Multiple sequence alignment - TraesCS6B01G249700

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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 TraesCS6B01G249700 chr6B 100.000 4768 0 0 1 4768 447896510 447891743 0.000000e+00 8805.0
1 TraesCS6B01G249700 chr6B 92.188 64 4 1 1488 1550 101541154 101541217 6.570000e-14 89.8
2 TraesCS6B01G249700 chr6B 90.164 61 4 2 1491 1550 42432692 42432751 1.420000e-10 78.7
3 TraesCS6B01G249700 chr6D 94.058 4796 202 34 2 4768 287031278 287026537 0.000000e+00 7201.0
4 TraesCS6B01G249700 chr6D 85.135 518 74 3 95 609 6830745 6831262 1.180000e-145 527.0
5 TraesCS6B01G249700 chr6D 90.909 55 5 0 40 94 461999060 461999114 1.840000e-09 75.0
6 TraesCS6B01G249700 chr6A 93.570 2846 107 33 1886 4681 438577468 438580287 0.000000e+00 4172.0
7 TraesCS6B01G249700 chr6A 96.333 900 20 2 821 1707 438575981 438576880 0.000000e+00 1467.0
8 TraesCS6B01G249700 chr6A 86.116 605 73 10 30 630 438574913 438575510 4.020000e-180 641.0
9 TraesCS6B01G249700 chr6A 95.804 286 10 2 1604 1888 438576877 438577161 1.210000e-125 460.0
10 TraesCS6B01G249700 chr6A 88.889 99 5 4 4584 4676 6418628 6418726 3.010000e-22 117.0
11 TraesCS6B01G249700 chr7D 83.876 614 73 14 94 703 104942005 104941414 3.220000e-156 562.0
12 TraesCS6B01G249700 chr7D 87.778 180 17 4 4584 4762 436466670 436466845 6.250000e-49 206.0
13 TraesCS6B01G249700 chr7D 87.222 180 18 4 4584 4762 292256294 292256469 2.910000e-47 200.0
14 TraesCS6B01G249700 chr7B 82.876 619 82 14 94 703 63626880 63626277 7.020000e-148 534.0
15 TraesCS6B01G249700 chr5B 84.526 517 74 6 96 609 423731089 423730576 1.530000e-139 507.0
16 TraesCS6B01G249700 chr5B 81.910 199 36 0 2613 2811 526576295 526576493 8.210000e-38 169.0
17 TraesCS6B01G249700 chr4A 84.291 522 76 5 91 609 472354065 472354583 5.510000e-139 505.0
18 TraesCS6B01G249700 chr4A 84.570 512 73 6 94 602 690147071 690146563 1.980000e-138 503.0
19 TraesCS6B01G249700 chr4A 88.333 180 17 4 4584 4762 107208661 107208837 3.740000e-51 213.0
20 TraesCS6B01G249700 chr4A 100.000 30 0 0 3068 3097 554932127 554932156 6.670000e-04 56.5
21 TraesCS6B01G249700 chr1D 83.939 523 76 7 91 610 470585405 470585922 1.190000e-135 494.0
22 TraesCS6B01G249700 chr5D 87.671 73 9 0 22 94 414238800 414238728 8.500000e-13 86.1
23 TraesCS6B01G249700 chr1A 94.444 54 3 0 41 94 564342736 564342683 3.060000e-12 84.2
24 TraesCS6B01G249700 chr1A 94.444 54 1 2 1496 1547 85844034 85844087 1.100000e-11 82.4
25 TraesCS6B01G249700 chr1A 94.444 54 1 2 1496 1547 85844087 85844034 1.100000e-11 82.4
26 TraesCS6B01G249700 chr1A 93.103 58 1 3 1492 1547 289338898 289338842 1.100000e-11 82.4
27 TraesCS6B01G249700 chr2D 86.486 74 10 0 22 95 10826725 10826652 1.100000e-11 82.4
28 TraesCS6B01G249700 chr2D 92.593 54 2 2 1497 1549 551877207 551877259 5.120000e-10 76.8
29 TraesCS6B01G249700 chr2D 87.931 58 7 0 38 95 27922516 27922459 8.560000e-08 69.4
30 TraesCS6B01G249700 chr3D 91.525 59 1 4 1493 1547 421666287 421666229 1.420000e-10 78.7
31 TraesCS6B01G249700 chr3D 81.000 100 16 3 1 99 123621471 123621568 5.120000e-10 76.8
32 TraesCS6B01G249700 chr5A 84.286 70 11 0 23 92 51227741 51227672 8.560000e-08 69.4


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 TraesCS6B01G249700 chr6B 447891743 447896510 4767 True 8805 8805 100.00000 1 4768 1 chr6B.!!$R1 4767
1 TraesCS6B01G249700 chr6D 287026537 287031278 4741 True 7201 7201 94.05800 2 4768 1 chr6D.!!$R1 4766
2 TraesCS6B01G249700 chr6D 6830745 6831262 517 False 527 527 85.13500 95 609 1 chr6D.!!$F1 514
3 TraesCS6B01G249700 chr6A 438574913 438580287 5374 False 1685 4172 92.95575 30 4681 4 chr6A.!!$F2 4651
4 TraesCS6B01G249700 chr7D 104941414 104942005 591 True 562 562 83.87600 94 703 1 chr7D.!!$R1 609
5 TraesCS6B01G249700 chr7B 63626277 63626880 603 True 534 534 82.87600 94 703 1 chr7B.!!$R1 609
6 TraesCS6B01G249700 chr5B 423730576 423731089 513 True 507 507 84.52600 96 609 1 chr5B.!!$R1 513
7 TraesCS6B01G249700 chr4A 472354065 472354583 518 False 505 505 84.29100 91 609 1 chr4A.!!$F2 518
8 TraesCS6B01G249700 chr4A 690146563 690147071 508 True 503 503 84.57000 94 602 1 chr4A.!!$R1 508
9 TraesCS6B01G249700 chr1D 470585405 470585922 517 False 494 494 83.93900 91 610 1 chr1D.!!$F1 519

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
80 82 0.168128 CGAATTTGCCAAGTCCGACC 59.832 55.0 0.00 0.0 0.00 4.79 F
796 1197 0.321919 ACGGACGAGCCTACACAGTA 60.322 55.0 0.00 0.0 0.00 2.74 F
797 1198 0.377554 CGGACGAGCCTACACAGTAG 59.622 60.0 0.00 0.0 0.00 2.57 F
1443 1857 0.885196 TTTGCATACGAAGGGTTGCC 59.115 50.0 0.00 0.0 34.10 4.52 F
2681 3537 0.251354 ATGATGCTTCTGCGGTCACT 59.749 50.0 0.88 0.0 43.34 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1938 0.762418 TGCCCCGTCCCATAATGTAG 59.238 55.00 0.00 0.0 0.00 2.74 R
2409 3263 2.489938 TCAACCTCAATACTGGCACC 57.510 50.00 0.00 0.0 0.00 5.01 R
2428 3282 4.122046 GCTTTTCAGTGGACAGCAATTTT 58.878 39.13 4.60 0.0 32.22 1.82 R
3266 4122 0.390998 GCCTCTGCTCAGAACTGGAC 60.391 60.00 7.57 0.0 36.94 4.02 R
4257 5130 0.106268 TTTGCCCCACTGCTCTTCAA 60.106 50.00 0.00 0.0 0.00 2.69 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
20 21 4.740822 GGATGCCCGGTTGGTGCT 62.741 66.667 0.00 0.00 36.04 4.40
28 29 4.980805 GGTTGGTGCTCGCGGACA 62.981 66.667 6.13 1.16 32.44 4.02
29 30 3.712881 GTTGGTGCTCGCGGACAC 61.713 66.667 19.85 19.85 36.03 3.67
60 61 4.636435 CGTGGGCGTTTGAGGGGT 62.636 66.667 0.00 0.00 0.00 4.95
63 64 4.011517 GGGCGTTTGAGGGGTCGA 62.012 66.667 0.00 0.00 0.00 4.20
78 80 1.153353 GTCGAATTTGCCAAGTCCGA 58.847 50.000 0.00 0.00 0.00 4.55
80 82 0.168128 CGAATTTGCCAAGTCCGACC 59.832 55.000 0.00 0.00 0.00 4.79
81 83 1.243902 GAATTTGCCAAGTCCGACCA 58.756 50.000 0.00 0.00 0.00 4.02
111 113 5.249780 TCTTACCAAAGGTGAAGCCATTA 57.750 39.130 0.00 0.00 40.61 1.90
119 121 1.467342 GGTGAAGCCATTACCGTTGAC 59.533 52.381 0.00 0.00 37.17 3.18
162 164 1.608590 CAGGACACGCCATCAAACTTT 59.391 47.619 0.00 0.00 40.02 2.66
297 299 0.322816 TCTGCATTTGCTCCTGGACC 60.323 55.000 3.94 0.00 42.66 4.46
298 300 0.323178 CTGCATTTGCTCCTGGACCT 60.323 55.000 3.94 0.00 42.66 3.85
301 303 0.394899 CATTTGCTCCTGGACCTCCC 60.395 60.000 0.00 0.00 34.29 4.30
380 382 2.165167 CATGTCCACCACAAAGATGCT 58.835 47.619 0.00 0.00 38.97 3.79
501 507 3.799755 GCATTGTCGTCACCGCCC 61.800 66.667 0.00 0.00 0.00 6.13
546 557 8.161425 ACAATTCAAAAACCTAAGCTACTAGGA 58.839 33.333 16.87 0.00 41.02 2.94
579 591 4.989279 AAAGCTAAAATGATCCGCACAT 57.011 36.364 0.00 0.00 0.00 3.21
591 603 2.184830 CGCACATGCAGGATCCAGG 61.185 63.158 15.82 6.81 42.21 4.45
609 625 0.838122 GGGACCCCCTCATCATCGAT 60.838 60.000 0.00 0.00 41.34 3.59
610 626 1.059913 GGACCCCCTCATCATCGATT 58.940 55.000 0.00 0.00 0.00 3.34
611 627 2.257207 GGACCCCCTCATCATCGATTA 58.743 52.381 0.00 0.00 0.00 1.75
612 628 2.840651 GGACCCCCTCATCATCGATTAT 59.159 50.000 0.00 0.00 0.00 1.28
613 629 3.118592 GGACCCCCTCATCATCGATTATC 60.119 52.174 0.00 0.00 0.00 1.75
614 630 3.515502 GACCCCCTCATCATCGATTATCA 59.484 47.826 0.00 0.00 0.00 2.15
615 631 3.517100 ACCCCCTCATCATCGATTATCAG 59.483 47.826 0.00 0.00 0.00 2.90
623 639 3.964909 TCATCGATTATCAGTCACCACG 58.035 45.455 0.00 0.00 0.00 4.94
670 705 2.278330 CCTTGCTGAAGGGTTGGCC 61.278 63.158 0.00 0.00 44.76 5.36
707 742 1.745489 GCGGCTAGGGTTCCTTGTG 60.745 63.158 0.00 0.00 34.61 3.33
708 743 1.078426 CGGCTAGGGTTCCTTGTGG 60.078 63.158 0.00 0.00 34.61 4.17
714 749 1.133809 AGGGTTCCTTGTGGCTAGCA 61.134 55.000 18.24 0.00 0.00 3.49
793 1194 1.303074 AGACGGACGAGCCTACACA 60.303 57.895 0.00 0.00 0.00 3.72
794 1195 1.136984 GACGGACGAGCCTACACAG 59.863 63.158 0.00 0.00 0.00 3.66
795 1196 1.584380 GACGGACGAGCCTACACAGT 61.584 60.000 0.00 0.00 0.00 3.55
796 1197 0.321919 ACGGACGAGCCTACACAGTA 60.322 55.000 0.00 0.00 0.00 2.74
797 1198 0.377554 CGGACGAGCCTACACAGTAG 59.622 60.000 0.00 0.00 0.00 2.57
798 1199 1.461559 GGACGAGCCTACACAGTAGT 58.538 55.000 0.00 0.00 0.00 2.73
799 1200 2.636830 GGACGAGCCTACACAGTAGTA 58.363 52.381 0.00 0.00 0.00 1.82
800 1201 2.613133 GGACGAGCCTACACAGTAGTAG 59.387 54.545 0.00 0.00 40.87 2.57
801 1202 3.269178 GACGAGCCTACACAGTAGTAGT 58.731 50.000 0.00 0.00 39.84 2.73
802 1203 4.437239 GACGAGCCTACACAGTAGTAGTA 58.563 47.826 0.00 0.00 39.84 1.82
803 1204 4.187694 ACGAGCCTACACAGTAGTAGTAC 58.812 47.826 0.00 0.00 39.84 2.73
804 1205 4.081198 ACGAGCCTACACAGTAGTAGTACT 60.081 45.833 8.14 8.14 40.38 2.73
805 1206 4.874966 CGAGCCTACACAGTAGTAGTACTT 59.125 45.833 8.40 0.00 37.40 2.24
806 1207 5.353678 CGAGCCTACACAGTAGTAGTACTTT 59.646 44.000 8.40 0.00 37.40 2.66
807 1208 6.128063 CGAGCCTACACAGTAGTAGTACTTTT 60.128 42.308 8.40 0.00 37.40 2.27
808 1209 7.536159 AGCCTACACAGTAGTAGTACTTTTT 57.464 36.000 8.40 0.00 37.40 1.94
956 1370 4.880426 TCTCCCCTCCCGCATCCC 62.880 72.222 0.00 0.00 0.00 3.85
1146 1560 1.005394 CCAGTTGCTTACGACCCGT 60.005 57.895 0.00 0.00 44.35 5.28
1208 1622 2.360350 TACCGAGGCCGACGAGTT 60.360 61.111 22.80 11.39 38.22 3.01
1345 1759 6.269315 CGTCTAGTTCTGAAGATGTGCTATT 58.731 40.000 0.00 0.00 0.00 1.73
1415 1829 6.700960 GCCTTAAATTGTGTATATGCATTGCA 59.299 34.615 14.72 14.72 44.86 4.08
1440 1854 3.004315 CACAAGTTTGCATACGAAGGGTT 59.996 43.478 1.44 0.00 0.00 4.11
1442 1856 1.539827 AGTTTGCATACGAAGGGTTGC 59.460 47.619 1.44 0.00 34.98 4.17
1443 1857 0.885196 TTTGCATACGAAGGGTTGCC 59.115 50.000 0.00 0.00 34.10 4.52
1482 1896 2.417719 ACATCTGTCGGACAGCTTTTC 58.582 47.619 28.92 0.00 45.54 2.29
1505 1919 3.119566 GCGGTTATTATCTACTCCCTCCG 60.120 52.174 0.00 0.00 37.71 4.63
1524 1938 3.067180 TCCGTCCCATAATGTAAGACGTC 59.933 47.826 7.70 7.70 46.62 4.34
1525 1939 3.067742 CCGTCCCATAATGTAAGACGTCT 59.932 47.826 13.58 13.58 46.62 4.18
1526 1940 4.276678 CCGTCCCATAATGTAAGACGTCTA 59.723 45.833 20.39 3.26 46.62 2.59
1657 2175 4.021456 TGAGTCGTTGGATGTAACATCTGT 60.021 41.667 0.00 0.00 0.00 3.41
1827 2347 9.826574 AAGTTTTACTTAGTGATCACTGTGTAA 57.173 29.630 33.76 31.64 42.52 2.41
1876 2396 6.825944 TTGTGTATGGCTTATGCTGTAAAA 57.174 33.333 0.13 0.00 39.59 1.52
2094 2923 7.595819 ATTGTTGTTTCTTCCTACATTTGGA 57.404 32.000 0.00 0.00 0.00 3.53
2110 2939 5.360714 ACATTTGGACCCTAATTGTATGCAG 59.639 40.000 0.00 0.00 0.00 4.41
2116 2945 5.758784 GGACCCTAATTGTATGCAGTTAGTC 59.241 44.000 19.62 13.99 40.88 2.59
2174 3003 6.453926 AGTTCTCTATCGTTTCTTAGTCCC 57.546 41.667 0.00 0.00 0.00 4.46
2176 3005 6.608002 AGTTCTCTATCGTTTCTTAGTCCCAT 59.392 38.462 0.00 0.00 0.00 4.00
2396 3250 7.101700 TGCAGATTATATGATAGCACAAGGAG 58.898 38.462 3.77 0.00 0.00 3.69
2409 3263 4.081420 AGCACAAGGAGATAAGGTACTGTG 60.081 45.833 0.00 0.00 40.86 3.66
2410 3264 4.759782 CACAAGGAGATAAGGTACTGTGG 58.240 47.826 0.00 0.00 40.86 4.17
2428 3282 1.702401 TGGTGCCAGTATTGAGGTTGA 59.298 47.619 0.00 0.00 0.00 3.18
2494 3349 8.046708 TGCTAACTACTATGAAATGTCATTGGT 58.953 33.333 3.06 6.56 42.03 3.67
2571 3427 9.748708 GAATAATAGCCTTGCACAATTTCAATA 57.251 29.630 0.00 0.00 0.00 1.90
2677 3533 1.522355 CCGATGATGCTTCTGCGGT 60.522 57.895 18.66 0.00 43.34 5.68
2681 3537 0.251354 ATGATGCTTCTGCGGTCACT 59.749 50.000 0.88 0.00 43.34 3.41
2869 3725 4.203226 ACTGAGAGAGATCGTATCTTGCA 58.797 43.478 0.00 0.00 40.38 4.08
3196 4052 9.313118 GGATATTTTGTTAACTGCATTTTAGGG 57.687 33.333 7.22 0.00 0.00 3.53
3219 4075 8.768397 AGGGTTATCACAGTACATCTGAATTTA 58.232 33.333 0.00 0.00 46.27 1.40
3266 4122 4.556135 GTCAAGTGCATTCATGATCAAACG 59.444 41.667 0.00 0.00 0.00 3.60
3375 4231 6.577039 GCAATCTTACATAGCATCCTCCCATA 60.577 42.308 0.00 0.00 0.00 2.74
3378 4234 8.860517 ATCTTACATAGCATCCTCCCATATTA 57.139 34.615 0.00 0.00 0.00 0.98
3474 4330 9.128404 TCTGATCTTTAATTCTGGGATTTGATG 57.872 33.333 0.00 0.00 0.00 3.07
3860 4716 9.926158 CACATGATAGAGTTAGATATTCTGCTT 57.074 33.333 0.00 0.00 0.00 3.91
3875 4731 0.250684 TGCTTCTCAAATGTGCCGGA 60.251 50.000 5.05 0.00 0.00 5.14
4044 4913 8.934023 AGATCCAAAAACCAGACAAGTAAATA 57.066 30.769 0.00 0.00 0.00 1.40
4068 4937 6.096673 TGTGGCTTATCTCGCTTTCATATA 57.903 37.500 0.00 0.00 0.00 0.86
4074 4943 8.721478 GGCTTATCTCGCTTTCATATATTTTCA 58.279 33.333 0.00 0.00 0.00 2.69
4211 5084 1.225855 AGCGCACGTCAAATTCTCAA 58.774 45.000 11.47 0.00 0.00 3.02
4226 5099 0.320683 CTCAACCGTGCACCTCATCA 60.321 55.000 12.15 0.00 0.00 3.07
4233 5106 0.890542 GTGCACCTCATCACCAAGCA 60.891 55.000 5.22 0.00 0.00 3.91
4245 5118 5.538053 TCATCACCAAGCACCTTATCAAAAA 59.462 36.000 0.00 0.00 0.00 1.94
4246 5119 5.195001 TCACCAAGCACCTTATCAAAAAC 57.805 39.130 0.00 0.00 0.00 2.43
4247 5120 4.646945 TCACCAAGCACCTTATCAAAAACA 59.353 37.500 0.00 0.00 0.00 2.83
4249 5122 4.649218 ACCAAGCACCTTATCAAAAACACT 59.351 37.500 0.00 0.00 0.00 3.55
4250 5123 5.221244 ACCAAGCACCTTATCAAAAACACTC 60.221 40.000 0.00 0.00 0.00 3.51
4253 5126 5.625150 AGCACCTTATCAAAAACACTCTCT 58.375 37.500 0.00 0.00 0.00 3.10
4255 5128 5.470098 GCACCTTATCAAAAACACTCTCTCA 59.530 40.000 0.00 0.00 0.00 3.27
4256 5129 6.348050 GCACCTTATCAAAAACACTCTCTCAG 60.348 42.308 0.00 0.00 0.00 3.35
4257 5130 6.708054 CACCTTATCAAAAACACTCTCTCAGT 59.292 38.462 0.00 0.00 34.67 3.41
4258 5131 7.227512 CACCTTATCAAAAACACTCTCTCAGTT 59.772 37.037 0.00 0.00 30.26 3.16
4259 5132 7.227512 ACCTTATCAAAAACACTCTCTCAGTTG 59.772 37.037 0.00 0.00 30.26 3.16
4260 5133 7.442364 CCTTATCAAAAACACTCTCTCAGTTGA 59.558 37.037 0.00 0.00 30.26 3.18
4261 5134 8.731275 TTATCAAAAACACTCTCTCAGTTGAA 57.269 30.769 0.00 0.00 30.26 2.69
4262 5135 6.668541 TCAAAAACACTCTCTCAGTTGAAG 57.331 37.500 0.00 0.00 30.26 3.02
4263 5136 6.406370 TCAAAAACACTCTCTCAGTTGAAGA 58.594 36.000 0.00 0.00 30.26 2.87
4264 5137 6.536582 TCAAAAACACTCTCTCAGTTGAAGAG 59.463 38.462 14.34 14.34 30.26 2.85
4265 5138 3.658757 ACACTCTCTCAGTTGAAGAGC 57.341 47.619 15.20 0.00 30.26 4.09
4266 5139 2.961741 ACACTCTCTCAGTTGAAGAGCA 59.038 45.455 15.20 0.00 30.26 4.26
4282 5155 2.113139 CAGTGGGGCAAACCGTCT 59.887 61.111 0.00 0.00 41.60 4.18
4289 5162 2.040012 TGGGGCAAACCGTCTAACATTA 59.960 45.455 0.00 0.00 41.60 1.90
4301 5174 2.758423 TCTAACATTACGCCTGCTCTCA 59.242 45.455 0.00 0.00 0.00 3.27
4316 5192 0.884514 TCTCAAGTCTCTCCGTGCTG 59.115 55.000 0.00 0.00 0.00 4.41
4320 5196 2.102420 TCAAGTCTCTCCGTGCTGAAAA 59.898 45.455 0.00 0.00 0.00 2.29
4563 5444 2.623763 TCCTGGCCCCCTCCTCTA 60.624 66.667 0.00 0.00 0.00 2.43
4659 5540 3.956744 AGCTTCTAGGTTTTCCATGTCC 58.043 45.455 0.00 0.00 43.73 4.02
4684 5565 5.522097 GTCTTTTGCTAGAAGCTACTCATCC 59.478 44.000 0.00 0.00 42.97 3.51
4748 5629 1.170442 TGCCGTCATAGAGTTCGTGA 58.830 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.264845 ACCAACCGGGCATCCCTT 61.265 61.111 6.32 0.00 42.67 3.95
60 61 1.153353 GTCGGACTTGGCAAATTCGA 58.847 50.000 8.15 8.15 0.00 3.71
63 64 1.923356 ATGGTCGGACTTGGCAAATT 58.077 45.000 8.23 0.00 0.00 1.82
78 80 5.630069 CACCTTTGGTAAGAGCATCTATGGT 60.630 44.000 0.00 0.00 38.29 3.55
80 82 5.674525 TCACCTTTGGTAAGAGCATCTATG 58.325 41.667 0.00 0.00 38.29 2.23
81 83 5.957771 TCACCTTTGGTAAGAGCATCTAT 57.042 39.130 0.00 0.00 38.29 1.98
111 113 0.966920 AGTCTGATTCGGTCAACGGT 59.033 50.000 0.00 0.00 44.45 4.83
119 121 1.207089 TGTTGCCCTAGTCTGATTCGG 59.793 52.381 0.00 0.00 0.00 4.30
143 145 1.981256 AAAGTTTGATGGCGTGTCCT 58.019 45.000 0.00 0.00 35.26 3.85
162 164 1.082019 TGGTGGGGTGCCAGATCTA 59.918 57.895 0.00 0.00 0.00 1.98
201 203 3.833650 TGATGGATGGCAAGTGTGATTTT 59.166 39.130 0.00 0.00 0.00 1.82
208 210 1.203052 GTGGTTGATGGATGGCAAGTG 59.797 52.381 0.00 0.00 0.00 3.16
301 303 1.218316 GTCTACGTGGAGCTTGGGG 59.782 63.158 0.12 0.00 0.00 4.96
316 318 2.597805 ACGTCTGCTCCCACGTCT 60.598 61.111 0.00 0.00 46.04 4.18
501 507 2.758770 TTCGACGTCTTGGCTTCGGG 62.759 60.000 14.70 0.00 32.17 5.14
546 557 6.958767 TCATTTTAGCTTTAGGTTCTAGGCT 58.041 36.000 0.00 0.00 0.00 4.58
579 591 2.692368 GGGTCCCTGGATCCTGCA 60.692 66.667 14.23 0.00 42.00 4.41
591 603 1.059913 AATCGATGATGAGGGGGTCC 58.940 55.000 0.00 0.00 0.00 4.46
602 618 3.243401 CCGTGGTGACTGATAATCGATGA 60.243 47.826 0.00 0.00 0.00 2.92
605 621 2.098607 GTCCGTGGTGACTGATAATCGA 59.901 50.000 0.00 0.00 32.39 3.59
609 625 1.200716 GTCGTCCGTGGTGACTGATAA 59.799 52.381 6.74 0.00 32.97 1.75
610 626 0.806868 GTCGTCCGTGGTGACTGATA 59.193 55.000 6.74 0.00 32.97 2.15
611 627 1.585006 GTCGTCCGTGGTGACTGAT 59.415 57.895 6.74 0.00 32.97 2.90
612 628 2.558286 GGTCGTCCGTGGTGACTGA 61.558 63.158 11.72 0.00 32.97 3.41
613 629 2.049433 GGTCGTCCGTGGTGACTG 60.049 66.667 11.72 0.00 32.97 3.51
614 630 2.083835 CTTGGTCGTCCGTGGTGACT 62.084 60.000 11.72 0.00 36.30 3.41
615 631 1.663702 CTTGGTCGTCCGTGGTGAC 60.664 63.158 0.00 5.76 36.30 3.67
743 1136 8.835439 GGGTATTTGATTCTTTGCTTTGAAAAA 58.165 29.630 0.00 0.00 0.00 1.94
744 1137 7.170658 CGGGTATTTGATTCTTTGCTTTGAAAA 59.829 33.333 0.00 0.00 0.00 2.29
810 1211 6.812998 ACTACTACTGTGTAGCACTCAAAAA 58.187 36.000 13.62 0.00 42.53 1.94
811 1212 6.401047 ACTACTACTGTGTAGCACTCAAAA 57.599 37.500 13.62 0.00 42.53 2.44
812 1213 6.713903 AGTACTACTACTGTGTAGCACTCAAA 59.286 38.462 13.10 0.00 40.96 2.69
813 1214 6.236409 AGTACTACTACTGTGTAGCACTCAA 58.764 40.000 13.10 0.00 40.96 3.02
814 1215 5.802465 AGTACTACTACTGTGTAGCACTCA 58.198 41.667 13.10 0.00 40.96 3.41
815 1216 6.479660 CCTAGTACTACTACTGTGTAGCACTC 59.520 46.154 18.24 8.56 42.71 3.51
816 1217 6.347696 CCTAGTACTACTACTGTGTAGCACT 58.652 44.000 18.51 18.51 44.60 4.40
817 1218 5.007528 GCCTAGTACTACTACTGTGTAGCAC 59.992 48.000 0.00 11.92 42.53 4.40
818 1219 5.121811 GCCTAGTACTACTACTGTGTAGCA 58.878 45.833 0.00 3.18 42.53 3.49
819 1220 5.121811 TGCCTAGTACTACTACTGTGTAGC 58.878 45.833 0.00 0.00 42.53 3.58
956 1370 1.272781 GTAGAGTGCTTGCTGCTACG 58.727 55.000 0.00 0.00 43.37 3.51
974 1388 1.790818 GGGGATAAAGGGAGAGACGT 58.209 55.000 0.00 0.00 0.00 4.34
1178 1592 3.861797 CGGTAGCCCCCAATCGCT 61.862 66.667 0.00 0.00 39.17 4.93
1345 1759 5.871524 AGAGACGTACGACATTGTAACTCTA 59.128 40.000 24.41 0.00 33.78 2.43
1415 1829 3.003275 CCTTCGTATGCAAACTTGTGTGT 59.997 43.478 0.00 0.00 0.00 3.72
1440 1854 0.973496 ATGCAAGCATGGTCATGGCA 60.973 50.000 6.76 12.65 37.70 4.92
1442 1856 3.119065 TGTTAATGCAAGCATGGTCATGG 60.119 43.478 8.50 0.00 39.16 3.66
1443 1857 4.112716 TGTTAATGCAAGCATGGTCATG 57.887 40.909 8.50 6.59 41.60 3.07
1482 1896 3.119566 GGAGGGAGTAGATAATAACCGCG 60.120 52.174 0.00 0.00 0.00 6.46
1505 1919 6.140303 TGTAGACGTCTTACATTATGGGAC 57.860 41.667 25.44 11.37 0.00 4.46
1524 1938 0.762418 TGCCCCGTCCCATAATGTAG 59.238 55.000 0.00 0.00 0.00 2.74
1525 1939 0.762418 CTGCCCCGTCCCATAATGTA 59.238 55.000 0.00 0.00 0.00 2.29
1526 1940 1.279025 ACTGCCCCGTCCCATAATGT 61.279 55.000 0.00 0.00 0.00 2.71
1617 2135 6.223852 ACGACTCACAGTTTCACAAAGATAT 58.776 36.000 0.00 0.00 0.00 1.63
1757 2277 2.965831 AGCTCACAAGGTTGTACTGAGA 59.034 45.455 9.52 0.00 39.91 3.27
1827 2347 7.690256 ACAGTTCCTTCAAACCTTCATACTAT 58.310 34.615 0.00 0.00 0.00 2.12
1876 2396 9.869757 ACTTTTTACATTAGTTGAAGTTTTGCT 57.130 25.926 0.00 0.00 0.00 3.91
1924 2753 6.683974 ATAGCTCAATGATGTGTACAAACC 57.316 37.500 0.00 0.00 0.00 3.27
2053 2882 6.186957 ACAACAATAGCATCTTCCCACATAA 58.813 36.000 0.00 0.00 0.00 1.90
2094 2923 6.308015 TGACTAACTGCATACAATTAGGGT 57.692 37.500 0.00 0.00 39.39 4.34
2154 2983 5.892119 ACATGGGACTAAGAAACGATAGAGA 59.108 40.000 0.00 0.00 41.38 3.10
2364 3218 6.897413 TGCTATCATATAATCTGCAGACCCTA 59.103 38.462 20.97 11.35 0.00 3.53
2396 3250 2.906354 CTGGCACCACAGTACCTTATC 58.094 52.381 0.00 0.00 33.81 1.75
2409 3263 2.489938 TCAACCTCAATACTGGCACC 57.510 50.000 0.00 0.00 0.00 5.01
2410 3264 4.846779 TTTTCAACCTCAATACTGGCAC 57.153 40.909 0.00 0.00 0.00 5.01
2416 3270 5.863935 GGACAGCAATTTTCAACCTCAATAC 59.136 40.000 0.00 0.00 0.00 1.89
2428 3282 4.122046 GCTTTTCAGTGGACAGCAATTTT 58.878 39.130 4.60 0.00 32.22 1.82
2534 3390 8.094548 TGCAAGGCTATTATTCTAACGATACAT 58.905 33.333 0.00 0.00 0.00 2.29
2869 3725 5.564550 AGTTATCAAAGTCAGCACCAATCT 58.435 37.500 0.00 0.00 0.00 2.40
3266 4122 0.390998 GCCTCTGCTCAGAACTGGAC 60.391 60.000 7.57 0.00 36.94 4.02
3449 4305 9.128404 TCATCAAATCCCAGAATTAAAGATCAG 57.872 33.333 0.00 0.00 0.00 2.90
3474 4330 6.645003 CCCTTGTTAAATGCAGTTAAACCTTC 59.355 38.462 19.88 8.73 0.00 3.46
3860 4716 1.833630 AGAGATCCGGCACATTTGAGA 59.166 47.619 0.00 0.00 0.00 3.27
3875 4731 3.439154 TGTCAAGAGCAGGAAGAGAGAT 58.561 45.455 0.00 0.00 0.00 2.75
4044 4913 3.266510 TGAAAGCGAGATAAGCCACAT 57.733 42.857 0.00 0.00 34.64 3.21
4068 4937 7.745620 AGAGTTGTTCTCCGTTTATGAAAAT 57.254 32.000 0.00 0.00 43.71 1.82
4074 4943 6.170506 TGCAATAGAGTTGTTCTCCGTTTAT 58.829 36.000 0.00 0.00 43.71 1.40
4131 5004 1.808411 TTTCACCGAGTGCATTCCTC 58.192 50.000 3.33 0.00 32.98 3.71
4211 5084 2.050836 TTGGTGATGAGGTGCACGGT 62.051 55.000 11.45 0.00 35.91 4.83
4226 5099 4.649218 AGTGTTTTTGATAAGGTGCTTGGT 59.351 37.500 0.00 0.00 0.00 3.67
4233 5106 6.831976 ACTGAGAGAGTGTTTTTGATAAGGT 58.168 36.000 0.00 0.00 31.75 3.50
4245 5118 2.961741 TGCTCTTCAACTGAGAGAGTGT 59.038 45.455 5.38 0.00 34.02 3.55
4246 5119 3.005684 ACTGCTCTTCAACTGAGAGAGTG 59.994 47.826 5.38 11.90 34.02 3.51
4247 5120 3.005684 CACTGCTCTTCAACTGAGAGAGT 59.994 47.826 5.38 3.70 35.94 3.24
4249 5122 2.298446 CCACTGCTCTTCAACTGAGAGA 59.702 50.000 5.38 2.62 33.68 3.10
4250 5123 2.612471 CCCACTGCTCTTCAACTGAGAG 60.612 54.545 0.00 0.00 33.68 3.20
4253 5126 0.397941 CCCCACTGCTCTTCAACTGA 59.602 55.000 0.00 0.00 0.00 3.41
4255 5128 1.073897 GCCCCACTGCTCTTCAACT 59.926 57.895 0.00 0.00 0.00 3.16
4256 5129 0.823356 TTGCCCCACTGCTCTTCAAC 60.823 55.000 0.00 0.00 0.00 3.18
4257 5130 0.106268 TTTGCCCCACTGCTCTTCAA 60.106 50.000 0.00 0.00 0.00 2.69
4258 5131 0.823356 GTTTGCCCCACTGCTCTTCA 60.823 55.000 0.00 0.00 0.00 3.02
4259 5132 1.527433 GGTTTGCCCCACTGCTCTTC 61.527 60.000 0.00 0.00 0.00 2.87
4260 5133 1.531602 GGTTTGCCCCACTGCTCTT 60.532 57.895 0.00 0.00 0.00 2.85
4261 5134 2.116125 GGTTTGCCCCACTGCTCT 59.884 61.111 0.00 0.00 0.00 4.09
4262 5135 3.365265 CGGTTTGCCCCACTGCTC 61.365 66.667 0.00 0.00 0.00 4.26
4263 5136 4.204028 ACGGTTTGCCCCACTGCT 62.204 61.111 0.00 0.00 0.00 4.24
4264 5137 2.741486 TAGACGGTTTGCCCCACTGC 62.741 60.000 0.00 0.00 0.00 4.40
4265 5138 0.250553 TTAGACGGTTTGCCCCACTG 60.251 55.000 0.00 0.00 0.00 3.66
4266 5139 0.250597 GTTAGACGGTTTGCCCCACT 60.251 55.000 0.00 0.00 0.00 4.00
4282 5155 3.056107 ACTTGAGAGCAGGCGTAATGTTA 60.056 43.478 0.00 0.00 0.00 2.41
4289 5162 0.897863 AGAGACTTGAGAGCAGGCGT 60.898 55.000 0.00 0.00 0.00 5.68
4301 5174 2.484889 GTTTTCAGCACGGAGAGACTT 58.515 47.619 0.00 0.00 0.00 3.01
4316 5192 1.121789 GATTTGCGCGGTTTCGTTTTC 59.878 47.619 8.83 0.00 38.89 2.29
4320 5196 0.671163 TAGGATTTGCGCGGTTTCGT 60.671 50.000 8.83 1.43 38.89 3.85
4659 5540 4.486090 TGAGTAGCTTCTAGCAAAAGACG 58.514 43.478 0.00 0.00 45.56 4.18
4684 5565 8.655651 TGCAATTTAGTAAGGGAAACAAAAAG 57.344 30.769 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.