Multiple sequence alignment - TraesCS2B01G408600

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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 TraesCS2B01G408600 chr2B 100.000 4387 0 0 1 4387 581591386 581595772 0.000000e+00 8102
1 TraesCS2B01G408600 chr2B 88.166 507 33 14 1 482 581585974 581586478 2.940000e-161 579
2 TraesCS2B01G408600 chr2B 73.721 430 71 25 40 447 763801042 763801451 3.560000e-26 130
3 TraesCS2B01G408600 chr2D 94.294 3943 151 32 483 4387 493195894 493199800 0.000000e+00 5967
4 TraesCS2B01G408600 chr2D 81.710 421 36 20 93 482 156022572 156022162 3.290000e-81 313
5 TraesCS2B01G408600 chr2D 84.925 199 10 7 483 675 87414806 87414990 2.690000e-42 183
6 TraesCS2B01G408600 chr2A 95.402 1457 50 6 2171 3626 640225657 640224217 0.000000e+00 2303
7 TraesCS2B01G408600 chr2A 88.454 1455 102 36 704 2131 640227302 640225887 0.000000e+00 1696
8 TraesCS2B01G408600 chr2A 91.214 774 47 14 3620 4387 640224187 640223429 0.000000e+00 1033
9 TraesCS2B01G408600 chr2A 84.211 418 31 22 93 482 32288352 32288762 1.490000e-99 374
10 TraesCS2B01G408600 chr3B 89.152 507 28 14 1 482 214539384 214539888 1.350000e-169 606
11 TraesCS2B01G408600 chr3B 87.992 508 33 11 1 482 196990742 196991247 3.810000e-160 575
12 TraesCS2B01G408600 chr3B 85.429 501 45 16 1 476 207441731 207441234 3.050000e-136 496
13 TraesCS2B01G408600 chr1B 88.409 509 29 17 1 482 278087972 278087467 1.760000e-163 586
14 TraesCS2B01G408600 chr1B 88.340 506 34 12 1 482 342579020 342579524 6.320000e-163 584
15 TraesCS2B01G408600 chr4A 86.863 510 35 6 1 486 113336562 113336061 3.860000e-150 542
16 TraesCS2B01G408600 chr4D 87.553 474 40 12 20 482 145679519 145679054 8.350000e-147 531
17 TraesCS2B01G408600 chr6B 85.216 487 57 10 1 476 503550757 503551239 1.830000e-133 486
18 TraesCS2B01G408600 chr5B 84.400 500 52 13 1 476 451203510 451204007 6.640000e-128 468
19 TraesCS2B01G408600 chr3A 84.010 419 30 24 93 482 4006854 4007264 6.930000e-98 368
20 TraesCS2B01G408600 chr3A 75.891 477 78 24 1 458 134799037 134799495 4.450000e-50 209
21 TraesCS2B01G408600 chr7A 83.571 420 32 24 93 483 720773580 720773169 4.170000e-95 359
22 TraesCS2B01G408600 chr1A 83.055 419 37 20 93 482 29999678 29999265 2.510000e-92 350
23 TraesCS2B01G408600 chr6A 77.609 527 64 31 1 482 25109576 25110093 2.010000e-68 270
24 TraesCS2B01G408600 chr6A 82.891 339 21 19 164 483 435814799 435814479 2.010000e-68 270


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 TraesCS2B01G408600 chr2B 581591386 581595772 4386 False 8102.000000 8102 100.000 1 4387 1 chr2B.!!$F2 4386
1 TraesCS2B01G408600 chr2B 581585974 581586478 504 False 579.000000 579 88.166 1 482 1 chr2B.!!$F1 481
2 TraesCS2B01G408600 chr2D 493195894 493199800 3906 False 5967.000000 5967 94.294 483 4387 1 chr2D.!!$F2 3904
3 TraesCS2B01G408600 chr2A 640223429 640227302 3873 True 1677.333333 2303 91.690 704 4387 3 chr2A.!!$R1 3683
4 TraesCS2B01G408600 chr3B 214539384 214539888 504 False 606.000000 606 89.152 1 482 1 chr3B.!!$F2 481
5 TraesCS2B01G408600 chr3B 196990742 196991247 505 False 575.000000 575 87.992 1 482 1 chr3B.!!$F1 481
6 TraesCS2B01G408600 chr1B 278087467 278087972 505 True 586.000000 586 88.409 1 482 1 chr1B.!!$R1 481
7 TraesCS2B01G408600 chr1B 342579020 342579524 504 False 584.000000 584 88.340 1 482 1 chr1B.!!$F1 481
8 TraesCS2B01G408600 chr4A 113336061 113336562 501 True 542.000000 542 86.863 1 486 1 chr4A.!!$R1 485
9 TraesCS2B01G408600 chr6A 25109576 25110093 517 False 270.000000 270 77.609 1 482 1 chr6A.!!$F1 481

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
482 552 0.096281 ACGTGTTTGTGTGCGAACAG 59.904 50.0 0.00 0.0 46.36 3.16 F
489 559 0.176910 TGTGTGCGAACAGAAGACCA 59.823 50.0 0.00 0.0 0.00 4.02 F
1515 1610 0.326264 GTGGATCTCACAGCCAGGTT 59.674 55.0 8.84 0.0 45.39 3.50 F
2372 2674 0.915872 TGGTCAGATCCACCATGGCT 60.916 55.0 13.04 0.0 39.11 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1716 0.761802 CACTAATCCTGCCCTCTCCC 59.238 60.000 0.0 0.0 0.00 4.30 R
1636 1731 0.830648 GCCTGCTACCACCATCACTA 59.169 55.000 0.0 0.0 0.00 2.74 R
3317 3619 1.317611 CGATAGCACTTGACGTTCACG 59.682 52.381 0.0 0.0 46.33 4.35 R
4143 4498 0.107508 TTCTCCAGTGCCATAGCTGC 60.108 55.000 0.0 0.0 40.80 5.25 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
174 213 1.811965 TGATGGCCGATTGAACAACAG 59.188 47.619 0.00 0.00 0.00 3.16
181 220 3.058293 GCCGATTGAACAACAGACAATCA 60.058 43.478 15.77 0.00 45.50 2.57
364 431 1.231928 GTGTGGGGTTTTGGGTCCT 59.768 57.895 0.00 0.00 0.00 3.85
391 459 1.523154 GCCCACCGAATTGTCTTGCA 61.523 55.000 0.00 0.00 0.00 4.08
460 530 3.434319 GGCGTCGAGGGTACACGA 61.434 66.667 7.31 6.00 35.49 4.35
482 552 0.096281 ACGTGTTTGTGTGCGAACAG 59.904 50.000 0.00 0.00 46.36 3.16
486 556 2.095213 GTGTTTGTGTGCGAACAGAAGA 59.905 45.455 6.19 0.00 46.36 2.87
487 557 2.095213 TGTTTGTGTGCGAACAGAAGAC 59.905 45.455 6.19 8.56 42.37 3.01
488 558 1.295792 TTGTGTGCGAACAGAAGACC 58.704 50.000 1.08 0.00 0.00 3.85
489 559 0.176910 TGTGTGCGAACAGAAGACCA 59.823 50.000 0.00 0.00 0.00 4.02
490 560 0.582005 GTGTGCGAACAGAAGACCAC 59.418 55.000 0.00 0.00 0.00 4.16
532 607 0.401738 TTGAGGAAACCAGGCAGAGG 59.598 55.000 0.00 0.00 0.00 3.69
544 619 1.517832 GCAGAGGTGCGGTGTATCT 59.482 57.895 0.00 0.00 40.71 1.98
582 657 2.167861 GTCAAGATCCAGCCGCGTC 61.168 63.158 4.92 0.00 0.00 5.19
596 671 4.514577 CGTCGCTCCTTCCCGCAT 62.515 66.667 0.00 0.00 0.00 4.73
606 681 1.798813 CCTTCCCGCATAGTAAATCGC 59.201 52.381 0.00 0.00 0.00 4.58
618 693 7.193595 GCATAGTAAATCGCCACAGTAAAATT 58.806 34.615 0.00 0.00 0.00 1.82
665 740 2.745281 GCCCTTTGTGCGACTGTTAATA 59.255 45.455 0.00 0.00 0.00 0.98
669 744 4.454504 CCTTTGTGCGACTGTTAATAGGTT 59.545 41.667 4.12 0.00 0.00 3.50
670 745 5.048991 CCTTTGTGCGACTGTTAATAGGTTT 60.049 40.000 4.12 0.00 0.00 3.27
671 746 6.148150 CCTTTGTGCGACTGTTAATAGGTTTA 59.852 38.462 4.12 0.00 0.00 2.01
672 747 7.308109 CCTTTGTGCGACTGTTAATAGGTTTAA 60.308 37.037 4.12 0.00 0.00 1.52
673 748 7.675962 TTGTGCGACTGTTAATAGGTTTAAT 57.324 32.000 4.12 0.00 0.00 1.40
674 749 7.675962 TGTGCGACTGTTAATAGGTTTAATT 57.324 32.000 4.12 0.00 0.00 1.40
675 750 8.774890 TGTGCGACTGTTAATAGGTTTAATTA 57.225 30.769 4.12 0.00 0.00 1.40
676 751 9.217278 TGTGCGACTGTTAATAGGTTTAATTAA 57.783 29.630 4.12 0.00 0.00 1.40
756 836 1.624336 TTTTGAGAATGGCAGCAGCT 58.376 45.000 0.00 0.00 41.70 4.24
946 1030 1.274069 ACCAGTCATCACCCAGATCCT 60.274 52.381 0.00 0.00 33.72 3.24
1061 1146 4.812476 CTTGGACGGCGGCGATGA 62.812 66.667 38.93 17.26 0.00 2.92
1150 1238 1.235696 GAGGAGGATGAGGAGGGCT 59.764 63.158 0.00 0.00 0.00 5.19
1305 1394 1.258445 GGTCTCCGAGAAGAAGGGCA 61.258 60.000 0.00 0.00 0.00 5.36
1376 1465 1.529865 GGCCTGTTCAGTTCGTGTTAC 59.470 52.381 0.00 0.00 0.00 2.50
1395 1484 3.407424 ACTTTGTGTGATCAGCAGCTA 57.593 42.857 0.00 0.00 0.00 3.32
1405 1494 6.471519 GTGTGATCAGCAGCTATTGATTTTTC 59.528 38.462 12.02 3.37 34.33 2.29
1437 1526 1.231928 GGAGGAGAGGAGGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
1457 1546 4.779733 GGGCTGGGAGAGGACGGA 62.780 72.222 0.00 0.00 0.00 4.69
1479 1568 3.132139 CGGAAGCAGCAGCAGCAT 61.132 61.111 12.92 0.00 45.49 3.79
1515 1610 0.326264 GTGGATCTCACAGCCAGGTT 59.674 55.000 8.84 0.00 45.39 3.50
1533 1628 2.648059 GTTTGTCCAGATGATCAGGGG 58.352 52.381 3.93 2.56 0.00 4.79
1544 1639 1.003580 TGATCAGGGGTGCTTTCAGTC 59.996 52.381 0.00 0.00 0.00 3.51
1569 1664 5.996513 CCCATTGTTTGAATTTCCATGTTGA 59.003 36.000 0.00 0.00 0.00 3.18
1581 1676 3.138304 TCCATGTTGAGTTGTAGTGTGC 58.862 45.455 0.00 0.00 0.00 4.57
1587 1682 4.058124 GTTGAGTTGTAGTGTGCTGATGA 58.942 43.478 0.00 0.00 0.00 2.92
1606 1701 5.357878 TGATGATGTAGCTGATTTGGGTTTC 59.642 40.000 0.00 0.00 0.00 2.78
1621 1716 6.702716 TTGGGTTTCTTTTTGTAGTACCAG 57.297 37.500 0.00 0.00 0.00 4.00
1624 1719 5.379187 GGTTTCTTTTTGTAGTACCAGGGA 58.621 41.667 0.00 0.00 0.00 4.20
1629 1724 2.544844 TTGTAGTACCAGGGAGAGGG 57.455 55.000 0.00 0.00 0.00 4.30
1634 1729 2.253656 TACCAGGGAGAGGGCAGGA 61.254 63.158 0.00 0.00 0.00 3.86
1635 1730 1.603633 TACCAGGGAGAGGGCAGGAT 61.604 60.000 0.00 0.00 0.00 3.24
1636 1731 1.695597 CCAGGGAGAGGGCAGGATT 60.696 63.158 0.00 0.00 0.00 3.01
1652 1747 3.134623 CAGGATTAGTGATGGTGGTAGCA 59.865 47.826 0.00 0.00 0.00 3.49
1693 1788 1.228063 AGCACACAGGAGGCAACAG 60.228 57.895 0.00 0.00 41.41 3.16
1708 1803 2.035066 GCAACAGCAGGTTTGATTCTGT 59.965 45.455 0.00 0.00 37.72 3.41
1720 1815 8.137437 CAGGTTTGATTCTGTTCTGTTATGTTT 58.863 33.333 0.00 0.00 0.00 2.83
1729 1824 9.950680 TTCTGTTCTGTTATGTTTGAATTTCTC 57.049 29.630 0.00 0.00 0.00 2.87
1937 2039 3.141767 ACTGTAGGGGAGAAAAAGCAC 57.858 47.619 0.00 0.00 0.00 4.40
2077 2188 4.452114 TGTAATCAGTGTCATGCAACAGAC 59.548 41.667 9.58 9.58 35.37 3.51
2152 2263 8.888579 ATAACTGAATTTTAGACCGATACTGG 57.111 34.615 0.00 0.00 0.00 4.00
2211 2513 6.183360 ACCTGTAGAATTCCTTCGGTAAGATC 60.183 42.308 0.65 0.00 36.45 2.75
2276 2578 5.544176 TCCTGTTTGAACTCTGAACTCCTAT 59.456 40.000 0.00 0.00 0.00 2.57
2372 2674 0.915872 TGGTCAGATCCACCATGGCT 60.916 55.000 13.04 0.00 39.11 4.75
2522 2824 8.943085 AGAAGGTTTATCAGAAGGATGATATGT 58.057 33.333 0.00 0.00 40.82 2.29
2696 2998 3.665675 GAGATTGCCCGGACAGCGT 62.666 63.158 0.73 0.00 0.00 5.07
2758 3060 6.013379 AGTCGTATCCCAAGACTATGATGAT 58.987 40.000 0.00 0.00 43.19 2.45
2954 3256 4.268644 CAGCAGTCTTGTATCGTTGTATGG 59.731 45.833 0.00 0.00 0.00 2.74
2973 3275 6.539826 TGTATGGAAATACATCTGACTGCAAG 59.460 38.462 0.00 0.00 34.17 4.01
3063 3365 2.589157 AAGACGGCGTGGGGAATCA 61.589 57.895 21.19 0.00 0.00 2.57
3080 3382 7.179269 GGGGAATCAGTGAGTATATAGTCTCT 58.821 42.308 16.71 15.26 31.64 3.10
3239 3541 2.755103 CTCTTTGATTGGTGTTAGCCCC 59.245 50.000 0.00 0.00 0.00 5.80
3281 3583 3.181445 ACACACTGTGCTTCTTTATGGGA 60.181 43.478 9.20 0.00 36.98 4.37
3317 3619 1.080974 CGATATCGGCCCGTACACC 60.081 63.158 17.51 0.00 35.37 4.16
3335 3637 1.000506 ACCGTGAACGTCAAGTGCTAT 59.999 47.619 1.75 0.00 37.74 2.97
3387 3689 3.726557 TTCCCATTGCTGAGAACTGAT 57.273 42.857 0.00 0.00 0.00 2.90
3417 3719 0.982704 ACTCATGACCTGCTTCTGCT 59.017 50.000 0.00 0.00 40.48 4.24
3435 3737 4.825085 TCTGCTGGTTTTTAATTCTTCGGT 59.175 37.500 0.00 0.00 0.00 4.69
3436 3738 4.865776 TGCTGGTTTTTAATTCTTCGGTG 58.134 39.130 0.00 0.00 0.00 4.94
3491 3793 6.804783 ACACTGTTGTTTAAGAAAAAGAACCG 59.195 34.615 7.70 4.82 28.43 4.44
3524 3826 5.767665 TCTGTTGTTACAATGCCACACTTAT 59.232 36.000 0.00 0.00 32.92 1.73
3578 3880 1.134491 TGCTGATGCTGACTGAGATGG 60.134 52.381 0.00 0.00 40.48 3.51
3663 4003 8.480133 TTGGGGTTTTAGCAAGTTTATTCTAA 57.520 30.769 0.00 0.00 0.00 2.10
3664 4004 8.117813 TGGGGTTTTAGCAAGTTTATTCTAAG 57.882 34.615 0.00 0.00 0.00 2.18
3665 4005 7.726738 TGGGGTTTTAGCAAGTTTATTCTAAGT 59.273 33.333 0.00 0.00 0.00 2.24
3666 4006 8.582437 GGGGTTTTAGCAAGTTTATTCTAAGTT 58.418 33.333 0.00 0.00 0.00 2.66
3715 4059 8.569641 CAGTTGAGGGTATAATAGACTAGTCAC 58.430 40.741 24.44 12.26 0.00 3.67
3719 4063 7.724506 TGAGGGTATAATAGACTAGTCACAAGG 59.275 40.741 24.44 0.00 0.00 3.61
3820 4164 1.028868 CCTGGCCTTTACAGCTCAGC 61.029 60.000 3.32 0.00 34.65 4.26
3872 4216 5.888901 TCTCTGTTCCTCCTGTAGTTAGAA 58.111 41.667 0.00 0.00 0.00 2.10
3873 4217 6.312529 TCTCTGTTCCTCCTGTAGTTAGAAA 58.687 40.000 0.00 0.00 0.00 2.52
3880 4224 7.171630 TCCTCCTGTAGTTAGAAATTCACTC 57.828 40.000 0.00 0.00 0.00 3.51
3985 4338 8.628882 AATAAAATAAAATAGCGTGCTTCCAC 57.371 30.769 0.00 0.00 38.62 4.02
4037 4390 8.766994 AATAGTAGGCACCATTTTCATGTATT 57.233 30.769 0.00 0.00 0.00 1.89
4119 4474 2.291996 ACCTATTTTTACCACCCCAGCC 60.292 50.000 0.00 0.00 0.00 4.85
4143 4498 7.533426 CCCTTCAAACTTTACTCATCAATCAG 58.467 38.462 0.00 0.00 0.00 2.90
4155 4510 1.671979 TCAATCAGCAGCTATGGCAC 58.328 50.000 3.10 0.00 41.70 5.01
4227 4588 5.810074 AGAACAACAAGAAAACAAAATCCGG 59.190 36.000 0.00 0.00 0.00 5.14
4250 4611 4.378770 GCAAAATCAAGAGCTCAACGATGA 60.379 41.667 17.77 11.88 0.00 2.92
4383 4745 1.475169 CCGCAGCCTCATCCTCCATA 61.475 60.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 431 1.068194 CAATTCGGTGGGCGCTTTTAA 60.068 47.619 7.64 0.00 0.00 1.52
461 531 1.325037 TGTTCGCACACAAACACGTAG 59.675 47.619 0.00 0.00 30.73 3.51
462 532 1.325037 CTGTTCGCACACAAACACGTA 59.675 47.619 0.00 0.00 32.28 3.57
470 540 0.176910 TGGTCTTCTGTTCGCACACA 59.823 50.000 0.00 0.00 0.00 3.72
482 552 1.671379 GCAACCTCCCGTGGTCTTC 60.671 63.158 0.00 0.00 39.83 2.87
505 575 2.625375 GGTTTCCTCAACCGTCACC 58.375 57.895 0.00 0.00 45.98 4.02
514 584 0.768221 ACCTCTGCCTGGTTTCCTCA 60.768 55.000 0.00 0.00 33.34 3.86
529 604 1.103803 TCTCAGATACACCGCACCTC 58.896 55.000 0.00 0.00 0.00 3.85
532 607 1.661112 GCTTTCTCAGATACACCGCAC 59.339 52.381 0.00 0.00 0.00 5.34
544 619 1.819288 CGTGGAGGAGTAGCTTTCTCA 59.181 52.381 16.61 4.12 34.04 3.27
582 657 0.387929 TTACTATGCGGGAAGGAGCG 59.612 55.000 0.00 0.00 35.87 5.03
596 671 6.373216 AGCAATTTTACTGTGGCGATTTACTA 59.627 34.615 0.00 0.00 0.00 1.82
618 693 4.457496 GCGCTAGCCACCTCAGCA 62.457 66.667 9.66 0.00 37.42 4.41
671 746 9.138596 ACCCACGCAGGTATTAATTAATTAATT 57.861 29.630 29.29 23.28 38.79 1.40
672 747 8.700439 ACCCACGCAGGTATTAATTAATTAAT 57.300 30.769 27.91 27.91 38.79 1.40
732 808 3.981211 TGCTGCCATTCTCAAAAAGAAC 58.019 40.909 0.00 0.00 46.61 3.01
756 836 5.543716 CGAAATCTCGTGCGTTAATTAACA 58.456 37.500 24.27 6.76 40.33 2.41
946 1030 0.535335 GTGGATCCGACTGGCTGTTA 59.465 55.000 7.39 0.00 34.14 2.41
1130 1215 1.532794 CCCTCCTCATCCTCCTCCG 60.533 68.421 0.00 0.00 0.00 4.63
1305 1394 3.144193 CTTCTCCTCCGGCTCGCT 61.144 66.667 0.00 0.00 0.00 4.93
1376 1465 4.393990 TCAATAGCTGCTGATCACACAAAG 59.606 41.667 13.43 0.00 0.00 2.77
1395 1484 8.034215 TCCTGAATGCAATTACGAAAAATCAAT 58.966 29.630 0.00 0.00 36.07 2.57
1405 1494 3.797039 TCTCCTCCTGAATGCAATTACG 58.203 45.455 0.00 0.00 36.07 3.18
1437 1526 3.151022 GTCCTCTCCCAGCCCTCG 61.151 72.222 0.00 0.00 0.00 4.63
1479 1568 0.816421 CACCATGCGCAGATGGATGA 60.816 55.000 31.47 0.00 45.24 2.92
1515 1610 1.561076 CACCCCTGATCATCTGGACAA 59.439 52.381 12.14 0.00 37.65 3.18
1533 1628 1.620822 ACAATGGGGACTGAAAGCAC 58.379 50.000 0.00 0.00 37.60 4.40
1544 1639 4.909001 ACATGGAAATTCAAACAATGGGG 58.091 39.130 0.00 0.00 0.00 4.96
1569 1664 4.277515 ACATCATCAGCACACTACAACT 57.722 40.909 0.00 0.00 0.00 3.16
1581 1676 4.458397 ACCCAAATCAGCTACATCATCAG 58.542 43.478 0.00 0.00 0.00 2.90
1587 1682 6.670695 AAAAGAAACCCAAATCAGCTACAT 57.329 33.333 0.00 0.00 0.00 2.29
1606 1701 4.323562 CCCTCTCCCTGGTACTACAAAAAG 60.324 50.000 0.00 0.00 0.00 2.27
1621 1716 0.761802 CACTAATCCTGCCCTCTCCC 59.238 60.000 0.00 0.00 0.00 4.30
1624 1719 2.053244 CCATCACTAATCCTGCCCTCT 58.947 52.381 0.00 0.00 0.00 3.69
1629 1724 2.717639 ACCACCATCACTAATCCTGC 57.282 50.000 0.00 0.00 0.00 4.85
1634 1729 2.158755 GCCTGCTACCACCATCACTAAT 60.159 50.000 0.00 0.00 0.00 1.73
1635 1730 1.209504 GCCTGCTACCACCATCACTAA 59.790 52.381 0.00 0.00 0.00 2.24
1636 1731 0.830648 GCCTGCTACCACCATCACTA 59.169 55.000 0.00 0.00 0.00 2.74
1652 1747 4.087892 CTGCTGGTGCGGTAGCCT 62.088 66.667 3.85 0.00 44.33 4.58
1693 1788 4.574599 AACAGAACAGAATCAAACCTGC 57.425 40.909 0.00 0.00 33.90 4.85
1720 1815 8.359642 CCCACAATTTTCAAGTAGAGAAATTCA 58.640 33.333 0.00 0.00 35.17 2.57
1937 2039 1.202927 ACCTGTTGTGGTCTTCCATGG 60.203 52.381 4.97 4.97 46.20 3.66
2033 2144 2.871096 ACCGAGAAAAGTATTGGCCA 57.129 45.000 0.00 0.00 0.00 5.36
2077 2188 1.531149 GGTGTTTGATGTCAGTGTCGG 59.469 52.381 0.00 0.00 0.00 4.79
2151 2262 3.524789 ACATAGGGGTAAAGGTAACCACC 59.475 47.826 0.00 0.00 41.71 4.61
2152 2263 4.849813 ACATAGGGGTAAAGGTAACCAC 57.150 45.455 0.00 0.00 39.09 4.16
2276 2578 6.422344 TTCACACTGTACCAACCAGTTATA 57.578 37.500 0.00 0.00 41.10 0.98
2372 2674 4.627015 TCCCTGGTAGGCTCTACATTTAA 58.373 43.478 12.53 0.00 32.73 1.52
2696 2998 2.231964 ACCGGTGCAAGTACTTAATCGA 59.768 45.455 19.47 0.00 0.00 3.59
2758 3060 2.231964 GGATGTCAGCATTGCCTTGAAA 59.768 45.455 4.70 0.00 35.07 2.69
2954 3256 6.968131 TGTACTTGCAGTCAGATGTATTTC 57.032 37.500 0.00 0.00 0.00 2.17
2981 3283 9.912634 CTTCTTCCAGATAAAACTGCAAAATAA 57.087 29.630 0.00 0.00 36.67 1.40
2984 3286 6.215845 GCTTCTTCCAGATAAAACTGCAAAA 58.784 36.000 0.00 0.00 36.67 2.44
3239 3541 1.803519 GAGTGCCAGCTCGAACTCG 60.804 63.158 3.46 0.00 41.45 4.18
3281 3583 2.042230 ACGCGGTTATCCTCCCCT 60.042 61.111 12.47 0.00 0.00 4.79
3317 3619 1.317611 CGATAGCACTTGACGTTCACG 59.682 52.381 0.00 0.00 46.33 4.35
3335 3637 4.938832 CCAATCTTGTTGTTACCCATACGA 59.061 41.667 0.00 0.00 0.00 3.43
3387 3689 4.067192 CAGGTCATGAGTCATCACACAAA 58.933 43.478 9.52 0.00 38.57 2.83
3417 3719 9.819267 AATTAAACACCGAAGAATTAAAAACCA 57.181 25.926 0.00 0.00 0.00 3.67
3491 3793 4.875544 TTGTAACAACAGAGTGAACAGC 57.124 40.909 0.00 0.00 0.00 4.40
3498 3800 3.315191 GTGTGGCATTGTAACAACAGAGT 59.685 43.478 0.00 0.00 0.00 3.24
3544 3846 3.391965 CATCAGCATCCTCTTCAGTAGC 58.608 50.000 0.00 0.00 0.00 3.58
3546 3848 3.036819 AGCATCAGCATCCTCTTCAGTA 58.963 45.455 0.00 0.00 45.49 2.74
3578 3880 6.150140 AGCTCATGACACAGAAAGTTAAATCC 59.850 38.462 0.00 0.00 0.00 3.01
3630 3970 3.818180 TGCTAAAACCCCAAGAAACGTA 58.182 40.909 0.00 0.00 0.00 3.57
3673 4017 6.874134 CCCTCAACTGATTACCTATATTTCCG 59.126 42.308 0.00 0.00 0.00 4.30
3715 4059 1.303282 GCCCCCTTGTACTCCCTTG 59.697 63.158 0.00 0.00 0.00 3.61
3719 4063 1.227383 CCATGCCCCCTTGTACTCC 59.773 63.158 0.00 0.00 0.00 3.85
3778 4122 6.429078 AGGACGGTTTTTCTTTGATAGGTTAC 59.571 38.462 0.00 0.00 0.00 2.50
3786 4130 1.679153 GCCAGGACGGTTTTTCTTTGA 59.321 47.619 0.00 0.00 36.97 2.69
3820 4164 4.711949 AAGCGGGCAGGTCAGCAG 62.712 66.667 0.00 0.00 35.83 4.24
3846 4190 2.820787 ACTACAGGAGGAACAGAGAACG 59.179 50.000 0.00 0.00 0.00 3.95
3975 4328 3.334691 TCTTTGGAATAGTGGAAGCACG 58.665 45.455 0.00 0.00 0.00 5.34
4037 4390 5.118990 GCCTCACATGAGCTAGTAATTTGA 58.881 41.667 0.00 0.00 40.75 2.69
4119 4474 7.025963 GCTGATTGATGAGTAAAGTTTGAAGG 58.974 38.462 0.00 0.00 0.00 3.46
4143 4498 0.107508 TTCTCCAGTGCCATAGCTGC 60.108 55.000 0.00 0.00 40.80 5.25
4197 4552 9.662545 ATTTTGTTTTCTTGTTGTTCTGTTTTG 57.337 25.926 0.00 0.00 0.00 2.44
4227 4588 3.542712 TCGTTGAGCTCTTGATTTTGC 57.457 42.857 16.19 0.00 0.00 3.68
4250 4611 1.975407 CCTCGGACGTGTACCCTGT 60.975 63.158 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.