Multiple sequence alignment - TraesCS1D01G433700

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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 TraesCS1D01G433700 chr1D 100.000 2276 0 0 1 2276 483005583 483003308 0.000000e+00 4204.0
1 TraesCS1D01G433700 chr1D 80.515 272 44 3 1910 2175 482931413 482931145 1.380000e-47 200.0
2 TraesCS1D01G433700 chr1D 91.667 48 2 2 1898 1944 483050163 483050209 5.250000e-07 65.8
3 TraesCS1D01G433700 chr4A 95.329 1306 58 1 1 1303 626488355 626487050 0.000000e+00 2071.0
4 TraesCS1D01G433700 chr5A 90.575 1305 115 7 1 1302 244703381 244702082 0.000000e+00 1722.0
5 TraesCS1D01G433700 chr3B 94.206 932 42 5 354 1275 779583691 779582762 0.000000e+00 1411.0
6 TraesCS1D01G433700 chr1B 93.827 405 24 1 1872 2276 671268680 671268277 1.930000e-170 608.0
7 TraesCS1D01G433700 chr1B 92.840 405 24 2 1872 2276 671329049 671328650 1.170000e-162 582.0
8 TraesCS1D01G433700 chr1B 92.840 405 24 2 1872 2276 671386755 671386356 1.170000e-162 582.0
9 TraesCS1D01G433700 chr1B 92.593 405 25 2 1872 2276 671358559 671358160 5.450000e-161 577.0
10 TraesCS1D01G433700 chr1B 88.947 380 33 8 1482 1860 671387494 671387123 5.730000e-126 460.0
11 TraesCS1D01G433700 chr1B 88.684 380 33 8 1482 1860 671329788 671329418 2.670000e-124 455.0
12 TraesCS1D01G433700 chr1B 88.684 380 33 8 1482 1860 671359297 671358927 2.670000e-124 455.0
13 TraesCS1D01G433700 chr1B 88.978 372 31 8 1482 1852 671276174 671275812 3.450000e-123 451.0
14 TraesCS1D01G433700 chr1B 93.333 120 7 1 2157 2276 671267520 671267402 2.320000e-40 176.0
15 TraesCS1D01G433700 chr1B 92.500 120 8 1 2157 2276 671327893 671327775 1.080000e-38 171.0
16 TraesCS1D01G433700 chr1B 92.500 120 8 1 2157 2276 671357403 671357285 1.080000e-38 171.0
17 TraesCS1D01G433700 chr1B 92.500 120 8 1 2157 2276 671385599 671385481 1.080000e-38 171.0
18 TraesCS1D01G433700 chr1B 91.667 48 2 2 1898 1944 671547917 671547963 5.250000e-07 65.8
19 TraesCS1D01G433700 chr1B 91.489 47 4 0 1898 1944 672819759 672819805 5.250000e-07 65.8
20 TraesCS1D01G433700 chr1A 90.909 440 32 4 1789 2228 579154994 579155425 3.260000e-163 584.0
21 TraesCS1D01G433700 chr1A 89.706 204 18 3 1482 1683 579154141 579154343 8.070000e-65 257.0
22 TraesCS1D01G433700 chr1A 92.424 66 0 4 1721 1785 579154341 579154402 3.110000e-14 89.8


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 TraesCS1D01G433700 chr1D 483003308 483005583 2275 True 4204.000000 4204 100.000000 1 2276 1 chr1D.!!$R2 2275
1 TraesCS1D01G433700 chr4A 626487050 626488355 1305 True 2071.000000 2071 95.329000 1 1303 1 chr4A.!!$R1 1302
2 TraesCS1D01G433700 chr5A 244702082 244703381 1299 True 1722.000000 1722 90.575000 1 1302 1 chr5A.!!$R1 1301
3 TraesCS1D01G433700 chr3B 779582762 779583691 929 True 1411.000000 1411 94.206000 354 1275 1 chr3B.!!$R1 921
4 TraesCS1D01G433700 chr1B 671385481 671387494 2013 True 404.333333 582 91.429000 1482 2276 3 chr1B.!!$R5 794
5 TraesCS1D01G433700 chr1B 671327775 671329788 2013 True 402.666667 582 91.341333 1482 2276 3 chr1B.!!$R3 794
6 TraesCS1D01G433700 chr1B 671357285 671359297 2012 True 401.000000 577 91.259000 1482 2276 3 chr1B.!!$R4 794
7 TraesCS1D01G433700 chr1B 671267402 671268680 1278 True 392.000000 608 93.580000 1872 2276 2 chr1B.!!$R2 404
8 TraesCS1D01G433700 chr1A 579154141 579155425 1284 False 310.266667 584 91.013000 1482 2228 3 chr1A.!!$F1 746

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
935 939 0.18135 GGGGTCTCGGATGCTTTCAT 59.819 55.0 0.0 0.0 35.17 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 2436 0.107459 AGATTTTCTGCCTCGGCTCC 60.107 55.0 9.65 0.0 42.51 4.7 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
64 65 0.843309 TTCTGCCCAGTTGGACAAGA 59.157 50.000 0.00 0.00 37.39 3.02
237 238 4.267928 GGCAACTATACTGTAAAGTCTGCG 59.732 45.833 0.00 0.00 32.72 5.18
261 262 1.729472 CGTTCTCTCGTGACTCGCAAT 60.729 52.381 0.00 0.00 39.67 3.56
306 307 5.183140 AGGGGTGAATACAAAAACTTCATCG 59.817 40.000 0.00 0.00 32.07 3.84
318 319 7.169982 ACAAAAACTTCATCGTCAAACAAACAA 59.830 29.630 0.00 0.00 0.00 2.83
477 478 4.832823 TGTCGGGCTATGAATGAAGATCTA 59.167 41.667 0.00 0.00 0.00 1.98
563 564 2.920524 TCTTCGTTTACCAACCTTGCA 58.079 42.857 0.00 0.00 0.00 4.08
765 769 2.603652 GGCGAAAGGGAGAAGGGGT 61.604 63.158 0.00 0.00 0.00 4.95
840 844 0.758734 ATGGTGCGCTAGCTATGGAA 59.241 50.000 13.93 0.00 45.42 3.53
891 895 3.014623 TCGGTCTCATCTCGCTTTTCTA 58.985 45.455 0.00 0.00 0.00 2.10
914 918 1.381851 CTTGGAGCAAGCCCCTTCT 59.618 57.895 0.00 0.00 34.63 2.85
935 939 0.181350 GGGGTCTCGGATGCTTTCAT 59.819 55.000 0.00 0.00 35.17 2.57
950 954 4.523943 TGCTTTCATGGCTGAATTACTTGT 59.476 37.500 0.00 0.00 40.95 3.16
973 977 4.801330 TTCAGAGAAGGCGTGATCTTTA 57.199 40.909 0.00 0.00 0.00 1.85
1154 1165 4.473196 TGTTGGGAGAGCCTGTAATATTCA 59.527 41.667 0.00 0.00 0.00 2.57
1157 1168 3.069729 GGGAGAGCCTGTAATATTCACGT 59.930 47.826 0.00 0.00 0.00 4.49
1378 1389 7.904558 AAGGAAAGAAGAATTGAAAAGGACT 57.095 32.000 0.00 0.00 0.00 3.85
1379 1390 7.517614 AGGAAAGAAGAATTGAAAAGGACTC 57.482 36.000 0.00 0.00 0.00 3.36
1380 1391 6.491745 AGGAAAGAAGAATTGAAAAGGACTCC 59.508 38.462 0.00 0.00 0.00 3.85
1381 1392 5.948992 AAGAAGAATTGAAAAGGACTCCG 57.051 39.130 0.00 0.00 0.00 4.63
1382 1393 3.753797 AGAAGAATTGAAAAGGACTCCGC 59.246 43.478 0.00 0.00 0.00 5.54
1383 1394 3.140325 AGAATTGAAAAGGACTCCGCA 57.860 42.857 0.00 0.00 0.00 5.69
1384 1395 3.690460 AGAATTGAAAAGGACTCCGCAT 58.310 40.909 0.00 0.00 0.00 4.73
1385 1396 4.843728 AGAATTGAAAAGGACTCCGCATA 58.156 39.130 0.00 0.00 0.00 3.14
1386 1397 5.253330 AGAATTGAAAAGGACTCCGCATAA 58.747 37.500 0.00 0.00 0.00 1.90
1387 1398 5.710099 AGAATTGAAAAGGACTCCGCATAAA 59.290 36.000 0.00 0.00 0.00 1.40
1388 1399 5.975693 ATTGAAAAGGACTCCGCATAAAA 57.024 34.783 0.00 0.00 0.00 1.52
1389 1400 5.975693 TTGAAAAGGACTCCGCATAAAAT 57.024 34.783 0.00 0.00 0.00 1.82
1390 1401 5.560966 TGAAAAGGACTCCGCATAAAATC 57.439 39.130 0.00 0.00 0.00 2.17
1391 1402 4.094294 TGAAAAGGACTCCGCATAAAATCG 59.906 41.667 0.00 0.00 0.00 3.34
1392 1403 2.981859 AGGACTCCGCATAAAATCGT 57.018 45.000 0.00 0.00 0.00 3.73
1393 1404 2.822764 AGGACTCCGCATAAAATCGTC 58.177 47.619 0.00 0.00 0.00 4.20
1394 1405 2.431057 AGGACTCCGCATAAAATCGTCT 59.569 45.455 0.00 0.00 0.00 4.18
1395 1406 3.635373 AGGACTCCGCATAAAATCGTCTA 59.365 43.478 0.00 0.00 0.00 2.59
1396 1407 3.982058 GGACTCCGCATAAAATCGTCTAG 59.018 47.826 0.00 0.00 0.00 2.43
1397 1408 3.978687 ACTCCGCATAAAATCGTCTAGG 58.021 45.455 0.00 0.00 0.00 3.02
1398 1409 3.383825 ACTCCGCATAAAATCGTCTAGGT 59.616 43.478 0.00 0.00 0.00 3.08
1399 1410 3.713288 TCCGCATAAAATCGTCTAGGTG 58.287 45.455 0.00 0.00 0.00 4.00
1400 1411 2.221055 CCGCATAAAATCGTCTAGGTGC 59.779 50.000 0.00 0.00 0.00 5.01
1401 1412 2.097396 CGCATAAAATCGTCTAGGTGCG 60.097 50.000 2.00 2.00 46.15 5.34
1402 1413 2.348591 GCATAAAATCGTCTAGGTGCGC 60.349 50.000 0.00 0.00 0.00 6.09
1403 1414 2.658373 TAAAATCGTCTAGGTGCGCA 57.342 45.000 5.66 5.66 0.00 6.09
1404 1415 1.803334 AAAATCGTCTAGGTGCGCAA 58.197 45.000 14.00 0.00 0.00 4.85
1405 1416 2.024176 AAATCGTCTAGGTGCGCAAT 57.976 45.000 14.00 6.64 0.00 3.56
1406 1417 2.882927 AATCGTCTAGGTGCGCAATA 57.117 45.000 14.00 7.63 0.00 1.90
1407 1418 2.135664 ATCGTCTAGGTGCGCAATAC 57.864 50.000 14.00 5.65 0.00 1.89
1408 1419 1.100510 TCGTCTAGGTGCGCAATACT 58.899 50.000 14.00 13.93 0.00 2.12
1409 1420 1.475280 TCGTCTAGGTGCGCAATACTT 59.525 47.619 14.00 0.00 0.00 2.24
1410 1421 1.588404 CGTCTAGGTGCGCAATACTTG 59.412 52.381 14.00 12.19 0.00 3.16
1411 1422 2.734175 CGTCTAGGTGCGCAATACTTGA 60.734 50.000 14.00 14.41 0.00 3.02
1412 1423 3.259064 GTCTAGGTGCGCAATACTTGAA 58.741 45.455 14.00 0.00 0.00 2.69
1413 1424 3.871594 GTCTAGGTGCGCAATACTTGAAT 59.128 43.478 14.00 0.00 0.00 2.57
1414 1425 5.047847 GTCTAGGTGCGCAATACTTGAATA 58.952 41.667 14.00 0.00 0.00 1.75
1415 1426 5.047847 TCTAGGTGCGCAATACTTGAATAC 58.952 41.667 14.00 0.00 0.00 1.89
1416 1427 3.605634 AGGTGCGCAATACTTGAATACA 58.394 40.909 14.00 0.00 0.00 2.29
1417 1428 4.199310 AGGTGCGCAATACTTGAATACAT 58.801 39.130 14.00 0.00 0.00 2.29
1418 1429 4.273480 AGGTGCGCAATACTTGAATACATC 59.727 41.667 14.00 0.00 0.00 3.06
1419 1430 4.273480 GGTGCGCAATACTTGAATACATCT 59.727 41.667 14.00 0.00 0.00 2.90
1420 1431 5.465390 GGTGCGCAATACTTGAATACATCTA 59.535 40.000 14.00 0.00 0.00 1.98
1421 1432 6.147821 GGTGCGCAATACTTGAATACATCTAT 59.852 38.462 14.00 0.00 0.00 1.98
1422 1433 7.330946 GGTGCGCAATACTTGAATACATCTATA 59.669 37.037 14.00 0.00 0.00 1.31
1423 1434 8.873830 GTGCGCAATACTTGAATACATCTATAT 58.126 33.333 14.00 0.00 0.00 0.86
1424 1435 8.872845 TGCGCAATACTTGAATACATCTATATG 58.127 33.333 8.16 0.00 39.17 1.78
1425 1436 7.848051 GCGCAATACTTGAATACATCTATATGC 59.152 37.037 0.30 0.00 36.50 3.14
1426 1437 8.872845 CGCAATACTTGAATACATCTATATGCA 58.127 33.333 0.00 0.00 36.50 3.96
1432 1443 9.650539 ACTTGAATACATCTATATGCATGTCTC 57.349 33.333 10.16 0.67 36.50 3.36
1433 1444 9.096160 CTTGAATACATCTATATGCATGTCTCC 57.904 37.037 10.16 0.00 36.50 3.71
1434 1445 7.559486 TGAATACATCTATATGCATGTCTCCC 58.441 38.462 10.16 0.00 36.50 4.30
1435 1446 7.401204 TGAATACATCTATATGCATGTCTCCCT 59.599 37.037 10.16 0.00 36.50 4.20
1436 1447 7.746243 ATACATCTATATGCATGTCTCCCTT 57.254 36.000 10.16 0.00 36.50 3.95
1437 1448 6.047511 ACATCTATATGCATGTCTCCCTTC 57.952 41.667 10.16 0.00 36.50 3.46
1438 1449 5.545335 ACATCTATATGCATGTCTCCCTTCA 59.455 40.000 10.16 0.00 36.50 3.02
1439 1450 6.043590 ACATCTATATGCATGTCTCCCTTCAA 59.956 38.462 10.16 0.00 36.50 2.69
1440 1451 6.499106 TCTATATGCATGTCTCCCTTCAAA 57.501 37.500 10.16 0.00 0.00 2.69
1441 1452 6.899089 TCTATATGCATGTCTCCCTTCAAAA 58.101 36.000 10.16 0.00 0.00 2.44
1442 1453 7.345691 TCTATATGCATGTCTCCCTTCAAAAA 58.654 34.615 10.16 0.00 0.00 1.94
1477 1488 8.509690 TCTAGACGTAATTTACCATCCTAATCG 58.490 37.037 1.04 0.00 0.00 3.34
1478 1489 7.281040 AGACGTAATTTACCATCCTAATCGA 57.719 36.000 1.04 0.00 0.00 3.59
1479 1490 7.144000 AGACGTAATTTACCATCCTAATCGAC 58.856 38.462 1.04 0.00 0.00 4.20
1480 1491 5.916883 ACGTAATTTACCATCCTAATCGACG 59.083 40.000 1.04 0.00 31.89 5.12
1547 1558 3.262686 GGAAAGCGGCGGATCGAC 61.263 66.667 9.78 0.00 0.00 4.20
1626 1638 2.071540 CGGGAAAAGAACGGTACTTCC 58.928 52.381 0.00 0.00 35.76 3.46
1629 1641 4.139786 GGGAAAAGAACGGTACTTCCTTT 58.860 43.478 7.42 0.86 36.57 3.11
1634 1646 3.957591 GAACGGTACTTCCTTTCTCCT 57.042 47.619 0.00 0.00 40.13 3.69
1640 1653 8.773033 AACGGTACTTCCTTTCTCCTATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1659 1673 2.182516 ATTTCGATCCCTCTCCCTGT 57.817 50.000 0.00 0.00 0.00 4.00
1677 1691 2.587247 TTGCCCGCTCTCTCAAGCT 61.587 57.895 0.00 0.00 40.23 3.74
1683 1697 1.066914 CGCTCTCTCAAGCTGTGTTC 58.933 55.000 0.00 0.00 40.23 3.18
1702 1716 1.525995 CCGGCGTGGGCATAAGATT 60.526 57.895 6.01 0.00 42.47 2.40
1715 1729 5.619625 GCATAAGATTTCCTAGATGCCAC 57.380 43.478 0.00 0.00 37.92 5.01
1733 1747 2.822255 GGCCGTTGCTGCCGATAA 60.822 61.111 0.00 0.00 39.48 1.75
1734 1748 2.186826 GGCCGTTGCTGCCGATAAT 61.187 57.895 0.00 0.00 39.48 1.28
1735 1749 1.279840 GCCGTTGCTGCCGATAATC 59.720 57.895 0.00 0.00 33.53 1.75
1785 1800 0.600057 CCCAGCCTTTTCTGTTGCTC 59.400 55.000 0.00 0.00 32.32 4.26
1786 1801 1.613836 CCAGCCTTTTCTGTTGCTCT 58.386 50.000 0.00 0.00 32.32 4.09
1788 1803 1.196354 CAGCCTTTTCTGTTGCTCTCG 59.804 52.381 0.00 0.00 30.08 4.04
1791 1806 1.517242 CTTTTCTGTTGCTCTCGCCT 58.483 50.000 0.00 0.00 34.43 5.52
1792 1807 1.462670 CTTTTCTGTTGCTCTCGCCTC 59.537 52.381 0.00 0.00 34.43 4.70
1793 1808 0.320771 TTTCTGTTGCTCTCGCCTCC 60.321 55.000 0.00 0.00 34.43 4.30
1794 1809 1.188219 TTCTGTTGCTCTCGCCTCCT 61.188 55.000 0.00 0.00 34.43 3.69
1795 1810 1.153667 CTGTTGCTCTCGCCTCCTC 60.154 63.158 0.00 0.00 34.43 3.71
1830 2435 7.485913 TGAATTCTGCGCAAATCTTAATCTTTC 59.514 33.333 13.05 6.97 0.00 2.62
1831 2436 4.897224 TCTGCGCAAATCTTAATCTTTCG 58.103 39.130 13.05 0.00 0.00 3.46
1837 2442 4.786609 GCAAATCTTAATCTTTCGGAGCCG 60.787 45.833 1.74 1.74 41.35 5.52
1855 2824 1.661112 CCGAGGCAGAAAATCTTCGAC 59.339 52.381 2.46 0.00 36.61 4.20
1860 2829 2.030946 GGCAGAAAATCTTCGACGGATG 59.969 50.000 0.00 0.00 36.61 3.51
1861 2830 2.537730 GCAGAAAATCTTCGACGGATGC 60.538 50.000 0.00 0.00 36.61 3.91
1862 2831 2.030946 CAGAAAATCTTCGACGGATGCC 59.969 50.000 0.00 0.00 36.61 4.40
1864 2833 5.534563 AGAAAATCTTCGACGGATGCCGA 62.535 47.826 13.39 0.00 42.22 5.54
1879 2848 1.866853 GCCGAGGCAGAAAACTTGGG 61.867 60.000 9.58 0.00 38.48 4.12
1903 2872 6.073276 GGGCGAAAAATTCAGCTTAATTTGTT 60.073 34.615 17.15 13.33 38.68 2.83
1907 2876 9.356929 CGAAAAATTCAGCTTAATTTGTTTGTC 57.643 29.630 17.15 10.00 38.68 3.18
2102 3071 1.875514 GCAGTGTGTGAGATGCAGAAA 59.124 47.619 0.00 0.00 38.54 2.52
2103 3072 2.095869 GCAGTGTGTGAGATGCAGAAAG 60.096 50.000 0.00 0.00 38.54 2.62
2148 3117 9.672673 AGTGATCTTTGCTATTTTCTAGCTTTA 57.327 29.630 0.00 0.00 40.95 1.85
2220 4066 4.010349 AGAATGGGTTCGTTTGGATCTTC 58.990 43.478 0.00 0.00 39.38 2.87
2235 4081 4.024048 TGGATCTTCGTTGTTTTCTTGCTC 60.024 41.667 0.00 0.00 0.00 4.26
2243 4089 4.035208 CGTTGTTTTCTTGCTCTGTAAGGT 59.965 41.667 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.866703 TGGTTTCATGGAACTGGTACA 57.133 42.857 16.48 2.91 0.00 2.90
64 65 1.405821 GTCGTCAATGAGGTCCGAGAT 59.594 52.381 2.75 0.00 0.00 2.75
237 238 2.846508 GCGAGTCACGAGAGAACGATAC 60.847 54.545 0.00 0.00 45.77 2.24
306 307 6.042143 AGATGACCACAATTGTTTGTTTGAC 58.958 36.000 8.77 0.00 43.57 3.18
318 319 5.388654 AGTTTCCAAAGAGATGACCACAAT 58.611 37.500 0.00 0.00 0.00 2.71
348 349 4.275936 CAGAACACTCGAACCTTTGGAATT 59.724 41.667 0.00 0.00 0.00 2.17
477 478 2.366266 ACAGTGAACCAAAGCATGCATT 59.634 40.909 21.98 12.12 0.00 3.56
563 564 3.511934 GTCTCTAGCCCATGTATCCGAAT 59.488 47.826 0.00 0.00 0.00 3.34
765 769 1.753470 CCAACATTGGCCTGGCAAA 59.247 52.632 22.05 17.05 42.21 3.68
865 869 1.945522 CGAGATGAGACCGAGCGAT 59.054 57.895 0.00 0.00 0.00 4.58
914 918 1.120530 GAAAGCATCCGAGACCCCTA 58.879 55.000 0.00 0.00 0.00 3.53
935 939 6.061441 TCTCTGAAAACAAGTAATTCAGCCA 58.939 36.000 17.22 8.39 46.06 4.75
950 954 3.685139 AGATCACGCCTTCTCTGAAAA 57.315 42.857 0.00 0.00 0.00 2.29
1154 1165 1.710013 CTTAGCACACCGATCAACGT 58.290 50.000 0.00 0.00 40.78 3.99
1157 1168 3.165058 CTAGCTTAGCACACCGATCAA 57.835 47.619 7.07 0.00 0.00 2.57
1352 1363 9.421399 AGTCCTTTTCAATTCTTCTTTCCTTTA 57.579 29.630 0.00 0.00 0.00 1.85
1353 1364 8.311395 AGTCCTTTTCAATTCTTCTTTCCTTT 57.689 30.769 0.00 0.00 0.00 3.11
1354 1365 7.014711 GGAGTCCTTTTCAATTCTTCTTTCCTT 59.985 37.037 0.41 0.00 0.00 3.36
1355 1366 6.491745 GGAGTCCTTTTCAATTCTTCTTTCCT 59.508 38.462 0.41 0.00 0.00 3.36
1356 1367 6.568653 CGGAGTCCTTTTCAATTCTTCTTTCC 60.569 42.308 7.77 0.00 0.00 3.13
1357 1368 6.374578 CGGAGTCCTTTTCAATTCTTCTTTC 58.625 40.000 7.77 0.00 0.00 2.62
1358 1369 5.278512 GCGGAGTCCTTTTCAATTCTTCTTT 60.279 40.000 7.77 0.00 0.00 2.52
1359 1370 4.216472 GCGGAGTCCTTTTCAATTCTTCTT 59.784 41.667 7.77 0.00 0.00 2.52
1360 1371 3.753797 GCGGAGTCCTTTTCAATTCTTCT 59.246 43.478 7.77 0.00 0.00 2.85
1361 1372 3.502211 TGCGGAGTCCTTTTCAATTCTTC 59.498 43.478 7.77 0.00 0.00 2.87
1362 1373 3.486383 TGCGGAGTCCTTTTCAATTCTT 58.514 40.909 7.77 0.00 0.00 2.52
1363 1374 3.140325 TGCGGAGTCCTTTTCAATTCT 57.860 42.857 7.77 0.00 0.00 2.40
1364 1375 5.560966 TTATGCGGAGTCCTTTTCAATTC 57.439 39.130 7.77 0.00 0.00 2.17
1365 1376 5.975693 TTTATGCGGAGTCCTTTTCAATT 57.024 34.783 7.77 0.00 0.00 2.32
1366 1377 5.975693 TTTTATGCGGAGTCCTTTTCAAT 57.024 34.783 7.77 0.00 0.00 2.57
1367 1378 5.391523 CGATTTTATGCGGAGTCCTTTTCAA 60.392 40.000 7.77 0.00 0.00 2.69
1368 1379 4.094294 CGATTTTATGCGGAGTCCTTTTCA 59.906 41.667 7.77 0.28 0.00 2.69
1369 1380 4.094442 ACGATTTTATGCGGAGTCCTTTTC 59.906 41.667 7.77 0.00 0.00 2.29
1370 1381 4.007659 ACGATTTTATGCGGAGTCCTTTT 58.992 39.130 7.77 0.00 0.00 2.27
1371 1382 3.606687 ACGATTTTATGCGGAGTCCTTT 58.393 40.909 7.77 0.00 0.00 3.11
1372 1383 3.118738 AGACGATTTTATGCGGAGTCCTT 60.119 43.478 7.77 0.00 0.00 3.36
1373 1384 2.431057 AGACGATTTTATGCGGAGTCCT 59.569 45.455 7.77 0.00 0.00 3.85
1374 1385 2.822764 AGACGATTTTATGCGGAGTCC 58.177 47.619 0.00 0.00 0.00 3.85
1375 1386 3.982058 CCTAGACGATTTTATGCGGAGTC 59.018 47.826 0.00 0.00 0.00 3.36
1376 1387 3.383825 ACCTAGACGATTTTATGCGGAGT 59.616 43.478 0.00 0.00 0.00 3.85
1377 1388 3.736252 CACCTAGACGATTTTATGCGGAG 59.264 47.826 0.00 0.00 0.00 4.63
1378 1389 3.713288 CACCTAGACGATTTTATGCGGA 58.287 45.455 0.00 0.00 0.00 5.54
1379 1390 2.221055 GCACCTAGACGATTTTATGCGG 59.779 50.000 0.00 0.00 0.00 5.69
1380 1391 3.505449 GCACCTAGACGATTTTATGCG 57.495 47.619 0.00 0.00 0.00 4.73
1381 1392 2.348591 GCGCACCTAGACGATTTTATGC 60.349 50.000 0.30 0.00 0.00 3.14
1382 1393 2.863740 TGCGCACCTAGACGATTTTATG 59.136 45.455 5.66 0.00 0.00 1.90
1383 1394 3.173668 TGCGCACCTAGACGATTTTAT 57.826 42.857 5.66 0.00 0.00 1.40
1384 1395 2.658373 TGCGCACCTAGACGATTTTA 57.342 45.000 5.66 0.00 0.00 1.52
1385 1396 1.803334 TTGCGCACCTAGACGATTTT 58.197 45.000 11.12 0.00 0.00 1.82
1386 1397 2.024176 ATTGCGCACCTAGACGATTT 57.976 45.000 11.12 0.00 0.00 2.17
1387 1398 2.100916 AGTATTGCGCACCTAGACGATT 59.899 45.455 11.12 0.00 0.00 3.34
1388 1399 1.681793 AGTATTGCGCACCTAGACGAT 59.318 47.619 11.12 0.00 0.00 3.73
1389 1400 1.100510 AGTATTGCGCACCTAGACGA 58.899 50.000 11.12 0.00 0.00 4.20
1390 1401 1.588404 CAAGTATTGCGCACCTAGACG 59.412 52.381 11.12 0.00 40.39 4.18
1399 1410 7.848051 GCATATAGATGTATTCAAGTATTGCGC 59.152 37.037 0.00 0.00 39.69 6.09
1400 1411 8.872845 TGCATATAGATGTATTCAAGTATTGCG 58.127 33.333 0.00 0.00 39.69 4.85
1406 1417 9.650539 GAGACATGCATATAGATGTATTCAAGT 57.349 33.333 0.00 0.00 36.36 3.16
1407 1418 9.096160 GGAGACATGCATATAGATGTATTCAAG 57.904 37.037 0.00 0.00 36.36 3.02
1408 1419 8.043113 GGGAGACATGCATATAGATGTATTCAA 58.957 37.037 0.00 0.00 36.36 2.69
1409 1420 7.401204 AGGGAGACATGCATATAGATGTATTCA 59.599 37.037 0.00 0.00 36.36 2.57
1410 1421 7.790027 AGGGAGACATGCATATAGATGTATTC 58.210 38.462 0.00 1.54 36.36 1.75
1411 1422 7.746243 AGGGAGACATGCATATAGATGTATT 57.254 36.000 0.00 0.00 36.36 1.89
1412 1423 7.401204 TGAAGGGAGACATGCATATAGATGTAT 59.599 37.037 0.00 0.00 38.77 2.29
1413 1424 6.725834 TGAAGGGAGACATGCATATAGATGTA 59.274 38.462 0.00 0.00 32.85 2.29
1414 1425 5.545335 TGAAGGGAGACATGCATATAGATGT 59.455 40.000 0.00 0.00 35.46 3.06
1415 1426 6.046290 TGAAGGGAGACATGCATATAGATG 57.954 41.667 0.00 0.00 36.02 2.90
1416 1427 6.692849 TTGAAGGGAGACATGCATATAGAT 57.307 37.500 0.00 0.00 0.00 1.98
1417 1428 6.499106 TTTGAAGGGAGACATGCATATAGA 57.501 37.500 0.00 0.00 0.00 1.98
1418 1429 7.572523 TTTTTGAAGGGAGACATGCATATAG 57.427 36.000 0.00 0.00 0.00 1.31
1451 1462 8.509690 CGATTAGGATGGTAAATTACGTCTAGA 58.490 37.037 0.00 0.00 0.00 2.43
1452 1463 8.509690 TCGATTAGGATGGTAAATTACGTCTAG 58.490 37.037 0.00 0.00 0.00 2.43
1453 1464 8.292448 GTCGATTAGGATGGTAAATTACGTCTA 58.708 37.037 0.00 0.00 0.00 2.59
1454 1465 7.144000 GTCGATTAGGATGGTAAATTACGTCT 58.856 38.462 0.00 0.00 0.00 4.18
1455 1466 6.087291 CGTCGATTAGGATGGTAAATTACGTC 59.913 42.308 0.00 0.00 0.00 4.34
1456 1467 5.916883 CGTCGATTAGGATGGTAAATTACGT 59.083 40.000 0.00 0.00 0.00 3.57
1457 1468 5.344128 CCGTCGATTAGGATGGTAAATTACG 59.656 44.000 0.00 0.00 38.14 3.18
1458 1469 6.364435 GTCCGTCGATTAGGATGGTAAATTAC 59.636 42.308 9.84 0.00 42.58 1.89
1459 1470 6.449698 GTCCGTCGATTAGGATGGTAAATTA 58.550 40.000 9.84 0.00 42.58 1.40
1460 1471 5.295152 GTCCGTCGATTAGGATGGTAAATT 58.705 41.667 9.84 0.00 42.58 1.82
1461 1472 4.558095 CGTCCGTCGATTAGGATGGTAAAT 60.558 45.833 15.01 0.00 42.58 1.40
1462 1473 3.243168 CGTCCGTCGATTAGGATGGTAAA 60.243 47.826 15.01 0.00 42.58 2.01
1463 1474 2.291465 CGTCCGTCGATTAGGATGGTAA 59.709 50.000 15.01 0.00 42.58 2.85
1464 1475 1.875514 CGTCCGTCGATTAGGATGGTA 59.124 52.381 15.01 0.00 42.58 3.25
1465 1476 0.666913 CGTCCGTCGATTAGGATGGT 59.333 55.000 15.01 0.00 42.58 3.55
1466 1477 3.474007 CGTCCGTCGATTAGGATGG 57.526 57.895 15.01 6.55 43.22 3.51
1467 1478 0.949397 TCCGTCCGTCGATTAGGATG 59.051 55.000 15.57 15.57 42.86 3.51
1468 1479 0.950116 GTCCGTCCGTCGATTAGGAT 59.050 55.000 9.84 0.00 42.86 3.24
1469 1480 1.431488 CGTCCGTCCGTCGATTAGGA 61.431 60.000 0.00 3.54 42.86 2.94
1470 1481 1.010350 CGTCCGTCCGTCGATTAGG 60.010 63.158 0.00 0.00 42.86 2.69
1471 1482 0.588233 CACGTCCGTCCGTCGATTAG 60.588 60.000 0.00 0.00 39.45 1.73
1472 1483 1.425031 CACGTCCGTCCGTCGATTA 59.575 57.895 0.00 0.00 39.45 1.75
1473 1484 2.177531 CACGTCCGTCCGTCGATT 59.822 61.111 0.00 0.00 39.45 3.34
1474 1485 4.471726 GCACGTCCGTCCGTCGAT 62.472 66.667 0.00 0.00 39.45 3.59
1480 1491 4.634133 TGTCACGCACGTCCGTCC 62.634 66.667 0.00 0.00 39.83 4.79
1531 1542 2.202756 AGTCGATCCGCCGCTTTC 60.203 61.111 0.00 0.00 0.00 2.62
1626 1638 9.810545 GAGGGATCGAAATTATATAGGAGAAAG 57.189 37.037 0.00 0.00 0.00 2.62
1629 1641 7.780745 GGAGAGGGATCGAAATTATATAGGAGA 59.219 40.741 0.00 0.00 0.00 3.71
1634 1646 7.189794 ACAGGGAGAGGGATCGAAATTATATA 58.810 38.462 0.00 0.00 0.00 0.86
1635 1647 6.026186 ACAGGGAGAGGGATCGAAATTATAT 58.974 40.000 0.00 0.00 0.00 0.86
1640 1653 2.171448 CAACAGGGAGAGGGATCGAAAT 59.829 50.000 0.00 0.00 0.00 2.17
1647 1660 2.610859 GGGCAACAGGGAGAGGGA 60.611 66.667 0.00 0.00 39.74 4.20
1659 1673 2.046892 GCTTGAGAGAGCGGGCAA 60.047 61.111 0.00 0.00 32.23 4.52
1694 1708 4.692625 CCGTGGCATCTAGGAAATCTTATG 59.307 45.833 0.00 0.00 0.00 1.90
1696 1710 3.494398 GCCGTGGCATCTAGGAAATCTTA 60.494 47.826 5.89 0.00 41.49 2.10
1702 1716 2.908015 GGCCGTGGCATCTAGGAA 59.092 61.111 13.76 0.00 44.11 3.36
1732 1746 2.174424 GAGCAAAGAGGATGGAGGGATT 59.826 50.000 0.00 0.00 0.00 3.01
1733 1747 1.773653 GAGCAAAGAGGATGGAGGGAT 59.226 52.381 0.00 0.00 0.00 3.85
1734 1748 1.207791 GAGCAAAGAGGATGGAGGGA 58.792 55.000 0.00 0.00 0.00 4.20
1735 1749 0.182299 GGAGCAAAGAGGATGGAGGG 59.818 60.000 0.00 0.00 0.00 4.30
1791 1806 3.962530 AATTCAGGGCGGGGGAGGA 62.963 63.158 0.00 0.00 0.00 3.71
1792 1807 3.420482 AATTCAGGGCGGGGGAGG 61.420 66.667 0.00 0.00 0.00 4.30
1793 1808 2.193248 GAATTCAGGGCGGGGGAG 59.807 66.667 0.00 0.00 0.00 4.30
1794 1809 2.286121 AGAATTCAGGGCGGGGGA 60.286 61.111 8.44 0.00 0.00 4.81
1795 1810 2.124151 CAGAATTCAGGGCGGGGG 60.124 66.667 8.44 0.00 0.00 5.40
1801 2406 1.747355 AGATTTGCGCAGAATTCAGGG 59.253 47.619 11.31 9.39 0.00 4.45
1830 2435 1.432270 GATTTTCTGCCTCGGCTCCG 61.432 60.000 9.65 1.14 42.51 4.63
1831 2436 0.107459 AGATTTTCTGCCTCGGCTCC 60.107 55.000 9.65 0.00 42.51 4.70
1837 2442 1.661112 CCGTCGAAGATTTTCTGCCTC 59.339 52.381 0.00 0.00 40.67 4.70
1843 2811 1.004927 CGGCATCCGTCGAAGATTTTC 60.005 52.381 0.00 0.00 45.23 2.29
1860 2829 1.581447 CCAAGTTTTCTGCCTCGGC 59.419 57.895 0.00 0.00 42.35 5.54
1861 2830 1.244019 CCCCAAGTTTTCTGCCTCGG 61.244 60.000 0.00 0.00 0.00 4.63
1862 2831 1.866853 GCCCCAAGTTTTCTGCCTCG 61.867 60.000 0.00 0.00 0.00 4.63
1864 2833 1.903404 CGCCCCAAGTTTTCTGCCT 60.903 57.895 0.00 0.00 0.00 4.75
1865 2834 1.460273 TTCGCCCCAAGTTTTCTGCC 61.460 55.000 0.00 0.00 0.00 4.85
1866 2835 0.387565 TTTCGCCCCAAGTTTTCTGC 59.612 50.000 0.00 0.00 0.00 4.26
1867 2836 2.880963 TTTTCGCCCCAAGTTTTCTG 57.119 45.000 0.00 0.00 0.00 3.02
1868 2837 4.141824 TGAATTTTTCGCCCCAAGTTTTCT 60.142 37.500 0.00 0.00 0.00 2.52
1869 2838 4.123506 TGAATTTTTCGCCCCAAGTTTTC 58.876 39.130 0.00 0.00 0.00 2.29
1870 2839 4.126437 CTGAATTTTTCGCCCCAAGTTTT 58.874 39.130 0.00 0.00 0.00 2.43
1879 2848 6.466308 ACAAATTAAGCTGAATTTTTCGCC 57.534 33.333 17.76 0.00 36.99 5.54
1903 2872 1.305201 GAAAAGACCCTGCACGACAA 58.695 50.000 0.00 0.00 0.00 3.18
1907 2876 1.901650 GCTCGAAAAGACCCTGCACG 61.902 60.000 0.00 0.00 0.00 5.34
1988 2957 5.278364 GGCCTTCAGAGCATAATCATCAAAG 60.278 44.000 0.00 0.00 0.00 2.77
1991 2960 3.393609 AGGCCTTCAGAGCATAATCATCA 59.606 43.478 0.00 0.00 0.00 3.07
2102 3071 5.887598 TCACTTGCTTGTTATGCCATATTCT 59.112 36.000 0.00 0.00 0.00 2.40
2103 3072 6.135290 TCACTTGCTTGTTATGCCATATTC 57.865 37.500 0.00 0.00 0.00 1.75
2148 3117 4.643784 AGACCTACAACGATTCGACCTTAT 59.356 41.667 13.95 0.00 0.00 1.73
2150 3119 2.824341 AGACCTACAACGATTCGACCTT 59.176 45.455 13.95 0.00 0.00 3.50
2220 4066 4.035208 ACCTTACAGAGCAAGAAAACAACG 59.965 41.667 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.