Multiple sequence alignment - TraesCS1B01G425500

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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 TraesCS1B01G425500 chr1B 100.000 2411 0 0 1 2411 651288151 651285741 0.000000e+00 4453
1 TraesCS1B01G425500 chr1B 83.524 613 54 27 996 1563 649670179 649670789 1.640000e-146 529
2 TraesCS1B01G425500 chr1D 84.354 1470 103 48 4 1416 469816277 469814878 0.000000e+00 1323
3 TraesCS1B01G425500 chr1D 89.327 609 36 14 1447 2034 469814877 469814277 0.000000e+00 737
4 TraesCS1B01G425500 chr1D 89.189 444 21 11 996 1412 469795522 469795965 1.640000e-146 529
5 TraesCS1B01G425500 chr1D 91.884 345 15 4 2068 2411 469814191 469813859 1.010000e-128 470
6 TraesCS1B01G425500 chr1A 83.488 1187 120 53 589 1745 562923867 562922727 0.000000e+00 1037
7 TraesCS1B01G425500 chr1A 86.167 600 54 20 1771 2360 562922729 562922149 2.630000e-174 621
8 TraesCS1B01G425500 chr1A 88.488 443 24 9 996 1411 562902457 562902899 5.950000e-141 510
9 TraesCS1B01G425500 chr7D 84.810 474 43 16 1106 1563 561875551 561876011 1.310000e-122 449
10 TraesCS1B01G425500 chr7B 85.809 451 30 11 996 1412 722094317 722094767 4.730000e-122 448
11 TraesCS1B01G425500 chr7B 85.646 209 20 7 4 207 601118626 601118423 6.750000e-51 211
12 TraesCS1B01G425500 chr3B 84.479 451 35 18 996 1412 379653682 379654131 1.720000e-111 412
13 TraesCS1B01G425500 chr5B 84.375 448 36 16 996 1409 328273751 328274198 2.230000e-110 409
14 TraesCS1B01G425500 chr6D 84.035 451 38 17 996 1412 17043024 17042574 1.040000e-108 403
15 TraesCS1B01G425500 chr6B 88.344 326 22 9 1102 1414 578774738 578775060 6.290000e-101 377


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 TraesCS1B01G425500 chr1B 651285741 651288151 2410 True 4453.000000 4453 100.000000 1 2411 1 chr1B.!!$R1 2410
1 TraesCS1B01G425500 chr1B 649670179 649670789 610 False 529.000000 529 83.524000 996 1563 1 chr1B.!!$F1 567
2 TraesCS1B01G425500 chr1D 469813859 469816277 2418 True 843.333333 1323 88.521667 4 2411 3 chr1D.!!$R1 2407
3 TraesCS1B01G425500 chr1A 562922149 562923867 1718 True 829.000000 1037 84.827500 589 2360 2 chr1A.!!$R1 1771

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
123 127 0.515564 CGGGGTTTGATCACGTTGAC 59.484 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2190 0.030773 CAAGAGCGCGTGATAGGCTA 59.969 55.0 8.43 0.0 37.1 3.93 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
57 61 8.671384 TTTATATATTTGGTCCTTCAAGTCCG 57.329 34.615 0.00 0.00 0.00 4.79
62 66 2.567985 TGGTCCTTCAAGTCCGAAAAC 58.432 47.619 0.00 0.00 0.00 2.43
63 67 1.878088 GGTCCTTCAAGTCCGAAAACC 59.122 52.381 0.00 0.00 0.00 3.27
105 109 1.531149 AGATTTTGAGCACGTTGACCG 59.469 47.619 0.00 0.00 44.03 4.79
114 118 0.887387 CACGTTGACCGGGGTTTGAT 60.887 55.000 6.32 0.00 42.24 2.57
116 120 0.604243 CGTTGACCGGGGTTTGATCA 60.604 55.000 6.32 0.00 0.00 2.92
117 121 0.879090 GTTGACCGGGGTTTGATCAC 59.121 55.000 6.32 0.00 0.00 3.06
118 122 0.604243 TTGACCGGGGTTTGATCACG 60.604 55.000 6.32 0.00 0.00 4.35
119 123 1.004200 GACCGGGGTTTGATCACGT 60.004 57.895 6.32 0.00 0.00 4.49
120 124 0.604511 GACCGGGGTTTGATCACGTT 60.605 55.000 6.32 0.00 0.00 3.99
121 125 0.887387 ACCGGGGTTTGATCACGTTG 60.887 55.000 6.32 0.00 0.00 4.10
122 126 0.604243 CCGGGGTTTGATCACGTTGA 60.604 55.000 0.00 0.00 0.00 3.18
123 127 0.515564 CGGGGTTTGATCACGTTGAC 59.484 55.000 0.00 0.00 0.00 3.18
124 128 0.879090 GGGGTTTGATCACGTTGACC 59.121 55.000 0.00 0.00 0.00 4.02
125 129 1.600023 GGGTTTGATCACGTTGACCA 58.400 50.000 0.00 0.00 0.00 4.02
126 130 1.535462 GGGTTTGATCACGTTGACCAG 59.465 52.381 0.00 0.00 0.00 4.00
127 131 2.218603 GGTTTGATCACGTTGACCAGT 58.781 47.619 0.00 0.00 0.00 4.00
128 132 2.616842 GGTTTGATCACGTTGACCAGTT 59.383 45.455 0.00 0.00 0.00 3.16
129 133 3.066203 GGTTTGATCACGTTGACCAGTTT 59.934 43.478 0.00 0.00 0.00 2.66
130 134 4.439563 GGTTTGATCACGTTGACCAGTTTT 60.440 41.667 0.00 0.00 0.00 2.43
131 135 3.961477 TGATCACGTTGACCAGTTTTG 57.039 42.857 0.00 0.00 0.00 2.44
132 136 3.536570 TGATCACGTTGACCAGTTTTGA 58.463 40.909 0.00 0.00 0.00 2.69
133 137 3.311322 TGATCACGTTGACCAGTTTTGAC 59.689 43.478 0.00 0.00 0.00 3.18
134 138 2.980568 TCACGTTGACCAGTTTTGACT 58.019 42.857 0.00 0.00 0.00 3.41
141 145 5.277974 CGTTGACCAGTTTTGACTGATGAAT 60.278 40.000 8.06 0.00 39.99 2.57
147 151 8.918202 ACCAGTTTTGACTGATGAATAGTAAA 57.082 30.769 8.06 0.00 39.99 2.01
207 215 3.883830 TTGTGACAACCAACATGCTTT 57.116 38.095 0.00 0.00 0.00 3.51
229 237 0.670706 TGCGCTTGGTGCATGTAAAA 59.329 45.000 9.73 0.00 44.36 1.52
254 262 8.746052 ATTTTGTGGTCAAATAATATCCGAGA 57.254 30.769 0.00 0.00 42.14 4.04
255 263 7.786178 TTTGTGGTCAAATAATATCCGAGAG 57.214 36.000 0.00 0.00 38.44 3.20
256 264 6.479972 TGTGGTCAAATAATATCCGAGAGT 57.520 37.500 0.00 0.00 0.00 3.24
257 265 6.884832 TGTGGTCAAATAATATCCGAGAGTT 58.115 36.000 0.00 0.00 0.00 3.01
258 266 6.761242 TGTGGTCAAATAATATCCGAGAGTTG 59.239 38.462 0.00 0.00 0.00 3.16
259 267 6.761714 GTGGTCAAATAATATCCGAGAGTTGT 59.238 38.462 0.00 0.00 0.00 3.32
260 268 7.924412 GTGGTCAAATAATATCCGAGAGTTGTA 59.076 37.037 0.00 0.00 0.00 2.41
261 269 8.141909 TGGTCAAATAATATCCGAGAGTTGTAG 58.858 37.037 0.00 0.00 0.00 2.74
262 270 8.142551 GGTCAAATAATATCCGAGAGTTGTAGT 58.857 37.037 0.00 0.00 0.00 2.73
355 367 1.065199 TCAGGCACCAAAGCATCTAGG 60.065 52.381 0.00 0.00 35.83 3.02
373 385 7.601856 CATCTAGGTTGCCACAAAATTTTAGA 58.398 34.615 2.44 0.00 0.00 2.10
424 436 3.146104 CTGTTCACCAGTCAAATCCCT 57.854 47.619 0.00 0.00 36.37 4.20
432 444 3.434309 CCAGTCAAATCCCTGGTCAAAT 58.566 45.455 0.00 0.00 42.72 2.32
466 478 2.159517 GGTCAGCGTGCTTAAAATCTGG 60.160 50.000 0.00 0.00 0.00 3.86
472 484 4.048504 GCGTGCTTAAAATCTGGTTTTGT 58.951 39.130 8.84 0.00 40.17 2.83
490 502 7.143340 GGTTTTGTACCAAACTTATCCAGTTC 58.857 38.462 18.79 0.00 43.58 3.01
498 510 6.833933 ACCAAACTTATCCAGTTCTGAAACTT 59.166 34.615 1.00 0.00 45.77 2.66
499 511 7.996644 ACCAAACTTATCCAGTTCTGAAACTTA 59.003 33.333 1.00 0.00 45.77 2.24
509 521 6.238759 CCAGTTCTGAAACTTAAAGGACCAAG 60.239 42.308 1.00 0.00 43.28 3.61
510 522 6.318900 CAGTTCTGAAACTTAAAGGACCAAGT 59.681 38.462 0.00 0.00 43.28 3.16
526 538 5.944007 GGACCAAGTGTGTATACCAAAAGAT 59.056 40.000 0.00 0.00 0.00 2.40
527 539 6.433093 GGACCAAGTGTGTATACCAAAAGATT 59.567 38.462 0.00 0.00 0.00 2.40
528 540 7.039993 GGACCAAGTGTGTATACCAAAAGATTT 60.040 37.037 0.00 0.00 0.00 2.17
529 541 8.245195 ACCAAGTGTGTATACCAAAAGATTTT 57.755 30.769 0.00 0.00 0.00 1.82
530 542 8.141268 ACCAAGTGTGTATACCAAAAGATTTTG 58.859 33.333 10.43 10.43 45.34 2.44
582 594 9.679661 AATTGAAGGGACAAAAACATAGTTTTT 57.320 25.926 13.18 13.18 33.44 1.94
617 629 6.924111 TGAAGCAACCTGATCCTAAATTTTC 58.076 36.000 0.00 0.00 0.00 2.29
618 630 5.567138 AGCAACCTGATCCTAAATTTTCG 57.433 39.130 0.00 0.00 0.00 3.46
619 631 5.253330 AGCAACCTGATCCTAAATTTTCGA 58.747 37.500 0.00 0.00 0.00 3.71
621 633 5.676331 GCAACCTGATCCTAAATTTTCGACC 60.676 44.000 0.00 0.00 0.00 4.79
622 634 5.174037 ACCTGATCCTAAATTTTCGACCA 57.826 39.130 0.00 0.00 0.00 4.02
623 635 4.941873 ACCTGATCCTAAATTTTCGACCAC 59.058 41.667 0.00 0.00 0.00 4.16
697 712 4.715523 CCACCCCGGCAATCGTGT 62.716 66.667 0.00 0.00 37.11 4.49
712 727 2.603473 TGTCCTGCCACGTAGCCT 60.603 61.111 2.86 0.00 0.00 4.58
805 820 0.884259 TGCACACAATCACACGGAGG 60.884 55.000 0.00 0.00 0.00 4.30
835 851 3.823330 GGTCGCCGTCGTCCTCAT 61.823 66.667 0.00 0.00 40.07 2.90
893 939 4.083862 GTGACGCCACCCCTCTCC 62.084 72.222 0.00 0.00 37.33 3.71
894 940 4.316823 TGACGCCACCCCTCTCCT 62.317 66.667 0.00 0.00 0.00 3.69
895 941 3.462678 GACGCCACCCCTCTCCTC 61.463 72.222 0.00 0.00 0.00 3.71
898 944 4.779733 GCCACCCCTCTCCTCCGA 62.780 72.222 0.00 0.00 0.00 4.55
899 945 2.283809 CCACCCCTCTCCTCCGAT 59.716 66.667 0.00 0.00 0.00 4.18
900 946 2.136878 CCACCCCTCTCCTCCGATG 61.137 68.421 0.00 0.00 0.00 3.84
901 947 1.075970 CACCCCTCTCCTCCGATGA 60.076 63.158 0.00 0.00 0.00 2.92
902 948 1.112315 CACCCCTCTCCTCCGATGAG 61.112 65.000 0.00 0.00 38.42 2.90
903 949 2.206536 CCCCTCTCCTCCGATGAGC 61.207 68.421 0.00 0.00 37.29 4.26
904 950 1.152567 CCCTCTCCTCCGATGAGCT 60.153 63.158 0.00 0.00 37.29 4.09
905 951 1.178534 CCCTCTCCTCCGATGAGCTC 61.179 65.000 6.82 6.82 37.29 4.09
910 956 0.753479 TCCTCCGATGAGCTCACCTC 60.753 60.000 20.97 13.06 41.15 3.85
955 1006 4.619227 CCCGTTGCCCGTCACACT 62.619 66.667 0.00 0.00 33.66 3.55
969 1036 2.203001 CACTCACACCACGGCACA 60.203 61.111 0.00 0.00 0.00 4.57
1196 1278 2.357517 CCTCAGCCACGTGGTGAC 60.358 66.667 33.92 18.73 46.14 3.67
1418 1512 2.607526 CGCTCTGGCTCTGAGACATATG 60.608 54.545 14.71 8.27 29.32 1.78
1419 1513 2.364970 GCTCTGGCTCTGAGACATATGT 59.635 50.000 14.71 8.43 29.32 2.29
1420 1514 3.571828 GCTCTGGCTCTGAGACATATGTA 59.428 47.826 14.71 0.00 29.32 2.29
1421 1515 4.220382 GCTCTGGCTCTGAGACATATGTAT 59.780 45.833 14.71 5.28 29.32 2.29
1422 1516 5.417266 GCTCTGGCTCTGAGACATATGTATA 59.583 44.000 14.71 0.00 29.32 1.47
1424 1518 5.412904 TCTGGCTCTGAGACATATGTATACG 59.587 44.000 14.71 0.00 29.32 3.06
1425 1519 5.070685 TGGCTCTGAGACATATGTATACGT 58.929 41.667 9.67 2.56 0.00 3.57
1427 1521 6.371825 TGGCTCTGAGACATATGTATACGTAG 59.628 42.308 9.67 4.05 0.00 3.51
1428 1522 6.594547 GGCTCTGAGACATATGTATACGTAGA 59.405 42.308 8.71 7.10 0.00 2.59
1430 1524 7.578169 TCTGAGACATATGTATACGTAGACG 57.422 40.000 15.04 0.00 46.33 4.18
1466 1588 6.996509 ACCGTTTGATTAGGAGTTAGTACAA 58.003 36.000 0.00 0.00 0.00 2.41
1504 1626 9.640952 TTCTCCTTCTTTTCATTTCTCCTTTTA 57.359 29.630 0.00 0.00 0.00 1.52
1529 1651 5.417894 ACTCGTGAGGTCATGTGAATTACTA 59.582 40.000 7.98 0.00 34.59 1.82
1570 1695 6.899089 TCTTGCTTGGGATCAATCAGTAATA 58.101 36.000 0.00 0.00 31.72 0.98
1577 1711 6.233434 TGGGATCAATCAGTAATAGTGATGC 58.767 40.000 11.01 0.00 38.23 3.91
1580 1714 8.263640 GGGATCAATCAGTAATAGTGATGCTAT 58.736 37.037 11.01 5.79 38.23 2.97
1636 1787 2.928116 GACCACACGCCTGTAAATAGAC 59.072 50.000 0.00 0.00 0.00 2.59
1649 1800 5.902681 TGTAAATAGACCGATGAGTGAAGG 58.097 41.667 0.00 0.00 0.00 3.46
1686 1837 7.435488 GTACTGGAGTATTTAGCACTGTATGTG 59.565 40.741 0.00 0.00 39.96 3.21
1707 1858 4.002982 TGAATGATGTTCGTTCCCTTCTG 58.997 43.478 6.93 0.00 40.69 3.02
1708 1859 3.703001 ATGATGTTCGTTCCCTTCTGT 57.297 42.857 0.00 0.00 0.00 3.41
1709 1860 4.819105 ATGATGTTCGTTCCCTTCTGTA 57.181 40.909 0.00 0.00 0.00 2.74
1710 1861 3.921677 TGATGTTCGTTCCCTTCTGTAC 58.078 45.455 0.00 0.00 0.00 2.90
1715 1866 2.783135 TCGTTCCCTTCTGTACGTACT 58.217 47.619 25.12 0.00 35.63 2.73
1813 1968 4.577283 TGTGTCGGATATTCTGATCGTGTA 59.423 41.667 0.00 0.00 33.80 2.90
1879 2034 8.456471 TCTCTTCTGTTTAATTAATCGACGAGA 58.544 33.333 19.19 19.19 0.00 4.04
1906 2062 9.759259 CAAATCTCTTTCCTTTGTTTTGAAAAC 57.241 29.630 13.55 13.55 0.00 2.43
1916 2072 7.067008 TCCTTTGTTTTGAAAACACAAAAACCA 59.933 29.630 21.77 3.44 46.43 3.67
1929 2085 6.638610 ACACAAAAACCAAGTTCATCATGAA 58.361 32.000 0.00 0.00 33.32 2.57
1932 2088 8.117988 CACAAAAACCAAGTTCATCATGAAAAG 58.882 33.333 0.29 0.00 38.22 2.27
1962 2118 5.341617 CCAGGCAAAGTAAACGTTTAACAA 58.658 37.500 21.67 0.00 0.00 2.83
1966 2122 5.684184 GGCAAAGTAAACGTTTAACAAGGAG 59.316 40.000 21.67 9.70 0.00 3.69
1995 2151 3.067180 CAGCATCACCACTGTCTGTTTTT 59.933 43.478 0.00 0.00 0.00 1.94
2002 2158 2.561569 CACTGTCTGTTTTTCCGAGGT 58.438 47.619 0.00 0.00 0.00 3.85
2008 2164 5.916318 TGTCTGTTTTTCCGAGGTACTAAA 58.084 37.500 0.00 0.00 41.55 1.85
2038 2194 1.580437 GAGACGCCGACCTATAGCC 59.420 63.158 0.00 0.00 0.00 3.93
2040 2196 0.399454 AGACGCCGACCTATAGCCTA 59.601 55.000 0.00 0.00 0.00 3.93
2041 2197 1.004511 AGACGCCGACCTATAGCCTAT 59.995 52.381 0.00 0.00 0.00 2.57
2042 2198 1.401199 GACGCCGACCTATAGCCTATC 59.599 57.143 0.00 0.00 0.00 2.08
2043 2199 1.271762 ACGCCGACCTATAGCCTATCA 60.272 52.381 0.00 0.00 0.00 2.15
2044 2200 1.132643 CGCCGACCTATAGCCTATCAC 59.867 57.143 0.00 0.00 0.00 3.06
2066 2238 2.031012 TCTTGAGGGCACTGCGTG 59.969 61.111 0.00 4.61 36.51 5.34
2160 2369 2.686405 TGCTCAAATGCCATTCAGCTAG 59.314 45.455 17.56 0.00 32.24 3.42
2165 2374 6.343716 TCAAATGCCATTCAGCTAGAAAAA 57.656 33.333 0.00 0.00 40.22 1.94
2166 2375 6.938507 TCAAATGCCATTCAGCTAGAAAAAT 58.061 32.000 0.00 0.00 40.22 1.82
2199 2408 0.510359 GAACGTCAAGCTCAGCACAG 59.490 55.000 0.00 0.00 0.00 3.66
2257 2466 6.750963 CCGAGTCTTGTCTTAAACATAGGTAC 59.249 42.308 0.00 0.00 37.82 3.34
2258 2467 7.362747 CCGAGTCTTGTCTTAAACATAGGTACT 60.363 40.741 0.00 0.00 37.82 2.73
2259 2468 7.697291 CGAGTCTTGTCTTAAACATAGGTACTC 59.303 40.741 0.00 0.00 37.82 2.59
2260 2469 8.418597 AGTCTTGTCTTAAACATAGGTACTCA 57.581 34.615 0.00 0.00 37.82 3.41
2272 2481 6.957631 ACATAGGTACTCATGACAAATGGAA 58.042 36.000 12.33 0.00 41.75 3.53
2278 2487 4.978099 ACTCATGACAAATGGAAGTCTGT 58.022 39.130 0.00 0.00 35.81 3.41
2292 2501 5.877012 TGGAAGTCTGTTCAAAGCATAGATC 59.123 40.000 0.00 0.00 0.00 2.75
2293 2502 5.006165 GGAAGTCTGTTCAAAGCATAGATCG 59.994 44.000 0.00 0.00 0.00 3.69
2294 2503 5.330455 AGTCTGTTCAAAGCATAGATCGA 57.670 39.130 0.00 0.00 0.00 3.59
2295 2504 5.911752 AGTCTGTTCAAAGCATAGATCGAT 58.088 37.500 0.00 0.00 0.00 3.59
2314 2523 4.213270 TCGATGCGTCAAATGAAAGAAACT 59.787 37.500 6.75 0.00 0.00 2.66
2364 2573 1.205657 GCTTCGCGTTCCGATAATGA 58.794 50.000 5.77 0.00 46.81 2.57
2365 2574 1.591158 GCTTCGCGTTCCGATAATGAA 59.409 47.619 5.77 0.00 46.81 2.57
2366 2575 2.221055 GCTTCGCGTTCCGATAATGAAT 59.779 45.455 5.77 0.00 46.81 2.57
2367 2576 3.787826 CTTCGCGTTCCGATAATGAATG 58.212 45.455 5.77 0.00 46.81 2.67
2394 2603 1.339727 CCACCTTTTCTTCTACCGGGG 60.340 57.143 6.32 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.271391 TGAGGGACCAAGTCTATACTTTTCAA 59.729 38.462 0.00 0.00 43.60 2.69
1 2 5.783360 TGAGGGACCAAGTCTATACTTTTCA 59.217 40.000 0.00 0.00 43.60 2.69
2 3 6.295719 TGAGGGACCAAGTCTATACTTTTC 57.704 41.667 0.00 0.00 43.60 2.29
56 60 2.475022 GCCGAAACTTATCCGGTTTTCG 60.475 50.000 20.39 20.39 44.63 3.46
57 61 2.159476 GGCCGAAACTTATCCGGTTTTC 60.159 50.000 0.00 3.54 44.63 2.29
62 66 1.455248 TTTGGCCGAAACTTATCCGG 58.545 50.000 1.75 0.00 45.51 5.14
63 67 3.127895 TGAATTTGGCCGAAACTTATCCG 59.872 43.478 10.16 0.00 0.00 4.18
74 78 2.925563 GCTCAAAATCTGAATTTGGCCG 59.074 45.455 15.95 7.98 38.12 6.13
76 80 3.365820 CGTGCTCAAAATCTGAATTTGGC 59.634 43.478 15.95 16.76 38.12 4.52
105 109 0.879090 GGTCAACGTGATCAAACCCC 59.121 55.000 0.00 0.00 0.00 4.95
114 118 2.980568 AGTCAAAACTGGTCAACGTGA 58.019 42.857 0.00 0.00 33.32 4.35
116 120 3.312421 CATCAGTCAAAACTGGTCAACGT 59.688 43.478 5.78 0.00 43.59 3.99
117 121 3.559655 TCATCAGTCAAAACTGGTCAACG 59.440 43.478 5.78 0.00 43.59 4.10
118 122 5.499139 TTCATCAGTCAAAACTGGTCAAC 57.501 39.130 5.78 0.00 43.59 3.18
119 123 6.998074 ACTATTCATCAGTCAAAACTGGTCAA 59.002 34.615 5.78 0.00 43.59 3.18
120 124 6.533730 ACTATTCATCAGTCAAAACTGGTCA 58.466 36.000 5.78 0.00 43.59 4.02
121 125 8.547967 TTACTATTCATCAGTCAAAACTGGTC 57.452 34.615 5.78 0.00 43.59 4.02
178 186 8.934825 GCATGTTGGTTGTCACAAAATTTATAT 58.065 29.630 0.00 0.00 0.00 0.86
180 188 6.991531 AGCATGTTGGTTGTCACAAAATTTAT 59.008 30.769 0.00 0.00 0.00 1.40
181 189 6.344500 AGCATGTTGGTTGTCACAAAATTTA 58.656 32.000 0.00 0.00 0.00 1.40
183 191 4.768583 AGCATGTTGGTTGTCACAAAATT 58.231 34.783 0.00 0.00 0.00 1.82
184 192 4.405116 AGCATGTTGGTTGTCACAAAAT 57.595 36.364 0.00 0.00 0.00 1.82
229 237 8.746052 TCTCGGATATTATTTGACCACAAAAT 57.254 30.769 0.00 0.00 46.77 1.82
292 302 2.427506 GAGGATCTCGTGGCAAAAAGT 58.572 47.619 0.00 0.00 0.00 2.66
416 428 2.899256 ACCACATTTGACCAGGGATTTG 59.101 45.455 0.00 0.00 0.00 2.32
424 436 2.035632 GGGTTTGACCACATTTGACCA 58.964 47.619 0.00 0.00 41.02 4.02
432 444 1.147376 CTGACCGGGTTTGACCACA 59.853 57.895 6.32 0.00 41.02 4.17
487 499 6.095021 ACACTTGGTCCTTTAAGTTTCAGAAC 59.905 38.462 0.00 0.00 35.08 3.01
490 502 5.357032 ACACACTTGGTCCTTTAAGTTTCAG 59.643 40.000 0.00 0.00 35.08 3.02
498 510 6.436738 TTGGTATACACACTTGGTCCTTTA 57.563 37.500 5.01 0.00 0.00 1.85
499 511 4.986054 TGGTATACACACTTGGTCCTTT 57.014 40.909 5.01 0.00 0.00 3.11
509 521 7.175990 TCCCTCAAAATCTTTTGGTATACACAC 59.824 37.037 13.77 0.00 45.68 3.82
510 522 7.175990 GTCCCTCAAAATCTTTTGGTATACACA 59.824 37.037 13.77 0.00 45.68 3.72
526 538 3.589735 TGTATAGGCTTGGTCCCTCAAAA 59.410 43.478 0.00 0.00 33.88 2.44
527 539 3.186283 TGTATAGGCTTGGTCCCTCAAA 58.814 45.455 0.00 0.00 33.88 2.69
528 540 2.840511 TGTATAGGCTTGGTCCCTCAA 58.159 47.619 0.00 0.00 33.88 3.02
529 541 2.561209 TGTATAGGCTTGGTCCCTCA 57.439 50.000 0.00 0.00 33.88 3.86
530 542 4.439253 AAATGTATAGGCTTGGTCCCTC 57.561 45.455 0.00 0.00 33.88 4.30
531 543 4.881157 AAAATGTATAGGCTTGGTCCCT 57.119 40.909 0.00 0.00 36.47 4.20
532 544 5.070685 CCTAAAATGTATAGGCTTGGTCCC 58.929 45.833 0.00 0.00 33.96 4.46
533 545 5.937111 TCCTAAAATGTATAGGCTTGGTCC 58.063 41.667 0.00 0.00 39.86 4.46
534 546 8.352942 CAATTCCTAAAATGTATAGGCTTGGTC 58.647 37.037 0.00 0.00 39.86 4.02
535 547 8.058847 TCAATTCCTAAAATGTATAGGCTTGGT 58.941 33.333 0.00 0.00 39.86 3.67
536 548 8.463930 TCAATTCCTAAAATGTATAGGCTTGG 57.536 34.615 0.00 0.00 39.86 3.61
537 549 9.956720 CTTCAATTCCTAAAATGTATAGGCTTG 57.043 33.333 0.00 0.00 39.86 4.01
538 550 9.136323 CCTTCAATTCCTAAAATGTATAGGCTT 57.864 33.333 0.00 0.00 39.86 4.35
582 594 3.381272 CAGGTTGCTTCAGTTTTCCAGAA 59.619 43.478 0.00 0.00 0.00 3.02
584 596 2.951642 TCAGGTTGCTTCAGTTTTCCAG 59.048 45.455 0.00 0.00 0.00 3.86
585 597 3.011566 TCAGGTTGCTTCAGTTTTCCA 57.988 42.857 0.00 0.00 0.00 3.53
586 598 3.057245 GGATCAGGTTGCTTCAGTTTTCC 60.057 47.826 0.00 0.00 0.00 3.13
587 599 3.823304 AGGATCAGGTTGCTTCAGTTTTC 59.177 43.478 0.00 0.00 0.00 2.29
592 604 6.521151 AAATTTAGGATCAGGTTGCTTCAG 57.479 37.500 0.00 0.00 0.00 3.02
697 712 3.449227 CGAGGCTACGTGGCAGGA 61.449 66.667 25.79 0.00 44.55 3.86
862 908 1.153823 GTCACCCGACGACCATCAG 60.154 63.158 0.00 0.00 31.07 2.90
863 909 2.967397 GTCACCCGACGACCATCA 59.033 61.111 0.00 0.00 31.07 3.07
889 935 0.753479 GGTGAGCTCATCGGAGGAGA 60.753 60.000 21.47 0.00 41.67 3.71
890 936 0.754957 AGGTGAGCTCATCGGAGGAG 60.755 60.000 21.47 14.94 41.67 3.69
891 937 0.753479 GAGGTGAGCTCATCGGAGGA 60.753 60.000 21.47 0.00 41.67 3.71
892 938 1.739049 GAGGTGAGCTCATCGGAGG 59.261 63.158 21.47 0.00 41.67 4.30
893 939 1.739049 GGAGGTGAGCTCATCGGAG 59.261 63.158 21.47 0.00 44.33 4.63
894 940 1.758514 GGGAGGTGAGCTCATCGGA 60.759 63.158 21.47 0.00 30.81 4.55
895 941 1.743321 GAGGGAGGTGAGCTCATCGG 61.743 65.000 21.47 0.00 30.81 4.18
896 942 1.739049 GAGGGAGGTGAGCTCATCG 59.261 63.158 21.47 0.00 30.81 3.84
897 943 1.406860 GGGAGGGAGGTGAGCTCATC 61.407 65.000 21.47 20.60 0.00 2.92
898 944 1.383803 GGGAGGGAGGTGAGCTCAT 60.384 63.158 21.47 4.21 0.00 2.90
899 945 2.039624 GGGAGGGAGGTGAGCTCA 59.960 66.667 13.74 13.74 0.00 4.26
900 946 0.912006 AAAGGGAGGGAGGTGAGCTC 60.912 60.000 6.82 6.82 0.00 4.09
901 947 0.476611 AAAAGGGAGGGAGGTGAGCT 60.477 55.000 0.00 0.00 0.00 4.09
902 948 1.286248 TAAAAGGGAGGGAGGTGAGC 58.714 55.000 0.00 0.00 0.00 4.26
903 949 4.660771 ACATATAAAAGGGAGGGAGGTGAG 59.339 45.833 0.00 0.00 0.00 3.51
904 950 4.641868 ACATATAAAAGGGAGGGAGGTGA 58.358 43.478 0.00 0.00 0.00 4.02
905 951 4.202472 GGACATATAAAAGGGAGGGAGGTG 60.202 50.000 0.00 0.00 0.00 4.00
910 956 3.498661 GGCTGGACATATAAAAGGGAGGG 60.499 52.174 0.00 0.00 0.00 4.30
946 997 1.949133 CGTGGTGTGAGTGTGACGG 60.949 63.158 0.00 0.00 0.00 4.79
955 1006 2.892914 CGTTGTGCCGTGGTGTGA 60.893 61.111 0.00 0.00 0.00 3.58
969 1036 3.398920 CTGATCAATCGGCGCGTT 58.601 55.556 8.43 0.00 0.00 4.84
1052 1119 3.764466 CCTCGGCAGGCTCGAACT 61.764 66.667 0.00 0.00 36.15 3.01
1438 1560 6.996509 ACTAACTCCTAATCAAACGGTTGTA 58.003 36.000 13.90 0.06 36.07 2.41
1466 1588 6.943899 AAAGAAGGAGAAGAGATTACTGGT 57.056 37.500 0.00 0.00 0.00 4.00
1504 1626 3.685139 ATTCACATGACCTCACGAGTT 57.315 42.857 0.00 0.00 0.00 3.01
1529 1651 0.039035 AGAGAGGAAGGTCGAGCAGT 59.961 55.000 18.15 3.71 0.00 4.40
1570 1695 9.700831 AAGAATTTAAACCCTAATAGCATCACT 57.299 29.630 0.00 0.00 0.00 3.41
1591 1740 9.665264 GTCGAAACTGAATTGACTTAAAAGAAT 57.335 29.630 0.00 0.00 0.00 2.40
1593 1742 7.281324 TGGTCGAAACTGAATTGACTTAAAAGA 59.719 33.333 0.00 0.00 0.00 2.52
1594 1743 7.376072 GTGGTCGAAACTGAATTGACTTAAAAG 59.624 37.037 0.00 0.00 0.00 2.27
1603 1752 2.903678 CGTGTGGTCGAAACTGAATTG 58.096 47.619 0.00 0.00 0.00 2.32
1608 1757 1.594293 AGGCGTGTGGTCGAAACTG 60.594 57.895 0.00 0.00 0.00 3.16
1636 1787 4.580995 AGTACATCTACCTTCACTCATCGG 59.419 45.833 0.00 0.00 0.00 4.18
1686 1837 4.003648 ACAGAAGGGAACGAACATCATTC 58.996 43.478 0.00 0.00 0.00 2.67
1707 1858 2.563471 AAGCTAGCTGCAGTACGTAC 57.437 50.000 20.16 18.10 45.94 3.67
1708 1859 2.876091 CAAAGCTAGCTGCAGTACGTA 58.124 47.619 20.16 0.00 45.94 3.57
1709 1860 1.714794 CAAAGCTAGCTGCAGTACGT 58.285 50.000 20.16 0.00 45.94 3.57
1710 1861 0.371645 GCAAAGCTAGCTGCAGTACG 59.628 55.000 20.16 4.77 45.94 3.67
1813 1968 2.112691 TGGGAGGAGGTTTCTCTTCTCT 59.887 50.000 6.88 0.00 44.27 3.10
1879 2034 9.500785 TTTTCAAAACAAAGGAAAGAGATTTGT 57.499 25.926 0.00 0.00 46.24 2.83
1890 2045 7.067008 TGGTTTTTGTGTTTTCAAAACAAAGGA 59.933 29.630 17.33 2.60 43.76 3.36
1906 2062 7.536895 TTTCATGATGAACTTGGTTTTTGTG 57.463 32.000 7.48 0.00 35.89 3.33
1916 2072 5.279156 GGGCTCAACTTTTCATGATGAACTT 60.279 40.000 7.48 0.00 35.89 2.66
1929 2085 1.043022 CTTTGCCTGGGCTCAACTTT 58.957 50.000 13.05 0.00 42.51 2.66
1932 2088 1.616159 TTACTTTGCCTGGGCTCAAC 58.384 50.000 13.05 0.00 42.51 3.18
1966 2122 0.835941 AGTGGTGATGCTGGGAGATC 59.164 55.000 0.00 0.00 0.00 2.75
1978 2134 2.093394 TCGGAAAAACAGACAGTGGTGA 60.093 45.455 0.00 0.00 0.00 4.02
1995 2151 2.028748 GCAACCAGTTTAGTACCTCGGA 60.029 50.000 0.00 0.00 0.00 4.55
2002 2158 2.297880 TCTCGCAGCAACCAGTTTAGTA 59.702 45.455 0.00 0.00 0.00 1.82
2008 2164 2.356313 CGTCTCGCAGCAACCAGT 60.356 61.111 0.00 0.00 0.00 4.00
2034 2190 0.030773 CAAGAGCGCGTGATAGGCTA 59.969 55.000 8.43 0.00 37.10 3.93
2035 2191 1.227089 CAAGAGCGCGTGATAGGCT 60.227 57.895 8.43 0.00 40.29 4.58
2038 2194 0.596083 CCCTCAAGAGCGCGTGATAG 60.596 60.000 8.43 1.98 32.16 2.08
2040 2196 2.185350 CCCTCAAGAGCGCGTGAT 59.815 61.111 8.43 0.00 32.16 3.06
2041 2197 4.742201 GCCCTCAAGAGCGCGTGA 62.742 66.667 8.43 5.90 0.00 4.35
2044 2200 4.749310 AGTGCCCTCAAGAGCGCG 62.749 66.667 0.00 0.00 44.16 6.86
2066 2238 6.292381 CGCTCTTTCATATTTGTACTAGTGCC 60.292 42.308 5.39 0.00 0.00 5.01
2160 2369 9.474249 GACGTTCTAACTGCAGTAATATTTTTC 57.526 33.333 22.01 7.35 0.00 2.29
2165 2374 6.255887 GCTTGACGTTCTAACTGCAGTAATAT 59.744 38.462 22.01 6.93 0.00 1.28
2166 2375 5.575606 GCTTGACGTTCTAACTGCAGTAATA 59.424 40.000 22.01 9.03 0.00 0.98
2181 2390 1.502163 GCTGTGCTGAGCTTGACGTT 61.502 55.000 5.83 0.00 35.95 3.99
2199 2408 1.329906 CTCATCTGAATCCGTGCAAGC 59.670 52.381 0.00 0.00 0.00 4.01
2257 2466 5.471116 TGAACAGACTTCCATTTGTCATGAG 59.529 40.000 0.00 0.00 35.81 2.90
2258 2467 5.375773 TGAACAGACTTCCATTTGTCATGA 58.624 37.500 0.00 0.00 35.81 3.07
2259 2468 5.694231 TGAACAGACTTCCATTTGTCATG 57.306 39.130 0.00 0.00 35.81 3.07
2260 2469 6.713762 TTTGAACAGACTTCCATTTGTCAT 57.286 33.333 0.00 0.00 35.81 3.06
2272 2481 5.330455 TCGATCTATGCTTTGAACAGACT 57.670 39.130 0.00 0.00 0.00 3.24
2292 2501 4.466828 AGTTTCTTTCATTTGACGCATCG 58.533 39.130 0.00 0.00 0.00 3.84
2293 2502 6.417635 TCAAAGTTTCTTTCATTTGACGCATC 59.582 34.615 0.00 0.00 36.89 3.91
2294 2503 6.198966 GTCAAAGTTTCTTTCATTTGACGCAT 59.801 34.615 12.28 0.00 46.54 4.73
2295 2504 5.514914 GTCAAAGTTTCTTTCATTTGACGCA 59.485 36.000 12.28 0.00 46.54 5.24
2314 2523 5.221880 GTCAGCAATGCACAATTAGTCAAA 58.778 37.500 8.35 0.00 0.00 2.69
2366 2575 4.469469 AGAAGAAAAGGTGGAATTCCCA 57.531 40.909 21.90 7.25 44.25 4.37
2367 2576 4.705507 GGTAGAAGAAAAGGTGGAATTCCC 59.294 45.833 21.90 12.59 34.29 3.97


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

AutoCloner maintained by Alex Coulton.