Multiple sequence alignment - TraesCS7A01G244000

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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 TraesCS7A01G244000 chr7A 100.000 5589 0 0 1 5589 220130047 220124459 0.000000e+00 10322.0
1 TraesCS7A01G244000 chr7D 91.868 4587 278 36 1058 5589 207787856 207783310 0.000000e+00 6316.0
2 TraesCS7A01G244000 chr7D 92.285 4459 267 41 1172 5589 207565206 207560784 0.000000e+00 6257.0
3 TraesCS7A01G244000 chr7D 91.238 2705 166 30 48 2714 207608367 207605696 0.000000e+00 3616.0
4 TraesCS7A01G244000 chr7D 90.256 1211 93 14 3 1205 207581473 207580280 0.000000e+00 1559.0
5 TraesCS7A01G244000 chr7D 90.759 1028 81 9 47 1067 207791385 207790365 0.000000e+00 1360.0
6 TraesCS7A01G244000 chr7D 89.981 1028 87 11 47 1067 207737645 207736627 0.000000e+00 1314.0
7 TraesCS7A01G244000 chr7D 82.540 126 21 1 294 418 207608371 207608246 5.920000e-20 110.0
8 TraesCS7A01G244000 chr7B 91.411 4436 323 30 993 5388 193523881 193528298 0.000000e+00 6028.0
9 TraesCS7A01G244000 chr7B 89.248 958 86 9 3 950 193522921 193523871 0.000000e+00 1182.0
10 TraesCS7A01G244000 chr7B 79.622 476 91 6 4877 5351 144112978 144113448 2.490000e-88 337.0
11 TraesCS7A01G244000 chr7B 87.047 193 25 0 5392 5584 380710372 380710180 9.430000e-53 219.0
12 TraesCS7A01G244000 chr3A 83.333 516 84 2 4874 5388 640842096 640842610 5.070000e-130 475.0
13 TraesCS7A01G244000 chr3A 79.431 457 90 3 4878 5333 25577229 25577682 2.510000e-83 320.0
14 TraesCS7A01G244000 chr5A 82.157 510 89 2 4878 5386 539071785 539071277 2.390000e-118 436.0
15 TraesCS7A01G244000 chr5A 82.731 249 34 6 175 420 4622867 4622625 4.390000e-51 213.0
16 TraesCS7A01G244000 chr1B 81.925 509 91 1 4879 5386 573579829 573580337 4.000000e-116 429.0
17 TraesCS7A01G244000 chr1B 82.374 278 37 10 451 720 596375665 596375392 1.210000e-56 231.0
18 TraesCS7A01G244000 chr1B 89.595 173 18 0 5391 5563 561253540 561253712 2.620000e-53 220.0
19 TraesCS7A01G244000 chr4D 82.468 462 76 2 4928 5387 399731099 399730641 3.140000e-107 399.0
20 TraesCS7A01G244000 chr3D 79.497 517 104 2 4874 5388 501308995 501309511 3.180000e-97 366.0
21 TraesCS7A01G244000 chr3D 89.947 189 18 1 5380 5567 390686810 390686998 5.590000e-60 243.0
22 TraesCS7A01G244000 chr4B 78.503 521 105 5 4873 5388 666328329 666328847 8.970000e-88 335.0
23 TraesCS7A01G244000 chr2B 81.694 366 66 1 4872 5237 3297482 3297118 2.530000e-78 303.0
24 TraesCS7A01G244000 chr1A 84.091 308 33 12 4 307 539176306 539176601 3.300000e-72 283.0
25 TraesCS7A01G244000 chr1A 83.544 158 14 7 724 877 539177021 539177170 2.720000e-28 137.0
26 TraesCS7A01G244000 chr1A 83.969 131 12 3 724 854 539181573 539181694 3.540000e-22 117.0
27 TraesCS7A01G244000 chr1A 85.393 89 13 0 290 378 426072538 426072626 5.960000e-15 93.5
28 TraesCS7A01G244000 chr5D 92.655 177 13 0 5390 5566 45339632 45339456 7.190000e-64 255.0
29 TraesCS7A01G244000 chr5D 92.571 175 13 0 5392 5566 218069895 218069721 9.290000e-63 252.0
30 TraesCS7A01G244000 chr5D 87.662 154 13 5 175 327 3925447 3925595 2.070000e-39 174.0
31 TraesCS7A01G244000 chr2A 92.571 175 13 0 5392 5566 623095800 623095974 9.290000e-63 252.0
32 TraesCS7A01G244000 chr2A 92.000 175 14 0 5392 5566 253384430 253384604 4.320000e-61 246.0
33 TraesCS7A01G244000 chr3B 89.000 200 22 0 5390 5589 624346328 624346527 1.200000e-61 248.0
34 TraesCS7A01G244000 chr5B 91.124 169 15 0 5398 5566 192651398 192651230 4.360000e-56 230.0
35 TraesCS7A01G244000 chr4A 83.133 249 33 6 175 420 18692850 18692608 9.430000e-53 219.0


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 TraesCS7A01G244000 chr7A 220124459 220130047 5588 True 10322 10322 100.0000 1 5589 1 chr7A.!!$R1 5588
1 TraesCS7A01G244000 chr7D 207560784 207565206 4422 True 6257 6257 92.2850 1172 5589 1 chr7D.!!$R1 4417
2 TraesCS7A01G244000 chr7D 207783310 207791385 8075 True 3838 6316 91.3135 47 5589 2 chr7D.!!$R5 5542
3 TraesCS7A01G244000 chr7D 207605696 207608371 2675 True 1863 3616 86.8890 48 2714 2 chr7D.!!$R4 2666
4 TraesCS7A01G244000 chr7D 207580280 207581473 1193 True 1559 1559 90.2560 3 1205 1 chr7D.!!$R2 1202
5 TraesCS7A01G244000 chr7D 207736627 207737645 1018 True 1314 1314 89.9810 47 1067 1 chr7D.!!$R3 1020
6 TraesCS7A01G244000 chr7B 193522921 193528298 5377 False 3605 6028 90.3295 3 5388 2 chr7B.!!$F2 5385
7 TraesCS7A01G244000 chr3A 640842096 640842610 514 False 475 475 83.3330 4874 5388 1 chr3A.!!$F2 514
8 TraesCS7A01G244000 chr5A 539071277 539071785 508 True 436 436 82.1570 4878 5386 1 chr5A.!!$R2 508
9 TraesCS7A01G244000 chr1B 573579829 573580337 508 False 429 429 81.9250 4879 5386 1 chr1B.!!$F2 507
10 TraesCS7A01G244000 chr3D 501308995 501309511 516 False 366 366 79.4970 4874 5388 1 chr3D.!!$F2 514
11 TraesCS7A01G244000 chr4B 666328329 666328847 518 False 335 335 78.5030 4873 5388 1 chr4B.!!$F1 515
12 TraesCS7A01G244000 chr1A 539176306 539177170 864 False 210 283 83.8175 4 877 2 chr1A.!!$F3 873

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
812 946 0.885196 AGACTTGACTCGGTCTCAGC 59.115 55.0 5.77 0.0 38.25 4.26 F
1222 3891 0.391130 CCACCTCGAGGCGAAAATCA 60.391 55.0 31.56 0.0 39.32 2.57 F
2083 4753 0.036388 GTCCCTGCTGATTTCGGTCA 60.036 55.0 0.00 0.0 0.00 4.02 F
2646 5362 0.178891 AGTGGATCTCCCTGGTGTGT 60.179 55.0 0.00 0.0 35.38 3.72 F
2915 5650 0.682209 GACTGGCCCTGATGCACAAT 60.682 55.0 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 4565 0.800683 GAATGATCACGTCCGTCGCA 60.801 55.0 0.00 0.0 44.19 5.10 R
2828 5563 0.252479 CTCCAGATGCTGCTTCCAGT 59.748 55.0 11.44 0.0 41.26 4.00 R
3763 6501 0.421904 AACCTGTATCCCCCAGACCT 59.578 55.0 0.00 0.0 31.38 3.85 R
4446 7188 1.107114 GAGATGCTCCGAGGTCTTCA 58.893 55.0 0.00 0.0 0.00 3.02 R
4817 7559 0.458669 GGCCATTTGACTCATGCCAG 59.541 55.0 0.00 0.0 0.00 4.85 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
119 124 9.725019 TGTATGTTGTTATTTCAGTCTGATCTT 57.275 29.630 2.68 0.00 0.00 2.40
172 177 6.696583 TGAAATTGTTTGTGTCACATTAGCTG 59.303 34.615 6.48 0.00 0.00 4.24
271 276 9.874205 AATTGTTTATGTCACCCATTTGAATAG 57.126 29.630 0.00 0.00 34.86 1.73
272 277 6.862209 TGTTTATGTCACCCATTTGAATAGC 58.138 36.000 0.00 0.00 34.86 2.97
345 350 7.696992 ATGAAACCGGTATTTCTTACATGTT 57.303 32.000 8.00 0.00 39.02 2.71
508 517 7.900782 TTTTGCTATTTCTGTAGTACACTCC 57.099 36.000 0.00 0.00 0.00 3.85
780 914 4.399112 CTTTTAAATGCACGCATGTACGA 58.601 39.130 5.06 0.00 36.68 3.43
800 934 4.038042 ACGAGTGTGAAATGAGAGACTTGA 59.962 41.667 0.00 0.00 0.00 3.02
812 946 0.885196 AGACTTGACTCGGTCTCAGC 59.115 55.000 5.77 0.00 38.25 4.26
849 986 2.112198 GGCATGGCCGAAATCACGA 61.112 57.895 8.35 0.00 39.62 4.35
870 1007 1.558756 TGGGCCCCAGCAATTTAAATG 59.441 47.619 22.27 0.00 42.56 2.32
875 1012 3.869526 GCCCCAGCAATTTAAATGCAGTT 60.870 43.478 18.49 4.23 46.22 3.16
892 1029 5.603596 TGCAGTTGCTTCAATGAAGAAAAT 58.396 33.333 25.54 18.13 38.72 1.82
968 1115 2.663196 GGTCAACCACCGCTAGCT 59.337 61.111 13.93 0.00 34.56 3.32
969 1116 1.741770 GGTCAACCACCGCTAGCTG 60.742 63.158 13.93 9.13 34.56 4.24
970 1117 2.047274 TCAACCACCGCTAGCTGC 60.047 61.111 13.93 0.00 38.57 5.25
971 1118 2.046892 CAACCACCGCTAGCTGCT 60.047 61.111 13.93 7.57 40.11 4.24
972 1119 2.046892 AACCACCGCTAGCTGCTG 60.047 61.111 13.43 7.35 40.11 4.41
1009 1156 0.617935 TTTGCGAGTCATGGATCCCA 59.382 50.000 9.90 0.00 38.19 4.37
1044 1191 3.504134 TCTCTCAAGAGTCAAACTCCTCG 59.496 47.826 6.91 0.00 46.18 4.63
1088 3756 0.737367 CAGAGCATCGACGGCAAGAA 60.737 55.000 12.80 0.00 42.67 2.52
1164 3833 2.283676 GACGTGGGACCCAGGAGA 60.284 66.667 34.54 1.26 41.36 3.71
1222 3891 0.391130 CCACCTCGAGGCGAAAATCA 60.391 55.000 31.56 0.00 39.32 2.57
1223 3892 1.438651 CACCTCGAGGCGAAAATCAA 58.561 50.000 31.56 0.00 39.32 2.57
1230 3899 1.464997 GAGGCGAAAATCAACGAGCTT 59.535 47.619 0.00 0.00 0.00 3.74
1368 4037 5.639506 CGAGTTGTTCAAGAGGTTCATACAT 59.360 40.000 0.00 0.00 0.00 2.29
1413 4082 2.817834 GCGCGGCATCTTGGTGTA 60.818 61.111 8.83 0.00 0.00 2.90
1426 4095 1.064003 TGGTGTACCCAACTGCTCAT 58.936 50.000 0.00 0.00 41.50 2.90
1503 4172 0.671796 TCGTCAAGAAGTTCCTCGCA 59.328 50.000 0.00 0.00 0.00 5.10
1504 4173 1.067974 TCGTCAAGAAGTTCCTCGCAA 59.932 47.619 0.00 0.00 0.00 4.85
1874 4543 0.994995 CAAGAGTGGTTGATCGAGCG 59.005 55.000 7.63 0.00 0.00 5.03
1896 4565 5.681179 GCGGTTAATACCAATTGCCAAAGAT 60.681 40.000 0.00 0.00 45.31 2.40
1974 4644 6.551385 AAGCTCTTTGTGTTCAGAGTATTG 57.449 37.500 0.00 0.00 0.00 1.90
1984 4654 4.275689 TGTTCAGAGTATTGTTTGCACTGG 59.724 41.667 0.00 0.00 31.31 4.00
2083 4753 0.036388 GTCCCTGCTGATTTCGGTCA 60.036 55.000 0.00 0.00 0.00 4.02
2133 4845 2.383527 GCCGTCGAAGGAGCAACAG 61.384 63.158 22.33 0.00 0.00 3.16
2550 5266 2.364972 TCAGATATGTCTCCGAGGCA 57.635 50.000 4.89 4.89 32.55 4.75
2646 5362 0.178891 AGTGGATCTCCCTGGTGTGT 60.179 55.000 0.00 0.00 35.38 3.72
2702 5418 4.662961 CTGTCCGCGTGACCAGCA 62.663 66.667 20.21 5.67 43.78 4.41
2825 5560 9.425893 GTGACTAATGTATTCAATCGTTCATTG 57.574 33.333 0.00 0.00 43.15 2.82
2828 5563 5.733226 ATGTATTCAATCGTTCATTGCGA 57.267 34.783 0.00 0.00 41.72 5.10
2872 5607 1.694150 TCCACTGCAGCTGAAGTACTT 59.306 47.619 27.30 8.13 30.45 2.24
2915 5650 0.682209 GACTGGCCCTGATGCACAAT 60.682 55.000 0.00 0.00 0.00 2.71
2984 5719 1.383803 GAGGCCTCTCACCCTGGAT 60.384 63.158 26.25 0.00 39.74 3.41
2988 5723 1.267574 GCCTCTCACCCTGGATGACA 61.268 60.000 0.00 0.00 0.00 3.58
3185 5920 1.107114 ACAGAGGCCAGTACATCGAG 58.893 55.000 5.01 0.00 0.00 4.04
3189 5924 0.972983 AGGCCAGTACATCGAGCTGT 60.973 55.000 5.01 0.00 0.00 4.40
3309 6044 3.144657 TCTTCCTGAGCTTGCATTTGA 57.855 42.857 0.00 0.00 0.00 2.69
3473 6210 9.522804 AATCTTAGTTTATTCGTTGCTCTAGAG 57.477 33.333 15.85 15.85 0.00 2.43
3489 6226 6.127423 TGCTCTAGAGTTTACTACCATGTTCC 60.127 42.308 20.75 0.00 0.00 3.62
3620 6357 9.294030 GACATTAGTCACATGAAAATGAAATCC 57.706 33.333 18.28 5.33 44.34 3.01
3652 6389 1.981256 TTCTGTTGGGAAGGAAGCAC 58.019 50.000 0.00 0.00 0.00 4.40
3733 6471 1.903404 GGGGGTGCAGGTTTGTCAG 60.903 63.158 0.00 0.00 0.00 3.51
3752 6490 1.600916 GGAAGCAGCAACCTCGGTT 60.601 57.895 0.00 0.00 39.13 4.44
3763 6501 5.642063 CAGCAACCTCGGTTTCTATCTTAAA 59.358 40.000 0.74 0.00 36.00 1.52
3892 6632 1.527380 GACCGAGGGTTGTGGCAAA 60.527 57.895 0.00 0.00 35.25 3.68
3893 6633 1.076632 ACCGAGGGTTGTGGCAAAA 60.077 52.632 0.00 0.00 27.29 2.44
3912 6652 3.322466 CGGCAGTGGGAGGAGGTT 61.322 66.667 0.00 0.00 0.00 3.50
3921 6661 2.371259 GGAGGAGGTTGAGGGGAGC 61.371 68.421 0.00 0.00 0.00 4.70
3950 6690 1.478288 GCTAAGCAATCCCTGGAGCAT 60.478 52.381 0.00 0.00 0.00 3.79
3981 6721 1.722636 GCATGCAGTTAGGCCTGAGC 61.723 60.000 17.99 14.27 34.23 4.26
3995 6735 4.615815 GAGCTGGATCGGCGGCAT 62.616 66.667 10.53 1.21 41.21 4.40
4020 6760 4.978099 AGAGGAAGAAGAGAAACATTGCA 58.022 39.130 0.00 0.00 0.00 4.08
4024 6764 6.479884 AGGAAGAAGAGAAACATTGCATACT 58.520 36.000 0.00 0.00 0.00 2.12
4026 6766 6.372659 GGAAGAAGAGAAACATTGCATACTGA 59.627 38.462 0.00 0.00 0.00 3.41
4052 6792 6.464222 TCGAGGTTGAAGATGAAGTATTGTT 58.536 36.000 0.00 0.00 0.00 2.83
4121 6862 2.037641 GACCCTTGCAAATTTTCAGGCT 59.962 45.455 0.00 0.00 0.00 4.58
4135 6876 3.055580 GGCTGCTAGCGCCTATCT 58.944 61.111 30.68 0.00 43.62 1.98
4142 6883 1.882989 CTAGCGCCTATCTGCTCCCC 61.883 65.000 2.29 0.00 42.48 4.81
4197 6938 7.662258 TCTGTTCGAATACACTTCCCAATAAAA 59.338 33.333 0.00 0.00 0.00 1.52
4260 7002 7.449704 AGGCAAGATTTCACTCACTCTTAAATT 59.550 33.333 0.00 0.00 0.00 1.82
4322 7064 2.107950 TTTTATCTCACAGGCCGTGG 57.892 50.000 21.98 14.91 46.36 4.94
4446 7188 8.874156 TGGTCTAGTCATATCTAAAGCATCATT 58.126 33.333 0.00 0.00 0.00 2.57
4484 7226 1.599047 CCTTCATCGTCCACCTGCT 59.401 57.895 0.00 0.00 0.00 4.24
4499 7241 2.158871 ACCTGCTTTTACCGACTGAACA 60.159 45.455 0.00 0.00 0.00 3.18
4520 7262 3.116096 TGCCAGTGTATACCTCCTTCT 57.884 47.619 0.00 0.00 0.00 2.85
4585 7327 2.157738 AGCAACAGCTTTGGTGAGATC 58.842 47.619 10.99 0.00 34.18 2.75
4587 7329 3.008375 AGCAACAGCTTTGGTGAGATCTA 59.992 43.478 10.99 0.00 34.18 1.98
4595 7337 5.127845 AGCTTTGGTGAGATCTAATCTTCGA 59.872 40.000 0.00 0.00 40.38 3.71
4611 7353 2.354109 TCGATGCTGATCTTATCCGC 57.646 50.000 0.00 0.00 39.57 5.54
4644 7386 7.706179 ACTCAAAAGGTGTTCACATGTATTTTG 59.294 33.333 0.00 7.91 37.60 2.44
4751 7493 9.042008 TCGTTATATCTCATTTAGGAAAAGTGC 57.958 33.333 0.00 0.00 0.00 4.40
4791 7533 6.801539 TCTACTTTTGTGAGCATTCGAAAT 57.198 33.333 0.00 0.00 0.00 2.17
4809 7551 0.108615 ATGACAGTTTCCGGCTCTCG 60.109 55.000 0.00 0.00 38.88 4.04
4823 7565 3.461773 CTCGGGTCCGTCTGGCAT 61.462 66.667 9.36 0.00 40.74 4.40
4825 7567 3.770040 CGGGTCCGTCTGGCATGA 61.770 66.667 0.00 0.00 34.14 3.07
4922 7664 1.280457 GAGAGAAAGCCTTCCTCCCA 58.720 55.000 0.00 0.00 31.28 4.37
4988 7734 1.977009 ACTCTGTCGGTCGATGGCA 60.977 57.895 0.00 0.00 0.00 4.92
5121 7869 7.962964 TCAATACTTCTCAAGTTCGTTCATT 57.037 32.000 0.00 0.00 42.81 2.57
5159 7907 1.405526 GCTCCGGTGTAGATTCTTGCA 60.406 52.381 0.00 0.00 0.00 4.08
5262 8012 5.666969 TTCAAGAATTCAACGACGACAAT 57.333 34.783 8.44 0.00 0.00 2.71
5271 8021 2.094659 CGACGACAATTGCGGCTCT 61.095 57.895 20.55 5.15 33.81 4.09
5312 8062 1.038280 ACGTGAACGAAGACTTCCCT 58.962 50.000 10.26 0.00 43.02 4.20
5333 8083 2.745821 TGCTGTCATCAACAAGATCAGC 59.254 45.455 10.22 10.22 46.73 4.26
5351 8101 2.070039 CCCGGCTCTGGTATGGGAA 61.070 63.158 0.00 0.00 42.77 3.97
5431 8181 4.752661 TTTTCGGTTTGATTAGGTTCGG 57.247 40.909 0.00 0.00 0.00 4.30
5436 8186 5.303971 TCGGTTTGATTAGGTTCGGTTTAA 58.696 37.500 0.00 0.00 0.00 1.52
5446 8196 5.826601 AGGTTCGGTTTAAACGGTTTTTA 57.173 34.783 21.13 3.60 0.00 1.52
5447 8197 6.389830 AGGTTCGGTTTAAACGGTTTTTAT 57.610 33.333 21.13 5.83 0.00 1.40
5448 8198 7.503521 AGGTTCGGTTTAAACGGTTTTTATA 57.496 32.000 21.13 2.36 0.00 0.98
5449 8199 7.359595 AGGTTCGGTTTAAACGGTTTTTATAC 58.640 34.615 21.13 5.25 0.00 1.47
5450 8200 7.228507 AGGTTCGGTTTAAACGGTTTTTATACT 59.771 33.333 21.13 9.70 0.00 2.12
5451 8201 7.860373 GGTTCGGTTTAAACGGTTTTTATACTT 59.140 33.333 21.13 0.00 0.00 2.24
5452 8202 8.891928 GTTCGGTTTAAACGGTTTTTATACTTC 58.108 33.333 21.13 0.00 0.00 3.01
5453 8203 7.287229 TCGGTTTAAACGGTTTTTATACTTCG 58.713 34.615 21.13 10.44 0.00 3.79
5454 8204 7.169982 TCGGTTTAAACGGTTTTTATACTTCGA 59.830 33.333 21.13 12.23 0.00 3.71
5491 8241 7.030075 TGTACATAGATACGGTTCGATTTCA 57.970 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.498054 ACTGATTATACAAAAGAGTGACATGG 57.502 34.615 0.00 0.00 0.00 3.66
327 332 9.849166 ACAAATTAAACATGTAAGAAATACCGG 57.151 29.630 0.00 0.00 33.27 5.28
485 494 7.241042 AGGAGTGTACTACAGAAATAGCAAA 57.759 36.000 0.00 0.00 0.00 3.68
487 496 6.852420 AAGGAGTGTACTACAGAAATAGCA 57.148 37.500 0.00 0.00 0.00 3.49
488 497 8.549338 AAAAAGGAGTGTACTACAGAAATAGC 57.451 34.615 0.00 0.00 0.00 2.97
714 727 3.512724 ACTGATTTGAAATCCTGCCCAAG 59.487 43.478 14.73 6.55 0.00 3.61
717 730 4.541973 AAACTGATTTGAAATCCTGCCC 57.458 40.909 14.73 0.00 0.00 5.36
770 901 2.666022 TCATTTCACACTCGTACATGCG 59.334 45.455 0.00 0.00 0.00 4.73
780 914 5.537188 GAGTCAAGTCTCTCATTTCACACT 58.463 41.667 0.00 0.00 0.00 3.55
812 946 1.593006 CCACTCGCTTTAAGCATACGG 59.407 52.381 17.51 7.79 42.58 4.02
839 973 2.186826 GGGGCCCATCGTGATTTCG 61.187 63.158 26.86 0.00 0.00 3.46
847 981 0.754957 TAAATTGCTGGGGCCCATCG 60.755 55.000 28.95 17.33 37.74 3.84
849 986 1.963985 TTTAAATTGCTGGGGCCCAT 58.036 45.000 28.95 13.14 37.74 4.00
870 1007 6.865205 ACTATTTTCTTCATTGAAGCAACTGC 59.135 34.615 19.53 0.00 39.29 4.40
918 1055 1.756538 CCTGCCAACTCAAAACCTGTT 59.243 47.619 0.00 0.00 0.00 3.16
966 1113 2.216898 CTTTATACCAGAGCCAGCAGC 58.783 52.381 0.00 0.00 44.25 5.25
967 1114 2.216898 GCTTTATACCAGAGCCAGCAG 58.783 52.381 0.00 0.00 0.00 4.24
968 1115 1.559219 TGCTTTATACCAGAGCCAGCA 59.441 47.619 0.00 0.00 35.59 4.41
969 1116 1.943340 GTGCTTTATACCAGAGCCAGC 59.057 52.381 0.00 0.00 35.59 4.85
970 1117 3.550437 AGTGCTTTATACCAGAGCCAG 57.450 47.619 0.00 0.00 35.59 4.85
971 1118 4.009675 CAAAGTGCTTTATACCAGAGCCA 58.990 43.478 0.00 0.00 35.59 4.75
972 1119 3.181496 GCAAAGTGCTTTATACCAGAGCC 60.181 47.826 0.00 0.00 40.96 4.70
982 1129 2.483877 CCATGACTCGCAAAGTGCTTTA 59.516 45.455 0.00 0.00 42.25 1.85
1009 1156 3.628032 TCTTGAGAGATAGCGACGACATT 59.372 43.478 0.00 0.00 0.00 2.71
1222 3891 2.657237 CGGGAGGTCAAGCTCGTT 59.343 61.111 3.35 0.00 0.00 3.85
1223 3892 4.070552 GCGGGAGGTCAAGCTCGT 62.071 66.667 3.35 0.00 0.00 4.18
1244 3913 0.663269 GGTTAAGTGCAAAGTGGCGC 60.663 55.000 0.00 0.00 44.42 6.53
1317 3986 2.913777 CGTTAGAGACGTCCATGTCA 57.086 50.000 13.01 0.00 46.49 3.58
1368 4037 3.201353 TCAATTTGGACTTCACCGTCA 57.799 42.857 0.00 0.00 35.63 4.35
1413 4082 1.003355 CCACGATGAGCAGTTGGGT 60.003 57.895 0.00 0.00 0.00 4.51
1503 4172 1.852067 CGTTGGTAGCTTTGGCGCTT 61.852 55.000 7.64 0.00 44.37 4.68
1504 4173 2.325082 CGTTGGTAGCTTTGGCGCT 61.325 57.895 7.64 0.00 44.37 5.92
1515 4184 1.272490 CCTGCTTGTCTCTCGTTGGTA 59.728 52.381 0.00 0.00 0.00 3.25
1874 4543 5.523552 GCATCTTTGGCAATTGGTATTAACC 59.476 40.000 7.72 0.00 46.98 2.85
1896 4565 0.800683 GAATGATCACGTCCGTCGCA 60.801 55.000 0.00 0.00 44.19 5.10
1984 4654 3.488090 GCGCCGGAAGTAGCACAC 61.488 66.667 5.05 0.00 0.00 3.82
2083 4753 2.424601 CCAACCTCGTCATGAATGCATT 59.575 45.455 12.83 12.83 30.68 3.56
2133 4845 4.724602 TGAGTCGCGTCCTGCTGC 62.725 66.667 5.77 0.00 43.27 5.25
2456 5172 3.137533 TCATCGTCAAACAGCATGAACA 58.862 40.909 0.00 0.00 39.69 3.18
2571 5287 2.027625 GAACTCCACGAACAGGCGG 61.028 63.158 0.00 0.00 35.12 6.13
2605 5321 2.876368 CTTGCTACCCCCTCGCCAAG 62.876 65.000 0.00 0.00 0.00 3.61
2789 5524 8.554835 TGAATACATTAGTCACGAAAAATGGA 57.445 30.769 0.00 0.00 34.38 3.41
2825 5560 1.449246 AGATGCTGCTTCCAGTCGC 60.449 57.895 11.44 0.00 41.26 5.19
2828 5563 0.252479 CTCCAGATGCTGCTTCCAGT 59.748 55.000 11.44 0.00 41.26 4.00
2872 5607 1.087202 CATCCGTCCCGCAAAATCGA 61.087 55.000 0.00 0.00 0.00 3.59
3185 5920 4.067896 TGAAGAGACTTTGGATCAACAGC 58.932 43.478 0.00 0.00 0.00 4.40
3189 5924 4.012374 GCCATGAAGAGACTTTGGATCAA 58.988 43.478 0.00 0.00 0.00 2.57
3309 6044 4.521146 CCCAGCATACTGTCAAGATCTTT 58.479 43.478 4.86 0.00 42.81 2.52
3345 6080 1.202486 CCATTCCTGCACATCAATGGC 60.202 52.381 7.80 0.00 39.07 4.40
3394 6130 4.225717 TGATCTGATCATCTTGTTGGGTGA 59.774 41.667 16.06 0.00 33.59 4.02
3473 6210 4.069304 TGCACTGGAACATGGTAGTAAAC 58.931 43.478 0.00 0.00 38.20 2.01
3598 6335 6.127758 CCCGGATTTCATTTTCATGTGACTAA 60.128 38.462 0.73 0.00 0.00 2.24
3606 6343 5.450412 CGAATGACCCGGATTTCATTTTCAT 60.450 40.000 20.35 5.02 41.52 2.57
3619 6356 2.024176 ACAGAAATCGAATGACCCGG 57.976 50.000 0.00 0.00 0.00 5.73
3620 6357 2.095853 CCAACAGAAATCGAATGACCCG 59.904 50.000 0.00 0.00 0.00 5.28
3677 6414 3.112263 ACAAGATGAAACCTATCCCCGA 58.888 45.455 0.00 0.00 0.00 5.14
3684 6421 9.101325 CCCCTAATATAGACAAGATGAAACCTA 57.899 37.037 0.00 0.00 0.00 3.08
3733 6471 2.747855 CCGAGGTTGCTGCTTCCC 60.748 66.667 0.00 0.00 0.00 3.97
3752 6490 4.967871 TCCCCCAGACCTTTAAGATAGAA 58.032 43.478 0.00 0.00 0.00 2.10
3763 6501 0.421904 AACCTGTATCCCCCAGACCT 59.578 55.000 0.00 0.00 31.38 3.85
3847 6587 2.103094 TCTAATCCTGCGAACCATCTGG 59.897 50.000 0.00 0.00 42.17 3.86
3851 6591 1.417890 CCCTCTAATCCTGCGAACCAT 59.582 52.381 0.00 0.00 0.00 3.55
3892 6632 3.322466 CTCCTCCCACTGCCGGTT 61.322 66.667 1.90 0.00 0.00 4.44
3932 6672 1.202687 CGATGCTCCAGGGATTGCTTA 60.203 52.381 1.88 0.00 0.00 3.09
3950 6690 4.166888 GCATGCCTCCTCCAGCGA 62.167 66.667 6.36 0.00 0.00 4.93
3981 6721 2.203056 TCAATGCCGCCGATCCAG 60.203 61.111 0.00 0.00 0.00 3.86
3994 6734 6.150809 GCAATGTTTCTCTTCTTCCTCTCAAT 59.849 38.462 0.00 0.00 0.00 2.57
3995 6735 5.471456 GCAATGTTTCTCTTCTTCCTCTCAA 59.529 40.000 0.00 0.00 0.00 3.02
4020 6760 6.471233 TCATCTTCAACCTCGAATCAGTAT 57.529 37.500 0.00 0.00 0.00 2.12
4024 6764 5.152623 ACTTCATCTTCAACCTCGAATCA 57.847 39.130 0.00 0.00 0.00 2.57
4026 6766 7.106239 ACAATACTTCATCTTCAACCTCGAAT 58.894 34.615 0.00 0.00 0.00 3.34
4052 6792 5.913137 ACTGTTGGTCAAAGATTCAACAA 57.087 34.783 14.75 0.00 45.54 2.83
4065 6805 5.104485 ACCCCTATTATCTCAACTGTTGGTC 60.104 44.000 19.55 0.00 0.00 4.02
4133 6874 6.229733 CACATTTTAAAATTTGGGGAGCAGA 58.770 36.000 16.12 0.00 0.00 4.26
4135 6876 4.759183 GCACATTTTAAAATTTGGGGAGCA 59.241 37.500 22.30 0.00 0.00 4.26
4172 6913 6.978343 TTATTGGGAAGTGTATTCGAACAG 57.022 37.500 0.00 0.00 0.00 3.16
4322 7064 1.329906 CTCTTCAACCATCATGCTCGC 59.670 52.381 0.00 0.00 0.00 5.03
4402 7144 1.342674 CCACTACCTAGGTGTAGCCCA 60.343 57.143 25.33 0.91 41.57 5.36
4409 7151 4.232188 TGACTAGACCACTACCTAGGTG 57.768 50.000 25.33 16.10 38.50 4.00
4446 7188 1.107114 GAGATGCTCCGAGGTCTTCA 58.893 55.000 0.00 0.00 0.00 3.02
4484 7226 2.811431 CTGGCATGTTCAGTCGGTAAAA 59.189 45.455 9.19 0.00 0.00 1.52
4499 7241 3.643792 GAGAAGGAGGTATACACTGGCAT 59.356 47.826 5.01 0.00 0.00 4.40
4520 7262 2.264480 CCGGCTCAACGTCATGGA 59.736 61.111 0.00 0.00 0.00 3.41
4585 7327 6.471841 CGGATAAGATCAGCATCGAAGATTAG 59.528 42.308 0.00 0.00 45.12 1.73
4587 7329 5.167121 CGGATAAGATCAGCATCGAAGATT 58.833 41.667 0.00 0.00 45.12 2.40
4611 7353 5.028375 GTGAACACCTTTTGAGTTCTTTCG 58.972 41.667 0.00 0.00 41.56 3.46
4751 7493 2.853235 AGAAGGGGGTAAAACTGACG 57.147 50.000 0.00 0.00 0.00 4.35
4791 7533 1.289066 CGAGAGCCGGAAACTGTCA 59.711 57.895 5.05 0.00 33.91 3.58
4809 7551 2.187946 CTCATGCCAGACGGACCC 59.812 66.667 0.00 0.00 0.00 4.46
4817 7559 0.458669 GGCCATTTGACTCATGCCAG 59.541 55.000 0.00 0.00 0.00 4.85
4823 7565 1.611491 GAAAACCGGCCATTTGACTCA 59.389 47.619 0.00 0.00 0.00 3.41
4825 7567 1.339929 GTGAAAACCGGCCATTTGACT 59.660 47.619 0.00 0.00 0.00 3.41
4902 7644 0.544223 GGGAGGAAGGCTTTCTCTCC 59.456 60.000 29.71 26.78 43.19 3.71
4903 7645 1.280457 TGGGAGGAAGGCTTTCTCTC 58.720 55.000 29.71 27.90 33.48 3.20
4906 7648 1.006400 CCAATGGGAGGAAGGCTTTCT 59.994 52.381 8.05 8.05 35.59 2.52
4941 7684 3.467226 GGGAGGCGAATCCACGGA 61.467 66.667 8.41 0.00 41.52 4.69
4988 7734 2.182312 TGGCACTAGGAATATCCTCCCT 59.818 50.000 1.36 0.00 45.66 4.20
5102 7850 3.815401 CCCAATGAACGAACTTGAGAAGT 59.185 43.478 0.00 0.00 45.46 3.01
5121 7869 0.458669 GCTCCGTCTAATTCGTCCCA 59.541 55.000 0.00 0.00 0.00 4.37
5285 8035 0.736325 CTTCGTTCACGTGCCCCTAG 60.736 60.000 11.67 1.56 40.80 3.02
5312 8062 2.745821 GCTGATCTTGTTGATGACAGCA 59.254 45.455 0.00 0.00 45.12 4.41
5333 8083 2.070039 TTCCCATACCAGAGCCGGG 61.070 63.158 2.18 0.00 38.34 5.73
5388 8138 1.376424 CGAATGCACAGCCTGACCT 60.376 57.895 0.00 0.00 0.00 3.85
5424 8174 4.717233 AAAAACCGTTTAAACCGAACCT 57.283 36.364 12.66 0.00 0.00 3.50
5430 8180 9.611284 AATCGAAGTATAAAAACCGTTTAAACC 57.389 29.630 12.66 0.00 0.00 3.27
5468 8218 7.137426 ACTGAAATCGAACCGTATCTATGTAC 58.863 38.462 0.00 0.00 0.00 2.90
5474 8224 7.650903 GGTTATTACTGAAATCGAACCGTATCT 59.349 37.037 0.00 0.00 30.29 1.98
5491 8241 9.863845 CCAAACCGAAATTAAATGGTTATTACT 57.136 29.630 0.00 0.00 43.64 2.24
5510 8260 4.082274 GGTTATTACCGAAACCAAACCG 57.918 45.455 0.00 0.00 43.84 4.44
5540 8290 0.594796 AAAAGCTCGCGCCAACTTTG 60.595 50.000 14.57 0.00 36.60 2.77
5548 8298 0.591236 TGTTGTTCAAAAGCTCGCGC 60.591 50.000 0.00 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.