Multiple sequence alignment - TraesCS6B01G339300

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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 TraesCS6B01G339300 chr6B 100.000 3289 0 0 1 3289 598449949 598453237 0.000000e+00 6074
1 TraesCS6B01G339300 chr6D 93.090 1505 68 19 105 1596 399758505 399759986 0.000000e+00 2170
2 TraesCS6B01G339300 chr6D 88.697 982 47 15 1660 2592 399759984 399760950 0.000000e+00 1140
3 TraesCS6B01G339300 chr6D 84.551 712 47 34 2635 3289 399760948 399761653 0.000000e+00 647
4 TraesCS6B01G339300 chr6D 95.890 73 1 2 1 73 399758434 399758504 2.070000e-22 117
5 TraesCS6B01G339300 chr6A 88.942 1682 88 43 1666 3289 545648664 545650305 0.000000e+00 1986
6 TraesCS6B01G339300 chr6A 93.974 1062 39 14 535 1586 545647612 545648658 0.000000e+00 1583
7 TraesCS6B01G339300 chr6A 87.129 404 38 7 102 501 545646851 545647244 2.330000e-121 446
8 TraesCS6B01G339300 chr6A 96.774 62 2 0 1 62 545646795 545646856 1.610000e-18 104
9 TraesCS6B01G339300 chr7B 83.871 279 36 8 990 1268 113060445 113060714 1.170000e-64 257
10 TraesCS6B01G339300 chr7D 82.979 282 36 7 990 1268 150900634 150900906 9.120000e-61 244
11 TraesCS6B01G339300 chr7A 83.456 272 33 8 1000 1268 150559748 150560010 3.280000e-60 243


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 TraesCS6B01G339300 chr6B 598449949 598453237 3288 False 6074.00 6074 100.00000 1 3289 1 chr6B.!!$F1 3288
1 TraesCS6B01G339300 chr6D 399758434 399761653 3219 False 1018.50 2170 90.55700 1 3289 4 chr6D.!!$F1 3288
2 TraesCS6B01G339300 chr6A 545646795 545650305 3510 False 1029.75 1986 91.70475 1 3289 4 chr6A.!!$F1 3288

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
403 406 0.102663 TAGTGCACGACGACCAACAA 59.897 50.0 12.01 0.00 0.00 2.83 F
753 1100 0.179145 ATCGCGAGGTCGAAAACGAT 60.179 50.0 16.66 5.28 42.15 3.73 F
1288 1639 0.242825 CAACGGTAGGCTTCGAGTCA 59.757 55.0 15.06 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1628 0.173708 AGAATCGGTGACTCGAAGCC 59.826 55.0 0.69 0.00 42.69 4.35 R
1605 1956 0.246635 TTTTTCCGGCGGAGAGAGAG 59.753 55.0 29.30 0.00 31.21 3.20 R
3032 3504 0.504384 CAGTATTCAATCGCCGCGAG 59.496 55.0 21.61 8.65 39.91 5.03 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
67 68 2.093075 ACAAGGGCAGATCAGTCATGAG 60.093 50.000 0.00 0.00 39.29 2.90
72 73 3.760684 GGGCAGATCAGTCATGAGTTTTT 59.239 43.478 0.00 0.00 39.29 1.94
100 101 1.821216 TTTTTGCGGGGAGATCAGTC 58.179 50.000 0.00 0.00 0.00 3.51
101 102 0.690192 TTTTGCGGGGAGATCAGTCA 59.310 50.000 0.00 0.00 0.00 3.41
102 103 0.911769 TTTGCGGGGAGATCAGTCAT 59.088 50.000 0.00 0.00 0.00 3.06
109 110 2.503356 GGGGAGATCAGTCATGAGTTGT 59.497 50.000 0.00 0.00 39.29 3.32
168 169 2.989639 CCTCTCCGTGGCATTCCA 59.010 61.111 0.00 0.00 40.85 3.53
169 170 1.528824 CCTCTCCGTGGCATTCCAT 59.471 57.895 0.00 0.00 45.62 3.41
170 171 0.107017 CCTCTCCGTGGCATTCCATT 60.107 55.000 0.00 0.00 45.62 3.16
171 172 1.303309 CTCTCCGTGGCATTCCATTC 58.697 55.000 0.00 0.00 45.62 2.67
288 289 3.049674 CATTCGGTGCGTGGTGCT 61.050 61.111 0.00 0.00 46.63 4.40
293 294 0.814410 TCGGTGCGTGGTGCTTTTAA 60.814 50.000 0.00 0.00 46.63 1.52
306 307 4.084380 GGTGCTTTTAATTCTTGCTGTTGC 60.084 41.667 0.00 0.00 40.20 4.17
308 309 3.121778 GCTTTTAATTCTTGCTGTTGCGG 59.878 43.478 0.00 0.00 43.34 5.69
311 312 0.318955 AATTCTTGCTGTTGCGGTGC 60.319 50.000 0.00 0.00 43.34 5.01
348 351 3.735746 GTGCAGGTGAATAGCAACAAAAC 59.264 43.478 0.00 0.00 40.35 2.43
350 353 4.824537 TGCAGGTGAATAGCAACAAAACTA 59.175 37.500 0.00 0.00 36.36 2.24
359 362 1.066908 GCAACAAAACTAGCACTGCCA 59.933 47.619 0.00 0.00 0.00 4.92
393 396 2.556257 TGCTTCAAGTTTAGTGCACGA 58.444 42.857 12.01 2.52 0.00 4.35
394 397 2.286833 TGCTTCAAGTTTAGTGCACGAC 59.713 45.455 12.01 11.71 0.00 4.34
395 398 2.659291 GCTTCAAGTTTAGTGCACGACG 60.659 50.000 12.01 0.00 0.00 5.12
396 399 2.495409 TCAAGTTTAGTGCACGACGA 57.505 45.000 12.01 3.33 0.00 4.20
403 406 0.102663 TAGTGCACGACGACCAACAA 59.897 50.000 12.01 0.00 0.00 2.83
407 410 1.185189 GCACGACGACCAACAAAAAC 58.815 50.000 0.00 0.00 0.00 2.43
414 417 1.555477 GACCAACAAAAACTGCACGG 58.445 50.000 0.00 0.00 0.00 4.94
416 419 1.754226 ACCAACAAAAACTGCACGGAT 59.246 42.857 0.00 0.00 0.00 4.18
433 436 4.451774 CACGGATGAATGCCAAACAATTTT 59.548 37.500 0.00 0.00 0.00 1.82
434 437 5.049543 CACGGATGAATGCCAAACAATTTTT 60.050 36.000 0.00 0.00 0.00 1.94
435 438 6.146837 CACGGATGAATGCCAAACAATTTTTA 59.853 34.615 0.00 0.00 0.00 1.52
437 440 6.545508 GGATGAATGCCAAACAATTTTTAGC 58.454 36.000 0.00 0.00 0.00 3.09
440 443 2.760374 TGCCAAACAATTTTTAGCGGG 58.240 42.857 0.00 0.00 0.00 6.13
442 445 2.549134 GCCAAACAATTTTTAGCGGGGT 60.549 45.455 0.00 0.00 0.00 4.95
444 447 3.063485 CAAACAATTTTTAGCGGGGTGG 58.937 45.455 0.00 0.00 0.00 4.61
445 448 2.296073 ACAATTTTTAGCGGGGTGGA 57.704 45.000 0.00 0.00 0.00 4.02
446 449 2.815158 ACAATTTTTAGCGGGGTGGAT 58.185 42.857 0.00 0.00 0.00 3.41
455 458 2.694616 GGGGTGGATGTAGGCCCA 60.695 66.667 0.00 0.00 42.79 5.36
457 460 2.001269 GGGTGGATGTAGGCCCAGT 61.001 63.158 0.00 0.00 40.76 4.00
475 478 1.086634 GTGTCAAGATCAGCTCGGCC 61.087 60.000 0.00 0.00 0.00 6.13
533 561 8.848474 GAATTCAATTAATTCGGGGAGATAGA 57.152 34.615 0.00 0.00 42.98 1.98
544 572 7.991647 TTCGGGGAGATAGATAGATAGTAGA 57.008 40.000 0.00 0.00 0.00 2.59
546 574 7.969004 TCGGGGAGATAGATAGATAGTAGATG 58.031 42.308 0.00 0.00 0.00 2.90
547 575 7.016760 TCGGGGAGATAGATAGATAGTAGATGG 59.983 44.444 0.00 0.00 0.00 3.51
548 576 7.016760 CGGGGAGATAGATAGATAGTAGATGGA 59.983 44.444 0.00 0.00 0.00 3.41
549 577 8.729047 GGGGAGATAGATAGATAGTAGATGGAA 58.271 40.741 0.00 0.00 0.00 3.53
550 578 9.793259 GGGAGATAGATAGATAGTAGATGGAAG 57.207 40.741 0.00 0.00 0.00 3.46
551 579 9.284968 GGAGATAGATAGATAGTAGATGGAAGC 57.715 40.741 0.00 0.00 0.00 3.86
568 909 4.234574 GGAAGCAAAACTGGTTAATTCGG 58.765 43.478 0.00 0.00 0.00 4.30
576 917 2.135933 CTGGTTAATTCGGCCGATCTC 58.864 52.381 31.56 16.93 0.00 2.75
648 989 2.359602 TCTCCGTCTCTCGCCGTT 60.360 61.111 0.00 0.00 38.35 4.44
649 990 1.970114 TCTCCGTCTCTCGCCGTTT 60.970 57.895 0.00 0.00 38.35 3.60
650 991 1.801913 CTCCGTCTCTCGCCGTTTG 60.802 63.158 0.00 0.00 38.35 2.93
721 1067 1.179174 TGCAGTACCTGACAGCGTCT 61.179 55.000 0.00 0.00 43.27 4.18
734 1080 1.590525 GCGTCTGTTCACGTGGTGA 60.591 57.895 17.00 6.19 42.04 4.02
750 1097 0.365859 GTGATCGCGAGGTCGAAAAC 59.634 55.000 16.66 0.00 46.72 2.43
751 1098 1.068832 TGATCGCGAGGTCGAAAACG 61.069 55.000 16.66 0.00 46.72 3.60
752 1099 0.795735 GATCGCGAGGTCGAAAACGA 60.796 55.000 16.66 2.99 42.15 3.85
753 1100 0.179145 ATCGCGAGGTCGAAAACGAT 60.179 50.000 16.66 5.28 42.15 3.73
839 1186 7.036220 CGTTGCTCTCTCTCCTCTTTATAAAA 58.964 38.462 0.00 0.00 0.00 1.52
840 1187 7.708752 CGTTGCTCTCTCTCCTCTTTATAAAAT 59.291 37.037 0.00 0.00 0.00 1.82
846 1193 8.643324 TCTCTCTCCTCTTTATAAAATACTGGC 58.357 37.037 0.00 0.00 0.00 4.85
932 1281 0.469917 GCCAAGCTATAGGACCAGCA 59.530 55.000 1.04 0.00 40.36 4.41
1236 1587 1.743252 CAAGCCCAAGGAGACGCTC 60.743 63.158 0.00 0.00 0.00 5.03
1288 1639 0.242825 CAACGGTAGGCTTCGAGTCA 59.757 55.000 15.06 0.00 0.00 3.41
1360 1711 1.360931 GGCATGGAAAAATGGTGCGC 61.361 55.000 0.00 0.00 36.70 6.09
1575 1926 7.268586 TGAGCTCTATTCAATCCAACTACTTC 58.731 38.462 16.19 0.00 0.00 3.01
1595 1946 5.362430 ACTTCTCTCTCTCTCTCTCTCTCTC 59.638 48.000 0.00 0.00 0.00 3.20
1596 1947 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1597 1948 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1598 1949 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1599 1950 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1600 1951 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1601 1952 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1602 1953 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1603 1954 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1604 1955 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1605 1956 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1606 1957 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1607 1958 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1608 1959 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1609 1960 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1610 1961 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1611 1962 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1612 1963 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1613 1964 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1614 1965 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1615 1966 2.959030 TCTCTCTCTCTCTCTCTCTCCG 59.041 54.545 0.00 0.00 0.00 4.63
1616 1967 1.412710 TCTCTCTCTCTCTCTCTCCGC 59.587 57.143 0.00 0.00 0.00 5.54
1617 1968 0.468226 TCTCTCTCTCTCTCTCCGCC 59.532 60.000 0.00 0.00 0.00 6.13
1618 1969 0.880278 CTCTCTCTCTCTCTCCGCCG 60.880 65.000 0.00 0.00 0.00 6.46
1619 1970 1.891919 CTCTCTCTCTCTCCGCCGG 60.892 68.421 0.00 0.00 0.00 6.13
1620 1971 2.190843 CTCTCTCTCTCCGCCGGA 59.809 66.667 5.05 5.37 0.00 5.14
1621 1972 1.452289 CTCTCTCTCTCCGCCGGAA 60.452 63.158 7.50 0.00 0.00 4.30
1622 1973 1.001269 TCTCTCTCTCCGCCGGAAA 60.001 57.895 7.50 0.00 0.00 3.13
1623 1974 0.611062 TCTCTCTCTCCGCCGGAAAA 60.611 55.000 7.50 0.00 0.00 2.29
1624 1975 0.246635 CTCTCTCTCCGCCGGAAAAA 59.753 55.000 7.50 0.00 0.00 1.94
1657 2008 6.441088 AGACCAGGTCTCATATAATTTCCC 57.559 41.667 17.31 0.00 38.71 3.97
1658 2009 5.310857 AGACCAGGTCTCATATAATTTCCCC 59.689 44.000 17.31 0.00 38.71 4.81
1659 2010 4.354087 ACCAGGTCTCATATAATTTCCCCC 59.646 45.833 0.00 0.00 0.00 5.40
1660 2011 4.603610 CCAGGTCTCATATAATTTCCCCCT 59.396 45.833 0.00 0.00 0.00 4.79
1663 2014 4.323562 GGTCTCATATAATTTCCCCCTCCG 60.324 50.000 0.00 0.00 0.00 4.63
1717 2068 0.530288 TGCGCCTTTAATTGCCTTCC 59.470 50.000 4.18 0.00 0.00 3.46
1759 2110 1.204704 TGTTCCTCGCGATTCTCATGT 59.795 47.619 10.36 0.00 0.00 3.21
1760 2111 1.855360 GTTCCTCGCGATTCTCATGTC 59.145 52.381 10.36 0.00 0.00 3.06
1761 2112 1.393603 TCCTCGCGATTCTCATGTCT 58.606 50.000 10.36 0.00 0.00 3.41
1791 2142 1.149361 TTCGTCCACACGCAACACTC 61.149 55.000 0.00 0.00 46.28 3.51
1792 2143 2.927618 CGTCCACACGCAACACTCG 61.928 63.158 0.00 0.00 39.69 4.18
1808 2178 7.029563 GCAACACTCGGAAGATGAATTTTATT 58.970 34.615 0.00 0.00 40.84 1.40
1831 2201 5.766150 TGGGTAATCGCCATTAGAATTTG 57.234 39.130 0.00 0.00 0.00 2.32
1832 2202 5.197451 TGGGTAATCGCCATTAGAATTTGT 58.803 37.500 0.00 0.00 0.00 2.83
1896 2268 5.333952 GCATTTAGCTCAATGGAGAGAATCG 60.334 44.000 19.58 0.00 44.26 3.34
1927 2299 4.000331 ACCTGACACTGACAATTCTCAG 58.000 45.455 8.98 8.98 43.06 3.35
1974 2353 1.371467 TGTGGTCCTGTGGATCCAAT 58.629 50.000 18.20 0.00 35.71 3.16
1998 2378 0.177836 TGATGCCATGTACCGTCCAG 59.822 55.000 0.00 0.00 0.00 3.86
2054 2442 8.357402 TGCAGAATGATAAAAGAATCATGATGG 58.643 33.333 9.46 0.00 44.08 3.51
2126 2516 1.134551 GCGAGATCCCTTTCTGCTTCT 60.135 52.381 0.00 0.00 0.00 2.85
2367 2758 3.564225 TCGACAGATTAATCTAGCTCGCA 59.436 43.478 17.53 10.72 34.85 5.10
2464 2884 1.712056 TTCAGGGTTTCTCGTCAGGA 58.288 50.000 0.00 0.00 0.00 3.86
2474 2894 5.125097 GGTTTCTCGTCAGGATCTGTTAGTA 59.875 44.000 0.00 0.00 32.61 1.82
2483 2903 5.888724 TCAGGATCTGTTAGTAAGAGTGAGG 59.111 44.000 6.92 0.00 32.61 3.86
2602 3024 1.401761 TGATGCCATTGCCATGTACC 58.598 50.000 0.00 0.00 36.33 3.34
2604 3026 1.755959 GATGCCATTGCCATGTACCAA 59.244 47.619 0.00 0.00 36.33 3.67
2605 3027 1.863325 TGCCATTGCCATGTACCAAT 58.137 45.000 0.00 0.00 36.33 3.16
2606 3028 1.481363 TGCCATTGCCATGTACCAATG 59.519 47.619 17.37 17.37 44.82 2.82
2607 3029 1.807377 GCCATTGCCATGTACCAATGC 60.807 52.381 18.27 12.96 44.22 3.56
2608 3030 1.481363 CCATTGCCATGTACCAATGCA 59.519 47.619 18.27 6.09 44.22 3.96
2609 3031 2.542597 CATTGCCATGTACCAATGCAC 58.457 47.619 14.18 0.00 41.02 4.57
2633 3055 0.532573 ACCTGTGCATCGATCTCGTT 59.467 50.000 0.00 0.00 40.80 3.85
2719 3144 2.939103 AGTTCTCAATCATAAGCACGGC 59.061 45.455 0.00 0.00 0.00 5.68
2772 3197 2.125269 GGTGGTGGGACGGAATCG 60.125 66.667 0.00 0.00 43.02 3.34
2838 3269 1.330521 CGGCGCTGCACATTAGTTTAT 59.669 47.619 7.64 0.00 0.00 1.40
2839 3270 2.719798 GGCGCTGCACATTAGTTTATG 58.280 47.619 7.64 0.00 0.00 1.90
2840 3271 2.111756 GCGCTGCACATTAGTTTATGC 58.888 47.619 0.00 0.00 38.59 3.14
2842 3273 3.611517 CGCTGCACATTAGTTTATGCTC 58.388 45.455 0.00 0.00 38.90 4.26
2843 3274 3.546815 CGCTGCACATTAGTTTATGCTCC 60.547 47.826 0.00 0.00 38.90 4.70
2844 3275 3.629398 GCTGCACATTAGTTTATGCTCCT 59.371 43.478 0.00 0.00 38.90 3.69
2845 3276 4.497006 GCTGCACATTAGTTTATGCTCCTG 60.497 45.833 0.00 0.00 38.90 3.86
2846 3277 3.378112 TGCACATTAGTTTATGCTCCTGC 59.622 43.478 0.00 0.00 38.90 4.85
2860 3298 4.067896 TGCTCCTGCAGAGAGTTTAAAAG 58.932 43.478 24.26 3.62 46.50 2.27
2874 3312 0.945813 TAAAAGTTTGACGCCCACGG 59.054 50.000 0.00 0.00 46.04 4.94
2898 3340 2.550855 CCTAAGCTCTGTCTGTTTGGCA 60.551 50.000 0.00 0.00 0.00 4.92
2978 3450 1.067295 AGGAGCTGACATTTCCACCA 58.933 50.000 0.00 0.00 33.32 4.17
3000 3472 5.769662 CCATAGATTAATGGCCAAGCTGTTA 59.230 40.000 10.96 0.00 40.07 2.41
3016 3488 7.309621 CCAAGCTGTTAGTTAGTTACTCCTACA 60.310 40.741 0.00 0.00 38.33 2.74
3024 3496 7.713734 AGTTAGTTACTCCTACATGTTGCTA 57.286 36.000 2.30 0.00 28.23 3.49
3028 3500 3.247006 ACTCCTACATGTTGCTAACCG 57.753 47.619 2.30 0.00 0.00 4.44
3164 3636 2.653115 GCAGCTTTTGGCCAGTCC 59.347 61.111 5.11 0.00 43.05 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.073125 TGACTGATCTCCCCGCAAAAA 59.927 47.619 0.00 0.00 0.00 1.94
82 83 0.690192 TGACTGATCTCCCCGCAAAA 59.310 50.000 0.00 0.00 0.00 2.44
83 84 0.911769 ATGACTGATCTCCCCGCAAA 59.088 50.000 0.00 0.00 0.00 3.68
84 85 0.178767 CATGACTGATCTCCCCGCAA 59.821 55.000 0.00 0.00 0.00 4.85
85 86 0.687427 TCATGACTGATCTCCCCGCA 60.687 55.000 0.00 0.00 0.00 5.69
86 87 0.033228 CTCATGACTGATCTCCCCGC 59.967 60.000 0.00 0.00 0.00 6.13
87 88 1.407936 ACTCATGACTGATCTCCCCG 58.592 55.000 0.00 0.00 0.00 5.73
88 89 2.503356 ACAACTCATGACTGATCTCCCC 59.497 50.000 6.99 0.00 0.00 4.81
89 90 3.055530 ACACAACTCATGACTGATCTCCC 60.056 47.826 6.99 0.00 0.00 4.30
90 91 4.199432 ACACAACTCATGACTGATCTCC 57.801 45.455 6.99 0.00 0.00 3.71
91 92 5.233902 GCATACACAACTCATGACTGATCTC 59.766 44.000 6.99 0.00 0.00 2.75
92 93 5.114780 GCATACACAACTCATGACTGATCT 58.885 41.667 6.99 0.00 0.00 2.75
93 94 4.872124 TGCATACACAACTCATGACTGATC 59.128 41.667 6.99 0.00 0.00 2.92
94 95 4.835678 TGCATACACAACTCATGACTGAT 58.164 39.130 6.99 0.00 0.00 2.90
95 96 4.270245 TGCATACACAACTCATGACTGA 57.730 40.909 6.99 0.00 0.00 3.41
96 97 6.856135 ATATGCATACACAACTCATGACTG 57.144 37.500 8.99 0.00 0.00 3.51
97 98 7.049754 TCAATATGCATACACAACTCATGACT 58.950 34.615 8.99 0.00 0.00 3.41
98 99 7.250445 TCAATATGCATACACAACTCATGAC 57.750 36.000 8.99 0.00 0.00 3.06
99 100 6.017687 GCTCAATATGCATACACAACTCATGA 60.018 38.462 8.99 0.00 0.00 3.07
100 101 6.140786 GCTCAATATGCATACACAACTCATG 58.859 40.000 8.99 0.00 0.00 3.07
101 102 5.240183 GGCTCAATATGCATACACAACTCAT 59.760 40.000 8.99 0.00 0.00 2.90
102 103 4.576053 GGCTCAATATGCATACACAACTCA 59.424 41.667 8.99 0.00 0.00 3.41
109 110 3.467374 TCGTGGCTCAATATGCATACA 57.533 42.857 8.99 0.00 0.00 2.29
138 139 0.765510 GGAGAGGCCCCGTGATAAAT 59.234 55.000 0.00 0.00 0.00 1.40
167 168 8.830201 TTTCCAAACTAAACCATTCATGAATG 57.170 30.769 32.70 32.70 45.77 2.67
168 169 9.439500 CATTTCCAAACTAAACCATTCATGAAT 57.561 29.630 15.36 15.36 0.00 2.57
169 170 7.387397 GCATTTCCAAACTAAACCATTCATGAA 59.613 33.333 11.26 11.26 0.00 2.57
170 171 6.873076 GCATTTCCAAACTAAACCATTCATGA 59.127 34.615 0.00 0.00 0.00 3.07
171 172 6.649973 TGCATTTCCAAACTAAACCATTCATG 59.350 34.615 0.00 0.00 0.00 3.07
288 289 4.047822 CACCGCAACAGCAAGAATTAAAA 58.952 39.130 0.00 0.00 0.00 1.52
293 294 1.286880 GCACCGCAACAGCAAGAAT 59.713 52.632 0.00 0.00 0.00 2.40
306 307 3.906008 CACGAGAATTTTAAAGTGCACCG 59.094 43.478 14.63 7.69 0.00 4.94
311 312 4.911610 CACCTGCACGAGAATTTTAAAGTG 59.088 41.667 0.00 0.04 0.00 3.16
364 367 6.035975 GCACTAAACTTGAAGCAAAATGTTGT 59.964 34.615 0.00 0.00 37.06 3.32
393 396 1.466697 CGTGCAGTTTTTGTTGGTCGT 60.467 47.619 0.00 0.00 0.00 4.34
394 397 1.187715 CGTGCAGTTTTTGTTGGTCG 58.812 50.000 0.00 0.00 0.00 4.79
395 398 1.133407 TCCGTGCAGTTTTTGTTGGTC 59.867 47.619 0.00 0.00 0.00 4.02
396 399 1.178276 TCCGTGCAGTTTTTGTTGGT 58.822 45.000 0.00 0.00 0.00 3.67
403 406 1.067635 GGCATTCATCCGTGCAGTTTT 60.068 47.619 0.00 0.00 43.00 2.43
407 410 0.527113 TTTGGCATTCATCCGTGCAG 59.473 50.000 0.00 0.00 43.00 4.41
414 417 6.242829 CGCTAAAAATTGTTTGGCATTCATC 58.757 36.000 8.21 0.00 0.00 2.92
416 419 4.450419 CCGCTAAAAATTGTTTGGCATTCA 59.550 37.500 8.21 0.00 0.00 2.57
433 436 1.692173 GCCTACATCCACCCCGCTAA 61.692 60.000 0.00 0.00 0.00 3.09
434 437 2.138179 GCCTACATCCACCCCGCTA 61.138 63.158 0.00 0.00 0.00 4.26
435 438 3.480133 GCCTACATCCACCCCGCT 61.480 66.667 0.00 0.00 0.00 5.52
437 440 3.873812 GGGCCTACATCCACCCCG 61.874 72.222 0.84 0.00 36.24 5.73
440 443 1.224592 CACTGGGCCTACATCCACC 59.775 63.158 4.53 0.00 0.00 4.61
442 445 0.546507 TGACACTGGGCCTACATCCA 60.547 55.000 4.53 0.00 0.00 3.41
444 447 1.555075 TCTTGACACTGGGCCTACATC 59.445 52.381 4.53 0.00 0.00 3.06
445 448 1.656587 TCTTGACACTGGGCCTACAT 58.343 50.000 4.53 0.00 0.00 2.29
446 449 1.555075 GATCTTGACACTGGGCCTACA 59.445 52.381 4.53 0.00 0.00 2.74
455 458 0.108424 GCCGAGCTGATCTTGACACT 60.108 55.000 0.00 0.00 0.00 3.55
457 460 1.219124 GGCCGAGCTGATCTTGACA 59.781 57.895 0.00 0.00 0.00 3.58
533 561 8.153550 CCAGTTTTGCTTCCATCTACTATCTAT 58.846 37.037 0.00 0.00 0.00 1.98
541 569 7.361713 CGAATTAACCAGTTTTGCTTCCATCTA 60.362 37.037 0.00 0.00 0.00 1.98
542 570 6.570378 CGAATTAACCAGTTTTGCTTCCATCT 60.570 38.462 0.00 0.00 0.00 2.90
543 571 5.572896 CGAATTAACCAGTTTTGCTTCCATC 59.427 40.000 0.00 0.00 0.00 3.51
544 572 5.469479 CGAATTAACCAGTTTTGCTTCCAT 58.531 37.500 0.00 0.00 0.00 3.41
546 574 4.234574 CCGAATTAACCAGTTTTGCTTCC 58.765 43.478 0.00 0.00 0.00 3.46
547 575 3.673338 GCCGAATTAACCAGTTTTGCTTC 59.327 43.478 0.00 0.00 0.00 3.86
548 576 3.554129 GGCCGAATTAACCAGTTTTGCTT 60.554 43.478 0.00 0.00 0.00 3.91
549 577 2.029380 GGCCGAATTAACCAGTTTTGCT 60.029 45.455 0.00 0.00 0.00 3.91
550 578 2.333926 GGCCGAATTAACCAGTTTTGC 58.666 47.619 0.00 0.00 0.00 3.68
551 579 2.226912 TCGGCCGAATTAACCAGTTTTG 59.773 45.455 28.99 0.00 0.00 2.44
576 917 1.581912 CGTCGTGTACGGATGACGG 60.582 63.158 16.30 2.97 46.84 4.79
721 1067 2.019408 CGCGATCACCACGTGAACA 61.019 57.895 19.30 0.00 45.96 3.18
750 1097 2.578713 CGGTGACCGGTTCGATCG 60.579 66.667 17.80 9.36 44.15 3.69
915 1264 1.202698 GGGTGCTGGTCCTATAGCTTG 60.203 57.143 0.00 0.00 40.52 4.01
920 1269 2.528134 GCTGGGTGCTGGTCCTATA 58.472 57.895 0.00 0.00 38.95 1.31
921 1270 3.324713 GCTGGGTGCTGGTCCTAT 58.675 61.111 0.00 0.00 38.95 2.57
997 1348 2.276740 CTGGCAGTTCCCCATCCC 59.723 66.667 6.28 0.00 0.00 3.85
1236 1587 2.439701 TAGACGTGGCCGAGGAGG 60.440 66.667 0.00 0.00 44.97 4.30
1277 1628 0.173708 AGAATCGGTGACTCGAAGCC 59.826 55.000 0.69 0.00 42.69 4.35
1360 1711 2.743928 GCCTTGGTCACCTCTGCG 60.744 66.667 0.00 0.00 0.00 5.18
1575 1926 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1595 1946 2.546795 GCGGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
1596 1947 1.412710 GCGGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
1597 1948 1.541233 GGCGGAGAGAGAGAGAGAGAG 60.541 61.905 0.00 0.00 0.00 3.20
1598 1949 0.468226 GGCGGAGAGAGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
1599 1950 0.880278 CGGCGGAGAGAGAGAGAGAG 60.880 65.000 0.00 0.00 0.00 3.20
1600 1951 1.145156 CGGCGGAGAGAGAGAGAGA 59.855 63.158 0.00 0.00 0.00 3.10
1601 1952 1.891919 CCGGCGGAGAGAGAGAGAG 60.892 68.421 24.41 0.00 0.00 3.20
1602 1953 1.911702 TTCCGGCGGAGAGAGAGAGA 61.912 60.000 29.30 8.02 31.21 3.10
1603 1954 1.032657 TTTCCGGCGGAGAGAGAGAG 61.033 60.000 29.30 0.00 31.21 3.20
1604 1955 0.611062 TTTTCCGGCGGAGAGAGAGA 60.611 55.000 29.30 9.70 31.21 3.10
1605 1956 0.246635 TTTTTCCGGCGGAGAGAGAG 59.753 55.000 29.30 0.00 31.21 3.20
1606 1957 2.358039 TTTTTCCGGCGGAGAGAGA 58.642 52.632 29.30 11.39 31.21 3.10
1634 1985 5.310857 GGGGAAATTATATGAGACCTGGTCT 59.689 44.000 28.70 28.70 46.42 3.85
1635 1986 5.515008 GGGGGAAATTATATGAGACCTGGTC 60.515 48.000 19.20 19.20 0.00 4.02
1636 1987 4.354087 GGGGGAAATTATATGAGACCTGGT 59.646 45.833 0.00 0.00 0.00 4.00
1637 1988 4.603610 AGGGGGAAATTATATGAGACCTGG 59.396 45.833 0.00 0.00 0.00 4.45
1638 1989 5.280727 GGAGGGGGAAATTATATGAGACCTG 60.281 48.000 0.00 0.00 0.00 4.00
1639 1990 4.852697 GGAGGGGGAAATTATATGAGACCT 59.147 45.833 0.00 0.00 0.00 3.85
1640 1991 4.323562 CGGAGGGGGAAATTATATGAGACC 60.324 50.000 0.00 0.00 0.00 3.85
1641 1992 4.833390 CGGAGGGGGAAATTATATGAGAC 58.167 47.826 0.00 0.00 0.00 3.36
1642 1993 3.263425 GCGGAGGGGGAAATTATATGAGA 59.737 47.826 0.00 0.00 0.00 3.27
1643 1994 3.610911 GCGGAGGGGGAAATTATATGAG 58.389 50.000 0.00 0.00 0.00 2.90
1644 1995 2.307686 GGCGGAGGGGGAAATTATATGA 59.692 50.000 0.00 0.00 0.00 2.15
1645 1996 2.723273 GGCGGAGGGGGAAATTATATG 58.277 52.381 0.00 0.00 0.00 1.78
1646 1997 1.280998 CGGCGGAGGGGGAAATTATAT 59.719 52.381 0.00 0.00 0.00 0.86
1647 1998 0.688487 CGGCGGAGGGGGAAATTATA 59.312 55.000 0.00 0.00 0.00 0.98
1648 1999 1.057851 TCGGCGGAGGGGGAAATTAT 61.058 55.000 7.21 0.00 0.00 1.28
1649 2000 1.057851 ATCGGCGGAGGGGGAAATTA 61.058 55.000 7.21 0.00 0.00 1.40
1650 2001 2.383601 ATCGGCGGAGGGGGAAATT 61.384 57.895 7.21 0.00 0.00 1.82
1651 2002 2.772622 ATCGGCGGAGGGGGAAAT 60.773 61.111 7.21 0.00 0.00 2.17
1652 2003 3.792736 CATCGGCGGAGGGGGAAA 61.793 66.667 7.21 0.00 0.00 3.13
1672 2023 1.672030 TGCAGAGAACGTGCATGGG 60.672 57.895 11.36 0.00 45.96 4.00
1717 2068 1.486726 CTAACCAGTAGCCCTTGGAGG 59.513 57.143 5.10 0.00 37.89 4.30
1727 2078 3.251571 GCGAGGAACAACTAACCAGTAG 58.748 50.000 0.00 0.00 33.48 2.57
1732 2083 2.005971 ATCGCGAGGAACAACTAACC 57.994 50.000 16.66 0.00 0.00 2.85
1759 2110 2.296471 GTGGACGAACTGAGGAAGAAGA 59.704 50.000 0.00 0.00 0.00 2.87
1760 2111 2.035961 TGTGGACGAACTGAGGAAGAAG 59.964 50.000 0.00 0.00 0.00 2.85
1761 2112 2.036387 TGTGGACGAACTGAGGAAGAA 58.964 47.619 0.00 0.00 0.00 2.52
1783 2134 4.425577 AAATTCATCTTCCGAGTGTTGC 57.574 40.909 0.00 0.00 0.00 4.17
1791 2142 9.463443 GATTACCCAAATAAAATTCATCTTCCG 57.537 33.333 0.00 0.00 0.00 4.30
1792 2143 9.463443 CGATTACCCAAATAAAATTCATCTTCC 57.537 33.333 0.00 0.00 0.00 3.46
1808 2178 5.654650 ACAAATTCTAATGGCGATTACCCAA 59.345 36.000 0.00 0.00 35.67 4.12
1858 2228 3.127030 GCTAAATGCTAACGGTTTCTGCT 59.873 43.478 0.00 0.00 38.95 4.24
1896 2268 2.367567 TCAGTGTCAGGTACTCCAAACC 59.632 50.000 0.00 0.00 34.60 3.27
1927 2299 4.734398 TTTATGCATGTCAATTGGGGAC 57.266 40.909 10.16 0.00 35.83 4.46
1974 2353 2.942376 GACGGTACATGGCATCAATCAA 59.058 45.455 0.00 0.00 0.00 2.57
2006 2386 7.290061 TGCATCCCTCTATTTTAAGCACTAAT 58.710 34.615 0.00 0.00 0.00 1.73
2010 2390 5.126067 TCTGCATCCCTCTATTTTAAGCAC 58.874 41.667 0.00 0.00 0.00 4.40
2054 2442 9.474249 GTTGCGACTCTTCACTATTTTATTTAC 57.526 33.333 0.00 0.00 0.00 2.01
2126 2516 2.203084 TTGCCGCGGTTCAGAACA 60.203 55.556 28.70 11.47 0.00 3.18
2367 2758 1.077086 TGGCAGCAACCCATGTGAT 59.923 52.632 0.00 0.00 0.00 3.06
2464 2884 4.142049 GCAGCCTCACTCTTACTAACAGAT 60.142 45.833 0.00 0.00 0.00 2.90
2494 2916 7.094377 GGTGCAAATGTATCAAGAGGAGTAAAA 60.094 37.037 0.00 0.00 0.00 1.52
2498 2920 4.018960 AGGTGCAAATGTATCAAGAGGAGT 60.019 41.667 0.00 0.00 0.00 3.85
2499 2921 4.334759 CAGGTGCAAATGTATCAAGAGGAG 59.665 45.833 0.00 0.00 0.00 3.69
2501 2923 4.264253 TCAGGTGCAAATGTATCAAGAGG 58.736 43.478 0.00 0.00 0.00 3.69
2633 3055 1.137697 ATGAGAGGCCATGAGCATGA 58.862 50.000 5.01 0.00 46.50 3.07
2765 3190 2.956964 GCTCTCCGCACGATTCCG 60.957 66.667 0.00 0.00 42.50 4.30
2772 3197 2.335712 CCCAAAAGGCTCTCCGCAC 61.336 63.158 0.00 0.00 41.67 5.34
2773 3198 2.034066 CCCAAAAGGCTCTCCGCA 59.966 61.111 0.00 0.00 41.67 5.69
2839 3270 4.068599 ACTTTTAAACTCTCTGCAGGAGC 58.931 43.478 23.94 0.00 41.60 4.70
2840 3271 6.260936 TCAAACTTTTAAACTCTCTGCAGGAG 59.739 38.462 22.96 22.96 43.12 3.69
2842 3273 6.202226 GTCAAACTTTTAAACTCTCTGCAGG 58.798 40.000 15.13 4.77 0.00 4.85
2843 3274 5.904080 CGTCAAACTTTTAAACTCTCTGCAG 59.096 40.000 7.63 7.63 0.00 4.41
2844 3275 5.729454 GCGTCAAACTTTTAAACTCTCTGCA 60.729 40.000 0.00 0.00 0.00 4.41
2845 3276 4.671068 GCGTCAAACTTTTAAACTCTCTGC 59.329 41.667 0.00 0.00 0.00 4.26
2846 3277 5.205565 GGCGTCAAACTTTTAAACTCTCTG 58.794 41.667 0.00 0.00 0.00 3.35
2860 3298 2.319841 GGTACCGTGGGCGTCAAAC 61.320 63.158 0.00 0.00 36.15 2.93
2874 3312 4.246458 CCAAACAGACAGAGCTTAGGTAC 58.754 47.826 0.00 0.00 0.00 3.34
2898 3340 1.420891 ACCATTGCCAAATGCCAAAGT 59.579 42.857 0.00 0.00 41.66 2.66
2906 3348 1.347378 GACCAACCACCATTGCCAAAT 59.653 47.619 0.00 0.00 0.00 2.32
2915 3357 0.537143 GAGCATGTGACCAACCACCA 60.537 55.000 0.00 0.00 36.26 4.17
2949 3421 0.861837 GTCAGCTCCTGTGTTGTTCG 59.138 55.000 0.00 0.00 32.61 3.95
2978 3450 6.605119 ACTAACAGCTTGGCCATTAATCTAT 58.395 36.000 6.09 0.00 0.00 1.98
3000 3472 6.607004 AGCAACATGTAGGAGTAACTAACT 57.393 37.500 0.00 0.00 42.80 2.24
3031 3503 1.201825 GTATTCAATCGCCGCGAGC 59.798 57.895 21.61 8.84 39.91 5.03
3032 3504 0.504384 CAGTATTCAATCGCCGCGAG 59.496 55.000 21.61 8.65 39.91 5.03
3034 3506 1.564622 CCAGTATTCAATCGCCGCG 59.435 57.895 6.39 6.39 0.00 6.46
3036 3508 0.583438 CTGCCAGTATTCAATCGCCG 59.417 55.000 0.00 0.00 0.00 6.46
3038 3510 1.016627 TGCTGCCAGTATTCAATCGC 58.983 50.000 0.00 0.00 0.00 4.58
3040 3512 3.304525 GCTGATGCTGCCAGTATTCAATC 60.305 47.826 0.00 0.00 36.03 2.67
3064 3536 5.932303 CACATTAACTAGTGGTAAGCACAGT 59.068 40.000 0.00 0.00 32.24 3.55
3161 3633 2.100631 CGGTTGATGCGTCCAGGAC 61.101 63.158 9.92 9.92 0.00 3.85
3164 3636 0.930310 CATACGGTTGATGCGTCCAG 59.070 55.000 2.83 0.00 0.00 3.86
3200 3680 1.024271 TTGATGGATAAAGCGGCTGC 58.976 50.000 10.33 10.33 43.24 5.25
3201 3681 3.489738 CCTTTTGATGGATAAAGCGGCTG 60.490 47.826 1.81 0.00 31.54 4.85
3202 3682 2.689983 CCTTTTGATGGATAAAGCGGCT 59.310 45.455 0.00 0.00 31.54 5.52
3211 3691 4.409574 TGCATAATTGGCCTTTTGATGGAT 59.590 37.500 3.32 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.