Multiple sequence alignment - TraesCS1B01G185500

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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 TraesCS1B01G185500 chr1B 100.000 2132 0 0 1 2132 332158612 332160743 0.000000e+00 3938
1 TraesCS1B01G185500 chr1D 90.502 1095 56 14 1038 2132 245975037 245973991 0.000000e+00 1402
2 TraesCS1B01G185500 chr1D 91.298 678 36 8 1 663 245980025 245979356 0.000000e+00 904
3 TraesCS1B01G185500 chr1D 91.667 240 16 3 711 947 245979358 245979120 1.580000e-86 329
4 TraesCS1B01G185500 chr1D 96.262 107 3 1 937 1042 245979157 245979051 7.820000e-40 174
5 TraesCS1B01G185500 chr1A 88.993 963 50 9 1170 2132 306640687 306639781 0.000000e+00 1140
6 TraesCS1B01G185500 chr1A 92.771 664 39 2 1 663 306641744 306641089 0.000000e+00 952
7 TraesCS1B01G185500 chr1A 91.358 243 14 6 711 947 306641091 306640850 2.040000e-85 326
8 TraesCS1B01G185500 chr1A 95.567 203 8 1 932 1133 306640892 306640690 7.340000e-85 324
9 TraesCS1B01G185500 chr6A 86.998 846 72 18 21 863 63118211 63117401 0.000000e+00 918
10 TraesCS1B01G185500 chr6A 87.892 223 14 7 1912 2126 63117284 63117067 1.260000e-62 250
11 TraesCS1B01G185500 chr6D 86.597 858 76 18 7 863 52338703 52337884 0.000000e+00 911
12 TraesCS1B01G185500 chr6D 86.358 799 80 11 1347 2132 52337669 52336887 0.000000e+00 845
13 TraesCS1B01G185500 chr6B 84.983 859 84 16 7 863 119127754 119126939 0.000000e+00 830
14 TraesCS1B01G185500 chr6B 85.375 800 74 20 1347 2132 119126720 119125950 0.000000e+00 789
15 TraesCS1B01G185500 chr6B 91.979 187 11 3 993 1178 22427143 22426960 2.100000e-65 259
16 TraesCS1B01G185500 chr7B 92.513 187 10 2 993 1178 45214990 45215173 4.510000e-67 265
17 TraesCS1B01G185500 chr3B 92.513 187 10 2 993 1178 201514300 201514117 4.510000e-67 265
18 TraesCS1B01G185500 chr3B 92.513 187 10 2 993 1178 201515879 201515696 4.510000e-67 265
19 TraesCS1B01G185500 chr3B 91.979 187 11 2 993 1178 201514837 201514654 2.100000e-65 259
20 TraesCS1B01G185500 chr3B 92.778 180 10 1 993 1172 201515349 201515173 7.550000e-65 257
21 TraesCS1B01G185500 chrUn 91.979 187 11 2 993 1178 445811864 445812047 2.100000e-65 259


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 TraesCS1B01G185500 chr1B 332158612 332160743 2131 False 3938.0 3938 100.000000 1 2132 1 chr1B.!!$F1 2131
1 TraesCS1B01G185500 chr1D 245973991 245975037 1046 True 1402.0 1402 90.502000 1038 2132 1 chr1D.!!$R1 1094
2 TraesCS1B01G185500 chr1D 245979051 245980025 974 True 469.0 904 93.075667 1 1042 3 chr1D.!!$R2 1041
3 TraesCS1B01G185500 chr1A 306639781 306641744 1963 True 685.5 1140 92.172250 1 2132 4 chr1A.!!$R1 2131
4 TraesCS1B01G185500 chr6A 63117067 63118211 1144 True 584.0 918 87.445000 21 2126 2 chr6A.!!$R1 2105
5 TraesCS1B01G185500 chr6D 52336887 52338703 1816 True 878.0 911 86.477500 7 2132 2 chr6D.!!$R1 2125
6 TraesCS1B01G185500 chr6B 119125950 119127754 1804 True 809.5 830 85.179000 7 2132 2 chr6B.!!$R2 2125
7 TraesCS1B01G185500 chr3B 201514117 201515879 1762 True 261.5 265 92.445750 993 1178 4 chr3B.!!$R1 185

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
565 577 1.247567 AAGAATTGGTTGGCCTCGTG 58.752 50.0 3.32 0.0 35.27 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 2978 0.46362 GCTGGTTTTGGCAGGTTCAA 59.536 50.0 0.0 0.0 0.0 2.69 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
116 117 5.008911 CCATCTCAGACTCATCACTAGACAG 59.991 48.000 0.00 0.00 0.00 3.51
153 154 4.530161 AGTTTCTCTGTCATAGAAGGCTGT 59.470 41.667 1.43 0.00 34.59 4.40
269 270 5.243507 TCATCAAATGCAACACCTGTTACAT 59.756 36.000 0.00 0.00 42.16 2.29
332 334 6.249260 CACAAAATAATAGCTTGCGAACTGTC 59.751 38.462 0.00 0.00 0.00 3.51
362 364 7.133891 AGTTCACGAGGTTGAAATTCTAATG 57.866 36.000 0.00 0.00 37.24 1.90
363 365 6.149474 AGTTCACGAGGTTGAAATTCTAATGG 59.851 38.462 0.00 0.00 37.24 3.16
369 371 5.264395 AGGTTGAAATTCTAATGGACCTGG 58.736 41.667 0.00 0.00 35.11 4.45
526 538 3.737559 AGGACTGCCAACATGGATAAA 57.262 42.857 0.00 0.00 40.96 1.40
545 557 6.318396 GGATAAAAGAAAGAGCTTCTGCAGAT 59.682 38.462 19.04 1.77 44.00 2.90
565 577 1.247567 AAGAATTGGTTGGCCTCGTG 58.752 50.000 3.32 0.00 35.27 4.35
583 595 5.163754 CCTCGTGGGAAAACTATGAAACATC 60.164 44.000 0.00 0.00 37.23 3.06
679 705 7.231317 TCAGAAGTGGTTTGCTAGATTGATTTT 59.769 33.333 0.00 0.00 0.00 1.82
681 707 5.473039 AGTGGTTTGCTAGATTGATTTTGC 58.527 37.500 0.00 0.00 0.00 3.68
688 714 7.928307 TTGCTAGATTGATTTTGCTACTTCT 57.072 32.000 0.00 0.00 0.00 2.85
737 763 6.724263 CCATAAACGCTTGCATTGATAACTA 58.276 36.000 0.00 0.00 0.00 2.24
787 816 6.043411 CCAGTAGTGGTAAATTGAGCTACTC 58.957 44.000 8.59 0.00 39.30 2.59
800 829 6.782082 TTGAGCTACTCACTTCTCATACAT 57.218 37.500 0.00 0.00 40.46 2.29
823 852 2.524569 AGCATTTTGTTGAAACGGGG 57.475 45.000 0.00 0.00 0.00 5.73
828 858 4.274705 GCATTTTGTTGAAACGGGGAAAAT 59.725 37.500 0.00 0.00 0.00 1.82
834 864 3.163616 TGAAACGGGGAAAATAAGGCT 57.836 42.857 0.00 0.00 0.00 4.58
940 977 7.521669 ACCAGGATTCCCTCAAAATAGAATAG 58.478 38.462 0.00 0.00 42.02 1.73
941 978 7.350921 ACCAGGATTCCCTCAAAATAGAATAGA 59.649 37.037 0.00 0.00 42.02 1.98
942 979 7.663493 CCAGGATTCCCTCAAAATAGAATAGAC 59.337 40.741 0.00 0.00 42.02 2.59
943 980 7.663493 CAGGATTCCCTCAAAATAGAATAGACC 59.337 40.741 0.00 0.00 42.02 3.85
944 981 7.350921 AGGATTCCCTCAAAATAGAATAGACCA 59.649 37.037 0.00 0.00 38.86 4.02
945 982 7.663493 GGATTCCCTCAAAATAGAATAGACCAG 59.337 40.741 0.00 0.00 0.00 4.00
946 983 6.500589 TCCCTCAAAATAGAATAGACCAGG 57.499 41.667 0.00 0.00 0.00 4.45
947 984 6.209774 TCCCTCAAAATAGAATAGACCAGGA 58.790 40.000 0.00 0.00 0.00 3.86
948 985 6.851836 TCCCTCAAAATAGAATAGACCAGGAT 59.148 38.462 0.00 0.00 0.00 3.24
949 986 7.350921 TCCCTCAAAATAGAATAGACCAGGATT 59.649 37.037 0.00 0.00 0.00 3.01
950 987 7.663493 CCCTCAAAATAGAATAGACCAGGATTC 59.337 40.741 0.00 0.00 33.11 2.52
951 988 7.663493 CCTCAAAATAGAATAGACCAGGATTCC 59.337 40.741 0.00 0.00 33.34 3.01
952 989 7.518188 TCAAAATAGAATAGACCAGGATTCCC 58.482 38.462 0.00 0.00 33.34 3.97
953 990 7.350921 TCAAAATAGAATAGACCAGGATTCCCT 59.649 37.037 0.00 0.00 45.74 4.20
954 991 6.943899 AATAGAATAGACCAGGATTCCCTC 57.056 41.667 0.00 0.00 42.02 4.30
955 992 4.286813 AGAATAGACCAGGATTCCCTCA 57.713 45.455 0.00 0.00 42.02 3.86
956 993 4.635473 AGAATAGACCAGGATTCCCTCAA 58.365 43.478 0.00 0.00 42.02 3.02
957 994 5.039645 AGAATAGACCAGGATTCCCTCAAA 58.960 41.667 0.00 0.00 42.02 2.69
958 995 5.492524 AGAATAGACCAGGATTCCCTCAAAA 59.507 40.000 0.00 0.00 42.02 2.44
959 996 6.161170 AGAATAGACCAGGATTCCCTCAAAAT 59.839 38.462 0.00 0.00 42.02 1.82
960 997 7.350921 AGAATAGACCAGGATTCCCTCAAAATA 59.649 37.037 0.00 0.00 42.02 1.40
961 998 5.379706 AGACCAGGATTCCCTCAAAATAG 57.620 43.478 0.00 0.00 42.02 1.73
962 999 5.039645 AGACCAGGATTCCCTCAAAATAGA 58.960 41.667 0.00 0.00 42.02 1.98
963 1000 5.492524 AGACCAGGATTCCCTCAAAATAGAA 59.507 40.000 0.00 0.00 42.02 2.10
964 1001 6.161170 AGACCAGGATTCCCTCAAAATAGAAT 59.839 38.462 0.00 0.00 42.02 2.40
1036 1073 2.329267 TGGTCGCCATCTCCATATCTT 58.671 47.619 0.00 0.00 0.00 2.40
1088 1125 2.863132 TATACCGTGTTTGGGCAACT 57.137 45.000 0.00 0.00 36.21 3.16
1119 1156 8.333908 CAACAATTAAGAGATCCATTCGAAGAG 58.666 37.037 3.35 0.00 38.43 2.85
1133 1170 3.538591 TCGAAGAGCACGGAGACTAATA 58.461 45.455 0.00 0.00 0.00 0.98
1134 1171 3.311871 TCGAAGAGCACGGAGACTAATAC 59.688 47.826 0.00 0.00 0.00 1.89
1135 1172 3.312973 CGAAGAGCACGGAGACTAATACT 59.687 47.826 0.00 0.00 0.00 2.12
1143 1180 7.384477 AGCACGGAGACTAATACTTTAAGTTT 58.616 34.615 1.94 0.81 0.00 2.66
1181 1636 8.030913 TCTGGGAGACTTCTTATAAAATACCC 57.969 38.462 0.00 0.00 0.00 3.69
1185 1640 9.775854 GGGAGACTTCTTATAAAATACCCTTAC 57.224 37.037 0.00 0.00 0.00 2.34
1195 1650 4.498894 AAATACCCTTACTACCAGGCAC 57.501 45.455 0.00 0.00 0.00 5.01
1220 1675 2.428544 TATAAGGCGCCCACACATTT 57.571 45.000 26.15 11.80 0.00 2.32
1262 1717 9.747898 ACCAATAGTTAGACCAATAAAATGTCA 57.252 29.630 0.00 0.00 0.00 3.58
1353 2336 8.910351 AAATATTATTGGTCTAGCTCTTGGTC 57.090 34.615 0.00 0.00 0.00 4.02
1354 2337 5.957771 ATTATTGGTCTAGCTCTTGGTCA 57.042 39.130 0.00 0.00 0.00 4.02
1355 2338 5.755409 TTATTGGTCTAGCTCTTGGTCAA 57.245 39.130 0.00 0.00 0.00 3.18
1356 2339 4.640771 ATTGGTCTAGCTCTTGGTCAAA 57.359 40.909 0.00 0.00 0.00 2.69
1357 2340 3.402628 TGGTCTAGCTCTTGGTCAAAC 57.597 47.619 0.00 0.00 0.00 2.93
1358 2341 2.972713 TGGTCTAGCTCTTGGTCAAACT 59.027 45.455 0.00 0.00 0.00 2.66
1359 2342 3.244215 TGGTCTAGCTCTTGGTCAAACTG 60.244 47.826 0.00 0.00 0.00 3.16
1365 2348 4.973168 AGCTCTTGGTCAAACTGAATGTA 58.027 39.130 0.00 0.00 0.00 2.29
1394 2377 6.119536 TGTGTGGGTGCCTTATATTTTAGAG 58.880 40.000 0.00 0.00 0.00 2.43
1430 2413 5.348164 ACAAATACAAAGGTGAAGTTGCAC 58.652 37.500 0.00 0.00 38.05 4.57
1461 2444 5.277058 GCTCGCATCTTCAGTTACTAAATGG 60.277 44.000 0.00 0.00 0.00 3.16
1472 2455 8.856153 TCAGTTACTAAATGGTATTTTGCAGA 57.144 30.769 0.00 0.00 0.00 4.26
1575 2746 8.884124 AAAGGAAGATGTTGGAAGATAATGAA 57.116 30.769 0.00 0.00 0.00 2.57
1585 2756 8.637099 TGTTGGAAGATAATGAATGAAACAACA 58.363 29.630 0.00 0.00 40.35 3.33
1593 2764 5.703978 ATGAATGAAACAACAACGATGGA 57.296 34.783 0.00 0.00 0.00 3.41
1716 2889 0.323178 CTTGGCACTTGAGGCATCCT 60.323 55.000 0.00 0.00 44.02 3.24
1767 2940 1.673626 CGCATTCTTGGCATTTGGCTT 60.674 47.619 5.67 0.00 44.01 4.35
1805 2978 6.206042 ACTATCAGTACTTTCCCAAGGATCT 58.794 40.000 0.00 0.00 33.82 2.75
1832 3007 1.888436 GCCAAAACCAGCCCTTAGCC 61.888 60.000 0.00 0.00 45.47 3.93
1906 3084 7.807433 TCACGAAAACAATTCATATTTCACAGG 59.193 33.333 0.00 0.00 32.64 4.00
1922 3100 2.032549 CACAGGCAGTTCGAACAAAGAG 60.033 50.000 28.78 17.39 0.00 2.85
1946 3124 7.390027 AGAATGTACAACTAATCAAGCAGAGT 58.610 34.615 0.00 0.00 0.00 3.24
1947 3125 8.531982 AGAATGTACAACTAATCAAGCAGAGTA 58.468 33.333 0.00 0.00 0.00 2.59
2094 3325 6.726490 ATACCATATGTATTACCTAGGCGG 57.274 41.667 9.30 0.00 36.77 6.13
2112 3343 2.544685 CGGGCAGACAAATCTCAGTAG 58.455 52.381 0.00 0.00 30.42 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.804712 TGCCAAAAGTTTATGTGCATTTTATG 58.195 30.769 0.00 0.00 0.00 1.90
15 16 5.609423 TCTTTGCCAAAAGTTTATGTGCAT 58.391 33.333 0.00 0.00 42.91 3.96
66 67 3.587797 TCTGATGTTCGTACCACTTCC 57.412 47.619 0.00 0.00 0.00 3.46
116 117 5.182760 ACAGAGAAACTTCATTTGGCTGATC 59.817 40.000 0.00 0.00 34.46 2.92
153 154 4.675303 CCTCCCCCTCCACCACCA 62.675 72.222 0.00 0.00 0.00 4.17
318 320 0.179073 ACTGTGACAGTTCGCAAGCT 60.179 50.000 13.33 0.00 42.59 3.74
319 321 1.457303 CTACTGTGACAGTTCGCAAGC 59.543 52.381 24.54 0.00 42.59 4.01
332 334 3.364889 TCAACCTCGTGAACTACTGTG 57.635 47.619 0.00 0.00 0.00 3.66
362 364 1.680860 CCCGATTTTACACCCAGGTCC 60.681 57.143 0.00 0.00 0.00 4.46
363 365 1.680860 CCCCGATTTTACACCCAGGTC 60.681 57.143 0.00 0.00 0.00 3.85
369 371 1.089112 CCGTTCCCCGATTTTACACC 58.911 55.000 0.00 0.00 39.56 4.16
429 431 0.843984 GGTATGCATACCCACCACCT 59.156 55.000 36.34 0.00 45.62 4.00
465 476 5.874810 TGAGAAGTGTGATTAACCATAGTGC 59.125 40.000 0.00 0.00 0.00 4.40
466 477 7.604164 ACTTGAGAAGTGTGATTAACCATAGTG 59.396 37.037 0.00 0.00 41.01 2.74
467 478 7.680730 ACTTGAGAAGTGTGATTAACCATAGT 58.319 34.615 0.00 0.00 41.01 2.12
468 479 9.653287 TTACTTGAGAAGTGTGATTAACCATAG 57.347 33.333 0.00 0.00 42.84 2.23
469 480 9.653287 CTTACTTGAGAAGTGTGATTAACCATA 57.347 33.333 0.00 0.00 42.84 2.74
470 481 8.375506 TCTTACTTGAGAAGTGTGATTAACCAT 58.624 33.333 0.00 0.00 42.84 3.55
471 482 7.732025 TCTTACTTGAGAAGTGTGATTAACCA 58.268 34.615 0.00 0.00 42.84 3.67
472 483 8.660373 CATCTTACTTGAGAAGTGTGATTAACC 58.340 37.037 0.00 0.00 42.84 2.85
526 538 6.047511 TCTTATCTGCAGAAGCTCTTTCTT 57.952 37.500 22.50 2.10 43.68 2.52
545 557 2.432444 CACGAGGCCAACCAATTCTTA 58.568 47.619 5.01 0.00 39.06 2.10
565 577 4.394920 TCTGCGATGTTTCATAGTTTTCCC 59.605 41.667 0.00 0.00 0.00 3.97
583 595 3.319405 ACTCCATACTCCATACTTCTGCG 59.681 47.826 0.00 0.00 0.00 5.18
651 677 6.240894 TCAATCTAGCAAACCACTTCTGAAT 58.759 36.000 0.00 0.00 0.00 2.57
655 681 7.373493 CAAAATCAATCTAGCAAACCACTTCT 58.627 34.615 0.00 0.00 0.00 2.85
679 705 9.658799 GCTTATATTATCCAATCAGAAGTAGCA 57.341 33.333 0.00 0.00 0.00 3.49
688 714 8.313292 GGCCAATTTGCTTATATTATCCAATCA 58.687 33.333 0.00 0.00 0.00 2.57
737 763 0.984995 GACCCTTCTACAGGCCTGTT 59.015 55.000 41.69 23.39 41.83 3.16
761 789 4.833390 AGCTCAATTTACCACTACTGGAC 58.167 43.478 0.00 0.00 40.55 4.02
787 816 8.239314 ACAAAATGCTTGTATGTATGAGAAGTG 58.761 33.333 0.00 0.00 0.00 3.16
800 829 4.363999 CCCGTTTCAACAAAATGCTTGTA 58.636 39.130 0.00 0.00 33.28 2.41
940 977 5.373812 TCTATTTTGAGGGAATCCTGGTC 57.626 43.478 0.00 0.00 45.05 4.02
941 978 5.796502 TTCTATTTTGAGGGAATCCTGGT 57.203 39.130 0.00 0.00 45.05 4.00
942 979 7.663493 GTCTATTCTATTTTGAGGGAATCCTGG 59.337 40.741 0.00 0.00 45.05 4.45
943 980 7.663493 GGTCTATTCTATTTTGAGGGAATCCTG 59.337 40.741 0.00 0.00 45.05 3.86
945 982 7.518188 TGGTCTATTCTATTTTGAGGGAATCC 58.482 38.462 0.00 0.00 31.89 3.01
946 983 7.663493 CCTGGTCTATTCTATTTTGAGGGAATC 59.337 40.741 0.00 0.00 31.89 2.52
947 984 7.129504 ACCTGGTCTATTCTATTTTGAGGGAAT 59.870 37.037 0.00 0.00 33.69 3.01
948 985 6.447084 ACCTGGTCTATTCTATTTTGAGGGAA 59.553 38.462 0.00 0.00 0.00 3.97
949 986 5.970640 ACCTGGTCTATTCTATTTTGAGGGA 59.029 40.000 0.00 0.00 0.00 4.20
950 987 6.126768 TGACCTGGTCTATTCTATTTTGAGGG 60.127 42.308 26.03 0.00 33.15 4.30
951 988 6.889198 TGACCTGGTCTATTCTATTTTGAGG 58.111 40.000 26.03 0.00 33.15 3.86
952 989 8.428063 AGATGACCTGGTCTATTCTATTTTGAG 58.572 37.037 26.03 0.00 33.15 3.02
953 990 8.324191 AGATGACCTGGTCTATTCTATTTTGA 57.676 34.615 26.03 2.90 33.15 2.69
954 991 8.970859 AAGATGACCTGGTCTATTCTATTTTG 57.029 34.615 26.03 0.00 33.15 2.44
956 993 8.652290 GGTAAGATGACCTGGTCTATTCTATTT 58.348 37.037 26.03 13.12 36.47 1.40
957 994 7.235812 GGGTAAGATGACCTGGTCTATTCTATT 59.764 40.741 26.03 13.68 39.66 1.73
958 995 6.726764 GGGTAAGATGACCTGGTCTATTCTAT 59.273 42.308 26.03 11.19 39.66 1.98
959 996 6.075984 GGGTAAGATGACCTGGTCTATTCTA 58.924 44.000 26.03 6.57 39.66 2.10
960 997 4.902448 GGGTAAGATGACCTGGTCTATTCT 59.098 45.833 26.03 20.60 39.66 2.40
961 998 4.902448 AGGGTAAGATGACCTGGTCTATTC 59.098 45.833 26.03 18.96 39.66 1.75
962 999 4.897051 AGGGTAAGATGACCTGGTCTATT 58.103 43.478 26.03 18.88 39.66 1.73
963 1000 4.561254 AGGGTAAGATGACCTGGTCTAT 57.439 45.455 26.03 17.53 39.66 1.98
964 1001 4.030913 CAAGGGTAAGATGACCTGGTCTA 58.969 47.826 26.03 13.79 39.66 2.59
1036 1073 6.358991 ACCCAGTAAAGCTTACAAGTAAACA 58.641 36.000 0.00 0.00 0.00 2.83
1076 1113 2.297701 GTTGAGAGAGTTGCCCAAACA 58.702 47.619 0.00 0.00 41.61 2.83
1119 1156 7.330208 TCAAACTTAAAGTATTAGTCTCCGTGC 59.670 37.037 0.00 0.00 0.00 5.34
1133 1170 5.382664 TGGGGAGACTTCAAACTTAAAGT 57.617 39.130 0.00 0.00 38.40 2.66
1134 1171 6.150140 CAGATGGGGAGACTTCAAACTTAAAG 59.850 42.308 0.00 0.00 0.00 1.85
1135 1172 6.003950 CAGATGGGGAGACTTCAAACTTAAA 58.996 40.000 0.00 0.00 0.00 1.52
1172 1209 5.727766 AGTGCCTGGTAGTAAGGGTATTTTA 59.272 40.000 0.00 0.00 35.17 1.52
1181 1636 9.490379 CCTTATATAAAAGTGCCTGGTAGTAAG 57.510 37.037 0.00 0.00 0.00 2.34
1185 1640 5.408604 CGCCTTATATAAAAGTGCCTGGTAG 59.591 44.000 0.00 0.00 0.00 3.18
1195 1650 3.880490 TGTGTGGGCGCCTTATATAAAAG 59.120 43.478 28.56 0.00 0.00 2.27
1337 2247 2.972713 AGTTTGACCAAGAGCTAGACCA 59.027 45.455 0.00 0.00 0.00 4.02
1352 2335 6.072008 CCCACACATTCATACATTCAGTTTGA 60.072 38.462 0.00 0.00 36.58 2.69
1353 2336 6.094719 CCCACACATTCATACATTCAGTTTG 58.905 40.000 0.00 0.00 0.00 2.93
1354 2337 5.774690 ACCCACACATTCATACATTCAGTTT 59.225 36.000 0.00 0.00 0.00 2.66
1355 2338 5.183713 CACCCACACATTCATACATTCAGTT 59.816 40.000 0.00 0.00 0.00 3.16
1356 2339 4.701651 CACCCACACATTCATACATTCAGT 59.298 41.667 0.00 0.00 0.00 3.41
1357 2340 4.439153 GCACCCACACATTCATACATTCAG 60.439 45.833 0.00 0.00 0.00 3.02
1358 2341 3.443329 GCACCCACACATTCATACATTCA 59.557 43.478 0.00 0.00 0.00 2.57
1359 2342 3.181487 GGCACCCACACATTCATACATTC 60.181 47.826 0.00 0.00 0.00 2.67
1365 2348 2.897271 TAAGGCACCCACACATTCAT 57.103 45.000 0.00 0.00 0.00 2.57
1394 2377 7.603024 ACCTTTGTATTTGTAGTACTCTTCTGC 59.397 37.037 0.00 0.00 0.00 4.26
1430 2413 1.793532 CTGAAGATGCGAGCTGCTATG 59.206 52.381 0.15 0.00 46.63 2.23
1461 2444 4.858935 TGAAGCTGTTGTCTGCAAAATAC 58.141 39.130 0.00 0.00 40.25 1.89
1472 2455 8.165239 TGTGTTATTAGAAATGAAGCTGTTGT 57.835 30.769 0.00 0.00 0.00 3.32
1520 2508 5.647658 TGAGTTATGACCACTTAAGCCATTG 59.352 40.000 1.29 0.00 0.00 2.82
1575 2746 6.429692 TGTTATCTCCATCGTTGTTGTTTCAT 59.570 34.615 0.00 0.00 0.00 2.57
1585 2756 7.348080 TCTTGAGTATGTTATCTCCATCGTT 57.652 36.000 0.00 0.00 0.00 3.85
1593 2764 7.301420 TCCTCCTCATCTTGAGTATGTTATCT 58.699 38.462 4.00 0.00 42.80 1.98
1716 2889 3.432749 GCATCAGGAGGAATTAGCTCACA 60.433 47.826 0.00 0.00 0.00 3.58
1767 2940 3.759086 ACTGATAGTCGAGAGAGCAAACA 59.241 43.478 0.00 0.00 43.49 2.83
1805 2978 0.463620 GCTGGTTTTGGCAGGTTCAA 59.536 50.000 0.00 0.00 0.00 2.69
1841 3019 9.244799 GAATTTCTGTCCTTCGTTATTGTTTTT 57.755 29.630 0.00 0.00 0.00 1.94
1842 3020 8.410141 TGAATTTCTGTCCTTCGTTATTGTTTT 58.590 29.630 0.00 0.00 0.00 2.43
1843 3021 7.860872 GTGAATTTCTGTCCTTCGTTATTGTTT 59.139 33.333 0.00 0.00 0.00 2.83
1844 3022 7.012894 TGTGAATTTCTGTCCTTCGTTATTGTT 59.987 33.333 0.00 0.00 0.00 2.83
1845 3023 6.485313 TGTGAATTTCTGTCCTTCGTTATTGT 59.515 34.615 0.00 0.00 0.00 2.71
1846 3024 6.898041 TGTGAATTTCTGTCCTTCGTTATTG 58.102 36.000 0.00 0.00 0.00 1.90
1847 3025 7.504924 TTGTGAATTTCTGTCCTTCGTTATT 57.495 32.000 0.00 0.00 0.00 1.40
1848 3026 7.504924 TTTGTGAATTTCTGTCCTTCGTTAT 57.495 32.000 0.00 0.00 0.00 1.89
1849 3027 6.928979 TTTGTGAATTTCTGTCCTTCGTTA 57.071 33.333 0.00 0.00 0.00 3.18
1850 3028 5.828299 TTTGTGAATTTCTGTCCTTCGTT 57.172 34.783 0.00 0.00 0.00 3.85
1851 3029 5.828299 TTTTGTGAATTTCTGTCCTTCGT 57.172 34.783 0.00 0.00 0.00 3.85
1902 3080 2.158957 TCTCTTTGTTCGAACTGCCTGT 60.159 45.455 27.32 0.00 0.00 4.00
1906 3084 4.474226 ACATTCTCTTTGTTCGAACTGC 57.526 40.909 27.32 3.51 0.00 4.40
1922 3100 7.602517 ACTCTGCTTGATTAGTTGTACATTC 57.397 36.000 0.00 0.00 0.00 2.67
1946 3124 4.469945 CAGGTTCCTTCCCTCAAGTACATA 59.530 45.833 0.00 0.00 0.00 2.29
1947 3125 3.264450 CAGGTTCCTTCCCTCAAGTACAT 59.736 47.826 0.00 0.00 0.00 2.29
2094 3325 3.196685 AGGTCTACTGAGATTTGTCTGCC 59.803 47.826 0.00 0.00 33.14 4.85


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

AutoCloner maintained by Alex Coulton.