Multiple sequence alignment - TraesCS7B01G095900

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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 TraesCS7B01G095900 chr7B 100.000 4113 0 0 1 4113 110702471 110698359 0.000000e+00 7596.0
1 TraesCS7B01G095900 chr7B 100.000 28 0 0 296 323 576035664 576035637 7.000000e-03 52.8
2 TraesCS7B01G095900 chr7D 91.184 3766 124 75 476 4113 147692213 147688528 0.000000e+00 4924.0
3 TraesCS7B01G095900 chr7D 93.793 290 17 1 4 293 147695896 147695608 6.310000e-118 435.0
4 TraesCS7B01G095900 chr7D 87.162 148 9 7 328 474 147692441 147692303 4.260000e-35 159.0
5 TraesCS7B01G095900 chr7A 88.361 3935 161 107 340 4113 148988916 148985118 0.000000e+00 4455.0
6 TraesCS7B01G095900 chr7A 86.452 155 14 7 23 174 148989189 148989039 3.290000e-36 163.0
7 TraesCS7B01G095900 chr7A 100.000 35 0 0 288 322 130123608 130123642 9.540000e-07 65.8
8 TraesCS7B01G095900 chr6A 100.000 35 0 0 288 322 176231382 176231348 9.540000e-07 65.8
9 TraesCS7B01G095900 chr6D 97.222 36 1 0 288 323 375891667 375891632 1.230000e-05 62.1
10 TraesCS7B01G095900 chr2B 97.222 36 1 0 288 323 698388358 698388323 1.230000e-05 62.1
11 TraesCS7B01G095900 chr4D 97.143 35 1 0 288 322 501793676 501793710 4.440000e-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 TraesCS7B01G095900 chr7B 110698359 110702471 4112 True 7596.000000 7596 100.0000 1 4113 1 chr7B.!!$R1 4112
1 TraesCS7B01G095900 chr7D 147688528 147695896 7368 True 1839.333333 4924 90.7130 4 4113 3 chr7D.!!$R1 4109
2 TraesCS7B01G095900 chr7A 148985118 148989189 4071 True 2309.000000 4455 87.4065 23 4113 2 chr7A.!!$R1 4090

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
291 317 0.248949 GCAACTAGGGGATCGTCGTC 60.249 60.0 0.00 0.0 0.0 4.20 F
709 3965 0.378257 GCACAGCGAGAGAGAGAGAG 59.622 60.0 0.00 0.0 0.0 3.20 F
1377 4678 0.173708 TGGTACGCGCATCACATACA 59.826 50.0 5.73 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 4672 0.320421 GGTGGTCTGCGTGTGTATGT 60.320 55.000 0.00 0.0 0.00 2.29 R
2220 5582 0.531311 TGCTACGATGGCAGCATCAG 60.531 55.000 2.73 0.0 42.68 2.90 R
3191 6614 1.151679 TTTGGCGTGGGATGGTTGA 59.848 52.632 0.00 0.0 0.00 3.18 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
44 45 1.186200 AGCATCACCTAGACTTCGCA 58.814 50.000 0.00 0.00 0.00 5.10
72 73 1.708341 ACAGAGCCAAAAATGCACCT 58.292 45.000 0.00 0.00 0.00 4.00
153 156 6.431234 ACGACTTCCTTCTTTAGCATTTTCAT 59.569 34.615 0.00 0.00 0.00 2.57
177 200 2.026822 ACTTTGTGGCAGTAGCTAGCAT 60.027 45.455 18.83 4.67 41.70 3.79
200 223 2.086054 AGCACATGTCTCGTTCTTCC 57.914 50.000 0.00 0.00 0.00 3.46
254 280 7.966246 AACATAAATCACACTTACACCGTTA 57.034 32.000 0.00 0.00 0.00 3.18
256 282 7.156673 ACATAAATCACACTTACACCGTTAGT 58.843 34.615 0.00 0.00 0.00 2.24
282 308 6.415573 AGAATTACAAGTAAGCAACTAGGGG 58.584 40.000 0.00 0.00 37.50 4.79
283 309 6.214819 AGAATTACAAGTAAGCAACTAGGGGA 59.785 38.462 0.00 0.00 37.50 4.81
284 310 6.576778 ATTACAAGTAAGCAACTAGGGGAT 57.423 37.500 0.00 0.00 37.50 3.85
285 311 4.489306 ACAAGTAAGCAACTAGGGGATC 57.511 45.455 0.00 0.00 37.50 3.36
286 312 3.118738 ACAAGTAAGCAACTAGGGGATCG 60.119 47.826 0.00 0.00 37.50 3.69
287 313 2.748388 AGTAAGCAACTAGGGGATCGT 58.252 47.619 0.00 0.00 36.36 3.73
288 314 2.694109 AGTAAGCAACTAGGGGATCGTC 59.306 50.000 0.00 0.00 36.36 4.20
289 315 0.460311 AAGCAACTAGGGGATCGTCG 59.540 55.000 0.00 0.00 0.00 5.12
290 316 0.683504 AGCAACTAGGGGATCGTCGT 60.684 55.000 0.00 0.00 0.00 4.34
291 317 0.248949 GCAACTAGGGGATCGTCGTC 60.249 60.000 0.00 0.00 0.00 4.20
292 318 1.390565 CAACTAGGGGATCGTCGTCT 58.609 55.000 0.00 0.00 0.00 4.18
294 320 0.545171 ACTAGGGGATCGTCGTCTGA 59.455 55.000 0.00 0.00 0.00 3.27
297 323 2.359981 AGGGGATCGTCGTCTGATAA 57.640 50.000 0.00 0.00 0.00 1.75
299 325 2.558795 AGGGGATCGTCGTCTGATAATG 59.441 50.000 0.00 0.00 0.00 1.90
300 326 2.296471 GGGGATCGTCGTCTGATAATGT 59.704 50.000 0.00 0.00 0.00 2.71
303 729 3.303857 GGATCGTCGTCTGATAATGTCGT 60.304 47.826 0.00 0.00 0.00 4.34
304 730 3.314763 TCGTCGTCTGATAATGTCGTC 57.685 47.619 0.00 0.00 0.00 4.20
307 733 3.548214 CGTCGTCTGATAATGTCGTCCAT 60.548 47.826 0.00 0.00 34.36 3.41
309 735 5.617087 CGTCGTCTGATAATGTCGTCCATAT 60.617 44.000 0.00 0.00 31.97 1.78
313 739 6.621613 GTCTGATAATGTCGTCCATATAGCA 58.378 40.000 0.00 0.00 31.97 3.49
318 744 2.031870 TGTCGTCCATATAGCAGTGCT 58.968 47.619 23.44 23.44 43.41 4.40
323 749 2.294791 GTCCATATAGCAGTGCTCGTCT 59.705 50.000 23.64 7.75 40.44 4.18
326 752 1.664873 TATAGCAGTGCTCGTCTCGT 58.335 50.000 23.64 0.00 40.44 4.18
416 3573 9.618890 TCCGTAGTAGAACAAGTATATACAAGT 57.381 33.333 15.18 9.57 0.00 3.16
436 3593 0.822121 AAAGACAACCAGGGAACGCC 60.822 55.000 0.00 0.00 0.00 5.68
512 3758 2.529151 CACCGCAATTAATCCACAAGC 58.471 47.619 0.00 0.00 0.00 4.01
541 3787 4.941713 ACCAAGAACAGTCCTCTCTCTAT 58.058 43.478 0.00 0.00 0.00 1.98
548 3794 8.017418 AGAACAGTCCTCTCTCTATATTTTGG 57.983 38.462 0.00 0.00 0.00 3.28
550 3796 5.071115 ACAGTCCTCTCTCTATATTTTGGGC 59.929 44.000 0.00 0.00 0.00 5.36
551 3797 4.595350 AGTCCTCTCTCTATATTTTGGGCC 59.405 45.833 0.00 0.00 0.00 5.80
552 3798 4.595350 GTCCTCTCTCTATATTTTGGGCCT 59.405 45.833 4.53 0.00 0.00 5.19
553 3799 4.594920 TCCTCTCTCTATATTTTGGGCCTG 59.405 45.833 4.53 0.00 0.00 4.85
554 3800 4.349342 CCTCTCTCTATATTTTGGGCCTGT 59.651 45.833 4.53 0.00 0.00 4.00
555 3801 5.163152 CCTCTCTCTATATTTTGGGCCTGTT 60.163 44.000 4.53 0.00 0.00 3.16
556 3802 5.930135 TCTCTCTATATTTTGGGCCTGTTC 58.070 41.667 4.53 0.00 0.00 3.18
633 3885 5.063312 ACCAAAAACACAAGCAGAATTTTCG 59.937 36.000 0.00 0.00 0.00 3.46
680 3936 2.669878 CAAAATGTGGACCCTGGGG 58.330 57.895 18.88 7.87 42.03 4.96
693 3949 4.986708 TGGGGAAAAGCCGGGCAC 62.987 66.667 23.09 9.21 37.63 5.01
694 3950 4.986708 GGGGAAAAGCCGGGCACA 62.987 66.667 23.09 0.00 37.63 4.57
695 3951 3.373565 GGGAAAAGCCGGGCACAG 61.374 66.667 23.09 0.00 37.63 3.66
696 3952 4.056125 GGAAAAGCCGGGCACAGC 62.056 66.667 23.09 7.59 0.00 4.40
697 3953 4.404654 GAAAAGCCGGGCACAGCG 62.405 66.667 23.09 0.00 34.20 5.18
703 3959 4.504916 CCGGGCACAGCGAGAGAG 62.505 72.222 0.00 0.00 0.00 3.20
704 3960 3.443925 CGGGCACAGCGAGAGAGA 61.444 66.667 0.00 0.00 0.00 3.10
705 3961 2.493973 GGGCACAGCGAGAGAGAG 59.506 66.667 0.00 0.00 0.00 3.20
706 3962 2.049185 GGGCACAGCGAGAGAGAGA 61.049 63.158 0.00 0.00 0.00 3.10
707 3963 1.433064 GGCACAGCGAGAGAGAGAG 59.567 63.158 0.00 0.00 0.00 3.20
708 3964 1.029408 GGCACAGCGAGAGAGAGAGA 61.029 60.000 0.00 0.00 0.00 3.10
709 3965 0.378257 GCACAGCGAGAGAGAGAGAG 59.622 60.000 0.00 0.00 0.00 3.20
710 3966 1.737838 CACAGCGAGAGAGAGAGAGT 58.262 55.000 0.00 0.00 0.00 3.24
711 3967 1.398041 CACAGCGAGAGAGAGAGAGTG 59.602 57.143 0.00 0.00 0.00 3.51
712 3968 1.277842 ACAGCGAGAGAGAGAGAGTGA 59.722 52.381 0.00 0.00 0.00 3.41
713 3969 2.290008 ACAGCGAGAGAGAGAGAGTGAA 60.290 50.000 0.00 0.00 0.00 3.18
714 3970 2.352651 CAGCGAGAGAGAGAGAGTGAAG 59.647 54.545 0.00 0.00 0.00 3.02
715 3971 1.670811 GCGAGAGAGAGAGAGTGAAGG 59.329 57.143 0.00 0.00 0.00 3.46
716 3972 2.939640 GCGAGAGAGAGAGAGTGAAGGT 60.940 54.545 0.00 0.00 0.00 3.50
717 3973 2.677836 CGAGAGAGAGAGAGTGAAGGTG 59.322 54.545 0.00 0.00 0.00 4.00
718 3974 2.423538 GAGAGAGAGAGAGTGAAGGTGC 59.576 54.545 0.00 0.00 0.00 5.01
719 3975 2.166829 GAGAGAGAGAGTGAAGGTGCA 58.833 52.381 0.00 0.00 0.00 4.57
720 3976 1.892474 AGAGAGAGAGTGAAGGTGCAC 59.108 52.381 8.80 8.80 39.05 4.57
721 3977 0.972883 AGAGAGAGTGAAGGTGCACC 59.027 55.000 29.22 29.22 39.59 5.01
870 4151 2.992124 TCACACACGGGAAAGAAAGA 57.008 45.000 0.00 0.00 0.00 2.52
944 4231 2.899044 CTCTCGATCGGCGTCTCCC 61.899 68.421 16.41 0.00 41.80 4.30
956 4243 1.990614 GTCTCCCTTTCCGCTCCCT 60.991 63.158 0.00 0.00 0.00 4.20
959 4246 4.803908 CCCTTTCCGCTCCCTGCC 62.804 72.222 0.00 0.00 38.78 4.85
960 4247 4.033776 CCTTTCCGCTCCCTGCCA 62.034 66.667 0.00 0.00 38.78 4.92
987 4274 4.521062 ATCTCCGGCTGCTCGTGC 62.521 66.667 1.71 1.71 40.20 5.34
1166 4462 1.208706 CCTTCTCCTCCCCTTCCTTC 58.791 60.000 0.00 0.00 0.00 3.46
1180 4476 3.053395 CCTTCCTTCCTTCCATCCATCAA 60.053 47.826 0.00 0.00 0.00 2.57
1247 4547 3.499737 CAACGTCCTGATGCCGCC 61.500 66.667 0.00 0.00 0.00 6.13
1291 4592 4.202010 GCTAATCTCTTTCTCGCTCTGTCT 60.202 45.833 0.00 0.00 0.00 3.41
1370 4671 1.146358 GAGGAACTGGTACGCGCATC 61.146 60.000 5.73 0.00 41.55 3.91
1371 4672 1.447140 GGAACTGGTACGCGCATCA 60.447 57.895 5.73 0.00 0.00 3.07
1372 4673 1.693083 GGAACTGGTACGCGCATCAC 61.693 60.000 5.73 0.65 0.00 3.06
1373 4674 1.005512 AACTGGTACGCGCATCACA 60.006 52.632 5.73 0.00 0.00 3.58
1374 4675 0.391130 AACTGGTACGCGCATCACAT 60.391 50.000 5.73 0.00 0.00 3.21
1375 4676 0.458260 ACTGGTACGCGCATCACATA 59.542 50.000 5.73 0.00 0.00 2.29
1376 4677 0.852777 CTGGTACGCGCATCACATAC 59.147 55.000 5.73 0.00 0.00 2.39
1377 4678 0.173708 TGGTACGCGCATCACATACA 59.826 50.000 5.73 0.00 0.00 2.29
1378 4679 0.575390 GGTACGCGCATCACATACAC 59.425 55.000 5.73 0.00 0.00 2.90
1395 4707 2.203280 CACGCAGACCACCCCAAA 60.203 61.111 0.00 0.00 0.00 3.28
1413 4727 3.124636 CCAAATCTTTTACCGTCGTCTGG 59.875 47.826 0.00 0.00 0.00 3.86
1673 5007 0.903236 GAAGGGTCAGTACTCCCCAC 59.097 60.000 23.25 15.16 44.40 4.61
1704 5038 7.013220 ACTGGCTTATGATCAGATTAGGTAGA 58.987 38.462 0.09 0.00 33.19 2.59
1758 5092 2.098117 GTGCTGCTGGATGATGGTTAAC 59.902 50.000 0.00 0.00 0.00 2.01
1776 5117 5.877012 GGTTAACTTAACTAACCAGGCTACC 59.123 44.000 5.42 0.00 45.21 3.18
1782 5127 3.476485 ACTAACCAGGCTACCTCTCTT 57.524 47.619 0.00 0.00 0.00 2.85
1797 5142 1.873591 TCTCTTTTCTTGGTCGCTTGC 59.126 47.619 0.00 0.00 0.00 4.01
1893 5238 0.341258 AGCCTCATCTCCTCCTGGAA 59.659 55.000 0.00 0.00 42.66 3.53
1916 5261 3.823330 CCGCCGACTCCGTAAGCT 61.823 66.667 0.00 0.00 0.00 3.74
1926 5271 2.711922 CCGTAAGCTGCTCCTCCGT 61.712 63.158 1.00 0.00 0.00 4.69
1954 5302 1.815421 CATTCGCCGCCAGCTTACT 60.815 57.895 0.00 0.00 40.39 2.24
1955 5303 1.815421 ATTCGCCGCCAGCTTACTG 60.815 57.895 0.00 0.00 44.05 2.74
1990 5338 3.455910 CCTTAACTGACCATCCTCCATGA 59.544 47.826 0.00 0.00 33.80 3.07
1991 5339 4.446371 CTTAACTGACCATCCTCCATGAC 58.554 47.826 0.00 0.00 33.80 3.06
1992 5340 1.207791 ACTGACCATCCTCCATGACC 58.792 55.000 0.00 0.00 33.80 4.02
1993 5341 1.206878 CTGACCATCCTCCATGACCA 58.793 55.000 0.00 0.00 33.80 4.02
1994 5342 1.773052 CTGACCATCCTCCATGACCAT 59.227 52.381 0.00 0.00 33.80 3.55
1995 5343 1.491754 TGACCATCCTCCATGACCATG 59.508 52.381 0.00 3.11 38.51 3.66
1996 5344 1.770658 GACCATCCTCCATGACCATGA 59.229 52.381 11.28 0.00 41.20 3.07
1997 5345 2.173356 GACCATCCTCCATGACCATGAA 59.827 50.000 11.28 0.00 41.20 2.57
1998 5346 2.582172 ACCATCCTCCATGACCATGAAA 59.418 45.455 11.28 0.00 41.20 2.69
1999 5347 3.205959 ACCATCCTCCATGACCATGAAAT 59.794 43.478 11.28 0.00 41.20 2.17
2000 5348 4.220724 CCATCCTCCATGACCATGAAATT 58.779 43.478 11.28 0.00 41.20 1.82
2001 5349 5.103558 ACCATCCTCCATGACCATGAAATTA 60.104 40.000 11.28 0.00 41.20 1.40
2264 5626 6.910536 AGATAGCATTACTGGTTTCTTTCG 57.089 37.500 0.48 0.00 37.75 3.46
2512 5886 1.513158 CAGCGCTGCTACTAGTGGT 59.487 57.895 26.68 0.00 36.40 4.16
2538 5912 4.814234 CGGCAGTGGCTTTAATTGATAGTA 59.186 41.667 15.48 0.00 40.87 1.82
3122 6516 0.250467 CGGGTTCTAGGCCATCCATG 60.250 60.000 5.01 0.00 33.74 3.66
3141 6551 1.127817 GTCGTCGTCGTCGTCGTTA 59.872 57.895 18.44 1.12 45.27 3.18
3147 6570 3.267687 GTCGTCGTCGTCGTTATTCTAG 58.732 50.000 11.41 0.00 38.33 2.43
3194 6617 6.930731 TCGATCATATTATTCCCACGATCAA 58.069 36.000 0.00 0.00 0.00 2.57
3230 6653 1.133790 CGACCAGGGACTAGTTAACCG 59.866 57.143 0.88 0.00 36.02 4.44
3268 6691 6.482641 ACAGTGTCTGATTATATCGTCGTACT 59.517 38.462 3.70 0.00 35.18 2.73
3300 6730 1.133790 ACTTGATCTGGCCGTACGTAC 59.866 52.381 15.90 15.90 0.00 3.67
3302 6732 2.330440 TGATCTGGCCGTACGTACTA 57.670 50.000 22.55 2.95 0.00 1.82
3303 6733 1.942657 TGATCTGGCCGTACGTACTAC 59.057 52.381 22.55 14.04 0.00 2.73
3373 6807 2.355756 GTCCATCGCATTTACACATGCT 59.644 45.455 4.28 0.00 46.43 3.79
3386 6820 7.920160 TTTACACATGCTTGTTATGAGATGA 57.080 32.000 1.83 0.00 32.34 2.92
3580 7014 2.478709 CGACCAATCTCAACTCCTCGAG 60.479 54.545 5.13 5.13 35.52 4.04
3583 7017 2.093764 CCAATCTCAACTCCTCGAGCTT 60.094 50.000 6.99 0.00 32.04 3.74
3586 7020 3.074675 TCTCAACTCCTCGAGCTTAGT 57.925 47.619 6.99 7.19 32.04 2.24
3587 7021 4.217836 TCTCAACTCCTCGAGCTTAGTA 57.782 45.455 6.99 0.00 32.04 1.82
3588 7022 4.193090 TCTCAACTCCTCGAGCTTAGTAG 58.807 47.826 6.99 5.73 32.04 2.57
3625 7063 7.085116 CCATGGAGTACGTACTATCTTTGATC 58.915 42.308 27.44 12.05 36.50 2.92
3653 7095 3.537580 CTCGGGATCGGGTGAAATTTTA 58.462 45.455 0.00 0.00 36.95 1.52
3654 7096 3.942748 CTCGGGATCGGGTGAAATTTTAA 59.057 43.478 0.00 0.00 36.95 1.52
3687 7129 1.448893 GTGGAGGCGCGGTCATAAA 60.449 57.895 8.83 0.00 0.00 1.40
3749 7193 6.485313 TGAAGGAGCTGTAAGAAAAATTTCGA 59.515 34.615 0.00 0.00 41.92 3.71
3875 7332 3.244976 GCACAACACAATTATCAGTGCC 58.755 45.455 0.00 0.00 43.54 5.01
3943 7406 0.452987 TTGAGCGAGGAAATGCATGC 59.547 50.000 11.82 11.82 0.00 4.06
3944 7407 0.677414 TGAGCGAGGAAATGCATGCA 60.677 50.000 25.04 25.04 0.00 3.96
3945 7408 0.029035 GAGCGAGGAAATGCATGCAG 59.971 55.000 26.69 11.42 0.00 4.41
3946 7409 0.679002 AGCGAGGAAATGCATGCAGT 60.679 50.000 26.69 21.79 0.00 4.40
3947 7410 0.524816 GCGAGGAAATGCATGCAGTG 60.525 55.000 26.69 12.10 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.058160 CTGGGAGGCAGCCAAACG 61.058 66.667 15.80 0.00 0.00 3.60
2 3 3.376918 GCTGGGAGGCAGCCAAAC 61.377 66.667 15.80 4.39 39.61 2.93
14 15 0.811616 GGTGATGCTTAGACGCTGGG 60.812 60.000 0.00 0.00 0.00 4.45
16 17 2.359214 TCTAGGTGATGCTTAGACGCTG 59.641 50.000 0.00 0.00 31.84 5.18
17 18 2.359531 GTCTAGGTGATGCTTAGACGCT 59.640 50.000 1.77 0.00 43.61 5.07
44 45 6.991531 TGCATTTTTGGCTCTGTTAGAAAAAT 59.008 30.769 0.00 0.00 34.42 1.82
72 73 5.841237 AGAGCAAAGGACATATAGCTTCCTA 59.159 40.000 4.31 0.00 38.93 2.94
153 156 4.000988 GCTAGCTACTGCCACAAAGTTAA 58.999 43.478 7.70 0.00 40.80 2.01
177 200 1.893137 AGAACGAGACATGTGCTACCA 59.107 47.619 1.15 0.00 0.00 3.25
254 280 9.654663 CCTAGTTGCTTACTTGTAATTCTTACT 57.345 33.333 0.00 0.00 38.33 2.24
256 282 8.044908 CCCCTAGTTGCTTACTTGTAATTCTTA 58.955 37.037 0.00 0.00 38.33 2.10
282 308 3.874706 ACGACATTATCAGACGACGATC 58.125 45.455 0.00 0.00 0.00 3.69
283 309 3.303857 GGACGACATTATCAGACGACGAT 60.304 47.826 0.00 0.00 0.00 3.73
284 310 2.031314 GGACGACATTATCAGACGACGA 59.969 50.000 0.00 0.00 0.00 4.20
285 311 2.223180 TGGACGACATTATCAGACGACG 60.223 50.000 0.00 0.00 0.00 5.12
286 312 3.416119 TGGACGACATTATCAGACGAC 57.584 47.619 0.00 0.00 0.00 4.34
287 313 5.959618 ATATGGACGACATTATCAGACGA 57.040 39.130 0.00 0.00 41.03 4.20
288 314 5.739630 GCTATATGGACGACATTATCAGACG 59.260 44.000 0.00 0.00 41.03 4.18
289 315 6.621613 TGCTATATGGACGACATTATCAGAC 58.378 40.000 0.00 0.00 41.03 3.51
290 316 6.434340 ACTGCTATATGGACGACATTATCAGA 59.566 38.462 0.00 0.00 41.03 3.27
291 317 6.529477 CACTGCTATATGGACGACATTATCAG 59.471 42.308 0.00 3.71 41.03 2.90
292 318 6.389906 CACTGCTATATGGACGACATTATCA 58.610 40.000 0.00 0.00 41.03 2.15
294 320 5.047021 AGCACTGCTATATGGACGACATTAT 60.047 40.000 0.21 0.00 37.86 1.28
297 323 2.630098 AGCACTGCTATATGGACGACAT 59.370 45.455 0.21 0.00 39.44 3.06
299 325 2.667137 GAGCACTGCTATATGGACGAC 58.333 52.381 2.71 0.00 39.88 4.34
300 326 1.266989 CGAGCACTGCTATATGGACGA 59.733 52.381 2.71 0.00 39.88 4.20
303 729 2.554462 GAGACGAGCACTGCTATATGGA 59.446 50.000 2.71 0.00 39.88 3.41
304 730 2.666895 CGAGACGAGCACTGCTATATGG 60.667 54.545 2.71 0.00 39.88 2.74
307 733 1.664873 ACGAGACGAGCACTGCTATA 58.335 50.000 2.71 0.00 39.88 1.31
309 735 1.445871 TAACGAGACGAGCACTGCTA 58.554 50.000 2.71 0.00 39.88 3.49
313 739 4.698583 AACTAATAACGAGACGAGCACT 57.301 40.909 0.00 0.00 0.00 4.40
318 744 6.367686 TGAGCATAACTAATAACGAGACGA 57.632 37.500 0.00 0.00 0.00 4.20
323 749 8.447833 CCAAACTTTGAGCATAACTAATAACGA 58.552 33.333 2.87 0.00 0.00 3.85
326 752 9.733556 TCTCCAAACTTTGAGCATAACTAATAA 57.266 29.630 2.87 0.00 0.00 1.40
390 3547 9.618890 ACTTGTATATACTTGTTCTACTACGGA 57.381 33.333 13.89 0.00 0.00 4.69
407 3564 7.504926 TCCCTGGTTGTCTTTACTTGTATAT 57.495 36.000 0.00 0.00 0.00 0.86
408 3565 6.938698 TCCCTGGTTGTCTTTACTTGTATA 57.061 37.500 0.00 0.00 0.00 1.47
416 3573 1.543871 GGCGTTCCCTGGTTGTCTTTA 60.544 52.381 0.00 0.00 0.00 1.85
436 3593 3.592814 CTGCCTCGCCCATGCATG 61.593 66.667 20.19 20.19 37.32 4.06
465 3623 2.115427 TGGGAATCGCTGAATACTCCA 58.885 47.619 0.00 0.00 0.00 3.86
512 3758 1.429463 GACTGTTCTTGGTACGGCTG 58.571 55.000 0.00 0.00 0.00 4.85
541 3787 0.606944 ACGCGAACAGGCCCAAAATA 60.607 50.000 15.93 0.00 0.00 1.40
633 3885 9.120538 TCTTATTATTAGTTGTGGGAAGAATGC 57.879 33.333 0.00 0.00 0.00 3.56
680 3936 4.404654 CGCTGTGCCCGGCTTTTC 62.405 66.667 11.61 0.00 41.05 2.29
693 3949 2.022764 TCACTCTCTCTCTCTCGCTG 57.977 55.000 0.00 0.00 0.00 5.18
694 3950 2.632377 CTTCACTCTCTCTCTCTCGCT 58.368 52.381 0.00 0.00 0.00 4.93
695 3951 1.670811 CCTTCACTCTCTCTCTCTCGC 59.329 57.143 0.00 0.00 0.00 5.03
696 3952 2.677836 CACCTTCACTCTCTCTCTCTCG 59.322 54.545 0.00 0.00 0.00 4.04
697 3953 2.423538 GCACCTTCACTCTCTCTCTCTC 59.576 54.545 0.00 0.00 0.00 3.20
699 3955 2.094752 GTGCACCTTCACTCTCTCTCTC 60.095 54.545 5.22 0.00 34.29 3.20
701 3957 1.067213 GGTGCACCTTCACTCTCTCTC 60.067 57.143 29.12 0.00 37.16 3.20
702 3958 0.972883 GGTGCACCTTCACTCTCTCT 59.027 55.000 29.12 0.00 37.16 3.10
703 3959 0.972883 AGGTGCACCTTCACTCTCTC 59.027 55.000 33.20 2.62 46.09 3.20
704 3960 3.155897 AGGTGCACCTTCACTCTCT 57.844 52.632 33.20 7.71 46.09 3.10
836 4117 1.040646 TGTGATCTCTCCGTATGGCC 58.959 55.000 0.00 0.00 34.14 5.36
956 4243 1.137675 CGGAGATGAGATTCAGTGGCA 59.862 52.381 0.00 0.00 0.00 4.92
959 4246 1.411977 AGCCGGAGATGAGATTCAGTG 59.588 52.381 5.05 0.00 0.00 3.66
960 4247 1.411977 CAGCCGGAGATGAGATTCAGT 59.588 52.381 5.05 0.00 0.00 3.41
998 4285 0.394080 GCTCAGCTGCTCCTCCATTT 60.394 55.000 9.47 0.00 0.00 2.32
1139 4427 2.304831 GGAGGAGAAGGCAGGGCTT 61.305 63.158 7.91 7.91 0.00 4.35
1166 4462 5.241064 GTGATGAAGATTGATGGATGGAAGG 59.759 44.000 0.00 0.00 0.00 3.46
1180 4476 0.459899 TACAGGCGCGTGATGAAGAT 59.540 50.000 34.34 14.06 0.00 2.40
1247 4547 0.392193 ATCGCCAAAGAGAGTGCAGG 60.392 55.000 0.00 0.00 0.00 4.85
1249 4549 1.159285 CAATCGCCAAAGAGAGTGCA 58.841 50.000 0.00 0.00 31.35 4.57
1291 4592 2.942804 TCCCATCTGCTCAAACAAACA 58.057 42.857 0.00 0.00 0.00 2.83
1370 4671 0.790207 GTGGTCTGCGTGTGTATGTG 59.210 55.000 0.00 0.00 0.00 3.21
1371 4672 0.320421 GGTGGTCTGCGTGTGTATGT 60.320 55.000 0.00 0.00 0.00 2.29
1372 4673 1.019278 GGGTGGTCTGCGTGTGTATG 61.019 60.000 0.00 0.00 0.00 2.39
1373 4674 1.295423 GGGTGGTCTGCGTGTGTAT 59.705 57.895 0.00 0.00 0.00 2.29
1374 4675 2.738480 GGGTGGTCTGCGTGTGTA 59.262 61.111 0.00 0.00 0.00 2.90
1375 4676 4.250305 GGGGTGGTCTGCGTGTGT 62.250 66.667 0.00 0.00 0.00 3.72
1376 4677 3.765894 TTGGGGTGGTCTGCGTGTG 62.766 63.158 0.00 0.00 0.00 3.82
1377 4678 2.351924 ATTTGGGGTGGTCTGCGTGT 62.352 55.000 0.00 0.00 0.00 4.49
1378 4679 1.586154 GATTTGGGGTGGTCTGCGTG 61.586 60.000 0.00 0.00 0.00 5.34
1395 4707 2.094338 GTCCCAGACGACGGTAAAAGAT 60.094 50.000 0.00 0.00 0.00 2.40
1413 4727 4.500887 GCAAGAAACCAAAACCCTAAGTCC 60.501 45.833 0.00 0.00 0.00 3.85
1673 5007 7.664082 AATCTGATCATAAGCCAGTTAATCG 57.336 36.000 0.00 0.00 0.00 3.34
1730 5064 3.612247 ATCCAGCAGCACCGGTGAC 62.612 63.158 38.30 26.95 36.48 3.67
1731 5065 3.321648 ATCCAGCAGCACCGGTGA 61.322 61.111 38.30 15.88 36.48 4.02
1732 5066 2.881539 ATCATCCAGCAGCACCGGTG 62.882 60.000 30.66 30.66 0.00 4.94
1733 5067 2.673200 ATCATCCAGCAGCACCGGT 61.673 57.895 0.00 0.00 0.00 5.28
1758 5092 4.957327 AGAGAGGTAGCCTGGTTAGTTAAG 59.043 45.833 0.00 0.00 31.76 1.85
1774 5115 1.694696 AGCGACCAAGAAAAGAGAGGT 59.305 47.619 0.00 0.00 34.76 3.85
1776 5117 2.096019 GCAAGCGACCAAGAAAAGAGAG 60.096 50.000 0.00 0.00 0.00 3.20
1782 5127 1.795170 GCAGGCAAGCGACCAAGAAA 61.795 55.000 0.00 0.00 0.00 2.52
1797 5142 2.025887 ACTTTCCCTATCAACCTGCAGG 60.026 50.000 31.60 31.60 42.17 4.85
1954 5302 5.586243 GTCAGTTAAGGATTGCATTAGCTCA 59.414 40.000 0.00 0.00 42.74 4.26
1955 5303 5.008118 GGTCAGTTAAGGATTGCATTAGCTC 59.992 44.000 0.00 0.00 42.74 4.09
1956 5304 4.884164 GGTCAGTTAAGGATTGCATTAGCT 59.116 41.667 0.00 0.00 42.74 3.32
1966 5314 3.736094 TGGAGGATGGTCAGTTAAGGAT 58.264 45.455 0.00 0.00 0.00 3.24
1990 5338 7.984617 CCGGGTCAATAATTTTAATTTCATGGT 59.015 33.333 0.00 0.00 0.00 3.55
1991 5339 7.984617 ACCGGGTCAATAATTTTAATTTCATGG 59.015 33.333 6.32 0.00 0.00 3.66
1992 5340 8.816144 CACCGGGTCAATAATTTTAATTTCATG 58.184 33.333 6.32 0.00 0.00 3.07
1993 5341 7.494298 GCACCGGGTCAATAATTTTAATTTCAT 59.506 33.333 6.32 0.00 0.00 2.57
1994 5342 6.814146 GCACCGGGTCAATAATTTTAATTTCA 59.186 34.615 6.32 0.00 0.00 2.69
1995 5343 6.814146 TGCACCGGGTCAATAATTTTAATTTC 59.186 34.615 6.32 0.00 0.00 2.17
1996 5344 6.702329 TGCACCGGGTCAATAATTTTAATTT 58.298 32.000 6.32 0.00 0.00 1.82
1997 5345 6.287589 TGCACCGGGTCAATAATTTTAATT 57.712 33.333 6.32 0.00 0.00 1.40
1998 5346 5.681179 GCTGCACCGGGTCAATAATTTTAAT 60.681 40.000 6.32 0.00 0.00 1.40
1999 5347 4.381079 GCTGCACCGGGTCAATAATTTTAA 60.381 41.667 6.32 0.00 0.00 1.52
2000 5348 3.129638 GCTGCACCGGGTCAATAATTTTA 59.870 43.478 6.32 0.00 0.00 1.52
2001 5349 2.094234 GCTGCACCGGGTCAATAATTTT 60.094 45.455 6.32 0.00 0.00 1.82
2097 5455 4.586001 AGGCAGAGAGCTTTTGATCAAAAA 59.414 37.500 28.49 15.77 44.79 1.94
2219 5581 1.839598 GCTACGATGGCAGCATCAGC 61.840 60.000 2.73 3.95 37.73 4.26
2220 5582 0.531311 TGCTACGATGGCAGCATCAG 60.531 55.000 2.73 0.00 42.68 2.90
2419 5793 2.170012 AGCCCGGTAGAATAAGACCA 57.830 50.000 0.00 0.00 35.26 4.02
2512 5886 1.742831 CAATTAAAGCCACTGCCGCTA 59.257 47.619 0.00 0.00 38.69 4.26
2538 5912 1.271379 TCACTCGTGCGACCAAATACT 59.729 47.619 0.00 0.00 0.00 2.12
3053 6441 1.255667 AAGTAGGACGACATGGCGGT 61.256 55.000 27.41 11.11 35.12 5.68
3116 6510 1.432251 GACGACGACGACCATGGAT 59.568 57.895 21.47 1.98 42.66 3.41
3117 6511 2.872557 GACGACGACGACCATGGA 59.127 61.111 21.47 0.00 42.66 3.41
3127 6537 2.923655 ACTAGAATAACGACGACGACGA 59.076 45.455 25.15 5.17 42.66 4.20
3191 6614 1.151679 TTTGGCGTGGGATGGTTGA 59.848 52.632 0.00 0.00 0.00 3.18
3194 6617 2.671619 CGTTTGGCGTGGGATGGT 60.672 61.111 0.00 0.00 35.54 3.55
3216 6639 3.602483 TGATTTGCGGTTAACTAGTCCC 58.398 45.455 5.42 0.00 0.00 4.46
3230 6653 2.029649 AGACACTGTGCCAATGATTTGC 60.030 45.455 7.90 0.00 0.00 3.68
3268 6691 2.422479 CAGATCAAGTCCGACGGAACTA 59.578 50.000 20.26 5.01 31.38 2.24
3300 6730 7.249147 ACTTCGTAGCTGTTACATTGTAGTAG 58.751 38.462 0.00 1.64 32.27 2.57
3302 6732 6.022163 ACTTCGTAGCTGTTACATTGTAGT 57.978 37.500 0.00 0.00 32.27 2.73
3303 6733 7.666531 CTACTTCGTAGCTGTTACATTGTAG 57.333 40.000 0.00 6.54 32.27 2.74
3373 6807 6.704937 GTCATGCATCTCTCATCTCATAACAA 59.295 38.462 0.00 0.00 0.00 2.83
3386 6820 1.485480 CCTCAGGTGTCATGCATCTCT 59.515 52.381 0.00 0.00 36.14 3.10
3580 7014 2.551887 GGTCCGTACCTAGCTACTAAGC 59.448 54.545 0.00 0.00 45.07 3.09
3583 7017 3.497405 CCATGGTCCGTACCTAGCTACTA 60.497 52.174 2.57 0.00 46.91 1.82
3586 7020 1.496001 TCCATGGTCCGTACCTAGCTA 59.504 52.381 12.58 0.00 46.91 3.32
3587 7021 0.260816 TCCATGGTCCGTACCTAGCT 59.739 55.000 12.58 0.00 46.91 3.32
3588 7022 0.674534 CTCCATGGTCCGTACCTAGC 59.325 60.000 12.58 0.00 46.91 3.42
3589 7023 2.068834 ACTCCATGGTCCGTACCTAG 57.931 55.000 12.58 0.28 46.91 3.02
3592 7030 0.383231 CGTACTCCATGGTCCGTACC 59.617 60.000 23.32 0.00 46.98 3.34
3607 7045 6.198591 GCACAAGGATCAAAGATAGTACGTAC 59.801 42.308 18.10 18.10 0.00 3.67
3608 7046 6.096423 AGCACAAGGATCAAAGATAGTACGTA 59.904 38.462 0.00 0.00 0.00 3.57
3609 7047 5.105310 AGCACAAGGATCAAAGATAGTACGT 60.105 40.000 0.00 0.00 0.00 3.57
3610 7048 5.352284 AGCACAAGGATCAAAGATAGTACG 58.648 41.667 0.00 0.00 0.00 3.67
3625 7063 2.202932 CCGATCCCGAGCACAAGG 60.203 66.667 0.00 0.00 38.22 3.61
3653 7095 4.157840 GCCTCCACCATTAAAATCTTCGTT 59.842 41.667 0.00 0.00 0.00 3.85
3654 7096 3.694566 GCCTCCACCATTAAAATCTTCGT 59.305 43.478 0.00 0.00 0.00 3.85
3783 7227 0.834612 ACGACTCAGGAACCCACAAA 59.165 50.000 0.00 0.00 0.00 2.83
3866 7320 1.112113 GTCCTCTTCCGGCACTGATA 58.888 55.000 0.00 0.00 0.00 2.15
3875 7332 2.277120 CGCGTACGTCCTCTTCCG 60.277 66.667 17.90 5.18 33.53 4.30
3943 7406 3.420606 CTCGCCTGCAGTGCACTG 61.421 66.667 37.09 37.09 46.40 3.66
3946 7409 4.933563 TTGCTCGCCTGCAGTGCA 62.934 61.111 18.58 18.58 44.27 4.57
3947 7410 4.395583 GTTGCTCGCCTGCAGTGC 62.396 66.667 13.81 8.58 44.27 4.40
3948 7411 2.962827 CTGTTGCTCGCCTGCAGTG 61.963 63.158 13.81 4.81 44.27 3.66
3949 7412 2.667536 CTGTTGCTCGCCTGCAGT 60.668 61.111 13.81 0.00 44.27 4.40
3950 7413 4.099170 GCTGTTGCTCGCCTGCAG 62.099 66.667 6.78 6.78 44.27 4.41


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

AutoCloner maintained by Alex Coulton.