Multiple sequence alignment - TraesCS1D01G331200

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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 TraesCS1D01G331200 chr1D 100.000 2314 0 0 1 2314 421463934 421466247 0.000000e+00 4274.0
1 TraesCS1D01G331200 chr1D 88.708 1355 76 30 563 1845 421225876 421227225 0.000000e+00 1583.0
2 TraesCS1D01G331200 chr1D 90.149 538 24 10 13 549 421225382 421225891 0.000000e+00 673.0
3 TraesCS1D01G331200 chr1D 89.224 232 19 4 1905 2135 421227236 421227462 4.420000e-73 285.0
4 TraesCS1D01G331200 chr1D 82.143 168 22 7 1265 1428 470339207 470339044 1.310000e-28 137.0
5 TraesCS1D01G331200 chr1D 100.000 31 0 0 2681 2711 421466614 421466644 1.050000e-04 58.4
6 TraesCS1D01G331200 chr1A 86.393 2021 142 55 267 2217 517519085 517521042 0.000000e+00 2085.0
7 TraesCS1D01G331200 chr1A 87.821 156 12 6 13 166 517518938 517519088 2.770000e-40 176.0
8 TraesCS1D01G331200 chr1B 89.172 1413 104 26 828 2220 570525832 570527215 0.000000e+00 1716.0
9 TraesCS1D01G331200 chr1B 85.145 828 53 29 13 831 570525042 570525808 0.000000e+00 784.0
10 TraesCS1D01G331200 chr1B 83.699 865 45 28 1363 2220 570831732 570832507 0.000000e+00 728.0
11 TraesCS1D01G331200 chr1B 87.852 461 32 13 930 1378 570825975 570826423 1.110000e-143 520.0
12 TraesCS1D01G331200 chr1B 79.781 638 63 33 1584 2194 570720196 570720794 1.170000e-108 403.0
13 TraesCS1D01G331200 chr1B 82.528 269 35 7 445 711 570814893 570815151 2.720000e-55 226.0
14 TraesCS1D01G331200 chr1B 94.853 136 4 3 699 831 570820643 570820778 2.740000e-50 209.0
15 TraesCS1D01G331200 chr1B 89.820 167 9 1 280 446 570704726 570704884 9.840000e-50 207.0
16 TraesCS1D01G331200 chr1B 89.820 167 9 1 280 446 570726669 570726827 9.840000e-50 207.0
17 TraesCS1D01G331200 chr1B 96.522 115 4 0 1374 1488 570831614 570831728 9.910000e-45 191.0
18 TraesCS1D01G331200 chr1B 90.654 107 8 1 830 936 570824812 570824916 1.010000e-29 141.0
19 TraesCS1D01G331200 chr5D 79.222 823 107 39 938 1716 556423349 556424151 5.180000e-142 514.0
20 TraesCS1D01G331200 chr5D 78.272 764 109 27 950 1661 559979041 559978283 3.200000e-119 438.0
21 TraesCS1D01G331200 chr5D 100.000 28 0 0 2684 2711 401392530 401392503 5.000000e-03 52.8
22 TraesCS1D01G331200 chr4A 78.369 883 124 39 835 1661 613544438 613543567 6.700000e-141 510.0
23 TraesCS1D01G331200 chr4A 82.367 431 68 6 1232 1655 604857066 604857495 4.260000e-98 368.0
24 TraesCS1D01G331200 chr5B 77.241 725 120 32 956 1651 694203704 694202996 1.520000e-102 383.0
25 TraesCS1D01G331200 chr2A 81.818 253 31 12 936 1179 643231162 643230916 5.920000e-47 198.0
26 TraesCS1D01G331200 chr2B 81.102 254 31 13 936 1179 585757421 585757175 1.280000e-43 187.0
27 TraesCS1D01G331200 chr3D 90.698 43 2 1 2270 2312 15929553 15929593 3.770000e-04 56.5


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 TraesCS1D01G331200 chr1D 421463934 421466644 2710 False 2166.2 4274 100.000000 1 2711 2 chr1D.!!$F2 2710
1 TraesCS1D01G331200 chr1D 421225382 421227462 2080 False 847.0 1583 89.360333 13 2135 3 chr1D.!!$F1 2122
2 TraesCS1D01G331200 chr1A 517518938 517521042 2104 False 1130.5 2085 87.107000 13 2217 2 chr1A.!!$F1 2204
3 TraesCS1D01G331200 chr1B 570525042 570527215 2173 False 1250.0 1716 87.158500 13 2220 2 chr1B.!!$F6 2207
4 TraesCS1D01G331200 chr1B 570831614 570832507 893 False 459.5 728 90.110500 1363 2220 2 chr1B.!!$F8 857
5 TraesCS1D01G331200 chr1B 570720196 570720794 598 False 403.0 403 79.781000 1584 2194 1 chr1B.!!$F2 610
6 TraesCS1D01G331200 chr1B 570824812 570826423 1611 False 330.5 520 89.253000 830 1378 2 chr1B.!!$F7 548
7 TraesCS1D01G331200 chr5D 556423349 556424151 802 False 514.0 514 79.222000 938 1716 1 chr5D.!!$F1 778
8 TraesCS1D01G331200 chr5D 559978283 559979041 758 True 438.0 438 78.272000 950 1661 1 chr5D.!!$R2 711
9 TraesCS1D01G331200 chr4A 613543567 613544438 871 True 510.0 510 78.369000 835 1661 1 chr4A.!!$R1 826
10 TraesCS1D01G331200 chr5B 694202996 694203704 708 True 383.0 383 77.241000 956 1651 1 chr5B.!!$R1 695

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
152 155 0.315568 AACCGTCTCACTCAGCTCAC 59.684 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 3185 0.036388 AACATGCCGTCGGTCTCAAT 60.036 50.0 13.94 0.0 0.0 2.57 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
125 128 2.415168 CACGTACCACCATTTGCAGTAG 59.585 50.000 0.00 0.00 0.00 2.57
143 146 5.050972 GCAGTAGCATAATTAACCGTCTCAC 60.051 44.000 0.00 0.00 41.58 3.51
144 147 6.273825 CAGTAGCATAATTAACCGTCTCACT 58.726 40.000 0.00 0.00 0.00 3.41
145 148 6.418226 CAGTAGCATAATTAACCGTCTCACTC 59.582 42.308 0.00 0.00 0.00 3.51
146 149 5.339008 AGCATAATTAACCGTCTCACTCA 57.661 39.130 0.00 0.00 0.00 3.41
147 150 5.352284 AGCATAATTAACCGTCTCACTCAG 58.648 41.667 0.00 0.00 0.00 3.35
148 151 4.025647 GCATAATTAACCGTCTCACTCAGC 60.026 45.833 0.00 0.00 0.00 4.26
149 152 3.963428 AATTAACCGTCTCACTCAGCT 57.037 42.857 0.00 0.00 0.00 4.24
150 153 3.512033 ATTAACCGTCTCACTCAGCTC 57.488 47.619 0.00 0.00 0.00 4.09
151 154 1.905637 TAACCGTCTCACTCAGCTCA 58.094 50.000 0.00 0.00 0.00 4.26
152 155 0.315568 AACCGTCTCACTCAGCTCAC 59.684 55.000 0.00 0.00 0.00 3.51
153 156 0.823769 ACCGTCTCACTCAGCTCACA 60.824 55.000 0.00 0.00 0.00 3.58
154 157 0.387878 CCGTCTCACTCAGCTCACAC 60.388 60.000 0.00 0.00 0.00 3.82
155 158 0.387878 CGTCTCACTCAGCTCACACC 60.388 60.000 0.00 0.00 0.00 4.16
156 159 0.676184 GTCTCACTCAGCTCACACCA 59.324 55.000 0.00 0.00 0.00 4.17
170 187 2.158534 TCACACCACCCAGCTAAATTGT 60.159 45.455 0.00 0.00 0.00 2.71
248 270 6.310941 TGGTGGATTGGTGGTAATAATATGG 58.689 40.000 0.00 0.00 0.00 2.74
340 367 1.738099 CTCACGTGCGGCTAAGCTT 60.738 57.895 11.67 3.48 38.13 3.74
349 381 0.745845 CGGCTAAGCTTGCTCACCAT 60.746 55.000 9.86 0.00 0.00 3.55
350 382 1.467920 GGCTAAGCTTGCTCACCATT 58.532 50.000 9.86 0.00 0.00 3.16
351 383 1.821136 GGCTAAGCTTGCTCACCATTT 59.179 47.619 9.86 0.00 0.00 2.32
352 384 2.416431 GGCTAAGCTTGCTCACCATTTG 60.416 50.000 9.86 0.00 0.00 2.32
353 385 2.489329 GCTAAGCTTGCTCACCATTTGA 59.511 45.455 9.86 0.00 0.00 2.69
400 433 2.308690 CACTACCACCCTCTAGCTACC 58.691 57.143 0.00 0.00 0.00 3.18
456 490 7.067859 TCAGCTACAACGATTAGTATTACCACT 59.932 37.037 0.00 0.00 0.00 4.00
473 507 7.728847 TTACCACTATGATTTTCCATGATCG 57.271 36.000 0.00 0.00 0.00 3.69
476 510 5.008911 CCACTATGATTTTCCATGATCGCAA 59.991 40.000 0.00 0.00 0.00 4.85
552 586 9.743581 AGCCAGATTCAATCCAAAATTTAAATT 57.256 25.926 7.64 7.64 0.00 1.82
553 587 9.777575 GCCAGATTCAATCCAAAATTTAAATTG 57.222 29.630 14.04 4.53 0.00 2.32
593 644 8.500753 AAAATTTACTGAGTTTTGAAAACCCC 57.499 30.769 16.45 9.88 0.00 4.95
682 733 0.322008 AGAACCTTGGCTGCTGCTAC 60.322 55.000 15.64 0.08 39.59 3.58
692 743 3.181471 TGGCTGCTGCTACTATCTTCTTC 60.181 47.826 15.64 0.00 39.59 2.87
736 787 1.152376 TGCATTTTGTGGAGCCCCA 60.152 52.632 0.00 0.00 40.95 4.96
1036 2252 2.642254 GCAGCAGCAGCATTTCCCA 61.642 57.895 4.63 0.00 45.49 4.37
1302 2590 2.100631 CAAGTTCGCGGCGGAGATT 61.101 57.895 23.46 8.92 0.00 2.40
1733 3049 0.600255 AACAAGAGAGTTGGCGACGG 60.600 55.000 0.00 0.00 0.00 4.79
1840 3180 5.948992 AGCTTGTGTAGGATTGAGAAAAC 57.051 39.130 0.00 0.00 0.00 2.43
1845 3185 5.856156 TGTGTAGGATTGAGAAAACGGTTA 58.144 37.500 0.00 0.00 0.00 2.85
1846 3186 6.469410 TGTGTAGGATTGAGAAAACGGTTAT 58.531 36.000 0.00 0.00 0.00 1.89
1886 3226 4.336889 TGGGTCTGAATTTAGATAGCCG 57.663 45.455 2.93 0.00 0.00 5.52
1887 3227 3.709653 TGGGTCTGAATTTAGATAGCCGT 59.290 43.478 2.93 0.00 0.00 5.68
1888 3228 4.058817 GGGTCTGAATTTAGATAGCCGTG 58.941 47.826 2.93 0.00 0.00 4.94
1889 3229 4.202223 GGGTCTGAATTTAGATAGCCGTGA 60.202 45.833 2.93 0.00 0.00 4.35
1896 3236 6.876789 TGAATTTAGATAGCCGTGAGTGAAAA 59.123 34.615 0.00 0.00 0.00 2.29
2003 3357 1.302192 GTGGCTTGGGTCGCTGTTA 60.302 57.895 0.00 0.00 0.00 2.41
2004 3358 0.676782 GTGGCTTGGGTCGCTGTTAT 60.677 55.000 0.00 0.00 0.00 1.89
2040 3413 9.801873 TTTCAAAAAGAATCAGAAAAGGTACAG 57.198 29.630 0.00 0.00 35.83 2.74
2049 3423 6.442541 TCAGAAAAGGTACAGGGATTGTTA 57.557 37.500 0.00 0.00 41.29 2.41
2053 3427 9.408648 CAGAAAAGGTACAGGGATTGTTATTAT 57.591 33.333 0.00 0.00 41.29 1.28
2070 3447 8.485976 TGTTATTATTATTTTTGGTTGGCAGC 57.514 30.769 0.00 0.00 0.00 5.25
2135 3513 3.316308 CAGGTCAAGTCCAAAGTCCAAAG 59.684 47.826 0.00 0.00 0.00 2.77
2136 3514 3.053619 AGGTCAAGTCCAAAGTCCAAAGT 60.054 43.478 0.00 0.00 0.00 2.66
2137 3515 3.315470 GGTCAAGTCCAAAGTCCAAAGTC 59.685 47.826 0.00 0.00 0.00 3.01
2138 3516 3.315470 GTCAAGTCCAAAGTCCAAAGTCC 59.685 47.826 0.00 0.00 0.00 3.85
2139 3517 3.053991 TCAAGTCCAAAGTCCAAAGTCCA 60.054 43.478 0.00 0.00 0.00 4.02
2140 3518 3.662759 AGTCCAAAGTCCAAAGTCCAA 57.337 42.857 0.00 0.00 0.00 3.53
2141 3519 3.976015 AGTCCAAAGTCCAAAGTCCAAA 58.024 40.909 0.00 0.00 0.00 3.28
2142 3520 3.699538 AGTCCAAAGTCCAAAGTCCAAAC 59.300 43.478 0.00 0.00 0.00 2.93
2154 3532 0.102300 GTCCAAACGCCTGCAAGTTT 59.898 50.000 8.30 8.30 40.74 2.66
2155 3533 0.383949 TCCAAACGCCTGCAAGTTTC 59.616 50.000 10.47 0.00 38.37 2.78
2220 3598 8.402326 TGCGTACAAGATAAACACAATACTAG 57.598 34.615 0.00 0.00 0.00 2.57
2221 3599 7.009815 TGCGTACAAGATAAACACAATACTAGC 59.990 37.037 0.00 0.00 0.00 3.42
2222 3600 7.009815 GCGTACAAGATAAACACAATACTAGCA 59.990 37.037 0.00 0.00 0.00 3.49
2223 3601 8.865978 CGTACAAGATAAACACAATACTAGCAA 58.134 33.333 0.00 0.00 0.00 3.91
2239 3617 5.086104 CTAGCAATACTAGTGGTTGGTGT 57.914 43.478 25.25 2.40 43.07 4.16
2240 3618 3.939066 AGCAATACTAGTGGTTGGTGTC 58.061 45.455 20.00 7.81 32.89 3.67
2241 3619 2.671396 GCAATACTAGTGGTTGGTGTCG 59.329 50.000 18.65 0.52 0.00 4.35
2242 3620 2.667473 ATACTAGTGGTTGGTGTCGC 57.333 50.000 5.39 0.00 0.00 5.19
2243 3621 0.604578 TACTAGTGGTTGGTGTCGCC 59.395 55.000 5.39 0.00 37.90 5.54
2244 3622 1.736645 CTAGTGGTTGGTGTCGCCG 60.737 63.158 0.00 0.00 41.21 6.46
2245 3623 2.149803 CTAGTGGTTGGTGTCGCCGA 62.150 60.000 0.00 0.00 41.21 5.54
2246 3624 1.537814 TAGTGGTTGGTGTCGCCGAT 61.538 55.000 0.00 0.00 41.21 4.18
2247 3625 2.358125 TGGTTGGTGTCGCCGATG 60.358 61.111 0.00 0.00 41.21 3.84
2248 3626 2.047655 GGTTGGTGTCGCCGATGA 60.048 61.111 0.00 0.00 41.21 2.92
2249 3627 1.669760 GGTTGGTGTCGCCGATGAA 60.670 57.895 0.00 0.00 41.21 2.57
2250 3628 1.495951 GTTGGTGTCGCCGATGAAC 59.504 57.895 0.00 0.00 41.21 3.18
2251 3629 1.669760 TTGGTGTCGCCGATGAACC 60.670 57.895 8.99 8.99 41.21 3.62
2252 3630 2.047655 GGTGTCGCCGATGAACCA 60.048 61.111 10.55 0.00 0.00 3.67
2253 3631 1.669760 GGTGTCGCCGATGAACCAA 60.670 57.895 10.55 0.00 0.00 3.67
2254 3632 1.024579 GGTGTCGCCGATGAACCAAT 61.025 55.000 10.55 0.00 0.00 3.16
2255 3633 0.373716 GTGTCGCCGATGAACCAATC 59.626 55.000 0.00 0.00 0.00 2.67
2266 3644 5.499139 GATGAACCAATCGAATTTAGGCA 57.501 39.130 0.00 0.00 0.00 4.75
2267 3645 6.076981 GATGAACCAATCGAATTTAGGCAT 57.923 37.500 0.00 0.00 0.00 4.40
2268 3646 5.499139 TGAACCAATCGAATTTAGGCATC 57.501 39.130 0.00 0.00 0.00 3.91
2269 3647 5.192927 TGAACCAATCGAATTTAGGCATCT 58.807 37.500 0.00 0.00 0.00 2.90
2270 3648 5.066375 TGAACCAATCGAATTTAGGCATCTG 59.934 40.000 0.00 0.00 0.00 2.90
2271 3649 4.526970 ACCAATCGAATTTAGGCATCTGT 58.473 39.130 0.00 0.00 0.00 3.41
2272 3650 5.680619 ACCAATCGAATTTAGGCATCTGTA 58.319 37.500 0.00 0.00 0.00 2.74
2273 3651 6.119536 ACCAATCGAATTTAGGCATCTGTAA 58.880 36.000 0.00 0.00 0.00 2.41
2274 3652 6.772716 ACCAATCGAATTTAGGCATCTGTAAT 59.227 34.615 0.00 0.00 0.00 1.89
2275 3653 7.080099 CCAATCGAATTTAGGCATCTGTAATG 58.920 38.462 0.00 0.00 0.00 1.90
2276 3654 6.808008 ATCGAATTTAGGCATCTGTAATGG 57.192 37.500 0.00 0.00 0.00 3.16
2277 3655 4.515191 TCGAATTTAGGCATCTGTAATGGC 59.485 41.667 3.60 3.60 43.88 4.40
2278 3656 4.275689 CGAATTTAGGCATCTGTAATGGCA 59.724 41.667 13.17 0.00 45.66 4.92
2279 3657 5.221028 CGAATTTAGGCATCTGTAATGGCAA 60.221 40.000 13.17 1.51 45.66 4.52
2280 3658 4.981806 TTTAGGCATCTGTAATGGCAAC 57.018 40.909 13.17 0.00 45.66 4.17
2281 3659 1.767759 AGGCATCTGTAATGGCAACC 58.232 50.000 13.17 0.00 45.66 3.77
2282 3660 0.746659 GGCATCTGTAATGGCAACCC 59.253 55.000 6.70 0.00 43.15 4.11
2304 3682 3.625745 AAAAACCTCTCGCATCCGT 57.374 47.368 0.00 0.00 35.54 4.69
2305 3683 1.439679 AAAAACCTCTCGCATCCGTC 58.560 50.000 0.00 0.00 35.54 4.79
2306 3684 0.608640 AAAACCTCTCGCATCCGTCT 59.391 50.000 0.00 0.00 35.54 4.18
2307 3685 0.108615 AAACCTCTCGCATCCGTCTG 60.109 55.000 0.00 0.00 35.54 3.51
2308 3686 2.279120 CCTCTCGCATCCGTCTGC 60.279 66.667 0.00 0.00 38.81 4.26
2703 4081 5.176407 TCACAACAAATCAAACTAACCGG 57.824 39.130 0.00 0.00 0.00 5.28
2704 4082 4.882427 TCACAACAAATCAAACTAACCGGA 59.118 37.500 9.46 0.00 0.00 5.14
2705 4083 4.973663 CACAACAAATCAAACTAACCGGAC 59.026 41.667 9.46 0.00 0.00 4.79
2706 4084 4.215965 CAACAAATCAAACTAACCGGACG 58.784 43.478 9.46 0.00 0.00 4.79
2707 4085 3.731089 ACAAATCAAACTAACCGGACGA 58.269 40.909 9.46 0.00 0.00 4.20
2708 4086 4.128643 ACAAATCAAACTAACCGGACGAA 58.871 39.130 9.46 0.00 0.00 3.85
2709 4087 4.575645 ACAAATCAAACTAACCGGACGAAA 59.424 37.500 9.46 0.00 0.00 3.46
2710 4088 5.239963 ACAAATCAAACTAACCGGACGAAAT 59.760 36.000 9.46 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.932200 AGCATAGCCGTTAATTAGAGCATC 59.068 41.667 6.32 0.00 0.00 3.91
7 8 4.899502 AGCATAGCCGTTAATTAGAGCAT 58.100 39.130 6.32 0.00 0.00 3.79
8 9 4.336889 AGCATAGCCGTTAATTAGAGCA 57.663 40.909 6.32 0.00 0.00 4.26
10 11 4.752101 AGCAAGCATAGCCGTTAATTAGAG 59.248 41.667 0.00 0.00 0.00 2.43
11 12 4.703897 AGCAAGCATAGCCGTTAATTAGA 58.296 39.130 0.00 0.00 0.00 2.10
13 14 4.036262 CCAAGCAAGCATAGCCGTTAATTA 59.964 41.667 0.00 0.00 0.00 1.40
14 15 3.181487 CCAAGCAAGCATAGCCGTTAATT 60.181 43.478 0.00 0.00 0.00 1.40
15 16 2.358898 CCAAGCAAGCATAGCCGTTAAT 59.641 45.455 0.00 0.00 0.00 1.40
16 17 1.742831 CCAAGCAAGCATAGCCGTTAA 59.257 47.619 0.00 0.00 0.00 2.01
18 19 0.322456 TCCAAGCAAGCATAGCCGTT 60.322 50.000 0.00 0.00 0.00 4.44
19 20 0.322456 TTCCAAGCAAGCATAGCCGT 60.322 50.000 0.00 0.00 0.00 5.68
125 128 4.025647 GCTGAGTGAGACGGTTAATTATGC 60.026 45.833 0.00 0.00 0.00 3.14
143 146 1.004080 CTGGGTGGTGTGAGCTGAG 60.004 63.158 0.00 0.00 0.00 3.35
144 147 3.150949 CTGGGTGGTGTGAGCTGA 58.849 61.111 0.00 0.00 0.00 4.26
145 148 1.830587 TAGCTGGGTGGTGTGAGCTG 61.831 60.000 0.00 0.00 41.84 4.24
146 149 1.127567 TTAGCTGGGTGGTGTGAGCT 61.128 55.000 0.00 0.00 44.05 4.09
147 150 0.250727 TTTAGCTGGGTGGTGTGAGC 60.251 55.000 0.00 0.00 0.00 4.26
148 151 2.489329 CAATTTAGCTGGGTGGTGTGAG 59.511 50.000 0.00 0.00 0.00 3.51
149 152 2.158534 ACAATTTAGCTGGGTGGTGTGA 60.159 45.455 0.00 0.00 0.00 3.58
150 153 2.238521 ACAATTTAGCTGGGTGGTGTG 58.761 47.619 0.00 0.00 0.00 3.82
151 154 2.675658 ACAATTTAGCTGGGTGGTGT 57.324 45.000 0.00 0.00 0.00 4.16
152 155 2.423538 GCTACAATTTAGCTGGGTGGTG 59.576 50.000 0.00 0.00 37.56 4.17
153 156 2.620627 GGCTACAATTTAGCTGGGTGGT 60.621 50.000 14.91 0.00 40.25 4.16
154 157 2.024414 GGCTACAATTTAGCTGGGTGG 58.976 52.381 14.91 0.00 40.25 4.61
155 158 2.684881 CTGGCTACAATTTAGCTGGGTG 59.315 50.000 14.91 0.00 40.25 4.61
156 159 2.308866 ACTGGCTACAATTTAGCTGGGT 59.691 45.455 14.91 10.41 40.25 4.51
170 187 2.354704 GCATAACACACTCCACTGGCTA 60.355 50.000 0.00 0.00 0.00 3.93
248 270 1.821332 GGCAGTGGCTACCATCTGC 60.821 63.158 22.26 22.26 46.97 4.26
349 381 2.099592 CCACTGCACTCAAAAGCTCAAA 59.900 45.455 0.00 0.00 0.00 2.69
350 382 1.677576 CCACTGCACTCAAAAGCTCAA 59.322 47.619 0.00 0.00 0.00 3.02
351 383 1.134128 TCCACTGCACTCAAAAGCTCA 60.134 47.619 0.00 0.00 0.00 4.26
352 384 1.534595 CTCCACTGCACTCAAAAGCTC 59.465 52.381 0.00 0.00 0.00 4.09
353 385 1.133976 ACTCCACTGCACTCAAAAGCT 60.134 47.619 0.00 0.00 0.00 3.74
354 386 1.002033 CACTCCACTGCACTCAAAAGC 60.002 52.381 0.00 0.00 0.00 3.51
355 387 2.292267 ACACTCCACTGCACTCAAAAG 58.708 47.619 0.00 0.00 0.00 2.27
356 388 2.418368 ACACTCCACTGCACTCAAAA 57.582 45.000 0.00 0.00 0.00 2.44
400 433 4.818546 CAGCTTAAGTATGATCAAGTGGGG 59.181 45.833 0.00 0.00 0.00 4.96
456 490 6.857451 CGAATTTGCGATCATGGAAAATCATA 59.143 34.615 0.00 0.00 31.02 2.15
473 507 2.788786 CCACCGAAATATGCGAATTTGC 59.211 45.455 10.99 10.99 0.00 3.68
476 510 1.953686 CCCCACCGAAATATGCGAATT 59.046 47.619 0.00 0.00 0.00 2.17
591 642 4.698575 TCGGAAATTCTTTTGGTTTTGGG 58.301 39.130 0.00 0.00 0.00 4.12
682 733 6.820656 ACTACAGCAATTGTGGAAGAAGATAG 59.179 38.462 7.40 3.01 40.46 2.08
692 743 5.627499 ATGTTACACTACAGCAATTGTGG 57.373 39.130 7.40 2.15 43.36 4.17
736 787 1.251251 CCTACTTGCCTTGCTTTGCT 58.749 50.000 0.00 0.00 0.00 3.91
805 867 5.791141 AGGGGAGGGTAGAATTGGTATTATC 59.209 44.000 0.00 0.00 0.00 1.75
811 873 1.203570 ACAGGGGAGGGTAGAATTGGT 60.204 52.381 0.00 0.00 0.00 3.67
906 1022 2.359850 GTGGTGCTTGGATCGGCA 60.360 61.111 3.14 3.14 36.01 5.69
1595 2903 2.060383 TCCTCCAGCTCCATCACCG 61.060 63.158 0.00 0.00 0.00 4.94
1733 3049 0.887933 ACAAATGGCGATCAACCCAC 59.112 50.000 0.00 0.00 33.17 4.61
1845 3185 0.036388 AACATGCCGTCGGTCTCAAT 60.036 50.000 13.94 0.00 0.00 2.57
1846 3186 0.250124 AAACATGCCGTCGGTCTCAA 60.250 50.000 13.94 0.00 0.00 3.02
1886 3226 5.879237 TGTCACTTCACATTTTTCACTCAC 58.121 37.500 0.00 0.00 0.00 3.51
1887 3227 6.507958 TTGTCACTTCACATTTTTCACTCA 57.492 33.333 0.00 0.00 0.00 3.41
1888 3228 7.489113 ACATTTGTCACTTCACATTTTTCACTC 59.511 33.333 0.00 0.00 0.00 3.51
1889 3229 7.322664 ACATTTGTCACTTCACATTTTTCACT 58.677 30.769 0.00 0.00 0.00 3.41
1896 3236 5.104982 ACCCAAACATTTGTCACTTCACATT 60.105 36.000 3.79 0.00 36.45 2.71
2049 3423 9.382275 CTTTAGCTGCCAACCAAAAATAATAAT 57.618 29.630 0.00 0.00 0.00 1.28
2053 3427 5.988561 CACTTTAGCTGCCAACCAAAAATAA 59.011 36.000 0.00 0.00 0.00 1.40
2055 3432 4.379652 CACTTTAGCTGCCAACCAAAAAT 58.620 39.130 0.00 0.00 0.00 1.82
2061 3438 1.877576 GCCCACTTTAGCTGCCAACC 61.878 60.000 0.00 0.00 0.00 3.77
2068 3445 2.675658 TTTTCCAGCCCACTTTAGCT 57.324 45.000 0.00 0.00 40.89 3.32
2096 3474 0.873312 CTGGTCGATCAGGACATGCG 60.873 60.000 18.34 0.00 38.70 4.73
2135 3513 0.102300 AAACTTGCAGGCGTTTGGAC 59.898 50.000 9.21 0.00 32.55 4.02
2136 3514 0.383949 GAAACTTGCAGGCGTTTGGA 59.616 50.000 13.33 0.00 33.82 3.53
2137 3515 0.102120 TGAAACTTGCAGGCGTTTGG 59.898 50.000 13.33 0.00 33.82 3.28
2138 3516 1.788308 CATGAAACTTGCAGGCGTTTG 59.212 47.619 13.33 0.50 33.82 2.93
2139 3517 1.408702 ACATGAAACTTGCAGGCGTTT 59.591 42.857 0.00 9.64 36.16 3.60
2140 3518 1.032014 ACATGAAACTTGCAGGCGTT 58.968 45.000 0.00 0.00 0.00 4.84
2141 3519 1.032014 AACATGAAACTTGCAGGCGT 58.968 45.000 0.00 0.00 0.00 5.68
2142 3520 1.411394 CAACATGAAACTTGCAGGCG 58.589 50.000 0.00 0.00 0.00 5.52
2154 3532 2.136298 ACCAACACACACCAACATGA 57.864 45.000 0.00 0.00 0.00 3.07
2155 3533 2.293122 CCTACCAACACACACCAACATG 59.707 50.000 0.00 0.00 0.00 3.21
2220 3598 2.671396 CGACACCAACCACTAGTATTGC 59.329 50.000 11.80 1.02 0.00 3.56
2221 3599 2.671396 GCGACACCAACCACTAGTATTG 59.329 50.000 10.71 10.71 0.00 1.90
2222 3600 2.354403 GGCGACACCAACCACTAGTATT 60.354 50.000 0.00 0.00 38.86 1.89
2223 3601 1.206371 GGCGACACCAACCACTAGTAT 59.794 52.381 0.00 0.00 38.86 2.12
2224 3602 0.604578 GGCGACACCAACCACTAGTA 59.395 55.000 0.00 0.00 38.86 1.82
2225 3603 1.370064 GGCGACACCAACCACTAGT 59.630 57.895 0.00 0.00 38.86 2.57
2226 3604 1.736645 CGGCGACACCAACCACTAG 60.737 63.158 0.00 0.00 39.03 2.57
2227 3605 1.537814 ATCGGCGACACCAACCACTA 61.538 55.000 13.76 0.00 39.03 2.74
2228 3606 2.879233 ATCGGCGACACCAACCACT 61.879 57.895 13.76 0.00 39.03 4.00
2229 3607 2.358247 ATCGGCGACACCAACCAC 60.358 61.111 13.76 0.00 39.03 4.16
2230 3608 2.358125 CATCGGCGACACCAACCA 60.358 61.111 13.76 0.00 39.03 3.67
2231 3609 1.669760 TTCATCGGCGACACCAACC 60.670 57.895 13.76 0.00 39.03 3.77
2232 3610 1.495951 GTTCATCGGCGACACCAAC 59.504 57.895 13.76 9.00 39.03 3.77
2233 3611 1.669760 GGTTCATCGGCGACACCAA 60.670 57.895 23.03 8.30 39.03 3.67
2234 3612 2.047655 GGTTCATCGGCGACACCA 60.048 61.111 23.03 3.30 39.03 4.17
2235 3613 1.024579 ATTGGTTCATCGGCGACACC 61.025 55.000 21.81 21.81 0.00 4.16
2236 3614 0.373716 GATTGGTTCATCGGCGACAC 59.626 55.000 13.76 9.58 0.00 3.67
2237 3615 1.081556 CGATTGGTTCATCGGCGACA 61.082 55.000 13.76 1.46 36.72 4.35
2238 3616 0.804544 TCGATTGGTTCATCGGCGAC 60.805 55.000 13.76 0.00 40.38 5.19
2239 3617 0.108567 TTCGATTGGTTCATCGGCGA 60.109 50.000 13.87 13.87 40.38 5.54
2240 3618 0.937304 ATTCGATTGGTTCATCGGCG 59.063 50.000 0.00 0.00 40.38 6.46
2241 3619 3.420839 AAATTCGATTGGTTCATCGGC 57.579 42.857 3.42 0.00 40.38 5.54
2242 3620 4.554723 GCCTAAATTCGATTGGTTCATCGG 60.555 45.833 3.42 0.00 40.38 4.18
2243 3621 4.035091 TGCCTAAATTCGATTGGTTCATCG 59.965 41.667 0.00 0.00 41.24 3.84
2244 3622 5.499139 TGCCTAAATTCGATTGGTTCATC 57.501 39.130 0.00 0.00 0.00 2.92
2245 3623 5.829924 AGATGCCTAAATTCGATTGGTTCAT 59.170 36.000 0.00 0.00 0.00 2.57
2246 3624 5.066375 CAGATGCCTAAATTCGATTGGTTCA 59.934 40.000 0.00 0.00 0.00 3.18
2247 3625 5.066505 ACAGATGCCTAAATTCGATTGGTTC 59.933 40.000 0.00 0.00 0.00 3.62
2248 3626 4.949856 ACAGATGCCTAAATTCGATTGGTT 59.050 37.500 0.00 0.00 0.00 3.67
2249 3627 4.526970 ACAGATGCCTAAATTCGATTGGT 58.473 39.130 0.00 0.00 0.00 3.67
2250 3628 6.618287 TTACAGATGCCTAAATTCGATTGG 57.382 37.500 0.00 0.00 0.00 3.16
2251 3629 7.080099 CCATTACAGATGCCTAAATTCGATTG 58.920 38.462 0.00 0.00 0.00 2.67
2252 3630 6.294176 GCCATTACAGATGCCTAAATTCGATT 60.294 38.462 0.00 0.00 0.00 3.34
2253 3631 5.182001 GCCATTACAGATGCCTAAATTCGAT 59.818 40.000 0.00 0.00 0.00 3.59
2254 3632 4.515191 GCCATTACAGATGCCTAAATTCGA 59.485 41.667 0.00 0.00 0.00 3.71
2255 3633 4.275689 TGCCATTACAGATGCCTAAATTCG 59.724 41.667 0.00 0.00 0.00 3.34
2256 3634 5.772825 TGCCATTACAGATGCCTAAATTC 57.227 39.130 0.00 0.00 0.00 2.17
2257 3635 5.163416 GGTTGCCATTACAGATGCCTAAATT 60.163 40.000 0.00 0.00 0.00 1.82
2258 3636 4.342092 GGTTGCCATTACAGATGCCTAAAT 59.658 41.667 0.00 0.00 0.00 1.40
2259 3637 3.699038 GGTTGCCATTACAGATGCCTAAA 59.301 43.478 0.00 0.00 0.00 1.85
2260 3638 3.287222 GGTTGCCATTACAGATGCCTAA 58.713 45.455 0.00 0.00 0.00 2.69
2261 3639 2.422803 GGGTTGCCATTACAGATGCCTA 60.423 50.000 0.00 0.00 0.00 3.93
2262 3640 1.686115 GGGTTGCCATTACAGATGCCT 60.686 52.381 0.00 0.00 0.00 4.75
2263 3641 0.746659 GGGTTGCCATTACAGATGCC 59.253 55.000 0.00 0.00 0.00 4.40
2264 3642 1.473258 TGGGTTGCCATTACAGATGC 58.527 50.000 0.00 0.00 0.00 3.91
2265 3643 5.850557 TTTATGGGTTGCCATTACAGATG 57.149 39.130 0.00 0.00 0.00 2.90
2266 3644 6.865834 TTTTTATGGGTTGCCATTACAGAT 57.134 33.333 0.00 0.00 0.00 2.90
2286 3664 1.002087 AGACGGATGCGAGAGGTTTTT 59.998 47.619 15.49 0.00 0.00 1.94
2287 3665 0.608640 AGACGGATGCGAGAGGTTTT 59.391 50.000 15.49 0.00 0.00 2.43
2288 3666 0.108615 CAGACGGATGCGAGAGGTTT 60.109 55.000 15.49 0.00 0.00 3.27
2289 3667 1.513158 CAGACGGATGCGAGAGGTT 59.487 57.895 15.49 0.00 0.00 3.50
2290 3668 3.069980 GCAGACGGATGCGAGAGGT 62.070 63.158 15.49 0.00 36.28 3.85
2291 3669 2.279120 GCAGACGGATGCGAGAGG 60.279 66.667 15.49 0.59 36.28 3.69
2680 4058 5.357314 TCCGGTTAGTTTGATTTGTTGTGAA 59.643 36.000 0.00 0.00 0.00 3.18
2681 4059 4.882427 TCCGGTTAGTTTGATTTGTTGTGA 59.118 37.500 0.00 0.00 0.00 3.58
2682 4060 4.973663 GTCCGGTTAGTTTGATTTGTTGTG 59.026 41.667 0.00 0.00 0.00 3.33
2683 4061 4.260866 CGTCCGGTTAGTTTGATTTGTTGT 60.261 41.667 0.00 0.00 0.00 3.32
2684 4062 4.024725 TCGTCCGGTTAGTTTGATTTGTTG 60.025 41.667 0.00 0.00 0.00 3.33
2685 4063 4.128643 TCGTCCGGTTAGTTTGATTTGTT 58.871 39.130 0.00 0.00 0.00 2.83
2686 4064 3.731089 TCGTCCGGTTAGTTTGATTTGT 58.269 40.909 0.00 0.00 0.00 2.83
2687 4065 4.735662 TTCGTCCGGTTAGTTTGATTTG 57.264 40.909 0.00 0.00 0.00 2.32
2688 4066 5.952526 ATTTCGTCCGGTTAGTTTGATTT 57.047 34.783 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.