Multiple sequence alignment - TraesCS1B01G269600

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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 TraesCS1B01G269600 chr1B 100.000 4543 0 0 1 4543 474121594 474117052 0.000000e+00 8390
1 TraesCS1B01G269600 chr1B 95.763 118 2 2 2292 2409 573578298 573578184 2.160000e-43 187
2 TraesCS1B01G269600 chr1D 94.292 4310 122 37 288 4542 351443034 351438794 0.000000e+00 6482
3 TraesCS1B01G269600 chr1D 89.892 277 8 5 1 257 351443304 351443028 5.630000e-89 339
4 TraesCS1B01G269600 chr1A 92.130 4625 204 71 26 4543 452284728 452280157 0.000000e+00 6377
5 TraesCS1B01G269600 chr3B 83.846 390 53 3 1424 1806 705151941 705152327 3.340000e-96 363
6 TraesCS1B01G269600 chr3D 84.615 273 26 9 3273 3530 532938005 532938276 1.620000e-64 257
7 TraesCS1B01G269600 chr3A 84.232 241 27 7 2724 2954 668686670 668686909 1.640000e-54 224
8 TraesCS1B01G269600 chr3A 86.765 204 17 6 3336 3530 668688056 668688258 7.650000e-53 219


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 TraesCS1B01G269600 chr1B 474117052 474121594 4542 True 8390.0 8390 100.0000 1 4543 1 chr1B.!!$R1 4542
1 TraesCS1B01G269600 chr1D 351438794 351443304 4510 True 3410.5 6482 92.0920 1 4542 2 chr1D.!!$R1 4541
2 TraesCS1B01G269600 chr1A 452280157 452284728 4571 True 6377.0 6377 92.1300 26 4543 1 chr1A.!!$R1 4517
3 TraesCS1B01G269600 chr3A 668686670 668688258 1588 False 221.5 224 85.4985 2724 3530 2 chr3A.!!$F1 806

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
742 835 0.033090 ACCCAACTCGACTCGGTTTC 59.967 55.000 0.0 0.0 0.00 2.78 F
776 869 0.097150 GCCCGATTCGTTTTCTGCTC 59.903 55.000 5.2 0.0 0.00 4.26 F
1774 1900 0.242825 TTGTCCGTCTCCACGCTTAG 59.757 55.000 0.0 0.0 45.29 2.18 F
2755 2885 1.197492 GACACAACAATGATGCTCGCA 59.803 47.619 0.0 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1776 2.525368 TGCTAAGTGCTCACTGGAGTA 58.475 47.619 2.97 1.75 43.37 2.59 R
2184 2314 2.838637 TCCCTGGAAACACAAAAGGT 57.161 45.000 0.00 0.00 35.60 3.50 R
2860 2999 1.089920 CTTGTCAATTCTGGCCTCCG 58.910 55.000 3.32 0.00 0.00 4.63 R
4308 5347 0.319555 TGGTTGTCTGCTCACGCTAC 60.320 55.000 0.00 0.00 36.97 3.58 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
45 46 5.431765 TGGTGAGATGAGAAGGAAATTAGC 58.568 41.667 0.00 0.00 0.00 3.09
148 155 2.755208 GCTAAACAAAACCAGGGGAGGT 60.755 50.000 0.00 0.00 45.91 3.85
187 194 1.517257 GAGTGCATGTCGACTCGGG 60.517 63.158 17.92 4.64 29.86 5.14
256 295 1.352352 CTGCAGAAGGAAAAGGAGGGA 59.648 52.381 8.42 0.00 0.00 4.20
259 298 2.911484 CAGAAGGAAAAGGAGGGATCG 58.089 52.381 0.00 0.00 0.00 3.69
260 299 1.210722 AGAAGGAAAAGGAGGGATCGC 59.789 52.381 0.54 0.54 0.00 4.58
263 302 1.153349 GAAAAGGAGGGATCGCGCT 60.153 57.895 12.99 0.00 40.40 5.92
511 596 1.454539 CCGACCCTTCCTGGTGTTT 59.545 57.895 0.00 0.00 39.24 2.83
577 667 1.878656 CGCACCGTCTTCTTCCTCCT 61.879 60.000 0.00 0.00 0.00 3.69
583 673 1.342175 CGTCTTCTTCCTCCTACCCCT 60.342 57.143 0.00 0.00 0.00 4.79
720 813 0.741915 GCAACCAACGAAGGGAAACA 59.258 50.000 0.00 0.00 0.00 2.83
721 814 1.535226 GCAACCAACGAAGGGAAACAC 60.535 52.381 0.00 0.00 0.00 3.32
742 835 0.033090 ACCCAACTCGACTCGGTTTC 59.967 55.000 0.00 0.00 0.00 2.78
756 849 1.058695 CGGTTTCCTCGATTCGTTTCG 59.941 52.381 5.89 3.85 40.46 3.46
759 852 0.738412 TTCCTCGATTCGTTTCGGCC 60.738 55.000 5.89 0.00 39.56 6.13
762 855 2.507547 CGATTCGTTTCGGCCCGA 60.508 61.111 0.00 0.00 35.50 5.14
763 856 1.881252 CGATTCGTTTCGGCCCGAT 60.881 57.895 6.69 0.00 35.23 4.18
764 857 1.426041 CGATTCGTTTCGGCCCGATT 61.426 55.000 6.69 0.00 35.23 3.34
766 859 1.426041 ATTCGTTTCGGCCCGATTCG 61.426 55.000 19.35 19.35 35.23 3.34
767 860 2.768503 TTCGTTTCGGCCCGATTCGT 62.769 55.000 22.59 0.00 35.23 3.85
768 861 2.385091 CGTTTCGGCCCGATTCGTT 61.385 57.895 6.69 0.00 35.23 3.85
769 862 1.871077 GTTTCGGCCCGATTCGTTT 59.129 52.632 6.69 0.00 35.23 3.60
770 863 0.239082 GTTTCGGCCCGATTCGTTTT 59.761 50.000 6.69 0.00 35.23 2.43
771 864 0.518195 TTTCGGCCCGATTCGTTTTC 59.482 50.000 6.69 0.00 35.23 2.29
772 865 0.320946 TTCGGCCCGATTCGTTTTCT 60.321 50.000 6.69 0.00 35.23 2.52
773 866 1.017177 TCGGCCCGATTCGTTTTCTG 61.017 55.000 0.00 0.00 0.00 3.02
774 867 1.136774 GGCCCGATTCGTTTTCTGC 59.863 57.895 5.20 0.00 0.00 4.26
775 868 1.305930 GGCCCGATTCGTTTTCTGCT 61.306 55.000 5.20 0.00 0.00 4.24
776 869 0.097150 GCCCGATTCGTTTTCTGCTC 59.903 55.000 5.20 0.00 0.00 4.26
777 870 0.370273 CCCGATTCGTTTTCTGCTCG 59.630 55.000 5.20 0.00 0.00 5.03
778 871 0.247301 CCGATTCGTTTTCTGCTCGC 60.247 55.000 5.20 0.00 0.00 5.03
779 872 0.716108 CGATTCGTTTTCTGCTCGCT 59.284 50.000 0.00 0.00 0.00 4.93
780 873 1.266598 CGATTCGTTTTCTGCTCGCTC 60.267 52.381 0.00 0.00 0.00 5.03
781 874 0.716108 ATTCGTTTTCTGCTCGCTCG 59.284 50.000 0.00 0.00 0.00 5.03
1272 1382 4.194720 CGCGTCCCCGAGAAGGAG 62.195 72.222 0.00 0.00 45.00 3.69
1274 1384 3.066233 GCGTCCCCGAGAAGGAGTC 62.066 68.421 0.00 0.00 45.00 3.36
1284 1394 2.104170 GAGAAGGAGTCCAAGGTCGAT 58.896 52.381 12.86 0.00 0.00 3.59
1344 1454 1.227350 CGGCATCAGCGAGGATGAA 60.227 57.895 17.65 0.00 46.00 2.57
1356 1466 1.332375 GAGGATGAAGACTCCGACTCG 59.668 57.143 0.00 0.00 37.88 4.18
1413 1523 3.531538 CAACTACGGCCACAACTATGAT 58.468 45.455 2.24 0.00 0.00 2.45
1425 1535 3.918591 ACAACTATGATGACGACAACGAC 59.081 43.478 0.00 0.00 42.66 4.34
1426 1536 2.782163 ACTATGATGACGACAACGACG 58.218 47.619 0.00 0.00 42.66 5.12
1427 1537 2.417586 ACTATGATGACGACAACGACGA 59.582 45.455 0.00 0.00 42.66 4.20
1428 1538 1.614385 ATGATGACGACAACGACGAC 58.386 50.000 0.00 0.00 42.66 4.34
1429 1539 0.723459 TGATGACGACAACGACGACG 60.723 55.000 5.58 5.58 42.66 5.12
1430 1540 0.451628 GATGACGACAACGACGACGA 60.452 55.000 15.32 0.00 42.66 4.20
1431 1541 0.452287 ATGACGACAACGACGACGAG 60.452 55.000 15.32 8.51 42.66 4.18
1432 1542 1.791283 GACGACAACGACGACGAGG 60.791 63.158 15.32 7.78 42.66 4.63
1433 1543 2.162921 GACGACAACGACGACGAGGA 62.163 60.000 15.32 0.00 42.66 3.71
1488 1601 2.741092 GAGGACCACCACGCTGAA 59.259 61.111 0.00 0.00 38.94 3.02
1491 1604 1.668151 GGACCACCACGCTGAAGAC 60.668 63.158 0.00 0.00 35.97 3.01
1625 1738 5.798125 CATGTATGGACTCCTATCTGTGT 57.202 43.478 0.00 0.00 0.00 3.72
1626 1739 6.166984 CATGTATGGACTCCTATCTGTGTT 57.833 41.667 0.00 0.00 0.00 3.32
1628 1741 5.269189 TGTATGGACTCCTATCTGTGTTCA 58.731 41.667 0.00 0.00 0.00 3.18
1630 1743 5.965033 ATGGACTCCTATCTGTGTTCATT 57.035 39.130 0.00 0.00 0.00 2.57
1631 1744 5.089970 TGGACTCCTATCTGTGTTCATTG 57.910 43.478 0.00 0.00 0.00 2.82
1632 1745 3.873952 GGACTCCTATCTGTGTTCATTGC 59.126 47.826 0.00 0.00 0.00 3.56
1650 1776 5.304101 TCATTGCCAAACCTGTTATTTGTCT 59.696 36.000 0.00 0.00 35.65 3.41
1774 1900 0.242825 TTGTCCGTCTCCACGCTTAG 59.757 55.000 0.00 0.00 45.29 2.18
2039 2169 7.066766 GGCAAATTACTTCTCTCATGTTCTGAT 59.933 37.037 0.00 0.00 32.10 2.90
2040 2170 8.457261 GCAAATTACTTCTCTCATGTTCTGATT 58.543 33.333 0.00 0.00 32.10 2.57
2186 2316 7.907214 ACTATTGTTGACATCTTCAGTTACC 57.093 36.000 0.00 0.00 34.94 2.85
2552 2682 7.530010 TCTTGCTATCTGAATTGTTTTAGTGC 58.470 34.615 0.00 0.00 0.00 4.40
2652 2782 4.894784 TGAAGATGGAAGTGAGTACAACC 58.105 43.478 0.00 0.00 0.00 3.77
2755 2885 1.197492 GACACAACAATGATGCTCGCA 59.803 47.619 0.00 0.00 0.00 5.10
2915 3054 2.557924 TGAGGCATACAAACCAGCAAAG 59.442 45.455 0.00 0.00 0.00 2.77
3060 3199 4.691216 GGTGAGATGAAGTACAAACAGACC 59.309 45.833 0.00 0.00 0.00 3.85
3091 3230 3.731652 TCGGTGTCGAAAGAAAACCTA 57.268 42.857 0.00 0.00 43.47 3.08
3160 3393 6.331845 AGCTATGATGATGCTTAAGATCTCG 58.668 40.000 6.67 0.00 32.61 4.04
3316 4334 0.035739 GGCTCCAGGAACGTTACCAA 59.964 55.000 6.97 0.00 0.00 3.67
3345 4370 5.336744 TGAAAATGGTTCGTGTTGTCTTTC 58.663 37.500 0.00 0.00 0.00 2.62
3347 4372 6.316640 TGAAAATGGTTCGTGTTGTCTTTCTA 59.683 34.615 0.00 0.00 0.00 2.10
3349 4374 6.481954 AATGGTTCGTGTTGTCTTTCTATC 57.518 37.500 0.00 0.00 0.00 2.08
3364 4389 9.988350 TGTCTTTCTATCGCAATATTTTCTTTC 57.012 29.630 0.00 0.00 0.00 2.62
3372 4397 8.847444 ATCGCAATATTTTCTTTCTTCACATC 57.153 30.769 0.00 0.00 0.00 3.06
3410 4443 4.985538 ACCTAACTGTACTCTTCCATCG 57.014 45.455 0.00 0.00 0.00 3.84
3419 4452 2.249413 CTCTTCCATCGGCCACAGCT 62.249 60.000 2.24 0.00 39.73 4.24
3455 4488 3.744660 GATACAAGTAATGGAGCTGGGG 58.255 50.000 0.00 0.00 0.00 4.96
3560 4594 5.455392 CGCTGATTCTTCTGTGATGTTTTT 58.545 37.500 0.00 0.00 34.31 1.94
3562 4596 5.860716 GCTGATTCTTCTGTGATGTTTTTCC 59.139 40.000 0.00 0.00 0.00 3.13
3567 4601 5.684704 TCTTCTGTGATGTTTTTCCTCACT 58.315 37.500 3.86 0.00 40.60 3.41
3589 4623 3.080319 TGATGAATTTGTCGCCATGTCA 58.920 40.909 0.00 0.00 0.00 3.58
3662 4697 9.927668 CCATATTTTTGAACATAAACACCTTCT 57.072 29.630 0.00 0.00 0.00 2.85
3847 4883 4.566004 GGCTGGTTAATTTTTCTTCCACC 58.434 43.478 0.00 0.00 0.00 4.61
3920 4956 3.305720 TCGGTACATTCCATCTAGCCTT 58.694 45.455 0.00 0.00 0.00 4.35
3928 4964 6.662755 ACATTCCATCTAGCCTTGACATTTA 58.337 36.000 0.00 0.00 0.00 1.40
3965 5001 3.381272 CGTGGGACATTCTTGGCATATTT 59.619 43.478 0.00 0.00 44.52 1.40
4034 5070 1.246056 TTGCTCCTCACATGCAAGCC 61.246 55.000 0.00 0.00 41.06 4.35
4082 5118 3.308402 CCTCTCCAATGGTGGTAATGTGT 60.308 47.826 0.00 0.00 46.11 3.72
4194 5230 7.375053 GTGGTTGCAAATTTCTAAGTTATCCA 58.625 34.615 0.00 0.00 0.00 3.41
4199 5236 5.449999 GCAAATTTCTAAGTTATCCACGGGG 60.450 44.000 0.00 0.00 0.00 5.73
4252 5290 3.362831 GCAAAAAGTGATGAAGATGTGCG 59.637 43.478 0.00 0.00 0.00 5.34
4308 5347 0.904649 TGGTCAGTCAGTATGGGCAG 59.095 55.000 0.00 0.00 36.16 4.85
4354 5393 0.029300 CCGCGCACCATTTATTCCTG 59.971 55.000 8.75 0.00 0.00 3.86
4391 5430 4.148079 TCCATTGTTGCATGTTCCAACTA 58.852 39.130 13.56 8.21 42.25 2.24
4455 5508 3.611517 CAAGCAAAGACTTGTGACTTCG 58.388 45.455 0.00 0.00 41.74 3.79
4489 5549 2.716017 GGAGTCTGGTCTGGCTCCG 61.716 68.421 11.68 0.00 38.22 4.63
4527 5587 1.831736 AGGTCAGCGTTACCAGCTATT 59.168 47.619 7.73 0.00 44.06 1.73
4528 5588 3.028850 AGGTCAGCGTTACCAGCTATTA 58.971 45.455 7.73 0.00 44.06 0.98
4529 5589 3.121544 GGTCAGCGTTACCAGCTATTAC 58.878 50.000 0.00 0.00 44.06 1.89
4530 5590 3.181478 GGTCAGCGTTACCAGCTATTACT 60.181 47.826 0.00 0.00 44.06 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.251016 TCTCACCAGATATCCCTCCAG 57.749 52.381 0.00 0.00 0.00 3.86
21 22 5.526846 GCTAATTTCCTTCTCATCTCACCAG 59.473 44.000 0.00 0.00 0.00 4.00
148 155 3.556038 TTTCTCCCGCCTCCCCTCA 62.556 63.158 0.00 0.00 0.00 3.86
187 194 0.679505 GCTTCTTTGGTTTGACCCCC 59.320 55.000 0.00 0.00 37.50 5.40
256 295 3.950794 TTCCTTCGGCAAGCGCGAT 62.951 57.895 12.10 0.00 39.92 4.58
259 298 1.442688 CTTTTCCTTCGGCAAGCGC 60.443 57.895 0.00 0.00 37.44 5.92
260 299 0.591170 TTCTTTTCCTTCGGCAAGCG 59.409 50.000 0.00 0.00 0.00 4.68
263 302 0.591170 CGCTTCTTTTCCTTCGGCAA 59.409 50.000 0.00 0.00 0.00 4.52
268 312 1.798813 TCGCTTCGCTTCTTTTCCTTC 59.201 47.619 0.00 0.00 0.00 3.46
284 328 3.986006 TCACCGGTTCGCTTCGCT 61.986 61.111 2.97 0.00 0.00 4.93
285 329 3.774702 GTCACCGGTTCGCTTCGC 61.775 66.667 2.97 0.00 0.00 4.70
286 330 3.467119 CGTCACCGGTTCGCTTCG 61.467 66.667 2.97 0.00 0.00 3.79
491 576 3.717294 CACCAGGAAGGGTCGGGG 61.717 72.222 0.00 0.00 43.89 5.73
603 693 1.279749 GGAAAGGGGGAGGTAGGGTG 61.280 65.000 0.00 0.00 0.00 4.61
674 767 1.007387 CAAGTGCCGGTTTCCTTGC 60.007 57.895 1.90 0.00 0.00 4.01
720 813 1.366366 CCGAGTCGAGTTGGGTTGT 59.634 57.895 17.80 0.00 0.00 3.32
721 814 0.249741 AACCGAGTCGAGTTGGGTTG 60.250 55.000 27.00 5.81 39.40 3.77
742 835 2.171725 GGGCCGAAACGAATCGAGG 61.172 63.158 10.55 8.16 45.48 4.63
756 849 1.136774 GCAGAAAACGAATCGGGCC 59.863 57.895 7.80 0.00 0.00 5.80
759 852 0.247301 GCGAGCAGAAAACGAATCGG 60.247 55.000 7.80 0.00 0.00 4.18
762 855 0.716108 CGAGCGAGCAGAAAACGAAT 59.284 50.000 0.00 0.00 0.00 3.34
763 856 1.886861 GCGAGCGAGCAGAAAACGAA 61.887 55.000 0.00 0.00 37.05 3.85
764 857 2.372690 GCGAGCGAGCAGAAAACGA 61.373 57.895 0.00 0.00 37.05 3.85
766 859 2.476499 GGCGAGCGAGCAGAAAAC 59.524 61.111 8.59 0.00 39.27 2.43
767 860 2.742372 GGGCGAGCGAGCAGAAAA 60.742 61.111 8.59 0.00 39.27 2.29
768 861 4.760047 GGGGCGAGCGAGCAGAAA 62.760 66.667 8.59 0.00 39.27 2.52
778 871 3.695022 AATCGACGAACGGGGCGAG 62.695 63.158 0.00 0.00 42.82 5.03
779 872 3.285523 AAATCGACGAACGGGGCGA 62.286 57.895 0.00 3.84 42.82 5.54
780 873 2.812178 AAATCGACGAACGGGGCG 60.812 61.111 0.00 0.00 42.82 6.13
781 874 1.087771 ATCAAATCGACGAACGGGGC 61.088 55.000 0.00 0.00 42.82 5.80
1054 1161 1.067084 CGATGGTCTCGCAGATGCT 59.933 57.895 2.95 0.00 41.14 3.79
1066 1173 0.692419 AGGATGGCCTTCTCGATGGT 60.692 55.000 17.48 0.00 43.90 3.55
1272 1382 0.175760 TGCTGCTATCGACCTTGGAC 59.824 55.000 0.00 0.00 0.00 4.02
1274 1384 1.156645 GCTGCTGCTATCGACCTTGG 61.157 60.000 8.53 0.00 36.03 3.61
1413 1523 1.083209 CTCGTCGTCGTTGTCGTCA 60.083 57.895 1.33 0.00 38.33 4.35
1425 1535 1.525077 CTCCTCCTCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
1426 1536 1.152839 CCTCCTCCTCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
1427 1537 1.619975 TCCTCCTCCTCCTCCTCGT 60.620 63.158 0.00 0.00 0.00 4.18
1428 1538 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1429 1539 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1430 1540 1.938596 TGCTCCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
1431 1541 1.457455 CTGCTCCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
1432 1542 1.457455 CCTGCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
1433 1543 1.938596 TCCTGCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
1625 1738 5.923204 ACAAATAACAGGTTTGGCAATGAA 58.077 33.333 0.00 0.00 40.08 2.57
1626 1739 5.304101 AGACAAATAACAGGTTTGGCAATGA 59.696 36.000 0.00 0.00 45.02 2.57
1628 1741 5.806654 AGACAAATAACAGGTTTGGCAAT 57.193 34.783 0.00 0.00 45.02 3.56
1630 1743 5.381757 AGTAGACAAATAACAGGTTTGGCA 58.618 37.500 7.14 0.00 45.02 4.92
1631 1744 5.106277 GGAGTAGACAAATAACAGGTTTGGC 60.106 44.000 3.97 0.40 43.37 4.52
1632 1745 6.001460 TGGAGTAGACAAATAACAGGTTTGG 58.999 40.000 3.97 0.00 40.08 3.28
1650 1776 2.525368 TGCTAAGTGCTCACTGGAGTA 58.475 47.619 2.97 1.75 43.37 2.59
1675 1801 5.632959 CACCGTTTGTGTTTTAGTTCAGAA 58.367 37.500 0.00 0.00 40.26 3.02
1774 1900 4.528920 TGTGGTATGCAAAATAGGTACCC 58.471 43.478 8.74 0.00 35.13 3.69
1794 1924 7.776969 AGCAACAAAACCAGATATCTCATATGT 59.223 33.333 1.03 2.41 0.00 2.29
2044 2174 6.464222 CAGATGGACTGGTACTAGTCAAAAA 58.536 40.000 32.45 19.02 46.97 1.94
2184 2314 2.838637 TCCCTGGAAACACAAAAGGT 57.161 45.000 0.00 0.00 35.60 3.50
2652 2782 4.040339 AGGGAAAACTAAGCAATTTGGGTG 59.960 41.667 0.00 0.00 0.00 4.61
2755 2885 5.948742 TTGTTTTCCCTCTTGTTTCCAAT 57.051 34.783 0.00 0.00 0.00 3.16
2860 2999 1.089920 CTTGTCAATTCTGGCCTCCG 58.910 55.000 3.32 0.00 0.00 4.63
3091 3230 2.905415 ACATCCACATGACCCATTGT 57.095 45.000 0.00 0.00 33.72 2.71
3160 3393 8.861086 TGGAGTCAAAGGATAGATATAAGTCAC 58.139 37.037 0.00 0.00 0.00 3.67
3316 4334 3.214328 ACACGAACCATTTTCAGCTTCT 58.786 40.909 0.00 0.00 0.00 2.85
3345 4370 9.941664 ATGTGAAGAAAGAAAATATTGCGATAG 57.058 29.630 0.00 0.00 0.00 2.08
3347 4372 8.680903 AGATGTGAAGAAAGAAAATATTGCGAT 58.319 29.630 0.00 0.00 0.00 4.58
3349 4374 9.941664 ATAGATGTGAAGAAAGAAAATATTGCG 57.058 29.630 0.00 0.00 0.00 4.85
3364 4389 7.621428 AAACCACAAGATCATAGATGTGAAG 57.379 36.000 13.62 4.77 44.52 3.02
3365 4390 7.552687 GGTAAACCACAAGATCATAGATGTGAA 59.447 37.037 13.62 0.14 44.52 3.18
3372 4397 8.041323 ACAGTTAGGTAAACCACAAGATCATAG 58.959 37.037 1.26 0.00 39.03 2.23
3419 4452 1.135228 TGTATCGTGCGCTGCTTCTTA 60.135 47.619 9.73 0.00 0.00 2.10
3455 4488 4.489306 ACTCTTAGGCTTTGGTATGTCC 57.511 45.455 0.00 0.00 0.00 4.02
3560 4594 3.436704 GCGACAAATTCATCAAGTGAGGA 59.563 43.478 0.00 0.00 38.29 3.71
3562 4596 3.189080 TGGCGACAAATTCATCAAGTGAG 59.811 43.478 0.00 0.00 36.07 3.51
3654 4689 2.304180 CCATCAGAGGTGAAGAAGGTGT 59.696 50.000 0.00 0.00 35.88 4.16
3847 4883 3.425162 ACAGCTTCCTTCCCAAGTAAG 57.575 47.619 0.00 0.00 0.00 2.34
3920 4956 8.233868 CACGGAATAAACTCATGTTAAATGTCA 58.766 33.333 0.00 0.00 34.96 3.58
3928 4964 4.007659 GTCCCACGGAATAAACTCATGTT 58.992 43.478 0.00 0.00 33.37 2.71
4082 5118 6.506147 CAAAGTCTGATCATGACCAAACAAA 58.494 36.000 16.74 0.00 35.21 2.83
4120 5156 5.593095 AGTTGACACTGACACTACTCTTACA 59.407 40.000 0.00 0.00 0.00 2.41
4194 5230 2.871453 ACAACTAAGCAATTTCCCCGT 58.129 42.857 0.00 0.00 0.00 5.28
4199 5236 9.860898 ATCTTTTCCATACAACTAAGCAATTTC 57.139 29.630 0.00 0.00 0.00 2.17
4252 5290 1.303091 ACGCTATCCCAAACGGCAAC 61.303 55.000 0.00 0.00 0.00 4.17
4308 5347 0.319555 TGGTTGTCTGCTCACGCTAC 60.320 55.000 0.00 0.00 36.97 3.58
4354 5393 6.529477 GCAACAATGGATAAGAAGAAGAAAGC 59.471 38.462 0.00 0.00 0.00 3.51
4454 5507 2.588877 CTACAATGGCCGGCTCCG 60.589 66.667 28.56 14.95 39.44 4.63
4455 5508 2.203209 CCTACAATGGCCGGCTCC 60.203 66.667 28.56 11.61 0.00 4.70
4489 5549 4.068599 GACCTAGCTATTTGCCAGATTCC 58.931 47.826 0.00 0.00 44.23 3.01


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

AutoCloner maintained by Alex Coulton.