Multiple sequence alignment - TraesCS2D01G192900

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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 TraesCS2D01G192900 chr2D 100.000 3692 0 0 1 3692 137025790 137029481 0.000000e+00 6818.0
1 TraesCS2D01G192900 chr2D 93.298 567 33 5 1 565 588287304 588286741 0.000000e+00 832.0
2 TraesCS2D01G192900 chr7A 95.055 2568 114 11 1133 3692 616935457 616932895 0.000000e+00 4026.0
3 TraesCS2D01G192900 chr7A 93.814 582 29 5 560 1136 616936120 616935541 0.000000e+00 869.0
4 TraesCS2D01G192900 chr6B 82.237 1779 265 36 1951 3692 2044368 2046132 0.000000e+00 1487.0
5 TraesCS2D01G192900 chr6B 83.893 298 44 3 1609 1905 2043766 2044060 7.810000e-72 281.0
6 TraesCS2D01G192900 chr6B 84.259 108 15 2 561 667 2034882 2034988 1.810000e-18 104.0
7 TraesCS2D01G192900 chr7D 79.073 2136 367 56 1610 3691 236782004 236779895 0.000000e+00 1395.0
8 TraesCS2D01G192900 chr7D 76.471 238 42 13 569 799 21286372 21286142 2.330000e-22 117.0
9 TraesCS2D01G192900 chr5D 94.523 566 29 2 1 565 352792651 352792087 0.000000e+00 872.0
10 TraesCS2D01G192900 chr5D 93.451 565 35 2 1 565 244418310 244417748 0.000000e+00 837.0
11 TraesCS2D01G192900 chr3D 93.497 569 36 1 1 569 460090025 460090592 0.000000e+00 845.0
12 TraesCS2D01G192900 chr3D 93.640 566 33 3 1 565 181529504 181530067 0.000000e+00 843.0
13 TraesCS2D01G192900 chr3D 93.451 565 36 1 1 565 506794999 506795562 0.000000e+00 837.0
14 TraesCS2D01G192900 chr6D 93.298 567 34 4 1 565 212875065 212875629 0.000000e+00 833.0
15 TraesCS2D01G192900 chr4D 93.286 566 36 2 1 565 47784765 47785329 0.000000e+00 833.0
16 TraesCS2D01G192900 chr6A 92.857 574 35 6 1 569 216363411 216363983 0.000000e+00 828.0
17 TraesCS2D01G192900 chr1B 82.677 381 66 0 2817 3197 639070630 639071010 4.570000e-89 339.0
18 TraesCS2D01G192900 chr3B 82.906 117 20 0 2473 2589 104326711 104326827 5.040000e-19 106.0
19 TraesCS2D01G192900 chr3B 83.158 95 9 4 566 656 759701565 759701474 3.060000e-11 80.5
20 TraesCS2D01G192900 chr2B 82.906 117 20 0 2473 2589 794922548 794922664 5.040000e-19 106.0
21 TraesCS2D01G192900 chr2B 82.906 117 20 0 2473 2589 794928525 794928641 5.040000e-19 106.0
22 TraesCS2D01G192900 chr2B 82.051 117 21 0 2473 2589 794916570 794916686 2.350000e-17 100.0
23 TraesCS2D01G192900 chr1A 75.200 250 48 13 557 799 26197611 26197369 5.040000e-19 106.0
24 TraesCS2D01G192900 chr1D 89.189 74 6 2 565 637 206836210 206836282 1.410000e-14 91.6
25 TraesCS2D01G192900 chr1D 84.211 95 8 4 566 656 485976763 485976672 6.570000e-13 86.1
26 TraesCS2D01G192900 chr5A 84.211 95 9 3 566 657 670407011 670406920 1.830000e-13 87.9
27 TraesCS2D01G192900 chr2A 94.000 50 3 0 566 615 394659562 394659513 3.950000e-10 76.8


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 TraesCS2D01G192900 chr2D 137025790 137029481 3691 False 6818.0 6818 100.0000 1 3692 1 chr2D.!!$F1 3691
1 TraesCS2D01G192900 chr2D 588286741 588287304 563 True 832.0 832 93.2980 1 565 1 chr2D.!!$R1 564
2 TraesCS2D01G192900 chr7A 616932895 616936120 3225 True 2447.5 4026 94.4345 560 3692 2 chr7A.!!$R1 3132
3 TraesCS2D01G192900 chr6B 2043766 2046132 2366 False 884.0 1487 83.0650 1609 3692 2 chr6B.!!$F2 2083
4 TraesCS2D01G192900 chr7D 236779895 236782004 2109 True 1395.0 1395 79.0730 1610 3691 1 chr7D.!!$R2 2081
5 TraesCS2D01G192900 chr5D 352792087 352792651 564 True 872.0 872 94.5230 1 565 1 chr5D.!!$R2 564
6 TraesCS2D01G192900 chr5D 244417748 244418310 562 True 837.0 837 93.4510 1 565 1 chr5D.!!$R1 564
7 TraesCS2D01G192900 chr3D 460090025 460090592 567 False 845.0 845 93.4970 1 569 1 chr3D.!!$F2 568
8 TraesCS2D01G192900 chr3D 181529504 181530067 563 False 843.0 843 93.6400 1 565 1 chr3D.!!$F1 564
9 TraesCS2D01G192900 chr3D 506794999 506795562 563 False 837.0 837 93.4510 1 565 1 chr3D.!!$F3 564
10 TraesCS2D01G192900 chr6D 212875065 212875629 564 False 833.0 833 93.2980 1 565 1 chr6D.!!$F1 564
11 TraesCS2D01G192900 chr4D 47784765 47785329 564 False 833.0 833 93.2860 1 565 1 chr4D.!!$F1 564
12 TraesCS2D01G192900 chr6A 216363411 216363983 572 False 828.0 828 92.8570 1 569 1 chr6A.!!$F1 568

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
764 772 0.179067 AGAACAACACTTTCGGCCGA 60.179 50.0 27.28 27.28 0.00 5.54 F
1151 1249 0.320374 AGTTCAGAACGGCCGATTCA 59.680 50.0 35.90 13.50 36.23 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2457 0.871722 TGACGGGAAATGCAACTTCG 59.128 50.0 0.0 0.0 0.0 3.79 R
2940 3311 1.289109 CGCCAACCCGTACTTCACAG 61.289 60.0 0.0 0.0 0.0 3.66 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
108 109 9.304731 CAATGAATTCTCTTGAAACTCAACAAA 57.695 29.630 7.05 0.00 34.20 2.83
131 132 2.245159 TGTTCTCAGTCACCAAGCAG 57.755 50.000 0.00 0.00 0.00 4.24
256 257 4.879104 AACGTTTCAACCGAACACATAA 57.121 36.364 0.00 0.00 0.00 1.90
270 271 5.007724 CGAACACATAAAAAGATAGGGGCTC 59.992 44.000 0.00 0.00 0.00 4.70
281 282 3.584848 AGATAGGGGCTCATAATTTCGCT 59.415 43.478 0.00 0.00 0.00 4.93
394 398 3.250744 CACATGATGCTTGCCAAAAGAG 58.749 45.455 0.00 0.00 0.00 2.85
469 476 5.570320 TGCTGAAAAGTAAAAGATAGGCCT 58.430 37.500 11.78 11.78 0.00 5.19
476 483 3.939592 AGTAAAAGATAGGCCTTTCGCAC 59.060 43.478 12.58 10.58 40.31 5.34
519 527 3.120121 GCGCTTTTTGTTTGTATGCTCAG 59.880 43.478 0.00 0.00 0.00 3.35
524 532 3.788227 TTGTTTGTATGCTCAGTCCCT 57.212 42.857 0.00 0.00 0.00 4.20
556 564 7.492020 GCAAAAGAATGTCACATTATATTGCCA 59.508 33.333 23.47 0.00 0.00 4.92
565 573 8.785946 TGTCACATTATATTGCCACTTATGATG 58.214 33.333 0.00 0.00 31.57 3.07
623 631 1.038681 TATCTGGACGGCGGCTGTTA 61.039 55.000 16.77 7.72 0.00 2.41
654 662 6.940739 AGATCTGTTGCTAGTGTAGTGAATT 58.059 36.000 0.00 0.00 0.00 2.17
656 664 7.880195 AGATCTGTTGCTAGTGTAGTGAATTTT 59.120 33.333 0.00 0.00 0.00 1.82
711 719 6.037830 GGCCAATACAAGTTGTATACGATGTT 59.962 38.462 25.11 9.01 42.29 2.71
719 727 2.899976 TGTATACGATGTTGGGTGCAG 58.100 47.619 0.00 0.00 0.00 4.41
730 738 1.003839 GGGTGCAGGAACGATGACA 60.004 57.895 0.00 0.00 0.00 3.58
751 759 4.887071 ACATTTCAGTGCAGGTAAGAACAA 59.113 37.500 0.00 0.00 0.00 2.83
764 772 0.179067 AGAACAACACTTTCGGCCGA 60.179 50.000 27.28 27.28 0.00 5.54
783 791 4.499040 GCCGATCGAAATAAATTGTGTTGG 59.501 41.667 18.66 0.00 0.00 3.77
784 792 4.499040 CCGATCGAAATAAATTGTGTTGGC 59.501 41.667 18.66 0.00 0.00 4.52
786 794 5.227805 CGATCGAAATAAATTGTGTTGGCAG 59.772 40.000 10.26 0.00 0.00 4.85
816 824 0.461163 TACGGGTGGTGAATGCATCG 60.461 55.000 0.00 0.00 0.00 3.84
827 835 0.881118 AATGCATCGCGTCCTGTTTT 59.119 45.000 5.77 0.00 0.00 2.43
887 895 4.749976 TGCTGTTCTTACCCAAAACAAAC 58.250 39.130 0.00 0.00 32.89 2.93
889 897 4.439016 GCTGTTCTTACCCAAAACAAACGA 60.439 41.667 0.00 0.00 32.89 3.85
981 989 2.414481 CTGGAATCGAGCTCAACAACAG 59.586 50.000 15.40 11.83 0.00 3.16
982 990 2.037121 TGGAATCGAGCTCAACAACAGA 59.963 45.455 15.40 0.72 0.00 3.41
984 992 3.686726 GGAATCGAGCTCAACAACAGAAT 59.313 43.478 15.40 0.00 0.00 2.40
985 993 4.436584 GGAATCGAGCTCAACAACAGAATG 60.437 45.833 15.40 0.00 46.00 2.67
1020 1031 5.390673 CGGAATGATTGCATCTCTAATGAGC 60.391 44.000 0.00 0.00 40.03 4.26
1032 1043 6.299805 TCTCTAATGAGCAGGTATGTTGTT 57.700 37.500 0.00 0.00 40.03 2.83
1068 1079 1.346062 ACATCGATCTGGATCTGGGG 58.654 55.000 0.00 0.00 35.72 4.96
1082 1093 0.690411 CTGGGGGCTGTCAGATCTCT 60.690 60.000 3.32 0.00 33.11 3.10
1093 1104 3.055819 TGTCAGATCTCTGGTTACCTTGC 60.056 47.826 2.07 0.00 43.91 4.01
1098 1109 2.609747 TCTCTGGTTACCTTGCTGACT 58.390 47.619 2.07 0.00 0.00 3.41
1151 1249 0.320374 AGTTCAGAACGGCCGATTCA 59.680 50.000 35.90 13.50 36.23 2.57
1167 1265 1.168407 TTCAGCTGCCAGCACTTGAC 61.168 55.000 20.53 0.00 45.56 3.18
1236 1334 2.467838 CAGATCGATCTTGTGCGTGAT 58.532 47.619 25.25 0.00 34.22 3.06
1252 1350 3.057019 CGTGATGTTTCCGAAGAAGACA 58.943 45.455 0.00 0.00 32.35 3.41
1261 1359 4.402056 TCCGAAGAAGACAACTCTGTTT 57.598 40.909 0.00 0.00 35.30 2.83
1273 1371 7.151308 AGACAACTCTGTTTCAACTAGATCTG 58.849 38.462 5.18 0.00 35.30 2.90
1274 1372 6.821388 ACAACTCTGTTTCAACTAGATCTGT 58.179 36.000 5.18 0.00 28.57 3.41
1297 1395 2.370189 GGAGGGTGGATCAGAAGGTATG 59.630 54.545 0.00 0.00 0.00 2.39
1305 1403 6.042093 GGTGGATCAGAAGGTATGTCATTCTA 59.958 42.308 0.00 0.00 43.91 2.10
1330 1428 5.461737 GCACAACAAGGATCGATTTCAAAAA 59.538 36.000 0.00 0.00 0.00 1.94
1353 1451 5.847111 AATTACACCGCAGACTATACTGA 57.153 39.130 0.00 0.00 39.94 3.41
1354 1452 5.847111 ATTACACCGCAGACTATACTGAA 57.153 39.130 0.00 0.00 39.94 3.02
1366 1464 7.495934 GCAGACTATACTGAAAAATCTTGGCTA 59.504 37.037 0.00 0.00 39.94 3.93
1383 1481 3.584406 TGGCTATAGCAATGCATAGGACT 59.416 43.478 25.53 0.00 44.36 3.85
1399 1497 7.766738 TGCATAGGACTGTTCGATTTGTAATAA 59.233 33.333 0.00 0.00 0.00 1.40
1435 1533 8.851960 AGAAACGGAAAATTTTGAAAGTAGAC 57.148 30.769 8.47 0.00 0.00 2.59
1504 1602 5.999205 TGCCATGTTTATTTTCCTGATGT 57.001 34.783 0.00 0.00 0.00 3.06
1507 1605 7.222872 TGCCATGTTTATTTTCCTGATGTTTT 58.777 30.769 0.00 0.00 0.00 2.43
1721 1820 3.068590 CAGGAAAACAGATGCAGTGGTTT 59.931 43.478 13.31 13.31 37.53 3.27
1744 1843 1.607148 CCTTCGGTTGGTCTGGTTTTC 59.393 52.381 0.00 0.00 0.00 2.29
1812 1911 3.752222 GAGCTAGGATTTGGCATCAGATG 59.248 47.826 5.98 5.98 0.00 2.90
1834 1933 1.470805 GGCAAAAGCAGAACCAACGTT 60.471 47.619 0.00 0.00 33.88 3.99
1840 1939 1.583495 GCAGAACCAACGTTAGGGGC 61.583 60.000 17.36 12.33 30.30 5.80
2130 2491 3.131400 TCCCGTCACATCGTCATATTGAA 59.869 43.478 0.00 0.00 0.00 2.69
2258 2620 5.514500 TTCACTAAAAGGTGCCTTAGGAT 57.486 39.130 0.69 0.00 37.16 3.24
2393 2756 5.507637 AGACACCGAGAGTAGGATAAGAAA 58.492 41.667 0.00 0.00 0.00 2.52
2547 2914 1.026718 AGAGTGTGCTTTATGCCGGC 61.027 55.000 22.73 22.73 42.00 6.13
2592 2959 7.898014 AGTAGAGAGTTTTGAATGGGTTTTT 57.102 32.000 0.00 0.00 0.00 1.94
2616 2983 5.192927 AGCGAATTTGTAAAGATGATGGGA 58.807 37.500 0.00 0.00 0.00 4.37
2660 3030 7.605410 TTTTAATAGGTAACACTACAGCAGC 57.395 36.000 0.00 0.00 41.41 5.25
2667 3037 4.330074 GGTAACACTACAGCAGCACTAATG 59.670 45.833 0.00 0.00 0.00 1.90
2794 3164 2.603473 CCCTGGGACGACTCACCA 60.603 66.667 7.01 0.00 0.00 4.17
2854 3225 7.048512 AGTCACTAGGGAGCAATTATACAAAC 58.951 38.462 0.00 0.00 0.00 2.93
2940 3311 4.202131 TGAAAACGGGTGGTCCAATTTAAC 60.202 41.667 0.00 0.00 34.36 2.01
3178 3549 3.013219 GCAGGAGGAAGGATTTCAAGAC 58.987 50.000 0.00 0.00 34.90 3.01
3202 3639 2.795329 AGGACAAGGCTGGTATGTTTG 58.205 47.619 0.00 0.00 0.00 2.93
3215 3652 9.726438 GGCTGGTATGTTTGATAGAATTATACT 57.274 33.333 0.00 0.00 0.00 2.12
3367 3804 6.630203 TTGGAAGGGTTCTTTATGTAGCTA 57.370 37.500 0.00 0.00 32.52 3.32
3622 4088 6.780706 TTTAACTGATGGTCTTTTCGTCTC 57.219 37.500 0.00 0.00 0.00 3.36
3643 4109 8.875803 CGTCTCTAGGTAATGATCATACTAGAC 58.124 40.741 25.54 21.42 34.78 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.466746 ACATGTGAATTGGTTGCTACTTTAT 57.533 32.000 0.00 0.00 0.00 1.40
108 109 3.324846 TGCTTGGTGACTGAGAACATAGT 59.675 43.478 0.00 0.00 0.00 2.12
152 153 4.944930 TGTGGAGCTCTTACTTAGACTCTC 59.055 45.833 14.64 0.00 34.34 3.20
256 257 5.241728 GCGAAATTATGAGCCCCTATCTTTT 59.758 40.000 0.00 0.00 0.00 2.27
270 271 3.757745 ACGTTGGGAAGCGAAATTATG 57.242 42.857 0.00 0.00 0.00 1.90
281 282 3.558321 CCTTGAGGTGAATACGTTGGGAA 60.558 47.826 0.00 0.00 0.00 3.97
306 308 9.655769 GTAGCATGAGTTATTATTGTTGTCATG 57.344 33.333 0.00 5.28 41.70 3.07
310 312 7.116075 TGGGTAGCATGAGTTATTATTGTTGT 58.884 34.615 0.00 0.00 0.00 3.32
447 454 6.516739 AAGGCCTATCTTTTACTTTTCAGC 57.483 37.500 5.16 0.00 0.00 4.26
469 476 0.603707 CTCTGCTTCCCTGTGCGAAA 60.604 55.000 0.00 0.00 0.00 3.46
519 527 3.181466 ACATTCTTTTGCACCAAAGGGAC 60.181 43.478 10.27 0.00 34.72 4.46
524 532 4.462508 TGTGACATTCTTTTGCACCAAA 57.537 36.364 0.00 0.00 0.00 3.28
556 564 2.698855 AGTGCGCTTCCATCATAAGT 57.301 45.000 9.73 0.00 0.00 2.24
565 573 1.081175 GAGCCAAAAGTGCGCTTCC 60.081 57.895 13.92 2.62 33.17 3.46
594 602 2.171725 GTCCAGATACAACGGGCGC 61.172 63.158 0.00 0.00 0.00 6.53
600 608 2.171725 GCCGCCGTCCAGATACAAC 61.172 63.158 0.00 0.00 0.00 3.32
623 631 5.799213 ACACTAGCAACAGATCTTAAAGCT 58.201 37.500 11.89 11.89 34.84 3.74
661 669 4.463070 ACTGTAGTTTTCCCCGCTTTAAA 58.537 39.130 0.00 0.00 0.00 1.52
663 671 3.325716 AGACTGTAGTTTTCCCCGCTTTA 59.674 43.478 0.00 0.00 0.00 1.85
680 688 3.149196 ACAACTTGTATTGGCCAGACTG 58.851 45.455 17.92 13.52 33.63 3.51
711 719 1.003839 GTCATCGTTCCTGCACCCA 60.004 57.895 0.00 0.00 0.00 4.51
719 727 2.483877 TGCACTGAAATGTCATCGTTCC 59.516 45.455 0.00 0.00 31.85 3.62
730 738 4.887071 TGTTGTTCTTACCTGCACTGAAAT 59.113 37.500 0.00 0.00 0.00 2.17
751 759 1.290955 TTCGATCGGCCGAAAGTGT 59.709 52.632 34.66 16.25 44.35 3.55
764 772 5.410067 CCTGCCAACACAATTTATTTCGAT 58.590 37.500 0.00 0.00 0.00 3.59
770 778 6.610830 TGATTATCCCTGCCAACACAATTTAT 59.389 34.615 0.00 0.00 0.00 1.40
783 791 3.074412 CACCCGTATTGATTATCCCTGC 58.926 50.000 0.00 0.00 0.00 4.85
784 792 3.072476 ACCACCCGTATTGATTATCCCTG 59.928 47.826 0.00 0.00 0.00 4.45
786 794 3.071892 TCACCACCCGTATTGATTATCCC 59.928 47.826 0.00 0.00 0.00 3.85
816 824 1.193874 CCTCGTACAAAAACAGGACGC 59.806 52.381 0.00 0.00 33.64 5.19
827 835 2.357009 GGAGTTCGCTATCCTCGTACAA 59.643 50.000 0.00 0.00 32.51 2.41
887 895 1.139095 GCCGGAGAGTAGTGGTTCG 59.861 63.158 5.05 0.00 0.00 3.95
889 897 1.303888 TCGCCGGAGAGTAGTGGTT 60.304 57.895 5.05 0.00 0.00 3.67
952 960 0.103208 GCTCGATTCCAGGACGACAT 59.897 55.000 0.00 0.00 32.72 3.06
959 967 1.734465 GTTGTTGAGCTCGATTCCAGG 59.266 52.381 7.00 0.00 0.00 4.45
981 989 6.566197 ATCATTCCGCTCTAAATTCCATTC 57.434 37.500 0.00 0.00 0.00 2.67
982 990 6.736794 GCAATCATTCCGCTCTAAATTCCATT 60.737 38.462 0.00 0.00 0.00 3.16
984 992 4.036734 GCAATCATTCCGCTCTAAATTCCA 59.963 41.667 0.00 0.00 0.00 3.53
985 993 4.036734 TGCAATCATTCCGCTCTAAATTCC 59.963 41.667 0.00 0.00 0.00 3.01
1032 1043 5.739959 TCGATGTATTTTCAGTTGGGATGA 58.260 37.500 0.00 0.00 0.00 2.92
1068 1079 2.159028 GGTAACCAGAGATCTGACAGCC 60.159 54.545 11.44 4.92 46.59 4.85
1082 1093 2.701423 TGTACAGTCAGCAAGGTAACCA 59.299 45.455 0.00 0.00 37.17 3.67
1093 1104 8.383619 GCTACAATACAGAAATTGTACAGTCAG 58.616 37.037 5.55 0.00 45.84 3.51
1098 1109 7.601130 AGTTCGCTACAATACAGAAATTGTACA 59.399 33.333 5.55 0.00 45.84 2.90
1136 1147 1.448540 AGCTGAATCGGCCGTTCTG 60.449 57.895 27.15 27.09 36.20 3.02
1151 1249 2.665008 TTCGTCAAGTGCTGGCAGCT 62.665 55.000 36.50 18.07 42.97 4.24
1167 1265 0.378962 CCTGGCTCTCTACGACTTCG 59.621 60.000 0.00 0.00 46.33 3.79
1236 1334 4.119862 CAGAGTTGTCTTCTTCGGAAACA 58.880 43.478 0.00 0.00 33.12 2.83
1252 1350 7.451877 TCCTACAGATCTAGTTGAAACAGAGTT 59.548 37.037 0.00 0.00 0.00 3.01
1261 1359 4.537751 CACCCTCCTACAGATCTAGTTGA 58.462 47.826 0.00 0.00 0.00 3.18
1273 1371 2.043227 CCTTCTGATCCACCCTCCTAC 58.957 57.143 0.00 0.00 0.00 3.18
1274 1372 1.651770 ACCTTCTGATCCACCCTCCTA 59.348 52.381 0.00 0.00 0.00 2.94
1297 1395 4.033358 CGATCCTTGTTGTGCTAGAATGAC 59.967 45.833 0.00 0.00 0.00 3.06
1305 1403 3.411446 TGAAATCGATCCTTGTTGTGCT 58.589 40.909 0.00 0.00 0.00 4.40
1330 1428 6.216801 TCAGTATAGTCTGCGGTGTAATTT 57.783 37.500 0.00 0.00 35.63 1.82
1341 1439 7.856145 AGCCAAGATTTTTCAGTATAGTCTG 57.144 36.000 0.00 0.00 36.85 3.51
1346 1444 9.845740 TTGCTATAGCCAAGATTTTTCAGTATA 57.154 29.630 21.84 0.00 41.18 1.47
1353 1451 6.224665 TGCATTGCTATAGCCAAGATTTTT 57.775 33.333 21.84 0.00 41.18 1.94
1354 1452 5.857471 TGCATTGCTATAGCCAAGATTTT 57.143 34.783 21.84 0.00 41.18 1.82
1366 1464 4.060900 CGAACAGTCCTATGCATTGCTAT 58.939 43.478 3.54 4.70 0.00 2.97
1405 1503 8.779303 ACTTTCAAAATTTTCCGTTTCTTTTGT 58.221 25.926 0.00 0.00 37.79 2.83
1411 1509 8.623310 TGTCTACTTTCAAAATTTTCCGTTTC 57.377 30.769 0.00 0.00 0.00 2.78
1412 1510 8.865978 GTTGTCTACTTTCAAAATTTTCCGTTT 58.134 29.630 0.00 0.00 0.00 3.60
1416 1514 7.980742 ACGTTGTCTACTTTCAAAATTTTCC 57.019 32.000 0.00 0.00 0.00 3.13
1423 1521 7.853929 GCTGAATAAACGTTGTCTACTTTCAAA 59.146 33.333 0.00 0.00 0.00 2.69
1435 1533 4.840772 CGTTTGAGAGCTGAATAAACGTTG 59.159 41.667 18.80 0.00 44.81 4.10
1538 1636 8.615878 AACAACATGCAGACTTAATGTTAGTA 57.384 30.769 10.69 0.00 41.39 1.82
1539 1637 7.510549 AACAACATGCAGACTTAATGTTAGT 57.489 32.000 10.69 9.19 41.39 2.24
1542 1640 8.359642 ACAATAACAACATGCAGACTTAATGTT 58.640 29.630 6.67 6.67 43.49 2.71
1547 1645 6.000840 TGGACAATAACAACATGCAGACTTA 58.999 36.000 0.00 0.00 0.00 2.24
1558 1656 8.419076 AATTGTTTCACTTGGACAATAACAAC 57.581 30.769 0.00 4.78 41.65 3.32
1612 1711 2.692368 ATGACCCCATGCCTCGGT 60.692 61.111 0.00 0.00 0.00 4.69
1744 1843 4.635765 TCATAAGCTTCACCCAAAGAATCG 59.364 41.667 0.00 0.00 0.00 3.34
1812 1911 1.067250 TTGGTTCTGCTTTTGCCGC 59.933 52.632 0.00 0.00 46.87 6.53
1840 1939 4.748102 AGAAGTTCTTGCATGCATTTTGTG 59.252 37.500 23.37 7.96 0.00 3.33
1858 1957 3.914426 ACAGAACAACCACAGAGAAGT 57.086 42.857 0.00 0.00 0.00 3.01
2096 2457 0.871722 TGACGGGAAATGCAACTTCG 59.128 50.000 0.00 0.00 0.00 3.79
2130 2491 6.998802 AGACACAAGCTCTCTAGTGTATTTT 58.001 36.000 8.26 0.00 44.48 1.82
2258 2620 5.714333 TCCTTGCTTATTTTTCCACATAGCA 59.286 36.000 0.00 0.00 0.00 3.49
2393 2756 6.349033 GCTACGTCCATTAGTCCACAAAATTT 60.349 38.462 0.00 0.00 0.00 1.82
2547 2914 1.913317 TCTCATCACGCATCAAGACG 58.087 50.000 0.00 0.00 0.00 4.18
2592 2959 6.353323 TCCCATCATCTTTACAAATTCGCTA 58.647 36.000 0.00 0.00 0.00 4.26
2616 2983 8.541899 TTAAAATTGTAACTGGTTTCTTCCCT 57.458 30.769 0.00 0.00 0.00 4.20
2824 3195 3.468071 TTGCTCCCTAGTGACTCCTTA 57.532 47.619 0.00 0.00 0.00 2.69
2854 3225 3.320541 ACTCTGTCCTGAAGTCTGACTTG 59.679 47.826 26.47 13.39 38.80 3.16
2923 3294 2.227865 CACAGTTAAATTGGACCACCCG 59.772 50.000 0.00 0.00 37.93 5.28
2940 3311 1.289109 CGCCAACCCGTACTTCACAG 61.289 60.000 0.00 0.00 0.00 3.66
3025 3396 8.816144 GTTCTTGTCATTTTTGCACAGAATTTA 58.184 29.630 0.00 0.00 0.00 1.40
3178 3549 3.157087 ACATACCAGCCTTGTCCTTTTG 58.843 45.455 0.00 0.00 0.00 2.44
3225 3662 8.732746 AAAAGTGTCAGTTCAAGTTACATACT 57.267 30.769 0.00 0.00 39.32 2.12
3231 3668 7.681939 AAGTGAAAAGTGTCAGTTCAAGTTA 57.318 32.000 0.00 0.00 36.63 2.24
3243 3680 5.394115 CCCTGCAGTTTAAAGTGAAAAGTGT 60.394 40.000 24.16 0.00 38.79 3.55
3610 4066 7.481642 TGATCATTACCTAGAGACGAAAAGAC 58.518 38.462 0.00 0.00 0.00 3.01
3643 4109 4.156182 GTGCTTTCGGGATTTTCTTAACG 58.844 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.