Multiple sequence alignment - TraesCS7D01G278000

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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 TraesCS7D01G278000 chr7D 100.000 2984 0 0 1 2984 267386836 267383853 0.000000e+00 5511
1 TraesCS7D01G278000 chr7B 94.702 2246 88 12 11 2234 247315739 247313503 0.000000e+00 3459
2 TraesCS7D01G278000 chr7B 88.408 716 64 8 2271 2984 247313501 247312803 0.000000e+00 845
3 TraesCS7D01G278000 chr7B 83.815 346 44 9 32 366 64693920 64693576 4.800000e-83 318
4 TraesCS7D01G278000 chr7B 83.478 345 45 9 32 365 530639179 530638836 8.030000e-81 311
5 TraesCS7D01G278000 chr7B 82.480 371 47 12 11 366 674200886 674201253 2.890000e-80 309
6 TraesCS7D01G278000 chr7A 96.426 1651 40 4 608 2245 293303846 293305490 0.000000e+00 2704
7 TraesCS7D01G278000 chr7A 85.561 561 49 15 11 551 293303045 293303593 2.600000e-155 558
8 TraesCS7D01G278000 chr7A 90.339 383 37 0 2271 2653 293305754 293306136 1.230000e-138 503
9 TraesCS7D01G278000 chr7A 90.120 334 31 2 2652 2984 293356643 293356975 1.640000e-117 433
10 TraesCS7D01G278000 chr1D 84.116 447 70 1 2538 2983 334611927 334612373 5.910000e-117 431
11 TraesCS7D01G278000 chr1D 84.196 367 46 5 11 366 15320143 15320508 2.200000e-91 346
12 TraesCS7D01G278000 chr2D 84.401 359 44 9 19 366 619364511 619364868 2.850000e-90 342
13 TraesCS7D01G278000 chr2A 83.740 369 45 10 11 366 61964142 61964508 4.770000e-88 335
14 TraesCS7D01G278000 chr2A 83.565 359 47 5 19 366 655832775 655833132 2.870000e-85 326
15 TraesCS7D01G278000 chr5B 84.104 346 43 9 32 366 521001259 521001603 1.030000e-84 324
16 TraesCS7D01G278000 chr5B 82.480 371 47 12 11 366 466784373 466784740 2.890000e-80 309
17 TraesCS7D01G278000 chr5B 82.948 346 47 9 32 366 637116142 637115798 4.830000e-78 302
18 TraesCS7D01G278000 chr2B 82.749 371 45 13 11 366 733092168 733091802 2.230000e-81 313
19 TraesCS7D01G278000 chr1B 82.480 371 47 12 11 366 96513213 96512846 2.890000e-80 309
20 TraesCS7D01G278000 chr5A 82.432 370 46 13 12 366 46013618 46013253 3.740000e-79 305
21 TraesCS7D01G278000 chr1A 82.210 371 48 8 11 366 542368739 542369106 1.340000e-78 303
22 TraesCS7D01G278000 chr6D 81.148 366 53 9 12 366 312823559 312823919 2.270000e-71 279
23 TraesCS7D01G278000 chr3A 78.551 345 67 7 11 350 695539866 695539524 1.390000e-53 220


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 TraesCS7D01G278000 chr7D 267383853 267386836 2983 True 5511 5511 100.000000 1 2984 1 chr7D.!!$R1 2983
1 TraesCS7D01G278000 chr7B 247312803 247315739 2936 True 2152 3459 91.555000 11 2984 2 chr7B.!!$R3 2973
2 TraesCS7D01G278000 chr7A 293303045 293306136 3091 False 1255 2704 90.775333 11 2653 3 chr7A.!!$F2 2642

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
627 847 0.035056 ATATCCTATTGGCAGCCGGC 60.035 55.0 21.89 21.89 43.74 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 3043 0.950555 TCTGACACACCGAGCATTGC 60.951 55.0 0.0 0.0 0.0 3.56 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
50 51 0.319555 TTCCCTTGTGAAGCTCGTCG 60.320 55.000 0.00 0.00 0.00 5.12
65 66 1.066114 CGTCGTCAAAGTCGGAGCTC 61.066 60.000 4.71 4.71 0.00 4.09
72 73 1.201647 CAAAGTCGGAGCTCTCGGTTA 59.798 52.381 14.64 0.00 0.00 2.85
129 140 2.281761 CTTCTGTGCGGGTTGGCT 60.282 61.111 0.00 0.00 0.00 4.75
155 166 5.573337 ATGATGAAGCTCTTTGGTTAAGC 57.427 39.130 0.00 0.00 36.40 3.09
165 176 2.510918 GGTTAAGCCGGAGTCGCC 60.511 66.667 5.05 0.00 34.56 5.54
168 179 2.585341 TTAAGCCGGAGTCGCCCAA 61.585 57.895 5.05 0.00 34.56 4.12
195 206 6.628185 GGAGGTAACCGATGATAACGATAAT 58.372 40.000 0.00 0.00 37.17 1.28
206 217 6.048073 TGATAACGATAATGCTTGCAACTC 57.952 37.500 0.00 0.00 0.00 3.01
207 218 5.584251 TGATAACGATAATGCTTGCAACTCA 59.416 36.000 0.00 0.00 0.00 3.41
213 224 0.723414 ATGCTTGCAACTCATCGACG 59.277 50.000 0.00 0.00 0.00 5.12
234 245 4.023707 ACGGATGTCTTTTCTTCTTTGCAG 60.024 41.667 0.00 0.00 0.00 4.41
247 258 2.490509 TCTTTGCAGCTCATGTTCCATG 59.509 45.455 0.00 0.00 0.00 3.66
282 293 1.280998 GGCCGGTAGTGCCCATATTAT 59.719 52.381 1.90 0.00 43.33 1.28
301 312 1.344065 TGTGGGTCTGGTTGTATCGT 58.656 50.000 0.00 0.00 0.00 3.73
328 339 3.754323 TGCCCGATTTTCGACAATTAACT 59.246 39.130 0.00 0.00 43.74 2.24
393 413 9.098355 GCCTTGTTTTAAGAAAAGAAATGTTCT 57.902 29.630 0.00 0.00 43.15 3.01
398 418 9.249457 GTTTTAAGAAAAGAAATGTTCTGAGGG 57.751 33.333 0.00 0.00 40.59 4.30
428 449 6.540914 ACCTTTTACATCAGACGTTCTTTTCA 59.459 34.615 0.00 0.00 0.00 2.69
627 847 0.035056 ATATCCTATTGGCAGCCGGC 60.035 55.000 21.89 21.89 43.74 6.13
660 880 6.598064 TGGCTAGTAGCTCTCAAAATTTAACC 59.402 38.462 21.20 0.05 41.99 2.85
695 915 2.041485 TGATTCCTTGGACAAGATGGCA 59.959 45.455 13.35 0.00 40.79 4.92
793 1013 0.892063 GTGCTCCGGAGAAGAGAAGT 59.108 55.000 35.69 0.00 0.00 3.01
867 1087 3.118542 CGTCGGTAAACTGCTTATACCC 58.881 50.000 0.00 0.00 36.54 3.69
881 1101 7.450323 ACTGCTTATACCCAATGTGTTAACTTT 59.550 33.333 7.22 0.00 0.00 2.66
926 1146 6.861572 TGCACCTAATTAAGATATCGTCTTCG 59.138 38.462 0.00 0.00 43.74 3.79
1932 2152 3.893763 CTGTCGCTCGCCGGATCT 61.894 66.667 5.05 0.00 37.59 2.75
2063 2296 0.677842 GTTCCCCGAGTGTACTGTGT 59.322 55.000 0.00 0.00 0.00 3.72
2064 2297 1.888512 GTTCCCCGAGTGTACTGTGTA 59.111 52.381 0.00 0.00 0.00 2.90
2065 2298 2.291209 TCCCCGAGTGTACTGTGTAA 57.709 50.000 0.00 0.00 0.00 2.41
2098 2331 3.314553 TCGCAACAGTTACTTAGCTGTC 58.685 45.455 6.26 0.00 45.17 3.51
2206 2439 3.831715 AACTTGTAAATTGCCGCTCTC 57.168 42.857 0.00 0.00 0.00 3.20
2240 2473 1.985334 CGGACAATGCTACACGTACA 58.015 50.000 0.00 0.00 0.00 2.90
2245 2478 5.615984 CGGACAATGCTACACGTACAAAAAT 60.616 40.000 0.00 0.00 0.00 1.82
2249 2726 8.496872 ACAATGCTACACGTACAAAAATTAAC 57.503 30.769 0.00 0.00 0.00 2.01
2252 2729 4.255861 GCTACACGTACAAAAATTAACGCG 59.744 41.667 3.53 3.53 38.87 6.01
2262 2739 6.818416 ACAAAAATTAACGCGAGAGTTCTAG 58.182 36.000 15.93 0.00 35.70 2.43
2263 2740 6.128634 ACAAAAATTAACGCGAGAGTTCTAGG 60.129 38.462 15.93 0.00 35.70 3.02
2264 2741 4.978083 AATTAACGCGAGAGTTCTAGGA 57.022 40.909 15.93 0.00 35.70 2.94
2265 2742 4.555348 ATTAACGCGAGAGTTCTAGGAG 57.445 45.455 15.93 0.00 35.70 3.69
2266 2743 1.823797 AACGCGAGAGTTCTAGGAGT 58.176 50.000 15.93 0.00 0.00 3.85
2267 2744 2.687700 ACGCGAGAGTTCTAGGAGTA 57.312 50.000 15.93 0.00 0.00 2.59
2268 2745 2.553086 ACGCGAGAGTTCTAGGAGTAG 58.447 52.381 15.93 0.00 0.00 2.57
2269 2746 2.168106 ACGCGAGAGTTCTAGGAGTAGA 59.832 50.000 15.93 0.00 33.12 2.59
2299 2776 7.114754 AGCTGATGTGAAGAAGATTAATTGGA 58.885 34.615 0.00 0.00 0.00 3.53
2300 2777 7.066766 AGCTGATGTGAAGAAGATTAATTGGAC 59.933 37.037 0.00 0.00 0.00 4.02
2309 2786 9.408648 GAAGAAGATTAATTGGACCAGGATTAA 57.591 33.333 11.90 11.90 31.90 1.40
2310 2787 9.768215 AAGAAGATTAATTGGACCAGGATTAAA 57.232 29.630 13.05 1.50 31.34 1.52
2367 2844 5.106118 GCCAAGAGGATTTGTTTAGAAGGTC 60.106 44.000 0.00 0.00 36.89 3.85
2369 2846 6.660949 CCAAGAGGATTTGTTTAGAAGGTCAT 59.339 38.462 0.00 0.00 36.89 3.06
2408 2885 9.291664 GGTCTATTCGTAGATGTAGCATTATTC 57.708 37.037 0.00 0.00 35.04 1.75
2417 2894 5.704515 AGATGTAGCATTATTCATGGAGCAC 59.295 40.000 0.00 0.00 32.81 4.40
2429 2906 1.131638 TGGAGCACCAGTGTTTCTCT 58.868 50.000 0.00 0.00 41.77 3.10
2433 2910 3.381590 GGAGCACCAGTGTTTCTCTTTTT 59.618 43.478 0.00 0.00 35.97 1.94
2434 2911 4.354587 GAGCACCAGTGTTTCTCTTTTTG 58.645 43.478 0.00 0.00 0.00 2.44
2451 2928 6.985117 TCTTTTTGCTTCTGCTTTGATACAT 58.015 32.000 0.00 0.00 40.48 2.29
2457 2944 5.129320 TGCTTCTGCTTTGATACATCCTCTA 59.871 40.000 0.00 0.00 40.48 2.43
2459 2946 7.015584 TGCTTCTGCTTTGATACATCCTCTATA 59.984 37.037 0.00 0.00 40.48 1.31
2460 2947 7.875041 GCTTCTGCTTTGATACATCCTCTATAA 59.125 37.037 0.00 0.00 36.03 0.98
2461 2948 9.770097 CTTCTGCTTTGATACATCCTCTATAAA 57.230 33.333 0.00 0.00 0.00 1.40
2462 2949 9.547753 TTCTGCTTTGATACATCCTCTATAAAC 57.452 33.333 0.00 0.00 0.00 2.01
2463 2950 8.704668 TCTGCTTTGATACATCCTCTATAAACA 58.295 33.333 0.00 0.00 0.00 2.83
2464 2951 9.499479 CTGCTTTGATACATCCTCTATAAACAT 57.501 33.333 0.00 0.00 0.00 2.71
2556 3043 1.753078 TCACATCTCGACCTCGGGG 60.753 63.158 0.00 0.00 40.92 5.73
2645 3132 4.457834 AAGAAGTATGACGAGTCCTTGG 57.542 45.455 0.34 0.00 0.00 3.61
2668 3155 5.039333 GGCTGCATGAAATCATAACACTTC 58.961 41.667 0.50 0.00 34.26 3.01
2671 3158 6.682113 GCTGCATGAAATCATAACACTTCCAT 60.682 38.462 0.00 0.00 34.26 3.41
2675 3162 5.953183 TGAAATCATAACACTTCCATGCAC 58.047 37.500 0.00 0.00 0.00 4.57
2678 3165 1.094785 ATAACACTTCCATGCACGCC 58.905 50.000 0.00 0.00 0.00 5.68
2707 3194 6.679884 GCAATTCAGAGCTAAGATTTTGGAGG 60.680 42.308 0.00 0.00 0.00 4.30
2719 3206 5.196695 AGATTTTGGAGGTTCTTCTATGCC 58.803 41.667 0.00 0.00 0.00 4.40
2747 3235 5.883673 TGGCCAACTAAAATAGTACATGGAC 59.116 40.000 0.61 0.00 40.89 4.02
2760 3248 4.825085 AGTACATGGACGTGGTTCAAATTT 59.175 37.500 1.41 0.00 0.00 1.82
2761 3249 4.237349 ACATGGACGTGGTTCAAATTTC 57.763 40.909 0.00 0.00 0.00 2.17
2810 3298 2.616510 CCTTTGGTGGTAGAGAAGGCAG 60.617 54.545 0.00 0.00 31.43 4.85
2823 3311 5.124645 AGAGAAGGCAGATTGCTAAGAATG 58.875 41.667 0.67 0.00 44.28 2.67
2824 3312 5.104610 AGAGAAGGCAGATTGCTAAGAATGA 60.105 40.000 0.67 0.00 44.28 2.57
2837 3325 2.957402 AGAATGAGGAGGTGCAACAA 57.043 45.000 3.64 0.00 39.98 2.83
2839 3327 2.158623 AGAATGAGGAGGTGCAACAACA 60.159 45.455 3.64 0.00 39.98 3.33
2844 3332 2.548480 GAGGAGGTGCAACAACAAGTAC 59.452 50.000 3.64 0.00 39.98 2.73
2849 3337 2.096174 GGTGCAACAACAAGTACGAACA 59.904 45.455 0.00 0.00 39.98 3.18
2850 3338 3.426426 GGTGCAACAACAAGTACGAACAA 60.426 43.478 0.00 0.00 39.98 2.83
2854 3342 4.584394 CAACAACAAGTACGAACAAGACC 58.416 43.478 0.00 0.00 0.00 3.85
2856 3344 3.117794 CAACAAGTACGAACAAGACCGA 58.882 45.455 0.00 0.00 0.00 4.69
2858 3346 2.099592 ACAAGTACGAACAAGACCGACA 59.900 45.455 0.00 0.00 0.00 4.35
2887 3375 6.511605 CGAGCACTAGCATAAAATTATGTGCA 60.512 38.462 19.76 0.00 45.49 4.57
2903 3391 1.069049 GTGCAATCAGTTGGCAAACCT 59.931 47.619 0.00 0.00 36.94 3.50
2908 3396 2.435372 TCAGTTGGCAAACCTTCAGT 57.565 45.000 0.00 0.00 36.94 3.41
2916 3404 1.915141 CAAACCTTCAGTGCTCCCAT 58.085 50.000 0.00 0.00 0.00 4.00
2965 3453 0.807496 GGTCAGCTGGTTCTGAATGC 59.193 55.000 15.13 0.00 43.89 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.280524 CTGCCGACAACCACCGAA 60.281 61.111 0.00 0.00 0.00 4.30
1 2 2.709125 CTTCTGCCGACAACCACCGA 62.709 60.000 0.00 0.00 0.00 4.69
2 3 2.280524 TTCTGCCGACAACCACCG 60.281 61.111 0.00 0.00 0.00 4.94
3 4 1.227853 ACTTCTGCCGACAACCACC 60.228 57.895 0.00 0.00 0.00 4.61
4 5 0.249911 AGACTTCTGCCGACAACCAC 60.250 55.000 0.00 0.00 0.00 4.16
5 6 0.468226 AAGACTTCTGCCGACAACCA 59.532 50.000 0.00 0.00 0.00 3.67
6 7 0.868406 CAAGACTTCTGCCGACAACC 59.132 55.000 0.00 0.00 0.00 3.77
7 8 0.235926 GCAAGACTTCTGCCGACAAC 59.764 55.000 0.00 0.00 0.00 3.32
8 9 0.179059 TGCAAGACTTCTGCCGACAA 60.179 50.000 0.00 0.00 0.00 3.18
9 10 0.035317 ATGCAAGACTTCTGCCGACA 59.965 50.000 0.00 0.00 0.00 4.35
50 51 0.456995 CCGAGAGCTCCGACTTTGAC 60.457 60.000 21.43 0.00 0.00 3.18
65 66 2.156446 ACACGCGCGAATAACCGAG 61.156 57.895 39.36 15.32 0.00 4.63
111 112 4.043200 GCCAACCCGCACAGAAGC 62.043 66.667 0.00 0.00 0.00 3.86
129 140 7.066284 GCTTAACCAAAGAGCTTCATCATAGAA 59.934 37.037 0.00 0.00 37.38 2.10
155 166 4.891727 CCGATTGGGCGACTCCGG 62.892 72.222 0.00 0.00 36.06 5.14
182 193 6.260714 TGAGTTGCAAGCATTATCGTTATCAT 59.739 34.615 0.00 0.00 0.00 2.45
187 198 4.494690 CGATGAGTTGCAAGCATTATCGTT 60.495 41.667 17.92 0.00 33.55 3.85
195 206 1.291184 CCGTCGATGAGTTGCAAGCA 61.291 55.000 6.11 1.14 0.00 3.91
213 224 4.022503 AGCTGCAAAGAAGAAAAGACATCC 60.023 41.667 1.02 0.00 0.00 3.51
247 258 2.200337 GGCCAACCTGACCACCAAC 61.200 63.158 0.00 0.00 0.00 3.77
282 293 1.344065 ACGATACAACCAGACCCACA 58.656 50.000 0.00 0.00 0.00 4.17
306 317 3.754323 AGTTAATTGTCGAAAATCGGGCA 59.246 39.130 0.16 0.00 40.88 5.36
307 318 4.095610 CAGTTAATTGTCGAAAATCGGGC 58.904 43.478 0.16 0.00 40.88 6.13
312 323 8.576442 AGAATTGTCCAGTTAATTGTCGAAAAT 58.424 29.630 0.00 0.00 0.00 1.82
319 330 7.227156 AGAGTGAGAATTGTCCAGTTAATTGT 58.773 34.615 0.00 0.00 0.00 2.71
328 339 8.924511 ATTAAGAAAAGAGTGAGAATTGTCCA 57.075 30.769 0.00 0.00 0.00 4.02
393 413 3.396276 TGATGTAAAAGGTCCAACCCTCA 59.604 43.478 0.00 0.00 39.75 3.86
398 418 4.062991 ACGTCTGATGTAAAAGGTCCAAC 58.937 43.478 0.00 0.00 0.00 3.77
428 449 5.721232 ACGATGAGTCTTAAGGATTTTCGT 58.279 37.500 13.90 13.90 32.51 3.85
627 847 2.623889 AGAGCTACTAGCCAACCGTATG 59.376 50.000 4.32 0.00 43.77 2.39
660 880 5.007039 CCAAGGAATCATATTCATATCGCCG 59.993 44.000 2.36 0.00 0.00 6.46
881 1101 5.347364 GTGCAAACTGCTTTTGTTTCAAGTA 59.653 36.000 11.49 0.00 45.70 2.24
926 1146 3.423154 CAGCGGCGAAAGGGACAC 61.423 66.667 12.98 0.00 0.00 3.67
1713 1933 1.377987 GTTCCACATAAGCCCCGCA 60.378 57.895 0.00 0.00 0.00 5.69
1932 2152 4.783621 GTGCTCGCCATCCTGCCA 62.784 66.667 0.00 0.00 0.00 4.92
2052 2285 6.281405 GCTAATGGCTATTACACAGTACACT 58.719 40.000 0.00 0.00 38.06 3.55
2098 2331 3.547868 CGAGATGGTGAATCGTTACACAG 59.452 47.826 0.00 0.00 40.54 3.66
2206 2439 2.183811 CCGCTGCTCCAGTGAGAG 59.816 66.667 7.31 0.00 43.78 3.20
2240 2473 6.161381 TCCTAGAACTCTCGCGTTAATTTTT 58.839 36.000 5.77 0.00 0.00 1.94
2245 2478 3.341823 ACTCCTAGAACTCTCGCGTTAA 58.658 45.455 5.77 0.00 0.00 2.01
2249 2726 2.823984 TCTACTCCTAGAACTCTCGCG 58.176 52.381 0.00 0.00 0.00 5.87
2252 2729 8.349983 CAGCTTTTATCTACTCCTAGAACTCTC 58.650 40.741 0.00 0.00 32.49 3.20
2262 2739 7.268586 TCTTCACATCAGCTTTTATCTACTCC 58.731 38.462 0.00 0.00 0.00 3.85
2263 2740 8.709386 TTCTTCACATCAGCTTTTATCTACTC 57.291 34.615 0.00 0.00 0.00 2.59
2264 2741 8.535335 TCTTCTTCACATCAGCTTTTATCTACT 58.465 33.333 0.00 0.00 0.00 2.57
2265 2742 8.709386 TCTTCTTCACATCAGCTTTTATCTAC 57.291 34.615 0.00 0.00 0.00 2.59
2266 2743 9.896645 AATCTTCTTCACATCAGCTTTTATCTA 57.103 29.630 0.00 0.00 0.00 1.98
2267 2744 8.804912 AATCTTCTTCACATCAGCTTTTATCT 57.195 30.769 0.00 0.00 0.00 1.98
2299 2776 1.619704 GCCCCAGCTTTTAATCCTGGT 60.620 52.381 12.73 0.00 43.61 4.00
2300 2777 1.114627 GCCCCAGCTTTTAATCCTGG 58.885 55.000 8.75 8.75 44.49 4.45
2320 2797 3.081061 CCATGAATTTCAACGGAGGTGA 58.919 45.455 11.11 0.00 0.00 4.02
2325 2802 1.181786 GCCCCATGAATTTCAACGGA 58.818 50.000 16.10 0.00 0.00 4.69
2367 2844 4.920640 ATAGACCACGAAGACCTACATG 57.079 45.455 0.00 0.00 0.00 3.21
2369 2846 3.376234 CGAATAGACCACGAAGACCTACA 59.624 47.826 0.00 0.00 0.00 2.74
2408 2885 1.808945 GAGAAACACTGGTGCTCCATG 59.191 52.381 8.18 11.03 43.43 3.66
2417 2894 5.039333 CAGAAGCAAAAAGAGAAACACTGG 58.961 41.667 0.00 0.00 0.00 4.00
2426 2903 6.441274 TGTATCAAAGCAGAAGCAAAAAGAG 58.559 36.000 0.00 0.00 45.49 2.85
2429 2906 6.015180 AGGATGTATCAAAGCAGAAGCAAAAA 60.015 34.615 0.00 0.00 45.49 1.94
2433 2910 4.080695 AGAGGATGTATCAAAGCAGAAGCA 60.081 41.667 0.00 0.00 45.49 3.91
2434 2911 4.450053 AGAGGATGTATCAAAGCAGAAGC 58.550 43.478 0.00 0.00 42.56 3.86
2459 2946 9.820725 CCACCATTGATATGTTTTGATATGTTT 57.179 29.630 0.00 0.00 0.00 2.83
2460 2947 9.199645 TCCACCATTGATATGTTTTGATATGTT 57.800 29.630 0.00 0.00 0.00 2.71
2461 2948 8.765488 TCCACCATTGATATGTTTTGATATGT 57.235 30.769 0.00 0.00 0.00 2.29
2462 2949 8.301720 CCTCCACCATTGATATGTTTTGATATG 58.698 37.037 0.00 0.00 0.00 1.78
2463 2950 8.006564 ACCTCCACCATTGATATGTTTTGATAT 58.993 33.333 0.00 0.00 0.00 1.63
2464 2951 7.353525 ACCTCCACCATTGATATGTTTTGATA 58.646 34.615 0.00 0.00 0.00 2.15
2465 2952 6.197168 ACCTCCACCATTGATATGTTTTGAT 58.803 36.000 0.00 0.00 0.00 2.57
2466 2953 5.579047 ACCTCCACCATTGATATGTTTTGA 58.421 37.500 0.00 0.00 0.00 2.69
2467 2954 5.163519 GGACCTCCACCATTGATATGTTTTG 60.164 44.000 0.00 0.00 35.64 2.44
2468 2955 4.956075 GGACCTCCACCATTGATATGTTTT 59.044 41.667 0.00 0.00 35.64 2.43
2556 3043 0.950555 TCTGACACACCGAGCATTGC 60.951 55.000 0.00 0.00 0.00 3.56
2594 3081 5.298276 CGGGCACATTTAAATAGAGCCTAAA 59.702 40.000 24.82 0.00 40.40 1.85
2596 3083 4.101898 TCGGGCACATTTAAATAGAGCCTA 59.898 41.667 24.82 16.38 40.40 3.93
2645 3132 4.644103 AGTGTTATGATTTCATGCAGCC 57.356 40.909 3.30 0.00 37.15 4.85
2675 3162 2.402388 CTCTGAATTGCTGCGGCG 59.598 61.111 13.96 0.51 42.25 6.46
2678 3165 2.274437 TCTTAGCTCTGAATTGCTGCG 58.726 47.619 0.00 0.00 40.08 5.18
2682 3169 6.199937 TCCAAAATCTTAGCTCTGAATTGC 57.800 37.500 0.00 0.00 0.00 3.56
2684 3171 6.488715 ACCTCCAAAATCTTAGCTCTGAATT 58.511 36.000 0.00 0.00 0.00 2.17
2687 3174 5.249393 AGAACCTCCAAAATCTTAGCTCTGA 59.751 40.000 0.00 0.00 0.00 3.27
2719 3206 7.706179 CCATGTACTATTTTAGTTGGCCAAATG 59.294 37.037 27.93 17.72 40.14 2.32
2731 3218 6.699366 TGAACCACGTCCATGTACTATTTTA 58.301 36.000 0.00 0.00 0.00 1.52
2736 3224 4.603989 TTTGAACCACGTCCATGTACTA 57.396 40.909 0.00 0.00 0.00 1.82
2738 3226 4.759516 AATTTGAACCACGTCCATGTAC 57.240 40.909 0.00 0.00 0.00 2.90
2747 3235 3.435327 TCATCTCCGAAATTTGAACCACG 59.565 43.478 0.00 0.00 0.00 4.94
2760 3248 0.394192 GTGGCCATGATCATCTCCGA 59.606 55.000 9.72 0.00 0.00 4.55
2761 3249 0.395686 AGTGGCCATGATCATCTCCG 59.604 55.000 9.72 0.00 0.00 4.63
2810 3298 3.563390 GCACCTCCTCATTCTTAGCAATC 59.437 47.826 0.00 0.00 0.00 2.67
2823 3311 1.680338 ACTTGTTGTTGCACCTCCTC 58.320 50.000 0.00 0.00 0.00 3.71
2824 3312 2.572290 GTACTTGTTGTTGCACCTCCT 58.428 47.619 0.00 0.00 0.00 3.69
2837 3325 2.099592 TGTCGGTCTTGTTCGTACTTGT 59.900 45.455 0.00 0.00 0.00 3.16
2839 3327 3.441496 TTGTCGGTCTTGTTCGTACTT 57.559 42.857 0.00 0.00 0.00 2.24
2844 3332 2.487406 CGAATTGTCGGTCTTGTTCG 57.513 50.000 0.00 0.00 43.81 3.95
2854 3342 1.629013 TGCTAGTGCTCGAATTGTCG 58.371 50.000 0.00 0.00 42.04 4.35
2856 3344 6.683974 ATTTTATGCTAGTGCTCGAATTGT 57.316 33.333 0.00 0.00 40.48 2.71
2858 3346 8.840321 ACATAATTTTATGCTAGTGCTCGAATT 58.160 29.630 9.65 0.00 43.30 2.17
2887 3375 3.068590 CACTGAAGGTTTGCCAACTGATT 59.931 43.478 0.17 0.00 37.19 2.57
2916 3404 2.196595 CCTCCTCCATTGGTTACTCCA 58.803 52.381 1.86 0.00 45.60 3.86


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

AutoCloner maintained by Alex Coulton.