Multiple sequence alignment - TraesCS3A01G187800

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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 TraesCS3A01G187800 chr3A 100.000 3451 0 0 1 3451 225896116 225892666 0.000000e+00 6373.0
1 TraesCS3A01G187800 chr3A 85.043 234 35 0 1548 1781 682479242 682479009 4.450000e-59 239.0
2 TraesCS3A01G187800 chr3A 90.278 72 5 2 1172 1242 682479386 682479316 3.670000e-15 93.5
3 TraesCS3A01G187800 chr3D 90.139 2880 109 59 667 3451 180471606 180468807 0.000000e+00 3583.0
4 TraesCS3A01G187800 chr3D 88.235 561 29 16 1 550 180472272 180471738 1.350000e-178 636.0
5 TraesCS3A01G187800 chr3D 83.830 235 38 0 1547 1781 546198933 546198699 1.250000e-54 224.0
6 TraesCS3A01G187800 chr3D 95.745 94 3 1 560 653 180471760 180471668 2.150000e-32 150.0
7 TraesCS3A01G187800 chr3D 96.000 50 2 0 1193 1242 546199055 546199006 7.940000e-12 82.4
8 TraesCS3A01G187800 chr3B 86.065 3380 178 122 157 3451 258722583 258719412 0.000000e+00 3362.0
9 TraesCS3A01G187800 chr3B 84.681 235 36 0 1547 1781 722590913 722590679 5.760000e-58 235.0
10 TraesCS3A01G187800 chr3B 83.019 106 14 4 1139 1242 722591091 722590988 3.670000e-15 93.5
11 TraesCS3A01G187800 chr4D 87.143 210 25 2 1549 1757 80836572 80836780 1.600000e-58 237.0
12 TraesCS3A01G187800 chr4D 85.308 211 29 2 1548 1757 28881790 28881999 2.090000e-52 217.0
13 TraesCS3A01G187800 chr4B 86.190 210 27 2 1549 1757 112921626 112921834 3.470000e-55 226.0
14 TraesCS3A01G187800 chr4B 84.834 211 30 2 1548 1757 41197714 41197923 9.700000e-51 211.0


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 TraesCS3A01G187800 chr3A 225892666 225896116 3450 True 6373.000000 6373 100.000 1 3451 1 chr3A.!!$R1 3450
1 TraesCS3A01G187800 chr3D 180468807 180472272 3465 True 1456.333333 3583 91.373 1 3451 3 chr3D.!!$R1 3450
2 TraesCS3A01G187800 chr3B 258719412 258722583 3171 True 3362.000000 3362 86.065 157 3451 1 chr3B.!!$R1 3294

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
653 665 0.031994 CAAAGCCAACCAAACCGAGG 59.968 55.0 0.0 0.0 0.00 4.63 F
654 666 0.396556 AAAGCCAACCAAACCGAGGT 60.397 50.0 0.0 0.0 42.34 3.85 F
969 1039 0.842635 CCCTCCAATCCTCCTCCTTG 59.157 60.0 0.0 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1590 0.035439 ACCCACGATCACCATTCACC 60.035 55.000 0.0 0.0 0.00 4.02 R
2230 2361 0.108615 GACCACCATGTCAGTCGGAG 60.109 60.000 0.0 0.0 35.29 4.63 R
2958 3129 2.439701 CCGGTCCGCTCCTAGTCA 60.440 66.667 5.5 0.0 0.00 3.41 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
54 55 1.486726 GTGGGGGAAGGTGTAGATGAG 59.513 57.143 0.00 0.00 0.00 2.90
99 100 2.034558 TGCTTGCTTTGCTTAGGTGTTC 59.965 45.455 0.00 0.00 0.00 3.18
114 115 7.121315 GCTTAGGTGTTCCAAATATTTGACTCT 59.879 37.037 26.32 18.93 40.55 3.24
120 121 3.374988 TCCAAATATTTGACTCTGCAGCG 59.625 43.478 26.32 5.22 40.55 5.18
128 129 0.801251 GACTCTGCAGCGCTGAAAAT 59.199 50.000 40.21 20.36 36.19 1.82
134 135 5.049818 ACTCTGCAGCGCTGAAAATATATTC 60.050 40.000 40.21 18.48 36.19 1.75
139 140 6.638063 TGCAGCGCTGAAAATATATTCAAATC 59.362 34.615 40.21 16.28 38.75 2.17
141 142 7.060403 GCAGCGCTGAAAATATATTCAAATCTC 59.940 37.037 40.21 11.87 38.75 2.75
191 202 0.680921 TGCAGCCTTGGGATAGCAAC 60.681 55.000 0.00 0.00 0.00 4.17
194 205 0.394899 AGCCTTGGGATAGCAACTGC 60.395 55.000 0.00 0.00 42.49 4.40
247 259 0.888736 TAAGCCTGCTTGCGCTCAAA 60.889 50.000 14.42 0.00 37.47 2.69
277 289 7.238571 GCGTATATTTGACATAAATAACGGGG 58.761 38.462 17.73 0.00 33.11 5.73
315 327 9.610705 AAATGCATGAGATGGATATAGATACAC 57.389 33.333 0.00 0.00 40.66 2.90
316 328 7.722949 TGCATGAGATGGATATAGATACACA 57.277 36.000 0.00 0.00 0.00 3.72
317 329 8.315220 TGCATGAGATGGATATAGATACACAT 57.685 34.615 0.00 0.00 0.00 3.21
318 330 8.419442 TGCATGAGATGGATATAGATACACATC 58.581 37.037 0.00 0.00 36.02 3.06
319 331 7.871973 GCATGAGATGGATATAGATACACATCC 59.128 40.741 0.00 0.00 36.32 3.51
341 353 6.414732 TCCCATAGTAATGTGGTGAAGAAAG 58.585 40.000 5.20 0.00 33.55 2.62
342 354 6.214615 TCCCATAGTAATGTGGTGAAGAAAGA 59.785 38.462 5.20 0.00 33.55 2.52
343 355 6.884295 CCCATAGTAATGTGGTGAAGAAAGAA 59.116 38.462 5.20 0.00 33.55 2.52
344 356 7.393234 CCCATAGTAATGTGGTGAAGAAAGAAA 59.607 37.037 5.20 0.00 33.55 2.52
345 357 8.960591 CCATAGTAATGTGGTGAAGAAAGAAAT 58.039 33.333 0.00 0.00 0.00 2.17
346 358 9.778993 CATAGTAATGTGGTGAAGAAAGAAATG 57.221 33.333 0.00 0.00 0.00 2.32
347 359 7.823745 AGTAATGTGGTGAAGAAAGAAATGT 57.176 32.000 0.00 0.00 0.00 2.71
348 360 7.651808 AGTAATGTGGTGAAGAAAGAAATGTG 58.348 34.615 0.00 0.00 0.00 3.21
349 361 4.916983 TGTGGTGAAGAAAGAAATGTGG 57.083 40.909 0.00 0.00 0.00 4.17
350 362 3.636300 TGTGGTGAAGAAAGAAATGTGGG 59.364 43.478 0.00 0.00 0.00 4.61
351 363 3.636764 GTGGTGAAGAAAGAAATGTGGGT 59.363 43.478 0.00 0.00 0.00 4.51
433 445 2.663196 GGACAGAGTTCCACCCCG 59.337 66.667 0.00 0.00 35.49 5.73
434 446 2.663196 GACAGAGTTCCACCCCGG 59.337 66.667 0.00 0.00 0.00 5.73
528 540 9.956720 AAAGAATCATTCATAAAATCACCGATC 57.043 29.630 0.00 0.00 0.00 3.69
529 541 8.915057 AGAATCATTCATAAAATCACCGATCT 57.085 30.769 0.00 0.00 0.00 2.75
530 542 8.997323 AGAATCATTCATAAAATCACCGATCTC 58.003 33.333 0.00 0.00 0.00 2.75
531 543 8.915057 AATCATTCATAAAATCACCGATCTCT 57.085 30.769 0.00 0.00 0.00 3.10
532 544 7.953158 TCATTCATAAAATCACCGATCTCTC 57.047 36.000 0.00 0.00 0.00 3.20
533 545 7.730084 TCATTCATAAAATCACCGATCTCTCT 58.270 34.615 0.00 0.00 0.00 3.10
534 546 7.869937 TCATTCATAAAATCACCGATCTCTCTC 59.130 37.037 0.00 0.00 0.00 3.20
535 547 6.968263 TCATAAAATCACCGATCTCTCTCT 57.032 37.500 0.00 0.00 0.00 3.10
536 548 6.976088 TCATAAAATCACCGATCTCTCTCTC 58.024 40.000 0.00 0.00 0.00 3.20
537 549 6.775142 TCATAAAATCACCGATCTCTCTCTCT 59.225 38.462 0.00 0.00 0.00 3.10
538 550 5.514274 AAAATCACCGATCTCTCTCTCTC 57.486 43.478 0.00 0.00 0.00 3.20
539 551 4.437682 AATCACCGATCTCTCTCTCTCT 57.562 45.455 0.00 0.00 0.00 3.10
540 552 3.469008 TCACCGATCTCTCTCTCTCTC 57.531 52.381 0.00 0.00 0.00 3.20
541 553 3.038280 TCACCGATCTCTCTCTCTCTCT 58.962 50.000 0.00 0.00 0.00 3.10
542 554 3.069586 TCACCGATCTCTCTCTCTCTCTC 59.930 52.174 0.00 0.00 0.00 3.20
543 555 3.070159 CACCGATCTCTCTCTCTCTCTCT 59.930 52.174 0.00 0.00 0.00 3.10
544 556 3.322254 ACCGATCTCTCTCTCTCTCTCTC 59.678 52.174 0.00 0.00 0.00 3.20
545 557 3.576118 CCGATCTCTCTCTCTCTCTCTCT 59.424 52.174 0.00 0.00 0.00 3.10
546 558 4.321601 CCGATCTCTCTCTCTCTCTCTCTC 60.322 54.167 0.00 0.00 0.00 3.20
547 559 4.522405 CGATCTCTCTCTCTCTCTCTCTCT 59.478 50.000 0.00 0.00 0.00 3.10
548 560 5.335583 CGATCTCTCTCTCTCTCTCTCTCTC 60.336 52.000 0.00 0.00 0.00 3.20
624 636 3.338249 TGCCATGAGTCTCAAAGTAAGC 58.662 45.455 6.64 4.68 0.00 3.09
653 665 0.031994 CAAAGCCAACCAAACCGAGG 59.968 55.000 0.00 0.00 0.00 4.63
654 666 0.396556 AAAGCCAACCAAACCGAGGT 60.397 50.000 0.00 0.00 42.34 3.85
751 813 4.081476 AGGAGGCATTAATTGGTTTCTTGC 60.081 41.667 0.00 0.00 0.00 4.01
761 823 4.679373 TTGGTTTCTTGCTTGGCATTTA 57.321 36.364 0.00 0.00 38.76 1.40
821 886 4.179599 CCTCCTCCTCCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
822 887 4.548513 CTCCTCCTCCCCCTCCCG 62.549 77.778 0.00 0.00 0.00 5.14
969 1039 0.842635 CCCTCCAATCCTCCTCCTTG 59.157 60.000 0.00 0.00 0.00 3.61
976 1046 3.350833 CAATCCTCCTCCTTGAACCTTG 58.649 50.000 0.00 0.00 0.00 3.61
977 1047 2.415983 TCCTCCTCCTTGAACCTTGA 57.584 50.000 0.00 0.00 0.00 3.02
978 1048 1.978580 TCCTCCTCCTTGAACCTTGAC 59.021 52.381 0.00 0.00 0.00 3.18
1017 1088 2.898705 AGAATGGCTCGTGAGATGAAC 58.101 47.619 0.00 0.00 40.84 3.18
1039 1110 1.535444 TTCTTCAGCCACCCTCCGA 60.535 57.895 0.00 0.00 0.00 4.55
1137 1214 3.013932 AAGCTCTGCTCCAGGGGG 61.014 66.667 0.00 0.00 38.25 5.40
1191 1268 4.189188 CTCGTCGGCCAGTACGGG 62.189 72.222 18.78 13.69 39.52 5.28
1241 1318 0.955178 CTCGACGGCAGATCAGGTAT 59.045 55.000 0.00 0.00 0.00 2.73
1242 1319 2.152016 CTCGACGGCAGATCAGGTATA 58.848 52.381 0.00 0.00 0.00 1.47
1311 1404 1.220529 TCGGATTCGAAGATGCATGC 58.779 50.000 11.82 11.82 43.03 4.06
1312 1405 0.939419 CGGATTCGAAGATGCATGCA 59.061 50.000 25.04 25.04 39.00 3.96
1313 1406 1.534163 CGGATTCGAAGATGCATGCAT 59.466 47.619 32.66 32.66 37.75 3.96
1334 1427 1.463056 TGAATGCGCAAACGGAACTAG 59.537 47.619 17.11 0.00 45.12 2.57
1341 1434 2.915463 CGCAAACGGAACTAGTCTACTG 59.085 50.000 0.00 0.00 34.97 2.74
1342 1435 2.666994 GCAAACGGAACTAGTCTACTGC 59.333 50.000 0.00 0.00 0.00 4.40
1343 1436 3.614390 GCAAACGGAACTAGTCTACTGCT 60.614 47.826 0.00 0.00 0.00 4.24
1344 1437 4.557205 CAAACGGAACTAGTCTACTGCTT 58.443 43.478 0.00 0.00 0.00 3.91
1361 1454 3.701241 TGCTTTGGTTTCTTTTACTGCG 58.299 40.909 0.00 0.00 0.00 5.18
1376 1469 1.274167 ACTGCGACCATCTTCCGTTTA 59.726 47.619 0.00 0.00 0.00 2.01
1377 1470 2.093658 ACTGCGACCATCTTCCGTTTAT 60.094 45.455 0.00 0.00 0.00 1.40
1378 1471 2.936498 CTGCGACCATCTTCCGTTTATT 59.064 45.455 0.00 0.00 0.00 1.40
1379 1472 3.340034 TGCGACCATCTTCCGTTTATTT 58.660 40.909 0.00 0.00 0.00 1.40
1380 1473 3.126171 TGCGACCATCTTCCGTTTATTTG 59.874 43.478 0.00 0.00 0.00 2.32
1381 1474 3.126343 GCGACCATCTTCCGTTTATTTGT 59.874 43.478 0.00 0.00 0.00 2.83
1382 1475 4.379082 GCGACCATCTTCCGTTTATTTGTT 60.379 41.667 0.00 0.00 0.00 2.83
1383 1476 5.695818 CGACCATCTTCCGTTTATTTGTTT 58.304 37.500 0.00 0.00 0.00 2.83
1384 1477 6.146898 CGACCATCTTCCGTTTATTTGTTTT 58.853 36.000 0.00 0.00 0.00 2.43
1401 1494 6.687081 TTGTTTTCGTGTGGATAACTTCTT 57.313 33.333 0.00 0.00 37.45 2.52
1402 1495 6.055231 TGTTTTCGTGTGGATAACTTCTTG 57.945 37.500 0.00 0.00 37.45 3.02
1403 1496 5.008217 TGTTTTCGTGTGGATAACTTCTTGG 59.992 40.000 0.00 0.00 37.45 3.61
1404 1497 4.610605 TTCGTGTGGATAACTTCTTGGA 57.389 40.909 0.00 0.00 0.00 3.53
1405 1498 3.921677 TCGTGTGGATAACTTCTTGGAC 58.078 45.455 0.00 0.00 0.00 4.02
1406 1499 3.576982 TCGTGTGGATAACTTCTTGGACT 59.423 43.478 0.00 0.00 0.00 3.85
1407 1500 4.039973 TCGTGTGGATAACTTCTTGGACTT 59.960 41.667 0.00 0.00 0.00 3.01
1408 1501 4.152402 CGTGTGGATAACTTCTTGGACTTG 59.848 45.833 0.00 0.00 0.00 3.16
1504 1611 1.737793 GTGAATGGTGATCGTGGGTTC 59.262 52.381 0.00 0.00 0.00 3.62
1508 1615 2.100631 GGTGATCGTGGGTTCTGCG 61.101 63.158 0.00 0.00 0.00 5.18
1509 1616 2.434185 TGATCGTGGGTTCTGCGC 60.434 61.111 0.00 0.00 0.00 6.09
1510 1617 3.195698 GATCGTGGGTTCTGCGCC 61.196 66.667 4.18 0.00 0.00 6.53
1563 1673 2.564721 AACAGGGAAAAGCTGCCGC 61.565 57.895 0.00 0.00 41.46 6.53
1877 1990 4.962836 GCACCAGCACCAGCACCT 62.963 66.667 0.00 0.00 45.49 4.00
1878 1991 2.981909 CACCAGCACCAGCACCTG 60.982 66.667 0.00 0.00 45.49 4.00
1947 2060 2.370123 ATGGGGGTGGCCATAGCT 60.370 61.111 9.72 0.00 39.73 3.32
1969 2082 2.746277 GGGTGTACAGCAAGGCCG 60.746 66.667 25.23 0.00 0.00 6.13
1970 2083 3.431725 GGTGTACAGCAAGGCCGC 61.432 66.667 19.87 0.00 0.00 6.53
1971 2084 2.358737 GTGTACAGCAAGGCCGCT 60.359 61.111 0.00 0.00 45.21 5.52
1972 2085 1.079405 GTGTACAGCAAGGCCGCTA 60.079 57.895 4.69 0.00 41.38 4.26
1973 2086 1.079405 TGTACAGCAAGGCCGCTAC 60.079 57.895 4.69 2.05 41.38 3.58
1974 2087 2.165301 GTACAGCAAGGCCGCTACG 61.165 63.158 4.69 0.00 41.38 3.51
2230 2361 1.134694 GCCAGCGTTTTGATCCGAC 59.865 57.895 0.00 0.00 0.00 4.79
2278 2409 2.808315 CTACGACATGGCTCCGCT 59.192 61.111 0.00 0.00 0.00 5.52
2306 2437 2.741092 GTGACCCAGGCGTTCTCA 59.259 61.111 0.00 0.00 0.00 3.27
2309 2440 3.607370 GACCCAGGCGTTCTCACCC 62.607 68.421 0.00 0.00 0.00 4.61
2505 2641 3.133542 GGAGGCCGATATCATCATCATCA 59.866 47.826 3.12 0.00 0.00 3.07
2508 2644 4.407945 AGGCCGATATCATCATCATCATCA 59.592 41.667 3.12 0.00 0.00 3.07
2511 2647 5.989777 GCCGATATCATCATCATCATCATCA 59.010 40.000 3.12 0.00 0.00 3.07
2665 2807 2.550830 TCACTCTCCTCAGTTTTGCC 57.449 50.000 0.00 0.00 0.00 4.52
2692 2834 7.386299 GCTGATTACAGTACTTATTCAGATGGG 59.614 40.741 23.43 4.84 45.04 4.00
2693 2835 8.547481 TGATTACAGTACTTATTCAGATGGGA 57.453 34.615 0.00 0.00 0.00 4.37
2694 2836 9.159254 TGATTACAGTACTTATTCAGATGGGAT 57.841 33.333 0.00 0.00 0.00 3.85
2914 3082 4.753107 ACGGCGAGAGAGAAACAAATTAAA 59.247 37.500 16.62 0.00 0.00 1.52
2917 3085 5.181433 GGCGAGAGAGAAACAAATTAAAGGT 59.819 40.000 0.00 0.00 0.00 3.50
2958 3129 3.884091 CGGTGCACTAGGAGTAAGACTAT 59.116 47.826 17.98 0.00 0.00 2.12
3087 3271 3.662247 AGAACGACGAGTCATTTTCCT 57.338 42.857 0.00 0.00 0.00 3.36
3093 3277 3.430931 GACGAGTCATTTTCCTCTCTCG 58.569 50.000 10.13 10.13 46.31 4.04
3105 3290 1.138859 CCTCTCTCGCTCTCTCTCTCA 59.861 57.143 0.00 0.00 0.00 3.27
3107 3292 0.930310 CTCTCGCTCTCTCTCTCACG 59.070 60.000 0.00 0.00 0.00 4.35
3108 3293 0.461163 TCTCGCTCTCTCTCTCACGG 60.461 60.000 0.00 0.00 0.00 4.94
3109 3294 1.436195 CTCGCTCTCTCTCTCACGGG 61.436 65.000 0.00 0.00 0.00 5.28
3110 3295 2.477176 CGCTCTCTCTCTCACGGGG 61.477 68.421 0.00 0.00 0.00 5.73
3111 3296 2.781158 GCTCTCTCTCTCACGGGGC 61.781 68.421 0.00 0.00 0.00 5.80
3232 3455 1.227674 GACGGATGGATGGTGCCTC 60.228 63.158 0.00 0.00 0.00 4.70
3353 3584 1.414919 TGACTCCGTTACCAGTTGCTT 59.585 47.619 0.00 0.00 0.00 3.91
3368 3607 2.177038 CTTCGTCACTCGCTCGCT 59.823 61.111 0.00 0.00 39.67 4.93
3369 3608 1.865622 CTTCGTCACTCGCTCGCTC 60.866 63.158 0.00 0.00 39.67 5.03
3370 3609 3.646735 TTCGTCACTCGCTCGCTCG 62.647 63.158 0.00 0.00 39.67 5.03
3372 3611 4.468615 GTCACTCGCTCGCTCGCT 62.469 66.667 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.390967 CACCTTCCCCCACAAAAGAAAAT 59.609 43.478 0.00 0.00 0.00 1.82
29 30 2.107552 TCTACACCTTCCCCCACAAAAG 59.892 50.000 0.00 0.00 0.00 2.27
31 32 1.822425 TCTACACCTTCCCCCACAAA 58.178 50.000 0.00 0.00 0.00 2.83
32 33 1.633432 CATCTACACCTTCCCCCACAA 59.367 52.381 0.00 0.00 0.00 3.33
54 55 6.373186 AGCTACCAAGTTTTTGTAACTCAC 57.627 37.500 0.00 0.00 32.21 3.51
99 100 3.688272 CGCTGCAGAGTCAAATATTTGG 58.312 45.455 24.40 11.53 38.66 3.28
114 115 5.497635 TTGAATATATTTTCAGCGCTGCA 57.502 34.783 32.44 20.57 36.97 4.41
151 152 9.285770 GCTGCAATTTTGGTTACTAGTAATTAC 57.714 33.333 18.03 7.57 0.00 1.89
155 156 6.007703 AGGCTGCAATTTTGGTTACTAGTAA 58.992 36.000 11.38 11.38 0.00 2.24
158 165 5.163513 CAAGGCTGCAATTTTGGTTACTAG 58.836 41.667 0.50 0.00 0.00 2.57
165 172 0.686224 TCCCAAGGCTGCAATTTTGG 59.314 50.000 13.22 13.22 39.77 3.28
171 178 0.039472 TTGCTATCCCAAGGCTGCAA 59.961 50.000 0.50 2.45 37.96 4.08
191 202 0.106066 TTTGGGGATATGGCTGGCAG 60.106 55.000 10.94 10.94 0.00 4.85
194 205 2.386829 ATGTTTGGGGATATGGCTGG 57.613 50.000 0.00 0.00 0.00 4.85
277 289 5.118990 TCTCATGCATTTACTACTTCTGCC 58.881 41.667 0.00 0.00 31.89 4.85
314 326 5.428457 TCTTCACCACATTACTATGGGATGT 59.572 40.000 0.00 0.00 37.35 3.06
315 327 5.928976 TCTTCACCACATTACTATGGGATG 58.071 41.667 0.00 0.00 37.35 3.51
316 328 6.575244 TTCTTCACCACATTACTATGGGAT 57.425 37.500 0.00 0.00 37.35 3.85
317 329 6.214615 TCTTTCTTCACCACATTACTATGGGA 59.785 38.462 0.00 0.00 37.35 4.37
318 330 6.414732 TCTTTCTTCACCACATTACTATGGG 58.585 40.000 0.00 0.00 40.59 4.00
319 331 7.921786 TTCTTTCTTCACCACATTACTATGG 57.078 36.000 0.00 0.00 42.13 2.74
332 344 4.501400 CCCAACCCACATTTCTTTCTTCAC 60.501 45.833 0.00 0.00 0.00 3.18
341 353 2.456577 AGCATACCCAACCCACATTTC 58.543 47.619 0.00 0.00 0.00 2.17
342 354 2.621556 AGCATACCCAACCCACATTT 57.378 45.000 0.00 0.00 0.00 2.32
343 355 2.682563 CGTAGCATACCCAACCCACATT 60.683 50.000 0.00 0.00 38.71 2.71
344 356 1.134220 CGTAGCATACCCAACCCACAT 60.134 52.381 0.00 0.00 38.71 3.21
345 357 0.250793 CGTAGCATACCCAACCCACA 59.749 55.000 0.00 0.00 38.71 4.17
346 358 0.463116 CCGTAGCATACCCAACCCAC 60.463 60.000 0.00 0.00 38.71 4.61
347 359 1.628238 CCCGTAGCATACCCAACCCA 61.628 60.000 0.00 0.00 38.71 4.51
348 360 1.147600 CCCGTAGCATACCCAACCC 59.852 63.158 0.00 0.00 38.71 4.11
349 361 1.147600 CCCCGTAGCATACCCAACC 59.852 63.158 0.00 0.00 38.71 3.77
350 362 0.463116 CACCCCGTAGCATACCCAAC 60.463 60.000 0.00 0.00 38.71 3.77
351 363 1.909228 CACCCCGTAGCATACCCAA 59.091 57.895 0.00 0.00 38.71 4.12
439 451 2.534396 CCAACCACTACCAGGGGCA 61.534 63.158 0.00 0.00 44.74 5.36
505 517 8.997323 AGAGATCGGTGATTTTATGAATGATTC 58.003 33.333 0.00 0.00 0.00 2.52
506 518 8.915057 AGAGATCGGTGATTTTATGAATGATT 57.085 30.769 0.00 0.00 0.00 2.57
508 520 7.730084 AGAGAGATCGGTGATTTTATGAATGA 58.270 34.615 0.00 0.00 0.00 2.57
509 521 7.871973 AGAGAGAGATCGGTGATTTTATGAATG 59.128 37.037 0.00 0.00 0.00 2.67
510 522 7.961351 AGAGAGAGATCGGTGATTTTATGAAT 58.039 34.615 0.00 0.00 0.00 2.57
511 523 7.286546 AGAGAGAGAGATCGGTGATTTTATGAA 59.713 37.037 0.00 0.00 0.00 2.57
513 525 6.980593 AGAGAGAGAGATCGGTGATTTTATG 58.019 40.000 0.00 0.00 0.00 1.90
515 527 6.361433 AGAGAGAGAGAGATCGGTGATTTTA 58.639 40.000 0.00 0.00 0.00 1.52
517 529 4.792068 AGAGAGAGAGAGATCGGTGATTT 58.208 43.478 0.00 0.00 0.00 2.17
518 530 4.103153 AGAGAGAGAGAGAGATCGGTGATT 59.897 45.833 0.00 0.00 0.00 2.57
520 532 3.038280 AGAGAGAGAGAGAGATCGGTGA 58.962 50.000 0.00 0.00 0.00 4.02
521 533 3.070159 AGAGAGAGAGAGAGAGATCGGTG 59.930 52.174 0.00 0.00 0.00 4.94
522 534 3.309296 AGAGAGAGAGAGAGAGATCGGT 58.691 50.000 0.00 0.00 0.00 4.69
523 535 3.576118 AGAGAGAGAGAGAGAGAGATCGG 59.424 52.174 0.00 0.00 0.00 4.18
524 536 4.522405 AGAGAGAGAGAGAGAGAGAGATCG 59.478 50.000 0.00 0.00 0.00 3.69
525 537 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
526 538 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
527 539 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
528 540 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
529 541 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
530 542 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
531 543 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
532 544 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
533 545 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
534 546 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
535 547 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
536 548 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
537 549 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
538 550 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
539 551 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
540 552 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
541 553 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
542 554 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
543 555 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
544 556 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
545 557 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
546 558 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
547 559 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
548 560 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
634 646 0.031994 CCTCGGTTTGGTTGGCTTTG 59.968 55.000 0.00 0.00 0.00 2.77
638 650 0.594602 GTAACCTCGGTTTGGTTGGC 59.405 55.000 6.65 0.00 46.14 4.52
653 665 7.800015 TTCTTTTCTTTTTCGGTTGTGTAAC 57.200 32.000 0.00 0.00 36.04 2.50
654 666 8.813643 TTTTCTTTTCTTTTTCGGTTGTGTAA 57.186 26.923 0.00 0.00 0.00 2.41
656 668 7.149307 TCTTTTCTTTTCTTTTTCGGTTGTGT 58.851 30.769 0.00 0.00 0.00 3.72
660 715 9.872757 GTTTTTCTTTTCTTTTCTTTTTCGGTT 57.127 25.926 0.00 0.00 0.00 4.44
695 756 8.356000 ACTTTATATCTCTCGGCTAAGCTAAT 57.644 34.615 0.00 0.00 0.00 1.73
696 757 7.762588 ACTTTATATCTCTCGGCTAAGCTAA 57.237 36.000 0.00 0.00 0.00 3.09
751 813 0.887933 ACCCGCAACTAAATGCCAAG 59.112 50.000 0.00 0.00 43.47 3.61
821 886 3.949113 GTCCCTCTCTAATATAGGAGGCG 59.051 52.174 12.66 8.68 39.71 5.52
822 887 5.198207 GAGTCCCTCTCTAATATAGGAGGC 58.802 50.000 12.66 4.98 39.71 4.70
946 1014 0.766288 GAGGAGGATTGGAGGGGAGG 60.766 65.000 0.00 0.00 0.00 4.30
948 1016 1.238896 AGGAGGAGGATTGGAGGGGA 61.239 60.000 0.00 0.00 0.00 4.81
969 1039 4.331968 TCTCTCTCTCTCTGTCAAGGTTC 58.668 47.826 0.00 0.00 0.00 3.62
976 1046 3.627395 TGGTCTCTCTCTCTCTCTGTC 57.373 52.381 0.00 0.00 0.00 3.51
977 1047 3.587061 TCTTGGTCTCTCTCTCTCTCTGT 59.413 47.826 0.00 0.00 0.00 3.41
978 1048 4.220693 TCTTGGTCTCTCTCTCTCTCTG 57.779 50.000 0.00 0.00 0.00 3.35
1191 1268 1.002011 GAGGTTCCAGTTCTGGGGC 60.002 63.158 17.37 10.80 0.00 5.80
1242 1319 9.227777 GAACTCCACATAGTATTAGGTTGTTTT 57.772 33.333 10.20 0.00 0.00 2.43
1311 1404 1.386412 GTTCCGTTTGCGCATTCAATG 59.614 47.619 12.75 8.36 36.67 2.82
1312 1405 1.269448 AGTTCCGTTTGCGCATTCAAT 59.731 42.857 12.75 0.00 36.67 2.57
1313 1406 0.665835 AGTTCCGTTTGCGCATTCAA 59.334 45.000 12.75 0.00 36.67 2.69
1334 1427 7.132863 CAGTAAAAGAAACCAAAGCAGTAGAC 58.867 38.462 0.00 0.00 0.00 2.59
1341 1434 3.729217 GTCGCAGTAAAAGAAACCAAAGC 59.271 43.478 0.00 0.00 0.00 3.51
1342 1435 4.201970 TGGTCGCAGTAAAAGAAACCAAAG 60.202 41.667 0.00 0.00 32.65 2.77
1343 1436 3.695060 TGGTCGCAGTAAAAGAAACCAAA 59.305 39.130 0.00 0.00 32.65 3.28
1344 1437 3.280295 TGGTCGCAGTAAAAGAAACCAA 58.720 40.909 0.00 0.00 32.65 3.67
1361 1454 6.304683 CGAAAACAAATAAACGGAAGATGGTC 59.695 38.462 0.00 0.00 0.00 4.02
1376 1469 7.272037 AGAAGTTATCCACACGAAAACAAAT 57.728 32.000 0.00 0.00 0.00 2.32
1377 1470 6.687081 AGAAGTTATCCACACGAAAACAAA 57.313 33.333 0.00 0.00 0.00 2.83
1378 1471 6.459024 CCAAGAAGTTATCCACACGAAAACAA 60.459 38.462 0.00 0.00 0.00 2.83
1379 1472 5.008217 CCAAGAAGTTATCCACACGAAAACA 59.992 40.000 0.00 0.00 0.00 2.83
1380 1473 5.237779 TCCAAGAAGTTATCCACACGAAAAC 59.762 40.000 0.00 0.00 0.00 2.43
1381 1474 5.237779 GTCCAAGAAGTTATCCACACGAAAA 59.762 40.000 0.00 0.00 0.00 2.29
1382 1475 4.753107 GTCCAAGAAGTTATCCACACGAAA 59.247 41.667 0.00 0.00 0.00 3.46
1383 1476 4.039973 AGTCCAAGAAGTTATCCACACGAA 59.960 41.667 0.00 0.00 0.00 3.85
1384 1477 3.576982 AGTCCAAGAAGTTATCCACACGA 59.423 43.478 0.00 0.00 0.00 4.35
1401 1494 7.703058 AGAAAGAAAGAAAGAAACAAGTCCA 57.297 32.000 0.00 0.00 0.00 4.02
1402 1495 8.029522 ACAAGAAAGAAAGAAAGAAACAAGTCC 58.970 33.333 0.00 0.00 0.00 3.85
1403 1496 8.972262 ACAAGAAAGAAAGAAAGAAACAAGTC 57.028 30.769 0.00 0.00 0.00 3.01
1449 1556 4.142902 CCGCAACACACTCCAAATTACTAG 60.143 45.833 0.00 0.00 0.00 2.57
1452 1559 2.292292 ACCGCAACACACTCCAAATTAC 59.708 45.455 0.00 0.00 0.00 1.89
1480 1587 1.339055 CCACGATCACCATTCACCACT 60.339 52.381 0.00 0.00 0.00 4.00
1481 1588 1.086696 CCACGATCACCATTCACCAC 58.913 55.000 0.00 0.00 0.00 4.16
1482 1589 0.035534 CCCACGATCACCATTCACCA 60.036 55.000 0.00 0.00 0.00 4.17
1483 1590 0.035439 ACCCACGATCACCATTCACC 60.035 55.000 0.00 0.00 0.00 4.02
1484 1591 1.737793 GAACCCACGATCACCATTCAC 59.262 52.381 0.00 0.00 0.00 3.18
1485 1592 1.628340 AGAACCCACGATCACCATTCA 59.372 47.619 0.00 0.00 0.00 2.57
1486 1593 2.009774 CAGAACCCACGATCACCATTC 58.990 52.381 0.00 0.00 0.00 2.67
1504 1611 2.515523 CCAGGAATCAGGGCGCAG 60.516 66.667 10.83 0.00 0.00 5.18
1508 1615 4.222810 ACAAAATAAACCAGGAATCAGGGC 59.777 41.667 0.00 0.00 0.00 5.19
1509 1616 5.480073 TCACAAAATAAACCAGGAATCAGGG 59.520 40.000 0.00 0.00 0.00 4.45
1510 1617 6.588719 TCACAAAATAAACCAGGAATCAGG 57.411 37.500 0.00 0.00 0.00 3.86
1563 1673 2.203280 TGGTTGAACCACCGCAGG 60.203 61.111 14.05 0.00 44.79 4.85
1781 1891 4.416738 AAGAGGAGGCGGGCTTGC 62.417 66.667 5.24 0.00 0.00 4.01
1841 1954 4.436998 GGTGCTGGAGGACGACGG 62.437 72.222 0.00 0.00 37.24 4.79
1877 1990 3.632080 CCCCGTGGTGCTGGTACA 61.632 66.667 0.00 0.00 0.00 2.90
1947 2060 1.546589 CCTTGCTGTACACCCCGGTA 61.547 60.000 0.00 0.00 0.00 4.02
2164 2277 2.246789 ACGACGCAACAAAACAACAAG 58.753 42.857 0.00 0.00 0.00 3.16
2230 2361 0.108615 GACCACCATGTCAGTCGGAG 60.109 60.000 0.00 0.00 35.29 4.63
2370 2501 3.789858 CTCGTGCTGCTGCTGCTG 61.790 66.667 27.67 20.72 40.48 4.41
2665 2807 7.115520 CCATCTGAATAAGTACTGTAATCAGCG 59.884 40.741 17.11 12.60 44.77 5.18
2692 2834 9.549509 TTACATTACATGCGACTTGTTTTAATC 57.450 29.630 0.00 0.00 0.00 1.75
2694 2836 9.335891 CATTACATTACATGCGACTTGTTTTAA 57.664 29.630 0.00 0.00 0.00 1.52
2695 2837 7.965655 CCATTACATTACATGCGACTTGTTTTA 59.034 33.333 0.00 0.00 0.00 1.52
2823 2991 4.162096 ACGGACATATCTAATGCTCGTC 57.838 45.455 0.00 0.00 0.00 4.20
2833 3001 3.973206 TGGACAACAACGGACATATCT 57.027 42.857 0.00 0.00 0.00 1.98
2902 3070 8.926715 AACTGAGTGAACCTTTAATTTGTTTC 57.073 30.769 0.00 0.00 0.00 2.78
2914 3082 4.560919 CGGCTTAGTAAACTGAGTGAACCT 60.561 45.833 4.12 0.00 32.74 3.50
2917 3085 3.322828 ACCGGCTTAGTAAACTGAGTGAA 59.677 43.478 0.00 0.00 32.74 3.18
2958 3129 2.439701 CCGGTCCGCTCCTAGTCA 60.440 66.667 5.50 0.00 0.00 3.41
3087 3271 1.470805 CGTGAGAGAGAGAGCGAGAGA 60.471 57.143 0.00 0.00 0.00 3.10
3093 3277 2.781158 GCCCCGTGAGAGAGAGAGC 61.781 68.421 0.00 0.00 0.00 4.09
3156 3354 3.453070 GAGAGGCCGAGACCATGCC 62.453 68.421 0.00 0.00 45.70 4.40
3158 3356 2.415010 CGAGAGGCCGAGACCATG 59.585 66.667 0.00 0.00 0.00 3.66
3185 3383 2.162921 CTCACGCGCAACAGTCCAAG 62.163 60.000 5.73 0.00 0.00 3.61
3353 3584 4.148645 CGAGCGAGCGAGTGACGA 62.149 66.667 0.00 0.00 45.77 4.20
3368 3607 2.813754 AGCAGCAATTACAGAAAAGCGA 59.186 40.909 0.00 0.00 0.00 4.93
3369 3608 3.207474 AGCAGCAATTACAGAAAAGCG 57.793 42.857 0.00 0.00 0.00 4.68
3370 3609 4.156739 AGGTAGCAGCAATTACAGAAAAGC 59.843 41.667 0.00 0.00 0.00 3.51
3371 3610 5.634896 CAGGTAGCAGCAATTACAGAAAAG 58.365 41.667 0.00 0.00 0.00 2.27
3372 3611 4.082787 GCAGGTAGCAGCAATTACAGAAAA 60.083 41.667 4.24 0.00 44.79 2.29


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

AutoCloner maintained by Alex Coulton.