Multiple sequence alignment - TraesCS7A01G313400

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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 TraesCS7A01G313400 chr7A 100.000 2276 0 0 1 2276 445483521 445481246 0.000000e+00 4204.0
1 TraesCS7A01G313400 chr7B 89.859 1913 113 36 410 2276 392804662 392802785 0.000000e+00 2383.0
2 TraesCS7A01G313400 chr7B 83.898 354 20 17 37 386 392806545 392806225 1.020000e-78 303.0
3 TraesCS7A01G313400 chr7D 85.096 1503 89 56 67 1490 393103398 393101952 0.000000e+00 1410.0
4 TraesCS7A01G313400 chr7D 93.557 776 38 6 1512 2276 393101753 393100979 0.000000e+00 1146.0
5 TraesCS7A01G313400 chr1B 89.295 383 30 8 1897 2276 375359595 375359969 9.520000e-129 470.0
6 TraesCS7A01G313400 chr5D 83.072 319 48 6 1883 2196 551124462 551124145 3.700000e-73 285.0
7 TraesCS7A01G313400 chr4B 96.000 75 2 1 1747 1820 642426335 642426261 1.100000e-23 121.0
8 TraesCS7A01G313400 chr1A 88.710 62 5 2 2217 2276 569672295 569672234 8.720000e-10 75.0
9 TraesCS7A01G313400 chr1A 88.710 62 5 2 2217 2276 569723206 569723145 8.720000e-10 75.0
10 TraesCS7A01G313400 chr4A 85.294 68 8 2 2211 2276 624470042 624470109 4.060000e-08 69.4


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 TraesCS7A01G313400 chr7A 445481246 445483521 2275 True 4204 4204 100.0000 1 2276 1 chr7A.!!$R1 2275
1 TraesCS7A01G313400 chr7B 392802785 392806545 3760 True 1343 2383 86.8785 37 2276 2 chr7B.!!$R1 2239
2 TraesCS7A01G313400 chr7D 393100979 393103398 2419 True 1278 1410 89.3265 67 2276 2 chr7D.!!$R1 2209

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
846 2416 0.037697 TACATGTCACGTGTCTGGCC 60.038 55.0 16.51 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 3940 1.13467 GGCGAGAACTACTTCCTGCAT 60.135 52.381 0.0 0.0 31.6 3.96 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
34 35 6.136541 AGTAGCACTCAAACAAAAGAAAGG 57.863 37.500 0.00 0.00 0.00 3.11
35 36 5.885912 AGTAGCACTCAAACAAAAGAAAGGA 59.114 36.000 0.00 0.00 0.00 3.36
36 37 5.659440 AGCACTCAAACAAAAGAAAGGAA 57.341 34.783 0.00 0.00 0.00 3.36
37 38 5.654497 AGCACTCAAACAAAAGAAAGGAAG 58.346 37.500 0.00 0.00 0.00 3.46
38 39 4.268644 GCACTCAAACAAAAGAAAGGAAGC 59.731 41.667 0.00 0.00 0.00 3.86
39 40 5.410067 CACTCAAACAAAAGAAAGGAAGCA 58.590 37.500 0.00 0.00 0.00 3.91
40 41 5.868801 CACTCAAACAAAAGAAAGGAAGCAA 59.131 36.000 0.00 0.00 0.00 3.91
41 42 6.536224 CACTCAAACAAAAGAAAGGAAGCAAT 59.464 34.615 0.00 0.00 0.00 3.56
42 43 6.536224 ACTCAAACAAAAGAAAGGAAGCAATG 59.464 34.615 0.00 0.00 0.00 2.82
43 44 6.638610 TCAAACAAAAGAAAGGAAGCAATGA 58.361 32.000 0.00 0.00 0.00 2.57
44 45 7.274447 TCAAACAAAAGAAAGGAAGCAATGAT 58.726 30.769 0.00 0.00 0.00 2.45
52 53 9.578576 AAAGAAAGGAAGCAATGATATAGCATA 57.421 29.630 3.46 0.00 0.00 3.14
62 63 7.279536 AGCAATGATATAGCATACTCAAATCGG 59.720 37.037 3.46 0.00 0.00 4.18
135 136 1.659233 TGGCACAAATTCAGGCGTG 59.341 52.632 0.00 0.00 31.92 5.34
136 137 3.846754 GCACAAATTCAGGCGTGC 58.153 55.556 0.35 0.00 46.85 5.34
138 139 3.389741 CACAAATTCAGGCGTGCTC 57.610 52.632 0.35 0.00 0.00 4.26
148 149 3.723348 GCGTGCTCCAAACCGGAC 61.723 66.667 9.46 0.00 39.64 4.79
149 150 2.280524 CGTGCTCCAAACCGGACA 60.281 61.111 9.46 0.00 39.64 4.02
190 191 2.328099 GGCAGGACAAACGCAGGAG 61.328 63.158 0.00 0.00 0.00 3.69
199 200 1.076332 AAACGCAGGAGCATTACGAC 58.924 50.000 0.00 0.00 42.27 4.34
204 205 0.249073 CAGGAGCATTACGACCGAGG 60.249 60.000 0.00 0.00 0.00 4.63
219 225 1.334243 CCGAGGTTCCGATGAGTAGAC 59.666 57.143 0.00 0.00 0.00 2.59
236 242 1.760613 AGACGGCCGATTCTATTCCAA 59.239 47.619 35.90 0.00 0.00 3.53
294 300 1.135139 CCGACACCGAGATGAGATGTT 59.865 52.381 0.00 0.00 38.22 2.71
386 396 2.956964 GGTCGGCGCTCTGAATCG 60.957 66.667 7.64 0.00 0.00 3.34
398 417 1.135046 CTGAATCGCGATCGCATCTT 58.865 50.000 36.45 25.59 42.06 2.40
399 418 0.854705 TGAATCGCGATCGCATCTTG 59.145 50.000 36.45 21.43 42.06 3.02
408 427 2.728318 CGATCGCATCTTGTCATCGATT 59.272 45.455 0.26 0.00 39.59 3.34
432 1981 4.933563 TGGTCGCAGCAGCAGCAA 62.934 61.111 10.77 0.00 45.49 3.91
476 2025 8.839310 ACAATATCCCATCTTTAATTCTCTCG 57.161 34.615 0.00 0.00 0.00 4.04
487 2036 5.723672 TTAATTCTCTCGAGGTCAACACT 57.276 39.130 13.56 0.00 0.00 3.55
513 2062 1.699634 AGCTTAACTGTCAGCTTCCCA 59.300 47.619 8.29 0.00 44.28 4.37
514 2063 1.807142 GCTTAACTGTCAGCTTCCCAC 59.193 52.381 0.00 0.00 32.87 4.61
515 2064 2.810400 GCTTAACTGTCAGCTTCCCACA 60.810 50.000 0.00 0.00 32.87 4.17
516 2065 3.679389 CTTAACTGTCAGCTTCCCACAT 58.321 45.455 0.00 0.00 0.00 3.21
517 2066 1.901591 AACTGTCAGCTTCCCACATG 58.098 50.000 0.00 0.00 0.00 3.21
518 2067 0.767375 ACTGTCAGCTTCCCACATGT 59.233 50.000 0.00 0.00 0.00 3.21
519 2068 1.977854 ACTGTCAGCTTCCCACATGTA 59.022 47.619 0.00 0.00 0.00 2.29
520 2069 2.371841 ACTGTCAGCTTCCCACATGTAA 59.628 45.455 0.00 0.00 0.00 2.41
521 2070 3.181445 ACTGTCAGCTTCCCACATGTAAA 60.181 43.478 0.00 0.00 0.00 2.01
742 2304 1.202417 GCATTCTGATCGAGTTCCCGA 60.202 52.381 0.00 0.00 43.16 5.14
746 2308 1.201647 TCTGATCGAGTTCCCGACAAC 59.798 52.381 0.00 0.00 41.70 3.32
756 2318 0.179234 TCCCGACAACTTGCACTCAA 59.821 50.000 0.00 0.00 0.00 3.02
757 2319 1.021202 CCCGACAACTTGCACTCAAA 58.979 50.000 0.00 0.00 0.00 2.69
758 2320 1.002468 CCCGACAACTTGCACTCAAAG 60.002 52.381 0.00 0.00 0.00 2.77
759 2321 1.002468 CCGACAACTTGCACTCAAAGG 60.002 52.381 0.00 0.00 0.00 3.11
760 2322 1.597937 CGACAACTTGCACTCAAAGGC 60.598 52.381 0.00 0.00 0.00 4.35
761 2323 0.746659 ACAACTTGCACTCAAAGGCC 59.253 50.000 0.00 0.00 0.00 5.19
763 2325 1.455383 AACTTGCACTCAAAGGCCGG 61.455 55.000 0.00 0.00 0.00 6.13
764 2326 3.273080 CTTGCACTCAAAGGCCGGC 62.273 63.158 21.18 21.18 0.00 6.13
765 2327 3.790416 TTGCACTCAAAGGCCGGCT 62.790 57.895 28.56 9.77 0.00 5.52
766 2328 3.741476 GCACTCAAAGGCCGGCTG 61.741 66.667 28.56 17.63 0.00 4.85
767 2329 2.281761 CACTCAAAGGCCGGCTGT 60.282 61.111 28.56 11.71 0.00 4.40
768 2330 1.898574 CACTCAAAGGCCGGCTGTT 60.899 57.895 28.56 17.60 0.00 3.16
769 2331 1.600916 ACTCAAAGGCCGGCTGTTC 60.601 57.895 28.56 9.72 0.00 3.18
770 2332 1.600636 CTCAAAGGCCGGCTGTTCA 60.601 57.895 28.56 6.19 0.00 3.18
771 2333 1.856265 CTCAAAGGCCGGCTGTTCAC 61.856 60.000 28.56 8.41 0.00 3.18
772 2334 1.898574 CAAAGGCCGGCTGTTCACT 60.899 57.895 28.56 11.02 0.00 3.41
773 2335 1.600916 AAAGGCCGGCTGTTCACTC 60.601 57.895 28.56 6.68 0.00 3.51
774 2336 2.337879 AAAGGCCGGCTGTTCACTCA 62.338 55.000 28.56 0.00 0.00 3.41
775 2337 2.045926 GGCCGGCTGTTCACTCAT 60.046 61.111 28.56 0.00 0.00 2.90
776 2338 2.401766 GGCCGGCTGTTCACTCATG 61.402 63.158 28.56 0.00 0.00 3.07
805 2367 8.055181 TCCATGAAGATAAGCTTAAGACCAATT 58.945 33.333 10.85 0.00 36.83 2.32
806 2368 8.689972 CCATGAAGATAAGCTTAAGACCAATTT 58.310 33.333 10.85 0.00 36.83 1.82
822 2384 3.616219 CAATTTACGGGAATCACTGGGA 58.384 45.455 0.00 0.00 0.00 4.37
838 2408 1.689813 TGGGAGTGTTACATGTCACGT 59.310 47.619 0.00 0.00 39.25 4.49
839 2409 2.066262 GGGAGTGTTACATGTCACGTG 58.934 52.381 9.94 9.94 39.25 4.49
840 2410 2.547218 GGGAGTGTTACATGTCACGTGT 60.547 50.000 16.51 8.00 39.25 4.49
841 2411 2.729882 GGAGTGTTACATGTCACGTGTC 59.270 50.000 16.51 10.98 39.25 3.67
843 2413 3.381045 AGTGTTACATGTCACGTGTCTG 58.619 45.455 16.51 13.38 39.25 3.51
844 2414 2.475111 GTGTTACATGTCACGTGTCTGG 59.525 50.000 16.51 8.86 0.00 3.86
845 2415 1.459592 GTTACATGTCACGTGTCTGGC 59.540 52.381 16.51 2.98 0.00 4.85
846 2416 0.037697 TACATGTCACGTGTCTGGCC 60.038 55.000 16.51 0.00 0.00 5.36
847 2417 1.301637 CATGTCACGTGTCTGGCCA 60.302 57.895 16.51 4.71 0.00 5.36
848 2418 0.884259 CATGTCACGTGTCTGGCCAA 60.884 55.000 16.51 0.00 0.00 4.52
849 2419 0.603707 ATGTCACGTGTCTGGCCAAG 60.604 55.000 16.51 0.66 0.00 3.61
850 2420 1.069090 GTCACGTGTCTGGCCAAGA 59.931 57.895 16.51 3.54 0.00 3.02
851 2421 0.320771 GTCACGTGTCTGGCCAAGAT 60.321 55.000 16.51 0.00 37.23 2.40
852 2422 0.320683 TCACGTGTCTGGCCAAGATG 60.321 55.000 16.51 4.86 37.23 2.90
853 2423 1.672356 ACGTGTCTGGCCAAGATGC 60.672 57.895 7.01 3.35 37.23 3.91
854 2424 1.672030 CGTGTCTGGCCAAGATGCA 60.672 57.895 7.01 0.00 37.23 3.96
855 2425 1.236616 CGTGTCTGGCCAAGATGCAA 61.237 55.000 7.01 0.00 37.23 4.08
856 2426 1.180029 GTGTCTGGCCAAGATGCAAT 58.820 50.000 7.01 0.00 37.23 3.56
857 2427 1.135199 GTGTCTGGCCAAGATGCAATG 60.135 52.381 7.01 0.00 37.23 2.82
858 2428 0.179119 GTCTGGCCAAGATGCAATGC 60.179 55.000 7.01 0.00 37.23 3.56
859 2429 0.612453 TCTGGCCAAGATGCAATGCA 60.612 50.000 11.44 11.44 44.86 3.96
860 2430 0.459585 CTGGCCAAGATGCAATGCAC 60.460 55.000 11.23 4.80 43.04 4.57
861 2431 1.186267 TGGCCAAGATGCAATGCACA 61.186 50.000 11.23 0.00 43.04 4.57
862 2432 0.738412 GGCCAAGATGCAATGCACAC 60.738 55.000 11.23 8.16 43.04 3.82
863 2433 0.038067 GCCAAGATGCAATGCACACA 60.038 50.000 11.23 0.00 43.04 3.72
864 2434 1.990799 CCAAGATGCAATGCACACAG 58.009 50.000 11.23 1.02 43.04 3.66
865 2435 1.346365 CAAGATGCAATGCACACAGC 58.654 50.000 11.23 0.00 43.04 4.40
875 2445 2.237066 GCACACAGCGGCCAAAAAC 61.237 57.895 2.24 0.00 0.00 2.43
886 2456 1.007964 CCAAAAACGGATGCACGCA 60.008 52.632 0.00 0.00 37.37 5.24
986 2588 1.929836 GCTCAGCAAATAGACTCCACG 59.070 52.381 0.00 0.00 0.00 4.94
990 2592 0.370273 GCAAATAGACTCCACGCACG 59.630 55.000 0.00 0.00 0.00 5.34
991 2593 1.710013 CAAATAGACTCCACGCACGT 58.290 50.000 0.00 0.00 0.00 4.49
1008 2610 1.957177 ACGTAGATCGAGATGGTGCAT 59.043 47.619 0.00 0.00 42.86 3.96
1072 2674 2.359967 GGGACCAAGAGGGAGACGG 61.360 68.421 0.00 0.00 41.15 4.79
1091 2693 3.519930 GGCGACGAGGAGGAGGAC 61.520 72.222 0.00 0.00 0.00 3.85
1107 2709 1.456287 GACAAGGAGGCAAGGTGGT 59.544 57.895 0.00 0.00 0.00 4.16
1292 2898 4.202060 CGCTTAGTTCATCAGCTCCTCTTA 60.202 45.833 0.00 0.00 0.00 2.10
1296 2902 4.873010 AGTTCATCAGCTCCTCTTACCTA 58.127 43.478 0.00 0.00 0.00 3.08
1301 2907 5.069648 TCATCAGCTCCTCTTACCTATGTTG 59.930 44.000 0.00 0.00 0.00 3.33
1302 2908 4.353777 TCAGCTCCTCTTACCTATGTTGT 58.646 43.478 0.00 0.00 0.00 3.32
1303 2909 5.516044 TCAGCTCCTCTTACCTATGTTGTA 58.484 41.667 0.00 0.00 0.00 2.41
1319 2925 9.042008 CCTATGTTGTATACACAGGTTGTAATC 57.958 37.037 4.68 0.00 44.86 1.75
1335 2941 2.029838 AATCGCCTGACTGGAATCAC 57.970 50.000 1.91 0.00 38.35 3.06
1337 2943 0.037326 TCGCCTGACTGGAATCACAC 60.037 55.000 1.91 0.00 38.35 3.82
1349 2955 1.852895 GAATCACACATAGTCCGCGTC 59.147 52.381 4.92 0.00 0.00 5.19
1357 2963 2.005960 ATAGTCCGCGTCAGCTCACC 62.006 60.000 4.92 0.00 42.32 4.02
1363 2969 3.699894 CGTCAGCTCACCCCTGCT 61.700 66.667 0.00 0.00 40.54 4.24
1381 2987 1.270839 GCTTTGTCAGTGGTAGGCTCA 60.271 52.381 0.00 0.00 0.00 4.26
1382 2988 2.693069 CTTTGTCAGTGGTAGGCTCAG 58.307 52.381 0.00 0.00 0.00 3.35
1383 2989 0.976641 TTGTCAGTGGTAGGCTCAGG 59.023 55.000 0.00 0.00 0.00 3.86
1384 2990 0.114364 TGTCAGTGGTAGGCTCAGGA 59.886 55.000 0.00 0.00 0.00 3.86
1385 2991 1.267121 GTCAGTGGTAGGCTCAGGAA 58.733 55.000 0.00 0.00 0.00 3.36
1386 2992 1.834263 GTCAGTGGTAGGCTCAGGAAT 59.166 52.381 0.00 0.00 0.00 3.01
1387 2993 2.111384 TCAGTGGTAGGCTCAGGAATC 58.889 52.381 0.00 0.00 0.00 2.52
1388 2994 1.833630 CAGTGGTAGGCTCAGGAATCA 59.166 52.381 0.00 0.00 0.00 2.57
1396 3009 1.948145 GGCTCAGGAATCAAGATGCTG 59.052 52.381 0.00 0.00 37.56 4.41
1401 3014 4.401022 TCAGGAATCAAGATGCTGTTGTT 58.599 39.130 0.00 0.00 37.49 2.83
1413 3026 9.630098 CAAGATGCTGTTGTTGTAAATATTTCT 57.370 29.630 3.39 0.00 0.00 2.52
1439 3056 6.809869 AGTTGAGTTTTCTCCCTCAATTTTG 58.190 36.000 5.49 0.00 46.20 2.44
1440 3057 5.789643 TGAGTTTTCTCCCTCAATTTTGG 57.210 39.130 0.00 0.00 45.63 3.28
1460 3077 6.855763 TTGGACTCCTCCGTAGTAAAATTA 57.144 37.500 0.00 0.00 39.88 1.40
1465 3086 7.500559 GGACTCCTCCGTAGTAAAATTAGTAGA 59.499 40.741 0.00 0.00 0.00 2.59
1541 3339 6.206243 ACAACTCTGATGCCATAATATCAAGC 59.794 38.462 0.00 0.00 33.30 4.01
1572 3370 5.455392 CAAAATTGTACAGAGCCAAGTGAG 58.545 41.667 0.00 0.00 0.00 3.51
1585 3383 2.031333 CCAAGTGAGTTCAAAGCTCTGC 60.031 50.000 0.00 0.00 34.30 4.26
1616 3414 0.725117 CCGACATCTTAAACCACCGC 59.275 55.000 0.00 0.00 0.00 5.68
1648 3448 3.011032 ACCCTCTCTGGAATCTTGCAAAT 59.989 43.478 0.00 0.00 38.35 2.32
1651 3451 4.461781 CCTCTCTGGAATCTTGCAAATTGT 59.538 41.667 0.00 0.00 38.35 2.71
1677 3477 7.442364 TCAGTTATAATTAAGGATCTGCAGCAC 59.558 37.037 9.47 5.09 0.00 4.40
1714 3514 1.402259 TCGCCTCTCTCTCGAATCAAC 59.598 52.381 0.00 0.00 0.00 3.18
1718 3518 0.456221 TCTCTCTCGAATCAACGCCC 59.544 55.000 0.00 0.00 0.00 6.13
1821 3621 4.814234 CAGCTACGTCCTGCCAAATTATAA 59.186 41.667 0.00 0.00 0.00 0.98
1847 3647 7.930217 TGAACTGGACATTAGTCTTTTTCTTG 58.070 34.615 0.00 0.00 44.36 3.02
1848 3648 7.556275 TGAACTGGACATTAGTCTTTTTCTTGT 59.444 33.333 0.00 0.00 44.36 3.16
1876 3677 2.618709 CTGTCAAGTCCCAAACTCCAAC 59.381 50.000 0.00 0.00 37.17 3.77
1918 3719 2.791655 TCAGCAAGTACTTCCGAGAGA 58.208 47.619 4.77 0.00 0.00 3.10
1923 3724 3.677424 GCAAGTACTTCCGAGAGATGCTT 60.677 47.826 4.77 0.00 0.00 3.91
1927 3728 2.457598 ACTTCCGAGAGATGCTTACCA 58.542 47.619 0.00 0.00 0.00 3.25
2004 3809 6.927294 TTGTAAAACGGCCAAATGAAAAAT 57.073 29.167 2.24 0.00 0.00 1.82
2008 3813 9.877178 TGTAAAACGGCCAAATGAAAAATATAT 57.123 25.926 2.24 0.00 0.00 0.86
2012 3817 9.744468 AAACGGCCAAATGAAAAATATATAGAC 57.256 29.630 2.24 0.00 0.00 2.59
2056 3861 5.241728 AGCATTTTACCTTCAAACTGAGACC 59.758 40.000 0.00 0.00 0.00 3.85
2083 3888 8.408043 TGAACATTAAAGATGTCTTTCATGGT 57.592 30.769 23.24 20.02 45.13 3.55
2138 3943 2.896243 CTTGTTGAGCTGACTGATGC 57.104 50.000 0.00 0.00 0.00 3.91
2234 4045 3.864789 AGTGGATTGGAACACTCAAGT 57.135 42.857 0.00 0.00 44.08 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.999431 CCTTTCTTTTGTTTGAGTGCTACTATA 58.001 33.333 0.00 0.00 0.00 1.31
9 10 7.719633 TCCTTTCTTTTGTTTGAGTGCTACTAT 59.280 33.333 0.00 0.00 0.00 2.12
10 11 7.051623 TCCTTTCTTTTGTTTGAGTGCTACTA 58.948 34.615 0.00 0.00 0.00 1.82
11 12 5.885912 TCCTTTCTTTTGTTTGAGTGCTACT 59.114 36.000 0.00 0.00 0.00 2.57
12 13 6.131544 TCCTTTCTTTTGTTTGAGTGCTAC 57.868 37.500 0.00 0.00 0.00 3.58
13 14 6.680378 GCTTCCTTTCTTTTGTTTGAGTGCTA 60.680 38.462 0.00 0.00 0.00 3.49
14 15 5.654497 CTTCCTTTCTTTTGTTTGAGTGCT 58.346 37.500 0.00 0.00 0.00 4.40
15 16 4.268644 GCTTCCTTTCTTTTGTTTGAGTGC 59.731 41.667 0.00 0.00 0.00 4.40
16 17 5.410067 TGCTTCCTTTCTTTTGTTTGAGTG 58.590 37.500 0.00 0.00 0.00 3.51
17 18 5.659440 TGCTTCCTTTCTTTTGTTTGAGT 57.341 34.783 0.00 0.00 0.00 3.41
18 19 6.757947 TCATTGCTTCCTTTCTTTTGTTTGAG 59.242 34.615 0.00 0.00 0.00 3.02
19 20 6.638610 TCATTGCTTCCTTTCTTTTGTTTGA 58.361 32.000 0.00 0.00 0.00 2.69
20 21 6.907206 TCATTGCTTCCTTTCTTTTGTTTG 57.093 33.333 0.00 0.00 0.00 2.93
23 24 8.193438 GCTATATCATTGCTTCCTTTCTTTTGT 58.807 33.333 0.00 0.00 0.00 2.83
24 25 8.192774 TGCTATATCATTGCTTCCTTTCTTTTG 58.807 33.333 0.00 0.00 32.18 2.44
25 26 8.297470 TGCTATATCATTGCTTCCTTTCTTTT 57.703 30.769 0.00 0.00 32.18 2.27
26 27 7.886629 TGCTATATCATTGCTTCCTTTCTTT 57.113 32.000 0.00 0.00 32.18 2.52
27 28 9.007901 GTATGCTATATCATTGCTTCCTTTCTT 57.992 33.333 0.00 0.00 32.18 2.52
28 29 8.381636 AGTATGCTATATCATTGCTTCCTTTCT 58.618 33.333 0.00 0.00 32.18 2.52
29 30 8.558973 AGTATGCTATATCATTGCTTCCTTTC 57.441 34.615 0.00 0.00 32.18 2.62
30 31 8.159447 TGAGTATGCTATATCATTGCTTCCTTT 58.841 33.333 0.00 0.00 32.18 3.11
31 32 7.683578 TGAGTATGCTATATCATTGCTTCCTT 58.316 34.615 0.00 0.00 32.18 3.36
32 33 7.250032 TGAGTATGCTATATCATTGCTTCCT 57.750 36.000 0.00 0.00 32.18 3.36
33 34 7.912056 TTGAGTATGCTATATCATTGCTTCC 57.088 36.000 0.00 0.00 32.18 3.46
34 35 9.985318 GATTTGAGTATGCTATATCATTGCTTC 57.015 33.333 0.00 0.00 32.18 3.86
35 36 8.663025 CGATTTGAGTATGCTATATCATTGCTT 58.337 33.333 0.00 0.00 32.18 3.91
36 37 7.279536 CCGATTTGAGTATGCTATATCATTGCT 59.720 37.037 0.00 0.00 32.18 3.91
37 38 7.065085 ACCGATTTGAGTATGCTATATCATTGC 59.935 37.037 0.00 0.00 0.00 3.56
38 39 8.484641 ACCGATTTGAGTATGCTATATCATTG 57.515 34.615 0.00 0.00 0.00 2.82
39 40 8.314021 TGACCGATTTGAGTATGCTATATCATT 58.686 33.333 0.00 0.00 0.00 2.57
40 41 7.840931 TGACCGATTTGAGTATGCTATATCAT 58.159 34.615 0.00 0.00 0.00 2.45
41 42 7.227049 TGACCGATTTGAGTATGCTATATCA 57.773 36.000 0.00 0.00 0.00 2.15
42 43 7.201478 GCTTGACCGATTTGAGTATGCTATATC 60.201 40.741 0.00 0.00 0.00 1.63
43 44 6.591834 GCTTGACCGATTTGAGTATGCTATAT 59.408 38.462 0.00 0.00 0.00 0.86
44 45 5.926542 GCTTGACCGATTTGAGTATGCTATA 59.073 40.000 0.00 0.00 0.00 1.31
52 53 2.334838 GTACGCTTGACCGATTTGAGT 58.665 47.619 0.00 0.00 0.00 3.41
62 63 1.945776 GCTGTGCTCGTACGCTTGAC 61.946 60.000 11.24 5.08 0.00 3.18
118 119 4.557942 CACGCCTGAATTTGTGCC 57.442 55.556 0.00 0.00 0.00 5.01
138 139 2.897846 TGCGTGTGTCCGGTTTGG 60.898 61.111 0.00 0.00 40.09 3.28
148 149 4.962122 GTGCTTGCGGTGCGTGTG 62.962 66.667 0.00 0.00 0.00 3.82
167 168 2.949106 CGTTTGTCCTGCCTGCTG 59.051 61.111 0.00 0.00 0.00 4.41
174 175 0.957395 ATGCTCCTGCGTTTGTCCTG 60.957 55.000 0.00 0.00 43.34 3.86
176 177 1.130561 GTAATGCTCCTGCGTTTGTCC 59.869 52.381 0.75 0.00 45.18 4.02
177 178 1.201921 CGTAATGCTCCTGCGTTTGTC 60.202 52.381 0.75 0.00 45.18 3.18
190 191 1.143969 CGGAACCTCGGTCGTAATGC 61.144 60.000 0.00 0.00 0.00 3.56
199 200 1.334243 GTCTACTCATCGGAACCTCGG 59.666 57.143 0.00 0.00 0.00 4.63
204 205 0.248949 GGCCGTCTACTCATCGGAAC 60.249 60.000 7.01 0.00 46.05 3.62
219 225 2.526304 TCTTGGAATAGAATCGGCCG 57.474 50.000 22.12 22.12 0.00 6.13
236 242 2.939103 CAGAATTCGGGCTTTCGATTCT 59.061 45.455 0.00 0.00 39.03 2.40
294 300 1.747924 CAACAGAGCATCCGAGAGAGA 59.252 52.381 0.00 0.00 33.66 3.10
334 340 3.138304 GGCGGCAGTCATTAACATGATA 58.862 45.455 3.07 0.00 41.64 2.15
335 341 1.949525 GGCGGCAGTCATTAACATGAT 59.050 47.619 3.07 0.00 41.64 2.45
386 396 0.160392 CGATGACAAGATGCGATCGC 59.840 55.000 32.48 32.48 42.35 4.58
398 417 2.103094 GACCAGATGGGAATCGATGACA 59.897 50.000 0.00 0.00 41.15 3.58
399 418 2.760374 GACCAGATGGGAATCGATGAC 58.240 52.381 0.00 0.00 41.15 3.06
408 427 3.002583 TGCTGCGACCAGATGGGA 61.003 61.111 3.48 0.00 41.77 4.37
476 2025 1.001406 AGCTAGCACAGTGTTGACCTC 59.999 52.381 18.83 0.00 0.00 3.85
487 2036 2.688507 GCTGACAGTTAAGCTAGCACA 58.311 47.619 18.83 0.00 36.47 4.57
513 2062 5.125417 CCGTCCTGAATCCATTTTTACATGT 59.875 40.000 2.69 2.69 0.00 3.21
514 2063 5.581605 CCGTCCTGAATCCATTTTTACATG 58.418 41.667 0.00 0.00 0.00 3.21
515 2064 4.097892 GCCGTCCTGAATCCATTTTTACAT 59.902 41.667 0.00 0.00 0.00 2.29
516 2065 3.442273 GCCGTCCTGAATCCATTTTTACA 59.558 43.478 0.00 0.00 0.00 2.41
517 2066 3.694566 AGCCGTCCTGAATCCATTTTTAC 59.305 43.478 0.00 0.00 0.00 2.01
518 2067 3.963129 AGCCGTCCTGAATCCATTTTTA 58.037 40.909 0.00 0.00 0.00 1.52
519 2068 2.807676 AGCCGTCCTGAATCCATTTTT 58.192 42.857 0.00 0.00 0.00 1.94
520 2069 2.493278 CAAGCCGTCCTGAATCCATTTT 59.507 45.455 0.00 0.00 0.00 1.82
521 2070 2.094675 CAAGCCGTCCTGAATCCATTT 58.905 47.619 0.00 0.00 0.00 2.32
662 2224 0.310543 GCGTGCATCTGGTTTTGACA 59.689 50.000 0.00 0.00 0.00 3.58
700 2262 4.440214 GCGTTTGTCTCGCCAATG 57.560 55.556 0.00 0.00 46.61 2.82
707 2269 2.977405 AATGCTTCTGCGTTTGTCTC 57.023 45.000 0.00 0.00 45.18 3.36
720 2282 2.739932 CGGGAACTCGATCAGAATGCTT 60.740 50.000 0.00 0.00 34.76 3.91
742 2304 0.746659 GGCCTTTGAGTGCAAGTTGT 59.253 50.000 4.48 0.00 35.04 3.32
746 2308 2.956987 CCGGCCTTTGAGTGCAAG 59.043 61.111 0.00 0.00 35.04 4.01
756 2318 2.032681 GAGTGAACAGCCGGCCTT 59.967 61.111 26.15 15.56 0.00 4.35
757 2319 2.596851 ATGAGTGAACAGCCGGCCT 61.597 57.895 26.15 12.29 0.00 5.19
758 2320 2.045926 ATGAGTGAACAGCCGGCC 60.046 61.111 26.15 8.39 0.00 6.13
759 2321 0.955428 TTCATGAGTGAACAGCCGGC 60.955 55.000 21.89 21.89 39.36 6.13
760 2322 1.667724 GATTCATGAGTGAACAGCCGG 59.332 52.381 0.00 0.00 46.43 6.13
761 2323 1.667724 GGATTCATGAGTGAACAGCCG 59.332 52.381 0.00 0.00 46.43 5.52
774 2336 9.282569 GTCTTAAGCTTATCTTCATGGATTCAT 57.717 33.333 7.08 0.00 36.25 2.57
775 2337 7.716998 GGTCTTAAGCTTATCTTCATGGATTCA 59.283 37.037 7.08 0.00 36.25 2.57
776 2338 7.716998 TGGTCTTAAGCTTATCTTCATGGATTC 59.283 37.037 7.08 0.00 36.25 2.52
785 2347 7.282450 CCCGTAAATTGGTCTTAAGCTTATCTT 59.718 37.037 7.08 0.00 38.79 2.40
797 2359 4.261801 CAGTGATTCCCGTAAATTGGTCT 58.738 43.478 0.00 0.00 0.00 3.85
805 2367 1.946984 ACTCCCAGTGATTCCCGTAA 58.053 50.000 0.00 0.00 0.00 3.18
806 2368 3.703804 ACTCCCAGTGATTCCCGTA 57.296 52.632 0.00 0.00 0.00 4.02
822 2384 3.381045 CAGACACGTGACATGTAACACT 58.619 45.455 25.01 4.23 35.23 3.55
838 2408 1.179152 CATTGCATCTTGGCCAGACA 58.821 50.000 5.11 0.00 32.83 3.41
839 2409 0.179119 GCATTGCATCTTGGCCAGAC 60.179 55.000 5.11 0.00 32.83 3.51
840 2410 0.612453 TGCATTGCATCTTGGCCAGA 60.612 50.000 7.38 6.43 31.71 3.86
841 2411 0.459585 GTGCATTGCATCTTGGCCAG 60.460 55.000 15.49 0.00 41.91 4.85
843 2413 0.738412 GTGTGCATTGCATCTTGGCC 60.738 55.000 15.49 0.00 41.91 5.36
844 2414 0.038067 TGTGTGCATTGCATCTTGGC 60.038 50.000 15.49 1.01 41.91 4.52
845 2415 1.990799 CTGTGTGCATTGCATCTTGG 58.009 50.000 15.49 1.34 41.91 3.61
846 2416 1.346365 GCTGTGTGCATTGCATCTTG 58.654 50.000 15.49 7.36 41.91 3.02
847 2417 0.109458 CGCTGTGTGCATTGCATCTT 60.109 50.000 15.49 0.00 41.91 2.40
848 2418 1.504900 CGCTGTGTGCATTGCATCT 59.495 52.632 15.49 0.00 41.91 2.90
849 2419 1.515519 CCGCTGTGTGCATTGCATC 60.516 57.895 15.49 11.58 41.91 3.91
850 2420 2.569657 CCGCTGTGTGCATTGCAT 59.430 55.556 15.49 0.00 41.91 3.96
851 2421 4.345962 GCCGCTGTGTGCATTGCA 62.346 61.111 7.38 7.38 43.06 4.08
853 2423 2.696409 TTTGGCCGCTGTGTGCATTG 62.696 55.000 0.00 0.00 43.06 2.82
854 2424 2.025767 TTTTGGCCGCTGTGTGCATT 62.026 50.000 0.00 0.00 43.06 3.56
855 2425 2.025767 TTTTTGGCCGCTGTGTGCAT 62.026 50.000 0.00 0.00 43.06 3.96
856 2426 2.714991 TTTTTGGCCGCTGTGTGCA 61.715 52.632 0.00 0.00 43.06 4.57
857 2427 2.105930 TTTTTGGCCGCTGTGTGC 59.894 55.556 0.00 0.00 38.57 4.57
858 2428 1.943693 CGTTTTTGGCCGCTGTGTG 60.944 57.895 0.00 0.00 0.00 3.82
859 2429 2.411290 CGTTTTTGGCCGCTGTGT 59.589 55.556 0.00 0.00 0.00 3.72
860 2430 2.141122 ATCCGTTTTTGGCCGCTGTG 62.141 55.000 0.00 0.00 0.00 3.66
861 2431 1.901464 ATCCGTTTTTGGCCGCTGT 60.901 52.632 0.00 0.00 0.00 4.40
862 2432 1.444212 CATCCGTTTTTGGCCGCTG 60.444 57.895 0.00 0.00 0.00 5.18
863 2433 2.961768 CATCCGTTTTTGGCCGCT 59.038 55.556 0.00 0.00 0.00 5.52
864 2434 2.809174 GCATCCGTTTTTGGCCGC 60.809 61.111 0.00 0.00 0.00 6.53
865 2435 1.732683 GTGCATCCGTTTTTGGCCG 60.733 57.895 0.00 0.00 0.00 6.13
866 2436 1.732683 CGTGCATCCGTTTTTGGCC 60.733 57.895 0.00 0.00 0.00 5.36
867 2437 2.371923 GCGTGCATCCGTTTTTGGC 61.372 57.895 0.00 0.00 0.00 4.52
868 2438 1.007964 TGCGTGCATCCGTTTTTGG 60.008 52.632 0.00 0.00 0.00 3.28
869 2439 1.595982 CGTGCGTGCATCCGTTTTTG 61.596 55.000 0.00 0.00 0.00 2.44
986 2588 1.759994 CACCATCTCGATCTACGTGC 58.240 55.000 0.00 0.00 43.13 5.34
990 2592 3.674682 GCCTATGCACCATCTCGATCTAC 60.675 52.174 0.00 0.00 37.47 2.59
991 2593 2.493675 GCCTATGCACCATCTCGATCTA 59.506 50.000 0.00 0.00 37.47 1.98
1008 2610 1.200716 CCTTCGTCGTGTGTAAGCCTA 59.799 52.381 0.00 0.00 0.00 3.93
1058 2660 4.148825 CCGCCGTCTCCCTCTTGG 62.149 72.222 0.00 0.00 0.00 3.61
1059 2661 4.821589 GCCGCCGTCTCCCTCTTG 62.822 72.222 0.00 0.00 0.00 3.02
1080 2682 1.334384 GCCTCCTTGTCCTCCTCCTC 61.334 65.000 0.00 0.00 0.00 3.71
1091 2693 1.604593 CCACCACCTTGCCTCCTTG 60.605 63.158 0.00 0.00 0.00 3.61
1169 2771 1.410882 AGTAGCTCCGCTTGAATCTCC 59.589 52.381 0.00 0.00 40.44 3.71
1173 2775 2.014068 GCCAAGTAGCTCCGCTTGAAT 61.014 52.381 20.39 0.00 43.29 2.57
1263 2865 1.887707 GATGAACTAAGCGGGGGCG 60.888 63.158 0.00 0.00 0.00 6.13
1266 2868 0.179000 AGCTGATGAACTAAGCGGGG 59.821 55.000 0.00 0.00 41.88 5.73
1269 2871 2.100584 AGAGGAGCTGATGAACTAAGCG 59.899 50.000 0.00 0.00 41.88 4.68
1296 2902 6.036735 GCGATTACAACCTGTGTATACAACAT 59.963 38.462 7.25 0.00 42.37 2.71
1301 2907 4.506654 CAGGCGATTACAACCTGTGTATAC 59.493 45.833 0.00 0.00 44.91 1.47
1302 2908 4.689071 CAGGCGATTACAACCTGTGTATA 58.311 43.478 0.00 0.00 44.91 1.47
1303 2909 3.531538 CAGGCGATTACAACCTGTGTAT 58.468 45.455 0.00 0.00 44.91 2.29
1319 2925 0.320683 TGTGTGATTCCAGTCAGGCG 60.321 55.000 0.00 0.00 37.29 5.52
1326 2932 2.205074 GCGGACTATGTGTGATTCCAG 58.795 52.381 0.00 0.00 0.00 3.86
1335 2941 0.867753 GAGCTGACGCGGACTATGTG 60.868 60.000 12.47 0.00 42.32 3.21
1337 2943 0.867753 GTGAGCTGACGCGGACTATG 60.868 60.000 12.47 0.00 42.32 2.23
1349 2955 1.228367 ACAAAGCAGGGGTGAGCTG 60.228 57.895 0.00 0.00 0.00 4.24
1357 2963 1.611673 CCTACCACTGACAAAGCAGGG 60.612 57.143 0.00 0.00 40.20 4.45
1358 2964 1.813513 CCTACCACTGACAAAGCAGG 58.186 55.000 0.00 0.00 40.20 4.85
1361 2967 1.270839 TGAGCCTACCACTGACAAAGC 60.271 52.381 0.00 0.00 0.00 3.51
1363 2969 1.347707 CCTGAGCCTACCACTGACAAA 59.652 52.381 0.00 0.00 0.00 2.83
1381 2987 4.147321 ACAACAACAGCATCTTGATTCCT 58.853 39.130 0.00 0.00 0.00 3.36
1382 2988 4.510038 ACAACAACAGCATCTTGATTCC 57.490 40.909 0.00 0.00 0.00 3.01
1383 2989 9.793252 ATATTTACAACAACAGCATCTTGATTC 57.207 29.630 0.00 0.00 0.00 2.52
1386 2992 9.624697 GAAATATTTACAACAACAGCATCTTGA 57.375 29.630 0.00 0.00 0.00 3.02
1387 2993 9.630098 AGAAATATTTACAACAACAGCATCTTG 57.370 29.630 0.00 0.00 0.00 3.02
1419 3032 5.536538 AGTCCAAAATTGAGGGAGAAAACTC 59.463 40.000 0.00 0.00 0.00 3.01
1429 3046 2.290323 ACGGAGGAGTCCAAAATTGAGG 60.290 50.000 12.86 0.00 44.18 3.86
1439 3056 6.462552 ACTAATTTTACTACGGAGGAGTCC 57.537 41.667 0.00 0.00 39.88 3.85
1440 3057 8.443953 TCTACTAATTTTACTACGGAGGAGTC 57.556 38.462 0.00 0.00 0.00 3.36
1460 3077 6.306643 AGCTTAATCCTTCTTTGCTCTACT 57.693 37.500 0.00 0.00 0.00 2.57
1465 3086 8.049721 ACTATGTAAGCTTAATCCTTCTTTGCT 58.950 33.333 7.99 0.00 0.00 3.91
1541 3339 4.201724 GCTCTGTACAATTTTGCTAGACGG 60.202 45.833 0.00 0.00 0.00 4.79
1572 3370 4.378874 GGTGATAACAGCAGAGCTTTGAAC 60.379 45.833 8.73 0.00 43.08 3.18
1585 3383 4.392921 AAGATGTCGGAGGTGATAACAG 57.607 45.455 0.00 0.00 0.00 3.16
1616 3414 2.497675 TCCAGAGAGGGTCAGATTTTCG 59.502 50.000 0.00 0.00 38.24 3.46
1648 3448 9.330063 CTGCAGATCCTTAATTATAACTGACAA 57.670 33.333 8.42 0.00 0.00 3.18
1651 3451 7.442364 GTGCTGCAGATCCTTAATTATAACTGA 59.558 37.037 20.43 0.00 0.00 3.41
1677 3477 1.746727 CGAAAGAGGCGTCGCATCAG 61.747 60.000 30.73 16.24 42.11 2.90
1714 3514 3.832615 AAGTAGGTTATAACAGGGGCG 57.167 47.619 17.16 0.00 0.00 6.13
1718 3518 9.262358 GCTATGAAGAAAGTAGGTTATAACAGG 57.738 37.037 17.16 0.00 0.00 4.00
1821 3621 8.571336 CAAGAAAAAGACTAATGTCCAGTTCAT 58.429 33.333 0.00 0.00 43.91 2.57
1844 3644 4.640201 TGGGACTTGACAGAAAAAGACAAG 59.360 41.667 0.00 0.00 41.98 3.16
1847 3647 5.125578 AGTTTGGGACTTGACAGAAAAAGAC 59.874 40.000 0.00 0.00 33.92 3.01
1848 3648 5.261216 AGTTTGGGACTTGACAGAAAAAGA 58.739 37.500 0.00 0.00 33.92 2.52
1855 3656 2.618709 GTTGGAGTTTGGGACTTGACAG 59.381 50.000 0.00 0.00 39.19 3.51
1876 3677 7.524367 GCTGATATTATTTTCATCACCCCCAAG 60.524 40.741 0.00 0.00 0.00 3.61
2025 3830 5.957842 TTGAAGGTAAAATGCTTGTCGAT 57.042 34.783 0.00 0.00 0.00 3.59
2056 3861 9.297586 CCATGAAAGACATCTTTAATGTTCATG 57.702 33.333 22.24 19.68 46.39 3.07
2083 3888 5.793817 ACATTCTAGCATACAACTCACACA 58.206 37.500 0.00 0.00 0.00 3.72
2135 3940 1.134670 GGCGAGAACTACTTCCTGCAT 60.135 52.381 0.00 0.00 31.60 3.96
2138 3943 2.338500 GTTGGCGAGAACTACTTCCTG 58.662 52.381 0.00 0.00 0.00 3.86
2205 4010 5.067805 AGTGTTCCAATCCACTTTTTCTCAC 59.932 40.000 0.00 0.00 38.76 3.51
2207 4012 5.299279 TGAGTGTTCCAATCCACTTTTTCTC 59.701 40.000 0.00 0.00 41.80 2.87


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

AutoCloner maintained by Alex Coulton.