Multiple sequence alignment - TraesCS7A01G349500

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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 TraesCS7A01G349500 chr7A 100.000 3328 0 0 1 3328 512327636 512330963 0.000000e+00 6146.0
1 TraesCS7A01G349500 chr7A 83.019 265 44 1 1290 1554 34106300 34106037 4.290000e-59 239.0
2 TraesCS7A01G349500 chr7A 82.707 266 43 3 1290 1554 34519329 34519066 2.000000e-57 233.0
3 TraesCS7A01G349500 chr7D 90.912 3081 140 64 4 3025 420743907 420740908 0.000000e+00 4010.0
4 TraesCS7A01G349500 chr7D 83.142 261 42 2 1295 1554 33754878 33755137 1.540000e-58 237.0
5 TraesCS7A01G349500 chr7B 90.222 3109 163 62 1 3025 436788888 436785837 0.000000e+00 3927.0
6 TraesCS7A01G349500 chr7B 85.662 272 22 10 3068 3326 436785371 436785104 1.520000e-68 270.0
7 TraesCS7A01G349500 chr7B 100.000 38 0 0 3027 3064 436785799 436785762 1.660000e-08 71.3
8 TraesCS7A01G349500 chr4A 84.151 265 39 3 1290 1553 691324117 691324379 1.530000e-63 254.0
9 TraesCS7A01G349500 chr4A 83.206 262 43 1 1290 1551 691247024 691247284 4.290000e-59 239.0
10 TraesCS7A01G349500 chr4A 82.707 266 43 3 1290 1554 691469856 691469593 2.000000e-57 233.0
11 TraesCS7A01G349500 chr4A 81.955 266 45 3 1290 1554 690881275 690881012 4.320000e-54 222.0
12 TraesCS7A01G349500 chr4A 80.556 144 28 0 1028 1171 690938216 690938073 9.760000e-21 111.0
13 TraesCS7A01G349500 chr1D 91.304 46 2 2 3070 3114 189529843 189529887 9.970000e-06 62.1


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 TraesCS7A01G349500 chr7A 512327636 512330963 3327 False 6146.000000 6146 100.000000 1 3328 1 chr7A.!!$F1 3327
1 TraesCS7A01G349500 chr7D 420740908 420743907 2999 True 4010.000000 4010 90.912000 4 3025 1 chr7D.!!$R1 3021
2 TraesCS7A01G349500 chr7B 436785104 436788888 3784 True 1422.766667 3927 91.961333 1 3326 3 chr7B.!!$R1 3325

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
835 863 0.966179 TGCGTGCTCTTCCTCTTGTA 59.034 50.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2770 2856 0.761802 CCAAGGCCCCACTATCTCTC 59.238 60.0 0.0 0.0 0.0 3.2 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
177 183 3.117963 AGTCTACCACTCTACCGCATAGT 60.118 47.826 0.00 0.00 32.13 2.12
178 184 4.102210 AGTCTACCACTCTACCGCATAGTA 59.898 45.833 0.00 0.00 32.13 1.82
179 185 4.213059 GTCTACCACTCTACCGCATAGTAC 59.787 50.000 0.00 0.00 32.13 2.73
201 207 7.828717 AGTACTACTTCTTACAGACTAACCCTC 59.171 40.741 0.00 0.00 0.00 4.30
202 208 5.951148 ACTACTTCTTACAGACTAACCCTCC 59.049 44.000 0.00 0.00 0.00 4.30
203 209 5.013258 ACTTCTTACAGACTAACCCTCCT 57.987 43.478 0.00 0.00 0.00 3.69
205 211 5.246429 ACTTCTTACAGACTAACCCTCCTTG 59.754 44.000 0.00 0.00 0.00 3.61
206 212 3.514309 TCTTACAGACTAACCCTCCTTGC 59.486 47.826 0.00 0.00 0.00 4.01
207 213 2.031495 ACAGACTAACCCTCCTTGCT 57.969 50.000 0.00 0.00 0.00 3.91
208 214 1.903183 ACAGACTAACCCTCCTTGCTC 59.097 52.381 0.00 0.00 0.00 4.26
209 215 1.902508 CAGACTAACCCTCCTTGCTCA 59.097 52.381 0.00 0.00 0.00 4.26
210 216 1.903183 AGACTAACCCTCCTTGCTCAC 59.097 52.381 0.00 0.00 0.00 3.51
233 239 4.836125 TGCTCTCTCCAACACATTTTTC 57.164 40.909 0.00 0.00 0.00 2.29
237 244 5.106752 GCTCTCTCCAACACATTTTTCTCTC 60.107 44.000 0.00 0.00 0.00 3.20
239 246 6.226787 TCTCTCCAACACATTTTTCTCTCTC 58.773 40.000 0.00 0.00 0.00 3.20
280 294 2.031258 TCGGCCTCGATAATTTTGCA 57.969 45.000 0.00 0.00 40.88 4.08
312 326 3.609879 CGCATCTGCAAAAGATCACACAA 60.610 43.478 2.72 0.00 44.24 3.33
461 475 5.319453 CAAGACATGCCTGGTCCATATTAT 58.681 41.667 0.00 0.00 35.89 1.28
484 498 2.103094 ACATGTGCATGGACGCTAGTAT 59.897 45.455 13.03 0.00 42.91 2.12
657 675 2.935481 TGGCTAACCCTGCTGCCT 60.935 61.111 0.00 0.00 45.11 4.75
661 679 4.096003 TAACCCTGCTGCCTCGCC 62.096 66.667 0.00 0.00 0.00 5.54
684 702 3.751518 CTTCCCCTTTCCATATAACCCG 58.248 50.000 0.00 0.00 0.00 5.28
695 714 3.306780 CCATATAACCCGTCACATCCTCC 60.307 52.174 0.00 0.00 0.00 4.30
736 755 3.243907 CGTCTTCCTCCTGTTTCTCTTGT 60.244 47.826 0.00 0.00 0.00 3.16
743 762 5.839063 TCCTCCTGTTTCTCTTGTTTCTCTA 59.161 40.000 0.00 0.00 0.00 2.43
747 766 8.651589 TCCTGTTTCTCTTGTTTCTCTATCTA 57.348 34.615 0.00 0.00 0.00 1.98
764 787 7.335673 TCTCTATCTATCTATCCTTCGTTGCTG 59.664 40.741 0.00 0.00 0.00 4.41
808 836 1.471684 CACAAAAGGCAGCAGGAGATC 59.528 52.381 0.00 0.00 0.00 2.75
830 858 1.004440 AAGGTGCGTGCTCTTCCTC 60.004 57.895 0.00 0.00 0.00 3.71
835 863 0.966179 TGCGTGCTCTTCCTCTTGTA 59.034 50.000 0.00 0.00 0.00 2.41
840 868 4.058817 CGTGCTCTTCCTCTTGTACTTTT 58.941 43.478 0.00 0.00 0.00 2.27
872 900 6.887886 ATCTATGCATGATGAGGAAGGTAT 57.112 37.500 10.16 0.00 0.00 2.73
883 911 9.621239 ATGATGAGGAAGGTATATAGAGGAAAA 57.379 33.333 0.00 0.00 0.00 2.29
885 913 9.936759 GATGAGGAAGGTATATAGAGGAAAAAG 57.063 37.037 0.00 0.00 0.00 2.27
926 954 3.737774 GCTTCTGATTTGGTTTTGCTGAC 59.262 43.478 0.00 0.00 0.00 3.51
930 958 2.224018 TGATTTGGTTTTGCTGACTGGC 60.224 45.455 0.00 0.00 0.00 4.85
939 967 1.002868 GCTGACTGGCTCCACACAT 60.003 57.895 0.00 0.00 0.00 3.21
940 968 1.303799 GCTGACTGGCTCCACACATG 61.304 60.000 0.00 0.00 0.00 3.21
1149 1187 2.354203 GGAGATCGACCTCAACAAGCTT 60.354 50.000 9.53 0.00 34.94 3.74
1213 1254 2.508526 CCCCATATTCAGGCAGCTAAC 58.491 52.381 0.00 0.00 0.00 2.34
1214 1255 2.158623 CCCCATATTCAGGCAGCTAACA 60.159 50.000 0.00 0.00 0.00 2.41
1215 1256 3.554934 CCCATATTCAGGCAGCTAACAA 58.445 45.455 0.00 0.00 0.00 2.83
1220 1261 7.362401 CCCATATTCAGGCAGCTAACAATAATC 60.362 40.741 0.00 0.00 0.00 1.75
1222 1263 6.630444 ATTCAGGCAGCTAACAATAATCTG 57.370 37.500 0.00 0.00 0.00 2.90
1223 1264 5.357742 TCAGGCAGCTAACAATAATCTGA 57.642 39.130 0.00 0.00 0.00 3.27
1230 1271 6.349115 GCAGCTAACAATAATCTGATGATGGG 60.349 42.308 0.00 0.00 32.44 4.00
1245 1286 8.944138 TCTGATGATGGGGTATTAATTAACTCA 58.056 33.333 0.00 0.00 0.00 3.41
1320 1361 4.175337 TGCAGGATAGGCACGGGC 62.175 66.667 0.00 0.00 36.11 6.13
1548 1589 1.878522 CATGCACGAGTACCGCCTC 60.879 63.158 0.00 0.00 43.32 4.70
1613 1654 4.095483 CAGACACAAACTGAAAGCAAGTCT 59.905 41.667 0.00 0.00 37.60 3.24
1769 1815 3.462678 GACGAGCTCCTCCACCCC 61.463 72.222 8.47 0.00 0.00 4.95
1778 1824 3.400054 CTCCACCCCTTCCCGGTC 61.400 72.222 0.00 0.00 0.00 4.79
2060 2109 0.179009 CCATCGGAATGCTCCACCAT 60.179 55.000 0.00 0.00 42.58 3.55
2061 2110 1.233019 CATCGGAATGCTCCACCATC 58.767 55.000 0.00 0.00 42.58 3.51
2062 2111 0.839277 ATCGGAATGCTCCACCATCA 59.161 50.000 0.00 0.00 42.58 3.07
2207 2265 0.029834 CAGCATCAATGGCGCCTTAC 59.970 55.000 29.70 9.91 36.08 2.34
2216 2277 3.804193 GCGCCTTACCAGCAGCAC 61.804 66.667 0.00 0.00 32.54 4.40
2328 2389 3.436243 CTCCTCAGGTTCTCCAAGTAGT 58.564 50.000 0.00 0.00 35.89 2.73
2452 2515 1.135527 TCTACCTTGGTACGGAATGCG 59.864 52.381 0.00 0.00 0.00 4.73
2471 2534 6.861065 ATGCGTCTAAATGTGTATAAAGGG 57.139 37.500 0.00 0.00 0.00 3.95
2474 2537 7.051623 TGCGTCTAAATGTGTATAAAGGGAAT 58.948 34.615 0.00 0.00 0.00 3.01
2510 2573 4.546570 GCTTCGAGTTTGCCTTAATTTGT 58.453 39.130 0.00 0.00 0.00 2.83
2518 2581 7.096230 CGAGTTTGCCTTAATTTGTTTAACCTG 60.096 37.037 0.00 0.00 0.00 4.00
2532 2595 4.679373 TTAACCTGCAAAATTTGGAGCA 57.321 36.364 19.73 5.49 46.38 4.26
2539 2602 6.014669 ACCTGCAAAATTTGGAGCAAGTATTA 60.015 34.615 19.73 0.00 46.38 0.98
2549 2612 7.709269 TTGGAGCAAGTATTATTTAGCTACG 57.291 36.000 0.00 0.00 35.74 3.51
2554 2617 8.467402 AGCAAGTATTATTTAGCTACGCTATG 57.533 34.615 0.00 0.00 41.01 2.23
2556 2619 7.063544 GCAAGTATTATTTAGCTACGCTATGCT 59.936 37.037 0.00 0.00 41.01 3.79
2568 2631 8.490110 TAGCTACGCTATGCTTATTAGAGCAGA 61.490 40.741 5.75 0.01 46.60 4.26
2594 2657 5.940470 AGGTCAGTTAATTTGCTCCACTAAG 59.060 40.000 0.00 0.00 0.00 2.18
2595 2658 5.123979 GGTCAGTTAATTTGCTCCACTAAGG 59.876 44.000 0.00 0.00 39.47 2.69
2596 2659 5.705905 GTCAGTTAATTTGCTCCACTAAGGT 59.294 40.000 0.00 0.00 39.02 3.50
2597 2660 5.705441 TCAGTTAATTTGCTCCACTAAGGTG 59.295 40.000 0.00 0.00 42.65 4.00
2650 2717 6.945072 ACTCGAAGTCACATTTACAAAGAAC 58.055 36.000 0.00 0.00 0.00 3.01
2669 2736 3.885484 ACAATCTAGCAATGCATACGC 57.115 42.857 8.35 12.04 39.24 4.42
2693 2778 1.222113 GGAGCTAGCCTGGTTGGAC 59.778 63.158 12.13 0.00 38.35 4.02
2696 2781 1.127567 AGCTAGCCTGGTTGGACACA 61.128 55.000 12.13 0.00 38.35 3.72
2715 2800 7.770433 TGGACACAATGAGGATATAGTTTTGAG 59.230 37.037 0.00 0.00 0.00 3.02
2742 2827 0.465460 TTTGGCTGGACTTGCTTCGT 60.465 50.000 0.00 0.00 0.00 3.85
2761 2847 4.817517 TCGTAGGTTTCTTGTTGGAGATC 58.182 43.478 0.00 0.00 0.00 2.75
2762 2848 4.282449 TCGTAGGTTTCTTGTTGGAGATCA 59.718 41.667 0.00 0.00 0.00 2.92
2763 2849 4.627467 CGTAGGTTTCTTGTTGGAGATCAG 59.373 45.833 0.00 0.00 0.00 2.90
2766 2852 4.137543 GGTTTCTTGTTGGAGATCAGTGT 58.862 43.478 0.00 0.00 0.00 3.55
2768 2854 4.687901 TTCTTGTTGGAGATCAGTGTGA 57.312 40.909 0.00 0.00 0.00 3.58
2769 2855 4.687901 TCTTGTTGGAGATCAGTGTGAA 57.312 40.909 0.00 0.00 0.00 3.18
2770 2856 4.635223 TCTTGTTGGAGATCAGTGTGAAG 58.365 43.478 0.00 0.00 0.00 3.02
2776 2864 4.608269 TGGAGATCAGTGTGAAGAGAGAT 58.392 43.478 0.00 0.00 0.00 2.75
2780 2868 6.238731 GGAGATCAGTGTGAAGAGAGATAGTG 60.239 46.154 0.00 0.00 0.00 2.74
2846 2937 4.277515 TCCCTTTCATGACTTCAGAGTG 57.722 45.455 0.00 0.00 35.88 3.51
2861 2952 4.792068 TCAGAGTGTCTGGTTTCCATTTT 58.208 39.130 4.14 0.00 44.39 1.82
2889 2991 8.212312 TCCTGTGTTTACTAAAGATGGTTGTTA 58.788 33.333 0.00 0.00 0.00 2.41
2891 2993 8.734218 TGTGTTTACTAAAGATGGTTGTTACA 57.266 30.769 0.00 0.00 0.00 2.41
2905 3007 4.808364 GGTTGTTACAGAAATTGCTTGCAA 59.192 37.500 10.57 10.57 0.00 4.08
2916 3018 9.272901 CAGAAATTGCTTGCAATTATTTCAATG 57.727 29.630 26.99 15.82 37.56 2.82
3074 3600 4.037327 GCCTTTTCCCATGAGAATTAGAGC 59.963 45.833 0.00 0.00 0.00 4.09
3080 3606 5.458595 TCCCATGAGAATTAGAGCTAGTGA 58.541 41.667 0.00 0.00 0.00 3.41
3128 3654 2.196742 AGGATTCAGGGGTGCTCATA 57.803 50.000 0.00 0.00 0.00 2.15
3142 3668 6.480981 GGGGTGCTCATAAATGATTTGATTTG 59.519 38.462 0.00 0.00 36.02 2.32
3193 3719 2.923121 TGAATGGTATCAAGCTGAGGC 58.077 47.619 0.00 0.00 39.06 4.70
3205 3731 2.738013 GCTGAGGCTTGAATTTGCTT 57.262 45.000 0.00 0.00 35.22 3.91
3226 3752 9.607285 TTGCTTTTTCAAAATACTAAGATCGAC 57.393 29.630 0.00 0.00 0.00 4.20
3227 3753 7.955324 TGCTTTTTCAAAATACTAAGATCGACG 59.045 33.333 0.00 0.00 0.00 5.12
3228 3754 7.955864 GCTTTTTCAAAATACTAAGATCGACGT 59.044 33.333 0.00 0.00 0.00 4.34
3230 3756 6.880822 TTCAAAATACTAAGATCGACGTGG 57.119 37.500 0.00 0.00 0.00 4.94
3232 3758 5.125900 TCAAAATACTAAGATCGACGTGGGA 59.874 40.000 0.00 0.00 0.00 4.37
3244 3776 2.221055 CGACGTGGGAGAAAAAGTTCAG 59.779 50.000 0.00 0.00 36.09 3.02
3252 3784 6.372937 GTGGGAGAAAAAGTTCAGGATTAGAG 59.627 42.308 0.00 0.00 36.09 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 207 1.675415 GGAGAGAGCAAGTGAGCAAGG 60.675 57.143 0.00 0.00 36.85 3.61
202 208 1.001746 TGGAGAGAGCAAGTGAGCAAG 59.998 52.381 0.00 0.00 36.85 4.01
203 209 1.051008 TGGAGAGAGCAAGTGAGCAA 58.949 50.000 0.00 0.00 36.85 3.91
205 211 1.270518 TGTTGGAGAGAGCAAGTGAGC 60.271 52.381 0.00 0.00 0.00 4.26
206 212 2.224137 TGTGTTGGAGAGAGCAAGTGAG 60.224 50.000 0.00 0.00 0.00 3.51
207 213 1.762370 TGTGTTGGAGAGAGCAAGTGA 59.238 47.619 0.00 0.00 0.00 3.41
208 214 2.245159 TGTGTTGGAGAGAGCAAGTG 57.755 50.000 0.00 0.00 0.00 3.16
209 215 3.498774 AATGTGTTGGAGAGAGCAAGT 57.501 42.857 0.00 0.00 0.00 3.16
210 216 4.843220 AAAATGTGTTGGAGAGAGCAAG 57.157 40.909 0.00 0.00 0.00 4.01
233 239 4.210120 CGGTGTTTGTTCTTTCTGAGAGAG 59.790 45.833 0.00 0.00 35.37 3.20
237 244 6.539649 TTATCGGTGTTTGTTCTTTCTGAG 57.460 37.500 0.00 0.00 0.00 3.35
239 246 6.015504 CGATTATCGGTGTTTGTTCTTTCTG 58.984 40.000 6.73 0.00 36.00 3.02
279 293 4.889112 AGATGCGCCCCTGCCATG 62.889 66.667 4.18 0.00 31.30 3.66
280 294 4.889112 CAGATGCGCCCCTGCCAT 62.889 66.667 4.18 0.00 33.04 4.40
348 362 0.676151 CTGGCCTCAGAAGGAGCAAC 60.676 60.000 3.32 0.00 46.67 4.17
350 364 1.130054 AACTGGCCTCAGAAGGAGCA 61.130 55.000 3.32 0.00 46.67 4.26
402 416 4.935578 AGGACTAAATGAAAAGAAGGGGG 58.064 43.478 0.00 0.00 0.00 5.40
461 475 2.093711 ACTAGCGTCCATGCACATGTAA 60.094 45.455 9.63 0.00 37.11 2.41
484 498 6.806668 TTGACCATACTGATAGGATCACAA 57.193 37.500 0.00 0.00 35.06 3.33
657 675 4.404098 GGAAAGGGGAAGCGGCGA 62.404 66.667 12.98 0.00 0.00 5.54
661 679 3.146847 GGTTATATGGAAAGGGGAAGCG 58.853 50.000 0.00 0.00 0.00 4.68
665 683 2.707257 GACGGGTTATATGGAAAGGGGA 59.293 50.000 0.00 0.00 0.00 4.81
684 702 1.208293 GGGAAGTGAGGAGGATGTGAC 59.792 57.143 0.00 0.00 0.00 3.67
695 714 1.457346 GATGGTGCAAGGGAAGTGAG 58.543 55.000 0.00 0.00 0.00 3.51
736 755 8.516234 GCAACGAAGGATAGATAGATAGAGAAA 58.484 37.037 0.00 0.00 0.00 2.52
743 762 5.279206 CCACAGCAACGAAGGATAGATAGAT 60.279 44.000 0.00 0.00 0.00 1.98
747 766 2.158900 CCCACAGCAACGAAGGATAGAT 60.159 50.000 0.00 0.00 0.00 1.98
808 836 1.294659 GAAGAGCACGCACCTTGGAG 61.295 60.000 0.00 0.00 0.00 3.86
817 845 1.067495 AGTACAAGAGGAAGAGCACGC 60.067 52.381 0.00 0.00 0.00 5.34
818 846 3.305398 AAGTACAAGAGGAAGAGCACG 57.695 47.619 0.00 0.00 0.00 5.34
840 868 7.675619 TCCTCATCATGCATAGATAGAGGTAAA 59.324 37.037 27.80 19.22 39.34 2.01
844 872 6.407187 CCTTCCTCATCATGCATAGATAGAGG 60.407 46.154 26.11 26.11 39.49 3.69
845 873 6.154877 ACCTTCCTCATCATGCATAGATAGAG 59.845 42.308 0.00 12.81 0.00 2.43
846 874 6.021672 ACCTTCCTCATCATGCATAGATAGA 58.978 40.000 0.00 0.00 0.00 1.98
848 876 7.984859 ATACCTTCCTCATCATGCATAGATA 57.015 36.000 0.00 0.00 0.00 1.98
849 877 6.887886 ATACCTTCCTCATCATGCATAGAT 57.112 37.500 0.00 2.20 0.00 1.98
872 900 8.325787 TCACATTAACAGCCTTTTTCCTCTATA 58.674 33.333 0.00 0.00 0.00 1.31
883 911 3.620966 GCTCCTCTCACATTAACAGCCTT 60.621 47.826 0.00 0.00 0.00 4.35
885 913 2.093235 AGCTCCTCTCACATTAACAGCC 60.093 50.000 0.00 0.00 0.00 4.85
939 967 2.158769 TGAGAAGAAGAAGCAAGCACCA 60.159 45.455 0.00 0.00 0.00 4.17
940 968 2.483491 CTGAGAAGAAGAAGCAAGCACC 59.517 50.000 0.00 0.00 0.00 5.01
941 969 3.397482 TCTGAGAAGAAGAAGCAAGCAC 58.603 45.455 0.00 0.00 0.00 4.40
942 970 3.758755 TCTGAGAAGAAGAAGCAAGCA 57.241 42.857 0.00 0.00 0.00 3.91
944 972 4.742417 TCGATCTGAGAAGAAGAAGCAAG 58.258 43.478 0.00 0.00 0.00 4.01
986 1024 0.603172 ATGCATGCTGGCTCTCGATC 60.603 55.000 20.33 0.00 34.04 3.69
987 1025 0.603172 GATGCATGCTGGCTCTCGAT 60.603 55.000 20.33 0.00 34.04 3.59
988 1026 1.227468 GATGCATGCTGGCTCTCGA 60.227 57.895 20.33 0.00 34.04 4.04
989 1027 2.252346 GGATGCATGCTGGCTCTCG 61.252 63.158 20.33 0.00 34.04 4.04
1149 1187 0.329261 CTTTGAGGTCCCATGGCTCA 59.671 55.000 14.51 14.51 0.00 4.26
1197 1238 8.159447 TCAGATTATTGTTAGCTGCCTGAATAT 58.841 33.333 0.00 0.00 0.00 1.28
1220 1261 9.224267 CTGAGTTAATTAATACCCCATCATCAG 57.776 37.037 0.31 0.00 0.00 2.90
1222 1263 9.965902 ATCTGAGTTAATTAATACCCCATCATC 57.034 33.333 0.31 0.00 0.00 2.92
1223 1264 9.965902 GATCTGAGTTAATTAATACCCCATCAT 57.034 33.333 0.31 0.00 0.00 2.45
1230 1271 7.652105 TCAGCACGATCTGAGTTAATTAATACC 59.348 37.037 0.31 0.00 38.11 2.73
1245 1286 4.747108 GCATATAGTTTGTCAGCACGATCT 59.253 41.667 0.00 0.00 0.00 2.75
1323 1364 3.887110 TGAAGAAGTACCACTCGTTCTGA 59.113 43.478 0.00 0.00 29.64 3.27
1613 1654 4.284490 AGAAAAGACAGCCAGTATCTGTGA 59.716 41.667 0.00 0.00 44.09 3.58
1744 1790 3.485431 GGAGCTCGTCGTCGTCGA 61.485 66.667 13.59 13.59 44.12 4.20
1769 1815 2.269241 GAAGCTGGGACCGGGAAG 59.731 66.667 6.32 0.00 0.00 3.46
1799 1845 1.139520 GTCCGTGGCCATTTGCATC 59.860 57.895 9.72 0.00 43.89 3.91
1809 1855 3.050275 GTGCTTCTGGTCCGTGGC 61.050 66.667 0.00 0.00 0.00 5.01
1810 1856 1.003355 ATGTGCTTCTGGTCCGTGG 60.003 57.895 0.00 0.00 0.00 4.94
2237 2298 2.282040 GTGCTGCTGCCTCCAAGT 60.282 61.111 13.47 0.00 38.71 3.16
2471 2534 7.399523 ACTCGAAGCGACATATACAAAAATTC 58.600 34.615 0.00 0.00 0.00 2.17
2474 2537 6.715344 AACTCGAAGCGACATATACAAAAA 57.285 33.333 0.00 0.00 0.00 1.94
2487 2550 3.471495 AATTAAGGCAAACTCGAAGCG 57.529 42.857 0.00 0.00 0.00 4.68
2510 2573 5.028549 TGCTCCAAATTTTGCAGGTTAAA 57.971 34.783 3.50 0.00 0.00 1.52
2554 2617 6.339587 ACTGACCTATCTGCTCTAATAAGC 57.660 41.667 0.00 0.00 42.82 3.09
2568 2631 6.067217 AGTGGAGCAAATTAACTGACCTAT 57.933 37.500 0.00 0.00 0.00 2.57
2573 2636 5.705441 CACCTTAGTGGAGCAAATTAACTGA 59.295 40.000 0.00 0.00 40.55 3.41
2650 2717 2.221749 ACGCGTATGCATTGCTAGATTG 59.778 45.455 11.67 7.05 42.97 2.67
2669 2736 1.448540 CCAGGCTAGCTCCACAACG 60.449 63.158 15.72 0.00 0.00 4.10
2693 2778 8.511604 AACCTCAAAACTATATCCTCATTGTG 57.488 34.615 0.00 0.00 0.00 3.33
2696 2781 9.753674 TTGAAACCTCAAAACTATATCCTCATT 57.246 29.630 0.00 0.00 38.65 2.57
2715 2800 3.392882 CAAGTCCAGCCAAATTGAAACC 58.607 45.455 0.00 0.00 0.00 3.27
2742 2827 5.071788 ACACTGATCTCCAACAAGAAACCTA 59.928 40.000 0.00 0.00 0.00 3.08
2761 2847 3.131933 CCCCACTATCTCTCTTCACACTG 59.868 52.174 0.00 0.00 0.00 3.66
2762 2848 3.370104 CCCCACTATCTCTCTTCACACT 58.630 50.000 0.00 0.00 0.00 3.55
2763 2849 2.159028 GCCCCACTATCTCTCTTCACAC 60.159 54.545 0.00 0.00 0.00 3.82
2766 2852 1.292242 AGGCCCCACTATCTCTCTTCA 59.708 52.381 0.00 0.00 0.00 3.02
2768 2854 2.122768 CAAGGCCCCACTATCTCTCTT 58.877 52.381 0.00 0.00 0.00 2.85
2769 2855 1.694048 CCAAGGCCCCACTATCTCTCT 60.694 57.143 0.00 0.00 0.00 3.10
2770 2856 0.761802 CCAAGGCCCCACTATCTCTC 59.238 60.000 0.00 0.00 0.00 3.20
2861 2952 7.558444 ACAACCATCTTTAGTAAACACAGGAAA 59.442 33.333 0.00 0.00 0.00 3.13
2867 2958 9.048446 TCTGTAACAACCATCTTTAGTAAACAC 57.952 33.333 0.00 0.00 0.00 3.32
3008 3111 6.147656 TGCATGCTCATAAATATCCTACAACG 59.852 38.462 20.33 0.00 0.00 4.10
3012 3115 7.854557 TCATGCATGCTCATAAATATCCTAC 57.145 36.000 22.25 0.00 0.00 3.18
3064 3203 8.305046 AGTTGATTCTCACTAGCTCTAATTCT 57.695 34.615 0.00 0.00 0.00 2.40
3115 3641 4.646040 TCAAATCATTTATGAGCACCCCTG 59.354 41.667 0.00 0.00 40.64 4.45
3168 3694 5.826737 CCTCAGCTTGATACCATTCAAATCT 59.173 40.000 0.00 0.00 35.31 2.40
3170 3696 4.340381 GCCTCAGCTTGATACCATTCAAAT 59.660 41.667 0.00 0.00 35.31 2.32
3203 3729 9.250986 CACGTCGATCTTAGTATTTTGAAAAAG 57.749 33.333 0.00 0.00 0.00 2.27
3204 3730 8.225107 CCACGTCGATCTTAGTATTTTGAAAAA 58.775 33.333 0.00 0.00 0.00 1.94
3205 3731 7.148540 CCCACGTCGATCTTAGTATTTTGAAAA 60.149 37.037 0.00 0.00 0.00 2.29
3220 3746 2.685100 ACTTTTTCTCCCACGTCGATC 58.315 47.619 0.00 0.00 0.00 3.69
3221 3747 2.833631 ACTTTTTCTCCCACGTCGAT 57.166 45.000 0.00 0.00 0.00 3.59
3223 3749 2.206750 TGAACTTTTTCTCCCACGTCG 58.793 47.619 0.00 0.00 32.36 5.12
3225 3751 2.171870 TCCTGAACTTTTTCTCCCACGT 59.828 45.455 0.00 0.00 32.36 4.49
3226 3752 2.846193 TCCTGAACTTTTTCTCCCACG 58.154 47.619 0.00 0.00 32.36 4.94
3227 3753 6.238648 TCTAATCCTGAACTTTTTCTCCCAC 58.761 40.000 0.00 0.00 32.36 4.61
3228 3754 6.448369 TCTAATCCTGAACTTTTTCTCCCA 57.552 37.500 0.00 0.00 32.36 4.37
3230 3756 6.176896 AGCTCTAATCCTGAACTTTTTCTCC 58.823 40.000 0.00 0.00 32.36 3.71
3232 3758 8.598041 TCTTAGCTCTAATCCTGAACTTTTTCT 58.402 33.333 0.00 0.00 32.36 2.52
3244 3776 7.252965 GAACCAATGTTCTTAGCTCTAATCC 57.747 40.000 0.00 0.00 46.03 3.01


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

AutoCloner maintained by Alex Coulton.