Multiple sequence alignment - TraesCS1D01G319800

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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 TraesCS1D01G319800 chr1D 100.000 6306 0 0 1 6306 413774440 413780745 0.000000e+00 11646.0
1 TraesCS1D01G319800 chr1D 85.626 1127 132 6 3038 4147 104294594 104293481 0.000000e+00 1157.0
2 TraesCS1D01G319800 chr1D 91.000 400 34 2 4318 4716 413731042 413731440 7.190000e-149 538.0
3 TraesCS1D01G319800 chr1D 89.535 86 9 0 4165 4250 413730918 413731003 6.680000e-20 110.0
4 TraesCS1D01G319800 chr3A 96.992 4155 108 6 7 4148 435361344 435357194 0.000000e+00 6964.0
5 TraesCS1D01G319800 chr3A 84.488 1992 302 7 5 1994 82462662 82460676 0.000000e+00 1960.0
6 TraesCS1D01G319800 chr2B 96.301 4109 133 8 1 4096 677673036 677677138 0.000000e+00 6728.0
7 TraesCS1D01G319800 chr2B 96.546 2519 80 5 117 2632 490797393 490794879 0.000000e+00 4163.0
8 TraesCS1D01G319800 chr2B 83.695 1981 311 11 1 1977 626299631 626301603 0.000000e+00 1858.0
9 TraesCS1D01G319800 chr2B 74.570 1164 248 29 3020 4148 8556596 8555446 3.440000e-127 466.0
10 TraesCS1D01G319800 chr4A 95.479 3605 155 6 1 3601 16257364 16260964 0.000000e+00 5747.0
11 TraesCS1D01G319800 chr4A 83.717 1953 305 11 1 1947 456464130 456466075 0.000000e+00 1832.0
12 TraesCS1D01G319800 chr4A 78.014 1128 184 42 4174 5279 710413397 710412312 0.000000e+00 651.0
13 TraesCS1D01G319800 chr4A 79.926 807 138 11 3266 4060 596975324 596976118 7.090000e-159 571.0
14 TraesCS1D01G319800 chr7B 96.992 2194 61 3 4 2194 221309960 221312151 0.000000e+00 3681.0
15 TraesCS1D01G319800 chr7B 86.667 135 18 0 3020 3154 64179799 64179933 3.940000e-32 150.0
16 TraesCS1D01G319800 chr1B 92.584 1645 85 6 4165 5801 558496144 558497759 0.000000e+00 2327.0
17 TraesCS1D01G319800 chr1B 87.979 574 58 4 4165 4729 558284945 558285516 0.000000e+00 667.0
18 TraesCS1D01G319800 chr1B 92.275 466 26 9 5841 6306 558499450 558499905 0.000000e+00 652.0
19 TraesCS1D01G319800 chr1B 86.335 483 54 5 4960 5431 558285510 558285991 3.370000e-142 516.0
20 TraesCS1D01G319800 chr1B 93.827 81 5 0 5848 5928 558497772 558497852 8.590000e-24 122.0
21 TraesCS1D01G319800 chr1B 100.000 38 0 0 5687 5724 558497854 558497891 3.150000e-08 71.3
22 TraesCS1D01G319800 chr1A 83.578 1979 313 11 1 1974 491997818 491999789 0.000000e+00 1844.0
23 TraesCS1D01G319800 chr1A 91.574 1163 78 15 4808 5962 510804335 510805485 0.000000e+00 1587.0
24 TraesCS1D01G319800 chr1A 84.716 1145 150 6 3019 4138 299263942 299265086 0.000000e+00 1122.0
25 TraesCS1D01G319800 chr1A 94.178 584 32 1 4165 4746 510803750 510804333 0.000000e+00 889.0
26 TraesCS1D01G319800 chr1A 86.063 574 53 11 4165 4729 510672980 510673535 5.440000e-165 592.0
27 TraesCS1D01G319800 chr1A 85.044 341 24 8 5980 6306 510805465 510805792 7.890000e-84 322.0
28 TraesCS1D01G319800 chr6D 83.608 909 121 7 3021 3913 456453353 456452457 0.000000e+00 828.0
29 TraesCS1D01G319800 chr3B 79.553 895 157 10 3266 4148 368933504 368934384 3.230000e-172 616.0
30 TraesCS1D01G319800 chr6B 79.106 895 157 13 3266 4148 613577030 613576154 1.960000e-164 590.0
31 TraesCS1D01G319800 chr4B 78.348 896 167 14 3266 4148 375397934 375397053 7.140000e-154 555.0
32 TraesCS1D01G319800 chr6A 79.814 644 110 11 3287 3920 603141389 603140756 9.640000e-123 451.0
33 TraesCS1D01G319800 chr5B 74.335 1165 247 32 3020 4149 637138385 637137238 1.250000e-121 448.0
34 TraesCS1D01G319800 chrUn 79.837 615 97 20 4165 4764 90118229 90117627 2.100000e-114 424.0
35 TraesCS1D01G319800 chr7A 78.613 519 97 10 4156 4673 24627390 24627895 1.310000e-86 331.0
36 TraesCS1D01G319800 chr7D 78.058 515 100 9 4159 4673 23510267 23510768 4.750000e-81 313.0


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 TraesCS1D01G319800 chr1D 413774440 413780745 6305 False 11646.000000 11646 100.000000 1 6306 1 chr1D.!!$F1 6305
1 TraesCS1D01G319800 chr1D 104293481 104294594 1113 True 1157.000000 1157 85.626000 3038 4147 1 chr1D.!!$R1 1109
2 TraesCS1D01G319800 chr1D 413730918 413731440 522 False 324.000000 538 90.267500 4165 4716 2 chr1D.!!$F2 551
3 TraesCS1D01G319800 chr3A 435357194 435361344 4150 True 6964.000000 6964 96.992000 7 4148 1 chr3A.!!$R2 4141
4 TraesCS1D01G319800 chr3A 82460676 82462662 1986 True 1960.000000 1960 84.488000 5 1994 1 chr3A.!!$R1 1989
5 TraesCS1D01G319800 chr2B 677673036 677677138 4102 False 6728.000000 6728 96.301000 1 4096 1 chr2B.!!$F2 4095
6 TraesCS1D01G319800 chr2B 490794879 490797393 2514 True 4163.000000 4163 96.546000 117 2632 1 chr2B.!!$R2 2515
7 TraesCS1D01G319800 chr2B 626299631 626301603 1972 False 1858.000000 1858 83.695000 1 1977 1 chr2B.!!$F1 1976
8 TraesCS1D01G319800 chr2B 8555446 8556596 1150 True 466.000000 466 74.570000 3020 4148 1 chr2B.!!$R1 1128
9 TraesCS1D01G319800 chr4A 16257364 16260964 3600 False 5747.000000 5747 95.479000 1 3601 1 chr4A.!!$F1 3600
10 TraesCS1D01G319800 chr4A 456464130 456466075 1945 False 1832.000000 1832 83.717000 1 1947 1 chr4A.!!$F2 1946
11 TraesCS1D01G319800 chr4A 710412312 710413397 1085 True 651.000000 651 78.014000 4174 5279 1 chr4A.!!$R1 1105
12 TraesCS1D01G319800 chr4A 596975324 596976118 794 False 571.000000 571 79.926000 3266 4060 1 chr4A.!!$F3 794
13 TraesCS1D01G319800 chr7B 221309960 221312151 2191 False 3681.000000 3681 96.992000 4 2194 1 chr7B.!!$F2 2190
14 TraesCS1D01G319800 chr1B 558496144 558499905 3761 False 793.075000 2327 94.671500 4165 6306 4 chr1B.!!$F2 2141
15 TraesCS1D01G319800 chr1B 558284945 558285991 1046 False 591.500000 667 87.157000 4165 5431 2 chr1B.!!$F1 1266
16 TraesCS1D01G319800 chr1A 491997818 491999789 1971 False 1844.000000 1844 83.578000 1 1974 1 chr1A.!!$F2 1973
17 TraesCS1D01G319800 chr1A 299263942 299265086 1144 False 1122.000000 1122 84.716000 3019 4138 1 chr1A.!!$F1 1119
18 TraesCS1D01G319800 chr1A 510803750 510805792 2042 False 932.666667 1587 90.265333 4165 6306 3 chr1A.!!$F4 2141
19 TraesCS1D01G319800 chr1A 510672980 510673535 555 False 592.000000 592 86.063000 4165 4729 1 chr1A.!!$F3 564
20 TraesCS1D01G319800 chr6D 456452457 456453353 896 True 828.000000 828 83.608000 3021 3913 1 chr6D.!!$R1 892
21 TraesCS1D01G319800 chr3B 368933504 368934384 880 False 616.000000 616 79.553000 3266 4148 1 chr3B.!!$F1 882
22 TraesCS1D01G319800 chr6B 613576154 613577030 876 True 590.000000 590 79.106000 3266 4148 1 chr6B.!!$R1 882
23 TraesCS1D01G319800 chr4B 375397053 375397934 881 True 555.000000 555 78.348000 3266 4148 1 chr4B.!!$R1 882
24 TraesCS1D01G319800 chr6A 603140756 603141389 633 True 451.000000 451 79.814000 3287 3920 1 chr6A.!!$R1 633
25 TraesCS1D01G319800 chr5B 637137238 637138385 1147 True 448.000000 448 74.335000 3020 4149 1 chr5B.!!$R1 1129
26 TraesCS1D01G319800 chrUn 90117627 90118229 602 True 424.000000 424 79.837000 4165 4764 1 chrUn.!!$R1 599
27 TraesCS1D01G319800 chr7A 24627390 24627895 505 False 331.000000 331 78.613000 4156 4673 1 chr7A.!!$F1 517
28 TraesCS1D01G319800 chr7D 23510267 23510768 501 False 313.000000 313 78.058000 4159 4673 1 chr7D.!!$F1 514


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
652 654 0.471617 CATAGGGGAGTCAAGGCCAG 59.528 60.000 5.01 0.00 0.00 4.85 F
973 975 1.200252 CTCGGAGCTCAAGTTCTTCGA 59.800 52.381 17.19 11.32 0.00 3.71 F
1828 1832 2.168313 TGATCGACATGCTGGAGCTTTA 59.832 45.455 0.00 0.00 42.66 1.85 F
2198 2205 0.250727 TGGACCAAACACCTAGCAGC 60.251 55.000 0.00 0.00 0.00 5.25 F
2483 2490 1.003233 GTGACGTCTTCCCCATCCTTT 59.997 52.381 17.92 0.00 0.00 3.11 F
3671 3688 1.229951 AGCACCTGAAGGGATCCCA 60.230 57.895 32.69 11.52 40.27 4.37 F
4070 4116 0.662619 CGCTTGCAGAAACAACCTGA 59.337 50.000 0.00 0.00 33.65 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 1832 0.678048 GCCGTTTGCCTCCAAGAGAT 60.678 55.000 0.00 0.0 31.52 2.75 R
1846 1850 1.142748 CCTCCTCGTCCTGTCATGC 59.857 63.158 0.00 0.0 0.00 4.06 R
3048 3055 0.108615 CTACGCAGACTCCACCCTTG 60.109 60.000 0.00 0.0 0.00 3.61 R
3671 3688 0.392706 TCATCGTGCTGTGGTCTGTT 59.607 50.000 0.00 0.0 0.00 3.16 R
4054 4094 1.214175 TCCCTCAGGTTGTTTCTGCAA 59.786 47.619 0.00 0.0 32.63 4.08 R
4526 4612 0.619255 TTCCATCGGAGTGGGGCTTA 60.619 55.000 6.62 0.0 39.80 3.09 R
5666 5786 1.220749 GCATGACTCCCTTACGGCA 59.779 57.895 0.00 0.0 0.00 5.69 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
165 166 5.045651 TGGAGAAGATCAAGCAAATACTCCA 60.046 40.000 0.00 0.00 45.57 3.86
356 358 1.903294 GAGCCTCATGGAGAGCACA 59.097 57.895 0.00 0.00 43.31 4.57
435 437 1.132500 CTCCGCCCCTTCCTTCTTAT 58.868 55.000 0.00 0.00 0.00 1.73
436 438 1.490910 CTCCGCCCCTTCCTTCTTATT 59.509 52.381 0.00 0.00 0.00 1.40
456 458 1.453015 AGGAGCACCACGTTTGCAA 60.453 52.632 18.65 0.00 42.83 4.08
621 623 1.199327 TCGTTGATCGCTTCGAGAACT 59.801 47.619 10.25 0.00 39.91 3.01
652 654 0.471617 CATAGGGGAGTCAAGGCCAG 59.528 60.000 5.01 0.00 0.00 4.85
788 790 1.528309 CGGTGACCCAACCAAGCTT 60.528 57.895 0.00 0.00 40.53 3.74
973 975 1.200252 CTCGGAGCTCAAGTTCTTCGA 59.800 52.381 17.19 11.32 0.00 3.71
1662 1666 3.716195 CTCACCCGGACCATGGCA 61.716 66.667 13.04 0.00 0.00 4.92
1697 1701 5.408604 ACGTAGTGAAGTTAATGCAGGAAAG 59.591 40.000 0.00 0.00 42.51 2.62
1828 1832 2.168313 TGATCGACATGCTGGAGCTTTA 59.832 45.455 0.00 0.00 42.66 1.85
1846 1850 2.691409 TATCTCTTGGAGGCAAACGG 57.309 50.000 0.00 0.00 0.00 4.44
2198 2205 0.250727 TGGACCAAACACCTAGCAGC 60.251 55.000 0.00 0.00 0.00 5.25
2458 2465 3.654020 GAAGGCATCCATCGCGGC 61.654 66.667 6.13 0.00 33.14 6.53
2483 2490 1.003233 GTGACGTCTTCCCCATCCTTT 59.997 52.381 17.92 0.00 0.00 3.11
3048 3055 3.554692 CGGCAAGCGTCGGTGATC 61.555 66.667 0.00 0.00 36.31 2.92
3054 3061 1.827399 AAGCGTCGGTGATCAAGGGT 61.827 55.000 0.00 0.00 0.00 4.34
3671 3688 1.229951 AGCACCTGAAGGGATCCCA 60.230 57.895 32.69 11.52 40.27 4.37
3939 3967 2.757508 CTCCCTGGAGCTCGAGCA 60.758 66.667 36.87 17.54 45.16 4.26
4070 4116 0.662619 CGCTTGCAGAAACAACCTGA 59.337 50.000 0.00 0.00 33.65 3.86
4159 4205 4.969196 CGGCGTCGGGATGGGATG 62.969 72.222 0.00 0.00 0.00 3.51
4160 4206 4.626081 GGCGTCGGGATGGGATGG 62.626 72.222 0.00 0.00 0.00 3.51
4161 4207 3.861797 GCGTCGGGATGGGATGGT 61.862 66.667 0.00 0.00 0.00 3.55
4162 4208 2.108976 CGTCGGGATGGGATGGTG 59.891 66.667 0.00 0.00 0.00 4.17
4163 4209 2.510906 GTCGGGATGGGATGGTGG 59.489 66.667 0.00 0.00 0.00 4.61
4526 4612 1.600916 GGAGCTCGTGTTTGGCCTT 60.601 57.895 7.83 0.00 0.00 4.35
4578 4664 1.114627 CCTCATGGTCGATGACAGGA 58.885 55.000 0.00 0.00 36.06 3.86
4589 4675 0.706433 ATGACAGGATTGGTGGCCTT 59.294 50.000 3.32 0.00 30.41 4.35
4844 4941 4.576463 ACGGAGGTGGTACGTATAAACTAG 59.424 45.833 0.00 0.00 39.30 2.57
4888 4985 6.610075 AGACATTATGGTTTGCTTTTCCAT 57.390 33.333 0.00 0.00 43.30 3.41
5060 5162 6.463995 TGAAGGTTAAGCTTTTTGTGACAT 57.536 33.333 20.20 0.00 0.00 3.06
5083 5185 8.829746 ACATAGATAATGAGCAATGGGATCTTA 58.170 33.333 0.00 0.00 39.07 2.10
5162 5264 5.823570 GCACTAGACTACTCTGTTGATCCTA 59.176 44.000 0.00 0.00 0.00 2.94
5231 5333 3.064271 GGCGTTGTACACAAAAGTGAAGA 59.936 43.478 0.00 0.00 37.63 2.87
5327 5429 6.674694 AACTAAGTCTGCTATCATTGCTTG 57.325 37.500 0.00 0.00 0.00 4.01
5346 5448 4.492895 GCTTGCATTCAATAAAATGTGGCG 60.493 41.667 0.00 0.00 38.60 5.69
5365 5467 2.726633 CGATTTTGCGACACAGGTTTT 58.273 42.857 0.00 0.00 0.00 2.43
5372 5474 2.483877 TGCGACACAGGTTTTCATCATC 59.516 45.455 0.00 0.00 0.00 2.92
5574 5693 1.418342 CGTATGAACTTGCGTCCCGG 61.418 60.000 0.00 0.00 0.00 5.73
5575 5694 0.108520 GTATGAACTTGCGTCCCGGA 60.109 55.000 0.73 0.00 0.00 5.14
5615 5734 4.600012 ATCAATGCGTCGAAGGTTTTAG 57.400 40.909 0.00 0.00 0.00 1.85
5731 5852 8.493547 GGTATAAGTATAACGATCAACAAAGCC 58.506 37.037 0.00 0.00 0.00 4.35
5750 5871 2.611518 CCTTGCAAACAACAACGGAAA 58.388 42.857 0.00 0.00 0.00 3.13
5801 5923 3.678289 ACAAATAGAGCTGTGCACATGA 58.322 40.909 22.00 4.37 0.00 3.07
5825 5947 6.877611 AACACACCTCATCGTTTAAGAAAT 57.122 33.333 0.00 0.00 0.00 2.17
5828 5950 8.197988 ACACACCTCATCGTTTAAGAAATATC 57.802 34.615 0.00 0.00 0.00 1.63
5831 5953 7.010183 ACACCTCATCGTTTAAGAAATATCGTG 59.990 37.037 0.00 0.00 0.00 4.35
5837 5959 9.644993 CATCGTTTAAGAAATATCGTGCATTTA 57.355 29.630 0.00 0.00 0.00 1.40
5876 5999 5.542635 AGTGGTTCCACTAGTACAGAAATGA 59.457 40.000 21.13 0.00 44.42 2.57
5950 7756 9.194972 CTCCATGTAATAGCCTATAAGAGATGA 57.805 37.037 0.00 0.00 0.00 2.92
5987 7793 6.633500 TTATTTTATTGCGGGAAGAGATGG 57.367 37.500 0.00 0.00 0.00 3.51
6019 7825 1.173913 GCAAAACTATTGGAGGCGGT 58.826 50.000 0.00 0.00 0.00 5.68
6023 7829 2.871096 AACTATTGGAGGCGGTTTCA 57.129 45.000 0.00 0.00 0.00 2.69
6075 7882 2.489971 GTGGTTCGTTTGATGAGACCA 58.510 47.619 0.00 0.00 0.00 4.02
6176 7984 0.179062 ACCTGGCGATGCTGAGATTC 60.179 55.000 0.00 0.00 0.00 2.52
6222 8043 3.508762 ACGTTCACGAACATCATAGTCC 58.491 45.455 6.30 0.00 43.02 3.85
6239 8060 3.384816 CCGCTCATATGCAAGTGGA 57.615 52.632 15.69 0.00 44.34 4.02
6254 8075 4.437930 GCAAGTGGATGTTGTATCTCAAGC 60.438 45.833 0.00 0.00 36.66 4.01
6263 8084 5.363101 TGTTGTATCTCAAGCTGGATCATC 58.637 41.667 0.00 0.00 36.66 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 2.633481 AGGCCTTCGACTCTGTTAAGTT 59.367 45.455 0.00 0.0 0.00 2.66
356 358 4.670621 GCAATCACGAAAATTATCGCGAAT 59.329 37.500 15.24 0.0 46.51 3.34
435 437 1.444119 GCAAACGTGGTGCTCCTGAA 61.444 55.000 15.34 0.0 39.00 3.02
436 438 1.891919 GCAAACGTGGTGCTCCTGA 60.892 57.895 15.34 0.0 39.00 3.86
456 458 3.222603 CAAACCTCCAGTGGCTAAACTT 58.777 45.455 3.51 0.0 0.00 2.66
599 601 0.519961 TCTCGAAGCGATCAACGACA 59.480 50.000 0.00 0.0 45.77 4.35
621 623 3.011821 ACTCCCCTATGTCTGAGAGTGAA 59.988 47.826 0.00 0.0 33.50 3.18
973 975 3.903090 CAAGAGGATAGGCTTCTCTCCAT 59.097 47.826 12.78 0.0 36.54 3.41
1662 1666 3.573110 ACTTCACTACGTACTGCCTTTCT 59.427 43.478 0.00 0.0 0.00 2.52
1697 1701 3.548770 TGGGATGATCTGCTTGTTGATC 58.451 45.455 0.00 0.0 39.43 2.92
1828 1832 0.678048 GCCGTTTGCCTCCAAGAGAT 60.678 55.000 0.00 0.0 31.52 2.75
1846 1850 1.142748 CCTCCTCGTCCTGTCATGC 59.857 63.158 0.00 0.0 0.00 4.06
2233 2240 3.325753 GCTCTGTCCAGCTGGGGT 61.326 66.667 32.23 0.0 36.38 4.95
2483 2490 2.198827 CCACACCTTAGGCATTGTCA 57.801 50.000 0.00 0.0 0.00 3.58
2648 2655 1.806690 GCCCTCCCCTACCCCAAAAA 61.807 60.000 0.00 0.0 0.00 1.94
2650 2657 2.615929 GCCCTCCCCTACCCCAAA 60.616 66.667 0.00 0.0 0.00 3.28
2690 2697 1.896660 TGCCTCGCACCACTTTTCC 60.897 57.895 0.00 0.0 31.71 3.13
2825 2832 4.415150 CCACTGATGGGCACGGCT 62.415 66.667 0.00 0.0 43.04 5.52
3048 3055 0.108615 CTACGCAGACTCCACCCTTG 60.109 60.000 0.00 0.0 0.00 3.61
3054 3061 2.360726 TCCGCTACGCAGACTCCA 60.361 61.111 0.00 0.0 0.00 3.86
3671 3688 0.392706 TCATCGTGCTGTGGTCTGTT 59.607 50.000 0.00 0.0 0.00 3.16
4008 4039 2.579201 CGCCAGATCCAGGTCGTT 59.421 61.111 3.95 0.0 0.00 3.85
4054 4094 1.214175 TCCCTCAGGTTGTTTCTGCAA 59.786 47.619 0.00 0.0 32.63 4.08
4148 4194 2.772191 TCCCACCATCCCATCCCG 60.772 66.667 0.00 0.0 0.00 5.14
4149 4195 2.768022 GGTCCCACCATCCCATCCC 61.768 68.421 0.00 0.0 38.42 3.85
4150 4196 2.927056 GGTCCCACCATCCCATCC 59.073 66.667 0.00 0.0 38.42 3.51
4151 4197 2.510906 CGGTCCCACCATCCCATC 59.489 66.667 0.00 0.0 38.47 3.51
4152 4198 3.809013 GCGGTCCCACCATCCCAT 61.809 66.667 0.00 0.0 38.47 4.00
4155 4201 4.176752 GAGGCGGTCCCACCATCC 62.177 72.222 0.00 0.0 38.47 3.51
4156 4202 1.760875 TAGAGGCGGTCCCACCATC 60.761 63.158 0.00 0.0 38.47 3.51
4157 4203 2.064581 GTAGAGGCGGTCCCACCAT 61.065 63.158 0.00 0.0 38.47 3.55
4158 4204 2.682494 GTAGAGGCGGTCCCACCA 60.682 66.667 0.00 0.0 38.47 4.17
4159 4205 3.468140 GGTAGAGGCGGTCCCACC 61.468 72.222 0.00 0.0 35.39 4.61
4160 4206 2.363925 AGGTAGAGGCGGTCCCAC 60.364 66.667 0.00 0.0 35.39 4.61
4161 4207 2.043248 GAGGTAGAGGCGGTCCCA 60.043 66.667 0.00 0.0 35.39 4.37
4162 4208 1.677637 CTTGAGGTAGAGGCGGTCCC 61.678 65.000 0.00 0.0 0.00 4.46
4163 4209 1.677637 CCTTGAGGTAGAGGCGGTCC 61.678 65.000 0.00 0.0 0.00 4.46
4245 4291 1.296392 CATTGCTCTGTGGGGTCGA 59.704 57.895 0.00 0.0 0.00 4.20
4422 4508 6.018588 TGTTTCACAAAGTAATCATCGTCGTT 60.019 34.615 0.00 0.0 0.00 3.85
4526 4612 0.619255 TTCCATCGGAGTGGGGCTTA 60.619 55.000 6.62 0.0 39.80 3.09
4578 4664 2.158475 TGAGAACTTGAAGGCCACCAAT 60.158 45.455 5.01 0.0 0.00 3.16
4589 4675 3.652869 AGACCCCATCTTTGAGAACTTGA 59.347 43.478 0.00 0.0 31.62 3.02
4798 4895 8.076781 CCGTTCATGAATATATATCGGTCCTAG 58.923 40.741 18.31 0.0 0.00 3.02
4844 4941 3.475566 TTACCTGATCAGCCTATGCAC 57.524 47.619 17.76 0.0 41.13 4.57
5231 5333 9.384764 GTAATTTCTAGCAAAGTAGTCCTTGAT 57.615 33.333 0.00 0.0 32.32 2.57
5327 5429 5.971895 AATCGCCACATTTTATTGAATGC 57.028 34.783 0.00 0.0 39.97 3.56
5346 5448 3.701241 TGAAAACCTGTGTCGCAAAATC 58.299 40.909 0.00 0.0 0.00 2.17
5365 5467 7.549839 TGCGATGATACATGAATAGATGATGA 58.450 34.615 0.00 0.0 0.00 2.92
5372 5474 5.668471 AGGGATGCGATGATACATGAATAG 58.332 41.667 0.00 0.0 0.00 1.73
5385 5487 4.632153 GTGAATACACTTAGGGATGCGAT 58.368 43.478 0.00 0.0 42.99 4.58
5489 5608 7.807977 ATCATCACATACCTTTTCATGGTAC 57.192 36.000 0.00 0.0 42.12 3.34
5574 5693 9.669353 CATTGATTACCATTGTAACTTAGCATC 57.331 33.333 0.00 0.0 39.66 3.91
5575 5694 8.137437 GCATTGATTACCATTGTAACTTAGCAT 58.863 33.333 0.00 0.0 39.66 3.79
5666 5786 1.220749 GCATGACTCCCTTACGGCA 59.779 57.895 0.00 0.0 0.00 5.69
5670 5790 9.425577 GAAGTATTATTAGCATGACTCCCTTAC 57.574 37.037 0.00 0.0 0.00 2.34
5731 5852 2.029124 GCTTTCCGTTGTTGTTTGCAAG 59.971 45.455 0.00 0.0 34.94 4.01
5750 5871 2.609350 CCATTTGCGCAACATTTAGCT 58.391 42.857 24.99 0.0 0.00 3.32
5801 5923 6.687081 TTTCTTAAACGATGAGGTGTGTTT 57.313 33.333 0.00 0.0 38.10 2.83
5921 7727 7.123397 TCTCTTATAGGCTATTACATGGAGCTG 59.877 40.741 13.08 0.0 36.43 4.24
5961 7767 8.143835 CCATCTCTTCCCGCAATAAAATAAAAT 58.856 33.333 0.00 0.0 0.00 1.82
5963 7769 6.605594 ACCATCTCTTCCCGCAATAAAATAAA 59.394 34.615 0.00 0.0 0.00 1.40
5966 7772 4.536765 ACCATCTCTTCCCGCAATAAAAT 58.463 39.130 0.00 0.0 0.00 1.82
5967 7773 3.963129 ACCATCTCTTCCCGCAATAAAA 58.037 40.909 0.00 0.0 0.00 1.52
5968 7774 3.644966 ACCATCTCTTCCCGCAATAAA 57.355 42.857 0.00 0.0 0.00 1.40
5969 7775 3.644966 AACCATCTCTTCCCGCAATAA 57.355 42.857 0.00 0.0 0.00 1.40
5970 7776 4.974645 ATAACCATCTCTTCCCGCAATA 57.025 40.909 0.00 0.0 0.00 1.90
5971 7777 3.864789 ATAACCATCTCTTCCCGCAAT 57.135 42.857 0.00 0.0 0.00 3.56
6019 7825 7.624360 ACTATATGCGATTCCACTTTTGAAA 57.376 32.000 0.00 0.0 0.00 2.69
6023 7829 9.436957 CCTAATACTATATGCGATTCCACTTTT 57.563 33.333 0.00 0.0 0.00 2.27
6075 7882 3.777522 CAAGGATCCCAGAAACTAGAGGT 59.222 47.826 8.55 0.0 0.00 3.85
6154 7962 1.589993 CTCAGCATCGCCAGGTACG 60.590 63.158 0.00 0.0 0.00 3.67
6162 7970 5.663795 TTAAATCAGAATCTCAGCATCGC 57.336 39.130 0.00 0.0 0.00 4.58
6168 7976 7.025963 GTGCCAAGTTTAAATCAGAATCTCAG 58.974 38.462 0.00 0.0 0.00 3.35
6176 7984 6.215121 TCAACATGTGCCAAGTTTAAATCAG 58.785 36.000 0.00 0.0 0.00 2.90
6222 8043 2.216046 ACATCCACTTGCATATGAGCG 58.784 47.619 6.97 0.0 37.31 5.03
6239 8060 5.363562 TGATCCAGCTTGAGATACAACAT 57.636 39.130 0.00 0.0 34.56 2.71
6263 8084 2.505650 TGTCATTGGGTGTATGGTGG 57.494 50.000 0.00 0.0 0.00 4.61



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

AutoCloner maintained by Alex Coulton.