Multiple sequence alignment - TraesCS7D01G238200

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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 TraesCS7D01G238200 chr7D 100.000 4356 0 0 1 4356 203408330 203403975 0.000000e+00 8045.0
1 TraesCS7D01G238200 chr7D 83.485 551 79 8 3816 4356 175442955 175442407 1.810000e-138 503.0
2 TraesCS7D01G238200 chr7A 93.300 2821 98 29 802 3581 215192976 215190206 0.000000e+00 4078.0
3 TraesCS7D01G238200 chr7A 91.393 732 55 5 6 732 215193930 215193202 0.000000e+00 996.0
4 TraesCS7D01G238200 chr7A 77.011 522 105 10 3834 4343 666593750 666594268 7.130000e-73 285.0
5 TraesCS7D01G238200 chr7A 78.423 241 42 8 355 588 486179231 486179468 9.760000e-32 148.0
6 TraesCS7D01G238200 chr7A 95.455 88 4 0 3637 3724 215189585 215189498 1.630000e-29 141.0
7 TraesCS7D01G238200 chr7A 89.423 104 9 2 633 735 682889608 682889710 3.540000e-26 130.0
8 TraesCS7D01G238200 chr7A 92.593 54 4 0 3593 3646 215190041 215189988 1.300000e-10 78.7
9 TraesCS7D01G238200 chr7B 92.339 1475 64 15 2221 3669 167007553 167006102 0.000000e+00 2052.0
10 TraesCS7D01G238200 chr7B 94.041 1309 40 7 901 2177 167008845 167007543 0.000000e+00 1951.0
11 TraesCS7D01G238200 chr7B 88.005 867 71 16 3 857 167013013 167012168 0.000000e+00 994.0
12 TraesCS7D01G238200 chr7B 85.921 554 58 11 3819 4356 167005743 167005194 1.360000e-159 573.0
13 TraesCS7D01G238200 chr5A 84.715 543 67 9 3817 4349 37642650 37643186 2.980000e-146 529.0
14 TraesCS7D01G238200 chr2A 84.392 551 70 8 3817 4356 747329318 747329863 1.070000e-145 527.0
15 TraesCS7D01G238200 chr5D 83.935 554 75 5 3817 4356 380519808 380520361 6.460000e-143 518.0
16 TraesCS7D01G238200 chr5D 81.982 111 13 5 631 734 287789115 287789225 2.160000e-13 87.9
17 TraesCS7D01G238200 chr3B 83.912 547 72 11 3819 4354 794589548 794590089 3.890000e-140 508.0
18 TraesCS7D01G238200 chr2D 85.336 491 59 5 3877 4356 136757874 136758362 3.030000e-136 496.0
19 TraesCS7D01G238200 chr2D 83.529 510 70 11 3858 4356 572039495 572040001 8.530000e-127 464.0
20 TraesCS7D01G238200 chr2D 79.098 244 44 6 356 595 18206501 18206741 1.250000e-35 161.0
21 TraesCS7D01G238200 chr2D 84.158 101 14 2 634 732 538270891 538270991 3.590000e-16 97.1
22 TraesCS7D01G238200 chr4B 83.427 531 78 4 3835 4356 443634547 443635076 6.550000e-133 484.0
23 TraesCS7D01G238200 chr4B 82.759 435 58 11 3835 4256 616970829 616971259 5.320000e-99 372.0
24 TraesCS7D01G238200 chr4B 80.342 234 41 4 360 590 108354732 108354963 5.790000e-39 172.0
25 TraesCS7D01G238200 chr4D 85.139 397 49 2 3855 4241 12357047 12356651 8.780000e-107 398.0
26 TraesCS7D01G238200 chr4D 86.179 123 14 1 3604 3726 285135510 285135629 3.540000e-26 130.0
27 TraesCS7D01G238200 chr3D 79.661 531 92 10 3839 4355 306267063 306266535 6.880000e-98 368.0
28 TraesCS7D01G238200 chr3D 80.690 145 25 3 452 595 595062142 595062000 4.610000e-20 110.0
29 TraesCS7D01G238200 chr1D 82.892 415 59 6 3877 4281 239554628 239554216 3.200000e-96 363.0
30 TraesCS7D01G238200 chr1D 80.814 172 32 1 3814 3984 437622528 437622357 2.730000e-27 134.0
31 TraesCS7D01G238200 chr6B 81.297 401 60 7 3857 4246 175336192 175335796 1.180000e-80 311.0
32 TraesCS7D01G238200 chr6B 84.255 235 37 0 3820 4054 510233326 510233092 3.390000e-56 230.0
33 TraesCS7D01G238200 chr6B 77.253 233 45 8 360 588 28115226 28114998 3.540000e-26 130.0
34 TraesCS7D01G238200 chr1A 77.354 446 84 11 3907 4341 585679548 585679987 9.350000e-62 248.0
35 TraesCS7D01G238200 chr1A 79.012 243 41 9 354 590 311849079 311849317 1.620000e-34 158.0
36 TraesCS7D01G238200 chr6D 77.056 231 48 5 360 588 16284486 16284259 1.270000e-25 128.0
37 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 186188794 186188908 4.610000e-20 110.0
38 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 221554706 221554592 4.610000e-20 110.0
39 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 229488314 229488200 4.610000e-20 110.0
40 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 304151668 304151554 4.610000e-20 110.0
41 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 386206114 386206000 4.610000e-20 110.0
42 TraesCS7D01G238200 chrUn 83.740 123 12 4 3604 3726 446244275 446244389 4.610000e-20 110.0
43 TraesCS7D01G238200 chrUn 93.243 74 3 1 3655 3726 86480633 86480560 1.660000e-19 108.0
44 TraesCS7D01G238200 chr4A 100.000 29 0 0 1339 1367 684965264 684965292 2.000000e-03 54.7


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 TraesCS7D01G238200 chr7D 203403975 203408330 4355 True 8045.000 8045 100.00000 1 4356 1 chr7D.!!$R2 4355
1 TraesCS7D01G238200 chr7D 175442407 175442955 548 True 503.000 503 83.48500 3816 4356 1 chr7D.!!$R1 540
2 TraesCS7D01G238200 chr7A 215189498 215193930 4432 True 1323.425 4078 93.18525 6 3724 4 chr7A.!!$R1 3718
3 TraesCS7D01G238200 chr7A 666593750 666594268 518 False 285.000 285 77.01100 3834 4343 1 chr7A.!!$F2 509
4 TraesCS7D01G238200 chr7B 167005194 167013013 7819 True 1392.500 2052 90.07650 3 4356 4 chr7B.!!$R1 4353
5 TraesCS7D01G238200 chr5A 37642650 37643186 536 False 529.000 529 84.71500 3817 4349 1 chr5A.!!$F1 532
6 TraesCS7D01G238200 chr2A 747329318 747329863 545 False 527.000 527 84.39200 3817 4356 1 chr2A.!!$F1 539
7 TraesCS7D01G238200 chr5D 380519808 380520361 553 False 518.000 518 83.93500 3817 4356 1 chr5D.!!$F2 539
8 TraesCS7D01G238200 chr3B 794589548 794590089 541 False 508.000 508 83.91200 3819 4354 1 chr3B.!!$F1 535
9 TraesCS7D01G238200 chr2D 572039495 572040001 506 False 464.000 464 83.52900 3858 4356 1 chr2D.!!$F4 498
10 TraesCS7D01G238200 chr4B 443634547 443635076 529 False 484.000 484 83.42700 3835 4356 1 chr4B.!!$F2 521
11 TraesCS7D01G238200 chr3D 306266535 306267063 528 True 368.000 368 79.66100 3839 4355 1 chr3D.!!$R1 516

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
539 546 0.107703 TGCCATCCTCGATGAACACC 60.108 55.000 3.18 0.0 42.09 4.16 F
816 979 1.002251 CGCCGTGCCTAAAAACTTGAA 60.002 47.619 0.00 0.0 0.00 2.69 F
1927 5401 0.106769 ATGTGCCAACCCATATGCGA 60.107 50.000 0.00 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 5345 0.621571 TCCCATCTCACCCTTCCCAG 60.622 60.0 0.0 0.0 0.00 4.45 R
2568 6042 0.471617 ACAAGCCTCAGAGCAGTTGT 59.528 50.0 0.0 0.0 34.23 3.32 R
3735 8012 0.107165 GGCTGCGTAATCCTCCCTTT 60.107 55.0 0.0 0.0 0.00 3.11 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
54 59 8.635765 AGTTTATAAGAAGCAGTTCATTTGGA 57.364 30.769 0.00 0.00 34.82 3.53
73 78 3.263170 TGGACGATTCTCCCAAAATCTCA 59.737 43.478 0.00 0.00 32.15 3.27
90 95 3.664107 TCTCAACAATTGGTTCTCCTCG 58.336 45.455 10.83 0.00 37.72 4.63
220 226 8.116026 AGTGGGTGGTATGATTCTAAAAATTCT 58.884 33.333 0.00 0.00 0.00 2.40
321 328 9.226345 GAAATGTAGTTTTATGTAATCTGCTGC 57.774 33.333 0.00 0.00 0.00 5.25
378 385 8.570068 AATACGGAAAGGCTAAAAATCTAACA 57.430 30.769 0.00 0.00 0.00 2.41
381 388 6.183360 ACGGAAAGGCTAAAAATCTAACATCG 60.183 38.462 0.00 0.00 0.00 3.84
403 410 6.703319 TCGGACTTTTAGACATGGTAAATCA 58.297 36.000 0.00 0.00 0.00 2.57
405 412 7.333423 TCGGACTTTTAGACATGGTAAATCAAG 59.667 37.037 0.00 0.00 0.00 3.02
412 419 5.699839 AGACATGGTAAATCAAGCGTTTTC 58.300 37.500 0.00 0.00 0.00 2.29
442 449 8.286097 TGCAATTTATATTGACGCGATAATGAA 58.714 29.630 15.93 8.77 43.12 2.57
450 457 6.749216 TTGACGCGATAATGAAAGATCTAC 57.251 37.500 15.93 0.00 0.00 2.59
475 482 2.224079 GCAAGCACGACAATTCTCTGAA 59.776 45.455 0.00 0.00 0.00 3.02
522 529 3.482786 CATGCTCGTGAACTAAACTTGC 58.517 45.455 0.00 0.00 0.00 4.01
539 546 0.107703 TGCCATCCTCGATGAACACC 60.108 55.000 3.18 0.00 42.09 4.16
548 555 3.118775 CCTCGATGAACACCCTTGTCATA 60.119 47.826 0.00 0.00 33.55 2.15
711 718 4.542735 GCAAATTAGTTTACAAGCACGGT 58.457 39.130 0.00 0.00 0.00 4.83
764 782 4.398988 TCAACTAAATTTGCCATGCTCGAT 59.601 37.500 0.00 0.00 0.00 3.59
816 979 1.002251 CGCCGTGCCTAAAAACTTGAA 60.002 47.619 0.00 0.00 0.00 2.69
830 993 7.873739 AAAAACTTGAAATTAGCTGGATTCG 57.126 32.000 0.00 0.00 0.00 3.34
833 998 5.253330 ACTTGAAATTAGCTGGATTCGGAA 58.747 37.500 0.00 0.00 0.00 4.30
1065 4509 1.747367 CGAGTCCTCCGCTGAGTCT 60.747 63.158 4.34 2.54 36.86 3.24
1198 4642 2.203337 GTGGCAGAGGTGGTGCAA 60.203 61.111 0.00 0.00 43.12 4.08
1444 4888 3.470567 GCGCTGACTCCGACAACG 61.471 66.667 0.00 0.00 39.43 4.10
1565 5009 4.835927 CGGGAAGAATCACCGGAG 57.164 61.111 9.46 0.00 43.69 4.63
1612 5062 2.266055 CTCACACCGCCTTCTCCC 59.734 66.667 0.00 0.00 0.00 4.30
1806 5277 1.537889 TGGGAGTAGTGTGGTGGGG 60.538 63.158 0.00 0.00 0.00 4.96
1808 5279 1.265454 GGGAGTAGTGTGGTGGGGAG 61.265 65.000 0.00 0.00 0.00 4.30
1817 5288 1.465188 TGGTGGGGAGATTGGGTGT 60.465 57.895 0.00 0.00 0.00 4.16
1833 5304 1.824852 GGTGTGGGAAATGGTGATTCC 59.175 52.381 0.00 0.00 44.61 3.01
1927 5401 0.106769 ATGTGCCAACCCATATGCGA 60.107 50.000 0.00 0.00 0.00 5.10
2056 5530 5.262422 GTTTGTACAAACCAATGCTTTTGC 58.738 37.500 32.27 9.89 43.52 3.68
2180 5654 9.956640 TTGATATTGTTATTTGCTTTTTGGGAT 57.043 25.926 0.00 0.00 0.00 3.85
2195 5669 7.068716 GCTTTTTGGGATGGAATGAACTATAGT 59.931 37.037 0.00 0.00 0.00 2.12
2440 5914 8.125978 AGTTGATTATGTTTGACATGACCAAT 57.874 30.769 0.00 0.00 39.53 3.16
2493 5967 5.057149 GTGGTCTACTGTGACATTCAGTTT 58.943 41.667 4.23 0.00 42.50 2.66
2568 6042 5.451242 GGTTGTCTGCTAACCATGTTTTGAA 60.451 40.000 0.00 0.00 45.43 2.69
2591 6065 1.001860 ACTGCTCTGAGGCTTGTCTTC 59.998 52.381 6.83 0.00 0.00 2.87
2595 6069 3.080319 GCTCTGAGGCTTGTCTTCAAAT 58.920 45.455 6.83 0.00 32.87 2.32
2674 6159 8.227119 TCGTGATATGATTTACCATTTTATGCG 58.773 33.333 0.00 0.00 0.00 4.73
2698 6184 7.326063 GCGTTAGTTTCAAGTAATCATTGCTTT 59.674 33.333 0.00 0.00 33.12 3.51
2704 6190 9.745323 GTTTCAAGTAATCATTGCTTTTAATGC 57.255 29.630 0.00 0.00 37.83 3.56
2705 6191 9.486497 TTTCAAGTAATCATTGCTTTTAATGCA 57.514 25.926 0.00 1.26 37.83 3.96
2706 6192 9.656040 TTCAAGTAATCATTGCTTTTAATGCAT 57.344 25.926 6.36 0.00 40.34 3.96
2752 6238 3.009033 TGGTGATCGGGAAAGAATCAACT 59.991 43.478 0.00 0.00 30.81 3.16
2769 6255 4.644498 TCAACTGATGATCTTGAAGCACA 58.356 39.130 0.00 0.00 31.50 4.57
2832 6318 7.719483 TCTGTTGAAGAAGCAAATGAAAAGAT 58.281 30.769 0.00 0.00 29.54 2.40
2833 6319 7.650504 TCTGTTGAAGAAGCAAATGAAAAGATG 59.349 33.333 0.00 0.00 29.54 2.90
2944 6430 0.392461 GGGCGTGGAGAAGTGCAATA 60.392 55.000 0.00 0.00 0.00 1.90
2992 6478 2.355132 GCCAGATCTTGATCAACTGCTG 59.645 50.000 15.65 15.30 0.00 4.41
3040 6526 1.558294 TGCATCATCCTGACAAGAGCT 59.442 47.619 0.00 0.00 0.00 4.09
3058 6544 1.476833 GCTTCTCAAACCTGGACACCA 60.477 52.381 0.00 0.00 0.00 4.17
3091 6577 2.419324 TCGAAAAGCTCTCTACGAGGAC 59.581 50.000 0.00 0.00 40.25 3.85
3140 6626 0.111089 GCTCGAACTCAAACTGCGTG 60.111 55.000 0.00 0.00 0.00 5.34
3178 6664 4.160329 CAGCAATACTAGGGGAGATGGTA 58.840 47.826 0.00 0.00 0.00 3.25
3343 6829 1.519455 GCCATCCTCGACCGAGTTG 60.519 63.158 16.86 13.40 40.44 3.16
3369 6855 3.946558 CCTACGTGAGCTTAGAAGTACCT 59.053 47.826 0.00 0.00 0.00 3.08
3370 6856 4.035441 CCTACGTGAGCTTAGAAGTACCTC 59.965 50.000 0.00 0.00 0.00 3.85
3371 6857 3.688235 ACGTGAGCTTAGAAGTACCTCT 58.312 45.455 0.00 0.00 0.00 3.69
3372 6858 4.841422 ACGTGAGCTTAGAAGTACCTCTA 58.159 43.478 0.00 0.00 0.00 2.43
3373 6859 4.635324 ACGTGAGCTTAGAAGTACCTCTAC 59.365 45.833 0.44 0.00 0.00 2.59
3374 6860 4.260294 CGTGAGCTTAGAAGTACCTCTACG 60.260 50.000 0.44 1.04 0.00 3.51
3375 6861 4.635324 GTGAGCTTAGAAGTACCTCTACGT 59.365 45.833 0.44 0.00 0.00 3.57
3376 6862 4.634883 TGAGCTTAGAAGTACCTCTACGTG 59.365 45.833 0.00 0.00 0.00 4.49
3377 6863 4.841422 AGCTTAGAAGTACCTCTACGTGA 58.159 43.478 0.00 0.00 0.00 4.35
3378 6864 4.877251 AGCTTAGAAGTACCTCTACGTGAG 59.123 45.833 0.00 3.02 42.30 3.51
3379 6865 4.496175 GCTTAGAAGTACCTCTACGTGAGC 60.496 50.000 0.00 4.31 41.35 4.26
3442 6928 4.957684 AGAAGAATATACCGGACAAGGG 57.042 45.455 9.46 0.00 35.02 3.95
3588 7228 5.482908 TCAGCTAATCACTGAGGAAAGTTC 58.517 41.667 0.00 0.00 39.21 3.01
3601 7241 4.618965 AGGAAAGTTCGTGTACTGAGTTC 58.381 43.478 0.00 0.00 0.00 3.01
3630 7270 1.533625 TGGGAAATGTTTGCGAGAGG 58.466 50.000 0.00 0.00 0.00 3.69
3693 7970 1.742411 CGGGTTGCGTCTGGTATGATT 60.742 52.381 0.00 0.00 0.00 2.57
3724 8001 7.931948 TGCTTTATCTAAACTAGGCAGGATAAC 59.068 37.037 0.00 0.00 0.00 1.89
3725 8002 8.151596 GCTTTATCTAAACTAGGCAGGATAACT 58.848 37.037 0.00 0.00 0.00 2.24
3726 8003 9.699703 CTTTATCTAAACTAGGCAGGATAACTC 57.300 37.037 0.00 0.00 0.00 3.01
3727 8004 9.435570 TTTATCTAAACTAGGCAGGATAACTCT 57.564 33.333 0.00 0.00 0.00 3.24
3728 8005 7.922699 ATCTAAACTAGGCAGGATAACTCTT 57.077 36.000 0.00 0.00 0.00 2.85
3729 8006 7.735326 TCTAAACTAGGCAGGATAACTCTTT 57.265 36.000 0.00 0.00 0.00 2.52
3730 8007 8.147244 TCTAAACTAGGCAGGATAACTCTTTT 57.853 34.615 0.00 0.00 0.00 2.27
3731 8008 8.603304 TCTAAACTAGGCAGGATAACTCTTTTT 58.397 33.333 0.00 0.00 0.00 1.94
3752 8029 5.890424 TTTTTAAAGGGAGGATTACGCAG 57.110 39.130 0.00 0.00 0.00 5.18
3753 8030 2.614829 TAAAGGGAGGATTACGCAGC 57.385 50.000 0.00 0.00 0.00 5.25
3754 8031 0.107165 AAAGGGAGGATTACGCAGCC 60.107 55.000 0.00 0.00 0.00 4.85
3755 8032 0.983378 AAGGGAGGATTACGCAGCCT 60.983 55.000 0.00 0.00 33.97 4.58
3756 8033 1.227674 GGGAGGATTACGCAGCCTG 60.228 63.158 0.00 0.00 30.70 4.85
3757 8034 1.227674 GGAGGATTACGCAGCCTGG 60.228 63.158 0.00 0.00 30.70 4.45
3758 8035 1.522569 GAGGATTACGCAGCCTGGT 59.477 57.895 0.00 0.00 30.70 4.00
3759 8036 0.750850 GAGGATTACGCAGCCTGGTA 59.249 55.000 0.00 0.00 30.70 3.25
3760 8037 1.138266 GAGGATTACGCAGCCTGGTAA 59.862 52.381 0.00 7.82 33.56 2.85
3761 8038 1.134491 AGGATTACGCAGCCTGGTAAC 60.134 52.381 7.61 3.94 31.99 2.50
3796 8073 0.761802 GGAGGATTACCCAGCCTCTG 59.238 60.000 6.13 0.00 45.87 3.35
3810 8087 3.036819 AGCCTCTGCAGTAGAATGATGA 58.963 45.455 14.67 0.00 41.13 2.92
3813 8090 4.213694 GCCTCTGCAGTAGAATGATGAATG 59.786 45.833 14.67 0.00 34.32 2.67
3852 8151 2.853731 TAGAGCAAGCTCGCTTAGAC 57.146 50.000 15.67 0.00 46.90 2.59
3901 8205 0.241481 GCCACAACCGGCGAAAATAA 59.759 50.000 9.30 0.00 43.52 1.40
3902 8206 1.135228 GCCACAACCGGCGAAAATAAT 60.135 47.619 9.30 0.00 43.52 1.28
3939 8249 4.954202 ACATCTGTTCTATTACTGGACCGA 59.046 41.667 0.00 0.00 0.00 4.69
3943 8253 5.421056 TCTGTTCTATTACTGGACCGACATT 59.579 40.000 0.00 0.00 0.00 2.71
3965 8275 5.506730 TCAAACTGGTTGTACATATCCCA 57.493 39.130 5.20 0.18 38.47 4.37
4194 8518 7.764141 TGTATATACTCCATTTAGCCACGTA 57.236 36.000 13.89 0.00 0.00 3.57
4208 8532 5.734855 AGCCACGTATCAAATAACATGTC 57.265 39.130 0.00 0.00 0.00 3.06
4320 8645 6.957920 TGGTTTCATCTTGATCACAAAAGA 57.042 33.333 0.00 0.00 36.87 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 40 4.637276 TCGTCCAAATGAACTGCTTCTTA 58.363 39.130 0.00 0.00 0.00 2.10
36 41 3.476552 TCGTCCAAATGAACTGCTTCTT 58.523 40.909 0.00 0.00 0.00 2.52
54 59 4.651778 TGTTGAGATTTTGGGAGAATCGT 58.348 39.130 0.00 0.00 38.29 3.73
73 78 3.721087 ATCCGAGGAGAACCAATTGTT 57.279 42.857 4.43 0.00 40.81 2.83
147 153 8.511604 ACCATATTTCTTGACAATCCTAACTG 57.488 34.615 0.00 0.00 0.00 3.16
186 192 6.268847 AGAATCATACCACCCACTAGATTCTC 59.731 42.308 0.00 0.00 43.83 2.87
220 226 6.356556 TCAGTTCTTTTGGTCATTTCTCTCA 58.643 36.000 0.00 0.00 0.00 3.27
228 234 7.442666 GTCTTTAGTCTCAGTTCTTTTGGTCAT 59.557 37.037 0.00 0.00 0.00 3.06
231 237 6.650120 TGTCTTTAGTCTCAGTTCTTTTGGT 58.350 36.000 0.00 0.00 0.00 3.67
321 328 8.925700 GCAGATTCCCAAAAGTTATGTAAAAAG 58.074 33.333 0.00 0.00 0.00 2.27
378 385 7.335627 TGATTTACCATGTCTAAAAGTCCGAT 58.664 34.615 0.00 0.00 0.00 4.18
381 388 7.251281 GCTTGATTTACCATGTCTAAAAGTCC 58.749 38.462 0.00 0.00 0.00 3.85
412 419 9.753669 TTATCGCGTCAATATAAATTGCAATAG 57.246 29.630 13.39 0.00 41.96 1.73
475 482 4.776795 ATTTGCCTCGGTTCGTATTTTT 57.223 36.364 0.00 0.00 0.00 1.94
493 500 2.297033 AGTTCACGAGCATGGCAAATTT 59.703 40.909 0.00 0.00 0.00 1.82
500 507 3.667960 GCAAGTTTAGTTCACGAGCATGG 60.668 47.826 0.00 0.00 0.00 3.66
510 517 3.596214 TCGAGGATGGCAAGTTTAGTTC 58.404 45.455 0.00 0.00 0.00 3.01
522 529 0.833287 AGGGTGTTCATCGAGGATGG 59.167 55.000 0.00 0.00 40.15 3.51
626 633 3.644966 TTCCATGCCTAAAACTCCGAT 57.355 42.857 0.00 0.00 0.00 4.18
665 672 6.735694 GCCATTCTCGCACCAATATAAATTGT 60.736 38.462 0.00 0.00 40.84 2.71
678 685 3.764885 ACTAATTTGCCATTCTCGCAC 57.235 42.857 0.00 0.00 35.56 5.34
732 739 4.379918 GGCAAATTTAGTTGAGGAGCACTC 60.380 45.833 1.81 1.81 46.78 3.51
740 758 4.100529 CGAGCATGGCAAATTTAGTTGAG 58.899 43.478 0.00 0.00 0.00 3.02
816 979 3.933861 AGGTTCCGAATCCAGCTAATT 57.066 42.857 0.00 0.00 0.00 1.40
830 993 4.492494 TCCTCCCGTATTAAAAGGTTCC 57.508 45.455 0.00 0.00 0.00 3.62
833 998 5.193124 AGGATTTCCTCCCGTATTAAAAGGT 59.807 40.000 0.00 0.00 44.77 3.50
862 4247 6.012508 TGGGTTATCAAGAGAAAGTGGAGAAT 60.013 38.462 0.00 0.00 0.00 2.40
1198 4642 3.112075 CTGTGCCGCGTCGTCATT 61.112 61.111 4.92 0.00 0.00 2.57
1363 4807 4.162690 ATCCGGGTCCAGCTTCGC 62.163 66.667 0.00 0.00 0.00 4.70
1364 4808 2.107141 GATCCGGGTCCAGCTTCG 59.893 66.667 2.19 0.00 0.00 3.79
1806 5277 2.102578 CCATTTCCCACACCCAATCTC 58.897 52.381 0.00 0.00 0.00 2.75
1808 5279 1.550072 CACCATTTCCCACACCCAATC 59.450 52.381 0.00 0.00 0.00 2.67
1817 5288 0.701731 ACCGGAATCACCATTTCCCA 59.298 50.000 9.46 0.00 39.63 4.37
1833 5304 1.012086 CCTCAACATCAGCATCACCG 58.988 55.000 0.00 0.00 0.00 4.94
1874 5345 0.621571 TCCCATCTCACCCTTCCCAG 60.622 60.000 0.00 0.00 0.00 4.45
2056 5530 9.630098 AAAATGCAGTAAGAACAAATACATCAG 57.370 29.630 0.00 0.00 0.00 2.90
2092 5566 7.615365 AGGAAATGTATGGCAGTTTGATCTTAA 59.385 33.333 0.00 0.00 35.34 1.85
2195 5669 6.635755 TCACTGATTGGTCATCGTATTACAA 58.364 36.000 0.00 0.00 34.08 2.41
2401 5875 6.429078 ACATAATCAACTACTGCAGCCATATG 59.571 38.462 15.27 12.90 0.00 1.78
2440 5914 7.831691 TCTACAAGGTGAAAATTCCAATGAA 57.168 32.000 0.00 0.00 34.33 2.57
2458 5932 6.046593 CACAGTAGACCACAAGTTTCTACAA 58.953 40.000 12.70 0.00 42.83 2.41
2493 5967 7.160726 TCACTGATCATTTATCGGATAATGCA 58.839 34.615 11.02 0.00 42.81 3.96
2568 6042 0.471617 ACAAGCCTCAGAGCAGTTGT 59.528 50.000 0.00 0.00 34.23 3.32
2595 6069 5.231702 CAATGACAAATGAAATGGACTGCA 58.768 37.500 0.00 0.00 0.00 4.41
2609 6089 9.239310 TGTCAGTACAAACCATGCAATGACAAA 62.239 37.037 8.88 0.00 41.20 2.83
2610 6090 7.853367 TGTCAGTACAAACCATGCAATGACAA 61.853 38.462 8.88 0.00 41.20 3.18
2645 6130 9.793259 ATAAAATGGTAAATCATATCACGACCT 57.207 29.630 0.00 0.00 0.00 3.85
2704 6190 9.486497 ACAAAGTTCTGTATCTCTGCATATATG 57.514 33.333 8.45 8.45 0.00 1.78
2705 6191 9.486497 CACAAAGTTCTGTATCTCTGCATATAT 57.514 33.333 0.00 0.00 0.00 0.86
2706 6192 7.928167 CCACAAAGTTCTGTATCTCTGCATATA 59.072 37.037 0.00 0.00 0.00 0.86
2707 6193 6.765036 CCACAAAGTTCTGTATCTCTGCATAT 59.235 38.462 0.00 0.00 0.00 1.78
2708 6194 6.108687 CCACAAAGTTCTGTATCTCTGCATA 58.891 40.000 0.00 0.00 0.00 3.14
2709 6195 4.940046 CCACAAAGTTCTGTATCTCTGCAT 59.060 41.667 0.00 0.00 0.00 3.96
2721 6207 1.697432 TCCCGATCACCACAAAGTTCT 59.303 47.619 0.00 0.00 0.00 3.01
2752 6238 5.433526 TCATCATGTGCTTCAAGATCATCA 58.566 37.500 0.00 0.00 33.03 3.07
2764 6250 2.885266 GCTCCATTCATCATCATGTGCT 59.115 45.455 0.00 0.00 0.00 4.40
2769 6255 3.813724 CGAGTTGCTCCATTCATCATCAT 59.186 43.478 0.00 0.00 0.00 2.45
2832 6318 4.080695 CCATCCTTGACTCAAGATCCTTCA 60.081 45.833 18.82 0.00 43.42 3.02
2833 6319 4.163078 TCCATCCTTGACTCAAGATCCTTC 59.837 45.833 18.82 0.00 43.42 3.46
2892 6378 7.416890 GGCTGAGAGCTTCTAGTTCAAGTATTA 60.417 40.741 0.00 0.00 41.99 0.98
2944 6430 1.417890 AGCTGGTTGTTAGCACTCTGT 59.582 47.619 0.00 0.00 43.53 3.41
2974 6460 3.271729 CTGCAGCAGTTGATCAAGATCT 58.728 45.455 14.90 0.00 38.60 2.75
2992 6478 0.813210 CCGCTTCCATCTTCTCCTGC 60.813 60.000 0.00 0.00 0.00 4.85
3058 6544 0.108138 CTTTTCGATCCTCGGCCACT 60.108 55.000 2.24 0.00 40.88 4.00
3061 6547 1.153349 AGCTTTTCGATCCTCGGCC 60.153 57.895 0.00 0.00 40.88 6.13
3106 6592 2.125912 AGCTGCTTGTAGTCGCCG 60.126 61.111 0.00 0.00 0.00 6.46
3140 6626 4.373116 TGCTCGGTTCTCGGCACC 62.373 66.667 0.00 0.00 39.08 5.01
3178 6664 2.999648 TGCGCCTCCAGCTTCTCT 61.000 61.111 4.18 0.00 40.39 3.10
3343 6829 3.693578 ACTTCTAAGCTCACGTAGGTACC 59.306 47.826 2.73 2.73 33.87 3.34
3369 6855 4.582869 TGGTACTTCTAAGCTCACGTAGA 58.417 43.478 0.00 0.00 35.44 2.59
3370 6856 4.634883 TCTGGTACTTCTAAGCTCACGTAG 59.365 45.833 0.00 0.00 0.00 3.51
3371 6857 4.582869 TCTGGTACTTCTAAGCTCACGTA 58.417 43.478 0.00 0.00 0.00 3.57
3372 6858 3.418995 TCTGGTACTTCTAAGCTCACGT 58.581 45.455 0.00 0.00 0.00 4.49
3373 6859 4.082679 ACTTCTGGTACTTCTAAGCTCACG 60.083 45.833 0.00 0.00 0.00 4.35
3374 6860 5.394224 ACTTCTGGTACTTCTAAGCTCAC 57.606 43.478 0.00 0.00 0.00 3.51
3375 6861 5.304614 ACAACTTCTGGTACTTCTAAGCTCA 59.695 40.000 0.00 0.00 0.00 4.26
3376 6862 5.785243 ACAACTTCTGGTACTTCTAAGCTC 58.215 41.667 0.00 0.00 0.00 4.09
3377 6863 5.810080 ACAACTTCTGGTACTTCTAAGCT 57.190 39.130 0.00 0.00 0.00 3.74
3378 6864 5.868258 GGTACAACTTCTGGTACTTCTAAGC 59.132 44.000 0.00 0.00 39.76 3.09
3379 6865 7.091443 CAGGTACAACTTCTGGTACTTCTAAG 58.909 42.308 0.00 0.00 39.76 2.18
3442 6928 3.366374 GCTGGCAAGTTTACACAAGGATC 60.366 47.826 0.00 0.00 0.00 3.36
3588 7228 6.036083 CCATTTCCAATAGAACTCAGTACACG 59.964 42.308 0.00 0.00 32.95 4.49
3601 7241 5.291614 CGCAAACATTTCCCATTTCCAATAG 59.708 40.000 0.00 0.00 0.00 1.73
3630 7270 3.582714 AGCAGAGTTTTAGCCAATTGC 57.417 42.857 0.00 0.00 41.71 3.56
3672 7949 1.813753 CATACCAGACGCAACCCGG 60.814 63.158 0.00 0.00 42.52 5.73
3693 7970 5.183228 GCCTAGTTTAGATAAAGCACACCA 58.817 41.667 0.00 0.00 0.00 4.17
3730 8007 4.157105 GCTGCGTAATCCTCCCTTTAAAAA 59.843 41.667 0.00 0.00 0.00 1.94
3731 8008 3.692593 GCTGCGTAATCCTCCCTTTAAAA 59.307 43.478 0.00 0.00 0.00 1.52
3732 8009 3.275999 GCTGCGTAATCCTCCCTTTAAA 58.724 45.455 0.00 0.00 0.00 1.52
3733 8010 2.420967 GGCTGCGTAATCCTCCCTTTAA 60.421 50.000 0.00 0.00 0.00 1.52
3734 8011 1.140252 GGCTGCGTAATCCTCCCTTTA 59.860 52.381 0.00 0.00 0.00 1.85
3735 8012 0.107165 GGCTGCGTAATCCTCCCTTT 60.107 55.000 0.00 0.00 0.00 3.11
3736 8013 0.983378 AGGCTGCGTAATCCTCCCTT 60.983 55.000 0.00 0.00 0.00 3.95
3737 8014 1.383248 AGGCTGCGTAATCCTCCCT 60.383 57.895 0.00 0.00 0.00 4.20
3738 8015 1.227674 CAGGCTGCGTAATCCTCCC 60.228 63.158 0.00 0.00 0.00 4.30
3739 8016 1.227674 CCAGGCTGCGTAATCCTCC 60.228 63.158 9.56 0.00 0.00 4.30
3740 8017 0.750850 TACCAGGCTGCGTAATCCTC 59.249 55.000 9.56 0.00 0.00 3.71
3741 8018 1.134491 GTTACCAGGCTGCGTAATCCT 60.134 52.381 22.63 0.00 0.00 3.24
3742 8019 1.134491 AGTTACCAGGCTGCGTAATCC 60.134 52.381 22.63 14.95 0.00 3.01
3743 8020 2.311124 AGTTACCAGGCTGCGTAATC 57.689 50.000 22.63 17.69 0.00 1.75
3744 8021 2.781681 AAGTTACCAGGCTGCGTAAT 57.218 45.000 22.63 11.48 0.00 1.89
3745 8022 2.554370 AAAGTTACCAGGCTGCGTAA 57.446 45.000 18.56 18.56 0.00 3.18
3746 8023 2.554370 AAAAGTTACCAGGCTGCGTA 57.446 45.000 9.56 10.18 0.00 4.42
3747 8024 1.687563 AAAAAGTTACCAGGCTGCGT 58.312 45.000 9.56 11.22 0.00 5.24
3772 8049 1.288037 GGCTGGGTAATCCTCCCTTTT 59.712 52.381 2.65 0.00 44.84 2.27
3776 8053 0.400670 AGAGGCTGGGTAATCCTCCC 60.401 60.000 0.00 0.00 45.73 4.30
3777 8054 0.761802 CAGAGGCTGGGTAATCCTCC 59.238 60.000 0.00 0.00 45.73 4.30
3787 8064 1.483827 TCATTCTACTGCAGAGGCTGG 59.516 52.381 23.35 5.77 42.66 4.85
3788 8065 2.975732 TCATTCTACTGCAGAGGCTG 57.024 50.000 23.35 10.82 43.82 4.85
3789 8066 3.036819 TCATCATTCTACTGCAGAGGCT 58.963 45.455 23.35 0.00 41.91 4.58
3796 8073 3.303593 CGGTGCATTCATCATTCTACTGC 60.304 47.826 0.00 0.00 0.00 4.40
3810 8087 9.391006 TCTAAATTATAGACTTTTCGGTGCATT 57.609 29.630 0.00 0.00 0.00 3.56
3813 8090 7.011109 TGCTCTAAATTATAGACTTTTCGGTGC 59.989 37.037 0.00 0.00 0.00 5.01
3919 8223 4.338012 TGTCGGTCCAGTAATAGAACAGA 58.662 43.478 0.00 0.00 0.00 3.41
3922 8228 5.657474 TGAATGTCGGTCCAGTAATAGAAC 58.343 41.667 0.00 0.00 0.00 3.01
3939 8249 6.377146 GGGATATGTACAACCAGTTTGAATGT 59.623 38.462 0.00 0.00 38.73 2.71
3943 8253 5.506730 TGGGATATGTACAACCAGTTTGA 57.493 39.130 0.00 0.00 38.73 2.69
3965 8275 2.505819 ACCCGATGAAAGATGGTAGCTT 59.494 45.455 0.00 0.00 0.00 3.74
3994 8304 5.721960 TGGAAGCCAGAGAGTCTTTAGTTAT 59.278 40.000 0.00 0.00 0.00 1.89
3999 8309 3.239449 TGTGGAAGCCAGAGAGTCTTTA 58.761 45.455 0.00 0.00 32.34 1.85
4004 8314 1.622811 CTCTTGTGGAAGCCAGAGAGT 59.377 52.381 14.21 0.00 38.81 3.24
4320 8645 3.113043 GGGAGGGTAGTCAAAGGTGTAT 58.887 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.