Multiple sequence alignment - TraesCS3D01G224000

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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 TraesCS3D01G224000 chr3D 100.000 3836 0 0 1 3836 305578667 305582502 0.000000e+00 7084.0
1 TraesCS3D01G224000 chr3D 93.046 417 27 2 1404 1819 573690588 573691003 3.280000e-170 608.0
2 TraesCS3D01G224000 chr3D 80.541 370 40 19 2668 3006 573691217 573691585 4.920000e-64 255.0
3 TraesCS3D01G224000 chr3D 91.489 141 11 1 988 1128 573690236 573690375 3.910000e-45 193.0
4 TraesCS3D01G224000 chr3D 92.523 107 8 0 1197 1303 573690411 573690517 1.850000e-33 154.0
5 TraesCS3D01G224000 chr3D 94.565 92 5 0 1931 2022 573691000 573691091 3.990000e-30 143.0
6 TraesCS3D01G224000 chr3D 94.545 55 3 0 2118 2172 582536283 582536337 6.830000e-13 86.1
7 TraesCS3D01G224000 chr3A 92.936 2095 85 25 7 2086 423618087 423620133 0.000000e+00 2990.0
8 TraesCS3D01G224000 chr3A 90.067 1802 98 38 2083 3836 423620377 423622145 0.000000e+00 2261.0
9 TraesCS3D01G224000 chr3A 93.029 416 27 2 1405 1819 708322768 708323182 1.180000e-169 606.0
10 TraesCS3D01G224000 chr3A 77.656 546 48 35 2495 3006 708325376 708325881 8.170000e-67 265.0
11 TraesCS3D01G224000 chr3A 81.375 349 32 20 2689 3006 708323419 708323765 1.770000e-63 254.0
12 TraesCS3D01G224000 chr3A 87.261 157 17 1 972 1125 708322389 708322545 3.940000e-40 176.0
13 TraesCS3D01G224000 chr3A 93.478 92 6 0 1931 2022 708323179 708323270 1.860000e-28 137.0
14 TraesCS3D01G224000 chr3A 95.402 87 3 1 2495 2581 708323264 708323349 1.860000e-28 137.0
15 TraesCS3D01G224000 chr3B 93.376 1872 90 13 1 1858 416153252 416151401 0.000000e+00 2739.0
16 TraesCS3D01G224000 chr3B 94.508 874 32 8 2139 3007 416150776 416149914 0.000000e+00 1334.0
17 TraesCS3D01G224000 chr3B 88.076 629 53 10 3227 3836 416139249 416138624 0.000000e+00 726.0
18 TraesCS3D01G224000 chr3B 92.326 417 30 2 1404 1819 763774075 763773660 3.300000e-165 592.0
19 TraesCS3D01G224000 chr3B 91.444 187 13 1 3046 3232 416147767 416147584 1.770000e-63 254.0
20 TraesCS3D01G224000 chr3B 80.495 364 39 16 2668 3001 763773445 763773084 2.290000e-62 250.0
21 TraesCS3D01G224000 chr3B 87.037 162 20 1 991 1152 763774421 763774261 8.470000e-42 182.0
22 TraesCS3D01G224000 chr3B 94.565 92 5 0 1931 2022 763773663 763773572 3.990000e-30 143.0
23 TraesCS3D01G224000 chr3B 88.496 113 7 4 1197 1303 763774249 763774137 8.650000e-27 132.0
24 TraesCS3D01G224000 chr3B 86.111 72 7 2 1885 1955 416151348 416151279 1.480000e-09 75.0


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 TraesCS3D01G224000 chr3D 305578667 305582502 3835 False 7084.0 7084 100.00000 1 3836 1 chr3D.!!$F1 3835
1 TraesCS3D01G224000 chr3D 573690236 573691585 1349 False 270.6 608 90.43280 988 3006 5 chr3D.!!$F3 2018
2 TraesCS3D01G224000 chr3A 423618087 423622145 4058 False 2625.5 2990 91.50150 7 3836 2 chr3A.!!$F1 3829
3 TraesCS3D01G224000 chr3A 708322389 708325881 3492 False 262.5 606 88.03350 972 3006 6 chr3A.!!$F2 2034
4 TraesCS3D01G224000 chr3B 416147584 416153252 5668 True 1100.5 2739 91.35975 1 3232 4 chr3B.!!$R2 3231
5 TraesCS3D01G224000 chr3B 416138624 416139249 625 True 726.0 726 88.07600 3227 3836 1 chr3B.!!$R1 609
6 TraesCS3D01G224000 chr3B 763773084 763774421 1337 True 259.8 592 88.58380 991 3001 5 chr3B.!!$R3 2010

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
109 111 0.037590 ATAAGCTCGTGGGGCAACAA 59.962 50.0 0.00 0.0 39.74 2.83 F
183 185 0.041982 GAAGAGGAGGAGGAGGTGGT 59.958 60.0 0.00 0.0 0.00 4.16 F
554 556 0.108329 GTAGTGTCCACGGTGATGGG 60.108 60.0 10.28 0.0 40.49 4.00 F
2392 2832 0.809636 GTGCACCAAAGCCACCAAAC 60.810 55.0 5.22 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1369 0.322975 ACAGGCCACATCTCACTCAC 59.677 55.000 5.01 0.00 0.00 3.51 R
1923 2007 0.883153 GTGAACATCACCTGCATGCA 59.117 50.000 21.29 21.29 41.37 3.96 R
2459 2899 0.315869 GTTTGTCAGCGACGTTGGTG 60.316 55.000 25.76 25.76 34.95 4.17 R
3431 8143 1.078710 ACTGGGGCTCTAGGAACGT 59.921 57.895 0.58 0.00 0.00 3.99 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
42 44 3.654414 CCTGCTTCAAAACTAGTCGTCT 58.346 45.455 0.00 0.00 0.00 4.18
61 63 0.416231 TAGGGTGGAGGGCAACTACT 59.584 55.000 0.00 0.00 0.00 2.57
64 66 0.912486 GGTGGAGGGCAACTACTGAT 59.088 55.000 0.00 0.00 0.00 2.90
72 74 3.461085 AGGGCAACTACTGATGATGGATT 59.539 43.478 0.00 0.00 0.00 3.01
81 83 3.208594 CTGATGATGGATTTGGCGAGAA 58.791 45.455 0.00 0.00 0.00 2.87
106 108 2.639065 CTTAATAAGCTCGTGGGGCAA 58.361 47.619 0.00 0.00 0.00 4.52
109 111 0.037590 ATAAGCTCGTGGGGCAACAA 59.962 50.000 0.00 0.00 39.74 2.83
119 121 1.271271 TGGGGCAACAAAATCCATTGC 60.271 47.619 0.00 0.00 46.39 3.56
141 143 4.199310 CAGTTGGAGGTTGTTTCTCTTCA 58.801 43.478 0.00 0.00 0.00 3.02
153 155 7.402640 GTTGTTTCTCTTCATATTCTTAGCCG 58.597 38.462 0.00 0.00 0.00 5.52
163 165 0.676466 TTCTTAGCCGCCACATGGTG 60.676 55.000 4.38 4.38 45.02 4.17
177 179 0.719015 ATGGTGGAAGAGGAGGAGGA 59.281 55.000 0.00 0.00 0.00 3.71
182 184 0.689412 GGAAGAGGAGGAGGAGGTGG 60.689 65.000 0.00 0.00 0.00 4.61
183 185 0.041982 GAAGAGGAGGAGGAGGTGGT 59.958 60.000 0.00 0.00 0.00 4.16
184 186 0.252467 AAGAGGAGGAGGAGGTGGTG 60.252 60.000 0.00 0.00 0.00 4.17
191 193 1.681486 GGAGGAGGTGGTGAGCTAGC 61.681 65.000 6.62 6.62 0.00 3.42
241 243 2.428925 GGGTCTTCGGCGGTGGATA 61.429 63.158 7.21 0.00 0.00 2.59
271 273 6.392354 CATGTACCATTGCTTTGATTTGAGT 58.608 36.000 0.00 0.00 0.00 3.41
308 310 2.046283 TGAAGTGAAGCTACGACACG 57.954 50.000 0.00 0.00 39.19 4.49
369 371 0.250597 AAAGTTGAGTGTACCGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
428 430 1.954927 CTTCCAGTTATTCCTCCCGC 58.045 55.000 0.00 0.00 0.00 6.13
472 474 2.359107 TGGCTTCAGCTCGGCTTG 60.359 61.111 0.00 0.00 36.40 4.01
487 489 2.616510 CGGCTTGAGTCTTTTCCATCCT 60.617 50.000 0.00 0.00 0.00 3.24
504 506 0.798776 CCTTGACATGAGTTGGCGTC 59.201 55.000 0.00 0.00 35.37 5.19
521 523 1.081641 TCGAAGCGACGACAAGGTC 60.082 57.895 0.00 0.00 37.37 3.85
554 556 0.108329 GTAGTGTCCACGGTGATGGG 60.108 60.000 10.28 0.00 40.49 4.00
567 569 2.508526 GTGATGGGGATCTTGGTATGC 58.491 52.381 0.00 0.00 0.00 3.14
574 576 1.271054 GGATCTTGGTATGCGGCTGAT 60.271 52.381 0.00 0.00 0.00 2.90
602 604 4.023279 CGAAAAAGGACCACATCACATTCA 60.023 41.667 0.00 0.00 0.00 2.57
610 612 4.206375 ACCACATCACATTCAACAACTCA 58.794 39.130 0.00 0.00 0.00 3.41
620 622 0.883833 CAACAACTCATGTCCAGGGC 59.116 55.000 0.00 0.00 42.99 5.19
661 663 4.100808 TGGGCTCAGTTGTAATTTTGCTTT 59.899 37.500 0.00 0.00 0.00 3.51
804 807 6.829849 AGGAAATGAATGCCTTGAAGAAAAA 58.170 32.000 0.00 0.00 0.00 1.94
935 938 2.373502 AGAACCAAGAAGTGCCTAGCTT 59.626 45.455 0.00 0.00 0.00 3.74
936 939 2.959465 ACCAAGAAGTGCCTAGCTTT 57.041 45.000 0.00 0.00 0.00 3.51
937 940 4.041691 AGAACCAAGAAGTGCCTAGCTTTA 59.958 41.667 0.00 0.00 0.00 1.85
962 965 1.877443 ACCAACGCACAACTAACCATC 59.123 47.619 0.00 0.00 0.00 3.51
1128 1134 1.152567 CTGGGTGCCCAAGGACAAA 60.153 57.895 11.54 0.00 46.63 2.83
1323 1368 3.949113 TGGTGATGCTACGTAGTACATGA 59.051 43.478 22.98 10.74 45.11 3.07
1324 1369 4.036380 TGGTGATGCTACGTAGTACATGAG 59.964 45.833 22.98 0.00 45.11 2.90
1325 1370 4.036498 GGTGATGCTACGTAGTACATGAGT 59.964 45.833 22.98 3.21 45.11 3.41
1326 1371 4.970611 GTGATGCTACGTAGTACATGAGTG 59.029 45.833 22.98 0.00 45.11 3.51
1360 1405 3.426292 GCCTGTTTCCGTTGAGATTAAGC 60.426 47.826 0.00 0.00 0.00 3.09
1604 1656 1.821332 GCCTTCAAGATGGCCGAGG 60.821 63.158 14.23 0.00 43.54 4.63
1907 1991 4.642445 TTTGGATGTGCATGATGTGATC 57.358 40.909 0.00 0.00 0.00 2.92
1918 2002 1.003464 TGATGTGATCTGTGGTGGGTG 59.997 52.381 0.00 0.00 0.00 4.61
1920 2004 2.034879 GTGATCTGTGGTGGGTGCG 61.035 63.158 0.00 0.00 0.00 5.34
1921 2005 3.127533 GATCTGTGGTGGGTGCGC 61.128 66.667 0.00 0.00 0.00 6.09
1922 2006 3.899981 GATCTGTGGTGGGTGCGCA 62.900 63.158 5.66 5.66 0.00 6.09
1923 2007 3.272364 ATCTGTGGTGGGTGCGCAT 62.272 57.895 15.91 0.00 0.00 4.73
1924 2008 3.740397 CTGTGGTGGGTGCGCATG 61.740 66.667 15.91 0.00 0.00 4.06
2129 2559 5.351948 AAAAACAGTACACCAATTTGCCT 57.648 34.783 0.00 0.00 0.00 4.75
2142 2572 5.167845 CCAATTTGCCTATTGGTTGTACAC 58.832 41.667 15.37 0.00 46.19 2.90
2187 2620 6.727824 TTGTACTCGTAGTAGTAGTCCAAC 57.272 41.667 0.00 0.00 32.69 3.77
2192 2625 6.179040 ACTCGTAGTAGTAGTCCAACTGATT 58.821 40.000 0.00 0.00 0.00 2.57
2221 2654 3.118482 TCAGGAGGACAGAAGCATTGATC 60.118 47.826 0.00 0.00 0.00 2.92
2392 2832 0.809636 GTGCACCAAAGCCACCAAAC 60.810 55.000 5.22 0.00 0.00 2.93
2459 2899 2.973694 TTCCCGTGATTACCAGTAGC 57.026 50.000 0.00 0.00 0.00 3.58
2465 2905 2.671396 CGTGATTACCAGTAGCACCAAC 59.329 50.000 0.00 0.00 0.00 3.77
2468 2908 2.443887 TTACCAGTAGCACCAACGTC 57.556 50.000 0.00 0.00 0.00 4.34
2663 3104 1.320344 TAAGCGTGTGAGCCGAGGAT 61.320 55.000 0.00 0.00 38.01 3.24
2664 3105 2.125512 GCGTGTGAGCCGAGGATT 60.126 61.111 0.00 0.00 0.00 3.01
2843 5409 4.762251 AGCTTCCAAGGAGTGACAAATTAC 59.238 41.667 0.00 0.00 0.00 1.89
2860 5430 0.548031 TACTAGGTCCATCGTCCCGT 59.452 55.000 0.00 0.00 0.00 5.28
2870 5444 0.739561 ATCGTCCCGTAGAGTGCTTC 59.260 55.000 0.00 0.00 0.00 3.86
2881 5455 5.377358 CGTAGAGTGCTTCATTTGTTCAAG 58.623 41.667 0.00 0.00 0.00 3.02
2903 5477 2.307686 GAGAACTGGGGTCCCATTTGTA 59.692 50.000 15.11 0.00 46.15 2.41
3013 5607 3.419264 TTGCAGCTAAACAGTTGTGTG 57.581 42.857 0.00 0.00 36.84 3.82
3028 5635 2.480224 GTGTGCATCACATACATGGC 57.520 50.000 12.63 0.00 46.32 4.40
3037 5644 5.478407 CATCACATACATGGCTAACGGATA 58.522 41.667 0.00 0.00 0.00 2.59
3086 7788 7.562454 AAATCTTTAACTCTCAAACGGTCAA 57.438 32.000 0.00 0.00 0.00 3.18
3111 7813 9.836864 AAAAGAGCAAAATTTGAAGGAGTTAAT 57.163 25.926 10.26 0.00 0.00 1.40
3131 7833 4.790718 ATTTTCATACCCACCCTACTCC 57.209 45.455 0.00 0.00 0.00 3.85
3142 7844 5.193124 ACCCACCCTACTCCCTTATTTTTAG 59.807 44.000 0.00 0.00 0.00 1.85
3172 7874 1.021390 GGACATGACACCGCTCCTTG 61.021 60.000 0.00 0.00 0.00 3.61
3290 7992 0.032815 TTGTCGGCGTCAGAATCACA 59.967 50.000 6.85 0.00 0.00 3.58
3326 8029 4.559099 ATTTCGTGAAATCATGCTTGTGCA 60.559 37.500 2.04 0.00 44.18 4.57
3327 8030 5.851972 ATTTCGTGAAATCATGCTTGTGCAT 60.852 36.000 2.04 0.00 45.01 3.96
3328 8031 6.625520 ATTTCGTGAAATCATGCTTGTGCATA 60.626 34.615 3.08 0.00 45.77 3.14
3329 8032 8.053664 ATTTCGTGAAATCATGCTTGTGCATAA 61.054 33.333 3.08 0.00 45.77 1.90
3341 8051 1.148048 TGCATAATGCTGGCGGCTA 59.852 52.632 20.66 4.66 45.31 3.93
3356 8066 0.462759 GGCTATGTGTGCTCACCTCC 60.463 60.000 15.83 7.96 43.26 4.30
3377 8087 2.821366 GCCTCCTCCGTCGTCGTA 60.821 66.667 0.71 0.00 35.01 3.43
3428 8140 0.315251 CCTTCTAGCGCATCATCGGA 59.685 55.000 11.47 0.00 0.00 4.55
3431 8143 1.164041 TCTAGCGCATCATCGGACGA 61.164 55.000 11.47 0.00 0.00 4.20
3445 8157 1.432657 GACGACGTTCCTAGAGCCC 59.567 63.158 0.13 0.00 0.00 5.19
3458 8170 3.252284 AGCCCCAGTGGTGTCCTG 61.252 66.667 8.74 0.00 36.04 3.86
3568 8289 2.758770 TTCGTGAAACTCCTCGCCGG 62.759 60.000 0.00 0.00 31.75 6.13
3569 8290 2.342648 GTGAAACTCCTCGCCGGT 59.657 61.111 1.90 0.00 0.00 5.28
3571 8292 2.434359 GAAACTCCTCGCCGGTGG 60.434 66.667 16.49 9.55 0.00 4.61
3572 8293 3.236003 GAAACTCCTCGCCGGTGGT 62.236 63.158 16.49 1.40 0.00 4.16
3665 8386 0.179081 GGGCGCGTCTAAAGGAAGAT 60.179 55.000 11.94 0.00 0.00 2.40
3672 8393 4.566759 CGCGTCTAAAGGAAGATGATGAAA 59.433 41.667 0.00 0.00 34.94 2.69
3697 8418 3.117512 AGACTTTCATGTGGGGTCAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
3724 8446 4.285003 TGAGGACTTAAATTGAGGGTTCGA 59.715 41.667 0.00 0.00 0.00 3.71
3738 8460 1.470458 GGTTCGATTAGGTCCGGTCAC 60.470 57.143 0.00 0.00 0.00 3.67
3743 8465 2.802057 CGATTAGGTCCGGTCACCATTC 60.802 54.545 14.39 7.00 39.16 2.67
3763 8485 8.462016 ACCATTCAACTTCTCAAACTATAATGC 58.538 33.333 0.00 0.00 0.00 3.56
3820 8542 2.390225 AGGGATCGGTTAGAGATGCT 57.610 50.000 0.00 0.00 36.79 3.79
3823 8545 2.029470 GGGATCGGTTAGAGATGCTCTG 60.029 54.545 7.19 0.00 41.37 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.272334 GGCGCCGACCATCATGTC 61.272 66.667 12.58 0.00 0.00 3.06
42 44 0.416231 AGTAGTTGCCCTCCACCCTA 59.584 55.000 0.00 0.00 0.00 3.53
61 63 2.945008 GTTCTCGCCAAATCCATCATCA 59.055 45.455 0.00 0.00 0.00 3.07
64 66 2.787473 AGTTCTCGCCAAATCCATCA 57.213 45.000 0.00 0.00 0.00 3.07
72 74 4.634443 GCTTATTAAGGAAGTTCTCGCCAA 59.366 41.667 2.25 0.00 0.00 4.52
81 83 3.118371 CCCCACGAGCTTATTAAGGAAGT 60.118 47.826 5.61 0.00 0.00 3.01
106 108 3.007182 CCTCCAACTGCAATGGATTTTGT 59.993 43.478 18.46 0.00 45.57 2.83
109 111 2.893424 ACCTCCAACTGCAATGGATTT 58.107 42.857 18.46 8.15 45.57 2.17
119 121 4.199310 TGAAGAGAAACAACCTCCAACTG 58.801 43.478 0.00 0.00 0.00 3.16
141 143 2.106511 ACCATGTGGCGGCTAAGAATAT 59.893 45.455 11.43 0.00 39.32 1.28
163 165 0.689412 CCACCTCCTCCTCCTCTTCC 60.689 65.000 0.00 0.00 0.00 3.46
177 179 2.352032 GGACGCTAGCTCACCACCT 61.352 63.158 13.93 0.00 0.00 4.00
182 184 1.351153 GAAGTTGGACGCTAGCTCAC 58.649 55.000 13.93 2.79 0.00 3.51
183 185 0.246635 GGAAGTTGGACGCTAGCTCA 59.753 55.000 13.93 5.69 0.00 4.26
184 186 0.533032 AGGAAGTTGGACGCTAGCTC 59.467 55.000 13.93 9.21 0.00 4.09
191 193 3.777465 TCGATCTAAGGAAGTTGGACG 57.223 47.619 0.00 0.00 0.00 4.79
241 243 2.795231 AGCAATGGTACATGCTCTGT 57.205 45.000 12.61 0.00 45.08 3.41
243 245 3.689347 TCAAAGCAATGGTACATGCTCT 58.311 40.909 17.07 4.45 46.55 4.09
271 273 0.516877 CAAAACGCCGCTGAGATGAA 59.483 50.000 0.00 0.00 0.00 2.57
308 310 4.458989 TCAACCATTGAAGCAACATAGGTC 59.541 41.667 0.00 0.00 36.59 3.85
369 371 1.448540 CTCTACGCAGCCACCCTTG 60.449 63.158 0.00 0.00 0.00 3.61
381 383 1.007964 CTGATGCCGGAGCTCTACG 60.008 63.158 14.64 9.59 40.80 3.51
428 430 3.285484 CCTCTCCTTTTGACATCATGGG 58.715 50.000 0.00 0.00 0.00 4.00
462 464 1.609320 GGAAAAGACTCAAGCCGAGCT 60.609 52.381 0.71 0.00 46.63 4.09
472 474 5.248640 TCATGTCAAGGATGGAAAAGACTC 58.751 41.667 0.00 0.00 0.00 3.36
474 476 5.006386 ACTCATGTCAAGGATGGAAAAGAC 58.994 41.667 0.00 0.00 0.00 3.01
476 478 5.336213 CCAACTCATGTCAAGGATGGAAAAG 60.336 44.000 0.00 0.00 30.53 2.27
478 480 4.081406 CCAACTCATGTCAAGGATGGAAA 58.919 43.478 0.00 0.00 30.53 3.13
487 489 0.032815 TCGACGCCAACTCATGTCAA 59.967 50.000 0.00 0.00 0.00 3.18
504 506 3.449042 GACCTTGTCGTCGCTTCG 58.551 61.111 0.00 0.00 0.00 3.79
539 541 1.615124 ATCCCCATCACCGTGGACA 60.615 57.895 0.00 0.00 42.02 4.02
554 556 0.106708 TCAGCCGCATACCAAGATCC 59.893 55.000 0.00 0.00 0.00 3.36
574 576 0.181587 TGTGGTCCTTTTTCGAGGCA 59.818 50.000 0.00 0.00 36.71 4.75
602 604 0.606401 CGCCCTGGACATGAGTTGTT 60.606 55.000 0.00 0.00 39.18 2.83
661 663 2.983192 TGTCACCAGGACCCATAGAAAA 59.017 45.455 0.00 0.00 46.38 2.29
668 670 0.986019 ACAACTGTCACCAGGACCCA 60.986 55.000 0.00 0.00 46.38 4.51
735 738 2.489528 TCTACCGATCTGGGGGAAAT 57.510 50.000 8.20 0.00 44.64 2.17
935 938 6.877855 TGGTTAGTTGTGCGTTGGTATAATAA 59.122 34.615 0.00 0.00 0.00 1.40
936 939 6.404708 TGGTTAGTTGTGCGTTGGTATAATA 58.595 36.000 0.00 0.00 0.00 0.98
937 940 5.247084 TGGTTAGTTGTGCGTTGGTATAAT 58.753 37.500 0.00 0.00 0.00 1.28
1128 1134 0.401395 TGGACTTGTCCTTGGGGAGT 60.401 55.000 19.11 0.00 43.12 3.85
1188 1209 4.001652 TCTTGCTCTGCTTCTTGATCTTG 58.998 43.478 0.00 0.00 0.00 3.02
1189 1210 4.002316 GTCTTGCTCTGCTTCTTGATCTT 58.998 43.478 0.00 0.00 0.00 2.40
1190 1211 3.598299 GTCTTGCTCTGCTTCTTGATCT 58.402 45.455 0.00 0.00 0.00 2.75
1191 1212 2.348059 CGTCTTGCTCTGCTTCTTGATC 59.652 50.000 0.00 0.00 0.00 2.92
1192 1213 2.028658 TCGTCTTGCTCTGCTTCTTGAT 60.029 45.455 0.00 0.00 0.00 2.57
1193 1214 1.341209 TCGTCTTGCTCTGCTTCTTGA 59.659 47.619 0.00 0.00 0.00 3.02
1323 1368 0.612229 CAGGCCACATCTCACTCACT 59.388 55.000 5.01 0.00 0.00 3.41
1324 1369 0.322975 ACAGGCCACATCTCACTCAC 59.677 55.000 5.01 0.00 0.00 3.51
1325 1370 1.059098 AACAGGCCACATCTCACTCA 58.941 50.000 5.01 0.00 0.00 3.41
1326 1371 2.079925 GAAACAGGCCACATCTCACTC 58.920 52.381 5.01 0.00 0.00 3.51
1360 1405 7.946768 CGTCGTGACAGCATGAATTATAATTAG 59.053 37.037 10.68 5.72 41.45 1.73
1660 1712 1.323271 TGGTCTCGCTGATGGAGTCC 61.323 60.000 0.73 0.73 39.31 3.85
1907 1991 3.740397 CATGCGCACCCACCACAG 61.740 66.667 14.90 0.00 0.00 3.66
1921 2005 1.474879 TGAACATCACCTGCATGCATG 59.525 47.619 22.97 22.70 0.00 4.06
1922 2006 1.475280 GTGAACATCACCTGCATGCAT 59.525 47.619 22.97 3.95 41.37 3.96
1923 2007 0.883153 GTGAACATCACCTGCATGCA 59.117 50.000 21.29 21.29 41.37 3.96
1924 2008 3.708195 GTGAACATCACCTGCATGC 57.292 52.632 11.82 11.82 41.37 4.06
2142 2572 6.127814 ACAAAGAGTCAAACATATCATGCTGG 60.128 38.462 0.00 0.00 0.00 4.85
2187 2620 3.945921 TGTCCTCCTGAGTACGTAATCAG 59.054 47.826 34.71 34.71 45.18 2.90
2192 2625 3.607741 CTTCTGTCCTCCTGAGTACGTA 58.392 50.000 0.00 0.00 0.00 3.57
2221 2654 2.710096 ACTCCCAACCATGAATACCG 57.290 50.000 0.00 0.00 0.00 4.02
2270 2704 4.142513 GGTAAGAGCATTGAAAGCCTTCAG 60.143 45.833 0.00 0.00 42.48 3.02
2392 2832 4.641396 TGCTTATATTCTTCACGGATGGG 58.359 43.478 0.00 0.00 0.00 4.00
2459 2899 0.315869 GTTTGTCAGCGACGTTGGTG 60.316 55.000 25.76 25.76 34.95 4.17
2465 2905 0.575390 AGAAACGTTTGTCAGCGACG 59.425 50.000 20.10 0.00 42.13 5.12
2468 2908 2.452006 ACAAGAAACGTTTGTCAGCG 57.548 45.000 20.10 6.77 33.72 5.18
2664 3105 8.732531 CCCGAAAACCATTTGTTAGTATCTAAA 58.267 33.333 0.00 0.00 35.67 1.85
2860 5430 5.620206 TCCTTGAACAAATGAAGCACTCTA 58.380 37.500 0.00 0.00 0.00 2.43
2903 5477 1.269726 CGGCCAAACAATCAAACTGCT 60.270 47.619 2.24 0.00 0.00 4.24
3013 5607 2.224079 CCGTTAGCCATGTATGTGATGC 59.776 50.000 0.00 0.00 0.00 3.91
3028 5635 6.071503 CCACCCTTATTACCTCTATCCGTTAG 60.072 46.154 0.00 0.00 0.00 2.34
3086 7788 9.836864 AATTAACTCCTTCAAATTTTGCTCTTT 57.163 25.926 4.19 0.00 0.00 2.52
3111 7813 2.848071 GGGAGTAGGGTGGGTATGAAAA 59.152 50.000 0.00 0.00 0.00 2.29
3117 7819 4.372953 AAATAAGGGAGTAGGGTGGGTA 57.627 45.455 0.00 0.00 0.00 3.69
3155 7857 0.396435 TTCAAGGAGCGGTGTCATGT 59.604 50.000 0.00 0.00 0.00 3.21
3172 7874 2.554462 GAGAGGCAAGGGAAGTTGTTTC 59.446 50.000 0.00 0.00 34.93 2.78
3282 7984 2.933287 TGGCCCCGGTGTGATTCT 60.933 61.111 0.00 0.00 0.00 2.40
3290 7992 1.677633 CGAAATTTCTGGCCCCGGT 60.678 57.895 15.92 0.00 0.00 5.28
3356 8066 3.432051 GACGACGGAGGAGGCCATG 62.432 68.421 5.01 0.00 0.00 3.66
3428 8140 2.050934 GGGGCTCTAGGAACGTCGT 61.051 63.158 0.00 0.00 0.00 4.34
3431 8143 1.078710 ACTGGGGCTCTAGGAACGT 59.921 57.895 0.58 0.00 0.00 3.99
3445 8157 2.253758 CGTTGCAGGACACCACTGG 61.254 63.158 0.00 0.00 36.48 4.00
3538 8258 1.619526 TTTCACGAAATAGCGCGCGT 61.620 50.000 32.35 20.00 37.48 6.01
3544 8264 2.029365 GCGAGGAGTTTCACGAAATAGC 59.971 50.000 0.00 0.00 32.36 2.97
3552 8272 2.027625 CACCGGCGAGGAGTTTCAC 61.028 63.158 9.30 0.00 45.00 3.18
3672 8393 2.711009 TGACCCCACATGAAAGTCTCTT 59.289 45.455 0.00 0.00 0.00 2.85
3697 8418 5.701224 ACCCTCAATTTAAGTCCTCAAACA 58.299 37.500 0.00 0.00 0.00 2.83
3724 8446 2.193127 TGAATGGTGACCGGACCTAAT 58.807 47.619 9.46 0.00 36.88 1.73
3738 8460 7.641411 CGCATTATAGTTTGAGAAGTTGAATGG 59.359 37.037 0.00 0.00 0.00 3.16
3743 8465 9.478019 CTTAACGCATTATAGTTTGAGAAGTTG 57.522 33.333 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.