Multiple sequence alignment - TraesCS3D01G434500

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 TraesCS3D01G434500 chr3D 100.000 3591 0 0 875 4465 546997416 547001006 0.000000e+00 6632.0
1 TraesCS3D01G434500 chr3D 100.000 588 0 0 1 588 546996542 546997129 0.000000e+00 1086.0
2 TraesCS3D01G434500 chr3A 93.282 1295 67 10 879 2155 683543988 683545280 0.000000e+00 1892.0
3 TraesCS3D01G434500 chr3A 92.537 1206 49 12 2298 3464 683545683 683546886 0.000000e+00 1690.0
4 TraesCS3D01G434500 chr3A 85.324 586 29 20 3595 4171 683547028 683547565 1.810000e-153 553.0
5 TraesCS3D01G434500 chr3A 83.908 522 29 23 84 556 683543360 683543875 8.810000e-122 448.0
6 TraesCS3D01G434500 chr3A 81.023 606 53 25 3894 4465 683680452 683681029 4.130000e-115 425.0
7 TraesCS3D01G434500 chr3A 87.544 281 23 3 4197 4465 24201618 24201338 9.320000e-82 315.0
8 TraesCS3D01G434500 chr3A 88.462 234 16 2 4241 4465 683547807 683548038 5.690000e-69 272.0
9 TraesCS3D01G434500 chr3B 90.189 1478 71 24 3023 4465 724185131 724186569 0.000000e+00 1858.0
10 TraesCS3D01G434500 chr3B 94.477 1213 49 7 958 2155 724182689 724183898 0.000000e+00 1853.0
11 TraesCS3D01G434500 chr3B 92.035 904 32 7 2158 3030 724183986 724184880 0.000000e+00 1234.0
12 TraesCS3D01G434500 chr3B 84.764 571 18 22 9 556 724182027 724182551 3.980000e-140 508.0
13 TraesCS3D01G434500 chr3B 96.429 56 2 0 879 934 724182636 724182691 4.760000e-15 93.5
14 TraesCS3D01G434500 chr3B 97.727 44 0 1 4197 4240 805483939 805483897 1.720000e-09 75.0
15 TraesCS3D01G434500 chr2A 88.849 278 20 2 4197 4465 5290188 5290463 9.260000e-87 331.0
16 TraesCS3D01G434500 chr7A 83.796 216 21 4 4234 4440 115587607 115587397 4.560000e-45 193.0
17 TraesCS3D01G434500 chr7A 87.302 63 5 2 4197 4259 454290791 454290732 8.010000e-08 69.4
18 TraesCS3D01G434500 chr6A 85.976 164 9 5 4234 4383 156674112 156673949 3.570000e-36 163.0
19 TraesCS3D01G434500 chr6A 84.810 158 11 4 4234 4378 519768176 519768333 3.600000e-31 147.0
20 TraesCS3D01G434500 chr2D 83.537 164 8 6 4234 4378 141501246 141501409 7.790000e-28 135.0
21 TraesCS3D01G434500 chr2B 100.000 42 0 0 4197 4238 681332000 681332041 1.330000e-10 78.7
22 TraesCS3D01G434500 chrUn 97.727 44 0 1 4197 4240 75923156 75923114 1.720000e-09 75.0
23 TraesCS3D01G434500 chr6B 95.745 47 1 1 4194 4240 9987597 9987642 1.720000e-09 75.0
24 TraesCS3D01G434500 chr6B 90.741 54 2 3 4188 4240 664040540 664040591 8.010000e-08 69.4
25 TraesCS3D01G434500 chr1B 97.727 44 0 1 4197 4240 299716697 299716739 1.720000e-09 75.0


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 TraesCS3D01G434500 chr3D 546996542 547001006 4464 False 3859.0 6632 100.0000 1 4465 2 chr3D.!!$F1 4464
1 TraesCS3D01G434500 chr3A 683543360 683548038 4678 False 971.0 1892 88.7026 84 4465 5 chr3A.!!$F2 4381
2 TraesCS3D01G434500 chr3A 683680452 683681029 577 False 425.0 425 81.0230 3894 4465 1 chr3A.!!$F1 571
3 TraesCS3D01G434500 chr3B 724182027 724186569 4542 False 1109.3 1858 91.5788 9 4465 5 chr3B.!!$F1 4456

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
564 684 0.036858 GCAGAGCTCCTTCCGTTTCT 60.037 55.0 10.93 0.0 0.0 2.52 F
953 1073 0.320374 ACTCGAGCATTTCCCGTTGA 59.680 50.0 13.61 0.0 0.0 3.18 F
1947 2106 0.747283 CGTCCGGTAGCCTCTACACT 60.747 60.0 0.00 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2490 0.305922 GCCAATAGCAGACATCGCAC 59.694 55.0 0.00 0.0 42.97 5.34 R
2577 3064 1.708822 AAATTCAAATGGCGCGGAAC 58.291 45.0 8.83 0.0 0.00 3.62 R
3724 4550 0.038166 TTGTTGTCCCCAGGCTCATC 59.962 55.0 0.00 0.0 0.00 2.92 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
17 18 3.408853 GGTTCCCCCTTCCCCTCG 61.409 72.222 0.00 0.00 0.00 4.63
27 28 3.283812 TTCCCCTCGCCTCGTCTCT 62.284 63.158 0.00 0.00 0.00 3.10
30 31 4.244802 CCTCGCCTCGTCTCTCGC 62.245 72.222 0.00 0.00 39.67 5.03
42 43 1.203523 GTCTCTCGCCCCTATGCTATG 59.796 57.143 0.00 0.00 0.00 2.23
70 71 1.677637 CTAGAGCCACCCCGAGGAAC 61.678 65.000 0.00 0.00 36.73 3.62
104 105 1.535028 GGTAAACGTAAACCCAACCGG 59.465 52.381 0.00 0.00 37.81 5.28
298 329 2.660802 GCCAATGCCTTTGCTGCT 59.339 55.556 0.00 0.00 38.71 4.24
307 338 1.002379 CTTTGCTGCTCCCTGCTCT 60.002 57.895 0.00 0.00 43.37 4.09
340 371 1.043116 CACCGTGAGAGCCTGGGATA 61.043 60.000 0.00 0.00 0.00 2.59
342 373 1.365633 CGTGAGAGCCTGGGATAGC 59.634 63.158 0.00 0.00 0.00 2.97
389 422 0.531200 CGACTTAAAGCTCCTCCCGT 59.469 55.000 0.00 0.00 0.00 5.28
476 526 4.454319 CTCTGCTCCGCTGCTGCT 62.454 66.667 14.03 0.00 36.97 4.24
522 582 1.623973 CGCCGTTTCCGTCTTCTTCC 61.624 60.000 0.00 0.00 0.00 3.46
564 684 0.036858 GCAGAGCTCCTTCCGTTTCT 60.037 55.000 10.93 0.00 0.00 2.52
582 702 0.605589 CTCTGTCCTCTTTCGGCTGT 59.394 55.000 0.00 0.00 0.00 4.40
914 1034 5.509716 TGCAGAAAATGGCATCTTGATAG 57.490 39.130 0.00 0.00 34.58 2.08
932 1052 7.786943 TCTTGATAGACCACTCTTTGATCCTAT 59.213 37.037 0.00 0.00 0.00 2.57
933 1053 7.921041 TGATAGACCACTCTTTGATCCTATT 57.079 36.000 0.00 0.00 0.00 1.73
934 1054 9.434275 TTGATAGACCACTCTTTGATCCTATTA 57.566 33.333 0.00 0.00 0.00 0.98
935 1055 8.861086 TGATAGACCACTCTTTGATCCTATTAC 58.139 37.037 0.00 0.00 0.00 1.89
936 1056 9.084533 GATAGACCACTCTTTGATCCTATTACT 57.915 37.037 0.00 0.00 0.00 2.24
937 1057 7.354751 AGACCACTCTTTGATCCTATTACTC 57.645 40.000 0.00 0.00 0.00 2.59
938 1058 6.039941 AGACCACTCTTTGATCCTATTACTCG 59.960 42.308 0.00 0.00 0.00 4.18
939 1059 5.892119 ACCACTCTTTGATCCTATTACTCGA 59.108 40.000 0.00 0.00 0.00 4.04
940 1060 6.039941 ACCACTCTTTGATCCTATTACTCGAG 59.960 42.308 11.84 11.84 0.00 4.04
941 1061 5.918011 CACTCTTTGATCCTATTACTCGAGC 59.082 44.000 13.61 0.00 0.00 5.03
942 1062 5.594725 ACTCTTTGATCCTATTACTCGAGCA 59.405 40.000 13.61 0.00 0.00 4.26
943 1063 6.266558 ACTCTTTGATCCTATTACTCGAGCAT 59.733 38.462 13.61 7.67 0.00 3.79
944 1064 7.055667 TCTTTGATCCTATTACTCGAGCATT 57.944 36.000 13.61 0.00 0.00 3.56
945 1065 7.500992 TCTTTGATCCTATTACTCGAGCATTT 58.499 34.615 13.61 0.00 0.00 2.32
946 1066 7.653713 TCTTTGATCCTATTACTCGAGCATTTC 59.346 37.037 13.61 0.00 0.00 2.17
947 1067 5.784177 TGATCCTATTACTCGAGCATTTCC 58.216 41.667 13.61 0.00 0.00 3.13
948 1068 4.602340 TCCTATTACTCGAGCATTTCCC 57.398 45.455 13.61 0.00 0.00 3.97
949 1069 3.005472 TCCTATTACTCGAGCATTTCCCG 59.995 47.826 13.61 0.00 0.00 5.14
950 1070 2.981859 ATTACTCGAGCATTTCCCGT 57.018 45.000 13.61 0.00 0.00 5.28
951 1071 2.754946 TTACTCGAGCATTTCCCGTT 57.245 45.000 13.61 0.00 0.00 4.44
952 1072 2.004583 TACTCGAGCATTTCCCGTTG 57.995 50.000 13.61 0.00 0.00 4.10
953 1073 0.320374 ACTCGAGCATTTCCCGTTGA 59.680 50.000 13.61 0.00 0.00 3.18
954 1074 1.002366 CTCGAGCATTTCCCGTTGAG 58.998 55.000 0.00 0.00 0.00 3.02
955 1075 1.019278 TCGAGCATTTCCCGTTGAGC 61.019 55.000 0.00 0.00 0.00 4.26
956 1076 1.425428 GAGCATTTCCCGTTGAGCG 59.575 57.895 0.00 0.00 40.95 5.03
957 1077 1.003839 AGCATTTCCCGTTGAGCGA 60.004 52.632 0.00 0.00 44.77 4.93
1061 1214 4.038080 CAAAACCCTCGCCGCCAC 62.038 66.667 0.00 0.00 0.00 5.01
1728 1887 2.740055 GTGAGGTCGCAGCAGGTG 60.740 66.667 0.00 0.00 0.00 4.00
1947 2106 0.747283 CGTCCGGTAGCCTCTACACT 60.747 60.000 0.00 0.00 0.00 3.55
1984 2152 8.594881 CTACCAAAGTAGCAGGTAAATCTATG 57.405 38.462 0.00 0.00 39.66 2.23
1986 2154 6.823689 ACCAAAGTAGCAGGTAAATCTATGTG 59.176 38.462 0.00 0.00 32.92 3.21
1989 2157 7.849804 AAGTAGCAGGTAAATCTATGTGTTG 57.150 36.000 0.00 0.00 0.00 3.33
1992 2160 6.054860 AGCAGGTAAATCTATGTGTTGTCT 57.945 37.500 0.00 0.00 0.00 3.41
2115 2288 7.855784 ATTATAATGAGGGGAAATTGAACCC 57.144 36.000 0.00 4.58 45.06 4.11
2139 2312 3.128242 GGCTATGCATCATTATCACTGCC 59.872 47.826 0.19 0.00 33.70 4.85
2145 2318 3.633525 GCATCATTATCACTGCCAGGAAA 59.366 43.478 0.00 0.00 0.00 3.13
2150 2323 5.425217 TCATTATCACTGCCAGGAAAGTAGA 59.575 40.000 0.00 0.00 0.00 2.59
2155 2328 5.211973 TCACTGCCAGGAAAGTAGATCTAT 58.788 41.667 5.57 0.00 0.00 1.98
2405 2891 9.233232 GCAACATTATATACTACCAAAACAAGC 57.767 33.333 0.00 0.00 0.00 4.01
2435 2921 5.521010 ACATTCCATTTCATTATTGCTTGCG 59.479 36.000 0.00 0.00 0.00 4.85
2443 2929 3.814842 TCATTATTGCTTGCGTCCATAGG 59.185 43.478 0.00 0.00 0.00 2.57
2464 2950 1.803334 TCTTTCGATTTGTGTCCCCG 58.197 50.000 0.00 0.00 0.00 5.73
2476 2962 1.673337 GTCCCCGGTTAACAGTGCC 60.673 63.158 8.10 0.00 0.00 5.01
2485 2971 5.120399 CCGGTTAACAGTGCCTAATCATTA 58.880 41.667 8.10 0.00 0.00 1.90
2494 2980 5.178996 CAGTGCCTAATCATTAGCTAGCAAG 59.821 44.000 18.83 3.40 32.42 4.01
2577 3064 6.379386 TGTGTTGACGATAAGTAGACTTCAG 58.621 40.000 0.00 0.00 37.40 3.02
2784 3271 1.597742 ATATTCCCGCATGAGCACAC 58.402 50.000 0.00 0.00 42.27 3.82
2822 3310 7.123383 CCACCCCCTGTTCTACTAAAAATATT 58.877 38.462 0.00 0.00 0.00 1.28
2930 3418 9.814899 CTTCTTCAGATAAGTACATCATCAGTT 57.185 33.333 0.00 0.00 0.00 3.16
3232 4026 2.593956 GGAAAGACCCCGCAGACCT 61.594 63.158 0.00 0.00 0.00 3.85
3425 4219 2.663188 GATCGGCCATCCAGCGAC 60.663 66.667 2.24 0.00 0.00 5.19
3475 4275 1.929836 CAGCTTCTAACTGCCATCGTC 59.070 52.381 0.00 0.00 0.00 4.20
3476 4276 0.924090 GCTTCTAACTGCCATCGTCG 59.076 55.000 0.00 0.00 0.00 5.12
3478 4278 2.607187 CTTCTAACTGCCATCGTCGTT 58.393 47.619 0.00 0.00 0.00 3.85
3481 4281 0.037697 TAACTGCCATCGTCGTTGCT 60.038 50.000 0.00 0.00 0.00 3.91
3483 4283 2.741985 TGCCATCGTCGTTGCTGG 60.742 61.111 0.00 0.60 0.00 4.85
3486 4286 1.573829 GCCATCGTCGTTGCTGGAAA 61.574 55.000 9.12 0.00 0.00 3.13
3515 4315 5.186215 TGAACTTCAGAACACCCGTATGATA 59.814 40.000 0.00 0.00 0.00 2.15
3527 4327 3.108881 CCGTATGATATTCCATCTCGCG 58.891 50.000 0.00 0.00 0.00 5.87
3666 4492 2.842256 GCCCATCAGCTTCATGGCG 61.842 63.158 14.08 9.58 39.78 5.69
3682 4508 2.918345 GCGCATGCTGGTGGTTGAA 61.918 57.895 17.13 0.00 38.39 2.69
3684 4510 0.457166 CGCATGCTGGTGGTTGAATG 60.457 55.000 17.13 0.00 0.00 2.67
3685 4511 0.889994 GCATGCTGGTGGTTGAATGA 59.110 50.000 11.37 0.00 0.00 2.57
3686 4512 1.135199 GCATGCTGGTGGTTGAATGAG 60.135 52.381 11.37 0.00 0.00 2.90
3687 4513 1.135199 CATGCTGGTGGTTGAATGAGC 60.135 52.381 0.00 0.00 0.00 4.26
3724 4550 0.323633 TGGTGATGTTCTGGCCATGG 60.324 55.000 5.51 7.63 0.00 3.66
3792 4627 6.763135 TGTTCTGTAGAATGGTGCATATCTTC 59.237 38.462 0.00 0.00 36.33 2.87
3793 4628 6.737720 TCTGTAGAATGGTGCATATCTTCT 57.262 37.500 0.00 0.00 0.00 2.85
3794 4629 7.129457 TCTGTAGAATGGTGCATATCTTCTT 57.871 36.000 8.45 0.00 0.00 2.52
3835 4670 0.114364 GGGGGAGGGTGATGTTTTGT 59.886 55.000 0.00 0.00 0.00 2.83
3914 4749 4.117372 CGTCCGTTCGACAAGCGC 62.117 66.667 0.00 0.00 42.07 5.92
3915 4750 4.117372 GTCCGTTCGACAAGCGCG 62.117 66.667 0.00 0.00 41.54 6.86
3980 4815 1.235281 TGTCTCACCACTCCGACTCG 61.235 60.000 0.00 0.00 0.00 4.18
4041 4876 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
4043 4878 1.001406 TGTGTGTGTGTGTGTGTGAGA 59.999 47.619 0.00 0.00 0.00 3.27
4045 4880 1.548269 TGTGTGTGTGTGTGTGAGAGA 59.452 47.619 0.00 0.00 0.00 3.10
4047 4882 2.099405 TGTGTGTGTGTGTGAGAGAGA 58.901 47.619 0.00 0.00 0.00 3.10
4049 4884 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
4050 4885 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
4051 4886 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
4068 4903 7.346471 AGAGAGAGAGAGAGTAAAATGTAGCT 58.654 38.462 0.00 0.00 0.00 3.32
4079 4914 8.531982 AGAGTAAAATGTAGCTATGTTCAGTGA 58.468 33.333 0.00 0.00 0.00 3.41
4080 4915 8.709386 AGTAAAATGTAGCTATGTTCAGTGAG 57.291 34.615 0.00 0.00 0.00 3.51
4084 4919 9.502091 AAAATGTAGCTATGTTCAGTGAGTAAA 57.498 29.630 0.00 0.00 0.00 2.01
4087 4922 8.479313 TGTAGCTATGTTCAGTGAGTAAAATG 57.521 34.615 0.00 0.00 0.00 2.32
4088 4923 8.094548 TGTAGCTATGTTCAGTGAGTAAAATGT 58.905 33.333 0.00 0.00 0.00 2.71
4089 4924 9.582431 GTAGCTATGTTCAGTGAGTAAAATGTA 57.418 33.333 0.00 0.00 0.00 2.29
4090 4925 8.709386 AGCTATGTTCAGTGAGTAAAATGTAG 57.291 34.615 0.00 0.00 0.00 2.74
4144 4985 1.574702 GGTGTGCGAAGTAACAGGCC 61.575 60.000 0.00 0.00 0.00 5.19
4195 5223 1.165907 TAACAGCACAGCACAGCACC 61.166 55.000 0.00 0.00 0.00 5.01
4286 5331 4.350368 AAGAATTTTTGGCCGTTGGATT 57.650 36.364 0.00 0.00 0.00 3.01
4403 5457 1.124780 TGTCCAAGAGACCAACGGAA 58.875 50.000 0.00 0.00 45.68 4.30
4432 5486 3.648982 CAGTGTTCGCAGCCGCAA 61.649 61.111 0.00 0.00 38.40 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.111053 GCGAGGGGAAGGGGGAAC 62.111 72.222 0.00 0.00 0.00 3.62
7 8 3.839432 GACGAGGCGAGGGGAAGG 61.839 72.222 0.00 0.00 0.00 3.46
10 11 3.700831 GAGAGACGAGGCGAGGGGA 62.701 68.421 0.00 0.00 0.00 4.81
27 28 1.371183 GCACATAGCATAGGGGCGA 59.629 57.895 0.00 0.00 43.99 5.54
70 71 2.533266 GTTTACCATACCACGGTCTCG 58.467 52.381 0.00 0.00 37.99 4.04
117 118 2.670592 CCCCCGTCCGTTTTCACC 60.671 66.667 0.00 0.00 0.00 4.02
119 120 2.745037 CTCCCCCGTCCGTTTTCA 59.255 61.111 0.00 0.00 0.00 2.69
120 121 2.046604 CCTCCCCCGTCCGTTTTC 60.047 66.667 0.00 0.00 0.00 2.29
122 123 4.644288 TCCCTCCCCCGTCCGTTT 62.644 66.667 0.00 0.00 0.00 3.60
123 124 3.937372 ATTCCCTCCCCCGTCCGTT 62.937 63.158 0.00 0.00 0.00 4.44
124 125 4.410033 ATTCCCTCCCCCGTCCGT 62.410 66.667 0.00 0.00 0.00 4.69
125 126 3.547513 GATTCCCTCCCCCGTCCG 61.548 72.222 0.00 0.00 0.00 4.79
126 127 3.169242 GGATTCCCTCCCCCGTCC 61.169 72.222 0.00 0.00 38.19 4.79
127 128 2.366435 TGGATTCCCTCCCCCGTC 60.366 66.667 0.00 0.00 44.23 4.79
216 221 2.999485 ATCTCGCAGCTCAGCACGT 61.999 57.895 11.38 0.00 33.40 4.49
298 329 3.991924 GAGGGGAGCAGAGCAGGGA 62.992 68.421 0.00 0.00 0.00 4.20
340 371 2.716017 CGGGGCGAGAAGAGAAGCT 61.716 63.158 0.00 0.00 0.00 3.74
342 373 2.202810 GCGGGGCGAGAAGAGAAG 60.203 66.667 0.00 0.00 0.00 2.85
469 519 4.834453 CCTCCTCCGCAGCAGCAG 62.834 72.222 0.82 0.00 42.27 4.24
472 522 4.527583 GCTCCTCCTCCGCAGCAG 62.528 72.222 0.00 0.00 0.00 4.24
522 582 4.339247 CAGGGTGCCAAAATTATACCTGAG 59.661 45.833 0.00 0.00 45.33 3.35
564 684 1.919240 TACAGCCGAAAGAGGACAGA 58.081 50.000 0.00 0.00 0.00 3.41
874 994 2.827322 TGCATGGTTCTTGCTTATGCTT 59.173 40.909 0.00 0.00 43.29 3.91
875 995 2.426024 CTGCATGGTTCTTGCTTATGCT 59.574 45.455 0.00 0.00 43.29 3.79
876 996 2.424601 TCTGCATGGTTCTTGCTTATGC 59.575 45.455 0.00 0.00 43.21 3.14
877 997 4.707030 TTCTGCATGGTTCTTGCTTATG 57.293 40.909 0.00 0.00 40.77 1.90
914 1034 6.039493 TCGAGTAATAGGATCAAAGAGTGGTC 59.961 42.308 0.00 0.00 36.53 4.02
932 1052 2.028839 TCAACGGGAAATGCTCGAGTAA 60.029 45.455 15.13 3.12 45.56 2.24
933 1053 1.546923 TCAACGGGAAATGCTCGAGTA 59.453 47.619 15.13 10.57 45.56 2.59
934 1054 0.320374 TCAACGGGAAATGCTCGAGT 59.680 50.000 15.13 0.00 45.56 4.18
935 1055 1.002366 CTCAACGGGAAATGCTCGAG 58.998 55.000 8.45 8.45 45.56 4.04
936 1056 1.019278 GCTCAACGGGAAATGCTCGA 61.019 55.000 0.00 0.00 45.56 4.04
938 1058 1.019278 TCGCTCAACGGGAAATGCTC 61.019 55.000 0.00 0.00 43.89 4.26
939 1059 0.392998 ATCGCTCAACGGGAAATGCT 60.393 50.000 0.00 0.00 43.89 3.79
940 1060 0.451783 AATCGCTCAACGGGAAATGC 59.548 50.000 0.00 0.00 43.89 3.56
941 1061 2.420022 AGAAATCGCTCAACGGGAAATG 59.580 45.455 0.00 0.00 43.89 2.32
942 1062 2.711542 AGAAATCGCTCAACGGGAAAT 58.288 42.857 0.00 0.00 43.89 2.17
943 1063 2.178912 AGAAATCGCTCAACGGGAAA 57.821 45.000 0.00 0.00 43.89 3.13
944 1064 2.073816 GAAGAAATCGCTCAACGGGAA 58.926 47.619 0.00 0.00 43.89 3.97
945 1065 1.275291 AGAAGAAATCGCTCAACGGGA 59.725 47.619 0.00 0.00 43.89 5.14
946 1066 1.661112 GAGAAGAAATCGCTCAACGGG 59.339 52.381 0.00 0.00 43.89 5.28
947 1067 2.611518 AGAGAAGAAATCGCTCAACGG 58.388 47.619 0.00 0.00 43.89 4.44
953 1073 1.760029 GGGAGGAGAGAAGAAATCGCT 59.240 52.381 0.00 0.00 41.30 4.93
954 1074 1.202592 GGGGAGGAGAGAAGAAATCGC 60.203 57.143 0.00 0.00 0.00 4.58
955 1075 1.067821 CGGGGAGGAGAGAAGAAATCG 59.932 57.143 0.00 0.00 0.00 3.34
956 1076 1.202592 GCGGGGAGGAGAGAAGAAATC 60.203 57.143 0.00 0.00 0.00 2.17
957 1077 0.833949 GCGGGGAGGAGAGAAGAAAT 59.166 55.000 0.00 0.00 0.00 2.17
1061 1214 2.123640 GGAGGACGAGGAGGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
1935 2094 1.285078 TCTGGAGCAGTGTAGAGGCTA 59.715 52.381 0.00 0.00 38.15 3.93
1947 2106 1.002430 CTTTGGTAGCACTCTGGAGCA 59.998 52.381 0.00 0.00 0.00 4.26
1979 2138 5.007626 GCACTGAAAACAGACAACACATAGA 59.992 40.000 0.00 0.00 0.00 1.98
1980 2139 5.008019 AGCACTGAAAACAGACAACACATAG 59.992 40.000 0.00 0.00 0.00 2.23
1984 2152 3.126858 TGAGCACTGAAAACAGACAACAC 59.873 43.478 0.00 0.00 0.00 3.32
1986 2154 4.355543 TTGAGCACTGAAAACAGACAAC 57.644 40.909 0.00 0.00 0.00 3.32
1989 2157 5.173774 TGAATTGAGCACTGAAAACAGAC 57.826 39.130 0.00 0.00 0.00 3.51
1992 2160 3.633525 AGCTGAATTGAGCACTGAAAACA 59.366 39.130 19.35 0.00 41.83 2.83
2097 2270 2.292455 CCTGGGTTCAATTTCCCCTCAT 60.292 50.000 7.42 0.00 42.80 2.90
2110 2283 2.283145 ATGATGCATAGCCTGGGTTC 57.717 50.000 2.65 0.00 0.00 3.62
2115 2288 4.142665 GCAGTGATAATGATGCATAGCCTG 60.143 45.833 0.00 0.00 38.54 4.85
2119 2292 4.395231 CCTGGCAGTGATAATGATGCATAG 59.605 45.833 14.43 0.00 40.46 2.23
2173 2436 8.817100 CATTGAGTTGTTTGCTTCGTATCTATA 58.183 33.333 0.00 0.00 0.00 1.31
2174 2437 7.334421 ACATTGAGTTGTTTGCTTCGTATCTAT 59.666 33.333 0.00 0.00 0.00 1.98
2223 2486 3.129109 CAATAGCAGACATCGCACATCT 58.871 45.455 0.00 0.00 0.00 2.90
2224 2487 2.222678 CCAATAGCAGACATCGCACATC 59.777 50.000 0.00 0.00 0.00 3.06
2225 2488 2.216046 CCAATAGCAGACATCGCACAT 58.784 47.619 0.00 0.00 0.00 3.21
2226 2489 1.655484 CCAATAGCAGACATCGCACA 58.345 50.000 0.00 0.00 0.00 4.57
2227 2490 0.305922 GCCAATAGCAGACATCGCAC 59.694 55.000 0.00 0.00 42.97 5.34
2228 2491 2.694065 GCCAATAGCAGACATCGCA 58.306 52.632 0.00 0.00 42.97 5.10
2405 2891 7.276218 AGCAATAATGAAATGGAATGTCAAACG 59.724 33.333 0.00 0.00 45.30 3.60
2464 2950 5.823045 AGCTAATGATTAGGCACTGTTAACC 59.177 40.000 13.60 0.00 41.52 2.85
2494 2980 2.939460 AAGGAAACACACAACAGTGC 57.061 45.000 0.00 0.00 43.23 4.40
2504 2990 7.657761 TCAGAAGAGTCTAATGAAAGGAAACAC 59.342 37.037 5.04 0.00 30.85 3.32
2577 3064 1.708822 AAATTCAAATGGCGCGGAAC 58.291 45.000 8.83 0.00 0.00 3.62
2784 3271 3.297620 GGTGGGCCAACAGCTGTG 61.298 66.667 22.49 14.24 43.05 3.66
2930 3418 6.183361 TGGTTGAAAGTCCTTCCCATAAGTTA 60.183 38.462 0.00 0.00 32.53 2.24
3269 4063 1.153568 CATGTGACGGAGCCATCGT 60.154 57.895 0.00 0.00 44.03 3.73
3425 4219 1.202973 CGAGCATGGCTACGAGTTCG 61.203 60.000 0.00 0.00 39.88 3.95
3466 4260 2.723586 TTCCAGCAACGACGATGGCA 62.724 55.000 0.00 0.00 32.63 4.92
3475 4275 4.228912 AGTTCAGAAATTTCCAGCAACG 57.771 40.909 14.61 0.00 0.00 4.10
3476 4276 5.591099 TGAAGTTCAGAAATTTCCAGCAAC 58.409 37.500 14.61 11.52 31.87 4.17
3509 4309 4.201822 CGACTCGCGAGATGGAATATCATA 60.202 45.833 40.58 0.00 44.57 2.15
3515 4315 1.299468 GCGACTCGCGAGATGGAAT 60.299 57.895 40.58 18.93 44.55 3.01
3544 4344 1.332889 TGATGATCCTGCGCCACTCT 61.333 55.000 4.18 0.00 0.00 3.24
3628 4454 2.331194 CAGCTATTTTGCCACACTTGC 58.669 47.619 0.00 0.00 0.00 4.01
3666 4492 0.889994 TCATTCAACCACCAGCATGC 59.110 50.000 10.51 10.51 31.97 4.06
3682 4508 6.655425 CCATCATCATCTTACATGAAGCTCAT 59.345 38.462 0.00 0.00 37.65 2.90
3684 4510 5.996513 ACCATCATCATCTTACATGAAGCTC 59.003 40.000 0.00 0.00 34.87 4.09
3685 4511 5.763698 CACCATCATCATCTTACATGAAGCT 59.236 40.000 0.00 0.00 34.87 3.74
3686 4512 5.761726 TCACCATCATCATCTTACATGAAGC 59.238 40.000 0.00 0.00 34.87 3.86
3687 4513 7.444487 ACATCACCATCATCATCTTACATGAAG 59.556 37.037 0.00 0.00 32.76 3.02
3724 4550 0.038166 TTGTTGTCCCCAGGCTCATC 59.962 55.000 0.00 0.00 0.00 2.92
3792 4627 2.490903 CAGCAAAGGGAGATCCAACAAG 59.509 50.000 0.47 0.00 38.24 3.16
3793 4628 2.158475 ACAGCAAAGGGAGATCCAACAA 60.158 45.455 0.47 0.00 38.24 2.83
3794 4629 1.425066 ACAGCAAAGGGAGATCCAACA 59.575 47.619 0.47 0.00 38.24 3.33
3835 4670 0.697658 TGATGGGTCAATGCACAGGA 59.302 50.000 0.00 0.00 0.00 3.86
3930 4765 2.460669 AGAGAAATGATGCCCAAACCC 58.539 47.619 0.00 0.00 0.00 4.11
4020 4855 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4041 4876 7.499232 GCTACATTTTACTCTCTCTCTCTCTCT 59.501 40.741 0.00 0.00 0.00 3.10
4043 4878 7.346471 AGCTACATTTTACTCTCTCTCTCTCT 58.654 38.462 0.00 0.00 0.00 3.10
4045 4880 9.066892 CATAGCTACATTTTACTCTCTCTCTCT 57.933 37.037 0.00 0.00 0.00 3.10
4047 4882 8.760980 ACATAGCTACATTTTACTCTCTCTCT 57.239 34.615 0.00 0.00 0.00 3.10
4049 4884 8.972127 TGAACATAGCTACATTTTACTCTCTCT 58.028 33.333 0.00 0.00 0.00 3.10
4050 4885 9.243637 CTGAACATAGCTACATTTTACTCTCTC 57.756 37.037 0.00 0.00 0.00 3.20
4051 4886 8.754080 ACTGAACATAGCTACATTTTACTCTCT 58.246 33.333 0.00 0.00 0.00 3.10
4068 4903 7.913789 ACCCTACATTTTACTCACTGAACATA 58.086 34.615 0.00 0.00 0.00 2.29
4079 4914 4.788617 ACATCCAGGACCCTACATTTTACT 59.211 41.667 0.00 0.00 0.00 2.24
4080 4915 4.881850 CACATCCAGGACCCTACATTTTAC 59.118 45.833 0.00 0.00 0.00 2.01
4084 4919 2.562296 ACACATCCAGGACCCTACATT 58.438 47.619 0.00 0.00 0.00 2.71
4087 4922 4.259356 GTTTTACACATCCAGGACCCTAC 58.741 47.826 0.00 0.00 0.00 3.18
4088 4923 3.055675 CGTTTTACACATCCAGGACCCTA 60.056 47.826 0.00 0.00 0.00 3.53
4089 4924 2.290071 CGTTTTACACATCCAGGACCCT 60.290 50.000 0.00 0.00 0.00 4.34
4090 4925 2.081462 CGTTTTACACATCCAGGACCC 58.919 52.381 0.00 0.00 0.00 4.46
4144 4985 2.252747 CTGTGTTGTGCTGTGTTGTTG 58.747 47.619 0.00 0.00 0.00 3.33
4333 5387 3.930229 CAGATCGTCCATTTTGTTACGGA 59.070 43.478 0.00 0.00 36.08 4.69
4381 5435 2.076863 CCGTTGGTCTCTTGGACATTC 58.923 52.381 0.00 0.00 46.16 2.67
4382 5436 1.697432 TCCGTTGGTCTCTTGGACATT 59.303 47.619 0.00 0.00 46.16 2.71


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

AutoCloner maintained by Alex Coulton.