Multiple sequence alignment - TraesCS3A01G400400

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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 TraesCS3A01G400400 chr3A 100.000 4052 0 0 1 4052 647147992 647143941 0.000000e+00 7483.0
1 TraesCS3A01G400400 chr3B 91.723 3407 200 34 110 3459 672384861 672381480 0.000000e+00 4654.0
2 TraesCS3A01G400400 chr3B 96.406 640 18 2 3418 4052 672381478 672380839 0.000000e+00 1050.0
3 TraesCS3A01G400400 chr3D 86.301 2847 246 69 308 3074 510287331 510284549 0.000000e+00 2964.0
4 TraesCS3A01G400400 chr3D 90.939 309 24 4 2259 2565 510266109 510265803 2.910000e-111 412.0
5 TraesCS3A01G400400 chr3D 91.163 215 12 5 1 208 510287639 510287425 6.630000e-73 285.0
6 TraesCS3A01G400400 chr3D 83.858 254 39 1 3298 3549 510284289 510284036 1.460000e-59 241.0
7 TraesCS3A01G400400 chr1A 91.667 60 4 1 3994 4052 279840664 279840605 9.330000e-12 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 TraesCS3A01G400400 chr3A 647143941 647147992 4051 True 7483.000000 7483 100.000000 1 4052 1 chr3A.!!$R1 4051
1 TraesCS3A01G400400 chr3B 672380839 672384861 4022 True 2852.000000 4654 94.064500 110 4052 2 chr3B.!!$R1 3942
2 TraesCS3A01G400400 chr3D 510284036 510287639 3603 True 1163.333333 2964 87.107333 1 3549 3 chr3D.!!$R2 3548

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
52 53 0.034283 GAGTCACCTCCGTCCTACCT 60.034 60.0 0.0 0.0 0.0 3.08 F
67 68 0.245539 TACCTTTTGCCCTCTCGTCG 59.754 55.0 0.0 0.0 0.0 5.12 F
1109 1193 0.257039 GTGCCAGATCCACCTCCATT 59.743 55.0 0.0 0.0 0.0 3.16 F
1840 1935 0.098905 TCTCGCTCATGTGTACTCGC 59.901 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1257 0.325671 GGACCTCCTCAGGGACATCA 60.326 60.0 0.00 0.0 45.53 3.07 R
1716 1811 0.851495 GCAGACGATCTTCAGCGATG 59.149 55.0 0.83 0.0 0.00 3.84 R
2625 2746 0.991146 GGGTGCCCCATTTGGAAAAT 59.009 50.0 5.45 0.0 44.65 1.82 R
3657 3912 0.604780 CTTGACAGGCACACAGAGGG 60.605 60.0 0.00 0.0 0.00 4.30 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
29 30 3.118775 TCCTTTCCACGTGAGGACATATG 60.119 47.826 19.30 0.00 37.42 1.78
38 39 3.119495 CGTGAGGACATATGTGTGAGTCA 60.119 47.826 14.43 5.69 39.09 3.41
39 40 4.177026 GTGAGGACATATGTGTGAGTCAC 58.823 47.826 14.43 16.68 46.31 3.67
51 52 0.323178 TGAGTCACCTCCGTCCTACC 60.323 60.000 0.00 0.00 36.86 3.18
52 53 0.034283 GAGTCACCTCCGTCCTACCT 60.034 60.000 0.00 0.00 0.00 3.08
53 54 0.408700 AGTCACCTCCGTCCTACCTT 59.591 55.000 0.00 0.00 0.00 3.50
64 65 0.902531 TCCTACCTTTTGCCCTCTCG 59.097 55.000 0.00 0.00 0.00 4.04
67 68 0.245539 TACCTTTTGCCCTCTCGTCG 59.754 55.000 0.00 0.00 0.00 5.12
216 224 2.116125 GTGGCCAAGCAGGAAGGT 59.884 61.111 7.24 0.00 41.22 3.50
217 225 1.378762 GTGGCCAAGCAGGAAGGTA 59.621 57.895 7.24 0.00 41.22 3.08
218 226 0.678048 GTGGCCAAGCAGGAAGGTAG 60.678 60.000 7.24 0.00 41.22 3.18
219 227 1.750780 GGCCAAGCAGGAAGGTAGC 60.751 63.158 0.00 0.00 41.22 3.58
266 296 1.185618 TGGAGACTGAAGGGACGGTG 61.186 60.000 0.00 0.00 0.00 4.94
277 307 4.927782 GACGGTGGTGGTGCTGCA 62.928 66.667 0.00 0.00 0.00 4.41
278 308 4.935495 ACGGTGGTGGTGCTGCAG 62.935 66.667 10.11 10.11 0.00 4.41
380 419 1.428219 CAGCTGCGATTTGCTCCAG 59.572 57.895 0.00 0.00 46.63 3.86
397 437 0.612174 CAGTCCAAGTCCCCTCTCGA 60.612 60.000 0.00 0.00 0.00 4.04
418 458 2.682494 TCCCTTCTTCCCCGTCGG 60.682 66.667 3.60 3.60 0.00 4.79
439 479 0.417437 TTCCCCTCTCTGATGGTCCA 59.583 55.000 0.00 0.00 0.00 4.02
494 534 4.225573 AGGAGCTGAAGAATATCTGAGCT 58.774 43.478 11.82 11.82 42.51 4.09
541 594 7.873739 AATTTGAGAGCCGTTTAGAAATTTG 57.126 32.000 0.00 0.00 0.00 2.32
610 666 2.314549 TGATTCCCTGGTTTATGGCCTT 59.685 45.455 3.32 0.00 0.00 4.35
624 684 2.238521 TGGCCTTTGTGATGTTCTTCC 58.761 47.619 3.32 0.00 0.00 3.46
631 691 1.377202 TGATGTTCTTCCGGGCAGC 60.377 57.895 0.00 0.00 0.00 5.25
665 728 4.788925 TTTCCCTCAGAGTTCAGGAAAA 57.211 40.909 13.46 2.07 42.18 2.29
702 765 9.241317 GATGTAATTATGTGCATCTTTTCCTTG 57.759 33.333 0.00 0.00 35.96 3.61
706 769 4.525912 ATGTGCATCTTTTCCTTGAACC 57.474 40.909 0.00 0.00 0.00 3.62
716 779 7.086685 TCTTTTCCTTGAACCCACTATTACT 57.913 36.000 0.00 0.00 0.00 2.24
717 780 7.523415 TCTTTTCCTTGAACCCACTATTACTT 58.477 34.615 0.00 0.00 0.00 2.24
718 781 8.662255 TCTTTTCCTTGAACCCACTATTACTTA 58.338 33.333 0.00 0.00 0.00 2.24
719 782 9.462606 CTTTTCCTTGAACCCACTATTACTTAT 57.537 33.333 0.00 0.00 0.00 1.73
720 783 9.816787 TTTTCCTTGAACCCACTATTACTTATT 57.183 29.630 0.00 0.00 0.00 1.40
722 785 9.895138 TTCCTTGAACCCACTATTACTTATTAC 57.105 33.333 0.00 0.00 0.00 1.89
802 867 8.918202 ATTTGCCCAAGATATCGAGTAATTAA 57.082 30.769 0.00 0.00 0.00 1.40
803 868 7.724305 TTGCCCAAGATATCGAGTAATTAAC 57.276 36.000 0.00 0.00 0.00 2.01
805 870 6.929049 TGCCCAAGATATCGAGTAATTAACAG 59.071 38.462 0.00 0.00 0.00 3.16
836 901 1.404035 GCCTTACGTTATGCCTTTGGG 59.596 52.381 0.00 0.00 0.00 4.12
854 919 7.069950 GCCTTTGGGTTCTTCCATCTATTTATT 59.930 37.037 0.00 0.00 36.58 1.40
875 940 8.617290 TTATTACAACTTCTTCCTGAACCTTC 57.383 34.615 0.00 0.00 0.00 3.46
882 947 4.357918 TCTTCCTGAACCTTCCTTCAAG 57.642 45.455 0.00 0.00 29.66 3.02
937 1002 3.875134 ACAAAAACTCGAGTAGGTTGTGG 59.125 43.478 27.34 15.37 43.55 4.17
966 1031 6.256975 CAGCTCTCTTCTCTCTTGATCATTTG 59.743 42.308 0.00 0.00 0.00 2.32
968 1033 6.629963 GCTCTCTTCTCTCTTGATCATTTGGA 60.630 42.308 0.00 0.00 0.00 3.53
1062 1143 0.905839 GCACGTTCGATGTCTACGAC 59.094 55.000 13.09 1.88 39.46 4.34
1108 1192 1.918253 GTGCCAGATCCACCTCCAT 59.082 57.895 0.00 0.00 0.00 3.41
1109 1193 0.257039 GTGCCAGATCCACCTCCATT 59.743 55.000 0.00 0.00 0.00 3.16
1110 1194 1.490490 GTGCCAGATCCACCTCCATTA 59.510 52.381 0.00 0.00 0.00 1.90
1172 1256 2.325583 AAAGAGGCTCGTTGTGTTCA 57.674 45.000 14.93 0.00 0.00 3.18
1173 1257 2.550830 AAGAGGCTCGTTGTGTTCAT 57.449 45.000 9.22 0.00 0.00 2.57
1174 1258 1.800805 AGAGGCTCGTTGTGTTCATG 58.199 50.000 9.22 0.00 0.00 3.07
1193 1277 1.381872 ATGTCCCTGAGGAGGTCCG 60.382 63.158 0.00 0.00 45.21 4.79
1297 1381 4.092771 CATTCCTGCATTCTTGTGAGTG 57.907 45.455 0.00 0.00 33.70 3.51
1323 1408 6.004574 AGTTTTCTGATTCCCTTCCTGTAAC 58.995 40.000 0.00 0.00 0.00 2.50
1324 1409 5.843019 TTTCTGATTCCCTTCCTGTAACT 57.157 39.130 0.00 0.00 0.00 2.24
1333 1418 2.026822 CCTTCCTGTAACTGCCTCACAT 60.027 50.000 0.00 0.00 0.00 3.21
1337 1422 3.264193 TCCTGTAACTGCCTCACATTCAT 59.736 43.478 0.00 0.00 0.00 2.57
1357 1442 6.121776 TCATTAGAACAGAGGCAGGTTTTA 57.878 37.500 0.00 0.00 0.00 1.52
1388 1473 6.925211 TGTAAGAAGATCTTGATCACGTCTT 58.075 36.000 14.00 9.75 37.29 3.01
1389 1474 7.378966 TGTAAGAAGATCTTGATCACGTCTTT 58.621 34.615 14.00 5.82 37.29 2.52
1415 1500 1.964223 GGCATCAGATCTCCCGTTCTA 59.036 52.381 0.00 0.00 0.00 2.10
1472 1557 6.070656 TGGTTTCAGAAACATCCTGATTTCT 58.929 36.000 24.37 0.00 44.19 2.52
1492 1577 1.028868 GGTGTCCCATCTGAAGCAGC 61.029 60.000 0.00 0.00 0.00 5.25
1508 1593 0.742281 CAGCCCGTGTCTTCATCAGG 60.742 60.000 0.00 0.00 0.00 3.86
1574 1659 5.698832 TGCCTGAATGTTTATGTTTCTTCG 58.301 37.500 0.00 0.00 0.00 3.79
1593 1678 4.884668 TCGGAGTTTTCAGTATGGTCTT 57.115 40.909 0.00 0.00 36.16 3.01
1594 1679 4.817517 TCGGAGTTTTCAGTATGGTCTTC 58.182 43.478 0.00 0.00 36.16 2.87
1596 1681 5.011738 TCGGAGTTTTCAGTATGGTCTTCTT 59.988 40.000 0.00 0.00 36.16 2.52
1598 1683 6.347725 CGGAGTTTTCAGTATGGTCTTCTTTG 60.348 42.308 0.00 0.00 36.16 2.77
1599 1684 6.710744 GGAGTTTTCAGTATGGTCTTCTTTGA 59.289 38.462 0.00 0.00 36.16 2.69
1600 1685 7.308049 GGAGTTTTCAGTATGGTCTTCTTTGAC 60.308 40.741 0.00 0.00 36.16 3.18
1601 1686 7.283329 AGTTTTCAGTATGGTCTTCTTTGACT 58.717 34.615 0.00 0.00 37.16 3.41
1603 1688 6.419484 TTCAGTATGGTCTTCTTTGACTCA 57.581 37.500 0.00 0.00 37.16 3.41
1604 1689 5.784177 TCAGTATGGTCTTCTTTGACTCAC 58.216 41.667 0.00 0.00 37.16 3.51
1605 1690 5.304357 TCAGTATGGTCTTCTTTGACTCACA 59.696 40.000 0.00 0.00 37.16 3.58
1606 1691 5.406780 CAGTATGGTCTTCTTTGACTCACAC 59.593 44.000 0.00 0.00 37.16 3.82
1609 1694 3.197766 TGGTCTTCTTTGACTCACACAGT 59.802 43.478 0.00 0.00 38.45 3.55
1625 1720 2.926200 CACAGTCTAGCCTTGACATTCG 59.074 50.000 8.94 0.00 36.94 3.34
1628 1723 1.661112 GTCTAGCCTTGACATTCGTGC 59.339 52.381 1.26 0.00 34.80 5.34
1681 1776 5.647225 GGATGAGATGAAGAAATATGCCCTC 59.353 44.000 0.00 0.00 0.00 4.30
1716 1811 4.082136 ACTCTCTCATGTTTTCTCGGTACC 60.082 45.833 0.16 0.16 0.00 3.34
1758 1853 1.715993 GACCAGCTCGAGAGGTTTTC 58.284 55.000 24.97 12.93 36.98 2.29
1813 1908 1.226435 GGCTAGACTCTGTGACGCG 60.226 63.158 3.53 3.53 0.00 6.01
1831 1926 2.178890 GCCAAGGCTCTCGCTCATG 61.179 63.158 3.29 0.00 38.26 3.07
1840 1935 0.098905 TCTCGCTCATGTGTACTCGC 59.901 55.000 0.00 0.00 0.00 5.03
1891 1986 2.368875 TCTGTCAGAAGGGTGGAAAGTC 59.631 50.000 0.00 0.00 0.00 3.01
2090 2211 1.136252 CACATGACGCACACACTTAGC 60.136 52.381 0.00 0.00 0.00 3.09
2102 2223 4.273480 CACACACTTAGCATGCTTATACCC 59.727 45.833 28.02 0.00 0.00 3.69
2159 2280 8.212995 ACATATTGTCATGGTTCATACTCATCA 58.787 33.333 0.00 0.00 0.00 3.07
2166 2287 6.988580 TCATGGTTCATACTCATCATTCTCAC 59.011 38.462 0.00 0.00 0.00 3.51
2179 2300 8.344446 TCATCATTCTCACAACTGAATTTGAT 57.656 30.769 0.00 0.00 31.35 2.57
2271 2392 5.683681 TGGAAGCTCTTGTTCATATATGCA 58.316 37.500 7.92 0.00 0.00 3.96
2426 2547 2.203195 TGCTCCAACTGCAAGCGT 60.203 55.556 3.06 0.00 38.90 5.07
2521 2642 2.550180 GAGGTCTCTTGTCTTTGTTGGC 59.450 50.000 0.00 0.00 0.00 4.52
2678 2799 5.918608 TCATCTCCATAAACTGAAGGTAGC 58.081 41.667 0.00 0.00 0.00 3.58
2700 2821 4.974645 TGGACTTACCAGACAGACAAAT 57.025 40.909 0.00 0.00 44.64 2.32
2740 2866 3.477210 AGACCAGGAAGAAGAACACAC 57.523 47.619 0.00 0.00 0.00 3.82
2767 2902 1.819288 TCTAGTTGCCTTCCTCACTCG 59.181 52.381 0.00 0.00 0.00 4.18
2779 2914 0.465705 CTCACTCGCCCACCATATGT 59.534 55.000 1.24 0.00 0.00 2.29
2784 2919 0.107410 TCGCCCACCATATGTTCCAC 60.107 55.000 1.24 0.00 0.00 4.02
2947 3082 3.425492 GCATCGGAGCAAGAAAGAAGAAC 60.425 47.826 0.00 0.00 0.00 3.01
3024 3159 4.390909 TCCGTCCTAAAAGCGAGAAAAATC 59.609 41.667 0.00 0.00 0.00 2.17
3161 3362 3.575399 CAGAAGGTGCTTTTGCCAC 57.425 52.632 0.00 0.00 46.87 5.01
3230 3434 1.539827 GAGGTGGTTAACATGCGCTTT 59.460 47.619 9.73 1.43 0.00 3.51
3327 3537 6.568844 GCAATTCCAGTGGAAACGTGTTAATA 60.569 38.462 27.93 1.13 45.41 0.98
3378 3588 2.554462 GAGTAGTCAGCCAGCATATCGA 59.446 50.000 0.00 0.00 0.00 3.59
3657 3912 0.108424 AAGCTCAGCACGAGGATGAC 60.108 55.000 0.00 0.00 42.55 3.06
3668 3923 1.986413 AGGATGACCCTCTGTGTGC 59.014 57.895 0.00 0.00 43.31 4.57
3669 3924 1.078143 GGATGACCCTCTGTGTGCC 60.078 63.158 0.00 0.00 0.00 5.01
3670 3925 1.557269 GGATGACCCTCTGTGTGCCT 61.557 60.000 0.00 0.00 0.00 4.75
3691 3946 2.411748 TGTCAAGTTATCTTTGCTCGCG 59.588 45.455 0.00 0.00 0.00 5.87
3729 3984 0.106469 GGCAAGAGGGAAAGGGATCC 60.106 60.000 1.92 1.92 38.86 3.36
3742 3997 3.346146 AGGGATCCGAATAGGGAGAAA 57.654 47.619 5.45 0.00 40.02 2.52
3745 4000 2.704065 GGATCCGAATAGGGAGAAACCA 59.296 50.000 0.00 0.00 40.02 3.67
3840 4095 8.685427 CCACATACCATATCAAATTCTGTCAAA 58.315 33.333 0.00 0.00 0.00 2.69
3842 4097 9.685276 ACATACCATATCAAATTCTGTCAAAGA 57.315 29.630 0.00 0.00 0.00 2.52
3859 4114 4.023536 TCAAAGACCGAAAGCAATACCAAC 60.024 41.667 0.00 0.00 0.00 3.77
3913 4168 4.294416 TCGATAGTACTGCTTTCAGCTC 57.706 45.455 5.39 0.00 39.86 4.09
4021 4279 0.182537 ACAGTAGTGGCCACAAGCAA 59.817 50.000 36.39 14.08 46.50 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.348064 ATGTCCTCACGTGGAAAGGA 58.652 50.000 17.95 17.95 37.93 3.36
38 39 0.323957 GCAAAAGGTAGGACGGAGGT 59.676 55.000 0.00 0.00 0.00 3.85
39 40 0.392595 GGCAAAAGGTAGGACGGAGG 60.393 60.000 0.00 0.00 0.00 4.30
51 52 0.951040 AAGCGACGAGAGGGCAAAAG 60.951 55.000 0.00 0.00 37.16 2.27
52 53 0.949105 GAAGCGACGAGAGGGCAAAA 60.949 55.000 0.00 0.00 37.16 2.44
53 54 1.374252 GAAGCGACGAGAGGGCAAA 60.374 57.895 0.00 0.00 37.16 3.68
239 268 2.163509 CCTTCAGTCTCCACTCTCGAA 58.836 52.381 0.00 0.00 0.00 3.71
244 274 0.528470 CGTCCCTTCAGTCTCCACTC 59.472 60.000 0.00 0.00 0.00 3.51
277 307 1.004161 GGAAGAGAAAGAAGCTGGGCT 59.996 52.381 0.00 0.00 42.56 5.19
278 308 1.458398 GGAAGAGAAAGAAGCTGGGC 58.542 55.000 0.00 0.00 0.00 5.36
279 309 1.677217 CGGGAAGAGAAAGAAGCTGGG 60.677 57.143 0.00 0.00 0.00 4.45
280 310 1.002544 ACGGGAAGAGAAAGAAGCTGG 59.997 52.381 0.00 0.00 0.00 4.85
282 312 1.067495 CGACGGGAAGAGAAAGAAGCT 60.067 52.381 0.00 0.00 0.00 3.74
283 313 1.336980 ACGACGGGAAGAGAAAGAAGC 60.337 52.381 0.00 0.00 0.00 3.86
380 419 0.612453 ACTCGAGAGGGGACTTGGAC 60.612 60.000 21.68 0.00 44.43 4.02
397 437 0.615261 GACGGGGAAGAAGGGAGACT 60.615 60.000 0.00 0.00 0.00 3.24
418 458 1.210722 GGACCATCAGAGAGGGGAAAC 59.789 57.143 2.59 0.00 37.87 2.78
439 479 1.216990 CTATGGCTCCCAGGTCCTTT 58.783 55.000 0.00 0.00 36.75 3.11
467 507 5.068855 TCAGATATTCTTCAGCTCCTCACTG 59.931 44.000 0.00 0.00 36.44 3.66
526 566 2.606108 CCCAGCAAATTTCTAAACGGC 58.394 47.619 0.00 0.00 0.00 5.68
529 569 4.321974 CCACTCCCCAGCAAATTTCTAAAC 60.322 45.833 0.00 0.00 0.00 2.01
535 575 2.250924 CTTCCACTCCCCAGCAAATTT 58.749 47.619 0.00 0.00 0.00 1.82
541 594 1.194781 TGAGACTTCCACTCCCCAGC 61.195 60.000 0.00 0.00 33.95 4.85
610 666 0.109532 TGCCCGGAAGAACATCACAA 59.890 50.000 0.73 0.00 0.00 3.33
624 684 3.508744 ATTGTAAGAATTTGCTGCCCG 57.491 42.857 0.00 0.00 0.00 6.13
631 691 8.115490 ACTCTGAGGGAAATTGTAAGAATTTG 57.885 34.615 9.85 0.00 30.68 2.32
665 728 8.093307 TGCACATAATTACATCCATGTTGTTTT 58.907 29.630 0.00 2.85 41.97 2.43
671 734 7.828508 AAGATGCACATAATTACATCCATGT 57.171 32.000 9.16 0.00 44.48 3.21
685 748 3.259123 GGGTTCAAGGAAAAGATGCACAT 59.741 43.478 0.00 0.00 0.00 3.21
779 844 7.276658 TGTTAATTACTCGATATCTTGGGCAA 58.723 34.615 0.34 0.00 0.00 4.52
783 848 9.529325 TTCACTGTTAATTACTCGATATCTTGG 57.471 33.333 0.34 0.00 0.00 3.61
802 867 3.067106 CGTAAGGCAAGTGATTCACTGT 58.933 45.455 19.65 7.70 44.62 3.55
803 868 3.067106 ACGTAAGGCAAGTGATTCACTG 58.933 45.455 19.65 14.10 43.30 3.66
805 870 5.560148 CATAACGTAAGGCAAGTGATTCAC 58.440 41.667 8.82 8.82 46.39 3.18
854 919 4.658901 AGGAAGGTTCAGGAAGAAGTTGTA 59.341 41.667 0.00 0.00 36.78 2.41
875 940 4.389077 CGCAAGTAGTACTTTCCTTGAAGG 59.611 45.833 23.22 4.45 36.03 3.46
882 947 1.393883 GCAGCGCAAGTAGTACTTTCC 59.606 52.381 13.00 6.60 36.03 3.13
937 1002 5.132897 TCAAGAGAGAAGAGAGCTGAAAC 57.867 43.478 0.00 0.00 0.00 2.78
966 1031 0.823356 TGCTTTGACCCTGCAAGTCC 60.823 55.000 12.65 0.39 33.48 3.85
968 1033 0.825010 CCTGCTTTGACCCTGCAAGT 60.825 55.000 0.00 0.00 36.22 3.16
1108 1192 4.919774 TGCCATAAGAAGTTCCAGGTAA 57.080 40.909 0.00 0.00 0.00 2.85
1109 1193 4.843728 CTTGCCATAAGAAGTTCCAGGTA 58.156 43.478 0.00 0.00 0.00 3.08
1110 1194 3.690460 CTTGCCATAAGAAGTTCCAGGT 58.310 45.455 0.00 0.00 0.00 4.00
1172 1256 1.694048 GGACCTCCTCAGGGACATCAT 60.694 57.143 0.00 0.00 45.53 2.45
1173 1257 0.325671 GGACCTCCTCAGGGACATCA 60.326 60.000 0.00 0.00 45.53 3.07
1174 1258 1.395826 CGGACCTCCTCAGGGACATC 61.396 65.000 0.00 0.00 45.53 3.06
1193 1277 2.360475 GCCTGTTCCAGCAGTCCC 60.360 66.667 0.00 0.00 34.84 4.46
1212 1296 4.080582 TCGGCTTGATATCCTTCCAAGAAA 60.081 41.667 0.00 0.00 39.55 2.52
1297 1381 3.192212 CAGGAAGGGAATCAGAAAACTGC 59.808 47.826 0.00 0.00 0.00 4.40
1312 1397 1.347707 TGTGAGGCAGTTACAGGAAGG 59.652 52.381 0.00 0.00 0.00 3.46
1323 1408 5.181009 TCTGTTCTAATGAATGTGAGGCAG 58.819 41.667 0.00 0.00 34.40 4.85
1324 1409 5.164620 TCTGTTCTAATGAATGTGAGGCA 57.835 39.130 0.00 0.00 34.40 4.75
1333 1418 4.640771 AACCTGCCTCTGTTCTAATGAA 57.359 40.909 0.00 0.00 0.00 2.57
1337 1422 6.779860 AGATTAAAACCTGCCTCTGTTCTAA 58.220 36.000 0.00 0.00 0.00 2.10
1382 1467 2.301870 TCTGATGCCCTGTAAAAGACGT 59.698 45.455 0.00 0.00 0.00 4.34
1388 1473 2.439507 GGGAGATCTGATGCCCTGTAAA 59.560 50.000 14.81 0.00 37.59 2.01
1389 1474 2.050144 GGGAGATCTGATGCCCTGTAA 58.950 52.381 14.81 0.00 37.59 2.41
1415 1500 7.038658 ACTCTAGCTTCTTCCAACATACTTCTT 60.039 37.037 0.00 0.00 0.00 2.52
1472 1557 3.665920 GCTGCTTCAGATGGGACACCA 62.666 57.143 0.00 0.00 40.75 4.17
1492 1577 2.076863 GAAACCTGATGAAGACACGGG 58.923 52.381 0.00 0.00 0.00 5.28
1508 1593 7.591006 TTCATACCGTGAAGAATACAGAAAC 57.409 36.000 0.00 0.00 41.79 2.78
1574 1659 6.710744 TCAAAGAAGACCATACTGAAAACTCC 59.289 38.462 0.00 0.00 0.00 3.85
1599 1684 2.297597 GTCAAGGCTAGACTGTGTGAGT 59.702 50.000 0.00 0.00 37.76 3.41
1600 1685 2.297315 TGTCAAGGCTAGACTGTGTGAG 59.703 50.000 0.00 0.00 36.94 3.51
1601 1686 2.316108 TGTCAAGGCTAGACTGTGTGA 58.684 47.619 0.00 0.00 36.94 3.58
1603 1688 3.615110 CGAATGTCAAGGCTAGACTGTGT 60.615 47.826 0.00 0.00 36.94 3.72
1604 1689 2.926200 CGAATGTCAAGGCTAGACTGTG 59.074 50.000 0.00 0.00 36.94 3.66
1605 1690 2.563179 ACGAATGTCAAGGCTAGACTGT 59.437 45.455 0.00 0.00 36.94 3.55
1606 1691 2.926200 CACGAATGTCAAGGCTAGACTG 59.074 50.000 0.00 0.00 36.94 3.51
1609 1694 1.405526 GGCACGAATGTCAAGGCTAGA 60.406 52.381 0.00 0.00 0.00 2.43
1610 1695 1.009829 GGCACGAATGTCAAGGCTAG 58.990 55.000 0.00 0.00 0.00 3.42
1611 1696 3.153024 GGCACGAATGTCAAGGCTA 57.847 52.632 0.00 0.00 0.00 3.93
1612 1697 3.987404 GGCACGAATGTCAAGGCT 58.013 55.556 0.00 0.00 0.00 4.58
1625 1720 0.868406 CACCAGAGAGAAAACGGCAC 59.132 55.000 0.00 0.00 0.00 5.01
1628 1723 1.801178 GCTTCACCAGAGAGAAAACGG 59.199 52.381 0.00 0.00 0.00 4.44
1681 1776 3.510388 TGAGAGAGTACGAGCAAATGG 57.490 47.619 0.00 0.00 0.00 3.16
1716 1811 0.851495 GCAGACGATCTTCAGCGATG 59.149 55.000 0.83 0.00 0.00 3.84
1758 1853 2.093973 ACCACGTTATCAGGAGCAAGAG 60.094 50.000 0.00 0.00 0.00 2.85
1831 1926 2.159240 TCCAGTGATCATGCGAGTACAC 60.159 50.000 0.00 0.00 0.00 2.90
1840 1935 5.296283 GGTCTTGAAATCTCCAGTGATCATG 59.704 44.000 0.00 0.00 0.00 3.07
1891 1986 2.438434 GGGTTGGCCCGTCTCATG 60.438 66.667 0.00 0.00 46.51 3.07
1983 2078 7.048512 GTGGAGTAACTAGTGATTAAGCCATT 58.951 38.462 0.00 0.00 0.00 3.16
2090 2211 2.138320 CTGACAGCGGGTATAAGCATG 58.862 52.381 0.00 0.00 35.48 4.06
2102 2223 5.453587 GCAGCTATAAAATTTTCTGACAGCG 59.546 40.000 17.15 11.91 0.00 5.18
2138 2259 7.341030 AGAATGATGAGTATGAACCATGACAA 58.659 34.615 0.00 0.00 0.00 3.18
2159 2280 6.208007 TCTGCATCAAATTCAGTTGTGAGAAT 59.792 34.615 0.00 0.00 36.09 2.40
2166 2287 5.399858 CCTTCTCTGCATCAAATTCAGTTG 58.600 41.667 0.00 0.00 0.00 3.16
2179 2300 2.775890 CTCTTTCTTGCCTTCTCTGCA 58.224 47.619 0.00 0.00 36.84 4.41
2271 2392 2.125773 ATCGTCCTACAACCGTCTCT 57.874 50.000 0.00 0.00 0.00 3.10
2412 2533 1.155889 CACATACGCTTGCAGTTGGA 58.844 50.000 0.00 0.00 0.00 3.53
2465 2586 4.015406 CTGCAGGTGCCCGGTGTA 62.015 66.667 5.57 0.00 41.18 2.90
2521 2642 4.945543 TGTGTCTGAATGAAATGATCCTGG 59.054 41.667 0.00 0.00 0.00 4.45
2625 2746 0.991146 GGGTGCCCCATTTGGAAAAT 59.009 50.000 5.45 0.00 44.65 1.82
2700 2821 9.383519 CTGGTCTTCTGAATTTTAACTGCTATA 57.616 33.333 0.00 0.00 0.00 1.31
2767 2902 3.586843 TGTGGAACATATGGTGGGC 57.413 52.632 7.80 0.00 45.67 5.36
2779 2914 7.123355 ATTGAGTTCAATTTCCTTTGTGGAA 57.877 32.000 1.58 0.00 43.48 3.53
2796 2931 3.950397 TCCTATTGCGGTCAATTGAGTT 58.050 40.909 8.80 0.00 42.51 3.01
2947 3082 3.696051 CACACCAATAGGACCCATTTGAG 59.304 47.826 0.00 0.00 38.69 3.02
3024 3159 1.180029 CAATTGGCTTGAGGGGTGAG 58.820 55.000 0.00 0.00 36.97 3.51
3161 3362 1.298413 CCAGCATAGTCGTCGACCG 60.298 63.158 21.40 11.62 32.18 4.79
3193 3396 1.474677 CCTCCCATGTGCAAGCTAGAG 60.475 57.143 0.00 0.00 0.00 2.43
3230 3434 1.660560 GCGGTAGGCGAGGTCAGTAA 61.661 60.000 0.00 0.00 0.00 2.24
3295 3505 0.809385 CCACTGGAATTGCAGAGCTG 59.191 55.000 30.84 18.95 0.00 4.24
3327 3537 3.338249 ACTCTTGCGCTAACACATGAAT 58.662 40.909 9.73 0.00 0.00 2.57
3378 3588 7.609097 TTCTTCTCTGCTCCATAGTAATCAT 57.391 36.000 0.00 0.00 0.00 2.45
3657 3912 0.604780 CTTGACAGGCACACAGAGGG 60.605 60.000 0.00 0.00 0.00 4.30
3668 3923 3.181516 GCGAGCAAAGATAACTTGACAGG 60.182 47.826 0.00 0.00 36.39 4.00
3669 3924 3.482598 CGCGAGCAAAGATAACTTGACAG 60.483 47.826 0.00 0.00 36.39 3.51
3670 3925 2.411748 CGCGAGCAAAGATAACTTGACA 59.588 45.455 0.00 0.00 36.39 3.58
3700 3955 4.020617 CTCTTGCCCTCCACCGCA 62.021 66.667 0.00 0.00 0.00 5.69
3729 3984 4.515567 GCCTATTTGGTTTCTCCCTATTCG 59.484 45.833 0.00 0.00 38.35 3.34
3742 3997 1.213296 AGGTGATCGGCCTATTTGGT 58.787 50.000 0.00 0.00 38.35 3.67
3745 4000 2.771943 TGAGAAGGTGATCGGCCTATTT 59.228 45.455 0.00 0.00 34.81 1.40
3840 4095 2.224670 TGGTTGGTATTGCTTTCGGTCT 60.225 45.455 0.00 0.00 0.00 3.85
3842 4097 2.279935 TGGTTGGTATTGCTTTCGGT 57.720 45.000 0.00 0.00 0.00 4.69
3859 4114 6.774656 ACTCTCCCTTTGCTTTATATCATTGG 59.225 38.462 0.00 0.00 0.00 3.16
4008 4266 1.885887 TCTTATGTTGCTTGTGGCCAC 59.114 47.619 29.67 29.67 40.92 5.01


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

AutoCloner maintained by Alex Coulton.