Multiple sequence alignment - TraesCS3D01G289000

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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 TraesCS3D01G289000 chr3D 100.000 2608 0 0 1593 4200 398300226 398302833 0.000000e+00 4817.0
1 TraesCS3D01G289000 chr3D 100.000 1214 0 0 1 1214 398298634 398299847 0.000000e+00 2242.0
2 TraesCS3D01G289000 chr3A 94.897 1901 68 13 1593 3492 517491504 517493376 0.000000e+00 2946.0
3 TraesCS3D01G289000 chr3A 94.744 723 28 6 497 1212 517490748 517491467 0.000000e+00 1116.0
4 TraesCS3D01G289000 chr3A 92.346 601 39 5 3493 4091 517493662 517494257 0.000000e+00 848.0
5 TraesCS3D01G289000 chr3B 94.314 1495 51 11 1991 3457 524326293 524327781 0.000000e+00 2259.0
6 TraesCS3D01G289000 chr3B 88.130 1171 92 20 48 1214 524324590 524325717 0.000000e+00 1349.0
7 TraesCS3D01G289000 chr3B 89.986 729 49 13 3493 4200 524328144 524328869 0.000000e+00 920.0
8 TraesCS3D01G289000 chr3B 94.402 393 12 1 1593 1985 524325752 524326134 2.800000e-166 595.0
9 TraesCS3D01G289000 chr3B 79.097 598 111 10 1 587 315387668 315388262 2.350000e-107 399.0
10 TraesCS3D01G289000 chr3B 100.000 29 0 0 4008 4036 828653650 828653622 2.000000e-03 54.7
11 TraesCS3D01G289000 chr3B 100.000 29 0 0 4008 4036 828681548 828681520 2.000000e-03 54.7
12 TraesCS3D01G289000 chr2B 82.031 512 75 11 1 502 182368165 182367661 1.810000e-113 420.0
13 TraesCS3D01G289000 chr2B 79.395 529 86 9 1 521 16850389 16850902 6.680000e-93 351.0
14 TraesCS3D01G289000 chr2B 76.298 578 109 15 80 635 217305576 217305005 2.470000e-72 283.0
15 TraesCS3D01G289000 chr6A 78.891 649 112 15 6 641 465392503 465391867 2.340000e-112 416.0
16 TraesCS3D01G289000 chr1A 78.571 630 109 18 1 614 547683398 547682779 3.940000e-105 392.0
17 TraesCS3D01G289000 chr1A 77.044 636 127 14 20 641 361213563 361212933 8.640000e-92 348.0
18 TraesCS3D01G289000 chr1A 81.771 192 31 4 1025 1214 535312152 535312341 1.560000e-34 158.0
19 TraesCS3D01G289000 chr4B 78.041 592 106 11 1 579 48646860 48646280 6.680000e-93 351.0
20 TraesCS3D01G289000 chr1B 83.333 342 44 12 175 506 649284993 649285331 1.900000e-78 303.0
21 TraesCS3D01G289000 chr1B 81.771 192 31 4 1025 1214 595176890 595177079 1.560000e-34 158.0
22 TraesCS3D01G289000 chr7D 76.817 509 93 14 153 641 577796603 577796100 3.220000e-66 263.0
23 TraesCS3D01G289000 chr4A 82.990 194 30 3 1022 1214 610490453 610490262 5.580000e-39 172.0
24 TraesCS3D01G289000 chr1D 81.250 192 32 4 1025 1214 439022278 439022467 7.270000e-33 152.0
25 TraesCS3D01G289000 chr5D 80.928 194 34 3 1022 1214 558247762 558247571 2.620000e-32 150.0
26 TraesCS3D01G289000 chr5B 80.928 194 34 3 1022 1214 704878541 704878732 2.620000e-32 150.0
27 TraesCS3D01G289000 chr2D 79.558 181 37 0 1032 1212 94319386 94319206 3.410000e-26 130.0


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 TraesCS3D01G289000 chr3D 398298634 398302833 4199 False 3529.500000 4817 100.000000 1 4200 2 chr3D.!!$F1 4199
1 TraesCS3D01G289000 chr3A 517490748 517494257 3509 False 1636.666667 2946 93.995667 497 4091 3 chr3A.!!$F1 3594
2 TraesCS3D01G289000 chr3B 524324590 524328869 4279 False 1280.750000 2259 91.708000 48 4200 4 chr3B.!!$F2 4152
3 TraesCS3D01G289000 chr3B 315387668 315388262 594 False 399.000000 399 79.097000 1 587 1 chr3B.!!$F1 586
4 TraesCS3D01G289000 chr2B 182367661 182368165 504 True 420.000000 420 82.031000 1 502 1 chr2B.!!$R1 501
5 TraesCS3D01G289000 chr2B 16850389 16850902 513 False 351.000000 351 79.395000 1 521 1 chr2B.!!$F1 520
6 TraesCS3D01G289000 chr2B 217305005 217305576 571 True 283.000000 283 76.298000 80 635 1 chr2B.!!$R2 555
7 TraesCS3D01G289000 chr6A 465391867 465392503 636 True 416.000000 416 78.891000 6 641 1 chr6A.!!$R1 635
8 TraesCS3D01G289000 chr1A 547682779 547683398 619 True 392.000000 392 78.571000 1 614 1 chr1A.!!$R2 613
9 TraesCS3D01G289000 chr1A 361212933 361213563 630 True 348.000000 348 77.044000 20 641 1 chr1A.!!$R1 621
10 TraesCS3D01G289000 chr4B 48646280 48646860 580 True 351.000000 351 78.041000 1 579 1 chr4B.!!$R1 578
11 TraesCS3D01G289000 chr7D 577796100 577796603 503 True 263.000000 263 76.817000 153 641 1 chr7D.!!$R1 488

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
262 271 0.842635 GTGATGCTGGGATCCTCCTT 59.157 55.000 12.58 0.0 36.57 3.36 F
382 394 0.968393 GAGAGCGGTGGGAAGAGAGT 60.968 60.000 0.00 0.0 0.00 3.24 F
719 772 1.062440 CAGCGCGTATTCATTGAGCAA 59.938 47.619 8.43 0.0 0.00 3.91 F
1721 1784 1.369625 ATCGTGGAATTCGGTTCAGC 58.630 50.000 0.00 0.0 38.64 4.26 F
2988 3231 0.106217 CAACAACCCACCCAAGACCT 60.106 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1992 0.482446 AACAGCCCCAAGATTCCACA 59.518 50.0 0.0 0.0 0.0 4.17 R
2162 2378 0.727457 CGATGCCGCTGATCTCGTAG 60.727 60.0 0.0 0.0 0.0 3.51 R
2170 2386 0.886938 TTTTCAACCGATGCCGCTGA 60.887 50.0 0.0 0.0 0.0 4.26 R
3132 3375 0.321346 TTCGATGCTGCTCTTGTCCA 59.679 50.0 0.0 0.0 0.0 4.02 R
3886 4489 0.532573 GTTGGATGACTGGCTCTCGA 59.467 55.0 0.0 0.0 0.0 4.04 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
50 51 1.977594 GCCATGGCGGTGTTTAGACG 61.978 60.000 23.48 0.00 36.97 4.18
56 58 1.740296 CGGTGTTTAGACGGCAGGG 60.740 63.158 0.00 0.00 0.00 4.45
169 176 4.404098 GGCCTTCCGCTTCCCGAA 62.404 66.667 0.00 0.00 40.02 4.30
173 180 1.019805 CCTTCCGCTTCCCGAACTTC 61.020 60.000 0.00 0.00 40.02 3.01
262 271 0.842635 GTGATGCTGGGATCCTCCTT 59.157 55.000 12.58 0.00 36.57 3.36
377 389 2.266055 GTGGAGAGCGGTGGGAAG 59.734 66.667 0.00 0.00 0.00 3.46
378 390 2.119611 TGGAGAGCGGTGGGAAGA 59.880 61.111 0.00 0.00 0.00 2.87
381 393 1.671901 GGAGAGCGGTGGGAAGAGAG 61.672 65.000 0.00 0.00 0.00 3.20
382 394 0.968393 GAGAGCGGTGGGAAGAGAGT 60.968 60.000 0.00 0.00 0.00 3.24
596 641 2.372040 TTTCGGTGTCCAGACCACGG 62.372 60.000 10.12 6.53 35.50 4.94
616 661 2.413634 GGGGTTCAAAACGTATGCGAAG 60.414 50.000 11.07 0.00 42.00 3.79
643 688 1.514087 GGTCGGCGTTGGAGATACA 59.486 57.895 6.85 0.00 0.00 2.29
719 772 1.062440 CAGCGCGTATTCATTGAGCAA 59.938 47.619 8.43 0.00 0.00 3.91
720 773 1.942657 AGCGCGTATTCATTGAGCAAT 59.057 42.857 8.43 0.00 0.00 3.56
822 885 2.683933 GTCTCCCTCCGCCTCCAA 60.684 66.667 0.00 0.00 0.00 3.53
823 886 2.683933 TCTCCCTCCGCCTCCAAC 60.684 66.667 0.00 0.00 0.00 3.77
824 887 4.148825 CTCCCTCCGCCTCCAACG 62.149 72.222 0.00 0.00 0.00 4.10
827 890 3.458163 CCTCCGCCTCCAACGCTA 61.458 66.667 0.00 0.00 0.00 4.26
828 891 2.577059 CTCCGCCTCCAACGCTAA 59.423 61.111 0.00 0.00 0.00 3.09
1655 1718 2.202298 CGAAATGCGTGGCGGTTC 60.202 61.111 0.00 0.00 34.64 3.62
1721 1784 1.369625 ATCGTGGAATTCGGTTCAGC 58.630 50.000 0.00 0.00 38.64 4.26
1748 1811 6.459573 GGGCAAATAATCTGCGATTTAGAACA 60.460 38.462 8.65 0.00 40.88 3.18
1854 1917 9.400638 TCATTTTACTTGGCATACTTTTAAACG 57.599 29.630 0.00 0.00 0.00 3.60
1888 1951 9.166173 TCAACTCTTGATTTGTTCTATATGTGG 57.834 33.333 1.68 0.00 34.08 4.17
1909 1972 5.122396 GTGGAATTCAACTAGCTTCGTTCAT 59.878 40.000 7.93 0.00 0.00 2.57
1910 1973 5.351465 TGGAATTCAACTAGCTTCGTTCATC 59.649 40.000 7.93 0.00 0.00 2.92
1929 1992 7.469870 CGTTCATCACTATCTCTTCTTGATCCT 60.470 40.741 0.00 0.00 0.00 3.24
1932 1995 6.462552 TCACTATCTCTTCTTGATCCTGTG 57.537 41.667 0.00 0.00 0.00 3.66
1933 1996 5.362143 TCACTATCTCTTCTTGATCCTGTGG 59.638 44.000 0.00 0.00 0.00 4.17
1934 1997 5.362143 CACTATCTCTTCTTGATCCTGTGGA 59.638 44.000 0.00 0.00 35.55 4.02
1935 1998 5.960811 ACTATCTCTTCTTGATCCTGTGGAA 59.039 40.000 0.00 0.00 34.34 3.53
1936 1999 5.972327 ATCTCTTCTTGATCCTGTGGAAT 57.028 39.130 0.00 0.00 34.34 3.01
1937 2000 5.350504 TCTCTTCTTGATCCTGTGGAATC 57.649 43.478 0.00 0.00 34.34 2.52
1938 2001 5.028802 TCTCTTCTTGATCCTGTGGAATCT 58.971 41.667 0.00 0.00 34.34 2.40
1939 2002 5.486775 TCTCTTCTTGATCCTGTGGAATCTT 59.513 40.000 0.00 0.00 34.34 2.40
1940 2003 5.494724 TCTTCTTGATCCTGTGGAATCTTG 58.505 41.667 0.00 0.00 34.34 3.02
1985 2048 3.253220 ACCACACCCACTTCCAGTATAA 58.747 45.455 0.00 0.00 0.00 0.98
1988 2051 5.222254 ACCACACCCACTTCCAGTATAATTT 60.222 40.000 0.00 0.00 0.00 1.82
2023 2239 5.396484 CCTTCTGTTGCAGTACATGATTTG 58.604 41.667 0.00 0.00 32.61 2.32
2068 2284 3.430218 GCATGATACCTCTTGTGCGTATC 59.570 47.826 0.00 0.00 39.10 2.24
2086 2302 7.433719 GTGCGTATCTGAGGCTATTCTAATATG 59.566 40.741 0.00 0.00 39.76 1.78
2107 2323 5.055642 TGTGTCACCTACTCGTTCTTATG 57.944 43.478 0.00 0.00 0.00 1.90
2162 2378 5.939296 TGGGAATTTGCAAATGAAGAATTCC 59.061 36.000 24.74 23.13 46.93 3.01
2170 2386 6.115446 TGCAAATGAAGAATTCCTACGAGAT 58.885 36.000 0.65 0.00 46.93 2.75
2230 2446 5.526115 CCAATATTCAGCCATTCATCACAC 58.474 41.667 0.00 0.00 0.00 3.82
2332 2548 6.845302 TGCATCACTAAATTTACAGCTTGAG 58.155 36.000 0.00 0.00 0.00 3.02
2392 2608 7.814587 GCTTTGGAAGACAAACTATTTGCTATT 59.185 33.333 1.23 0.00 43.81 1.73
2453 2669 3.940209 TTGTGAATGCACCTGGATTTC 57.060 42.857 0.00 0.00 44.51 2.17
2485 2701 6.423302 GCTTCGTAGAACAATCTGATCATCAT 59.577 38.462 0.00 0.00 45.90 2.45
2527 2743 6.156602 TGCCTAAACCAATTTCATTCCATGAT 59.843 34.615 0.00 0.00 39.39 2.45
2533 2749 5.365605 ACCAATTTCATTCCATGATGATGCT 59.634 36.000 0.00 0.00 39.39 3.79
2534 2750 6.126883 ACCAATTTCATTCCATGATGATGCTT 60.127 34.615 0.00 0.00 39.39 3.91
2600 2816 4.520492 CACCAGCTCATGAACTTTTTAGGT 59.480 41.667 0.00 0.00 0.00 3.08
2662 2878 5.180304 GGAGAATTTCTTCAAAGAAGCGAGT 59.820 40.000 0.00 0.00 45.01 4.18
2688 2904 6.576185 AGGCATTTGGTAATGATGTTTCATC 58.424 36.000 2.25 3.16 41.83 2.92
2744 2960 5.227569 TGTTCTTACAGAGCTCCATTCAA 57.772 39.130 10.93 0.00 0.00 2.69
2758 3001 2.616510 CCATTCAACTGGGGAGAGTGAC 60.617 54.545 0.00 0.00 32.28 3.67
2830 3073 3.426615 AGGAGATTCACACTCTTCTCGT 58.573 45.455 0.00 0.00 36.34 4.18
2876 3119 2.207580 GAGAGTCCTCTGCTTCCCC 58.792 63.158 0.60 0.00 40.61 4.81
2932 3175 6.778069 AGGTCTCCGAGATAGATGTCAATTTA 59.222 38.462 0.33 0.00 0.00 1.40
2952 3195 7.817418 ATTTAGAACCTGCTGTTACAGAAAA 57.183 32.000 17.40 0.00 40.25 2.29
2988 3231 0.106217 CAACAACCCACCCAAGACCT 60.106 55.000 0.00 0.00 0.00 3.85
2998 3241 0.322008 CCCAAGACCTTCCTGCTGAC 60.322 60.000 0.00 0.00 0.00 3.51
3047 3290 4.020617 CCGAGCAGCCTGGGTTGA 62.021 66.667 7.64 0.00 32.73 3.18
3132 3375 0.382873 GACCGCGGAAGTTTTTGGTT 59.617 50.000 35.90 3.54 0.00 3.67
3135 3378 0.382515 CGCGGAAGTTTTTGGTTGGA 59.617 50.000 0.00 0.00 0.00 3.53
3143 3386 3.096092 AGTTTTTGGTTGGACAAGAGCA 58.904 40.909 0.00 0.00 0.00 4.26
3144 3387 3.131046 AGTTTTTGGTTGGACAAGAGCAG 59.869 43.478 0.00 0.00 0.00 4.24
3145 3388 1.032014 TTTGGTTGGACAAGAGCAGC 58.968 50.000 0.00 0.00 0.00 5.25
3146 3389 0.106769 TTGGTTGGACAAGAGCAGCA 60.107 50.000 0.00 0.00 0.00 4.41
3255 3499 5.161943 ACCAGTACAGAAACATTAGGACC 57.838 43.478 0.00 0.00 0.00 4.46
3308 3552 7.693951 GCTAACATTTACTTTGCAGTGTATCAG 59.306 37.037 2.46 0.00 34.06 2.90
3314 3558 7.744087 TTACTTTGCAGTGTATCAGAATTGT 57.256 32.000 2.46 0.00 34.06 2.71
3318 3562 4.388485 TGCAGTGTATCAGAATTGTGTGT 58.612 39.130 2.11 0.00 0.00 3.72
3319 3563 4.213906 TGCAGTGTATCAGAATTGTGTGTG 59.786 41.667 2.11 0.00 0.00 3.82
3347 3591 7.448420 AGATTGTTGCAGACTATGTGCTATAT 58.552 34.615 0.00 0.00 41.78 0.86
3348 3592 8.588472 AGATTGTTGCAGACTATGTGCTATATA 58.412 33.333 0.00 0.00 41.78 0.86
3385 3629 7.718272 ACGTTCATACTTTGTTAGCTAAACA 57.282 32.000 7.99 6.23 46.41 2.83
3402 3646 6.543831 AGCTAAACATTCAGATACCATTGTCC 59.456 38.462 0.00 0.00 0.00 4.02
3526 4113 0.829182 CTTGGCTCAAAACTGGGCCT 60.829 55.000 16.63 0.00 44.36 5.19
3595 4193 7.264294 ACTGGAGGAGAGATATTTTCAAGTT 57.736 36.000 0.00 0.00 0.00 2.66
3600 4198 7.600752 GGAGGAGAGATATTTTCAAGTTATCGG 59.399 40.741 0.00 0.00 0.00 4.18
3630 4228 2.029110 GGCACTGGAAGCTTGCAAAATA 60.029 45.455 21.68 0.00 37.66 1.40
3631 4229 2.989166 GCACTGGAAGCTTGCAAAATAC 59.011 45.455 21.68 6.28 36.12 1.89
3632 4230 3.305608 GCACTGGAAGCTTGCAAAATACT 60.306 43.478 21.68 0.00 36.12 2.12
3633 4231 4.082787 GCACTGGAAGCTTGCAAAATACTA 60.083 41.667 21.68 0.00 36.12 1.82
3705 4303 1.662438 CTCTGGTCTCGAGTCCCTGC 61.662 65.000 23.33 1.96 0.00 4.85
3790 4388 3.659735 CAGACTTATTTGTGCTAACGCG 58.340 45.455 3.53 3.53 39.65 6.01
3814 4412 3.728718 CGTGGTACTTGCAAATTGTGAAC 59.271 43.478 0.00 0.00 0.00 3.18
3828 4426 3.159353 TGTGAACCGTATCCGATCTTG 57.841 47.619 0.00 0.00 35.63 3.02
3860 4459 0.618458 TTAGGGCATCTCCAACGCTT 59.382 50.000 0.00 0.00 36.21 4.68
3959 4563 4.482990 ACCAAACTGGAGGAAATTCATGT 58.517 39.130 0.00 0.00 40.96 3.21
3963 4567 6.868339 CCAAACTGGAGGAAATTCATGTAAAC 59.132 38.462 0.00 0.00 40.96 2.01
3966 4570 4.912586 TGGAGGAAATTCATGTAAACCGA 58.087 39.130 0.00 0.00 0.00 4.69
4009 4613 6.996282 CCGGACATATTTTCACTAAACCCTAT 59.004 38.462 0.00 0.00 0.00 2.57
4038 4642 2.254546 AATCTAAATGATCGCCGGCA 57.745 45.000 28.98 14.46 33.57 5.69
4094 4698 3.708220 CTCCGCCTTCGCAGTCTCC 62.708 68.421 0.00 0.00 34.03 3.71
4105 4709 0.892814 GCAGTCTCCAGCTTTGCCTT 60.893 55.000 0.00 0.00 0.00 4.35
4120 4727 2.352805 CTTGGCCTCCACCACCTC 59.647 66.667 3.32 0.00 40.19 3.85
4125 4732 3.636231 CCTCCACCACCTCCGCAA 61.636 66.667 0.00 0.00 0.00 4.85
4164 4771 0.733150 GATCAACCCGCCAAGCTTAC 59.267 55.000 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.954118 TGGTGTCCCCTGCCGTCT 62.954 66.667 0.00 0.00 0.00 4.18
50 51 4.489771 CCGATGGTGTCCCCTGCC 62.490 72.222 0.00 0.00 0.00 4.85
56 58 4.176752 GGAGCCCCGATGGTGTCC 62.177 72.222 0.00 0.00 36.04 4.02
85 87 4.736896 GACGTGGTGGAGGTCGCC 62.737 72.222 0.00 0.00 46.03 5.54
169 176 0.321996 GACCGCAAAGGAGGAGAAGT 59.678 55.000 0.00 0.00 45.00 3.01
173 180 1.160137 CAAAGACCGCAAAGGAGGAG 58.840 55.000 0.00 0.00 45.00 3.69
262 271 1.074090 TTGGAGGTGGTGGAGGTGA 60.074 57.895 0.00 0.00 0.00 4.02
350 362 1.691219 GCTCTCCACCCAATTCCCA 59.309 57.895 0.00 0.00 0.00 4.37
377 389 1.087501 GCGACAAAATCCCCACTCTC 58.912 55.000 0.00 0.00 0.00 3.20
378 390 0.673644 CGCGACAAAATCCCCACTCT 60.674 55.000 0.00 0.00 0.00 3.24
381 393 1.238625 TTCCGCGACAAAATCCCCAC 61.239 55.000 8.23 0.00 0.00 4.61
382 394 0.537600 TTTCCGCGACAAAATCCCCA 60.538 50.000 8.23 0.00 0.00 4.96
542 586 0.241213 CATGTATCGATCCGCCGAGT 59.759 55.000 0.00 0.00 42.21 4.18
596 641 2.413634 CCTTCGCATACGTTTTGAACCC 60.414 50.000 0.00 0.00 41.18 4.11
616 661 0.239082 CAACGCCGACCCTTAAAACC 59.761 55.000 0.00 0.00 0.00 3.27
643 688 9.411189 TGGCGACCCTTTTATTACTTTTATTAT 57.589 29.630 0.00 0.00 0.00 1.28
659 705 1.077501 CATCCACATGGCGACCCTT 60.078 57.895 0.00 0.00 34.44 3.95
661 707 2.114670 CACATCCACATGGCGACCC 61.115 63.158 0.00 0.00 33.82 4.46
663 709 1.377202 ACCACATCCACATGGCGAC 60.377 57.895 0.00 0.00 39.84 5.19
719 772 4.458829 TGACGCGGAGAGGGGGAT 62.459 66.667 12.47 0.00 37.07 3.85
811 874 0.387929 TATTAGCGTTGGAGGCGGAG 59.612 55.000 0.00 0.00 33.62 4.63
812 875 0.825410 TTATTAGCGTTGGAGGCGGA 59.175 50.000 0.00 0.00 33.62 5.54
814 877 0.935196 GGTTATTAGCGTTGGAGGCG 59.065 55.000 0.00 0.00 33.62 5.52
815 878 2.327200 AGGTTATTAGCGTTGGAGGC 57.673 50.000 0.00 0.00 0.00 4.70
816 879 3.871594 CAGAAGGTTATTAGCGTTGGAGG 59.128 47.826 0.00 0.00 0.00 4.30
817 880 3.871594 CCAGAAGGTTATTAGCGTTGGAG 59.128 47.826 0.00 0.00 0.00 3.86
818 881 3.516300 TCCAGAAGGTTATTAGCGTTGGA 59.484 43.478 1.71 1.71 35.89 3.53
819 882 3.869065 TCCAGAAGGTTATTAGCGTTGG 58.131 45.455 0.00 0.00 35.89 3.77
820 883 5.873179 TTTCCAGAAGGTTATTAGCGTTG 57.127 39.130 0.00 0.00 35.89 4.10
821 884 7.362660 GGAATTTTCCAGAAGGTTATTAGCGTT 60.363 37.037 4.43 0.00 46.76 4.84
822 885 6.095021 GGAATTTTCCAGAAGGTTATTAGCGT 59.905 38.462 4.43 0.00 46.76 5.07
823 886 6.495706 GGAATTTTCCAGAAGGTTATTAGCG 58.504 40.000 4.43 0.00 46.76 4.26
1655 1718 1.162698 CCTCACATGTCAGCACAAGG 58.837 55.000 0.00 0.00 35.64 3.61
1721 1784 3.996150 AATCGCAGATTATTTGCCCAG 57.004 42.857 2.09 0.00 45.12 4.45
1748 1811 5.972107 AGAGCAATAAATCACAAGCACTT 57.028 34.783 0.00 0.00 0.00 3.16
1854 1917 6.136541 ACAAATCAAGAGTTGACCTTTGTC 57.863 37.500 16.05 0.00 43.75 3.18
1888 1951 6.091441 AGTGATGAACGAAGCTAGTTGAATTC 59.909 38.462 11.59 0.00 31.14 2.17
1909 1972 5.362143 CCACAGGATCAAGAAGAGATAGTGA 59.638 44.000 0.00 0.00 30.69 3.41
1910 1973 5.362143 TCCACAGGATCAAGAAGAGATAGTG 59.638 44.000 0.00 0.00 0.00 2.74
1929 1992 0.482446 AACAGCCCCAAGATTCCACA 59.518 50.000 0.00 0.00 0.00 4.17
1932 1995 1.546029 GTCAAACAGCCCCAAGATTCC 59.454 52.381 0.00 0.00 0.00 3.01
1933 1996 2.238521 TGTCAAACAGCCCCAAGATTC 58.761 47.619 0.00 0.00 0.00 2.52
1934 1997 2.380064 TGTCAAACAGCCCCAAGATT 57.620 45.000 0.00 0.00 0.00 2.40
1935 1998 2.380064 TTGTCAAACAGCCCCAAGAT 57.620 45.000 0.00 0.00 0.00 2.40
1936 1999 2.151502 TTTGTCAAACAGCCCCAAGA 57.848 45.000 0.00 0.00 0.00 3.02
1937 2000 4.599047 TTATTTGTCAAACAGCCCCAAG 57.401 40.909 0.00 0.00 0.00 3.61
1938 2001 5.359194 TTTTATTTGTCAAACAGCCCCAA 57.641 34.783 0.00 0.00 0.00 4.12
1939 2002 5.306678 AGATTTTATTTGTCAAACAGCCCCA 59.693 36.000 0.00 0.00 0.00 4.96
1940 2003 5.793817 AGATTTTATTTGTCAAACAGCCCC 58.206 37.500 0.00 0.00 0.00 5.80
1985 2048 6.260714 GCAACAGAAGGGAAACAAATTGAAAT 59.739 34.615 0.00 0.00 0.00 2.17
1988 2051 4.161189 TGCAACAGAAGGGAAACAAATTGA 59.839 37.500 0.00 0.00 0.00 2.57
2023 2239 6.040247 GCATTACCATTACCAAGGCTAAAAC 58.960 40.000 0.00 0.00 0.00 2.43
2068 2284 6.870965 GGTGACACATATTAGAATAGCCTCAG 59.129 42.308 8.08 0.00 0.00 3.35
2086 2302 5.056894 ACATAAGAACGAGTAGGTGACAC 57.943 43.478 0.00 0.00 0.00 3.67
2107 2323 4.283978 GGATCTACCTTCCTAAAGCCCTAC 59.716 50.000 0.00 0.00 35.41 3.18
2162 2378 0.727457 CGATGCCGCTGATCTCGTAG 60.727 60.000 0.00 0.00 0.00 3.51
2170 2386 0.886938 TTTTCAACCGATGCCGCTGA 60.887 50.000 0.00 0.00 0.00 4.26
2320 2536 6.260936 CAGTTTTCTTCCTCTCAAGCTGTAAA 59.739 38.462 0.00 0.00 0.00 2.01
2332 2548 6.883744 ACTCTCCATATCAGTTTTCTTCCTC 58.116 40.000 0.00 0.00 0.00 3.71
2392 2608 9.499479 GATATAAGATTTTTCTGCTGATCCTCA 57.501 33.333 0.00 0.00 0.00 3.86
2453 2669 7.030165 TCAGATTGTTCTACGAAGCTAGAAAG 58.970 38.462 0.00 0.00 34.09 2.62
2485 2701 1.625818 GGCAGTCTCCTCTTCTTTCCA 59.374 52.381 0.00 0.00 0.00 3.53
2527 2743 1.951209 TCCCCTGAGTACAAGCATCA 58.049 50.000 0.00 0.00 0.00 3.07
2533 2749 2.409064 TCTGGTTCCCCTGAGTACAA 57.591 50.000 0.00 0.00 34.10 2.41
2534 2750 2.642171 ATCTGGTTCCCCTGAGTACA 57.358 50.000 0.00 0.00 41.43 2.90
2582 2798 6.500684 TGATGACCTAAAAAGTTCATGAGC 57.499 37.500 0.50 0.50 0.00 4.26
2662 2878 5.479724 TGAAACATCATTACCAAATGCCTCA 59.520 36.000 0.00 0.00 41.96 3.86
2688 2904 0.914644 ACCTGGGACATCACCATCAG 59.085 55.000 0.00 0.00 38.20 2.90
2830 3073 1.889170 CTGGCGGACTCTGCTATATCA 59.111 52.381 9.76 0.00 0.00 2.15
2876 3119 1.718396 TCTGCACGAGAATGAGCTTG 58.282 50.000 0.00 0.00 0.00 4.01
2932 3175 4.520492 CCATTTTCTGTAACAGCAGGTTCT 59.480 41.667 0.00 0.00 40.96 3.01
2952 3195 3.033909 TGTTGATCTCTCGATGGACCAT 58.966 45.455 6.71 6.71 0.00 3.55
2998 3241 2.605818 CTGCCAAAATCCATCATTTGCG 59.394 45.455 0.00 0.00 34.69 4.85
3047 3290 2.759114 CTCCTGGTGTGCATGGGT 59.241 61.111 0.00 0.00 0.00 4.51
3132 3375 0.321346 TTCGATGCTGCTCTTGTCCA 59.679 50.000 0.00 0.00 0.00 4.02
3135 3378 1.001293 TCTGTTCGATGCTGCTCTTGT 59.999 47.619 0.00 0.00 0.00 3.16
3255 3499 1.077930 CTCACTGGGAGGTGCCATG 60.078 63.158 0.00 0.00 40.13 3.66
3274 3518 5.743872 GCAAAGTAAATGTTAGCAGGCATAC 59.256 40.000 0.00 0.00 0.00 2.39
3282 3526 7.526608 TGATACACTGCAAAGTAAATGTTAGC 58.473 34.615 2.44 0.00 0.00 3.09
3308 3552 5.976534 TGCAACAATCTAACACACACAATTC 59.023 36.000 0.00 0.00 0.00 2.17
3314 3558 4.450976 AGTCTGCAACAATCTAACACACA 58.549 39.130 0.00 0.00 0.00 3.72
3318 3562 5.122239 GCACATAGTCTGCAACAATCTAACA 59.878 40.000 0.00 0.00 34.56 2.41
3319 3563 5.352569 AGCACATAGTCTGCAACAATCTAAC 59.647 40.000 0.00 0.00 37.08 2.34
3348 3592 9.745880 CAAAGTATGAACGTATATCAAGGTAGT 57.254 33.333 0.00 0.00 0.00 2.73
3382 3626 4.635765 CGTGGACAATGGTATCTGAATGTT 59.364 41.667 0.00 0.00 0.00 2.71
3385 3629 4.162320 AGTCGTGGACAATGGTATCTGAAT 59.838 41.667 0.00 0.00 34.60 2.57
3392 3636 1.250328 ACGAGTCGTGGACAATGGTA 58.750 50.000 19.16 0.00 39.18 3.25
3595 4193 1.448893 GTGCCAGGAAACGCCGATA 60.449 57.895 0.00 0.00 43.43 2.92
3600 4198 1.856265 CTTCCAGTGCCAGGAAACGC 61.856 60.000 0.00 0.00 44.07 4.84
3630 4228 7.330900 AGTACTACAACGCATCTGTAATAGT 57.669 36.000 0.00 0.00 31.39 2.12
3631 4229 6.856938 GGAGTACTACAACGCATCTGTAATAG 59.143 42.308 0.00 0.00 0.00 1.73
3632 4230 6.512253 CGGAGTACTACAACGCATCTGTAATA 60.512 42.308 5.80 0.00 0.00 0.98
3633 4231 5.589192 GGAGTACTACAACGCATCTGTAAT 58.411 41.667 0.00 0.00 0.00 1.89
3705 4303 3.191371 GCTGGTTGTTCTACCCTTTGATG 59.809 47.826 1.53 0.00 37.39 3.07
3735 4333 1.201921 CGAAGCGAAAGAAATGTCCGG 60.202 52.381 0.00 0.00 0.00 5.14
3790 4388 1.000717 ACAATTTGCAAGTACCACGCC 60.001 47.619 0.00 0.00 0.00 5.68
3879 4482 1.377366 GACTGGCTCTCGACGGATGA 61.377 60.000 0.00 0.00 0.00 2.92
3886 4489 0.532573 GTTGGATGACTGGCTCTCGA 59.467 55.000 0.00 0.00 0.00 4.04
3888 4491 1.086634 GCGTTGGATGACTGGCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
3889 4492 1.078848 GCGTTGGATGACTGGCTCT 60.079 57.895 0.00 0.00 0.00 4.09
3959 4563 7.964011 GGAATGTAATGAATTTCGTTCGGTTTA 59.036 33.333 7.12 0.00 39.80 2.01
3963 4567 4.961551 CGGAATGTAATGAATTTCGTTCGG 59.038 41.667 7.12 7.62 39.80 4.30
3966 4570 5.413213 TGTCCGGAATGTAATGAATTTCGTT 59.587 36.000 5.23 8.79 34.78 3.85
4009 4613 9.140286 CGGCGATCATTTAGATTAGATTTAGAA 57.860 33.333 0.00 0.00 37.00 2.10
4079 4683 2.507992 CTGGAGACTGCGAAGGCG 60.508 66.667 0.00 0.00 44.10 5.52
4094 4698 2.643232 GGAGGCCAAGGCAAAGCTG 61.643 63.158 13.87 0.00 44.11 4.24
4150 4757 2.351276 CAGGTAAGCTTGGCGGGT 59.649 61.111 9.86 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.