Multiple sequence alignment - TraesCS5B01G392000

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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 TraesCS5B01G392000 chr5B 100.000 4525 0 0 1 4525 570933580 570938104 0.000000e+00 8357.0
1 TraesCS5B01G392000 chr5B 95.075 1543 51 7 1991 3521 571173722 571175251 0.000000e+00 2405.0
2 TraesCS5B01G392000 chr5B 90.134 821 69 4 1183 1995 571122770 571123586 0.000000e+00 1057.0
3 TraesCS5B01G392000 chr5B 85.053 843 93 11 69 883 571121725 571122562 0.000000e+00 828.0
4 TraesCS5B01G392000 chr5B 88.263 426 28 11 4114 4525 571175949 571176366 1.460000e-134 490.0
5 TraesCS5B01G392000 chr5B 89.846 325 18 4 3512 3821 571175419 571175743 1.960000e-108 403.0
6 TraesCS5B01G392000 chr5B 89.655 174 10 3 3907 4075 571175771 571175941 9.860000e-52 215.0
7 TraesCS5B01G392000 chr5B 75.943 212 33 8 913 1124 571122568 571122761 4.820000e-15 93.5
8 TraesCS5B01G392000 chr5D 90.224 3386 227 51 1175 4525 464077311 464080627 0.000000e+00 4324.0
9 TraesCS5B01G392000 chr5D 88.745 924 50 14 170 1078 464076392 464077276 0.000000e+00 1081.0
10 TraesCS5B01G392000 chr5D 95.376 173 8 0 1 173 464076190 464076362 4.460000e-70 276.0
11 TraesCS5B01G392000 chr5A 91.875 2043 100 26 2360 4374 584508105 584510109 0.000000e+00 2793.0
12 TraesCS5B01G392000 chr5A 91.667 876 58 7 1 866 584490885 584491755 0.000000e+00 1199.0
13 TraesCS5B01G392000 chr5A 87.212 1040 115 13 1157 2183 584507037 584508071 0.000000e+00 1168.0
14 TraesCS5B01G392000 chr5A 95.556 135 3 2 4366 4499 584510043 584510175 3.550000e-51 213.0
15 TraesCS5B01G392000 chr3B 88.589 1297 139 6 2363 3657 671746429 671745140 0.000000e+00 1567.0
16 TraesCS5B01G392000 chr3B 76.492 1089 184 44 1166 2211 671747489 671746430 1.110000e-145 527.0
17 TraesCS5B01G392000 chr2B 88.124 1221 135 5 2362 3579 752829850 752828637 0.000000e+00 1443.0
18 TraesCS5B01G392000 chr2B 82.848 892 118 21 1 886 752831916 752831054 0.000000e+00 767.0
19 TraesCS5B01G392000 chr2B 76.217 1068 189 35 1179 2209 752830889 752829850 5.220000e-139 505.0
20 TraesCS5B01G392000 chr2B 86.624 157 11 6 2215 2366 190023042 190022891 1.010000e-36 165.0
21 TraesCS5B01G392000 chr2D 87.624 1212 147 2 2364 3575 617072832 617071624 0.000000e+00 1404.0
22 TraesCS5B01G392000 chr2D 81.096 894 122 24 1 886 617074899 617074045 0.000000e+00 671.0
23 TraesCS5B01G392000 chr2D 75.311 1045 192 37 1179 2188 617073881 617072868 1.490000e-119 440.0
24 TraesCS5B01G392000 chr2A 87.418 1216 141 10 2364 3575 747143715 747142508 0.000000e+00 1387.0
25 TraesCS5B01G392000 chr2A 81.006 895 122 27 1 886 747145786 747144931 0.000000e+00 667.0
26 TraesCS5B01G392000 chr2A 79.889 900 129 26 1 886 746978766 746977905 2.990000e-171 612.0
27 TraesCS5B01G392000 chr2A 75.215 1045 195 39 1179 2188 747144766 747143751 1.930000e-118 436.0
28 TraesCS5B01G392000 chr2A 76.840 462 81 16 1223 1668 746977602 746977151 2.100000e-58 237.0
29 TraesCS5B01G392000 chr3A 83.349 1087 173 3 2411 3490 10952685 10951600 0.000000e+00 998.0
30 TraesCS5B01G392000 chrUn 82.353 1088 182 8 2411 3490 36344511 36345596 0.000000e+00 937.0
31 TraesCS5B01G392000 chr7B 86.624 157 11 4 2215 2366 505937315 505937466 1.010000e-36 165.0
32 TraesCS5B01G392000 chr7B 83.125 160 15 8 2216 2369 245994268 245994115 7.900000e-28 135.0
33 TraesCS5B01G392000 chr6A 85.256 156 14 3 2215 2366 184388178 184388328 7.840000e-33 152.0
34 TraesCS5B01G392000 chr6A 84.713 157 13 5 2215 2366 65858234 65858084 3.650000e-31 147.0
35 TraesCS5B01G392000 chr1A 87.218 133 11 4 2215 2342 555641257 555641126 3.650000e-31 147.0
36 TraesCS5B01G392000 chr4A 83.871 155 17 4 2215 2366 136431522 136431373 1.700000e-29 141.0


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 TraesCS5B01G392000 chr5B 570933580 570938104 4524 False 8357.000000 8357 100.000000 1 4525 1 chr5B.!!$F1 4524
1 TraesCS5B01G392000 chr5B 571173722 571176366 2644 False 878.250000 2405 90.709750 1991 4525 4 chr5B.!!$F3 2534
2 TraesCS5B01G392000 chr5B 571121725 571123586 1861 False 659.500000 1057 83.710000 69 1995 3 chr5B.!!$F2 1926
3 TraesCS5B01G392000 chr5D 464076190 464080627 4437 False 1893.666667 4324 91.448333 1 4525 3 chr5D.!!$F1 4524
4 TraesCS5B01G392000 chr5A 584507037 584510175 3138 False 1391.333333 2793 91.547667 1157 4499 3 chr5A.!!$F2 3342
5 TraesCS5B01G392000 chr5A 584490885 584491755 870 False 1199.000000 1199 91.667000 1 866 1 chr5A.!!$F1 865
6 TraesCS5B01G392000 chr3B 671745140 671747489 2349 True 1047.000000 1567 82.540500 1166 3657 2 chr3B.!!$R1 2491
7 TraesCS5B01G392000 chr2B 752828637 752831916 3279 True 905.000000 1443 82.396333 1 3579 3 chr2B.!!$R2 3578
8 TraesCS5B01G392000 chr2D 617071624 617074899 3275 True 838.333333 1404 81.343667 1 3575 3 chr2D.!!$R1 3574
9 TraesCS5B01G392000 chr2A 747142508 747145786 3278 True 830.000000 1387 81.213000 1 3575 3 chr2A.!!$R2 3574
10 TraesCS5B01G392000 chr2A 746977151 746978766 1615 True 424.500000 612 78.364500 1 1668 2 chr2A.!!$R1 1667
11 TraesCS5B01G392000 chr3A 10951600 10952685 1085 True 998.000000 998 83.349000 2411 3490 1 chr3A.!!$R1 1079
12 TraesCS5B01G392000 chrUn 36344511 36345596 1085 False 937.000000 937 82.353000 2411 3490 1 chrUn.!!$F1 1079

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
910 1000 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.0 0.0 0.00 3.82 F
1040 1145 0.107848 CGTTCACCATCCCCTACCAC 60.108 60.0 0.0 0.0 0.00 4.16 F
1139 1274 0.396435 CCTTCCCACTACACTGTGCA 59.604 55.0 7.9 0.0 36.68 4.57 F
1691 1884 1.021390 GGTGGATTGTCTGAGCACCG 61.021 60.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2229 0.532573 TGAGAAGATGAGCCACCGAC 59.467 55.000 0.00 0.00 0.00 4.79 R
2717 2966 1.195442 TAACGTGGTGGATCCTGCCA 61.195 55.000 20.09 20.09 37.07 4.92 R
3095 3344 2.292267 CTGGATATGACGCCAAAGCTT 58.708 47.619 0.00 0.00 36.60 3.74 R
3657 4119 4.537135 ATTTCACGCTCGATACCCATAT 57.463 40.909 0.00 0.00 0.00 1.78 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
117 118 1.135575 GTGAATTTCCTTGAGCAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
222 256 4.148825 ATCGTGCAGGCGGAGGTC 62.149 66.667 0.35 0.00 0.00 3.85
436 489 1.109609 ATCTCTGCTGCATCGAGACA 58.890 50.000 19.84 3.87 36.70 3.41
468 521 7.174599 CAGTTTCTGAAGAAATCTTGGTCATCT 59.825 37.037 8.64 0.00 44.69 2.90
469 522 7.174599 AGTTTCTGAAGAAATCTTGGTCATCTG 59.825 37.037 8.64 0.00 44.69 2.90
555 608 9.464714 GCGACAAGAAATATACTCATCTTTCTA 57.535 33.333 0.00 0.00 36.87 2.10
738 804 4.043200 GGCTTTGGCTGTGCGTCC 62.043 66.667 0.00 0.00 38.73 4.79
806 890 5.967088 ACACTGACATGTATCAACTACCTC 58.033 41.667 0.00 0.00 0.00 3.85
811 895 3.181475 ACATGTATCAACTACCTCGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
908 998 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
909 999 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
910 1000 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
958 1059 5.192176 TGGCAGCAGTGATGTTTTCATATA 58.808 37.500 10.56 0.00 41.05 0.86
960 1061 6.147581 GGCAGCAGTGATGTTTTCATATATG 58.852 40.000 10.56 6.36 41.05 1.78
961 1062 5.628193 GCAGCAGTGATGTTTTCATATATGC 59.372 40.000 10.56 0.00 41.05 3.14
962 1063 6.731164 CAGCAGTGATGTTTTCATATATGCA 58.269 36.000 7.92 0.74 40.80 3.96
963 1064 7.368059 CAGCAGTGATGTTTTCATATATGCAT 58.632 34.615 3.79 3.79 40.80 3.96
995 1096 2.292016 TGTGGCACGTATTTCTTTGTGG 59.708 45.455 13.77 0.00 33.04 4.17
1011 1116 3.581265 TGTGGTGACATATGGATGCAT 57.419 42.857 7.80 4.68 46.14 3.96
1032 1137 1.338674 TGATGTGGACGTTCACCATCC 60.339 52.381 24.06 10.65 39.69 3.51
1040 1145 0.107848 CGTTCACCATCCCCTACCAC 60.108 60.000 0.00 0.00 0.00 4.16
1041 1146 1.286248 GTTCACCATCCCCTACCACT 58.714 55.000 0.00 0.00 0.00 4.00
1042 1147 2.474112 GTTCACCATCCCCTACCACTA 58.526 52.381 0.00 0.00 0.00 2.74
1043 1148 2.169978 GTTCACCATCCCCTACCACTAC 59.830 54.545 0.00 0.00 0.00 2.73
1044 1149 1.129058 CACCATCCCCTACCACTACC 58.871 60.000 0.00 0.00 0.00 3.18
1045 1150 0.720232 ACCATCCCCTACCACTACCA 59.280 55.000 0.00 0.00 0.00 3.25
1062 1176 5.127194 CACTACCAGGTCTTTCTACATGCTA 59.873 44.000 0.00 0.00 29.97 3.49
1066 1180 6.116126 ACCAGGTCTTTCTACATGCTATTTC 58.884 40.000 0.00 0.00 29.97 2.17
1068 1182 6.825721 CCAGGTCTTTCTACATGCTATTTCTT 59.174 38.462 0.00 0.00 29.97 2.52
1085 1199 8.951969 GCTATTTCTTAATCTTTTCAAGCATCG 58.048 33.333 0.00 0.00 0.00 3.84
1090 1204 1.453155 TCTTTTCAAGCATCGCTCCC 58.547 50.000 0.00 0.00 38.25 4.30
1120 1234 5.576774 CAGTGTTTGTTTTCTTTTCACCCTC 59.423 40.000 0.00 0.00 0.00 4.30
1124 1238 5.592104 TTGTTTTCTTTTCACCCTCCTTC 57.408 39.130 0.00 0.00 0.00 3.46
1125 1239 3.958147 TGTTTTCTTTTCACCCTCCTTCC 59.042 43.478 0.00 0.00 0.00 3.46
1127 1241 1.827792 TCTTTTCACCCTCCTTCCCA 58.172 50.000 0.00 0.00 0.00 4.37
1128 1242 1.423921 TCTTTTCACCCTCCTTCCCAC 59.576 52.381 0.00 0.00 0.00 4.61
1138 1273 0.685097 TCCTTCCCACTACACTGTGC 59.315 55.000 7.90 0.00 36.68 4.57
1139 1274 0.396435 CCTTCCCACTACACTGTGCA 59.604 55.000 7.90 0.00 36.68 4.57
1153 1318 3.304721 TGCATGGTTGTGCCCAGC 61.305 61.111 0.00 0.00 44.43 4.85
1154 1319 4.073200 GCATGGTTGTGCCCAGCC 62.073 66.667 0.00 0.00 42.00 4.85
1164 1329 1.074775 TGCCCAGCCAACTACAAGG 59.925 57.895 0.00 0.00 0.00 3.61
1213 1378 3.302740 GCAAGAGCTAAACAATCGATCGG 60.303 47.826 16.41 1.30 37.91 4.18
1214 1379 4.112634 CAAGAGCTAAACAATCGATCGGA 58.887 43.478 16.41 2.25 0.00 4.55
1248 1417 2.116772 ATGGTGGTTGCTGCTGCT 59.883 55.556 17.00 0.00 40.48 4.24
1249 1418 2.273179 ATGGTGGTTGCTGCTGCTG 61.273 57.895 17.00 0.77 40.48 4.41
1250 1419 4.353437 GGTGGTTGCTGCTGCTGC 62.353 66.667 22.51 22.51 40.48 5.25
1270 1439 3.894547 TTTCCTGGCCGCGGTTCTC 62.895 63.158 28.70 14.43 0.00 2.87
1328 1521 1.178534 CCCTCCTTTTTCTTGCGGCA 61.179 55.000 0.00 0.00 0.00 5.69
1331 1524 2.289010 CCTCCTTTTTCTTGCGGCAATT 60.289 45.455 16.80 0.00 0.00 2.32
1346 1539 1.165270 CAATTTCCAGGACGTCCACC 58.835 55.000 35.00 10.80 38.89 4.61
1360 1553 2.598787 CCACCACCCTTTCCGCCTA 61.599 63.158 0.00 0.00 0.00 3.93
1460 1653 1.628340 CAGGGACATACTTGGTCACCA 59.372 52.381 0.00 0.00 39.53 4.17
1656 1849 2.203153 ACAGCCGACCACCAACAC 60.203 61.111 0.00 0.00 0.00 3.32
1668 1861 3.321111 ACCACCAACACTAGTGACTACAG 59.679 47.826 29.30 14.83 36.01 2.74
1691 1884 1.021390 GGTGGATTGTCTGAGCACCG 61.021 60.000 0.00 0.00 0.00 4.94
1727 1920 6.083630 GTCTATGTGCTGATCGACTCTTATC 58.916 44.000 0.00 0.00 0.00 1.75
1941 2145 3.614159 TCTATACGTATGCACACCGTC 57.386 47.619 18.37 0.00 36.12 4.79
1972 2187 8.028354 TGTTTTGAAACATATATGCCTGACTTG 58.972 33.333 12.79 0.00 43.45 3.16
2128 2350 2.103094 TCCACTGAACACCTTCACTCAG 59.897 50.000 0.00 0.00 40.92 3.35
2532 2781 2.516930 AGCAAATGATCGGCCCGG 60.517 61.111 1.90 0.00 0.00 5.73
2570 2819 3.684305 CAGATATTGTTGCGGTCACAAGA 59.316 43.478 0.00 0.00 0.00 3.02
2717 2966 2.030027 TCAGTGAGGTCTCCACCATT 57.970 50.000 0.00 0.00 46.68 3.16
3095 3344 2.042297 AGCTCCTGAGATGATATCCCGA 59.958 50.000 0.00 0.00 0.00 5.14
3491 3758 0.106894 CTACCATTTCGGAGGAGGGC 59.893 60.000 0.00 0.00 38.63 5.19
3582 4031 5.637006 TGCAGTAATGGTTGTTATGAACC 57.363 39.130 0.00 0.00 45.06 3.62
3591 4040 4.432712 GGTTGTTATGAACCATGGAATGC 58.567 43.478 21.47 4.85 44.97 3.56
3657 4119 6.993786 TGTTCATCCGAAATACAAGCATAA 57.006 33.333 0.00 0.00 31.43 1.90
3662 4124 8.267620 TCATCCGAAATACAAGCATAATATGG 57.732 34.615 2.13 0.00 0.00 2.74
3671 4133 5.178797 ACAAGCATAATATGGGTATCGAGC 58.821 41.667 2.13 0.00 0.00 5.03
3768 4232 6.012745 AGAGGATTATACATGGGGAAAATGC 58.987 40.000 0.00 0.00 0.00 3.56
3840 4322 0.662619 TTCTTCTGGCGCTGTTTGTG 59.337 50.000 7.64 0.00 0.00 3.33
3841 4323 0.179059 TCTTCTGGCGCTGTTTGTGA 60.179 50.000 7.64 0.00 0.00 3.58
3845 4328 1.680735 TCTGGCGCTGTTTGTGATTTT 59.319 42.857 7.64 0.00 0.00 1.82
3850 4333 3.115554 GCGCTGTTTGTGATTTTCAAGT 58.884 40.909 0.00 0.00 0.00 3.16
3855 4338 4.681744 TGTTTGTGATTTTCAAGTCCTGC 58.318 39.130 0.00 0.00 0.00 4.85
3862 4345 0.250901 TTTCAAGTCCTGCAGCTCCC 60.251 55.000 8.66 0.00 0.00 4.30
3888 4376 0.698238 ACATCCTTGCAGCCCAACTA 59.302 50.000 0.00 0.00 0.00 2.24
3918 4406 4.898829 TCAAACCATGACACTGTTCAAG 57.101 40.909 0.00 0.00 31.50 3.02
3922 4410 1.195448 CCATGACACTGTTCAAGACGC 59.805 52.381 0.00 0.00 0.00 5.19
3929 4417 3.243737 ACACTGTTCAAGACGCTATGACA 60.244 43.478 0.00 0.00 0.00 3.58
4021 4514 5.503927 ACTTTCAACAGATCAGGTATGCAT 58.496 37.500 3.79 3.79 0.00 3.96
4024 4517 6.441093 TTCAACAGATCAGGTATGCATTTC 57.559 37.500 3.54 0.00 0.00 2.17
4043 4536 4.385358 TTCTTTTTCAGTGAGGTTTGCC 57.615 40.909 0.00 0.00 0.00 4.52
4075 4568 0.458370 GTGCAGCCGGGCAAAATAAG 60.458 55.000 23.09 2.80 46.93 1.73
4078 4571 1.735700 GCAGCCGGGCAAAATAAGTTC 60.736 52.381 23.09 0.00 0.00 3.01
4079 4572 1.818674 CAGCCGGGCAAAATAAGTTCT 59.181 47.619 23.09 0.00 0.00 3.01
4087 4585 5.414765 CGGGCAAAATAAGTTCTAAGGAAGT 59.585 40.000 0.00 0.00 36.75 3.01
4095 4598 2.143925 GTTCTAAGGAAGTTGCGTGCT 58.856 47.619 0.00 0.00 31.46 4.40
4096 4599 2.543777 TCTAAGGAAGTTGCGTGCTT 57.456 45.000 0.00 0.00 0.00 3.91
4150 4653 9.594478 TGACATGAATTACACTTTATCACGTAT 57.406 29.630 0.00 0.00 0.00 3.06
4191 4700 4.864806 TCAAAGAGCGCTTGAATGTAGTAG 59.135 41.667 13.26 0.00 33.79 2.57
4226 4735 5.105269 GGAAACTTGTGTTTTTAGGGGTGAA 60.105 40.000 0.00 0.00 45.36 3.18
4229 4738 3.955524 TGTGTTTTTAGGGGTGAAGGA 57.044 42.857 0.00 0.00 0.00 3.36
4243 4765 3.006247 GTGAAGGAAGCTTGCCTCTAAG 58.994 50.000 15.04 0.00 33.76 2.18
4249 4771 2.682155 AGCTTGCCTCTAAGTGCTAC 57.318 50.000 0.00 0.00 0.00 3.58
4250 4772 2.183679 AGCTTGCCTCTAAGTGCTACT 58.816 47.619 0.00 0.00 0.00 2.57
4251 4773 2.569404 AGCTTGCCTCTAAGTGCTACTT 59.431 45.455 6.74 6.74 41.97 2.24
4351 4878 4.498520 CGTCTGCCGTCGCCTCAT 62.499 66.667 0.00 0.00 0.00 2.90
4352 4879 2.805546 GTCTGCCGTCGCCTCATA 59.194 61.111 0.00 0.00 0.00 2.15
4390 4917 1.141881 GCATCCAGGTCATCGTCGT 59.858 57.895 0.00 0.00 0.00 4.34
4454 4982 4.383861 CCTGCTCTCGCCTGCACA 62.384 66.667 0.00 0.00 35.20 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 0.179032 TTGTCGGCTGCTCAAGGAAA 60.179 50.000 0.00 0.00 0.00 3.13
104 105 1.004560 CTTGTCGGCTGCTCAAGGA 60.005 57.895 16.99 1.25 36.09 3.36
117 118 0.877743 GTGGAGCTGGAAAGCTTGTC 59.122 55.000 0.00 0.00 46.36 3.18
180 214 0.664767 ACAAGCTCGTCTCGACAAGC 60.665 55.000 1.85 1.85 0.00 4.01
198 232 1.349627 CGCCTGCACGATGATTCAC 59.650 57.895 0.00 0.00 34.06 3.18
360 407 3.303791 CCAGCAACACATCATCATCATCG 60.304 47.826 0.00 0.00 0.00 3.84
573 626 0.541863 ACCTGGCTTACCTTCATCCG 59.458 55.000 0.00 0.00 36.63 4.18
662 723 2.040412 GACTCATGGACAGGGGAAGTTT 59.960 50.000 0.00 0.00 0.00 2.66
755 839 6.015265 GGTCTGGGATTCTAATGTAGTCTACC 60.015 46.154 7.56 0.00 0.00 3.18
756 840 6.778559 AGGTCTGGGATTCTAATGTAGTCTAC 59.221 42.308 2.81 2.81 0.00 2.59
757 841 6.778069 CAGGTCTGGGATTCTAATGTAGTCTA 59.222 42.308 0.00 0.00 0.00 2.59
758 842 5.600484 CAGGTCTGGGATTCTAATGTAGTCT 59.400 44.000 0.00 0.00 0.00 3.24
759 843 5.598830 TCAGGTCTGGGATTCTAATGTAGTC 59.401 44.000 0.00 0.00 0.00 2.59
811 895 2.477845 GCATATGCCGCTGCGATC 59.522 61.111 25.45 14.99 41.78 3.69
886 976 5.179182 CACACACACACACACACACATATAT 59.821 40.000 0.00 0.00 0.00 0.86
888 978 3.312146 CACACACACACACACACACATAT 59.688 43.478 0.00 0.00 0.00 1.78
889 979 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
891 981 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
892 982 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
893 983 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
894 984 1.152510 TGACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
895 985 3.614399 TGACACACACACACACACA 57.386 47.368 0.00 0.00 0.00 3.72
958 1059 7.219322 ACGTGCCACATATATATATGATGCAT 58.781 34.615 32.06 23.56 44.19 3.96
960 1061 8.763049 ATACGTGCCACATATATATATGATGC 57.237 34.615 30.76 28.35 42.05 3.91
971 1072 5.163663 CCACAAAGAAATACGTGCCACATAT 60.164 40.000 0.00 0.00 0.00 1.78
975 1076 2.292292 ACCACAAAGAAATACGTGCCAC 59.708 45.455 0.00 0.00 0.00 5.01
989 1090 3.694926 TGCATCCATATGTCACCACAAA 58.305 40.909 1.24 0.00 35.64 2.83
995 1096 5.458015 CACATCAATGCATCCATATGTCAC 58.542 41.667 0.00 0.00 31.46 3.67
1011 1116 2.422597 GATGGTGAACGTCCACATCAA 58.577 47.619 7.39 0.00 38.74 2.57
1032 1137 2.249309 AAGACCTGGTAGTGGTAGGG 57.751 55.000 0.00 0.00 38.03 3.53
1040 1145 4.744795 AGCATGTAGAAAGACCTGGTAG 57.255 45.455 0.00 0.00 0.00 3.18
1041 1146 6.808321 AATAGCATGTAGAAAGACCTGGTA 57.192 37.500 0.00 0.00 34.10 3.25
1042 1147 5.700402 AATAGCATGTAGAAAGACCTGGT 57.300 39.130 0.00 0.00 31.81 4.00
1043 1148 6.352516 AGAAATAGCATGTAGAAAGACCTGG 58.647 40.000 0.00 0.00 0.00 4.45
1044 1149 7.856145 AAGAAATAGCATGTAGAAAGACCTG 57.144 36.000 0.00 0.00 0.00 4.00
1078 1192 2.042831 GCACAAGGGAGCGATGCTT 61.043 57.895 0.00 0.00 39.88 3.91
1085 1199 0.031178 CAAACACTGCACAAGGGAGC 59.969 55.000 0.00 0.00 38.79 4.70
1090 1204 5.844301 AAAGAAAACAAACACTGCACAAG 57.156 34.783 0.00 0.00 0.00 3.16
1120 1234 0.396435 TGCACAGTGTAGTGGGAAGG 59.604 55.000 1.61 0.00 39.87 3.46
1124 1238 0.036732 ACCATGCACAGTGTAGTGGG 59.963 55.000 19.18 12.88 39.87 4.61
1125 1239 1.536766 CAACCATGCACAGTGTAGTGG 59.463 52.381 15.46 15.46 39.87 4.00
1127 1241 2.221169 CACAACCATGCACAGTGTAGT 58.779 47.619 1.61 0.00 0.00 2.73
1128 1242 1.069022 GCACAACCATGCACAGTGTAG 60.069 52.381 1.61 0.00 45.39 2.74
1138 1273 2.208619 TTGGCTGGGCACAACCATG 61.209 57.895 12.87 0.00 42.14 3.66
1139 1274 2.200930 TTGGCTGGGCACAACCAT 59.799 55.556 12.87 0.00 42.14 3.55
1153 1318 4.072839 GACTTTCCTTCCCTTGTAGTTGG 58.927 47.826 0.00 0.00 0.00 3.77
1154 1319 4.974399 AGACTTTCCTTCCCTTGTAGTTG 58.026 43.478 0.00 0.00 0.00 3.16
1155 1320 5.132144 TGAAGACTTTCCTTCCCTTGTAGTT 59.868 40.000 0.00 0.00 41.29 2.24
1164 1329 3.004839 GCTTGGTTGAAGACTTTCCTTCC 59.995 47.826 0.00 0.00 41.29 3.46
1208 1373 1.402259 AGGCATCGACGATATCCGATC 59.598 52.381 10.57 8.58 42.79 3.69
1213 1378 2.534298 CATGGAGGCATCGACGATATC 58.466 52.381 10.57 8.90 0.00 1.63
1214 1379 1.205655 CCATGGAGGCATCGACGATAT 59.794 52.381 10.57 0.00 0.00 1.63
1250 1419 3.051392 GAACCGCGGCCAGGAAATG 62.051 63.158 28.58 0.00 0.00 2.32
1270 1439 2.819595 CCCTCAACATCCACGGCG 60.820 66.667 4.80 4.80 0.00 6.46
1328 1521 0.768622 TGGTGGACGTCCTGGAAATT 59.231 50.000 33.39 0.00 36.82 1.82
1331 1524 2.513259 GGTGGTGGACGTCCTGGAA 61.513 63.158 33.39 12.38 36.82 3.53
1346 1539 0.676782 CCTTGTAGGCGGAAAGGGTG 60.677 60.000 7.11 0.00 37.42 4.61
1360 1553 1.220206 CTCAGCTGGATCGCCTTGT 59.780 57.895 15.13 0.00 34.31 3.16
1471 1664 4.039973 ACGACCCAGAAGTATGAAAGTTCA 59.960 41.667 0.00 0.00 39.63 3.18
1647 1840 3.572682 TCTGTAGTCACTAGTGTTGGTGG 59.427 47.826 21.99 10.17 36.53 4.61
1656 1849 1.743958 CCACCGGTCTGTAGTCACTAG 59.256 57.143 2.59 0.00 0.00 2.57
1668 1861 0.741221 GCTCAGACAATCCACCGGTC 60.741 60.000 2.59 0.00 0.00 4.79
1691 1884 2.094417 GCACATAGACGAAAGAAGTGCC 59.906 50.000 0.00 0.00 43.54 5.01
1727 1920 4.699257 AGAAGGCTTAAGCTTCTCAACATG 59.301 41.667 25.88 0.00 41.70 3.21
1972 2187 7.364522 TGCATACAATGAAGAAAGTGTAGAC 57.635 36.000 0.00 0.00 30.45 2.59
2013 2229 0.532573 TGAGAAGATGAGCCACCGAC 59.467 55.000 0.00 0.00 0.00 4.79
2342 2586 3.262420 CTCCCTCCGTTCACAAATACAG 58.738 50.000 0.00 0.00 0.00 2.74
2343 2587 2.635915 ACTCCCTCCGTTCACAAATACA 59.364 45.455 0.00 0.00 0.00 2.29
2344 2588 3.329929 ACTCCCTCCGTTCACAAATAC 57.670 47.619 0.00 0.00 0.00 1.89
2345 2589 4.091549 ACTACTCCCTCCGTTCACAAATA 58.908 43.478 0.00 0.00 0.00 1.40
2346 2590 2.904434 ACTACTCCCTCCGTTCACAAAT 59.096 45.455 0.00 0.00 0.00 2.32
2532 2781 7.442656 ACAATATCTGTGTAGGCATACCTTAC 58.557 38.462 6.00 0.00 39.39 2.34
2570 2819 2.107204 ACCCAGCTTGTCTCTGAAATGT 59.893 45.455 0.00 0.00 33.54 2.71
2717 2966 1.195442 TAACGTGGTGGATCCTGCCA 61.195 55.000 20.09 20.09 37.07 4.92
3095 3344 2.292267 CTGGATATGACGCCAAAGCTT 58.708 47.619 0.00 0.00 36.60 3.74
3491 3758 6.827641 TCGAACATAAAGGAAATTTCACTCG 58.172 36.000 19.49 13.30 32.01 4.18
3547 3996 4.984161 CCATTACTGCAACTTTTCACAAGG 59.016 41.667 0.00 0.00 0.00 3.61
3582 4031 6.144854 CAGTATAAAACATCCGCATTCCATG 58.855 40.000 0.00 0.00 0.00 3.66
3657 4119 4.537135 ATTTCACGCTCGATACCCATAT 57.463 40.909 0.00 0.00 0.00 1.78
3662 4124 4.795970 ATGAAATTTCACGCTCGATACC 57.204 40.909 22.71 0.00 40.49 2.73
3671 4133 5.389725 GCAATGGGACAAATGAAATTTCACG 60.390 40.000 22.71 15.87 44.81 4.35
3732 4195 9.941664 CATGTATAATCCTCTGTGTTCATTTTC 57.058 33.333 0.00 0.00 0.00 2.29
3768 4232 8.628882 TCAGAAAATATGTCATGTACGTACTG 57.371 34.615 25.12 19.39 32.37 2.74
3840 4322 2.163211 GGAGCTGCAGGACTTGAAAATC 59.837 50.000 17.12 0.00 0.00 2.17
3841 4323 2.165998 GGAGCTGCAGGACTTGAAAAT 58.834 47.619 17.12 0.00 0.00 1.82
3845 4328 2.947532 CGGGAGCTGCAGGACTTGA 61.948 63.158 17.12 0.00 0.00 3.02
3850 4333 3.473647 CCATCGGGAGCTGCAGGA 61.474 66.667 17.12 3.92 35.59 3.86
3855 4338 1.890979 GATGTGCCATCGGGAGCTG 60.891 63.158 0.00 0.00 35.59 4.24
3862 4345 1.725665 CTGCAAGGATGTGCCATCG 59.274 57.895 8.49 0.00 44.26 3.84
3888 4376 4.586001 AGTGTCATGGTTTGATGCTTCTTT 59.414 37.500 0.88 0.00 36.54 2.52
3982 4470 6.150307 TGTTGAAAGTAGTTGCAGAAAACTGA 59.850 34.615 0.00 0.00 40.58 3.41
3993 4481 7.413438 GCATACCTGATCTGTTGAAAGTAGTTG 60.413 40.741 0.00 0.00 0.00 3.16
3996 4484 6.108687 TGCATACCTGATCTGTTGAAAGTAG 58.891 40.000 0.00 0.00 0.00 2.57
4021 4514 4.466015 AGGCAAACCTCACTGAAAAAGAAA 59.534 37.500 0.00 0.00 46.34 2.52
4043 4536 1.287730 GCTGCACTGACAACGGAGAG 61.288 60.000 0.00 0.00 0.00 3.20
4075 4568 2.143925 AGCACGCAACTTCCTTAGAAC 58.856 47.619 0.00 0.00 0.00 3.01
4078 4571 3.555518 GAAAAGCACGCAACTTCCTTAG 58.444 45.455 0.00 0.00 0.00 2.18
4079 4572 2.032377 CGAAAAGCACGCAACTTCCTTA 60.032 45.455 0.00 0.00 0.00 2.69
4191 4700 8.487313 AAAACACAAGTTTCCTCCAAATTTAC 57.513 30.769 0.00 0.00 46.79 2.01
4226 4735 1.339535 GCACTTAGAGGCAAGCTTCCT 60.340 52.381 14.87 14.87 36.46 3.36
4229 4738 2.569404 AGTAGCACTTAGAGGCAAGCTT 59.431 45.455 0.00 0.00 33.83 3.74
4243 4765 2.906354 CCCCACATGTAGAAGTAGCAC 58.094 52.381 0.00 0.00 0.00 4.40
4249 4771 1.819632 GGCGCCCCACATGTAGAAG 60.820 63.158 18.11 0.00 0.00 2.85
4250 4772 2.270850 GGCGCCCCACATGTAGAA 59.729 61.111 18.11 0.00 0.00 2.10
4251 4773 4.155733 CGGCGCCCCACATGTAGA 62.156 66.667 23.46 0.00 0.00 2.59
4351 4878 3.712907 GGCGGTTGGCAGGGAGTA 61.713 66.667 0.00 0.00 46.16 2.59
4390 4917 0.171903 GTTAAGGCGACGGCAGTCTA 59.828 55.000 24.23 6.33 44.93 2.59


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

AutoCloner maintained by Alex Coulton.