Multiple sequence alignment - TraesCS2D01G219100

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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 TraesCS2D01G219100 chr2D 100.000 4203 0 0 1 4203 183380408 183376206 0.000000e+00 7762
1 TraesCS2D01G219100 chr2B 93.680 3592 114 45 674 4203 239198015 239194475 0.000000e+00 5271
2 TraesCS2D01G219100 chr2B 90.691 376 29 5 316 691 239198418 239198049 2.920000e-136 496
3 TraesCS2D01G219100 chr2B 88.820 322 31 4 2 322 239199101 239198784 1.420000e-104 390
4 TraesCS2D01G219100 chr2A 93.651 2268 93 17 376 2625 197793578 197791344 0.000000e+00 3343
5 TraesCS2D01G219100 chr2A 92.431 1057 42 19 2742 3768 197791345 197790297 0.000000e+00 1474
6 TraesCS2D01G219100 chr2A 91.716 1014 53 11 2219 3209 619125407 619126412 0.000000e+00 1378
7 TraesCS2D01G219100 chr2A 90.331 362 8 6 3835 4196 197790119 197789785 2.300000e-122 449
8 TraesCS2D01G219100 chr2A 92.388 289 20 1 2923 3209 481011343 481011055 1.090000e-110 411
9 TraesCS2D01G219100 chr2A 88.474 321 30 6 3 322 197794340 197794026 8.530000e-102 381
10 TraesCS2D01G219100 chr2A 91.358 162 5 5 3757 3918 197790263 197790111 3.290000e-51 213
11 TraesCS2D01G219100 chr7A 91.815 1014 54 10 2219 3209 706110838 706109831 0.000000e+00 1386
12 TraesCS2D01G219100 chr7A 93.439 442 25 2 2770 3209 205042375 205041936 0.000000e+00 652
13 TraesCS2D01G219100 chr7A 92.329 365 18 4 2219 2577 205042728 205042368 1.040000e-140 510
14 TraesCS2D01G219100 chr4A 91.716 1014 56 11 2219 3209 480996365 480997373 0.000000e+00 1382
15 TraesCS2D01G219100 chr4A 92.098 367 19 4 2219 2579 256221504 256221142 3.750000e-140 508
16 TraesCS2D01G219100 chr5A 91.429 1015 56 16 2219 3209 435166325 435167332 0.000000e+00 1363
17 TraesCS2D01G219100 chr5A 90.944 1027 62 11 2207 3209 458455758 458456777 0.000000e+00 1352
18 TraesCS2D01G219100 chr5A 89.183 416 25 10 2351 2750 234866132 234866543 6.270000e-138 501
19 TraesCS2D01G219100 chr1A 90.056 714 47 10 2514 3209 204558600 204557893 0.000000e+00 904


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 TraesCS2D01G219100 chr2D 183376206 183380408 4202 True 7762.000000 7762 100.000000 1 4203 1 chr2D.!!$R1 4202
1 TraesCS2D01G219100 chr2B 239194475 239199101 4626 True 2052.333333 5271 91.063667 2 4203 3 chr2B.!!$R1 4201
2 TraesCS2D01G219100 chr2A 619125407 619126412 1005 False 1378.000000 1378 91.716000 2219 3209 1 chr2A.!!$F1 990
3 TraesCS2D01G219100 chr2A 197789785 197794340 4555 True 1172.000000 3343 91.249000 3 4196 5 chr2A.!!$R2 4193
4 TraesCS2D01G219100 chr7A 706109831 706110838 1007 True 1386.000000 1386 91.815000 2219 3209 1 chr7A.!!$R1 990
5 TraesCS2D01G219100 chr7A 205041936 205042728 792 True 581.000000 652 92.884000 2219 3209 2 chr7A.!!$R2 990
6 TraesCS2D01G219100 chr4A 480996365 480997373 1008 False 1382.000000 1382 91.716000 2219 3209 1 chr4A.!!$F1 990
7 TraesCS2D01G219100 chr5A 435166325 435167332 1007 False 1363.000000 1363 91.429000 2219 3209 1 chr5A.!!$F2 990
8 TraesCS2D01G219100 chr5A 458455758 458456777 1019 False 1352.000000 1352 90.944000 2207 3209 1 chr5A.!!$F3 1002
9 TraesCS2D01G219100 chr1A 204557893 204558600 707 True 904.000000 904 90.056000 2514 3209 1 chr1A.!!$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
479 899 0.393808 TTAGCGGAGGGGAAATGTGC 60.394 55.0 0.00 0.0 0.00 4.57 F
1798 2279 0.179000 CCCCTGGTCGATTGGAAGAG 59.821 60.0 0.00 0.0 0.00 2.85 F
2805 3319 0.527600 CGCAGCGTGTCCATAGCTTA 60.528 55.0 6.65 0.0 39.48 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2541 0.538287 ACCAGAGCAAGTTTCCTGCC 60.538 55.0 0.00 0.0 0.00 4.85 R
3063 3586 0.393537 ATTCCAGCTGTAGCCTGCAC 60.394 55.0 13.81 0.0 43.38 4.57 R
3740 4310 0.395586 AAGCACTCAACCACCAGCAA 60.396 50.0 0.00 0.0 0.00 3.91 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
24 25 4.637534 GCAACTTGTGACATATGAGGTGAT 59.362 41.667 10.38 0.00 0.00 3.06
62 63 9.743581 TTATGCATATAACACATCCATCTCAAT 57.256 29.630 7.36 0.00 0.00 2.57
73 74 9.060347 ACACATCCATCTCAATATGACAAATAC 57.940 33.333 0.00 0.00 0.00 1.89
74 75 8.509690 CACATCCATCTCAATATGACAAATACC 58.490 37.037 0.00 0.00 0.00 2.73
87 88 3.537580 ACAAATACCGTTGTGTGTGACT 58.462 40.909 0.00 0.00 40.22 3.41
125 148 7.878547 TGAACATGGCAATAACAAGATATGA 57.121 32.000 0.00 0.00 0.00 2.15
126 149 8.291191 TGAACATGGCAATAACAAGATATGAA 57.709 30.769 0.00 0.00 0.00 2.57
127 150 8.190122 TGAACATGGCAATAACAAGATATGAAC 58.810 33.333 0.00 0.00 0.00 3.18
128 151 7.643569 ACATGGCAATAACAAGATATGAACA 57.356 32.000 0.00 0.00 0.00 3.18
129 152 8.241497 ACATGGCAATAACAAGATATGAACAT 57.759 30.769 0.00 0.00 0.00 2.71
130 153 8.139350 ACATGGCAATAACAAGATATGAACATG 58.861 33.333 0.00 0.00 36.48 3.21
131 154 7.878547 TGGCAATAACAAGATATGAACATGA 57.121 32.000 0.00 0.00 0.00 3.07
132 155 7.933396 TGGCAATAACAAGATATGAACATGAG 58.067 34.615 0.00 0.00 0.00 2.90
133 156 7.013559 TGGCAATAACAAGATATGAACATGAGG 59.986 37.037 0.00 0.00 0.00 3.86
134 157 7.013655 GGCAATAACAAGATATGAACATGAGGT 59.986 37.037 0.00 0.00 0.00 3.85
135 158 8.072567 GCAATAACAAGATATGAACATGAGGTC 58.927 37.037 0.00 0.00 0.00 3.85
136 159 9.112725 CAATAACAAGATATGAACATGAGGTCA 57.887 33.333 0.00 0.00 0.00 4.02
137 160 9.685276 AATAACAAGATATGAACATGAGGTCAA 57.315 29.630 0.00 0.00 0.00 3.18
138 161 7.621428 AACAAGATATGAACATGAGGTCAAG 57.379 36.000 0.00 0.00 0.00 3.02
139 162 6.950842 ACAAGATATGAACATGAGGTCAAGA 58.049 36.000 0.00 0.00 0.00 3.02
140 163 7.397221 ACAAGATATGAACATGAGGTCAAGAA 58.603 34.615 0.00 0.00 0.00 2.52
141 164 7.335422 ACAAGATATGAACATGAGGTCAAGAAC 59.665 37.037 0.00 0.00 0.00 3.01
142 165 6.950842 AGATATGAACATGAGGTCAAGAACA 58.049 36.000 0.00 0.00 0.00 3.18
143 166 7.397221 AGATATGAACATGAGGTCAAGAACAA 58.603 34.615 0.00 0.00 0.00 2.83
144 167 5.954296 ATGAACATGAGGTCAAGAACAAG 57.046 39.130 0.00 0.00 0.00 3.16
145 168 5.034852 TGAACATGAGGTCAAGAACAAGA 57.965 39.130 0.00 0.00 0.00 3.02
146 169 5.624159 TGAACATGAGGTCAAGAACAAGAT 58.376 37.500 0.00 0.00 0.00 2.40
147 170 6.768483 TGAACATGAGGTCAAGAACAAGATA 58.232 36.000 0.00 0.00 0.00 1.98
156 179 6.429385 AGGTCAAGAACAAGATAAAAGCTCAG 59.571 38.462 0.00 0.00 0.00 3.35
162 185 5.368256 ACAAGATAAAAGCTCAGCAACTG 57.632 39.130 0.00 0.00 0.00 3.16
219 242 8.574196 AGTGCAACATAAAATTCTAAACACAC 57.426 30.769 0.00 0.00 41.43 3.82
245 268 7.487829 CCAAAATAGAAACAAATATGGTCACCG 59.512 37.037 0.00 0.00 0.00 4.94
257 280 1.140052 TGGTCACCGTGTTGAGAACAT 59.860 47.619 0.00 0.00 44.35 2.71
279 302 9.754382 AACATAAAATACAAGGAATCATGCATC 57.246 29.630 0.00 0.00 0.00 3.91
316 339 1.333636 TTTTTGTGGTGGCCAGGTGG 61.334 55.000 5.11 0.00 32.34 4.61
324 725 3.721706 GGCCAGGTGGGAGGAGTG 61.722 72.222 0.00 0.00 40.01 3.51
338 739 5.133221 GGGAGGAGTGTATTTATGCAACAT 58.867 41.667 0.00 0.00 0.00 2.71
402 822 6.528072 GTGAACCATTAGCTTTAAGTTCATGC 59.472 38.462 18.84 8.68 43.68 4.06
403 823 5.582689 ACCATTAGCTTTAAGTTCATGCC 57.417 39.130 0.00 0.00 0.00 4.40
476 896 0.814010 CGGTTAGCGGAGGGGAAATG 60.814 60.000 0.00 0.00 0.00 2.32
479 899 0.393808 TTAGCGGAGGGGAAATGTGC 60.394 55.000 0.00 0.00 0.00 4.57
509 929 2.618045 GGAACCAATCCGGACAAGATGT 60.618 50.000 6.12 0.00 38.79 3.06
524 944 5.734720 ACAAGATGTATGAGGAAACACGAT 58.265 37.500 0.00 0.00 0.00 3.73
624 1044 0.578211 GACGCTCGAAACCGACAAAA 59.422 50.000 6.77 0.00 32.06 2.44
625 1045 1.004715 GACGCTCGAAACCGACAAAAA 60.005 47.619 6.77 0.00 32.06 1.94
626 1046 1.600485 ACGCTCGAAACCGACAAAAAT 59.400 42.857 6.77 0.00 32.06 1.82
627 1047 2.230864 CGCTCGAAACCGACAAAAATC 58.769 47.619 0.00 0.00 32.06 2.17
628 1048 2.349060 CGCTCGAAACCGACAAAAATCA 60.349 45.455 0.00 0.00 32.06 2.57
629 1049 3.623863 GCTCGAAACCGACAAAAATCAA 58.376 40.909 0.00 0.00 32.06 2.57
630 1050 3.664025 GCTCGAAACCGACAAAAATCAAG 59.336 43.478 0.00 0.00 32.06 3.02
631 1051 3.623863 TCGAAACCGACAAAAATCAAGC 58.376 40.909 0.00 0.00 0.00 4.01
639 1059 3.701241 GACAAAAATCAAGCAACGGTCA 58.299 40.909 0.00 0.00 0.00 4.02
661 1081 6.419413 GTCATGCGGACTGTTAATTTTTGAAA 59.581 34.615 1.39 0.00 43.46 2.69
702 1172 3.380320 GCTGTTGTGTTGTAAGGGAAACT 59.620 43.478 0.00 0.00 0.00 2.66
744 1214 9.158097 TGAAAGTAGAAACCCCTAACTAACTTA 57.842 33.333 0.00 0.00 0.00 2.24
797 1267 1.064060 CTAACCGCTATGCAACAAGGC 59.936 52.381 0.00 0.00 0.00 4.35
1129 1610 0.179171 CGCCGACTCGATACACAAGT 60.179 55.000 0.00 0.00 0.00 3.16
1137 1618 2.852413 CTCGATACACAAGTTACTGCGG 59.148 50.000 0.00 0.00 0.00 5.69
1356 1837 0.990374 AGGAGCTCTTCATGTGGCTT 59.010 50.000 14.64 0.00 35.01 4.35
1540 2021 4.410555 GGGATAGTCCAGGTGAGATTTTCT 59.589 45.833 0.00 0.00 38.64 2.52
1608 2089 4.619852 GAAGTTCCCCTTCTCGCC 57.380 61.111 0.00 0.00 45.19 5.54
1611 2092 3.703127 GTTCCCCTTCTCGCCGGT 61.703 66.667 1.90 0.00 0.00 5.28
1784 2265 1.135024 CGCAAACATTGGATTCCCCTG 60.135 52.381 0.00 0.24 35.38 4.45
1798 2279 0.179000 CCCCTGGTCGATTGGAAGAG 59.821 60.000 0.00 0.00 0.00 2.85
1860 2342 6.173191 GGAATTTCTTCCGTTTCGATTGTA 57.827 37.500 0.00 0.00 41.60 2.41
2031 2513 6.770785 TGGGTGATTAATGGCTTCAGTTATAC 59.229 38.462 0.00 0.00 0.00 1.47
2032 2514 6.998673 GGGTGATTAATGGCTTCAGTTATACT 59.001 38.462 0.00 0.00 0.00 2.12
2041 2524 6.106673 TGGCTTCAGTTATACTTAGCTGAAC 58.893 40.000 0.00 6.15 45.26 3.18
2058 2541 4.414852 CTGAACTTGGGCACAATAAATCG 58.585 43.478 0.00 0.00 35.73 3.34
2249 2737 4.706476 TGGGAATTGGAGCTCATTAAGTTG 59.294 41.667 17.19 0.00 0.00 3.16
2250 2738 4.706962 GGGAATTGGAGCTCATTAAGTTGT 59.293 41.667 17.19 0.00 0.00 3.32
2579 3078 0.887933 GGAATCAACCACACGCCAAT 59.112 50.000 0.00 0.00 0.00 3.16
2580 3079 1.272212 GGAATCAACCACACGCCAATT 59.728 47.619 0.00 0.00 0.00 2.32
2629 3142 2.108362 GCTACCGGGATGGGTTCG 59.892 66.667 6.32 0.00 44.64 3.95
2691 3204 0.820226 TCTCATCGCCTGTCCTTCTG 59.180 55.000 0.00 0.00 0.00 3.02
2770 3284 2.297033 GGAGAAAAGCTGATGCCACAAA 59.703 45.455 0.00 0.00 40.80 2.83
2805 3319 0.527600 CGCAGCGTGTCCATAGCTTA 60.528 55.000 6.65 0.00 39.48 3.09
2806 3320 1.651987 GCAGCGTGTCCATAGCTTAA 58.348 50.000 0.00 0.00 39.48 1.85
3024 3543 2.955477 ACTAGTAGTTTACCTGCGCC 57.045 50.000 4.18 0.00 0.00 6.53
3038 3560 2.819595 CGCCCAGTTGTATGCGCT 60.820 61.111 9.73 0.00 40.58 5.92
3063 3586 6.128117 TGTTTTAAATTACCGCTGAAGCCTAG 60.128 38.462 0.00 0.00 37.91 3.02
3065 3588 2.604046 ATTACCGCTGAAGCCTAGTG 57.396 50.000 0.00 0.00 37.91 2.74
3115 3640 3.462021 AGAAGTGTCTGAACAAGCTGTC 58.538 45.455 0.00 0.00 37.08 3.51
3177 3702 2.788807 AGAGGATAGAGGCAGAAGGAGA 59.211 50.000 0.00 0.00 0.00 3.71
3183 3708 2.187100 AGAGGCAGAAGGAGAAGAAGG 58.813 52.381 0.00 0.00 0.00 3.46
3244 3779 3.447229 GGAGGAGGAGAGAGAAAGACAAG 59.553 52.174 0.00 0.00 0.00 3.16
3472 4019 0.942962 GCATGCTCCTGTGTGATAGC 59.057 55.000 11.37 0.00 35.51 2.97
3502 4049 6.055588 AGTATTAAGTTTGTCAGTGCTGTGT 58.944 36.000 0.00 0.00 0.00 3.72
3503 4050 5.835113 ATTAAGTTTGTCAGTGCTGTGTT 57.165 34.783 0.00 0.00 0.00 3.32
3504 4051 6.935741 ATTAAGTTTGTCAGTGCTGTGTTA 57.064 33.333 0.00 0.00 0.00 2.41
3505 4052 4.616181 AAGTTTGTCAGTGCTGTGTTAC 57.384 40.909 0.00 0.00 0.00 2.50
3506 4053 3.605634 AGTTTGTCAGTGCTGTGTTACA 58.394 40.909 0.00 0.00 0.00 2.41
3507 4054 4.006989 AGTTTGTCAGTGCTGTGTTACAA 58.993 39.130 0.00 0.40 0.00 2.41
3508 4055 4.095610 GTTTGTCAGTGCTGTGTTACAAC 58.904 43.478 4.40 0.00 0.00 3.32
3599 4153 2.716424 TGTGTGGGATTCTTCCTTCCTT 59.284 45.455 0.00 0.00 42.20 3.36
3662 4221 2.357881 CGTCTGCCAGCTCAGCAA 60.358 61.111 9.15 0.00 40.35 3.91
3738 4308 1.737355 TTCTTGTGTTGCCTGCCTGC 61.737 55.000 0.00 0.00 0.00 4.85
3739 4309 3.216944 CTTGTGTTGCCTGCCTGCC 62.217 63.158 0.00 0.00 0.00 4.85
3740 4310 3.736996 TTGTGTTGCCTGCCTGCCT 62.737 57.895 0.00 0.00 0.00 4.75
3741 4311 2.914097 GTGTTGCCTGCCTGCCTT 60.914 61.111 0.00 0.00 0.00 4.35
3762 4332 1.270839 GCTGGTGGTTGAGTGCTTCTA 60.271 52.381 0.00 0.00 0.00 2.10
3785 4400 4.202367 ACTGCTTAGGTATGGTGATTAGCC 60.202 45.833 0.00 0.00 0.00 3.93
3941 4615 4.685924 ACCTGAAGTGCAAAAACATCTTG 58.314 39.130 0.00 0.00 0.00 3.02
3976 4651 4.876679 GGAGGGAGTATAAGCTGTTTTGAC 59.123 45.833 0.00 0.00 0.00 3.18
4000 4675 8.567285 ACAGTTTATAAATCAGAAACAGAGGG 57.433 34.615 0.31 0.00 40.17 4.30
4001 4676 8.383175 ACAGTTTATAAATCAGAAACAGAGGGA 58.617 33.333 0.31 0.00 40.17 4.20
4002 4677 8.669243 CAGTTTATAAATCAGAAACAGAGGGAC 58.331 37.037 0.31 0.00 40.17 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.005650 CACCTCATATGTCACAAGTTGCT 58.994 43.478 1.81 0.0 0.00 3.91
52 53 6.826668 ACGGTATTTGTCATATTGAGATGGA 58.173 36.000 0.00 0.0 0.00 3.41
62 63 5.177881 GTCACACACAACGGTATTTGTCATA 59.822 40.000 0.00 0.0 37.62 2.15
73 74 1.374560 TTCCAAGTCACACACAACGG 58.625 50.000 0.00 0.0 0.00 4.44
74 75 2.160615 TGTTTCCAAGTCACACACAACG 59.839 45.455 0.00 0.0 0.00 4.10
87 88 6.528321 TGCCATGTTCATATTTTGTTTCCAA 58.472 32.000 0.00 0.0 0.00 3.53
123 146 5.034852 TCTTGTTCTTGACCTCATGTTCA 57.965 39.130 0.00 0.0 0.00 3.18
124 147 7.672983 TTATCTTGTTCTTGACCTCATGTTC 57.327 36.000 0.00 0.0 0.00 3.18
125 148 8.463930 TTTTATCTTGTTCTTGACCTCATGTT 57.536 30.769 0.00 0.0 0.00 2.71
126 149 7.308830 GCTTTTATCTTGTTCTTGACCTCATGT 60.309 37.037 0.00 0.0 0.00 3.21
127 150 7.025963 GCTTTTATCTTGTTCTTGACCTCATG 58.974 38.462 0.00 0.0 0.00 3.07
128 151 6.944862 AGCTTTTATCTTGTTCTTGACCTCAT 59.055 34.615 0.00 0.0 0.00 2.90
129 152 6.299141 AGCTTTTATCTTGTTCTTGACCTCA 58.701 36.000 0.00 0.0 0.00 3.86
130 153 6.428159 TGAGCTTTTATCTTGTTCTTGACCTC 59.572 38.462 0.00 0.0 0.00 3.85
131 154 6.299141 TGAGCTTTTATCTTGTTCTTGACCT 58.701 36.000 0.00 0.0 0.00 3.85
132 155 6.560253 TGAGCTTTTATCTTGTTCTTGACC 57.440 37.500 0.00 0.0 0.00 4.02
133 156 6.082984 GCTGAGCTTTTATCTTGTTCTTGAC 58.917 40.000 0.00 0.0 0.00 3.18
134 157 5.764686 TGCTGAGCTTTTATCTTGTTCTTGA 59.235 36.000 5.83 0.0 0.00 3.02
135 158 6.005583 TGCTGAGCTTTTATCTTGTTCTTG 57.994 37.500 5.83 0.0 0.00 3.02
136 159 6.264067 AGTTGCTGAGCTTTTATCTTGTTCTT 59.736 34.615 5.83 0.0 0.00 2.52
137 160 5.767168 AGTTGCTGAGCTTTTATCTTGTTCT 59.233 36.000 5.83 0.0 0.00 3.01
138 161 5.855395 CAGTTGCTGAGCTTTTATCTTGTTC 59.145 40.000 5.83 0.0 32.44 3.18
139 162 5.278660 CCAGTTGCTGAGCTTTTATCTTGTT 60.279 40.000 5.83 0.0 32.44 2.83
140 163 4.217118 CCAGTTGCTGAGCTTTTATCTTGT 59.783 41.667 5.83 0.0 32.44 3.16
141 164 4.217118 ACCAGTTGCTGAGCTTTTATCTTG 59.783 41.667 5.83 0.0 32.44 3.02
142 165 4.401925 ACCAGTTGCTGAGCTTTTATCTT 58.598 39.130 5.83 0.0 32.44 2.40
143 166 4.026356 ACCAGTTGCTGAGCTTTTATCT 57.974 40.909 5.83 0.0 32.44 1.98
144 167 4.773323 AACCAGTTGCTGAGCTTTTATC 57.227 40.909 5.83 0.0 32.44 1.75
145 168 4.829492 AGAAACCAGTTGCTGAGCTTTTAT 59.171 37.500 5.83 0.0 32.44 1.40
146 169 4.207165 AGAAACCAGTTGCTGAGCTTTTA 58.793 39.130 5.83 0.0 32.44 1.52
147 170 3.026694 AGAAACCAGTTGCTGAGCTTTT 58.973 40.909 5.83 0.0 32.44 2.27
156 179 2.430694 ACTTTGGGAAGAAACCAGTTGC 59.569 45.455 0.00 0.0 39.57 4.17
162 185 1.760029 TGGCAACTTTGGGAAGAAACC 59.240 47.619 0.00 0.0 36.69 3.27
219 242 7.487829 CGGTGACCATATTTGTTTCTATTTTGG 59.512 37.037 1.11 0.0 0.00 3.28
257 280 6.039159 TGCGATGCATGATTCCTTGTATTTTA 59.961 34.615 2.46 0.0 31.71 1.52
316 339 5.822519 TGATGTTGCATAAATACACTCCTCC 59.177 40.000 0.00 0.0 0.00 4.30
324 725 9.701098 ATCCATTTGATGATGTTGCATAAATAC 57.299 29.630 0.00 0.0 30.54 1.89
476 896 2.034221 GGTTCCACTGGAGGGCAC 59.966 66.667 0.00 0.0 31.21 5.01
479 899 0.034089 GGATTGGTTCCACTGGAGGG 60.034 60.000 0.00 0.0 44.74 4.30
509 929 2.419990 CCTGGCATCGTGTTTCCTCATA 60.420 50.000 0.00 0.0 0.00 2.15
561 981 0.593773 CGTGCTTTTTGGTCAACCCG 60.594 55.000 0.00 0.0 35.15 5.28
562 982 0.458260 ACGTGCTTTTTGGTCAACCC 59.542 50.000 0.00 0.0 34.29 4.11
624 1044 0.168788 CGCATGACCGTTGCTTGATT 59.831 50.000 0.00 0.0 37.96 2.57
625 1045 1.647545 CCGCATGACCGTTGCTTGAT 61.648 55.000 0.00 0.0 37.96 2.57
626 1046 2.324330 CCGCATGACCGTTGCTTGA 61.324 57.895 0.00 0.0 37.96 3.02
627 1047 2.176546 CCGCATGACCGTTGCTTG 59.823 61.111 0.00 0.0 37.96 4.01
628 1048 2.031919 TCCGCATGACCGTTGCTT 59.968 55.556 0.00 0.0 37.96 3.91
629 1049 2.742372 GTCCGCATGACCGTTGCT 60.742 61.111 0.00 0.0 38.09 3.91
630 1050 2.742372 AGTCCGCATGACCGTTGC 60.742 61.111 0.00 0.0 45.68 4.17
631 1051 1.227999 AACAGTCCGCATGACCGTTG 61.228 55.000 0.00 0.0 41.83 4.10
639 1059 7.961325 AATTTCAAAAATTAACAGTCCGCAT 57.039 28.000 0.00 0.0 0.00 4.73
661 1081 5.460646 ACAGCGACGATGAAAATTCAAAAT 58.539 33.333 21.46 0.0 41.13 1.82
702 1172 5.083533 ACTTTCATTTTTGCTGGTCACAA 57.916 34.783 0.00 0.0 0.00 3.33
744 1214 4.032960 TGCCCTTCGCATATATGGAAAT 57.967 40.909 14.51 0.0 44.64 2.17
797 1267 6.698766 CCTTTGTTTGGAAGATTTCTGTTGAG 59.301 38.462 0.00 0.0 0.00 3.02
1046 1527 1.537397 AGGAAGAGGCACAGGCAGA 60.537 57.895 0.00 0.0 43.71 4.26
1356 1837 2.285368 AGGATGCCCTTCACCGGA 60.285 61.111 9.46 0.0 40.78 5.14
1611 2092 4.236147 TGATTGGACGTCGAAATAAACGA 58.764 39.130 17.11 0.0 41.29 3.85
1784 2265 2.415512 CGTTTTCCTCTTCCAATCGACC 59.584 50.000 0.00 0.0 0.00 4.79
1798 2279 2.092323 CTCAAGAATCCCCCGTTTTCC 58.908 52.381 0.00 0.0 0.00 3.13
1860 2342 1.270839 CCACTGACCCAGAACGATTGT 60.271 52.381 0.45 0.0 35.18 2.71
1998 2480 2.486548 CCATTAATCACCCACCCCTACG 60.487 54.545 0.00 0.0 0.00 3.51
2000 2482 1.497286 GCCATTAATCACCCACCCCTA 59.503 52.381 0.00 0.0 0.00 3.53
2031 2513 1.896220 TGTGCCCAAGTTCAGCTAAG 58.104 50.000 0.00 0.0 0.00 2.18
2032 2514 2.356665 TTGTGCCCAAGTTCAGCTAA 57.643 45.000 0.00 0.0 0.00 3.09
2041 2524 1.476085 TGCCGATTTATTGTGCCCAAG 59.524 47.619 0.00 0.0 33.17 3.61
2058 2541 0.538287 ACCAGAGCAAGTTTCCTGCC 60.538 55.000 0.00 0.0 0.00 4.85
2216 2699 7.397221 TGAGCTCCAATTCCCATTACTATATG 58.603 38.462 12.15 0.0 0.00 1.78
2222 2710 6.547510 ACTTAATGAGCTCCAATTCCCATTAC 59.452 38.462 12.15 0.0 0.00 1.89
2382 2879 3.192633 ACCATCACAAAATTAGGTTCGGC 59.807 43.478 0.00 0.0 0.00 5.54
2579 3078 6.607004 ACGGATTAAGGAGAGAGAGAAAAA 57.393 37.500 0.00 0.0 0.00 1.94
2580 3079 6.607004 AACGGATTAAGGAGAGAGAGAAAA 57.393 37.500 0.00 0.0 0.00 2.29
2621 3122 2.627699 ACAATCTTGCAAACGAACCCAT 59.372 40.909 0.00 0.0 0.00 4.00
2629 3142 7.599998 ACATGGAAAGATAACAATCTTGCAAAC 59.400 33.333 0.00 0.0 40.47 2.93
2770 3284 2.244651 GCGTTCTTGCGAGGTGTGT 61.245 57.895 0.00 0.0 0.00 3.72
2787 3301 1.651987 TTAAGCTATGGACACGCTGC 58.348 50.000 0.00 0.0 33.64 5.25
2805 3319 4.104897 ACTTCTAGAACTTCCCTGGCTTTT 59.895 41.667 0.00 0.0 0.00 2.27
2806 3320 3.653352 ACTTCTAGAACTTCCCTGGCTTT 59.347 43.478 0.00 0.0 0.00 3.51
3001 3519 4.497173 GGCGCAGGTAAACTACTAGTACTC 60.497 50.000 10.83 0.0 0.00 2.59
3024 3543 2.704725 AAAACAGCGCATACAACTGG 57.295 45.000 11.47 0.0 35.70 4.00
3038 3560 4.521256 AGGCTTCAGCGGTAATTTAAAACA 59.479 37.500 0.00 0.0 43.26 2.83
3063 3586 0.393537 ATTCCAGCTGTAGCCTGCAC 60.394 55.000 13.81 0.0 43.38 4.57
3065 3588 1.943340 GTTATTCCAGCTGTAGCCTGC 59.057 52.381 13.81 0.0 43.38 4.85
3177 3702 1.774217 TGGTCCAGGTGCCCTTCTT 60.774 57.895 0.00 0.0 0.00 2.52
3183 3708 2.930562 ACCTCTGGTCCAGGTGCC 60.931 66.667 19.11 0.0 43.10 5.01
3244 3779 2.405172 GTGAACTTGTCTCGGTCTTCC 58.595 52.381 0.00 0.0 0.00 3.46
3472 4019 7.041780 AGCACTGACAAACTTAATACTCAACTG 60.042 37.037 0.00 0.0 0.00 3.16
3502 4049 8.516234 TGTTCTTTTCTTGCTTGTAAGTTGTAA 58.484 29.630 0.00 0.0 0.00 2.41
3503 4050 8.046294 TGTTCTTTTCTTGCTTGTAAGTTGTA 57.954 30.769 0.00 0.0 0.00 2.41
3504 4051 6.919721 TGTTCTTTTCTTGCTTGTAAGTTGT 58.080 32.000 0.00 0.0 0.00 3.32
3505 4052 7.009540 CCTTGTTCTTTTCTTGCTTGTAAGTTG 59.990 37.037 0.00 0.0 0.00 3.16
3506 4053 7.035612 CCTTGTTCTTTTCTTGCTTGTAAGTT 58.964 34.615 0.00 0.0 0.00 2.66
3507 4054 6.152831 ACCTTGTTCTTTTCTTGCTTGTAAGT 59.847 34.615 0.00 0.0 0.00 2.24
3508 4055 6.564328 ACCTTGTTCTTTTCTTGCTTGTAAG 58.436 36.000 0.00 0.0 0.00 2.34
3599 4153 1.432807 AGCCAAGGAAGGAATTCCCAA 59.567 47.619 21.22 0.0 42.06 4.12
3662 4221 3.325753 GTGGCCAGCTCACTCCCT 61.326 66.667 5.11 0.0 32.78 4.20
3738 4308 1.799258 GCACTCAACCACCAGCAAGG 61.799 60.000 0.00 0.0 45.67 3.61
3739 4309 0.820891 AGCACTCAACCACCAGCAAG 60.821 55.000 0.00 0.0 0.00 4.01
3740 4310 0.395586 AAGCACTCAACCACCAGCAA 60.396 50.000 0.00 0.0 0.00 3.91
3741 4311 0.819259 GAAGCACTCAACCACCAGCA 60.819 55.000 0.00 0.0 0.00 4.41
3762 4332 4.202367 GGCTAATCACCATACCTAAGCAGT 60.202 45.833 0.00 0.0 0.00 4.40
3915 4589 5.536161 AGATGTTTTTGCACTTCAGGTACAT 59.464 36.000 0.00 0.0 0.00 2.29
3941 4615 3.900966 ACTCCCTCCGTACCAAAATAC 57.099 47.619 0.00 0.0 0.00 1.89
3976 4651 8.669243 GTCCCTCTGTTTCTGATTTATAAACTG 58.331 37.037 0.00 0.0 34.84 3.16
4085 4761 3.497031 GCAGTAAAGCGACGGGGC 61.497 66.667 0.00 0.0 0.00 5.80


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

AutoCloner maintained by Alex Coulton.