Multiple sequence alignment - TraesCS3D01G065200

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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 TraesCS3D01G065200 chr3D 100.000 3287 0 0 1 3287 28596140 28592854 0.000000e+00 6071
1 TraesCS3D01G065200 chr3D 88.742 151 14 3 3121 3270 28869128 28868980 7.250000e-42 182
2 TraesCS3D01G065200 chr3D 86.228 167 19 4 3121 3286 28548914 28548751 9.370000e-41 178
3 TraesCS3D01G065200 chr6B 92.407 2621 138 24 688 3284 131689416 131691999 0.000000e+00 3681
4 TraesCS3D01G065200 chr6B 92.805 681 39 7 1 679 131688700 131689372 0.000000e+00 977
5 TraesCS3D01G065200 chr3A 85.848 749 67 23 1939 2672 38298455 38299179 0.000000e+00 760
6 TraesCS3D01G065200 chr3A 92.233 309 22 2 2981 3287 38299508 38299816 1.400000e-118 436
7 TraesCS3D01G065200 chr3A 95.516 223 6 2 2711 2929 38299284 38299506 1.450000e-93 353
8 TraesCS3D01G065200 chr3A 88.344 163 16 3 3121 3282 38282695 38282535 3.350000e-45 193
9 TraesCS3D01G065200 chr3B 88.424 311 33 3 595 904 49010591 49010283 4.010000e-99 372
10 TraesCS3D01G065200 chr3B 87.417 151 16 3 3121 3270 49151241 49151389 1.570000e-38 171


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 TraesCS3D01G065200 chr3D 28592854 28596140 3286 True 6071.000000 6071 100.000 1 3287 1 chr3D.!!$R2 3286
1 TraesCS3D01G065200 chr6B 131688700 131691999 3299 False 2329.000000 3681 92.606 1 3284 2 chr6B.!!$F1 3283
2 TraesCS3D01G065200 chr3A 38298455 38299816 1361 False 516.333333 760 91.199 1939 3287 3 chr3A.!!$F1 1348

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
37 38 0.320247 CTGAGTGGTCAGGTCAGTGC 60.320 60.0 0.00 0.0 45.85 4.40 F
921 959 0.455972 CCGGTATGGCGCAGTTTTTG 60.456 55.0 10.83 0.0 0.00 2.44 F
2151 2198 0.321996 GCTTGGTCTTCCGAAGAGGT 59.678 55.0 11.24 0.0 41.99 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1967 1.065564 AGAAGGACAGCTTCAGGATGC 60.066 52.381 0.0 0.0 34.20 3.91 R
2184 2231 0.836606 TGAGGAGCAACAGTTCACCA 59.163 50.000 0.0 0.0 0.00 4.17 R
2964 3123 0.327924 ACCAATGCCAGACGGAATGA 59.672 50.000 0.0 0.0 26.98 2.57 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
20 21 2.176546 CGGTGGCGTTGCAATCTG 59.823 61.111 0.59 0.00 0.00 2.90
36 37 2.301296 AATCTGAGTGGTCAGGTCAGTG 59.699 50.000 2.66 0.00 43.94 3.66
37 38 0.320247 CTGAGTGGTCAGGTCAGTGC 60.320 60.000 0.00 0.00 45.85 4.40
38 39 1.004440 GAGTGGTCAGGTCAGTGCC 60.004 63.158 0.00 0.00 0.00 5.01
60 61 4.291513 CCTTTCTCCTAAACCCCTAAACCT 59.708 45.833 0.00 0.00 0.00 3.50
207 209 4.828925 GAGCTGACTGGCGAGGGC 62.829 72.222 0.00 1.72 37.29 5.19
236 238 3.196685 AGGTAACAATCTGAGAGGTCAGC 59.803 47.826 0.00 0.00 45.12 4.26
268 270 2.375014 AACCCCTAAACCCTTGTGTG 57.625 50.000 0.00 0.00 0.00 3.82
294 296 1.550976 GACCTGAACTCCAATCGGACT 59.449 52.381 0.00 0.00 35.91 3.85
303 305 1.067846 TCCAATCGGACTCGTCAGTTG 60.068 52.381 0.00 3.41 35.91 3.16
361 363 3.019564 GTCCTGCTATGCTTGTTTCCAT 58.980 45.455 0.00 0.00 0.00 3.41
411 413 2.731572 AGTACCCGCTAGCTAACTGAA 58.268 47.619 13.93 0.00 0.00 3.02
413 415 1.558233 ACCCGCTAGCTAACTGAAGT 58.442 50.000 13.93 0.00 0.00 3.01
417 419 2.353803 CCGCTAGCTAACTGAAGTTGGT 60.354 50.000 13.93 4.72 38.55 3.67
433 435 3.689649 AGTTGGTCGTGCAAGGATATTTC 59.310 43.478 0.00 0.00 31.14 2.17
434 436 2.639065 TGGTCGTGCAAGGATATTTCC 58.361 47.619 0.00 0.00 42.96 3.13
435 437 1.947456 GGTCGTGCAAGGATATTTCCC 59.053 52.381 0.00 0.00 43.76 3.97
489 491 3.772387 TGGGGCTGTGATGTTTTGATTA 58.228 40.909 0.00 0.00 0.00 1.75
490 492 3.763360 TGGGGCTGTGATGTTTTGATTAG 59.237 43.478 0.00 0.00 0.00 1.73
491 493 3.763897 GGGGCTGTGATGTTTTGATTAGT 59.236 43.478 0.00 0.00 0.00 2.24
492 494 4.220602 GGGGCTGTGATGTTTTGATTAGTT 59.779 41.667 0.00 0.00 0.00 2.24
493 495 5.402398 GGGCTGTGATGTTTTGATTAGTTC 58.598 41.667 0.00 0.00 0.00 3.01
506 508 1.986698 TTAGTTCGTTCGCTGCTACC 58.013 50.000 0.00 0.00 0.00 3.18
507 509 1.171308 TAGTTCGTTCGCTGCTACCT 58.829 50.000 0.00 0.00 0.00 3.08
546 548 3.762823 TGTGTGCCAATTCATGCAGATTA 59.237 39.130 0.00 0.00 38.34 1.75
553 555 5.607477 CCAATTCATGCAGATTATTGCCTT 58.393 37.500 0.00 0.00 43.43 4.35
554 556 5.465390 CCAATTCATGCAGATTATTGCCTTG 59.535 40.000 0.00 0.00 43.43 3.61
571 573 4.156556 TGCCTTGTAGCTTAAGATTTGCTG 59.843 41.667 6.67 0.00 37.62 4.41
576 578 6.241207 TGTAGCTTAAGATTTGCTGTTCAC 57.759 37.500 6.67 0.00 37.62 3.18
594 596 5.127031 TGTTCACATAGTTCATCTCGGATCA 59.873 40.000 0.00 0.00 0.00 2.92
599 601 8.678199 TCACATAGTTCATCTCGGATCATATAC 58.322 37.037 0.00 0.00 0.00 1.47
606 608 4.436242 TCTCGGATCATATACGGAAAGC 57.564 45.455 0.00 0.00 37.17 3.51
635 637 5.128663 TGCTCTAGTACATCCTGTTTATGCA 59.871 40.000 0.00 0.00 0.00 3.96
639 641 7.620880 TCTAGTACATCCTGTTTATGCAAAGT 58.379 34.615 0.00 0.00 0.00 2.66
642 644 8.630054 AGTACATCCTGTTTATGCAAAGTTTA 57.370 30.769 0.00 0.00 0.00 2.01
644 646 6.389906 ACATCCTGTTTATGCAAAGTTTAGC 58.610 36.000 0.00 0.00 0.00 3.09
646 648 6.012658 TCCTGTTTATGCAAAGTTTAGCAG 57.987 37.500 14.88 5.81 44.94 4.24
649 651 5.782047 TGTTTATGCAAAGTTTAGCAGCAT 58.218 33.333 13.67 13.67 44.94 3.79
657 659 5.234972 GCAAAGTTTAGCAGCATCAAGTTTT 59.765 36.000 0.00 0.00 0.00 2.43
665 667 4.060205 GCAGCATCAAGTTTTTGTCCATT 58.940 39.130 0.00 0.00 35.73 3.16
668 670 5.178067 CAGCATCAAGTTTTTGTCCATTTCC 59.822 40.000 0.00 0.00 35.73 3.13
669 671 4.452114 GCATCAAGTTTTTGTCCATTTCCC 59.548 41.667 0.00 0.00 35.73 3.97
673 675 4.519540 AGTTTTTGTCCATTTCCCATCG 57.480 40.909 0.00 0.00 0.00 3.84
679 681 6.875948 TTTGTCCATTTCCCATCGTATATG 57.124 37.500 0.00 0.00 0.00 1.78
680 682 4.905429 TGTCCATTTCCCATCGTATATGG 58.095 43.478 0.00 0.00 38.88 2.74
682 684 5.072464 TGTCCATTTCCCATCGTATATGGAA 59.928 40.000 5.59 0.00 42.12 3.53
684 686 6.149474 GTCCATTTCCCATCGTATATGGAAAG 59.851 42.308 5.59 2.08 46.69 2.62
685 687 6.003950 CCATTTCCCATCGTATATGGAAAGT 58.996 40.000 5.59 0.00 46.69 2.66
687 689 7.014230 CCATTTCCCATCGTATATGGAAAGTTT 59.986 37.037 5.59 0.00 46.69 2.66
688 690 9.062524 CATTTCCCATCGTATATGGAAAGTTTA 57.937 33.333 5.59 0.00 46.69 2.01
689 691 9.807921 ATTTCCCATCGTATATGGAAAGTTTAT 57.192 29.630 5.59 0.00 46.69 1.40
705 743 8.677300 GGAAAGTTTATGATGCTATTCTGTTGA 58.323 33.333 0.00 0.00 0.00 3.18
732 770 9.599866 CATGTAGGAGTATTTGTGATCTTTACA 57.400 33.333 0.00 0.00 0.00 2.41
738 776 8.831550 GGAGTATTTGTGATCTTTACAATCCTC 58.168 37.037 0.00 3.00 37.81 3.71
740 778 9.388506 AGTATTTGTGATCTTTACAATCCTCTG 57.611 33.333 0.00 0.00 37.81 3.35
757 795 9.948964 CAATCCTCTGTATCCATCATAAATGTA 57.051 33.333 0.00 0.00 0.00 2.29
790 828 5.722021 AACAGGGCAATAAGTTTTGGTAG 57.278 39.130 0.00 0.00 0.00 3.18
906 944 8.392612 CGTTGTTATGATTTTAGATTTACCGGT 58.607 33.333 13.98 13.98 0.00 5.28
911 949 6.870971 TGATTTTAGATTTACCGGTATGGC 57.129 37.500 16.67 7.55 43.94 4.40
921 959 0.455972 CCGGTATGGCGCAGTTTTTG 60.456 55.000 10.83 0.00 0.00 2.44
933 971 5.688176 GGCGCAGTTTTTGAATGTTTTAGTA 59.312 36.000 10.83 0.00 0.00 1.82
934 972 6.364976 GGCGCAGTTTTTGAATGTTTTAGTAT 59.635 34.615 10.83 0.00 0.00 2.12
935 973 7.095816 GGCGCAGTTTTTGAATGTTTTAGTATT 60.096 33.333 10.83 0.00 0.00 1.89
936 974 7.735586 GCGCAGTTTTTGAATGTTTTAGTATTG 59.264 33.333 0.30 0.00 0.00 1.90
976 1014 7.408756 TGCAGCATTAGATGTTCCTAAATTT 57.591 32.000 0.00 0.00 32.95 1.82
978 1016 8.965819 TGCAGCATTAGATGTTCCTAAATTTTA 58.034 29.630 0.00 0.00 32.95 1.52
1020 1058 1.191535 TGGCTGATGCTAGTTACCGT 58.808 50.000 0.00 0.00 39.59 4.83
1022 1060 1.136305 GGCTGATGCTAGTTACCGTCA 59.864 52.381 0.00 0.00 39.59 4.35
1051 1089 1.432270 GGATGCAGCTAAGTGTCGCC 61.432 60.000 0.22 0.00 0.00 5.54
1055 1093 1.066502 TGCAGCTAAGTGTCGCCATTA 60.067 47.619 0.00 0.00 0.00 1.90
1062 1100 4.752101 GCTAAGTGTCGCCATTATGAGAAT 59.248 41.667 0.00 0.00 0.00 2.40
1065 1103 4.632153 AGTGTCGCCATTATGAGAATACC 58.368 43.478 0.00 0.00 0.00 2.73
1083 1121 6.591834 AGAATACCGTCATTTCTCAAACTGAG 59.408 38.462 0.00 0.00 45.59 3.35
1085 1123 2.160417 CCGTCATTTCTCAAACTGAGGC 59.840 50.000 3.92 0.00 44.39 4.70
1098 1136 1.167851 CTGAGGCCATTTTTCGCAGA 58.832 50.000 5.01 0.00 31.53 4.26
1102 1140 1.531739 GGCCATTTTTCGCAGACCCA 61.532 55.000 0.00 0.00 34.32 4.51
1113 1151 1.838112 GCAGACCCATCAACATCCAA 58.162 50.000 0.00 0.00 0.00 3.53
1240 1278 6.231211 TCTTTTATGTCAGTTCCTGGAGTTC 58.769 40.000 0.00 0.00 31.51 3.01
1266 1304 3.106827 TGATGGCAGACCTGTTCAGATA 58.893 45.455 1.00 0.00 36.63 1.98
1308 1346 9.436957 AGTTACATCGTATGTTTTCTCAAATCT 57.563 29.630 5.94 0.00 41.63 2.40
1452 1490 7.888021 ACAATGGATATGTTGTGGAGTTTCTTA 59.112 33.333 0.00 0.00 37.19 2.10
1482 1520 8.193953 AGAATCAAAGAATTATGTTGTTGGGT 57.806 30.769 0.00 0.00 0.00 4.51
1484 1522 8.606040 AATCAAAGAATTATGTTGTTGGGTTG 57.394 30.769 0.00 0.00 0.00 3.77
1535 1573 1.623311 GCTGCCCCTTGGTTTGTATTT 59.377 47.619 0.00 0.00 0.00 1.40
1536 1574 2.612721 GCTGCCCCTTGGTTTGTATTTG 60.613 50.000 0.00 0.00 0.00 2.32
1538 1576 3.515104 CTGCCCCTTGGTTTGTATTTGAT 59.485 43.478 0.00 0.00 0.00 2.57
1540 1578 4.464597 TGCCCCTTGGTTTGTATTTGATAC 59.535 41.667 0.00 0.00 36.29 2.24
1555 1593 8.536175 TGTATTTGATACAGTGACATTACCTCA 58.464 33.333 0.00 0.00 40.60 3.86
1556 1594 9.378551 GTATTTGATACAGTGACATTACCTCAA 57.621 33.333 0.00 0.00 35.81 3.02
1566 1604 5.749109 GTGACATTACCTCAATACTTCGGAG 59.251 44.000 0.00 0.00 0.00 4.63
1582 1620 4.149511 TCGGAGAATGCATACCAATCAA 57.850 40.909 0.00 0.00 0.00 2.57
1600 1638 4.737855 TCAACTATCCCTTGAGCTACAC 57.262 45.455 0.00 0.00 0.00 2.90
1719 1757 6.056428 AGTGATTAGCGAAACGAAACTTTT 57.944 33.333 0.00 0.00 0.00 2.27
1797 1835 6.069440 TGGACTTCTTTTCCACATATCTGGAT 60.069 38.462 0.00 0.00 40.18 3.41
1914 1952 2.093235 GTGGGCTAGAGACAATGCTCTT 60.093 50.000 11.26 0.00 42.41 2.85
1919 1957 5.363939 GGCTAGAGACAATGCTCTTAATGT 58.636 41.667 11.26 0.00 42.41 2.71
1929 1967 4.707030 TGCTCTTAATGTCAATTGGCAG 57.293 40.909 18.95 4.78 30.80 4.85
1930 1968 3.119388 TGCTCTTAATGTCAATTGGCAGC 60.119 43.478 18.95 14.81 30.80 5.25
1935 1973 2.154567 ATGTCAATTGGCAGCATCCT 57.845 45.000 18.95 0.00 30.80 3.24
1936 1974 1.179152 TGTCAATTGGCAGCATCCTG 58.821 50.000 9.09 0.00 42.13 3.86
1977 2015 5.762218 ACTACTGCATGATTATTCCAAGCTC 59.238 40.000 0.00 0.00 0.00 4.09
1980 2018 3.317149 TGCATGATTATTCCAAGCTCTGC 59.683 43.478 0.00 0.00 0.00 4.26
2094 2132 4.381612 CGTACCCTGTCTGATGCTAAGAAA 60.382 45.833 0.00 0.00 0.00 2.52
2097 2135 3.944015 CCCTGTCTGATGCTAAGAAAAGG 59.056 47.826 0.00 0.00 32.89 3.11
2105 2143 1.271926 TGCTAAGAAAAGGTGGGAGCC 60.272 52.381 0.00 0.00 0.00 4.70
2124 2162 3.770263 CCATATGAGGCCAAATATGCG 57.230 47.619 23.09 15.98 36.05 4.73
2151 2198 0.321996 GCTTGGTCTTCCGAAGAGGT 59.678 55.000 11.24 0.00 41.99 3.85
2156 2203 1.134670 GGTCTTCCGAAGAGGTGATGG 60.135 57.143 11.24 0.00 41.99 3.51
2184 2231 7.595488 AGATTATATTGGAATCTTTGGTGGGT 58.405 34.615 0.00 0.00 40.04 4.51
2199 2246 0.465460 TGGGTGGTGAACTGTTGCTC 60.465 55.000 0.00 0.00 0.00 4.26
2223 2270 8.918202 TCCTCAATTACAATTACAAGTTCTGT 57.082 30.769 0.00 0.00 42.47 3.41
2260 2307 3.873952 GAGACAAGCAGGTTATGATGGTC 59.126 47.826 0.00 0.00 46.80 4.02
2278 2325 4.219115 TGGTCAATGGTTTGAAAGGCTTA 58.781 39.130 0.00 0.00 43.29 3.09
2279 2326 4.280677 TGGTCAATGGTTTGAAAGGCTTAG 59.719 41.667 0.00 0.00 43.29 2.18
2640 2720 8.432110 AAACATTTGGATTTGTGGAAAACTAC 57.568 30.769 0.00 0.00 0.00 2.73
2641 2721 7.360113 ACATTTGGATTTGTGGAAAACTACT 57.640 32.000 0.00 0.00 0.00 2.57
2688 2768 5.384063 TTTCTTTTTCACTGTGCTGTTGA 57.616 34.783 2.12 0.00 0.00 3.18
2693 2773 2.988010 TCACTGTGCTGTTGAGACTT 57.012 45.000 2.12 0.00 0.00 3.01
2843 2999 6.178507 CGTGTATGAAGCATAACTTTCTTCG 58.821 40.000 0.00 0.00 39.29 3.79
2963 3122 1.743958 GCTTGGTGAGAGACGTAGCTA 59.256 52.381 0.00 0.00 31.97 3.32
2964 3123 2.359531 GCTTGGTGAGAGACGTAGCTAT 59.640 50.000 0.00 0.00 31.97 2.97
2965 3124 3.549221 GCTTGGTGAGAGACGTAGCTATC 60.549 52.174 0.00 0.00 31.97 2.08
2966 3125 3.277142 TGGTGAGAGACGTAGCTATCA 57.723 47.619 0.00 0.00 34.06 2.15
2967 3126 3.821748 TGGTGAGAGACGTAGCTATCAT 58.178 45.455 5.07 0.00 38.27 2.45
2969 3128 4.276183 TGGTGAGAGACGTAGCTATCATTC 59.724 45.833 5.07 2.84 38.27 2.67
2971 3130 3.498777 TGAGAGACGTAGCTATCATTCCG 59.501 47.826 0.00 0.00 31.71 4.30
2972 3131 3.478509 AGAGACGTAGCTATCATTCCGT 58.521 45.455 4.69 4.69 0.00 4.69
2973 3132 3.499157 AGAGACGTAGCTATCATTCCGTC 59.501 47.826 19.13 19.13 43.52 4.79
2974 3133 3.900388 GACGTAGCTATCATTCCGTCT 57.100 47.619 19.35 0.00 40.91 4.18
2975 3134 3.556513 GACGTAGCTATCATTCCGTCTG 58.443 50.000 19.35 0.00 40.91 3.51
2976 3135 2.293677 ACGTAGCTATCATTCCGTCTGG 59.706 50.000 0.00 0.00 0.00 3.86
2977 3136 2.678324 GTAGCTATCATTCCGTCTGGC 58.322 52.381 0.00 0.00 34.14 4.85
2978 3137 1.123077 AGCTATCATTCCGTCTGGCA 58.877 50.000 0.00 0.00 34.14 4.92
2979 3138 1.696336 AGCTATCATTCCGTCTGGCAT 59.304 47.619 0.00 0.00 34.14 4.40
2980 3139 2.105477 AGCTATCATTCCGTCTGGCATT 59.895 45.455 0.00 0.00 34.14 3.56
2981 3140 2.225019 GCTATCATTCCGTCTGGCATTG 59.775 50.000 0.00 0.00 34.14 2.82
2982 3141 1.683943 ATCATTCCGTCTGGCATTGG 58.316 50.000 0.00 0.00 34.14 3.16
3068 3227 6.373495 ACAGAAAGTTTCGGTTCAGTTTACTT 59.627 34.615 14.64 0.00 34.38 2.24
3076 3235 8.981647 GTTTCGGTTCAGTTTACTTACAAGATA 58.018 33.333 0.00 0.00 0.00 1.98
3183 3342 2.164422 GCAAAACAGATGCCTAGAACCC 59.836 50.000 0.00 0.00 37.85 4.11
3187 3346 1.051812 CAGATGCCTAGAACCCGGAT 58.948 55.000 0.73 0.00 0.00 4.18
3229 3388 0.239347 CTCCCAACGCAAAAGCTCAG 59.761 55.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.421268 ACCTGACCACTCAGATTGCAA 59.579 47.619 0.00 0.00 46.32 4.08
12 13 1.002430 GACCTGACCACTCAGATTGCA 59.998 52.381 0.00 0.00 46.32 4.08
20 21 1.004440 GGCACTGACCTGACCACTC 60.004 63.158 0.00 0.00 0.00 3.51
36 37 4.015084 GTTTAGGGGTTTAGGAGAAAGGC 58.985 47.826 0.00 0.00 0.00 4.35
37 38 4.291513 AGGTTTAGGGGTTTAGGAGAAAGG 59.708 45.833 0.00 0.00 0.00 3.11
38 39 5.013808 TGAGGTTTAGGGGTTTAGGAGAAAG 59.986 44.000 0.00 0.00 0.00 2.62
155 157 4.724602 GTCTCGCAGTCGCAGCCA 62.725 66.667 0.00 0.00 38.40 4.75
157 159 3.474034 GTGTCTCGCAGTCGCAGC 61.474 66.667 0.00 0.00 38.40 5.25
163 165 1.951130 CGCAGTTGTGTCTCGCAGT 60.951 57.895 0.00 0.00 0.00 4.40
207 209 1.207089 TCAGATTGTTACCTCAGGCCG 59.793 52.381 0.00 0.00 0.00 6.13
236 238 6.268158 GGGTTTAGGGGTTATAGAAGAGAGAG 59.732 46.154 0.00 0.00 0.00 3.20
268 270 0.395312 TTGGAGTTCAGGTCGGGAAC 59.605 55.000 0.00 0.00 43.82 3.62
294 296 0.251653 AGGTAGGAGCCAACTGACGA 60.252 55.000 0.00 0.00 0.00 4.20
303 305 4.065789 CGATTGGATTTTAGGTAGGAGCC 58.934 47.826 0.00 0.00 0.00 4.70
411 413 3.350219 AATATCCTTGCACGACCAACT 57.650 42.857 0.00 0.00 0.00 3.16
413 415 3.013921 GGAAATATCCTTGCACGACCAA 58.986 45.455 0.00 0.00 42.93 3.67
417 419 2.917933 CAGGGAAATATCCTTGCACGA 58.082 47.619 0.00 0.00 44.74 4.35
435 437 4.861102 AAAGCCCTGAACTTCAAATCAG 57.139 40.909 0.00 0.00 42.15 2.90
489 491 0.388649 CAGGTAGCAGCGAACGAACT 60.389 55.000 0.00 0.00 0.00 3.01
490 492 0.666577 ACAGGTAGCAGCGAACGAAC 60.667 55.000 0.00 0.00 0.00 3.95
491 493 0.032952 AACAGGTAGCAGCGAACGAA 59.967 50.000 0.00 0.00 0.00 3.85
492 494 0.032952 AAACAGGTAGCAGCGAACGA 59.967 50.000 0.00 0.00 0.00 3.85
493 495 1.705256 TAAACAGGTAGCAGCGAACG 58.295 50.000 0.00 0.00 0.00 3.95
506 508 5.556758 GCACACACATTGCATGTTTAAACAG 60.557 40.000 24.22 17.02 42.70 3.16
507 509 4.269603 GCACACACATTGCATGTTTAAACA 59.730 37.500 22.58 22.58 42.70 2.83
546 548 5.420104 AGCAAATCTTAAGCTACAAGGCAAT 59.580 36.000 0.00 0.00 36.73 3.56
553 555 5.762711 TGTGAACAGCAAATCTTAAGCTACA 59.237 36.000 0.00 0.00 36.73 2.74
554 556 6.241207 TGTGAACAGCAAATCTTAAGCTAC 57.759 37.500 0.00 0.00 36.73 3.58
571 573 5.592054 TGATCCGAGATGAACTATGTGAAC 58.408 41.667 0.00 0.00 0.00 3.18
576 578 7.012421 TCCGTATATGATCCGAGATGAACTATG 59.988 40.741 0.00 0.00 0.00 2.23
606 608 3.651206 CAGGATGTACTAGAGCATGCAG 58.349 50.000 21.98 11.36 36.17 4.41
635 637 6.818142 ACAAAAACTTGATGCTGCTAAACTTT 59.182 30.769 0.00 0.00 0.00 2.66
639 641 5.163468 TGGACAAAAACTTGATGCTGCTAAA 60.163 36.000 0.00 0.00 0.00 1.85
642 644 2.694628 TGGACAAAAACTTGATGCTGCT 59.305 40.909 0.00 0.00 0.00 4.24
644 646 5.178067 GGAAATGGACAAAAACTTGATGCTG 59.822 40.000 0.00 0.00 0.00 4.41
646 648 4.452114 GGGAAATGGACAAAAACTTGATGC 59.548 41.667 0.00 0.00 0.00 3.91
649 651 5.508825 CGATGGGAAATGGACAAAAACTTGA 60.509 40.000 0.00 0.00 0.00 3.02
657 659 5.072464 TCCATATACGATGGGAAATGGACAA 59.928 40.000 3.81 0.00 38.31 3.18
665 667 8.433599 TCATAAACTTTCCATATACGATGGGAA 58.566 33.333 3.81 0.65 39.60 3.97
668 670 8.177663 GCATCATAAACTTTCCATATACGATGG 58.822 37.037 0.00 0.00 40.48 3.51
669 671 8.939929 AGCATCATAAACTTTCCATATACGATG 58.060 33.333 0.00 0.00 0.00 3.84
679 681 8.677300 TCAACAGAATAGCATCATAAACTTTCC 58.323 33.333 0.00 0.00 0.00 3.13
680 682 9.495754 GTCAACAGAATAGCATCATAAACTTTC 57.504 33.333 0.00 0.00 0.00 2.62
682 684 8.565896 TGTCAACAGAATAGCATCATAAACTT 57.434 30.769 0.00 0.00 0.00 2.66
684 686 8.400947 ACATGTCAACAGAATAGCATCATAAAC 58.599 33.333 0.00 0.00 0.00 2.01
685 687 8.510243 ACATGTCAACAGAATAGCATCATAAA 57.490 30.769 0.00 0.00 0.00 1.40
687 689 7.874528 CCTACATGTCAACAGAATAGCATCATA 59.125 37.037 0.00 0.00 0.00 2.15
688 690 6.709397 CCTACATGTCAACAGAATAGCATCAT 59.291 38.462 0.00 0.00 0.00 2.45
689 691 6.051074 CCTACATGTCAACAGAATAGCATCA 58.949 40.000 0.00 0.00 0.00 3.07
697 735 7.387673 CACAAATACTCCTACATGTCAACAGAA 59.612 37.037 0.00 0.00 0.00 3.02
705 743 9.601217 GTAAAGATCACAAATACTCCTACATGT 57.399 33.333 2.69 2.69 0.00 3.21
757 795 6.948309 ACTTATTGCCCTGTTTCATAGTTTCT 59.052 34.615 0.00 0.00 0.00 2.52
811 849 4.639334 AGCGCTTCATTCACAGATATCAT 58.361 39.130 2.64 0.00 0.00 2.45
854 892 5.711976 ACACAAAAGGCTATAATGCAAGACT 59.288 36.000 0.00 0.00 30.16 3.24
867 905 0.530288 AACAACGCACACAAAAGGCT 59.470 45.000 0.00 0.00 0.00 4.58
906 944 3.932545 ACATTCAAAAACTGCGCCATA 57.067 38.095 4.18 0.00 0.00 2.74
911 949 8.963130 TCAATACTAAAACATTCAAAAACTGCG 58.037 29.630 0.00 0.00 0.00 5.18
933 971 5.522460 GCTGCATTGCAAGTAATCAATCAAT 59.478 36.000 13.18 0.00 38.41 2.57
934 972 4.865925 GCTGCATTGCAAGTAATCAATCAA 59.134 37.500 13.18 0.00 38.41 2.57
935 973 4.082136 TGCTGCATTGCAAGTAATCAATCA 60.082 37.500 13.18 0.00 40.29 2.57
936 974 4.426416 TGCTGCATTGCAAGTAATCAATC 58.574 39.130 13.18 0.00 40.29 2.67
976 1014 8.896744 CATCTTCAACCTGCAATAAGAGAATAA 58.103 33.333 0.00 0.00 30.30 1.40
978 1016 6.320672 CCATCTTCAACCTGCAATAAGAGAAT 59.679 38.462 0.00 0.00 30.30 2.40
998 1036 2.036475 CGGTAACTAGCATCAGCCATCT 59.964 50.000 0.00 0.00 43.56 2.90
999 1037 2.224066 ACGGTAACTAGCATCAGCCATC 60.224 50.000 0.00 0.00 43.56 3.51
1020 1058 4.301505 GCATCCCGCAGTCTTTGA 57.698 55.556 0.00 0.00 41.79 2.69
1083 1121 1.215382 GGGTCTGCGAAAAATGGCC 59.785 57.895 0.00 0.00 0.00 5.36
1085 1123 1.818060 TGATGGGTCTGCGAAAAATGG 59.182 47.619 0.00 0.00 0.00 3.16
1098 1136 1.203162 TGCCTTTGGATGTTGATGGGT 60.203 47.619 0.00 0.00 0.00 4.51
1102 1140 2.173519 CAGGTGCCTTTGGATGTTGAT 58.826 47.619 0.00 0.00 0.00 2.57
1113 1151 2.683211 AAAGGTCATTCAGGTGCCTT 57.317 45.000 0.00 0.00 37.27 4.35
1240 1278 5.011431 TCTGAACAGGTCTGCCATCATATAG 59.989 44.000 1.93 0.00 37.19 1.31
1266 1304 2.683933 CTAGGGGCCGTGACTGGT 60.684 66.667 9.43 0.00 0.00 4.00
1335 1373 3.312421 ACAACACATCACAGTTGCTACAC 59.688 43.478 0.13 0.00 46.79 2.90
1390 1428 4.724279 ATGGTGTGGTAAGTCTTTTCCT 57.276 40.909 0.00 0.00 0.00 3.36
1395 1433 4.431416 TGACAATGGTGTGGTAAGTCTT 57.569 40.909 0.00 0.00 38.41 3.01
1466 1504 6.575162 ACTCTCAACCCAACAACATAATTC 57.425 37.500 0.00 0.00 0.00 2.17
1473 1511 4.809426 CCGATATACTCTCAACCCAACAAC 59.191 45.833 0.00 0.00 0.00 3.32
1482 1520 9.481340 CTGATTTTCAATCCGATATACTCTCAA 57.519 33.333 0.00 0.00 0.00 3.02
1484 1522 9.352784 CTCTGATTTTCAATCCGATATACTCTC 57.647 37.037 0.00 0.00 0.00 3.20
1535 1573 8.306313 AGTATTGAGGTAATGTCACTGTATCA 57.694 34.615 0.00 0.00 0.00 2.15
1536 1574 9.250624 GAAGTATTGAGGTAATGTCACTGTATC 57.749 37.037 0.00 0.00 0.00 2.24
1538 1576 7.255569 CGAAGTATTGAGGTAATGTCACTGTA 58.744 38.462 0.00 0.00 0.00 2.74
1540 1578 5.520288 CCGAAGTATTGAGGTAATGTCACTG 59.480 44.000 0.00 0.00 0.00 3.66
1555 1593 5.290493 TGGTATGCATTCTCCGAAGTATT 57.710 39.130 3.54 0.00 0.00 1.89
1556 1594 4.955811 TGGTATGCATTCTCCGAAGTAT 57.044 40.909 3.54 0.00 0.00 2.12
1566 1604 6.006449 AGGGATAGTTGATTGGTATGCATTC 58.994 40.000 3.54 0.00 0.00 2.67
1582 1620 5.900123 ACATTAGTGTAGCTCAAGGGATAGT 59.100 40.000 0.00 0.00 36.63 2.12
1733 1771 2.093447 CCAGCTCCGAATAAGACCAAGT 60.093 50.000 0.00 0.00 0.00 3.16
1766 1804 3.228188 TGGAAAAGAAGTCCACTGCAT 57.772 42.857 0.00 0.00 40.33 3.96
1797 1835 3.701542 CTGTAGACTGCTGGTGAGGATTA 59.298 47.826 0.00 0.00 0.00 1.75
1914 1952 3.382227 CAGGATGCTGCCAATTGACATTA 59.618 43.478 7.12 0.00 0.00 1.90
1919 1957 2.097036 CTTCAGGATGCTGCCAATTGA 58.903 47.619 9.76 0.00 34.76 2.57
1929 1967 1.065564 AGAAGGACAGCTTCAGGATGC 60.066 52.381 0.00 0.00 34.20 3.91
1930 1968 2.738000 CGAGAAGGACAGCTTCAGGATG 60.738 54.545 0.00 0.00 37.36 3.51
1935 1973 1.964223 AGTTCGAGAAGGACAGCTTCA 59.036 47.619 0.00 0.00 33.57 3.02
1936 1974 2.734276 AGTTCGAGAAGGACAGCTTC 57.266 50.000 0.00 0.00 0.00 3.86
1944 1982 3.510388 TCATGCAGTAGTTCGAGAAGG 57.490 47.619 0.00 0.00 0.00 3.46
1998 2036 6.146760 AGGGATCTCAACATAATACTGGAGT 58.853 40.000 0.00 0.00 0.00 3.85
1999 2037 6.678568 AGGGATCTCAACATAATACTGGAG 57.321 41.667 0.00 0.00 0.00 3.86
2000 2038 7.451731 AAAGGGATCTCAACATAATACTGGA 57.548 36.000 0.00 0.00 0.00 3.86
2001 2039 7.995488 AGAAAAGGGATCTCAACATAATACTGG 59.005 37.037 0.00 0.00 0.00 4.00
2094 2132 1.143813 CCTCATATGGCTCCCACCTT 58.856 55.000 2.13 0.00 35.80 3.50
2105 2143 4.005650 ACTCGCATATTTGGCCTCATATG 58.994 43.478 21.70 21.70 36.71 1.78
2124 2162 0.957888 GGAAGACCAAGCCAGCACTC 60.958 60.000 0.00 0.00 35.97 3.51
2151 2198 8.945195 AAGATTCCAATATAATCTTGCCATCA 57.055 30.769 10.01 0.00 46.71 3.07
2184 2231 0.836606 TGAGGAGCAACAGTTCACCA 59.163 50.000 0.00 0.00 0.00 4.17
2223 2270 5.046376 TGCTTGTCTCATCTGAATCCTTGTA 60.046 40.000 0.00 0.00 0.00 2.41
2260 2307 4.255833 TGCTAAGCCTTTCAAACCATTG 57.744 40.909 0.00 0.00 37.92 2.82
2639 2719 2.754867 GCTCTAGTCCTAGCCCATGAGT 60.755 54.545 0.00 0.00 33.32 3.41
2640 2720 1.892474 GCTCTAGTCCTAGCCCATGAG 59.108 57.143 0.00 0.00 33.32 2.90
2641 2721 1.217942 TGCTCTAGTCCTAGCCCATGA 59.782 52.381 0.00 0.00 37.97 3.07
2693 2773 6.483640 GTCCTCAGAGAGCTAAGAAACAAAAA 59.516 38.462 0.00 0.00 0.00 1.94
2843 2999 7.520451 AGTAAACCCCAAAGATAAAACTGAC 57.480 36.000 0.00 0.00 0.00 3.51
2932 3091 6.529477 CGTCTCTCACCAAGCATATATACATG 59.471 42.308 0.00 0.00 0.00 3.21
2936 3095 6.127980 GCTACGTCTCTCACCAAGCATATATA 60.128 42.308 0.00 0.00 32.01 0.86
2939 3098 3.243569 GCTACGTCTCTCACCAAGCATAT 60.244 47.826 0.00 0.00 32.01 1.78
2963 3122 1.064463 ACCAATGCCAGACGGAATGAT 60.064 47.619 0.00 0.00 26.98 2.45
2964 3123 0.327924 ACCAATGCCAGACGGAATGA 59.672 50.000 0.00 0.00 26.98 2.57
2965 3124 0.452987 CACCAATGCCAGACGGAATG 59.547 55.000 0.00 0.00 26.98 2.67
2966 3125 0.680921 CCACCAATGCCAGACGGAAT 60.681 55.000 0.00 0.00 27.70 3.01
2967 3126 1.303236 CCACCAATGCCAGACGGAA 60.303 57.895 0.00 0.00 0.00 4.30
2969 3128 1.024579 GTACCACCAATGCCAGACGG 61.025 60.000 0.00 0.00 0.00 4.79
2971 3130 1.271379 ACAGTACCACCAATGCCAGAC 60.271 52.381 0.00 0.00 0.00 3.51
2972 3131 1.003118 GACAGTACCACCAATGCCAGA 59.997 52.381 0.00 0.00 0.00 3.86
2973 3132 1.003580 AGACAGTACCACCAATGCCAG 59.996 52.381 0.00 0.00 0.00 4.85
2974 3133 1.064003 AGACAGTACCACCAATGCCA 58.936 50.000 0.00 0.00 0.00 4.92
2975 3134 1.453155 CAGACAGTACCACCAATGCC 58.547 55.000 0.00 0.00 0.00 4.40
2976 3135 1.453155 CCAGACAGTACCACCAATGC 58.547 55.000 0.00 0.00 0.00 3.56
2977 3136 1.003580 AGCCAGACAGTACCACCAATG 59.996 52.381 0.00 0.00 0.00 2.82
2978 3137 1.362224 AGCCAGACAGTACCACCAAT 58.638 50.000 0.00 0.00 0.00 3.16
2979 3138 2.018355 TAGCCAGACAGTACCACCAA 57.982 50.000 0.00 0.00 0.00 3.67
2980 3139 1.831106 CATAGCCAGACAGTACCACCA 59.169 52.381 0.00 0.00 0.00 4.17
2981 3140 1.831736 ACATAGCCAGACAGTACCACC 59.168 52.381 0.00 0.00 0.00 4.61
2982 3141 3.611766 AACATAGCCAGACAGTACCAC 57.388 47.619 0.00 0.00 0.00 4.16
3068 3227 9.109393 GAGAAACCATGCATTTACTATCTTGTA 57.891 33.333 0.00 0.00 0.00 2.41
3076 3235 6.435277 ACTTCATGAGAAACCATGCATTTACT 59.565 34.615 0.00 0.00 42.63 2.24
3128 3287 9.520204 GTGATTGAAAATACATGTGGAAATAGG 57.480 33.333 9.11 0.00 0.00 2.57
3150 3309 1.884579 CTGTTTTGCTGCCTCTGTGAT 59.115 47.619 0.00 0.00 0.00 3.06
3176 3335 2.840640 TTCTCCTGATCCGGGTTCTA 57.159 50.000 0.00 0.00 0.00 2.10
3183 3342 4.280425 TCTTCATCTCATTCTCCTGATCCG 59.720 45.833 0.00 0.00 0.00 4.18
3187 3346 6.159299 GATGTCTTCATCTCATTCTCCTGA 57.841 41.667 1.58 0.00 44.86 3.86
3229 3388 2.047179 GGAACACACCTCTCCGGC 60.047 66.667 0.00 0.00 35.61 6.13
3239 3398 1.484653 CGTGGATATCCTGGGAACACA 59.515 52.381 22.35 0.00 36.82 3.72
3240 3399 1.810412 GCGTGGATATCCTGGGAACAC 60.810 57.143 22.35 9.38 36.82 3.32


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

AutoCloner maintained by Alex Coulton.