Multiple sequence alignment - TraesCS4D01G260000

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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 TraesCS4D01G260000 chr4D 100.000 2111 0 0 1 2111 428984678 428986788 0.000000e+00 3899.0
1 TraesCS4D01G260000 chr4D 95.231 671 32 0 1441 2111 277425961 277425291 0.000000e+00 1062.0
2 TraesCS4D01G260000 chr3D 98.957 671 7 0 1441 2111 536024767 536024097 0.000000e+00 1201.0
3 TraesCS4D01G260000 chr3D 97.765 671 15 0 1441 2111 91812386 91811716 0.000000e+00 1157.0
4 TraesCS4D01G260000 chr3D 96.125 671 26 0 1441 2111 48158668 48157998 0.000000e+00 1096.0
5 TraesCS4D01G260000 chr3D 97.674 43 0 1 264 306 17372451 17372492 2.910000e-09 73.1
6 TraesCS4D01G260000 chr6D 96.870 671 21 0 1441 2111 445339559 445338889 0.000000e+00 1123.0
7 TraesCS4D01G260000 chr6D 82.274 299 31 18 876 1162 87463268 87463556 2.710000e-59 239.0
8 TraesCS4D01G260000 chr6D 87.437 199 24 1 971 1169 87465870 87466067 5.860000e-56 228.0
9 TraesCS4D01G260000 chr7D 96.721 671 22 0 1441 2111 397177598 397178268 0.000000e+00 1118.0
10 TraesCS4D01G260000 chr2D 94.933 671 34 0 1441 2111 52849124 52848454 0.000000e+00 1051.0
11 TraesCS4D01G260000 chr2D 94.784 671 35 0 1441 2111 553907029 553907699 0.000000e+00 1046.0
12 TraesCS4D01G260000 chr5D 94.784 671 35 0 1441 2111 525462169 525462839 0.000000e+00 1046.0
13 TraesCS4D01G260000 chr4B 87.680 763 53 19 711 1439 527119919 527120674 0.000000e+00 850.0
14 TraesCS4D01G260000 chr4B 88.640 669 43 12 1 653 527119254 527119905 0.000000e+00 784.0
15 TraesCS4D01G260000 chr4A 90.754 411 28 7 1037 1439 37277359 37276951 6.630000e-150 540.0
16 TraesCS4D01G260000 chr4A 89.062 256 12 6 305 544 37278475 37278220 9.460000e-79 303.0
17 TraesCS4D01G260000 chr4A 89.109 101 7 2 543 643 37277795 37277699 2.840000e-24 122.0
18 TraesCS4D01G260000 chr6A 82.042 284 40 10 891 1169 105591207 105591484 4.530000e-57 231.0
19 TraesCS4D01G260000 chr3A 88.000 200 18 6 971 1166 645405904 645406101 4.530000e-57 231.0
20 TraesCS4D01G260000 chr6B 87.000 200 24 2 960 1158 166114789 166114987 7.580000e-55 224.0
21 TraesCS4D01G260000 chr7B 85.990 207 26 3 961 1165 593016161 593015956 3.530000e-53 219.0
22 TraesCS4D01G260000 chr3B 84.071 226 31 5 960 1181 669634881 669635105 1.640000e-51 213.0
23 TraesCS4D01G260000 chr5B 96.970 33 1 0 276 308 572000546 572000514 2.930000e-04 56.5


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 TraesCS4D01G260000 chr4D 428984678 428986788 2110 False 3899.000000 3899 100.000000 1 2111 1 chr4D.!!$F1 2110
1 TraesCS4D01G260000 chr4D 277425291 277425961 670 True 1062.000000 1062 95.231000 1441 2111 1 chr4D.!!$R1 670
2 TraesCS4D01G260000 chr3D 536024097 536024767 670 True 1201.000000 1201 98.957000 1441 2111 1 chr3D.!!$R3 670
3 TraesCS4D01G260000 chr3D 91811716 91812386 670 True 1157.000000 1157 97.765000 1441 2111 1 chr3D.!!$R2 670
4 TraesCS4D01G260000 chr3D 48157998 48158668 670 True 1096.000000 1096 96.125000 1441 2111 1 chr3D.!!$R1 670
5 TraesCS4D01G260000 chr6D 445338889 445339559 670 True 1123.000000 1123 96.870000 1441 2111 1 chr6D.!!$R1 670
6 TraesCS4D01G260000 chr6D 87463268 87466067 2799 False 233.500000 239 84.855500 876 1169 2 chr6D.!!$F1 293
7 TraesCS4D01G260000 chr7D 397177598 397178268 670 False 1118.000000 1118 96.721000 1441 2111 1 chr7D.!!$F1 670
8 TraesCS4D01G260000 chr2D 52848454 52849124 670 True 1051.000000 1051 94.933000 1441 2111 1 chr2D.!!$R1 670
9 TraesCS4D01G260000 chr2D 553907029 553907699 670 False 1046.000000 1046 94.784000 1441 2111 1 chr2D.!!$F1 670
10 TraesCS4D01G260000 chr5D 525462169 525462839 670 False 1046.000000 1046 94.784000 1441 2111 1 chr5D.!!$F1 670
11 TraesCS4D01G260000 chr4B 527119254 527120674 1420 False 817.000000 850 88.160000 1 1439 2 chr4B.!!$F1 1438
12 TraesCS4D01G260000 chr4A 37276951 37278475 1524 True 321.666667 540 89.641667 305 1439 3 chr4A.!!$R1 1134

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
866 1316 0.040425 GCACGAACGCCTTTGTTCAT 60.04 50.0 7.33 0.0 46.77 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 5158 1.134461 GCCACTCTGAGATGCATGAGT 60.134 52.381 12.44 7.85 36.25 3.41 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
42 43 4.787598 CATTAGCACCTTTGGATAATCGC 58.212 43.478 0.00 0.00 0.00 4.58
77 78 3.557264 GGGGGAAAATATCTAGTGCTCCG 60.557 52.174 0.00 0.00 0.00 4.63
79 80 3.557264 GGGAAAATATCTAGTGCTCCGGG 60.557 52.174 0.00 0.00 0.00 5.73
102 104 0.320683 TCATGTGCCAAGACTCACGG 60.321 55.000 0.00 0.00 36.06 4.94
106 108 2.435059 GCCAAGACTCACGGGAGC 60.435 66.667 16.39 7.86 45.42 4.70
108 110 1.605058 GCCAAGACTCACGGGAGCTA 61.605 60.000 16.39 0.00 45.42 3.32
112 114 1.025812 AGACTCACGGGAGCTATTCG 58.974 55.000 16.39 0.00 45.42 3.34
137 139 8.961092 CGATCTATGAATTTTATGCACAAAAGG 58.039 33.333 9.05 0.00 31.29 3.11
183 185 2.486472 AGGTCAAACAGATCCAGCAG 57.514 50.000 0.00 0.00 0.00 4.24
191 193 0.107312 CAGATCCAGCAGGTCCCAAG 60.107 60.000 0.00 0.00 35.89 3.61
198 200 2.413142 GCAGGTCCCAAGATGCAGC 61.413 63.158 0.00 0.00 38.54 5.25
205 207 1.147824 CCAAGATGCAGCCCGATCT 59.852 57.895 0.00 0.00 0.00 2.75
206 208 0.394192 CCAAGATGCAGCCCGATCTA 59.606 55.000 0.00 0.00 0.00 1.98
215 217 1.417890 CAGCCCGATCTAAGGTCCAAT 59.582 52.381 0.00 0.00 0.00 3.16
216 218 1.417890 AGCCCGATCTAAGGTCCAATG 59.582 52.381 0.00 0.00 0.00 2.82
234 236 3.224324 GCCGAGGAGCCCGTATCA 61.224 66.667 0.00 0.00 0.00 2.15
235 237 2.728817 CCGAGGAGCCCGTATCAC 59.271 66.667 0.00 0.00 0.00 3.06
236 238 2.728817 CGAGGAGCCCGTATCACC 59.271 66.667 0.00 0.00 0.00 4.02
237 239 2.728817 GAGGAGCCCGTATCACCG 59.271 66.667 0.00 0.00 0.00 4.94
238 240 2.043248 AGGAGCCCGTATCACCGT 60.043 61.111 0.00 0.00 0.00 4.83
239 241 0.820891 GAGGAGCCCGTATCACCGTA 60.821 60.000 0.00 0.00 0.00 4.02
240 242 0.396139 AGGAGCCCGTATCACCGTAA 60.396 55.000 0.00 0.00 0.00 3.18
241 243 0.249197 GGAGCCCGTATCACCGTAAC 60.249 60.000 0.00 0.00 0.00 2.50
242 244 0.249197 GAGCCCGTATCACCGTAACC 60.249 60.000 0.00 0.00 0.00 2.85
252 254 0.949105 CACCGTAACCTGAGCACCAC 60.949 60.000 0.00 0.00 0.00 4.16
255 257 1.078709 CGTAACCTGAGCACCACATG 58.921 55.000 0.00 0.00 0.00 3.21
270 273 2.286872 CACATGCTCACTCCAAGGATC 58.713 52.381 0.00 0.00 0.00 3.36
286 289 0.924090 GATCGGCTAGCAAACTGTCG 59.076 55.000 18.24 9.00 0.00 4.35
290 293 1.130613 GCTAGCAAACTGTCGTGCG 59.869 57.895 10.63 0.68 45.62 5.34
299 302 3.360249 AACTGTCGTGCGTAAAGTAGT 57.640 42.857 0.00 0.00 0.00 2.73
384 389 1.210870 GAACCAAACACGTACGCTGA 58.789 50.000 16.72 0.00 0.00 4.26
385 390 1.796459 GAACCAAACACGTACGCTGAT 59.204 47.619 16.72 5.04 0.00 2.90
408 426 8.375506 TGATCTTGTGGTTTCTAATCTTGTACT 58.624 33.333 0.00 0.00 0.00 2.73
448 467 3.374058 GGGTTTGACAAGACGTGATATGG 59.626 47.826 0.00 0.00 0.00 2.74
484 503 5.559148 AGTTGTTTTTGGGCATGGATTTA 57.441 34.783 0.00 0.00 0.00 1.40
546 992 3.065095 ACGACTCGCTGTAACTCCTAATC 59.935 47.826 0.00 0.00 0.00 1.75
557 1003 7.575720 GCTGTAACTCCTAATCATTTTGTGCTT 60.576 37.037 0.00 0.00 0.00 3.91
558 1004 8.856153 TGTAACTCCTAATCATTTTGTGCTTA 57.144 30.769 0.00 0.00 0.00 3.09
559 1005 9.290988 TGTAACTCCTAATCATTTTGTGCTTAA 57.709 29.630 0.00 0.00 0.00 1.85
586 1032 2.553602 TGACCAAGCATGACACATCAAC 59.446 45.455 0.00 0.00 38.69 3.18
588 1034 2.165167 CCAAGCATGACACATCAACCT 58.835 47.619 0.00 0.00 38.69 3.50
592 1038 1.665679 GCATGACACATCAACCTACCG 59.334 52.381 0.00 0.00 38.69 4.02
597 1043 2.735134 GACACATCAACCTACCGTGTTC 59.265 50.000 0.00 0.00 40.72 3.18
599 1045 1.342174 ACATCAACCTACCGTGTTCGT 59.658 47.619 0.00 0.00 35.01 3.85
631 1077 3.310774 GTGATGCGAATTATGTGCAGTCT 59.689 43.478 0.00 0.00 42.65 3.24
653 1099 0.667993 TCCTTGAAAGGCAAAGCACG 59.332 50.000 4.08 0.00 46.06 5.34
654 1100 0.667993 CCTTGAAAGGCAAAGCACGA 59.332 50.000 0.00 0.00 39.76 4.35
655 1101 1.066908 CCTTGAAAGGCAAAGCACGAA 59.933 47.619 0.00 0.00 39.76 3.85
656 1102 2.388121 CTTGAAAGGCAAAGCACGAAG 58.612 47.619 0.00 0.00 35.74 3.79
666 1112 3.084579 GCACGAAGCGTCATCCAG 58.915 61.111 0.00 0.00 38.32 3.86
667 1113 1.446099 GCACGAAGCGTCATCCAGA 60.446 57.895 0.00 0.00 38.32 3.86
668 1114 1.687494 GCACGAAGCGTCATCCAGAC 61.687 60.000 0.00 0.00 44.02 3.51
669 1115 0.109086 CACGAAGCGTCATCCAGACT 60.109 55.000 0.00 0.00 45.32 3.24
670 1116 0.171455 ACGAAGCGTCATCCAGACTC 59.829 55.000 0.00 0.00 45.32 3.36
671 1117 0.863538 CGAAGCGTCATCCAGACTCG 60.864 60.000 0.00 0.00 45.32 4.18
672 1118 0.171455 GAAGCGTCATCCAGACTCGT 59.829 55.000 0.00 0.00 45.32 4.18
673 1119 0.171455 AAGCGTCATCCAGACTCGTC 59.829 55.000 0.00 0.00 45.32 4.20
674 1120 0.960861 AGCGTCATCCAGACTCGTCA 60.961 55.000 0.00 0.00 45.32 4.35
675 1121 0.798771 GCGTCATCCAGACTCGTCAC 60.799 60.000 0.00 0.00 45.32 3.67
676 1122 0.521735 CGTCATCCAGACTCGTCACA 59.478 55.000 0.00 0.00 45.32 3.58
677 1123 1.068541 CGTCATCCAGACTCGTCACAA 60.069 52.381 0.00 0.00 45.32 3.33
678 1124 2.416027 CGTCATCCAGACTCGTCACAAT 60.416 50.000 0.00 0.00 45.32 2.71
679 1125 3.589988 GTCATCCAGACTCGTCACAATT 58.410 45.455 0.00 0.00 44.09 2.32
680 1126 3.614616 GTCATCCAGACTCGTCACAATTC 59.385 47.826 0.00 0.00 44.09 2.17
681 1127 3.258123 TCATCCAGACTCGTCACAATTCA 59.742 43.478 0.00 0.00 0.00 2.57
682 1128 3.026630 TCCAGACTCGTCACAATTCAC 57.973 47.619 0.00 0.00 0.00 3.18
683 1129 1.721389 CCAGACTCGTCACAATTCACG 59.279 52.381 0.00 0.00 37.36 4.35
684 1130 2.394708 CAGACTCGTCACAATTCACGT 58.605 47.619 0.00 0.00 37.30 4.49
685 1131 2.794910 CAGACTCGTCACAATTCACGTT 59.205 45.455 0.00 0.00 37.30 3.99
686 1132 3.050619 AGACTCGTCACAATTCACGTTC 58.949 45.455 0.00 1.39 37.30 3.95
687 1133 2.792674 GACTCGTCACAATTCACGTTCA 59.207 45.455 0.00 0.00 37.30 3.18
688 1134 3.390135 ACTCGTCACAATTCACGTTCAT 58.610 40.909 0.00 0.00 37.30 2.57
689 1135 3.184379 ACTCGTCACAATTCACGTTCATG 59.816 43.478 0.00 0.00 37.30 3.07
690 1136 3.385577 TCGTCACAATTCACGTTCATGA 58.614 40.909 0.00 0.00 37.30 3.07
691 1137 3.428534 TCGTCACAATTCACGTTCATGAG 59.571 43.478 0.00 0.00 37.30 2.90
692 1138 3.428534 CGTCACAATTCACGTTCATGAGA 59.571 43.478 0.00 0.00 0.00 3.27
693 1139 4.084589 CGTCACAATTCACGTTCATGAGAA 60.085 41.667 0.00 0.00 0.00 2.87
694 1140 5.377358 GTCACAATTCACGTTCATGAGAAG 58.623 41.667 0.00 0.00 33.63 2.85
695 1141 4.452114 TCACAATTCACGTTCATGAGAAGG 59.548 41.667 0.00 0.00 43.42 3.46
696 1142 3.189287 ACAATTCACGTTCATGAGAAGGC 59.811 43.478 0.00 0.00 41.98 4.35
697 1143 2.542020 TTCACGTTCATGAGAAGGCA 57.458 45.000 0.00 0.00 41.98 4.75
698 1144 2.542020 TCACGTTCATGAGAAGGCAA 57.458 45.000 0.00 0.00 41.98 4.52
699 1145 2.844946 TCACGTTCATGAGAAGGCAAA 58.155 42.857 0.00 0.00 41.98 3.68
700 1146 3.411446 TCACGTTCATGAGAAGGCAAAT 58.589 40.909 0.00 0.00 41.98 2.32
701 1147 3.436704 TCACGTTCATGAGAAGGCAAATC 59.563 43.478 0.00 0.00 41.98 2.17
702 1148 3.189080 CACGTTCATGAGAAGGCAAATCA 59.811 43.478 0.00 0.00 41.98 2.57
703 1149 3.189287 ACGTTCATGAGAAGGCAAATCAC 59.811 43.478 0.00 0.00 41.98 3.06
704 1150 3.189080 CGTTCATGAGAAGGCAAATCACA 59.811 43.478 0.00 0.00 33.63 3.58
705 1151 4.479619 GTTCATGAGAAGGCAAATCACAC 58.520 43.478 0.00 0.00 33.63 3.82
706 1152 2.743664 TCATGAGAAGGCAAATCACACG 59.256 45.455 0.00 0.00 0.00 4.49
707 1153 1.522668 TGAGAAGGCAAATCACACGG 58.477 50.000 0.00 0.00 0.00 4.94
708 1154 1.202758 TGAGAAGGCAAATCACACGGT 60.203 47.619 0.00 0.00 0.00 4.83
709 1155 2.037902 TGAGAAGGCAAATCACACGGTA 59.962 45.455 0.00 0.00 0.00 4.02
725 1171 4.000325 CACGGTATGATTCTGTGTTTCCA 59.000 43.478 3.18 0.00 37.40 3.53
735 1181 8.690203 TGATTCTGTGTTTCCAATCTTTTCTA 57.310 30.769 0.00 0.00 0.00 2.10
743 1192 9.673454 GTGTTTCCAATCTTTTCTATTTAACGT 57.327 29.630 0.00 0.00 0.00 3.99
794 1243 1.439644 GATGAGGACTGACTCGGGC 59.560 63.158 0.00 0.00 40.39 6.13
819 1268 1.741770 GAGGCCTGCACGACGAAAT 60.742 57.895 12.00 0.00 0.00 2.17
839 1289 7.920682 ACGAAATGCTTAAAACTGAAACTTCAT 59.079 29.630 0.00 0.00 36.46 2.57
852 1302 7.041721 ACTGAAACTTCATATATTCTGCACGA 58.958 34.615 0.00 0.00 36.46 4.35
866 1316 0.040425 GCACGAACGCCTTTGTTCAT 60.040 50.000 7.33 0.00 46.77 2.57
871 1321 2.066262 GAACGCCTTTGTTCATCGAGA 58.934 47.619 1.98 0.00 45.92 4.04
872 1322 1.714794 ACGCCTTTGTTCATCGAGAG 58.285 50.000 0.00 0.00 0.00 3.20
873 1323 4.162255 GAACGCCTTTGTTCATCGAGAGA 61.162 47.826 1.98 0.00 45.92 3.10
936 1386 3.923864 AGCAGTGCAACGACCGGA 61.924 61.111 19.20 0.00 45.86 5.14
944 1394 2.026590 AACGACCGGACGACACAC 59.973 61.111 31.92 0.57 37.03 3.82
945 1395 2.773745 AACGACCGGACGACACACA 61.774 57.895 31.92 0.00 37.03 3.72
953 1403 3.168528 ACGACACACAAGGGCCCT 61.169 61.111 22.28 22.28 0.00 5.19
954 1404 2.669569 CGACACACAAGGGCCCTG 60.670 66.667 29.50 21.81 0.00 4.45
957 1407 0.618458 GACACACAAGGGCCCTGATA 59.382 55.000 29.50 0.00 0.00 2.15
958 1408 1.004277 GACACACAAGGGCCCTGATAA 59.996 52.381 29.50 0.00 0.00 1.75
965 1431 2.317530 GGGCCCTGATAAACCCTCA 58.682 57.895 17.04 0.00 39.42 3.86
968 1435 0.919710 GCCCTGATAAACCCTCACCT 59.080 55.000 0.00 0.00 0.00 4.00
1073 4224 0.110486 AGCCAAAAGGCCGAGAAAGA 59.890 50.000 2.33 0.00 35.12 2.52
1352 4517 0.674581 TGCACATTGCTCGGGAGAAG 60.675 55.000 0.00 0.00 45.31 2.85
1360 4525 3.485463 TGCTCGGGAGAAGAAGAAAAA 57.515 42.857 0.00 0.00 39.18 1.94
1389 4558 5.658190 AGTGCCATCTTTGCCTTTGTATATT 59.342 36.000 0.00 0.00 0.00 1.28
1394 4563 7.257722 CCATCTTTGCCTTTGTATATTCGTTT 58.742 34.615 0.00 0.00 0.00 3.60
1395 4564 7.432252 CCATCTTTGCCTTTGTATATTCGTTTC 59.568 37.037 0.00 0.00 0.00 2.78
1421 4590 3.813166 CCTCGTGGTGATGTGTACTTTTT 59.187 43.478 0.00 0.00 0.00 1.94
1494 4663 1.070445 GGCGAGACCCATCCATCAG 59.930 63.158 0.00 0.00 0.00 2.90
1623 4792 2.469826 GCGTGGAACATCATATGTCGA 58.530 47.619 1.90 0.00 44.07 4.20
1989 5158 4.704540 CCACCTTTCATGGCACTTATACAA 59.295 41.667 0.00 0.00 0.00 2.41
2092 5261 2.472909 GGGCAATACACAGCTCGGC 61.473 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.755469 CCCCCAATCCTTGCACGG 60.755 66.667 1.99 1.99 0.00 4.94
59 60 3.067833 GCCCGGAGCACTAGATATTTTC 58.932 50.000 0.73 0.00 42.97 2.29
79 80 1.975363 GAGTCTTGGCACATGAGCGC 61.975 60.000 9.09 0.00 43.19 5.92
86 87 2.099652 CTCCCGTGAGTCTTGGCACA 62.100 60.000 0.00 0.00 34.78 4.57
91 92 2.796383 CGAATAGCTCCCGTGAGTCTTG 60.796 54.545 0.00 0.00 40.95 3.02
112 114 8.758715 GCCTTTTGTGCATAAAATTCATAGATC 58.241 33.333 19.86 2.05 0.00 2.75
137 139 2.222227 ATTTTCAGACTCCCAAGGGC 57.778 50.000 0.00 0.00 34.68 5.19
183 185 2.440980 GGGCTGCATCTTGGGACC 60.441 66.667 0.50 0.00 0.00 4.46
191 193 0.394565 ACCTTAGATCGGGCTGCATC 59.605 55.000 0.50 0.00 0.00 3.91
198 200 1.543429 GCCATTGGACCTTAGATCGGG 60.543 57.143 6.95 1.79 0.00 5.14
205 207 0.619255 TCCTCGGCCATTGGACCTTA 60.619 55.000 6.95 0.00 0.00 2.69
206 208 1.915078 CTCCTCGGCCATTGGACCTT 61.915 60.000 6.95 0.00 0.00 3.50
232 234 1.116536 TGGTGCTCAGGTTACGGTGA 61.117 55.000 0.00 0.00 0.00 4.02
233 235 0.949105 GTGGTGCTCAGGTTACGGTG 60.949 60.000 0.00 0.00 0.00 4.94
234 236 1.370064 GTGGTGCTCAGGTTACGGT 59.630 57.895 0.00 0.00 0.00 4.83
235 237 0.036388 ATGTGGTGCTCAGGTTACGG 60.036 55.000 0.00 0.00 0.00 4.02
236 238 1.078709 CATGTGGTGCTCAGGTTACG 58.921 55.000 0.00 0.00 0.00 3.18
252 254 1.579698 CGATCCTTGGAGTGAGCATG 58.420 55.000 0.00 0.00 0.00 4.06
255 257 1.522580 GCCGATCCTTGGAGTGAGC 60.523 63.158 0.00 0.00 0.00 4.26
270 273 1.781555 CACGACAGTTTGCTAGCCG 59.218 57.895 13.29 9.00 0.00 5.52
286 289 3.737774 AGAACCGAAACTACTTTACGCAC 59.262 43.478 0.00 0.00 0.00 5.34
290 293 6.914215 CCCAAAAAGAACCGAAACTACTTTAC 59.086 38.462 0.00 0.00 31.86 2.01
299 302 5.112686 CAACAATCCCAAAAAGAACCGAAA 58.887 37.500 0.00 0.00 0.00 3.46
384 389 7.119846 GCAGTACAAGATTAGAAACCACAAGAT 59.880 37.037 0.00 0.00 0.00 2.40
385 390 6.426937 GCAGTACAAGATTAGAAACCACAAGA 59.573 38.462 0.00 0.00 0.00 3.02
408 426 0.889994 CCATGCCAACTAGCTTTGCA 59.110 50.000 0.00 6.37 0.00 4.08
448 467 4.365899 AAACAACTTCAAGGAACGGAAC 57.634 40.909 0.00 0.00 0.00 3.62
484 503 1.599419 GCATCACGTCGTTGGCTTTTT 60.599 47.619 0.00 0.00 0.00 1.94
546 992 8.586570 TTGGTCAAGTTATTAAGCACAAAATG 57.413 30.769 0.00 0.00 0.00 2.32
557 1003 6.000840 TGTGTCATGCTTGGTCAAGTTATTA 58.999 36.000 11.71 0.00 40.45 0.98
558 1004 4.826733 TGTGTCATGCTTGGTCAAGTTATT 59.173 37.500 11.71 0.00 40.45 1.40
559 1005 4.397420 TGTGTCATGCTTGGTCAAGTTAT 58.603 39.130 11.71 5.10 40.45 1.89
586 1032 0.863144 CACCAAACGAACACGGTAGG 59.137 55.000 0.00 0.00 0.00 3.18
588 1034 0.461516 TGCACCAAACGAACACGGTA 60.462 50.000 0.00 0.00 0.00 4.02
592 1038 0.859788 CACGTGCACCAAACGAACAC 60.860 55.000 12.15 0.00 43.68 3.32
597 1043 4.513275 CATCACGTGCACCAAACG 57.487 55.556 11.67 0.95 46.32 3.60
659 1105 3.258123 TGAATTGTGACGAGTCTGGATGA 59.742 43.478 1.72 0.00 0.00 2.92
660 1106 3.369147 GTGAATTGTGACGAGTCTGGATG 59.631 47.826 1.72 0.00 0.00 3.51
661 1107 3.589988 GTGAATTGTGACGAGTCTGGAT 58.410 45.455 1.72 0.00 0.00 3.41
662 1108 2.607038 CGTGAATTGTGACGAGTCTGGA 60.607 50.000 1.72 0.00 37.81 3.86
663 1109 1.721389 CGTGAATTGTGACGAGTCTGG 59.279 52.381 1.72 0.00 37.81 3.86
664 1110 2.394708 ACGTGAATTGTGACGAGTCTG 58.605 47.619 1.72 0.00 38.94 3.51
665 1111 2.795175 ACGTGAATTGTGACGAGTCT 57.205 45.000 1.72 0.00 38.94 3.24
666 1112 2.792674 TGAACGTGAATTGTGACGAGTC 59.207 45.455 7.94 0.00 38.94 3.36
667 1113 2.816689 TGAACGTGAATTGTGACGAGT 58.183 42.857 7.94 0.00 38.94 4.18
668 1114 3.428534 TCATGAACGTGAATTGTGACGAG 59.571 43.478 0.00 0.00 38.94 4.18
669 1115 3.385577 TCATGAACGTGAATTGTGACGA 58.614 40.909 0.00 0.00 38.94 4.20
670 1116 3.428534 TCTCATGAACGTGAATTGTGACG 59.571 43.478 0.00 0.00 41.41 4.35
671 1117 4.990543 TCTCATGAACGTGAATTGTGAC 57.009 40.909 0.00 0.00 0.00 3.67
672 1118 4.452114 CCTTCTCATGAACGTGAATTGTGA 59.548 41.667 0.00 0.00 0.00 3.58
673 1119 4.715896 CCTTCTCATGAACGTGAATTGTG 58.284 43.478 0.00 0.00 0.00 3.33
674 1120 3.189287 GCCTTCTCATGAACGTGAATTGT 59.811 43.478 0.00 0.00 0.00 2.71
675 1121 3.189080 TGCCTTCTCATGAACGTGAATTG 59.811 43.478 0.00 0.00 0.00 2.32
676 1122 3.411446 TGCCTTCTCATGAACGTGAATT 58.589 40.909 0.00 0.00 0.00 2.17
677 1123 3.057969 TGCCTTCTCATGAACGTGAAT 57.942 42.857 0.00 0.00 0.00 2.57
678 1124 2.542020 TGCCTTCTCATGAACGTGAA 57.458 45.000 0.00 0.00 0.00 3.18
679 1125 2.542020 TTGCCTTCTCATGAACGTGA 57.458 45.000 0.00 0.00 0.00 4.35
680 1126 3.189080 TGATTTGCCTTCTCATGAACGTG 59.811 43.478 0.00 0.00 0.00 4.49
681 1127 3.189287 GTGATTTGCCTTCTCATGAACGT 59.811 43.478 0.00 0.00 0.00 3.99
682 1128 3.189080 TGTGATTTGCCTTCTCATGAACG 59.811 43.478 0.00 0.00 0.00 3.95
683 1129 4.479619 GTGTGATTTGCCTTCTCATGAAC 58.520 43.478 0.00 0.00 0.00 3.18
684 1130 3.189080 CGTGTGATTTGCCTTCTCATGAA 59.811 43.478 0.00 0.00 0.00 2.57
685 1131 2.743664 CGTGTGATTTGCCTTCTCATGA 59.256 45.455 0.00 0.00 0.00 3.07
686 1132 2.159476 CCGTGTGATTTGCCTTCTCATG 60.159 50.000 0.00 0.00 0.00 3.07
687 1133 2.086869 CCGTGTGATTTGCCTTCTCAT 58.913 47.619 0.00 0.00 0.00 2.90
688 1134 1.202758 ACCGTGTGATTTGCCTTCTCA 60.203 47.619 0.00 0.00 0.00 3.27
689 1135 1.523758 ACCGTGTGATTTGCCTTCTC 58.476 50.000 0.00 0.00 0.00 2.87
690 1136 2.851263 TACCGTGTGATTTGCCTTCT 57.149 45.000 0.00 0.00 0.00 2.85
691 1137 3.006940 TCATACCGTGTGATTTGCCTTC 58.993 45.455 0.00 0.00 0.00 3.46
692 1138 3.066291 TCATACCGTGTGATTTGCCTT 57.934 42.857 0.00 0.00 0.00 4.35
693 1139 2.779755 TCATACCGTGTGATTTGCCT 57.220 45.000 0.00 0.00 0.00 4.75
694 1140 3.627577 AGAATCATACCGTGTGATTTGCC 59.372 43.478 20.55 10.95 44.10 4.52
695 1141 4.094887 ACAGAATCATACCGTGTGATTTGC 59.905 41.667 20.55 11.51 44.10 3.68
696 1142 5.122239 ACACAGAATCATACCGTGTGATTTG 59.878 40.000 20.55 19.94 44.10 2.32
697 1143 5.245531 ACACAGAATCATACCGTGTGATTT 58.754 37.500 20.55 10.68 44.10 2.17
698 1144 4.832248 ACACAGAATCATACCGTGTGATT 58.168 39.130 19.93 19.93 46.07 2.57
699 1145 4.471904 ACACAGAATCATACCGTGTGAT 57.528 40.909 5.01 5.01 40.84 3.06
700 1146 3.953712 ACACAGAATCATACCGTGTGA 57.046 42.857 7.72 0.00 40.84 3.58
701 1147 4.142902 GGAAACACAGAATCATACCGTGTG 60.143 45.833 0.00 0.00 40.51 3.82
702 1148 4.000988 GGAAACACAGAATCATACCGTGT 58.999 43.478 0.00 0.00 42.36 4.49
703 1149 4.000325 TGGAAACACAGAATCATACCGTG 59.000 43.478 0.00 0.00 33.40 4.94
704 1150 4.280436 TGGAAACACAGAATCATACCGT 57.720 40.909 0.00 0.00 33.40 4.83
705 1151 5.586243 AGATTGGAAACACAGAATCATACCG 59.414 40.000 0.00 0.00 42.67 4.02
706 1152 7.396540 AAGATTGGAAACACAGAATCATACC 57.603 36.000 0.00 0.00 42.67 2.73
707 1153 9.346725 GAAAAGATTGGAAACACAGAATCATAC 57.653 33.333 0.00 0.00 42.67 2.39
708 1154 9.300681 AGAAAAGATTGGAAACACAGAATCATA 57.699 29.630 0.00 0.00 42.67 2.15
709 1155 8.186709 AGAAAAGATTGGAAACACAGAATCAT 57.813 30.769 0.00 0.00 42.67 2.45
737 1183 7.360607 GCCTCAGTTAGCTAATCAAAACGTTAA 60.361 37.037 9.88 0.00 0.00 2.01
743 1192 6.570378 GCTTTGCCTCAGTTAGCTAATCAAAA 60.570 38.462 9.88 3.96 0.00 2.44
749 1198 2.711542 GGCTTTGCCTCAGTTAGCTAA 58.288 47.619 0.86 0.86 46.69 3.09
750 1199 2.403252 GGCTTTGCCTCAGTTAGCTA 57.597 50.000 0.73 0.00 46.69 3.32
751 1200 3.256281 GGCTTTGCCTCAGTTAGCT 57.744 52.632 0.73 0.00 46.69 3.32
769 1218 1.200252 AGTCAGTCCTCATCGTTGTCG 59.800 52.381 0.00 0.00 38.55 4.35
776 1225 1.040339 AGCCCGAGTCAGTCCTCATC 61.040 60.000 0.00 0.00 0.00 2.92
777 1226 0.259065 TAGCCCGAGTCAGTCCTCAT 59.741 55.000 0.00 0.00 0.00 2.90
794 1243 2.125106 GTGCAGGCCTCGGGTTAG 60.125 66.667 0.00 0.00 0.00 2.34
800 1249 4.717629 TTCGTCGTGCAGGCCTCG 62.718 66.667 0.00 3.52 0.00 4.63
839 1289 2.882927 AGGCGTTCGTGCAGAATATA 57.117 45.000 0.00 0.00 41.49 0.86
848 1298 1.721489 CGATGAACAAAGGCGTTCGTG 60.721 52.381 3.40 0.00 46.77 4.35
852 1302 2.069273 CTCTCGATGAACAAAGGCGTT 58.931 47.619 0.00 0.00 0.00 4.84
889 1339 2.647875 CGCGCCCCAATCAAAACA 59.352 55.556 0.00 0.00 0.00 2.83
931 1381 2.420043 CCTTGTGTGTCGTCCGGT 59.580 61.111 0.00 0.00 0.00 5.28
936 1386 3.168528 AGGGCCCTTGTGTGTCGT 61.169 61.111 22.28 0.00 0.00 4.34
944 1394 3.207452 GGGTTTATCAGGGCCCTTG 57.793 57.895 26.10 18.33 38.12 3.61
1073 4224 2.240667 AGGGCAGCAGAACAACTCATAT 59.759 45.455 0.00 0.00 0.00 1.78
1216 4379 0.519077 GCTTCAACTTCAAGCCCTCG 59.481 55.000 0.00 0.00 40.45 4.63
1389 4558 0.031585 CACCACGAGGACAGAAACGA 59.968 55.000 5.68 0.00 38.69 3.85
1394 4563 0.603065 CACATCACCACGAGGACAGA 59.397 55.000 5.68 0.80 38.69 3.41
1395 4564 0.318441 ACACATCACCACGAGGACAG 59.682 55.000 5.68 0.00 38.69 3.51
1421 4590 3.016736 GGCAAGGAAAGATTCATCCGAA 58.983 45.455 3.65 0.00 40.78 4.30
1439 4608 2.281484 GAACAAGACGCCCTGGCA 60.281 61.111 9.17 0.00 42.06 4.92
1989 5158 1.134461 GCCACTCTGAGATGCATGAGT 60.134 52.381 12.44 7.85 36.25 3.41
2079 5248 3.075005 ACGGGCCGAGCTGTGTAT 61.075 61.111 35.78 2.80 0.00 2.29
2092 5261 1.299468 GCAGAGCTCGATACACGGG 60.299 63.158 8.37 0.00 46.38 5.28


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

AutoCloner maintained by Alex Coulton.