Multiple sequence alignment - TraesCS6D01G260900

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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 TraesCS6D01G260900 chr6D 100.000 3309 0 0 1 3309 368373257 368369949 0.000000e+00 6111.0
1 TraesCS6D01G260900 chr6D 86.975 1405 162 16 827 2214 368741232 368739832 0.000000e+00 1561.0
2 TraesCS6D01G260900 chr6D 89.757 1191 120 2 1025 2214 367864908 367866097 0.000000e+00 1522.0
3 TraesCS6D01G260900 chr6D 88.747 1253 116 10 949 2200 367875875 367877103 0.000000e+00 1509.0
4 TraesCS6D01G260900 chr6D 86.885 122 14 2 2661 2780 336478376 336478255 5.760000e-28 135.0
5 TraesCS6D01G260900 chr6A 93.500 2754 111 24 331 3035 509286480 509283746 0.000000e+00 4032.0
6 TraesCS6D01G260900 chr6A 89.840 1191 119 2 1025 2214 508293992 508295181 0.000000e+00 1528.0
7 TraesCS6D01G260900 chr6A 90.059 1177 106 3 1025 2200 508333673 508334839 0.000000e+00 1515.0
8 TraesCS6D01G260900 chr6A 87.237 1238 154 4 978 2214 509562335 509561101 0.000000e+00 1408.0
9 TraesCS6D01G260900 chr6A 88.889 279 14 7 3033 3309 509283701 509283438 8.850000e-86 327.0
10 TraesCS6D01G260900 chr6B 89.924 1191 118 2 1025 2214 554165584 554164395 0.000000e+00 1533.0
11 TraesCS6D01G260900 chr6B 88.437 1254 127 9 949 2199 554123812 554122574 0.000000e+00 1496.0
12 TraesCS6D01G260900 chr6B 84.634 807 71 22 2 804 553049458 553050215 0.000000e+00 754.0
13 TraesCS6D01G260900 chr6B 92.135 178 8 5 2287 2460 553052223 553052398 2.550000e-61 246.0
14 TraesCS6D01G260900 chr6B 86.239 218 23 4 2549 2766 674554865 674555075 2.570000e-56 230.0
15 TraesCS6D01G260900 chr6B 83.168 202 21 6 2608 2808 66786418 66786607 4.390000e-39 172.0
16 TraesCS6D01G260900 chr5A 84.400 250 24 8 1 239 477686168 477685923 7.140000e-57 231.0
17 TraesCS6D01G260900 chr5B 80.240 334 42 13 1 324 450412709 450412390 2.570000e-56 230.0
18 TraesCS6D01G260900 chr5B 81.857 237 34 8 1 235 101827496 101827267 1.210000e-44 191.0
19 TraesCS6D01G260900 chr5B 84.211 114 14 4 2670 2780 690899466 690899578 1.260000e-19 108.0
20 TraesCS6D01G260900 chr4A 84.362 243 28 8 1 239 628933551 628933315 2.570000e-56 230.0
21 TraesCS6D01G260900 chr4A 80.275 218 24 6 2549 2765 103073310 103073509 2.660000e-31 147.0
22 TraesCS6D01G260900 chr7D 83.658 257 25 9 2545 2800 289248408 289248168 3.320000e-55 226.0
23 TraesCS6D01G260900 chr7D 85.388 219 23 5 2549 2767 27220661 27220870 5.560000e-53 219.0
24 TraesCS6D01G260900 chr7D 86.957 115 15 0 2687 2801 436741318 436741204 2.680000e-26 130.0
25 TraesCS6D01G260900 chr4B 83.951 243 25 10 1 240 566593461 566593692 1.550000e-53 220.0
26 TraesCS6D01G260900 chr4B 79.675 246 38 10 1 239 328276896 328276656 2.040000e-37 167.0
27 TraesCS6D01G260900 chr4D 83.750 240 29 9 1 236 319113042 319112809 5.560000e-53 219.0
28 TraesCS6D01G260900 chr4D 83.182 220 29 3 2548 2767 451277516 451277727 9.370000e-46 195.0
29 TraesCS6D01G260900 chr2D 81.579 266 41 5 2543 2806 60120881 60120622 2.590000e-51 213.0
30 TraesCS6D01G260900 chr3D 82.353 255 28 11 2548 2801 143237818 143237580 4.330000e-49 206.0
31 TraesCS6D01G260900 chr5D 81.092 238 38 6 1 232 539470093 539470329 2.030000e-42 183.0
32 TraesCS6D01G260900 chr7B 92.241 116 7 2 2545 2659 362034136 362034022 2.640000e-36 163.0
33 TraesCS6D01G260900 chr3B 85.047 107 15 1 2678 2783 576023429 576023323 1.260000e-19 108.0
34 TraesCS6D01G260900 chr3B 76.344 186 34 7 2582 2764 67378577 67378399 1.260000e-14 91.6
35 TraesCS6D01G260900 chr7A 86.667 60 7 1 2582 2640 181795767 181795826 7.660000e-07 65.8


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 TraesCS6D01G260900 chr6D 368369949 368373257 3308 True 6111.0 6111 100.0000 1 3309 1 chr6D.!!$R2 3308
1 TraesCS6D01G260900 chr6D 368739832 368741232 1400 True 1561.0 1561 86.9750 827 2214 1 chr6D.!!$R3 1387
2 TraesCS6D01G260900 chr6D 367864908 367866097 1189 False 1522.0 1522 89.7570 1025 2214 1 chr6D.!!$F1 1189
3 TraesCS6D01G260900 chr6D 367875875 367877103 1228 False 1509.0 1509 88.7470 949 2200 1 chr6D.!!$F2 1251
4 TraesCS6D01G260900 chr6A 509283438 509286480 3042 True 2179.5 4032 91.1945 331 3309 2 chr6A.!!$R2 2978
5 TraesCS6D01G260900 chr6A 508293992 508295181 1189 False 1528.0 1528 89.8400 1025 2214 1 chr6A.!!$F1 1189
6 TraesCS6D01G260900 chr6A 508333673 508334839 1166 False 1515.0 1515 90.0590 1025 2200 1 chr6A.!!$F2 1175
7 TraesCS6D01G260900 chr6A 509561101 509562335 1234 True 1408.0 1408 87.2370 978 2214 1 chr6A.!!$R1 1236
8 TraesCS6D01G260900 chr6B 554164395 554165584 1189 True 1533.0 1533 89.9240 1025 2214 1 chr6B.!!$R2 1189
9 TraesCS6D01G260900 chr6B 554122574 554123812 1238 True 1496.0 1496 88.4370 949 2199 1 chr6B.!!$R1 1250
10 TraesCS6D01G260900 chr6B 553049458 553052398 2940 False 500.0 754 88.3845 2 2460 2 chr6B.!!$F3 2458

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
186 189 0.250467 AATGAACGCAGACAGGCTGT 60.250 50.000 22.26 22.26 46.62 4.40 F
323 326 0.459585 TCGGCGTATTGGAGTTGCTC 60.460 55.000 6.85 0.00 0.00 4.26 F
1247 1701 1.356979 CGACCTCGTCATCATCGCT 59.643 57.895 0.00 0.00 32.09 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2553 1.753078 GGCAAGGGGGTTCGATTCC 60.753 63.158 0.0 0.0 0.0 3.01 R
2272 2730 7.819900 AGTAGTTATTTTTCAATCGACTGAGCT 59.180 33.333 0.0 0.0 0.0 4.09 R
2683 3346 0.040958 GCAAGCCTGACAACTTCGTG 60.041 55.000 0.0 0.0 0.0 4.35 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
105 106 7.761409 TGGTTGTGAAACTATGAGATATTTGC 58.239 34.615 0.00 0.00 38.04 3.68
128 130 9.755804 TTGCATTTGTTTGAATTATGTGAACTA 57.244 25.926 0.00 0.00 0.00 2.24
133 135 7.681939 TGTTTGAATTATGTGAACTAGGGTC 57.318 36.000 0.00 0.00 0.00 4.46
183 186 2.422276 AAAAATGAACGCAGACAGGC 57.578 45.000 0.00 0.00 0.00 4.85
184 187 1.609208 AAAATGAACGCAGACAGGCT 58.391 45.000 0.00 0.00 0.00 4.58
186 189 0.250467 AATGAACGCAGACAGGCTGT 60.250 50.000 22.26 22.26 46.62 4.40
190 193 2.029518 CGCAGACAGGCTGTGTGA 59.970 61.111 39.28 0.00 43.48 3.58
234 237 3.656045 CACGGCCGACCCAAACAC 61.656 66.667 35.90 0.00 0.00 3.32
235 238 4.178169 ACGGCCGACCCAAACACA 62.178 61.111 35.90 0.00 0.00 3.72
236 239 2.902846 CGGCCGACCCAAACACAA 60.903 61.111 24.07 0.00 0.00 3.33
237 240 2.482333 CGGCCGACCCAAACACAAA 61.482 57.895 24.07 0.00 0.00 2.83
238 241 1.817209 GGCCGACCCAAACACAAAA 59.183 52.632 0.00 0.00 0.00 2.44
241 244 1.404315 GCCGACCCAAACACAAAAACA 60.404 47.619 0.00 0.00 0.00 2.83
244 247 3.318017 CGACCCAAACACAAAAACACAA 58.682 40.909 0.00 0.00 0.00 3.33
251 254 4.625607 AACACAAAAACACAAAAGGGGA 57.374 36.364 0.00 0.00 0.00 4.81
257 260 0.549469 AACACAAAAGGGGACGGACT 59.451 50.000 0.00 0.00 0.00 3.85
259 262 1.770061 ACACAAAAGGGGACGGACTAA 59.230 47.619 0.00 0.00 0.00 2.24
298 301 4.673534 AAAACGAACAAAACGTGTCTCT 57.326 36.364 0.00 0.00 40.60 3.10
299 302 3.651562 AACGAACAAAACGTGTCTCTG 57.348 42.857 0.00 0.00 40.60 3.35
301 304 2.601763 ACGAACAAAACGTGTCTCTGTC 59.398 45.455 0.00 0.00 40.60 3.51
323 326 0.459585 TCGGCGTATTGGAGTTGCTC 60.460 55.000 6.85 0.00 0.00 4.26
366 369 4.665833 ATAAACGAGGTGAATCGATGGA 57.334 40.909 0.00 0.00 45.56 3.41
426 430 2.229302 GCAGGATCTACACCGGTATCTC 59.771 54.545 6.87 1.22 0.00 2.75
474 478 2.387476 TAGCATGGATCAGCAGCGGG 62.387 60.000 0.00 0.00 0.00 6.13
606 617 1.541147 CGTGGGTGATGCATGTCTTTT 59.459 47.619 2.46 0.00 0.00 2.27
617 628 9.754382 GTGATGCATGTCTTTTATATTGGATTT 57.246 29.630 2.46 0.00 0.00 2.17
640 651 6.317789 TCAAGCTCTTTTCTACATTGTTGG 57.682 37.500 0.00 0.00 0.00 3.77
654 665 8.314021 TCTACATTGTTGGCATATATGACCTAG 58.686 37.037 16.15 11.17 33.92 3.02
686 697 8.586570 CAAGCAGTTGTATTTTTGGTTGAATA 57.413 30.769 8.99 0.00 46.38 1.75
762 778 7.122204 TCGATCAGTTAACTATCCAAGTTCAGA 59.878 37.037 8.04 0.00 45.64 3.27
797 813 3.887741 TGTGTTGTCATGAATGAAAGCG 58.112 40.909 0.00 0.00 38.75 4.68
813 857 1.671379 GCGGGTCCAGTCCAAGTTC 60.671 63.158 0.00 0.00 0.00 3.01
1247 1701 1.356979 CGACCTCGTCATCATCGCT 59.643 57.895 0.00 0.00 32.09 4.93
1290 1744 3.866582 GGATCCCAGCACTCCCGG 61.867 72.222 0.00 0.00 0.00 5.73
1419 1873 1.364626 CCTGCTGCTCGACAACATCC 61.365 60.000 0.00 0.00 0.00 3.51
1859 2313 4.012895 GTGAACGCGTGGCTGGTG 62.013 66.667 14.98 0.00 0.00 4.17
2006 2463 4.517815 ACCACGGACACGCACGTT 62.518 61.111 0.00 0.00 46.04 3.99
2096 2553 2.287069 CCTCGGCGAGTACTATCAGTTG 60.287 54.545 32.41 11.13 0.00 3.16
2238 2695 5.942236 CACCAAGTAATCCCATCCATATCTG 59.058 44.000 0.00 0.00 0.00 2.90
2272 2730 1.340088 TACGTGTTGGGAGTGCCTAA 58.660 50.000 1.06 0.00 31.46 2.69
2340 2998 1.079819 CATCGTGGTTCAGTCGCCT 60.080 57.895 0.00 0.00 0.00 5.52
2417 3077 3.130340 TGGCTTCTTCTTTGGTTGTTGTC 59.870 43.478 0.00 0.00 0.00 3.18
2427 3087 1.150536 GTTGTTGTCTGGGCTGGGA 59.849 57.895 0.00 0.00 0.00 4.37
2501 3164 5.360649 TCCCCGTGATGATGTACAATAAA 57.639 39.130 0.00 0.00 0.00 1.40
2506 3169 6.966632 CCCGTGATGATGTACAATAAAACTTG 59.033 38.462 0.00 0.00 0.00 3.16
2546 3209 5.048713 CCTTGTGTGGTTGTATTCTCTTTCC 60.049 44.000 0.00 0.00 0.00 3.13
2565 3228 9.231297 CTCTTTCCAAAATGATAAGTACCTGAA 57.769 33.333 0.00 0.00 0.00 3.02
2571 3234 7.414540 CCAAAATGATAAGTACCTGAAGTCAGC 60.415 40.741 2.59 0.00 42.47 4.26
2580 3243 1.135915 CCTGAAGTCAGCTACGAGCAT 59.864 52.381 2.59 0.00 45.56 3.79
2586 3249 1.039856 TCAGCTACGAGCATATGGCA 58.960 50.000 4.56 0.00 45.56 4.92
2627 3290 3.242543 GCAATTCTAGTGACGCAAGGATG 60.243 47.826 0.00 0.00 46.39 3.51
2628 3291 2.672961 TTCTAGTGACGCAAGGATGG 57.327 50.000 0.00 0.00 46.39 3.51
2632 3295 0.537143 AGTGACGCAAGGATGGCAAA 60.537 50.000 0.00 0.00 46.39 3.68
2665 3328 6.919662 ACACACACTGCAATTTTCTATTTCTG 59.080 34.615 0.00 0.00 0.00 3.02
2693 3356 5.751243 AATAAACTGAAGCACGAAGTTGT 57.249 34.783 0.00 0.00 41.61 3.32
2696 3359 2.205074 ACTGAAGCACGAAGTTGTCAG 58.795 47.619 0.00 0.00 41.61 3.51
2697 3360 1.528586 CTGAAGCACGAAGTTGTCAGG 59.471 52.381 0.00 0.00 41.61 3.86
2703 3366 1.166531 ACGAAGTTGTCAGGCTTGCC 61.167 55.000 2.97 2.97 37.78 4.52
2726 3389 1.324736 CTAAAGTTGTCATCCTCGCGC 59.675 52.381 0.00 0.00 0.00 6.86
2768 3431 0.109781 GTTCGATTTGCCATGTGCGT 60.110 50.000 0.00 0.00 45.60 5.24
2778 3449 1.351430 CCATGTGCGTGTACCTGACG 61.351 60.000 0.17 0.17 39.87 4.35
2797 3468 3.508762 ACGTTCGAGCGTTATCAGATTT 58.491 40.909 22.04 0.00 43.04 2.17
2808 3479 7.746929 AGCGTTATCAGATTTCTTCTCTTTTG 58.253 34.615 0.00 0.00 29.93 2.44
2810 3481 7.148407 GCGTTATCAGATTTCTTCTCTTTTGGA 60.148 37.037 0.00 0.00 29.93 3.53
2811 3482 8.386606 CGTTATCAGATTTCTTCTCTTTTGGAG 58.613 37.037 0.00 0.00 43.12 3.86
2812 3483 9.225436 GTTATCAGATTTCTTCTCTTTTGGAGT 57.775 33.333 0.00 0.00 42.40 3.85
2833 3505 7.289317 TGGAGTAAGATATCCGGTGAACTTTAT 59.711 37.037 0.00 0.00 38.52 1.40
2885 3557 1.438651 TCTTGCGTATCCAAGCACAC 58.561 50.000 0.00 0.00 43.69 3.82
2943 3615 4.156556 TGCAAGCAATGATTCTGTTCCTAC 59.843 41.667 0.00 0.00 0.00 3.18
2966 3638 7.251704 ACTAGGTGCATTCTCGAAATTATTG 57.748 36.000 0.00 0.00 0.00 1.90
3005 3679 5.627499 TGAGGCAAAAATACTGATGTCAC 57.373 39.130 0.00 0.00 0.00 3.67
3090 3811 7.159322 ACTAGTTCTCACGTTGATATGTTCT 57.841 36.000 0.00 0.00 0.00 3.01
3145 3867 4.460505 ACTGTAATACGTTTTTGCTTCGC 58.539 39.130 0.00 0.00 0.00 4.70
3147 3869 2.341318 AATACGTTTTTGCTTCGCCC 57.659 45.000 0.00 0.00 0.00 6.13
3148 3870 1.530323 ATACGTTTTTGCTTCGCCCT 58.470 45.000 0.00 0.00 0.00 5.19
3206 3929 0.463295 AGCATCTCCAAGCCATGTCG 60.463 55.000 0.00 0.00 0.00 4.35
3213 3936 2.276201 TCCAAGCCATGTCGTAAATCG 58.724 47.619 0.00 0.00 41.41 3.34
3220 3943 1.062002 CATGTCGTAAATCGGGCACAC 59.938 52.381 0.00 0.00 40.32 3.82
3225 3948 3.619929 GTCGTAAATCGGGCACACTAAAT 59.380 43.478 0.00 0.00 40.32 1.40
3226 3949 3.619483 TCGTAAATCGGGCACACTAAATG 59.381 43.478 0.00 0.00 40.32 2.32
3227 3950 3.372822 CGTAAATCGGGCACACTAAATGT 59.627 43.478 0.00 0.00 37.76 2.71
3228 3951 4.493545 CGTAAATCGGGCACACTAAATGTC 60.494 45.833 0.00 0.00 36.07 3.06
3229 3952 2.038387 ATCGGGCACACTAAATGTCC 57.962 50.000 0.00 0.00 40.64 4.02
3231 3954 1.800681 GGGCACACTAAATGTCCGC 59.199 57.895 0.00 0.00 40.64 5.54
3232 3955 1.423845 GGCACACTAAATGTCCGCG 59.576 57.895 0.00 0.00 40.64 6.46
3233 3956 1.423845 GCACACTAAATGTCCGCGG 59.576 57.895 22.12 22.12 40.64 6.46
3234 3957 1.017177 GCACACTAAATGTCCGCGGA 61.017 55.000 27.28 27.28 40.64 5.54
3235 3958 0.719465 CACACTAAATGTCCGCGGAC 59.281 55.000 43.88 43.88 40.64 4.79
3299 4022 6.187727 TCCAACCCTATATCTCAAATGTCC 57.812 41.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 7.761409 TGCAAATATCTCATAGTTTCACAACC 58.239 34.615 0.00 0.00 32.70 3.77
104 105 8.863049 CCTAGTTCACATAATTCAAACAAATGC 58.137 33.333 0.00 0.00 0.00 3.56
105 106 9.357652 CCCTAGTTCACATAATTCAAACAAATG 57.642 33.333 0.00 0.00 0.00 2.32
168 171 0.952497 CACAGCCTGTCTGCGTTCAT 60.952 55.000 0.00 0.00 46.76 2.57
169 172 1.595109 CACAGCCTGTCTGCGTTCA 60.595 57.895 0.00 0.00 46.76 3.18
170 173 1.595382 ACACAGCCTGTCTGCGTTC 60.595 57.895 0.00 0.00 46.76 3.95
172 175 2.104572 ATCACACAGCCTGTCTGCGT 62.105 55.000 0.00 0.00 46.76 5.24
174 177 1.357258 CGATCACACAGCCTGTCTGC 61.357 60.000 0.00 0.00 46.76 4.26
176 179 0.969149 TTCGATCACACAGCCTGTCT 59.031 50.000 0.00 0.00 0.00 3.41
178 181 2.254546 TTTTCGATCACACAGCCTGT 57.745 45.000 0.00 0.00 0.00 4.00
180 183 1.470098 GCATTTTCGATCACACAGCCT 59.530 47.619 0.00 0.00 0.00 4.58
181 184 1.791555 CGCATTTTCGATCACACAGCC 60.792 52.381 0.00 0.00 0.00 4.85
183 186 2.474526 GGACGCATTTTCGATCACACAG 60.475 50.000 0.00 0.00 0.00 3.66
184 187 1.463056 GGACGCATTTTCGATCACACA 59.537 47.619 0.00 0.00 0.00 3.72
185 188 1.526986 CGGACGCATTTTCGATCACAC 60.527 52.381 0.00 0.00 0.00 3.82
186 189 0.718904 CGGACGCATTTTCGATCACA 59.281 50.000 0.00 0.00 0.00 3.58
187 190 0.586502 GCGGACGCATTTTCGATCAC 60.587 55.000 12.31 0.00 41.49 3.06
188 191 1.713246 GCGGACGCATTTTCGATCA 59.287 52.632 12.31 0.00 41.49 2.92
189 192 1.366494 CGCGGACGCATTTTCGATC 60.366 57.895 17.35 0.00 42.06 3.69
190 193 2.701006 CGCGGACGCATTTTCGAT 59.299 55.556 17.35 0.00 42.06 3.59
231 234 3.615351 CGTCCCCTTTTGTGTTTTTGTGT 60.615 43.478 0.00 0.00 0.00 3.72
232 235 2.926838 CGTCCCCTTTTGTGTTTTTGTG 59.073 45.455 0.00 0.00 0.00 3.33
233 236 2.093921 CCGTCCCCTTTTGTGTTTTTGT 60.094 45.455 0.00 0.00 0.00 2.83
234 237 2.166664 TCCGTCCCCTTTTGTGTTTTTG 59.833 45.455 0.00 0.00 0.00 2.44
235 238 2.166870 GTCCGTCCCCTTTTGTGTTTTT 59.833 45.455 0.00 0.00 0.00 1.94
236 239 1.752498 GTCCGTCCCCTTTTGTGTTTT 59.248 47.619 0.00 0.00 0.00 2.43
237 240 1.064240 AGTCCGTCCCCTTTTGTGTTT 60.064 47.619 0.00 0.00 0.00 2.83
238 241 0.549469 AGTCCGTCCCCTTTTGTGTT 59.451 50.000 0.00 0.00 0.00 3.32
241 244 1.072806 GGTTAGTCCGTCCCCTTTTGT 59.927 52.381 0.00 0.00 0.00 2.83
283 286 1.931172 CCGACAGAGACACGTTTTGTT 59.069 47.619 0.00 0.00 39.17 2.83
290 293 2.176055 CCGACCGACAGAGACACG 59.824 66.667 0.00 0.00 0.00 4.49
295 298 0.866061 CAATACGCCGACCGACAGAG 60.866 60.000 0.00 0.00 41.02 3.35
298 301 2.182284 CCAATACGCCGACCGACA 59.818 61.111 0.00 0.00 41.02 4.35
299 302 1.588139 CTCCAATACGCCGACCGAC 60.588 63.158 0.00 0.00 41.02 4.79
301 304 1.153706 AACTCCAATACGCCGACCG 60.154 57.895 0.00 0.00 44.21 4.79
366 369 1.475751 GCCGTTCCATGGATCATGAGT 60.476 52.381 17.06 0.00 43.81 3.41
474 478 0.882042 CACAGGAGACACAGCCACAC 60.882 60.000 0.00 0.00 0.00 3.82
617 628 5.278463 GCCAACAATGTAGAAAAGAGCTTGA 60.278 40.000 0.00 0.00 0.00 3.02
629 640 8.314021 TCTAGGTCATATATGCCAACAATGTAG 58.686 37.037 21.03 14.22 0.00 2.74
640 651 6.367422 GCTTGAACACTCTAGGTCATATATGC 59.633 42.308 7.92 3.51 0.00 3.14
654 665 6.198966 CCAAAAATACAACTGCTTGAACACTC 59.801 38.462 0.00 0.00 0.00 3.51
738 754 8.254508 AGTCTGAACTTGGATAGTTAACTGATC 58.745 37.037 18.56 14.99 47.00 2.92
762 778 4.766373 TGACAACACATGGCATTCATTAGT 59.234 37.500 0.00 0.00 44.10 2.24
797 813 0.250770 GGTGAACTTGGACTGGACCC 60.251 60.000 0.00 0.00 0.00 4.46
813 857 0.957395 AGTCAAATGAGGCTGCGGTG 60.957 55.000 0.00 0.00 0.00 4.94
994 1417 1.637553 ACAGAAAGCCCTGGTGATCAT 59.362 47.619 0.00 0.00 38.44 2.45
1247 1701 3.766691 GCGGCGTACAGGAGGGAA 61.767 66.667 9.37 0.00 0.00 3.97
1290 1744 4.446413 GCCCAGCTGTTGCATGGC 62.446 66.667 13.81 13.20 45.79 4.40
2006 2463 2.343758 GAGAAGAGGTGGTGCGCA 59.656 61.111 5.66 5.66 0.00 6.09
2096 2553 1.753078 GGCAAGGGGGTTCGATTCC 60.753 63.158 0.00 0.00 0.00 3.01
2272 2730 7.819900 AGTAGTTATTTTTCAATCGACTGAGCT 59.180 33.333 0.00 0.00 0.00 4.09
2340 2998 1.269883 CGTAGGTGGTAGCACAACACA 60.270 52.381 25.23 3.64 36.87 3.72
2388 3048 3.131046 ACCAAAGAAGAAGCCAACACTTG 59.869 43.478 0.00 0.00 0.00 3.16
2389 3049 3.365472 ACCAAAGAAGAAGCCAACACTT 58.635 40.909 0.00 0.00 0.00 3.16
2390 3050 3.018423 ACCAAAGAAGAAGCCAACACT 57.982 42.857 0.00 0.00 0.00 3.55
2394 3054 3.513515 ACAACAACCAAAGAAGAAGCCAA 59.486 39.130 0.00 0.00 0.00 4.52
2407 3067 1.152777 CCAGCCCAGACAACAACCA 60.153 57.895 0.00 0.00 0.00 3.67
2417 3077 2.081161 AAGCCCTATCCCAGCCCAG 61.081 63.158 0.00 0.00 0.00 4.45
2478 3141 5.560722 TTATTGTACATCATCACGGGGAT 57.439 39.130 0.00 0.00 36.39 3.85
2546 3209 7.467623 GCTGACTTCAGGTACTTATCATTTTG 58.532 38.462 8.32 0.00 43.94 2.44
2565 3228 1.000283 GCCATATGCTCGTAGCTGACT 60.000 52.381 0.00 0.00 42.97 3.41
2571 3234 3.317150 TCGATTTGCCATATGCTCGTAG 58.683 45.455 0.00 0.00 42.00 3.51
2594 3257 4.092821 TCACTAGAATTGCCATCGAAAACG 59.907 41.667 0.00 0.00 0.00 3.60
2627 3290 4.290155 CAGTGTGTGTCAACTAATTTGCC 58.710 43.478 0.00 0.00 34.88 4.52
2628 3291 3.730715 GCAGTGTGTGTCAACTAATTTGC 59.269 43.478 0.00 0.00 34.88 3.68
2632 3295 5.772825 AATTGCAGTGTGTGTCAACTAAT 57.227 34.783 0.00 0.00 0.00 1.73
2665 3328 8.556517 ACTTCGTGCTTCAGTTTATTTTTAAC 57.443 30.769 0.00 0.00 0.00 2.01
2683 3346 0.040958 GCAAGCCTGACAACTTCGTG 60.041 55.000 0.00 0.00 0.00 4.35
2685 3348 1.165907 TGGCAAGCCTGACAACTTCG 61.166 55.000 12.96 0.00 37.77 3.79
2693 3356 2.656947 ACTTTAGTTGGCAAGCCTGA 57.343 45.000 12.96 0.00 36.94 3.86
2726 3389 4.497473 TTTTCGATGGCAAGTTTAGTGG 57.503 40.909 0.00 0.00 0.00 4.00
2768 3431 1.208358 CGCTCGAACGTCAGGTACA 59.792 57.895 0.00 0.00 0.00 2.90
2778 3449 5.517054 AGAAGAAATCTGATAACGCTCGAAC 59.483 40.000 0.00 0.00 36.88 3.95
2797 3468 7.201920 CCGGATATCTTACTCCAAAAGAGAAGA 60.202 40.741 0.00 2.68 46.50 2.87
2808 3479 5.532664 AAGTTCACCGGATATCTTACTCC 57.467 43.478 9.46 0.00 0.00 3.85
2810 3481 9.901172 AAAATAAAGTTCACCGGATATCTTACT 57.099 29.630 9.46 0.00 0.00 2.24
2839 3511 9.550406 AAAATAAATCGTTCGGTATCCTGATAA 57.450 29.630 0.00 0.00 0.00 1.75
2847 3519 6.685403 CGCAAGAAAAATAAATCGTTCGGTAT 59.315 34.615 0.00 0.00 43.02 2.73
2851 3523 5.968251 ACGCAAGAAAAATAAATCGTTCG 57.032 34.783 0.00 0.00 43.62 3.95
2885 3557 1.144936 GGATCAGCCTCACCCTTCG 59.855 63.158 0.00 0.00 0.00 3.79
2905 3577 7.544915 TCATTGCTTGCAATAAAAATTCGATCA 59.455 29.630 18.74 0.00 0.00 2.92
2910 3582 9.485591 CAGAATCATTGCTTGCAATAAAAATTC 57.514 29.630 18.74 20.39 0.00 2.17
2943 3615 7.225538 ACTCAATAATTTCGAGAATGCACCTAG 59.774 37.037 0.00 0.00 0.00 3.02
3048 3769 9.053840 AGAACTAGTATCGAAAATCTCATCGTA 57.946 33.333 0.00 0.00 39.91 3.43
3145 3867 0.536687 TACGGCGAGGATGTCTAGGG 60.537 60.000 16.62 0.00 0.00 3.53
3147 3869 1.595466 ACTACGGCGAGGATGTCTAG 58.405 55.000 16.62 4.47 0.00 2.43
3148 3870 2.048444 AACTACGGCGAGGATGTCTA 57.952 50.000 16.62 0.00 0.00 2.59
3189 3912 2.602257 TACGACATGGCTTGGAGATG 57.398 50.000 0.00 0.00 0.00 2.90
3199 3922 0.655733 GTGCCCGATTTACGACATGG 59.344 55.000 0.00 0.00 45.77 3.66
3206 3929 4.201881 GGACATTTAGTGTGCCCGATTTAC 60.202 45.833 0.00 0.00 42.75 2.01
3213 3936 1.800681 GCGGACATTTAGTGTGCCC 59.199 57.895 0.00 0.00 45.43 5.36
3232 3955 1.447314 GAACCCGTCGGTCATGTCC 60.447 63.158 11.06 0.00 43.71 4.02
3233 3956 1.012486 GTGAACCCGTCGGTCATGTC 61.012 60.000 11.06 0.58 43.71 3.06
3234 3957 1.005394 GTGAACCCGTCGGTCATGT 60.005 57.895 11.06 0.00 43.71 3.21
3235 3958 2.092291 CGTGAACCCGTCGGTCATG 61.092 63.158 11.06 9.90 43.71 3.07
3236 3959 2.260434 CGTGAACCCGTCGGTCAT 59.740 61.111 11.06 0.00 43.71 3.06
3237 3960 3.980989 CCGTGAACCCGTCGGTCA 61.981 66.667 11.06 5.45 43.71 4.02
3238 3961 3.673484 TCCGTGAACCCGTCGGTC 61.673 66.667 11.06 2.48 43.71 4.79
3240 3963 4.729856 GGTCCGTGAACCCGTCGG 62.730 72.222 3.60 3.60 44.76 4.79
3246 3969 1.142531 GTATCCGGGTCCGTGAACC 59.857 63.158 0.00 0.00 35.78 3.62
3267 3990 2.056906 ATAGGGTTGGATGGCGGCTC 62.057 60.000 11.43 5.18 0.00 4.70
3270 3993 1.909302 AGATATAGGGTTGGATGGCGG 59.091 52.381 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.