Multiple sequence alignment - TraesCS7A01G115800

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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 TraesCS7A01G115800 chr7A 100.000 2321 0 0 1 2321 73944036 73946356 0.000000e+00 4287.0
1 TraesCS7A01G115800 chr7A 92.262 672 44 8 285 951 642889035 642889703 0.000000e+00 946.0
2 TraesCS7A01G115800 chr7A 85.698 895 82 19 680 1565 642889527 642890384 0.000000e+00 902.0
3 TraesCS7A01G115800 chr7A 85.610 820 64 29 1556 2321 680378971 680378152 0.000000e+00 811.0
4 TraesCS7A01G115800 chr7A 82.500 600 90 10 286 877 725604824 725605416 1.590000e-141 512.0
5 TraesCS7A01G115800 chr7A 93.197 147 8 2 139 283 680379103 680378957 5.020000e-52 215.0
6 TraesCS7A01G115800 chr3B 92.278 777 46 11 797 1564 750902010 750901239 0.000000e+00 1090.0
7 TraesCS7A01G115800 chr3B 87.725 611 56 15 286 888 750902450 750901851 0.000000e+00 695.0
8 TraesCS7A01G115800 chr3B 85.185 216 27 5 706 918 750902064 750901851 1.400000e-52 217.0
9 TraesCS7A01G115800 chr4D 89.627 858 52 21 709 1565 408578700 408579521 0.000000e+00 1057.0
10 TraesCS7A01G115800 chr4D 85.762 604 72 12 286 885 408578314 408578907 5.440000e-176 627.0
11 TraesCS7A01G115800 chrUn 90.026 772 59 12 1566 2321 26079952 26079183 0.000000e+00 983.0
12 TraesCS7A01G115800 chrUn 87.625 299 27 6 2 290 26080240 26079942 2.860000e-89 339.0
13 TraesCS7A01G115800 chr2D 90.014 701 55 9 1566 2252 532646294 532645595 0.000000e+00 893.0
14 TraesCS7A01G115800 chr2D 87.000 300 28 6 2 290 532646583 532646284 6.180000e-86 327.0
15 TraesCS7A01G115800 chr7B 86.763 763 74 15 1573 2321 219506370 219505621 0.000000e+00 824.0
16 TraesCS7A01G115800 chr7B 83.646 373 39 10 1574 1932 443743491 443743855 4.780000e-87 331.0
17 TraesCS7A01G115800 chr7B 88.931 262 27 2 2 261 219506665 219506404 2.880000e-84 322.0
18 TraesCS7A01G115800 chr7B 90.698 129 11 1 2190 2317 443743868 443743996 1.100000e-38 171.0
19 TraesCS7A01G115800 chr1A 90.110 637 52 8 1696 2321 480836751 480836115 0.000000e+00 817.0
20 TraesCS7A01G115800 chr1A 85.753 372 36 8 1574 1930 504087440 504087809 6.050000e-101 377.0
21 TraesCS7A01G115800 chr1A 92.517 147 9 2 139 283 480837059 480836913 2.340000e-50 209.0
22 TraesCS7A01G115800 chr1A 91.729 133 10 1 2190 2321 504087824 504087956 1.420000e-42 183.0
23 TraesCS7A01G115800 chr6A 85.488 820 65 30 1556 2321 255035732 255036551 0.000000e+00 806.0
24 TraesCS7A01G115800 chr6A 88.088 638 48 9 1696 2321 15630562 15631183 0.000000e+00 732.0
25 TraesCS7A01G115800 chr6A 93.197 147 8 2 139 283 255035600 255035746 5.020000e-52 215.0
26 TraesCS7A01G115800 chr6A 93.333 135 8 1 139 272 15630211 15630345 5.060000e-47 198.0
27 TraesCS7A01G115800 chr5B 81.588 554 68 19 286 813 255409798 255410343 5.930000e-116 427.0
28 TraesCS7A01G115800 chr5B 77.122 271 55 5 800 1064 255410197 255410466 1.440000e-32 150.0
29 TraesCS7A01G115800 chr5B 79.355 155 27 3 1412 1565 255409946 255409796 1.130000e-18 104.0
30 TraesCS7A01G115800 chr5B 87.500 80 6 4 286 362 645923538 645923460 3.180000e-14 89.8
31 TraesCS7A01G115800 chr4B 79.534 601 87 23 286 869 108343413 108343994 1.670000e-106 396.0
32 TraesCS7A01G115800 chr5D 89.032 155 13 2 2171 2321 543467409 543467563 3.040000e-44 189.0
33 TraesCS7A01G115800 chr2A 85.030 167 22 1 1397 1563 1495248 1495411 1.430000e-37 167.0
34 TraesCS7A01G115800 chr2A 87.179 117 14 1 284 399 1495413 1495297 5.200000e-27 132.0


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 TraesCS7A01G115800 chr7A 73944036 73946356 2320 False 4287.000000 4287 100.0000 1 2321 1 chr7A.!!$F1 2320
1 TraesCS7A01G115800 chr7A 642889035 642890384 1349 False 924.000000 946 88.9800 285 1565 2 chr7A.!!$F3 1280
2 TraesCS7A01G115800 chr7A 680378152 680379103 951 True 513.000000 811 89.4035 139 2321 2 chr7A.!!$R1 2182
3 TraesCS7A01G115800 chr7A 725604824 725605416 592 False 512.000000 512 82.5000 286 877 1 chr7A.!!$F2 591
4 TraesCS7A01G115800 chr3B 750901239 750902450 1211 True 667.333333 1090 88.3960 286 1564 3 chr3B.!!$R1 1278
5 TraesCS7A01G115800 chr4D 408578314 408579521 1207 False 842.000000 1057 87.6945 286 1565 2 chr4D.!!$F1 1279
6 TraesCS7A01G115800 chrUn 26079183 26080240 1057 True 661.000000 983 88.8255 2 2321 2 chrUn.!!$R1 2319
7 TraesCS7A01G115800 chr2D 532645595 532646583 988 True 610.000000 893 88.5070 2 2252 2 chr2D.!!$R1 2250
8 TraesCS7A01G115800 chr7B 219505621 219506665 1044 True 573.000000 824 87.8470 2 2321 2 chr7B.!!$R1 2319
9 TraesCS7A01G115800 chr7B 443743491 443743996 505 False 251.000000 331 87.1720 1574 2317 2 chr7B.!!$F1 743
10 TraesCS7A01G115800 chr1A 480836115 480837059 944 True 513.000000 817 91.3135 139 2321 2 chr1A.!!$R1 2182
11 TraesCS7A01G115800 chr1A 504087440 504087956 516 False 280.000000 377 88.7410 1574 2321 2 chr1A.!!$F1 747
12 TraesCS7A01G115800 chr6A 255035600 255036551 951 False 510.500000 806 89.3425 139 2321 2 chr6A.!!$F2 2182
13 TraesCS7A01G115800 chr6A 15630211 15631183 972 False 465.000000 732 90.7105 139 2321 2 chr6A.!!$F1 2182
14 TraesCS7A01G115800 chr5B 255409798 255410466 668 False 288.500000 427 79.3550 286 1064 2 chr5B.!!$F1 778
15 TraesCS7A01G115800 chr4B 108343413 108343994 581 False 396.000000 396 79.5340 286 869 1 chr4B.!!$F1 583

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
55 56 0.108041 TCTCGCTGCTGCATGAATGA 60.108 50.0 16.29 2.66 39.64 2.57 F
91 94 0.379669 ACGGCGTGTAGTAGATTCGG 59.620 55.0 13.76 0.00 0.00 4.30 F
1264 1419 0.394352 CCCATTCCTACACTGCCACC 60.394 60.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1423 0.469917 AGTGGCAGCAGTACAACACT 59.530 50.0 0.00 0.00 38.32 3.55 R
1270 1425 0.534877 CCAGTGGCAGCAGTACAACA 60.535 55.0 0.00 0.00 0.00 3.33 R
2104 2362 1.609208 AGAAACATGCGCAAGGAAGT 58.391 45.0 17.11 5.52 42.86 3.01 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
38 39 7.041303 TCACGTCTCACTAATCGCTAATTATCT 60.041 37.037 0.00 0.00 0.00 1.98
55 56 0.108041 TCTCGCTGCTGCATGAATGA 60.108 50.000 16.29 2.66 39.64 2.57
91 94 0.379669 ACGGCGTGTAGTAGATTCGG 59.620 55.000 13.76 0.00 0.00 4.30
107 110 3.423154 GGTTTCTCCACGGCTGCG 61.423 66.667 0.00 0.00 35.97 5.18
108 111 2.665185 GTTTCTCCACGGCTGCGT 60.665 61.111 0.00 0.00 0.00 5.24
128 131 2.680339 GTGAAGCTAGGATTCTTGCACC 59.320 50.000 10.20 1.69 42.71 5.01
236 239 4.963318 TCTATCTAGATGGGCTTGGTTG 57.037 45.455 15.79 0.00 0.00 3.77
240 243 2.912956 TCTAGATGGGCTTGGTTGTTCT 59.087 45.455 0.00 0.00 0.00 3.01
263 274 5.508280 ACCTAAAGCCCATGTAACTAACA 57.492 39.130 0.00 0.00 43.86 2.41
283 294 9.821662 ACTAACACATCTAATTTCGCTAAAAAC 57.178 29.630 0.00 0.00 0.00 2.43
284 295 9.820229 CTAACACATCTAATTTCGCTAAAAACA 57.180 29.630 0.00 0.00 0.00 2.83
313 325 8.632906 AAATTGCAAAAACCATCATAATTGGA 57.367 26.923 1.71 0.00 37.69 3.53
338 351 5.640147 ACCCTAATTCAGAAAACCATCACA 58.360 37.500 0.00 0.00 0.00 3.58
486 503 0.670546 AAATCTCACGGTGTCTGGCG 60.671 55.000 8.17 0.00 0.00 5.69
571 602 0.897863 CAGGGGGAAAAATCACGCCA 60.898 55.000 0.00 0.00 40.20 5.69
663 694 5.263599 CTCCACCTCATCTATCTATGCTCT 58.736 45.833 0.00 0.00 0.00 4.09
993 1148 1.654954 CTACAGAGTACGGGCACGCT 61.655 60.000 9.12 0.00 46.04 5.07
1011 1166 2.747460 GCAGCGATGGCAGGAACA 60.747 61.111 1.46 0.00 43.41 3.18
1090 1245 1.493871 CTCATGAGGGCCATCTCCTTT 59.506 52.381 19.75 0.00 34.21 3.11
1097 1252 1.228510 GCCATCTCCTTTCCCCCTG 59.771 63.158 0.00 0.00 0.00 4.45
1237 1392 1.429825 CTACCTCGCACTCAGGTCG 59.570 63.158 0.00 0.00 43.68 4.79
1239 1394 4.803426 CCTCGCACTCAGGTCGCC 62.803 72.222 0.00 0.00 0.00 5.54
1257 1412 1.819632 CGGCAGCCCATTCCTACAC 60.820 63.158 5.63 0.00 0.00 2.90
1258 1413 1.609783 GGCAGCCCATTCCTACACT 59.390 57.895 0.00 0.00 0.00 3.55
1259 1414 0.749454 GGCAGCCCATTCCTACACTG 60.749 60.000 0.00 0.00 0.00 3.66
1260 1415 1.379642 GCAGCCCATTCCTACACTGC 61.380 60.000 0.00 0.00 43.09 4.40
1261 1416 0.749454 CAGCCCATTCCTACACTGCC 60.749 60.000 0.00 0.00 0.00 4.85
1262 1417 1.207488 AGCCCATTCCTACACTGCCA 61.207 55.000 0.00 0.00 0.00 4.92
1263 1418 1.032114 GCCCATTCCTACACTGCCAC 61.032 60.000 0.00 0.00 0.00 5.01
1264 1419 0.394352 CCCATTCCTACACTGCCACC 60.394 60.000 0.00 0.00 0.00 4.61
1265 1420 0.744414 CCATTCCTACACTGCCACCG 60.744 60.000 0.00 0.00 0.00 4.94
1266 1421 1.078426 ATTCCTACACTGCCACCGC 60.078 57.895 0.00 0.00 0.00 5.68
1267 1422 2.536997 ATTCCTACACTGCCACCGCC 62.537 60.000 0.00 0.00 0.00 6.13
1268 1423 4.015406 CCTACACTGCCACCGCCA 62.015 66.667 0.00 0.00 0.00 5.69
1269 1424 2.434884 CTACACTGCCACCGCCAG 60.435 66.667 0.00 0.00 0.00 4.85
1270 1425 3.238497 TACACTGCCACCGCCAGT 61.238 61.111 0.00 0.00 0.00 4.00
1271 1426 3.529341 TACACTGCCACCGCCAGTG 62.529 63.158 17.20 17.20 46.83 3.66
1272 1427 4.935495 CACTGCCACCGCCAGTGT 62.935 66.667 12.11 0.00 45.74 3.55
1273 1428 4.189580 ACTGCCACCGCCAGTGTT 62.190 61.111 1.26 0.00 45.74 3.32
1274 1429 3.663176 CTGCCACCGCCAGTGTTG 61.663 66.667 1.26 0.00 45.74 3.33
1275 1430 4.497984 TGCCACCGCCAGTGTTGT 62.498 61.111 1.26 0.00 45.74 3.32
1276 1431 2.281208 GCCACCGCCAGTGTTGTA 60.281 61.111 1.26 0.00 45.74 2.41
1277 1432 2.613506 GCCACCGCCAGTGTTGTAC 61.614 63.158 1.26 0.00 45.74 2.90
1278 1433 1.070786 CCACCGCCAGTGTTGTACT 59.929 57.895 0.00 0.00 45.74 2.73
1350 1528 5.167303 AGGAAATTACTCAACAGGACCTC 57.833 43.478 0.00 0.00 0.00 3.85
1444 1622 5.854010 TGTCAAACGGCTCTAATAGATCT 57.146 39.130 0.00 0.00 0.00 2.75
1480 1658 5.353111 TGAAAACTGTCAGTACAATCGTGA 58.647 37.500 5.77 0.00 34.49 4.35
1481 1659 5.813157 TGAAAACTGTCAGTACAATCGTGAA 59.187 36.000 5.77 0.00 34.49 3.18
1482 1660 6.481976 TGAAAACTGTCAGTACAATCGTGAAT 59.518 34.615 5.77 0.00 34.49 2.57
1486 1664 6.452242 ACTGTCAGTACAATCGTGAATGTTA 58.548 36.000 2.87 0.00 34.49 2.41
1487 1665 7.097192 ACTGTCAGTACAATCGTGAATGTTAT 58.903 34.615 2.87 0.00 34.49 1.89
1488 1666 7.602644 ACTGTCAGTACAATCGTGAATGTTATT 59.397 33.333 2.87 0.00 34.49 1.40
1489 1667 8.317891 TGTCAGTACAATCGTGAATGTTATTT 57.682 30.769 0.00 0.00 30.91 1.40
1490 1668 8.227119 TGTCAGTACAATCGTGAATGTTATTTG 58.773 33.333 0.00 0.00 30.91 2.32
1491 1669 8.440059 GTCAGTACAATCGTGAATGTTATTTGA 58.560 33.333 0.00 0.00 0.00 2.69
1492 1670 8.994170 TCAGTACAATCGTGAATGTTATTTGAA 58.006 29.630 0.00 0.00 0.00 2.69
1493 1671 9.605955 CAGTACAATCGTGAATGTTATTTGAAA 57.394 29.630 0.00 0.00 0.00 2.69
1530 1708 8.930846 ATAGATGATGGTTTTCTGAATTAGGG 57.069 34.615 0.00 0.00 0.00 3.53
1531 1709 6.735556 AGATGATGGTTTTCTGAATTAGGGT 58.264 36.000 0.00 0.00 0.00 4.34
1532 1710 6.830838 AGATGATGGTTTTCTGAATTAGGGTC 59.169 38.462 0.00 0.00 0.00 4.46
1533 1711 5.261216 TGATGGTTTTCTGAATTAGGGTCC 58.739 41.667 0.00 0.00 0.00 4.46
1534 1712 4.042271 TGGTTTTCTGAATTAGGGTCCC 57.958 45.455 0.00 0.00 0.00 4.46
1535 1713 3.660669 TGGTTTTCTGAATTAGGGTCCCT 59.339 43.478 16.73 16.73 37.71 4.20
1536 1714 4.853276 TGGTTTTCTGAATTAGGGTCCCTA 59.147 41.667 14.22 14.22 34.61 3.53
1547 1725 3.652057 AGGGTCCCTAATTGTGATGTG 57.348 47.619 9.39 0.00 28.47 3.21
1548 1726 2.919602 AGGGTCCCTAATTGTGATGTGT 59.080 45.455 9.39 0.00 28.47 3.72
1549 1727 3.333680 AGGGTCCCTAATTGTGATGTGTT 59.666 43.478 9.39 0.00 28.47 3.32
1550 1728 4.086457 GGGTCCCTAATTGTGATGTGTTT 58.914 43.478 0.00 0.00 0.00 2.83
1551 1729 4.526650 GGGTCCCTAATTGTGATGTGTTTT 59.473 41.667 0.00 0.00 0.00 2.43
1552 1730 5.011635 GGGTCCCTAATTGTGATGTGTTTTT 59.988 40.000 0.00 0.00 0.00 1.94
1553 1731 5.925969 GGTCCCTAATTGTGATGTGTTTTTG 59.074 40.000 0.00 0.00 0.00 2.44
1554 1732 5.405269 GTCCCTAATTGTGATGTGTTTTTGC 59.595 40.000 0.00 0.00 0.00 3.68
1555 1733 5.069648 TCCCTAATTGTGATGTGTTTTTGCA 59.930 36.000 0.00 0.00 0.00 4.08
1556 1734 5.757320 CCCTAATTGTGATGTGTTTTTGCAA 59.243 36.000 0.00 0.00 0.00 4.08
1557 1735 6.427547 CCCTAATTGTGATGTGTTTTTGCAAT 59.572 34.615 0.00 0.00 0.00 3.56
1558 1736 7.041235 CCCTAATTGTGATGTGTTTTTGCAATT 60.041 33.333 0.00 0.00 38.25 2.32
1559 1737 8.344098 CCTAATTGTGATGTGTTTTTGCAATTT 58.656 29.630 0.00 0.00 36.72 1.82
1562 1740 7.840342 TTGTGATGTGTTTTTGCAATTTACT 57.160 28.000 0.00 0.00 0.00 2.24
1563 1741 7.462109 TGTGATGTGTTTTTGCAATTTACTC 57.538 32.000 0.00 0.94 0.00 2.59
1566 1744 7.010923 GTGATGTGTTTTTGCAATTTACTCCAA 59.989 33.333 0.00 0.00 0.00 3.53
1569 1747 8.273780 TGTGTTTTTGCAATTTACTCCAAAAT 57.726 26.923 0.00 0.00 37.13 1.82
1571 1749 9.644993 GTGTTTTTGCAATTTACTCCAAAATAC 57.355 29.630 0.00 0.00 37.13 1.89
1619 1806 3.366476 GCTTATCGCAGTAGGTCGATGAT 60.366 47.826 7.30 0.00 44.10 2.45
1625 1812 2.159099 GCAGTAGGTCGATGATGGTTCA 60.159 50.000 0.00 0.00 36.00 3.18
1636 1823 1.633432 TGATGGTTCATCTTCCCCGTT 59.367 47.619 9.00 0.00 41.06 4.44
1665 1856 3.723235 CTGCTAGACGCCGCCACAT 62.723 63.158 0.00 0.00 38.05 3.21
1691 1930 1.526575 CCCATGAAACGGCAGCAACT 61.527 55.000 0.00 0.00 0.00 3.16
1692 1931 1.164411 CCATGAAACGGCAGCAACTA 58.836 50.000 0.00 0.00 0.00 2.24
1698 1944 5.637006 TGAAACGGCAGCAACTAATAAAT 57.363 34.783 0.00 0.00 0.00 1.40
1750 2002 3.587061 CCCTCCATTACCCTACATATGCA 59.413 47.826 1.58 0.00 0.00 3.96
1792 2044 0.681733 AGCCATCGCCTCATCGTAAT 59.318 50.000 0.00 0.00 34.57 1.89
1867 2125 4.228567 TGACGGAACCGCAGCACA 62.229 61.111 13.32 3.86 44.19 4.57
1895 2153 4.980805 GTCACCGGTGCCTCGCAA 62.981 66.667 30.25 7.86 41.47 4.85
1938 2196 0.899720 GTATGGTCTTCACCCGGTCA 59.100 55.000 0.00 0.00 42.99 4.02
1951 2209 2.825836 GGTCAAGGCTGCCATCGG 60.826 66.667 22.65 7.00 0.00 4.18
2010 2268 2.657296 CGTTGTCCGTCGTGCAGT 60.657 61.111 0.00 0.00 0.00 4.40
2019 2277 1.670087 CCGTCGTGCAGTCTTTCAGAT 60.670 52.381 0.00 0.00 0.00 2.90
2071 2329 4.367023 GCCGGTCCACGTGCAGTA 62.367 66.667 10.91 0.00 42.24 2.74
2104 2362 2.071778 ACAAGAGGAGCTTTTGGCAA 57.928 45.000 0.00 0.00 44.79 4.52
2105 2363 1.683385 ACAAGAGGAGCTTTTGGCAAC 59.317 47.619 0.00 0.00 44.79 4.17
2136 2395 3.809279 GCATGTTTCTTTTGTTTCCCCAG 59.191 43.478 0.00 0.00 0.00 4.45
2145 2404 6.843752 TCTTTTGTTTCCCCAGTATCACTAA 58.156 36.000 0.00 0.00 0.00 2.24
2191 2452 8.681486 ATCATTGTAATATGCAAGCTGAACTA 57.319 30.769 0.00 0.00 0.00 2.24
2220 2484 2.012673 GCGTCAATCTTCCAATCAGCT 58.987 47.619 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.842462 ACGTGACTGCACCAGGGA 60.842 61.111 0.00 0.00 42.09 4.20
3 4 0.941463 GTGAGACGTGACTGCACCAG 60.941 60.000 0.00 0.00 42.09 4.00
12 13 4.895224 ATTAGCGATTAGTGAGACGTGA 57.105 40.909 0.00 0.00 0.00 4.35
38 39 1.698714 CGTCATTCATGCAGCAGCGA 61.699 55.000 0.00 0.00 46.23 4.93
107 110 2.680339 GGTGCAAGAATCCTAGCTTCAC 59.320 50.000 0.00 0.00 0.00 3.18
108 111 2.573462 AGGTGCAAGAATCCTAGCTTCA 59.427 45.455 0.00 0.00 0.00 3.02
121 124 6.808008 TTTCTCTTGAATTCTAGGTGCAAG 57.192 37.500 15.49 9.36 37.79 4.01
150 153 7.044314 GGCACGTTGTATATTAGATGCAAAAAC 60.044 37.037 0.00 0.00 33.48 2.43
165 168 5.353123 CCTTACAATAACTGGCACGTTGTAT 59.647 40.000 11.08 2.45 35.80 2.29
167 170 3.500680 CCTTACAATAACTGGCACGTTGT 59.499 43.478 11.08 9.01 36.94 3.32
235 238 5.249852 AGTTACATGGGCTTTAGGTAGAACA 59.750 40.000 0.00 0.00 0.00 3.18
236 239 5.742063 AGTTACATGGGCTTTAGGTAGAAC 58.258 41.667 0.00 0.00 0.00 3.01
240 243 6.013553 TGTGTTAGTTACATGGGCTTTAGGTA 60.014 38.462 0.00 0.00 39.39 3.08
281 292 7.856145 TGATGGTTTTTGCAATTTACTTGTT 57.144 28.000 0.00 0.00 37.18 2.83
282 293 9.553064 TTATGATGGTTTTTGCAATTTACTTGT 57.447 25.926 0.00 0.00 37.18 3.16
303 315 7.690454 TCTGAATTAGGGTCTCCAATTATGA 57.310 36.000 0.00 0.00 34.83 2.15
313 325 5.946377 GTGATGGTTTTCTGAATTAGGGTCT 59.054 40.000 0.00 0.00 0.00 3.85
363 378 4.644234 TGAAAACTGTCAGCAGAATGGAAA 59.356 37.500 0.00 0.00 45.28 3.13
364 379 4.206375 TGAAAACTGTCAGCAGAATGGAA 58.794 39.130 0.00 0.00 45.28 3.53
365 380 3.819368 TGAAAACTGTCAGCAGAATGGA 58.181 40.909 0.00 0.00 45.28 3.41
424 439 4.692930 GCCCCATCTGCCAGAAAT 57.307 55.556 0.00 0.00 0.00 2.17
481 498 1.350193 CAGCTTACTGTACACGCCAG 58.650 55.000 0.00 0.00 39.22 4.85
620 651 2.043852 AGATCACGGAGGCGGAGT 60.044 61.111 0.00 0.00 0.00 3.85
718 749 4.393155 TGCTTGGTCGATGCCGCT 62.393 61.111 0.00 0.00 35.37 5.52
993 1148 2.747460 GTTCCTGCCATCGCTGCA 60.747 61.111 0.00 0.00 37.17 4.41
1090 1245 3.562232 AACGGCGAAACAGGGGGA 61.562 61.111 16.62 0.00 0.00 4.81
1216 1371 2.701780 CCTGAGTGCGAGGTAGCGT 61.702 63.158 0.00 0.00 40.67 5.07
1237 1392 4.189580 TAGGAATGGGCTGCCGGC 62.190 66.667 22.73 22.73 40.90 6.13
1239 1394 1.819632 GTGTAGGAATGGGCTGCCG 60.820 63.158 13.40 0.00 0.00 5.69
1240 1395 0.749454 CAGTGTAGGAATGGGCTGCC 60.749 60.000 11.05 11.05 0.00 4.85
1268 1423 0.469917 AGTGGCAGCAGTACAACACT 59.530 50.000 0.00 0.00 38.32 3.55
1269 1424 0.588252 CAGTGGCAGCAGTACAACAC 59.412 55.000 0.00 0.00 0.00 3.32
1270 1425 0.534877 CCAGTGGCAGCAGTACAACA 60.535 55.000 0.00 0.00 0.00 3.33
1271 1426 2.247790 CCAGTGGCAGCAGTACAAC 58.752 57.895 0.00 0.00 0.00 3.32
1272 1427 4.798433 CCAGTGGCAGCAGTACAA 57.202 55.556 0.00 0.00 0.00 2.41
1350 1528 0.956410 AGAGTGAGGAGACGGACGTG 60.956 60.000 0.53 0.00 0.00 4.49
1504 1682 9.359653 CCCTAATTCAGAAAACCATCATCTATT 57.640 33.333 0.00 0.00 0.00 1.73
1505 1683 8.506083 ACCCTAATTCAGAAAACCATCATCTAT 58.494 33.333 0.00 0.00 0.00 1.98
1506 1684 7.872138 ACCCTAATTCAGAAAACCATCATCTA 58.128 34.615 0.00 0.00 0.00 1.98
1507 1685 6.735556 ACCCTAATTCAGAAAACCATCATCT 58.264 36.000 0.00 0.00 0.00 2.90
1508 1686 6.039829 GGACCCTAATTCAGAAAACCATCATC 59.960 42.308 0.00 0.00 0.00 2.92
1509 1687 5.893824 GGACCCTAATTCAGAAAACCATCAT 59.106 40.000 0.00 0.00 0.00 2.45
1510 1688 5.261216 GGACCCTAATTCAGAAAACCATCA 58.739 41.667 0.00 0.00 0.00 3.07
1511 1689 4.645136 GGGACCCTAATTCAGAAAACCATC 59.355 45.833 2.09 0.00 0.00 3.51
1512 1690 4.294970 AGGGACCCTAATTCAGAAAACCAT 59.705 41.667 12.85 0.00 28.47 3.55
1513 1691 3.660669 AGGGACCCTAATTCAGAAAACCA 59.339 43.478 12.85 0.00 28.47 3.67
1514 1692 4.317530 AGGGACCCTAATTCAGAAAACC 57.682 45.455 12.85 0.00 28.47 3.27
1526 1704 4.108570 ACACATCACAATTAGGGACCCTA 58.891 43.478 16.95 16.95 34.61 3.53
1527 1705 2.919602 ACACATCACAATTAGGGACCCT 59.080 45.455 19.48 19.48 37.71 4.34
1528 1706 3.366052 ACACATCACAATTAGGGACCC 57.634 47.619 0.59 0.59 27.79 4.46
1529 1707 5.722021 AAAACACATCACAATTAGGGACC 57.278 39.130 0.00 0.00 27.79 4.46
1530 1708 5.405269 GCAAAAACACATCACAATTAGGGAC 59.595 40.000 0.00 0.00 27.79 4.46
1531 1709 5.069648 TGCAAAAACACATCACAATTAGGGA 59.930 36.000 0.00 0.00 0.00 4.20
1532 1710 5.295950 TGCAAAAACACATCACAATTAGGG 58.704 37.500 0.00 0.00 0.00 3.53
1533 1711 6.841443 TTGCAAAAACACATCACAATTAGG 57.159 33.333 0.00 0.00 0.00 2.69
1536 1714 8.891720 AGTAAATTGCAAAAACACATCACAATT 58.108 25.926 1.71 0.00 37.73 2.32
1537 1715 8.436046 AGTAAATTGCAAAAACACATCACAAT 57.564 26.923 1.71 0.00 0.00 2.71
1538 1716 7.010923 GGAGTAAATTGCAAAAACACATCACAA 59.989 33.333 1.71 0.00 0.00 3.33
1539 1717 6.478344 GGAGTAAATTGCAAAAACACATCACA 59.522 34.615 1.71 0.00 0.00 3.58
1540 1718 6.478344 TGGAGTAAATTGCAAAAACACATCAC 59.522 34.615 1.71 0.00 0.00 3.06
1541 1719 6.577103 TGGAGTAAATTGCAAAAACACATCA 58.423 32.000 1.71 0.07 0.00 3.07
1542 1720 7.475771 TTGGAGTAAATTGCAAAAACACATC 57.524 32.000 1.71 0.00 0.00 3.06
1543 1721 7.856145 TTTGGAGTAAATTGCAAAAACACAT 57.144 28.000 1.71 0.00 35.79 3.21
1544 1722 7.672983 TTTTGGAGTAAATTGCAAAAACACA 57.327 28.000 1.71 3.25 42.72 3.72
1545 1723 9.644993 GTATTTTGGAGTAAATTGCAAAAACAC 57.355 29.630 1.71 0.71 46.52 3.32
1546 1724 8.831550 GGTATTTTGGAGTAAATTGCAAAAACA 58.168 29.630 1.71 0.00 46.52 2.83
1547 1725 9.051679 AGGTATTTTGGAGTAAATTGCAAAAAC 57.948 29.630 1.71 1.89 46.52 2.43
1550 1728 9.699703 GTTAGGTATTTTGGAGTAAATTGCAAA 57.300 29.630 1.71 0.00 36.74 3.68
1551 1729 8.024285 CGTTAGGTATTTTGGAGTAAATTGCAA 58.976 33.333 0.00 0.00 0.00 4.08
1552 1730 7.531716 CGTTAGGTATTTTGGAGTAAATTGCA 58.468 34.615 0.00 0.00 0.00 4.08
1553 1731 6.471198 GCGTTAGGTATTTTGGAGTAAATTGC 59.529 38.462 0.00 0.00 0.00 3.56
1554 1732 7.531716 TGCGTTAGGTATTTTGGAGTAAATTG 58.468 34.615 0.00 0.00 0.00 2.32
1555 1733 7.690952 TGCGTTAGGTATTTTGGAGTAAATT 57.309 32.000 0.00 0.00 0.00 1.82
1556 1734 7.773690 AGATGCGTTAGGTATTTTGGAGTAAAT 59.226 33.333 0.00 0.00 0.00 1.40
1557 1735 7.107542 AGATGCGTTAGGTATTTTGGAGTAAA 58.892 34.615 0.00 0.00 0.00 2.01
1558 1736 6.646267 AGATGCGTTAGGTATTTTGGAGTAA 58.354 36.000 0.00 0.00 0.00 2.24
1559 1737 6.229936 AGATGCGTTAGGTATTTTGGAGTA 57.770 37.500 0.00 0.00 0.00 2.59
1560 1738 5.099042 AGATGCGTTAGGTATTTTGGAGT 57.901 39.130 0.00 0.00 0.00 3.85
1561 1739 7.441157 TGATTAGATGCGTTAGGTATTTTGGAG 59.559 37.037 0.00 0.00 0.00 3.86
1562 1740 7.276658 TGATTAGATGCGTTAGGTATTTTGGA 58.723 34.615 0.00 0.00 0.00 3.53
1563 1741 7.490962 TGATTAGATGCGTTAGGTATTTTGG 57.509 36.000 0.00 0.00 0.00 3.28
1569 1747 8.467598 GGATAGATTGATTAGATGCGTTAGGTA 58.532 37.037 0.00 0.00 0.00 3.08
1571 1749 6.473778 CGGATAGATTGATTAGATGCGTTAGG 59.526 42.308 0.00 0.00 0.00 2.69
1619 1806 0.768622 ACAACGGGGAAGATGAACCA 59.231 50.000 0.00 0.00 0.00 3.67
1625 1812 3.223674 AGACAAAACAACGGGGAAGAT 57.776 42.857 0.00 0.00 0.00 2.40
1636 1823 2.800544 GCGTCTAGCAGAAGACAAAACA 59.199 45.455 12.54 0.00 45.13 2.83
1665 1856 1.004320 CCGTTTCATGGGGTGTCGA 60.004 57.895 0.00 0.00 0.00 4.20
1691 1930 4.708909 TGTGGTGAATGCTGCCATTTATTA 59.291 37.500 0.00 0.00 41.60 0.98
1692 1931 3.514706 TGTGGTGAATGCTGCCATTTATT 59.485 39.130 0.00 0.00 41.60 1.40
1698 1944 0.966875 GGATGTGGTGAATGCTGCCA 60.967 55.000 0.00 0.00 0.00 4.92
1750 2002 6.093357 GCTGCTTAAATCTAGCACTTTCTTCT 59.907 38.462 0.00 0.00 43.30 2.85
1792 2044 3.690280 TGATGGCGAGTGGCGTGA 61.690 61.111 0.00 0.00 44.92 4.35
1867 2125 4.320456 CGGTGACCAGCTGCAGGT 62.320 66.667 17.19 17.19 43.46 4.00
1914 2172 1.473677 CGGGTGAAGACCATACGTACA 59.526 52.381 0.00 0.00 45.25 2.90
2019 2277 2.621407 GGCATGAACAAAGGGATGAGGA 60.621 50.000 0.00 0.00 0.00 3.71
2071 2329 2.613977 CCTCTTGTTCCTCTCGCACAAT 60.614 50.000 0.00 0.00 30.18 2.71
2104 2362 1.609208 AGAAACATGCGCAAGGAAGT 58.391 45.000 17.11 5.52 42.86 3.01
2105 2363 2.712057 AAGAAACATGCGCAAGGAAG 57.288 45.000 17.11 4.80 45.01 3.46
2136 2395 1.949465 CCCGGTTGCCTTAGTGATAC 58.051 55.000 0.00 0.00 0.00 2.24
2145 2404 4.394712 CGAGAAGCCCGGTTGCCT 62.395 66.667 0.00 0.00 0.00 4.75
2166 2427 7.578310 AGTTCAGCTTGCATATTACAATGAT 57.422 32.000 0.00 0.00 0.00 2.45
2191 2452 4.717877 TGGAAGATTGACGCCAATGATAT 58.282 39.130 0.20 0.00 42.66 1.63


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

AutoCloner maintained by Alex Coulton.