Multiple sequence alignment - TraesCS5D01G428200

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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 TraesCS5D01G428200 chr5D 100.000 2671 0 0 1 2671 486038329 486035659 0.000000e+00 4933.0
1 TraesCS5D01G428200 chr5D 85.588 451 63 2 1 450 76030573 76031022 3.110000e-129 472.0
2 TraesCS5D01G428200 chr5B 91.863 1106 50 15 908 2008 597087378 597086308 0.000000e+00 1507.0
3 TraesCS5D01G428200 chr5B 86.806 720 83 8 2 709 597088297 597087578 0.000000e+00 793.0
4 TraesCS5D01G428200 chr5B 94.526 274 15 0 2398 2671 597085861 597085588 8.840000e-115 424.0
5 TraesCS5D01G428200 chr5B 87.268 377 29 8 2033 2401 597086317 597085952 1.910000e-111 412.0
6 TraesCS5D01G428200 chr5B 90.476 42 4 0 1320 1361 597086872 597086831 3.710000e-04 56.5
7 TraesCS5D01G428200 chr5A 88.926 605 46 13 1760 2356 606814819 606814228 0.000000e+00 726.0
8 TraesCS5D01G428200 chr5A 93.103 290 20 0 2382 2671 606813891 606813602 2.460000e-115 425.0
9 TraesCS5D01G428200 chr7D 85.746 449 63 1 1 448 4582283 4582731 8.650000e-130 473.0
10 TraesCS5D01G428200 chr4A 86.270 437 59 1 1 436 94978346 94978782 8.650000e-130 473.0
11 TraesCS5D01G428200 chr1A 85.619 452 60 5 1 449 447639527 447639976 1.120000e-128 470.0
12 TraesCS5D01G428200 chr3D 85.523 449 63 2 2 449 601004415 601003968 4.030000e-128 468.0
13 TraesCS5D01G428200 chr3D 85.177 452 64 3 1 450 562514563 562514113 6.740000e-126 460.0
14 TraesCS5D01G428200 chr2B 86.041 437 60 1 1 436 95792389 95792825 4.030000e-128 468.0
15 TraesCS5D01G428200 chr1B 86.041 437 60 1 1 436 57805075 57805511 4.030000e-128 468.0
16 TraesCS5D01G428200 chr2D 85.714 441 62 1 1 440 113920092 113920532 5.210000e-127 464.0


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 TraesCS5D01G428200 chr5D 486035659 486038329 2670 True 4933.0 4933 100.0000 1 2671 1 chr5D.!!$R1 2670
1 TraesCS5D01G428200 chr5B 597085588 597088297 2709 True 638.5 1507 90.1878 2 2671 5 chr5B.!!$R1 2669
2 TraesCS5D01G428200 chr5A 606813602 606814819 1217 True 575.5 726 91.0145 1760 2671 2 chr5A.!!$R1 911

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
155 156 0.243907 ACAGTCGGGAAGTCATCGTG 59.756 55.0 0.00 0.00 0.00 4.35 F
234 235 0.252742 AGAACGGAGGGATCCAACCT 60.253 55.0 15.23 0.59 42.18 3.50 F
289 290 0.321653 CCGAGAAAGTCCACCAAGGG 60.322 60.0 0.00 0.00 38.24 3.95 F
393 394 0.390860 ATTCCATCTTCTCGGAGCCG 59.609 55.0 1.74 1.74 41.35 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1067 1114 0.037326 CGGCTACATCACTGTGGTGT 60.037 55.0 27.71 27.71 45.01 4.16 R
1068 1115 0.037326 ACGGCTACATCACTGTGGTG 60.037 55.0 19.03 19.03 44.23 4.17 R
1130 1181 0.461516 CGCCTCTCAGCACACATGAT 60.462 55.0 0.00 0.00 0.00 2.45 R
1717 1768 0.598419 GCAGTTGCTTCCCAGTTTGC 60.598 55.0 0.00 0.00 38.21 3.68 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
61 62 1.467035 CCACCTAGCGACGACTACAAC 60.467 57.143 0.00 0.00 0.00 3.32
71 72 3.050619 GACGACTACAACCACTGAAGTG 58.949 50.000 3.35 3.35 45.23 3.16
102 103 3.770040 CCACCGTCATCGCCCTCA 61.770 66.667 0.00 0.00 35.54 3.86
104 105 3.771160 ACCGTCATCGCCCTCACC 61.771 66.667 0.00 0.00 35.54 4.02
137 138 4.319261 CGGCCAAAACTTGTTGTAGTAGAC 60.319 45.833 2.24 0.00 0.00 2.59
139 140 5.277828 GGCCAAAACTTGTTGTAGTAGACAG 60.278 44.000 0.00 0.00 39.88 3.51
141 142 6.511282 GCCAAAACTTGTTGTAGTAGACAGTC 60.511 42.308 0.00 0.00 39.88 3.51
155 156 0.243907 ACAGTCGGGAAGTCATCGTG 59.756 55.000 0.00 0.00 0.00 4.35
156 157 0.458543 CAGTCGGGAAGTCATCGTGG 60.459 60.000 0.00 0.00 0.00 4.94
160 161 1.475280 TCGGGAAGTCATCGTGGTAAG 59.525 52.381 0.00 0.00 0.00 2.34
178 179 2.344129 GCCCTATAGGACCAGCGC 59.656 66.667 21.07 9.90 38.24 5.92
180 181 1.367840 CCCTATAGGACCAGCGCAC 59.632 63.158 21.07 0.00 38.24 5.34
181 182 1.367840 CCTATAGGACCAGCGCACC 59.632 63.158 14.11 7.54 37.39 5.01
184 185 0.686441 TATAGGACCAGCGCACCAGT 60.686 55.000 11.47 0.00 0.00 4.00
188 189 1.738099 GACCAGCGCACCAGTACAG 60.738 63.158 11.47 0.00 0.00 2.74
192 193 1.003355 AGCGCACCAGTACAGCAAT 60.003 52.632 11.47 0.00 0.00 3.56
194 195 1.982073 GCGCACCAGTACAGCAATCC 61.982 60.000 0.30 0.00 0.00 3.01
199 200 1.078497 CAGTACAGCAATCCCCGCA 60.078 57.895 0.00 0.00 0.00 5.69
211 212 0.895530 TCCCCGCAGTTGAAGAGTAG 59.104 55.000 0.00 0.00 0.00 2.57
217 218 3.190744 CCGCAGTTGAAGAGTAGTGTAGA 59.809 47.826 0.00 0.00 0.00 2.59
220 221 4.617645 GCAGTTGAAGAGTAGTGTAGAACG 59.382 45.833 0.00 0.00 0.00 3.95
234 235 0.252742 AGAACGGAGGGATCCAACCT 60.253 55.000 15.23 0.59 42.18 3.50
244 245 2.427506 GGATCCAACCTGAAGACACAC 58.572 52.381 6.95 0.00 0.00 3.82
254 255 3.181482 CCTGAAGACACACGAGCATAGAT 60.181 47.826 0.00 0.00 0.00 1.98
271 272 5.704888 CATAGATGAACTACGACCTGATCC 58.295 45.833 0.00 0.00 33.62 3.36
275 276 2.286872 GAACTACGACCTGATCCGAGA 58.713 52.381 0.00 0.00 0.00 4.04
278 279 2.683867 ACTACGACCTGATCCGAGAAAG 59.316 50.000 0.00 0.00 0.00 2.62
279 280 1.546961 ACGACCTGATCCGAGAAAGT 58.453 50.000 0.00 0.00 0.00 2.66
289 290 0.321653 CCGAGAAAGTCCACCAAGGG 60.322 60.000 0.00 0.00 38.24 3.95
297 298 2.124570 CCACCAAGGGCAGATCCG 60.125 66.667 0.00 0.00 34.94 4.18
299 300 3.011517 ACCAAGGGCAGATCCGCT 61.012 61.111 0.03 0.00 34.94 5.52
317 318 1.005037 TGCGGACACATCTCCACAC 60.005 57.895 0.00 0.00 0.00 3.82
336 337 2.782222 GCCCACCGACGATGCTAGA 61.782 63.158 0.00 0.00 0.00 2.43
337 338 2.041976 CCCACCGACGATGCTAGAT 58.958 57.895 0.00 0.00 0.00 1.98
361 362 4.849329 CCGTGACGGCGCCTAGAC 62.849 72.222 26.68 16.09 41.17 2.59
375 376 2.960163 CCTAGACGGGGAGAACCTTAT 58.040 52.381 0.00 0.00 40.03 1.73
380 381 2.438392 GACGGGGAGAACCTTATTCCAT 59.562 50.000 0.00 0.00 40.03 3.41
393 394 0.390860 ATTCCATCTTCTCGGAGCCG 59.609 55.000 1.74 1.74 41.35 5.52
417 418 2.476519 GCCGTCTCGACTTTCTGAGTAG 60.477 54.545 0.00 0.00 39.19 2.57
422 423 4.004314 TCTCGACTTTCTGAGTAGGACAG 58.996 47.826 0.00 0.00 39.19 3.51
443 444 7.234661 ACAGAAACCCTAACAAAACTCAAAA 57.765 32.000 0.00 0.00 0.00 2.44
461 474 1.826340 AAAAACATGGAAGGCGGGCC 61.826 55.000 0.18 0.18 0.00 5.80
493 506 2.041115 GCGGAAGGCAGAAGAACCC 61.041 63.158 0.00 0.00 42.87 4.11
524 537 4.847444 GAAGGAGGAGGCGGCTGC 62.847 72.222 23.28 23.28 41.71 5.25
540 553 1.342555 CTGCGACGTTTATCGGTCAA 58.657 50.000 0.00 0.00 42.49 3.18
551 564 5.791480 CGTTTATCGGTCAACCAAATTACAC 59.209 40.000 0.00 0.00 35.14 2.90
573 586 7.231467 ACACATTGTAAAACCTAGAGTTCCAT 58.769 34.615 0.00 0.00 37.88 3.41
647 660 5.912892 TGAAAGGAAAGGGTCAAACATTTC 58.087 37.500 0.00 0.00 0.00 2.17
648 661 4.584327 AAGGAAAGGGTCAAACATTTCG 57.416 40.909 0.00 0.00 33.45 3.46
652 665 2.951229 AGGGTCAAACATTTCGGACT 57.049 45.000 0.00 0.00 0.00 3.85
674 687 2.631160 AAAAGTGACACGACATGGGA 57.369 45.000 0.00 0.00 0.00 4.37
675 688 2.631160 AAAGTGACACGACATGGGAA 57.369 45.000 0.00 0.00 0.00 3.97
709 722 2.042162 AGACCACCTGGCAATCAGATTT 59.958 45.455 0.00 0.00 46.18 2.17
710 723 2.827921 GACCACCTGGCAATCAGATTTT 59.172 45.455 0.00 0.00 46.18 1.82
711 724 3.242011 ACCACCTGGCAATCAGATTTTT 58.758 40.909 0.00 0.00 46.18 1.94
735 748 5.723672 TTTTTGCGGGGTAAAATATGTCA 57.276 34.783 0.00 0.00 28.52 3.58
736 749 4.974368 TTTGCGGGGTAAAATATGTCAG 57.026 40.909 0.00 0.00 0.00 3.51
737 750 3.916359 TGCGGGGTAAAATATGTCAGA 57.084 42.857 0.00 0.00 0.00 3.27
738 751 4.431416 TGCGGGGTAAAATATGTCAGAT 57.569 40.909 0.00 0.00 0.00 2.90
739 752 4.787551 TGCGGGGTAAAATATGTCAGATT 58.212 39.130 0.00 0.00 0.00 2.40
744 757 7.623506 GCGGGGTAAAATATGTCAGATTAATCG 60.624 40.741 9.78 5.54 0.00 3.34
763 776 4.433186 TCGCACAATTATTGGAGTTTGG 57.567 40.909 9.88 0.00 34.12 3.28
799 815 8.825667 ATTTGTTTATTTGTCAGGCGTTTATT 57.174 26.923 0.00 0.00 0.00 1.40
800 816 8.649973 TTTGTTTATTTGTCAGGCGTTTATTT 57.350 26.923 0.00 0.00 0.00 1.40
801 817 8.649973 TTGTTTATTTGTCAGGCGTTTATTTT 57.350 26.923 0.00 0.00 0.00 1.82
834 850 3.552604 TTTTGTATGCTGCCGACTTTC 57.447 42.857 0.00 0.00 0.00 2.62
844 860 1.820581 CCGACTTTCATAGGCCCGA 59.179 57.895 0.00 0.00 0.00 5.14
870 886 6.784031 AGAAGAGAAACAATGTACCATTCCT 58.216 36.000 0.00 0.00 0.00 3.36
876 892 4.487714 ACAATGTACCATTCCTCGTCAT 57.512 40.909 0.00 0.00 0.00 3.06
878 894 5.984725 ACAATGTACCATTCCTCGTCATTA 58.015 37.500 0.00 0.00 0.00 1.90
999 1046 8.294577 ACAATACATATGTCGACGTGTATACAT 58.705 33.333 26.96 18.21 36.92 2.29
1067 1114 5.865085 AGAACAAATACTCTGTGGTAGCAA 58.135 37.500 0.00 0.00 0.00 3.91
1068 1115 5.701290 AGAACAAATACTCTGTGGTAGCAAC 59.299 40.000 0.00 0.00 0.00 4.17
1091 1142 1.014044 ACAGTGATGTAGCCGTTGCG 61.014 55.000 0.00 0.00 44.33 4.85
1129 1180 4.579869 AGTATCGACATGGCAAAAGAACT 58.420 39.130 0.00 0.00 0.00 3.01
1130 1181 5.730550 AGTATCGACATGGCAAAAGAACTA 58.269 37.500 0.00 0.00 0.00 2.24
1133 1184 4.574892 TCGACATGGCAAAAGAACTATCA 58.425 39.130 0.00 0.00 0.00 2.15
1207 1258 0.548031 ACATTGATGCTCGGGATGGT 59.452 50.000 0.00 0.00 0.00 3.55
1253 1304 0.950071 GCACAACAATTGCGGGCATT 60.950 50.000 15.80 0.00 0.00 3.56
1285 1336 0.031994 AACTTTGGCACGACAATGGC 59.968 50.000 3.82 0.00 45.14 4.40
1315 1366 0.820891 GGCATCGTCATCTTGGGCAT 60.821 55.000 0.00 0.00 0.00 4.40
1328 1379 0.482446 TGGGCATGGAAGGAACAACT 59.518 50.000 0.00 0.00 0.00 3.16
1333 1384 2.173519 CATGGAAGGAACAACTGGCAT 58.826 47.619 0.00 0.00 0.00 4.40
1358 1409 3.550431 AGTGTCACCTGCGGCACT 61.550 61.111 0.00 0.00 37.36 4.40
1370 1421 3.064324 GGCACTGTGGGCATGGTC 61.064 66.667 10.21 0.00 0.00 4.02
1372 1423 2.747460 CACTGTGGGCATGGTCGG 60.747 66.667 0.00 0.00 0.00 4.79
1389 1440 2.890474 GCATAGGTGGCACGGTCG 60.890 66.667 12.17 1.41 0.00 4.79
1414 1465 2.034066 CACCGTGGGAACAGGCAT 59.966 61.111 0.00 0.00 44.71 4.40
1466 1517 4.418328 GTGGGCACGGTGGGCATA 62.418 66.667 10.60 0.00 34.52 3.14
1467 1518 4.108299 TGGGCACGGTGGGCATAG 62.108 66.667 10.60 0.00 34.52 2.23
1468 1519 4.875713 GGGCACGGTGGGCATAGG 62.876 72.222 10.60 0.00 34.52 2.57
1469 1520 4.109675 GGCACGGTGGGCATAGGT 62.110 66.667 10.60 0.00 0.00 3.08
1470 1521 2.824041 GCACGGTGGGCATAGGTG 60.824 66.667 10.60 0.00 0.00 4.00
1471 1522 2.124736 CACGGTGGGCATAGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
1480 1531 1.153168 GCATAGGTGGCACGGTCAT 60.153 57.895 12.17 0.00 0.00 3.06
1588 1639 4.683334 GTCGGCCAAGTTGCGTGC 62.683 66.667 2.24 0.00 0.00 5.34
1615 1666 0.668706 CACGTGTTGCTGGAGAGGAG 60.669 60.000 7.58 0.00 0.00 3.69
1717 1768 3.123804 GGATGGCTTACTGTCGTGTATG 58.876 50.000 0.00 0.00 0.00 2.39
1718 1769 2.004583 TGGCTTACTGTCGTGTATGC 57.995 50.000 11.87 11.87 40.56 3.14
1786 1837 1.009335 CCGATGTCAATGCATGGCG 60.009 57.895 0.00 0.00 36.00 5.69
1836 1888 2.432628 GGTCGTTGGCCAGACTCG 60.433 66.667 20.92 16.82 37.52 4.18
1860 1912 1.160137 GGTAGGCAGCACAACTTCTG 58.840 55.000 0.00 0.00 0.00 3.02
1913 1965 6.071463 GTGTACGTTAGTGAGAAAAATGCAG 58.929 40.000 0.00 0.00 0.00 4.41
2006 2060 3.775661 AATAAAAATGCTAACGCGGCT 57.224 38.095 12.47 0.00 39.65 5.52
2010 2064 1.369091 AAATGCTAACGCGGCTCTGG 61.369 55.000 12.47 0.00 39.65 3.86
2022 2076 0.322816 GGCTCTGGTGATCTTTGGCA 60.323 55.000 0.00 0.00 0.00 4.92
2071 2125 2.414138 GCATTTGGATGTGCTTTGCTTC 59.586 45.455 0.00 0.00 38.30 3.86
2072 2126 3.863400 GCATTTGGATGTGCTTTGCTTCT 60.863 43.478 0.00 0.00 38.30 2.85
2073 2127 4.312443 CATTTGGATGTGCTTTGCTTCTT 58.688 39.130 0.00 0.00 0.00 2.52
2074 2128 4.405116 TTTGGATGTGCTTTGCTTCTTT 57.595 36.364 0.00 0.00 0.00 2.52
2075 2129 3.648339 TGGATGTGCTTTGCTTCTTTC 57.352 42.857 0.00 0.00 0.00 2.62
2076 2130 3.225104 TGGATGTGCTTTGCTTCTTTCT 58.775 40.909 0.00 0.00 0.00 2.52
2077 2131 3.638160 TGGATGTGCTTTGCTTCTTTCTT 59.362 39.130 0.00 0.00 0.00 2.52
2078 2132 4.099881 TGGATGTGCTTTGCTTCTTTCTTT 59.900 37.500 0.00 0.00 0.00 2.52
2079 2133 5.052481 GGATGTGCTTTGCTTCTTTCTTTT 58.948 37.500 0.00 0.00 0.00 2.27
2113 2174 6.639563 TCAAGACGATTTGATTACATCCTGA 58.360 36.000 0.00 0.00 32.39 3.86
2226 2290 5.566469 TCTTTGGACGAATGAAATAAGGGT 58.434 37.500 0.00 0.00 0.00 4.34
2333 2402 0.109597 GACAATGAGGCAAACCAGCG 60.110 55.000 0.00 0.00 39.06 5.18
2374 2747 0.529773 TTTCCGCGTGGCAGCTATAG 60.530 55.000 11.05 0.00 34.14 1.31
2376 2749 1.227263 CCGCGTGGCAGCTATAGTT 60.227 57.895 0.00 0.00 34.40 2.24
2377 2750 1.215655 CCGCGTGGCAGCTATAGTTC 61.216 60.000 0.00 0.00 34.40 3.01
2380 2753 1.478137 CGTGGCAGCTATAGTTCGAC 58.522 55.000 0.84 0.00 0.00 4.20
2430 2904 1.140652 CCAACCACCCAAGCATGTTTT 59.859 47.619 0.00 0.00 0.00 2.43
2490 2964 6.241385 CGTCAAATTATCTCCTTTTCACGTC 58.759 40.000 0.00 0.00 0.00 4.34
2531 3005 1.664016 GCCAACATGACTCGCAACAAG 60.664 52.381 0.00 0.00 0.00 3.16
2546 3020 3.181491 GCAACAAGCTGAGTAAACCAACA 60.181 43.478 0.00 0.00 41.15 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.251354 TCGTCGCTAGGTGGTCTACT 59.749 55.000 0.00 0.00 0.00 2.57
61 62 1.805869 CCTTCTGCTCACTTCAGTGG 58.194 55.000 7.11 0.00 45.65 4.00
89 90 4.873129 CGGGTGAGGGCGATGACG 62.873 72.222 0.00 0.00 42.93 4.35
116 117 5.296035 ACTGTCTACTACAACAAGTTTTGGC 59.704 40.000 0.00 0.00 37.74 4.52
117 118 6.292168 CGACTGTCTACTACAACAAGTTTTGG 60.292 42.308 6.21 0.00 37.74 3.28
124 125 3.489355 TCCCGACTGTCTACTACAACAA 58.511 45.455 6.21 0.00 37.74 2.83
137 138 0.458543 CCACGATGACTTCCCGACTG 60.459 60.000 0.00 0.00 0.00 3.51
139 140 0.813184 TACCACGATGACTTCCCGAC 59.187 55.000 0.00 0.00 0.00 4.79
141 142 1.470979 CCTTACCACGATGACTTCCCG 60.471 57.143 0.00 0.00 0.00 5.14
176 177 1.369091 GGGATTGCTGTACTGGTGCG 61.369 60.000 1.65 0.00 0.00 5.34
178 179 0.744414 CGGGGATTGCTGTACTGGTG 60.744 60.000 1.65 0.00 0.00 4.17
180 181 1.819632 GCGGGGATTGCTGTACTGG 60.820 63.158 1.65 0.00 0.00 4.00
181 182 1.078497 TGCGGGGATTGCTGTACTG 60.078 57.895 0.00 0.00 0.00 2.74
184 185 0.676466 CAACTGCGGGGATTGCTGTA 60.676 55.000 0.00 0.00 42.63 2.74
188 189 0.960364 TCTTCAACTGCGGGGATTGC 60.960 55.000 0.00 0.00 0.00 3.56
192 193 0.895530 CTACTCTTCAACTGCGGGGA 59.104 55.000 0.00 0.00 0.00 4.81
194 195 1.000955 ACACTACTCTTCAACTGCGGG 59.999 52.381 0.00 0.00 0.00 6.13
199 200 5.068636 TCCGTTCTACACTACTCTTCAACT 58.931 41.667 0.00 0.00 0.00 3.16
211 212 1.481871 TGGATCCCTCCGTTCTACAC 58.518 55.000 9.90 0.00 45.37 2.90
217 218 0.546747 TCAGGTTGGATCCCTCCGTT 60.547 55.000 9.90 0.00 45.37 4.44
220 221 1.210722 GTCTTCAGGTTGGATCCCTCC 59.789 57.143 9.90 11.60 42.45 4.30
234 235 3.443681 TCATCTATGCTCGTGTGTCTTCA 59.556 43.478 0.00 0.00 0.00 3.02
244 245 3.251245 AGGTCGTAGTTCATCTATGCTCG 59.749 47.826 0.00 0.00 36.05 5.03
254 255 2.014857 CTCGGATCAGGTCGTAGTTCA 58.985 52.381 0.00 0.00 0.00 3.18
271 272 0.955919 GCCCTTGGTGGACTTTCTCG 60.956 60.000 0.00 0.00 38.35 4.04
275 276 0.779997 ATCTGCCCTTGGTGGACTTT 59.220 50.000 0.00 0.00 38.35 2.66
278 279 1.077429 GGATCTGCCCTTGGTGGAC 60.077 63.158 0.00 0.00 38.35 4.02
279 280 2.669133 CGGATCTGCCCTTGGTGGA 61.669 63.158 0.00 0.00 38.35 4.02
297 298 2.103042 GTGGAGATGTGTCCGCAGC 61.103 63.158 5.01 0.00 45.16 5.25
300 301 2.094659 CGTGTGGAGATGTGTCCGC 61.095 63.158 3.01 3.01 45.91 5.54
301 302 2.094659 GCGTGTGGAGATGTGTCCG 61.095 63.158 0.00 0.00 39.81 4.79
302 303 1.741770 GGCGTGTGGAGATGTGTCC 60.742 63.158 0.00 0.00 37.10 4.02
317 318 4.201679 TAGCATCGTCGGTGGGCG 62.202 66.667 7.76 0.00 0.00 6.13
346 347 4.849329 CCGTCTAGGCGCCGTCAC 62.849 72.222 23.20 17.17 0.00 3.67
352 353 3.145551 TTCTCCCCGTCTAGGCGC 61.146 66.667 12.24 0.00 39.21 6.53
353 354 2.783288 GGTTCTCCCCGTCTAGGCG 61.783 68.421 10.46 10.46 39.21 5.52
355 356 2.449137 TAAGGTTCTCCCCGTCTAGG 57.551 55.000 0.00 0.00 40.63 3.02
361 362 2.706190 AGATGGAATAAGGTTCTCCCCG 59.294 50.000 0.00 0.00 0.00 5.73
370 371 3.556004 GGCTCCGAGAAGATGGAATAAGG 60.556 52.174 0.00 0.00 32.89 2.69
375 376 1.816537 CGGCTCCGAGAAGATGGAA 59.183 57.895 1.35 0.00 42.83 3.53
393 394 3.179939 GAAAGTCGAGACGGCGGC 61.180 66.667 13.24 8.92 36.23 6.53
398 399 3.001414 TCCTACTCAGAAAGTCGAGACG 58.999 50.000 0.00 0.00 39.55 4.18
409 410 3.544698 AGGGTTTCTGTCCTACTCAGA 57.455 47.619 0.00 0.00 39.71 3.27
417 418 4.885325 TGAGTTTTGTTAGGGTTTCTGTCC 59.115 41.667 0.00 0.00 0.00 4.02
443 444 2.282783 GGCCCGCCTTCCATGTTTT 61.283 57.895 0.00 0.00 0.00 2.43
477 490 1.210722 CCTAGGGTTCTTCTGCCTTCC 59.789 57.143 0.00 0.00 0.00 3.46
479 492 0.621082 GCCTAGGGTTCTTCTGCCTT 59.379 55.000 11.72 0.00 0.00 4.35
483 496 3.441500 AAAAGGCCTAGGGTTCTTCTG 57.558 47.619 5.16 0.00 0.00 3.02
519 532 1.749609 GACCGATAAACGTCGCAGCC 61.750 60.000 0.00 0.00 40.17 4.85
524 537 1.700523 TGGTTGACCGATAAACGTCG 58.299 50.000 0.00 0.00 40.78 5.12
540 553 9.357161 TCTAGGTTTTACAATGTGTAATTTGGT 57.643 29.630 0.00 0.00 41.83 3.67
551 564 6.150976 TGCATGGAACTCTAGGTTTTACAATG 59.849 38.462 0.00 0.00 38.41 2.82
613 626 7.947890 TGACCCTTTCCTTTCAGTTTACAATAT 59.052 33.333 0.00 0.00 0.00 1.28
647 660 2.034001 GTCGTGTCACTTTTTCAGTCCG 60.034 50.000 0.65 0.00 30.92 4.79
648 661 2.933906 TGTCGTGTCACTTTTTCAGTCC 59.066 45.455 0.65 0.00 30.92 3.85
652 665 2.616376 CCCATGTCGTGTCACTTTTTCA 59.384 45.455 0.65 0.00 0.00 2.69
713 726 5.477291 TCTGACATATTTTACCCCGCAAAAA 59.523 36.000 0.00 0.00 0.00 1.94
714 727 5.010933 TCTGACATATTTTACCCCGCAAAA 58.989 37.500 0.00 0.00 0.00 2.44
715 728 4.590918 TCTGACATATTTTACCCCGCAAA 58.409 39.130 0.00 0.00 0.00 3.68
716 729 4.223556 TCTGACATATTTTACCCCGCAA 57.776 40.909 0.00 0.00 0.00 4.85
717 730 3.916359 TCTGACATATTTTACCCCGCA 57.084 42.857 0.00 0.00 0.00 5.69
718 731 6.870971 TTAATCTGACATATTTTACCCCGC 57.129 37.500 0.00 0.00 0.00 6.13
719 732 7.623506 GCGATTAATCTGACATATTTTACCCCG 60.624 40.741 13.45 0.00 0.00 5.73
720 733 7.174253 TGCGATTAATCTGACATATTTTACCCC 59.826 37.037 13.45 0.00 0.00 4.95
721 734 8.015658 GTGCGATTAATCTGACATATTTTACCC 58.984 37.037 13.45 0.00 0.00 3.69
722 735 8.556194 TGTGCGATTAATCTGACATATTTTACC 58.444 33.333 13.45 0.00 0.00 2.85
723 736 9.929722 TTGTGCGATTAATCTGACATATTTTAC 57.070 29.630 13.45 0.00 0.00 2.01
730 743 8.077991 CCAATAATTGTGCGATTAATCTGACAT 58.922 33.333 13.45 4.96 0.00 3.06
731 744 7.281999 TCCAATAATTGTGCGATTAATCTGACA 59.718 33.333 13.45 11.90 0.00 3.58
732 745 7.639039 TCCAATAATTGTGCGATTAATCTGAC 58.361 34.615 13.45 9.67 0.00 3.51
733 746 7.498900 ACTCCAATAATTGTGCGATTAATCTGA 59.501 33.333 13.45 0.00 0.00 3.27
734 747 7.642669 ACTCCAATAATTGTGCGATTAATCTG 58.357 34.615 13.45 8.13 0.00 2.90
735 748 7.807977 ACTCCAATAATTGTGCGATTAATCT 57.192 32.000 13.45 0.00 0.00 2.40
736 749 8.745837 CAAACTCCAATAATTGTGCGATTAATC 58.254 33.333 5.30 5.30 0.00 1.75
737 750 7.706179 CCAAACTCCAATAATTGTGCGATTAAT 59.294 33.333 0.00 0.00 0.00 1.40
738 751 7.032580 CCAAACTCCAATAATTGTGCGATTAA 58.967 34.615 0.00 0.00 0.00 1.40
739 752 6.151985 ACCAAACTCCAATAATTGTGCGATTA 59.848 34.615 0.00 0.00 0.00 1.75
744 757 7.954788 TTTAACCAAACTCCAATAATTGTGC 57.045 32.000 0.00 0.00 0.00 4.57
801 817 6.646240 GCAGCATACAAAATCTGAAGGAAAAA 59.354 34.615 0.00 0.00 0.00 1.94
823 839 0.815615 GGGCCTATGAAAGTCGGCAG 60.816 60.000 0.84 0.00 44.23 4.85
834 850 3.543680 TTCTCTTCTTTCGGGCCTATG 57.456 47.619 0.84 0.00 0.00 2.23
870 886 9.647797 ACTATTGTACATCAAAGTTAATGACGA 57.352 29.630 0.00 1.51 39.62 4.20
906 922 7.786118 GCAACATTTCTACGTGTATATGTTACG 59.214 37.037 15.65 0.00 42.98 3.18
1021 1068 7.847487 TCTTTTCAAGTGTATGTCTTACGTTG 58.153 34.615 0.00 0.00 33.15 4.10
1024 1071 7.847487 TGTTCTTTTCAAGTGTATGTCTTACG 58.153 34.615 0.00 0.00 33.15 3.18
1067 1114 0.037326 CGGCTACATCACTGTGGTGT 60.037 55.000 27.71 27.71 45.01 4.16
1068 1115 0.037326 ACGGCTACATCACTGTGGTG 60.037 55.000 19.03 19.03 44.23 4.17
1086 1137 1.793613 GCGCACTTCATGTCGCAAC 60.794 57.895 0.30 0.00 46.43 4.17
1091 1142 1.438651 TACTTGGCGCACTTCATGTC 58.561 50.000 10.83 0.00 0.00 3.06
1129 1180 1.202452 CGCCTCTCAGCACACATGATA 60.202 52.381 0.00 0.00 0.00 2.15
1130 1181 0.461516 CGCCTCTCAGCACACATGAT 60.462 55.000 0.00 0.00 0.00 2.45
1133 1184 2.435586 GCGCCTCTCAGCACACAT 60.436 61.111 0.00 0.00 0.00 3.21
1174 1225 1.472082 TCAATGTGCCTATGCCGTTTG 59.528 47.619 0.00 0.00 36.33 2.93
1207 1258 1.760029 TGACAATGCCGCAGATACCTA 59.240 47.619 0.00 0.00 0.00 3.08
1253 1304 1.530419 AAAGTTGACCATGCCGCCA 60.530 52.632 0.00 0.00 0.00 5.69
1315 1366 2.290896 CCTATGCCAGTTGTTCCTTCCA 60.291 50.000 0.00 0.00 0.00 3.53
1328 1379 3.680620 GACACTGCCGCCTATGCCA 62.681 63.158 0.00 0.00 0.00 4.92
1333 1384 2.603473 AGGTGACACTGCCGCCTA 60.603 61.111 5.39 0.00 42.27 3.93
1358 1409 2.607411 CTATGCCGACCATGCCCACA 62.607 60.000 0.00 0.00 35.34 4.17
1370 1421 4.467084 ACCGTGCCACCTATGCCG 62.467 66.667 0.00 0.00 0.00 5.69
1372 1423 2.890474 CGACCGTGCCACCTATGC 60.890 66.667 0.00 0.00 0.00 3.14
1449 1500 4.418328 TATGCCCACCGTGCCCAC 62.418 66.667 0.00 0.00 0.00 4.61
1450 1501 4.108299 CTATGCCCACCGTGCCCA 62.108 66.667 0.00 0.00 0.00 5.36
1451 1502 4.875713 CCTATGCCCACCGTGCCC 62.876 72.222 0.00 0.00 0.00 5.36
1452 1503 4.109675 ACCTATGCCCACCGTGCC 62.110 66.667 0.00 0.00 0.00 5.01
1453 1504 2.824041 CACCTATGCCCACCGTGC 60.824 66.667 0.00 0.00 0.00 5.34
1454 1505 2.124736 CCACCTATGCCCACCGTG 60.125 66.667 0.00 0.00 0.00 4.94
1455 1506 4.109675 GCCACCTATGCCCACCGT 62.110 66.667 0.00 0.00 0.00 4.83
1456 1507 4.108299 TGCCACCTATGCCCACCG 62.108 66.667 0.00 0.00 0.00 4.94
1457 1508 2.440247 GTGCCACCTATGCCCACC 60.440 66.667 0.00 0.00 0.00 4.61
1458 1509 2.824041 CGTGCCACCTATGCCCAC 60.824 66.667 0.00 0.00 0.00 4.61
1459 1510 4.108299 CCGTGCCACCTATGCCCA 62.108 66.667 0.00 0.00 0.00 5.36
1460 1511 4.109675 ACCGTGCCACCTATGCCC 62.110 66.667 0.00 0.00 0.00 5.36
1461 1512 2.513897 GACCGTGCCACCTATGCC 60.514 66.667 0.00 0.00 0.00 4.40
1462 1513 1.153168 ATGACCGTGCCACCTATGC 60.153 57.895 0.00 0.00 0.00 3.14
1463 1514 0.815213 CCATGACCGTGCCACCTATG 60.815 60.000 0.00 0.00 0.00 2.23
1464 1515 1.526887 CCATGACCGTGCCACCTAT 59.473 57.895 0.00 0.00 0.00 2.57
1465 1516 2.986290 CCATGACCGTGCCACCTA 59.014 61.111 0.00 0.00 0.00 3.08
1466 1517 4.722700 GCCATGACCGTGCCACCT 62.723 66.667 0.00 0.00 0.00 4.00
1475 1526 4.722700 ACAGTGCCGGCCATGACC 62.723 66.667 28.78 9.58 0.00 4.02
1497 1548 2.594592 GACCTTGCCGGCAGTTGT 60.595 61.111 30.75 26.00 35.61 3.32
1498 1549 3.726517 CGACCTTGCCGGCAGTTG 61.727 66.667 30.75 23.83 35.61 3.16
1555 1606 1.810532 GACACTACTCCTCCGGCTG 59.189 63.158 0.00 0.00 0.00 4.85
1684 1735 3.584733 AAGCCATCCCAGATAAACTCC 57.415 47.619 0.00 0.00 0.00 3.85
1690 1741 2.628178 CGACAGTAAGCCATCCCAGATA 59.372 50.000 0.00 0.00 0.00 1.98
1691 1742 1.414181 CGACAGTAAGCCATCCCAGAT 59.586 52.381 0.00 0.00 0.00 2.90
1696 1747 2.953466 TACACGACAGTAAGCCATCC 57.047 50.000 0.00 0.00 0.00 3.51
1717 1768 0.598419 GCAGTTGCTTCCCAGTTTGC 60.598 55.000 0.00 0.00 38.21 3.68
1718 1769 0.746063 TGCAGTTGCTTCCCAGTTTG 59.254 50.000 5.62 0.00 42.66 2.93
1786 1837 2.786777 CCATTACCGGGGCTATAAACC 58.213 52.381 6.32 0.00 0.00 3.27
1798 1850 3.003689 CCAATCTAAGCAAGCCATTACCG 59.996 47.826 0.00 0.00 0.00 4.02
1836 1888 1.301401 TTGTGCTGCCTACCACGAC 60.301 57.895 0.00 0.00 34.77 4.34
1913 1965 1.109323 CCGGGAATTTGAGCCATCCC 61.109 60.000 0.00 0.00 46.69 3.85
1958 2010 3.728385 ATAAGGAAAGTTGAGCCAGCT 57.272 42.857 0.00 0.00 0.00 4.24
1959 2011 4.013050 AGAATAAGGAAAGTTGAGCCAGC 58.987 43.478 0.00 0.00 0.00 4.85
1960 2012 5.006386 ACAGAATAAGGAAAGTTGAGCCAG 58.994 41.667 0.00 0.00 0.00 4.85
1961 2013 4.985538 ACAGAATAAGGAAAGTTGAGCCA 58.014 39.130 0.00 0.00 0.00 4.75
1962 2014 5.003804 TGACAGAATAAGGAAAGTTGAGCC 58.996 41.667 0.00 0.00 0.00 4.70
2006 2060 2.886523 CACTTTGCCAAAGATCACCAGA 59.113 45.455 23.32 0.00 41.02 3.86
2010 2064 5.125100 TCATTCACTTTGCCAAAGATCAC 57.875 39.130 23.32 0.00 41.02 3.06
2022 2076 2.224523 TGGAGCCGAGTTCATTCACTTT 60.225 45.455 0.00 0.00 0.00 2.66
2101 2162 7.254590 CCGAAAAGAATCAGTCAGGATGTAATC 60.255 40.741 0.00 0.00 44.55 1.75
2113 2174 2.372172 ACTGGTCCCGAAAAGAATCAGT 59.628 45.455 0.00 0.00 0.00 3.41
2206 2270 7.113437 TCAATACCCTTATTTCATTCGTCCAA 58.887 34.615 0.00 0.00 0.00 3.53
2333 2402 6.481434 AAAGTGTCCTCCACCTACATATAC 57.519 41.667 0.00 0.00 45.74 1.47
2356 2425 1.067416 CTATAGCTGCCACGCGGAA 59.933 57.895 12.47 0.00 37.02 4.30
2357 2426 1.672854 AACTATAGCTGCCACGCGGA 61.673 55.000 12.47 0.00 37.02 5.54
2380 2753 5.808042 ATGTACAAAGACAAGCTGCTATG 57.192 39.130 0.90 6.44 31.83 2.23
2430 2904 1.285667 TGTGGTGGATAGGTCGGACTA 59.714 52.381 8.23 0.00 0.00 2.59
2490 2964 2.563179 CAACCCCCGACTATCTATCTGG 59.437 54.545 0.00 0.00 0.00 3.86
2531 3005 5.065988 TGTTCTCTTTGTTGGTTTACTCAGC 59.934 40.000 0.00 0.00 0.00 4.26
2539 3013 6.099341 GTCATGTTTGTTCTCTTTGTTGGTT 58.901 36.000 0.00 0.00 0.00 3.67
2546 3020 9.883142 TTTTATTTGGTCATGTTTGTTCTCTTT 57.117 25.926 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.