Multiple sequence alignment - TraesCS7D01G458800

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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 TraesCS7D01G458800 chr7D 100.000 4858 0 0 1 4858 576339803 576334946 0.000000e+00 8972.0
1 TraesCS7D01G458800 chr7D 87.037 54 5 2 3087 3140 518639167 518639218 5.250000e-05 60.2
2 TraesCS7D01G458800 chr7A 96.504 2603 81 6 1 2600 667480865 667478270 0.000000e+00 4294.0
3 TraesCS7D01G458800 chr7A 80.127 2677 387 75 9 2607 705136187 705138796 0.000000e+00 1862.0
4 TraesCS7D01G458800 chr7A 90.319 909 53 17 3524 4425 667478254 667477374 0.000000e+00 1158.0
5 TraesCS7D01G458800 chr7A 84.661 502 33 19 4147 4642 667477363 667476900 1.230000e-125 460.0
6 TraesCS7D01G458800 chr7A 84.058 345 40 10 2686 3018 705138942 705139283 7.850000e-83 318.0
7 TraesCS7D01G458800 chr7A 88.646 229 14 5 4641 4858 667476846 667476619 8.010000e-68 268.0
8 TraesCS7D01G458800 chr7A 78.316 475 57 19 3671 4127 705141577 705142023 1.040000e-66 265.0
9 TraesCS7D01G458800 chr7A 79.070 301 36 18 4285 4567 705142284 705142575 1.070000e-41 182.0
10 TraesCS7D01G458800 chr7B 94.436 1959 93 8 1 1954 639089987 639088040 0.000000e+00 3000.0
11 TraesCS7D01G458800 chr7B 87.679 1745 123 45 3138 4858 639086755 639085079 0.000000e+00 1947.0
12 TraesCS7D01G458800 chr7B 80.539 2672 400 73 17 2607 704088366 704090998 0.000000e+00 1943.0
13 TraesCS7D01G458800 chr7B 80.329 2674 402 80 17 2607 704153206 704155838 0.000000e+00 1910.0
14 TraesCS7D01G458800 chr7B 94.536 1153 46 9 1934 3082 639087892 639086753 0.000000e+00 1764.0
15 TraesCS7D01G458800 chr7B 80.607 1021 104 49 3140 4097 704091699 704092688 0.000000e+00 702.0
16 TraesCS7D01G458800 chr7B 80.507 1026 103 46 3140 4099 704156537 704157531 0.000000e+00 697.0
17 TraesCS7D01G458800 chr7B 82.544 401 40 15 2683 3071 704155980 704156362 4.690000e-85 326.0
18 TraesCS7D01G458800 chr7B 83.908 348 41 10 2683 3018 704091140 704091484 7.850000e-83 318.0
19 TraesCS7D01G458800 chr7B 79.155 355 43 17 4228 4567 704092856 704093194 2.940000e-52 217.0
20 TraesCS7D01G458800 chr3D 87.403 1413 134 26 1692 3073 181109593 181108194 0.000000e+00 1583.0
21 TraesCS7D01G458800 chr3D 85.324 879 88 16 3358 4227 181107834 181106988 0.000000e+00 870.0
22 TraesCS7D01G458800 chr3D 86.066 122 10 7 4251 4366 181106509 181106389 1.840000e-24 124.0
23 TraesCS7D01G458800 chr3A 88.132 910 90 13 2171 3073 227918108 227919006 0.000000e+00 1066.0
24 TraesCS7D01G458800 chr3A 86.207 754 74 13 3358 4105 227919282 227920011 0.000000e+00 789.0
25 TraesCS7D01G458800 chr3A 82.000 400 44 10 1779 2165 227917556 227917940 1.020000e-81 315.0
26 TraesCS7D01G458800 chr3A 87.288 118 8 6 4251 4362 227920763 227920879 1.420000e-25 128.0
27 TraesCS7D01G458800 chr3B 83.111 225 30 6 4641 4858 259372521 259372298 1.070000e-46 198.0
28 TraesCS7D01G458800 chr3B 76.675 403 48 26 4251 4615 259373024 259372630 1.070000e-41 182.0
29 TraesCS7D01G458800 chr3B 95.455 44 1 1 3109 3151 698423924 698423881 8.720000e-08 69.4
30 TraesCS7D01G458800 chr3B 92.000 50 2 2 3097 3146 755082004 755082051 8.720000e-08 69.4
31 TraesCS7D01G458800 chr2D 92.157 51 4 0 3097 3147 625150374 625150424 6.740000e-09 73.1
32 TraesCS7D01G458800 chr6B 95.349 43 2 0 3101 3143 454559966 454560008 8.720000e-08 69.4
33 TraesCS7D01G458800 chr1D 90.566 53 2 3 3109 3160 407873363 407873313 3.140000e-07 67.6
34 TraesCS7D01G458800 chr5D 90.000 50 5 0 3109 3158 346885148 346885197 1.130000e-06 65.8
35 TraesCS7D01G458800 chr1A 93.333 45 2 1 3108 3152 85036583 85036540 1.130000e-06 65.8
36 TraesCS7D01G458800 chr6D 87.037 54 6 1 3088 3141 451070056 451070108 5.250000e-05 60.2


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 TraesCS7D01G458800 chr7D 576334946 576339803 4857 True 8972.000000 8972 100.000000 1 4858 1 chr7D.!!$R1 4857
1 TraesCS7D01G458800 chr7A 667476619 667480865 4246 True 1545.000000 4294 90.032500 1 4858 4 chr7A.!!$R1 4857
2 TraesCS7D01G458800 chr7A 705136187 705142575 6388 False 656.750000 1862 80.392750 9 4567 4 chr7A.!!$F1 4558
3 TraesCS7D01G458800 chr7B 639085079 639089987 4908 True 2237.000000 3000 92.217000 1 4858 3 chr7B.!!$R1 4857
4 TraesCS7D01G458800 chr7B 704153206 704157531 4325 False 977.666667 1910 81.126667 17 4099 3 chr7B.!!$F2 4082
5 TraesCS7D01G458800 chr7B 704088366 704093194 4828 False 795.000000 1943 81.052250 17 4567 4 chr7B.!!$F1 4550
6 TraesCS7D01G458800 chr3D 181106389 181109593 3204 True 859.000000 1583 86.264333 1692 4366 3 chr3D.!!$R1 2674
7 TraesCS7D01G458800 chr3A 227917556 227920879 3323 False 574.500000 1066 85.906750 1779 4362 4 chr3A.!!$F1 2583

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
183 192 1.351017 TCAACCAGGATGTGAAGGACC 59.649 52.381 0.00 0.0 0.0 4.46 F
362 377 1.482593 AGGATCGAGACCATTCACACC 59.517 52.381 12.78 0.0 0.0 4.16 F
1338 1393 1.066071 TCGATGCGGTAACATTCCCAA 60.066 47.619 0.00 0.0 0.0 4.12 F
2884 3408 1.406614 CCTCATGAGCCAGTTCTGGAC 60.407 57.143 21.32 14.1 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1112 1.550976 GCTCTACTAACCTGTGGTGCT 59.449 52.381 0.00 0.00 35.34 4.40 R
2318 2745 1.212616 GTGACTGAGTGCACACAGAC 58.787 55.000 39.44 34.11 37.86 3.51 R
3123 3905 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37 R
4238 7081 1.074889 ACCTGTAAGCGGGGTCAAAAT 59.925 47.619 0.00 0.00 45.50 1.82 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
146 155 1.866483 TAGTGAGACCCGGGCCTGTA 61.866 60.000 24.08 2.73 0.00 2.74
183 192 1.351017 TCAACCAGGATGTGAAGGACC 59.649 52.381 0.00 0.00 0.00 4.46
362 377 1.482593 AGGATCGAGACCATTCACACC 59.517 52.381 12.78 0.00 0.00 4.16
376 391 4.846779 TTCACACCAAGGCAGAATTTAC 57.153 40.909 0.00 0.00 0.00 2.01
627 656 1.668419 CTGTCTAATTGCGGGGAAGG 58.332 55.000 0.00 0.00 0.00 3.46
634 663 4.594854 TGCGGGGAAGGCAAAGCA 62.595 61.111 0.00 0.00 37.49 3.91
647 676 2.442413 GCAAAGCACCCAACATACCTA 58.558 47.619 0.00 0.00 0.00 3.08
780 810 7.441458 GTCCTACTGCCATTACAAAGGTATAAG 59.559 40.741 0.00 0.00 0.00 1.73
883 913 6.096423 GTCTGGTGTATGTTACTCTGATACCA 59.904 42.308 0.00 0.00 34.77 3.25
933 964 7.881775 ATGTTCACAGGGTCTAAAAATATCC 57.118 36.000 0.00 0.00 0.00 2.59
993 1040 6.855914 CGTTGCGTGCCAATAATTATAATTCT 59.144 34.615 13.95 2.15 35.55 2.40
1011 1058 1.767088 TCTGATCCAATGCTGAGGGAG 59.233 52.381 0.00 0.00 33.47 4.30
1020 1067 2.202987 CTGAGGGAGTGCGGCATC 60.203 66.667 5.72 4.94 0.00 3.91
1065 1112 2.041350 AGTCGAGGGTAGAGTCCTTCAA 59.959 50.000 0.00 0.00 33.91 2.69
1119 1167 6.998074 TCTTTTCACTGGATGTATGTCTTTGT 59.002 34.615 0.00 0.00 0.00 2.83
1120 1168 7.502226 TCTTTTCACTGGATGTATGTCTTTGTT 59.498 33.333 0.00 0.00 0.00 2.83
1121 1169 6.558771 TTCACTGGATGTATGTCTTTGTTG 57.441 37.500 0.00 0.00 0.00 3.33
1338 1393 1.066071 TCGATGCGGTAACATTCCCAA 60.066 47.619 0.00 0.00 0.00 4.12
1399 1463 5.982890 AGATGTGGGGAGTTGTTAATTTG 57.017 39.130 0.00 0.00 0.00 2.32
1480 1544 6.890268 AGAAGGGAACTGTGAGTTAACTTTTT 59.110 34.615 10.02 0.00 42.68 1.94
1650 1714 7.138736 TCAGCAGATTAAAGCAAAGTTAACAC 58.861 34.615 8.61 0.00 0.00 3.32
1706 1770 4.963318 TCCTGAGAAGAACAGTGACATT 57.037 40.909 0.00 0.00 34.04 2.71
1910 1984 6.207691 TGCTAAAGATAAATGCCAAGGTTC 57.792 37.500 0.00 0.00 0.00 3.62
2224 2647 4.141620 GCTGATGGTCCTGGAGAGATTTTA 60.142 45.833 0.00 0.00 0.00 1.52
2235 2658 4.994852 TGGAGAGATTTTACAACCGACAAG 59.005 41.667 0.00 0.00 0.00 3.16
2318 2745 4.201753 CCAATCATGTCAAAGTACAGAGCG 60.202 45.833 0.00 0.00 31.70 5.03
2692 3207 5.409826 GTCTTGTCCCTTGATGTTAAGAGTG 59.590 44.000 0.00 0.00 0.00 3.51
2716 3232 6.127730 TGCAAACTGACTCTAATACTCGATGA 60.128 38.462 0.00 0.00 0.00 2.92
2884 3408 1.406614 CCTCATGAGCCAGTTCTGGAC 60.407 57.143 21.32 14.10 0.00 4.02
3010 3539 2.844946 TCACACGAGATTTTTCCTGCA 58.155 42.857 0.00 0.00 0.00 4.41
3073 3602 8.148999 CCCTGGTAACCTACATCTTTTATCTAC 58.851 40.741 0.00 0.00 0.00 2.59
3094 3876 4.894784 ACACACCTACCACAGAACTATTG 58.105 43.478 0.00 0.00 0.00 1.90
3099 3881 6.932960 ACACCTACCACAGAACTATTGTTTAC 59.067 38.462 0.00 0.00 36.39 2.01
3100 3882 7.159372 CACCTACCACAGAACTATTGTTTACT 58.841 38.462 0.00 0.00 36.39 2.24
3101 3883 8.308931 CACCTACCACAGAACTATTGTTTACTA 58.691 37.037 0.00 0.00 36.39 1.82
3102 3884 8.309656 ACCTACCACAGAACTATTGTTTACTAC 58.690 37.037 0.00 0.00 36.39 2.73
3103 3885 8.529476 CCTACCACAGAACTATTGTTTACTACT 58.471 37.037 0.00 0.00 36.39 2.57
3104 3886 9.924650 CTACCACAGAACTATTGTTTACTACTT 57.075 33.333 0.00 0.00 36.39 2.24
3127 3909 9.362151 ACTTATTTTGAGACACTTATTTTGGGA 57.638 29.630 0.00 0.00 0.00 4.37
3128 3910 9.626045 CTTATTTTGAGACACTTATTTTGGGAC 57.374 33.333 0.00 0.00 0.00 4.46
3129 3911 5.682943 TTTGAGACACTTATTTTGGGACG 57.317 39.130 0.00 0.00 0.00 4.79
3130 3912 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3131 3913 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3132 3914 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3133 3915 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3134 3916 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3135 3917 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3136 3918 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3241 4027 2.766828 AGGTACTGTGGTTGATAGAGGC 59.233 50.000 0.00 0.00 37.18 4.70
3283 4069 5.808042 ATGATTTCTACATGTGTGCTCAC 57.192 39.130 9.11 11.94 44.08 3.51
3292 4078 3.051479 TGTGCTCACGCTGGCATG 61.051 61.111 0.00 0.00 40.66 4.06
3315 4105 6.341316 TGATTGTATGTTCTCTCTACCTTGC 58.659 40.000 0.00 0.00 0.00 4.01
3374 4164 9.587772 GCTTACTTGAATCTAAGTCATTCTACA 57.412 33.333 0.00 0.00 41.01 2.74
3389 4192 4.986054 TTCTACATTTGTGTACCAGGGT 57.014 40.909 0.00 0.00 0.00 4.34
3404 4207 0.611714 AGGGTACTACAAGGCCAACG 59.388 55.000 5.01 0.00 0.00 4.10
3425 4228 0.246635 ACTACCATGTGCTCCACGAC 59.753 55.000 0.00 0.00 37.14 4.34
3569 4385 8.192774 TCACTGCATCCTTTTGATATTTCAATC 58.807 33.333 0.00 0.00 41.38 2.67
3710 6059 1.008327 TCCCTCTCAGTTGCTCCCATA 59.992 52.381 0.00 0.00 0.00 2.74
3830 6182 3.084579 CCTCGTCTGCATCGCAAC 58.915 61.111 6.57 0.00 38.41 4.17
3932 6287 1.299541 CTACATGGAACCGGTCATGC 58.700 55.000 27.56 12.69 43.12 4.06
3998 6356 6.382859 TGCTAGATTTAGTGGGTGTTATCTCA 59.617 38.462 0.00 0.00 0.00 3.27
4216 7042 6.863126 AGTTTTGTGATTATGTACTTTGCTGC 59.137 34.615 0.00 0.00 0.00 5.25
4232 7071 4.186856 TGCTGCCAATTTACTTAAAGGC 57.813 40.909 0.00 0.00 39.89 4.35
4238 7081 4.349365 CCAATTTACTTAAAGGCCCTGGA 58.651 43.478 0.00 0.00 0.00 3.86
4437 7843 8.031277 GCAATCAAGAAGTAATTTCCAGATGTT 58.969 33.333 0.00 0.00 36.40 2.71
4450 7856 9.533253 AATTTCCAGATGTTAAAACTGAAGTTG 57.467 29.630 0.00 0.00 38.44 3.16
4454 7860 7.338196 TCCAGATGTTAAAACTGAAGTTGTGAA 59.662 33.333 0.00 0.00 38.44 3.18
4492 7898 5.005740 TCAGATCAGTGCAAAAATAGCAGT 58.994 37.500 0.00 0.00 45.98 4.40
4533 7939 6.536582 CGTCAAACCTCATCTAGTCAATCAAT 59.463 38.462 0.00 0.00 0.00 2.57
4535 7941 7.768120 GTCAAACCTCATCTAGTCAATCAATCT 59.232 37.037 0.00 0.00 0.00 2.40
4539 7945 8.311395 ACCTCATCTAGTCAATCAATCTAACA 57.689 34.615 0.00 0.00 0.00 2.41
4585 7992 0.394352 ATCAAAGTCCCCGCATGGTC 60.394 55.000 0.00 0.00 0.00 4.02
4591 7998 2.189521 CCCCGCATGGTCTGTACC 59.810 66.667 0.00 0.00 46.98 3.34
4605 8012 5.411781 GGTCTGTACCAATCACTAGTGAAG 58.588 45.833 28.43 22.11 45.98 3.02
4609 8016 5.020795 TGTACCAATCACTAGTGAAGCCTA 58.979 41.667 28.43 13.21 43.58 3.93
4621 8028 6.929606 ACTAGTGAAGCCTAGTTTACAACAAG 59.070 38.462 0.00 0.00 44.01 3.16
4622 8029 5.681639 AGTGAAGCCTAGTTTACAACAAGT 58.318 37.500 0.00 0.00 0.00 3.16
4623 8030 5.527582 AGTGAAGCCTAGTTTACAACAAGTG 59.472 40.000 0.00 0.00 0.00 3.16
4687 8149 8.676397 AGGTAGGAATCAGATGAATCATATCA 57.324 34.615 0.00 0.00 27.20 2.15
4694 8156 9.491675 GAATCAGATGAATCATATCACAAGTCT 57.508 33.333 0.00 0.00 30.82 3.24
4703 8165 5.264395 TCATATCACAAGTCTCTGAGGTGA 58.736 41.667 14.11 14.11 42.07 4.02
4705 8167 2.950781 TCACAAGTCTCTGAGGTGAGT 58.049 47.619 4.59 0.00 33.88 3.41
4706 8168 2.887783 TCACAAGTCTCTGAGGTGAGTC 59.112 50.000 4.59 0.00 33.88 3.36
4707 8169 1.883275 ACAAGTCTCTGAGGTGAGTCG 59.117 52.381 4.59 0.00 35.68 4.18
4711 8174 1.403679 GTCTCTGAGGTGAGTCGATGG 59.596 57.143 4.59 0.00 35.68 3.51
4720 8183 4.566987 AGGTGAGTCGATGGTTTTTCTAC 58.433 43.478 0.00 0.00 0.00 2.59
4735 8198 9.354673 TGGTTTTTCTACAGAATTGATTCTTCT 57.645 29.630 3.54 0.00 44.28 2.85
4777 8248 8.762645 AGGCGATCTATGATCTTCCAATATTTA 58.237 33.333 13.79 0.00 0.00 1.40
4778 8249 9.553064 GGCGATCTATGATCTTCCAATATTTAT 57.447 33.333 6.09 0.00 0.00 1.40
4840 8312 5.426689 AACTCAAGACCATCTATCAGCAA 57.573 39.130 0.00 0.00 0.00 3.91
4846 8318 6.709397 TCAAGACCATCTATCAGCAAATCATC 59.291 38.462 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.932303 TGCAAATTAGGCCTCGAGATAATAC 59.068 40.000 9.68 9.01 0.00 1.89
8 9 4.040339 TCATGCAAATTAGGCCTCGAGATA 59.960 41.667 9.68 0.64 0.00 1.98
146 155 6.712547 CCTGGTTGAAGAGTAGAAAGTCAATT 59.287 38.462 0.00 0.00 31.38 2.32
362 377 5.584649 TCCAGTAATCGTAAATTCTGCCTTG 59.415 40.000 0.00 0.00 0.00 3.61
376 391 4.868171 TCTTTTCGGACAATCCAGTAATCG 59.132 41.667 0.00 0.00 35.91 3.34
627 656 1.256812 AGGTATGTTGGGTGCTTTGC 58.743 50.000 0.00 0.00 0.00 3.68
634 663 0.539986 CAGCGGTAGGTATGTTGGGT 59.460 55.000 0.00 0.00 0.00 4.51
780 810 1.663643 TGCAACGTTGACAGTGACTTC 59.336 47.619 31.62 10.10 0.00 3.01
993 1040 1.211212 CACTCCCTCAGCATTGGATCA 59.789 52.381 0.00 0.00 0.00 2.92
1011 1058 1.623359 GATCTATCGAGATGCCGCAC 58.377 55.000 0.00 0.00 42.80 5.34
1020 1067 6.869315 TGAGTAAACTCTGGATCTATCGAG 57.131 41.667 11.22 0.00 43.25 4.04
1065 1112 1.550976 GCTCTACTAACCTGTGGTGCT 59.449 52.381 0.00 0.00 35.34 4.40
1119 1167 2.309528 CCTGCATAGTAGGCGTTCAA 57.690 50.000 1.88 0.00 0.00 2.69
1338 1393 2.544721 TGAACCTCTGGAGAGCAGAAT 58.455 47.619 0.00 0.00 40.75 2.40
1399 1463 4.388773 TCTTCAACATTACATCGTGCAGAC 59.611 41.667 0.00 0.00 0.00 3.51
1561 1625 4.842531 TGATGCCTCTCCTCAATTACAA 57.157 40.909 0.00 0.00 0.00 2.41
1604 1668 2.808906 ACATAGCCTCCACCCTTTTC 57.191 50.000 0.00 0.00 0.00 2.29
1650 1714 5.050023 GGAGAAAGAGAAAGTCTGGTTTTCG 60.050 44.000 0.00 0.00 39.07 3.46
1706 1770 3.263170 TGAGGTAGCAGAGCAAACCATAA 59.737 43.478 13.63 0.00 38.67 1.90
1910 1984 5.407691 AGATGCAAATATAGATCACACTGCG 59.592 40.000 0.00 0.00 0.00 5.18
2235 2658 1.972978 ACCTGGGTGAGTAAGCGAC 59.027 57.895 0.00 0.00 0.00 5.19
2318 2745 1.212616 GTGACTGAGTGCACACAGAC 58.787 55.000 39.44 34.11 37.86 3.51
2473 2901 6.421801 AGTGAGCAACAAAACAAAAGCATATC 59.578 34.615 0.00 0.00 0.00 1.63
2666 3156 6.126863 TCTTAACATCAAGGGACAAGACAT 57.873 37.500 0.00 0.00 0.00 3.06
2692 3207 6.197468 GTCATCGAGTATTAGAGTCAGTTTGC 59.803 42.308 0.00 0.00 0.00 3.68
2716 3232 5.705905 GGTGCCAAAGTAAACTTAGAGATGT 59.294 40.000 0.00 0.00 34.61 3.06
3010 3539 4.916041 TGATCAGGTCTCTGTCCATTTT 57.084 40.909 0.00 0.00 41.59 1.82
3073 3602 4.894784 ACAATAGTTCTGTGGTAGGTGTG 58.105 43.478 0.00 0.00 0.00 3.82
3101 3883 9.362151 TCCCAAAATAAGTGTCTCAAAATAAGT 57.638 29.630 0.00 0.00 0.00 2.24
3102 3884 9.626045 GTCCCAAAATAAGTGTCTCAAAATAAG 57.374 33.333 0.00 0.00 0.00 1.73
3103 3885 8.293867 CGTCCCAAAATAAGTGTCTCAAAATAA 58.706 33.333 0.00 0.00 0.00 1.40
3104 3886 7.094549 CCGTCCCAAAATAAGTGTCTCAAAATA 60.095 37.037 0.00 0.00 0.00 1.40
3105 3887 6.294508 CCGTCCCAAAATAAGTGTCTCAAAAT 60.295 38.462 0.00 0.00 0.00 1.82
3106 3888 5.009210 CCGTCCCAAAATAAGTGTCTCAAAA 59.991 40.000 0.00 0.00 0.00 2.44
3107 3889 4.517453 CCGTCCCAAAATAAGTGTCTCAAA 59.483 41.667 0.00 0.00 0.00 2.69
3108 3890 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3109 3891 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3110 3892 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3111 3893 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3112 3894 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3113 3895 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3114 3896 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3115 3897 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3116 3898 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3117 3899 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3118 3900 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3119 3901 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3120 3902 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3121 3903 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3122 3904 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
3123 3905 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
3124 3906 1.201424 AATTGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
3125 3907 3.007635 CAAAATTGTACTCCCTCCGTCC 58.992 50.000 0.00 0.00 0.00 4.79
3126 3908 3.671716 ACAAAATTGTACTCCCTCCGTC 58.328 45.455 0.00 0.00 40.16 4.79
3127 3909 3.782656 ACAAAATTGTACTCCCTCCGT 57.217 42.857 0.00 0.00 40.16 4.69
3128 3910 4.574828 CCATACAAAATTGTACTCCCTCCG 59.425 45.833 8.09 0.00 45.47 4.63
3129 3911 5.589050 GTCCATACAAAATTGTACTCCCTCC 59.411 44.000 8.09 0.00 45.47 4.30
3130 3912 6.415573 AGTCCATACAAAATTGTACTCCCTC 58.584 40.000 8.09 0.00 45.47 4.30
3131 3913 6.388619 AGTCCATACAAAATTGTACTCCCT 57.611 37.500 8.09 1.15 45.47 4.20
3132 3914 8.456471 GTTTAGTCCATACAAAATTGTACTCCC 58.544 37.037 8.09 0.00 45.47 4.30
3133 3915 9.005777 TGTTTAGTCCATACAAAATTGTACTCC 57.994 33.333 8.09 0.00 45.47 3.85
3136 3918 9.124807 GCTTGTTTAGTCCATACAAAATTGTAC 57.875 33.333 8.09 0.00 45.47 2.90
3241 4027 4.040829 TCATAGTTACTGGGATGGCAGATG 59.959 45.833 0.00 0.00 0.00 2.90
3256 4042 8.257306 TGAGCACACATGTAGAAATCATAGTTA 58.743 33.333 0.00 0.00 0.00 2.24
3283 4069 2.615447 AGAACATACAATCATGCCAGCG 59.385 45.455 0.00 0.00 0.00 5.18
3292 4078 5.460419 CGCAAGGTAGAGAGAACATACAATC 59.540 44.000 0.00 0.00 0.00 2.67
3382 4185 0.178885 TGGCCTTGTAGTACCCTGGT 60.179 55.000 3.32 0.00 0.00 4.00
3389 4192 0.682852 AGTGCGTTGGCCTTGTAGTA 59.317 50.000 3.32 0.00 38.85 1.82
3528 4331 2.419713 GCAGTGATGATCAGAGGCAAGA 60.420 50.000 0.09 0.00 0.00 3.02
3569 4385 2.561569 ACCTGAAACGAGTTCACAAGG 58.438 47.619 0.00 0.00 41.47 3.61
3830 6182 4.147826 CAGAAGAACATCGATGACGCTATG 59.852 45.833 31.33 19.30 39.58 2.23
3932 6287 1.744368 AGCGCTCAGGCATGAACAG 60.744 57.895 2.64 0.00 38.60 3.16
3998 6356 7.144722 TGATAGCAATCAAAGATTGTTCGTT 57.855 32.000 17.93 4.65 39.20 3.85
4141 6692 2.672651 CCGTTGGACATGCTGCCA 60.673 61.111 0.00 0.00 0.00 4.92
4216 7042 4.349365 TCCAGGGCCTTTAAGTAAATTGG 58.651 43.478 1.32 0.00 0.00 3.16
4232 7071 2.052104 GCGGGGTCAAAATCCAGGG 61.052 63.158 0.00 0.00 0.00 4.45
4238 7081 1.074889 ACCTGTAAGCGGGGTCAAAAT 59.925 47.619 0.00 0.00 45.50 1.82
4437 7843 7.853929 GCGAATTACTTCACAACTTCAGTTTTA 59.146 33.333 0.00 0.00 35.83 1.52
4438 7844 6.691388 GCGAATTACTTCACAACTTCAGTTTT 59.309 34.615 0.00 0.00 35.83 2.43
4447 7853 8.175069 TCTGAATAATGCGAATTACTTCACAAC 58.825 33.333 12.97 0.00 27.95 3.32
4450 7856 8.551205 TGATCTGAATAATGCGAATTACTTCAC 58.449 33.333 12.97 7.81 0.00 3.18
4454 7860 7.307632 GCACTGATCTGAATAATGCGAATTACT 60.308 37.037 6.60 0.00 0.00 2.24
4461 7867 4.541085 TTGCACTGATCTGAATAATGCG 57.459 40.909 6.60 0.00 34.32 4.73
4509 7915 7.768120 AGATTGATTGACTAGATGAGGTTTGAC 59.232 37.037 0.00 0.00 0.00 3.18
4512 7918 9.606631 GTTAGATTGATTGACTAGATGAGGTTT 57.393 33.333 0.00 0.00 0.00 3.27
4514 7920 8.311395 TGTTAGATTGATTGACTAGATGAGGT 57.689 34.615 0.00 0.00 0.00 3.85
4533 7939 9.958180 TGGAGTCAAAATATGAGAAATGTTAGA 57.042 29.630 0.00 0.00 39.19 2.10
4585 7992 4.081420 AGGCTTCACTAGTGATTGGTACAG 60.081 45.833 25.68 18.12 39.64 2.74
4655 8117 9.129532 GATTCATCTGATTCCTACCTCAAATTT 57.870 33.333 0.00 0.00 0.00 1.82
4668 8130 9.491675 AGACTTGTGATATGATTCATCTGATTC 57.508 33.333 1.55 0.00 0.00 2.52
4687 8149 1.883275 CGACTCACCTCAGAGACTTGT 59.117 52.381 0.00 0.00 38.98 3.16
4694 8156 1.924731 AACCATCGACTCACCTCAGA 58.075 50.000 0.00 0.00 0.00 3.27
4703 8165 6.934645 TCAATTCTGTAGAAAAACCATCGACT 59.065 34.615 0.00 0.00 37.61 4.18
4705 8167 7.921786 ATCAATTCTGTAGAAAAACCATCGA 57.078 32.000 0.00 0.00 37.61 3.59
4706 8168 8.454106 AGAATCAATTCTGTAGAAAAACCATCG 58.546 33.333 4.47 0.00 44.91 3.84
4735 8198 6.427441 AGATCGCCTCATCTATATGAAGGTA 58.573 40.000 7.77 0.90 41.57 3.08
4737 8200 5.850557 AGATCGCCTCATCTATATGAAGG 57.149 43.478 0.00 0.00 41.57 3.46
4777 8248 3.963428 AGGTAAGTTCGAGCACTGAAT 57.037 42.857 1.01 0.00 0.00 2.57
4778 8249 3.069016 TCAAGGTAAGTTCGAGCACTGAA 59.931 43.478 1.01 0.00 0.00 3.02
4780 8251 3.026630 TCAAGGTAAGTTCGAGCACTG 57.973 47.619 1.01 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.