Multiple sequence alignment - TraesCS3A01G276500

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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 TraesCS3A01G276500 chr3A 100.000 4062 0 0 1 4062 506444865 506440804 0.000000e+00 7502.0
1 TraesCS3A01G276500 chr3B 91.025 2663 126 46 359 2955 499176497 499173882 0.000000e+00 3489.0
2 TraesCS3A01G276500 chr3B 92.165 1136 43 19 2952 4047 499173785 499172656 0.000000e+00 1563.0
3 TraesCS3A01G276500 chr3B 93.365 211 10 1 2 212 499177084 499176878 3.940000e-80 309.0
4 TraesCS3A01G276500 chr3D 97.188 1956 41 6 2119 4062 383546790 383544837 0.000000e+00 3295.0
5 TraesCS3A01G276500 chr3D 92.048 1660 82 23 352 1999 383548528 383546907 0.000000e+00 2289.0
6 TraesCS3A01G276500 chr3D 92.833 293 14 3 1 291 383548809 383548522 6.280000e-113 418.0
7 TraesCS3A01G276500 chr1D 91.358 81 5 1 1741 1821 355319154 355319076 4.290000e-20 110.0
8 TraesCS3A01G276500 chr1A 89.610 77 6 2 1741 1817 395177530 395177604 3.340000e-16 97.1
9 TraesCS3A01G276500 chr7D 89.610 77 5 2 1741 1816 454079149 454079075 1.200000e-15 95.3
10 TraesCS3A01G276500 chr4B 89.474 76 6 1 1742 1817 106227479 106227406 1.200000e-15 95.3
11 TraesCS3A01G276500 chr4B 89.189 74 6 1 1741 1814 366930229 366930300 1.550000e-14 91.6
12 TraesCS3A01G276500 chr5B 86.747 83 7 3 1741 1823 250597074 250596996 5.590000e-14 89.8
13 TraesCS3A01G276500 chr2D 87.500 80 7 2 1741 1819 58651783 58651860 5.590000e-14 89.8


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 TraesCS3A01G276500 chr3A 506440804 506444865 4061 True 7502.000000 7502 100.000 1 4062 1 chr3A.!!$R1 4061
1 TraesCS3A01G276500 chr3B 499172656 499177084 4428 True 1787.000000 3489 92.185 2 4047 3 chr3B.!!$R1 4045
2 TraesCS3A01G276500 chr3D 383544837 383548809 3972 True 2000.666667 3295 94.023 1 4062 3 chr3D.!!$R1 4061

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
798 1075 0.032217 CCCTTGCTCTCTCTCCCTCT 60.032 60.000 0.00 0.0 0.00 3.69 F
813 1090 0.108615 CCTCTCTTTCATCCGCGTGT 60.109 55.000 4.92 0.0 0.00 4.49 F
816 1093 0.366871 CTCTTTCATCCGCGTGTTCG 59.633 55.000 4.92 0.0 40.37 3.95 F
1486 1785 1.002134 ATGTGGGAAGGAACTGGCG 60.002 57.895 0.00 0.0 40.86 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2552 0.399091 AGCTGCAGCCCCTCTGTATA 60.399 55.000 34.39 0.00 44.66 1.47 R
2583 2928 0.599060 TGCACTGCAACATGGTCATG 59.401 50.000 0.00 9.19 38.02 3.07 R
2624 2969 1.005037 TGCTCCTTGCTGTGTACGG 60.005 57.895 0.00 0.00 43.37 4.02 R
3118 3566 1.210722 CCCCTGCTTCTTAGGAGTTCC 59.789 57.143 0.00 0.00 38.10 3.62 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
85 86 2.487428 CACTCACGCTCTCCTCCG 59.513 66.667 0.00 0.00 0.00 4.63
86 87 2.752238 ACTCACGCTCTCCTCCGG 60.752 66.667 0.00 0.00 0.00 5.14
87 88 3.522731 CTCACGCTCTCCTCCGGG 61.523 72.222 0.00 0.00 0.00 5.73
189 192 3.393800 GGCAAAAGAAAGAAGAAAGCCC 58.606 45.455 0.00 0.00 33.68 5.19
281 284 0.960364 GCCAAGGTGCCATTTCTCGA 60.960 55.000 0.00 0.00 0.00 4.04
282 285 0.804989 CCAAGGTGCCATTTCTCGAC 59.195 55.000 0.00 0.00 0.00 4.20
283 286 0.804989 CAAGGTGCCATTTCTCGACC 59.195 55.000 0.00 0.00 0.00 4.79
284 287 0.322546 AAGGTGCCATTTCTCGACCC 60.323 55.000 0.00 0.00 0.00 4.46
285 288 1.749258 GGTGCCATTTCTCGACCCC 60.749 63.158 0.00 0.00 0.00 4.95
286 289 1.749258 GTGCCATTTCTCGACCCCC 60.749 63.158 0.00 0.00 0.00 5.40
301 304 2.841595 CCCCCTCTCCACATACCTC 58.158 63.158 0.00 0.00 0.00 3.85
302 305 0.266152 CCCCCTCTCCACATACCTCT 59.734 60.000 0.00 0.00 0.00 3.69
303 306 1.710816 CCCCTCTCCACATACCTCTC 58.289 60.000 0.00 0.00 0.00 3.20
304 307 1.710816 CCCTCTCCACATACCTCTCC 58.289 60.000 0.00 0.00 0.00 3.71
305 308 1.219213 CCCTCTCCACATACCTCTCCT 59.781 57.143 0.00 0.00 0.00 3.69
306 309 2.447429 CCCTCTCCACATACCTCTCCTA 59.553 54.545 0.00 0.00 0.00 2.94
307 310 3.499563 CCCTCTCCACATACCTCTCCTAG 60.500 56.522 0.00 0.00 0.00 3.02
308 311 3.153919 CTCTCCACATACCTCTCCTAGC 58.846 54.545 0.00 0.00 0.00 3.42
309 312 2.786445 TCTCCACATACCTCTCCTAGCT 59.214 50.000 0.00 0.00 0.00 3.32
310 313 3.981375 TCTCCACATACCTCTCCTAGCTA 59.019 47.826 0.00 0.00 0.00 3.32
311 314 4.042311 TCTCCACATACCTCTCCTAGCTAG 59.958 50.000 14.20 14.20 0.00 3.42
312 315 2.823154 CCACATACCTCTCCTAGCTAGC 59.177 54.545 15.74 6.62 0.00 3.42
313 316 3.499563 CCACATACCTCTCCTAGCTAGCT 60.500 52.174 23.12 23.12 0.00 3.32
314 317 4.263550 CCACATACCTCTCCTAGCTAGCTA 60.264 50.000 22.85 22.85 0.00 3.32
315 318 4.698304 CACATACCTCTCCTAGCTAGCTAC 59.302 50.000 20.67 0.00 0.00 3.58
316 319 2.963599 ACCTCTCCTAGCTAGCTACC 57.036 55.000 20.67 0.00 0.00 3.18
317 320 1.426215 ACCTCTCCTAGCTAGCTACCC 59.574 57.143 20.67 0.00 0.00 3.69
318 321 1.425831 CCTCTCCTAGCTAGCTACCCA 59.574 57.143 20.67 2.24 0.00 4.51
319 322 2.042433 CCTCTCCTAGCTAGCTACCCAT 59.958 54.545 20.67 0.00 0.00 4.00
320 323 3.352648 CTCTCCTAGCTAGCTACCCATC 58.647 54.545 20.67 0.00 0.00 3.51
321 324 2.041891 TCTCCTAGCTAGCTACCCATCC 59.958 54.545 20.67 0.00 0.00 3.51
322 325 1.178276 CCTAGCTAGCTACCCATCCG 58.822 60.000 20.67 8.95 0.00 4.18
323 326 0.528470 CTAGCTAGCTACCCATCCGC 59.472 60.000 20.67 0.00 0.00 5.54
324 327 0.112606 TAGCTAGCTACCCATCCGCT 59.887 55.000 20.67 6.63 37.77 5.52
325 328 0.760945 AGCTAGCTACCCATCCGCTT 60.761 55.000 17.69 0.00 35.33 4.68
326 329 0.319986 GCTAGCTACCCATCCGCTTC 60.320 60.000 7.70 0.00 35.33 3.86
327 330 0.318762 CTAGCTACCCATCCGCTTCC 59.681 60.000 0.00 0.00 35.33 3.46
328 331 0.397957 TAGCTACCCATCCGCTTCCA 60.398 55.000 0.00 0.00 35.33 3.53
329 332 1.523938 GCTACCCATCCGCTTCCAC 60.524 63.158 0.00 0.00 0.00 4.02
330 333 1.972660 GCTACCCATCCGCTTCCACT 61.973 60.000 0.00 0.00 0.00 4.00
331 334 0.541863 CTACCCATCCGCTTCCACTT 59.458 55.000 0.00 0.00 0.00 3.16
332 335 0.251916 TACCCATCCGCTTCCACTTG 59.748 55.000 0.00 0.00 0.00 3.16
333 336 1.750399 CCCATCCGCTTCCACTTGG 60.750 63.158 0.00 0.00 0.00 3.61
334 337 2.409870 CCATCCGCTTCCACTTGGC 61.410 63.158 0.00 0.00 34.44 4.52
335 338 2.044946 ATCCGCTTCCACTTGGCC 60.045 61.111 0.00 0.00 34.44 5.36
336 339 2.905996 ATCCGCTTCCACTTGGCCA 61.906 57.895 0.00 0.00 34.44 5.36
337 340 2.215451 ATCCGCTTCCACTTGGCCAT 62.215 55.000 6.09 0.00 34.44 4.40
338 341 1.978617 CCGCTTCCACTTGGCCATT 60.979 57.895 6.09 0.00 34.44 3.16
339 342 1.535204 CCGCTTCCACTTGGCCATTT 61.535 55.000 6.09 0.00 34.44 2.32
340 343 0.109132 CGCTTCCACTTGGCCATTTC 60.109 55.000 6.09 0.00 34.44 2.17
341 344 0.247460 GCTTCCACTTGGCCATTTCC 59.753 55.000 6.09 0.00 34.44 3.13
342 345 0.897621 CTTCCACTTGGCCATTTCCC 59.102 55.000 6.09 0.00 34.44 3.97
343 346 0.189574 TTCCACTTGGCCATTTCCCA 59.810 50.000 6.09 0.00 34.44 4.37
344 347 0.413037 TCCACTTGGCCATTTCCCAT 59.587 50.000 6.09 0.00 34.44 4.00
345 348 0.826062 CCACTTGGCCATTTCCCATC 59.174 55.000 6.09 0.00 31.26 3.51
346 349 0.826062 CACTTGGCCATTTCCCATCC 59.174 55.000 6.09 0.00 31.26 3.51
347 350 0.325577 ACTTGGCCATTTCCCATCCC 60.326 55.000 6.09 0.00 31.26 3.85
350 353 1.001503 GGCCATTTCCCATCCCACA 59.998 57.895 0.00 0.00 0.00 4.17
354 357 1.218704 CCATTTCCCATCCCACATCCT 59.781 52.381 0.00 0.00 0.00 3.24
383 620 0.038435 CGGAGCTCATCATCATCGCT 60.038 55.000 17.19 0.00 0.00 4.93
384 621 1.604947 CGGAGCTCATCATCATCGCTT 60.605 52.381 17.19 0.00 0.00 4.68
385 622 1.799403 GGAGCTCATCATCATCGCTTG 59.201 52.381 17.19 0.00 0.00 4.01
386 623 1.799403 GAGCTCATCATCATCGCTTGG 59.201 52.381 9.40 0.00 0.00 3.61
393 636 1.202687 TCATCATCGCTTGGCCTAAGG 60.203 52.381 3.32 1.28 36.87 2.69
407 650 0.723981 CTAAGGCTCGCTTCAACTGC 59.276 55.000 0.00 0.00 0.00 4.40
421 664 0.321475 AACTGCCTGCTCTTCTCAGC 60.321 55.000 0.00 0.00 40.13 4.26
427 670 1.202557 CCTGCTCTTCTCAGCTCATCC 60.203 57.143 0.00 0.00 40.39 3.51
464 714 4.131596 GTGTTAACTGTGGCTTCTGGTTA 58.868 43.478 7.22 0.00 0.00 2.85
465 715 4.760204 GTGTTAACTGTGGCTTCTGGTTAT 59.240 41.667 7.22 0.00 0.00 1.89
466 716 5.240844 GTGTTAACTGTGGCTTCTGGTTATT 59.759 40.000 7.22 0.00 0.00 1.40
472 722 3.572255 TGTGGCTTCTGGTTATTTTGGTC 59.428 43.478 0.00 0.00 0.00 4.02
474 724 5.007682 GTGGCTTCTGGTTATTTTGGTCTA 58.992 41.667 0.00 0.00 0.00 2.59
485 735 7.175990 TGGTTATTTTGGTCTACTTTGCTAAGG 59.824 37.037 12.54 0.00 35.61 2.69
517 781 3.629858 GCCAATTAAAGAGGCTGCG 57.370 52.632 0.00 0.00 44.92 5.18
600 864 3.922910 TGATCTCTGACTTGACTGCTTG 58.077 45.455 0.00 0.00 0.00 4.01
646 910 2.898705 CTCGCTAGCCATTCTTCTGTT 58.101 47.619 9.66 0.00 0.00 3.16
655 927 3.950395 GCCATTCTTCTGTTTCTAGCCAT 59.050 43.478 0.00 0.00 0.00 4.40
659 931 3.866651 TCTTCTGTTTCTAGCCATGAGC 58.133 45.455 0.00 0.00 44.25 4.26
674 946 1.229428 TGAGCTTTTCTGCTTCCGTG 58.771 50.000 0.00 0.00 44.17 4.94
750 1027 5.711036 TCTTCCTCGCTAGAAAGTAGAAACT 59.289 40.000 0.00 0.00 37.65 2.66
775 1052 4.286297 TGATTTGATCTCAAGTTCCCGT 57.714 40.909 0.00 0.00 37.15 5.28
796 1073 1.002792 CCCCTTGCTCTCTCTCCCT 59.997 63.158 0.00 0.00 0.00 4.20
798 1075 0.032217 CCCTTGCTCTCTCTCCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
799 1076 1.402787 CCTTGCTCTCTCTCCCTCTC 58.597 60.000 0.00 0.00 0.00 3.20
800 1077 1.063717 CCTTGCTCTCTCTCCCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
803 1080 2.733956 TGCTCTCTCTCCCTCTCTTTC 58.266 52.381 0.00 0.00 0.00 2.62
804 1081 2.042297 TGCTCTCTCTCCCTCTCTTTCA 59.958 50.000 0.00 0.00 0.00 2.69
805 1082 3.299503 GCTCTCTCTCCCTCTCTTTCAT 58.700 50.000 0.00 0.00 0.00 2.57
806 1083 3.319122 GCTCTCTCTCCCTCTCTTTCATC 59.681 52.174 0.00 0.00 0.00 2.92
807 1084 3.891366 CTCTCTCTCCCTCTCTTTCATCC 59.109 52.174 0.00 0.00 0.00 3.51
808 1085 2.622942 CTCTCTCCCTCTCTTTCATCCG 59.377 54.545 0.00 0.00 0.00 4.18
809 1086 1.068434 CTCTCCCTCTCTTTCATCCGC 59.932 57.143 0.00 0.00 0.00 5.54
810 1087 0.249238 CTCCCTCTCTTTCATCCGCG 60.249 60.000 0.00 0.00 0.00 6.46
811 1088 0.970937 TCCCTCTCTTTCATCCGCGT 60.971 55.000 4.92 0.00 0.00 6.01
812 1089 0.807667 CCCTCTCTTTCATCCGCGTG 60.808 60.000 4.92 0.00 0.00 5.34
813 1090 0.108615 CCTCTCTTTCATCCGCGTGT 60.109 55.000 4.92 0.00 0.00 4.49
814 1091 1.673033 CCTCTCTTTCATCCGCGTGTT 60.673 52.381 4.92 0.00 0.00 3.32
815 1092 1.656095 CTCTCTTTCATCCGCGTGTTC 59.344 52.381 4.92 0.00 0.00 3.18
816 1093 0.366871 CTCTTTCATCCGCGTGTTCG 59.633 55.000 4.92 0.00 40.37 3.95
831 1108 1.667830 TTCGCCGCTTTGACCTCAG 60.668 57.895 0.00 0.00 0.00 3.35
850 1127 1.449601 CATACGCTTCCCGCTGGTT 60.450 57.895 0.00 0.00 41.76 3.67
915 1192 6.154203 TGTCTCCTCTCATATCATTGACAC 57.846 41.667 0.00 0.00 0.00 3.67
1089 1366 2.441901 AGCCTGAGAGGAGGAGCG 60.442 66.667 0.00 0.00 37.67 5.03
1271 1551 1.215647 CTAGACACTCCACGGCCAC 59.784 63.158 2.24 0.00 0.00 5.01
1305 1585 3.330720 ACCGGAGCAAAGAGGGGG 61.331 66.667 9.46 0.00 0.00 5.40
1347 1627 3.430098 CCAAAGCACAAGGTAACAAGCAA 60.430 43.478 0.00 0.00 41.41 3.91
1353 1633 5.126384 AGCACAAGGTAACAAGCAACTTTTA 59.874 36.000 0.00 0.00 41.41 1.52
1486 1785 1.002134 ATGTGGGAAGGAACTGGCG 60.002 57.895 0.00 0.00 40.86 5.69
1487 1786 1.488705 ATGTGGGAAGGAACTGGCGA 61.489 55.000 0.00 0.00 40.86 5.54
1489 1788 1.026718 GTGGGAAGGAACTGGCGATG 61.027 60.000 0.00 0.00 40.86 3.84
1490 1789 1.452108 GGGAAGGAACTGGCGATGG 60.452 63.158 0.00 0.00 40.86 3.51
1491 1790 1.602237 GGAAGGAACTGGCGATGGA 59.398 57.895 0.00 0.00 40.86 3.41
1506 1805 3.181465 GCGATGGAGGAGGAAAATACAGA 60.181 47.826 0.00 0.00 0.00 3.41
1640 1939 1.999634 ATACCCCTGCATGGTGCCTC 62.000 60.000 16.24 0.00 44.23 4.70
1644 1943 3.138798 CTGCATGGTGCCTCTGCC 61.139 66.667 11.71 0.00 44.23 4.85
1700 1999 5.153513 GCGTTTGCTTTGATAGTTCATTCA 58.846 37.500 0.00 0.00 38.39 2.57
1763 2062 8.288208 CGGACTAAAACGTGTCTATATACATCT 58.712 37.037 4.05 0.00 34.01 2.90
1818 2119 3.611766 ATGAACGGAGGGAGTAGTTTG 57.388 47.619 0.00 0.00 0.00 2.93
1834 2135 1.225376 TTTGCAGTGGCGTAAGGTCG 61.225 55.000 0.00 0.00 45.35 4.79
2015 2319 1.135402 GTGGCGCTTACCTTTGGATTG 60.135 52.381 7.64 0.00 0.00 2.67
2075 2394 5.163744 TGTGTGTGTGTGTGTATTTTGGTAC 60.164 40.000 0.00 0.00 0.00 3.34
2097 2416 4.232221 CCAAGTGCAGTGCAAATAGAAAG 58.768 43.478 21.67 4.14 41.47 2.62
2207 2552 3.511934 AGAACTCACCGTGCTCTAATCTT 59.488 43.478 0.00 0.00 0.00 2.40
2307 2652 1.152567 CAAACAGCCCCCTGAACCA 60.153 57.895 0.00 0.00 41.77 3.67
2429 2774 1.699656 GCAGCATGTGACAGCTACGG 61.700 60.000 8.74 0.65 39.50 4.02
2624 2969 0.248565 GGGACCCGTCTAAGGTTGAC 59.751 60.000 0.00 0.00 37.88 3.18
2903 3248 3.869623 GCTCAGAGCTTTCCCATGA 57.130 52.632 15.78 0.00 38.45 3.07
2913 3258 2.620585 GCTTTCCCATGATCTGGTAAGC 59.379 50.000 17.85 17.85 45.57 3.09
2914 3259 3.889815 CTTTCCCATGATCTGGTAAGCA 58.110 45.455 0.00 0.00 44.30 3.91
2915 3260 4.272489 CTTTCCCATGATCTGGTAAGCAA 58.728 43.478 0.00 0.00 44.30 3.91
3109 3557 0.250467 ATGTTGCTCACTGAAGCCGT 60.250 50.000 4.78 0.00 41.77 5.68
3118 3566 4.143094 GCTCACTGAAGCCGTAAACTAAAG 60.143 45.833 0.00 0.00 36.22 1.85
3201 3675 8.767478 CTTTTTGAGGATTAGTAGTTCGGTAA 57.233 34.615 0.00 0.00 0.00 2.85
3304 3781 8.868635 ACCTTGTATTTAACGCTATAGTTCTC 57.131 34.615 0.84 0.00 35.70 2.87
3473 3952 9.851686 TTCATGTGGAATATGCTATAGAAGTTT 57.148 29.630 3.21 0.00 35.17 2.66
3500 3979 2.001076 AAAAAGGCTGAAGGGTCCAG 57.999 50.000 0.00 0.00 34.88 3.86
3519 3998 5.932303 GTCCAGTAGCTGAGTTGTTAATTCA 59.068 40.000 0.00 0.00 32.44 2.57
3657 4136 2.099756 GCTGGGCATCAAACTACCAATC 59.900 50.000 0.00 0.00 0.00 2.67
3665 4144 2.565391 TCAAACTACCAATCGCTCCTCA 59.435 45.455 0.00 0.00 0.00 3.86
3666 4145 3.197766 TCAAACTACCAATCGCTCCTCAT 59.802 43.478 0.00 0.00 0.00 2.90
3667 4146 4.404394 TCAAACTACCAATCGCTCCTCATA 59.596 41.667 0.00 0.00 0.00 2.15
3669 4148 3.833732 ACTACCAATCGCTCCTCATAGA 58.166 45.455 0.00 0.00 0.00 1.98
3670 4149 3.823873 ACTACCAATCGCTCCTCATAGAG 59.176 47.826 0.00 0.00 36.92 2.43
3718 4203 2.352715 GGCCAACCTTTTCATCCTTTCG 60.353 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 161 2.095461 CTTTCTTTTGCCCCTAGAGCC 58.905 52.381 0.00 0.00 0.00 4.70
169 172 4.058721 TGGGCTTTCTTCTTTCTTTTGC 57.941 40.909 0.00 0.00 0.00 3.68
283 286 0.266152 AGAGGTATGTGGAGAGGGGG 59.734 60.000 0.00 0.00 0.00 5.40
284 287 1.710816 GAGAGGTATGTGGAGAGGGG 58.289 60.000 0.00 0.00 0.00 4.79
285 288 1.219213 AGGAGAGGTATGTGGAGAGGG 59.781 57.143 0.00 0.00 0.00 4.30
286 289 2.765689 AGGAGAGGTATGTGGAGAGG 57.234 55.000 0.00 0.00 0.00 3.69
287 290 3.153919 GCTAGGAGAGGTATGTGGAGAG 58.846 54.545 0.00 0.00 0.00 3.20
288 291 2.786445 AGCTAGGAGAGGTATGTGGAGA 59.214 50.000 0.00 0.00 32.80 3.71
289 292 3.237268 AGCTAGGAGAGGTATGTGGAG 57.763 52.381 0.00 0.00 32.80 3.86
290 293 3.498841 GCTAGCTAGGAGAGGTATGTGGA 60.499 52.174 22.10 0.00 37.51 4.02
291 294 2.823154 GCTAGCTAGGAGAGGTATGTGG 59.177 54.545 22.10 0.00 37.51 4.17
292 295 3.761897 AGCTAGCTAGGAGAGGTATGTG 58.238 50.000 17.69 0.00 37.51 3.21
293 296 4.263594 GGTAGCTAGCTAGGAGAGGTATGT 60.264 50.000 24.78 0.00 37.51 2.29
294 297 4.266714 GGTAGCTAGCTAGGAGAGGTATG 58.733 52.174 24.78 0.00 37.51 2.39
295 298 3.267551 GGGTAGCTAGCTAGGAGAGGTAT 59.732 52.174 24.78 0.00 37.51 2.73
296 299 2.643801 GGGTAGCTAGCTAGGAGAGGTA 59.356 54.545 24.78 5.59 37.09 3.08
297 300 1.426215 GGGTAGCTAGCTAGGAGAGGT 59.574 57.143 24.78 6.63 39.82 3.85
298 301 1.425831 TGGGTAGCTAGCTAGGAGAGG 59.574 57.143 24.78 0.00 0.00 3.69
299 302 2.961531 TGGGTAGCTAGCTAGGAGAG 57.038 55.000 24.78 0.00 0.00 3.20
300 303 2.041891 GGATGGGTAGCTAGCTAGGAGA 59.958 54.545 24.78 9.60 0.00 3.71
301 304 2.452505 GGATGGGTAGCTAGCTAGGAG 58.547 57.143 24.78 0.00 0.00 3.69
302 305 1.271982 CGGATGGGTAGCTAGCTAGGA 60.272 57.143 24.78 11.71 0.00 2.94
303 306 1.178276 CGGATGGGTAGCTAGCTAGG 58.822 60.000 24.78 6.64 0.00 3.02
304 307 0.528470 GCGGATGGGTAGCTAGCTAG 59.472 60.000 24.78 16.84 0.00 3.42
305 308 0.112606 AGCGGATGGGTAGCTAGCTA 59.887 55.000 20.67 20.67 39.74 3.32
306 309 0.760945 AAGCGGATGGGTAGCTAGCT 60.761 55.000 23.12 23.12 40.78 3.32
307 310 0.319986 GAAGCGGATGGGTAGCTAGC 60.320 60.000 14.67 14.67 40.78 3.42
308 311 0.318762 GGAAGCGGATGGGTAGCTAG 59.681 60.000 0.00 0.00 40.78 3.42
309 312 0.397957 TGGAAGCGGATGGGTAGCTA 60.398 55.000 0.00 0.00 40.78 3.32
310 313 1.689233 TGGAAGCGGATGGGTAGCT 60.689 57.895 0.00 0.00 43.90 3.32
311 314 1.523938 GTGGAAGCGGATGGGTAGC 60.524 63.158 0.00 0.00 0.00 3.58
312 315 0.541863 AAGTGGAAGCGGATGGGTAG 59.458 55.000 0.00 0.00 0.00 3.18
313 316 0.251916 CAAGTGGAAGCGGATGGGTA 59.748 55.000 0.00 0.00 0.00 3.69
314 317 1.002134 CAAGTGGAAGCGGATGGGT 60.002 57.895 0.00 0.00 0.00 4.51
315 318 1.750399 CCAAGTGGAAGCGGATGGG 60.750 63.158 0.00 0.00 37.39 4.00
316 319 2.409870 GCCAAGTGGAAGCGGATGG 61.410 63.158 0.18 0.00 37.39 3.51
317 320 2.409870 GGCCAAGTGGAAGCGGATG 61.410 63.158 0.00 0.00 37.39 3.51
318 321 2.044946 GGCCAAGTGGAAGCGGAT 60.045 61.111 0.00 0.00 37.39 4.18
319 322 2.424842 AATGGCCAAGTGGAAGCGGA 62.425 55.000 10.96 0.00 37.39 5.54
320 323 1.535204 AAATGGCCAAGTGGAAGCGG 61.535 55.000 10.96 0.00 37.39 5.52
321 324 0.109132 GAAATGGCCAAGTGGAAGCG 60.109 55.000 10.96 0.00 37.39 4.68
322 325 0.247460 GGAAATGGCCAAGTGGAAGC 59.753 55.000 10.96 0.00 37.39 3.86
323 326 0.897621 GGGAAATGGCCAAGTGGAAG 59.102 55.000 10.96 0.00 37.39 3.46
324 327 0.189574 TGGGAAATGGCCAAGTGGAA 59.810 50.000 10.96 0.00 37.39 3.53
325 328 0.413037 ATGGGAAATGGCCAAGTGGA 59.587 50.000 10.96 0.00 37.39 4.02
326 329 0.826062 GATGGGAAATGGCCAAGTGG 59.174 55.000 10.96 0.00 38.53 4.00
327 330 0.826062 GGATGGGAAATGGCCAAGTG 59.174 55.000 10.96 0.00 0.00 3.16
328 331 0.325577 GGGATGGGAAATGGCCAAGT 60.326 55.000 10.96 0.00 0.00 3.16
329 332 0.325484 TGGGATGGGAAATGGCCAAG 60.325 55.000 10.96 0.00 0.00 3.61
330 333 0.617249 GTGGGATGGGAAATGGCCAA 60.617 55.000 10.96 0.00 0.00 4.52
331 334 1.001503 GTGGGATGGGAAATGGCCA 59.998 57.895 8.56 8.56 0.00 5.36
332 335 0.398948 ATGTGGGATGGGAAATGGCC 60.399 55.000 0.00 0.00 0.00 5.36
333 336 1.043022 GATGTGGGATGGGAAATGGC 58.957 55.000 0.00 0.00 0.00 4.40
334 337 1.218704 AGGATGTGGGATGGGAAATGG 59.781 52.381 0.00 0.00 0.00 3.16
335 338 2.313317 CAGGATGTGGGATGGGAAATG 58.687 52.381 0.00 0.00 0.00 2.32
336 339 1.412074 GCAGGATGTGGGATGGGAAAT 60.412 52.381 0.00 0.00 39.31 2.17
337 340 0.033208 GCAGGATGTGGGATGGGAAA 60.033 55.000 0.00 0.00 39.31 3.13
338 341 0.920763 AGCAGGATGTGGGATGGGAA 60.921 55.000 0.00 0.00 39.31 3.97
339 342 0.920763 AAGCAGGATGTGGGATGGGA 60.921 55.000 0.00 0.00 39.31 4.37
340 343 0.754217 CAAGCAGGATGTGGGATGGG 60.754 60.000 0.00 0.00 39.31 4.00
341 344 1.389609 GCAAGCAGGATGTGGGATGG 61.390 60.000 0.00 0.00 39.31 3.51
342 345 0.395311 AGCAAGCAGGATGTGGGATG 60.395 55.000 0.00 0.00 39.31 3.51
343 346 0.333993 AAGCAAGCAGGATGTGGGAT 59.666 50.000 0.00 0.00 39.31 3.85
344 347 0.322816 GAAGCAAGCAGGATGTGGGA 60.323 55.000 0.00 0.00 39.31 4.37
345 348 1.318158 GGAAGCAAGCAGGATGTGGG 61.318 60.000 0.00 0.00 39.31 4.61
346 349 1.651240 CGGAAGCAAGCAGGATGTGG 61.651 60.000 0.00 0.00 39.31 4.17
347 350 1.651240 CCGGAAGCAAGCAGGATGTG 61.651 60.000 0.00 0.00 39.31 3.21
350 353 1.222936 CTCCGGAAGCAAGCAGGAT 59.777 57.895 5.23 0.00 0.00 3.24
393 636 2.866028 CAGGCAGTTGAAGCGAGC 59.134 61.111 0.00 0.00 0.00 5.03
407 650 1.202557 GGATGAGCTGAGAAGAGCAGG 60.203 57.143 0.00 0.00 41.83 4.85
421 664 1.912043 AGAAACTCACCAGGGGATGAG 59.088 52.381 0.00 0.00 46.49 2.90
427 670 2.348411 AACACAGAAACTCACCAGGG 57.652 50.000 0.00 0.00 0.00 4.45
464 714 5.641155 ACCCTTAGCAAAGTAGACCAAAAT 58.359 37.500 0.00 0.00 0.00 1.82
465 715 5.056553 ACCCTTAGCAAAGTAGACCAAAA 57.943 39.130 0.00 0.00 0.00 2.44
466 716 4.717279 ACCCTTAGCAAAGTAGACCAAA 57.283 40.909 0.00 0.00 0.00 3.28
472 722 4.092968 CGCACTTTACCCTTAGCAAAGTAG 59.907 45.833 0.00 0.00 39.78 2.57
474 724 2.812011 CGCACTTTACCCTTAGCAAAGT 59.188 45.455 0.00 0.00 41.86 2.66
485 735 2.432206 ATTGGCAAACGCACTTTACC 57.568 45.000 3.01 0.00 0.00 2.85
513 777 2.919807 GCAAGAAAAGAAGAAGCCGCAG 60.920 50.000 0.00 0.00 0.00 5.18
517 781 2.887152 TGAGGCAAGAAAAGAAGAAGCC 59.113 45.455 0.00 0.00 40.85 4.35
617 881 4.196826 GCTAGCGAGCGTGCGTTG 62.197 66.667 2.13 0.00 39.39 4.10
655 927 1.229428 CACGGAAGCAGAAAAGCTCA 58.771 50.000 0.00 0.00 45.89 4.26
659 931 1.884235 AGGACACGGAAGCAGAAAAG 58.116 50.000 0.00 0.00 0.00 2.27
660 932 2.218603 GAAGGACACGGAAGCAGAAAA 58.781 47.619 0.00 0.00 0.00 2.29
661 933 1.140052 TGAAGGACACGGAAGCAGAAA 59.860 47.619 0.00 0.00 0.00 2.52
662 934 0.756294 TGAAGGACACGGAAGCAGAA 59.244 50.000 0.00 0.00 0.00 3.02
663 935 0.976641 ATGAAGGACACGGAAGCAGA 59.023 50.000 0.00 0.00 0.00 4.26
674 946 8.336801 ACAATAAGGAAGTAAACATGAAGGAC 57.663 34.615 0.00 0.00 0.00 3.85
750 1027 4.766891 GGGAACTTGAGATCAAATCAACCA 59.233 41.667 0.00 0.00 35.15 3.67
775 1052 1.280457 GGAGAGAGAGCAAGGGGAAA 58.720 55.000 0.00 0.00 0.00 3.13
796 1073 1.710013 GAACACGCGGATGAAAGAGA 58.290 50.000 12.47 0.00 0.00 3.10
798 1075 1.623081 GCGAACACGCGGATGAAAGA 61.623 55.000 12.47 0.00 42.84 2.52
799 1076 1.225745 GCGAACACGCGGATGAAAG 60.226 57.895 12.47 0.00 42.84 2.62
800 1077 2.857448 GCGAACACGCGGATGAAA 59.143 55.556 12.47 0.00 42.84 2.69
809 1086 2.127758 GTCAAAGCGGCGAACACG 60.128 61.111 12.98 0.00 0.00 4.49
810 1087 2.171489 GAGGTCAAAGCGGCGAACAC 62.171 60.000 12.98 0.00 0.00 3.32
811 1088 1.959226 GAGGTCAAAGCGGCGAACA 60.959 57.895 12.98 0.00 0.00 3.18
812 1089 1.901650 CTGAGGTCAAAGCGGCGAAC 61.902 60.000 12.98 0.00 0.00 3.95
813 1090 1.667830 CTGAGGTCAAAGCGGCGAA 60.668 57.895 12.98 0.00 0.00 4.70
814 1091 2.048222 CTGAGGTCAAAGCGGCGA 60.048 61.111 12.98 0.00 0.00 5.54
815 1092 3.793144 GCTGAGGTCAAAGCGGCG 61.793 66.667 0.51 0.51 0.00 6.46
816 1093 0.744414 TATGCTGAGGTCAAAGCGGC 60.744 55.000 0.00 0.00 42.54 6.53
817 1094 1.009829 GTATGCTGAGGTCAAAGCGG 58.990 55.000 0.00 0.00 42.54 5.52
845 1122 3.125316 CCTAGCTAAAAGTGCGAAACCAG 59.875 47.826 0.00 0.00 35.28 4.00
850 1127 2.762535 AGCCTAGCTAAAAGTGCGAA 57.237 45.000 0.00 0.00 36.99 4.70
993 1270 3.452627 TGGAGCTTTCTTCCATAGGACTC 59.547 47.826 0.00 0.00 0.00 3.36
1212 1492 2.202987 GGGCTCTCCTGATGCACG 60.203 66.667 0.00 0.00 0.00 5.34
1271 1551 3.968568 TGGTGGTCGTCGTCGTGG 61.969 66.667 1.33 0.00 38.33 4.94
1275 1555 4.712425 CCGGTGGTGGTCGTCGTC 62.712 72.222 0.00 0.00 0.00 4.20
1277 1557 4.415332 CTCCGGTGGTGGTCGTCG 62.415 72.222 0.00 0.00 0.00 5.12
1278 1558 4.736896 GCTCCGGTGGTGGTCGTC 62.737 72.222 0.00 0.00 0.00 4.20
1305 1585 0.602905 CCTCAACCGTGTCCAGGAAC 60.603 60.000 0.00 0.00 0.00 3.62
1347 1627 3.716601 AGCGCAAAAGCACAATAAAAGT 58.283 36.364 11.47 0.00 40.15 2.66
1353 1633 0.388659 TCCAAGCGCAAAAGCACAAT 59.611 45.000 11.47 0.00 40.15 2.71
1365 1655 1.135689 GCTGTTACCATGTTCCAAGCG 60.136 52.381 0.00 0.00 0.00 4.68
1486 1785 4.745172 GCCTCTGTATTTTCCTCCTCCATC 60.745 50.000 0.00 0.00 0.00 3.51
1487 1786 3.137360 GCCTCTGTATTTTCCTCCTCCAT 59.863 47.826 0.00 0.00 0.00 3.41
1489 1788 2.158740 GGCCTCTGTATTTTCCTCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
1490 1789 2.483889 CGGCCTCTGTATTTTCCTCCTC 60.484 54.545 0.00 0.00 0.00 3.71
1491 1790 1.486726 CGGCCTCTGTATTTTCCTCCT 59.513 52.381 0.00 0.00 0.00 3.69
1506 1805 3.881019 TTCCTCTCACCGACGGCCT 62.881 63.158 15.39 0.00 0.00 5.19
1640 1939 2.419324 GTGAGAGCAGAAAAGATGGCAG 59.581 50.000 0.00 0.00 0.00 4.85
1644 1943 3.439476 CCTTGGTGAGAGCAGAAAAGATG 59.561 47.826 0.00 0.00 0.00 2.90
1787 2088 5.996644 TCCCTCCGTTCATACAAATACAAT 58.003 37.500 0.00 0.00 0.00 2.71
1790 2091 5.019785 ACTCCCTCCGTTCATACAAATAC 57.980 43.478 0.00 0.00 0.00 1.89
1796 2097 4.430908 CAAACTACTCCCTCCGTTCATAC 58.569 47.826 0.00 0.00 0.00 2.39
1804 2105 1.339151 CCACTGCAAACTACTCCCTCC 60.339 57.143 0.00 0.00 0.00 4.30
1818 2119 2.813908 CCGACCTTACGCCACTGC 60.814 66.667 0.00 0.00 0.00 4.40
1834 2135 5.763204 TCATGTTGACCAACTAAGAAGAACC 59.237 40.000 13.26 0.00 41.67 3.62
1873 2177 4.122046 CAAGCTTTTGGAAAGGAAACCTG 58.878 43.478 0.00 0.00 32.13 4.00
2027 2331 7.082602 CACACACACTACCACTACTTTACTAG 58.917 42.308 0.00 0.00 0.00 2.57
2030 2334 5.461078 CACACACACACTACCACTACTTTAC 59.539 44.000 0.00 0.00 0.00 2.01
2031 2335 5.127519 ACACACACACACTACCACTACTTTA 59.872 40.000 0.00 0.00 0.00 1.85
2032 2336 4.081309 ACACACACACACTACCACTACTTT 60.081 41.667 0.00 0.00 0.00 2.66
2033 2337 3.449737 ACACACACACACTACCACTACTT 59.550 43.478 0.00 0.00 0.00 2.24
2043 2347 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
2075 2394 3.921119 TTCTATTTGCACTGCACTTGG 57.079 42.857 2.26 0.00 38.71 3.61
2097 2416 6.726490 TTATGGTCACTCTAGTATTCACCC 57.274 41.667 0.00 0.00 0.00 4.61
2207 2552 0.399091 AGCTGCAGCCCCTCTGTATA 60.399 55.000 34.39 0.00 44.66 1.47
2429 2774 2.783135 TGACAGCCAATGAAAGTCTCC 58.217 47.619 0.00 0.00 0.00 3.71
2583 2928 0.599060 TGCACTGCAACATGGTCATG 59.401 50.000 0.00 9.19 38.02 3.07
2624 2969 1.005037 TGCTCCTTGCTGTGTACGG 60.005 57.895 0.00 0.00 43.37 4.02
2913 3258 2.857592 ACAGAAAAGTGCAGCTGTTG 57.142 45.000 16.64 4.20 38.34 3.33
2915 3260 4.823989 AGATTAACAGAAAAGTGCAGCTGT 59.176 37.500 16.64 0.00 42.91 4.40
3109 3557 7.970102 TGCTTCTTAGGAGTTCCTTTAGTTTA 58.030 34.615 5.91 0.00 46.09 2.01
3118 3566 1.210722 CCCCTGCTTCTTAGGAGTTCC 59.789 57.143 0.00 0.00 38.10 3.62
3304 3781 5.670097 CGCCAAATCTATGTAACTGAATCG 58.330 41.667 0.00 0.00 0.00 3.34
3473 3952 6.183361 GGACCCTTCAGCCTTTTTATATCCTA 60.183 42.308 0.00 0.00 0.00 2.94
3519 3998 5.897250 GGGGTGTGGTTGGAAAGATAATATT 59.103 40.000 0.00 0.00 0.00 1.28
3593 4072 7.687757 GCACATATTTTACTTTCGGCAATTTTG 59.312 33.333 0.00 0.00 0.00 2.44
3665 4144 6.098838 TGTGTAGTCATGATCTTTGCCTCTAT 59.901 38.462 0.00 0.00 0.00 1.98
3666 4145 5.422012 TGTGTAGTCATGATCTTTGCCTCTA 59.578 40.000 0.00 0.00 0.00 2.43
3667 4146 4.223700 TGTGTAGTCATGATCTTTGCCTCT 59.776 41.667 0.00 0.00 0.00 3.69
3669 4148 4.256920 GTGTGTAGTCATGATCTTTGCCT 58.743 43.478 0.00 0.00 0.00 4.75
3670 4149 4.002982 TGTGTGTAGTCATGATCTTTGCC 58.997 43.478 0.00 0.00 0.00 4.52
3671 4150 4.093998 CCTGTGTGTAGTCATGATCTTTGC 59.906 45.833 0.00 0.00 0.00 3.68
3672 4151 5.482006 TCCTGTGTGTAGTCATGATCTTTG 58.518 41.667 0.00 0.00 0.00 2.77
3673 4152 5.337894 CCTCCTGTGTGTAGTCATGATCTTT 60.338 44.000 0.00 0.00 0.00 2.52
3680 4165 0.905357 GCCCTCCTGTGTGTAGTCAT 59.095 55.000 0.00 0.00 0.00 3.06
3705 4190 2.813754 CACAGAGGCGAAAGGATGAAAA 59.186 45.455 0.00 0.00 0.00 2.29
3718 4203 3.801698 TGATTCTTAGCATCACAGAGGC 58.198 45.455 0.00 0.00 39.81 4.70


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

AutoCloner maintained by Alex Coulton.