Multiple sequence alignment - TraesCS6A01G108300

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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 TraesCS6A01G108300 chr6A 100.000 3558 0 0 1 3558 77101127 77097570 0.000000e+00 6571.0
1 TraesCS6A01G108300 chr6A 90.541 74 7 0 11 84 77109592 77109519 8.130000e-17 99.0
2 TraesCS6A01G108300 chr6D 94.287 2818 88 30 107 2877 60488891 60486100 0.000000e+00 4244.0
3 TraesCS6A01G108300 chr6D 89.357 498 46 3 2911 3407 60485703 60485212 1.400000e-173 619.0
4 TraesCS6A01G108300 chr6D 94.406 143 8 0 3416 3558 60485054 60484912 1.660000e-53 220.0
5 TraesCS6A01G108300 chr6D 90.756 119 9 1 9 127 60488958 60488842 1.320000e-34 158.0
6 TraesCS6A01G108300 chr6B 91.465 2566 116 44 579 3093 134665246 134662733 0.000000e+00 3430.0
7 TraesCS6A01G108300 chr6B 86.926 283 18 14 312 578 134665562 134665283 2.080000e-77 300.0
8 TraesCS6A01G108300 chr2A 85.267 2138 129 79 748 2802 175467327 175469361 0.000000e+00 2032.0
9 TraesCS6A01G108300 chr2A 87.261 157 13 4 592 747 175467126 175467276 4.720000e-39 172.0
10 TraesCS6A01G108300 chr2A 79.874 159 32 0 1087 1245 54882364 54882522 2.240000e-22 117.0
11 TraesCS6A01G108300 chr2A 85.217 115 9 2 2846 2953 175469505 175469618 1.040000e-20 111.0
12 TraesCS6A01G108300 chr2A 92.000 50 4 0 3295 3344 175471943 175471992 1.770000e-08 71.3
13 TraesCS6A01G108300 chr2B 85.014 2122 147 76 748 2802 223153836 223155853 0.000000e+00 1999.0
14 TraesCS6A01G108300 chr2B 88.199 161 11 5 588 747 223153632 223153785 6.070000e-43 185.0
15 TraesCS6A01G108300 chr2B 82.051 156 28 0 1095 1250 85074008 85074163 2.230000e-27 134.0
16 TraesCS6A01G108300 chr2B 80.952 168 29 2 1083 1250 85177929 85177765 2.880000e-26 130.0
17 TraesCS6A01G108300 chr2B 86.957 115 7 2 2846 2953 223155995 223156108 4.820000e-24 122.0
18 TraesCS6A01G108300 chr2B 89.362 47 3 2 2760 2804 223155951 223155997 1.380000e-04 58.4
19 TraesCS6A01G108300 chr2D 84.942 2145 120 84 748 2802 175330904 175332935 0.000000e+00 1984.0
20 TraesCS6A01G108300 chr2D 88.608 158 11 4 591 747 175330702 175330853 6.070000e-43 185.0
21 TraesCS6A01G108300 chr2D 79.762 168 31 2 1083 1250 54317505 54317669 6.240000e-23 119.0
22 TraesCS6A01G108300 chr2D 86.207 58 7 1 200 257 643799774 643799718 1.070000e-05 62.1
23 TraesCS6A01G108300 chr3D 83.884 242 30 7 1490 1731 39325676 39325444 4.620000e-54 222.0
24 TraesCS6A01G108300 chr3D 78.544 261 39 7 1464 1723 148224359 148224603 4.760000e-34 156.0
25 TraesCS6A01G108300 chr5A 82.745 255 27 9 1478 1731 317247919 317247681 1.000000e-50 211.0
26 TraesCS6A01G108300 chr5B 82.072 251 28 9 1478 1727 267779036 267778802 7.790000e-47 198.0
27 TraesCS6A01G108300 chr5D 81.526 249 29 9 1478 1725 238066460 238066692 4.690000e-44 189.0
28 TraesCS6A01G108300 chr3B 78.491 265 39 9 1461 1723 214284993 214284745 1.320000e-34 158.0
29 TraesCS6A01G108300 chr3A 86.014 143 19 1 1461 1602 165088449 165088307 6.150000e-33 152.0
30 TraesCS6A01G108300 chr4D 93.617 94 2 2 895 984 484166802 484166709 1.720000e-28 137.0
31 TraesCS6A01G108300 chrUn 90.000 50 5 0 207 256 22442972 22443021 8.240000e-07 65.8


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 TraesCS6A01G108300 chr6A 77097570 77101127 3557 True 6571.000 6571 100.00000 1 3558 1 chr6A.!!$R1 3557
1 TraesCS6A01G108300 chr6D 60484912 60488958 4046 True 1310.250 4244 92.20150 9 3558 4 chr6D.!!$R1 3549
2 TraesCS6A01G108300 chr6B 134662733 134665562 2829 True 1865.000 3430 89.19550 312 3093 2 chr6B.!!$R1 2781
3 TraesCS6A01G108300 chr2A 175467126 175471992 4866 False 596.575 2032 87.43625 592 3344 4 chr2A.!!$F2 2752
4 TraesCS6A01G108300 chr2B 223153632 223156108 2476 False 591.100 1999 87.38300 588 2953 4 chr2B.!!$F2 2365
5 TraesCS6A01G108300 chr2D 175330702 175332935 2233 False 1084.500 1984 86.77500 591 2802 2 chr2D.!!$F2 2211

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
987 1153 0.179043 GCTAGCTTGCTAGGGGGAAC 60.179 60.000 25.23 8.73 0.00 3.62 F
1287 1464 1.268032 CGGCCGTGCTTGATTTATCAC 60.268 52.381 19.50 0.00 36.36 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 2773 0.108520 TTCCAGTTCACGCCGGATAC 60.109 55.0 5.05 0.0 0.00 2.24 R
3245 5978 0.743345 GGCGTCCGTGGAAAGCTTAT 60.743 55.0 0.00 0.0 32.92 1.73 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
29 30 7.123098 TGCCACAGATGAAGAAACATTTATGAT 59.877 33.333 0.00 0.00 0.00 2.45
69 70 4.670227 CTAACTAGCAGCAGGTTGTTTC 57.330 45.455 12.58 0.00 40.59 2.78
71 72 0.798776 CTAGCAGCAGGTTGTTTCCG 59.201 55.000 0.00 0.00 0.00 4.30
104 105 1.609501 AGCTAGTGGTTCCCGCAGA 60.610 57.895 0.00 0.00 36.32 4.26
134 135 5.723672 ACTAGCAACTAGTTGTTCTAGCA 57.276 39.130 30.49 16.17 43.82 3.49
135 136 5.715070 ACTAGCAACTAGTTGTTCTAGCAG 58.285 41.667 30.49 23.28 43.82 4.24
136 137 5.336849 ACTAGCAACTAGTTGTTCTAGCAGG 60.337 44.000 30.49 18.80 43.82 4.85
137 138 7.476440 ACTAGCAACTAGTTGTTCTAGCAGGA 61.476 42.308 30.49 14.60 43.82 3.86
138 139 8.880078 ACTAGCAACTAGTTGTTCTAGCAGGAA 61.880 40.741 30.49 14.08 43.82 3.36
161 162 2.464157 AACTAGCAGCCAGTTGACTC 57.536 50.000 5.32 0.00 34.96 3.36
162 163 0.244994 ACTAGCAGCCAGTTGACTCG 59.755 55.000 0.00 0.00 0.00 4.18
178 179 1.550976 ACTCGGGAACTTTCTAGCAGG 59.449 52.381 0.00 0.00 0.00 4.85
183 184 2.351455 GGAACTTTCTAGCAGGCAGAC 58.649 52.381 0.00 0.00 0.00 3.51
257 258 4.103153 AGAACTTGAACTCTGATGGGTTGA 59.897 41.667 0.00 0.00 0.00 3.18
267 268 4.104086 TCTGATGGGTTGAAGATACCTGT 58.896 43.478 0.00 0.00 35.92 4.00
268 269 4.536090 TCTGATGGGTTGAAGATACCTGTT 59.464 41.667 0.00 0.00 35.92 3.16
275 276 6.011981 TGGGTTGAAGATACCTGTTTTCCTAT 60.012 38.462 0.00 0.00 35.92 2.57
276 277 7.183112 TGGGTTGAAGATACCTGTTTTCCTATA 59.817 37.037 0.00 0.00 35.92 1.31
277 278 7.715686 GGGTTGAAGATACCTGTTTTCCTATAG 59.284 40.741 0.00 0.00 35.92 1.31
278 279 7.226918 GGTTGAAGATACCTGTTTTCCTATAGC 59.773 40.741 0.00 0.00 32.75 2.97
279 280 7.676683 TGAAGATACCTGTTTTCCTATAGCT 57.323 36.000 0.00 0.00 0.00 3.32
290 291 9.347934 CTGTTTTCCTATAGCTATCTAATCACG 57.652 37.037 10.16 0.00 0.00 4.35
332 333 2.227194 GACGAACTGGTTGGTTCCATT 58.773 47.619 2.95 0.00 41.58 3.16
394 411 4.503910 CCTTGATTAGTTGATGGTCACGA 58.496 43.478 0.00 0.00 0.00 4.35
619 682 1.910580 GAGGAAGCGGAATGGGTGGA 61.911 60.000 0.00 0.00 0.00 4.02
620 683 1.452108 GGAAGCGGAATGGGTGGAG 60.452 63.158 0.00 0.00 0.00 3.86
826 959 4.593864 GATCACTCGCCCGCCTCC 62.594 72.222 0.00 0.00 0.00 4.30
852 990 4.796231 CTCCTCCCAACCGTCGCG 62.796 72.222 0.00 0.00 0.00 5.87
880 1018 0.473117 TCCCACTCCGTTCCTTCCTT 60.473 55.000 0.00 0.00 0.00 3.36
882 1020 0.685097 CCACTCCGTTCCTTCCTTCA 59.315 55.000 0.00 0.00 0.00 3.02
975 1141 3.564225 GTGTGTTTGTTGGTAGCTAGCTT 59.436 43.478 24.88 7.25 0.00 3.74
984 1150 0.682292 GTAGCTAGCTTGCTAGGGGG 59.318 60.000 26.87 6.94 44.93 5.40
985 1151 0.561184 TAGCTAGCTTGCTAGGGGGA 59.439 55.000 24.88 4.94 43.74 4.81
986 1152 0.326618 AGCTAGCTTGCTAGGGGGAA 60.327 55.000 21.42 0.00 42.10 3.97
987 1153 0.179043 GCTAGCTTGCTAGGGGGAAC 60.179 60.000 25.23 8.73 0.00 3.62
1029 1196 2.107953 GGCAGCTCCGACTCATCC 59.892 66.667 0.00 0.00 0.00 3.51
1278 1455 2.607668 TATCTCGTCGGCCGTGCTTG 62.608 60.000 27.15 12.83 37.94 4.01
1279 1456 4.717629 CTCGTCGGCCGTGCTTGA 62.718 66.667 27.15 15.14 37.94 3.02
1287 1464 1.268032 CGGCCGTGCTTGATTTATCAC 60.268 52.381 19.50 0.00 36.36 3.06
1350 1531 7.984859 TCCATCCATCTCATGCTTATACTAT 57.015 36.000 0.00 0.00 0.00 2.12
1351 1532 8.384693 TCCATCCATCTCATGCTTATACTATT 57.615 34.615 0.00 0.00 0.00 1.73
1352 1533 8.262933 TCCATCCATCTCATGCTTATACTATTG 58.737 37.037 0.00 0.00 0.00 1.90
1455 1640 4.726351 GCGCTCGGGATCGGGATC 62.726 72.222 0.00 0.00 39.73 3.36
2422 2661 4.380531 TGTCCGCATTTATGAATCCTCTC 58.619 43.478 0.00 0.00 0.00 3.20
2531 2773 0.322456 TTTCCAGCATCCCGTCCAAG 60.322 55.000 0.00 0.00 0.00 3.61
2635 2912 2.222027 AGCCAGTAGTTGTTGCAGTTC 58.778 47.619 0.00 0.00 0.00 3.01
2722 3004 2.510691 GCTGCATTGCACCATGGC 60.511 61.111 13.04 5.63 33.79 4.40
2734 3016 0.321298 ACCATGGCCACGTACTTGTC 60.321 55.000 8.16 0.00 0.00 3.18
2758 3040 4.859798 CGAACTTGCTAGCCATATAGTAGC 59.140 45.833 13.29 0.00 39.76 3.58
2958 3719 1.952102 TTTGGCCGGGTCTAGCTACG 61.952 60.000 2.18 0.00 0.00 3.51
2976 4010 6.936279 AGCTACGCATCATGTATAAATAGGT 58.064 36.000 0.00 0.00 0.00 3.08
3011 4045 3.077229 GCAACGCATGGTAATTGCATA 57.923 42.857 3.06 0.00 45.38 3.14
3016 4050 2.601979 CGCATGGTAATTGCATACACGG 60.602 50.000 0.00 0.00 40.14 4.94
3038 4072 5.491982 GGGTATGATTCATCTACATGGACC 58.508 45.833 1.55 2.67 0.00 4.46
3105 4140 8.319146 ACTACTATGTTGCAGTGGTTTAGTTAT 58.681 33.333 0.00 0.00 34.44 1.89
3106 4141 7.996098 ACTATGTTGCAGTGGTTTAGTTATT 57.004 32.000 0.00 0.00 0.00 1.40
3144 4234 5.699839 CCCTTATGCGCCAATCTTTTATAC 58.300 41.667 4.18 0.00 0.00 1.47
3236 5969 8.405531 CAAAGGAAAACTTCATCTTGACAGTTA 58.594 33.333 0.00 0.00 38.85 2.24
3245 5978 8.314021 ACTTCATCTTGACAGTTATCACATGTA 58.686 33.333 0.00 0.00 0.00 2.29
3246 5979 9.322773 CTTCATCTTGACAGTTATCACATGTAT 57.677 33.333 0.00 0.00 0.00 2.29
3252 5985 9.102757 CTTGACAGTTATCACATGTATAAGCTT 57.897 33.333 3.48 3.48 0.00 3.74
3261 5994 4.034048 CACATGTATAAGCTTTCCACGGAC 59.966 45.833 3.20 0.00 0.00 4.79
3298 6063 3.060940 CGCGCTCATGTAAGTTCTATGTG 60.061 47.826 5.56 0.00 0.00 3.21
3345 6110 4.576463 GGGAAAGATATGTGCACGAAAGAT 59.424 41.667 13.13 1.83 0.00 2.40
3346 6111 5.504665 GGGAAAGATATGTGCACGAAAGATG 60.505 44.000 13.13 0.00 0.00 2.90
3372 6137 6.926630 AGTACATCTCTATTCCATCCTTCC 57.073 41.667 0.00 0.00 0.00 3.46
3374 6139 7.021873 AGTACATCTCTATTCCATCCTTCCAT 58.978 38.462 0.00 0.00 0.00 3.41
3375 6140 6.776887 ACATCTCTATTCCATCCTTCCATT 57.223 37.500 0.00 0.00 0.00 3.16
3398 6163 0.877071 AGCTTTCAAGATGTGTGCCG 59.123 50.000 0.00 0.00 0.00 5.69
3402 6167 1.960417 TTCAAGATGTGTGCCGTGAA 58.040 45.000 0.00 0.00 0.00 3.18
3407 6172 5.610398 TCAAGATGTGTGCCGTGAATATAT 58.390 37.500 0.00 0.00 0.00 0.86
3408 6173 5.696270 TCAAGATGTGTGCCGTGAATATATC 59.304 40.000 0.00 0.00 0.00 1.63
3409 6174 4.569943 AGATGTGTGCCGTGAATATATCC 58.430 43.478 0.00 0.00 0.00 2.59
3410 6175 3.120321 TGTGTGCCGTGAATATATCCC 57.880 47.619 0.00 0.00 0.00 3.85
3411 6176 2.436173 TGTGTGCCGTGAATATATCCCA 59.564 45.455 0.00 0.00 0.00 4.37
3412 6177 3.118223 TGTGTGCCGTGAATATATCCCAA 60.118 43.478 0.00 0.00 0.00 4.12
3414 6179 3.118223 TGTGCCGTGAATATATCCCAACA 60.118 43.478 0.00 0.00 0.00 3.33
3419 6333 4.755123 CCGTGAATATATCCCAACACCTTC 59.245 45.833 0.00 0.00 0.00 3.46
3432 6346 1.337823 ACACCTTCGGTCATGTAGCAC 60.338 52.381 0.00 0.00 31.02 4.40
3438 6352 1.136891 TCGGTCATGTAGCACCATCTG 59.863 52.381 2.56 0.00 32.33 2.90
3471 6385 0.684805 AAGGGACTACTGCCTCGAGG 60.685 60.000 27.83 27.83 37.20 4.63
3534 6448 5.467738 ACATATTCTCTCATGAGGTACCCA 58.532 41.667 22.42 6.92 40.58 4.51
3551 6465 2.644798 ACCCATTTCTCACTAGCCAACT 59.355 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.197721 GTTTCTTCATCTGTGGCACGG 59.802 52.381 20.50 20.50 0.00 4.94
1 2 1.872952 TGTTTCTTCATCTGTGGCACG 59.127 47.619 13.77 8.10 0.00 5.34
2 3 4.510038 AATGTTTCTTCATCTGTGGCAC 57.490 40.909 11.55 11.55 0.00 5.01
3 4 6.433716 TCATAAATGTTTCTTCATCTGTGGCA 59.566 34.615 0.00 0.00 0.00 4.92
4 5 6.855836 TCATAAATGTTTCTTCATCTGTGGC 58.144 36.000 0.00 0.00 0.00 5.01
29 30 3.034721 AGCCAACACGAAGAACGAATA 57.965 42.857 0.00 0.00 45.77 1.75
139 140 3.555966 AGTCAACTGGCTGCTAGTTTTT 58.444 40.909 25.97 13.14 36.29 1.94
140 141 3.142174 GAGTCAACTGGCTGCTAGTTTT 58.858 45.455 25.97 15.65 36.29 2.43
141 142 2.772287 GAGTCAACTGGCTGCTAGTTT 58.228 47.619 25.97 14.02 36.29 2.66
142 143 1.337260 CGAGTCAACTGGCTGCTAGTT 60.337 52.381 23.41 23.41 38.84 2.24
143 144 0.244994 CGAGTCAACTGGCTGCTAGT 59.755 55.000 13.27 13.27 0.00 2.57
144 145 0.459237 CCGAGTCAACTGGCTGCTAG 60.459 60.000 11.77 11.77 0.00 3.42
161 162 0.036388 TGCCTGCTAGAAAGTTCCCG 60.036 55.000 0.00 0.00 0.00 5.14
162 163 1.279271 TCTGCCTGCTAGAAAGTTCCC 59.721 52.381 0.00 0.00 0.00 3.97
178 179 7.137426 GGATTATCATGATTCTGTTTGTCTGC 58.863 38.462 14.65 0.00 0.00 4.26
235 236 4.389374 TCAACCCATCAGAGTTCAAGTTC 58.611 43.478 0.00 0.00 0.00 3.01
236 237 4.437682 TCAACCCATCAGAGTTCAAGTT 57.562 40.909 0.00 0.00 0.00 2.66
249 250 5.016831 GGAAAACAGGTATCTTCAACCCAT 58.983 41.667 0.00 0.00 37.77 4.00
267 268 7.453752 ACCCGTGATTAGATAGCTATAGGAAAA 59.546 37.037 6.13 0.00 0.00 2.29
268 269 6.952358 ACCCGTGATTAGATAGCTATAGGAAA 59.048 38.462 6.13 0.00 0.00 3.13
332 333 3.260884 GGTGACCTCATTTCAGACACCTA 59.739 47.826 0.00 0.00 41.73 3.08
484 501 2.633967 TCGTAGCTTCCTGGGTGTTTTA 59.366 45.455 0.00 0.00 0.00 1.52
826 959 0.689412 GTTGGGAGGAGAGGAGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
852 990 2.484742 ACGGAGTGGGATTTGTTACC 57.515 50.000 0.00 0.00 42.51 2.85
880 1018 5.337571 CCAAAGCTTCTAGGTAGTGTGATGA 60.338 44.000 0.00 0.00 0.00 2.92
882 1020 4.624125 GCCAAAGCTTCTAGGTAGTGTGAT 60.624 45.833 0.00 0.00 35.50 3.06
938 1104 0.462581 CACACCAGATGATCCCACCG 60.463 60.000 0.00 0.00 0.00 4.94
975 1141 0.902531 CTTCTTCGTTCCCCCTAGCA 59.097 55.000 0.00 0.00 0.00 3.49
984 1150 3.181485 ACCTCATCGGATCTTCTTCGTTC 60.181 47.826 0.00 0.00 36.31 3.95
985 1151 2.761208 ACCTCATCGGATCTTCTTCGTT 59.239 45.455 0.00 0.00 36.31 3.85
986 1152 2.359531 GACCTCATCGGATCTTCTTCGT 59.640 50.000 0.00 0.00 36.31 3.85
987 1153 2.287909 GGACCTCATCGGATCTTCTTCG 60.288 54.545 0.00 0.00 36.31 3.79
1252 1425 2.904011 GGCCGACGAGATAGACATAG 57.096 55.000 0.00 0.00 0.00 2.23
1278 1455 0.247894 TTTGCGGCGCGTGATAAATC 60.248 50.000 28.09 0.00 0.00 2.17
1279 1456 0.380378 ATTTGCGGCGCGTGATAAAT 59.620 45.000 28.09 22.20 0.00 1.40
1350 1531 9.352784 GAATATAAAAATACTTGTGCACAGCAA 57.647 29.630 20.59 9.50 41.47 3.91
1351 1532 8.739039 AGAATATAAAAATACTTGTGCACAGCA 58.261 29.630 20.59 9.51 35.60 4.41
1352 1533 9.573133 AAGAATATAAAAATACTTGTGCACAGC 57.427 29.630 20.59 0.00 0.00 4.40
1400 1585 5.608437 ACAGGATCACATACATAACCCAGAT 59.392 40.000 0.00 0.00 0.00 2.90
1401 1586 4.968719 ACAGGATCACATACATAACCCAGA 59.031 41.667 0.00 0.00 0.00 3.86
1402 1587 5.296151 ACAGGATCACATACATAACCCAG 57.704 43.478 0.00 0.00 0.00 4.45
1403 1588 4.202212 CGACAGGATCACATACATAACCCA 60.202 45.833 0.00 0.00 0.00 4.51
1404 1589 4.202223 ACGACAGGATCACATACATAACCC 60.202 45.833 0.00 0.00 0.00 4.11
1405 1590 4.745125 CACGACAGGATCACATACATAACC 59.255 45.833 0.00 0.00 0.00 2.85
1406 1591 4.209288 GCACGACAGGATCACATACATAAC 59.791 45.833 0.00 0.00 0.00 1.89
1453 1638 1.347050 CGCCTTCTCTGATGGATGGAT 59.653 52.381 4.02 0.00 31.99 3.41
1454 1639 0.755079 CGCCTTCTCTGATGGATGGA 59.245 55.000 4.02 0.00 31.99 3.41
1455 1640 0.755079 TCGCCTTCTCTGATGGATGG 59.245 55.000 4.02 0.00 0.00 3.51
1456 1641 1.539929 GGTCGCCTTCTCTGATGGATG 60.540 57.143 4.02 0.00 0.00 3.51
1563 1748 2.584608 CCGGTGGCCTTCCAGTAG 59.415 66.667 3.32 0.00 44.48 2.57
2128 2355 1.968540 GTCTGCTGTGAACAGGCCC 60.969 63.158 12.20 0.00 43.94 5.80
2404 2643 3.077359 GGGGAGAGGATTCATAAATGCG 58.923 50.000 0.00 0.00 38.19 4.73
2531 2773 0.108520 TTCCAGTTCACGCCGGATAC 60.109 55.000 5.05 0.00 0.00 2.24
2635 2912 1.060713 CACTGAAAGCGACTACCACG 58.939 55.000 0.00 0.00 37.60 4.94
2722 3004 1.790623 CAAGTTCGGACAAGTACGTGG 59.209 52.381 13.47 0.00 38.28 4.94
2734 3016 4.258702 ACTATATGGCTAGCAAGTTCGG 57.741 45.455 18.24 3.30 0.00 4.30
2758 3040 7.203910 ACTTCGAAAATACTCCTAGCTATGTG 58.796 38.462 0.00 0.00 0.00 3.21
2901 3306 6.580788 TGGGGTTTGTAATCAATTGCATATG 58.419 36.000 0.00 0.00 32.55 1.78
2909 3314 5.255397 TCTGACTGGGGTTTGTAATCAAT 57.745 39.130 0.00 0.00 33.32 2.57
2958 3719 9.219603 ACATACACACCTATTTATACATGATGC 57.780 33.333 0.00 0.00 0.00 3.91
2976 4010 5.864628 TGCGTTGCTTATTTACATACACA 57.135 34.783 0.00 0.00 0.00 3.72
3011 4045 5.511373 CCATGTAGATGAATCATACCCGTGT 60.511 44.000 0.46 0.00 0.00 4.49
3016 4050 6.365970 AGGTCCATGTAGATGAATCATACC 57.634 41.667 0.46 0.00 0.00 2.73
3025 4059 9.424319 GTTATACAATGTAGGTCCATGTAGATG 57.576 37.037 0.00 0.00 0.00 2.90
3061 4095 5.748592 AGTAGTTCACAAAACTTCATTCGC 58.251 37.500 0.00 0.00 0.00 4.70
3062 4096 8.495949 ACATAGTAGTTCACAAAACTTCATTCG 58.504 33.333 0.00 0.00 0.00 3.34
3067 4102 7.414436 TGCAACATAGTAGTTCACAAAACTTC 58.586 34.615 0.00 0.00 0.00 3.01
3071 4106 6.238621 CCACTGCAACATAGTAGTTCACAAAA 60.239 38.462 0.00 0.00 31.85 2.44
3105 4140 5.534654 GCATAAGGGCCACTCACATAATTAA 59.465 40.000 6.18 0.00 0.00 1.40
3106 4141 5.070001 GCATAAGGGCCACTCACATAATTA 58.930 41.667 6.18 0.00 0.00 1.40
3107 4142 3.891366 GCATAAGGGCCACTCACATAATT 59.109 43.478 6.18 0.00 0.00 1.40
3236 5969 4.816385 CCGTGGAAAGCTTATACATGTGAT 59.184 41.667 9.11 0.96 0.00 3.06
3245 5978 0.743345 GGCGTCCGTGGAAAGCTTAT 60.743 55.000 0.00 0.00 32.92 1.73
3246 5979 1.375013 GGCGTCCGTGGAAAGCTTA 60.375 57.895 0.00 0.00 32.92 3.09
3252 5985 3.588817 TAGGGAGGCGTCCGTGGAA 62.589 63.158 26.45 7.82 45.05 3.53
3261 5994 2.280186 GCGGTGATTAGGGAGGCG 60.280 66.667 0.00 0.00 0.00 5.52
3345 6110 8.783660 AAGGATGGAATAGAGATGTACTTACA 57.216 34.615 0.00 0.00 40.98 2.41
3346 6111 8.308207 GGAAGGATGGAATAGAGATGTACTTAC 58.692 40.741 0.00 0.00 0.00 2.34
3355 6120 7.211897 TGAAAATGGAAGGATGGAATAGAGA 57.788 36.000 0.00 0.00 0.00 3.10
3363 6128 4.221262 TGAAAGCTGAAAATGGAAGGATGG 59.779 41.667 0.00 0.00 0.00 3.51
3372 6137 5.107607 GCACACATCTTGAAAGCTGAAAATG 60.108 40.000 1.14 0.00 0.00 2.32
3374 6139 4.362279 GCACACATCTTGAAAGCTGAAAA 58.638 39.130 1.14 0.00 0.00 2.29
3375 6140 3.243501 GGCACACATCTTGAAAGCTGAAA 60.244 43.478 1.14 0.00 0.00 2.69
3398 6163 5.924475 CGAAGGTGTTGGGATATATTCAC 57.076 43.478 0.00 0.00 0.00 3.18
3419 6333 1.134699 ACAGATGGTGCTACATGACCG 60.135 52.381 0.00 0.00 34.69 4.79
3432 6346 6.326583 TCCCTTAGTCCATAGTAAACAGATGG 59.673 42.308 7.43 7.43 41.36 3.51
3438 6352 7.683945 GCAGTAGTCCCTTAGTCCATAGTAAAC 60.684 44.444 0.00 0.00 0.00 2.01
3471 6385 5.651139 GGAAAAGGGGGAAGTAATAGTGAAC 59.349 44.000 0.00 0.00 0.00 3.18
3508 6422 5.046950 GGTACCTCATGAGAGAATATGTCCC 60.047 48.000 24.62 7.96 44.98 4.46
3509 6423 6.031751 GGTACCTCATGAGAGAATATGTCC 57.968 45.833 24.62 10.38 44.98 4.02


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

AutoCloner maintained by Alex Coulton.