Multiple sequence alignment - TraesCS5A01G128000

Loading Multiple Alignment...

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 TraesCS5A01G128000 chr5A 100.000 2831 0 0 1 2831 285305198 285308028 0.000000e+00 5228.0
1 TraesCS5A01G128000 chr5A 93.904 853 35 5 27 866 285213703 285214551 0.000000e+00 1271.0
2 TraesCS5A01G128000 chr5A 80.376 372 55 16 2466 2831 678664334 678663975 1.670000e-67 267.0
3 TraesCS5A01G128000 chr5A 97.500 40 0 1 1500 1539 285306664 285306702 1.820000e-07 67.6
4 TraesCS5A01G128000 chr5A 97.500 40 0 1 1467 1505 285306697 285306736 1.820000e-07 67.6
5 TraesCS5A01G128000 chr5D 93.452 901 36 9 620 1505 216098185 216099077 0.000000e+00 1315.0
6 TraesCS5A01G128000 chr5D 89.520 229 5 4 1606 1833 216099331 216099541 3.590000e-69 272.0
7 TraesCS5A01G128000 chr5D 89.506 162 15 2 1828 1989 216099796 216099955 1.330000e-48 204.0
8 TraesCS5A01G128000 chr5D 97.345 113 3 0 1500 1612 216099038 216099150 2.880000e-45 193.0
9 TraesCS5A01G128000 chr5D 95.652 115 5 0 2021 2135 216100262 216100376 4.820000e-43 185.0
10 TraesCS5A01G128000 chr5B 93.740 655 26 5 862 1505 232213912 232214562 0.000000e+00 968.0
11 TraesCS5A01G128000 chr5B 86.806 576 35 20 307 869 232213192 232213739 3.120000e-169 604.0
12 TraesCS5A01G128000 chr5B 80.519 462 53 11 2335 2766 319898740 319898286 1.270000e-83 320.0
13 TraesCS5A01G128000 chr5B 79.680 438 62 21 2296 2714 377607508 377607079 9.920000e-75 291.0
14 TraesCS5A01G128000 chr5B 91.837 196 8 2 1606 1801 232214816 232215003 1.670000e-67 267.0
15 TraesCS5A01G128000 chr5B 96.460 113 4 0 1500 1612 232214523 232214635 1.340000e-43 187.0
16 TraesCS5A01G128000 chr5B 92.800 125 9 0 2017 2141 232217845 232217969 6.230000e-42 182.0
17 TraesCS5A01G128000 chr4D 82.648 559 73 16 2287 2828 471821953 471822504 9.180000e-130 473.0
18 TraesCS5A01G128000 chr4D 81.301 492 54 22 2335 2820 53225108 53225567 5.760000e-97 364.0
19 TraesCS5A01G128000 chr4D 75.751 433 59 29 1095 1485 97420858 97420430 2.900000e-40 176.0
20 TraesCS5A01G128000 chr6D 84.040 495 53 17 2335 2826 77680753 77680282 1.200000e-123 453.0
21 TraesCS5A01G128000 chr6D 80.000 505 72 18 2335 2820 7473560 7473066 2.090000e-91 346.0
22 TraesCS5A01G128000 chr6D 90.558 233 17 5 2287 2515 403025100 403024869 1.270000e-78 303.0
23 TraesCS5A01G128000 chr6D 78.000 350 43 19 2475 2820 403024949 403024630 3.720000e-44 189.0
24 TraesCS5A01G128000 chr3D 83.267 502 55 19 2335 2822 550418974 550419460 4.330000e-118 435.0
25 TraesCS5A01G128000 chr2A 83.439 471 55 13 2335 2787 427332797 427333262 1.570000e-112 416.0
26 TraesCS5A01G128000 chr2A 95.652 46 2 0 2296 2341 427332739 427332784 1.090000e-09 75.0
27 TraesCS5A01G128000 chr7A 80.594 505 50 24 2335 2803 170074873 170074381 2.090000e-91 346.0
28 TraesCS5A01G128000 chr6A 80.478 502 51 18 2335 2831 487697027 487696568 9.710000e-90 340.0
29 TraesCS5A01G128000 chr1D 79.438 569 48 33 2242 2770 307669163 307669702 3.490000e-89 339.0
30 TraesCS5A01G128000 chr1D 84.548 343 35 8 2242 2569 209733998 209734337 9.780000e-85 324.0
31 TraesCS5A01G128000 chr1D 85.283 265 31 7 2570 2828 209734555 209734817 1.670000e-67 267.0
32 TraesCS5A01G128000 chr1D 77.605 451 75 20 2335 2769 52219556 52219996 1.680000e-62 250.0
33 TraesCS5A01G128000 chr4A 84.548 343 31 15 2499 2825 543754828 543754492 1.270000e-83 320.0
34 TraesCS5A01G128000 chr4A 76.214 412 52 29 1095 1465 478742871 478743277 2.900000e-40 176.0
35 TraesCS5A01G128000 chr1B 76.285 506 92 20 2335 2828 307168193 307168682 7.830000e-61 244.0
36 TraesCS5A01G128000 chr6B 79.511 327 45 19 2505 2818 350137537 350137220 2.210000e-51 213.0
37 TraesCS5A01G128000 chr4B 77.112 367 49 24 1095 1430 139138715 139138353 2.240000e-41 180.0


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 TraesCS5A01G128000 chr5A 285305198 285308028 2830 False 1787.733333 5228 98.333333 1 2831 3 chr5A.!!$F2 2830
1 TraesCS5A01G128000 chr5A 285213703 285214551 848 False 1271.000000 1271 93.904000 27 866 1 chr5A.!!$F1 839
2 TraesCS5A01G128000 chr5D 216098185 216100376 2191 False 433.800000 1315 93.095000 620 2135 5 chr5D.!!$F1 1515
3 TraesCS5A01G128000 chr5B 232213192 232217969 4777 False 441.600000 968 92.328600 307 2141 5 chr5B.!!$F1 1834
4 TraesCS5A01G128000 chr4D 471821953 471822504 551 False 473.000000 473 82.648000 2287 2828 1 chr4D.!!$F2 541
5 TraesCS5A01G128000 chr2A 427332739 427333262 523 False 245.500000 416 89.545500 2296 2787 2 chr2A.!!$F1 491
6 TraesCS5A01G128000 chr1D 307669163 307669702 539 False 339.000000 339 79.438000 2242 2770 1 chr1D.!!$F2 528
7 TraesCS5A01G128000 chr1D 209733998 209734817 819 False 295.500000 324 84.915500 2242 2828 2 chr1D.!!$F3 586

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
995 1197 0.670162 CCCAACAGCACAAACTCCTG 59.33 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 5737 0.109132 CATGGGGCTCTTGCGTTTTC 60.109 55.0 0.0 0.0 40.82 2.29 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
21 22 4.664150 ATCTTTTGCCTCCGTTTCAAAA 57.336 36.364 0.00 0.00 37.36 2.44
22 23 4.457834 TCTTTTGCCTCCGTTTCAAAAA 57.542 36.364 0.00 0.00 38.65 1.94
58 59 2.849880 ATATTTCATGTGGCGTGTGC 57.150 45.000 0.00 0.00 41.71 4.57
110 111 3.317430 GGATTAGATGGGCAAAAGAGCAG 59.683 47.826 0.00 0.00 35.83 4.24
135 136 4.505367 TGGTTCTAGGGTTTAAAGAGGGA 58.495 43.478 0.00 0.00 0.00 4.20
145 146 6.952358 AGGGTTTAAAGAGGGATTTAAAGGTC 59.048 38.462 4.99 0.00 42.35 3.85
191 192 3.830178 TGAAGACCGACAGGAGAAACATA 59.170 43.478 0.00 0.00 41.02 2.29
214 215 2.879103 ACTGGTCAAATAGGGTGTGG 57.121 50.000 0.00 0.00 0.00 4.17
224 225 7.093509 GGTCAAATAGGGTGTGGAAATGTAAAT 60.094 37.037 0.00 0.00 0.00 1.40
421 422 7.284716 TCTGAGATTCGTTATAAAGCTACAGGA 59.715 37.037 0.00 0.00 0.00 3.86
434 435 7.889589 AAAGCTACAGGATTTATGCAAAAAC 57.110 32.000 0.00 0.00 31.22 2.43
531 532 4.274459 GCTCACAGAGACAAGTTTTGACAT 59.726 41.667 0.00 0.00 0.00 3.06
539 540 7.756722 CAGAGACAAGTTTTGACATCACTTTTT 59.243 33.333 0.00 0.00 0.00 1.94
551 552 8.523523 TGACATCACTTTTTCATATTTTGCAG 57.476 30.769 0.00 0.00 0.00 4.41
583 584 2.430465 ACTGCACATCCTAAGCAACTG 58.570 47.619 0.00 0.00 37.89 3.16
603 617 6.604735 ACTGCGCATTTACCTCTATAAAAG 57.395 37.500 12.24 0.00 0.00 2.27
611 625 5.641789 TTACCTCTATAAAAGAAGGGGCC 57.358 43.478 0.00 0.00 32.46 5.80
612 626 3.470868 ACCTCTATAAAAGAAGGGGCCA 58.529 45.455 4.39 0.00 32.46 5.36
613 627 3.856206 ACCTCTATAAAAGAAGGGGCCAA 59.144 43.478 4.39 0.00 32.46 4.52
869 890 9.373603 TGCCATGATTGAGAATAATTTGAAAAG 57.626 29.630 0.00 0.00 0.00 2.27
886 1088 2.808906 AAGGACAAACATAGAGGCCC 57.191 50.000 0.00 0.00 0.00 5.80
896 1098 3.081804 ACATAGAGGCCCAAAACTTTCG 58.918 45.455 0.00 0.00 0.00 3.46
924 1126 2.487746 AAATTGGGGTTGAACCACCT 57.512 45.000 15.07 0.00 42.39 4.00
995 1197 0.670162 CCCAACAGCACAAACTCCTG 59.330 55.000 0.00 0.00 0.00 3.86
1220 1431 3.153919 GAGAACACCAACCCTAAATGCA 58.846 45.455 0.00 0.00 0.00 3.96
1236 1447 4.611310 AATGCATCATCGTCAAGAACTG 57.389 40.909 0.00 0.00 0.00 3.16
1240 1451 0.976641 TCATCGTCAAGAACTGCCCT 59.023 50.000 0.00 0.00 0.00 5.19
1471 1682 2.441001 CTGCATGGGGAAGGTTCTATCT 59.559 50.000 0.00 0.00 0.00 1.98
1472 1683 2.173356 TGCATGGGGAAGGTTCTATCTG 59.827 50.000 0.00 0.00 0.00 2.90
1473 1684 2.487986 GCATGGGGAAGGTTCTATCTGG 60.488 54.545 0.00 0.00 0.00 3.86
1474 1685 2.961536 TGGGGAAGGTTCTATCTGGA 57.038 50.000 0.00 0.00 0.00 3.86
1475 1686 2.478292 TGGGGAAGGTTCTATCTGGAC 58.522 52.381 0.00 0.00 0.00 4.02
1476 1687 1.413077 GGGGAAGGTTCTATCTGGACG 59.587 57.143 0.00 0.00 0.00 4.79
1477 1688 2.385803 GGGAAGGTTCTATCTGGACGA 58.614 52.381 0.00 0.00 0.00 4.20
1478 1689 2.362717 GGGAAGGTTCTATCTGGACGAG 59.637 54.545 0.00 0.00 0.00 4.18
1479 1690 3.288964 GGAAGGTTCTATCTGGACGAGA 58.711 50.000 0.00 0.00 34.25 4.04
1480 1691 3.316868 GGAAGGTTCTATCTGGACGAGAG 59.683 52.174 0.00 0.00 32.80 3.20
1481 1692 2.303175 AGGTTCTATCTGGACGAGAGC 58.697 52.381 0.00 0.00 32.80 4.09
1482 1693 1.002251 GGTTCTATCTGGACGAGAGCG 60.002 57.143 0.00 0.00 44.79 5.03
1483 1694 0.663688 TTCTATCTGGACGAGAGCGC 59.336 55.000 0.00 0.00 42.48 5.92
1484 1695 1.082431 CTATCTGGACGAGAGCGCG 60.082 63.158 0.00 0.00 42.48 6.86
1485 1696 1.499688 CTATCTGGACGAGAGCGCGA 61.500 60.000 12.10 0.00 42.48 5.87
1486 1697 1.773054 TATCTGGACGAGAGCGCGAC 61.773 60.000 12.10 2.22 42.48 5.19
1487 1698 4.838486 CTGGACGAGAGCGCGACC 62.838 72.222 12.10 7.98 44.37 4.79
1504 1715 3.610669 CGCTGCCGGGAGCTATCT 61.611 66.667 39.69 0.00 44.23 1.98
1662 2060 4.063967 CGCGTGTAGGGCTGGTGA 62.064 66.667 0.00 0.00 0.00 4.02
1681 2079 5.186215 TGGTGATGGTGAATACTACTCGAAA 59.814 40.000 0.00 0.00 0.00 3.46
1687 2085 5.407387 TGGTGAATACTACTCGAAAACTTGC 59.593 40.000 0.00 0.00 0.00 4.01
1718 2116 1.149148 GTCTGGTTCGTGGCTTTCTC 58.851 55.000 0.00 0.00 0.00 2.87
1763 2161 3.153024 GGCGTGTAGATTTGCCAGA 57.847 52.632 0.00 0.00 46.76 3.86
1764 2162 1.448985 GGCGTGTAGATTTGCCAGAA 58.551 50.000 0.00 0.00 46.76 3.02
1814 2212 8.204160 TGAGTTTGAGGTACCATGTAGATAATG 58.796 37.037 15.94 0.00 0.00 1.90
1839 2497 6.909550 ATTAGGACTCAGAGATATGTGACC 57.090 41.667 3.79 0.00 0.00 4.02
1877 2535 7.097192 TGATACAAATTTCAGCTTCGTCTACT 58.903 34.615 0.00 0.00 0.00 2.57
1886 2544 1.536331 GCTTCGTCTACTCTATCCCGG 59.464 57.143 0.00 0.00 0.00 5.73
1896 2554 2.091830 ACTCTATCCCGGAGATGTGTGA 60.092 50.000 0.73 2.10 36.33 3.58
1897 2555 2.959030 CTCTATCCCGGAGATGTGTGAA 59.041 50.000 0.73 0.00 36.33 3.18
1898 2556 2.693591 TCTATCCCGGAGATGTGTGAAC 59.306 50.000 0.73 0.00 36.33 3.18
1899 2557 1.275666 ATCCCGGAGATGTGTGAACA 58.724 50.000 0.73 0.00 32.41 3.18
1902 2560 2.009774 CCCGGAGATGTGTGAACATTC 58.990 52.381 0.73 0.00 0.00 2.67
1942 2600 4.794278 TCACTTTGTATCGGTTCAGCTA 57.206 40.909 0.00 0.00 0.00 3.32
1947 2605 7.820386 TCACTTTGTATCGGTTCAGCTATTTAA 59.180 33.333 0.00 0.00 0.00 1.52
1981 2639 9.988350 ATATAAAGCTGAATGAAACGTGTTTAG 57.012 29.630 0.00 0.00 32.11 1.85
2009 2705 5.282129 TGAGGGGTTAACTATACCATGACA 58.718 41.667 5.42 1.60 37.40 3.58
2032 5542 6.127423 ACAGTCATATACGAGCTAGTGGTTTT 60.127 38.462 10.02 0.00 0.00 2.43
2058 5568 9.910267 TGATGAAGATTTGAATTCTATCCAAGA 57.090 29.630 7.05 0.00 0.00 3.02
2141 5651 8.981659 CCCCTATCCTTTTGTCAATTCTTTTAT 58.018 33.333 0.00 0.00 0.00 1.40
2147 5657 9.020731 TCCTTTTGTCAATTCTTTTATACTCCC 57.979 33.333 0.00 0.00 0.00 4.30
2148 5658 9.025041 CCTTTTGTCAATTCTTTTATACTCCCT 57.975 33.333 0.00 0.00 0.00 4.20
2150 5660 8.575649 TTTGTCAATTCTTTTATACTCCCTCC 57.424 34.615 0.00 0.00 0.00 4.30
2151 5661 6.346096 TGTCAATTCTTTTATACTCCCTCCG 58.654 40.000 0.00 0.00 0.00 4.63
2152 5662 6.070424 TGTCAATTCTTTTATACTCCCTCCGT 60.070 38.462 0.00 0.00 0.00 4.69
2153 5663 6.479331 GTCAATTCTTTTATACTCCCTCCGTC 59.521 42.308 0.00 0.00 0.00 4.79
2154 5664 5.548181 ATTCTTTTATACTCCCTCCGTCC 57.452 43.478 0.00 0.00 0.00 4.79
2155 5665 3.303049 TCTTTTATACTCCCTCCGTCCC 58.697 50.000 0.00 0.00 0.00 4.46
2156 5666 2.852714 TTTATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
2157 5667 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2158 5668 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2159 5669 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2160 5670 1.732117 TACTCCCTCCGTCCCAAAAA 58.268 50.000 0.00 0.00 0.00 1.94
2187 5697 6.530019 AAAAAGAGAAACAAGCTTCCTTCA 57.470 33.333 15.90 0.00 0.00 3.02
2188 5698 6.530019 AAAAGAGAAACAAGCTTCCTTCAA 57.470 33.333 15.90 0.00 0.00 2.69
2189 5699 6.530019 AAAGAGAAACAAGCTTCCTTCAAA 57.470 33.333 15.90 0.00 0.00 2.69
2190 5700 6.530019 AAGAGAAACAAGCTTCCTTCAAAA 57.470 33.333 15.90 0.00 0.00 2.44
2191 5701 6.530019 AGAGAAACAAGCTTCCTTCAAAAA 57.470 33.333 15.90 0.00 0.00 1.94
2218 5728 9.956640 AGAACAAGAGAATCAATCTATGAAACT 57.043 29.630 0.00 0.00 42.54 2.66
2219 5729 9.985318 GAACAAGAGAATCAATCTATGAAACTG 57.015 33.333 0.00 0.00 42.54 3.16
2220 5730 9.730705 AACAAGAGAATCAATCTATGAAACTGA 57.269 29.630 0.00 0.00 42.54 3.41
2221 5731 9.381033 ACAAGAGAATCAATCTATGAAACTGAG 57.619 33.333 0.00 0.00 42.54 3.35
2222 5732 9.597170 CAAGAGAATCAATCTATGAAACTGAGA 57.403 33.333 0.00 0.00 42.54 3.27
2233 5743 8.299262 TCTATGAAACTGAGAAAGAGAAAACG 57.701 34.615 0.00 0.00 0.00 3.60
2234 5744 5.156804 TGAAACTGAGAAAGAGAAAACGC 57.843 39.130 0.00 0.00 0.00 4.84
2235 5745 4.634004 TGAAACTGAGAAAGAGAAAACGCA 59.366 37.500 0.00 0.00 0.00 5.24
2236 5746 5.123186 TGAAACTGAGAAAGAGAAAACGCAA 59.877 36.000 0.00 0.00 0.00 4.85
2238 5748 4.442706 ACTGAGAAAGAGAAAACGCAAGA 58.557 39.130 0.00 0.00 43.62 3.02
2239 5749 4.509600 ACTGAGAAAGAGAAAACGCAAGAG 59.490 41.667 0.00 0.00 43.62 2.85
2240 5750 3.248602 TGAGAAAGAGAAAACGCAAGAGC 59.751 43.478 0.00 0.00 43.62 4.09
2250 5760 2.677524 GCAAGAGCCCCATGTGCA 60.678 61.111 7.16 0.00 35.28 4.57
2341 5860 8.715191 AAGTTGCTAAATTGTTGAATTGTTCA 57.285 26.923 0.00 0.00 38.04 3.18
2421 5960 9.932699 TGCAATTTCAAAAATAATGTTTGTCTG 57.067 25.926 0.00 0.00 37.28 3.51
2422 5961 9.384682 GCAATTTCAAAAATAATGTTTGTCTGG 57.615 29.630 0.86 0.00 37.28 3.86
2698 6491 8.839310 TTTGAAAAGATGTTCACTTTTTCCAA 57.161 26.923 0.00 0.00 44.20 3.53
2717 6510 6.155475 TCCAAAAATGTTCACGAATTTCCT 57.845 33.333 0.00 0.00 0.00 3.36
2719 6512 7.142680 TCCAAAAATGTTCACGAATTTCCTAC 58.857 34.615 0.00 0.00 0.00 3.18
2728 6522 4.446385 TCACGAATTTCCTACAACTGTTCG 59.554 41.667 0.00 0.00 41.69 3.95
2734 6528 5.666969 TTTCCTACAACTGTTCGTCAATG 57.333 39.130 0.00 0.00 0.00 2.82
2828 6643 3.383620 TCGCAAATTTGAAACATGGCT 57.616 38.095 22.31 0.00 0.00 4.75
2829 6644 3.058450 TCGCAAATTTGAAACATGGCTG 58.942 40.909 22.31 1.33 0.00 4.85
2830 6645 3.058450 CGCAAATTTGAAACATGGCTGA 58.942 40.909 22.31 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.664150 TTTTGAAACGGAGGCAAAAGAT 57.336 36.364 0.00 0.00 36.80 2.40
1 2 4.457834 TTTTTGAAACGGAGGCAAAAGA 57.542 36.364 0.00 0.00 41.02 2.52
41 42 0.241749 CAGCACACGCCACATGAAAT 59.758 50.000 0.00 0.00 39.83 2.17
52 53 3.725895 GCATACTCAAATCACAGCACACG 60.726 47.826 0.00 0.00 0.00 4.49
58 59 4.926860 TGAACGCATACTCAAATCACAG 57.073 40.909 0.00 0.00 0.00 3.66
110 111 5.886474 CCCTCTTTAAACCCTAGAACCAATC 59.114 44.000 0.00 0.00 0.00 2.67
145 146 6.308766 CAGCAAAATTAGATGGAAAAGGAACG 59.691 38.462 0.00 0.00 0.00 3.95
161 162 2.554032 CCTGTCGGTCTTCAGCAAAATT 59.446 45.455 0.00 0.00 0.00 1.82
191 192 2.901839 ACACCCTATTTGACCAGTACGT 59.098 45.455 0.00 0.00 0.00 3.57
224 225 7.551585 ACACATTGTTGTCCATTTCAACTAAA 58.448 30.769 9.57 0.00 43.54 1.85
409 410 8.032451 GGTTTTTGCATAAATCCTGTAGCTTTA 58.968 33.333 5.60 0.00 0.00 1.85
421 422 3.063485 GTGTGGCGGTTTTTGCATAAAT 58.937 40.909 5.60 0.00 0.00 1.40
512 513 5.431765 AGTGATGTCAAAACTTGTCTCTGT 58.568 37.500 0.00 0.00 0.00 3.41
531 532 7.862372 GTCTGACTGCAAAATATGAAAAAGTGA 59.138 33.333 0.00 0.00 0.00 3.41
539 540 7.175467 AGTTTGATGTCTGACTGCAAAATATGA 59.825 33.333 21.28 5.23 31.19 2.15
551 552 3.120060 GGATGTGCAGTTTGATGTCTGAC 60.120 47.826 0.00 0.00 34.02 3.51
583 584 6.293462 CCCTTCTTTTATAGAGGTAAATGCGC 60.293 42.308 0.00 0.00 33.51 6.09
603 617 1.006220 CACGCTTTTTGGCCCCTTC 60.006 57.895 0.00 0.00 0.00 3.46
611 625 4.278858 TCAATCTCGAAACACGCTTTTTG 58.721 39.130 0.00 0.00 42.26 2.44
612 626 4.545823 TCAATCTCGAAACACGCTTTTT 57.454 36.364 0.00 0.00 42.26 1.94
613 627 4.749245 ATCAATCTCGAAACACGCTTTT 57.251 36.364 0.00 0.00 42.26 2.27
814 835 5.687166 AGTTCATTACCCTCGTTCCATAA 57.313 39.130 0.00 0.00 0.00 1.90
869 890 2.507407 TTGGGCCTCTATGTTTGTCC 57.493 50.000 4.53 0.00 0.00 4.02
896 1098 0.312729 AACCCCAATTTTCGTGCGAC 59.687 50.000 0.00 0.00 0.00 5.19
924 1126 7.069331 TGTCATTTTCTCCTTTTCTTTGCCTTA 59.931 33.333 0.00 0.00 0.00 2.69
995 1197 1.082366 CGTGTGCGGCTTGGTTTAC 60.082 57.895 0.00 0.00 0.00 2.01
1136 1347 4.790861 GGCGACGTCTTCCCCGAC 62.791 72.222 14.70 0.00 0.00 4.79
1141 1352 2.087009 CGACAAGGCGACGTCTTCC 61.087 63.158 12.63 14.19 0.00 3.46
1155 1366 4.337060 CGCCTGTGACGTCCGACA 62.337 66.667 14.12 10.78 0.00 4.35
1220 1431 1.556911 AGGGCAGTTCTTGACGATGAT 59.443 47.619 0.00 0.00 34.72 2.45
1435 1646 2.358737 CAGGACACCTTGGGCGAC 60.359 66.667 0.00 0.00 0.00 5.19
1486 1697 4.671569 GATAGCTCCCGGCAGCGG 62.672 72.222 12.78 0.00 44.82 5.52
1487 1698 3.610669 AGATAGCTCCCGGCAGCG 61.611 66.667 12.78 0.00 44.82 5.18
1488 1699 2.030262 CAGATAGCTCCCGGCAGC 59.970 66.667 10.19 10.19 44.79 5.25
1489 1700 1.834378 TCCAGATAGCTCCCGGCAG 60.834 63.158 0.00 0.00 44.79 4.85
1490 1701 2.134287 GTCCAGATAGCTCCCGGCA 61.134 63.158 0.00 0.00 44.79 5.69
1491 1702 2.737830 GTCCAGATAGCTCCCGGC 59.262 66.667 0.00 0.00 42.19 6.13
1492 1703 1.519751 CTCGTCCAGATAGCTCCCGG 61.520 65.000 0.00 0.00 0.00 5.73
1493 1704 0.535328 TCTCGTCCAGATAGCTCCCG 60.535 60.000 0.00 0.00 0.00 5.14
1494 1705 1.243902 CTCTCGTCCAGATAGCTCCC 58.756 60.000 0.00 0.00 0.00 4.30
1495 1706 0.596082 GCTCTCGTCCAGATAGCTCC 59.404 60.000 0.00 0.00 43.35 4.70
1496 1707 0.237235 CGCTCTCGTCCAGATAGCTC 59.763 60.000 0.00 0.00 44.18 4.09
1497 1708 1.791103 GCGCTCTCGTCCAGATAGCT 61.791 60.000 0.00 0.00 44.18 3.32
1498 1709 1.371145 GCGCTCTCGTCCAGATAGC 60.371 63.158 0.00 0.00 43.28 2.97
1499 1710 1.082431 CGCGCTCTCGTCCAGATAG 60.082 63.158 5.56 0.00 38.14 2.08
1500 1711 1.523032 TCGCGCTCTCGTCCAGATA 60.523 57.895 5.56 0.00 38.14 1.98
1501 1712 2.824489 TCGCGCTCTCGTCCAGAT 60.824 61.111 5.56 0.00 38.14 2.90
1502 1713 3.800863 GTCGCGCTCTCGTCCAGA 61.801 66.667 5.56 0.00 38.14 3.86
1503 1714 4.838486 GGTCGCGCTCTCGTCCAG 62.838 72.222 5.56 0.00 37.55 3.86
1657 2055 4.274978 TCGAGTAGTATTCACCATCACCA 58.725 43.478 0.00 0.00 0.00 4.17
1658 2056 4.913335 TCGAGTAGTATTCACCATCACC 57.087 45.455 0.00 0.00 0.00 4.02
1659 2057 6.812160 AGTTTTCGAGTAGTATTCACCATCAC 59.188 38.462 0.00 0.00 0.00 3.06
1660 2058 6.931838 AGTTTTCGAGTAGTATTCACCATCA 58.068 36.000 0.00 0.00 0.00 3.07
1661 2059 7.674240 GCAAGTTTTCGAGTAGTATTCACCATC 60.674 40.741 0.00 0.00 0.00 3.51
1662 2060 6.092259 GCAAGTTTTCGAGTAGTATTCACCAT 59.908 38.462 0.00 0.00 0.00 3.55
1687 2085 3.191581 ACGAACCAGACTGTCATCTACTG 59.808 47.826 10.88 0.00 0.00 2.74
1718 2116 4.022935 TCTGAAAGCATAGCAACAACCAAG 60.023 41.667 0.00 0.00 0.00 3.61
1814 2212 7.232534 AGGTCACATATCTCTGAGTCCTAATTC 59.767 40.741 4.32 0.00 0.00 2.17
1839 2497 8.843262 TGAAATTTGTATCATCTGCCAATCTAG 58.157 33.333 0.00 0.00 0.00 2.43
1877 2535 2.693591 GTTCACACATCTCCGGGATAGA 59.306 50.000 0.00 0.00 32.64 1.98
1912 2570 7.227711 TGAACCGATACAAAGTGATGAGAAAAA 59.772 33.333 0.00 0.00 0.00 1.94
1968 2626 4.562757 CCCTCATCCTCTAAACACGTTTCA 60.563 45.833 0.00 0.00 34.23 2.69
1974 2632 5.045797 AGTTAACCCCTCATCCTCTAAACAC 60.046 44.000 0.88 0.00 0.00 3.32
1980 2638 5.102783 TGGTATAGTTAACCCCTCATCCTCT 60.103 44.000 0.88 0.00 36.06 3.69
1981 2639 5.152934 TGGTATAGTTAACCCCTCATCCTC 58.847 45.833 0.88 0.00 36.06 3.71
2009 2705 6.096423 TCAAAACCACTAGCTCGTATATGACT 59.904 38.462 0.00 0.00 0.00 3.41
2032 5542 9.910267 TCTTGGATAGAATTCAAATCTTCATCA 57.090 29.630 8.44 1.42 0.00 3.07
2088 5598 1.743958 CGACCCAAGTACGACTCTCAT 59.256 52.381 0.00 0.00 0.00 2.90
2141 5651 1.732117 TTTTTGGGACGGAGGGAGTA 58.268 50.000 0.00 0.00 0.00 2.59
2142 5652 2.547171 TTTTTGGGACGGAGGGAGT 58.453 52.632 0.00 0.00 0.00 3.85
2164 5674 6.530019 TGAAGGAAGCTTGTTTCTCTTTTT 57.470 33.333 2.10 0.00 0.00 1.94
2165 5675 6.530019 TTGAAGGAAGCTTGTTTCTCTTTT 57.470 33.333 2.10 0.00 0.00 2.27
2166 5676 6.530019 TTTGAAGGAAGCTTGTTTCTCTTT 57.470 33.333 2.10 0.00 0.00 2.52
2167 5677 6.530019 TTTTGAAGGAAGCTTGTTTCTCTT 57.470 33.333 2.10 0.00 0.00 2.85
2168 5678 6.530019 TTTTTGAAGGAAGCTTGTTTCTCT 57.470 33.333 2.10 0.00 0.00 3.10
2192 5702 9.956640 AGTTTCATAGATTGATTCTCTTGTTCT 57.043 29.630 0.00 0.00 35.79 3.01
2193 5703 9.985318 CAGTTTCATAGATTGATTCTCTTGTTC 57.015 33.333 0.00 0.00 35.79 3.18
2194 5704 9.730705 TCAGTTTCATAGATTGATTCTCTTGTT 57.269 29.630 0.00 0.00 35.79 2.83
2195 5705 9.381033 CTCAGTTTCATAGATTGATTCTCTTGT 57.619 33.333 0.00 0.00 35.79 3.16
2196 5706 9.597170 TCTCAGTTTCATAGATTGATTCTCTTG 57.403 33.333 0.00 0.00 35.79 3.02
2207 5717 8.930760 CGTTTTCTCTTTCTCAGTTTCATAGAT 58.069 33.333 0.00 0.00 0.00 1.98
2208 5718 7.095607 GCGTTTTCTCTTTCTCAGTTTCATAGA 60.096 37.037 0.00 0.00 0.00 1.98
2209 5719 7.012358 GCGTTTTCTCTTTCTCAGTTTCATAG 58.988 38.462 0.00 0.00 0.00 2.23
2210 5720 6.481976 TGCGTTTTCTCTTTCTCAGTTTCATA 59.518 34.615 0.00 0.00 0.00 2.15
2211 5721 5.296780 TGCGTTTTCTCTTTCTCAGTTTCAT 59.703 36.000 0.00 0.00 0.00 2.57
2212 5722 4.634004 TGCGTTTTCTCTTTCTCAGTTTCA 59.366 37.500 0.00 0.00 0.00 2.69
2213 5723 5.156804 TGCGTTTTCTCTTTCTCAGTTTC 57.843 39.130 0.00 0.00 0.00 2.78
2214 5724 5.354234 TCTTGCGTTTTCTCTTTCTCAGTTT 59.646 36.000 0.00 0.00 0.00 2.66
2215 5725 4.876107 TCTTGCGTTTTCTCTTTCTCAGTT 59.124 37.500 0.00 0.00 0.00 3.16
2216 5726 4.442706 TCTTGCGTTTTCTCTTTCTCAGT 58.557 39.130 0.00 0.00 0.00 3.41
2217 5727 4.610231 GCTCTTGCGTTTTCTCTTTCTCAG 60.610 45.833 0.00 0.00 0.00 3.35
2218 5728 3.248602 GCTCTTGCGTTTTCTCTTTCTCA 59.751 43.478 0.00 0.00 0.00 3.27
2219 5729 3.364465 GGCTCTTGCGTTTTCTCTTTCTC 60.364 47.826 0.00 0.00 40.82 2.87
2220 5730 2.550180 GGCTCTTGCGTTTTCTCTTTCT 59.450 45.455 0.00 0.00 40.82 2.52
2221 5731 2.350868 GGGCTCTTGCGTTTTCTCTTTC 60.351 50.000 0.00 0.00 40.82 2.62
2222 5732 1.609072 GGGCTCTTGCGTTTTCTCTTT 59.391 47.619 0.00 0.00 40.82 2.52
2223 5733 1.239347 GGGCTCTTGCGTTTTCTCTT 58.761 50.000 0.00 0.00 40.82 2.85
2224 5734 0.606673 GGGGCTCTTGCGTTTTCTCT 60.607 55.000 0.00 0.00 40.82 3.10
2225 5735 0.889186 TGGGGCTCTTGCGTTTTCTC 60.889 55.000 0.00 0.00 40.82 2.87
2226 5736 0.251341 ATGGGGCTCTTGCGTTTTCT 60.251 50.000 0.00 0.00 40.82 2.52
2227 5737 0.109132 CATGGGGCTCTTGCGTTTTC 60.109 55.000 0.00 0.00 40.82 2.29
2228 5738 0.827507 ACATGGGGCTCTTGCGTTTT 60.828 50.000 0.00 0.00 40.82 2.43
2229 5739 1.228552 ACATGGGGCTCTTGCGTTT 60.229 52.632 0.00 0.00 40.82 3.60
2230 5740 1.973281 CACATGGGGCTCTTGCGTT 60.973 57.895 0.00 0.00 40.82 4.84
2231 5741 2.360350 CACATGGGGCTCTTGCGT 60.360 61.111 0.00 0.00 40.82 5.24
2232 5742 3.818787 GCACATGGGGCTCTTGCG 61.819 66.667 0.00 0.00 40.82 4.85
2233 5743 2.677524 TGCACATGGGGCTCTTGC 60.678 61.111 12.08 4.48 38.76 4.01
2234 5744 2.050350 CCTGCACATGGGGCTCTTG 61.050 63.158 12.08 0.00 0.00 3.02
2235 5745 2.357836 CCTGCACATGGGGCTCTT 59.642 61.111 12.08 0.00 0.00 2.85
2236 5746 3.736224 CCCTGCACATGGGGCTCT 61.736 66.667 12.08 0.00 40.97 4.09
2341 5860 9.781633 TCATTTCCTGAACATTTTTCAAATCAT 57.218 25.926 0.00 0.00 0.00 2.45
2348 5867 9.977762 GCATTTATCATTTCCTGAACATTTTTC 57.022 29.630 0.00 0.00 37.44 2.29
2490 6031 8.764287 GGTGAACATTTTTCAAAATTCTCGAAT 58.236 29.630 0.00 0.00 36.52 3.34
2645 6435 9.166173 TCATGAATATTTCTGAAATCGTGAACT 57.834 29.630 18.22 0.00 32.38 3.01
2664 6455 9.991906 AGTGAACATCTTTTCAAAATCATGAAT 57.008 25.926 0.00 0.00 38.98 2.57
2698 6491 7.647715 CAGTTGTAGGAAATTCGTGAACATTTT 59.352 33.333 11.98 0.00 0.00 1.82
2717 6510 4.884458 TTTGCATTGACGAACAGTTGTA 57.116 36.364 0.00 0.00 0.00 2.41
2741 6535 5.793030 TTTTTACAAATCCGGGAACATGT 57.207 34.783 0.00 9.22 0.00 3.21
2772 6569 8.777865 TCAAATTGTGTACATTTTTCAAACCA 57.222 26.923 0.00 0.00 29.96 3.67
2773 6570 9.092876 TCTCAAATTGTGTACATTTTTCAAACC 57.907 29.630 0.00 0.00 29.96 3.27
2803 6618 5.433855 CCATGTTTCAAATTTGCGAACAAG 58.566 37.500 27.96 24.91 37.43 3.16


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

AutoCloner maintained by Alex Coulton.