Multiple sequence alignment - TraesCS2B01G469400

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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 TraesCS2B01G469400 chr2B 100.000 4370 0 0 1 4370 665666957 665671326 0.000000e+00 8070
1 TraesCS2B01G469400 chr2B 91.364 220 18 1 4151 4370 748058916 748059134 2.550000e-77 300
2 TraesCS2B01G469400 chr2D 93.417 4208 170 42 1 4142 557662674 557666840 0.000000e+00 6137
3 TraesCS2B01G469400 chr2D 91.781 219 14 4 4152 4370 317886472 317886686 7.100000e-78 302
4 TraesCS2B01G469400 chr2A 93.381 4049 190 33 1 4022 698079869 698083866 0.000000e+00 5921
5 TraesCS2B01G469400 chr2A 92.784 97 5 2 3818 3912 698086205 698086301 5.890000e-29 139
6 TraesCS2B01G469400 chr7D 90.135 446 29 5 125 555 635099374 635099819 2.280000e-157 566
7 TraesCS2B01G469400 chr7D 92.166 217 15 2 4154 4370 597084518 597084304 5.490000e-79 305
8 TraesCS2B01G469400 chr5B 87.302 441 24 5 129 554 380782289 380782712 3.950000e-130 475
9 TraesCS2B01G469400 chr5B 92.694 219 14 2 4152 4370 461598760 461598976 9.120000e-82 315
10 TraesCS2B01G469400 chr5B 92.166 217 15 2 4154 4370 94128244 94128458 5.490000e-79 305
11 TraesCS2B01G469400 chr4A 86.907 443 24 7 129 555 688921101 688921525 2.380000e-127 466
12 TraesCS2B01G469400 chr4A 85.034 441 34 11 129 554 696397211 696397634 1.880000e-113 420
13 TraesCS2B01G469400 chr4A 91.928 223 16 2 4146 4368 637197230 637197450 1.180000e-80 311
14 TraesCS2B01G469400 chr1D 91.593 226 16 3 4145 4370 9309996 9310218 4.240000e-80 309
15 TraesCS2B01G469400 chr3D 91.781 219 14 3 4154 4370 361385579 361385795 7.100000e-78 302
16 TraesCS2B01G469400 chr6D 91.364 220 16 3 4151 4370 60514261 60514477 9.190000e-77 298


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 TraesCS2B01G469400 chr2B 665666957 665671326 4369 False 8070 8070 100.0000 1 4370 1 chr2B.!!$F1 4369
1 TraesCS2B01G469400 chr2D 557662674 557666840 4166 False 6137 6137 93.4170 1 4142 1 chr2D.!!$F2 4141
2 TraesCS2B01G469400 chr2A 698079869 698086301 6432 False 3030 5921 93.0825 1 4022 2 chr2A.!!$F1 4021

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
741 795 0.463654 ACGTCTGTTTCTGCCTGCAA 60.464 50.0 0.00 0.0 0.00 4.08 F
1299 1353 0.108615 CGCTGTCGGGTGAGAATCTT 60.109 55.0 0.00 0.0 34.92 2.40 F
2739 2793 0.114954 TGCTCAAGGCCTCCCAAAAT 59.885 50.0 5.23 0.0 40.92 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 2634 1.020861 CAATCTGTACCAGCTGCGCA 61.021 55.0 10.98 10.98 0.0 6.09 R
3249 3303 0.036388 GAGCATCCCGGAACTTGTCA 60.036 55.0 0.73 0.00 0.0 3.58 R
4221 4580 0.546598 CTCGCCCCCAGACCTATTTT 59.453 55.0 0.00 0.00 0.0 1.82 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
54 55 4.942481 CGAATCCGGCATCGCGGA 62.942 66.667 14.35 4.25 36.22 5.54
55 56 3.038417 GAATCCGGCATCGCGGAG 61.038 66.667 6.13 0.00 35.55 4.63
56 57 4.609018 AATCCGGCATCGCGGAGG 62.609 66.667 6.13 2.93 35.55 4.30
127 129 4.803426 GCAGACCTCTGACGCCCG 62.803 72.222 6.49 0.00 46.59 6.13
213 235 1.002033 AGCTTTGCTCTGCTTTGTTCG 60.002 47.619 0.00 0.00 35.86 3.95
392 425 3.550275 TCGCATTCTGATTTGTACGCTAC 59.450 43.478 0.00 0.00 0.00 3.58
402 435 2.414994 TGTACGCTACCTGCTAGTCT 57.585 50.000 0.00 0.00 40.11 3.24
403 436 3.548745 TGTACGCTACCTGCTAGTCTA 57.451 47.619 0.00 0.00 40.11 2.59
404 437 3.201290 TGTACGCTACCTGCTAGTCTAC 58.799 50.000 0.00 0.00 40.11 2.59
405 438 1.297664 ACGCTACCTGCTAGTCTACG 58.702 55.000 0.00 0.00 40.11 3.51
424 457 1.135859 CGCCTTCAGATTTCACTGTGC 60.136 52.381 2.12 0.00 38.79 4.57
441 474 4.399303 ACTGTGCATAATTGTTCTAAGGGC 59.601 41.667 0.00 0.00 0.00 5.19
460 493 1.811558 GCACACAGAAGCTCAACCTCA 60.812 52.381 0.00 0.00 0.00 3.86
470 503 4.708726 AGCTCAACCTCATGTAAATTGC 57.291 40.909 0.00 0.00 0.00 3.56
488 521 4.758773 TTGCATCATATCCAGTCACTCA 57.241 40.909 0.00 0.00 0.00 3.41
490 523 4.638304 TGCATCATATCCAGTCACTCATG 58.362 43.478 0.00 0.00 0.00 3.07
492 525 5.305128 TGCATCATATCCAGTCACTCATGTA 59.695 40.000 0.00 0.00 0.00 2.29
503 536 7.819415 TCCAGTCACTCATGTAAACATAGAAAG 59.181 37.037 0.00 0.00 34.26 2.62
533 566 2.508526 ACATTCAAGAACTGTCAGGCC 58.491 47.619 4.53 0.00 0.00 5.19
534 567 1.466167 CATTCAAGAACTGTCAGGCCG 59.534 52.381 4.53 0.00 0.00 6.13
536 569 2.032681 AAGAACTGTCAGGCCGGC 59.967 61.111 21.18 21.18 0.00 6.13
537 570 2.818169 AAGAACTGTCAGGCCGGCA 61.818 57.895 30.85 4.32 0.00 5.69
554 594 1.691196 GCATGCCCAGGTTGCTATTA 58.309 50.000 6.36 0.00 33.61 0.98
557 597 3.553508 GCATGCCCAGGTTGCTATTAATG 60.554 47.826 6.36 0.00 33.61 1.90
618 663 3.737663 GCAGAAATGGCAAACAGTCACAA 60.738 43.478 0.00 0.00 32.48 3.33
619 664 3.798337 CAGAAATGGCAAACAGTCACAAC 59.202 43.478 0.00 0.00 32.48 3.32
627 672 4.290155 GCAAACAGTCACAACCACATAAG 58.710 43.478 0.00 0.00 0.00 1.73
634 679 5.405571 CAGTCACAACCACATAAGTCTACAC 59.594 44.000 0.00 0.00 0.00 2.90
635 680 5.304614 AGTCACAACCACATAAGTCTACACT 59.695 40.000 0.00 0.00 0.00 3.55
676 722 5.044179 TCCCCAACTCAATCTGGAATGTATT 60.044 40.000 0.00 0.00 34.35 1.89
677 723 6.159575 TCCCCAACTCAATCTGGAATGTATTA 59.840 38.462 0.00 0.00 34.35 0.98
709 755 7.930513 TTAGAGTTAACAGATCGCACATATG 57.069 36.000 8.61 0.00 0.00 1.78
733 787 6.094325 TGTTTTCACCATTTACGTCTGTTTCT 59.906 34.615 0.00 0.00 0.00 2.52
741 795 0.463654 ACGTCTGTTTCTGCCTGCAA 60.464 50.000 0.00 0.00 0.00 4.08
788 842 4.066490 TGTATTTTGGTGTCCTGTTACCG 58.934 43.478 0.00 0.00 39.87 4.02
880 934 7.537596 TGGCTTCTCCAAGAAAATCATTTTA 57.462 32.000 0.00 0.00 43.21 1.52
883 937 7.493645 GGCTTCTCCAAGAAAATCATTTTATGG 59.506 37.037 16.26 16.26 39.35 2.74
888 942 8.721019 TCCAAGAAAATCATTTTATGGATTGC 57.279 30.769 19.25 0.00 40.71 3.56
911 965 8.958119 TGCTAATTGTTCTCTATTTATCCGTT 57.042 30.769 0.00 0.00 0.00 4.44
926 980 0.888736 CCGTTGTTCACATGCCCAGA 60.889 55.000 0.00 0.00 0.00 3.86
941 995 3.026694 GCCCAGAATTTGTAGCTCCAAT 58.973 45.455 0.00 0.00 0.00 3.16
1008 1062 1.514678 GCAGTTGAACCATGACCGCA 61.515 55.000 0.00 0.00 0.00 5.69
1029 1083 0.912006 AGACCAAGAAGAGGAGCCCC 60.912 60.000 0.00 0.00 0.00 5.80
1035 1089 3.003763 AAGAGGAGCCCCGTGGAC 61.004 66.667 0.00 0.00 37.58 4.02
1212 1266 2.100087 GGAGCTCTGTAGGCTTCACTAC 59.900 54.545 14.64 0.00 42.83 2.73
1299 1353 0.108615 CGCTGTCGGGTGAGAATCTT 60.109 55.000 0.00 0.00 34.92 2.40
1473 1527 2.223572 CCAAGGCAAGTTTCACACTGTC 60.224 50.000 0.00 0.00 35.12 3.51
1578 1632 8.200024 AGATACCTATGATGAAGCTGTACATT 57.800 34.615 0.00 0.00 0.00 2.71
1683 1737 0.984230 AGGCCTCTTTGGATCGTCAA 59.016 50.000 0.00 0.00 38.35 3.18
1806 1860 7.715265 TGAAGAGTCAACACTAGAATTTGAC 57.285 36.000 19.45 19.45 46.31 3.18
1856 1910 1.035139 CACATATCCCTTGGCCTTGC 58.965 55.000 3.32 0.00 0.00 4.01
2308 2362 7.289317 AGGACTCGTATGAAAGGATGGTTATAA 59.711 37.037 0.00 0.00 0.00 0.98
2349 2403 1.081094 TGAATGTCGCAGCATGTCAG 58.919 50.000 0.00 0.00 39.31 3.51
2467 2521 5.246307 AGGATTTGGTAAGCTACTTGTCAC 58.754 41.667 0.00 0.00 0.00 3.67
2557 2611 2.526304 TGACGGTCTTCTGAAGTTGG 57.474 50.000 16.43 9.36 0.00 3.77
2580 2634 8.887264 TGGTACATAATGGTAGTTTGGAAATT 57.113 30.769 0.00 0.00 0.00 1.82
2706 2760 2.647299 TGGGAAGCCTCATTCTGGTTTA 59.353 45.455 0.00 0.00 0.00 2.01
2739 2793 0.114954 TGCTCAAGGCCTCCCAAAAT 59.885 50.000 5.23 0.00 40.92 1.82
2745 2799 2.285024 GGCCTCCCAAAATGCAGCA 61.285 57.895 0.00 0.00 0.00 4.41
2903 2957 1.084370 GTGGTATCGACTGCACAGCC 61.084 60.000 0.00 0.00 0.00 4.85
2952 3006 3.392616 AGGTCATTTCTGGTTCACTCAGT 59.607 43.478 0.00 0.00 34.15 3.41
3063 3117 3.807622 TGAAACTGTTAGAGGAGTTTGCG 59.192 43.478 0.00 0.00 41.43 4.85
3088 3142 0.883833 CAGATTTCACACCACTGGGC 59.116 55.000 0.00 0.00 37.90 5.36
3094 3148 3.161450 ACACCACTGGGCTGTCGT 61.161 61.111 0.00 0.00 37.90 4.34
3104 3158 1.271163 TGGGCTGTCGTCCCTTAAAAG 60.271 52.381 0.00 0.00 44.23 2.27
3129 3183 6.277918 GAAACAAGTTTCAAAGATTGCCTG 57.722 37.500 18.09 0.00 46.03 4.85
3189 3243 0.176680 ACGCCGAGAGCTTCATGAAT 59.823 50.000 8.96 0.00 40.39 2.57
3249 3303 3.521126 ACAAGAAGGTAGCCATCATCTGT 59.479 43.478 0.00 0.00 0.00 3.41
3258 3312 3.341823 AGCCATCATCTGTGACAAGTTC 58.658 45.455 0.00 0.00 37.14 3.01
3297 3351 1.039856 TGTTTGGGAGCCTTTCAAGC 58.960 50.000 0.00 0.00 0.00 4.01
3300 3354 0.540365 TTGGGAGCCTTTCAAGCAGG 60.540 55.000 0.00 0.00 34.08 4.85
3304 3358 0.519077 GAGCCTTTCAAGCAGGAACG 59.481 55.000 0.00 0.00 32.41 3.95
3352 3406 1.339438 TGGATGTGCTGAAGAGAAGGC 60.339 52.381 0.00 0.00 0.00 4.35
3402 3456 4.082625 TGTTGCATCTGAAATAAGCTGGTG 60.083 41.667 0.00 0.00 0.00 4.17
3406 3460 0.099436 CTGAAATAAGCTGGTGCCGC 59.901 55.000 0.00 0.00 40.80 6.53
3418 3472 0.320421 GGTGCCGCTTGAGTAGAACA 60.320 55.000 0.00 0.00 0.00 3.18
3419 3473 1.676014 GGTGCCGCTTGAGTAGAACAT 60.676 52.381 0.00 0.00 0.00 2.71
3667 3723 8.079809 GCTATTAAAGGCTTAAGTTGACACAAA 58.920 33.333 0.00 0.00 30.59 2.83
3672 3728 4.461081 AGGCTTAAGTTGACACAAACACAA 59.539 37.500 4.02 0.00 32.21 3.33
3675 3731 3.866883 AAGTTGACACAAACACAAGGG 57.133 42.857 0.00 0.00 32.21 3.95
3717 3773 4.051922 AGTAACTGTGAAGAAAGCTGTCG 58.948 43.478 0.00 0.00 0.00 4.35
3770 3826 6.981722 TCCATTGCTTAAAGAGAAAACCTTC 58.018 36.000 0.00 0.00 0.00 3.46
3814 3870 0.037605 AGGACGGTGAAGGTTTAGCG 60.038 55.000 4.74 4.74 42.83 4.26
3844 3900 7.171337 TGGCTTTGATGAAAATTACTTCTTTGC 59.829 33.333 0.00 0.00 0.00 3.68
3930 3991 0.532115 GCTTTCCGCCACCAAATCAT 59.468 50.000 0.00 0.00 0.00 2.45
3933 3994 1.626686 TTCCGCCACCAAATCATTGT 58.373 45.000 0.00 0.00 34.60 2.71
4042 4218 9.265901 GTAATATTTCTTAGCTTGCTGATCAGA 57.734 33.333 27.04 8.75 0.00 3.27
4052 4228 4.732938 GCTTGCTGATCAGATTTAGGCAAC 60.733 45.833 27.04 12.01 35.03 4.17
4057 4233 2.024176 TCAGATTTAGGCAACGAGGC 57.976 50.000 0.00 0.00 46.39 4.70
4082 4262 7.647715 GCATTCTCAAACTGCAACTTAGTTTTA 59.352 33.333 0.00 0.00 43.71 1.52
4083 4263 9.515020 CATTCTCAAACTGCAACTTAGTTTTAA 57.485 29.630 0.00 0.00 43.71 1.52
4142 4325 8.396272 TGATTTCCCTTTTTAGAAACTGAGAG 57.604 34.615 0.00 0.00 34.97 3.20
4145 4328 4.104102 TCCCTTTTTAGAAACTGAGAGCCA 59.896 41.667 0.00 0.00 0.00 4.75
4156 4339 3.799281 CTGAGAGCCAGTTCCTTAGAG 57.201 52.381 0.00 0.00 38.10 2.43
4157 4340 1.827969 TGAGAGCCAGTTCCTTAGAGC 59.172 52.381 0.00 0.00 0.00 4.09
4159 4342 2.433970 GAGAGCCAGTTCCTTAGAGCAT 59.566 50.000 0.00 0.00 0.00 3.79
4160 4343 2.433970 AGAGCCAGTTCCTTAGAGCATC 59.566 50.000 0.00 0.00 0.00 3.91
4173 4532 0.674895 GAGCATCTTCAGCCGTTGGT 60.675 55.000 0.00 0.00 0.00 3.67
4174 4533 0.674895 AGCATCTTCAGCCGTTGGTC 60.675 55.000 0.00 0.00 0.00 4.02
4175 4534 1.648467 GCATCTTCAGCCGTTGGTCC 61.648 60.000 0.00 0.00 0.00 4.46
4176 4535 1.026718 CATCTTCAGCCGTTGGTCCC 61.027 60.000 0.00 0.00 0.00 4.46
4177 4536 2.198304 ATCTTCAGCCGTTGGTCCCC 62.198 60.000 0.00 0.00 0.00 4.81
4178 4537 3.920093 CTTCAGCCGTTGGTCCCCC 62.920 68.421 0.00 0.00 0.00 5.40
4180 4539 4.722700 CAGCCGTTGGTCCCCCAG 62.723 72.222 0.00 0.00 43.15 4.45
4195 4554 1.828224 CCAGGGGGCGCCTAAAATC 60.828 63.158 28.56 8.16 0.00 2.17
4201 4560 2.407616 GCGCCTAAAATCGCCACC 59.592 61.111 0.00 0.00 45.01 4.61
4203 4562 1.721487 CGCCTAAAATCGCCACCTG 59.279 57.895 0.00 0.00 0.00 4.00
4204 4563 1.714899 CGCCTAAAATCGCCACCTGG 61.715 60.000 0.00 0.00 38.53 4.45
4205 4564 1.384222 GCCTAAAATCGCCACCTGGG 61.384 60.000 0.00 0.00 40.85 4.45
4223 4582 3.597728 GGTGACCCGGCGCAAAAA 61.598 61.111 10.83 0.00 0.00 1.94
4238 4597 3.588742 AAAAATAGGTCTGGGGGCG 57.411 52.632 0.00 0.00 0.00 6.13
4240 4599 0.546598 AAAATAGGTCTGGGGGCGAG 59.453 55.000 0.00 0.00 0.00 5.03
4241 4600 0.620700 AAATAGGTCTGGGGGCGAGT 60.621 55.000 0.00 0.00 0.00 4.18
4242 4601 0.620700 AATAGGTCTGGGGGCGAGTT 60.621 55.000 0.00 0.00 0.00 3.01
4244 4603 4.410400 GGTCTGGGGGCGAGTTGG 62.410 72.222 0.00 0.00 0.00 3.77
4317 5555 9.771534 TTTGTATAGCAAATTTAGGCAAAGTTT 57.228 25.926 3.62 0.00 41.68 2.66
4318 5556 8.755696 TGTATAGCAAATTTAGGCAAAGTTTG 57.244 30.769 11.41 11.41 29.91 2.93
4320 5558 7.889589 ATAGCAAATTTAGGCAAAGTTTGAC 57.110 32.000 19.82 17.00 39.66 3.18
4336 5574 5.959652 GTTTGACTAAAACACGCCAAATT 57.040 34.783 0.00 0.00 46.30 1.82
4337 5575 6.339194 GTTTGACTAAAACACGCCAAATTT 57.661 33.333 0.00 0.00 46.30 1.82
4338 5576 6.407623 GTTTGACTAAAACACGCCAAATTTC 58.592 36.000 0.00 0.00 46.30 2.17
4340 5578 3.634283 ACTAAAACACGCCAAATTTCGG 58.366 40.909 4.55 3.83 0.00 4.30
4341 5579 1.213491 AAAACACGCCAAATTTCGGC 58.787 45.000 16.94 16.94 46.62 5.54
4350 5588 2.142319 CCAAATTTCGGCAAACTTGGG 58.858 47.619 11.98 0.00 42.71 4.12
4351 5589 1.530720 CAAATTTCGGCAAACTTGGGC 59.469 47.619 0.00 0.00 27.24 5.36
4360 6325 4.097286 TCGGCAAACTTGGGCTTTATATTC 59.903 41.667 0.00 0.00 0.00 1.75
4362 6327 5.109210 GGCAAACTTGGGCTTTATATTCAC 58.891 41.667 0.00 0.00 0.00 3.18
4368 6333 5.891551 ACTTGGGCTTTATATTCACGGATTT 59.108 36.000 0.00 0.00 0.00 2.17
4369 6334 7.057894 ACTTGGGCTTTATATTCACGGATTTA 58.942 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.496336 ATGAAGCTGGGCGGCCTC 62.496 66.667 29.87 18.36 0.00 4.70
54 55 4.052518 AATGAAGCTGGGCGGCCT 62.053 61.111 29.87 8.67 0.00 5.19
55 56 3.521796 GAATGAAGCTGGGCGGCC 61.522 66.667 23.42 23.42 0.00 6.13
56 57 3.521796 GGAATGAAGCTGGGCGGC 61.522 66.667 0.00 0.00 0.00 6.53
57 58 2.830370 GGGAATGAAGCTGGGCGG 60.830 66.667 0.00 0.00 0.00 6.13
58 59 2.830370 GGGGAATGAAGCTGGGCG 60.830 66.667 0.00 0.00 0.00 6.13
59 60 2.442830 GGGGGAATGAAGCTGGGC 60.443 66.667 0.00 0.00 0.00 5.36
213 235 0.320683 AACGTAACGGCAGTAACCCC 60.321 55.000 0.00 0.00 0.00 4.95
329 362 4.018609 CGATTAGCGCTGTCCTGG 57.981 61.111 22.90 0.00 0.00 4.45
402 435 3.325870 CACAGTGAAATCTGAAGGCGTA 58.674 45.455 0.00 0.00 38.63 4.42
403 436 2.146342 CACAGTGAAATCTGAAGGCGT 58.854 47.619 0.00 0.00 38.63 5.68
404 437 1.135859 GCACAGTGAAATCTGAAGGCG 60.136 52.381 4.15 0.00 38.63 5.52
405 438 1.881973 TGCACAGTGAAATCTGAAGGC 59.118 47.619 4.15 2.77 38.63 4.35
424 457 5.647658 TCTGTGTGCCCTTAGAACAATTATG 59.352 40.000 0.00 0.00 0.00 1.90
441 474 2.245159 TGAGGTTGAGCTTCTGTGTG 57.755 50.000 0.00 0.00 0.00 3.82
460 493 7.722728 AGTGACTGGATATGATGCAATTTACAT 59.277 33.333 0.00 0.00 0.00 2.29
470 503 7.712205 TGTTTACATGAGTGACTGGATATGATG 59.288 37.037 0.00 0.00 0.00 3.07
519 552 2.032681 GCCGGCCTGACAGTTCTT 59.967 61.111 18.11 0.00 0.00 2.52
533 566 3.993614 TAGCAACCTGGGCATGCCG 62.994 63.158 29.90 18.88 40.93 5.69
534 567 1.044790 AATAGCAACCTGGGCATGCC 61.045 55.000 29.47 29.47 40.93 4.40
536 569 3.638160 ACATTAATAGCAACCTGGGCATG 59.362 43.478 0.00 0.00 0.00 4.06
537 570 3.914771 ACATTAATAGCAACCTGGGCAT 58.085 40.909 0.00 0.00 0.00 4.40
557 597 8.992073 AGAGCAATTGAAATATGGTTGAAAAAC 58.008 29.630 10.34 0.00 0.00 2.43
575 615 5.953183 TGCGATGTATTTTCAAGAGCAATT 58.047 33.333 0.00 0.00 0.00 2.32
595 635 1.001487 TGACTGTTTGCCATTTCTGCG 60.001 47.619 0.00 0.00 0.00 5.18
634 679 7.561356 AGTTGGGGAGAAATGGTGAAAATATAG 59.439 37.037 0.00 0.00 0.00 1.31
635 680 7.418378 AGTTGGGGAGAAATGGTGAAAATATA 58.582 34.615 0.00 0.00 0.00 0.86
688 734 6.589830 AACATATGTGCGATCTGTTAACTC 57.410 37.500 9.63 0.00 0.00 3.01
701 747 6.090129 ACGTAAATGGTGAAAACATATGTGC 58.910 36.000 9.63 3.00 0.00 4.57
709 755 6.413818 CAGAAACAGACGTAAATGGTGAAAAC 59.586 38.462 0.00 0.00 0.00 2.43
741 795 0.250513 GATTCCTTGACGGCTCAGGT 59.749 55.000 6.93 0.00 0.00 4.00
788 842 3.057033 TCAGTACGAGTTTAGGCCTTGAC 60.057 47.826 12.58 10.64 0.00 3.18
894 948 7.591006 TGTGAACAACGGATAAATAGAGAAC 57.409 36.000 0.00 0.00 0.00 3.01
895 949 7.201609 GCATGTGAACAACGGATAAATAGAGAA 60.202 37.037 0.00 0.00 0.00 2.87
896 950 6.257849 GCATGTGAACAACGGATAAATAGAGA 59.742 38.462 0.00 0.00 0.00 3.10
902 956 2.490115 GGGCATGTGAACAACGGATAAA 59.510 45.455 0.00 0.00 0.00 1.40
905 959 0.251121 TGGGCATGTGAACAACGGAT 60.251 50.000 0.00 0.00 0.00 4.18
911 965 2.964464 ACAAATTCTGGGCATGTGAACA 59.036 40.909 0.00 0.00 0.00 3.18
926 980 7.951347 ATGAGAAGAATTGGAGCTACAAATT 57.049 32.000 17.06 11.02 33.48 1.82
963 1017 9.276397 CAAAACAAAATGGAAAACAGTCATTTC 57.724 29.630 0.00 0.00 39.34 2.17
964 1018 7.754475 GCAAAACAAAATGGAAAACAGTCATTT 59.246 29.630 0.00 0.00 41.22 2.32
1008 1062 0.980423 GGCTCCTCTTCTTGGTCTGT 59.020 55.000 0.00 0.00 0.00 3.41
1035 1089 1.227380 GATAGCAGCGTCCCCACTG 60.227 63.158 0.00 0.00 36.96 3.66
1299 1353 1.826340 TAGCAACCTCCTGCAAGCGA 61.826 55.000 0.00 0.00 45.18 4.93
1473 1527 2.847327 TCAGCTCCAAAGTCTTCAGG 57.153 50.000 0.00 0.00 0.00 3.86
1560 1614 6.988580 CCTTCTCAATGTACAGCTTCATCATA 59.011 38.462 0.33 0.00 0.00 2.15
1578 1632 2.037251 CTCACCGGAAACTTCCTTCTCA 59.963 50.000 9.46 0.00 45.33 3.27
1683 1737 1.466360 GCACGCATTCGCTCATCTTTT 60.466 47.619 0.00 0.00 39.84 2.27
1806 1860 3.220110 TGCTCGGTATACTGGAGTAAGG 58.780 50.000 18.98 3.01 33.76 2.69
1856 1910 7.699391 TGTAGTAATATTCTCGAAACTTGTCCG 59.301 37.037 0.00 0.00 0.00 4.79
1997 2051 2.613977 CCCTCTGCAGTTCGAAGAACAT 60.614 50.000 14.67 0.00 45.90 2.71
2152 2206 3.754965 ACTTCTTCATGGTTGCAGCTAA 58.245 40.909 0.00 0.00 0.00 3.09
2467 2521 2.303022 AGGAGTTGACCACTACACCATG 59.697 50.000 0.00 0.00 39.17 3.66
2557 2611 7.431084 CGCAATTTCCAAACTACCATTATGTAC 59.569 37.037 0.00 0.00 0.00 2.90
2580 2634 1.020861 CAATCTGTACCAGCTGCGCA 61.021 55.000 10.98 10.98 0.00 6.09
2739 2793 6.324512 AGGTTATTAATCCATTGAATGCTGCA 59.675 34.615 4.13 4.13 0.00 4.41
2745 2799 5.476945 GGCCGAGGTTATTAATCCATTGAAT 59.523 40.000 0.00 0.00 0.00 2.57
2952 3006 7.343057 ACTGTTATTATGGAGTCTGAGATGTGA 59.657 37.037 0.00 0.00 0.00 3.58
3063 3117 3.499918 CAGTGGTGTGAAATCTGTCTTCC 59.500 47.826 0.00 0.00 0.00 3.46
3104 3158 4.511454 GGCAATCTTTGAAACTTGTTTCCC 59.489 41.667 19.53 9.76 0.00 3.97
3117 3171 2.099141 TCTCGACCAGGCAATCTTTG 57.901 50.000 0.00 0.00 0.00 2.77
3129 3183 0.747255 TCAGCTGCCTAATCTCGACC 59.253 55.000 9.47 0.00 0.00 4.79
3157 3211 3.286751 GGCGTGGTTGCTCAGCAA 61.287 61.111 8.40 8.40 46.80 3.91
3189 3243 1.829849 CTCTTCTCCCTGATCACAGCA 59.170 52.381 0.00 0.00 42.25 4.41
3249 3303 0.036388 GAGCATCCCGGAACTTGTCA 60.036 55.000 0.73 0.00 0.00 3.58
3270 3324 1.576421 GCTCCCAAACAAGCTGTCG 59.424 57.895 0.00 0.00 35.60 4.35
3297 3351 1.069765 ACTCTGCACCACGTTCCTG 59.930 57.895 0.00 0.00 0.00 3.86
3300 3354 2.939022 GCACTCTGCACCACGTTC 59.061 61.111 0.00 0.00 44.26 3.95
3352 3406 7.188468 GCTAATCTCAGCTAAAATCCTTCAG 57.812 40.000 0.00 0.00 38.57 3.02
3377 3431 5.887598 ACCAGCTTATTTCAGATGCAACATA 59.112 36.000 0.00 0.00 0.00 2.29
3402 3456 4.939509 TTAAATGTTCTACTCAAGCGGC 57.060 40.909 0.00 0.00 0.00 6.53
3419 3473 9.660180 ACAAGGTTTTACAGAAGCAAATTTAAA 57.340 25.926 0.00 0.00 0.00 1.52
3667 3723 1.153046 CGGACACCAACCCTTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
3672 3728 1.486145 CCCTTACGGACACCAACCCT 61.486 60.000 0.00 0.00 0.00 4.34
3675 3731 0.672711 GCTCCCTTACGGACACCAAC 60.673 60.000 0.00 0.00 34.86 3.77
3717 3773 5.023533 TGATTACCAGCACCAGTCTATTC 57.976 43.478 0.00 0.00 0.00 1.75
3770 3826 4.993029 AGTCTCTCTCCCTAAACAATCG 57.007 45.455 0.00 0.00 0.00 3.34
3814 3870 5.482006 AGTAATTTTCATCAAAGCCAAGCC 58.518 37.500 0.00 0.00 0.00 4.35
3844 3900 5.684184 GGACGTTTAAAGTTTTGCTAACTGG 59.316 40.000 5.71 0.00 0.00 4.00
3950 4011 5.049129 GCAAGACTGACACTGATAGCTTTTT 60.049 40.000 0.00 0.00 0.00 1.94
3954 4015 2.830923 AGCAAGACTGACACTGATAGCT 59.169 45.455 0.00 0.00 0.00 3.32
3971 4032 7.045948 AGGAAACTACCTCATTGCCTAGCAA 62.046 44.000 4.23 4.23 46.95 3.91
4042 4218 2.945668 GAGAATGCCTCGTTGCCTAAAT 59.054 45.455 0.00 0.00 31.32 1.40
4052 4228 1.159285 TGCAGTTTGAGAATGCCTCG 58.841 50.000 0.00 0.00 44.92 4.63
4057 4233 7.992180 AAAACTAAGTTGCAGTTTGAGAATG 57.008 32.000 4.85 0.00 43.62 2.67
4100 4282 3.961484 ATCAGGAGGATTTTCCCCTTC 57.039 47.619 2.02 0.00 35.77 3.46
4111 4293 6.463053 TTCTAAAAAGGGAAATCAGGAGGA 57.537 37.500 0.00 0.00 0.00 3.71
4142 4325 2.998316 AGATGCTCTAAGGAACTGGC 57.002 50.000 0.00 0.00 40.86 4.85
4146 4329 3.202097 GGCTGAAGATGCTCTAAGGAAC 58.798 50.000 0.00 0.00 0.00 3.62
4147 4330 2.159043 CGGCTGAAGATGCTCTAAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
4148 4331 1.410517 CGGCTGAAGATGCTCTAAGGA 59.589 52.381 0.00 0.00 0.00 3.36
4149 4332 1.137872 ACGGCTGAAGATGCTCTAAGG 59.862 52.381 0.00 0.00 0.00 2.69
4150 4333 2.593346 ACGGCTGAAGATGCTCTAAG 57.407 50.000 0.00 0.00 0.00 2.18
4151 4334 2.621338 CAACGGCTGAAGATGCTCTAA 58.379 47.619 0.00 0.00 0.00 2.10
4152 4335 1.134699 CCAACGGCTGAAGATGCTCTA 60.135 52.381 0.00 0.00 0.00 2.43
4156 4339 1.648467 GGACCAACGGCTGAAGATGC 61.648 60.000 0.00 0.00 0.00 3.91
4157 4340 1.026718 GGGACCAACGGCTGAAGATG 61.027 60.000 0.00 0.00 0.00 2.90
4159 4342 2.747686 GGGACCAACGGCTGAAGA 59.252 61.111 0.00 0.00 0.00 2.87
4176 4535 3.373932 ATTTTAGGCGCCCCCTGGG 62.374 63.158 26.15 5.50 45.91 4.45
4177 4536 1.828224 GATTTTAGGCGCCCCCTGG 60.828 63.158 26.15 0.00 45.91 4.45
4178 4537 2.186826 CGATTTTAGGCGCCCCCTG 61.187 63.158 26.15 2.62 45.91 4.45
4180 4539 3.592814 GCGATTTTAGGCGCCCCC 61.593 66.667 26.15 5.00 46.93 5.40
4185 4544 1.714899 CCAGGTGGCGATTTTAGGCG 61.715 60.000 0.00 0.00 36.92 5.52
4187 4546 0.751643 CCCCAGGTGGCGATTTTAGG 60.752 60.000 0.00 0.00 0.00 2.69
4188 4547 0.751643 CCCCCAGGTGGCGATTTTAG 60.752 60.000 0.00 0.00 0.00 1.85
4189 4548 1.304952 CCCCCAGGTGGCGATTTTA 59.695 57.895 0.00 0.00 0.00 1.52
4190 4549 2.037208 CCCCCAGGTGGCGATTTT 59.963 61.111 0.00 0.00 0.00 1.82
4206 4565 3.597728 TTTTTGCGCCGGGTCACC 61.598 61.111 4.18 0.00 0.00 4.02
4220 4579 0.996583 TCGCCCCCAGACCTATTTTT 59.003 50.000 0.00 0.00 0.00 1.94
4221 4580 0.546598 CTCGCCCCCAGACCTATTTT 59.453 55.000 0.00 0.00 0.00 1.82
4222 4581 0.620700 ACTCGCCCCCAGACCTATTT 60.621 55.000 0.00 0.00 0.00 1.40
4223 4582 0.620700 AACTCGCCCCCAGACCTATT 60.621 55.000 0.00 0.00 0.00 1.73
4224 4583 1.003051 AACTCGCCCCCAGACCTAT 59.997 57.895 0.00 0.00 0.00 2.57
4226 4585 3.322466 CAACTCGCCCCCAGACCT 61.322 66.667 0.00 0.00 0.00 3.85
4227 4586 4.410400 CCAACTCGCCCCCAGACC 62.410 72.222 0.00 0.00 0.00 3.85
4295 5533 8.802267 AGTCAAACTTTGCCTAAATTTGCTATA 58.198 29.630 0.00 0.00 31.64 1.31
4296 5534 7.670364 AGTCAAACTTTGCCTAAATTTGCTAT 58.330 30.769 0.00 0.00 31.64 2.97
4297 5535 7.049799 AGTCAAACTTTGCCTAAATTTGCTA 57.950 32.000 0.00 0.00 31.64 3.49
4299 5537 7.707774 TTAGTCAAACTTTGCCTAAATTTGC 57.292 32.000 0.00 0.00 29.18 3.68
4300 5538 9.914923 GTTTTAGTCAAACTTTGCCTAAATTTG 57.085 29.630 15.15 0.00 39.79 2.32
4301 5539 9.660180 TGTTTTAGTCAAACTTTGCCTAAATTT 57.340 25.926 15.15 0.00 44.68 1.82
4302 5540 9.093970 GTGTTTTAGTCAAACTTTGCCTAAATT 57.906 29.630 15.15 0.00 44.68 1.82
4305 5543 6.259638 CGTGTTTTAGTCAAACTTTGCCTAA 58.740 36.000 1.67 1.67 44.68 2.69
4306 5544 5.731126 GCGTGTTTTAGTCAAACTTTGCCTA 60.731 40.000 1.87 0.00 44.68 3.93
4307 5545 4.668289 CGTGTTTTAGTCAAACTTTGCCT 58.332 39.130 1.87 0.00 44.68 4.75
4308 5546 3.242016 GCGTGTTTTAGTCAAACTTTGCC 59.758 43.478 1.87 0.00 44.68 4.52
4309 5547 3.242016 GGCGTGTTTTAGTCAAACTTTGC 59.758 43.478 1.87 3.23 44.68 3.68
4310 5548 4.416620 TGGCGTGTTTTAGTCAAACTTTG 58.583 39.130 1.87 0.00 44.68 2.77
4311 5549 4.705337 TGGCGTGTTTTAGTCAAACTTT 57.295 36.364 1.87 0.00 44.68 2.66
4312 5550 4.705337 TTGGCGTGTTTTAGTCAAACTT 57.295 36.364 1.87 0.00 44.68 2.66
4313 5551 4.705337 TTTGGCGTGTTTTAGTCAAACT 57.295 36.364 1.87 0.00 44.68 2.66
4314 5552 5.959652 AATTTGGCGTGTTTTAGTCAAAC 57.040 34.783 0.00 0.00 43.43 2.93
4315 5553 5.230306 CGAAATTTGGCGTGTTTTAGTCAAA 59.770 36.000 0.00 0.00 44.49 2.69
4317 5555 4.283678 CGAAATTTGGCGTGTTTTAGTCA 58.716 39.130 0.00 0.00 0.00 3.41
4318 5556 3.666797 CCGAAATTTGGCGTGTTTTAGTC 59.333 43.478 0.00 0.00 0.00 2.59
4320 5558 2.407026 GCCGAAATTTGGCGTGTTTTAG 59.593 45.455 8.71 0.00 43.70 1.85
4321 5559 2.395654 GCCGAAATTTGGCGTGTTTTA 58.604 42.857 8.71 0.00 43.70 1.52
4322 5560 1.213491 GCCGAAATTTGGCGTGTTTT 58.787 45.000 8.71 0.00 43.70 2.43
4323 5561 2.893671 GCCGAAATTTGGCGTGTTT 58.106 47.368 8.71 0.00 43.70 2.83
4324 5562 4.645692 GCCGAAATTTGGCGTGTT 57.354 50.000 8.71 0.00 43.70 3.32
4331 5569 1.530720 GCCCAAGTTTGCCGAAATTTG 59.469 47.619 0.00 0.00 38.10 2.32
4332 5570 1.416030 AGCCCAAGTTTGCCGAAATTT 59.584 42.857 0.00 0.00 0.00 1.82
4333 5571 1.047801 AGCCCAAGTTTGCCGAAATT 58.952 45.000 0.00 0.00 0.00 1.82
4335 5573 0.827368 AAAGCCCAAGTTTGCCGAAA 59.173 45.000 0.00 0.00 0.00 3.46
4336 5574 1.693627 TAAAGCCCAAGTTTGCCGAA 58.306 45.000 0.00 0.00 0.00 4.30
4337 5575 1.917872 ATAAAGCCCAAGTTTGCCGA 58.082 45.000 0.00 0.00 0.00 5.54
4338 5576 4.142271 TGAATATAAAGCCCAAGTTTGCCG 60.142 41.667 0.00 0.00 0.00 5.69
4340 5578 4.798387 CGTGAATATAAAGCCCAAGTTTGC 59.202 41.667 0.00 0.00 0.00 3.68
4341 5579 5.124776 TCCGTGAATATAAAGCCCAAGTTTG 59.875 40.000 0.00 0.00 0.00 2.93
4342 5580 5.258051 TCCGTGAATATAAAGCCCAAGTTT 58.742 37.500 0.00 0.00 0.00 2.66
4343 5581 4.850680 TCCGTGAATATAAAGCCCAAGTT 58.149 39.130 0.00 0.00 0.00 2.66
4344 5582 4.497291 TCCGTGAATATAAAGCCCAAGT 57.503 40.909 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.