Multiple sequence alignment - TraesCS3A01G247200

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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 TraesCS3A01G247200 chr3A 100.000 5140 0 0 1 5140 465224412 465229551 0.000000e+00 9492.0
1 TraesCS3A01G247200 chr3B 91.829 3439 146 52 1 3381 438383231 438379870 0.000000e+00 4669.0
2 TraesCS3A01G247200 chr3B 93.683 1124 43 16 3438 4547 438379830 438378721 0.000000e+00 1657.0
3 TraesCS3A01G247200 chr3B 89.917 605 46 10 4542 5140 438378451 438377856 0.000000e+00 765.0
4 TraesCS3A01G247200 chr3D 93.357 2785 83 36 206 2934 339477382 339474644 0.000000e+00 4024.0
5 TraesCS3A01G247200 chr3D 92.910 2172 90 34 2998 5140 339474635 339472499 0.000000e+00 3099.0
6 TraesCS3A01G247200 chr3D 91.795 195 12 2 1 192 339477780 339477587 8.480000e-68 268.0
7 TraesCS3A01G247200 chr3D 82.353 85 13 2 16 98 384637561 384637645 7.140000e-09 73.1
8 TraesCS3A01G247200 chr1B 87.054 224 26 3 1345 1566 652782336 652782558 3.070000e-62 250.0
9 TraesCS3A01G247200 chr1D 86.607 224 27 3 1345 1566 470220191 470220413 1.430000e-60 244.0
10 TraesCS3A01G247200 chr1A 86.607 224 27 3 1345 1566 563819050 563819272 1.430000e-60 244.0
11 TraesCS3A01G247200 chr2D 79.429 175 32 4 1355 1527 52227343 52227515 2.510000e-23 121.0
12 TraesCS3A01G247200 chr2B 78.857 175 33 4 1355 1527 81755685 81755857 1.170000e-21 115.0
13 TraesCS3A01G247200 chr2A 78.857 175 33 4 1355 1527 53782753 53782925 1.170000e-21 115.0
14 TraesCS3A01G247200 chr4D 78.395 162 31 4 1355 1514 306795500 306795659 9.110000e-18 102.0
15 TraesCS3A01G247200 chr7D 85.263 95 12 2 11 104 553846876 553846783 4.240000e-16 97.1
16 TraesCS3A01G247200 chr5D 89.231 65 6 1 15 78 402191715 402191779 4.270000e-11 80.5


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 TraesCS3A01G247200 chr3A 465224412 465229551 5139 False 9492.000000 9492 100.000000 1 5140 1 chr3A.!!$F1 5139
1 TraesCS3A01G247200 chr3B 438377856 438383231 5375 True 2363.666667 4669 91.809667 1 5140 3 chr3B.!!$R1 5139
2 TraesCS3A01G247200 chr3D 339472499 339477780 5281 True 2463.666667 4024 92.687333 1 5140 3 chr3D.!!$R1 5139

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
970 1228 0.032678 CGGGGAGGAACATCAGATCG 59.967 60.0 0.00 0.0 0.0 3.69 F
975 1233 0.103208 AGGAACATCAGATCGTCGCC 59.897 55.0 0.00 0.0 0.0 5.54 F
2542 2812 0.173708 CTTCACGGACTAGAGGCCAC 59.826 60.0 5.01 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2669 2941 0.108992 AATTTGCACTGCCTCATGCG 60.109 50.000 0.0 0.0 45.13 4.73 R
2850 3122 4.213906 GCTGACAAATTCCACCCATTTTTG 59.786 41.667 0.0 0.0 34.34 2.44 R
4153 4471 0.758734 TGATTAGTGCGATGGGGAGG 59.241 55.000 0.0 0.0 0.00 4.30 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
105 111 8.997621 AATGAATCAAATGACATCTCTTTTGG 57.002 30.769 8.72 0.00 39.97 3.28
182 188 1.399440 CCATTGACTCGAAGCACATGG 59.601 52.381 0.00 10.77 0.00 3.66
242 439 2.886523 ACACATGGAATATTGATGGGCG 59.113 45.455 0.00 0.00 0.00 6.13
271 469 2.154462 GCTTAGAACAGTGGTGCACAT 58.846 47.619 20.43 0.20 36.74 3.21
326 524 7.762382 TCGAATTCGACATGCATATAGTAGAT 58.238 34.615 25.96 0.00 44.22 1.98
392 616 1.379527 GTTTAACCTGCGATCCCCAG 58.620 55.000 0.00 1.91 0.00 4.45
393 617 0.393808 TTTAACCTGCGATCCCCAGC 60.394 55.000 3.15 0.00 0.00 4.85
394 618 2.265467 TTAACCTGCGATCCCCAGCC 62.265 60.000 3.15 0.00 0.00 4.85
454 683 3.821033 AGCAAAAGGGCACTAACAGTAAG 59.179 43.478 0.00 0.00 35.83 2.34
687 922 1.884579 GCATGCATGTATCCCCAAGAG 59.115 52.381 26.79 0.00 0.00 2.85
728 963 1.819229 GTGCTGCTCCTGCTAGCTA 59.181 57.895 17.23 1.31 43.19 3.32
729 964 0.249405 GTGCTGCTCCTGCTAGCTAG 60.249 60.000 16.84 16.84 43.19 3.42
869 1104 3.386592 GGAGACCTGAGCAGTGCT 58.613 61.111 19.86 19.86 43.88 4.40
887 1145 0.308376 CTTAGCTAGGCGTCGTCTCC 59.692 60.000 0.73 0.00 0.00 3.71
928 1186 2.509336 CGCGCTCCACCCTAACTG 60.509 66.667 5.56 0.00 0.00 3.16
929 1187 2.125106 GCGCTCCACCCTAACTGG 60.125 66.667 0.00 0.00 0.00 4.00
930 1188 2.125106 CGCTCCACCCTAACTGGC 60.125 66.667 0.00 0.00 0.00 4.85
931 1189 2.272471 GCTCCACCCTAACTGGCC 59.728 66.667 0.00 0.00 0.00 5.36
970 1228 0.032678 CGGGGAGGAACATCAGATCG 59.967 60.000 0.00 0.00 0.00 3.69
972 1230 1.069358 GGGGAGGAACATCAGATCGTC 59.931 57.143 0.00 0.00 32.62 4.20
973 1231 1.269309 GGGAGGAACATCAGATCGTCG 60.269 57.143 0.00 0.00 33.73 5.12
974 1232 1.482278 GAGGAACATCAGATCGTCGC 58.518 55.000 0.00 0.00 0.00 5.19
975 1233 0.103208 AGGAACATCAGATCGTCGCC 59.897 55.000 0.00 0.00 0.00 5.54
976 1234 0.179111 GGAACATCAGATCGTCGCCA 60.179 55.000 0.00 0.00 0.00 5.69
977 1235 1.640428 GAACATCAGATCGTCGCCAA 58.360 50.000 0.00 0.00 0.00 4.52
978 1236 1.590238 GAACATCAGATCGTCGCCAAG 59.410 52.381 0.00 0.00 0.00 3.61
979 1237 0.179100 ACATCAGATCGTCGCCAAGG 60.179 55.000 0.00 0.00 0.00 3.61
980 1238 0.877649 CATCAGATCGTCGCCAAGGG 60.878 60.000 0.00 0.00 0.00 3.95
981 1239 2.650813 ATCAGATCGTCGCCAAGGGC 62.651 60.000 0.00 0.00 46.75 5.19
996 1254 3.097614 CAAGGGCAGTAGTAGTACCACT 58.902 50.000 4.02 0.00 0.00 4.00
1156 1417 2.045926 CCGGCCACTCCTTCAAGG 60.046 66.667 2.24 0.00 36.46 3.61
1217 1478 1.822581 CACATGATCACTTGCATGCG 58.177 50.000 14.09 1.59 44.30 4.73
1303 1573 2.750712 ACGGGGGTCAAATTGATTAACG 59.249 45.455 0.00 5.39 0.00 3.18
1305 1575 3.093814 GGGGGTCAAATTGATTAACGGT 58.906 45.455 0.00 0.00 0.00 4.83
1309 1579 5.158494 GGGTCAAATTGATTAACGGTTGAC 58.842 41.667 3.07 11.71 42.51 3.18
1322 1592 2.295349 ACGGTTGACTATATACGCAGGG 59.705 50.000 0.00 0.00 0.00 4.45
1413 1683 2.815647 CGCTCTTCAACTCCGGCC 60.816 66.667 0.00 0.00 0.00 6.13
1427 1697 2.668632 GGCCTGATCAACCCGACA 59.331 61.111 0.00 0.00 0.00 4.35
1679 1949 3.060866 GTGGCTCCCACGTCTTCT 58.939 61.111 0.00 0.00 44.95 2.85
1928 2198 0.249073 CGATCTTCCTGCAGTACCCG 60.249 60.000 13.81 4.64 0.00 5.28
2128 2398 2.357154 GGCTTGGTCAATACTGGTCCAT 60.357 50.000 0.00 0.00 30.92 3.41
2179 2449 0.472471 AGCGACCCCTTCTTGAACAA 59.528 50.000 0.00 0.00 0.00 2.83
2181 2451 1.235724 CGACCCCTTCTTGAACAACC 58.764 55.000 0.00 0.00 0.00 3.77
2253 2523 1.139455 TGGTACAATACGGCTTAGGCC 59.861 52.381 5.63 5.63 46.56 5.19
2282 2552 4.537433 CCTGCTACCTCTGCGGCC 62.537 72.222 0.00 0.00 35.62 6.13
2316 2586 2.125147 CTGCTTCGCCGGATTCCA 60.125 61.111 5.05 0.00 0.00 3.53
2387 2657 3.605664 GCAACCACTGCCACCACC 61.606 66.667 0.00 0.00 46.13 4.61
2461 2731 7.489113 GCTTAATCTTGGTACACCATTTTGATG 59.511 37.037 1.05 0.00 46.97 3.07
2496 2766 5.183331 TCACGCCCTCTCACTATATTATCAC 59.817 44.000 0.00 0.00 0.00 3.06
2542 2812 0.173708 CTTCACGGACTAGAGGCCAC 59.826 60.000 5.01 0.00 0.00 5.01
2611 2881 1.173043 TTTGGATGTTAGCTTGCCCG 58.827 50.000 0.00 0.00 0.00 6.13
2831 3103 3.011818 CTCCAAGCTGTACATCATGCAA 58.988 45.455 7.48 0.00 0.00 4.08
2850 3122 3.361940 GCAAGCATGACTTTTCGCTAAAC 59.638 43.478 0.00 0.00 36.04 2.01
2936 3208 3.373439 GCTGTACTCCATGAGCAAAAGAG 59.627 47.826 0.00 0.00 32.04 2.85
2938 3210 4.825422 TGTACTCCATGAGCAAAAGAGAG 58.175 43.478 0.00 0.00 32.04 3.20
2940 3212 4.205065 ACTCCATGAGCAAAAGAGAGAG 57.795 45.455 0.00 0.00 32.04 3.20
2942 3214 4.081531 ACTCCATGAGCAAAAGAGAGAGAG 60.082 45.833 0.00 0.00 32.04 3.20
2943 3215 4.092279 TCCATGAGCAAAAGAGAGAGAGA 58.908 43.478 0.00 0.00 0.00 3.10
2944 3216 4.160065 TCCATGAGCAAAAGAGAGAGAGAG 59.840 45.833 0.00 0.00 0.00 3.20
2945 3217 4.160065 CCATGAGCAAAAGAGAGAGAGAGA 59.840 45.833 0.00 0.00 0.00 3.10
2946 3218 5.345702 CATGAGCAAAAGAGAGAGAGAGAG 58.654 45.833 0.00 0.00 0.00 3.20
2947 3219 4.661222 TGAGCAAAAGAGAGAGAGAGAGA 58.339 43.478 0.00 0.00 0.00 3.10
2948 3220 4.701651 TGAGCAAAAGAGAGAGAGAGAGAG 59.298 45.833 0.00 0.00 0.00 3.20
2949 3221 4.922206 AGCAAAAGAGAGAGAGAGAGAGA 58.078 43.478 0.00 0.00 0.00 3.10
2950 3222 4.946157 AGCAAAAGAGAGAGAGAGAGAGAG 59.054 45.833 0.00 0.00 0.00 3.20
2951 3223 4.943705 GCAAAAGAGAGAGAGAGAGAGAGA 59.056 45.833 0.00 0.00 0.00 3.10
2952 3224 5.065731 GCAAAAGAGAGAGAGAGAGAGAGAG 59.934 48.000 0.00 0.00 0.00 3.20
2953 3225 6.409704 CAAAAGAGAGAGAGAGAGAGAGAGA 58.590 44.000 0.00 0.00 0.00 3.10
2954 3226 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
2955 3227 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2956 3228 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2957 3229 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2958 3230 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2959 3231 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2960 3232 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2961 3233 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2971 3243 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2975 3247 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2979 3251 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2983 3255 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3115 3387 3.851620 CACCCATATGCGTGCATTC 57.148 52.632 13.20 0.00 37.82 2.67
3141 3413 6.139048 TGCATGGATCTATTTCACATGTTG 57.861 37.500 0.00 0.00 40.63 3.33
3174 3446 4.104383 AGACTTGAAGGAATGGAAGCAA 57.896 40.909 0.00 0.00 0.00 3.91
3252 3524 8.246180 ACATTGCTTAGTTATTGAAAGATGTGG 58.754 33.333 0.00 0.00 0.00 4.17
3273 3545 2.079925 GGAGCAGATTGGTCTTGTCAC 58.920 52.381 8.02 0.00 43.82 3.67
3289 3563 0.391228 TCACGCACACATGTGGTAGT 59.609 50.000 28.64 20.55 45.72 2.73
3331 3605 6.954487 AAAAACTCTTTGTAGTACTTGGGG 57.046 37.500 0.00 0.00 0.00 4.96
3342 3616 6.371278 TGTAGTACTTGGGGAAGGAGTATAG 58.629 44.000 0.00 0.00 0.00 1.31
3367 3641 3.954258 TGATCCGAAGCTGACAGATTAGA 59.046 43.478 14.20 10.81 0.00 2.10
3376 3650 7.117812 CGAAGCTGACAGATTAGAGGTTAAAAA 59.882 37.037 5.82 0.00 0.00 1.94
3394 3689 4.481368 AAAACAACCAAAAGGAGGGAAC 57.519 40.909 0.00 0.00 0.00 3.62
3444 3745 3.526931 ACACTGGATTCTATCGTGGTG 57.473 47.619 0.00 0.00 33.34 4.17
3509 3810 2.148916 TGTCACGGCAACTTGTCTAG 57.851 50.000 0.00 0.00 37.10 2.43
3519 3820 3.373439 GCAACTTGTCTAGCATCAAGAGG 59.627 47.826 20.51 14.86 42.22 3.69
3560 3861 2.224549 TGCGTGTGAAGAATTTTACCGG 59.775 45.455 0.00 0.00 0.00 5.28
3570 3871 7.491048 GTGAAGAATTTTACCGGGTACGTATAA 59.509 37.037 6.34 0.00 38.78 0.98
3572 3873 6.515832 AGAATTTTACCGGGTACGTATAAGG 58.484 40.000 6.34 5.11 38.78 2.69
3577 3885 1.251251 CGGGTACGTATAAGGAGGGG 58.749 60.000 0.00 0.00 34.81 4.79
3642 3956 0.447801 CGGTCAAATTTCCTCCTGCG 59.552 55.000 0.00 0.00 0.00 5.18
3686 4000 1.796017 TCACATTATACAGGGGGCGA 58.204 50.000 0.00 0.00 0.00 5.54
3872 4186 2.821366 CATGCAGGACCAGCGGAC 60.821 66.667 4.22 0.00 33.85 4.79
4127 4441 1.751927 CGGCGGGGTCTACTACTGT 60.752 63.158 0.00 0.00 0.00 3.55
4153 4471 1.626654 ATATAGCATGAACCGCGCGC 61.627 55.000 27.36 23.91 0.00 6.86
4189 4507 6.132658 ACTAATCAAGTGATGCTCCTCTCTA 58.867 40.000 0.00 0.00 36.93 2.43
4334 4652 0.441533 CTTGTGAGCAGTGATCGTGC 59.558 55.000 11.08 11.08 41.54 5.34
4446 4765 2.546162 GGTTCGCCTATGCTACTCCTTC 60.546 54.545 0.00 0.00 34.43 3.46
4653 5245 2.409715 CCAGAACGATGCTATACATGCG 59.590 50.000 0.00 0.00 39.84 4.73
4683 5275 7.227512 ACGTATAGTACTAAGTGCTACCGAAAT 59.772 37.037 6.70 0.00 33.97 2.17
4693 5285 2.822561 TGCTACCGAAATTTGCCAATGA 59.177 40.909 0.00 0.00 0.00 2.57
4912 5509 4.067192 ACAGCCCAAAGATTGCATTTTTC 58.933 39.130 0.00 0.00 0.00 2.29
4928 5526 8.458212 TGCATTTTTCCAAAACAAAATTTCAC 57.542 26.923 0.00 0.00 31.54 3.18
4932 5530 6.410243 TTTCCAAAACAAAATTTCACGGAC 57.590 33.333 0.00 0.00 0.00 4.79
4973 5571 8.419076 ACAAGTTTCCACATAATTTGTTTCAC 57.581 30.769 0.00 0.00 36.00 3.18
5080 5678 2.671396 GCTAGTCCATACACAACAACCG 59.329 50.000 0.00 0.00 0.00 4.44
5086 5684 4.736307 GTCCATACACAACAACCGTTTTTC 59.264 41.667 0.00 0.00 31.13 2.29
5090 5688 6.311690 CCATACACAACAACCGTTTTTCTTTT 59.688 34.615 0.00 0.00 31.13 2.27
5132 5730 0.314302 CTCACGTCAACTCGAGGGTT 59.686 55.000 18.41 0.01 33.65 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.508875 GTCGAGGTTCATGTTTATTTTCCTTTA 58.491 33.333 0.00 0.00 0.00 1.85
37 38 6.148811 TGAGTCGAGGTTCATGTTTATTTTCC 59.851 38.462 0.00 0.00 0.00 3.13
80 83 8.038944 CCCAAAAGAGATGTCATTTGATTCATT 58.961 33.333 18.85 0.00 41.77 2.57
126 132 1.995991 CGCACGTTACCGGATTCAG 59.004 57.895 9.46 0.00 38.78 3.02
134 140 0.791422 TGTATGTTGCGCACGTTACC 59.209 50.000 11.12 0.00 0.00 2.85
234 431 2.346766 AGCATTGATTACGCCCATCA 57.653 45.000 0.00 0.00 0.00 3.07
242 439 6.546395 CACCACTGTTCTAAGCATTGATTAC 58.454 40.000 0.00 0.00 0.00 1.89
326 524 6.101332 CCTGCACAAAACGGTATACTACTAA 58.899 40.000 2.25 0.00 0.00 2.24
332 530 2.081462 AGCCTGCACAAAACGGTATAC 58.919 47.619 0.00 0.00 0.00 1.47
335 533 1.791103 GCAGCCTGCACAAAACGGTA 61.791 55.000 12.82 0.00 44.26 4.02
336 534 3.119193 CAGCCTGCACAAAACGGT 58.881 55.556 0.00 0.00 0.00 4.83
337 535 2.355009 GCAGCCTGCACAAAACGG 60.355 61.111 12.82 0.00 44.26 4.44
392 616 2.436646 CGTGATGGTCACCTGGGC 60.437 66.667 0.00 0.00 44.20 5.36
393 617 2.436646 GCGTGATGGTCACCTGGG 60.437 66.667 0.00 0.00 44.20 4.45
394 618 2.034879 GTGCGTGATGGTCACCTGG 61.035 63.158 0.00 0.00 44.20 4.45
395 619 2.382746 CGTGCGTGATGGTCACCTG 61.383 63.158 0.00 0.00 44.20 4.00
396 620 2.048222 CGTGCGTGATGGTCACCT 60.048 61.111 0.00 0.00 44.20 4.00
454 683 4.785453 CCTGCGTTCCTGCCTCCC 62.785 72.222 0.00 0.00 0.00 4.30
695 930 2.429930 CACGACCCCTCCTGCAAA 59.570 61.111 0.00 0.00 0.00 3.68
730 965 5.220931 GGCAATAAATGGAGTGCTGAAGTAG 60.221 44.000 0.00 0.00 40.23 2.57
731 966 4.640201 GGCAATAAATGGAGTGCTGAAGTA 59.360 41.667 0.00 0.00 40.23 2.24
869 1104 0.107312 AGGAGACGACGCCTAGCTAA 60.107 55.000 8.59 0.00 44.15 3.09
887 1145 0.525668 CAGGGATCGACGAAACGGAG 60.526 60.000 0.00 0.00 0.00 4.63
914 1172 2.272471 GGCCAGTTAGGGTGGAGC 59.728 66.667 0.00 0.00 37.23 4.70
915 1173 2.584608 CGGCCAGTTAGGGTGGAG 59.415 66.667 2.24 0.00 37.23 3.86
930 1188 4.007940 CAACACAACGACGGCCGG 62.008 66.667 31.76 15.62 43.93 6.13
931 1189 4.659874 GCAACACAACGACGGCCG 62.660 66.667 26.86 26.86 45.44 6.13
954 1212 1.866063 GCGACGATCTGATGTTCCTCC 60.866 57.143 0.00 0.00 0.00 4.30
974 1232 2.167900 GTGGTACTACTACTGCCCTTGG 59.832 54.545 1.48 0.00 0.00 3.61
975 1233 3.097614 AGTGGTACTACTACTGCCCTTG 58.902 50.000 10.57 0.00 38.55 3.61
976 1234 3.469750 AGTGGTACTACTACTGCCCTT 57.530 47.619 10.57 0.00 38.55 3.95
977 1235 3.895998 GTAGTGGTACTACTACTGCCCT 58.104 50.000 31.36 5.67 45.70 5.19
987 1245 2.026641 GACGCCATGGTAGTGGTACTA 58.973 52.381 14.67 0.00 41.47 1.82
988 1246 0.822164 GACGCCATGGTAGTGGTACT 59.178 55.000 14.67 0.00 41.47 2.73
989 1247 0.526954 CGACGCCATGGTAGTGGTAC 60.527 60.000 14.67 1.73 41.47 3.34
990 1248 1.811195 CGACGCCATGGTAGTGGTA 59.189 57.895 14.67 0.00 41.47 3.25
991 1249 2.577059 CGACGCCATGGTAGTGGT 59.423 61.111 14.67 3.97 41.47 4.16
992 1250 2.890474 GCGACGCCATGGTAGTGG 60.890 66.667 14.67 15.56 42.35 4.00
1156 1417 0.400670 ATACCTGAGGAGAAGGGGGC 60.401 60.000 4.99 0.00 39.30 5.80
1217 1478 6.492087 ACAAGACAGAACCCTATCTATCTAGC 59.508 42.308 0.00 0.00 32.12 3.42
1303 1573 2.612221 GGCCCTGCGTATATAGTCAACC 60.612 54.545 0.00 0.00 0.00 3.77
1305 1575 2.299013 CAGGCCCTGCGTATATAGTCAA 59.701 50.000 0.00 0.00 0.00 3.18
1309 1579 2.760650 TGATCAGGCCCTGCGTATATAG 59.239 50.000 5.66 0.00 0.00 1.31
1314 1584 2.434843 CCTGATCAGGCCCTGCGTA 61.435 63.158 28.45 0.00 42.44 4.42
1413 1683 2.444624 CGCGTGTCGGGTTGATCAG 61.445 63.158 0.00 0.00 35.14 2.90
1679 1949 0.324460 GGTCGGAGGAGGAAGAGGAA 60.324 60.000 0.00 0.00 0.00 3.36
1833 2103 2.362120 CGGAGTAGACACGGGGGT 60.362 66.667 0.00 0.00 0.00 4.95
1941 2211 4.459089 GAGCTCCCCCGCAGACAC 62.459 72.222 0.87 0.00 0.00 3.67
2034 2304 1.600636 CGTTGCAGAGCCCCAAGAA 60.601 57.895 0.00 0.00 0.00 2.52
2128 2398 2.202610 CGAGCTGATCAACGCCGA 60.203 61.111 0.00 0.00 0.00 5.54
2179 2449 0.537371 CTCTTCTTTGGCAACGGGGT 60.537 55.000 0.00 0.00 42.51 4.95
2181 2451 2.257353 CCTCTTCTTTGGCAACGGG 58.743 57.895 0.00 0.00 42.51 5.28
2282 2552 1.302832 AGGAGGAGGCAAAACAGCG 60.303 57.895 0.00 0.00 34.64 5.18
2387 2657 7.309177 AGTTACTATTGTAGCTGATAGCATCG 58.691 38.462 0.00 0.00 45.56 3.84
2461 2731 2.293399 AGAGGGCGTGAATGAACAAAAC 59.707 45.455 0.00 0.00 0.00 2.43
2496 2766 3.950087 ACACTTACATACGCATGCATG 57.050 42.857 22.70 22.70 35.39 4.06
2611 2881 4.951094 TGGGTATACCTAAACAATGGCAAC 59.049 41.667 21.25 0.33 41.11 4.17
2669 2941 0.108992 AATTTGCACTGCCTCATGCG 60.109 50.000 0.00 0.00 45.13 4.73
2831 3103 4.829064 TTGTTTAGCGAAAAGTCATGCT 57.171 36.364 0.00 0.00 41.32 3.79
2850 3122 4.213906 GCTGACAAATTCCACCCATTTTTG 59.786 41.667 0.00 0.00 34.34 2.44
2936 3208 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2938 3210 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2940 3212 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2942 3214 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2943 3215 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2944 3216 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2945 3217 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2946 3218 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2947 3219 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2948 3220 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2949 3221 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2950 3222 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2951 3223 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2952 3224 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2953 3225 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2954 3226 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2955 3227 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2956 3228 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2957 3229 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2958 3230 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2959 3231 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2960 3232 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2961 3233 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2971 3243 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2975 3247 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2979 3251 6.070021 TCACAAATCTCTCTCTCTCTCTCTCT 60.070 42.308 0.00 0.00 0.00 3.10
2983 3255 5.595542 CCATCACAAATCTCTCTCTCTCTCT 59.404 44.000 0.00 0.00 0.00 3.10
3126 3398 9.288576 AGTCTTTTCATCAACATGTGAAATAGA 57.711 29.630 0.00 7.87 42.12 1.98
3141 3413 8.663911 CATTCCTTCAAGTCTAGTCTTTTCATC 58.336 37.037 0.00 0.00 0.00 2.92
3174 3446 7.948034 TTTTGGAATCTTATATGGAACCGTT 57.052 32.000 0.00 0.00 0.00 4.44
3241 3513 1.361204 TCTGCTCCCCACATCTTTCA 58.639 50.000 0.00 0.00 0.00 2.69
3243 3515 2.622452 CCAATCTGCTCCCCACATCTTT 60.622 50.000 0.00 0.00 0.00 2.52
3252 3524 1.003580 TGACAAGACCAATCTGCTCCC 59.996 52.381 0.00 0.00 34.48 4.30
3273 3545 2.363788 ACTACTACCACATGTGTGCG 57.636 50.000 23.79 11.64 44.34 5.34
3312 3586 4.286291 CCTTCCCCAAGTACTACAAAGAGT 59.714 45.833 0.00 0.00 0.00 3.24
3313 3587 4.530946 TCCTTCCCCAAGTACTACAAAGAG 59.469 45.833 0.00 0.00 0.00 2.85
3314 3588 4.495565 TCCTTCCCCAAGTACTACAAAGA 58.504 43.478 0.00 0.00 0.00 2.52
3316 3590 4.237018 ACTCCTTCCCCAAGTACTACAAA 58.763 43.478 0.00 0.00 0.00 2.83
3318 3592 3.555117 ACTCCTTCCCCAAGTACTACA 57.445 47.619 0.00 0.00 0.00 2.74
3326 3600 5.132144 GGATCAAACTATACTCCTTCCCCAA 59.868 44.000 0.00 0.00 0.00 4.12
3329 3603 4.587684 TCGGATCAAACTATACTCCTTCCC 59.412 45.833 0.00 0.00 0.00 3.97
3331 3605 5.692654 GCTTCGGATCAAACTATACTCCTTC 59.307 44.000 0.00 0.00 0.00 3.46
3342 3616 2.688507 TCTGTCAGCTTCGGATCAAAC 58.311 47.619 0.00 0.00 0.00 2.93
3376 3650 1.412505 GGGTTCCCTCCTTTTGGTTGT 60.413 52.381 0.00 0.00 41.38 3.32
3429 3724 2.213499 CTTGCCACCACGATAGAATCC 58.787 52.381 0.00 0.00 41.38 3.01
3433 3728 1.220749 GGCTTGCCACCACGATAGA 59.779 57.895 6.79 0.00 41.38 1.98
3444 3745 1.533625 TATGAGTTGTGTGGCTTGCC 58.466 50.000 4.43 4.43 0.00 4.52
3509 3810 3.356529 TCCTCCTTTTCCTCTTGATGC 57.643 47.619 0.00 0.00 0.00 3.91
3519 3820 2.474410 TCCGCTTCTTCCTCCTTTTC 57.526 50.000 0.00 0.00 0.00 2.29
3560 3861 0.972134 GCCCCCTCCTTATACGTACC 59.028 60.000 0.00 0.00 0.00 3.34
3642 3956 2.126888 TTAAGCAAGCAAGCGCGC 60.127 55.556 26.66 26.66 45.49 6.86
3686 4000 3.714391 GCACGGTCGATCTAGGTAAAAT 58.286 45.455 0.00 0.00 0.00 1.82
3872 4186 3.496131 CCCGCGAACCCAACATCG 61.496 66.667 8.23 0.00 41.81 3.84
4153 4471 0.758734 TGATTAGTGCGATGGGGAGG 59.241 55.000 0.00 0.00 0.00 4.30
4334 4652 9.801873 ATTGATCAGAAATTTGGTAATAAACGG 57.198 29.630 0.00 0.00 0.00 4.44
4368 4687 6.124088 TCATGATGATGGAGTATATCGACG 57.876 41.667 0.00 0.00 0.00 5.12
4446 4765 2.589014 GAGGCTCATGTTGCGAAAAAG 58.411 47.619 10.25 0.00 0.00 2.27
4490 4809 6.932400 ACCAAAACAGTAGATTTGATCGTACA 59.068 34.615 0.00 0.00 39.16 2.90
4501 4820 7.081976 GCGACATTAAAACCAAAACAGTAGAT 58.918 34.615 0.00 0.00 0.00 1.98
4562 5154 5.833131 TGTCTATCAGCCTATACATGTGTGA 59.167 40.000 9.11 2.26 0.00 3.58
4668 5260 3.413327 TGGCAAATTTCGGTAGCACTTA 58.587 40.909 0.00 0.00 0.00 2.24
4683 5275 3.013921 GTTCCCGAGTATCATTGGCAAA 58.986 45.455 3.01 0.00 33.17 3.68
4812 5406 5.398416 GTCTTTTTCTTGTACGCCATTTGTC 59.602 40.000 0.00 0.00 0.00 3.18
4895 5491 6.793349 TGTTTTGGAAAAATGCAATCTTTGG 58.207 32.000 0.00 0.00 0.00 3.28
4898 5494 9.872721 AATTTTGTTTTGGAAAAATGCAATCTT 57.127 22.222 0.00 0.00 36.40 2.40
4912 5509 3.558006 GGGTCCGTGAAATTTTGTTTTGG 59.442 43.478 0.00 0.00 0.00 3.28
4928 5526 0.179084 ATGTGTTCGCTATGGGTCCG 60.179 55.000 0.00 0.00 0.00 4.79
4932 5530 3.531538 ACTTGTATGTGTTCGCTATGGG 58.468 45.455 0.00 0.00 0.00 4.00
5057 5655 4.261801 GGTTGTTGTGTATGGACTAGCAT 58.738 43.478 0.00 0.00 0.00 3.79
5063 5661 3.974871 AAACGGTTGTTGTGTATGGAC 57.025 42.857 0.00 0.00 38.62 4.02


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

AutoCloner maintained by Alex Coulton.