Multiple sequence alignment - TraesCS6D01G287600

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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 TraesCS6D01G287600 chr6D 100.000 2830 0 0 1 2830 396917980 396915151 0.000000e+00 5227.0
1 TraesCS6D01G287600 chr6D 94.684 301 13 3 2532 2830 205298751 205298452 5.520000e-127 464.0
2 TraesCS6D01G287600 chr6D 93.115 305 16 4 2248 2548 17972237 17972540 2.590000e-120 442.0
3 TraesCS6D01G287600 chr6D 93.836 292 16 2 2257 2547 39567602 39567312 3.350000e-119 438.0
4 TraesCS6D01G287600 chr6D 93.559 295 17 2 2255 2548 141275516 141275223 3.350000e-119 438.0
5 TraesCS6D01G287600 chr6D 92.763 304 17 5 2248 2548 352834920 352834619 4.330000e-118 435.0
6 TraesCS6D01G287600 chr6D 100.000 94 0 0 361 454 396917526 396917433 1.040000e-39 174.0
7 TraesCS6D01G287600 chr6D 100.000 94 0 0 455 548 396917620 396917527 1.040000e-39 174.0
8 TraesCS6D01G287600 chr6B 89.332 1706 73 44 455 2092 593363738 593362074 0.000000e+00 2041.0
9 TraesCS6D01G287600 chr6B 93.187 455 28 3 1 454 593364099 593363647 0.000000e+00 665.0
10 TraesCS6D01G287600 chr6B 95.681 301 11 2 2532 2830 706133961 706134261 1.520000e-132 483.0
11 TraesCS6D01G287600 chr6B 98.438 128 1 1 2093 2220 593360144 593360018 1.020000e-54 224.0
12 TraesCS6D01G287600 chr6B 97.143 35 0 1 2205 2238 593360001 593359967 1.100000e-04 58.4
13 TraesCS6D01G287600 chr6A 94.613 891 30 9 455 1327 543217232 543216342 0.000000e+00 1363.0
14 TraesCS6D01G287600 chr6A 87.535 714 62 14 1361 2055 543216359 543215654 0.000000e+00 800.0
15 TraesCS6D01G287600 chr6A 95.197 458 18 3 1 454 543217594 543217137 0.000000e+00 721.0
16 TraesCS6D01G287600 chr6A 89.447 199 13 3 2055 2245 543214594 543214396 7.830000e-61 244.0
17 TraesCS6D01G287600 chr4D 96.194 289 8 2 2544 2830 385586725 385586438 1.190000e-128 470.0
18 TraesCS6D01G287600 chr4D 94.198 293 15 2 2257 2548 189733422 189733713 2.000000e-121 446.0
19 TraesCS6D01G287600 chr4D 93.878 294 15 3 2257 2548 385587096 385586804 9.310000e-120 440.0
20 TraesCS6D01G287600 chr3D 96.181 288 9 2 2544 2830 115643437 115643151 1.190000e-128 470.0
21 TraesCS6D01G287600 chr3D 94.667 300 12 4 2533 2830 451438862 451439159 1.990000e-126 462.0
22 TraesCS6D01G287600 chr3D 94.352 301 14 3 2532 2830 15282188 15281889 2.570000e-125 459.0
23 TraesCS6D01G287600 chr7B 96.167 287 9 1 2544 2830 50890787 50890503 4.270000e-128 468.0
24 TraesCS6D01G287600 chr2D 96.167 287 10 1 2544 2830 580227282 580226997 4.270000e-128 468.0
25 TraesCS6D01G287600 chr2D 93.485 307 13 7 2245 2548 399663454 399663152 1.550000e-122 449.0
26 TraesCS6D01G287600 chr7D 94.667 300 13 3 2533 2830 438545929 438546227 1.990000e-126 462.0
27 TraesCS6D01G287600 chr7D 93.443 305 14 6 2248 2548 561873396 561873698 5.560000e-122 448.0
28 TraesCS6D01G287600 chr7D 93.919 296 13 3 2257 2548 75958724 75958430 2.590000e-120 442.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G287600 chr6D 396915151 396917980 2829 True 1858.333333 5227 100.000 1 2830 3 chr6D.!!$R5 2829
1 TraesCS6D01G287600 chr6B 593359967 593364099 4132 True 747.100000 2041 94.525 1 2238 4 chr6B.!!$R1 2237
2 TraesCS6D01G287600 chr6A 543214396 543217594 3198 True 782.000000 1363 91.698 1 2245 4 chr6A.!!$R1 2244
3 TraesCS6D01G287600 chr4D 385586438 385587096 658 True 455.000000 470 95.036 2257 2830 2 chr4D.!!$R1 573

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
509 512 0.034089 ACAGGGGGCTTTGCTCATAC 60.034 55.0 0.0 0.0 0.0 2.39 F
512 515 0.106015 GGGGGCTTTGCTCATACCAT 60.106 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1770 0.025898 TCATCGTCGTCGTCGTCATC 59.974 55.0 11.41 0.00 38.33 2.92 R
1935 2004 0.180406 ATGGTGACCGGTGAATAGCC 59.820 55.0 14.63 0.36 0.00 3.93 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
92 93 5.807011 GGCTGCATTAAAACCATTACTGAAG 59.193 40.000 0.50 0.00 0.00 3.02
96 97 5.339990 CATTAAAACCATTACTGAAGCCCG 58.660 41.667 0.00 0.00 0.00 6.13
98 99 3.706600 AAACCATTACTGAAGCCCGTA 57.293 42.857 0.00 0.00 0.00 4.02
134 135 1.405256 CCAAGGCAGAGAGTACAGCAG 60.405 57.143 0.00 0.00 0.00 4.24
135 136 0.901124 AAGGCAGAGAGTACAGCAGG 59.099 55.000 0.00 0.00 0.00 4.85
140 141 1.134753 CAGAGAGTACAGCAGGCAGAG 59.865 57.143 0.00 0.00 0.00 3.35
146 147 0.687757 TACAGCAGGCAGAGGGGTAG 60.688 60.000 0.00 0.00 0.00 3.18
149 151 1.381872 GCAGGCAGAGGGGTAGAGA 60.382 63.158 0.00 0.00 0.00 3.10
161 163 5.248705 AGAGGGGTAGAGAAAAACGAAGATT 59.751 40.000 0.00 0.00 0.00 2.40
174 176 1.755179 GAAGATTAGCAGCTGCCCAA 58.245 50.000 34.39 27.29 43.38 4.12
391 394 3.530910 AAGGAACTGACGTGGCGGG 62.531 63.158 0.00 0.00 40.86 6.13
427 430 2.603021 TGCTCATACCATCTCTCCTCC 58.397 52.381 0.00 0.00 0.00 4.30
428 431 2.178764 TGCTCATACCATCTCTCCTCCT 59.821 50.000 0.00 0.00 0.00 3.69
431 434 4.335416 CTCATACCATCTCTCCTCCTCTC 58.665 52.174 0.00 0.00 0.00 3.20
432 435 3.075283 TCATACCATCTCTCCTCCTCTCC 59.925 52.174 0.00 0.00 0.00 3.71
433 436 1.619298 ACCATCTCTCCTCCTCTCCT 58.381 55.000 0.00 0.00 0.00 3.69
434 437 1.499007 ACCATCTCTCCTCCTCTCCTC 59.501 57.143 0.00 0.00 0.00 3.71
435 438 1.203050 CCATCTCTCCTCCTCTCCTCC 60.203 61.905 0.00 0.00 0.00 4.30
436 439 1.498576 CATCTCTCCTCCTCTCCTCCA 59.501 57.143 0.00 0.00 0.00 3.86
437 440 1.919933 TCTCTCCTCCTCTCCTCCAT 58.080 55.000 0.00 0.00 0.00 3.41
438 441 2.222271 TCTCTCCTCCTCTCCTCCATT 58.778 52.381 0.00 0.00 0.00 3.16
439 442 2.589664 TCTCTCCTCCTCTCCTCCATTT 59.410 50.000 0.00 0.00 0.00 2.32
440 443 2.965147 CTCTCCTCCTCTCCTCCATTTC 59.035 54.545 0.00 0.00 0.00 2.17
441 444 2.046292 CTCCTCCTCTCCTCCATTTCC 58.954 57.143 0.00 0.00 0.00 3.13
442 445 1.135960 CCTCCTCTCCTCCATTTCCC 58.864 60.000 0.00 0.00 0.00 3.97
443 446 1.344906 CCTCCTCTCCTCCATTTCCCT 60.345 57.143 0.00 0.00 0.00 4.20
444 447 2.046292 CTCCTCTCCTCCATTTCCCTC 58.954 57.143 0.00 0.00 0.00 4.30
445 448 1.653918 TCCTCTCCTCCATTTCCCTCT 59.346 52.381 0.00 0.00 0.00 3.69
446 449 2.046447 TCCTCTCCTCCATTTCCCTCTT 59.954 50.000 0.00 0.00 0.00 2.85
447 450 2.172293 CCTCTCCTCCATTTCCCTCTTG 59.828 54.545 0.00 0.00 0.00 3.02
448 451 2.843113 CTCTCCTCCATTTCCCTCTTGT 59.157 50.000 0.00 0.00 0.00 3.16
449 452 2.573462 TCTCCTCCATTTCCCTCTTGTG 59.427 50.000 0.00 0.00 0.00 3.33
450 453 2.307098 CTCCTCCATTTCCCTCTTGTGT 59.693 50.000 0.00 0.00 0.00 3.72
451 454 2.716424 TCCTCCATTTCCCTCTTGTGTT 59.284 45.455 0.00 0.00 0.00 3.32
452 455 3.140144 TCCTCCATTTCCCTCTTGTGTTT 59.860 43.478 0.00 0.00 0.00 2.83
453 456 3.507622 CCTCCATTTCCCTCTTGTGTTTC 59.492 47.826 0.00 0.00 0.00 2.78
454 457 3.146066 TCCATTTCCCTCTTGTGTTTCG 58.854 45.455 0.00 0.00 0.00 3.46
455 458 2.884639 CCATTTCCCTCTTGTGTTTCGT 59.115 45.455 0.00 0.00 0.00 3.85
456 459 4.069304 CCATTTCCCTCTTGTGTTTCGTA 58.931 43.478 0.00 0.00 0.00 3.43
457 460 4.517453 CCATTTCCCTCTTGTGTTTCGTAA 59.483 41.667 0.00 0.00 0.00 3.18
458 461 5.449304 CATTTCCCTCTTGTGTTTCGTAAC 58.551 41.667 0.00 0.00 34.75 2.50
459 462 3.823281 TCCCTCTTGTGTTTCGTAACA 57.177 42.857 3.22 3.22 41.82 2.41
460 463 3.724374 TCCCTCTTGTGTTTCGTAACAG 58.276 45.455 7.95 0.00 44.53 3.16
461 464 3.133362 TCCCTCTTGTGTTTCGTAACAGT 59.867 43.478 7.95 0.00 44.53 3.55
462 465 3.875134 CCCTCTTGTGTTTCGTAACAGTT 59.125 43.478 7.95 0.00 44.53 3.16
463 466 4.260620 CCCTCTTGTGTTTCGTAACAGTTG 60.261 45.833 7.95 1.91 44.53 3.16
464 467 4.569162 CCTCTTGTGTTTCGTAACAGTTGA 59.431 41.667 7.95 5.84 44.53 3.18
465 468 5.064198 CCTCTTGTGTTTCGTAACAGTTGAA 59.936 40.000 7.95 0.00 44.53 2.69
466 469 5.860641 TCTTGTGTTTCGTAACAGTTGAAC 58.139 37.500 7.95 0.00 44.53 3.18
467 470 5.408909 TCTTGTGTTTCGTAACAGTTGAACA 59.591 36.000 7.95 0.00 44.53 3.18
468 471 5.608676 TGTGTTTCGTAACAGTTGAACAA 57.391 34.783 7.95 0.00 44.53 2.83
469 472 5.623335 TGTGTTTCGTAACAGTTGAACAAG 58.377 37.500 7.95 0.00 44.53 3.16
470 473 5.025826 GTGTTTCGTAACAGTTGAACAAGG 58.974 41.667 7.95 0.00 44.53 3.61
471 474 4.936411 TGTTTCGTAACAGTTGAACAAGGA 59.064 37.500 3.22 0.00 39.29 3.36
472 475 5.411977 TGTTTCGTAACAGTTGAACAAGGAA 59.588 36.000 3.22 0.00 39.29 3.36
473 476 5.473796 TTCGTAACAGTTGAACAAGGAAC 57.526 39.130 0.00 0.00 0.00 3.62
474 477 6.402875 GTTTCGTAACAGTTGAACAAGGAACT 60.403 38.462 0.00 0.00 35.25 3.01
479 482 3.261981 AGTTGAACAAGGAACTGACGT 57.738 42.857 0.00 0.00 40.86 4.34
480 483 2.936498 AGTTGAACAAGGAACTGACGTG 59.064 45.455 0.00 0.00 40.86 4.49
481 484 1.948104 TGAACAAGGAACTGACGTGG 58.052 50.000 0.00 0.00 40.86 4.94
482 485 0.586802 GAACAAGGAACTGACGTGGC 59.413 55.000 0.00 0.00 40.86 5.01
483 486 1.157870 AACAAGGAACTGACGTGGCG 61.158 55.000 0.00 0.00 40.86 5.69
484 487 2.030562 AAGGAACTGACGTGGCGG 59.969 61.111 0.00 0.00 40.86 6.13
485 488 3.530910 AAGGAACTGACGTGGCGGG 62.531 63.158 0.00 0.00 40.86 6.13
501 504 4.678743 GGCGGAACAGGGGGCTTT 62.679 66.667 0.00 0.00 0.00 3.51
502 505 3.373565 GCGGAACAGGGGGCTTTG 61.374 66.667 0.00 0.00 0.00 2.77
503 506 3.373565 CGGAACAGGGGGCTTTGC 61.374 66.667 0.00 0.00 0.00 3.68
504 507 2.118294 GGAACAGGGGGCTTTGCT 59.882 61.111 0.00 0.00 0.00 3.91
505 508 1.979155 GGAACAGGGGGCTTTGCTC 60.979 63.158 0.00 0.00 0.00 4.26
506 509 1.228552 GAACAGGGGGCTTTGCTCA 60.229 57.895 0.00 0.00 0.00 4.26
507 510 0.613012 GAACAGGGGGCTTTGCTCAT 60.613 55.000 0.00 0.00 0.00 2.90
508 511 0.704076 AACAGGGGGCTTTGCTCATA 59.296 50.000 0.00 0.00 0.00 2.15
509 512 0.034089 ACAGGGGGCTTTGCTCATAC 60.034 55.000 0.00 0.00 0.00 2.39
510 513 0.753111 CAGGGGGCTTTGCTCATACC 60.753 60.000 0.00 0.00 0.00 2.73
511 514 1.214305 AGGGGGCTTTGCTCATACCA 61.214 55.000 0.00 0.00 0.00 3.25
512 515 0.106015 GGGGGCTTTGCTCATACCAT 60.106 55.000 0.00 0.00 0.00 3.55
513 516 1.322442 GGGGCTTTGCTCATACCATC 58.678 55.000 0.00 0.00 0.00 3.51
514 517 1.133668 GGGGCTTTGCTCATACCATCT 60.134 52.381 0.00 0.00 0.00 2.90
515 518 2.225467 GGGCTTTGCTCATACCATCTC 58.775 52.381 0.00 0.00 0.00 2.75
516 519 2.158696 GGGCTTTGCTCATACCATCTCT 60.159 50.000 0.00 0.00 0.00 3.10
517 520 3.137533 GGCTTTGCTCATACCATCTCTC 58.862 50.000 0.00 0.00 0.00 3.20
518 521 3.137533 GCTTTGCTCATACCATCTCTCC 58.862 50.000 0.00 0.00 0.00 3.71
519 522 3.181456 GCTTTGCTCATACCATCTCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
520 523 4.630111 CTTTGCTCATACCATCTCTCCTC 58.370 47.826 0.00 0.00 0.00 3.71
521 524 2.603021 TGCTCATACCATCTCTCCTCC 58.397 52.381 0.00 0.00 0.00 4.30
522 525 2.178764 TGCTCATACCATCTCTCCTCCT 59.821 50.000 0.00 0.00 0.00 3.69
523 526 2.825532 GCTCATACCATCTCTCCTCCTC 59.174 54.545 0.00 0.00 0.00 3.71
524 527 3.500289 GCTCATACCATCTCTCCTCCTCT 60.500 52.174 0.00 0.00 0.00 3.69
525 528 4.335416 CTCATACCATCTCTCCTCCTCTC 58.665 52.174 0.00 0.00 0.00 3.20
701 714 1.905215 ACTGCATACTCTCACCTGCTT 59.095 47.619 0.00 0.00 35.66 3.91
772 786 4.813526 CTCGACGGTCGTCAGGCG 62.814 72.222 27.53 1.14 44.77 5.52
934 963 2.166664 CGATCCTCTTTCTTCTTCCCGT 59.833 50.000 0.00 0.00 0.00 5.28
944 973 1.327690 TTCTTCCCGTGCTAGCCGAT 61.328 55.000 22.12 0.00 0.00 4.18
948 977 3.536917 CCGTGCTAGCCGATCCCA 61.537 66.667 22.12 0.00 0.00 4.37
954 983 0.667792 GCTAGCCGATCCCATTCGAC 60.668 60.000 2.29 0.00 41.62 4.20
1350 1379 4.382320 GGTGCGTACCGGAAGCCA 62.382 66.667 9.46 0.00 37.19 4.75
1413 1442 1.135859 CGCAAGAAGAATGTGAGTGCC 60.136 52.381 0.00 0.00 43.02 5.01
1449 1503 4.024641 GGACTTTGTTACGTTTCGGAATGT 60.025 41.667 6.53 6.53 38.50 2.71
1460 1522 1.225983 CGGAATGTATGGGCCCACA 59.774 57.895 31.51 23.21 0.00 4.17
1486 1548 0.395312 GTTGACTCCGTTCCCCTGAA 59.605 55.000 0.00 0.00 0.00 3.02
1602 1665 1.152963 AAGCCACGGCACAAGAAGT 60.153 52.632 11.35 0.00 44.88 3.01
1625 1688 1.922220 CGATGACGACGACGACGAC 60.922 63.158 25.15 19.21 41.06 4.34
1628 1691 1.642037 ATGACGACGACGACGACCAT 61.642 55.000 25.15 21.34 42.66 3.55
1658 1721 0.713883 CGCGCTACAAGAAACGTGAT 59.286 50.000 5.56 0.00 38.23 3.06
1673 1736 1.181001 GTGATGACGACGACGATGAC 58.819 55.000 15.32 0.00 42.66 3.06
1763 1829 4.317628 CGTTACAAGCACGATGATGATGAG 60.318 45.833 0.00 0.00 40.20 2.90
1826 1892 0.944311 GCCGCCACGATTACGATGAT 60.944 55.000 0.00 0.00 42.66 2.45
1900 1968 1.600957 CGGCTTTGCATCGATGAATCT 59.399 47.619 29.20 0.00 0.00 2.40
1904 1972 3.252701 GCTTTGCATCGATGAATCTCCAT 59.747 43.478 29.20 0.00 0.00 3.41
1908 1976 3.817084 TGCATCGATGAATCTCCATTTCC 59.183 43.478 29.20 6.72 0.00 3.13
1948 2017 2.799126 TCATTTGGCTATTCACCGGT 57.201 45.000 0.00 0.00 0.00 5.28
2136 5205 1.745489 CTGGCGGTTACTGCTTCCC 60.745 63.158 16.20 0.00 0.00 3.97
2240 5341 0.034896 ATGCGTTTGTCTCCTTCGGT 59.965 50.000 0.00 0.00 0.00 4.69
2245 5346 3.387397 CGTTTGTCTCCTTCGGTACTTT 58.613 45.455 0.00 0.00 0.00 2.66
2246 5347 3.805971 CGTTTGTCTCCTTCGGTACTTTT 59.194 43.478 0.00 0.00 0.00 2.27
2247 5348 4.271776 CGTTTGTCTCCTTCGGTACTTTTT 59.728 41.667 0.00 0.00 0.00 1.94
2277 5378 1.677052 GGAAAAACTAACGCCCACACA 59.323 47.619 0.00 0.00 0.00 3.72
2305 5406 0.536233 TTTGCACATAGCCCACACGT 60.536 50.000 0.00 0.00 44.83 4.49
2334 5435 2.487762 ACCACTCATTTTGCCACGTATG 59.512 45.455 0.00 0.00 0.00 2.39
2369 5470 6.907206 TCAGCAGAAATCTTTTTGGTTTTG 57.093 33.333 0.00 0.00 31.72 2.44
2440 5541 5.321516 CGTTTTCACCATTAAATCCGTCTC 58.678 41.667 0.00 0.00 0.00 3.36
2465 5566 4.527038 ACGAGATCTTCAAAACTAGACCCA 59.473 41.667 0.00 0.00 0.00 4.51
2466 5567 5.187967 ACGAGATCTTCAAAACTAGACCCAT 59.812 40.000 0.00 0.00 0.00 4.00
2470 5571 7.918076 AGATCTTCAAAACTAGACCCATTGTA 58.082 34.615 0.00 0.00 0.00 2.41
2477 5578 8.768397 TCAAAACTAGACCCATTGTAGATATGT 58.232 33.333 0.00 0.00 0.00 2.29
2520 5623 5.990996 CCAAAAGTTGCCATGATTTTACACT 59.009 36.000 0.00 0.00 0.00 3.55
2540 5643 4.568359 CACTGTAGTTGCCATAGTGCTTAG 59.432 45.833 0.00 0.00 33.28 2.18
2579 5764 9.512588 TTTTTGTATGAACCATGGCAATTTTAT 57.487 25.926 13.04 3.50 0.00 1.40
2580 5765 8.489990 TTTGTATGAACCATGGCAATTTTATG 57.510 30.769 13.04 0.00 0.00 1.90
2591 5776 5.280164 TGGCAATTTTATGTGCATGTATCG 58.720 37.500 0.00 0.00 42.74 2.92
2638 5823 7.475840 CATGGCAAGTCTAGTTTCTTAATTCC 58.524 38.462 0.00 0.00 0.00 3.01
2639 5824 5.944007 TGGCAAGTCTAGTTTCTTAATTCCC 59.056 40.000 0.00 0.00 0.00 3.97
2713 5898 5.571784 AACATATCATGGCAACTTCAGTG 57.428 39.130 0.00 0.00 37.61 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.357760 TGCTTGGTTCGCGGGTAC 60.358 61.111 6.13 1.97 0.00 3.34
134 135 2.712709 GTTTTTCTCTACCCCTCTGCC 58.287 52.381 0.00 0.00 0.00 4.85
135 136 2.028385 TCGTTTTTCTCTACCCCTCTGC 60.028 50.000 0.00 0.00 0.00 4.26
140 141 5.293814 GCTAATCTTCGTTTTTCTCTACCCC 59.706 44.000 0.00 0.00 0.00 4.95
146 147 5.319931 CAGCTGCTAATCTTCGTTTTTCTC 58.680 41.667 0.00 0.00 0.00 2.87
149 151 3.366374 GGCAGCTGCTAATCTTCGTTTTT 60.366 43.478 35.82 0.00 41.70 1.94
161 163 2.047274 GACGTTGGGCAGCTGCTA 60.047 61.111 35.82 23.19 41.70 3.49
174 176 3.773119 ACAATTCCTGTAGGTATGGACGT 59.227 43.478 0.00 0.00 36.10 4.34
391 394 3.373565 CAAAGCCCCCTGTTCCGC 61.374 66.667 0.00 0.00 0.00 5.54
392 395 3.373565 GCAAAGCCCCCTGTTCCG 61.374 66.667 0.00 0.00 0.00 4.30
427 430 2.843113 ACAAGAGGGAAATGGAGGAGAG 59.157 50.000 0.00 0.00 0.00 3.20
428 431 2.573462 CACAAGAGGGAAATGGAGGAGA 59.427 50.000 0.00 0.00 0.00 3.71
431 434 2.887151 ACACAAGAGGGAAATGGAGG 57.113 50.000 0.00 0.00 0.00 4.30
432 435 3.189287 CGAAACACAAGAGGGAAATGGAG 59.811 47.826 0.00 0.00 0.00 3.86
433 436 3.146066 CGAAACACAAGAGGGAAATGGA 58.854 45.455 0.00 0.00 0.00 3.41
434 437 2.884639 ACGAAACACAAGAGGGAAATGG 59.115 45.455 0.00 0.00 0.00 3.16
435 438 5.008217 TGTTACGAAACACAAGAGGGAAATG 59.992 40.000 0.00 0.00 40.69 2.32
436 439 5.127491 TGTTACGAAACACAAGAGGGAAAT 58.873 37.500 0.00 0.00 40.69 2.17
437 440 4.515361 TGTTACGAAACACAAGAGGGAAA 58.485 39.130 0.00 0.00 40.69 3.13
438 441 4.124238 CTGTTACGAAACACAAGAGGGAA 58.876 43.478 0.00 0.00 40.69 3.97
439 442 3.133362 ACTGTTACGAAACACAAGAGGGA 59.867 43.478 0.00 0.00 40.69 4.20
440 443 3.463944 ACTGTTACGAAACACAAGAGGG 58.536 45.455 0.00 0.00 40.69 4.30
441 444 4.569162 TCAACTGTTACGAAACACAAGAGG 59.431 41.667 0.00 0.00 40.69 3.69
442 445 5.712217 TCAACTGTTACGAAACACAAGAG 57.288 39.130 0.00 0.00 40.69 2.85
443 446 5.408909 TGTTCAACTGTTACGAAACACAAGA 59.591 36.000 0.00 0.00 40.69 3.02
444 447 5.623335 TGTTCAACTGTTACGAAACACAAG 58.377 37.500 0.00 0.00 40.69 3.16
445 448 5.608676 TGTTCAACTGTTACGAAACACAA 57.391 34.783 0.00 0.00 40.69 3.33
446 449 5.391097 CCTTGTTCAACTGTTACGAAACACA 60.391 40.000 0.00 0.00 40.69 3.72
447 450 5.025826 CCTTGTTCAACTGTTACGAAACAC 58.974 41.667 0.00 0.00 40.69 3.32
448 451 4.936411 TCCTTGTTCAACTGTTACGAAACA 59.064 37.500 0.00 0.00 43.32 2.83
449 452 5.473796 TCCTTGTTCAACTGTTACGAAAC 57.526 39.130 0.00 0.00 36.07 2.78
450 453 5.644636 AGTTCCTTGTTCAACTGTTACGAAA 59.355 36.000 0.00 0.00 31.42 3.46
451 454 5.064198 CAGTTCCTTGTTCAACTGTTACGAA 59.936 40.000 4.03 0.00 43.07 3.85
452 455 4.569162 CAGTTCCTTGTTCAACTGTTACGA 59.431 41.667 4.03 0.00 43.07 3.43
453 456 4.569162 TCAGTTCCTTGTTCAACTGTTACG 59.431 41.667 10.71 0.00 46.51 3.18
454 457 5.501897 CGTCAGTTCCTTGTTCAACTGTTAC 60.502 44.000 10.71 3.56 46.51 2.50
455 458 4.569162 CGTCAGTTCCTTGTTCAACTGTTA 59.431 41.667 10.71 0.00 46.51 2.41
456 459 3.374058 CGTCAGTTCCTTGTTCAACTGTT 59.626 43.478 10.71 0.00 46.51 3.16
457 460 2.936498 CGTCAGTTCCTTGTTCAACTGT 59.064 45.455 10.71 0.00 46.51 3.55
459 462 2.936498 CACGTCAGTTCCTTGTTCAACT 59.064 45.455 0.00 0.00 32.87 3.16
460 463 2.031683 CCACGTCAGTTCCTTGTTCAAC 59.968 50.000 0.00 0.00 0.00 3.18
461 464 2.285083 CCACGTCAGTTCCTTGTTCAA 58.715 47.619 0.00 0.00 0.00 2.69
462 465 1.948104 CCACGTCAGTTCCTTGTTCA 58.052 50.000 0.00 0.00 0.00 3.18
463 466 0.586802 GCCACGTCAGTTCCTTGTTC 59.413 55.000 0.00 0.00 0.00 3.18
464 467 1.157870 CGCCACGTCAGTTCCTTGTT 61.158 55.000 0.00 0.00 0.00 2.83
465 468 1.594293 CGCCACGTCAGTTCCTTGT 60.594 57.895 0.00 0.00 0.00 3.16
466 469 2.317609 CCGCCACGTCAGTTCCTTG 61.318 63.158 0.00 0.00 0.00 3.61
467 470 2.030562 CCGCCACGTCAGTTCCTT 59.969 61.111 0.00 0.00 0.00 3.36
468 471 4.003788 CCCGCCACGTCAGTTCCT 62.004 66.667 0.00 0.00 0.00 3.36
484 487 4.678743 AAAGCCCCCTGTTCCGCC 62.679 66.667 0.00 0.00 0.00 6.13
485 488 3.373565 CAAAGCCCCCTGTTCCGC 61.374 66.667 0.00 0.00 0.00 5.54
486 489 3.373565 GCAAAGCCCCCTGTTCCG 61.374 66.667 0.00 0.00 0.00 4.30
487 490 1.979155 GAGCAAAGCCCCCTGTTCC 60.979 63.158 0.00 0.00 0.00 3.62
488 491 0.613012 ATGAGCAAAGCCCCCTGTTC 60.613 55.000 0.00 0.00 0.00 3.18
489 492 0.704076 TATGAGCAAAGCCCCCTGTT 59.296 50.000 0.00 0.00 0.00 3.16
490 493 0.034089 GTATGAGCAAAGCCCCCTGT 60.034 55.000 0.00 0.00 0.00 4.00
491 494 0.753111 GGTATGAGCAAAGCCCCCTG 60.753 60.000 0.00 0.00 0.00 4.45
492 495 1.214305 TGGTATGAGCAAAGCCCCCT 61.214 55.000 0.00 0.00 0.00 4.79
493 496 0.106015 ATGGTATGAGCAAAGCCCCC 60.106 55.000 0.00 0.00 0.00 5.40
494 497 1.133668 AGATGGTATGAGCAAAGCCCC 60.134 52.381 0.00 0.00 0.00 5.80
495 498 2.158696 AGAGATGGTATGAGCAAAGCCC 60.159 50.000 0.00 0.00 0.00 5.19
496 499 3.137533 GAGAGATGGTATGAGCAAAGCC 58.862 50.000 0.00 0.00 0.00 4.35
497 500 3.137533 GGAGAGATGGTATGAGCAAAGC 58.862 50.000 0.00 0.00 0.00 3.51
498 501 4.502950 GGAGGAGAGATGGTATGAGCAAAG 60.503 50.000 0.00 0.00 0.00 2.77
499 502 3.389329 GGAGGAGAGATGGTATGAGCAAA 59.611 47.826 0.00 0.00 0.00 3.68
500 503 2.968574 GGAGGAGAGATGGTATGAGCAA 59.031 50.000 0.00 0.00 0.00 3.91
501 504 2.178764 AGGAGGAGAGATGGTATGAGCA 59.821 50.000 0.00 0.00 0.00 4.26
502 505 2.825532 GAGGAGGAGAGATGGTATGAGC 59.174 54.545 0.00 0.00 0.00 4.26
503 506 4.335416 GAGAGGAGGAGAGATGGTATGAG 58.665 52.174 0.00 0.00 0.00 2.90
504 507 3.075283 GGAGAGGAGGAGAGATGGTATGA 59.925 52.174 0.00 0.00 0.00 2.15
505 508 3.075882 AGGAGAGGAGGAGAGATGGTATG 59.924 52.174 0.00 0.00 0.00 2.39
506 509 3.333680 GAGGAGAGGAGGAGAGATGGTAT 59.666 52.174 0.00 0.00 0.00 2.73
507 510 2.714250 GAGGAGAGGAGGAGAGATGGTA 59.286 54.545 0.00 0.00 0.00 3.25
508 511 1.499007 GAGGAGAGGAGGAGAGATGGT 59.501 57.143 0.00 0.00 0.00 3.55
509 512 1.203050 GGAGGAGAGGAGGAGAGATGG 60.203 61.905 0.00 0.00 0.00 3.51
510 513 1.498576 TGGAGGAGAGGAGGAGAGATG 59.501 57.143 0.00 0.00 0.00 2.90
511 514 1.919933 TGGAGGAGAGGAGGAGAGAT 58.080 55.000 0.00 0.00 0.00 2.75
512 515 1.919933 ATGGAGGAGAGGAGGAGAGA 58.080 55.000 0.00 0.00 0.00 3.10
513 516 2.773525 AATGGAGGAGAGGAGGAGAG 57.226 55.000 0.00 0.00 0.00 3.20
514 517 2.359781 GGAAATGGAGGAGAGGAGGAGA 60.360 54.545 0.00 0.00 0.00 3.71
515 518 2.046292 GGAAATGGAGGAGAGGAGGAG 58.954 57.143 0.00 0.00 0.00 3.69
516 519 1.344496 GGGAAATGGAGGAGAGGAGGA 60.344 57.143 0.00 0.00 0.00 3.71
517 520 1.135960 GGGAAATGGAGGAGAGGAGG 58.864 60.000 0.00 0.00 0.00 4.30
518 521 2.046292 GAGGGAAATGGAGGAGAGGAG 58.954 57.143 0.00 0.00 0.00 3.69
519 522 1.653918 AGAGGGAAATGGAGGAGAGGA 59.346 52.381 0.00 0.00 0.00 3.71
520 523 2.172293 CAAGAGGGAAATGGAGGAGAGG 59.828 54.545 0.00 0.00 0.00 3.69
521 524 2.843113 ACAAGAGGGAAATGGAGGAGAG 59.157 50.000 0.00 0.00 0.00 3.20
522 525 2.573462 CACAAGAGGGAAATGGAGGAGA 59.427 50.000 0.00 0.00 0.00 3.71
523 526 2.307098 ACACAAGAGGGAAATGGAGGAG 59.693 50.000 0.00 0.00 0.00 3.69
524 527 2.348472 ACACAAGAGGGAAATGGAGGA 58.652 47.619 0.00 0.00 0.00 3.71
525 528 2.887151 ACACAAGAGGGAAATGGAGG 57.113 50.000 0.00 0.00 0.00 4.30
701 714 2.027285 TGCCTGTAAATAGCAGCACAGA 60.027 45.455 10.66 0.00 40.67 3.41
772 786 3.880846 CTCGCTCCATTTGCCGCC 61.881 66.667 0.00 0.00 0.00 6.13
859 873 2.990479 GGTCAAGCGGAGATGGGT 59.010 61.111 0.00 0.00 0.00 4.51
934 963 1.112916 TCGAATGGGATCGGCTAGCA 61.113 55.000 18.24 0.00 42.92 3.49
944 973 1.382695 GGAGAGGGGTCGAATGGGA 60.383 63.158 0.00 0.00 0.00 4.37
948 977 1.455959 CTCCGGAGAGGGGTCGAAT 60.456 63.158 28.21 0.00 41.52 3.34
1449 1503 2.665089 CGGTGTCTGTGGGCCCATA 61.665 63.158 31.45 26.12 0.00 2.74
1460 1522 0.031721 GAACGGAGTCAACGGTGTCT 59.968 55.000 0.00 0.00 45.00 3.41
1486 1548 7.758528 GCAGAAAAATACAGCAAGAGATGATTT 59.241 33.333 0.00 0.00 34.60 2.17
1602 1665 2.202260 GTCGTCGTCATCGTCGCA 60.202 61.111 0.00 0.00 44.86 5.10
1603 1666 3.295462 CGTCGTCGTCATCGTCGC 61.295 66.667 0.00 0.00 44.86 5.19
1625 1688 4.598894 CGCGGCCTCCTCTCATGG 62.599 72.222 0.00 0.00 0.00 3.66
1628 1691 4.815108 TAGCGCGGCCTCCTCTCA 62.815 66.667 8.83 0.00 0.00 3.27
1643 1706 3.057739 CGTCGTCATCACGTTTCTTGTAG 59.942 47.826 0.00 0.00 46.76 2.74
1658 1721 1.131218 GTCGTCATCGTCGTCGTCA 59.869 57.895 1.33 0.00 38.33 4.35
1673 1736 1.991430 CGGCTTTCTGTCATCGTCG 59.009 57.895 0.00 0.00 0.00 5.12
1707 1770 0.025898 TCATCGTCGTCGTCGTCATC 59.974 55.000 11.41 0.00 38.33 2.92
1763 1829 1.224075 TCCTATCATCGTCGTCGTCC 58.776 55.000 1.33 0.00 38.33 4.79
1826 1892 4.528920 TCATGTCATGATGCCTTGATCAA 58.471 39.130 11.62 8.12 35.97 2.57
1935 2004 0.180406 ATGGTGACCGGTGAATAGCC 59.820 55.000 14.63 0.36 0.00 3.93
1948 2017 2.837498 CATACGATTGGAGCATGGTGA 58.163 47.619 0.00 0.00 0.00 4.02
2042 2117 3.016736 ACCGTTTATCTGCATTTCAGGG 58.983 45.455 0.00 0.00 43.06 4.45
2044 2119 4.944962 TCACCGTTTATCTGCATTTCAG 57.055 40.909 0.00 0.00 44.21 3.02
2136 5205 0.802994 TACGCTGGGCAATTACGACG 60.803 55.000 0.00 0.00 0.00 5.12
2250 5351 3.003585 GGGCGTTAGTTTTTCCGAAGAAA 59.996 43.478 0.00 0.00 40.26 2.52
2251 5352 2.549329 GGGCGTTAGTTTTTCCGAAGAA 59.451 45.455 0.00 0.00 0.00 2.52
2252 5353 2.145536 GGGCGTTAGTTTTTCCGAAGA 58.854 47.619 0.00 0.00 0.00 2.87
2253 5354 1.874872 TGGGCGTTAGTTTTTCCGAAG 59.125 47.619 0.00 0.00 0.00 3.79
2254 5355 1.603326 GTGGGCGTTAGTTTTTCCGAA 59.397 47.619 0.00 0.00 0.00 4.30
2255 5356 1.228533 GTGGGCGTTAGTTTTTCCGA 58.771 50.000 0.00 0.00 0.00 4.55
2277 5378 3.776158 ATGTGCAAACGCCCACAT 58.224 50.000 0.00 0.78 44.81 3.21
2295 5396 1.913262 TGATGGAGACGTGTGGGCT 60.913 57.895 0.00 0.00 0.00 5.19
2305 5406 3.084039 GCAAAATGAGTGGTGATGGAGA 58.916 45.455 0.00 0.00 0.00 3.71
2334 5435 5.585445 AGATTTCTGCTGATGTCATCTGTTC 59.415 40.000 17.91 6.13 0.00 3.18
2403 5504 6.505272 TGGTGAAAACGGATTTTTAATTCGT 58.495 32.000 0.07 0.07 38.17 3.85
2440 5541 4.794246 GGTCTAGTTTTGAAGATCTCGTCG 59.206 45.833 0.00 0.00 0.00 5.12
2520 5623 4.466370 AGTCTAAGCACTATGGCAACTACA 59.534 41.667 0.00 0.00 35.83 2.74
2557 5742 7.040494 CACATAAAATTGCCATGGTTCATACA 58.960 34.615 14.67 0.00 0.00 2.29
2579 5764 1.748950 ATTGCCACGATACATGCACA 58.251 45.000 0.00 0.00 32.63 4.57
2580 5765 2.849880 AATTGCCACGATACATGCAC 57.150 45.000 0.00 0.00 32.63 4.57
2591 5776 6.734104 TGCACCATAAATTAAAATTGCCAC 57.266 33.333 0.00 0.00 0.00 5.01
2713 5898 5.005971 GCACATGAATTGCCATGATGTTTAC 59.994 40.000 12.68 0.00 44.98 2.01


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

AutoCloner maintained by Alex Coulton.