Multiple sequence alignment - TraesCS4A01G095800

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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 TraesCS4A01G095800 chr4A 100.000 2843 0 0 1 2843 103766149 103768991 0.000000e+00 5251
1 TraesCS4A01G095800 chr4A 89.212 241 25 1 2148 2388 695669120 695668881 1.660000e-77 300
2 TraesCS4A01G095800 chr4B 93.995 2198 86 24 683 2843 446342705 446344893 0.000000e+00 3286
3 TraesCS4A01G095800 chr4B 92.975 484 30 4 1904 2387 560292808 560292329 0.000000e+00 702
4 TraesCS4A01G095800 chr4B 90.756 238 21 1 2148 2385 648942480 648942716 1.640000e-82 316
5 TraesCS4A01G095800 chr4B 76.993 552 50 27 170 683 446342155 446342667 7.870000e-61 244
6 TraesCS4A01G095800 chr4B 95.050 101 4 1 1808 1908 560294617 560294518 1.050000e-34 158
7 TraesCS4A01G095800 chr4D 92.015 2367 89 49 532 2843 360943565 360941244 0.000000e+00 3232
8 TraesCS4A01G095800 chr4D 76.696 575 81 28 1 552 360944129 360943585 1.300000e-68 270
9 TraesCS4A01G095800 chr3B 91.586 725 45 9 1735 2451 356022087 356022803 0.000000e+00 987
10 TraesCS4A01G095800 chr3B 91.551 722 48 12 1735 2451 661974731 661975444 0.000000e+00 983
11 TraesCS4A01G095800 chr3B 91.453 117 10 0 1142 1258 116690152 116690036 8.150000e-36 161
12 TraesCS4A01G095800 chr6B 92.178 652 43 6 1735 2385 251103294 251103938 0.000000e+00 915
13 TraesCS4A01G095800 chr6B 92.179 537 37 4 1852 2388 306015091 306014560 0.000000e+00 754
14 TraesCS4A01G095800 chr1B 86.567 201 17 7 910 1102 42067455 42067257 2.220000e-51 213
15 TraesCS4A01G095800 chr2D 89.583 96 8 2 1128 1222 102626735 102626641 1.380000e-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 TraesCS4A01G095800 chr4A 103766149 103768991 2842 False 5251 5251 100.0000 1 2843 1 chr4A.!!$F1 2842
1 TraesCS4A01G095800 chr4B 446342155 446344893 2738 False 1765 3286 85.4940 170 2843 2 chr4B.!!$F2 2673
2 TraesCS4A01G095800 chr4B 560292329 560294617 2288 True 430 702 94.0125 1808 2387 2 chr4B.!!$R1 579
3 TraesCS4A01G095800 chr4D 360941244 360944129 2885 True 1751 3232 84.3555 1 2843 2 chr4D.!!$R1 2842
4 TraesCS4A01G095800 chr3B 356022087 356022803 716 False 987 987 91.5860 1735 2451 1 chr3B.!!$F1 716
5 TraesCS4A01G095800 chr3B 661974731 661975444 713 False 983 983 91.5510 1735 2451 1 chr3B.!!$F2 716
6 TraesCS4A01G095800 chr6B 251103294 251103938 644 False 915 915 92.1780 1735 2385 1 chr6B.!!$F1 650
7 TraesCS4A01G095800 chr6B 306014560 306015091 531 True 754 754 92.1790 1852 2388 1 chr6B.!!$R1 536

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
662 757 0.03563 CTGAGGCTTTGACTCCCTGG 60.036 60.0 0.0 0.0 36.76 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 4249 0.034186 CATCCCTGTTTAGCAGCCCA 60.034 55.0 0.0 0.0 43.71 5.36 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 4.512198 TGATCGGACAAAAATAACGTGTGT 59.488 37.500 0.00 0.00 0.00 3.72
56 57 2.959599 GTGTGTGCACGTCAGCGA 60.960 61.111 13.13 0.00 42.00 4.93
57 58 2.202810 TGTGTGCACGTCAGCGAA 60.203 55.556 13.13 0.00 42.00 4.70
70 71 4.202326 CGTCAGCGAAAGAGTAGTATACG 58.798 47.826 0.00 0.00 43.55 3.06
71 72 4.260132 CGTCAGCGAAAGAGTAGTATACGT 60.260 45.833 0.00 0.00 43.55 3.57
72 73 5.051441 CGTCAGCGAAAGAGTAGTATACGTA 60.051 44.000 0.00 0.00 43.55 3.57
73 74 7.040671 CGTCAGCGAAAGAGTAGTATACGTAC 61.041 46.154 0.00 1.40 43.55 3.67
74 75 9.794536 CGTCAGCGAAAGAGTAGTATACGTACC 62.795 48.148 0.00 0.00 43.55 3.34
85 97 5.429957 AGTATACGTACCGTCAAGGAATC 57.570 43.478 0.00 0.00 45.00 2.52
89 101 1.738030 CGTACCGTCAAGGAATCCCAC 60.738 57.143 0.00 0.00 45.00 4.61
117 129 9.846248 AAAAACAAACGATAGAGTAGTATACGT 57.154 29.630 0.00 0.00 43.87 3.57
119 131 9.922305 AAACAAACGATAGAGTAGTATACGTAC 57.078 33.333 0.00 1.40 43.87 3.67
125 137 8.465336 ACGATAGAGTAGTATACGTACCGTGTG 61.465 44.444 0.00 0.00 43.87 3.82
128 140 1.462616 AGTATACGTACCGTGTGGCA 58.537 50.000 0.00 0.00 41.39 4.92
133 145 1.462616 ACGTACCGTGTGGCAGTATA 58.537 50.000 0.00 0.00 39.18 1.47
135 147 2.428171 ACGTACCGTGTGGCAGTATATT 59.572 45.455 0.00 0.00 39.18 1.28
138 150 5.221303 ACGTACCGTGTGGCAGTATATTTAT 60.221 40.000 0.00 0.00 39.18 1.40
141 153 7.381948 CGTACCGTGTGGCAGTATATTTATAAA 59.618 37.037 0.00 0.00 39.70 1.40
142 154 9.044150 GTACCGTGTGGCAGTATATTTATAAAA 57.956 33.333 1.21 0.00 39.70 1.52
144 156 8.617809 ACCGTGTGGCAGTATATTTATAAAAAG 58.382 33.333 1.21 0.00 39.70 2.27
174 186 5.946486 AGAAAAGAACTTGGAGAGGTGAAT 58.054 37.500 0.00 0.00 0.00 2.57
181 195 7.974504 AGAACTTGGAGAGGTGAATAGTAAAA 58.025 34.615 0.00 0.00 0.00 1.52
182 196 8.606830 AGAACTTGGAGAGGTGAATAGTAAAAT 58.393 33.333 0.00 0.00 0.00 1.82
245 259 1.869774 TGAGTGTGTGATGACTGTGC 58.130 50.000 0.00 0.00 0.00 4.57
269 283 5.277250 CCAATTTTTAGCGTGTTTGCACATT 60.277 36.000 0.00 0.00 45.50 2.71
270 284 5.982465 ATTTTTAGCGTGTTTGCACATTT 57.018 30.435 0.00 0.00 45.50 2.32
273 287 2.575694 AGCGTGTTTGCACATTTGAA 57.424 40.000 0.00 0.00 45.50 2.69
287 305 6.207221 TGCACATTTGAATAGCTCTCAGAAAA 59.793 34.615 0.00 0.00 0.00 2.29
288 306 6.746364 GCACATTTGAATAGCTCTCAGAAAAG 59.254 38.462 0.00 0.00 0.00 2.27
289 307 7.361542 GCACATTTGAATAGCTCTCAGAAAAGA 60.362 37.037 0.00 0.00 0.00 2.52
290 308 8.509690 CACATTTGAATAGCTCTCAGAAAAGAA 58.490 33.333 0.00 0.00 0.00 2.52
291 309 9.240734 ACATTTGAATAGCTCTCAGAAAAGAAT 57.759 29.630 0.00 0.00 0.00 2.40
298 316 8.956533 ATAGCTCTCAGAAAAGAATTAAGACC 57.043 34.615 0.00 0.00 0.00 3.85
306 324 9.354673 TCAGAAAAGAATTAAGACCTGTGAAAT 57.645 29.630 0.00 0.00 0.00 2.17
307 325 9.971922 CAGAAAAGAATTAAGACCTGTGAAATT 57.028 29.630 0.00 0.00 0.00 1.82
330 348 6.854496 TTTTTACTAGTTCGTGCACTGATT 57.146 33.333 16.19 8.04 0.00 2.57
331 349 7.949903 TTTTTACTAGTTCGTGCACTGATTA 57.050 32.000 16.19 8.66 0.00 1.75
333 351 4.111375 ACTAGTTCGTGCACTGATTAGG 57.889 45.455 16.19 0.00 0.00 2.69
338 377 2.959516 TCGTGCACTGATTAGGTTGAG 58.040 47.619 16.19 0.00 0.00 3.02
376 415 0.179137 TGCTTAGATGTCCGAGCACG 60.179 55.000 0.00 0.00 39.97 5.34
377 416 0.179134 GCTTAGATGTCCGAGCACGT 60.179 55.000 2.18 0.00 37.88 4.49
380 419 0.172578 TAGATGTCCGAGCACGTTGG 59.827 55.000 2.18 0.00 37.88 3.77
385 424 0.442699 GTCCGAGCACGTTGGAAATC 59.557 55.000 2.18 0.00 40.85 2.17
387 426 1.225745 CGAGCACGTTGGAAATCGC 60.226 57.895 0.00 0.00 34.56 4.58
421 460 2.415893 GCACCCAAACATCTTCCATTCG 60.416 50.000 0.00 0.00 0.00 3.34
423 462 3.505680 CACCCAAACATCTTCCATTCGAA 59.494 43.478 0.00 0.00 0.00 3.71
424 463 4.022416 CACCCAAACATCTTCCATTCGAAA 60.022 41.667 0.00 0.00 0.00 3.46
471 510 8.687301 GTGTTTCCATTATTTTGTTAGTGTTCG 58.313 33.333 0.00 0.00 0.00 3.95
472 511 8.407064 TGTTTCCATTATTTTGTTAGTGTTCGT 58.593 29.630 0.00 0.00 0.00 3.85
473 512 8.898792 GTTTCCATTATTTTGTTAGTGTTCGTC 58.101 33.333 0.00 0.00 0.00 4.20
476 515 6.953743 CCATTATTTTGTTAGTGTTCGTCGAG 59.046 38.462 0.00 0.00 0.00 4.04
477 516 7.148705 CCATTATTTTGTTAGTGTTCGTCGAGA 60.149 37.037 0.00 0.00 0.00 4.04
478 517 7.878477 TTATTTTGTTAGTGTTCGTCGAGAT 57.122 32.000 0.00 0.00 0.00 2.75
479 518 8.969121 TTATTTTGTTAGTGTTCGTCGAGATA 57.031 30.769 0.00 0.00 0.00 1.98
515 555 4.570930 GGAAATGGATATTCGAGGACCTC 58.429 47.826 11.87 11.87 0.00 3.85
631 726 2.919043 GAACCATCCATCCCGCCT 59.081 61.111 0.00 0.00 0.00 5.52
662 757 0.035630 CTGAGGCTTTGACTCCCTGG 60.036 60.000 0.00 0.00 36.76 4.45
665 760 2.361737 GCTTTGACTCCCTGGCCC 60.362 66.667 0.00 0.00 0.00 5.80
798 931 3.175710 ACCCACTCACCCACCACC 61.176 66.667 0.00 0.00 0.00 4.61
967 1127 3.255379 GTCCACGGCTCGATTCGC 61.255 66.667 0.00 0.00 0.00 4.70
982 1142 2.678580 CGCCCGGGGGATTTGTTT 60.679 61.111 33.13 0.00 37.50 2.83
988 1148 2.355986 GGGGGATTTGTTTCGGGGC 61.356 63.158 0.00 0.00 0.00 5.80
989 1149 1.304962 GGGGATTTGTTTCGGGGCT 60.305 57.895 0.00 0.00 0.00 5.19
991 1151 0.973632 GGGATTTGTTTCGGGGCTTT 59.026 50.000 0.00 0.00 0.00 3.51
993 1153 2.412870 GGATTTGTTTCGGGGCTTTTG 58.587 47.619 0.00 0.00 0.00 2.44
995 1155 1.196012 TTTGTTTCGGGGCTTTTGGT 58.804 45.000 0.00 0.00 0.00 3.67
996 1156 0.747852 TTGTTTCGGGGCTTTTGGTC 59.252 50.000 0.00 0.00 0.00 4.02
998 1158 0.826256 GTTTCGGGGCTTTTGGTCCT 60.826 55.000 0.00 0.00 40.18 3.85
1116 1281 2.811317 CTCGAGCAGTTCCCGCAC 60.811 66.667 0.00 0.00 0.00 5.34
1206 1371 4.459089 GGCTCGCTCTCCGGCTTT 62.459 66.667 0.00 0.00 37.59 3.51
1284 1449 3.049080 GCACCTCCTCATGGGGTCC 62.049 68.421 12.53 0.00 35.59 4.46
1374 1539 4.194720 GCGGTCGAGTCGATGCCT 62.195 66.667 24.15 0.00 38.42 4.75
1383 1548 1.810030 GTCGATGCCTTCCGTGACC 60.810 63.158 0.00 0.00 0.00 4.02
1901 2066 7.973048 TGATAGTGGTGAATAAGTAGGAGTT 57.027 36.000 0.00 0.00 0.00 3.01
2076 3956 1.000171 CAAGCCCAAGCCTTCAAGAAC 60.000 52.381 0.00 0.00 41.25 3.01
2096 3976 3.403038 ACGGGATAGCAGTGAATTATGC 58.597 45.455 0.00 2.36 42.87 3.14
2139 4019 7.859875 GCAATATTCTAGGCAAAGAGAACAATC 59.140 37.037 0.00 0.00 34.61 2.67
2142 4022 1.168714 AGGCAAAGAGAACAATCGGC 58.831 50.000 0.00 0.00 0.00 5.54
2317 4198 8.979574 GTTTCAACATAAGATATCCTTAGACCG 58.020 37.037 0.00 0.00 40.40 4.79
2339 4220 3.749609 GGTCATAAGTTGTAACAACGGCT 59.250 43.478 1.07 0.00 0.00 5.52
2353 4234 3.308866 ACAACGGCTATCGATTTACTTGC 59.691 43.478 1.71 0.00 42.43 4.01
2358 4239 4.034048 CGGCTATCGATTTACTTGCAGTTT 59.966 41.667 1.71 0.00 42.43 2.66
2360 4241 4.730521 GCTATCGATTTACTTGCAGTTTGC 59.269 41.667 1.71 0.00 45.29 3.68
2361 4242 3.552604 TCGATTTACTTGCAGTTTGCC 57.447 42.857 0.00 0.00 44.23 4.52
2368 4249 1.956477 ACTTGCAGTTTGCCGAATCTT 59.044 42.857 0.00 0.00 44.23 2.40
2380 4261 1.401905 CCGAATCTTGGGCTGCTAAAC 59.598 52.381 0.00 0.00 0.00 2.01
2390 4271 2.799176 CTGCTAAACAGGGATGGCC 58.201 57.895 0.00 0.00 43.19 5.36
2393 4274 0.255890 GCTAAACAGGGATGGCCTGA 59.744 55.000 3.32 0.00 38.52 3.86
2397 4278 0.038744 AACAGGGATGGCCTGAACAG 59.961 55.000 3.32 0.00 38.52 3.16
2398 4279 1.751927 CAGGGATGGCCTGAACAGC 60.752 63.158 3.32 0.00 37.47 4.40
2464 4354 5.539955 ACCATGCTGGACTCTTAATGTTTTT 59.460 36.000 8.91 0.00 40.96 1.94
2540 4430 5.350365 GCTCAACCGATTCAAGTGTTATGTA 59.650 40.000 0.00 0.00 0.00 2.29
2622 4512 5.239525 GGGCCATATGAGTGAAGTGATTAAC 59.760 44.000 4.39 0.00 0.00 2.01
2641 4531 7.485913 TGATTAACGAAGAAATGTCTACCGTAC 59.514 37.037 12.04 6.83 40.32 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.188194 CGTTATTTTTGTCCGATCATCGAC 58.812 41.667 9.16 5.68 43.74 4.20
44 45 0.312729 TACTCTTTCGCTGACGTGCA 59.687 50.000 0.00 0.00 41.18 4.57
70 71 1.276989 TGTGGGATTCCTTGACGGTAC 59.723 52.381 2.01 0.00 0.00 3.34
71 72 1.646912 TGTGGGATTCCTTGACGGTA 58.353 50.000 2.01 0.00 0.00 4.02
72 73 0.768622 TTGTGGGATTCCTTGACGGT 59.231 50.000 2.01 0.00 0.00 4.83
73 74 1.904287 TTTGTGGGATTCCTTGACGG 58.096 50.000 2.01 0.00 0.00 4.79
116 128 8.592105 TTTATAAATATACTGCCACACGGTAC 57.408 34.615 0.00 0.00 42.95 3.34
117 129 9.610705 TTTTTATAAATATACTGCCACACGGTA 57.389 29.630 0.00 0.00 44.27 4.02
118 130 8.508883 TTTTTATAAATATACTGCCACACGGT 57.491 30.769 0.00 0.00 42.04 4.83
119 131 8.832521 TCTTTTTATAAATATACTGCCACACGG 58.167 33.333 0.00 0.00 0.00 4.94
147 159 6.663523 TCACCTCTCCAAGTTCTTTTCTTTTT 59.336 34.615 0.00 0.00 0.00 1.94
152 164 6.937465 ACTATTCACCTCTCCAAGTTCTTTTC 59.063 38.462 0.00 0.00 0.00 2.29
153 165 6.842676 ACTATTCACCTCTCCAAGTTCTTTT 58.157 36.000 0.00 0.00 0.00 2.27
154 166 6.441088 ACTATTCACCTCTCCAAGTTCTTT 57.559 37.500 0.00 0.00 0.00 2.52
155 167 7.554959 TTACTATTCACCTCTCCAAGTTCTT 57.445 36.000 0.00 0.00 0.00 2.52
156 168 7.554959 TTTACTATTCACCTCTCCAAGTTCT 57.445 36.000 0.00 0.00 0.00 3.01
157 169 8.794335 ATTTTACTATTCACCTCTCCAAGTTC 57.206 34.615 0.00 0.00 0.00 3.01
213 227 7.661027 TCATCACACACTCAAACATTTCTCATA 59.339 33.333 0.00 0.00 0.00 2.15
220 234 4.883585 ACAGTCATCACACACTCAAACATT 59.116 37.500 0.00 0.00 0.00 2.71
245 259 4.114098 GTGCAAACACGCTAAAAATTGG 57.886 40.909 0.00 0.00 36.98 3.16
273 287 8.767436 AGGTCTTAATTCTTTTCTGAGAGCTAT 58.233 33.333 0.00 0.00 38.34 2.97
307 325 6.854496 AATCAGTGCACGAACTAGTAAAAA 57.146 33.333 12.01 0.00 0.00 1.94
308 326 6.588756 CCTAATCAGTGCACGAACTAGTAAAA 59.411 38.462 12.01 0.00 0.00 1.52
320 338 5.438761 AAAACTCAACCTAATCAGTGCAC 57.561 39.130 9.40 9.40 0.00 4.57
351 390 2.100584 CTCGGACATCTAAGCAGCTCTT 59.899 50.000 0.00 4.26 38.79 2.85
358 397 0.179134 ACGTGCTCGGACATCTAAGC 60.179 55.000 13.32 0.00 41.85 3.09
361 400 0.172578 CCAACGTGCTCGGACATCTA 59.827 55.000 13.32 0.00 41.85 1.98
376 415 1.004595 GGTCCGTAGCGATTTCCAAC 58.995 55.000 0.00 0.00 0.00 3.77
377 416 0.899720 AGGTCCGTAGCGATTTCCAA 59.100 50.000 0.00 0.00 0.00 3.53
380 419 1.557651 GTGAGGTCCGTAGCGATTTC 58.442 55.000 0.00 0.00 0.00 2.17
385 424 4.111016 TGCGTGAGGTCCGTAGCG 62.111 66.667 0.00 0.00 0.00 4.26
387 426 2.181021 GGTGCGTGAGGTCCGTAG 59.819 66.667 0.00 0.00 0.00 3.51
452 491 7.726079 TCTCGACGAACACTAACAAAATAATG 58.274 34.615 0.00 0.00 0.00 1.90
461 500 5.808403 ACTCATATCTCGACGAACACTAAC 58.192 41.667 0.00 0.00 0.00 2.34
462 501 6.432607 AACTCATATCTCGACGAACACTAA 57.567 37.500 0.00 0.00 0.00 2.24
463 502 6.255950 CAAACTCATATCTCGACGAACACTA 58.744 40.000 0.00 0.00 0.00 2.74
464 503 4.966965 AACTCATATCTCGACGAACACT 57.033 40.909 0.00 0.00 0.00 3.55
466 505 4.421058 CCAAACTCATATCTCGACGAACA 58.579 43.478 0.00 0.00 0.00 3.18
467 506 3.797256 CCCAAACTCATATCTCGACGAAC 59.203 47.826 0.00 0.00 0.00 3.95
468 507 3.446161 ACCCAAACTCATATCTCGACGAA 59.554 43.478 0.00 0.00 0.00 3.85
469 508 3.021695 ACCCAAACTCATATCTCGACGA 58.978 45.455 0.00 0.00 0.00 4.20
471 510 3.718815 GGACCCAAACTCATATCTCGAC 58.281 50.000 0.00 0.00 0.00 4.20
472 511 2.361119 CGGACCCAAACTCATATCTCGA 59.639 50.000 0.00 0.00 0.00 4.04
473 512 2.545952 CCGGACCCAAACTCATATCTCG 60.546 54.545 0.00 0.00 0.00 4.04
476 515 3.553828 TTCCGGACCCAAACTCATATC 57.446 47.619 1.83 0.00 0.00 1.63
477 516 4.207165 CATTTCCGGACCCAAACTCATAT 58.793 43.478 1.83 0.00 0.00 1.78
478 517 3.616219 CATTTCCGGACCCAAACTCATA 58.384 45.455 1.83 0.00 0.00 2.15
479 518 2.446435 CATTTCCGGACCCAAACTCAT 58.554 47.619 1.83 0.00 0.00 2.90
515 555 2.383298 TTTCGAAGTGAAAAGCAGCG 57.617 45.000 0.00 0.00 43.46 5.18
582 660 2.356313 CCCGGATCGGCGATTCTG 60.356 66.667 24.81 18.04 46.86 3.02
631 726 1.992277 GCCTCAGCCAAGGGAGAGA 60.992 63.158 4.27 0.00 36.88 3.10
665 760 2.029073 ACGTTGACCGGTCAGCTG 59.971 61.111 37.80 32.43 41.13 4.24
798 931 1.356494 GGAGAGGGGAGGGGAATTGG 61.356 65.000 0.00 0.00 0.00 3.16
951 1111 4.508128 GGCGAATCGAGCCGTGGA 62.508 66.667 6.91 0.00 45.58 4.02
967 1127 2.049767 CCGAAACAAATCCCCCGGG 61.050 63.158 15.80 15.80 33.94 5.73
982 1142 1.497309 ATCAGGACCAAAAGCCCCGA 61.497 55.000 0.00 0.00 0.00 5.14
988 1148 0.804989 GACGCCATCAGGACCAAAAG 59.195 55.000 0.00 0.00 36.89 2.27
989 1149 0.953471 CGACGCCATCAGGACCAAAA 60.953 55.000 0.00 0.00 36.89 2.44
991 1151 2.264480 CGACGCCATCAGGACCAA 59.736 61.111 0.00 0.00 36.89 3.67
993 1153 2.202756 GACGACGCCATCAGGACC 60.203 66.667 0.00 0.00 36.89 4.46
995 1155 3.458163 GGGACGACGCCATCAGGA 61.458 66.667 9.90 0.00 36.89 3.86
996 1156 4.530857 GGGGACGACGCCATCAGG 62.531 72.222 15.65 0.00 46.50 3.86
1206 1371 1.472904 CCGTCCTCGTAGTAGAGCTCA 60.473 57.143 17.77 0.00 36.95 4.26
1901 2066 4.973211 CCTGGGGTTTCCTCCTTATACTAA 59.027 45.833 0.00 0.00 36.20 2.24
1980 3860 8.770828 CCAACTCTAAATTCTTAAAACGAGACA 58.229 33.333 0.00 0.00 0.00 3.41
2076 3956 2.413112 CGCATAATTCACTGCTATCCCG 59.587 50.000 6.15 0.00 36.23 5.14
2096 3976 0.321564 TGCCAGTGACTGATTTCCCG 60.322 55.000 15.33 0.00 32.44 5.14
2139 4019 2.279582 ATACAGAAGTGAGAACGCCG 57.720 50.000 0.00 0.00 0.00 6.46
2142 4022 6.129393 CACAAACAATACAGAAGTGAGAACG 58.871 40.000 0.00 0.00 0.00 3.95
2195 4075 4.529769 TGGGACCAACATAATGCAAAATCA 59.470 37.500 0.00 0.00 0.00 2.57
2262 4142 7.691993 AAGAGGTTTAGGCAGAGGAATAATA 57.308 36.000 0.00 0.00 0.00 0.98
2314 4195 3.742369 CGTTGTTACAACTTATGACCGGT 59.258 43.478 23.27 6.92 0.00 5.28
2315 4196 3.123959 CCGTTGTTACAACTTATGACCGG 59.876 47.826 23.27 14.19 0.00 5.28
2317 4198 3.749609 AGCCGTTGTTACAACTTATGACC 59.250 43.478 23.27 6.20 0.00 4.02
2353 4234 0.109132 GCCCAAGATTCGGCAAACTG 60.109 55.000 0.00 0.00 45.01 3.16
2360 4241 1.401905 GTTTAGCAGCCCAAGATTCGG 59.598 52.381 0.00 0.00 0.00 4.30
2361 4242 2.083774 TGTTTAGCAGCCCAAGATTCG 58.916 47.619 0.00 0.00 0.00 3.34
2368 4249 0.034186 CATCCCTGTTTAGCAGCCCA 60.034 55.000 0.00 0.00 43.71 5.36
2390 4271 5.618056 AACATCACTTGTATGCTGTTCAG 57.382 39.130 0.00 0.00 34.65 3.02
2393 4274 6.579666 ATCAAACATCACTTGTATGCTGTT 57.420 33.333 0.00 0.00 39.87 3.16
2442 4331 9.643693 AAATAAAAACATTAAGAGTCCAGCATG 57.356 29.630 0.00 0.00 0.00 4.06
2464 4354 8.560355 TGTTTCTCTATTTAGCAGTGCAAATA 57.440 30.769 19.20 20.51 0.00 1.40
2540 4430 8.637196 TCTAGATCGGTATCTCAATGTTACAT 57.363 34.615 0.00 0.00 41.71 2.29
2551 4441 8.527810 GGAAGAAATCAATCTAGATCGGTATCT 58.472 37.037 5.51 5.25 44.80 1.98
2622 4512 6.116680 ACTAGTACGGTAGACATTTCTTCG 57.883 41.667 0.00 0.00 35.03 3.79
2783 4677 6.548321 TGGAAAACAATAACATGGTACTCCT 58.452 36.000 0.00 0.00 34.23 3.69
2787 4681 8.138712 TGAACTTGGAAAACAATAACATGGTAC 58.861 33.333 0.00 0.00 38.65 3.34


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

AutoCloner maintained by Alex Coulton.