Multiple sequence alignment - TraesCS5A01G147300

Loading Multiple Alignment...

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 TraesCS5A01G147300 chr5A 100.000 2432 0 0 1 2432 325180121 325182552 0.000000e+00 4492.0
1 TraesCS5A01G147300 chr5A 94.595 37 2 0 2382 2418 470919797 470919833 9.390000e-05 58.4
2 TraesCS5A01G147300 chr5B 87.943 846 79 19 1579 2412 34545808 34546642 0.000000e+00 976.0
3 TraesCS5A01G147300 chr5B 83.918 1026 115 13 549 1558 698002601 698003592 0.000000e+00 935.0
4 TraesCS5A01G147300 chr5B 87.211 735 77 12 1615 2344 594156699 594157421 0.000000e+00 821.0
5 TraesCS5A01G147300 chr5B 88.203 551 58 3 1 544 273458027 273458577 0.000000e+00 651.0
6 TraesCS5A01G147300 chr7D 87.957 847 72 23 1580 2414 133609060 133609888 0.000000e+00 972.0
7 TraesCS5A01G147300 chr7D 87.839 847 73 23 1580 2414 133495441 133494613 0.000000e+00 966.0
8 TraesCS5A01G147300 chr7D 91.456 316 27 0 1052 1367 614352430 614352115 3.710000e-118 435.0
9 TraesCS5A01G147300 chr7D 86.614 127 11 4 549 669 30832442 30832316 4.220000e-28 135.0
10 TraesCS5A01G147300 chr2D 87.825 846 75 18 1581 2414 599216419 599215590 0.000000e+00 966.0
11 TraesCS5A01G147300 chr2D 90.143 700 54 12 1737 2432 180995212 180995900 0.000000e+00 896.0
12 TraesCS5A01G147300 chr6D 87.879 792 61 11 1608 2368 12660215 12661002 0.000000e+00 898.0
13 TraesCS5A01G147300 chr5D 90.505 653 46 9 1769 2414 421866610 421867253 0.000000e+00 848.0
14 TraesCS5A01G147300 chr5D 87.931 406 45 3 143 544 231789404 231788999 2.190000e-130 475.0
15 TraesCS5A01G147300 chr3D 87.637 728 44 24 1697 2414 30352622 30353313 0.000000e+00 804.0
16 TraesCS5A01G147300 chr3D 86.447 546 59 8 1053 1585 31419047 31418504 3.480000e-163 584.0
17 TraesCS5A01G147300 chr3D 83.871 341 26 17 577 906 555034582 555034904 5.080000e-77 298.0
18 TraesCS5A01G147300 chr3D 89.362 188 14 4 549 730 501815560 501815747 5.230000e-57 231.0
19 TraesCS5A01G147300 chr2A 90.988 577 41 10 1844 2414 105547798 105547227 0.000000e+00 767.0
20 TraesCS5A01G147300 chr2A 87.440 629 55 17 1581 2204 698294001 698293392 0.000000e+00 702.0
21 TraesCS5A01G147300 chr2A 85.561 187 20 5 549 729 3514221 3514406 3.190000e-44 189.0
22 TraesCS5A01G147300 chr2A 82.993 147 19 4 549 689 274466 274612 7.060000e-26 128.0
23 TraesCS5A01G147300 chr2A 90.526 95 9 0 332 426 679266304 679266210 2.540000e-25 126.0
24 TraesCS5A01G147300 chr2A 97.059 34 1 0 113 146 611169046 611169079 9.390000e-05 58.4
25 TraesCS5A01G147300 chr7B 89.826 403 29 5 1172 1563 462813943 462813542 7.760000e-140 507.0
26 TraesCS5A01G147300 chr7B 91.139 316 28 0 1052 1367 706384311 706384626 1.730000e-116 429.0
27 TraesCS5A01G147300 chr4B 86.816 402 41 5 1173 1563 665226606 665227006 2.870000e-119 438.0
28 TraesCS5A01G147300 chr4A 86.104 403 44 7 1172 1563 608584023 608583622 8.040000e-115 424.0
29 TraesCS5A01G147300 chr3B 90.506 316 30 0 1052 1367 29245558 29245873 3.740000e-113 418.0
30 TraesCS5A01G147300 chr3B 85.100 349 33 11 1251 1585 130115730 130116073 3.000000e-89 339.0
31 TraesCS5A01G147300 chr7A 89.241 316 34 0 1052 1367 706399487 706399172 1.750000e-106 396.0
32 TraesCS5A01G147300 chr7A 85.039 127 13 4 549 669 4804676 4804550 9.130000e-25 124.0
33 TraesCS5A01G147300 chr1D 88.125 320 24 6 1278 1585 482914770 482914453 3.820000e-98 368.0
34 TraesCS5A01G147300 chr2B 87.654 324 28 6 1251 1563 298514394 298514072 1.370000e-97 366.0
35 TraesCS5A01G147300 chr2B 83.668 349 34 12 1251 1585 105743403 105743742 8.450000e-80 307.0
36 TraesCS5A01G147300 chr3A 84.153 366 31 13 549 906 51776901 51777247 1.800000e-86 329.0
37 TraesCS5A01G147300 chr3A 86.916 214 27 1 210 423 144533687 144533899 3.130000e-59 239.0
38 TraesCS5A01G147300 chr6B 86.614 127 11 4 549 669 705319404 705319278 4.220000e-28 135.0
39 TraesCS5A01G147300 chr1A 86.290 124 10 6 549 665 57962124 57962001 7.060000e-26 128.0


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 TraesCS5A01G147300 chr5A 325180121 325182552 2431 False 4492 4492 100.000 1 2432 1 chr5A.!!$F1 2431
1 TraesCS5A01G147300 chr5B 34545808 34546642 834 False 976 976 87.943 1579 2412 1 chr5B.!!$F1 833
2 TraesCS5A01G147300 chr5B 698002601 698003592 991 False 935 935 83.918 549 1558 1 chr5B.!!$F4 1009
3 TraesCS5A01G147300 chr5B 594156699 594157421 722 False 821 821 87.211 1615 2344 1 chr5B.!!$F3 729
4 TraesCS5A01G147300 chr5B 273458027 273458577 550 False 651 651 88.203 1 544 1 chr5B.!!$F2 543
5 TraesCS5A01G147300 chr7D 133609060 133609888 828 False 972 972 87.957 1580 2414 1 chr7D.!!$F1 834
6 TraesCS5A01G147300 chr7D 133494613 133495441 828 True 966 966 87.839 1580 2414 1 chr7D.!!$R2 834
7 TraesCS5A01G147300 chr2D 599215590 599216419 829 True 966 966 87.825 1581 2414 1 chr2D.!!$R1 833
8 TraesCS5A01G147300 chr2D 180995212 180995900 688 False 896 896 90.143 1737 2432 1 chr2D.!!$F1 695
9 TraesCS5A01G147300 chr6D 12660215 12661002 787 False 898 898 87.879 1608 2368 1 chr6D.!!$F1 760
10 TraesCS5A01G147300 chr5D 421866610 421867253 643 False 848 848 90.505 1769 2414 1 chr5D.!!$F1 645
11 TraesCS5A01G147300 chr3D 30352622 30353313 691 False 804 804 87.637 1697 2414 1 chr3D.!!$F1 717
12 TraesCS5A01G147300 chr3D 31418504 31419047 543 True 584 584 86.447 1053 1585 1 chr3D.!!$R1 532
13 TraesCS5A01G147300 chr2A 105547227 105547798 571 True 767 767 90.988 1844 2414 1 chr2A.!!$R1 570
14 TraesCS5A01G147300 chr2A 698293392 698294001 609 True 702 702 87.440 1581 2204 1 chr2A.!!$R3 623

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
673 687 0.248289 GTCCACACTTAAGCGGGCTA 59.752 55.0 1.29 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1754 0.780002 GACAAAAGCTGTTGCATGCG 59.22 50.0 16.88 0.0 38.84 4.73 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
26 27 3.770040 CGGTGAGCCATGGACGGA 61.770 66.667 18.40 0.00 34.09 4.69
33 34 3.770040 CCATGGACGGAGCCGACA 61.770 66.667 16.83 13.86 42.83 4.35
37 38 2.750637 GGACGGAGCCGACAGAGA 60.751 66.667 16.83 0.00 42.83 3.10
48 49 3.251245 AGCCGACAGAGACGTAGATTATG 59.749 47.826 0.00 0.00 0.00 1.90
59 60 5.744345 AGACGTAGATTATGCAAGAAACTCG 59.256 40.000 0.00 2.11 0.00 4.18
61 62 5.288712 ACGTAGATTATGCAAGAAACTCGTG 59.711 40.000 0.00 0.00 0.00 4.35
64 65 4.997395 AGATTATGCAAGAAACTCGTGTGT 59.003 37.500 0.00 0.00 0.00 3.72
71 72 4.447724 GCAAGAAACTCGTGTGTAGATCAA 59.552 41.667 0.00 0.00 0.00 2.57
78 79 5.403246 ACTCGTGTGTAGATCAACATCTTC 58.597 41.667 0.00 0.00 40.18 2.87
79 80 5.184096 ACTCGTGTGTAGATCAACATCTTCT 59.816 40.000 0.00 0.00 40.18 2.85
96 97 5.576337 TCTTCTTCGTCTGAATTCGTTTG 57.424 39.130 0.04 0.00 32.61 2.93
106 107 6.303259 CGTCTGAATTCGTTTGAAGAAATTCC 59.697 38.462 0.04 0.00 37.57 3.01
107 108 7.138736 GTCTGAATTCGTTTGAAGAAATTCCA 58.861 34.615 0.04 0.00 37.57 3.53
110 111 7.656412 TGAATTCGTTTGAAGAAATTCCATCA 58.344 30.769 0.04 0.00 37.57 3.07
114 115 6.980593 TCGTTTGAAGAAATTCCATCACATT 58.019 32.000 0.00 0.00 0.00 2.71
115 116 7.083858 TCGTTTGAAGAAATTCCATCACATTC 58.916 34.615 0.00 0.00 0.00 2.67
148 152 2.471818 CGACATGCCTCTTCTGATCTG 58.528 52.381 0.00 0.00 0.00 2.90
179 183 7.888021 TCAGCCCTAAATTAAATCTTTCAGACA 59.112 33.333 0.00 0.00 0.00 3.41
180 184 8.522830 CAGCCCTAAATTAAATCTTTCAGACAA 58.477 33.333 0.00 0.00 0.00 3.18
181 185 8.523658 AGCCCTAAATTAAATCTTTCAGACAAC 58.476 33.333 0.00 0.00 0.00 3.32
191 195 6.712241 ATCTTTCAGACAACGACAGTTATG 57.288 37.500 0.00 0.00 38.79 1.90
196 200 4.754618 TCAGACAACGACAGTTATGCAATT 59.245 37.500 0.00 0.00 38.79 2.32
204 208 3.932710 GACAGTTATGCAATTCAGACGGA 59.067 43.478 0.00 0.00 0.00 4.69
207 211 5.163723 ACAGTTATGCAATTCAGACGGAATG 60.164 40.000 1.36 0.00 45.46 2.67
209 213 3.770263 ATGCAATTCAGACGGAATGTG 57.230 42.857 1.36 4.45 45.46 3.21
219 223 2.029380 AGACGGAATGTGTCGTTGATGA 60.029 45.455 0.00 0.00 41.24 2.92
225 229 4.911610 GGAATGTGTCGTTGATGAAAACTG 59.088 41.667 0.00 0.00 0.00 3.16
261 265 5.632959 TGTTTTATTCGCCTCAAATTACCG 58.367 37.500 0.00 0.00 0.00 4.02
272 276 5.408604 GCCTCAAATTACCGTACATCCTATG 59.591 44.000 0.00 0.00 0.00 2.23
274 278 5.302360 TCAAATTACCGTACATCCTATGGC 58.698 41.667 0.00 0.00 33.60 4.40
275 279 3.975168 ATTACCGTACATCCTATGGCC 57.025 47.619 0.00 0.00 33.60 5.36
285 289 5.387113 ACATCCTATGGCCATCAACTTTA 57.613 39.130 24.80 0.84 33.60 1.85
342 346 3.253955 GCACGGCGATGAAAGTGT 58.746 55.556 16.62 0.00 36.99 3.55
347 351 0.389817 CGGCGATGAAAGTGTCTCCA 60.390 55.000 0.00 0.00 0.00 3.86
352 356 0.687354 ATGAAAGTGTCTCCAGCGGT 59.313 50.000 0.00 0.00 0.00 5.68
385 393 1.066605 GCATGCACTTGATTAGGCTGG 59.933 52.381 14.21 0.00 0.00 4.85
459 467 3.662759 TGGATTTCATTGGTACTCCCC 57.337 47.619 0.00 0.00 0.00 4.81
512 520 3.984292 GCTCATGCTTGAACGGAAG 57.016 52.632 3.65 0.00 36.03 3.46
533 541 8.567948 CGGAAGTGCCTATCATTAAAATATGTT 58.432 33.333 0.00 0.00 0.00 2.71
593 601 8.567285 AACTACCATTTTCTCACTAATCCTTG 57.433 34.615 0.00 0.00 0.00 3.61
641 650 3.007940 GCCTGATTTGGCCCTTTTAAACT 59.992 43.478 0.00 0.00 46.82 2.66
642 651 4.504864 GCCTGATTTGGCCCTTTTAAACTT 60.505 41.667 0.00 0.00 46.82 2.66
643 652 5.620206 CCTGATTTGGCCCTTTTAAACTTT 58.380 37.500 0.00 0.00 0.00 2.66
646 655 7.255104 CCTGATTTGGCCCTTTTAAACTTTTTC 60.255 37.037 0.00 0.00 0.00 2.29
647 656 7.342581 TGATTTGGCCCTTTTAAACTTTTTCT 58.657 30.769 0.00 0.00 0.00 2.52
655 669 7.634210 GCCCTTTTAAACTTTTTCTAGTTGGGT 60.634 37.037 0.00 0.00 38.06 4.51
662 676 4.079958 ACTTTTTCTAGTTGGGTCCACACT 60.080 41.667 0.00 8.87 0.00 3.55
666 680 4.884668 TCTAGTTGGGTCCACACTTAAG 57.115 45.455 0.00 0.00 0.00 1.85
673 687 0.248289 GTCCACACTTAAGCGGGCTA 59.752 55.000 1.29 0.00 0.00 3.93
675 689 1.348366 TCCACACTTAAGCGGGCTAAA 59.652 47.619 1.29 0.00 0.00 1.85
699 713 3.622166 TCAATCGGGTCCCTAGTTTTC 57.378 47.619 6.29 0.00 0.00 2.29
707 721 4.581409 CGGGTCCCTAGTTTTCTTTTCAAA 59.419 41.667 6.29 0.00 0.00 2.69
838 852 2.125753 GTGGCCGACTCTGAGCTG 60.126 66.667 4.19 0.00 0.00 4.24
839 853 2.601666 TGGCCGACTCTGAGCTGT 60.602 61.111 4.19 0.00 0.00 4.40
884 898 3.161450 GCTGGCCGACCTCCCATA 61.161 66.667 0.00 0.00 36.63 2.74
924 938 0.538746 GGGGAAGAAAAAGGTGGCGA 60.539 55.000 0.00 0.00 0.00 5.54
1010 1024 3.376078 CACCAGCATGCGCCCTTT 61.376 61.111 13.01 0.00 39.83 3.11
1017 1031 2.044946 ATGCGCCCTTTCCCTGTC 60.045 61.111 4.18 0.00 0.00 3.51
1026 1040 1.584380 CTTTCCCTGTCTGCAGCAGC 61.584 60.000 24.24 13.15 41.26 5.25
1047 1061 2.167861 GCGAAGGCCAGCTAACTCG 61.168 63.158 5.01 2.36 0.00 4.18
1050 1064 0.802607 GAAGGCCAGCTAACTCGTCG 60.803 60.000 5.01 0.00 0.00 5.12
1195 1209 2.423018 AGCTGCACGTGCTCTTGA 59.577 55.556 37.59 18.88 42.66 3.02
1201 1215 1.737735 CACGTGCTCTTGATCGCCA 60.738 57.895 0.82 0.00 0.00 5.69
1266 1281 1.623811 GTGCTCCAGGAACTCAACCTA 59.376 52.381 0.00 0.00 34.60 3.08
1399 1421 4.196193 AGACGAGGTGTTTGTTGAAATGA 58.804 39.130 0.00 0.00 0.00 2.57
1448 1473 1.064003 TAGACACTGTGTGGGCCAAT 58.936 50.000 19.62 0.00 37.94 3.16
1450 1475 1.423541 AGACACTGTGTGGGCCAATTA 59.576 47.619 19.62 0.00 37.94 1.40
1460 1485 5.660417 TGTGTGGGCCAATTATGTCATAATT 59.340 36.000 20.52 20.52 44.07 1.40
1476 1501 5.957796 GTCATAATTGAGTTTAAACGAGGCG 59.042 40.000 12.54 0.00 30.85 5.52
1480 1505 5.622770 ATTGAGTTTAAACGAGGCGAATT 57.377 34.783 12.54 0.00 0.00 2.17
1485 1510 0.321741 TAAACGAGGCGAATTGGGCA 60.322 50.000 16.18 0.00 34.40 5.36
1486 1511 0.965363 AAACGAGGCGAATTGGGCAT 60.965 50.000 16.18 0.69 34.40 4.40
1493 1518 2.236893 AGGCGAATTGGGCATTTTTCAT 59.763 40.909 16.18 0.00 34.40 2.57
1543 1569 6.924111 AGTGAAAAATGATAGTTTTCCGCAT 58.076 32.000 10.68 0.00 42.00 4.73
1558 1584 7.383843 AGTTTTCCGCATAAATTTGTAAAGTGG 59.616 33.333 0.00 0.00 0.00 4.00
1563 1589 6.745450 CCGCATAAATTTGTAAAGTGGTAGTG 59.255 38.462 0.00 0.00 0.00 2.74
1564 1590 6.250527 CGCATAAATTTGTAAAGTGGTAGTGC 59.749 38.462 0.00 0.00 0.00 4.40
1565 1591 7.087639 GCATAAATTTGTAAAGTGGTAGTGCA 58.912 34.615 0.00 0.00 0.00 4.57
1568 1595 6.709018 AATTTGTAAAGTGGTAGTGCAAGT 57.291 33.333 0.00 0.00 0.00 3.16
1599 1626 8.442384 GTTTCACCGAATAAGTAATTTTACCGA 58.558 33.333 0.00 0.00 34.19 4.69
1604 1631 6.037391 CCGAATAAGTAATTTTACCGAAGCCA 59.963 38.462 0.00 0.00 34.19 4.75
1607 1634 4.296621 AGTAATTTTACCGAAGCCAGGT 57.703 40.909 0.98 0.98 45.28 4.00
1628 1655 3.847671 TGTACCAGTGTTGAATCCACA 57.152 42.857 0.00 0.00 35.24 4.17
1635 1662 3.312421 CAGTGTTGAATCCACACTTCGTT 59.688 43.478 16.22 0.00 42.12 3.85
1653 1680 3.367932 TCGTTCATTTCGTCAAGATCTGC 59.632 43.478 0.00 0.00 0.00 4.26
1659 1686 0.317160 TCGTCAAGATCTGCGTGGTT 59.683 50.000 0.00 0.00 0.00 3.67
1677 1704 5.516339 CGTGGTTTTCGTCGGTATAAACTAT 59.484 40.000 0.00 0.00 32.53 2.12
1727 1754 4.643334 GGTAATACAAATGTGGGTCCCTTC 59.357 45.833 10.00 3.07 0.00 3.46
1756 1783 3.631250 ACAGCTTTTGTCAGGGAAAAGA 58.369 40.909 8.75 0.00 41.15 2.52
1760 1787 4.651045 AGCTTTTGTCAGGGAAAAGAACAT 59.349 37.500 8.75 0.00 41.15 2.71
1763 1790 6.983890 GCTTTTGTCAGGGAAAAGAACATTTA 59.016 34.615 8.75 0.00 41.15 1.40
1764 1791 7.042725 GCTTTTGTCAGGGAAAAGAACATTTAC 60.043 37.037 8.75 0.00 41.15 2.01
1765 1792 7.411486 TTTGTCAGGGAAAAGAACATTTACA 57.589 32.000 0.00 0.00 0.00 2.41
1766 1793 7.595819 TTGTCAGGGAAAAGAACATTTACAT 57.404 32.000 0.00 0.00 0.00 2.29
1767 1794 8.698973 TTGTCAGGGAAAAGAACATTTACATA 57.301 30.769 0.00 0.00 0.00 2.29
1768 1795 8.106247 TGTCAGGGAAAAGAACATTTACATAC 57.894 34.615 0.00 0.00 0.00 2.39
1769 1796 7.721842 TGTCAGGGAAAAGAACATTTACATACA 59.278 33.333 0.00 0.00 0.00 2.29
1770 1797 8.739972 GTCAGGGAAAAGAACATTTACATACAT 58.260 33.333 0.00 0.00 0.00 2.29
1771 1798 8.739039 TCAGGGAAAAGAACATTTACATACATG 58.261 33.333 0.00 0.00 0.00 3.21
1772 1799 7.489113 CAGGGAAAAGAACATTTACATACATGC 59.511 37.037 0.00 0.00 0.00 4.06
1802 1831 8.419450 ACATATATTATCCTCTCTCTCTCCCT 57.581 38.462 0.00 0.00 0.00 4.20
1812 1841 1.282447 TCTCTCTCCCTACGCAAGACT 59.718 52.381 0.00 0.00 43.62 3.24
1932 1962 4.399303 ACAAGACCTTTGAAACAAGACCAG 59.601 41.667 0.00 0.00 0.00 4.00
2121 2152 9.197694 CATTTGAACGTATTTGAAATAACCCAA 57.802 29.630 0.00 0.46 0.00 4.12
2138 2169 6.836577 AACCCAATTAACATTTTTCACACG 57.163 33.333 0.00 0.00 0.00 4.49
2139 2170 4.747605 ACCCAATTAACATTTTTCACACGC 59.252 37.500 0.00 0.00 0.00 5.34
2142 2173 5.107530 CCAATTAACATTTTTCACACGCCAG 60.108 40.000 0.00 0.00 0.00 4.85
2218 2256 7.488150 AGAAAGAAAATTTCACTCGTTCCAAAC 59.512 33.333 8.55 0.00 30.71 2.93
2421 2498 8.941977 AGAAAACACATTACGCTCAATTACATA 58.058 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.752683 AATCTACGTCTCTGTCGGCT 58.247 50.000 0.00 0.00 0.00 5.52
32 33 6.754209 AGTTTCTTGCATAATCTACGTCTCTG 59.246 38.462 0.00 0.00 0.00 3.35
33 34 6.868622 AGTTTCTTGCATAATCTACGTCTCT 58.131 36.000 0.00 0.00 0.00 3.10
37 38 5.288712 CACGAGTTTCTTGCATAATCTACGT 59.711 40.000 0.00 0.00 0.00 3.57
48 49 3.987868 TGATCTACACACGAGTTTCTTGC 59.012 43.478 0.00 0.00 0.00 4.01
59 60 5.864474 ACGAAGAAGATGTTGATCTACACAC 59.136 40.000 12.25 9.59 38.03 3.82
61 62 6.252441 CAGACGAAGAAGATGTTGATCTACAC 59.748 42.308 12.25 6.90 38.03 2.90
64 65 6.759497 TCAGACGAAGAAGATGTTGATCTA 57.241 37.500 0.00 0.00 38.03 1.98
71 72 4.810790 ACGAATTCAGACGAAGAAGATGT 58.189 39.130 6.22 0.00 33.74 3.06
78 79 5.576337 TCTTCAAACGAATTCAGACGAAG 57.424 39.130 6.22 11.26 33.74 3.79
79 80 5.977171 TTCTTCAAACGAATTCAGACGAA 57.023 34.783 6.22 4.56 35.05 3.85
96 97 7.701445 AGATTCGAATGTGATGGAATTTCTTC 58.299 34.615 16.96 0.00 29.79 2.87
106 107 3.060003 GCTCGGAAGATTCGAATGTGATG 60.060 47.826 16.96 5.06 40.84 3.07
107 108 3.126831 GCTCGGAAGATTCGAATGTGAT 58.873 45.455 16.96 0.00 40.84 3.06
110 111 1.134367 TCGCTCGGAAGATTCGAATGT 59.866 47.619 16.96 9.03 40.34 2.71
114 115 0.738975 ATGTCGCTCGGAAGATTCGA 59.261 50.000 0.00 0.00 40.77 3.71
115 116 0.848942 CATGTCGCTCGGAAGATTCG 59.151 55.000 0.00 0.00 40.84 3.34
175 179 4.754618 TGAATTGCATAACTGTCGTTGTCT 59.245 37.500 0.00 0.00 34.59 3.41
179 183 4.143115 CGTCTGAATTGCATAACTGTCGTT 60.143 41.667 0.00 0.00 37.15 3.85
180 184 3.367932 CGTCTGAATTGCATAACTGTCGT 59.632 43.478 0.00 0.00 0.00 4.34
181 185 3.242091 CCGTCTGAATTGCATAACTGTCG 60.242 47.826 0.00 0.00 0.00 4.35
186 190 5.030295 CACATTCCGTCTGAATTGCATAAC 58.970 41.667 0.00 0.00 41.85 1.89
191 195 2.474526 CGACACATTCCGTCTGAATTGC 60.475 50.000 0.00 0.00 41.85 3.56
196 200 1.338655 TCAACGACACATTCCGTCTGA 59.661 47.619 0.00 0.00 38.13 3.27
204 208 4.202000 TGCAGTTTTCATCAACGACACATT 60.202 37.500 0.00 0.00 0.00 2.71
207 211 3.035942 GTGCAGTTTTCATCAACGACAC 58.964 45.455 0.00 0.00 33.28 3.67
209 213 3.035942 GTGTGCAGTTTTCATCAACGAC 58.964 45.455 0.00 0.00 0.00 4.34
219 223 4.981806 ACATGTTGTAGTGTGCAGTTTT 57.018 36.364 0.00 0.00 0.00 2.43
225 229 5.059221 GCGAATAAAACATGTTGTAGTGTGC 59.941 40.000 13.25 12.44 0.00 4.57
261 265 4.357918 AGTTGATGGCCATAGGATGTAC 57.642 45.455 20.84 3.78 0.00 2.90
306 310 2.277084 GCGACGAGTAACCCATCAATT 58.723 47.619 0.00 0.00 0.00 2.32
334 338 0.249868 CACCGCTGGAGACACTTTCA 60.250 55.000 1.50 0.00 35.60 2.69
364 372 1.019673 AGCCTAATCAAGTGCATGCG 58.980 50.000 14.09 0.00 0.00 4.73
371 379 4.019174 CAAATCCACCAGCCTAATCAAGT 58.981 43.478 0.00 0.00 0.00 3.16
385 393 8.990163 TCTTTAATATAGGTTCCCAAATCCAC 57.010 34.615 0.00 0.00 0.00 4.02
402 410 7.446931 TGCAGTGTTGTCTTCCAATCTTTAATA 59.553 33.333 0.00 0.00 35.02 0.98
417 425 1.544686 CGTTGGTTTGCAGTGTTGTC 58.455 50.000 0.00 0.00 0.00 3.18
446 454 2.434702 GAGTAGTGGGGGAGTACCAATG 59.565 54.545 0.00 0.00 42.91 2.82
449 457 0.337428 GGAGTAGTGGGGGAGTACCA 59.663 60.000 0.00 0.00 42.91 3.25
459 467 1.046204 GGTATTCCCGGGAGTAGTGG 58.954 60.000 25.02 0.00 0.00 4.00
499 507 0.394938 TAGGCACTTCCGTTCAAGCA 59.605 50.000 0.00 0.00 41.75 3.91
504 512 6.431198 TTTTAATGATAGGCACTTCCGTTC 57.569 37.500 0.00 0.00 41.75 3.95
507 515 8.099364 ACATATTTTAATGATAGGCACTTCCG 57.901 34.615 0.00 0.00 41.75 4.30
545 553 9.830975 AGTTTTCAACATAAATTTGTAAAGCCT 57.169 25.926 0.00 0.00 0.00 4.58
559 567 9.349713 AGTGAGAAAATGGTAGTTTTCAACATA 57.650 29.630 12.83 0.00 45.85 2.29
560 568 8.237811 AGTGAGAAAATGGTAGTTTTCAACAT 57.762 30.769 12.83 0.00 45.85 2.71
561 569 7.639113 AGTGAGAAAATGGTAGTTTTCAACA 57.361 32.000 12.83 9.85 45.85 3.33
564 572 9.010029 GGATTAGTGAGAAAATGGTAGTTTTCA 57.990 33.333 12.83 0.00 45.85 2.69
573 581 8.792830 TTAGTCAAGGATTAGTGAGAAAATGG 57.207 34.615 0.00 0.00 0.00 3.16
622 631 7.342581 AGAAAAAGTTTAAAAGGGCCAAATCA 58.657 30.769 6.18 0.00 0.00 2.57
631 640 7.924412 GGACCCAACTAGAAAAAGTTTAAAAGG 59.076 37.037 0.00 0.00 37.61 3.11
641 650 4.513406 AGTGTGGACCCAACTAGAAAAA 57.487 40.909 0.00 0.00 0.00 1.94
642 651 4.513406 AAGTGTGGACCCAACTAGAAAA 57.487 40.909 0.00 0.00 0.00 2.29
643 652 5.617252 CTTAAGTGTGGACCCAACTAGAAA 58.383 41.667 0.00 0.00 0.00 2.52
646 655 3.335579 GCTTAAGTGTGGACCCAACTAG 58.664 50.000 4.02 0.00 0.00 2.57
647 656 2.289195 CGCTTAAGTGTGGACCCAACTA 60.289 50.000 7.91 0.00 0.00 2.24
655 669 0.978151 TTAGCCCGCTTAAGTGTGGA 59.022 50.000 21.01 4.92 39.82 4.02
675 689 4.586306 AACTAGGGACCCGATTGATTTT 57.414 40.909 4.40 0.00 0.00 1.82
679 693 3.178865 AGAAAACTAGGGACCCGATTGA 58.821 45.455 4.40 0.00 0.00 2.57
707 721 3.084786 GCTACAGGACTGGATTGCTTTT 58.915 45.455 4.14 0.00 34.19 2.27
798 812 4.711949 ACAGCTGCCTCCGCCAAG 62.712 66.667 15.27 0.00 0.00 3.61
838 852 2.359478 CCCACGGTAACCAGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
839 853 4.338710 GCCCACGGTAACCAGCCA 62.339 66.667 0.00 0.00 0.00 4.75
869 883 3.151710 CGTATGGGAGGTCGGCCA 61.152 66.667 9.71 0.00 37.19 5.36
904 918 1.532604 CGCCACCTTTTTCTTCCCCC 61.533 60.000 0.00 0.00 0.00 5.40
909 923 1.792118 GCCGTCGCCACCTTTTTCTT 61.792 55.000 0.00 0.00 0.00 2.52
997 1011 4.052518 AGGGAAAGGGCGCATGCT 62.053 61.111 17.13 0.00 42.25 3.79
998 1012 3.830192 CAGGGAAAGGGCGCATGC 61.830 66.667 10.83 7.91 41.71 4.06
1004 1018 1.676967 CTGCAGACAGGGAAAGGGC 60.677 63.158 8.42 0.00 40.48 5.19
1010 1024 4.025858 GGCTGCTGCAGACAGGGA 62.026 66.667 32.30 2.63 44.63 4.20
1017 1031 3.800863 CTTCGCTGGCTGCTGCAG 61.801 66.667 24.80 24.80 41.91 4.41
1026 1040 2.109126 GTTAGCTGGCCTTCGCTGG 61.109 63.158 20.26 0.00 37.05 4.85
1032 1046 1.215647 CGACGAGTTAGCTGGCCTT 59.784 57.895 3.32 0.00 0.00 4.35
1183 1197 1.690283 CTGGCGATCAAGAGCACGTG 61.690 60.000 12.28 12.28 34.54 4.49
1184 1198 1.446792 CTGGCGATCAAGAGCACGT 60.447 57.895 0.00 0.00 34.54 4.49
1193 1207 2.434185 GGTCGTTGCTGGCGATCA 60.434 61.111 0.00 0.00 39.10 2.92
1195 1209 2.125512 GAGGTCGTTGCTGGCGAT 60.126 61.111 0.00 0.00 40.59 4.58
1201 1215 4.070552 GCCGGAGAGGTCGTTGCT 62.071 66.667 5.05 0.00 43.70 3.91
1247 1262 2.024176 TAGGTTGAGTTCCTGGAGCA 57.976 50.000 13.26 2.83 36.60 4.26
1257 1272 1.403780 GCGTTGTCGGATAGGTTGAGT 60.404 52.381 0.00 0.00 37.56 3.41
1374 1396 3.254470 TCAACAAACACCTCGTCTTCA 57.746 42.857 0.00 0.00 0.00 3.02
1399 1421 6.712114 TGCTCCTCCTATATCTCTCTTAGT 57.288 41.667 0.00 0.00 0.00 2.24
1450 1475 7.472543 GCCTCGTTTAAACTCAATTATGACAT 58.527 34.615 16.01 0.00 0.00 3.06
1460 1485 3.187637 CCAATTCGCCTCGTTTAAACTCA 59.812 43.478 16.01 2.15 0.00 3.41
1470 1495 0.173255 AAAATGCCCAATTCGCCTCG 59.827 50.000 0.00 0.00 0.00 4.63
1474 1499 4.180057 TGTATGAAAAATGCCCAATTCGC 58.820 39.130 0.00 0.00 0.00 4.70
1476 1501 6.114767 ACCATGTATGAAAAATGCCCAATTC 58.885 36.000 0.00 0.00 0.00 2.17
1480 1505 5.268387 ACTACCATGTATGAAAAATGCCCA 58.732 37.500 0.00 0.00 0.00 5.36
1515 1540 9.010366 GCGGAAAACTATCATTTTTCACTAATC 57.990 33.333 9.18 0.00 42.41 1.75
1538 1564 6.745450 CACTACCACTTTACAAATTTATGCGG 59.255 38.462 0.00 0.00 0.00 5.69
1539 1565 6.250527 GCACTACCACTTTACAAATTTATGCG 59.749 38.462 0.00 0.00 0.00 4.73
1543 1569 8.228035 ACTTGCACTACCACTTTACAAATTTA 57.772 30.769 0.00 0.00 0.00 1.40
1558 1584 2.033151 GTGAAACCGTGACTTGCACTAC 60.033 50.000 0.00 0.00 45.49 2.73
1599 1626 0.843984 ACACTGGTACAACCTGGCTT 59.156 50.000 7.73 0.00 41.00 4.35
1604 1631 3.137544 TGGATTCAACACTGGTACAACCT 59.862 43.478 0.00 0.00 39.58 3.50
1607 1634 3.880490 GTGTGGATTCAACACTGGTACAA 59.120 43.478 15.76 0.00 38.70 2.41
1635 1662 2.667969 CACGCAGATCTTGACGAAATGA 59.332 45.455 14.58 0.00 32.89 2.57
1653 1680 3.674753 AGTTTATACCGACGAAAACCACG 59.325 43.478 0.00 0.00 33.33 4.94
1659 1686 9.096160 TGCAATTAATAGTTTATACCGACGAAA 57.904 29.630 0.00 0.00 0.00 3.46
1677 1704 2.603075 AGAGTTGGGGCTGCAATTAA 57.397 45.000 0.50 0.00 0.00 1.40
1727 1754 0.780002 GACAAAAGCTGTTGCATGCG 59.220 50.000 16.88 0.00 38.84 4.73
1756 1783 7.880160 ATGTACCAGCATGTATGTAAATGTT 57.120 32.000 0.00 0.00 0.00 2.71
1766 1793 9.715119 AGAGGATAATATATGTACCAGCATGTA 57.285 33.333 0.00 0.00 0.00 2.29
1767 1794 8.615360 AGAGGATAATATATGTACCAGCATGT 57.385 34.615 0.00 0.00 0.00 3.21
1768 1795 8.922237 AGAGAGGATAATATATGTACCAGCATG 58.078 37.037 0.00 0.00 0.00 4.06
1769 1796 9.142014 GAGAGAGGATAATATATGTACCAGCAT 57.858 37.037 0.00 0.00 0.00 3.79
1770 1797 8.340002 AGAGAGAGGATAATATATGTACCAGCA 58.660 37.037 0.00 0.00 0.00 4.41
1771 1798 8.760980 AGAGAGAGGATAATATATGTACCAGC 57.239 38.462 0.00 0.00 0.00 4.85
1835 1864 7.901029 TCAAAGCATATTTACCATCCAAAACA 58.099 30.769 0.00 0.00 0.00 2.83
1836 1865 8.770438 TTCAAAGCATATTTACCATCCAAAAC 57.230 30.769 0.00 0.00 0.00 2.43
2121 2152 5.446143 TCTGGCGTGTGAAAAATGTTAAT 57.554 34.783 0.00 0.00 0.00 1.40
2129 2160 3.577649 TGTTTTTCTGGCGTGTGAAAA 57.422 38.095 7.23 7.23 39.47 2.29
2134 2165 4.111916 CTGAAATTGTTTTTCTGGCGTGT 58.888 39.130 0.42 0.00 0.00 4.49
2136 2167 4.647424 TCTGAAATTGTTTTTCTGGCGT 57.353 36.364 5.50 0.00 0.00 5.68
2138 2169 8.397148 TCATTTTTCTGAAATTGTTTTTCTGGC 58.603 29.630 3.31 0.00 31.39 4.85
2185 2223 7.644157 ACGAGTGAAATTTTCTTTCTTAACTGC 59.356 33.333 10.33 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.