Multiple sequence alignment - TraesCS5B01G048100

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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 TraesCS5B01G048100 chr5B 100.000 2393 0 0 1 2393 54201634 54199242 0.000000e+00 4420.0
1 TraesCS5B01G048100 chr5B 93.436 777 49 2 724 1499 237158134 237157359 0.000000e+00 1151.0
2 TraesCS5B01G048100 chr5B 85.819 684 67 16 1700 2355 54395904 54395223 0.000000e+00 699.0
3 TraesCS5B01G048100 chr5B 94.072 388 19 3 187 574 54435738 54435355 9.530000e-164 586.0
4 TraesCS5B01G048100 chr5B 92.593 216 11 2 1498 1712 54435158 54434947 2.990000e-79 305.0
5 TraesCS5B01G048100 chr5B 92.000 125 6 2 575 699 54435316 54435196 3.160000e-39 172.0
6 TraesCS5B01G048100 chr5B 94.872 39 2 0 2355 2393 54395199 54395161 7.140000e-06 62.1
7 TraesCS5B01G048100 chr6B 96.525 777 26 1 723 1498 68901588 68902364 0.000000e+00 1284.0
8 TraesCS5B01G048100 chr6B 95.231 692 33 0 723 1414 502298875 502299566 0.000000e+00 1096.0
9 TraesCS5B01G048100 chr6B 83.794 253 30 6 224 470 715631949 715631702 1.850000e-56 230.0
10 TraesCS5B01G048100 chr7A 93.557 776 49 1 723 1497 270771795 270772570 0.000000e+00 1155.0
11 TraesCS5B01G048100 chr3B 92.720 783 53 4 718 1498 125892819 125893599 0.000000e+00 1127.0
12 TraesCS5B01G048100 chr3D 92.387 775 50 3 723 1497 540373366 540374131 0.000000e+00 1096.0
13 TraesCS5B01G048100 chr4B 91.517 778 64 2 724 1500 435170989 435170213 0.000000e+00 1070.0
14 TraesCS5B01G048100 chr4B 83.051 118 18 2 2038 2155 54865065 54864950 3.250000e-19 106.0
15 TraesCS5B01G048100 chr7B 91.176 782 67 2 717 1497 592907592 592908372 0.000000e+00 1061.0
16 TraesCS5B01G048100 chr7D 90.244 779 69 7 723 1498 7796640 7797414 0.000000e+00 1011.0
17 TraesCS5B01G048100 chr5D 86.845 821 53 21 1498 2287 50993634 50992838 0.000000e+00 867.0
18 TraesCS5B01G048100 chr5D 94.709 378 20 0 187 564 51327385 51327008 2.650000e-164 588.0
19 TraesCS5B01G048100 chr5D 94.180 378 22 0 187 564 51250821 51250444 5.740000e-161 577.0
20 TraesCS5B01G048100 chr5D 96.364 330 11 1 187 515 50994138 50993809 2.090000e-150 542.0
21 TraesCS5B01G048100 chr5D 90.296 371 26 6 1987 2355 51325333 51324971 5.980000e-131 477.0
22 TraesCS5B01G048100 chr5D 89.730 370 29 7 1987 2355 51248770 51248409 4.660000e-127 464.0
23 TraesCS5B01G048100 chr5D 95.745 188 7 1 1 187 50994355 50994168 3.870000e-78 302.0
24 TraesCS5B01G048100 chr5D 95.213 188 9 0 1 188 51251037 51250850 5.000000e-77 298.0
25 TraesCS5B01G048100 chr5D 94.681 188 10 0 1 188 51327601 51327414 2.330000e-75 292.0
26 TraesCS5B01G048100 chr5D 91.469 211 9 3 1498 1703 51250225 51250019 5.040000e-72 281.0
27 TraesCS5B01G048100 chr5D 91.469 211 9 3 1498 1703 51326789 51326583 5.040000e-72 281.0
28 TraesCS5B01G048100 chr5D 88.995 209 19 4 1720 1928 51249974 51249770 3.050000e-64 255.0
29 TraesCS5B01G048100 chr5D 88.995 209 19 4 1720 1928 51326538 51326334 3.050000e-64 255.0
30 TraesCS5B01G048100 chr5D 85.256 156 12 6 574 726 50993799 50993652 1.480000e-32 150.0
31 TraesCS5B01G048100 chr5D 84.314 153 11 4 577 726 51250385 51250243 1.150000e-28 137.0
32 TraesCS5B01G048100 chr5D 100.000 31 0 0 2355 2385 51248387 51248357 9.240000e-05 58.4
33 TraesCS5B01G048100 chr5D 100.000 31 0 0 2355 2385 51324949 51324919 9.240000e-05 58.4
34 TraesCS5B01G048100 chr5A 95.745 329 14 0 187 515 40483703 40483375 4.530000e-147 531.0
35 TraesCS5B01G048100 chr5A 91.975 324 23 2 1592 1912 40483141 40482818 3.630000e-123 451.0
36 TraesCS5B01G048100 chr5A 95.213 188 7 2 1 187 40483919 40483733 1.800000e-76 296.0
37 TraesCS5B01G048100 chr5A 83.226 310 26 8 1938 2245 40482753 40482468 6.560000e-66 261.0
38 TraesCS5B01G048100 chr6D 85.830 247 30 2 224 470 469395691 469395450 8.490000e-65 257.0
39 TraesCS5B01G048100 chr6A 85.020 247 32 2 224 470 614524558 614524317 1.840000e-61 246.0
40 TraesCS5B01G048100 chrUn 89.305 187 17 2 1720 1906 480276357 480276540 5.140000e-57 231.0
41 TraesCS5B01G048100 chrUn 92.073 164 4 3 1545 1703 480276153 480276312 3.100000e-54 222.0
42 TraesCS5B01G048100 chr4D 84.496 129 16 2 2001 2126 37611210 37611083 8.980000e-25 124.0


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 TraesCS5B01G048100 chr5B 54199242 54201634 2392 True 4420.000000 4420 100.000000 1 2393 1 chr5B.!!$R1 2392
1 TraesCS5B01G048100 chr5B 237157359 237158134 775 True 1151.000000 1151 93.436000 724 1499 1 chr5B.!!$R2 775
2 TraesCS5B01G048100 chr5B 54395161 54395904 743 True 380.550000 699 90.345500 1700 2393 2 chr5B.!!$R3 693
3 TraesCS5B01G048100 chr5B 54434947 54435738 791 True 354.333333 586 92.888333 187 1712 3 chr5B.!!$R4 1525
4 TraesCS5B01G048100 chr6B 68901588 68902364 776 False 1284.000000 1284 96.525000 723 1498 1 chr6B.!!$F1 775
5 TraesCS5B01G048100 chr6B 502298875 502299566 691 False 1096.000000 1096 95.231000 723 1414 1 chr6B.!!$F2 691
6 TraesCS5B01G048100 chr7A 270771795 270772570 775 False 1155.000000 1155 93.557000 723 1497 1 chr7A.!!$F1 774
7 TraesCS5B01G048100 chr3B 125892819 125893599 780 False 1127.000000 1127 92.720000 718 1498 1 chr3B.!!$F1 780
8 TraesCS5B01G048100 chr3D 540373366 540374131 765 False 1096.000000 1096 92.387000 723 1497 1 chr3D.!!$F1 774
9 TraesCS5B01G048100 chr4B 435170213 435170989 776 True 1070.000000 1070 91.517000 724 1500 1 chr4B.!!$R2 776
10 TraesCS5B01G048100 chr7B 592907592 592908372 780 False 1061.000000 1061 91.176000 717 1497 1 chr7B.!!$F1 780
11 TraesCS5B01G048100 chr7D 7796640 7797414 774 False 1011.000000 1011 90.244000 723 1498 1 chr7D.!!$F1 775
12 TraesCS5B01G048100 chr5D 50992838 50994355 1517 True 465.250000 867 91.052500 1 2287 4 chr5D.!!$R1 2286
13 TraesCS5B01G048100 chr5D 51324919 51327601 2682 True 325.233333 588 93.358333 1 2385 6 chr5D.!!$R3 2384
14 TraesCS5B01G048100 chr5D 51248357 51251037 2680 True 295.771429 577 91.985857 1 2385 7 chr5D.!!$R2 2384
15 TraesCS5B01G048100 chr5A 40482468 40483919 1451 True 384.750000 531 91.539750 1 2245 4 chr5A.!!$R1 2244

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
922 1046 1.270839 ACCCTCACCATGACTTTGTCG 60.271 52.381 0.0 0.0 34.95 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 3268 3.05845 TGCTCCAACATCGCAATTTTTG 58.942 40.909 0.0 0.0 0.0 2.44 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
45 46 2.002586 CTTGCAGTTGGTCGGATACTG 58.997 52.381 11.29 11.29 41.64 2.74
67 68 2.571212 TGTGCTCCTTTTGTGTACCAG 58.429 47.619 0.00 0.00 0.00 4.00
171 173 8.970859 ATCTATGCTCACTTTAGCTTGTAAAT 57.029 30.769 0.00 0.00 43.19 1.40
447 479 3.390639 CCTAGATCCTGCAGTCATCCTTT 59.609 47.826 13.81 1.31 0.00 3.11
571 612 4.085357 TGGTGGTATCTGAATACATGCC 57.915 45.455 0.00 0.00 39.69 4.40
695 774 3.266772 TCTTGGTTGGTGCTCCTTATCAT 59.733 43.478 6.34 0.00 34.23 2.45
698 777 5.387113 TGGTTGGTGCTCCTTATCATATT 57.613 39.130 6.34 0.00 34.23 1.28
849 973 3.016971 TCCCTCACCCATGGGCTG 61.017 66.667 31.73 25.41 43.04 4.85
922 1046 1.270839 ACCCTCACCATGACTTTGTCG 60.271 52.381 0.00 0.00 34.95 4.35
1340 1465 4.911514 TCCGGTTCAAAAAGAAAGAAGG 57.088 40.909 0.00 0.00 38.13 3.46
1351 1476 9.739276 TCAAAAAGAAAGAAGGCAATATCTCTA 57.261 29.630 0.00 0.00 0.00 2.43
1521 1649 8.924511 AACATACTTTAATCATGTGGGATAGG 57.075 34.615 0.00 0.00 33.31 2.57
1522 1650 8.275187 ACATACTTTAATCATGTGGGATAGGA 57.725 34.615 0.00 0.00 31.83 2.94
1523 1651 8.157476 ACATACTTTAATCATGTGGGATAGGAC 58.843 37.037 0.00 0.00 31.83 3.85
1524 1652 6.575244 ACTTTAATCATGTGGGATAGGACA 57.425 37.500 0.00 0.00 0.00 4.02
1525 1653 7.154191 ACTTTAATCATGTGGGATAGGACAT 57.846 36.000 0.00 0.00 32.90 3.06
1526 1654 7.227156 ACTTTAATCATGTGGGATAGGACATC 58.773 38.462 0.00 0.00 30.14 3.06
1527 1655 3.969287 ATCATGTGGGATAGGACATCG 57.031 47.619 0.00 0.00 30.14 3.84
1528 1656 2.677914 TCATGTGGGATAGGACATCGT 58.322 47.619 0.00 0.00 30.14 3.73
1529 1657 2.365293 TCATGTGGGATAGGACATCGTG 59.635 50.000 0.00 0.00 30.14 4.35
1530 1658 1.119684 TGTGGGATAGGACATCGTGG 58.880 55.000 0.00 0.00 0.00 4.94
1531 1659 0.249911 GTGGGATAGGACATCGTGGC 60.250 60.000 0.00 0.00 0.00 5.01
1537 1665 3.630289 GGACATCGTGGCCCTACT 58.370 61.111 0.00 0.00 40.64 2.57
1538 1666 2.816746 GGACATCGTGGCCCTACTA 58.183 57.895 0.00 0.00 40.64 1.82
1539 1667 0.388294 GGACATCGTGGCCCTACTAC 59.612 60.000 0.00 0.00 40.64 2.73
1540 1668 0.388294 GACATCGTGGCCCTACTACC 59.612 60.000 0.00 0.00 0.00 3.18
1541 1669 1.047034 ACATCGTGGCCCTACTACCC 61.047 60.000 0.00 0.00 0.00 3.69
1542 1670 0.759436 CATCGTGGCCCTACTACCCT 60.759 60.000 0.00 0.00 0.00 4.34
1543 1671 0.031414 ATCGTGGCCCTACTACCCTT 60.031 55.000 0.00 0.00 0.00 3.95
1544 1672 0.252375 TCGTGGCCCTACTACCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
1545 1673 0.616891 CGTGGCCCTACTACCCTTTT 59.383 55.000 0.00 0.00 0.00 2.27
1546 1674 1.406477 CGTGGCCCTACTACCCTTTTC 60.406 57.143 0.00 0.00 0.00 2.29
1547 1675 1.914108 GTGGCCCTACTACCCTTTTCT 59.086 52.381 0.00 0.00 0.00 2.52
1548 1676 1.913419 TGGCCCTACTACCCTTTTCTG 59.087 52.381 0.00 0.00 0.00 3.02
1549 1677 2.193993 GGCCCTACTACCCTTTTCTGA 58.806 52.381 0.00 0.00 0.00 3.27
1550 1678 2.093075 GGCCCTACTACCCTTTTCTGAC 60.093 54.545 0.00 0.00 0.00 3.51
1551 1679 2.570302 GCCCTACTACCCTTTTCTGACA 59.430 50.000 0.00 0.00 0.00 3.58
1552 1680 3.369576 GCCCTACTACCCTTTTCTGACAG 60.370 52.174 0.00 0.00 0.00 3.51
1553 1681 3.369576 CCCTACTACCCTTTTCTGACAGC 60.370 52.174 0.00 0.00 0.00 4.40
1554 1682 2.861147 ACTACCCTTTTCTGACAGCC 57.139 50.000 0.00 0.00 0.00 4.85
1555 1683 1.002087 ACTACCCTTTTCTGACAGCCG 59.998 52.381 0.00 0.00 0.00 5.52
1556 1684 0.321298 TACCCTTTTCTGACAGCCGC 60.321 55.000 0.00 0.00 0.00 6.53
1557 1685 1.600636 CCCTTTTCTGACAGCCGCA 60.601 57.895 0.00 0.00 0.00 5.69
1558 1686 1.580845 CCCTTTTCTGACAGCCGCAG 61.581 60.000 0.00 0.00 34.71 5.18
1559 1687 1.208614 CTTTTCTGACAGCCGCAGC 59.791 57.895 0.00 0.00 40.32 5.25
1569 1697 2.253452 GCCGCAGCTTCACAGTTG 59.747 61.111 0.00 0.00 34.41 3.16
1570 1698 2.949106 CCGCAGCTTCACAGTTGG 59.051 61.111 0.00 0.00 31.96 3.77
1571 1699 2.253452 CGCAGCTTCACAGTTGGC 59.747 61.111 0.00 0.00 31.96 4.52
1572 1700 2.545596 CGCAGCTTCACAGTTGGCA 61.546 57.895 0.00 0.00 31.96 4.92
1573 1701 1.859427 CGCAGCTTCACAGTTGGCAT 61.859 55.000 0.00 0.00 31.96 4.40
1574 1702 0.388134 GCAGCTTCACAGTTGGCATG 60.388 55.000 0.00 0.00 31.96 4.06
1575 1703 0.242825 CAGCTTCACAGTTGGCATGG 59.757 55.000 0.00 0.00 0.00 3.66
1576 1704 0.178981 AGCTTCACAGTTGGCATGGT 60.179 50.000 0.00 0.00 0.00 3.55
1577 1705 1.073763 AGCTTCACAGTTGGCATGGTA 59.926 47.619 0.00 0.00 0.00 3.25
1578 1706 1.470098 GCTTCACAGTTGGCATGGTAG 59.530 52.381 0.00 0.00 0.00 3.18
1579 1707 2.875672 GCTTCACAGTTGGCATGGTAGA 60.876 50.000 0.00 0.00 0.00 2.59
1580 1708 3.614092 CTTCACAGTTGGCATGGTAGAT 58.386 45.455 0.00 0.00 0.00 1.98
1581 1709 3.719268 TCACAGTTGGCATGGTAGATT 57.281 42.857 0.00 0.00 0.00 2.40
1582 1710 4.032960 TCACAGTTGGCATGGTAGATTT 57.967 40.909 0.00 0.00 0.00 2.17
1583 1711 4.009675 TCACAGTTGGCATGGTAGATTTC 58.990 43.478 0.00 0.00 0.00 2.17
1584 1712 3.758023 CACAGTTGGCATGGTAGATTTCA 59.242 43.478 0.00 0.00 0.00 2.69
1585 1713 4.218200 CACAGTTGGCATGGTAGATTTCAA 59.782 41.667 0.00 0.00 0.00 2.69
1586 1714 4.218417 ACAGTTGGCATGGTAGATTTCAAC 59.782 41.667 0.00 0.00 34.87 3.18
1587 1715 3.763897 AGTTGGCATGGTAGATTTCAACC 59.236 43.478 0.00 0.00 35.12 3.77
1588 1716 2.364632 TGGCATGGTAGATTTCAACCG 58.635 47.619 0.00 0.00 38.70 4.44
1589 1717 2.290641 TGGCATGGTAGATTTCAACCGT 60.291 45.455 0.00 0.00 38.70 4.83
1590 1718 2.354821 GGCATGGTAGATTTCAACCGTC 59.645 50.000 0.00 0.00 38.70 4.79
1602 1730 3.482722 TCAACCGTCGACTTATCTGAC 57.517 47.619 14.70 0.00 0.00 3.51
1604 1732 0.731417 ACCGTCGACTTATCTGACCG 59.269 55.000 14.70 0.00 0.00 4.79
1620 1748 2.679934 CCGCGCAGATTGCAACAGA 61.680 57.895 8.75 0.00 45.36 3.41
1621 1749 1.207339 CGCGCAGATTGCAACAGAA 59.793 52.632 8.75 0.00 45.36 3.02
1624 1752 1.069022 GCGCAGATTGCAACAGAAAGA 60.069 47.619 0.00 0.00 45.36 2.52
1630 1758 6.385033 GCAGATTGCAACAGAAAGAAAGTAT 58.615 36.000 0.00 0.00 44.26 2.12
1632 1760 7.587629 CAGATTGCAACAGAAAGAAAGTATGA 58.412 34.615 0.00 0.00 0.00 2.15
1712 1845 7.161773 AGACGTACCATTACTAAGTGCTTAA 57.838 36.000 0.00 0.00 0.00 1.85
1718 1879 9.379791 GTACCATTACTAAGTGCTTAAACTCAT 57.620 33.333 0.00 0.00 0.00 2.90
1740 1901 6.782494 TCATTATGTCTAATCCCTACTCTGCA 59.218 38.462 0.00 0.00 0.00 4.41
1764 1925 6.918022 CAGGTTTGTCTCAAATAAGTGGTTTC 59.082 38.462 0.00 0.00 0.00 2.78
1780 1941 4.567159 GTGGTTTCGAGCTCTGGTATTTAG 59.433 45.833 12.85 0.00 0.00 1.85
1786 1947 4.464951 TCGAGCTCTGGTATTTAGTGGAAA 59.535 41.667 12.85 0.00 0.00 3.13
1798 1959 5.860941 TTTAGTGGAAATTTGTTCAGGCA 57.139 34.783 0.00 0.00 0.00 4.75
1854 2015 8.041323 TCAGGTATGTTGTTTTCTCTAGGATTC 58.959 37.037 0.00 0.00 0.00 2.52
1896 2059 8.818622 ACCAGTACATATTTCTGACTAGTACA 57.181 34.615 0.00 0.00 34.41 2.90
1929 2105 8.403236 ACAATCAGACTGTTTTTAACCTTGTAC 58.597 33.333 1.59 0.00 0.00 2.90
1930 2106 8.402472 CAATCAGACTGTTTTTAACCTTGTACA 58.598 33.333 1.59 0.00 0.00 2.90
1931 2107 8.691661 ATCAGACTGTTTTTAACCTTGTACAT 57.308 30.769 1.59 0.00 0.00 2.29
2069 3187 4.438797 CGATTAGATTTGCCATGCGAAAAG 59.561 41.667 0.00 0.00 35.42 2.27
2122 3240 5.811399 TTTGCCATATTCTACGGTGAAAG 57.189 39.130 0.00 0.00 0.00 2.62
2134 3252 4.067972 ACGGTGAAAGTTGTCATGTAGT 57.932 40.909 0.00 0.00 0.00 2.73
2294 3414 9.665719 TTAGAGCATTGTGTCTGAATATTACAA 57.334 29.630 3.80 3.80 35.93 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.000447 GTATCCGACCAACTGCAAGAC 59.000 52.381 0.00 0.00 37.43 3.01
45 46 2.685897 TGGTACACAAAAGGAGCACAAC 59.314 45.455 0.00 0.00 0.00 3.32
67 68 2.352323 CCCACCAATAAAACGGAAGCAC 60.352 50.000 0.00 0.00 0.00 4.40
171 173 0.181587 TCGCTTGGTTGTGGAAGGAA 59.818 50.000 0.00 0.00 0.00 3.36
301 333 9.942850 TTCAAGTGATCACTCTATGTAATCAAA 57.057 29.630 28.01 9.53 41.58 2.69
311 343 7.122204 TCGGAAGTAATTCAAGTGATCACTCTA 59.878 37.037 28.01 16.28 41.58 2.43
447 479 5.538433 TGCATATACCAGCAGTATACAGTGA 59.462 40.000 5.50 0.00 44.76 3.41
571 612 4.635765 TCGAATCTCCAAACCTTAATGCTG 59.364 41.667 0.00 0.00 0.00 4.41
661 740 5.625197 GCACCAACCAAGATCAGCATTAATT 60.625 40.000 0.00 0.00 0.00 1.40
662 741 4.142093 GCACCAACCAAGATCAGCATTAAT 60.142 41.667 0.00 0.00 0.00 1.40
663 742 3.193267 GCACCAACCAAGATCAGCATTAA 59.807 43.478 0.00 0.00 0.00 1.40
695 774 9.378551 AGTTTATTCTTCATAGAACACGCAATA 57.621 29.630 0.00 0.00 42.91 1.90
698 777 6.402118 GCAGTTTATTCTTCATAGAACACGCA 60.402 38.462 0.00 0.00 42.91 5.24
922 1046 2.211468 ATCGGAACCTTGGAAGCCCC 62.211 60.000 0.00 0.00 0.00 5.80
1071 1195 5.423015 GCATAAGAACAGTTGGAGATGAGA 58.577 41.667 0.00 0.00 0.00 3.27
1340 1465 4.633565 GCCATTGCCTAGTAGAGATATTGC 59.366 45.833 0.00 0.00 0.00 3.56
1351 1476 4.923415 AGAAAGTTAAGCCATTGCCTAGT 58.077 39.130 0.00 0.00 38.69 2.57
1500 1628 7.684317 TGTCCTATCCCACATGATTAAAGTA 57.316 36.000 0.00 0.00 0.00 2.24
1501 1629 6.575244 TGTCCTATCCCACATGATTAAAGT 57.425 37.500 0.00 0.00 0.00 2.66
1502 1630 6.369890 CGATGTCCTATCCCACATGATTAAAG 59.630 42.308 0.00 0.00 33.22 1.85
1503 1631 6.183361 ACGATGTCCTATCCCACATGATTAAA 60.183 38.462 0.00 0.00 33.22 1.52
1504 1632 5.306937 ACGATGTCCTATCCCACATGATTAA 59.693 40.000 0.00 0.00 33.22 1.40
1505 1633 4.838423 ACGATGTCCTATCCCACATGATTA 59.162 41.667 0.00 0.00 33.22 1.75
1506 1634 3.648067 ACGATGTCCTATCCCACATGATT 59.352 43.478 0.00 0.00 33.22 2.57
1507 1635 3.007290 CACGATGTCCTATCCCACATGAT 59.993 47.826 0.00 0.00 33.22 2.45
1508 1636 2.365293 CACGATGTCCTATCCCACATGA 59.635 50.000 0.00 0.00 33.22 3.07
1509 1637 2.548707 CCACGATGTCCTATCCCACATG 60.549 54.545 0.00 0.00 33.22 3.21
1510 1638 1.694150 CCACGATGTCCTATCCCACAT 59.306 52.381 0.00 0.00 35.88 3.21
1511 1639 1.119684 CCACGATGTCCTATCCCACA 58.880 55.000 0.00 0.00 0.00 4.17
1512 1640 0.249911 GCCACGATGTCCTATCCCAC 60.250 60.000 0.00 0.00 0.00 4.61
1513 1641 1.407656 GGCCACGATGTCCTATCCCA 61.408 60.000 0.00 0.00 0.00 4.37
1514 1642 1.371558 GGCCACGATGTCCTATCCC 59.628 63.158 0.00 0.00 0.00 3.85
1515 1643 1.122019 AGGGCCACGATGTCCTATCC 61.122 60.000 6.18 0.00 0.00 2.59
1516 1644 1.272769 GTAGGGCCACGATGTCCTATC 59.727 57.143 6.18 4.02 34.77 2.08
1517 1645 1.133136 AGTAGGGCCACGATGTCCTAT 60.133 52.381 6.18 1.09 34.77 2.57
1518 1646 0.260816 AGTAGGGCCACGATGTCCTA 59.739 55.000 6.18 5.41 0.00 2.94
1519 1647 0.260816 TAGTAGGGCCACGATGTCCT 59.739 55.000 6.18 7.24 0.00 3.85
1520 1648 0.388294 GTAGTAGGGCCACGATGTCC 59.612 60.000 6.18 0.00 0.00 4.02
1521 1649 0.388294 GGTAGTAGGGCCACGATGTC 59.612 60.000 6.18 0.00 0.00 3.06
1522 1650 1.047034 GGGTAGTAGGGCCACGATGT 61.047 60.000 6.18 0.00 0.00 3.06
1523 1651 0.759436 AGGGTAGTAGGGCCACGATG 60.759 60.000 6.18 0.00 0.00 3.84
1524 1652 0.031414 AAGGGTAGTAGGGCCACGAT 60.031 55.000 6.18 0.00 0.00 3.73
1525 1653 0.252375 AAAGGGTAGTAGGGCCACGA 60.252 55.000 6.18 0.00 0.00 4.35
1526 1654 0.616891 AAAAGGGTAGTAGGGCCACG 59.383 55.000 6.18 0.00 0.00 4.94
1527 1655 1.914108 AGAAAAGGGTAGTAGGGCCAC 59.086 52.381 6.18 1.63 0.00 5.01
1528 1656 1.913419 CAGAAAAGGGTAGTAGGGCCA 59.087 52.381 6.18 0.00 0.00 5.36
1529 1657 2.093075 GTCAGAAAAGGGTAGTAGGGCC 60.093 54.545 0.00 0.00 0.00 5.80
1530 1658 2.570302 TGTCAGAAAAGGGTAGTAGGGC 59.430 50.000 0.00 0.00 0.00 5.19
1531 1659 3.369576 GCTGTCAGAAAAGGGTAGTAGGG 60.370 52.174 3.32 0.00 0.00 3.53
1532 1660 3.369576 GGCTGTCAGAAAAGGGTAGTAGG 60.370 52.174 3.32 0.00 0.00 3.18
1533 1661 3.676324 CGGCTGTCAGAAAAGGGTAGTAG 60.676 52.174 3.32 0.00 0.00 2.57
1534 1662 2.232941 CGGCTGTCAGAAAAGGGTAGTA 59.767 50.000 3.32 0.00 0.00 1.82
1535 1663 1.002087 CGGCTGTCAGAAAAGGGTAGT 59.998 52.381 3.32 0.00 0.00 2.73
1536 1664 1.726853 CGGCTGTCAGAAAAGGGTAG 58.273 55.000 3.32 0.00 0.00 3.18
1537 1665 0.321298 GCGGCTGTCAGAAAAGGGTA 60.321 55.000 3.32 0.00 0.00 3.69
1538 1666 1.600916 GCGGCTGTCAGAAAAGGGT 60.601 57.895 3.32 0.00 0.00 4.34
1539 1667 1.580845 CTGCGGCTGTCAGAAAAGGG 61.581 60.000 3.32 0.00 33.54 3.95
1540 1668 1.871772 CTGCGGCTGTCAGAAAAGG 59.128 57.895 3.32 0.00 33.54 3.11
1541 1669 1.208614 GCTGCGGCTGTCAGAAAAG 59.791 57.895 11.21 0.00 33.54 2.27
1542 1670 3.343972 GCTGCGGCTGTCAGAAAA 58.656 55.556 11.21 0.00 33.54 2.29
1552 1680 2.253452 CAACTGTGAAGCTGCGGC 59.747 61.111 10.33 10.33 39.06 6.53
1553 1681 2.949106 CCAACTGTGAAGCTGCGG 59.051 61.111 0.00 0.00 0.00 5.69
1554 1682 1.859427 ATGCCAACTGTGAAGCTGCG 61.859 55.000 0.00 0.00 0.00 5.18
1555 1683 0.388134 CATGCCAACTGTGAAGCTGC 60.388 55.000 0.00 0.00 0.00 5.25
1556 1684 0.242825 CCATGCCAACTGTGAAGCTG 59.757 55.000 0.00 0.00 0.00 4.24
1557 1685 0.178981 ACCATGCCAACTGTGAAGCT 60.179 50.000 0.00 0.00 0.00 3.74
1558 1686 1.470098 CTACCATGCCAACTGTGAAGC 59.530 52.381 0.00 0.00 0.00 3.86
1559 1687 3.057969 TCTACCATGCCAACTGTGAAG 57.942 47.619 0.00 0.00 0.00 3.02
1560 1688 3.719268 ATCTACCATGCCAACTGTGAA 57.281 42.857 0.00 0.00 0.00 3.18
1561 1689 3.719268 AATCTACCATGCCAACTGTGA 57.281 42.857 0.00 0.00 0.00 3.58
1562 1690 3.758023 TGAAATCTACCATGCCAACTGTG 59.242 43.478 0.00 0.00 0.00 3.66
1563 1691 4.032960 TGAAATCTACCATGCCAACTGT 57.967 40.909 0.00 0.00 0.00 3.55
1564 1692 4.380867 GGTTGAAATCTACCATGCCAACTG 60.381 45.833 8.83 0.00 40.66 3.16
1565 1693 3.763897 GGTTGAAATCTACCATGCCAACT 59.236 43.478 8.83 0.00 40.66 3.16
1566 1694 3.427503 CGGTTGAAATCTACCATGCCAAC 60.428 47.826 13.19 0.00 40.94 3.77
1567 1695 2.752354 CGGTTGAAATCTACCATGCCAA 59.248 45.455 13.19 0.00 40.94 4.52
1568 1696 2.290641 ACGGTTGAAATCTACCATGCCA 60.291 45.455 13.19 0.00 40.94 4.92
1569 1697 2.354821 GACGGTTGAAATCTACCATGCC 59.645 50.000 13.19 0.00 40.94 4.40
1570 1698 2.030457 CGACGGTTGAAATCTACCATGC 59.970 50.000 13.19 2.56 40.94 4.06
1571 1699 3.306166 GTCGACGGTTGAAATCTACCATG 59.694 47.826 13.19 3.71 40.94 3.66
1572 1700 3.194968 AGTCGACGGTTGAAATCTACCAT 59.805 43.478 10.46 0.00 40.94 3.55
1573 1701 2.559668 AGTCGACGGTTGAAATCTACCA 59.440 45.455 10.46 0.00 40.94 3.25
1574 1702 3.227810 AGTCGACGGTTGAAATCTACC 57.772 47.619 10.46 4.23 38.19 3.18
1575 1703 6.196724 CAGATAAGTCGACGGTTGAAATCTAC 59.803 42.308 10.46 0.00 0.00 2.59
1576 1704 6.094464 TCAGATAAGTCGACGGTTGAAATCTA 59.906 38.462 10.46 1.38 0.00 1.98
1577 1705 5.103000 CAGATAAGTCGACGGTTGAAATCT 58.897 41.667 10.46 8.76 0.00 2.40
1578 1706 5.004535 GTCAGATAAGTCGACGGTTGAAATC 59.995 44.000 10.46 6.76 0.00 2.17
1579 1707 4.863131 GTCAGATAAGTCGACGGTTGAAAT 59.137 41.667 10.46 0.00 0.00 2.17
1580 1708 4.232221 GTCAGATAAGTCGACGGTTGAAA 58.768 43.478 10.46 0.00 0.00 2.69
1581 1709 3.366679 GGTCAGATAAGTCGACGGTTGAA 60.367 47.826 10.46 0.00 32.43 2.69
1582 1710 2.163010 GGTCAGATAAGTCGACGGTTGA 59.837 50.000 10.46 8.35 32.43 3.18
1583 1711 2.527100 GGTCAGATAAGTCGACGGTTG 58.473 52.381 10.46 6.13 32.43 3.77
1584 1712 1.131883 CGGTCAGATAAGTCGACGGTT 59.868 52.381 10.46 2.33 32.43 4.44
1585 1713 0.731417 CGGTCAGATAAGTCGACGGT 59.269 55.000 10.46 4.91 32.43 4.83
1586 1714 0.591741 GCGGTCAGATAAGTCGACGG 60.592 60.000 10.46 0.00 34.57 4.79
1587 1715 0.924363 CGCGGTCAGATAAGTCGACG 60.924 60.000 10.46 0.00 32.43 5.12
1588 1716 1.201098 GCGCGGTCAGATAAGTCGAC 61.201 60.000 8.83 7.70 0.00 4.20
1589 1717 1.063649 GCGCGGTCAGATAAGTCGA 59.936 57.895 8.83 0.00 0.00 4.20
1590 1718 1.202973 CTGCGCGGTCAGATAAGTCG 61.203 60.000 8.83 0.00 36.19 4.18
1624 1752 9.300681 TGGTTTCAATCTGAAGAATCATACTTT 57.699 29.630 0.00 0.00 37.70 2.66
1630 1758 6.247676 TCCATGGTTTCAATCTGAAGAATCA 58.752 36.000 12.58 1.52 37.70 2.57
1632 1760 6.487828 TCTCCATGGTTTCAATCTGAAGAAT 58.512 36.000 12.58 0.00 37.70 2.40
1712 1845 8.865090 CAGAGTAGGGATTAGACATAATGAGTT 58.135 37.037 0.00 0.00 31.57 3.01
1718 1879 5.540337 CCTGCAGAGTAGGGATTAGACATAA 59.460 44.000 17.39 0.00 0.00 1.90
1740 1901 6.238648 CGAAACCACTTATTTGAGACAAACCT 60.239 38.462 0.00 0.00 0.00 3.50
1764 1925 4.386867 TTCCACTAAATACCAGAGCTCG 57.613 45.455 8.37 3.24 0.00 5.03
1780 1941 4.058721 AGTTGCCTGAACAAATTTCCAC 57.941 40.909 0.00 0.00 36.98 4.02
1786 1947 3.656559 GATGCAAGTTGCCTGAACAAAT 58.343 40.909 24.59 8.96 44.23 2.32
1798 1959 5.277490 GCATGTATGTATCACGATGCAAGTT 60.277 40.000 1.85 0.00 37.00 2.66
1898 2061 9.403583 AGGTTAAAAACAGTCTGATTGTTCTTA 57.596 29.630 17.26 12.14 37.77 2.10
1902 2065 7.836842 ACAAGGTTAAAAACAGTCTGATTGTT 58.163 30.769 12.14 12.14 40.30 2.83
1934 2137 6.918569 CGACAGAGAGAGAAAAACTTACAGAA 59.081 38.462 0.00 0.00 0.00 3.02
2034 3152 8.735315 TGGCAAATCTAATCGTCAGATTTTTAA 58.265 29.630 14.58 5.38 45.88 1.52
2149 3268 3.058450 TGCTCCAACATCGCAATTTTTG 58.942 40.909 0.00 0.00 0.00 2.44
2254 3374 6.869913 ACAATGCTCTAATTTGTGTGAAATGG 59.130 34.615 0.00 0.00 32.61 3.16


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

AutoCloner maintained by Alex Coulton.