Multiple sequence alignment - TraesCS2D01G097700

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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 TraesCS2D01G097700 chr2D 100.000 5018 0 0 1 5018 49884467 49879450 0.000000e+00 9267.0
1 TraesCS2D01G097700 chr2B 94.446 2899 134 12 2086 4980 77175273 77172398 0.000000e+00 4436.0
2 TraesCS2D01G097700 chr2B 89.033 1769 111 25 1 1716 77177399 77175661 0.000000e+00 2115.0
3 TraesCS2D01G097700 chr2B 95.821 335 13 1 1723 2057 77175606 77175273 1.590000e-149 540.0
4 TraesCS2D01G097700 chr2B 83.962 212 27 2 4393 4598 1678828 1678618 3.960000e-46 196.0
5 TraesCS2D01G097700 chr2A 92.715 2114 112 19 1733 3830 51588961 51586874 0.000000e+00 3013.0
6 TraesCS2D01G097700 chr2A 94.351 1186 53 9 3826 5004 51586795 51585617 0.000000e+00 1807.0
7 TraesCS2D01G097700 chr2A 90.842 808 52 8 931 1716 51589831 51589024 0.000000e+00 1062.0
8 TraesCS2D01G097700 chr2A 87.715 757 58 14 47 794 51590560 51589830 0.000000e+00 850.0
9 TraesCS2D01G097700 chr2A 100.000 30 0 0 4989 5018 51585617 51585588 7.020000e-04 56.5
10 TraesCS2D01G097700 chr7A 86.512 215 20 5 4391 4598 605163508 605163720 1.410000e-55 228.0
11 TraesCS2D01G097700 chr7A 83.886 211 27 3 4393 4597 694564747 694564538 1.430000e-45 195.0
12 TraesCS2D01G097700 chr4B 85.915 213 21 5 4393 4598 391595573 391595363 8.460000e-53 219.0
13 TraesCS2D01G097700 chr7B 84.434 212 26 2 4393 4598 654701522 654701732 8.520000e-48 202.0


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 TraesCS2D01G097700 chr2D 49879450 49884467 5017 True 9267.000000 9267 100.0000 1 5018 1 chr2D.!!$R1 5017
1 TraesCS2D01G097700 chr2B 77172398 77177399 5001 True 2363.666667 4436 93.1000 1 4980 3 chr2B.!!$R2 4979
2 TraesCS2D01G097700 chr2A 51585588 51590560 4972 True 1357.700000 3013 93.1246 47 5018 5 chr2A.!!$R1 4971

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
312 324 0.385974 GTGCAACATTCCGTCAGCAC 60.386 55.000 0.00 0.00 45.95 4.40 F
1195 1239 0.667792 GTTGGTCGAGCAGGTCAGAC 60.668 60.000 17.81 8.22 0.00 3.51 F
1644 1697 0.536260 TGGAATACGTTACGGGTGGG 59.464 55.000 10.20 0.00 0.00 4.61 F
2778 2889 1.070134 GACCAGCGCATAACTATCCCA 59.930 52.381 11.47 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1646 0.677731 TTCTCGCCTTGCTTCCCATG 60.678 55.0 0.00 0.0 0.00 3.66 R
2671 2782 0.255890 AGAGCCACCACTTGTGTTGT 59.744 50.0 0.00 0.0 43.85 3.32 R
2991 3102 0.625849 TGCCCTTCCATTTCCTCCTC 59.374 55.0 0.00 0.0 0.00 3.71 R
4367 4571 0.103572 ACCTGTTGCTTGCTTGCTTG 59.896 50.0 3.47 0.0 0.00 4.01 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
27 28 4.357279 GGTGCTGGCTGCCTCCTT 62.357 66.667 21.03 0.00 42.00 3.36
283 295 3.853330 CCGGCTTGCGTGTCGATG 61.853 66.667 4.34 0.00 0.00 3.84
312 324 0.385974 GTGCAACATTCCGTCAGCAC 60.386 55.000 0.00 0.00 45.95 4.40
315 327 1.511850 CAACATTCCGTCAGCACAGA 58.488 50.000 0.00 0.00 0.00 3.41
332 344 1.476085 CAGACTTGCATCCTCGTCTCT 59.524 52.381 0.00 0.00 34.72 3.10
337 349 1.323271 TGCATCCTCGTCTCTCCCAC 61.323 60.000 0.00 0.00 0.00 4.61
347 359 1.078848 CTCTCCCACTTCCGCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
384 398 2.830370 GCCATGGAGCTTTCCGGG 60.830 66.667 18.40 0.00 0.00 5.73
386 400 1.000896 CCATGGAGCTTTCCGGGTT 60.001 57.895 5.56 0.00 0.00 4.11
447 478 2.852075 TTCCCTTCCCAGTGCCGT 60.852 61.111 0.00 0.00 0.00 5.68
448 479 2.457323 TTCCCTTCCCAGTGCCGTT 61.457 57.895 0.00 0.00 0.00 4.44
449 480 2.002018 TTCCCTTCCCAGTGCCGTTT 62.002 55.000 0.00 0.00 0.00 3.60
491 522 7.112779 TCTTCATCCTTTCTTGGTTAATCTCC 58.887 38.462 0.00 0.00 0.00 3.71
492 523 6.387192 TCATCCTTTCTTGGTTAATCTCCA 57.613 37.500 0.00 0.00 0.00 3.86
526 557 6.890663 TTTTTCAGCAGTTTTGACATTCAG 57.109 33.333 0.00 0.00 0.00 3.02
544 576 6.151144 ACATTCAGTTTTCTAAATCCTTCCCG 59.849 38.462 0.00 0.00 0.00 5.14
557 589 1.202580 CCTTCCCGAGGCTTACATCAG 60.203 57.143 0.00 0.00 39.09 2.90
564 596 1.153369 GGCTTACATCAGAGCGCCA 60.153 57.895 2.29 0.00 39.78 5.69
596 629 1.066143 TCCGTCTGAGATTTCAAGGGC 60.066 52.381 0.00 0.00 31.69 5.19
598 631 1.756430 GTCTGAGATTTCAAGGGCCC 58.244 55.000 16.46 16.46 31.69 5.80
599 632 1.283321 GTCTGAGATTTCAAGGGCCCT 59.717 52.381 22.28 22.28 31.69 5.19
600 633 2.505819 GTCTGAGATTTCAAGGGCCCTA 59.494 50.000 28.96 10.31 31.69 3.53
601 634 2.774234 TCTGAGATTTCAAGGGCCCTAG 59.226 50.000 28.96 15.86 31.69 3.02
760 795 4.315588 CTTCCAGGAAGCTGCAGG 57.684 61.111 16.65 0.00 32.78 4.85
803 838 5.278315 GCCGATTTGGTTTCAGTTTCTAAGT 60.278 40.000 0.00 0.00 41.21 2.24
805 840 6.017440 CCGATTTGGTTTCAGTTTCTAAGTCA 60.017 38.462 0.00 0.00 0.00 3.41
894 929 1.078567 CCCTTGCCTGAGCTGTCTC 60.079 63.158 0.00 0.00 40.80 3.36
921 956 1.688197 CCTGTGTTGGGTGCTGAATTT 59.312 47.619 0.00 0.00 0.00 1.82
966 1001 4.320608 TGTTCAAAAATGGCAGGTCTTC 57.679 40.909 0.00 0.00 0.00 2.87
1167 1211 1.338020 CTTGACAAGGCCAAGGTTCAC 59.662 52.381 5.01 0.00 37.83 3.18
1195 1239 0.667792 GTTGGTCGAGCAGGTCAGAC 60.668 60.000 17.81 8.22 0.00 3.51
1215 1259 8.284945 TCAGACCATTTTCTGATAATTTCCTG 57.715 34.615 0.00 0.00 45.79 3.86
1254 1299 6.543465 TGTTTCCTGGATATTTCACAGCATAG 59.457 38.462 0.00 0.00 0.00 2.23
1255 1300 6.499106 TTCCTGGATATTTCACAGCATAGA 57.501 37.500 0.00 0.00 0.00 1.98
1268 1313 3.054802 ACAGCATAGAGAAAGTTCCCTGG 60.055 47.826 0.00 0.00 0.00 4.45
1471 1516 2.046285 CCCCAATGTTGTCCGCCTC 61.046 63.158 0.00 0.00 0.00 4.70
1489 1541 2.291540 CCTCCATGAGGTAAAGGCCAAA 60.292 50.000 5.01 0.00 44.25 3.28
1566 1618 6.970484 ACATTCAAATCTACAGTTCACAACC 58.030 36.000 0.00 0.00 0.00 3.77
1579 1632 6.377146 ACAGTTCACAACCAACTATTTGACTT 59.623 34.615 0.00 0.00 34.24 3.01
1584 1637 6.038161 TCACAACCAACTATTTGACTTCACTG 59.962 38.462 0.00 0.00 34.24 3.66
1593 1646 6.929606 ACTATTTGACTTCACTGTAACAGGTC 59.070 38.462 0.00 0.00 35.51 3.85
1608 1661 2.409870 GGTCATGGGAAGCAAGGCG 61.410 63.158 0.00 0.00 0.00 5.52
1632 1685 7.218963 GCGAGAATTTTCATTGTTCTGGAATAC 59.781 37.037 0.00 0.00 32.67 1.89
1635 1688 8.576442 AGAATTTTCATTGTTCTGGAATACGTT 58.424 29.630 0.00 0.00 31.41 3.99
1644 1697 0.536260 TGGAATACGTTACGGGTGGG 59.464 55.000 10.20 0.00 0.00 4.61
1688 1744 7.328737 CGTTAGTACTACTGCATCTCTTGTTTT 59.671 37.037 0.91 0.00 0.00 2.43
1689 1745 8.436200 GTTAGTACTACTGCATCTCTTGTTTTG 58.564 37.037 0.91 0.00 0.00 2.44
1698 1754 6.913170 TGCATCTCTTGTTTTGTATTTCTCC 58.087 36.000 0.00 0.00 0.00 3.71
1699 1755 6.489700 TGCATCTCTTGTTTTGTATTTCTCCA 59.510 34.615 0.00 0.00 0.00 3.86
1717 1773 1.770658 CCATGATGGGAGTTAGCAGGA 59.229 52.381 2.79 0.00 32.67 3.86
1718 1774 2.374504 CCATGATGGGAGTTAGCAGGAT 59.625 50.000 2.79 0.00 32.67 3.24
1719 1775 3.584406 CCATGATGGGAGTTAGCAGGATA 59.416 47.826 2.79 0.00 32.67 2.59
1720 1776 4.226846 CCATGATGGGAGTTAGCAGGATAT 59.773 45.833 2.79 0.00 32.67 1.63
1721 1777 5.280882 CCATGATGGGAGTTAGCAGGATATT 60.281 44.000 2.79 0.00 32.67 1.28
1722 1778 5.912149 TGATGGGAGTTAGCAGGATATTT 57.088 39.130 0.00 0.00 0.00 1.40
1723 1779 6.266131 TGATGGGAGTTAGCAGGATATTTT 57.734 37.500 0.00 0.00 0.00 1.82
1724 1780 6.672593 TGATGGGAGTTAGCAGGATATTTTT 58.327 36.000 0.00 0.00 0.00 1.94
1749 1853 9.881529 TTTACACGACGCTTTTATTAATTTCTT 57.118 25.926 0.00 0.00 0.00 2.52
1816 1920 1.293924 CCCGCAGATACTTTCAGCAG 58.706 55.000 0.00 0.00 36.71 4.24
1884 1988 1.338337 AGATCTGAAGGTACATCGCCG 59.662 52.381 0.00 0.00 0.00 6.46
2060 2164 4.124238 GCAGGCGAAGGTAATAACACATA 58.876 43.478 0.00 0.00 0.00 2.29
2067 2173 7.012044 GGCGAAGGTAATAACACATAACAATCT 59.988 37.037 0.00 0.00 0.00 2.40
2080 2186 8.318412 ACACATAACAATCTTATAGACCACACA 58.682 33.333 0.00 0.00 0.00 3.72
2082 2188 9.905713 ACATAACAATCTTATAGACCACACAAT 57.094 29.630 0.00 0.00 0.00 2.71
2092 2198 4.445452 AGACCACACAATTGATTGCATC 57.555 40.909 13.59 8.47 41.38 3.91
2116 2222 8.087982 TCTCTGTAGTTTTTGTTGATGTCATC 57.912 34.615 5.83 5.83 0.00 2.92
2302 2408 4.288626 TGCTACCCAATATCCAGGTTATCC 59.711 45.833 0.00 0.00 35.02 2.59
2493 2599 6.744537 GCTGTACATTTGCATTTACTCTCTTG 59.255 38.462 0.00 0.00 0.00 3.02
2636 2743 9.263538 TCACATTCCATTTCTGAAATTTGAAAG 57.736 29.630 20.09 18.59 35.93 2.62
2666 2773 3.131046 CCAAAAGGTCAACAGAACTGCTT 59.869 43.478 1.46 0.00 27.57 3.91
2671 2782 3.327757 AGGTCAACAGAACTGCTTCCATA 59.672 43.478 1.46 0.00 0.00 2.74
2766 2877 1.154413 CATTGTCGTTGACCAGCGC 60.154 57.895 0.00 0.00 34.98 5.92
2778 2889 1.070134 GACCAGCGCATAACTATCCCA 59.930 52.381 11.47 0.00 0.00 4.37
2787 2898 5.334105 GCGCATAACTATCCCACAACTATTG 60.334 44.000 0.30 0.00 0.00 1.90
2793 2904 7.923414 AACTATCCCACAACTATTGAAAGAC 57.077 36.000 0.00 0.00 0.00 3.01
2839 2950 4.051237 GCCACCTGTTTTTGATGAGAAAC 58.949 43.478 0.00 0.00 36.53 2.78
2991 3102 4.826556 TGGTTTCCAGGAAAAACAAGTTG 58.173 39.130 16.70 0.00 38.16 3.16
3002 3113 5.985530 GGAAAAACAAGTTGAGGAGGAAATG 59.014 40.000 10.54 0.00 0.00 2.32
3032 3143 1.267732 CCAGCTTCGATGAACGCATTC 60.268 52.381 1.89 0.00 42.26 2.67
3053 3164 8.551205 GCATTCGAGTTGATATCACTGAATAAA 58.449 33.333 4.48 0.00 0.00 1.40
3062 3173 8.948631 TGATATCACTGAATAAAGGACTGAAC 57.051 34.615 0.00 0.00 0.00 3.18
3066 3177 6.698380 TCACTGAATAAAGGACTGAACCTAC 58.302 40.000 0.00 0.00 39.62 3.18
3067 3178 5.577164 CACTGAATAAAGGACTGAACCTACG 59.423 44.000 0.00 0.00 39.62 3.51
3068 3179 4.501071 TGAATAAAGGACTGAACCTACGC 58.499 43.478 0.00 0.00 39.62 4.42
3098 3209 8.650143 TTTTTGAAGCTGATAAGGTTAGGAAT 57.350 30.769 0.00 0.00 0.00 3.01
3103 3214 7.336931 TGAAGCTGATAAGGTTAGGAATTGTTC 59.663 37.037 0.00 0.00 0.00 3.18
3120 3231 1.203052 GTTCCAGCATTGTGTCCCATG 59.797 52.381 0.00 0.00 0.00 3.66
3139 3250 6.825213 TCCCATGAATCTCTTTACAACATCTG 59.175 38.462 0.00 0.00 0.00 2.90
3163 3274 9.853555 CTGTATATTTATGGCAACTTTTCACAA 57.146 29.630 0.00 0.00 37.61 3.33
3164 3275 9.853555 TGTATATTTATGGCAACTTTTCACAAG 57.146 29.630 0.00 0.00 37.61 3.16
3169 3280 2.159114 TGGCAACTTTTCACAAGAAGCC 60.159 45.455 12.19 12.19 39.40 4.35
3171 3282 3.493176 GGCAACTTTTCACAAGAAGCCAT 60.493 43.478 13.45 0.00 39.06 4.40
3178 3297 4.771590 TTCACAAGAAGCCATGCTAAAG 57.228 40.909 0.00 0.00 38.25 1.85
3265 3384 6.980593 AGAAATCATCAGTCGGATAGAAGAG 58.019 40.000 0.00 0.00 33.95 2.85
3338 3457 2.310945 CCAAGCATCCTCCCATGGATAT 59.689 50.000 15.22 0.00 44.38 1.63
3359 3478 8.129211 GGATATGACTTTTAACATAGGTTGTGC 58.871 37.037 2.37 0.00 38.99 4.57
3539 3658 4.297299 ACACAGCAGTTTGAGAAATGTG 57.703 40.909 0.00 0.00 41.68 3.21
3571 3690 9.752961 CAATGTAATGCAATTATTGATCAAGGA 57.247 29.630 14.54 5.19 41.51 3.36
3586 3705 6.962182 TGATCAAGGATGACATTTCTAGGTT 58.038 36.000 0.00 0.00 38.69 3.50
3691 3810 9.383519 CTCTTGAATATTGTGGTTCTTTAGCTA 57.616 33.333 0.00 0.00 0.00 3.32
3771 3890 8.556213 TTTTTATTCTATACAAGTGCGGAAGT 57.444 30.769 0.00 0.00 0.00 3.01
3788 3907 0.537188 AGTGCCCATGAAGGACTACG 59.463 55.000 7.87 0.00 41.22 3.51
3809 3928 3.560503 GCACACGTAATTTAAGCAAGCA 58.439 40.909 0.00 0.00 0.00 3.91
3846 4049 4.518970 TCAGTACCCAACAAAGAAGAATGC 59.481 41.667 0.00 0.00 0.00 3.56
3888 4091 6.647334 TTATTCTTGTGGTTGCAAATCAGA 57.353 33.333 0.00 0.00 37.82 3.27
3932 4135 4.946784 ACTGACTCGGCATTAATTGTTC 57.053 40.909 0.00 0.00 0.00 3.18
3942 4145 5.028375 GGCATTAATTGTTCGCAGTTCTAC 58.972 41.667 0.00 0.00 0.00 2.59
3957 4160 4.811024 CAGTTCTACAAAACACTCTCTGCA 59.189 41.667 0.00 0.00 0.00 4.41
4080 4283 9.961265 TTAGGTTCTCATGTATATAGTTGTTCG 57.039 33.333 0.00 0.00 0.00 3.95
4087 4290 9.302345 CTCATGTATATAGTTGTTCGTTGTTCT 57.698 33.333 0.00 0.00 0.00 3.01
4101 4304 4.380678 TCGTTGTTCTTTGTAGATTCGTCG 59.619 41.667 0.00 0.00 0.00 5.12
4233 4436 9.982291 GAAGGAAAGGTTAAAATTTTGTTTGTC 57.018 29.630 13.76 4.22 0.00 3.18
4238 4441 7.924103 AGGTTAAAATTTTGTTTGTCTAGCG 57.076 32.000 13.76 0.00 0.00 4.26
4242 4445 3.806316 ATTTTGTTTGTCTAGCGTCGG 57.194 42.857 0.00 0.00 0.00 4.79
4246 4449 0.388134 GTTTGTCTAGCGTCGGAGCA 60.388 55.000 5.88 0.00 40.15 4.26
4322 4526 4.920340 CGGGACTGATTTATTCTCATCTCG 59.080 45.833 0.00 0.00 0.00 4.04
4351 4555 2.934553 GCTAATACGGTGAACAAGGTCC 59.065 50.000 0.00 0.00 0.00 4.46
4391 4595 2.891112 CAAGCAAGCAACAGGTTTCAA 58.109 42.857 0.00 0.00 0.00 2.69
4410 4614 1.169577 AACACCAACGCAACTCAACA 58.830 45.000 0.00 0.00 0.00 3.33
4421 4625 2.629022 CAACTCAACAAGCGAAGTTCG 58.371 47.619 20.87 20.87 43.89 3.95
4490 4694 2.006888 CACGCCGACATTGTCCTTATT 58.993 47.619 11.12 0.00 0.00 1.40
4497 4701 4.572389 CCGACATTGTCCTTATTTCCTGAG 59.428 45.833 11.12 0.00 0.00 3.35
4524 4728 0.114954 AATTTGAGGCCTTGGGAGCA 59.885 50.000 6.77 0.00 0.00 4.26
4650 4854 9.612620 ATTCACAAGAAATTTCGACAGTTATTC 57.387 29.630 12.42 0.00 37.29 1.75
4810 5017 4.200838 TGTACAGATTTCGCCTTGATCA 57.799 40.909 0.00 0.00 0.00 2.92
4958 5166 0.809385 CATGGAACCAGAAGCAGCAG 59.191 55.000 0.00 0.00 0.00 4.24
4961 5169 1.908619 TGGAACCAGAAGCAGCAGATA 59.091 47.619 0.00 0.00 0.00 1.98
4970 5178 2.035530 AGCAGCAGATAGTTTGGAGC 57.964 50.000 0.00 0.00 0.00 4.70
4980 5188 2.957402 AGTTTGGAGCACATCTTCCA 57.043 45.000 0.00 0.00 0.00 3.53
4981 5189 3.446442 AGTTTGGAGCACATCTTCCAT 57.554 42.857 0.00 0.00 31.71 3.41
4986 5194 1.674962 GGAGCACATCTTCCATTGAGC 59.325 52.381 0.00 0.00 0.00 4.26
4987 5195 1.674962 GAGCACATCTTCCATTGAGCC 59.325 52.381 0.00 0.00 30.91 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.610327 CTCACGAGGAGGGAGGAGA 59.390 63.158 0.00 0.00 46.56 3.71
143 144 3.546815 CGAGAATTCCGGTGAATCAATGC 60.547 47.826 0.00 0.00 40.34 3.56
149 150 0.541863 AGGCGAGAATTCCGGTGAAT 59.458 50.000 15.15 0.00 43.08 2.57
312 324 1.476085 AGAGACGAGGATGCAAGTCTG 59.524 52.381 16.71 0.00 43.17 3.51
315 327 0.820871 GGAGAGACGAGGATGCAAGT 59.179 55.000 0.00 0.00 0.00 3.16
337 349 1.678970 CCCTTTCCCCAAGCGGAAG 60.679 63.158 0.00 0.00 42.81 3.46
347 359 2.094700 GCGTCATTTCTTTCCCTTTCCC 60.095 50.000 0.00 0.00 0.00 3.97
384 398 1.606601 GAGAAACCCCAGCCCCAAC 60.607 63.158 0.00 0.00 0.00 3.77
386 400 2.121506 AGAGAAACCCCAGCCCCA 60.122 61.111 0.00 0.00 0.00 4.96
447 478 3.076621 AGATTTCGTGCAGCATCTGAAA 58.923 40.909 17.53 17.53 32.44 2.69
448 479 2.703416 AGATTTCGTGCAGCATCTGAA 58.297 42.857 0.00 0.62 32.44 3.02
449 480 2.391616 AGATTTCGTGCAGCATCTGA 57.608 45.000 0.00 0.00 32.44 3.27
516 547 8.576442 GGAAGGATTTAGAAAACTGAATGTCAA 58.424 33.333 0.00 0.00 0.00 3.18
523 554 5.488341 CTCGGGAAGGATTTAGAAAACTGA 58.512 41.667 0.00 0.00 0.00 3.41
524 555 5.803020 CTCGGGAAGGATTTAGAAAACTG 57.197 43.478 0.00 0.00 0.00 3.16
526 557 4.867182 AGCCTCGGGAAGGATTTAGAAAAC 60.867 45.833 0.00 0.00 42.73 2.43
544 576 0.878086 GGCGCTCTGATGTAAGCCTC 60.878 60.000 7.64 0.00 41.21 4.70
557 589 1.265365 GATATTTTCTGCCTGGCGCTC 59.735 52.381 14.98 0.00 38.78 5.03
564 596 3.706594 TCTCAGACGGATATTTTCTGCCT 59.293 43.478 4.91 0.00 37.31 4.75
568 600 7.497249 CCTTGAAATCTCAGACGGATATTTTCT 59.503 37.037 1.59 0.00 33.80 2.52
569 601 7.254932 CCCTTGAAATCTCAGACGGATATTTTC 60.255 40.741 1.59 0.00 33.80 2.29
570 602 6.543831 CCCTTGAAATCTCAGACGGATATTTT 59.456 38.462 1.59 0.00 33.80 1.82
642 677 1.468736 GGATCTCGCCGTTAAACGTCT 60.469 52.381 0.00 0.00 40.58 4.18
643 678 0.919300 GGATCTCGCCGTTAAACGTC 59.081 55.000 0.00 0.00 40.58 4.34
665 700 3.423154 GGGGCGAAACGTCAGCAG 61.423 66.667 11.08 0.00 30.88 4.24
760 795 1.061799 CAACGTGCAAGCTTCATCGC 61.062 55.000 0.00 0.00 0.00 4.58
844 879 4.883026 CAGGACAAATGCTGCAGC 57.117 55.556 31.89 31.89 37.48 5.25
894 929 1.904865 ACCCAACACAGGCAGCATG 60.905 57.895 5.26 5.26 40.87 4.06
900 935 1.181098 ATTCAGCACCCAACACAGGC 61.181 55.000 0.00 0.00 0.00 4.85
966 1001 0.321671 TTTCCTCAAGCCAGTCTCCG 59.678 55.000 0.00 0.00 0.00 4.63
1167 1211 2.280524 TCGACCAACCCGTGCTTG 60.281 61.111 0.00 0.00 0.00 4.01
1195 1239 6.632909 TGCACAGGAAATTATCAGAAAATGG 58.367 36.000 0.00 0.00 0.00 3.16
1237 1282 8.443953 AACTTTCTCTATGCTGTGAAATATCC 57.556 34.615 0.00 0.00 31.78 2.59
1254 1299 2.363683 CATGAGCCAGGGAACTTTCTC 58.636 52.381 0.00 0.00 40.21 2.87
1255 1300 1.615384 GCATGAGCCAGGGAACTTTCT 60.615 52.381 0.00 0.00 40.21 2.52
1268 1313 5.655488 TCAGTTCTAGTAGAAAGCATGAGC 58.345 41.667 14.20 0.00 35.75 4.26
1471 1516 2.807676 AGTTTGGCCTTTACCTCATGG 58.192 47.619 3.32 0.00 39.83 3.66
1546 1598 6.119536 AGTTGGTTGTGAACTGTAGATTTGA 58.880 36.000 0.00 0.00 32.30 2.69
1550 1602 7.936847 TCAAATAGTTGGTTGTGAACTGTAGAT 59.063 33.333 2.65 0.00 35.30 1.98
1554 1606 5.885912 AGTCAAATAGTTGGTTGTGAACTGT 59.114 36.000 2.65 0.00 35.30 3.55
1560 1612 6.183360 ACAGTGAAGTCAAATAGTTGGTTGTG 60.183 38.462 2.65 0.00 35.29 3.33
1562 1614 6.377327 ACAGTGAAGTCAAATAGTTGGTTG 57.623 37.500 2.65 0.00 35.29 3.77
1566 1618 7.226720 ACCTGTTACAGTGAAGTCAAATAGTTG 59.773 37.037 11.68 0.00 35.95 3.16
1579 1632 2.615391 TCCCATGACCTGTTACAGTGA 58.385 47.619 11.68 0.00 0.00 3.41
1584 1637 2.489938 TGCTTCCCATGACCTGTTAC 57.510 50.000 0.00 0.00 0.00 2.50
1593 1646 0.677731 TTCTCGCCTTGCTTCCCATG 60.678 55.000 0.00 0.00 0.00 3.66
1608 1661 8.237267 ACGTATTCCAGAACAATGAAAATTCTC 58.763 33.333 0.00 0.00 30.17 2.87
1632 1685 3.366739 GAGCTCCCCACCCGTAACG 62.367 68.421 0.87 0.00 0.00 3.18
1635 1688 3.326385 ATGGAGCTCCCCACCCGTA 62.326 63.158 29.95 9.07 39.34 4.02
1644 1697 3.883830 ACGATGATATCATGGAGCTCC 57.116 47.619 28.20 26.78 36.57 4.70
1698 1754 3.784511 ATCCTGCTAACTCCCATCATG 57.215 47.619 0.00 0.00 0.00 3.07
1699 1755 6.460103 AAATATCCTGCTAACTCCCATCAT 57.540 37.500 0.00 0.00 0.00 2.45
1722 1778 9.881529 AGAAATTAATAAAAGCGTCGTGTAAAA 57.118 25.926 0.00 0.00 0.00 1.52
1723 1779 9.881529 AAGAAATTAATAAAAGCGTCGTGTAAA 57.118 25.926 0.00 0.00 0.00 2.01
1724 1780 9.532697 GAAGAAATTAATAAAAGCGTCGTGTAA 57.467 29.630 0.00 0.00 0.00 2.41
1726 1782 7.803724 AGAAGAAATTAATAAAAGCGTCGTGT 58.196 30.769 0.00 0.00 0.00 4.49
1727 1783 9.749490 TTAGAAGAAATTAATAAAAGCGTCGTG 57.251 29.630 0.00 0.00 0.00 4.35
1728 1784 9.750882 GTTAGAAGAAATTAATAAAAGCGTCGT 57.249 29.630 0.00 0.00 0.00 4.34
1729 1785 9.968743 AGTTAGAAGAAATTAATAAAAGCGTCG 57.031 29.630 0.00 0.00 0.00 5.12
1742 1846 7.122799 GGCCTGGTTATGAAGTTAGAAGAAATT 59.877 37.037 0.00 0.00 0.00 1.82
1749 1853 2.419574 GCGGCCTGGTTATGAAGTTAGA 60.420 50.000 0.00 0.00 0.00 2.10
1816 1920 5.003778 GCAATAATCAACAGCGTTGATCAAC 59.996 40.000 25.68 25.68 38.11 3.18
1884 1988 4.821935 CCAAGGGGTTGAGTGGTC 57.178 61.111 0.00 0.00 0.00 4.02
2023 2127 1.934399 GCCTGCTCAGATATCGCACTC 60.934 57.143 0.00 0.00 0.00 3.51
2060 2164 8.862325 TCAATTGTGTGGTCTATAAGATTGTT 57.138 30.769 5.13 0.00 0.00 2.83
2067 2173 7.643569 ATGCAATCAATTGTGTGGTCTATAA 57.356 32.000 5.13 0.00 39.88 0.98
2070 2176 5.565592 GATGCAATCAATTGTGTGGTCTA 57.434 39.130 5.13 0.00 44.70 2.59
2084 2190 7.362662 TCAACAAAAACTACAGAGATGCAATC 58.637 34.615 0.00 0.00 46.04 2.67
2092 2198 8.092521 AGATGACATCAACAAAAACTACAGAG 57.907 34.615 17.57 0.00 0.00 3.35
2116 2222 9.813446 ATCGGAGGTTACAGTTTAATAAGTTAG 57.187 33.333 0.00 0.00 0.00 2.34
2302 2408 4.393062 CGCACCATTATAGCCCTTATCTTG 59.607 45.833 0.00 0.00 0.00 3.02
2432 2538 8.192110 TGGCAATTAACGTATTTTCTTATTCCC 58.808 33.333 0.00 0.00 0.00 3.97
2493 2599 2.481795 GCTCCAGAGATCTGTCAAGAGC 60.482 54.545 17.31 17.31 42.64 4.09
2636 2743 1.269723 GTTGACCTTTTGGCTGGCTAC 59.730 52.381 2.00 0.00 45.59 3.58
2666 2773 2.857483 CCACCACTTGTGTTGTATGGA 58.143 47.619 0.00 0.00 43.85 3.41
2671 2782 0.255890 AGAGCCACCACTTGTGTTGT 59.744 50.000 0.00 0.00 43.85 3.32
2701 2812 7.589081 TCCCTAAGTAATGTAGTCATAGACCA 58.411 38.462 0.00 0.00 33.49 4.02
2723 2834 3.957591 ACCGAGTAAGAAAGAACTCCC 57.042 47.619 0.00 0.00 39.16 4.30
2766 2877 9.613428 TCTTTCAATAGTTGTGGGATAGTTATG 57.387 33.333 0.00 0.00 0.00 1.90
2778 2889 4.998051 ACCATGGGTCTTTCAATAGTTGT 58.002 39.130 18.09 0.00 0.00 3.32
2811 2922 7.118723 TCTCATCAAAAACAGGTGGCTTATAT 58.881 34.615 0.00 0.00 0.00 0.86
2814 2925 4.724399 TCTCATCAAAAACAGGTGGCTTA 58.276 39.130 0.00 0.00 0.00 3.09
2855 2966 2.098607 CCGAAAGCAGCATCAACATCAT 59.901 45.455 0.00 0.00 0.00 2.45
2896 3007 7.330208 CAGCTTTTCCAGTGAAAATAAGATTGG 59.670 37.037 0.00 0.00 46.44 3.16
2898 3009 7.955918 ACAGCTTTTCCAGTGAAAATAAGATT 58.044 30.769 0.00 0.00 46.44 2.40
2904 3015 5.509670 GGCTAACAGCTTTTCCAGTGAAAAT 60.510 40.000 0.00 0.00 46.44 1.82
2954 3065 6.183361 CCTGGAAACCATAGTAACCATCCATA 60.183 42.308 0.00 0.00 35.35 2.74
2968 3079 5.188751 TCAACTTGTTTTTCCTGGAAACCAT 59.811 36.000 21.00 5.12 36.43 3.55
2971 3082 5.105513 TCCTCAACTTGTTTTTCCTGGAAAC 60.106 40.000 21.00 12.32 37.48 2.78
2991 3102 0.625849 TGCCCTTCCATTTCCTCCTC 59.374 55.000 0.00 0.00 0.00 3.71
3002 3113 2.753446 GAAGCTGGCTGCCCTTCC 60.753 66.667 20.57 6.64 44.23 3.46
3032 3143 7.923344 AGTCCTTTATTCAGTGATATCAACTCG 59.077 37.037 7.07 0.00 0.00 4.18
3053 3164 3.418684 AAATTGCGTAGGTTCAGTCCT 57.581 42.857 0.00 0.00 41.20 3.85
3098 3209 1.327303 GGGACACAATGCTGGAACAA 58.673 50.000 0.00 0.00 38.70 2.83
3147 3258 3.493176 GGCTTCTTGTGAAAAGTTGCCAT 60.493 43.478 13.47 0.00 37.02 4.40
3149 3260 2.159114 TGGCTTCTTGTGAAAAGTTGCC 60.159 45.455 12.12 12.12 37.30 4.52
3154 3265 3.655276 AGCATGGCTTCTTGTGAAAAG 57.345 42.857 0.00 0.00 33.89 2.27
3163 3274 6.447162 GTTAACAAACTTTAGCATGGCTTCT 58.553 36.000 0.00 0.00 40.44 2.85
3164 3275 5.633601 GGTTAACAAACTTTAGCATGGCTTC 59.366 40.000 8.10 0.00 40.44 3.86
3166 3277 4.586841 TGGTTAACAAACTTTAGCATGGCT 59.413 37.500 8.10 0.00 43.41 4.75
3169 3280 7.651304 TGTCATTGGTTAACAAACTTTAGCATG 59.349 33.333 8.10 0.00 43.46 4.06
3171 3282 7.067615 TCTGTCATTGGTTAACAAACTTTAGCA 59.932 33.333 8.10 0.00 43.46 3.49
3178 3297 7.699566 TGTACTTCTGTCATTGGTTAACAAAC 58.300 34.615 8.10 0.00 43.46 2.93
3338 3457 5.057819 TCGCACAACCTATGTTAAAAGTCA 58.942 37.500 0.00 0.00 41.46 3.41
3548 3667 9.134055 TCATCCTTGATCAATAATTGCATTACA 57.866 29.630 8.96 0.00 0.00 2.41
3571 3690 6.209391 CCACTTGGAAAACCTAGAAATGTCAT 59.791 38.462 0.00 0.00 37.39 3.06
3586 3705 2.892852 CAAAGATGGAGCCACTTGGAAA 59.107 45.455 0.00 0.00 37.39 3.13
3766 3885 0.329596 AGTCCTTCATGGGCACTTCC 59.670 55.000 0.00 0.00 44.59 3.46
3767 3886 2.633488 GTAGTCCTTCATGGGCACTTC 58.367 52.381 0.00 0.00 44.59 3.01
3768 3887 1.066143 CGTAGTCCTTCATGGGCACTT 60.066 52.381 0.00 0.00 44.59 3.16
3769 3888 0.537188 CGTAGTCCTTCATGGGCACT 59.463 55.000 0.00 0.00 44.59 4.40
3770 3889 1.090052 GCGTAGTCCTTCATGGGCAC 61.090 60.000 0.00 0.00 44.59 5.01
3771 3890 1.220749 GCGTAGTCCTTCATGGGCA 59.779 57.895 0.00 0.00 44.59 5.36
3788 3907 3.560503 TGCTTGCTTAAATTACGTGTGC 58.439 40.909 0.00 0.00 0.00 4.57
3809 3928 6.182507 TGGGTACTGATTGTGTTCTAAGTT 57.817 37.500 0.00 0.00 0.00 2.66
3875 4078 7.816031 CCATTGGATATAATCTGATTTGCAACC 59.184 37.037 8.38 7.15 0.00 3.77
3888 4091 9.807921 CAGTAAGGTTTACCCATTGGATATAAT 57.192 33.333 3.62 0.00 36.42 1.28
3932 4135 4.051922 AGAGAGTGTTTTGTAGAACTGCG 58.948 43.478 0.00 0.00 0.00 5.18
3942 4145 5.929697 TTATCTGTGCAGAGAGTGTTTTG 57.070 39.130 19.31 0.00 41.33 2.44
3957 4160 5.393866 ACCCAAACAACATCCTTTATCTGT 58.606 37.500 0.00 0.00 0.00 3.41
4078 4281 4.380678 CGACGAATCTACAAAGAACAACGA 59.619 41.667 0.00 0.00 34.73 3.85
4080 4283 4.143179 CCCGACGAATCTACAAAGAACAAC 60.143 45.833 0.00 0.00 34.73 3.32
4087 4290 1.274167 AGCACCCGACGAATCTACAAA 59.726 47.619 0.00 0.00 0.00 2.83
4101 4304 4.035278 GCTCTATATACATCGAGCACCC 57.965 50.000 13.92 0.00 45.08 4.61
4233 4436 0.945099 TCAGTATGCTCCGACGCTAG 59.055 55.000 0.00 0.00 34.76 3.42
4238 4441 5.378292 TCTTGATATCAGTATGCTCCGAC 57.622 43.478 5.39 0.00 34.76 4.79
4322 4526 2.833794 TCACCGTATTAGCCTCATTGC 58.166 47.619 0.00 0.00 0.00 3.56
4351 4555 1.945394 GCTTGCTGTATCCAGATGGTG 59.055 52.381 0.00 0.00 41.50 4.17
4364 4568 0.528901 TGTTGCTTGCTTGCTTGCTG 60.529 50.000 10.35 0.00 0.00 4.41
4365 4569 0.249322 CTGTTGCTTGCTTGCTTGCT 60.249 50.000 10.35 0.00 0.00 3.91
4366 4570 1.219522 CCTGTTGCTTGCTTGCTTGC 61.220 55.000 3.47 0.00 0.00 4.01
4367 4571 0.103572 ACCTGTTGCTTGCTTGCTTG 59.896 50.000 3.47 0.00 0.00 4.01
4391 4595 1.169577 TGTTGAGTTGCGTTGGTGTT 58.830 45.000 0.00 0.00 0.00 3.32
4410 4614 1.014564 GCAGTAGCCGAACTTCGCTT 61.015 55.000 5.61 0.00 38.82 4.68
4490 4694 4.323333 CCTCAAATTCAGAGAGCTCAGGAA 60.323 45.833 17.77 15.77 35.09 3.36
4497 4701 2.416680 AGGCCTCAAATTCAGAGAGC 57.583 50.000 0.00 9.71 35.09 4.09
4524 4728 3.196469 TGGAAGATCTCAAGAACGCAGAT 59.804 43.478 0.00 0.00 0.00 2.90
4650 4854 0.745845 CTCCCCTGTCTTTCCATGCG 60.746 60.000 0.00 0.00 0.00 4.73
4810 5017 0.912486 GATGTGGCCTACAAGGACCT 59.088 55.000 3.32 0.00 45.26 3.85
4903 5110 3.430790 GGTTGAATGATTTAGGGCAAGGC 60.431 47.826 0.00 0.00 0.00 4.35
4958 5166 4.517285 TGGAAGATGTGCTCCAAACTATC 58.483 43.478 0.00 0.00 0.00 2.08
4961 5169 2.957402 TGGAAGATGTGCTCCAAACT 57.043 45.000 0.00 0.00 0.00 2.66
4970 5178 4.730949 ATTTGGCTCAATGGAAGATGTG 57.269 40.909 0.00 0.00 0.00 3.21
4980 5188 4.098894 AGGACATGGAAATTTGGCTCAAT 58.901 39.130 0.00 0.00 0.00 2.57
4981 5189 3.509442 AGGACATGGAAATTTGGCTCAA 58.491 40.909 0.00 0.00 0.00 3.02
4986 5194 9.408648 AGTATTTACTAGGACATGGAAATTTGG 57.591 33.333 0.00 0.00 34.13 3.28


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

AutoCloner maintained by Alex Coulton.