Multiple sequence alignment - TraesCS7D01G207800

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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 TraesCS7D01G207800 chr7D 100.000 3320 0 0 1 3320 165155520 165152201 0.000000e+00 6131
1 TraesCS7D01G207800 chr7B 91.217 2744 109 46 662 3320 128446785 128444089 0.000000e+00 3611
2 TraesCS7D01G207800 chr7B 84.863 621 67 16 1 621 128447388 128446795 4.740000e-168 601
3 TraesCS7D01G207800 chr7A 93.921 2188 66 17 521 2650 166989325 166987147 0.000000e+00 3241
4 TraesCS7D01G207800 chr7A 84.488 361 50 3 1 357 166989845 166989487 5.270000e-93 351
5 TraesCS7D01G207800 chr7A 85.629 334 24 10 2658 2988 166987085 166986773 2.470000e-86 329
6 TraesCS7D01G207800 chr7A 86.705 173 9 11 3160 3320 166986683 166986513 2.630000e-41 180
7 TraesCS7D01G207800 chr7A 84.298 121 10 6 405 525 166989479 166989368 3.500000e-20 110
8 TraesCS7D01G207800 chr5B 88.303 436 50 1 1685 2120 254501350 254501784 3.800000e-144 521
9 TraesCS7D01G207800 chr1A 91.457 199 17 0 1685 1883 277625470 277625272 1.170000e-69 274
10 TraesCS7D01G207800 chr1A 91.623 191 16 0 1687 1877 277622954 277622764 7.060000e-67 265
11 TraesCS7D01G207800 chr1A 91.099 191 17 0 1687 1877 277617006 277616816 3.290000e-65 259
12 TraesCS7D01G207800 chr1A 91.099 191 17 0 1687 1877 277618988 277618798 3.290000e-65 259
13 TraesCS7D01G207800 chr1A 91.099 191 17 0 1687 1877 277620971 277620781 3.290000e-65 259
14 TraesCS7D01G207800 chr1A 91.099 191 17 0 1687 1877 277625015 277624825 3.290000e-65 259
15 TraesCS7D01G207800 chr4A 93.684 95 6 0 1862 1956 494075117 494075211 3.450000e-30 143


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 TraesCS7D01G207800 chr7D 165152201 165155520 3319 True 6131.0 6131 100.0000 1 3320 1 chr7D.!!$R1 3319
1 TraesCS7D01G207800 chr7B 128444089 128447388 3299 True 2106.0 3611 88.0400 1 3320 2 chr7B.!!$R1 3319
2 TraesCS7D01G207800 chr7A 166986513 166989845 3332 True 842.2 3241 87.0082 1 3320 5 chr7A.!!$R1 3319
3 TraesCS7D01G207800 chr1A 277616816 277625470 8654 True 262.5 274 91.2460 1685 1883 6 chr1A.!!$R1 198

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
212 216 0.039437 AGAGCACGACGGTGTTAGTG 60.039 55.0 0.00 0.0 46.13 2.74 F
218 222 0.169672 CGACGGTGTTAGTGGACGAT 59.830 55.0 0.00 0.0 0.00 3.73 F
276 280 0.530744 AGCTTGGCGATCGAGTGTTA 59.469 50.0 21.57 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 10333 1.837538 TAACAAGCAACCAGACGCGC 61.838 55.000 5.73 0.0 0.00 6.86 R
2243 10410 6.952935 AAGAGACAGCGAAATAACAGTAAG 57.047 37.500 0.00 0.0 0.00 2.34 R
2413 10601 3.041351 AGCACGCGCATTTCGTCA 61.041 55.556 5.73 0.0 42.27 4.35 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
25 26 2.047655 TGGAATCGAAACGCGCCT 60.048 55.556 5.73 0.00 40.61 5.52
30 31 1.225376 AATCGAAACGCGCCTTCACA 61.225 50.000 18.33 7.28 40.61 3.58
31 32 1.897398 ATCGAAACGCGCCTTCACAC 61.897 55.000 18.33 0.00 40.61 3.82
56 57 1.132643 CGTGGTTTTTGTTGGAACCGA 59.867 47.619 0.00 0.00 46.55 4.69
107 108 3.914364 CGGAGTTTGCTGCTATGTTTTTC 59.086 43.478 0.00 0.00 0.00 2.29
119 120 5.538053 TGCTATGTTTTTCTGGTGGAATCAA 59.462 36.000 0.00 0.00 33.53 2.57
120 121 6.041409 TGCTATGTTTTTCTGGTGGAATCAAA 59.959 34.615 0.00 0.00 33.53 2.69
123 124 6.232581 TGTTTTTCTGGTGGAATCAAATGT 57.767 33.333 0.00 0.00 33.53 2.71
131 132 6.930164 TCTGGTGGAATCAAATGTCAATTTTG 59.070 34.615 0.00 0.00 33.59 2.44
134 135 5.702209 GTGGAATCAAATGTCAATTTTGGCT 59.298 36.000 0.00 0.00 33.59 4.75
193 197 7.780008 TTTCTGTTCGTTGAGTTCTTCAATA 57.220 32.000 0.00 0.00 46.85 1.90
196 200 6.863645 TCTGTTCGTTGAGTTCTTCAATAGAG 59.136 38.462 0.00 0.00 46.85 2.43
201 205 4.783764 TGAGTTCTTCAATAGAGCACGA 57.216 40.909 0.00 0.00 36.63 4.35
212 216 0.039437 AGAGCACGACGGTGTTAGTG 60.039 55.000 0.00 0.00 46.13 2.74
215 219 1.280206 GCACGACGGTGTTAGTGGAC 61.280 60.000 0.00 0.00 46.13 4.02
218 222 0.169672 CGACGGTGTTAGTGGACGAT 59.830 55.000 0.00 0.00 0.00 3.73
221 225 1.822990 ACGGTGTTAGTGGACGATGAT 59.177 47.619 0.00 0.00 0.00 2.45
224 228 2.550978 GTGTTAGTGGACGATGATGGG 58.449 52.381 0.00 0.00 0.00 4.00
242 246 1.754745 GGAACCAGAGCCTGTGACA 59.245 57.895 0.00 0.00 0.00 3.58
272 276 2.103042 GCAAGCTTGGCGATCGAGT 61.103 57.895 27.10 0.00 0.00 4.18
274 278 1.016130 CAAGCTTGGCGATCGAGTGT 61.016 55.000 21.57 0.00 0.00 3.55
276 280 0.530744 AGCTTGGCGATCGAGTGTTA 59.469 50.000 21.57 0.00 0.00 2.41
286 290 3.585862 GATCGAGTGTTAGAACAAGCCA 58.414 45.455 0.00 0.00 41.21 4.75
311 315 2.257691 AGAGCTGCATCCATGATGAC 57.742 50.000 8.21 0.90 42.09 3.06
359 363 4.059304 TGCAATCCCCGTGGCCAT 62.059 61.111 9.72 0.00 0.00 4.40
374 378 4.082523 CATGTGGCGGGACCTCGT 62.083 66.667 4.61 0.00 40.22 4.18
387 391 4.813526 CTCGTCGGTGCTCGTCGG 62.814 72.222 15.60 6.73 46.82 4.79
393 397 4.760047 GGTGCTCGTCGGCCACAT 62.760 66.667 2.24 0.00 0.00 3.21
395 399 4.794439 TGCTCGTCGGCCACATCG 62.794 66.667 2.24 1.15 0.00 3.84
401 405 3.060000 TCGGCCACATCGACGACT 61.060 61.111 2.24 0.00 0.00 4.18
402 406 2.880879 CGGCCACATCGACGACTG 60.881 66.667 2.24 2.70 0.00 3.51
446 450 2.305607 TATGGAAGCGGCAAGGGGT 61.306 57.895 1.45 0.00 0.00 4.95
472 476 2.149383 TGGGGAAGCAGTGCTCTGT 61.149 57.895 20.03 1.96 43.05 3.41
474 478 1.072159 GGGAAGCAGTGCTCTGTGT 59.928 57.895 20.03 1.04 43.05 3.72
487 491 3.257469 CTCTGTGTATGGTGAGCATGT 57.743 47.619 7.49 0.00 0.00 3.21
490 494 1.339920 TGTGTATGGTGAGCATGTGGG 60.340 52.381 7.49 0.00 0.00 4.61
492 496 1.632920 TGTATGGTGAGCATGTGGGAA 59.367 47.619 7.49 0.00 0.00 3.97
493 497 2.292267 GTATGGTGAGCATGTGGGAAG 58.708 52.381 7.49 0.00 0.00 3.46
495 499 0.770499 TGGTGAGCATGTGGGAAGAA 59.230 50.000 0.00 0.00 0.00 2.52
496 500 1.271543 TGGTGAGCATGTGGGAAGAAG 60.272 52.381 0.00 0.00 0.00 2.85
497 501 1.003580 GGTGAGCATGTGGGAAGAAGA 59.996 52.381 0.00 0.00 0.00 2.87
499 503 2.746362 GTGAGCATGTGGGAAGAAGAAG 59.254 50.000 0.00 0.00 0.00 2.85
500 504 2.639347 TGAGCATGTGGGAAGAAGAAGA 59.361 45.455 0.00 0.00 0.00 2.87
501 505 3.006247 GAGCATGTGGGAAGAAGAAGAC 58.994 50.000 0.00 0.00 0.00 3.01
502 506 1.734465 GCATGTGGGAAGAAGAAGACG 59.266 52.381 0.00 0.00 0.00 4.18
646 725 4.143030 CCATAACTGAACAAGCGAGTCAAG 60.143 45.833 0.00 0.00 0.00 3.02
657 736 1.656652 CGAGTCAAGTATGGCCCAAG 58.343 55.000 0.00 0.00 0.00 3.61
658 737 1.383523 GAGTCAAGTATGGCCCAAGC 58.616 55.000 0.00 0.00 38.76 4.01
659 738 0.698238 AGTCAAGTATGGCCCAAGCA 59.302 50.000 0.00 0.00 42.56 3.91
660 739 1.075374 AGTCAAGTATGGCCCAAGCAA 59.925 47.619 0.00 0.00 42.56 3.91
683 762 2.973082 GCACCAAGCCCAATCACC 59.027 61.111 0.00 0.00 37.23 4.02
724 803 0.751452 TTTTACCAAAACACCCCCGC 59.249 50.000 0.00 0.00 0.00 6.13
774 853 1.169577 AAACAACACGTGAGCAACCA 58.830 45.000 25.01 0.00 0.00 3.67
811 890 2.041405 CCTCCACCTCTCCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
981 1061 1.692519 CACCCTATAAACCTCCTCCGG 59.307 57.143 0.00 0.00 0.00 5.14
1030 1110 4.227134 CGCCAGTCCCATCTCCCG 62.227 72.222 0.00 0.00 0.00 5.14
1225 1307 2.047655 TACAAGAAGGCGGTGGCG 60.048 61.111 0.00 0.00 41.24 5.69
1639 1721 1.115467 TCGAGGGCATCTTCTTCTCC 58.885 55.000 0.00 0.00 0.00 3.71
1909 6419 1.135373 AGCCAGTACATCGAGTTCGTG 60.135 52.381 1.07 2.62 40.80 4.35
2217 10384 5.826737 AGTAGTAGTAGCGGTGATACATGTT 59.173 40.000 2.30 0.00 0.00 2.71
2243 10410 3.068873 TGGGTGCTCCACAATGTTTTTAC 59.931 43.478 7.20 0.00 41.46 2.01
2430 10618 2.111932 TTTGACGAAATGCGCGTGCT 62.112 50.000 23.16 0.72 46.04 4.40
2460 10648 2.658707 GCGCACAGAGTGTTCGACC 61.659 63.158 0.30 0.00 39.26 4.79
2641 10831 2.420628 TTTGCACGAAATCTTGGCTG 57.579 45.000 0.00 0.00 0.00 4.85
2660 10904 1.134220 TGTTTTCGCAGACTTGGGAGT 60.134 47.619 0.00 0.00 45.56 3.85
2668 10912 2.032681 ACTTGGGAGTCGCTTGGC 59.967 61.111 8.82 0.00 0.00 4.52
2678 10922 2.488153 GAGTCGCTTGGCTTTATTTGGT 59.512 45.455 0.00 0.00 0.00 3.67
2709 10953 1.884579 GCGGAGGAATCTACCGTATGA 59.115 52.381 16.19 0.00 46.95 2.15
2759 11005 2.800250 CCCAAAAGCAAGATCCTCTGT 58.200 47.619 0.00 0.00 0.00 3.41
2760 11006 2.490903 CCCAAAAGCAAGATCCTCTGTG 59.509 50.000 0.00 0.00 0.00 3.66
2770 11016 4.640789 AGATCCTCTGTGAACGTGATAC 57.359 45.455 0.00 0.00 0.00 2.24
2786 11032 0.825010 ATACGGGCTGGGTAGTACGG 60.825 60.000 0.00 0.00 32.21 4.02
2787 11033 2.909457 TACGGGCTGGGTAGTACGGG 62.909 65.000 0.00 0.00 32.21 5.28
2789 11035 1.076044 GGGCTGGGTAGTACGGGTA 60.076 63.158 0.00 0.00 0.00 3.69
2790 11036 1.395045 GGGCTGGGTAGTACGGGTAC 61.395 65.000 0.70 0.70 36.35 3.34
2792 11038 0.743097 GCTGGGTAGTACGGGTACTG 59.257 60.000 19.10 5.56 45.25 2.74
2793 11039 0.743097 CTGGGTAGTACGGGTACTGC 59.257 60.000 19.10 17.44 45.25 4.40
2810 11056 3.889815 ACTGCTACTGTACCGGTACATA 58.110 45.455 39.92 30.34 44.15 2.29
2819 11065 6.465948 ACTGTACCGGTACATAAAAATGTCA 58.534 36.000 39.92 18.09 44.15 3.58
2861 11107 3.319135 AGCTGACTGACAAGCAAGG 57.681 52.632 0.71 0.00 0.00 3.61
2914 11167 1.623811 AGTGGCCTCATGTTTCTACGT 59.376 47.619 3.32 0.00 0.00 3.57
2921 11174 1.808390 ATGTTTCTACGTCGGCCGC 60.808 57.895 23.51 15.21 41.42 6.53
2957 11210 4.681978 AACCGGACTGCTGCGACC 62.682 66.667 9.46 0.00 31.75 4.79
2979 11232 0.746204 TCTGCAACGTCCAAACTGCA 60.746 50.000 9.74 9.74 0.00 4.41
2988 11241 1.336755 GTCCAAACTGCATGTTCCGTT 59.663 47.619 0.00 0.00 38.03 4.44
2991 11244 2.605338 CCAAACTGCATGTTCCGTTCAG 60.605 50.000 0.00 0.00 38.03 3.02
3020 11280 2.223641 CGGTTATGGCTGTACGAAGCTA 60.224 50.000 5.29 0.00 43.06 3.32
3038 11298 0.243907 TAGCAGCGTCCAAGTGTCTC 59.756 55.000 0.00 0.00 0.00 3.36
3044 11304 1.269998 GCGTCCAAGTGTCTCTGTAGT 59.730 52.381 0.00 0.00 0.00 2.73
3045 11305 2.922758 GCGTCCAAGTGTCTCTGTAGTG 60.923 54.545 0.00 0.00 0.00 2.74
3047 11307 2.628657 GTCCAAGTGTCTCTGTAGTGGT 59.371 50.000 0.00 0.00 0.00 4.16
3048 11308 2.891580 TCCAAGTGTCTCTGTAGTGGTC 59.108 50.000 0.00 0.00 0.00 4.02
3049 11309 2.894126 CCAAGTGTCTCTGTAGTGGTCT 59.106 50.000 0.00 0.00 0.00 3.85
3050 11310 4.079970 CCAAGTGTCTCTGTAGTGGTCTA 58.920 47.826 0.00 0.00 0.00 2.59
3051 11311 4.156922 CCAAGTGTCTCTGTAGTGGTCTAG 59.843 50.000 0.00 0.00 0.00 2.43
3052 11312 4.644163 AGTGTCTCTGTAGTGGTCTAGT 57.356 45.455 0.00 0.00 0.00 2.57
3053 11313 5.758790 AGTGTCTCTGTAGTGGTCTAGTA 57.241 43.478 0.00 0.00 0.00 1.82
3054 11314 6.316280 AGTGTCTCTGTAGTGGTCTAGTAT 57.684 41.667 0.00 0.00 0.00 2.12
3055 11315 7.434927 AGTGTCTCTGTAGTGGTCTAGTATA 57.565 40.000 0.00 0.00 0.00 1.47
3056 11316 7.502696 AGTGTCTCTGTAGTGGTCTAGTATAG 58.497 42.308 0.00 0.00 41.04 1.31
3057 11317 6.707161 GTGTCTCTGTAGTGGTCTAGTATAGG 59.293 46.154 0.00 0.00 39.78 2.57
3058 11318 6.614496 TGTCTCTGTAGTGGTCTAGTATAGGA 59.386 42.308 0.00 0.00 39.78 2.94
3059 11319 7.156673 GTCTCTGTAGTGGTCTAGTATAGGAG 58.843 46.154 0.00 0.00 39.78 3.69
3060 11320 6.845446 TCTCTGTAGTGGTCTAGTATAGGAGT 59.155 42.308 0.00 0.00 39.78 3.85
3061 11321 8.009513 TCTCTGTAGTGGTCTAGTATAGGAGTA 58.990 40.741 0.00 0.00 39.78 2.59
3062 11322 8.192743 TCTGTAGTGGTCTAGTATAGGAGTAG 57.807 42.308 0.00 0.00 39.78 2.57
3066 11326 9.088987 GTAGTGGTCTAGTATAGGAGTAGTACT 57.911 40.741 1.37 1.37 39.78 2.73
3108 11369 1.363807 CACACCAGACGAGAGCACA 59.636 57.895 0.00 0.00 0.00 4.57
3117 11378 1.227823 CGAGAGCACACCCAAACCA 60.228 57.895 0.00 0.00 0.00 3.67
3127 11392 2.570284 CCCAAACCAAACGGGGAGC 61.570 63.158 0.00 0.00 43.57 4.70
3186 11470 4.717313 GGTCGTGTTCCCTGCCCC 62.717 72.222 0.00 0.00 0.00 5.80
3249 11535 3.694072 TCCAACACTTTCTGGACTTGTTG 59.306 43.478 5.90 5.90 44.32 3.33
3252 11538 5.124776 CCAACACTTTCTGGACTTGTTGTTA 59.875 40.000 10.83 0.00 43.57 2.41
3253 11539 5.813080 ACACTTTCTGGACTTGTTGTTAC 57.187 39.130 0.00 0.00 0.00 2.50
3254 11540 4.331717 ACACTTTCTGGACTTGTTGTTACG 59.668 41.667 0.00 0.00 0.00 3.18
3255 11541 3.875134 ACTTTCTGGACTTGTTGTTACGG 59.125 43.478 0.00 0.00 0.00 4.02
3256 11542 1.873698 TCTGGACTTGTTGTTACGGC 58.126 50.000 0.00 0.00 0.00 5.68
3258 11544 2.629137 TCTGGACTTGTTGTTACGGCTA 59.371 45.455 0.00 0.00 0.00 3.93
3259 11545 2.993899 CTGGACTTGTTGTTACGGCTAG 59.006 50.000 0.00 0.00 0.00 3.42
3260 11546 2.629137 TGGACTTGTTGTTACGGCTAGA 59.371 45.455 0.00 0.00 0.00 2.43
3263 11549 4.802563 GGACTTGTTGTTACGGCTAGATAC 59.197 45.833 0.00 0.00 0.00 2.24
3264 11550 5.393896 GGACTTGTTGTTACGGCTAGATACT 60.394 44.000 0.00 0.00 0.00 2.12
3265 11551 6.034161 ACTTGTTGTTACGGCTAGATACTT 57.966 37.500 0.00 0.00 0.00 2.24
3266 11552 7.161773 ACTTGTTGTTACGGCTAGATACTTA 57.838 36.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.632046 GAAGGCGCGTTTCGATTCCA 61.632 55.000 17.42 0.00 41.67 3.53
30 31 3.053849 AACAAAAACCACGCCGCGT 62.054 52.632 13.85 13.85 42.36 6.01
31 32 2.278271 AACAAAAACCACGCCGCG 60.278 55.556 12.14 12.14 0.00 6.46
35 36 1.282817 GGTTCCAACAAAAACCACGC 58.717 50.000 0.00 0.00 43.63 5.34
56 57 5.412904 GTCCAATTGTAGCAAAAGAGCTAGT 59.587 40.000 4.43 0.00 46.90 2.57
107 108 6.148150 CCAAAATTGACATTTGATTCCACCAG 59.852 38.462 3.56 0.00 39.56 4.00
119 120 3.390639 TGGTTCCAGCCAAAATTGACATT 59.609 39.130 0.00 0.00 35.25 2.71
120 121 2.971330 TGGTTCCAGCCAAAATTGACAT 59.029 40.909 0.00 0.00 35.25 3.06
123 124 4.703379 AAATGGTTCCAGCCAAAATTGA 57.297 36.364 0.00 0.00 42.48 2.57
155 159 3.981071 ACAGAAATCTCCGATGGTCAA 57.019 42.857 0.00 0.00 0.00 3.18
193 197 0.039437 CACTAACACCGTCGTGCTCT 60.039 55.000 0.00 0.00 44.40 4.09
196 200 1.007038 TCCACTAACACCGTCGTGC 60.007 57.895 0.00 0.00 44.40 5.34
201 205 1.250328 TCATCGTCCACTAACACCGT 58.750 50.000 0.00 0.00 0.00 4.83
212 216 0.179045 CTGGTTCCCCATCATCGTCC 60.179 60.000 0.00 0.00 40.90 4.79
215 219 0.533755 GCTCTGGTTCCCCATCATCG 60.534 60.000 0.00 0.00 40.90 3.84
218 222 1.229951 AGGCTCTGGTTCCCCATCA 60.230 57.895 0.00 0.00 40.90 3.07
221 225 2.121963 ACAGGCTCTGGTTCCCCA 60.122 61.111 7.06 0.00 38.87 4.96
224 228 0.603975 GTGTCACAGGCTCTGGTTCC 60.604 60.000 0.00 0.00 35.51 3.62
230 234 0.250945 TCTCTCGTGTCACAGGCTCT 60.251 55.000 3.42 0.00 0.00 4.09
235 239 0.109365 CAGCCTCTCTCGTGTCACAG 60.109 60.000 3.42 0.29 0.00 3.66
242 246 1.825281 AAGCTTGCAGCCTCTCTCGT 61.825 55.000 0.00 0.00 43.77 4.18
260 264 2.029739 TGTTCTAACACTCGATCGCCAA 60.030 45.455 11.09 0.00 33.17 4.52
272 276 5.586243 GCTCTAATGATGGCTTGTTCTAACA 59.414 40.000 0.00 0.00 37.08 2.41
274 278 5.819379 CAGCTCTAATGATGGCTTGTTCTAA 59.181 40.000 0.00 0.00 32.30 2.10
276 280 4.197750 CAGCTCTAATGATGGCTTGTTCT 58.802 43.478 0.00 0.00 32.30 3.01
286 290 4.635699 TCATGGATGCAGCTCTAATGAT 57.364 40.909 0.22 0.00 0.00 2.45
387 391 2.152699 CGTCAGTCGTCGATGTGGC 61.153 63.158 4.21 0.00 34.52 5.01
395 399 3.371063 TCTGCCCCGTCAGTCGTC 61.371 66.667 0.00 0.00 37.94 4.20
401 405 2.280552 GGTAGTGTCTGCCCCGTCA 61.281 63.158 0.00 0.00 29.85 4.35
402 406 1.542187 AAGGTAGTGTCTGCCCCGTC 61.542 60.000 0.57 0.00 36.92 4.79
472 476 1.284313 TCCCACATGCTCACCATACA 58.716 50.000 0.00 0.00 31.47 2.29
474 478 2.195727 TCTTCCCACATGCTCACCATA 58.804 47.619 0.00 0.00 31.47 2.74
484 488 3.307059 CCTTCGTCTTCTTCTTCCCACAT 60.307 47.826 0.00 0.00 0.00 3.21
487 491 2.563179 CTCCTTCGTCTTCTTCTTCCCA 59.437 50.000 0.00 0.00 0.00 4.37
490 494 2.826725 TCCCTCCTTCGTCTTCTTCTTC 59.173 50.000 0.00 0.00 0.00 2.87
492 496 2.606751 TCCCTCCTTCGTCTTCTTCT 57.393 50.000 0.00 0.00 0.00 2.85
493 497 2.761208 TCATCCCTCCTTCGTCTTCTTC 59.239 50.000 0.00 0.00 0.00 2.87
495 499 2.104170 GTCATCCCTCCTTCGTCTTCT 58.896 52.381 0.00 0.00 0.00 2.85
496 500 1.137282 GGTCATCCCTCCTTCGTCTTC 59.863 57.143 0.00 0.00 0.00 2.87
497 501 1.196012 GGTCATCCCTCCTTCGTCTT 58.804 55.000 0.00 0.00 0.00 3.01
526 577 2.357034 ATTCGGTCGCGTGCAACT 60.357 55.556 5.77 0.00 31.75 3.16
588 639 1.591703 GCCTGTTTAGCCCAAAGCC 59.408 57.895 0.00 0.00 45.47 4.35
646 725 0.607620 TTGCTTTGCTTGGGCCATAC 59.392 50.000 7.26 2.62 37.74 2.39
657 736 1.957695 GGCTTGGTGCTTGCTTTGC 60.958 57.895 0.00 0.00 42.39 3.68
658 737 1.301165 GGGCTTGGTGCTTGCTTTG 60.301 57.895 0.00 0.00 42.39 2.77
659 738 1.336632 TTGGGCTTGGTGCTTGCTTT 61.337 50.000 0.00 0.00 42.39 3.51
660 739 1.123246 ATTGGGCTTGGTGCTTGCTT 61.123 50.000 0.00 0.00 42.39 3.91
678 757 2.171448 GGTGCTGGAAGTATCTGGTGAT 59.829 50.000 0.00 0.00 35.30 3.06
683 762 0.181350 GGGGGTGCTGGAAGTATCTG 59.819 60.000 0.00 0.00 35.30 2.90
1030 1110 4.393834 GGAAGGATTTCTGCTAGGGATTC 58.606 47.826 0.00 0.00 33.68 2.52
1285 1367 2.202492 CGCTCGTCGTTGGAGAGG 60.202 66.667 0.00 0.00 33.27 3.69
2168 10333 1.837538 TAACAAGCAACCAGACGCGC 61.838 55.000 5.73 0.00 0.00 6.86
2243 10410 6.952935 AAGAGACAGCGAAATAACAGTAAG 57.047 37.500 0.00 0.00 0.00 2.34
2413 10601 3.041351 AGCACGCGCATTTCGTCA 61.041 55.556 5.73 0.00 42.27 4.35
2446 10634 1.873591 GCATTTGGTCGAACACTCTGT 59.126 47.619 0.44 0.00 0.00 3.41
2450 10638 1.574428 GCGCATTTGGTCGAACACT 59.426 52.632 0.44 0.00 0.00 3.55
2452 10640 2.248135 ACGCGCATTTGGTCGAACA 61.248 52.632 5.73 0.00 0.00 3.18
2460 10648 2.580326 GGATGGCACGCGCATTTG 60.580 61.111 5.73 1.65 41.24 2.32
2641 10831 1.594331 ACTCCCAAGTCTGCGAAAAC 58.406 50.000 0.00 0.00 0.00 2.43
2660 10904 3.068873 ACAAACCAAATAAAGCCAAGCGA 59.931 39.130 0.00 0.00 0.00 4.93
2668 10912 5.791480 CCGCTACGTAACAAACCAAATAAAG 59.209 40.000 0.00 0.00 0.00 1.85
2678 10922 3.194116 AGATTCCTCCGCTACGTAACAAA 59.806 43.478 0.00 0.00 0.00 2.83
2709 10953 2.863809 ACTGCCCAAGATCTCGTTTTT 58.136 42.857 0.00 0.00 0.00 1.94
2759 11005 1.216977 CCAGCCCGTATCACGTTCA 59.783 57.895 0.00 0.00 40.58 3.18
2760 11006 1.520787 CCCAGCCCGTATCACGTTC 60.521 63.158 0.00 0.00 40.58 3.95
2770 11016 2.909457 TACCCGTACTACCCAGCCCG 62.909 65.000 0.00 0.00 0.00 6.13
2787 11033 3.009723 TGTACCGGTACAGTAGCAGTAC 58.990 50.000 37.58 21.86 40.77 2.73
2789 11035 2.205022 TGTACCGGTACAGTAGCAGT 57.795 50.000 37.58 7.18 40.77 4.40
2810 11056 9.912634 CAAACCTACATTAGACATGACATTTTT 57.087 29.630 0.00 0.00 0.00 1.94
2819 11065 4.630069 GTCACGCAAACCTACATTAGACAT 59.370 41.667 0.00 0.00 0.00 3.06
2829 11075 0.391228 TCAGCTGTCACGCAAACCTA 59.609 50.000 14.67 0.00 0.00 3.08
2861 11107 0.240945 CACAACAAAGTGCCCGATCC 59.759 55.000 0.00 0.00 32.04 3.36
2945 11198 1.875813 CAGATCGGTCGCAGCAGTC 60.876 63.158 0.00 0.00 0.00 3.51
2957 11210 1.136252 CAGTTTGGACGTTGCAGATCG 60.136 52.381 0.00 6.50 0.00 3.69
2979 11232 2.417719 GAAGCTGACTGAACGGAACAT 58.582 47.619 0.00 0.00 0.00 2.71
2988 11241 1.405526 GCCATAACCGAAGCTGACTGA 60.406 52.381 0.00 0.00 0.00 3.41
2991 11244 3.460648 AGCCATAACCGAAGCTGAC 57.539 52.632 0.00 0.00 33.41 3.51
3020 11280 1.005630 GAGACACTTGGACGCTGCT 60.006 57.895 0.00 0.00 0.00 4.24
3038 11298 7.965718 ACTACTCCTATACTAGACCACTACAG 58.034 42.308 0.00 0.00 0.00 2.74
3044 11304 6.558014 AGCAGTACTACTCCTATACTAGACCA 59.442 42.308 0.00 0.00 0.00 4.02
3045 11305 6.875195 CAGCAGTACTACTCCTATACTAGACC 59.125 46.154 0.00 0.00 0.00 3.85
3047 11307 6.270463 AGCAGCAGTACTACTCCTATACTAGA 59.730 42.308 0.00 0.00 0.00 2.43
3048 11308 6.469410 AGCAGCAGTACTACTCCTATACTAG 58.531 44.000 0.00 0.00 0.00 2.57
3049 11309 6.436738 AGCAGCAGTACTACTCCTATACTA 57.563 41.667 0.00 0.00 0.00 1.82
3050 11310 5.313280 AGCAGCAGTACTACTCCTATACT 57.687 43.478 0.00 0.00 0.00 2.12
3051 11311 5.120519 CGTAGCAGCAGTACTACTCCTATAC 59.879 48.000 0.00 0.00 37.26 1.47
3052 11312 5.236282 CGTAGCAGCAGTACTACTCCTATA 58.764 45.833 0.00 0.00 37.26 1.31
3053 11313 4.066490 CGTAGCAGCAGTACTACTCCTAT 58.934 47.826 0.00 0.00 37.26 2.57
3054 11314 3.464907 CGTAGCAGCAGTACTACTCCTA 58.535 50.000 0.00 0.00 37.26 2.94
3055 11315 2.290464 CGTAGCAGCAGTACTACTCCT 58.710 52.381 0.00 0.00 37.26 3.69
3056 11316 1.334243 CCGTAGCAGCAGTACTACTCC 59.666 57.143 0.00 0.00 37.26 3.85
3057 11317 2.286872 TCCGTAGCAGCAGTACTACTC 58.713 52.381 0.00 0.00 37.26 2.59
3058 11318 2.093075 TCTCCGTAGCAGCAGTACTACT 60.093 50.000 0.00 0.00 37.26 2.57
3059 11319 2.286872 TCTCCGTAGCAGCAGTACTAC 58.713 52.381 0.00 0.00 36.28 2.73
3060 11320 2.704464 TCTCCGTAGCAGCAGTACTA 57.296 50.000 0.00 0.00 0.00 1.82
3061 11321 1.835494 TTCTCCGTAGCAGCAGTACT 58.165 50.000 0.00 0.00 0.00 2.73
3062 11322 2.099263 TGATTCTCCGTAGCAGCAGTAC 59.901 50.000 0.00 0.00 0.00 2.73
3066 11326 0.179100 GCTGATTCTCCGTAGCAGCA 60.179 55.000 8.08 0.00 36.24 4.41
3100 11360 1.067060 GTTTGGTTTGGGTGTGCTCTC 59.933 52.381 0.00 0.00 0.00 3.20
3108 11369 1.152631 CTCCCCGTTTGGTTTGGGT 60.153 57.895 0.00 0.00 41.63 4.51
3136 11401 2.028733 CCATTTTGGCGCCACTTGC 61.029 57.895 32.95 0.00 0.00 4.01
3138 11403 0.467804 AAACCATTTTGGCGCCACTT 59.532 45.000 32.95 14.47 42.67 3.16
3139 11404 0.033366 GAAACCATTTTGGCGCCACT 59.967 50.000 32.95 14.70 42.67 4.00
3186 11470 0.996727 CTGCTTTTCCCGTTTTCGCG 60.997 55.000 0.00 0.00 42.58 5.87
3249 11535 9.525409 TCAAGAAAATAAGTATCTAGCCGTAAC 57.475 33.333 0.00 0.00 0.00 2.50
3252 11538 7.210873 CCTCAAGAAAATAAGTATCTAGCCGT 58.789 38.462 0.00 0.00 0.00 5.68
3253 11539 6.647067 CCCTCAAGAAAATAAGTATCTAGCCG 59.353 42.308 0.00 0.00 0.00 5.52
3254 11540 6.937465 CCCCTCAAGAAAATAAGTATCTAGCC 59.063 42.308 0.00 0.00 0.00 3.93
3255 11541 7.736893 TCCCCTCAAGAAAATAAGTATCTAGC 58.263 38.462 0.00 0.00 0.00 3.42
3256 11542 8.371699 CCTCCCCTCAAGAAAATAAGTATCTAG 58.628 40.741 0.00 0.00 0.00 2.43
3258 11544 6.101881 CCCTCCCCTCAAGAAAATAAGTATCT 59.898 42.308 0.00 0.00 0.00 1.98
3259 11545 6.299922 CCCTCCCCTCAAGAAAATAAGTATC 58.700 44.000 0.00 0.00 0.00 2.24
3260 11546 5.399152 GCCCTCCCCTCAAGAAAATAAGTAT 60.399 44.000 0.00 0.00 0.00 2.12
3263 11549 3.053320 AGCCCTCCCCTCAAGAAAATAAG 60.053 47.826 0.00 0.00 0.00 1.73
3264 11550 2.926329 AGCCCTCCCCTCAAGAAAATAA 59.074 45.455 0.00 0.00 0.00 1.40
3265 11551 2.573463 AGCCCTCCCCTCAAGAAAATA 58.427 47.619 0.00 0.00 0.00 1.40
3266 11552 1.387119 AGCCCTCCCCTCAAGAAAAT 58.613 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.