Multiple sequence alignment - TraesCS1D01G405200

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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 TraesCS1D01G405200 chr1D 100.000 2423 0 0 1 2423 469816305 469813883 0.000000e+00 4475.0
1 TraesCS1D01G405200 chr1D 90.991 444 25 7 996 1424 469795522 469795965 3.470000e-163 584.0
2 TraesCS1D01G405200 chr1B 84.482 1495 105 48 4 1428 651288173 651286736 0.000000e+00 1358.0
3 TraesCS1D01G405200 chr1B 89.327 609 36 14 1429 2029 651286705 651286118 0.000000e+00 737.0
4 TraesCS1D01G405200 chr1B 90.541 444 24 8 996 1424 649670179 649670619 2.700000e-159 571.0
5 TraesCS1D01G405200 chr1B 91.589 321 14 4 2115 2423 651286084 651285765 4.790000e-117 431.0
6 TraesCS1D01G405200 chr1A 88.305 838 45 20 604 1427 562923828 562923030 0.000000e+00 955.0
7 TraesCS1D01G405200 chr1A 90.971 443 25 7 996 1423 562902457 562902899 1.250000e-162 582.0
8 TraesCS1D01G405200 chr1A 89.600 375 19 8 2026 2400 562922503 562922149 2.200000e-125 459.0
9 TraesCS1D01G405200 chr1A 93.860 228 13 1 1766 1992 562922729 562922502 2.310000e-90 342.0
10 TraesCS1D01G405200 chr1A 89.352 216 12 3 1530 1736 562922940 562922727 6.640000e-66 261.0
11 TraesCS1D01G405200 chr1A 100.000 28 0 0 2396 2423 562921903 562921876 4.000000e-03 52.8
12 TraesCS1D01G405200 chr7D 87.013 462 33 15 1106 1541 561875551 561876011 1.670000e-136 496.0
13 TraesCS1D01G405200 chr7D 86.275 153 19 2 1 152 591483747 591483596 5.360000e-37 165.0
14 TraesCS1D01G405200 chr7B 86.475 451 39 7 996 1424 722094317 722094767 2.180000e-130 475.0
15 TraesCS1D01G405200 chr6D 85.144 451 45 16 996 1424 17043024 17042574 2.210000e-120 442.0
16 TraesCS1D01G405200 chr6D 85.616 146 19 2 1 145 78819094 78818950 4.170000e-33 152.0
17 TraesCS1D01G405200 chr6D 91.753 97 8 0 441 537 471924880 471924784 4.200000e-28 135.0
18 TraesCS1D01G405200 chr6B 91.104 326 25 4 1102 1426 578774738 578775060 2.860000e-119 438.0
19 TraesCS1D01G405200 chr6A 81.448 442 50 18 118 537 614871370 614871801 1.390000e-87 333.0
20 TraesCS1D01G405200 chr4D 77.002 487 72 21 1 457 456128158 456127682 2.410000e-60 243.0
21 TraesCS1D01G405200 chr4D 78.723 282 41 12 8 284 505385885 505386152 1.150000e-38 171.0
22 TraesCS1D01G405200 chr4B 75.944 503 63 36 1 453 593435096 593434602 3.160000e-49 206.0
23 TraesCS1D01G405200 chr3B 76.072 443 60 24 127 537 82824970 82825398 3.180000e-44 189.0
24 TraesCS1D01G405200 chr3B 87.943 141 14 3 1 140 82825454 82825316 1.930000e-36 163.0
25 TraesCS1D01G405200 chr3B 83.459 133 19 2 405 537 63430048 63429919 1.180000e-23 121.0
26 TraesCS1D01G405200 chr3D 73.805 565 93 39 1 537 97058077 97058614 3.200000e-39 172.0
27 TraesCS1D01G405200 chr5A 76.751 357 52 18 4 333 672335635 672335987 1.150000e-38 171.0
28 TraesCS1D01G405200 chr5A 80.591 237 24 13 310 537 672336196 672336419 1.930000e-36 163.0
29 TraesCS1D01G405200 chrUn 76.533 375 49 17 199 537 81723414 81723785 4.140000e-38 169.0
30 TraesCS1D01G405200 chr7A 79.200 250 40 10 4 252 273649618 273649380 1.930000e-36 163.0
31 TraesCS1D01G405200 chr5D 80.357 224 37 5 113 335 441916639 441916856 1.930000e-36 163.0
32 TraesCS1D01G405200 chr4A 77.152 302 51 8 1 284 669995589 669995288 2.490000e-35 159.0
33 TraesCS1D01G405200 chr5B 80.822 146 19 5 399 536 537962667 537962523 3.290000e-19 106.0


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 TraesCS1D01G405200 chr1D 469813883 469816305 2422 True 4475.00 4475 100.0000 1 2423 1 chr1D.!!$R1 2422
1 TraesCS1D01G405200 chr1B 651285765 651288173 2408 True 842.00 1358 88.4660 4 2423 3 chr1B.!!$R1 2419
2 TraesCS1D01G405200 chr1A 562921876 562923828 1952 True 413.96 955 92.2234 604 2423 5 chr1A.!!$R1 1819

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
142 143 0.66102 CACGTTGACCAGGGTTTGAC 59.339 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
1924 2076 0.316204 CTTTGCCTGGGCTCAAGTTG 59.684 55.0 13.05 0.0 42.51 3.16 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
27 28 8.803235 AGTATGTTTTTGATCCCTTAAGTTTCC 58.197 33.333 0.97 0.00 0.00 3.13
84 85 8.331931 TGGTATATATTTGGTCCTTCAAGTCT 57.668 34.615 0.00 0.00 0.00 3.24
85 86 9.442062 TGGTATATATTTGGTCCTTCAAGTCTA 57.558 33.333 0.00 0.00 0.00 2.59
133 134 2.290367 CAGATTTTGAGCACGTTGACCA 59.710 45.455 0.00 0.00 0.00 4.02
142 143 0.661020 CACGTTGACCAGGGTTTGAC 59.339 55.000 0.00 0.00 0.00 3.18
150 170 1.165270 CCAGGGTTTGACCGATGAAC 58.835 55.000 3.37 0.00 39.83 3.18
156 176 4.007659 GGGTTTGACCGATGAACAGTAAT 58.992 43.478 0.00 0.00 39.83 1.89
158 178 5.048294 GGGTTTGACCGATGAACAGTAATTT 60.048 40.000 0.00 0.00 39.83 1.82
160 180 6.921307 GGTTTGACCGATGAACAGTAATTTTT 59.079 34.615 0.00 0.00 0.00 1.94
220 240 2.867287 TGTGACAACCAACATGCTTG 57.133 45.000 0.00 0.00 0.00 4.01
242 262 1.213537 GCGCTTGGTGCATGTGAAT 59.786 52.632 0.00 0.00 43.06 2.57
267 287 6.935741 TTTGTGGTCAAATAATATCCGAGG 57.064 37.500 0.00 0.00 38.44 4.63
268 288 5.880164 TGTGGTCAAATAATATCCGAGGA 57.120 39.130 0.00 0.00 0.00 3.71
269 289 5.853936 TGTGGTCAAATAATATCCGAGGAG 58.146 41.667 0.00 0.00 0.00 3.69
270 290 4.691216 GTGGTCAAATAATATCCGAGGAGC 59.309 45.833 0.00 0.00 0.00 4.70
271 291 4.593206 TGGTCAAATAATATCCGAGGAGCT 59.407 41.667 0.00 0.00 0.00 4.09
272 292 4.932200 GGTCAAATAATATCCGAGGAGCTG 59.068 45.833 0.00 0.00 0.00 4.24
273 293 5.511545 GGTCAAATAATATCCGAGGAGCTGT 60.512 44.000 0.00 0.00 0.00 4.40
274 294 6.295123 GGTCAAATAATATCCGAGGAGCTGTA 60.295 42.308 0.00 0.00 0.00 2.74
275 295 6.809196 GTCAAATAATATCCGAGGAGCTGTAG 59.191 42.308 0.00 0.00 0.00 2.74
276 296 6.493802 TCAAATAATATCCGAGGAGCTGTAGT 59.506 38.462 0.00 0.00 0.00 2.73
277 297 7.668469 TCAAATAATATCCGAGGAGCTGTAGTA 59.332 37.037 0.00 0.00 0.00 1.82
345 365 1.493772 TCGGATGTCGAAACACACAC 58.506 50.000 0.00 0.00 45.86 3.82
346 366 1.202428 TCGGATGTCGAAACACACACA 60.202 47.619 0.00 0.00 45.86 3.72
372 392 1.908619 TCAGGCACCAAAGCATCTAGA 59.091 47.619 0.00 0.00 35.83 2.43
390 410 7.761249 GCATCTAGATTGCCACAAAATTTTAGT 59.239 33.333 1.33 1.95 0.00 2.24
439 461 3.763057 AGTGTTCACCAGTTAAATCCCC 58.237 45.455 0.00 0.00 0.00 4.81
447 469 2.490509 CCAGTTAAATCCCCGGTCAAAC 59.509 50.000 0.00 0.00 0.00 2.93
481 503 2.742053 GGTCAGCGTGCTTAAAATCTGA 59.258 45.455 0.00 0.00 0.00 3.27
487 509 5.061311 CAGCGTGCTTAAAATCTGATTTTGG 59.939 40.000 29.33 23.05 42.08 3.28
501 523 5.714806 TCTGATTTTGGACCAAACTTATCCC 59.285 40.000 19.42 2.96 32.79 3.85
502 524 5.650283 TGATTTTGGACCAAACTTATCCCT 58.350 37.500 19.42 0.00 32.79 4.20
505 527 6.816616 TTTTGGACCAAACTTATCCCTTTT 57.183 33.333 19.42 0.00 32.79 2.27
513 535 7.272244 ACCAAACTTATCCCTTTTTGAAACTG 58.728 34.615 0.00 0.00 31.79 3.16
514 536 6.705825 CCAAACTTATCCCTTTTTGAAACTGG 59.294 38.462 0.00 0.00 31.79 4.00
582 619 8.887036 ATTGAAGGGACAAAAACATAGTTTTC 57.113 30.769 8.16 0.00 33.44 2.29
584 621 8.754991 TGAAGGGACAAAAACATAGTTTTCTA 57.245 30.769 8.16 0.00 36.78 2.10
666 725 4.664267 AGAGAGCCAGCCACCCCA 62.664 66.667 0.00 0.00 0.00 4.96
672 731 2.682846 CCAGCCACCCCAGCAATA 59.317 61.111 0.00 0.00 0.00 1.90
762 835 1.667349 GCGTTGCATGCACACAATCG 61.667 55.000 22.58 17.68 0.00 3.34
836 909 1.324736 CCAAGAGAAGAACGCATACGC 59.675 52.381 0.00 0.00 45.53 4.42
837 910 1.992667 CAAGAGAAGAACGCATACGCA 59.007 47.619 0.00 0.00 45.53 5.24
889 979 4.265056 GTGACGCCACCCCACCTT 62.265 66.667 0.00 0.00 37.33 3.50
897 987 1.852626 CACCCCACCTTCCTCCCTT 60.853 63.158 0.00 0.00 0.00 3.95
898 988 1.072143 ACCCCACCTTCCTCCCTTT 60.072 57.895 0.00 0.00 0.00 3.11
899 989 0.704813 ACCCCACCTTCCTCCCTTTT 60.705 55.000 0.00 0.00 0.00 2.27
900 990 1.378732 CCCCACCTTCCTCCCTTTTA 58.621 55.000 0.00 0.00 0.00 1.52
901 991 1.714217 CCCCACCTTCCTCCCTTTTAA 59.286 52.381 0.00 0.00 0.00 1.52
943 1033 2.279851 TTGCTCGTCACACCACGG 60.280 61.111 0.00 0.00 40.35 4.94
964 1054 2.773745 GCAAGCTGCACACACCACA 61.774 57.895 1.02 0.00 44.26 4.17
967 1057 4.318021 GCTGCACACACCACAGCG 62.318 66.667 0.00 0.00 46.38 5.18
968 1058 3.653009 CTGCACACACCACAGCGG 61.653 66.667 0.00 0.00 42.50 5.52
1404 1494 1.264749 TGCCCATACTCAAGGACGCT 61.265 55.000 0.00 0.00 0.00 5.07
1448 1568 9.877178 AGACATTTTGATTAGGAGTTAGTACAG 57.123 33.333 0.00 0.00 0.00 2.74
1477 1600 9.045745 AGTAATCTCTTCTCCTTCTCATTTCTT 57.954 33.333 0.00 0.00 0.00 2.52
1508 1631 4.494484 TCGTGAGGTCATGTGAATTACTG 58.506 43.478 0.00 0.00 34.59 2.74
1555 1679 5.132480 TGGGATCAATCAGTAATGGTGATGA 59.868 40.000 12.86 0.00 34.78 2.92
1558 1682 7.551974 GGGATCAATCAGTAATGGTGATGATAG 59.448 40.741 12.86 0.00 34.78 2.08
1559 1683 8.099537 GGATCAATCAGTAATGGTGATGATAGT 58.900 37.037 12.86 0.00 34.78 2.12
1560 1684 9.499479 GATCAATCAGTAATGGTGATGATAGTT 57.501 33.333 12.86 0.00 34.78 2.24
1562 1686 9.987272 TCAATCAGTAATGGTGATGATAGTTAG 57.013 33.333 0.00 0.00 34.78 2.34
1563 1687 8.715998 CAATCAGTAATGGTGATGATAGTTAGC 58.284 37.037 0.00 0.00 34.78 3.09
1564 1688 7.603180 TCAGTAATGGTGATGATAGTTAGCT 57.397 36.000 0.00 0.00 0.00 3.32
1565 1689 8.706322 TCAGTAATGGTGATGATAGTTAGCTA 57.294 34.615 0.00 0.00 0.00 3.32
1566 1690 8.797438 TCAGTAATGGTGATGATAGTTAGCTAG 58.203 37.037 0.00 0.00 0.00 3.42
1567 1691 8.797438 CAGTAATGGTGATGATAGTTAGCTAGA 58.203 37.037 0.00 0.00 0.00 2.43
1568 1692 8.798402 AGTAATGGTGATGATAGTTAGCTAGAC 58.202 37.037 0.00 0.00 0.00 2.59
1569 1693 5.690997 TGGTGATGATAGTTAGCTAGACG 57.309 43.478 0.00 0.00 0.00 4.18
1570 1694 5.374071 TGGTGATGATAGTTAGCTAGACGA 58.626 41.667 0.00 0.00 0.00 4.20
1571 1695 6.004574 TGGTGATGATAGTTAGCTAGACGAT 58.995 40.000 0.00 0.00 0.00 3.73
1572 1696 6.072452 TGGTGATGATAGTTAGCTAGACGATG 60.072 42.308 0.00 0.00 0.00 3.84
1573 1697 6.149640 GGTGATGATAGTTAGCTAGACGATGA 59.850 42.308 0.00 0.00 0.00 2.92
1577 1701 9.104965 GATGATAGTTAGCTAGACGATGATAGT 57.895 37.037 0.00 0.00 0.00 2.12
1578 1702 8.850007 TGATAGTTAGCTAGACGATGATAGTT 57.150 34.615 0.00 0.00 0.00 2.24
1646 1793 9.127006 CTGTAAATAGATCGATGAGTGAAGATG 57.873 37.037 0.54 0.00 0.00 2.90
1655 1802 5.009110 TCGATGAGTGAAGATGGATGTACTC 59.991 44.000 0.00 0.00 36.11 2.59
1689 1836 5.756195 TTAGCACTCCATGTAAATGATGC 57.244 39.130 8.08 8.08 0.00 3.91
1746 1897 5.188434 GGTTCTCTGGATGACAATCAATCA 58.812 41.667 0.00 0.00 34.17 2.57
1747 1898 5.649395 GGTTCTCTGGATGACAATCAATCAA 59.351 40.000 0.00 0.00 34.17 2.57
1748 1899 6.320672 GGTTCTCTGGATGACAATCAATCAAT 59.679 38.462 0.00 0.00 34.17 2.57
1749 1900 7.416022 GTTCTCTGGATGACAATCAATCAATC 58.584 38.462 0.00 0.00 34.17 2.67
1803 1954 4.122776 GCACTGTGTCGGATATTCTGATT 58.877 43.478 9.86 0.00 33.80 2.57
1861 2012 7.869800 AGCTGAACAATTTCTCTTCTGTTTAG 58.130 34.615 0.00 0.00 38.03 1.85
1862 2013 6.580416 GCTGAACAATTTCTCTTCTGTTTAGC 59.420 38.462 12.71 12.71 46.89 3.09
1868 2019 8.951243 ACAATTTCTCTTCTGTTTAGCTAATCC 58.049 33.333 7.08 1.93 0.00 3.01
1924 2076 3.498397 ACAACAACCGAGTTCATCATGAC 59.502 43.478 0.00 0.00 0.00 3.06
1967 2119 8.385898 AGTAAACGTTTAACATGGAAATCTCA 57.614 30.769 21.67 0.00 0.00 3.27
1978 2130 0.445436 GAAATCTCACAGCAGCACCG 59.555 55.000 0.00 0.00 0.00 4.94
1997 2149 1.578206 GCTGTCTGTTTTCCCGAGGC 61.578 60.000 0.00 0.00 0.00 4.70
2003 2155 1.804748 CTGTTTTCCCGAGGCACTAAC 59.195 52.381 0.00 0.00 41.55 2.34
2046 2198 3.689649 ACCTACGGCTTCAACATTGATTC 59.310 43.478 0.00 0.00 37.00 2.52
2052 2204 3.091545 GCTTCAACATTGATTCCCCTGA 58.908 45.455 0.00 0.00 37.00 3.86
2077 2229 1.739562 CTCTTGAGGGCACTGCGTC 60.740 63.158 0.00 0.00 0.00 5.19
2079 2231 2.031012 TTGAGGGCACTGCGTCTG 59.969 61.111 0.00 0.00 0.00 3.51
2080 2232 4.687215 TGAGGGCACTGCGTCTGC 62.687 66.667 0.00 0.00 43.20 4.26
2091 2243 4.012895 CGTCTGCGTGGCACCAAC 62.013 66.667 12.86 10.44 33.79 3.77
2092 2244 3.660111 GTCTGCGTGGCACCAACC 61.660 66.667 12.86 0.00 33.79 3.77
2093 2245 4.947147 TCTGCGTGGCACCAACCC 62.947 66.667 12.86 0.00 33.79 4.11
2095 2247 4.594854 TGCGTGGCACCAACCCAT 62.595 61.111 12.86 0.00 34.34 4.00
2096 2248 3.302344 GCGTGGCACCAACCCATT 61.302 61.111 12.86 0.00 34.34 3.16
2097 2249 2.650196 CGTGGCACCAACCCATTG 59.350 61.111 12.86 0.00 34.34 2.82
2098 2250 1.900981 CGTGGCACCAACCCATTGA 60.901 57.895 12.86 0.00 38.15 2.57
2099 2251 1.665442 GTGGCACCAACCCATTGAC 59.335 57.895 6.29 0.00 38.15 3.18
2100 2252 0.827507 GTGGCACCAACCCATTGACT 60.828 55.000 6.29 0.00 38.15 3.41
2101 2253 0.827089 TGGCACCAACCCATTGACTG 60.827 55.000 0.00 0.00 38.15 3.51
2102 2254 0.539438 GGCACCAACCCATTGACTGA 60.539 55.000 0.00 0.00 38.15 3.41
2103 2255 1.327303 GCACCAACCCATTGACTGAA 58.673 50.000 0.00 0.00 38.15 3.02
2104 2256 1.686052 GCACCAACCCATTGACTGAAA 59.314 47.619 0.00 0.00 38.15 2.69
2117 2269 3.141398 TGACTGAAACAAGATGGAGCAC 58.859 45.455 0.00 0.00 0.00 4.40
2124 2276 3.784701 ACAAGATGGAGCACTAGTACG 57.215 47.619 0.00 0.00 0.00 3.67
2181 2333 4.634443 ACGTTGAATAACTACCCATTGCTC 59.366 41.667 0.00 0.00 34.60 4.26
2242 2394 2.341257 CAGTTAGCACGTCAAGCTCAT 58.659 47.619 1.67 0.00 42.32 2.90
2244 2396 1.321743 GTTAGCACGTCAAGCTCATCG 59.678 52.381 1.67 0.00 42.32 3.84
2354 2514 7.044052 GCATAGATGCGTAAAATGAAAGAAACC 60.044 37.037 0.00 0.00 44.67 3.27
2382 2542 1.165284 TTGTGCATTGCTGACGCTGA 61.165 50.000 10.49 0.00 36.97 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.803235 GGAAACTTAAGGGATCAAAAACATACT 58.197 33.333 7.53 0.00 0.00 2.12
2 3 8.581578 TGGAAACTTAAGGGATCAAAAACATAC 58.418 33.333 7.53 0.00 0.00 2.39
26 27 5.045869 TGAGGGACCAAGTCTATACTTTTGG 60.046 44.000 0.00 0.82 43.60 3.28
27 28 6.049955 TGAGGGACCAAGTCTATACTTTTG 57.950 41.667 0.00 0.00 43.60 2.44
90 91 6.953520 TCTGAATTTGGACCAAACTTATCCAT 59.046 34.615 21.85 0.57 42.09 3.41
91 92 6.310941 TCTGAATTTGGACCAAACTTATCCA 58.689 36.000 21.85 11.70 40.83 3.41
102 103 4.925646 GTGCTCAAAATCTGAATTTGGACC 59.074 41.667 15.95 7.27 38.12 4.46
104 105 4.278170 ACGTGCTCAAAATCTGAATTTGGA 59.722 37.500 15.95 4.57 38.12 3.53
133 134 1.420138 ACTGTTCATCGGTCAAACCCT 59.580 47.619 0.00 0.00 33.75 4.34
197 217 4.199432 AGCATGTTGGTTGTCACAAAAA 57.801 36.364 0.00 0.00 0.00 1.94
239 259 9.796120 TCGGATATTATTTGACCACAAAAATTC 57.204 29.630 0.00 0.00 46.77 2.17
242 262 7.612244 TCCTCGGATATTATTTGACCACAAAAA 59.388 33.333 0.00 0.00 46.77 1.94
307 327 2.699954 GAGGATCTCGTGGCAAAAAGA 58.300 47.619 0.00 0.00 0.00 2.52
345 365 3.204526 TGCTTTGGTGCCTGAAAATTTG 58.795 40.909 0.00 0.00 0.00 2.32
346 366 3.557228 TGCTTTGGTGCCTGAAAATTT 57.443 38.095 0.00 0.00 0.00 1.82
419 441 2.486592 CGGGGATTTAACTGGTGAACAC 59.513 50.000 0.00 0.00 0.00 3.32
431 453 1.810959 CACGTTTGACCGGGGATTTA 58.189 50.000 6.32 0.00 0.00 1.40
439 461 0.028374 GGTTTGACCACGTTTGACCG 59.972 55.000 0.00 0.00 38.42 4.79
447 469 1.959226 CTGACCGGGTTTGACCACG 60.959 63.158 6.32 0.92 41.02 4.94
481 503 7.387265 AAAAGGGATAAGTTTGGTCCAAAAT 57.613 32.000 18.74 15.10 35.03 1.82
487 509 7.438160 CAGTTTCAAAAAGGGATAAGTTTGGTC 59.562 37.037 0.00 0.00 32.91 4.02
513 535 4.563140 TTGGTATACACTTGGTCCTTCC 57.437 45.455 5.01 0.00 0.00 3.46
514 536 6.235664 TCTTTTGGTATACACTTGGTCCTTC 58.764 40.000 5.01 0.00 0.00 3.46
589 629 1.556911 ACGAGGATCAGGTTGCTTCAT 59.443 47.619 0.00 0.00 33.17 2.57
638 697 1.760086 GGCTCTCTCCTGCTGCCTA 60.760 63.158 0.00 0.00 40.36 3.93
647 706 3.791586 GGGTGGCTGGCTCTCTCC 61.792 72.222 2.00 0.00 0.00 3.71
666 725 0.391661 CGTGGCAGGTCACTATTGCT 60.392 55.000 2.26 0.00 37.93 3.91
672 731 2.657237 GCTACGTGGCAGGTCACT 59.343 61.111 19.95 0.00 35.63 3.41
762 835 2.499732 CTTTTTCGCGCTCCGTGC 60.500 61.111 5.56 0.00 37.28 5.34
835 908 2.824041 CCGGCCAGGTGTGTATGC 60.824 66.667 2.24 0.00 34.51 3.14
836 909 2.824041 GCCGGCCAGGTGTGTATG 60.824 66.667 18.11 0.00 43.70 2.39
837 910 4.467084 CGCCGGCCAGGTGTGTAT 62.467 66.667 23.46 0.00 45.30 2.29
889 979 7.724061 GCTGGACATATAAATTAAAAGGGAGGA 59.276 37.037 0.00 0.00 0.00 3.71
897 987 6.296026 AGCGAGGCTGGACATATAAATTAAA 58.704 36.000 0.00 0.00 37.57 1.52
898 988 5.865085 AGCGAGGCTGGACATATAAATTAA 58.135 37.500 0.00 0.00 37.57 1.40
899 989 5.479306 GAGCGAGGCTGGACATATAAATTA 58.521 41.667 0.00 0.00 39.88 1.40
900 990 4.319177 GAGCGAGGCTGGACATATAAATT 58.681 43.478 0.00 0.00 39.88 1.82
901 991 3.307059 GGAGCGAGGCTGGACATATAAAT 60.307 47.826 0.00 0.00 39.88 1.40
967 1057 3.330853 GATCGATCGGTGCGTGCC 61.331 66.667 16.41 0.00 0.00 5.01
968 1058 2.580470 CTGATCGATCGGTGCGTGC 61.580 63.158 23.61 0.00 0.00 5.34
980 1070 2.351322 CGACCTCGACGCTGATCG 60.351 66.667 0.00 0.00 43.02 3.69
1265 1355 4.778415 CGTCTCCAGTCACCGCCG 62.778 72.222 0.00 0.00 0.00 6.46
1269 1359 4.436998 CCGGCGTCTCCAGTCACC 62.437 72.222 6.01 0.00 34.01 4.02
1365 1455 2.755876 AGCTCGCCGGAGATGTGA 60.756 61.111 8.83 0.00 43.27 3.58
1448 1568 4.404073 TGAGAAGGAGAAGAGATTACTGGC 59.596 45.833 0.00 0.00 0.00 4.85
1477 1600 3.069586 ACATGACCTCACGAGTCAAAAGA 59.930 43.478 0.00 0.00 0.00 2.52
1508 1631 1.140804 GAGAGGAAGGTCGAGCAGC 59.859 63.158 18.15 7.77 0.00 5.25
1586 1733 9.724839 TGGTCGAAACTAAATTCACTTAAAAAG 57.275 29.630 0.00 0.00 0.00 2.27
1587 1734 9.505995 GTGGTCGAAACTAAATTCACTTAAAAA 57.494 29.630 0.00 0.00 0.00 1.94
1675 1822 3.003689 GGGAACGAGCATCATTTACATGG 59.996 47.826 0.00 0.00 33.17 3.66
1676 1823 3.879295 AGGGAACGAGCATCATTTACATG 59.121 43.478 0.00 0.00 33.17 3.21
1689 1836 1.272490 TGCTGTACAGAAGGGAACGAG 59.728 52.381 27.08 0.00 0.00 4.18
1746 1897 5.280654 ACATGGCAAAAACAGAACAGATT 57.719 34.783 0.00 0.00 0.00 2.40
1747 1898 4.942761 ACATGGCAAAAACAGAACAGAT 57.057 36.364 0.00 0.00 0.00 2.90
1748 1899 4.734398 AACATGGCAAAAACAGAACAGA 57.266 36.364 0.00 0.00 0.00 3.41
1749 1900 5.350914 TGAAAACATGGCAAAAACAGAACAG 59.649 36.000 0.00 0.00 0.00 3.16
1803 1954 3.711704 AGGAGGTTTCTCTTCTCAACACA 59.288 43.478 0.00 0.00 39.86 3.72
1861 2012 2.545946 GAGATTTGCCTCGTGGATTAGC 59.454 50.000 7.92 0.00 34.57 3.09
1862 2013 4.065321 AGAGATTTGCCTCGTGGATTAG 57.935 45.455 7.92 0.00 38.19 1.73
1868 2019 3.984292 GCAAGAGATTTGCCTCGTG 57.016 52.632 0.54 0.00 42.76 4.35
1906 2058 3.748048 AGTTGTCATGATGAACTCGGTTG 59.252 43.478 14.35 0.00 0.00 3.77
1924 2076 0.316204 CTTTGCCTGGGCTCAAGTTG 59.684 55.000 13.05 0.00 42.51 3.16
1978 2130 1.578206 GCCTCGGGAAAACAGACAGC 61.578 60.000 0.00 0.00 0.00 4.40
1997 2149 0.602638 TCGCAGCAACCAGGTTAGTG 60.603 55.000 3.89 6.62 0.00 2.74
2003 2155 3.114616 CGTCTCGCAGCAACCAGG 61.115 66.667 0.00 0.00 0.00 4.45
2029 2181 1.134946 GGGGAATCAATGTTGAAGCCG 59.865 52.381 0.00 0.00 41.13 5.52
2046 2198 2.110967 CAAGAGCGCATGTCAGGGG 61.111 63.158 11.47 0.00 0.00 4.79
2052 2204 2.437359 GCCCTCAAGAGCGCATGT 60.437 61.111 11.47 0.00 32.73 3.21
2079 2231 3.302344 AATGGGTTGGTGCCACGC 61.302 61.111 0.00 0.00 0.00 5.34
2080 2232 1.900981 TCAATGGGTTGGTGCCACG 60.901 57.895 0.00 0.00 35.99 4.94
2081 2233 0.827507 AGTCAATGGGTTGGTGCCAC 60.828 55.000 0.00 0.00 35.99 5.01
2082 2234 0.827089 CAGTCAATGGGTTGGTGCCA 60.827 55.000 0.00 0.00 35.99 4.92
2083 2235 0.539438 TCAGTCAATGGGTTGGTGCC 60.539 55.000 0.00 0.00 35.99 5.01
2084 2236 1.327303 TTCAGTCAATGGGTTGGTGC 58.673 50.000 0.00 0.00 35.99 5.01
2085 2237 2.692557 TGTTTCAGTCAATGGGTTGGTG 59.307 45.455 0.00 0.00 35.99 4.17
2086 2238 3.025322 TGTTTCAGTCAATGGGTTGGT 57.975 42.857 0.00 0.00 35.99 3.67
2087 2239 3.636300 TCTTGTTTCAGTCAATGGGTTGG 59.364 43.478 0.00 0.00 35.99 3.77
2088 2240 4.916983 TCTTGTTTCAGTCAATGGGTTG 57.083 40.909 0.00 0.00 36.65 3.77
2089 2241 4.281688 CCATCTTGTTTCAGTCAATGGGTT 59.718 41.667 0.00 0.00 0.00 4.11
2090 2242 3.828451 CCATCTTGTTTCAGTCAATGGGT 59.172 43.478 0.00 0.00 0.00 4.51
2091 2243 4.081406 TCCATCTTGTTTCAGTCAATGGG 58.919 43.478 0.00 0.00 30.46 4.00
2092 2244 4.380233 GCTCCATCTTGTTTCAGTCAATGG 60.380 45.833 0.00 0.00 0.00 3.16
2093 2245 4.216902 TGCTCCATCTTGTTTCAGTCAATG 59.783 41.667 0.00 0.00 0.00 2.82
2094 2246 4.217118 GTGCTCCATCTTGTTTCAGTCAAT 59.783 41.667 0.00 0.00 0.00 2.57
2095 2247 3.565482 GTGCTCCATCTTGTTTCAGTCAA 59.435 43.478 0.00 0.00 0.00 3.18
2096 2248 3.141398 GTGCTCCATCTTGTTTCAGTCA 58.859 45.455 0.00 0.00 0.00 3.41
2097 2249 3.406764 AGTGCTCCATCTTGTTTCAGTC 58.593 45.455 0.00 0.00 0.00 3.51
2098 2250 3.498774 AGTGCTCCATCTTGTTTCAGT 57.501 42.857 0.00 0.00 0.00 3.41
2099 2251 4.573900 ACTAGTGCTCCATCTTGTTTCAG 58.426 43.478 0.00 0.00 0.00 3.02
2100 2252 4.623932 ACTAGTGCTCCATCTTGTTTCA 57.376 40.909 0.00 0.00 0.00 2.69
2101 2253 4.563184 CGTACTAGTGCTCCATCTTGTTTC 59.437 45.833 5.39 0.00 0.00 2.78
2102 2254 4.219944 TCGTACTAGTGCTCCATCTTGTTT 59.780 41.667 5.39 0.00 0.00 2.83
2103 2255 3.762288 TCGTACTAGTGCTCCATCTTGTT 59.238 43.478 5.39 0.00 0.00 2.83
2104 2256 3.353557 TCGTACTAGTGCTCCATCTTGT 58.646 45.455 5.39 0.00 0.00 3.16
2117 2269 7.378728 TCAACGCTCATTTCATATTCGTACTAG 59.621 37.037 0.00 0.00 0.00 2.57
2124 2276 8.304202 AGATAGTCAACGCTCATTTCATATTC 57.696 34.615 0.00 0.00 0.00 1.75
2244 2396 0.874390 TCTGAATCCGTGCAAGTTGC 59.126 50.000 21.17 21.17 45.29 4.17
2354 2514 4.855388 GTCAGCAATGCACAATTAGTCAAG 59.145 41.667 8.35 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.