Multiple sequence alignment - TraesCS2A01G196800

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 TraesCS2A01G196800 chr2A 100.000 5651 0 0 1 5651 166635558 166629908 0.000000e+00 10436.0
1 TraesCS2A01G196800 chr2A 92.424 1584 78 13 2466 4042 447943107 447944655 0.000000e+00 2222.0
2 TraesCS2A01G196800 chr2A 86.334 1822 186 31 2614 4393 197562010 197563810 0.000000e+00 1927.0
3 TraesCS2A01G196800 chr2A 87.129 1383 109 25 1039 2381 197560642 197561995 0.000000e+00 1504.0
4 TraesCS2A01G196800 chr2A 87.013 1232 116 19 3198 4393 197333272 197334495 0.000000e+00 1349.0
5 TraesCS2A01G196800 chr2A 89.603 731 69 4 1 724 29274143 29273413 0.000000e+00 922.0
6 TraesCS2A01G196800 chr2A 95.740 493 19 2 2466 2958 398765493 398765003 0.000000e+00 793.0
7 TraesCS2A01G196800 chr2A 95.538 493 20 2 2466 2958 398506563 398506073 0.000000e+00 787.0
8 TraesCS2A01G196800 chr2A 85.202 669 90 7 2477 3139 197332613 197333278 0.000000e+00 678.0
9 TraesCS2A01G196800 chr2A 88.350 412 42 3 5243 5651 197563957 197564365 1.830000e-134 490.0
10 TraesCS2A01G196800 chr2A 94.783 230 10 2 2213 2442 447942904 447943131 1.940000e-94 357.0
11 TraesCS2A01G196800 chr2A 93.939 231 12 1 2213 2443 398506766 398506538 1.170000e-91 348.0
12 TraesCS2A01G196800 chr2A 93.506 231 13 1 2213 2443 398765696 398765468 5.420000e-90 342.0
13 TraesCS2A01G196800 chr2A 79.302 430 55 17 3869 4270 166257755 166257332 2.590000e-68 270.0
14 TraesCS2A01G196800 chr2A 95.652 46 2 0 5185 5230 166256698 166256653 2.180000e-09 75.0
15 TraesCS2A01G196800 chr2B 94.283 5440 182 53 242 5651 214320089 214314749 0.000000e+00 8203.0
16 TraesCS2A01G196800 chr2B 93.305 478 22 2 1056 1530 281487341 281486871 0.000000e+00 697.0
17 TraesCS2A01G196800 chr2B 92.371 485 25 4 1051 1530 673104350 673104827 0.000000e+00 680.0
18 TraesCS2A01G196800 chr2B 92.469 478 26 4 1056 1530 310456434 310456904 0.000000e+00 675.0
19 TraesCS2A01G196800 chr2B 92.259 478 27 2 1056 1530 677947594 677947124 0.000000e+00 669.0
20 TraesCS2A01G196800 chr2B 90.341 352 34 0 5300 5651 214283305 214282954 3.990000e-126 462.0
21 TraesCS2A01G196800 chr2B 85.774 239 31 3 26 261 612095144 612094906 3.380000e-62 250.0
22 TraesCS2A01G196800 chr2D 95.229 4947 150 32 727 5651 156714162 156709280 0.000000e+00 7749.0
23 TraesCS2A01G196800 chr2D 90.399 1104 84 11 1270 2367 182570519 182571606 0.000000e+00 1432.0
24 TraesCS2A01G196800 chr2D 88.210 687 58 9 3729 4393 182572865 182573550 0.000000e+00 798.0
25 TraesCS2A01G196800 chr2D 82.621 702 84 15 2466 3139 182571689 182572380 2.270000e-163 586.0
26 TraesCS2A01G196800 chr2D 89.078 412 39 3 5243 5651 182573697 182574105 1.820000e-139 507.0
27 TraesCS2A01G196800 chr2D 86.207 464 37 11 5188 5651 156594705 156594269 1.420000e-130 477.0
28 TraesCS2A01G196800 chr2D 80.238 420 57 13 3869 4265 156595773 156595357 5.540000e-75 292.0
29 TraesCS2A01G196800 chr2D 74.379 523 98 22 3070 3572 48566041 48566547 2.080000e-44 191.0
30 TraesCS2A01G196800 chr4A 91.108 731 55 7 3 724 65714408 65715137 0.000000e+00 981.0
31 TraesCS2A01G196800 chr4A 91.960 398 22 4 1136 1530 670970357 670969967 2.980000e-152 549.0
32 TraesCS2A01G196800 chr5A 90.574 732 61 5 1 724 700671675 700670944 0.000000e+00 963.0
33 TraesCS2A01G196800 chr5A 87.296 551 63 4 181 724 510491055 510491605 1.730000e-174 623.0
34 TraesCS2A01G196800 chr3D 90.424 731 62 5 1 724 300679916 300680645 0.000000e+00 955.0
35 TraesCS2A01G196800 chr3D 89.134 543 48 7 193 724 23089594 23089052 0.000000e+00 665.0
36 TraesCS2A01G196800 chr6A 87.962 731 62 5 1 724 546925896 546926607 0.000000e+00 839.0
37 TraesCS2A01G196800 chr6A 75.407 492 87 23 3097 3572 32811586 32811113 2.060000e-49 207.0
38 TraesCS2A01G196800 chr6A 73.879 513 99 23 3071 3572 46698241 46697753 7.530000e-39 172.0
39 TraesCS2A01G196800 chr4B 93.096 478 23 2 1056 1530 639306252 639306722 0.000000e+00 691.0
40 TraesCS2A01G196800 chr4B 92.259 478 27 2 1056 1530 367623270 367623740 0.000000e+00 669.0
41 TraesCS2A01G196800 chr5B 92.469 478 26 2 1056 1530 18174942 18175412 0.000000e+00 675.0
42 TraesCS2A01G196800 chr1B 92.259 478 27 4 1056 1530 649829135 649828665 0.000000e+00 669.0
43 TraesCS2A01G196800 chr1B 90.503 358 32 2 5295 5651 148414117 148414473 6.630000e-129 472.0
44 TraesCS2A01G196800 chr1B 81.915 94 6 5 5185 5278 148414034 148414116 1.020000e-07 69.4
45 TraesCS2A01G196800 chr7B 92.519 401 20 4 1133 1530 271756811 271756418 2.960000e-157 566.0
46 TraesCS2A01G196800 chr4D 88.027 451 45 6 282 724 465182961 465183410 5.020000e-145 525.0
47 TraesCS2A01G196800 chr5D 89.277 401 41 1 327 727 519644724 519644326 8.450000e-138 501.0
48 TraesCS2A01G196800 chr1A 89.944 358 34 2 5295 5651 90161333 90161689 1.430000e-125 460.0
49 TraesCS2A01G196800 chr1A 95.111 225 9 1 2216 2440 512491084 512491306 2.500000e-93 353.0
50 TraesCS2A01G196800 chr1A 95.625 160 7 0 2466 2625 512491284 512491443 2.020000e-64 257.0
51 TraesCS2A01G196800 chr1D 89.385 358 36 2 5295 5651 93102998 93103354 3.110000e-122 449.0
52 TraesCS2A01G196800 chr6D 74.899 494 81 31 3097 3572 29926159 29926627 9.670000e-43 185.0
53 TraesCS2A01G196800 chrUn 74.125 514 97 25 3071 3572 27474181 27474670 4.500000e-41 180.0


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 TraesCS2A01G196800 chr2A 166629908 166635558 5650 True 10436.00 10436 100.0000 1 5651 1 chr2A.!!$R2 5650
1 TraesCS2A01G196800 chr2A 197560642 197564365 3723 False 1307.00 1927 87.2710 1039 5651 3 chr2A.!!$F2 4612
2 TraesCS2A01G196800 chr2A 447942904 447944655 1751 False 1289.50 2222 93.6035 2213 4042 2 chr2A.!!$F3 1829
3 TraesCS2A01G196800 chr2A 197332613 197334495 1882 False 1013.50 1349 86.1075 2477 4393 2 chr2A.!!$F1 1916
4 TraesCS2A01G196800 chr2A 29273413 29274143 730 True 922.00 922 89.6030 1 724 1 chr2A.!!$R1 723
5 TraesCS2A01G196800 chr2A 398506073 398506766 693 True 567.50 787 94.7385 2213 2958 2 chr2A.!!$R4 745
6 TraesCS2A01G196800 chr2A 398765003 398765696 693 True 567.50 793 94.6230 2213 2958 2 chr2A.!!$R5 745
7 TraesCS2A01G196800 chr2B 214314749 214320089 5340 True 8203.00 8203 94.2830 242 5651 1 chr2B.!!$R2 5409
8 TraesCS2A01G196800 chr2D 156709280 156714162 4882 True 7749.00 7749 95.2290 727 5651 1 chr2D.!!$R1 4924
9 TraesCS2A01G196800 chr2D 182570519 182574105 3586 False 830.75 1432 87.5770 1270 5651 4 chr2D.!!$F2 4381
10 TraesCS2A01G196800 chr2D 156594269 156595773 1504 True 384.50 477 83.2225 3869 5651 2 chr2D.!!$R2 1782
11 TraesCS2A01G196800 chr4A 65714408 65715137 729 False 981.00 981 91.1080 3 724 1 chr4A.!!$F1 721
12 TraesCS2A01G196800 chr5A 700670944 700671675 731 True 963.00 963 90.5740 1 724 1 chr5A.!!$R1 723
13 TraesCS2A01G196800 chr5A 510491055 510491605 550 False 623.00 623 87.2960 181 724 1 chr5A.!!$F1 543
14 TraesCS2A01G196800 chr3D 300679916 300680645 729 False 955.00 955 90.4240 1 724 1 chr3D.!!$F1 723
15 TraesCS2A01G196800 chr3D 23089052 23089594 542 True 665.00 665 89.1340 193 724 1 chr3D.!!$R1 531
16 TraesCS2A01G196800 chr6A 546925896 546926607 711 False 839.00 839 87.9620 1 724 1 chr6A.!!$F1 723

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
617 632 0.032952 TTTGCTCGTGTAGAAGGCGT 59.967 50.000 0.00 0.00 0.00 5.68 F
1513 1567 0.107945 AGCCTGAATCTCGTGCTTCC 60.108 55.000 0.00 0.00 0.00 3.46 F
2450 2545 1.153997 GACCTCACGTCGGAAGCTC 60.154 63.158 7.38 0.00 0.00 4.09 F
2470 2565 1.370587 GGAGAGACCTCACGTCGGAG 61.371 65.000 7.38 1.78 46.92 4.63 F
2981 3109 1.686115 GGTGCAGGCAATTCCCTATGT 60.686 52.381 0.00 0.00 32.78 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2522 0.036448 TTCCGACGTGAGGTCTCTCT 59.964 55.000 0.00 0.0 43.79 3.10 R
2473 2568 0.250597 TTCACGTGAGGTCTCTCCGA 60.251 55.000 19.11 0.0 41.99 4.55 R
4025 4192 1.358759 CACAACACTTGGCCGGAAC 59.641 57.895 5.05 0.0 34.12 3.62 R
4321 4507 1.736126 CACATCTGCCACACTGTCATC 59.264 52.381 0.00 0.0 0.00 2.92 R
4721 4962 1.135689 CCGCTTCAGTGTATGCCAAAC 60.136 52.381 0.00 0.0 0.00 2.93 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
82 84 3.196901 TGGATGCCTCTAAGCGTTTCTTA 59.803 43.478 0.00 0.00 36.25 2.10
111 113 6.016192 AGCTATCTTGATTCAATCATTGGCAG 60.016 38.462 0.00 0.00 39.39 4.85
135 137 2.989571 AGGTGGACCTTTCCTCTGAAAT 59.010 45.455 0.00 0.00 46.09 2.17
150 153 9.822727 TTCCTCTGAAATAAGTAAGGGAAAATT 57.177 29.630 0.00 0.00 0.00 1.82
182 185 6.363882 TCATGTGATAATATTGTTGCCCAGA 58.636 36.000 0.00 0.00 0.00 3.86
236 239 1.680249 GGAGTGCTCCCAAATCTGGAC 60.680 57.143 6.98 0.00 46.92 4.02
253 256 2.377628 GACGGGTCAAGCTGTCCACA 62.378 60.000 9.52 0.00 0.00 4.17
280 287 1.067060 TCTTATGGTGATGACGGCTCG 59.933 52.381 0.00 0.00 0.00 5.03
303 310 3.559171 GCAGGTTCTGGAATGGTACTTCA 60.559 47.826 0.00 0.00 31.21 3.02
333 347 5.528320 TGCGATCATATTTTCTTCATGCAGA 59.472 36.000 0.00 0.00 0.00 4.26
350 364 5.518848 TGCAGACAATTGTTTTCATGTCT 57.481 34.783 13.36 0.00 45.41 3.41
475 489 1.704628 TCAAGTTGATCCAGGCCAAGA 59.295 47.619 5.01 0.00 0.00 3.02
480 494 0.620556 TGATCCAGGCCAAGAAGGTC 59.379 55.000 5.01 0.00 44.66 3.85
556 571 9.952188 CTCTTCGTGATTCTTGTATTACTCATA 57.048 33.333 0.00 0.00 0.00 2.15
616 631 0.438830 GTTTGCTCGTGTAGAAGGCG 59.561 55.000 0.00 0.00 0.00 5.52
617 632 0.032952 TTTGCTCGTGTAGAAGGCGT 59.967 50.000 0.00 0.00 0.00 5.68
649 664 0.248289 GATTGGTTCGGGTCCTTCGA 59.752 55.000 0.00 0.00 34.62 3.71
653 668 0.248289 GGTTCGGGTCCTTCGAATGA 59.752 55.000 0.00 0.00 46.17 2.57
687 702 9.464714 CTAGCTACGATTAATTGTATGAACTGT 57.535 33.333 14.65 0.59 0.00 3.55
844 865 1.363744 GCGAACTTCCTCTGACATGG 58.636 55.000 0.00 0.00 0.00 3.66
877 898 4.024641 CGTCCACCTTTATAAATAACCGCC 60.025 45.833 0.00 0.00 0.00 6.13
900 921 6.143206 CCCATCCTTTCCCCAAATAACTAAT 58.857 40.000 0.00 0.00 0.00 1.73
1042 1063 3.190878 GGGACGATGGCAAGCAAG 58.809 61.111 0.00 0.00 0.00 4.01
1154 1175 2.910479 TGTCTCGTCGCCACCACT 60.910 61.111 0.00 0.00 0.00 4.00
1230 1281 2.032860 AATCCATCTCCTCGCCACCG 62.033 60.000 0.00 0.00 0.00 4.94
1281 1332 0.811616 CCGGGAGCCAAATCTTCGAG 60.812 60.000 0.00 0.00 0.00 4.04
1374 1425 0.663153 GCGACCTGCTGTGTTTTCTT 59.337 50.000 0.00 0.00 41.73 2.52
1375 1426 1.597937 GCGACCTGCTGTGTTTTCTTG 60.598 52.381 0.00 0.00 41.73 3.02
1376 1427 1.002468 CGACCTGCTGTGTTTTCTTGG 60.002 52.381 0.00 0.00 0.00 3.61
1377 1428 2.024414 GACCTGCTGTGTTTTCTTGGT 58.976 47.619 0.00 0.00 0.00 3.67
1378 1429 2.427095 GACCTGCTGTGTTTTCTTGGTT 59.573 45.455 0.00 0.00 0.00 3.67
1379 1430 2.831526 ACCTGCTGTGTTTTCTTGGTTT 59.168 40.909 0.00 0.00 0.00 3.27
1380 1431 3.119137 ACCTGCTGTGTTTTCTTGGTTTC 60.119 43.478 0.00 0.00 0.00 2.78
1469 1523 6.483640 GGCCAAGACGTTATTGAGAAAGATAT 59.516 38.462 14.10 0.00 0.00 1.63
1513 1567 0.107945 AGCCTGAATCTCGTGCTTCC 60.108 55.000 0.00 0.00 0.00 3.46
1531 1585 4.813697 GCTTCCTGATTACTCTGTGATTCC 59.186 45.833 0.00 0.00 0.00 3.01
1734 1789 2.094854 GTGCTCTTCTTGCAATCTTGGG 60.095 50.000 0.00 0.00 42.41 4.12
1744 1799 4.362470 TGCAATCTTGGGATATGGAGAG 57.638 45.455 0.00 0.00 0.00 3.20
1748 1803 4.906747 ATCTTGGGATATGGAGAGAAGC 57.093 45.455 0.00 0.00 0.00 3.86
1749 1804 3.933886 TCTTGGGATATGGAGAGAAGCT 58.066 45.455 0.00 0.00 0.00 3.74
1898 1955 5.119694 TGGGAACATGTTTTTGTTTTAGGC 58.880 37.500 13.36 0.00 39.85 3.93
1911 1968 4.013728 TGTTTTAGGCCGTGCATATCTTT 58.986 39.130 0.00 0.00 0.00 2.52
2149 2206 8.673711 CCGAAATTTGGTCTAAAAGATGTGATA 58.326 33.333 0.00 0.00 0.00 2.15
2246 2303 2.634982 TTCGGATTTTGCAGCATCAC 57.365 45.000 0.00 0.00 0.00 3.06
2401 2496 3.507622 CCCATCTCTTGTGGAAAAGGTTC 59.492 47.826 0.00 0.00 39.12 3.62
2427 2522 2.461695 AGAGAAGGAATCGGAAGCTCA 58.538 47.619 0.00 0.00 0.00 4.26
2450 2545 1.153997 GACCTCACGTCGGAAGCTC 60.154 63.158 7.38 0.00 0.00 4.09
2451 2546 2.202492 CCTCACGTCGGAAGCTCG 60.202 66.667 0.00 0.00 0.00 5.03
2452 2547 2.202492 CTCACGTCGGAAGCTCGG 60.202 66.667 0.00 0.00 33.89 4.63
2453 2548 2.670592 TCACGTCGGAAGCTCGGA 60.671 61.111 0.00 0.00 33.89 4.55
2454 2549 2.202492 CACGTCGGAAGCTCGGAG 60.202 66.667 0.00 0.00 33.89 4.63
2455 2550 2.359602 ACGTCGGAAGCTCGGAGA 60.360 61.111 9.69 0.00 33.89 3.71
2466 2561 4.298009 TCGGAGAGACCTCACGTC 57.702 61.111 11.72 0.00 41.20 4.34
2467 2562 1.740664 TCGGAGAGACCTCACGTCG 60.741 63.158 11.72 0.00 46.92 5.12
2468 2563 2.751913 CGGAGAGACCTCACGTCGG 61.752 68.421 0.00 0.00 46.92 4.79
2469 2564 1.376942 GGAGAGACCTCACGTCGGA 60.377 63.158 7.38 0.00 46.92 4.55
2470 2565 1.370587 GGAGAGACCTCACGTCGGAG 61.371 65.000 7.38 1.78 46.92 4.63
2529 2625 9.416284 TGACTCCTTTTAGTCTTTGGTTATTTT 57.584 29.630 5.68 0.00 45.12 1.82
2559 2655 2.057137 ACCCATGAAATGTCGGGATG 57.943 50.000 2.98 0.00 44.81 3.51
2981 3109 1.686115 GGTGCAGGCAATTCCCTATGT 60.686 52.381 0.00 0.00 32.78 2.29
3055 3186 7.229907 ACAGAATATATGCTGTGAATGCAATCA 59.770 33.333 23.35 0.00 43.26 2.57
3186 3317 8.150945 CCTTAGTATACTACAGGATGCATGTTT 58.849 37.037 23.36 0.00 42.53 2.83
3566 3709 9.371136 CTCAAGTCTGAAGCTTATTGTTATGTA 57.629 33.333 0.00 0.00 0.00 2.29
3902 4061 5.019470 TGTATGGAATGGTTACCAAATGCA 58.981 37.500 8.63 12.45 39.69 3.96
3989 4149 2.214376 AAAACGCAGATTGATCCCCA 57.786 45.000 0.00 0.00 0.00 4.96
4025 4192 5.047802 AGGTGATATGTTTGGTTTTCTGCAG 60.048 40.000 7.63 7.63 0.00 4.41
4073 4240 4.040339 TGCTTCCATCTCACTGACTTAACA 59.960 41.667 0.00 0.00 0.00 2.41
4192 4377 5.488919 TCAGTCATCAACCTATCTTTCCCTT 59.511 40.000 0.00 0.00 0.00 3.95
4265 4451 6.398234 TTTCCTCAGATTAGTAGCAGCTAG 57.602 41.667 1.02 0.00 0.00 3.42
4321 4507 5.476091 GGATATACCTGGACTTGGAGAAG 57.524 47.826 0.00 0.00 35.41 2.85
4581 4768 4.360563 CTGATGATGTGTACGTTAGTCCC 58.639 47.826 0.00 0.00 0.00 4.46
4629 4816 3.262420 GCTGTTCACGATCAACCACTAT 58.738 45.455 0.00 0.00 0.00 2.12
4636 4823 3.804325 CACGATCAACCACTATGACATCC 59.196 47.826 0.00 0.00 0.00 3.51
4671 4903 4.489306 AGTCTCCCATTGCTAGGTTAAC 57.511 45.455 0.00 0.00 0.00 2.01
4721 4962 3.756434 GCTGAGCTCTAGGTGGTAGATAG 59.244 52.174 16.19 0.00 37.14 2.08
4745 4986 1.369091 GCATACACTGAAGCGGGTGG 61.369 60.000 0.00 0.00 37.72 4.61
4758 4999 1.663695 CGGGTGGGCTTATACTTGTG 58.336 55.000 0.00 0.00 0.00 3.33
4808 5085 8.794335 AGGATAGAAAAACAAGGTCTGATTAC 57.206 34.615 0.00 0.00 0.00 1.89
4980 5257 6.091986 GGTGCTATTTCTCTCTATATTGCAGC 59.908 42.308 0.00 0.00 38.95 5.25
5048 5326 4.880120 AGGAGAATGTGCTTGTATGACATG 59.120 41.667 0.00 0.00 30.69 3.21
5078 5356 2.337583 TGAACGTGCTGATTCAGTAGC 58.662 47.619 14.90 2.68 40.29 3.58
5212 5521 0.725784 CGGAAGAACGTTGCATGCAC 60.726 55.000 22.58 14.60 0.00 4.57
5267 5576 5.748592 AGAACGAAATCAAACAACAGTAGC 58.251 37.500 0.00 0.00 0.00 3.58
5278 5587 7.806690 TCAAACAACAGTAGCATTATCAGTTC 58.193 34.615 0.00 0.00 0.00 3.01
5302 5628 1.283321 ACAAGGGGAGCCTTCAGAATC 59.717 52.381 0.00 0.00 0.00 2.52
5543 5871 1.442017 GTCAACAATGCGGTTCGGC 60.442 57.895 0.00 0.00 0.00 5.54
5609 5937 0.317160 CCTGAGGTAGTGTCGCACAA 59.683 55.000 11.58 0.00 36.74 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 7.228906 CCAATGATTGAATCAAGATAGCTCACT 59.771 37.037 12.36 0.00 43.50 3.41
170 173 0.604578 GCATGTGTCTGGGCAACAAT 59.395 50.000 0.00 0.00 39.74 2.71
174 177 0.251634 TATCGCATGTGTCTGGGCAA 59.748 50.000 6.09 0.00 0.00 4.52
182 185 8.250332 ACCATTTTCTTTTATTATCGCATGTGT 58.750 29.630 6.09 0.00 0.00 3.72
236 239 1.669115 CTGTGGACAGCTTGACCCG 60.669 63.158 0.00 0.00 37.15 5.28
253 256 3.070159 CGTCATCACCATAAGACCCATCT 59.930 47.826 0.00 0.00 36.42 2.90
280 287 1.282157 AGTACCATTCCAGAACCTGCC 59.718 52.381 0.00 0.00 0.00 4.85
303 310 7.558161 TGAAGAAAATATGATCGCACATCTT 57.442 32.000 0.00 0.00 0.00 2.40
333 347 7.232127 AGAGAATCCAGACATGAAAACAATTGT 59.768 33.333 4.92 4.92 33.66 2.71
393 407 6.693545 GGTCACTTCTCTGTATTACGAATGAG 59.306 42.308 0.00 0.00 0.00 2.90
475 489 4.515944 CGAGTAGACCAATCTATCGACCTT 59.484 45.833 0.00 0.00 39.66 3.50
480 494 3.188873 GGGACGAGTAGACCAATCTATCG 59.811 52.174 0.00 11.31 39.66 2.92
488 502 4.831155 CCATAATAAGGGACGAGTAGACCA 59.169 45.833 0.00 0.00 36.37 4.02
577 592 6.128172 GCAAACTTGGCTATGATATCGCTAAT 60.128 38.462 0.00 0.00 0.00 1.73
582 597 4.143242 CGAGCAAACTTGGCTATGATATCG 60.143 45.833 0.00 0.00 42.78 2.92
597 612 0.438830 CGCCTTCTACACGAGCAAAC 59.561 55.000 0.00 0.00 0.00 2.93
616 631 5.220854 CCGAACCAATCCAAGTCATGATTAC 60.221 44.000 0.00 0.00 0.00 1.89
617 632 4.881273 CCGAACCAATCCAAGTCATGATTA 59.119 41.667 0.00 0.00 0.00 1.75
649 664 3.409570 TCGTAGCTAGCTCCGTATCATT 58.590 45.455 26.18 0.36 0.00 2.57
653 668 6.072064 ACAATTAATCGTAGCTAGCTCCGTAT 60.072 38.462 26.18 18.74 0.00 3.06
777 796 7.003402 TGTCTGGATTTTCCCCTTAAAAATG 57.997 36.000 0.00 0.00 36.66 2.32
784 805 4.750941 TCAATTGTCTGGATTTTCCCCTT 58.249 39.130 5.13 0.00 35.03 3.95
877 898 6.838612 TGATTAGTTATTTGGGGAAAGGATGG 59.161 38.462 0.00 0.00 0.00 3.51
1040 1061 2.032071 CACGGGCCGGTTCTTCTT 59.968 61.111 31.78 2.61 0.00 2.52
1041 1062 3.239253 ACACGGGCCGGTTCTTCT 61.239 61.111 31.78 3.51 0.00 2.85
1042 1063 3.047877 CACACGGGCCGGTTCTTC 61.048 66.667 31.78 0.00 0.00 2.87
1154 1175 3.068691 CGGGCGGAGGAGAGTGAA 61.069 66.667 0.00 0.00 0.00 3.18
1281 1332 3.984749 GAGCTCGATCTCCCGGCC 61.985 72.222 4.91 0.00 0.00 6.13
1456 1510 5.303971 CCGGAGCTGAATATCTTTCTCAAT 58.696 41.667 0.00 0.00 0.00 2.57
1469 1523 0.179032 TTGTTCTTGCCGGAGCTGAA 60.179 50.000 5.05 0.00 40.80 3.02
1513 1567 5.426504 AGCAAGGAATCACAGAGTAATCAG 58.573 41.667 0.00 0.00 0.00 2.90
1531 1585 4.500603 AGAATGCACAAAGAAGAGCAAG 57.499 40.909 0.00 0.00 38.54 4.01
1734 1789 6.041523 AGAGGTTGTTAGCTTCTCTCCATATC 59.958 42.308 0.00 0.00 29.81 1.63
1744 1799 4.258702 TCACAGAGAGGTTGTTAGCTTC 57.741 45.455 0.00 0.00 30.79 3.86
1748 1803 6.925211 TGACTAATCACAGAGAGGTTGTTAG 58.075 40.000 0.00 0.00 0.00 2.34
1749 1804 6.911250 TGACTAATCACAGAGAGGTTGTTA 57.089 37.500 0.00 0.00 0.00 2.41
1796 1851 2.125512 GTACAGGCAGAGCACCCG 60.126 66.667 0.00 0.00 0.00 5.28
1898 1955 4.060900 AGCACTGATAAAGATATGCACGG 58.939 43.478 0.00 0.00 35.51 4.94
2149 2206 5.395879 GGTTTCAAGTACCAACCAACCAAAT 60.396 40.000 8.35 0.00 39.93 2.32
2246 2303 6.865726 AGAATCTAATAGCAGTATCGCACAAG 59.134 38.462 0.00 0.00 0.00 3.16
2283 2344 9.327731 AGAATACGAAATAGGGGAATAAGAGAT 57.672 33.333 0.00 0.00 0.00 2.75
2284 2345 8.722622 AGAATACGAAATAGGGGAATAAGAGA 57.277 34.615 0.00 0.00 0.00 3.10
2401 2496 4.568760 GCTTCCGATTCCTTCTCTACAAAG 59.431 45.833 0.00 0.00 0.00 2.77
2427 2522 0.036448 TTCCGACGTGAGGTCTCTCT 59.964 55.000 0.00 0.00 43.79 3.10
2450 2545 2.751913 CCGACGTGAGGTCTCTCCG 61.752 68.421 0.00 4.71 43.79 4.63
2451 2546 1.370587 CTCCGACGTGAGGTCTCTCC 61.371 65.000 0.00 0.00 43.79 3.71
2452 2547 1.370587 CCTCCGACGTGAGGTCTCTC 61.371 65.000 18.79 0.00 45.76 3.20
2453 2548 1.377463 CCTCCGACGTGAGGTCTCT 60.377 63.158 18.79 0.00 45.76 3.10
2454 2549 3.188965 CCTCCGACGTGAGGTCTC 58.811 66.667 18.79 0.00 45.76 3.36
2459 2554 4.180946 CCGAGCCTCCGACGTGAG 62.181 72.222 0.00 0.00 0.00 3.51
2460 2555 4.710167 TCCGAGCCTCCGACGTGA 62.710 66.667 0.00 0.00 0.00 4.35
2461 2556 4.180946 CTCCGAGCCTCCGACGTG 62.181 72.222 0.00 0.00 0.00 4.49
2462 2557 4.405671 TCTCCGAGCCTCCGACGT 62.406 66.667 0.00 0.00 0.00 4.34
2463 2558 3.578272 CTCTCCGAGCCTCCGACG 61.578 72.222 0.00 0.00 0.00 5.12
2464 2559 2.124653 TCTCTCCGAGCCTCCGAC 60.125 66.667 0.00 0.00 0.00 4.79
2465 2560 2.124653 GTCTCTCCGAGCCTCCGA 60.125 66.667 0.00 0.00 0.00 4.55
2466 2561 3.213402 GGTCTCTCCGAGCCTCCG 61.213 72.222 0.00 0.00 34.06 4.63
2467 2562 1.826487 GAGGTCTCTCCGAGCCTCC 60.826 68.421 16.63 3.00 42.01 4.30
2468 2563 1.077357 TGAGGTCTCTCCGAGCCTC 60.077 63.158 18.86 18.86 44.88 4.70
2469 2564 1.379309 GTGAGGTCTCTCCGAGCCT 60.379 63.158 6.57 6.57 41.03 4.58
2470 2565 2.766400 CGTGAGGTCTCTCCGAGCC 61.766 68.421 0.00 0.00 41.03 4.70
2471 2566 2.041686 ACGTGAGGTCTCTCCGAGC 61.042 63.158 14.13 0.00 41.99 5.03
2472 2567 0.673956 TCACGTGAGGTCTCTCCGAG 60.674 60.000 15.76 8.67 41.99 4.63
2473 2568 0.250597 TTCACGTGAGGTCTCTCCGA 60.251 55.000 19.11 0.00 41.99 4.55
2559 2655 3.652057 TCCATCTGACCTGGGATTTTC 57.348 47.619 0.00 0.00 34.36 2.29
2981 3109 6.154192 TCCAACATAATGATTTAAGGCTTGCA 59.846 34.615 10.69 3.28 0.00 4.08
3055 3186 0.696501 AAATAGCGGTCACCAAGGGT 59.303 50.000 0.00 0.00 35.62 4.34
3056 3187 2.169769 TCTAAATAGCGGTCACCAAGGG 59.830 50.000 0.00 0.00 0.00 3.95
3186 3317 7.766278 GCATAAACAAAGAGAGTTAGATCAGGA 59.234 37.037 0.00 0.00 0.00 3.86
3566 3709 5.757988 TGTTAAGTTGGGTCCTAAGTTGTT 58.242 37.500 16.28 0.00 0.00 2.83
3659 3803 5.779529 AGCATTTCAGTGTTCAATGAAGT 57.220 34.783 13.70 9.66 36.81 3.01
3989 4149 7.500227 CCAAACATATCACCTGTCAGTTGATAT 59.500 37.037 21.24 21.24 33.86 1.63
4025 4192 1.358759 CACAACACTTGGCCGGAAC 59.641 57.895 5.05 0.00 34.12 3.62
4192 4377 3.364460 AACATGAATCGGGATGAACCA 57.636 42.857 0.00 0.00 41.20 3.67
4321 4507 1.736126 CACATCTGCCACACTGTCATC 59.264 52.381 0.00 0.00 0.00 2.92
4354 4540 4.034048 GCACGACATTGATGTAAAGGTAGG 59.966 45.833 0.00 0.00 41.95 3.18
4394 4581 3.199946 TGAGGGTCATGTATCCAAGAACC 59.800 47.826 0.00 0.00 44.75 3.62
4395 4582 4.487714 TGAGGGTCATGTATCCAAGAAC 57.512 45.455 0.00 0.00 0.00 3.01
4490 4677 1.751927 GCCAAGGCCCACATCTGAG 60.752 63.158 0.00 0.00 34.56 3.35
4597 4784 1.743252 TGAACAGCACGTGCACACA 60.743 52.632 39.21 28.14 45.16 3.72
4618 4805 5.305644 GGTAGAGGATGTCATAGTGGTTGAT 59.694 44.000 0.00 0.00 0.00 2.57
4629 4816 7.306013 AGACTTATATTGGGTAGAGGATGTCA 58.694 38.462 0.00 0.00 0.00 3.58
4636 4823 7.390027 CAATGGGAGACTTATATTGGGTAGAG 58.610 42.308 0.00 0.00 0.00 2.43
4721 4962 1.135689 CCGCTTCAGTGTATGCCAAAC 60.136 52.381 0.00 0.00 0.00 2.93
4745 4986 6.442513 AGAAAGAATGCACAAGTATAAGCC 57.557 37.500 0.00 0.00 0.00 4.35
4758 4999 9.713740 CTTATATGTCAACAGAAGAAAGAATGC 57.286 33.333 0.00 0.00 0.00 3.56
4797 5073 6.722129 ACTAGTCACAGAAAGTAATCAGACCT 59.278 38.462 0.00 0.00 0.00 3.85
4808 5085 5.119898 GCACATCAGAACTAGTCACAGAAAG 59.880 44.000 0.00 0.00 0.00 2.62
4902 5179 4.438145 CGAGCAACTTCGACTATCATACAC 59.562 45.833 0.00 0.00 43.03 2.90
4980 5257 3.727518 TGTTGATAATTTTCACGTCGCG 58.272 40.909 0.00 0.00 0.00 5.87
5048 5326 1.457303 CAGCACGTTCAGACTTACTGC 59.543 52.381 0.00 0.00 45.38 4.40
5078 5356 7.933728 TTTCATGTCAAATGTTGATGTTCTG 57.066 32.000 0.00 0.00 42.47 3.02
5212 5521 3.412237 TCCCCTCTTCTAAAACGTTGG 57.588 47.619 0.00 0.00 0.00 3.77
5267 5576 5.500234 TCCCCTTGTTCTGAACTGATAATG 58.500 41.667 20.18 4.79 0.00 1.90
5302 5628 2.008329 GAGAAGATGCTGTGCTTCAGG 58.992 52.381 0.00 0.00 43.78 3.86
5531 5859 3.127533 GCAGAGCCGAACCGCATT 61.128 61.111 0.00 0.00 0.00 3.56
5543 5871 2.360350 AATGGCACCACCGCAGAG 60.360 61.111 0.00 0.00 43.94 3.35
5551 5879 1.303561 GCAGTGGAGAATGGCACCA 60.304 57.895 0.00 0.00 34.66 4.17


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

AutoCloner maintained by Alex Coulton.