Multiple sequence alignment - TraesCS3A01G321700

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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 TraesCS3A01G321700 chr3A 100.000 7033 0 0 1 7033 565350931 565357963 0.000000e+00 12988
1 TraesCS3A01G321700 chr3A 97.173 2653 69 3 1790 4441 560189712 560187065 0.000000e+00 4479
2 TraesCS3A01G321700 chr3A 94.562 331 10 3 1477 1799 560203057 560202727 8.140000e-139 505
3 TraesCS3A01G321700 chr3B 95.958 5987 143 30 878 6821 552926159 552932089 0.000000e+00 9624
4 TraesCS3A01G321700 chr3B 90.875 800 43 10 93 886 552925351 552926126 0.000000e+00 1046
5 TraesCS3A01G321700 chr3B 94.872 78 4 0 1 78 552925285 552925362 9.580000e-24 122
6 TraesCS3A01G321700 chr3D 96.835 4076 65 18 875 4930 423858474 423854443 0.000000e+00 6754
7 TraesCS3A01G321700 chr3D 97.030 1549 32 4 4932 6475 423854304 423852765 0.000000e+00 2593
8 TraesCS3A01G321700 chr3D 88.207 831 36 24 96 886 423859315 423858507 0.000000e+00 935
9 TraesCS3A01G321700 chr3D 96.774 248 3 2 6625 6872 423852659 423852417 6.570000e-110 409
10 TraesCS3A01G321700 chr3D 94.958 119 4 2 6916 7033 423852164 423852047 1.200000e-42 185
11 TraesCS3A01G321700 chr6A 78.718 390 57 10 6453 6821 55034767 55035151 3.280000e-58 237
12 TraesCS3A01G321700 chr6A 86.471 170 17 5 6445 6612 481078623 481078788 1.560000e-41 182


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 TraesCS3A01G321700 chr3A 565350931 565357963 7032 False 12988.000000 12988 100.000000 1 7033 1 chr3A.!!$F1 7032
1 TraesCS3A01G321700 chr3A 560187065 560189712 2647 True 4479.000000 4479 97.173000 1790 4441 1 chr3A.!!$R1 2651
2 TraesCS3A01G321700 chr3B 552925285 552932089 6804 False 3597.333333 9624 93.901667 1 6821 3 chr3B.!!$F1 6820
3 TraesCS3A01G321700 chr3D 423852047 423859315 7268 True 2175.200000 6754 94.760800 96 7033 5 chr3D.!!$R1 6937

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
915 999 0.030603 ATCCCTCCTCCTCTTCCACC 60.031 60.000 0.00 0.0 0.00 4.61 F
933 1017 1.229359 CCCCTCCTACTCCTGCGTA 59.771 63.158 0.00 0.0 0.00 4.42 F
1629 1726 2.355756 TCTCAGCATTAAAATCGCAGCC 59.644 45.455 0.00 0.0 0.00 4.85 F
1867 1976 5.108330 GCGCAACAATCTACTTCTATACGAC 60.108 44.000 0.30 0.0 0.00 4.34 F
2981 3106 4.012374 ACACCAGATGTTAATCCTGCAAG 58.988 43.478 0.00 0.0 38.98 4.01 F
3030 3155 2.030946 GCACGACCAGAGCAATTATGTC 59.969 50.000 0.00 0.0 36.42 3.06 F
3819 3945 2.198827 AATTGACGGATGCAACTCCA 57.801 45.000 7.13 0.0 34.78 3.86 F
4930 5059 2.290641 GACCAACTGTGCCTACTTTGTG 59.709 50.000 0.00 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1973 2.766313 TGAATCTTGTTCCTGTGGTCG 58.234 47.619 0.00 0.00 0.00 4.79 R
2795 2920 5.394115 CCATTACAGTTTTCCTGCATAACCC 60.394 44.000 0.00 0.00 45.68 4.11 R
2981 3106 1.620822 TTCTTTGCCCTTCTCAAGCC 58.379 50.000 0.00 0.00 0.00 4.35 R
3030 3155 2.023673 TCACCCTCTTTTGTGTTGCTG 58.976 47.619 0.00 0.00 34.14 4.41 R
4896 5025 3.057033 ACAGTTGGTCGTACAGGACATAC 60.057 47.826 4.63 2.23 38.70 2.39 R
4912 5041 5.034554 CATACACAAAGTAGGCACAGTTG 57.965 43.478 0.00 0.00 35.85 3.16 R
5774 6047 0.883833 CATGGACAAGACAACAGCCC 59.116 55.000 0.00 0.00 0.00 5.19 R
6566 6840 0.116143 ATTAGCCAAGCAAACCCCCA 59.884 50.000 0.00 0.00 0.00 4.96 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
62 63 3.753272 GTCCTTGTGTACATGACATTGCT 59.247 43.478 0.00 0.00 41.14 3.91
78 79 6.584942 TGACATTGCTGTTTTCTACTACTACG 59.415 38.462 0.00 0.00 35.14 3.51
79 80 6.453092 ACATTGCTGTTTTCTACTACTACGT 58.547 36.000 0.00 0.00 28.70 3.57
80 81 6.927381 ACATTGCTGTTTTCTACTACTACGTT 59.073 34.615 0.00 0.00 28.70 3.99
81 82 7.440255 ACATTGCTGTTTTCTACTACTACGTTT 59.560 33.333 0.00 0.00 28.70 3.60
82 83 7.775397 TTGCTGTTTTCTACTACTACGTTTT 57.225 32.000 0.00 0.00 0.00 2.43
83 84 7.775397 TGCTGTTTTCTACTACTACGTTTTT 57.225 32.000 0.00 0.00 0.00 1.94
130 131 4.094294 TCAAAATAAGTGTAGCGGACATGC 59.906 41.667 0.00 0.00 41.14 4.06
148 149 6.873076 GGACATGCCATTTATTTTGAAACAGA 59.127 34.615 0.00 0.00 36.34 3.41
151 152 6.662865 TGCCATTTATTTTGAAACAGAGGA 57.337 33.333 0.00 0.00 0.00 3.71
190 191 8.639761 TCCTACTGTACATTCTTATAAGGCTTC 58.360 37.037 12.54 0.77 0.00 3.86
236 241 1.468520 ACACAAACATACCAGCATCGC 59.531 47.619 0.00 0.00 0.00 4.58
242 247 0.602106 CATACCAGCATCGCTCCCTG 60.602 60.000 0.00 0.00 36.40 4.45
243 248 1.050988 ATACCAGCATCGCTCCCTGT 61.051 55.000 0.00 0.00 36.40 4.00
244 249 1.264749 TACCAGCATCGCTCCCTGTT 61.265 55.000 0.00 0.00 36.40 3.16
245 250 1.377725 CCAGCATCGCTCCCTGTTT 60.378 57.895 0.00 0.00 36.40 2.83
434 453 4.214971 TCCTCGCGAGTCCATAATAAGTAC 59.785 45.833 32.41 0.00 0.00 2.73
435 454 4.215827 CCTCGCGAGTCCATAATAAGTACT 59.784 45.833 32.41 0.00 0.00 2.73
436 455 5.354054 TCGCGAGTCCATAATAAGTACTC 57.646 43.478 3.71 0.00 34.55 2.59
437 456 4.214971 TCGCGAGTCCATAATAAGTACTCC 59.785 45.833 3.71 0.00 34.42 3.85
457 478 3.056107 TCCCTCCGTAGTTCATTCAACAG 60.056 47.826 0.00 0.00 37.48 3.16
481 502 2.316792 CGTGTTATCTCCCGCTTATCG 58.683 52.381 0.00 0.00 38.08 2.92
596 635 4.585526 TCGGATCGCCACCATCGC 62.586 66.667 0.00 0.00 0.00 4.58
613 652 2.585247 CCTTCGTCCCCGCGATTC 60.585 66.667 8.23 0.00 40.76 2.52
616 655 2.955751 CTTCGTCCCCGCGATTCCTC 62.956 65.000 8.23 0.00 40.76 3.71
617 656 4.587189 CGTCCCCGCGATTCCTCC 62.587 72.222 8.23 0.00 0.00 4.30
618 657 3.155167 GTCCCCGCGATTCCTCCT 61.155 66.667 8.23 0.00 0.00 3.69
619 658 2.365105 TCCCCGCGATTCCTCCTT 60.365 61.111 8.23 0.00 0.00 3.36
620 659 1.993391 TCCCCGCGATTCCTCCTTT 60.993 57.895 8.23 0.00 0.00 3.11
621 660 1.523938 CCCCGCGATTCCTCCTTTC 60.524 63.158 8.23 0.00 0.00 2.62
622 661 1.523938 CCCGCGATTCCTCCTTTCC 60.524 63.158 8.23 0.00 0.00 3.13
623 662 1.523938 CCGCGATTCCTCCTTTCCC 60.524 63.158 8.23 0.00 0.00 3.97
624 663 1.883084 CGCGATTCCTCCTTTCCCG 60.883 63.158 0.00 0.00 0.00 5.14
631 670 4.989168 CGATTCCTCCTTTCCCGTAATAAG 59.011 45.833 0.00 0.00 0.00 1.73
639 678 1.044231 TCCCGTAATAAGCCCGCAGA 61.044 55.000 0.00 0.00 0.00 4.26
679 718 2.922234 GATGGAGGAAGCCCAGGG 59.078 66.667 0.00 0.00 37.08 4.45
915 999 0.030603 ATCCCTCCTCCTCTTCCACC 60.031 60.000 0.00 0.00 0.00 4.61
930 1014 2.066999 CACCCCCTCCTACTCCTGC 61.067 68.421 0.00 0.00 0.00 4.85
931 1015 2.840102 CCCCCTCCTACTCCTGCG 60.840 72.222 0.00 0.00 0.00 5.18
932 1016 2.042843 CCCCTCCTACTCCTGCGT 60.043 66.667 0.00 0.00 0.00 5.24
933 1017 1.229359 CCCCTCCTACTCCTGCGTA 59.771 63.158 0.00 0.00 0.00 4.42
962 1046 3.188786 CGCGCTCTTTTCCGAGGG 61.189 66.667 5.56 0.00 44.21 4.30
1166 1253 4.915667 GCGTTAAGCCTTTTGGTTTTCTAG 59.084 41.667 0.00 0.00 40.21 2.43
1629 1726 2.355756 TCTCAGCATTAAAATCGCAGCC 59.644 45.455 0.00 0.00 0.00 4.85
1864 1973 6.420903 TGATGCGCAACAATCTACTTCTATAC 59.579 38.462 18.75 0.00 0.00 1.47
1867 1976 5.108330 GCGCAACAATCTACTTCTATACGAC 60.108 44.000 0.30 0.00 0.00 4.34
2739 2864 5.393135 GGCAGGTTTTCTAGATAACCAAAGC 60.393 44.000 33.31 30.60 42.48 3.51
2795 2920 6.516718 ACTGTAATGGTAATCAGGAAGATCG 58.483 40.000 0.00 0.00 35.39 3.69
2981 3106 4.012374 ACACCAGATGTTAATCCTGCAAG 58.988 43.478 0.00 0.00 38.98 4.01
3030 3155 2.030946 GCACGACCAGAGCAATTATGTC 59.969 50.000 0.00 0.00 36.42 3.06
3100 3225 4.080863 GTCCTAGGATGAAAGCTCCAAAGA 60.081 45.833 16.27 0.00 35.08 2.52
3249 3374 6.438741 TGTCTTCTCTGACTAATGGATCAACT 59.561 38.462 0.00 0.00 37.79 3.16
3443 3568 5.831525 CCCCTCATCAATCAGAAATCAATCA 59.168 40.000 0.00 0.00 0.00 2.57
3548 3673 2.936919 ACTCTTGATGTGGCTGTTGA 57.063 45.000 0.00 0.00 0.00 3.18
3566 3691 3.751479 TGAGACTTTAGCTGCTGACAA 57.249 42.857 13.43 1.57 0.00 3.18
3819 3945 2.198827 AATTGACGGATGCAACTCCA 57.801 45.000 7.13 0.00 34.78 3.86
4102 4228 4.141482 GGTTGGCTATCTCCAGTGGAATAA 60.141 45.833 14.17 2.02 37.44 1.40
4368 4495 7.641411 CCTCATGATAATTTAGAAGCAAACACG 59.359 37.037 0.00 0.00 0.00 4.49
4896 5025 6.992123 TCCTTGTACAAACATCCTATGCTATG 59.008 38.462 10.03 0.00 34.97 2.23
4912 5041 3.317149 TGCTATGTATGTCCTGTACGACC 59.683 47.826 0.00 0.00 31.35 4.79
4930 5059 2.290641 GACCAACTGTGCCTACTTTGTG 59.709 50.000 0.00 0.00 0.00 3.33
5194 5460 3.560025 GGTGATCCTTGACAGATGGTTGT 60.560 47.826 0.00 0.00 0.00 3.32
5195 5461 4.074970 GTGATCCTTGACAGATGGTTGTT 58.925 43.478 0.00 0.00 0.00 2.83
5217 5483 4.905429 TGTCACCAATAATGCACACTACT 58.095 39.130 0.00 0.00 0.00 2.57
5745 6018 3.131577 TCAGTTTGTAGTCAGTTCACGGT 59.868 43.478 0.00 0.00 0.00 4.83
5776 6049 8.682936 ACAGATTAATAGAAATGCTTAGTGGG 57.317 34.615 0.00 0.00 0.00 4.61
5777 6050 7.229506 ACAGATTAATAGAAATGCTTAGTGGGC 59.770 37.037 0.00 0.00 0.00 5.36
5778 6051 7.446625 CAGATTAATAGAAATGCTTAGTGGGCT 59.553 37.037 0.00 0.00 0.00 5.19
5779 6052 6.942532 TTAATAGAAATGCTTAGTGGGCTG 57.057 37.500 0.00 0.00 0.00 4.85
5780 6053 2.887151 AGAAATGCTTAGTGGGCTGT 57.113 45.000 0.00 0.00 0.00 4.40
5952 6225 1.447314 GGCTGGAAACTACCGTCGG 60.447 63.158 10.48 10.48 0.00 4.79
5954 6227 0.735287 GCTGGAAACTACCGTCGGAC 60.735 60.000 20.51 0.00 0.00 4.79
6044 6317 1.153369 CACCTGATGGCAGTACCCG 60.153 63.158 0.00 0.00 40.63 5.28
6074 6347 1.012086 GATTTCCGTCTTTACCGCCC 58.988 55.000 0.00 0.00 0.00 6.13
6075 6348 0.741927 ATTTCCGTCTTTACCGCCCG 60.742 55.000 0.00 0.00 0.00 6.13
6109 6382 1.355563 CCAGCGATGCAAGCATGAG 59.644 57.895 12.94 7.43 36.70 2.90
6111 6384 1.292992 CAGCGATGCAAGCATGAGTA 58.707 50.000 12.94 0.00 36.70 2.59
6230 6503 7.704271 TGAGAGATTGAGGTTGTACTAATACG 58.296 38.462 0.00 0.00 33.60 3.06
6315 6588 4.201950 GCTGCCAGGATAGTACAAAATGTG 60.202 45.833 0.00 0.00 0.00 3.21
6368 6641 1.474077 GTTCATTGCTTGCGGGATTCT 59.526 47.619 0.00 0.00 0.00 2.40
6382 6655 2.098117 GGGATTCTTTTCGTGAGGCATG 59.902 50.000 0.00 0.00 0.00 4.06
6447 6720 3.084039 TGAGTTGATCACCCAGCATTTC 58.916 45.455 0.00 0.00 31.12 2.17
6486 6760 8.489990 TGCAATTGTATAAAACATCATTTGGG 57.510 30.769 7.40 0.00 38.10 4.12
6598 6872 4.618927 GCTTGGCTAATTCATGAGCAAACA 60.619 41.667 6.95 0.00 40.64 2.83
6605 6879 2.728690 TCATGAGCAAACATGTTGCC 57.271 45.000 21.59 12.83 45.98 4.52
6612 6886 3.689347 AGCAAACATGTTGCCATCTCTA 58.311 40.909 21.59 0.00 45.98 2.43
6663 6937 6.294473 CCTAATCACCATGTAATGCTCTCTT 58.706 40.000 0.00 0.00 44.97 2.85
6678 6952 3.681034 GCTCTCTTCATGCTGCTAAAGGA 60.681 47.826 0.00 1.95 0.00 3.36
6713 6987 6.404623 GCCATAATGTTTGACATAACAGCAGA 60.405 38.462 8.47 0.00 37.97 4.26
6827 7103 1.306825 ACAGGCAGGGAGCTCTGAT 60.307 57.895 14.64 0.00 44.79 2.90
6872 7148 8.585881 TCCTATAATGTATCCAACACTAGCTTC 58.414 37.037 0.00 0.00 42.09 3.86
6873 7149 8.367911 CCTATAATGTATCCAACACTAGCTTCA 58.632 37.037 0.00 0.00 42.09 3.02
6874 7150 9.197694 CTATAATGTATCCAACACTAGCTTCAC 57.802 37.037 0.00 0.00 42.09 3.18
6875 7151 4.882842 TGTATCCAACACTAGCTTCACA 57.117 40.909 0.00 0.00 31.43 3.58
6876 7152 5.420725 TGTATCCAACACTAGCTTCACAT 57.579 39.130 0.00 0.00 31.43 3.21
6877 7153 5.178061 TGTATCCAACACTAGCTTCACATG 58.822 41.667 0.00 0.00 31.43 3.21
6878 7154 3.769739 TCCAACACTAGCTTCACATGT 57.230 42.857 0.00 0.00 0.00 3.21
6879 7155 4.085357 TCCAACACTAGCTTCACATGTT 57.915 40.909 0.00 0.00 33.86 2.71
6880 7156 4.460263 TCCAACACTAGCTTCACATGTTT 58.540 39.130 0.00 0.00 31.25 2.83
6881 7157 4.887071 TCCAACACTAGCTTCACATGTTTT 59.113 37.500 0.00 0.00 31.25 2.43
6882 7158 5.359576 TCCAACACTAGCTTCACATGTTTTT 59.640 36.000 0.00 0.00 31.25 1.94
6908 7184 2.562125 TTTTTGAGGAATCGCCGGG 58.438 52.632 2.18 0.00 43.43 5.73
6909 7185 0.963355 TTTTTGAGGAATCGCCGGGG 60.963 55.000 13.31 13.31 43.43 5.73
6910 7186 2.830186 TTTTGAGGAATCGCCGGGGG 62.830 60.000 19.63 4.42 43.43 5.40
6954 7440 3.168035 TCACCTGTATTGGCCACAAAT 57.832 42.857 3.88 0.00 40.55 2.32
6957 7443 1.549620 CCTGTATTGGCCACAAATGCA 59.450 47.619 3.88 5.62 40.55 3.96
6989 7475 5.476599 TGTTAACTTTCAACCATCCATCAGG 59.523 40.000 7.22 0.00 0.00 3.86
6990 7476 2.450476 ACTTTCAACCATCCATCAGGC 58.550 47.619 0.00 0.00 33.74 4.85
7014 7500 5.811100 CGGTTTAGTCCATCTAGACTTTTCC 59.189 44.000 0.00 0.41 44.83 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 9.439500 TTTTGAAACGTAGTAGTATAATTGCCT 57.561 29.630 0.00 0.00 45.00 4.75
96 97 8.919661 GCTACACTTATTTTGAAACGTAGTAGT 58.080 33.333 0.00 0.00 45.00 2.73
97 98 8.100306 CGCTACACTTATTTTGAAACGTAGTAG 58.900 37.037 0.00 0.00 45.00 2.57
98 99 7.062138 CCGCTACACTTATTTTGAAACGTAGTA 59.938 37.037 0.00 0.00 45.00 1.82
100 101 6.089820 TCCGCTACACTTATTTTGAAACGTAG 59.910 38.462 0.00 0.00 0.00 3.51
101 102 5.925397 TCCGCTACACTTATTTTGAAACGTA 59.075 36.000 0.00 0.00 0.00 3.57
102 103 4.751098 TCCGCTACACTTATTTTGAAACGT 59.249 37.500 0.00 0.00 0.00 3.99
130 131 9.793252 CATACTCCTCTGTTTCAAAATAAATGG 57.207 33.333 0.00 0.00 0.00 3.16
216 221 1.468520 GCGATGCTGGTATGTTTGTGT 59.531 47.619 0.00 0.00 0.00 3.72
236 241 4.577283 TGGAACGAAAAAGTAAACAGGGAG 59.423 41.667 0.00 0.00 0.00 4.30
268 287 3.599343 AGCTGCTTTGTTATGATGACGA 58.401 40.909 0.00 0.00 0.00 4.20
269 288 3.620374 AGAGCTGCTTTGTTATGATGACG 59.380 43.478 2.53 0.00 0.00 4.35
270 289 4.201891 CCAGAGCTGCTTTGTTATGATGAC 60.202 45.833 17.58 0.00 0.00 3.06
434 453 3.056107 TGTTGAATGAACTACGGAGGGAG 60.056 47.826 0.00 0.00 35.37 4.30
435 454 2.901192 TGTTGAATGAACTACGGAGGGA 59.099 45.455 0.00 0.00 35.37 4.20
436 455 3.262420 CTGTTGAATGAACTACGGAGGG 58.738 50.000 0.00 0.00 35.37 4.30
437 456 2.673368 GCTGTTGAATGAACTACGGAGG 59.327 50.000 0.00 0.00 35.37 4.30
457 478 2.108362 CGGGAGATAACACGGGGC 59.892 66.667 0.00 0.00 0.00 5.80
481 502 2.311688 CTGTAGGTGACGGGGATGGC 62.312 65.000 0.00 0.00 0.00 4.40
613 652 2.486727 GGGCTTATTACGGGAAAGGAGG 60.487 54.545 0.00 0.00 0.00 4.30
616 655 1.589803 CGGGCTTATTACGGGAAAGG 58.410 55.000 0.00 0.00 0.00 3.11
617 656 0.942252 GCGGGCTTATTACGGGAAAG 59.058 55.000 0.00 0.00 0.00 2.62
618 657 0.252479 TGCGGGCTTATTACGGGAAA 59.748 50.000 0.00 0.00 0.00 3.13
619 658 0.179067 CTGCGGGCTTATTACGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
620 659 1.044231 TCTGCGGGCTTATTACGGGA 61.044 55.000 0.00 0.00 0.00 5.14
621 660 0.878961 GTCTGCGGGCTTATTACGGG 60.879 60.000 0.00 0.00 0.00 5.28
622 661 1.213094 CGTCTGCGGGCTTATTACGG 61.213 60.000 0.00 0.00 0.00 4.02
623 662 0.526954 ACGTCTGCGGGCTTATTACG 60.527 55.000 0.00 0.00 43.45 3.18
624 663 2.497107 TACGTCTGCGGGCTTATTAC 57.503 50.000 0.00 0.00 43.45 1.89
668 707 3.003763 ACGACTCCCTGGGCTTCC 61.004 66.667 8.22 0.00 0.00 3.46
679 718 3.106407 GCCTGCGACACACGACTC 61.106 66.667 0.00 0.00 45.77 3.36
885 969 1.003718 GGAGGGATTTATCGGCGGG 60.004 63.158 7.21 0.00 0.00 6.13
915 999 1.108132 GTACGCAGGAGTAGGAGGGG 61.108 65.000 0.00 0.00 0.00 4.79
1081 1165 2.800544 GCCGAGAAAAGCGAGCATATAA 59.199 45.455 0.00 0.00 0.00 0.98
1082 1166 2.404215 GCCGAGAAAAGCGAGCATATA 58.596 47.619 0.00 0.00 0.00 0.86
1083 1167 1.221414 GCCGAGAAAAGCGAGCATAT 58.779 50.000 0.00 0.00 0.00 1.78
1084 1168 0.810031 GGCCGAGAAAAGCGAGCATA 60.810 55.000 0.00 0.00 0.00 3.14
1085 1169 2.109126 GGCCGAGAAAAGCGAGCAT 61.109 57.895 0.00 0.00 0.00 3.79
1086 1170 2.742372 GGCCGAGAAAAGCGAGCA 60.742 61.111 0.00 0.00 0.00 4.26
1166 1253 6.750501 TGTGATGCTACTAATGTCGTTCTTAC 59.249 38.462 0.00 0.00 0.00 2.34
1234 1321 0.661020 ACGCAAGGCAACACAACTAC 59.339 50.000 0.00 0.00 46.39 2.73
1235 1322 3.088259 ACGCAAGGCAACACAACTA 57.912 47.368 0.00 0.00 46.39 2.24
1629 1726 2.479566 TTCTTGTGCTTAGGCTGGAG 57.520 50.000 0.00 0.00 39.59 3.86
1864 1973 2.766313 TGAATCTTGTTCCTGTGGTCG 58.234 47.619 0.00 0.00 0.00 4.79
1867 1976 5.765182 ACTTACTTGAATCTTGTTCCTGTGG 59.235 40.000 0.00 0.00 0.00 4.17
2112 2237 6.148150 TGGTAGACGAAATAAAGTGCGAAAAT 59.852 34.615 0.00 0.00 0.00 1.82
2795 2920 5.394115 CCATTACAGTTTTCCTGCATAACCC 60.394 44.000 0.00 0.00 45.68 4.11
2981 3106 1.620822 TTCTTTGCCCTTCTCAAGCC 58.379 50.000 0.00 0.00 0.00 4.35
3030 3155 2.023673 TCACCCTCTTTTGTGTTGCTG 58.976 47.619 0.00 0.00 34.14 4.41
3249 3374 8.684386 TCTGATTGGTAGTTTTATCAAACACA 57.316 30.769 5.36 0.00 44.32 3.72
3475 3600 6.799512 GCATAGAATTGCTACCATTCAAAGT 58.200 36.000 0.00 0.00 39.57 2.66
3548 3673 2.370189 AGGTTGTCAGCAGCTAAAGTCT 59.630 45.455 0.00 0.00 0.00 3.24
3566 3691 2.224867 CCAGGTGACTCCATTTGAAGGT 60.225 50.000 0.00 0.00 40.21 3.50
3819 3945 9.467258 GCACAAAAATCACTATATACATTGCAT 57.533 29.630 0.00 0.00 0.00 3.96
3829 3955 7.392953 TGGATTGACAGCACAAAAATCACTATA 59.607 33.333 0.00 0.00 33.44 1.31
4102 4228 8.598041 ACTCTTTCTGTGATTATGGTCTTTAGT 58.402 33.333 0.00 0.00 0.00 2.24
4368 4495 7.384660 CCTCTTCTATCAACATATTCAGCAGAC 59.615 40.741 0.00 0.00 0.00 3.51
4810 4939 9.496710 TCTCCCAGTAATTTCTATGGTAAAGTA 57.503 33.333 0.00 0.00 0.00 2.24
4896 5025 3.057033 ACAGTTGGTCGTACAGGACATAC 60.057 47.826 4.63 2.23 38.70 2.39
4912 5041 5.034554 CATACACAAAGTAGGCACAGTTG 57.965 43.478 0.00 0.00 35.85 3.16
5195 5461 4.905429 AGTAGTGTGCATTATTGGTGACA 58.095 39.130 0.00 0.00 39.83 3.58
5217 5483 2.102252 ACGCAAGAAAAAGCCATCCAAA 59.898 40.909 0.00 0.00 43.62 3.28
5334 5605 9.799106 AGACATTATTTTTCGAATATCAGGGAT 57.201 29.630 0.00 0.00 0.00 3.85
5472 5745 4.211125 TCTATCCAGTGCTCCTGTAAGAG 58.789 47.826 3.76 0.00 39.74 2.85
5473 5746 4.251103 TCTATCCAGTGCTCCTGTAAGA 57.749 45.455 3.76 1.50 39.74 2.10
5774 6047 0.883833 CATGGACAAGACAACAGCCC 59.116 55.000 0.00 0.00 0.00 5.19
5775 6048 1.267806 CACATGGACAAGACAACAGCC 59.732 52.381 0.00 0.00 0.00 4.85
5776 6049 2.221169 TCACATGGACAAGACAACAGC 58.779 47.619 0.00 0.00 0.00 4.40
5777 6050 4.790878 CAATCACATGGACAAGACAACAG 58.209 43.478 0.00 0.00 0.00 3.16
5778 6051 3.004629 GCAATCACATGGACAAGACAACA 59.995 43.478 0.00 0.00 0.00 3.33
5779 6052 3.004629 TGCAATCACATGGACAAGACAAC 59.995 43.478 0.00 0.00 0.00 3.32
5780 6053 3.220940 TGCAATCACATGGACAAGACAA 58.779 40.909 0.00 0.00 0.00 3.18
5822 6095 3.636300 TGACAGGACCAAAACCATTGAAG 59.364 43.478 0.00 0.00 0.00 3.02
5952 6225 4.314948 GCTTCTTGCTAAGTTCTTCGTC 57.685 45.455 0.00 0.00 38.95 4.20
6061 6334 0.945265 TGAAACGGGCGGTAAAGACG 60.945 55.000 0.00 0.00 0.00 4.18
6109 6382 2.228822 CCAGACAAGCCAACACCAATAC 59.771 50.000 0.00 0.00 0.00 1.89
6111 6384 1.331214 CCAGACAAGCCAACACCAAT 58.669 50.000 0.00 0.00 0.00 3.16
6156 6429 0.603569 CTACACCAAGCCTCGTGAGT 59.396 55.000 2.00 0.00 34.05 3.41
6230 6503 6.307155 CAATCCCATCGTAAAATAGAATCGC 58.693 40.000 0.00 0.00 0.00 4.58
6300 6573 7.323656 GTCAACAGTTGCACATTTTGTACTATC 59.676 37.037 8.58 0.00 0.00 2.08
6368 6641 5.446143 ACAATTAACATGCCTCACGAAAA 57.554 34.783 0.00 0.00 0.00 2.29
6382 6655 9.143631 ACCGAGTGTTTAGTACATACAATTAAC 57.856 33.333 0.00 0.00 39.39 2.01
6486 6760 6.427853 TGCTGGTGCTATATGATTGTAATGAC 59.572 38.462 0.00 0.00 40.48 3.06
6556 6830 0.405585 CAAACCCCCAGATCAGTGGT 59.594 55.000 0.00 0.00 35.60 4.16
6560 6834 1.180029 CAAGCAAACCCCCAGATCAG 58.820 55.000 0.00 0.00 0.00 2.90
6562 6836 1.607801 GCCAAGCAAACCCCCAGATC 61.608 60.000 0.00 0.00 0.00 2.75
6563 6837 1.610379 GCCAAGCAAACCCCCAGAT 60.610 57.895 0.00 0.00 0.00 2.90
6564 6838 1.431195 TAGCCAAGCAAACCCCCAGA 61.431 55.000 0.00 0.00 0.00 3.86
6565 6839 0.541764 TTAGCCAAGCAAACCCCCAG 60.542 55.000 0.00 0.00 0.00 4.45
6566 6840 0.116143 ATTAGCCAAGCAAACCCCCA 59.884 50.000 0.00 0.00 0.00 4.96
6567 6841 1.207089 GAATTAGCCAAGCAAACCCCC 59.793 52.381 0.00 0.00 0.00 5.40
6598 6872 9.102532 CCTGAAGATAGGTAGAGATGGCAACAT 62.103 44.444 0.00 0.00 46.35 2.71
6605 6879 8.642935 TGTTATCCTGAAGATAGGTAGAGATG 57.357 38.462 0.00 0.00 38.69 2.90
6663 6937 3.943381 CTGTGATTCCTTTAGCAGCATGA 59.057 43.478 0.00 0.00 39.69 3.07
6678 6952 5.126061 GTCAAACATTATGGCTCCTGTGATT 59.874 40.000 0.00 0.00 0.00 2.57
6713 6987 6.343716 AGATCATAGCTGAATCTGATCGTT 57.656 37.500 0.00 0.00 45.48 3.85
6890 7166 0.963355 CCCCGGCGATTCCTCAAAAA 60.963 55.000 9.30 0.00 0.00 1.94
6891 7167 1.377987 CCCCGGCGATTCCTCAAAA 60.378 57.895 9.30 0.00 0.00 2.44
6892 7168 2.270850 CCCCGGCGATTCCTCAAA 59.729 61.111 9.30 0.00 0.00 2.69
6893 7169 3.792736 CCCCCGGCGATTCCTCAA 61.793 66.667 9.30 0.00 0.00 3.02
6917 7193 1.274703 TGAAGCTGTGGGGATCCTCC 61.275 60.000 9.81 10.72 35.23 4.30
6954 7440 3.882288 TGAAAGTTAACACAGATGCTGCA 59.118 39.130 4.13 4.13 34.37 4.41
6957 7443 4.887071 TGGTTGAAAGTTAACACAGATGCT 59.113 37.500 8.61 0.00 0.00 3.79
6989 7475 4.388378 AAGTCTAGATGGACTAAACCGC 57.612 45.455 0.00 0.00 44.67 5.68
6990 7476 5.811100 GGAAAAGTCTAGATGGACTAAACCG 59.189 44.000 0.00 0.00 44.67 4.44
7014 7500 1.752198 TCCGGACCAGGTCAAGTTG 59.248 57.895 21.75 5.14 33.68 3.16


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

AutoCloner maintained by Alex Coulton.