Multiple sequence alignment - TraesCS2B01G160500

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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 TraesCS2B01G160500 chr2B 100.000 3665 0 0 1 3665 134044878 134041214 0.000000e+00 6769.0
1 TraesCS2B01G160500 chr2A 88.915 2111 124 42 650 2725 82344896 82342861 0.000000e+00 2501.0
2 TraesCS2B01G160500 chr2A 96.784 653 19 2 1 651 82345631 82344979 0.000000e+00 1088.0
3 TraesCS2B01G160500 chr2A 82.227 467 61 11 2758 3221 82342532 82342085 2.060000e-102 383.0
4 TraesCS2B01G160500 chr2A 83.486 109 15 1 3557 3665 82340712 82340607 8.380000e-17 99.0
5 TraesCS2B01G160500 chr2D 89.143 1621 115 30 1121 2720 82180213 82178633 0.000000e+00 1962.0
6 TraesCS2B01G160500 chr2D 89.803 1118 66 29 1 1076 82181325 82180214 0.000000e+00 1389.0
7 TraesCS2B01G160500 chr2D 84.149 511 58 13 3031 3524 82176494 82175990 1.190000e-129 473.0
8 TraesCS2B01G160500 chr2D 80.095 422 48 14 1 410 82186035 82185638 7.750000e-72 281.0
9 TraesCS2B01G160500 chr2D 85.577 104 13 2 3555 3656 82175557 82175454 1.390000e-19 108.0
10 TraesCS2B01G160500 chr2D 89.583 48 5 0 3243 3290 541077848 541077801 1.100000e-05 62.1
11 TraesCS2B01G160500 chr3A 79.348 276 51 5 3237 3508 700251933 700251660 4.830000e-44 189.0
12 TraesCS2B01G160500 chr3D 76.190 273 52 8 3241 3502 407212542 407212812 8.260000e-27 132.0
13 TraesCS2B01G160500 chr1A 78.713 202 31 9 3235 3426 468606090 468606289 1.380000e-24 124.0
14 TraesCS2B01G160500 chr7A 89.362 47 3 1 3455 3501 521456728 521456684 1.420000e-04 58.4


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 TraesCS2B01G160500 chr2B 134041214 134044878 3664 True 6769.00 6769 100.000 1 3665 1 chr2B.!!$R1 3664
1 TraesCS2B01G160500 chr2A 82340607 82345631 5024 True 1017.75 2501 87.853 1 3665 4 chr2A.!!$R1 3664
2 TraesCS2B01G160500 chr2D 82175454 82181325 5871 True 983.00 1962 87.168 1 3656 4 chr2D.!!$R3 3655

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
400 404 1.128692 GCTGTACCGATTGTTCAGTGC 59.871 52.381 0.00 0.0 42.54 4.40 F
1386 1531 0.037697 TGGCGAAACATCGTGCTACT 60.038 50.000 0.00 0.0 35.26 2.57 F
1902 2056 0.027324 GATCGTCGTCGTCCAGTACC 59.973 60.000 1.33 0.0 38.33 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1968 0.179081 GTGCGTCTTATCCTGGGGAC 60.179 60.0 0.00 0.0 32.98 4.46 R
2662 2840 0.251634 TGTGCCGTGCATCTGGATTA 59.748 50.0 6.77 0.0 41.91 1.75 R
3520 6238 0.319986 TGCGTGGCAATGACGACTAA 60.320 50.0 0.00 0.0 39.21 2.24 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
86 87 3.570939 GCACCGTAAGCGATCTTTTAG 57.429 47.619 0.00 0.00 41.33 1.85
156 157 1.533994 GAGGTTTTGCTGGGGCCTT 60.534 57.895 0.84 0.00 37.74 4.35
160 161 1.765657 TTTTGCTGGGGCCTTTGCT 60.766 52.632 0.84 0.00 37.74 3.91
238 239 5.199024 TCTTTTGGTGTCCAATGTTCATG 57.801 39.130 1.97 0.00 43.55 3.07
400 404 1.128692 GCTGTACCGATTGTTCAGTGC 59.871 52.381 0.00 0.00 42.54 4.40
494 498 7.254932 GGCTCATTACTGAATCAAAGTATCCAC 60.255 40.741 0.00 0.00 30.46 4.02
730 849 6.875726 TGAGTCTTGAGTATGAAGGACATTTG 59.124 38.462 0.00 0.00 40.07 2.32
751 873 4.842574 TGCAGGACAAATAATGCTGTCTA 58.157 39.130 2.56 0.00 41.43 2.59
903 1029 2.898738 CTGCATCACGAGCTCCCT 59.101 61.111 8.47 0.00 0.00 4.20
962 1088 1.375396 CACGGCCAAGAATCGTCCA 60.375 57.895 2.24 0.00 34.73 4.02
1148 1287 2.440430 CTTCTCCGCCCTCTCCGA 60.440 66.667 0.00 0.00 0.00 4.55
1204 1343 0.681733 TCTCCAGCGTCTTCTTTGCT 59.318 50.000 0.00 0.00 40.16 3.91
1223 1368 2.801679 GCTGCTTCTCTGATACTGATGC 59.198 50.000 0.00 0.00 0.00 3.91
1281 1426 1.740664 GGACGGGAAAGACGAAGCC 60.741 63.158 0.00 0.00 34.93 4.35
1312 1457 3.837146 AGATCGGGAAGCATGACTATGAT 59.163 43.478 0.00 0.00 36.36 2.45
1321 1466 6.203723 GGAAGCATGACTATGATTGGTAAGAC 59.796 42.308 0.00 0.00 42.55 3.01
1328 1473 6.932400 TGACTATGATTGGTAAGACAAAACGT 59.068 34.615 0.00 0.00 33.48 3.99
1329 1474 7.095397 TGACTATGATTGGTAAGACAAAACGTG 60.095 37.037 0.00 0.00 33.48 4.49
1330 1475 6.932400 ACTATGATTGGTAAGACAAAACGTGA 59.068 34.615 0.00 0.00 33.48 4.35
1332 1477 5.996219 TGATTGGTAAGACAAAACGTGATG 58.004 37.500 0.00 0.00 33.48 3.07
1337 1482 5.760743 TGGTAAGACAAAACGTGATGATGAA 59.239 36.000 7.75 0.00 0.00 2.57
1338 1483 6.429692 TGGTAAGACAAAACGTGATGATGAAT 59.570 34.615 7.75 0.00 0.00 2.57
1340 1485 4.726416 AGACAAAACGTGATGATGAATGC 58.274 39.130 7.75 0.00 0.00 3.56
1341 1486 3.836949 ACAAAACGTGATGATGAATGCC 58.163 40.909 7.75 0.00 0.00 4.40
1365 1510 0.465824 GGCATTCAGATCAGCTGCCT 60.466 55.000 9.47 5.69 46.97 4.75
1386 1531 0.037697 TGGCGAAACATCGTGCTACT 60.038 50.000 0.00 0.00 35.26 2.57
1412 1557 7.106239 AGTACCTATTTCTCTGACATTGTTGG 58.894 38.462 0.00 0.00 0.00 3.77
1414 1559 4.096984 CCTATTTCTCTGACATTGTTGGGC 59.903 45.833 0.00 0.00 0.00 5.36
1591 1736 4.915806 ACGTAGTGATCAGGCTAAAGCTTG 60.916 45.833 0.00 7.71 44.72 4.01
1595 1746 0.253044 ATCAGGCTAAAGCTTGGCGA 59.747 50.000 13.36 11.04 46.52 5.54
1601 1752 2.099756 GGCTAAAGCTTGGCGATCATTT 59.900 45.455 15.40 0.00 41.70 2.32
1602 1753 3.366719 GCTAAAGCTTGGCGATCATTTC 58.633 45.455 0.00 0.00 38.21 2.17
1603 1754 4.087327 GCTAAAGCTTGGCGATCATTTCG 61.087 47.826 0.00 0.00 43.63 3.46
1761 1915 3.771160 AGCGCGTCCGGGAAATCT 61.771 61.111 8.43 0.00 34.32 2.40
1827 1981 1.074775 TCCCCGTCCCCAGGATAAG 60.075 63.158 0.00 0.00 32.73 1.73
1839 1993 1.588139 GGATAAGACGCACGGACGG 60.588 63.158 4.37 0.00 37.37 4.79
1841 1995 2.877360 GATAAGACGCACGGACGGCA 62.877 60.000 7.96 0.00 46.03 5.69
1842 1996 2.292794 ATAAGACGCACGGACGGCAT 62.293 55.000 7.96 0.00 46.03 4.40
1896 2050 1.226603 CAAGGGATCGTCGTCGTCC 60.227 63.158 12.51 12.51 36.92 4.79
1902 2056 0.027324 GATCGTCGTCGTCCAGTACC 59.973 60.000 1.33 0.00 38.33 3.34
1903 2057 1.699656 ATCGTCGTCGTCCAGTACCG 61.700 60.000 1.33 0.00 38.33 4.02
1904 2058 2.482374 GTCGTCGTCCAGTACCGG 59.518 66.667 0.00 0.00 0.00 5.28
1905 2059 2.747460 TCGTCGTCCAGTACCGGG 60.747 66.667 6.32 0.00 0.00 5.73
1906 2060 4.487412 CGTCGTCCAGTACCGGGC 62.487 72.222 6.32 0.00 0.00 6.13
1907 2061 4.139234 GTCGTCCAGTACCGGGCC 62.139 72.222 6.32 0.00 0.00 5.80
1910 2064 3.468140 GTCCAGTACCGGGCCCTC 61.468 72.222 22.43 7.63 0.00 4.30
1979 2133 1.893801 CCCGAAGTCAACTACCAGAGT 59.106 52.381 0.00 0.00 41.56 3.24
1992 2146 1.445754 CAGAGTGGCGTCAGAGCAG 60.446 63.158 0.00 0.00 39.27 4.24
2021 2175 3.049674 CAGACGTGGCGGCATTGT 61.050 61.111 17.19 17.44 37.34 2.71
2078 2232 0.804364 GATGCAATGTCAACGGCTCA 59.196 50.000 0.00 0.00 0.00 4.26
2079 2233 0.806868 ATGCAATGTCAACGGCTCAG 59.193 50.000 0.00 0.00 0.00 3.35
2080 2234 1.236616 TGCAATGTCAACGGCTCAGG 61.237 55.000 0.00 0.00 0.00 3.86
2081 2235 1.503542 CAATGTCAACGGCTCAGGC 59.496 57.895 0.00 0.00 37.82 4.85
2121 2287 2.665777 CAGTATGGTGAAGACGCGG 58.334 57.895 12.47 0.00 0.00 6.46
2188 2354 3.536917 CATCCCCGGCGACTGCTA 61.537 66.667 9.30 0.00 42.25 3.49
2239 2405 6.441093 TGTTAGCCAGCAAAAGATTATCAG 57.559 37.500 0.00 0.00 0.00 2.90
2240 2406 5.163622 TGTTAGCCAGCAAAAGATTATCAGC 60.164 40.000 0.00 0.00 0.00 4.26
2660 2838 3.998672 GGAGCCGTTCCACGTGGA 61.999 66.667 33.23 33.23 46.01 4.02
2678 2856 1.537202 GGAATAATCCAGATGCACGGC 59.463 52.381 0.00 0.00 45.79 5.68
2679 2857 2.221169 GAATAATCCAGATGCACGGCA 58.779 47.619 0.00 1.01 44.86 5.69
2680 2858 1.597742 ATAATCCAGATGCACGGCAC 58.402 50.000 0.50 0.00 43.04 5.01
2681 2859 0.251634 TAATCCAGATGCACGGCACA 59.748 50.000 0.50 0.00 43.04 4.57
2682 2860 1.028330 AATCCAGATGCACGGCACAG 61.028 55.000 0.50 0.00 43.04 3.66
2685 2863 3.321648 AGATGCACGGCACAGGGA 61.322 61.111 0.50 0.00 43.04 4.20
2728 2906 4.503741 CAACTTGGTTGGTAATCACCTG 57.496 45.455 2.82 0.00 45.98 4.00
2729 2907 3.876309 ACTTGGTTGGTAATCACCTGT 57.124 42.857 0.00 0.00 45.98 4.00
2730 2908 3.486383 ACTTGGTTGGTAATCACCTGTG 58.514 45.455 0.00 0.00 45.98 3.66
2732 2910 1.143889 TGGTTGGTAATCACCTGTGCA 59.856 47.619 0.00 0.00 45.98 4.57
2733 2911 1.812571 GGTTGGTAATCACCTGTGCAG 59.187 52.381 0.00 0.00 45.98 4.41
2734 2912 2.504367 GTTGGTAATCACCTGTGCAGT 58.496 47.619 0.00 0.00 45.98 4.40
2747 2925 3.249091 CTGTGCAGTGTACATGACTCTC 58.751 50.000 14.74 0.00 29.24 3.20
2753 2931 4.162072 CAGTGTACATGACTCTCTGTTCG 58.838 47.826 0.00 0.00 29.24 3.95
2754 2932 3.191581 AGTGTACATGACTCTCTGTTCGG 59.808 47.826 0.00 0.00 0.00 4.30
2755 2933 2.492088 TGTACATGACTCTCTGTTCGGG 59.508 50.000 0.00 0.00 0.00 5.14
2762 4548 1.204941 ACTCTCTGTTCGGGAAATCGG 59.795 52.381 0.00 0.00 0.00 4.18
2785 4571 1.207339 CAGCAGACGCGATTTTGCA 59.793 52.632 15.93 0.00 45.49 4.08
2786 4572 0.179181 CAGCAGACGCGATTTTGCAT 60.179 50.000 15.93 4.37 45.49 3.96
2787 4573 0.179181 AGCAGACGCGATTTTGCATG 60.179 50.000 15.93 0.07 45.49 4.06
2788 4574 1.135699 GCAGACGCGATTTTGCATGG 61.136 55.000 15.93 0.00 36.59 3.66
2789 4575 1.135699 CAGACGCGATTTTGCATGGC 61.136 55.000 15.93 0.00 34.15 4.40
2791 4577 2.181273 CGCGATTTTGCATGGCCA 59.819 55.556 8.56 8.56 34.15 5.36
2812 4598 2.571212 ACATTTGGTTTGCGTCAGAGA 58.429 42.857 0.00 0.00 0.00 3.10
2829 4615 6.259608 CGTCAGAGATAAATTGGCATCTTTCT 59.740 38.462 0.00 0.00 31.63 2.52
2832 4618 8.708378 TCAGAGATAAATTGGCATCTTTCTAGA 58.292 33.333 0.00 0.00 31.63 2.43
2840 4626 5.086104 TGGCATCTTTCTAGACCTTGTAC 57.914 43.478 0.00 0.00 31.99 2.90
2849 4635 8.647796 TCTTTCTAGACCTTGTACAATGAAAGA 58.352 33.333 23.70 23.70 42.15 2.52
2857 4643 6.088824 CCTTGTACAATGAAAGATGCTTGAC 58.911 40.000 9.13 0.00 0.00 3.18
2949 4735 8.730680 TCTAACCATCTTCTCTAAACATTTTGC 58.269 33.333 0.00 0.00 0.00 3.68
2957 4743 8.845227 TCTTCTCTAAACATTTTGCATTGTACA 58.155 29.630 0.00 0.00 0.00 2.90
2959 4745 9.979578 TTCTCTAAACATTTTGCATTGTACAAT 57.020 25.926 15.47 15.47 0.00 2.71
2985 4771 1.003118 AGTATGCTTGGCTTGAACGGA 59.997 47.619 0.00 0.00 0.00 4.69
2987 4773 0.537143 ATGCTTGGCTTGAACGGACA 60.537 50.000 0.00 0.00 0.00 4.02
2994 4780 2.499693 TGGCTTGAACGGACATGATCTA 59.500 45.455 0.00 0.00 0.00 1.98
3002 4788 2.097629 ACGGACATGATCTACGTCACAG 59.902 50.000 0.00 0.00 31.39 3.66
3012 4798 0.594110 TACGTCACAGCGTCATCACA 59.406 50.000 0.00 0.00 44.55 3.58
3013 4799 0.249280 ACGTCACAGCGTCATCACAA 60.249 50.000 0.00 0.00 41.71 3.33
3014 4800 0.436150 CGTCACAGCGTCATCACAAG 59.564 55.000 0.00 0.00 0.00 3.16
3015 4801 0.792640 GTCACAGCGTCATCACAAGG 59.207 55.000 0.00 0.00 0.00 3.61
3017 4803 1.672356 ACAGCGTCATCACAAGGCC 60.672 57.895 0.00 0.00 0.00 5.19
3018 4804 1.672030 CAGCGTCATCACAAGGCCA 60.672 57.895 5.01 0.00 0.00 5.36
3019 4805 1.073025 AGCGTCATCACAAGGCCAA 59.927 52.632 5.01 0.00 0.00 4.52
3021 4807 1.926511 GCGTCATCACAAGGCCAAGG 61.927 60.000 5.01 0.00 0.00 3.61
3028 5049 1.776710 ACAAGGCCAAGGGTGGGTA 60.777 57.895 5.01 0.00 46.09 3.69
3029 5050 1.304134 CAAGGCCAAGGGTGGGTAC 60.304 63.158 5.01 0.00 46.09 3.34
3071 5094 4.207891 TGCTTTTCTATGGTCAGACCTC 57.792 45.455 20.82 0.00 39.58 3.85
3078 5101 5.667539 TCTATGGTCAGACCTCTTTCTTG 57.332 43.478 20.82 3.01 39.58 3.02
3090 5113 4.644685 ACCTCTTTCTTGTTTTTGCAGCTA 59.355 37.500 0.00 0.00 0.00 3.32
3091 5114 4.978580 CCTCTTTCTTGTTTTTGCAGCTAC 59.021 41.667 0.00 0.00 0.00 3.58
3135 5158 7.069950 TCTGTATTTGCATCACACTCCTACTAT 59.930 37.037 0.00 0.00 0.00 2.12
3140 5163 6.392625 TGCATCACACTCCTACTATTACTC 57.607 41.667 0.00 0.00 0.00 2.59
3143 5166 5.728937 TCACACTCCTACTATTACTCCCT 57.271 43.478 0.00 0.00 0.00 4.20
3145 5168 5.193124 TCACACTCCTACTATTACTCCCTCA 59.807 44.000 0.00 0.00 0.00 3.86
3150 5175 6.834969 ACTCCTACTATTACTCCCTCAAGTTC 59.165 42.308 0.00 0.00 0.00 3.01
3155 5180 6.712276 ACTATTACTCCCTCAAGTTCCAAAG 58.288 40.000 0.00 0.00 0.00 2.77
3161 5186 5.770162 ACTCCCTCAAGTTCCAAAGTAATTG 59.230 40.000 0.00 0.00 38.84 2.32
3295 5999 8.292448 TGTCTTAAAATGAAGCATCAAGAGAAC 58.708 33.333 0.00 0.00 39.49 3.01
3307 6011 4.898829 TCAAGAGAACACAAACACCATG 57.101 40.909 0.00 0.00 0.00 3.66
3309 6013 4.576053 TCAAGAGAACACAAACACCATGAG 59.424 41.667 0.00 0.00 0.00 2.90
3317 6021 2.483877 ACAAACACCATGAGCATACACG 59.516 45.455 0.00 0.00 0.00 4.49
3319 6023 0.036483 ACACCATGAGCATACACGCA 60.036 50.000 0.00 0.00 0.00 5.24
3325 6029 0.391130 TGAGCATACACGCAACCTCC 60.391 55.000 0.00 0.00 0.00 4.30
3338 6042 2.548480 GCAACCTCCGCATAAATAGGAC 59.452 50.000 0.00 0.00 33.16 3.85
3370 6074 7.113658 ACCAACACCAACACATACATAAAAA 57.886 32.000 0.00 0.00 0.00 1.94
3376 6080 6.693545 CACCAACACATACATAAAAACACGTT 59.306 34.615 0.00 0.00 0.00 3.99
3407 6111 5.500234 AGCAAGTCATATAAGACCAAAGCA 58.500 37.500 4.52 0.00 39.34 3.91
3420 6124 1.608025 CCAAAGCAGTGTAGGCGAGAA 60.608 52.381 0.00 0.00 36.08 2.87
3474 6187 6.693978 CGACAAACTACGACAATGACCATATA 59.306 38.462 0.00 0.00 0.00 0.86
3489 6207 5.301551 TGACCATATATGCACCAACCATTTC 59.698 40.000 7.24 0.00 0.00 2.17
3504 6222 4.401022 ACCATTTCATGACATCACACAGT 58.599 39.130 0.00 0.00 0.00 3.55
3509 6227 2.295909 TCATGACATCACACAGTCGACA 59.704 45.455 19.50 0.00 37.58 4.35
3520 6238 5.527214 TCACACAGTCGACAAAATTCTTCAT 59.473 36.000 19.50 0.00 0.00 2.57
3527 6377 6.645415 AGTCGACAAAATTCTTCATTAGTCGT 59.355 34.615 19.50 0.00 45.14 4.34
3536 6386 3.932710 TCTTCATTAGTCGTCATTGCCAC 59.067 43.478 0.00 0.00 0.00 5.01
3553 6403 0.672401 CACGCATAACCAACTCGGGT 60.672 55.000 0.00 0.00 45.04 5.28
3563 6683 2.067605 AACTCGGGTCACCACCACA 61.068 57.895 0.00 0.00 45.94 4.17
3602 6722 2.166907 TCACCACCACCAAACCATTT 57.833 45.000 0.00 0.00 0.00 2.32
3605 6725 2.298729 CACCACCACCAAACCATTTAGG 59.701 50.000 0.00 0.00 45.67 2.69
3635 6755 1.259840 GGCAACCACATCAGGCCAAT 61.260 55.000 5.01 0.00 44.01 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.258123 TGATGTGTCTCTCCGAAATGACA 59.742 43.478 0.00 0.00 37.14 3.58
86 87 1.266466 GTAGCCAACGACGTAGAAGC 58.734 55.000 0.00 1.97 0.00 3.86
156 157 1.317613 ACCATTCGAAGCAACAGCAA 58.682 45.000 3.35 0.00 0.00 3.91
160 161 0.958091 CCCAACCATTCGAAGCAACA 59.042 50.000 3.35 0.00 0.00 3.33
238 239 6.380095 TGTAAACACACAGGTTTTGATACC 57.620 37.500 0.00 0.00 41.07 2.73
400 404 6.677781 ACCATATGTGAACCATTTTCTACG 57.322 37.500 1.24 0.00 34.86 3.51
443 447 1.909302 TCCCCCTAAAAGAGAGCACAG 59.091 52.381 0.00 0.00 0.00 3.66
494 498 7.660030 ATTACTAATTCAGGGGAACAAATGG 57.340 36.000 0.00 0.00 35.46 3.16
730 849 5.818136 TTAGACAGCATTATTTGTCCTGC 57.182 39.130 1.34 0.00 43.64 4.85
746 868 6.009589 TGCATTTCTCTTCCCATTTTAGACA 58.990 36.000 0.00 0.00 0.00 3.41
747 869 6.515272 TGCATTTCTCTTCCCATTTTAGAC 57.485 37.500 0.00 0.00 0.00 2.59
751 873 6.656270 GGAATTTGCATTTCTCTTCCCATTTT 59.344 34.615 9.11 0.00 0.00 1.82
903 1029 6.566079 ATTGACTGATATGACAAGGGAAGA 57.434 37.500 0.00 0.00 0.00 2.87
962 1088 4.965814 TCTTCTGTTCTCTCTGTTGCAAT 58.034 39.130 0.59 0.00 0.00 3.56
1097 1236 4.785453 CCTTGGTGCCGGCTCTCC 62.785 72.222 29.70 25.27 0.00 3.71
1098 1237 3.706373 TCCTTGGTGCCGGCTCTC 61.706 66.667 29.70 17.79 0.00 3.20
1099 1238 4.021925 GTCCTTGGTGCCGGCTCT 62.022 66.667 29.70 0.00 0.00 4.09
1103 1242 3.649277 CTCTCGTCCTTGGTGCCGG 62.649 68.421 0.00 0.00 0.00 6.13
1104 1243 2.125912 CTCTCGTCCTTGGTGCCG 60.126 66.667 0.00 0.00 0.00 5.69
1105 1244 2.435059 GCTCTCGTCCTTGGTGCC 60.435 66.667 0.00 0.00 0.00 5.01
1106 1245 1.078848 ATGCTCTCGTCCTTGGTGC 60.079 57.895 0.00 0.00 0.00 5.01
1107 1246 0.803768 CGATGCTCTCGTCCTTGGTG 60.804 60.000 1.70 0.00 42.56 4.17
1108 1247 1.513158 CGATGCTCTCGTCCTTGGT 59.487 57.895 1.70 0.00 42.56 3.67
1109 1248 4.409342 CGATGCTCTCGTCCTTGG 57.591 61.111 1.70 0.00 42.56 3.61
1148 1287 1.959282 ACTTACTCTCGTCGGTTTGGT 59.041 47.619 0.00 0.00 0.00 3.67
1172 1311 2.797156 CGCTGGAGATAATTCAGGAACG 59.203 50.000 0.00 0.00 0.00 3.95
1204 1343 4.439968 CTTGCATCAGTATCAGAGAAGCA 58.560 43.478 0.00 0.00 0.00 3.91
1266 1411 1.741770 CTGGGCTTCGTCTTTCCCG 60.742 63.158 0.00 0.00 41.65 5.14
1312 1457 5.760743 TCATCATCACGTTTTGTCTTACCAA 59.239 36.000 0.00 0.00 0.00 3.67
1321 1466 3.835779 TGGCATTCATCATCACGTTTTG 58.164 40.909 0.00 0.00 0.00 2.44
1340 1485 2.693591 AGCTGATCTGAATGCCATTTGG 59.306 45.455 3.42 0.00 38.53 3.28
1341 1486 3.706698 CAGCTGATCTGAATGCCATTTG 58.293 45.455 8.42 0.00 45.72 2.32
1412 1557 1.659098 CCTACGAACAACGATGAAGCC 59.341 52.381 0.00 0.00 45.77 4.35
1414 1559 2.607187 AGCCTACGAACAACGATGAAG 58.393 47.619 0.00 0.00 45.77 3.02
1508 1653 1.512734 GCGAATTGCTCTTGGCGTG 60.513 57.895 0.00 0.00 45.43 5.34
1581 1726 3.366719 GAAATGATCGCCAAGCTTTAGC 58.633 45.455 0.00 1.56 42.49 3.09
1595 1746 1.949525 GCTGCACCATACCGAAATGAT 59.050 47.619 0.00 0.00 0.00 2.45
1601 1752 1.676678 GGAGAGCTGCACCATACCGA 61.677 60.000 1.02 0.00 0.00 4.69
1602 1753 1.227380 GGAGAGCTGCACCATACCG 60.227 63.158 1.02 0.00 0.00 4.02
1603 1754 1.147153 GGGAGAGCTGCACCATACC 59.853 63.158 1.02 0.00 0.00 2.73
1604 1755 1.227380 CGGGAGAGCTGCACCATAC 60.227 63.158 1.02 0.00 0.00 2.39
1605 1756 2.434843 CCGGGAGAGCTGCACCATA 61.435 63.158 1.02 0.00 0.00 2.74
1635 1786 2.097038 CGACGAGCTGCTTCCCTTG 61.097 63.158 2.53 0.00 0.00 3.61
1667 1818 3.444805 GACCAGAGGACGCGAGCT 61.445 66.667 15.93 0.31 0.00 4.09
1814 1968 0.179081 GTGCGTCTTATCCTGGGGAC 60.179 60.000 0.00 0.00 32.98 4.46
1830 1984 4.760047 ACCTGATGCCGTCCGTGC 62.760 66.667 0.00 0.00 0.00 5.34
1876 2030 1.651240 GACGACGACGATCCCTTGGA 61.651 60.000 15.32 0.00 42.66 3.53
1962 2116 2.689646 GCCACTCTGGTAGTTGACTTC 58.310 52.381 0.00 0.00 40.46 3.01
2015 2169 4.383602 AACGTGCCGCGACAATGC 62.384 61.111 8.23 1.50 44.77 3.56
2018 2172 4.927444 TCGAACGTGCCGCGACAA 62.927 61.111 8.23 0.00 44.77 3.18
2024 2178 3.467119 CGAACCTCGAACGTGCCG 61.467 66.667 4.46 4.46 43.74 5.69
2134 2300 2.817396 GCTCCTCTGCTTCACGGC 60.817 66.667 0.00 0.00 0.00 5.68
2218 2384 4.035558 CGCTGATAATCTTTTGCTGGCTAA 59.964 41.667 0.00 0.00 0.00 3.09
2263 2429 2.737376 GGCCTTGTCGTCGTGGAC 60.737 66.667 0.00 2.36 37.45 4.02
2583 2761 4.495939 CCGTCGTCGTCGTCCTCG 62.496 72.222 10.76 3.89 38.33 4.63
2595 2773 2.178521 CTCCCGTCTTCACCGTCG 59.821 66.667 0.00 0.00 0.00 5.12
2659 2837 2.031682 GTGCCGTGCATCTGGATTATTC 60.032 50.000 6.77 0.00 41.91 1.75
2660 2838 1.949525 GTGCCGTGCATCTGGATTATT 59.050 47.619 6.77 0.00 41.91 1.40
2662 2840 0.251634 TGTGCCGTGCATCTGGATTA 59.748 50.000 6.77 0.00 41.91 1.75
2663 2841 1.002257 TGTGCCGTGCATCTGGATT 60.002 52.632 6.77 0.00 41.91 3.01
2665 2843 2.046988 CTGTGCCGTGCATCTGGA 60.047 61.111 6.77 0.00 41.91 3.86
2667 2845 3.129502 CCCTGTGCCGTGCATCTG 61.130 66.667 1.90 1.77 41.91 2.90
2668 2846 3.320879 CTCCCTGTGCCGTGCATCT 62.321 63.158 1.90 0.00 41.91 2.90
2669 2847 2.821366 CTCCCTGTGCCGTGCATC 60.821 66.667 1.90 0.00 41.91 3.91
2676 2854 3.161450 TATCCCGCTCCCTGTGCC 61.161 66.667 0.00 0.00 0.00 5.01
2677 2855 2.109181 GTATCCCGCTCCCTGTGC 59.891 66.667 0.00 0.00 0.00 4.57
2678 2856 1.043116 TCAGTATCCCGCTCCCTGTG 61.043 60.000 0.00 0.00 0.00 3.66
2679 2857 0.325296 TTCAGTATCCCGCTCCCTGT 60.325 55.000 0.00 0.00 0.00 4.00
2680 2858 0.830648 TTTCAGTATCCCGCTCCCTG 59.169 55.000 0.00 0.00 0.00 4.45
2681 2859 1.807814 ATTTCAGTATCCCGCTCCCT 58.192 50.000 0.00 0.00 0.00 4.20
2682 2860 2.222027 CAATTTCAGTATCCCGCTCCC 58.778 52.381 0.00 0.00 0.00 4.30
2685 2863 1.680338 GCCAATTTCAGTATCCCGCT 58.320 50.000 0.00 0.00 0.00 5.52
2725 2903 2.028658 AGAGTCATGTACACTGCACAGG 60.029 50.000 0.00 0.00 0.00 4.00
2726 2904 3.056962 AGAGAGTCATGTACACTGCACAG 60.057 47.826 0.00 0.00 0.00 3.66
2728 2906 3.249091 CAGAGAGTCATGTACACTGCAC 58.751 50.000 0.00 0.00 0.00 4.57
2729 2907 2.893489 ACAGAGAGTCATGTACACTGCA 59.107 45.455 0.00 0.00 32.86 4.41
2730 2908 3.584406 ACAGAGAGTCATGTACACTGC 57.416 47.619 0.00 0.00 32.86 4.40
2732 2910 3.191581 CCGAACAGAGAGTCATGTACACT 59.808 47.826 0.00 0.00 0.00 3.55
2733 2911 3.502920 CCGAACAGAGAGTCATGTACAC 58.497 50.000 0.00 0.00 0.00 2.90
2734 2912 2.492088 CCCGAACAGAGAGTCATGTACA 59.508 50.000 0.00 0.00 0.00 2.90
2747 2925 1.090052 GCTCCCGATTTCCCGAACAG 61.090 60.000 0.00 0.00 0.00 3.16
2753 2931 2.517166 GCTGGCTCCCGATTTCCC 60.517 66.667 0.00 0.00 0.00 3.97
2754 2932 1.821332 CTGCTGGCTCCCGATTTCC 60.821 63.158 0.00 0.00 0.00 3.13
2755 2933 1.092345 GTCTGCTGGCTCCCGATTTC 61.092 60.000 0.00 0.00 0.00 2.17
2762 4548 4.521062 ATCGCGTCTGCTGGCTCC 62.521 66.667 5.77 0.00 39.65 4.70
2777 4563 3.119779 CCAAATGTTGGCCATGCAAAATC 60.120 43.478 6.09 0.00 45.17 2.17
2791 4577 2.948979 TCTCTGACGCAAACCAAATGTT 59.051 40.909 0.00 0.00 39.43 2.71
2804 4590 5.998454 AAGATGCCAATTTATCTCTGACG 57.002 39.130 0.00 0.00 32.71 4.35
2806 4592 8.708378 TCTAGAAAGATGCCAATTTATCTCTGA 58.292 33.333 0.00 0.00 32.71 3.27
2812 4598 7.836183 ACAAGGTCTAGAAAGATGCCAATTTAT 59.164 33.333 0.00 0.00 33.30 1.40
2829 4615 6.711277 AGCATCTTTCATTGTACAAGGTCTA 58.289 36.000 18.86 4.59 0.00 2.59
2832 4618 5.769662 TCAAGCATCTTTCATTGTACAAGGT 59.230 36.000 18.86 3.41 0.00 3.50
2881 4667 9.778741 ATCGATGTTTATTTATAGAAGCCAGAA 57.221 29.630 0.00 0.00 0.00 3.02
2882 4668 9.208022 CATCGATGTTTATTTATAGAAGCCAGA 57.792 33.333 17.50 0.00 0.00 3.86
2928 4714 7.816031 ACAATGCAAAATGTTTAGAGAAGATGG 59.184 33.333 0.00 0.00 0.00 3.51
2949 4735 6.914215 CAAGCATACTTAGGCATTGTACAATG 59.086 38.462 34.41 34.41 41.64 2.82
2957 4743 3.303351 AGCCAAGCATACTTAGGCATT 57.697 42.857 16.60 0.83 45.18 3.56
2959 4745 2.026356 TCAAGCCAAGCATACTTAGGCA 60.026 45.455 16.60 0.30 45.18 4.75
2961 4747 3.063997 CGTTCAAGCCAAGCATACTTAGG 59.936 47.826 0.00 0.00 33.74 2.69
2966 4752 1.130561 GTCCGTTCAAGCCAAGCATAC 59.869 52.381 0.00 0.00 0.00 2.39
2985 4771 1.472878 ACGCTGTGACGTAGATCATGT 59.527 47.619 0.00 0.00 46.19 3.21
3002 4788 1.503542 CTTGGCCTTGTGATGACGC 59.496 57.895 3.32 0.00 0.00 5.19
3012 4798 2.544745 GGTACCCACCCTTGGCCTT 61.545 63.158 3.32 0.00 42.35 4.35
3013 4799 2.939353 GGTACCCACCCTTGGCCT 60.939 66.667 3.32 0.00 42.35 5.19
3014 4800 3.261677 TGGTACCCACCCTTGGCC 61.262 66.667 10.07 0.00 45.11 5.36
3015 4801 1.571773 ATCTGGTACCCACCCTTGGC 61.572 60.000 10.07 0.00 45.11 4.52
3017 4803 2.844348 AGTTATCTGGTACCCACCCTTG 59.156 50.000 10.07 0.00 45.11 3.61
3018 4804 3.216230 AGTTATCTGGTACCCACCCTT 57.784 47.619 10.07 0.00 45.11 3.95
3019 4805 2.844348 CAAGTTATCTGGTACCCACCCT 59.156 50.000 10.07 0.00 45.11 4.34
3021 4807 3.994931 ACAAGTTATCTGGTACCCACC 57.005 47.619 10.07 0.00 46.00 4.61
3025 5046 8.665685 CAAATAGTGAACAAGTTATCTGGTACC 58.334 37.037 4.43 4.43 0.00 3.34
3028 5049 6.942576 AGCAAATAGTGAACAAGTTATCTGGT 59.057 34.615 0.00 0.00 0.00 4.00
3029 5050 7.383102 AGCAAATAGTGAACAAGTTATCTGG 57.617 36.000 0.00 0.00 0.00 3.86
3071 5094 7.417612 TCTAAGTAGCTGCAAAAACAAGAAAG 58.582 34.615 4.12 0.00 0.00 2.62
3078 5101 8.748380 AATTTGATCTAAGTAGCTGCAAAAAC 57.252 30.769 4.12 0.00 0.00 2.43
3135 5158 6.503560 TTACTTTGGAACTTGAGGGAGTAA 57.496 37.500 0.00 0.00 0.00 2.24
3140 5163 6.648879 TTCAATTACTTTGGAACTTGAGGG 57.351 37.500 0.00 0.00 35.92 4.30
3274 5978 7.509141 TGTGTTCTCTTGATGCTTCATTTTA 57.491 32.000 2.75 0.00 0.00 1.52
3295 5999 3.667695 CGTGTATGCTCATGGTGTTTGTG 60.668 47.826 0.00 0.00 0.00 3.33
3307 6011 1.421410 CGGAGGTTGCGTGTATGCTC 61.421 60.000 0.00 0.00 35.36 4.26
3309 6013 3.089784 CGGAGGTTGCGTGTATGC 58.910 61.111 0.00 0.00 0.00 3.14
3317 6021 2.548480 GTCCTATTTATGCGGAGGTTGC 59.452 50.000 0.00 0.00 0.00 4.17
3319 6023 2.805657 GCGTCCTATTTATGCGGAGGTT 60.806 50.000 0.00 0.00 35.67 3.50
3325 6029 1.930503 TGTGTGCGTCCTATTTATGCG 59.069 47.619 0.00 0.00 0.00 4.73
3338 6042 0.800300 GTTGGTGTTGGTTGTGTGCG 60.800 55.000 0.00 0.00 0.00 5.34
3370 6074 0.944386 CTTGCTAGTTGCCAACGTGT 59.056 50.000 1.20 0.00 42.00 4.49
3376 6080 6.049149 GTCTTATATGACTTGCTAGTTGCCA 58.951 40.000 10.70 0.00 36.08 4.92
3395 6099 2.611971 CGCCTACACTGCTTTGGTCTTA 60.612 50.000 0.00 0.00 0.00 2.10
3451 6164 7.042051 GCATATATGGTCATTGTCGTAGTTTGT 60.042 37.037 14.51 0.00 0.00 2.83
3474 6187 2.898612 TGTCATGAAATGGTTGGTGCAT 59.101 40.909 0.00 0.00 46.73 3.96
3489 6207 2.676076 TGTCGACTGTGTGATGTCATG 58.324 47.619 17.92 0.00 33.18 3.07
3504 6222 6.643360 TGACGACTAATGAAGAATTTTGTCGA 59.357 34.615 20.32 3.06 45.94 4.20
3509 6227 7.029563 GGCAATGACGACTAATGAAGAATTTT 58.970 34.615 0.00 0.00 0.00 1.82
3520 6238 0.319986 TGCGTGGCAATGACGACTAA 60.320 50.000 0.00 0.00 39.21 2.24
3527 6377 1.201181 GTTGGTTATGCGTGGCAATGA 59.799 47.619 0.00 0.00 43.62 2.57
3536 6386 0.390603 TGACCCGAGTTGGTTATGCG 60.391 55.000 0.00 0.00 39.24 4.73
3553 6403 4.248842 CAGCCCGTGTGGTGGTGA 62.249 66.667 0.00 0.00 36.57 4.02
3563 6683 0.541998 TCCATATCCGATCAGCCCGT 60.542 55.000 0.00 0.00 0.00 5.28
3602 6722 3.054655 GTGGTTGCCCTTATTCAGACCTA 60.055 47.826 0.00 0.00 0.00 3.08
3605 6725 2.790433 TGTGGTTGCCCTTATTCAGAC 58.210 47.619 0.00 0.00 0.00 3.51
3625 6745 2.172505 TGTCGTCCATAATTGGCCTGAT 59.827 45.455 3.32 0.00 43.29 2.90
3628 6748 2.799126 TTGTCGTCCATAATTGGCCT 57.201 45.000 3.32 0.00 43.29 5.19
3631 6751 4.199310 ACCTCATTGTCGTCCATAATTGG 58.801 43.478 0.00 0.00 45.15 3.16
3646 6768 4.519610 GGTGGCCACAACCTCATT 57.480 55.556 35.78 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.