Multiple sequence alignment - TraesCS2B01G293700

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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 TraesCS2B01G293700 chr2B 100.000 3833 0 0 1 3833 409665615 409661783 0.000000e+00 7079
1 TraesCS2B01G293700 chr2B 98.540 548 8 0 3286 3833 161702035 161702582 0.000000e+00 968
2 TraesCS2B01G293700 chr2B 97.662 556 13 0 3278 3833 52430961 52431516 0.000000e+00 955
3 TraesCS2B01G293700 chr2A 92.860 3011 139 30 79 3068 455495759 455492804 0.000000e+00 4300
4 TraesCS2B01G293700 chr2D 94.517 2608 82 14 633 3228 344339730 344337172 0.000000e+00 3967
5 TraesCS2B01G293700 chr2D 82.060 563 68 16 1 549 344340331 344339788 2.100000e-122 449
6 TraesCS2B01G293700 chr1B 98.182 550 10 0 3284 3833 656506499 656505950 0.000000e+00 961
7 TraesCS2B01G293700 chr1B 97.814 549 12 0 3285 3833 343954645 343955193 0.000000e+00 948
8 TraesCS2B01G293700 chr1B 97.148 561 11 3 3274 3833 427964158 427964714 0.000000e+00 942
9 TraesCS2B01G293700 chr7B 98.175 548 10 0 3286 3833 458854607 458854060 0.000000e+00 957
10 TraesCS2B01G293700 chr7B 96.991 565 16 1 3269 3833 23388194 23387631 0.000000e+00 948
11 TraesCS2B01G293700 chr7A 97.826 552 10 2 3283 3833 162727985 162728535 0.000000e+00 952
12 TraesCS2B01G293700 chr4A 97.993 548 11 0 3286 3833 562280658 562280111 0.000000e+00 952


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 TraesCS2B01G293700 chr2B 409661783 409665615 3832 True 7079 7079 100.0000 1 3833 1 chr2B.!!$R1 3832
1 TraesCS2B01G293700 chr2B 161702035 161702582 547 False 968 968 98.5400 3286 3833 1 chr2B.!!$F2 547
2 TraesCS2B01G293700 chr2B 52430961 52431516 555 False 955 955 97.6620 3278 3833 1 chr2B.!!$F1 555
3 TraesCS2B01G293700 chr2A 455492804 455495759 2955 True 4300 4300 92.8600 79 3068 1 chr2A.!!$R1 2989
4 TraesCS2B01G293700 chr2D 344337172 344340331 3159 True 2208 3967 88.2885 1 3228 2 chr2D.!!$R1 3227
5 TraesCS2B01G293700 chr1B 656505950 656506499 549 True 961 961 98.1820 3284 3833 1 chr1B.!!$R1 549
6 TraesCS2B01G293700 chr1B 343954645 343955193 548 False 948 948 97.8140 3285 3833 1 chr1B.!!$F1 548
7 TraesCS2B01G293700 chr1B 427964158 427964714 556 False 942 942 97.1480 3274 3833 1 chr1B.!!$F2 559
8 TraesCS2B01G293700 chr7B 458854060 458854607 547 True 957 957 98.1750 3286 3833 1 chr7B.!!$R2 547
9 TraesCS2B01G293700 chr7B 23387631 23388194 563 True 948 948 96.9910 3269 3833 1 chr7B.!!$R1 564
10 TraesCS2B01G293700 chr7A 162727985 162728535 550 False 952 952 97.8260 3283 3833 1 chr7A.!!$F1 550
11 TraesCS2B01G293700 chr4A 562280111 562280658 547 True 952 952 97.9930 3286 3833 1 chr4A.!!$R1 547

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
559 574 0.035725 AAAAGCGTACTACCTGGCCC 60.036 55.0 0.00 0.0 0.00 5.80 F
1221 1253 0.596083 CCATGCTCTTCTACGCCTCG 60.596 60.0 0.00 0.0 0.00 4.63 F
2211 2255 0.458197 ATCTCTCGTCGTCGTCGTCT 60.458 55.0 11.41 0.0 38.33 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1437 0.109272 TCGTCTTGCTCGTGGTCATC 60.109 55.000 0.00 0.0 0.00 2.92 R
2799 2843 1.211969 GACGCGCTGTCTCCTTGTA 59.788 57.895 20.14 0.0 44.58 2.41 R
3113 3159 3.044986 CCAAAACTTGATGTGCTGTTCG 58.955 45.455 0.00 0.0 0.00 3.95 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
25 26 2.872245 CCTTCTTCACTTTTGTCTGCGA 59.128 45.455 0.00 0.00 0.00 5.10
39 40 2.347755 GTCTGCGATTTACGGGAGAAAC 59.652 50.000 0.00 0.00 42.83 2.78
41 42 1.002201 TGCGATTTACGGGAGAAACCA 59.998 47.619 0.00 0.00 42.83 3.67
46 47 1.331214 TTACGGGAGAAACCACGTCT 58.669 50.000 0.00 0.00 42.34 4.18
52 53 1.605712 GGAGAAACCACGTCTGGACTG 60.606 57.143 0.00 0.00 40.55 3.51
57 58 2.574018 CCACGTCTGGACTGCTCCA 61.574 63.158 0.00 0.00 45.11 3.86
59 60 2.126307 CGTCTGGACTGCTCCACG 60.126 66.667 0.00 0.00 42.15 4.94
63 64 3.302347 CTGGACTGCTCCACGGACC 62.302 68.421 0.00 0.00 42.15 4.46
66 67 3.343788 GACTGCTCCACGGACCGAG 62.344 68.421 23.38 13.45 0.00 4.63
70 71 2.927580 GCTCCACGGACCGAGACAA 61.928 63.158 23.38 0.86 0.00 3.18
73 74 0.682852 TCCACGGACCGAGACAAATT 59.317 50.000 23.38 0.00 0.00 1.82
75 76 1.997606 CCACGGACCGAGACAAATTAC 59.002 52.381 23.38 0.00 0.00 1.89
77 78 1.619827 ACGGACCGAGACAAATTACCA 59.380 47.619 23.38 0.00 0.00 3.25
85 93 3.432252 CGAGACAAATTACCAGCTTTCGT 59.568 43.478 0.00 0.00 0.00 3.85
89 97 4.606961 ACAAATTACCAGCTTTCGTTGTG 58.393 39.130 0.00 0.00 0.00 3.33
127 140 2.282407 ACTGTTGCGGAAAGTTTACGT 58.718 42.857 20.86 0.00 0.00 3.57
134 147 1.523934 CGGAAAGTTTACGTGTTCGCT 59.476 47.619 12.25 0.00 41.18 4.93
137 150 4.317980 CGGAAAGTTTACGTGTTCGCTTTA 60.318 41.667 12.25 0.00 41.18 1.85
157 170 5.537300 TTAGAGATGCCCTTACTGACATC 57.463 43.478 0.00 0.00 39.35 3.06
193 206 5.374071 ACCAAAGTAACCGTTGATCTCTTT 58.626 37.500 0.00 0.00 32.55 2.52
196 209 6.856426 CCAAAGTAACCGTTGATCTCTTTTTC 59.144 38.462 0.00 0.00 32.55 2.29
203 216 6.729187 ACCGTTGATCTCTTTTTCTTCTTTG 58.271 36.000 0.00 0.00 0.00 2.77
205 218 7.148069 ACCGTTGATCTCTTTTTCTTCTTTGTT 60.148 33.333 0.00 0.00 0.00 2.83
239 252 6.808008 AGAATCACCATTTACTTGACAGTG 57.192 37.500 0.00 0.00 34.06 3.66
241 254 7.450074 AGAATCACCATTTACTTGACAGTGTA 58.550 34.615 0.00 0.00 34.06 2.90
264 277 1.402968 ACTGCACGCATCAATTCATCC 59.597 47.619 0.00 0.00 0.00 3.51
265 278 1.402613 CTGCACGCATCAATTCATCCA 59.597 47.619 0.00 0.00 0.00 3.41
313 326 3.780294 TGGACATTATACTCCAGCAAGGT 59.220 43.478 0.00 0.00 39.02 3.50
315 328 5.163343 TGGACATTATACTCCAGCAAGGTAC 60.163 44.000 0.00 0.00 39.02 3.34
318 331 5.661312 ACATTATACTCCAGCAAGGTACAGA 59.339 40.000 0.00 0.00 39.02 3.41
325 338 1.808945 CAGCAAGGTACAGAAGGCAAG 59.191 52.381 0.00 0.00 0.00 4.01
329 342 0.615850 AGGTACAGAAGGCAAGAGGC 59.384 55.000 0.00 0.00 43.74 4.70
338 351 4.065110 GCAAGAGGCCAAACGTCT 57.935 55.556 5.01 0.00 45.32 4.18
400 415 0.040067 GACAAAACGCAAGGCTGAGG 60.040 55.000 0.00 0.00 46.39 3.86
404 419 3.772853 AACGCAAGGCTGAGGTGCA 62.773 57.895 9.36 0.00 46.39 4.57
423 438 5.221244 GGTGCAAGGTAAATTTGTCTCTTGT 60.221 40.000 17.51 0.00 35.43 3.16
424 439 6.016610 GGTGCAAGGTAAATTTGTCTCTTGTA 60.017 38.462 17.51 13.67 35.43 2.41
425 440 7.309194 GGTGCAAGGTAAATTTGTCTCTTGTAT 60.309 37.037 17.51 0.00 35.43 2.29
426 441 8.082242 GTGCAAGGTAAATTTGTCTCTTGTATT 58.918 33.333 17.51 0.00 35.43 1.89
427 442 8.081633 TGCAAGGTAAATTTGTCTCTTGTATTG 58.918 33.333 17.51 0.00 35.43 1.90
436 451 1.207089 TCTCTTGTATTGAGGGCGTGG 59.793 52.381 0.00 0.00 32.78 4.94
447 462 2.285977 GAGGGCGTGGGTTGTATTTAG 58.714 52.381 0.00 0.00 0.00 1.85
454 469 2.758423 GTGGGTTGTATTTAGGCCTTGG 59.242 50.000 12.58 0.00 0.00 3.61
457 472 3.699538 GGGTTGTATTTAGGCCTTGGAAG 59.300 47.826 12.58 0.00 0.00 3.46
499 514 1.532505 GCTGTGCGATGCGATCAATTT 60.533 47.619 0.00 0.00 0.00 1.82
550 565 1.946267 CCGGCAACAAAAGCGTACT 59.054 52.632 0.00 0.00 0.00 2.73
551 566 1.149987 CCGGCAACAAAAGCGTACTA 58.850 50.000 0.00 0.00 0.00 1.82
552 567 1.136169 CCGGCAACAAAAGCGTACTAC 60.136 52.381 0.00 0.00 0.00 2.73
553 568 1.136169 CGGCAACAAAAGCGTACTACC 60.136 52.381 0.00 0.00 0.00 3.18
554 569 2.148768 GGCAACAAAAGCGTACTACCT 58.851 47.619 0.00 0.00 0.00 3.08
555 570 2.095919 GGCAACAAAAGCGTACTACCTG 60.096 50.000 0.00 0.00 0.00 4.00
556 571 2.095919 GCAACAAAAGCGTACTACCTGG 60.096 50.000 0.00 0.00 0.00 4.45
557 572 1.804601 ACAAAAGCGTACTACCTGGC 58.195 50.000 0.00 0.00 0.00 4.85
559 574 0.035725 AAAAGCGTACTACCTGGCCC 60.036 55.000 0.00 0.00 0.00 5.80
561 576 1.328430 AAGCGTACTACCTGGCCCTC 61.328 60.000 0.00 0.00 0.00 4.30
596 614 1.142097 GGAGAGACCAGCTTACGCC 59.858 63.158 0.00 0.00 38.79 5.68
857 888 1.938585 CCGGCCATCCTATCCTCTTA 58.061 55.000 2.24 0.00 0.00 2.10
858 889 2.257207 CCGGCCATCCTATCCTCTTAA 58.743 52.381 2.24 0.00 0.00 1.85
859 890 2.840651 CCGGCCATCCTATCCTCTTAAT 59.159 50.000 2.24 0.00 0.00 1.40
950 982 2.083002 ACGTACGGTCTCTTTCTCTCC 58.917 52.381 21.06 0.00 0.00 3.71
960 992 2.166459 CTCTTTCTCTCCCACACGCATA 59.834 50.000 0.00 0.00 0.00 3.14
1221 1253 0.596083 CCATGCTCTTCTACGCCTCG 60.596 60.000 0.00 0.00 0.00 4.63
1224 1256 2.119655 GCTCTTCTACGCCTCGGGA 61.120 63.158 0.00 0.00 0.00 5.14
1226 1258 0.748729 CTCTTCTACGCCTCGGGAGT 60.749 60.000 4.87 4.87 39.46 3.85
1287 1319 4.087892 ATCCACGCGCAGGAGCTT 62.088 61.111 22.86 6.95 38.83 3.74
1296 1328 1.803519 GCAGGAGCTTCTCGACACG 60.804 63.158 0.00 0.00 37.91 4.49
1382 1426 1.810755 CCGCCAAGATGATGATGATGG 59.189 52.381 0.00 0.00 0.00 3.51
1383 1427 2.501261 CGCCAAGATGATGATGATGGT 58.499 47.619 0.00 0.00 0.00 3.55
1384 1428 2.225727 CGCCAAGATGATGATGATGGTG 59.774 50.000 0.00 0.00 32.78 4.17
1385 1429 3.483421 GCCAAGATGATGATGATGGTGA 58.517 45.455 0.00 0.00 0.00 4.02
1386 1430 3.502595 GCCAAGATGATGATGATGGTGAG 59.497 47.826 0.00 0.00 0.00 3.51
1387 1431 4.072839 CCAAGATGATGATGATGGTGAGG 58.927 47.826 0.00 0.00 0.00 3.86
1388 1432 4.445879 CCAAGATGATGATGATGGTGAGGT 60.446 45.833 0.00 0.00 0.00 3.85
1389 1433 5.131067 CAAGATGATGATGATGGTGAGGTT 58.869 41.667 0.00 0.00 0.00 3.50
1390 1434 4.715713 AGATGATGATGATGGTGAGGTTG 58.284 43.478 0.00 0.00 0.00 3.77
1391 1435 4.411212 AGATGATGATGATGGTGAGGTTGA 59.589 41.667 0.00 0.00 0.00 3.18
1392 1436 4.783560 TGATGATGATGGTGAGGTTGAT 57.216 40.909 0.00 0.00 0.00 2.57
1393 1437 4.457466 TGATGATGATGGTGAGGTTGATG 58.543 43.478 0.00 0.00 0.00 3.07
1394 1438 4.164604 TGATGATGATGGTGAGGTTGATGA 59.835 41.667 0.00 0.00 0.00 2.92
1395 1439 4.783560 TGATGATGGTGAGGTTGATGAT 57.216 40.909 0.00 0.00 0.00 2.45
1396 1440 4.457466 TGATGATGGTGAGGTTGATGATG 58.543 43.478 0.00 0.00 0.00 3.07
1399 1443 2.787473 TGGTGAGGTTGATGATGACC 57.213 50.000 0.00 0.00 36.15 4.02
1410 1454 1.929836 GATGATGACCACGAGCAAGAC 59.070 52.381 0.00 0.00 0.00 3.01
1426 1470 0.976641 AGACGATGACCAAAGCCTGA 59.023 50.000 0.00 0.00 0.00 3.86
1428 1472 1.667724 GACGATGACCAAAGCCTGATG 59.332 52.381 0.00 0.00 0.00 3.07
1432 1476 0.770499 TGACCAAAGCCTGATGGACA 59.230 50.000 3.95 1.46 39.12 4.02
1437 1481 0.610232 AAAGCCTGATGGACACCTGC 60.610 55.000 0.00 0.00 34.57 4.85
1518 1562 4.760047 ATCTTCAAGGCGCGCCGT 62.760 61.111 41.70 37.62 41.95 5.68
1702 1746 3.610791 CTCTGCGACCGCGTCTTCA 62.611 63.158 4.92 3.36 45.51 3.02
2115 2159 5.453339 GCTGGCTCACATATACTTCTACCAA 60.453 44.000 0.00 0.00 0.00 3.67
2211 2255 0.458197 ATCTCTCGTCGTCGTCGTCT 60.458 55.000 11.41 0.00 38.33 4.18
2789 2833 1.621814 AGAGGTTCCGGTCGAAATCAA 59.378 47.619 0.00 0.00 30.39 2.57
2799 2843 4.381505 CCGGTCGAAATCAAAAATGGGAAT 60.382 41.667 0.00 0.00 0.00 3.01
2870 2914 3.071602 GGTAGCCAGCTTCAGGATATGAA 59.928 47.826 0.00 0.00 45.79 2.57
2871 2915 4.263243 GGTAGCCAGCTTCAGGATATGAAT 60.263 45.833 0.00 0.00 46.71 2.57
2872 2916 5.046304 GGTAGCCAGCTTCAGGATATGAATA 60.046 44.000 0.00 0.00 46.71 1.75
2873 2917 5.775813 AGCCAGCTTCAGGATATGAATAT 57.224 39.130 0.00 0.00 46.71 1.28
2874 2918 5.498393 AGCCAGCTTCAGGATATGAATATG 58.502 41.667 0.00 0.00 46.71 1.78
2875 2919 5.250082 AGCCAGCTTCAGGATATGAATATGA 59.750 40.000 0.00 0.00 46.71 2.15
2876 2920 6.069556 AGCCAGCTTCAGGATATGAATATGAT 60.070 38.462 0.00 0.00 46.71 2.45
2877 2921 7.126879 AGCCAGCTTCAGGATATGAATATGATA 59.873 37.037 0.00 0.00 46.71 2.15
2878 2922 7.226325 GCCAGCTTCAGGATATGAATATGATAC 59.774 40.741 0.00 0.00 46.71 2.24
2879 2923 8.484575 CCAGCTTCAGGATATGAATATGATACT 58.515 37.037 0.00 0.00 46.71 2.12
3031 3075 2.731341 CGGAGCAACGAAGAAGACGTAT 60.731 50.000 0.00 0.00 43.16 3.06
3061 3105 5.723492 TGAAATGCATCGAAGTCTGTATG 57.277 39.130 0.00 0.00 0.00 2.39
3076 3122 9.850628 GAAGTCTGTATGTAAGTGTGTGTATTA 57.149 33.333 0.00 0.00 0.00 0.98
3101 3147 8.814038 AGATTTGGCTCAATATAACTTTGTCT 57.186 30.769 0.00 0.00 0.00 3.41
3102 3148 8.897752 AGATTTGGCTCAATATAACTTTGTCTC 58.102 33.333 0.00 0.00 0.00 3.36
3132 3178 4.630894 TTCGAACAGCACATCAAGTTTT 57.369 36.364 0.00 0.00 0.00 2.43
3171 3217 4.283467 GGTCCTTTTACCCTGCAAGAAAAT 59.717 41.667 0.00 0.00 34.07 1.82
3172 3218 5.221641 GGTCCTTTTACCCTGCAAGAAAATT 60.222 40.000 0.00 0.00 34.07 1.82
3239 3285 9.079833 TGTATATTTACGGAACTTTTTCTCTCG 57.920 33.333 0.00 0.00 31.71 4.04
3240 3286 9.294030 GTATATTTACGGAACTTTTTCTCTCGA 57.706 33.333 0.00 0.00 31.71 4.04
3241 3287 8.767478 ATATTTACGGAACTTTTTCTCTCGAA 57.233 30.769 0.00 0.00 31.71 3.71
3242 3288 6.907206 TTTACGGAACTTTTTCTCTCGAAA 57.093 33.333 0.00 0.00 37.36 3.46
3243 3289 6.907206 TTACGGAACTTTTTCTCTCGAAAA 57.093 33.333 0.00 0.00 44.89 2.29
3244 3290 7.486802 TTACGGAACTTTTTCTCTCGAAAAT 57.513 32.000 1.61 0.00 45.60 1.82
3245 3291 6.373186 ACGGAACTTTTTCTCTCGAAAATT 57.627 33.333 1.61 0.00 45.60 1.82
3246 3292 6.792326 ACGGAACTTTTTCTCTCGAAAATTT 58.208 32.000 1.61 0.00 45.60 1.82
3247 3293 7.922837 ACGGAACTTTTTCTCTCGAAAATTTA 58.077 30.769 0.00 0.00 45.60 1.40
3248 3294 8.565416 ACGGAACTTTTTCTCTCGAAAATTTAT 58.435 29.630 0.00 0.00 45.60 1.40
3274 3320 7.838079 ATATTACATGTATGTGGGCATTTGT 57.162 32.000 6.36 0.00 41.89 2.83
3275 3321 3.872511 ACATGTATGTGGGCATTTGTG 57.127 42.857 0.00 0.00 40.03 3.33
3276 3322 3.429492 ACATGTATGTGGGCATTTGTGA 58.571 40.909 0.00 0.00 40.03 3.58
3277 3323 4.025360 ACATGTATGTGGGCATTTGTGAT 58.975 39.130 0.00 0.00 40.03 3.06
3278 3324 4.467082 ACATGTATGTGGGCATTTGTGATT 59.533 37.500 0.00 0.00 40.03 2.57
3279 3325 4.453177 TGTATGTGGGCATTTGTGATTG 57.547 40.909 0.00 0.00 36.58 2.67
3280 3326 3.831333 TGTATGTGGGCATTTGTGATTGT 59.169 39.130 0.00 0.00 36.58 2.71
3281 3327 5.012893 TGTATGTGGGCATTTGTGATTGTA 58.987 37.500 0.00 0.00 36.58 2.41
3282 3328 5.655974 TGTATGTGGGCATTTGTGATTGTAT 59.344 36.000 0.00 0.00 36.58 2.29
3522 3571 1.153628 GCCCGACTGCTATGACGTT 60.154 57.895 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.185594 CCGTAAATCGCAGACAAAAGTGA 59.814 43.478 0.00 0.00 42.51 3.41
18 19 2.288961 TTCTCCCGTAAATCGCAGAC 57.711 50.000 0.00 0.00 42.51 3.51
22 23 1.395954 GTGGTTTCTCCCGTAAATCGC 59.604 52.381 0.00 0.00 38.35 4.58
25 26 2.301009 AGACGTGGTTTCTCCCGTAAAT 59.699 45.455 0.00 0.00 40.94 1.40
39 40 2.262915 GGAGCAGTCCAGACGTGG 59.737 66.667 0.00 0.00 46.63 4.94
52 53 2.430382 TTTGTCTCGGTCCGTGGAGC 62.430 60.000 11.88 8.03 39.05 4.70
57 58 1.619827 TGGTAATTTGTCTCGGTCCGT 59.380 47.619 11.88 0.00 0.00 4.69
59 60 2.007608 GCTGGTAATTTGTCTCGGTCC 58.992 52.381 0.00 0.00 0.00 4.46
63 64 3.432252 ACGAAAGCTGGTAATTTGTCTCG 59.568 43.478 0.00 0.00 0.00 4.04
66 67 4.675114 CACAACGAAAGCTGGTAATTTGTC 59.325 41.667 0.00 0.00 0.00 3.18
70 71 3.282831 GCACAACGAAAGCTGGTAATT 57.717 42.857 0.00 0.00 0.00 1.40
99 107 0.320073 TTCCGCAACAGTTAGGACCG 60.320 55.000 8.73 0.00 31.69 4.79
105 113 3.870419 ACGTAAACTTTCCGCAACAGTTA 59.130 39.130 0.00 0.00 30.37 2.24
106 114 2.679336 ACGTAAACTTTCCGCAACAGTT 59.321 40.909 0.00 0.00 31.90 3.16
109 122 2.008329 ACACGTAAACTTTCCGCAACA 58.992 42.857 0.00 0.00 0.00 3.33
127 140 1.555075 AGGGCATCTCTAAAGCGAACA 59.445 47.619 0.00 0.00 0.00 3.18
134 147 5.663106 AGATGTCAGTAAGGGCATCTCTAAA 59.337 40.000 4.56 0.00 42.88 1.85
137 150 3.652055 AGATGTCAGTAAGGGCATCTCT 58.348 45.455 4.56 0.00 42.88 3.10
157 170 5.048294 GGTTACTTTGGTACCCAAACATGAG 60.048 44.000 10.07 1.05 46.92 2.90
159 172 4.320641 CGGTTACTTTGGTACCCAAACATG 60.321 45.833 10.07 0.00 46.92 3.21
217 230 6.560253 ACACTGTCAAGTAAATGGTGATTC 57.440 37.500 0.00 0.00 33.79 2.52
220 233 6.413783 TCTACACTGTCAAGTAAATGGTGA 57.586 37.500 0.00 0.00 33.79 4.02
221 234 6.706270 AGTTCTACACTGTCAAGTAAATGGTG 59.294 38.462 0.00 0.00 33.79 4.17
239 252 3.125146 TGAATTGATGCGTGCAGTTCTAC 59.875 43.478 0.00 0.00 34.34 2.59
241 254 2.153645 TGAATTGATGCGTGCAGTTCT 58.846 42.857 0.00 0.00 34.34 3.01
307 320 2.079925 CTCTTGCCTTCTGTACCTTGC 58.920 52.381 0.00 0.00 0.00 4.01
373 388 0.313672 TTGCGTTTTGTCTCCATGCC 59.686 50.000 0.00 0.00 0.00 4.40
400 415 5.831997 ACAAGAGACAAATTTACCTTGCAC 58.168 37.500 15.12 0.00 35.67 4.57
404 419 9.014297 CCTCAATACAAGAGACAAATTTACCTT 57.986 33.333 0.00 0.00 35.09 3.50
423 438 1.277579 TACAACCCACGCCCTCAATA 58.722 50.000 0.00 0.00 0.00 1.90
424 439 0.623723 ATACAACCCACGCCCTCAAT 59.376 50.000 0.00 0.00 0.00 2.57
425 440 0.402504 AATACAACCCACGCCCTCAA 59.597 50.000 0.00 0.00 0.00 3.02
426 441 0.402504 AAATACAACCCACGCCCTCA 59.597 50.000 0.00 0.00 0.00 3.86
427 442 2.285977 CTAAATACAACCCACGCCCTC 58.714 52.381 0.00 0.00 0.00 4.30
436 451 3.699538 CCTTCCAAGGCCTAAATACAACC 59.300 47.826 5.16 0.00 39.76 3.77
454 469 0.519077 CGAAGCTGCTTCCAACCTTC 59.481 55.000 30.56 9.81 37.20 3.46
457 472 1.301677 CCTCGAAGCTGCTTCCAACC 61.302 60.000 30.56 11.63 37.20 3.77
461 476 1.153469 CCTCCTCGAAGCTGCTTCC 60.153 63.158 30.56 16.48 37.20 3.46
499 514 2.710220 TTACAAGAGAGCAACGCGTA 57.290 45.000 14.46 0.00 0.00 4.42
550 565 1.229359 CTCCTACGAGGGCCAGGTA 59.771 63.158 6.18 6.41 35.59 3.08
551 566 1.578215 TACTCCTACGAGGGCCAGGT 61.578 60.000 6.18 5.38 40.77 4.00
552 567 0.178958 ATACTCCTACGAGGGCCAGG 60.179 60.000 6.18 3.28 40.77 4.45
553 568 1.705873 AATACTCCTACGAGGGCCAG 58.294 55.000 6.18 0.96 40.77 4.85
554 569 1.760613 CAAATACTCCTACGAGGGCCA 59.239 52.381 6.18 0.00 40.77 5.36
555 570 1.070289 CCAAATACTCCTACGAGGGCC 59.930 57.143 0.00 0.00 40.77 5.80
556 571 1.070289 CCCAAATACTCCTACGAGGGC 59.930 57.143 0.00 0.00 40.77 5.19
557 572 2.102588 CACCCAAATACTCCTACGAGGG 59.897 54.545 0.00 0.00 40.77 4.30
559 574 3.028850 TCCACCCAAATACTCCTACGAG 58.971 50.000 0.00 0.00 42.32 4.18
561 576 3.028850 TCTCCACCCAAATACTCCTACG 58.971 50.000 0.00 0.00 0.00 3.51
596 614 1.293924 GATGTGGAGATTGGACTGCG 58.706 55.000 0.00 0.00 0.00 5.18
762 793 2.660552 AAACGTGACACCTCGGCG 60.661 61.111 0.00 0.00 33.99 6.46
857 888 1.084289 GCGAGGCGGAGTTTGTTATT 58.916 50.000 0.00 0.00 0.00 1.40
858 889 0.743345 GGCGAGGCGGAGTTTGTTAT 60.743 55.000 0.00 0.00 0.00 1.89
859 890 1.375013 GGCGAGGCGGAGTTTGTTA 60.375 57.895 0.00 0.00 0.00 2.41
914 946 2.456119 CGTTGCTTAGCGGCAGAGG 61.456 63.158 1.45 0.00 43.39 3.69
1287 1319 4.794439 CGCATGGCCGTGTCGAGA 62.794 66.667 27.24 0.00 0.00 4.04
1329 1361 2.781406 GGGAGGGAGGTGAGGAGT 59.219 66.667 0.00 0.00 0.00 3.85
1382 1426 2.002586 CGTGGTCATCATCAACCTCAC 58.997 52.381 0.00 0.00 36.47 3.51
1383 1427 1.899142 TCGTGGTCATCATCAACCTCA 59.101 47.619 0.00 0.00 36.47 3.86
1384 1428 2.544685 CTCGTGGTCATCATCAACCTC 58.455 52.381 0.00 0.00 36.47 3.85
1385 1429 1.406069 GCTCGTGGTCATCATCAACCT 60.406 52.381 0.00 0.00 36.47 3.50
1386 1430 1.009829 GCTCGTGGTCATCATCAACC 58.990 55.000 0.00 0.00 36.03 3.77
1387 1431 1.725641 TGCTCGTGGTCATCATCAAC 58.274 50.000 0.00 0.00 0.00 3.18
1388 1432 2.028203 TCTTGCTCGTGGTCATCATCAA 60.028 45.455 0.00 0.00 0.00 2.57
1389 1433 1.550072 TCTTGCTCGTGGTCATCATCA 59.450 47.619 0.00 0.00 0.00 3.07
1390 1434 1.929836 GTCTTGCTCGTGGTCATCATC 59.070 52.381 0.00 0.00 0.00 2.92
1391 1435 1.737029 CGTCTTGCTCGTGGTCATCAT 60.737 52.381 0.00 0.00 0.00 2.45
1392 1436 0.388520 CGTCTTGCTCGTGGTCATCA 60.389 55.000 0.00 0.00 0.00 3.07
1393 1437 0.109272 TCGTCTTGCTCGTGGTCATC 60.109 55.000 0.00 0.00 0.00 2.92
1394 1438 0.532573 ATCGTCTTGCTCGTGGTCAT 59.467 50.000 0.00 0.00 0.00 3.06
1395 1439 0.388520 CATCGTCTTGCTCGTGGTCA 60.389 55.000 0.00 0.00 0.00 4.02
1396 1440 0.109272 TCATCGTCTTGCTCGTGGTC 60.109 55.000 0.00 0.00 0.00 4.02
1399 1443 0.388520 TGGTCATCGTCTTGCTCGTG 60.389 55.000 0.00 0.00 0.00 4.35
1410 1454 1.019673 CCATCAGGCTTTGGTCATCG 58.980 55.000 5.28 0.00 0.00 3.84
1426 1470 2.046892 GTGAGCGCAGGTGTCCAT 60.047 61.111 11.47 0.00 39.88 3.41
1428 1472 3.537206 AAGGTGAGCGCAGGTGTCC 62.537 63.158 11.47 2.95 39.88 4.02
1702 1746 4.814294 GCCCTCGTTGTCGCCGAT 62.814 66.667 0.00 0.00 36.96 4.18
1860 1904 1.837090 GATGGCCGGGAGTATGGTT 59.163 57.895 2.18 0.00 0.00 3.67
2115 2159 1.956159 GCTCCTACTCCGACTCCTTGT 60.956 57.143 0.00 0.00 0.00 3.16
2601 2645 2.223829 CCGGTAGAAGAGCCTGTACATG 60.224 54.545 0.00 0.00 0.00 3.21
2789 2833 4.706962 GCTGTCTCCTTGTATTCCCATTTT 59.293 41.667 0.00 0.00 0.00 1.82
2799 2843 1.211969 GACGCGCTGTCTCCTTGTA 59.788 57.895 20.14 0.00 44.58 2.41
2872 2916 8.690884 GCACCAGAGATATGTATGTAGTATCAT 58.309 37.037 0.00 0.00 0.00 2.45
2873 2917 7.890655 AGCACCAGAGATATGTATGTAGTATCA 59.109 37.037 0.00 0.00 0.00 2.15
2874 2918 8.187480 CAGCACCAGAGATATGTATGTAGTATC 58.813 40.741 0.00 0.00 0.00 2.24
2875 2919 7.671819 ACAGCACCAGAGATATGTATGTAGTAT 59.328 37.037 0.00 0.00 0.00 2.12
2876 2920 7.004691 ACAGCACCAGAGATATGTATGTAGTA 58.995 38.462 0.00 0.00 0.00 1.82
2877 2921 5.835819 ACAGCACCAGAGATATGTATGTAGT 59.164 40.000 0.00 0.00 0.00 2.73
2878 2922 6.155136 CACAGCACCAGAGATATGTATGTAG 58.845 44.000 0.00 0.00 0.00 2.74
2879 2923 5.509670 GCACAGCACCAGAGATATGTATGTA 60.510 44.000 0.00 0.00 0.00 2.29
2880 2924 4.741837 GCACAGCACCAGAGATATGTATGT 60.742 45.833 0.00 0.00 0.00 2.29
2881 2925 3.744942 GCACAGCACCAGAGATATGTATG 59.255 47.826 0.00 0.00 0.00 2.39
2882 2926 3.553715 CGCACAGCACCAGAGATATGTAT 60.554 47.826 0.00 0.00 0.00 2.29
2883 2927 2.223805 CGCACAGCACCAGAGATATGTA 60.224 50.000 0.00 0.00 0.00 2.29
2884 2928 1.472201 CGCACAGCACCAGAGATATGT 60.472 52.381 0.00 0.00 0.00 2.29
2885 2929 1.215244 CGCACAGCACCAGAGATATG 58.785 55.000 0.00 0.00 0.00 1.78
3011 3055 2.342910 TACGTCTTCTTCGTTGCTCC 57.657 50.000 0.00 0.00 41.72 4.70
3031 3075 6.543465 AGACTTCGATGCATTTCAAATCCATA 59.457 34.615 0.00 0.00 0.00 2.74
3061 3105 7.333423 TGAGCCAAATCTAATACACACACTTAC 59.667 37.037 0.00 0.00 0.00 2.34
3076 3122 8.814038 AGACAAAGTTATATTGAGCCAAATCT 57.186 30.769 0.00 0.00 0.00 2.40
3108 3154 4.630894 ACTTGATGTGCTGTTCGAAAAA 57.369 36.364 0.00 0.00 0.00 1.94
3111 3157 4.350346 CAAAACTTGATGTGCTGTTCGAA 58.650 39.130 0.00 0.00 0.00 3.71
3112 3158 3.243035 CCAAAACTTGATGTGCTGTTCGA 60.243 43.478 0.00 0.00 0.00 3.71
3113 3159 3.044986 CCAAAACTTGATGTGCTGTTCG 58.955 45.455 0.00 0.00 0.00 3.95
3114 3160 4.045636 ACCAAAACTTGATGTGCTGTTC 57.954 40.909 0.00 0.00 0.00 3.18
3115 3161 4.470334 AACCAAAACTTGATGTGCTGTT 57.530 36.364 0.00 0.00 0.00 3.16
3132 3178 9.027202 GTAAAAGGACCCTATTATTTCAAACCA 57.973 33.333 0.00 0.00 0.00 3.67
3248 3294 9.360901 ACAAATGCCCACATACATGTAATATTA 57.639 29.630 10.14 0.00 39.39 0.98
3249 3295 8.143193 CACAAATGCCCACATACATGTAATATT 58.857 33.333 10.14 0.00 39.39 1.28
3250 3296 7.505248 TCACAAATGCCCACATACATGTAATAT 59.495 33.333 10.14 0.00 39.39 1.28
3251 3297 6.830838 TCACAAATGCCCACATACATGTAATA 59.169 34.615 10.14 0.00 39.39 0.98
3252 3298 5.655974 TCACAAATGCCCACATACATGTAAT 59.344 36.000 10.14 0.00 39.39 1.89
3253 3299 5.012893 TCACAAATGCCCACATACATGTAA 58.987 37.500 10.14 0.00 39.39 2.41
3254 3300 4.593956 TCACAAATGCCCACATACATGTA 58.406 39.130 8.27 8.27 39.39 2.29
3255 3301 3.429492 TCACAAATGCCCACATACATGT 58.571 40.909 2.69 2.69 42.84 3.21
3256 3302 4.659111 ATCACAAATGCCCACATACATG 57.341 40.909 0.00 0.00 34.62 3.21
3257 3303 4.467082 ACAATCACAAATGCCCACATACAT 59.533 37.500 0.00 0.00 34.62 2.29
3258 3304 3.831333 ACAATCACAAATGCCCACATACA 59.169 39.130 0.00 0.00 34.62 2.29
3259 3305 4.454728 ACAATCACAAATGCCCACATAC 57.545 40.909 0.00 0.00 34.62 2.39
3260 3306 6.154192 ACAATACAATCACAAATGCCCACATA 59.846 34.615 0.00 0.00 34.62 2.29
3261 3307 5.046448 ACAATACAATCACAAATGCCCACAT 60.046 36.000 0.00 0.00 38.49 3.21
3262 3308 4.282957 ACAATACAATCACAAATGCCCACA 59.717 37.500 0.00 0.00 0.00 4.17
3263 3309 4.626604 CACAATACAATCACAAATGCCCAC 59.373 41.667 0.00 0.00 0.00 4.61
3264 3310 4.282957 ACACAATACAATCACAAATGCCCA 59.717 37.500 0.00 0.00 0.00 5.36
3265 3311 4.819769 ACACAATACAATCACAAATGCCC 58.180 39.130 0.00 0.00 0.00 5.36
3266 3312 7.273381 GTCTAACACAATACAATCACAAATGCC 59.727 37.037 0.00 0.00 0.00 4.40
3267 3313 8.023128 AGTCTAACACAATACAATCACAAATGC 58.977 33.333 0.00 0.00 0.00 3.56
3268 3314 9.333497 CAGTCTAACACAATACAATCACAAATG 57.667 33.333 0.00 0.00 0.00 2.32
3269 3315 9.066892 ACAGTCTAACACAATACAATCACAAAT 57.933 29.630 0.00 0.00 0.00 2.32
3270 3316 8.445275 ACAGTCTAACACAATACAATCACAAA 57.555 30.769 0.00 0.00 0.00 2.83
3271 3317 9.719355 ATACAGTCTAACACAATACAATCACAA 57.281 29.630 0.00 0.00 0.00 3.33
3272 3318 9.719355 AATACAGTCTAACACAATACAATCACA 57.281 29.630 0.00 0.00 0.00 3.58
3281 3327 9.502091 ACACATGTAAATACAGTCTAACACAAT 57.498 29.630 0.00 0.00 39.92 2.71
3282 3328 8.896320 ACACATGTAAATACAGTCTAACACAA 57.104 30.769 0.00 0.00 39.92 3.33


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

AutoCloner maintained by Alex Coulton.