Multiple sequence alignment - TraesCS2D01G144100

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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 TraesCS2D01G144100 chr2D 100.000 4359 0 0 1 4359 85671750 85676108 0.000000e+00 8050.0
1 TraesCS2D01G144100 chr2D 93.647 2062 106 10 1542 3589 84916312 84918362 0.000000e+00 3059.0
2 TraesCS2D01G144100 chr2D 93.394 1877 114 9 1526 3395 85388858 85390731 0.000000e+00 2771.0
3 TraesCS2D01G144100 chr2D 86.983 991 54 31 600 1522 84915346 84916329 0.000000e+00 1046.0
4 TraesCS2D01G144100 chr2D 85.083 1019 78 34 600 1582 85387904 85388884 0.000000e+00 972.0
5 TraesCS2D01G144100 chr2D 91.341 589 45 3 1 585 84914773 84915359 0.000000e+00 800.0
6 TraesCS2D01G144100 chr2D 89.171 591 54 5 1 585 85387331 85387917 0.000000e+00 728.0
7 TraesCS2D01G144100 chr2D 78.899 109 5 12 1428 1522 142675724 142675620 1.690000e-04 58.4
8 TraesCS2D01G144100 chr2B 90.145 3450 222 45 1 3395 136804453 136807839 0.000000e+00 4379.0
9 TraesCS2D01G144100 chr2B 92.805 3030 106 48 699 3698 137187588 137190535 0.000000e+00 4285.0
10 TraesCS2D01G144100 chr2B 93.889 1849 108 3 1552 3395 137608121 137609969 0.000000e+00 2784.0
11 TraesCS2D01G144100 chr2B 94.272 1711 97 1 1686 3395 136951179 136952889 0.000000e+00 2615.0
12 TraesCS2D01G144100 chr2B 83.706 1387 117 44 1 1336 136949423 136950751 0.000000e+00 1208.0
13 TraesCS2D01G144100 chr2B 90.104 576 51 6 13 585 137606760 137607332 0.000000e+00 743.0
14 TraesCS2D01G144100 chr2B 96.296 297 10 1 1337 1633 136950886 136951181 1.820000e-133 486.0
15 TraesCS2D01G144100 chr2B 92.771 332 11 3 4041 4359 137191140 137191471 6.600000e-128 468.0
16 TraesCS2D01G144100 chr2B 91.049 324 11 2 1229 1552 137607846 137608151 5.210000e-114 422.0
17 TraesCS2D01G144100 chr2B 95.528 246 5 4 3776 4017 137190905 137191148 5.290000e-104 388.0
18 TraesCS2D01G144100 chr2B 87.234 282 30 3 5 282 137144533 137144812 2.530000e-82 316.0
19 TraesCS2D01G144100 chr2B 95.833 192 8 0 954 1145 137607627 137607818 1.180000e-80 311.0
20 TraesCS2D01G144100 chr2B 88.636 132 14 1 455 585 137185829 137185960 4.510000e-35 159.0
21 TraesCS2D01G144100 chr2B 93.827 81 4 1 264 344 137744551 137744630 2.130000e-23 121.0
22 TraesCS2D01G144100 chr2B 91.892 37 3 0 1630 1666 496960228 496960192 8.000000e-03 52.8
23 TraesCS2D01G144100 chr2A 91.123 1532 121 11 1878 3401 84154118 84152594 0.000000e+00 2061.0
24 TraesCS2D01G144100 chr2A 84.706 425 52 7 3535 3956 84152506 84152092 3.140000e-111 412.0
25 TraesCS2D01G144100 chr2A 93.750 96 6 0 1288 1383 84154377 84154282 1.260000e-30 145.0
26 TraesCS2D01G144100 chrUn 76.138 1274 268 26 2119 3373 320961871 320963127 1.710000e-178 636.0
27 TraesCS2D01G144100 chrUn 75.743 1278 251 39 2119 3373 232156516 232157757 4.860000e-164 588.0
28 TraesCS2D01G144100 chr3B 76.387 1262 249 31 2119 3361 824391358 824392589 6.150000e-178 634.0
29 TraesCS2D01G144100 chr3B 77.778 144 21 11 1655 1789 513534614 513534755 1.300000e-10 78.7
30 TraesCS2D01G144100 chr7A 75.113 1330 275 43 2120 3423 32413303 32414602 4.890000e-159 571.0
31 TraesCS2D01G144100 chr7A 73.504 1253 261 50 2156 3377 15695271 15696483 4.060000e-110 409.0
32 TraesCS2D01G144100 chr7A 80.628 191 29 6 1684 1868 522982770 522982958 1.630000e-29 141.0
33 TraesCS2D01G144100 chr7A 80.714 140 14 7 1494 1632 733798047 733797920 3.590000e-16 97.1
34 TraesCS2D01G144100 chr5D 83.594 128 10 5 1496 1623 234843128 234843244 4.610000e-20 110.0
35 TraesCS2D01G144100 chr7D 80.147 136 17 5 1482 1617 633355340 633355465 4.640000e-15 93.5
36 TraesCS2D01G144100 chr7D 100.000 30 0 0 641 670 613966034 613966005 6.090000e-04 56.5
37 TraesCS2D01G144100 chr7B 78.723 141 17 10 1393 1522 600963435 600963573 1.000000e-11 82.4
38 TraesCS2D01G144100 chr4D 78.049 123 16 5 1497 1615 88516324 88516209 2.810000e-07 67.6
39 TraesCS2D01G144100 chr1A 94.444 36 2 0 1563 1598 543652838 543652803 6.090000e-04 56.5


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 TraesCS2D01G144100 chr2D 85671750 85676108 4358 False 8050.000000 8050 100.000000 1 4359 1 chr2D.!!$F1 4358
1 TraesCS2D01G144100 chr2D 84914773 84918362 3589 False 1635.000000 3059 90.657000 1 3589 3 chr2D.!!$F2 3588
2 TraesCS2D01G144100 chr2D 85387331 85390731 3400 False 1490.333333 2771 89.216000 1 3395 3 chr2D.!!$F3 3394
3 TraesCS2D01G144100 chr2B 136804453 136807839 3386 False 4379.000000 4379 90.145000 1 3395 1 chr2B.!!$F1 3394
4 TraesCS2D01G144100 chr2B 136949423 136952889 3466 False 1436.333333 2615 91.424667 1 3395 3 chr2B.!!$F4 3394
5 TraesCS2D01G144100 chr2B 137185829 137191471 5642 False 1325.000000 4285 92.435000 455 4359 4 chr2B.!!$F5 3904
6 TraesCS2D01G144100 chr2B 137606760 137609969 3209 False 1065.000000 2784 92.718750 13 3395 4 chr2B.!!$F6 3382
7 TraesCS2D01G144100 chr2A 84152092 84154377 2285 True 872.666667 2061 89.859667 1288 3956 3 chr2A.!!$R1 2668
8 TraesCS2D01G144100 chrUn 320961871 320963127 1256 False 636.000000 636 76.138000 2119 3373 1 chrUn.!!$F2 1254
9 TraesCS2D01G144100 chrUn 232156516 232157757 1241 False 588.000000 588 75.743000 2119 3373 1 chrUn.!!$F1 1254
10 TraesCS2D01G144100 chr3B 824391358 824392589 1231 False 634.000000 634 76.387000 2119 3361 1 chr3B.!!$F2 1242
11 TraesCS2D01G144100 chr7A 32413303 32414602 1299 False 571.000000 571 75.113000 2120 3423 1 chr7A.!!$F2 1303
12 TraesCS2D01G144100 chr7A 15695271 15696483 1212 False 409.000000 409 73.504000 2156 3377 1 chr7A.!!$F1 1221

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
507 518 0.035056 CTTGGGGAGAATTGGCGACT 60.035 55.000 0.00 0.0 0.0 4.18 F
1058 2691 0.687354 CCTAGGTCTGCACACCTGTT 59.313 55.000 22.63 0.2 47.0 3.16 F
1074 2707 1.007238 CTGTTACCTCTCCCTCCCTCA 59.993 57.143 0.00 0.0 0.0 3.86 F
1222 2866 1.027357 GGCCACGAATGAATGATGCT 58.973 50.000 0.00 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 3669 0.555769 GGGGGTGATATTTGGGAGCA 59.444 55.000 0.0 0.0 0.00 4.26 R
2529 4511 0.397957 TGGAGCATTACGGGGAGCTA 60.398 55.000 0.0 0.0 37.48 3.32 R
3047 5053 2.183478 TCGGCTGAAGAATCAAAGCA 57.817 45.000 0.0 0.0 34.49 3.91 R
3596 5627 4.683832 ACTAACCAGTAGTCGATTGCATC 58.316 43.478 0.0 0.0 38.84 3.91 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
31 32 1.395826 CCCTAGGTCCGAGCTCCTTG 61.396 65.000 8.47 0.73 35.51 3.61
74 75 6.753107 TCTATGATGTCGTGTTCACTCTTA 57.247 37.500 1.53 0.00 0.00 2.10
76 77 4.848562 TGATGTCGTGTTCACTCTTAGT 57.151 40.909 1.53 0.00 0.00 2.24
91 92 0.618458 TTAGTGGCACCATCCTGGAC 59.382 55.000 15.27 0.00 40.96 4.02
92 93 0.546507 TAGTGGCACCATCCTGGACA 60.547 55.000 15.27 0.00 40.96 4.02
103 104 2.601240 TCCTGGACATTGATTTGGCA 57.399 45.000 0.00 0.00 0.00 4.92
211 217 1.558294 TGTGGTAGTCGGCTCTCTAGA 59.442 52.381 0.00 0.00 0.00 2.43
215 221 3.215975 GGTAGTCGGCTCTCTAGATGTT 58.784 50.000 0.00 0.00 0.00 2.71
233 239 4.980805 TGCGGGCTCGTTGTGGTC 62.981 66.667 8.30 0.00 38.89 4.02
344 353 0.890683 GCCAACCTTGCATAGTGCTT 59.109 50.000 3.41 0.00 45.31 3.91
365 374 1.274167 TGTCGCTCGTTTATTCCTGGT 59.726 47.619 0.00 0.00 0.00 4.00
428 438 1.396653 CTTGGATCTTCATGTGGCCC 58.603 55.000 0.00 0.00 0.00 5.80
483 494 5.186021 TGGTTGCTTCCTTTAAGTCAAAACA 59.814 36.000 0.00 0.00 37.53 2.83
503 514 0.533951 CTTGCTTGGGGAGAATTGGC 59.466 55.000 0.00 0.00 0.00 4.52
507 518 0.035056 CTTGGGGAGAATTGGCGACT 60.035 55.000 0.00 0.00 0.00 4.18
573 584 7.022979 CAGTGTGTGGTTTATATTGTGTCATG 58.977 38.462 0.00 0.00 0.00 3.07
574 585 6.714810 AGTGTGTGGTTTATATTGTGTCATGT 59.285 34.615 0.00 0.00 0.00 3.21
575 586 6.801377 GTGTGTGGTTTATATTGTGTCATGTG 59.199 38.462 0.00 0.00 0.00 3.21
576 587 5.799936 GTGTGGTTTATATTGTGTCATGTGC 59.200 40.000 0.00 0.00 0.00 4.57
577 588 5.474876 TGTGGTTTATATTGTGTCATGTGCA 59.525 36.000 0.00 0.00 0.00 4.57
578 589 6.029607 GTGGTTTATATTGTGTCATGTGCAG 58.970 40.000 0.00 0.00 0.00 4.41
579 590 5.709631 TGGTTTATATTGTGTCATGTGCAGT 59.290 36.000 0.00 0.00 0.00 4.40
580 591 6.029607 GGTTTATATTGTGTCATGTGCAGTG 58.970 40.000 0.00 0.00 0.00 3.66
581 592 6.128035 GGTTTATATTGTGTCATGTGCAGTGA 60.128 38.462 0.00 0.00 0.00 3.41
582 593 6.667007 TTATATTGTGTCATGTGCAGTGAG 57.333 37.500 2.11 0.00 0.00 3.51
583 594 2.330440 TTGTGTCATGTGCAGTGAGT 57.670 45.000 2.11 0.00 0.00 3.41
584 595 2.330440 TGTGTCATGTGCAGTGAGTT 57.670 45.000 2.11 0.00 0.00 3.01
585 596 2.642427 TGTGTCATGTGCAGTGAGTTT 58.358 42.857 2.11 0.00 0.00 2.66
586 597 3.016031 TGTGTCATGTGCAGTGAGTTTT 58.984 40.909 2.11 0.00 0.00 2.43
587 598 3.443329 TGTGTCATGTGCAGTGAGTTTTT 59.557 39.130 2.11 0.00 0.00 1.94
630 641 9.254133 CAGTGAGTTGTATAGTTTATCATCTGG 57.746 37.037 0.00 0.00 0.00 3.86
688 713 8.451687 TCTTAATCATTGAAAATGAGTTTGCG 57.548 30.769 8.07 0.00 0.00 4.85
704 729 7.346695 TGAGTTTGCGCCGTTTATTTATATAC 58.653 34.615 4.18 0.00 0.00 1.47
881 2472 2.216940 CGTAAGAAAACACGCAGACGAA 59.783 45.455 0.00 0.00 40.99 3.85
902 2508 2.024941 AGGAGCCCATCGATTCCTTTTT 60.025 45.455 10.08 0.00 36.69 1.94
904 2510 3.951680 GGAGCCCATCGATTCCTTTTTAA 59.048 43.478 6.61 0.00 0.00 1.52
905 2511 4.584743 GGAGCCCATCGATTCCTTTTTAAT 59.415 41.667 6.61 0.00 0.00 1.40
906 2512 5.507985 GGAGCCCATCGATTCCTTTTTAATG 60.508 44.000 6.61 0.00 0.00 1.90
909 2515 5.591099 CCCATCGATTCCTTTTTAATGTGG 58.409 41.667 0.00 0.00 0.00 4.17
948 2557 4.070552 GCCTGACCGCCTCTTCGT 62.071 66.667 0.00 0.00 0.00 3.85
949 2558 2.657237 CCTGACCGCCTCTTCGTT 59.343 61.111 0.00 0.00 0.00 3.85
1058 2691 0.687354 CCTAGGTCTGCACACCTGTT 59.313 55.000 22.63 0.20 47.00 3.16
1074 2707 1.007238 CTGTTACCTCTCCCTCCCTCA 59.993 57.143 0.00 0.00 0.00 3.86
1083 2716 1.198759 TCCCTCCCTCACTTTTCCCG 61.199 60.000 0.00 0.00 0.00 5.14
1222 2866 1.027357 GGCCACGAATGAATGATGCT 58.973 50.000 0.00 0.00 0.00 3.79
1423 3201 3.686016 ACTTGTGGTCGCCTGAATTTAT 58.314 40.909 0.00 0.00 0.00 1.40
1436 3214 7.038659 CGCCTGAATTTATTAATTTGGGTCAA 58.961 34.615 0.00 0.00 34.16 3.18
1559 3367 4.090090 GGTATCTATCTTAGGCTGGCAGA 58.910 47.826 20.86 0.00 0.00 4.26
1674 3483 4.699522 GGTTCAGGGAGCGCCGTT 62.700 66.667 2.29 0.00 33.83 4.44
1742 3552 4.039366 GTGAGGGAAGAGAAACAGTACACT 59.961 45.833 0.00 0.00 0.00 3.55
1748 3558 5.278660 GGAAGAGAAACAGTACACTTACCGA 60.279 44.000 0.00 0.00 0.00 4.69
1791 3601 1.134818 TGTCCGTTGGATCTTGATCCG 60.135 52.381 20.69 11.34 43.62 4.18
1846 3657 2.896410 CGTTTTCAGATTTTCACGCGAG 59.104 45.455 15.93 4.59 0.00 5.03
1894 3845 2.430465 CCCCTAATGCATGATTCGGAG 58.570 52.381 0.00 0.00 29.80 4.63
2074 4031 6.554334 TTGTGTTTCTCCTTAATGTGTAGC 57.446 37.500 0.00 0.00 0.00 3.58
2111 4071 5.353400 GCCTAAGTACTACCACATTTCCAAC 59.647 44.000 0.00 0.00 0.00 3.77
2529 4511 1.751924 AGACTTATCTCTTCGCCGCTT 59.248 47.619 0.00 0.00 0.00 4.68
2917 4905 2.129555 ATCCCAGCGTGCAGGAAGTT 62.130 55.000 11.29 0.00 32.26 2.66
3043 5049 2.875296 AGCAATGGCACCTTTCAAGTA 58.125 42.857 0.00 0.00 44.61 2.24
3047 5053 4.082026 GCAATGGCACCTTTCAAGTATTCT 60.082 41.667 0.00 0.00 40.72 2.40
3453 5474 2.408271 TATTGAGCTCAAGCCAGTGG 57.592 50.000 31.14 4.20 43.38 4.00
3463 5484 2.371841 TCAAGCCAGTGGTGTAGTGAAT 59.628 45.455 11.74 0.00 30.94 2.57
3699 5730 3.064271 TCGCGGCAAGGTAATGTAAATTC 59.936 43.478 6.13 0.00 0.00 2.17
3723 5754 4.986659 GCAGCATTGTTTCTTTTGATCTGT 59.013 37.500 0.00 0.00 0.00 3.41
3728 5759 5.705609 TTGTTTCTTTTGATCTGTAGGCC 57.294 39.130 0.00 0.00 0.00 5.19
3739 5770 2.889512 TCTGTAGGCCAGAGTTTGAGA 58.110 47.619 5.01 0.00 45.34 3.27
3967 6292 6.324819 CGACTGAAATGTAGCATCCATTTTT 58.675 36.000 8.89 0.17 41.34 1.94
3990 6315 1.066757 TCTCTTGCTGCTATGAGCTCG 59.933 52.381 9.64 0.00 42.97 5.03
4010 6335 3.250280 TCGGCAGCGTGTTATTTTGTTAA 59.750 39.130 0.00 0.00 0.00 2.01
4011 6336 3.602062 CGGCAGCGTGTTATTTTGTTAAG 59.398 43.478 0.00 0.00 0.00 1.85
4012 6337 4.611807 CGGCAGCGTGTTATTTTGTTAAGA 60.612 41.667 0.00 0.00 0.00 2.10
4013 6338 5.216648 GGCAGCGTGTTATTTTGTTAAGAA 58.783 37.500 0.00 0.00 0.00 2.52
4014 6339 5.342259 GGCAGCGTGTTATTTTGTTAAGAAG 59.658 40.000 0.00 0.00 0.00 2.85
4015 6340 6.140110 GCAGCGTGTTATTTTGTTAAGAAGA 58.860 36.000 0.00 0.00 0.00 2.87
4016 6341 6.635239 GCAGCGTGTTATTTTGTTAAGAAGAA 59.365 34.615 0.00 0.00 0.00 2.52
4017 6342 7.326063 GCAGCGTGTTATTTTGTTAAGAAGAAT 59.674 33.333 0.00 0.00 0.00 2.40
4018 6343 8.840867 CAGCGTGTTATTTTGTTAAGAAGAATC 58.159 33.333 0.00 0.00 0.00 2.52
4019 6344 8.564574 AGCGTGTTATTTTGTTAAGAAGAATCA 58.435 29.630 0.00 0.00 0.00 2.57
4020 6345 8.840867 GCGTGTTATTTTGTTAAGAAGAATCAG 58.159 33.333 0.00 0.00 0.00 2.90
4021 6346 9.878599 CGTGTTATTTTGTTAAGAAGAATCAGT 57.121 29.630 0.00 0.00 0.00 3.41
4024 6349 9.052080 GTTATTTTGTTAAGAAGAATCAGTCGC 57.948 33.333 0.00 0.00 0.00 5.19
4025 6350 6.612247 TTTTGTTAAGAAGAATCAGTCGCA 57.388 33.333 0.00 0.00 0.00 5.10
4026 6351 6.612247 TTTGTTAAGAAGAATCAGTCGCAA 57.388 33.333 0.00 0.00 0.00 4.85
4027 6352 6.612247 TTGTTAAGAAGAATCAGTCGCAAA 57.388 33.333 0.00 0.00 0.00 3.68
4028 6353 6.612247 TGTTAAGAAGAATCAGTCGCAAAA 57.388 33.333 0.00 0.00 0.00 2.44
4029 6354 7.022055 TGTTAAGAAGAATCAGTCGCAAAAA 57.978 32.000 0.00 0.00 0.00 1.94
4119 6444 3.316308 AGTGATTTAATCGATGCCTTGGC 59.684 43.478 0.00 4.43 0.00 4.52
4267 6592 1.682854 CTCTGTCCTCTCCTGATCTGC 59.317 57.143 0.00 0.00 0.00 4.26
4289 6627 5.357878 TGCATCAGATTTATCAACACCCTTC 59.642 40.000 0.00 0.00 0.00 3.46
4297 6635 1.682740 TCAACACCCTTCGGTTTTCC 58.317 50.000 0.00 0.00 42.04 3.13
4298 6636 1.064611 TCAACACCCTTCGGTTTTCCA 60.065 47.619 0.00 0.00 42.04 3.53
4299 6637 1.336755 CAACACCCTTCGGTTTTCCAG 59.663 52.381 0.00 0.00 42.04 3.86
4316 6654 0.958876 CAGCACCAATCTCAGCAGCA 60.959 55.000 0.00 0.00 0.00 4.41
4340 6678 3.295973 GTCCCTTGTAGATCTCTCAGCT 58.704 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.067582 GTCATCATCGTCCGGACCC 59.932 63.158 28.52 5.39 0.00 4.46
91 92 3.368739 GGGTCTTTCCTGCCAAATCAATG 60.369 47.826 0.00 0.00 36.25 2.82
92 93 2.833943 GGGTCTTTCCTGCCAAATCAAT 59.166 45.455 0.00 0.00 36.25 2.57
103 104 1.454539 CCAACCACGGGTCTTTCCT 59.545 57.895 0.00 0.00 33.12 3.36
211 217 1.896660 ACAACGAGCCCGCAAACAT 60.897 52.632 0.00 0.00 39.95 2.71
215 221 4.555709 ACCACAACGAGCCCGCAA 62.556 61.111 0.00 0.00 39.95 4.85
233 239 3.485463 TGACTCCACTACAACAAAGGG 57.515 47.619 0.00 0.00 0.00 3.95
235 241 6.128007 ACAGTTTTGACTCCACTACAACAAAG 60.128 38.462 0.00 0.00 0.00 2.77
344 353 2.289195 ACCAGGAATAAACGAGCGACAA 60.289 45.455 0.00 0.00 0.00 3.18
428 438 1.081892 CACATCGAAGTGGCAGAAGG 58.918 55.000 12.86 0.00 35.88 3.46
483 494 1.928868 CCAATTCTCCCCAAGCAAGT 58.071 50.000 0.00 0.00 0.00 3.16
503 514 4.380841 TTGTACCTTAGTGGCATAGTCG 57.619 45.455 0.00 0.00 40.22 4.18
507 518 4.221262 ACGAGTTTGTACCTTAGTGGCATA 59.779 41.667 0.00 0.00 40.22 3.14
587 598 0.600557 CTGCACATACCCCGCAAAAA 59.399 50.000 0.00 0.00 34.75 1.94
588 599 0.538516 ACTGCACATACCCCGCAAAA 60.539 50.000 0.00 0.00 34.75 2.44
589 600 1.074072 ACTGCACATACCCCGCAAA 59.926 52.632 0.00 0.00 34.75 3.68
590 601 1.673993 CACTGCACATACCCCGCAA 60.674 57.895 0.00 0.00 34.75 4.85
591 602 2.046411 CACTGCACATACCCCGCA 60.046 61.111 0.00 0.00 0.00 5.69
592 603 1.815421 CTCACTGCACATACCCCGC 60.815 63.158 0.00 0.00 0.00 6.13
593 604 0.036388 AACTCACTGCACATACCCCG 60.036 55.000 0.00 0.00 0.00 5.73
594 605 1.271379 ACAACTCACTGCACATACCCC 60.271 52.381 0.00 0.00 0.00 4.95
595 606 2.185004 ACAACTCACTGCACATACCC 57.815 50.000 0.00 0.00 0.00 3.69
596 607 5.661458 ACTATACAACTCACTGCACATACC 58.339 41.667 0.00 0.00 0.00 2.73
597 608 7.596749 AAACTATACAACTCACTGCACATAC 57.403 36.000 0.00 0.00 0.00 2.39
630 641 7.381408 GTGTTGCCCAGTTAATTAGAGAAAAAC 59.619 37.037 0.00 0.00 0.00 2.43
724 2290 2.567615 AGTACACAGGGAGAAGCGAAAT 59.432 45.455 0.00 0.00 0.00 2.17
881 2472 1.216990 AAAGGAATCGATGGGCTCCT 58.783 50.000 10.08 10.08 40.10 3.69
902 2508 0.809636 CACCGATCGCTGCCACATTA 60.810 55.000 10.32 0.00 0.00 1.90
904 2510 2.512286 CACCGATCGCTGCCACAT 60.512 61.111 10.32 0.00 0.00 3.21
905 2511 4.758251 CCACCGATCGCTGCCACA 62.758 66.667 10.32 0.00 0.00 4.17
909 2515 3.567797 GAAGCCACCGATCGCTGC 61.568 66.667 10.32 11.42 34.94 5.25
993 2618 3.589881 GATGGCTGCATGGTCGCC 61.590 66.667 6.96 6.96 44.02 5.54
1055 2688 1.089978 TGAGGGAGGGAGAGGTAACA 58.910 55.000 0.00 0.00 41.41 2.41
1058 2691 1.394532 AAGTGAGGGAGGGAGAGGTA 58.605 55.000 0.00 0.00 0.00 3.08
1074 2707 1.730851 AGGAAGAGGACGGGAAAAGT 58.269 50.000 0.00 0.00 0.00 2.66
1083 2716 4.762251 ACAAATTTGCACTAGGAAGAGGAC 59.238 41.667 18.12 0.00 0.00 3.85
1222 2866 3.785859 GTGCATCTCGGCAGGGGA 61.786 66.667 0.00 0.00 45.96 4.81
1423 3201 5.802956 GCGAAATTCGATTGACCCAAATTAA 59.197 36.000 20.38 0.00 43.74 1.40
1436 3214 2.004583 TCCTTCACGCGAAATTCGAT 57.995 45.000 20.38 2.99 43.74 3.59
1559 3367 5.952947 CCCCTAAGATAGATAATGAGGTCGT 59.047 44.000 0.00 0.00 0.00 4.34
1742 3552 5.800296 TCATCTTCAACCTCAAATCGGTAA 58.200 37.500 0.00 0.00 33.53 2.85
1748 3558 6.014840 ACAATGCTTCATCTTCAACCTCAAAT 60.015 34.615 0.00 0.00 0.00 2.32
1791 3601 1.981495 CCCCCTCCTATCTCAACCATC 59.019 57.143 0.00 0.00 0.00 3.51
1858 3669 0.555769 GGGGGTGATATTTGGGAGCA 59.444 55.000 0.00 0.00 0.00 4.26
1964 3920 8.063200 ACAATTAAAATAAGCTACCCCAGAAC 57.937 34.615 0.00 0.00 0.00 3.01
2074 4031 3.601443 ACTTAGGCTCTTACTGCAGTG 57.399 47.619 29.57 13.80 0.00 3.66
2529 4511 0.397957 TGGAGCATTACGGGGAGCTA 60.398 55.000 0.00 0.00 37.48 3.32
2917 4905 2.771943 GTCCTCTCCCCATACAACATCA 59.228 50.000 0.00 0.00 0.00 3.07
3043 5049 3.128242 CGGCTGAAGAATCAAAGCAGAAT 59.872 43.478 0.00 0.00 34.49 2.40
3047 5053 2.183478 TCGGCTGAAGAATCAAAGCA 57.817 45.000 0.00 0.00 34.49 3.91
3596 5627 4.683832 ACTAACCAGTAGTCGATTGCATC 58.316 43.478 0.00 0.00 38.84 3.91
3699 5730 4.089493 CAGATCAAAAGAAACAATGCTGCG 59.911 41.667 0.00 0.00 0.00 5.18
3770 5801 3.518992 TCACTCTAAAGGTTTTGGGGG 57.481 47.619 0.00 0.00 0.00 5.40
3967 6292 3.937706 GAGCTCATAGCAGCAAGAGAAAA 59.062 43.478 9.40 0.00 45.56 2.29
3970 6295 1.066757 CGAGCTCATAGCAGCAAGAGA 59.933 52.381 15.40 0.00 45.56 3.10
3971 6296 1.489574 CGAGCTCATAGCAGCAAGAG 58.510 55.000 15.40 0.00 45.56 2.85
3975 6300 2.107750 GCCGAGCTCATAGCAGCA 59.892 61.111 15.40 0.00 45.56 4.41
3979 6304 3.034923 CGCTGCCGAGCTCATAGC 61.035 66.667 15.40 17.42 43.77 2.97
3990 6315 4.789784 TCTTAACAAAATAACACGCTGCC 58.210 39.130 0.00 0.00 0.00 4.85
4233 6558 6.731467 AGAGGACAGAGAAGAGAGAAACTAT 58.269 40.000 0.00 0.00 0.00 2.12
4248 6573 1.006400 TGCAGATCAGGAGAGGACAGA 59.994 52.381 0.00 0.00 0.00 3.41
4267 6592 6.052840 CGAAGGGTGTTGATAAATCTGATG 57.947 41.667 0.00 0.00 0.00 3.07
4289 6627 1.200020 GAGATTGGTGCTGGAAAACCG 59.800 52.381 0.00 0.00 39.47 4.44
4297 6635 0.958876 TGCTGCTGAGATTGGTGCTG 60.959 55.000 0.00 0.00 0.00 4.41
4298 6636 0.251033 TTGCTGCTGAGATTGGTGCT 60.251 50.000 0.00 0.00 0.00 4.40
4299 6637 0.109412 GTTGCTGCTGAGATTGGTGC 60.109 55.000 0.00 0.00 0.00 5.01
4316 6654 3.697045 CTGAGAGATCTACAAGGGACGTT 59.303 47.826 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.