Multiple sequence alignment - TraesCS2A01G134000

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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 TraesCS2A01G134000 chr2A 100.000 7167 0 0 1 7167 80586526 80593692 0.000000e+00 13236
1 TraesCS2A01G134000 chr2D 96.485 4495 125 14 2684 7167 79983670 79988142 0.000000e+00 7395
2 TraesCS2A01G134000 chr2D 93.882 2321 78 27 322 2608 79981356 79983646 0.000000e+00 3441
3 TraesCS2A01G134000 chr2D 87.850 214 15 3 3 215 79980968 79981171 2.580000e-59 241
4 TraesCS2A01G134000 chr2D 90.541 74 7 0 237 310 79981240 79981313 1.650000e-16 99
5 TraesCS2A01G134000 chr2B 97.138 4263 103 8 2906 7167 131570634 131574878 0.000000e+00 7179
6 TraesCS2A01G134000 chr2B 92.997 1942 81 26 893 2804 131568644 131570560 0.000000e+00 2782
7 TraesCS2A01G134000 chr2B 84.605 708 46 25 216 880 131567914 131568601 0.000000e+00 645
8 TraesCS2A01G134000 chr2B 91.457 199 15 1 19 215 131567685 131567883 9.160000e-69 272
9 TraesCS2A01G134000 chr4B 91.631 466 25 7 2102 2563 653276407 653276862 3.650000e-177 632
10 TraesCS2A01G134000 chr4B 98.726 157 2 0 1515 1671 653276255 653276411 5.470000e-71 279


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 TraesCS2A01G134000 chr2A 80586526 80593692 7166 False 13236.0 13236 100.00000 1 7167 1 chr2A.!!$F1 7166
1 TraesCS2A01G134000 chr2D 79980968 79988142 7174 False 2794.0 7395 92.18950 3 7167 4 chr2D.!!$F1 7164
2 TraesCS2A01G134000 chr2B 131567685 131574878 7193 False 2719.5 7179 91.54925 19 7167 4 chr2B.!!$F1 7148
3 TraesCS2A01G134000 chr4B 653276255 653276862 607 False 455.5 632 95.17850 1515 2563 2 chr4B.!!$F1 1048

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
269 319 0.107993 CGGCAGAAAGGCAGAGATCA 60.108 55.0 0.0 0.0 44.47 2.92 F
460 546 0.170339 CGGCCCAAGATCGGAAAAAC 59.830 55.0 0.0 0.0 0.00 2.43 F
916 1067 0.810648 GATTGCCGCTCCATTGTTGA 59.189 50.0 0.0 0.0 0.00 3.18 F
2481 2654 1.093159 GAGCTGAACTGGGAATGCTG 58.907 55.0 0.0 0.0 0.00 4.41 F
2611 2784 1.148157 CTCACATCGATCCACACGGC 61.148 60.0 0.0 0.0 0.00 5.68 F
3545 3745 0.179045 ATGGCTACAATGTCGAGGGC 60.179 55.0 0.0 0.0 0.00 5.19 F
4853 5053 0.249741 GTGATCCCATCCGTAACCCG 60.250 60.0 0.0 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2284 1.156736 CGAACGGCTTCTTGGTGATT 58.843 50.000 0.00 0.00 0.00 2.57 R
2235 2404 3.323136 GGCAGCGCGACGATGTAG 61.323 66.667 12.10 0.00 45.34 2.74 R
2665 2852 0.318441 TGGGCGTCAGAACTCAGAAG 59.682 55.000 0.00 0.00 0.00 2.85 R
3461 3661 1.377594 CAGGTATGCTGCAGTGCCA 60.378 57.895 16.64 5.17 0.00 4.92 R
4505 4705 0.035152 CAGCCAGTATGCCCTTGTCA 60.035 55.000 0.00 0.00 31.97 3.58 R
5211 5411 1.202371 TGCAGAGGCGGTATTAGTTCG 60.202 52.381 0.00 0.00 45.35 3.95 R
6686 6895 1.280457 GGAGTTGGTCTGATCCAGGT 58.720 55.000 0.00 0.00 38.80 4.00 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
45 46 2.806244 CCTTCACCTAAAGACACAACCG 59.194 50.000 0.00 0.00 0.00 4.44
52 53 1.578583 AAAGACACAACCGACCGAAG 58.421 50.000 0.00 0.00 0.00 3.79
54 55 0.748450 AGACACAACCGACCGAAGAA 59.252 50.000 0.00 0.00 0.00 2.52
57 58 0.865769 CACAACCGACCGAAGAAAGG 59.134 55.000 0.00 0.00 0.00 3.11
59 60 0.882927 CAACCGACCGAAGAAAGGCA 60.883 55.000 0.00 0.00 0.00 4.75
66 67 1.639298 CCGAAGAAAGGCAAGGCTCG 61.639 60.000 0.00 0.00 0.00 5.03
114 115 1.552226 CTAAACCGCAATGCAGCATG 58.448 50.000 9.18 4.58 40.87 4.06
118 119 0.317799 ACCGCAATGCAGCATGAAAA 59.682 45.000 9.18 0.00 39.69 2.29
133 134 3.795688 TGAAAATCTTGGCAGAGACCT 57.204 42.857 2.25 0.00 30.36 3.85
134 135 4.104383 TGAAAATCTTGGCAGAGACCTT 57.896 40.909 2.25 0.30 30.36 3.50
140 141 6.814954 AATCTTGGCAGAGACCTTAGAATA 57.185 37.500 2.25 0.00 30.36 1.75
148 149 4.985409 CAGAGACCTTAGAATATCGCCAAC 59.015 45.833 0.00 0.00 0.00 3.77
217 250 5.274718 ACTAAGATTCATAACACGAGAGCG 58.725 41.667 0.00 0.00 44.79 5.03
269 319 0.107993 CGGCAGAAAGGCAGAGATCA 60.108 55.000 0.00 0.00 44.47 2.92
275 325 2.087646 GAAAGGCAGAGATCACAACCC 58.912 52.381 0.00 0.00 0.00 4.11
287 337 1.228862 ACAACCCTTGTCCCCATGC 60.229 57.895 0.00 0.00 40.56 4.06
322 378 0.614697 TCCAGAGCTTCGGACCATCA 60.615 55.000 1.04 0.00 0.00 3.07
323 379 0.179089 CCAGAGCTTCGGACCATCAG 60.179 60.000 0.00 0.00 0.00 2.90
362 448 0.887836 GAACCCCTTCCACGAACCAC 60.888 60.000 0.00 0.00 0.00 4.16
421 507 3.763671 GGCACCACCAAACTGGAG 58.236 61.111 0.00 0.00 40.96 3.86
434 520 2.376808 ACTGGAGAGCATCAAACGAG 57.623 50.000 0.00 0.00 37.82 4.18
452 538 0.749454 AGAATGCACGGCCCAAGATC 60.749 55.000 0.00 0.00 0.00 2.75
453 539 2.051804 GAATGCACGGCCCAAGATCG 62.052 60.000 0.00 0.00 0.00 3.69
455 541 4.467084 GCACGGCCCAAGATCGGA 62.467 66.667 0.00 0.00 0.00 4.55
460 546 0.170339 CGGCCCAAGATCGGAAAAAC 59.830 55.000 0.00 0.00 0.00 2.43
463 562 2.036604 GGCCCAAGATCGGAAAAACAAA 59.963 45.455 0.00 0.00 0.00 2.83
679 781 2.282180 GCTTTTCTCACCCCCGCA 60.282 61.111 0.00 0.00 0.00 5.69
680 782 2.626780 GCTTTTCTCACCCCCGCAC 61.627 63.158 0.00 0.00 0.00 5.34
768 889 1.453928 GGCCACCCTCCATACTTGC 60.454 63.158 0.00 0.00 0.00 4.01
772 893 1.463674 CACCCTCCATACTTGCCAAC 58.536 55.000 0.00 0.00 0.00 3.77
803 924 4.767255 CCCGAGCTGGCACACTCC 62.767 72.222 0.00 0.00 34.59 3.85
828 949 3.223589 GCTCCTCGCCTCCTCCTC 61.224 72.222 0.00 0.00 0.00 3.71
829 950 2.520741 CTCCTCGCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
830 951 4.144727 TCCTCGCCTCCTCCTCCC 62.145 72.222 0.00 0.00 0.00 4.30
876 997 2.800544 ACGACAACAGAATCCAAGAACG 59.199 45.455 0.00 0.00 0.00 3.95
916 1067 0.810648 GATTGCCGCTCCATTGTTGA 59.189 50.000 0.00 0.00 0.00 3.18
917 1068 1.202114 GATTGCCGCTCCATTGTTGAA 59.798 47.619 0.00 0.00 0.00 2.69
918 1069 1.255882 TTGCCGCTCCATTGTTGAAT 58.744 45.000 0.00 0.00 0.00 2.57
923 1074 3.181487 GCCGCTCCATTGTTGAATAACAT 60.181 43.478 0.00 0.00 45.56 2.71
925 1076 5.510671 CCGCTCCATTGTTGAATAACATAC 58.489 41.667 0.00 0.00 45.56 2.39
927 1078 5.965334 CGCTCCATTGTTGAATAACATACAC 59.035 40.000 0.00 0.00 45.56 2.90
928 1079 6.183360 CGCTCCATTGTTGAATAACATACACT 60.183 38.462 0.00 0.00 45.56 3.55
930 1081 7.624360 TCCATTGTTGAATAACATACACTCC 57.376 36.000 0.00 0.00 45.56 3.85
931 1082 7.402054 TCCATTGTTGAATAACATACACTCCT 58.598 34.615 0.00 0.00 45.56 3.69
983 1140 4.514066 GTGTGAGGGCCCGTATTATTTTAG 59.486 45.833 18.44 0.00 0.00 1.85
1326 1495 2.663196 GAGTTCGAGGTGGTGGGG 59.337 66.667 0.00 0.00 0.00 4.96
2115 2284 3.129502 CGCTACCTCGTCGACCCA 61.130 66.667 10.58 0.00 0.00 4.51
2235 2404 2.125512 ATGAAGCTCGACGTGCCC 60.126 61.111 17.52 10.82 0.00 5.36
2316 2485 1.609783 CCTTCACCCCATCCAGGTC 59.390 63.158 0.00 0.00 34.56 3.85
2481 2654 1.093159 GAGCTGAACTGGGAATGCTG 58.907 55.000 0.00 0.00 0.00 4.41
2608 2781 1.863454 GCATCTCACATCGATCCACAC 59.137 52.381 0.00 0.00 0.00 3.82
2611 2784 1.148157 CTCACATCGATCCACACGGC 61.148 60.000 0.00 0.00 0.00 5.68
2614 2787 1.153568 CATCGATCCACACGGCTGT 60.154 57.895 0.00 0.00 0.00 4.40
2621 2808 1.600636 CCACACGGCTGTTGTCCAT 60.601 57.895 0.00 0.00 0.00 3.41
2626 2813 2.083774 CACGGCTGTTGTCCATATTGT 58.916 47.619 0.00 0.00 0.00 2.71
2632 2819 4.332819 GGCTGTTGTCCATATTGTACTGTC 59.667 45.833 0.00 0.00 0.00 3.51
2633 2820 4.935205 GCTGTTGTCCATATTGTACTGTCA 59.065 41.667 0.00 0.00 0.00 3.58
2635 2822 6.094048 GCTGTTGTCCATATTGTACTGTCAAT 59.906 38.462 0.00 9.35 40.50 2.57
2641 2828 7.495606 TGTCCATATTGTACTGTCAATGCTAAG 59.504 37.037 12.59 0.00 38.32 2.18
2661 2848 7.650834 CTAAGGAGCAAAAGCTAGCTTATAG 57.349 40.000 29.52 21.42 42.04 1.31
2664 2851 5.602978 AGGAGCAAAAGCTAGCTTATAGGTA 59.397 40.000 29.52 0.00 42.04 3.08
2665 2852 5.697178 GGAGCAAAAGCTAGCTTATAGGTAC 59.303 44.000 29.52 22.18 42.04 3.34
2666 2853 6.463190 GGAGCAAAAGCTAGCTTATAGGTACT 60.463 42.308 29.52 18.56 42.04 2.73
2667 2854 6.890293 AGCAAAAGCTAGCTTATAGGTACTT 58.110 36.000 29.52 14.80 37.67 2.24
2668 2855 6.987404 AGCAAAAGCTAGCTTATAGGTACTTC 59.013 38.462 29.52 11.42 37.67 3.01
2669 2856 6.987404 GCAAAAGCTAGCTTATAGGTACTTCT 59.013 38.462 29.52 7.22 35.85 2.85
2670 2857 7.042389 GCAAAAGCTAGCTTATAGGTACTTCTG 60.042 40.741 29.52 9.81 35.85 3.02
2678 2865 7.120051 AGCTTATAGGTACTTCTGAGTTCTGA 58.880 38.462 0.00 0.00 41.75 3.27
2681 2868 2.229302 AGGTACTTCTGAGTTCTGACGC 59.771 50.000 0.00 0.00 37.33 5.19
2732 2922 6.805713 TGAACTCATCGACATATTAGCTCAA 58.194 36.000 0.00 0.00 0.00 3.02
2766 2964 2.301346 ACTGTCAAGCTGAAAACTGGG 58.699 47.619 0.00 0.00 0.00 4.45
2815 3013 8.940952 CAAACCTTCAACCATGTTTAAGAAAAA 58.059 29.630 3.18 0.00 30.29 1.94
2914 3112 4.684242 TCAACTAACGTAACTGTCATGCTG 59.316 41.667 0.00 0.00 0.00 4.41
2952 3150 3.487574 CGCTCAGTTGATCGATTAACTCC 59.512 47.826 27.27 18.47 34.82 3.85
2962 3160 7.582667 TGATCGATTAACTCCTGTATCTTGA 57.417 36.000 0.00 0.00 0.00 3.02
3030 3228 4.286549 AGCCTGCTAATCTGCTATGAGAAT 59.713 41.667 0.00 0.00 30.97 2.40
3072 3270 3.446442 AAAGTCCAGTGCATCCTGATT 57.554 42.857 5.92 0.00 34.23 2.57
3090 3288 8.613922 TCCTGATTATGCCTATCTATCATCAA 57.386 34.615 0.00 0.00 0.00 2.57
3094 3292 9.039165 TGATTATGCCTATCTATCATCAAGTCA 57.961 33.333 0.00 0.00 0.00 3.41
3119 3317 6.408858 AGTTCAATGAATAGTAACAGCACG 57.591 37.500 0.00 0.00 0.00 5.34
3122 3320 4.561213 TCAATGAATAGTAACAGCACGTCG 59.439 41.667 0.00 0.00 0.00 5.12
3136 3334 1.654105 CACGTCGCAAGGTTAAGCTAG 59.346 52.381 7.76 3.21 38.47 3.42
3172 3370 7.040271 ACTGACTGAACTTCTACTTACTCCTTC 60.040 40.741 0.00 0.00 0.00 3.46
3191 3390 8.477256 ACTCCTTCAAAATGAAACAAAAGATCA 58.523 29.630 0.00 0.00 35.73 2.92
3193 3392 9.263538 TCCTTCAAAATGAAACAAAAGATCATG 57.736 29.630 0.00 0.00 35.73 3.07
3196 3395 9.597170 TTCAAAATGAAACAAAAGATCATGTGA 57.403 25.926 0.00 0.00 32.71 3.58
3221 3420 7.305474 AGGACAAAATTTAATACTTCACTGCG 58.695 34.615 0.00 0.00 0.00 5.18
3275 3474 5.710513 TCCACTTTCATGTCAAATTCCTG 57.289 39.130 0.00 0.00 0.00 3.86
3297 3497 9.196139 TCCTGATAATTAATTTTTGGGGTAGTG 57.804 33.333 5.91 0.00 0.00 2.74
3331 3531 5.645624 TGGCCGAAAACATTATACATGTTG 58.354 37.500 2.30 0.00 40.94 3.33
3461 3661 1.331214 CACCAGACAAGGGCAATGTT 58.669 50.000 0.00 0.00 0.00 2.71
3545 3745 0.179045 ATGGCTACAATGTCGAGGGC 60.179 55.000 0.00 0.00 0.00 5.19
3956 4156 2.570284 GCCCGGGAAACAAGTTGGG 61.570 63.158 29.31 0.00 39.72 4.12
4415 4615 3.077484 ACATTGGTGAACATAGCTGCT 57.923 42.857 7.57 7.57 0.00 4.24
4505 4705 4.332683 TGAAGATGTCTACAGGGGTAGT 57.667 45.455 2.19 0.00 45.85 2.73
4572 4772 1.373748 GCTTCACGAGGTGCCGTAA 60.374 57.895 0.00 0.00 41.29 3.18
4823 5023 1.210478 GAGGGAAGCTATGTTGAGCCA 59.790 52.381 0.00 0.00 43.97 4.75
4853 5053 0.249741 GTGATCCCATCCGTAACCCG 60.250 60.000 0.00 0.00 0.00 5.28
5048 5248 1.226323 CAAGACCTACGGCGAGTCG 60.226 63.158 16.62 8.54 35.65 4.18
5211 5411 6.314896 CAGAGATCTTTTCATCAACCAGGTAC 59.685 42.308 0.00 0.00 0.00 3.34
5289 5489 8.743085 ATTCATCACTTAACTCATGCACTAAT 57.257 30.769 0.00 0.00 0.00 1.73
5470 5670 5.045012 TCTCAAATGCATCAGGCTCTTAT 57.955 39.130 0.00 0.00 45.15 1.73
5488 5688 6.252869 GCTCTTATTCGTCGAATGTGAACTTA 59.747 38.462 26.79 4.88 33.95 2.24
5551 5751 0.036164 ACATGTACCTGAGCCGCAAA 59.964 50.000 5.05 0.00 0.00 3.68
5974 6174 2.223745 TGGGTTTACGAGGAAGCAAAC 58.776 47.619 0.00 0.00 0.00 2.93
6022 6222 0.615331 GGAAGAGGCTGATGGACACA 59.385 55.000 0.00 0.00 0.00 3.72
6385 6594 4.640364 TGCTGTCACATGTTCATCTACAA 58.360 39.130 0.00 0.00 0.00 2.41
7065 7274 5.349543 GCTTCTTTTGTAATTGGCTTGATGG 59.650 40.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.387220 GGTATAAGCATGGGAGGATATAACCT 59.613 42.308 0.24 0.24 43.64 3.50
1 2 6.387220 AGGTATAAGCATGGGAGGATATAACC 59.613 42.308 0.00 0.00 0.00 2.85
7 8 4.042187 GTGAAGGTATAAGCATGGGAGGAT 59.958 45.833 0.00 0.00 0.00 3.24
16 17 6.014070 TGTGTCTTTAGGTGAAGGTATAAGCA 60.014 38.462 0.00 0.00 0.00 3.91
45 46 0.606673 AGCCTTGCCTTTCTTCGGTC 60.607 55.000 0.00 0.00 0.00 4.79
52 53 2.041115 GTCCCGAGCCTTGCCTTTC 61.041 63.158 0.00 0.00 0.00 2.62
54 55 3.249189 TGTCCCGAGCCTTGCCTT 61.249 61.111 0.00 0.00 0.00 4.35
57 58 2.032681 AAGTGTCCCGAGCCTTGC 59.967 61.111 0.00 0.00 0.00 4.01
59 60 2.750350 CCAAGTGTCCCGAGCCTT 59.250 61.111 0.00 0.00 0.00 4.35
66 67 1.098712 TGAAACGTGCCAAGTGTCCC 61.099 55.000 0.00 0.00 0.00 4.46
114 115 5.491982 TCTAAGGTCTCTGCCAAGATTTTC 58.508 41.667 0.00 0.00 0.00 2.29
118 119 6.295011 CGATATTCTAAGGTCTCTGCCAAGAT 60.295 42.308 0.00 0.00 0.00 2.40
133 134 6.277605 TCTTCGATTGTTGGCGATATTCTAA 58.722 36.000 0.00 0.00 36.31 2.10
134 135 5.838529 TCTTCGATTGTTGGCGATATTCTA 58.161 37.500 0.00 0.00 36.31 2.10
140 141 3.119849 CCTTTTCTTCGATTGTTGGCGAT 60.120 43.478 0.00 0.00 36.31 4.58
148 149 3.308530 GGTTGTGCCTTTTCTTCGATTG 58.691 45.455 0.00 0.00 0.00 2.67
183 186 2.159421 TGAATCTTAGTCGACGTCAGCC 60.159 50.000 17.16 2.03 0.00 4.85
237 270 1.076777 CTGCCGTGGGAATGGGATT 60.077 57.895 0.00 0.00 0.00 3.01
322 378 2.887738 TTTGGTGGTTTGCTGGGCCT 62.888 55.000 4.53 0.00 0.00 5.19
323 379 2.439104 TTTGGTGGTTTGCTGGGCC 61.439 57.895 0.00 0.00 0.00 5.80
362 448 0.179936 TTGTGGGGCCTTTTGCTTTG 59.820 50.000 0.84 0.00 40.92 2.77
408 494 1.271543 TGATGCTCTCCAGTTTGGTGG 60.272 52.381 0.00 0.00 39.03 4.61
417 503 3.264947 CATTCTCGTTTGATGCTCTCCA 58.735 45.455 0.00 0.00 0.00 3.86
418 504 2.031437 GCATTCTCGTTTGATGCTCTCC 59.969 50.000 0.00 0.00 35.55 3.71
420 506 2.417933 GTGCATTCTCGTTTGATGCTCT 59.582 45.455 8.73 0.00 38.88 4.09
421 507 2.778659 GTGCATTCTCGTTTGATGCTC 58.221 47.619 8.73 2.18 38.88 4.26
434 520 1.729881 GATCTTGGGCCGTGCATTC 59.270 57.895 0.00 0.00 0.00 2.67
452 538 2.324860 GCGGATTCCTTTGTTTTTCCG 58.675 47.619 4.87 4.87 46.66 4.30
453 539 2.036604 TGGCGGATTCCTTTGTTTTTCC 59.963 45.455 0.30 0.00 0.00 3.13
455 541 3.462982 GTTGGCGGATTCCTTTGTTTTT 58.537 40.909 0.30 0.00 0.00 1.94
460 546 1.154035 GCGTTGGCGGATTCCTTTG 60.154 57.895 0.30 0.00 38.78 2.77
490 589 2.895424 AACCTCCTGCCTTCCCGTG 61.895 63.158 0.00 0.00 0.00 4.94
491 590 2.529389 AACCTCCTGCCTTCCCGT 60.529 61.111 0.00 0.00 0.00 5.28
492 591 2.045926 CAACCTCCTGCCTTCCCG 60.046 66.667 0.00 0.00 0.00 5.14
493 592 2.356667 CCAACCTCCTGCCTTCCC 59.643 66.667 0.00 0.00 0.00 3.97
750 860 1.453928 GCAAGTATGGAGGGTGGCC 60.454 63.158 0.00 0.00 0.00 5.36
768 889 4.519213 TCGGGAATGTATAGGTTTGTTGG 58.481 43.478 0.00 0.00 0.00 3.77
772 893 3.809832 CAGCTCGGGAATGTATAGGTTTG 59.190 47.826 0.00 0.00 0.00 2.93
824 945 4.761304 AGGGGAGGAGGGGGAGGA 62.761 72.222 0.00 0.00 0.00 3.71
830 951 4.421554 TGAGGCAGGGGAGGAGGG 62.422 72.222 0.00 0.00 0.00 4.30
831 952 2.767496 CTGAGGCAGGGGAGGAGG 60.767 72.222 0.00 0.00 0.00 4.30
832 953 1.761667 CTCTGAGGCAGGGGAGGAG 60.762 68.421 0.00 0.00 31.51 3.69
844 965 0.673985 TGTTGTCGTGTCCCTCTGAG 59.326 55.000 0.00 0.00 0.00 3.35
876 997 1.305718 ACTGAGAGGGTGGCTCTCC 60.306 63.158 0.00 0.00 44.83 3.71
916 1067 8.605325 AACTACCACTAGGAGTGTATGTTATT 57.395 34.615 5.92 0.00 44.50 1.40
917 1068 8.605325 AAACTACCACTAGGAGTGTATGTTAT 57.395 34.615 5.92 0.00 44.50 1.89
918 1069 8.426569 AAAACTACCACTAGGAGTGTATGTTA 57.573 34.615 5.92 0.00 44.50 2.41
967 1124 1.808343 CCGGCTAAAATAATACGGGCC 59.192 52.381 0.00 0.00 37.80 5.80
983 1140 0.036875 CATCTTTATCCCCTCCCGGC 59.963 60.000 0.00 0.00 0.00 6.13
989 1146 1.068741 GCGACGACATCTTTATCCCCT 59.931 52.381 0.00 0.00 0.00 4.79
1326 1495 1.901085 CAGCTCCTCCACCAGGTAC 59.099 63.158 0.00 0.00 43.95 3.34
1388 1557 1.445410 CCGATGAAGACGTTGGCGA 60.445 57.895 0.00 0.00 42.00 5.54
1530 1699 2.440980 GCCATGCTGAAGGACCCC 60.441 66.667 0.00 0.00 0.00 4.95
1533 1702 2.747460 TGCGCCATGCTGAAGGAC 60.747 61.111 4.18 0.00 46.63 3.85
2115 2284 1.156736 CGAACGGCTTCTTGGTGATT 58.843 50.000 0.00 0.00 0.00 2.57
2235 2404 3.323136 GGCAGCGCGACGATGTAG 61.323 66.667 12.10 0.00 45.34 2.74
2481 2654 3.068024 TCCCTGCATCAAACACAAGAAAC 59.932 43.478 0.00 0.00 0.00 2.78
2608 2781 3.309682 CAGTACAATATGGACAACAGCCG 59.690 47.826 0.00 0.00 32.29 5.52
2611 2784 7.466805 CATTGACAGTACAATATGGACAACAG 58.533 38.462 0.00 0.00 38.25 3.16
2614 2787 6.179756 AGCATTGACAGTACAATATGGACAA 58.820 36.000 0.00 0.00 38.25 3.18
2656 2843 6.183360 GCGTCAGAACTCAGAAGTACCTATAA 60.183 42.308 0.00 0.00 33.48 0.98
2661 2848 2.597520 GCGTCAGAACTCAGAAGTACC 58.402 52.381 0.00 0.00 33.48 3.34
2664 2851 0.318762 GGGCGTCAGAACTCAGAAGT 59.681 55.000 0.00 0.00 37.32 3.01
2665 2852 0.318441 TGGGCGTCAGAACTCAGAAG 59.682 55.000 0.00 0.00 0.00 2.85
2666 2853 0.976641 ATGGGCGTCAGAACTCAGAA 59.023 50.000 0.00 0.00 0.00 3.02
2667 2854 0.532573 GATGGGCGTCAGAACTCAGA 59.467 55.000 0.00 0.00 0.00 3.27
2668 2855 0.534412 AGATGGGCGTCAGAACTCAG 59.466 55.000 0.00 0.00 0.00 3.35
2669 2856 0.532573 GAGATGGGCGTCAGAACTCA 59.467 55.000 0.00 0.00 0.00 3.41
2670 2857 0.820871 AGAGATGGGCGTCAGAACTC 59.179 55.000 0.00 0.00 0.00 3.01
2681 2868 4.826274 TTACACCTCAAGAAGAGATGGG 57.174 45.455 0.00 0.00 42.70 4.00
2732 2922 7.664731 TCAGCTTGACAGTAAACTAGTAGTAGT 59.335 37.037 2.50 4.29 41.61 2.73
2745 2943 3.135712 TCCCAGTTTTCAGCTTGACAGTA 59.864 43.478 0.00 0.00 0.00 2.74
2746 2944 2.092429 TCCCAGTTTTCAGCTTGACAGT 60.092 45.455 0.00 0.00 0.00 3.55
2766 2964 6.094719 TGATGCACAAATTGAATAAGCAGTC 58.905 36.000 0.00 3.46 33.69 3.51
2835 3033 7.669089 AGGGGACTCAAATTTTCTTAAAACA 57.331 32.000 0.00 0.00 32.90 2.83
2837 3035 8.866093 CCTAAGGGGACTCAAATTTTCTTAAAA 58.134 33.333 0.00 0.00 42.68 1.52
2914 3112 4.745620 ACTGAGCGAGTAGTTTCAGTTTTC 59.254 41.667 0.45 0.00 45.80 2.29
2952 3150 4.396166 GTGGGTGAATGGTTCAAGATACAG 59.604 45.833 0.00 0.00 42.15 2.74
2962 3160 2.091885 ACTGTTCAGTGGGTGAATGGTT 60.092 45.455 4.58 0.00 46.99 3.67
3047 3245 3.128242 CAGGATGCACTGGACTTTTCATC 59.872 47.826 0.00 0.00 34.84 2.92
3072 3270 8.874156 ACTTTGACTTGATGATAGATAGGCATA 58.126 33.333 0.00 0.00 0.00 3.14
3090 3288 8.507249 GCTGTTACTATTCATTGAACTTTGACT 58.493 33.333 0.15 0.00 0.00 3.41
3094 3292 7.041372 ACGTGCTGTTACTATTCATTGAACTTT 60.041 33.333 0.15 0.00 0.00 2.66
3107 3305 1.667756 CCTTGCGACGTGCTGTTACTA 60.668 52.381 0.00 0.00 46.63 1.82
3119 3317 1.722011 TGCTAGCTTAACCTTGCGAC 58.278 50.000 17.23 0.00 36.56 5.19
3122 3320 3.182182 GCATTTGCTAGCTTAACCTTGC 58.818 45.455 17.23 12.48 38.21 4.01
3136 3334 4.756084 AGTTCAGTCAGTTAGCATTTGC 57.244 40.909 0.00 0.00 42.49 3.68
3172 3370 8.492748 CCTCACATGATCTTTTGTTTCATTTTG 58.507 33.333 0.00 0.00 0.00 2.44
3193 3392 9.612620 CAGTGAAGTATTAAATTTTGTCCTCAC 57.387 33.333 0.00 3.82 0.00 3.51
3196 3395 7.305474 CGCAGTGAAGTATTAAATTTTGTCCT 58.695 34.615 0.00 0.00 0.00 3.85
3289 3488 2.092914 CCATGAGGAGTTTCACTACCCC 60.093 54.545 0.00 0.00 36.89 4.95
3297 3497 1.821216 TTTCGGCCATGAGGAGTTTC 58.179 50.000 2.24 0.00 36.89 2.78
3312 3512 5.676744 CCGAGCAACATGTATAATGTTTTCG 59.323 40.000 18.54 18.54 39.94 3.46
3331 3531 1.394917 CTGTGCATACAAGAACCGAGC 59.605 52.381 0.00 0.00 36.14 5.03
3461 3661 1.377594 CAGGTATGCTGCAGTGCCA 60.378 57.895 16.64 5.17 0.00 4.92
3491 3691 4.898265 TCCTTGAGGACAGAATAGATGGAG 59.102 45.833 0.00 0.00 39.78 3.86
3545 3745 2.251818 TCTTCAGGTGTCTCTGGAAGG 58.748 52.381 0.00 0.00 35.58 3.46
3956 4156 1.607628 GGGAAGCATGCATCACTCATC 59.392 52.381 23.12 5.75 0.00 2.92
4055 4255 5.559035 GCTTATAGTGTTTGCATAGCTTCGG 60.559 44.000 0.00 0.00 0.00 4.30
4415 4615 1.984570 CTCCTCTGGGCGGTCAAGA 60.985 63.158 0.00 0.00 0.00 3.02
4505 4705 0.035152 CAGCCAGTATGCCCTTGTCA 60.035 55.000 0.00 0.00 31.97 3.58
4823 5023 3.017581 GGATCACCACCAGGGCCT 61.018 66.667 0.00 0.00 42.05 5.19
5048 5248 2.753043 CACATCACCTGGGCCAGC 60.753 66.667 28.51 0.00 0.00 4.85
5211 5411 1.202371 TGCAGAGGCGGTATTAGTTCG 60.202 52.381 0.00 0.00 45.35 3.95
5470 5670 3.644823 TGCTAAGTTCACATTCGACGAA 58.355 40.909 13.48 13.48 0.00 3.85
5488 5688 2.298610 CATGATGCATTCTCCACTGCT 58.701 47.619 0.00 0.00 39.16 4.24
5551 5751 4.673580 GCATCACTGTCGAATGCAAAAGAT 60.674 41.667 12.90 0.00 38.08 2.40
5911 6111 3.609853 TGCACTCCATCCAACAGTATTC 58.390 45.455 0.00 0.00 0.00 1.75
5974 6174 4.872124 TCTTCATCTTCGATGAATGTGGTG 59.128 41.667 16.84 7.14 37.40 4.17
6022 6222 3.193479 GCTTCCTGAACGAATTGGGATTT 59.807 43.478 0.00 0.00 0.00 2.17
6348 6557 5.414454 TGTGACAGCAAAGTACCAATATTCC 59.586 40.000 0.00 0.00 0.00 3.01
6349 6558 6.494893 TGTGACAGCAAAGTACCAATATTC 57.505 37.500 0.00 0.00 0.00 1.75
6350 6559 6.434028 ACATGTGACAGCAAAGTACCAATATT 59.566 34.615 0.00 0.00 0.00 1.28
6351 6560 5.945784 ACATGTGACAGCAAAGTACCAATAT 59.054 36.000 0.00 0.00 0.00 1.28
6352 6561 5.312895 ACATGTGACAGCAAAGTACCAATA 58.687 37.500 0.00 0.00 0.00 1.90
6353 6562 4.144297 ACATGTGACAGCAAAGTACCAAT 58.856 39.130 0.00 0.00 0.00 3.16
6354 6563 3.550820 ACATGTGACAGCAAAGTACCAA 58.449 40.909 0.00 0.00 0.00 3.67
6355 6564 3.207265 ACATGTGACAGCAAAGTACCA 57.793 42.857 0.00 0.00 0.00 3.25
6356 6565 3.563808 TGAACATGTGACAGCAAAGTACC 59.436 43.478 0.00 0.00 0.00 3.34
6357 6566 4.811555 TGAACATGTGACAGCAAAGTAC 57.188 40.909 0.00 0.00 0.00 2.73
6385 6594 8.758829 TGACACTCCATTGTCTGTTACTATATT 58.241 33.333 4.97 0.00 45.34 1.28
6399 6608 8.647143 AAACAGTTAAAAATGACACTCCATTG 57.353 30.769 0.00 0.00 36.90 2.82
6686 6895 1.280457 GGAGTTGGTCTGATCCAGGT 58.720 55.000 0.00 0.00 38.80 4.00
7065 7274 3.486875 CGGTTGACAGTTTTCCAGTTCAC 60.487 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.