Multiple sequence alignment - TraesCS4D01G036300

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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 TraesCS4D01G036300 chr4D 100.000 2516 0 0 1 2516 16153134 16155649 0.000000e+00 4647.0
1 TraesCS4D01G036300 chr4D 82.640 697 84 20 1389 2070 16199502 16200176 1.300000e-162 582.0
2 TraesCS4D01G036300 chr4D 86.585 410 39 10 2110 2516 16197209 16197605 2.970000e-119 438.0
3 TraesCS4D01G036300 chr4D 95.161 124 4 1 1947 2070 16201740 16201861 7.100000e-46 195.0
4 TraesCS4D01G036300 chr4D 79.931 289 33 12 2110 2381 16200366 16200646 3.300000e-44 189.0
5 TraesCS4D01G036300 chr4D 89.726 146 12 2 1926 2070 16196873 16197016 1.540000e-42 183.0
6 TraesCS4D01G036300 chr4D 97.059 34 1 0 2072 2105 16200312 16200345 9.720000e-05 58.4
7 TraesCS4D01G036300 chr4B 84.292 1426 104 48 707 2070 27930729 27932096 0.000000e+00 1282.0
8 TraesCS4D01G036300 chr4B 85.762 597 39 17 1 572 27929932 27930507 7.750000e-165 590.0
9 TraesCS4D01G036300 chr4B 78.838 723 95 26 1389 2070 27936795 27937500 3.840000e-118 435.0
10 TraesCS4D01G036300 chr4B 83.333 408 34 19 2114 2516 27932441 27932819 1.850000e-91 346.0
11 TraesCS4D01G036300 chr4B 81.250 384 55 12 2147 2516 27939467 27939847 6.810000e-76 294.0
12 TraesCS4D01G036300 chr4B 80.070 286 33 11 2110 2378 27937703 27937981 9.190000e-45 191.0
13 TraesCS4D01G036300 chr4B 89.062 128 8 2 1947 2070 27939122 27939247 1.210000e-33 154.0
14 TraesCS4D01G036300 chr4A 87.919 596 39 9 1141 1721 584346559 584345982 0.000000e+00 671.0
15 TraesCS4D01G036300 chr4A 86.364 528 26 19 685 1192 584347076 584346575 3.680000e-148 534.0
16 TraesCS4D01G036300 chr4A 81.547 569 60 16 1389 1931 584339418 584338869 6.430000e-116 427.0
17 TraesCS4D01G036300 chr4A 86.828 372 19 4 1729 2073 584344303 584343935 3.040000e-104 388.0
18 TraesCS4D01G036300 chr4A 83.610 421 50 7 2110 2516 584280803 584280388 6.570000e-101 377.0
19 TraesCS4D01G036300 chr4A 82.270 423 55 8 1389 1799 584342375 584341961 5.150000e-92 348.0
20 TraesCS4D01G036300 chr4A 95.812 191 7 1 2326 2516 584341356 584341167 8.740000e-80 307.0
21 TraesCS4D01G036300 chr4A 79.545 396 53 20 293 671 584347513 584347129 8.930000e-65 257.0
22 TraesCS4D01G036300 chr4A 93.103 145 8 1 1929 2073 584341841 584341699 7.050000e-51 211.0
23 TraesCS4D01G036300 chr4A 89.412 170 10 3 2110 2279 584341529 584341368 9.120000e-50 207.0
24 TraesCS4D01G036300 chr4A 91.096 146 10 2 1929 2073 584338835 584338692 7.100000e-46 195.0
25 TraesCS4D01G036300 chr4A 90.551 127 10 2 1947 2073 584281114 584280990 1.550000e-37 167.0
26 TraesCS4D01G036300 chr4A 80.973 226 24 6 2110 2322 584338497 584338278 7.200000e-36 161.0
27 TraesCS4D01G036300 chr4A 95.455 44 2 0 2067 2110 584341595 584341552 1.250000e-08 71.3
28 TraesCS4D01G036300 chr4A 97.500 40 1 0 2072 2111 584338559 584338520 4.490000e-08 69.4
29 TraesCS4D01G036300 chr5A 87.755 49 4 2 1120 1166 504567593 504567545 3.500000e-04 56.5
30 TraesCS4D01G036300 chr5A 92.105 38 3 0 1119 1156 504567600 504567563 1.000000e-03 54.7
31 TraesCS4D01G036300 chr5A 100.000 28 0 0 1120 1147 469789033 469789060 5.000000e-03 52.8
32 TraesCS4D01G036300 chr5A 100.000 28 0 0 1120 1147 469789039 469789066 5.000000e-03 52.8
33 TraesCS4D01G036300 chr5A 100.000 28 0 0 1120 1147 469789075 469789102 5.000000e-03 52.8


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 TraesCS4D01G036300 chr4D 16153134 16155649 2515 False 4647.000000 4647 100.000000 1 2516 1 chr4D.!!$F1 2515
1 TraesCS4D01G036300 chr4D 16196873 16201861 4988 False 274.233333 582 88.517000 1389 2516 6 chr4D.!!$F2 1127
2 TraesCS4D01G036300 chr4B 27929932 27939847 9915 False 470.285714 1282 83.229571 1 2516 7 chr4B.!!$F1 2515
3 TraesCS4D01G036300 chr4A 584338278 584347513 9235 True 295.900000 671 88.294154 293 2516 13 chr4A.!!$R2 2223
4 TraesCS4D01G036300 chr4A 584280388 584281114 726 True 272.000000 377 87.080500 1947 2516 2 chr4A.!!$R1 569

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
949 1131 0.465705 CTCATCAGCTCCGGCCTTTA 59.534 55.0 0.0 0.0 39.73 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 3830 1.698532 GTCTCCCCTGATCATCATGCT 59.301 52.381 0.0 0.0 0.0 3.79 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
26 28 3.001086 TGGAGTGATATAGGGGGCTCTA 58.999 50.000 0.00 0.00 0.00 2.43
30 32 3.018149 GTGATATAGGGGGCTCTACTCG 58.982 54.545 0.00 0.00 0.00 4.18
31 33 2.025226 TGATATAGGGGGCTCTACTCGG 60.025 54.545 0.00 0.00 0.00 4.63
34 36 2.923634 TAGGGGGCTCTACTCGGCAC 62.924 65.000 0.00 0.00 0.00 5.01
54 56 1.136085 CGTTTGTTGTATGCCGGAGTG 60.136 52.381 5.05 0.00 0.00 3.51
56 58 2.264005 TTGTTGTATGCCGGAGTGTT 57.736 45.000 5.05 0.00 0.00 3.32
59 61 0.981183 TTGTATGCCGGAGTGTTCCT 59.019 50.000 5.05 0.00 41.67 3.36
75 77 2.893489 GTTCCTGGACTGATTTGGCTTT 59.107 45.455 0.00 0.00 0.00 3.51
76 78 2.795329 TCCTGGACTGATTTGGCTTTC 58.205 47.619 0.00 0.00 0.00 2.62
88 90 1.075659 GGCTTTCCTGGGAACTGCT 59.924 57.895 18.73 0.00 35.57 4.24
116 136 0.804989 GCTGTTCACTGTATGGCCAC 59.195 55.000 8.16 0.00 0.00 5.01
123 143 1.065199 CACTGTATGGCCACCTGACAT 60.065 52.381 8.16 0.00 0.00 3.06
136 156 6.397272 GCCACCTGACATGAAATTTCAAATA 58.603 36.000 23.91 10.43 41.13 1.40
146 166 9.362539 ACATGAAATTTCAAATACTTCAGATGC 57.637 29.630 23.91 0.00 41.13 3.91
164 184 7.330262 TCAGATGCTTCATGTGAATTGTACTA 58.670 34.615 4.46 0.00 40.36 1.82
168 188 8.654230 ATGCTTCATGTGAATTGTACTAGTAG 57.346 34.615 1.87 0.00 33.01 2.57
210 230 6.137794 TCTTTGCCGAATTTTACACTGAAA 57.862 33.333 0.00 0.00 0.00 2.69
211 231 6.565234 TCTTTGCCGAATTTTACACTGAAAA 58.435 32.000 0.00 0.00 33.04 2.29
228 248 4.054671 TGAAAATTGAATGTGAAACCGGC 58.945 39.130 0.00 0.00 34.36 6.13
229 249 3.742433 AAATTGAATGTGAAACCGGCA 57.258 38.095 0.00 0.00 34.36 5.69
230 250 3.959535 AATTGAATGTGAAACCGGCAT 57.040 38.095 0.00 0.00 34.36 4.40
231 251 3.959535 ATTGAATGTGAAACCGGCATT 57.040 38.095 0.00 1.98 35.78 3.56
232 252 5.398603 AATTGAATGTGAAACCGGCATTA 57.601 34.783 0.00 0.00 33.56 1.90
233 253 4.433186 TTGAATGTGAAACCGGCATTAG 57.567 40.909 0.00 0.00 33.56 1.73
234 254 3.417101 TGAATGTGAAACCGGCATTAGT 58.583 40.909 0.00 0.00 33.56 2.24
235 255 3.823873 TGAATGTGAAACCGGCATTAGTT 59.176 39.130 0.00 0.00 33.56 2.24
242 262 0.676782 ACCGGCATTAGTTCCTGCAC 60.677 55.000 0.00 0.00 40.18 4.57
359 383 4.556233 TCACCTCATCTTAACACACTTCG 58.444 43.478 0.00 0.00 0.00 3.79
382 406 9.667107 TTCGGATATCCTTTTTGATATATGACC 57.333 33.333 19.61 0.00 37.91 4.02
384 408 9.448438 CGGATATCCTTTTTGATATATGACCAA 57.552 33.333 19.61 0.00 37.91 3.67
441 468 5.277442 CCATTTTGAATTGGTTGCAAGACAC 60.277 40.000 0.00 0.00 0.00 3.67
444 471 1.606668 GAATTGGTTGCAAGACACGGA 59.393 47.619 0.00 0.00 0.00 4.69
447 474 0.813610 TGGTTGCAAGACACGGACAG 60.814 55.000 0.00 0.00 0.00 3.51
450 477 1.400494 GTTGCAAGACACGGACAGTTT 59.600 47.619 0.00 0.00 0.00 2.66
457 484 1.002792 GACACGGACAGTTTTGCCTTC 60.003 52.381 0.00 0.00 0.00 3.46
494 522 1.026182 CGGGCACTTTGAGCTATGCA 61.026 55.000 0.00 0.00 39.92 3.96
497 525 1.747355 GGCACTTTGAGCTATGCACAT 59.253 47.619 0.00 0.00 39.92 3.21
514 542 3.115556 TGGCACGCCAAAGAACAC 58.884 55.556 8.67 0.00 44.12 3.32
579 712 7.359262 TCTGTATGAATGTGTTTAGGTTTCG 57.641 36.000 0.00 0.00 0.00 3.46
646 784 0.884704 TTGAGAAAGAGCACGGGCAC 60.885 55.000 14.57 5.35 44.61 5.01
647 785 1.301716 GAGAAAGAGCACGGGCACA 60.302 57.895 14.57 0.00 44.61 4.57
671 809 8.254508 ACACTTTGCTAACAGGTGAAAATTAAA 58.745 29.630 5.92 0.00 35.94 1.52
672 810 9.092876 CACTTTGCTAACAGGTGAAAATTAAAA 57.907 29.630 0.00 0.00 35.02 1.52
673 811 9.660180 ACTTTGCTAACAGGTGAAAATTAAAAA 57.340 25.926 0.00 0.00 0.00 1.94
787 964 5.156804 CCTTATTAAGGCGATGTGTGAAC 57.843 43.478 9.51 0.00 42.78 3.18
842 1019 1.580845 CGCAAAGCCTGAGGTCTTGG 61.581 60.000 13.97 10.08 0.00 3.61
936 1118 0.698238 CACCCCCAAGAACCTCATCA 59.302 55.000 0.00 0.00 0.00 3.07
944 1126 1.522580 GAACCTCATCAGCTCCGGC 60.523 63.158 0.00 0.00 39.06 6.13
946 1128 3.160047 CCTCATCAGCTCCGGCCT 61.160 66.667 0.00 0.00 39.73 5.19
948 1130 1.222936 CTCATCAGCTCCGGCCTTT 59.777 57.895 0.00 0.00 39.73 3.11
949 1131 0.465705 CTCATCAGCTCCGGCCTTTA 59.534 55.000 0.00 0.00 39.73 1.85
950 1132 0.908910 TCATCAGCTCCGGCCTTTAA 59.091 50.000 0.00 0.00 39.73 1.52
951 1133 1.490490 TCATCAGCTCCGGCCTTTAAT 59.510 47.619 0.00 0.00 39.73 1.40
953 1135 1.204146 TCAGCTCCGGCCTTTAATCT 58.796 50.000 0.00 0.00 39.73 2.40
956 1138 0.470341 GCTCCGGCCTTTAATCTCCT 59.530 55.000 0.00 0.00 0.00 3.69
957 1139 1.541452 GCTCCGGCCTTTAATCTCCTC 60.541 57.143 0.00 0.00 0.00 3.71
958 1140 2.043227 CTCCGGCCTTTAATCTCCTCT 58.957 52.381 0.00 0.00 0.00 3.69
961 1143 1.587547 GGCCTTTAATCTCCTCTGCG 58.412 55.000 0.00 0.00 0.00 5.18
987 1169 1.694169 AGGCATCGAATCCCCCACT 60.694 57.895 0.00 0.00 0.00 4.00
1076 1276 1.536073 GCCAAGAAGCCCAAACCTCC 61.536 60.000 0.00 0.00 0.00 4.30
1135 1335 2.035442 AAGAAGCCGAAGCCGAAGC 61.035 57.895 0.00 0.00 41.25 3.86
1136 1336 3.500642 GAAGCCGAAGCCGAAGCC 61.501 66.667 0.00 0.00 41.25 4.35
1141 1341 3.854459 CGAAGCCGAAGCCGAAGC 61.854 66.667 0.00 0.00 41.25 3.86
1142 1342 3.500642 GAAGCCGAAGCCGAAGCC 61.501 66.667 0.00 0.00 41.25 4.35
1147 1401 3.188786 CGAAGCCGAAGCCGAAGG 61.189 66.667 0.00 0.00 46.25 3.46
1212 1466 2.676463 GCAGAAGGAGAGCAACGAGATT 60.676 50.000 0.00 0.00 0.00 2.40
1237 1491 0.250513 GATCTTCGAGGCCACCAAGT 59.749 55.000 5.01 0.00 0.00 3.16
1238 1492 0.250513 ATCTTCGAGGCCACCAAGTC 59.749 55.000 5.01 0.00 0.00 3.01
1239 1493 1.376037 CTTCGAGGCCACCAAGTCC 60.376 63.158 5.01 0.00 0.00 3.85
1240 1494 3.234630 TTCGAGGCCACCAAGTCCG 62.235 63.158 5.01 0.00 0.00 4.79
1241 1495 3.691342 CGAGGCCACCAAGTCCGA 61.691 66.667 5.01 0.00 0.00 4.55
1242 1496 2.047179 GAGGCCACCAAGTCCGAC 60.047 66.667 5.01 0.00 0.00 4.79
1243 1497 2.847234 AGGCCACCAAGTCCGACA 60.847 61.111 5.01 0.00 0.00 4.35
1244 1498 2.112297 GGCCACCAAGTCCGACAA 59.888 61.111 0.00 0.00 0.00 3.18
1245 1499 1.966451 GGCCACCAAGTCCGACAAG 60.966 63.158 0.00 0.00 0.00 3.16
1275 1529 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1347 1610 3.260632 AGAAGAAGAGCAAGAAGGAGACC 59.739 47.826 0.00 0.00 0.00 3.85
1348 1611 2.614259 AGAAGAGCAAGAAGGAGACCA 58.386 47.619 0.00 0.00 0.00 4.02
1350 1613 2.317371 AGAGCAAGAAGGAGACCAGA 57.683 50.000 0.00 0.00 0.00 3.86
1353 1616 0.980423 GCAAGAAGGAGACCAGAGGT 59.020 55.000 0.00 0.00 39.44 3.85
1356 1619 3.198853 GCAAGAAGGAGACCAGAGGTAAT 59.801 47.826 0.00 0.00 35.25 1.89
1386 1649 1.064166 CCTGGCCAAGATGATGAGGTT 60.064 52.381 7.01 0.00 0.00 3.50
1431 1694 1.097547 CCAATGACGGGCTCACCATC 61.098 60.000 0.00 0.00 40.22 3.51
1464 1727 2.282462 CTCGGGTTTGGCAAGGCT 60.282 61.111 0.00 0.00 0.00 4.58
1516 1779 1.624865 CTGCGACTGCTGCTTCTGAC 61.625 60.000 0.00 0.00 43.34 3.51
1625 1888 0.640768 GTGCTTAGACGTGTGATCGC 59.359 55.000 0.00 0.00 0.00 4.58
1627 1890 0.917259 GCTTAGACGTGTGATCGCAG 59.083 55.000 9.75 6.68 0.00 5.18
1669 1944 8.940952 GTCAGTTTTACAAGAGCTCAAGATTAT 58.059 33.333 17.77 0.00 0.00 1.28
1670 1945 9.507329 TCAGTTTTACAAGAGCTCAAGATTATT 57.493 29.630 17.77 0.00 0.00 1.40
1721 1996 6.312426 CAGTTGGTTGTTTCAGCATTTTGTTA 59.688 34.615 0.00 0.00 0.00 2.41
1724 1999 6.634805 TGGTTGTTTCAGCATTTTGTTAAGA 58.365 32.000 0.00 0.00 0.00 2.10
1725 2000 7.099764 TGGTTGTTTCAGCATTTTGTTAAGAA 58.900 30.769 0.00 0.00 0.00 2.52
1726 2001 7.604164 TGGTTGTTTCAGCATTTTGTTAAGAAA 59.396 29.630 0.00 0.00 0.00 2.52
1766 3712 6.840780 AAAGTAAAATTCTGTCTGATGGGG 57.159 37.500 0.00 0.00 0.00 4.96
1927 3873 6.119536 ACAGAAACACCATTTAGTCAACTGA 58.880 36.000 0.00 0.00 0.00 3.41
1940 6149 7.540474 TTAGTCAACTGAAGTAGTGGATCTT 57.460 36.000 0.00 0.00 41.36 2.40
2023 6235 8.515414 GGAACTGTTGCAGAGTTTAATTCTTAT 58.485 33.333 12.91 0.00 33.71 1.73
2141 6791 3.536956 TTAGCCAAGGTAAGATGTCCG 57.463 47.619 0.00 0.00 0.00 4.79
2170 6820 3.146104 ACTATGGCTTGTTGAAGTGCT 57.854 42.857 0.00 0.00 0.00 4.40
2181 6831 6.840789 GCTTGTTGAAGTGCTTTTAAAAATCG 59.159 34.615 1.66 0.00 0.00 3.34
2219 6874 8.623903 TGGCTTGTTCTTATATAGCATTTCAAG 58.376 33.333 0.00 0.00 33.60 3.02
2280 6947 4.463186 GTGTATGGTCTGTAGTGAAGAGGT 59.537 45.833 0.00 0.00 0.00 3.85
2311 6978 7.440523 AGATCACCTTTTTCTGACATTGTAC 57.559 36.000 0.00 0.00 0.00 2.90
2312 6979 7.227156 AGATCACCTTTTTCTGACATTGTACT 58.773 34.615 0.00 0.00 0.00 2.73
2313 6980 8.375506 AGATCACCTTTTTCTGACATTGTACTA 58.624 33.333 0.00 0.00 0.00 1.82
2314 6981 7.962964 TCACCTTTTTCTGACATTGTACTAG 57.037 36.000 0.00 0.00 0.00 2.57
2315 6982 7.506114 TCACCTTTTTCTGACATTGTACTAGT 58.494 34.615 0.00 0.00 0.00 2.57
2316 6983 8.644216 TCACCTTTTTCTGACATTGTACTAGTA 58.356 33.333 0.00 0.00 0.00 1.82
2318 6985 7.597743 ACCTTTTTCTGACATTGTACTAGTACG 59.402 37.037 24.36 14.68 38.85 3.67
2319 6986 7.063074 CCTTTTTCTGACATTGTACTAGTACGG 59.937 40.741 24.36 18.86 38.85 4.02
2320 6987 6.579666 TTTCTGACATTGTACTAGTACGGT 57.420 37.500 24.36 21.39 38.85 4.83
2321 6988 6.579666 TTCTGACATTGTACTAGTACGGTT 57.420 37.500 24.36 11.36 38.85 4.44
2322 6989 5.946298 TCTGACATTGTACTAGTACGGTTG 58.054 41.667 24.36 21.78 38.85 3.77
2323 6990 5.474532 TCTGACATTGTACTAGTACGGTTGT 59.525 40.000 24.36 24.16 38.85 3.32
2324 6991 5.702865 TGACATTGTACTAGTACGGTTGTC 58.297 41.667 31.37 31.37 39.51 3.18
2335 7002 7.217200 ACTAGTACGGTTGTCGGTTAGATATA 58.783 38.462 0.00 0.00 44.45 0.86
2425 7100 4.000325 TGTGTTTCGATGGTAAGATGTGG 59.000 43.478 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 1.529438 CATACAACAAACGTGCCGAGT 59.471 47.619 0.00 0.00 0.00 4.18
31 33 0.727793 CCGGCATACAACAAACGTGC 60.728 55.000 0.00 0.00 35.17 5.34
34 36 1.136085 CACTCCGGCATACAACAAACG 60.136 52.381 0.00 0.00 0.00 3.60
54 56 2.206576 AGCCAAATCAGTCCAGGAAC 57.793 50.000 0.00 0.00 0.00 3.62
56 58 2.555227 GGAAAGCCAAATCAGTCCAGGA 60.555 50.000 0.00 0.00 0.00 3.86
59 61 2.517959 CAGGAAAGCCAAATCAGTCCA 58.482 47.619 0.00 0.00 36.29 4.02
75 77 1.734655 AGAGAAAGCAGTTCCCAGGA 58.265 50.000 0.00 0.00 36.86 3.86
76 78 2.575805 AAGAGAAAGCAGTTCCCAGG 57.424 50.000 0.00 0.00 36.86 4.45
88 90 6.166279 CCATACAGTGAACAGCTAAGAGAAA 58.834 40.000 0.00 0.00 0.00 2.52
116 136 9.350357 CTGAAGTATTTGAAATTTCATGTCAGG 57.650 33.333 21.10 8.86 37.00 3.86
123 143 9.630098 GAAGCATCTGAAGTATTTGAAATTTCA 57.370 29.630 16.91 16.91 34.92 2.69
136 156 5.475909 ACAATTCACATGAAGCATCTGAAGT 59.524 36.000 0.00 0.00 33.68 3.01
174 194 8.506168 AATTCGGCAAAGATTCATAAGAAGTA 57.494 30.769 0.00 0.00 37.14 2.24
210 230 3.959535 ATGCCGGTTTCACATTCAATT 57.040 38.095 1.90 0.00 0.00 2.32
211 231 3.959535 AATGCCGGTTTCACATTCAAT 57.040 38.095 1.90 0.00 27.91 2.57
228 248 3.009723 ACCATTCGTGCAGGAACTAATG 58.990 45.455 23.02 16.61 36.02 1.90
229 249 3.009723 CACCATTCGTGCAGGAACTAAT 58.990 45.455 23.02 5.60 33.15 1.73
230 250 2.037902 TCACCATTCGTGCAGGAACTAA 59.962 45.455 23.02 2.33 42.69 2.24
231 251 1.621317 TCACCATTCGTGCAGGAACTA 59.379 47.619 23.02 2.72 42.69 2.24
232 252 0.396435 TCACCATTCGTGCAGGAACT 59.604 50.000 23.02 10.41 42.69 3.01
233 253 1.453155 ATCACCATTCGTGCAGGAAC 58.547 50.000 23.02 0.00 42.69 3.62
234 254 3.205338 CATATCACCATTCGTGCAGGAA 58.795 45.455 22.83 22.83 42.69 3.36
235 255 2.485302 CCATATCACCATTCGTGCAGGA 60.485 50.000 4.68 4.68 42.69 3.86
242 262 2.613595 CCACACACCATATCACCATTCG 59.386 50.000 0.00 0.00 0.00 3.34
413 440 4.378774 TGCAACCAATTCAAAATGGACTG 58.621 39.130 3.87 2.56 39.12 3.51
441 468 1.318576 AAGGAAGGCAAAACTGTCCG 58.681 50.000 0.00 0.00 33.38 4.79
444 471 2.170397 CCCAAAAGGAAGGCAAAACTGT 59.830 45.455 0.00 0.00 38.24 3.55
447 474 1.765904 TCCCCAAAAGGAAGGCAAAAC 59.234 47.619 0.00 0.00 38.24 2.43
450 477 0.178935 CCTCCCCAAAAGGAAGGCAA 60.179 55.000 0.00 0.00 38.24 4.52
457 484 1.244019 CGTGCTTCCTCCCCAAAAGG 61.244 60.000 0.00 0.00 35.05 3.11
481 509 2.486951 GCCATGTGCATAGCTCAAAG 57.513 50.000 0.00 0.00 40.77 2.77
494 522 1.106351 TGTTCTTTGGCGTGCCATGT 61.106 50.000 15.40 0.00 46.64 3.21
497 525 2.829206 CGTGTTCTTTGGCGTGCCA 61.829 57.895 10.06 10.06 45.63 4.92
501 529 1.063469 CAAAGTCGTGTTCTTTGGCGT 59.937 47.619 9.61 0.00 44.33 5.68
505 533 2.450160 GTGCCAAAGTCGTGTTCTTTG 58.550 47.619 10.29 10.29 46.27 2.77
514 542 4.701956 ATATTTGAAGGTGCCAAAGTCG 57.298 40.909 0.00 0.00 37.00 4.18
553 581 7.957484 CGAAACCTAAACACATTCATACAGAAG 59.043 37.037 0.00 0.00 40.15 2.85
556 584 6.542852 CCGAAACCTAAACACATTCATACAG 58.457 40.000 0.00 0.00 0.00 2.74
597 730 0.824595 AAACAACGGGCCCTTACCAC 60.825 55.000 22.43 0.00 0.00 4.16
598 731 0.106116 AAAACAACGGGCCCTTACCA 60.106 50.000 22.43 0.00 0.00 3.25
599 732 1.042229 AAAAACAACGGGCCCTTACC 58.958 50.000 22.43 0.00 0.00 2.85
646 784 8.641499 TTTAATTTTCACCTGTTAGCAAAGTG 57.359 30.769 3.76 3.76 32.99 3.16
647 785 9.660180 TTTTTAATTTTCACCTGTTAGCAAAGT 57.340 25.926 0.00 0.00 0.00 2.66
699 854 7.669722 AGCCAGATTAATTTTCACCTCAACTAA 59.330 33.333 0.00 0.00 0.00 2.24
700 855 7.175104 AGCCAGATTAATTTTCACCTCAACTA 58.825 34.615 0.00 0.00 0.00 2.24
701 856 6.012745 AGCCAGATTAATTTTCACCTCAACT 58.987 36.000 0.00 0.00 0.00 3.16
703 858 6.071391 GGAAGCCAGATTAATTTTCACCTCAA 60.071 38.462 0.00 0.00 0.00 3.02
704 859 5.418840 GGAAGCCAGATTAATTTTCACCTCA 59.581 40.000 0.00 0.00 0.00 3.86
735 912 3.394719 GAAGCGAGATTAATGACCCCTC 58.605 50.000 0.00 0.00 0.00 4.30
785 962 0.753848 CCCAACCCAGGAACGTTGTT 60.754 55.000 5.00 0.00 38.12 2.83
786 963 1.152839 CCCAACCCAGGAACGTTGT 60.153 57.895 5.00 0.00 38.12 3.32
787 964 2.561037 GCCCAACCCAGGAACGTTG 61.561 63.158 5.00 0.00 39.25 4.10
821 998 0.603975 AAGACCTCAGGCTTTGCGTC 60.604 55.000 0.00 0.00 0.00 5.19
824 1001 0.538287 ACCAAGACCTCAGGCTTTGC 60.538 55.000 0.00 0.00 0.00 3.68
842 1019 1.337917 GGAAGAAGAAGGTGGGTCGAC 60.338 57.143 7.13 7.13 0.00 4.20
936 1118 0.470341 GGAGATTAAAGGCCGGAGCT 59.530 55.000 5.05 0.00 39.73 4.09
944 1126 1.587547 GCCGCAGAGGAGATTAAAGG 58.412 55.000 0.00 0.00 45.00 3.11
946 1128 0.179084 CCGCCGCAGAGGAGATTAAA 60.179 55.000 0.00 0.00 43.02 1.52
948 1130 3.129300 CCGCCGCAGAGGAGATTA 58.871 61.111 0.00 0.00 43.02 1.75
949 1131 4.537433 GCCGCCGCAGAGGAGATT 62.537 66.667 0.00 0.00 43.02 2.40
961 1143 4.838152 TTCGATGCCTCTGCCGCC 62.838 66.667 0.00 0.00 36.33 6.13
987 1169 1.213619 TGGCCATTGGAGGATGTGGA 61.214 55.000 0.00 0.00 33.53 4.02
1050 1232 1.143183 GGGCTTCTTGGCGTCGATA 59.857 57.895 0.00 0.00 42.84 2.92
1076 1276 2.506438 GCTCCTCGACGGGTTTCG 60.506 66.667 0.00 0.00 45.88 3.46
1113 1313 2.360475 GGCTTCGGCTTCTTGGCT 60.360 61.111 0.00 0.00 41.44 4.75
1135 1335 2.507110 TTCTGCTCCTTCGGCTTCGG 62.507 60.000 0.00 0.00 34.13 4.30
1136 1336 1.079819 TTCTGCTCCTTCGGCTTCG 60.080 57.895 0.00 0.00 0.00 3.79
1138 1338 1.194781 TCCTTCTGCTCCTTCGGCTT 61.195 55.000 0.00 0.00 0.00 4.35
1141 1341 1.519719 CCTCCTTCTGCTCCTTCGG 59.480 63.158 0.00 0.00 0.00 4.30
1142 1342 1.519719 CCCTCCTTCTGCTCCTTCG 59.480 63.158 0.00 0.00 0.00 3.79
1147 1401 1.077858 CCTTGCCCTCCTTCTGCTC 60.078 63.158 0.00 0.00 0.00 4.26
1158 1412 2.270527 GCAGAGACCTCCTTGCCC 59.729 66.667 1.20 0.00 0.00 5.36
1159 1413 2.129555 TTGGCAGAGACCTCCTTGCC 62.130 60.000 18.14 18.14 42.28 4.52
1237 1491 2.317609 GCTTGCGCTTCTTGTCGGA 61.318 57.895 9.73 0.00 0.00 4.55
1238 1492 2.174349 GCTTGCGCTTCTTGTCGG 59.826 61.111 9.73 0.00 0.00 4.79
1239 1493 1.154525 CAGCTTGCGCTTCTTGTCG 60.155 57.895 9.73 0.00 46.47 4.35
1240 1494 1.441682 GCAGCTTGCGCTTCTTGTC 60.442 57.895 9.73 0.00 46.47 3.18
1241 1495 2.641559 GCAGCTTGCGCTTCTTGT 59.358 55.556 9.73 0.00 46.47 3.16
1275 1529 1.916206 GCTTCTTGGACCCCTCCTCC 61.916 65.000 0.00 0.00 37.48 4.30
1318 1581 5.474578 TTCTTGCTCTTCTTCTTGCTAGA 57.525 39.130 0.00 0.00 36.04 2.43
1347 1610 0.179034 GCTCCCAGCCATTACCTCTG 60.179 60.000 0.00 0.00 34.48 3.35
1348 1611 2.225792 GCTCCCAGCCATTACCTCT 58.774 57.895 0.00 0.00 34.48 3.69
1368 1631 1.634973 TCAACCTCATCATCTTGGCCA 59.365 47.619 0.00 0.00 0.00 5.36
1374 1637 3.134442 GCTTCTCCTCAACCTCATCATCT 59.866 47.826 0.00 0.00 0.00 2.90
1431 1694 3.170810 GAGCTCGTCGGCGGAGTAG 62.171 68.421 10.62 0.00 38.89 2.57
1563 1826 3.490761 GCATTACAACAAACACCACTGCT 60.491 43.478 0.00 0.00 0.00 4.24
1735 3681 8.349983 TCAGACAGAATTTTACTTTAAACAGCC 58.650 33.333 0.00 0.00 0.00 4.85
1743 3689 5.716703 CCCCCATCAGACAGAATTTTACTTT 59.283 40.000 0.00 0.00 0.00 2.66
1766 3712 7.260603 CAATACCTCAACAAGATCAATTTCCC 58.739 38.462 0.00 0.00 0.00 3.97
1875 3821 6.662234 CCCCTGATCATCATGCTATAACAATT 59.338 38.462 0.00 0.00 0.00 2.32
1884 3830 1.698532 GTCTCCCCTGATCATCATGCT 59.301 52.381 0.00 0.00 0.00 3.79
1927 3873 7.554959 TTCTTAACCTCAAGATCCACTACTT 57.445 36.000 0.00 0.00 34.59 2.24
1940 6149 9.796120 CTTAACAAAACAACATTCTTAACCTCA 57.204 29.630 0.00 0.00 0.00 3.86
2023 6235 8.660435 AGATTAGCCTGCCTAACATATTTTCTA 58.340 33.333 0.00 0.00 38.77 2.10
2024 6236 7.521669 AGATTAGCCTGCCTAACATATTTTCT 58.478 34.615 0.00 0.00 38.77 2.52
2227 6882 7.176589 ACCTTTCTTAATAGACTGTCCTCAG 57.823 40.000 3.76 0.00 46.18 3.35
2229 6884 8.968969 TCTTACCTTTCTTAATAGACTGTCCTC 58.031 37.037 3.76 0.00 0.00 3.71
2280 6947 4.844085 TCAGAAAAAGGTGATCTAGGGTCA 59.156 41.667 0.00 0.00 0.00 4.02
2311 6978 4.889832 ATCTAACCGACAACCGTACTAG 57.110 45.455 0.00 0.00 36.31 2.57
2312 6979 8.506437 CAATATATCTAACCGACAACCGTACTA 58.494 37.037 0.00 0.00 36.31 1.82
2313 6980 7.013655 ACAATATATCTAACCGACAACCGTACT 59.986 37.037 0.00 0.00 36.31 2.73
2314 6981 7.141363 ACAATATATCTAACCGACAACCGTAC 58.859 38.462 0.00 0.00 36.31 3.67
2315 6982 7.275888 ACAATATATCTAACCGACAACCGTA 57.724 36.000 0.00 0.00 36.31 4.02
2316 6983 6.152932 ACAATATATCTAACCGACAACCGT 57.847 37.500 0.00 0.00 36.31 4.83
2425 7100 2.185387 TCCCTACCTGCCACTAAGTTC 58.815 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.