Multiple sequence alignment - TraesCS6A01G168900

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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 TraesCS6A01G168900 chr6A 100.000 4046 0 0 1 4046 176295054 176291009 0.000000e+00 7472.0
1 TraesCS6A01G168900 chr6A 90.978 1574 124 13 1477 3048 175997191 175995634 0.000000e+00 2104.0
2 TraesCS6A01G168900 chr6A 89.677 155 14 2 1096 1249 176002955 176002802 3.190000e-46 196.0
3 TraesCS6A01G168900 chr6D 95.890 2555 65 20 669 3215 135042166 135039644 0.000000e+00 4100.0
4 TraesCS6A01G168900 chr6D 95.814 2556 67 18 669 3215 134588716 134586192 0.000000e+00 4091.0
5 TraesCS6A01G168900 chr6D 90.010 1962 169 17 1096 3048 134742432 134740489 0.000000e+00 2512.0
6 TraesCS6A01G168900 chr6D 89.690 1969 167 22 1096 3048 134337497 134335549 0.000000e+00 2479.0
7 TraesCS6A01G168900 chr6D 89.329 834 86 3 3215 4046 349734727 349735559 0.000000e+00 1044.0
8 TraesCS6A01G168900 chr6D 87.726 554 46 15 30 577 135042709 135042172 9.550000e-176 627.0
9 TraesCS6A01G168900 chr6D 87.545 554 47 17 30 577 134589259 134588722 4.440000e-174 621.0
10 TraesCS6A01G168900 chr6D 92.308 78 6 0 1710 1787 33243212 33243135 1.190000e-20 111.0
11 TraesCS6A01G168900 chr6B 95.423 2556 83 13 669 3215 233674436 233671906 0.000000e+00 4041.0
12 TraesCS6A01G168900 chr6B 90.311 1961 165 16 1096 3048 233088913 233086970 0.000000e+00 2545.0
13 TraesCS6A01G168900 chr6B 85.902 532 35 16 49 577 233674936 233674442 7.700000e-147 531.0
14 TraesCS6A01G168900 chr6B 80.734 109 19 2 2441 2548 479079564 479079457 2.590000e-12 84.2
15 TraesCS6A01G168900 chr2D 91.856 835 66 2 3214 4046 145724983 145725817 0.000000e+00 1164.0
16 TraesCS6A01G168900 chr2D 91.765 85 7 0 588 672 627553866 627553782 7.100000e-23 119.0
17 TraesCS6A01G168900 chr7B 87.784 835 100 2 3214 4046 324399526 324398692 0.000000e+00 976.0
18 TraesCS6A01G168900 chr7B 85.048 836 121 4 3214 4046 579678260 579679094 0.000000e+00 848.0
19 TraesCS6A01G168900 chr1B 85.988 835 114 3 3214 4046 288039495 288038662 0.000000e+00 891.0
20 TraesCS6A01G168900 chr1B 92.771 83 6 0 588 670 392736122 392736040 1.980000e-23 121.0
21 TraesCS6A01G168900 chr5B 85.066 837 120 5 3214 4046 390522114 390521279 0.000000e+00 848.0
22 TraesCS6A01G168900 chr5B 84.946 837 121 5 3214 4046 390401249 390400414 0.000000e+00 843.0
23 TraesCS6A01G168900 chr1D 83.134 836 135 6 3214 4046 293609485 293610317 0.000000e+00 758.0
24 TraesCS6A01G168900 chr1D 91.304 92 7 1 581 672 462461619 462461529 1.530000e-24 124.0
25 TraesCS6A01G168900 chr1D 91.860 86 6 1 588 673 397231882 397231798 7.100000e-23 119.0
26 TraesCS6A01G168900 chr4A 81.993 833 148 2 3215 4046 361716190 361717021 0.000000e+00 706.0
27 TraesCS6A01G168900 chr7D 75.221 565 98 18 2193 2743 30130409 30129873 3.150000e-56 230.0
28 TraesCS6A01G168900 chr7D 91.860 86 7 0 588 673 34494601 34494516 1.980000e-23 121.0
29 TraesCS6A01G168900 chrUn 91.765 85 7 0 585 669 5551070 5551154 7.100000e-23 119.0
30 TraesCS6A01G168900 chrUn 91.765 85 7 0 585 669 13209343 13209427 7.100000e-23 119.0
31 TraesCS6A01G168900 chr3D 88.776 98 10 1 575 672 358187496 358187592 7.100000e-23 119.0
32 TraesCS6A01G168900 chr3D 91.011 89 7 1 581 669 576600557 576600644 7.100000e-23 119.0


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 TraesCS6A01G168900 chr6A 176291009 176295054 4045 True 7472.0 7472 100.0000 1 4046 1 chr6A.!!$R3 4045
1 TraesCS6A01G168900 chr6A 175995634 175997191 1557 True 2104.0 2104 90.9780 1477 3048 1 chr6A.!!$R1 1571
2 TraesCS6A01G168900 chr6D 134740489 134742432 1943 True 2512.0 2512 90.0100 1096 3048 1 chr6D.!!$R3 1952
3 TraesCS6A01G168900 chr6D 134335549 134337497 1948 True 2479.0 2479 89.6900 1096 3048 1 chr6D.!!$R2 1952
4 TraesCS6A01G168900 chr6D 135039644 135042709 3065 True 2363.5 4100 91.8080 30 3215 2 chr6D.!!$R5 3185
5 TraesCS6A01G168900 chr6D 134586192 134589259 3067 True 2356.0 4091 91.6795 30 3215 2 chr6D.!!$R4 3185
6 TraesCS6A01G168900 chr6D 349734727 349735559 832 False 1044.0 1044 89.3290 3215 4046 1 chr6D.!!$F1 831
7 TraesCS6A01G168900 chr6B 233086970 233088913 1943 True 2545.0 2545 90.3110 1096 3048 1 chr6B.!!$R1 1952
8 TraesCS6A01G168900 chr6B 233671906 233674936 3030 True 2286.0 4041 90.6625 49 3215 2 chr6B.!!$R3 3166
9 TraesCS6A01G168900 chr2D 145724983 145725817 834 False 1164.0 1164 91.8560 3214 4046 1 chr2D.!!$F1 832
10 TraesCS6A01G168900 chr7B 324398692 324399526 834 True 976.0 976 87.7840 3214 4046 1 chr7B.!!$R1 832
11 TraesCS6A01G168900 chr7B 579678260 579679094 834 False 848.0 848 85.0480 3214 4046 1 chr7B.!!$F1 832
12 TraesCS6A01G168900 chr1B 288038662 288039495 833 True 891.0 891 85.9880 3214 4046 1 chr1B.!!$R1 832
13 TraesCS6A01G168900 chr5B 390521279 390522114 835 True 848.0 848 85.0660 3214 4046 1 chr5B.!!$R2 832
14 TraesCS6A01G168900 chr5B 390400414 390401249 835 True 843.0 843 84.9460 3214 4046 1 chr5B.!!$R1 832
15 TraesCS6A01G168900 chr1D 293609485 293610317 832 False 758.0 758 83.1340 3214 4046 1 chr1D.!!$F1 832
16 TraesCS6A01G168900 chr4A 361716190 361717021 831 False 706.0 706 81.9930 3215 4046 1 chr4A.!!$F1 831
17 TraesCS6A01G168900 chr7D 30129873 30130409 536 True 230.0 230 75.2210 2193 2743 1 chr7D.!!$R1 550

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
675 684 0.035152 TACGGAGGGAGTAGTTGCGA 60.035 55.000 0.00 0.00 0.00 5.10 F
960 994 0.740868 CGTGCCCACTCATCATCGTT 60.741 55.000 0.00 0.00 0.00 3.85 F
963 997 1.003003 TGCCCACTCATCATCGTTTGA 59.997 47.619 0.00 0.00 39.12 2.69 F
1980 2023 1.052617 TTGTGGAAGACGGTCATCCA 58.947 50.000 26.39 26.39 41.43 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2017 1.910580 GAACGCCCTTCCCTGGATGA 61.911 60.000 0.00 0.0 0.00 2.92 R
1980 2023 2.203938 TCCAGAACGCCCTTCCCT 60.204 61.111 0.00 0.0 0.00 4.20 R
2124 2167 3.058708 CGAGTTCCGAGTACTTGTACACA 60.059 47.826 9.32 0.0 41.76 3.72 R
3291 3370 0.730265 GTGCCGGATGTTCGCATTTA 59.270 50.000 5.05 0.0 38.08 1.40 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
23 24 6.406692 TCTAGGATTTTCGGGTAGATCTTG 57.593 41.667 0.00 0.00 0.00 3.02
24 25 3.809905 AGGATTTTCGGGTAGATCTTGC 58.190 45.455 0.00 0.00 0.00 4.01
25 26 3.456277 AGGATTTTCGGGTAGATCTTGCT 59.544 43.478 0.00 0.00 0.00 3.91
26 27 3.561725 GGATTTTCGGGTAGATCTTGCTG 59.438 47.826 0.00 0.00 0.00 4.41
27 28 2.691409 TTTCGGGTAGATCTTGCTGG 57.309 50.000 0.00 0.00 0.00 4.85
28 29 1.568504 TTCGGGTAGATCTTGCTGGT 58.431 50.000 0.00 0.00 0.00 4.00
36 37 1.375098 GATCTTGCTGGTGAGGCTGC 61.375 60.000 0.00 0.00 0.00 5.25
110 111 3.760035 ACTCCCGTCGCTCGCAAT 61.760 61.111 0.00 0.00 38.35 3.56
141 142 2.561549 TTATTCCGTCCGCCCGTCAC 62.562 60.000 0.00 0.00 0.00 3.67
202 203 1.136984 GCAGGTCGTCGTCCACTAG 59.863 63.158 11.13 0.00 0.00 2.57
272 273 2.170397 TCATCATACGCCATGTCCAACT 59.830 45.455 0.00 0.00 35.96 3.16
288 289 1.115326 AACTTTCCTTGCACCTGGCC 61.115 55.000 0.00 0.00 43.89 5.36
319 324 3.195661 GCTCGGATGGTAGAATTTTCGT 58.804 45.455 0.00 0.00 0.00 3.85
329 334 9.314321 GATGGTAGAATTTTCGTATCTTCAGAA 57.686 33.333 0.00 0.00 0.00 3.02
361 366 3.503363 GTGCCGCATCTGGTCTGC 61.503 66.667 0.00 0.00 36.26 4.26
454 461 3.949754 TGATGGTTGAATCTGATTGCTCC 59.050 43.478 7.78 7.36 0.00 4.70
456 463 2.290260 TGGTTGAATCTGATTGCTCCGT 60.290 45.455 7.78 0.00 0.00 4.69
473 480 2.108157 TGGTGCGCGTCTTCACTT 59.892 55.556 8.43 0.00 33.91 3.16
494 501 5.940470 ACTTCCAGTAGAAATGGTGTGAATC 59.060 40.000 0.00 0.00 39.01 2.52
572 581 9.628500 AAAGGTTTAGATCACTACAAAAAGAGT 57.372 29.630 0.00 0.00 0.00 3.24
573 582 8.608844 AGGTTTAGATCACTACAAAAAGAGTG 57.391 34.615 0.00 0.00 43.70 3.51
593 602 9.440761 AAGAGTGATAGTATTGTTATTCCCTCT 57.559 33.333 0.00 0.00 0.00 3.69
613 622 9.750783 TCCCTCTATAAACTAATATAAGAGCGT 57.249 33.333 0.00 0.00 0.00 5.07
673 682 3.538634 ATTTACGGAGGGAGTAGTTGC 57.461 47.619 0.00 0.00 0.00 4.17
674 683 0.813184 TTACGGAGGGAGTAGTTGCG 59.187 55.000 0.00 0.00 0.00 4.85
675 684 0.035152 TACGGAGGGAGTAGTTGCGA 60.035 55.000 0.00 0.00 0.00 5.10
693 702 2.418197 GCGACCACAATACCTGAGCTTA 60.418 50.000 0.00 0.00 0.00 3.09
773 782 2.704572 AGGAGAGCGAAAGGTTTGATG 58.295 47.619 0.00 0.00 45.11 3.07
787 796 3.633986 GGTTTGATGATTGACTCCCCATC 59.366 47.826 0.00 0.00 36.77 3.51
825 834 2.996395 CTCCAGCTGCACATCCCT 59.004 61.111 8.66 0.00 0.00 4.20
826 835 1.302285 CTCCAGCTGCACATCCCTT 59.698 57.895 8.66 0.00 0.00 3.95
828 837 1.001764 CCAGCTGCACATCCCTTCA 60.002 57.895 8.66 0.00 0.00 3.02
953 987 4.415150 CCTGGCGTGCCCACTCAT 62.415 66.667 8.69 0.00 39.18 2.90
954 988 2.821366 CTGGCGTGCCCACTCATC 60.821 66.667 8.69 0.00 39.18 2.92
955 989 3.610619 CTGGCGTGCCCACTCATCA 62.611 63.158 8.69 0.00 39.18 3.07
956 990 2.124570 GGCGTGCCCACTCATCAT 60.125 61.111 0.00 0.00 0.00 2.45
957 991 2.182842 GGCGTGCCCACTCATCATC 61.183 63.158 0.00 0.00 0.00 2.92
958 992 2.528743 GCGTGCCCACTCATCATCG 61.529 63.158 0.00 0.00 0.00 3.84
959 993 1.153568 CGTGCCCACTCATCATCGT 60.154 57.895 0.00 0.00 0.00 3.73
960 994 0.740868 CGTGCCCACTCATCATCGTT 60.741 55.000 0.00 0.00 0.00 3.85
961 995 1.453155 GTGCCCACTCATCATCGTTT 58.547 50.000 0.00 0.00 0.00 3.60
962 996 1.131126 GTGCCCACTCATCATCGTTTG 59.869 52.381 0.00 0.00 0.00 2.93
963 997 1.003003 TGCCCACTCATCATCGTTTGA 59.997 47.619 0.00 0.00 39.12 2.69
964 998 1.398390 GCCCACTCATCATCGTTTGAC 59.602 52.381 0.00 0.00 37.11 3.18
965 999 2.936993 GCCCACTCATCATCGTTTGACT 60.937 50.000 0.00 0.00 37.11 3.41
966 1000 2.932614 CCCACTCATCATCGTTTGACTC 59.067 50.000 0.00 0.00 37.11 3.36
1003 1037 3.174573 GCGCAACCGAAGCAATGC 61.175 61.111 0.30 0.00 36.29 3.56
1974 2017 2.280592 GGCGTTGTGGAAGACGGT 60.281 61.111 0.00 0.00 39.52 4.83
1980 2023 1.052617 TTGTGGAAGACGGTCATCCA 58.947 50.000 26.39 26.39 41.43 3.41
1995 2038 1.915078 ATCCAGGGAAGGGCGTTCTG 61.915 60.000 18.29 10.33 35.25 3.02
2124 2167 2.997897 GCGGTGGAGTCCCTGACT 60.998 66.667 6.74 0.00 46.42 3.41
2559 2617 2.032981 CGCCAAGGTGTCAAGCTTT 58.967 52.632 0.00 0.00 42.19 3.51
3048 3106 3.606595 TCGATCGTCGGGAGATAGTAT 57.393 47.619 15.94 0.00 43.27 2.12
3049 3107 4.725790 TCGATCGTCGGGAGATAGTATA 57.274 45.455 15.94 0.00 43.27 1.47
3050 3108 4.680702 TCGATCGTCGGGAGATAGTATAG 58.319 47.826 15.94 0.00 43.27 1.31
3051 3109 3.803231 CGATCGTCGGGAGATAGTATAGG 59.197 52.174 7.03 0.00 43.27 2.57
3052 3110 4.441217 CGATCGTCGGGAGATAGTATAGGA 60.441 50.000 7.03 0.00 43.27 2.94
3062 3120 6.296547 GGGAGATAGTATAGGAGTACTCAGCA 60.297 46.154 23.91 8.79 36.39 4.41
3066 3124 7.668052 AGATAGTATAGGAGTACTCAGCAAAGG 59.332 40.741 23.91 0.00 36.39 3.11
3138 3217 8.460831 TTTCTTTTTAGTTGAAGAGTGCAAAC 57.539 30.769 0.00 0.00 33.77 2.93
3201 3280 7.803279 TGTGATTCGAGTCATGTATAGTACT 57.197 36.000 14.12 0.00 0.00 2.73
3202 3281 8.221965 TGTGATTCGAGTCATGTATAGTACTT 57.778 34.615 14.12 0.00 0.00 2.24
3203 3282 8.343366 TGTGATTCGAGTCATGTATAGTACTTC 58.657 37.037 14.12 0.00 0.00 3.01
3204 3283 8.343366 GTGATTCGAGTCATGTATAGTACTTCA 58.657 37.037 14.12 0.00 0.00 3.02
3205 3284 9.067986 TGATTCGAGTCATGTATAGTACTTCAT 57.932 33.333 6.51 1.43 0.00 2.57
3206 3285 9.900710 GATTCGAGTCATGTATAGTACTTCATT 57.099 33.333 0.00 0.00 0.00 2.57
3208 3287 9.731819 TTCGAGTCATGTATAGTACTTCATTTC 57.268 33.333 0.00 2.22 0.00 2.17
3209 3288 8.899771 TCGAGTCATGTATAGTACTTCATTTCA 58.100 33.333 0.00 0.00 0.00 2.69
3210 3289 9.516314 CGAGTCATGTATAGTACTTCATTTCAA 57.484 33.333 0.00 0.00 0.00 2.69
3291 3370 5.385198 ACATGATTACAGGAAGTGTGGTTT 58.615 37.500 0.00 0.00 40.69 3.27
3304 3383 4.794169 AGTGTGGTTTAAATGCGAACATC 58.206 39.130 0.00 0.00 34.62 3.06
3371 3452 7.606839 ACAGCTAAACTAACTCCTCATAAAACC 59.393 37.037 0.00 0.00 0.00 3.27
3391 3472 2.224769 CCTTGTAGACCACCAACACCAT 60.225 50.000 0.00 0.00 0.00 3.55
3421 3502 1.810532 GACCACTCGGCTACCTCAG 59.189 63.158 0.00 0.00 34.57 3.35
3433 3514 4.559153 GGCTACCTCAGTTAACGTACAAA 58.441 43.478 0.00 0.00 0.00 2.83
3565 3647 1.004277 TGTCCGCCCATAGAAAGCTTT 59.996 47.619 12.53 12.53 0.00 3.51
3585 3667 1.884075 TTCGTGCTCGTAGCCACCAT 61.884 55.000 8.17 0.00 41.51 3.55
3623 3705 0.741221 GCGAGTGATTGAGGGGTGTC 60.741 60.000 0.00 0.00 0.00 3.67
3681 3763 1.202043 CGAGCGTACAGACACTGTAGG 60.202 57.143 20.12 20.12 45.88 3.18
3706 3788 7.711772 GGAGAATATGATCAGCATTATCCTCAG 59.288 40.741 25.30 0.00 37.18 3.35
3729 3811 0.040514 GCAAACACGTGTAGCATGCA 60.041 50.000 29.93 2.77 32.80 3.96
3741 3823 0.917533 AGCATGCAGAACTCCCATCT 59.082 50.000 21.98 0.00 0.00 2.90
3755 3837 1.397390 CCATCTTGAAGCCCATGCCC 61.397 60.000 0.00 0.00 38.69 5.36
3835 3917 0.332972 CTTAAGAGGGCCCCAGCTTT 59.667 55.000 21.43 8.62 39.73 3.51
3856 3938 0.179020 CCAGACACACTTTGCCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
3879 3961 2.298163 GGATTTAGGCCATCCATTGCAG 59.702 50.000 14.35 0.00 40.21 4.41
3927 4009 4.495422 AGTATTGTCCAGACGATGAACAC 58.505 43.478 10.28 1.64 36.19 3.32
3954 4037 3.376935 AAGGCATCCTGCTCGGTCG 62.377 63.158 0.00 0.00 44.28 4.79
3955 4038 4.899239 GGCATCCTGCTCGGTCGG 62.899 72.222 0.00 0.00 44.28 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.991687 GCAAGATCTACCCGAAAATCCTAG 59.008 45.833 0.00 0.00 0.00 3.02
3 4 3.456277 AGCAAGATCTACCCGAAAATCCT 59.544 43.478 0.00 0.00 0.00 3.24
4 5 3.561725 CAGCAAGATCTACCCGAAAATCC 59.438 47.826 0.00 0.00 0.00 3.01
5 6 3.561725 CCAGCAAGATCTACCCGAAAATC 59.438 47.826 0.00 0.00 0.00 2.17
6 7 3.054361 ACCAGCAAGATCTACCCGAAAAT 60.054 43.478 0.00 0.00 0.00 1.82
7 8 2.304761 ACCAGCAAGATCTACCCGAAAA 59.695 45.455 0.00 0.00 0.00 2.29
8 9 1.906574 ACCAGCAAGATCTACCCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
9 10 1.207089 CACCAGCAAGATCTACCCGAA 59.793 52.381 0.00 0.00 0.00 4.30
10 11 0.824109 CACCAGCAAGATCTACCCGA 59.176 55.000 0.00 0.00 0.00 5.14
11 12 0.824109 TCACCAGCAAGATCTACCCG 59.176 55.000 0.00 0.00 0.00 5.28
12 13 1.139853 CCTCACCAGCAAGATCTACCC 59.860 57.143 0.00 0.00 0.00 3.69
13 14 1.474143 GCCTCACCAGCAAGATCTACC 60.474 57.143 0.00 0.00 0.00 3.18
14 15 1.484240 AGCCTCACCAGCAAGATCTAC 59.516 52.381 0.00 0.00 0.00 2.59
15 16 1.483827 CAGCCTCACCAGCAAGATCTA 59.516 52.381 0.00 0.00 0.00 1.98
16 17 0.252479 CAGCCTCACCAGCAAGATCT 59.748 55.000 0.00 0.00 0.00 2.75
17 18 1.375098 GCAGCCTCACCAGCAAGATC 61.375 60.000 0.00 0.00 0.00 2.75
18 19 1.378250 GCAGCCTCACCAGCAAGAT 60.378 57.895 0.00 0.00 0.00 2.40
19 20 2.033141 GCAGCCTCACCAGCAAGA 59.967 61.111 0.00 0.00 0.00 3.02
20 21 3.060615 GGCAGCCTCACCAGCAAG 61.061 66.667 3.29 0.00 0.00 4.01
152 153 1.522569 GAGGGAGGAACGGTCATGG 59.477 63.158 1.31 0.00 0.00 3.66
202 203 5.221891 TCAATATTCAAAGCAACTCTCGC 57.778 39.130 0.00 0.00 0.00 5.03
272 273 2.597217 CGGCCAGGTGCAAGGAAA 60.597 61.111 2.24 0.00 43.89 3.13
288 289 1.301244 CATCCGAGCCTTCCATCCG 60.301 63.158 0.00 0.00 0.00 4.18
319 324 7.397476 ACCTACATGTCTGAACTTCTGAAGATA 59.603 37.037 23.36 8.29 0.00 1.98
329 334 1.066858 CGGCACCTACATGTCTGAACT 60.067 52.381 0.00 0.00 0.00 3.01
361 366 0.532862 ATTATTCCCGAGCACAGCCG 60.533 55.000 0.00 0.00 0.00 5.52
391 398 7.327975 CCTGGTTTACCAAATTAATCCCTTTC 58.672 38.462 2.81 0.00 46.97 2.62
408 415 2.825532 GGCTTCTGATTTGCCTGGTTTA 59.174 45.455 8.84 0.00 43.05 2.01
409 416 1.620323 GGCTTCTGATTTGCCTGGTTT 59.380 47.619 8.84 0.00 43.05 3.27
456 463 1.954146 GAAGTGAAGACGCGCACCA 60.954 57.895 5.73 0.00 35.67 4.17
473 480 4.536090 AGGATTCACACCATTTCTACTGGA 59.464 41.667 0.00 0.00 37.22 3.86
549 557 8.603242 TCACTCTTTTTGTAGTGATCTAAACC 57.397 34.615 1.19 0.00 45.40 3.27
567 576 9.440761 AGAGGGAATAACAATACTATCACTCTT 57.559 33.333 0.00 0.00 0.00 2.85
587 596 9.750783 ACGCTCTTATATTAGTTTATAGAGGGA 57.249 33.333 16.73 0.00 37.30 4.20
647 656 7.876582 GCAACTACTCCCTCCGTAAATTAATAT 59.123 37.037 0.00 0.00 0.00 1.28
648 657 7.212274 GCAACTACTCCCTCCGTAAATTAATA 58.788 38.462 0.00 0.00 0.00 0.98
649 658 6.053650 GCAACTACTCCCTCCGTAAATTAAT 58.946 40.000 0.00 0.00 0.00 1.40
650 659 5.422145 GCAACTACTCCCTCCGTAAATTAA 58.578 41.667 0.00 0.00 0.00 1.40
651 660 4.440525 CGCAACTACTCCCTCCGTAAATTA 60.441 45.833 0.00 0.00 0.00 1.40
652 661 3.677976 CGCAACTACTCCCTCCGTAAATT 60.678 47.826 0.00 0.00 0.00 1.82
653 662 2.159142 CGCAACTACTCCCTCCGTAAAT 60.159 50.000 0.00 0.00 0.00 1.40
654 663 1.203052 CGCAACTACTCCCTCCGTAAA 59.797 52.381 0.00 0.00 0.00 2.01
655 664 0.813184 CGCAACTACTCCCTCCGTAA 59.187 55.000 0.00 0.00 0.00 3.18
656 665 0.035152 TCGCAACTACTCCCTCCGTA 60.035 55.000 0.00 0.00 0.00 4.02
657 666 1.303888 TCGCAACTACTCCCTCCGT 60.304 57.895 0.00 0.00 0.00 4.69
658 667 1.139095 GTCGCAACTACTCCCTCCG 59.861 63.158 0.00 0.00 0.00 4.63
659 668 1.255667 TGGTCGCAACTACTCCCTCC 61.256 60.000 0.00 0.00 0.00 4.30
660 669 0.108756 GTGGTCGCAACTACTCCCTC 60.109 60.000 0.00 0.00 34.28 4.30
661 670 0.830444 TGTGGTCGCAACTACTCCCT 60.830 55.000 0.00 0.00 37.72 4.20
662 671 0.034337 TTGTGGTCGCAACTACTCCC 59.966 55.000 0.00 0.00 37.72 4.30
663 672 2.094762 ATTGTGGTCGCAACTACTCC 57.905 50.000 0.00 0.00 37.72 3.85
664 673 2.928116 GGTATTGTGGTCGCAACTACTC 59.072 50.000 0.00 0.00 37.72 2.59
665 674 2.565834 AGGTATTGTGGTCGCAACTACT 59.434 45.455 0.00 0.00 37.72 2.57
666 675 2.671396 CAGGTATTGTGGTCGCAACTAC 59.329 50.000 0.00 4.43 37.39 2.73
667 676 2.563620 TCAGGTATTGTGGTCGCAACTA 59.436 45.455 0.00 0.00 0.00 2.24
673 682 2.386661 AAGCTCAGGTATTGTGGTCG 57.613 50.000 0.00 0.00 31.22 4.79
674 683 4.770795 ACATAAGCTCAGGTATTGTGGTC 58.229 43.478 0.00 0.00 31.22 4.02
675 684 4.844349 ACATAAGCTCAGGTATTGTGGT 57.156 40.909 0.00 0.00 32.81 4.16
723 732 9.075678 AGTCTTTCATTTGATCATTTCTCTTGT 57.924 29.630 0.00 0.00 0.00 3.16
773 782 1.216990 ACTGGGATGGGGAGTCAATC 58.783 55.000 0.00 0.00 0.00 2.67
856 865 1.610038 TCAAAGGTCGTCGCTTCTACA 59.390 47.619 0.00 0.00 0.00 2.74
857 866 1.984297 GTCAAAGGTCGTCGCTTCTAC 59.016 52.381 0.00 0.00 0.00 2.59
949 983 4.115401 TGAGGAGTCAAACGATGATGAG 57.885 45.455 0.00 0.00 40.97 2.90
950 984 4.442052 GGATGAGGAGTCAAACGATGATGA 60.442 45.833 0.00 0.00 40.97 2.92
951 985 3.806521 GGATGAGGAGTCAAACGATGATG 59.193 47.826 0.00 0.00 40.97 3.07
952 986 3.181461 GGGATGAGGAGTCAAACGATGAT 60.181 47.826 0.00 0.00 40.97 2.45
953 987 2.168521 GGGATGAGGAGTCAAACGATGA 59.831 50.000 0.00 0.00 35.88 2.92
954 988 2.555199 GGGATGAGGAGTCAAACGATG 58.445 52.381 0.00 0.00 35.88 3.84
955 989 1.486726 GGGGATGAGGAGTCAAACGAT 59.513 52.381 0.00 0.00 35.88 3.73
956 990 0.902531 GGGGATGAGGAGTCAAACGA 59.097 55.000 0.00 0.00 35.88 3.85
957 991 0.905357 AGGGGATGAGGAGTCAAACG 59.095 55.000 0.00 0.00 35.88 3.60
958 992 3.348119 GAAAGGGGATGAGGAGTCAAAC 58.652 50.000 0.00 0.00 35.88 2.93
959 993 2.308866 GGAAAGGGGATGAGGAGTCAAA 59.691 50.000 0.00 0.00 35.88 2.69
960 994 1.916181 GGAAAGGGGATGAGGAGTCAA 59.084 52.381 0.00 0.00 35.88 3.18
961 995 1.203428 TGGAAAGGGGATGAGGAGTCA 60.203 52.381 0.00 0.00 37.02 3.41
962 996 1.584724 TGGAAAGGGGATGAGGAGTC 58.415 55.000 0.00 0.00 0.00 3.36
963 997 1.918957 CTTGGAAAGGGGATGAGGAGT 59.081 52.381 0.00 0.00 41.27 3.85
964 998 2.200081 TCTTGGAAAGGGGATGAGGAG 58.800 52.381 0.00 0.00 46.24 3.69
965 999 2.359376 TCTTGGAAAGGGGATGAGGA 57.641 50.000 0.00 0.00 46.24 3.71
966 1000 2.947695 GCTTCTTGGAAAGGGGATGAGG 60.948 54.545 0.00 0.00 46.24 3.86
1170 1204 2.668212 GCGTTGCAGGTGTAGCCA 60.668 61.111 0.00 0.00 40.61 4.75
1974 2017 1.910580 GAACGCCCTTCCCTGGATGA 61.911 60.000 0.00 0.00 0.00 2.92
1980 2023 2.203938 TCCAGAACGCCCTTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
2124 2167 3.058708 CGAGTTCCGAGTACTTGTACACA 60.059 47.826 9.32 0.00 41.76 3.72
3048 3106 3.507411 ACACCTTTGCTGAGTACTCCTA 58.493 45.455 20.11 1.43 0.00 2.94
3049 3107 2.300437 GACACCTTTGCTGAGTACTCCT 59.700 50.000 20.11 0.00 0.00 3.69
3050 3108 2.300437 AGACACCTTTGCTGAGTACTCC 59.700 50.000 20.11 6.32 0.00 3.85
3051 3109 3.669251 AGACACCTTTGCTGAGTACTC 57.331 47.619 16.32 16.32 0.00 2.59
3052 3110 4.423625 AAAGACACCTTTGCTGAGTACT 57.576 40.909 0.00 0.00 40.83 2.73
3062 3120 6.126409 TGTCCATAACAGAAAAGACACCTTT 58.874 36.000 0.00 0.00 37.50 3.11
3268 3347 4.640771 ACCACACTTCCTGTAATCATGT 57.359 40.909 0.00 0.00 0.00 3.21
3272 3351 6.806739 GCATTTAAACCACACTTCCTGTAATC 59.193 38.462 0.00 0.00 0.00 1.75
3279 3358 3.907894 TCGCATTTAAACCACACTTCC 57.092 42.857 0.00 0.00 0.00 3.46
3291 3370 0.730265 GTGCCGGATGTTCGCATTTA 59.270 50.000 5.05 0.00 38.08 1.40
3304 3383 2.098233 GTGTATCCGTGTGTGCCGG 61.098 63.158 0.00 0.00 46.83 6.13
3371 3452 2.631160 TGGTGTTGGTGGTCTACAAG 57.369 50.000 0.00 0.00 0.00 3.16
3391 3472 3.755628 GTGGTCGCAGGCGGTAGA 61.756 66.667 14.24 0.00 40.25 2.59
3421 3502 6.890558 TGGAGCTTGTTATTTGTACGTTAAC 58.109 36.000 0.00 0.00 0.00 2.01
3467 3549 8.543774 AGAGAAATGCAAGAGTCTTTAATAGGA 58.456 33.333 1.56 0.00 0.00 2.94
3506 3588 0.968901 AGTCACGGCGGTTCTATGGA 60.969 55.000 13.24 0.00 0.00 3.41
3565 3647 1.373748 GGTGGCTACGAGCACGAAA 60.374 57.895 11.40 0.00 44.75 3.46
3585 3667 6.016192 CACTCGCTAATGAGAATACCCTAGAA 60.016 42.308 0.00 0.00 39.35 2.10
3623 3705 1.379916 TGGGACACCCTGCAGATTG 59.620 57.895 17.39 13.96 45.70 2.67
3681 3763 7.225145 GCTGAGGATAATGCTGATCATATTCTC 59.775 40.741 12.65 12.65 34.33 2.87
3706 3788 1.082104 GCTACACGTGTTTGCAGGC 60.082 57.895 28.55 16.56 34.13 4.85
3729 3811 1.283321 GGGCTTCAAGATGGGAGTTCT 59.717 52.381 0.00 0.00 0.00 3.01
3741 3823 2.681064 GCTGGGCATGGGCTTCAA 60.681 61.111 0.00 0.00 40.87 2.69
3755 3837 2.219325 GACGTCAGACAGGAGGGCTG 62.219 65.000 11.55 0.00 0.00 4.85
3835 3917 1.679139 CTGGCAAAGTGTGTCTGGAA 58.321 50.000 0.00 0.00 30.97 3.53
3856 3938 2.757606 GCAATGGATGGCCTAAATCCCT 60.758 50.000 16.08 5.50 42.63 4.20
3879 3961 3.431486 CCAAGTCAGTCTATTCCAGCCTC 60.431 52.174 0.00 0.00 0.00 4.70
3927 4009 1.019673 CAGGATGCCTTCAATGGACG 58.980 55.000 0.00 0.00 0.00 4.79
3954 4037 3.106407 GACTGTGCGCAGACGTCC 61.106 66.667 32.90 12.32 45.28 4.79


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

AutoCloner maintained by Alex Coulton.