Multiple sequence alignment - TraesCS7D01G172300

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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 TraesCS7D01G172300 chr7D 100.000 5621 0 0 1 5621 124523254 124517634 0.000000e+00 10381.0
1 TraesCS7D01G172300 chr7B 93.805 4859 172 48 821 5621 86229571 86224784 0.000000e+00 7186.0
2 TraesCS7D01G172300 chr7A 93.351 3023 135 31 740 3725 126949204 126946211 0.000000e+00 4409.0
3 TraesCS7D01G172300 chr7A 93.805 1372 39 14 3818 5151 126946179 126944816 0.000000e+00 2021.0
4 TraesCS7D01G172300 chr7A 87.842 732 56 16 1 705 126950411 126949686 0.000000e+00 828.0
5 TraesCS7D01G172300 chr7A 92.920 452 21 6 5174 5621 126944484 126944040 0.000000e+00 647.0
6 TraesCS7D01G172300 chr7A 87.562 201 22 2 1170 1370 599065052 599064855 4.380000e-56 230.0
7 TraesCS7D01G172300 chr7A 91.195 159 14 0 1212 1370 71602007 71601849 3.410000e-52 217.0
8 TraesCS7D01G172300 chr7A 84.270 89 10 2 3679 3764 437764 437677 3.610000e-12 84.2
9 TraesCS7D01G172300 chr2A 84.615 273 25 12 1029 1301 675368273 675368018 7.230000e-64 255.0
10 TraesCS7D01G172300 chr3A 81.288 326 38 16 1048 1369 698038491 698038797 5.630000e-60 243.0
11 TraesCS7D01G172300 chr3A 85.981 214 26 3 1158 1370 680168634 680168424 5.670000e-55 226.0
12 TraesCS7D01G172300 chr3A 81.250 96 14 4 3680 3773 147790966 147790873 2.170000e-09 75.0
13 TraesCS7D01G172300 chr3A 87.302 63 6 2 3329 3391 66225392 66225452 2.810000e-08 71.3
14 TraesCS7D01G172300 chr1A 80.233 344 32 13 1029 1372 425580767 425581074 5.670000e-55 226.0
15 TraesCS7D01G172300 chr6A 84.878 205 27 3 1158 1361 16324937 16325138 2.650000e-48 204.0
16 TraesCS7D01G172300 chr1B 90.588 85 5 2 3680 3764 502803805 502803886 5.950000e-20 110.0
17 TraesCS7D01G172300 chr1B 88.710 62 6 1 3327 3387 205875690 205875751 2.170000e-09 75.0
18 TraesCS7D01G172300 chr1B 88.525 61 5 2 3328 3387 675255057 675254998 7.810000e-09 73.1
19 TraesCS7D01G172300 chr1B 88.525 61 4 3 3328 3387 544715351 544715293 2.810000e-08 71.3
20 TraesCS7D01G172300 chr6B 88.043 92 10 1 3680 3771 68850643 68850733 2.140000e-19 108.0
21 TraesCS7D01G172300 chr5A 96.552 58 2 0 1314 1371 131654089 131654146 4.640000e-16 97.1
22 TraesCS7D01G172300 chr1D 83.810 105 10 6 3660 3764 376260310 376260407 6.000000e-15 93.5
23 TraesCS7D01G172300 chr1D 89.189 74 5 2 3691 3764 376239716 376239786 7.760000e-14 89.8
24 TraesCS7D01G172300 chr1D 87.179 78 5 4 3695 3770 376255174 376255248 3.610000e-12 84.2
25 TraesCS7D01G172300 chr4A 84.091 88 11 1 3680 3764 744387282 744387369 1.300000e-11 82.4
26 TraesCS7D01G172300 chr3D 88.889 63 4 2 3329 3391 57158550 57158609 2.170000e-09 75.0
27 TraesCS7D01G172300 chr3B 87.500 64 6 2 3329 3392 90115653 90115714 7.810000e-09 73.1
28 TraesCS7D01G172300 chr6D 88.525 61 4 3 3327 3386 316281816 316281874 2.810000e-08 71.3


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 TraesCS7D01G172300 chr7D 124517634 124523254 5620 True 10381.00 10381 100.0000 1 5621 1 chr7D.!!$R1 5620
1 TraesCS7D01G172300 chr7B 86224784 86229571 4787 True 7186.00 7186 93.8050 821 5621 1 chr7B.!!$R1 4800
2 TraesCS7D01G172300 chr7A 126944040 126950411 6371 True 1976.25 4409 91.9795 1 5621 4 chr7A.!!$R4 5620

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
285 295 0.321653 CCAGACCTGTTGGCACCTAC 60.322 60.000 0.00 0.0 36.63 3.18 F
307 317 0.895100 TGAGACAAATGGGTGCTGCC 60.895 55.000 0.00 0.0 0.00 4.85 F
412 422 1.211457 AGGTGGCTGATTCCTGATCAC 59.789 52.381 0.00 0.0 39.83 3.06 F
1424 1916 1.212935 ACACCTGCTGGTTTTGACTCT 59.787 47.619 13.36 0.0 46.05 3.24 F
2296 2810 1.003696 CCCACCCTTTCCTGTCTCTTC 59.996 57.143 0.00 0.0 0.00 2.87 F
3318 3835 0.692476 ACCACTAGCATGCCAACAGA 59.308 50.000 15.66 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 1999 0.519961 GCGTAATCGGCACCACTTTT 59.480 50.000 0.00 0.00 37.56 2.27 R
1669 2163 1.144969 CTTTCGTACTTCTGCCGCAA 58.855 50.000 0.00 0.00 0.00 4.85 R
1925 2425 1.305201 CTTACAACCGTGCCAACTGT 58.695 50.000 0.00 0.00 0.00 3.55 R
2540 3054 2.030185 GGACTGATCGGCGCTATCTAAA 60.030 50.000 19.30 4.12 0.00 1.85 R
3426 3947 0.178955 TACCGTTGGTCTGTGGAGGA 60.179 55.000 0.00 0.00 37.09 3.71 R
4994 5576 1.134175 GATAAACCCAACCATGGCACG 59.866 52.381 13.04 0.00 46.09 5.34 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
23 24 2.482374 GCATCAGTGCGAGTTGCC 59.518 61.111 0.00 0.00 45.60 4.52
53 54 0.322456 CCCATCGTGCTTCAAAGGGA 60.322 55.000 0.00 0.00 36.96 4.20
96 97 0.877071 CGAGGCTCAATGTTGCAAGT 59.123 50.000 15.95 0.00 0.00 3.16
98 99 2.483877 CGAGGCTCAATGTTGCAAGTTA 59.516 45.455 15.95 0.00 0.00 2.24
113 122 3.364964 GCAAGTTAACGCTACAAGCATGT 60.365 43.478 0.00 0.00 42.58 3.21
156 165 1.646540 CCGTTGTGCTTCTTTGCGA 59.353 52.632 0.00 0.00 35.36 5.10
159 168 1.530852 CGTTGTGCTTCTTTGCGACAA 60.531 47.619 0.00 0.00 34.36 3.18
164 173 2.013400 TGCTTCTTTGCGACAAGAACA 58.987 42.857 5.58 6.64 35.36 3.18
167 176 3.605692 GCTTCTTTGCGACAAGAACAGAG 60.606 47.826 5.58 0.00 32.23 3.35
170 179 1.662517 TTGCGACAAGAACAGAGCAA 58.337 45.000 0.00 0.00 41.48 3.91
182 191 3.883830 ACAGAGCAATAGAGTGTCAGG 57.116 47.619 0.00 0.00 0.00 3.86
209 218 3.058160 GCAGGGCGTCTGTTGCAT 61.058 61.111 6.79 0.00 45.08 3.96
217 226 1.069022 GCGTCTGTTGCATGTCATTGT 60.069 47.619 0.00 0.00 0.00 2.71
221 230 1.717113 CTGTTGCATGTCATTGTTGCG 59.283 47.619 0.00 0.00 39.23 4.85
229 238 2.096406 CATTGTTGCGAGTCGGCG 59.904 61.111 15.52 0.00 35.06 6.46
250 260 2.751688 GCGGGGTGGGTCTTGTTA 59.248 61.111 0.00 0.00 0.00 2.41
251 261 1.673337 GCGGGGTGGGTCTTGTTAC 60.673 63.158 0.00 0.00 0.00 2.50
280 290 0.976641 CTACTCCAGACCTGTTGGCA 59.023 55.000 0.00 0.00 35.62 4.92
281 291 0.685097 TACTCCAGACCTGTTGGCAC 59.315 55.000 0.00 0.00 35.62 5.01
284 294 0.472925 TCCAGACCTGTTGGCACCTA 60.473 55.000 0.00 0.00 35.62 3.08
285 295 0.321653 CCAGACCTGTTGGCACCTAC 60.322 60.000 0.00 0.00 36.63 3.18
307 317 0.895100 TGAGACAAATGGGTGCTGCC 60.895 55.000 0.00 0.00 0.00 4.85
309 319 2.203480 ACAAATGGGTGCTGCCGT 60.203 55.556 0.00 0.00 38.44 5.68
332 342 2.357517 AGCTCGTGGTTTGCGGAG 60.358 61.111 0.00 0.00 0.00 4.63
359 369 1.599797 CGGGGGAAGTGTGTGGTTC 60.600 63.158 0.00 0.00 0.00 3.62
403 413 1.296715 GGTGTCGAGGTGGCTGATT 59.703 57.895 0.00 0.00 0.00 2.57
411 421 1.487976 GAGGTGGCTGATTCCTGATCA 59.512 52.381 0.00 0.00 42.42 2.92
412 422 1.211457 AGGTGGCTGATTCCTGATCAC 59.789 52.381 0.00 0.00 39.83 3.06
528 542 6.033341 TGAATATGTTTTAAAGGTGCGATGC 58.967 36.000 0.00 0.00 0.00 3.91
615 643 6.447084 ACATCCTTAATTTTCTACTCCCTCCA 59.553 38.462 0.00 0.00 0.00 3.86
673 701 9.817809 GGATGTATCTAGACATGTGTTAGAAAA 57.182 33.333 16.47 8.55 40.18 2.29
675 703 8.997621 TGTATCTAGACATGTGTTAGAAAACC 57.002 34.615 16.47 8.50 34.49 3.27
696 724 4.421948 CCAAGAGGTAAGATACGTGTGTC 58.578 47.826 0.00 0.00 0.00 3.67
705 733 9.656040 AGGTAAGATACGTGTGTCTAGATATAG 57.344 37.037 0.00 0.00 30.59 1.31
706 734 9.650539 GGTAAGATACGTGTGTCTAGATATAGA 57.349 37.037 0.00 0.00 30.59 1.98
754 1234 9.826574 AGGTAATATTTTATTACTTGTCGCTCA 57.173 29.630 14.01 0.00 35.46 4.26
772 1252 4.383052 CGCTCAGACGGATATATGTTTCAC 59.617 45.833 0.00 0.00 0.00 3.18
780 1260 6.161381 ACGGATATATGTTTCACCGGAATAC 58.839 40.000 9.46 1.57 43.76 1.89
783 1263 6.309737 GGATATATGTTTCACCGGAATACGTC 59.690 42.308 9.46 0.00 42.24 4.34
1059 1550 4.019513 ATGTCCGACCCCTCCCCA 62.020 66.667 0.00 0.00 0.00 4.96
1061 1552 1.968541 ATGTCCGACCCCTCCCCATA 61.969 60.000 0.00 0.00 0.00 2.74
1388 1879 3.168528 CCATGTACCCCCTCCCCG 61.169 72.222 0.00 0.00 0.00 5.73
1424 1916 1.212935 ACACCTGCTGGTTTTGACTCT 59.787 47.619 13.36 0.00 46.05 3.24
1450 1944 6.183360 TGGTTTTATGCTTTTACTGACGGTTT 60.183 34.615 0.00 0.00 0.00 3.27
1505 1999 2.235761 GGTGTTAGGGAAGGGGGCA 61.236 63.158 0.00 0.00 0.00 5.36
1574 2068 3.008704 TCATGTGATAGATCATGCCAGGG 59.991 47.826 0.00 0.00 40.54 4.45
1632 2126 2.648059 CTGCAAGAGAGTTTATGGGGG 58.352 52.381 0.00 0.00 34.07 5.40
1659 2153 7.241042 TGAGGTTTATGCTGACTTAAGTAGT 57.759 36.000 8.42 0.00 40.71 2.73
1669 2163 7.667557 TGCTGACTTAAGTAGTGAGTTTATGT 58.332 34.615 8.42 0.00 39.93 2.29
1720 2219 9.277565 CAATACAAAATTAGGAACTCAATGACG 57.722 33.333 0.00 0.00 41.75 4.35
1925 2425 1.144093 CCCACACCAACCCTACTTTGA 59.856 52.381 0.00 0.00 0.00 2.69
1932 2432 2.884639 CCAACCCTACTTTGACAGTTGG 59.115 50.000 5.42 5.42 45.76 3.77
1950 2450 1.274167 TGGCACGGTTGTAAGGACTAG 59.726 52.381 0.00 0.00 0.00 2.57
2040 2554 7.390027 TGAGATAATGAGCCTCTAATTAAGCC 58.610 38.462 0.00 0.00 0.00 4.35
2052 2566 7.472543 CCTCTAATTAAGCCAATGTGTGTAAC 58.527 38.462 0.00 0.00 37.35 2.50
2216 2730 2.669364 CACTGCAGGTTTGATTCTTGC 58.331 47.619 19.93 0.00 38.17 4.01
2234 2748 6.560253 TCTTGCTGGAACTGTTTCTTATTC 57.440 37.500 0.00 0.00 31.71 1.75
2296 2810 1.003696 CCCACCCTTTCCTGTCTCTTC 59.996 57.143 0.00 0.00 0.00 2.87
2362 2876 4.701651 TCAAAGCAGTAATGCAGCAAGTAT 59.298 37.500 18.53 0.00 37.25 2.12
2382 2896 9.653287 CAAGTATAAGTTACAAGATTCCACTGA 57.347 33.333 0.00 0.00 0.00 3.41
2432 2946 4.464244 TCACCATGGTTTTGACTTTTCACA 59.536 37.500 16.84 0.00 0.00 3.58
2531 3045 3.822735 TGACTTCTTTTTCTGCATCAGGG 59.177 43.478 0.00 0.00 31.51 4.45
2540 3054 3.060479 TCTGCATCAGGGGTATAAGGT 57.940 47.619 0.00 0.00 31.51 3.50
2704 3218 2.489722 GCAAGGAAAAGTTAGAGGCCTG 59.510 50.000 12.00 0.00 0.00 4.85
3086 3603 1.499007 ACTGGTTTTGATGGTGTCCCT 59.501 47.619 0.00 0.00 0.00 4.20
3318 3835 0.692476 ACCACTAGCATGCCAACAGA 59.308 50.000 15.66 0.00 0.00 3.41
3325 3842 3.756933 AGCATGCCAACAGAAAAATGT 57.243 38.095 15.66 0.00 33.96 2.71
3326 3843 3.656559 AGCATGCCAACAGAAAAATGTC 58.343 40.909 15.66 0.00 31.50 3.06
3542 4066 6.820656 ACATCAGTTGATCAATAACACTCCTC 59.179 38.462 12.12 0.00 31.21 3.71
3689 4219 7.130099 TCTAACAGAATAACATACTCCCTCCA 58.870 38.462 0.00 0.00 0.00 3.86
3692 4222 6.595682 ACAGAATAACATACTCCCTCCAATG 58.404 40.000 0.00 0.00 0.00 2.82
3734 4278 6.761099 CTCTATACAATGTATAGAGGCCGT 57.239 41.667 38.29 11.16 44.73 5.68
3746 4290 7.051623 TGTATAGAGGCCGTGTCAATTAATTT 58.948 34.615 0.00 0.00 0.00 1.82
3806 4350 1.168714 GAGGTGGGCTTGAACACATC 58.831 55.000 0.00 0.00 40.49 3.06
3906 4457 2.019249 TGCCTCATCTTGTAATGCTGC 58.981 47.619 0.00 0.00 0.00 5.25
3947 4498 5.049680 GTGCTCAGACAAAACCGAAAGATTA 60.050 40.000 0.00 0.00 0.00 1.75
3948 4499 5.529430 TGCTCAGACAAAACCGAAAGATTAA 59.471 36.000 0.00 0.00 0.00 1.40
4106 4674 5.591877 GGATGAACTGTCCTTTGCTATGATT 59.408 40.000 0.00 0.00 32.85 2.57
4259 4827 4.779993 AGTCTTCACAACTTCCTTCCTT 57.220 40.909 0.00 0.00 0.00 3.36
4394 4962 1.203287 GCTCTCATGAAAACTTGGCCC 59.797 52.381 0.00 0.00 0.00 5.80
4448 5016 6.659242 GGATGTCTTGAAGAAAATGGAGGTAA 59.341 38.462 0.00 0.00 0.00 2.85
4490 5059 5.822204 AGATACACTCAGGACTCTTGTACT 58.178 41.667 0.00 0.00 38.01 2.73
4493 5062 4.950050 ACACTCAGGACTCTTGTACTTTG 58.050 43.478 0.00 0.00 34.53 2.77
4587 5156 4.168101 TCTTCATACCACCTGGAAAGAGT 58.832 43.478 0.00 0.00 38.94 3.24
4665 5242 5.009610 ACGGAGTTTGAGCACACATATTTTT 59.990 36.000 0.00 0.00 37.78 1.94
4717 5294 2.080286 ACTATATTAAGCCGCTGCCG 57.920 50.000 0.00 0.00 38.69 5.69
4765 5343 8.732746 AAATAATTCACGGTTAGCTCTGTAAT 57.267 30.769 0.00 0.00 0.00 1.89
4833 5411 9.692749 TTTCGCCATTGTACTCTAGAAATATAG 57.307 33.333 0.00 0.00 0.00 1.31
4994 5576 7.687941 TGAAAGAGAAAACATGATTAGGACC 57.312 36.000 0.00 0.00 0.00 4.46
5025 5610 5.044772 TGGTTGGGTTTATCATACTGCCTTA 60.045 40.000 0.00 0.00 0.00 2.69
5071 5656 4.201851 CCTCTTGCCATCAGAATTTACACG 60.202 45.833 0.00 0.00 0.00 4.49
5096 5681 4.073052 TGGTCATGCCAAACGGAC 57.927 55.556 6.42 0.00 45.94 4.79
5125 5710 7.654022 AACTTCACCAAATCTTGTTCCTTTA 57.346 32.000 0.00 0.00 0.00 1.85
5179 6074 2.880890 GGAGCGATGGAGTGCAATTTAT 59.119 45.455 0.00 0.00 0.00 1.40
5231 6132 6.824305 TCATGGAAAGAAAAGAAGATGGTC 57.176 37.500 0.00 0.00 0.00 4.02
5246 6147 2.027625 GGTCGAAGTGGAACCAGCG 61.028 63.158 0.00 0.00 37.80 5.18
5341 6244 6.437162 ACAAGAGAAATTTATAGGCTTGCCAA 59.563 34.615 14.54 0.00 35.83 4.52
5342 6245 7.039082 ACAAGAGAAATTTATAGGCTTGCCAAA 60.039 33.333 14.54 6.28 35.83 3.28
5347 6250 7.565029 AGAAATTTATAGGCTTGCCAAATAGGT 59.435 33.333 14.54 1.66 40.61 3.08
5447 6350 7.922811 GCAAACTGCTTTTAGGCTCATTTATAT 59.077 33.333 0.00 0.00 40.96 0.86
5567 6471 2.859165 TTTGCTGCTACTGCTAGGTT 57.141 45.000 0.00 0.00 40.48 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.449388 GCTCCCTTTGAAGCACGATG 59.551 55.000 0.00 0.00 0.00 3.84
37 38 1.021390 CGCTCCCTTTGAAGCACGAT 61.021 55.000 0.00 0.00 0.00 3.73
53 54 4.280494 AGCAACACCGACGACGCT 62.280 61.111 0.64 0.00 38.29 5.07
85 86 4.822036 TGTAGCGTTAACTTGCAACATT 57.178 36.364 3.71 0.00 0.00 2.71
96 97 1.392168 GCGACATGCTTGTAGCGTTAA 59.608 47.619 19.16 0.00 46.26 2.01
98 99 1.787847 GCGACATGCTTGTAGCGTT 59.212 52.632 19.16 0.00 46.26 4.84
120 129 2.629656 GCGACCACCTTTGCAGCAT 61.630 57.895 0.00 0.00 0.00 3.79
121 130 3.286751 GCGACCACCTTTGCAGCA 61.287 61.111 0.00 0.00 0.00 4.41
122 131 4.043200 GGCGACCACCTTTGCAGC 62.043 66.667 0.00 0.00 0.00 5.25
123 132 3.726517 CGGCGACCACCTTTGCAG 61.727 66.667 0.00 0.00 0.00 4.41
124 133 4.555709 ACGGCGACCACCTTTGCA 62.556 61.111 16.62 0.00 0.00 4.08
156 165 5.220710 ACACTCTATTGCTCTGTTCTTGT 57.779 39.130 0.00 0.00 0.00 3.16
159 168 4.081752 CCTGACACTCTATTGCTCTGTTCT 60.082 45.833 0.00 0.00 0.00 3.01
164 173 2.826488 ACCCTGACACTCTATTGCTCT 58.174 47.619 0.00 0.00 0.00 4.09
167 176 1.740025 GCAACCCTGACACTCTATTGC 59.260 52.381 0.00 0.00 34.77 3.56
170 179 2.026822 CCTTGCAACCCTGACACTCTAT 60.027 50.000 0.00 0.00 0.00 1.98
196 205 0.523072 AATGACATGCAACAGACGCC 59.477 50.000 0.00 0.00 0.00 5.68
207 216 1.201954 CCGACTCGCAACAATGACATG 60.202 52.381 0.00 0.00 0.00 3.21
208 217 1.078709 CCGACTCGCAACAATGACAT 58.921 50.000 0.00 0.00 0.00 3.06
209 218 1.565156 GCCGACTCGCAACAATGACA 61.565 55.000 0.00 0.00 0.00 3.58
234 243 1.375013 CGTAACAAGACCCACCCCG 60.375 63.158 0.00 0.00 0.00 5.73
239 248 1.267806 GTCGACTCGTAACAAGACCCA 59.732 52.381 8.70 0.00 0.00 4.51
240 249 1.267806 TGTCGACTCGTAACAAGACCC 59.732 52.381 17.92 0.00 0.00 4.46
241 250 2.031333 AGTGTCGACTCGTAACAAGACC 60.031 50.000 17.92 0.00 0.00 3.85
246 256 2.738846 GGAGTAGTGTCGACTCGTAACA 59.261 50.000 17.92 0.00 43.62 2.41
250 260 1.001746 TCTGGAGTAGTGTCGACTCGT 59.998 52.381 17.92 3.57 43.62 4.18
251 261 1.394227 GTCTGGAGTAGTGTCGACTCG 59.606 57.143 17.92 0.00 43.62 4.18
284 294 0.889186 GCACCCATTTGTCTCACCGT 60.889 55.000 0.00 0.00 0.00 4.83
285 295 0.606401 AGCACCCATTTGTCTCACCG 60.606 55.000 0.00 0.00 0.00 4.94
294 304 4.319133 CTACGGCAGCACCCATTT 57.681 55.556 0.00 0.00 33.26 2.32
307 317 2.814183 AAACCACGAGCTCCGCTACG 62.814 60.000 8.47 0.00 39.88 3.51
309 319 1.080093 CAAACCACGAGCTCCGCTA 60.080 57.895 8.47 0.00 39.88 4.26
343 353 2.258726 GCGAACCACACACTTCCCC 61.259 63.158 0.00 0.00 0.00 4.81
371 381 0.253327 GACACCCACCCTTCTCATCC 59.747 60.000 0.00 0.00 0.00 3.51
403 413 2.981302 CACCAGCCGTGATCAGGA 59.019 61.111 16.84 0.00 46.20 3.86
523 537 4.782156 TGTATGGAATAAAATGCGCATCG 58.218 39.130 25.53 0.00 0.00 3.84
528 542 7.413644 TGTGTGTATGTATGGAATAAAATGCG 58.586 34.615 0.00 0.00 0.00 4.73
605 633 1.368374 CTTTTGGGGTGGAGGGAGTA 58.632 55.000 0.00 0.00 0.00 2.59
675 703 5.312120 AGACACACGTATCTTACCTCTTG 57.688 43.478 0.00 0.00 0.00 3.02
705 733 9.023967 ACCTTCGTATGTATGTATTTAAACGTC 57.976 33.333 0.00 0.00 0.00 4.34
706 734 8.931385 ACCTTCGTATGTATGTATTTAAACGT 57.069 30.769 0.00 0.00 0.00 3.99
738 1218 3.441222 TCCGTCTGAGCGACAAGTAATAA 59.559 43.478 0.00 0.00 42.98 1.40
739 1219 3.011818 TCCGTCTGAGCGACAAGTAATA 58.988 45.455 0.00 0.00 42.98 0.98
740 1220 1.816835 TCCGTCTGAGCGACAAGTAAT 59.183 47.619 0.00 0.00 42.98 1.89
741 1221 1.241165 TCCGTCTGAGCGACAAGTAA 58.759 50.000 0.00 0.00 42.98 2.24
742 1222 1.460504 ATCCGTCTGAGCGACAAGTA 58.539 50.000 0.00 0.00 42.98 2.24
749 1229 4.383052 GTGAAACATATATCCGTCTGAGCG 59.617 45.833 0.00 0.00 36.32 5.03
754 1234 3.893200 TCCGGTGAAACATATATCCGTCT 59.107 43.478 0.00 0.00 39.98 4.18
757 1237 5.287752 CGTATTCCGGTGAAACATATATCCG 59.712 44.000 0.00 2.15 39.98 4.18
762 1242 4.374399 GGACGTATTCCGGTGAAACATAT 58.626 43.478 0.00 0.00 42.24 1.78
780 1260 4.280929 TGTCCCTATGAATGTATCTGGACG 59.719 45.833 0.00 0.00 0.00 4.79
783 1263 6.179906 ACTTGTCCCTATGAATGTATCTGG 57.820 41.667 0.00 0.00 0.00 3.86
865 1345 1.414378 GGCCCGTTTCGTTTTTCATG 58.586 50.000 0.00 0.00 0.00 3.07
873 1356 2.281276 GAGTTGGGCCCGTTTCGT 60.281 61.111 19.37 0.00 0.00 3.85
874 1357 3.053896 GGAGTTGGGCCCGTTTCG 61.054 66.667 19.37 0.00 0.00 3.46
903 1386 2.270205 CGAGGTTGGCTCATGGCT 59.730 61.111 6.20 0.00 41.46 4.75
904 1387 3.512516 GCGAGGTTGGCTCATGGC 61.513 66.667 0.00 0.00 40.90 4.40
905 1388 3.197790 CGCGAGGTTGGCTCATGG 61.198 66.667 0.00 0.00 0.00 3.66
906 1389 3.869272 GCGCGAGGTTGGCTCATG 61.869 66.667 12.10 0.00 0.00 3.07
1388 1879 4.516195 GTCGAGAGAAGGGCGGGC 62.516 72.222 0.00 0.00 45.01 6.13
1424 1916 5.299782 ACCGTCAGTAAAAGCATAAAACCAA 59.700 36.000 0.00 0.00 0.00 3.67
1450 1944 2.904866 GCACCACGCAACCTCCAA 60.905 61.111 0.00 0.00 41.79 3.53
1505 1999 0.519961 GCGTAATCGGCACCACTTTT 59.480 50.000 0.00 0.00 37.56 2.27
1574 2068 2.159382 TGACTCGGAAAAAGGATTGCC 58.841 47.619 0.00 0.00 0.00 4.52
1632 2126 7.617041 ACTTAAGTCAGCATAAACCTCAATC 57.383 36.000 1.12 0.00 0.00 2.67
1659 2153 2.177394 TCTGCCGCAACATAAACTCA 57.823 45.000 0.00 0.00 0.00 3.41
1669 2163 1.144969 CTTTCGTACTTCTGCCGCAA 58.855 50.000 0.00 0.00 0.00 4.85
1693 2192 9.076596 GTCATTGAGTTCCTAATTTTGTATTGC 57.923 33.333 0.00 0.00 0.00 3.56
1720 2219 3.609853 TCATATTGCCAGTGGTTGAGAC 58.390 45.455 11.74 0.00 0.00 3.36
1764 2263 4.065789 AGAAACGATTCCTTTCCTCACAC 58.934 43.478 1.30 0.00 36.12 3.82
1925 2425 1.305201 CTTACAACCGTGCCAACTGT 58.695 50.000 0.00 0.00 0.00 3.55
1932 2432 2.005560 GCCTAGTCCTTACAACCGTGC 61.006 57.143 0.00 0.00 0.00 5.34
2040 2554 9.973246 GTTCAAGATATACAGTTACACACATTG 57.027 33.333 0.00 0.00 0.00 2.82
2286 2800 9.126151 TGACTATACTTATTCAGAAGAGACAGG 57.874 37.037 3.87 0.00 0.00 4.00
2362 2876 6.426937 GCAGTTCAGTGGAATCTTGTAACTTA 59.573 38.462 0.00 0.00 35.05 2.24
2455 2969 3.068590 GCAATATTGGGCAACATGCTACT 59.931 43.478 17.02 0.00 44.28 2.57
2531 3045 4.082571 TCGGCGCTATCTAAACCTTATACC 60.083 45.833 7.64 0.00 0.00 2.73
2540 3054 2.030185 GGACTGATCGGCGCTATCTAAA 60.030 50.000 19.30 4.12 0.00 1.85
2641 3155 6.929625 TGGAACATTTGTTGTCTTTGAAGAA 58.070 32.000 0.00 0.00 37.68 2.52
2657 3171 9.492973 CTCAAATTAATTGTTCCTTGGAACATT 57.507 29.630 28.85 23.48 43.54 2.71
2955 3470 6.720288 AGAAGACTACAGTAACCCGCATATAT 59.280 38.462 0.00 0.00 0.00 0.86
3086 3603 5.988561 GCAACCATGAATTACCTGAAAAACA 59.011 36.000 0.00 0.00 0.00 2.83
3342 3863 2.284112 AGTCTTTCCCGCCCGGTA 60.284 61.111 0.00 0.00 0.00 4.02
3386 3907 7.149307 GCCTTACCTAAACATTGTTGCTTAAA 58.851 34.615 2.13 0.00 0.00 1.52
3426 3947 0.178955 TACCGTTGGTCTGTGGAGGA 60.179 55.000 0.00 0.00 37.09 3.71
3491 4014 5.535030 GGGTTCCAAACAGAGTGTTAATTCT 59.465 40.000 0.00 0.00 40.14 2.40
3492 4015 5.535030 AGGGTTCCAAACAGAGTGTTAATTC 59.465 40.000 0.00 0.00 40.14 2.17
3542 4066 5.066117 TGCAGAGGTATAGTTCACTCTTACG 59.934 44.000 0.00 0.00 38.18 3.18
3661 4185 8.611051 AGGGAGTATGTTATTCTGTTAGAAGT 57.389 34.615 0.00 0.00 37.69 3.01
3662 4186 8.145122 GGAGGGAGTATGTTATTCTGTTAGAAG 58.855 40.741 0.00 0.00 37.69 2.85
3664 4188 7.130099 TGGAGGGAGTATGTTATTCTGTTAGA 58.870 38.462 0.00 0.00 0.00 2.10
3692 4222 0.928451 GGCCGCGTCAATTAATTCGC 60.928 55.000 19.07 19.07 44.23 4.70
3734 4278 4.887071 CCCTCCGATCCAAATTAATTGACA 59.113 41.667 0.39 0.00 41.85 3.58
3746 4290 2.544844 AAACTACTCCCTCCGATCCA 57.455 50.000 0.00 0.00 0.00 3.41
3906 4457 2.478894 AGCACCGACAATTTAAGACGTG 59.521 45.455 0.00 0.00 0.00 4.49
3965 4516 1.203052 GGGGATGACAAATGTGCACAG 59.797 52.381 25.84 14.19 0.00 3.66
3972 4523 0.687427 GGGGGTGGGGATGACAAATG 60.687 60.000 0.00 0.00 0.00 2.32
3979 4530 2.279743 CACATGGGGGTGGGGATG 59.720 66.667 0.00 0.00 35.13 3.51
3980 4531 2.129397 TCACATGGGGGTGGGGAT 59.871 61.111 0.00 0.00 39.27 3.85
3981 4532 2.938798 GTCACATGGGGGTGGGGA 60.939 66.667 0.00 0.00 39.27 4.81
4259 4827 5.333581 TCTCTTTCTATGTCCTCCTGAACA 58.666 41.667 0.00 0.00 0.00 3.18
4394 4962 3.214696 ACCAACCTGAAGAAACCAGAG 57.785 47.619 0.00 0.00 33.65 3.35
4448 5016 7.766278 GTGTATCTTATGTTTCTGTCACCATCT 59.234 37.037 0.00 0.00 0.00 2.90
4490 5059 8.780249 GTTTTAGGATGTTAGTAGTCAAGCAAA 58.220 33.333 0.00 0.00 0.00 3.68
4493 5062 8.035984 AGAGTTTTAGGATGTTAGTAGTCAAGC 58.964 37.037 0.00 0.00 0.00 4.01
4557 5126 5.050490 CCAGGTGGTATGAAGATTAAGTCG 58.950 45.833 0.00 0.00 0.00 4.18
4587 5156 6.065976 ACCTCATTGATATGTTGGTTGAGA 57.934 37.500 0.00 0.00 36.81 3.27
4665 5242 3.305539 GCCATCACAGCATTTCAAGTGAA 60.306 43.478 0.00 0.00 43.38 3.18
4742 5320 7.497595 TCATTACAGAGCTAACCGTGAATTAT 58.502 34.615 0.00 0.00 0.00 1.28
4839 5417 9.898152 AAATCCAGAAACAGGAAACAAAATAAA 57.102 25.926 0.00 0.00 38.93 1.40
4841 5419 9.974980 GTAAATCCAGAAACAGGAAACAAAATA 57.025 29.630 0.00 0.00 38.93 1.40
4842 5420 8.482128 TGTAAATCCAGAAACAGGAAACAAAAT 58.518 29.630 0.00 0.00 38.93 1.82
4843 5421 7.841956 TGTAAATCCAGAAACAGGAAACAAAA 58.158 30.769 0.00 0.00 38.93 2.44
4968 5550 9.396022 GGTCCTAATCATGTTTTCTCTTTCATA 57.604 33.333 0.00 0.00 0.00 2.15
4991 5573 3.061848 CCCAACCATGGCACGGTC 61.062 66.667 13.04 0.00 46.09 4.79
4994 5576 1.134175 GATAAACCCAACCATGGCACG 59.866 52.381 13.04 0.00 46.09 5.34
5025 5610 8.306313 AGGACAAAGAGAACCAAATTTTTACT 57.694 30.769 0.00 0.00 0.00 2.24
5033 5618 3.632145 GCAAGAGGACAAAGAGAACCAAA 59.368 43.478 0.00 0.00 0.00 3.28
5146 5731 2.050836 ATCGCTCCCCACACACACAA 62.051 55.000 0.00 0.00 0.00 3.33
5148 5733 2.034879 CATCGCTCCCCACACACAC 61.035 63.158 0.00 0.00 0.00 3.82
5149 5734 2.347114 CATCGCTCCCCACACACA 59.653 61.111 0.00 0.00 0.00 3.72
5150 5735 2.436646 CCATCGCTCCCCACACAC 60.437 66.667 0.00 0.00 0.00 3.82
5151 5736 2.606213 TCCATCGCTCCCCACACA 60.606 61.111 0.00 0.00 0.00 3.72
5153 5738 2.284625 ACTCCATCGCTCCCCACA 60.285 61.111 0.00 0.00 0.00 4.17
5160 5745 3.065786 CACATAAATTGCACTCCATCGCT 59.934 43.478 0.00 0.00 0.00 4.93
5231 6132 1.504359 TTTACGCTGGTTCCACTTCG 58.496 50.000 0.00 0.00 0.00 3.79
5246 6147 6.127758 TGACCTATGGCATTTGTGTCATTTAC 60.128 38.462 4.78 0.00 0.00 2.01
5306 6207 5.612725 AAATTTCTCTTGTGGCTGGAAAA 57.387 34.783 0.00 0.00 31.24 2.29
5317 6218 6.455360 TGGCAAGCCTATAAATTTCTCTTG 57.545 37.500 12.96 4.09 36.94 3.02
5447 6350 4.079672 TGTTTCAGTAAAACCCCTTCCTCA 60.080 41.667 0.00 0.00 45.58 3.86


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

AutoCloner maintained by Alex Coulton.