Multiple sequence alignment - TraesCS1D01G287100

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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 TraesCS1D01G287100 chr1D 100.000 4528 0 0 1 4528 385619138 385614611 0.000000e+00 8362.0
1 TraesCS1D01G287100 chr1B 91.867 3738 179 55 1 3669 517905432 517901751 0.000000e+00 5103.0
2 TraesCS1D01G287100 chr1B 97.826 46 1 0 3666 3711 517901594 517901549 3.750000e-11 80.5
3 TraesCS1D01G287100 chr1A 95.177 1472 54 9 2241 3711 485339150 485337695 0.000000e+00 2309.0
4 TraesCS1D01G287100 chr1A 88.164 1901 98 47 1 1841 485341386 485339553 0.000000e+00 2146.0
5 TraesCS1D01G287100 chr1A 94.966 298 11 2 1930 2226 485339558 485339264 8.870000e-127 464.0
6 TraesCS1D01G287100 chr1A 90.690 290 21 5 3711 3995 137734006 137734294 9.190000e-102 381.0
7 TraesCS1D01G287100 chr1A 88.215 297 24 10 3707 3995 412040470 412040177 1.210000e-90 344.0
8 TraesCS1D01G287100 chr3D 92.533 750 36 11 3790 4528 294326339 294327079 0.000000e+00 1057.0
9 TraesCS1D01G287100 chr3D 92.000 125 4 1 4105 4229 294326622 294326740 2.170000e-38 171.0
10 TraesCS1D01G287100 chr4A 92.042 754 30 17 3790 4528 502347862 502348600 0.000000e+00 1033.0
11 TraesCS1D01G287100 chr4A 89.667 300 27 1 4230 4525 608555314 608555613 3.310000e-101 379.0
12 TraesCS1D01G287100 chr4A 87.847 288 30 4 3711 3995 282610010 282609725 2.610000e-87 333.0
13 TraesCS1D01G287100 chr6D 91.497 294 18 6 3707 3995 414564741 414565032 9.130000e-107 398.0
14 TraesCS1D01G287100 chr6D 88.136 295 24 8 3711 3995 413771161 413771454 1.560000e-89 340.0
15 TraesCS1D01G287100 chr2D 91.379 290 20 4 3711 3995 620304478 620304189 4.250000e-105 392.0
16 TraesCS1D01G287100 chr5D 88.779 303 30 1 4230 4528 563973781 563973479 7.160000e-98 368.0
17 TraesCS1D01G287100 chr3B 87.713 293 27 7 3711 3995 5347411 5347702 2.610000e-87 333.0


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 TraesCS1D01G287100 chr1D 385614611 385619138 4527 True 8362.000000 8362 100.0000 1 4528 1 chr1D.!!$R1 4527
1 TraesCS1D01G287100 chr1B 517901549 517905432 3883 True 2591.750000 5103 94.8465 1 3711 2 chr1B.!!$R1 3710
2 TraesCS1D01G287100 chr1A 485337695 485341386 3691 True 1639.666667 2309 92.7690 1 3711 3 chr1A.!!$R2 3710
3 TraesCS1D01G287100 chr3D 294326339 294327079 740 False 614.000000 1057 92.2665 3790 4528 2 chr3D.!!$F1 738
4 TraesCS1D01G287100 chr4A 502347862 502348600 738 False 1033.000000 1033 92.0420 3790 4528 1 chr4A.!!$F1 738

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
199 200 1.285641 GTGGAACCAACATGCGGTG 59.714 57.895 8.12 0.0 36.67 4.94 F
1098 1152 1.008309 GACGGCATAGAGGACGAGC 60.008 63.158 0.00 0.0 43.61 5.03 F
1854 1920 0.906066 ATGCATCAGCCATTGCCAAA 59.094 45.000 0.00 0.0 41.13 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1478 0.102663 GACGAAGACGGGAGGATTCC 59.897 60.0 0.0 0.0 44.46 3.01 R
2106 2204 0.179134 GGTCTGAACCCTCGTCATCG 60.179 60.0 0.0 0.0 39.93 3.84 R
3770 4131 0.105862 ACCGAATATGGGAGGGACGA 60.106 55.0 0.0 0.0 0.00 4.20 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
151 152 4.666928 TTACAAAAACCGATTAGTCCGC 57.333 40.909 0.00 0.00 0.00 5.54
199 200 1.285641 GTGGAACCAACATGCGGTG 59.714 57.895 8.12 0.00 36.67 4.94
308 309 1.525619 GTCGGCGGCAATATTCTGTAC 59.474 52.381 6.63 0.00 0.00 2.90
336 337 2.128507 GCTACTCCCCACCTCCTCG 61.129 68.421 0.00 0.00 0.00 4.63
337 338 2.043248 TACTCCCCACCTCCTCGC 60.043 66.667 0.00 0.00 0.00 5.03
581 599 3.240631 GCGCAAATTAAAGCCTCGAAATC 59.759 43.478 0.30 0.00 0.00 2.17
762 812 1.442857 GGTGATATCGGCGAGCTCG 60.443 63.158 31.37 31.37 43.27 5.03
763 813 1.442857 GTGATATCGGCGAGCTCGG 60.443 63.158 35.10 20.83 40.23 4.63
764 814 2.179517 GATATCGGCGAGCTCGGG 59.820 66.667 35.10 11.31 40.23 5.14
765 815 2.597805 ATATCGGCGAGCTCGGGT 60.598 61.111 35.10 19.58 40.23 5.28
766 816 1.303074 ATATCGGCGAGCTCGGGTA 60.303 57.895 35.10 21.07 40.23 3.69
829 883 2.923035 GCCGGGCTAGATGGGCTA 60.923 66.667 12.87 0.00 42.29 3.93
842 896 2.804912 GGGCTAGACTAACGGGCCC 61.805 68.421 13.57 13.57 46.55 5.80
843 897 2.804912 GGCTAGACTAACGGGCCCC 61.805 68.421 18.66 0.00 35.96 5.80
858 912 4.410400 CCCGGGAAGTGTGGGCTC 62.410 72.222 18.48 0.00 35.82 4.70
867 921 1.968540 GTGTGGGCTCTGAGGTTGC 60.969 63.158 6.83 0.00 0.00 4.17
880 934 3.365265 GTTGCTTCGTGGGCTGGG 61.365 66.667 0.00 0.00 0.00 4.45
1093 1147 1.660355 GCATCGACGGCATAGAGGA 59.340 57.895 6.06 0.00 0.00 3.71
1097 1151 1.158484 TCGACGGCATAGAGGACGAG 61.158 60.000 0.00 0.00 43.61 4.18
1098 1152 1.008309 GACGGCATAGAGGACGAGC 60.008 63.158 0.00 0.00 43.61 5.03
1099 1153 2.336809 CGGCATAGAGGACGAGCC 59.663 66.667 0.00 0.00 43.61 4.70
1100 1154 2.336809 GGCATAGAGGACGAGCCG 59.663 66.667 0.00 0.00 43.43 5.52
1101 1155 2.336809 GCATAGAGGACGAGCCGG 59.663 66.667 0.00 0.00 43.43 6.13
1102 1156 2.336809 CATAGAGGACGAGCCGGC 59.663 66.667 21.89 21.89 43.43 6.13
1175 1229 4.674662 TCACATTTTTGTTTTGCTCGATCG 59.325 37.500 9.36 9.36 0.00 3.69
1176 1230 4.674662 CACATTTTTGTTTTGCTCGATCGA 59.325 37.500 18.32 18.32 0.00 3.59
1177 1231 5.343058 CACATTTTTGTTTTGCTCGATCGAT 59.657 36.000 19.78 0.00 0.00 3.59
1178 1232 5.569059 ACATTTTTGTTTTGCTCGATCGATC 59.431 36.000 19.78 15.57 0.00 3.69
1213 1272 1.908344 TGATGCTAGTTTTGCTGCCA 58.092 45.000 0.00 0.00 0.00 4.92
1220 1279 4.168760 GCTAGTTTTGCTGCCATAAACAG 58.831 43.478 18.06 14.68 34.93 3.16
1230 1289 4.285292 CTGCCATAAACAGCATTCGATTC 58.715 43.478 0.00 0.00 0.00 2.52
1232 1291 3.316308 GCCATAAACAGCATTCGATTCCT 59.684 43.478 0.00 0.00 0.00 3.36
1235 1294 5.333339 CCATAAACAGCATTCGATTCCTACG 60.333 44.000 0.00 0.00 0.00 3.51
1243 1302 4.259850 GCATTCGATTCCTACGTGTTCTTC 60.260 45.833 0.00 0.00 0.00 2.87
1244 1303 3.498927 TCGATTCCTACGTGTTCTTCC 57.501 47.619 0.00 0.00 0.00 3.46
1249 1308 4.451629 TTCCTACGTGTTCTTCCTGATC 57.548 45.455 0.00 0.00 0.00 2.92
1259 1318 5.860716 GTGTTCTTCCTGATCTTTGCATTTC 59.139 40.000 0.00 0.00 0.00 2.17
1270 1329 6.431852 TGATCTTTGCATTTCTGTCATCTCAA 59.568 34.615 0.00 0.00 0.00 3.02
1389 1448 3.591023 GAGAAGGAAGACAAGCAGGTAC 58.409 50.000 0.00 0.00 0.00 3.34
1390 1449 3.243724 AGAAGGAAGACAAGCAGGTACT 58.756 45.455 0.00 0.00 43.88 2.73
1391 1450 4.417437 AGAAGGAAGACAAGCAGGTACTA 58.583 43.478 0.00 0.00 36.02 1.82
1392 1451 4.838986 AGAAGGAAGACAAGCAGGTACTAA 59.161 41.667 0.00 0.00 36.02 2.24
1393 1452 5.485708 AGAAGGAAGACAAGCAGGTACTAAT 59.514 40.000 0.00 0.00 36.02 1.73
1394 1453 5.763876 AGGAAGACAAGCAGGTACTAATT 57.236 39.130 0.00 0.00 36.02 1.40
1395 1454 5.491982 AGGAAGACAAGCAGGTACTAATTG 58.508 41.667 0.00 0.00 36.02 2.32
1396 1455 5.248477 AGGAAGACAAGCAGGTACTAATTGA 59.752 40.000 0.00 0.00 36.02 2.57
1397 1456 5.938125 GGAAGACAAGCAGGTACTAATTGAA 59.062 40.000 0.00 0.00 36.02 2.69
1398 1457 6.430000 GGAAGACAAGCAGGTACTAATTGAAA 59.570 38.462 0.00 0.00 36.02 2.69
1399 1458 6.803154 AGACAAGCAGGTACTAATTGAAAC 57.197 37.500 0.00 0.00 36.02 2.78
1400 1459 5.705905 AGACAAGCAGGTACTAATTGAAACC 59.294 40.000 0.00 0.00 36.02 3.27
1402 1461 3.007635 AGCAGGTACTAATTGAAACCGC 58.992 45.455 0.00 1.76 36.02 5.68
1403 1462 2.222953 GCAGGTACTAATTGAAACCGCG 60.223 50.000 0.00 0.00 36.02 6.46
1404 1463 2.004733 AGGTACTAATTGAAACCGCGC 58.995 47.619 0.00 0.00 36.02 6.86
1405 1464 1.733360 GGTACTAATTGAAACCGCGCA 59.267 47.619 8.75 0.00 0.00 6.09
1406 1465 2.222953 GGTACTAATTGAAACCGCGCAG 60.223 50.000 8.75 0.00 0.00 5.18
1419 1478 4.018609 CGCAGCTCATTCCTACGG 57.981 61.111 0.00 0.00 0.00 4.02
1420 1479 1.592669 CGCAGCTCATTCCTACGGG 60.593 63.158 0.00 0.00 0.00 5.28
1440 1499 1.664321 AATCCTCCCGTCTTCGTCGG 61.664 60.000 0.00 0.00 46.49 4.79
1854 1920 0.906066 ATGCATCAGCCATTGCCAAA 59.094 45.000 0.00 0.00 41.13 3.28
1866 1932 4.301628 CCATTGCCAAACTTGTTTCTCTC 58.698 43.478 0.00 0.00 0.00 3.20
1892 1958 6.551227 GGGAGGCCAAAATCTGAATAGTTATT 59.449 38.462 5.01 0.00 0.00 1.40
1914 1980 5.739752 TCTGAATGTTGAACAGAACACAG 57.260 39.130 3.74 8.48 38.64 3.66
1922 2016 5.163248 TGTTGAACAGAACACAGGGAAGATA 60.163 40.000 0.00 0.00 30.75 1.98
1957 2054 7.148836 GCATGATCACATTTCGATCTACTAGTG 60.149 40.741 5.39 0.00 40.03 2.74
2086 2184 1.446966 GAAGCGCCAGACAGAGGAC 60.447 63.158 2.29 0.00 0.00 3.85
2234 2332 4.426416 GAGCATCATCTCATAGCTAGCTG 58.574 47.826 27.68 12.64 35.36 4.24
2425 2622 2.487934 CATCGGATCTCCATTGTGGAC 58.512 52.381 0.00 0.00 42.67 4.02
2427 2624 0.459899 CGGATCTCCATTGTGGACGA 59.540 55.000 0.00 0.00 42.67 4.20
2451 2648 2.027073 TGGCTCGACGTGTTCATGC 61.027 57.895 0.00 0.00 0.00 4.06
2473 2670 1.273048 CTCTGCTGAACTCACTCTGCT 59.727 52.381 0.00 0.00 40.04 4.24
2476 2673 1.139654 TGCTGAACTCACTCTGCTTGT 59.860 47.619 4.47 0.00 40.04 3.16
2542 2739 2.520741 CTCGGGGAGAGGGAGAGC 60.521 72.222 0.00 0.00 43.20 4.09
2752 2949 1.918293 TCCAGATTCCCACCACGCT 60.918 57.895 0.00 0.00 0.00 5.07
3046 3243 2.896443 CCTGGGAACGAGAGAGGC 59.104 66.667 0.00 0.00 0.00 4.70
3379 3576 2.797156 GCAGCACGATAACTGTATGAGG 59.203 50.000 0.00 0.00 36.26 3.86
3598 3799 3.057526 GCTTGTGAGTGGATTTTGTACCC 60.058 47.826 0.00 0.00 0.00 3.69
3617 3818 0.809636 CAACGTGCATGGATCCGCTA 60.810 55.000 11.36 0.00 0.00 4.26
3635 3836 3.381949 GCTATCCACGTTAGATGTGTCC 58.618 50.000 7.89 0.00 33.37 4.02
3642 3843 0.172803 GTTAGATGTGTCCGCCGAGT 59.827 55.000 0.00 0.00 0.00 4.18
3711 4072 7.148507 CGCCATATTTTCTCTCAATGGATAGTC 60.149 40.741 3.89 0.00 39.60 2.59
3712 4073 7.882271 GCCATATTTTCTCTCAATGGATAGTCT 59.118 37.037 3.89 0.00 39.60 3.24
3713 4074 9.434420 CCATATTTTCTCTCAATGGATAGTCTC 57.566 37.037 0.00 0.00 39.60 3.36
3719 4080 9.653516 TTTCTCTCAATGGATAGTCTCTATTCT 57.346 33.333 0.00 0.00 33.16 2.40
3720 4081 9.653516 TTCTCTCAATGGATAGTCTCTATTCTT 57.346 33.333 0.00 0.00 33.16 2.52
3734 4095 8.842280 AGTCTCTATTCTTAATAGACGACTTGG 58.158 37.037 21.02 8.44 44.83 3.61
3735 4096 8.623030 GTCTCTATTCTTAATAGACGACTTGGT 58.377 37.037 19.07 0.00 43.64 3.67
3736 4097 8.622157 TCTCTATTCTTAATAGACGACTTGGTG 58.378 37.037 5.47 0.00 43.64 4.17
3737 4098 8.515695 TCTATTCTTAATAGACGACTTGGTGA 57.484 34.615 5.47 0.00 43.64 4.02
3738 4099 8.963725 TCTATTCTTAATAGACGACTTGGTGAA 58.036 33.333 5.47 0.00 43.64 3.18
3739 4100 9.751542 CTATTCTTAATAGACGACTTGGTGAAT 57.248 33.333 0.00 1.36 42.80 2.57
3741 4102 9.751542 ATTCTTAATAGACGACTTGGTGAATAG 57.248 33.333 0.00 0.00 0.00 1.73
3742 4103 8.289939 TCTTAATAGACGACTTGGTGAATAGT 57.710 34.615 0.00 0.00 0.00 2.12
3743 4104 8.404000 TCTTAATAGACGACTTGGTGAATAGTC 58.596 37.037 0.00 0.00 37.90 2.59
3744 4105 6.777213 AATAGACGACTTGGTGAATAGTCT 57.223 37.500 0.00 0.91 38.86 3.24
3745 4106 6.777213 ATAGACGACTTGGTGAATAGTCTT 57.223 37.500 0.00 0.00 38.86 3.01
3746 4107 5.061920 AGACGACTTGGTGAATAGTCTTC 57.938 43.478 0.00 0.00 38.96 2.87
3747 4108 3.834610 ACGACTTGGTGAATAGTCTTCG 58.165 45.455 0.00 0.00 38.86 3.79
3748 4109 2.599082 CGACTTGGTGAATAGTCTTCGC 59.401 50.000 0.00 0.00 38.86 4.70
3749 4110 2.599082 GACTTGGTGAATAGTCTTCGCG 59.401 50.000 0.00 0.00 38.17 5.87
3750 4111 1.927174 CTTGGTGAATAGTCTTCGCGG 59.073 52.381 6.13 0.00 0.00 6.46
3751 4112 0.892755 TGGTGAATAGTCTTCGCGGT 59.107 50.000 6.13 0.00 0.00 5.68
3752 4113 1.274167 TGGTGAATAGTCTTCGCGGTT 59.726 47.619 6.13 0.00 0.00 4.44
3753 4114 2.289195 TGGTGAATAGTCTTCGCGGTTT 60.289 45.455 6.13 0.00 0.00 3.27
3754 4115 3.056678 TGGTGAATAGTCTTCGCGGTTTA 60.057 43.478 6.13 0.00 0.00 2.01
3755 4116 4.117685 GGTGAATAGTCTTCGCGGTTTAT 58.882 43.478 6.13 0.00 0.00 1.40
3756 4117 4.569564 GGTGAATAGTCTTCGCGGTTTATT 59.430 41.667 6.13 4.24 0.00 1.40
3757 4118 5.064325 GGTGAATAGTCTTCGCGGTTTATTT 59.936 40.000 6.13 0.00 0.00 1.40
3758 4119 6.402875 GGTGAATAGTCTTCGCGGTTTATTTT 60.403 38.462 6.13 0.00 0.00 1.82
3759 4120 6.681599 GTGAATAGTCTTCGCGGTTTATTTTC 59.318 38.462 6.13 3.85 0.00 2.29
3760 4121 3.717350 AGTCTTCGCGGTTTATTTTCG 57.283 42.857 6.13 0.00 0.00 3.46
3761 4122 2.159747 AGTCTTCGCGGTTTATTTTCGC 60.160 45.455 6.13 0.00 45.15 4.70
3762 4123 2.070783 TCTTCGCGGTTTATTTTCGCT 58.929 42.857 6.13 0.00 46.23 4.93
3763 4124 2.159761 TCTTCGCGGTTTATTTTCGCTG 60.160 45.455 6.13 0.00 46.23 5.18
3764 4125 0.444651 TCGCGGTTTATTTTCGCTGG 59.555 50.000 6.13 0.00 46.23 4.85
3765 4126 0.167251 CGCGGTTTATTTTCGCTGGT 59.833 50.000 0.00 0.00 46.23 4.00
3766 4127 1.400500 CGCGGTTTATTTTCGCTGGTT 60.400 47.619 0.00 0.00 46.23 3.67
3767 4128 2.668250 GCGGTTTATTTTCGCTGGTTT 58.332 42.857 0.00 0.00 45.16 3.27
3768 4129 3.054166 GCGGTTTATTTTCGCTGGTTTT 58.946 40.909 0.00 0.00 45.16 2.43
3769 4130 3.491639 GCGGTTTATTTTCGCTGGTTTTT 59.508 39.130 0.00 0.00 45.16 1.94
3787 4148 2.902705 TTTCGTCCCTCCCATATTCG 57.097 50.000 0.00 0.00 0.00 3.34
3788 4149 1.045407 TTCGTCCCTCCCATATTCGG 58.955 55.000 0.00 0.00 0.00 4.30
3815 4176 1.605058 CGTCATCCTTCCACCTCCGT 61.605 60.000 0.00 0.00 0.00 4.69
3850 4211 1.498166 CGCGAAATAAACCCGTGCA 59.502 52.632 0.00 0.00 0.00 4.57
3920 4288 3.365265 CCAACCAGCCCTTCGCAC 61.365 66.667 0.00 0.00 41.38 5.34
3984 4355 1.887707 GCGGCCGATCCTAACCTTG 60.888 63.158 33.48 0.00 0.00 3.61
4248 4655 0.396435 TGCTCACCAAGATGTTCGGT 59.604 50.000 0.00 0.00 0.00 4.69
4302 4709 0.984230 TCAAGAAGATGCGGGAGGTT 59.016 50.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 1.860950 CCTTCGACTTGTATGGCATCG 59.139 52.381 1.65 0.48 32.57 3.84
196 197 4.020128 AGACTCTGGTTAGTTTGATCCACC 60.020 45.833 0.00 0.00 0.00 4.61
199 200 4.508662 CCAGACTCTGGTTAGTTTGATCC 58.491 47.826 16.18 0.00 45.82 3.36
230 231 1.026182 TGCTGAAGCCGGTAAGCATG 61.026 55.000 15.46 0.00 40.59 4.06
328 329 4.021925 GTTGCAGGGCGAGGAGGT 62.022 66.667 0.00 0.00 0.00 3.85
336 337 3.590466 ATCTGGTGGGTTGCAGGGC 62.590 63.158 0.00 0.00 0.00 5.19
337 338 0.967380 GAATCTGGTGGGTTGCAGGG 60.967 60.000 0.00 0.00 0.00 4.45
463 476 4.928520 GGGGATGGAGGGAGGGGG 62.929 77.778 0.00 0.00 0.00 5.40
476 489 0.469917 GATGATCTGGCTTTCGGGGA 59.530 55.000 0.00 0.00 0.00 4.81
581 599 2.031163 GGCGAGATCGATTGGGGG 59.969 66.667 6.39 0.00 43.02 5.40
604 622 1.054978 GTATTTCGCCCTCCCCTCCT 61.055 60.000 0.00 0.00 0.00 3.69
619 637 2.590092 GCCCGTGCCTGAGGTATT 59.410 61.111 0.00 0.00 0.00 1.89
665 714 1.651240 TAGAACCTTCGTCTCCGCCG 61.651 60.000 0.00 0.00 0.00 6.46
676 725 1.354705 GAGGCCAAACCCTAGAACCTT 59.645 52.381 5.01 0.00 40.58 3.50
680 729 1.559065 CCGGAGGCCAAACCCTAGAA 61.559 60.000 5.01 0.00 46.14 2.10
762 812 2.819284 CCCAATCGGCTCCCTACCC 61.819 68.421 0.00 0.00 0.00 3.69
763 813 1.759459 CTCCCAATCGGCTCCCTACC 61.759 65.000 0.00 0.00 0.00 3.18
764 814 1.749033 CTCCCAATCGGCTCCCTAC 59.251 63.158 0.00 0.00 0.00 3.18
765 815 1.459539 CCTCCCAATCGGCTCCCTA 60.460 63.158 0.00 0.00 0.00 3.53
766 816 2.770048 CCTCCCAATCGGCTCCCT 60.770 66.667 0.00 0.00 0.00 4.20
821 875 0.033642 GCCCGTTAGTCTAGCCCATC 59.966 60.000 0.00 0.00 0.00 3.51
842 896 3.322466 AGAGCCCACACTTCCCGG 61.322 66.667 0.00 0.00 0.00 5.73
843 897 2.046892 CAGAGCCCACACTTCCCG 60.047 66.667 0.00 0.00 0.00 5.14
844 898 1.298014 CTCAGAGCCCACACTTCCC 59.702 63.158 0.00 0.00 0.00 3.97
845 899 1.298014 CCTCAGAGCCCACACTTCC 59.702 63.158 0.00 0.00 0.00 3.46
848 902 1.757306 CAACCTCAGAGCCCACACT 59.243 57.895 0.00 0.00 0.00 3.55
850 904 1.708993 AAGCAACCTCAGAGCCCACA 61.709 55.000 0.00 0.00 0.00 4.17
857 911 1.371183 CCCACGAAGCAACCTCAGA 59.629 57.895 0.00 0.00 0.00 3.27
858 912 2.328099 GCCCACGAAGCAACCTCAG 61.328 63.158 0.00 0.00 0.00 3.35
867 921 2.919494 GCAAACCCAGCCCACGAAG 61.919 63.158 0.00 0.00 0.00 3.79
1101 1155 4.742201 TCTGTCTTCTGCCGGCGC 62.742 66.667 23.90 0.00 0.00 6.53
1102 1156 2.048222 TTCTGTCTTCTGCCGGCG 60.048 61.111 23.90 16.91 0.00 6.46
1138 1192 2.550830 ATGTGAACACCAGAGACCAC 57.449 50.000 2.46 0.00 0.00 4.16
1139 1193 3.576078 AAATGTGAACACCAGAGACCA 57.424 42.857 2.46 0.00 0.00 4.02
1140 1194 4.097892 ACAAAAATGTGAACACCAGAGACC 59.902 41.667 2.46 0.00 0.00 3.85
1141 1195 5.248870 ACAAAAATGTGAACACCAGAGAC 57.751 39.130 2.46 0.00 0.00 3.36
1147 1201 5.544136 AGCAAAACAAAAATGTGAACACC 57.456 34.783 2.46 0.00 0.00 4.16
1175 1229 4.707030 TCAATCAACATTGCCACAGATC 57.293 40.909 0.00 0.00 39.56 2.75
1176 1230 4.679639 GCATCAATCAACATTGCCACAGAT 60.680 41.667 0.00 0.00 39.56 2.90
1177 1231 3.367600 GCATCAATCAACATTGCCACAGA 60.368 43.478 0.00 0.00 39.56 3.41
1178 1232 2.927477 GCATCAATCAACATTGCCACAG 59.073 45.455 0.00 0.00 39.56 3.66
1213 1272 5.234329 CACGTAGGAATCGAATGCTGTTTAT 59.766 40.000 4.56 0.00 0.00 1.40
1220 1279 3.187700 AGAACACGTAGGAATCGAATGC 58.812 45.455 0.00 0.00 0.00 3.56
1230 1289 4.457834 AAGATCAGGAAGAACACGTAGG 57.542 45.455 0.00 0.00 0.00 3.18
1232 1291 3.994392 GCAAAGATCAGGAAGAACACGTA 59.006 43.478 0.00 0.00 0.00 3.57
1235 1294 5.382618 AATGCAAAGATCAGGAAGAACAC 57.617 39.130 0.00 0.00 0.00 3.32
1243 1302 5.357314 AGATGACAGAAATGCAAAGATCAGG 59.643 40.000 0.00 0.00 0.00 3.86
1244 1303 6.093633 TGAGATGACAGAAATGCAAAGATCAG 59.906 38.462 0.00 0.00 0.00 2.90
1249 1308 4.849926 CGTTGAGATGACAGAAATGCAAAG 59.150 41.667 0.00 0.00 0.00 2.77
1259 1318 4.639135 TCACCTATCGTTGAGATGACAG 57.361 45.455 0.00 0.00 40.40 3.51
1270 1329 1.064296 CGCGCTCTTCACCTATCGT 59.936 57.895 5.56 0.00 0.00 3.73
1389 1448 0.447801 AGCTGCGCGGTTTCAATTAG 59.552 50.000 19.23 0.00 0.00 1.73
1390 1449 0.446222 GAGCTGCGCGGTTTCAATTA 59.554 50.000 19.23 0.00 0.00 1.40
1391 1450 1.210155 GAGCTGCGCGGTTTCAATT 59.790 52.632 19.23 0.00 0.00 2.32
1392 1451 1.308069 ATGAGCTGCGCGGTTTCAAT 61.308 50.000 23.09 9.53 0.00 2.57
1393 1452 1.514678 AATGAGCTGCGCGGTTTCAA 61.515 50.000 23.09 7.82 0.00 2.69
1394 1453 1.911293 GAATGAGCTGCGCGGTTTCA 61.911 55.000 22.03 22.03 0.00 2.69
1395 1454 1.226128 GAATGAGCTGCGCGGTTTC 60.226 57.895 19.23 16.01 0.00 2.78
1396 1455 2.690778 GGAATGAGCTGCGCGGTTT 61.691 57.895 19.23 6.59 0.00 3.27
1397 1456 2.238847 TAGGAATGAGCTGCGCGGTT 62.239 55.000 19.23 12.78 0.00 4.44
1398 1457 2.721167 TAGGAATGAGCTGCGCGGT 61.721 57.895 19.23 11.01 0.00 5.68
1399 1458 2.106938 TAGGAATGAGCTGCGCGG 59.893 61.111 13.18 13.18 0.00 6.46
1400 1459 2.580470 CGTAGGAATGAGCTGCGCG 61.580 63.158 0.00 0.00 0.00 6.86
1419 1478 0.102663 GACGAAGACGGGAGGATTCC 59.897 60.000 0.00 0.00 44.46 3.01
1420 1479 0.248539 CGACGAAGACGGGAGGATTC 60.249 60.000 0.00 0.00 42.66 2.52
1436 1495 3.103911 CGTCGACTGCAACCCGAC 61.104 66.667 14.70 19.10 46.27 4.79
1444 1503 1.132640 GGTCATTTGCGTCGACTGC 59.867 57.895 20.46 20.46 0.00 4.40
1479 1542 2.900273 CCGGCTTCTTGGATCGGA 59.100 61.111 0.00 0.00 42.94 4.55
1480 1543 2.897350 GCCGGCTTCTTGGATCGG 60.897 66.667 22.15 0.00 43.13 4.18
1650 1713 1.738830 GTCGTTCCGGCGGATTTGA 60.739 57.895 31.59 23.45 0.00 2.69
1799 1865 1.745141 GCAAGCCGTCTGAATCCTGAT 60.745 52.381 0.00 0.00 0.00 2.90
1854 1920 0.321996 GCCTCCCGAGAGAAACAAGT 59.678 55.000 0.00 0.00 43.39 3.16
1866 1932 1.767759 ATTCAGATTTTGGCCTCCCG 58.232 50.000 3.32 0.00 0.00 5.14
1892 1958 4.576053 CCTGTGTTCTGTTCAACATTCAGA 59.424 41.667 0.00 0.00 38.53 3.27
1898 1964 3.054728 TCTTCCCTGTGTTCTGTTCAACA 60.055 43.478 0.00 0.00 33.75 3.33
1902 1968 6.710744 TCTTTTATCTTCCCTGTGTTCTGTTC 59.289 38.462 0.00 0.00 0.00 3.18
1905 1971 7.693969 AATCTTTTATCTTCCCTGTGTTCTG 57.306 36.000 0.00 0.00 0.00 3.02
1906 1972 7.309438 GCAAATCTTTTATCTTCCCTGTGTTCT 60.309 37.037 0.00 0.00 0.00 3.01
1907 1973 6.808704 GCAAATCTTTTATCTTCCCTGTGTTC 59.191 38.462 0.00 0.00 0.00 3.18
1908 1974 6.267471 TGCAAATCTTTTATCTTCCCTGTGTT 59.733 34.615 0.00 0.00 0.00 3.32
1910 1976 6.271488 TGCAAATCTTTTATCTTCCCTGTG 57.729 37.500 0.00 0.00 0.00 3.66
1912 1978 7.104043 TCATGCAAATCTTTTATCTTCCCTG 57.896 36.000 0.00 0.00 0.00 4.45
1913 1979 7.562454 TGATCATGCAAATCTTTTATCTTCCCT 59.438 33.333 12.19 0.00 0.00 4.20
1914 1980 7.650903 GTGATCATGCAAATCTTTTATCTTCCC 59.349 37.037 0.00 0.00 0.00 3.97
1922 2016 7.092079 TCGAAATGTGATCATGCAAATCTTTT 58.908 30.769 0.00 9.57 34.19 2.27
2080 2178 2.878429 CTGTACAGCGCGTCCTCT 59.122 61.111 10.54 0.00 0.00 3.69
2105 2203 0.802607 GTCTGAACCCTCGTCATCGC 60.803 60.000 0.00 0.00 36.96 4.58
2106 2204 0.179134 GGTCTGAACCCTCGTCATCG 60.179 60.000 0.00 0.00 39.93 3.84
2381 2578 1.226435 CTGGTGAGAGAGCGCGTAC 60.226 63.158 8.43 1.75 0.00 3.67
2387 2584 0.972983 TGGCTACCTGGTGAGAGAGC 60.973 60.000 10.23 9.84 0.00 4.09
2388 2585 1.686052 GATGGCTACCTGGTGAGAGAG 59.314 57.143 10.23 0.00 0.00 3.20
2425 2622 2.801162 CGTCGAGCCACAGTGTCG 60.801 66.667 7.14 7.14 34.98 4.35
2427 2624 2.027605 CACGTCGAGCCACAGTGT 59.972 61.111 0.00 0.00 0.00 3.55
2451 2648 1.067000 CAGAGTGAGTTCAGCAGAGGG 60.067 57.143 0.00 0.00 0.00 4.30
2473 2670 1.153269 TGCAACCGAGACAGCACAA 60.153 52.632 0.00 0.00 31.05 3.33
2476 2673 1.595109 CACTGCAACCGAGACAGCA 60.595 57.895 0.00 0.00 34.72 4.41
2916 3113 3.715097 GTGCTCCTGGCTGCTCCT 61.715 66.667 11.56 0.00 42.39 3.69
3379 3576 8.476925 CGAAACTAGGCAACAAAATAAGAAAAC 58.523 33.333 0.00 0.00 41.41 2.43
3598 3799 0.809636 TAGCGGATCCATGCACGTTG 60.810 55.000 13.41 0.00 0.00 4.10
3617 3818 1.470979 GCGGACACATCTAACGTGGAT 60.471 52.381 0.00 0.00 38.74 3.41
3635 3836 4.723862 CGATTAATCAAGAAAAACTCGGCG 59.276 41.667 15.57 0.00 0.00 6.46
3712 4073 8.515695 TCACCAAGTCGTCTATTAAGAATAGA 57.484 34.615 5.07 5.07 45.66 1.98
3713 4074 9.751542 ATTCACCAAGTCGTCTATTAAGAATAG 57.248 33.333 0.58 0.58 41.77 1.73
3715 4076 9.751542 CTATTCACCAAGTCGTCTATTAAGAAT 57.248 33.333 0.00 0.00 32.16 2.40
3716 4077 8.746530 ACTATTCACCAAGTCGTCTATTAAGAA 58.253 33.333 0.00 0.00 32.16 2.52
3717 4078 8.289939 ACTATTCACCAAGTCGTCTATTAAGA 57.710 34.615 0.00 0.00 0.00 2.10
3718 4079 8.407064 AGACTATTCACCAAGTCGTCTATTAAG 58.593 37.037 0.00 0.00 45.47 1.85
3719 4080 8.289939 AGACTATTCACCAAGTCGTCTATTAA 57.710 34.615 0.00 0.00 45.47 1.40
3720 4081 7.876936 AGACTATTCACCAAGTCGTCTATTA 57.123 36.000 0.00 0.00 45.47 0.98
3721 4082 6.777213 AGACTATTCACCAAGTCGTCTATT 57.223 37.500 0.00 0.00 45.47 1.73
3722 4083 6.458478 CGAAGACTATTCACCAAGTCGTCTAT 60.458 42.308 13.71 0.00 44.20 1.98
3723 4084 5.163784 CGAAGACTATTCACCAAGTCGTCTA 60.164 44.000 13.71 0.00 44.20 2.59
3724 4085 4.379603 CGAAGACTATTCACCAAGTCGTCT 60.380 45.833 13.71 0.00 44.20 4.18
3725 4086 3.852536 CGAAGACTATTCACCAAGTCGTC 59.147 47.826 7.93 7.93 45.47 4.20
3726 4087 3.834610 CGAAGACTATTCACCAAGTCGT 58.165 45.455 0.00 0.00 45.47 4.34
3727 4088 2.599082 GCGAAGACTATTCACCAAGTCG 59.401 50.000 0.00 0.00 45.47 4.18
3728 4089 2.599082 CGCGAAGACTATTCACCAAGTC 59.401 50.000 0.00 0.00 42.02 3.01
3729 4090 2.607187 CGCGAAGACTATTCACCAAGT 58.393 47.619 0.00 0.00 0.00 3.16
3730 4091 1.927174 CCGCGAAGACTATTCACCAAG 59.073 52.381 8.23 0.00 0.00 3.61
3731 4092 1.274167 ACCGCGAAGACTATTCACCAA 59.726 47.619 8.23 0.00 0.00 3.67
3732 4093 0.892755 ACCGCGAAGACTATTCACCA 59.107 50.000 8.23 0.00 0.00 4.17
3733 4094 2.005971 AACCGCGAAGACTATTCACC 57.994 50.000 8.23 0.00 0.00 4.02
3734 4095 5.713822 AATAAACCGCGAAGACTATTCAC 57.286 39.130 8.23 0.00 0.00 3.18
3735 4096 6.454583 CGAAAATAAACCGCGAAGACTATTCA 60.455 38.462 8.23 0.00 0.00 2.57
3736 4097 5.894807 CGAAAATAAACCGCGAAGACTATTC 59.105 40.000 8.23 3.85 0.00 1.75
3737 4098 5.725864 GCGAAAATAAACCGCGAAGACTATT 60.726 40.000 8.23 0.32 39.54 1.73
3738 4099 4.260091 GCGAAAATAAACCGCGAAGACTAT 60.260 41.667 8.23 0.00 39.54 2.12
3739 4100 3.061161 GCGAAAATAAACCGCGAAGACTA 59.939 43.478 8.23 0.00 39.54 2.59
3740 4101 2.159747 GCGAAAATAAACCGCGAAGACT 60.160 45.455 8.23 0.00 39.54 3.24
3741 4102 2.163638 GCGAAAATAAACCGCGAAGAC 58.836 47.619 8.23 0.00 39.54 3.01
3742 4103 2.513964 GCGAAAATAAACCGCGAAGA 57.486 45.000 8.23 0.00 39.54 2.87
3766 4127 3.537580 CGAATATGGGAGGGACGAAAAA 58.462 45.455 0.00 0.00 0.00 1.94
3767 4128 2.158871 CCGAATATGGGAGGGACGAAAA 60.159 50.000 0.00 0.00 0.00 2.29
3768 4129 1.414919 CCGAATATGGGAGGGACGAAA 59.585 52.381 0.00 0.00 0.00 3.46
3769 4130 1.045407 CCGAATATGGGAGGGACGAA 58.955 55.000 0.00 0.00 0.00 3.85
3770 4131 0.105862 ACCGAATATGGGAGGGACGA 60.106 55.000 0.00 0.00 0.00 4.20
3771 4132 0.756903 AACCGAATATGGGAGGGACG 59.243 55.000 0.28 0.00 0.00 4.79
3772 4133 3.292492 AAAACCGAATATGGGAGGGAC 57.708 47.619 0.28 0.00 0.00 4.46
3805 4166 1.180456 TGCGAGTTAACGGAGGTGGA 61.180 55.000 0.00 0.00 0.00 4.02
3815 4176 1.294138 CGGGAGGGTTGCGAGTTAA 59.706 57.895 0.00 0.00 0.00 2.01
3920 4288 2.031163 GAAGGGATGGATCGGGCG 59.969 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.