Multiple sequence alignment - TraesCS1B01G094700

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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 TraesCS1B01G094700 chr1B 100.000 6588 0 0 1 6588 96587262 96593849 0.000000e+00 12166.0
1 TraesCS1B01G094700 chr1D 95.201 5043 141 21 1604 6588 60223620 60218621 0.000000e+00 7878.0
2 TraesCS1B01G094700 chr1D 93.531 1484 62 13 1 1466 60225320 60223853 0.000000e+00 2178.0
3 TraesCS1B01G094700 chr1D 96.094 128 5 0 1480 1607 60223869 60223742 6.690000e-50 209.0
4 TraesCS1B01G094700 chr1A 96.577 3418 83 10 1480 4865 58907257 58903842 0.000000e+00 5633.0
5 TraesCS1B01G094700 chr1A 94.911 1631 61 10 4871 6492 58903701 58902084 0.000000e+00 2532.0
6 TraesCS1B01G094700 chr1A 93.289 1490 60 15 1 1466 58908714 58907241 0.000000e+00 2161.0
7 TraesCS1B01G094700 chr5A 82.796 93 15 1 6497 6588 338379547 338379639 1.520000e-11 82.4


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 TraesCS1B01G094700 chr1B 96587262 96593849 6587 False 12166.000000 12166 100.000000 1 6588 1 chr1B.!!$F1 6587
1 TraesCS1B01G094700 chr1D 60218621 60225320 6699 True 3421.666667 7878 94.942000 1 6588 3 chr1D.!!$R1 6587
2 TraesCS1B01G094700 chr1A 58902084 58908714 6630 True 3442.000000 5633 94.925667 1 6492 3 chr1A.!!$R1 6491

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
930 973 0.324285 GGGCATCTCAGATAGGCCTG 59.676 60.0 17.99 0.0 44.04 4.85 F
1581 1625 0.111253 CTCTCCCCTGTTTTGTGGCT 59.889 55.0 0.00 0.0 0.00 4.75 F
3084 3258 0.533755 ATAGGTTGCGAGCATCTGGC 60.534 55.0 5.82 0.0 45.30 4.85 F
4194 4389 1.060713 CGCACTTCCTTGTGTAGTCG 58.939 55.0 0.00 0.0 39.89 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2449 2.035066 GGAAAGTGCAGCAATGAAGTGT 59.965 45.455 0.0 0.0 0.00 3.55 R
3390 3564 1.072331 GCAAACCTCACCTCTTCTGGA 59.928 52.381 0.0 0.0 0.00 3.86 R
4872 5073 0.603569 CAAGTGACCTAGCCAGTCGT 59.396 55.000 0.0 0.0 37.04 4.34 R
6127 6467 0.179000 GAAGTCCCTCACGATGCCAT 59.821 55.000 0.0 0.0 0.00 4.40 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
109 132 7.713734 ACATGAATGAATCAAATTGTCTCCT 57.286 32.000 0.00 0.00 42.54 3.69
118 141 8.912988 TGAATCAAATTGTCTCCTTTGTTACTT 58.087 29.630 0.00 0.00 34.66 2.24
121 144 8.925161 TCAAATTGTCTCCTTTGTTACTTTTG 57.075 30.769 0.00 0.00 34.66 2.44
132 155 7.228706 TCCTTTGTTACTTTTGTTGATCTCCTC 59.771 37.037 0.00 0.00 0.00 3.71
133 156 6.539649 TTGTTACTTTTGTTGATCTCCTCG 57.460 37.500 0.00 0.00 0.00 4.63
134 157 5.607477 TGTTACTTTTGTTGATCTCCTCGT 58.393 37.500 0.00 0.00 0.00 4.18
135 158 6.053005 TGTTACTTTTGTTGATCTCCTCGTT 58.947 36.000 0.00 0.00 0.00 3.85
136 159 6.018262 TGTTACTTTTGTTGATCTCCTCGTTG 60.018 38.462 0.00 0.00 0.00 4.10
137 160 4.703897 ACTTTTGTTGATCTCCTCGTTGA 58.296 39.130 0.00 0.00 0.00 3.18
138 161 4.752101 ACTTTTGTTGATCTCCTCGTTGAG 59.248 41.667 0.00 0.00 0.00 3.02
179 202 4.379813 CGGCAACATCATTGGGAATATAGC 60.380 45.833 0.00 0.00 0.00 2.97
181 204 5.010922 GGCAACATCATTGGGAATATAGCAA 59.989 40.000 0.00 0.00 0.00 3.91
220 248 4.220382 AGGATGATGAATCGGATGAGAGAC 59.780 45.833 0.00 0.00 35.99 3.36
228 256 2.060980 GGATGAGAGACCAGGGCGT 61.061 63.158 0.00 0.00 0.00 5.68
346 374 4.787280 AGACGGGGAGGGAGGCAG 62.787 72.222 0.00 0.00 0.00 4.85
347 375 4.779733 GACGGGGAGGGAGGCAGA 62.780 72.222 0.00 0.00 0.00 4.26
348 376 4.787280 ACGGGGAGGGAGGCAGAG 62.787 72.222 0.00 0.00 0.00 3.35
349 377 4.465446 CGGGGAGGGAGGCAGAGA 62.465 72.222 0.00 0.00 0.00 3.10
350 378 2.445654 GGGGAGGGAGGCAGAGAG 60.446 72.222 0.00 0.00 0.00 3.20
351 379 2.693017 GGGAGGGAGGCAGAGAGA 59.307 66.667 0.00 0.00 0.00 3.10
352 380 1.457455 GGGAGGGAGGCAGAGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
353 381 1.618030 GGAGGGAGGCAGAGAGAGA 59.382 63.158 0.00 0.00 0.00 3.10
361 389 1.133976 AGGCAGAGAGAGAGAGAGAGC 60.134 57.143 0.00 0.00 0.00 4.09
558 595 6.095160 CCCTCCATCTATATTGTACGTACCTC 59.905 46.154 22.43 0.00 0.00 3.85
571 608 1.461559 GTACCTCTGTACTCCTGCGT 58.538 55.000 0.00 0.00 43.33 5.24
637 674 1.506493 CTAGTGATGGATCCTTGCGC 58.494 55.000 14.23 0.00 0.00 6.09
751 788 1.376166 CCGCGGTGGGTGTTGATTA 60.376 57.895 19.50 0.00 0.00 1.75
767 804 7.763985 GGTGTTGATTAATTAGGGGTTTTCATG 59.236 37.037 0.00 0.00 0.00 3.07
770 807 7.416964 TGATTAATTAGGGGTTTTCATGGTG 57.583 36.000 0.00 0.00 0.00 4.17
771 808 7.185565 TGATTAATTAGGGGTTTTCATGGTGA 58.814 34.615 0.00 0.00 0.00 4.02
774 811 0.409484 AGGGGTTTTCATGGTGAGGG 59.591 55.000 0.00 0.00 0.00 4.30
802 845 8.146412 ACCTAATTATCGTTCAATGTAGGGTAC 58.854 37.037 0.00 0.00 32.75 3.34
896 939 1.203287 GAGCCTTGCATTTCTGGTTCC 59.797 52.381 0.00 0.00 0.00 3.62
908 951 0.798776 CTGGTTCCGCTTGTAGCTTG 59.201 55.000 0.00 0.00 39.60 4.01
928 971 1.130054 TGGGGCATCTCAGATAGGCC 61.130 60.000 16.67 16.67 45.15 5.19
930 973 0.324285 GGGCATCTCAGATAGGCCTG 59.676 60.000 17.99 0.00 44.04 4.85
982 1025 0.813821 GTTCAGCAGGATTTGGAGCC 59.186 55.000 0.00 0.00 0.00 4.70
1118 1161 3.118298 GCCGGGGGAATTAGTAAGTACAA 60.118 47.826 2.18 0.00 0.00 2.41
1120 1163 4.162888 CCGGGGGAATTAGTAAGTACAACT 59.837 45.833 0.00 6.21 0.00 3.16
1266 1310 8.977267 ATATCTTCTTTCCTCTTTCTTCATGG 57.023 34.615 0.00 0.00 0.00 3.66
1322 1366 3.370953 GGCCCATTGAGTACACTTGATCT 60.371 47.826 0.00 0.00 0.00 2.75
1388 1432 8.707938 AATTTGGCTCTCAACTTATAATTTGC 57.292 30.769 9.98 0.28 34.67 3.68
1392 1436 5.745769 GGCTCTCAACTTATAATTTGCTTGC 59.254 40.000 9.98 11.76 0.00 4.01
1458 1502 1.607148 ACAGCGCAACCTACCTTTTTC 59.393 47.619 11.47 0.00 0.00 2.29
1459 1503 1.606668 CAGCGCAACCTACCTTTTTCA 59.393 47.619 11.47 0.00 0.00 2.69
1460 1504 1.880027 AGCGCAACCTACCTTTTTCAG 59.120 47.619 11.47 0.00 0.00 3.02
1461 1505 1.877443 GCGCAACCTACCTTTTTCAGA 59.123 47.619 0.30 0.00 0.00 3.27
1462 1506 2.350484 GCGCAACCTACCTTTTTCAGAC 60.350 50.000 0.30 0.00 0.00 3.51
1463 1507 2.875933 CGCAACCTACCTTTTTCAGACA 59.124 45.455 0.00 0.00 0.00 3.41
1464 1508 3.502211 CGCAACCTACCTTTTTCAGACAT 59.498 43.478 0.00 0.00 0.00 3.06
1465 1509 4.023193 CGCAACCTACCTTTTTCAGACATT 60.023 41.667 0.00 0.00 0.00 2.71
1466 1510 5.507315 CGCAACCTACCTTTTTCAGACATTT 60.507 40.000 0.00 0.00 0.00 2.32
1467 1511 6.280643 GCAACCTACCTTTTTCAGACATTTT 58.719 36.000 0.00 0.00 0.00 1.82
1468 1512 6.761242 GCAACCTACCTTTTTCAGACATTTTT 59.239 34.615 0.00 0.00 0.00 1.94
1563 1607 9.151471 CTTTGATTCATTTTGATTGATTCAGCT 57.849 29.630 0.00 0.00 35.85 4.24
1576 1620 2.276732 TTCAGCTCTCCCCTGTTTTG 57.723 50.000 0.00 0.00 0.00 2.44
1581 1625 0.111253 CTCTCCCCTGTTTTGTGGCT 59.889 55.000 0.00 0.00 0.00 4.75
1679 1848 8.939929 CCATACTACTGTGGATAAATATGCTTG 58.060 37.037 0.00 0.00 37.72 4.01
2001 2171 5.676532 AATTGCCATTTGTGTTGTCATTG 57.323 34.783 0.00 0.00 0.00 2.82
2136 2306 0.615331 GGCATCAGGTCACCTTCTCA 59.385 55.000 0.00 0.00 0.00 3.27
2141 2311 1.552337 TCAGGTCACCTTCTCATGCTC 59.448 52.381 0.00 0.00 0.00 4.26
2230 2400 8.465273 AATGCTCTACTACTTTCCTTGTTTTT 57.535 30.769 0.00 0.00 0.00 1.94
3021 3195 9.111519 TCCCCAGTTTAATATGAATCTGCTATA 57.888 33.333 5.60 0.00 0.00 1.31
3057 3231 5.233225 TGCTGTTCTCTCATAGTTCTTGTG 58.767 41.667 0.00 0.00 0.00 3.33
3084 3258 0.533755 ATAGGTTGCGAGCATCTGGC 60.534 55.000 5.82 0.00 45.30 4.85
3327 3501 3.861840 TCAGATGATCAAACGAGGAACC 58.138 45.455 0.00 0.00 0.00 3.62
3364 3538 6.874134 ACTAACTGTTGATTCAGTGTCCATAC 59.126 38.462 2.69 0.00 46.25 2.39
3390 3564 6.268387 AGAAAAATGGTTCATGTCCACTGATT 59.732 34.615 12.84 7.58 37.81 2.57
3464 3638 5.945191 TGATTATCTGGCATTGAACTGTTCA 59.055 36.000 18.69 18.69 38.04 3.18
3469 3643 5.499313 TCTGGCATTGAACTGTTCATGATA 58.501 37.500 22.60 9.35 39.84 2.15
3530 3704 8.525290 AATATGTAATAGTGCTTCCAGCTTTT 57.475 30.769 0.00 0.00 35.31 2.27
3558 3732 6.808212 GTGTAGCTTGCAAAACATATCATTGT 59.192 34.615 0.00 0.00 0.00 2.71
3588 3762 7.235399 ACATTGGAAATCTTAGGGTGTCAAAAT 59.765 33.333 0.00 0.00 0.00 1.82
3596 3770 2.086869 AGGGTGTCAAAATGCGATCAG 58.913 47.619 0.00 0.00 0.00 2.90
3642 3816 5.789574 AGTTATTGGTTGTCTTCCCCATA 57.210 39.130 0.00 0.00 0.00 2.74
3719 3898 1.615392 GTGGGAACTGCAAAGCTCAAT 59.385 47.619 0.00 0.00 0.00 2.57
3808 3987 6.238731 CCAGTAAAATATATATGGGCATGGCG 60.239 42.308 13.76 0.00 0.00 5.69
3963 4158 6.327934 CCTTGTTGCTCTTCCATGAAATTAG 58.672 40.000 0.00 0.00 0.00 1.73
4194 4389 1.060713 CGCACTTCCTTGTGTAGTCG 58.939 55.000 0.00 0.00 39.89 4.18
4215 4410 3.829601 CGGAGGGAGCTATCTGATTTAGT 59.170 47.826 0.00 0.00 0.00 2.24
4516 4711 3.075882 TCTTCCCTGGGTTTCACAATGAT 59.924 43.478 13.56 0.00 0.00 2.45
4744 4945 5.407387 GTCGTAAGTAGTTTTCAGGATGCAA 59.593 40.000 0.00 0.00 35.00 4.08
4866 5067 7.099764 GTCAGGATGTAGGTGGATAACATATG 58.900 42.308 0.00 0.00 37.40 1.78
4867 5068 6.787458 TCAGGATGTAGGTGGATAACATATGT 59.213 38.462 1.41 1.41 37.40 2.29
4868 5069 7.953493 TCAGGATGTAGGTGGATAACATATGTA 59.047 37.037 9.21 0.00 37.40 2.29
4870 5071 7.733047 AGGATGTAGGTGGATAACATATGTACA 59.267 37.037 9.21 6.77 34.09 2.90
4871 5072 8.540388 GGATGTAGGTGGATAACATATGTACAT 58.460 37.037 13.93 13.93 34.09 2.29
4885 5221 3.008835 TGTACATACGACTGGCTAGGT 57.991 47.619 0.85 0.00 0.00 3.08
5052 5389 7.229506 GGCCACTTGAGAATTTAGTAGCATATT 59.770 37.037 0.00 0.00 29.78 1.28
5091 5428 3.181487 GCATCGTTTGCCCATGTAGATTT 60.181 43.478 2.29 0.00 46.15 2.17
5182 5519 5.356751 TGCTACACTGTTTGAAAATGTCAGT 59.643 36.000 0.00 0.00 37.61 3.41
5257 5594 4.842574 TCAATAACAGTGCAGGCATAGAA 58.157 39.130 0.00 0.00 0.00 2.10
5794 6131 3.893813 GGATGCTTGCCTGGATTATCTTT 59.106 43.478 0.00 0.00 0.00 2.52
5829 6166 7.392673 ACCTCGATACAGAAACTAACACTTAGA 59.607 37.037 0.00 0.00 36.73 2.10
6034 6374 3.906720 ATGTAGTTGGCGGATACACTT 57.093 42.857 0.00 0.00 32.58 3.16
6054 6394 5.178252 CACTTAACTCATGACACAGGTGAAG 59.822 44.000 6.40 7.34 0.00 3.02
6078 6418 3.819337 CTCTGGCAGGTAATTCATGATGG 59.181 47.826 15.73 0.00 0.00 3.51
6080 6420 1.267806 GGCAGGTAATTCATGATGGCG 59.732 52.381 0.00 0.00 0.00 5.69
6095 6435 0.323633 TGGCGGTGGCTACTGTACTA 60.324 55.000 11.04 0.00 39.81 1.82
6096 6436 0.101939 GGCGGTGGCTACTGTACTAC 59.898 60.000 11.04 0.00 39.81 2.73
6097 6437 1.101331 GCGGTGGCTACTGTACTACT 58.899 55.000 11.04 0.00 35.54 2.57
6105 6445 7.433425 CGGTGGCTACTGTACTACTTTATAAAC 59.567 40.741 0.00 0.00 0.00 2.01
6127 6467 7.661127 AACTATTCGTTATGTGTGCTTGTTA 57.339 32.000 0.00 0.00 33.05 2.41
6148 6488 1.519455 GCATCGTGAGGGACTTCCG 60.519 63.158 0.00 0.00 41.55 4.30
6223 6563 3.822996 CGGTACTTATATCGGCTCAGTG 58.177 50.000 0.00 0.00 30.83 3.66
6276 6616 3.701040 ACAATGTTGCAAGAGTGGACTTT 59.299 39.130 25.05 3.86 0.00 2.66
6277 6617 4.160252 ACAATGTTGCAAGAGTGGACTTTT 59.840 37.500 25.05 3.16 0.00 2.27
6278 6618 5.359576 ACAATGTTGCAAGAGTGGACTTTTA 59.640 36.000 25.05 0.00 0.00 1.52
6279 6619 4.893424 TGTTGCAAGAGTGGACTTTTAC 57.107 40.909 0.00 0.00 0.00 2.01
6280 6620 4.265893 TGTTGCAAGAGTGGACTTTTACA 58.734 39.130 0.00 0.00 0.00 2.41
6281 6621 4.887071 TGTTGCAAGAGTGGACTTTTACAT 59.113 37.500 0.00 0.00 0.00 2.29
6282 6622 5.359576 TGTTGCAAGAGTGGACTTTTACATT 59.640 36.000 0.00 0.00 0.00 2.71
6283 6623 6.127479 TGTTGCAAGAGTGGACTTTTACATTT 60.127 34.615 0.00 0.00 0.00 2.32
6284 6624 5.830912 TGCAAGAGTGGACTTTTACATTTG 58.169 37.500 0.00 0.00 0.00 2.32
6285 6625 5.221224 TGCAAGAGTGGACTTTTACATTTGG 60.221 40.000 0.00 0.00 0.00 3.28
6358 6702 0.329931 TGTAATCGTTGGGTGCCCAT 59.670 50.000 11.20 0.00 46.64 4.00
6411 6755 2.298729 GTTGTTATGCTTTCCAAGGCCA 59.701 45.455 5.01 0.00 0.00 5.36
6420 6764 2.990740 TTCCAAGGCCAGTTGGTTAT 57.009 45.000 20.21 0.00 46.31 1.89
6430 6778 5.665812 AGGCCAGTTGGTTATTCTCTGTATA 59.334 40.000 5.01 0.00 37.57 1.47
6431 6779 5.758784 GGCCAGTTGGTTATTCTCTGTATAC 59.241 44.000 0.00 0.00 37.57 1.47
6466 6814 1.000731 GGGCATTGTTGTTGCTGCTAA 59.999 47.619 0.00 0.00 40.03 3.09
6468 6816 2.331194 GCATTGTTGTTGCTGCTAAGG 58.669 47.619 0.00 0.00 37.14 2.69
6485 6833 0.886563 AGGCTGCTTCTGTTGAATGC 59.113 50.000 0.00 0.00 0.00 3.56
6486 6834 0.108945 GGCTGCTTCTGTTGAATGCC 60.109 55.000 0.00 0.00 36.56 4.40
6487 6835 0.599558 GCTGCTTCTGTTGAATGCCA 59.400 50.000 0.00 0.00 0.00 4.92
6488 6836 1.402456 GCTGCTTCTGTTGAATGCCAG 60.402 52.381 0.00 0.00 0.00 4.85
6489 6837 1.201647 CTGCTTCTGTTGAATGCCAGG 59.798 52.381 0.00 0.00 0.00 4.45
6490 6838 0.108945 GCTTCTGTTGAATGCCAGGC 60.109 55.000 3.66 3.66 0.00 4.85
6491 6839 1.542492 CTTCTGTTGAATGCCAGGCT 58.458 50.000 14.15 0.00 0.00 4.58
6492 6840 1.201647 CTTCTGTTGAATGCCAGGCTG 59.798 52.381 14.15 7.75 0.00 4.85
6493 6841 1.214589 CTGTTGAATGCCAGGCTGC 59.785 57.895 14.15 5.45 0.00 5.25
6494 6842 1.228644 TGTTGAATGCCAGGCTGCT 60.229 52.632 14.15 0.00 0.00 4.24
6495 6843 0.828762 TGTTGAATGCCAGGCTGCTT 60.829 50.000 14.15 3.45 0.00 3.91
6496 6844 0.108945 GTTGAATGCCAGGCTGCTTC 60.109 55.000 14.15 13.13 0.00 3.86
6497 6845 0.251474 TTGAATGCCAGGCTGCTTCT 60.251 50.000 14.15 0.00 0.00 2.85
6498 6846 0.963856 TGAATGCCAGGCTGCTTCTG 60.964 55.000 14.15 0.00 0.00 3.02
6499 6847 0.964358 GAATGCCAGGCTGCTTCTGT 60.964 55.000 14.15 0.00 0.00 3.41
6500 6848 0.541296 AATGCCAGGCTGCTTCTGTT 60.541 50.000 14.15 0.00 0.00 3.16
6501 6849 1.248785 ATGCCAGGCTGCTTCTGTTG 61.249 55.000 14.15 0.00 0.00 3.33
6502 6850 1.601759 GCCAGGCTGCTTCTGTTGA 60.602 57.895 9.56 0.00 0.00 3.18
6503 6851 1.174712 GCCAGGCTGCTTCTGTTGAA 61.175 55.000 9.56 0.00 0.00 2.69
6504 6852 1.542492 CCAGGCTGCTTCTGTTGAAT 58.458 50.000 9.56 0.00 0.00 2.57
6524 6872 1.908483 CCAGGCTCCAGGGTACTTC 59.092 63.158 0.00 0.00 0.00 3.01
6541 6889 8.262933 AGGGTACTTCTGGTTACATAATGTTAC 58.737 37.037 0.00 0.00 0.00 2.50
6552 6900 8.881743 GGTTACATAATGTTACAACAACCGATA 58.118 33.333 0.00 0.00 43.03 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.445452 ACCTGCTTGTATTTGCATGAAG 57.555 40.909 0.00 0.00 38.59 3.02
53 54 8.175925 TGTTGAATTGATGAATTGGTTCTGTA 57.824 30.769 0.00 0.00 35.33 2.74
109 132 6.540914 ACGAGGAGATCAACAAAAGTAACAAA 59.459 34.615 0.00 0.00 0.00 2.83
132 155 6.481954 AAAGTAATAAGTGCTTCCTCAACG 57.518 37.500 0.00 0.00 29.75 4.10
133 156 6.402226 CCGAAAGTAATAAGTGCTTCCTCAAC 60.402 42.308 0.00 0.00 29.75 3.18
134 157 5.642063 CCGAAAGTAATAAGTGCTTCCTCAA 59.358 40.000 0.00 0.00 29.75 3.02
135 158 5.175859 CCGAAAGTAATAAGTGCTTCCTCA 58.824 41.667 0.00 0.00 29.75 3.86
136 159 4.034163 GCCGAAAGTAATAAGTGCTTCCTC 59.966 45.833 0.00 0.00 29.75 3.71
137 160 3.939592 GCCGAAAGTAATAAGTGCTTCCT 59.060 43.478 0.00 0.00 29.75 3.36
138 161 3.687698 TGCCGAAAGTAATAAGTGCTTCC 59.312 43.478 0.00 0.00 29.75 3.46
139 162 4.939509 TGCCGAAAGTAATAAGTGCTTC 57.060 40.909 0.00 0.00 29.75 3.86
148 171 4.142182 CCCAATGATGTTGCCGAAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
151 174 1.545582 CCCAATGATGTTGCCGAAAGT 59.454 47.619 0.00 0.00 0.00 2.66
179 202 7.054491 TCATCCTTCCTTTCTTTTTCCTTTG 57.946 36.000 0.00 0.00 0.00 2.77
181 204 7.012607 TCATCATCCTTCCTTTCTTTTTCCTT 58.987 34.615 0.00 0.00 0.00 3.36
228 256 0.669318 GTCAGTGGATCGAACGGCAA 60.669 55.000 0.00 0.00 0.00 4.52
265 293 3.238497 CACGTGGAGGGTGGGTGA 61.238 66.667 7.95 0.00 0.00 4.02
346 374 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
347 375 2.363680 CTCTCTCGCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
348 376 2.362397 TCTCTCTCGCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
349 377 2.363680 CTCTCTCTCGCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
350 378 2.362397 TCTCTCTCTCGCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
351 379 2.363680 CTCTCTCTCTCGCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
352 380 2.546795 CCTCTCTCTCTCGCTCTCTCTC 60.547 59.091 0.00 0.00 0.00 3.20
353 381 1.414181 CCTCTCTCTCTCGCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
361 389 1.498865 GCGCTCTCCTCTCTCTCTCG 61.499 65.000 0.00 0.00 0.00 4.04
558 595 2.577112 CGCGACGCAGGAGTACAG 60.577 66.667 21.35 0.00 0.00 2.74
571 608 2.443952 ATCCAGATCCCCACGCGA 60.444 61.111 15.93 0.00 0.00 5.87
612 649 1.660355 GATCCATCACTAGCGCGGA 59.340 57.895 8.83 0.00 0.00 5.54
620 657 1.153086 GGCGCAAGGATCCATCACT 60.153 57.895 15.82 0.00 38.28 3.41
734 771 1.091537 ATTAATCAACACCCACCGCG 58.908 50.000 0.00 0.00 0.00 6.46
739 776 4.957606 ACCCCTAATTAATCAACACCCA 57.042 40.909 0.00 0.00 0.00 4.51
751 788 4.352893 CCTCACCATGAAAACCCCTAATT 58.647 43.478 0.00 0.00 0.00 1.40
767 804 4.684484 ACGATAATTAGGTTCCCTCACC 57.316 45.455 0.00 0.00 34.61 4.02
770 807 6.766467 ACATTGAACGATAATTAGGTTCCCTC 59.234 38.462 20.70 6.09 39.36 4.30
771 808 6.659824 ACATTGAACGATAATTAGGTTCCCT 58.340 36.000 20.70 10.98 39.36 4.20
774 811 7.713942 ACCCTACATTGAACGATAATTAGGTTC 59.286 37.037 18.42 18.42 40.26 3.62
802 845 0.668706 CTGGGGCAGATCTTATCGCG 60.669 60.000 0.00 0.00 32.44 5.87
908 951 0.036022 GCCTATCTGAGATGCCCCAC 59.964 60.000 4.96 0.00 0.00 4.61
928 971 2.671070 GCGTTTTGGGCAGATAAACCAG 60.671 50.000 0.00 0.00 35.37 4.00
930 973 1.544246 AGCGTTTTGGGCAGATAAACC 59.456 47.619 0.00 0.00 0.00 3.27
982 1025 7.151308 AGGAGCATCTTATTTCATTACTCTCG 58.849 38.462 0.00 0.00 33.73 4.04
1118 1161 5.221501 CCAAATGGAAGAACATTGTCCAAGT 60.222 40.000 0.00 0.00 44.41 3.16
1120 1163 4.898265 TCCAAATGGAAGAACATTGTCCAA 59.102 37.500 0.00 0.00 44.41 3.53
1177 1220 6.988580 TCTAAATATCAGCATCTGAACTGTGG 59.011 38.462 9.90 0.00 44.04 4.17
1216 1260 4.466015 AGCTCCAAAACAACTCTTTCCAAA 59.534 37.500 0.00 0.00 0.00 3.28
1217 1261 4.023291 AGCTCCAAAACAACTCTTTCCAA 58.977 39.130 0.00 0.00 0.00 3.53
1302 1346 4.163078 AGGAGATCAAGTGTACTCAATGGG 59.837 45.833 0.00 0.00 0.00 4.00
1322 1366 3.332485 AGGTTTTGCATAAGGGTGTAGGA 59.668 43.478 0.00 0.00 0.00 2.94
1388 1432 7.044798 ACTAAGCTAGGAATAGAAGTTGCAAG 58.955 38.462 0.00 0.00 0.00 4.01
1392 1436 9.255304 GAATGACTAAGCTAGGAATAGAAGTTG 57.745 37.037 0.00 0.00 0.00 3.16
1467 1511 5.069251 TCTGAAAAAGGTAATCCCGCAAAAA 59.931 36.000 0.00 0.00 38.74 1.94
1468 1512 4.585162 TCTGAAAAAGGTAATCCCGCAAAA 59.415 37.500 0.00 0.00 38.74 2.44
1469 1513 4.022676 GTCTGAAAAAGGTAATCCCGCAAA 60.023 41.667 0.00 0.00 38.74 3.68
1470 1514 3.504520 GTCTGAAAAAGGTAATCCCGCAA 59.495 43.478 0.00 0.00 38.74 4.85
1471 1515 3.078837 GTCTGAAAAAGGTAATCCCGCA 58.921 45.455 0.00 0.00 38.74 5.69
1472 1516 3.078837 TGTCTGAAAAAGGTAATCCCGC 58.921 45.455 0.00 0.00 38.74 6.13
1473 1517 5.414454 TCAATGTCTGAAAAAGGTAATCCCG 59.586 40.000 0.00 0.00 38.74 5.14
1474 1518 6.834168 TCAATGTCTGAAAAAGGTAATCCC 57.166 37.500 0.00 0.00 0.00 3.85
1487 1531 4.284829 TGTGTGCCTATTCAATGTCTGA 57.715 40.909 0.00 0.00 0.00 3.27
1540 1584 8.063200 AGAGCTGAATCAATCAAAATGAATCA 57.937 30.769 0.00 0.00 37.67 2.57
1563 1607 1.073284 GTAGCCACAAAACAGGGGAGA 59.927 52.381 0.00 0.00 0.00 3.71
1576 1620 4.261801 AGTGGTGATTACAATGTAGCCAC 58.738 43.478 20.23 20.23 43.74 5.01
1581 1625 5.962031 ACTAGGGAGTGGTGATTACAATGTA 59.038 40.000 0.00 0.00 33.41 2.29
1626 1795 9.753674 AGGAGAAAATCATTAATCAGTAACCAA 57.246 29.630 0.00 0.00 0.00 3.67
1629 1798 9.396022 TGGAGGAGAAAATCATTAATCAGTAAC 57.604 33.333 0.00 0.00 0.00 2.50
1660 1829 8.660435 AGGTATACAAGCATATTTATCCACAGT 58.340 33.333 5.01 0.00 0.00 3.55
1679 1848 9.639601 AAATAAAGCAAAGCAAAAGAGGTATAC 57.360 29.630 0.00 0.00 0.00 1.47
1724 1893 9.784531 ATGTTATAAGCTCTGCAGTAATTACAT 57.215 29.630 17.65 12.55 0.00 2.29
1753 1922 8.852135 CCAGTTTAATTAACCAAACACTTCCTA 58.148 33.333 13.41 0.00 37.16 2.94
1813 1983 7.120923 TGGGAGATACAACTCATAAAGGTAC 57.879 40.000 0.00 0.00 38.51 3.34
1828 1998 5.292101 CGTGAGAGTTTGAATTGGGAGATAC 59.708 44.000 0.00 0.00 0.00 2.24
1830 2000 4.256920 CGTGAGAGTTTGAATTGGGAGAT 58.743 43.478 0.00 0.00 0.00 2.75
2001 2171 8.715998 CAGAAATATGTCATATTCCTACAGCAC 58.284 37.037 16.66 3.48 34.50 4.40
2136 2306 5.277683 CGCAAGCTGAATATACAAAGAGCAT 60.278 40.000 0.00 0.00 0.00 3.79
2141 2311 3.621794 GCCGCAAGCTGAATATACAAAG 58.378 45.455 0.00 0.00 38.99 2.77
2216 2386 7.582667 ACTGCATAGTAAAAACAAGGAAAGT 57.417 32.000 0.00 0.00 34.74 2.66
2279 2449 2.035066 GGAAAGTGCAGCAATGAAGTGT 59.965 45.455 0.00 0.00 0.00 3.55
2369 2539 6.611642 TGGCTGTATTCTTAGGAGATACTGTT 59.388 38.462 0.00 0.00 0.00 3.16
2524 2695 4.036498 ACTCTAAATCCTCGATGTACCACG 59.964 45.833 0.00 3.02 0.00 4.94
2536 2707 8.985315 TGCAAAATCATCATACTCTAAATCCT 57.015 30.769 0.00 0.00 0.00 3.24
2871 3042 7.649705 TGTAAAAGCAACATCGCATTTTCTTAA 59.350 29.630 0.00 0.00 34.83 1.85
3021 3195 7.436118 TGAGAGAACAGCAAAAGCAAATAAAT 58.564 30.769 0.00 0.00 0.00 1.40
3024 3198 6.579666 ATGAGAGAACAGCAAAAGCAAATA 57.420 33.333 0.00 0.00 0.00 1.40
3057 3231 5.696724 AGATGCTCGCAACCTATACAAATAC 59.303 40.000 0.00 0.00 0.00 1.89
3084 3258 3.961480 TGATATGCCAGATAAGGACGG 57.039 47.619 0.00 0.00 0.00 4.79
3234 3408 7.448748 AGTAACAACCAGTCACATAAATTCC 57.551 36.000 0.00 0.00 0.00 3.01
3364 3538 5.009911 TCAGTGGACATGAACCATTTTTCTG 59.990 40.000 16.35 16.50 39.69 3.02
3390 3564 1.072331 GCAAACCTCACCTCTTCTGGA 59.928 52.381 0.00 0.00 0.00 3.86
3442 3616 6.604396 TCATGAACAGTTCAATGCCAGATAAT 59.396 34.615 19.92 0.00 43.95 1.28
3469 3643 8.993121 CAGATGAAACTTTACTCAAGTATGTGT 58.007 33.333 0.00 0.00 45.77 3.72
3530 3704 5.240403 TGATATGTTTTGCAAGCTACACACA 59.760 36.000 11.68 9.79 0.00 3.72
3558 3732 6.074648 ACACCCTAAGATTTCCAATGTGAAA 58.925 36.000 0.00 0.73 38.51 2.69
3596 3770 8.952278 ACTAGCAGTATAACTATCTCACTATGC 58.048 37.037 0.00 0.00 0.00 3.14
3642 3816 7.610305 CCTAAGGTCACCAAGTGTACATAAAAT 59.390 37.037 0.00 0.00 34.79 1.82
3808 3987 6.064846 TCTCTTCTTTTTCTGAATGTGCAC 57.935 37.500 10.75 10.75 0.00 4.57
3916 4111 5.794687 CGCAATCCTAATTGTGTTCTACA 57.205 39.130 4.03 0.00 44.66 2.74
3963 4158 4.142026 GGTAATAAGCAAACCATGTTCCCC 60.142 45.833 0.00 0.00 33.28 4.81
4194 4389 5.512232 CCAACTAAATCAGATAGCTCCCTCC 60.512 48.000 0.00 0.00 0.00 4.30
4516 4711 2.449518 TCTGGCCAACCACTCCCA 60.450 61.111 7.01 0.00 42.67 4.37
4744 4945 8.040727 GCAAAATTTAATGGGTTATTCACCTCT 58.959 33.333 0.00 0.00 46.38 3.69
4866 5067 2.947652 TGACCTAGCCAGTCGTATGTAC 59.052 50.000 0.00 0.00 37.04 2.90
4867 5068 2.947652 GTGACCTAGCCAGTCGTATGTA 59.052 50.000 0.00 0.00 37.04 2.29
4868 5069 1.749634 GTGACCTAGCCAGTCGTATGT 59.250 52.381 0.00 0.00 37.04 2.29
4870 5071 2.427453 CAAGTGACCTAGCCAGTCGTAT 59.573 50.000 0.00 0.00 37.04 3.06
4871 5072 1.816835 CAAGTGACCTAGCCAGTCGTA 59.183 52.381 0.00 0.00 37.04 3.43
4872 5073 0.603569 CAAGTGACCTAGCCAGTCGT 59.396 55.000 0.00 0.00 37.04 4.34
4873 5074 0.888619 TCAAGTGACCTAGCCAGTCG 59.111 55.000 0.00 0.00 37.04 4.18
5052 5389 4.336993 ACGATGCTTTTGAACACCACTTAA 59.663 37.500 0.00 0.00 0.00 1.85
5055 5392 2.297701 ACGATGCTTTTGAACACCACT 58.702 42.857 0.00 0.00 0.00 4.00
5091 5428 7.371126 TGTGCGAAATTACATATCAGTGAAA 57.629 32.000 0.00 0.00 0.00 2.69
5182 5519 3.134623 GTGGTGGGTGATACAGATGATCA 59.865 47.826 0.00 0.00 0.00 2.92
5197 5534 0.538516 TTGTCCAATTCCGTGGTGGG 60.539 55.000 0.00 0.00 39.88 4.61
5257 5594 4.529897 TCATAGCTGACATTTTGATGCCT 58.470 39.130 0.00 0.00 0.00 4.75
5930 6270 3.572255 AGAAACCAAGCTCGCCAAAAATA 59.428 39.130 0.00 0.00 0.00 1.40
6034 6374 4.588951 AGTCTTCACCTGTGTCATGAGTTA 59.411 41.667 0.00 0.00 0.00 2.24
6054 6394 4.142609 TCATGAATTACCTGCCAGAGTC 57.857 45.455 0.00 0.00 0.00 3.36
6078 6418 1.101331 AGTAGTACAGTAGCCACCGC 58.899 55.000 2.52 0.00 0.00 5.68
6080 6420 8.473219 AGTTTATAAAGTAGTACAGTAGCCACC 58.527 37.037 3.63 0.00 0.00 4.61
6105 6445 7.125755 CCATAACAAGCACACATAACGAATAG 58.874 38.462 0.00 0.00 0.00 1.73
6109 6449 3.126171 GCCATAACAAGCACACATAACGA 59.874 43.478 0.00 0.00 0.00 3.85
6127 6467 0.179000 GAAGTCCCTCACGATGCCAT 59.821 55.000 0.00 0.00 0.00 4.40
6181 6521 4.692625 CCGCAAGAGAAATGATGGTATAGG 59.307 45.833 0.00 0.00 43.02 2.57
6223 6563 2.158559 TCACATACACAACATGGGCAC 58.841 47.619 0.00 0.00 0.00 5.01
6276 6616 5.707242 TGCGGAAATGTAACCAAATGTAA 57.293 34.783 0.00 0.00 0.00 2.41
6277 6617 5.707242 TTGCGGAAATGTAACCAAATGTA 57.293 34.783 0.00 0.00 0.00 2.29
6278 6618 4.592485 TTGCGGAAATGTAACCAAATGT 57.408 36.364 0.00 0.00 0.00 2.71
6279 6619 6.329496 ACTATTGCGGAAATGTAACCAAATG 58.671 36.000 0.00 0.00 0.00 2.32
6280 6620 6.377146 AGACTATTGCGGAAATGTAACCAAAT 59.623 34.615 0.00 0.00 0.00 2.32
6281 6621 5.708230 AGACTATTGCGGAAATGTAACCAAA 59.292 36.000 0.00 0.00 0.00 3.28
6282 6622 5.250200 AGACTATTGCGGAAATGTAACCAA 58.750 37.500 0.00 0.00 0.00 3.67
6283 6623 4.839121 AGACTATTGCGGAAATGTAACCA 58.161 39.130 0.00 0.00 0.00 3.67
6284 6624 4.272748 GGAGACTATTGCGGAAATGTAACC 59.727 45.833 0.00 0.00 0.00 2.85
6285 6625 5.006746 CAGGAGACTATTGCGGAAATGTAAC 59.993 44.000 0.00 0.00 40.21 2.50
6358 6702 1.004560 CCTCCAGCGAAGACAGCAA 60.005 57.895 0.00 0.00 37.01 3.91
6411 6755 8.287350 TCTAGGGTATACAGAGAATAACCAACT 58.713 37.037 5.01 0.00 38.88 3.16
6420 6764 7.721842 CAGAACATCTCTAGGGTATACAGAGAA 59.278 40.741 19.64 8.47 45.80 2.87
6430 6778 1.273838 TGCCCAGAACATCTCTAGGGT 60.274 52.381 0.00 0.00 41.28 4.34
6431 6779 1.500474 TGCCCAGAACATCTCTAGGG 58.500 55.000 0.00 0.00 41.74 3.53
6466 6814 0.886563 GCATTCAACAGAAGCAGCCT 59.113 50.000 0.00 0.00 0.00 4.58
6468 6816 0.599558 TGGCATTCAACAGAAGCAGC 59.400 50.000 0.00 0.00 0.00 5.25
6485 6833 1.201647 CATTCAACAGAAGCAGCCTGG 59.798 52.381 3.97 0.00 36.03 4.45
6486 6834 1.402456 GCATTCAACAGAAGCAGCCTG 60.402 52.381 0.00 0.00 37.64 4.85
6487 6835 0.886563 GCATTCAACAGAAGCAGCCT 59.113 50.000 0.00 0.00 0.00 4.58
6488 6836 0.108945 GGCATTCAACAGAAGCAGCC 60.109 55.000 0.00 0.00 33.52 4.85
6489 6837 0.599558 TGGCATTCAACAGAAGCAGC 59.400 50.000 0.00 0.00 0.00 5.25
6490 6838 1.201647 CCTGGCATTCAACAGAAGCAG 59.798 52.381 0.00 0.00 36.86 4.24
6491 6839 1.250328 CCTGGCATTCAACAGAAGCA 58.750 50.000 0.00 0.00 36.86 3.91
6492 6840 0.108945 GCCTGGCATTCAACAGAAGC 60.109 55.000 15.17 0.00 36.86 3.86
6493 6841 1.471684 GAGCCTGGCATTCAACAGAAG 59.528 52.381 22.65 0.00 36.86 2.85
6494 6842 1.538047 GAGCCTGGCATTCAACAGAA 58.462 50.000 22.65 0.00 36.86 3.02
6495 6843 0.322816 GGAGCCTGGCATTCAACAGA 60.323 55.000 22.65 0.00 36.86 3.41
6496 6844 0.609957 TGGAGCCTGGCATTCAACAG 60.610 55.000 22.65 0.00 34.54 3.16
6497 6845 0.609957 CTGGAGCCTGGCATTCAACA 60.610 55.000 22.65 8.87 0.00 3.33
6498 6846 1.318158 CCTGGAGCCTGGCATTCAAC 61.318 60.000 22.65 4.50 0.00 3.18
6499 6847 1.000521 CCTGGAGCCTGGCATTCAA 60.001 57.895 22.65 2.88 0.00 2.69
6500 6848 2.679092 CCTGGAGCCTGGCATTCA 59.321 61.111 22.65 14.11 0.00 2.57
6501 6849 1.635817 TACCCTGGAGCCTGGCATTC 61.636 60.000 22.65 10.54 34.26 2.67
6502 6850 1.619363 TACCCTGGAGCCTGGCATT 60.619 57.895 22.65 0.00 34.26 3.56
6503 6851 2.042762 TACCCTGGAGCCTGGCAT 59.957 61.111 22.65 5.85 34.26 4.40
6504 6852 3.009115 GTACCCTGGAGCCTGGCA 61.009 66.667 22.65 0.00 34.26 4.92
6524 6872 7.018826 CGGTTGTTGTAACATTATGTAACCAG 58.981 38.462 19.26 11.57 38.95 4.00
6541 6889 3.627577 CCCAGGAGATTTATCGGTTGTTG 59.372 47.826 0.00 0.00 0.00 3.33
6552 6900 3.075882 TCACATTCCAACCCAGGAGATTT 59.924 43.478 0.00 0.00 39.25 2.17


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

AutoCloner maintained by Alex Coulton.