Multiple sequence alignment - TraesCS5D01G460600

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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 TraesCS5D01G460600 chr5D 100.000 3318 0 0 1 3318 505122734 505126051 0.000000e+00 6128.0
1 TraesCS5D01G460600 chr5D 88.394 853 42 18 2411 3242 29466118 29466934 0.000000e+00 974.0
2 TraesCS5D01G460600 chr5D 94.636 522 16 4 2445 2966 447516218 447515709 0.000000e+00 798.0
3 TraesCS5D01G460600 chr5D 85.266 638 61 13 2703 3318 182438764 182438138 7.810000e-176 627.0
4 TraesCS5D01G460600 chr5A 89.833 3403 183 62 4 3318 632662810 632666137 0.000000e+00 4217.0
5 TraesCS5D01G460600 chr5A 87.166 187 10 4 20 192 632650714 632650900 2.020000e-47 200.0
6 TraesCS5D01G460600 chr5A 100.000 28 0 0 1 28 632650685 632650712 6.000000e-03 52.8
7 TraesCS5D01G460600 chr5B 88.929 3080 163 64 1 2987 634980531 634983525 0.000000e+00 3635.0
8 TraesCS5D01G460600 chr5B 86.601 306 22 8 3018 3318 634983584 634983875 1.490000e-83 320.0
9 TraesCS5D01G460600 chr1D 89.202 852 38 16 2411 3242 288277481 288278298 0.000000e+00 1014.0
10 TraesCS5D01G460600 chr3D 88.498 852 45 16 2411 3242 47562871 47563689 0.000000e+00 981.0
11 TraesCS5D01G460600 chr3D 94.466 524 14 6 2445 2966 562942030 562941520 0.000000e+00 793.0
12 TraesCS5D01G460600 chr3D 84.123 422 37 15 2918 3318 313254609 313255021 6.720000e-102 381.0
13 TraesCS5D01G460600 chr7D 88.187 855 47 15 2411 3245 577029774 577028954 0.000000e+00 970.0
14 TraesCS5D01G460600 chr6D 87.156 872 52 23 2391 3242 227946478 227947309 0.000000e+00 935.0
15 TraesCS5D01G460600 chr7A 86.916 642 48 17 2700 3318 360266678 360267306 0.000000e+00 688.0
16 TraesCS5D01G460600 chr6A 86.613 620 47 21 2722 3318 290275034 290275640 0.000000e+00 652.0
17 TraesCS5D01G460600 chr1A 84.779 565 53 15 2776 3318 401151858 401152411 1.350000e-148 536.0
18 TraesCS5D01G460600 chr2A 84.382 461 39 16 2882 3318 405140666 405141117 3.960000e-114 422.0
19 TraesCS5D01G460600 chr2A 83.913 460 43 18 2882 3318 396000683 396000232 8.570000e-111 411.0
20 TraesCS5D01G460600 chr2A 83.987 306 36 12 1209 1504 775611482 775611180 7.010000e-72 281.0
21 TraesCS5D01G460600 chr2D 84.834 422 36 12 2918 3318 121235065 121235479 1.850000e-107 399.0
22 TraesCS5D01G460600 chr4B 83.660 306 37 12 1209 1504 624392984 624393286 3.260000e-70 276.0
23 TraesCS5D01G460600 chr6B 83.007 306 39 12 1209 1504 497825513 497825211 7.060000e-67 265.0
24 TraesCS5D01G460600 chrUn 83.929 280 32 12 1209 1478 478759970 478760246 4.250000e-64 255.0


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 TraesCS5D01G460600 chr5D 505122734 505126051 3317 False 6128.0 6128 100.000 1 3318 1 chr5D.!!$F2 3317
1 TraesCS5D01G460600 chr5D 29466118 29466934 816 False 974.0 974 88.394 2411 3242 1 chr5D.!!$F1 831
2 TraesCS5D01G460600 chr5D 447515709 447516218 509 True 798.0 798 94.636 2445 2966 1 chr5D.!!$R2 521
3 TraesCS5D01G460600 chr5D 182438138 182438764 626 True 627.0 627 85.266 2703 3318 1 chr5D.!!$R1 615
4 TraesCS5D01G460600 chr5A 632662810 632666137 3327 False 4217.0 4217 89.833 4 3318 1 chr5A.!!$F1 3314
5 TraesCS5D01G460600 chr5B 634980531 634983875 3344 False 1977.5 3635 87.765 1 3318 2 chr5B.!!$F1 3317
6 TraesCS5D01G460600 chr1D 288277481 288278298 817 False 1014.0 1014 89.202 2411 3242 1 chr1D.!!$F1 831
7 TraesCS5D01G460600 chr3D 47562871 47563689 818 False 981.0 981 88.498 2411 3242 1 chr3D.!!$F1 831
8 TraesCS5D01G460600 chr3D 562941520 562942030 510 True 793.0 793 94.466 2445 2966 1 chr3D.!!$R1 521
9 TraesCS5D01G460600 chr7D 577028954 577029774 820 True 970.0 970 88.187 2411 3245 1 chr7D.!!$R1 834
10 TraesCS5D01G460600 chr6D 227946478 227947309 831 False 935.0 935 87.156 2391 3242 1 chr6D.!!$F1 851
11 TraesCS5D01G460600 chr7A 360266678 360267306 628 False 688.0 688 86.916 2700 3318 1 chr7A.!!$F1 618
12 TraesCS5D01G460600 chr6A 290275034 290275640 606 False 652.0 652 86.613 2722 3318 1 chr6A.!!$F1 596
13 TraesCS5D01G460600 chr1A 401151858 401152411 553 False 536.0 536 84.779 2776 3318 1 chr1A.!!$F1 542

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
590 668 0.104409 ACCAACTCAGAGAAGGGGGT 60.104 55.0 3.79 1.2 0.0 4.95 F
1526 1649 0.324943 ATCCGGTTGGTTGGTCTGAG 59.675 55.0 0.00 0.0 36.3 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2402 0.611896 CCGGCACCCCTGAAGAAAAT 60.612 55.0 0.0 0.0 0.00 1.82 R
3131 3337 0.388134 CATTGCTCGCTTGCTGCTTT 60.388 50.0 0.0 0.0 40.11 3.51 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
55 56 7.437862 TCTTGTTGCAAAATATTCTGAAACCAC 59.562 33.333 9.69 0.00 31.02 4.16
56 57 5.988561 TGTTGCAAAATATTCTGAAACCACC 59.011 36.000 9.69 0.00 31.02 4.61
152 166 1.073931 TAATCCGGACCCCCAAAACA 58.926 50.000 6.12 0.00 0.00 2.83
221 235 2.919494 CGCTGTTCACTTTGGGGCC 61.919 63.158 0.00 0.00 0.00 5.80
223 237 1.527433 GCTGTTCACTTTGGGGCCTC 61.527 60.000 0.84 0.00 0.00 4.70
224 238 1.228124 TGTTCACTTTGGGGCCTCG 60.228 57.895 0.84 0.00 0.00 4.63
225 239 2.282180 TTCACTTTGGGGCCTCGC 60.282 61.111 0.84 0.00 0.00 5.03
340 385 2.810164 CCCGGAAATTTTTACCCCTCA 58.190 47.619 0.73 0.00 0.00 3.86
360 419 2.546368 CACGAGAGAGAGGGAATCTACG 59.454 54.545 0.00 0.00 38.84 3.51
488 556 5.048846 TGCAACTTTACTTTCTTCCTCCT 57.951 39.130 0.00 0.00 0.00 3.69
490 558 6.597562 TGCAACTTTACTTTCTTCCTCCTTA 58.402 36.000 0.00 0.00 0.00 2.69
571 649 5.175127 GTTGGAAAGAAAAAGGAAACAGCA 58.825 37.500 0.00 0.00 0.00 4.41
590 668 0.104409 ACCAACTCAGAGAAGGGGGT 60.104 55.000 3.79 1.20 0.00 4.95
637 727 1.187567 AAAGAAAAGCGGGCATGGCT 61.188 50.000 19.78 3.98 44.02 4.75
638 728 1.880819 AAGAAAAGCGGGCATGGCTG 61.881 55.000 23.24 23.24 41.39 4.85
639 729 3.360956 GAAAAGCGGGCATGGCTGG 62.361 63.158 27.62 16.74 41.39 4.85
657 747 4.215742 CTGGCGGGCATGGCAATG 62.216 66.667 22.06 11.08 44.45 2.82
673 763 4.912395 TGGGCCGCTTGCTTTGGT 62.912 61.111 0.00 0.00 40.92 3.67
823 913 1.166973 TTCTACTTCCCCCTCCCCCT 61.167 60.000 0.00 0.00 0.00 4.79
825 915 2.623297 CTACTTCCCCCTCCCCCTCC 62.623 70.000 0.00 0.00 0.00 4.30
826 916 4.845307 CTTCCCCCTCCCCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
928 1029 4.958897 CCCACGCCCACCGGAAAA 62.959 66.667 9.46 0.00 42.52 2.29
929 1030 3.361977 CCACGCCCACCGGAAAAG 61.362 66.667 9.46 0.00 42.52 2.27
930 1031 3.361977 CACGCCCACCGGAAAAGG 61.362 66.667 9.46 3.65 42.52 3.11
1098 1204 4.572571 TTGGTGGTCGTGGTGGCC 62.573 66.667 0.00 0.00 0.00 5.36
1186 1292 2.045047 AGGAGGACTCTGGAGGATTTCA 59.955 50.000 2.58 0.00 0.00 2.69
1263 1369 4.223032 CCTATCCACAACAGGTACTTCACT 59.777 45.833 0.00 0.00 34.60 3.41
1264 1370 5.421056 CCTATCCACAACAGGTACTTCACTA 59.579 44.000 0.00 0.00 34.60 2.74
1272 1378 5.211174 ACAGGTACTTCACTACACCTTTC 57.789 43.478 0.00 0.00 39.40 2.62
1274 1380 5.365895 ACAGGTACTTCACTACACCTTTCTT 59.634 40.000 0.00 0.00 39.40 2.52
1275 1381 5.927115 CAGGTACTTCACTACACCTTTCTTC 59.073 44.000 0.00 0.00 39.40 2.87
1276 1382 5.601313 AGGTACTTCACTACACCTTTCTTCA 59.399 40.000 0.00 0.00 38.23 3.02
1277 1383 5.927115 GGTACTTCACTACACCTTTCTTCAG 59.073 44.000 0.00 0.00 0.00 3.02
1278 1384 5.615925 ACTTCACTACACCTTTCTTCAGT 57.384 39.130 0.00 0.00 0.00 3.41
1279 1385 5.360591 ACTTCACTACACCTTTCTTCAGTG 58.639 41.667 0.00 0.00 37.53 3.66
1289 1396 4.160252 ACCTTTCTTCAGTGTGTTGCATTT 59.840 37.500 0.00 0.00 0.00 2.32
1298 1405 4.053295 AGTGTGTTGCATTTCAAGATTGC 58.947 39.130 0.00 0.00 34.91 3.56
1311 1418 6.409524 TTCAAGATTGCCTCTGAATTTTGT 57.590 33.333 0.00 0.00 33.29 2.83
1315 1422 5.075493 AGATTGCCTCTGAATTTTGTGAGT 58.925 37.500 0.00 0.00 31.12 3.41
1321 1444 5.523369 CCTCTGAATTTTGTGAGTTGGTTC 58.477 41.667 0.00 0.00 0.00 3.62
1323 1446 5.200483 TCTGAATTTTGTGAGTTGGTTCCT 58.800 37.500 0.00 0.00 0.00 3.36
1324 1447 5.656416 TCTGAATTTTGTGAGTTGGTTCCTT 59.344 36.000 0.00 0.00 0.00 3.36
1325 1448 6.154363 TCTGAATTTTGTGAGTTGGTTCCTTT 59.846 34.615 0.00 0.00 0.00 3.11
1326 1449 6.337356 TGAATTTTGTGAGTTGGTTCCTTTC 58.663 36.000 0.00 0.00 0.00 2.62
1327 1450 6.154363 TGAATTTTGTGAGTTGGTTCCTTTCT 59.846 34.615 0.00 0.00 0.00 2.52
1328 1451 5.576447 TTTTGTGAGTTGGTTCCTTTCTC 57.424 39.130 0.00 0.00 0.00 2.87
1329 1452 4.503714 TTGTGAGTTGGTTCCTTTCTCT 57.496 40.909 0.00 0.00 0.00 3.10
1330 1453 3.808728 TGTGAGTTGGTTCCTTTCTCTG 58.191 45.455 0.00 0.00 0.00 3.35
1331 1454 3.199946 TGTGAGTTGGTTCCTTTCTCTGT 59.800 43.478 0.00 0.00 0.00 3.41
1332 1455 4.200092 GTGAGTTGGTTCCTTTCTCTGTT 58.800 43.478 0.00 0.00 0.00 3.16
1333 1456 4.640647 GTGAGTTGGTTCCTTTCTCTGTTT 59.359 41.667 0.00 0.00 0.00 2.83
1342 1465 6.460261 GGTTCCTTTCTCTGTTTTCCTCTTTG 60.460 42.308 0.00 0.00 0.00 2.77
1343 1466 4.580580 TCCTTTCTCTGTTTTCCTCTTTGC 59.419 41.667 0.00 0.00 0.00 3.68
1376 1499 7.042321 CCAACTTCAGTTCGTATGTTAGTTTCA 60.042 37.037 0.00 0.00 35.83 2.69
1470 1593 7.255277 GGCCATGAATATTGTCTAGGTTTCTTC 60.255 40.741 0.00 0.00 0.00 2.87
1487 1610 4.981806 TCTTCAAGTTTGGTTCTGTTGG 57.018 40.909 0.00 0.00 0.00 3.77
1523 1646 1.700739 TGTTATCCGGTTGGTTGGTCT 59.299 47.619 0.00 0.00 36.30 3.85
1524 1647 2.081462 GTTATCCGGTTGGTTGGTCTG 58.919 52.381 0.00 0.00 36.30 3.51
1525 1648 1.646912 TATCCGGTTGGTTGGTCTGA 58.353 50.000 0.00 0.00 36.30 3.27
1526 1649 0.324943 ATCCGGTTGGTTGGTCTGAG 59.675 55.000 0.00 0.00 36.30 3.35
1527 1650 1.966451 CCGGTTGGTTGGTCTGAGC 60.966 63.158 0.00 0.00 0.00 4.26
1528 1651 1.966451 CGGTTGGTTGGTCTGAGCC 60.966 63.158 4.17 0.00 0.00 4.70
1529 1652 1.456287 GGTTGGTTGGTCTGAGCCT 59.544 57.895 4.17 0.00 0.00 4.58
1530 1653 0.606673 GGTTGGTTGGTCTGAGCCTC 60.607 60.000 4.17 0.00 0.00 4.70
1583 1708 3.632333 CAGTGGGGTGACAGACTCTATA 58.368 50.000 0.00 0.00 0.00 1.31
1586 1711 3.381908 GTGGGGTGACAGACTCTATACTG 59.618 52.174 0.00 0.00 39.65 2.74
1717 1842 5.874810 TCTAGTGTTTAATGTGCCATCTGAC 59.125 40.000 0.00 0.00 0.00 3.51
1763 1889 4.614946 GCATTCCATATGCTCTGTTTTCC 58.385 43.478 0.00 0.00 41.52 3.13
1939 2065 1.758280 CACCCACATTCCCCAATGATG 59.242 52.381 1.73 0.00 41.97 3.07
2178 2309 9.712359 CATGATTAACTATCAACACAACAGATG 57.288 33.333 0.00 0.00 45.99 2.90
2179 2310 8.267620 TGATTAACTATCAACACAACAGATGG 57.732 34.615 0.00 0.00 40.29 3.51
2180 2311 7.882791 TGATTAACTATCAACACAACAGATGGT 59.117 33.333 0.00 0.00 40.29 3.55
2266 2401 4.033009 TCATCACCCTCTAATCTGCTGAA 58.967 43.478 0.00 0.00 0.00 3.02
2267 2402 4.471025 TCATCACCCTCTAATCTGCTGAAA 59.529 41.667 0.00 0.00 0.00 2.69
2371 2506 2.124320 CGGTTATGGTGGGGCAGG 60.124 66.667 0.00 0.00 0.00 4.85
2372 2507 2.675242 CGGTTATGGTGGGGCAGGA 61.675 63.158 0.00 0.00 0.00 3.86
2402 2549 3.444916 CATTGCATTGCATCTCCTGAAC 58.555 45.455 12.95 0.00 38.76 3.18
2767 2928 2.038659 TGCCCACTTTCTTTTTCCCTG 58.961 47.619 0.00 0.00 0.00 4.45
2809 2970 3.093057 ACCACACAGTAAGTTTTGGCAA 58.907 40.909 0.00 0.00 35.16 4.52
2856 3021 3.017265 GTCAGCAAACAAGGACCAATG 57.983 47.619 0.00 0.00 0.00 2.82
2897 3070 4.809426 CACCTAATAAAGTAACCCAGCTCG 59.191 45.833 0.00 0.00 0.00 5.03
3062 3265 4.701765 ACAATAAGCAATTTGCCACAACA 58.298 34.783 17.51 0.00 46.52 3.33
3067 3270 5.579564 AAGCAATTTGCCACAACAAAAAT 57.420 30.435 17.51 0.00 46.52 1.82
3095 3301 8.757164 AAAAGAAACAGGTGAAAACTAAAGTG 57.243 30.769 0.00 0.00 0.00 3.16
3098 3304 7.114095 AGAAACAGGTGAAAACTAAAGTGGTA 58.886 34.615 0.00 0.00 0.00 3.25
3123 3329 4.429854 AAGAGAAAGCAGAGGAACAACT 57.570 40.909 0.00 0.00 0.00 3.16
3131 3337 1.228245 GAGGAACAACTGCCAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
3132 3338 0.823356 GAGGAACAACTGCCAGCCAA 60.823 55.000 0.00 0.00 0.00 4.52
3164 3384 0.904394 GCAATGCTTTTCCTCCCCCA 60.904 55.000 0.00 0.00 0.00 4.96
3191 3411 1.767681 CCTTCTGATTCCCTCCTCCTG 59.232 57.143 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.524355 CTACATGCGAAATCAGCTCGG 59.476 52.381 0.00 0.00 36.80 4.63
56 57 1.524355 CCTACATGCGAAATCAGCTCG 59.476 52.381 0.00 0.00 39.33 5.03
221 235 2.288825 TGGTAAAAGTGAGTGAGGCGAG 60.289 50.000 0.00 0.00 0.00 5.03
223 237 2.163818 TGGTAAAAGTGAGTGAGGCG 57.836 50.000 0.00 0.00 0.00 5.52
224 238 2.162408 GCATGGTAAAAGTGAGTGAGGC 59.838 50.000 0.00 0.00 0.00 4.70
225 239 2.749621 GGCATGGTAAAAGTGAGTGAGG 59.250 50.000 0.00 0.00 0.00 3.86
340 385 2.171027 ACGTAGATTCCCTCTCTCTCGT 59.829 50.000 0.00 0.00 35.28 4.18
360 419 3.844577 TTGAACTGGAGCTACGTAGAC 57.155 47.619 26.53 17.34 0.00 2.59
396 455 2.695359 TGCGCTCCGTCTTTATTTTCT 58.305 42.857 9.73 0.00 0.00 2.52
467 526 6.711194 AGTAAGGAGGAAGAAAGTAAAGTTGC 59.289 38.462 0.00 0.00 0.00 4.17
488 556 5.221742 TGAGTGAGAGAGTGAGAGTGAGTAA 60.222 44.000 0.00 0.00 0.00 2.24
490 558 3.072330 TGAGTGAGAGAGTGAGAGTGAGT 59.928 47.826 0.00 0.00 0.00 3.41
571 649 0.104409 ACCCCCTTCTCTGAGTTGGT 60.104 55.000 4.32 3.07 0.00 3.67
590 668 2.051518 CATGGCGCCCCTGCTTTTA 61.052 57.895 26.77 0.73 34.43 1.52
614 704 0.392336 ATGCCCGCTTTTCTTTTGCA 59.608 45.000 0.00 0.00 0.00 4.08
640 730 4.215742 CATTGCCATGCCCGCCAG 62.216 66.667 0.00 0.00 0.00 4.85
653 743 1.738830 CAAAGCAAGCGGCCCATTG 60.739 57.895 9.70 9.70 46.50 2.82
654 744 2.658422 CAAAGCAAGCGGCCCATT 59.342 55.556 0.00 0.00 46.50 3.16
655 745 3.384532 CCAAAGCAAGCGGCCCAT 61.385 61.111 0.00 0.00 46.50 4.00
656 746 4.912395 ACCAAAGCAAGCGGCCCA 62.912 61.111 0.00 0.00 46.50 5.36
657 747 4.362476 CACCAAAGCAAGCGGCCC 62.362 66.667 0.00 0.00 46.50 5.80
659 749 3.903932 GAGCACCAAAGCAAGCGGC 62.904 63.158 0.00 0.00 45.30 6.53
660 750 2.256461 GAGCACCAAAGCAAGCGG 59.744 61.111 0.00 0.00 36.85 5.52
661 751 2.192608 GAGGAGCACCAAAGCAAGCG 62.193 60.000 2.07 0.00 38.94 4.68
662 752 1.583477 GAGGAGCACCAAAGCAAGC 59.417 57.895 2.07 0.00 38.94 4.01
663 753 1.871772 CGAGGAGCACCAAAGCAAG 59.128 57.895 2.07 0.00 38.94 4.01
664 754 4.063529 CGAGGAGCACCAAAGCAA 57.936 55.556 2.07 0.00 38.94 3.91
914 1015 3.122727 TTCCTTTTCCGGTGGGCGT 62.123 57.895 0.00 0.00 0.00 5.68
919 1020 3.630312 TGTTTCTTCTTCCTTTTCCGGTG 59.370 43.478 0.00 0.00 0.00 4.94
920 1021 3.883489 CTGTTTCTTCTTCCTTTTCCGGT 59.117 43.478 0.00 0.00 0.00 5.28
921 1022 4.134563 TCTGTTTCTTCTTCCTTTTCCGG 58.865 43.478 0.00 0.00 0.00 5.14
922 1023 4.214332 CCTCTGTTTCTTCTTCCTTTTCCG 59.786 45.833 0.00 0.00 0.00 4.30
923 1024 5.377478 TCCTCTGTTTCTTCTTCCTTTTCC 58.623 41.667 0.00 0.00 0.00 3.13
924 1025 6.292150 TCTCCTCTGTTTCTTCTTCCTTTTC 58.708 40.000 0.00 0.00 0.00 2.29
925 1026 6.253946 TCTCCTCTGTTTCTTCTTCCTTTT 57.746 37.500 0.00 0.00 0.00 2.27
926 1027 5.221823 CCTCTCCTCTGTTTCTTCTTCCTTT 60.222 44.000 0.00 0.00 0.00 3.11
927 1028 4.285775 CCTCTCCTCTGTTTCTTCTTCCTT 59.714 45.833 0.00 0.00 0.00 3.36
928 1029 3.837731 CCTCTCCTCTGTTTCTTCTTCCT 59.162 47.826 0.00 0.00 0.00 3.36
929 1030 3.055458 CCCTCTCCTCTGTTTCTTCTTCC 60.055 52.174 0.00 0.00 0.00 3.46
930 1031 3.835395 TCCCTCTCCTCTGTTTCTTCTTC 59.165 47.826 0.00 0.00 0.00 2.87
1186 1292 2.732619 GGAAAGGATCGTCGGCCCT 61.733 63.158 0.00 0.00 0.00 5.19
1263 1369 3.625764 GCAACACACTGAAGAAAGGTGTA 59.374 43.478 0.00 0.00 41.45 2.90
1264 1370 2.423538 GCAACACACTGAAGAAAGGTGT 59.576 45.455 0.00 0.00 43.93 4.16
1272 1378 4.923893 TCTTGAAATGCAACACACTGAAG 58.076 39.130 0.00 0.00 31.96 3.02
1274 1380 5.283294 CAATCTTGAAATGCAACACACTGA 58.717 37.500 0.00 0.00 31.96 3.41
1275 1381 4.084745 GCAATCTTGAAATGCAACACACTG 60.085 41.667 0.00 0.00 39.81 3.66
1276 1382 4.053295 GCAATCTTGAAATGCAACACACT 58.947 39.130 0.00 0.00 39.81 3.55
1277 1383 3.184986 GGCAATCTTGAAATGCAACACAC 59.815 43.478 11.80 0.00 41.80 3.82
1278 1384 3.069872 AGGCAATCTTGAAATGCAACACA 59.930 39.130 11.80 0.00 41.80 3.72
1279 1385 3.656559 AGGCAATCTTGAAATGCAACAC 58.343 40.909 11.80 0.00 41.80 3.32
1289 1396 5.535783 TCACAAAATTCAGAGGCAATCTTGA 59.464 36.000 0.00 0.00 35.47 3.02
1298 1405 5.507985 GGAACCAACTCACAAAATTCAGAGG 60.508 44.000 0.00 0.00 32.52 3.69
1311 1418 4.503714 AACAGAGAAAGGAACCAACTCA 57.496 40.909 0.00 0.00 0.00 3.41
1315 1422 4.867086 AGGAAAACAGAGAAAGGAACCAA 58.133 39.130 0.00 0.00 0.00 3.67
1321 1444 4.555511 CGCAAAGAGGAAAACAGAGAAAGG 60.556 45.833 0.00 0.00 0.00 3.11
1323 1446 3.945285 ACGCAAAGAGGAAAACAGAGAAA 59.055 39.130 0.00 0.00 0.00 2.52
1324 1447 3.541632 ACGCAAAGAGGAAAACAGAGAA 58.458 40.909 0.00 0.00 0.00 2.87
1325 1448 3.194005 ACGCAAAGAGGAAAACAGAGA 57.806 42.857 0.00 0.00 0.00 3.10
1326 1449 3.312421 TGAACGCAAAGAGGAAAACAGAG 59.688 43.478 0.00 0.00 0.00 3.35
1327 1450 3.275143 TGAACGCAAAGAGGAAAACAGA 58.725 40.909 0.00 0.00 0.00 3.41
1328 1451 3.691049 TGAACGCAAAGAGGAAAACAG 57.309 42.857 0.00 0.00 0.00 3.16
1329 1452 3.004315 GGATGAACGCAAAGAGGAAAACA 59.996 43.478 0.00 0.00 0.00 2.83
1330 1453 3.004315 TGGATGAACGCAAAGAGGAAAAC 59.996 43.478 0.00 0.00 0.00 2.43
1331 1454 3.218453 TGGATGAACGCAAAGAGGAAAA 58.782 40.909 0.00 0.00 0.00 2.29
1332 1455 2.857483 TGGATGAACGCAAAGAGGAAA 58.143 42.857 0.00 0.00 0.00 3.13
1333 1456 2.552315 GTTGGATGAACGCAAAGAGGAA 59.448 45.455 0.00 0.00 0.00 3.36
1342 1465 2.411547 CGAACTGAAGTTGGATGAACGC 60.412 50.000 0.00 0.00 39.80 4.84
1343 1466 2.800544 ACGAACTGAAGTTGGATGAACG 59.199 45.455 11.55 4.80 39.80 3.95
1376 1499 1.656587 TTACAGGGCCACATGACTCT 58.343 50.000 6.18 0.00 0.00 3.24
1470 1593 4.815269 TCAAACCAACAGAACCAAACTTG 58.185 39.130 0.00 0.00 0.00 3.16
1487 1610 7.812669 ACCGGATAACATTTTCAGATTTCAAAC 59.187 33.333 9.46 0.00 0.00 2.93
1523 1646 2.587247 GGCACACCTCAGAGGCTCA 61.587 63.158 17.31 0.00 39.63 4.26
1524 1647 2.267324 GGCACACCTCAGAGGCTC 59.733 66.667 17.31 6.34 39.63 4.70
1525 1648 2.527624 TGGCACACCTCAGAGGCT 60.528 61.111 17.31 0.84 39.63 4.58
1602 1727 6.582672 GGCAGTAAGAGTGCTTTATTTCAAAC 59.417 38.462 6.27 0.00 43.82 2.93
1682 1807 9.577110 CACATTAAACACTAGACGTATTTCCTA 57.423 33.333 0.00 0.00 0.00 2.94
1684 1809 7.178074 GCACATTAAACACTAGACGTATTTCC 58.822 38.462 0.00 0.00 0.00 3.13
1717 1842 1.274728 AGAGTGAACTAGTGCAGCCTG 59.725 52.381 2.90 0.00 0.00 4.85
1723 1848 3.577649 TGCTACAGAGTGAACTAGTGC 57.422 47.619 0.00 0.00 0.00 4.40
1763 1889 4.724074 TGCCCAGCATAAGAAAATTCAG 57.276 40.909 0.00 0.00 31.71 3.02
1953 2081 7.220683 GCGACAACAACAAAAATATCATATGCT 59.779 33.333 0.00 0.00 0.00 3.79
2113 2241 8.464770 TTGACTGCTTTCATGCAAATAATTAC 57.535 30.769 0.00 0.00 42.83 1.89
2178 2309 2.094338 CCCTACACTGAACCGTTAGACC 60.094 54.545 0.00 0.00 0.00 3.85
2179 2310 2.560105 ACCCTACACTGAACCGTTAGAC 59.440 50.000 0.00 0.00 0.00 2.59
2180 2311 2.821969 GACCCTACACTGAACCGTTAGA 59.178 50.000 0.00 0.00 0.00 2.10
2266 2401 1.256812 CGGCACCCCTGAAGAAAATT 58.743 50.000 0.00 0.00 0.00 1.82
2267 2402 0.611896 CCGGCACCCCTGAAGAAAAT 60.612 55.000 0.00 0.00 0.00 1.82
2371 2506 1.931172 GCAATGCAATGCACCATCTTC 59.069 47.619 21.74 0.00 45.70 2.87
2372 2507 2.018542 GCAATGCAATGCACCATCTT 57.981 45.000 21.74 0.00 45.70 2.40
2402 2549 2.689983 AGCTCTTGTTTGTTGTCCCTTG 59.310 45.455 0.00 0.00 0.00 3.61
2767 2928 4.691216 GGTTCTGAAACTGATACAGTGACC 59.309 45.833 5.17 0.00 44.62 4.02
2809 2970 7.213678 TCTTGTTTGTTTGTTTGTTTCCTCTT 58.786 30.769 0.00 0.00 0.00 2.85
2897 3070 1.003696 ACTGGCAAAAGCCTCTCTACC 59.996 52.381 8.11 0.00 0.00 3.18
2998 3171 8.200792 TGGATGCTGTGTGTTTAAAATAAGTTT 58.799 29.630 0.00 0.00 0.00 2.66
3005 3178 5.330455 TGTTGGATGCTGTGTGTTTAAAA 57.670 34.783 0.00 0.00 0.00 1.52
3077 3283 4.820173 GCTACCACTTTAGTTTTCACCTGT 59.180 41.667 0.00 0.00 0.00 4.00
3088 3294 5.470098 TGCTTTCTCTTTGCTACCACTTTAG 59.530 40.000 0.00 0.00 0.00 1.85
3094 3300 3.557898 CCTCTGCTTTCTCTTTGCTACCA 60.558 47.826 0.00 0.00 0.00 3.25
3095 3301 3.006247 CCTCTGCTTTCTCTTTGCTACC 58.994 50.000 0.00 0.00 0.00 3.18
3098 3304 3.145286 GTTCCTCTGCTTTCTCTTTGCT 58.855 45.455 0.00 0.00 0.00 3.91
3123 3329 2.838693 TTGCTGCTTTGGCTGGCA 60.839 55.556 0.00 0.00 42.23 4.92
3131 3337 0.388134 CATTGCTCGCTTGCTGCTTT 60.388 50.000 0.00 0.00 40.11 3.51
3132 3338 1.211969 CATTGCTCGCTTGCTGCTT 59.788 52.632 0.00 0.00 40.11 3.91
3143 3362 0.820226 GGGGAGGAAAAGCATTGCTC 59.180 55.000 12.39 13.17 38.25 4.26
3164 3384 2.040412 GAGGGAATCAGAAGGGTGTGTT 59.960 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.