Multiple sequence alignment - TraesCS4D01G176000

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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 TraesCS4D01G176000 chr4D 100.000 3301 0 0 1 3301 305139845 305143145 0.000000e+00 6096.0
1 TraesCS4D01G176000 chr4D 100.000 140 0 0 3508 3647 305143352 305143491 3.610000e-65 259.0
2 TraesCS4D01G176000 chr4A 90.334 3114 128 51 4 3033 173629215 173632239 0.000000e+00 3923.0
3 TraesCS4D01G176000 chr4A 90.000 140 2 3 3508 3640 173638179 173638313 1.740000e-38 171.0
4 TraesCS4D01G176000 chr4A 92.661 109 8 0 3047 3155 173632296 173632404 1.360000e-34 158.0
5 TraesCS4D01G176000 chr4A 85.714 119 9 4 3172 3286 173637981 173638095 6.400000e-23 119.0
6 TraesCS4D01G176000 chr4A 100.000 30 0 0 3020 3049 173632256 173632285 5.090000e-04 56.5
7 TraesCS4D01G176000 chr4B 90.535 3064 107 58 1 2964 381372602 381375582 0.000000e+00 3882.0
8 TraesCS4D01G176000 chr4B 83.636 275 7 13 3000 3272 381375577 381375815 1.320000e-54 224.0
9 TraesCS4D01G176000 chr4B 90.714 140 6 2 3508 3647 381375917 381376049 2.890000e-41 180.0
10 TraesCS4D01G176000 chr2D 85.081 248 34 2 1478 1725 417544117 417544361 2.170000e-62 250.0
11 TraesCS4D01G176000 chr2B 84.400 250 32 6 1478 1725 489419049 489419293 4.710000e-59 239.0
12 TraesCS4D01G176000 chr2B 82.166 157 27 1 1204 1359 83955362 83955206 2.280000e-27 134.0
13 TraesCS4D01G176000 chr2A 84.426 244 31 6 1484 1725 572615833 572615595 2.190000e-57 233.0
14 TraesCS4D01G176000 chr2A 82.432 222 34 3 1497 1714 625957808 625958028 4.810000e-44 189.0
15 TraesCS4D01G176000 chr5A 82.759 261 33 10 1472 1725 317240005 317239750 4.740000e-54 222.0
16 TraesCS4D01G176000 chr5D 82.375 261 34 10 1472 1725 238073371 238073626 2.210000e-52 217.0
17 TraesCS4D01G176000 chr5B 80.843 261 38 10 1472 1725 267760739 267760484 1.030000e-45 195.0
18 TraesCS4D01G176000 chr7A 81.466 232 38 4 1491 1718 489163235 489163465 6.220000e-43 185.0
19 TraesCS4D01G176000 chr7D 81.034 232 39 4 1491 1718 438368650 438368880 2.890000e-41 180.0
20 TraesCS4D01G176000 chr7B 80.603 232 40 4 1491 1718 455272021 455271791 1.350000e-39 174.0
21 TraesCS4D01G176000 chr7B 78.947 228 41 4 1492 1714 436787584 436787359 8.160000e-32 148.0
22 TraesCS4D01G176000 chr3A 76.506 166 31 5 1198 1359 586423070 586422909 2.330000e-12 84.2


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 TraesCS4D01G176000 chr4D 305139845 305143491 3646 False 3177.500000 6096 100.000000 1 3647 2 chr4D.!!$F1 3646
1 TraesCS4D01G176000 chr4A 173629215 173632404 3189 False 1379.166667 3923 94.331667 4 3155 3 chr4A.!!$F1 3151
2 TraesCS4D01G176000 chr4B 381372602 381376049 3447 False 1428.666667 3882 88.295000 1 3647 3 chr4B.!!$F1 3646

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
273 275 0.101759 GGCACGTCGCTCCTGTAATA 59.898 55.0 9.31 0.0 41.91 0.98 F
1071 1136 0.106719 CTCTCCCTCTTCCTCTCGCT 60.107 60.0 0.00 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 1139 0.179094 GACGCCGAGAGAGAGAGAGA 60.179 60.0 0.0 0.0 0.0 3.10 R
3049 3219 0.536724 GCCCAAAACCATGATCCACC 59.463 55.0 0.0 0.0 0.0 4.61 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
120 121 3.482232 CTCCCCGATGATGGCACCC 62.482 68.421 0.00 0.00 0.00 4.61
184 186 1.004504 GTCGGATGCTCATCGCTTTTC 60.005 52.381 4.02 0.00 38.69 2.29
185 187 1.009078 CGGATGCTCATCGCTTTTCA 58.991 50.000 4.02 0.00 38.69 2.69
186 188 1.004185 CGGATGCTCATCGCTTTTCAG 60.004 52.381 4.02 0.00 38.69 3.02
188 190 2.421424 GGATGCTCATCGCTTTTCAGTT 59.579 45.455 4.02 0.00 38.69 3.16
189 191 2.975410 TGCTCATCGCTTTTCAGTTG 57.025 45.000 0.00 0.00 40.11 3.16
250 252 4.803426 GTGGTCGCGGGCTCTCTG 62.803 72.222 6.13 0.00 0.00 3.35
272 274 1.153628 GGCACGTCGCTCCTGTAAT 60.154 57.895 9.31 0.00 41.91 1.89
273 275 0.101759 GGCACGTCGCTCCTGTAATA 59.898 55.000 9.31 0.00 41.91 0.98
274 276 1.470285 GGCACGTCGCTCCTGTAATAA 60.470 52.381 9.31 0.00 41.91 1.40
435 438 6.120905 ACCTCTGATCATCCTTTGATTTGAG 58.879 40.000 0.00 0.00 45.29 3.02
437 440 6.038382 CCTCTGATCATCCTTTGATTTGAGTG 59.962 42.308 0.00 5.98 45.29 3.51
468 471 6.675413 ACTGGATGTGGTTAGTGTTACTAA 57.325 37.500 0.00 0.00 38.28 2.24
517 520 2.356069 GCGGATGGGTTGAATTCTTCTC 59.644 50.000 7.05 0.44 0.00 2.87
529 532 0.674581 TTCTTCTCGCTGCATGTGGG 60.675 55.000 0.00 0.00 0.00 4.61
568 572 5.048013 GGTTTCCTTCCAAAGTCAGGTAATG 60.048 44.000 0.00 0.00 0.00 1.90
763 803 8.545229 AAAATACTCTGAATGTGAGAGAGTTG 57.455 34.615 6.23 0.00 43.13 3.16
764 804 4.533919 ACTCTGAATGTGAGAGAGTTGG 57.466 45.455 0.00 0.00 43.13 3.77
765 805 3.260380 ACTCTGAATGTGAGAGAGTTGGG 59.740 47.826 0.00 0.00 43.13 4.12
776 835 2.121228 AGTTGGGGTTGGGGCCTA 60.121 61.111 0.84 0.00 0.00 3.93
780 839 2.615929 GGGGTTGGGGCCTAAGGA 60.616 66.667 1.07 0.00 0.00 3.36
842 901 1.574702 GAGTTGCTTACGGGCCACAC 61.575 60.000 4.39 0.00 31.42 3.82
843 902 2.281900 TTGCTTACGGGCCACACC 60.282 61.111 4.39 0.00 37.93 4.16
873 932 1.126296 GCGCGGTAAGAAGTGAAAGAC 59.874 52.381 8.83 0.00 0.00 3.01
889 948 4.658786 ACGGGAGGGGTCTTGGCT 62.659 66.667 0.00 0.00 0.00 4.75
941 1001 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
942 1002 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
944 1004 3.963374 TCTCTCTCTCTCTCTCTCTCTGG 59.037 52.174 0.00 0.00 0.00 3.86
1008 1068 2.685380 CCCGGCCCAGTCTCTCTT 60.685 66.667 0.00 0.00 0.00 2.85
1069 1134 1.106944 GCCTCTCCCTCTTCCTCTCG 61.107 65.000 0.00 0.00 0.00 4.04
1070 1135 1.106944 CCTCTCCCTCTTCCTCTCGC 61.107 65.000 0.00 0.00 0.00 5.03
1071 1136 0.106719 CTCTCCCTCTTCCTCTCGCT 60.107 60.000 0.00 0.00 0.00 4.93
1072 1137 0.106918 TCTCCCTCTTCCTCTCGCTC 60.107 60.000 0.00 0.00 0.00 5.03
1073 1138 1.076632 TCCCTCTTCCTCTCGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
1074 1139 1.076339 CCCTCTTCCTCTCGCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
1075 1140 1.106944 CCCTCTTCCTCTCGCTCCTC 61.107 65.000 0.00 0.00 0.00 3.71
1076 1141 0.106719 CCTCTTCCTCTCGCTCCTCT 60.107 60.000 0.00 0.00 0.00 3.69
1077 1142 1.308998 CTCTTCCTCTCGCTCCTCTC 58.691 60.000 0.00 0.00 0.00 3.20
1078 1143 0.916086 TCTTCCTCTCGCTCCTCTCT 59.084 55.000 0.00 0.00 0.00 3.10
1079 1144 1.134220 TCTTCCTCTCGCTCCTCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
1080 1145 0.916086 TTCCTCTCGCTCCTCTCTCT 59.084 55.000 0.00 0.00 0.00 3.10
1081 1146 0.468226 TCCTCTCGCTCCTCTCTCTC 59.532 60.000 0.00 0.00 0.00 3.20
1110 1175 3.339141 GCGTCCATTTCCTCTTCTTCTT 58.661 45.455 0.00 0.00 0.00 2.52
1116 1181 5.249393 TCCATTTCCTCTTCTTCTTGCTAGT 59.751 40.000 0.00 0.00 0.00 2.57
1124 1189 5.368145 TCTTCTTCTTGCTAGTTTGCTTCA 58.632 37.500 0.00 0.00 0.00 3.02
1125 1190 5.822519 TCTTCTTCTTGCTAGTTTGCTTCAA 59.177 36.000 0.00 0.00 0.00 2.69
1166 1245 1.215647 GATGTCTGAGGCGTCGGTT 59.784 57.895 14.58 2.03 0.00 4.44
1167 1246 0.389948 GATGTCTGAGGCGTCGGTTT 60.390 55.000 14.58 1.69 0.00 3.27
1379 1464 5.657302 AGGTACACAACACACCCAAATTAAA 59.343 36.000 0.00 0.00 32.43 1.52
1416 1505 3.834489 TCTCTCATCTTGCTTGATCCC 57.166 47.619 0.00 0.00 0.00 3.85
1422 1511 1.755783 CTTGCTTGATCCCAGCCCC 60.756 63.158 10.66 0.00 0.00 5.80
1463 1552 2.340577 CCTTACTTACTCGCGTGTTTCG 59.659 50.000 19.81 10.31 43.12 3.46
1464 1553 2.686558 TACTTACTCGCGTGTTTCGT 57.313 45.000 19.81 15.10 42.13 3.85
1489 1578 2.272146 GGCAAGGCGAAGATGGGA 59.728 61.111 0.00 0.00 0.00 4.37
1770 1862 0.110192 GTTTGCTTTCGCTCCTTCCG 60.110 55.000 0.00 0.00 36.97 4.30
1781 1873 3.071023 TCGCTCCTTCCGGATTCATTATT 59.929 43.478 4.15 0.00 39.01 1.40
1811 1903 8.586879 ATTTCTCTCCTTAATTTCTTTCTGGG 57.413 34.615 0.00 0.00 0.00 4.45
1817 1909 8.611257 TCTCCTTAATTTCTTTCTGGGTTCATA 58.389 33.333 0.00 0.00 0.00 2.15
1961 2059 1.142748 AGCTCCTTCGGCTTCATCG 59.857 57.895 0.00 0.00 36.56 3.84
1962 2060 1.884926 GCTCCTTCGGCTTCATCGG 60.885 63.158 0.00 0.00 0.00 4.18
2143 2241 0.385751 ACATGATGTACTCGAGCCCG 59.614 55.000 13.61 0.00 37.07 6.13
2152 2250 0.035247 ACTCGAGCCCGTACTTCTCT 60.035 55.000 13.61 0.00 37.05 3.10
2335 2433 2.095161 ACCGTCGTCTCAGAATCAAGAC 60.095 50.000 5.93 5.93 38.81 3.01
2423 2521 0.462759 GGAGCTGCACCTACCACATC 60.463 60.000 8.98 0.00 0.00 3.06
2424 2522 0.462759 GAGCTGCACCTACCACATCC 60.463 60.000 1.02 0.00 0.00 3.51
2425 2523 1.200760 AGCTGCACCTACCACATCCA 61.201 55.000 1.02 0.00 0.00 3.41
2426 2524 1.026718 GCTGCACCTACCACATCCAC 61.027 60.000 0.00 0.00 0.00 4.02
2427 2525 0.324614 CTGCACCTACCACATCCACA 59.675 55.000 0.00 0.00 0.00 4.17
2428 2526 0.991146 TGCACCTACCACATCCACAT 59.009 50.000 0.00 0.00 0.00 3.21
2443 2542 2.057316 CCACATGATTCTCGCTCGATC 58.943 52.381 0.00 0.00 0.00 3.69
2604 2714 1.621317 GACCTCCAGGGATTAGCTAGC 59.379 57.143 6.62 6.62 40.27 3.42
2605 2715 1.221781 ACCTCCAGGGATTAGCTAGCT 59.778 52.381 23.12 23.12 40.27 3.32
2608 2718 4.295238 ACCTCCAGGGATTAGCTAGCTATA 59.705 45.833 24.69 15.51 40.27 1.31
2609 2719 4.892934 CCTCCAGGGATTAGCTAGCTATAG 59.107 50.000 24.69 10.90 37.23 1.31
2610 2720 4.873010 TCCAGGGATTAGCTAGCTATAGG 58.127 47.826 24.69 18.07 0.00 2.57
2611 2721 3.386402 CCAGGGATTAGCTAGCTATAGGC 59.614 52.174 24.69 13.62 42.19 3.93
2724 2845 2.886862 ACTAGCAGTAGCAGCATGAG 57.113 50.000 0.00 0.00 45.49 2.90
2725 2846 2.382882 ACTAGCAGTAGCAGCATGAGA 58.617 47.619 0.00 0.00 45.49 3.27
2726 2847 2.964464 ACTAGCAGTAGCAGCATGAGAT 59.036 45.455 0.00 0.00 45.49 2.75
2727 2848 2.242047 AGCAGTAGCAGCATGAGATG 57.758 50.000 0.00 0.00 45.49 2.90
2728 2849 1.202663 AGCAGTAGCAGCATGAGATGG 60.203 52.381 0.00 0.00 45.49 3.51
2729 2850 1.202615 GCAGTAGCAGCATGAGATGGA 60.203 52.381 0.00 0.00 39.69 3.41
2730 2851 2.756829 CAGTAGCAGCATGAGATGGAG 58.243 52.381 0.00 0.00 39.69 3.86
2897 3037 7.095102 TGAGTTTGACATGTCACTATGTGAATG 60.095 37.037 27.88 10.28 44.49 2.67
2905 3045 5.255687 TGTCACTATGTGAATGGATGCTTT 58.744 37.500 1.73 0.00 44.49 3.51
2928 3068 4.038282 TGTGTTCTCTCTGTACCGCTTTAA 59.962 41.667 0.00 0.00 0.00 1.52
2929 3069 4.621886 GTGTTCTCTCTGTACCGCTTTAAG 59.378 45.833 0.00 0.00 0.00 1.85
2934 3074 3.006537 TCTCTGTACCGCTTTAAGCTTGT 59.993 43.478 15.29 13.56 39.60 3.16
2944 3084 6.964934 ACCGCTTTAAGCTTGTTAATTAATCG 59.035 34.615 15.29 0.89 39.60 3.34
2952 3092 5.883673 AGCTTGTTAATTAATCGCTGGGTTA 59.116 36.000 14.23 0.00 0.00 2.85
2960 3100 2.403252 ATCGCTGGGTTACTCCTTTG 57.597 50.000 0.00 0.00 36.25 2.77
2964 3104 1.886655 GCTGGGTTACTCCTTTGTGGG 60.887 57.143 0.00 0.00 36.20 4.61
2965 3105 0.111639 TGGGTTACTCCTTTGTGGGC 59.888 55.000 0.00 0.00 36.20 5.36
2966 3106 0.958876 GGGTTACTCCTTTGTGGGCG 60.959 60.000 0.00 0.00 36.20 6.13
2967 3107 1.583495 GGTTACTCCTTTGTGGGCGC 61.583 60.000 0.00 0.00 36.20 6.53
2968 3108 0.887387 GTTACTCCTTTGTGGGCGCA 60.887 55.000 10.83 0.00 36.20 6.09
2991 3131 1.082679 CGACGAGACGAGAGGCACTA 61.083 60.000 0.00 0.00 46.78 2.74
3001 3141 2.097791 CGAGAGGCACTAGTACCAGTTC 59.902 54.545 14.76 7.52 41.55 3.01
3049 3219 5.495640 GAAATCTAGCAAGGGGAGATATGG 58.504 45.833 0.00 0.00 29.71 2.74
3104 3287 2.046314 CGGGCTTGGTTGGATCGT 60.046 61.111 0.00 0.00 0.00 3.73
3107 3290 2.106683 GGCTTGGTTGGATCGTCCG 61.107 63.158 0.59 0.00 40.17 4.79
3161 3344 1.593006 CAGTTGGTGAACTCGACACAC 59.407 52.381 6.93 5.42 40.68 3.82
3162 3345 1.206132 AGTTGGTGAACTCGACACACA 59.794 47.619 6.93 0.77 38.01 3.72
3173 3356 3.370366 ACTCGACACACATAGACGTACTC 59.630 47.826 0.00 0.00 0.00 2.59
3175 3358 2.676839 CGACACACATAGACGTACTCCT 59.323 50.000 0.00 0.00 0.00 3.69
3176 3359 3.485381 CGACACACATAGACGTACTCCTG 60.485 52.174 0.00 0.00 0.00 3.86
3179 3362 3.626217 CACACATAGACGTACTCCTGCTA 59.374 47.826 0.00 0.00 0.00 3.49
3180 3363 3.878103 ACACATAGACGTACTCCTGCTAG 59.122 47.826 0.00 0.00 0.00 3.42
3181 3364 3.251245 CACATAGACGTACTCCTGCTAGG 59.749 52.174 0.00 0.00 36.46 3.02
3182 3365 1.964552 TAGACGTACTCCTGCTAGGC 58.035 55.000 0.00 0.00 34.61 3.93
3183 3366 1.096386 AGACGTACTCCTGCTAGGCG 61.096 60.000 0.00 0.00 34.61 5.52
3184 3367 2.026301 CGTACTCCTGCTAGGCGC 59.974 66.667 0.00 0.00 34.61 6.53
3185 3368 2.417936 GTACTCCTGCTAGGCGCC 59.582 66.667 21.89 21.89 38.05 6.53
3186 3369 3.217017 TACTCCTGCTAGGCGCCG 61.217 66.667 23.20 9.22 38.05 6.46
3187 3370 3.709348 TACTCCTGCTAGGCGCCGA 62.709 63.158 23.20 16.40 38.05 5.54
3188 3371 4.277593 CTCCTGCTAGGCGCCGAG 62.278 72.222 29.96 29.96 38.05 4.63
3191 3374 3.217017 CTGCTAGGCGCCGAGGTA 61.217 66.667 33.55 19.78 38.05 3.08
3192 3375 3.200887 CTGCTAGGCGCCGAGGTAG 62.201 68.421 33.55 23.95 38.05 3.18
3193 3376 3.979739 GCTAGGCGCCGAGGTAGG 61.980 72.222 33.55 13.08 0.00 3.18
3266 3449 0.172352 GCTCTCTCGTGTCTCCAAGG 59.828 60.000 0.00 0.00 0.00 3.61
3267 3450 0.172352 CTCTCTCGTGTCTCCAAGGC 59.828 60.000 0.00 0.00 0.00 4.35
3268 3451 0.251386 TCTCTCGTGTCTCCAAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
3269 3452 0.172352 CTCTCGTGTCTCCAAGGCTC 59.828 60.000 0.00 0.00 0.00 4.70
3271 3454 1.533033 TCGTGTCTCCAAGGCTCCA 60.533 57.895 0.00 0.00 0.00 3.86
3275 3458 1.743252 GTCTCCAAGGCTCCAAGCG 60.743 63.158 0.00 0.00 43.62 4.68
3276 3459 1.913262 TCTCCAAGGCTCCAAGCGA 60.913 57.895 0.00 0.00 43.62 4.93
3277 3460 1.222936 CTCCAAGGCTCCAAGCGAT 59.777 57.895 0.00 0.00 43.62 4.58
3278 3461 0.813210 CTCCAAGGCTCCAAGCGATC 60.813 60.000 0.00 0.00 43.62 3.69
3288 3533 1.595093 CCAAGCGATCAACCAACCCC 61.595 60.000 0.00 0.00 0.00 4.95
3531 3776 1.821241 CTTGTCGCTCACACACACGG 61.821 60.000 0.00 0.00 33.41 4.94
3619 3864 2.221749 CACAGCACACACAGACACATAC 59.778 50.000 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 0.109723 TTCCCTTTCCCAAGTGGACG 59.890 55.000 0.00 0.00 45.11 4.79
272 274 6.403855 CGAGACTTTCTTGGGTTGTTTGTTTA 60.404 38.462 0.00 0.00 0.00 2.01
273 275 5.621329 CGAGACTTTCTTGGGTTGTTTGTTT 60.621 40.000 0.00 0.00 0.00 2.83
274 276 4.142469 CGAGACTTTCTTGGGTTGTTTGTT 60.142 41.667 0.00 0.00 0.00 2.83
468 471 2.930040 CCACAACGCGAGAAACATAGAT 59.070 45.455 15.93 0.00 0.00 1.98
475 478 2.975799 GGGCCACAACGCGAGAAA 60.976 61.111 15.93 0.00 0.00 2.52
517 520 3.740397 CCACACCCACATGCAGCG 61.740 66.667 0.00 0.00 0.00 5.18
529 532 0.395173 AAACCGGCATATCCCCACAC 60.395 55.000 0.00 0.00 0.00 3.82
596 601 8.501070 ACCCACAGTAGTACTAGTAGTTCATAT 58.499 37.037 15.34 0.00 0.00 1.78
631 650 8.261522 GGACAGAACCTGACTTCTTCTTATATT 58.738 37.037 0.45 0.00 35.18 1.28
632 651 7.400339 TGGACAGAACCTGACTTCTTCTTATAT 59.600 37.037 0.45 0.00 35.18 0.86
633 652 6.724441 TGGACAGAACCTGACTTCTTCTTATA 59.276 38.462 0.45 0.00 35.18 0.98
763 803 2.224805 CTTCCTTAGGCCCCAACCCC 62.225 65.000 0.00 0.00 0.00 4.95
764 804 1.212250 TCTTCCTTAGGCCCCAACCC 61.212 60.000 0.00 0.00 0.00 4.11
765 805 0.256177 CTCTTCCTTAGGCCCCAACC 59.744 60.000 0.00 0.00 0.00 3.77
776 835 4.385088 GGCTCTTGATTCATCCTCTTCCTT 60.385 45.833 0.00 0.00 0.00 3.36
780 839 4.792513 ATGGCTCTTGATTCATCCTCTT 57.207 40.909 0.00 0.00 0.00 2.85
844 903 3.629491 CTTACCGCGCGCAGTTGTG 62.629 63.158 32.61 13.47 0.00 3.33
845 904 3.411351 CTTACCGCGCGCAGTTGT 61.411 61.111 32.61 22.69 0.00 3.32
846 905 2.548587 CTTCTTACCGCGCGCAGTTG 62.549 60.000 32.61 20.79 0.00 3.16
847 906 2.356553 TTCTTACCGCGCGCAGTT 60.357 55.556 32.61 16.60 0.00 3.16
873 932 3.787001 GAGCCAAGACCCCTCCCG 61.787 72.222 0.00 0.00 0.00 5.14
941 1001 4.742201 CCACGCGGTCACTCCCAG 62.742 72.222 12.47 0.00 0.00 4.45
1008 1068 0.037160 GGCGGGTTTAGGAACAAGGA 59.963 55.000 0.00 0.00 37.51 3.36
1069 1134 1.541233 CCGAGAGAGAGAGAGAGGAGC 60.541 61.905 0.00 0.00 0.00 4.70
1070 1135 1.541233 GCCGAGAGAGAGAGAGAGGAG 60.541 61.905 0.00 0.00 0.00 3.69
1071 1136 0.468226 GCCGAGAGAGAGAGAGAGGA 59.532 60.000 0.00 0.00 0.00 3.71
1072 1137 0.880278 CGCCGAGAGAGAGAGAGAGG 60.880 65.000 0.00 0.00 0.00 3.69
1073 1138 0.179084 ACGCCGAGAGAGAGAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1074 1139 0.179094 GACGCCGAGAGAGAGAGAGA 60.179 60.000 0.00 0.00 0.00 3.10
1075 1140 1.157870 GGACGCCGAGAGAGAGAGAG 61.158 65.000 0.00 0.00 0.00 3.20
1076 1141 1.153329 GGACGCCGAGAGAGAGAGA 60.153 63.158 0.00 0.00 0.00 3.10
1077 1142 0.817634 ATGGACGCCGAGAGAGAGAG 60.818 60.000 0.00 0.00 0.00 3.20
1078 1143 0.394488 AATGGACGCCGAGAGAGAGA 60.394 55.000 0.00 0.00 0.00 3.10
1079 1144 0.457851 AAATGGACGCCGAGAGAGAG 59.542 55.000 0.00 0.00 0.00 3.20
1080 1145 0.456221 GAAATGGACGCCGAGAGAGA 59.544 55.000 0.00 0.00 0.00 3.10
1081 1146 0.528684 GGAAATGGACGCCGAGAGAG 60.529 60.000 0.00 0.00 0.00 3.20
1110 1175 3.068024 CCCAACTTTGAAGCAAACTAGCA 59.932 43.478 0.00 0.00 36.85 3.49
1116 1181 1.134551 GTGCCCCAACTTTGAAGCAAA 60.135 47.619 7.26 0.00 37.61 3.68
1166 1245 0.250989 CCACCTCCGCCTGGTTTAAA 60.251 55.000 0.00 0.00 35.28 1.52
1167 1246 1.128809 TCCACCTCCGCCTGGTTTAA 61.129 55.000 0.00 0.00 35.28 1.52
1480 1569 2.433970 CCACTCCTTCTCTCCCATCTTC 59.566 54.545 0.00 0.00 0.00 2.87
1489 1578 5.743422 GCAAAAGAAGTACCACTCCTTCTCT 60.743 44.000 2.68 0.00 45.01 3.10
1624 1713 1.272490 AGCGTCTTCTTCATTCCGACA 59.728 47.619 0.00 0.00 0.00 4.35
1790 1882 6.942576 TGAACCCAGAAAGAAATTAAGGAGAG 59.057 38.462 0.00 0.00 0.00 3.20
1961 2059 1.002544 CCCAGAGTCAAGGAAGTCACC 59.997 57.143 3.38 0.00 0.00 4.02
1962 2060 1.002544 CCCCAGAGTCAAGGAAGTCAC 59.997 57.143 3.38 0.00 0.00 3.67
2080 2178 2.421424 CTGTTCCATCTTAACCTGCAGC 59.579 50.000 8.66 0.00 0.00 5.25
2083 2181 2.162408 GTGCTGTTCCATCTTAACCTGC 59.838 50.000 0.00 0.00 0.00 4.85
2143 2241 1.142097 GGCCGGCAGAGAGAAGTAC 59.858 63.158 30.85 1.22 0.00 2.73
2335 2433 2.668457 CTCGTCGAATTGGTCAAGGAAG 59.332 50.000 0.00 0.00 0.00 3.46
2423 2521 2.057316 GATCGAGCGAGAATCATGTGG 58.943 52.381 0.00 0.00 33.17 4.17
2424 2522 1.712877 CGATCGAGCGAGAATCATGTG 59.287 52.381 20.02 0.00 33.17 3.21
2425 2523 1.335415 CCGATCGAGCGAGAATCATGT 60.335 52.381 26.68 0.00 33.17 3.21
2426 2524 1.334994 CCGATCGAGCGAGAATCATG 58.665 55.000 26.68 0.24 33.17 3.07
2427 2525 0.955178 ACCGATCGAGCGAGAATCAT 59.045 50.000 26.68 0.00 33.17 2.45
2428 2526 0.738975 AACCGATCGAGCGAGAATCA 59.261 50.000 26.68 0.00 33.17 2.57
2443 2542 2.004583 TAATCAACGAGCCAGAACCG 57.995 50.000 0.00 0.00 0.00 4.44
2553 2659 4.223953 TGTCTGGATAGTAACCTGATCCC 58.776 47.826 8.90 0.00 38.75 3.85
2897 3037 3.406764 ACAGAGAGAACACAAAGCATCC 58.593 45.455 0.00 0.00 0.00 3.51
2905 3045 1.617322 AGCGGTACAGAGAGAACACA 58.383 50.000 0.00 0.00 0.00 3.72
2928 3068 4.270008 ACCCAGCGATTAATTAACAAGCT 58.730 39.130 14.44 14.44 0.00 3.74
2929 3069 4.632538 ACCCAGCGATTAATTAACAAGC 57.367 40.909 0.00 6.66 0.00 4.01
2934 3074 6.243216 AGGAGTAACCCAGCGATTAATTAA 57.757 37.500 0.00 0.00 40.05 1.40
2944 3084 1.534729 CCACAAAGGAGTAACCCAGC 58.465 55.000 0.00 0.00 41.22 4.85
2952 3092 2.193536 GTTGCGCCCACAAAGGAGT 61.194 57.895 4.18 0.00 41.22 3.85
2964 3104 3.524759 CGTCTCGTCGAGTTGCGC 61.525 66.667 21.15 0.00 40.61 6.09
2965 3105 2.172659 TCGTCTCGTCGAGTTGCG 59.827 61.111 21.15 21.15 42.69 4.85
3001 3141 2.439701 CCCCATGAGCAGCACCAG 60.440 66.667 0.00 0.00 0.00 4.00
3049 3219 0.536724 GCCCAAAACCATGATCCACC 59.463 55.000 0.00 0.00 0.00 4.61
3095 3278 3.064931 GGGAATAATCGGACGATCCAAC 58.935 50.000 7.75 1.42 35.91 3.77
3107 3290 1.861971 GACGTGGTCCGGGAATAATC 58.138 55.000 0.00 0.00 42.24 1.75
3161 3344 2.226912 GCCTAGCAGGAGTACGTCTATG 59.773 54.545 0.00 0.00 37.67 2.23
3162 3345 2.506444 GCCTAGCAGGAGTACGTCTAT 58.494 52.381 0.00 0.00 37.67 1.98
3184 3367 1.332997 CTTGTACGTAGCCTACCTCGG 59.667 57.143 0.00 0.00 0.00 4.63
3185 3368 1.268437 GCTTGTACGTAGCCTACCTCG 60.268 57.143 8.24 0.00 32.45 4.63
3186 3369 2.022934 AGCTTGTACGTAGCCTACCTC 58.977 52.381 14.19 0.00 39.47 3.85
3187 3370 1.749634 CAGCTTGTACGTAGCCTACCT 59.250 52.381 14.19 0.00 39.47 3.08
3188 3371 1.801765 GCAGCTTGTACGTAGCCTACC 60.802 57.143 14.19 0.00 39.47 3.18
3189 3372 1.135199 TGCAGCTTGTACGTAGCCTAC 60.135 52.381 14.19 0.00 39.47 3.18
3190 3373 1.134367 CTGCAGCTTGTACGTAGCCTA 59.866 52.381 14.19 3.27 39.47 3.93
3191 3374 0.108615 CTGCAGCTTGTACGTAGCCT 60.109 55.000 14.19 2.35 39.47 4.58
3192 3375 1.696832 GCTGCAGCTTGTACGTAGCC 61.697 60.000 31.33 0.00 39.47 3.93
3193 3376 1.696832 GGCTGCAGCTTGTACGTAGC 61.697 60.000 35.82 13.26 41.70 3.58
3194 3377 0.108615 AGGCTGCAGCTTGTACGTAG 60.109 55.000 35.82 0.00 41.70 3.51
3195 3378 0.320374 AAGGCTGCAGCTTGTACGTA 59.680 50.000 35.82 0.00 41.70 3.57
3196 3379 0.320374 TAAGGCTGCAGCTTGTACGT 59.680 50.000 35.82 19.99 41.70 3.57
3197 3380 1.594862 GATAAGGCTGCAGCTTGTACG 59.405 52.381 35.82 0.00 41.70 3.67
3198 3381 2.869192 GAGATAAGGCTGCAGCTTGTAC 59.131 50.000 35.82 23.51 41.70 2.90
3247 3430 0.172352 CCTTGGAGACACGAGAGAGC 59.828 60.000 0.00 0.00 42.67 4.09
3248 3431 0.172352 GCCTTGGAGACACGAGAGAG 59.828 60.000 0.00 0.00 42.67 3.20
3266 3449 0.169009 GTTGGTTGATCGCTTGGAGC 59.831 55.000 0.00 0.00 38.02 4.70
3267 3450 0.804989 GGTTGGTTGATCGCTTGGAG 59.195 55.000 0.00 0.00 0.00 3.86
3268 3451 0.608035 GGGTTGGTTGATCGCTTGGA 60.608 55.000 0.00 0.00 0.00 3.53
3269 3452 1.595093 GGGGTTGGTTGATCGCTTGG 61.595 60.000 0.00 0.00 0.00 3.61
3271 3454 0.609131 CTGGGGTTGGTTGATCGCTT 60.609 55.000 0.00 0.00 0.00 4.68
3275 3458 1.026718 CGAGCTGGGGTTGGTTGATC 61.027 60.000 0.00 0.00 0.00 2.92
3276 3459 1.002134 CGAGCTGGGGTTGGTTGAT 60.002 57.895 0.00 0.00 0.00 2.57
3277 3460 2.144078 TCGAGCTGGGGTTGGTTGA 61.144 57.895 0.00 0.00 0.00 3.18
3278 3461 1.966451 GTCGAGCTGGGGTTGGTTG 60.966 63.158 0.00 0.00 0.00 3.77
3605 3850 3.005791 TCACCTCTGTATGTGTCTGTGTG 59.994 47.826 0.00 0.00 34.14 3.82
3606 3851 3.230976 TCACCTCTGTATGTGTCTGTGT 58.769 45.455 0.00 0.00 34.14 3.72
3607 3852 3.367806 CCTCACCTCTGTATGTGTCTGTG 60.368 52.174 0.00 0.00 34.14 3.66
3612 3857 0.532573 CGCCTCACCTCTGTATGTGT 59.467 55.000 0.00 0.00 34.14 3.72


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

AutoCloner maintained by Alex Coulton.