Multiple sequence alignment - TraesCS7B01G480800

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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 TraesCS7B01G480800 chr7B 100.000 1713 0 0 804 2516 734408425 734406713 0.000000e+00 3164
1 TraesCS7B01G480800 chr7B 100.000 419 0 0 1 419 734409228 734408810 0.000000e+00 774
2 TraesCS7B01G480800 chr7B 78.426 1080 150 41 861 1888 734380071 734379023 5.910000e-176 627
3 TraesCS7B01G480800 chr7B 79.373 606 105 12 988 1590 734426981 734426393 2.330000e-110 409
4 TraesCS7B01G480800 chr7B 89.506 162 17 0 988 1149 734417183 734417022 3.280000e-49 206
5 TraesCS7B01G480800 chr7D 84.366 1695 147 52 841 2478 638296306 638297939 0.000000e+00 1554
6 TraesCS7B01G480800 chr7D 87.027 740 88 5 848 1583 638287868 638288603 0.000000e+00 828
7 TraesCS7B01G480800 chr7D 80.351 855 123 30 894 1727 638330497 638331327 7.700000e-170 606
8 TraesCS7B01G480800 chr7D 80.502 877 85 32 1632 2467 638288599 638289430 5.990000e-166 593
9 TraesCS7B01G480800 chr7D 78.479 618 99 20 988 1590 638273937 638274535 8.500000e-100 374
10 TraesCS7B01G480800 chr7D 91.549 142 11 1 3 143 638287355 638287496 7.100000e-46 195
11 TraesCS7B01G480800 chr7A 85.727 1093 92 36 849 1906 727774293 727773230 0.000000e+00 1096
12 TraesCS7B01G480800 chr7A 91.047 793 60 6 804 1595 727788682 727787900 0.000000e+00 1061
13 TraesCS7B01G480800 chr7A 81.443 970 135 30 894 1840 727722394 727721447 0.000000e+00 752
14 TraesCS7B01G480800 chr7A 82.460 496 62 19 1867 2342 727773241 727772751 6.480000e-111 411
15 TraesCS7B01G480800 chr7A 81.621 506 38 15 1642 2116 727787521 727787040 3.950000e-98 368
16 TraesCS7B01G480800 chr7A 76.641 518 91 21 865 1379 727581428 727580938 2.480000e-65 259
17 TraesCS7B01G480800 chr7A 74.757 515 101 22 865 1378 727584332 727583846 1.180000e-48 204


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 TraesCS7B01G480800 chr7B 734406713 734409228 2515 True 1969.000000 3164 100.000000 1 2516 2 chr7B.!!$R4 2515
1 TraesCS7B01G480800 chr7B 734379023 734380071 1048 True 627.000000 627 78.426000 861 1888 1 chr7B.!!$R1 1027
2 TraesCS7B01G480800 chr7B 734426393 734426981 588 True 409.000000 409 79.373000 988 1590 1 chr7B.!!$R3 602
3 TraesCS7B01G480800 chr7D 638296306 638297939 1633 False 1554.000000 1554 84.366000 841 2478 1 chr7D.!!$F2 1637
4 TraesCS7B01G480800 chr7D 638330497 638331327 830 False 606.000000 606 80.351000 894 1727 1 chr7D.!!$F3 833
5 TraesCS7B01G480800 chr7D 638287355 638289430 2075 False 538.666667 828 86.359333 3 2467 3 chr7D.!!$F4 2464
6 TraesCS7B01G480800 chr7D 638273937 638274535 598 False 374.000000 374 78.479000 988 1590 1 chr7D.!!$F1 602
7 TraesCS7B01G480800 chr7A 727772751 727774293 1542 True 753.500000 1096 84.093500 849 2342 2 chr7A.!!$R3 1493
8 TraesCS7B01G480800 chr7A 727721447 727722394 947 True 752.000000 752 81.443000 894 1840 1 chr7A.!!$R1 946
9 TraesCS7B01G480800 chr7A 727787040 727788682 1642 True 714.500000 1061 86.334000 804 2116 2 chr7A.!!$R4 1312
10 TraesCS7B01G480800 chr7A 727580938 727584332 3394 True 231.500000 259 75.699000 865 1379 2 chr7A.!!$R2 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
28 29 0.031449 GAGCTAGACCGAGGATGTGC 59.969 60.0 0.0 0.0 0.00 4.57 F
336 396 0.462759 AGCCAGCAATAGAGCCGAAC 60.463 55.0 0.0 0.0 34.23 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1480 0.032678 CGCCGATGAGTATGAAGGCT 59.967 55.0 2.75 0.0 42.16 4.58 R
1878 2479 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.00 3.72 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
18 19 2.128729 AGGGCAATCGAGCTAGACC 58.871 57.895 0.00 0.00 34.17 3.85
19 20 1.300233 GGGCAATCGAGCTAGACCG 60.300 63.158 0.00 0.00 34.17 4.79
28 29 0.031449 GAGCTAGACCGAGGATGTGC 59.969 60.000 0.00 0.00 0.00 4.57
56 57 5.418310 TTGCACTTTAGTTTTCCTTCGAG 57.582 39.130 0.00 0.00 0.00 4.04
86 87 4.275196 CCATCAGTCAAGTTGCTATCATGG 59.725 45.833 0.00 7.54 0.00 3.66
92 93 1.755179 AGTTGCTATCATGGTGTGCC 58.245 50.000 0.00 0.00 0.00 5.01
94 95 1.375853 TTGCTATCATGGTGTGCCGC 61.376 55.000 0.00 0.00 37.67 6.53
163 192 8.494433 TGACTACTAAAAGGCAATAGATTCCAT 58.506 33.333 0.00 0.00 29.20 3.41
166 195 6.672593 ACTAAAAGGCAATAGATTCCATCCA 58.327 36.000 0.00 0.00 0.00 3.41
167 196 5.859205 AAAAGGCAATAGATTCCATCCAC 57.141 39.130 0.00 0.00 0.00 4.02
177 206 9.081204 CAATAGATTCCATCCACCAAATATTCA 57.919 33.333 0.00 0.00 0.00 2.57
178 207 8.874744 ATAGATTCCATCCACCAAATATTCAG 57.125 34.615 0.00 0.00 0.00 3.02
181 210 5.715439 TCCATCCACCAAATATTCAGAGT 57.285 39.130 0.00 0.00 0.00 3.24
182 211 5.684704 TCCATCCACCAAATATTCAGAGTC 58.315 41.667 0.00 0.00 0.00 3.36
227 258 4.556233 CGATTAATCGGGATGCTCAGTTA 58.444 43.478 26.61 0.00 45.93 2.24
228 259 5.171476 CGATTAATCGGGATGCTCAGTTAT 58.829 41.667 26.61 0.00 45.93 1.89
229 260 5.639506 CGATTAATCGGGATGCTCAGTTATT 59.360 40.000 26.61 0.00 45.93 1.40
230 261 6.147821 CGATTAATCGGGATGCTCAGTTATTT 59.852 38.462 26.61 0.00 45.93 1.40
231 262 6.618287 TTAATCGGGATGCTCAGTTATTTG 57.382 37.500 0.00 0.00 0.00 2.32
232 263 3.627395 TCGGGATGCTCAGTTATTTGT 57.373 42.857 0.00 0.00 0.00 2.83
233 264 3.950397 TCGGGATGCTCAGTTATTTGTT 58.050 40.909 0.00 0.00 0.00 2.83
234 265 3.938963 TCGGGATGCTCAGTTATTTGTTC 59.061 43.478 0.00 0.00 0.00 3.18
235 266 3.689161 CGGGATGCTCAGTTATTTGTTCA 59.311 43.478 0.00 0.00 0.00 3.18
236 267 4.155826 CGGGATGCTCAGTTATTTGTTCAA 59.844 41.667 0.00 0.00 0.00 2.69
237 268 5.644644 GGGATGCTCAGTTATTTGTTCAAG 58.355 41.667 0.00 0.00 0.00 3.02
238 269 5.415701 GGGATGCTCAGTTATTTGTTCAAGA 59.584 40.000 0.00 0.00 0.00 3.02
264 301 2.370189 AGAAGAAGTGGACAAGAGGTGG 59.630 50.000 0.00 0.00 0.00 4.61
272 309 1.689273 GGACAAGAGGTGGATATCGCT 59.311 52.381 0.00 0.00 0.00 4.93
291 328 5.575957 TCGCTAAAGGTAGAGAAATACACG 58.424 41.667 0.00 0.00 33.72 4.49
292 329 4.738740 CGCTAAAGGTAGAGAAATACACGG 59.261 45.833 0.00 0.00 29.12 4.94
293 330 5.449588 CGCTAAAGGTAGAGAAATACACGGA 60.450 44.000 0.00 0.00 29.12 4.69
294 331 5.747675 GCTAAAGGTAGAGAAATACACGGAC 59.252 44.000 0.00 0.00 0.00 4.79
295 332 5.997384 AAAGGTAGAGAAATACACGGACT 57.003 39.130 0.00 0.00 0.00 3.85
296 333 7.201767 GCTAAAGGTAGAGAAATACACGGACTA 60.202 40.741 0.00 0.00 0.00 2.59
297 334 6.696441 AAGGTAGAGAAATACACGGACTAG 57.304 41.667 0.00 0.00 0.00 2.57
298 335 5.753716 AGGTAGAGAAATACACGGACTAGT 58.246 41.667 0.00 0.00 0.00 2.57
299 336 6.186234 AGGTAGAGAAATACACGGACTAGTT 58.814 40.000 0.00 0.00 0.00 2.24
300 337 6.662663 AGGTAGAGAAATACACGGACTAGTTT 59.337 38.462 0.00 0.00 0.00 2.66
301 338 7.178097 AGGTAGAGAAATACACGGACTAGTTTT 59.822 37.037 0.00 0.00 0.00 2.43
303 340 5.638234 AGAGAAATACACGGACTAGTTTTGC 59.362 40.000 0.00 0.00 0.00 3.68
304 341 5.302360 AGAAATACACGGACTAGTTTTGCA 58.698 37.500 0.00 0.00 0.00 4.08
307 344 2.634600 ACACGGACTAGTTTTGCACAA 58.365 42.857 0.00 0.00 0.00 3.33
308 345 2.612212 ACACGGACTAGTTTTGCACAAG 59.388 45.455 0.00 0.00 0.00 3.16
328 388 1.332997 GCACTAGCAAGCCAGCAATAG 59.667 52.381 0.55 0.00 41.58 1.73
331 391 1.872313 CTAGCAAGCCAGCAATAGAGC 59.128 52.381 0.55 0.00 36.85 4.09
336 396 0.462759 AGCCAGCAATAGAGCCGAAC 60.463 55.000 0.00 0.00 34.23 3.95
342 402 4.024556 CCAGCAATAGAGCCGAACTAAATG 60.025 45.833 0.00 0.00 34.23 2.32
351 411 6.640518 AGAGCCGAACTAAATGACAAATCTA 58.359 36.000 0.00 0.00 0.00 1.98
389 450 9.027129 GTTTTTACTTTACCAAATGAACCTGTC 57.973 33.333 0.00 0.00 0.00 3.51
413 474 4.794169 AGACAAATTGAATGTACAACGCC 58.206 39.130 0.00 0.00 32.50 5.68
415 476 4.295051 ACAAATTGAATGTACAACGCCAC 58.705 39.130 0.00 0.00 32.50 5.01
836 897 3.181466 GGAAAACAGGGCACAAGAACAAT 60.181 43.478 0.00 0.00 0.00 2.71
837 898 4.038642 GGAAAACAGGGCACAAGAACAATA 59.961 41.667 0.00 0.00 0.00 1.90
838 899 4.584327 AAACAGGGCACAAGAACAATAC 57.416 40.909 0.00 0.00 0.00 1.89
839 900 3.508845 ACAGGGCACAAGAACAATACT 57.491 42.857 0.00 0.00 0.00 2.12
845 906 6.010219 AGGGCACAAGAACAATACTACAATT 58.990 36.000 0.00 0.00 0.00 2.32
855 916 9.787435 AGAACAATACTACAATTCTACAAACCA 57.213 29.630 0.00 0.00 0.00 3.67
966 1027 3.472726 ACCACGACCACCACCGTT 61.473 61.111 0.00 0.00 36.83 4.44
1265 1335 2.786495 CGTGGTCGGAGGATGAGGG 61.786 68.421 0.00 0.00 0.00 4.30
1299 1369 2.665000 CATGTGCACCGGGAGACT 59.335 61.111 15.69 0.00 0.00 3.24
1383 1453 1.002430 GAGTTCACTGCCATCACAGGA 59.998 52.381 0.00 0.00 42.21 3.86
1404 1480 1.536073 CCGTCTGCTGGTTCTCAGGA 61.536 60.000 0.00 0.00 43.54 3.86
1418 1494 3.921104 TCTCAGGAGCCTTCATACTCAT 58.079 45.455 0.00 0.00 34.48 2.90
1510 1592 2.426522 GCATGGTGTTGCTTCTCTGTA 58.573 47.619 0.00 0.00 39.57 2.74
1518 1602 5.040635 GTGTTGCTTCTCTGTATCTAGCTC 58.959 45.833 0.00 0.00 33.15 4.09
1579 1711 3.705638 CTGAGCGTGCGTGTGTGG 61.706 66.667 0.00 0.00 0.00 4.17
1597 2076 2.172372 GGATGCTCTGCTCTGCGTG 61.172 63.158 0.00 0.00 0.00 5.34
1598 2077 2.125229 ATGCTCTGCTCTGCGTGG 60.125 61.111 0.00 0.00 0.00 4.94
1599 2078 2.569072 GATGCTCTGCTCTGCGTGGA 62.569 60.000 0.00 0.00 0.00 4.02
1602 2081 1.023513 GCTCTGCTCTGCGTGGATTT 61.024 55.000 0.00 0.00 0.00 2.17
1605 2084 3.201290 CTCTGCTCTGCGTGGATTTTAT 58.799 45.455 0.00 0.00 0.00 1.40
1606 2085 4.371786 CTCTGCTCTGCGTGGATTTTATA 58.628 43.478 0.00 0.00 0.00 0.98
1732 2225 1.145119 ACTTTGGGGTGTTTCCTCCTC 59.855 52.381 0.00 0.00 35.35 3.71
1736 2229 1.423794 GGGGTGTTTCCTCCTCCACA 61.424 60.000 0.00 0.00 36.25 4.17
1760 2291 3.187842 GTGGCTCCTTTTGGTTTAGTACG 59.812 47.826 0.00 0.00 41.38 3.67
1765 2296 6.104665 GCTCCTTTTGGTTTAGTACGAGTAT 58.895 40.000 0.00 0.00 41.38 2.12
1780 2311 4.371786 ACGAGTATACTACGTGGATTCGA 58.628 43.478 21.54 0.00 38.79 3.71
1795 2326 5.800438 GTGGATTCGAGGAAATTAAGCAAAC 59.200 40.000 0.00 0.00 0.00 2.93
1877 2478 1.102809 ACCAGCCATGTGTGTGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
1878 2479 1.102809 CCAGCCATGTGTGTGTGTGT 61.103 55.000 0.00 0.00 0.00 3.72
1879 2480 0.029700 CAGCCATGTGTGTGTGTGTG 59.970 55.000 0.00 0.00 0.00 3.82
1880 2481 0.394216 AGCCATGTGTGTGTGTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
1881 2482 0.248580 GCCATGTGTGTGTGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
1882 2483 1.093972 CCATGTGTGTGTGTGTGTGT 58.906 50.000 0.00 0.00 0.00 3.72
1883 2484 1.202166 CCATGTGTGTGTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
1884 2485 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
1885 2486 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1886 2487 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1887 2488 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1888 2489 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1889 2490 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1890 2491 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1891 2492 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1892 2493 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1893 2494 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1894 2495 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1895 2496 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1896 2497 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1920 2521 4.332543 GTGTGTGTGAAAAGATGAGACACA 59.667 41.667 0.00 0.00 43.44 3.72
1941 2542 6.093633 ACACACTTTACTTCTTTTGACCTGTC 59.906 38.462 0.00 0.00 0.00 3.51
1953 2562 1.202806 TGACCTGTCTTTTGCTCCCAG 60.203 52.381 0.00 0.00 0.00 4.45
2133 3213 5.130705 AGTGTATACTCTGTCCCAGATGA 57.869 43.478 6.65 0.00 39.92 2.92
2140 3220 5.287674 ACTCTGTCCCAGATGACAATATG 57.712 43.478 0.00 0.00 44.19 1.78
2151 3231 6.293081 CCAGATGACAATATGGAATTGACGTC 60.293 42.308 9.11 9.11 46.42 4.34
2162 3242 1.414158 ATTGACGTCCGATCTGGGAT 58.586 50.000 14.12 0.00 38.61 3.85
2166 3246 2.361119 TGACGTCCGATCTGGGATTAAG 59.639 50.000 14.12 0.00 38.61 1.85
2171 3251 1.284982 CGATCTGGGATTAAGCCGCG 61.285 60.000 3.16 0.00 0.00 6.46
2173 3253 1.407656 ATCTGGGATTAAGCCGCGGA 61.408 55.000 33.48 8.40 36.51 5.54
2178 3258 0.461339 GGATTAAGCCGCGGAGAACA 60.461 55.000 33.48 8.30 0.00 3.18
2182 3262 2.676632 TAAGCCGCGGAGAACAAATA 57.323 45.000 33.48 5.94 0.00 1.40
2249 3332 2.741985 CCATCCAGTGCGACGCAA 60.742 61.111 26.29 9.58 41.47 4.85
2278 3362 1.080298 GCCACTTGCATTGCTGTCC 60.080 57.895 10.49 0.00 40.77 4.02
2298 3382 1.273327 CTTCCCCAGCGCAATTCTTTT 59.727 47.619 11.47 0.00 0.00 2.27
2319 3404 2.278854 TGCCAAAAAGAAAAGCACAGC 58.721 42.857 0.00 0.00 0.00 4.40
2331 3416 4.639078 AAAGCACAGCCCCAAAAATATT 57.361 36.364 0.00 0.00 0.00 1.28
2344 3429 8.022550 GCCCCAAAAATATTGAATGTCAAAAAG 58.977 33.333 0.00 0.00 40.12 2.27
2368 3460 9.774742 AAGATGAAACATAAAGAATAACGCTTC 57.225 29.630 0.00 0.00 0.00 3.86
2369 3461 8.116753 AGATGAAACATAAAGAATAACGCTTCG 58.883 33.333 0.00 0.00 0.00 3.79
2370 3462 6.019152 TGAAACATAAAGAATAACGCTTCGC 58.981 36.000 0.00 0.00 0.00 4.70
2371 3463 5.539582 AACATAAAGAATAACGCTTCGCA 57.460 34.783 0.00 0.00 0.00 5.10
2372 3464 5.734855 ACATAAAGAATAACGCTTCGCAT 57.265 34.783 0.00 0.00 0.00 4.73
2374 3466 5.523916 ACATAAAGAATAACGCTTCGCATCT 59.476 36.000 0.00 0.00 0.00 2.90
2375 3467 6.700081 ACATAAAGAATAACGCTTCGCATCTA 59.300 34.615 0.00 0.00 0.00 1.98
2376 3468 7.223971 ACATAAAGAATAACGCTTCGCATCTAA 59.776 33.333 0.00 0.00 0.00 2.10
2377 3469 6.417191 AAAGAATAACGCTTCGCATCTAAA 57.583 33.333 0.00 0.00 0.00 1.85
2378 3470 5.391060 AGAATAACGCTTCGCATCTAAAC 57.609 39.130 0.00 0.00 0.00 2.01
2379 3471 4.270325 AGAATAACGCTTCGCATCTAAACC 59.730 41.667 0.00 0.00 0.00 3.27
2380 3472 1.803334 AACGCTTCGCATCTAAACCA 58.197 45.000 0.00 0.00 0.00 3.67
2385 3477 4.165779 CGCTTCGCATCTAAACCATTTTT 58.834 39.130 0.00 0.00 0.00 1.94
2425 3538 9.918630 ATCATGAGTTTGCCAATTTAATATAGC 57.081 29.630 0.09 0.00 0.00 2.97
2467 4498 9.730420 AAACTTTAATTGCCACGATATTATGAC 57.270 29.630 0.00 0.00 0.00 3.06
2474 4505 6.117911 TGCCACGATATTATGACAAACAAG 57.882 37.500 0.00 0.00 0.00 3.16
2478 4509 7.376866 GCCACGATATTATGACAAACAAGAATG 59.623 37.037 0.00 0.00 0.00 2.67
2480 4511 8.611757 CACGATATTATGACAAACAAGAATGGA 58.388 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.739338 CGGTCTAGCTCGATTGCCCT 61.739 60.000 0.00 0.00 0.00 5.19
1 2 1.300233 CGGTCTAGCTCGATTGCCC 60.300 63.158 0.00 0.00 0.00 5.36
9 10 0.031449 GCACATCCTCGGTCTAGCTC 59.969 60.000 0.00 0.00 0.00 4.09
28 29 7.454260 AAGGAAAACTAAAGTGCAAGGATAG 57.546 36.000 0.00 0.00 0.00 2.08
36 37 4.510340 TCACTCGAAGGAAAACTAAAGTGC 59.490 41.667 0.00 0.00 35.09 4.40
56 57 3.373439 GCAACTTGACTGATGGAGATCAC 59.627 47.826 0.00 0.00 34.71 3.06
72 73 2.094675 GGCACACCATGATAGCAACTT 58.905 47.619 0.00 0.00 35.26 2.66
86 87 1.806758 GCCATTCATTGCGGCACAC 60.807 57.895 0.05 0.00 45.52 3.82
94 95 4.024641 TCAGAATCGATTCGCCATTCATTG 60.025 41.667 27.69 18.45 41.56 2.82
104 105 7.685532 TTTAGTCTCAATCAGAATCGATTCG 57.314 36.000 27.69 22.39 41.56 3.34
105 106 9.092876 ACTTTTAGTCTCAATCAGAATCGATTC 57.907 33.333 27.16 27.16 33.27 2.52
106 107 9.442047 AACTTTTAGTCTCAATCAGAATCGATT 57.558 29.630 11.20 11.20 36.00 3.34
143 145 6.015940 GGTGGATGGAATCTATTGCCTTTTAG 60.016 42.308 0.00 0.00 44.71 1.85
144 146 5.833131 GGTGGATGGAATCTATTGCCTTTTA 59.167 40.000 0.00 0.00 44.71 1.52
207 238 6.772716 ACAAATAACTGAGCATCCCGATTAAT 59.227 34.615 0.00 0.00 0.00 1.40
213 244 3.689161 TGAACAAATAACTGAGCATCCCG 59.311 43.478 0.00 0.00 0.00 5.14
215 246 6.500684 TCTTGAACAAATAACTGAGCATCC 57.499 37.500 0.00 0.00 0.00 3.51
224 255 9.617975 CTTCTTCTCCAATCTTGAACAAATAAC 57.382 33.333 0.00 0.00 0.00 1.89
227 258 7.255730 CCACTTCTTCTCCAATCTTGAACAAAT 60.256 37.037 0.00 0.00 0.00 2.32
228 259 6.039717 CCACTTCTTCTCCAATCTTGAACAAA 59.960 38.462 0.00 0.00 0.00 2.83
229 260 5.532406 CCACTTCTTCTCCAATCTTGAACAA 59.468 40.000 0.00 0.00 0.00 2.83
230 261 5.065914 CCACTTCTTCTCCAATCTTGAACA 58.934 41.667 0.00 0.00 0.00 3.18
231 262 5.180304 GTCCACTTCTTCTCCAATCTTGAAC 59.820 44.000 0.00 0.00 0.00 3.18
232 263 5.163205 TGTCCACTTCTTCTCCAATCTTGAA 60.163 40.000 0.00 0.00 0.00 2.69
233 264 4.347876 TGTCCACTTCTTCTCCAATCTTGA 59.652 41.667 0.00 0.00 0.00 3.02
234 265 4.645535 TGTCCACTTCTTCTCCAATCTTG 58.354 43.478 0.00 0.00 0.00 3.02
235 266 4.982241 TGTCCACTTCTTCTCCAATCTT 57.018 40.909 0.00 0.00 0.00 2.40
236 267 4.594920 TCTTGTCCACTTCTTCTCCAATCT 59.405 41.667 0.00 0.00 0.00 2.40
237 268 4.899502 TCTTGTCCACTTCTTCTCCAATC 58.100 43.478 0.00 0.00 0.00 2.67
238 269 4.263243 CCTCTTGTCCACTTCTTCTCCAAT 60.263 45.833 0.00 0.00 0.00 3.16
264 301 9.344309 GTGTATTTCTCTACCTTTAGCGATATC 57.656 37.037 0.00 0.00 0.00 1.63
272 309 7.831193 ACTAGTCCGTGTATTTCTCTACCTTTA 59.169 37.037 0.00 0.00 0.00 1.85
303 340 0.520404 CTGGCTTGCTAGTGCTTGTG 59.480 55.000 0.00 0.00 40.48 3.33
304 341 1.239968 GCTGGCTTGCTAGTGCTTGT 61.240 55.000 7.75 0.00 40.48 3.16
307 344 0.323178 ATTGCTGGCTTGCTAGTGCT 60.323 50.000 7.75 0.00 40.48 4.40
308 345 1.332997 CTATTGCTGGCTTGCTAGTGC 59.667 52.381 7.75 0.60 40.20 4.40
311 348 1.872313 GCTCTATTGCTGGCTTGCTAG 59.128 52.381 1.49 1.49 0.00 3.42
318 378 0.462759 AGTTCGGCTCTATTGCTGGC 60.463 55.000 0.00 0.00 39.62 4.85
328 388 5.803020 AGATTTGTCATTTAGTTCGGCTC 57.197 39.130 0.00 0.00 0.00 4.70
362 422 8.755028 ACAGGTTCATTTGGTAAAGTAAAAACT 58.245 29.630 0.00 0.00 0.00 2.66
363 423 8.936070 ACAGGTTCATTTGGTAAAGTAAAAAC 57.064 30.769 0.00 0.00 0.00 2.43
364 424 8.750298 TGACAGGTTCATTTGGTAAAGTAAAAA 58.250 29.630 0.00 0.00 0.00 1.94
372 433 5.441500 TGTCTTGACAGGTTCATTTGGTAA 58.558 37.500 0.00 0.00 32.84 2.85
376 437 6.979817 TCAATTTGTCTTGACAGGTTCATTTG 59.020 34.615 3.61 3.19 32.84 2.32
381 442 6.507023 ACATTCAATTTGTCTTGACAGGTTC 58.493 36.000 3.61 0.00 34.96 3.62
382 443 6.469782 ACATTCAATTTGTCTTGACAGGTT 57.530 33.333 3.61 1.22 34.96 3.50
383 444 6.545666 TGTACATTCAATTTGTCTTGACAGGT 59.454 34.615 3.61 0.00 34.96 4.00
389 450 5.116983 GGCGTTGTACATTCAATTTGTCTTG 59.883 40.000 0.00 0.00 0.00 3.02
809 870 1.140312 TGTGCCCTGTTTTCCTCTCT 58.860 50.000 0.00 0.00 0.00 3.10
1238 1302 4.135153 CCGACCACGCTCCTCCAG 62.135 72.222 0.00 0.00 38.29 3.86
1281 1351 1.613317 TAGTCTCCCGGTGCACATGG 61.613 60.000 20.43 19.00 0.00 3.66
1395 1465 3.449018 TGAGTATGAAGGCTCCTGAGAAC 59.551 47.826 0.00 0.00 0.00 3.01
1397 1467 3.388552 TGAGTATGAAGGCTCCTGAGA 57.611 47.619 0.00 0.00 0.00 3.27
1404 1480 0.032678 CGCCGATGAGTATGAAGGCT 59.967 55.000 2.75 0.00 42.16 4.58
1443 1519 2.659610 GCTCTCGCCAAGACTGGT 59.340 61.111 0.00 0.00 45.53 4.00
1510 1592 3.169099 AGTTCACACACCAGAGCTAGAT 58.831 45.455 0.00 0.00 0.00 1.98
1518 1602 1.338337 AGTCGAGAGTTCACACACCAG 59.662 52.381 0.00 0.00 0.00 4.00
1579 1711 2.172372 CACGCAGAGCAGAGCATCC 61.172 63.158 0.00 0.00 33.66 3.51
1597 2076 1.422402 TGACCCCCGGCTATAAAATCC 59.578 52.381 0.00 0.00 0.00 3.01
1598 2077 2.943036 TGACCCCCGGCTATAAAATC 57.057 50.000 0.00 0.00 0.00 2.17
1599 2078 2.041216 GGATGACCCCCGGCTATAAAAT 59.959 50.000 0.00 0.00 0.00 1.82
1602 2081 1.189524 CGGATGACCCCCGGCTATAA 61.190 60.000 0.00 0.00 43.05 0.98
1736 2229 2.227194 CTAAACCAAAAGGAGCCACGT 58.773 47.619 0.00 0.00 0.00 4.49
1760 2291 4.993584 TCCTCGAATCCACGTAGTATACTC 59.006 45.833 9.12 0.62 41.61 2.59
1765 2296 5.587388 AATTTCCTCGAATCCACGTAGTA 57.413 39.130 0.00 0.00 41.61 1.82
1780 2311 6.478512 TTCAAGTGGTTTGCTTAATTTCCT 57.521 33.333 0.00 0.00 36.70 3.36
1795 2326 6.455647 TGATCACTACTAGTGTTTCAAGTGG 58.544 40.000 17.17 3.94 46.03 4.00
1877 2478 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1878 2479 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1879 2480 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1880 2481 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1881 2482 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1882 2483 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1883 2484 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1884 2485 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1885 2486 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1886 2487 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1887 2488 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
1888 2489 1.884235 TTCACACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
1889 2490 2.979401 TTTCACACACACACACACAC 57.021 45.000 0.00 0.00 0.00 3.82
1890 2491 3.142174 TCTTTTCACACACACACACACA 58.858 40.909 0.00 0.00 0.00 3.72
1891 2492 3.822594 TCTTTTCACACACACACACAC 57.177 42.857 0.00 0.00 0.00 3.82
1892 2493 4.006319 TCATCTTTTCACACACACACACA 58.994 39.130 0.00 0.00 0.00 3.72
1893 2494 4.332543 TCTCATCTTTTCACACACACACAC 59.667 41.667 0.00 0.00 0.00 3.82
1894 2495 4.332543 GTCTCATCTTTTCACACACACACA 59.667 41.667 0.00 0.00 0.00 3.72
1895 2496 4.332543 TGTCTCATCTTTTCACACACACAC 59.667 41.667 0.00 0.00 0.00 3.82
1896 2497 4.332543 GTGTCTCATCTTTTCACACACACA 59.667 41.667 0.00 0.00 37.81 3.72
1920 2521 7.939784 AAAGACAGGTCAAAAGAAGTAAAGT 57.060 32.000 1.84 0.00 0.00 2.66
1941 2542 5.520376 TTTCTTCTTTCTGGGAGCAAAAG 57.480 39.130 0.00 0.00 0.00 2.27
1953 2562 2.789339 GCACCGCAAGTTTTCTTCTTTC 59.211 45.455 0.00 0.00 38.17 2.62
2124 3195 6.064060 GTCAATTCCATATTGTCATCTGGGA 58.936 40.000 0.00 0.00 29.23 4.37
2126 3197 5.528690 ACGTCAATTCCATATTGTCATCTGG 59.471 40.000 0.00 0.00 0.00 3.86
2133 3213 4.131649 TCGGACGTCAATTCCATATTGT 57.868 40.909 18.91 0.00 31.94 2.71
2140 3220 1.571919 CCAGATCGGACGTCAATTCC 58.428 55.000 18.91 0.00 36.56 3.01
2151 3231 0.951040 GCGGCTTAATCCCAGATCGG 60.951 60.000 0.00 0.00 0.00 4.18
2162 3242 1.816074 ATTTGTTCTCCGCGGCTTAA 58.184 45.000 23.51 11.59 0.00 1.85
2166 3246 2.716398 GAATTATTTGTTCTCCGCGGC 58.284 47.619 23.51 6.96 0.00 6.53
2171 3251 7.095695 TCCCAAATCGAATTATTTGTTCTCC 57.904 36.000 11.09 0.00 42.68 3.71
2173 3253 8.066612 ACATCCCAAATCGAATTATTTGTTCT 57.933 30.769 11.09 0.00 42.68 3.01
2212 3293 1.265905 GTTGCCCGAGTGAACGAAAAT 59.734 47.619 0.00 0.00 35.09 1.82
2225 3306 3.443045 GCACTGGATGGTTGCCCG 61.443 66.667 0.00 0.00 0.00 6.13
2234 3315 2.434884 CCTTGCGTCGCACTGGAT 60.435 61.111 25.66 0.00 38.71 3.41
2278 3362 0.890683 AAAGAATTGCGCTGGGGAAG 59.109 50.000 9.73 0.00 0.00 3.46
2298 3382 2.677337 GCTGTGCTTTTCTTTTTGGCAA 59.323 40.909 0.00 0.00 34.65 4.52
2313 3398 3.608316 TCAATATTTTTGGGGCTGTGC 57.392 42.857 0.00 0.00 0.00 4.57
2319 3404 9.282569 TCTTTTTGACATTCAATATTTTTGGGG 57.717 29.630 0.00 0.00 36.11 4.96
2344 3429 8.246184 CGAAGCGTTATTCTTTATGTTTCATC 57.754 34.615 0.00 0.00 0.00 2.92
2385 3477 7.226441 CAAACTCATGATATATGTCCAGGGAA 58.774 38.462 0.00 0.00 0.00 3.97
2386 3478 6.745190 GCAAACTCATGATATATGTCCAGGGA 60.745 42.308 0.00 0.00 0.00 4.20
2388 3480 5.413833 GGCAAACTCATGATATATGTCCAGG 59.586 44.000 0.00 0.00 0.00 4.45
2389 3481 5.999600 TGGCAAACTCATGATATATGTCCAG 59.000 40.000 0.00 0.00 0.00 3.86
2390 3482 5.939447 TGGCAAACTCATGATATATGTCCA 58.061 37.500 0.00 3.54 0.00 4.02
2442 4473 8.898761 TGTCATAATATCGTGGCAATTAAAGTT 58.101 29.630 0.00 0.00 0.00 2.66
2443 4474 8.445275 TGTCATAATATCGTGGCAATTAAAGT 57.555 30.769 0.00 0.00 0.00 2.66
2452 4483 6.358118 TCTTGTTTGTCATAATATCGTGGC 57.642 37.500 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.