Multiple sequence alignment - TraesCS7A01G326300

Loading Multiple Alignment...

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 TraesCS7A01G326300 chr7A 100.000 5359 0 0 1 5359 474290933 474296291 0.000000e+00 9897.0
1 TraesCS7A01G326300 chr7D 94.777 3676 118 20 1180 4815 412881584 412885225 0.000000e+00 5657.0
2 TraesCS7A01G326300 chr7D 87.928 1052 45 26 128 1133 412880576 412881591 0.000000e+00 1164.0
3 TraesCS7A01G326300 chr7D 94.960 496 19 4 4870 5359 412885233 412885728 0.000000e+00 773.0
4 TraesCS7A01G326300 chr7B 92.893 3194 106 32 469 3627 427298215 427301322 0.000000e+00 4529.0
5 TraesCS7A01G326300 chr7B 92.897 1605 47 23 3805 5359 427301322 427302909 0.000000e+00 2270.0
6 TraesCS7A01G326300 chr7B 85.616 438 35 12 12 434 427297790 427298214 8.240000e-118 435.0
7 TraesCS7A01G326300 chr7B 90.123 162 16 0 3643 3804 102234317 102234478 1.510000e-50 211.0
8 TraesCS7A01G326300 chr4D 90.184 163 16 0 3643 3805 64390632 64390470 4.200000e-51 213.0
9 TraesCS7A01G326300 chr4D 90.123 162 16 0 3643 3804 334164391 334164552 1.510000e-50 211.0
10 TraesCS7A01G326300 chr4D 88.172 93 11 0 5267 5359 89537694 89537786 1.580000e-20 111.0
11 TraesCS7A01G326300 chr3B 89.412 170 17 1 3639 3807 716149102 716148933 4.200000e-51 213.0
12 TraesCS7A01G326300 chr3B 91.250 80 7 0 5278 5357 647680840 647680761 5.670000e-20 110.0
13 TraesCS7A01G326300 chr6B 89.697 165 16 1 3641 3805 15042422 15042259 5.440000e-50 209.0
14 TraesCS7A01G326300 chr2D 88.889 171 18 1 3641 3811 99959429 99959260 5.440000e-50 209.0
15 TraesCS7A01G326300 chr4A 87.640 178 18 4 3641 3817 137967142 137966968 2.530000e-48 204.0
16 TraesCS7A01G326300 chr4A 89.091 165 16 2 3641 3804 137972667 137972830 2.530000e-48 204.0
17 TraesCS7A01G326300 chr4A 87.912 91 11 0 5269 5359 502028118 502028208 2.040000e-19 108.0
18 TraesCS7A01G326300 chr4A 83.673 98 14 2 108 204 231287750 231287846 2.060000e-14 91.6
19 TraesCS7A01G326300 chr4A 86.585 82 8 2 117 198 564649562 564649484 2.660000e-13 87.9
20 TraesCS7A01G326300 chr1A 77.231 325 53 14 5036 5357 466927361 466927667 2.570000e-38 171.0
21 TraesCS7A01G326300 chr1A 83.871 93 11 3 117 206 580496708 580496617 9.560000e-13 86.1
22 TraesCS7A01G326300 chr1B 77.019 322 53 15 5036 5357 491982666 491982966 1.190000e-36 165.0
23 TraesCS7A01G326300 chr1D 76.398 322 55 15 5036 5357 367429177 367429477 2.580000e-33 154.0
24 TraesCS7A01G326300 chr3A 93.506 77 5 0 5281 5357 627864990 627864914 1.220000e-21 115.0
25 TraesCS7A01G326300 chr3A 85.057 87 12 1 108 194 34532544 34532629 2.660000e-13 87.9
26 TraesCS7A01G326300 chr4B 89.011 91 10 0 5269 5359 126597589 126597679 4.390000e-21 113.0
27 TraesCS7A01G326300 chr4B 85.882 85 9 2 117 201 171146648 171146567 2.660000e-13 87.9
28 TraesCS7A01G326300 chr5B 82.692 104 12 5 117 214 383540021 383539918 2.660000e-13 87.9
29 TraesCS7A01G326300 chr5A 86.250 80 10 1 108 187 377183547 377183625 9.560000e-13 86.1


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 TraesCS7A01G326300 chr7A 474290933 474296291 5358 False 9897.000000 9897 100.000000 1 5359 1 chr7A.!!$F1 5358
1 TraesCS7A01G326300 chr7D 412880576 412885728 5152 False 2531.333333 5657 92.555000 128 5359 3 chr7D.!!$F1 5231
2 TraesCS7A01G326300 chr7B 427297790 427302909 5119 False 2411.333333 4529 90.468667 12 5359 3 chr7B.!!$F2 5347

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
832 868 0.105913 CCCCTCACCCTCTCTAGACC 60.106 65.000 0.00 0.00 0.00 3.85 F
1524 1609 0.249996 GCACAGGGCTTGCAAACATT 60.250 50.000 0.00 0.00 39.93 2.71 F
1610 1695 0.570727 AAATGGGGAAGGGGGTTTGT 59.429 50.000 0.00 0.00 0.00 2.83 F
1741 1829 0.693049 AATCTGGTGTGGTGGGAGAC 59.307 55.000 0.00 0.00 0.00 3.36 F
1773 1861 1.474677 CCAGATGCCAAGGCTACTCTG 60.475 57.143 21.45 21.45 42.51 3.35 F
3652 3757 1.486211 ACATCCTTGTACTCCCTCCG 58.514 55.000 0.00 0.00 33.16 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1972 1.338674 TGAATTGTCAGGGCTACGGTG 60.339 52.381 0.0 0.00 0.00 4.94 R
2895 2986 1.064505 GCACACCATTGACCATGATCG 59.935 52.381 0.0 0.00 34.31 3.69 R
3570 3675 7.949690 AATCATCCAATGAGATTTCAAGTGA 57.050 32.000 0.0 0.00 43.53 3.41 R
3685 3790 4.634184 TTTGCTCCGTATGTAGTCTCTC 57.366 45.455 0.0 0.00 0.00 3.20 R
3732 3837 6.095021 GGACTGCATACGGATGTATATAGACA 59.905 42.308 9.9 2.07 39.28 3.41 R
5190 5339 1.813513 CTCCAGCCGTCAAGTTCATT 58.186 50.000 0.0 0.00 0.00 2.57 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
104 106 1.208844 TGGGCGTGGGGAAGGATTAA 61.209 55.000 0.00 0.00 0.00 1.40
111 113 2.026542 GTGGGGAAGGATTAAACGAGGT 60.027 50.000 0.00 0.00 0.00 3.85
115 117 2.095372 GGAAGGATTAAACGAGGTTGCG 59.905 50.000 0.00 0.00 37.29 4.85
125 127 2.027625 GAGGTTGCGTCGAACCCAG 61.028 63.158 17.51 0.00 45.85 4.45
126 128 3.047877 GGTTGCGTCGAACCCAGG 61.048 66.667 12.77 0.00 39.74 4.45
128 130 2.029964 TTGCGTCGAACCCAGGAC 59.970 61.111 0.00 0.00 0.00 3.85
167 173 3.134804 GGAGTACTTCACCACTATGCCAT 59.865 47.826 0.00 0.00 0.00 4.40
168 174 4.384208 GGAGTACTTCACCACTATGCCATT 60.384 45.833 0.00 0.00 0.00 3.16
189 195 4.986054 TCCTGCCCTTTCTAACAAACTA 57.014 40.909 0.00 0.00 0.00 2.24
195 201 7.610305 CCTGCCCTTTCTAACAAACTAGAAATA 59.390 37.037 0.00 0.00 43.54 1.40
266 272 6.628856 GTCATGAATAATTGAAACACGGATCG 59.371 38.462 0.00 0.00 0.00 3.69
349 360 2.368548 TGTGATCCTTATGCTATGCCGT 59.631 45.455 0.00 0.00 0.00 5.68
552 579 7.930865 TCAGAAAGAGAAAGAAAAAGAGAGAGG 59.069 37.037 0.00 0.00 0.00 3.69
632 662 3.787001 CGTTGCCTCCTCCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
633 663 3.412408 GTTGCCTCCTCCCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
634 664 4.760220 TTGCCTCCTCCCCTCCCC 62.760 72.222 0.00 0.00 0.00 4.81
636 666 4.890306 GCCTCCTCCCCTCCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
656 686 2.159128 TCGTCTAGAGTCTAGACCCACG 60.159 54.545 37.45 30.38 40.48 4.94
717 747 1.198867 CCAGCCAGATATCTCGTCTCG 59.801 57.143 1.03 0.00 0.00 4.04
750 780 1.215647 CACCGAGGAAGAAGACCCG 59.784 63.158 0.00 0.00 0.00 5.28
832 868 0.105913 CCCCTCACCCTCTCTAGACC 60.106 65.000 0.00 0.00 0.00 3.85
851 887 3.892588 GACCAAATCTACGAGAGAGGGAT 59.107 47.826 0.00 0.00 37.70 3.85
896 949 1.381522 GAGAGGTCGGAGGAGTACAC 58.618 60.000 0.00 0.00 0.00 2.90
903 956 1.681327 GGAGGAGTACACGGGCTGA 60.681 63.158 0.00 0.00 0.00 4.26
946 999 2.939103 CGACTGGTGGATTCCATTTCTC 59.061 50.000 9.01 1.54 35.28 2.87
964 1029 3.330720 CCCTTCTTGCTCCGGGGT 61.331 66.667 1.62 0.00 32.91 4.95
1119 1196 6.973642 TGGATAGTTGGATTCAGAAAATCCT 58.026 36.000 15.71 1.54 45.01 3.24
1133 1211 2.725221 AATCCTTGTGCTCTGGATCC 57.275 50.000 4.20 4.20 39.43 3.36
1136 1214 1.487976 TCCTTGTGCTCTGGATCCATC 59.512 52.381 16.63 8.32 0.00 3.51
1172 1250 4.827087 CGCAGTGCCATCTCCGCT 62.827 66.667 10.11 0.00 0.00 5.52
1186 1264 2.952978 TCTCCGCTACTCCTTCTGATTC 59.047 50.000 0.00 0.00 0.00 2.52
1192 1270 3.614616 GCTACTCCTTCTGATTCGTTGTG 59.385 47.826 0.00 0.00 0.00 3.33
1220 1298 2.202756 CTAACCTGGCGAGGCGAC 60.203 66.667 15.66 0.00 44.33 5.19
1233 1311 1.446272 GGCGACGAAGAAGTGGGAG 60.446 63.158 0.00 0.00 0.00 4.30
1256 1334 2.711547 GGGGTAACTGCTCCTGGATAAT 59.288 50.000 0.00 0.00 0.00 1.28
1424 1505 5.787494 TCCTCTCCCCAATAAGATAATCCAG 59.213 44.000 0.00 0.00 0.00 3.86
1430 1511 5.705400 CCCAATAAGATAATCCAGTTGGGT 58.295 41.667 14.81 0.00 45.77 4.51
1433 1518 2.736670 AGATAATCCAGTTGGGTGGC 57.263 50.000 0.00 0.00 37.53 5.01
1452 1537 3.219281 GGCCCAAGTTCTTGTCTTTGTA 58.781 45.455 10.93 0.00 0.00 2.41
1455 1540 4.497507 GCCCAAGTTCTTGTCTTTGTACAC 60.498 45.833 10.93 0.00 0.00 2.90
1494 1579 2.045536 CCAGGGCTCAGGTTGCTC 60.046 66.667 0.00 0.00 0.00 4.26
1495 1580 2.600729 CCAGGGCTCAGGTTGCTCT 61.601 63.158 0.00 0.00 42.78 4.09
1524 1609 0.249996 GCACAGGGCTTGCAAACATT 60.250 50.000 0.00 0.00 39.93 2.71
1525 1610 1.504359 CACAGGGCTTGCAAACATTG 58.496 50.000 0.00 0.97 0.00 2.82
1536 1621 1.939969 CAAACATTGCGTTGCATTGC 58.060 45.000 12.15 0.46 41.68 3.56
1537 1622 1.260825 CAAACATTGCGTTGCATTGCA 59.739 42.857 7.38 7.38 41.68 4.08
1563 1648 4.911390 ACTCCATCAGTTCAAGGGTTTAG 58.089 43.478 0.00 0.00 26.56 1.85
1566 1651 4.844085 TCCATCAGTTCAAGGGTTTAGAGA 59.156 41.667 0.00 0.00 0.00 3.10
1589 1674 1.288037 GGGAAGGGCAATTTAGAGGGT 59.712 52.381 0.00 0.00 0.00 4.34
1594 1679 4.337264 AGGGCAATTTAGAGGGTCAAAT 57.663 40.909 0.00 0.00 0.00 2.32
1600 1685 4.965283 ATTTAGAGGGTCAAATGGGGAA 57.035 40.909 0.00 0.00 0.00 3.97
1605 1690 1.001631 GGTCAAATGGGGAAGGGGG 59.998 63.158 0.00 0.00 0.00 5.40
1608 1693 0.871024 TCAAATGGGGAAGGGGGTTT 59.129 50.000 0.00 0.00 0.00 3.27
1609 1694 0.983467 CAAATGGGGAAGGGGGTTTG 59.017 55.000 0.00 0.00 0.00 2.93
1610 1695 0.570727 AAATGGGGAAGGGGGTTTGT 59.429 50.000 0.00 0.00 0.00 2.83
1611 1696 1.473550 AATGGGGAAGGGGGTTTGTA 58.526 50.000 0.00 0.00 0.00 2.41
1612 1697 1.706539 ATGGGGAAGGGGGTTTGTAT 58.293 50.000 0.00 0.00 0.00 2.29
1613 1698 0.707616 TGGGGAAGGGGGTTTGTATG 59.292 55.000 0.00 0.00 0.00 2.39
1614 1699 1.004436 GGGGAAGGGGGTTTGTATGA 58.996 55.000 0.00 0.00 0.00 2.15
1615 1700 1.063942 GGGGAAGGGGGTTTGTATGAG 60.064 57.143 0.00 0.00 0.00 2.90
1616 1701 1.920351 GGGAAGGGGGTTTGTATGAGA 59.080 52.381 0.00 0.00 0.00 3.27
1617 1702 2.310647 GGGAAGGGGGTTTGTATGAGAA 59.689 50.000 0.00 0.00 0.00 2.87
1741 1829 0.693049 AATCTGGTGTGGTGGGAGAC 59.307 55.000 0.00 0.00 0.00 3.36
1773 1861 1.474677 CCAGATGCCAAGGCTACTCTG 60.475 57.143 21.45 21.45 42.51 3.35
1884 1972 3.129287 CAGGGTATGCAATTCTGGTTGTC 59.871 47.826 0.00 0.00 0.00 3.18
1923 2011 7.175467 ACAATTCATGTGAGTAAGCATTCTTCA 59.825 33.333 0.00 0.00 41.93 3.02
2006 2094 3.242739 ACAGTTCATGTGTTTGCTTCGTC 60.243 43.478 0.00 0.00 41.91 4.20
2054 2142 4.800993 CGACGTATTTTCTGAGAGCTTCAT 59.199 41.667 0.00 0.00 34.68 2.57
2134 2225 4.112716 TGCATATCAACATGTTTGGCAG 57.887 40.909 8.77 0.00 0.00 4.85
2150 2241 1.687563 GCAGGGTGTAGTTTTGTGGT 58.312 50.000 0.00 0.00 0.00 4.16
2270 2361 9.823647 AAGACTTTGTGATGTGGATATAGTTAG 57.176 33.333 0.00 0.00 0.00 2.34
2271 2362 8.982723 AGACTTTGTGATGTGGATATAGTTAGT 58.017 33.333 0.00 0.00 0.00 2.24
2272 2363 9.601217 GACTTTGTGATGTGGATATAGTTAGTT 57.399 33.333 0.00 0.00 0.00 2.24
2715 2806 9.462174 TTGTGAATTTTACTTCATGCTACTTTG 57.538 29.630 0.00 0.00 37.47 2.77
2863 2954 5.878133 GAGTTTTCTCATGATTCTTCAGCC 58.122 41.667 0.00 0.00 45.53 4.85
2895 2986 2.093128 TCCAGTTCCCTCGGATAAAAGC 60.093 50.000 0.00 0.00 0.00 3.51
3230 3321 4.673580 GCAGCAATCCTGTGTTTCTATGTG 60.674 45.833 0.00 0.00 43.71 3.21
3422 3513 4.969133 AGGTTAGTCCCCTAAACCTATGT 58.031 43.478 4.22 0.00 41.05 2.29
3570 3675 6.765036 CACTGGCTAATCTGAAATGTAGTGAT 59.235 38.462 0.00 0.00 35.15 3.06
3571 3676 6.989169 ACTGGCTAATCTGAAATGTAGTGATC 59.011 38.462 0.00 0.00 0.00 2.92
3572 3677 6.888105 TGGCTAATCTGAAATGTAGTGATCA 58.112 36.000 0.00 0.00 0.00 2.92
3573 3678 6.763135 TGGCTAATCTGAAATGTAGTGATCAC 59.237 38.462 18.47 18.47 0.00 3.06
3574 3679 6.989169 GGCTAATCTGAAATGTAGTGATCACT 59.011 38.462 30.11 30.11 45.02 3.41
3575 3680 7.497249 GGCTAATCTGAAATGTAGTGATCACTT 59.503 37.037 32.14 15.06 42.54 3.16
3576 3681 8.333908 GCTAATCTGAAATGTAGTGATCACTTG 58.666 37.037 32.14 12.72 42.54 3.16
3577 3682 9.591792 CTAATCTGAAATGTAGTGATCACTTGA 57.408 33.333 32.14 19.37 42.54 3.02
3578 3683 8.853077 AATCTGAAATGTAGTGATCACTTGAA 57.147 30.769 32.14 18.41 42.54 2.69
3652 3757 1.486211 ACATCCTTGTACTCCCTCCG 58.514 55.000 0.00 0.00 33.16 4.63
3666 3771 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
3685 3790 9.883142 AATACAAGTCTTTCTAGAGATTCCAAG 57.117 33.333 0.00 0.00 0.00 3.61
3711 3816 5.918608 AGACTACATACGGAGCAAAATGAT 58.081 37.500 0.00 0.00 0.00 2.45
3718 3823 4.946784 ACGGAGCAAAATGATTGACTAC 57.053 40.909 0.00 0.00 0.00 2.73
3773 3878 9.796120 GTATGCAGTCCATATTAGAATCTCTAC 57.204 37.037 0.00 0.00 38.60 2.59
3776 3881 8.363390 TGCAGTCCATATTAGAATCTCTACAAG 58.637 37.037 0.00 0.00 0.00 3.16
3780 3885 8.308207 GTCCATATTAGAATCTCTACAAGGACC 58.692 40.741 0.00 0.00 34.39 4.46
3932 4039 0.943835 GCAACCAACCCAATGCGTTC 60.944 55.000 0.00 0.00 0.00 3.95
3986 4093 1.082104 GTGCACGAAAAGGAAGCCG 60.082 57.895 0.00 0.00 0.00 5.52
4196 4303 1.250154 TGGGCACTACAAGCAATGGC 61.250 55.000 0.00 0.00 41.61 4.40
4235 4342 3.196469 GTGATTCAGACACTGAGATCCCA 59.804 47.826 0.98 0.00 41.75 4.37
4372 4479 2.776694 CGCTGATTGTATATGAGCGC 57.223 50.000 0.00 0.00 45.13 5.92
4373 4480 1.391485 CGCTGATTGTATATGAGCGCC 59.609 52.381 2.29 0.00 45.13 6.53
4376 4483 1.003118 TGATTGTATATGAGCGCCCCC 59.997 52.381 2.29 0.00 0.00 5.40
4436 4543 3.374402 CTCGTCAGTGAGGGCCGT 61.374 66.667 12.65 0.00 32.18 5.68
4447 4554 3.068064 GGGCCGTGGGATGTTTGG 61.068 66.667 0.00 0.00 0.00 3.28
4461 4568 6.671340 TGGGATGTTTGGAATTTGGATGAATA 59.329 34.615 0.00 0.00 0.00 1.75
4511 4618 3.707316 TGTAGGATTTGGGGAATGTTGG 58.293 45.455 0.00 0.00 0.00 3.77
4559 4666 8.668353 TCTGTAAACATCTCAGTTATGCATTTC 58.332 33.333 3.54 0.00 0.00 2.17
4757 4884 3.676646 GCTGGTTTGACATGCAGAATTTC 59.323 43.478 0.00 0.00 0.00 2.17
4768 4895 7.124599 TGACATGCAGAATTTCAATCCCTATTT 59.875 33.333 0.00 0.00 0.00 1.40
4790 4917 4.797471 TGACTGTTTGCAGCATGATTTAC 58.203 39.130 0.00 0.00 46.30 2.01
4833 4960 4.847367 GCCATTGGCCAGGGGAGG 62.847 72.222 24.61 15.52 44.06 4.30
4849 4976 2.165437 GGGAGGAAAAATGCACGCATAA 59.835 45.455 4.68 0.00 35.31 1.90
4851 4978 4.432712 GGAGGAAAAATGCACGCATAATT 58.567 39.130 4.68 3.58 35.31 1.40
4852 4979 4.504097 GGAGGAAAAATGCACGCATAATTC 59.496 41.667 4.68 11.90 35.31 2.17
4855 4982 5.931146 AGGAAAAATGCACGCATAATTCAAA 59.069 32.000 21.47 0.00 35.07 2.69
4856 4983 6.091169 AGGAAAAATGCACGCATAATTCAAAG 59.909 34.615 21.47 0.00 35.07 2.77
4857 4984 6.090628 GGAAAAATGCACGCATAATTCAAAGA 59.909 34.615 21.47 0.00 35.07 2.52
4858 4985 7.201548 GGAAAAATGCACGCATAATTCAAAGAT 60.202 33.333 21.47 2.72 35.07 2.40
4860 4987 8.700722 AAAATGCACGCATAATTCAAAGATTA 57.299 26.923 4.68 0.00 35.31 1.75
4862 4989 8.876275 AATGCACGCATAATTCAAAGATTATT 57.124 26.923 4.68 0.00 35.31 1.40
4899 5048 4.397103 TCAGAGGCATGAAAAACATAGCAG 59.603 41.667 0.00 0.00 37.46 4.24
4979 5128 7.412137 AATCAACAACAGCAATAGAAAAAGC 57.588 32.000 0.00 0.00 0.00 3.51
4999 5148 5.640189 AGCAAAAGATCTTGATGGACTTG 57.360 39.130 9.17 8.89 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.948309 AGCTTTTCTTCATACTGGGTATGTTT 59.052 34.615 14.67 0.00 44.21 2.83
64 65 3.564225 CACCTAACGTGGAAGCTTTTCTT 59.436 43.478 0.00 0.00 38.96 2.52
65 66 3.139077 CACCTAACGTGGAAGCTTTTCT 58.861 45.455 0.00 0.00 38.96 2.52
104 106 1.952635 GGTTCGACGCAACCTCGTT 60.953 57.895 16.89 0.00 43.42 3.85
111 113 2.029964 GTCCTGGGTTCGACGCAA 59.970 61.111 0.00 0.00 40.62 4.85
115 117 0.037232 CAAGAGGTCCTGGGTTCGAC 60.037 60.000 0.00 0.00 0.00 4.20
125 127 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
126 128 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
128 130 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
162 164 0.998928 TAGAAAGGGCAGGAATGGCA 59.001 50.000 4.13 0.00 35.93 4.92
167 173 4.178956 AGTTTGTTAGAAAGGGCAGGAA 57.821 40.909 0.00 0.00 0.00 3.36
168 174 3.876309 AGTTTGTTAGAAAGGGCAGGA 57.124 42.857 0.00 0.00 0.00 3.86
208 214 7.189693 TGAATATGGACGAAATTCTATGTGC 57.810 36.000 0.00 0.00 32.12 4.57
292 298 6.990341 TGATTAAGATCCATGTGTCAACTG 57.010 37.500 0.00 0.00 0.00 3.16
349 360 3.597182 TCTGCATATTGGAGTGGGGATA 58.403 45.455 0.00 0.00 37.12 2.59
552 579 3.070748 GGGACACTTTTCTCTCTTCTGC 58.929 50.000 0.00 0.00 0.00 4.26
632 662 2.224354 GGGTCTAGACTCTAGACGAGGG 60.224 59.091 28.47 1.24 44.33 4.30
633 663 2.435069 TGGGTCTAGACTCTAGACGAGG 59.565 54.545 28.47 1.85 44.33 4.63
634 664 3.460103 GTGGGTCTAGACTCTAGACGAG 58.540 54.545 28.47 3.83 43.53 4.18
635 665 2.159128 CGTGGGTCTAGACTCTAGACGA 60.159 54.545 28.47 19.60 43.53 4.20
636 666 2.203401 CGTGGGTCTAGACTCTAGACG 58.797 57.143 28.47 19.64 43.53 4.18
690 720 3.549794 GAGATATCTGGCTGGCAAAACT 58.450 45.455 10.74 0.98 0.00 2.66
691 721 2.289002 CGAGATATCTGGCTGGCAAAAC 59.711 50.000 10.74 0.00 0.00 2.43
692 722 2.092968 ACGAGATATCTGGCTGGCAAAA 60.093 45.455 10.74 0.00 0.00 2.44
717 747 1.813178 TCGGTGTGACAGAGATGAGAC 59.187 52.381 0.00 0.00 0.00 3.36
832 868 6.488683 ACTCTTATCCCTCTCTCGTAGATTTG 59.511 42.308 0.00 0.00 33.89 2.32
1119 1196 0.178767 CCGATGGATCCAGAGCACAA 59.821 55.000 21.33 0.00 0.00 3.33
1156 1234 1.884926 GTAGCGGAGATGGCACTGC 60.885 63.158 0.00 0.00 37.27 4.40
1157 1235 0.249238 GAGTAGCGGAGATGGCACTG 60.249 60.000 0.00 0.00 0.00 3.66
1169 1247 2.853731 ACGAATCAGAAGGAGTAGCG 57.146 50.000 0.00 0.00 0.00 4.26
1172 1250 4.866508 ACACAACGAATCAGAAGGAGTA 57.133 40.909 0.00 0.00 0.00 2.59
1186 1264 4.809426 AGGTTAGACAGAAAGAACACAACG 59.191 41.667 0.00 0.00 0.00 4.10
1192 1270 2.737252 CGCCAGGTTAGACAGAAAGAAC 59.263 50.000 0.00 0.00 0.00 3.01
1220 1298 2.125512 CCCGCTCCCACTTCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
1233 1311 2.125106 CAGGAGCAGTTACCCCGC 60.125 66.667 0.00 0.00 0.00 6.13
1256 1334 4.502604 GCTAACCAGATAAAGATACGGGCA 60.503 45.833 0.00 0.00 0.00 5.36
1384 1462 3.554692 GACGGTCGCCATTCGCTG 61.555 66.667 0.00 0.00 38.27 5.18
1387 1465 2.582498 GAGGACGGTCGCCATTCG 60.582 66.667 1.43 0.00 40.15 3.34
1430 1511 2.031120 CAAAGACAAGAACTTGGGCCA 58.969 47.619 17.05 0.00 44.45 5.36
1433 1518 4.638421 TGTGTACAAAGACAAGAACTTGGG 59.362 41.667 17.05 5.57 44.45 4.12
1437 1522 4.080526 AGGGTGTGTACAAAGACAAGAACT 60.081 41.667 0.00 0.00 29.45 3.01
1452 1537 0.182537 TTAGCAGCAACAGGGTGTGT 59.817 50.000 0.00 0.00 46.68 3.72
1494 1579 1.822990 AGCCCTGTGCATGATTTTCAG 59.177 47.619 0.00 0.00 44.83 3.02
1495 1580 1.927487 AGCCCTGTGCATGATTTTCA 58.073 45.000 0.00 0.00 44.83 2.69
1528 1613 3.419943 TGATGGAGTAGTTGCAATGCAA 58.580 40.909 17.55 17.55 46.80 4.08
1529 1614 3.011818 CTGATGGAGTAGTTGCAATGCA 58.988 45.455 2.72 2.72 36.47 3.96
1530 1615 3.012518 ACTGATGGAGTAGTTGCAATGC 58.987 45.455 0.59 0.00 30.86 3.56
1531 1616 4.696877 TGAACTGATGGAGTAGTTGCAATG 59.303 41.667 0.59 0.00 37.27 2.82
1532 1617 4.910195 TGAACTGATGGAGTAGTTGCAAT 58.090 39.130 0.59 0.00 37.27 3.56
1533 1618 4.350368 TGAACTGATGGAGTAGTTGCAA 57.650 40.909 0.00 0.00 37.27 4.08
1534 1619 4.318332 CTTGAACTGATGGAGTAGTTGCA 58.682 43.478 0.00 0.00 37.27 4.08
1535 1620 3.686726 CCTTGAACTGATGGAGTAGTTGC 59.313 47.826 0.00 0.00 37.27 4.17
1536 1621 4.256920 CCCTTGAACTGATGGAGTAGTTG 58.743 47.826 0.00 0.00 37.27 3.16
1537 1622 3.910627 ACCCTTGAACTGATGGAGTAGTT 59.089 43.478 0.00 0.00 39.67 2.24
1538 1623 3.521727 ACCCTTGAACTGATGGAGTAGT 58.478 45.455 0.00 0.00 33.09 2.73
1539 1624 4.559862 AACCCTTGAACTGATGGAGTAG 57.440 45.455 0.00 0.00 33.09 2.57
1540 1625 4.993705 AAACCCTTGAACTGATGGAGTA 57.006 40.909 0.00 0.00 33.09 2.59
1563 1648 4.600062 TCTAAATTGCCCTTCCCTTTCTC 58.400 43.478 0.00 0.00 0.00 2.87
1566 1651 3.566553 CCCTCTAAATTGCCCTTCCCTTT 60.567 47.826 0.00 0.00 0.00 3.11
1589 1674 0.871024 AAACCCCCTTCCCCATTTGA 59.129 50.000 0.00 0.00 0.00 2.69
1594 1679 0.707616 CATACAAACCCCCTTCCCCA 59.292 55.000 0.00 0.00 0.00 4.96
1600 1685 5.074746 AGTTTTTCTCATACAAACCCCCT 57.925 39.130 0.00 0.00 31.83 4.79
1605 1690 9.134734 TGTCAACAAAGTTTTTCTCATACAAAC 57.865 29.630 0.00 0.00 0.00 2.93
1608 1693 8.902806 AGATGTCAACAAAGTTTTTCTCATACA 58.097 29.630 0.00 0.00 0.00 2.29
1609 1694 9.736023 AAGATGTCAACAAAGTTTTTCTCATAC 57.264 29.630 0.00 0.00 0.00 2.39
1610 1695 9.950680 GAAGATGTCAACAAAGTTTTTCTCATA 57.049 29.630 0.00 0.00 0.00 2.15
1611 1696 8.469200 TGAAGATGTCAACAAAGTTTTTCTCAT 58.531 29.630 0.00 0.00 31.51 2.90
1612 1697 7.754924 GTGAAGATGTCAACAAAGTTTTTCTCA 59.245 33.333 0.00 0.00 38.23 3.27
1613 1698 7.970614 AGTGAAGATGTCAACAAAGTTTTTCTC 59.029 33.333 0.00 0.00 38.23 2.87
1614 1699 7.830739 AGTGAAGATGTCAACAAAGTTTTTCT 58.169 30.769 0.00 0.00 38.23 2.52
1615 1700 7.970614 AGAGTGAAGATGTCAACAAAGTTTTTC 59.029 33.333 0.00 0.00 38.23 2.29
1616 1701 7.756722 CAGAGTGAAGATGTCAACAAAGTTTTT 59.243 33.333 0.00 0.00 38.23 1.94
1617 1702 7.253422 CAGAGTGAAGATGTCAACAAAGTTTT 58.747 34.615 0.00 0.00 38.23 2.43
1773 1861 2.723658 CACGATCAGCGAGAAAGATAGC 59.276 50.000 0.00 0.00 44.57 2.97
1800 1888 3.885484 AAGATGCAGAAGACAACAACG 57.115 42.857 0.00 0.00 0.00 4.10
1884 1972 1.338674 TGAATTGTCAGGGCTACGGTG 60.339 52.381 0.00 0.00 0.00 4.94
1923 2011 7.519057 TCAGCATAACTCTGTAGTAGATAGGT 58.481 38.462 0.00 0.00 33.75 3.08
2006 2094 3.492102 TCAGGACTTTTCTCCAACTGG 57.508 47.619 0.00 0.00 31.94 4.00
2118 2209 1.619827 CACCCTGCCAAACATGTTGAT 59.380 47.619 12.82 0.00 0.00 2.57
2134 2225 3.215975 TGCTAACCACAAAACTACACCC 58.784 45.455 0.00 0.00 0.00 4.61
2150 2241 5.401531 AATGGTCTCGAACTAACTGCTAA 57.598 39.130 0.00 0.00 0.00 3.09
2269 2360 2.484264 GGTTCTTAGCATGTTCGCAACT 59.516 45.455 0.00 0.00 0.00 3.16
2270 2361 2.484264 AGGTTCTTAGCATGTTCGCAAC 59.516 45.455 0.00 0.00 0.00 4.17
2271 2362 2.778299 AGGTTCTTAGCATGTTCGCAA 58.222 42.857 0.00 0.00 0.00 4.85
2272 2363 2.472695 AGGTTCTTAGCATGTTCGCA 57.527 45.000 0.00 0.00 0.00 5.10
2435 2526 5.460646 CAAGTACAGTGTTTTATTGGCTGG 58.539 41.667 0.00 0.00 0.00 4.85
2715 2806 9.946165 GGATACTATAATTTGGCAGTTGTTTAC 57.054 33.333 0.00 0.00 0.00 2.01
2863 2954 2.043227 GGGAACTGGAGAGTATGAGGG 58.957 57.143 0.00 0.00 0.00 4.30
2895 2986 1.064505 GCACACCATTGACCATGATCG 59.935 52.381 0.00 0.00 34.31 3.69
3570 3675 7.949690 AATCATCCAATGAGATTTCAAGTGA 57.050 32.000 0.00 0.00 43.53 3.41
3571 3676 8.997621 AAAATCATCCAATGAGATTTCAAGTG 57.002 30.769 0.00 0.00 43.53 3.16
3572 3677 9.649167 GAAAAATCATCCAATGAGATTTCAAGT 57.351 29.630 16.96 1.87 43.53 3.16
3573 3678 9.095065 GGAAAAATCATCCAATGAGATTTCAAG 57.905 33.333 20.24 0.00 42.94 3.02
3574 3679 8.595421 TGGAAAAATCATCCAATGAGATTTCAA 58.405 29.630 20.24 13.09 43.84 2.69
3575 3680 8.136563 TGGAAAAATCATCCAATGAGATTTCA 57.863 30.769 20.24 9.14 43.84 2.69
3666 3771 7.339466 AGTCTCTCTTGGAATCTCTAGAAAGAC 59.661 40.741 0.00 0.00 0.00 3.01
3685 3790 4.634184 TTTGCTCCGTATGTAGTCTCTC 57.366 45.455 0.00 0.00 0.00 3.20
3711 3816 8.405418 AGACATAGTTTAGAGTGTGTAGTCAA 57.595 34.615 0.00 0.00 31.57 3.18
3732 3837 6.095021 GGACTGCATACGGATGTATATAGACA 59.905 42.308 9.90 2.07 39.28 3.41
3752 3857 9.083422 TCCTTGTAGAGATTCTAATATGGACTG 57.917 37.037 0.00 0.00 29.58 3.51
3780 3885 7.173722 TCTACTCCCTCCGTTCCTAAATATAG 58.826 42.308 0.00 0.00 0.00 1.31
3896 4003 4.754618 TGGTTGCTGTACTTGTACTTGATG 59.245 41.667 11.53 0.46 0.00 3.07
3932 4039 0.946700 TGTGTATGCAACCACGGTCG 60.947 55.000 12.70 0.00 34.28 4.79
3986 4093 1.537135 GCTCGCAGGTTGATCCTAGAC 60.537 57.143 0.00 0.00 46.24 2.59
4160 4267 2.354203 GCCCAACTCTAAGTCACTCAGG 60.354 54.545 0.00 0.00 0.00 3.86
4196 4303 2.463876 TCACTTCTGCGATATCTTGCG 58.536 47.619 0.34 0.00 34.16 4.85
4235 4342 6.440647 TCTCAGTAATGGTTCTGGTCATAACT 59.559 38.462 0.00 0.00 33.13 2.24
4372 4479 2.025887 ACTATTTCTCACTGCAAGGGGG 60.026 50.000 0.00 0.00 41.61 5.40
4373 4480 3.356529 ACTATTTCTCACTGCAAGGGG 57.643 47.619 0.00 0.00 38.52 4.79
4376 4483 6.376978 CCTGAAAACTATTTCTCACTGCAAG 58.623 40.000 3.31 0.00 44.32 4.01
4436 4543 4.423913 TCATCCAAATTCCAAACATCCCA 58.576 39.130 0.00 0.00 0.00 4.37
4447 4554 7.553334 AGCATATGCCATATTCATCCAAATTC 58.447 34.615 23.96 0.00 43.38 2.17
4511 4618 6.314896 CAGAAAGAGACCTATCACCAATCAAC 59.685 42.308 0.00 0.00 0.00 3.18
4559 4666 9.831737 CTACAATCTCTTAAAACCTTCACAATG 57.168 33.333 0.00 0.00 0.00 2.82
4594 4701 7.505585 TCTTCCTGGAATCTTGCTAAAAAGAAA 59.494 33.333 10.03 0.00 39.54 2.52
4595 4702 7.004086 TCTTCCTGGAATCTTGCTAAAAAGAA 58.996 34.615 10.03 0.00 39.54 2.52
4596 4703 6.542821 TCTTCCTGGAATCTTGCTAAAAAGA 58.457 36.000 10.03 0.00 40.36 2.52
4597 4704 6.432472 ACTCTTCCTGGAATCTTGCTAAAAAG 59.568 38.462 10.03 0.00 0.00 2.27
4757 4884 5.389859 TGCAAACAGTCAAATAGGGATTG 57.610 39.130 0.00 0.00 0.00 2.67
4768 4895 4.520111 AGTAAATCATGCTGCAAACAGTCA 59.480 37.500 6.36 0.00 46.30 3.41
4790 4917 6.749578 GTGTACTCACATGAAGTCATCTGTAG 59.250 42.308 0.00 0.00 43.37 2.74
4833 4960 7.048000 TCTTTGAATTATGCGTGCATTTTTC 57.952 32.000 13.20 15.20 37.82 2.29
4858 4985 9.241919 TGCCTCTGAACTTTTCATGATAAATAA 57.758 29.630 0.00 0.00 39.30 1.40
4860 4987 7.707624 TGCCTCTGAACTTTTCATGATAAAT 57.292 32.000 0.00 0.00 39.30 1.40
4862 4989 6.885918 TCATGCCTCTGAACTTTTCATGATAA 59.114 34.615 0.00 0.00 39.30 1.75
4867 4994 6.409524 TTTTCATGCCTCTGAACTTTTCAT 57.590 33.333 0.00 0.00 39.30 2.57
4899 5048 5.515270 GCAAGAAATATAAAGGTTTGGTCGC 59.485 40.000 0.00 0.00 0.00 5.19
4979 5128 6.016860 TGTGACAAGTCCATCAAGATCTTTTG 60.017 38.462 4.86 8.59 0.00 2.44
5183 5332 2.131972 CCGTCAAGTTCATTGTCGTCA 58.868 47.619 6.52 0.00 45.22 4.35
5190 5339 1.813513 CTCCAGCCGTCAAGTTCATT 58.186 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.