Multiple sequence alignment - TraesCS2A01G233600

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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 TraesCS2A01G233600 chr2A 100.000 4276 0 0 1 4276 278912320 278908045 0.000000e+00 7897.0
1 TraesCS2A01G233600 chr2D 91.369 2433 86 29 1892 4261 204503149 204505520 0.000000e+00 3216.0
2 TraesCS2A01G233600 chr2D 94.994 1638 59 11 320 1941 204501617 204503247 0.000000e+00 2549.0
3 TraesCS2A01G233600 chr2D 91.000 100 9 0 312 411 204501496 204501595 7.460000e-28 135.0
4 TraesCS2A01G233600 chr2B 97.182 1845 42 8 1 1842 258658135 258659972 0.000000e+00 3110.0
5 TraesCS2A01G233600 chr2B 95.169 1718 55 6 1857 3565 258660585 258662283 0.000000e+00 2687.0
6 TraesCS2A01G233600 chr2B 86.636 651 23 29 3668 4276 258662334 258662962 0.000000e+00 662.0
7 TraesCS2A01G233600 chr2B 90.604 149 6 1 1842 1990 258660529 258660669 1.570000e-44 191.0
8 TraesCS2A01G233600 chr2B 90.909 99 9 0 1843 1941 258660620 258660718 2.680000e-27 134.0
9 TraesCS2A01G233600 chr7A 94.558 147 8 0 8 154 538361735 538361881 1.200000e-55 228.0
10 TraesCS2A01G233600 chr4D 95.139 144 7 0 11 154 23322867 23322724 1.200000e-55 228.0
11 TraesCS2A01G233600 chr5D 93.878 147 9 0 8 154 62177129 62177275 5.570000e-54 222.0
12 TraesCS2A01G233600 chr5D 94.444 144 8 0 11 154 322978620 322978477 5.570000e-54 222.0
13 TraesCS2A01G233600 chr5B 94.444 144 8 0 11 154 220640578 220640721 5.570000e-54 222.0
14 TraesCS2A01G233600 chr3D 94.444 144 8 0 11 154 376923784 376923641 5.570000e-54 222.0
15 TraesCS2A01G233600 chr4B 93.750 144 9 0 11 154 648316508 648316365 2.590000e-52 217.0
16 TraesCS2A01G233600 chr4B 93.151 146 9 1 11 156 654180225 654180369 3.350000e-51 213.0
17 TraesCS2A01G233600 chr6A 100.000 28 0 0 4082 4109 125161408 125161435 8.000000e-03 52.8
18 TraesCS2A01G233600 chr3B 100.000 28 0 0 4082 4109 522783953 522783980 8.000000e-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 TraesCS2A01G233600 chr2A 278908045 278912320 4275 True 7897.000000 7897 100.000000 1 4276 1 chr2A.!!$R1 4275
1 TraesCS2A01G233600 chr2D 204501496 204505520 4024 False 1966.666667 3216 92.454333 312 4261 3 chr2D.!!$F1 3949
2 TraesCS2A01G233600 chr2B 258658135 258662962 4827 False 1356.800000 3110 92.100000 1 4276 5 chr2B.!!$F1 4275

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
100 101 0.032615 TGCCAAAGACCCAAAGTGGT 60.033 50.000 0.00 0.0 42.79 4.16 F
944 1072 1.604438 CGGCCACCTTTTTGCTTAACC 60.604 52.381 2.24 0.0 0.00 2.85 F
1797 1926 0.813184 TACTACCCAGTTTCTCGGCG 59.187 55.000 0.00 0.0 36.14 6.46 F
3056 3787 1.000607 GGGGAAGCGTTGAAGGAAAAC 60.001 52.381 0.00 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1215 0.473694 TGGAGGAGGAAAGAGCCACA 60.474 55.0 0.00 0.00 0.00 4.17 R
2849 3580 0.389556 TCTTGCTCTGAGCTGCTTCG 60.390 55.0 28.04 11.35 42.97 3.79 R
3107 3838 0.179140 GCAAGCTCGAGTCTCCAGAG 60.179 60.0 15.13 0.00 35.28 3.35 R
4091 4880 0.247185 GACTGCTCTGCTCTGCTCTT 59.753 55.0 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
82 83 2.890371 GCAGGGAAAGGCTGCATG 59.110 61.111 0.50 0.00 42.98 4.06
100 101 0.032615 TGCCAAAGACCCAAAGTGGT 60.033 50.000 0.00 0.00 42.79 4.16
121 122 3.286725 ACCCTTCCCCGGACCCTA 61.287 66.667 0.73 0.00 0.00 3.53
211 212 8.380099 TGTACCTGGATCATTTACTACAAAAGT 58.620 33.333 0.00 0.00 42.62 2.66
233 234 8.614994 AAGTTTGAAAGTTATTTTGAGTGTCG 57.385 30.769 0.00 0.00 0.00 4.35
237 238 6.556212 TGAAAGTTATTTTGAGTGTCGCAAA 58.444 32.000 0.00 0.00 31.92 3.68
238 239 7.199766 TGAAAGTTATTTTGAGTGTCGCAAAT 58.800 30.769 0.00 0.00 33.67 2.32
240 241 8.728088 AAAGTTATTTTGAGTGTCGCAAATAG 57.272 30.769 0.00 0.00 33.67 1.73
447 563 6.017400 ACATCTGCCACTGTTTAGATTTTG 57.983 37.500 0.00 0.00 0.00 2.44
571 693 3.968649 TGGGTAGTCGGCAAATTATAGGA 59.031 43.478 0.00 0.00 0.00 2.94
706 828 4.225267 CCCTTAACTTATCAGACCCTGTGT 59.775 45.833 0.00 0.00 32.61 3.72
822 949 5.065218 GTGTCGCTTGTCATTATTCTGGAAT 59.935 40.000 1.40 1.40 34.93 3.01
866 993 9.267084 GCTTCCAATATGTTGTTTCCTTTTTAA 57.733 29.630 1.26 0.00 33.36 1.52
927 1054 1.816074 TAACAACATCCCTGTTCGGC 58.184 50.000 0.00 0.00 43.76 5.54
944 1072 1.604438 CGGCCACCTTTTTGCTTAACC 60.604 52.381 2.24 0.00 0.00 2.85
953 1081 6.016555 ACCTTTTTGCTTAACCATAGTGGAT 58.983 36.000 2.45 0.00 40.96 3.41
1087 1215 1.676014 GCTCGCAAACCTGGACAGTAT 60.676 52.381 0.00 0.00 0.00 2.12
1122 1250 0.963225 TCCATTTCACTCGGTCGTCA 59.037 50.000 0.00 0.00 0.00 4.35
1202 1330 2.031012 CCAGCAGACACGGAAGCA 59.969 61.111 0.00 0.00 0.00 3.91
1386 1514 2.711922 GGCACCGTCTCTCCGTGAT 61.712 63.158 0.00 0.00 0.00 3.06
1797 1926 0.813184 TACTACCCAGTTTCTCGGCG 59.187 55.000 0.00 0.00 36.14 6.46
2535 3266 5.526506 TTATCCCTTCTACGGAAGCTAAC 57.473 43.478 0.00 0.00 45.44 2.34
2552 3283 3.118519 GCTAACATAAACTCCCTCCCGAA 60.119 47.826 0.00 0.00 0.00 4.30
2683 3414 6.047511 AGTATATGAGGTGATCCTTGATGC 57.952 41.667 0.00 0.00 45.24 3.91
2700 3431 2.180204 GCGATCATCGGTTGTGGGG 61.180 63.158 9.59 0.00 40.84 4.96
2762 3493 1.137086 CGTTATCTGGAGGGACAGGTG 59.863 57.143 0.00 0.00 38.98 4.00
2801 3532 1.643811 AGCTTCCTAGAGAGGGTGAGT 59.356 52.381 0.00 0.00 43.94 3.41
2821 3552 7.331193 GGTGAGTACGATGATCAAAACTTACTT 59.669 37.037 16.94 6.04 0.00 2.24
2849 3580 3.669023 CGCAGAGCAATGAAAGGAAAGAC 60.669 47.826 0.00 0.00 0.00 3.01
2899 3630 3.829026 GCAAAGAATCCAAGAAAGAGGGT 59.171 43.478 0.00 0.00 0.00 4.34
2903 3634 4.171234 AGAATCCAAGAAAGAGGGTGAGA 58.829 43.478 0.00 0.00 0.00 3.27
2942 3673 1.773653 GATCCTTCAAGCCCTCAGGAT 59.226 52.381 0.00 5.07 46.93 3.24
2944 3675 1.561542 TCCTTCAAGCCCTCAGGATTC 59.438 52.381 0.00 0.00 40.74 2.52
2945 3676 1.563410 CCTTCAAGCCCTCAGGATTCT 59.437 52.381 0.00 0.00 40.74 2.40
2947 3678 1.661463 TCAAGCCCTCAGGATTCTGT 58.339 50.000 0.00 0.00 40.74 3.41
3056 3787 1.000607 GGGGAAGCGTTGAAGGAAAAC 60.001 52.381 0.00 0.00 0.00 2.43
3107 3838 0.598562 TGACAGCAGAGTCGTCTTCC 59.401 55.000 0.00 0.00 41.41 3.46
3144 3875 2.203070 CGGAATCAAGGAGGCGGG 60.203 66.667 0.00 0.00 0.00 6.13
3262 3993 4.452733 GGCCGAGGAGACCAACCG 62.453 72.222 0.00 0.00 0.00 4.44
3283 4018 3.509575 CGGATCTTCCTCTGATAAGGGAG 59.490 52.174 0.00 0.00 42.74 4.30
3326 4061 3.756434 TCTTGGGCATTGTACAAAGTAGC 59.244 43.478 13.23 13.61 0.00 3.58
3335 4070 2.366266 TGTACAAAGTAGCGGACCTGTT 59.634 45.455 0.00 0.00 0.00 3.16
3378 4115 6.854381 AGTTTACTGTTTTATGTAGCGTTTGC 59.146 34.615 0.00 0.00 43.24 3.68
3408 4152 2.224113 GGTCGTGGTGAGTGAAAACCTA 60.224 50.000 0.00 0.00 37.36 3.08
3458 4202 2.058595 CGTGTAGGCTGGTAGGGCT 61.059 63.158 0.00 0.00 44.34 5.19
3469 4213 0.764752 GGTAGGGCTAGGTGGATGCT 60.765 60.000 0.00 0.00 0.00 3.79
3492 4236 0.454285 CAACCTTTGTGGCGTATGCG 60.454 55.000 0.00 0.00 44.10 4.73
3535 4279 1.482593 CCTCTCCAGTTAATCTGCGGT 59.517 52.381 0.00 0.00 42.38 5.68
3551 4295 0.040781 CGGTACTTGCGTTTTGGTGG 60.041 55.000 0.00 0.00 0.00 4.61
3554 4298 1.025812 TACTTGCGTTTTGGTGGTGG 58.974 50.000 0.00 0.00 0.00 4.61
3588 4332 1.388888 CTCTGTGTTTTCTTTGCGCG 58.611 50.000 0.00 0.00 0.00 6.86
3599 4343 1.202475 TCTTTGCGCGGTAGATATGCA 60.202 47.619 8.83 0.00 0.00 3.96
3641 4385 1.312815 GCCAGGATAGGATGTTGCAC 58.687 55.000 0.00 0.00 0.00 4.57
3642 4386 1.972872 CCAGGATAGGATGTTGCACC 58.027 55.000 0.00 0.00 0.00 5.01
3643 4387 1.212688 CCAGGATAGGATGTTGCACCA 59.787 52.381 0.00 0.00 0.00 4.17
3644 4388 2.357050 CCAGGATAGGATGTTGCACCAA 60.357 50.000 0.00 0.00 0.00 3.67
3645 4389 2.947652 CAGGATAGGATGTTGCACCAAG 59.052 50.000 0.00 0.00 0.00 3.61
3646 4390 2.578021 AGGATAGGATGTTGCACCAAGT 59.422 45.455 0.00 0.00 0.00 3.16
3647 4391 3.780294 AGGATAGGATGTTGCACCAAGTA 59.220 43.478 0.00 0.00 0.00 2.24
3648 4392 4.130118 GGATAGGATGTTGCACCAAGTAG 58.870 47.826 0.00 0.00 0.00 2.57
3649 4393 4.141711 GGATAGGATGTTGCACCAAGTAGA 60.142 45.833 0.00 0.00 0.00 2.59
3650 4394 5.455326 GGATAGGATGTTGCACCAAGTAGAT 60.455 44.000 0.00 0.00 0.00 1.98
3651 4395 6.239600 GGATAGGATGTTGCACCAAGTAGATA 60.240 42.308 0.00 0.00 0.00 1.98
3652 4396 5.028549 AGGATGTTGCACCAAGTAGATAG 57.971 43.478 0.00 0.00 0.00 2.08
3653 4397 4.716784 AGGATGTTGCACCAAGTAGATAGA 59.283 41.667 0.00 0.00 0.00 1.98
3654 4398 5.053145 GGATGTTGCACCAAGTAGATAGAG 58.947 45.833 0.00 0.00 0.00 2.43
3655 4399 3.861840 TGTTGCACCAAGTAGATAGAGC 58.138 45.455 0.00 0.00 0.00 4.09
3656 4400 3.260632 TGTTGCACCAAGTAGATAGAGCA 59.739 43.478 0.00 0.00 0.00 4.26
3657 4401 3.808466 TGCACCAAGTAGATAGAGCAG 57.192 47.619 0.00 0.00 0.00 4.24
3658 4402 3.099905 TGCACCAAGTAGATAGAGCAGT 58.900 45.455 0.00 0.00 0.00 4.40
3659 4403 4.278310 TGCACCAAGTAGATAGAGCAGTA 58.722 43.478 0.00 0.00 0.00 2.74
3660 4404 4.895889 TGCACCAAGTAGATAGAGCAGTAT 59.104 41.667 0.00 0.00 0.00 2.12
3661 4405 5.010112 TGCACCAAGTAGATAGAGCAGTATC 59.990 44.000 0.00 0.00 0.00 2.24
3662 4406 5.010112 GCACCAAGTAGATAGAGCAGTATCA 59.990 44.000 7.78 0.00 32.57 2.15
3663 4407 6.442952 CACCAAGTAGATAGAGCAGTATCAC 58.557 44.000 7.78 4.79 32.57 3.06
3664 4408 5.239744 ACCAAGTAGATAGAGCAGTATCACG 59.760 44.000 7.78 0.00 32.57 4.35
3726 4470 7.444299 CCCAATCTTGAATTTTGAGAGGAAAA 58.556 34.615 0.00 0.00 0.00 2.29
3727 4471 7.933033 CCCAATCTTGAATTTTGAGAGGAAAAA 59.067 33.333 0.00 0.00 0.00 1.94
3744 4488 0.527565 AAAATGTCGCAGTCATGGCC 59.472 50.000 0.00 0.00 36.24 5.36
3756 4503 2.124151 ATGGCCGGGTGAGAATGC 60.124 61.111 2.18 0.00 0.00 3.56
3769 4516 3.065371 GTGAGAATGCAGGGAAATTACCG 59.935 47.826 0.00 0.00 0.00 4.02
3773 4520 1.529226 TGCAGGGAAATTACCGTGTG 58.471 50.000 0.00 0.00 44.50 3.82
3819 4604 6.406400 CCCTACTCCTACTCATCAACAAGAAG 60.406 46.154 0.00 0.00 0.00 2.85
3836 4624 5.472820 ACAAGAAGCAATCTGAAGGAGAAAG 59.527 40.000 0.00 0.00 38.79 2.62
3964 4752 1.153901 GCGAGCTTGCAATGCATGT 60.154 52.632 21.53 8.88 39.85 3.21
3973 4761 0.604578 GCAATGCATGTTGTCCTGGT 59.395 50.000 0.00 0.00 0.00 4.00
4007 4795 4.308458 CACGGGCGTCCACTGGAA 62.308 66.667 6.96 0.00 31.38 3.53
4010 4798 4.717313 GGGCGTCCACTGGAACCC 62.717 72.222 17.93 17.93 41.30 4.11
4067 4856 3.643320 CCAGAGTCAGGCCAGTCATAATA 59.357 47.826 5.01 0.00 0.00 0.98
4068 4857 4.101585 CCAGAGTCAGGCCAGTCATAATAA 59.898 45.833 5.01 0.00 0.00 1.40
4086 4875 8.977412 TCATAATAATATATGACCGCCAAGAGA 58.023 33.333 0.00 0.00 37.37 3.10
4091 4880 1.561643 ATGACCGCCAAGAGAAGAGA 58.438 50.000 0.00 0.00 0.00 3.10
4094 4883 1.546476 GACCGCCAAGAGAAGAGAAGA 59.454 52.381 0.00 0.00 0.00 2.87
4095 4884 1.548269 ACCGCCAAGAGAAGAGAAGAG 59.452 52.381 0.00 0.00 0.00 2.85
4156 4946 2.037687 TGCCCTTGCCCATTCCAG 59.962 61.111 0.00 0.00 36.33 3.86
4204 5010 0.322008 CACCCTGGTTTGCTCTCTCC 60.322 60.000 0.00 0.00 0.00 3.71
4265 5075 2.686915 TCCGTCTAGGATCGTCCTTTTC 59.313 50.000 11.09 3.27 46.91 2.29
4268 5078 4.352887 CGTCTAGGATCGTCCTTTTCTTC 58.647 47.826 11.09 0.00 46.91 2.87
4273 5083 7.388224 GTCTAGGATCGTCCTTTTCTTCTTTTT 59.612 37.037 11.09 0.00 46.91 1.94
4274 5084 6.319141 AGGATCGTCCTTTTCTTCTTTTTG 57.681 37.500 1.23 0.00 46.91 2.44
4275 5085 6.062095 AGGATCGTCCTTTTCTTCTTTTTGA 58.938 36.000 1.23 0.00 46.91 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.396276 TGTTTCCAGGACTTGAACCCATA 59.604 43.478 0.00 0.00 0.00 2.74
29 30 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
80 81 1.341080 CCACTTTGGGTCTTTGGCAT 58.659 50.000 0.00 0.00 32.67 4.40
82 83 2.820845 ACCACTTTGGGTCTTTGGC 58.179 52.632 0.00 0.00 43.37 4.52
114 115 4.832608 CCCGCTTGCGTAGGGTCC 62.833 72.222 13.97 0.00 40.27 4.46
121 122 3.019003 ATGTAGCTCCCGCTTGCGT 62.019 57.895 13.97 0.00 46.47 5.24
144 145 4.994756 AGTTTTGGGGGCAGCCCG 62.995 66.667 25.18 0.00 46.66 6.13
156 157 3.140623 GCACCAAATCATGCCAAGTTTT 58.859 40.909 0.00 0.00 35.73 2.43
181 182 8.319057 TGTAGTAAATGATCCAGGTACAAGAT 57.681 34.615 0.00 0.00 0.00 2.40
211 212 6.556212 TGCGACACTCAAAATAACTTTCAAA 58.444 32.000 0.00 0.00 0.00 2.69
217 218 7.435068 ACTATTTGCGACACTCAAAATAACT 57.565 32.000 0.00 0.00 37.04 2.24
237 238 7.962441 ACAAAACAAAATAAGAGGGCAACTAT 58.038 30.769 0.00 0.00 0.00 2.12
238 239 7.354751 ACAAAACAAAATAAGAGGGCAACTA 57.645 32.000 0.00 0.00 0.00 2.24
240 241 6.918892 AACAAAACAAAATAAGAGGGCAAC 57.081 33.333 0.00 0.00 0.00 4.17
378 492 3.126831 GGCAGAAATATCAGTGAGGTCG 58.873 50.000 0.00 0.00 0.00 4.79
423 537 6.449698 CAAAATCTAAACAGTGGCAGATGTT 58.550 36.000 11.22 11.22 41.28 2.71
427 541 4.724399 TCCAAAATCTAAACAGTGGCAGA 58.276 39.130 0.00 0.00 0.00 4.26
447 563 2.733956 TCCATGGCCACTATTTGTTCC 58.266 47.619 8.16 0.00 0.00 3.62
706 828 9.781834 CGGAATATTTTGAGCAGTAAAATAACA 57.218 29.630 13.24 0.00 40.98 2.41
927 1054 5.469479 CACTATGGTTAAGCAAAAAGGTGG 58.531 41.667 12.00 0.00 0.00 4.61
944 1072 6.122277 AGGTAAATGTTCCACATCCACTATG 58.878 40.000 0.00 0.00 37.97 2.23
1087 1215 0.473694 TGGAGGAGGAAAGAGCCACA 60.474 55.000 0.00 0.00 0.00 4.17
1097 1225 1.195115 CCGAGTGAAATGGAGGAGGA 58.805 55.000 0.00 0.00 0.00 3.71
1098 1226 0.905357 ACCGAGTGAAATGGAGGAGG 59.095 55.000 0.00 0.00 0.00 4.30
1099 1227 1.469940 CGACCGAGTGAAATGGAGGAG 60.470 57.143 0.00 0.00 0.00 3.69
1122 1250 7.121759 AGCTTGTCAGTACATATTTTTGCTCAT 59.878 33.333 0.00 0.00 34.97 2.90
1602 1730 4.514066 CCAACCAAATATAGAAGGTACGCC 59.486 45.833 0.00 0.00 33.15 5.68
2535 3266 3.134804 ACTCATTCGGGAGGGAGTTTATG 59.865 47.826 0.00 0.00 37.31 1.90
2552 3283 5.060427 ACTCTGTCCAGCTATAGACTCAT 57.940 43.478 3.21 0.00 34.02 2.90
2683 3414 1.089481 CACCCCACAACCGATGATCG 61.089 60.000 8.05 8.05 40.07 3.69
2801 3532 6.592607 GTGGGAAGTAAGTTTTGATCATCGTA 59.407 38.462 0.00 0.00 0.00 3.43
2821 3552 2.046023 CATTGCTCTGCGGTGGGA 60.046 61.111 0.00 0.00 0.00 4.37
2849 3580 0.389556 TCTTGCTCTGAGCTGCTTCG 60.390 55.000 28.04 11.35 42.97 3.79
2899 3630 4.422073 TCAGAGAGCAAAGGTTTTCTCA 57.578 40.909 5.16 0.00 38.78 3.27
2903 3634 4.764308 GGATCTTCAGAGAGCAAAGGTTTT 59.236 41.667 0.00 0.00 40.07 2.43
2942 3673 1.479323 GCATACCGGTCTACCACAGAA 59.521 52.381 12.40 0.00 34.17 3.02
2944 3675 0.821517 TGCATACCGGTCTACCACAG 59.178 55.000 12.40 0.00 35.14 3.66
2945 3676 0.821517 CTGCATACCGGTCTACCACA 59.178 55.000 12.40 0.98 35.14 4.17
2947 3678 0.324923 ACCTGCATACCGGTCTACCA 60.325 55.000 12.40 3.43 35.14 3.25
3056 3787 1.750930 CCAGGGATCCATCACCTCG 59.249 63.158 15.23 0.00 30.66 4.63
3107 3838 0.179140 GCAAGCTCGAGTCTCCAGAG 60.179 60.000 15.13 0.00 35.28 3.35
3144 3875 0.392595 GTTCCGGATTCCTCACACCC 60.393 60.000 4.15 0.00 0.00 4.61
3262 3993 4.283212 CACTCCCTTATCAGAGGAAGATCC 59.717 50.000 0.00 0.00 39.25 3.36
3378 4115 2.113139 ACCACGACCAAAGGCCTG 59.887 61.111 5.69 0.00 0.00 4.85
3492 4236 1.160137 GATAGCACATCCAATCCGGC 58.840 55.000 0.00 0.00 33.14 6.13
3499 4243 4.202716 TGGAGAGGATAGATAGCACATCCA 60.203 45.833 12.53 0.00 40.67 3.41
3551 4295 2.417097 GGCCACAAAGCACACCAC 59.583 61.111 0.00 0.00 0.00 4.16
3554 4298 1.529244 AGAGGGCCACAAAGCACAC 60.529 57.895 6.18 0.00 39.23 3.82
3588 4332 2.874701 CCTGCACTTGTGCATATCTACC 59.125 50.000 25.63 0.00 44.47 3.18
3599 4343 0.892358 CTGTCATGGCCTGCACTTGT 60.892 55.000 3.32 0.00 0.00 3.16
3607 4351 0.395311 CTGGCATTCTGTCATGGCCT 60.395 55.000 3.32 0.00 46.73 5.19
3641 4385 5.239744 ACGTGATACTGCTCTATCTACTTGG 59.760 44.000 0.00 0.00 0.00 3.61
3642 4386 6.139435 CACGTGATACTGCTCTATCTACTTG 58.861 44.000 10.90 0.00 0.00 3.16
3643 4387 5.278071 GCACGTGATACTGCTCTATCTACTT 60.278 44.000 22.23 0.00 0.00 2.24
3644 4388 4.214545 GCACGTGATACTGCTCTATCTACT 59.785 45.833 22.23 0.00 0.00 2.57
3645 4389 4.468643 GCACGTGATACTGCTCTATCTAC 58.531 47.826 22.23 0.00 0.00 2.59
3646 4390 3.186613 CGCACGTGATACTGCTCTATCTA 59.813 47.826 22.23 0.00 0.00 1.98
3647 4391 2.031595 CGCACGTGATACTGCTCTATCT 60.032 50.000 22.23 0.00 0.00 1.98
3648 4392 2.311462 CGCACGTGATACTGCTCTATC 58.689 52.381 22.23 0.00 0.00 2.08
3649 4393 1.001268 CCGCACGTGATACTGCTCTAT 60.001 52.381 22.23 0.00 0.00 1.98
3650 4394 0.380733 CCGCACGTGATACTGCTCTA 59.619 55.000 22.23 0.00 0.00 2.43
3651 4395 1.139734 CCGCACGTGATACTGCTCT 59.860 57.895 22.23 0.00 0.00 4.09
3652 4396 1.153823 ACCGCACGTGATACTGCTC 60.154 57.895 22.23 0.00 0.00 4.26
3653 4397 1.446099 CACCGCACGTGATACTGCT 60.446 57.895 22.23 0.00 46.20 4.24
3654 4398 2.452813 CCACCGCACGTGATACTGC 61.453 63.158 22.23 0.62 46.20 4.40
3655 4399 1.076533 GACCACCGCACGTGATACTG 61.077 60.000 22.23 7.81 46.20 2.74
3656 4400 1.214589 GACCACCGCACGTGATACT 59.785 57.895 22.23 0.00 46.20 2.12
3657 4401 0.801067 GAGACCACCGCACGTGATAC 60.801 60.000 22.23 0.00 46.20 2.24
3658 4402 0.963856 AGAGACCACCGCACGTGATA 60.964 55.000 22.23 0.00 46.20 2.15
3659 4403 2.214181 GAGAGACCACCGCACGTGAT 62.214 60.000 22.23 0.00 46.20 3.06
3660 4404 2.910479 AGAGACCACCGCACGTGA 60.910 61.111 22.23 0.00 46.20 4.35
3661 4405 2.430921 GAGAGACCACCGCACGTG 60.431 66.667 12.28 12.28 42.62 4.49
3662 4406 2.910479 TGAGAGACCACCGCACGT 60.910 61.111 0.00 0.00 0.00 4.49
3663 4407 2.126307 CTGAGAGACCACCGCACG 60.126 66.667 0.00 0.00 0.00 5.34
3664 4408 0.247736 ATTCTGAGAGACCACCGCAC 59.752 55.000 0.00 0.00 0.00 5.34
3726 4470 1.647545 CGGCCATGACTGCGACATTT 61.648 55.000 2.24 0.00 0.00 2.32
3727 4471 2.108514 CGGCCATGACTGCGACATT 61.109 57.895 2.24 0.00 0.00 2.71
3728 4472 2.512286 CGGCCATGACTGCGACAT 60.512 61.111 2.24 0.00 0.00 3.06
3744 4488 0.322456 TTTCCCTGCATTCTCACCCG 60.322 55.000 0.00 0.00 0.00 5.28
3756 4503 0.808755 GGCACACGGTAATTTCCCTG 59.191 55.000 0.00 0.00 0.00 4.45
3792 4546 2.966516 GTTGATGAGTAGGAGTAGGGGG 59.033 54.545 0.00 0.00 0.00 5.40
3819 4604 2.163211 GCCACTTTCTCCTTCAGATTGC 59.837 50.000 0.00 0.00 0.00 3.56
3943 4731 2.001361 ATGCATTGCAAGCTCGCTCC 62.001 55.000 16.46 0.00 43.62 4.70
3964 4752 0.681564 AAACGTGGCAACCAGGACAA 60.682 50.000 12.90 0.00 41.36 3.18
4007 4795 4.457496 CTCGCGCTGACATGGGGT 62.457 66.667 5.56 0.00 0.00 4.95
4010 4798 4.827087 AGGCTCGCGCTGACATGG 62.827 66.667 5.56 0.00 36.09 3.66
4067 4856 5.540337 TCTCTTCTCTTGGCGGTCATATATT 59.460 40.000 0.00 0.00 0.00 1.28
4068 4857 5.080337 TCTCTTCTCTTGGCGGTCATATAT 58.920 41.667 0.00 0.00 0.00 0.86
4086 4875 1.205417 GCTCTGCTCTGCTCTTCTCTT 59.795 52.381 0.00 0.00 0.00 2.85
4091 4880 0.247185 GACTGCTCTGCTCTGCTCTT 59.753 55.000 0.00 0.00 0.00 2.85
4094 4883 2.980475 GGACTGCTCTGCTCTGCT 59.020 61.111 0.00 0.00 0.00 4.24
4095 4884 2.508887 CGGACTGCTCTGCTCTGC 60.509 66.667 0.00 0.00 0.00 4.26
4156 4946 2.062519 GAAGACGAAGGAAGTGCAGAC 58.937 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.