Multiple sequence alignment - TraesCS7D01G179800

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 TraesCS7D01G179800 chr7D 100.000 4173 0 0 1 4173 133227827 133223655 0.000000e+00 7707
1 TraesCS7D01G179800 chr7D 98.361 61 0 1 4114 4173 524334662 524334602 5.710000e-19 106
2 TraesCS7D01G179800 chr7A 91.638 3480 150 55 693 4090 131835489 131832069 0.000000e+00 4684
3 TraesCS7D01G179800 chr7A 93.575 716 23 11 1 694 131836233 131835519 0.000000e+00 1046
4 TraesCS7D01G179800 chr7B 92.368 1782 66 25 2374 4112 94310239 94308485 0.000000e+00 2473
5 TraesCS7D01G179800 chr7B 91.592 1665 88 13 692 2331 94311874 94310237 0.000000e+00 2252
6 TraesCS7D01G179800 chr7B 93.247 696 29 11 5 694 94312586 94311903 0.000000e+00 1009
7 TraesCS7D01G179800 chr7B 98.305 59 1 0 4115 4173 674767618 674767676 2.050000e-18 104
8 TraesCS7D01G179800 chr3B 77.820 1578 236 68 705 2226 785427862 785426343 0.000000e+00 870
9 TraesCS7D01G179800 chr3B 100.000 55 0 0 4119 4173 761488401 761488347 7.380000e-18 102
10 TraesCS7D01G179800 chr6A 77.856 709 116 25 2497 3173 552832981 552832282 6.500000e-108 401
11 TraesCS7D01G179800 chr6A 77.258 299 57 10 1025 1316 552833334 552833040 9.280000e-37 165
12 TraesCS7D01G179800 chr6D 77.926 299 55 9 1025 1316 407208866 407208572 4.290000e-40 176
13 TraesCS7D01G179800 chr6D 82.209 163 29 0 1025 1187 406345708 406345546 1.560000e-29 141
14 TraesCS7D01G179800 chr6B 77.365 296 62 5 1025 1316 611349223 611348929 1.990000e-38 171
15 TraesCS7D01G179800 chr4A 100.000 58 0 0 4116 4173 659628421 659628478 1.590000e-19 108
16 TraesCS7D01G179800 chrUn 95.455 66 3 0 4107 4172 50075405 50075470 5.710000e-19 106
17 TraesCS7D01G179800 chrUn 95.455 66 3 0 4107 4172 328634075 328634140 5.710000e-19 106
18 TraesCS7D01G179800 chrUn 95.455 66 3 0 4107 4172 397695860 397695795 5.710000e-19 106
19 TraesCS7D01G179800 chr5D 96.825 63 2 0 4111 4173 236155871 236155933 5.710000e-19 106
20 TraesCS7D01G179800 chr5D 98.361 61 0 1 4114 4173 445794274 445794214 5.710000e-19 106


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 TraesCS7D01G179800 chr7D 133223655 133227827 4172 True 7707.000000 7707 100.000000 1 4173 1 chr7D.!!$R1 4172
1 TraesCS7D01G179800 chr7A 131832069 131836233 4164 True 2865.000000 4684 92.606500 1 4090 2 chr7A.!!$R1 4089
2 TraesCS7D01G179800 chr7B 94308485 94312586 4101 True 1911.333333 2473 92.402333 5 4112 3 chr7B.!!$R1 4107
3 TraesCS7D01G179800 chr3B 785426343 785427862 1519 True 870.000000 870 77.820000 705 2226 1 chr3B.!!$R2 1521
4 TraesCS7D01G179800 chr6A 552832282 552833334 1052 True 283.000000 401 77.557000 1025 3173 2 chr6A.!!$R1 2148

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
360 381 0.032952 GTACTCGCTGGTTGGTGTGA 59.967 55.000 0.00 0.00 0.00 3.58 F
366 389 0.179045 GCTGGTTGGTGTGAGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41 F
847 915 0.457443 GCATAGGAAAGCACCTTGGC 59.543 55.000 2.69 4.15 41.00 4.52 F
852 920 1.006922 GAAAGCACCTTGGCACTGC 60.007 57.895 3.35 3.35 35.83 4.40 F
1771 1894 1.122227 TCGGCTGGATGACATGATCA 58.878 50.000 0.00 0.00 43.13 2.92 F
2178 2321 1.146359 ACATGGTGCCATATCCTGCAT 59.854 47.619 3.07 0.00 40.07 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1926 0.456628 CATTCATGCCCATGTTGCGA 59.543 50.000 8.02 0.00 39.72 5.10 R
2073 2216 2.980379 TGACAACACTACCCATAACCCA 59.020 45.455 0.00 0.00 0.00 4.51 R
2507 2650 0.866061 TTGAGAGATCGCGCGCTTAC 60.866 55.000 30.48 18.73 0.00 2.34 R
2932 3081 4.111016 TAGCAGTCGTCCACGCGG 62.111 66.667 12.47 0.00 39.60 6.46 R
3018 3182 1.093159 GTAGTCCTCGTCGTCCATGT 58.907 55.000 0.00 0.00 0.00 3.21 R
4103 4354 0.249398 AACACTATCTGGGGTCGTGC 59.751 55.000 0.00 0.00 0.00 5.34 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
360 381 0.032952 GTACTCGCTGGTTGGTGTGA 59.967 55.000 0.00 0.00 0.00 3.58
366 389 0.179045 GCTGGTTGGTGTGAGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
410 433 4.680237 GGCCGGCTTTTGGTTGGC 62.680 66.667 28.56 0.41 44.98 4.52
434 457 1.429825 CATCTTGCTGCTGCTGCTC 59.570 57.895 27.67 8.99 40.48 4.26
604 630 5.791336 AAAGAAAGTTCATGTTTCCTCCC 57.209 39.130 4.20 0.00 34.93 4.30
606 632 3.399305 AGAAAGTTCATGTTTCCTCCCCT 59.601 43.478 4.20 0.00 34.93 4.79
697 753 1.889170 CAGGTCAGGGGAAGCTTTTTC 59.111 52.381 0.00 0.00 0.00 2.29
698 754 1.783365 AGGTCAGGGGAAGCTTTTTCT 59.217 47.619 0.00 0.00 0.00 2.52
701 757 2.816672 GTCAGGGGAAGCTTTTTCTCTG 59.183 50.000 15.07 15.07 0.00 3.35
710 766 6.291377 GGAAGCTTTTTCTCTGGGAATTTTT 58.709 36.000 0.00 0.00 33.53 1.94
845 913 4.454678 TCATAGCATAGGAAAGCACCTTG 58.545 43.478 2.69 3.55 41.00 3.61
847 915 0.457443 GCATAGGAAAGCACCTTGGC 59.543 55.000 2.69 4.15 41.00 4.52
852 920 1.006922 GAAAGCACCTTGGCACTGC 60.007 57.895 3.35 3.35 35.83 4.40
899 967 5.809001 TGAATGTGCTACTTCAATCCTTCT 58.191 37.500 0.00 0.00 0.00 2.85
1281 1362 2.355115 GTGTCCGGGCTTCCCAAT 59.645 61.111 7.97 0.00 45.83 3.16
1513 1615 3.602489 GCTTTCGTGCGGAATAAGTTTTC 59.398 43.478 0.00 0.00 33.85 2.29
1771 1894 1.122227 TCGGCTGGATGACATGATCA 58.878 50.000 0.00 0.00 43.13 2.92
1803 1926 2.427506 GCCCAAATCTCTGAGAAACGT 58.572 47.619 12.00 0.00 0.00 3.99
1828 1951 4.271533 GCAACATGGGCATGAATGTTAATG 59.728 41.667 16.65 10.09 43.41 1.90
1986 2115 9.810231 ATTCAATCATTTAAAAACAATTGTCGC 57.190 25.926 12.39 0.00 30.85 5.19
1989 2118 6.191534 TCATTTAAAAACAATTGTCGCACG 57.808 33.333 12.39 0.00 0.00 5.34
2059 2201 3.266510 TGGAGTATCATTCCAGTGCAC 57.733 47.619 9.40 9.40 39.74 4.57
2061 2203 2.205074 GAGTATCATTCCAGTGCACCG 58.795 52.381 14.63 2.26 33.17 4.94
2072 2215 5.227569 TCCAGTGCACCGATCATAAATAT 57.772 39.130 14.63 0.00 0.00 1.28
2073 2216 5.620206 TCCAGTGCACCGATCATAAATATT 58.380 37.500 14.63 0.00 0.00 1.28
2081 2224 7.094420 TGCACCGATCATAAATATTGGGTTATG 60.094 37.037 0.00 0.00 38.51 1.90
2085 2228 8.050325 CCGATCATAAATATTGGGTTATGGGTA 58.950 37.037 0.00 0.00 37.98 3.69
2097 2240 3.439129 GGTTATGGGTAGTGTTGTCAAGC 59.561 47.826 0.00 0.00 0.00 4.01
2099 2242 3.508845 ATGGGTAGTGTTGTCAAGCTT 57.491 42.857 0.00 0.00 0.00 3.74
2178 2321 1.146359 ACATGGTGCCATATCCTGCAT 59.854 47.619 3.07 0.00 40.07 3.96
2185 2328 4.565444 GGTGCCATATCCTGCATATGTGTA 60.565 45.833 4.29 0.00 42.14 2.90
2314 2457 1.291132 GAACTCAGTTCATAGCCGCC 58.709 55.000 13.01 0.00 41.62 6.13
2316 2459 2.202878 TCAGTTCATAGCCGCCGC 60.203 61.111 0.00 0.00 0.00 6.53
2455 2598 3.262420 CTTCTGTTTACCGGTGATCCTG 58.738 50.000 19.93 7.19 0.00 3.86
2456 2599 2.253610 TCTGTTTACCGGTGATCCTGT 58.746 47.619 19.93 0.00 35.43 4.00
2457 2600 2.232941 TCTGTTTACCGGTGATCCTGTC 59.767 50.000 19.93 0.00 33.39 3.51
2458 2601 1.276989 TGTTTACCGGTGATCCTGTCC 59.723 52.381 19.93 0.00 33.39 4.02
2476 2619 8.236585 TCCTGTCCATCCATAATATTTTGTTG 57.763 34.615 5.36 3.22 0.00 3.33
2507 2650 1.679153 ACCCTACCGTGTTTGCTTTTG 59.321 47.619 0.00 0.00 0.00 2.44
2932 3081 3.732849 CTCAAGGTCCTGGGCCCC 61.733 72.222 22.27 2.51 0.00 5.80
3179 3356 1.550524 CGGAGTCTCCATGAACCAAGA 59.449 52.381 19.15 0.00 35.91 3.02
3180 3357 2.169352 CGGAGTCTCCATGAACCAAGAT 59.831 50.000 19.15 0.00 35.91 2.40
3217 3394 2.765122 AGCTGTCAAGAGAAGTGAAGC 58.235 47.619 0.00 0.00 33.27 3.86
3368 3560 3.824133 CAGATATTGGCCTGGATGTTGA 58.176 45.455 3.32 0.00 0.00 3.18
3457 3650 7.280876 TCAATATGAACTGTTGAGAATACTGCC 59.719 37.037 0.00 0.00 30.85 4.85
3461 3654 1.348594 GTTGAGAATACTGCCGCGC 59.651 57.895 0.00 0.00 0.00 6.86
3492 3685 7.330700 TGATTTTTCGTTTTTGTTTCTGAAGCT 59.669 29.630 5.84 0.00 0.00 3.74
3502 3695 4.914983 TGTTTCTGAAGCTTCTGGATCAT 58.085 39.130 27.06 0.00 0.00 2.45
3582 3781 4.666253 CTGGTGGTGGTGGCAGGG 62.666 72.222 0.00 0.00 0.00 4.45
3596 3795 3.013932 AGGGGCTGCTGGAGAAGG 61.014 66.667 0.00 0.00 0.00 3.46
3607 3806 0.772384 TGGAGAAGGGGCGGTAAAAA 59.228 50.000 0.00 0.00 0.00 1.94
3627 3826 2.042404 GCTCTGGGCTCCTCTGATGG 62.042 65.000 0.00 0.00 38.06 3.51
3668 3875 2.667536 AGCAGAGCCAACAGTGCG 60.668 61.111 0.00 0.00 40.97 5.34
3812 4034 0.611062 ATCTTGTGACGGACGGAGGA 60.611 55.000 0.00 0.00 0.00 3.71
3830 4052 2.975489 AGGAGGTGTCTTGTTGTCAGAT 59.025 45.455 0.00 0.00 0.00 2.90
4030 4281 2.697263 TGGGATGGGAGCAGCCAT 60.697 61.111 0.00 0.00 38.95 4.40
4085 4336 2.295349 AGGCACACTTTTCAATGCTCTG 59.705 45.455 0.00 0.00 38.18 3.35
4093 4344 2.877097 TTCAATGCTCTGGTTAGGCA 57.123 45.000 0.00 0.00 40.32 4.75
4095 4346 2.436417 TCAATGCTCTGGTTAGGCAAC 58.564 47.619 0.00 0.00 39.46 4.17
4107 4358 4.025401 GGCAACCTCCAACGCACG 62.025 66.667 0.00 0.00 0.00 5.34
4113 4364 4.308458 CTCCAACGCACGACCCCA 62.308 66.667 0.00 0.00 0.00 4.96
4114 4365 4.308458 TCCAACGCACGACCCCAG 62.308 66.667 0.00 0.00 0.00 4.45
4115 4366 4.308458 CCAACGCACGACCCCAGA 62.308 66.667 0.00 0.00 0.00 3.86
4116 4367 2.047274 CAACGCACGACCCCAGAT 60.047 61.111 0.00 0.00 0.00 2.90
4117 4368 1.216977 CAACGCACGACCCCAGATA 59.783 57.895 0.00 0.00 0.00 1.98
4118 4369 0.806102 CAACGCACGACCCCAGATAG 60.806 60.000 0.00 0.00 0.00 2.08
4119 4370 1.255667 AACGCACGACCCCAGATAGT 61.256 55.000 0.00 0.00 0.00 2.12
4120 4371 1.226974 CGCACGACCCCAGATAGTG 60.227 63.158 0.00 0.00 36.05 2.74
4121 4372 1.898154 GCACGACCCCAGATAGTGT 59.102 57.895 0.00 0.00 35.46 3.55
4122 4373 0.249398 GCACGACCCCAGATAGTGTT 59.751 55.000 0.00 0.00 35.46 3.32
4123 4374 2.007049 GCACGACCCCAGATAGTGTTG 61.007 57.143 0.00 0.00 35.46 3.33
4124 4375 1.548719 CACGACCCCAGATAGTGTTGA 59.451 52.381 0.00 0.00 0.00 3.18
4125 4376 1.825474 ACGACCCCAGATAGTGTTGAG 59.175 52.381 0.00 0.00 0.00 3.02
4126 4377 1.825474 CGACCCCAGATAGTGTTGAGT 59.175 52.381 0.00 0.00 0.00 3.41
4127 4378 3.021695 CGACCCCAGATAGTGTTGAGTA 58.978 50.000 0.00 0.00 0.00 2.59
4128 4379 3.446161 CGACCCCAGATAGTGTTGAGTAA 59.554 47.826 0.00 0.00 0.00 2.24
4129 4380 4.081862 CGACCCCAGATAGTGTTGAGTAAA 60.082 45.833 0.00 0.00 0.00 2.01
4130 4381 5.395324 CGACCCCAGATAGTGTTGAGTAAAT 60.395 44.000 0.00 0.00 0.00 1.40
4131 4382 6.183360 CGACCCCAGATAGTGTTGAGTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
4132 4383 7.125792 ACCCCAGATAGTGTTGAGTAAATAG 57.874 40.000 0.00 0.00 0.00 1.73
4133 4384 6.099845 ACCCCAGATAGTGTTGAGTAAATAGG 59.900 42.308 0.00 0.00 0.00 2.57
4134 4385 5.992217 CCCAGATAGTGTTGAGTAAATAGGC 59.008 44.000 0.00 0.00 0.00 3.93
4135 4386 6.408092 CCCAGATAGTGTTGAGTAAATAGGCA 60.408 42.308 0.00 0.00 0.00 4.75
4136 4387 7.047891 CCAGATAGTGTTGAGTAAATAGGCAA 58.952 38.462 0.00 0.00 0.00 4.52
4137 4388 7.716998 CCAGATAGTGTTGAGTAAATAGGCAAT 59.283 37.037 0.00 0.00 0.00 3.56
4138 4389 9.113838 CAGATAGTGTTGAGTAAATAGGCAATT 57.886 33.333 0.00 0.00 0.00 2.32
4139 4390 9.686683 AGATAGTGTTGAGTAAATAGGCAATTT 57.313 29.630 2.34 2.34 40.87 1.82
4140 4391 9.937175 GATAGTGTTGAGTAAATAGGCAATTTC 57.063 33.333 0.00 0.00 38.71 2.17
4141 4392 9.686683 ATAGTGTTGAGTAAATAGGCAATTTCT 57.313 29.630 0.00 0.00 38.71 2.52
4142 4393 8.045176 AGTGTTGAGTAAATAGGCAATTTCTC 57.955 34.615 0.00 7.49 38.71 2.87
4143 4394 6.961554 GTGTTGAGTAAATAGGCAATTTCTCG 59.038 38.462 0.00 0.00 38.71 4.04
4144 4395 6.876789 TGTTGAGTAAATAGGCAATTTCTCGA 59.123 34.615 0.00 5.03 38.71 4.04
4145 4396 7.552687 TGTTGAGTAAATAGGCAATTTCTCGAT 59.447 33.333 0.00 0.00 38.71 3.59
4146 4397 8.398665 GTTGAGTAAATAGGCAATTTCTCGATT 58.601 33.333 0.00 0.00 38.71 3.34
4147 4398 9.607988 TTGAGTAAATAGGCAATTTCTCGATTA 57.392 29.630 0.00 0.00 38.71 1.75
4148 4399 9.607988 TGAGTAAATAGGCAATTTCTCGATTAA 57.392 29.630 0.00 0.00 38.71 1.40
4157 4408 8.912988 AGGCAATTTCTCGATTAAATTAATCCA 58.087 29.630 17.23 6.53 41.10 3.41
4158 4409 8.968242 GGCAATTTCTCGATTAAATTAATCCAC 58.032 33.333 17.23 0.00 41.10 4.02
4159 4410 8.682016 GCAATTTCTCGATTAAATTAATCCACG 58.318 33.333 17.23 8.92 41.10 4.94
4160 4411 9.929722 CAATTTCTCGATTAAATTAATCCACGA 57.070 29.630 17.23 12.07 41.10 4.35
4162 4413 8.712285 TTTCTCGATTAAATTAATCCACGAGT 57.288 30.769 22.80 0.00 41.10 4.18
4163 4414 9.806203 TTTCTCGATTAAATTAATCCACGAGTA 57.194 29.630 22.80 16.29 41.10 2.59
4164 4415 9.806203 TTCTCGATTAAATTAATCCACGAGTAA 57.194 29.630 22.80 16.72 41.10 2.24
4165 4416 9.806203 TCTCGATTAAATTAATCCACGAGTAAA 57.194 29.630 22.80 10.58 41.10 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 1.871676 AGACCCGTCTTTTTCTTTCGC 59.128 47.619 0.00 0.00 36.31 4.70
206 222 0.106819 TACTCCGGTCTCTACAGGCC 60.107 60.000 0.00 0.00 41.67 5.19
213 229 7.340256 CCAATCTATATACTACTCCGGTCTCT 58.660 42.308 0.00 0.00 0.00 3.10
434 457 0.174845 TATCCAAGAACCAGACGCGG 59.825 55.000 12.47 0.00 0.00 6.46
604 630 1.445095 CGAGATGGCTGGGAGAAGG 59.555 63.158 0.00 0.00 0.00 3.46
606 632 0.909610 AACCGAGATGGCTGGGAGAA 60.910 55.000 0.00 0.00 42.14 2.87
670 696 1.544825 TTCCCCTGACCTGCGAAGAG 61.545 60.000 0.00 0.00 0.00 2.85
710 766 2.529780 TAAAACCCAGCGAAGACGAA 57.470 45.000 0.00 0.00 42.66 3.85
716 775 5.523438 ACAGAAAAATAAAACCCAGCGAA 57.477 34.783 0.00 0.00 0.00 4.70
842 910 4.272018 GTGACTCATATTAGCAGTGCCAAG 59.728 45.833 12.58 1.72 0.00 3.61
845 913 3.134458 GGTGACTCATATTAGCAGTGCC 58.866 50.000 12.58 0.00 0.00 5.01
847 915 5.604565 TCATGGTGACTCATATTAGCAGTG 58.395 41.667 0.00 0.00 0.00 3.66
852 920 9.551734 TCAGAATTTCATGGTGACTCATATTAG 57.448 33.333 0.00 0.00 0.00 1.73
899 967 6.463995 AAAATTTCCTTAGTTCACACAGCA 57.536 33.333 0.00 0.00 0.00 4.41
993 1071 0.107459 GGTGCTCTTCCATCCCTGAC 60.107 60.000 0.00 0.00 0.00 3.51
1281 1362 2.971660 TGAAGGTGAACAACGAGTCA 57.028 45.000 0.00 0.00 0.00 3.41
1771 1894 1.338136 ATTTGGGCCCTCGATCGTCT 61.338 55.000 25.70 0.00 0.00 4.18
1803 1926 0.456628 CATTCATGCCCATGTTGCGA 59.543 50.000 8.02 0.00 39.72 5.10
1828 1951 8.538856 GCATATGATTCTCTAATGAATAGACGC 58.461 37.037 6.97 0.00 36.86 5.19
1893 2021 5.246883 AGCAGCAAGGAAAGTAATTTTGGAT 59.753 36.000 0.00 0.00 0.00 3.41
1973 2101 5.096849 ACTAAAACGTGCGACAATTGTTTT 58.903 33.333 13.36 9.63 43.08 2.43
2059 2201 6.889722 ACCCATAACCCAATATTTATGATCGG 59.110 38.462 6.48 3.29 37.73 4.18
2061 2203 9.975218 ACTACCCATAACCCAATATTTATGATC 57.025 33.333 6.48 0.00 37.73 2.92
2072 2215 3.394940 TGACAACACTACCCATAACCCAA 59.605 43.478 0.00 0.00 0.00 4.12
2073 2216 2.980379 TGACAACACTACCCATAACCCA 59.020 45.455 0.00 0.00 0.00 4.51
2081 2224 3.127425 AGAAGCTTGACAACACTACCC 57.873 47.619 2.10 0.00 0.00 3.69
2085 2228 3.134458 GTGCTAGAAGCTTGACAACACT 58.866 45.455 2.10 0.00 42.97 3.55
2097 2240 7.170658 GCAAGAGGAGTATTATTGTGCTAGAAG 59.829 40.741 0.00 0.00 0.00 2.85
2099 2242 6.325028 AGCAAGAGGAGTATTATTGTGCTAGA 59.675 38.462 0.00 0.00 38.00 2.43
2178 2321 6.654582 ACATGTTCTTCTGCATTGTACACATA 59.345 34.615 0.00 0.00 0.00 2.29
2185 2328 5.518848 TTGAACATGTTCTTCTGCATTGT 57.481 34.783 32.57 0.00 40.14 2.71
2314 2457 5.445142 CCTGCTCGATTAAATGCTATTAGCG 60.445 44.000 10.94 0.00 46.26 4.26
2316 2459 7.041780 ACAACCTGCTCGATTAAATGCTATTAG 60.042 37.037 0.00 0.00 0.00 1.73
2446 2589 4.647564 ATTATGGATGGACAGGATCACC 57.352 45.455 0.00 0.00 0.00 4.02
2455 2598 9.520204 CAGTTCAACAAAATATTATGGATGGAC 57.480 33.333 0.00 0.00 0.00 4.02
2456 2599 9.253832 ACAGTTCAACAAAATATTATGGATGGA 57.746 29.630 0.00 0.00 0.00 3.41
2476 2619 2.094854 CACGGTAGGGTCAGTACAGTTC 60.095 54.545 0.00 0.00 27.84 3.01
2507 2650 0.866061 TTGAGAGATCGCGCGCTTAC 60.866 55.000 30.48 18.73 0.00 2.34
2932 3081 4.111016 TAGCAGTCGTCCACGCGG 62.111 66.667 12.47 0.00 39.60 6.46
3018 3182 1.093159 GTAGTCCTCGTCGTCCATGT 58.907 55.000 0.00 0.00 0.00 3.21
3179 3356 7.114754 TGACAGCTTATTGATGAAGAGGAAAT 58.885 34.615 0.00 0.00 35.75 2.17
3180 3357 6.475504 TGACAGCTTATTGATGAAGAGGAAA 58.524 36.000 0.00 0.00 35.75 3.13
3368 3560 1.709578 TCCAGACAAGCTCACTCACT 58.290 50.000 0.00 0.00 0.00 3.41
3410 3603 8.922058 ATTGATGATTTGTTGCTCTATGTTTC 57.078 30.769 0.00 0.00 0.00 2.78
3457 3650 2.137395 CGAAAAATCACCACGCGCG 61.137 57.895 30.96 30.96 0.00 6.86
3461 3654 5.443142 AACAAAAACGAAAAATCACCACG 57.557 34.783 0.00 0.00 0.00 4.94
3467 3660 7.675478 AGCTTCAGAAACAAAAACGAAAAATC 58.325 30.769 0.00 0.00 0.00 2.17
3492 3685 1.211212 CCAGCCACTCATGATCCAGAA 59.789 52.381 0.00 0.00 0.00 3.02
3502 3695 2.033141 GCAGAAGCCAGCCACTCA 59.967 61.111 0.00 0.00 33.58 3.41
3537 3730 2.963371 GTCTTCTCCACGCCTCGT 59.037 61.111 0.00 0.00 42.36 4.18
3582 3781 4.811364 GCCCCTTCTCCAGCAGCC 62.811 72.222 0.00 0.00 0.00 4.85
3596 3795 1.313091 CCCAGAGCTTTTTACCGCCC 61.313 60.000 0.00 0.00 0.00 6.13
3647 3846 2.360852 CTGTTGGCTCTGCTGGGG 60.361 66.667 0.00 0.00 0.00 4.96
3812 4034 2.158769 TGCATCTGACAACAAGACACCT 60.159 45.455 0.00 0.00 0.00 4.00
4030 4281 1.228831 CATCCTGGCAACACCCCAA 60.229 57.895 0.00 0.00 46.17 4.12
4093 4344 2.280592 GGTCGTGCGTTGGAGGTT 60.281 61.111 0.00 0.00 0.00 3.50
4103 4354 0.249398 AACACTATCTGGGGTCGTGC 59.751 55.000 0.00 0.00 0.00 5.34
4107 4358 5.416271 TTTACTCAACACTATCTGGGGTC 57.584 43.478 0.00 0.00 0.00 4.46
4112 4363 8.668510 ATTGCCTATTTACTCAACACTATCTG 57.331 34.615 0.00 0.00 0.00 2.90
4113 4364 9.686683 AAATTGCCTATTTACTCAACACTATCT 57.313 29.630 0.00 0.00 34.69 1.98
4114 4365 9.937175 GAAATTGCCTATTTACTCAACACTATC 57.063 33.333 0.00 0.00 36.59 2.08
4115 4366 9.686683 AGAAATTGCCTATTTACTCAACACTAT 57.313 29.630 0.00 0.00 36.59 2.12
4116 4367 9.162764 GAGAAATTGCCTATTTACTCAACACTA 57.837 33.333 0.00 0.00 36.59 2.74
4117 4368 7.148407 CGAGAAATTGCCTATTTACTCAACACT 60.148 37.037 0.00 0.00 36.59 3.55
4118 4369 6.961554 CGAGAAATTGCCTATTTACTCAACAC 59.038 38.462 0.00 0.00 36.59 3.32
4119 4370 6.876789 TCGAGAAATTGCCTATTTACTCAACA 59.123 34.615 0.00 0.00 36.59 3.33
4120 4371 7.303634 TCGAGAAATTGCCTATTTACTCAAC 57.696 36.000 0.00 0.00 36.59 3.18
4121 4372 8.506168 AATCGAGAAATTGCCTATTTACTCAA 57.494 30.769 0.00 0.00 36.59 3.02
4122 4373 9.607988 TTAATCGAGAAATTGCCTATTTACTCA 57.392 29.630 0.00 0.00 36.59 3.41
4131 4382 8.912988 TGGATTAATTTAATCGAGAAATTGCCT 58.087 29.630 22.08 11.75 44.24 4.75
4132 4383 8.968242 GTGGATTAATTTAATCGAGAAATTGCC 58.032 33.333 22.08 19.77 44.24 4.52
4133 4384 8.682016 CGTGGATTAATTTAATCGAGAAATTGC 58.318 33.333 22.08 14.50 44.24 3.56
4134 4385 9.929722 TCGTGGATTAATTTAATCGAGAAATTG 57.070 29.630 22.08 10.11 44.24 2.32
4136 4387 9.326413 ACTCGTGGATTAATTTAATCGAGAAAT 57.674 29.630 27.80 14.36 44.24 2.17
4137 4388 8.712285 ACTCGTGGATTAATTTAATCGAGAAA 57.288 30.769 27.80 13.16 44.24 2.52
4138 4389 9.806203 TTACTCGTGGATTAATTTAATCGAGAA 57.194 29.630 27.80 19.77 44.24 2.87
4139 4390 9.806203 TTTACTCGTGGATTAATTTAATCGAGA 57.194 29.630 27.80 20.93 44.24 4.04


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

AutoCloner maintained by Alex Coulton.