Multiple sequence alignment - TraesCS5B01G154700

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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 TraesCS5B01G154700 chr5B 100.000 8166 0 0 1 8166 285050856 285042691 0.000000e+00 15080
1 TraesCS5B01G154700 chr5A 96.881 4232 110 13 3775 7997 335300690 335296472 0.000000e+00 7064
2 TraesCS5B01G154700 chr5A 94.444 3834 125 31 3 3781 335304515 335300715 0.000000e+00 5819
3 TraesCS5B01G154700 chr5A 92.899 169 8 2 8000 8164 335296408 335296240 8.190000e-60 243
4 TraesCS5B01G154700 chr5D 94.737 4275 133 26 3775 7993 252625030 252620792 0.000000e+00 6564
5 TraesCS5B01G154700 chr5D 94.017 2624 111 13 1 2603 252628982 252626384 0.000000e+00 3934
6 TraesCS5B01G154700 chr5D 94.903 1334 43 6 2468 3781 252626383 252625055 0.000000e+00 2063


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 TraesCS5B01G154700 chr5B 285042691 285050856 8165 True 15080.000000 15080 100.000000 1 8166 1 chr5B.!!$R1 8165
1 TraesCS5B01G154700 chr5A 335296240 335304515 8275 True 4375.333333 7064 94.741333 3 8164 3 chr5A.!!$R1 8161
2 TraesCS5B01G154700 chr5D 252620792 252628982 8190 True 4187.000000 6564 94.552333 1 7993 3 chr5D.!!$R1 7992

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
761 785 0.404346 TTCCCTTCCCTTCCCCAACT 60.404 55.000 0.00 0.00 0.00 3.16 F
1688 1729 0.743345 GTGTGACAGGTAATCCCCGC 60.743 60.000 0.00 0.00 0.00 6.13 F
1741 1783 1.228063 CGAGGGCTGCCATGCTTAT 60.228 57.895 22.05 0.00 0.00 1.73 F
2690 2872 2.227388 CCTGTTTCAGTCTTGGCATGAC 59.773 50.000 22.06 22.06 34.88 3.06 F
4230 4488 0.403655 TGCAGAATACCACAGGCCAA 59.596 50.000 5.01 0.00 0.00 4.52 F
5420 5678 0.178918 AGAGGGGCTAGGACCTATGC 60.179 60.000 0.46 7.91 37.18 3.14 F
5692 5950 1.344114 TGGAAATCAAAAGGCACCAGC 59.656 47.619 0.00 0.00 41.10 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1783 0.107214 GGAATCTCCGGTTGATGGCA 60.107 55.000 0.00 0.00 0.00 4.92 R
3629 3818 2.106566 ACTGTGGTTCCACATTGCAAA 58.893 42.857 22.45 1.11 44.56 3.68 R
3660 3850 3.225104 AGAGCAAAACAGATGGAGCAAA 58.775 40.909 0.00 0.00 0.00 3.68 R
4543 4801 0.924090 CTCGTTCTGATACTTGCCGC 59.076 55.000 0.00 0.00 0.00 6.53 R
5647 5905 1.268999 GGTGCGTTGAAAAGTGCATCA 60.269 47.619 0.00 0.00 40.03 3.07 R
7072 7375 1.403814 ACATCCTCGACATGTCCGAT 58.596 50.000 20.03 14.53 35.35 4.18 R
7495 7798 2.151502 TGACCAAGCAAGGGAACAAA 57.848 45.000 0.00 0.00 0.00 2.83 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
34 35 4.363999 CATAAGTTGTAGAGAAGAGGCCG 58.636 47.826 0.00 0.00 0.00 6.13
108 109 6.772605 TCCATATCTCGAATGTCCATCAATT 58.227 36.000 0.00 0.00 0.00 2.32
163 170 1.647346 TGACACACACAAGGTTCGAC 58.353 50.000 0.00 0.00 0.00 4.20
171 178 3.247648 CACACAAGGTTCGACGAAGAAAT 59.752 43.478 11.25 0.00 0.00 2.17
309 317 2.014128 CCGACATAACCAATCACCCAC 58.986 52.381 0.00 0.00 0.00 4.61
425 434 2.472488 CCAATGCTCTGTTTTCGTTTGC 59.528 45.455 0.00 0.00 0.00 3.68
438 447 6.201044 TGTTTTCGTTTGCTTCTGTTGAAAAA 59.799 30.769 0.00 0.00 36.12 1.94
473 484 7.068226 ACACCTAATTCTTTACATAACCCATGC 59.932 37.037 0.00 0.00 38.29 4.06
481 492 1.735571 ACATAACCCATGCGACGTTTC 59.264 47.619 0.00 0.00 38.29 2.78
493 504 3.649096 CGTTTCCACGGTGCATCA 58.351 55.556 1.68 0.00 43.16 3.07
494 505 2.170738 CGTTTCCACGGTGCATCAT 58.829 52.632 1.68 0.00 43.16 2.45
528 539 1.810151 GCACGTTCAACATACCATGGT 59.190 47.619 23.55 23.55 33.60 3.55
545 556 6.479006 ACCATGGTATCCAATCTACATGATG 58.521 40.000 18.10 0.00 36.95 3.07
637 655 2.409870 GCACATGGTAGGGCACAGC 61.410 63.158 0.00 0.00 0.00 4.40
706 726 2.435693 CCCTTCTCCGCCCTACCTG 61.436 68.421 0.00 0.00 0.00 4.00
733 753 0.528684 CGTCGCCATCTCCTTCCTTC 60.529 60.000 0.00 0.00 0.00 3.46
741 765 1.558233 TCTCCTTCCTTCCCTTCGTC 58.442 55.000 0.00 0.00 0.00 4.20
761 785 0.404346 TTCCCTTCCCTTCCCCAACT 60.404 55.000 0.00 0.00 0.00 3.16
1023 1059 2.107141 GTTCGCCTGATCCCTCCG 59.893 66.667 0.00 0.00 0.00 4.63
1055 1091 0.817634 CCCCATAATCTTCCGCGCAA 60.818 55.000 8.75 0.00 0.00 4.85
1087 1123 1.766496 TCCGATCGGAAATTTAGGCCT 59.234 47.619 33.96 11.78 42.05 5.19
1236 1277 5.391433 CGCGTTCGTTTTATGTGAATATTCC 59.609 40.000 12.90 5.17 0.00 3.01
1268 1309 3.808618 GCTTCCTGTAGCTATGGGATTGG 60.809 52.174 15.34 11.01 38.15 3.16
1269 1310 3.344535 TCCTGTAGCTATGGGATTGGA 57.655 47.619 11.93 3.81 0.00 3.53
1292 1333 6.479990 GGAGCTATATGGATTTTGTTTTTGGC 59.520 38.462 0.00 0.00 0.00 4.52
1522 1563 6.242829 GCTCTTTCATTGTTTTGTTTGTGTG 58.757 36.000 0.00 0.00 0.00 3.82
1688 1729 0.743345 GTGTGACAGGTAATCCCCGC 60.743 60.000 0.00 0.00 0.00 6.13
1741 1783 1.228063 CGAGGGCTGCCATGCTTAT 60.228 57.895 22.05 0.00 0.00 1.73
1828 1870 4.122776 CGATGATAGCCTTGCAACTTACT 58.877 43.478 0.00 0.00 0.00 2.24
2076 2118 4.388577 AGTTTTGGATTCTGTTAGGCCT 57.611 40.909 11.78 11.78 0.00 5.19
2096 2138 6.070194 AGGCCTAGTGACACTGTAAATTGTAT 60.070 38.462 18.58 0.00 0.00 2.29
2097 2139 6.598064 GGCCTAGTGACACTGTAAATTGTATT 59.402 38.462 18.58 0.00 0.00 1.89
2099 2141 7.962918 GCCTAGTGACACTGTAAATTGTATTTG 59.037 37.037 18.58 0.00 0.00 2.32
2123 2165 5.989777 GTGACGCCAACATTACTATTATCCT 59.010 40.000 0.00 0.00 0.00 3.24
2259 2304 5.983720 GGTATCAGCGTGTATGTCTACAAAT 59.016 40.000 0.00 0.00 39.51 2.32
2323 2369 9.090692 CGATGCTACAATCACATTGATATATCA 57.909 33.333 11.49 11.49 42.83 2.15
2436 2482 7.065803 CAGAAAGTAAAGTGAGAGTTTGGTTGA 59.934 37.037 0.00 0.00 0.00 3.18
2570 2752 5.511545 CCGAGGGCTGCTAGAATTTTATAGT 60.512 44.000 0.00 0.00 0.00 2.12
2626 2808 6.108687 CCACATGAAAGATGTAGCTGTCTAA 58.891 40.000 0.00 0.00 0.00 2.10
2690 2872 2.227388 CCTGTTTCAGTCTTGGCATGAC 59.773 50.000 22.06 22.06 34.88 3.06
2735 2917 5.067805 GGATGAGACATTTCCCATGTTTACC 59.932 44.000 0.00 0.00 31.52 2.85
2736 2918 4.991776 TGAGACATTTCCCATGTTTACCA 58.008 39.130 0.00 0.00 31.52 3.25
2848 3030 3.907474 TGGGTACTCCATGTTTCTCTCAA 59.093 43.478 0.00 0.00 41.46 3.02
2935 3117 7.255208 GGAAAACGTGGACTTTGGAATAACTTA 60.255 37.037 0.00 0.00 0.00 2.24
3068 3250 3.005472 CGAGTGAAAACTCTGGTGGACTA 59.995 47.826 4.51 0.00 34.74 2.59
3069 3251 4.322049 CGAGTGAAAACTCTGGTGGACTAT 60.322 45.833 4.51 0.00 34.74 2.12
3070 3252 5.105877 CGAGTGAAAACTCTGGTGGACTATA 60.106 44.000 4.51 0.00 34.74 1.31
3075 3257 6.440647 TGAAAACTCTGGTGGACTATATGTCT 59.559 38.462 0.00 0.00 44.74 3.41
3103 3285 9.628500 TCATGTCTACTCAGAGCTATTTAGTAA 57.372 33.333 0.00 0.00 0.00 2.24
3153 3335 5.478679 AGATGTATGGTTCCTATTCTCTCCG 59.521 44.000 0.00 0.00 0.00 4.63
3160 3342 4.750598 GGTTCCTATTCTCTCCGTAATTGC 59.249 45.833 0.00 0.00 0.00 3.56
3188 3370 6.658816 ACACCATTAGATGTGTTCAAATGCTA 59.341 34.615 0.00 0.00 0.00 3.49
3335 3524 4.806952 ATACCCTGTCTCTTCTCTAGCT 57.193 45.455 0.00 0.00 0.00 3.32
3357 3546 8.606040 AGCTGTTTTGCACAATATTGTTATTT 57.394 26.923 18.50 0.00 39.91 1.40
3629 3818 7.230712 CCAGGTAACACTTGACTTCCTTTTAAT 59.769 37.037 0.00 0.00 41.41 1.40
3797 4054 3.271729 GCCTAGTAGGAAGTTTTGCCTC 58.728 50.000 21.02 0.00 37.67 4.70
3824 4081 6.432162 CGATGGATTTGGATTTGGATGTCTAT 59.568 38.462 0.00 0.00 0.00 1.98
4230 4488 0.403655 TGCAGAATACCACAGGCCAA 59.596 50.000 5.01 0.00 0.00 4.52
4447 4705 2.927553 AATCAAAATCAGAGGCGCAC 57.072 45.000 10.83 2.06 0.00 5.34
4543 4801 5.180117 CACAGTACTGAAAATGACTGAAGGG 59.820 44.000 29.30 0.00 41.51 3.95
4691 4949 4.239428 TCAGCCTGGAATGATGATGAAA 57.761 40.909 0.00 0.00 0.00 2.69
4779 5037 3.512724 CCTTCAGCATCCTCAAAACCAAT 59.487 43.478 0.00 0.00 0.00 3.16
4885 5143 1.000052 TGTGTGCCACATTCAGCAATG 60.000 47.619 0.00 0.00 44.57 2.82
4909 5167 5.238868 GTCTGGTTCTGTTTTAAAGAGGGAC 59.761 44.000 2.04 2.30 0.00 4.46
4918 5176 3.604875 TTAAAGAGGGACGATGGTGAC 57.395 47.619 0.00 0.00 0.00 3.67
5116 5374 1.065102 CTTGCTGGGCTTTCATCATCG 59.935 52.381 0.00 0.00 0.00 3.84
5225 5483 5.506982 GCTTCTCCTTTGAATGACATATGGC 60.507 44.000 7.80 4.20 0.00 4.40
5350 5608 1.304630 TTCTGGCACCATGCTGCAT 60.305 52.632 14.72 9.81 44.28 3.96
5385 5643 4.065088 TCAACTGACAATGCTTCTACCAC 58.935 43.478 0.00 0.00 0.00 4.16
5420 5678 0.178918 AGAGGGGCTAGGACCTATGC 60.179 60.000 0.46 7.91 37.18 3.14
5430 5688 2.050144 AGGACCTATGCATACACCTGG 58.950 52.381 16.10 12.16 0.00 4.45
5608 5866 3.521560 GGATGAGTCGTATTCAACTGCA 58.478 45.455 0.00 0.00 0.00 4.41
5692 5950 1.344114 TGGAAATCAAAAGGCACCAGC 59.656 47.619 0.00 0.00 41.10 4.85
5926 6184 6.750501 GTGAGTATTGATACTTGCGTGTTCTA 59.249 38.462 5.22 0.00 43.27 2.10
5934 6192 8.887036 TGATACTTGCGTGTTCTATATTTCAT 57.113 30.769 0.00 0.00 0.00 2.57
5966 6224 2.621055 AGTATTTTTGTGCCGCAGTTGA 59.379 40.909 0.00 0.00 0.00 3.18
6016 6274 8.586570 TGTGATTTATTTCAAATGTTGTCACC 57.413 30.769 12.97 2.60 0.00 4.02
6157 6424 9.480053 GTGATTTTTATATATGTGCAATGGCTT 57.520 29.630 0.00 0.00 41.91 4.35
6195 6462 1.738099 CGCAGGGTCTTCAAGGTCG 60.738 63.158 0.00 0.00 0.00 4.79
6219 6486 4.803329 AATATCTGCACCTCCTGGATTT 57.197 40.909 0.00 0.00 37.04 2.17
6234 6501 1.718757 GATTTGCGGCACCAGCTAGG 61.719 60.000 0.05 0.00 45.67 3.02
6565 6868 6.719829 AGGTTTGTTTACTTCCCCTATCTTTG 59.280 38.462 0.00 0.00 0.00 2.77
7165 7468 8.842358 TGTATAACAGAACCTTTGGACTTTAG 57.158 34.615 0.00 0.00 0.00 1.85
7404 7707 6.035843 CCACCAATTTGATATACTTGTGTGC 58.964 40.000 0.00 0.00 0.00 4.57
7494 7797 1.599071 CGGCACATTAATGATCGCTGT 59.401 47.619 22.16 0.00 0.00 4.40
7495 7798 2.032054 CGGCACATTAATGATCGCTGTT 59.968 45.455 22.16 0.00 0.00 3.16
7518 7821 2.238521 GTTCCCTTGCTTGGTCATCAA 58.761 47.619 0.00 0.00 0.00 2.57
7519 7822 2.827921 GTTCCCTTGCTTGGTCATCAAT 59.172 45.455 0.00 0.00 34.45 2.57
7520 7823 2.726821 TCCCTTGCTTGGTCATCAATC 58.273 47.619 0.00 0.00 34.45 2.67
7521 7824 2.041485 TCCCTTGCTTGGTCATCAATCA 59.959 45.455 0.00 0.00 34.45 2.57
7552 7855 4.933330 TCTAGGCGAAGTCATACATGAAC 58.067 43.478 0.00 0.00 38.75 3.18
7553 7856 3.610040 AGGCGAAGTCATACATGAACA 57.390 42.857 0.00 0.00 38.75 3.18
7554 7857 3.525537 AGGCGAAGTCATACATGAACAG 58.474 45.455 0.00 0.00 38.75 3.16
7555 7858 3.055819 AGGCGAAGTCATACATGAACAGT 60.056 43.478 0.00 0.00 38.75 3.55
7631 7936 0.109226 AGAGAGACACCGTTTAGCGC 60.109 55.000 0.00 0.00 39.71 5.92
7651 7956 3.671459 CGCGTATGTTCTATTTCGCCATA 59.329 43.478 0.00 0.00 40.43 2.74
7889 8202 8.215926 TGTTTGTTACTAGCTGTAATGTGTTT 57.784 30.769 0.00 0.00 42.36 2.83
7974 8298 0.389817 TGAACATTCCTCTGCCGTCG 60.390 55.000 0.00 0.00 0.00 5.12
7997 8321 4.219288 GTGAAATTGAATCCAGCAGTTCCT 59.781 41.667 0.00 0.00 0.00 3.36
7998 8322 4.219070 TGAAATTGAATCCAGCAGTTCCTG 59.781 41.667 0.00 0.00 34.12 3.86
7999 8323 2.957402 TTGAATCCAGCAGTTCCTGT 57.043 45.000 0.00 0.00 33.43 4.00
8000 8324 2.479566 TGAATCCAGCAGTTCCTGTC 57.520 50.000 0.00 0.00 33.43 3.51
8002 8326 2.289882 TGAATCCAGCAGTTCCTGTCTG 60.290 50.000 8.00 8.00 36.31 3.51
8009 8333 1.073897 AGTTCCTGTCTGCTTGCCC 59.926 57.895 0.00 0.00 0.00 5.36
8010 8334 1.973812 GTTCCTGTCTGCTTGCCCC 60.974 63.158 0.00 0.00 0.00 5.80
8011 8335 3.210012 TTCCTGTCTGCTTGCCCCC 62.210 63.158 0.00 0.00 0.00 5.40
8054 8440 7.882179 ACATCCTAACAGTTTGAAACCAATAC 58.118 34.615 4.14 0.00 0.00 1.89
8061 8450 6.492254 ACAGTTTGAAACCAATACGAAGAAC 58.508 36.000 4.14 0.00 0.00 3.01
8072 8461 6.095720 ACCAATACGAAGAACAACAAGGAAAA 59.904 34.615 0.00 0.00 0.00 2.29
8073 8462 7.145323 CCAATACGAAGAACAACAAGGAAAAT 58.855 34.615 0.00 0.00 0.00 1.82
8088 8477 6.149474 ACAAGGAAAATAACAGTTCCAGATCG 59.851 38.462 5.31 0.00 44.94 3.69
8164 8553 6.971184 GTCATCCACAGCTTTCAAATCATTAG 59.029 38.462 0.00 0.00 0.00 1.73
8165 8554 5.314923 TCCACAGCTTTCAAATCATTAGC 57.685 39.130 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.632118 ACTTTTCTTTCCCTCTTTACCTCC 58.368 41.667 0.00 0.00 0.00 4.30
115 116 4.410743 GTTGCTTGCCGCCAGAGC 62.411 66.667 0.00 0.00 38.05 4.09
135 136 0.615850 TGTGTGTGTCACCACCTTCA 59.384 50.000 16.95 6.61 45.61 3.02
141 142 1.745232 GAACCTTGTGTGTGTCACCA 58.255 50.000 0.00 0.00 45.61 4.17
163 170 4.790140 CCTTTCGCTTCATCAATTTCTTCG 59.210 41.667 0.00 0.00 0.00 3.79
171 178 7.630242 ATTTATCTTCCTTTCGCTTCATCAA 57.370 32.000 0.00 0.00 0.00 2.57
222 230 2.093152 GTCGACGAATATTGGTTGCGTT 59.907 45.455 11.88 0.00 35.09 4.84
267 275 5.525199 GGGTTCTCTCTCGATTGACTAATC 58.475 45.833 0.00 0.00 39.44 1.75
277 285 2.681848 GTTATGTCGGGTTCTCTCTCGA 59.318 50.000 0.00 0.00 0.00 4.04
285 293 2.681344 GGTGATTGGTTATGTCGGGTTC 59.319 50.000 0.00 0.00 0.00 3.62
293 301 3.282021 CTCCAGTGGGTGATTGGTTATG 58.718 50.000 9.92 0.00 33.08 1.90
309 317 2.557056 TCTTATATTCGTCGCCCTCCAG 59.443 50.000 0.00 0.00 0.00 3.86
321 329 5.505819 GCCTCCGGTGCTTTTTCTTATATTC 60.506 44.000 0.00 0.00 0.00 1.75
356 364 2.605818 CGACCGATTTTCTCGCCAAATA 59.394 45.455 0.00 0.00 46.25 1.40
365 373 3.207778 TGTTGTTTCCGACCGATTTTCT 58.792 40.909 0.00 0.00 0.00 2.52
411 420 4.155099 TCAACAGAAGCAAACGAAAACAGA 59.845 37.500 0.00 0.00 0.00 3.41
412 421 4.411327 TCAACAGAAGCAAACGAAAACAG 58.589 39.130 0.00 0.00 0.00 3.16
468 479 2.474266 CGTGGAAACGTCGCATGG 59.526 61.111 0.00 0.00 0.00 3.66
473 484 2.222953 GATGCACCGTGGAAACGTCG 62.223 60.000 0.00 0.00 0.00 5.12
481 492 2.564771 AGTCATTATGATGCACCGTGG 58.435 47.619 0.00 0.00 33.14 4.94
485 496 5.461078 GCAATTGAAGTCATTATGATGCACC 59.539 40.000 10.34 0.00 33.14 5.01
486 497 6.037726 TGCAATTGAAGTCATTATGATGCAC 58.962 36.000 10.34 0.00 35.39 4.57
487 498 6.037726 GTGCAATTGAAGTCATTATGATGCA 58.962 36.000 10.34 11.74 37.70 3.96
488 499 5.172591 CGTGCAATTGAAGTCATTATGATGC 59.827 40.000 10.34 3.08 33.14 3.91
489 500 6.260377 ACGTGCAATTGAAGTCATTATGATG 58.740 36.000 10.34 0.00 34.46 3.07
490 501 6.441093 ACGTGCAATTGAAGTCATTATGAT 57.559 33.333 10.34 0.00 0.00 2.45
491 502 5.878332 ACGTGCAATTGAAGTCATTATGA 57.122 34.783 10.34 0.00 0.00 2.15
492 503 6.085573 TGAACGTGCAATTGAAGTCATTATG 58.914 36.000 10.34 0.00 0.00 1.90
493 504 6.252967 TGAACGTGCAATTGAAGTCATTAT 57.747 33.333 10.34 0.00 0.00 1.28
494 505 5.681337 TGAACGTGCAATTGAAGTCATTA 57.319 34.783 10.34 0.00 0.00 1.90
545 556 7.462571 AACCCAAACATAGAAATGGAACTAC 57.537 36.000 0.00 0.00 37.43 2.73
639 657 2.107953 GATCGCCTCCTCCTGTGC 59.892 66.667 0.00 0.00 0.00 4.57
640 658 2.025767 CTGGATCGCCTCCTCCTGTG 62.026 65.000 5.59 0.00 45.21 3.66
641 659 1.760086 CTGGATCGCCTCCTCCTGT 60.760 63.158 5.59 0.00 45.21 4.00
642 660 2.506061 CCTGGATCGCCTCCTCCTG 61.506 68.421 5.59 0.00 45.21 3.86
643 661 2.123077 CCTGGATCGCCTCCTCCT 60.123 66.667 5.59 0.00 45.21 3.69
644 662 3.237741 CCCTGGATCGCCTCCTCC 61.238 72.222 0.00 0.00 45.21 4.30
706 726 2.202349 GATGGCGACGCAAAGCAC 60.202 61.111 23.09 3.15 34.54 4.40
733 753 0.910088 AGGGAAGGGAAGACGAAGGG 60.910 60.000 0.00 0.00 0.00 3.95
741 765 0.039764 GTTGGGGAAGGGAAGGGAAG 59.960 60.000 0.00 0.00 0.00 3.46
1055 1091 3.616219 TCCGATCGGATTGAACCAAATT 58.384 40.909 32.59 0.00 39.76 1.82
1087 1123 5.654650 ACATCAAATTAATAAACGCAGGGGA 59.345 36.000 0.00 0.00 0.00 4.81
1268 1309 6.479990 GGCCAAAAACAAAATCCATATAGCTC 59.520 38.462 0.00 0.00 0.00 4.09
1269 1310 6.348498 GGCCAAAAACAAAATCCATATAGCT 58.652 36.000 0.00 0.00 0.00 3.32
1292 1333 4.278419 AGAAACGTCAAATTTCCAAGAGGG 59.722 41.667 0.00 0.00 36.84 4.30
1522 1563 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
1688 1729 6.662414 TGCATATAAAGTGAAAGTTCGAGG 57.338 37.500 0.00 0.00 0.00 4.63
1741 1783 0.107214 GGAATCTCCGGTTGATGGCA 60.107 55.000 0.00 0.00 0.00 4.92
2057 2099 5.013704 TCACTAGGCCTAACAGAATCCAAAA 59.986 40.000 14.85 0.00 0.00 2.44
2076 2118 9.549078 TCACAAATACAATTTACAGTGTCACTA 57.451 29.630 4.85 0.00 32.24 2.74
2096 2138 5.950758 AATAGTAATGTTGGCGTCACAAA 57.049 34.783 0.00 0.00 31.17 2.83
2097 2139 6.259167 GGATAATAGTAATGTTGGCGTCACAA 59.741 38.462 0.00 0.00 0.00 3.33
2099 2141 5.989777 AGGATAATAGTAATGTTGGCGTCAC 59.010 40.000 0.00 0.00 0.00 3.67
2123 2165 3.878103 TGCGCTCAAGTACCTAAAACAAA 59.122 39.130 9.73 0.00 0.00 2.83
2259 2304 9.176460 TGCATATTGAAAAGATCATTAGTGTCA 57.824 29.630 0.00 0.00 38.03 3.58
2323 2369 6.724905 ACACAAAGGTAGGATAGTAGTCACTT 59.275 38.462 0.00 0.00 36.14 3.16
2436 2482 7.728532 ACTTTTGATGGAAAACCACCTAATACT 59.271 33.333 0.00 0.00 30.13 2.12
2477 2523 4.405680 AGGACATGTCATGTTAGAATCGGA 59.594 41.667 26.47 0.00 45.03 4.55
2593 2775 4.832266 ACATCTTTCATGTGGCCTGTAAAA 59.168 37.500 3.32 0.00 0.00 1.52
2598 2780 2.357009 GCTACATCTTTCATGTGGCCTG 59.643 50.000 3.32 0.00 46.43 4.85
2626 2808 7.703058 AAAAGATTCCTGGATTTTACGACAT 57.297 32.000 0.00 0.00 0.00 3.06
2735 2917 4.445452 AGCAATAACTGAACTGGCATTG 57.555 40.909 0.00 0.00 0.00 2.82
2736 2918 4.768968 AGAAGCAATAACTGAACTGGCATT 59.231 37.500 0.00 0.00 0.00 3.56
2935 3117 3.821033 GGTGTACTTCATTCAACAGCCTT 59.179 43.478 0.00 0.00 34.99 4.35
2998 3180 5.474876 ACTGATGTTTCCTTTAAGCCTTCTG 59.525 40.000 0.00 0.00 0.00 3.02
3068 3250 8.108999 AGCTCTGAGTAGACATGATAGACATAT 58.891 37.037 6.53 0.00 37.46 1.78
3069 3251 7.457561 AGCTCTGAGTAGACATGATAGACATA 58.542 38.462 6.53 0.00 37.46 2.29
3070 3252 6.306199 AGCTCTGAGTAGACATGATAGACAT 58.694 40.000 6.53 0.00 40.17 3.06
3075 3257 9.800572 ACTAAATAGCTCTGAGTAGACATGATA 57.199 33.333 6.53 0.00 0.00 2.15
3103 3285 8.768397 TGTATTGGTTATCCATTAAGAGTGAGT 58.232 33.333 0.00 0.00 43.91 3.41
3153 3335 4.574828 ACATCTAATGGTGTCCGCAATTAC 59.425 41.667 0.00 0.00 33.60 1.89
3160 3342 3.595173 TGAACACATCTAATGGTGTCCG 58.405 45.455 0.00 0.00 46.82 4.79
3188 3370 9.137459 ACATATCACAGTAATAACTAGTGAGCT 57.863 33.333 0.00 0.00 42.08 4.09
3319 3508 4.388469 GCAAAACAGCTAGAGAAGAGACAG 59.612 45.833 0.00 0.00 0.00 3.51
3357 3546 7.090173 GCTCTGCAACAATAGAAAACCATTAA 58.910 34.615 0.00 0.00 0.00 1.40
3508 3697 2.912295 TGGATTCCCACATGTCTGAGAA 59.088 45.455 0.00 0.00 37.58 2.87
3629 3818 2.106566 ACTGTGGTTCCACATTGCAAA 58.893 42.857 22.45 1.11 44.56 3.68
3660 3850 3.225104 AGAGCAAAACAGATGGAGCAAA 58.775 40.909 0.00 0.00 0.00 3.68
3797 4054 4.581824 ACATCCAAATCCAAATCCATCGAG 59.418 41.667 0.00 0.00 0.00 4.04
4230 4488 3.136443 TGTTTGGAGGTGACAGTCTTGAT 59.864 43.478 1.31 0.00 0.00 2.57
4339 4597 6.149633 CCTGTACAGACCAAAATTTAGCAAC 58.850 40.000 24.68 0.00 0.00 4.17
4351 4609 1.229820 ATGCCCCCTGTACAGACCA 60.230 57.895 24.68 14.32 0.00 4.02
4355 4613 1.153369 CACGATGCCCCCTGTACAG 60.153 63.158 16.34 16.34 0.00 2.74
4543 4801 0.924090 CTCGTTCTGATACTTGCCGC 59.076 55.000 0.00 0.00 0.00 6.53
4691 4949 6.231258 TGAAGTCTCATCTGATGCTACAAT 57.769 37.500 12.78 6.52 0.00 2.71
4779 5037 2.354729 CAATCTGGCCCGGTTCCA 59.645 61.111 11.63 11.63 0.00 3.53
4885 5143 5.238868 GTCCCTCTTTAAAACAGAACCAGAC 59.761 44.000 0.00 0.00 0.00 3.51
4909 5167 3.066900 CCCTAAGTCTACTGTCACCATCG 59.933 52.174 0.00 0.00 0.00 3.84
4918 5176 4.767928 ACTTCTGTGTCCCTAAGTCTACTG 59.232 45.833 0.00 0.00 0.00 2.74
4926 5184 3.150458 TCTCGACTTCTGTGTCCCTAA 57.850 47.619 0.00 0.00 33.70 2.69
4928 5186 1.889829 CTTCTCGACTTCTGTGTCCCT 59.110 52.381 0.00 0.00 33.70 4.20
5116 5374 6.482524 AGAAAGTACAGGGTCCTTATTTTCC 58.517 40.000 15.06 0.00 0.00 3.13
5225 5483 2.189594 TCAGTGGCCACAGAAGAATG 57.810 50.000 36.39 23.44 0.00 2.67
5313 5571 5.511373 CCAGAAGTTCTACCATCACTTGTCA 60.511 44.000 4.74 0.00 30.71 3.58
5350 5608 6.428083 TTGTCAGTTGAAGATAACCTGGTA 57.572 37.500 0.00 0.00 0.00 3.25
5385 5643 1.726791 CCTCTTGACGTCCATTCAACG 59.273 52.381 14.12 0.00 45.37 4.10
5400 5658 1.763192 GCATAGGTCCTAGCCCCTCTT 60.763 57.143 4.57 0.00 32.08 2.85
5430 5688 7.679638 GCATACCAGAATGTTCAGAAACCATAC 60.680 40.741 0.00 0.00 34.28 2.39
5519 5777 4.385825 TCGTCTTTATTTCCACTTGCAGT 58.614 39.130 0.00 0.00 0.00 4.40
5523 5781 3.127030 GCCCTCGTCTTTATTTCCACTTG 59.873 47.826 0.00 0.00 0.00 3.16
5647 5905 1.268999 GGTGCGTTGAAAAGTGCATCA 60.269 47.619 0.00 0.00 40.03 3.07
5692 5950 6.835914 AGCAAACGAAAATCTAGACTCATTG 58.164 36.000 0.00 2.76 0.00 2.82
5934 6192 6.045955 GGCACAAAAATACTTTCCTGTTCAA 58.954 36.000 0.00 0.00 0.00 2.69
5992 6250 8.702438 CAGGTGACAACATTTGAAATAAATCAC 58.298 33.333 11.93 11.93 0.00 3.06
6036 6294 4.852134 AAAAATACTGCAGTGCACATCA 57.148 36.364 29.57 14.69 33.79 3.07
6058 6316 2.746904 CAATGTTTACCCATGCTCGACA 59.253 45.455 0.00 0.00 0.00 4.35
6059 6317 2.477863 GCAATGTTTACCCATGCTCGAC 60.478 50.000 0.00 0.00 0.00 4.20
6061 6319 1.472082 TGCAATGTTTACCCATGCTCG 59.528 47.619 0.00 0.00 0.00 5.03
6132 6390 9.478768 CAAGCCATTGCACATATATAAAAATCA 57.521 29.630 0.00 0.00 41.13 2.57
6133 6391 9.480053 ACAAGCCATTGCACATATATAAAAATC 57.520 29.630 0.00 0.00 40.27 2.17
6134 6392 9.835389 AACAAGCCATTGCACATATATAAAAAT 57.165 25.926 0.00 0.00 40.27 1.82
6135 6393 9.096160 CAACAAGCCATTGCACATATATAAAAA 57.904 29.630 0.00 0.00 40.27 1.94
6136 6394 8.645730 CAACAAGCCATTGCACATATATAAAA 57.354 30.769 0.00 0.00 40.27 1.52
6157 6424 3.852939 GCGAATGAAACACATCAGCAACA 60.853 43.478 0.00 0.00 39.39 3.33
6195 6462 4.156455 TCCAGGAGGTGCAGATATTTTC 57.844 45.455 0.00 0.00 35.89 2.29
6565 6868 9.435688 AATTATTATTGGTTTTGGAGAAGCAAC 57.564 29.630 4.61 0.00 46.08 4.17
6667 6970 9.019656 GTGTGTCTAGATATCTGAGGTTGATAT 57.980 37.037 15.79 0.00 39.13 1.63
6894 7197 5.371526 TCTGAATAGGGTTGAATGCATCTC 58.628 41.667 0.00 0.60 0.00 2.75
7072 7375 1.403814 ACATCCTCGACATGTCCGAT 58.596 50.000 20.03 14.53 35.35 4.18
7165 7468 7.040409 AGGTCAATATTCACCTTCAAAGACAAC 60.040 37.037 4.99 0.00 40.35 3.32
7367 7670 7.959689 TCAAATTGGTGGATAAAATGTTGTG 57.040 32.000 0.00 0.00 0.00 3.33
7433 7736 6.455647 TCACAACACCACACAAAACAAAATA 58.544 32.000 0.00 0.00 0.00 1.40
7440 7743 2.293677 ACGTTCACAACACCACACAAAA 59.706 40.909 0.00 0.00 0.00 2.44
7494 7797 2.461695 TGACCAAGCAAGGGAACAAAA 58.538 42.857 0.00 0.00 0.00 2.44
7495 7798 2.151502 TGACCAAGCAAGGGAACAAA 57.848 45.000 0.00 0.00 0.00 2.83
7552 7855 5.989477 TCCATATACTTCAAGGACCAACTG 58.011 41.667 0.00 0.00 0.00 3.16
7553 7856 6.831664 ATCCATATACTTCAAGGACCAACT 57.168 37.500 0.00 0.00 0.00 3.16
7554 7857 7.506114 TGTATCCATATACTTCAAGGACCAAC 58.494 38.462 0.00 0.00 39.05 3.77
7555 7858 7.684317 TGTATCCATATACTTCAAGGACCAA 57.316 36.000 0.00 0.00 39.05 3.67
7631 7936 6.033619 GCTACTATGGCGAAATAGAACATACG 59.966 42.308 10.70 0.00 34.73 3.06
7651 7956 6.438763 GCAAGAAAACATTTACACAGCTACT 58.561 36.000 0.00 0.00 0.00 2.57
7889 8202 4.734398 TCCAAAAAGCTTGCTTGAGAAA 57.266 36.364 18.60 3.71 0.00 2.52
7974 8298 4.219288 AGGAACTGCTGGATTCAATTTCAC 59.781 41.667 0.00 0.00 37.18 3.18
8009 8333 1.061657 TCATCCTTGGTAGGGTAGGGG 60.062 57.143 0.00 0.00 42.26 4.79
8010 8334 2.047830 GTCATCCTTGGTAGGGTAGGG 58.952 57.143 0.00 0.00 42.26 3.53
8011 8335 2.759355 TGTCATCCTTGGTAGGGTAGG 58.241 52.381 0.00 0.00 42.26 3.18
8012 8336 3.325135 GGATGTCATCCTTGGTAGGGTAG 59.675 52.174 22.64 0.00 46.19 3.18
8013 8337 3.314693 GGATGTCATCCTTGGTAGGGTA 58.685 50.000 22.64 0.00 46.19 3.69
8015 8339 2.938956 GGATGTCATCCTTGGTAGGG 57.061 55.000 22.64 0.00 46.19 3.53
8054 8440 7.193595 ACTGTTATTTTCCTTGTTGTTCTTCG 58.806 34.615 0.00 0.00 0.00 3.79
8061 8450 7.038154 TCTGGAACTGTTATTTTCCTTGTTG 57.962 36.000 0.00 0.00 41.76 3.33
8072 8461 3.627395 TTGGCGATCTGGAACTGTTAT 57.373 42.857 0.00 0.00 0.00 1.89
8073 8462 3.197766 AGATTGGCGATCTGGAACTGTTA 59.802 43.478 16.53 0.00 43.52 2.41
8088 8477 4.872124 GGAATTTGATGGTGAAAGATTGGC 59.128 41.667 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.