Multiple sequence alignment - TraesCS6D01G383200

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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 TraesCS6D01G383200 chr6D 100.000 4911 0 0 1 4911 462415003 462410093 0.000000e+00 9070.0
1 TraesCS6D01G383200 chr6D 91.319 2396 133 34 1741 4099 452100142 452097785 0.000000e+00 3203.0
2 TraesCS6D01G383200 chr6D 98.051 1180 23 0 176 1355 452101596 452100417 0.000000e+00 2052.0
3 TraesCS6D01G383200 chr6D 82.866 677 67 15 4252 4909 452085397 452084751 3.320000e-156 562.0
4 TraesCS6D01G383200 chr6D 90.541 148 14 0 4099 4246 452097339 452097192 3.880000e-46 196.0
5 TraesCS6D01G383200 chr6D 96.154 104 4 0 1361 1464 452100382 452100279 2.350000e-38 171.0
6 TraesCS6D01G383200 chr6D 88.889 45 5 0 4043 4087 433308779 433308735 6.870000e-04 56.5
7 TraesCS6D01G383200 chr6A 91.843 2084 110 20 1946 3992 609167735 609165675 0.000000e+00 2852.0
8 TraesCS6D01G383200 chr6A 93.811 921 45 10 3993 4911 609165571 609164661 0.000000e+00 1375.0
9 TraesCS6D01G383200 chr6A 85.363 936 61 35 399 1295 609169242 609168344 0.000000e+00 900.0
10 TraesCS6D01G383200 chr6A 90.426 470 38 4 1566 2033 609168198 609167734 3.250000e-171 612.0
11 TraesCS6D01G383200 chr6A 100.000 32 0 0 1361 1392 609168267 609168236 5.310000e-05 60.2
12 TraesCS6D01G383200 chr6B 84.870 1573 158 38 1418 2974 704881439 704879931 0.000000e+00 1513.0
13 TraesCS6D01G383200 chr6B 83.464 1403 118 50 23 1355 704882926 704881568 0.000000e+00 1201.0
14 TraesCS6D01G383200 chr6B 77.431 802 113 34 4140 4911 704873926 704873163 2.730000e-112 416.0
15 TraesCS6D01G383200 chr6B 91.892 74 6 0 1361 1434 704881534 704881461 2.420000e-18 104.0
16 TraesCS6D01G383200 chr6B 86.275 51 6 1 4043 4093 665586442 665586393 2.000000e-03 54.7
17 TraesCS6D01G383200 chr1B 88.506 174 13 3 1 168 491633927 491634099 2.320000e-48 204.0
18 TraesCS6D01G383200 chr3A 88.000 50 6 0 4048 4097 420834388 420834437 5.310000e-05 60.2
19 TraesCS6D01G383200 chr4D 100.000 31 0 0 4045 4075 490090932 490090962 1.910000e-04 58.4


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 TraesCS6D01G383200 chr6D 462410093 462415003 4910 True 9070.000000 9070 100.00000 1 4911 1 chr6D.!!$R3 4910
1 TraesCS6D01G383200 chr6D 452097192 452101596 4404 True 1405.500000 3203 94.01625 176 4246 4 chr6D.!!$R4 4070
2 TraesCS6D01G383200 chr6D 452084751 452085397 646 True 562.000000 562 82.86600 4252 4909 1 chr6D.!!$R2 657
3 TraesCS6D01G383200 chr6A 609164661 609169242 4581 True 1159.840000 2852 92.28860 399 4911 5 chr6A.!!$R1 4512
4 TraesCS6D01G383200 chr6B 704879931 704882926 2995 True 939.333333 1513 86.74200 23 2974 3 chr6B.!!$R3 2951
5 TraesCS6D01G383200 chr6B 704873163 704873926 763 True 416.000000 416 77.43100 4140 4911 1 chr6B.!!$R2 771

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
75 76 0.035458 GCTGCAGACGCCCCTTATAT 59.965 55.000 20.43 0.0 37.32 0.86 F
140 141 0.531532 GGCGACCATCCAGTCATCAG 60.532 60.000 0.00 0.0 36.52 2.90 F
142 143 0.531532 CGACCATCCAGTCATCAGCC 60.532 60.000 0.00 0.0 36.52 4.85 F
170 171 1.152694 ATCGCCATGACCCCATTGG 60.153 57.895 0.00 0.0 41.37 3.16 F
1857 2021 1.227704 TTGTGCCGGTGATTCGTGT 60.228 52.632 1.90 0.0 0.00 4.49 F
2936 3194 0.040067 GCCACGAGGTTTGCTTGAAG 60.040 55.000 0.00 0.0 37.19 3.02 F
3821 4140 0.459585 GGCGAAAGATACCACTGCGA 60.460 55.000 0.00 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2092 0.694444 ACACAGACAAGGGGACAGGT 60.694 55.000 0.00 0.00 0.00 4.00 R
2030 2285 1.397672 TCATCTCGAGAGAAGCCCAG 58.602 55.000 21.52 3.38 41.36 4.45 R
2031 2286 2.079170 ATCATCTCGAGAGAAGCCCA 57.921 50.000 21.52 0.00 41.36 5.36 R
2135 2393 4.873010 AGAGGTAGGAGCTTCATCAGTAA 58.127 43.478 0.00 0.00 0.00 2.24 R
3838 4157 1.194547 GGGCACGCGTACATGATATTG 59.805 52.381 13.44 0.00 0.00 1.90 R
3882 4201 0.179045 ACAGGCAAGCAACTTCGTCT 60.179 50.000 0.00 0.00 0.00 4.18 R
4731 5634 3.008594 TGAGCGAACAATTTCCTAAGGGA 59.991 43.478 0.00 0.00 40.36 4.20 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
21 22 3.664107 GACACATGAACCTAAGCACAGA 58.336 45.455 0.00 0.00 0.00 3.41
27 28 4.727507 TGAACCTAAGCACAGAGATCTC 57.272 45.455 15.29 15.29 0.00 2.75
73 74 2.190578 GCTGCAGACGCCCCTTAT 59.809 61.111 20.43 0.00 37.32 1.73
74 75 1.445942 GCTGCAGACGCCCCTTATA 59.554 57.895 20.43 0.00 37.32 0.98
75 76 0.035458 GCTGCAGACGCCCCTTATAT 59.965 55.000 20.43 0.00 37.32 0.86
76 77 1.800805 CTGCAGACGCCCCTTATATG 58.199 55.000 8.42 0.00 37.32 1.78
89 90 6.457799 CGCCCCTTATATGTAGTCAAACAAAC 60.458 42.308 0.00 0.00 32.02 2.93
92 93 6.182634 CCTTATATGTAGTCAAACAAACGCG 58.817 40.000 3.53 3.53 32.02 6.01
110 111 1.406341 GCGGGCATAACTAGAACACCA 60.406 52.381 0.00 0.00 0.00 4.17
111 112 2.550978 CGGGCATAACTAGAACACCAG 58.449 52.381 0.00 0.00 0.00 4.00
114 115 2.092914 GGCATAACTAGAACACCAGGCT 60.093 50.000 0.00 0.00 0.00 4.58
117 118 2.841442 AACTAGAACACCAGGCTGAC 57.159 50.000 17.94 1.98 0.00 3.51
120 121 1.620819 CTAGAACACCAGGCTGACAGT 59.379 52.381 17.94 8.35 0.00 3.55
123 124 2.670934 CACCAGGCTGACAGTGGC 60.671 66.667 17.94 0.00 34.40 5.01
127 128 4.008933 AGGCTGACAGTGGCGACC 62.009 66.667 3.99 0.00 35.01 4.79
129 130 2.046892 GCTGACAGTGGCGACCAT 60.047 61.111 3.99 0.00 35.28 3.55
131 132 1.448540 CTGACAGTGGCGACCATCC 60.449 63.158 0.00 0.00 35.28 3.51
139 140 1.264045 TGGCGACCATCCAGTCATCA 61.264 55.000 0.00 0.00 36.52 3.07
140 141 0.531532 GGCGACCATCCAGTCATCAG 60.532 60.000 0.00 0.00 36.52 2.90
141 142 1.156645 GCGACCATCCAGTCATCAGC 61.157 60.000 0.00 0.00 36.52 4.26
142 143 0.531532 CGACCATCCAGTCATCAGCC 60.532 60.000 0.00 0.00 36.52 4.85
149 150 2.110967 CAGTCATCAGCCGGCAAGG 61.111 63.158 31.54 18.32 44.97 3.61
168 169 1.829533 GCATCGCCATGACCCCATT 60.830 57.895 0.00 0.00 30.57 3.16
170 171 1.152694 ATCGCCATGACCCCATTGG 60.153 57.895 0.00 0.00 41.37 3.16
213 226 2.911143 CCGCTCCCAGCAACCTAT 59.089 61.111 0.00 0.00 42.58 2.57
224 237 3.136443 CCAGCAACCTATCCAATCCACTA 59.864 47.826 0.00 0.00 0.00 2.74
297 310 5.511373 CCAGAGTAACAAACAGATCACCTCA 60.511 44.000 0.00 0.00 0.00 3.86
1001 1059 2.417515 CCAGTTCCTCTTCTCTTACCGC 60.418 54.545 0.00 0.00 0.00 5.68
1355 1436 1.608590 TGCTTAGTTTCAGCAACCAGC 59.391 47.619 0.00 0.00 44.42 4.85
1430 1540 7.398047 TGGTTTTCCTGCTAGTAGTACTGATAA 59.602 37.037 13.29 0.54 41.38 1.75
1480 1628 4.952071 TGTTCTTTGCCCAATTGAATGA 57.048 36.364 7.12 0.00 0.00 2.57
1481 1629 4.630111 TGTTCTTTGCCCAATTGAATGAC 58.370 39.130 7.12 0.00 0.00 3.06
1483 1631 3.509442 TCTTTGCCCAATTGAATGACCT 58.491 40.909 7.12 0.00 0.00 3.85
1484 1632 3.511146 TCTTTGCCCAATTGAATGACCTC 59.489 43.478 7.12 0.00 0.00 3.85
1485 1633 2.601240 TGCCCAATTGAATGACCTCA 57.399 45.000 7.12 0.00 0.00 3.86
1486 1634 2.886913 TGCCCAATTGAATGACCTCAA 58.113 42.857 7.12 0.00 39.56 3.02
1487 1635 2.562298 TGCCCAATTGAATGACCTCAAC 59.438 45.455 7.12 0.00 38.12 3.18
1488 1636 2.827921 GCCCAATTGAATGACCTCAACT 59.172 45.455 7.12 0.00 38.12 3.16
1502 1652 2.293399 CCTCAACTGTTTGGTTGGTAGC 59.707 50.000 7.37 0.00 44.52 3.58
1508 1658 3.003480 CTGTTTGGTTGGTAGCTAGCTC 58.997 50.000 23.26 12.82 0.00 4.09
1510 1660 1.651737 TTGGTTGGTAGCTAGCTCCA 58.348 50.000 23.26 23.60 0.00 3.86
1512 1662 3.040655 TGGTTGGTAGCTAGCTCCATA 57.959 47.619 26.41 18.01 0.00 2.74
1517 1667 5.233988 GTTGGTAGCTAGCTCCATATTGAG 58.766 45.833 26.41 0.00 35.40 3.02
1521 1671 6.126768 TGGTAGCTAGCTCCATATTGAGTTTT 60.127 38.462 23.26 0.00 34.74 2.43
1528 1678 9.553064 CTAGCTCCATATTGAGTTTTAATCTGT 57.447 33.333 5.75 0.00 34.74 3.41
1532 1682 9.778993 CTCCATATTGAGTTTTAATCTGTGTTG 57.221 33.333 0.00 0.00 0.00 3.33
1540 1690 5.711976 AGTTTTAATCTGTGTTGGCAGCTAT 59.288 36.000 2.28 0.00 36.49 2.97
1541 1691 6.884295 AGTTTTAATCTGTGTTGGCAGCTATA 59.116 34.615 2.28 0.00 36.49 1.31
1547 1703 4.002982 CTGTGTTGGCAGCTATAGTGAAA 58.997 43.478 2.28 0.00 0.00 2.69
1551 1707 5.801947 GTGTTGGCAGCTATAGTGAAATTTG 59.198 40.000 2.28 0.00 0.00 2.32
1587 1751 2.513204 CGCCCCTGACTGAGCATG 60.513 66.667 0.00 0.00 0.00 4.06
1613 1777 6.605471 TCTCAAGAGCCTGTATTAGTTGAA 57.395 37.500 0.00 0.00 0.00 2.69
1617 1781 7.624549 TCAAGAGCCTGTATTAGTTGAATCTT 58.375 34.615 0.00 0.00 0.00 2.40
1644 1808 2.226962 AATGCAGGTTGAGCTTGGAT 57.773 45.000 0.00 0.00 36.84 3.41
1645 1809 2.226962 ATGCAGGTTGAGCTTGGATT 57.773 45.000 0.00 0.00 31.54 3.01
1650 1814 2.624838 CAGGTTGAGCTTGGATTGTTGT 59.375 45.455 0.00 0.00 0.00 3.32
1652 1816 2.887152 GGTTGAGCTTGGATTGTTGTCT 59.113 45.455 0.00 0.00 0.00 3.41
1674 1838 6.039493 GTCTTCCATGAAATCTGATGCTTCAT 59.961 38.462 10.39 10.39 39.74 2.57
1683 1847 7.609146 TGAAATCTGATGCTTCATTTGTCTAGT 59.391 33.333 2.33 0.00 0.00 2.57
1720 1884 5.273944 CGCCTTTCATCCATTTAGTTTAGC 58.726 41.667 0.00 0.00 0.00 3.09
1723 1887 6.753744 GCCTTTCATCCATTTAGTTTAGCTTG 59.246 38.462 0.00 0.00 0.00 4.01
1724 1888 7.362920 GCCTTTCATCCATTTAGTTTAGCTTGA 60.363 37.037 0.00 0.00 0.00 3.02
1725 1889 8.522830 CCTTTCATCCATTTAGTTTAGCTTGAA 58.477 33.333 0.00 0.00 0.00 2.69
1728 1892 8.268850 TCATCCATTTAGTTTAGCTTGAAGTC 57.731 34.615 0.00 0.00 0.00 3.01
1732 1896 9.383519 TCCATTTAGTTTAGCTTGAAGTCTATG 57.616 33.333 0.00 0.00 0.00 2.23
1735 1899 7.834068 TTAGTTTAGCTTGAAGTCTATGCAG 57.166 36.000 0.00 0.00 0.00 4.41
1846 2010 4.142708 TGTGTTTATTATCTGCTTGTGCCG 60.143 41.667 0.00 0.00 38.71 5.69
1857 2021 1.227704 TTGTGCCGGTGATTCGTGT 60.228 52.632 1.90 0.00 0.00 4.49
1878 2042 6.642950 CGTGTGGATGGATATCTCTAAGAAAC 59.357 42.308 2.05 0.00 33.68 2.78
1902 2070 3.199727 TGGAATGCTAGCACCTTGTATGA 59.800 43.478 22.07 0.00 0.00 2.15
1954 2122 5.046591 CCCCTTGTCTGTGTATGTTTCTCTA 60.047 44.000 0.00 0.00 0.00 2.43
2066 2324 9.664332 CTCGAGATGATATTCCATTAGGATTTT 57.336 33.333 6.58 0.00 45.26 1.82
2153 2411 6.446318 CAGATCTTACTGATGAAGCTCCTAC 58.554 44.000 0.00 0.00 39.94 3.18
2207 2465 4.974368 TTACTGAAAATTATGTGCCCGG 57.026 40.909 0.00 0.00 0.00 5.73
2216 2474 3.358111 TTATGTGCCCGGAAGAAATGA 57.642 42.857 0.73 0.00 0.00 2.57
2221 2479 4.082845 TGTGCCCGGAAGAAATGATTTAA 58.917 39.130 0.73 0.00 0.00 1.52
2361 2619 3.521531 AGGGAGTTCTCAAGGATCTTTCC 59.478 47.826 2.24 0.00 42.96 3.13
2418 2676 8.023021 ACCATCACAGAAGCTAATGTTATCTA 57.977 34.615 1.10 0.00 0.00 1.98
2653 2911 7.484035 ACAATTTCGCCTTATCTATCAGTTC 57.516 36.000 0.00 0.00 0.00 3.01
2732 2990 7.812309 TTGAAGACAAGTCTATATGTGTTCG 57.188 36.000 2.72 0.00 46.82 3.95
2782 3040 9.372369 GATATTACTAGCATGGTGGATACTTTC 57.628 37.037 15.72 1.49 37.61 2.62
2840 3098 4.404507 TGAACGTTATGCAGCTCTTTTC 57.595 40.909 0.00 0.00 0.00 2.29
2894 3152 3.988976 TCTGCTGTTATTGAGGCTCTT 57.011 42.857 16.72 5.93 0.00 2.85
2936 3194 0.040067 GCCACGAGGTTTGCTTGAAG 60.040 55.000 0.00 0.00 37.19 3.02
3040 3337 5.882557 TGGCATGCTAAAGAAAAACCAAAAA 59.117 32.000 18.92 0.00 0.00 1.94
3333 3630 3.740115 GGTAACTGACACCACATGACTT 58.260 45.455 0.00 0.00 36.01 3.01
3341 3638 1.267806 CACCACATGACTTTGCCAGAC 59.732 52.381 0.00 0.00 0.00 3.51
3445 3758 2.521126 GAATTTTCCAAGGACCCCGAA 58.479 47.619 0.00 0.00 0.00 4.30
3472 3785 1.876156 GTCTCCCAAAGCTGTGAAGTG 59.124 52.381 5.12 0.00 0.00 3.16
3607 3921 6.739550 GCGTAAATGTTAACATGTGTACCTTC 59.260 38.462 21.46 10.63 36.56 3.46
3634 3948 2.408050 CAGTTTCTGTTCCTCCAGACG 58.592 52.381 0.00 0.00 41.05 4.18
3640 3954 1.118965 TGTTCCTCCAGACGCCTCAA 61.119 55.000 0.00 0.00 0.00 3.02
3670 3984 4.087892 TCCTGAGCCCAGCTTCGC 62.088 66.667 0.00 0.00 39.88 4.70
3757 4071 1.301479 GTGTCGTCGCCCTTTTCCT 60.301 57.895 0.00 0.00 0.00 3.36
3796 4115 1.220749 GCTTGACACCGGGATAGCA 59.779 57.895 6.32 0.00 0.00 3.49
3819 4138 0.739813 ACGGCGAAAGATACCACTGC 60.740 55.000 16.62 0.00 0.00 4.40
3821 4140 0.459585 GGCGAAAGATACCACTGCGA 60.460 55.000 0.00 0.00 0.00 5.10
3838 4157 2.674852 TGCGAAATTGCTCTCTGATGAC 59.325 45.455 0.00 0.00 35.36 3.06
3882 4201 6.425721 CCCGTGAAAACAGAAACTGATACTTA 59.574 38.462 5.76 0.00 35.18 2.24
3889 4208 8.522178 AAACAGAAACTGATACTTAGACGAAG 57.478 34.615 5.76 0.00 36.90 3.79
3893 4212 6.586844 AGAAACTGATACTTAGACGAAGTTGC 59.413 38.462 6.26 0.69 46.79 4.17
3981 4307 5.991933 ACTATCACACTGTCACAGAAGAT 57.008 39.130 13.14 13.22 35.18 2.40
4052 4481 8.512138 CAAATCAAGTATACCTCTTCCGTTTTT 58.488 33.333 0.00 0.00 0.00 1.94
4064 4493 8.370182 ACCTCTTCCGTTTTTATTTACTCTGTA 58.630 33.333 0.00 0.00 0.00 2.74
4171 5046 4.037803 GGTTTAAGGAAAAACCGTGCCTTA 59.962 41.667 2.97 0.00 46.51 2.69
4235 5111 3.238108 TCGATCAAAGCAAGAGAGACC 57.762 47.619 0.00 0.00 0.00 3.85
4249 5125 2.597510 GACCAACAAAGGCGCCCT 60.598 61.111 26.15 7.54 33.87 5.19
4331 5226 6.438425 AGGAGGGTCTATTGTTAGTTCGTTTA 59.562 38.462 0.00 0.00 0.00 2.01
4423 5322 8.970691 ACATTACATAAATTTTCTGAGCACAC 57.029 30.769 0.00 0.00 0.00 3.82
4763 5666 7.382218 AGGAAATTGTTCGCTCATTTGTAAAAG 59.618 33.333 0.00 0.00 34.28 2.27
4785 5688 8.940768 AAAGAATGTTCGAATTTCTGGAAAAA 57.059 26.923 20.44 0.00 33.56 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.664107 TCTGTGCTTAGGTTCATGTGTC 58.336 45.455 0.00 0.00 0.00 3.67
1 2 3.324846 TCTCTGTGCTTAGGTTCATGTGT 59.675 43.478 0.00 0.00 0.00 3.72
2 3 3.930336 TCTCTGTGCTTAGGTTCATGTG 58.070 45.455 0.00 0.00 0.00 3.21
3 4 4.469227 AGATCTCTGTGCTTAGGTTCATGT 59.531 41.667 0.00 0.00 0.00 3.21
4 5 5.021033 AGATCTCTGTGCTTAGGTTCATG 57.979 43.478 0.00 0.00 0.00 3.07
5 6 4.961730 AGAGATCTCTGTGCTTAGGTTCAT 59.038 41.667 24.56 0.00 38.75 2.57
6 7 4.348486 AGAGATCTCTGTGCTTAGGTTCA 58.652 43.478 24.56 0.00 38.75 3.18
19 20 8.324306 TGTTGAATAATTGGAACAGAGATCTCT 58.676 33.333 19.92 19.92 42.39 3.10
20 21 8.498054 TGTTGAATAATTGGAACAGAGATCTC 57.502 34.615 15.29 15.29 42.39 2.75
27 28 8.246180 ACAGCTTATGTTGAATAATTGGAACAG 58.754 33.333 0.00 0.00 39.96 3.16
36 37 4.875544 GCCGACAGCTTATGTTGAATAA 57.124 40.909 0.00 0.00 45.05 1.40
61 62 3.840991 TGACTACATATAAGGGGCGTCT 58.159 45.455 0.00 0.00 0.00 4.18
62 63 4.595762 TTGACTACATATAAGGGGCGTC 57.404 45.455 0.00 0.00 0.00 5.19
68 69 6.182634 CGCGTTTGTTTGACTACATATAAGG 58.817 40.000 0.00 0.00 0.00 2.69
69 70 6.182634 CCGCGTTTGTTTGACTACATATAAG 58.817 40.000 4.92 0.00 0.00 1.73
71 72 4.567558 CCCGCGTTTGTTTGACTACATATA 59.432 41.667 4.92 0.00 0.00 0.86
73 74 2.737783 CCCGCGTTTGTTTGACTACATA 59.262 45.455 4.92 0.00 0.00 2.29
74 75 1.533731 CCCGCGTTTGTTTGACTACAT 59.466 47.619 4.92 0.00 0.00 2.29
75 76 0.938713 CCCGCGTTTGTTTGACTACA 59.061 50.000 4.92 0.00 0.00 2.74
76 77 0.385098 GCCCGCGTTTGTTTGACTAC 60.385 55.000 4.92 0.00 0.00 2.73
89 90 0.928229 GTGTTCTAGTTATGCCCGCG 59.072 55.000 0.00 0.00 0.00 6.46
92 93 2.919228 CCTGGTGTTCTAGTTATGCCC 58.081 52.381 0.00 0.00 0.00 5.36
110 111 4.008933 GGTCGCCACTGTCAGCCT 62.009 66.667 0.00 0.00 0.00 4.58
111 112 3.612247 ATGGTCGCCACTGTCAGCC 62.612 63.158 0.00 0.00 35.80 4.85
114 115 2.171209 CTGGATGGTCGCCACTGTCA 62.171 60.000 0.50 0.00 35.80 3.58
117 118 1.448540 GACTGGATGGTCGCCACTG 60.449 63.158 0.50 0.00 35.80 3.66
120 121 1.264045 TGATGACTGGATGGTCGCCA 61.264 55.000 1.01 1.01 38.91 5.69
123 124 0.531532 GGCTGATGACTGGATGGTCG 60.532 60.000 0.00 0.00 38.91 4.79
127 128 1.890979 GCCGGCTGATGACTGGATG 60.891 63.158 22.15 0.00 0.00 3.51
129 130 2.526450 CTTGCCGGCTGATGACTGGA 62.526 60.000 29.70 0.00 0.00 3.86
131 132 2.110967 CCTTGCCGGCTGATGACTG 61.111 63.158 29.70 8.14 0.00 3.51
168 169 4.641645 CGTGCCCTGCTGAACCCA 62.642 66.667 0.00 0.00 0.00 4.51
213 226 5.261216 GGTTTGGAAATCTAGTGGATTGGA 58.739 41.667 2.06 0.00 43.17 3.53
224 237 2.105821 TGGTCTGACGGTTTGGAAATCT 59.894 45.455 1.07 0.00 0.00 2.40
253 266 2.032924 GGTCCTCTTTGTTGTTGGTTCG 59.967 50.000 0.00 0.00 0.00 3.95
255 268 3.023832 CTGGTCCTCTTTGTTGTTGGTT 58.976 45.455 0.00 0.00 0.00 3.67
297 310 2.093447 CCGTTTGTGAGCCTAGAGGATT 60.093 50.000 0.00 0.00 37.39 3.01
652 678 1.838073 GAATCCACCCACCTCCGTGT 61.838 60.000 0.00 0.00 38.41 4.49
653 679 1.078426 GAATCCACCCACCTCCGTG 60.078 63.158 0.00 0.00 39.91 4.94
1355 1436 1.088340 CGCTCAATCAGGTCCTGCAG 61.088 60.000 14.64 6.78 0.00 4.41
1356 1437 1.078918 CGCTCAATCAGGTCCTGCA 60.079 57.895 14.64 3.80 0.00 4.41
1357 1438 2.467826 GCGCTCAATCAGGTCCTGC 61.468 63.158 14.64 0.00 0.00 4.85
1358 1439 1.078918 TGCGCTCAATCAGGTCCTG 60.079 57.895 13.21 13.21 0.00 3.86
1359 1440 1.220206 CTGCGCTCAATCAGGTCCT 59.780 57.895 9.73 0.00 0.00 3.85
1458 1606 5.055812 GTCATTCAATTGGGCAAAGAACAA 58.944 37.500 5.42 0.00 0.00 2.83
1484 1632 3.058224 GCTAGCTACCAACCAAACAGTTG 60.058 47.826 7.70 0.00 45.46 3.16
1485 1633 3.146847 GCTAGCTACCAACCAAACAGTT 58.853 45.455 7.70 0.00 0.00 3.16
1486 1634 2.372172 AGCTAGCTACCAACCAAACAGT 59.628 45.455 17.69 0.00 0.00 3.55
1487 1635 3.003480 GAGCTAGCTACCAACCAAACAG 58.997 50.000 19.38 0.00 0.00 3.16
1488 1636 2.290071 GGAGCTAGCTACCAACCAAACA 60.290 50.000 19.38 0.00 0.00 2.83
1502 1652 9.553064 ACAGATTAAAACTCAATATGGAGCTAG 57.447 33.333 7.05 0.00 38.50 3.42
1508 1658 7.489113 GCCAACACAGATTAAAACTCAATATGG 59.511 37.037 0.00 0.00 30.63 2.74
1510 1660 8.121305 TGCCAACACAGATTAAAACTCAATAT 57.879 30.769 0.00 0.00 0.00 1.28
1512 1662 6.403866 TGCCAACACAGATTAAAACTCAAT 57.596 33.333 0.00 0.00 0.00 2.57
1517 1667 4.243007 AGCTGCCAACACAGATTAAAAC 57.757 40.909 0.00 0.00 40.25 2.43
1521 1671 5.128663 TCACTATAGCTGCCAACACAGATTA 59.871 40.000 0.00 0.00 40.25 1.75
1528 1678 5.709631 TCAAATTTCACTATAGCTGCCAACA 59.290 36.000 0.00 0.00 0.00 3.33
1532 1682 6.261826 ACAGATCAAATTTCACTATAGCTGCC 59.738 38.462 0.00 0.00 0.00 4.85
1547 1703 7.254932 GGCGAAGAAGCTATTAACAGATCAAAT 60.255 37.037 0.00 0.00 37.29 2.32
1551 1707 4.449405 GGGCGAAGAAGCTATTAACAGATC 59.551 45.833 0.00 0.00 37.29 2.75
1587 1751 5.799827 ACTAATACAGGCTCTTGAGATCC 57.200 43.478 1.30 0.00 0.00 3.36
1613 1777 4.951715 TCAACCTGCATTATCAGCAAAGAT 59.048 37.500 0.00 0.00 42.17 2.40
1617 1781 2.424601 GCTCAACCTGCATTATCAGCAA 59.575 45.455 0.00 0.00 42.17 3.91
1628 1792 1.251251 ACAATCCAAGCTCAACCTGC 58.749 50.000 0.00 0.00 0.00 4.85
1629 1793 2.624838 ACAACAATCCAAGCTCAACCTG 59.375 45.455 0.00 0.00 0.00 4.00
1644 1808 6.570957 GCATCAGATTTCATGGAAGACAACAA 60.571 38.462 0.00 0.00 0.00 2.83
1645 1809 5.106038 GCATCAGATTTCATGGAAGACAACA 60.106 40.000 0.00 0.00 0.00 3.33
1650 1814 5.503002 TGAAGCATCAGATTTCATGGAAGA 58.497 37.500 0.00 0.00 0.00 2.87
1652 1816 6.785337 AATGAAGCATCAGATTTCATGGAA 57.215 33.333 10.03 0.00 39.82 3.53
1674 1838 3.702045 CCAAAACCACCCAACTAGACAAA 59.298 43.478 0.00 0.00 0.00 2.83
1683 1847 3.541713 GGCGCCAAAACCACCCAA 61.542 61.111 24.80 0.00 0.00 4.12
1720 1884 9.371136 TCATAAACTAACTGCATAGACTTCAAG 57.629 33.333 1.33 0.00 0.00 3.02
1724 1888 9.726438 ACTTTCATAAACTAACTGCATAGACTT 57.274 29.630 1.33 0.00 0.00 3.01
1725 1889 9.372369 GACTTTCATAAACTAACTGCATAGACT 57.628 33.333 1.33 0.00 0.00 3.24
1728 1892 8.723942 AGGACTTTCATAAACTAACTGCATAG 57.276 34.615 0.00 0.00 0.00 2.23
1732 1896 6.874134 TGAGAGGACTTTCATAAACTAACTGC 59.126 38.462 0.00 0.00 0.00 4.40
1735 1899 7.873505 AGTGTGAGAGGACTTTCATAAACTAAC 59.126 37.037 0.00 0.00 0.00 2.34
1846 2010 2.332063 ATCCATCCACACGAATCACC 57.668 50.000 0.00 0.00 0.00 4.02
1857 2021 6.270927 CCAGGTTTCTTAGAGATATCCATCCA 59.729 42.308 0.00 0.00 0.00 3.41
1878 2042 1.340405 ACAAGGTGCTAGCATTCCAGG 60.340 52.381 22.51 15.56 0.00 4.45
1924 2092 0.694444 ACACAGACAAGGGGACAGGT 60.694 55.000 0.00 0.00 0.00 4.00
2026 2281 2.248248 TCTCGAGAGAAGCCCAGAAAA 58.752 47.619 12.08 0.00 41.32 2.29
2028 2283 1.753649 CATCTCGAGAGAAGCCCAGAA 59.246 52.381 21.52 0.00 41.36 3.02
2030 2285 1.397672 TCATCTCGAGAGAAGCCCAG 58.602 55.000 21.52 3.38 41.36 4.45
2031 2286 2.079170 ATCATCTCGAGAGAAGCCCA 57.921 50.000 21.52 0.00 41.36 5.36
2034 2289 5.384063 TGGAATATCATCTCGAGAGAAGC 57.616 43.478 21.52 6.12 41.36 3.86
2040 2297 9.664332 AAAATCCTAATGGAATATCATCTCGAG 57.336 33.333 5.93 5.93 46.80 4.04
2066 2324 7.151999 TCAAAACTAAGCAAAGTGAACAAGA 57.848 32.000 0.00 0.00 0.00 3.02
2102 2360 9.078753 GTACTAAGAGCAGATCTGAAGTAAAAC 57.921 37.037 27.04 10.43 38.28 2.43
2135 2393 4.873010 AGAGGTAGGAGCTTCATCAGTAA 58.127 43.478 0.00 0.00 0.00 2.24
2233 2491 3.612860 GCAGCTGAGCATTCAAGAAAATG 59.387 43.478 20.43 0.00 39.22 2.32
2361 2619 1.434696 GCGGACAATTGGATGCAGG 59.565 57.895 10.83 0.00 0.00 4.85
2445 2703 5.737353 TCAATAAACATATTGCGCTTCTCG 58.263 37.500 9.73 0.00 37.36 4.04
2718 2976 7.695820 ACTAGAGACAACGAACACATATAGAC 58.304 38.462 0.00 0.00 0.00 2.59
2732 2990 7.205992 TCAAGATGATGCATACTAGAGACAAC 58.794 38.462 0.00 0.00 0.00 3.32
2840 3098 1.518572 ACCGTCATTCCTAAGCGCG 60.519 57.895 0.00 0.00 0.00 6.86
2894 3152 2.945008 CAGAAGAGCACTTTTCACACCA 59.055 45.455 0.00 0.00 36.39 4.17
3040 3337 3.069158 GCAAGAAGATGCAGGCCAAATAT 59.931 43.478 5.01 0.00 45.70 1.28
3118 3415 6.013842 AGGCACTAAAACAGCAAGAATAAC 57.986 37.500 0.00 0.00 36.02 1.89
3278 3575 2.772691 GGCCTCAGCAGCTTCATGC 61.773 63.158 0.00 0.00 46.88 4.06
3319 3616 1.267806 CTGGCAAAGTCATGTGGTGTC 59.732 52.381 0.00 0.00 0.00 3.67
3445 3758 1.201429 AGCTTTGGGAGACGATGGGT 61.201 55.000 0.00 0.00 0.00 4.51
3472 3785 4.166888 TCGAGCATGCTGAGGGCC 62.167 66.667 28.27 8.49 40.92 5.80
3581 3894 5.701750 AGGTACACATGTTAACATTTACGCA 59.298 36.000 18.50 0.00 33.61 5.24
3582 3895 6.173191 AGGTACACATGTTAACATTTACGC 57.827 37.500 18.50 12.53 33.61 4.42
3607 3921 4.761739 TGGAGGAACAGAAACTGCATAAAG 59.238 41.667 0.00 0.00 34.37 1.85
3634 3948 2.033141 TCCTGCTGCACTTGAGGC 59.967 61.111 0.00 0.00 0.00 4.70
3640 3954 3.067091 CAGGACTCCTGCTGCACT 58.933 61.111 12.34 0.00 45.13 4.40
3670 3984 6.348498 TGACAGGTCCATCAAAGTATGTATG 58.652 40.000 0.00 0.00 0.00 2.39
3796 4115 3.058501 CAGTGGTATCTTTCGCCGTTTTT 60.059 43.478 0.00 0.00 0.00 1.94
3819 4138 4.934075 TTGTCATCAGAGAGCAATTTCG 57.066 40.909 0.00 0.00 0.00 3.46
3821 4140 8.568794 CATGATATTGTCATCAGAGAGCAATTT 58.431 33.333 0.00 0.00 45.76 1.82
3838 4157 1.194547 GGGCACGCGTACATGATATTG 59.805 52.381 13.44 0.00 0.00 1.90
3882 4201 0.179045 ACAGGCAAGCAACTTCGTCT 60.179 50.000 0.00 0.00 0.00 4.18
3889 4208 0.675633 ACAATCCACAGGCAAGCAAC 59.324 50.000 0.00 0.00 0.00 4.17
3893 4212 0.892755 ATGCACAATCCACAGGCAAG 59.107 50.000 0.00 0.00 38.08 4.01
4012 4441 4.935808 ACTTGATTTGGTGTCGATAGTTCC 59.064 41.667 0.00 0.00 37.40 3.62
4171 5046 1.196808 CTAGCACGTGCCAAAACGATT 59.803 47.619 35.51 17.02 46.49 3.34
4235 5111 2.956987 CAGAGGGCGCCTTTGTTG 59.043 61.111 28.56 14.82 31.98 3.33
4249 5125 0.249868 CACAGAAACGACCCTGCAGA 60.250 55.000 17.39 0.00 33.90 4.26
4331 5226 8.644216 ACAAAAGTAAAGAACGGGGAAATAATT 58.356 29.630 0.00 0.00 0.00 1.40
4731 5634 3.008594 TGAGCGAACAATTTCCTAAGGGA 59.991 43.478 0.00 0.00 40.36 4.20
4787 5690 9.523730 GTGAACATTTTTAAACACAAGTTGAAC 57.476 29.630 10.54 0.00 38.17 3.18
4789 5692 9.134734 GAGTGAACATTTTTAAACACAAGTTGA 57.865 29.630 10.54 0.00 38.17 3.18


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

AutoCloner maintained by Alex Coulton.