Multiple sequence alignment - TraesCS2D01G000500

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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 TraesCS2D01G000500 chr2D 100.000 4119 0 0 842 4960 273562 277680 0.000000e+00 7607.0
1 TraesCS2D01G000500 chr2D 100.000 565 0 0 1 565 272721 273285 0.000000e+00 1044.0
2 TraesCS2D01G000500 chr2A 95.301 4171 94 40 842 4960 262278 258158 0.000000e+00 6523.0
3 TraesCS2D01G000500 chr2A 83.706 313 15 18 32 335 262815 262530 3.810000e-66 263.0
4 TraesCS2D01G000500 chr2A 93.519 108 3 1 446 549 262406 262299 1.850000e-34 158.0
5 TraesCS2D01G000500 chr2B 92.255 3809 113 58 978 4719 11076062 11079755 0.000000e+00 5232.0
6 TraesCS2D01G000500 chr2B 91.946 149 12 0 32 180 11075265 11075413 5.030000e-50 209.0
7 TraesCS2D01G000500 chr2B 95.455 66 3 0 219 284 11075411 11075476 6.790000e-19 106.0
8 TraesCS2D01G000500 chr2B 91.781 73 4 2 313 384 11075542 11075613 3.160000e-17 100.0
9 TraesCS2D01G000500 chr6B 80.228 526 93 9 1160 1678 704971903 704972424 7.790000e-103 385.0
10 TraesCS2D01G000500 chr6B 79.225 284 54 4 1178 1457 562489849 562489567 5.070000e-45 193.0
11 TraesCS2D01G000500 chr6B 100.000 28 0 0 2778 2805 632180649 632180622 9.000000e-03 52.8
12 TraesCS2D01G000500 chr6A 73.973 511 122 7 1178 1678 562688500 562687991 3.920000e-46 196.0
13 TraesCS2D01G000500 chr6A 79.152 283 56 2 1178 1457 517559719 517559437 5.070000e-45 193.0
14 TraesCS2D01G000500 chr6A 100.000 28 0 0 2778 2805 562686924 562686897 9.000000e-03 52.8
15 TraesCS2D01G000500 chr5D 71.783 443 113 12 1199 1635 2671159 2670723 1.130000e-21 115.0
16 TraesCS2D01G000500 chr6D 100.000 28 0 0 2778 2805 419267067 419267040 9.000000e-03 52.8


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 TraesCS2D01G000500 chr2D 272721 277680 4959 False 4325.500000 7607 100.00000 1 4960 2 chr2D.!!$F1 4959
1 TraesCS2D01G000500 chr2A 258158 262815 4657 True 2314.666667 6523 90.84200 32 4960 3 chr2A.!!$R1 4928
2 TraesCS2D01G000500 chr2B 11075265 11079755 4490 False 1411.750000 5232 92.85925 32 4719 4 chr2B.!!$F1 4687
3 TraesCS2D01G000500 chr6B 704971903 704972424 521 False 385.000000 385 80.22800 1160 1678 1 chr6B.!!$F1 518

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
871 1037 0.679321 CCTTCCTTCCTTGAGCCAGC 60.679 60.000 0.0 0.0 0.00 4.85 F
1413 1656 1.073199 CAAGTTCCTCACCGCCCTT 59.927 57.895 0.0 0.0 0.00 3.95 F
3103 3354 1.200716 CTTTGTGCGGAATGCTGTGAT 59.799 47.619 0.0 0.0 46.63 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2717 2960 2.224744 TGACTTATTTGGCTGGCAGACA 60.225 45.455 21.61 21.61 0.00 3.41 R
3201 3457 0.316204 AACAGCATGAACAAGCAGCC 59.684 50.000 0.00 0.00 39.69 4.85 R
4779 5105 0.393132 GGCGGGGAGGAAAGAAGAAG 60.393 60.000 0.00 0.00 0.00 2.85 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
19 20 1.763968 GGAAAGGGAAGGGAAATCGG 58.236 55.000 0.00 0.00 0.00 4.18
20 21 1.005569 GGAAAGGGAAGGGAAATCGGT 59.994 52.381 0.00 0.00 0.00 4.69
21 22 2.240414 GGAAAGGGAAGGGAAATCGGTA 59.760 50.000 0.00 0.00 0.00 4.02
22 23 3.542648 GAAAGGGAAGGGAAATCGGTAG 58.457 50.000 0.00 0.00 0.00 3.18
23 24 2.265526 AGGGAAGGGAAATCGGTAGT 57.734 50.000 0.00 0.00 0.00 2.73
24 25 3.409804 AGGGAAGGGAAATCGGTAGTA 57.590 47.619 0.00 0.00 0.00 1.82
25 26 3.306613 AGGGAAGGGAAATCGGTAGTAG 58.693 50.000 0.00 0.00 0.00 2.57
26 27 3.036819 GGGAAGGGAAATCGGTAGTAGT 58.963 50.000 0.00 0.00 0.00 2.73
27 28 4.078980 AGGGAAGGGAAATCGGTAGTAGTA 60.079 45.833 0.00 0.00 0.00 1.82
28 29 4.280425 GGGAAGGGAAATCGGTAGTAGTAG 59.720 50.000 0.00 0.00 0.00 2.57
29 30 4.280425 GGAAGGGAAATCGGTAGTAGTAGG 59.720 50.000 0.00 0.00 0.00 3.18
30 31 4.803329 AGGGAAATCGGTAGTAGTAGGA 57.197 45.455 0.00 0.00 0.00 2.94
65 66 8.424274 GATGAGAATCTCCTTTTCTCTTCTTC 57.576 38.462 7.91 6.41 46.03 2.87
66 67 6.706295 TGAGAATCTCCTTTTCTCTTCTTCC 58.294 40.000 7.91 0.00 46.03 3.46
76 83 6.206438 CCTTTTCTCTTCTTCCCTTCTTCTTG 59.794 42.308 0.00 0.00 0.00 3.02
182 210 4.554363 CCGGCGGTAGAGCTCGTG 62.554 72.222 19.97 0.51 37.29 4.35
184 212 4.874977 GGCGGTAGAGCTCGTGCC 62.875 72.222 20.35 20.35 40.80 5.01
186 214 4.554363 CGGTAGAGCTCGTGCCGG 62.554 72.222 27.26 15.32 40.80 6.13
187 215 3.138798 GGTAGAGCTCGTGCCGGA 61.139 66.667 5.05 0.00 40.80 5.14
188 216 2.409651 GTAGAGCTCGTGCCGGAG 59.590 66.667 5.05 0.00 40.80 4.63
189 217 2.113433 GTAGAGCTCGTGCCGGAGA 61.113 63.158 5.05 0.00 40.80 3.71
190 218 1.152943 TAGAGCTCGTGCCGGAGAT 60.153 57.895 5.05 0.00 40.80 2.75
191 219 0.752009 TAGAGCTCGTGCCGGAGATT 60.752 55.000 5.05 0.00 40.80 2.40
192 220 1.590259 GAGCTCGTGCCGGAGATTC 60.590 63.158 5.05 0.00 40.80 2.52
193 221 2.956964 GCTCGTGCCGGAGATTCG 60.957 66.667 5.05 1.34 36.08 3.34
194 222 2.956964 CTCGTGCCGGAGATTCGC 60.957 66.667 5.05 0.00 36.08 4.70
195 223 4.508128 TCGTGCCGGAGATTCGCC 62.508 66.667 5.05 0.00 0.00 5.54
196 224 4.514577 CGTGCCGGAGATTCGCCT 62.515 66.667 5.05 0.00 0.00 5.52
197 225 2.892425 GTGCCGGAGATTCGCCTG 60.892 66.667 5.05 0.00 0.00 4.85
198 226 4.838152 TGCCGGAGATTCGCCTGC 62.838 66.667 5.05 14.41 34.62 4.85
200 228 4.918201 CCGGAGATTCGCCTGCCC 62.918 72.222 0.00 0.00 0.00 5.36
201 229 3.854669 CGGAGATTCGCCTGCCCT 61.855 66.667 4.86 0.00 0.00 5.19
202 230 2.110006 GGAGATTCGCCTGCCCTC 59.890 66.667 0.00 0.00 0.00 4.30
203 231 2.110006 GAGATTCGCCTGCCCTCC 59.890 66.667 0.00 0.00 0.00 4.30
204 232 3.468326 GAGATTCGCCTGCCCTCCC 62.468 68.421 0.00 0.00 0.00 4.30
205 233 3.483869 GATTCGCCTGCCCTCCCT 61.484 66.667 0.00 0.00 0.00 4.20
206 234 3.468326 GATTCGCCTGCCCTCCCTC 62.468 68.421 0.00 0.00 0.00 4.30
216 244 4.806339 CCTCCCTCCCGGCCTCTT 62.806 72.222 0.00 0.00 0.00 2.85
217 245 3.157949 CTCCCTCCCGGCCTCTTC 61.158 72.222 0.00 0.00 0.00 2.87
218 246 4.798682 TCCCTCCCGGCCTCTTCC 62.799 72.222 0.00 0.00 0.00 3.46
219 247 4.806339 CCCTCCCGGCCTCTTCCT 62.806 72.222 0.00 0.00 0.00 3.36
225 253 3.532155 CGGCCTCTTCCTCCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
228 256 3.532155 CCTCTTCCTCCTCCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
335 400 8.202745 ACTACGACACTAGTATAAGTTGGTAC 57.797 38.462 0.00 0.00 0.00 3.34
384 449 5.163764 CGGATTTCGTTCCTGAATGAATTCA 60.164 40.000 24.04 11.26 43.43 2.57
386 451 5.371115 TTTCGTTCCTGAATGAATTCACC 57.629 39.130 11.07 6.51 43.43 4.02
387 452 3.343617 TCGTTCCTGAATGAATTCACCC 58.656 45.455 11.07 6.14 41.51 4.61
388 453 2.095853 CGTTCCTGAATGAATTCACCCG 59.904 50.000 11.07 2.47 41.51 5.28
389 454 3.343617 GTTCCTGAATGAATTCACCCGA 58.656 45.455 11.07 0.00 41.51 5.14
390 455 3.266510 TCCTGAATGAATTCACCCGAG 57.733 47.619 11.07 4.62 41.51 4.63
392 457 3.772572 TCCTGAATGAATTCACCCGAGTA 59.227 43.478 11.07 0.00 41.51 2.59
393 458 4.408921 TCCTGAATGAATTCACCCGAGTAT 59.591 41.667 11.07 0.00 41.51 2.12
394 459 4.512944 CCTGAATGAATTCACCCGAGTATG 59.487 45.833 11.07 0.00 41.51 2.39
395 460 4.450976 TGAATGAATTCACCCGAGTATGG 58.549 43.478 11.07 0.00 41.51 2.74
397 462 3.992943 TGAATTCACCCGAGTATGGTT 57.007 42.857 3.38 0.00 32.46 3.67
398 463 5.623956 ATGAATTCACCCGAGTATGGTTA 57.376 39.130 11.07 0.00 32.46 2.85
399 464 5.018539 TGAATTCACCCGAGTATGGTTAG 57.981 43.478 3.38 0.00 32.46 2.34
400 465 4.712829 TGAATTCACCCGAGTATGGTTAGA 59.287 41.667 3.38 0.00 32.46 2.10
401 466 5.188163 TGAATTCACCCGAGTATGGTTAGAA 59.812 40.000 3.38 0.00 32.46 2.10
402 467 5.687166 ATTCACCCGAGTATGGTTAGAAA 57.313 39.130 0.00 0.00 32.46 2.52
403 468 4.730949 TCACCCGAGTATGGTTAGAAAG 57.269 45.455 0.00 0.00 32.46 2.62
404 469 4.346730 TCACCCGAGTATGGTTAGAAAGA 58.653 43.478 0.00 0.00 32.46 2.52
405 470 4.773674 TCACCCGAGTATGGTTAGAAAGAA 59.226 41.667 0.00 0.00 32.46 2.52
406 471 5.246656 TCACCCGAGTATGGTTAGAAAGAAA 59.753 40.000 0.00 0.00 32.46 2.52
429 561 7.846101 AAGAATTTTGGTCAGAGGATTTCTT 57.154 32.000 0.00 0.00 32.41 2.52
430 562 7.459795 AGAATTTTGGTCAGAGGATTTCTTC 57.540 36.000 0.00 0.00 32.41 2.87
432 564 7.727634 AGAATTTTGGTCAGAGGATTTCTTCTT 59.272 33.333 0.00 0.00 32.41 2.52
436 568 5.799213 TGGTCAGAGGATTTCTTCTTTCTC 58.201 41.667 0.00 0.00 32.41 2.87
437 569 5.545723 TGGTCAGAGGATTTCTTCTTTCTCT 59.454 40.000 0.00 0.00 32.41 3.10
438 570 6.043706 TGGTCAGAGGATTTCTTCTTTCTCTT 59.956 38.462 0.00 0.00 32.41 2.85
439 571 6.593770 GGTCAGAGGATTTCTTCTTTCTCTTC 59.406 42.308 0.00 0.00 32.41 2.87
440 572 7.386059 GTCAGAGGATTTCTTCTTTCTCTTCT 58.614 38.462 0.00 0.00 32.41 2.85
443 575 9.369904 CAGAGGATTTCTTCTTTCTCTTCTTAG 57.630 37.037 0.00 0.00 32.41 2.18
557 715 5.408356 GCTTGAGCATTTGATTGACTTGAT 58.592 37.500 0.00 0.00 41.59 2.57
558 716 5.288712 GCTTGAGCATTTGATTGACTTGATG 59.711 40.000 0.00 0.00 41.59 3.07
559 717 4.740268 TGAGCATTTGATTGACTTGATGC 58.260 39.130 0.00 0.00 39.97 3.91
560 718 4.218852 TGAGCATTTGATTGACTTGATGCA 59.781 37.500 8.58 0.00 41.60 3.96
561 719 4.744570 AGCATTTGATTGACTTGATGCAG 58.255 39.130 8.58 0.00 41.60 4.41
562 720 4.461431 AGCATTTGATTGACTTGATGCAGA 59.539 37.500 8.58 0.00 41.60 4.26
563 721 4.798907 GCATTTGATTGACTTGATGCAGAG 59.201 41.667 0.00 0.00 39.58 3.35
564 722 4.430137 TTTGATTGACTTGATGCAGAGC 57.570 40.909 0.00 0.00 0.00 4.09
871 1037 0.679321 CCTTCCTTCCTTGAGCCAGC 60.679 60.000 0.00 0.00 0.00 4.85
875 1041 2.034687 TTCCTTGAGCCAGCCAGC 59.965 61.111 0.00 0.00 0.00 4.85
1413 1656 1.073199 CAAGTTCCTCACCGCCCTT 59.927 57.895 0.00 0.00 0.00 3.95
2951 3200 4.755411 TCTGTCTCGTCAGTTTTTCAGTT 58.245 39.130 0.00 0.00 36.85 3.16
2952 3201 5.175859 TCTGTCTCGTCAGTTTTTCAGTTT 58.824 37.500 0.00 0.00 36.85 2.66
2953 3202 5.291128 TCTGTCTCGTCAGTTTTTCAGTTTC 59.709 40.000 0.00 0.00 36.85 2.78
2956 3205 6.148811 TGTCTCGTCAGTTTTTCAGTTTCTTT 59.851 34.615 0.00 0.00 0.00 2.52
3013 3264 9.489084 CAGGCTAGCATGTAGTTACAATTATTA 57.511 33.333 20.93 0.00 39.99 0.98
3080 3331 1.805254 CTGGATTTTCCTGCCAGCG 59.195 57.895 0.00 0.00 42.30 5.18
3103 3354 1.200716 CTTTGTGCGGAATGCTGTGAT 59.799 47.619 0.00 0.00 46.63 3.06
3150 3401 6.754193 TCAAACTGGGCGAAATAAGATTTTT 58.246 32.000 0.00 0.00 0.00 1.94
3227 3483 4.337836 TGCTTGTTCATGCTGTTGAAACTA 59.662 37.500 10.95 0.00 37.36 2.24
3228 3484 4.913924 GCTTGTTCATGCTGTTGAAACTAG 59.086 41.667 3.91 0.00 37.36 2.57
3229 3485 5.506317 GCTTGTTCATGCTGTTGAAACTAGT 60.506 40.000 0.00 0.00 37.36 2.57
3256 3512 2.164827 TGAACATGATGTGATTGGCTGC 59.835 45.455 0.00 0.00 0.00 5.25
3298 3554 9.940166 TTGTTTTCGGTAACTATCTTTTTCTTC 57.060 29.630 3.00 0.00 0.00 2.87
3707 3966 0.111061 AGTGCATGACCTCCTTTGCA 59.889 50.000 0.00 0.00 42.41 4.08
3996 4267 7.496920 TCTTGATAGATTGTTGTAGCTTGATGG 59.503 37.037 0.00 0.00 0.00 3.51
4009 4280 2.952310 GCTTGATGGGTAGTTGATTCCC 59.048 50.000 0.00 0.00 41.41 3.97
4328 4615 0.670162 CTAGCAGAGCAGAGGAGAGC 59.330 60.000 0.00 0.00 0.00 4.09
4329 4616 0.033699 TAGCAGAGCAGAGGAGAGCA 60.034 55.000 0.00 0.00 0.00 4.26
4330 4617 1.142314 GCAGAGCAGAGGAGAGCAG 59.858 63.158 0.00 0.00 0.00 4.24
4331 4618 1.321805 GCAGAGCAGAGGAGAGCAGA 61.322 60.000 0.00 0.00 0.00 4.26
4372 4659 0.112218 TGGTCCAGTGAATTGGGGTG 59.888 55.000 0.00 0.00 38.81 4.61
4373 4660 1.250840 GGTCCAGTGAATTGGGGTGC 61.251 60.000 0.00 0.00 38.81 5.01
4584 4892 8.522542 AGACCTACTAGTAGTACAAAGGAATG 57.477 38.462 24.84 10.09 0.00 2.67
4590 4898 8.890410 ACTAGTAGTACAAAGGAATGTTAGGA 57.110 34.615 0.00 0.00 34.75 2.94
4591 4899 8.968969 ACTAGTAGTACAAAGGAATGTTAGGAG 58.031 37.037 0.00 0.00 34.75 3.69
4593 4901 6.729569 AGTAGTACAAAGGAATGTTAGGAGGT 59.270 38.462 2.52 0.00 34.75 3.85
4594 4902 5.805728 AGTACAAAGGAATGTTAGGAGGTG 58.194 41.667 0.00 0.00 34.75 4.00
4595 4903 4.724279 ACAAAGGAATGTTAGGAGGTGT 57.276 40.909 0.00 0.00 0.00 4.16
4597 4905 5.805728 ACAAAGGAATGTTAGGAGGTGTAG 58.194 41.667 0.00 0.00 0.00 2.74
4598 4906 5.546499 ACAAAGGAATGTTAGGAGGTGTAGA 59.454 40.000 0.00 0.00 0.00 2.59
4599 4907 6.043938 ACAAAGGAATGTTAGGAGGTGTAGAA 59.956 38.462 0.00 0.00 0.00 2.10
4758 5084 0.110486 GGAGACACTTGGCAAAGGGA 59.890 55.000 10.97 0.00 39.36 4.20
4792 5118 6.701145 AAAAACACCTCTTCTTCTTTCCTC 57.299 37.500 0.00 0.00 0.00 3.71
4793 5119 4.359434 AACACCTCTTCTTCTTTCCTCC 57.641 45.455 0.00 0.00 0.00 4.30
4794 5120 2.640332 ACACCTCTTCTTCTTTCCTCCC 59.360 50.000 0.00 0.00 0.00 4.30
4795 5121 2.026729 CACCTCTTCTTCTTTCCTCCCC 60.027 54.545 0.00 0.00 0.00 4.81
4796 5122 1.208293 CCTCTTCTTCTTTCCTCCCCG 59.792 57.143 0.00 0.00 0.00 5.73
4801 5127 2.258748 CTTCTTTCCTCCCCGCCTCC 62.259 65.000 0.00 0.00 0.00 4.30
4827 5153 2.964039 TCCTCCTCCCCCATCCCA 60.964 66.667 0.00 0.00 0.00 4.37
4901 5241 0.531200 AAGGTCCTTGTCGTCGATCC 59.469 55.000 2.38 0.00 0.00 3.36
4918 5258 1.552578 TCCGTCGAATCCTCCTCAAA 58.447 50.000 0.00 0.00 0.00 2.69
4921 5261 1.067142 CGTCGAATCCTCCTCAAACCA 60.067 52.381 0.00 0.00 0.00 3.67
4926 5266 2.698855 ATCCTCCTCAAACCATCACG 57.301 50.000 0.00 0.00 0.00 4.35
4932 5272 2.028476 TCCTCAAACCATCACGACGATT 60.028 45.455 0.00 0.00 29.21 3.34
4935 5275 1.060553 CAAACCATCACGACGATTCCG 59.939 52.381 0.00 0.00 42.50 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.005569 ACCGATTTCCCTTCCCTTTCC 59.994 52.381 0.00 0.00 0.00 3.13
1 2 2.509166 ACCGATTTCCCTTCCCTTTC 57.491 50.000 0.00 0.00 0.00 2.62
2 3 2.917600 ACTACCGATTTCCCTTCCCTTT 59.082 45.455 0.00 0.00 0.00 3.11
3 4 2.558974 ACTACCGATTTCCCTTCCCTT 58.441 47.619 0.00 0.00 0.00 3.95
4 5 2.265526 ACTACCGATTTCCCTTCCCT 57.734 50.000 0.00 0.00 0.00 4.20
5 6 3.036819 ACTACTACCGATTTCCCTTCCC 58.963 50.000 0.00 0.00 0.00 3.97
6 7 4.280425 CCTACTACTACCGATTTCCCTTCC 59.720 50.000 0.00 0.00 0.00 3.46
7 8 5.136105 TCCTACTACTACCGATTTCCCTTC 58.864 45.833 0.00 0.00 0.00 3.46
8 9 5.134725 TCCTACTACTACCGATTTCCCTT 57.865 43.478 0.00 0.00 0.00 3.95
9 10 4.447470 CCTCCTACTACTACCGATTTCCCT 60.447 50.000 0.00 0.00 0.00 4.20
10 11 3.825585 CCTCCTACTACTACCGATTTCCC 59.174 52.174 0.00 0.00 0.00 3.97
11 12 4.723309 TCCTCCTACTACTACCGATTTCC 58.277 47.826 0.00 0.00 0.00 3.13
12 13 4.761227 CCTCCTCCTACTACTACCGATTTC 59.239 50.000 0.00 0.00 0.00 2.17
13 14 4.414846 TCCTCCTCCTACTACTACCGATTT 59.585 45.833 0.00 0.00 0.00 2.17
14 15 3.979347 TCCTCCTCCTACTACTACCGATT 59.021 47.826 0.00 0.00 0.00 3.34
15 16 3.583966 CTCCTCCTCCTACTACTACCGAT 59.416 52.174 0.00 0.00 0.00 4.18
16 17 2.971330 CTCCTCCTCCTACTACTACCGA 59.029 54.545 0.00 0.00 0.00 4.69
17 18 2.038820 CCTCCTCCTCCTACTACTACCG 59.961 59.091 0.00 0.00 0.00 4.02
18 19 3.325605 TCCTCCTCCTCCTACTACTACC 58.674 54.545 0.00 0.00 0.00 3.18
19 20 4.233729 TCTCCTCCTCCTCCTACTACTAC 58.766 52.174 0.00 0.00 0.00 2.73
20 21 4.573059 TCTCCTCCTCCTCCTACTACTA 57.427 50.000 0.00 0.00 0.00 1.82
21 22 3.441505 TCTCCTCCTCCTCCTACTACT 57.558 52.381 0.00 0.00 0.00 2.57
22 23 3.653836 TCATCTCCTCCTCCTCCTACTAC 59.346 52.174 0.00 0.00 0.00 2.73
23 24 3.913799 CTCATCTCCTCCTCCTCCTACTA 59.086 52.174 0.00 0.00 0.00 1.82
24 25 2.716424 CTCATCTCCTCCTCCTCCTACT 59.284 54.545 0.00 0.00 0.00 2.57
25 26 2.714250 TCTCATCTCCTCCTCCTCCTAC 59.286 54.545 0.00 0.00 0.00 3.18
26 27 3.082116 TCTCATCTCCTCCTCCTCCTA 57.918 52.381 0.00 0.00 0.00 2.94
27 28 1.919933 TCTCATCTCCTCCTCCTCCT 58.080 55.000 0.00 0.00 0.00 3.69
28 29 2.765689 TTCTCATCTCCTCCTCCTCC 57.234 55.000 0.00 0.00 0.00 4.30
29 30 4.118168 AGATTCTCATCTCCTCCTCCTC 57.882 50.000 0.00 0.00 34.26 3.71
63 64 3.864789 AGAGCAACAAGAAGAAGGGAA 57.135 42.857 0.00 0.00 0.00 3.97
64 65 3.864789 AAGAGCAACAAGAAGAAGGGA 57.135 42.857 0.00 0.00 0.00 4.20
65 66 3.005155 CCAAAGAGCAACAAGAAGAAGGG 59.995 47.826 0.00 0.00 0.00 3.95
66 67 3.885297 TCCAAAGAGCAACAAGAAGAAGG 59.115 43.478 0.00 0.00 0.00 3.46
76 83 0.804989 CGGTGGATCCAAAGAGCAAC 59.195 55.000 18.20 0.45 35.57 4.17
183 211 4.918201 GGGCAGGCGAATCTCCGG 62.918 72.222 0.00 0.00 0.00 5.14
184 212 3.798954 GAGGGCAGGCGAATCTCCG 62.799 68.421 0.00 0.00 0.00 4.63
185 213 2.110006 GAGGGCAGGCGAATCTCC 59.890 66.667 0.00 0.00 0.00 3.71
186 214 2.110006 GGAGGGCAGGCGAATCTC 59.890 66.667 0.00 0.00 0.00 2.75
187 215 3.483869 GGGAGGGCAGGCGAATCT 61.484 66.667 0.00 0.00 0.00 2.40
188 216 3.468326 GAGGGAGGGCAGGCGAATC 62.468 68.421 0.00 0.00 0.00 2.52
189 217 3.483869 GAGGGAGGGCAGGCGAAT 61.484 66.667 0.00 0.00 0.00 3.34
204 232 3.157949 GGAGGAAGAGGCCGGGAG 61.158 72.222 2.18 0.00 0.00 4.30
205 233 3.680920 GAGGAGGAAGAGGCCGGGA 62.681 68.421 2.18 0.00 0.00 5.14
206 234 3.157949 GAGGAGGAAGAGGCCGGG 61.158 72.222 2.18 0.00 0.00 5.73
207 235 3.157949 GGAGGAGGAAGAGGCCGG 61.158 72.222 0.00 0.00 0.00 6.13
208 236 3.532155 CGGAGGAGGAAGAGGCCG 61.532 72.222 0.00 0.00 0.00 6.13
209 237 3.855853 GCGGAGGAGGAAGAGGCC 61.856 72.222 0.00 0.00 0.00 5.19
210 238 3.855853 GGCGGAGGAGGAAGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
211 239 3.532155 CGGCGGAGGAGGAAGAGG 61.532 72.222 0.00 0.00 0.00 3.69
212 240 4.214327 GCGGCGGAGGAGGAAGAG 62.214 72.222 9.78 0.00 0.00 2.85
234 262 2.224548 ACATCCCTTATTAAGCGGAGGC 60.225 50.000 17.89 0.00 34.87 4.70
314 342 7.226325 AGCTAGTACCAACTTATACTAGTGTCG 59.774 40.741 5.39 0.00 46.79 4.35
384 449 5.482878 TCTTTCTTTCTAACCATACTCGGGT 59.517 40.000 0.00 0.00 41.41 5.28
386 451 8.494016 AATTCTTTCTTTCTAACCATACTCGG 57.506 34.615 0.00 0.00 0.00 4.63
392 457 8.923270 TGACCAAAATTCTTTCTTTCTAACCAT 58.077 29.630 0.00 0.00 0.00 3.55
393 458 8.299990 TGACCAAAATTCTTTCTTTCTAACCA 57.700 30.769 0.00 0.00 0.00 3.67
394 459 8.630037 TCTGACCAAAATTCTTTCTTTCTAACC 58.370 33.333 0.00 0.00 0.00 2.85
395 460 9.670719 CTCTGACCAAAATTCTTTCTTTCTAAC 57.329 33.333 0.00 0.00 0.00 2.34
397 462 8.217799 TCCTCTGACCAAAATTCTTTCTTTCTA 58.782 33.333 0.00 0.00 0.00 2.10
398 463 7.062957 TCCTCTGACCAAAATTCTTTCTTTCT 58.937 34.615 0.00 0.00 0.00 2.52
399 464 7.277174 TCCTCTGACCAAAATTCTTTCTTTC 57.723 36.000 0.00 0.00 0.00 2.62
400 465 7.846101 ATCCTCTGACCAAAATTCTTTCTTT 57.154 32.000 0.00 0.00 0.00 2.52
401 466 7.846101 AATCCTCTGACCAAAATTCTTTCTT 57.154 32.000 0.00 0.00 0.00 2.52
402 467 7.727634 AGAAATCCTCTGACCAAAATTCTTTCT 59.272 33.333 0.00 0.00 31.12 2.52
403 468 7.890515 AGAAATCCTCTGACCAAAATTCTTTC 58.109 34.615 0.00 0.00 31.12 2.62
404 469 7.846101 AGAAATCCTCTGACCAAAATTCTTT 57.154 32.000 0.00 0.00 31.12 2.52
405 470 7.727634 AGAAGAAATCCTCTGACCAAAATTCTT 59.272 33.333 0.00 0.00 37.32 2.52
406 471 7.237255 AGAAGAAATCCTCTGACCAAAATTCT 58.763 34.615 0.00 0.00 33.37 2.40
429 561 8.133024 AGCAAGAAGATCTAAGAAGAGAAAGA 57.867 34.615 0.00 0.00 34.49 2.52
430 562 8.776376 AAGCAAGAAGATCTAAGAAGAGAAAG 57.224 34.615 0.00 0.00 34.49 2.62
432 564 9.213799 GAAAAGCAAGAAGATCTAAGAAGAGAA 57.786 33.333 0.00 0.00 34.49 2.87
436 568 8.321650 ACAGAAAAGCAAGAAGATCTAAGAAG 57.678 34.615 0.00 0.00 0.00 2.85
437 569 8.682936 AACAGAAAAGCAAGAAGATCTAAGAA 57.317 30.769 0.00 0.00 0.00 2.52
438 570 8.682936 AAACAGAAAAGCAAGAAGATCTAAGA 57.317 30.769 0.00 0.00 0.00 2.10
439 571 8.782144 AGAAACAGAAAAGCAAGAAGATCTAAG 58.218 33.333 0.00 0.00 0.00 2.18
440 572 8.682936 AGAAACAGAAAAGCAAGAAGATCTAA 57.317 30.769 0.00 0.00 0.00 2.10
443 575 8.563732 AGTAAGAAACAGAAAAGCAAGAAGATC 58.436 33.333 0.00 0.00 0.00 2.75
483 615 5.386060 TCTTTCTTTCTTTTTCCCTCCCTC 58.614 41.667 0.00 0.00 0.00 4.30
871 1037 0.037512 CTGACTGACTGACTGGCTGG 60.038 60.000 0.00 0.00 0.00 4.85
875 1041 1.336702 GCTGACTGACTGACTGACTGG 60.337 57.143 0.00 0.00 0.00 4.00
1413 1656 4.373116 GCGGTGGCGAAGGAGACA 62.373 66.667 0.00 0.00 0.00 3.41
2717 2960 2.224744 TGACTTATTTGGCTGGCAGACA 60.225 45.455 21.61 21.61 0.00 3.41
2864 3113 9.288576 CTTCAATAAGCATGGAGTCCAATAATA 57.711 33.333 17.71 8.16 36.95 0.98
2865 3114 8.000709 TCTTCAATAAGCATGGAGTCCAATAAT 58.999 33.333 17.71 6.06 32.77 1.28
2866 3115 7.345691 TCTTCAATAAGCATGGAGTCCAATAA 58.654 34.615 17.71 0.58 32.77 1.40
2973 3222 5.183228 TGCTAGCCTGAATGTTTAGTTACC 58.817 41.667 13.29 0.00 0.00 2.85
3039 3290 9.912634 CCAGTGTAATTTGACAGTTTCATAATT 57.087 29.630 0.00 0.00 32.84 1.40
3080 3331 1.535462 ACAGCATTCCGCACAAAGTAC 59.465 47.619 0.00 0.00 46.13 2.73
3103 3354 3.324846 ACCACAGTCAAGTGCTGAAGATA 59.675 43.478 8.94 0.00 38.18 1.98
3195 3449 3.129988 AGCATGAACAAGCAGCCTAAATC 59.870 43.478 0.00 0.00 0.00 2.17
3201 3457 0.316204 AACAGCATGAACAAGCAGCC 59.684 50.000 0.00 0.00 39.69 4.85
3227 3483 7.012704 GCCAATCACATCATGTTCACTAATACT 59.987 37.037 0.00 0.00 0.00 2.12
3228 3484 7.012704 AGCCAATCACATCATGTTCACTAATAC 59.987 37.037 0.00 0.00 0.00 1.89
3229 3485 7.012610 CAGCCAATCACATCATGTTCACTAATA 59.987 37.037 0.00 0.00 0.00 0.98
3256 3512 3.369546 AACAAGCACCGGAATTCTTTG 57.630 42.857 9.46 6.40 0.00 2.77
3298 3554 2.606725 GAGGAATGAACTGATGAGCACG 59.393 50.000 0.00 0.00 0.00 5.34
3557 3816 3.458118 TGAAGTTGGGGATCGGTGATAAT 59.542 43.478 0.00 0.00 0.00 1.28
3848 4107 3.980989 CGGTCCCGGACGTTGTCA 61.981 66.667 11.55 0.00 33.68 3.58
3933 4192 4.991153 TGTGCTGAAGGACTCTATACAG 57.009 45.455 3.55 0.00 37.28 2.74
3996 4267 5.183228 TCGATCAAAAGGGAATCAACTACC 58.817 41.667 0.00 0.00 0.00 3.18
4009 4280 5.505173 AACCTGGCATAATCGATCAAAAG 57.495 39.130 0.00 0.00 0.00 2.27
4327 4614 4.272991 CCAGATTAGAAGCATCTTGTCTGC 59.727 45.833 19.59 0.00 40.74 4.26
4328 4615 5.426504 ACCAGATTAGAAGCATCTTGTCTG 58.573 41.667 18.70 18.70 41.20 3.51
4329 4616 5.424895 AGACCAGATTAGAAGCATCTTGTCT 59.575 40.000 10.31 10.31 43.76 3.41
4330 4617 5.523188 CAGACCAGATTAGAAGCATCTTGTC 59.477 44.000 0.00 2.16 40.98 3.18
4331 4618 5.426504 CAGACCAGATTAGAAGCATCTTGT 58.573 41.667 0.00 0.00 37.10 3.16
4372 4659 1.070601 AGCCACCAAACCAAATCAAGC 59.929 47.619 0.00 0.00 0.00 4.01
4373 4660 2.758009 CAGCCACCAAACCAAATCAAG 58.242 47.619 0.00 0.00 0.00 3.02
4538 4836 9.713713 AGGTCTTTATCTTTCTTTCTACAAGAC 57.286 33.333 0.00 0.00 37.80 3.01
4566 4874 8.414778 CCTCCTAACATTCCTTTGTACTACTAG 58.585 40.741 0.00 0.00 0.00 2.57
4584 4892 9.010029 TCATTCAAATTTTCTACACCTCCTAAC 57.990 33.333 0.00 0.00 0.00 2.34
4589 4897 7.875971 ACACTCATTCAAATTTTCTACACCTC 58.124 34.615 0.00 0.00 0.00 3.85
4590 4898 7.823745 ACACTCATTCAAATTTTCTACACCT 57.176 32.000 0.00 0.00 0.00 4.00
4591 4899 9.612620 CTAACACTCATTCAAATTTTCTACACC 57.387 33.333 0.00 0.00 0.00 4.16
4593 4901 9.567776 TCCTAACACTCATTCAAATTTTCTACA 57.432 29.630 0.00 0.00 0.00 2.74
4595 4903 9.231297 CCTCCTAACACTCATTCAAATTTTCTA 57.769 33.333 0.00 0.00 0.00 2.10
4597 4905 7.809806 CACCTCCTAACACTCATTCAAATTTTC 59.190 37.037 0.00 0.00 0.00 2.29
4598 4906 7.287696 ACACCTCCTAACACTCATTCAAATTTT 59.712 33.333 0.00 0.00 0.00 1.82
4599 4907 6.777580 ACACCTCCTAACACTCATTCAAATTT 59.222 34.615 0.00 0.00 0.00 1.82
4774 5100 2.026729 GGGGAGGAAAGAAGAAGAGGTG 60.027 54.545 0.00 0.00 0.00 4.00
4775 5101 2.270858 GGGGAGGAAAGAAGAAGAGGT 58.729 52.381 0.00 0.00 0.00 3.85
4776 5102 1.208293 CGGGGAGGAAAGAAGAAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
4777 5103 1.406205 GCGGGGAGGAAAGAAGAAGAG 60.406 57.143 0.00 0.00 0.00 2.85
4778 5104 0.613777 GCGGGGAGGAAAGAAGAAGA 59.386 55.000 0.00 0.00 0.00 2.87
4779 5105 0.393132 GGCGGGGAGGAAAGAAGAAG 60.393 60.000 0.00 0.00 0.00 2.85
4780 5106 0.840722 AGGCGGGGAGGAAAGAAGAA 60.841 55.000 0.00 0.00 0.00 2.52
4781 5107 1.229529 AGGCGGGGAGGAAAGAAGA 60.230 57.895 0.00 0.00 0.00 2.87
4782 5108 1.222113 GAGGCGGGGAGGAAAGAAG 59.778 63.158 0.00 0.00 0.00 2.85
4783 5109 2.298661 GGAGGCGGGGAGGAAAGAA 61.299 63.158 0.00 0.00 0.00 2.52
4784 5110 2.687566 GGAGGCGGGGAGGAAAGA 60.688 66.667 0.00 0.00 0.00 2.52
4785 5111 2.689034 AGGAGGCGGGGAGGAAAG 60.689 66.667 0.00 0.00 0.00 2.62
4786 5112 2.687566 GAGGAGGCGGGGAGGAAA 60.688 66.667 0.00 0.00 0.00 3.13
4787 5113 3.684628 AGAGGAGGCGGGGAGGAA 61.685 66.667 0.00 0.00 0.00 3.36
4788 5114 4.465446 CAGAGGAGGCGGGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
4794 5120 3.535962 GAGAGGCAGAGGAGGCGG 61.536 72.222 0.00 0.00 39.37 6.13
4795 5121 3.535962 GGAGAGGCAGAGGAGGCG 61.536 72.222 0.00 0.00 39.37 5.52
4796 5122 2.042025 AGGAGAGGCAGAGGAGGC 60.042 66.667 0.00 0.00 0.00 4.70
4801 5127 1.457455 GGGAGGAGGAGAGGCAGAG 60.457 68.421 0.00 0.00 0.00 3.35
4875 5214 1.299976 GACAAGGACCTTCGGCCAT 59.700 57.895 2.91 0.00 0.00 4.40
4901 5241 1.067142 TGGTTTGAGGAGGATTCGACG 60.067 52.381 0.00 0.00 0.00 5.12
4918 5258 1.518572 GCGGAATCGTCGTGATGGT 60.519 57.895 0.00 0.00 37.39 3.55
4921 5261 1.065928 GAGGCGGAATCGTCGTGAT 59.934 57.895 0.00 0.00 46.91 3.06
4926 5266 2.417936 GGGAGAGGCGGAATCGTC 59.582 66.667 0.00 0.00 42.03 4.20


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

AutoCloner maintained by Alex Coulton.