Multiple sequence alignment - TraesCS6B01G010700

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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 TraesCS6B01G010700 chr6B 100.000 2382 0 0 1 2382 6508869 6511250 0.000000e+00 4399.0
1 TraesCS6B01G010700 chr6B 93.510 678 35 8 32 705 446416975 446417647 0.000000e+00 1000.0
2 TraesCS6B01G010700 chr6B 92.920 678 33 6 32 695 688940774 688941450 0.000000e+00 972.0
3 TraesCS6B01G010700 chr6D 86.673 1043 112 20 692 1725 3217907 3218931 0.000000e+00 1131.0
4 TraesCS6B01G010700 chr6D 86.306 628 70 10 920 1545 3195005 3195618 0.000000e+00 669.0
5 TraesCS6B01G010700 chr6D 100.000 28 0 0 1692 1719 160853788 160853761 4.000000e-03 52.8
6 TraesCS6B01G010700 chr1B 95.421 677 27 4 32 706 525802761 525803435 0.000000e+00 1075.0
7 TraesCS6B01G010700 chr1B 92.805 681 32 8 32 698 625950935 625950258 0.000000e+00 970.0
8 TraesCS6B01G010700 chr4A 95.401 674 21 8 32 698 615529442 615528772 0.000000e+00 1064.0
9 TraesCS6B01G010700 chr4A 80.172 116 20 3 2011 2124 719794296 719794182 1.520000e-12 84.2
10 TraesCS6B01G010700 chr3A 94.845 679 26 6 32 705 737389418 737390092 0.000000e+00 1051.0
11 TraesCS6B01G010700 chr3A 84.848 396 46 5 1784 2178 732360871 732360489 1.030000e-103 387.0
12 TraesCS6B01G010700 chr3B 94.395 678 23 7 32 695 588409920 588410596 0.000000e+00 1027.0
13 TraesCS6B01G010700 chr3B 93.204 103 7 0 1773 1875 773730036 773730138 4.100000e-33 152.0
14 TraesCS6B01G010700 chr7B 93.935 676 28 5 32 695 592779886 592779212 0.000000e+00 1009.0
15 TraesCS6B01G010700 chr7B 92.669 682 33 9 32 698 135020450 135019771 0.000000e+00 966.0
16 TraesCS6B01G010700 chr7A 91.640 622 44 2 1769 2382 17896369 17895748 0.000000e+00 854.0
17 TraesCS6B01G010700 chr5D 91.774 620 42 6 1771 2382 21601928 21601310 0.000000e+00 854.0
18 TraesCS6B01G010700 chr5D 91.493 529 38 6 1772 2294 21566230 21566757 0.000000e+00 721.0
19 TraesCS6B01G010700 chr5D 90.217 92 9 0 2289 2380 21584125 21584216 1.160000e-23 121.0
20 TraesCS6B01G010700 chr2A 91.148 610 50 4 1775 2382 717015298 717015905 0.000000e+00 824.0
21 TraesCS6B01G010700 chr2A 84.899 298 38 5 1776 2067 92680807 92681103 6.440000e-76 294.0
22 TraesCS6B01G010700 chr6A 87.561 611 66 6 920 1528 2039604 2040206 0.000000e+00 699.0
23 TraesCS6B01G010700 chr6A 88.235 51 4 2 1187 1236 12146507 12146556 2.560000e-05 60.2
24 TraesCS6B01G010700 chrUn 84.375 96 14 1 2030 2124 16700071 16699976 2.520000e-15 93.5
25 TraesCS6B01G010700 chrUn 84.375 96 14 1 2030 2124 141674483 141674388 2.520000e-15 93.5
26 TraesCS6B01G010700 chr7D 80.328 122 20 4 2006 2124 518628809 518628689 3.260000e-14 89.8
27 TraesCS6B01G010700 chr4B 100.000 32 0 0 1 32 33962134 33962103 2.560000e-05 60.2
28 TraesCS6B01G010700 chr4B 100.000 32 0 0 1 32 33964450 33964419 2.560000e-05 60.2


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 TraesCS6B01G010700 chr6B 6508869 6511250 2381 False 4399 4399 100.000 1 2382 1 chr6B.!!$F1 2381
1 TraesCS6B01G010700 chr6B 446416975 446417647 672 False 1000 1000 93.510 32 705 1 chr6B.!!$F2 673
2 TraesCS6B01G010700 chr6B 688940774 688941450 676 False 972 972 92.920 32 695 1 chr6B.!!$F3 663
3 TraesCS6B01G010700 chr6D 3217907 3218931 1024 False 1131 1131 86.673 692 1725 1 chr6D.!!$F2 1033
4 TraesCS6B01G010700 chr6D 3195005 3195618 613 False 669 669 86.306 920 1545 1 chr6D.!!$F1 625
5 TraesCS6B01G010700 chr1B 525802761 525803435 674 False 1075 1075 95.421 32 706 1 chr1B.!!$F1 674
6 TraesCS6B01G010700 chr1B 625950258 625950935 677 True 970 970 92.805 32 698 1 chr1B.!!$R1 666
7 TraesCS6B01G010700 chr4A 615528772 615529442 670 True 1064 1064 95.401 32 698 1 chr4A.!!$R1 666
8 TraesCS6B01G010700 chr3A 737389418 737390092 674 False 1051 1051 94.845 32 705 1 chr3A.!!$F1 673
9 TraesCS6B01G010700 chr3B 588409920 588410596 676 False 1027 1027 94.395 32 695 1 chr3B.!!$F1 663
10 TraesCS6B01G010700 chr7B 592779212 592779886 674 True 1009 1009 93.935 32 695 1 chr7B.!!$R2 663
11 TraesCS6B01G010700 chr7B 135019771 135020450 679 True 966 966 92.669 32 698 1 chr7B.!!$R1 666
12 TraesCS6B01G010700 chr7A 17895748 17896369 621 True 854 854 91.640 1769 2382 1 chr7A.!!$R1 613
13 TraesCS6B01G010700 chr5D 21601310 21601928 618 True 854 854 91.774 1771 2382 1 chr5D.!!$R1 611
14 TraesCS6B01G010700 chr5D 21566230 21566757 527 False 721 721 91.493 1772 2294 1 chr5D.!!$F1 522
15 TraesCS6B01G010700 chr2A 717015298 717015905 607 False 824 824 91.148 1775 2382 1 chr2A.!!$F2 607
16 TraesCS6B01G010700 chr6A 2039604 2040206 602 False 699 699 87.561 920 1528 1 chr6A.!!$F1 608

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
971 1000 0.243907 CGGTCTGATCACTTCACCGT 59.756 55.0 17.07 0.0 38.52 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2285 1.000827 CATCTGCCGCTCCACTACTAG 60.001 57.143 0.0 0.0 0.0 2.57 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
24 25 4.818546 AGTCATATTTGCAGTAGGACATGC 59.181 41.667 20.63 0.00 42.86 4.06
25 26 4.023707 GTCATATTTGCAGTAGGACATGCC 60.024 45.833 16.31 0.00 41.85 4.40
26 27 2.512692 ATTTGCAGTAGGACATGCCA 57.487 45.000 8.58 0.00 41.85 4.92
27 28 1.533625 TTTGCAGTAGGACATGCCAC 58.466 50.000 8.58 5.28 41.85 5.01
28 29 0.399833 TTGCAGTAGGACATGCCACA 59.600 50.000 8.58 0.00 41.85 4.17
29 30 0.620030 TGCAGTAGGACATGCCACAT 59.380 50.000 8.58 0.00 41.85 3.21
30 31 1.303309 GCAGTAGGACATGCCACATC 58.697 55.000 8.58 0.00 40.02 3.06
276 278 1.678101 GTTGCCTCCTATCAATGCCAC 59.322 52.381 0.00 0.00 0.00 5.01
397 399 9.859427 ACATTGTATTGTTCATGAACTATTTGG 57.141 29.630 31.04 20.81 41.67 3.28
703 727 6.709846 GCTGTTGGAGATGCTCTAAGATAATT 59.290 38.462 0.00 0.00 31.92 1.40
704 728 7.307870 GCTGTTGGAGATGCTCTAAGATAATTG 60.308 40.741 0.00 0.00 31.92 2.32
713 737 5.130975 TGCTCTAAGATAATTGCAGGGAGAA 59.869 40.000 0.00 0.00 0.00 2.87
717 741 4.429854 AGATAATTGCAGGGAGAAGGTC 57.570 45.455 0.00 0.00 0.00 3.85
725 749 2.678336 GCAGGGAGAAGGTCGTAATTTG 59.322 50.000 0.00 0.00 0.00 2.32
726 750 2.678336 CAGGGAGAAGGTCGTAATTTGC 59.322 50.000 0.00 0.00 0.00 3.68
742 766 7.278203 TCGTAATTTGCAAGATAATCGTTGGTA 59.722 33.333 0.00 0.00 0.00 3.25
754 778 3.202829 TCGTTGGTAGAAAAGGCAAGT 57.797 42.857 0.00 0.00 0.00 3.16
766 790 5.944007 AGAAAAGGCAAGTTATACGTTGGAT 59.056 36.000 0.00 0.00 0.00 3.41
767 791 7.107542 AGAAAAGGCAAGTTATACGTTGGATA 58.892 34.615 0.00 0.00 0.00 2.59
768 792 6.920569 AAAGGCAAGTTATACGTTGGATAG 57.079 37.500 0.00 0.00 0.00 2.08
770 794 6.420913 AGGCAAGTTATACGTTGGATAGAT 57.579 37.500 0.00 0.00 0.00 1.98
771 795 7.534723 AGGCAAGTTATACGTTGGATAGATA 57.465 36.000 0.00 0.00 0.00 1.98
773 797 7.014905 AGGCAAGTTATACGTTGGATAGATACA 59.985 37.037 0.00 0.00 0.00 2.29
774 798 7.328737 GGCAAGTTATACGTTGGATAGATACAG 59.671 40.741 0.00 0.00 0.00 2.74
790 814 2.949177 ACAGGTGTAAACATGGCAGA 57.051 45.000 2.26 0.00 0.00 4.26
802 826 3.869272 GGCAGACAATCGCGGCTG 61.869 66.667 6.13 6.53 0.00 4.85
806 830 0.729116 CAGACAATCGCGGCTGATTT 59.271 50.000 6.13 8.58 36.46 2.17
807 831 0.729116 AGACAATCGCGGCTGATTTG 59.271 50.000 6.13 12.59 36.46 2.32
810 834 1.331756 ACAATCGCGGCTGATTTGATC 59.668 47.619 6.13 0.00 36.46 2.92
820 844 4.673761 CGGCTGATTTGATCATTTGATTCG 59.326 41.667 0.00 0.00 38.85 3.34
838 862 6.042777 TGATTCGACCATAACACAGAAGATC 58.957 40.000 0.00 0.00 0.00 2.75
856 880 6.213195 AGAAGATCAGTTTCCATTCTCTCTGT 59.787 38.462 0.00 0.00 0.00 3.41
868 892 5.355596 CATTCTCTCTGTACCCATGAAGAC 58.644 45.833 0.00 0.00 0.00 3.01
880 904 4.141158 ACCCATGAAGACCATTTATCCCTC 60.141 45.833 0.00 0.00 31.94 4.30
883 907 5.458654 CCATGAAGACCATTTATCCCTCCAT 60.459 44.000 0.00 0.00 31.94 3.41
886 910 3.680169 AGACCATTTATCCCTCCATGGA 58.320 45.455 15.27 15.27 38.88 3.41
887 911 3.654806 AGACCATTTATCCCTCCATGGAG 59.345 47.826 31.69 31.69 38.88 3.86
888 912 2.108952 ACCATTTATCCCTCCATGGAGC 59.891 50.000 32.97 0.00 38.88 4.70
896 924 1.747145 CTCCATGGAGCGAGCATCT 59.253 57.895 28.45 0.00 35.31 2.90
916 944 5.521516 TCTCGTCGTAGTACAAGTACAAG 57.478 43.478 12.43 3.89 38.48 3.16
918 946 5.871524 TCTCGTCGTAGTACAAGTACAAGAT 59.128 40.000 12.43 0.00 38.48 2.40
935 964 6.674694 ACAAGATATACGTACGCCTATAGG 57.325 41.667 16.72 15.01 38.53 2.57
954 983 1.153489 CAGTGCTCCAGTCCATCGG 60.153 63.158 0.00 0.00 0.00 4.18
970 999 0.526211 TCGGTCTGATCACTTCACCG 59.474 55.000 18.41 18.41 42.46 4.94
971 1000 0.243907 CGGTCTGATCACTTCACCGT 59.756 55.000 17.07 0.00 38.52 4.83
972 1001 1.732732 CGGTCTGATCACTTCACCGTC 60.733 57.143 17.07 0.00 38.52 4.79
973 1002 1.404315 GGTCTGATCACTTCACCGTCC 60.404 57.143 0.00 0.00 0.00 4.79
974 1003 1.546476 GTCTGATCACTTCACCGTCCT 59.454 52.381 0.00 0.00 0.00 3.85
975 1004 1.819288 TCTGATCACTTCACCGTCCTC 59.181 52.381 0.00 0.00 0.00 3.71
976 1005 1.546029 CTGATCACTTCACCGTCCTCA 59.454 52.381 0.00 0.00 0.00 3.86
977 1006 1.272490 TGATCACTTCACCGTCCTCAC 59.728 52.381 0.00 0.00 0.00 3.51
998 1027 4.393990 CACTCATCAGCATACACAACACAT 59.606 41.667 0.00 0.00 0.00 3.21
1018 1047 3.220674 TGATGAACAACCACATGACCA 57.779 42.857 0.00 0.00 0.00 4.02
1027 1056 1.746239 CACATGACCAGCATCCGCA 60.746 57.895 0.00 0.00 42.27 5.69
1062 1091 0.755698 TCACCGTATGCCTCCTCCTC 60.756 60.000 0.00 0.00 0.00 3.71
1100 1129 6.183360 CGATGTAAGATCCACATTTTCAACGA 60.183 38.462 10.89 0.00 36.76 3.85
1101 1130 7.465916 CGATGTAAGATCCACATTTTCAACGAT 60.466 37.037 10.89 0.00 36.76 3.73
1120 1149 3.423206 CGATTGCTTGTGTTGCTTCTTTC 59.577 43.478 0.00 0.00 0.00 2.62
1134 1163 7.394077 TGTTGCTTCTTTCTTAATCATGGATCA 59.606 33.333 0.00 0.00 0.00 2.92
1144 1173 2.353357 TCATGGATCAATCACCCTGC 57.647 50.000 0.00 0.00 0.00 4.85
1152 1181 4.202090 GGATCAATCACCCTGCTTTCAATC 60.202 45.833 0.00 0.00 0.00 2.67
1159 1188 8.469200 CAATCACCCTGCTTTCAATCTTATTTA 58.531 33.333 0.00 0.00 0.00 1.40
1161 1190 8.593945 TCACCCTGCTTTCAATCTTATTTAAT 57.406 30.769 0.00 0.00 0.00 1.40
1182 1211 1.879380 CATCTGTTTTCGTTCAGGCCA 59.121 47.619 5.01 0.00 33.13 5.36
1198 1227 2.721859 CAGATCATCGACGGCGGA 59.278 61.111 12.58 0.00 38.28 5.54
1251 1280 1.727335 GTGCGCCTACAAGAAAGACTC 59.273 52.381 4.18 0.00 0.00 3.36
1465 1496 7.630470 TTTAGAAAAATTGTACAATGCACGG 57.370 32.000 21.46 0.00 0.00 4.94
1488 1519 1.529438 GGTCGATGCGTGTGAAAGAAA 59.471 47.619 0.00 0.00 0.00 2.52
1531 1562 6.566079 ATCATCATCTTTCCCTCACAAGTA 57.434 37.500 0.00 0.00 0.00 2.24
1532 1563 5.982356 TCATCATCTTTCCCTCACAAGTAG 58.018 41.667 0.00 0.00 0.00 2.57
1533 1564 5.485353 TCATCATCTTTCCCTCACAAGTAGT 59.515 40.000 0.00 0.00 0.00 2.73
1569 1600 3.974642 GGAACAACCATACTCCCCTATCT 59.025 47.826 0.00 0.00 38.79 1.98
1574 1605 5.162760 ACAACCATACTCCCCTATCTATGGA 60.163 44.000 9.10 0.00 38.55 3.41
1575 1606 4.949121 ACCATACTCCCCTATCTATGGAC 58.051 47.826 9.10 0.00 38.55 4.02
1579 1610 4.678538 ACTCCCCTATCTATGGACTACC 57.321 50.000 0.00 0.00 0.00 3.18
1590 1621 2.217510 TGGACTACCACTCTCCTCAC 57.782 55.000 0.00 0.00 41.77 3.51
1592 1623 1.096416 GACTACCACTCTCCTCACCG 58.904 60.000 0.00 0.00 0.00 4.94
1601 1632 2.290768 ACTCTCCTCACCGTAAGCTACA 60.291 50.000 0.00 0.00 0.00 2.74
1608 1639 3.994392 CTCACCGTAAGCTACAAACACAT 59.006 43.478 0.00 0.00 0.00 3.21
1625 1656 3.260475 ACATCTGGTAATGTGCGCTAA 57.740 42.857 9.73 0.00 38.43 3.09
1632 1663 5.414454 TCTGGTAATGTGCGCTAATTTCTTT 59.586 36.000 9.73 0.23 0.00 2.52
1634 1665 7.282224 TCTGGTAATGTGCGCTAATTTCTTTAT 59.718 33.333 9.73 0.00 0.00 1.40
1668 1699 4.966466 TATATGTGCGCTGCAAAGGGCT 62.966 50.000 9.73 0.00 46.16 5.19
1669 1700 3.982241 GTGCGCTGCAAAGGGCTT 61.982 61.111 9.73 0.00 46.16 4.35
1673 1704 1.956043 CGCTGCAAAGGGCTTACAA 59.044 52.632 0.00 0.00 45.15 2.41
1677 1708 2.932187 GCTGCAAAGGGCTTACAAATGG 60.932 50.000 0.00 0.00 45.15 3.16
1688 1720 4.926832 GGCTTACAAATGGTTTTTACGCAT 59.073 37.500 0.00 0.00 0.00 4.73
1843 1879 3.672808 GCCTCATCTATGGTTGGATCAG 58.327 50.000 0.00 0.00 0.00 2.90
1892 1930 1.820906 CCACATCATCCCACAGCCG 60.821 63.158 0.00 0.00 0.00 5.52
1971 2022 0.111253 CCCACTCTGCCTCACCTTTT 59.889 55.000 0.00 0.00 0.00 2.27
2013 2064 1.687840 ACACACTATAGCCCGGGCA 60.688 57.895 45.13 31.09 44.88 5.36
2178 2229 2.357517 CTTGTTCGTGCTCCGGCT 60.358 61.111 0.00 0.00 39.59 5.52
2203 2254 1.375396 CGCAGTCCACGGATTTCCA 60.375 57.895 0.00 0.00 35.14 3.53
2234 2285 0.179073 AGTGTATGCGTGATGGGAGC 60.179 55.000 0.00 0.00 0.00 4.70
2236 2287 1.068588 GTGTATGCGTGATGGGAGCTA 59.931 52.381 0.00 0.00 0.00 3.32
2239 2290 1.704641 ATGCGTGATGGGAGCTAGTA 58.295 50.000 0.00 0.00 0.00 1.82
2291 2342 0.249911 GCTCGACGGAATGGGCTATT 60.250 55.000 0.00 0.00 0.00 1.73
2295 2346 1.202533 CGACGGAATGGGCTATTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
2298 2349 2.026262 ACGGAATGGGCTATTGTCTGTT 60.026 45.455 0.00 0.00 0.00 3.16
2307 2358 2.186076 CTATTGTCTGTTCTCGCGGAC 58.814 52.381 6.13 4.99 43.21 4.79
2340 2391 3.550431 GCGGCCCCTAGCATCTCA 61.550 66.667 0.00 0.00 46.50 3.27
2347 2398 0.680618 CCCTAGCATCTCAGAGCAGG 59.319 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.991606 GCATGTCCTACTGCAAATATGACTA 59.008 40.000 11.74 3.20 38.28 2.59
1 2 4.818546 GCATGTCCTACTGCAAATATGACT 59.181 41.667 11.74 0.40 38.28 3.41
2 3 4.023707 GGCATGTCCTACTGCAAATATGAC 60.024 45.833 0.00 0.00 40.18 3.06
3 4 4.136796 GGCATGTCCTACTGCAAATATGA 58.863 43.478 0.00 0.00 40.18 2.15
4 5 3.884693 TGGCATGTCCTACTGCAAATATG 59.115 43.478 0.00 0.00 40.18 1.78
6 7 3.278574 GTGGCATGTCCTACTGCAAATA 58.721 45.455 0.00 0.00 40.18 1.40
7 8 2.094675 GTGGCATGTCCTACTGCAAAT 58.905 47.619 0.00 0.00 40.18 2.32
8 9 1.202867 TGTGGCATGTCCTACTGCAAA 60.203 47.619 0.00 0.00 40.18 3.68
9 10 0.399833 TGTGGCATGTCCTACTGCAA 59.600 50.000 0.00 0.00 40.18 4.08
10 11 0.620030 ATGTGGCATGTCCTACTGCA 59.380 50.000 0.00 0.00 40.18 4.41
11 12 1.303309 GATGTGGCATGTCCTACTGC 58.697 55.000 0.00 0.00 37.66 4.40
12 13 2.169144 TCTGATGTGGCATGTCCTACTG 59.831 50.000 0.00 0.00 35.26 2.74
13 14 2.470990 TCTGATGTGGCATGTCCTACT 58.529 47.619 0.00 0.00 35.26 2.57
14 15 2.988010 TCTGATGTGGCATGTCCTAC 57.012 50.000 0.00 0.00 35.26 3.18
15 16 2.773661 ACATCTGATGTGGCATGTCCTA 59.226 45.455 21.71 0.00 43.01 2.94
16 17 1.562942 ACATCTGATGTGGCATGTCCT 59.437 47.619 21.71 0.00 43.01 3.85
17 18 2.048444 ACATCTGATGTGGCATGTCC 57.952 50.000 21.71 0.00 43.01 4.02
26 27 5.563876 AATGCTCTATCCACATCTGATGT 57.436 39.130 17.24 17.24 46.22 3.06
27 28 5.181433 CCAAATGCTCTATCCACATCTGATG 59.819 44.000 15.83 15.83 0.00 3.07
28 29 5.314529 CCAAATGCTCTATCCACATCTGAT 58.685 41.667 0.00 0.00 0.00 2.90
29 30 4.445305 CCCAAATGCTCTATCCACATCTGA 60.445 45.833 0.00 0.00 0.00 3.27
30 31 3.819337 CCCAAATGCTCTATCCACATCTG 59.181 47.826 0.00 0.00 0.00 2.90
40 41 4.621274 GCTTGCAAAATCCCAAATGCTCTA 60.621 41.667 0.00 0.00 39.49 2.43
318 320 0.679002 CCATGCCCACCACTCTTCAG 60.679 60.000 0.00 0.00 0.00 3.02
543 558 1.068333 AGCAGTGCGCAAAAATACAGG 60.068 47.619 14.00 0.00 46.13 4.00
703 727 1.568504 ATTACGACCTTCTCCCTGCA 58.431 50.000 0.00 0.00 0.00 4.41
704 728 2.678336 CAAATTACGACCTTCTCCCTGC 59.322 50.000 0.00 0.00 0.00 4.85
713 737 5.815740 ACGATTATCTTGCAAATTACGACCT 59.184 36.000 0.00 0.00 0.00 3.85
717 741 6.255215 ACCAACGATTATCTTGCAAATTACG 58.745 36.000 0.00 4.88 0.00 3.18
725 749 6.487103 CCTTTTCTACCAACGATTATCTTGC 58.513 40.000 0.00 0.00 0.00 4.01
726 750 6.093495 TGCCTTTTCTACCAACGATTATCTTG 59.907 38.462 0.00 0.00 0.00 3.02
742 766 5.310451 TCCAACGTATAACTTGCCTTTTCT 58.690 37.500 0.00 0.00 0.00 2.52
754 778 7.828508 ACACCTGTATCTATCCAACGTATAA 57.171 36.000 0.00 0.00 0.00 0.98
766 790 5.423931 TCTGCCATGTTTACACCTGTATCTA 59.576 40.000 0.00 0.00 0.00 1.98
767 791 4.225042 TCTGCCATGTTTACACCTGTATCT 59.775 41.667 0.00 0.00 0.00 1.98
768 792 4.332819 GTCTGCCATGTTTACACCTGTATC 59.667 45.833 0.00 0.00 0.00 2.24
770 794 3.071747 TGTCTGCCATGTTTACACCTGTA 59.928 43.478 0.00 0.00 0.00 2.74
771 795 2.158682 TGTCTGCCATGTTTACACCTGT 60.159 45.455 0.00 0.00 0.00 4.00
773 797 2.949177 TGTCTGCCATGTTTACACCT 57.051 45.000 0.00 0.00 0.00 4.00
774 798 3.426159 CGATTGTCTGCCATGTTTACACC 60.426 47.826 0.00 0.00 0.00 4.16
790 814 1.331756 GATCAAATCAGCCGCGATTGT 59.668 47.619 8.23 0.00 35.77 2.71
802 826 9.173939 GTTATGGTCGAATCAAATGATCAAATC 57.826 33.333 0.00 0.00 32.75 2.17
806 830 6.597280 TGTGTTATGGTCGAATCAAATGATCA 59.403 34.615 0.00 0.00 32.75 2.92
807 831 7.011389 TCTGTGTTATGGTCGAATCAAATGATC 59.989 37.037 0.00 0.00 32.75 2.92
810 834 6.421377 TCTGTGTTATGGTCGAATCAAATG 57.579 37.500 0.00 0.00 0.00 2.32
820 844 6.092807 GGAAACTGATCTTCTGTGTTATGGTC 59.907 42.308 0.00 0.00 0.00 4.02
838 862 4.020218 TGGGTACAGAGAGAATGGAAACTG 60.020 45.833 0.00 0.00 0.00 3.16
856 880 4.981647 AGGGATAAATGGTCTTCATGGGTA 59.018 41.667 0.00 0.00 35.99 3.69
868 892 2.800250 GCTCCATGGAGGGATAAATGG 58.200 52.381 36.92 14.01 42.19 3.16
880 904 1.664017 CGAGATGCTCGCTCCATGG 60.664 63.158 4.97 4.97 46.75 3.66
896 924 7.776933 ATATCTTGTACTTGTACTACGACGA 57.223 36.000 0.00 0.19 0.00 4.20
898 926 8.543774 ACGTATATCTTGTACTTGTACTACGAC 58.456 37.037 22.58 9.48 34.15 4.34
901 929 9.784824 CGTACGTATATCTTGTACTTGTACTAC 57.215 37.037 7.22 4.72 37.04 2.73
935 964 1.812922 CGATGGACTGGAGCACTGC 60.813 63.158 0.00 0.00 0.00 4.40
946 975 2.166459 TGAAGTGATCAGACCGATGGAC 59.834 50.000 0.00 0.00 33.17 4.02
954 983 1.546476 AGGACGGTGAAGTGATCAGAC 59.454 52.381 0.00 0.00 39.19 3.51
970 999 3.118992 TGTGTATGCTGATGAGTGAGGAC 60.119 47.826 0.00 0.00 0.00 3.85
971 1000 3.099141 TGTGTATGCTGATGAGTGAGGA 58.901 45.455 0.00 0.00 0.00 3.71
972 1001 3.531934 TGTGTATGCTGATGAGTGAGG 57.468 47.619 0.00 0.00 0.00 3.86
973 1002 4.092529 GTGTTGTGTATGCTGATGAGTGAG 59.907 45.833 0.00 0.00 0.00 3.51
974 1003 3.996363 GTGTTGTGTATGCTGATGAGTGA 59.004 43.478 0.00 0.00 0.00 3.41
975 1004 3.747529 TGTGTTGTGTATGCTGATGAGTG 59.252 43.478 0.00 0.00 0.00 3.51
976 1005 4.006780 TGTGTTGTGTATGCTGATGAGT 57.993 40.909 0.00 0.00 0.00 3.41
977 1006 4.632688 TCATGTGTTGTGTATGCTGATGAG 59.367 41.667 0.00 0.00 0.00 2.90
998 1027 3.148412 CTGGTCATGTGGTTGTTCATCA 58.852 45.455 0.00 0.00 0.00 3.07
1027 1056 1.160137 GTGAGAAGAAGCGCAACCAT 58.840 50.000 11.47 0.00 0.00 3.55
1062 1091 1.365368 TACATCGTGCATTGGTGGCG 61.365 55.000 7.05 0.00 0.00 5.69
1100 1129 4.660789 AGAAAGAAGCAACACAAGCAAT 57.339 36.364 0.00 0.00 0.00 3.56
1101 1130 4.454728 AAGAAAGAAGCAACACAAGCAA 57.545 36.364 0.00 0.00 0.00 3.91
1120 1149 5.048224 GCAGGGTGATTGATCCATGATTAAG 60.048 44.000 0.00 0.00 37.66 1.85
1134 1163 7.486407 AAATAAGATTGAAAGCAGGGTGATT 57.514 32.000 0.00 0.00 0.00 2.57
1159 1188 3.191371 GGCCTGAACGAAAACAGATGATT 59.809 43.478 0.00 0.00 36.38 2.57
1161 1190 2.151202 GGCCTGAACGAAAACAGATGA 58.849 47.619 0.00 0.00 36.38 2.92
1173 1202 1.576356 GTCGATGATCTGGCCTGAAC 58.424 55.000 17.04 14.46 0.00 3.18
1182 1211 2.556459 CCTCCGCCGTCGATGATCT 61.556 63.158 6.11 0.00 38.10 2.75
1198 1227 3.512680 CAAACTAATCTTCTCGTCGCCT 58.487 45.455 0.00 0.00 0.00 5.52
1251 1280 1.792367 TGTCGAGTTTGCAGAATGACG 59.208 47.619 0.00 0.00 39.69 4.35
1441 1472 7.203910 ACCGTGCATTGTACAATTTTTCTAAA 58.796 30.769 18.50 0.00 0.00 1.85
1444 1475 5.195001 ACCGTGCATTGTACAATTTTTCT 57.805 34.783 18.50 0.00 0.00 2.52
1448 1479 2.095466 CCGACCGTGCATTGTACAATTT 60.095 45.455 18.50 0.00 0.00 1.82
1465 1496 1.279527 TTTCACACGCATCGACCGAC 61.280 55.000 13.45 0.00 0.00 4.79
1505 1536 6.157645 ACTTGTGAGGGAAAGATGATGATACT 59.842 38.462 0.00 0.00 0.00 2.12
1548 1579 6.295916 CCATAGATAGGGGAGTATGGTTGTTC 60.296 46.154 0.00 0.00 37.98 3.18
1557 1588 5.014966 GTGGTAGTCCATAGATAGGGGAGTA 59.985 48.000 0.00 0.00 46.20 2.59
1569 1600 3.372784 GGTGAGGAGAGTGGTAGTCCATA 60.373 52.174 0.00 0.00 46.20 2.74
1574 1605 0.404812 ACGGTGAGGAGAGTGGTAGT 59.595 55.000 0.00 0.00 0.00 2.73
1575 1606 2.414994 TACGGTGAGGAGAGTGGTAG 57.585 55.000 0.00 0.00 0.00 3.18
1579 1610 1.178276 AGCTTACGGTGAGGAGAGTG 58.822 55.000 1.90 0.00 0.00 3.51
1581 1612 2.366533 TGTAGCTTACGGTGAGGAGAG 58.633 52.381 0.00 0.00 0.00 3.20
1590 1621 3.370978 CCAGATGTGTTTGTAGCTTACGG 59.629 47.826 0.00 0.00 0.00 4.02
1592 1623 7.119262 ACATTACCAGATGTGTTTGTAGCTTAC 59.881 37.037 0.00 0.00 38.75 2.34
1608 1639 4.513442 AGAAATTAGCGCACATTACCAGA 58.487 39.130 11.47 0.00 0.00 3.86
1634 1665 9.767684 GCAGCGCACATATATTTATTTAATGTA 57.232 29.630 11.47 0.00 0.00 2.29
1640 1671 6.642131 CCTTTGCAGCGCACATATATTTATTT 59.358 34.615 11.47 0.00 38.71 1.40
1641 1672 6.151691 CCTTTGCAGCGCACATATATTTATT 58.848 36.000 11.47 0.00 38.71 1.40
1650 1681 4.060038 GCCCTTTGCAGCGCACAT 62.060 61.111 11.47 0.00 38.71 3.21
1655 1686 0.313672 TTTGTAAGCCCTTTGCAGCG 59.686 50.000 0.00 0.00 44.83 5.18
1657 1688 2.299867 ACCATTTGTAAGCCCTTTGCAG 59.700 45.455 0.00 0.00 44.83 4.41
1668 1699 9.692749 TGATAAATGCGTAAAAACCATTTGTAA 57.307 25.926 7.79 0.00 38.98 2.41
1669 1700 9.862371 ATGATAAATGCGTAAAAACCATTTGTA 57.138 25.926 7.79 0.00 38.98 2.41
1673 1704 9.598517 AATCATGATAAATGCGTAAAAACCATT 57.401 25.926 9.04 0.00 0.00 3.16
1765 1797 9.411189 TGGGCGTTAGTATTTTCCTAATTTAAT 57.589 29.630 0.00 0.00 0.00 1.40
1766 1798 8.676401 GTGGGCGTTAGTATTTTCCTAATTTAA 58.324 33.333 0.00 0.00 0.00 1.52
1767 1799 7.828223 TGTGGGCGTTAGTATTTTCCTAATTTA 59.172 33.333 0.00 0.00 0.00 1.40
1776 1808 2.481185 CACGTGTGGGCGTTAGTATTTT 59.519 45.455 7.58 0.00 43.83 1.82
1843 1879 5.402270 ACAATGCTCTAAAAATCGTGCAAAC 59.598 36.000 0.00 0.00 33.97 2.93
1971 2022 2.529643 TGCGGGTAGGTGGGGAAA 60.530 61.111 0.00 0.00 0.00 3.13
2178 2229 4.680237 CGTGGACTGCGGGCTTCA 62.680 66.667 0.00 0.00 0.00 3.02
2188 2239 1.079127 CGCTGGAAATCCGTGGACT 60.079 57.895 0.00 0.00 39.43 3.85
2203 2254 1.845266 CATACACTCAATCTCGCGCT 58.155 50.000 5.56 0.00 0.00 5.92
2234 2285 1.000827 CATCTGCCGCTCCACTACTAG 60.001 57.143 0.00 0.00 0.00 2.57
2236 2287 1.680522 CCATCTGCCGCTCCACTACT 61.681 60.000 0.00 0.00 0.00 2.57
2239 2290 4.479993 GCCATCTGCCGCTCCACT 62.480 66.667 0.00 0.00 0.00 4.00
2291 2342 2.254350 CGTCCGCGAGAACAGACA 59.746 61.111 8.23 0.00 41.33 3.41
2347 2398 4.176752 ATTCCCTTCGGCGCTCCC 62.177 66.667 7.64 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.