Multiple sequence alignment - TraesCS7A01G110500

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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 TraesCS7A01G110500 chr7A 100.000 4492 0 0 1 4492 67674562 67670071 0.000000e+00 8296
1 TraesCS7A01G110500 chr7A 82.097 782 57 33 3745 4491 67678811 67679544 3.870000e-165 592
2 TraesCS7A01G110500 chr7A 76.703 558 81 36 1183 1731 629879594 629879077 9.580000e-67 265
3 TraesCS7A01G110500 chr7B 91.899 3123 153 43 184 3251 5058108 5061185 0.000000e+00 4274
4 TraesCS7A01G110500 chr7B 87.863 1310 98 35 3215 4491 5061184 5062465 0.000000e+00 1482
5 TraesCS7A01G110500 chr7B 84.375 256 18 12 4122 4375 5052376 5052141 9.720000e-57 231
6 TraesCS7A01G110500 chr7B 75.227 440 49 31 3822 4244 5145922 5146318 2.160000e-33 154
7 TraesCS7A01G110500 chr7B 89.431 123 8 3 4373 4490 5152845 5152967 2.800000e-32 150
8 TraesCS7A01G110500 chr7B 82.090 134 11 5 11 137 5057801 5057928 7.950000e-18 102
9 TraesCS7A01G110500 chr7D 96.361 2116 75 2 1137 3251 64011878 64013992 0.000000e+00 3480
10 TraesCS7A01G110500 chr7D 88.796 1321 66 39 3215 4491 64013991 64015273 0.000000e+00 1544
11 TraesCS7A01G110500 chr7D 87.674 860 48 23 389 1218 64011059 64011890 0.000000e+00 948
12 TraesCS7A01G110500 chr7D 86.000 350 27 16 4150 4491 64003842 64003507 5.530000e-94 355
13 TraesCS7A01G110500 chr7D 80.211 379 31 12 1 340 64010686 64011059 1.250000e-60 244
14 TraesCS7A01G110500 chr7D 88.557 201 20 2 3942 4141 64005871 64005673 1.610000e-59 241
15 TraesCS7A01G110500 chr2B 79.868 606 85 19 1230 1827 708391507 708392083 4.180000e-110 409
16 TraesCS7A01G110500 chr2B 79.832 595 87 17 1236 1827 66034137 66033573 1.950000e-108 403
17 TraesCS7A01G110500 chr2B 90.476 105 10 0 1736 1840 128531570 128531466 6.060000e-29 139
18 TraesCS7A01G110500 chr4A 81.081 296 44 10 1538 1827 714217636 714217925 4.520000e-55 226
19 TraesCS7A01G110500 chr2A 83.249 197 30 3 1604 1798 764660949 764660754 1.280000e-40 178
20 TraesCS7A01G110500 chr1B 89.524 105 11 0 1736 1840 189691025 189690921 2.820000e-27 134
21 TraesCS7A01G110500 chr4D 84.091 132 14 3 1722 1853 48514605 48514729 2.190000e-23 121


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 TraesCS7A01G110500 chr7A 67670071 67674562 4491 True 8296.000000 8296 100.0000 1 4492 1 chr7A.!!$R1 4491
1 TraesCS7A01G110500 chr7A 67678811 67679544 733 False 592.000000 592 82.0970 3745 4491 1 chr7A.!!$F1 746
2 TraesCS7A01G110500 chr7A 629879077 629879594 517 True 265.000000 265 76.7030 1183 1731 1 chr7A.!!$R2 548
3 TraesCS7A01G110500 chr7B 5057801 5062465 4664 False 1952.666667 4274 87.2840 11 4491 3 chr7B.!!$F3 4480
4 TraesCS7A01G110500 chr7D 64010686 64015273 4587 False 1554.000000 3480 88.2605 1 4491 4 chr7D.!!$F1 4490
5 TraesCS7A01G110500 chr7D 64003507 64005871 2364 True 298.000000 355 87.2785 3942 4491 2 chr7D.!!$R1 549
6 TraesCS7A01G110500 chr2B 708391507 708392083 576 False 409.000000 409 79.8680 1230 1827 1 chr2B.!!$F1 597
7 TraesCS7A01G110500 chr2B 66033573 66034137 564 True 403.000000 403 79.8320 1236 1827 1 chr2B.!!$R1 591

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
437 604 0.324285 ACCAGGTACGAGACGAGACT 59.676 55.0 0.00 0.0 0.00 3.24 F
450 617 0.509499 CGAGACTAGACGAGATCGCC 59.491 60.0 1.39 0.0 44.43 5.54 F
2300 2629 0.607620 GGCTTGCCAAGTTTGCCATA 59.392 50.0 6.28 0.0 42.79 2.74 F
3065 3394 0.332293 TCATCCATGGCACCACACAT 59.668 50.0 6.96 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2557 1.064946 GTCGGTGAGATCCTCGCAG 59.935 63.158 9.37 5.74 42.14 5.18 R
2309 2638 1.800586 CCATCTGACGTGACAAGGTTG 59.199 52.381 0.00 0.00 0.00 3.77 R
3339 3704 0.035152 ATCATCGCAAGCAACCCAGA 60.035 50.000 0.00 0.00 37.18 3.86 R
4463 6733 0.179124 CTGAGACGCCTCCAGCTAAC 60.179 60.000 0.00 0.00 40.39 2.34 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
69 71 3.581024 TGCTTTGCAGTGATCCAATTC 57.419 42.857 0.00 0.00 33.32 2.17
70 72 2.231964 TGCTTTGCAGTGATCCAATTCC 59.768 45.455 0.00 0.00 33.32 3.01
71 73 2.231964 GCTTTGCAGTGATCCAATTCCA 59.768 45.455 0.00 0.00 0.00 3.53
72 74 3.841643 CTTTGCAGTGATCCAATTCCAC 58.158 45.455 0.00 0.00 0.00 4.02
75 77 4.508551 TGCAGTGATCCAATTCCACTAT 57.491 40.909 0.00 0.00 38.93 2.12
76 78 5.628797 TGCAGTGATCCAATTCCACTATA 57.371 39.130 0.00 0.00 38.93 1.31
77 79 5.368145 TGCAGTGATCCAATTCCACTATAC 58.632 41.667 0.00 0.00 38.93 1.47
78 80 4.449068 GCAGTGATCCAATTCCACTATACG 59.551 45.833 0.00 0.00 38.93 3.06
79 81 5.601662 CAGTGATCCAATTCCACTATACGT 58.398 41.667 0.00 0.00 38.93 3.57
87 89 7.658261 TCCAATTCCACTATACGTATCTCAAG 58.342 38.462 12.24 6.44 0.00 3.02
133 144 5.193527 TGAAATCCCCTCATTCTGTTATGGA 59.806 40.000 0.00 0.00 0.00 3.41
137 148 6.187727 TCCCCTCATTCTGTTATGGATTAC 57.812 41.667 0.00 0.00 0.00 1.89
140 151 5.073691 CCCTCATTCTGTTATGGATTACCCT 59.926 44.000 0.00 0.00 35.38 4.34
141 152 6.234177 CCTCATTCTGTTATGGATTACCCTC 58.766 44.000 0.00 0.00 35.38 4.30
154 317 5.162870 TGGATTACCCTCTAGCTGATTCCTA 60.163 44.000 0.00 0.00 35.38 2.94
164 327 1.772182 CTGATTCCTACATCGACCGC 58.228 55.000 0.00 0.00 0.00 5.68
172 335 1.779025 TACATCGACCGCTCTACCGC 61.779 60.000 0.00 0.00 0.00 5.68
193 356 4.033129 CGCGTTATTTCCGTATTTCTGGAA 59.967 41.667 0.00 0.00 42.35 3.53
197 360 6.413818 CGTTATTTCCGTATTTCTGGAATTGC 59.586 38.462 0.00 0.00 43.44 3.56
202 365 2.618709 CGTATTTCTGGAATTGCTCCCC 59.381 50.000 0.00 0.00 44.69 4.81
214 377 2.513897 CTCCCCGACGAAATGGGC 60.514 66.667 0.00 0.00 44.58 5.36
256 419 1.210722 GACCCCCATCTGAGAAACTCC 59.789 57.143 0.00 0.00 0.00 3.85
287 450 7.009448 CCATAATCCAATTTTCACACATTGACG 59.991 37.037 0.00 0.00 32.91 4.35
291 454 4.320861 CCAATTTTCACACATTGACGCCTA 60.321 41.667 0.00 0.00 32.91 3.93
292 455 4.685169 ATTTTCACACATTGACGCCTAG 57.315 40.909 0.00 0.00 32.26 3.02
293 456 2.831685 TTCACACATTGACGCCTAGT 57.168 45.000 0.00 0.00 32.26 2.57
308 475 3.181479 CGCCTAGTCTGCTACCAAACATA 60.181 47.826 0.00 0.00 0.00 2.29
317 484 4.689071 TGCTACCAAACATACATAGGTCG 58.311 43.478 0.00 0.00 33.91 4.79
319 486 5.114081 GCTACCAAACATACATAGGTCGTT 58.886 41.667 0.00 0.00 33.91 3.85
334 501 0.534203 TCGTTGCCTCCAACCAACTC 60.534 55.000 1.43 0.00 46.76 3.01
363 530 2.667473 AATTCCCCAACTACTCGTCG 57.333 50.000 0.00 0.00 0.00 5.12
371 538 3.823330 CTACTCGTCGGCCCGCTT 61.823 66.667 0.00 0.00 0.00 4.68
433 600 3.991999 CCACCAGGTACGAGACGA 58.008 61.111 0.00 0.00 0.00 4.20
434 601 1.801332 CCACCAGGTACGAGACGAG 59.199 63.158 0.00 0.00 0.00 4.18
435 602 0.675837 CCACCAGGTACGAGACGAGA 60.676 60.000 0.00 0.00 0.00 4.04
436 603 0.447011 CACCAGGTACGAGACGAGAC 59.553 60.000 0.00 0.00 0.00 3.36
437 604 0.324285 ACCAGGTACGAGACGAGACT 59.676 55.000 0.00 0.00 0.00 3.24
450 617 0.509499 CGAGACTAGACGAGATCGCC 59.491 60.000 1.39 0.00 44.43 5.54
451 618 0.869730 GAGACTAGACGAGATCGCCC 59.130 60.000 1.39 0.00 44.43 6.13
491 658 4.584518 CACCAGCAGCACACCCCA 62.585 66.667 0.00 0.00 0.00 4.96
556 723 1.080569 GCAGCCAACCAACCAATCG 60.081 57.895 0.00 0.00 0.00 3.34
557 724 1.586028 CAGCCAACCAACCAATCGG 59.414 57.895 0.00 0.00 38.77 4.18
558 725 2.261361 GCCAACCAACCAATCGGC 59.739 61.111 0.00 0.00 34.57 5.54
841 1053 1.276622 GGCAGGAGGAGGAGTACAAA 58.723 55.000 0.00 0.00 0.00 2.83
925 1137 0.888619 CGGGGAAGAAAAGGAAAGCC 59.111 55.000 0.00 0.00 0.00 4.35
927 1139 0.888619 GGGAAGAAAAGGAAAGCCGG 59.111 55.000 0.00 0.00 39.96 6.13
928 1140 1.546998 GGGAAGAAAAGGAAAGCCGGA 60.547 52.381 5.05 0.00 39.96 5.14
929 1141 1.813178 GGAAGAAAAGGAAAGCCGGAG 59.187 52.381 5.05 0.00 39.96 4.63
930 1142 1.200252 GAAGAAAAGGAAAGCCGGAGC 59.800 52.381 5.05 0.00 39.96 4.70
931 1143 0.609406 AGAAAAGGAAAGCCGGAGCC 60.609 55.000 5.05 0.00 41.25 4.70
961 1173 3.305471 GCTGTCGAGTATATCACTTCCCC 60.305 52.174 0.00 0.00 37.72 4.81
1017 1233 1.991230 CACCCAAATCCGTCCTCCT 59.009 57.895 0.00 0.00 0.00 3.69
1136 1378 4.463879 CTGCTGGACCTGCCGGAG 62.464 72.222 19.56 7.71 46.81 4.63
1161 1471 4.519437 TGCTGCTCATCCTCGGCG 62.519 66.667 0.00 0.00 37.40 6.46
1286 1605 3.066233 GACGGCCGACTTCCTCCTC 62.066 68.421 35.90 11.99 0.00 3.71
1419 1739 1.608717 CTCCTCCTCCAACCACCTCG 61.609 65.000 0.00 0.00 0.00 4.63
2050 2379 1.692042 CTGGGCTGGAGGACCTCAT 60.692 63.158 23.06 0.00 45.52 2.90
2189 2518 2.507102 CTGCATCTCGACGGCGTT 60.507 61.111 16.19 0.00 38.98 4.84
2228 2557 1.658095 GAGTCGCTCTGCATCAAGAAC 59.342 52.381 0.00 0.00 0.00 3.01
2255 2584 4.803426 CTCACCGACGCCAGCCTC 62.803 72.222 0.00 0.00 0.00 4.70
2300 2629 0.607620 GGCTTGCCAAGTTTGCCATA 59.392 50.000 6.28 0.00 42.79 2.74
2309 2638 3.514645 CAAGTTTGCCATACAAGGATGC 58.485 45.455 0.00 0.00 40.06 3.91
2345 2674 0.839853 ATGGGATCAGGAGGCTAGCC 60.840 60.000 27.19 27.19 0.00 3.93
2432 2761 1.073722 CCTTGCTGCTCTGAACCCA 59.926 57.895 0.00 0.00 0.00 4.51
2711 3040 1.144936 GCTCGATAGCTGCCCTGTT 59.855 57.895 0.00 0.00 45.85 3.16
2747 3076 1.120530 TTAAGGTGGAGGGCGATCTC 58.879 55.000 0.00 0.00 0.00 2.75
2753 3082 2.519780 GAGGGCGATCTCCGGACT 60.520 66.667 0.00 0.00 39.04 3.85
2829 3158 2.042831 GCGCTGGCCAAGATGAAGT 61.043 57.895 7.01 0.00 0.00 3.01
2858 3187 2.895372 GAGGCGGTGGGTTATGCG 60.895 66.667 0.00 0.00 0.00 4.73
2891 3220 2.057922 ACGGGGCATATGGATCTTTCT 58.942 47.619 4.56 0.00 0.00 2.52
2975 3304 2.359975 CCGCCCCAAGACAAGGAC 60.360 66.667 0.00 0.00 0.00 3.85
3065 3394 0.332293 TCATCCATGGCACCACACAT 59.668 50.000 6.96 0.00 0.00 3.21
3149 3478 1.794714 ACTATCCAGCACCGGAGAAT 58.205 50.000 9.46 0.00 38.83 2.40
3185 3514 1.099879 AGATGCGGGCTGAATCTTGC 61.100 55.000 11.29 0.00 0.00 4.01
3194 3523 1.826385 CTGAATCTTGCCTCCGGTTT 58.174 50.000 0.00 0.00 0.00 3.27
3239 3603 5.580297 GCAATTTCGGCAAATTCCTGATTAA 59.420 36.000 5.15 0.00 39.75 1.40
3240 3604 6.455513 GCAATTTCGGCAAATTCCTGATTAAC 60.456 38.462 5.15 0.00 39.75 2.01
3273 3637 3.623060 GTGCACCATTACAGTGATTCGAT 59.377 43.478 5.22 0.00 37.42 3.59
3331 3696 1.261480 AGTCACCCAGAGTGCTACTG 58.739 55.000 0.00 0.00 46.81 2.74
3333 3698 1.618837 GTCACCCAGAGTGCTACTGAA 59.381 52.381 0.00 0.00 46.81 3.02
3338 3703 3.702045 ACCCAGAGTGCTACTGAAGTATC 59.298 47.826 0.00 0.00 37.54 2.24
3339 3704 3.957497 CCCAGAGTGCTACTGAAGTATCT 59.043 47.826 0.00 0.00 37.54 1.98
3340 3705 4.037446 CCCAGAGTGCTACTGAAGTATCTC 59.963 50.000 0.00 1.32 37.54 2.75
3359 3724 0.813184 CTGGGTTGCTTGCGATGATT 59.187 50.000 0.00 0.00 0.00 2.57
3361 3726 0.803380 GGGTTGCTTGCGATGATTGC 60.803 55.000 0.00 0.00 0.00 3.56
3427 3792 2.421424 GACAATGCCTGATCAAGTGACC 59.579 50.000 0.00 0.00 0.00 4.02
3621 3988 6.140737 GCAAGAGAAATTGGCGTTATTATTCG 59.859 38.462 0.00 0.00 0.00 3.34
3661 4029 9.730420 GTTTGAGCTCTGTAAACATTAGAAAAA 57.270 29.630 16.19 0.00 35.11 1.94
3702 4070 4.016444 TCATATGCCCTTGTTCTTCAACC 58.984 43.478 0.00 0.00 32.18 3.77
3719 4090 3.119531 TCAACCGCCACATTTCATCATTC 60.120 43.478 0.00 0.00 0.00 2.67
3732 4103 4.515028 TCATCATTCTGAAGATGGCCTT 57.485 40.909 19.96 0.00 41.45 4.35
3783 4155 1.145803 GGAGAAACTGGTGCGTACAC 58.854 55.000 5.86 0.00 46.66 2.90
3784 4156 1.270147 GGAGAAACTGGTGCGTACACT 60.270 52.381 5.86 0.00 46.57 3.55
3833 4209 1.532868 GCTGTGTCCTTGTGCTTACTG 59.467 52.381 0.00 0.00 0.00 2.74
3855 4235 0.813821 GTCTCCTTTGCCTTGCATCC 59.186 55.000 0.00 0.00 38.76 3.51
3856 4236 0.677731 TCTCCTTTGCCTTGCATCCG 60.678 55.000 0.00 0.00 38.76 4.18
3910 4298 5.629435 GCAAACAGGTTTAACAATCTGCTAC 59.371 40.000 0.00 0.00 44.13 3.58
3912 4300 6.560253 AACAGGTTTAACAATCTGCTACAG 57.440 37.500 0.00 0.00 44.13 2.74
3913 4301 5.865085 ACAGGTTTAACAATCTGCTACAGA 58.135 37.500 0.00 0.00 44.13 3.41
3914 4302 5.701290 ACAGGTTTAACAATCTGCTACAGAC 59.299 40.000 0.00 0.00 44.13 3.51
3915 4303 5.934625 CAGGTTTAACAATCTGCTACAGACT 59.065 40.000 0.00 0.00 43.63 3.24
3916 4304 7.097192 CAGGTTTAACAATCTGCTACAGACTA 58.903 38.462 0.00 0.00 43.63 2.59
3917 4305 7.276658 CAGGTTTAACAATCTGCTACAGACTAG 59.723 40.741 0.00 0.00 43.63 2.57
3949 4337 5.405269 TGACATGAGATGAACTTGTAACACG 59.595 40.000 0.00 0.00 0.00 4.49
3950 4338 4.152402 ACATGAGATGAACTTGTAACACGC 59.848 41.667 0.00 0.00 0.00 5.34
3955 4343 3.120321 TGAACTTGTAACACGCCTGAT 57.880 42.857 0.00 0.00 0.00 2.90
3966 4354 2.301870 ACACGCCTGATCCAAGAAAGTA 59.698 45.455 0.00 0.00 0.00 2.24
3973 4362 2.635915 TGATCCAAGAAAGTACACCCGT 59.364 45.455 0.00 0.00 0.00 5.28
4029 4432 9.133627 GAATGCTGAAATTAACTTTCTTCCTTC 57.866 33.333 9.98 7.52 43.14 3.46
4073 4476 1.163554 GAAGCTTCTGCAAGGTCCAG 58.836 55.000 19.44 0.00 39.53 3.86
4103 4507 1.604947 CCATCATCAGAGCAGGCTACG 60.605 57.143 0.00 0.00 0.00 3.51
4117 4527 2.679837 AGGCTACGACAATTTGCTGATG 59.320 45.455 0.00 0.00 0.00 3.07
4120 4530 2.907910 ACGACAATTTGCTGATGCTC 57.092 45.000 0.00 0.00 40.48 4.26
4150 6385 0.252103 AGGCCCCGAACTAACTGAGA 60.252 55.000 0.00 0.00 0.00 3.27
4244 6485 4.571984 TCGGAACATATTGCACAAGATCTG 59.428 41.667 0.00 0.00 0.00 2.90
4275 6517 0.676782 CGCCCTTCCAAGTTCCGATT 60.677 55.000 0.00 0.00 0.00 3.34
4306 6548 1.593196 TTGTCAAAGCGAAGTCCCAG 58.407 50.000 0.00 0.00 0.00 4.45
4364 6606 1.402107 AAAGGCACCCAAGCACCAAG 61.402 55.000 0.00 0.00 35.83 3.61
4366 6608 1.228429 GGCACCCAAGCACCAAGTA 60.228 57.895 0.00 0.00 35.83 2.24
4367 6609 1.524008 GGCACCCAAGCACCAAGTAC 61.524 60.000 0.00 0.00 35.83 2.73
4370 6612 0.553819 ACCCAAGCACCAAGTACCAA 59.446 50.000 0.00 0.00 0.00 3.67
4371 6613 1.247567 CCCAAGCACCAAGTACCAAG 58.752 55.000 0.00 0.00 0.00 3.61
4372 6614 0.598065 CCAAGCACCAAGTACCAAGC 59.402 55.000 0.00 0.00 0.00 4.01
4379 6633 3.805807 GCACCAAGTACCAAGCACTCTTA 60.806 47.826 0.00 0.00 0.00 2.10
4463 6733 4.320870 TGCCTTCTTTTCGGGTTAAGTAG 58.679 43.478 0.00 0.00 0.00 2.57
4491 6761 1.979693 GGCGTCTCAGTGGAGGAGT 60.980 63.158 5.75 0.00 41.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.037697 GTGTCATGGTGCCTCGTACA 60.038 55.000 0.00 0.00 0.00 2.90
9 10 0.901827 ATGTGTCATGGTGCCTCGTA 59.098 50.000 0.00 0.00 0.00 3.43
66 68 6.650427 TGCTTGAGATACGTATAGTGGAAT 57.350 37.500 8.34 0.00 0.00 3.01
68 70 6.128363 CGTATGCTTGAGATACGTATAGTGGA 60.128 42.308 8.34 0.00 42.33 4.02
69 71 6.022208 CGTATGCTTGAGATACGTATAGTGG 58.978 44.000 8.34 0.00 42.33 4.00
70 72 5.508573 GCGTATGCTTGAGATACGTATAGTG 59.491 44.000 8.34 0.00 46.72 2.74
71 73 5.391736 GGCGTATGCTTGAGATACGTATAGT 60.392 44.000 8.34 0.00 46.72 2.12
72 74 5.029014 GGCGTATGCTTGAGATACGTATAG 58.971 45.833 8.34 3.33 46.72 1.31
75 77 2.030540 GGGCGTATGCTTGAGATACGTA 60.031 50.000 6.92 0.00 46.72 3.57
76 78 1.269621 GGGCGTATGCTTGAGATACGT 60.270 52.381 6.92 0.00 46.72 3.57
78 80 2.821991 AGGGCGTATGCTTGAGATAC 57.178 50.000 6.92 0.00 42.25 2.24
79 81 3.838244 AAAGGGCGTATGCTTGAGATA 57.162 42.857 6.92 0.00 42.25 1.98
87 89 0.468648 AGAGGGTAAAGGGCGTATGC 59.531 55.000 0.00 0.00 41.71 3.14
93 95 3.994931 TTTCACTAGAGGGTAAAGGGC 57.005 47.619 0.00 0.00 0.00 5.19
133 144 5.716979 TGTAGGAATCAGCTAGAGGGTAAT 58.283 41.667 0.00 0.00 0.00 1.89
137 148 3.192422 CGATGTAGGAATCAGCTAGAGGG 59.808 52.174 0.00 0.00 0.00 4.30
140 151 3.821600 GGTCGATGTAGGAATCAGCTAGA 59.178 47.826 0.00 0.00 0.00 2.43
141 152 3.365465 CGGTCGATGTAGGAATCAGCTAG 60.365 52.174 0.00 0.00 0.00 3.42
154 317 3.108343 CGGTAGAGCGGTCGATGT 58.892 61.111 9.28 0.00 0.00 3.06
164 327 2.199291 ACGGAAATAACGCGGTAGAG 57.801 50.000 10.76 1.32 34.00 2.43
172 335 6.413818 GCAATTCCAGAAATACGGAAATAACG 59.586 38.462 0.00 0.00 44.25 3.18
173 336 7.480810 AGCAATTCCAGAAATACGGAAATAAC 58.519 34.615 0.00 0.00 44.25 1.89
193 356 0.748005 CCATTTCGTCGGGGAGCAAT 60.748 55.000 0.00 0.00 0.00 3.56
197 360 2.513897 GCCCATTTCGTCGGGGAG 60.514 66.667 8.34 0.00 45.08 4.30
202 365 1.004927 GAATCTTCGCCCATTTCGTCG 60.005 52.381 0.00 0.00 0.00 5.12
214 377 2.483889 GCAGGTTAGGGGAGAATCTTCG 60.484 54.545 0.00 0.00 33.73 3.79
256 419 5.874261 GTGTGAAAATTGGATTATGGTTGGG 59.126 40.000 0.00 0.00 0.00 4.12
287 450 2.762535 TGTTTGGTAGCAGACTAGGC 57.237 50.000 15.61 0.00 0.00 3.93
291 454 5.425539 ACCTATGTATGTTTGGTAGCAGACT 59.574 40.000 15.61 5.30 0.00 3.24
292 455 5.671493 ACCTATGTATGTTTGGTAGCAGAC 58.329 41.667 8.56 8.56 0.00 3.51
293 456 5.451381 CGACCTATGTATGTTTGGTAGCAGA 60.451 44.000 0.00 0.00 0.00 4.26
294 457 4.745125 CGACCTATGTATGTTTGGTAGCAG 59.255 45.833 0.00 0.00 0.00 4.24
295 458 4.160814 ACGACCTATGTATGTTTGGTAGCA 59.839 41.667 0.00 0.00 0.00 3.49
308 475 0.981183 TTGGAGGCAACGACCTATGT 59.019 50.000 0.00 0.00 41.32 2.29
317 484 1.949257 CGAGTTGGTTGGAGGCAAC 59.051 57.895 0.00 0.00 0.00 4.17
319 486 2.281484 GCGAGTTGGTTGGAGGCA 60.281 61.111 0.00 0.00 0.00 4.75
387 554 2.045926 GGCTAGCTGTGTGTGGGG 60.046 66.667 15.72 0.00 0.00 4.96
433 600 0.881159 CGGGCGATCTCGTCTAGTCT 60.881 60.000 4.03 0.00 44.45 3.24
434 601 0.879400 TCGGGCGATCTCGTCTAGTC 60.879 60.000 4.03 0.00 44.45 2.59
435 602 1.145598 TCGGGCGATCTCGTCTAGT 59.854 57.895 4.03 0.00 44.45 2.57
436 603 1.570475 GTCGGGCGATCTCGTCTAG 59.430 63.158 4.03 0.00 44.45 2.43
437 604 1.890979 GGTCGGGCGATCTCGTCTA 60.891 63.158 4.03 0.00 44.45 2.59
491 658 5.364735 GGGGGAGTTGAATGAATGAATGAAT 59.635 40.000 0.00 0.00 0.00 2.57
541 708 2.261361 GCCGATTGGTTGGTTGGC 59.739 61.111 0.00 0.00 37.71 4.52
556 723 3.206211 CTCGCTCGATCTCTGGGCC 62.206 68.421 0.00 0.00 0.00 5.80
557 724 2.334653 CTCGCTCGATCTCTGGGC 59.665 66.667 0.00 0.00 0.00 5.36
558 725 2.128853 GAGCTCGCTCGATCTCTGGG 62.129 65.000 13.80 0.00 35.30 4.45
817 1021 0.548682 ACTCCTCCTCCTGCCATTGT 60.549 55.000 0.00 0.00 0.00 2.71
841 1053 7.867160 TTTATCCTCTTATCCCCTTCGTATT 57.133 36.000 0.00 0.00 0.00 1.89
894 1106 2.158561 CTTCCCCGCTTTGCCCTTTG 62.159 60.000 0.00 0.00 0.00 2.77
998 1214 1.749258 GGAGGACGGATTTGGGTGC 60.749 63.158 0.00 0.00 0.00 5.01
1000 1216 1.272554 GGAGGAGGACGGATTTGGGT 61.273 60.000 0.00 0.00 0.00 4.51
1004 1220 2.732619 GCGGGAGGAGGACGGATTT 61.733 63.158 0.00 0.00 0.00 2.17
1027 1243 2.040359 CCCTTCCTCCTCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
1028 1244 2.040359 CCCCTTCCTCCTCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1030 1246 1.208706 CTTTCCCCTTCCTCCTCTCC 58.791 60.000 0.00 0.00 0.00 3.71
1032 1248 0.916845 GGCTTTCCCCTTCCTCCTCT 60.917 60.000 0.00 0.00 0.00 3.69
1033 1249 1.610327 GGCTTTCCCCTTCCTCCTC 59.390 63.158 0.00 0.00 0.00 3.71
1034 1250 2.301738 CGGCTTTCCCCTTCCTCCT 61.302 63.158 0.00 0.00 0.00 3.69
1035 1251 2.272471 CGGCTTTCCCCTTCCTCC 59.728 66.667 0.00 0.00 0.00 4.30
1036 1252 2.272471 CCGGCTTTCCCCTTCCTC 59.728 66.667 0.00 0.00 0.00 3.71
1037 1253 4.048470 GCCGGCTTTCCCCTTCCT 62.048 66.667 22.15 0.00 0.00 3.36
1139 1381 2.124653 AGGATGAGCAGCAGCAGC 60.125 61.111 3.17 0.46 45.49 5.25
1140 1382 1.883544 CGAGGATGAGCAGCAGCAG 60.884 63.158 3.17 0.00 45.49 4.24
1141 1383 2.186125 CGAGGATGAGCAGCAGCA 59.814 61.111 3.17 0.00 45.49 4.41
1142 1384 2.588314 CCGAGGATGAGCAGCAGC 60.588 66.667 0.00 0.00 42.56 5.25
1143 1385 2.588314 GCCGAGGATGAGCAGCAG 60.588 66.667 0.00 0.00 0.00 4.24
1144 1386 4.519437 CGCCGAGGATGAGCAGCA 62.519 66.667 0.00 0.00 0.00 4.41
1272 1591 2.428085 GGAGGAGGAGGAAGTCGGC 61.428 68.421 0.00 0.00 0.00 5.54
2012 2341 2.280797 AGCGCGGCAAAGAAGTCA 60.281 55.556 8.83 0.00 0.00 3.41
2014 2343 3.050275 GGAGCGCGGCAAAGAAGT 61.050 61.111 8.83 0.00 0.00 3.01
2117 2446 1.890894 CGTCAGGACCTTGATCCGT 59.109 57.895 0.00 0.00 44.22 4.69
2172 2501 2.507102 AACGCCGTCGAGATGCAG 60.507 61.111 0.00 0.00 39.41 4.41
2228 2557 1.064946 GTCGGTGAGATCCTCGCAG 59.935 63.158 9.37 5.74 42.14 5.18
2309 2638 1.800586 CCATCTGACGTGACAAGGTTG 59.199 52.381 0.00 0.00 0.00 3.77
2753 3082 1.561717 CGTGAAATGGACGCGGACAA 61.562 55.000 12.47 0.00 37.56 3.18
2891 3220 1.906574 AGATAAAACCGCTCCCACTGA 59.093 47.619 0.00 0.00 0.00 3.41
2975 3304 4.003788 AGGCTCCGGTGGTTCACG 62.004 66.667 0.00 0.00 34.83 4.35
3065 3394 3.332919 GAAGAAGCTCATGAAGTGCTCA 58.667 45.455 8.26 0.00 45.71 4.26
3149 3478 4.377897 GCATCTCTGTGATCATCATGTCA 58.622 43.478 0.00 0.00 32.05 3.58
3239 3603 2.268076 GGTGCACCCAATTCAGCGT 61.268 57.895 26.31 0.00 0.00 5.07
3240 3604 2.267351 TGGTGCACCCAATTCAGCG 61.267 57.895 32.62 0.00 41.50 5.18
3331 3696 2.680339 GCAAGCAACCCAGAGATACTTC 59.320 50.000 0.00 0.00 0.00 3.01
3333 3698 1.406069 CGCAAGCAACCCAGAGATACT 60.406 52.381 0.00 0.00 0.00 2.12
3338 3703 0.674581 TCATCGCAAGCAACCCAGAG 60.675 55.000 0.00 0.00 37.18 3.35
3339 3704 0.035152 ATCATCGCAAGCAACCCAGA 60.035 50.000 0.00 0.00 37.18 3.86
3340 3705 0.813184 AATCATCGCAAGCAACCCAG 59.187 50.000 0.00 0.00 37.18 4.45
3359 3724 4.253685 GAGCAATTCCAGTTACTACAGCA 58.746 43.478 0.00 0.00 0.00 4.41
3361 3726 5.482908 ACTGAGCAATTCCAGTTACTACAG 58.517 41.667 0.00 0.00 40.40 2.74
3427 3792 6.043327 TGCAAATAAAGATTCGATACCACG 57.957 37.500 0.00 0.00 0.00 4.94
3621 3988 7.029563 CAGAGCTCAAACATTACAATTTACCC 58.970 38.462 17.77 0.00 0.00 3.69
3661 4029 1.873591 GACAAACAAGTGACTGCCGAT 59.126 47.619 0.00 0.00 0.00 4.18
3719 4090 5.920193 TTTTGGAATAAGGCCATCTTCAG 57.080 39.130 5.01 0.00 36.93 3.02
3783 4155 0.322975 ACTTCCCAGTGCTGCTACAG 59.677 55.000 0.00 0.00 34.12 2.74
3784 4156 0.764890 AACTTCCCAGTGCTGCTACA 59.235 50.000 0.00 0.00 31.60 2.74
3833 4209 1.174712 TGCAAGGCAAAGGAGACAGC 61.175 55.000 0.00 0.00 34.76 4.40
3855 4235 1.737793 GAACTTATGGTCAACCCTGCG 59.262 52.381 0.00 0.00 34.29 5.18
3856 4236 2.790433 TGAACTTATGGTCAACCCTGC 58.210 47.619 0.00 0.00 34.29 4.85
3898 4286 5.478679 ACTCACTAGTCTGTAGCAGATTGTT 59.521 40.000 1.99 0.00 42.73 2.83
3910 4298 5.877564 TCTCATGTCAGTACTCACTAGTCTG 59.122 44.000 0.00 0.00 37.15 3.51
3912 4300 6.540551 TCATCTCATGTCAGTACTCACTAGTC 59.459 42.308 0.00 0.00 37.15 2.59
3913 4301 6.418946 TCATCTCATGTCAGTACTCACTAGT 58.581 40.000 0.00 0.00 39.91 2.57
3914 4302 6.934048 TCATCTCATGTCAGTACTCACTAG 57.066 41.667 0.00 0.00 32.21 2.57
3915 4303 6.887002 AGTTCATCTCATGTCAGTACTCACTA 59.113 38.462 0.00 0.00 32.21 2.74
3916 4304 5.714333 AGTTCATCTCATGTCAGTACTCACT 59.286 40.000 0.00 0.00 34.42 3.41
3917 4305 5.960113 AGTTCATCTCATGTCAGTACTCAC 58.040 41.667 0.00 0.00 0.00 3.51
3949 4337 3.010420 GGTGTACTTTCTTGGATCAGGC 58.990 50.000 0.00 0.00 0.00 4.85
3950 4338 3.610911 GGGTGTACTTTCTTGGATCAGG 58.389 50.000 0.00 0.00 0.00 3.86
3955 4343 2.040939 TGACGGGTGTACTTTCTTGGA 58.959 47.619 0.00 0.00 0.00 3.53
3966 4354 4.295141 TGGAATTCTTAATGACGGGTGT 57.705 40.909 5.23 0.00 0.00 4.16
3973 4362 8.712103 AGTCAGATCAGATGGAATTCTTAATGA 58.288 33.333 5.23 6.00 0.00 2.57
4103 4507 2.907910 ACGAGCATCAGCAAATTGTC 57.092 45.000 0.00 0.00 45.49 3.18
4117 4527 1.592400 GGGCCTTTGGGTTAACGAGC 61.592 60.000 0.84 0.00 34.45 5.03
4120 4530 2.337246 CGGGGCCTTTGGGTTAACG 61.337 63.158 0.84 0.00 34.45 3.18
4150 6385 1.579429 GCGATTTGCGGAACCACTT 59.421 52.632 0.00 0.00 41.29 3.16
4275 6517 1.403679 CTTTGACAAAACGCACCTGGA 59.596 47.619 0.00 0.00 0.00 3.86
4306 6548 2.680339 CCCAAAGAGGAGAAAGAATCGC 59.320 50.000 0.00 0.00 41.22 4.58
4364 6606 4.022242 TCTGTCACTAAGAGTGCTTGGTAC 60.022 45.833 1.60 0.00 45.54 3.34
4366 6608 2.965831 TCTGTCACTAAGAGTGCTTGGT 59.034 45.455 1.60 0.00 45.54 3.67
4367 6609 3.256879 TCTCTGTCACTAAGAGTGCTTGG 59.743 47.826 1.60 0.00 45.54 3.61
4370 6612 3.088532 CCTCTCTGTCACTAAGAGTGCT 58.911 50.000 1.60 0.00 45.54 4.40
4371 6613 2.823154 ACCTCTCTGTCACTAAGAGTGC 59.177 50.000 1.60 0.00 45.54 4.40
4372 6614 4.394920 GAGACCTCTCTGTCACTAAGAGTG 59.605 50.000 0.00 0.00 42.20 3.51
4463 6733 0.179124 CTGAGACGCCTCCAGCTAAC 60.179 60.000 0.00 0.00 40.39 2.34


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

AutoCloner maintained by Alex Coulton.