Multiple sequence alignment - TraesCS2D01G456300

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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 TraesCS2D01G456300 chr2D 100.000 4673 0 0 1 4673 564087357 564092029 0.000000e+00 8630
1 TraesCS2D01G456300 chr2B 94.365 4685 170 40 6 4635 675348023 675352668 0.000000e+00 7103
2 TraesCS2D01G456300 chr2A 95.868 4332 131 18 326 4627 704768995 704773308 0.000000e+00 6964
3 TraesCS2D01G456300 chr2A 87.919 298 20 6 6 287 704768697 704768994 2.080000e-88 337


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 TraesCS2D01G456300 chr2D 564087357 564092029 4672 False 8630.0 8630 100.0000 1 4673 1 chr2D.!!$F1 4672
1 TraesCS2D01G456300 chr2B 675348023 675352668 4645 False 7103.0 7103 94.3650 6 4635 1 chr2B.!!$F1 4629
2 TraesCS2D01G456300 chr2A 704768697 704773308 4611 False 3650.5 6964 91.8935 6 4627 2 chr2A.!!$F1 4621

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
298 315 0.178990 AAGAGGTGTCCAAGCAACCC 60.179 55.000 0.00 0.00 0.00 4.11 F
962 1004 0.462047 CCCACTTGTCATACTCCGCC 60.462 60.000 0.00 0.00 0.00 6.13 F
1460 1502 1.065199 GGAGACCTTCATGTCCATGCA 60.065 52.381 2.33 0.00 38.65 3.96 F
1466 1508 1.399440 CTTCATGTCCATGCACCGAAG 59.601 52.381 2.33 2.62 38.65 3.79 F
3510 3552 0.743097 GGATCATGAACTTGCCTGCC 59.257 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2285 0.327259 AAGAGAATGCAGCTGCCTCA 59.673 50.000 34.64 18.12 41.18 3.86 R
2277 2319 1.069090 GACAACAGCTCGGGTGTGA 59.931 57.895 0.00 0.00 43.73 3.58 R
2973 3015 1.134788 CCTGGAGATACGTTGTGGTCC 60.135 57.143 0.00 0.00 0.00 4.46 R
3528 3570 2.927871 GCAAATGCGCAGGTTCTTCATT 60.928 45.455 18.32 0.00 0.00 2.57 R
4465 4514 0.391228 TAGTTGCGTGAACTGCCTGA 59.609 50.000 11.03 0.00 45.05 3.86 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
147 150 4.754618 CACTAATTCTGCAAGTACACCACA 59.245 41.667 0.00 0.00 33.76 4.17
148 151 4.755123 ACTAATTCTGCAAGTACACCACAC 59.245 41.667 0.00 0.00 33.76 3.82
149 152 2.700722 TTCTGCAAGTACACCACACA 57.299 45.000 0.00 0.00 33.76 3.72
150 153 2.700722 TCTGCAAGTACACCACACAA 57.299 45.000 0.00 0.00 33.76 3.33
190 207 1.915489 TCAAGCACATACCCCTGACAT 59.085 47.619 0.00 0.00 0.00 3.06
199 216 1.153369 CCCCTGACATAGCACACCG 60.153 63.158 0.00 0.00 0.00 4.94
265 282 4.695928 CCTGCAGTTCATGATGATATGGAG 59.304 45.833 13.81 16.65 33.52 3.86
287 304 8.772250 TGGAGATGATAAGAAAATAAGAGGTGT 58.228 33.333 0.00 0.00 0.00 4.16
291 308 9.396022 GATGATAAGAAAATAAGAGGTGTCCAA 57.604 33.333 0.00 0.00 0.00 3.53
292 309 8.792830 TGATAAGAAAATAAGAGGTGTCCAAG 57.207 34.615 0.00 0.00 0.00 3.61
294 311 4.985538 AGAAAATAAGAGGTGTCCAAGCA 58.014 39.130 0.00 0.00 0.00 3.91
296 313 5.241728 AGAAAATAAGAGGTGTCCAAGCAAC 59.758 40.000 0.00 0.00 0.00 4.17
298 315 0.178990 AAGAGGTGTCCAAGCAACCC 60.179 55.000 0.00 0.00 0.00 4.11
299 316 1.062488 AGAGGTGTCCAAGCAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
300 317 0.890996 GAGGTGTCCAAGCAACCCTG 60.891 60.000 0.00 0.00 0.00 4.45
314 331 2.559668 CAACCCTGCAGTTCATGTGAAT 59.440 45.455 13.81 0.00 36.33 2.57
320 337 6.095440 ACCCTGCAGTTCATGTGAATAAATAC 59.905 38.462 13.81 0.00 36.33 1.89
413 439 9.120538 TGGAAATGGAACTAAATTATCAGCTAC 57.879 33.333 0.00 0.00 0.00 3.58
414 440 9.343539 GGAAATGGAACTAAATTATCAGCTACT 57.656 33.333 0.00 0.00 0.00 2.57
419 445 9.595823 TGGAACTAAATTATCAGCTACTACAAC 57.404 33.333 0.00 0.00 0.00 3.32
420 446 9.595823 GGAACTAAATTATCAGCTACTACAACA 57.404 33.333 0.00 0.00 0.00 3.33
427 460 9.672673 AATTATCAGCTACTACAACACTTGATT 57.327 29.630 0.00 0.00 0.00 2.57
431 464 6.209589 TCAGCTACTACAACACTTGATTCTCT 59.790 38.462 0.00 0.00 0.00 3.10
435 468 6.031751 ACTACAACACTTGATTCTCTCCTC 57.968 41.667 0.00 0.00 0.00 3.71
446 479 2.284405 TCTCCTCCCCCGTCAACC 60.284 66.667 0.00 0.00 0.00 3.77
455 488 1.202842 CCCCCGTCAACCCCATATTAC 60.203 57.143 0.00 0.00 0.00 1.89
456 489 1.772453 CCCCGTCAACCCCATATTACT 59.228 52.381 0.00 0.00 0.00 2.24
457 490 2.974099 CCCCGTCAACCCCATATTACTA 59.026 50.000 0.00 0.00 0.00 1.82
459 492 4.383173 CCCGTCAACCCCATATTACTAAC 58.617 47.826 0.00 0.00 0.00 2.34
460 493 4.383173 CCGTCAACCCCATATTACTAACC 58.617 47.826 0.00 0.00 0.00 2.85
462 495 5.305128 CCGTCAACCCCATATTACTAACCTA 59.695 44.000 0.00 0.00 0.00 3.08
542 582 1.017701 GGAAACGGCGGATTCGAACT 61.018 55.000 13.24 0.00 39.00 3.01
552 592 1.588861 GGATTCGAACTCTAAGCACGC 59.411 52.381 0.00 0.00 0.00 5.34
554 594 1.415374 TTCGAACTCTAAGCACGCAC 58.585 50.000 0.00 0.00 0.00 5.34
556 596 1.674611 CGAACTCTAAGCACGCACCG 61.675 60.000 0.00 0.00 0.00 4.94
750 791 4.214327 CGCTCCTCTTCCTCGCCC 62.214 72.222 0.00 0.00 0.00 6.13
770 811 3.147595 CGTGGGATCGAGCTGGGA 61.148 66.667 0.00 0.00 0.00 4.37
793 834 2.507992 CTCGCGAGCAAGGACAGG 60.508 66.667 25.07 0.00 0.00 4.00
822 863 2.258591 GCAGACGACGGAGCAGAA 59.741 61.111 0.00 0.00 0.00 3.02
836 878 1.362406 GCAGAACTACAGAAGGCGGC 61.362 60.000 0.00 0.00 0.00 6.53
889 931 5.379732 TTCACATTTGGAAAACGGTATCC 57.620 39.130 6.06 6.06 36.21 2.59
900 942 2.354305 GGTATCCGCGCCAGTACG 60.354 66.667 0.00 0.00 0.00 3.67
902 944 1.648720 GTATCCGCGCCAGTACGTA 59.351 57.895 0.00 0.00 34.88 3.57
903 945 0.658536 GTATCCGCGCCAGTACGTAC 60.659 60.000 18.10 18.10 34.88 3.67
904 946 1.785041 TATCCGCGCCAGTACGTACC 61.785 60.000 21.80 6.26 34.88 3.34
962 1004 0.462047 CCCACTTGTCATACTCCGCC 60.462 60.000 0.00 0.00 0.00 6.13
1275 1317 3.918220 CTGCGCGGCGAGATCAAC 61.918 66.667 28.54 6.77 0.00 3.18
1311 1353 5.895636 TCACCCACAACATAATGATGAAC 57.104 39.130 0.00 0.00 36.48 3.18
1460 1502 1.065199 GGAGACCTTCATGTCCATGCA 60.065 52.381 2.33 0.00 38.65 3.96
1466 1508 1.399440 CTTCATGTCCATGCACCGAAG 59.601 52.381 2.33 2.62 38.65 3.79
1684 1726 6.121776 TCAGTCAGATTAAAAGGCCAACTA 57.878 37.500 5.01 0.00 0.00 2.24
1881 1923 3.055819 ACAATAGAGGTGTGCGTCTTGAT 60.056 43.478 0.00 0.00 40.04 2.57
1932 1974 7.094248 ACTGCATGTGCTAAATTGTCTTCATTA 60.094 33.333 6.55 0.00 42.66 1.90
2166 2208 3.871485 ACTGTTCAATCAGATGAGAGCC 58.129 45.455 0.65 0.00 38.63 4.70
2243 2285 5.188434 CAACAGGATGGATATGTGTCTTGT 58.812 41.667 0.00 0.00 43.62 3.16
2277 2319 5.240403 GCATTCTCTTTCTCTGAAAAGTGGT 59.760 40.000 10.15 2.65 37.49 4.16
2328 2370 9.866655 AATTCCCTTATCTCTATGTATGCAAAA 57.133 29.630 0.00 0.00 0.00 2.44
2790 2832 3.790089 AGTCGGAAGGATTTGGTTTCT 57.210 42.857 0.00 0.00 0.00 2.52
3510 3552 0.743097 GGATCATGAACTTGCCTGCC 59.257 55.000 0.00 0.00 0.00 4.85
3795 3837 4.193826 TCTGTCCACTATTTGTCTGAGC 57.806 45.455 0.00 0.00 0.00 4.26
3964 4007 4.737855 AGCATATCTAGTTCACACGGTT 57.262 40.909 0.00 0.00 0.00 4.44
4077 4120 8.034804 CCATTTTAAGAGTTAACAATTCCAGGG 58.965 37.037 8.61 0.00 0.00 4.45
4259 4302 2.736721 TCGAAAATCGCAGGAAGTCTTG 59.263 45.455 0.00 0.00 40.21 3.02
4465 4514 4.889409 TGACAAAAGAGAGCAAAATCAGGT 59.111 37.500 0.00 0.00 0.00 4.00
4468 4517 5.009410 ACAAAAGAGAGCAAAATCAGGTCAG 59.991 40.000 0.00 0.00 36.03 3.51
4469 4518 3.347077 AGAGAGCAAAATCAGGTCAGG 57.653 47.619 0.00 0.00 36.03 3.86
4470 4519 1.742268 GAGAGCAAAATCAGGTCAGGC 59.258 52.381 0.00 0.00 36.03 4.85
4471 4520 1.074405 AGAGCAAAATCAGGTCAGGCA 59.926 47.619 0.00 0.00 36.03 4.75
4472 4521 1.471684 GAGCAAAATCAGGTCAGGCAG 59.528 52.381 0.00 0.00 33.87 4.85
4473 4522 1.202976 AGCAAAATCAGGTCAGGCAGT 60.203 47.619 0.00 0.00 0.00 4.40
4474 4523 1.615392 GCAAAATCAGGTCAGGCAGTT 59.385 47.619 0.00 0.00 0.00 3.16
4475 4524 2.352127 GCAAAATCAGGTCAGGCAGTTC 60.352 50.000 0.00 0.00 0.00 3.01
4476 4525 2.886523 CAAAATCAGGTCAGGCAGTTCA 59.113 45.455 0.00 0.00 0.00 3.18
4477 4526 2.191128 AATCAGGTCAGGCAGTTCAC 57.809 50.000 0.00 0.00 0.00 3.18
4478 4527 0.036952 ATCAGGTCAGGCAGTTCACG 60.037 55.000 0.00 0.00 0.00 4.35
4479 4528 2.031163 AGGTCAGGCAGTTCACGC 59.969 61.111 0.00 0.00 0.00 5.34
4480 4529 2.280797 GGTCAGGCAGTTCACGCA 60.281 61.111 0.00 0.00 0.00 5.24
4510 4559 9.940166 AACTTATTTTTGTTACTAACAGAACCG 57.060 29.630 4.74 0.00 43.27 4.44
4519 4568 8.075593 TGTTACTAACAGAACCGTAAACATTC 57.924 34.615 0.00 0.00 36.25 2.67
4542 4603 2.090524 GCAAATGAGCTGCGTTGGC 61.091 57.895 0.00 0.00 35.40 4.52
4593 4654 6.284459 ACTATCTTTTGGAGCAGCACTATAC 58.716 40.000 0.00 0.00 0.00 1.47
4598 4661 0.034059 GGAGCAGCACTATACGGCAT 59.966 55.000 0.00 0.00 0.00 4.40
4607 4670 6.978659 GCAGCACTATACGGCATAAATCTATA 59.021 38.462 0.00 0.00 0.00 1.31
4644 4707 4.723879 AAAAATGATTCCGCAAAAACCG 57.276 36.364 0.00 0.00 0.00 4.44
4645 4708 3.378911 AAATGATTCCGCAAAAACCGT 57.621 38.095 0.00 0.00 0.00 4.83
4646 4709 2.346099 ATGATTCCGCAAAAACCGTG 57.654 45.000 0.00 0.00 0.00 4.94
4647 4710 0.318275 TGATTCCGCAAAAACCGTGC 60.318 50.000 0.00 0.00 38.68 5.34
4648 4711 0.039527 GATTCCGCAAAAACCGTGCT 60.040 50.000 0.00 0.00 39.95 4.40
4649 4712 0.039527 ATTCCGCAAAAACCGTGCTC 60.040 50.000 0.00 0.00 39.95 4.26
4650 4713 1.377366 TTCCGCAAAAACCGTGCTCA 61.377 50.000 0.00 0.00 39.95 4.26
4651 4714 1.064946 CCGCAAAAACCGTGCTCAA 59.935 52.632 0.00 0.00 39.95 3.02
4652 4715 0.526524 CCGCAAAAACCGTGCTCAAA 60.527 50.000 0.00 0.00 39.95 2.69
4653 4716 1.486439 CGCAAAAACCGTGCTCAAAT 58.514 45.000 0.00 0.00 39.95 2.32
4654 4717 2.605823 CCGCAAAAACCGTGCTCAAATA 60.606 45.455 0.00 0.00 39.95 1.40
4655 4718 2.656422 CGCAAAAACCGTGCTCAAATAG 59.344 45.455 0.00 0.00 39.95 1.73
4656 4719 3.608241 CGCAAAAACCGTGCTCAAATAGA 60.608 43.478 0.00 0.00 39.95 1.98
4658 4721 4.556699 GCAAAAACCGTGCTCAAATAGAGT 60.557 41.667 0.00 0.00 46.47 3.24
4659 4722 4.749245 AAAACCGTGCTCAAATAGAGTG 57.251 40.909 0.00 0.00 46.47 3.51
4660 4723 1.726853 ACCGTGCTCAAATAGAGTGC 58.273 50.000 0.00 0.00 46.47 4.40
4661 4724 1.001974 ACCGTGCTCAAATAGAGTGCA 59.998 47.619 0.00 0.00 46.47 4.57
4662 4725 1.394917 CCGTGCTCAAATAGAGTGCAC 59.605 52.381 9.40 9.40 46.94 4.57
4666 4729 4.212143 TGCTCAAATAGAGTGCACATCT 57.788 40.909 21.04 19.51 46.47 2.90
4667 4730 4.582869 TGCTCAAATAGAGTGCACATCTT 58.417 39.130 21.04 3.26 46.47 2.40
4668 4731 4.393990 TGCTCAAATAGAGTGCACATCTTG 59.606 41.667 21.04 13.97 46.47 3.02
4669 4732 4.633126 GCTCAAATAGAGTGCACATCTTGA 59.367 41.667 21.04 17.07 46.47 3.02
4670 4733 5.122869 GCTCAAATAGAGTGCACATCTTGAA 59.877 40.000 21.04 4.87 46.47 2.69
4671 4734 6.675002 GCTCAAATAGAGTGCACATCTTGAAG 60.675 42.308 21.04 13.15 46.47 3.02
4672 4735 6.233434 TCAAATAGAGTGCACATCTTGAAGT 58.767 36.000 21.04 1.22 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.189594 TTGGACAGCACATCTCAAGG 57.810 50.000 0.00 0.00 0.00 3.61
1 2 3.119602 CCATTTGGACAGCACATCTCAAG 60.120 47.826 0.00 0.00 37.39 3.02
2 3 2.821378 CCATTTGGACAGCACATCTCAA 59.179 45.455 0.00 0.00 37.39 3.02
3 4 2.040145 TCCATTTGGACAGCACATCTCA 59.960 45.455 0.00 0.00 39.78 3.27
4 5 2.715046 TCCATTTGGACAGCACATCTC 58.285 47.619 0.00 0.00 39.78 2.75
147 150 1.651987 CCTACACGGCGAATCATTGT 58.348 50.000 16.62 9.07 0.00 2.71
190 207 0.830444 ACTTGTCCTCCGGTGTGCTA 60.830 55.000 0.00 0.00 0.00 3.49
199 216 0.608640 ACACATCCGACTTGTCCTCC 59.391 55.000 0.00 0.00 0.00 4.30
265 282 8.964476 TGGACACCTCTTATTTTCTTATCATC 57.036 34.615 0.00 0.00 0.00 2.92
276 293 3.421844 GGTTGCTTGGACACCTCTTATT 58.578 45.455 0.00 0.00 0.00 1.40
292 309 5.174120 ATTCACATGAACTGCAGGGTTGC 62.174 47.826 19.93 0.00 42.83 4.17
294 311 2.363306 TTCACATGAACTGCAGGGTT 57.637 45.000 19.93 4.61 31.20 4.11
296 313 5.587388 ATTTATTCACATGAACTGCAGGG 57.413 39.130 19.93 4.42 36.80 4.45
298 315 7.482743 GTGTGTATTTATTCACATGAACTGCAG 59.517 37.037 13.48 13.48 44.48 4.41
299 316 7.304735 GTGTGTATTTATTCACATGAACTGCA 58.695 34.615 0.00 0.00 44.48 4.41
300 317 7.725610 GTGTGTATTTATTCACATGAACTGC 57.274 36.000 0.00 0.00 44.48 4.40
306 323 7.881516 CACATCGTGTGTATTTATTCACATG 57.118 36.000 12.72 12.72 46.54 3.21
324 341 9.729023 TTTAGGTTTATATGATTTTGCACATCG 57.271 29.630 0.00 0.00 0.00 3.84
336 353 7.767198 CCTTCGTGGAGTTTTAGGTTTATATGA 59.233 37.037 0.00 0.00 38.35 2.15
358 383 3.569701 TCACTGGCTTGACAAATTCCTTC 59.430 43.478 0.00 0.00 0.00 3.46
413 439 5.415221 GGAGGAGAGAATCAAGTGTTGTAG 58.585 45.833 0.00 0.00 37.82 2.74
414 440 4.223032 GGGAGGAGAGAATCAAGTGTTGTA 59.777 45.833 0.00 0.00 37.82 2.41
418 444 2.192263 GGGGAGGAGAGAATCAAGTGT 58.808 52.381 0.00 0.00 37.82 3.55
419 445 1.488393 GGGGGAGGAGAGAATCAAGTG 59.512 57.143 0.00 0.00 37.82 3.16
420 446 1.886422 GGGGGAGGAGAGAATCAAGT 58.114 55.000 0.00 0.00 37.82 3.16
421 447 0.755686 CGGGGGAGGAGAGAATCAAG 59.244 60.000 0.00 0.00 37.82 3.02
423 449 0.397254 GACGGGGGAGGAGAGAATCA 60.397 60.000 0.00 0.00 37.82 2.57
427 460 1.305046 GTTGACGGGGGAGGAGAGA 60.305 63.158 0.00 0.00 0.00 3.10
435 468 1.142060 TAATATGGGGTTGACGGGGG 58.858 55.000 0.00 0.00 0.00 5.40
455 488 9.613428 TGGTGATTACTGATTTCAATAGGTTAG 57.387 33.333 0.00 0.00 0.00 2.34
456 489 9.967451 TTGGTGATTACTGATTTCAATAGGTTA 57.033 29.630 0.00 0.00 0.00 2.85
457 490 8.739972 GTTGGTGATTACTGATTTCAATAGGTT 58.260 33.333 0.00 0.00 0.00 3.50
459 492 8.279970 TGTTGGTGATTACTGATTTCAATAGG 57.720 34.615 0.00 0.00 0.00 2.57
460 493 9.166173 TCTGTTGGTGATTACTGATTTCAATAG 57.834 33.333 0.00 0.00 0.00 1.73
462 495 7.094205 GGTCTGTTGGTGATTACTGATTTCAAT 60.094 37.037 0.00 0.00 0.00 2.57
542 582 1.358725 GATTGCGGTGCGTGCTTAGA 61.359 55.000 0.00 0.00 0.00 2.10
552 592 1.665679 GTACATGTCCTGATTGCGGTG 59.334 52.381 0.00 0.00 0.00 4.94
554 594 1.935873 CTGTACATGTCCTGATTGCGG 59.064 52.381 0.00 0.00 0.00 5.69
556 596 4.194640 ACATCTGTACATGTCCTGATTGC 58.805 43.478 0.00 0.00 30.76 3.56
793 834 1.135731 CGTCTGCGTCTCTCTGACC 59.864 63.158 0.00 0.00 42.49 4.02
822 863 2.885861 CTCGCCGCCTTCTGTAGT 59.114 61.111 0.00 0.00 0.00 2.73
836 878 3.437795 CCTTGCCTTGCCTGCTCG 61.438 66.667 0.00 0.00 0.00 5.03
850 892 3.942748 TGTGAAAGCGTAAAGTGTTCCTT 59.057 39.130 0.00 0.00 33.79 3.36
889 931 1.010419 AAAAGGTACGTACTGGCGCG 61.010 55.000 24.07 0.00 34.88 6.86
900 942 1.133730 TGGGTGTGGACCAAAAGGTAC 60.134 52.381 0.00 0.00 45.25 3.34
902 944 0.106217 CTGGGTGTGGACCAAAAGGT 60.106 55.000 0.00 0.00 45.25 3.50
903 945 0.827507 CCTGGGTGTGGACCAAAAGG 60.828 60.000 0.00 0.00 45.25 3.11
904 946 1.463553 GCCTGGGTGTGGACCAAAAG 61.464 60.000 0.00 0.00 45.25 2.27
962 1004 1.587054 GAGGTGAGGTGGACGTGAG 59.413 63.158 0.00 0.00 0.00 3.51
993 1035 1.154488 CGTCGCCACCATTCAAACG 60.154 57.895 0.00 0.00 0.00 3.60
1274 1316 1.374252 GTGATGACGTTGGGCTCGT 60.374 57.895 0.00 3.18 44.27 4.18
1275 1317 2.100631 GGTGATGACGTTGGGCTCG 61.101 63.158 0.00 0.00 0.00 5.03
1374 1416 1.625818 GTGTTCCAGGAGGTGACATCT 59.374 52.381 0.00 0.00 35.58 2.90
1437 1479 1.279496 TGGACATGAAGGTCTCCAGG 58.721 55.000 0.00 0.00 37.91 4.45
1460 1502 4.698625 AGGAGTCCCCGCTTCGGT 62.699 66.667 5.25 0.00 46.80 4.69
1466 1508 3.860930 TTTGGCAAGGAGTCCCCGC 62.861 63.158 5.25 8.81 40.87 6.13
1482 1524 1.652563 GCCGAAAGTGAAGGCGTTT 59.347 52.632 0.00 0.00 41.53 3.60
1800 1842 1.134580 CCACTCTGAGACAATGCGGAT 60.135 52.381 12.44 0.00 0.00 4.18
1881 1923 7.652105 GTCAGAGAACTAGTGTATGTTGTTGAA 59.348 37.037 0.00 0.00 0.00 2.69
1932 1974 0.919710 GGAGTTGCTTACCCCATCCT 59.080 55.000 0.00 0.00 0.00 3.24
2166 2208 2.858941 CTGATCAACTGTCATCAGCTCG 59.141 50.000 13.69 0.00 44.77 5.03
2243 2285 0.327259 AAGAGAATGCAGCTGCCTCA 59.673 50.000 34.64 18.12 41.18 3.86
2277 2319 1.069090 GACAACAGCTCGGGTGTGA 59.931 57.895 0.00 0.00 43.73 3.58
2328 2370 2.029623 GCATTCTGGAGATTGCCACAT 58.970 47.619 10.99 0.00 42.41 3.21
2973 3015 1.134788 CCTGGAGATACGTTGTGGTCC 60.135 57.143 0.00 0.00 0.00 4.46
3528 3570 2.927871 GCAAATGCGCAGGTTCTTCATT 60.928 45.455 18.32 0.00 0.00 2.57
3795 3837 1.892209 ACCAACTGGCGAACCTAAAG 58.108 50.000 0.00 0.00 39.32 1.85
3964 4007 2.627699 TCTACATATCACTCGCCATGCA 59.372 45.455 0.00 0.00 0.00 3.96
4077 4120 9.742144 TCAGTGAATTACCTCCTACTATATCTC 57.258 37.037 0.00 0.00 0.00 2.75
4259 4302 1.853963 TCCTGTCTTCCTGCTCTACC 58.146 55.000 0.00 0.00 0.00 3.18
4465 4514 0.391228 TAGTTGCGTGAACTGCCTGA 59.609 50.000 11.03 0.00 45.05 3.86
4468 4517 1.226746 AGTTAGTTGCGTGAACTGCC 58.773 50.000 11.03 3.36 45.05 4.85
4469 4518 4.663636 ATAAGTTAGTTGCGTGAACTGC 57.336 40.909 11.03 5.46 45.05 4.40
4470 4519 7.431084 ACAAAAATAAGTTAGTTGCGTGAACTG 59.569 33.333 11.03 0.00 45.05 3.16
4472 4521 7.673810 ACAAAAATAAGTTAGTTGCGTGAAC 57.326 32.000 0.00 0.00 34.40 3.18
4473 4522 9.224058 GTAACAAAAATAAGTTAGTTGCGTGAA 57.776 29.630 0.00 0.00 31.45 3.18
4474 4523 8.614346 AGTAACAAAAATAAGTTAGTTGCGTGA 58.386 29.630 0.00 0.00 31.63 4.35
4475 4524 8.776680 AGTAACAAAAATAAGTTAGTTGCGTG 57.223 30.769 0.00 0.00 31.63 5.34
4519 4568 2.838386 ACGCAGCTCATTTGCTAATG 57.162 45.000 13.83 13.83 41.98 1.90
4535 4596 0.445436 CTGTCTTCATCAGCCAACGC 59.555 55.000 0.00 0.00 0.00 4.84
4542 4603 2.159071 CCAGAGAGGCTGTCTTCATCAG 60.159 54.545 12.08 0.00 43.33 2.90
4593 4654 5.977635 TCCAGTGGATATAGATTTATGCCG 58.022 41.667 8.12 0.00 0.00 5.69
4627 4690 1.668628 GCACGGTTTTTGCGGAATCAT 60.669 47.619 0.00 0.00 0.00 2.45
4631 4694 1.357334 GAGCACGGTTTTTGCGGAA 59.643 52.632 0.00 0.00 45.15 4.30
4635 4698 3.896122 TCTATTTGAGCACGGTTTTTGC 58.104 40.909 0.00 0.00 40.52 3.68
4636 4699 4.911610 CACTCTATTTGAGCACGGTTTTTG 59.088 41.667 0.00 0.00 46.41 2.44
4637 4700 4.556699 GCACTCTATTTGAGCACGGTTTTT 60.557 41.667 0.00 0.00 46.41 1.94
4638 4701 3.058224 GCACTCTATTTGAGCACGGTTTT 60.058 43.478 0.00 0.00 46.41 2.43
4639 4702 2.484264 GCACTCTATTTGAGCACGGTTT 59.516 45.455 0.00 0.00 46.41 3.27
4640 4703 2.076863 GCACTCTATTTGAGCACGGTT 58.923 47.619 0.00 0.00 46.41 4.44
4641 4704 1.001974 TGCACTCTATTTGAGCACGGT 59.998 47.619 0.00 0.00 46.41 4.83
4642 4705 1.394917 GTGCACTCTATTTGAGCACGG 59.605 52.381 10.32 0.00 46.41 4.94
4643 4706 2.795121 GTGCACTCTATTTGAGCACG 57.205 50.000 10.32 0.00 46.41 5.34
4645 4708 4.212143 AGATGTGCACTCTATTTGAGCA 57.788 40.909 19.41 0.00 46.41 4.26
4646 4709 4.633126 TCAAGATGTGCACTCTATTTGAGC 59.367 41.667 19.41 0.00 46.41 4.26
4648 4711 6.233434 ACTTCAAGATGTGCACTCTATTTGA 58.767 36.000 19.41 16.20 0.00 2.69
4649 4712 6.492007 ACTTCAAGATGTGCACTCTATTTG 57.508 37.500 19.41 14.35 0.00 2.32


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

AutoCloner maintained by Alex Coulton.