0.00 31.45 2.01
420 466 3.695606 AGTGGTCGCGGCACATCT 61.696 61.111 14.93 1.29 0.00 2.90
435 485 3.881092 CTCGTCGCACGCACTCAGT 62.881 63.158 4.15 0.00 42.21 3.41
437 487 3.189010 TTCTCGTCGCACGCACTCA 62.189 57.895 4.15 0.00 42.21 3.41
683 739 1.737793 CTAAGCCCACGTCCAAATCAC 59.262 52.381 0.00 0.00 0.00 3.06
782 838 2.683362 GGTGGTAGGTTTCAAGCATAGC 59.317 50.000 0.00 0.00 0.00 2.97
783 839 3.950397 TGGTGGTAGGTTTCAAGCATAG 58.050 45.455 0.00 0.00 0.00 2.23
784 840 4.584638 ATGGTGGTAGGTTTCAAGCATA 57.415 40.909 0.00 0.00 0.00 3.14
785 841 2.969821 TGGTGGTAGGTTTCAAGCAT 57.030 45.000 0.00 0.00 0.00 3.79
786 842 2.969821 ATGGTGGTAGGTTTCAAGCA 57.030 45.000 0.00 0.00 0.00 3.91
879 941 8.686334 CCAATAGTTGCACCATTTTATAGAACT 58.314 33.333 0.00 0.00 0.00 3.01
880 942 8.466798 ACCAATAGTTGCACCATTTTATAGAAC 58.533 33.333 0.00 0.00 0.00 3.01
881 943 8.588290 ACCAATAGTTGCACCATTTTATAGAA 57.412 30.769 0.00 0.00 0.00 2.10
927 989 0.813184 CCGAATGCAAGCTGGAACAT 59.187 50.000 0.00 0.00 38.20 2.71
955 1017 4.643463 TCTCTCTCTCTAACACGAACACT 58.357 43.478 0.00 0.00 0.00 3.55
968 1030 4.646945 TCTCTCTGTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
969 1031 4.614475 TCTCTCTGTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
984 1046 1.270412 GCCATGGATGAGCTCTCTCTG 60.270 57.143 18.40 10.58 40.03 3.35
1059 1121 1.286354 GCGTGCTTGCATGCATTGTT 61.286 50.000 27.53 0.00 45.23 2.83
1137 1203 0.676466 CAATGCACGTCTAAGGGCCA 60.676 55.000 6.18 0.00 40.47 5.36
1215 1319 3.549221 GCGAAGTCGATCTTAAGCTAGCT 60.549 47.826 12.68 12.68 43.02 3.32
1216 1320 2.722116 GCGAAGTCGATCTTAAGCTAGC 59.278 50.000 6.62 6.62 43.02 3.42
1217 1321 3.003897 AGGCGAAGTCGATCTTAAGCTAG 59.996 47.826 4.59 0.00 43.02 3.42
1218 1322 2.950309 AGGCGAAGTCGATCTTAAGCTA 59.050 45.455 4.59 0.00 43.02 3.32
1389 1517 3.252554 TGAAACCCAAGCTAACCCAAT 57.747 42.857 0.00 0.00 0.00 3.16
1601 1825 3.515502 TGGACCTGAACTAGTTGATGAGG 59.484 47.826 14.14 14.09 0.00 3.86
1623 1847 1.043022 CACTCCTTGCTGGGCTTTTT 58.957 50.000 0.00 0.00 36.20 1.94
1681 1905 6.935741 TGCGCTACATTCCTACAAATTTAT 57.064 33.333 9.73 0.00 0.00 1.40
1685 1909 4.708177 AGATGCGCTACATTCCTACAAAT 58.292 39.130 9.73 0.00 39.84 2.32
1686 1910 4.119862 GAGATGCGCTACATTCCTACAAA 58.880 43.478 9.73 0.00 39.84 2.83
1687 1911 3.384789 AGAGATGCGCTACATTCCTACAA 59.615 43.478 9.73 0.00 39.84 2.41
1693 2223 5.293079 AGAAAAGAAGAGATGCGCTACATTC 59.707 40.000 9.73 10.76 39.84 2.67
1744 2282 4.398358 TCAGTCCCATCTCTTTAGTGTACG 59.602 45.833 0.00 0.00 0.00 3.67
1881 2419 9.512435 GACGTACTGAGATAATTAGCTTAAACA 57.488 33.333 4.45 0.00 0.00 2.83
1882 2420 8.966194 GGACGTACTGAGATAATTAGCTTAAAC 58.034 37.037 4.45 1.86 0.00 2.01
1883 2421 8.910944 AGGACGTACTGAGATAATTAGCTTAAA 58.089 33.333 0.00 0.00 0.00 1.52
1886 2424 6.963083 AGGACGTACTGAGATAATTAGCTT 57.037 37.500 0.00 0.00 0.00 3.74
1887 2425 6.963083 AAGGACGTACTGAGATAATTAGCT 57.037 37.500 0.00 2.14 0.00 3.32
1904 2443 1.566018 GGTCGTGCCTGAAAAGGACG 61.566 60.000 0.00 0.00 35.43 4.79
1990 2529 3.379057 AGGTTTGTAAAGTTGGTGAACGG 59.621 43.478 0.00 0.00 37.15 4.44
2056 2596 5.509501 CCAATTTGTGCTACATCTGTTTGGT 60.510 40.000 0.00 0.00 0.00 3.67
2059 2599 5.789643 ACCAATTTGTGCTACATCTGTTT 57.210 34.783 0.00 0.00 0.00 2.83
2082 2625 2.346803 GCCACTCGTCTGCATCTTTTA 58.653 47.619 0.00 0.00 0.00 1.52
2084 2627 0.674895 GGCCACTCGTCTGCATCTTT 60.675 55.000 0.00 0.00 0.00 2.52
2087 2630 1.812922 CAGGCCACTCGTCTGCATC 60.813 63.158 5.01 0.00 0.00 3.91
2096 2639 4.943705 TCATATGAAACTTTCAGGCCACTC 59.056 41.667 5.01 0.00 43.98 3.51
2101 2644 7.118101 TGCAAAATTCATATGAAACTTTCAGGC 59.882 33.333 21.50 19.55 43.98 4.85
2191 2738 3.343941 TTGTAACCAGCTCGCCTTATT 57.656 42.857 0.00 0.00 0.00 1.40
2326 2878 6.995091 CCTCAAATCTCCGAATAATTTCCTCT 59.005 38.462 0.00 0.00 0.00 3.69
2362 2914 3.438781 TCCGAAATGTGTTATTCACCTGC 59.561 43.478 0.00 0.00 45.61 4.85
2425 3031 6.607019 TCACCTATTGGTAAAAGAAACCTGT 58.393 36.000 0.00 0.00 46.60 4.00
2463 3096 5.804944 TCTCCTTCCTCATCATCTTGATC 57.195 43.478 0.00 0.00 34.28 2.92
2621 3254 3.795623 TCGAGTGACCCACTTATTAGC 57.204 47.619 0.82 0.00 45.44 3.09
2626 3259 4.157289 GTGTTAGATCGAGTGACCCACTTA 59.843 45.833 0.82 0.00 45.44 2.24
2657 3294 6.757897 TCATTAATGTCCACATTCTGTTCC 57.242 37.500 14.97 0.00 44.67 3.62
2756 3547 5.393962 CCACTTTGTGTACTACTACGTACC 58.606 45.833 0.00 0.00 39.14 3.34
2757 3548 5.393962 CCCACTTTGTGTACTACTACGTAC 58.606 45.833 0.00 0.00 40.06 3.67
2759 3550 3.256631 CCCCACTTTGTGTACTACTACGT 59.743 47.826 0.00 0.00 0.00 3.57
2760 3551 3.367703 CCCCCACTTTGTGTACTACTACG 60.368 52.174 0.00 0.00 0.00 3.51
2784 3581 6.320171 TCGCTAACTGCTTGTTAACTACTAG 58.680 40.000 7.22 3.47 40.24 2.57
2785 3582 6.258230 TCGCTAACTGCTTGTTAACTACTA 57.742 37.500 7.22 0.00 40.24 1.82
2786 3583 5.130292 TCGCTAACTGCTTGTTAACTACT 57.870 39.130 7.22 0.00 40.24 2.57
2787 3584 7.434307 TCATATCGCTAACTGCTTGTTAACTAC 59.566 37.037 7.22 0.00 40.24 2.73
2869 3940 7.436080 GTCACAATTTCATTCAATCGCCATATT 59.564 33.333 0.00 0.00 0.00 1.28
2870 3941 6.919662 GTCACAATTTCATTCAATCGCCATAT 59.080 34.615 0.00 0.00 0.00 1.78
2871 3942 6.264832 GTCACAATTTCATTCAATCGCCATA 58.735 36.000 0.00 0.00 0.00 2.74
2872 3943 5.104374 GTCACAATTTCATTCAATCGCCAT 58.896 37.500 0.00 0.00 0.00 4.40
2873 3944 4.484236 GTCACAATTTCATTCAATCGCCA 58.516 39.130 0.00 0.00 0.00 5.69
2874 3945 3.543494 CGTCACAATTTCATTCAATCGCC 59.457 43.478 0.00 0.00 0.00 5.54
2875 3946 4.158384 ACGTCACAATTTCATTCAATCGC 58.842 39.130 0.00 0.00 0.00 4.58
2876 3947 5.850653 TCAACGTCACAATTTCATTCAATCG 59.149 36.000 0.00 0.00 0.00 3.34
3079 4153 4.073052 TGACGGAGCGGCAAAAAT 57.927 50.000 1.45 0.00 44.01 1.82
3085 4159 2.125512 ATCAACTGACGGAGCGGC 60.126 61.111 0.00 0.00 34.27 6.53
3086 4160 1.079819 ACATCAACTGACGGAGCGG 60.080 57.895 0.00 0.00 0.00 5.52
3159 4243 4.317839 CGCTTGAATATTGGCACTACGTAC 60.318 45.833 0.00 0.00 0.00 3.67
3269 4354 3.184379 GCCGAAATTCAAAGGAACAAAGC 59.816 43.478 0.00 0.00 35.46 3.51
3282 4367 5.416947 TCCTAGTCTTTAGTGCCGAAATTC 58.583 41.667 0.00 0.00 0.00 2.17
3290 4375 7.349412 TCTTTATCCTCCTAGTCTTTAGTGC 57.651 40.000 0.00 0.00 0.00 4.40
3369 4458 0.805614 ACCAGATCGAGAGACACACG 59.194 55.000 0.00 0.00 46.97 4.49
3413 4502 1.195448 GACGACACTCATGGTTGCAAG 59.805 52.381 0.00 0.00 0.00 4.01
3476 4568 3.475566 ACGAGGTAAGCATGCATACAT 57.524 42.857 28.47 24.15 36.79 2.29
3477 4569 2.979814 ACGAGGTAAGCATGCATACA 57.020 45.000 28.47 6.00 0.00 2.29
3478 4570 3.621268 TCAAACGAGGTAAGCATGCATAC 59.379 43.478 21.83 21.83 0.00 2.39
3479 4571 3.867857 TCAAACGAGGTAAGCATGCATA 58.132 40.909 21.98 9.95 0.00 3.14
3513 4605 2.164422 TGTATGCCTCTCAGAGAACACG 59.836 50.000 2.09 0.00 0.00 4.49
3611 4707 1.631405 TGCCTGGGTTGAAATTCAGG 58.369 50.000 4.60 4.60 46.93 3.86
3653 4749 4.819630 TCCAATTCCGTGGAAAGCATATAC 59.180 41.667 5.27 0.00 44.91 1.47
3715 4811 3.730715 GCAAGCACGAAATACAATATGGC 59.269 43.478 0.00 0.00 0.00 4.40
3740 5100 3.300667 CTTGCGTCAGCTTGTCGGC 62.301 63.158 0.00 0.00 45.42 5.54
3796 5156 2.514824 CCCTGCCTTTCGCTAGCC 60.515 66.667 9.66 0.00 38.78 3.93
3904 5269 1.860950 CCTCCATCTTTCACGTATGCG 59.139 52.381 0.19 0.19 44.93 4.73
3905 5270 2.158957 TCCCTCCATCTTTCACGTATGC 60.159 50.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.