Multiple sequence alignment - TraesCS3A01G529600

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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 TraesCS3A01G529600 chr3A 100.000 2399 0 0 1 2399 742932438 742930040 0.000000e+00 4431.0
1 TraesCS3A01G529600 chr3A 88.288 222 26 0 2013 2234 742962794 742962573 1.410000e-67 267.0
2 TraesCS3A01G529600 chr3D 92.681 1626 73 23 783 2399 609366504 609364916 0.000000e+00 2302.0
3 TraesCS3A01G529600 chr3D 78.182 440 58 14 1155 1580 609352451 609352036 1.840000e-61 246.0
4 TraesCS3A01G529600 chr3B 90.602 1660 77 20 783 2399 820116999 820115376 0.000000e+00 2128.0
5 TraesCS3A01G529600 chr3B 86.578 1274 128 18 1138 2399 820176635 820177877 0.000000e+00 1365.0
6 TraesCS3A01G529600 chr3B 81.903 746 86 19 1021 1736 820216380 820217106 3.440000e-163 584.0
7 TraesCS3A01G529600 chr3B 84.247 584 79 9 802 1379 820109965 820109389 7.490000e-155 556.0
8 TraesCS3A01G529600 chr3B 88.717 452 47 2 1951 2399 819990408 819990858 1.250000e-152 549.0
9 TraesCS3A01G529600 chr3B 93.768 353 22 0 2046 2398 820184424 820184776 4.540000e-147 531.0
10 TraesCS3A01G529600 chr3B 87.111 450 54 2 1951 2397 820124469 820124021 7.650000e-140 507.0
11 TraesCS3A01G529600 chr3B 88.235 102 7 3 1703 1803 820090881 820090784 1.510000e-22 117.0
12 TraesCS3A01G529600 chr1B 96.529 461 16 0 1 461 160661255 160661715 0.000000e+00 763.0
13 TraesCS3A01G529600 chr1B 94.309 246 10 3 539 784 160661712 160661953 8.100000e-100 374.0
14 TraesCS3A01G529600 chr2A 80.952 105 18 2 2296 2399 763332877 763332980 5.500000e-12 82.4
15 TraesCS3A01G529600 chr2D 88.525 61 7 0 2339 2399 568410297 568410237 9.200000e-10 75.0
16 TraesCS3A01G529600 chr2D 88.525 61 7 0 2339 2399 568727432 568727372 9.200000e-10 75.0


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 TraesCS3A01G529600 chr3A 742930040 742932438 2398 True 4431.0 4431 100.000 1 2399 1 chr3A.!!$R1 2398
1 TraesCS3A01G529600 chr3D 609364916 609366504 1588 True 2302.0 2302 92.681 783 2399 1 chr3D.!!$R2 1616
2 TraesCS3A01G529600 chr3B 820115376 820116999 1623 True 2128.0 2128 90.602 783 2399 1 chr3B.!!$R3 1616
3 TraesCS3A01G529600 chr3B 820176635 820177877 1242 False 1365.0 1365 86.578 1138 2399 1 chr3B.!!$F2 1261
4 TraesCS3A01G529600 chr3B 820216380 820217106 726 False 584.0 584 81.903 1021 1736 1 chr3B.!!$F4 715
5 TraesCS3A01G529600 chr3B 820109389 820109965 576 True 556.0 556 84.247 802 1379 1 chr3B.!!$R2 577
6 TraesCS3A01G529600 chr1B 160661255 160661953 698 False 568.5 763 95.419 1 784 2 chr1B.!!$F1 783

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
355 356 0.037697 AGTGCCGAGTTCGTATGCAA 60.038 50.0 5.71 0.0 36.24 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1481 0.105964 TCCACAGGTTCACCAACTCG 59.894 55.0 0.0 0.0 38.89 4.18 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
120 121 2.203549 CTCTTCCCCAAGCTCCACCC 62.204 65.000 0.00 0.00 0.00 4.61
123 124 2.935481 CCCCAAGCTCCACCCTGA 60.935 66.667 0.00 0.00 0.00 3.86
242 243 0.379669 GCCTGCATATGTGTGTGCTC 59.620 55.000 4.29 0.00 42.33 4.26
243 244 1.741528 CCTGCATATGTGTGTGCTCA 58.258 50.000 4.29 0.00 42.33 4.26
271 272 4.107051 GCTGGCCGTGTGTGATGC 62.107 66.667 0.00 0.00 0.00 3.91
305 306 2.423185 TGTATATGCTGTTTGGTGCTGC 59.577 45.455 0.00 0.00 0.00 5.25
317 318 2.422597 TGGTGCTGCTGTACACATTAC 58.577 47.619 13.41 0.00 38.57 1.89
336 337 6.821160 ACATTACGTGACATGTATGGATTTGA 59.179 34.615 8.32 0.00 31.60 2.69
355 356 0.037697 AGTGCCGAGTTCGTATGCAA 60.038 50.000 5.71 0.00 36.24 4.08
383 384 5.181811 TGTTCACTGGATGCTATGTTTCTTG 59.818 40.000 0.00 0.00 0.00 3.02
408 409 6.509317 AATTTTGTTTGCAATACACGTGAG 57.491 33.333 25.01 9.97 34.18 3.51
461 462 4.389374 CTGTACAGAACTGGGACAACAAT 58.611 43.478 18.45 0.00 38.70 2.71
463 464 5.302360 TGTACAGAACTGGGACAACAATAC 58.698 41.667 6.76 0.00 38.70 1.89
464 465 4.431416 ACAGAACTGGGACAACAATACA 57.569 40.909 6.76 0.00 38.70 2.29
465 466 4.985538 ACAGAACTGGGACAACAATACAT 58.014 39.130 6.76 0.00 38.70 2.29
466 467 6.121776 ACAGAACTGGGACAACAATACATA 57.878 37.500 6.76 0.00 38.70 2.29
467 468 6.721318 ACAGAACTGGGACAACAATACATAT 58.279 36.000 6.76 0.00 38.70 1.78
468 469 7.175104 ACAGAACTGGGACAACAATACATATT 58.825 34.615 6.76 0.00 38.70 1.28
469 470 7.669722 ACAGAACTGGGACAACAATACATATTT 59.330 33.333 6.76 0.00 38.70 1.40
470 471 7.970061 CAGAACTGGGACAACAATACATATTTG 59.030 37.037 0.00 0.00 38.70 2.32
471 472 7.669722 AGAACTGGGACAACAATACATATTTGT 59.330 33.333 0.00 0.00 38.70 2.83
472 473 7.391148 ACTGGGACAACAATACATATTTGTC 57.609 36.000 7.03 7.03 38.70 3.18
473 474 7.175104 ACTGGGACAACAATACATATTTGTCT 58.825 34.615 12.92 0.00 38.70 3.41
474 475 7.669722 ACTGGGACAACAATACATATTTGTCTT 59.330 33.333 12.92 0.00 38.70 3.01
475 476 8.415950 TGGGACAACAATACATATTTGTCTTT 57.584 30.769 12.92 0.00 35.40 2.52
476 477 8.303156 TGGGACAACAATACATATTTGTCTTTG 58.697 33.333 12.92 9.08 35.40 2.77
477 478 8.303876 GGGACAACAATACATATTTGTCTTTGT 58.696 33.333 12.92 9.99 40.90 2.83
478 479 9.691362 GGACAACAATACATATTTGTCTTTGTT 57.309 29.630 17.09 17.09 44.62 2.83
485 486 9.787532 AATACATATTTGTCTTTGTTTCATCCG 57.212 29.630 0.00 0.00 37.28 4.18
486 487 7.447374 ACATATTTGTCTTTGTTTCATCCGA 57.553 32.000 0.00 0.00 0.00 4.55
487 488 7.881142 ACATATTTGTCTTTGTTTCATCCGAA 58.119 30.769 0.00 0.00 0.00 4.30
488 489 8.522830 ACATATTTGTCTTTGTTTCATCCGAAT 58.477 29.630 0.00 0.00 0.00 3.34
489 490 8.800972 CATATTTGTCTTTGTTTCATCCGAATG 58.199 33.333 0.00 0.00 0.00 2.67
490 491 5.766150 TTGTCTTTGTTTCATCCGAATGT 57.234 34.783 0.00 0.00 34.32 2.71
491 492 6.869315 TTGTCTTTGTTTCATCCGAATGTA 57.131 33.333 0.00 0.00 34.32 2.29
492 493 6.236017 TGTCTTTGTTTCATCCGAATGTAC 57.764 37.500 0.00 0.00 34.32 2.90
493 494 5.760743 TGTCTTTGTTTCATCCGAATGTACA 59.239 36.000 0.00 0.00 34.32 2.90
494 495 6.261158 TGTCTTTGTTTCATCCGAATGTACAA 59.739 34.615 0.00 2.18 37.06 2.41
495 496 7.136119 GTCTTTGTTTCATCCGAATGTACAAA 58.864 34.615 13.62 13.62 41.08 2.83
496 497 7.112984 GTCTTTGTTTCATCCGAATGTACAAAC 59.887 37.037 11.46 3.11 39.98 2.93
497 498 6.378710 TTGTTTCATCCGAATGTACAAACA 57.621 33.333 0.00 0.00 36.29 2.83
498 499 5.996219 TGTTTCATCCGAATGTACAAACAG 58.004 37.500 0.00 0.00 39.49 3.16
499 500 5.529430 TGTTTCATCCGAATGTACAAACAGT 59.471 36.000 0.00 0.00 39.49 3.55
500 501 6.706716 TGTTTCATCCGAATGTACAAACAGTA 59.293 34.615 0.00 0.00 39.49 2.74
512 513 2.812011 ACAAACAGTACTGAATTCCGGC 59.188 45.455 29.30 0.00 0.00 6.13
513 514 3.074412 CAAACAGTACTGAATTCCGGCT 58.926 45.455 29.30 0.03 0.00 5.52
514 515 3.418684 AACAGTACTGAATTCCGGCTT 57.581 42.857 29.30 6.81 0.00 4.35
515 516 2.699954 ACAGTACTGAATTCCGGCTTG 58.300 47.619 29.30 0.00 0.00 4.01
516 517 2.038557 ACAGTACTGAATTCCGGCTTGT 59.961 45.455 29.30 0.00 0.00 3.16
517 518 2.673368 CAGTACTGAATTCCGGCTTGTC 59.327 50.000 18.45 0.00 0.00 3.18
518 519 2.301870 AGTACTGAATTCCGGCTTGTCA 59.698 45.455 2.27 0.00 0.00 3.58
519 520 2.496899 ACTGAATTCCGGCTTGTCAT 57.503 45.000 2.27 0.00 0.00 3.06
520 521 2.795329 ACTGAATTCCGGCTTGTCATT 58.205 42.857 2.27 0.00 0.00 2.57
521 522 2.489329 ACTGAATTCCGGCTTGTCATTG 59.511 45.455 2.27 0.00 0.00 2.82
522 523 2.489329 CTGAATTCCGGCTTGTCATTGT 59.511 45.455 2.27 0.00 0.00 2.71
523 524 3.680490 TGAATTCCGGCTTGTCATTGTA 58.320 40.909 2.27 0.00 0.00 2.41
524 525 3.689161 TGAATTCCGGCTTGTCATTGTAG 59.311 43.478 2.27 0.00 0.00 2.74
525 526 2.851263 TTCCGGCTTGTCATTGTAGT 57.149 45.000 0.00 0.00 0.00 2.73
526 527 2.851263 TCCGGCTTGTCATTGTAGTT 57.149 45.000 0.00 0.00 0.00 2.24
527 528 2.695359 TCCGGCTTGTCATTGTAGTTC 58.305 47.619 0.00 0.00 0.00 3.01
528 529 2.301870 TCCGGCTTGTCATTGTAGTTCT 59.698 45.455 0.00 0.00 0.00 3.01
529 530 3.074412 CCGGCTTGTCATTGTAGTTCTT 58.926 45.455 0.00 0.00 0.00 2.52
530 531 3.502211 CCGGCTTGTCATTGTAGTTCTTT 59.498 43.478 0.00 0.00 0.00 2.52
531 532 4.023193 CCGGCTTGTCATTGTAGTTCTTTT 60.023 41.667 0.00 0.00 0.00 2.27
532 533 5.507315 CCGGCTTGTCATTGTAGTTCTTTTT 60.507 40.000 0.00 0.00 0.00 1.94
586 587 9.594478 TGCTTAACTCGATGATTTAACTTATGA 57.406 29.630 0.00 0.00 0.00 2.15
660 661 7.999450 TCCGGTTAAACATTTGTAAACCTAT 57.001 32.000 18.36 0.00 39.83 2.57
661 662 7.818642 TCCGGTTAAACATTTGTAAACCTATG 58.181 34.615 18.36 11.10 39.83 2.23
761 762 7.703058 AACCAATCTACAAAACAATAGAGGG 57.297 36.000 0.00 0.00 34.39 4.30
770 771 0.107654 ACAATAGAGGGCGTTCAGGC 60.108 55.000 0.00 0.00 45.91 4.85
788 789 4.473196 TCAGGCCATTTTGGTATGTCTCTA 59.527 41.667 5.01 0.00 40.46 2.43
915 917 0.855349 GAATATCTGGAGCACGCACG 59.145 55.000 0.00 0.00 0.00 5.34
1041 1046 3.459227 TGATGATAGGTTCATTGGCAGGA 59.541 43.478 0.00 0.00 45.29 3.86
1052 1081 1.368641 TTGGCAGGAATCGTTCATCG 58.631 50.000 0.00 0.00 41.41 3.84
1053 1082 0.249120 TGGCAGGAATCGTTCATCGT 59.751 50.000 0.00 0.00 40.80 3.73
1054 1083 0.652592 GGCAGGAATCGTTCATCGTG 59.347 55.000 0.00 0.00 40.80 4.35
1055 1084 1.359848 GCAGGAATCGTTCATCGTGT 58.640 50.000 0.00 0.00 40.80 4.49
1056 1085 1.324736 GCAGGAATCGTTCATCGTGTC 59.675 52.381 0.00 0.00 40.80 3.67
1057 1086 2.881074 CAGGAATCGTTCATCGTGTCT 58.119 47.619 1.25 0.00 40.80 3.41
1058 1087 3.254060 CAGGAATCGTTCATCGTGTCTT 58.746 45.455 1.25 0.00 40.80 3.01
1059 1088 3.679980 CAGGAATCGTTCATCGTGTCTTT 59.320 43.478 1.25 0.00 40.80 2.52
1060 1089 4.862574 CAGGAATCGTTCATCGTGTCTTTA 59.137 41.667 1.25 0.00 40.80 1.85
1061 1090 5.520288 CAGGAATCGTTCATCGTGTCTTTAT 59.480 40.000 1.25 0.00 40.80 1.40
1062 1091 5.749109 AGGAATCGTTCATCGTGTCTTTATC 59.251 40.000 1.25 0.00 40.80 1.75
1175 1204 3.096852 TCACACTCGTGGATATTCCTGT 58.903 45.455 1.77 0.00 43.79 4.00
1450 1496 0.393077 ACCTCGAGTTGGTGAACCTG 59.607 55.000 12.31 0.00 36.30 4.00
1461 1509 0.250338 GTGAACCTGTGGACCACTCC 60.250 60.000 24.81 10.01 35.11 3.85
1573 1649 6.801539 TTAAGATCAATTAATAGCCTGGCG 57.198 37.500 13.96 0.00 0.00 5.69
1597 1673 3.641434 ATCTGTGCCAAGCATTCTAGT 57.359 42.857 0.00 0.00 41.91 2.57
1622 1722 3.513515 TGAAAGCTGGTTGGACAAAACTT 59.486 39.130 0.00 0.00 0.00 2.66
1662 1762 0.397941 CTCTTGGCTGACTGTTGGGA 59.602 55.000 0.00 0.00 0.00 4.37
1840 1945 7.504403 TGATGTTTCCTTTTTCTGGCAATAAA 58.496 30.769 0.00 0.00 0.00 1.40
1941 2046 7.009179 TCCATATGGGTCATATTCTTGAGAC 57.991 40.000 21.78 0.00 35.18 3.36
1970 2075 9.113838 CGGAGGTAGTAGTGACTTAAGTTATTA 57.886 37.037 10.02 4.01 37.10 0.98
1981 2086 8.995220 GTGACTTAAGTTATTATCCACACAACA 58.005 33.333 10.02 0.00 0.00 3.33
1998 2103 5.046231 ACACAACAAAAATGTAAACAGGGGT 60.046 36.000 0.00 0.00 0.00 4.95
2074 2179 2.029918 GCCGAGTTGCTTTCCAAGATTT 60.030 45.455 0.00 0.00 33.21 2.17
2077 2182 3.908382 CGAGTTGCTTTCCAAGATTTTCG 59.092 43.478 0.00 0.00 33.21 3.46
2096 2201 2.367241 TCGACATCCAACAGAAACTGGA 59.633 45.455 0.00 0.00 45.65 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 1.746220 GTGACAGGTCGCTGAGTATCT 59.254 52.381 5.76 0.00 37.16 1.98
236 237 0.381445 GCACACACACATTGAGCACA 59.619 50.000 0.00 0.00 0.00 4.57
242 243 1.007038 GGCCAGCACACACACATTG 60.007 57.895 0.00 0.00 0.00 2.82
243 244 2.554636 CGGCCAGCACACACACATT 61.555 57.895 2.24 0.00 0.00 2.71
271 272 3.875727 AGCATATACACAAGCTTCAGCAG 59.124 43.478 0.00 0.00 45.16 4.24
286 287 2.684374 CAGCAGCACCAAACAGCATATA 59.316 45.455 0.00 0.00 0.00 0.86
317 318 4.494690 GCACTCAAATCCATACATGTCACG 60.495 45.833 0.00 0.00 0.00 4.35
336 337 0.037697 TTGCATACGAACTCGGCACT 60.038 50.000 3.88 0.00 44.95 4.40
355 356 5.045012 ACATAGCATCCAGTGAACATGAT 57.955 39.130 0.00 0.00 0.00 2.45
383 384 7.383050 TCACGTGTATTGCAAACAAAATTAC 57.617 32.000 16.51 0.00 39.77 1.89
408 409 0.879765 AATGAGCACAAGCAGACAGC 59.120 50.000 0.00 0.00 45.49 4.40
461 462 8.554835 TCGGATGAAACAAAGACAAATATGTA 57.445 30.769 0.00 0.00 40.74 2.29
463 464 8.800972 CATTCGGATGAAACAAAGACAAATATG 58.199 33.333 0.00 0.00 37.71 1.78
464 465 8.522830 ACATTCGGATGAAACAAAGACAAATAT 58.477 29.630 11.64 0.00 37.71 1.28
465 466 7.881142 ACATTCGGATGAAACAAAGACAAATA 58.119 30.769 11.64 0.00 37.71 1.40
466 467 6.748132 ACATTCGGATGAAACAAAGACAAAT 58.252 32.000 11.64 0.00 37.71 2.32
467 468 6.142818 ACATTCGGATGAAACAAAGACAAA 57.857 33.333 11.64 0.00 37.71 2.83
468 469 5.766150 ACATTCGGATGAAACAAAGACAA 57.234 34.783 11.64 0.00 37.71 3.18
469 470 5.760743 TGTACATTCGGATGAAACAAAGACA 59.239 36.000 11.64 0.00 37.71 3.41
470 471 6.236017 TGTACATTCGGATGAAACAAAGAC 57.764 37.500 11.64 0.00 37.71 3.01
471 472 6.869315 TTGTACATTCGGATGAAACAAAGA 57.131 33.333 19.98 5.32 38.48 2.52
472 473 6.915300 TGTTTGTACATTCGGATGAAACAAAG 59.085 34.615 27.39 0.00 43.97 2.77
473 474 6.796426 TGTTTGTACATTCGGATGAAACAAA 58.204 32.000 25.06 25.06 42.80 2.83
474 475 6.038825 ACTGTTTGTACATTCGGATGAAACAA 59.961 34.615 17.90 18.44 37.20 2.83
475 476 5.529430 ACTGTTTGTACATTCGGATGAAACA 59.471 36.000 11.64 15.04 36.21 2.83
476 477 5.997385 ACTGTTTGTACATTCGGATGAAAC 58.003 37.500 11.64 11.20 37.71 2.78
490 491 3.998341 GCCGGAATTCAGTACTGTTTGTA 59.002 43.478 21.99 0.00 0.00 2.41
491 492 2.812011 GCCGGAATTCAGTACTGTTTGT 59.188 45.455 21.99 6.77 0.00 2.83
492 493 3.074412 AGCCGGAATTCAGTACTGTTTG 58.926 45.455 21.99 7.41 0.00 2.93
493 494 3.418684 AGCCGGAATTCAGTACTGTTT 57.581 42.857 21.99 16.29 0.00 2.83
494 495 3.074412 CAAGCCGGAATTCAGTACTGTT 58.926 45.455 21.99 10.46 0.00 3.16
495 496 2.038557 ACAAGCCGGAATTCAGTACTGT 59.961 45.455 21.99 3.28 0.00 3.55
496 497 2.673368 GACAAGCCGGAATTCAGTACTG 59.327 50.000 17.17 17.17 0.00 2.74
497 498 2.301870 TGACAAGCCGGAATTCAGTACT 59.698 45.455 5.05 0.26 0.00 2.73
498 499 2.695359 TGACAAGCCGGAATTCAGTAC 58.305 47.619 5.05 0.00 0.00 2.73
499 500 3.627395 ATGACAAGCCGGAATTCAGTA 57.373 42.857 5.05 0.00 0.00 2.74
500 501 2.489329 CAATGACAAGCCGGAATTCAGT 59.511 45.455 5.05 0.00 0.00 3.41
501 502 2.489329 ACAATGACAAGCCGGAATTCAG 59.511 45.455 5.05 2.79 0.00 3.02
502 503 2.513753 ACAATGACAAGCCGGAATTCA 58.486 42.857 5.05 1.06 0.00 2.57
503 504 3.689649 ACTACAATGACAAGCCGGAATTC 59.310 43.478 5.05 0.00 0.00 2.17
504 505 3.686016 ACTACAATGACAAGCCGGAATT 58.314 40.909 5.05 0.00 0.00 2.17
505 506 3.350219 ACTACAATGACAAGCCGGAAT 57.650 42.857 5.05 0.00 0.00 3.01
506 507 2.851263 ACTACAATGACAAGCCGGAA 57.149 45.000 5.05 0.00 0.00 4.30
507 508 2.301870 AGAACTACAATGACAAGCCGGA 59.698 45.455 5.05 0.00 0.00 5.14
508 509 2.699954 AGAACTACAATGACAAGCCGG 58.300 47.619 0.00 0.00 0.00 6.13
509 510 4.749245 AAAGAACTACAATGACAAGCCG 57.251 40.909 0.00 0.00 0.00 5.52
537 538 9.851686 AGCATCTATCACTTTATGGATTTTGTA 57.148 29.630 0.00 0.00 0.00 2.41
538 539 8.757982 AGCATCTATCACTTTATGGATTTTGT 57.242 30.769 0.00 0.00 0.00 2.83
543 544 9.717942 GAGTTAAGCATCTATCACTTTATGGAT 57.282 33.333 0.00 0.00 0.00 3.41
544 545 7.867909 CGAGTTAAGCATCTATCACTTTATGGA 59.132 37.037 0.00 0.00 0.00 3.41
545 546 7.867909 TCGAGTTAAGCATCTATCACTTTATGG 59.132 37.037 0.00 0.00 0.00 2.74
546 547 8.803201 TCGAGTTAAGCATCTATCACTTTATG 57.197 34.615 0.00 0.00 0.00 1.90
547 548 9.416794 CATCGAGTTAAGCATCTATCACTTTAT 57.583 33.333 0.00 0.00 0.00 1.40
654 655 7.280205 GTCGTAGATGACCAATTTTCATAGGTT 59.720 37.037 0.18 0.00 40.67 3.50
655 656 6.761714 GTCGTAGATGACCAATTTTCATAGGT 59.238 38.462 0.18 0.00 40.67 3.08
656 657 6.761242 TGTCGTAGATGACCAATTTTCATAGG 59.239 38.462 0.00 0.00 40.67 2.57
657 658 7.770801 TGTCGTAGATGACCAATTTTCATAG 57.229 36.000 0.00 0.00 40.67 2.23
660 661 6.708502 TCTTTGTCGTAGATGACCAATTTTCA 59.291 34.615 0.00 0.00 40.67 2.69
661 662 7.129109 TCTTTGTCGTAGATGACCAATTTTC 57.871 36.000 0.00 0.00 40.67 2.29
761 762 0.885196 TACCAAAATGGCCTGAACGC 59.115 50.000 3.32 0.00 42.67 4.84
770 771 7.554118 ACACTTCATAGAGACATACCAAAATGG 59.446 37.037 0.00 0.00 45.02 3.16
776 777 7.239763 TGAAACACTTCATAGAGACATACCA 57.760 36.000 0.00 0.00 36.62 3.25
915 917 4.846779 TTTGGATGTGAACACTTTAGCC 57.153 40.909 6.51 0.00 0.00 3.93
1009 1012 4.528206 TGAACCTATCATCACACAGTGTCT 59.472 41.667 2.14 0.00 31.91 3.41
1041 1046 6.535150 ACATGATAAAGACACGATGAACGATT 59.465 34.615 0.00 0.00 45.77 3.34
1052 1081 6.808212 CCAAATTGACCACATGATAAAGACAC 59.192 38.462 0.00 0.00 0.00 3.67
1053 1082 6.572119 GCCAAATTGACCACATGATAAAGACA 60.572 38.462 0.00 0.00 0.00 3.41
1054 1083 5.807011 GCCAAATTGACCACATGATAAAGAC 59.193 40.000 0.00 0.00 0.00 3.01
1055 1084 5.479724 TGCCAAATTGACCACATGATAAAGA 59.520 36.000 0.00 0.00 0.00 2.52
1056 1085 5.577945 GTGCCAAATTGACCACATGATAAAG 59.422 40.000 0.00 0.00 0.00 1.85
1057 1086 5.477510 GTGCCAAATTGACCACATGATAAA 58.522 37.500 0.00 0.00 0.00 1.40
1058 1087 4.081752 GGTGCCAAATTGACCACATGATAA 60.082 41.667 14.97 0.00 0.00 1.75
1059 1088 3.446873 GGTGCCAAATTGACCACATGATA 59.553 43.478 14.97 0.00 0.00 2.15
1060 1089 2.234414 GGTGCCAAATTGACCACATGAT 59.766 45.455 14.97 0.00 0.00 2.45
1061 1090 1.617850 GGTGCCAAATTGACCACATGA 59.382 47.619 14.97 0.00 0.00 3.07
1062 1091 1.338011 GGGTGCCAAATTGACCACATG 60.338 52.381 14.97 0.00 0.00 3.21
1175 1204 2.630098 GGCATCACTAGAGCATGAGGTA 59.370 50.000 0.00 0.00 0.00 3.08
1435 1481 0.105964 TCCACAGGTTCACCAACTCG 59.894 55.000 0.00 0.00 38.89 4.18
1573 1649 2.621998 AGAATGCTTGGCACAGATATGC 59.378 45.455 0.00 0.00 43.04 3.14
1597 1673 3.569194 TTGTCCAACCAGCTTTCAGTA 57.431 42.857 0.00 0.00 0.00 2.74
1622 1722 1.189752 CTGCTGGTCAGGAAGCTAGA 58.810 55.000 0.00 0.00 40.21 2.43
1642 1742 0.109342 CCCAACAGTCAGCCAAGAGT 59.891 55.000 0.00 0.00 0.00 3.24
1645 1745 1.691196 TTTCCCAACAGTCAGCCAAG 58.309 50.000 0.00 0.00 0.00 3.61
1823 1928 5.187576 TCCATCCTTTATTGCCAGAAAAAGG 59.812 40.000 6.39 6.39 46.14 3.11
1825 1930 5.779771 AGTCCATCCTTTATTGCCAGAAAAA 59.220 36.000 0.00 0.00 0.00 1.94
1874 1979 8.439971 ACTAGGCACATTATTCATAGATTTGGA 58.560 33.333 0.00 0.00 0.00 3.53
1941 2046 2.021355 AGTCACTACTACCTCCGTCG 57.979 55.000 0.00 0.00 32.84 5.12
1970 2075 6.760770 CCTGTTTACATTTTTGTTGTGTGGAT 59.239 34.615 0.00 0.00 0.00 3.41
1971 2076 6.102663 CCTGTTTACATTTTTGTTGTGTGGA 58.897 36.000 0.00 0.00 0.00 4.02
1981 2086 3.313791 AGCCACCCCTGTTTACATTTTT 58.686 40.909 0.00 0.00 0.00 1.94
1998 2103 1.825090 CATGTTGCTAGTCCAAGCCA 58.175 50.000 0.00 0.00 42.05 4.75
2074 2179 3.138304 CCAGTTTCTGTTGGATGTCGAA 58.862 45.455 0.00 0.00 36.55 3.71
2077 2182 3.476552 TGTCCAGTTTCTGTTGGATGTC 58.523 45.455 0.00 0.00 44.74 3.06
2113 2218 2.935481 CTGGAGGAAGGTGGCCCA 60.935 66.667 0.00 0.00 0.00 5.36
2367 2472 0.174845 CTGCGGATGGAACTCGGTAA 59.825 55.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.