Multiple sequence alignment - TraesCS2D01G211300

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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 TraesCS2D01G211300 chr2D 100.000 4252 0 0 1 4252 168424012 168428263 0.000000e+00 7853.0
1 TraesCS2D01G211300 chr2D 85.577 104 13 2 3911 4013 607673040 607672938 1.620000e-19 108.0
2 TraesCS2D01G211300 chr2D 89.412 85 8 1 1980 2063 74975910 74975994 5.810000e-19 106.0
3 TraesCS2D01G211300 chr2A 92.115 2790 161 27 1356 4106 182009672 182006903 0.000000e+00 3879.0
4 TraesCS2D01G211300 chr2A 90.952 630 39 12 759 1370 182010319 182009690 0.000000e+00 832.0
5 TraesCS2D01G211300 chr2A 91.443 596 32 6 1 580 182011499 182010907 0.000000e+00 800.0
6 TraesCS2D01G211300 chr2A 93.750 64 4 0 4189 4252 181857596 181857533 3.500000e-16 97.1
7 TraesCS2D01G211300 chr2B 88.026 927 45 24 671 1561 229790157 229789261 0.000000e+00 1037.0
8 TraesCS2D01G211300 chr2B 88.313 753 59 9 2216 2944 229788484 229787737 0.000000e+00 876.0
9 TraesCS2D01G211300 chr2B 93.466 551 30 2 2944 3488 229787683 229787133 0.000000e+00 813.0
10 TraesCS2D01G211300 chr2B 92.152 446 26 6 3480 3916 229786282 229785837 4.670000e-174 621.0
11 TraesCS2D01G211300 chr2B 91.709 398 30 3 1588 1982 229789261 229788864 2.230000e-152 549.0
12 TraesCS2D01G211300 chr2B 85.029 521 27 19 140 637 229790737 229790245 2.300000e-132 483.0
13 TraesCS2D01G211300 chr2B 91.166 283 23 2 3911 4192 229784772 229784491 2.400000e-102 383.0
14 TraesCS2D01G211300 chr2B 94.702 151 8 0 3 153 229790911 229790761 7.110000e-58 235.0
15 TraesCS2D01G211300 chr2B 91.489 141 11 1 2062 2201 229788866 229788726 4.340000e-45 193.0
16 TraesCS2D01G211300 chr2B 92.941 85 5 1 1980 2063 247368622 247368538 5.770000e-24 122.0
17 TraesCS2D01G211300 chr2B 91.860 86 6 1 1980 2064 788025911 788025996 7.470000e-23 119.0
18 TraesCS2D01G211300 chr2B 92.958 71 4 1 4182 4252 229782062 229781993 7.520000e-18 102.0
19 TraesCS2D01G211300 chr5A 82.159 908 96 32 2658 3536 486062126 486062996 0.000000e+00 719.0
20 TraesCS2D01G211300 chr7D 91.195 159 14 0 2754 2912 59672260 59672102 2.570000e-52 217.0
21 TraesCS2D01G211300 chr5D 91.195 159 14 0 2754 2912 220776190 220776032 2.570000e-52 217.0
22 TraesCS2D01G211300 chr1A 91.860 86 7 0 1978 2063 330769234 330769319 2.080000e-23 121.0
23 TraesCS2D01G211300 chr1B 91.860 86 6 1 1979 2063 597156803 597156888 7.470000e-23 119.0
24 TraesCS2D01G211300 chr4D 89.535 86 7 2 1980 2064 20114855 20114939 1.620000e-19 108.0
25 TraesCS2D01G211300 chr4A 89.412 85 8 1 1980 2063 697388805 697388889 5.810000e-19 106.0
26 TraesCS2D01G211300 chr6D 87.640 89 10 1 1979 2066 343295806 343295718 7.520000e-18 102.0


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 TraesCS2D01G211300 chr2D 168424012 168428263 4251 False 7853.0 7853 100.000000 1 4252 1 chr2D.!!$F2 4251
1 TraesCS2D01G211300 chr2A 182006903 182011499 4596 True 1837.0 3879 91.503333 1 4106 3 chr2A.!!$R2 4105
2 TraesCS2D01G211300 chr2B 229781993 229790911 8918 True 529.2 1037 90.901000 3 4252 10 chr2B.!!$R2 4249
3 TraesCS2D01G211300 chr5A 486062126 486062996 870 False 719.0 719 82.159000 2658 3536 1 chr5A.!!$F1 878

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
770 1303 0.039618 GGGAATGTTTGGGCTCAGGA 59.960 55.0 0.00 0.00 0.00 3.86 F
1369 1970 0.106519 AGTTCACTGGCTTTGTGGCT 60.107 50.0 6.16 3.46 42.34 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2281 0.105408 AGGGTGTTCGCGTTACTTGT 59.895 50.0 5.77 0.0 0.00 3.16 R
3359 4319 0.237498 AAGCGTTGTAAAGAAGCCGC 59.763 50.0 0.00 0.0 41.29 6.53 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
38 39 2.443952 ATCGGGATGTGGCTCGGA 60.444 61.111 0.00 0.00 0.00 4.55
40 41 1.821061 ATCGGGATGTGGCTCGGATC 61.821 60.000 0.00 0.00 0.00 3.36
96 97 2.590007 CGCAGGGATGCTGCTACC 60.590 66.667 0.00 4.17 44.88 3.18
315 353 2.738743 TCCAGAAAAATGGAGGCCATC 58.261 47.619 5.01 0.00 44.40 3.51
316 354 2.312741 TCCAGAAAAATGGAGGCCATCT 59.687 45.455 5.01 0.00 44.40 2.90
359 402 4.886489 GGAGTAGGACCAGTAGTAAATCGT 59.114 45.833 0.00 0.00 0.00 3.73
381 424 2.139917 CGTTCAAGATGTTTCCGGTCA 58.860 47.619 0.00 0.00 0.00 4.02
383 426 3.002862 CGTTCAAGATGTTTCCGGTCAAA 59.997 43.478 0.00 0.00 0.00 2.69
384 427 4.287720 GTTCAAGATGTTTCCGGTCAAAC 58.712 43.478 10.96 10.96 36.87 2.93
401 444 4.851558 GTCAAACCGTGTAATCTTTGATGC 59.148 41.667 0.00 0.00 35.61 3.91
415 458 1.298157 TGATGCGTACTTGTGGCAGC 61.298 55.000 8.98 8.98 42.94 5.25
446 499 6.830114 ATTCAGTTGCTAGTATTAACTCGC 57.170 37.500 0.00 0.00 43.05 5.03
666 1160 2.408241 GGTCCCGACTCCTGACTCG 61.408 68.421 0.00 0.00 0.00 4.18
667 1161 1.376942 GTCCCGACTCCTGACTCGA 60.377 63.158 0.00 0.00 31.24 4.04
668 1162 1.376942 TCCCGACTCCTGACTCGAC 60.377 63.158 0.00 0.00 31.24 4.20
669 1163 2.751913 CCCGACTCCTGACTCGACG 61.752 68.421 0.00 0.00 31.24 5.12
681 1210 3.610791 CTCGACGCCTGCGAAGTGA 62.611 63.158 19.52 8.72 42.83 3.41
769 1302 0.972471 GGGGAATGTTTGGGCTCAGG 60.972 60.000 0.00 0.00 0.00 3.86
770 1303 0.039618 GGGAATGTTTGGGCTCAGGA 59.960 55.000 0.00 0.00 0.00 3.86
771 1304 1.342374 GGGAATGTTTGGGCTCAGGAT 60.342 52.381 0.00 0.00 0.00 3.24
793 1326 3.676291 TTTTAGGCAATTTGGGCTCAC 57.324 42.857 0.00 0.00 43.38 3.51
807 1340 1.135517 GGCTCACTTGAGAGAGACGTC 60.136 57.143 7.70 7.70 44.74 4.34
808 1341 1.537638 GCTCACTTGAGAGAGACGTCA 59.462 52.381 19.50 0.00 44.74 4.35
809 1342 2.163412 GCTCACTTGAGAGAGACGTCAT 59.837 50.000 19.50 5.56 44.74 3.06
810 1343 3.757184 CTCACTTGAGAGAGACGTCATG 58.243 50.000 19.50 1.22 44.74 3.07
811 1344 2.489722 TCACTTGAGAGAGACGTCATGG 59.510 50.000 19.50 1.47 0.00 3.66
813 1346 0.532573 TTGAGAGAGACGTCATGGGC 59.467 55.000 19.50 4.60 0.00 5.36
814 1347 1.323271 TGAGAGAGACGTCATGGGCC 61.323 60.000 19.50 0.00 0.00 5.80
815 1348 1.000993 AGAGAGACGTCATGGGCCT 59.999 57.895 19.50 4.44 0.00 5.19
816 1349 0.259065 AGAGAGACGTCATGGGCCTA 59.741 55.000 19.50 0.00 0.00 3.93
939 1483 4.724602 GCGGCGCAGAGAGACACA 62.725 66.667 29.21 0.00 0.00 3.72
940 1484 2.049156 CGGCGCAGAGAGACACAA 60.049 61.111 10.83 0.00 0.00 3.33
941 1485 2.375766 CGGCGCAGAGAGACACAAC 61.376 63.158 10.83 0.00 0.00 3.32
942 1486 2.029844 GGCGCAGAGAGACACAACC 61.030 63.158 10.83 0.00 0.00 3.77
944 1488 1.285950 CGCAGAGAGACACAACCGA 59.714 57.895 0.00 0.00 0.00 4.69
945 1489 1.004277 CGCAGAGAGACACAACCGAC 61.004 60.000 0.00 0.00 0.00 4.79
1027 1572 1.733526 GGCCGCAACAAGAACAAGT 59.266 52.632 0.00 0.00 0.00 3.16
1112 1657 0.676782 GCAGAAGCCCCACAACGTAT 60.677 55.000 0.00 0.00 33.58 3.06
1114 1659 1.737793 CAGAAGCCCCACAACGTATTC 59.262 52.381 0.00 0.00 0.00 1.75
1116 1661 1.737793 GAAGCCCCACAACGTATTCTG 59.262 52.381 0.00 0.00 0.00 3.02
1179 1724 3.261897 TCCACTCTCTTTGACCCTGATTC 59.738 47.826 0.00 0.00 0.00 2.52
1180 1725 3.008375 CCACTCTCTTTGACCCTGATTCA 59.992 47.826 0.00 0.00 0.00 2.57
1192 1737 3.506067 ACCCTGATTCATTCCGTGTTTTC 59.494 43.478 0.00 0.00 0.00 2.29
1290 1835 2.161609 GTGAGCAAAAGGATTACACCGG 59.838 50.000 0.00 0.00 34.73 5.28
1303 1848 7.046033 AGGATTACACCGGTTACTTCTTATTG 58.954 38.462 2.97 0.00 34.73 1.90
1359 1928 4.453819 GGTCAATCTTTCTGAGTTCACTGG 59.546 45.833 0.00 0.00 0.00 4.00
1363 1932 4.156455 TCTTTCTGAGTTCACTGGCTTT 57.844 40.909 0.00 0.00 0.00 3.51
1365 1934 3.281727 TTCTGAGTTCACTGGCTTTGT 57.718 42.857 0.00 0.00 0.00 2.83
1369 1970 0.106519 AGTTCACTGGCTTTGTGGCT 60.107 50.000 6.16 3.46 42.34 4.75
1393 1994 8.040727 GCTGTTTAAATTGGGGAATTTGAGTAT 58.959 33.333 0.00 0.00 34.51 2.12
1395 1996 8.247562 TGTTTAAATTGGGGAATTTGAGTATCG 58.752 33.333 0.00 0.00 38.61 2.92
1397 1998 5.835113 AATTGGGGAATTTGAGTATCGTG 57.165 39.130 0.00 0.00 38.61 4.35
1398 1999 3.992943 TGGGGAATTTGAGTATCGTGT 57.007 42.857 0.00 0.00 38.61 4.49
1399 2000 5.423704 TTGGGGAATTTGAGTATCGTGTA 57.576 39.130 0.00 0.00 38.61 2.90
1400 2001 5.423704 TGGGGAATTTGAGTATCGTGTAA 57.576 39.130 0.00 0.00 38.61 2.41
1401 2002 5.996644 TGGGGAATTTGAGTATCGTGTAAT 58.003 37.500 0.00 0.00 38.61 1.89
1405 2016 7.186804 GGGAATTTGAGTATCGTGTAATTGTG 58.813 38.462 0.00 0.00 38.61 3.33
1410 2021 5.984725 TGAGTATCGTGTAATTGTGGGATT 58.015 37.500 0.00 0.00 38.61 3.01
1412 2023 7.557724 TGAGTATCGTGTAATTGTGGGATTAA 58.442 34.615 0.00 0.00 38.61 1.40
1422 2033 2.496111 TGTGGGATTAACCGAACACAC 58.504 47.619 0.00 0.00 40.11 3.82
1442 2053 8.445275 ACACACACTGATTAGTTTGACATTAA 57.555 30.769 10.46 0.00 36.87 1.40
1494 2112 4.512484 TGGATGATTCATACAGCGTTTCA 58.488 39.130 7.51 0.00 28.55 2.69
1519 2137 2.644887 TGCATGAGGGCACACTTTC 58.355 52.632 0.00 0.00 39.25 2.62
1523 2141 2.036346 GCATGAGGGCACACTTTCTTTT 59.964 45.455 0.00 0.00 0.00 2.27
1565 2183 5.570234 AGCGTTTGTACCTTCTTTTTCAA 57.430 34.783 0.00 0.00 0.00 2.69
1566 2184 5.337554 AGCGTTTGTACCTTCTTTTTCAAC 58.662 37.500 0.00 0.00 0.00 3.18
1567 2185 5.096849 GCGTTTGTACCTTCTTTTTCAACA 58.903 37.500 0.00 0.00 0.00 3.33
1572 2190 4.647399 TGTACCTTCTTTTTCAACAAGGGG 59.353 41.667 1.81 0.00 39.93 4.79
1575 2193 4.215109 CCTTCTTTTTCAACAAGGGGAGA 58.785 43.478 0.00 0.00 33.04 3.71
1586 2204 5.312178 TCAACAAGGGGAGAAGGAAAATAGA 59.688 40.000 0.00 0.00 0.00 1.98
1649 2268 2.860582 GCTAGACCATAGCTCGAGCAAC 60.861 54.545 36.87 20.19 45.16 4.17
1662 2281 3.318886 TCGAGCAACGTTACAGCATAAA 58.681 40.909 11.17 0.00 43.13 1.40
1666 2285 4.783242 AGCAACGTTACAGCATAAACAAG 58.217 39.130 11.17 0.00 0.00 3.16
1693 2316 2.736347 GAACACCCTAGCTACTCCTCA 58.264 52.381 0.00 0.00 0.00 3.86
1698 2321 1.410932 CCCTAGCTACTCCTCACAGCT 60.411 57.143 0.55 0.55 46.91 4.24
1709 2332 0.179116 CTCACAGCTCTGCGTGCTAT 60.179 55.000 5.13 0.00 38.92 2.97
1729 2352 4.978083 ATCAATAGTTGAAAGCCTGCAG 57.022 40.909 6.78 6.78 43.95 4.41
1736 2359 0.472044 TGAAAGCCTGCAGTACCACA 59.528 50.000 13.81 4.59 0.00 4.17
1867 2490 4.195225 TGTATGTGTAATCGAGTTGGCA 57.805 40.909 0.00 0.00 0.00 4.92
1868 2491 4.180817 TGTATGTGTAATCGAGTTGGCAG 58.819 43.478 0.00 0.00 0.00 4.85
1889 2512 7.094377 TGGCAGTAGATAGTTTCAAATGTTTCC 60.094 37.037 0.00 0.00 0.00 3.13
1943 2566 3.189287 CACTCCACTAATGTTGTTGCTCC 59.811 47.826 0.00 0.00 0.00 4.70
1960 2583 1.341531 CTCCGGCTAACTAGGATGGTG 59.658 57.143 0.00 0.00 33.04 4.17
1971 2594 2.586648 AGGATGGTGGGTCTGAAAAC 57.413 50.000 0.00 0.00 0.00 2.43
1989 2612 9.310449 TCTGAAAACTGTATTCTACTACCTCTT 57.690 33.333 0.00 0.00 0.00 2.85
2028 2651 6.767080 ACGTTTTTGCAGTTCAATTTAAACC 58.233 32.000 0.00 0.00 32.96 3.27
2035 2658 5.525378 TGCAGTTCAATTTAAACCGCAAAAT 59.475 32.000 8.29 0.00 37.16 1.82
2156 2780 3.118261 TCCCTCATCTGGTTGCTGTATTC 60.118 47.826 0.00 0.00 0.00 1.75
2175 2799 2.875296 TCTACTGGCCAAACTGCAAAT 58.125 42.857 7.01 0.00 0.00 2.32
2208 2832 6.671614 TTTGAGTTGTTCAAGTTACATCGT 57.328 33.333 0.00 0.00 46.01 3.73
2215 2839 8.086522 AGTTGTTCAAGTTACATCGTACTGTAT 58.913 33.333 0.00 0.00 31.94 2.29
2280 3132 7.816640 TGCTAGAGGTTAAAGTAATGCAAAAG 58.183 34.615 0.00 0.00 0.00 2.27
2301 3153 4.090090 AGTAATAGGTGCTGACACTGACT 58.910 43.478 0.00 0.00 46.57 3.41
2302 3154 3.325293 AATAGGTGCTGACACTGACTG 57.675 47.619 0.00 0.00 46.57 3.51
2308 3160 2.294791 GTGCTGACACTGACTGTAGAGT 59.705 50.000 0.00 0.00 43.85 3.24
2379 3231 8.602424 TCCCTTAGATCAGTTACTGAAATTTGA 58.398 33.333 19.42 7.54 44.04 2.69
2432 3284 4.523943 CCTGTCACCTTTTCATCAATTCCA 59.476 41.667 0.00 0.00 0.00 3.53
2554 3406 8.674173 AGTAGATCCTGAGGATTAAGAGTATCA 58.326 37.037 16.38 0.00 43.27 2.15
2594 3446 6.795399 TGCTTTATCTTTTGGCATTAGCTAC 58.205 36.000 0.00 0.00 41.70 3.58
2686 3559 6.663944 AGATTGTCCATAACGTTTTCTAGC 57.336 37.500 5.91 0.00 0.00 3.42
2732 3606 7.773690 ACATAAAGTAAATATGTCCCTGGTGTC 59.226 37.037 0.00 0.00 39.20 3.67
2761 3635 8.442632 TCTTCCTAATGCATCAGATGTTTAAG 57.557 34.615 12.18 7.32 0.00 1.85
2815 3689 5.474532 TCTTTTTCTCATTGTCAGACCATGG 59.525 40.000 11.19 11.19 0.00 3.66
2928 3812 1.419387 GGCTGTTCCCTGATATGCTCT 59.581 52.381 0.00 0.00 0.00 4.09
3088 4040 9.635404 TTTTACCTGATCACCTTTCTCTTTAAA 57.365 29.630 0.00 0.00 0.00 1.52
3282 4234 7.445707 TCAGTGGTTAGCATAATTTTGTGTACA 59.554 33.333 0.00 0.00 0.00 2.90
3359 4319 4.142609 TGCCTCTAAAGATTGCCACTAG 57.857 45.455 0.00 0.00 0.00 2.57
3426 4386 7.070821 CCTGGTATTGGTTAGTACAGTAGGAAT 59.929 40.741 0.00 0.00 0.00 3.01
3485 5304 4.865776 TCGCAAAGTTGGAAGGTAAATTG 58.134 39.130 0.00 0.00 0.00 2.32
3550 5369 4.027674 TGCACCACTAAGCAAATCCTTA 57.972 40.909 0.00 0.00 37.90 2.69
3621 5441 3.931907 AATCCTCGATTTGATGTGGGA 57.068 42.857 0.00 0.00 0.00 4.37
3714 5535 1.842562 ACCATCTAGAGCATTGCAGGT 59.157 47.619 11.91 4.17 0.00 4.00
3725 5546 2.592102 ATTGCAGGTCAATGTGGAGT 57.408 45.000 0.00 0.00 43.40 3.85
3838 5664 2.106683 GCCATCAAACGTCTCCCCG 61.107 63.158 0.00 0.00 0.00 5.73
3867 5695 1.297598 CGGATCGGCGCAATTGAAC 60.298 57.895 10.83 0.00 0.00 3.18
4000 6898 8.075761 ACTTCCTTAAACTGTTAGACCGATAT 57.924 34.615 0.00 0.00 0.00 1.63
4097 6996 8.900781 CCTGAACAAAGATTCATCTACATTGAT 58.099 33.333 6.69 0.00 37.93 2.57
4113 7012 6.205101 ACATTGATCTTTGCTTCATTCTCC 57.795 37.500 0.00 0.00 0.00 3.71
4154 7053 2.139888 ATTGCGCGTGTGCCAAATGA 62.140 50.000 8.43 0.00 35.75 2.57
4170 7069 4.439700 CCAAATGAGCCAGATGATCAACAC 60.440 45.833 0.00 0.00 0.00 3.32
4172 7071 1.629861 TGAGCCAGATGATCAACACCA 59.370 47.619 0.00 0.00 0.00 4.17
4192 7091 1.185618 TAGTTCGCTGCACCTCAGGT 61.186 55.000 0.00 0.00 43.06 4.00
4239 9576 1.303317 GGTTGCGACTTGGGACCAT 60.303 57.895 3.59 0.00 0.00 3.55
4240 9577 1.305930 GGTTGCGACTTGGGACCATC 61.306 60.000 3.59 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.971386 ACCTGACCACGTAAACGGAT 59.029 50.000 7.50 0.00 44.95 4.18
40 41 1.585297 AAACCTGACCACGTAAACGG 58.415 50.000 7.50 0.00 44.95 4.44
96 97 1.021390 CCAAAGGACGGCACTGCTAG 61.021 60.000 0.00 0.00 0.00 3.42
294 332 2.925966 TGGCCTCCATTTTTCTGGAT 57.074 45.000 3.32 0.00 44.23 3.41
310 348 1.743996 GTCACTTTCCTGGAGATGGC 58.256 55.000 0.00 0.00 0.00 4.40
311 349 1.406069 CCGTCACTTTCCTGGAGATGG 60.406 57.143 7.34 7.34 0.00 3.51
313 351 1.276421 CACCGTCACTTTCCTGGAGAT 59.724 52.381 0.00 0.00 0.00 2.75
314 352 0.679505 CACCGTCACTTTCCTGGAGA 59.320 55.000 0.00 0.00 0.00 3.71
315 353 0.393077 ACACCGTCACTTTCCTGGAG 59.607 55.000 0.00 0.00 0.00 3.86
316 354 1.616865 CTACACCGTCACTTTCCTGGA 59.383 52.381 0.00 0.00 0.00 3.86
359 402 2.803956 GACCGGAAACATCTTGAACGAA 59.196 45.455 9.46 0.00 0.00 3.85
381 424 3.500680 ACGCATCAAAGATTACACGGTTT 59.499 39.130 0.00 0.00 0.00 3.27
383 426 2.695359 ACGCATCAAAGATTACACGGT 58.305 42.857 0.00 0.00 0.00 4.83
384 427 3.863424 AGTACGCATCAAAGATTACACGG 59.137 43.478 0.00 0.00 0.00 4.94
392 435 1.804151 GCCACAAGTACGCATCAAAGA 59.196 47.619 0.00 0.00 0.00 2.52
401 444 0.163788 CTTTCGCTGCCACAAGTACG 59.836 55.000 0.00 0.00 0.00 3.67
415 458 7.470289 AATACTAGCAACTGAATAGCTTTCG 57.530 36.000 0.00 0.00 39.68 3.46
446 499 5.361285 AGGCATGTAAACTAGTAGTCCTCAG 59.639 44.000 2.58 0.00 0.00 3.35
514 571 8.805175 TCTTAATTGATTGATCAGGCAAGAAAA 58.195 29.630 14.85 9.44 38.19 2.29
515 572 8.246180 GTCTTAATTGATTGATCAGGCAAGAAA 58.754 33.333 14.85 11.12 38.19 2.52
516 573 7.394077 TGTCTTAATTGATTGATCAGGCAAGAA 59.606 33.333 14.85 11.24 38.19 2.52
517 574 6.885918 TGTCTTAATTGATTGATCAGGCAAGA 59.114 34.615 14.85 6.66 38.19 3.02
520 577 5.066893 GCTGTCTTAATTGATTGATCAGGCA 59.933 40.000 0.00 0.00 38.19 4.75
597 756 5.435686 AGCAAACCCATGACTAGATGTAA 57.564 39.130 0.00 0.00 0.00 2.41
598 757 5.423931 TGTAGCAAACCCATGACTAGATGTA 59.576 40.000 0.00 0.00 0.00 2.29
663 1157 3.175240 CACTTCGCAGGCGTCGAG 61.175 66.667 13.83 12.06 40.74 4.04
666 1160 2.383527 CCTTCACTTCGCAGGCGTC 61.384 63.158 13.83 0.00 40.74 5.19
667 1161 2.357517 CCTTCACTTCGCAGGCGT 60.358 61.111 13.83 0.00 40.74 5.68
668 1162 3.793144 GCCTTCACTTCGCAGGCG 61.793 66.667 7.46 7.46 43.73 5.52
681 1210 5.301805 CCAGATAATAATTTTCCCGTGCCTT 59.698 40.000 0.00 0.00 0.00 4.35
753 1286 4.541973 AAAATCCTGAGCCCAAACATTC 57.458 40.909 0.00 0.00 0.00 2.67
793 1326 1.470632 GCCCATGACGTCTCTCTCAAG 60.471 57.143 17.92 0.00 0.00 3.02
807 1340 0.957395 CGGCTAGCAATAGGCCCATG 60.957 60.000 18.24 0.00 46.50 3.66
808 1341 1.376466 CGGCTAGCAATAGGCCCAT 59.624 57.895 18.24 0.00 46.50 4.00
809 1342 2.040009 GACGGCTAGCAATAGGCCCA 62.040 60.000 18.24 0.00 46.50 5.36
810 1343 1.301795 GACGGCTAGCAATAGGCCC 60.302 63.158 18.24 0.00 46.50 5.80
811 1344 1.301795 GGACGGCTAGCAATAGGCC 60.302 63.158 18.24 12.24 46.50 5.19
813 1346 1.270358 GGAAGGACGGCTAGCAATAGG 60.270 57.143 18.24 2.30 0.00 2.57
814 1347 1.412710 TGGAAGGACGGCTAGCAATAG 59.587 52.381 18.24 7.11 0.00 1.73
815 1348 1.491668 TGGAAGGACGGCTAGCAATA 58.508 50.000 18.24 0.00 0.00 1.90
816 1349 0.618458 TTGGAAGGACGGCTAGCAAT 59.382 50.000 18.24 2.87 0.00 3.56
928 1472 0.038159 GGGTCGGTTGTGTCTCTCTG 60.038 60.000 0.00 0.00 0.00 3.35
934 1478 2.356673 GGTCGGGTCGGTTGTGTC 60.357 66.667 0.00 0.00 0.00 3.67
938 1482 2.613506 GCTTTGGTCGGGTCGGTTG 61.614 63.158 0.00 0.00 0.00 3.77
939 1483 2.281276 GCTTTGGTCGGGTCGGTT 60.281 61.111 0.00 0.00 0.00 4.44
940 1484 4.675029 CGCTTTGGTCGGGTCGGT 62.675 66.667 0.00 0.00 0.00 4.69
1112 1657 4.526970 AGACAAAGGCTCAAAAGACAGAA 58.473 39.130 0.00 0.00 30.24 3.02
1114 1659 4.907879 AAGACAAAGGCTCAAAAGACAG 57.092 40.909 0.00 0.00 30.24 3.51
1116 1661 5.506686 AGAAAGACAAAGGCTCAAAAGAC 57.493 39.130 0.00 0.00 0.00 3.01
1163 1708 3.624861 CGGAATGAATCAGGGTCAAAGAG 59.375 47.826 0.00 0.00 0.00 2.85
1164 1709 3.009033 ACGGAATGAATCAGGGTCAAAGA 59.991 43.478 0.00 0.00 0.00 2.52
1166 1711 3.081061 CACGGAATGAATCAGGGTCAAA 58.919 45.455 0.00 0.00 0.00 2.69
1179 1724 1.627864 AAGGGGGAAAACACGGAATG 58.372 50.000 0.00 0.00 0.00 2.67
1180 1725 2.244695 GAAAGGGGGAAAACACGGAAT 58.755 47.619 0.00 0.00 0.00 3.01
1192 1737 3.204827 CATCGCTGCGAAAGGGGG 61.205 66.667 29.48 10.35 39.99 5.40
1290 1835 8.541133 AAACAGAGAGAGCAATAAGAAGTAAC 57.459 34.615 0.00 0.00 0.00 2.50
1303 1848 3.127721 GGCAACCAATAAACAGAGAGAGC 59.872 47.826 0.00 0.00 0.00 4.09
1359 1928 3.498018 CCCAATTTAAACAGCCACAAAGC 59.502 43.478 0.00 0.00 0.00 3.51
1363 1932 2.964209 TCCCCAATTTAAACAGCCACA 58.036 42.857 0.00 0.00 0.00 4.17
1365 1934 5.072329 TCAAATTCCCCAATTTAAACAGCCA 59.928 36.000 0.00 0.00 39.75 4.75
1369 1970 8.247562 CGATACTCAAATTCCCCAATTTAAACA 58.752 33.333 0.00 0.00 39.75 2.83
1393 1994 3.933955 CGGTTAATCCCACAATTACACGA 59.066 43.478 0.00 0.00 0.00 4.35
1395 1996 5.181622 TGTTCGGTTAATCCCACAATTACAC 59.818 40.000 0.00 0.00 0.00 2.90
1397 1998 5.181622 TGTGTTCGGTTAATCCCACAATTAC 59.818 40.000 0.00 0.00 34.58 1.89
1398 1999 5.181622 GTGTGTTCGGTTAATCCCACAATTA 59.818 40.000 3.01 0.00 37.53 1.40
1399 2000 4.022676 GTGTGTTCGGTTAATCCCACAATT 60.023 41.667 3.01 0.00 37.53 2.32
1400 2001 3.504520 GTGTGTTCGGTTAATCCCACAAT 59.495 43.478 3.01 0.00 37.53 2.71
1401 2002 2.879646 GTGTGTTCGGTTAATCCCACAA 59.120 45.455 3.01 0.00 37.53 3.33
1405 2016 2.482721 CAGTGTGTGTTCGGTTAATCCC 59.517 50.000 0.00 0.00 0.00 3.85
1410 2021 5.204409 ACTAATCAGTGTGTGTTCGGTTA 57.796 39.130 0.00 0.00 32.25 2.85
1412 2023 3.746045 ACTAATCAGTGTGTGTTCGGT 57.254 42.857 0.00 0.00 32.25 4.69
1442 2053 7.692460 TTTCATGCAGAGTTCTTCATAATGT 57.308 32.000 0.00 0.00 29.00 2.71
1494 2112 2.428171 GTGTGCCCTCATGCATAAACAT 59.572 45.455 0.00 0.00 44.30 2.71
1519 2137 3.727723 GCTTGCGCATGCTCTATAAAAAG 59.272 43.478 33.57 15.46 43.34 2.27
1523 2141 1.952193 TGCTTGCGCATGCTCTATAA 58.048 45.000 37.63 20.95 42.25 0.98
1565 2183 6.447084 TGTATCTATTTTCCTTCTCCCCTTGT 59.553 38.462 0.00 0.00 0.00 3.16
1566 2184 6.900194 TGTATCTATTTTCCTTCTCCCCTTG 58.100 40.000 0.00 0.00 0.00 3.61
1567 2185 6.101881 CCTGTATCTATTTTCCTTCTCCCCTT 59.898 42.308 0.00 0.00 0.00 3.95
1572 2190 7.713073 CCAACTCCTGTATCTATTTTCCTTCTC 59.287 40.741 0.00 0.00 0.00 2.87
1575 2193 6.663734 CCCAACTCCTGTATCTATTTTCCTT 58.336 40.000 0.00 0.00 0.00 3.36
1586 2204 0.254178 CAGCAGCCCAACTCCTGTAT 59.746 55.000 0.00 0.00 0.00 2.29
1605 2224 1.087501 GACCTTTTGATCTCGGCACC 58.912 55.000 0.00 0.00 0.00 5.01
1662 2281 0.105408 AGGGTGTTCGCGTTACTTGT 59.895 50.000 5.77 0.00 0.00 3.16
1666 2285 0.108945 AGCTAGGGTGTTCGCGTTAC 60.109 55.000 5.77 6.59 0.00 2.50
1698 2321 4.385358 TCAACTATTGATAGCACGCAGA 57.615 40.909 0.00 0.00 34.08 4.26
1709 2332 3.754965 ACTGCAGGCTTTCAACTATTGA 58.245 40.909 19.93 0.00 38.04 2.57
1729 2352 4.002982 TCAATGATGAAGCAGTGTGGTAC 58.997 43.478 0.00 0.00 35.53 3.34
1736 2359 5.860182 CGAACAAAATCAATGATGAAGCAGT 59.140 36.000 0.00 0.00 39.49 4.40
1817 2440 3.935203 AGGTAATGCTCGACAATGTCTTG 59.065 43.478 11.92 5.11 38.39 3.02
1867 2490 8.784043 GTGTGGAAACATTTGAAACTATCTACT 58.216 33.333 0.00 0.00 46.14 2.57
1868 2491 8.021396 GGTGTGGAAACATTTGAAACTATCTAC 58.979 37.037 0.00 0.00 46.14 2.59
1943 2566 0.393077 CCCACCATCCTAGTTAGCCG 59.607 60.000 0.00 0.00 0.00 5.52
1960 2583 7.040494 GGTAGTAGAATACAGTTTTCAGACCC 58.960 42.308 6.53 0.00 46.26 4.46
2028 2651 9.019764 CCTTACCAAAATATAAGACATTTTGCG 57.980 33.333 12.75 9.64 45.58 4.85
2035 2658 7.404980 ACTCCCTCCTTACCAAAATATAAGACA 59.595 37.037 0.00 0.00 31.20 3.41
2052 2675 4.415224 TTCAAGTAAGGTACTCCCTCCT 57.585 45.455 0.00 0.00 45.47 3.69
2156 2780 4.989279 ATATTTGCAGTTTGGCCAGTAG 57.011 40.909 5.11 0.00 0.00 2.57
2205 2829 5.878116 CCCATGGAAAAGAAATACAGTACGA 59.122 40.000 15.22 0.00 0.00 3.43
2222 3073 2.517959 CTCAACAGCTTTTCCCATGGA 58.482 47.619 15.22 0.00 0.00 3.41
2255 3107 7.447238 ACTTTTGCATTACTTTAACCTCTAGCA 59.553 33.333 0.00 0.00 0.00 3.49
2280 3132 4.177026 CAGTCAGTGTCAGCACCTATTAC 58.823 47.826 0.00 0.00 46.35 1.89
2301 3153 5.001232 GGCAAGTTCCAATAACACTCTACA 58.999 41.667 0.00 0.00 0.00 2.74
2302 3154 5.246307 AGGCAAGTTCCAATAACACTCTAC 58.754 41.667 0.00 0.00 0.00 2.59
2308 3160 4.700213 GCTAAGAGGCAAGTTCCAATAACA 59.300 41.667 0.00 0.00 0.00 2.41
2379 3231 3.377172 CGAGTGAAGGGTGACAAACTTTT 59.623 43.478 0.00 0.00 0.00 2.27
2479 3331 7.121315 ACAAGATTTAACTAGCCTTGGATTGAC 59.879 37.037 0.00 0.00 38.70 3.18
2484 3336 8.325787 TGAATACAAGATTTAACTAGCCTTGGA 58.674 33.333 0.00 0.00 38.70 3.53
2554 3406 4.861102 AAAGCAAAACAGCAGCTTATCT 57.139 36.364 0.00 0.00 46.95 1.98
2686 3559 9.764363 TTTATGTATTCCAGTAGAACAGCTATG 57.236 33.333 0.00 0.00 37.29 2.23
2732 3606 6.242508 CATCTGATGCATTAGGAAGATGTG 57.757 41.667 17.59 3.58 37.38 3.21
2761 3635 9.060347 TGACAATTCAAATATCTGATCTTAGCC 57.940 33.333 0.00 0.00 0.00 3.93
2928 3812 3.572255 GGGTGCCACTAATTCACTTTCAA 59.428 43.478 0.00 0.00 0.00 2.69
3282 4234 8.211629 GGTTGATCTACAGGTGGAAATATACTT 58.788 37.037 9.51 0.00 0.00 2.24
3359 4319 0.237498 AAGCGTTGTAAAGAAGCCGC 59.763 50.000 0.00 0.00 41.29 6.53
3361 4321 4.689345 TCTCTTAAGCGTTGTAAAGAAGCC 59.311 41.667 0.00 0.00 0.00 4.35
3426 4386 5.085920 AGAATGTGATGAAAAACCCCATCA 58.914 37.500 0.00 0.00 44.66 3.07
3485 5304 4.349663 TTTGTTGCTACGATGGCATTAC 57.650 40.909 0.00 0.00 39.54 1.89
3550 5369 9.014297 CACACTAATTTTTACCTTCTGATTCCT 57.986 33.333 0.00 0.00 0.00 3.36
3571 5390 0.037303 CCAGGAGCCATCAACACACT 59.963 55.000 0.00 0.00 0.00 3.55
3714 5535 3.186702 TGAACGAACACTCCACATTGA 57.813 42.857 0.00 0.00 0.00 2.57
3838 5664 2.892425 CGATCCGCTGAAGCACCC 60.892 66.667 2.79 0.00 42.21 4.61
3963 6861 9.642343 ACAGTTTAAGGAAGTTAATTTTCTCCT 57.358 29.630 0.00 0.00 30.46 3.69
3979 6877 7.817962 CCCATATATCGGTCTAACAGTTTAAGG 59.182 40.741 0.00 0.00 0.00 2.69
4097 6996 2.040813 AGCCAGGAGAATGAAGCAAAGA 59.959 45.455 0.00 0.00 0.00 2.52
4113 7012 1.092348 CATCACACATGACCAGCCAG 58.908 55.000 0.00 0.00 37.79 4.85
4154 7053 3.457380 ACTATGGTGTTGATCATCTGGCT 59.543 43.478 0.00 0.00 0.00 4.75
4170 7069 0.108186 TGAGGTGCAGCGAACTATGG 60.108 55.000 10.78 0.00 0.00 2.74
4172 7071 0.176680 CCTGAGGTGCAGCGAACTAT 59.823 55.000 10.78 0.00 43.50 2.12
4192 7091 0.382158 CGCTGCTAGCTGCTACTACA 59.618 55.000 34.44 5.33 39.60 2.74
4193 7092 0.663688 TCGCTGCTAGCTGCTACTAC 59.336 55.000 34.44 13.11 39.60 2.73
4226 9563 0.037697 TCAACGATGGTCCCAAGTCG 60.038 55.000 7.58 7.58 39.78 4.18


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

AutoCloner maintained by Alex Coulton.