Multiple sequence alignment - TraesCS6D01G268700

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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 TraesCS6D01G268700 chr6D 100.000 4289 0 0 1 4289 379047514 379051802 0.000000e+00 7921.0
1 TraesCS6D01G268700 chr6B 90.569 4220 192 52 190 4284 565392441 565396579 0.000000e+00 5398.0
2 TraesCS6D01G268700 chr6B 80.666 1712 316 14 1301 3003 63150988 63149283 0.000000e+00 1314.0
3 TraesCS6D01G268700 chr6B 80.264 1439 269 14 1574 3003 63169006 63167574 0.000000e+00 1070.0
4 TraesCS6D01G268700 chr6B 84.028 144 22 1 712 854 440962969 440962826 2.080000e-28 137.0
5 TraesCS6D01G268700 chr6A 92.475 3442 175 37 190 3559 520439937 520443366 0.000000e+00 4844.0
6 TraesCS6D01G268700 chr6A 82.271 502 50 20 3638 4116 520508353 520508838 8.640000e-107 398.0
7 TraesCS6D01G268700 chr6A 94.118 68 3 1 3566 3632 520508230 520508297 7.590000e-18 102.0
8 TraesCS6D01G268700 chr3D 80.333 300 44 8 574 861 583966763 583966467 3.360000e-51 213.0
9 TraesCS6D01G268700 chr4A 78.351 291 49 5 574 854 6046911 6046625 4.410000e-40 176.0
10 TraesCS6D01G268700 chr4A 78.926 242 39 7 627 858 66603306 66603067 2.070000e-33 154.0
11 TraesCS6D01G268700 chr5A 80.252 238 34 6 626 854 620181800 620182033 2.650000e-37 167.0
12 TraesCS6D01G268700 chr5A 77.860 271 48 6 593 854 603532797 603532530 1.600000e-34 158.0
13 TraesCS6D01G268700 chr1A 79.310 232 36 6 632 854 372891535 372891307 7.430000e-33 152.0
14 TraesCS6D01G268700 chr4B 84.722 144 21 1 712 854 210129037 210129180 4.470000e-30 143.0
15 TraesCS6D01G268700 chr1D 84.028 144 22 1 712 854 406764541 406764398 2.080000e-28 137.0
16 TraesCS6D01G268700 chr2D 98.507 67 1 0 4218 4284 557163685 557163619 7.530000e-23 119.0
17 TraesCS6D01G268700 chr5B 94.030 67 4 0 4218 4284 548688216 548688282 7.590000e-18 102.0
18 TraesCS6D01G268700 chr2B 92.537 67 5 0 4218 4284 664385009 664384943 3.530000e-16 97.1
19 TraesCS6D01G268700 chr2A 92.188 64 5 0 4221 4284 667009711 667009648 1.640000e-14 91.6


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 TraesCS6D01G268700 chr6D 379047514 379051802 4288 False 7921 7921 100.0000 1 4289 1 chr6D.!!$F1 4288
1 TraesCS6D01G268700 chr6B 565392441 565396579 4138 False 5398 5398 90.5690 190 4284 1 chr6B.!!$F1 4094
2 TraesCS6D01G268700 chr6B 63149283 63150988 1705 True 1314 1314 80.6660 1301 3003 1 chr6B.!!$R1 1702
3 TraesCS6D01G268700 chr6B 63167574 63169006 1432 True 1070 1070 80.2640 1574 3003 1 chr6B.!!$R2 1429
4 TraesCS6D01G268700 chr6A 520439937 520443366 3429 False 4844 4844 92.4750 190 3559 1 chr6A.!!$F1 3369
5 TraesCS6D01G268700 chr6A 520508230 520508838 608 False 250 398 88.1945 3566 4116 2 chr6A.!!$F2 550

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
581 626 0.112606 CCGGAGAGACATAGGGGCTA 59.887 60.000 0.00 0.0 0.00 3.93 F
859 923 1.410153 CAATCCAAACAGCCCATAGCC 59.590 52.381 0.00 0.0 45.47 3.93 F
1007 1093 1.474478 TGACAGCGCCAAAGACAAAAA 59.526 42.857 2.29 0.0 0.00 1.94 F
1974 2072 2.639286 CGCCGCTTTGTTGAGCTT 59.361 55.556 0.00 0.0 40.52 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1907 0.482446 ACCCTGGCAAACTCATTGGA 59.518 50.000 0.00 0.0 39.54 3.53 R
1815 1910 2.969821 TGTACCCTGGCAAACTCATT 57.030 45.000 0.00 0.0 0.00 2.57 R
2925 3023 2.685017 TGCTCCTGATGCGGGACT 60.685 61.111 0.00 0.0 33.41 3.85 R
3851 4020 1.071385 AGGCCACTCAACAAGTCTGAG 59.929 52.381 5.01 0.0 44.90 3.35 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
138 139 9.923143 AAAATTTAAAACTATGCTTGTACTCCC 57.077 29.630 0.00 0.00 0.00 4.30
139 140 8.879427 AATTTAAAACTATGCTTGTACTCCCT 57.121 30.769 0.00 0.00 0.00 4.20
140 141 7.916914 TTTAAAACTATGCTTGTACTCCCTC 57.083 36.000 0.00 0.00 0.00 4.30
141 142 4.489306 AAACTATGCTTGTACTCCCTCC 57.511 45.455 0.00 0.00 0.00 4.30
142 143 2.032620 ACTATGCTTGTACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
143 144 2.032620 CTATGCTTGTACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
144 145 0.824759 ATGCTTGTACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
145 146 1.255667 TGCTTGTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
146 147 1.807886 CTTGTACTCCCTCCGTCCG 59.192 63.158 0.00 0.00 0.00 4.79
147 148 0.679002 CTTGTACTCCCTCCGTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
148 149 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
149 150 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
150 151 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
151 152 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
152 153 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
153 154 0.391263 CTCCCTCCGTCCGAAAAAGG 60.391 60.000 0.00 0.00 0.00 3.11
154 155 1.123246 TCCCTCCGTCCGAAAAAGGT 61.123 55.000 0.00 0.00 0.00 3.50
155 156 0.250597 CCCTCCGTCCGAAAAAGGTT 60.251 55.000 0.00 0.00 0.00 3.50
156 157 1.601166 CCTCCGTCCGAAAAAGGTTT 58.399 50.000 0.00 0.00 0.00 3.27
157 158 2.550639 CCCTCCGTCCGAAAAAGGTTTA 60.551 50.000 0.00 0.00 0.00 2.01
158 159 2.481568 CCTCCGTCCGAAAAAGGTTTAC 59.518 50.000 0.00 0.00 0.00 2.01
159 160 3.132925 CTCCGTCCGAAAAAGGTTTACA 58.867 45.455 0.00 0.00 0.00 2.41
160 161 3.742385 TCCGTCCGAAAAAGGTTTACAT 58.258 40.909 0.00 0.00 0.00 2.29
161 162 3.499157 TCCGTCCGAAAAAGGTTTACATG 59.501 43.478 0.00 0.00 0.00 3.21
162 163 3.251487 CCGTCCGAAAAAGGTTTACATGT 59.749 43.478 2.69 2.69 0.00 3.21
163 164 4.451774 CCGTCCGAAAAAGGTTTACATGTA 59.548 41.667 0.08 0.08 0.00 2.29
164 165 5.122711 CCGTCCGAAAAAGGTTTACATGTAT 59.877 40.000 6.36 0.00 0.00 2.29
165 166 6.313411 CCGTCCGAAAAAGGTTTACATGTATA 59.687 38.462 6.36 0.00 0.00 1.47
166 167 7.148440 CCGTCCGAAAAAGGTTTACATGTATAA 60.148 37.037 6.36 1.70 0.00 0.98
167 168 8.229137 CGTCCGAAAAAGGTTTACATGTATAAA 58.771 33.333 6.36 0.00 0.00 1.40
168 169 9.896263 GTCCGAAAAAGGTTTACATGTATAAAA 57.104 29.630 6.36 0.00 0.00 1.52
170 171 9.902196 CCGAAAAAGGTTTACATGTATAAAAGT 57.098 29.630 6.36 0.00 0.00 2.66
197 198 4.499472 TCGGAGGGAGGGATTATAATGTT 58.501 43.478 1.78 0.00 0.00 2.71
344 375 7.750655 AGTACCAAGAAGAAGAAAAGGAGAAT 58.249 34.615 0.00 0.00 0.00 2.40
348 379 8.851145 ACCAAGAAGAAGAAAAGGAGAATAAAC 58.149 33.333 0.00 0.00 0.00 2.01
413 444 4.854173 ACCCAAAGAAAACTGGCAAAAAT 58.146 34.783 0.00 0.00 0.00 1.82
414 445 5.260424 ACCCAAAGAAAACTGGCAAAAATT 58.740 33.333 0.00 0.00 0.00 1.82
416 447 6.542005 ACCCAAAGAAAACTGGCAAAAATTAG 59.458 34.615 0.00 0.00 0.00 1.73
422 453 6.980397 AGAAAACTGGCAAAAATTAGACACAG 59.020 34.615 0.00 0.00 0.00 3.66
427 458 6.980397 ACTGGCAAAAATTAGACACAGAAAAG 59.020 34.615 0.00 0.00 0.00 2.27
432 464 9.689075 GCAAAAATTAGACACAGAAAAGAAAAC 57.311 29.630 0.00 0.00 0.00 2.43
433 465 9.885743 CAAAAATTAGACACAGAAAAGAAAACG 57.114 29.630 0.00 0.00 0.00 3.60
434 466 9.849166 AAAAATTAGACACAGAAAAGAAAACGA 57.151 25.926 0.00 0.00 0.00 3.85
524 569 3.738481 AGCTAATTGGCCGGCCCA 61.738 61.111 41.75 33.21 43.51 5.36
539 584 2.960129 CCATAGTCGTTCGCCCGC 60.960 66.667 0.00 0.00 0.00 6.13
581 626 0.112606 CCGGAGAGACATAGGGGCTA 59.887 60.000 0.00 0.00 0.00 3.93
590 635 4.536765 AGACATAGGGGCTATTTGGTTTG 58.463 43.478 0.00 0.00 0.00 2.93
593 638 5.445964 ACATAGGGGCTATTTGGTTTGTAG 58.554 41.667 0.00 0.00 0.00 2.74
600 645 5.072040 GCTATTTGGTTTGTAGCCACATT 57.928 39.130 0.00 0.00 35.86 2.71
607 652 4.343526 TGGTTTGTAGCCACATTTTGTCAT 59.656 37.500 0.00 0.00 33.76 3.06
615 660 5.531634 AGCCACATTTTGTCATACTTTGTG 58.468 37.500 0.00 0.00 34.30 3.33
629 674 3.674997 ACTTTGTGACACCGCATCTTAT 58.325 40.909 2.45 0.00 32.17 1.73
653 698 4.038642 GCAAGTTTGACCAAATTAGGTGGA 59.961 41.667 1.57 0.00 43.38 4.02
659 704 7.507616 AGTTTGACCAAATTAGGTGGATGTTTA 59.492 33.333 1.57 0.00 43.38 2.01
666 711 9.238368 CCAAATTAGGTGGATGTTTAGTTCTAA 57.762 33.333 0.00 0.00 38.54 2.10
673 718 6.128007 GGTGGATGTTTAGTTCTAACCACATG 60.128 42.308 20.89 0.00 45.36 3.21
679 724 6.938030 TGTTTAGTTCTAACCACATGTAAGGG 59.062 38.462 0.00 0.00 0.00 3.95
687 732 7.466804 TCTAACCACATGTAAGGGAAGATTTT 58.533 34.615 7.66 0.00 0.00 1.82
717 770 2.000447 GAGCATTGAACCCGTAGACAC 59.000 52.381 0.00 0.00 0.00 3.67
749 802 9.000486 GTGTAGGAAGATTACTTTAAACAAGCT 58.000 33.333 0.00 0.00 36.39 3.74
774 827 5.982890 AGTGTGGCTAACAATTTAAGCAT 57.017 34.783 5.95 0.00 41.57 3.79
779 838 6.127925 TGTGGCTAACAATTTAAGCATCTCAG 60.128 38.462 5.95 0.00 35.24 3.35
800 859 6.869695 TCAGGTAAGATAAGTGCGACAAATA 58.130 36.000 0.00 0.00 0.00 1.40
851 914 5.886960 AAGATAGTCACAATCCAAACAGC 57.113 39.130 0.00 0.00 0.00 4.40
853 916 1.620822 AGTCACAATCCAAACAGCCC 58.379 50.000 0.00 0.00 0.00 5.19
859 923 1.410153 CAATCCAAACAGCCCATAGCC 59.590 52.381 0.00 0.00 45.47 3.93
925 991 5.694458 ACCGTCCAAATTAATTGCTTGTTTC 59.306 36.000 0.39 0.00 37.73 2.78
948 1014 4.328983 CAGCATCAGCCTTTTTGCATAAAG 59.671 41.667 19.26 19.26 43.56 1.85
1007 1093 1.474478 TGACAGCGCCAAAGACAAAAA 59.526 42.857 2.29 0.00 0.00 1.94
1974 2072 2.639286 CGCCGCTTTGTTGAGCTT 59.361 55.556 0.00 0.00 40.52 3.74
2276 2374 3.517296 TGCTTTACAGGGGTTGAATGA 57.483 42.857 0.00 0.00 0.00 2.57
2616 2714 5.592282 TGTTACAGTTGTTGACATTGATGGT 59.408 36.000 0.00 0.00 0.00 3.55
2838 2936 3.745799 TGCTAAAGGATTCAACGTTCCA 58.254 40.909 0.00 0.00 34.27 3.53
2925 3023 5.551583 AGGGCCATACTTGTTGGATATCATA 59.448 40.000 6.18 0.00 36.26 2.15
3107 3205 3.833070 ACTACTAGGGGTTCAACTGTGAG 59.167 47.826 0.00 0.00 34.49 3.51
3151 3249 8.955388 TGCTTGTTTCATTCATATAAGCTTGTA 58.045 29.630 9.86 7.40 39.63 2.41
3221 3319 4.082665 AGGGATGTGCTGTCATAAGATG 57.917 45.455 0.00 0.00 0.00 2.90
3350 3448 6.428159 CCTTTCTGTTACTTTACATGTCTGCT 59.572 38.462 0.00 0.00 0.00 4.24
3361 3459 1.802960 CATGTCTGCTGTGTCAGGTTC 59.197 52.381 0.00 0.00 34.91 3.62
3402 3508 1.543871 GGTGGTCGGCAGGTTTTAGAA 60.544 52.381 0.00 0.00 0.00 2.10
3463 3574 5.953571 ACAGTTGGGAGGAAAAATAGAAGT 58.046 37.500 0.00 0.00 0.00 3.01
3500 3611 1.717032 TATCAAGCCCGCTATCCAGT 58.283 50.000 0.00 0.00 0.00 4.00
3577 3688 1.671901 CCGGCTTGAGAGGAGAGACC 61.672 65.000 0.00 0.00 39.35 3.85
3636 3798 7.864379 CAGCTTTTTGAGATAGAGAGAGAGATC 59.136 40.741 0.00 0.00 0.00 2.75
3648 3810 1.554160 AGAGAGATCCTGCAACTGTGG 59.446 52.381 0.00 0.00 0.00 4.17
3663 3827 1.406539 CTGTGGTTTGTCTTGCTGCTT 59.593 47.619 0.00 0.00 0.00 3.91
3664 3828 1.134753 TGTGGTTTGTCTTGCTGCTTG 59.865 47.619 0.00 0.00 0.00 4.01
3665 3829 1.134946 GTGGTTTGTCTTGCTGCTTGT 59.865 47.619 0.00 0.00 0.00 3.16
3666 3830 2.357637 GTGGTTTGTCTTGCTGCTTGTA 59.642 45.455 0.00 0.00 0.00 2.41
3667 3831 2.357637 TGGTTTGTCTTGCTGCTTGTAC 59.642 45.455 0.00 0.00 0.00 2.90
3668 3832 2.357637 GGTTTGTCTTGCTGCTTGTACA 59.642 45.455 0.00 0.00 0.00 2.90
3669 3833 3.548818 GGTTTGTCTTGCTGCTTGTACAG 60.549 47.826 0.00 0.00 40.80 2.74
3725 3891 2.413239 CCAGTTGTGCTGCTGTTATTCG 60.413 50.000 0.00 0.00 43.71 3.34
3726 3892 2.224079 CAGTTGTGCTGCTGTTATTCGT 59.776 45.455 0.00 0.00 38.52 3.85
3727 3893 3.431912 CAGTTGTGCTGCTGTTATTCGTA 59.568 43.478 0.00 0.00 38.52 3.43
3728 3894 3.432252 AGTTGTGCTGCTGTTATTCGTAC 59.568 43.478 0.00 0.00 0.00 3.67
3729 3895 3.313012 TGTGCTGCTGTTATTCGTACT 57.687 42.857 0.00 0.00 0.00 2.73
3730 3896 2.993220 TGTGCTGCTGTTATTCGTACTG 59.007 45.455 0.00 0.00 0.00 2.74
3747 3913 6.151691 TCGTACTGGTACTGATTGTTGTTAC 58.848 40.000 8.89 0.00 34.04 2.50
3840 4009 7.324935 TGGATTGAATGATTTGAGAAATGGTG 58.675 34.615 0.00 0.00 0.00 4.17
3841 4010 7.178805 TGGATTGAATGATTTGAGAAATGGTGA 59.821 33.333 0.00 0.00 0.00 4.02
3842 4011 7.490402 GGATTGAATGATTTGAGAAATGGTGAC 59.510 37.037 0.00 0.00 0.00 3.67
3843 4012 7.528996 TTGAATGATTTGAGAAATGGTGACT 57.471 32.000 0.00 0.00 0.00 3.41
3844 4013 6.916440 TGAATGATTTGAGAAATGGTGACTG 58.084 36.000 0.00 0.00 0.00 3.51
3845 4014 4.771590 TGATTTGAGAAATGGTGACTGC 57.228 40.909 0.00 0.00 0.00 4.40
3846 4015 4.401022 TGATTTGAGAAATGGTGACTGCT 58.599 39.130 0.00 0.00 0.00 4.24
3847 4016 4.828939 TGATTTGAGAAATGGTGACTGCTT 59.171 37.500 0.00 0.00 0.00 3.91
3848 4017 5.302568 TGATTTGAGAAATGGTGACTGCTTT 59.697 36.000 0.00 0.00 0.00 3.51
3849 4018 4.836125 TTGAGAAATGGTGACTGCTTTC 57.164 40.909 0.00 0.00 0.00 2.62
3850 4019 3.149196 TGAGAAATGGTGACTGCTTTCC 58.851 45.455 0.00 0.00 0.00 3.13
3851 4020 2.489722 GAGAAATGGTGACTGCTTTCCC 59.510 50.000 0.00 0.00 0.00 3.97
3852 4021 2.108952 AGAAATGGTGACTGCTTTCCCT 59.891 45.455 0.00 0.00 0.00 4.20
3853 4022 2.206576 AATGGTGACTGCTTTCCCTC 57.793 50.000 0.00 0.00 0.00 4.30
3854 4023 1.067295 ATGGTGACTGCTTTCCCTCA 58.933 50.000 0.00 0.00 0.00 3.86
3997 4188 1.003718 GTCCAGGTTTCCGGTGGAG 60.004 63.158 10.85 0.00 41.11 3.86
4006 4197 0.895530 TTCCGGTGGAGCAAGTCTAG 59.104 55.000 0.00 0.00 31.21 2.43
4009 4200 0.888619 CGGTGGAGCAAGTCTAGACA 59.111 55.000 24.44 0.00 0.00 3.41
4053 4244 7.118390 TGTCAGCTTATTCTGCTCTTTAGTTTC 59.882 37.037 0.00 0.00 38.92 2.78
4054 4245 7.118390 GTCAGCTTATTCTGCTCTTTAGTTTCA 59.882 37.037 0.00 0.00 38.92 2.69
4055 4246 7.332926 TCAGCTTATTCTGCTCTTTAGTTTCAG 59.667 37.037 0.00 0.00 38.92 3.02
4056 4247 7.118971 CAGCTTATTCTGCTCTTTAGTTTCAGT 59.881 37.037 0.00 0.00 38.92 3.41
4057 4248 7.663493 AGCTTATTCTGCTCTTTAGTTTCAGTT 59.337 33.333 0.00 0.00 35.67 3.16
4058 4249 8.293157 GCTTATTCTGCTCTTTAGTTTCAGTTT 58.707 33.333 0.00 0.00 0.00 2.66
4061 4252 7.730364 TTCTGCTCTTTAGTTTCAGTTTAGG 57.270 36.000 0.00 0.00 0.00 2.69
4062 4253 6.827727 TCTGCTCTTTAGTTTCAGTTTAGGT 58.172 36.000 0.00 0.00 0.00 3.08
4063 4254 6.706270 TCTGCTCTTTAGTTTCAGTTTAGGTG 59.294 38.462 0.00 0.00 0.00 4.00
4179 4389 6.532826 TCCTTTAAAACGCTCCCTAGTTTTA 58.467 36.000 8.79 8.79 45.33 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 9.923143 GGGAGTACAAGCATAGTTTTAAATTTT 57.077 29.630 0.00 0.00 0.00 1.82
113 114 9.309224 AGGGAGTACAAGCATAGTTTTAAATTT 57.691 29.630 0.00 0.00 0.00 1.82
114 115 8.879427 AGGGAGTACAAGCATAGTTTTAAATT 57.121 30.769 0.00 0.00 0.00 1.82
115 116 7.556635 GGAGGGAGTACAAGCATAGTTTTAAAT 59.443 37.037 0.00 0.00 0.00 1.40
116 117 6.882678 GGAGGGAGTACAAGCATAGTTTTAAA 59.117 38.462 0.00 0.00 0.00 1.52
117 118 6.412214 GGAGGGAGTACAAGCATAGTTTTAA 58.588 40.000 0.00 0.00 0.00 1.52
118 119 5.394883 CGGAGGGAGTACAAGCATAGTTTTA 60.395 44.000 0.00 0.00 0.00 1.52
119 120 4.623171 CGGAGGGAGTACAAGCATAGTTTT 60.623 45.833 0.00 0.00 0.00 2.43
120 121 3.118738 CGGAGGGAGTACAAGCATAGTTT 60.119 47.826 0.00 0.00 0.00 2.66
121 122 2.431057 CGGAGGGAGTACAAGCATAGTT 59.569 50.000 0.00 0.00 0.00 2.24
122 123 2.032620 CGGAGGGAGTACAAGCATAGT 58.967 52.381 0.00 0.00 0.00 2.12
123 124 2.032620 ACGGAGGGAGTACAAGCATAG 58.967 52.381 0.00 0.00 0.00 2.23
124 125 2.029623 GACGGAGGGAGTACAAGCATA 58.970 52.381 0.00 0.00 0.00 3.14
125 126 0.824759 GACGGAGGGAGTACAAGCAT 59.175 55.000 0.00 0.00 0.00 3.79
126 127 1.255667 GGACGGAGGGAGTACAAGCA 61.256 60.000 0.00 0.00 0.00 3.91
127 128 1.516423 GGACGGAGGGAGTACAAGC 59.484 63.158 0.00 0.00 0.00 4.01
128 129 0.679002 TCGGACGGAGGGAGTACAAG 60.679 60.000 0.00 0.00 0.00 3.16
129 130 0.251297 TTCGGACGGAGGGAGTACAA 60.251 55.000 0.00 0.00 0.00 2.41
130 131 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
131 132 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
132 133 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
133 134 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
134 135 0.391263 CCTTTTTCGGACGGAGGGAG 60.391 60.000 0.00 0.00 0.00 4.30
135 136 1.123246 ACCTTTTTCGGACGGAGGGA 61.123 55.000 5.15 0.00 0.00 4.20
136 137 0.250597 AACCTTTTTCGGACGGAGGG 60.251 55.000 5.15 0.00 0.00 4.30
137 138 1.601166 AAACCTTTTTCGGACGGAGG 58.399 50.000 0.00 0.00 0.00 4.30
138 139 3.132925 TGTAAACCTTTTTCGGACGGAG 58.867 45.455 0.00 0.00 0.00 4.63
139 140 3.191078 TGTAAACCTTTTTCGGACGGA 57.809 42.857 0.00 0.00 0.00 4.69
140 141 3.251487 ACATGTAAACCTTTTTCGGACGG 59.749 43.478 0.00 0.00 0.00 4.79
141 142 4.477302 ACATGTAAACCTTTTTCGGACG 57.523 40.909 0.00 0.00 0.00 4.79
142 143 9.896263 TTTTATACATGTAAACCTTTTTCGGAC 57.104 29.630 10.14 0.00 0.00 4.79
144 145 9.902196 ACTTTTATACATGTAAACCTTTTTCGG 57.098 29.630 10.14 0.00 0.00 4.30
171 172 5.979656 TTATAATCCCTCCCTCCGAAAAA 57.020 39.130 0.00 0.00 0.00 1.94
172 173 5.371472 ACATTATAATCCCTCCCTCCGAAAA 59.629 40.000 0.00 0.00 0.00 2.29
173 174 4.911522 ACATTATAATCCCTCCCTCCGAAA 59.088 41.667 0.00 0.00 0.00 3.46
174 175 4.499472 ACATTATAATCCCTCCCTCCGAA 58.501 43.478 0.00 0.00 0.00 4.30
175 176 4.141990 ACATTATAATCCCTCCCTCCGA 57.858 45.455 0.00 0.00 0.00 4.55
176 177 4.910458 AACATTATAATCCCTCCCTCCG 57.090 45.455 0.00 0.00 0.00 4.63
177 178 6.500751 TGACTAACATTATAATCCCTCCCTCC 59.499 42.308 0.00 0.00 0.00 4.30
178 179 7.554959 TGACTAACATTATAATCCCTCCCTC 57.445 40.000 0.00 0.00 0.00 4.30
179 180 8.525729 AATGACTAACATTATAATCCCTCCCT 57.474 34.615 0.00 0.00 45.92 4.20
237 239 9.313118 CACATGTCTACTTTTACACATATGCTA 57.687 33.333 1.58 0.00 0.00 3.49
239 241 7.974675 ACACATGTCTACTTTTACACATATGC 58.025 34.615 1.58 0.00 28.50 3.14
323 354 8.300286 GGTTTATTCTCCTTTTCTTCTTCTTGG 58.700 37.037 0.00 0.00 0.00 3.61
324 355 8.850156 TGGTTTATTCTCCTTTTCTTCTTCTTG 58.150 33.333 0.00 0.00 0.00 3.02
388 419 3.535280 TGCCAGTTTTCTTTGGGTTTC 57.465 42.857 0.00 0.00 34.96 2.78
394 425 8.116136 GTGTCTAATTTTTGCCAGTTTTCTTTG 58.884 33.333 0.00 0.00 0.00 2.77
395 426 7.821846 TGTGTCTAATTTTTGCCAGTTTTCTTT 59.178 29.630 0.00 0.00 0.00 2.52
440 472 9.768662 GGTTCAGTCCGGTTTTCTTTATATATA 57.231 33.333 0.00 0.00 0.00 0.86
442 474 6.757947 CGGTTCAGTCCGGTTTTCTTTATATA 59.242 38.462 0.00 0.00 45.88 0.86
444 476 4.931002 CGGTTCAGTCCGGTTTTCTTTATA 59.069 41.667 0.00 0.00 45.88 0.98
507 552 1.715019 TATGGGCCGGCCAATTAGCT 61.715 55.000 44.46 23.00 37.98 3.32
524 569 2.104331 CTGCGGGCGAACGACTAT 59.896 61.111 0.00 0.00 35.47 2.12
539 584 3.717707 ACCGATTCGTATGAATGGTCTG 58.282 45.455 14.93 4.29 44.79 3.51
581 626 5.679601 ACAAAATGTGGCTACAAACCAAAT 58.320 33.333 7.10 0.00 40.84 2.32
590 635 6.582295 CACAAAGTATGACAAAATGTGGCTAC 59.418 38.462 0.00 0.00 35.56 3.58
593 638 5.402270 GTCACAAAGTATGACAAAATGTGGC 59.598 40.000 0.00 0.00 44.87 5.01
607 652 2.831685 AGATGCGGTGTCACAAAGTA 57.168 45.000 5.12 0.00 0.00 2.24
621 666 5.870978 ATTTGGTCAAACTTGCATAAGATGC 59.129 36.000 4.46 4.46 43.82 3.91
629 674 4.202202 CCACCTAATTTGGTCAAACTTGCA 60.202 41.667 8.74 0.00 38.45 4.08
634 679 5.722021 ACATCCACCTAATTTGGTCAAAC 57.278 39.130 8.74 0.00 38.45 2.93
640 685 7.703058 AGAACTAAACATCCACCTAATTTGG 57.297 36.000 4.22 4.22 35.18 3.28
653 698 7.610305 CCCTTACATGTGGTTAGAACTAAACAT 59.390 37.037 14.09 9.78 43.69 2.71
659 704 5.546499 TCTTCCCTTACATGTGGTTAGAACT 59.454 40.000 9.11 0.00 0.00 3.01
693 738 4.081365 TGTCTACGGGTTCAATGCTCATAA 60.081 41.667 0.00 0.00 0.00 1.90
694 739 3.449377 TGTCTACGGGTTCAATGCTCATA 59.551 43.478 0.00 0.00 0.00 2.15
695 740 2.236146 TGTCTACGGGTTCAATGCTCAT 59.764 45.455 0.00 0.00 0.00 2.90
702 747 4.095185 CACTTTTTGTGTCTACGGGTTCAA 59.905 41.667 0.00 0.00 41.53 2.69
736 789 5.359860 AGCCACACTTTAGCTTGTTTAAAGT 59.640 36.000 5.86 5.86 46.71 2.66
745 798 6.405278 AAATTGTTAGCCACACTTTAGCTT 57.595 33.333 0.00 0.00 36.70 3.74
746 799 7.519032 TTAAATTGTTAGCCACACTTTAGCT 57.481 32.000 0.00 0.00 40.01 3.32
747 800 6.308041 GCTTAAATTGTTAGCCACACTTTAGC 59.692 38.462 8.36 9.82 40.01 3.09
749 802 7.278461 TGCTTAAATTGTTAGCCACACTTTA 57.722 32.000 5.53 5.53 38.72 1.85
771 824 3.738282 CGCACTTATCTTACCTGAGATGC 59.262 47.826 0.00 0.00 37.01 3.91
774 827 4.014406 TGTCGCACTTATCTTACCTGAGA 58.986 43.478 0.00 0.00 0.00 3.27
779 838 6.565999 GCCATATTTGTCGCACTTATCTTACC 60.566 42.308 0.00 0.00 0.00 2.85
853 916 1.026182 TTTGCACTCGCCAGGCTATG 61.026 55.000 10.54 5.97 37.32 2.23
859 923 2.472861 CGTATCTATTTGCACTCGCCAG 59.527 50.000 0.00 0.00 37.32 4.85
901 966 4.864704 ACAAGCAATTAATTTGGACGGT 57.135 36.364 0.00 0.00 35.75 4.83
902 967 5.694006 TGAAACAAGCAATTAATTTGGACGG 59.306 36.000 0.00 0.00 35.75 4.79
903 968 6.616260 GCTGAAACAAGCAATTAATTTGGACG 60.616 38.462 0.00 0.00 43.01 4.79
925 991 2.380084 ATGCAAAAAGGCTGATGCTG 57.620 45.000 16.95 0.76 39.49 4.41
948 1014 2.293170 GGTTCAGATTGGGCTAGCTTC 58.707 52.381 15.72 8.13 0.00 3.86
1007 1093 0.631212 GAATTGGGGAGGGGTGATGT 59.369 55.000 0.00 0.00 0.00 3.06
1800 1895 0.608130 TCATTGGAGTGTCCCAGACG 59.392 55.000 0.00 0.00 37.53 4.18
1812 1907 0.482446 ACCCTGGCAAACTCATTGGA 59.518 50.000 0.00 0.00 39.54 3.53
1815 1910 2.969821 TGTACCCTGGCAAACTCATT 57.030 45.000 0.00 0.00 0.00 2.57
2276 2374 5.893255 TGTGCTTTGCTCCCATTTAATAGAT 59.107 36.000 0.00 0.00 0.00 1.98
2616 2714 5.497464 TGTTCATGAGGAAACTACCATCA 57.503 39.130 0.00 0.00 44.43 3.07
2661 2759 3.341823 CTTCACTGGGAGGTTCTCAATG 58.658 50.000 0.00 0.00 31.08 2.82
2925 3023 2.685017 TGCTCCTGATGCGGGACT 60.685 61.111 0.00 0.00 33.41 3.85
3107 3205 1.985684 GCAAACTAGAAAACGCATGGC 59.014 47.619 0.00 0.00 0.00 4.40
3151 3249 5.718607 ACTACAGGGTTCGGAACTAAGTAAT 59.281 40.000 19.40 7.75 0.00 1.89
3221 3319 4.515191 TGTAGGACAAGAAACTTGCATGAC 59.485 41.667 6.60 6.03 0.00 3.06
3361 3459 2.543861 CCTCCATCGGTCGTTATGTCAG 60.544 54.545 0.00 0.00 0.00 3.51
3432 3543 4.553330 TTCCTCCCAACTGTATTCAGAC 57.447 45.455 6.32 0.00 43.76 3.51
3470 3581 4.819630 AGCGGGCTTGATAAATTAATCGAA 59.180 37.500 0.00 0.00 0.00 3.71
3472 3583 4.749245 AGCGGGCTTGATAAATTAATCG 57.251 40.909 0.00 0.00 0.00 3.34
3485 3596 1.789523 TTAGACTGGATAGCGGGCTT 58.210 50.000 0.00 0.00 0.00 4.35
3500 3611 8.932945 CACTGTCTAGTGCTTGATAAATTAGA 57.067 34.615 0.00 0.00 46.93 2.10
3577 3688 2.357517 AACACAGCCGAAGCCTCG 60.358 61.111 0.00 0.00 45.02 4.63
3623 3735 4.206375 CAGTTGCAGGATCTCTCTCTCTA 58.794 47.826 0.00 0.00 0.00 2.43
3636 3798 1.392589 AGACAAACCACAGTTGCAGG 58.607 50.000 0.00 0.00 35.97 4.85
3648 3810 3.621794 CTGTACAAGCAGCAAGACAAAC 58.378 45.455 0.00 0.00 0.00 2.93
3663 3827 3.081804 TCAATGTCTCTCTCGCTGTACA 58.918 45.455 0.00 0.00 0.00 2.90
3664 3828 3.375610 TCTCAATGTCTCTCTCGCTGTAC 59.624 47.826 0.00 0.00 0.00 2.90
3665 3829 3.610911 TCTCAATGTCTCTCTCGCTGTA 58.389 45.455 0.00 0.00 0.00 2.74
3666 3830 2.423185 CTCTCAATGTCTCTCTCGCTGT 59.577 50.000 0.00 0.00 0.00 4.40
3667 3831 2.682352 TCTCTCAATGTCTCTCTCGCTG 59.318 50.000 0.00 0.00 0.00 5.18
3668 3832 2.997980 TCTCTCAATGTCTCTCTCGCT 58.002 47.619 0.00 0.00 0.00 4.93
3669 3833 3.988379 ATCTCTCAATGTCTCTCTCGC 57.012 47.619 0.00 0.00 0.00 5.03
3670 3834 6.558771 ACATATCTCTCAATGTCTCTCTCG 57.441 41.667 0.00 0.00 30.54 4.04
3671 3835 8.846943 TCTACATATCTCTCAATGTCTCTCTC 57.153 38.462 0.00 0.00 37.50 3.20
3725 3891 6.927381 ACAGTAACAACAATCAGTACCAGTAC 59.073 38.462 0.00 0.00 36.35 2.73
3726 3892 7.058023 ACAGTAACAACAATCAGTACCAGTA 57.942 36.000 0.00 0.00 0.00 2.74
3727 3893 5.925509 ACAGTAACAACAATCAGTACCAGT 58.074 37.500 0.00 0.00 0.00 4.00
3728 3894 6.658831 CAACAGTAACAACAATCAGTACCAG 58.341 40.000 0.00 0.00 0.00 4.00
3729 3895 5.008217 GCAACAGTAACAACAATCAGTACCA 59.992 40.000 0.00 0.00 0.00 3.25
3730 3896 5.238650 AGCAACAGTAACAACAATCAGTACC 59.761 40.000 0.00 0.00 0.00 3.34
3840 4009 2.224402 ACAAGTCTGAGGGAAAGCAGTC 60.224 50.000 0.00 0.00 33.90 3.51
3841 4010 1.771255 ACAAGTCTGAGGGAAAGCAGT 59.229 47.619 0.00 0.00 33.90 4.40
3842 4011 2.551459 CAACAAGTCTGAGGGAAAGCAG 59.449 50.000 0.00 0.00 0.00 4.24
3843 4012 2.172505 TCAACAAGTCTGAGGGAAAGCA 59.827 45.455 0.00 0.00 0.00 3.91
3844 4013 2.810852 CTCAACAAGTCTGAGGGAAAGC 59.189 50.000 0.00 0.00 37.29 3.51
3845 4014 3.812053 CACTCAACAAGTCTGAGGGAAAG 59.188 47.826 4.96 0.00 45.58 2.62
3846 4015 3.433598 CCACTCAACAAGTCTGAGGGAAA 60.434 47.826 3.66 0.00 45.58 3.13
3847 4016 2.104792 CCACTCAACAAGTCTGAGGGAA 59.895 50.000 3.66 0.00 45.58 3.97
3848 4017 1.694150 CCACTCAACAAGTCTGAGGGA 59.306 52.381 3.66 0.00 45.58 4.20
3849 4018 1.879796 GCCACTCAACAAGTCTGAGGG 60.880 57.143 4.96 0.18 43.88 4.30
3850 4019 1.517242 GCCACTCAACAAGTCTGAGG 58.483 55.000 4.96 0.00 43.88 3.86
3851 4020 1.071385 AGGCCACTCAACAAGTCTGAG 59.929 52.381 5.01 0.00 44.90 3.35
3852 4021 1.131638 AGGCCACTCAACAAGTCTGA 58.868 50.000 5.01 0.00 35.45 3.27
3853 4022 1.605710 CAAGGCCACTCAACAAGTCTG 59.394 52.381 5.01 0.00 35.45 3.51
3854 4023 1.490490 TCAAGGCCACTCAACAAGTCT 59.510 47.619 5.01 0.00 35.45 3.24
3977 4167 2.738480 CACCGGAAACCTGGACGA 59.262 61.111 9.46 0.00 0.00 4.20
3978 4168 2.358247 CCACCGGAAACCTGGACG 60.358 66.667 9.46 0.00 0.00 4.79
3979 4169 1.003718 CTCCACCGGAAACCTGGAC 60.004 63.158 9.46 0.00 31.84 4.02
3997 4188 2.726760 CTCAACGTGTGTCTAGACTTGC 59.273 50.000 23.01 13.53 0.00 4.01
4006 4197 0.944386 ACATTGGCTCAACGTGTGTC 59.056 50.000 0.00 0.00 0.00 3.67
4009 4200 1.748493 ACAAACATTGGCTCAACGTGT 59.252 42.857 0.00 0.00 34.12 4.49
4053 4244 4.743493 ACAAAACAACTGCACCTAAACTG 58.257 39.130 0.00 0.00 0.00 3.16
4054 4245 5.400066 AACAAAACAACTGCACCTAAACT 57.600 34.783 0.00 0.00 0.00 2.66
4055 4246 6.586844 TGTAAACAAAACAACTGCACCTAAAC 59.413 34.615 0.00 0.00 0.00 2.01
4056 4247 6.688578 TGTAAACAAAACAACTGCACCTAAA 58.311 32.000 0.00 0.00 0.00 1.85
4057 4248 6.151312 TCTGTAAACAAAACAACTGCACCTAA 59.849 34.615 0.00 0.00 0.00 2.69
4058 4249 5.648526 TCTGTAAACAAAACAACTGCACCTA 59.351 36.000 0.00 0.00 0.00 3.08
4059 4250 4.461081 TCTGTAAACAAAACAACTGCACCT 59.539 37.500 0.00 0.00 0.00 4.00
4060 4251 4.739195 TCTGTAAACAAAACAACTGCACC 58.261 39.130 0.00 0.00 0.00 5.01
4061 4252 6.695245 CAATCTGTAAACAAAACAACTGCAC 58.305 36.000 0.00 0.00 0.00 4.57
4062 4253 5.290643 GCAATCTGTAAACAAAACAACTGCA 59.709 36.000 0.00 0.00 31.29 4.41
4063 4254 5.519927 AGCAATCTGTAAACAAAACAACTGC 59.480 36.000 0.00 0.00 0.00 4.40
4119 4322 1.134848 GTCGAGCAAGCAAGGATCTCT 60.135 52.381 0.00 0.00 0.00 3.10
4130 4333 1.202973 CGTATCCGCAGTCGAGCAAG 61.203 60.000 0.00 0.00 38.10 4.01
4150 4353 4.010349 AGGGAGCGTTTTAAAGGATTCAG 58.990 43.478 1.30 0.00 0.00 3.02
4165 4368 7.095270 TCTCTAAAACTTAAAACTAGGGAGCG 58.905 38.462 0.00 0.00 0.00 5.03
4206 4416 1.029947 CGACCCAGTAATGTTGCCCC 61.030 60.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.