Multiple sequence alignment - TraesCS2D01G556800

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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 TraesCS2D01G556800 chr2D 100.000 3817 0 0 1 3817 630092719 630088903 0.000000e+00 7049.0
1 TraesCS2D01G556800 chr2D 91.720 2017 98 27 1845 3817 629726424 629728415 0.000000e+00 2736.0
2 TraesCS2D01G556800 chr2D 88.564 1609 102 38 1812 3367 629990565 629988986 0.000000e+00 1877.0
3 TraesCS2D01G556800 chr2D 85.837 1631 111 57 1835 3390 630632943 630634528 0.000000e+00 1622.0
4 TraesCS2D01G556800 chr2D 86.776 794 70 15 1 770 630629634 630630416 0.000000e+00 852.0
5 TraesCS2D01G556800 chr2D 87.267 589 45 12 962 1537 630631836 630632407 0.000000e+00 645.0
6 TraesCS2D01G556800 chr2D 83.406 687 72 17 104 762 629992145 629991473 1.960000e-167 599.0
7 TraesCS2D01G556800 chr2D 86.414 449 44 9 1114 1553 629991180 629990740 3.450000e-130 475.0
8 TraesCS2D01G556800 chr2D 76.854 890 118 40 1918 2780 30661434 30660606 4.560000e-114 422.0
9 TraesCS2D01G556800 chr2D 85.377 212 24 6 3192 3403 630049712 630049508 2.990000e-51 213.0
10 TraesCS2D01G556800 chr2A 91.143 1050 51 18 2111 3141 760772006 760773032 0.000000e+00 1386.0
11 TraesCS2D01G556800 chr2A 91.675 949 55 14 2111 3043 760508799 760507859 0.000000e+00 1293.0
12 TraesCS2D01G556800 chr2A 89.692 844 48 21 2108 2926 760490412 760489583 0.000000e+00 1040.0
13 TraesCS2D01G556800 chr2A 94.016 635 26 7 3185 3817 760773036 760773660 0.000000e+00 952.0
14 TraesCS2D01G556800 chr2A 82.585 936 72 45 622 1528 760770439 760771312 0.000000e+00 741.0
15 TraesCS2D01G556800 chr2A 90.606 330 20 7 1219 1537 760509435 760509106 9.800000e-116 427.0
16 TraesCS2D01G556800 chr2A 83.954 349 33 12 2923 3264 760478652 760478320 2.860000e-81 313.0
17 TraesCS2D01G556800 chr2A 80.100 402 50 22 3437 3817 33005922 33006314 4.860000e-69 272.0
18 TraesCS2D01G556800 chr2A 88.750 160 14 3 3250 3408 760477048 760476892 3.890000e-45 193.0
19 TraesCS2D01G556800 chr2A 77.532 316 47 17 3520 3817 33022675 33022984 6.560000e-38 169.0
20 TraesCS2D01G556800 chr2A 78.095 315 31 19 1672 1982 760771728 760772008 8.480000e-37 165.0
21 TraesCS2D01G556800 chr2A 77.061 279 33 22 2804 3060 78804047 78803778 8.600000e-27 132.0
22 TraesCS2D01G556800 chr2A 94.366 71 2 2 3267 3337 760507282 760507214 1.450000e-19 108.0
23 TraesCS2D01G556800 chr2A 96.226 53 2 0 699 751 760510495 760510443 1.890000e-13 87.9
24 TraesCS2D01G556800 chr2A 94.118 51 3 0 1128 1178 760509496 760509446 1.140000e-10 78.7
25 TraesCS2D01G556800 chr2A 92.157 51 4 0 3767 3817 760506922 760506872 5.290000e-09 73.1
26 TraesCS2D01G556800 chr2B 83.127 1612 128 61 1845 3390 773732533 773734066 0.000000e+00 1338.0
27 TraesCS2D01G556800 chr2B 84.406 917 100 19 1 910 773730863 773731743 0.000000e+00 861.0
28 TraesCS2D01G556800 chr2B 92.338 509 17 8 2917 3419 147797800 147798292 0.000000e+00 704.0
29 TraesCS2D01G556800 chr2B 81.455 701 53 36 996 1667 773731839 773732491 1.580000e-138 503.0
30 TraesCS2D01G556800 chr2B 76.404 890 132 42 1915 2780 50483626 50484461 3.550000e-110 409.0
31 TraesCS2D01G556800 chr2B 87.052 363 26 11 991 1348 773078844 773078498 1.290000e-104 390.0
32 TraesCS2D01G556800 chr2B 85.470 234 16 7 674 901 773082936 773082715 1.070000e-55 228.0
33 TraesCS2D01G556800 chr2B 84.615 156 9 5 3492 3636 147799126 147799277 1.430000e-29 141.0
34 TraesCS2D01G556800 chr2B 75.500 200 27 16 2804 2988 121510690 121510498 1.140000e-10 78.7
35 TraesCS2D01G556800 chr7D 90.244 41 4 0 290 330 83384650 83384610 2.000000e-03 54.7


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 TraesCS2D01G556800 chr2D 630088903 630092719 3816 True 7049.000000 7049 100.000000 1 3817 1 chr2D.!!$R3 3816
1 TraesCS2D01G556800 chr2D 629726424 629728415 1991 False 2736.000000 2736 91.720000 1845 3817 1 chr2D.!!$F1 1972
2 TraesCS2D01G556800 chr2D 630629634 630634528 4894 False 1039.666667 1622 86.626667 1 3390 3 chr2D.!!$F2 3389
3 TraesCS2D01G556800 chr2D 629988986 629992145 3159 True 983.666667 1877 86.128000 104 3367 3 chr2D.!!$R4 3263
4 TraesCS2D01G556800 chr2D 30660606 30661434 828 True 422.000000 422 76.854000 1918 2780 1 chr2D.!!$R1 862
5 TraesCS2D01G556800 chr2A 760489583 760490412 829 True 1040.000000 1040 89.692000 2108 2926 1 chr2A.!!$R2 818
6 TraesCS2D01G556800 chr2A 760770439 760773660 3221 False 811.000000 1386 86.459750 622 3817 4 chr2A.!!$F3 3195
7 TraesCS2D01G556800 chr2A 760506872 760510495 3623 True 344.616667 1293 93.191333 699 3817 6 chr2A.!!$R4 3118
8 TraesCS2D01G556800 chr2A 760476892 760478652 1760 True 253.000000 313 86.352000 2923 3408 2 chr2A.!!$R3 485
9 TraesCS2D01G556800 chr2B 773730863 773734066 3203 False 900.666667 1338 82.996000 1 3390 3 chr2B.!!$F3 3389
10 TraesCS2D01G556800 chr2B 147797800 147799277 1477 False 422.500000 704 88.476500 2917 3636 2 chr2B.!!$F2 719
11 TraesCS2D01G556800 chr2B 50483626 50484461 835 False 409.000000 409 76.404000 1915 2780 1 chr2B.!!$F1 865
12 TraesCS2D01G556800 chr2B 773078498 773082936 4438 True 309.000000 390 86.261000 674 1348 2 chr2B.!!$R2 674

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
853 2035 1.143305 CACTCGGTGCTGTCAAGAAG 58.857 55.0 0.00 0.0 0.0 2.85 F
1528 6865 0.249155 GTGTCCTTCGTCGTCCAACA 60.249 55.0 0.00 0.0 0.0 3.33 F
1841 7203 0.393820 AAAATGTTGCCCCAGCTGTG 59.606 50.0 13.81 0.0 40.8 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 7721 0.713883 GTACGCACACGATTGTCCAG 59.286 55.000 0.00 0.0 43.93 3.86 R
2632 8500 2.032071 CGCCGTCCAAAGGTTCCT 59.968 61.111 0.00 0.0 0.00 3.36 R
3479 11176 5.689383 TCTAGTTGTACGAGTTACCGTTT 57.311 39.130 4.47 0.0 43.20 3.60 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
51 53 5.783100 AATATGCGCCAAACATTTTTCAG 57.217 34.783 4.18 0.00 0.00 3.02
62 64 8.082242 GCCAAACATTTTTCAGTAAGTGATAGT 58.918 33.333 0.00 0.00 34.17 2.12
187 189 7.519809 TGTGCTAAACATTTGTCAGTATGTGAC 60.520 37.037 3.62 3.62 44.36 3.67
207 209 7.320399 TGTGACAGACATCTTTAATACACGAT 58.680 34.615 0.00 0.00 0.00 3.73
288 291 4.973663 CGTGGGACTTTTTAAACACATGAC 59.026 41.667 0.00 0.00 0.00 3.06
336 339 9.216087 TGAATATTGTTAAATACGCAATGAACG 57.784 29.630 0.00 0.00 34.97 3.95
345 348 3.111958 ACGCAATGAACGTATTTTCCG 57.888 42.857 0.00 0.00 43.02 4.30
359 362 7.142680 ACGTATTTTCCGAACAAAAATGATGT 58.857 30.769 0.00 0.00 37.04 3.06
360 363 7.650104 ACGTATTTTCCGAACAAAAATGATGTT 59.350 29.630 0.00 0.00 43.37 2.71
399 403 8.469200 TGGACAAATTTTGAAATAGGCTATCTG 58.531 33.333 15.81 0.00 0.00 2.90
418 426 5.600908 TCTGTATTTTCAAGTACGCAACC 57.399 39.130 0.00 0.00 0.00 3.77
444 452 8.355806 CAGCTTTTATTTTCGAAAATACACGAC 58.644 33.333 32.65 23.01 39.75 4.34
501 509 8.951954 AAATATACACGACGCACATTTTAAAA 57.048 26.923 2.51 2.51 0.00 1.52
515 523 8.652463 GCACATTTTAAAAGCGTGGTAAATATT 58.348 29.630 23.96 0.00 0.00 1.28
554 585 8.075593 AGATCAACACATTTTAAATGCACAAC 57.924 30.769 16.57 4.32 0.00 3.32
577 610 5.988561 ACATTTGAAAAATGTGCACGGTAAT 59.011 32.000 15.57 0.00 39.22 1.89
681 714 1.184431 TGCGTAACCGGTAAGGATCA 58.816 50.000 8.00 0.00 45.00 2.92
683 716 1.406539 GCGTAACCGGTAAGGATCAGA 59.593 52.381 8.00 0.00 45.00 3.27
695 728 3.438297 AGGATCAGATAAACGTGACGG 57.562 47.619 10.66 0.00 0.00 4.79
697 730 3.194968 AGGATCAGATAAACGTGACGGTT 59.805 43.478 14.41 14.41 40.82 4.44
819 1992 6.493116 GGATAGATCAAAGTGTGAAAGCATG 58.507 40.000 0.00 0.00 40.50 4.06
831 2004 4.746611 TGTGAAAGCATGCATAGACGATAG 59.253 41.667 21.98 0.00 46.19 2.08
853 2035 1.143305 CACTCGGTGCTGTCAAGAAG 58.857 55.000 0.00 0.00 0.00 2.85
896 2078 5.798125 TGAGAGTCAGTCAAGAAACAGAT 57.202 39.130 0.00 0.00 0.00 2.90
988 6244 4.717629 TCCCTCACTGAACGCGCG 62.718 66.667 30.96 30.96 0.00 6.86
989 6245 4.717629 CCCTCACTGAACGCGCGA 62.718 66.667 39.36 14.09 0.00 5.87
1027 6285 1.896694 CTCACTCTCACTGGGGAGC 59.103 63.158 0.00 0.00 34.84 4.70
1029 6287 1.979155 CACTCTCACTGGGGAGCGA 60.979 63.158 0.00 0.00 34.84 4.93
1030 6288 1.228894 ACTCTCACTGGGGAGCGAA 60.229 57.895 0.00 0.00 34.84 4.70
1034 6292 1.160137 CTCACTGGGGAGCGAAAAAG 58.840 55.000 0.00 0.00 0.00 2.27
1081 6361 4.284746 GCAAGGTATCCTATTCCTAGCACT 59.715 45.833 0.00 0.00 31.13 4.40
1082 6362 5.567823 GCAAGGTATCCTATTCCTAGCACTC 60.568 48.000 0.00 0.00 31.13 3.51
1083 6363 4.679331 AGGTATCCTATTCCTAGCACTCC 58.321 47.826 0.00 0.00 28.47 3.85
1084 6364 3.444388 GGTATCCTATTCCTAGCACTCCG 59.556 52.174 0.00 0.00 0.00 4.63
1086 6366 2.584236 TCCTATTCCTAGCACTCCGTC 58.416 52.381 0.00 0.00 0.00 4.79
1126 6406 2.969300 GATCGAGGAGGGAGGAGCGT 62.969 65.000 0.00 0.00 0.00 5.07
1298 6600 1.842007 CTGGGGTGATCATGAGGGG 59.158 63.158 0.00 0.00 0.00 4.79
1425 6727 2.264480 CGGTGCGTCCTCCAATCA 59.736 61.111 0.00 0.00 0.00 2.57
1443 6761 1.854939 TCATTCTTGGATGGATGGGCT 59.145 47.619 0.00 0.00 0.00 5.19
1528 6865 0.249155 GTGTCCTTCGTCGTCCAACA 60.249 55.000 0.00 0.00 0.00 3.33
1576 6913 5.163120 ACATCTACATCTGCCTTTGGATGAT 60.163 40.000 9.47 0.00 41.05 2.45
1577 6914 5.378230 TCTACATCTGCCTTTGGATGATT 57.622 39.130 9.47 0.00 41.05 2.57
1578 6915 6.499106 TCTACATCTGCCTTTGGATGATTA 57.501 37.500 9.47 0.00 41.05 1.75
1579 6916 6.291377 TCTACATCTGCCTTTGGATGATTAC 58.709 40.000 9.47 0.00 41.05 1.89
1580 6917 4.858850 ACATCTGCCTTTGGATGATTACA 58.141 39.130 9.47 0.00 41.05 2.41
1581 6918 5.452255 ACATCTGCCTTTGGATGATTACAT 58.548 37.500 9.47 0.00 41.05 2.29
1582 6919 6.604171 ACATCTGCCTTTGGATGATTACATA 58.396 36.000 9.47 0.00 41.05 2.29
1583 6920 6.713903 ACATCTGCCTTTGGATGATTACATAG 59.286 38.462 9.47 0.00 41.05 2.23
1584 6921 6.499106 TCTGCCTTTGGATGATTACATAGA 57.501 37.500 0.00 0.00 36.82 1.98
1589 6926 6.057533 CCTTTGGATGATTACATAGACTGCA 58.942 40.000 0.00 0.00 36.82 4.41
1593 6930 5.999600 TGGATGATTACATAGACTGCATTGG 59.000 40.000 0.00 0.00 36.82 3.16
1599 6936 3.368248 ACATAGACTGCATTGGCCAATT 58.632 40.909 28.68 14.40 40.13 2.32
1600 6937 3.382546 ACATAGACTGCATTGGCCAATTC 59.617 43.478 28.68 24.01 40.13 2.17
1610 6947 2.957402 TGGCCAATTCTTCAGTGTCT 57.043 45.000 0.61 0.00 0.00 3.41
1614 6951 3.557898 GGCCAATTCTTCAGTGTCTCTCA 60.558 47.826 0.00 0.00 0.00 3.27
1626 6963 2.874701 GTGTCTCTCACTGCAACACATT 59.125 45.455 10.02 0.00 43.13 2.71
1629 6969 4.202253 TGTCTCTCACTGCAACACATTAGT 60.202 41.667 0.00 0.00 0.00 2.24
1633 6973 4.515191 TCTCACTGCAACACATTAGTTTCC 59.485 41.667 0.00 0.00 0.00 3.13
1639 6979 5.321102 TGCAACACATTAGTTTCCCAGTAT 58.679 37.500 0.00 0.00 0.00 2.12
1673 7016 4.870991 CGAGTCCTCCTTAATTCTCCAAAC 59.129 45.833 0.00 0.00 0.00 2.93
1704 7047 5.634859 GCTCATATTTATTTGGGCATTTCGG 59.365 40.000 0.89 0.00 39.21 4.30
1708 7051 8.519526 TCATATTTATTTGGGCATTTCGGTATC 58.480 33.333 0.00 0.00 0.00 2.24
1736 7085 5.352569 ACGCATTTTTGGATCTTCTAGTCTG 59.647 40.000 0.00 0.00 0.00 3.51
1737 7086 5.220739 CGCATTTTTGGATCTTCTAGTCTGG 60.221 44.000 0.00 0.00 0.00 3.86
1738 7087 5.449725 GCATTTTTGGATCTTCTAGTCTGGC 60.450 44.000 0.00 0.00 0.00 4.85
1739 7088 4.908601 TTTTGGATCTTCTAGTCTGGCA 57.091 40.909 0.00 0.00 0.00 4.92
1740 7089 5.441718 TTTTGGATCTTCTAGTCTGGCAT 57.558 39.130 0.00 0.00 0.00 4.40
1741 7090 4.679373 TTGGATCTTCTAGTCTGGCATC 57.321 45.455 0.00 0.00 0.00 3.91
1758 7107 2.911484 CATCCTGAAAGAGGCAGTACC 58.089 52.381 0.00 0.00 42.47 3.34
1774 7123 4.155462 GCAGTACCATTAGATGATGCCATG 59.845 45.833 0.00 0.00 32.09 3.66
1798 7159 2.776312 CATGATCATGCTCCTTGTGC 57.224 50.000 22.20 0.00 31.39 4.57
1831 7193 7.031372 TCAGCTGATTCATCTAAAAATGTTGC 58.969 34.615 13.74 0.00 0.00 4.17
1841 7203 0.393820 AAAATGTTGCCCCAGCTGTG 59.606 50.000 13.81 0.00 40.80 3.66
1871 7249 4.632688 GGATGCAGCAATGTTTAGCATTTT 59.367 37.500 3.51 0.00 44.82 1.82
1883 7261 7.239166 TGTTTAGCATTTTTGCGAAAATCAA 57.761 28.000 19.77 12.15 42.14 2.57
1910 7691 3.471680 TGATCGTCACATTTGTGTGGAA 58.528 40.909 10.30 0.00 45.76 3.53
1940 7721 7.186804 CGGAATTCAGAATGGTGTAATTGTAC 58.813 38.462 7.93 0.00 36.16 2.90
1990 7781 6.391227 TCCTTGAGGAAAACATTTGAAGAC 57.609 37.500 0.00 0.00 42.18 3.01
1996 7787 6.262273 TGAGGAAAACATTTGAAGACCTACAC 59.738 38.462 0.00 0.00 0.00 2.90
2025 7821 3.865571 TGGGGGTAGTATATTGAGGACC 58.134 50.000 0.00 0.00 0.00 4.46
2045 7845 5.178809 GGACCATATATGCGAAACAAGTACC 59.821 44.000 7.24 0.00 0.00 3.34
2106 7921 3.726291 TTTTTCACTTGCTGTTAGCCC 57.274 42.857 0.00 0.00 41.51 5.19
2165 7999 5.654603 TTGCTCTTCCGTAGATGAACTTA 57.345 39.130 0.00 0.00 30.92 2.24
2166 8000 5.654603 TGCTCTTCCGTAGATGAACTTAA 57.345 39.130 0.00 0.00 30.92 1.85
2167 8001 6.222038 TGCTCTTCCGTAGATGAACTTAAT 57.778 37.500 0.00 0.00 30.92 1.40
2168 8002 6.640518 TGCTCTTCCGTAGATGAACTTAATT 58.359 36.000 0.00 0.00 30.92 1.40
2209 8043 0.824109 TACCTCGTAGCAGCAGCAAT 59.176 50.000 3.17 0.00 45.49 3.56
2210 8044 0.460987 ACCTCGTAGCAGCAGCAATC 60.461 55.000 3.17 0.00 45.49 2.67
2406 8253 9.777297 ATTGTGTTTTGAATAGGCAAATTAAGT 57.223 25.926 0.00 0.00 37.57 2.24
2632 8500 1.743623 CGTGTGCCGGCCTTTATCA 60.744 57.895 26.77 10.51 0.00 2.15
3057 9348 3.643792 CTGGATCTTAGGTCCGGAGATTT 59.356 47.826 15.04 0.00 43.50 2.17
3070 9361 5.357596 GTCCGGAGATTTCTCACTTAGTACT 59.642 44.000 3.06 0.00 44.60 2.73
3086 9377 3.585862 AGTACTGTTGCCACTTACGATG 58.414 45.455 0.00 0.00 0.00 3.84
3087 9378 1.808411 ACTGTTGCCACTTACGATGG 58.192 50.000 0.00 0.00 40.50 3.51
3510 11968 6.686130 ACTCGTACAACTAGAAAATTGTCG 57.314 37.500 0.00 3.61 39.67 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 8.110271 TCACCCCATATTGAAGTGTTGTATTTA 58.890 33.333 0.00 0.00 0.00 1.40
153 155 8.932945 TGACAAATGTTTAGCACACATTAAAA 57.067 26.923 8.17 0.00 42.80 1.52
160 162 6.578545 CACATACTGACAAATGTTTAGCACAC 59.421 38.462 1.28 0.00 38.61 3.82
175 177 8.709386 ATTAAAGATGTCTGTCACATACTGAC 57.291 34.615 7.87 7.87 46.53 3.51
187 189 8.579682 TGATCATCGTGTATTAAAGATGTCTG 57.420 34.615 0.00 0.00 40.75 3.51
207 209 9.323985 TGTGAATCATGAATTAACGTATGATCA 57.676 29.630 9.13 0.00 38.83 2.92
399 403 4.156182 GCTGGTTGCGTACTTGAAAATAC 58.844 43.478 0.00 0.00 0.00 1.89
418 426 8.355806 GTCGTGTATTTTCGAAAATAAAAGCTG 58.644 33.333 33.70 22.12 41.14 4.24
554 585 5.896922 TTACCGTGCACATTTTTCAAATG 57.103 34.783 18.64 7.52 0.00 2.32
656 689 2.743126 CCTTACCGGTTACGCATTTCAA 59.257 45.455 15.04 0.00 39.22 2.69
666 699 5.360714 ACGTTTATCTGATCCTTACCGGTTA 59.639 40.000 15.04 1.26 0.00 2.85
669 702 4.049186 CACGTTTATCTGATCCTTACCGG 58.951 47.826 0.00 0.00 0.00 5.28
681 714 2.611224 GGTCCAACCGTCACGTTTATCT 60.611 50.000 0.00 0.00 0.00 1.98
683 716 1.799544 GGTCCAACCGTCACGTTTAT 58.200 50.000 0.00 0.00 0.00 1.40
695 728 0.180406 ATCCACTATGCCGGTCCAAC 59.820 55.000 1.90 0.00 0.00 3.77
697 730 0.689412 TCATCCACTATGCCGGTCCA 60.689 55.000 1.90 0.00 35.38 4.02
775 808 3.891400 CCGCGTCCCCATGCAATG 61.891 66.667 4.92 0.00 46.21 2.82
819 1992 3.497640 ACCGAGTGTACTATCGTCTATGC 59.502 47.826 15.78 0.00 37.23 3.14
831 2004 1.000607 TCTTGACAGCACCGAGTGTAC 60.001 52.381 6.02 0.00 35.75 2.90
832 2005 1.324383 TCTTGACAGCACCGAGTGTA 58.676 50.000 6.02 0.00 35.75 2.90
833 2006 0.464036 TTCTTGACAGCACCGAGTGT 59.536 50.000 6.02 0.00 35.75 3.55
834 2007 1.143305 CTTCTTGACAGCACCGAGTG 58.857 55.000 0.25 0.25 36.51 3.51
853 2035 2.237751 CGTCCGGGATCGTCAATGC 61.238 63.158 0.00 0.00 33.95 3.56
874 2056 5.798125 ATCTGTTTCTTGACTGACTCTCA 57.202 39.130 0.00 0.00 31.59 3.27
896 2078 1.641192 TCCACCTGAGGCTCTTCTCTA 59.359 52.381 16.72 0.00 34.98 2.43
988 6244 3.444805 AGCCGGAGAGTGAGCGTC 61.445 66.667 5.05 0.00 0.00 5.19
989 6245 3.753434 CAGCCGGAGAGTGAGCGT 61.753 66.667 5.05 0.00 0.00 5.07
1027 6285 6.077838 CGGTGGTTTTCTATTCTCTTTTTCG 58.922 40.000 0.00 0.00 0.00 3.46
1029 6287 5.243060 CCCGGTGGTTTTCTATTCTCTTTTT 59.757 40.000 0.00 0.00 0.00 1.94
1030 6288 4.765339 CCCGGTGGTTTTCTATTCTCTTTT 59.235 41.667 0.00 0.00 0.00 2.27
1034 6292 2.014857 GCCCGGTGGTTTTCTATTCTC 58.985 52.381 0.00 0.00 0.00 2.87
1126 6406 0.035317 AAGTGCAGCATCGTCTTCCA 59.965 50.000 0.00 0.00 0.00 3.53
1201 6494 2.660064 GCACCATCTCCACCTCCGT 61.660 63.158 0.00 0.00 0.00 4.69
1354 6656 4.498520 CATGACGGCGAGCGAGGT 62.499 66.667 16.62 0.00 0.00 3.85
1425 6727 1.133262 CCAGCCCATCCATCCAAGAAT 60.133 52.381 0.00 0.00 0.00 2.40
1443 6761 2.610859 GGAGGAGAAGGTGGGCCA 60.611 66.667 0.00 0.00 37.19 5.36
1449 6767 1.306568 GAGCAGGGGAGGAGAAGGT 60.307 63.158 0.00 0.00 0.00 3.50
1516 6853 1.671328 TGCAAATTTGTTGGACGACGA 59.329 42.857 19.03 0.00 0.00 4.20
1576 6913 3.643199 TGGCCAATGCAGTCTATGTAA 57.357 42.857 0.61 0.00 40.13 2.41
1577 6914 3.643199 TTGGCCAATGCAGTCTATGTA 57.357 42.857 16.05 0.00 40.13 2.29
1578 6915 2.512692 TTGGCCAATGCAGTCTATGT 57.487 45.000 16.05 0.00 40.13 2.29
1579 6916 3.635373 AGAATTGGCCAATGCAGTCTATG 59.365 43.478 33.69 0.00 40.13 2.23
1580 6917 3.907221 AGAATTGGCCAATGCAGTCTAT 58.093 40.909 33.69 16.11 40.13 1.98
1581 6918 3.370840 AGAATTGGCCAATGCAGTCTA 57.629 42.857 33.69 4.70 40.13 2.59
1582 6919 2.226962 AGAATTGGCCAATGCAGTCT 57.773 45.000 33.69 26.62 40.13 3.24
1583 6920 2.231964 TGAAGAATTGGCCAATGCAGTC 59.768 45.455 33.69 28.35 40.13 3.51
1584 6921 2.232941 CTGAAGAATTGGCCAATGCAGT 59.767 45.455 33.69 22.81 40.13 4.40
1589 6926 3.760684 GAGACACTGAAGAATTGGCCAAT 59.239 43.478 25.73 25.73 0.00 3.16
1593 6930 3.434984 GTGAGAGACACTGAAGAATTGGC 59.565 47.826 0.00 0.00 45.13 4.52
1610 6947 4.515191 GGAAACTAATGTGTTGCAGTGAGA 59.485 41.667 0.00 0.00 0.00 3.27
1614 6951 3.561143 TGGGAAACTAATGTGTTGCAGT 58.439 40.909 0.00 0.00 0.00 4.40
1633 6973 9.804758 GGAGGACTCGATAATAATTTATACTGG 57.195 37.037 0.00 0.00 0.00 4.00
1650 6990 4.737855 TTGGAGAATTAAGGAGGACTCG 57.262 45.455 0.00 0.00 0.00 4.18
1673 7016 7.211573 TGCCCAAATAAATATGAGCATTTCAG 58.788 34.615 0.00 0.00 39.68 3.02
1704 7047 6.604735 AGATCCAAAAATGCGTACAGATAC 57.395 37.500 0.00 0.00 0.00 2.24
1708 7051 5.551760 AGAAGATCCAAAAATGCGTACAG 57.448 39.130 0.00 0.00 0.00 2.74
1741 7090 3.356529 AATGGTACTGCCTCTTTCAGG 57.643 47.619 0.00 0.00 46.82 3.86
1798 7159 8.883954 TTTAGATGAATCAGCTGAGATAACAG 57.116 34.615 22.96 0.00 40.43 3.16
1831 7193 0.754957 TCCAAACAACACAGCTGGGG 60.755 55.000 22.46 13.54 0.00 4.96
1841 7203 2.758009 ACATTGCTGCATCCAAACAAC 58.242 42.857 1.84 0.00 0.00 3.32
1901 7682 3.891977 TGAATTCCGGATTTTCCACACAA 59.108 39.130 19.50 3.26 35.91 3.33
1910 7691 4.344104 ACACCATTCTGAATTCCGGATTT 58.656 39.130 4.15 8.45 0.00 2.17
1940 7721 0.713883 GTACGCACACGATTGTCCAG 59.286 55.000 0.00 0.00 43.93 3.86
1990 7781 1.982958 ACCCCCAACACTAAGTGTAGG 59.017 52.381 0.00 0.00 46.79 3.18
1996 7787 7.369551 TCAATATACTACCCCCAACACTAAG 57.630 40.000 0.00 0.00 0.00 2.18
2025 7821 6.844696 ACTGGTACTTGTTTCGCATATATG 57.155 37.500 8.45 8.45 0.00 1.78
2045 7845 7.254898 CCATCTAATTGGTGCACTAACATACTG 60.255 40.741 18.60 12.49 31.74 2.74
2097 7912 2.993899 CTGAGTTGTAACGGGCTAACAG 59.006 50.000 0.00 0.00 0.00 3.16
2098 7913 2.629137 TCTGAGTTGTAACGGGCTAACA 59.371 45.455 0.00 0.00 0.00 2.41
2101 7916 4.098960 CCTATTCTGAGTTGTAACGGGCTA 59.901 45.833 0.00 0.00 0.00 3.93
2102 7917 3.118738 CCTATTCTGAGTTGTAACGGGCT 60.119 47.826 0.00 0.00 0.00 5.19
2103 7918 3.195661 CCTATTCTGAGTTGTAACGGGC 58.804 50.000 0.00 0.00 0.00 6.13
2106 7921 4.730949 TCCCCTATTCTGAGTTGTAACG 57.269 45.455 0.00 0.00 0.00 3.18
2135 7957 4.385825 TCTACGGAAGAGCAAACAAACAT 58.614 39.130 0.00 0.00 0.00 2.71
2165 7999 5.858581 GCTGCTCAAACGAACAAGAATAATT 59.141 36.000 0.00 0.00 0.00 1.40
2166 8000 5.182001 AGCTGCTCAAACGAACAAGAATAAT 59.818 36.000 0.00 0.00 0.00 1.28
2167 8001 4.515191 AGCTGCTCAAACGAACAAGAATAA 59.485 37.500 0.00 0.00 0.00 1.40
2168 8002 4.065088 AGCTGCTCAAACGAACAAGAATA 58.935 39.130 0.00 0.00 0.00 1.75
2209 8043 1.672030 CTCCACAGGCATTGCACGA 60.672 57.895 11.39 0.00 0.00 4.35
2210 8044 2.872557 CTCCACAGGCATTGCACG 59.127 61.111 11.39 2.94 0.00 5.34
2451 8305 3.450457 ACAAAACATCAGGGTCAAAAGCA 59.550 39.130 0.00 0.00 0.00 3.91
2632 8500 2.032071 CGCCGTCCAAAGGTTCCT 59.968 61.111 0.00 0.00 0.00 3.36
3479 11176 5.689383 TCTAGTTGTACGAGTTACCGTTT 57.311 39.130 4.47 0.00 43.20 3.60


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

AutoCloner maintained by Alex Coulton.