Multiple sequence alignment - TraesCS3A01G055700

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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 TraesCS3A01G055700 chr3A 100.000 2654 0 0 1 2654 32153995 32151342 0.000000e+00 4902
1 TraesCS3A01G055700 chr3A 83.333 450 40 15 1000 1441 731227167 731226745 1.490000e-102 383
2 TraesCS3A01G055700 chr3A 82.927 451 49 10 992 1441 32253046 32252623 5.360000e-102 381
3 TraesCS3A01G055700 chr3A 91.667 192 16 0 284 475 32192591 32192400 1.570000e-67 267
4 TraesCS3A01G055700 chr3B 90.991 2664 159 43 47 2654 40247771 40245133 0.000000e+00 3515
5 TraesCS3A01G055700 chr3B 84.889 450 43 11 993 1441 40866850 40866425 5.250000e-117 431
6 TraesCS3A01G055700 chr3B 88.144 194 20 3 285 476 702692940 702692748 7.390000e-56 228
7 TraesCS3A01G055700 chr3D 88.719 1764 117 39 179 1897 23065540 23063814 0.000000e+00 2080
8 TraesCS3A01G055700 chr3D 96.788 716 21 1 1941 2654 23063817 23063102 0.000000e+00 1194
9 TraesCS3A01G055700 chr3D 84.667 450 44 10 993 1441 23174593 23174168 2.440000e-115 425
10 TraesCS3A01G055700 chr3D 86.411 287 29 10 205 485 23088419 23088137 3.320000e-79 305
11 TraesCS3A01G055700 chr1D 88.170 1716 116 46 179 1848 225395865 225397539 0.000000e+00 1964
12 TraesCS3A01G055700 chr1D 90.816 196 16 2 282 476 356143344 356143538 7.290000e-66 261
13 TraesCS3A01G055700 chr2D 89.286 420 43 2 2196 2614 419040492 419040910 2.340000e-145 525
14 TraesCS3A01G055700 chr2A 89.048 420 44 2 2196 2614 570785191 570784773 1.090000e-143 520
15 TraesCS3A01G055700 chr2B 88.571 420 46 2 2196 2614 491181324 491181742 2.360000e-140 508
16 TraesCS3A01G055700 chr4A 84.264 394 60 2 2223 2615 580908038 580907646 1.490000e-102 383
17 TraesCS3A01G055700 chr4A 90.355 197 15 4 282 476 577540896 577541090 3.390000e-64 255
18 TraesCS3A01G055700 chr5D 91.795 195 16 0 282 476 546817804 546817998 3.370000e-69 272


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 TraesCS3A01G055700 chr3A 32151342 32153995 2653 True 4902 4902 100.0000 1 2654 1 chr3A.!!$R1 2653
1 TraesCS3A01G055700 chr3B 40245133 40247771 2638 True 3515 3515 90.9910 47 2654 1 chr3B.!!$R1 2607
2 TraesCS3A01G055700 chr3D 23063102 23065540 2438 True 1637 2080 92.7535 179 2654 2 chr3D.!!$R3 2475
3 TraesCS3A01G055700 chr1D 225395865 225397539 1674 False 1964 1964 88.1700 179 1848 1 chr1D.!!$F1 1669

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
39 40 0.035317 AAATGACTGGACAGAGCGCA 59.965 50.0 11.47 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1994 0.111061 AGCAACCACAATCCAGAGCA 59.889 50.0 0.0 0.0 0.0 4.26 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
27 28 8.422577 AAAATAAACCTAAGCAGGAAATGACT 57.577 30.769 0.00 0.00 45.91 3.41
28 29 7.396540 AATAAACCTAAGCAGGAAATGACTG 57.603 36.000 0.00 0.00 45.91 3.51
29 30 3.356529 ACCTAAGCAGGAAATGACTGG 57.643 47.619 0.00 0.00 45.91 4.00
30 31 2.912956 ACCTAAGCAGGAAATGACTGGA 59.087 45.455 0.00 0.00 45.91 3.86
31 32 3.274288 CCTAAGCAGGAAATGACTGGAC 58.726 50.000 0.00 0.00 45.91 4.02
32 33 2.957402 AAGCAGGAAATGACTGGACA 57.043 45.000 0.00 0.00 36.48 4.02
33 34 2.486472 AGCAGGAAATGACTGGACAG 57.514 50.000 0.00 0.00 36.48 3.51
34 35 1.980765 AGCAGGAAATGACTGGACAGA 59.019 47.619 6.29 0.00 36.48 3.41
35 36 2.027377 AGCAGGAAATGACTGGACAGAG 60.027 50.000 6.29 0.00 36.48 3.35
36 37 2.354259 CAGGAAATGACTGGACAGAGC 58.646 52.381 6.29 0.00 32.38 4.09
37 38 1.066573 AGGAAATGACTGGACAGAGCG 60.067 52.381 6.29 0.00 0.00 5.03
38 39 0.723981 GAAATGACTGGACAGAGCGC 59.276 55.000 0.00 0.00 0.00 5.92
39 40 0.035317 AAATGACTGGACAGAGCGCA 59.965 50.000 11.47 0.00 0.00 6.09
40 41 0.671781 AATGACTGGACAGAGCGCAC 60.672 55.000 11.47 2.25 0.00 5.34
41 42 2.433318 GACTGGACAGAGCGCACC 60.433 66.667 11.47 5.39 0.00 5.01
42 43 2.919856 ACTGGACAGAGCGCACCT 60.920 61.111 11.47 2.70 0.00 4.00
43 44 1.595993 GACTGGACAGAGCGCACCTA 61.596 60.000 11.47 0.00 0.00 3.08
44 45 1.153745 CTGGACAGAGCGCACCTAC 60.154 63.158 11.47 4.12 0.00 3.18
45 46 1.599606 CTGGACAGAGCGCACCTACT 61.600 60.000 11.47 0.00 0.00 2.57
63 64 9.402320 GCACCTACTATTCTATCTATCTGATGA 57.598 37.037 0.00 0.00 36.65 2.92
97 98 1.633774 GAGGTCCAGTCCAGAAGTGA 58.366 55.000 0.00 0.00 0.00 3.41
98 99 1.971357 GAGGTCCAGTCCAGAAGTGAA 59.029 52.381 0.00 0.00 0.00 3.18
99 100 1.974236 AGGTCCAGTCCAGAAGTGAAG 59.026 52.381 0.00 0.00 0.00 3.02
100 101 1.609320 GGTCCAGTCCAGAAGTGAAGC 60.609 57.143 0.00 0.00 0.00 3.86
101 102 0.687354 TCCAGTCCAGAAGTGAAGCC 59.313 55.000 0.00 0.00 0.00 4.35
102 103 0.689623 CCAGTCCAGAAGTGAAGCCT 59.310 55.000 0.00 0.00 0.00 4.58
104 105 2.149578 CAGTCCAGAAGTGAAGCCTTG 58.850 52.381 0.00 0.00 0.00 3.61
105 106 1.771255 AGTCCAGAAGTGAAGCCTTGT 59.229 47.619 0.00 0.00 0.00 3.16
119 122 6.003326 TGAAGCCTTGTACAATCAAGAATGA 58.997 36.000 9.13 0.00 45.11 2.57
149 152 3.867216 GCAGGGACCTACGTGTAACAAAT 60.867 47.826 0.00 0.00 35.74 2.32
184 187 2.667536 AGTGCACGCAGAAGGCAG 60.668 61.111 12.01 0.00 45.17 4.85
203 206 1.415659 AGAGAGATCATCGCCCAAAGG 59.584 52.381 0.00 0.00 0.00 3.11
209 212 0.918983 TCATCGCCCAAAGGAAGGAT 59.081 50.000 0.00 0.00 33.47 3.24
225 228 5.667626 AGGAAGGATCTATTTGTAAGCTCCA 59.332 40.000 0.00 0.00 32.71 3.86
236 239 7.883229 ATTTGTAAGCTCCAAAAATAAACGG 57.117 32.000 13.56 0.00 35.60 4.44
242 245 1.896465 TCCAAAAATAAACGGGGGCAG 59.104 47.619 0.00 0.00 0.00 4.85
243 246 1.674519 CCAAAAATAAACGGGGGCAGC 60.675 52.381 0.00 0.00 0.00 5.25
254 257 2.285024 GGGGCAGCAATGAAAGGCA 61.285 57.895 0.00 0.00 0.00 4.75
268 271 1.921869 AAGGCACCGGGGGACTTATG 61.922 60.000 17.92 0.00 0.00 1.90
280 283 4.514401 GGGGACTTATGTGTAAGGAACTG 58.486 47.826 0.88 0.00 41.33 3.16
390 393 9.098355 CTTCTCTGTATCGTTCCAATTTTATCA 57.902 33.333 0.00 0.00 0.00 2.15
400 403 5.464588 TCCAATTTTATCAGATGTCCCCA 57.535 39.130 0.00 0.00 0.00 4.96
446 450 0.375803 GGCTTATAAACCGGTGCGTG 59.624 55.000 8.52 0.00 0.00 5.34
476 480 0.693622 TGGCCGATGTGGGACTAAAA 59.306 50.000 0.00 0.00 35.49 1.52
477 481 1.092348 GGCCGATGTGGGACTAAAAC 58.908 55.000 0.00 0.00 38.63 2.43
478 482 0.725117 GCCGATGTGGGACTAAAACG 59.275 55.000 0.00 0.00 38.63 3.60
480 484 0.725117 CGATGTGGGACTAAAACGCC 59.275 55.000 0.00 0.00 0.00 5.68
481 485 1.816074 GATGTGGGACTAAAACGCCA 58.184 50.000 0.00 0.00 0.00 5.69
482 486 1.737793 GATGTGGGACTAAAACGCCAG 59.262 52.381 0.00 0.00 0.00 4.85
483 487 0.887387 TGTGGGACTAAAACGCCAGC 60.887 55.000 0.00 0.00 0.00 4.85
485 489 1.375013 GGGACTAAAACGCCAGCGA 60.375 57.895 20.32 0.00 42.83 4.93
488 492 0.714439 GACTAAAACGCCAGCGAGTC 59.286 55.000 20.32 16.27 42.83 3.36
498 502 3.069318 AGCGAGTCCGTTCCTCCC 61.069 66.667 0.00 0.00 38.24 4.30
502 506 2.203788 AGTCCGTTCCTCCCAGCA 60.204 61.111 0.00 0.00 0.00 4.41
503 507 1.827399 GAGTCCGTTCCTCCCAGCAA 61.827 60.000 0.00 0.00 0.00 3.91
504 508 1.201429 AGTCCGTTCCTCCCAGCAAT 61.201 55.000 0.00 0.00 0.00 3.56
507 511 2.464459 CGTTCCTCCCAGCAATCGC 61.464 63.158 0.00 0.00 38.99 4.58
532 537 3.844090 GACCAGCCTCGCTCCTCC 61.844 72.222 0.00 0.00 36.40 4.30
802 820 2.821366 TCGAGGTACGGACGAGCC 60.821 66.667 0.00 0.00 42.82 4.70
904 927 2.903855 TAGATCCGCCCCGTCGTC 60.904 66.667 0.00 0.00 0.00 4.20
945 968 4.851179 TCCCTCGCTCGCTCGCTA 62.851 66.667 0.00 0.00 0.00 4.26
946 969 4.615834 CCCTCGCTCGCTCGCTAC 62.616 72.222 0.00 0.00 0.00 3.58
998 1030 3.793957 ATCGATCCCTCCGCCTCGT 62.794 63.158 0.00 0.00 33.10 4.18
1006 1038 1.513158 CTCCGCCTCGTCATGAAGT 59.487 57.895 8.54 0.00 0.00 3.01
1071 1103 3.881104 GGTTCGGGTGGTGGTGGT 61.881 66.667 0.00 0.00 0.00 4.16
1496 1540 1.078143 CTCAGGAAAGGGGAAGGCG 60.078 63.158 0.00 0.00 0.00 5.52
1499 1543 4.360405 GGAAAGGGGAAGGCGGCA 62.360 66.667 13.08 0.00 0.00 5.69
1500 1544 2.751837 GAAAGGGGAAGGCGGCAG 60.752 66.667 13.08 0.00 0.00 4.85
1587 1631 4.194640 TCTTTCAGAGCATGCCTAATCAC 58.805 43.478 15.66 0.00 0.00 3.06
1622 1666 2.309755 AGAAAGATGAGGGTGATGGCAA 59.690 45.455 0.00 0.00 0.00 4.52
1698 1742 1.892474 AGTCTGGACAAGAGAGAGCAC 59.108 52.381 3.51 0.00 34.84 4.40
1702 1746 1.345741 TGGACAAGAGAGAGCACAAGG 59.654 52.381 0.00 0.00 0.00 3.61
1707 1751 3.898123 ACAAGAGAGAGCACAAGGAGTTA 59.102 43.478 0.00 0.00 0.00 2.24
1708 1752 4.530161 ACAAGAGAGAGCACAAGGAGTTAT 59.470 41.667 0.00 0.00 0.00 1.89
1710 1754 4.348486 AGAGAGAGCACAAGGAGTTATGA 58.652 43.478 0.00 0.00 0.00 2.15
1711 1755 4.159506 AGAGAGAGCACAAGGAGTTATGAC 59.840 45.833 0.00 0.00 0.00 3.06
1712 1756 3.834813 AGAGAGCACAAGGAGTTATGACA 59.165 43.478 0.00 0.00 0.00 3.58
1713 1757 4.081752 AGAGAGCACAAGGAGTTATGACAG 60.082 45.833 0.00 0.00 0.00 3.51
1714 1758 3.834813 AGAGCACAAGGAGTTATGACAGA 59.165 43.478 0.00 0.00 0.00 3.41
1715 1759 4.081752 AGAGCACAAGGAGTTATGACAGAG 60.082 45.833 0.00 0.00 0.00 3.35
1716 1760 3.834813 AGCACAAGGAGTTATGACAGAGA 59.165 43.478 0.00 0.00 0.00 3.10
1717 1761 3.929610 GCACAAGGAGTTATGACAGAGAC 59.070 47.826 0.00 0.00 0.00 3.36
1723 1788 3.764434 GGAGTTATGACAGAGACAGTGGA 59.236 47.826 0.00 0.00 0.00 4.02
1737 1802 2.807247 GTGGAACTGCAAGGTGGTT 58.193 52.632 0.00 0.00 39.30 3.67
1761 1826 9.236006 GTTGGATTATGCTGTTCTAATATGGAT 57.764 33.333 0.00 0.00 0.00 3.41
1771 1836 8.531982 GCTGTTCTAATATGGATAGGTGTATGA 58.468 37.037 0.00 0.00 0.00 2.15
1789 1854 9.847706 GGTGTATGAGTACTGATATGTCATAAG 57.152 37.037 0.00 0.00 33.13 1.73
1790 1855 9.847706 GTGTATGAGTACTGATATGTCATAAGG 57.152 37.037 0.00 0.00 33.13 2.69
1823 1891 3.996957 TGTGGATAGGTGTATGGGTACA 58.003 45.455 0.00 0.00 38.46 2.90
1827 1895 5.307196 GTGGATAGGTGTATGGGTACAGATT 59.693 44.000 0.00 0.00 41.29 2.40
1848 1919 5.761165 TTGGTTGGTAGTTTAGTTGAAGC 57.239 39.130 0.00 0.00 0.00 3.86
1893 1964 5.525012 CCATACCATATAGCACATGGAATCG 59.475 44.000 15.73 4.08 44.95 3.34
1920 1991 1.758862 GGAGAAATGGCCCCAAATCTG 59.241 52.381 0.00 0.00 0.00 2.90
1923 1994 1.901833 GAAATGGCCCCAAATCTGTGT 59.098 47.619 0.00 0.00 0.00 3.72
1934 2005 3.119602 CCAAATCTGTGTGCTCTGGATTG 60.120 47.826 0.00 0.00 0.00 2.67
1947 2018 2.821378 TCTGGATTGTGGTTGCTTGATG 59.179 45.455 0.00 0.00 0.00 3.07
1949 2020 2.557924 TGGATTGTGGTTGCTTGATGTC 59.442 45.455 0.00 0.00 0.00 3.06
1955 2026 2.349886 GTGGTTGCTTGATGTCGATCTC 59.650 50.000 0.00 0.00 0.00 2.75
2105 2178 5.521906 TTTAAGCTTGCATGTGGTTGTTA 57.478 34.783 9.86 0.00 0.00 2.41
2165 2238 8.206867 TGAAATTTCTCGATACTCCAGATTGAT 58.793 33.333 18.64 0.00 0.00 2.57
2277 2350 1.034838 AGCAGGCTGAGAGGTACGAG 61.035 60.000 20.86 0.00 0.00 4.18
2334 2407 0.539669 TTGACTCCGAGGAGCTCACA 60.540 55.000 17.19 10.87 45.54 3.58
2418 2491 1.035139 GGCGCATCATTTCCTCCATT 58.965 50.000 10.83 0.00 0.00 3.16
2502 2575 2.777832 AGATTGAGGTTGAGCTCACC 57.222 50.000 18.03 19.98 0.00 4.02
2556 2629 0.916358 CCCACCTTGTCCCCTCATCT 60.916 60.000 0.00 0.00 0.00 2.90
2618 2691 7.598759 AGGGTGATTACTACAGGTATTACAG 57.401 40.000 0.00 0.00 0.00 2.74
2633 2706 8.097038 CAGGTATTACAGTAATGTCCAGCATAT 58.903 37.037 21.29 6.49 36.67 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.870116 AGTCATTTCCTGCTTAGGTTTATTTTT 58.130 29.630 0.00 0.00 0.00 1.94
2 3 8.306761 CAGTCATTTCCTGCTTAGGTTTATTTT 58.693 33.333 0.00 0.00 0.00 1.82
3 4 7.093771 CCAGTCATTTCCTGCTTAGGTTTATTT 60.094 37.037 0.00 0.00 0.00 1.40
4 5 6.378280 CCAGTCATTTCCTGCTTAGGTTTATT 59.622 38.462 0.00 0.00 0.00 1.40
5 6 5.888161 CCAGTCATTTCCTGCTTAGGTTTAT 59.112 40.000 0.00 0.00 0.00 1.40
6 7 5.013704 TCCAGTCATTTCCTGCTTAGGTTTA 59.986 40.000 0.00 0.00 0.00 2.01
7 8 4.082125 CCAGTCATTTCCTGCTTAGGTTT 58.918 43.478 0.00 0.00 0.00 3.27
8 9 3.330701 TCCAGTCATTTCCTGCTTAGGTT 59.669 43.478 0.00 0.00 0.00 3.50
9 10 2.912956 TCCAGTCATTTCCTGCTTAGGT 59.087 45.455 0.00 0.00 0.00 3.08
10 11 3.274288 GTCCAGTCATTTCCTGCTTAGG 58.726 50.000 0.00 0.00 0.00 2.69
11 12 3.937706 CTGTCCAGTCATTTCCTGCTTAG 59.062 47.826 0.00 0.00 0.00 2.18
12 13 3.582647 TCTGTCCAGTCATTTCCTGCTTA 59.417 43.478 0.00 0.00 0.00 3.09
13 14 2.373169 TCTGTCCAGTCATTTCCTGCTT 59.627 45.455 0.00 0.00 0.00 3.91
14 15 1.980765 TCTGTCCAGTCATTTCCTGCT 59.019 47.619 0.00 0.00 0.00 4.24
15 16 2.354259 CTCTGTCCAGTCATTTCCTGC 58.646 52.381 0.00 0.00 0.00 4.85
16 17 2.354259 GCTCTGTCCAGTCATTTCCTG 58.646 52.381 0.00 0.00 0.00 3.86
17 18 1.066573 CGCTCTGTCCAGTCATTTCCT 60.067 52.381 0.00 0.00 0.00 3.36
18 19 1.363744 CGCTCTGTCCAGTCATTTCC 58.636 55.000 0.00 0.00 0.00 3.13
19 20 0.723981 GCGCTCTGTCCAGTCATTTC 59.276 55.000 0.00 0.00 0.00 2.17
20 21 0.035317 TGCGCTCTGTCCAGTCATTT 59.965 50.000 9.73 0.00 0.00 2.32
21 22 0.671781 GTGCGCTCTGTCCAGTCATT 60.672 55.000 9.73 0.00 0.00 2.57
22 23 1.079543 GTGCGCTCTGTCCAGTCAT 60.080 57.895 9.73 0.00 0.00 3.06
23 24 2.340078 GTGCGCTCTGTCCAGTCA 59.660 61.111 9.73 0.00 0.00 3.41
24 25 1.595993 TAGGTGCGCTCTGTCCAGTC 61.596 60.000 9.73 0.00 0.00 3.51
25 26 1.606601 TAGGTGCGCTCTGTCCAGT 60.607 57.895 9.73 0.00 0.00 4.00
26 27 1.153745 GTAGGTGCGCTCTGTCCAG 60.154 63.158 9.73 0.00 0.00 3.86
27 28 0.323087 TAGTAGGTGCGCTCTGTCCA 60.323 55.000 9.73 0.00 0.00 4.02
28 29 1.033574 ATAGTAGGTGCGCTCTGTCC 58.966 55.000 9.73 3.50 0.00 4.02
29 30 2.359531 AGAATAGTAGGTGCGCTCTGTC 59.640 50.000 9.73 4.84 0.00 3.51
30 31 2.379972 AGAATAGTAGGTGCGCTCTGT 58.620 47.619 9.73 0.00 0.00 3.41
31 32 4.457603 AGATAGAATAGTAGGTGCGCTCTG 59.542 45.833 9.73 0.00 0.00 3.35
32 33 4.658063 AGATAGAATAGTAGGTGCGCTCT 58.342 43.478 9.73 9.10 0.00 4.09
33 34 6.540914 AGATAGATAGAATAGTAGGTGCGCTC 59.459 42.308 9.73 4.47 0.00 5.03
34 35 6.317642 CAGATAGATAGAATAGTAGGTGCGCT 59.682 42.308 9.73 0.00 0.00 5.92
35 36 6.316640 TCAGATAGATAGAATAGTAGGTGCGC 59.683 42.308 0.00 0.00 0.00 6.09
36 37 7.851387 TCAGATAGATAGAATAGTAGGTGCG 57.149 40.000 0.00 0.00 0.00 5.34
37 38 9.402320 TCATCAGATAGATAGAATAGTAGGTGC 57.598 37.037 0.00 0.00 34.43 5.01
63 64 3.652869 TGGACCTCCACTTCTCTTTTCAT 59.347 43.478 0.00 0.00 42.01 2.57
69 70 1.551329 GGACTGGACCTCCACTTCTCT 60.551 57.143 0.00 0.00 42.01 3.10
97 98 5.769662 TGTCATTCTTGATTGTACAAGGCTT 59.230 36.000 14.65 0.00 44.84 4.35
98 99 5.316167 TGTCATTCTTGATTGTACAAGGCT 58.684 37.500 14.65 0.00 44.84 4.58
99 100 5.627499 TGTCATTCTTGATTGTACAAGGC 57.373 39.130 14.65 9.13 44.84 4.35
100 101 6.969366 TGTTGTCATTCTTGATTGTACAAGG 58.031 36.000 14.65 4.65 44.84 3.61
101 102 7.864686 TCTGTTGTCATTCTTGATTGTACAAG 58.135 34.615 14.65 0.00 45.73 3.16
102 103 7.520453 GCTCTGTTGTCATTCTTGATTGTACAA 60.520 37.037 11.41 11.41 33.56 2.41
104 105 6.073058 TGCTCTGTTGTCATTCTTGATTGTAC 60.073 38.462 0.00 0.00 33.56 2.90
105 106 5.997129 TGCTCTGTTGTCATTCTTGATTGTA 59.003 36.000 0.00 0.00 33.56 2.41
119 122 0.977395 GTAGGTCCCTGCTCTGTTGT 59.023 55.000 0.00 0.00 0.00 3.32
149 152 2.230508 CACTGTGGCCGACTAGTCTTAA 59.769 50.000 20.34 1.18 0.00 1.85
177 180 1.605202 GGCGATGATCTCTCTGCCTTC 60.605 57.143 16.47 0.00 39.38 3.46
184 187 1.414181 TCCTTTGGGCGATGATCTCTC 59.586 52.381 0.00 0.00 0.00 3.20
203 206 7.865706 TTTGGAGCTTACAAATAGATCCTTC 57.134 36.000 11.96 0.00 46.03 3.46
209 212 9.834628 CGTTTATTTTTGGAGCTTACAAATAGA 57.165 29.630 15.44 7.94 37.62 1.98
225 228 1.343069 TGCTGCCCCCGTTTATTTTT 58.657 45.000 0.00 0.00 0.00 1.94
236 239 2.285024 TGCCTTTCATTGCTGCCCC 61.285 57.895 0.00 0.00 0.00 5.80
242 245 2.573340 CCCGGTGCCTTTCATTGC 59.427 61.111 0.00 0.00 0.00 3.56
243 246 2.350458 CCCCCGGTGCCTTTCATTG 61.350 63.158 0.00 0.00 0.00 2.82
254 257 1.835531 CTTACACATAAGTCCCCCGGT 59.164 52.381 0.00 0.00 34.21 5.28
268 271 1.067071 CGGTCCCTCAGTTCCTTACAC 60.067 57.143 0.00 0.00 0.00 2.90
400 403 4.016706 CAGCGGACCCGTCCCTTT 62.017 66.667 10.37 0.00 46.96 3.11
476 480 4.719369 GAACGGACTCGCTGGCGT 62.719 66.667 14.55 0.00 40.63 5.68
478 482 3.991536 GAGGAACGGACTCGCTGGC 62.992 68.421 0.00 0.00 40.63 4.85
480 484 2.182030 GGAGGAACGGACTCGCTG 59.818 66.667 0.00 0.00 40.63 5.18
481 485 3.069318 GGGAGGAACGGACTCGCT 61.069 66.667 11.28 0.00 42.58 4.93
482 486 3.358076 CTGGGAGGAACGGACTCGC 62.358 68.421 11.54 11.54 45.11 5.03
483 487 2.885861 CTGGGAGGAACGGACTCG 59.114 66.667 0.00 0.00 43.02 4.18
485 489 1.201429 ATTGCTGGGAGGAACGGACT 61.201 55.000 0.00 0.00 0.00 3.85
488 492 1.815421 CGATTGCTGGGAGGAACGG 60.815 63.158 0.00 0.00 0.00 4.44
502 506 3.390521 TGGTCGGGAGCAGCGATT 61.391 61.111 0.00 0.00 34.41 3.34
515 519 3.844090 GGAGGAGCGAGGCTGGTC 61.844 72.222 0.00 0.00 39.88 4.02
616 621 1.723542 CGCTGATAATGATGGTCTCGC 59.276 52.381 0.00 0.00 0.00 5.03
802 820 3.711782 AAGGGGAGGGGAGGGGAG 61.712 72.222 0.00 0.00 0.00 4.30
814 837 3.023735 CTGGGGGAAGGGAAGGGG 61.024 72.222 0.00 0.00 0.00 4.79
872 895 1.668751 GATCTAGATCTAGAGCGGCGG 59.331 57.143 30.77 6.79 44.47 6.13
1053 1085 3.879885 CCACCACCACCCGAACCA 61.880 66.667 0.00 0.00 0.00 3.67
1188 1229 2.286121 ACATCACCCCCATCCGGT 60.286 61.111 0.00 0.00 0.00 5.28
1200 1241 1.695114 CCCCCAGATACGGCACATCA 61.695 60.000 0.00 0.00 0.00 3.07
1342 1383 2.284995 GAGGTCAGCCCACTCCCT 60.285 66.667 0.00 0.00 34.66 4.20
1344 1385 3.775654 CCGAGGTCAGCCCACTCC 61.776 72.222 0.00 0.00 34.66 3.85
1622 1666 0.981277 CCCACCTCCACCCTTATCGT 60.981 60.000 0.00 0.00 0.00 3.73
1698 1742 5.167121 CACTGTCTCTGTCATAACTCCTTG 58.833 45.833 0.00 0.00 0.00 3.61
1702 1746 5.047660 AGTTCCACTGTCTCTGTCATAACTC 60.048 44.000 0.00 0.00 0.00 3.01
1707 1751 3.674528 CAGTTCCACTGTCTCTGTCAT 57.325 47.619 0.00 0.00 41.19 3.06
1723 1788 2.086610 AATCCAACCACCTTGCAGTT 57.913 45.000 0.00 0.00 0.00 3.16
1771 1836 7.014711 CAGGTGACCTTATGACATATCAGTACT 59.985 40.741 0.00 0.00 38.57 2.73
1774 1839 5.070981 CCAGGTGACCTTATGACATATCAGT 59.929 44.000 0.00 0.00 38.57 3.41
1781 1846 4.042809 ACATTTCCAGGTGACCTTATGACA 59.957 41.667 0.00 0.00 0.00 3.58
1789 1854 2.514458 ATCCACATTTCCAGGTGACC 57.486 50.000 0.00 0.00 37.18 4.02
1790 1855 3.054361 ACCTATCCACATTTCCAGGTGAC 60.054 47.826 0.00 0.00 37.18 3.67
1823 1891 6.206829 GCTTCAACTAAACTACCAACCAATCT 59.793 38.462 0.00 0.00 0.00 2.40
1827 1895 3.810941 CGCTTCAACTAAACTACCAACCA 59.189 43.478 0.00 0.00 0.00 3.67
1848 1919 2.184322 CCCATCTGTCCCGTGACG 59.816 66.667 0.00 0.00 44.86 4.35
1876 1947 4.456911 CCAAAGCGATTCCATGTGCTATAT 59.543 41.667 0.00 0.00 36.49 0.86
1877 1948 3.814842 CCAAAGCGATTCCATGTGCTATA 59.185 43.478 0.00 0.00 36.49 1.31
1878 1949 2.620115 CCAAAGCGATTCCATGTGCTAT 59.380 45.455 0.00 0.00 36.49 2.97
1879 1950 2.016318 CCAAAGCGATTCCATGTGCTA 58.984 47.619 0.00 0.00 36.49 3.49
1880 1951 0.813184 CCAAAGCGATTCCATGTGCT 59.187 50.000 0.00 0.00 39.89 4.40
1893 1964 1.617018 GGGCCATTTCTCCCCAAAGC 61.617 60.000 4.39 0.00 38.70 3.51
1920 1991 1.267806 CAACCACAATCCAGAGCACAC 59.732 52.381 0.00 0.00 0.00 3.82
1923 1994 0.111061 AGCAACCACAATCCAGAGCA 59.889 50.000 0.00 0.00 0.00 4.26
1934 2005 2.349886 GAGATCGACATCAAGCAACCAC 59.650 50.000 0.00 0.00 0.00 4.16
1947 2018 9.762062 CAACATACTATATACTGTGAGATCGAC 57.238 37.037 0.00 0.00 0.00 4.20
1949 2020 8.454894 AGCAACATACTATATACTGTGAGATCG 58.545 37.037 0.00 0.00 0.00 3.69
2122 2195 8.239998 AGAAATTTCAGTTAGCTAAATGTCAGC 58.760 33.333 27.65 15.84 39.41 4.26
2165 2238 3.135712 TGGCTTCTAACAGTCACCAAAGA 59.864 43.478 0.00 0.00 0.00 2.52
2277 2350 3.198635 TCTCCATGAACTCAACCATCTCC 59.801 47.826 0.00 0.00 0.00 3.71
2334 2407 2.493907 GAAGGTTGCGCTCCTCGACT 62.494 60.000 21.00 8.92 41.67 4.18
2418 2491 0.901124 GGCTCTCTTCCTTCTGCTCA 59.099 55.000 0.00 0.00 0.00 4.26
2502 2575 5.541953 TGAGGATACCATCACAGATCTTG 57.458 43.478 0.00 0.00 37.17 3.02
2556 2629 1.203187 ACCTTGGACTCTGGAGCAGTA 60.203 52.381 0.00 0.00 32.61 2.74
2618 2691 5.409826 GCAGGAACTATATGCTGGACATTAC 59.590 44.000 0.00 0.00 38.99 1.89


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

AutoCloner maintained by Alex Coulton.