Multiple sequence alignment - TraesCS2D01G178800

Loading Multiple Alignment...

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 TraesCS2D01G178800 chr2D 100.000 2615 0 0 1 2615 122395649 122398263 0.000000e+00 4830.0
1 TraesCS2D01G178800 chr2D 77.211 588 97 21 1041 1617 26941693 26941132 2.530000e-80 309.0
2 TraesCS2D01G178800 chr2D 92.913 127 9 0 310 436 357698038 357697912 4.440000e-43 185.0
3 TraesCS2D01G178800 chr2D 79.651 172 27 7 1176 1343 400373433 400373266 1.640000e-22 117.0
4 TraesCS2D01G178800 chr2B 89.587 1018 65 17 1635 2615 175414921 175415934 0.000000e+00 1254.0
5 TraesCS2D01G178800 chr2B 92.611 812 49 4 832 1637 175413224 175414030 0.000000e+00 1157.0
6 TraesCS2D01G178800 chr2B 83.333 366 24 13 464 799 175412576 175412934 1.180000e-78 303.0
7 TraesCS2D01G178800 chr2B 79.326 445 79 13 1016 1454 737458102 737457665 1.520000e-77 300.0
8 TraesCS2D01G178800 chr2B 86.364 242 23 8 3 240 175412030 175412265 3.340000e-64 255.0
9 TraesCS2D01G178800 chr2B 77.828 221 42 6 1183 1398 565036947 565036729 2.110000e-26 130.0
10 TraesCS2D01G178800 chr2A 91.076 818 57 11 757 1563 126645159 126645971 0.000000e+00 1092.0
11 TraesCS2D01G178800 chr2A 88.662 882 54 24 1768 2615 126646633 126647502 0.000000e+00 1033.0
12 TraesCS2D01G178800 chr2A 91.519 283 18 3 464 745 126644523 126644800 4.080000e-103 385.0
13 TraesCS2D01G178800 chr2A 91.707 205 13 4 1565 1768 126646135 126646336 5.510000e-72 281.0
14 TraesCS2D01G178800 chr2A 84.553 246 30 7 1 241 126644085 126644327 1.210000e-58 237.0
15 TraesCS2D01G178800 chr2A 73.427 715 147 30 629 1323 731378605 731377914 7.280000e-56 228.0
16 TraesCS2D01G178800 chr2A 95.833 72 3 0 240 311 126644382 126644453 1.640000e-22 117.0
17 TraesCS2D01G178800 chr2A 100.000 33 0 0 434 466 126644451 126644483 7.810000e-06 62.1
18 TraesCS2D01G178800 chr1B 77.555 998 162 36 605 1581 186451330 186450374 1.770000e-151 545.0
19 TraesCS2D01G178800 chr1B 90.909 132 12 0 309 440 627700673 627700804 7.440000e-41 178.0
20 TraesCS2D01G178800 chr1A 86.019 515 65 5 1064 1576 133411320 133410811 1.770000e-151 545.0
21 TraesCS2D01G178800 chr6D 78.778 622 107 14 1021 1622 269235483 269234867 6.780000e-106 394.0
22 TraesCS2D01G178800 chr5D 86.111 288 36 4 1214 1501 547251179 547251462 9.090000e-80 307.0
23 TraesCS2D01G178800 chr5D 100.000 32 0 0 1425 1456 296999118 296999087 2.810000e-05 60.2
24 TraesCS2D01G178800 chr1D 91.304 138 12 0 302 439 158107781 158107644 3.440000e-44 189.0
25 TraesCS2D01G178800 chr3D 92.913 127 9 0 310 436 593115352 593115226 4.440000e-43 185.0
26 TraesCS2D01G178800 chr7D 91.538 130 10 1 310 439 462136389 462136261 7.440000e-41 178.0
27 TraesCS2D01G178800 chr4B 91.406 128 11 0 309 436 554115890 554116017 2.670000e-40 176.0
28 TraesCS2D01G178800 chr4B 88.356 146 14 3 292 437 626638032 626638174 3.460000e-39 172.0
29 TraesCS2D01G178800 chr6A 89.209 139 13 2 301 439 28664746 28664610 3.460000e-39 172.0
30 TraesCS2D01G178800 chr4D 88.112 143 16 1 302 444 295432377 295432518 4.480000e-38 169.0
31 TraesCS2D01G178800 chr4D 100.000 32 0 0 1425 1456 209865389 209865420 2.810000e-05 60.2
32 TraesCS2D01G178800 chr6B 75.410 305 68 6 1068 1369 19036939 19037239 9.760000e-30 141.0
33 TraesCS2D01G178800 chr5A 73.121 346 63 16 1004 1344 7827572 7827892 2.140000e-16 97.1


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 TraesCS2D01G178800 chr2D 122395649 122398263 2614 False 4830.000000 4830 100.000000 1 2615 1 chr2D.!!$F1 2614
1 TraesCS2D01G178800 chr2D 26941132 26941693 561 True 309.000000 309 77.211000 1041 1617 1 chr2D.!!$R1 576
2 TraesCS2D01G178800 chr2B 175412030 175415934 3904 False 742.250000 1254 87.973750 3 2615 4 chr2B.!!$F1 2612
3 TraesCS2D01G178800 chr2A 126644085 126647502 3417 False 458.157143 1092 91.907143 1 2615 7 chr2A.!!$F1 2614
4 TraesCS2D01G178800 chr2A 731377914 731378605 691 True 228.000000 228 73.427000 629 1323 1 chr2A.!!$R1 694
5 TraesCS2D01G178800 chr1B 186450374 186451330 956 True 545.000000 545 77.555000 605 1581 1 chr1B.!!$R1 976
6 TraesCS2D01G178800 chr1A 133410811 133411320 509 True 545.000000 545 86.019000 1064 1576 1 chr1A.!!$R1 512
7 TraesCS2D01G178800 chr6D 269234867 269235483 616 True 394.000000 394 78.778000 1021 1622 1 chr6D.!!$R1 601

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
624 881 0.177373 CACCTAGCCGACCCCTAAAC 59.823 60.0 0.0 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 4483 0.034198 TCCCGCGTTCATGTCAAGAA 59.966 50.0 4.92 0.0 0.0 2.52 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
39 40 1.548973 GAACACACAGCACGACCGAG 61.549 60.000 0.00 0.00 0.00 4.63
40 41 2.734723 CACACAGCACGACCGAGG 60.735 66.667 0.00 0.00 0.00 4.63
41 42 3.991051 ACACAGCACGACCGAGGG 61.991 66.667 0.00 0.00 0.00 4.30
42 43 3.680786 CACAGCACGACCGAGGGA 61.681 66.667 0.00 0.00 0.00 4.20
43 44 3.374402 ACAGCACGACCGAGGGAG 61.374 66.667 0.00 0.00 0.00 4.30
44 45 4.803426 CAGCACGACCGAGGGAGC 62.803 72.222 0.00 0.00 0.00 4.70
61 62 3.763897 GGGAGCACTGGTAATTGATTGTT 59.236 43.478 0.00 0.00 0.00 2.83
67 78 5.126061 GCACTGGTAATTGATTGTTGATCCT 59.874 40.000 0.00 0.00 33.60 3.24
83 94 0.984230 TCCTGTAGGACAGCAAAGGG 59.016 55.000 0.00 0.00 44.63 3.95
88 99 1.134068 GTAGGACAGCAAAGGGATCCC 60.134 57.143 24.59 24.59 0.00 3.85
92 103 1.271840 ACAGCAAAGGGATCCCGCTA 61.272 55.000 25.83 0.00 41.95 4.26
100 111 1.442148 GGATCCCGCTACTGTGGTC 59.558 63.158 0.00 0.00 42.08 4.02
118 129 4.630069 GTGGTCGCTGATGTTAGTAATGTT 59.370 41.667 0.00 0.00 0.00 2.71
137 148 7.436320 AATGTTATAAAATCTGGCCATTGGT 57.564 32.000 5.51 0.00 0.00 3.67
141 152 5.852282 ATAAAATCTGGCCATTGGTGTAC 57.148 39.130 5.51 0.00 0.00 2.90
143 154 0.618458 ATCTGGCCATTGGTGTACGT 59.382 50.000 5.51 0.00 0.00 3.57
181 194 4.341235 TGTATGCCTACTATTTGAGCGAGT 59.659 41.667 0.74 0.00 0.00 4.18
197 210 5.580691 TGAGCGAGTGAAATAATGTAACTGG 59.419 40.000 0.00 0.00 0.00 4.00
277 347 6.122277 TCTCATTCTCTTGTGTTTTCCTGTT 58.878 36.000 0.00 0.00 0.00 3.16
291 361 6.127842 TGTTTTCCTGTTCCTTCAAACACTAC 60.128 38.462 0.00 0.00 35.39 2.73
320 390 4.569719 AAAAATCATGTACTCCCTCCGT 57.430 40.909 0.00 0.00 0.00 4.69
321 391 3.821421 AAATCATGTACTCCCTCCGTC 57.179 47.619 0.00 0.00 0.00 4.79
322 392 2.757894 ATCATGTACTCCCTCCGTCT 57.242 50.000 0.00 0.00 0.00 4.18
323 393 2.054232 TCATGTACTCCCTCCGTCTC 57.946 55.000 0.00 0.00 0.00 3.36
324 394 1.283905 TCATGTACTCCCTCCGTCTCA 59.716 52.381 0.00 0.00 0.00 3.27
325 395 2.100197 CATGTACTCCCTCCGTCTCAA 58.900 52.381 0.00 0.00 0.00 3.02
326 396 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
327 397 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
328 398 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
329 399 3.581332 TGTACTCCCTCCGTCTCAAAATT 59.419 43.478 0.00 0.00 0.00 1.82
330 400 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
331 401 2.637872 ACTCCCTCCGTCTCAAAATTCA 59.362 45.455 0.00 0.00 0.00 2.57
332 402 3.264450 ACTCCCTCCGTCTCAAAATTCAT 59.736 43.478 0.00 0.00 0.00 2.57
333 403 3.609853 TCCCTCCGTCTCAAAATTCATG 58.390 45.455 0.00 0.00 0.00 3.07
334 404 3.009033 TCCCTCCGTCTCAAAATTCATGT 59.991 43.478 0.00 0.00 0.00 3.21
335 405 3.375299 CCCTCCGTCTCAAAATTCATGTC 59.625 47.826 0.00 0.00 0.00 3.06
336 406 4.256920 CCTCCGTCTCAAAATTCATGTCT 58.743 43.478 0.00 0.00 0.00 3.41
337 407 4.697352 CCTCCGTCTCAAAATTCATGTCTT 59.303 41.667 0.00 0.00 0.00 3.01
338 408 5.874810 CCTCCGTCTCAAAATTCATGTCTTA 59.125 40.000 0.00 0.00 0.00 2.10
339 409 6.036517 CCTCCGTCTCAAAATTCATGTCTTAG 59.963 42.308 0.00 0.00 0.00 2.18
340 410 6.697395 TCCGTCTCAAAATTCATGTCTTAGA 58.303 36.000 0.00 0.00 0.00 2.10
341 411 6.590292 TCCGTCTCAAAATTCATGTCTTAGAC 59.410 38.462 5.27 5.27 0.00 2.59
342 412 6.591834 CCGTCTCAAAATTCATGTCTTAGACT 59.408 38.462 13.86 0.00 33.15 3.24
343 413 7.118390 CCGTCTCAAAATTCATGTCTTAGACTT 59.882 37.037 13.86 4.38 33.15 3.01
344 414 7.954248 CGTCTCAAAATTCATGTCTTAGACTTG 59.046 37.037 18.50 18.50 38.51 3.16
345 415 8.778358 GTCTCAAAATTCATGTCTTAGACTTGT 58.222 33.333 22.02 6.80 38.37 3.16
346 416 8.993121 TCTCAAAATTCATGTCTTAGACTTGTC 58.007 33.333 22.02 0.00 38.37 3.18
347 417 8.908786 TCAAAATTCATGTCTTAGACTTGTCT 57.091 30.769 22.02 8.41 38.37 3.41
348 418 9.996554 TCAAAATTCATGTCTTAGACTTGTCTA 57.003 29.630 22.02 6.41 38.37 2.59
354 424 9.569167 TTCATGTCTTAGACTTGTCTAAATACG 57.431 33.333 22.02 11.06 38.37 3.06
355 425 8.188799 TCATGTCTTAGACTTGTCTAAATACGG 58.811 37.037 22.02 15.98 38.37 4.02
356 426 7.692460 TGTCTTAGACTTGTCTAAATACGGA 57.308 36.000 19.65 12.43 32.51 4.69
357 427 8.289939 TGTCTTAGACTTGTCTAAATACGGAT 57.710 34.615 19.65 0.00 32.51 4.18
358 428 8.188799 TGTCTTAGACTTGTCTAAATACGGATG 58.811 37.037 19.65 9.16 32.51 3.51
359 429 8.189460 GTCTTAGACTTGTCTAAATACGGATGT 58.811 37.037 19.65 0.00 32.51 3.06
360 430 9.399797 TCTTAGACTTGTCTAAATACGGATGTA 57.600 33.333 19.65 0.00 32.51 2.29
363 433 8.466617 AGACTTGTCTAAATACGGATGTATCT 57.533 34.615 0.89 0.00 40.42 1.98
364 434 9.570468 AGACTTGTCTAAATACGGATGTATCTA 57.430 33.333 0.89 0.00 40.42 1.98
366 436 9.962783 ACTTGTCTAAATACGGATGTATCTAAC 57.037 33.333 0.00 0.00 40.42 2.34
367 437 9.961265 CTTGTCTAAATACGGATGTATCTAACA 57.039 33.333 0.00 0.00 40.42 2.41
427 497 9.463443 AAATTTAAGACAAGAATTTTGAGACGG 57.537 29.630 0.00 0.00 31.00 4.79
428 498 7.795482 TTTAAGACAAGAATTTTGAGACGGA 57.205 32.000 7.18 0.00 0.00 4.69
429 499 7.795482 TTAAGACAAGAATTTTGAGACGGAA 57.205 32.000 7.18 0.00 0.00 4.30
430 500 5.931441 AGACAAGAATTTTGAGACGGAAG 57.069 39.130 7.18 0.00 0.00 3.46
431 501 4.757149 AGACAAGAATTTTGAGACGGAAGG 59.243 41.667 7.18 0.00 0.00 3.46
432 502 4.714632 ACAAGAATTTTGAGACGGAAGGA 58.285 39.130 7.18 0.00 0.00 3.36
472 700 3.581332 ACGTAGGATTCAAGAGAAACCCA 59.419 43.478 0.00 0.00 45.16 4.51
522 750 6.292542 CGTACTGCTTGAATAAGATGTCATGG 60.293 42.308 0.00 0.00 35.92 3.66
523 751 5.748402 ACTGCTTGAATAAGATGTCATGGA 58.252 37.500 0.00 0.00 35.92 3.41
558 787 1.134788 AGCAACTCTAACCGATTCCCG 60.135 52.381 0.00 0.00 38.18 5.14
561 790 3.187700 CAACTCTAACCGATTCCCGAAG 58.812 50.000 0.00 0.00 41.76 3.79
570 799 3.007182 ACCGATTCCCGAAGACACTTTAA 59.993 43.478 0.00 0.00 41.76 1.52
572 801 4.092968 CCGATTCCCGAAGACACTTTAAAG 59.907 45.833 13.76 13.76 41.76 1.85
624 881 0.177373 CACCTAGCCGACCCCTAAAC 59.823 60.000 0.00 0.00 0.00 2.01
684 941 4.868734 CCGACTCTTATATTTAATCGGCCC 59.131 45.833 0.00 0.00 40.93 5.80
822 1431 3.145551 CCTAGTAGCACCCGCCGT 61.146 66.667 0.00 0.00 39.83 5.68
838 1700 3.637273 GTGCTCGTCCCCCACCTT 61.637 66.667 0.00 0.00 0.00 3.50
848 1710 2.171870 GTCCCCCACCTTAATTCGATCA 59.828 50.000 0.00 0.00 0.00 2.92
864 1726 3.116300 CGATCAATTTCTCGTCACCGAT 58.884 45.455 0.00 0.00 43.27 4.18
932 1800 2.494918 GCACCTAGTCGCCATCGT 59.505 61.111 0.00 0.00 36.96 3.73
947 1815 3.191371 GCCATCGTGTTTTGGAGAGATTT 59.809 43.478 0.00 0.00 34.81 2.17
979 1847 3.461773 CGGGCATCCACCTCGAGT 61.462 66.667 12.31 0.00 0.00 4.18
1179 2054 1.729881 GAGCATGCCGAAACATCCC 59.270 57.895 15.66 0.00 0.00 3.85
1232 2108 3.262420 GAGTGAGTGCCATTTCATACGT 58.738 45.455 0.00 0.00 0.00 3.57
1261 2137 6.445475 TCTTCAAATTCATCGCAATGTGAAA 58.555 32.000 0.00 0.00 38.82 2.69
1483 2380 8.934023 AGGGAAAAGAAACAATGTAGTCAATA 57.066 30.769 0.00 0.00 0.00 1.90
1542 2441 5.992217 AGCAGTTAAGGAAGTAGTGTTTCTG 59.008 40.000 0.00 0.00 0.00 3.02
1664 3618 7.700234 TCGATGGACCAAAAATAAATGAATTCG 59.300 33.333 0.00 0.00 0.00 3.34
1760 3716 1.475682 CTATAGGATACCGGGCCGTTC 59.524 57.143 26.32 17.63 37.17 3.95
1795 4052 2.623889 AGAGATTAGACGGGATCGGTTG 59.376 50.000 0.00 0.00 41.39 3.77
1933 4190 3.525609 TCCAAGCCACCACAAGGAATATA 59.474 43.478 0.00 0.00 38.69 0.86
1972 4232 3.006940 ACAGAACACGCTTTCAACTTCA 58.993 40.909 0.00 0.00 0.00 3.02
1981 4241 3.748048 CGCTTTCAACTTCAGAATCCTGA 59.252 43.478 0.00 0.00 46.95 3.86
2022 4282 4.615912 GCCAAACATAACGATGTGAGCTTT 60.616 41.667 0.00 0.00 45.93 3.51
2048 4308 2.727123 TCAACTGCCAGGTTTCTTCA 57.273 45.000 0.00 0.00 0.00 3.02
2049 4309 3.011566 TCAACTGCCAGGTTTCTTCAA 57.988 42.857 0.00 0.00 0.00 2.69
2061 4321 5.929992 CAGGTTTCTTCAATGAAATGCACAT 59.070 36.000 0.00 0.00 38.09 3.21
2069 4329 9.708092 TCTTCAATGAAATGCACATAAAAATCA 57.292 25.926 0.00 0.00 0.00 2.57
2113 4373 3.731652 TTTCTTTGCATGTGAACCCAG 57.268 42.857 0.00 0.00 0.00 4.45
2121 4381 2.569059 CATGTGAACCCAGCTCTATGG 58.431 52.381 0.00 0.00 40.29 2.74
2129 4389 5.191722 TGAACCCAGCTCTATGGATTAAAGT 59.808 40.000 0.00 0.00 43.57 2.66
2134 4394 4.514441 CAGCTCTATGGATTAAAGTGCAGG 59.486 45.833 0.00 0.00 33.36 4.85
2137 4397 5.698545 GCTCTATGGATTAAAGTGCAGGTAG 59.301 44.000 0.00 0.00 31.73 3.18
2180 4441 5.003804 ACGCAATAGGAAACATTCAGAACT 58.996 37.500 0.00 0.00 0.00 3.01
2184 4445 6.096001 GCAATAGGAAACATTCAGAACTGGAT 59.904 38.462 1.93 0.00 0.00 3.41
2198 4459 3.014304 ACTGGATGCTGCAGAATTCAT 57.986 42.857 16.62 10.12 38.14 2.57
2215 4477 7.012138 CAGAATTCATATGGTCCTGAGTTTCTG 59.988 40.741 8.44 13.85 37.25 3.02
2219 4481 3.983044 ATGGTCCTGAGTTTCTGGTAC 57.017 47.619 2.53 0.00 36.89 3.34
2220 4482 1.975680 TGGTCCTGAGTTTCTGGTACC 59.024 52.381 4.43 4.43 36.89 3.34
2221 4483 2.258109 GGTCCTGAGTTTCTGGTACCT 58.742 52.381 14.36 0.00 36.89 3.08
2223 4485 3.306849 GGTCCTGAGTTTCTGGTACCTTC 60.307 52.174 14.36 2.29 36.89 3.46
2224 4486 3.579151 GTCCTGAGTTTCTGGTACCTTCT 59.421 47.826 14.36 4.20 36.89 2.85
2225 4487 4.040584 GTCCTGAGTTTCTGGTACCTTCTT 59.959 45.833 14.36 0.00 36.89 2.52
2226 4488 4.040461 TCCTGAGTTTCTGGTACCTTCTTG 59.960 45.833 14.36 0.00 36.89 3.02
2227 4489 4.040461 CCTGAGTTTCTGGTACCTTCTTGA 59.960 45.833 14.36 1.04 31.65 3.02
2228 4490 4.957296 TGAGTTTCTGGTACCTTCTTGAC 58.043 43.478 14.36 4.71 0.00 3.18
2229 4491 4.407621 TGAGTTTCTGGTACCTTCTTGACA 59.592 41.667 14.36 3.81 0.00 3.58
2252 4541 4.951254 TGAACGCGGGAAGAATAATCATA 58.049 39.130 12.47 0.00 0.00 2.15
2258 4547 6.812160 ACGCGGGAAGAATAATCATATCTAAC 59.188 38.462 12.47 0.00 0.00 2.34
2369 4658 0.109723 AACCTTTTCAGCGGCTACCA 59.890 50.000 0.26 0.00 0.00 3.25
2470 4759 2.561478 TTCGGAAGGAAAAGGAGGTG 57.439 50.000 0.00 0.00 0.00 4.00
2474 4763 2.614734 CGGAAGGAAAAGGAGGTGGTAC 60.615 54.545 0.00 0.00 0.00 3.34
2552 4841 2.985139 CCAGTCATCATCGTCATCATCG 59.015 50.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.318017 GTCGTGCTGTGTGTTCTTCTAT 58.682 45.455 0.00 0.00 0.00 1.98
15 16 2.545113 GGTCGTGCTGTGTGTTCTTCTA 60.545 50.000 0.00 0.00 0.00 2.10
16 17 1.571919 GTCGTGCTGTGTGTTCTTCT 58.428 50.000 0.00 0.00 0.00 2.85
39 40 3.356290 ACAATCAATTACCAGTGCTCCC 58.644 45.455 0.00 0.00 0.00 4.30
40 41 4.458989 TCAACAATCAATTACCAGTGCTCC 59.541 41.667 0.00 0.00 0.00 4.70
41 42 5.627499 TCAACAATCAATTACCAGTGCTC 57.373 39.130 0.00 0.00 0.00 4.26
42 43 5.126061 GGATCAACAATCAATTACCAGTGCT 59.874 40.000 0.00 0.00 35.96 4.40
43 44 5.126061 AGGATCAACAATCAATTACCAGTGC 59.874 40.000 0.00 0.00 35.96 4.40
44 45 6.151648 ACAGGATCAACAATCAATTACCAGTG 59.848 38.462 0.00 0.00 35.96 3.66
45 46 6.248433 ACAGGATCAACAATCAATTACCAGT 58.752 36.000 0.00 0.00 35.96 4.00
46 47 6.764308 ACAGGATCAACAATCAATTACCAG 57.236 37.500 0.00 0.00 35.96 4.00
61 62 2.237143 CCTTTGCTGTCCTACAGGATCA 59.763 50.000 8.99 1.43 45.89 2.92
67 78 1.559682 GGATCCCTTTGCTGTCCTACA 59.440 52.381 0.00 0.00 0.00 2.74
79 90 1.338136 CCACAGTAGCGGGATCCCTT 61.338 60.000 28.42 18.27 0.00 3.95
83 94 1.065928 CGACCACAGTAGCGGGATC 59.934 63.158 0.00 0.00 0.00 3.36
92 103 1.618837 ACTAACATCAGCGACCACAGT 59.381 47.619 0.00 0.00 0.00 3.55
118 129 5.529430 CGTACACCAATGGCCAGATTTTATA 59.471 40.000 13.05 0.00 0.00 0.98
277 347 4.764050 TGGTGAAGTAGTGTTTGAAGGA 57.236 40.909 0.00 0.00 0.00 3.36
308 378 3.889520 ATTTTGAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
309 379 3.835978 TGAATTTTGAGACGGAGGGAGTA 59.164 43.478 0.00 0.00 0.00 2.59
310 380 2.637872 TGAATTTTGAGACGGAGGGAGT 59.362 45.455 0.00 0.00 0.00 3.85
311 381 3.334583 TGAATTTTGAGACGGAGGGAG 57.665 47.619 0.00 0.00 0.00 4.30
312 382 3.009033 ACATGAATTTTGAGACGGAGGGA 59.991 43.478 0.00 0.00 0.00 4.20
313 383 3.347216 ACATGAATTTTGAGACGGAGGG 58.653 45.455 0.00 0.00 0.00 4.30
314 384 4.256920 AGACATGAATTTTGAGACGGAGG 58.743 43.478 0.00 0.00 0.00 4.30
315 385 5.869753 AAGACATGAATTTTGAGACGGAG 57.130 39.130 0.00 0.00 0.00 4.63
316 386 6.590292 GTCTAAGACATGAATTTTGAGACGGA 59.410 38.462 0.00 0.00 32.09 4.69
317 387 6.591834 AGTCTAAGACATGAATTTTGAGACGG 59.408 38.462 0.00 0.00 36.70 4.79
318 388 7.588143 AGTCTAAGACATGAATTTTGAGACG 57.412 36.000 0.00 0.00 36.70 4.18
319 389 8.778358 ACAAGTCTAAGACATGAATTTTGAGAC 58.222 33.333 0.00 4.17 35.25 3.36
320 390 8.908786 ACAAGTCTAAGACATGAATTTTGAGA 57.091 30.769 0.00 0.00 35.25 3.27
321 391 8.997323 AGACAAGTCTAAGACATGAATTTTGAG 58.003 33.333 0.00 0.00 38.35 3.02
322 392 8.908786 AGACAAGTCTAAGACATGAATTTTGA 57.091 30.769 0.00 0.00 38.35 2.69
337 407 9.570468 AGATACATCCGTATTTAGACAAGTCTA 57.430 33.333 5.86 5.86 38.48 2.59
338 408 8.466617 AGATACATCCGTATTTAGACAAGTCT 57.533 34.615 7.96 7.96 38.48 3.24
340 410 9.962783 GTTAGATACATCCGTATTTAGACAAGT 57.037 33.333 0.00 0.00 38.48 3.16
341 411 9.961265 TGTTAGATACATCCGTATTTAGACAAG 57.039 33.333 0.00 0.00 38.48 3.16
401 471 9.463443 CCGTCTCAAAATTCTTGTCTTAAATTT 57.537 29.630 0.00 0.00 34.86 1.82
402 472 8.846211 TCCGTCTCAAAATTCTTGTCTTAAATT 58.154 29.630 0.00 0.00 0.00 1.82
403 473 8.391075 TCCGTCTCAAAATTCTTGTCTTAAAT 57.609 30.769 0.00 0.00 0.00 1.40
404 474 7.795482 TCCGTCTCAAAATTCTTGTCTTAAA 57.205 32.000 0.00 0.00 0.00 1.52
405 475 7.041372 CCTTCCGTCTCAAAATTCTTGTCTTAA 60.041 37.037 0.00 0.00 0.00 1.85
406 476 6.426937 CCTTCCGTCTCAAAATTCTTGTCTTA 59.573 38.462 0.00 0.00 0.00 2.10
407 477 5.239525 CCTTCCGTCTCAAAATTCTTGTCTT 59.760 40.000 0.00 0.00 0.00 3.01
408 478 4.757149 CCTTCCGTCTCAAAATTCTTGTCT 59.243 41.667 0.00 0.00 0.00 3.41
409 479 4.755123 TCCTTCCGTCTCAAAATTCTTGTC 59.245 41.667 0.00 0.00 0.00 3.18
410 480 4.714632 TCCTTCCGTCTCAAAATTCTTGT 58.285 39.130 0.00 0.00 0.00 3.16
411 481 4.757149 ACTCCTTCCGTCTCAAAATTCTTG 59.243 41.667 0.00 0.00 0.00 3.02
412 482 4.974399 ACTCCTTCCGTCTCAAAATTCTT 58.026 39.130 0.00 0.00 0.00 2.52
413 483 4.625607 ACTCCTTCCGTCTCAAAATTCT 57.374 40.909 0.00 0.00 0.00 2.40
414 484 5.480205 ACTACTCCTTCCGTCTCAAAATTC 58.520 41.667 0.00 0.00 0.00 2.17
415 485 5.485209 ACTACTCCTTCCGTCTCAAAATT 57.515 39.130 0.00 0.00 0.00 1.82
416 486 5.485209 AACTACTCCTTCCGTCTCAAAAT 57.515 39.130 0.00 0.00 0.00 1.82
417 487 4.950205 AACTACTCCTTCCGTCTCAAAA 57.050 40.909 0.00 0.00 0.00 2.44
418 488 4.950205 AAACTACTCCTTCCGTCTCAAA 57.050 40.909 0.00 0.00 0.00 2.69
419 489 7.707624 TTATAAACTACTCCTTCCGTCTCAA 57.292 36.000 0.00 0.00 0.00 3.02
420 490 7.341256 ACATTATAAACTACTCCTTCCGTCTCA 59.659 37.037 0.00 0.00 0.00 3.27
421 491 7.714703 ACATTATAAACTACTCCTTCCGTCTC 58.285 38.462 0.00 0.00 0.00 3.36
422 492 7.657023 ACATTATAAACTACTCCTTCCGTCT 57.343 36.000 0.00 0.00 0.00 4.18
423 493 7.763071 ACAACATTATAAACTACTCCTTCCGTC 59.237 37.037 0.00 0.00 0.00 4.79
424 494 7.618137 ACAACATTATAAACTACTCCTTCCGT 58.382 34.615 0.00 0.00 0.00 4.69
425 495 9.028185 GTACAACATTATAAACTACTCCTTCCG 57.972 37.037 0.00 0.00 0.00 4.30
426 496 9.028185 CGTACAACATTATAAACTACTCCTTCC 57.972 37.037 0.00 0.00 0.00 3.46
427 497 9.578439 ACGTACAACATTATAAACTACTCCTTC 57.422 33.333 0.00 0.00 0.00 3.46
430 500 9.455847 CCTACGTACAACATTATAAACTACTCC 57.544 37.037 0.00 0.00 0.00 3.85
472 700 3.525199 ACCCTAGTGCCTCTTTGATTCAT 59.475 43.478 0.00 0.00 0.00 2.57
522 750 3.815401 AGTTGCTCTAACACAACCACATC 59.185 43.478 2.47 0.00 45.79 3.06
523 751 3.815401 GAGTTGCTCTAACACAACCACAT 59.185 43.478 2.47 0.00 45.79 3.21
572 801 9.334947 AGTGAAGTAAAAGTTAAAGGTTACTCC 57.665 33.333 6.47 0.00 36.11 3.85
584 840 6.602009 AGGTGCAGTTTAGTGAAGTAAAAGTT 59.398 34.615 0.00 0.00 0.00 2.66
594 850 1.067142 CGGCTAGGTGCAGTTTAGTGA 60.067 52.381 0.00 0.00 45.15 3.41
684 941 0.250989 TTTTTACTCAGCGGGTGGGG 60.251 55.000 12.28 5.86 0.00 4.96
793 1398 1.673808 CTACTAGGGGTCACCGGTGC 61.674 65.000 30.25 23.00 46.96 5.01
800 1405 1.380785 CGGGTGCTACTAGGGGTCA 60.381 63.158 0.00 0.00 0.00 4.02
822 1431 0.912487 ATTAAGGTGGGGGACGAGCA 60.912 55.000 0.00 0.00 39.21 4.26
838 1700 6.583912 GGTGACGAGAAATTGATCGAATTA 57.416 37.500 16.80 1.13 41.40 1.40
864 1726 4.142752 CGTAGATCCGCCGATTTATAGTCA 60.143 45.833 0.00 0.00 0.00 3.41
903 1765 0.738975 CTAGGTGCGTCGAATCTGGA 59.261 55.000 0.00 0.00 0.00 3.86
932 1800 4.141274 TCCCTGTCAAATCTCTCCAAAACA 60.141 41.667 0.00 0.00 0.00 2.83
947 1815 2.355986 CCCGGTTCGATCCCTGTCA 61.356 63.158 6.94 0.00 0.00 3.58
992 1863 2.223745 GAGAGGAGGACATACCGAGAC 58.776 57.143 0.00 0.00 44.74 3.36
1179 2054 3.308530 GCACTTGAAGAAAACCCATTCG 58.691 45.455 0.00 0.00 34.46 3.34
1232 2108 5.687770 TTGCGATGAATTTGAAGAACAGA 57.312 34.783 0.00 0.00 0.00 3.41
1483 2380 5.296283 CGATCAATGCTTTCTCCATCTCTTT 59.704 40.000 0.00 0.00 0.00 2.52
1577 2638 6.538742 CCAATTCTTCGCTAAGAGAACCAATA 59.461 38.462 0.55 0.00 42.60 1.90
1664 3618 7.919690 ACTTACCGGAGTAAAAACTTAAACAC 58.080 34.615 9.46 0.00 37.99 3.32
1720 3675 2.494073 AGAGGACTACTTTCGCTCCTTG 59.506 50.000 0.00 0.00 33.00 3.61
1784 4041 2.106683 GCAACTCCAACCGATCCCG 61.107 63.158 0.00 0.00 0.00 5.14
1795 4052 2.545731 GCAGTAGCTAAGAGCAACTCC 58.454 52.381 0.00 0.00 45.56 3.85
1941 4198 6.092944 TGAAAGCGTGTTCTGTTCTTTCTTTA 59.907 34.615 12.36 0.00 41.67 1.85
1942 4199 4.965119 AAGCGTGTTCTGTTCTTTCTTT 57.035 36.364 0.00 0.00 0.00 2.52
1944 4201 3.938963 TGAAAGCGTGTTCTGTTCTTTCT 59.061 39.130 12.36 0.00 41.67 2.52
1954 4214 3.944422 TCTGAAGTTGAAAGCGTGTTC 57.056 42.857 0.00 0.00 0.00 3.18
1972 4232 1.115467 CCGCTGTAGGTCAGGATTCT 58.885 55.000 0.00 0.00 43.78 2.40
1981 4241 1.219124 CATGTGCTCCGCTGTAGGT 59.781 57.895 0.00 0.00 0.00 3.08
1986 4246 2.628696 TTTGGCATGTGCTCCGCTG 61.629 57.895 4.84 0.00 41.70 5.18
2022 4282 5.324409 AGAAACCTGGCAGTTGATGATTTA 58.676 37.500 14.43 0.00 0.00 1.40
2049 4309 8.938906 GGACTTTGATTTTTATGTGCATTTCAT 58.061 29.630 0.00 0.00 0.00 2.57
2095 4355 0.961019 GCTGGGTTCACATGCAAAGA 59.039 50.000 0.00 0.00 0.00 2.52
2101 4361 2.171237 TCCATAGAGCTGGGTTCACATG 59.829 50.000 0.00 0.00 36.89 3.21
2113 4373 4.455606 ACCTGCACTTTAATCCATAGAGC 58.544 43.478 0.00 0.00 0.00 4.09
2121 4381 5.818136 TGCATTCTACCTGCACTTTAATC 57.182 39.130 0.00 0.00 44.30 1.75
2157 4418 5.003804 AGTTCTGAATGTTTCCTATTGCGT 58.996 37.500 0.00 0.00 0.00 5.24
2166 4427 4.730657 CAGCATCCAGTTCTGAATGTTTC 58.269 43.478 1.00 0.00 0.00 2.78
2180 4441 3.824443 CCATATGAATTCTGCAGCATCCA 59.176 43.478 9.47 0.00 0.00 3.41
2184 4445 3.117776 AGGACCATATGAATTCTGCAGCA 60.118 43.478 9.47 0.00 0.00 4.41
2185 4446 3.252701 CAGGACCATATGAATTCTGCAGC 59.747 47.826 9.47 0.00 0.00 5.25
2198 4459 3.773119 GGTACCAGAAACTCAGGACCATA 59.227 47.826 7.15 0.00 29.93 2.74
2215 4477 2.415512 GCGTTCATGTCAAGAAGGTACC 59.584 50.000 2.73 2.73 34.37 3.34
2219 4481 0.443869 CCGCGTTCATGTCAAGAAGG 59.556 55.000 4.92 6.21 34.84 3.46
2220 4482 0.443869 CCCGCGTTCATGTCAAGAAG 59.556 55.000 4.92 0.00 0.00 2.85
2221 4483 0.034198 TCCCGCGTTCATGTCAAGAA 59.966 50.000 4.92 0.00 0.00 2.52
2223 4485 0.443869 CTTCCCGCGTTCATGTCAAG 59.556 55.000 4.92 0.00 0.00 3.02
2224 4486 0.034198 TCTTCCCGCGTTCATGTCAA 59.966 50.000 4.92 0.00 0.00 3.18
2225 4487 0.034198 TTCTTCCCGCGTTCATGTCA 59.966 50.000 4.92 0.00 0.00 3.58
2226 4488 1.369625 ATTCTTCCCGCGTTCATGTC 58.630 50.000 4.92 0.00 0.00 3.06
2227 4489 2.684001 TATTCTTCCCGCGTTCATGT 57.316 45.000 4.92 0.00 0.00 3.21
2228 4490 3.559655 TGATTATTCTTCCCGCGTTCATG 59.440 43.478 4.92 0.00 0.00 3.07
2229 4491 3.804036 TGATTATTCTTCCCGCGTTCAT 58.196 40.909 4.92 0.00 0.00 2.57
2252 4541 7.723172 AGGTAGTGCGTAATTAGGTAGTTAGAT 59.277 37.037 8.57 0.00 0.00 1.98
2258 4547 5.068198 TGGAAGGTAGTGCGTAATTAGGTAG 59.932 44.000 7.00 0.00 0.00 3.18
2369 4658 8.158132 AGATGAAGACTGCTATGATTGATGATT 58.842 33.333 0.00 0.00 0.00 2.57
2445 4734 2.039746 TCCTTTTCCTTCCGAATCAGCA 59.960 45.455 0.00 0.00 0.00 4.41
2446 4735 2.680339 CTCCTTTTCCTTCCGAATCAGC 59.320 50.000 0.00 0.00 0.00 4.26
2454 4743 2.374170 TGTACCACCTCCTTTTCCTTCC 59.626 50.000 0.00 0.00 0.00 3.46
2470 4759 8.208718 TGTTCAATTCATATTACTGCTGTACC 57.791 34.615 2.52 0.00 0.00 3.34
2552 4841 3.357166 ACTCCGCAGAATATCGAGTTC 57.643 47.619 5.45 5.45 0.00 3.01


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

AutoCloner maintained by Alex Coulton.