Multiple sequence alignment - TraesCS1D01G105600

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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 TraesCS1D01G105600 chr1D 100.000 5444 0 0 1 5444 97540112 97534669 0.000000e+00 10054
1 TraesCS1D01G105600 chr1B 91.212 2401 130 45 2564 4899 155739653 155742037 0.000000e+00 3190
2 TraesCS1D01G105600 chr1B 96.835 1738 44 4 364 2098 155737213 155738942 0.000000e+00 2894
3 TraesCS1D01G105600 chr1B 88.831 385 19 10 1 364 155736005 155736386 8.320000e-123 451
4 TraesCS1D01G105600 chr1B 93.370 181 7 2 2134 2314 155738941 155739116 4.180000e-66 263
5 TraesCS1D01G105600 chr1B 85.845 219 17 7 5021 5232 155743264 155743475 2.550000e-53 220
6 TraesCS1D01G105600 chr1B 89.051 137 9 1 5224 5360 155744136 155744266 1.210000e-36 165
7 TraesCS1D01G105600 chr1B 94.382 89 5 0 5356 5444 155746572 155746660 2.640000e-28 137
8 TraesCS1D01G105600 chr1B 97.368 76 2 0 4897 4972 155742063 155742138 4.430000e-26 130
9 TraesCS1D01G105600 chr1A 95.301 1745 55 17 650 2385 92574700 92572974 0.000000e+00 2743
10 TraesCS1D01G105600 chr1A 95.939 1256 30 9 2564 3808 92572817 92571572 0.000000e+00 2017
11 TraesCS1D01G105600 chr1A 89.011 1092 69 23 3840 4886 92571583 92570498 0.000000e+00 1304
12 TraesCS1D01G105600 chr1A 91.682 553 32 5 1 539 92575252 92574700 0.000000e+00 754
13 TraesCS1D01G105600 chrUn 98.496 133 2 0 2435 2567 17025390 17025258 9.120000e-58 235
14 TraesCS1D01G105600 chrUn 98.496 133 2 0 2435 2567 17027623 17027491 9.120000e-58 235
15 TraesCS1D01G105600 chrUn 98.496 133 2 0 2435 2567 292131056 292131188 9.120000e-58 235
16 TraesCS1D01G105600 chrUn 98.496 133 2 0 2435 2567 302852126 302852258 9.120000e-58 235
17 TraesCS1D01G105600 chrUn 98.496 133 2 0 2435 2567 302859429 302859297 9.120000e-58 235
18 TraesCS1D01G105600 chr3A 99.219 128 1 0 2439 2566 182282824 182282951 1.180000e-56 231
19 TraesCS1D01G105600 chr3B 96.992 133 4 0 2435 2567 17593616 17593484 1.970000e-54 224
20 TraesCS1D01G105600 chr7A 95.000 140 7 0 2440 2579 59200258 59200119 2.550000e-53 220
21 TraesCS1D01G105600 chr4A 94.406 143 7 1 2424 2566 200095995 200095854 9.180000e-53 219


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 TraesCS1D01G105600 chr1D 97534669 97540112 5443 True 10054.00 10054 100.00000 1 5444 1 chr1D.!!$R1 5443
1 TraesCS1D01G105600 chr1B 155736005 155746660 10655 False 931.25 3190 92.11175 1 5444 8 chr1B.!!$F1 5443
2 TraesCS1D01G105600 chr1A 92570498 92575252 4754 True 1704.50 2743 92.98325 1 4886 4 chr1A.!!$R1 4885
3 TraesCS1D01G105600 chrUn 17025258 17027623 2365 True 235.00 235 98.49600 2435 2567 2 chrUn.!!$R2 132

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
304 327 0.320683 TTCTGTGCCATGGACTGTCG 60.321 55.000 18.40 0.0 0.00 4.35 F
834 1688 0.604511 GGTTTGGACCACCACTACCG 60.605 60.000 0.00 0.0 46.80 4.02 F
1017 1871 2.361119 GCAGATGGATGCATGTGATTGT 59.639 45.455 25.55 0.0 45.77 2.71 F
1467 2321 3.118629 TCACACATGAGATAAGGAGCACC 60.119 47.826 0.00 0.0 0.00 5.01 F
2399 3683 3.274288 GTTTCCTCCTGGCACTAATGAG 58.726 50.000 0.00 0.0 0.00 2.90 F
3167 6143 4.003648 GCTGCCTTTACAGATGTAAGTGT 58.996 43.478 5.63 0.0 41.03 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 2195 1.040646 ACCTCTCTCGCAACTTCACA 58.959 50.000 0.00 0.0 0.00 3.58 R
1876 2730 3.675775 GCAACAACTTCAACAAGCTCCAA 60.676 43.478 0.00 0.0 32.09 3.53 R
2874 5739 1.138459 CTCTCGACGTGCTGCATCT 59.862 57.895 5.27 0.0 0.00 2.90 R
3060 6036 5.821516 AAACATCGTTGGTCAAAGTTACA 57.178 34.783 0.00 0.0 0.00 2.41 R
3472 6448 0.105039 GAAGCATACGGGTCCCTCAG 59.895 60.000 6.29 0.0 0.00 3.35 R
5090 9274 0.037734 GATGAAGGTCCACCCGGTTT 59.962 55.000 0.00 0.0 38.74 3.27 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
83 85 4.961511 TGCCGCGTCGTCTTGCTT 62.962 61.111 4.92 0.00 0.00 3.91
198 202 3.002791 TCAAGCAGTCAAGCTATTTCGG 58.997 45.455 0.00 0.00 45.89 4.30
237 242 6.690194 ATCTCAAGCAGTTTGATAATGACC 57.310 37.500 0.00 0.00 44.48 4.02
238 243 5.809001 TCTCAAGCAGTTTGATAATGACCT 58.191 37.500 0.00 0.00 44.48 3.85
239 244 5.645067 TCTCAAGCAGTTTGATAATGACCTG 59.355 40.000 0.00 0.00 44.48 4.00
240 245 4.156556 TCAAGCAGTTTGATAATGACCTGC 59.843 41.667 0.00 0.00 40.82 4.85
279 291 2.969628 TCAATTTGGGTTGGGTCATGT 58.030 42.857 0.00 0.00 0.00 3.21
304 327 0.320683 TTCTGTGCCATGGACTGTCG 60.321 55.000 18.40 0.00 0.00 4.35
312 335 5.245075 TGTGCCATGGACTGTCGATATAATA 59.755 40.000 18.40 0.00 0.00 0.98
423 1273 3.697045 CAGGGTCAAAGTGTGGTGTTTAA 59.303 43.478 0.00 0.00 0.00 1.52
431 1281 5.821516 AAGTGTGGTGTTTAATTTCACGA 57.178 34.783 0.00 0.00 35.67 4.35
499 1352 6.657541 TCTTTTTCACTAGTGTCTTTGTTGGT 59.342 34.615 21.99 0.00 0.00 3.67
508 1361 5.747342 AGTGTCTTTGTTGGTAGGTGTAAA 58.253 37.500 0.00 0.00 0.00 2.01
517 1370 7.499321 TGTTGGTAGGTGTAAATTAGTGTTG 57.501 36.000 0.00 0.00 0.00 3.33
590 1444 9.746457 ATCCTTACTTCTAAATTTTCTTCTGCT 57.254 29.630 0.00 0.00 0.00 4.24
596 1450 7.285401 ACTTCTAAATTTTCTTCTGCTTGGTGA 59.715 33.333 0.00 0.00 0.00 4.02
605 1459 1.270826 TCTGCTTGGTGAGAGAAGACG 59.729 52.381 0.00 0.00 0.00 4.18
611 1465 2.525368 TGGTGAGAGAAGACGGATTGA 58.475 47.619 0.00 0.00 0.00 2.57
616 1470 5.064071 GGTGAGAGAAGACGGATTGAAAATC 59.936 44.000 0.00 0.00 0.00 2.17
623 1477 1.597663 ACGGATTGAAAATCGCGATCC 59.402 47.619 23.92 16.99 41.16 3.36
625 1479 2.222027 GGATTGAAAATCGCGATCCCT 58.778 47.619 23.92 9.72 39.45 4.20
663 1517 5.651139 ACCAGCTAGAGTTTATTCGTGTAGA 59.349 40.000 0.00 0.00 0.00 2.59
767 1621 9.774742 CTTGACTGTATTTTTCATAGCTTAACC 57.225 33.333 0.00 0.00 0.00 2.85
768 1622 8.276252 TGACTGTATTTTTCATAGCTTAACCC 57.724 34.615 0.00 0.00 0.00 4.11
834 1688 0.604511 GGTTTGGACCACCACTACCG 60.605 60.000 0.00 0.00 46.80 4.02
1017 1871 2.361119 GCAGATGGATGCATGTGATTGT 59.639 45.455 25.55 0.00 45.77 2.71
1333 2187 4.096833 TGCTTGTGCACATAATTCCTGATC 59.903 41.667 22.39 0.00 45.31 2.92
1341 2195 5.587844 GCACATAATTCCTGATCTGTTGAGT 59.412 40.000 0.00 0.00 0.00 3.41
1467 2321 3.118629 TCACACATGAGATAAGGAGCACC 60.119 47.826 0.00 0.00 0.00 5.01
1635 2489 6.823689 GCTTAGTTGTTCCTATCAATCTTCCA 59.176 38.462 0.00 0.00 0.00 3.53
2099 2968 8.190122 TCAATGGATAAATGTGTATGCTTTGTC 58.810 33.333 8.91 0.00 37.78 3.18
2122 2991 8.204160 TGTCTGTGAATAAGAGTTTTGAAGAGA 58.796 33.333 0.00 0.00 0.00 3.10
2123 2992 9.046296 GTCTGTGAATAAGAGTTTTGAAGAGAA 57.954 33.333 0.00 0.00 0.00 2.87
2124 2993 9.784531 TCTGTGAATAAGAGTTTTGAAGAGAAT 57.215 29.630 0.00 0.00 0.00 2.40
2127 2996 9.617975 GTGAATAAGAGTTTTGAAGAGAATTGG 57.382 33.333 0.00 0.00 0.00 3.16
2128 2997 9.354673 TGAATAAGAGTTTTGAAGAGAATTGGT 57.645 29.630 0.00 0.00 0.00 3.67
2133 3002 8.753497 AGAGTTTTGAAGAGAATTGGTTAACT 57.247 30.769 5.42 0.00 0.00 2.24
2134 3003 8.624776 AGAGTTTTGAAGAGAATTGGTTAACTG 58.375 33.333 5.42 0.00 0.00 3.16
2135 3004 8.519799 AGTTTTGAAGAGAATTGGTTAACTGA 57.480 30.769 5.42 0.00 0.00 3.41
2136 3005 8.966868 AGTTTTGAAGAGAATTGGTTAACTGAA 58.033 29.630 5.42 0.00 0.00 3.02
2270 3142 9.082313 CCTTTTCCCTAATATGATATTGCTTGT 57.918 33.333 7.91 0.00 0.00 3.16
2339 3520 6.204359 GCACTTGTATGCATCCTTGATTTAG 58.796 40.000 0.19 0.00 45.39 1.85
2359 3540 9.669353 GATTTAGTTATTGGAAGTATGCATGTG 57.331 33.333 10.16 0.00 0.00 3.21
2369 3550 5.764686 GGAAGTATGCATGTGGTCATCATTA 59.235 40.000 10.16 0.00 31.15 1.90
2399 3683 3.274288 GTTTCCTCCTGGCACTAATGAG 58.726 50.000 0.00 0.00 0.00 2.90
2615 4596 6.147328 GTCAGTTTACTTGGGCTACAACTAAG 59.853 42.308 0.00 0.00 34.76 2.18
2616 4597 5.001874 AGTTTACTTGGGCTACAACTAAGC 58.998 41.667 0.00 0.00 39.33 3.09
2874 5739 4.729552 AATGGAGCAGAATATTGCCCTA 57.270 40.909 0.00 0.00 45.18 3.53
3167 6143 4.003648 GCTGCCTTTACAGATGTAAGTGT 58.996 43.478 5.63 0.00 41.03 3.55
3168 6144 4.455877 GCTGCCTTTACAGATGTAAGTGTT 59.544 41.667 5.63 0.00 41.03 3.32
3472 6448 1.602311 CATAGCCAGGCCAGATTCAC 58.398 55.000 8.22 0.00 0.00 3.18
3549 6525 1.859302 TGGTTGTTCAGGTTTGCCTT 58.141 45.000 0.00 0.00 44.18 4.35
3553 6529 3.447742 GTTGTTCAGGTTTGCCTTTGAG 58.552 45.455 0.00 0.00 44.18 3.02
3609 6585 0.179124 GCCGAAAGTTGCCACAAACA 60.179 50.000 0.00 0.00 32.21 2.83
3644 6620 6.699575 ACACCATAACTTTCTAATGATGCC 57.300 37.500 0.00 0.00 0.00 4.40
3679 6677 4.323417 CCAAGTTAATGCAGTGGTACTCA 58.677 43.478 0.00 0.00 0.00 3.41
3713 6711 4.908601 TTAGCATTCCAAAGAGACCTCA 57.091 40.909 0.00 0.00 0.00 3.86
3766 6764 7.811713 CCTGAAGAGAAAAAGAATGATTTGGAC 59.188 37.037 0.00 0.00 0.00 4.02
3877 6907 0.698238 TTGTGGCTGCCCATAGAAGT 59.302 50.000 17.53 0.00 44.51 3.01
3878 6908 0.035152 TGTGGCTGCCCATAGAAGTG 60.035 55.000 17.53 0.00 44.51 3.16
3883 6913 1.486726 GCTGCCCATAGAAGTGGTACT 59.513 52.381 0.00 0.00 37.57 2.73
4302 7334 1.407618 ACGCCCAAGAAGAAACCAAAC 59.592 47.619 0.00 0.00 0.00 2.93
4308 7340 3.305897 CCAAGAAGAAACCAAACGCAAAC 59.694 43.478 0.00 0.00 0.00 2.93
4320 7352 2.126110 GCAAACGCAAATCCCCGG 60.126 61.111 0.00 0.00 0.00 5.73
4338 7370 0.883814 GGAGAATGATGGCGCCTCTG 60.884 60.000 29.70 0.00 0.00 3.35
4350 7382 1.006922 GCCTCTGCAACCAAGCAAC 60.007 57.895 0.00 0.00 45.13 4.17
4353 7385 1.153066 TCTGCAACCAAGCAACGGA 60.153 52.632 0.00 0.00 45.13 4.69
4434 7466 3.305619 TAGGGCCCGCTACCAGTCA 62.306 63.158 18.44 0.00 0.00 3.41
4437 7469 1.077716 GGCCCGCTACCAGTCAATT 60.078 57.895 0.00 0.00 0.00 2.32
4452 7484 0.445436 CAATTGCGTGAGAGGCAGAC 59.555 55.000 0.00 0.00 40.30 3.51
4454 7486 1.877576 ATTGCGTGAGAGGCAGACGA 61.878 55.000 0.00 0.00 40.30 4.20
4455 7487 2.505118 GCGTGAGAGGCAGACGAC 60.505 66.667 0.00 0.00 35.05 4.34
4456 7488 2.202362 CGTGAGAGGCAGACGACG 60.202 66.667 0.00 0.00 35.05 5.12
4459 7491 4.838486 GAGAGGCAGACGACGCGG 62.838 72.222 12.47 0.00 0.00 6.46
4526 7576 2.031683 CCGAAATTGGTACGCTCCATTC 59.968 50.000 0.05 2.38 37.33 2.67
4531 7581 0.174845 TGGTACGCTCCATTCGAAGG 59.825 55.000 3.35 2.70 31.96 3.46
4547 7597 3.615709 GGGTGGGTGTTTGGCTGC 61.616 66.667 0.00 0.00 0.00 5.25
4582 7642 5.607939 TTTCCTACTGAGTTGAGTTGTGA 57.392 39.130 0.00 0.00 0.00 3.58
4583 7643 5.808366 TTCCTACTGAGTTGAGTTGTGAT 57.192 39.130 0.00 0.00 0.00 3.06
4801 7875 3.913089 TCATCGGATGAATGACGTATGG 58.087 45.455 17.94 0.00 36.11 2.74
4802 7876 2.148916 TCGGATGAATGACGTATGGC 57.851 50.000 0.00 0.00 0.00 4.40
4822 7900 1.201845 CGTGTCACACAGATGATTGCG 60.202 52.381 9.06 0.00 33.40 4.85
4829 7907 3.188254 CACACAGATGATTGCGGTTTGTA 59.812 43.478 0.00 0.00 0.00 2.41
4927 8034 3.755378 AGCTGCCATTTTAGAGTGACAAG 59.245 43.478 0.00 0.00 0.00 3.16
4952 8059 2.358898 CCGGCCATTCTCCTAACATTTG 59.641 50.000 2.24 0.00 0.00 2.32
4998 9110 9.025041 AGGATTTTAACTCCTTACATTTTGAGG 57.975 33.333 0.00 0.00 40.29 3.86
5008 9120 5.515886 CCTTACATTTTGAGGTTACTCCCCA 60.516 44.000 0.00 0.00 43.29 4.96
5014 9126 4.620086 TTGAGGTTACTCCCCATAGAGA 57.380 45.455 0.00 0.00 43.29 3.10
5023 9207 0.918983 CCCCATAGAGAAGCAACCCA 59.081 55.000 0.00 0.00 0.00 4.51
5057 9241 8.187913 TGTTCAATTTAGGTGATGGATTTTCA 57.812 30.769 0.00 0.00 0.00 2.69
5058 9242 8.087750 TGTTCAATTTAGGTGATGGATTTTCAC 58.912 33.333 0.00 0.00 42.20 3.18
5059 9243 7.773489 TCAATTTAGGTGATGGATTTTCACA 57.227 32.000 6.20 0.00 44.22 3.58
5060 9244 7.601856 TCAATTTAGGTGATGGATTTTCACAC 58.398 34.615 6.20 0.00 44.22 3.82
5061 9245 7.451255 TCAATTTAGGTGATGGATTTTCACACT 59.549 33.333 6.20 3.91 44.22 3.55
5062 9246 7.781324 ATTTAGGTGATGGATTTTCACACTT 57.219 32.000 6.20 0.00 44.22 3.16
5100 9284 3.450507 GGAAACCAAACCGGGTGG 58.549 61.111 21.57 21.57 41.32 4.61
5101 9285 1.152715 GGAAACCAAACCGGGTGGA 60.153 57.895 27.99 0.00 41.32 4.02
5102 9286 1.457823 GGAAACCAAACCGGGTGGAC 61.458 60.000 27.99 18.47 41.32 4.02
5103 9287 1.456145 AAACCAAACCGGGTGGACC 60.456 57.895 27.99 0.00 41.32 4.46
5104 9288 1.940242 AAACCAAACCGGGTGGACCT 61.940 55.000 27.99 12.28 41.32 3.85
5109 9300 0.037734 AAACCGGGTGGACCTTCATC 59.962 55.000 6.32 0.00 39.21 2.92
5145 9336 5.733620 ATTCAAATCACATCACAAGGCTT 57.266 34.783 0.00 0.00 0.00 4.35
5150 9341 1.699083 TCACATCACAAGGCTTGAGGA 59.301 47.619 32.50 26.32 0.00 3.71
5153 9344 2.040813 ACATCACAAGGCTTGAGGACAT 59.959 45.455 32.50 16.75 0.00 3.06
5157 9348 2.229784 CACAAGGCTTGAGGACATTTCC 59.770 50.000 32.50 0.00 43.22 3.13
5187 9378 1.859080 GATGAACGCCACGAAGTATCC 59.141 52.381 0.00 0.00 41.61 2.59
5228 9419 2.203800 TCGATCCACGTATCAGCAAC 57.796 50.000 0.00 0.00 43.13 4.17
5263 10123 5.171476 ACCAATGAACTAGTGTCGATGAAG 58.829 41.667 0.00 0.00 0.00 3.02
5264 10124 5.047306 ACCAATGAACTAGTGTCGATGAAGA 60.047 40.000 0.00 0.00 0.00 2.87
5266 10126 6.019237 CCAATGAACTAGTGTCGATGAAGATG 60.019 42.308 0.00 0.00 0.00 2.90
5267 10127 5.897377 TGAACTAGTGTCGATGAAGATGA 57.103 39.130 0.00 0.00 0.00 2.92
5268 10128 6.267496 TGAACTAGTGTCGATGAAGATGAA 57.733 37.500 0.00 0.00 0.00 2.57
5269 10129 6.687604 TGAACTAGTGTCGATGAAGATGAAA 58.312 36.000 0.00 0.00 0.00 2.69
5270 10130 6.586463 TGAACTAGTGTCGATGAAGATGAAAC 59.414 38.462 0.00 0.00 0.00 2.78
5271 10131 6.274157 ACTAGTGTCGATGAAGATGAAACT 57.726 37.500 0.00 0.00 0.00 2.66
5272 10132 6.692486 ACTAGTGTCGATGAAGATGAAACTT 58.308 36.000 0.00 0.00 0.00 2.66
5273 10133 7.155328 ACTAGTGTCGATGAAGATGAAACTTT 58.845 34.615 0.00 0.00 0.00 2.66
5288 10148 6.647334 TGAAACTTTGTGATATGCTTGGAA 57.353 33.333 0.00 0.00 0.00 3.53
5305 10165 4.179926 TGGAAGAACATCTCTCTTGACG 57.820 45.455 0.00 0.00 33.24 4.35
5308 10168 1.895798 AGAACATCTCTCTTGACGCCA 59.104 47.619 0.00 0.00 0.00 5.69
5315 10175 0.750249 TCTCTTGACGCCACAGTTGA 59.250 50.000 0.00 0.00 0.00 3.18
5316 10176 1.344438 TCTCTTGACGCCACAGTTGAT 59.656 47.619 0.00 0.00 0.00 2.57
5334 10194 4.406648 TGATGGCGATCAAACTATGTCT 57.593 40.909 9.17 0.00 35.55 3.41
5350 10210 1.431633 TGTCTCCACTCCCTCTAACCA 59.568 52.381 0.00 0.00 0.00 3.67
5366 12536 6.030548 TCTAACCAGACACAAGATTCTCTG 57.969 41.667 0.00 0.00 0.00 3.35
5372 12542 1.637553 ACACAAGATTCTCTGGCCCAT 59.362 47.619 0.00 0.00 0.00 4.00
5374 12544 1.134280 ACAAGATTCTCTGGCCCATCG 60.134 52.381 0.00 0.00 0.00 3.84
5421 12591 1.959226 CGGTGGTTGGGTTGAGTCG 60.959 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 1.444119 GCACGCCTTGTCTTGACCAA 61.444 55.000 0.00 0.00 0.00 3.67
113 115 1.608590 CTCTTTTCTTTGCCCGCTCAA 59.391 47.619 0.00 0.00 0.00 3.02
114 116 1.202758 TCTCTTTTCTTTGCCCGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
119 121 3.153130 AGCTTCTCTCTTTTCTTTGCCC 58.847 45.455 0.00 0.00 0.00 5.36
198 202 8.031848 TGCTTGAGATTTTTATTTGCAATTCC 57.968 30.769 0.00 0.00 0.00 3.01
232 237 5.069119 TCGATTCAGTATTACAGCAGGTCAT 59.931 40.000 0.00 0.00 0.00 3.06
233 238 4.401202 TCGATTCAGTATTACAGCAGGTCA 59.599 41.667 0.00 0.00 0.00 4.02
234 239 4.933330 TCGATTCAGTATTACAGCAGGTC 58.067 43.478 0.00 0.00 0.00 3.85
235 240 5.537300 ATCGATTCAGTATTACAGCAGGT 57.463 39.130 0.00 0.00 0.00 4.00
237 242 7.468922 TGAAATCGATTCAGTATTACAGCAG 57.531 36.000 11.83 0.00 43.08 4.24
304 327 8.748412 AGGTCTGTGAAGCTGAGATATTATATC 58.252 37.037 4.15 4.15 0.00 1.63
312 335 2.496871 CTGAGGTCTGTGAAGCTGAGAT 59.503 50.000 0.00 0.00 30.71 2.75
378 1223 5.649395 TGAATCCAACTCTGAACCATCATTC 59.351 40.000 0.00 0.00 34.37 2.67
379 1224 5.573219 TGAATCCAACTCTGAACCATCATT 58.427 37.500 0.00 0.00 34.37 2.57
423 1273 1.298859 GCTCCAAGGCGTCGTGAAAT 61.299 55.000 3.97 0.00 0.00 2.17
431 1281 2.281761 CCACAAGCTCCAAGGCGT 60.282 61.111 0.00 0.00 37.29 5.68
499 1352 8.336806 CAAACGAACAACACTAATTTACACCTA 58.663 33.333 0.00 0.00 0.00 3.08
508 1361 4.277174 TGCCATCAAACGAACAACACTAAT 59.723 37.500 0.00 0.00 0.00 1.73
517 1370 5.041951 TCAACTAATGCCATCAAACGAAC 57.958 39.130 0.00 0.00 0.00 3.95
590 1444 2.897326 TCAATCCGTCTTCTCTCACCAA 59.103 45.455 0.00 0.00 0.00 3.67
596 1450 3.619038 GCGATTTTCAATCCGTCTTCTCT 59.381 43.478 0.00 0.00 0.00 3.10
605 1459 2.031682 CAGGGATCGCGATTTTCAATCC 60.032 50.000 24.55 18.12 36.06 3.01
611 1465 3.753294 ATAGTCAGGGATCGCGATTTT 57.247 42.857 24.55 9.05 0.00 1.82
616 1470 2.802787 AGAAATAGTCAGGGATCGCG 57.197 50.000 0.00 0.00 0.00 5.87
623 1477 3.462021 GCTGGTGCTAGAAATAGTCAGG 58.538 50.000 0.00 0.00 36.03 3.86
663 1517 3.414486 AAAAACGCAGTGCTACCCT 57.586 47.368 14.33 0.00 45.00 4.34
764 1618 0.404426 GGCTCTAGTTGGGTTGGGTT 59.596 55.000 0.00 0.00 0.00 4.11
765 1619 0.475828 AGGCTCTAGTTGGGTTGGGT 60.476 55.000 0.00 0.00 0.00 4.51
766 1620 0.035056 CAGGCTCTAGTTGGGTTGGG 60.035 60.000 0.00 0.00 0.00 4.12
767 1621 0.693049 ACAGGCTCTAGTTGGGTTGG 59.307 55.000 0.00 0.00 0.00 3.77
768 1622 1.347707 TGACAGGCTCTAGTTGGGTTG 59.652 52.381 0.00 0.00 0.00 3.77
931 1785 7.776107 TGACCTGTGAAAACATAACATCAAAA 58.224 30.769 0.00 0.00 0.00 2.44
1017 1871 1.948611 GCCTGCCAAAGTGGTTCGATA 60.949 52.381 0.00 0.00 40.46 2.92
1080 1934 3.066203 TCGAGAAGTATGCAAGTGCGATA 59.934 43.478 0.00 0.00 45.83 2.92
1333 2187 1.933181 TCGCAACTTCACACTCAACAG 59.067 47.619 0.00 0.00 0.00 3.16
1341 2195 1.040646 ACCTCTCTCGCAACTTCACA 58.959 50.000 0.00 0.00 0.00 3.58
1876 2730 3.675775 GCAACAACTTCAACAAGCTCCAA 60.676 43.478 0.00 0.00 32.09 3.53
2018 2872 6.944234 AGAAATATACAAAAGCAGCCCTAC 57.056 37.500 0.00 0.00 0.00 3.18
2079 2936 7.751732 TCACAGACAAAGCATACACATTTATC 58.248 34.615 0.00 0.00 0.00 1.75
2122 2991 7.271511 TCAATTGCAACTTCAGTTAACCAATT 58.728 30.769 0.00 13.76 38.89 2.32
2123 2992 6.815089 TCAATTGCAACTTCAGTTAACCAAT 58.185 32.000 0.00 0.00 36.32 3.16
2124 2993 6.127479 ACTCAATTGCAACTTCAGTTAACCAA 60.127 34.615 0.00 0.00 36.32 3.67
2125 2994 5.359576 ACTCAATTGCAACTTCAGTTAACCA 59.640 36.000 0.00 0.00 36.32 3.67
2126 2995 5.831997 ACTCAATTGCAACTTCAGTTAACC 58.168 37.500 0.00 0.00 36.32 2.85
2127 2996 8.743099 GTTAACTCAATTGCAACTTCAGTTAAC 58.257 33.333 28.01 28.01 43.31 2.01
2128 2997 7.918562 GGTTAACTCAATTGCAACTTCAGTTAA 59.081 33.333 20.39 20.39 36.32 2.01
2129 2998 7.284489 AGGTTAACTCAATTGCAACTTCAGTTA 59.716 33.333 0.00 9.37 36.32 2.24
2130 2999 6.096846 AGGTTAACTCAATTGCAACTTCAGTT 59.903 34.615 0.00 10.35 39.12 3.16
2131 3000 5.594317 AGGTTAACTCAATTGCAACTTCAGT 59.406 36.000 0.00 0.00 0.00 3.41
2132 3001 6.076981 AGGTTAACTCAATTGCAACTTCAG 57.923 37.500 0.00 0.00 0.00 3.02
2133 3002 6.770785 ACTAGGTTAACTCAATTGCAACTTCA 59.229 34.615 0.00 0.00 0.00 3.02
2134 3003 7.203255 ACTAGGTTAACTCAATTGCAACTTC 57.797 36.000 0.00 0.00 0.00 3.01
2135 3004 8.685838 TTACTAGGTTAACTCAATTGCAACTT 57.314 30.769 0.00 0.00 0.00 2.66
2136 3005 8.685838 TTTACTAGGTTAACTCAATTGCAACT 57.314 30.769 0.00 0.00 0.00 3.16
2270 3142 9.613428 CTTGTCAGGATATAAACCAATTACTCA 57.387 33.333 0.00 0.00 0.00 3.41
2339 3520 5.356751 TGACCACATGCATACTTCCAATAAC 59.643 40.000 0.00 0.00 0.00 1.89
2359 3540 9.788960 GAGGAAACAAAAGTATTAATGATGACC 57.211 33.333 0.00 0.00 0.00 4.02
2369 3550 4.280929 GTGCCAGGAGGAAACAAAAGTATT 59.719 41.667 0.00 0.00 36.89 1.89
2399 3683 9.693157 CAAACACAATGAAATCAGAAGAAAAAC 57.307 29.630 0.00 0.00 0.00 2.43
2874 5739 1.138459 CTCTCGACGTGCTGCATCT 59.862 57.895 5.27 0.00 0.00 2.90
3060 6036 5.821516 AAACATCGTTGGTCAAAGTTACA 57.178 34.783 0.00 0.00 0.00 2.41
3167 6143 8.227791 GTCGAAATATTAAAACTGCTGTCAGAA 58.772 33.333 3.32 0.00 42.95 3.02
3168 6144 7.602644 AGTCGAAATATTAAAACTGCTGTCAGA 59.397 33.333 3.32 0.00 42.95 3.27
3260 6236 7.175990 TCAAATTAACCACCTACAAGATGAACC 59.824 37.037 0.00 0.00 0.00 3.62
3472 6448 0.105039 GAAGCATACGGGTCCCTCAG 59.895 60.000 6.29 0.00 0.00 3.35
3549 6525 1.649321 AGGAGTGAGTGGATGCTCAA 58.351 50.000 0.00 0.00 45.75 3.02
3553 6529 3.006247 GAGAAAAGGAGTGAGTGGATGC 58.994 50.000 0.00 0.00 0.00 3.91
3877 6907 9.796180 TTTTTGCTCCTTAATTAGTTAGTACCA 57.204 29.630 0.00 0.00 0.00 3.25
3883 6913 7.177744 CCCCTGTTTTTGCTCCTTAATTAGTTA 59.822 37.037 0.00 0.00 0.00 2.24
3932 6963 4.764172 ACATCAGGTCTTCTGCTAACATC 58.236 43.478 0.00 0.00 43.06 3.06
3993 7024 1.062198 TGAGCCATATCCTCTGGTCCA 60.062 52.381 0.00 0.00 36.10 4.02
4308 7340 0.463654 TCATTCTCCGGGGATTTGCG 60.464 55.000 3.90 0.00 0.00 4.85
4320 7352 1.505477 GCAGAGGCGCCATCATTCTC 61.505 60.000 31.54 15.73 0.00 2.87
4338 7370 2.050077 GCTCCGTTGCTTGGTTGC 60.050 61.111 0.00 0.00 0.00 4.17
4412 7444 2.918276 GGTAGCGGGCCCTAGGAG 60.918 72.222 22.43 4.41 0.00 3.69
4434 7466 1.016130 CGTCTGCCTCTCACGCAATT 61.016 55.000 0.00 0.00 35.40 2.32
4437 7469 2.983592 TCGTCTGCCTCTCACGCA 60.984 61.111 0.00 0.00 33.46 5.24
4461 7493 3.997064 CTCCCGCCAGTCGAGCTTG 62.997 68.421 0.00 0.00 41.67 4.01
4496 7546 3.969981 CGTACCAATTTCGGTCACAAAAC 59.030 43.478 0.00 0.00 40.67 2.43
4512 7562 0.174845 CCTTCGAATGGAGCGTACCA 59.825 55.000 0.00 5.31 44.41 3.25
4526 7576 2.561037 GCCAAACACCCACCCTTCG 61.561 63.158 0.00 0.00 0.00 3.79
4531 7581 2.521708 AGCAGCCAAACACCCACC 60.522 61.111 0.00 0.00 0.00 4.61
4797 7871 1.548269 TCATCTGTGTGACACGCCATA 59.452 47.619 16.24 2.49 37.14 2.74
4798 7872 0.321346 TCATCTGTGTGACACGCCAT 59.679 50.000 16.24 5.85 37.14 4.40
4800 7874 1.129251 CAATCATCTGTGTGACACGCC 59.871 52.381 16.24 2.53 37.14 5.68
4801 7875 1.464687 GCAATCATCTGTGTGACACGC 60.465 52.381 11.51 12.29 37.14 5.34
4802 7876 1.201845 CGCAATCATCTGTGTGACACG 60.202 52.381 11.51 6.25 37.14 4.49
4804 7878 1.270785 ACCGCAATCATCTGTGTGACA 60.271 47.619 0.00 0.00 0.00 3.58
4805 7879 1.442769 ACCGCAATCATCTGTGTGAC 58.557 50.000 0.00 0.00 0.00 3.67
4822 7900 3.733727 CGAAAATGCAACCAGTACAAACC 59.266 43.478 0.00 0.00 0.00 3.27
4829 7907 1.285641 CCGCGAAAATGCAACCAGT 59.714 52.632 8.23 0.00 34.15 4.00
4876 7954 1.463444 GTGTTCTTACATGCACGACCC 59.537 52.381 0.00 0.00 36.50 4.46
4927 8034 0.393808 TTAGGAGAATGGCCGGTTGC 60.394 55.000 1.90 0.00 40.16 4.17
4998 9110 4.443621 GTTGCTTCTCTATGGGGAGTAAC 58.556 47.826 0.00 0.00 35.11 2.50
5000 9112 3.039011 GGTTGCTTCTCTATGGGGAGTA 58.961 50.000 0.00 0.00 35.11 2.59
5023 9207 5.774690 TCACCTAAATTGAACATTGGAAGCT 59.225 36.000 0.00 0.00 0.00 3.74
5030 9214 9.657419 GAAAATCCATCACCTAAATTGAACATT 57.343 29.630 0.00 0.00 0.00 2.71
5057 9241 6.223852 CACTACAATGGAGAAGTGTAAGTGT 58.776 40.000 0.00 0.00 38.77 3.55
5058 9242 5.639506 CCACTACAATGGAGAAGTGTAAGTG 59.360 44.000 0.00 0.00 43.02 3.16
5059 9243 5.280011 CCCACTACAATGGAGAAGTGTAAGT 60.280 44.000 0.00 0.00 43.02 2.24
5060 9244 5.178797 CCCACTACAATGGAGAAGTGTAAG 58.821 45.833 0.00 0.00 43.02 2.34
5061 9245 4.019681 CCCCACTACAATGGAGAAGTGTAA 60.020 45.833 0.00 0.00 43.02 2.41
5062 9246 3.517901 CCCCACTACAATGGAGAAGTGTA 59.482 47.826 0.00 0.00 43.02 2.90
5090 9274 0.037734 GATGAAGGTCCACCCGGTTT 59.962 55.000 0.00 0.00 38.74 3.27
5096 9280 4.446371 CAATACTGAGATGAAGGTCCACC 58.554 47.826 0.00 0.00 0.00 4.61
5097 9281 4.162320 TCCAATACTGAGATGAAGGTCCAC 59.838 45.833 0.00 0.00 0.00 4.02
5100 9284 9.213799 GAATAATCCAATACTGAGATGAAGGTC 57.786 37.037 0.00 0.00 0.00 3.85
5101 9285 8.717717 TGAATAATCCAATACTGAGATGAAGGT 58.282 33.333 0.00 0.00 0.00 3.50
5102 9286 9.565090 TTGAATAATCCAATACTGAGATGAAGG 57.435 33.333 0.00 0.00 0.00 3.46
5137 9328 2.519013 GGAAATGTCCTCAAGCCTTGT 58.481 47.619 4.04 0.00 41.24 3.16
5157 9348 1.303309 GGCGTTCATCCTCCATCAAG 58.697 55.000 0.00 0.00 0.00 3.02
5164 9355 0.389948 ACTTCGTGGCGTTCATCCTC 60.390 55.000 0.00 0.00 0.00 3.71
5170 9361 1.717194 TTGGATACTTCGTGGCGTTC 58.283 50.000 0.00 0.00 37.61 3.95
5187 9378 2.703798 CCTCCGCCCACTTGCATTG 61.704 63.158 0.00 0.00 0.00 2.82
5200 9391 1.167155 ACGTGGATCGATCTCCTCCG 61.167 60.000 23.96 18.94 42.86 4.63
5228 9419 5.633830 AGTTCATTGGTCATGTTAGCTTG 57.366 39.130 0.00 0.00 34.06 4.01
5263 10123 6.855836 TCCAAGCATATCACAAAGTTTCATC 58.144 36.000 0.00 0.00 0.00 2.92
5264 10124 6.839124 TCCAAGCATATCACAAAGTTTCAT 57.161 33.333 0.00 0.00 0.00 2.57
5266 10126 6.913170 TCTTCCAAGCATATCACAAAGTTTC 58.087 36.000 0.00 0.00 0.00 2.78
5267 10127 6.899393 TCTTCCAAGCATATCACAAAGTTT 57.101 33.333 0.00 0.00 0.00 2.66
5268 10128 6.265196 TGTTCTTCCAAGCATATCACAAAGTT 59.735 34.615 0.00 0.00 0.00 2.66
5269 10129 5.769662 TGTTCTTCCAAGCATATCACAAAGT 59.230 36.000 0.00 0.00 0.00 2.66
5270 10130 6.258230 TGTTCTTCCAAGCATATCACAAAG 57.742 37.500 0.00 0.00 0.00 2.77
5271 10131 6.660521 AGATGTTCTTCCAAGCATATCACAAA 59.339 34.615 0.00 0.00 0.00 2.83
5272 10132 6.182627 AGATGTTCTTCCAAGCATATCACAA 58.817 36.000 0.00 0.00 0.00 3.33
5273 10133 5.748402 AGATGTTCTTCCAAGCATATCACA 58.252 37.500 0.00 0.00 0.00 3.58
5288 10148 1.895798 TGGCGTCAAGAGAGATGTTCT 59.104 47.619 0.00 0.00 39.43 3.01
5308 10168 2.783135 AGTTTGATCGCCATCAACTGT 58.217 42.857 6.21 0.00 46.71 3.55
5315 10175 3.134623 TGGAGACATAGTTTGATCGCCAT 59.865 43.478 0.00 0.00 36.30 4.40
5316 10176 2.499693 TGGAGACATAGTTTGATCGCCA 59.500 45.455 0.00 0.00 38.52 5.69
5334 10194 1.431633 TGTCTGGTTAGAGGGAGTGGA 59.568 52.381 0.00 0.00 32.48 4.02
5409 12579 2.093394 TCACTTGTTCGACTCAACCCAA 60.093 45.455 0.00 0.00 0.00 4.12
5421 12591 4.860072 GGAGGATTGTTGTTCACTTGTTC 58.140 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.