Multiple sequence alignment - TraesCS1A01G374000

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 TraesCS1A01G374000 chr1A 100.000 2417 0 0 1 2417 549600583 549598167 0.000000e+00 4464
1 TraesCS1A01G374000 chr1A 93.250 2148 132 6 185 2323 254401276 254403419 0.000000e+00 3151
2 TraesCS1A01G374000 chr3D 94.504 2147 103 8 185 2323 543499392 543501531 0.000000e+00 3297
3 TraesCS1A01G374000 chr3D 94.035 2146 115 8 185 2323 542834731 542836870 0.000000e+00 3241
4 TraesCS1A01G374000 chr3D 93.398 2151 120 12 185 2323 461559723 461561863 0.000000e+00 3166
5 TraesCS1A01G374000 chr3D 91.979 187 15 0 1 187 542834420 542834606 1.840000e-66 263
6 TraesCS1A01G374000 chr4D 94.027 2143 114 6 185 2323 130442898 130440766 0.000000e+00 3236
7 TraesCS1A01G374000 chr4D 93.727 2152 118 12 185 2322 303073190 303075338 0.000000e+00 3210
8 TraesCS1A01G374000 chr4D 91.979 187 15 0 1 187 502779720 502779906 1.840000e-66 263
9 TraesCS1A01G374000 chr2D 93.910 2151 115 8 185 2323 634063024 634060878 0.000000e+00 3232
10 TraesCS1A01G374000 chr5A 93.942 2146 116 8 185 2322 524396550 524398689 0.000000e+00 3230
11 TraesCS1A01G374000 chr7D 93.671 2149 118 9 185 2323 116648241 116650381 0.000000e+00 3199
12 TraesCS1A01G374000 chr7D 91.979 187 15 0 1 187 116647929 116648115 1.840000e-66 263
13 TraesCS1A01G374000 chr6A 93.048 187 13 0 1 187 587656458 587656272 8.510000e-70 274
14 TraesCS1A01G374000 chr1D 93.048 187 13 0 1 187 362592700 362592514 8.510000e-70 274
15 TraesCS1A01G374000 chr1B 91.667 192 15 1 1 191 536921195 536921004 5.120000e-67 265
16 TraesCS1A01G374000 chr1B 98.913 92 1 0 2326 2417 626507535 626507444 5.350000e-37 165
17 TraesCS1A01G374000 chr6D 91.979 187 15 0 1 187 36262052 36262238 1.840000e-66 263
18 TraesCS1A01G374000 chr5D 91.979 187 15 0 1 187 238121900 238122086 1.840000e-66 263
19 TraesCS1A01G374000 chr4B 91.979 187 15 0 1 187 446327202 446327388 1.840000e-66 263


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 TraesCS1A01G374000 chr1A 549598167 549600583 2416 True 4464 4464 100.000 1 2417 1 chr1A.!!$R1 2416
1 TraesCS1A01G374000 chr1A 254401276 254403419 2143 False 3151 3151 93.250 185 2323 1 chr1A.!!$F1 2138
2 TraesCS1A01G374000 chr3D 543499392 543501531 2139 False 3297 3297 94.504 185 2323 1 chr3D.!!$F2 2138
3 TraesCS1A01G374000 chr3D 461559723 461561863 2140 False 3166 3166 93.398 185 2323 1 chr3D.!!$F1 2138
4 TraesCS1A01G374000 chr3D 542834420 542836870 2450 False 1752 3241 93.007 1 2323 2 chr3D.!!$F3 2322
5 TraesCS1A01G374000 chr4D 130440766 130442898 2132 True 3236 3236 94.027 185 2323 1 chr4D.!!$R1 2138
6 TraesCS1A01G374000 chr4D 303073190 303075338 2148 False 3210 3210 93.727 185 2322 1 chr4D.!!$F1 2137
7 TraesCS1A01G374000 chr2D 634060878 634063024 2146 True 3232 3232 93.910 185 2323 1 chr2D.!!$R1 2138
8 TraesCS1A01G374000 chr5A 524396550 524398689 2139 False 3230 3230 93.942 185 2322 1 chr5A.!!$F1 2137
9 TraesCS1A01G374000 chr7D 116647929 116650381 2452 False 1731 3199 92.825 1 2323 2 chr7D.!!$F1 2322

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
634 779 0.450184 GTGCACTTGAACACCGTTGT 59.55 50.0 10.32 0.0 37.67 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2367 0.108186 TTGCCTGCATCTAGTGTCCG 60.108 55.0 0.0 0.0 0.0 4.79 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
38 39 4.040217 CAGCTAGGGTTTGATCTAGATGCT 59.960 45.833 10.74 6.28 41.17 3.79
44 45 4.706962 GGGTTTGATCTAGATGCTTGGTTT 59.293 41.667 10.74 0.00 0.00 3.27
59 60 6.953101 TGCTTGGTTTATTAGTGGTCTGATA 58.047 36.000 0.00 0.00 0.00 2.15
65 66 8.544622 TGGTTTATTAGTGGTCTGATATGTGAA 58.455 33.333 0.00 0.00 0.00 3.18
72 73 7.423844 AGTGGTCTGATATGTGAACTGATAA 57.576 36.000 0.00 0.00 0.00 1.75
74 75 7.343057 AGTGGTCTGATATGTGAACTGATAAGA 59.657 37.037 0.00 0.00 0.00 2.10
86 87 9.049523 TGTGAACTGATAAGATTGATTGCTATC 57.950 33.333 0.76 0.76 0.00 2.08
87 88 8.219769 GTGAACTGATAAGATTGATTGCTATCG 58.780 37.037 3.70 0.00 33.23 2.92
117 118 6.696042 TGCAATTTATGGTAGGGCTAGATA 57.304 37.500 0.00 0.00 0.00 1.98
168 169 8.921205 AGTAGTAGAGTTTGAAGTTGAACCTTA 58.079 33.333 0.00 0.00 0.00 2.69
218 348 6.883744 TGAACCATGTACATGTATGCTTCTA 58.116 36.000 29.25 12.10 37.11 2.10
219 349 7.508687 TGAACCATGTACATGTATGCTTCTAT 58.491 34.615 29.25 5.40 37.11 1.98
240 370 7.969004 TCTATTTTCATGGATTGTCCGGTATA 58.031 34.615 0.00 0.00 40.17 1.47
253 383 4.100344 TGTCCGGTATATTGTGTGCTATGT 59.900 41.667 0.00 0.00 0.00 2.29
324 454 1.276622 TCTTAGTCAGGCCCTTGTCC 58.723 55.000 0.00 0.00 0.00 4.02
411 541 1.241165 TTCAGAGGTGTTCGCGTCTA 58.759 50.000 5.77 0.00 33.01 2.59
425 555 3.252701 TCGCGTCTAATTCCCTCTATGTC 59.747 47.826 5.77 0.00 0.00 3.06
453 583 3.129792 CTCGTTGAGCCAACTCCTC 57.870 57.895 13.76 0.00 42.74 3.71
511 656 3.258123 GCAAAGGCAAAGAAGGATGGTAA 59.742 43.478 0.00 0.00 40.72 2.85
586 731 3.690460 TGTGTGAGCTCATCTCTAGTGA 58.310 45.455 21.47 0.00 42.38 3.41
597 742 6.238648 GCTCATCTCTAGTGAAGTTAGGACTC 60.239 46.154 0.00 0.00 34.21 3.36
634 779 0.450184 GTGCACTTGAACACCGTTGT 59.550 50.000 10.32 0.00 37.67 3.32
639 784 2.418628 CACTTGAACACCGTTGTGAAGT 59.581 45.455 5.30 5.30 45.76 3.01
789 934 3.373439 CACTTGCTCCATAGTTCTGAAGC 59.627 47.826 0.00 0.00 0.00 3.86
804 949 2.507110 GAAGCCAGAGCACTACGCCA 62.507 60.000 0.00 0.00 44.04 5.69
904 1049 7.285401 ACAACACTTGTGTTTCATTCTTAGGAT 59.715 33.333 15.46 0.00 43.48 3.24
916 1061 3.438131 TCTTAGGATCACCCAAGGGAT 57.562 47.619 13.15 0.00 38.96 3.85
925 1070 0.779997 ACCCAAGGGATGCTGAGTTT 59.220 50.000 13.15 0.00 38.96 2.66
942 1088 3.882888 GAGTTTCTCAACACACCATCCAA 59.117 43.478 0.00 0.00 35.05 3.53
985 1131 3.254024 TTCTCCTTCGGGCTGGCAC 62.254 63.158 2.88 0.00 34.44 5.01
1119 1266 0.109532 TCGACAAGCCATTTGACCCA 59.890 50.000 0.00 0.00 39.21 4.51
1171 1318 4.423913 CCTGATGGAGGAGGAGATCAATA 58.576 47.826 0.00 0.00 46.33 1.90
1304 1451 2.775856 GCGACGAGGCTCTCATGGA 61.776 63.158 13.50 0.00 0.00 3.41
1387 1535 1.372997 CGGAGGGTGTTGTGTCTCG 60.373 63.158 0.00 0.00 0.00 4.04
1488 1649 0.247537 CGACGATGACGATGACGACA 60.248 55.000 0.00 0.00 45.90 4.35
1723 1888 4.448537 TGTTTGTGTGCTACTTTGCTTT 57.551 36.364 0.00 0.00 0.00 3.51
1724 1889 4.172505 TGTTTGTGTGCTACTTTGCTTTG 58.827 39.130 0.00 0.00 0.00 2.77
1774 1941 1.884579 ACTCTTGCTCTTGTGCATTGG 59.115 47.619 0.00 0.00 42.96 3.16
1775 1942 0.599558 TCTTGCTCTTGTGCATTGGC 59.400 50.000 0.00 0.00 42.96 4.52
1776 1943 0.601558 CTTGCTCTTGTGCATTGGCT 59.398 50.000 0.00 0.00 42.96 4.75
1827 1994 6.612863 GGTAAGGTCCCAGAGGTTTATAGTTA 59.387 42.308 0.00 0.00 0.00 2.24
1965 2132 1.295792 GTTGACAGTCGCAAGGTTGA 58.704 50.000 0.00 0.00 38.47 3.18
1972 2139 1.021968 GTCGCAAGGTTGAAGGTGTT 58.978 50.000 0.00 0.00 38.47 3.32
1999 2166 2.151202 GATCGTCAGTTTGGGCTGAAA 58.849 47.619 0.00 0.00 45.75 2.69
2034 2201 2.492088 TCATCTTCGTCCAGTTCATCGT 59.508 45.455 0.00 0.00 0.00 3.73
2135 2302 0.797542 GTATGCAACCAAACGCCGTA 59.202 50.000 0.00 0.00 0.00 4.02
2200 2367 4.675114 GCATTTGCGTATTACCTAATGCAC 59.325 41.667 23.00 8.66 44.29 4.57
2253 2421 3.388024 GCAGATGGTGTATTAGGGTCTGA 59.612 47.826 0.00 0.00 34.95 3.27
2264 2432 7.067494 GTGTATTAGGGTCTGATTTTGCTCAAT 59.933 37.037 0.00 0.00 0.00 2.57
2296 2464 2.166254 TGAGAAGTGTATGCGATGCAGA 59.834 45.455 0.00 0.00 43.65 4.26
2301 2469 4.123497 AGTGTATGCGATGCAGAAACTA 57.877 40.909 7.43 0.00 45.02 2.24
2304 2472 5.586243 AGTGTATGCGATGCAGAAACTATTT 59.414 36.000 7.43 0.00 45.02 1.40
2323 2491 1.752683 TACAACGGCAACCAAACACT 58.247 45.000 0.00 0.00 0.00 3.55
2324 2492 0.892063 ACAACGGCAACCAAACACTT 59.108 45.000 0.00 0.00 0.00 3.16
2325 2493 1.135228 ACAACGGCAACCAAACACTTC 60.135 47.619 0.00 0.00 0.00 3.01
2326 2494 0.458260 AACGGCAACCAAACACTTCC 59.542 50.000 0.00 0.00 0.00 3.46
2327 2495 0.395173 ACGGCAACCAAACACTTCCT 60.395 50.000 0.00 0.00 0.00 3.36
2328 2496 0.030638 CGGCAACCAAACACTTCCTG 59.969 55.000 0.00 0.00 0.00 3.86
2329 2497 1.111277 GGCAACCAAACACTTCCTGT 58.889 50.000 0.00 0.00 32.89 4.00
2330 2498 2.303175 GGCAACCAAACACTTCCTGTA 58.697 47.619 0.00 0.00 30.51 2.74
2331 2499 2.890945 GGCAACCAAACACTTCCTGTAT 59.109 45.455 0.00 0.00 30.51 2.29
2332 2500 3.305335 GGCAACCAAACACTTCCTGTATG 60.305 47.826 0.00 0.00 30.51 2.39
2333 2501 3.568007 GCAACCAAACACTTCCTGTATGA 59.432 43.478 0.00 0.00 30.51 2.15
2334 2502 4.037446 GCAACCAAACACTTCCTGTATGAA 59.963 41.667 0.00 0.00 30.51 2.57
2335 2503 5.278957 GCAACCAAACACTTCCTGTATGAAT 60.279 40.000 0.00 0.00 30.51 2.57
2336 2504 6.738453 GCAACCAAACACTTCCTGTATGAATT 60.738 38.462 0.00 0.00 30.51 2.17
2337 2505 6.575162 ACCAAACACTTCCTGTATGAATTC 57.425 37.500 0.00 0.00 30.51 2.17
2338 2506 6.068010 ACCAAACACTTCCTGTATGAATTCA 58.932 36.000 11.26 11.26 30.51 2.57
2339 2507 6.207417 ACCAAACACTTCCTGTATGAATTCAG 59.793 38.462 14.54 0.00 30.51 3.02
2340 2508 5.886960 AACACTTCCTGTATGAATTCAGC 57.113 39.130 14.54 9.72 30.51 4.26
2341 2509 4.265073 ACACTTCCTGTATGAATTCAGCC 58.735 43.478 14.54 7.19 0.00 4.85
2342 2510 4.263462 ACACTTCCTGTATGAATTCAGCCA 60.263 41.667 14.54 11.29 0.00 4.75
2343 2511 4.701651 CACTTCCTGTATGAATTCAGCCAA 59.298 41.667 14.54 0.00 0.00 4.52
2344 2512 5.359009 CACTTCCTGTATGAATTCAGCCAAT 59.641 40.000 14.54 0.00 0.00 3.16
2345 2513 5.591877 ACTTCCTGTATGAATTCAGCCAATC 59.408 40.000 14.54 1.66 0.00 2.67
2346 2514 5.378230 TCCTGTATGAATTCAGCCAATCT 57.622 39.130 14.54 0.00 0.00 2.40
2347 2515 5.128205 TCCTGTATGAATTCAGCCAATCTG 58.872 41.667 14.54 1.65 44.21 2.90
2348 2516 4.261489 CCTGTATGAATTCAGCCAATCTGC 60.261 45.833 14.54 0.00 42.56 4.26
2349 2517 3.313249 TGTATGAATTCAGCCAATCTGCG 59.687 43.478 14.54 0.00 42.56 5.18
2350 2518 1.825090 TGAATTCAGCCAATCTGCGT 58.175 45.000 3.38 0.00 42.56 5.24
2351 2519 2.161855 TGAATTCAGCCAATCTGCGTT 58.838 42.857 3.38 0.00 42.56 4.84
2352 2520 2.095110 TGAATTCAGCCAATCTGCGTTG 60.095 45.455 3.38 0.00 42.56 4.10
2353 2521 0.171903 ATTCAGCCAATCTGCGTTGC 59.828 50.000 0.00 0.00 42.56 4.17
2354 2522 1.171549 TTCAGCCAATCTGCGTTGCA 61.172 50.000 0.00 0.00 42.56 4.08
2355 2523 1.443194 CAGCCAATCTGCGTTGCAC 60.443 57.895 0.00 0.00 35.78 4.57
2356 2524 2.502510 GCCAATCTGCGTTGCACG 60.503 61.111 4.61 4.61 45.88 5.34
2370 2538 2.432456 CACGCTTGCTCCGCACTA 60.432 61.111 0.00 0.00 38.71 2.74
2371 2539 2.125912 ACGCTTGCTCCGCACTAG 60.126 61.111 0.00 0.00 38.71 2.57
2372 2540 3.558411 CGCTTGCTCCGCACTAGC 61.558 66.667 3.16 3.16 38.71 3.42
2373 2541 2.125350 GCTTGCTCCGCACTAGCT 60.125 61.111 5.52 0.00 38.77 3.32
2374 2542 1.141881 GCTTGCTCCGCACTAGCTA 59.858 57.895 5.52 0.00 38.77 3.32
2375 2543 0.873743 GCTTGCTCCGCACTAGCTAG 60.874 60.000 19.44 19.44 43.07 3.42
2376 2544 0.873743 CTTGCTCCGCACTAGCTAGC 60.874 60.000 20.91 6.62 43.60 3.42
2377 2545 2.028337 GCTCCGCACTAGCTAGCC 59.972 66.667 20.91 10.93 39.88 3.93
2378 2546 2.786495 GCTCCGCACTAGCTAGCCA 61.786 63.158 20.91 0.00 39.88 4.75
2379 2547 1.066587 CTCCGCACTAGCTAGCCAC 59.933 63.158 20.91 9.21 39.10 5.01
2380 2548 2.278857 CCGCACTAGCTAGCCACG 60.279 66.667 20.91 19.55 39.10 4.94
2381 2549 2.490217 CGCACTAGCTAGCCACGT 59.510 61.111 20.91 3.00 39.10 4.49
2382 2550 1.586564 CGCACTAGCTAGCCACGTC 60.587 63.158 20.91 3.02 39.10 4.34
2383 2551 1.810532 GCACTAGCTAGCCACGTCT 59.189 57.895 20.91 0.00 37.91 4.18
2384 2552 1.022735 GCACTAGCTAGCCACGTCTA 58.977 55.000 20.91 0.00 37.91 2.59
2385 2553 1.268640 GCACTAGCTAGCCACGTCTAC 60.269 57.143 20.91 0.00 37.91 2.59
2386 2554 2.014857 CACTAGCTAGCCACGTCTACA 58.985 52.381 20.91 0.00 0.00 2.74
2387 2555 2.015587 ACTAGCTAGCCACGTCTACAC 58.984 52.381 20.91 0.00 0.00 2.90
2388 2556 2.014857 CTAGCTAGCCACGTCTACACA 58.985 52.381 12.13 0.00 0.00 3.72
2389 2557 0.811915 AGCTAGCCACGTCTACACAG 59.188 55.000 12.13 0.00 0.00 3.66
2390 2558 0.526662 GCTAGCCACGTCTACACAGT 59.473 55.000 2.29 0.00 0.00 3.55
2391 2559 1.732732 GCTAGCCACGTCTACACAGTG 60.733 57.143 2.29 0.00 35.79 3.66
2392 2560 1.540267 CTAGCCACGTCTACACAGTGT 59.460 52.381 11.87 11.87 34.34 3.55
2393 2561 1.612676 AGCCACGTCTACACAGTGTA 58.387 50.000 12.97 12.97 34.34 2.90
2411 2579 4.505313 TGTAGACTACACTTGTGCTCAG 57.495 45.455 11.37 0.00 32.89 3.35
2412 2580 2.447244 AGACTACACTTGTGCTCAGC 57.553 50.000 0.10 0.00 0.00 4.26
2413 2581 1.967066 AGACTACACTTGTGCTCAGCT 59.033 47.619 0.00 0.00 0.00 4.24
2414 2582 2.029470 AGACTACACTTGTGCTCAGCTC 60.029 50.000 0.00 0.00 0.00 4.09
2415 2583 1.688735 ACTACACTTGTGCTCAGCTCA 59.311 47.619 0.00 0.00 0.00 4.26
2416 2584 2.288702 ACTACACTTGTGCTCAGCTCAG 60.289 50.000 0.96 0.00 33.64 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.202305 GCATCTAGATCAAACCCTAGCTGT 60.202 45.833 1.03 0.00 33.82 4.40
38 39 8.544622 TCACATATCAGACCACTAATAAACCAA 58.455 33.333 0.00 0.00 0.00 3.67
44 45 8.533569 TCAGTTCACATATCAGACCACTAATA 57.466 34.615 0.00 0.00 0.00 0.98
59 60 7.876936 AGCAATCAATCTTATCAGTTCACAT 57.123 32.000 0.00 0.00 0.00 3.21
65 66 6.146837 GCACGATAGCAATCAATCTTATCAGT 59.853 38.462 0.00 0.00 42.67 3.41
72 73 2.138320 CCGCACGATAGCAATCAATCT 58.862 47.619 0.00 0.00 42.67 2.40
74 75 1.953559 ACCGCACGATAGCAATCAAT 58.046 45.000 0.00 0.00 42.67 2.57
102 103 4.846367 TGCTTGAATATCTAGCCCTACCAT 59.154 41.667 10.46 0.00 43.03 3.55
117 118 2.814805 AGCCTACCACATGCTTGAAT 57.185 45.000 6.60 0.00 29.17 2.57
168 169 6.600427 TCACTATCATGATTCAACACAAGCAT 59.400 34.615 14.65 0.00 32.53 3.79
218 348 7.505585 ACAATATACCGGACAATCCATGAAAAT 59.494 33.333 9.46 0.00 35.91 1.82
219 349 6.831353 ACAATATACCGGACAATCCATGAAAA 59.169 34.615 9.46 0.00 35.91 2.29
240 370 6.875948 TTGACAGTAAACATAGCACACAAT 57.124 33.333 0.00 0.00 0.00 2.71
253 383 2.410392 CGTAGCACGCATTGACAGTAAA 59.590 45.455 0.00 0.00 33.65 2.01
335 465 2.290641 GACAAACGATGGAGCAAACTGT 59.709 45.455 0.00 0.00 0.00 3.55
366 496 1.758440 GCCATCTCGGACATAGGCCA 61.758 60.000 5.01 0.00 36.56 5.36
367 497 1.004440 GCCATCTCGGACATAGGCC 60.004 63.158 0.00 0.00 36.56 5.19
411 541 4.656112 CACTACTGGGACATAGAGGGAATT 59.344 45.833 0.00 0.00 38.20 2.17
425 555 3.425578 CTCAACGAGCACTACTGGG 57.574 57.895 0.00 0.00 0.00 4.45
511 656 1.873591 GCCACTTCATGTTGTTCGACT 59.126 47.619 0.00 0.00 0.00 4.18
586 731 2.339769 AGCCCTTGTGAGTCCTAACTT 58.660 47.619 0.00 0.00 35.28 2.66
597 742 0.111253 ACCTCCTTGAAGCCCTTGTG 59.889 55.000 0.00 0.00 0.00 3.33
634 779 3.635373 ACAGAACTCGAACACCTACTTCA 59.365 43.478 0.00 0.00 0.00 3.02
639 784 1.616865 CCCACAGAACTCGAACACCTA 59.383 52.381 0.00 0.00 0.00 3.08
789 934 2.510238 GCTGGCGTAGTGCTCTGG 60.510 66.667 0.00 0.00 45.43 3.86
804 949 2.511600 GCTAACCGCGACATGGCT 60.512 61.111 8.23 0.00 0.00 4.75
904 1049 0.842030 ACTCAGCATCCCTTGGGTGA 60.842 55.000 5.51 1.39 35.47 4.02
916 1061 2.288666 GGTGTGTTGAGAAACTCAGCA 58.711 47.619 12.70 12.70 46.35 4.41
925 1070 3.897239 AGTTTTGGATGGTGTGTTGAGA 58.103 40.909 0.00 0.00 0.00 3.27
942 1088 1.271543 TGCTGCATCTGGCTGTAGTTT 60.272 47.619 0.00 0.00 45.15 2.66
985 1131 2.131709 CCATGGCATGCTTCCCAGG 61.132 63.158 22.02 8.48 34.01 4.45
1007 1153 2.121506 AACCAAGAGGCTCCCCCA 60.122 61.111 11.71 0.00 39.06 4.96
1119 1266 5.103301 TCTCTTCCTCTTCCTATCATGGACT 60.103 44.000 0.00 0.00 35.58 3.85
1171 1318 2.753452 CCTCAGTCATGCTGCAAAAGAT 59.247 45.455 6.36 0.00 44.66 2.40
1304 1451 2.350514 GCAGGTGGCTGAGAGCTT 59.649 61.111 0.00 0.00 41.99 3.74
1325 1472 3.305516 CACCCTGGGCCTTGTTGC 61.306 66.667 14.08 0.00 0.00 4.17
1370 1518 1.004918 CCGAGACACAACACCCTCC 60.005 63.158 0.00 0.00 0.00 4.30
1371 1519 1.004918 CCCGAGACACAACACCCTC 60.005 63.158 0.00 0.00 0.00 4.30
1723 1888 1.913778 ATCAATGGAGCACACAAGCA 58.086 45.000 0.00 0.00 36.85 3.91
1724 1889 2.991190 CAAATCAATGGAGCACACAAGC 59.009 45.455 0.00 0.00 0.00 4.01
1774 1941 3.200522 GCATACCACTTGCCCAGC 58.799 61.111 0.00 0.00 33.95 4.85
1827 1994 0.112995 TGCACTGGCTTCTTCCCATT 59.887 50.000 0.00 0.00 41.91 3.16
1911 2078 0.981183 TTGCACCCACTCGGAGTAAT 59.019 50.000 10.87 0.00 34.64 1.89
1965 2132 2.635915 TGACGATCCACCTTAACACCTT 59.364 45.455 0.00 0.00 0.00 3.50
1972 2139 2.027561 CCCAAACTGACGATCCACCTTA 60.028 50.000 0.00 0.00 0.00 2.69
1999 2166 5.788450 ACGAAGATGATGAAGTTCTTCAGT 58.212 37.500 21.74 13.37 43.50 3.41
2022 2189 2.289631 ACAGCAATGACGATGAACTGGA 60.290 45.455 0.00 0.00 0.00 3.86
2034 2201 1.100463 ACGCCACAACACAGCAATGA 61.100 50.000 0.00 0.00 0.00 2.57
2135 2302 3.607163 CCCAAGCGGCACATGAAT 58.393 55.556 0.00 0.00 0.00 2.57
2200 2367 0.108186 TTGCCTGCATCTAGTGTCCG 60.108 55.000 0.00 0.00 0.00 4.79
2253 2421 6.240894 TCAACCTAGTCTGATTGAGCAAAAT 58.759 36.000 0.00 0.00 0.00 1.82
2264 2432 5.105716 GCATACACTTCTCAACCTAGTCTGA 60.106 44.000 0.00 0.00 0.00 3.27
2271 2439 3.525537 CATCGCATACACTTCTCAACCT 58.474 45.455 0.00 0.00 0.00 3.50
2296 2464 5.517322 TTGGTTGCCGTTGTAAATAGTTT 57.483 34.783 0.00 0.00 0.00 2.66
2301 2469 3.131400 AGTGTTTGGTTGCCGTTGTAAAT 59.869 39.130 0.00 0.00 0.00 1.40
2304 2472 1.752683 AGTGTTTGGTTGCCGTTGTA 58.247 45.000 0.00 0.00 0.00 2.41
2323 2491 5.759059 AGATTGGCTGAATTCATACAGGAA 58.241 37.500 8.96 0.00 35.05 3.36
2324 2492 5.378230 AGATTGGCTGAATTCATACAGGA 57.622 39.130 8.96 0.00 35.05 3.86
2338 2506 2.956987 GTGCAACGCAGATTGGCT 59.043 55.556 0.00 0.00 40.08 4.75
2361 2529 1.066587 GTGGCTAGCTAGTGCGGAG 59.933 63.158 21.62 0.00 45.42 4.63
2362 2530 2.771639 CGTGGCTAGCTAGTGCGGA 61.772 63.158 21.62 0.00 45.42 5.54
2363 2531 2.278857 CGTGGCTAGCTAGTGCGG 60.279 66.667 21.62 6.17 45.42 5.69
2364 2532 1.586564 GACGTGGCTAGCTAGTGCG 60.587 63.158 21.62 22.13 45.42 5.34
2365 2533 1.022735 TAGACGTGGCTAGCTAGTGC 58.977 55.000 21.62 9.45 40.05 4.40
2366 2534 2.014857 TGTAGACGTGGCTAGCTAGTG 58.985 52.381 21.62 11.73 0.00 2.74
2367 2535 2.015587 GTGTAGACGTGGCTAGCTAGT 58.984 52.381 21.62 12.02 0.00 2.57
2368 2536 2.014857 TGTGTAGACGTGGCTAGCTAG 58.985 52.381 16.84 16.84 0.00 3.42
2369 2537 2.014857 CTGTGTAGACGTGGCTAGCTA 58.985 52.381 15.72 5.44 0.00 3.32
2370 2538 0.811915 CTGTGTAGACGTGGCTAGCT 59.188 55.000 15.72 0.00 0.00 3.32
2371 2539 0.526662 ACTGTGTAGACGTGGCTAGC 59.473 55.000 6.04 6.04 0.00 3.42
2372 2540 1.540267 ACACTGTGTAGACGTGGCTAG 59.460 52.381 12.53 0.00 33.56 3.42
2373 2541 1.612676 ACACTGTGTAGACGTGGCTA 58.387 50.000 12.53 0.00 33.56 3.93
2374 2542 1.612676 TACACTGTGTAGACGTGGCT 58.387 50.000 16.26 0.00 33.56 4.75
2390 2558 3.305403 GCTGAGCACAAGTGTAGTCTACA 60.305 47.826 8.70 8.70 36.08 2.74
2391 2559 3.057174 AGCTGAGCACAAGTGTAGTCTAC 60.057 47.826 7.39 2.81 0.00 2.59
2392 2560 3.157881 AGCTGAGCACAAGTGTAGTCTA 58.842 45.455 7.39 0.00 0.00 2.59
2393 2561 1.967066 AGCTGAGCACAAGTGTAGTCT 59.033 47.619 7.39 0.00 0.00 3.24
2394 2562 2.288457 TGAGCTGAGCACAAGTGTAGTC 60.288 50.000 7.39 0.00 0.00 2.59
2395 2563 1.688735 TGAGCTGAGCACAAGTGTAGT 59.311 47.619 7.39 0.00 0.00 2.73
2396 2564 2.335752 CTGAGCTGAGCACAAGTGTAG 58.664 52.381 7.39 0.00 0.00 2.74
2397 2565 2.445565 CTGAGCTGAGCACAAGTGTA 57.554 50.000 7.39 0.00 0.00 2.90
2398 2566 3.302375 CTGAGCTGAGCACAAGTGT 57.698 52.632 7.39 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.