Multiple sequence alignment - TraesCS4A01G003800

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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 TraesCS4A01G003800 chr4A 100.000 4070 0 0 1 4070 2937907 2941976 0.000000e+00 7516.0
1 TraesCS4A01G003800 chr4D 92.766 2737 136 28 684 3378 468606369 468603653 0.000000e+00 3901.0
2 TraesCS4A01G003800 chr4D 90.950 674 47 7 3405 4070 468603654 468602987 0.000000e+00 894.0
3 TraesCS4A01G003800 chr4D 85.989 364 32 10 303 650 468606818 468606458 4.970000e-99 372.0
4 TraesCS4A01G003800 chr4B 94.290 1401 69 6 1981 3378 588205571 588204179 0.000000e+00 2134.0
5 TraesCS4A01G003800 chr4B 86.657 1379 86 44 684 1991 588207139 588205788 0.000000e+00 1437.0
6 TraesCS4A01G003800 chr4B 91.458 679 47 7 3401 4070 588204184 588203508 0.000000e+00 922.0
7 TraesCS4A01G003800 chr4B 81.358 692 94 23 1 687 588207855 588207194 7.750000e-147 531.0
8 TraesCS4A01G003800 chr6A 95.833 48 1 1 509 555 611070255 611070208 4.360000e-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 TraesCS4A01G003800 chr4A 2937907 2941976 4069 False 7516.000000 7516 100.000000 1 4070 1 chr4A.!!$F1 4069
1 TraesCS4A01G003800 chr4D 468602987 468606818 3831 True 1722.333333 3901 89.901667 303 4070 3 chr4D.!!$R1 3767
2 TraesCS4A01G003800 chr4B 588203508 588207855 4347 True 1256.000000 2134 88.440750 1 4070 4 chr4B.!!$R1 4069

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
387 388 0.611896 AATCGCCCAAAGTCAAGGGG 60.612 55.0 0.0 0.0 45.58 4.79 F
886 1011 0.819666 GCCCCATTTCCCGCTAGAAG 60.820 60.0 0.0 0.0 0.00 2.85 F
2403 2791 0.950836 TTGCTGTCCACAAATCCACG 59.049 50.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2438 0.179137 GCGGCTGCATTTCCTTTACC 60.179 55.0 14.08 0.0 42.15 2.85 R
2652 3040 0.744281 CGAGGGCAGTTTTTGTGGTT 59.256 50.0 0.00 0.0 0.00 3.67 R
3850 4250 0.108585 ACTGTGGATTGCAGACGGTT 59.891 50.0 0.00 0.0 37.40 4.44 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
30 31 4.998033 ACAATGTCAAAATTGCATGCATGA 59.002 33.333 30.64 19.07 40.54 3.07
31 32 5.121611 ACAATGTCAAAATTGCATGCATGAG 59.878 36.000 30.64 12.03 40.54 2.90
37 38 5.744819 TCAAAATTGCATGCATGAGTATTCG 59.255 36.000 30.64 17.03 0.00 3.34
40 41 6.375945 AATTGCATGCATGAGTATTCGTAA 57.624 33.333 30.64 6.62 0.00 3.18
60 61 5.704053 CGTAACAAGGGGTTAACTCTTTGAT 59.296 40.000 30.61 23.14 43.30 2.57
61 62 6.206048 CGTAACAAGGGGTTAACTCTTTGATT 59.794 38.462 30.61 22.49 43.30 2.57
110 111 8.985805 ACAATTCTAGTTGAGTACCTTAAAACG 58.014 33.333 0.40 0.00 33.37 3.60
149 150 3.384467 AGGACCAAAATTCAACACACCTG 59.616 43.478 0.00 0.00 0.00 4.00
152 153 5.507315 GGACCAAAATTCAACACACCTGTAG 60.507 44.000 0.00 0.00 0.00 2.74
154 155 5.420739 ACCAAAATTCAACACACCTGTAGTT 59.579 36.000 0.00 0.00 0.00 2.24
155 156 5.977129 CCAAAATTCAACACACCTGTAGTTC 59.023 40.000 0.00 0.00 0.00 3.01
156 157 6.405286 CCAAAATTCAACACACCTGTAGTTCA 60.405 38.462 0.00 0.00 0.00 3.18
157 158 6.767524 AAATTCAACACACCTGTAGTTCAA 57.232 33.333 0.00 0.00 0.00 2.69
158 159 6.959639 AATTCAACACACCTGTAGTTCAAT 57.040 33.333 0.00 0.00 0.00 2.57
159 160 6.959639 ATTCAACACACCTGTAGTTCAATT 57.040 33.333 0.00 0.00 0.00 2.32
160 161 6.767524 TTCAACACACCTGTAGTTCAATTT 57.232 33.333 0.00 0.00 0.00 1.82
161 162 6.767524 TCAACACACCTGTAGTTCAATTTT 57.232 33.333 0.00 0.00 0.00 1.82
162 163 7.867305 TCAACACACCTGTAGTTCAATTTTA 57.133 32.000 0.00 0.00 0.00 1.52
163 164 8.282455 TCAACACACCTGTAGTTCAATTTTAA 57.718 30.769 0.00 0.00 0.00 1.52
164 165 8.740906 TCAACACACCTGTAGTTCAATTTTAAA 58.259 29.630 0.00 0.00 0.00 1.52
165 166 8.803799 CAACACACCTGTAGTTCAATTTTAAAC 58.196 33.333 0.00 0.00 0.00 2.01
166 167 8.288689 ACACACCTGTAGTTCAATTTTAAACT 57.711 30.769 0.00 3.80 39.07 2.66
167 168 8.745590 ACACACCTGTAGTTCAATTTTAAACTT 58.254 29.630 3.67 0.00 37.02 2.66
168 169 9.233232 CACACCTGTAGTTCAATTTTAAACTTC 57.767 33.333 3.67 0.83 37.02 3.01
169 170 9.185680 ACACCTGTAGTTCAATTTTAAACTTCT 57.814 29.630 3.67 0.00 37.02 2.85
251 252 2.124277 AAATCTTAGCCACGGGTTCC 57.876 50.000 0.00 0.00 0.00 3.62
254 255 1.078426 CTTAGCCACGGGTTCCCAG 60.078 63.158 8.70 3.78 0.00 4.45
256 257 0.912487 TTAGCCACGGGTTCCCAGAT 60.912 55.000 8.70 0.00 0.00 2.90
257 258 1.335132 TAGCCACGGGTTCCCAGATC 61.335 60.000 8.70 0.00 0.00 2.75
260 261 1.141881 CACGGGTTCCCAGATCGAG 59.858 63.158 8.70 0.00 0.00 4.04
267 268 1.617018 TTCCCAGATCGAGCCACCAG 61.617 60.000 0.00 0.00 0.00 4.00
275 276 3.311110 GAGCCACCAGACCCGTCA 61.311 66.667 0.00 0.00 0.00 4.35
278 279 2.879233 GCCACCAGACCCGTCAGAA 61.879 63.158 0.00 0.00 0.00 3.02
290 291 0.803768 CGTCAGAAGACATCGGGCAG 60.804 60.000 0.00 0.00 45.23 4.85
362 363 1.064463 TCTTTAGCATCCAAGCCCCAG 60.064 52.381 0.00 0.00 34.23 4.45
378 379 2.033448 AGCCGTCAATCGCCCAAA 59.967 55.556 0.00 0.00 38.35 3.28
382 383 0.953471 CCGTCAATCGCCCAAAGTCA 60.953 55.000 0.00 0.00 38.35 3.41
387 388 0.611896 AATCGCCCAAAGTCAAGGGG 60.612 55.000 0.00 0.00 45.58 4.79
403 404 1.553690 GGGGTTCCACTCTGCTAGCA 61.554 60.000 18.22 18.22 0.00 3.49
408 409 1.446792 CCACTCTGCTAGCACCACG 60.447 63.158 14.93 4.08 0.00 4.94
409 410 2.097038 CACTCTGCTAGCACCACGC 61.097 63.158 14.93 0.00 42.91 5.34
410 411 2.510238 CTCTGCTAGCACCACGCC 60.510 66.667 14.93 0.00 44.04 5.68
411 412 3.300934 CTCTGCTAGCACCACGCCA 62.301 63.158 14.93 0.00 44.04 5.69
470 472 9.691362 AAGGAAATGTTAATACAATGTTCACAC 57.309 29.630 0.00 0.00 37.91 3.82
484 497 4.681744 TGTTCACACATCTTTTGAAAGCC 58.318 39.130 0.00 0.00 35.99 4.35
497 510 7.950512 TCTTTTGAAAGCCTGTATCATTCAAA 58.049 30.769 7.63 7.63 44.00 2.69
609 626 8.441312 AAATGTCAGCAGAATTTCAAACAAAT 57.559 26.923 0.00 0.00 0.00 2.32
613 630 9.545105 TGTCAGCAGAATTTCAAACAAATATTT 57.455 25.926 0.00 0.00 0.00 1.40
615 632 9.761504 TCAGCAGAATTTCAAACAAATATTTCA 57.238 25.926 0.00 0.00 0.00 2.69
639 656 6.534436 CACACCATTCAAAGAAATGTTCAACA 59.466 34.615 0.00 0.00 35.31 3.33
723 800 9.912634 AAATGTGTATTGGAAAAAGTAGACATG 57.087 29.630 0.00 0.00 33.17 3.21
724 801 8.635765 ATGTGTATTGGAAAAAGTAGACATGT 57.364 30.769 0.00 0.00 32.09 3.21
725 802 9.733556 ATGTGTATTGGAAAAAGTAGACATGTA 57.266 29.630 0.00 0.00 32.09 2.29
726 803 9.733556 TGTGTATTGGAAAAAGTAGACATGTAT 57.266 29.630 0.00 0.00 0.00 2.29
832 957 1.310904 GTACAAACCAAGGCCGAACA 58.689 50.000 0.00 0.00 0.00 3.18
839 964 1.660264 CAAGGCCGAACAAAACCGC 60.660 57.895 0.00 0.00 0.00 5.68
881 1006 4.489771 CGAGCCCCATTTCCCGCT 62.490 66.667 0.00 0.00 0.00 5.52
883 1008 1.227973 GAGCCCCATTTCCCGCTAG 60.228 63.158 0.00 0.00 0.00 3.42
886 1011 0.819666 GCCCCATTTCCCGCTAGAAG 60.820 60.000 0.00 0.00 0.00 2.85
1108 1242 2.584673 CTCGCCAAGGAGAAGGAGA 58.415 57.895 0.00 0.00 36.08 3.71
1191 1325 1.060622 CGTCGACGAGCAGGTCTAC 59.939 63.158 33.35 4.23 43.02 2.59
1212 1346 1.765314 CAATCCACCTCTCCTCGGAAT 59.235 52.381 0.00 0.00 0.00 3.01
1272 1406 8.432110 TTTATCTTGCTACGATTTGCTGATTA 57.568 30.769 0.00 0.00 0.00 1.75
1285 1419 5.857471 TTGCTGATTAATTTGGGATCTGG 57.143 39.130 0.00 0.00 0.00 3.86
1293 1427 2.786512 TTTGGGATCTGGGCAGGTGC 62.787 60.000 0.00 0.00 41.14 5.01
1414 1548 3.269520 GGTATCGCCTTCTTCCGAC 57.730 57.895 0.00 0.00 36.18 4.79
1460 1595 5.410439 GCACAAATTTCATTTCTGCTTGGAT 59.590 36.000 3.11 0.00 39.87 3.41
1467 1602 7.707624 TTTCATTTCTGCTTGGATTACTGAT 57.292 32.000 0.00 0.00 0.00 2.90
1535 1670 3.448093 TTTGGCCTGTTGATGTATGGA 57.552 42.857 3.32 0.00 0.00 3.41
1586 1721 2.047179 GCCTCCACGACCTTGACC 60.047 66.667 0.00 0.00 0.00 4.02
1715 1850 7.094592 GCCTCTGTACTCTCTTTTAAATGCTTT 60.095 37.037 0.00 0.00 0.00 3.51
1716 1851 8.447053 CCTCTGTACTCTCTTTTAAATGCTTTC 58.553 37.037 0.00 0.00 0.00 2.62
1718 1853 9.337396 TCTGTACTCTCTTTTAAATGCTTTCAA 57.663 29.630 0.00 0.00 0.00 2.69
1766 1901 4.813697 AGCTGTCTTGAACTTTCAGTCTTC 59.186 41.667 0.00 0.00 38.61 2.87
1776 1911 4.258543 ACTTTCAGTCTTCGTGGACAAAA 58.741 39.130 11.56 10.08 38.57 2.44
1827 1987 2.560981 TCTATCAACCAACGCTCACAGA 59.439 45.455 0.00 0.00 0.00 3.41
1871 2031 4.764823 TGTTAGCTAACAGGTTTGGGAATG 59.235 41.667 30.81 0.00 40.93 2.67
1905 2065 1.063266 ACAACCACATGAAACAGGGGT 60.063 47.619 0.00 0.00 0.00 4.95
1906 2066 2.175931 ACAACCACATGAAACAGGGGTA 59.824 45.455 0.00 0.00 0.00 3.69
2024 2412 1.246649 TGCGATCTTGGTTTGCACAT 58.753 45.000 0.00 0.00 0.00 3.21
2036 2424 1.179152 TTGCACATCCAGATTGCCAG 58.821 50.000 0.00 0.00 35.26 4.85
2050 2438 1.187974 TGCCAGATTTGATGCCTTGG 58.812 50.000 0.00 0.00 0.00 3.61
2094 2482 9.734620 GCATTTGATTGCTAGATTTGTAACATA 57.265 29.630 0.00 0.00 39.57 2.29
2101 2489 6.539324 TGCTAGATTTGTAACATAAACGCAC 58.461 36.000 0.00 0.00 0.00 5.34
2403 2791 0.950836 TTGCTGTCCACAAATCCACG 59.049 50.000 0.00 0.00 0.00 4.94
2429 2817 3.011818 TGCATCAGTGGATCATGTCAAC 58.988 45.455 0.00 0.00 0.00 3.18
2451 2839 3.181510 CGCACCTTTATGTAAGTTCCTGC 60.182 47.826 0.00 0.00 31.56 4.85
2455 2843 4.202524 ACCTTTATGTAAGTTCCTGCCACA 60.203 41.667 0.00 0.00 31.56 4.17
2467 2855 2.041620 TCCTGCCACATTTAGCTTCCTT 59.958 45.455 0.00 0.00 0.00 3.36
2477 2865 8.023706 CCACATTTAGCTTCCTTCTTTTCTAAC 58.976 37.037 0.00 0.00 0.00 2.34
2490 2878 6.385649 TCTTTTCTAACGCCTTCATTGTTT 57.614 33.333 0.00 0.00 0.00 2.83
2568 2956 1.331756 CACACACAGTTCAAGTGGAGC 59.668 52.381 0.00 0.00 41.21 4.70
2595 2983 0.975887 ATGTCCCAACATTTGCACCC 59.024 50.000 0.00 0.00 43.74 4.61
2610 2998 3.561143 TGCACCCTACAAAGTTGAATGT 58.439 40.909 0.00 0.00 0.00 2.71
2634 3022 4.335594 GTGTTCTACCCATTGATACTTGCC 59.664 45.833 0.00 0.00 0.00 4.52
2652 3040 2.112928 AGTGGCGGTCATGCACAA 59.887 55.556 0.00 0.00 36.28 3.33
2670 3058 2.093711 ACAAACCACAAAAACTGCCCTC 60.094 45.455 0.00 0.00 0.00 4.30
2823 3211 8.825667 TGTTTTATTGAACTTATTTTCCCTGC 57.174 30.769 0.00 0.00 0.00 4.85
3136 3524 6.704056 AAACTCTTCCAAAGGAGAGGATTA 57.296 37.500 3.51 0.00 34.02 1.75
3165 3553 7.109501 TGCTACATGTAGTGTTACCATGAAAT 58.890 34.615 28.95 0.00 42.29 2.17
3193 3581 7.763172 CTCAGTTGAGTATTCCATACTGTTC 57.237 40.000 1.03 0.00 45.64 3.18
3307 3699 3.443329 TGAGTTTCAATATGGCATTGCGT 59.557 39.130 4.78 0.00 0.00 5.24
3310 3702 6.147864 AGTTTCAATATGGCATTGCGTAAT 57.852 33.333 4.78 0.00 0.00 1.89
3319 3711 6.826893 ATGGCATTGCGTAATTTTCAATAC 57.173 33.333 1.91 0.00 0.00 1.89
3337 3729 6.338146 TCAATACGGAACTGTATTCAGAAGG 58.662 40.000 13.88 5.09 41.79 3.46
3347 3739 4.661222 TGTATTCAGAAGGCCATGTTTGA 58.339 39.130 5.01 0.00 0.00 2.69
3385 3777 3.433513 GGATTGCTCCAAAAGATCTGC 57.566 47.619 0.00 0.00 41.64 4.26
3386 3778 2.223433 GGATTGCTCCAAAAGATCTGCG 60.223 50.000 0.00 0.00 41.64 5.18
3387 3779 0.523072 TTGCTCCAAAAGATCTGCGC 59.477 50.000 0.00 0.00 0.00 6.09
3388 3780 0.606130 TGCTCCAAAAGATCTGCGCA 60.606 50.000 10.98 10.98 0.00 6.09
3389 3781 0.737219 GCTCCAAAAGATCTGCGCAT 59.263 50.000 12.24 0.00 0.00 4.73
3390 3782 1.942657 GCTCCAAAAGATCTGCGCATA 59.057 47.619 12.24 3.38 0.00 3.14
3391 3783 2.551459 GCTCCAAAAGATCTGCGCATAT 59.449 45.455 12.24 9.95 0.00 1.78
3392 3784 3.364764 GCTCCAAAAGATCTGCGCATATC 60.365 47.826 23.94 23.94 0.00 1.63
3393 3785 4.063689 CTCCAAAAGATCTGCGCATATCT 58.936 43.478 27.21 27.21 33.87 1.98
3394 3786 5.213891 TCCAAAAGATCTGCGCATATCTA 57.786 39.130 31.14 17.07 32.17 1.98
3395 3787 5.798132 TCCAAAAGATCTGCGCATATCTAT 58.202 37.500 31.14 22.29 32.17 1.98
3396 3788 5.871524 TCCAAAAGATCTGCGCATATCTATC 59.128 40.000 31.14 19.11 32.17 2.08
3397 3789 5.640783 CCAAAAGATCTGCGCATATCTATCA 59.359 40.000 31.14 0.00 32.17 2.15
3398 3790 6.148315 CCAAAAGATCTGCGCATATCTATCAA 59.852 38.462 31.14 0.00 32.17 2.57
3399 3791 6.718454 AAAGATCTGCGCATATCTATCAAC 57.282 37.500 31.14 9.03 32.17 3.18
3400 3792 5.657826 AGATCTGCGCATATCTATCAACT 57.342 39.130 30.29 10.34 30.65 3.16
3401 3793 5.649557 AGATCTGCGCATATCTATCAACTC 58.350 41.667 30.29 7.66 30.65 3.01
3402 3794 4.179926 TCTGCGCATATCTATCAACTCC 57.820 45.455 12.24 0.00 0.00 3.85
3403 3795 3.056536 TCTGCGCATATCTATCAACTCCC 60.057 47.826 12.24 0.00 0.00 4.30
3404 3796 2.632512 TGCGCATATCTATCAACTCCCA 59.367 45.455 5.66 0.00 0.00 4.37
3405 3797 3.070878 TGCGCATATCTATCAACTCCCAA 59.929 43.478 5.66 0.00 0.00 4.12
3413 3805 5.531122 TCTATCAACTCCCAAGTATTCGG 57.469 43.478 0.00 0.00 33.48 4.30
3416 3808 1.065418 CAACTCCCAAGTATTCGGCCT 60.065 52.381 0.00 0.00 33.48 5.19
3423 3815 3.340034 CCAAGTATTCGGCCTACACAAA 58.660 45.455 0.00 0.00 0.00 2.83
3424 3816 3.754323 CCAAGTATTCGGCCTACACAAAA 59.246 43.478 0.00 0.00 0.00 2.44
3433 3826 5.945155 TCGGCCTACACAAAATTTTCATAC 58.055 37.500 0.00 0.00 0.00 2.39
3497 3890 7.103641 TCTTTCGATACTCCAAAAGCAACTAT 58.896 34.615 0.00 0.00 0.00 2.12
3535 3928 5.704515 GCATGCATAGAATCAACCAGTATCT 59.295 40.000 14.21 0.00 0.00 1.98
3570 3965 7.845066 ACCGTTTCTTCCTTTATCTGAATAC 57.155 36.000 0.00 0.00 0.00 1.89
3651 4048 9.433153 CTGCAGTATATACATGTTGATGATTCT 57.567 33.333 15.18 0.00 33.36 2.40
3684 4081 3.258372 ACATCACGGTCTACATGAAGTGT 59.742 43.478 0.00 0.00 44.95 3.55
3700 4097 4.024387 TGAAGTGTGAAATGTAACGGAAGC 60.024 41.667 0.00 0.00 0.00 3.86
3705 4102 6.021596 GTGTGAAATGTAACGGAAGCAATAG 58.978 40.000 0.00 0.00 0.00 1.73
3708 4105 5.182190 TGAAATGTAACGGAAGCAATAGCAA 59.818 36.000 0.00 0.00 45.49 3.91
3742 4142 8.788409 AAAATTTGATCAGTTTCTCGTTCTTC 57.212 30.769 8.16 0.00 0.00 2.87
3796 4196 4.079253 TCAAGTTTCTTGGATTGTAGCCC 58.921 43.478 9.18 0.00 0.00 5.19
3805 4205 1.134068 GGATTGTAGCCCAGTTCCCTC 60.134 57.143 0.00 0.00 0.00 4.30
3850 4250 4.814234 GCCCATTGATGTCTAATAACACGA 59.186 41.667 0.00 0.00 30.55 4.35
3853 4253 6.238374 CCCATTGATGTCTAATAACACGAACC 60.238 42.308 0.00 0.00 30.55 3.62
3903 4303 5.789574 ATTAAACCCACAAGGATGGACTA 57.210 39.130 0.00 0.00 43.02 2.59
3915 4315 6.835488 ACAAGGATGGACTATATGCAAACAAT 59.165 34.615 0.00 0.00 29.34 2.71
3916 4316 7.998383 ACAAGGATGGACTATATGCAAACAATA 59.002 33.333 0.00 0.00 29.34 1.90
3994 4397 2.273619 AGAGGGAGCTTTCCAGTGATT 58.726 47.619 9.32 0.00 0.00 2.57
3997 4400 1.066143 GGGAGCTTTCCAGTGATTCGA 60.066 52.381 0.00 0.00 0.00 3.71
3999 4402 1.663135 GAGCTTTCCAGTGATTCGAGC 59.337 52.381 0.00 0.00 0.00 5.03
4042 4445 5.709164 GCCATATATTTCAATCAGCCAGAGT 59.291 40.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.121611 ACTCATGCATGCAATTTTGACATTG 59.878 36.000 26.68 14.13 37.23 2.82
9 10 5.242434 ACTCATGCATGCAATTTTGACATT 58.758 33.333 26.68 0.00 0.00 2.71
11 12 4.260139 ACTCATGCATGCAATTTTGACA 57.740 36.364 26.68 2.39 0.00 3.58
21 22 4.794248 TGTTACGAATACTCATGCATGC 57.206 40.909 22.25 11.82 0.00 4.06
30 31 6.212187 AGAGTTAACCCCTTGTTACGAATACT 59.788 38.462 0.88 0.00 39.13 2.12
31 32 6.401394 AGAGTTAACCCCTTGTTACGAATAC 58.599 40.000 0.88 0.00 39.13 1.89
37 38 7.520451 AATCAAAGAGTTAACCCCTTGTTAC 57.480 36.000 10.47 0.00 39.13 2.50
40 41 7.432148 AAAAATCAAAGAGTTAACCCCTTGT 57.568 32.000 10.47 1.56 0.00 3.16
93 94 9.750882 GACATAAATCGTTTTAAGGTACTCAAC 57.249 33.333 2.96 0.00 38.49 3.18
115 116 9.844257 TTGAATTTTGGTCCTAAAAATTGACAT 57.156 25.926 14.35 0.00 43.68 3.06
137 138 6.767524 AAATTGAACTACAGGTGTGTTGAA 57.232 33.333 0.00 0.00 38.19 2.69
139 140 8.803799 GTTTAAAATTGAACTACAGGTGTGTTG 58.196 33.333 0.00 0.00 38.19 3.33
211 212 8.027771 AGATTTTGAGTTCTTGATCTTCATTGC 58.972 33.333 0.00 0.00 0.00 3.56
251 252 1.142748 GTCTGGTGGCTCGATCTGG 59.857 63.158 0.00 0.00 0.00 3.86
254 255 2.501610 GGGTCTGGTGGCTCGATC 59.498 66.667 0.00 0.00 0.00 3.69
256 257 4.988716 ACGGGTCTGGTGGCTCGA 62.989 66.667 0.00 0.00 0.00 4.04
257 258 4.436998 GACGGGTCTGGTGGCTCG 62.437 72.222 0.00 0.00 0.00 5.03
260 261 2.788191 CTTCTGACGGGTCTGGTGGC 62.788 65.000 5.97 0.00 0.00 5.01
267 268 0.179134 CCGATGTCTTCTGACGGGTC 60.179 60.000 0.00 0.00 45.70 4.46
275 276 0.324738 TCTCCTGCCCGATGTCTTCT 60.325 55.000 0.00 0.00 0.00 2.85
278 279 1.760086 CCTCTCCTGCCCGATGTCT 60.760 63.158 0.00 0.00 0.00 3.41
290 291 0.531753 GGATCTTCTTGCGCCTCTCC 60.532 60.000 4.18 0.00 0.00 3.71
318 319 4.459089 GGAGGTCAGACCGGCAGC 62.459 72.222 14.32 2.82 44.90 5.25
326 327 2.680352 GACGGGCTGGAGGTCAGA 60.680 66.667 0.00 0.00 46.18 3.27
327 328 1.831652 AAAGACGGGCTGGAGGTCAG 61.832 60.000 0.00 0.00 46.03 3.51
328 329 0.543410 TAAAGACGGGCTGGAGGTCA 60.543 55.000 0.00 0.00 33.18 4.02
375 376 2.158608 AGAGTGGAACCCCTTGACTTTG 60.159 50.000 0.00 0.00 37.80 2.77
378 379 1.059913 CAGAGTGGAACCCCTTGACT 58.940 55.000 0.00 0.00 37.80 3.41
382 383 1.280457 CTAGCAGAGTGGAACCCCTT 58.720 55.000 0.00 0.00 37.80 3.95
387 388 0.321671 TGGTGCTAGCAGAGTGGAAC 59.678 55.000 20.03 3.12 0.00 3.62
403 404 1.178534 CCCAGATTTGTTGGCGTGGT 61.179 55.000 0.00 0.00 34.26 4.16
408 409 0.897621 CCTTCCCCAGATTTGTTGGC 59.102 55.000 0.00 0.00 34.26 4.52
409 410 1.560505 CCCTTCCCCAGATTTGTTGG 58.439 55.000 0.00 0.00 35.41 3.77
410 411 0.897621 GCCCTTCCCCAGATTTGTTG 59.102 55.000 0.00 0.00 0.00 3.33
411 412 0.611896 CGCCCTTCCCCAGATTTGTT 60.612 55.000 0.00 0.00 0.00 2.83
423 424 1.523758 AAATGTCACTGACGCCCTTC 58.476 50.000 4.71 0.00 34.95 3.46
465 467 3.953612 ACAGGCTTTCAAAAGATGTGTGA 59.046 39.130 6.67 0.00 36.64 3.58
466 468 4.311816 ACAGGCTTTCAAAAGATGTGTG 57.688 40.909 6.67 0.00 36.64 3.82
468 470 6.258230 TGATACAGGCTTTCAAAAGATGTG 57.742 37.500 17.24 9.35 37.74 3.21
469 471 7.177216 TGAATGATACAGGCTTTCAAAAGATGT 59.823 33.333 6.67 11.37 39.35 3.06
470 472 7.541162 TGAATGATACAGGCTTTCAAAAGATG 58.459 34.615 6.67 6.63 38.28 2.90
473 475 8.592105 TTTTGAATGATACAGGCTTTCAAAAG 57.408 30.769 22.05 0.00 44.86 2.27
590 607 9.801714 GTGAAATATTTGTTTGAAATTCTGCTG 57.198 29.630 5.17 0.00 0.00 4.41
591 608 9.545105 TGTGAAATATTTGTTTGAAATTCTGCT 57.455 25.926 5.17 0.00 0.00 4.24
609 626 9.474920 GAACATTTCTTTGAATGGTGTGAAATA 57.525 29.630 0.00 0.00 37.08 1.40
613 630 6.462552 TGAACATTTCTTTGAATGGTGTGA 57.537 33.333 3.06 0.00 37.08 3.58
614 631 6.534436 TGTTGAACATTTCTTTGAATGGTGTG 59.466 34.615 0.00 0.00 37.08 3.82
615 632 6.638610 TGTTGAACATTTCTTTGAATGGTGT 58.361 32.000 0.00 0.00 37.08 4.16
778 879 4.260784 GCTTCAGCGTGGATTTTTATCGAT 60.261 41.667 2.16 2.16 0.00 3.59
865 990 1.227973 CTAGCGGGAAATGGGGCTC 60.228 63.158 0.00 0.00 36.97 4.70
866 991 1.279025 TTCTAGCGGGAAATGGGGCT 61.279 55.000 0.00 0.00 39.44 5.19
868 993 0.837272 TCTTCTAGCGGGAAATGGGG 59.163 55.000 0.00 0.00 0.00 4.96
869 994 1.202698 CCTCTTCTAGCGGGAAATGGG 60.203 57.143 0.00 0.00 0.00 4.00
881 1006 0.736325 GCGCTTCGTTGCCTCTTCTA 60.736 55.000 0.00 0.00 0.00 2.10
883 1008 2.476499 GCGCTTCGTTGCCTCTTC 59.524 61.111 0.00 0.00 0.00 2.87
1041 1175 1.152839 CTCCTCCTCCTCGTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1108 1242 2.960688 GCTTCTTGGCCGAGGAGGT 61.961 63.158 27.31 0.00 43.70 3.85
1191 1325 0.687757 TCCGAGGAGAGGTGGATTGG 60.688 60.000 0.00 0.00 0.00 3.16
1212 1346 1.305046 GAAGAGGTGGGTCGGAGGA 60.305 63.158 0.00 0.00 0.00 3.71
1272 1406 0.712380 ACCTGCCCAGATCCCAAATT 59.288 50.000 0.00 0.00 0.00 1.82
1301 1435 3.607661 GGGATCTCGGCGAGGGAC 61.608 72.222 33.93 23.72 27.95 4.46
1427 1561 1.274798 GAAATTTGTGCGGTGCCGTG 61.275 55.000 12.46 0.00 42.09 4.94
1460 1595 8.865590 TTCATTTCGATCGACATTATCAGTAA 57.134 30.769 19.26 5.63 0.00 2.24
1467 1602 5.174943 CGACCATTCATTTCGATCGACATTA 59.825 40.000 19.26 5.60 34.62 1.90
1535 1670 3.507622 GCAACAGCTTCTTAGACCCAAAT 59.492 43.478 0.00 0.00 0.00 2.32
1586 1721 3.498018 TGACCACAATGACAGTGAAATCG 59.502 43.478 10.34 0.00 39.30 3.34
1661 1796 6.931281 GCAATTATACAGGCAAGAGATCAGTA 59.069 38.462 0.00 0.00 0.00 2.74
1662 1797 5.762218 GCAATTATACAGGCAAGAGATCAGT 59.238 40.000 0.00 0.00 0.00 3.41
1667 1802 4.336433 GCAAGCAATTATACAGGCAAGAGA 59.664 41.667 0.00 0.00 0.00 3.10
1776 1911 4.037803 GCCAATTCAGCCATTTTTGGTTTT 59.962 37.500 0.00 0.00 39.21 2.43
1827 1987 5.574188 ACAGAGGTTAAAGCCAATTGATCT 58.426 37.500 7.12 0.42 0.00 2.75
1871 2031 7.648142 TCATGTGGTTGTTTCATCTACTTTTC 58.352 34.615 0.00 0.00 0.00 2.29
2007 2395 1.811965 TGGATGTGCAAACCAAGATCG 59.188 47.619 5.48 0.00 0.00 3.69
2024 2412 2.691526 GCATCAAATCTGGCAATCTGGA 59.308 45.455 0.00 0.00 0.00 3.86
2036 2424 4.391405 CCTTTACCCAAGGCATCAAATC 57.609 45.455 0.00 0.00 46.18 2.17
2050 2438 0.179137 GCGGCTGCATTTCCTTTACC 60.179 55.000 14.08 0.00 42.15 2.85
2094 2482 4.911514 ATTGGTACTTCAAAGTGCGTTT 57.088 36.364 5.66 0.00 41.76 3.60
2101 2489 5.006386 AGAGGCAGAATTGGTACTTCAAAG 58.994 41.667 0.00 0.00 0.00 2.77
2258 2646 7.323656 GTCTGGTTGTTCAAAAACGAGATAATG 59.676 37.037 8.29 0.00 42.09 1.90
2318 2706 5.999600 TGCAGGTCCATCTATATTGTGAATG 59.000 40.000 0.00 0.00 0.00 2.67
2403 2791 3.192001 ACATGATCCACTGATGCAACAAC 59.808 43.478 0.00 0.00 0.00 3.32
2451 2839 6.581171 AGAAAAGAAGGAAGCTAAATGTGG 57.419 37.500 0.00 0.00 0.00 4.17
2455 2843 6.127980 GGCGTTAGAAAAGAAGGAAGCTAAAT 60.128 38.462 0.00 0.00 0.00 1.40
2467 2855 6.385649 AAACAATGAAGGCGTTAGAAAAGA 57.614 33.333 0.00 0.00 0.00 2.52
2477 2865 4.881850 AGGATACCTTAAACAATGAAGGCG 59.118 41.667 0.54 0.00 45.28 5.52
2490 2878 7.990886 CAGTAATTGCCAGTTTAGGATACCTTA 59.009 37.037 0.00 0.00 34.61 2.69
2595 2983 7.352739 GGTAGAACACACATTCAACTTTGTAG 58.647 38.462 0.00 0.00 0.00 2.74
2610 2998 4.941263 GCAAGTATCAATGGGTAGAACACA 59.059 41.667 0.00 0.00 35.08 3.72
2634 3022 1.794151 TTTGTGCATGACCGCCACTG 61.794 55.000 0.00 0.00 0.00 3.66
2652 3040 0.744281 CGAGGGCAGTTTTTGTGGTT 59.256 50.000 0.00 0.00 0.00 3.67
2670 3058 3.487574 GTGTCAGACTCTGAAGAACAACG 59.512 47.826 10.45 0.00 42.46 4.10
3087 3475 7.028962 TGCTGAATCAAATAATCAACCGAAAG 58.971 34.615 0.00 0.00 0.00 2.62
3136 3524 6.294361 TGGTAACACTACATGTAGCAGATT 57.706 37.500 28.88 19.84 46.17 2.40
3187 3575 9.373450 AGTGATGGATAATCTATGTAGAACAGT 57.627 33.333 0.00 0.00 35.69 3.55
3209 3597 8.750515 TCAGCCATTTCATAAATCATAAGTGA 57.249 30.769 0.00 0.00 39.04 3.41
3217 3607 6.535865 TGCAACATTCAGCCATTTCATAAATC 59.464 34.615 0.00 0.00 0.00 2.17
3218 3608 6.408035 TGCAACATTCAGCCATTTCATAAAT 58.592 32.000 0.00 0.00 0.00 1.40
3219 3609 5.791666 TGCAACATTCAGCCATTTCATAAA 58.208 33.333 0.00 0.00 0.00 1.40
3226 3616 3.688694 AACATGCAACATTCAGCCATT 57.311 38.095 0.00 0.00 0.00 3.16
3255 3645 9.635520 AAAATGCTGAGACAAAGAAAGATAATG 57.364 29.630 0.00 0.00 0.00 1.90
3310 3702 8.610248 TTCTGAATACAGTTCCGTATTGAAAA 57.390 30.769 1.27 0.00 41.14 2.29
3319 3711 2.280628 GGCCTTCTGAATACAGTTCCG 58.719 52.381 0.00 0.00 43.81 4.30
3332 3724 5.759059 TCAAGATATCAAACATGGCCTTCT 58.241 37.500 3.32 0.00 0.00 2.85
3337 3729 6.420008 GCTTTGATCAAGATATCAAACATGGC 59.580 38.462 8.41 6.69 46.04 4.40
3378 3770 5.394005 GGAGTTGATAGATATGCGCAGATCT 60.394 44.000 39.77 39.77 41.68 2.75
3379 3771 4.803088 GGAGTTGATAGATATGCGCAGATC 59.197 45.833 32.24 32.24 0.00 2.75
3380 3772 4.382470 GGGAGTTGATAGATATGCGCAGAT 60.382 45.833 18.97 18.97 0.00 2.90
3381 3773 3.056536 GGGAGTTGATAGATATGCGCAGA 60.057 47.826 18.32 13.18 0.00 4.26
3382 3774 3.257393 GGGAGTTGATAGATATGCGCAG 58.743 50.000 18.32 0.00 0.00 5.18
3383 3775 2.632512 TGGGAGTTGATAGATATGCGCA 59.367 45.455 14.96 14.96 0.00 6.09
3384 3776 3.319137 TGGGAGTTGATAGATATGCGC 57.681 47.619 0.00 0.00 0.00 6.09
3385 3777 4.887748 ACTTGGGAGTTGATAGATATGCG 58.112 43.478 0.00 0.00 29.87 4.73
3386 3778 7.276658 CGAATACTTGGGAGTTGATAGATATGC 59.723 40.741 0.00 0.00 37.33 3.14
3387 3779 7.761704 CCGAATACTTGGGAGTTGATAGATATG 59.238 40.741 0.00 0.00 37.33 1.78
3388 3780 7.579723 GCCGAATACTTGGGAGTTGATAGATAT 60.580 40.741 0.00 0.00 37.33 1.63
3389 3781 6.295123 GCCGAATACTTGGGAGTTGATAGATA 60.295 42.308 0.00 0.00 37.33 1.98
3390 3782 5.511545 GCCGAATACTTGGGAGTTGATAGAT 60.512 44.000 0.00 0.00 37.33 1.98
3391 3783 4.202223 GCCGAATACTTGGGAGTTGATAGA 60.202 45.833 0.00 0.00 37.33 1.98
3392 3784 4.058817 GCCGAATACTTGGGAGTTGATAG 58.941 47.826 0.00 0.00 37.33 2.08
3393 3785 3.181458 GGCCGAATACTTGGGAGTTGATA 60.181 47.826 0.00 0.00 37.33 2.15
3394 3786 2.421529 GGCCGAATACTTGGGAGTTGAT 60.422 50.000 0.00 0.00 37.33 2.57
3395 3787 1.065709 GGCCGAATACTTGGGAGTTGA 60.066 52.381 0.00 0.00 37.33 3.18
3396 3788 1.065418 AGGCCGAATACTTGGGAGTTG 60.065 52.381 0.00 0.00 37.33 3.16
3397 3789 1.286248 AGGCCGAATACTTGGGAGTT 58.714 50.000 0.00 0.00 37.33 3.01
3398 3790 1.761198 GTAGGCCGAATACTTGGGAGT 59.239 52.381 0.00 0.00 39.97 3.85
3399 3791 1.760613 TGTAGGCCGAATACTTGGGAG 59.239 52.381 0.00 0.00 0.00 4.30
3400 3792 1.483415 GTGTAGGCCGAATACTTGGGA 59.517 52.381 0.00 0.00 0.00 4.37
3401 3793 1.208535 TGTGTAGGCCGAATACTTGGG 59.791 52.381 0.00 0.00 0.00 4.12
3402 3794 2.684001 TGTGTAGGCCGAATACTTGG 57.316 50.000 0.00 0.00 0.00 3.61
3403 3795 5.560966 ATTTTGTGTAGGCCGAATACTTG 57.439 39.130 0.00 0.00 0.00 3.16
3404 3796 6.584185 AAATTTTGTGTAGGCCGAATACTT 57.416 33.333 0.00 0.00 0.00 2.24
3405 3797 6.207810 TGAAAATTTTGTGTAGGCCGAATACT 59.792 34.615 8.47 0.00 0.00 2.12
3413 3805 8.495148 CCAAAAGTATGAAAATTTTGTGTAGGC 58.505 33.333 8.47 0.00 40.59 3.93
3416 3808 9.319143 CACCCAAAAGTATGAAAATTTTGTGTA 57.681 29.630 8.47 0.00 40.59 2.90
3423 3815 7.501892 ACAAATGCACCCAAAAGTATGAAAATT 59.498 29.630 0.00 0.00 0.00 1.82
3424 3816 6.997476 ACAAATGCACCCAAAAGTATGAAAAT 59.003 30.769 0.00 0.00 0.00 1.82
3433 3826 4.057406 TGAGAACAAATGCACCCAAAAG 57.943 40.909 0.00 0.00 0.00 2.27
3478 3871 6.914757 GCATGAATAGTTGCTTTTGGAGTATC 59.085 38.462 0.00 0.00 35.95 2.24
3548 3941 6.755141 TCCGTATTCAGATAAAGGAAGAAACG 59.245 38.462 0.00 0.00 29.28 3.60
3643 4040 9.335891 CGTGATGTTCTATGTACTAGAATCATC 57.664 37.037 24.20 24.20 45.78 2.92
3651 4048 7.049754 TGTAGACCGTGATGTTCTATGTACTA 58.950 38.462 0.00 0.00 0.00 1.82
3660 4057 4.327357 CACTTCATGTAGACCGTGATGTTC 59.673 45.833 6.32 0.00 41.97 3.18
3666 4063 3.297830 TCACACTTCATGTAGACCGTG 57.702 47.619 6.32 9.85 40.64 4.94
3684 4081 4.697828 TGCTATTGCTTCCGTTACATTTCA 59.302 37.500 0.00 0.00 40.48 2.69
3705 4102 9.463443 AACTGATCAAATTTTAGTGTACTTTGC 57.537 29.630 0.00 0.00 0.00 3.68
3742 4142 2.950309 AGCTGAGATGCTTTTATGGCTG 59.050 45.455 0.00 0.00 40.93 4.85
3763 4163 5.365605 TCCAAGAAACTTGACTGAAGGTCTA 59.634 40.000 12.25 0.00 44.74 2.59
3796 4196 2.951642 TGACAAAGCAAAGAGGGAACTG 59.048 45.455 0.00 0.00 44.43 3.16
3805 4205 4.321745 GCGTATTCATGTGACAAAGCAAAG 59.678 41.667 0.00 0.00 0.00 2.77
3850 4250 0.108585 ACTGTGGATTGCAGACGGTT 59.891 50.000 0.00 0.00 37.40 4.44
3888 4288 4.356405 TGCATATAGTCCATCCTTGTGG 57.644 45.455 0.00 0.00 40.76 4.17
3891 4291 6.698008 TTGTTTGCATATAGTCCATCCTTG 57.302 37.500 0.00 0.00 0.00 3.61
3943 4343 2.099405 CCCGTATGTCCCAGCATTTTT 58.901 47.619 0.00 0.00 0.00 1.94
3948 4348 0.618107 TTACCCCGTATGTCCCAGCA 60.618 55.000 0.00 0.00 0.00 4.41
3949 4349 0.179065 GTTACCCCGTATGTCCCAGC 60.179 60.000 0.00 0.00 0.00 4.85
3961 4364 2.369203 GCTCCCTCTTATCAGTTACCCC 59.631 54.545 0.00 0.00 0.00 4.95
3994 4397 4.518590 TGGATTTCAGTTTTCATTGCTCGA 59.481 37.500 0.00 0.00 0.00 4.04
3997 4400 4.562143 GGCTGGATTTCAGTTTTCATTGCT 60.562 41.667 0.00 0.00 45.08 3.91
3999 4402 4.885413 TGGCTGGATTTCAGTTTTCATTG 58.115 39.130 0.00 0.00 45.08 2.82
4042 4445 1.250154 CCCCGTACTTCCACGTACCA 61.250 60.000 0.00 0.00 40.31 3.25


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

AutoCloner maintained by Alex Coulton.