Multiple sequence alignment - TraesCS3B01G331600

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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 TraesCS3B01G331600 chr3B 100.000 3878 0 0 556 4433 536983428 536987305 0.000000e+00 7162.0
1 TraesCS3B01G331600 chr3B 100.000 263 0 0 1 263 536982873 536983135 1.850000e-133 486.0
2 TraesCS3B01G331600 chr3B 93.333 60 3 1 557 615 62308030 62307971 2.200000e-13 87.9
3 TraesCS3B01G331600 chr3B 89.552 67 4 3 557 622 756117537 756117473 1.020000e-11 82.4
4 TraesCS3B01G331600 chr3B 100.000 30 0 0 1533 1562 245509906 245509877 6.190000e-04 56.5
5 TraesCS3B01G331600 chr3D 94.241 1719 80 8 2100 3803 410664709 410666423 0.000000e+00 2608.0
6 TraesCS3B01G331600 chr3D 90.757 1493 84 18 627 2103 410663173 410664627 0.000000e+00 1943.0
7 TraesCS3B01G331600 chr3D 98.596 641 6 1 3796 4433 410666599 410667239 0.000000e+00 1131.0
8 TraesCS3B01G331600 chr3D 84.364 275 28 5 1 263 410662828 410663099 5.690000e-64 255.0
9 TraesCS3B01G331600 chr3D 89.552 67 5 2 557 622 567196609 567196544 2.840000e-12 84.2
10 TraesCS3B01G331600 chr3A 93.302 1269 62 9 2099 3351 540970668 540969407 0.000000e+00 1851.0
11 TraesCS3B01G331600 chr3A 89.226 1253 74 23 662 1902 540972182 540970979 0.000000e+00 1509.0
12 TraesCS3B01G331600 chr3A 94.631 745 28 7 3696 4433 540968731 540967992 0.000000e+00 1144.0
13 TraesCS3B01G331600 chr3A 92.541 362 24 2 3337 3698 540969390 540969032 2.360000e-142 516.0
14 TraesCS3B01G331600 chr3A 96.774 217 7 0 1887 2103 540970962 540970746 3.260000e-96 363.0
15 TraesCS3B01G331600 chr4A 94.444 54 3 0 559 612 155806612 155806665 2.840000e-12 84.2
16 TraesCS3B01G331600 chr1A 96.154 52 0 2 562 612 527083975 527084025 2.840000e-12 84.2
17 TraesCS3B01G331600 chr1A 88.406 69 4 4 557 623 537097602 537097668 3.680000e-11 80.5
18 TraesCS3B01G331600 chrUn 89.552 67 4 3 557 622 320256143 320256079 1.020000e-11 82.4
19 TraesCS3B01G331600 chrUn 89.552 67 4 3 557 622 357700793 357700729 1.020000e-11 82.4
20 TraesCS3B01G331600 chr1D 86.957 69 8 1 557 624 277349070 277349002 4.750000e-10 76.8


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 TraesCS3B01G331600 chr3B 536982873 536987305 4432 False 3824.00 7162 100.0000 1 4433 2 chr3B.!!$F1 4432
1 TraesCS3B01G331600 chr3D 410662828 410667239 4411 False 1484.25 2608 91.9895 1 4433 4 chr3D.!!$F1 4432
2 TraesCS3B01G331600 chr3A 540967992 540972182 4190 True 1076.60 1851 93.2948 662 4433 5 chr3A.!!$R1 3771

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
777 820 0.399454 ACAGCAGCACTTCTGACCAT 59.601 50.0 4.28 0.0 45.72 3.55 F
1479 1539 0.238817 TTTACGTTGCGGGAACATGC 59.761 50.0 12.89 0.0 33.73 4.06 F
2018 2113 0.103937 CCTCGCCAAAAACCAAAGCA 59.896 50.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1797 1.477700 TGCGGTACTTTATGCGGTACT 59.522 47.619 0.00 0.00 38.52 2.73 R
3208 3413 0.520404 GCAGATGTGACACAAGCCAG 59.480 55.000 13.23 3.54 0.00 4.85 R
3676 3912 0.252375 AAATGCATGAGCCAGGGGTT 60.252 50.000 0.00 0.00 41.13 4.11 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
64 65 5.862924 TCTCACTGTAGCAATTGTTTAGC 57.137 39.130 7.40 0.00 0.00 3.09
134 137 9.190317 GAAGAAAATTTGTATCTATTCACCCCT 57.810 33.333 0.00 0.00 0.00 4.79
146 149 8.940012 ATCTATTCACCCCTTCTATATCCATT 57.060 34.615 0.00 0.00 0.00 3.16
147 150 8.757307 TCTATTCACCCCTTCTATATCCATTT 57.243 34.615 0.00 0.00 0.00 2.32
148 151 8.826765 TCTATTCACCCCTTCTATATCCATTTC 58.173 37.037 0.00 0.00 0.00 2.17
149 152 6.840090 TTCACCCCTTCTATATCCATTTCA 57.160 37.500 0.00 0.00 0.00 2.69
161 164 9.919416 TCTATATCCATTTCAATCCTTTCAACA 57.081 29.630 0.00 0.00 0.00 3.33
168 171 7.485913 CCATTTCAATCCTTTCAACAAGTATCG 59.514 37.037 0.00 0.00 0.00 2.92
170 173 4.941263 TCAATCCTTTCAACAAGTATCGGG 59.059 41.667 0.00 0.00 0.00 5.14
194 197 3.303461 CCTCGTGCTCTATGAGTAGAACG 60.303 52.174 0.00 0.00 40.22 3.95
195 198 3.528532 TCGTGCTCTATGAGTAGAACGA 58.471 45.455 1.52 1.52 42.98 3.85
212 225 8.138712 AGTAGAACGAGCAATTAGATTTCTAGG 58.861 37.037 0.00 0.00 0.00 3.02
234 247 2.697229 GGCCCCTCGTGTAGTAGTATTT 59.303 50.000 0.00 0.00 0.00 1.40
235 248 3.243670 GGCCCCTCGTGTAGTAGTATTTC 60.244 52.174 0.00 0.00 0.00 2.17
579 592 7.701809 GCTAAATAGTGATCTAAACGCTCTT 57.298 36.000 0.00 0.00 0.00 2.85
580 593 8.798748 GCTAAATAGTGATCTAAACGCTCTTA 57.201 34.615 0.00 0.00 0.00 2.10
581 594 9.413048 GCTAAATAGTGATCTAAACGCTCTTAT 57.587 33.333 0.00 0.00 0.00 1.73
596 609 8.608844 AACGCTCTTATATTTCTTTATGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
597 610 7.162082 ACGCTCTTATATTTCTTTATGGAGGG 58.838 38.462 0.00 0.00 35.06 4.30
598 611 7.016268 ACGCTCTTATATTTCTTTATGGAGGGA 59.984 37.037 0.00 0.00 34.22 4.20
599 612 7.547370 CGCTCTTATATTTCTTTATGGAGGGAG 59.453 40.741 0.00 0.00 33.23 4.30
600 613 8.379331 GCTCTTATATTTCTTTATGGAGGGAGT 58.621 37.037 0.00 0.00 0.00 3.85
642 685 9.546428 AAACTTGATCAACCTTCCAAAATTTAG 57.454 29.630 3.38 0.00 0.00 1.85
646 689 3.257127 TCAACCTTCCAAAATTTAGCCGG 59.743 43.478 0.00 0.00 0.00 6.13
648 691 2.176045 CCTTCCAAAATTTAGCCGGGT 58.824 47.619 12.58 12.58 0.00 5.28
692 735 9.880157 TTTAATATGGAGGTAGTACAACAACTC 57.120 33.333 2.06 0.00 0.00 3.01
730 773 4.314121 AGCAGTACAGCTCTTCTTTGAAG 58.686 43.478 6.99 1.23 42.18 3.02
731 774 4.061596 GCAGTACAGCTCTTCTTTGAAGT 58.938 43.478 2.52 0.00 0.00 3.01
774 817 2.064762 CAGTACAGCAGCACTTCTGAC 58.935 52.381 4.28 0.00 45.72 3.51
775 818 1.001406 AGTACAGCAGCACTTCTGACC 59.999 52.381 4.28 0.00 45.72 4.02
776 819 1.047801 TACAGCAGCACTTCTGACCA 58.952 50.000 4.28 0.00 45.72 4.02
777 820 0.399454 ACAGCAGCACTTCTGACCAT 59.601 50.000 4.28 0.00 45.72 3.55
798 841 5.461078 CCATGAAAAGAGCACAGAACAAAAG 59.539 40.000 0.00 0.00 0.00 2.27
854 897 1.755008 GTGGACTAGGGAGCTCGCT 60.755 63.158 32.68 32.68 42.15 4.93
914 964 2.265589 AACAGTAGTTTCCCCGGTTG 57.734 50.000 0.00 0.00 33.11 3.77
937 987 4.873129 CGCACCATCCTCCGGACG 62.873 72.222 0.00 0.00 32.98 4.79
957 1007 2.058595 GCCTCCCAGCTCCTTCGTA 61.059 63.158 0.00 0.00 0.00 3.43
958 1008 2.022240 GCCTCCCAGCTCCTTCGTAG 62.022 65.000 0.00 0.00 0.00 3.51
959 1009 1.439644 CTCCCAGCTCCTTCGTAGC 59.560 63.158 0.00 0.00 40.40 3.58
967 1017 3.835378 GCTCCTTCGTAGCTACCTATC 57.165 52.381 18.16 0.00 37.01 2.08
968 1018 2.488937 GCTCCTTCGTAGCTACCTATCC 59.511 54.545 18.16 0.00 37.01 2.59
969 1019 3.811454 GCTCCTTCGTAGCTACCTATCCT 60.811 52.174 18.16 0.00 37.01 3.24
970 1020 3.752665 TCCTTCGTAGCTACCTATCCTG 58.247 50.000 18.16 2.45 0.00 3.86
971 1021 2.229302 CCTTCGTAGCTACCTATCCTGC 59.771 54.545 18.16 0.00 0.00 4.85
972 1022 1.520494 TCGTAGCTACCTATCCTGCG 58.480 55.000 18.16 3.37 36.30 5.18
978 1028 3.497332 AGCTACCTATCCTGCGACAATA 58.503 45.455 0.00 0.00 0.00 1.90
1168 1222 1.202114 TGCTCCGGATGCAAAATTCAC 59.798 47.619 21.42 0.00 37.51 3.18
1321 1375 0.898789 GTTCGGTGAGTCTCCTCCCA 60.899 60.000 9.48 0.00 36.86 4.37
1325 1379 1.408969 GGTGAGTCTCCTCCCATCTC 58.591 60.000 3.90 0.00 36.86 2.75
1333 1387 4.917040 AGTCTCCTCCCATCTCTCACTATA 59.083 45.833 0.00 0.00 0.00 1.31
1392 1452 6.425577 AAATTTTGATTTCCGCATCAATGG 57.574 33.333 0.00 0.00 41.72 3.16
1431 1491 1.374252 AAGCGTTCGCTGTAGGTGG 60.374 57.895 20.05 0.00 41.76 4.61
1479 1539 0.238817 TTTACGTTGCGGGAACATGC 59.761 50.000 12.89 0.00 33.73 4.06
1502 1562 4.630069 CCGATTCCTTCAAACTAACGACAT 59.370 41.667 0.00 0.00 0.00 3.06
1531 1591 1.794512 CAAAATCCTTTGTTGCCGGG 58.205 50.000 2.18 0.00 37.69 5.73
1577 1637 0.874390 GCCATGCGTGTTCTGAAGAA 59.126 50.000 4.96 0.00 0.00 2.52
1592 1654 7.875041 TGTTCTGAAGAATTTTCCACAAAAACA 59.125 29.630 0.00 0.00 39.59 2.83
1650 1712 3.265737 GGCCAATGGGGTCCTAAATTTTT 59.734 43.478 0.00 0.00 39.65 1.94
1660 1722 7.356839 TGGGGTCCTAAATTTTTATATACCCCT 59.643 37.037 26.92 0.00 46.41 4.79
1702 1764 2.778679 CGAGCTGCGTTTGGCTAC 59.221 61.111 0.00 0.00 44.05 3.58
1733 1796 3.007506 TGTTAAGATCGCTCCTTTGTCCA 59.992 43.478 0.00 0.00 0.00 4.02
1734 1797 2.859165 AAGATCGCTCCTTTGTCCAA 57.141 45.000 0.00 0.00 0.00 3.53
1735 1798 2.393271 AGATCGCTCCTTTGTCCAAG 57.607 50.000 0.00 0.00 0.00 3.61
1736 1799 1.625818 AGATCGCTCCTTTGTCCAAGT 59.374 47.619 0.00 0.00 0.00 3.16
1737 1800 2.832129 AGATCGCTCCTTTGTCCAAGTA 59.168 45.455 0.00 0.00 0.00 2.24
1738 1801 2.450609 TCGCTCCTTTGTCCAAGTAC 57.549 50.000 0.00 0.00 0.00 2.73
1739 1802 1.001633 TCGCTCCTTTGTCCAAGTACC 59.998 52.381 0.00 0.00 0.00 3.34
1740 1803 1.439679 GCTCCTTTGTCCAAGTACCG 58.560 55.000 0.00 0.00 0.00 4.02
1741 1804 1.439679 CTCCTTTGTCCAAGTACCGC 58.560 55.000 0.00 0.00 0.00 5.68
1742 1805 0.759959 TCCTTTGTCCAAGTACCGCA 59.240 50.000 0.00 0.00 0.00 5.69
1743 1806 1.349688 TCCTTTGTCCAAGTACCGCAT 59.650 47.619 0.00 0.00 0.00 4.73
1744 1807 2.568062 TCCTTTGTCCAAGTACCGCATA 59.432 45.455 0.00 0.00 0.00 3.14
1799 1862 6.150976 CAGGAGTGTTAGTTTCCAAATGCATA 59.849 38.462 0.00 0.00 33.32 3.14
1807 1870 6.336842 AGTTTCCAAATGCATATCCTATGC 57.663 37.500 0.00 11.31 44.76 3.14
1820 1883 6.183360 GCATATCCTATGCAAGACATGATCAC 60.183 42.308 12.93 0.00 44.00 3.06
1833 1896 6.602278 AGACATGATCACCATTGATGAGATT 58.398 36.000 0.00 0.00 42.95 2.40
1835 1898 6.362248 ACATGATCACCATTGATGAGATTCA 58.638 36.000 0.00 0.00 42.95 2.57
1837 1900 5.747342 TGATCACCATTGATGAGATTCACA 58.253 37.500 0.00 0.00 42.95 3.58
2006 2101 1.271856 TATTCAGTTGGACCTCGCCA 58.728 50.000 0.00 0.00 35.78 5.69
2018 2113 0.103937 CCTCGCCAAAAACCAAAGCA 59.896 50.000 0.00 0.00 0.00 3.91
2062 2157 2.232696 TGGTACGCTTGTGAGAATAGCA 59.767 45.455 0.00 0.00 34.62 3.49
2369 2549 4.280174 GGTTCGGACTATATACTGCCAGAA 59.720 45.833 0.00 0.00 0.00 3.02
2440 2631 1.602377 CGGGGACAAAAAGACTGTCAC 59.398 52.381 10.88 1.18 44.91 3.67
2456 2647 5.852738 CTGTCACCAGTGTTTCTATGAAG 57.147 43.478 0.00 0.00 33.80 3.02
2462 2653 8.086522 GTCACCAGTGTTTCTATGAAGTACTTA 58.913 37.037 8.42 0.00 0.00 2.24
2862 3053 8.502387 TGTAACATTGCCATTTTTAAATGAAGC 58.498 29.630 15.02 11.45 46.72 3.86
3093 3298 4.323028 CCAGAGCTCTGTCTGAAAATACCA 60.323 45.833 35.47 0.00 46.02 3.25
3097 3302 6.059787 AGCTCTGTCTGAAAATACCATCTT 57.940 37.500 0.00 0.00 0.00 2.40
3161 3366 7.866898 CACCATGTTGTTCTATGACATTTTCAA 59.133 33.333 0.00 0.00 37.92 2.69
3187 3392 5.391312 AAGTTTCATGCTGTATTTCCACC 57.609 39.130 0.00 0.00 0.00 4.61
3208 3413 4.106197 CCACTAGCGTAACACTCTCATTC 58.894 47.826 0.00 0.00 0.00 2.67
3239 3444 4.746611 TGTCACATCTGCATCATCGATAAC 59.253 41.667 0.00 0.00 0.00 1.89
3272 3477 5.047802 CACAGGATGGCACTTACTTTTGAAT 60.048 40.000 0.00 0.00 43.62 2.57
3276 3481 6.071728 AGGATGGCACTTACTTTTGAATGAAG 60.072 38.462 0.00 0.00 0.00 3.02
3284 3489 6.547510 ACTTACTTTTGAATGAAGAGCTTGGT 59.452 34.615 0.00 0.00 0.00 3.67
3295 3500 5.404946 TGAAGAGCTTGGTATACGTGTAAC 58.595 41.667 0.00 0.00 0.00 2.50
3345 3581 9.155975 CAGCTCAAGATACTATTGTACTTTGTT 57.844 33.333 0.00 0.00 32.16 2.83
3638 3874 7.466746 TGTTCTCCCCTCATTAATTTTTCAG 57.533 36.000 0.00 0.00 0.00 3.02
3641 3877 4.340617 TCCCCTCATTAATTTTTCAGCGT 58.659 39.130 0.00 0.00 0.00 5.07
3642 3878 5.502079 TCCCCTCATTAATTTTTCAGCGTA 58.498 37.500 0.00 0.00 0.00 4.42
3658 3894 4.754618 TCAGCGTAATGTTTGAGACAACAT 59.245 37.500 0.00 0.00 42.62 2.71
3663 3899 6.582295 GCGTAATGTTTGAGACAACATTGAAT 59.418 34.615 17.95 0.00 45.83 2.57
3676 3912 7.502226 AGACAACATTGAATGGTAAAGTCAGAA 59.498 33.333 10.27 0.00 33.60 3.02
3688 3924 0.768221 AGTCAGAAACCCCTGGCTCA 60.768 55.000 0.00 0.00 45.11 4.26
3698 3934 1.187974 CCCTGGCTCATGCATTTTGA 58.812 50.000 0.00 0.00 41.91 2.69
3717 4256 2.614520 TGACGTTGGAATTTCGCAGAAA 59.385 40.909 6.26 6.26 45.90 2.52
3735 4274 5.792468 GCAGAAAAGCGAGAAAATAACTGAG 59.208 40.000 0.00 0.00 0.00 3.35
3739 4278 1.671328 GCGAGAAAATAACTGAGCCCC 59.329 52.381 0.00 0.00 0.00 5.80
3740 4279 2.289565 CGAGAAAATAACTGAGCCCCC 58.710 52.381 0.00 0.00 0.00 5.40
3741 4280 2.355716 CGAGAAAATAACTGAGCCCCCA 60.356 50.000 0.00 0.00 0.00 4.96
3751 4290 1.351017 CTGAGCCCCCAACAAACTAGA 59.649 52.381 0.00 0.00 0.00 2.43
3760 4301 2.032030 CCAACAAACTAGACTTGTGGCG 60.032 50.000 13.33 7.38 37.10 5.69
3788 4329 4.012374 GTTGCAAGATCCCAGATGAGAAA 58.988 43.478 0.00 0.00 0.00 2.52
3840 4564 3.012934 ACGGGGAAAGGAAACATATGG 57.987 47.619 7.80 0.00 0.00 2.74
3864 4588 2.664402 ACAAGGCACAGTTTCATCCT 57.336 45.000 0.00 0.00 0.00 3.24
3949 4673 7.287810 AGAAGGAACTAAAATGGTACACAACT 58.712 34.615 0.00 0.00 39.59 3.16
4180 4908 2.301870 TGTCTAAATGCCCACTCGAAGT 59.698 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.220755 ACAAGTGTACTAAATGTGTTCACAAT 57.779 30.769 9.68 0.00 32.77 2.71
111 114 9.190317 AGAAGGGGTGAATAGATACAAATTTTC 57.810 33.333 0.00 0.00 0.00 2.29
119 122 8.840200 TGGATATAGAAGGGGTGAATAGATAC 57.160 38.462 0.00 0.00 0.00 2.24
122 125 8.757307 AAATGGATATAGAAGGGGTGAATAGA 57.243 34.615 0.00 0.00 0.00 1.98
123 126 8.605947 TGAAATGGATATAGAAGGGGTGAATAG 58.394 37.037 0.00 0.00 0.00 1.73
140 143 7.307131 ACTTGTTGAAAGGATTGAAATGGAT 57.693 32.000 0.00 0.00 0.00 3.41
146 149 5.414454 CCCGATACTTGTTGAAAGGATTGAA 59.586 40.000 0.00 0.00 0.00 2.69
147 150 4.941263 CCCGATACTTGTTGAAAGGATTGA 59.059 41.667 0.00 0.00 0.00 2.57
148 151 4.700213 ACCCGATACTTGTTGAAAGGATTG 59.300 41.667 0.00 0.00 0.00 2.67
149 152 4.918588 ACCCGATACTTGTTGAAAGGATT 58.081 39.130 0.00 0.00 0.00 3.01
160 163 0.527817 GCACGAGGACCCGATACTTG 60.528 60.000 9.04 0.00 0.00 3.16
161 164 0.683504 AGCACGAGGACCCGATACTT 60.684 55.000 9.04 0.00 0.00 2.24
168 171 0.671251 CTCATAGAGCACGAGGACCC 59.329 60.000 0.00 0.00 0.00 4.46
170 173 3.468770 TCTACTCATAGAGCACGAGGAC 58.531 50.000 0.00 0.00 32.16 3.85
194 197 4.075682 GGCCCCTAGAAATCTAATTGCTC 58.924 47.826 0.00 0.00 28.94 4.26
195 198 3.181428 GGGCCCCTAGAAATCTAATTGCT 60.181 47.826 12.23 0.00 31.60 3.91
212 225 0.106519 TACTACTACACGAGGGGCCC 60.107 60.000 17.12 17.12 0.00 5.80
219 232 8.728337 ACTCATACAGAAATACTACTACACGA 57.272 34.615 0.00 0.00 0.00 4.35
555 568 7.701809 AAGAGCGTTTAGATCACTATTTAGC 57.298 36.000 0.00 0.00 37.82 3.09
570 583 9.057089 CCTCCATAAAGAAATATAAGAGCGTTT 57.943 33.333 0.00 0.00 0.00 3.60
571 584 7.661847 CCCTCCATAAAGAAATATAAGAGCGTT 59.338 37.037 0.00 0.00 0.00 4.84
572 585 7.016268 TCCCTCCATAAAGAAATATAAGAGCGT 59.984 37.037 0.00 0.00 0.00 5.07
573 586 7.386851 TCCCTCCATAAAGAAATATAAGAGCG 58.613 38.462 0.00 0.00 0.00 5.03
574 587 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
614 627 8.887036 AATTTTGGAAGGTTGATCAAGTTTAC 57.113 30.769 8.80 7.68 0.00 2.01
632 645 3.349022 TCTGTACCCGGCTAAATTTTGG 58.651 45.455 0.00 0.00 0.00 3.28
642 685 4.083484 GCATATTAACATTCTGTACCCGGC 60.083 45.833 0.00 0.00 0.00 6.13
665 708 9.886132 AGTTGTTGTACTACCTCCATATTAAAG 57.114 33.333 4.98 0.00 0.00 1.85
692 735 1.743252 GCTCAGAGTCTTTGCGGGG 60.743 63.158 0.00 0.00 0.00 5.73
721 764 9.052759 GTACTACTCATTTTCCACTTCAAAGAA 57.947 33.333 0.00 0.00 0.00 2.52
725 768 7.771361 TGTTGTACTACTCATTTTCCACTTCAA 59.229 33.333 8.88 0.00 0.00 2.69
730 773 7.699566 TGTTTGTTGTACTACTCATTTTCCAC 58.300 34.615 8.88 0.00 0.00 4.02
731 774 7.554835 ACTGTTTGTTGTACTACTCATTTTCCA 59.445 33.333 8.88 0.00 0.00 3.53
774 817 4.572985 TTGTTCTGTGCTCTTTTCATGG 57.427 40.909 0.00 0.00 0.00 3.66
775 818 5.461078 CCTTTTGTTCTGTGCTCTTTTCATG 59.539 40.000 0.00 0.00 0.00 3.07
776 819 5.452356 CCCTTTTGTTCTGTGCTCTTTTCAT 60.452 40.000 0.00 0.00 0.00 2.57
777 820 4.142182 CCCTTTTGTTCTGTGCTCTTTTCA 60.142 41.667 0.00 0.00 0.00 2.69
798 841 1.610379 AGGTTTGCAGATTGCCCCC 60.610 57.895 0.00 0.00 44.23 5.40
854 897 2.125391 GCAGCAGCGGATGTGAGA 60.125 61.111 3.61 0.00 31.62 3.27
937 987 4.847444 GAAGGAGCTGGGAGGCGC 62.847 72.222 0.00 0.00 37.29 6.53
952 1002 1.878088 CGCAGGATAGGTAGCTACGAA 59.122 52.381 17.48 8.41 0.00 3.85
957 1007 1.776662 TTGTCGCAGGATAGGTAGCT 58.223 50.000 0.00 0.00 0.00 3.32
958 1008 2.821991 ATTGTCGCAGGATAGGTAGC 57.178 50.000 0.00 0.00 0.00 3.58
959 1009 3.056749 GGGTATTGTCGCAGGATAGGTAG 60.057 52.174 0.00 0.00 0.00 3.18
960 1010 2.895404 GGGTATTGTCGCAGGATAGGTA 59.105 50.000 0.00 0.00 0.00 3.08
961 1011 1.692519 GGGTATTGTCGCAGGATAGGT 59.307 52.381 0.00 0.00 0.00 3.08
962 1012 1.691976 TGGGTATTGTCGCAGGATAGG 59.308 52.381 0.00 0.00 0.00 2.57
963 1013 3.032017 CTGGGTATTGTCGCAGGATAG 57.968 52.381 0.00 0.00 42.20 2.08
968 1018 2.173669 CGCCTGGGTATTGTCGCAG 61.174 63.158 0.00 0.00 44.38 5.18
969 1019 2.125310 CGCCTGGGTATTGTCGCA 60.125 61.111 0.00 0.00 0.00 5.10
970 1020 2.895372 CCGCCTGGGTATTGTCGC 60.895 66.667 0.00 0.00 0.00 5.19
1081 1131 0.030092 TTCGGGAGATTCCTGGGGAT 60.030 55.000 4.20 0.00 43.23 3.85
1325 1379 9.338291 GCAAATTGCAACATCATATATAGTGAG 57.662 33.333 13.73 0.00 44.26 3.51
1392 1452 7.700656 ACGCTTGTTGGATAGCATTTTATAAAC 59.299 33.333 0.00 0.00 37.23 2.01
1415 1475 1.153628 ATCCACCTACAGCGAACGC 60.154 57.895 11.31 11.31 42.33 4.84
1464 1524 4.459331 CGGCATGTTCCCGCAACG 62.459 66.667 0.00 0.00 39.22 4.10
1479 1539 3.991773 TGTCGTTAGTTTGAAGGAATCGG 59.008 43.478 0.00 0.00 0.00 4.18
1481 1541 8.797266 AAAAATGTCGTTAGTTTGAAGGAATC 57.203 30.769 0.00 0.00 0.00 2.52
1508 1568 3.553922 CCGGCAACAAAGGATTTTGCTAA 60.554 43.478 5.59 0.00 46.05 3.09
1509 1569 2.029470 CCGGCAACAAAGGATTTTGCTA 60.029 45.455 5.59 0.00 46.05 3.49
1529 1589 2.562298 TCAGAAACACATGGCAATTCCC 59.438 45.455 0.00 0.00 0.00 3.97
1531 1591 5.125100 TCTTCAGAAACACATGGCAATTC 57.875 39.130 0.00 0.00 0.00 2.17
1577 1637 6.428385 TTTGCGAATGTTTTTGTGGAAAAT 57.572 29.167 0.00 0.00 39.29 1.82
1592 1654 3.624777 AGGAGGAATGACATTTGCGAAT 58.375 40.909 1.39 0.00 0.00 3.34
1607 1669 1.798735 CGAACGTTCGCTAGGAGGA 59.201 57.895 34.54 0.00 44.26 3.71
1650 1712 7.758820 TTTCCTTTCTCAACAGGGGTATATA 57.241 36.000 0.00 0.00 0.00 0.86
1660 1722 6.474102 GCAAACGTTTATTTCCTTTCTCAACA 59.526 34.615 14.20 0.00 0.00 3.33
1733 1796 2.094078 TGCGGTACTTTATGCGGTACTT 60.094 45.455 0.00 0.00 38.52 2.24
1734 1797 1.477700 TGCGGTACTTTATGCGGTACT 59.522 47.619 0.00 0.00 38.52 2.73
1735 1798 1.925229 TGCGGTACTTTATGCGGTAC 58.075 50.000 0.00 0.00 37.97 3.34
1736 1799 2.894763 ATGCGGTACTTTATGCGGTA 57.105 45.000 0.00 0.00 0.00 4.02
1737 1800 2.894763 TATGCGGTACTTTATGCGGT 57.105 45.000 0.00 0.00 0.00 5.68
1738 1801 4.742438 ATTTATGCGGTACTTTATGCGG 57.258 40.909 0.00 0.00 0.00 5.69
1739 1802 5.985781 AGAATTTATGCGGTACTTTATGCG 58.014 37.500 0.00 0.00 0.00 4.73
1740 1803 7.913297 TCAAAGAATTTATGCGGTACTTTATGC 59.087 33.333 0.00 0.00 35.03 3.14
1741 1804 9.950680 ATCAAAGAATTTATGCGGTACTTTATG 57.049 29.630 0.00 0.00 35.03 1.90
1744 1807 9.705290 AAAATCAAAGAATTTATGCGGTACTTT 57.295 25.926 0.00 0.00 35.03 2.66
1799 1862 4.103627 TGGTGATCATGTCTTGCATAGGAT 59.896 41.667 0.00 0.00 35.74 3.24
1807 1870 5.820947 TCTCATCAATGGTGATCATGTCTTG 59.179 40.000 0.00 1.54 42.88 3.02
1835 1898 8.809066 TGCCTAATCCGTTAACTATATGTATGT 58.191 33.333 3.71 0.00 0.00 2.29
1859 1922 5.237815 TCGGAAATCACATACTATGGATGC 58.762 41.667 1.11 0.00 33.60 3.91
2006 2101 4.094146 CACATTTCCGTTGCTTTGGTTTTT 59.906 37.500 0.00 0.00 0.00 1.94
2018 2113 3.937814 TGCTCTATGACACATTTCCGTT 58.062 40.909 0.00 0.00 0.00 4.44
2062 2157 7.437713 TGAAGGTAGTCCTGTCATTATCAAT 57.562 36.000 0.00 0.00 44.35 2.57
2173 2353 4.819630 ACATTTCCTCGTTGCTAAACTTCA 59.180 37.500 0.00 0.00 33.87 3.02
2340 2520 5.050295 GCAGTATATAGTCCGAACCTTTTGC 60.050 44.000 0.00 0.00 0.00 3.68
2440 2631 9.436957 AACATAAGTACTTCATAGAAACACTGG 57.563 33.333 12.39 0.00 0.00 4.00
2632 2823 1.952102 AAGCCCAGAATGCCGCAATG 61.952 55.000 0.00 0.00 32.92 2.82
2828 3019 3.500448 TGGCAATGTTACAGTTGAGGA 57.500 42.857 10.20 0.00 0.00 3.71
2862 3053 8.665685 GGACTTGTGGTAATACAAAGATAACAG 58.334 37.037 6.70 0.00 39.81 3.16
3072 3277 5.424895 AGATGGTATTTTCAGACAGAGCTCT 59.575 40.000 11.45 11.45 0.00 4.09
3161 3366 7.147976 GTGGAAATACAGCATGAAACTTTCTT 58.852 34.615 0.00 0.00 39.69 2.52
3187 3392 4.795795 CAGAATGAGAGTGTTACGCTAGTG 59.204 45.833 0.59 0.59 39.69 2.74
3208 3413 0.520404 GCAGATGTGACACAAGCCAG 59.480 55.000 13.23 3.54 0.00 4.85
3239 3444 1.539388 TGCCATCCTGTGCGTTAAAAG 59.461 47.619 0.00 0.00 0.00 2.27
3272 3477 5.184479 AGTTACACGTATACCAAGCTCTTCA 59.816 40.000 0.00 0.00 0.00 3.02
3276 3481 4.561606 CACAGTTACACGTATACCAAGCTC 59.438 45.833 0.00 0.00 0.00 4.09
3284 3489 7.646526 GTGCATAGAATCACAGTTACACGTATA 59.353 37.037 0.00 0.00 33.63 1.47
3295 3500 6.986231 TGTAGTAATGGTGCATAGAATCACAG 59.014 38.462 0.00 0.00 35.04 3.66
3362 3598 4.082571 ACTTTTCCCTGCGAAGAATGAATG 60.083 41.667 0.00 0.00 0.00 2.67
3366 3602 3.923017 AACTTTTCCCTGCGAAGAATG 57.077 42.857 0.00 0.00 0.00 2.67
3448 3684 2.829720 TGTCGTAGGCAGGATGTACTTT 59.170 45.455 0.00 0.00 36.97 2.66
3658 3894 4.830600 GGGGTTTCTGACTTTACCATTCAA 59.169 41.667 0.00 0.00 32.20 2.69
3663 3899 2.107552 CCAGGGGTTTCTGACTTTACCA 59.892 50.000 0.00 0.00 36.93 3.25
3676 3912 0.252375 AAATGCATGAGCCAGGGGTT 60.252 50.000 0.00 0.00 41.13 4.11
3688 3924 4.385447 CGAAATTCCAACGTCAAAATGCAT 59.615 37.500 0.00 0.00 0.00 3.96
3698 3934 3.628017 CTTTTCTGCGAAATTCCAACGT 58.372 40.909 4.91 0.00 0.00 3.99
3717 4256 3.010420 GGGCTCAGTTATTTTCTCGCTT 58.990 45.455 0.00 0.00 0.00 4.68
3731 4270 1.351017 TCTAGTTTGTTGGGGGCTCAG 59.649 52.381 0.00 0.00 0.00 3.35
3735 4274 1.886542 CAAGTCTAGTTTGTTGGGGGC 59.113 52.381 0.00 0.00 0.00 5.80
3739 4278 2.032030 CGCCACAAGTCTAGTTTGTTGG 60.032 50.000 11.09 14.51 36.67 3.77
3740 4279 2.602217 GCGCCACAAGTCTAGTTTGTTG 60.602 50.000 0.00 9.72 36.67 3.33
3741 4280 1.602377 GCGCCACAAGTCTAGTTTGTT 59.398 47.619 0.00 0.00 36.67 2.83
3840 4564 4.537015 GATGAAACTGTGCCTTGTAACAC 58.463 43.478 0.00 0.00 37.31 3.32
3949 4673 1.267121 AGAGTCGCCTTTAGCCTCAA 58.733 50.000 0.00 0.00 38.78 3.02
4180 4908 2.363306 ACATCTTGTTGCTGGGAACA 57.637 45.000 3.65 3.65 39.59 3.18


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

AutoCloner maintained by Alex Coulton.