Multiple sequence alignment - TraesCS4D01G332800

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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 TraesCS4D01G332800 chr4D 100.000 3480 0 0 1 3480 490331923 490328444 0.000000e+00 6427.0
1 TraesCS4D01G332800 chr4D 98.144 2856 32 5 565 3418 490975445 490978281 0.000000e+00 4961.0
2 TraesCS4D01G332800 chr4D 92.683 287 20 1 210 496 490975028 490975313 2.500000e-111 412.0
3 TraesCS4D01G332800 chr4D 100.000 37 0 0 3442 3478 490978281 490978317 6.230000e-08 69.4
4 TraesCS4D01G332800 chr4D 95.122 41 2 0 2681 2721 490329199 490329159 8.060000e-07 65.8
5 TraesCS4D01G332800 chr4D 95.122 41 2 0 2725 2765 490329243 490329203 8.060000e-07 65.8
6 TraesCS4D01G332800 chr4D 95.122 41 2 0 2725 2765 490977559 490977599 8.060000e-07 65.8
7 TraesCS4D01G332800 chr4D 95.122 41 2 0 2681 2721 490977603 490977643 8.060000e-07 65.8
8 TraesCS4D01G332800 chr5A 93.519 2191 97 27 461 2638 671754133 671751975 0.000000e+00 3217.0
9 TraesCS4D01G332800 chr5A 93.388 2193 98 27 461 2638 671624987 671622827 0.000000e+00 3203.0
10 TraesCS4D01G332800 chr5A 93.333 2190 95 27 461 2638 671822122 671819972 0.000000e+00 3188.0
11 TraesCS4D01G332800 chr5A 86.536 713 88 6 1587 2295 641725397 641726105 0.000000e+00 778.0
12 TraesCS4D01G332800 chr4B 94.029 1859 79 17 632 2484 629963561 629961729 0.000000e+00 2789.0
13 TraesCS4D01G332800 chr4B 87.425 167 15 4 470 635 629964475 629964314 1.650000e-43 187.0
14 TraesCS4D01G332800 chr5D 86.816 713 86 6 1587 2295 513926335 513927043 0.000000e+00 789.0
15 TraesCS4D01G332800 chr5B 86.676 713 87 7 1587 2295 644874555 644875263 0.000000e+00 784.0
16 TraesCS4D01G332800 chr5B 94.064 219 13 0 243 461 619136417 619136635 2.000000e-87 333.0
17 TraesCS4D01G332800 chr5B 93.607 219 14 0 243 461 619189588 619189806 9.310000e-86 327.0
18 TraesCS4D01G332800 chr5B 92.237 219 17 0 243 461 619069640 619069858 9.380000e-81 311.0
19 TraesCS4D01G332800 chr5B 90.909 220 19 1 243 461 619105570 619105789 9.450000e-76 294.0
20 TraesCS4D01G332800 chr7D 89.498 219 23 0 243 461 49472931 49473149 9.510000e-71 278.0
21 TraesCS4D01G332800 chr6D 89.041 219 24 0 243 461 402894732 402894950 4.430000e-69 272.0
22 TraesCS4D01G332800 chr6D 92.857 112 8 0 113 224 58822675 58822564 2.780000e-36 163.0
23 TraesCS4D01G332800 chr6B 88.546 227 22 3 1 224 385763995 385764220 4.430000e-69 272.0
24 TraesCS4D01G332800 chr4A 88.393 224 24 1 1 224 304078158 304077937 5.730000e-68 268.0
25 TraesCS4D01G332800 chr2D 89.545 220 10 3 5 224 573230357 573230563 2.060000e-67 267.0
26 TraesCS4D01G332800 chr2D 85.845 219 30 1 243 461 557681455 557681238 7.510000e-57 231.0
27 TraesCS4D01G332800 chr1B 86.758 219 26 3 243 459 468508954 468509171 1.250000e-59 241.0
28 TraesCS4D01G332800 chr3B 85.897 234 22 2 1 224 549486806 549486574 4.490000e-59 239.0
29 TraesCS4D01G332800 chr3B 83.408 223 18 5 9 230 263504696 263504900 4.590000e-44 189.0
30 TraesCS4D01G332800 chr7B 85.909 220 26 2 9 224 456604609 456604827 2.700000e-56 230.0
31 TraesCS4D01G332800 chr3D 85.268 224 8 5 1 224 433110814 433111012 1.270000e-49 207.0
32 TraesCS4D01G332800 chr3D 91.525 118 9 1 107 224 575777084 575776968 1.000000e-35 161.0
33 TraesCS4D01G332800 chr3D 80.543 221 25 6 18 229 141629698 141629487 1.670000e-33 154.0
34 TraesCS4D01G332800 chr1D 82.203 236 20 8 2 229 207572187 207571966 2.130000e-42 183.0
35 TraesCS4D01G332800 chr1D 99.010 101 1 0 1 101 138057208 138057308 7.670000e-42 182.0
36 TraesCS4D01G332800 chr1D 97.030 101 3 0 1 101 476667691 476667791 1.660000e-38 171.0
37 TraesCS4D01G332800 chr7A 83.838 198 12 3 33 229 115585339 115585517 1.660000e-38 171.0


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 TraesCS4D01G332800 chr4D 490328444 490331923 3479 True 2186.2 6427 96.7480 1 3480 3 chr4D.!!$R1 3479
1 TraesCS4D01G332800 chr4D 490975028 490978317 3289 False 1114.8 4961 96.2142 210 3478 5 chr4D.!!$F1 3268
2 TraesCS4D01G332800 chr5A 671751975 671754133 2158 True 3217.0 3217 93.5190 461 2638 1 chr5A.!!$R2 2177
3 TraesCS4D01G332800 chr5A 671622827 671624987 2160 True 3203.0 3203 93.3880 461 2638 1 chr5A.!!$R1 2177
4 TraesCS4D01G332800 chr5A 671819972 671822122 2150 True 3188.0 3188 93.3330 461 2638 1 chr5A.!!$R3 2177
5 TraesCS4D01G332800 chr5A 641725397 641726105 708 False 778.0 778 86.5360 1587 2295 1 chr5A.!!$F1 708
6 TraesCS4D01G332800 chr4B 629961729 629964475 2746 True 1488.0 2789 90.7270 470 2484 2 chr4B.!!$R1 2014
7 TraesCS4D01G332800 chr5D 513926335 513927043 708 False 789.0 789 86.8160 1587 2295 1 chr5D.!!$F1 708
8 TraesCS4D01G332800 chr5B 644874555 644875263 708 False 784.0 784 86.6760 1587 2295 1 chr5B.!!$F5 708

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
255 256 0.469917 ATAGTGCATCTCCCAACGGG 59.530 55.0 0.0 0.0 46.11 5.28 F
314 315 0.736636 TGAGTAGCGACCACATACGG 59.263 55.0 0.0 0.0 0.00 4.02 F
316 317 0.737219 AGTAGCGACCACATACGGAC 59.263 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 2107 1.731969 GTAGCGGACGACGTTGCTT 60.732 57.895 26.54 14.8 46.52 3.91 R
1495 2369 9.588096 ACCAAGAAAGAAAGAACCATAACTTAT 57.412 29.630 0.00 0.0 0.00 1.73 R
2766 3649 4.422073 TCTTCCGGTGAAATAGATGCAT 57.578 40.909 0.00 0.0 0.00 3.96 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
45 46 6.904954 GTTGGAAACGTGTATATGTTGTTG 57.095 37.500 0.00 0.00 36.92 3.33
46 47 5.614923 TGGAAACGTGTATATGTTGTTGG 57.385 39.130 0.00 0.00 36.21 3.77
47 48 5.306394 TGGAAACGTGTATATGTTGTTGGA 58.694 37.500 0.00 0.00 36.21 3.53
48 49 5.763698 TGGAAACGTGTATATGTTGTTGGAA 59.236 36.000 0.00 0.00 36.21 3.53
49 50 6.262496 TGGAAACGTGTATATGTTGTTGGAAA 59.738 34.615 0.00 0.00 36.21 3.13
65 66 6.243811 GTTGGAAACGTATTGTTGGTATGA 57.756 37.500 0.00 0.00 40.84 2.15
66 67 6.848451 GTTGGAAACGTATTGTTGGTATGAT 58.152 36.000 0.00 0.00 40.84 2.45
67 68 7.309920 GTTGGAAACGTATTGTTGGTATGATT 58.690 34.615 0.00 0.00 40.84 2.57
68 69 6.847400 TGGAAACGTATTGTTGGTATGATTG 58.153 36.000 0.00 0.00 40.84 2.67
69 70 6.431543 TGGAAACGTATTGTTGGTATGATTGT 59.568 34.615 0.00 0.00 40.84 2.71
70 71 7.040340 TGGAAACGTATTGTTGGTATGATTGTT 60.040 33.333 0.00 0.00 40.84 2.83
71 72 7.272515 GGAAACGTATTGTTGGTATGATTGTTG 59.727 37.037 0.00 0.00 40.84 3.33
72 73 7.441890 AACGTATTGTTGGTATGATTGTTGA 57.558 32.000 0.00 0.00 40.00 3.18
73 74 7.441890 ACGTATTGTTGGTATGATTGTTGAA 57.558 32.000 0.00 0.00 0.00 2.69
74 75 7.877003 ACGTATTGTTGGTATGATTGTTGAAA 58.123 30.769 0.00 0.00 0.00 2.69
75 76 8.519526 ACGTATTGTTGGTATGATTGTTGAAAT 58.480 29.630 0.00 0.00 0.00 2.17
76 77 9.352784 CGTATTGTTGGTATGATTGTTGAAATT 57.647 29.630 0.00 0.00 0.00 1.82
92 93 8.939201 TGTTGAAATTATGTTCAAATGTGTGT 57.061 26.923 2.14 0.00 46.28 3.72
93 94 8.815189 TGTTGAAATTATGTTCAAATGTGTGTG 58.185 29.630 2.14 0.00 46.28 3.82
94 95 8.816144 GTTGAAATTATGTTCAAATGTGTGTGT 58.184 29.630 2.14 0.00 46.28 3.72
95 96 8.350238 TGAAATTATGTTCAAATGTGTGTGTG 57.650 30.769 0.00 0.00 34.59 3.82
96 97 7.978414 TGAAATTATGTTCAAATGTGTGTGTGT 59.022 29.630 0.00 0.00 34.59 3.72
97 98 7.697352 AATTATGTTCAAATGTGTGTGTGTG 57.303 32.000 0.00 0.00 0.00 3.82
98 99 4.717233 ATGTTCAAATGTGTGTGTGTGT 57.283 36.364 0.00 0.00 0.00 3.72
99 100 3.831112 TGTTCAAATGTGTGTGTGTGTG 58.169 40.909 0.00 0.00 0.00 3.82
100 101 3.254411 TGTTCAAATGTGTGTGTGTGTGT 59.746 39.130 0.00 0.00 0.00 3.72
101 102 4.455877 TGTTCAAATGTGTGTGTGTGTGTA 59.544 37.500 0.00 0.00 0.00 2.90
102 103 5.124617 TGTTCAAATGTGTGTGTGTGTGTAT 59.875 36.000 0.00 0.00 0.00 2.29
103 104 6.316390 TGTTCAAATGTGTGTGTGTGTGTATA 59.684 34.615 0.00 0.00 0.00 1.47
104 105 7.012799 TGTTCAAATGTGTGTGTGTGTGTATAT 59.987 33.333 0.00 0.00 0.00 0.86
105 106 8.499967 GTTCAAATGTGTGTGTGTGTGTATATA 58.500 33.333 0.00 0.00 0.00 0.86
106 107 8.785329 TCAAATGTGTGTGTGTGTGTATATAT 57.215 30.769 0.00 0.00 0.00 0.86
107 108 9.877178 TCAAATGTGTGTGTGTGTGTATATATA 57.123 29.630 0.00 0.00 0.00 0.86
157 158 9.767228 ATGTGAAATTCTGTCAAATTGAATGAA 57.233 25.926 12.04 12.04 31.70 2.57
158 159 9.767228 TGTGAAATTCTGTCAAATTGAATGAAT 57.233 25.926 14.57 14.57 34.42 2.57
185 186 3.275617 AAAAACAGGAAAAACAGGGGC 57.724 42.857 0.00 0.00 0.00 5.80
186 187 2.174685 AAACAGGAAAAACAGGGGCT 57.825 45.000 0.00 0.00 0.00 5.19
187 188 3.322191 AAACAGGAAAAACAGGGGCTA 57.678 42.857 0.00 0.00 0.00 3.93
188 189 3.542969 AACAGGAAAAACAGGGGCTAT 57.457 42.857 0.00 0.00 0.00 2.97
189 190 4.668138 AACAGGAAAAACAGGGGCTATA 57.332 40.909 0.00 0.00 0.00 1.31
190 191 3.964411 ACAGGAAAAACAGGGGCTATAC 58.036 45.455 0.00 0.00 0.00 1.47
191 192 3.332485 ACAGGAAAAACAGGGGCTATACA 59.668 43.478 0.00 0.00 0.00 2.29
192 193 3.947834 CAGGAAAAACAGGGGCTATACAG 59.052 47.826 0.00 0.00 0.00 2.74
193 194 3.053619 AGGAAAAACAGGGGCTATACAGG 60.054 47.826 0.00 0.00 0.00 4.00
194 195 2.437085 AAAACAGGGGCTATACAGGC 57.563 50.000 0.00 0.00 46.47 4.85
211 212 2.949106 CACTTTGCCGTCTGCTGG 59.051 61.111 0.00 0.00 42.00 4.85
227 228 1.228644 TGGCTGATGGCAAAGTGCT 60.229 52.632 0.00 0.00 46.03 4.40
236 237 3.153369 TGGCAAAGTGCTTGATTCCTA 57.847 42.857 0.00 0.00 44.28 2.94
255 256 0.469917 ATAGTGCATCTCCCAACGGG 59.530 55.000 0.00 0.00 46.11 5.28
281 282 1.004200 AGTAACCAAACGCTCCCCG 60.004 57.895 0.00 0.00 44.21 5.73
283 284 2.215625 TAACCAAACGCTCCCCGGA 61.216 57.895 0.73 0.00 42.52 5.14
312 313 2.223525 GGAGTGAGTAGCGACCACATAC 60.224 54.545 16.49 9.69 32.33 2.39
314 315 0.736636 TGAGTAGCGACCACATACGG 59.263 55.000 0.00 0.00 0.00 4.02
315 316 1.019673 GAGTAGCGACCACATACGGA 58.980 55.000 0.00 0.00 0.00 4.69
316 317 0.737219 AGTAGCGACCACATACGGAC 59.263 55.000 0.00 0.00 0.00 4.79
327 328 2.930040 CACATACGGACTAAAGCAGTGG 59.070 50.000 0.00 0.00 37.72 4.00
349 350 4.221924 GGCCCTAAAGATAACCTGCAAAAA 59.778 41.667 0.00 0.00 0.00 1.94
366 367 6.454795 TGCAAAAAGTGGATATTTGTCTTCC 58.545 36.000 0.00 0.00 36.63 3.46
368 369 7.450014 TGCAAAAAGTGGATATTTGTCTTCCTA 59.550 33.333 0.00 0.00 36.63 2.94
395 396 6.806388 AAAACCAAATCATTCCTGCAATTC 57.194 33.333 0.00 0.00 0.00 2.17
431 432 5.968387 ATAAAGCACATACTTCTACACGC 57.032 39.130 0.00 0.00 0.00 5.34
442 443 4.740268 ACTTCTACACGCATATGTTTCGA 58.260 39.130 4.29 0.00 33.85 3.71
464 465 1.136110 GTCTCTGCCTCTACTCCTTGC 59.864 57.143 0.00 0.00 0.00 4.01
466 467 1.520342 CTGCCTCTACTCCTTGCGC 60.520 63.158 0.00 0.00 0.00 6.09
564 565 2.315720 AAAGAGGAGGCCATGCTTTT 57.684 45.000 5.01 0.00 0.00 2.27
576 679 0.835941 ATGCTTTTGCCCAACCAACA 59.164 45.000 0.00 0.00 46.87 3.33
584 687 1.599797 CCCAACCAACAGGTCGACC 60.600 63.158 27.67 27.67 33.53 4.79
706 1570 5.761234 TGAGACAAAGTTTATGCCTACGTTT 59.239 36.000 0.00 0.00 0.00 3.60
2643 3525 5.836898 TCAAGATGGTAAGGTATACGTGGAT 59.163 40.000 0.00 0.00 0.00 3.41
2658 3540 5.833406 ACGTGGATGATCAATTTTGCATA 57.167 34.783 0.00 0.00 0.00 3.14
2766 3649 5.113383 CCTTGAGTAACCGTAATGTATGCA 58.887 41.667 0.00 0.00 0.00 3.96
2976 3859 0.251386 TAAACAGGGATTTGCCGGCA 60.251 50.000 29.03 29.03 37.63 5.69
3012 3895 2.450609 TTGGCGACTTGAACCTACTC 57.549 50.000 0.00 0.00 0.00 2.59
3013 3896 0.242825 TGGCGACTTGAACCTACTCG 59.757 55.000 0.00 0.00 0.00 4.18
3014 3897 0.243095 GGCGACTTGAACCTACTCGT 59.757 55.000 0.00 0.00 0.00 4.18
3015 3898 1.615502 GCGACTTGAACCTACTCGTC 58.384 55.000 0.00 0.00 0.00 4.20
3016 3899 1.068748 GCGACTTGAACCTACTCGTCA 60.069 52.381 0.00 0.00 0.00 4.35
3017 3900 2.606308 GCGACTTGAACCTACTCGTCAA 60.606 50.000 0.00 0.00 0.00 3.18
3018 3901 2.978489 CGACTTGAACCTACTCGTCAAC 59.022 50.000 0.00 0.00 0.00 3.18
3019 3902 3.549423 CGACTTGAACCTACTCGTCAACA 60.549 47.826 0.00 0.00 0.00 3.33
3020 3903 3.714391 ACTTGAACCTACTCGTCAACAC 58.286 45.455 0.00 0.00 0.00 3.32
3021 3904 2.806608 TGAACCTACTCGTCAACACC 57.193 50.000 0.00 0.00 0.00 4.16
3022 3905 1.001048 TGAACCTACTCGTCAACACCG 60.001 52.381 0.00 0.00 0.00 4.94
3023 3906 0.316204 AACCTACTCGTCAACACCGG 59.684 55.000 0.00 0.00 0.00 5.28
3024 3907 0.538057 ACCTACTCGTCAACACCGGA 60.538 55.000 9.46 0.00 0.00 5.14
3025 3908 0.815734 CCTACTCGTCAACACCGGAT 59.184 55.000 9.46 0.00 0.00 4.18
3172 4055 7.214467 ACGTTGGAAAAATAGATCATGTGTT 57.786 32.000 0.00 0.00 0.00 3.32
3238 4121 3.082579 GCTTGGATCGGCGGTCTCT 62.083 63.158 20.81 0.00 0.00 3.10
3264 4147 1.909700 TGTCCATTGCTTCTCAACCC 58.090 50.000 0.00 0.00 37.53 4.11
3284 4167 3.555586 CCCAACCTGGATTTGAGCAAAAG 60.556 47.826 0.00 0.00 40.96 2.27
3340 4223 1.657751 GCGGATGGCTTCTTTCCCAC 61.658 60.000 0.07 0.00 39.11 4.61
3352 4235 0.771127 TTTCCCACAGTGGAAGAGGG 59.229 55.000 22.37 2.75 44.87 4.30
3362 4245 1.613630 GGAAGAGGGGTGGAGCTCA 60.614 63.158 17.19 0.00 0.00 4.26
3371 4254 1.612395 GGTGGAGCTCAGTCCCTCTG 61.612 65.000 17.19 0.00 44.85 3.35
3398 4281 4.770010 GGAACCTGTTCATGGTTTTGGATA 59.230 41.667 11.78 0.00 46.59 2.59
3399 4282 5.245075 GGAACCTGTTCATGGTTTTGGATAA 59.755 40.000 11.78 0.00 46.59 1.75
3426 4309 9.755122 AAAAACTAAGGGATACTGCTAAGAAAT 57.245 29.630 0.00 0.00 0.00 2.17
3427 4310 9.755122 AAAACTAAGGGATACTGCTAAGAAATT 57.245 29.630 0.00 0.00 0.00 1.82
3433 4316 9.620259 AAGGGATACTGCTAAGAAATTAAAGAG 57.380 33.333 0.00 0.00 0.00 2.85
3434 4317 8.773216 AGGGATACTGCTAAGAAATTAAAGAGT 58.227 33.333 0.00 0.00 0.00 3.24
3435 4318 9.397280 GGGATACTGCTAAGAAATTAAAGAGTT 57.603 33.333 0.00 0.00 0.00 3.01
3438 4321 9.959721 ATACTGCTAAGAAATTAAAGAGTTGGA 57.040 29.630 0.00 0.00 0.00 3.53
3439 4322 8.329203 ACTGCTAAGAAATTAAAGAGTTGGAG 57.671 34.615 0.00 0.00 0.00 3.86
3440 4323 7.094592 ACTGCTAAGAAATTAAAGAGTTGGAGC 60.095 37.037 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.168451 ACGTTTCCAACAACATGAACATATATA 57.832 29.630 0.00 0.00 0.00 0.86
7 8 7.967854 CACGTTTCCAACAACATGAACATATAT 59.032 33.333 0.00 0.00 0.00 0.86
8 9 7.041030 ACACGTTTCCAACAACATGAACATATA 60.041 33.333 0.00 0.00 0.00 0.86
9 10 6.148948 CACGTTTCCAACAACATGAACATAT 58.851 36.000 0.00 0.00 0.00 1.78
10 11 5.066634 ACACGTTTCCAACAACATGAACATA 59.933 36.000 0.00 0.00 0.00 2.29
11 12 4.142271 ACACGTTTCCAACAACATGAACAT 60.142 37.500 0.00 0.00 0.00 2.71
12 13 3.191581 ACACGTTTCCAACAACATGAACA 59.808 39.130 0.00 0.00 0.00 3.18
13 14 3.765026 ACACGTTTCCAACAACATGAAC 58.235 40.909 0.00 0.00 0.00 3.18
14 15 5.759506 ATACACGTTTCCAACAACATGAA 57.240 34.783 0.00 0.00 0.00 2.57
15 16 6.428465 ACATATACACGTTTCCAACAACATGA 59.572 34.615 0.00 0.00 0.00 3.07
16 17 6.607689 ACATATACACGTTTCCAACAACATG 58.392 36.000 0.00 0.00 0.00 3.21
17 18 6.811253 ACATATACACGTTTCCAACAACAT 57.189 33.333 0.00 0.00 0.00 2.71
18 19 6.038382 ACAACATATACACGTTTCCAACAACA 59.962 34.615 0.00 0.00 0.00 3.33
19 20 6.432107 ACAACATATACACGTTTCCAACAAC 58.568 36.000 0.00 0.00 0.00 3.32
20 21 6.621316 ACAACATATACACGTTTCCAACAA 57.379 33.333 0.00 0.00 0.00 2.83
21 22 6.431278 CAACAACATATACACGTTTCCAACA 58.569 36.000 0.00 0.00 0.00 3.33
22 23 5.854338 CCAACAACATATACACGTTTCCAAC 59.146 40.000 0.00 0.00 0.00 3.77
23 24 5.763698 TCCAACAACATATACACGTTTCCAA 59.236 36.000 0.00 0.00 0.00 3.53
24 25 5.306394 TCCAACAACATATACACGTTTCCA 58.694 37.500 0.00 0.00 0.00 3.53
25 26 5.866335 TCCAACAACATATACACGTTTCC 57.134 39.130 0.00 0.00 0.00 3.13
26 27 6.301372 CGTTTCCAACAACATATACACGTTTC 59.699 38.462 0.00 0.00 0.00 2.78
27 28 6.137415 CGTTTCCAACAACATATACACGTTT 58.863 36.000 0.00 0.00 0.00 3.60
28 29 5.236911 ACGTTTCCAACAACATATACACGTT 59.763 36.000 0.00 0.00 33.61 3.99
29 30 4.751098 ACGTTTCCAACAACATATACACGT 59.249 37.500 0.00 0.00 32.59 4.49
30 31 5.272167 ACGTTTCCAACAACATATACACG 57.728 39.130 0.00 0.00 0.00 4.49
31 32 8.231837 ACAATACGTTTCCAACAACATATACAC 58.768 33.333 0.00 0.00 0.00 2.90
32 33 8.325421 ACAATACGTTTCCAACAACATATACA 57.675 30.769 0.00 0.00 0.00 2.29
33 34 9.057365 CAACAATACGTTTCCAACAACATATAC 57.943 33.333 0.00 0.00 34.86 1.47
34 35 8.237949 CCAACAATACGTTTCCAACAACATATA 58.762 33.333 0.00 0.00 34.86 0.86
35 36 7.087639 CCAACAATACGTTTCCAACAACATAT 58.912 34.615 0.00 0.00 34.86 1.78
36 37 6.039493 ACCAACAATACGTTTCCAACAACATA 59.961 34.615 0.00 0.00 34.86 2.29
37 38 5.163499 ACCAACAATACGTTTCCAACAACAT 60.163 36.000 0.00 0.00 34.86 2.71
38 39 4.158025 ACCAACAATACGTTTCCAACAACA 59.842 37.500 0.00 0.00 34.86 3.33
39 40 4.674475 ACCAACAATACGTTTCCAACAAC 58.326 39.130 0.00 0.00 34.86 3.32
40 41 4.985538 ACCAACAATACGTTTCCAACAA 57.014 36.364 0.00 0.00 34.86 2.83
41 42 5.763698 TCATACCAACAATACGTTTCCAACA 59.236 36.000 0.00 0.00 34.86 3.33
42 43 6.243811 TCATACCAACAATACGTTTCCAAC 57.756 37.500 0.00 0.00 34.86 3.77
43 44 7.040340 ACAATCATACCAACAATACGTTTCCAA 60.040 33.333 0.00 0.00 34.86 3.53
44 45 6.431543 ACAATCATACCAACAATACGTTTCCA 59.568 34.615 0.00 0.00 34.86 3.53
45 46 6.848451 ACAATCATACCAACAATACGTTTCC 58.152 36.000 0.00 0.00 34.86 3.13
46 47 8.018520 TCAACAATCATACCAACAATACGTTTC 58.981 33.333 0.00 0.00 34.86 2.78
47 48 7.877003 TCAACAATCATACCAACAATACGTTT 58.123 30.769 0.00 0.00 34.86 3.60
48 49 7.441890 TCAACAATCATACCAACAATACGTT 57.558 32.000 0.00 0.00 38.83 3.99
49 50 7.441890 TTCAACAATCATACCAACAATACGT 57.558 32.000 0.00 0.00 0.00 3.57
50 51 8.909708 ATTTCAACAATCATACCAACAATACG 57.090 30.769 0.00 0.00 0.00 3.06
66 67 9.376075 ACACACATTTGAACATAATTTCAACAA 57.624 25.926 0.00 0.00 43.57 2.83
67 68 8.815189 CACACACATTTGAACATAATTTCAACA 58.185 29.630 0.00 0.00 43.57 3.33
68 69 8.816144 ACACACACATTTGAACATAATTTCAAC 58.184 29.630 0.00 0.00 43.57 3.18
69 70 8.815189 CACACACACATTTGAACATAATTTCAA 58.185 29.630 0.00 0.00 42.47 2.69
70 71 7.978414 ACACACACACATTTGAACATAATTTCA 59.022 29.630 0.00 0.00 33.55 2.69
71 72 8.268052 CACACACACACATTTGAACATAATTTC 58.732 33.333 0.00 0.00 0.00 2.17
72 73 7.763528 ACACACACACACATTTGAACATAATTT 59.236 29.630 0.00 0.00 0.00 1.82
73 74 7.222417 CACACACACACACATTTGAACATAATT 59.778 33.333 0.00 0.00 0.00 1.40
74 75 6.696583 CACACACACACACATTTGAACATAAT 59.303 34.615 0.00 0.00 0.00 1.28
75 76 6.032717 CACACACACACACATTTGAACATAA 58.967 36.000 0.00 0.00 0.00 1.90
76 77 5.124617 ACACACACACACACATTTGAACATA 59.875 36.000 0.00 0.00 0.00 2.29
77 78 4.082300 ACACACACACACACATTTGAACAT 60.082 37.500 0.00 0.00 0.00 2.71
78 79 3.254411 ACACACACACACACATTTGAACA 59.746 39.130 0.00 0.00 0.00 3.18
79 80 3.832276 ACACACACACACACATTTGAAC 58.168 40.909 0.00 0.00 0.00 3.18
80 81 5.826601 ATACACACACACACACATTTGAA 57.173 34.783 0.00 0.00 0.00 2.69
81 82 8.785329 ATATATACACACACACACACATTTGA 57.215 30.769 0.00 0.00 0.00 2.69
131 132 9.767228 TTCATTCAATTTGACAGAATTTCACAT 57.233 25.926 0.00 0.00 30.04 3.21
132 133 9.767228 ATTCATTCAATTTGACAGAATTTCACA 57.233 25.926 14.91 0.00 30.60 3.58
165 166 2.843730 AGCCCCTGTTTTTCCTGTTTTT 59.156 40.909 0.00 0.00 0.00 1.94
166 167 2.477245 AGCCCCTGTTTTTCCTGTTTT 58.523 42.857 0.00 0.00 0.00 2.43
167 168 2.174685 AGCCCCTGTTTTTCCTGTTT 57.825 45.000 0.00 0.00 0.00 2.83
168 169 3.542969 ATAGCCCCTGTTTTTCCTGTT 57.457 42.857 0.00 0.00 0.00 3.16
169 170 3.332485 TGTATAGCCCCTGTTTTTCCTGT 59.668 43.478 0.00 0.00 0.00 4.00
170 171 3.947834 CTGTATAGCCCCTGTTTTTCCTG 59.052 47.826 0.00 0.00 0.00 3.86
171 172 3.053619 CCTGTATAGCCCCTGTTTTTCCT 60.054 47.826 0.00 0.00 0.00 3.36
172 173 3.288092 CCTGTATAGCCCCTGTTTTTCC 58.712 50.000 0.00 0.00 0.00 3.13
173 174 2.688446 GCCTGTATAGCCCCTGTTTTTC 59.312 50.000 0.00 0.00 0.00 2.29
174 175 2.042433 TGCCTGTATAGCCCCTGTTTTT 59.958 45.455 0.00 0.00 0.00 1.94
175 176 1.638589 TGCCTGTATAGCCCCTGTTTT 59.361 47.619 0.00 0.00 0.00 2.43
176 177 1.064685 GTGCCTGTATAGCCCCTGTTT 60.065 52.381 0.00 0.00 0.00 2.83
177 178 0.546598 GTGCCTGTATAGCCCCTGTT 59.453 55.000 0.00 0.00 0.00 3.16
178 179 0.326618 AGTGCCTGTATAGCCCCTGT 60.327 55.000 0.00 0.00 0.00 4.00
179 180 0.839946 AAGTGCCTGTATAGCCCCTG 59.160 55.000 0.00 0.00 0.00 4.45
180 181 1.212935 CAAAGTGCCTGTATAGCCCCT 59.787 52.381 0.00 0.00 0.00 4.79
181 182 1.680338 CAAAGTGCCTGTATAGCCCC 58.320 55.000 0.00 0.00 0.00 5.80
182 183 1.025041 GCAAAGTGCCTGTATAGCCC 58.975 55.000 0.00 0.00 37.42 5.19
201 202 2.513204 CCATCAGCCAGCAGACGG 60.513 66.667 0.00 0.00 0.00 4.79
202 203 3.200593 GCCATCAGCCAGCAGACG 61.201 66.667 0.00 0.00 34.35 4.18
203 204 1.246056 TTTGCCATCAGCCAGCAGAC 61.246 55.000 0.00 0.00 42.71 3.51
204 205 0.963856 CTTTGCCATCAGCCAGCAGA 60.964 55.000 0.00 0.00 42.71 4.26
205 206 1.248785 ACTTTGCCATCAGCCAGCAG 61.249 55.000 0.00 0.00 42.71 4.24
206 207 1.228644 ACTTTGCCATCAGCCAGCA 60.229 52.632 0.00 0.00 42.71 4.41
207 208 1.214589 CACTTTGCCATCAGCCAGC 59.785 57.895 0.00 0.00 42.71 4.85
208 209 1.214589 GCACTTTGCCATCAGCCAG 59.785 57.895 0.00 0.00 42.71 4.85
211 212 0.599558 TCAAGCACTTTGCCATCAGC 59.400 50.000 0.00 0.00 46.52 4.26
216 217 1.999648 AGGAATCAAGCACTTTGCCA 58.000 45.000 0.00 0.00 46.52 4.92
227 228 4.907269 TGGGAGATGCACTATAGGAATCAA 59.093 41.667 4.43 0.00 0.00 2.57
236 237 4.819759 CTACCCGTTGGGAGATGCACTAT 61.820 52.174 9.30 0.00 46.90 2.12
255 256 3.858247 AGCGTTTGGTTACTGGATCTAC 58.142 45.455 0.00 0.00 0.00 2.59
312 313 1.745489 GGGCCACTGCTTTAGTCCG 60.745 63.158 4.39 0.00 37.60 4.79
314 315 2.781681 TTAGGGCCACTGCTTTAGTC 57.218 50.000 6.18 0.00 37.60 2.59
315 316 2.642807 TCTTTAGGGCCACTGCTTTAGT 59.357 45.455 6.18 0.00 41.36 2.24
316 317 3.350219 TCTTTAGGGCCACTGCTTTAG 57.650 47.619 6.18 0.00 37.74 1.85
327 328 5.047306 ACTTTTTGCAGGTTATCTTTAGGGC 60.047 40.000 0.00 0.00 0.00 5.19
366 367 9.434420 TTGCAGGAATGATTTGGTTTTTAATAG 57.566 29.630 0.00 0.00 0.00 1.73
368 369 8.866970 ATTGCAGGAATGATTTGGTTTTTAAT 57.133 26.923 0.00 0.00 0.00 1.40
395 396 7.886629 ATGTGCTTTATTATGGGCTATATGG 57.113 36.000 0.00 0.00 0.00 2.74
423 424 4.678622 ACATCGAAACATATGCGTGTAGA 58.321 39.130 1.58 0.00 0.00 2.59
431 432 4.375272 AGGCAGAGACATCGAAACATATG 58.625 43.478 0.00 0.00 0.00 1.78
442 443 3.030291 CAAGGAGTAGAGGCAGAGACAT 58.970 50.000 0.00 0.00 0.00 3.06
464 465 1.790123 CGTTCCAAATCATCCAACGCG 60.790 52.381 3.53 3.53 34.08 6.01
466 467 3.000041 TCTCGTTCCAAATCATCCAACG 59.000 45.455 0.00 0.00 40.90 4.10
584 687 3.577805 ATTAAATTCAGAGGACGGGGG 57.422 47.619 0.00 0.00 0.00 5.40
589 692 9.674068 ACTCTCCTAAAATTAAATTCAGAGGAC 57.326 33.333 0.00 0.00 31.03 3.85
1233 2107 1.731969 GTAGCGGACGACGTTGCTT 60.732 57.895 26.54 14.80 46.52 3.91
1495 2369 9.588096 ACCAAGAAAGAAAGAACCATAACTTAT 57.412 29.630 0.00 0.00 0.00 1.73
2766 3649 4.422073 TCTTCCGGTGAAATAGATGCAT 57.578 40.909 0.00 0.00 0.00 3.96
2895 3778 0.107165 GAAGCACTCCGGCCCTAATT 60.107 55.000 0.00 0.00 0.00 1.40
2902 3785 2.092882 GTACACGAAGCACTCCGGC 61.093 63.158 0.00 0.00 0.00 6.13
2976 3859 2.169810 AATCACCACCCAAGGGCCT 61.170 57.895 0.00 0.00 39.32 5.19
3012 3895 2.093783 GCTCTTTTATCCGGTGTTGACG 59.906 50.000 0.00 0.00 0.00 4.35
3013 3896 3.071479 TGCTCTTTTATCCGGTGTTGAC 58.929 45.455 0.00 0.00 0.00 3.18
3014 3897 3.410631 TGCTCTTTTATCCGGTGTTGA 57.589 42.857 0.00 0.00 0.00 3.18
3015 3898 3.252215 TGTTGCTCTTTTATCCGGTGTTG 59.748 43.478 0.00 0.00 0.00 3.33
3016 3899 3.482436 TGTTGCTCTTTTATCCGGTGTT 58.518 40.909 0.00 0.00 0.00 3.32
3017 3900 3.134574 TGTTGCTCTTTTATCCGGTGT 57.865 42.857 0.00 0.00 0.00 4.16
3018 3901 4.414852 CATTGTTGCTCTTTTATCCGGTG 58.585 43.478 0.00 0.00 0.00 4.94
3019 3902 3.119495 GCATTGTTGCTCTTTTATCCGGT 60.119 43.478 0.00 0.00 45.77 5.28
3020 3903 3.438360 GCATTGTTGCTCTTTTATCCGG 58.562 45.455 0.00 0.00 45.77 5.14
3125 4008 4.500116 GCTCAGGCTCGGTCGACC 62.500 72.222 25.28 25.28 35.22 4.79
3172 4055 2.108075 TCCTCCCAAGAATTTGTGCAGA 59.892 45.455 0.00 0.00 32.21 4.26
3238 4121 3.084039 GAGAAGCAATGGACAATGGTCA 58.916 45.455 1.86 0.00 46.17 4.02
3264 4147 3.321682 TCCTTTTGCTCAAATCCAGGTTG 59.678 43.478 9.92 0.00 31.20 3.77
3284 4167 3.185246 TCAAATCTGAATCTCCGCTCC 57.815 47.619 0.00 0.00 0.00 4.70
3340 4223 1.986413 CTCCACCCCTCTTCCACTG 59.014 63.158 0.00 0.00 0.00 3.66
3352 4235 1.305718 AGAGGGACTGAGCTCCACC 60.306 63.158 12.15 11.46 41.55 4.61
3371 4254 0.698818 ACCATGAACAGGTTCCCCTC 59.301 55.000 9.49 0.00 39.89 4.30
3417 4300 6.092259 TCGCTCCAACTCTTTAATTTCTTAGC 59.908 38.462 0.00 0.00 0.00 3.09
3418 4301 7.413109 GGTCGCTCCAACTCTTTAATTTCTTAG 60.413 40.741 0.00 0.00 35.97 2.18
3419 4302 6.370718 GGTCGCTCCAACTCTTTAATTTCTTA 59.629 38.462 0.00 0.00 35.97 2.10
3420 4303 5.181433 GGTCGCTCCAACTCTTTAATTTCTT 59.819 40.000 0.00 0.00 35.97 2.52
3421 4304 4.695928 GGTCGCTCCAACTCTTTAATTTCT 59.304 41.667 0.00 0.00 35.97 2.52
3422 4305 4.435651 CGGTCGCTCCAACTCTTTAATTTC 60.436 45.833 0.00 0.00 35.57 2.17
3423 4306 3.435671 CGGTCGCTCCAACTCTTTAATTT 59.564 43.478 0.00 0.00 35.57 1.82
3424 4307 3.000727 CGGTCGCTCCAACTCTTTAATT 58.999 45.455 0.00 0.00 35.57 1.40
3425 4308 2.618053 CGGTCGCTCCAACTCTTTAAT 58.382 47.619 0.00 0.00 35.57 1.40
3426 4309 1.337447 CCGGTCGCTCCAACTCTTTAA 60.337 52.381 0.00 0.00 35.57 1.52
3427 4310 0.245539 CCGGTCGCTCCAACTCTTTA 59.754 55.000 0.00 0.00 35.57 1.85
3428 4311 1.004918 CCGGTCGCTCCAACTCTTT 60.005 57.895 0.00 0.00 35.57 2.52
3429 4312 2.207924 ACCGGTCGCTCCAACTCTT 61.208 57.895 0.00 0.00 35.57 2.85
3430 4313 2.600769 ACCGGTCGCTCCAACTCT 60.601 61.111 0.00 0.00 35.57 3.24
3431 4314 2.432628 CACCGGTCGCTCCAACTC 60.433 66.667 2.59 0.00 35.57 3.01
3432 4315 4.003788 CCACCGGTCGCTCCAACT 62.004 66.667 2.59 0.00 35.57 3.16
3433 4316 1.952102 TATCCACCGGTCGCTCCAAC 61.952 60.000 2.59 0.00 35.57 3.77
3434 4317 1.672854 CTATCCACCGGTCGCTCCAA 61.673 60.000 2.59 0.00 35.57 3.53
3435 4318 2.043752 TATCCACCGGTCGCTCCA 60.044 61.111 2.59 0.00 35.57 3.86
3436 4319 2.728817 CTATCCACCGGTCGCTCC 59.271 66.667 2.59 0.00 0.00 4.70
3437 4320 1.389609 TTCCTATCCACCGGTCGCTC 61.390 60.000 2.59 0.00 0.00 5.03
3438 4321 0.974010 TTTCCTATCCACCGGTCGCT 60.974 55.000 2.59 0.00 0.00 4.93
3439 4322 0.808847 GTTTCCTATCCACCGGTCGC 60.809 60.000 2.59 0.00 0.00 5.19
3440 4323 0.526954 CGTTTCCTATCCACCGGTCG 60.527 60.000 2.59 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.