Multiple sequence alignment - TraesCS7B01G411600

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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 TraesCS7B01G411600 chr7B 100.000 3944 0 0 1 3944 680071705 680075648 0.000000e+00 7284.0
1 TraesCS7B01G411600 chr7B 92.914 1891 78 20 1201 3066 707878724 707880583 0.000000e+00 2699.0
2 TraesCS7B01G411600 chr7B 92.540 630 33 8 3317 3944 707881132 707881749 0.000000e+00 891.0
3 TraesCS7B01G411600 chr7B 90.476 336 24 2 3609 3944 707883198 707883525 1.680000e-118 436.0
4 TraesCS7B01G411600 chr7B 95.789 190 7 1 3059 3247 707880730 707880919 4.950000e-79 305.0
5 TraesCS7B01G411600 chr7B 86.381 257 35 0 169 425 707875961 707876217 8.340000e-72 281.0
6 TraesCS7B01G411600 chr7B 78.300 447 45 21 996 1409 707831773 707832200 1.420000e-59 241.0
7 TraesCS7B01G411600 chr7B 87.079 178 8 4 1014 1191 707878503 707878665 1.870000e-43 187.0
8 TraesCS7B01G411600 chr7B 91.045 134 9 1 1229 1362 707867373 707867503 1.130000e-40 178.0
9 TraesCS7B01G411600 chr7B 90.110 91 6 1 874 964 707876738 707876825 8.960000e-22 115.0
10 TraesCS7B01G411600 chr7D 93.397 2499 83 21 822 3261 600862519 600864994 0.000000e+00 3626.0
11 TraesCS7B01G411600 chr7D 91.202 682 35 7 3264 3944 600865088 600865745 0.000000e+00 904.0
12 TraesCS7B01G411600 chr7D 83.333 222 28 6 423 639 600861825 600862042 3.110000e-46 196.0
13 TraesCS7B01G411600 chr7D 92.727 110 7 1 1299 1408 103195096 103194988 1.470000e-34 158.0
14 TraesCS7B01G411600 chr7D 80.612 98 16 3 263 359 2404910 2404815 5.470000e-09 73.1
15 TraesCS7B01G411600 chr6D 83.811 1569 176 45 2423 3944 471112251 471113788 0.000000e+00 1419.0
16 TraesCS7B01G411600 chr6D 85.182 1073 102 25 2367 3401 471277080 471276027 0.000000e+00 1048.0
17 TraesCS7B01G411600 chr6D 86.979 768 61 19 2502 3261 459552023 459551287 0.000000e+00 828.0
18 TraesCS7B01G411600 chr6D 84.840 686 45 32 1023 1657 459553448 459552771 1.550000e-178 636.0
19 TraesCS7B01G411600 chr6D 88.250 400 30 10 3264 3647 459551180 459550782 2.780000e-126 462.0
20 TraesCS7B01G411600 chr6D 75.912 274 49 10 429 691 434774729 434774462 1.490000e-24 124.0
21 TraesCS7B01G411600 chr6D 78.571 168 20 10 2086 2246 459552417 459552259 3.240000e-16 97.1
22 TraesCS7B01G411600 chr6B 82.906 1404 163 42 2582 3944 719425313 719423946 0.000000e+00 1192.0
23 TraesCS7B01G411600 chr6B 87.149 996 101 13 2364 3345 719307903 719308885 0.000000e+00 1105.0
24 TraesCS7B01G411600 chr7A 91.789 682 33 6 3264 3944 692784956 692785615 0.000000e+00 928.0
25 TraesCS7B01G411600 chr7A 96.997 333 6 1 2918 3250 692784569 692784897 1.240000e-154 556.0
26 TraesCS7B01G411600 chr7A 87.277 393 24 11 902 1270 692784169 692784559 3.640000e-115 425.0
27 TraesCS7B01G411600 chr7A 78.774 424 55 12 4 427 692782895 692783283 6.540000e-63 252.0
28 TraesCS7B01G411600 chr7A 80.612 98 17 2 263 359 3766155 3766059 1.520000e-09 75.0
29 TraesCS7B01G411600 chr2B 86.053 760 66 13 2525 3261 771415462 771416204 0.000000e+00 780.0
30 TraesCS7B01G411600 chr2B 88.689 389 27 10 3266 3647 771416318 771416696 3.590000e-125 459.0
31 TraesCS7B01G411600 chr2B 87.949 390 32 7 3264 3647 771480347 771480727 2.800000e-121 446.0
32 TraesCS7B01G411600 chr2B 95.455 44 2 0 2436 2479 771415396 771415439 1.970000e-08 71.3
33 TraesCS7B01G411600 chr6A 83.684 760 60 25 1155 1892 616095386 616094669 0.000000e+00 658.0
34 TraesCS7B01G411600 chr6A 87.152 467 48 4 2367 2826 616057203 616056742 1.620000e-143 520.0
35 TraesCS7B01G411600 chr6A 86.364 462 38 10 2820 3261 616056291 616055835 7.670000e-132 481.0
36 TraesCS7B01G411600 chr6A 82.323 198 30 5 2014 2207 616094440 616094244 2.440000e-37 167.0
37 TraesCS7B01G411600 chr3A 85.400 637 55 24 1017 1627 574317298 574317922 9.300000e-176 627.0
38 TraesCS7B01G411600 chr3A 78.280 686 102 31 3288 3944 574280179 574279512 7.940000e-107 398.0
39 TraesCS7B01G411600 chr3A 92.636 258 16 2 2712 2966 574319003 574319260 6.230000e-98 368.0
40 TraesCS7B01G411600 chr3A 91.045 134 7 3 1299 1428 502781032 502781164 4.050000e-40 176.0
41 TraesCS7B01G411600 chr3A 90.909 77 6 1 2292 2368 574318475 574318550 6.970000e-18 102.0
42 TraesCS7B01G411600 chr4B 81.633 98 16 2 263 359 595288510 595288414 3.270000e-11 80.5
43 TraesCS7B01G411600 chr1D 81.915 94 17 0 257 350 174777621 174777714 3.270000e-11 80.5
44 TraesCS7B01G411600 chrUn 82.022 89 14 2 263 350 35058134 35058221 1.520000e-09 75.0
45 TraesCS7B01G411600 chr4A 82.222 90 13 3 264 350 518935384 518935295 1.520000e-09 75.0
46 TraesCS7B01G411600 chr2A 81.818 88 16 0 263 350 695175490 695175577 1.520000e-09 75.0


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 TraesCS7B01G411600 chr7B 680071705 680075648 3943 False 7284.000000 7284 100.000000 1 3944 1 chr7B.!!$F1 3943
1 TraesCS7B01G411600 chr7B 707875961 707883525 7564 False 702.000000 2699 90.755571 169 3944 7 chr7B.!!$F4 3775
2 TraesCS7B01G411600 chr7D 600861825 600865745 3920 False 1575.333333 3626 89.310667 423 3944 3 chr7D.!!$F1 3521
3 TraesCS7B01G411600 chr6D 471112251 471113788 1537 False 1419.000000 1419 83.811000 2423 3944 1 chr6D.!!$F1 1521
4 TraesCS7B01G411600 chr6D 471276027 471277080 1053 True 1048.000000 1048 85.182000 2367 3401 1 chr6D.!!$R2 1034
5 TraesCS7B01G411600 chr6D 459550782 459553448 2666 True 505.775000 828 84.660000 1023 3647 4 chr6D.!!$R3 2624
6 TraesCS7B01G411600 chr6B 719423946 719425313 1367 True 1192.000000 1192 82.906000 2582 3944 1 chr6B.!!$R1 1362
7 TraesCS7B01G411600 chr6B 719307903 719308885 982 False 1105.000000 1105 87.149000 2364 3345 1 chr6B.!!$F1 981
8 TraesCS7B01G411600 chr7A 692782895 692785615 2720 False 540.250000 928 88.709250 4 3944 4 chr7A.!!$F1 3940
9 TraesCS7B01G411600 chr2B 771415396 771416696 1300 False 436.766667 780 90.065667 2436 3647 3 chr2B.!!$F2 1211
10 TraesCS7B01G411600 chr6A 616055835 616057203 1368 True 500.500000 520 86.758000 2367 3261 2 chr6A.!!$R1 894
11 TraesCS7B01G411600 chr6A 616094244 616095386 1142 True 412.500000 658 83.003500 1155 2207 2 chr6A.!!$R2 1052
12 TraesCS7B01G411600 chr3A 574279512 574280179 667 True 398.000000 398 78.280000 3288 3944 1 chr3A.!!$R1 656
13 TraesCS7B01G411600 chr3A 574317298 574319260 1962 False 365.666667 627 89.648333 1017 2966 3 chr3A.!!$F2 1949

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
134 135 0.038310 TCCTCTCAGGAGCACGAAGA 59.962 55.0 0.00 0.00 40.06 2.87 F
869 1219 0.045008 TACACCAATCCCTGCCCCTA 59.955 55.0 0.00 0.00 0.00 3.53 F
1714 3990 0.518559 GTTGCGCGCTAACTGCTTAC 60.519 55.0 33.29 6.19 40.11 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 3990 1.233019 GGCGGATGATGAGTCATTGG 58.767 55.0 7.16 0.0 44.96 3.16 R
1921 4386 1.398958 TTGCACAAACTGCCTTCCCC 61.399 55.0 0.00 0.0 46.51 4.81 R
3648 7281 0.823356 TGGTTTCTGCAAGGTGGAGC 60.823 55.0 0.00 0.0 35.65 4.70 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
39 40 4.722535 TTGCTCGCCCCTCCTCCT 62.723 66.667 0.00 0.00 0.00 3.69
94 95 2.663196 CCCTGTCGTTGTCCCCTC 59.337 66.667 0.00 0.00 0.00 4.30
96 97 1.913762 CCTGTCGTTGTCCCCTCCT 60.914 63.158 0.00 0.00 0.00 3.69
99 100 1.911766 GTCGTTGTCCCCTCCTCCA 60.912 63.158 0.00 0.00 0.00 3.86
114 115 4.463879 CCACCTGCTCCAGCTCCG 62.464 72.222 0.00 0.00 42.66 4.63
121 122 2.781158 GCTCCAGCTCCGTCCTCTC 61.781 68.421 0.00 0.00 38.21 3.20
129 130 1.662438 CTCCGTCCTCTCAGGAGCAC 61.662 65.000 0.00 0.00 46.90 4.40
134 135 0.038310 TCCTCTCAGGAGCACGAAGA 59.962 55.000 0.00 0.00 40.06 2.87
136 137 1.173043 CTCTCAGGAGCACGAAGAGT 58.827 55.000 0.00 0.00 32.43 3.24
141 142 1.048601 AGGAGCACGAAGAGTTTGGA 58.951 50.000 0.00 0.00 0.00 3.53
155 156 0.821711 TTTGGACAAACGGGAGGCTG 60.822 55.000 0.00 0.00 0.00 4.85
158 159 3.876589 GACAAACGGGAGGCTGCGA 62.877 63.158 0.00 0.00 0.00 5.10
224 225 2.357034 GCGGTGTGGTCGACATGT 60.357 61.111 18.91 0.00 36.78 3.21
246 247 2.678934 CGAGTCCGGAAGTGGGGA 60.679 66.667 5.23 0.00 0.00 4.81
339 340 1.131638 CCTAGCATCAACAGGGCCTA 58.868 55.000 5.28 0.00 0.00 3.93
399 400 2.659610 GACCTCTTGCTCTGCGGT 59.340 61.111 0.00 0.00 0.00 5.68
400 401 1.739562 GACCTCTTGCTCTGCGGTG 60.740 63.158 0.00 0.00 0.00 4.94
416 417 3.319198 TGGCGAGGAGGGTGAACC 61.319 66.667 0.00 0.00 40.67 3.62
538 571 1.377202 GCCTCATTTGCCGGAGACA 60.377 57.895 5.05 0.00 32.87 3.41
541 574 0.745845 CTCATTTGCCGGAGACAGGG 60.746 60.000 5.05 0.00 32.87 4.45
546 579 4.785453 GCCGGAGACAGGGCCAAG 62.785 72.222 5.05 0.00 43.64 3.61
547 580 3.003173 CCGGAGACAGGGCCAAGA 61.003 66.667 6.18 0.00 0.00 3.02
548 581 2.592993 CCGGAGACAGGGCCAAGAA 61.593 63.158 6.18 0.00 0.00 2.52
549 582 1.078848 CGGAGACAGGGCCAAGAAG 60.079 63.158 6.18 0.00 0.00 2.85
550 583 1.544825 CGGAGACAGGGCCAAGAAGA 61.545 60.000 6.18 0.00 0.00 2.87
551 584 0.915364 GGAGACAGGGCCAAGAAGAT 59.085 55.000 6.18 0.00 0.00 2.40
552 585 1.407989 GGAGACAGGGCCAAGAAGATG 60.408 57.143 6.18 0.00 0.00 2.90
553 586 1.556911 GAGACAGGGCCAAGAAGATGA 59.443 52.381 6.18 0.00 0.00 2.92
554 587 1.280421 AGACAGGGCCAAGAAGATGAC 59.720 52.381 6.18 0.00 0.00 3.06
556 589 0.250234 CAGGGCCAAGAAGATGACGA 59.750 55.000 6.18 0.00 0.00 4.20
558 591 0.462759 GGGCCAAGAAGATGACGAGG 60.463 60.000 4.39 0.00 0.00 4.63
559 592 0.537188 GGCCAAGAAGATGACGAGGA 59.463 55.000 0.00 0.00 0.00 3.71
560 593 1.066143 GGCCAAGAAGATGACGAGGAA 60.066 52.381 0.00 0.00 0.00 3.36
561 594 2.275318 GCCAAGAAGATGACGAGGAAG 58.725 52.381 0.00 0.00 0.00 3.46
562 595 2.093973 GCCAAGAAGATGACGAGGAAGA 60.094 50.000 0.00 0.00 0.00 2.87
563 596 3.516615 CCAAGAAGATGACGAGGAAGAC 58.483 50.000 0.00 0.00 0.00 3.01
567 600 1.384525 AGATGACGAGGAAGACGAGG 58.615 55.000 0.00 0.00 34.70 4.63
568 601 0.248702 GATGACGAGGAAGACGAGGC 60.249 60.000 0.00 0.00 34.70 4.70
569 602 0.681564 ATGACGAGGAAGACGAGGCT 60.682 55.000 0.00 0.00 34.70 4.58
605 641 2.202743 CGTCGTCGTCCATGGCAT 60.203 61.111 6.96 0.00 0.00 4.40
606 642 1.065109 CGTCGTCGTCCATGGCATA 59.935 57.895 6.96 0.00 0.00 3.14
611 647 2.584970 CGTCCATGGCATACGCGT 60.585 61.111 19.17 19.17 39.92 6.01
615 651 3.952675 CATGGCATACGCGTGGGC 61.953 66.667 24.59 25.03 39.92 5.36
691 908 2.304831 GGCAAGAGGGAGAAGGGCT 61.305 63.158 0.00 0.00 0.00 5.19
735 1027 3.903090 ACCCAAATTTGAGCCTGAAATGA 59.097 39.130 19.86 0.00 0.00 2.57
775 1069 1.442017 GGACATGCGTTCGTTTGGC 60.442 57.895 0.00 0.00 0.00 4.52
805 1154 1.210478 TGGGCCATTAGAGTTGCTCTC 59.790 52.381 0.00 2.14 40.34 3.20
806 1155 1.576356 GGCCATTAGAGTTGCTCTCG 58.424 55.000 0.00 0.00 46.86 4.04
808 1157 1.740380 GCCATTAGAGTTGCTCTCGCA 60.740 52.381 1.54 0.00 46.86 5.10
824 1173 8.102800 TGCTCTCGCATAAATTTCATATGAAT 57.897 30.769 18.61 7.09 42.25 2.57
869 1219 0.045008 TACACCAATCCCTGCCCCTA 59.955 55.000 0.00 0.00 0.00 3.53
908 1382 2.421529 CCCTTCCCCTTAATCTCCAACG 60.422 54.545 0.00 0.00 0.00 4.10
926 1400 2.685100 ACGGTAAAGCTACACTTCAGC 58.315 47.619 0.00 0.00 37.75 4.26
927 1401 1.654105 CGGTAAAGCTACACTTCAGCG 59.346 52.381 0.00 0.00 40.83 5.18
928 1402 2.955614 GGTAAAGCTACACTTCAGCGA 58.044 47.619 0.00 0.00 43.97 4.93
939 1413 5.156804 ACACTTCAGCGAGTAACAAAAAG 57.843 39.130 0.00 0.00 0.00 2.27
940 1414 4.873827 ACACTTCAGCGAGTAACAAAAAGA 59.126 37.500 0.00 0.00 0.00 2.52
958 1433 8.194769 ACAAAAAGAAATCCGTACAAAATGTCT 58.805 29.630 0.00 0.00 0.00 3.41
964 1439 5.796350 ATCCGTACAAAATGTCTGTAAGC 57.204 39.130 0.00 0.00 31.27 3.09
967 1442 4.433805 CCGTACAAAATGTCTGTAAGCGTC 60.434 45.833 0.00 0.00 31.27 5.19
1142 3272 4.530857 CACATCCTCGCCCGGACC 62.531 72.222 0.73 0.00 35.52 4.46
1212 3391 2.352032 CCTCACCCTCGACCTGGAC 61.352 68.421 0.00 0.00 0.00 4.02
1216 3395 3.450115 CCCTCGACCTGGACGACC 61.450 72.222 16.84 0.00 35.88 4.79
1628 3871 5.220586 GCAATGCATCATGGACAGAAATTTG 60.221 40.000 0.00 0.00 0.00 2.32
1629 3872 5.670792 ATGCATCATGGACAGAAATTTGT 57.329 34.783 0.00 0.00 0.00 2.83
1630 3873 5.471556 TGCATCATGGACAGAAATTTGTT 57.528 34.783 0.00 0.00 0.00 2.83
1666 3911 1.996191 GAAAGTCTCGACACTGCCATC 59.004 52.381 0.00 0.00 0.00 3.51
1714 3990 0.518559 GTTGCGCGCTAACTGCTTAC 60.519 55.000 33.29 6.19 40.11 2.34
1723 3999 3.307242 CGCTAACTGCTTACCAATGACTC 59.693 47.826 0.00 0.00 40.11 3.36
1753 4029 2.180204 CCCAAATCGCTAGCACCGG 61.180 63.158 16.45 0.00 0.00 5.28
1827 4137 1.608590 CCGCACTTCTGAAACCATGTT 59.391 47.619 0.00 0.00 0.00 2.71
1865 4175 6.039382 ACAAACATCCTACAGAGTTTCAAACC 59.961 38.462 0.00 0.00 32.34 3.27
1892 4202 5.005779 CACATTTTACAACTAGCTAGCTCGG 59.994 44.000 23.26 17.52 0.00 4.63
1921 4386 0.678395 ATCTGGCATGCTAGGACTCG 59.322 55.000 28.28 5.33 0.00 4.18
1998 4466 3.615155 GTCTTCCTTCATTCCTCCTTGG 58.385 50.000 0.00 0.00 37.10 3.61
2048 4518 7.278424 TGCTATATTTTTCCAAGCATGAAAAGC 59.722 33.333 0.00 8.00 41.30 3.51
2051 4521 4.669206 TTTTCCAAGCATGAAAAGCTGA 57.331 36.364 0.00 0.00 42.53 4.26
2061 4531 5.243283 AGCATGAAAAGCTGATCTGTTTCTT 59.757 36.000 0.00 7.35 41.61 2.52
2067 4537 7.172190 TGAAAAGCTGATCTGTTTCTTGTAGAG 59.828 37.037 13.32 0.00 32.41 2.43
2078 4548 8.208224 TCTGTTTCTTGTAGAGGTATTGTTTCA 58.792 33.333 0.00 0.00 0.00 2.69
2132 4604 3.558931 TCTTTCAGTTGGAGCTGACAA 57.441 42.857 0.00 0.00 44.23 3.18
2145 4617 1.369091 CTGACAAGGCGGCATGTACC 61.369 60.000 20.23 9.32 0.00 3.34
2230 4712 4.333926 GCTCTGGTTCTAGTAATTGCAAGG 59.666 45.833 4.94 0.00 0.00 3.61
2262 4880 6.923508 TGTTGAATAAGTATCTCATACCGCAG 59.076 38.462 0.00 0.00 36.40 5.18
2306 4946 3.609853 TGGTTCTATTAGCAAGGCTGTG 58.390 45.455 0.07 0.00 40.10 3.66
2340 4980 3.237268 TCCATTGTTGGCTGTTAAGGT 57.763 42.857 0.00 0.00 43.29 3.50
2365 5046 5.169295 GGGATACTATATTCTGGCGTTGTC 58.831 45.833 0.00 0.00 0.00 3.18
3083 6529 1.202428 GGGAACTAGACCTGCGACATC 60.202 57.143 0.00 0.00 0.00 3.06
3142 6594 4.313020 AATCTCTTTGGCAGTTCCTCAT 57.687 40.909 0.00 0.00 35.26 2.90
3261 6715 7.364056 CCTGAAATGATATGTGGGTGAATTTGT 60.364 37.037 0.00 0.00 0.00 2.83
3278 6878 8.697067 GTGAATTTGTGAGAATTCTTCATGTTG 58.303 33.333 9.87 0.00 43.28 3.33
3352 6954 0.110486 ACCAACAGGTAACAGCCCAG 59.890 55.000 0.00 0.00 41.41 4.45
3454 7082 5.175126 TCAGAAAAGTAGAAGCGAAGAAACG 59.825 40.000 0.00 0.00 0.00 3.60
3583 7214 5.431765 TCATGGCTTTTCCTCTATGAGTTC 58.568 41.667 0.00 0.00 35.26 3.01
3584 7215 4.908601 TGGCTTTTCCTCTATGAGTTCA 57.091 40.909 0.00 0.00 35.26 3.18
3634 7267 1.632589 GAAACAAGGGACCAGGCAAT 58.367 50.000 0.00 0.00 0.00 3.56
3653 7286 3.311110 GTGACCTCCACGGCTCCA 61.311 66.667 0.00 0.00 35.86 3.86
3654 7287 3.311110 TGACCTCCACGGCTCCAC 61.311 66.667 0.00 0.00 35.61 4.02
3688 7321 4.392047 CAAGATCATAGGTGGCATTGCTA 58.608 43.478 8.82 0.00 0.00 3.49
3802 7441 3.626924 GCCACCACGGAGACCACT 61.627 66.667 0.00 0.00 36.56 4.00
3879 7518 1.731433 CCGGTCGAAGGGCTAATCGA 61.731 60.000 0.00 5.89 45.01 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.824166 GAGCAATGGCAGCGCACG 62.824 66.667 11.47 0.01 44.61 5.34
16 17 4.809496 AGGGGCGAGCAATGGCAG 62.809 66.667 0.00 0.00 44.61 4.85
22 23 4.722535 AGGAGGAGGGGCGAGCAA 62.723 66.667 0.00 0.00 0.00 3.91
80 81 1.911766 GGAGGAGGGGACAACGACA 60.912 63.158 0.00 0.00 0.00 4.35
85 86 1.538876 CAGGTGGAGGAGGGGACAA 60.539 63.158 0.00 0.00 0.00 3.18
89 90 3.086600 GAGCAGGTGGAGGAGGGG 61.087 72.222 0.00 0.00 0.00 4.79
94 95 3.007920 AGCTGGAGCAGGTGGAGG 61.008 66.667 0.65 0.00 40.87 4.30
96 97 3.005539 GGAGCTGGAGCAGGTGGA 61.006 66.667 0.00 0.00 42.53 4.02
99 100 3.386237 GACGGAGCTGGAGCAGGT 61.386 66.667 0.00 0.00 45.28 4.00
121 122 1.151668 CCAAACTCTTCGTGCTCCTG 58.848 55.000 0.00 0.00 0.00 3.86
129 130 1.263217 CCCGTTTGTCCAAACTCTTCG 59.737 52.381 17.90 6.94 46.21 3.79
134 135 0.822121 GCCTCCCGTTTGTCCAAACT 60.822 55.000 17.90 0.00 46.21 2.66
136 137 0.821711 CAGCCTCCCGTTTGTCCAAA 60.822 55.000 0.00 0.00 0.00 3.28
141 142 3.936203 TCGCAGCCTCCCGTTTGT 61.936 61.111 0.00 0.00 0.00 2.83
177 178 3.542864 TACTACCCCCACCGTGCCA 62.543 63.158 0.00 0.00 0.00 4.92
178 179 2.684655 TACTACCCCCACCGTGCC 60.685 66.667 0.00 0.00 0.00 5.01
182 183 3.534056 CGGCTACTACCCCCACCG 61.534 72.222 0.00 0.00 0.00 4.94
211 212 2.356913 CCGCACATGTCGACCACA 60.357 61.111 14.12 0.00 40.18 4.17
237 238 1.002502 CCCCTTCGTTCCCCACTTC 60.003 63.158 0.00 0.00 0.00 3.01
330 331 2.683933 CCACGAGGTAGGCCCTGT 60.684 66.667 0.00 0.00 46.51 4.00
383 384 2.345244 CACCGCAGAGCAAGAGGT 59.655 61.111 0.00 0.00 39.91 3.85
399 400 3.319198 GGTTCACCCTCCTCGCCA 61.319 66.667 0.00 0.00 0.00 5.69
512 545 0.899717 GGCAAATGAGGCAAGGTCCA 60.900 55.000 0.00 0.00 0.00 4.02
515 548 1.978617 CCGGCAAATGAGGCAAGGT 60.979 57.895 0.00 0.00 0.00 3.50
525 558 2.044946 GCCCTGTCTCCGGCAAAT 60.045 61.111 0.00 0.00 45.01 2.32
538 571 0.539051 CTCGTCATCTTCTTGGCCCT 59.461 55.000 0.00 0.00 0.00 5.19
541 574 2.093973 TCTTCCTCGTCATCTTCTTGGC 60.094 50.000 0.00 0.00 0.00 4.52
545 578 2.680841 CTCGTCTTCCTCGTCATCTTCT 59.319 50.000 0.00 0.00 0.00 2.85
546 579 2.223386 CCTCGTCTTCCTCGTCATCTTC 60.223 54.545 0.00 0.00 0.00 2.87
547 580 1.746220 CCTCGTCTTCCTCGTCATCTT 59.254 52.381 0.00 0.00 0.00 2.40
548 581 1.384525 CCTCGTCTTCCTCGTCATCT 58.615 55.000 0.00 0.00 0.00 2.90
549 582 0.248702 GCCTCGTCTTCCTCGTCATC 60.249 60.000 0.00 0.00 0.00 2.92
550 583 0.681564 AGCCTCGTCTTCCTCGTCAT 60.682 55.000 0.00 0.00 0.00 3.06
551 584 1.303398 AGCCTCGTCTTCCTCGTCA 60.303 57.895 0.00 0.00 0.00 4.35
552 585 1.430228 GAGCCTCGTCTTCCTCGTC 59.570 63.158 0.00 0.00 0.00 4.20
553 586 2.400158 CGAGCCTCGTCTTCCTCGT 61.400 63.158 5.82 0.00 41.47 4.18
554 587 2.405594 CGAGCCTCGTCTTCCTCG 59.594 66.667 5.82 0.00 40.76 4.63
563 596 2.278206 CCACGATGACGAGCCTCG 60.278 66.667 13.52 13.52 46.93 4.63
567 600 2.509336 CCACCCACGATGACGAGC 60.509 66.667 0.00 0.00 42.66 5.03
568 601 2.184322 CCCACCCACGATGACGAG 59.816 66.667 0.00 0.00 42.66 4.18
569 602 4.077184 GCCCACCCACGATGACGA 62.077 66.667 0.00 0.00 42.66 4.20
628 664 1.895131 CATTCCCCACACTTTCCCAAG 59.105 52.381 0.00 0.00 35.92 3.61
629 665 1.482177 CCATTCCCCACACTTTCCCAA 60.482 52.381 0.00 0.00 0.00 4.12
630 666 0.114168 CCATTCCCCACACTTTCCCA 59.886 55.000 0.00 0.00 0.00 4.37
640 854 4.738998 CAGCGCCACCATTCCCCA 62.739 66.667 2.29 0.00 0.00 4.96
676 890 0.692756 GGCTAGCCCTTCTCCCTCTT 60.693 60.000 24.19 0.00 0.00 2.85
679 893 2.444895 CGGCTAGCCCTTCTCCCT 60.445 66.667 28.09 0.00 0.00 4.20
713 1005 3.903090 TCATTTCAGGCTCAAATTTGGGT 59.097 39.130 19.08 0.00 0.00 4.51
735 1027 1.737355 TTTTCGTCCGTCCCGTGACT 61.737 55.000 0.00 0.00 39.47 3.41
761 1055 2.860293 CGAGCCAAACGAACGCAT 59.140 55.556 0.00 0.00 0.00 4.73
847 1196 0.331616 GGGCAGGGATTGGTGTAGTT 59.668 55.000 0.00 0.00 0.00 2.24
908 1382 2.924290 CTCGCTGAAGTGTAGCTTTACC 59.076 50.000 0.00 0.00 39.00 2.85
926 1400 6.879962 TGTACGGATTTCTTTTTGTTACTCG 58.120 36.000 0.00 0.00 0.00 4.18
927 1401 9.505995 TTTTGTACGGATTTCTTTTTGTTACTC 57.494 29.630 0.00 0.00 0.00 2.59
939 1413 6.741358 GCTTACAGACATTTTGTACGGATTTC 59.259 38.462 0.00 0.00 31.17 2.17
940 1414 6.608610 GCTTACAGACATTTTGTACGGATTT 58.391 36.000 0.00 0.00 31.17 2.17
958 1433 1.456296 TCTCTAAGGCGACGCTTACA 58.544 50.000 20.77 2.83 0.00 2.41
992 2717 3.921021 CGGATAATACACCATCTTCTCGC 59.079 47.826 0.00 0.00 0.00 5.03
1118 3248 3.083997 GCGAGGATGTGAGGGGGT 61.084 66.667 0.00 0.00 0.00 4.95
1550 3773 2.999648 AGAAGCAGCGGCAGGAGA 61.000 61.111 12.44 0.00 44.61 3.71
1628 3871 4.336713 ACTTTCTTTCACTTGGCTCTGAAC 59.663 41.667 0.00 0.00 0.00 3.18
1629 3872 4.526970 ACTTTCTTTCACTTGGCTCTGAA 58.473 39.130 0.00 0.00 0.00 3.02
1630 3873 4.130118 GACTTTCTTTCACTTGGCTCTGA 58.870 43.478 0.00 0.00 0.00 3.27
1666 3911 6.435591 TGCTATGATGTAGAGTAGGATTCAGG 59.564 42.308 0.00 0.00 0.00 3.86
1714 3990 1.233019 GGCGGATGATGAGTCATTGG 58.767 55.000 7.16 0.00 44.96 3.16
1723 3999 2.133742 GATTTGGGCGGCGGATGATG 62.134 60.000 9.78 0.00 0.00 3.07
1753 4029 4.097863 GCGGCAGTAACAACGGGC 62.098 66.667 0.00 0.00 0.00 6.13
1827 4137 3.592059 GATGTTTGTAGACGGGTAAGCA 58.408 45.455 0.00 0.00 0.00 3.91
1865 4175 4.494199 GCTAGCTAGTTGTAAAATGTGGCG 60.494 45.833 21.62 0.00 0.00 5.69
1892 4202 3.853475 AGCATGCCAGATTAAACTTTGC 58.147 40.909 15.66 0.00 0.00 3.68
1921 4386 1.398958 TTGCACAAACTGCCTTCCCC 61.399 55.000 0.00 0.00 46.51 4.81
1952 4420 1.707117 CGATACGATGCGAGTTTACCG 59.293 52.381 0.00 0.00 0.00 4.02
1998 4466 4.574674 TTATATCCATGATGCTGGGGTC 57.425 45.455 0.00 0.00 36.89 4.46
2048 4518 8.037758 ACAATACCTCTACAAGAAACAGATCAG 58.962 37.037 0.00 0.00 0.00 2.90
2051 4521 9.220767 GAAACAATACCTCTACAAGAAACAGAT 57.779 33.333 0.00 0.00 0.00 2.90
2145 4617 1.944709 TCATCTCTGGCAAATGCATCG 59.055 47.619 0.00 0.00 44.36 3.84
2281 4899 4.943705 CAGCCTTGCTAATAGAACCAAAGA 59.056 41.667 0.00 0.00 36.40 2.52
2306 4946 9.194101 AGCCAACAATGGATCTAATGACCAAAC 62.194 40.741 0.54 0.00 43.38 2.93
2340 4980 3.786553 ACGCCAGAATATAGTATCCCCA 58.213 45.455 0.00 0.00 0.00 4.96
2365 5046 3.289076 GCGGTTCTTTCAAAAAGAGTCG 58.711 45.455 15.57 15.57 0.00 4.18
2960 6232 9.650714 ACAGGTTACAAGATACCTACATACATA 57.349 33.333 0.00 0.00 42.81 2.29
2961 6233 8.421784 CACAGGTTACAAGATACCTACATACAT 58.578 37.037 0.00 0.00 42.81 2.29
2962 6234 7.398047 ACACAGGTTACAAGATACCTACATACA 59.602 37.037 0.00 0.00 42.81 2.29
2963 6235 7.705325 CACACAGGTTACAAGATACCTACATAC 59.295 40.741 0.00 0.00 42.81 2.39
3278 6878 3.494251 CCAGCAAAAACATAACACTTGCC 59.506 43.478 1.71 0.00 42.63 4.52
3352 6954 2.271944 AAACCTGTGTTGGCCTACTC 57.728 50.000 18.31 14.91 34.13 2.59
3454 7082 1.077915 GAGCTGCTCTTGTCTGCTTC 58.922 55.000 21.93 0.00 38.55 3.86
3596 7227 1.427020 GAGCTTGTGAATGAGCGGC 59.573 57.895 0.00 0.00 0.00 6.53
3634 7267 1.681327 GGAGCCGTGGAGGTCACTA 60.681 63.158 0.00 0.00 43.94 2.74
3647 7280 1.527433 GGTTTCTGCAAGGTGGAGCC 61.527 60.000 0.00 0.00 35.65 4.70
3648 7281 0.823356 TGGTTTCTGCAAGGTGGAGC 60.823 55.000 0.00 0.00 35.65 4.70
3649 7282 1.610522 CTTGGTTTCTGCAAGGTGGAG 59.389 52.381 0.00 0.00 37.15 3.86
3650 7283 1.214175 TCTTGGTTTCTGCAAGGTGGA 59.786 47.619 0.00 0.00 0.00 4.02
3651 7284 1.691196 TCTTGGTTTCTGCAAGGTGG 58.309 50.000 0.00 0.00 0.00 4.61
3652 7285 2.886523 TGATCTTGGTTTCTGCAAGGTG 59.113 45.455 0.00 0.00 0.00 4.00
3653 7286 3.228188 TGATCTTGGTTTCTGCAAGGT 57.772 42.857 0.00 0.00 0.00 3.50
3654 7287 4.337555 CCTATGATCTTGGTTTCTGCAAGG 59.662 45.833 0.00 0.00 0.00 3.61
3688 7321 2.273449 CCGAAGAGGGCTGGCATT 59.727 61.111 2.88 0.00 35.97 3.56
3802 7441 1.307866 CAAGGGGGAGGGGAAGCTA 60.308 63.158 0.00 0.00 0.00 3.32
3874 7513 1.065701 CGAGACGGGAAGATGTCGATT 59.934 52.381 0.00 0.00 40.05 3.34
3897 7536 0.179037 AGAGTTGCTGCTGCTTGACA 60.179 50.000 17.00 0.00 40.48 3.58
3901 7540 0.110104 AAGGAGAGTTGCTGCTGCTT 59.890 50.000 17.00 2.48 45.46 3.91


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

AutoCloner maintained by Alex Coulton.