Multiple sequence alignment - TraesCS2D01G099500

Loading Multiple Alignment...

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 TraesCS2D01G099500 chr2D 100.000 4558 0 0 1 4558 51248010 51252567 0.000000e+00 8418.0
1 TraesCS2D01G099500 chr2D 92.063 315 25 0 888 1202 51248200 51248514 1.160000e-120 444.0
2 TraesCS2D01G099500 chr2D 92.063 315 25 0 191 505 51248897 51249211 1.160000e-120 444.0
3 TraesCS2D01G099500 chr2D 94.949 99 3 2 105 202 188886079 188886176 2.200000e-33 154.0
4 TraesCS2D01G099500 chr2D 94.898 98 3 2 106 202 165009325 165009229 7.900000e-33 152.0
5 TraesCS2D01G099500 chr2D 81.203 133 20 3 3846 3978 404896868 404896741 8.070000e-18 102.0
6 TraesCS2D01G099500 chr2D 80.198 101 10 6 3877 3975 56528598 56528690 2.940000e-07 67.6
7 TraesCS2D01G099500 chr2A 93.561 3603 161 25 982 4558 52746130 52749687 0.000000e+00 5302.0
8 TraesCS2D01G099500 chr2A 91.855 221 18 0 285 505 52746130 52746350 4.430000e-80 309.0
9 TraesCS2D01G099500 chr2A 84.252 254 37 2 2175 2426 52559608 52559356 1.270000e-60 244.0
10 TraesCS2D01G099500 chr2A 92.593 135 10 0 862 996 52745975 52746109 1.290000e-45 195.0
11 TraesCS2D01G099500 chr2A 90.826 109 10 0 191 299 52746001 52746109 3.670000e-31 147.0
12 TraesCS2D01G099500 chr2A 89.474 57 5 1 3873 3928 57925578 57925634 2.270000e-08 71.3
13 TraesCS2D01G099500 chr2B 91.800 1878 103 13 2699 4555 80197993 80199840 0.000000e+00 2567.0
14 TraesCS2D01G099500 chr2B 94.176 601 28 6 1497 2091 80196725 80197324 0.000000e+00 909.0
15 TraesCS2D01G099500 chr2B 94.062 320 14 3 897 1212 80195986 80196304 8.870000e-132 481.0
16 TraesCS2D01G099500 chr2B 90.879 307 27 1 192 497 80195977 80196283 1.180000e-110 411.0
17 TraesCS2D01G099500 chr2B 98.039 153 2 1 1217 1369 80196341 80196492 9.720000e-67 265.0
18 TraesCS2D01G099500 chr2B 85.433 254 34 2 2175 2426 79678268 79678016 1.260000e-65 261.0
19 TraesCS2D01G099500 chr5B 94.059 101 6 0 108 208 432174788 432174688 2.200000e-33 154.0
20 TraesCS2D01G099500 chr7A 86.232 138 19 0 61 198 20733061 20732924 2.840000e-32 150.0
21 TraesCS2D01G099500 chr5A 94.845 97 4 1 109 205 367782484 367782389 2.840000e-32 150.0
22 TraesCS2D01G099500 chr5A 90.991 111 7 3 87 195 328936561 328936670 3.670000e-31 147.0
23 TraesCS2D01G099500 chr1D 91.818 110 6 3 98 205 447863818 447863710 2.840000e-32 150.0
24 TraesCS2D01G099500 chr4B 91.743 109 5 4 89 194 2432002 2431895 1.020000e-31 148.0
25 TraesCS2D01G099500 chr1A 91.589 107 7 2 95 199 133417563 133417457 3.670000e-31 147.0
26 TraesCS2D01G099500 chr1B 77.698 139 24 7 3839 3976 156569206 156569074 1.360000e-10 78.7
27 TraesCS2D01G099500 chr1B 100.000 29 0 0 811 839 577833909 577833937 2.000000e-03 54.7
28 TraesCS2D01G099500 chr7B 100.000 37 0 0 804 840 432497667 432497631 8.180000e-08 69.4


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 TraesCS2D01G099500 chr2D 51248010 51252567 4557 False 8418.00 8418 100.00000 1 4558 1 chr2D.!!$F1 4557
1 TraesCS2D01G099500 chr2D 51248200 51249211 1011 False 444.00 444 92.06300 191 1202 2 chr2D.!!$F4 1011
2 TraesCS2D01G099500 chr2A 52745975 52749687 3712 False 1488.25 5302 92.20875 191 4558 4 chr2A.!!$F2 4367
3 TraesCS2D01G099500 chr2B 80195977 80199840 3863 False 926.60 2567 93.79120 192 4555 5 chr2B.!!$F1 4363

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
22 23 5.646577 AGCGTTCAGATCACTAAAGTAGT 57.353 39.130 0.00 0.0 40.28 2.73 F
1373 1450 4.699735 TCGGTCGTACCAAGTAGTTCAATA 59.300 41.667 5.15 0.0 38.47 1.90 F
1684 1898 0.674895 GATTCAGGCTCGCTGTGGTT 60.675 55.000 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1480 0.037419 AAATGTGCGTGCATTTCCCC 60.037 50.000 11.61 0.0 43.23 4.81 R
2907 3252 1.372087 CGACCAGATGGGCTGCTTTC 61.372 60.000 2.62 0.0 42.58 2.62 R
3573 3918 1.216930 ACCTAAACAAAGTGGCACCCT 59.783 47.619 15.27 0.0 0.00 4.34 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
22 23 5.646577 AGCGTTCAGATCACTAAAGTAGT 57.353 39.130 0.00 0.00 40.28 2.73
23 24 6.754702 AGCGTTCAGATCACTAAAGTAGTA 57.245 37.500 0.00 0.00 37.23 1.82
24 25 7.154435 AGCGTTCAGATCACTAAAGTAGTAA 57.846 36.000 0.00 0.00 37.23 2.24
25 26 7.773149 AGCGTTCAGATCACTAAAGTAGTAAT 58.227 34.615 0.00 0.00 37.23 1.89
26 27 7.916450 AGCGTTCAGATCACTAAAGTAGTAATC 59.084 37.037 0.00 0.00 37.23 1.75
27 28 7.916450 GCGTTCAGATCACTAAAGTAGTAATCT 59.084 37.037 0.00 0.00 43.07 2.40
117 118 9.740239 TGATGTATACGAAAAATGTACTACCTC 57.260 33.333 0.00 0.00 0.00 3.85
118 119 9.962783 GATGTATACGAAAAATGTACTACCTCT 57.037 33.333 0.00 0.00 0.00 3.69
119 120 9.745880 ATGTATACGAAAAATGTACTACCTCTG 57.254 33.333 0.00 0.00 0.00 3.35
120 121 8.742777 TGTATACGAAAAATGTACTACCTCTGT 58.257 33.333 0.00 0.00 0.00 3.41
124 125 8.302965 ACGAAAAATGTACTACCTCTGTAAAC 57.697 34.615 0.00 0.00 0.00 2.01
125 126 8.146412 ACGAAAAATGTACTACCTCTGTAAACT 58.854 33.333 0.00 0.00 0.00 2.66
126 127 9.630098 CGAAAAATGTACTACCTCTGTAAACTA 57.370 33.333 0.00 0.00 0.00 2.24
170 171 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
171 172 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
172 173 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
173 174 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
185 186 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
186 187 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
188 189 8.516811 AACGCTCTTATATTAGTTTACGGATG 57.483 34.615 0.00 0.00 0.00 3.51
189 190 7.088905 ACGCTCTTATATTAGTTTACGGATGG 58.911 38.462 0.00 0.00 0.00 3.51
1316 1393 5.700832 CAGGAAGCTGTACTGAATGTAACAA 59.299 40.000 3.61 0.00 34.21 2.83
1317 1394 5.701290 AGGAAGCTGTACTGAATGTAACAAC 59.299 40.000 3.61 0.00 32.25 3.32
1373 1450 4.699735 TCGGTCGTACCAAGTAGTTCAATA 59.300 41.667 5.15 0.00 38.47 1.90
1377 1454 7.063780 CGGTCGTACCAAGTAGTTCAATAATTT 59.936 37.037 5.15 0.00 38.47 1.82
1379 1456 8.715088 GTCGTACCAAGTAGTTCAATAATTTGT 58.285 33.333 0.00 0.00 34.32 2.83
1380 1457 9.275398 TCGTACCAAGTAGTTCAATAATTTGTT 57.725 29.630 0.00 0.00 34.32 2.83
1447 1524 6.000246 TGCATCTTTATATCAAGACCCACA 58.000 37.500 1.43 0.00 35.57 4.17
1450 1527 6.488006 GCATCTTTATATCAAGACCCACACAT 59.512 38.462 1.43 0.00 35.57 3.21
1452 1529 9.212641 CATCTTTATATCAAGACCCACACATAG 57.787 37.037 1.43 0.00 35.57 2.23
1491 1572 6.183360 CCAGCACAACTTACTGAATTACTAGC 60.183 42.308 0.00 0.00 33.10 3.42
1495 1576 5.875359 ACAACTTACTGAATTACTAGCTGCC 59.125 40.000 0.00 0.00 0.00 4.85
1503 1711 4.585162 TGAATTACTAGCTGCCTCTACTCC 59.415 45.833 0.00 0.00 0.00 3.85
1522 1730 4.235360 CTCCGTGAACTAACTGACGAAAT 58.765 43.478 0.00 0.00 33.64 2.17
1528 1736 7.339207 CGTGAACTAACTGACGAAATAAAACA 58.661 34.615 0.00 0.00 33.64 2.83
1581 1790 0.753111 GTGACCATGAGGCAATCCCC 60.753 60.000 0.00 0.00 39.06 4.81
1684 1898 0.674895 GATTCAGGCTCGCTGTGGTT 60.675 55.000 0.00 0.00 0.00 3.67
1774 1988 1.280133 CTCACAGCAAGGGATGAGGAA 59.720 52.381 0.00 0.00 35.87 3.36
1776 1990 2.089980 CACAGCAAGGGATGAGGAAAG 58.910 52.381 0.00 0.00 33.73 2.62
1783 1997 4.268359 CAAGGGATGAGGAAAGAGGAAAG 58.732 47.826 0.00 0.00 0.00 2.62
1966 2184 4.024387 TGAATGTCTTGCCGTTTGTACTTC 60.024 41.667 0.00 0.00 0.00 3.01
1968 2186 4.325028 TGTCTTGCCGTTTGTACTTCTA 57.675 40.909 0.00 0.00 0.00 2.10
1973 2191 4.794278 TGCCGTTTGTACTTCTATGAGA 57.206 40.909 0.00 0.00 0.00 3.27
1976 2194 4.619863 GCCGTTTGTACTTCTATGAGACCA 60.620 45.833 0.00 0.00 0.00 4.02
1980 2198 7.382488 CCGTTTGTACTTCTATGAGACCATATG 59.618 40.741 0.00 0.00 34.96 1.78
1991 2209 8.911965 TCTATGAGACCATATGATGAAGATAGC 58.088 37.037 3.65 0.00 34.96 2.97
1996 2214 5.752650 ACCATATGATGAAGATAGCATGGG 58.247 41.667 3.65 0.00 36.76 4.00
1999 2217 3.136009 TGATGAAGATAGCATGGGCAG 57.864 47.619 0.00 0.00 44.61 4.85
2105 2323 8.041323 GTGGGTATGTATTTCTCAGAAAAGAGA 58.959 37.037 3.35 0.00 42.62 3.10
2410 2631 4.278170 CCATGTTAGCAAAACCAGTCTTCA 59.722 41.667 0.00 0.00 0.00 3.02
2431 2652 4.274705 TCAAACTGCTTGAATGTTCGCTAA 59.725 37.500 0.00 0.00 41.21 3.09
2439 2660 5.697473 TTGAATGTTCGCTAAAATGGACA 57.303 34.783 0.00 0.00 0.00 4.02
2586 2917 4.804139 CCACTACCTTACTAAGCATTGACG 59.196 45.833 0.00 0.00 0.00 4.35
2645 2987 5.733620 AGGCACATTGAATTTGAAGTGAT 57.266 34.783 0.00 0.00 0.00 3.06
2674 3016 9.787435 TTTTGACTGATACACTACAAAATAGGT 57.213 29.630 0.00 0.00 34.09 3.08
2679 3021 8.041323 ACTGATACACTACAAAATAGGTTCCTG 58.959 37.037 1.12 0.00 0.00 3.86
2738 3082 2.851195 ACTTGTCGACTTGCTTTGGAT 58.149 42.857 17.92 0.00 0.00 3.41
2907 3252 0.830648 TTCTGGTTCAGCTATCGGGG 59.169 55.000 0.00 0.00 0.00 5.73
2923 3268 1.755783 GGGAAAGCAGCCCATCTGG 60.756 63.158 3.89 0.00 45.31 3.86
2938 3283 3.243737 CCATCTGGTCGAATCGGTGATTA 60.244 47.826 1.76 0.00 31.89 1.75
3144 3489 4.651778 TGTAAATGGCAGCTTTAGTCACT 58.348 39.130 0.00 0.00 0.00 3.41
3188 3533 0.911769 TCCACCAGAGAATGCCGAAT 59.088 50.000 0.00 0.00 0.00 3.34
3573 3918 2.231721 TGGTGATCGATGGTTACACGAA 59.768 45.455 0.54 0.00 39.38 3.85
3574 3919 2.858344 GGTGATCGATGGTTACACGAAG 59.142 50.000 0.54 0.00 39.38 3.79
3673 4019 4.678287 CAGCAAACATGATTATCATTCGCC 59.322 41.667 4.77 0.00 34.28 5.54
3781 4130 6.208007 TCAGTTTCTTACGACCAGTCTATTGA 59.792 38.462 0.00 0.00 0.00 2.57
3792 4141 6.114187 ACCAGTCTATTGATGTTTGTCTGA 57.886 37.500 0.00 0.00 0.00 3.27
3795 4144 6.820152 CCAGTCTATTGATGTTTGTCTGATGA 59.180 38.462 0.00 0.00 0.00 2.92
3844 4193 1.366111 TTCATCGTAAGCCAAGCCGC 61.366 55.000 0.00 0.00 37.18 6.53
3851 4200 2.789845 TAAGCCAAGCCGCGTTAGCA 62.790 55.000 4.92 0.00 45.49 3.49
3881 4230 2.102578 CCCCATTGGATCACCTTGTTC 58.897 52.381 3.62 0.00 35.39 3.18
3930 4280 1.822186 GTGTTGTCGGGTGGCAAGT 60.822 57.895 0.00 0.00 0.00 3.16
3973 4323 2.511600 CCCGCCTCGCTTGGTTAG 60.512 66.667 0.00 0.00 0.00 2.34
3985 4335 4.876107 TCGCTTGGTTAGATGAAAATCCTC 59.124 41.667 0.00 0.00 0.00 3.71
4004 4354 1.202879 TCCTGCGTTTGGTTGATCCTT 60.203 47.619 0.00 0.00 37.07 3.36
4010 4360 3.262420 CGTTTGGTTGATCCTTCGAGAT 58.738 45.455 0.00 0.00 37.07 2.75
4019 4369 3.317711 TGATCCTTCGAGATCTCTGAAGC 59.682 47.826 30.88 23.63 42.68 3.86
4020 4370 2.028130 TCCTTCGAGATCTCTGAAGCC 58.972 52.381 30.88 8.06 38.10 4.35
4021 4371 1.753649 CCTTCGAGATCTCTGAAGCCA 59.246 52.381 30.88 14.29 38.10 4.75
4022 4372 2.167281 CCTTCGAGATCTCTGAAGCCAA 59.833 50.000 30.88 14.04 38.10 4.52
4023 4373 3.368843 CCTTCGAGATCTCTGAAGCCAAA 60.369 47.826 30.88 13.57 38.10 3.28
4024 4374 3.516981 TCGAGATCTCTGAAGCCAAAG 57.483 47.619 20.26 1.20 0.00 2.77
4025 4375 1.932511 CGAGATCTCTGAAGCCAAAGC 59.067 52.381 20.26 0.00 40.32 3.51
4026 4376 2.287769 GAGATCTCTGAAGCCAAAGCC 58.712 52.381 15.80 0.00 41.25 4.35
4027 4377 1.632409 AGATCTCTGAAGCCAAAGCCA 59.368 47.619 0.00 0.00 41.25 4.75
4028 4378 2.040813 AGATCTCTGAAGCCAAAGCCAA 59.959 45.455 0.00 0.00 41.25 4.52
4029 4379 1.901591 TCTCTGAAGCCAAAGCCAAG 58.098 50.000 0.00 0.00 41.25 3.61
4036 4386 1.183676 AGCCAAAGCCAAGCTCCTTG 61.184 55.000 0.00 0.00 38.25 3.61
4070 4420 5.195379 GTGTTTGTTGTATGTTGTCGTCTC 58.805 41.667 0.00 0.00 0.00 3.36
4075 4425 4.167268 GTTGTATGTTGTCGTCTCCTCTC 58.833 47.826 0.00 0.00 0.00 3.20
4110 4460 2.288666 TGAGTTGTTGTTGTGCTCCTC 58.711 47.619 0.00 0.00 0.00 3.71
4132 4482 3.120854 CGTGAGCTTTGTAAACTGCTCTC 60.121 47.826 15.26 12.09 46.36 3.20
4151 4501 3.775316 TCTCCCCTTCTTAATCACTGGAC 59.225 47.826 0.00 0.00 0.00 4.02
4232 4582 2.614779 CGATGATGCTGTTGAGTGACT 58.385 47.619 0.00 0.00 0.00 3.41
4278 4632 7.442666 ACAACTTATCTTTCTCAGTGTTTCTCC 59.557 37.037 0.00 0.00 0.00 3.71
4302 4656 0.110295 TACATGCTGCCACAGGTGTT 59.890 50.000 0.00 0.00 35.00 3.32
4337 4694 1.153509 GGCAAGGTGATGGCAATGC 60.154 57.895 0.00 0.00 44.66 3.56
4363 4720 2.266689 GCGACGGGGCCTAAGAAA 59.733 61.111 0.84 0.00 0.00 2.52
4435 4792 0.613777 AGGTACAGCTTTCTTCCCCG 59.386 55.000 0.00 0.00 0.00 5.73
4526 4899 3.625764 TGTGTTTCTGCCTGTTTGTAGAC 59.374 43.478 0.00 0.00 0.00 2.59
4542 4915 7.652105 TGTTTGTAGACTATAATCTGATTCGCC 59.348 37.037 6.10 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.646577 ACTACTTTAGTGATCTGAACGCT 57.353 39.130 6.26 6.26 37.69 5.07
1 2 7.988904 ATTACTACTTTAGTGATCTGAACGC 57.011 36.000 0.00 0.00 39.81 4.84
91 92 9.740239 GAGGTAGTACATTTTTCGTATACATCA 57.260 33.333 3.32 0.00 0.00 3.07
92 93 9.962783 AGAGGTAGTACATTTTTCGTATACATC 57.037 33.333 3.32 0.00 0.00 3.06
93 94 9.745880 CAGAGGTAGTACATTTTTCGTATACAT 57.254 33.333 3.32 0.00 0.00 2.29
94 95 8.742777 ACAGAGGTAGTACATTTTTCGTATACA 58.257 33.333 3.32 0.00 0.00 2.29
98 99 9.410556 GTTTACAGAGGTAGTACATTTTTCGTA 57.589 33.333 2.06 0.00 0.00 3.43
99 100 8.146412 AGTTTACAGAGGTAGTACATTTTTCGT 58.854 33.333 2.06 0.00 0.00 3.85
100 101 8.530269 AGTTTACAGAGGTAGTACATTTTTCG 57.470 34.615 2.06 0.00 0.00 3.46
146 147 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
147 148 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
159 160 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
160 161 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
162 163 8.975439 CATCCGTAAACTAATATAAGAGCGTTT 58.025 33.333 0.00 0.00 0.00 3.60
163 164 7.597743 CCATCCGTAAACTAATATAAGAGCGTT 59.402 37.037 0.00 0.00 0.00 4.84
164 165 7.040201 TCCATCCGTAAACTAATATAAGAGCGT 60.040 37.037 0.00 0.00 0.00 5.07
165 166 7.310664 TCCATCCGTAAACTAATATAAGAGCG 58.689 38.462 0.00 0.00 0.00 5.03
166 167 8.305317 ACTCCATCCGTAAACTAATATAAGAGC 58.695 37.037 0.00 0.00 0.00 4.09
172 173 9.706691 CATTGTACTCCATCCGTAAACTAATAT 57.293 33.333 0.00 0.00 0.00 1.28
173 174 8.698210 ACATTGTACTCCATCCGTAAACTAATA 58.302 33.333 0.00 0.00 0.00 0.98
174 175 7.562135 ACATTGTACTCCATCCGTAAACTAAT 58.438 34.615 0.00 0.00 0.00 1.73
175 176 6.938507 ACATTGTACTCCATCCGTAAACTAA 58.061 36.000 0.00 0.00 0.00 2.24
176 177 6.534475 ACATTGTACTCCATCCGTAAACTA 57.466 37.500 0.00 0.00 0.00 2.24
177 178 5.416271 ACATTGTACTCCATCCGTAAACT 57.584 39.130 0.00 0.00 0.00 2.66
178 179 6.490566 AAACATTGTACTCCATCCGTAAAC 57.509 37.500 0.00 0.00 0.00 2.01
179 180 7.228906 TCAAAAACATTGTACTCCATCCGTAAA 59.771 33.333 0.00 0.00 0.00 2.01
180 181 6.711194 TCAAAAACATTGTACTCCATCCGTAA 59.289 34.615 0.00 0.00 0.00 3.18
181 182 6.231951 TCAAAAACATTGTACTCCATCCGTA 58.768 36.000 0.00 0.00 0.00 4.02
182 183 5.067273 TCAAAAACATTGTACTCCATCCGT 58.933 37.500 0.00 0.00 0.00 4.69
183 184 5.621197 TCAAAAACATTGTACTCCATCCG 57.379 39.130 0.00 0.00 0.00 4.18
184 185 6.332630 CCATCAAAAACATTGTACTCCATCC 58.667 40.000 0.00 0.00 0.00 3.51
185 186 6.332630 CCCATCAAAAACATTGTACTCCATC 58.667 40.000 0.00 0.00 0.00 3.51
186 187 5.337491 GCCCATCAAAAACATTGTACTCCAT 60.337 40.000 0.00 0.00 0.00 3.41
187 188 4.021544 GCCCATCAAAAACATTGTACTCCA 60.022 41.667 0.00 0.00 0.00 3.86
188 189 4.494484 GCCCATCAAAAACATTGTACTCC 58.506 43.478 0.00 0.00 0.00 3.85
189 190 4.220602 AGGCCCATCAAAAACATTGTACTC 59.779 41.667 0.00 0.00 0.00 2.59
1316 1393 3.195610 TGCTAATCTGACGAAGATGGTGT 59.804 43.478 6.21 0.00 45.37 4.16
1317 1394 3.785486 TGCTAATCTGACGAAGATGGTG 58.215 45.455 6.21 2.54 45.37 4.17
1384 1461 7.610580 TTCCCCAATCATTGAACTACTTTTT 57.389 32.000 0.00 0.00 0.00 1.94
1386 1463 7.614494 CATTTCCCCAATCATTGAACTACTTT 58.386 34.615 0.00 0.00 0.00 2.66
1388 1465 5.127682 GCATTTCCCCAATCATTGAACTACT 59.872 40.000 0.00 0.00 0.00 2.57
1389 1466 5.105392 TGCATTTCCCCAATCATTGAACTAC 60.105 40.000 0.00 0.00 0.00 2.73
1390 1467 5.022122 TGCATTTCCCCAATCATTGAACTA 58.978 37.500 0.00 0.00 0.00 2.24
1391 1468 3.839490 TGCATTTCCCCAATCATTGAACT 59.161 39.130 0.00 0.00 0.00 3.01
1392 1469 3.934579 GTGCATTTCCCCAATCATTGAAC 59.065 43.478 0.00 0.00 0.00 3.18
1393 1470 3.368220 CGTGCATTTCCCCAATCATTGAA 60.368 43.478 0.00 0.00 0.00 2.69
1394 1471 2.166050 CGTGCATTTCCCCAATCATTGA 59.834 45.455 0.00 0.00 0.00 2.57
1395 1472 2.542597 CGTGCATTTCCCCAATCATTG 58.457 47.619 0.00 0.00 0.00 2.82
1396 1473 1.134729 GCGTGCATTTCCCCAATCATT 60.135 47.619 0.00 0.00 0.00 2.57
1397 1474 0.461135 GCGTGCATTTCCCCAATCAT 59.539 50.000 0.00 0.00 0.00 2.45
1398 1475 0.897401 TGCGTGCATTTCCCCAATCA 60.897 50.000 0.00 0.00 0.00 2.57
1399 1476 0.458370 GTGCGTGCATTTCCCCAATC 60.458 55.000 0.00 0.00 0.00 2.67
1400 1477 1.184322 TGTGCGTGCATTTCCCCAAT 61.184 50.000 0.00 0.00 0.00 3.16
1401 1478 1.184322 ATGTGCGTGCATTTCCCCAA 61.184 50.000 0.00 0.00 0.00 4.12
1402 1479 1.184322 AATGTGCGTGCATTTCCCCA 61.184 50.000 0.00 0.00 35.76 4.96
1403 1480 0.037419 AAATGTGCGTGCATTTCCCC 60.037 50.000 11.61 0.00 43.23 4.81
1404 1481 1.794512 AAAATGTGCGTGCATTTCCC 58.205 45.000 15.78 0.00 45.17 3.97
1405 1482 2.662520 GCAAAAATGTGCGTGCATTTCC 60.663 45.455 15.78 7.53 45.17 3.13
1406 1483 2.562948 GCAAAAATGTGCGTGCATTTC 58.437 42.857 15.78 4.82 45.17 2.17
1447 1524 4.012374 CTGGAAAAGTGGTGATGCTATGT 58.988 43.478 0.00 0.00 0.00 2.29
1450 1527 2.224744 TGCTGGAAAAGTGGTGATGCTA 60.225 45.455 0.00 0.00 0.00 3.49
1452 1529 0.961019 TGCTGGAAAAGTGGTGATGC 59.039 50.000 0.00 0.00 0.00 3.91
1491 1572 1.178276 AGTTCACGGAGTAGAGGCAG 58.822 55.000 0.00 0.00 41.61 4.85
1495 1576 4.435784 CGTCAGTTAGTTCACGGAGTAGAG 60.436 50.000 0.00 0.00 41.61 2.43
1503 1711 7.339207 TGTTTTATTTCGTCAGTTAGTTCACG 58.661 34.615 0.00 0.00 0.00 4.35
1522 1730 5.798125 TGGAACCATCAAAGCATGTTTTA 57.202 34.783 7.25 0.00 0.00 1.52
1528 1736 2.961062 GCCTATGGAACCATCAAAGCAT 59.039 45.455 9.75 0.00 37.82 3.79
1581 1790 4.450419 GGAGATGATGCTTATCACCTTTCG 59.550 45.833 0.00 0.00 33.95 3.46
1596 1805 2.868583 CAATGCGAGTTTCGGAGATGAT 59.131 45.455 0.34 0.00 44.87 2.45
1675 1889 0.250124 TTCCACCAGTAACCACAGCG 60.250 55.000 0.00 0.00 0.00 5.18
1684 1898 2.409064 TCCCTCTGTTTCCACCAGTA 57.591 50.000 0.00 0.00 0.00 2.74
1774 1988 0.890996 CAACCGCAGCCTTTCCTCTT 60.891 55.000 0.00 0.00 0.00 2.85
1776 1990 1.301677 CTCAACCGCAGCCTTTCCTC 61.302 60.000 0.00 0.00 0.00 3.71
1783 1997 3.553095 AAGGGACTCAACCGCAGCC 62.553 63.158 0.00 0.00 38.49 4.85
1966 2184 8.693625 TGCTATCTTCATCATATGGTCTCATAG 58.306 37.037 2.13 4.07 39.02 2.23
1968 2186 7.492077 TGCTATCTTCATCATATGGTCTCAT 57.508 36.000 2.13 0.00 37.40 2.90
1973 2191 5.752650 CCCATGCTATCTTCATCATATGGT 58.247 41.667 2.13 0.00 33.66 3.55
1976 2194 5.045066 ACTGCCCATGCTATCTTCATCATAT 60.045 40.000 0.00 0.00 38.71 1.78
1980 2198 2.812591 CACTGCCCATGCTATCTTCATC 59.187 50.000 0.00 0.00 38.71 2.92
1991 2209 1.604308 TTCACCTGCACTGCCCATG 60.604 57.895 0.00 0.00 0.00 3.66
1996 2214 0.665369 GCATTGTTCACCTGCACTGC 60.665 55.000 0.00 0.00 35.96 4.40
1999 2217 0.038892 CCTGCATTGTTCACCTGCAC 60.039 55.000 0.00 0.00 40.75 4.57
2410 2631 4.829064 TTAGCGAACATTCAAGCAGTTT 57.171 36.364 0.00 0.00 0.00 2.66
2439 2660 2.567615 GTGGCATACGAGGGAGGAATAT 59.432 50.000 0.00 0.00 0.00 1.28
2564 2793 4.267928 GCGTCAATGCTTAGTAAGGTAGTG 59.732 45.833 11.84 2.64 0.00 2.74
2586 2917 9.463443 AAACAGATAAATCAGTTTTGTAACAGC 57.537 29.630 7.44 0.00 41.69 4.40
2654 2996 8.041323 ACAGGAACCTATTTTGTAGTGTATCAG 58.959 37.037 0.00 0.00 0.00 2.90
2673 3015 4.021916 TGCTACTAAGTAGGGACAGGAAC 58.978 47.826 0.00 0.00 36.71 3.62
2674 3016 4.326600 TGCTACTAAGTAGGGACAGGAA 57.673 45.455 0.00 0.00 36.71 3.36
2679 3021 5.855740 AAGACATGCTACTAAGTAGGGAC 57.144 43.478 0.00 0.00 36.71 4.46
2907 3252 1.372087 CGACCAGATGGGCTGCTTTC 61.372 60.000 2.62 0.00 42.58 2.62
2923 3268 6.578020 TGTTTGTATAATCACCGATTCGAC 57.422 37.500 7.83 0.00 33.95 4.20
2938 3283 5.023533 ACTGCCTCGTCATATGTTTGTAT 57.976 39.130 1.90 0.00 0.00 2.29
3018 3363 4.574013 CCTGATGTGGATTTCTTCAGTAGC 59.426 45.833 0.00 0.00 36.21 3.58
3133 3478 2.269172 GTTAGGCCGAGTGACTAAAGC 58.731 52.381 0.00 0.00 0.00 3.51
3188 3533 2.650116 GGACTCCCGCAGCTTCTCA 61.650 63.158 0.00 0.00 0.00 3.27
3242 3587 3.381333 CTCGCTCAGCATGGCCTCA 62.381 63.158 3.32 0.00 36.16 3.86
3573 3918 1.216930 ACCTAAACAAAGTGGCACCCT 59.783 47.619 15.27 0.00 0.00 4.34
3574 3919 1.699730 ACCTAAACAAAGTGGCACCC 58.300 50.000 15.27 0.00 0.00 4.61
3689 4035 4.213059 GCTGAGACCTCTTATTATTGCAGC 59.787 45.833 0.00 0.00 38.29 5.25
3781 4130 6.432162 GCACCCATATATCATCAGACAAACAT 59.568 38.462 0.00 0.00 0.00 2.71
3792 4141 5.339778 CCTTGATCAGGCACCCATATATCAT 60.340 44.000 0.00 0.00 35.13 2.45
3795 4144 4.581309 CCTTGATCAGGCACCCATATAT 57.419 45.455 0.00 0.00 35.13 0.86
3844 4193 1.737793 GGGGATCACAACTTGCTAACG 59.262 52.381 0.00 0.00 0.00 3.18
3881 4230 0.397254 AGGGAGGTGTCTCGTATGGG 60.397 60.000 0.00 0.00 40.85 4.00
3930 4280 0.916809 GAGCTTTGGCCCCCTAGTTA 59.083 55.000 0.00 0.00 39.73 2.24
3963 4313 4.035675 GGAGGATTTTCATCTAACCAAGCG 59.964 45.833 0.00 0.00 0.00 4.68
3973 4323 3.428045 CCAAACGCAGGAGGATTTTCATC 60.428 47.826 0.00 0.00 0.00 2.92
3985 4335 1.200020 GAAGGATCAACCAAACGCAGG 59.800 52.381 0.00 0.00 42.04 4.85
4004 4354 2.417924 GCTTTGGCTTCAGAGATCTCGA 60.418 50.000 16.97 13.92 35.22 4.04
4010 4360 1.901591 CTTGGCTTTGGCTTCAGAGA 58.098 50.000 0.00 0.00 38.73 3.10
4019 4369 1.815003 CTACAAGGAGCTTGGCTTTGG 59.185 52.381 0.00 0.00 44.81 3.28
4020 4370 1.200948 GCTACAAGGAGCTTGGCTTTG 59.799 52.381 0.00 0.00 44.81 2.77
4021 4371 1.539157 GCTACAAGGAGCTTGGCTTT 58.461 50.000 0.00 0.00 44.81 3.51
4022 4372 0.674895 CGCTACAAGGAGCTTGGCTT 60.675 55.000 2.37 0.00 44.81 4.35
4023 4373 1.078848 CGCTACAAGGAGCTTGGCT 60.079 57.895 2.37 0.00 44.81 4.75
4024 4374 1.376037 ACGCTACAAGGAGCTTGGC 60.376 57.895 2.37 0.00 44.81 4.52
4025 4375 0.320771 ACACGCTACAAGGAGCTTGG 60.321 55.000 14.32 1.27 43.93 3.61
4026 4376 1.512926 AACACGCTACAAGGAGCTTG 58.487 50.000 9.02 9.02 44.86 4.01
4027 4377 1.873591 CAAACACGCTACAAGGAGCTT 59.126 47.619 2.37 0.00 40.51 3.74
4028 4378 1.202651 ACAAACACGCTACAAGGAGCT 60.203 47.619 2.37 0.00 40.51 4.09
4029 4379 1.069906 CACAAACACGCTACAAGGAGC 60.070 52.381 0.00 0.00 39.20 4.70
4036 4386 3.494232 ACAACAAACACAAACACGCTAC 58.506 40.909 0.00 0.00 0.00 3.58
4089 4439 2.289002 GAGGAGCACAACAACAACTCAG 59.711 50.000 0.00 0.00 0.00 3.35
4132 4482 3.878778 CAGTCCAGTGATTAAGAAGGGG 58.121 50.000 0.00 0.00 0.00 4.79
4151 4501 0.993746 GAAAAGCAACAGCGTCGCAG 60.994 55.000 21.09 14.65 0.00 5.18
4232 4582 1.974957 TGATTCGGGTCTTGAACTGGA 59.025 47.619 0.00 0.00 0.00 3.86
4278 4632 3.538379 TGTGGCAGCATGTACAGAG 57.462 52.632 0.33 0.00 39.31 3.35
4302 4656 0.465705 GCCAGAAGACGATGATCCCA 59.534 55.000 0.00 0.00 0.00 4.37
4355 4712 2.678336 GCACCGGATTCTGTTTCTTAGG 59.322 50.000 9.46 0.00 0.00 2.69
4363 4720 0.392998 GACATGGCACCGGATTCTGT 60.393 55.000 9.46 4.66 0.00 3.41
4435 4792 1.523938 GACGGCCATTCCTAGTGCC 60.524 63.158 2.24 0.00 40.54 5.01
4473 4830 1.967779 TGAACCAAGATGAGACGACCA 59.032 47.619 0.00 0.00 0.00 4.02
4526 4899 3.610242 GTGCTCGGCGAATCAGATTATAG 59.390 47.826 12.13 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.