Multiple sequence alignment - TraesCS3A01G247000

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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 TraesCS3A01G247000 chr3A 100.000 3064 0 0 1 3064 464913374 464916437 0.000000e+00 5659
1 TraesCS3A01G247000 chr3A 82.857 350 58 2 2717 3064 556675384 556675035 2.290000e-81 313
2 TraesCS3A01G247000 chr3B 91.286 2100 66 40 489 2562 438538554 438536546 0.000000e+00 2756
3 TraesCS3A01G247000 chr3B 91.209 273 20 3 9 280 438539072 438538803 4.830000e-98 368
4 TraesCS3A01G247000 chr3B 83.333 216 5 4 265 452 438538768 438538556 1.460000e-38 171
5 TraesCS3A01G247000 chr3D 93.878 1568 64 9 1499 3064 339846589 339845052 0.000000e+00 2335
6 TraesCS3A01G247000 chr3D 93.665 1026 33 20 489 1500 339847624 339846617 0.000000e+00 1506
7 TraesCS3A01G247000 chr3D 84.615 481 23 23 1 452 339848084 339847626 6.070000e-117 431
8 TraesCS3A01G247000 chr3D 82.486 354 60 2 2713 3064 213677784 213677431 2.970000e-80 309
9 TraesCS3A01G247000 chr1D 86.131 411 55 2 1630 2039 470075907 470075498 2.800000e-120 442
10 TraesCS3A01G247000 chr1D 85.532 235 33 1 993 1227 470076714 470076481 8.490000e-61 244
11 TraesCS3A01G247000 chr1B 85.610 410 59 0 1630 2039 652458175 652457766 6.070000e-117 431
12 TraesCS3A01G247000 chr1B 86.818 220 29 0 1008 1227 652458941 652458722 2.360000e-61 246
13 TraesCS3A01G247000 chr1A 85.680 412 55 3 1630 2039 563685114 563684705 6.070000e-117 431
14 TraesCS3A01G247000 chr1A 85.020 247 35 2 988 1232 563685887 563685641 1.820000e-62 250
15 TraesCS3A01G247000 chr7D 87.324 355 42 3 2709 3060 472803834 472803480 1.320000e-108 403
16 TraesCS3A01G247000 chr2A 85.387 349 48 3 2713 3060 470230639 470230985 2.900000e-95 359
17 TraesCS3A01G247000 chr2A 82.571 350 59 2 2717 3064 728087384 728087035 1.070000e-79 307
18 TraesCS3A01G247000 chr7B 84.286 350 52 3 2713 3060 511470558 511470210 3.780000e-89 339
19 TraesCS3A01G247000 chr4A 84.286 350 52 3 2713 3060 492895118 492894770 3.780000e-89 339
20 TraesCS3A01G247000 chr2D 83.908 348 52 4 2713 3058 352188230 352188575 2.280000e-86 329
21 TraesCS3A01G247000 chr5A 85.714 210 30 0 1019 1228 383883145 383882936 3.980000e-54 222
22 TraesCS3A01G247000 chr5A 80.861 209 38 2 1021 1228 526393850 526394057 2.440000e-36 163
23 TraesCS3A01G247000 chr5D 84.689 209 32 0 1019 1227 291501065 291500857 3.100000e-50 209
24 TraesCS3A01G247000 chr5B 84.689 209 32 0 1019 1227 332202989 332202781 3.100000e-50 209


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 TraesCS3A01G247000 chr3A 464913374 464916437 3063 False 5659.000000 5659 100.000000 1 3064 1 chr3A.!!$F1 3063
1 TraesCS3A01G247000 chr3B 438536546 438539072 2526 True 1098.333333 2756 88.609333 9 2562 3 chr3B.!!$R1 2553
2 TraesCS3A01G247000 chr3D 339845052 339848084 3032 True 1424.000000 2335 90.719333 1 3064 3 chr3D.!!$R2 3063
3 TraesCS3A01G247000 chr1D 470075498 470076714 1216 True 343.000000 442 85.831500 993 2039 2 chr1D.!!$R1 1046
4 TraesCS3A01G247000 chr1B 652457766 652458941 1175 True 338.500000 431 86.214000 1008 2039 2 chr1B.!!$R1 1031
5 TraesCS3A01G247000 chr1A 563684705 563685887 1182 True 340.500000 431 85.350000 988 2039 2 chr1A.!!$R1 1051

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
462 542 0.03601 ACGTGATGAAGGAAGGCCAG 60.036 55.0 5.01 0.0 36.29 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2725 0.459489 CTCCGGCAGAGAGAAAGAGG 59.541 60.0 0.0 0.0 46.5 3.69 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
65 69 8.868522 ATTGTTTCTGTTATTGGAGAGATTGA 57.131 30.769 0.00 0.00 0.00 2.57
71 75 7.724287 TCTGTTATTGGAGAGATTGATCTGAG 58.276 38.462 0.00 0.00 37.25 3.35
129 134 4.154195 GCTTTGGACGACAATGTTCTGTAT 59.846 41.667 0.00 0.00 39.21 2.29
168 173 1.153329 TCCGTCGTGCAGTTTGGTT 60.153 52.632 0.00 0.00 0.00 3.67
207 212 1.461778 CTCGAATCTGAACTCGCTCG 58.538 55.000 7.44 0.00 35.04 5.03
209 214 0.910513 CGAATCTGAACTCGCTCGTG 59.089 55.000 0.45 0.00 0.00 4.35
213 218 3.570926 ATCTGAACTCGCTCGTGTTTA 57.429 42.857 10.40 6.40 32.85 2.01
221 226 0.304705 CGCTCGTGTTTATGATGGGC 59.695 55.000 0.00 0.00 0.00 5.36
226 231 2.163412 TCGTGTTTATGATGGGCTTTGC 59.837 45.455 0.00 0.00 0.00 3.68
244 249 8.207521 GGCTTTGCCTTAATTTTATTGCATTA 57.792 30.769 0.73 0.00 46.69 1.90
245 250 8.839343 GGCTTTGCCTTAATTTTATTGCATTAT 58.161 29.630 0.73 0.00 46.69 1.28
271 276 8.674263 ATTTGTATTTTCTGCCATTGTTTTCA 57.326 26.923 0.00 0.00 0.00 2.69
435 515 3.016971 TCTGCACCCATCCCCAGG 61.017 66.667 0.00 0.00 0.00 4.45
452 532 3.566322 CCCAGGTAACAAAACGTGATGAA 59.434 43.478 7.75 0.00 37.42 2.57
453 533 4.320202 CCCAGGTAACAAAACGTGATGAAG 60.320 45.833 7.75 0.00 37.42 3.02
454 534 4.320202 CCAGGTAACAAAACGTGATGAAGG 60.320 45.833 7.75 0.00 37.42 3.46
455 535 4.513692 CAGGTAACAAAACGTGATGAAGGA 59.486 41.667 7.75 0.00 37.42 3.36
456 536 5.008217 CAGGTAACAAAACGTGATGAAGGAA 59.992 40.000 7.75 0.00 37.42 3.36
457 537 5.238650 AGGTAACAAAACGTGATGAAGGAAG 59.761 40.000 7.75 0.00 41.41 3.46
458 538 4.568152 AACAAAACGTGATGAAGGAAGG 57.432 40.909 7.75 0.00 0.00 3.46
459 539 2.293399 ACAAAACGTGATGAAGGAAGGC 59.707 45.455 7.75 0.00 0.00 4.35
460 540 1.534729 AAACGTGATGAAGGAAGGCC 58.465 50.000 0.00 0.00 0.00 5.19
461 541 0.400213 AACGTGATGAAGGAAGGCCA 59.600 50.000 5.01 0.00 36.29 5.36
462 542 0.036010 ACGTGATGAAGGAAGGCCAG 60.036 55.000 5.01 0.00 36.29 4.85
463 543 0.036010 CGTGATGAAGGAAGGCCAGT 60.036 55.000 5.01 0.00 36.29 4.00
464 544 1.743996 GTGATGAAGGAAGGCCAGTC 58.256 55.000 5.01 0.69 36.29 3.51
465 545 0.250234 TGATGAAGGAAGGCCAGTCG 59.750 55.000 5.01 0.00 36.29 4.18
466 546 1.078143 ATGAAGGAAGGCCAGTCGC 60.078 57.895 5.01 0.00 36.29 5.19
467 547 2.815647 GAAGGAAGGCCAGTCGCG 60.816 66.667 5.01 0.00 38.94 5.87
478 558 4.927782 AGTCGCGCCAACTGCCAA 62.928 61.111 9.14 0.00 36.24 4.52
479 559 3.959975 GTCGCGCCAACTGCCAAA 61.960 61.111 0.00 0.00 36.24 3.28
480 560 2.983030 TCGCGCCAACTGCCAAAT 60.983 55.556 0.00 0.00 36.24 2.32
481 561 2.806198 CGCGCCAACTGCCAAATG 60.806 61.111 0.00 0.00 36.24 2.32
482 562 2.650196 GCGCCAACTGCCAAATGA 59.350 55.556 0.00 0.00 36.24 2.57
483 563 1.444895 GCGCCAACTGCCAAATGAG 60.445 57.895 0.00 0.00 36.24 2.90
484 564 1.444895 CGCCAACTGCCAAATGAGC 60.445 57.895 0.00 0.00 36.24 4.26
485 565 1.667151 GCCAACTGCCAAATGAGCA 59.333 52.632 0.00 0.00 38.82 4.26
486 566 0.668401 GCCAACTGCCAAATGAGCAC 60.668 55.000 0.00 0.00 36.01 4.40
487 567 0.675083 CCAACTGCCAAATGAGCACA 59.325 50.000 0.00 0.00 36.01 4.57
776 868 1.269703 GGCGACCCCTTCTTCCCTTA 61.270 60.000 0.00 0.00 0.00 2.69
931 1040 3.461458 GGAAGGGGAAGGAGATCAAATCT 59.539 47.826 0.00 0.00 43.70 2.40
1244 1356 2.699321 GGTACCAATACTCTCCACCTCC 59.301 54.545 7.15 0.00 0.00 4.30
1322 1927 1.420138 TCTTTCTTTCTCCCACCGCTT 59.580 47.619 0.00 0.00 0.00 4.68
1343 1948 2.991190 TGCCGTCGATTCAGTTTAGTTC 59.009 45.455 0.00 0.00 0.00 3.01
1388 1993 7.358066 TCGATCGTAGTAATTGATGACTAACC 58.642 38.462 15.94 0.00 30.15 2.85
1458 2063 7.806690 TCAATAGCAATCTGTAAACAACTCAC 58.193 34.615 0.00 0.00 0.00 3.51
1462 2067 5.468072 AGCAATCTGTAAACAACTCACTCTG 59.532 40.000 0.00 0.00 0.00 3.35
1481 2086 1.618343 TGAACTGCAGATGTCCTTCGA 59.382 47.619 23.35 1.14 0.00 3.71
1488 2094 3.450817 TGCAGATGTCCTTCGAAATAGGA 59.549 43.478 0.00 0.00 39.46 2.94
1497 2103 8.529424 TGTCCTTCGAAATAGGAGTATCTTTA 57.471 34.615 4.53 0.00 42.31 1.85
1529 2164 0.592637 TGTGCATCTTTCTGGTTGCG 59.407 50.000 0.00 0.00 37.92 4.85
1580 2215 6.653320 CAGTACCAAGTTGGCTAATCACTTTA 59.347 38.462 22.25 0.00 42.67 1.85
1581 2216 5.959618 ACCAAGTTGGCTAATCACTTTAC 57.040 39.130 22.25 0.00 42.67 2.01
1582 2217 4.454504 ACCAAGTTGGCTAATCACTTTACG 59.545 41.667 22.25 0.00 42.67 3.18
1583 2218 4.454504 CCAAGTTGGCTAATCACTTTACGT 59.545 41.667 9.46 0.00 0.00 3.57
1588 2223 4.168014 TGGCTAATCACTTTACGTACGTG 58.832 43.478 30.25 16.37 0.00 4.49
1621 2256 2.829003 CACCCGCGGCTCTCTCTA 60.829 66.667 22.85 0.00 0.00 2.43
2076 2725 1.135333 CGGCCTAGTCAAACTCTCTCC 59.865 57.143 0.00 0.00 0.00 3.71
2077 2726 1.483004 GGCCTAGTCAAACTCTCTCCC 59.517 57.143 0.00 0.00 0.00 4.30
2078 2727 2.462723 GCCTAGTCAAACTCTCTCCCT 58.537 52.381 0.00 0.00 0.00 4.20
2079 2728 2.429250 GCCTAGTCAAACTCTCTCCCTC 59.571 54.545 0.00 0.00 0.00 4.30
2080 2729 3.880117 GCCTAGTCAAACTCTCTCCCTCT 60.880 52.174 0.00 0.00 0.00 3.69
2081 2730 4.349365 CCTAGTCAAACTCTCTCCCTCTT 58.651 47.826 0.00 0.00 0.00 2.85
2082 2731 4.775253 CCTAGTCAAACTCTCTCCCTCTTT 59.225 45.833 0.00 0.00 0.00 2.52
2083 2732 4.882842 AGTCAAACTCTCTCCCTCTTTC 57.117 45.455 0.00 0.00 0.00 2.62
2084 2733 4.488770 AGTCAAACTCTCTCCCTCTTTCT 58.511 43.478 0.00 0.00 0.00 2.52
2085 2734 4.526650 AGTCAAACTCTCTCCCTCTTTCTC 59.473 45.833 0.00 0.00 0.00 2.87
2147 2796 2.906354 CTAGGGTGTAACAGGCATGTC 58.094 52.381 3.65 0.00 39.29 3.06
2229 2878 9.657419 TTGATATCATATGCTTGATTGATACGT 57.343 29.630 6.17 0.00 37.51 3.57
2522 3171 9.899226 GGAAGGATATGCATAATTTAAGAACAC 57.101 33.333 11.13 0.00 0.00 3.32
2552 3201 3.316573 GACGCAAGCCCTACCAGCT 62.317 63.158 0.00 0.00 44.19 4.24
2636 3285 8.138074 GCTTCTTTAAGGGATATAAAAGCCAAG 58.862 37.037 0.00 0.00 32.98 3.61
2687 3336 5.116180 GGATACAACTCCGATCATGTGAAA 58.884 41.667 0.00 0.00 0.00 2.69
2706 3355 5.068067 GTGAAACTGGGCTTTAAGGTTAACA 59.932 40.000 8.10 0.00 0.00 2.41
2707 3356 5.300792 TGAAACTGGGCTTTAAGGTTAACAG 59.699 40.000 8.10 0.00 0.00 3.16
2723 3372 7.918076 AGGTTAACAGAAGAGGTCATATTTGA 58.082 34.615 8.10 0.00 0.00 2.69
2724 3373 8.552296 AGGTTAACAGAAGAGGTCATATTTGAT 58.448 33.333 8.10 0.00 33.56 2.57
2732 3381 4.971282 AGAGGTCATATTTGATGAGTGGGA 59.029 41.667 0.00 0.00 33.56 4.37
2737 3386 6.239120 GGTCATATTTGATGAGTGGGAAATGG 60.239 42.308 0.00 0.00 33.56 3.16
2768 3417 9.715121 AAAATTAACATTTGAGAAGATGCATGT 57.285 25.926 2.46 0.00 32.57 3.21
2772 3421 7.876936 AACATTTGAGAAGATGCATGTATCT 57.123 32.000 19.38 19.38 39.03 1.98
2779 3428 7.927048 TGAGAAGATGCATGTATCTCAAATTG 58.073 34.615 24.20 0.00 42.44 2.32
2782 3431 7.338703 AGAAGATGCATGTATCTCAAATTGTGT 59.661 33.333 24.20 7.54 36.42 3.72
2802 3451 9.769093 ATTGTGTCACTAGAAAAATTATAACGC 57.231 29.630 4.27 0.00 0.00 4.84
2840 3491 6.096141 TCTGTTAACTGAGGAGATGATCTCAC 59.904 42.308 22.67 15.93 45.12 3.51
2881 3532 5.715439 TTGGGATGAACACCTAATCAGAT 57.285 39.130 0.00 0.00 0.00 2.90
2903 3554 1.696063 ACTATGTGGCCCATTGATGC 58.304 50.000 17.69 0.00 34.86 3.91
2909 3560 1.153784 GGCCCATTGATGCACAACG 60.154 57.895 0.00 0.00 41.52 4.10
2918 3569 3.829886 TGATGCACAACGGATTCTTTC 57.170 42.857 0.00 0.00 0.00 2.62
2923 3574 3.380004 TGCACAACGGATTCTTTCAGTTT 59.620 39.130 0.00 0.00 40.23 2.66
2957 3608 6.971726 ACATGATATGCCAGATTTCATTGT 57.028 33.333 0.00 0.00 0.00 2.71
3021 3672 0.914417 ATTCCGTGGAGTGGGACCAT 60.914 55.000 0.00 0.00 39.69 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 69 2.729479 CGGCTGGGCACTCTCAGAT 61.729 63.158 0.00 0.00 33.11 2.90
142 147 1.271379 ACTGCACGACGGAGTTGAATA 59.729 47.619 0.00 0.00 45.30 1.75
168 173 5.355630 TCGAGGTTTTGTTTCTCATGTTTCA 59.644 36.000 0.00 0.00 0.00 2.69
207 212 2.892374 GGCAAAGCCCATCATAAACAC 58.108 47.619 0.00 0.00 44.06 3.32
245 250 9.770097 TGAAAACAATGGCAGAAAATACAAATA 57.230 25.926 0.00 0.00 0.00 1.40
248 253 9.941325 ATATGAAAACAATGGCAGAAAATACAA 57.059 25.926 0.00 0.00 0.00 2.41
283 288 4.488770 ACAAAAACACCATATGTCCCCTT 58.511 39.130 1.24 0.00 42.31 3.95
290 295 8.977505 CCACTAAGAAAACAAAAACACCATATG 58.022 33.333 0.00 0.00 0.00 1.78
295 349 5.290885 CAGCCACTAAGAAAACAAAAACACC 59.709 40.000 0.00 0.00 0.00 4.16
435 515 5.449304 CCTTCCTTCATCACGTTTTGTTAC 58.551 41.667 0.00 0.00 0.00 2.50
461 541 4.927782 TTGGCAGTTGGCGCGACT 62.928 61.111 15.80 2.55 46.16 4.18
462 542 3.267597 ATTTGGCAGTTGGCGCGAC 62.268 57.895 12.10 8.22 46.16 5.19
463 543 2.983030 ATTTGGCAGTTGGCGCGA 60.983 55.556 12.10 0.00 46.16 5.87
464 544 2.806198 CATTTGGCAGTTGGCGCG 60.806 61.111 0.00 0.00 46.16 6.86
465 545 1.444895 CTCATTTGGCAGTTGGCGC 60.445 57.895 0.00 0.00 46.16 6.53
466 546 1.444895 GCTCATTTGGCAGTTGGCG 60.445 57.895 1.08 0.00 46.16 5.69
467 547 0.668401 GTGCTCATTTGGCAGTTGGC 60.668 55.000 0.00 0.00 40.54 4.52
468 548 0.675083 TGTGCTCATTTGGCAGTTGG 59.325 50.000 0.00 0.00 40.54 3.77
469 549 1.774639 GTGTGCTCATTTGGCAGTTG 58.225 50.000 0.00 0.00 40.54 3.16
470 550 0.311790 CGTGTGCTCATTTGGCAGTT 59.688 50.000 0.00 0.00 40.54 3.16
471 551 0.534877 TCGTGTGCTCATTTGGCAGT 60.535 50.000 0.00 0.00 40.54 4.40
472 552 0.592637 TTCGTGTGCTCATTTGGCAG 59.407 50.000 0.00 0.00 40.54 4.85
473 553 1.028130 TTTCGTGTGCTCATTTGGCA 58.972 45.000 0.00 0.00 37.36 4.92
474 554 2.132740 TTTTCGTGTGCTCATTTGGC 57.867 45.000 0.00 0.00 0.00 4.52
475 555 3.899734 TCATTTTCGTGTGCTCATTTGG 58.100 40.909 0.00 0.00 0.00 3.28
476 556 5.107760 CCTTTCATTTTCGTGTGCTCATTTG 60.108 40.000 0.00 0.00 0.00 2.32
477 557 4.984161 CCTTTCATTTTCGTGTGCTCATTT 59.016 37.500 0.00 0.00 0.00 2.32
478 558 4.278170 TCCTTTCATTTTCGTGTGCTCATT 59.722 37.500 0.00 0.00 0.00 2.57
479 559 3.820467 TCCTTTCATTTTCGTGTGCTCAT 59.180 39.130 0.00 0.00 0.00 2.90
480 560 3.210227 TCCTTTCATTTTCGTGTGCTCA 58.790 40.909 0.00 0.00 0.00 4.26
481 561 3.498397 TCTCCTTTCATTTTCGTGTGCTC 59.502 43.478 0.00 0.00 0.00 4.26
482 562 3.476552 TCTCCTTTCATTTTCGTGTGCT 58.523 40.909 0.00 0.00 0.00 4.40
483 563 3.896648 TCTCCTTTCATTTTCGTGTGC 57.103 42.857 0.00 0.00 0.00 4.57
484 564 4.222114 GCTTCTCCTTTCATTTTCGTGTG 58.778 43.478 0.00 0.00 0.00 3.82
485 565 3.882888 TGCTTCTCCTTTCATTTTCGTGT 59.117 39.130 0.00 0.00 0.00 4.49
486 566 4.488126 TGCTTCTCCTTTCATTTTCGTG 57.512 40.909 0.00 0.00 0.00 4.35
487 567 5.299279 TCTTTGCTTCTCCTTTCATTTTCGT 59.701 36.000 0.00 0.00 0.00 3.85
704 790 1.646189 GAGGTAGAGAAAGCCAAGCG 58.354 55.000 0.00 0.00 0.00 4.68
877 976 3.256704 TCCTCTCCTCTCCTATCCTCTC 58.743 54.545 0.00 0.00 0.00 3.20
878 977 3.115962 TCTCCTCTCCTCTCCTATCCTCT 60.116 52.174 0.00 0.00 0.00 3.69
879 978 3.256704 TCTCCTCTCCTCTCCTATCCTC 58.743 54.545 0.00 0.00 0.00 3.71
880 979 3.260205 CTCTCCTCTCCTCTCCTATCCT 58.740 54.545 0.00 0.00 0.00 3.24
881 980 2.308866 CCTCTCCTCTCCTCTCCTATCC 59.691 59.091 0.00 0.00 0.00 2.59
882 981 2.290960 GCCTCTCCTCTCCTCTCCTATC 60.291 59.091 0.00 0.00 0.00 2.08
883 982 1.710809 GCCTCTCCTCTCCTCTCCTAT 59.289 57.143 0.00 0.00 0.00 2.57
884 983 1.145571 GCCTCTCCTCTCCTCTCCTA 58.854 60.000 0.00 0.00 0.00 2.94
885 984 1.930520 GCCTCTCCTCTCCTCTCCT 59.069 63.158 0.00 0.00 0.00 3.69
931 1040 3.196039 TCGATCAACCGATGGTTTCCTAA 59.804 43.478 0.00 0.00 44.33 2.69
1244 1356 1.172175 GGGCAAAAGAGAAGGAGCAG 58.828 55.000 0.00 0.00 0.00 4.24
1322 1927 2.736144 ACTAAACTGAATCGACGGCA 57.264 45.000 0.00 0.00 0.00 5.69
1361 1966 9.053135 GTTAGTCATCAATTACTACGATCGATC 57.947 37.037 24.34 15.68 0.00 3.69
1365 1970 7.431249 TGGGTTAGTCATCAATTACTACGATC 58.569 38.462 0.00 0.00 0.00 3.69
1366 1971 7.356089 TGGGTTAGTCATCAATTACTACGAT 57.644 36.000 0.00 0.00 0.00 3.73
1367 1972 6.778834 TGGGTTAGTCATCAATTACTACGA 57.221 37.500 0.00 0.00 0.00 3.43
1368 1973 6.479001 CCTTGGGTTAGTCATCAATTACTACG 59.521 42.308 0.00 0.00 0.00 3.51
1369 1974 7.494952 GTCCTTGGGTTAGTCATCAATTACTAC 59.505 40.741 0.00 0.00 0.00 2.73
1370 1975 7.402071 AGTCCTTGGGTTAGTCATCAATTACTA 59.598 37.037 0.00 0.00 0.00 1.82
1371 1976 6.215636 AGTCCTTGGGTTAGTCATCAATTACT 59.784 38.462 0.00 0.00 0.00 2.24
1375 1980 5.256474 CAAGTCCTTGGGTTAGTCATCAAT 58.744 41.667 0.00 0.00 36.95 2.57
1377 1982 3.559171 GCAAGTCCTTGGGTTAGTCATCA 60.559 47.826 8.97 0.00 40.74 3.07
1378 1983 3.010420 GCAAGTCCTTGGGTTAGTCATC 58.990 50.000 8.97 0.00 40.74 2.92
1379 1984 2.615493 CGCAAGTCCTTGGGTTAGTCAT 60.615 50.000 14.06 0.00 45.06 3.06
1388 1993 1.363744 GAGTCATCGCAAGTCCTTGG 58.636 55.000 8.97 0.23 40.74 3.61
1462 2067 2.370281 TCGAAGGACATCTGCAGTTC 57.630 50.000 14.67 7.97 0.00 3.01
1497 2103 7.919091 CAGAAAGATGCACATTGTATTGCTAAT 59.081 33.333 0.00 0.00 39.62 1.73
1529 2164 3.057876 TCAATGTGGAAATGCGGTTACAC 60.058 43.478 7.44 7.44 0.00 2.90
1620 2255 1.113788 GCCCGGTACCTACACACATA 58.886 55.000 10.90 0.00 0.00 2.29
1621 2256 1.619807 GGCCCGGTACCTACACACAT 61.620 60.000 10.90 0.00 0.00 3.21
2076 2725 0.459489 CTCCGGCAGAGAGAAAGAGG 59.541 60.000 0.00 0.00 46.50 3.69
2147 2796 2.124122 TCAATAATCATCACGGTCGCG 58.876 47.619 0.00 0.00 0.00 5.87
2228 2877 8.304202 AGTACTACACGCTGTATGTATAGTAC 57.696 38.462 11.72 11.72 39.89 2.73
2229 2878 9.411801 GTAGTACTACACGCTGTATGTATAGTA 57.588 37.037 25.02 0.00 36.15 1.82
2230 2879 7.386299 GGTAGTACTACACGCTGTATGTATAGT 59.614 40.741 29.38 0.00 37.78 2.12
2231 2880 7.411264 CGGTAGTACTACACGCTGTATGTATAG 60.411 44.444 29.38 3.64 37.78 1.31
2232 2881 6.366061 CGGTAGTACTACACGCTGTATGTATA 59.634 42.308 29.38 0.00 37.78 1.47
2233 2882 5.178252 CGGTAGTACTACACGCTGTATGTAT 59.822 44.000 29.38 0.00 37.78 2.29
2309 2958 3.253188 ACCAATGAAATGGAGTGAACACG 59.747 43.478 0.00 0.00 43.54 4.49
2569 3218 5.278660 GCATTTTGCAATATCCTTCTCCGAT 60.279 40.000 0.00 0.00 44.26 4.18
2570 3219 4.036734 GCATTTTGCAATATCCTTCTCCGA 59.963 41.667 0.00 0.00 44.26 4.55
2571 3220 4.293415 GCATTTTGCAATATCCTTCTCCG 58.707 43.478 0.00 0.00 44.26 4.63
2643 3292 4.780554 TCCCACACCATGTAGACTTTGATA 59.219 41.667 0.00 0.00 0.00 2.15
2653 3302 3.199071 GGAGTTGTATCCCACACCATGTA 59.801 47.826 0.00 0.00 36.69 2.29
2687 3336 4.717279 TCTGTTAACCTTAAAGCCCAGT 57.283 40.909 2.48 0.00 0.00 4.00
2706 3355 6.409005 CCCACTCATCAAATATGACCTCTTCT 60.409 42.308 0.00 0.00 38.69 2.85
2707 3356 5.762218 CCCACTCATCAAATATGACCTCTTC 59.238 44.000 0.00 0.00 38.69 2.87
2777 3426 8.231837 GGCGTTATAATTTTTCTAGTGACACAA 58.768 33.333 8.59 0.00 0.00 3.33
2779 3428 7.971455 AGGCGTTATAATTTTTCTAGTGACAC 58.029 34.615 0.00 0.00 0.00 3.67
2782 3431 9.321562 CCTTAGGCGTTATAATTTTTCTAGTGA 57.678 33.333 0.00 0.00 0.00 3.41
2812 3462 5.016051 TCATCTCCTCAGTTAACAGATGC 57.984 43.478 20.28 0.00 40.16 3.91
2840 3491 2.426024 CAATTGTTGGAGGCAGGATCAG 59.574 50.000 0.00 0.00 0.00 2.90
2881 3532 3.636300 GCATCAATGGGCCACATAGTTTA 59.364 43.478 9.28 0.00 39.40 2.01
2903 3554 4.970003 GTGAAACTGAAAGAATCCGTTGTG 59.030 41.667 0.00 0.00 35.88 3.33
2923 3574 3.126073 GCATATCATGTTGCGAGAGTGA 58.874 45.455 0.00 0.00 0.00 3.41
2982 3633 0.608640 AAGCTGGTCGAACCGAGAAT 59.391 50.000 0.00 0.00 42.58 2.40
3021 3672 8.292444 AGTATTTTAATTTGCTGCCATACTGA 57.708 30.769 0.00 0.00 0.00 3.41
3029 3680 8.413229 TCCCATTAGAGTATTTTAATTTGCTGC 58.587 33.333 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.