Multiple sequence alignment - TraesCS1D01G104000

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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 TraesCS1D01G104000 chr1D 100.000 2570 0 0 1 2570 93820406 93822975 0.000000e+00 4747
1 TraesCS1D01G104000 chr1D 97.895 95 2 0 1517 1611 93821829 93821923 5.690000e-37 165
2 TraesCS1D01G104000 chr1D 97.895 95 2 0 1424 1518 93821922 93822016 5.690000e-37 165
3 TraesCS1D01G104000 chr1A 96.740 1135 33 4 391 1525 327383983 327382853 0.000000e+00 1888
4 TraesCS1D01G104000 chr1A 96.454 1128 35 3 391 1518 335871678 335872800 0.000000e+00 1857
5 TraesCS1D01G104000 chr1A 95.510 735 29 2 785 1518 335905867 335906598 0.000000e+00 1171
6 TraesCS1D01G104000 chr1A 97.273 550 15 0 1517 2066 327382952 327382403 0.000000e+00 933
7 TraesCS1D01G104000 chr1A 96.909 550 17 0 1517 2066 335872706 335873255 0.000000e+00 922
8 TraesCS1D01G104000 chr1A 96.909 550 17 0 1517 2066 335906504 335907053 0.000000e+00 922
9 TraesCS1D01G104000 chr1A 95.922 515 17 3 2058 2570 242861678 242862190 0.000000e+00 832
10 TraesCS1D01G104000 chr1A 98.280 407 7 0 1 407 327384291 327383885 0.000000e+00 713
11 TraesCS1D01G104000 chr1A 98.284 408 6 1 1 407 335871369 335871776 0.000000e+00 713
12 TraesCS1D01G104000 chr1A 97.549 408 9 1 1 407 335905236 335905643 0.000000e+00 697
13 TraesCS1D01G104000 chr2A 92.885 773 55 0 740 1512 347862158 347862930 0.000000e+00 1123
14 TraesCS1D01G104000 chr2A 94.584 517 28 0 1517 2033 347862842 347863358 0.000000e+00 800
15 TraesCS1D01G104000 chr7A 90.734 777 64 4 740 1512 354945785 354946557 0.000000e+00 1029
16 TraesCS1D01G104000 chr7A 93.012 415 19 3 1 407 354945163 354945575 4.730000e-167 597
17 TraesCS1D01G104000 chr7A 90.238 420 41 0 1517 1936 354946469 354946888 1.340000e-152 549
18 TraesCS1D01G104000 chr5A 93.010 701 48 1 740 1440 337891382 337890683 0.000000e+00 1022
19 TraesCS1D01G104000 chr7B 94.128 579 30 4 740 1318 336259342 336259916 0.000000e+00 878
20 TraesCS1D01G104000 chr7B 93.308 523 33 1 1511 2033 530665248 530665768 0.000000e+00 771
21 TraesCS1D01G104000 chr7B 95.422 415 10 2 1 407 345988392 345988805 0.000000e+00 652
22 TraesCS1D01G104000 chr7B 96.307 352 12 1 391 742 336259032 336259382 6.170000e-161 577
23 TraesCS1D01G104000 chr7B 98.450 129 2 0 279 407 336259002 336259130 7.150000e-56 228
24 TraesCS1D01G104000 chr5B 93.610 579 33 2 740 1318 22034211 22033637 0.000000e+00 861
25 TraesCS1D01G104000 chr5B 93.092 579 35 3 740 1318 463403890 463403317 0.000000e+00 843
26 TraesCS1D01G104000 chr5B 93.976 415 17 2 1 407 389235646 389236060 2.810000e-174 621
27 TraesCS1D01G104000 chr5B 96.875 352 10 1 391 742 463404200 463403850 2.850000e-164 588
28 TraesCS1D01G104000 chr5B 94.886 352 17 1 391 742 22034521 22034171 1.340000e-152 549
29 TraesCS1D01G104000 chr5B 95.522 335 15 0 1517 1851 115862160 115861826 1.050000e-148 536
30 TraesCS1D01G104000 chr5B 98.450 129 2 0 279 407 463404230 463404102 7.150000e-56 228
31 TraesCS1D01G104000 chr5B 92.308 156 10 2 1370 1525 115862214 115862061 1.200000e-53 220
32 TraesCS1D01G104000 chr5D 96.086 511 16 1 2060 2570 230669117 230669623 0.000000e+00 830
33 TraesCS1D01G104000 chr5D 95.508 512 16 4 2060 2570 488622798 488622293 0.000000e+00 811
34 TraesCS1D01G104000 chr5D 95.117 512 21 1 2059 2570 434649003 434648496 0.000000e+00 804
35 TraesCS1D01G104000 chr5D 95.446 505 19 1 2066 2570 317180778 317180278 0.000000e+00 802
36 TraesCS1D01G104000 chr6D 95.842 505 17 2 2066 2570 37850558 37851058 0.000000e+00 813
37 TraesCS1D01G104000 chr6D 95.842 505 17 1 2066 2570 425413553 425413053 0.000000e+00 813
38 TraesCS1D01G104000 chr2D 95.652 506 19 3 2066 2570 579350220 579349717 0.000000e+00 809
39 TraesCS1D01G104000 chr4A 95.050 505 24 1 2066 2570 583086625 583086122 0.000000e+00 793
40 TraesCS1D01G104000 chr4A 93.103 145 8 1 1894 2036 15918902 15918758 7.200000e-51 211
41 TraesCS1D01G104000 chr4A 90.850 153 12 1 1886 2036 682752730 682752882 1.210000e-48 204
42 TraesCS1D01G104000 chr2B 95.181 415 12 1 1 407 388578059 388577645 0.000000e+00 649
43 TraesCS1D01G104000 chr2B 93.735 415 18 1 1 407 746312437 746312023 1.310000e-172 616
44 TraesCS1D01G104000 chr2B 95.184 353 14 3 391 742 388577743 388577393 2.890000e-154 555
45 TraesCS1D01G104000 chr2B 91.447 152 9 2 1887 2036 733164607 733164756 3.350000e-49 206
46 TraesCS1D01G104000 chr3B 94.458 415 15 1 1 407 648407035 648407449 1.300000e-177 632
47 TraesCS1D01G104000 chr3B 96.875 352 10 1 391 742 589660358 589660008 2.850000e-164 588
48 TraesCS1D01G104000 chr3B 94.901 353 16 2 391 742 455491349 455491700 3.740000e-153 551
49 TraesCS1D01G104000 chr3B 98.450 129 2 0 279 407 589660388 589660260 7.150000e-56 228
50 TraesCS1D01G104000 chr6B 94.349 407 15 1 9 407 185001125 185001531 3.630000e-173 617
51 TraesCS1D01G104000 chr6B 96.023 352 12 2 391 742 587741854 587742203 2.870000e-159 571
52 TraesCS1D01G104000 chr6B 97.674 129 3 0 279 407 587741824 587741952 3.330000e-54 222
53 TraesCS1D01G104000 chr4B 93.731 335 21 0 1517 1851 242921216 242920882 1.060000e-138 503
54 TraesCS1D01G104000 chr4D 90.909 154 11 2 1886 2036 451039472 451039625 1.210000e-48 204


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 TraesCS1D01G104000 chr1D 93820406 93822975 2569 False 1692.333333 4747 98.596667 1 2570 3 chr1D.!!$F1 2569
1 TraesCS1D01G104000 chr1A 327382403 327384291 1888 True 1178.000000 1888 97.431000 1 2066 3 chr1A.!!$R1 2065
2 TraesCS1D01G104000 chr1A 335871369 335873255 1886 False 1164.000000 1857 97.215667 1 2066 3 chr1A.!!$F2 2065
3 TraesCS1D01G104000 chr1A 335905236 335907053 1817 False 930.000000 1171 96.656000 1 2066 3 chr1A.!!$F3 2065
4 TraesCS1D01G104000 chr1A 242861678 242862190 512 False 832.000000 832 95.922000 2058 2570 1 chr1A.!!$F1 512
5 TraesCS1D01G104000 chr2A 347862158 347863358 1200 False 961.500000 1123 93.734500 740 2033 2 chr2A.!!$F1 1293
6 TraesCS1D01G104000 chr7A 354945163 354946888 1725 False 725.000000 1029 91.328000 1 1936 3 chr7A.!!$F1 1935
7 TraesCS1D01G104000 chr5A 337890683 337891382 699 True 1022.000000 1022 93.010000 740 1440 1 chr5A.!!$R1 700
8 TraesCS1D01G104000 chr7B 530665248 530665768 520 False 771.000000 771 93.308000 1511 2033 1 chr7B.!!$F2 522
9 TraesCS1D01G104000 chr7B 336259002 336259916 914 False 561.000000 878 96.295000 279 1318 3 chr7B.!!$F3 1039
10 TraesCS1D01G104000 chr5B 22033637 22034521 884 True 705.000000 861 94.248000 391 1318 2 chr5B.!!$R1 927
11 TraesCS1D01G104000 chr5B 463403317 463404230 913 True 553.000000 843 96.139000 279 1318 3 chr5B.!!$R3 1039
12 TraesCS1D01G104000 chr5D 230669117 230669623 506 False 830.000000 830 96.086000 2060 2570 1 chr5D.!!$F1 510
13 TraesCS1D01G104000 chr5D 488622293 488622798 505 True 811.000000 811 95.508000 2060 2570 1 chr5D.!!$R3 510
14 TraesCS1D01G104000 chr5D 434648496 434649003 507 True 804.000000 804 95.117000 2059 2570 1 chr5D.!!$R2 511
15 TraesCS1D01G104000 chr5D 317180278 317180778 500 True 802.000000 802 95.446000 2066 2570 1 chr5D.!!$R1 504
16 TraesCS1D01G104000 chr6D 37850558 37851058 500 False 813.000000 813 95.842000 2066 2570 1 chr6D.!!$F1 504
17 TraesCS1D01G104000 chr6D 425413053 425413553 500 True 813.000000 813 95.842000 2066 2570 1 chr6D.!!$R1 504
18 TraesCS1D01G104000 chr2D 579349717 579350220 503 True 809.000000 809 95.652000 2066 2570 1 chr2D.!!$R1 504
19 TraesCS1D01G104000 chr4A 583086122 583086625 503 True 793.000000 793 95.050000 2066 2570 1 chr4A.!!$R2 504
20 TraesCS1D01G104000 chr2B 388577393 388578059 666 True 602.000000 649 95.182500 1 742 2 chr2B.!!$R2 741

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
252 254 1.188863 GGTGCATCAAATGGCTTCCT 58.811 50.0 0.0 0.0 0.00 3.36 F
1503 1592 2.067365 AGGGGAGTTGTTGGTCAAAC 57.933 50.0 0.0 0.0 37.81 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2145 0.756294 TGACACCGACACTCACCATT 59.244 50.000 0.0 0.0 0.00 3.16 R
2509 2605 1.203262 CCTGGATTAGGGGGTATCCGA 60.203 57.143 0.0 0.0 42.67 4.55 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
104 106 4.414852 TGCTCAAGAAATTTGATAAGCGC 58.585 39.130 0.00 0.00 0.00 5.92
252 254 1.188863 GGTGCATCAAATGGCTTCCT 58.811 50.000 0.00 0.00 0.00 3.36
389 399 6.780706 TGTAGTAGTAGTTTTTCTTGCAGC 57.219 37.500 0.00 0.00 0.00 5.25
396 406 5.823045 AGTAGTTTTTCTTGCAGCTTGTAGT 59.177 36.000 0.00 0.00 0.00 2.73
409 419 6.647895 TGCAGCTTGTAGTAGTAGTTTTTACC 59.352 38.462 0.00 0.00 0.00 2.85
882 967 5.367945 TGGGTCTAAAACTTGACTGAACT 57.632 39.130 0.00 0.00 34.01 3.01
913 998 4.853007 AGTTTAGCTCAGCCTCATTTGAT 58.147 39.130 0.00 0.00 0.00 2.57
958 1043 9.892987 CGCAGAATATATATTCGTTCTTGAATC 57.107 33.333 23.50 8.04 45.10 2.52
1206 1291 2.656002 CTCGGTGATCAGGTCCTTCTA 58.344 52.381 0.00 0.00 0.00 2.10
1254 1339 3.066814 GTCCCTCCTGTACGCCGT 61.067 66.667 0.00 0.00 0.00 5.68
1458 1547 8.870116 TCTAGCATTGCTATTATTCTGAACCTA 58.130 33.333 18.29 0.00 40.54 3.08
1459 1548 7.976135 AGCATTGCTATTATTCTGAACCTAG 57.024 36.000 10.00 0.00 36.99 3.02
1460 1549 7.512992 AGCATTGCTATTATTCTGAACCTAGT 58.487 34.615 10.00 0.00 36.99 2.57
1461 1550 8.651389 AGCATTGCTATTATTCTGAACCTAGTA 58.349 33.333 10.00 0.00 36.99 1.82
1462 1551 9.442047 GCATTGCTATTATTCTGAACCTAGTAT 57.558 33.333 0.16 0.00 0.00 2.12
1464 1553 9.950496 ATTGCTATTATTCTGAACCTAGTATGG 57.050 33.333 0.00 0.00 0.00 2.74
1465 1554 7.386851 TGCTATTATTCTGAACCTAGTATGGC 58.613 38.462 0.00 0.00 0.00 4.40
1466 1555 6.819146 GCTATTATTCTGAACCTAGTATGGCC 59.181 42.308 0.00 0.00 0.00 5.36
1467 1556 7.310734 GCTATTATTCTGAACCTAGTATGGCCT 60.311 40.741 3.32 0.00 0.00 5.19
1468 1557 4.965200 ATTCTGAACCTAGTATGGCCTC 57.035 45.455 3.32 0.00 0.00 4.70
1469 1558 3.398318 TCTGAACCTAGTATGGCCTCA 57.602 47.619 3.32 0.00 0.00 3.86
1470 1559 3.719871 TCTGAACCTAGTATGGCCTCAA 58.280 45.455 3.32 0.00 0.00 3.02
1471 1560 4.101114 TCTGAACCTAGTATGGCCTCAAA 58.899 43.478 3.32 0.00 0.00 2.69
1472 1561 4.534500 TCTGAACCTAGTATGGCCTCAAAA 59.466 41.667 3.32 0.00 0.00 2.44
1473 1562 5.191722 TCTGAACCTAGTATGGCCTCAAAAT 59.808 40.000 3.32 0.00 0.00 1.82
1474 1563 5.192927 TGAACCTAGTATGGCCTCAAAATG 58.807 41.667 3.32 0.00 0.00 2.32
1475 1564 5.045213 TGAACCTAGTATGGCCTCAAAATGA 60.045 40.000 3.32 0.00 0.00 2.57
1476 1565 5.450818 ACCTAGTATGGCCTCAAAATGAA 57.549 39.130 3.32 0.00 0.00 2.57
1477 1566 5.193679 ACCTAGTATGGCCTCAAAATGAAC 58.806 41.667 3.32 0.00 0.00 3.18
1478 1567 5.044846 ACCTAGTATGGCCTCAAAATGAACT 60.045 40.000 3.32 0.00 0.00 3.01
1479 1568 5.297776 CCTAGTATGGCCTCAAAATGAACTG 59.702 44.000 3.32 0.00 0.00 3.16
1480 1569 4.922206 AGTATGGCCTCAAAATGAACTGA 58.078 39.130 3.32 0.00 0.00 3.41
1481 1570 5.324409 AGTATGGCCTCAAAATGAACTGAA 58.676 37.500 3.32 0.00 0.00 3.02
1482 1571 5.774690 AGTATGGCCTCAAAATGAACTGAAA 59.225 36.000 3.32 0.00 0.00 2.69
1483 1572 5.750352 ATGGCCTCAAAATGAACTGAAAT 57.250 34.783 3.32 0.00 0.00 2.17
1484 1573 6.855763 ATGGCCTCAAAATGAACTGAAATA 57.144 33.333 3.32 0.00 0.00 1.40
1485 1574 6.271488 TGGCCTCAAAATGAACTGAAATAG 57.729 37.500 3.32 0.00 0.00 1.73
1486 1575 5.185635 TGGCCTCAAAATGAACTGAAATAGG 59.814 40.000 3.32 0.00 0.00 2.57
1487 1576 5.394553 GGCCTCAAAATGAACTGAAATAGGG 60.395 44.000 0.00 0.00 0.00 3.53
1488 1577 5.394553 GCCTCAAAATGAACTGAAATAGGGG 60.395 44.000 0.00 0.00 0.00 4.79
1489 1578 5.951747 CCTCAAAATGAACTGAAATAGGGGA 59.048 40.000 0.00 0.00 0.00 4.81
1490 1579 6.096001 CCTCAAAATGAACTGAAATAGGGGAG 59.904 42.308 0.00 0.00 0.00 4.30
1491 1580 6.552008 TCAAAATGAACTGAAATAGGGGAGT 58.448 36.000 0.00 0.00 0.00 3.85
1492 1581 7.010160 TCAAAATGAACTGAAATAGGGGAGTT 58.990 34.615 0.00 0.00 0.00 3.01
1493 1582 6.840780 AAATGAACTGAAATAGGGGAGTTG 57.159 37.500 0.00 0.00 0.00 3.16
1494 1583 4.993705 TGAACTGAAATAGGGGAGTTGT 57.006 40.909 0.00 0.00 0.00 3.32
1495 1584 5.319043 TGAACTGAAATAGGGGAGTTGTT 57.681 39.130 0.00 0.00 0.00 2.83
1496 1585 5.070001 TGAACTGAAATAGGGGAGTTGTTG 58.930 41.667 0.00 0.00 0.00 3.33
1497 1586 4.034285 ACTGAAATAGGGGAGTTGTTGG 57.966 45.455 0.00 0.00 0.00 3.77
1498 1587 3.397955 ACTGAAATAGGGGAGTTGTTGGT 59.602 43.478 0.00 0.00 0.00 3.67
1499 1588 4.010349 CTGAAATAGGGGAGTTGTTGGTC 58.990 47.826 0.00 0.00 0.00 4.02
1500 1589 3.396276 TGAAATAGGGGAGTTGTTGGTCA 59.604 43.478 0.00 0.00 0.00 4.02
1501 1590 4.141135 TGAAATAGGGGAGTTGTTGGTCAA 60.141 41.667 0.00 0.00 0.00 3.18
1502 1591 4.463050 AATAGGGGAGTTGTTGGTCAAA 57.537 40.909 0.00 0.00 37.81 2.69
1503 1592 2.067365 AGGGGAGTTGTTGGTCAAAC 57.933 50.000 0.00 0.00 37.81 2.93
1519 1608 6.092092 TGGTCAAACAAATAATTCAGCATCG 58.908 36.000 0.00 0.00 0.00 3.84
1545 1634 9.698309 GTCTTGTCTAGCATTGCTATTATTCTA 57.302 33.333 18.29 0.00 40.54 2.10
1797 1886 5.090652 TGTCAGTAGTTTGTTCAATTCGC 57.909 39.130 0.00 0.00 0.00 4.70
2056 2145 5.008316 GGAAGCTTGAAAGTTCGGTTTTCTA 59.992 40.000 2.10 1.97 35.94 2.10
2163 2254 2.024414 GGACATGATGTTTACCCAGGC 58.976 52.381 0.00 0.00 0.00 4.85
2196 2288 5.070823 TCGATGGAGGTAATACCCTACTT 57.929 43.478 5.71 0.00 39.75 2.24
2279 2371 4.079096 AGAGGCTAAACCCTAGAAGCTAGA 60.079 45.833 0.00 0.00 40.58 2.43
2416 2512 0.832983 TTGCCAAGCTTGCCTTCCAT 60.833 50.000 21.43 0.00 0.00 3.41
2429 2525 1.005215 CCTTCCATGCCAAGGAGAGTT 59.995 52.381 13.98 0.00 42.94 3.01
2430 2526 2.556114 CCTTCCATGCCAAGGAGAGTTT 60.556 50.000 13.98 0.00 42.94 2.66
2495 2591 0.821711 CAACAGTCCGGCCAAAGGAA 60.822 55.000 2.24 0.00 39.84 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.916360 AACTGGTTTGAATTATGGATGTGT 57.084 33.333 0.00 0.00 0.00 3.72
252 254 7.601886 CACATTTTATGCTTCCACAAATACCAA 59.398 33.333 0.00 0.00 0.00 3.67
388 398 6.863126 TCACGGTAAAAACTACTACTACAAGC 59.137 38.462 0.00 0.00 0.00 4.01
389 399 8.801715 TTCACGGTAAAAACTACTACTACAAG 57.198 34.615 0.00 0.00 0.00 3.16
396 406 8.711457 GCTTATGTTTCACGGTAAAAACTACTA 58.289 33.333 15.20 6.11 36.54 1.82
409 419 7.321271 CACTGTAAAAAGAGCTTATGTTTCACG 59.679 37.037 0.00 0.00 0.00 4.35
558 568 8.505625 GTCATCCATAATGTTGCAAAACAAAAT 58.494 29.630 0.00 0.00 40.82 1.82
882 967 3.815401 GGCTGAGCTAAACTTCAGTTCAA 59.185 43.478 3.72 0.00 37.25 2.69
913 998 4.120589 TGCGTTGTGTGTGTATCTGTTTA 58.879 39.130 0.00 0.00 0.00 2.01
1300 1385 1.592400 CGACCCAGTAGAGCGGACAA 61.592 60.000 0.00 0.00 0.00 3.18
1458 1547 4.922206 TCAGTTCATTTTGAGGCCATACT 58.078 39.130 5.01 0.00 0.00 2.12
1459 1548 5.643379 TTCAGTTCATTTTGAGGCCATAC 57.357 39.130 5.01 0.00 0.00 2.39
1460 1549 6.855763 ATTTCAGTTCATTTTGAGGCCATA 57.144 33.333 5.01 0.00 0.00 2.74
1461 1550 5.750352 ATTTCAGTTCATTTTGAGGCCAT 57.250 34.783 5.01 0.00 0.00 4.40
1462 1551 5.185635 CCTATTTCAGTTCATTTTGAGGCCA 59.814 40.000 5.01 0.00 0.00 5.36
1463 1552 5.394553 CCCTATTTCAGTTCATTTTGAGGCC 60.395 44.000 0.00 0.00 0.00 5.19
1464 1553 5.394553 CCCCTATTTCAGTTCATTTTGAGGC 60.395 44.000 0.00 0.00 0.00 4.70
1465 1554 5.951747 TCCCCTATTTCAGTTCATTTTGAGG 59.048 40.000 0.00 0.00 0.00 3.86
1466 1555 6.660949 ACTCCCCTATTTCAGTTCATTTTGAG 59.339 38.462 0.00 0.00 0.00 3.02
1467 1556 6.552008 ACTCCCCTATTTCAGTTCATTTTGA 58.448 36.000 0.00 0.00 0.00 2.69
1468 1557 6.840780 ACTCCCCTATTTCAGTTCATTTTG 57.159 37.500 0.00 0.00 0.00 2.44
1469 1558 6.782494 ACAACTCCCCTATTTCAGTTCATTTT 59.218 34.615 0.00 0.00 0.00 1.82
1470 1559 6.314917 ACAACTCCCCTATTTCAGTTCATTT 58.685 36.000 0.00 0.00 0.00 2.32
1471 1560 5.892348 ACAACTCCCCTATTTCAGTTCATT 58.108 37.500 0.00 0.00 0.00 2.57
1472 1561 5.520748 ACAACTCCCCTATTTCAGTTCAT 57.479 39.130 0.00 0.00 0.00 2.57
1473 1562 4.993705 ACAACTCCCCTATTTCAGTTCA 57.006 40.909 0.00 0.00 0.00 3.18
1474 1563 4.459337 CCAACAACTCCCCTATTTCAGTTC 59.541 45.833 0.00 0.00 0.00 3.01
1475 1564 4.141018 ACCAACAACTCCCCTATTTCAGTT 60.141 41.667 0.00 0.00 0.00 3.16
1476 1565 3.397955 ACCAACAACTCCCCTATTTCAGT 59.602 43.478 0.00 0.00 0.00 3.41
1477 1566 4.010349 GACCAACAACTCCCCTATTTCAG 58.990 47.826 0.00 0.00 0.00 3.02
1478 1567 3.396276 TGACCAACAACTCCCCTATTTCA 59.604 43.478 0.00 0.00 0.00 2.69
1479 1568 4.028993 TGACCAACAACTCCCCTATTTC 57.971 45.455 0.00 0.00 0.00 2.17
1480 1569 4.463050 TTGACCAACAACTCCCCTATTT 57.537 40.909 0.00 0.00 33.18 1.40
1481 1570 4.149598 GTTTGACCAACAACTCCCCTATT 58.850 43.478 0.00 0.00 38.29 1.73
1482 1571 3.139397 TGTTTGACCAACAACTCCCCTAT 59.861 43.478 0.00 0.00 42.76 2.57
1483 1572 2.510382 TGTTTGACCAACAACTCCCCTA 59.490 45.455 0.00 0.00 42.76 3.53
1484 1573 1.286553 TGTTTGACCAACAACTCCCCT 59.713 47.619 0.00 0.00 42.76 4.79
1485 1574 1.770294 TGTTTGACCAACAACTCCCC 58.230 50.000 0.00 0.00 42.76 4.81
1492 1581 6.577103 TGCTGAATTATTTGTTTGACCAACA 58.423 32.000 0.00 0.00 44.11 3.33
1493 1582 7.410728 CGATGCTGAATTATTTGTTTGACCAAC 60.411 37.037 0.00 0.00 35.71 3.77
1494 1583 6.585702 CGATGCTGAATTATTTGTTTGACCAA 59.414 34.615 0.00 0.00 0.00 3.67
1495 1584 6.092092 CGATGCTGAATTATTTGTTTGACCA 58.908 36.000 0.00 0.00 0.00 4.02
1496 1585 6.092748 ACGATGCTGAATTATTTGTTTGACC 58.907 36.000 0.00 0.00 0.00 4.02
1497 1586 7.023575 AGACGATGCTGAATTATTTGTTTGAC 58.976 34.615 0.00 0.00 0.00 3.18
1498 1587 7.144722 AGACGATGCTGAATTATTTGTTTGA 57.855 32.000 0.00 0.00 0.00 2.69
1499 1588 7.326789 ACAAGACGATGCTGAATTATTTGTTTG 59.673 33.333 0.00 0.00 0.00 2.93
1500 1589 7.370383 ACAAGACGATGCTGAATTATTTGTTT 58.630 30.769 0.00 0.00 0.00 2.83
1501 1590 6.913170 ACAAGACGATGCTGAATTATTTGTT 58.087 32.000 0.00 0.00 0.00 2.83
1502 1591 6.372659 AGACAAGACGATGCTGAATTATTTGT 59.627 34.615 0.00 0.00 0.00 2.83
1503 1592 6.779117 AGACAAGACGATGCTGAATTATTTG 58.221 36.000 0.00 0.00 0.00 2.32
1504 1593 6.992063 AGACAAGACGATGCTGAATTATTT 57.008 33.333 0.00 0.00 0.00 1.40
1505 1594 6.201806 GCTAGACAAGACGATGCTGAATTATT 59.798 38.462 0.00 0.00 0.00 1.40
1506 1595 5.694006 GCTAGACAAGACGATGCTGAATTAT 59.306 40.000 0.00 0.00 0.00 1.28
1507 1596 5.043903 GCTAGACAAGACGATGCTGAATTA 58.956 41.667 0.00 0.00 0.00 1.40
1508 1597 3.868077 GCTAGACAAGACGATGCTGAATT 59.132 43.478 0.00 0.00 0.00 2.17
1509 1598 3.118992 TGCTAGACAAGACGATGCTGAAT 60.119 43.478 0.00 0.00 0.00 2.57
1514 1603 2.286067 GCAATGCTAGACAAGACGATGC 60.286 50.000 0.00 0.00 0.00 3.91
1515 1604 3.193263 AGCAATGCTAGACAAGACGATG 58.807 45.455 5.69 0.00 36.99 3.84
1519 1608 8.600449 AGAATAATAGCAATGCTAGACAAGAC 57.400 34.615 20.25 8.38 44.66 3.01
1545 1634 7.893833 AGTTTATTTTGAGGCCATACTAGGTTT 59.106 33.333 5.01 0.00 0.00 3.27
1551 1640 7.775053 TTTCAGTTTATTTTGAGGCCATACT 57.225 32.000 5.01 0.00 0.00 2.12
1606 1695 2.645838 ACTGAGTGTCCAAACATGCT 57.354 45.000 0.00 0.00 37.81 3.79
1797 1886 2.791383 TCAAACAAATCCCAAGCGTG 57.209 45.000 0.00 0.00 0.00 5.34
1873 1962 7.947890 TCAAAATTTGAGAACTATACCTTGGGT 59.052 33.333 4.03 0.00 35.64 4.51
2056 2145 0.756294 TGACACCGACACTCACCATT 59.244 50.000 0.00 0.00 0.00 3.16
2163 2254 3.610669 CCATCGAGAGGGCCCGAG 61.611 72.222 18.44 9.41 38.25 4.63
2196 2288 5.106876 TCATCAAGATCAATCAAGCAGGA 57.893 39.130 0.00 0.00 0.00 3.86
2279 2371 7.175104 ACCAAGAACAACAATCATACCATAGT 58.825 34.615 0.00 0.00 0.00 2.12
2416 2512 1.339055 CGGATGAAACTCTCCTTGGCA 60.339 52.381 0.00 0.00 0.00 4.92
2509 2605 1.203262 CCTGGATTAGGGGGTATCCGA 60.203 57.143 0.00 0.00 42.67 4.55


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

AutoCloner maintained by Alex Coulton.