Multiple sequence alignment - TraesCS6B01G058200

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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 TraesCS6B01G058200 chr6B 100.000 2759 0 0 1 2759 38710193 38712951 0.000000e+00 5096.0
1 TraesCS6B01G058200 chr6B 93.103 203 8 3 1 197 715075583 715075381 2.690000e-75 292.0
2 TraesCS6B01G058200 chr6B 91.716 169 10 1 186 354 715074673 715074509 5.940000e-57 231.0
3 TraesCS6B01G058200 chr5D 89.140 2035 205 9 730 2759 388112376 388114399 0.000000e+00 2519.0
4 TraesCS6B01G058200 chr5D 91.566 83 7 0 181 263 302880898 302880980 6.240000e-22 115.0
5 TraesCS6B01G058200 chr3A 87.187 2037 248 12 732 2759 654279030 654281062 0.000000e+00 2303.0
6 TraesCS6B01G058200 chr3A 84.016 2027 302 16 728 2750 40833695 40835703 0.000000e+00 1929.0
7 TraesCS6B01G058200 chr7A 86.969 2049 243 8 734 2759 563248051 563250098 0.000000e+00 2283.0
8 TraesCS6B01G058200 chr6A 86.572 2033 262 10 730 2758 544159660 544161685 0.000000e+00 2231.0
9 TraesCS6B01G058200 chr4A 83.580 2028 309 19 728 2750 82740212 82742220 0.000000e+00 1879.0
10 TraesCS6B01G058200 chr4A 82.776 389 26 17 1 355 677874459 677874840 2.670000e-80 309.0
11 TraesCS6B01G058200 chr4A 100.000 31 0 0 692 722 329169534 329169564 1.070000e-04 58.4
12 TraesCS6B01G058200 chr7D 86.924 1606 204 6 1157 2759 91749559 91751161 0.000000e+00 1797.0
13 TraesCS6B01G058200 chr7D 86.737 1606 207 6 1157 2759 91779888 91781490 0.000000e+00 1781.0
14 TraesCS6B01G058200 chr7D 89.055 201 15 3 1 197 264030360 264030163 2.750000e-60 243.0
15 TraesCS6B01G058200 chr7D 92.771 83 6 0 181 263 264030148 264030066 1.340000e-23 121.0
16 TraesCS6B01G058200 chr7D 100.000 31 0 0 692 722 383894694 383894724 1.070000e-04 58.4
17 TraesCS6B01G058200 chr3B 82.759 1566 263 7 733 2296 74271298 74269738 0.000000e+00 1389.0
18 TraesCS6B01G058200 chr3B 87.624 202 18 5 1 197 780612548 780612349 7.690000e-56 228.0
19 TraesCS6B01G058200 chr3B 93.750 80 5 0 184 263 780612331 780612252 1.340000e-23 121.0
20 TraesCS6B01G058200 chr1D 89.570 1093 113 1 1668 2759 452245107 452246199 0.000000e+00 1386.0
21 TraesCS6B01G058200 chr1D 100.000 31 0 0 692 722 388611528 388611498 1.070000e-04 58.4
22 TraesCS6B01G058200 chr2D 85.356 519 55 10 182 692 31508089 31508594 4.070000e-143 518.0
23 TraesCS6B01G058200 chr2D 91.457 199 13 2 1 197 31507878 31508074 1.260000e-68 270.0
24 TraesCS6B01G058200 chr2D 86.567 201 19 4 1 197 35561436 35561240 5.980000e-52 215.0
25 TraesCS6B01G058200 chr2D 76.112 427 55 21 247 652 35561127 35560727 2.180000e-41 180.0
26 TraesCS6B01G058200 chr2D 91.566 83 7 0 181 263 35561225 35561143 6.240000e-22 115.0
27 TraesCS6B01G058200 chr2A 82.806 506 51 13 193 692 765603814 765604289 1.180000e-113 420.0
28 TraesCS6B01G058200 chr2A 94.500 200 8 2 1 197 765603328 765603527 3.450000e-79 305.0
29 TraesCS6B01G058200 chr7B 80.272 441 47 22 1 408 706618229 706618662 2.080000e-76 296.0
30 TraesCS6B01G058200 chr7B 85.268 224 23 6 185 408 706704592 706704805 3.580000e-54 222.0
31 TraesCS6B01G058200 chr4B 84.483 290 31 10 2 287 498418043 498417764 9.730000e-70 274.0


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 TraesCS6B01G058200 chr6B 38710193 38712951 2758 False 5096.0 5096 100.0000 1 2759 1 chr6B.!!$F1 2758
1 TraesCS6B01G058200 chr6B 715074509 715075583 1074 True 261.5 292 92.4095 1 354 2 chr6B.!!$R1 353
2 TraesCS6B01G058200 chr5D 388112376 388114399 2023 False 2519.0 2519 89.1400 730 2759 1 chr5D.!!$F2 2029
3 TraesCS6B01G058200 chr3A 654279030 654281062 2032 False 2303.0 2303 87.1870 732 2759 1 chr3A.!!$F2 2027
4 TraesCS6B01G058200 chr3A 40833695 40835703 2008 False 1929.0 1929 84.0160 728 2750 1 chr3A.!!$F1 2022
5 TraesCS6B01G058200 chr7A 563248051 563250098 2047 False 2283.0 2283 86.9690 734 2759 1 chr7A.!!$F1 2025
6 TraesCS6B01G058200 chr6A 544159660 544161685 2025 False 2231.0 2231 86.5720 730 2758 1 chr6A.!!$F1 2028
7 TraesCS6B01G058200 chr4A 82740212 82742220 2008 False 1879.0 1879 83.5800 728 2750 1 chr4A.!!$F1 2022
8 TraesCS6B01G058200 chr7D 91749559 91751161 1602 False 1797.0 1797 86.9240 1157 2759 1 chr7D.!!$F1 1602
9 TraesCS6B01G058200 chr7D 91779888 91781490 1602 False 1781.0 1781 86.7370 1157 2759 1 chr7D.!!$F2 1602
10 TraesCS6B01G058200 chr3B 74269738 74271298 1560 True 1389.0 1389 82.7590 733 2296 1 chr3B.!!$R1 1563
11 TraesCS6B01G058200 chr1D 452245107 452246199 1092 False 1386.0 1386 89.5700 1668 2759 1 chr1D.!!$F1 1091
12 TraesCS6B01G058200 chr2D 31507878 31508594 716 False 394.0 518 88.4065 1 692 2 chr2D.!!$F1 691
13 TraesCS6B01G058200 chr2A 765603328 765604289 961 False 362.5 420 88.6530 1 692 2 chr2A.!!$F1 691

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
649 1648 0.179009 CCATGATGATGGGGCGAGTT 60.179 55.0 2.74 0.0 45.11 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 3136 0.32016 GAACTGTCGCGGGTTTACCT 60.32 55.0 6.13 0.0 36.97 3.08 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
102 103 5.716228 TGTTTCCATTCCATGTGCTTCTATT 59.284 36.000 0.00 0.00 0.00 1.73
103 104 5.840243 TTCCATTCCATGTGCTTCTATTG 57.160 39.130 0.00 0.00 0.00 1.90
105 106 4.079844 TCCATTCCATGTGCTTCTATTGGA 60.080 41.667 0.00 0.00 34.74 3.53
210 1197 7.716799 AGCAAATATGTAATTTGTGGGAAGA 57.283 32.000 11.03 0.00 40.19 2.87
265 1256 7.833285 ATCACAACCTACCAAAACAATTAGT 57.167 32.000 0.00 0.00 0.00 2.24
356 1347 2.619177 CGGGAGGAGATGCTATATACGG 59.381 54.545 0.00 0.00 0.00 4.02
357 1348 3.684697 CGGGAGGAGATGCTATATACGGA 60.685 52.174 0.00 0.00 0.00 4.69
408 1399 2.238521 AGGAAGGAAAAATTCAGCGCA 58.761 42.857 11.47 0.00 0.00 6.09
410 1401 3.259123 AGGAAGGAAAAATTCAGCGCATT 59.741 39.130 11.47 0.00 0.00 3.56
419 1410 2.588027 TTCAGCGCATTACCATCGTA 57.412 45.000 11.47 0.00 0.00 3.43
431 1422 6.681777 CATTACCATCGTATCAGATCAGACA 58.318 40.000 0.00 0.00 0.00 3.41
433 1424 5.598416 ACCATCGTATCAGATCAGACAAA 57.402 39.130 0.00 0.00 0.00 2.83
434 1425 5.352284 ACCATCGTATCAGATCAGACAAAC 58.648 41.667 0.00 0.00 0.00 2.93
435 1426 5.105351 ACCATCGTATCAGATCAGACAAACA 60.105 40.000 0.00 0.00 0.00 2.83
436 1427 5.812127 CCATCGTATCAGATCAGACAAACAA 59.188 40.000 0.00 0.00 0.00 2.83
437 1428 6.237942 CCATCGTATCAGATCAGACAAACAAC 60.238 42.308 0.00 0.00 0.00 3.32
438 1429 4.857037 TCGTATCAGATCAGACAAACAACG 59.143 41.667 0.00 0.00 0.00 4.10
439 1430 4.031765 CGTATCAGATCAGACAAACAACGG 59.968 45.833 0.00 0.00 0.00 4.44
459 1450 1.334869 GAATGTTAATCCAGCGGCCAG 59.665 52.381 2.24 0.00 0.00 4.85
480 1471 4.338682 CAGCCAGACGAAGGTACTAATAGT 59.661 45.833 0.00 0.00 38.49 2.12
486 1477 6.037940 CAGACGAAGGTACTAATAGTGCAGTA 59.962 42.308 10.50 3.17 38.49 2.74
535 1526 2.931713 GATCTGGTCGTACCGCGGTG 62.932 65.000 40.02 24.81 42.58 4.94
544 1535 1.068474 GTACCGCGGTGCATATGATC 58.932 55.000 40.02 14.27 0.00 2.92
546 1537 2.471607 CGCGGTGCATATGATCGC 59.528 61.111 20.23 20.23 42.51 4.58
574 1565 0.818296 TCTAGTTCGAGGCTTGCCTC 59.182 55.000 26.80 26.80 0.00 4.70
649 1648 0.179009 CCATGATGATGGGGCGAGTT 60.179 55.000 2.74 0.00 45.11 3.01
650 1649 0.949397 CATGATGATGGGGCGAGTTG 59.051 55.000 0.00 0.00 0.00 3.16
651 1650 0.839277 ATGATGATGGGGCGAGTTGA 59.161 50.000 0.00 0.00 0.00 3.18
652 1651 0.839277 TGATGATGGGGCGAGTTGAT 59.161 50.000 0.00 0.00 0.00 2.57
666 1665 4.206609 GCGAGTTGATGTATTTCGTAGACC 59.793 45.833 0.00 0.00 34.32 3.85
668 1667 5.977725 CGAGTTGATGTATTTCGTAGACCAT 59.022 40.000 0.00 0.00 34.32 3.55
669 1668 6.475727 CGAGTTGATGTATTTCGTAGACCATT 59.524 38.462 0.00 0.00 34.32 3.16
674 1673 7.496747 TGATGTATTTCGTAGACCATTCATCA 58.503 34.615 0.00 0.00 39.59 3.07
682 1681 7.519032 TCGTAGACCATTCATCATACATACA 57.481 36.000 0.00 0.00 0.00 2.29
684 1683 8.082242 TCGTAGACCATTCATCATACATACAAG 58.918 37.037 0.00 0.00 0.00 3.16
692 1691 8.762426 CATTCATCATACATACAAGAGTGAGTG 58.238 37.037 0.00 0.00 0.00 3.51
693 1692 6.276091 TCATCATACATACAAGAGTGAGTGC 58.724 40.000 0.00 0.00 0.00 4.40
694 1693 5.921962 TCATACATACAAGAGTGAGTGCT 57.078 39.130 0.00 0.00 0.00 4.40
695 1694 5.895928 TCATACATACAAGAGTGAGTGCTC 58.104 41.667 0.00 0.00 35.82 4.26
696 1695 3.601443 ACATACAAGAGTGAGTGCTCC 57.399 47.619 0.00 0.00 36.20 4.70
697 1696 2.094494 ACATACAAGAGTGAGTGCTCCG 60.094 50.000 0.00 0.00 36.20 4.63
698 1697 0.243907 TACAAGAGTGAGTGCTCCGC 59.756 55.000 0.00 0.00 36.20 5.54
699 1698 1.291588 CAAGAGTGAGTGCTCCGCT 59.708 57.895 0.00 0.00 36.20 5.52
700 1699 1.013005 CAAGAGTGAGTGCTCCGCTG 61.013 60.000 0.00 0.00 36.20 5.18
701 1700 2.778309 AAGAGTGAGTGCTCCGCTGC 62.778 60.000 0.00 0.00 36.20 5.25
702 1701 3.580100 GAGTGAGTGCTCCGCTGCA 62.580 63.158 0.00 0.00 41.05 4.41
703 1702 3.117171 GTGAGTGCTCCGCTGCAG 61.117 66.667 10.11 10.11 44.20 4.41
705 1704 3.117171 GAGTGCTCCGCTGCAGTG 61.117 66.667 20.56 20.56 45.47 3.66
715 1714 3.773117 GCTGCAGTGCGTGTTAATT 57.227 47.368 16.64 0.00 0.00 1.40
716 1715 1.330306 GCTGCAGTGCGTGTTAATTG 58.670 50.000 16.64 0.00 0.00 2.32
717 1716 1.069296 GCTGCAGTGCGTGTTAATTGA 60.069 47.619 16.64 0.00 0.00 2.57
718 1717 2.604373 GCTGCAGTGCGTGTTAATTGAA 60.604 45.455 16.64 0.00 0.00 2.69
719 1718 3.228749 CTGCAGTGCGTGTTAATTGAAG 58.771 45.455 11.20 0.00 0.00 3.02
720 1719 2.616376 TGCAGTGCGTGTTAATTGAAGT 59.384 40.909 11.20 0.00 0.00 3.01
721 1720 3.810386 TGCAGTGCGTGTTAATTGAAGTA 59.190 39.130 11.20 0.00 0.00 2.24
722 1721 4.454161 TGCAGTGCGTGTTAATTGAAGTAT 59.546 37.500 11.20 0.00 0.00 2.12
723 1722 5.639931 TGCAGTGCGTGTTAATTGAAGTATA 59.360 36.000 11.20 0.00 0.00 1.47
724 1723 6.147985 TGCAGTGCGTGTTAATTGAAGTATAA 59.852 34.615 11.20 0.00 0.00 0.98
725 1724 7.148323 TGCAGTGCGTGTTAATTGAAGTATAAT 60.148 33.333 11.20 0.00 0.00 1.28
726 1725 7.373441 GCAGTGCGTGTTAATTGAAGTATAATC 59.627 37.037 0.00 0.00 0.00 1.75
745 1744 2.294074 TCAGGTTTTTCCCTCACGTTG 58.706 47.619 0.00 0.00 36.75 4.10
755 1757 0.666374 CCTCACGTTGGGGTTTTGTC 59.334 55.000 0.00 0.00 31.83 3.18
761 1763 2.092592 ACGTTGGGGTTTTGTCTTCTCT 60.093 45.455 0.00 0.00 0.00 3.10
772 1774 0.387565 GTCTTCTCTGAGGCGATCCC 59.612 60.000 4.59 0.00 0.00 3.85
786 1788 3.837213 ATCCCCCGCCTCCTAGAGC 62.837 68.421 0.00 0.00 0.00 4.09
948 1955 2.521126 TCGGGTGAGACTACAACATGA 58.479 47.619 0.00 0.00 0.00 3.07
953 1960 3.921021 GGTGAGACTACAACATGACTTCG 59.079 47.826 0.00 0.00 0.00 3.79
962 1969 3.623960 ACAACATGACTTCGGACGAAAAA 59.376 39.130 8.59 0.00 33.34 1.94
1009 2016 4.642437 ACGTAGAGAAGATGATGCAAGAGA 59.358 41.667 0.00 0.00 0.00 3.10
1017 2024 2.519771 TGATGCAAGAGATTGGGCTT 57.480 45.000 0.00 0.00 0.00 4.35
1028 2035 2.092158 AGATTGGGCTTAAGGAAGAGGC 60.092 50.000 4.29 0.00 34.25 4.70
1080 2087 1.220206 CCCTGAAGATGCAGCTCGT 59.780 57.895 4.22 0.00 34.56 4.18
1254 2263 0.179936 GGGAGAGGGTGATGCAAGAG 59.820 60.000 0.00 0.00 0.00 2.85
1280 2289 0.547471 TGGCACTTCAGGGGAGATGA 60.547 55.000 0.00 0.00 0.00 2.92
1356 2366 6.126215 TGGACACAATAGATATTTGGGTCCAT 60.126 38.462 27.75 0.00 43.74 3.41
1389 2399 1.308998 CCGACTTGTTTGCTCACCTT 58.691 50.000 0.00 0.00 0.00 3.50
1411 2421 3.842925 GAACCACTTGCGGGCAGGA 62.843 63.158 9.90 0.00 0.00 3.86
1419 2429 0.764369 TTGCGGGCAGGATAGGAGAT 60.764 55.000 0.00 0.00 0.00 2.75
1583 2593 0.467290 AAGTTGCCCGATTGGTGTGT 60.467 50.000 0.00 0.00 36.04 3.72
1625 2635 3.553828 TCTCTTCAAAGAACACGGGTT 57.446 42.857 0.56 0.56 40.76 4.11
1710 2720 4.270153 AGAGGGCCTGGTGGTGGA 62.270 66.667 12.95 0.00 35.27 4.02
1749 2759 1.019805 GCAAAGGAGGACGTACTGGC 61.020 60.000 4.10 0.00 0.00 4.85
1756 2766 0.683504 AGGACGTACTGGCGGAAGAT 60.684 55.000 0.00 0.00 35.98 2.40
1761 2771 1.202417 CGTACTGGCGGAAGATGACAT 60.202 52.381 0.00 0.00 0.00 3.06
1765 2775 2.501723 ACTGGCGGAAGATGACATAACT 59.498 45.455 0.00 0.00 0.00 2.24
1788 2798 1.748493 GGCAATAACCGCTTTGATGGA 59.252 47.619 0.00 0.00 0.00 3.41
1794 2804 0.107017 ACCGCTTTGATGGAGATGGG 60.107 55.000 0.00 0.00 0.00 4.00
1812 2822 1.528129 GGAGGGAGAAGCAAACACAG 58.472 55.000 0.00 0.00 0.00 3.66
1846 2856 2.565391 TCAGAACCGGCTCAAGATACAA 59.435 45.455 7.76 0.00 0.00 2.41
1879 2889 4.590487 CTCGTAAAAGGGCGAGCA 57.410 55.556 1.06 0.00 46.01 4.26
1895 2905 0.109153 AGCAGCACAGGACATGTCAA 59.891 50.000 26.47 0.00 41.41 3.18
1941 2951 2.196997 CTGGCTTGGGACCCGATCAA 62.197 60.000 5.91 0.00 0.00 2.57
2010 3020 3.425162 AAAAGAGATCCCAAGCGAACT 57.575 42.857 0.00 0.00 0.00 3.01
2023 3033 2.180276 AGCGAACTAGATTGGTGACCT 58.820 47.619 2.11 0.00 0.00 3.85
2048 3058 3.699538 GGTCAGGAAGGTTTCAACAACTT 59.300 43.478 0.00 0.00 0.00 2.66
2116 3126 6.272318 CAATGAGTGCTTTTTGTTGGAACTA 58.728 36.000 0.00 0.00 0.00 2.24
2261 3271 7.416664 GCTGGAACATTAGGCTTTGATAATTCA 60.417 37.037 0.00 0.00 38.20 2.57
2378 3388 2.637382 TGATGCTAGGGTCACAGAAACA 59.363 45.455 0.00 0.00 0.00 2.83
2384 3394 0.467290 GGGTCACAGAAACAGGCCAA 60.467 55.000 5.01 0.00 0.00 4.52
2565 3575 2.868044 GCGGATAGGAGTAATGCACAGG 60.868 54.545 0.00 0.00 0.00 4.00
2645 3656 0.884514 GCCCTGGACTTTTGAGAAGC 59.115 55.000 0.00 0.00 0.00 3.86
2685 3713 1.070786 GCAGGGTCCGTCTTGACAA 59.929 57.895 1.59 0.00 36.97 3.18
2715 3743 0.898326 TCGGCTAGTTGGACAGCTCA 60.898 55.000 0.00 0.00 37.91 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 2.409651 GCAAACGCCGTGGAAACA 59.590 55.556 0.00 0.00 38.70 2.83
113 115 2.724358 CGCAAACGCCGTGGAAAC 60.724 61.111 0.00 0.00 0.00 2.78
114 116 2.762234 AACGCAAACGCCGTGGAAA 61.762 52.632 0.00 0.00 45.53 3.13
120 125 1.792057 CTTAGCAACGCAAACGCCG 60.792 57.895 0.00 0.00 45.53 6.46
217 1208 3.181539 GCTTCGAACAAACAAACGCAAAA 60.182 39.130 0.00 0.00 0.00 2.44
219 1210 1.914700 GCTTCGAACAAACAAACGCAA 59.085 42.857 0.00 0.00 0.00 4.85
220 1211 1.135660 TGCTTCGAACAAACAAACGCA 60.136 42.857 0.00 0.00 0.00 5.24
221 1212 1.540407 TGCTTCGAACAAACAAACGC 58.460 45.000 0.00 0.00 0.00 4.84
222 1213 3.788694 TGATTGCTTCGAACAAACAAACG 59.211 39.130 15.57 0.00 28.34 3.60
234 1225 2.422597 TGGTAGGTTGTGATTGCTTCG 58.577 47.619 0.00 0.00 0.00 3.79
297 1288 8.744008 TCGATAATTAATTCTGTGCTACTAGC 57.256 34.615 3.39 0.61 42.82 3.42
302 1293 8.585018 TCTCCATCGATAATTAATTCTGTGCTA 58.415 33.333 3.39 0.00 0.00 3.49
356 1347 2.983229 TCTAGTCACTCCCACGTACTC 58.017 52.381 0.00 0.00 0.00 2.59
357 1348 3.345414 CTTCTAGTCACTCCCACGTACT 58.655 50.000 0.00 0.00 0.00 2.73
359 1350 2.089980 GCTTCTAGTCACTCCCACGTA 58.910 52.381 0.00 0.00 0.00 3.57
361 1352 0.888619 TGCTTCTAGTCACTCCCACG 59.111 55.000 0.00 0.00 0.00 4.94
363 1354 1.895798 CAGTGCTTCTAGTCACTCCCA 59.104 52.381 10.53 0.00 41.19 4.37
364 1355 2.171840 TCAGTGCTTCTAGTCACTCCC 58.828 52.381 10.53 0.00 41.19 4.30
365 1356 4.464069 AATCAGTGCTTCTAGTCACTCC 57.536 45.455 10.53 0.00 41.19 3.85
366 1357 6.039616 CCTAAATCAGTGCTTCTAGTCACTC 58.960 44.000 10.53 0.00 41.19 3.51
367 1358 5.717178 TCCTAAATCAGTGCTTCTAGTCACT 59.283 40.000 8.50 8.50 43.67 3.41
368 1359 5.967088 TCCTAAATCAGTGCTTCTAGTCAC 58.033 41.667 0.00 0.00 0.00 3.67
369 1360 6.351371 CCTTCCTAAATCAGTGCTTCTAGTCA 60.351 42.308 0.00 0.00 0.00 3.41
370 1361 6.045955 CCTTCCTAAATCAGTGCTTCTAGTC 58.954 44.000 0.00 0.00 0.00 2.59
408 1399 6.901081 TGTCTGATCTGATACGATGGTAAT 57.099 37.500 5.52 0.00 31.15 1.89
410 1401 6.096282 TGTTTGTCTGATCTGATACGATGGTA 59.904 38.462 5.52 0.00 0.00 3.25
419 1410 4.271696 TCCGTTGTTTGTCTGATCTGAT 57.728 40.909 5.52 0.00 0.00 2.90
431 1422 4.614993 CGCTGGATTAACATTCCGTTGTTT 60.615 41.667 1.67 0.00 40.25 2.83
433 1424 2.418628 CGCTGGATTAACATTCCGTTGT 59.581 45.455 0.00 0.00 38.63 3.32
434 1425 2.223249 CCGCTGGATTAACATTCCGTTG 60.223 50.000 0.00 0.00 38.63 4.10
435 1426 2.014128 CCGCTGGATTAACATTCCGTT 58.986 47.619 0.00 0.00 41.91 4.44
436 1427 1.663695 CCGCTGGATTAACATTCCGT 58.336 50.000 0.00 0.00 35.94 4.69
437 1428 0.307760 GCCGCTGGATTAACATTCCG 59.692 55.000 0.00 0.00 35.94 4.30
438 1429 0.668535 GGCCGCTGGATTAACATTCC 59.331 55.000 0.00 0.00 0.00 3.01
439 1430 1.334869 CTGGCCGCTGGATTAACATTC 59.665 52.381 0.00 0.00 0.00 2.67
459 1450 4.608951 CACTATTAGTACCTTCGTCTGGC 58.391 47.826 0.00 0.00 0.00 4.85
480 1471 9.489084 GTTGTGATATATTCTGGTATTACTGCA 57.511 33.333 0.00 0.00 0.00 4.41
535 1526 0.737715 GACCTCCGGCGATCATATGC 60.738 60.000 9.30 0.00 0.00 3.14
544 1535 1.728672 GAACTAGAGACCTCCGGCG 59.271 63.158 0.00 0.00 0.00 6.46
546 1537 1.301423 CTCGAACTAGAGACCTCCGG 58.699 60.000 0.00 0.00 40.57 5.14
610 1609 1.074248 CCGGCCCACTTACACCTTT 59.926 57.895 0.00 0.00 0.00 3.11
636 1635 1.199615 TACATCAACTCGCCCCATCA 58.800 50.000 0.00 0.00 0.00 3.07
639 1638 2.639065 GAAATACATCAACTCGCCCCA 58.361 47.619 0.00 0.00 0.00 4.96
649 1648 7.496747 TGATGAATGGTCTACGAAATACATCA 58.503 34.615 0.00 0.00 38.24 3.07
650 1649 7.946655 TGATGAATGGTCTACGAAATACATC 57.053 36.000 0.00 0.00 0.00 3.06
651 1650 9.424319 GTATGATGAATGGTCTACGAAATACAT 57.576 33.333 0.00 0.00 0.00 2.29
652 1651 8.417884 TGTATGATGAATGGTCTACGAAATACA 58.582 33.333 0.00 0.00 0.00 2.29
666 1665 8.762426 CACTCACTCTTGTATGTATGATGAATG 58.238 37.037 0.00 0.00 0.00 2.67
668 1667 6.758416 GCACTCACTCTTGTATGTATGATGAA 59.242 38.462 0.00 0.00 0.00 2.57
669 1668 6.097412 AGCACTCACTCTTGTATGTATGATGA 59.903 38.462 0.00 0.00 0.00 2.92
674 1673 4.202060 CGGAGCACTCACTCTTGTATGTAT 60.202 45.833 0.00 0.00 36.87 2.29
697 1696 1.069296 TCAATTAACACGCACTGCAGC 60.069 47.619 15.27 0.00 0.00 5.25
698 1697 2.967459 TCAATTAACACGCACTGCAG 57.033 45.000 13.48 13.48 0.00 4.41
699 1698 2.616376 ACTTCAATTAACACGCACTGCA 59.384 40.909 1.11 0.00 0.00 4.41
700 1699 3.268013 ACTTCAATTAACACGCACTGC 57.732 42.857 0.00 0.00 0.00 4.40
701 1700 8.387354 TGATTATACTTCAATTAACACGCACTG 58.613 33.333 0.00 0.00 0.00 3.66
702 1701 8.487313 TGATTATACTTCAATTAACACGCACT 57.513 30.769 0.00 0.00 0.00 4.40
703 1702 7.850982 CCTGATTATACTTCAATTAACACGCAC 59.149 37.037 0.00 0.00 0.00 5.34
704 1703 7.551262 ACCTGATTATACTTCAATTAACACGCA 59.449 33.333 0.00 0.00 0.00 5.24
705 1704 7.916552 ACCTGATTATACTTCAATTAACACGC 58.083 34.615 0.00 0.00 0.00 5.34
712 1711 9.547279 AGGGAAAAACCTGATTATACTTCAATT 57.453 29.630 0.00 0.00 40.04 2.32
713 1712 9.190317 GAGGGAAAAACCTGATTATACTTCAAT 57.810 33.333 0.00 0.00 42.10 2.57
714 1713 8.167392 TGAGGGAAAAACCTGATTATACTTCAA 58.833 33.333 0.00 0.00 42.10 2.69
715 1714 7.610305 GTGAGGGAAAAACCTGATTATACTTCA 59.390 37.037 0.00 0.00 42.10 3.02
716 1715 7.201617 CGTGAGGGAAAAACCTGATTATACTTC 60.202 40.741 0.00 0.00 42.10 3.01
717 1716 6.598064 CGTGAGGGAAAAACCTGATTATACTT 59.402 38.462 0.00 0.00 42.10 2.24
718 1717 6.113411 CGTGAGGGAAAAACCTGATTATACT 58.887 40.000 0.00 0.00 42.10 2.12
719 1718 5.878669 ACGTGAGGGAAAAACCTGATTATAC 59.121 40.000 0.00 0.00 42.10 1.47
720 1719 6.057321 ACGTGAGGGAAAAACCTGATTATA 57.943 37.500 0.00 0.00 42.10 0.98
721 1720 4.918588 ACGTGAGGGAAAAACCTGATTAT 58.081 39.130 0.00 0.00 42.10 1.28
722 1721 4.360951 ACGTGAGGGAAAAACCTGATTA 57.639 40.909 0.00 0.00 42.10 1.75
723 1722 3.223674 ACGTGAGGGAAAAACCTGATT 57.776 42.857 0.00 0.00 42.10 2.57
724 1723 2.884639 CAACGTGAGGGAAAAACCTGAT 59.115 45.455 0.00 0.00 42.10 2.90
725 1724 2.294074 CAACGTGAGGGAAAAACCTGA 58.706 47.619 0.00 0.00 42.10 3.86
726 1725 1.336755 CCAACGTGAGGGAAAAACCTG 59.663 52.381 0.00 0.00 42.10 4.00
745 1744 2.784347 CCTCAGAGAAGACAAAACCCC 58.216 52.381 0.00 0.00 0.00 4.95
755 1757 1.745264 GGGGATCGCCTCAGAGAAG 59.255 63.158 21.11 0.00 33.55 2.85
786 1788 4.760047 CGACAGGGACGGCCAAGG 62.760 72.222 11.00 0.00 35.15 3.61
810 1813 2.439104 GCAGGCAGGGGAGGTAGAG 61.439 68.421 0.00 0.00 0.00 2.43
813 1817 1.541368 AAAGCAGGCAGGGGAGGTA 60.541 57.895 0.00 0.00 0.00 3.08
908 1914 0.686441 TGGAGATCGGATCGGGTTGT 60.686 55.000 12.08 0.00 0.00 3.32
962 1969 3.717294 CCCCCACAGCGCTAGGTT 61.717 66.667 22.24 1.19 0.00 3.50
974 1981 1.001020 TCTACGTCGCTAACCCCCA 60.001 57.895 0.00 0.00 0.00 4.96
1009 2016 1.063642 GGCCTCTTCCTTAAGCCCAAT 60.064 52.381 0.00 0.00 37.66 3.16
1017 2024 0.976073 CGTCCAGGGCCTCTTCCTTA 60.976 60.000 0.95 0.00 31.06 2.69
1028 2035 1.003116 CGAATACTACGTCGTCCAGGG 60.003 57.143 0.00 0.00 32.61 4.45
1044 2051 0.034059 GGATGTCGGCCTCATCGAAT 59.966 55.000 22.50 4.90 41.54 3.34
1254 2263 2.757099 CTGAAGTGCCATGGCCCC 60.757 66.667 33.44 23.16 41.09 5.80
1280 2289 5.645067 CCATCGTATGGCTTGATAATGACAT 59.355 40.000 1.69 0.00 44.70 3.06
1356 2366 2.353357 AGTCGGGTACGTCATGGATA 57.647 50.000 0.00 0.00 41.85 2.59
1389 2399 0.250945 TGCCCGCAAGTGGTTCAATA 60.251 50.000 0.00 0.00 0.00 1.90
1411 2421 6.431234 GGTTCAACAAACAAGACATCTCCTAT 59.569 38.462 0.00 0.00 39.81 2.57
1419 2429 3.963129 AGGAGGTTCAACAAACAAGACA 58.037 40.909 0.00 0.00 39.81 3.41
1467 2477 6.549364 TCACTTCAATTCTTACCCAAACACAT 59.451 34.615 0.00 0.00 0.00 3.21
1468 2478 5.888724 TCACTTCAATTCTTACCCAAACACA 59.111 36.000 0.00 0.00 0.00 3.72
1488 2498 4.646492 ACATTCTTCAAAGGCTTTGTCACT 59.354 37.500 32.46 16.14 41.36 3.41
1583 2593 1.283613 GACCCAACATCCCACATACCA 59.716 52.381 0.00 0.00 0.00 3.25
1643 2653 5.620206 TCAGATCTTTGAACACTAAGGCAA 58.380 37.500 0.00 0.00 0.00 4.52
1733 2743 2.348888 CCGCCAGTACGTCCTCCTT 61.349 63.158 0.00 0.00 0.00 3.36
1749 2759 3.126831 GCCTGAGTTATGTCATCTTCCG 58.873 50.000 0.00 0.00 0.00 4.30
1756 2766 4.188462 CGGTTATTGCCTGAGTTATGTCA 58.812 43.478 0.00 0.00 0.00 3.58
1761 2771 3.343941 AAGCGGTTATTGCCTGAGTTA 57.656 42.857 0.00 0.00 0.00 2.24
1765 2775 2.192664 TCAAAGCGGTTATTGCCTGA 57.807 45.000 0.00 0.00 0.00 3.86
1788 2798 1.283321 GTTTGCTTCTCCCTCCCATCT 59.717 52.381 0.00 0.00 0.00 2.90
1794 2804 1.072331 TCCTGTGTTTGCTTCTCCCTC 59.928 52.381 0.00 0.00 0.00 4.30
1812 2822 3.462021 CGGTTCTGATTGATCTTCCTCC 58.538 50.000 0.00 0.00 0.00 4.30
1846 2856 2.530701 ACGAGAAGACTCCTCCATGTT 58.469 47.619 0.00 0.00 39.76 2.71
1879 2889 1.888215 CTGTTGACATGTCCTGTGCT 58.112 50.000 22.85 0.00 38.54 4.40
1941 2951 1.614241 CCACGGGCACTAAGGCTAGT 61.614 60.000 0.00 0.00 43.56 2.57
1979 2989 3.245264 GGGATCTCTTTTTGGAGGTGGAA 60.245 47.826 0.00 0.00 34.39 3.53
2010 3020 3.703804 ACCCGAGGTCACCAATCTA 57.296 52.632 0.00 0.00 0.00 1.98
2023 3033 1.133363 TTGAAACCTTCCTGACCCGA 58.867 50.000 0.00 0.00 0.00 5.14
2048 3058 4.830600 GGGAGGTCACCAAATTCTTAACAA 59.169 41.667 0.00 0.00 0.00 2.83
2116 3126 1.153429 GGTTTACCTGCTCCGCGAT 60.153 57.895 8.23 0.00 0.00 4.58
2126 3136 0.320160 GAACTGTCGCGGGTTTACCT 60.320 55.000 6.13 0.00 36.97 3.08
2384 3394 1.522355 CGTGATGCGCCAAGGATCT 60.522 57.895 4.18 0.00 46.37 2.75
2541 3551 3.832490 TGTGCATTACTCCTATCCGCTAT 59.168 43.478 0.00 0.00 0.00 2.97
2565 3575 1.804151 TGCATCACGGAAAGCTTGTAC 59.196 47.619 0.00 0.00 0.00 2.90
2645 3656 1.265454 AAGCTCCCTCCTGTAACCCG 61.265 60.000 0.00 0.00 0.00 5.28
2715 3743 9.983024 AGTGATATAGTGTAGCTAGTGGATATT 57.017 33.333 0.00 0.00 32.45 1.28


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

AutoCloner maintained by Alex Coulton.