Multiple sequence alignment - TraesCS3A01G207700

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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 TraesCS3A01G207700 chr3A 100.000 4396 0 0 1 4396 365953965 365958360 0.000000e+00 8118.0
1 TraesCS3A01G207700 chr3A 80.942 467 80 7 2159 2619 581621336 581620873 1.160000e-95 361.0
2 TraesCS3A01G207700 chr2D 95.560 1689 53 6 2708 4375 361712270 361710583 0.000000e+00 2684.0
3 TraesCS3A01G207700 chr2D 93.833 1654 96 5 1055 2704 361713978 361712327 0.000000e+00 2484.0
4 TraesCS3A01G207700 chr5A 86.870 2300 256 23 389 2660 536255008 536257289 0.000000e+00 2532.0
5 TraesCS3A01G207700 chr5A 78.041 592 114 7 2031 2608 43690756 43691345 4.180000e-95 359.0
6 TraesCS3A01G207700 chr5A 79.917 483 79 15 1539 2017 431660914 431660446 5.450000e-89 339.0
7 TraesCS3A01G207700 chr5A 88.199 161 18 1 2708 2868 536258770 536258929 1.610000e-44 191.0
8 TraesCS3A01G207700 chr5A 93.023 129 9 0 2830 2958 536258931 536259059 5.800000e-44 189.0
9 TraesCS3A01G207700 chr5A 95.556 45 2 0 2659 2703 536258675 536258719 6.100000e-09 73.1
10 TraesCS3A01G207700 chr1B 86.564 2069 248 20 656 2709 529585465 529583412 0.000000e+00 2254.0
11 TraesCS3A01G207700 chr1B 89.496 1428 87 20 2971 4375 154145160 154143773 0.000000e+00 1748.0
12 TraesCS3A01G207700 chr1B 88.584 692 37 10 6 660 529588642 529587956 0.000000e+00 802.0
13 TraesCS3A01G207700 chr1B 90.079 252 23 2 2708 2958 529583367 529583117 4.240000e-85 326.0
14 TraesCS3A01G207700 chr5D 92.554 1437 74 18 2969 4378 551022186 551023616 0.000000e+00 2030.0
15 TraesCS3A01G207700 chr5D 91.922 1436 83 19 2969 4377 254535854 254537283 0.000000e+00 1978.0
16 TraesCS3A01G207700 chr5D 84.629 579 50 15 109 653 328909225 328909798 1.390000e-149 540.0
17 TraesCS3A01G207700 chr4D 91.905 1433 84 17 2969 4375 40828748 40827322 0.000000e+00 1975.0
18 TraesCS3A01G207700 chr4D 87.897 661 66 7 2052 2709 3241029 3240380 0.000000e+00 765.0
19 TraesCS3A01G207700 chr4D 94.783 230 12 0 2729 2958 3240315 3240086 4.180000e-95 359.0
20 TraesCS3A01G207700 chr4D 76.786 616 123 17 2015 2620 31461590 31462195 1.180000e-85 327.0
21 TraesCS3A01G207700 chr7A 91.550 1432 87 17 2969 4375 678174263 678175685 0.000000e+00 1943.0
22 TraesCS3A01G207700 chr7A 80.603 928 144 25 1718 2622 287209964 287210878 0.000000e+00 684.0
23 TraesCS3A01G207700 chr7A 74.110 618 121 14 2015 2624 539328554 539327968 7.400000e-53 219.0
24 TraesCS3A01G207700 chr7D 91.347 1433 80 19 2969 4376 509916424 509917837 0.000000e+00 1919.0
25 TraesCS3A01G207700 chr2A 91.035 1439 95 16 2969 4379 721732388 721730956 0.000000e+00 1912.0
26 TraesCS3A01G207700 chr2A 89.923 1429 85 17 2971 4376 195110033 195108641 0.000000e+00 1786.0
27 TraesCS3A01G207700 chr1A 90.356 1431 78 18 2971 4376 14531395 14532790 0.000000e+00 1823.0
28 TraesCS3A01G207700 chr1D 90.957 940 63 11 4 930 141595546 141594616 0.000000e+00 1245.0
29 TraesCS3A01G207700 chr1D 86.786 840 107 4 1396 2234 141594609 141593773 0.000000e+00 933.0
30 TraesCS3A01G207700 chr1D 87.064 487 49 8 2228 2709 141576555 141576078 5.000000e-149 538.0
31 TraesCS3A01G207700 chr1D 89.558 249 25 1 2708 2956 141576033 141575786 9.180000e-82 315.0
32 TraesCS3A01G207700 chr1D 81.315 289 50 4 1730 2017 477859228 477858943 9.510000e-57 231.0
33 TraesCS3A01G207700 chr2B 86.224 980 104 17 3043 3994 131078148 131077172 0.000000e+00 1033.0
34 TraesCS3A01G207700 chr2B 85.901 383 27 12 1 373 52112265 52111900 2.480000e-102 383.0
35 TraesCS3A01G207700 chr2B 85.417 384 32 6 1 374 58917552 58917921 1.150000e-100 377.0
36 TraesCS3A01G207700 chr5B 86.243 756 70 22 47 791 667515413 667514681 0.000000e+00 789.0
37 TraesCS3A01G207700 chr5B 84.775 578 50 14 109 653 382225768 382226340 2.990000e-151 545.0
38 TraesCS3A01G207700 chr3D 85.677 384 30 11 1 374 569275027 569274659 8.920000e-102 381.0
39 TraesCS3A01G207700 chr3D 75.000 856 161 33 1641 2463 96407953 96408788 3.250000e-91 346.0
40 TraesCS3A01G207700 chr3D 81.229 293 53 2 1720 2012 54398690 54398400 7.350000e-58 235.0
41 TraesCS3A01G207700 chr4A 84.211 380 36 11 1 370 728719942 728720307 9.050000e-92 348.0
42 TraesCS3A01G207700 chr4A 75.910 577 127 9 2017 2586 651571462 651572033 7.200000e-73 285.0
43 TraesCS3A01G207700 chr3B 91.633 251 19 2 2708 2958 817243996 817244244 3.250000e-91 346.0
44 TraesCS3A01G207700 chr3B 88.764 267 26 2 2441 2704 817243671 817243936 1.520000e-84 324.0
45 TraesCS3A01G207700 chr3B 79.521 376 71 6 1641 2014 147562074 147562445 3.370000e-66 263.0
46 TraesCS3A01G207700 chr3B 80.602 299 54 3 1718 2016 84781362 84781068 1.230000e-55 228.0
47 TraesCS3A01G207700 chr7B 83.333 384 39 14 1 374 687448719 687448351 9.110000e-87 331.0


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 TraesCS3A01G207700 chr3A 365953965 365958360 4395 False 8118.000000 8118 100.0000 1 4396 1 chr3A.!!$F1 4395
1 TraesCS3A01G207700 chr2D 361710583 361713978 3395 True 2584.000000 2684 94.6965 1055 4375 2 chr2D.!!$R1 3320
2 TraesCS3A01G207700 chr5A 536255008 536259059 4051 False 746.275000 2532 90.9120 389 2958 4 chr5A.!!$F2 2569
3 TraesCS3A01G207700 chr5A 43690756 43691345 589 False 359.000000 359 78.0410 2031 2608 1 chr5A.!!$F1 577
4 TraesCS3A01G207700 chr1B 154143773 154145160 1387 True 1748.000000 1748 89.4960 2971 4375 1 chr1B.!!$R1 1404
5 TraesCS3A01G207700 chr1B 529583117 529588642 5525 True 1127.333333 2254 88.4090 6 2958 3 chr1B.!!$R2 2952
6 TraesCS3A01G207700 chr5D 551022186 551023616 1430 False 2030.000000 2030 92.5540 2969 4378 1 chr5D.!!$F3 1409
7 TraesCS3A01G207700 chr5D 254535854 254537283 1429 False 1978.000000 1978 91.9220 2969 4377 1 chr5D.!!$F1 1408
8 TraesCS3A01G207700 chr5D 328909225 328909798 573 False 540.000000 540 84.6290 109 653 1 chr5D.!!$F2 544
9 TraesCS3A01G207700 chr4D 40827322 40828748 1426 True 1975.000000 1975 91.9050 2969 4375 1 chr4D.!!$R1 1406
10 TraesCS3A01G207700 chr4D 3240086 3241029 943 True 562.000000 765 91.3400 2052 2958 2 chr4D.!!$R2 906
11 TraesCS3A01G207700 chr4D 31461590 31462195 605 False 327.000000 327 76.7860 2015 2620 1 chr4D.!!$F1 605
12 TraesCS3A01G207700 chr7A 678174263 678175685 1422 False 1943.000000 1943 91.5500 2969 4375 1 chr7A.!!$F2 1406
13 TraesCS3A01G207700 chr7A 287209964 287210878 914 False 684.000000 684 80.6030 1718 2622 1 chr7A.!!$F1 904
14 TraesCS3A01G207700 chr7A 539327968 539328554 586 True 219.000000 219 74.1100 2015 2624 1 chr7A.!!$R1 609
15 TraesCS3A01G207700 chr7D 509916424 509917837 1413 False 1919.000000 1919 91.3470 2969 4376 1 chr7D.!!$F1 1407
16 TraesCS3A01G207700 chr2A 721730956 721732388 1432 True 1912.000000 1912 91.0350 2969 4379 1 chr2A.!!$R2 1410
17 TraesCS3A01G207700 chr2A 195108641 195110033 1392 True 1786.000000 1786 89.9230 2971 4376 1 chr2A.!!$R1 1405
18 TraesCS3A01G207700 chr1A 14531395 14532790 1395 False 1823.000000 1823 90.3560 2971 4376 1 chr1A.!!$F1 1405
19 TraesCS3A01G207700 chr1D 141593773 141595546 1773 True 1089.000000 1245 88.8715 4 2234 2 chr1D.!!$R3 2230
20 TraesCS3A01G207700 chr1D 141575786 141576555 769 True 426.500000 538 88.3110 2228 2956 2 chr1D.!!$R2 728
21 TraesCS3A01G207700 chr2B 131077172 131078148 976 True 1033.000000 1033 86.2240 3043 3994 1 chr2B.!!$R2 951
22 TraesCS3A01G207700 chr5B 667514681 667515413 732 True 789.000000 789 86.2430 47 791 1 chr5B.!!$R1 744
23 TraesCS3A01G207700 chr5B 382225768 382226340 572 False 545.000000 545 84.7750 109 653 1 chr5B.!!$F1 544
24 TraesCS3A01G207700 chr3D 96407953 96408788 835 False 346.000000 346 75.0000 1641 2463 1 chr3D.!!$F1 822
25 TraesCS3A01G207700 chr4A 651571462 651572033 571 False 285.000000 285 75.9100 2017 2586 1 chr4A.!!$F1 569
26 TraesCS3A01G207700 chr3B 817243671 817244244 573 False 335.000000 346 90.1985 2441 2958 2 chr3B.!!$F2 517

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
817 3378 0.042881 GTCCCTTACCTCTCACCCCT 59.957 60.0 0.0 0.0 0.0 4.79 F
2234 4864 0.482446 TGATGGCAAAGGGTGAGGTT 59.518 50.0 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 5151 0.401738 TCTTCCAAAGCTGACCTGGG 59.598 55.0 0.0 0.0 0.0 4.45 R
3798 7958 0.617413 CAGACCACATGCTTCTCCCT 59.383 55.0 0.0 0.0 0.0 4.20 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
25 26 7.266400 GGAGATTACTTTACTTCAGGGTACAG 58.734 42.308 0.00 0.00 0.00 2.74
165 188 2.096516 CAGAACTCTCGCTGTTTCTTGC 60.097 50.000 0.00 0.00 0.00 4.01
206 233 5.313712 AGTGTCCAAGGTAATCAAAATCGT 58.686 37.500 0.00 0.00 0.00 3.73
211 238 4.625311 CCAAGGTAATCAAAATCGTTTGGC 59.375 41.667 0.00 0.00 43.70 4.52
327 361 1.171308 CCTGAATGAGTGCCCACAAG 58.829 55.000 0.82 0.00 0.00 3.16
328 362 1.546323 CCTGAATGAGTGCCCACAAGT 60.546 52.381 0.82 0.00 0.00 3.16
329 363 2.290260 CCTGAATGAGTGCCCACAAGTA 60.290 50.000 0.82 0.00 0.00 2.24
386 426 3.904339 GTCTAAAGGCCATCCAGATCCTA 59.096 47.826 5.01 0.00 33.74 2.94
407 449 6.043474 TCCTACTCCTGTACCTTTGCTAAAAA 59.957 38.462 0.00 0.00 0.00 1.94
448 495 8.885722 TGAAGGTACATTACGTGAAAATTATCC 58.114 33.333 0.00 0.00 0.00 2.59
462 509 8.810427 GTGAAAATTATCCATGTTGTGCTATTG 58.190 33.333 0.00 0.00 0.00 1.90
530 588 9.337396 CTTACCTTGTATTGTATGAATGCCTAA 57.663 33.333 0.00 0.00 0.00 2.69
660 3221 7.010339 AGAACCAAGCTACTCTTTTAGTCAT 57.990 36.000 0.00 0.00 39.80 3.06
718 3279 5.705609 TCAAACACCTTGAGATTAAAGCC 57.294 39.130 0.00 0.00 39.20 4.35
817 3378 0.042881 GTCCCTTACCTCTCACCCCT 59.957 60.000 0.00 0.00 0.00 4.79
870 3432 4.033776 CTTTGCCGCCTCCCTCCA 62.034 66.667 0.00 0.00 0.00 3.86
887 3452 4.988716 ACTCCACCCTCGCCGTCA 62.989 66.667 0.00 0.00 0.00 4.35
926 3491 2.187073 CCAAGCAAAGCTAGGGCAG 58.813 57.895 6.90 0.00 38.25 4.85
970 3536 4.461119 TCCTCGCTGGAGATTGGT 57.539 55.556 0.00 0.00 43.27 3.67
1004 3570 2.351276 GCTTGTCGGGGACATGGT 59.649 61.111 11.91 0.00 42.40 3.55
1008 3574 2.436646 GTCGGGGACATGGTGCTG 60.437 66.667 0.00 0.00 32.09 4.41
1249 3816 4.609018 CCCTGGCTCGCCCGTATG 62.609 72.222 5.33 0.00 35.87 2.39
1469 4039 1.183030 TGGTGACGTGAAGGTCCGAT 61.183 55.000 0.00 0.00 36.07 4.18
1498 4068 0.974525 AGGTAGTAGGTTGGGTCGCC 60.975 60.000 0.00 0.00 0.00 5.54
1588 4159 1.203001 TGCCTTCTCCGGGTCAAAATT 60.203 47.619 0.00 0.00 0.00 1.82
1597 4169 2.258286 GTCAAAATTGGCGGCGCT 59.742 55.556 32.30 9.47 0.00 5.92
1610 4182 4.283403 GCGCTTGGGTTGCTTGCA 62.283 61.111 0.00 0.00 0.00 4.08
1611 4183 2.652530 CGCTTGGGTTGCTTGCAT 59.347 55.556 0.00 0.00 0.00 3.96
1726 4299 3.626924 GGTCCAGGTGGTGCTCGT 61.627 66.667 0.00 0.00 36.34 4.18
1728 4301 1.227853 GTCCAGGTGGTGCTCGTTT 60.228 57.895 0.00 0.00 36.34 3.60
1751 4324 1.818060 GGTGGTCATGTTAGCATTGCA 59.182 47.619 11.91 0.00 31.99 4.08
1791 4372 1.666209 GGTGACCCATGGAAATGGCG 61.666 60.000 15.22 0.00 40.35 5.69
1795 4376 2.105528 CCATGGAAATGGCGCTGC 59.894 61.111 5.56 0.00 34.56 5.25
1848 4429 4.760047 GCCGGTGGCTGTCGACAT 62.760 66.667 20.40 0.00 46.69 3.06
2056 4673 2.664851 CCACGCGGTTGCTCTTCA 60.665 61.111 12.47 0.00 39.65 3.02
2170 4799 0.893727 GTGGGGTGGCGTCTTGATTT 60.894 55.000 0.00 0.00 0.00 2.17
2234 4864 0.482446 TGATGGCAAAGGGTGAGGTT 59.518 50.000 0.00 0.00 0.00 3.50
2439 5072 4.935808 GGAGTTTAGGTGTATGAGGTTGTG 59.064 45.833 0.00 0.00 0.00 3.33
2512 5151 1.423845 CTGCGTGTGCCGTATTTCC 59.576 57.895 0.00 0.00 41.78 3.13
2667 6696 0.194587 CCTGGGTATGGGGAGGAGAT 59.805 60.000 0.00 0.00 0.00 2.75
2714 6818 3.322466 CACCGCCTCCTTCCTGGT 61.322 66.667 0.00 0.00 37.07 4.00
2743 6847 2.963101 GGCTCAAAGGGGTAAGTTTTGT 59.037 45.455 0.00 0.00 34.35 2.83
2959 7104 9.663904 AATGCAACGTTATATGTATTTTAGCTG 57.336 29.630 0.00 0.00 29.20 4.24
3038 7187 7.425577 CAATATTCCTGATATTGTGCGAGAA 57.574 36.000 9.51 0.00 46.59 2.87
3047 7197 7.430502 CCTGATATTGTGCGAGAATTCTTTTTC 59.569 37.037 9.87 2.51 0.00 2.29
3066 7216 8.091449 TCTTTTTCTTAGCCTTGAAAACAACAA 58.909 29.630 7.53 0.00 40.46 2.83
3320 7473 9.054922 CATATGTTCCTTTGTTTCCAAATGTTT 57.945 29.630 0.00 0.00 39.72 2.83
3410 7563 1.202806 TCCTGAAGCTCCAAGTTGGTG 60.203 52.381 21.35 19.50 39.03 4.17
3500 7653 2.645802 GTTTCCAGTGGTGTGGTGTTA 58.354 47.619 9.54 0.00 38.88 2.41
3503 7656 1.140052 TCCAGTGGTGTGGTGTTACAG 59.860 52.381 9.54 0.00 38.88 2.74
3521 7678 6.479990 TGTTACAGAAAAGACATGAGTGACTG 59.520 38.462 0.00 4.54 30.82 3.51
3641 7800 8.021898 TGTCTTCCAGATCATTGTGATGTATA 57.978 34.615 0.00 0.00 37.20 1.47
3700 7859 0.472471 TCTTGGGCCGAAACTGAACT 59.528 50.000 0.54 0.00 0.00 3.01
3800 7960 4.880537 CTGCAGCGCCTCGGTAGG 62.881 72.222 2.29 0.00 46.76 3.18
4177 8367 1.906105 ATACCCGATTGTGCCCGTGT 61.906 55.000 0.00 0.00 0.00 4.49
4247 8437 9.868277 ATAATTTCCAGCAAAATATTTTCGTGA 57.132 25.926 10.53 3.27 0.00 4.35
4289 8479 7.914871 CGACATTCCTATGCTATCTTATCTCTG 59.085 40.741 0.00 0.00 35.03 3.35
4294 8484 5.754406 CCTATGCTATCTTATCTCTGCATGC 59.246 44.000 11.82 11.82 40.65 4.06
4312 8502 5.345472 TGCATGCGAAATTAAACAGTCATTG 59.655 36.000 14.09 0.00 0.00 2.82
4378 8569 3.058363 GCACGGGCACTCTACTAGTATAC 60.058 52.174 3.77 0.00 40.72 1.47
4379 8570 4.132336 CACGGGCACTCTACTAGTATACA 58.868 47.826 2.33 0.00 35.76 2.29
4380 8571 4.760715 CACGGGCACTCTACTAGTATACAT 59.239 45.833 2.33 0.00 35.76 2.29
4381 8572 5.241064 CACGGGCACTCTACTAGTATACATT 59.759 44.000 2.33 0.00 35.76 2.71
4382 8573 5.241064 ACGGGCACTCTACTAGTATACATTG 59.759 44.000 2.33 0.00 35.76 2.82
4383 8574 5.335740 CGGGCACTCTACTAGTATACATTGG 60.336 48.000 2.33 0.00 35.76 3.16
4384 8575 5.539193 GGGCACTCTACTAGTATACATTGGT 59.461 44.000 2.33 0.00 35.76 3.67
4385 8576 6.718454 GGGCACTCTACTAGTATACATTGGTA 59.282 42.308 2.33 0.00 35.76 3.25
4386 8577 7.094291 GGGCACTCTACTAGTATACATTGGTAG 60.094 44.444 2.33 7.37 35.76 3.18
4387 8578 7.447853 GGCACTCTACTAGTATACATTGGTAGT 59.552 40.741 2.33 6.34 35.76 2.73
4388 8579 8.291032 GCACTCTACTAGTATACATTGGTAGTG 58.709 40.741 2.33 11.97 35.76 2.74
4389 8580 9.557061 CACTCTACTAGTATACATTGGTAGTGA 57.443 37.037 17.16 10.22 35.76 3.41
4390 8581 9.781633 ACTCTACTAGTATACATTGGTAGTGAG 57.218 37.037 17.16 16.79 36.36 3.51
4391 8582 9.221933 CTCTACTAGTATACATTGGTAGTGAGG 57.778 40.741 2.33 0.72 31.88 3.86
4392 8583 8.942033 TCTACTAGTATACATTGGTAGTGAGGA 58.058 37.037 2.33 2.69 31.88 3.71
4393 8584 9.221933 CTACTAGTATACATTGGTAGTGAGGAG 57.778 40.741 2.33 0.00 31.88 3.69
4394 8585 7.813331 ACTAGTATACATTGGTAGTGAGGAGA 58.187 38.462 5.50 0.00 31.88 3.71
4395 8586 6.963083 AGTATACATTGGTAGTGAGGAGAC 57.037 41.667 5.50 0.00 31.88 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.179076 TGTACCCTGAAGTAAAGTAATCTCC 57.821 40.000 0.00 0.00 0.00 3.71
1 2 7.123847 TCCTGTACCCTGAAGTAAAGTAATCTC 59.876 40.741 0.00 0.00 0.00 2.75
2 3 6.958192 TCCTGTACCCTGAAGTAAAGTAATCT 59.042 38.462 0.00 0.00 0.00 2.40
12 13 3.261897 CAGAACATCCTGTACCCTGAAGT 59.738 47.826 0.00 0.00 29.74 3.01
78 79 6.200878 AGGAAAGGAAGGAAGTCAATGTAA 57.799 37.500 0.00 0.00 0.00 2.41
79 80 5.843019 AGGAAAGGAAGGAAGTCAATGTA 57.157 39.130 0.00 0.00 0.00 2.29
206 233 4.329831 GGCAAGGGTATCGCCAAA 57.670 55.556 0.00 0.00 45.52 3.28
211 238 1.392589 AATTGCAGGCAAGGGTATCG 58.607 50.000 12.66 0.00 39.47 2.92
252 282 0.037697 AGCGCCGTTCAACTGTCATA 60.038 50.000 2.29 0.00 0.00 2.15
253 283 1.291877 GAGCGCCGTTCAACTGTCAT 61.292 55.000 2.29 0.00 0.00 3.06
254 284 1.954146 GAGCGCCGTTCAACTGTCA 60.954 57.895 2.29 0.00 0.00 3.58
265 295 1.191096 GCACATAAATTTGAGCGCCG 58.809 50.000 2.29 0.00 0.00 6.46
301 335 2.749621 GGGCACTCATTCAGGTAAACAG 59.250 50.000 0.00 0.00 0.00 3.16
327 361 5.011090 TCAGATTAGCATCACACCTGTAC 57.989 43.478 0.00 0.00 0.00 2.90
328 362 5.395657 CCTTCAGATTAGCATCACACCTGTA 60.396 44.000 0.00 0.00 0.00 2.74
329 363 4.511527 CTTCAGATTAGCATCACACCTGT 58.488 43.478 0.00 0.00 0.00 4.00
412 459 8.661257 CACGTAATGTACCTTCATCATAACAAA 58.339 33.333 0.00 0.00 0.00 2.83
426 473 8.617809 ACATGGATAATTTTCACGTAATGTACC 58.382 33.333 0.00 0.00 0.00 3.34
448 495 4.095483 GTCTTCCTCCAATAGCACAACATG 59.905 45.833 0.00 0.00 0.00 3.21
462 509 4.273724 GTGAGAAAACAAGTGTCTTCCTCC 59.726 45.833 0.00 0.00 0.00 4.30
660 3221 8.975663 AGATGATTCAATCTTCTTGCTGATTA 57.024 30.769 9.51 0.00 39.83 1.75
718 3279 6.072397 TGTGTTTGTTTCGGTATAAAGATGGG 60.072 38.462 0.00 0.00 0.00 4.00
788 3349 3.108376 GAGGTAAGGGACTGGATCAGTT 58.892 50.000 1.90 0.00 45.44 3.16
791 3352 2.314852 TGAGAGGTAAGGGACTGGATCA 59.685 50.000 0.00 0.00 40.86 2.92
817 3378 2.124612 TCGTCCACGGGAGCGATA 60.125 61.111 0.00 0.00 40.29 2.92
840 3402 0.888619 GGCAAAGCTAGGTTTCACCC 59.111 55.000 16.80 13.18 39.75 4.61
843 3405 1.241315 GGCGGCAAAGCTAGGTTTCA 61.241 55.000 16.80 0.00 37.29 2.69
870 3432 4.988716 TGACGGCGAGGGTGGAGT 62.989 66.667 16.62 0.00 0.00 3.85
987 3553 2.040544 CACCATGTCCCCGACAAGC 61.041 63.158 0.00 0.00 45.96 4.01
1046 3612 3.580319 GGAACCCCCACACAGCCT 61.580 66.667 0.00 0.00 34.14 4.58
1051 3617 3.182996 ACCCTGGAACCCCCACAC 61.183 66.667 0.00 0.00 40.82 3.82
1304 3871 4.790962 CATGGTCAGCCGCTGCCT 62.791 66.667 24.89 13.67 38.69 4.75
1412 3982 3.387374 ACAACCATTCAGCCACAAATTCA 59.613 39.130 0.00 0.00 0.00 2.57
1469 4039 1.846439 ACCTACTACCTACGGCTACCA 59.154 52.381 0.00 0.00 0.00 3.25
1483 4053 3.387947 CCGGCGACCCAACCTACT 61.388 66.667 9.30 0.00 0.00 2.57
1527 4097 2.184167 CCGCCACCGACAACAAACT 61.184 57.895 0.00 0.00 36.29 2.66
1597 4169 1.554160 CCCATAATGCAAGCAACCCAA 59.446 47.619 0.00 0.00 0.00 4.12
1607 4179 0.537143 GTCGCCATCCCCATAATGCA 60.537 55.000 0.00 0.00 0.00 3.96
1610 4182 0.034896 GTCGTCGCCATCCCCATAAT 59.965 55.000 0.00 0.00 0.00 1.28
1611 4183 1.331399 TGTCGTCGCCATCCCCATAA 61.331 55.000 0.00 0.00 0.00 1.90
1726 4299 2.937519 TGCTAACATGACCACCACAAA 58.062 42.857 0.00 0.00 0.00 2.83
1728 4301 2.819019 CAATGCTAACATGACCACCACA 59.181 45.455 0.00 0.00 36.36 4.17
1751 4324 2.824041 GCCAATCCGCACACCGAT 60.824 61.111 0.00 0.00 40.02 4.18
1779 4352 2.278336 CGCAGCGCCATTTCCATG 60.278 61.111 2.29 0.00 0.00 3.66
1848 4429 1.294138 GGGGACACGATTCCGACAA 59.706 57.895 0.00 0.00 36.38 3.18
2120 4738 1.154016 CACGTCTGAGCTACCCGTG 60.154 63.158 11.59 11.59 42.19 4.94
2170 4799 2.158769 CGATGTCAGATCCCCAAATCCA 60.159 50.000 0.00 0.00 0.00 3.41
2234 4864 2.106511 AGGCACAGAGCTTTTGTTAGGA 59.893 45.455 2.38 0.00 44.79 2.94
2439 5072 2.460757 TAACTAAACACCCTCACGCC 57.539 50.000 0.00 0.00 0.00 5.68
2506 5145 2.291540 CCAAAGCTGACCTGGGGAAATA 60.292 50.000 0.00 0.00 0.00 1.40
2512 5151 0.401738 TCTTCCAAAGCTGACCTGGG 59.598 55.000 0.00 0.00 0.00 4.45
2608 5248 2.445145 TCCCACATCCCTCTCAAAACAA 59.555 45.455 0.00 0.00 0.00 2.83
2667 6696 3.396276 TCTGTTTCTCCCCCATTTGTACA 59.604 43.478 0.00 0.00 0.00 2.90
2704 6734 1.538876 CCCCAGTGACCAGGAAGGA 60.539 63.158 0.00 0.00 41.22 3.36
2705 6735 2.606587 CCCCCAGTGACCAGGAAGG 61.607 68.421 0.00 0.00 45.67 3.46
2706 6736 3.081554 CCCCCAGTGACCAGGAAG 58.918 66.667 0.00 0.00 0.00 3.46
2714 6818 2.538141 CCCTTTGAGCCCCCAGTGA 61.538 63.158 0.00 0.00 0.00 3.41
2743 6847 1.776667 CTCCTAATTGCCCATCTCCCA 59.223 52.381 0.00 0.00 0.00 4.37
3038 7187 9.098355 GTTGTTTTCAAGGCTAAGAAAAAGAAT 57.902 29.630 21.81 0.00 43.09 2.40
3047 7197 6.038714 AGACTCTTGTTGTTTTCAAGGCTAAG 59.961 38.462 5.95 0.00 41.52 2.18
3105 7258 4.637276 TGGCCATGTAATTATCCTGTACG 58.363 43.478 0.00 0.00 0.00 3.67
3410 7563 6.015940 GGAACTCCATCAATATTCAATGGGAC 60.016 42.308 19.45 11.73 40.34 4.46
3478 7631 1.153046 ACCACACCACTGGAAACGG 60.153 57.895 0.71 0.00 44.60 4.44
3500 7653 3.812053 GCAGTCACTCATGTCTTTTCTGT 59.188 43.478 0.00 0.00 0.00 3.41
3503 7656 4.818534 TTGCAGTCACTCATGTCTTTTC 57.181 40.909 0.00 0.00 0.00 2.29
3521 7678 4.498009 CCACCGGAGACATTTTGATATTGC 60.498 45.833 9.46 0.00 0.00 3.56
3641 7800 3.537206 GAGAACTGCAGCCACCCGT 62.537 63.158 15.27 0.00 0.00 5.28
3700 7859 4.946160 ATGGATTACTTGTTGGGGAGAA 57.054 40.909 0.00 0.00 0.00 2.87
3776 7935 1.493950 CGAGGCGCTGCAGGAATTAG 61.494 60.000 17.12 0.00 0.00 1.73
3798 7958 0.617413 CAGACCACATGCTTCTCCCT 59.383 55.000 0.00 0.00 0.00 4.20
3800 7960 1.277557 AGACAGACCACATGCTTCTCC 59.722 52.381 0.00 0.00 0.00 3.71
3801 7961 2.740981 CAAGACAGACCACATGCTTCTC 59.259 50.000 0.00 0.00 0.00 2.87
4027 8213 6.303259 GTCTAGTTGTTGCGCTTAAGAAATTG 59.697 38.462 9.73 0.99 0.00 2.32
4139 8329 8.215050 TCGGGTATTTATTGTAGTCCAATTCAT 58.785 33.333 0.00 0.00 41.01 2.57
4247 8437 2.587753 CGGTGCCTTGTCACGTGT 60.588 61.111 16.51 0.00 37.83 4.49
4289 8479 5.345741 ACAATGACTGTTTAATTTCGCATGC 59.654 36.000 7.91 7.91 32.99 4.06
4326 8516 7.492994 GCCACGGGCTTTTGAAATATTTTATTA 59.507 33.333 1.43 0.00 46.69 0.98
4329 8519 5.172205 GCCACGGGCTTTTGAAATATTTTA 58.828 37.500 1.43 0.00 46.69 1.52


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

AutoCloner maintained by Alex Coulton.