Multiple sequence alignment - TraesCS3B01G208300

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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 TraesCS3B01G208300 chr3B 100.000 4705 0 0 1 4705 244387257 244382553 0.000000e+00 8689.0
1 TraesCS3B01G208300 chr3B 97.368 76 2 0 4179 4254 244383041 244382966 3.820000e-26 130.0
2 TraesCS3B01G208300 chr3B 97.368 76 2 0 4217 4292 244383079 244383004 3.820000e-26 130.0
3 TraesCS3B01G208300 chr3B 94.737 38 2 0 4179 4216 244383003 244382966 5.080000e-05 60.2
4 TraesCS3B01G208300 chr3B 94.737 38 2 0 4255 4292 244383079 244383042 5.080000e-05 60.2
5 TraesCS3B01G208300 chr3D 96.060 2868 76 15 1409 4254 169450166 169447314 0.000000e+00 4636.0
6 TraesCS3B01G208300 chr3D 92.842 1411 49 23 1 1371 169451860 169450462 0.000000e+00 1999.0
7 TraesCS3B01G208300 chr3D 94.845 485 14 5 4224 4705 169447382 169446906 0.000000e+00 747.0
8 TraesCS3B01G208300 chr3D 100.000 31 0 0 4262 4292 169447382 169447352 1.830000e-04 58.4
9 TraesCS3B01G208300 chr3A 95.857 2872 87 15 1409 4254 197850952 197853817 0.000000e+00 4615.0
10 TraesCS3B01G208300 chr3A 90.729 1413 80 22 1 1371 197849257 197850660 0.000000e+00 1836.0
11 TraesCS3B01G208300 chr3A 92.771 249 14 1 4217 4465 197853742 197853986 1.610000e-94 357.0
12 TraesCS3B01G208300 chr3A 85.572 201 8 2 4505 4705 197854064 197854243 1.730000e-44 191.0
13 TraesCS3B01G208300 chr3A 94.737 38 2 0 4255 4292 197853742 197853779 5.080000e-05 60.2
14 TraesCS3B01G208300 chr3A 94.737 38 2 0 4179 4216 197853780 197853817 5.080000e-05 60.2


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 TraesCS3B01G208300 chr3B 244382553 244387257 4704 True 8689.000000 8689 100.00000 1 4705 1 chr3B.!!$R1 4704
1 TraesCS3B01G208300 chr3D 169446906 169451860 4954 True 1860.100000 4636 95.93675 1 4705 4 chr3D.!!$R1 4704
2 TraesCS3B01G208300 chr3A 197849257 197854243 4986 False 1186.566667 4615 92.40050 1 4705 6 chr3A.!!$F1 4704

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
901 924 0.468400 GAGAGAGGGGGTACTGCGAT 60.468 60.000 0.00 0.0 0.00 4.58 F
1284 1331 0.032130 TGAGCCTTCTCGTGTCACAC 59.968 55.000 0.00 0.0 42.26 3.82 F
2809 3132 1.207329 CTGGACCTGGTGTTAGTAGCC 59.793 57.143 2.82 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2495 1.805345 GATGATGCAGCAGTATCTGGC 59.195 52.381 11.66 0.0 37.69 4.85 R
2965 3301 0.034670 ATGCCCAGCAGAAAGGAGAC 60.035 55.000 0.00 0.0 43.65 3.36 R
3872 4222 0.734889 GGGAATCAATGTCCTGCACG 59.265 55.000 0.00 0.0 35.33 5.34 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
189 198 4.039357 ACGTCTCACCTCACGCGG 62.039 66.667 12.47 0.00 39.73 6.46
559 581 1.153469 GAGAAGAGGCGCCTTCCTG 60.153 63.158 33.34 0.00 42.58 3.86
586 608 4.645921 GCTTTTGCCGCGGTTGCT 62.646 61.111 28.70 0.00 40.15 3.91
707 730 1.610327 CTCCTCTCCTCGAGTCCCA 59.390 63.158 12.31 0.00 38.11 4.37
746 769 3.097162 GATTCGGGGCCCCTTCCT 61.097 66.667 38.17 19.98 0.00 3.36
755 778 2.434331 CCCCTTCCTGCGAAACCA 59.566 61.111 0.00 0.00 0.00 3.67
898 921 1.762858 GGGAGAGAGGGGGTACTGC 60.763 68.421 0.00 0.00 0.00 4.40
899 922 2.128507 GGAGAGAGGGGGTACTGCG 61.129 68.421 0.00 0.00 0.00 5.18
901 924 0.468400 GAGAGAGGGGGTACTGCGAT 60.468 60.000 0.00 0.00 0.00 4.58
903 926 1.217183 AGAGAGGGGGTACTGCGATAA 59.783 52.381 0.00 0.00 0.00 1.75
904 927 1.614413 GAGAGGGGGTACTGCGATAAG 59.386 57.143 0.00 0.00 0.00 1.73
906 929 2.037144 GAGGGGGTACTGCGATAAGAA 58.963 52.381 0.00 0.00 0.00 2.52
909 932 3.577415 AGGGGGTACTGCGATAAGAATAC 59.423 47.826 0.00 0.00 0.00 1.89
910 933 3.577415 GGGGGTACTGCGATAAGAATACT 59.423 47.826 0.00 0.00 0.00 2.12
911 934 4.768968 GGGGGTACTGCGATAAGAATACTA 59.231 45.833 0.00 0.00 0.00 1.82
912 935 5.421374 GGGGGTACTGCGATAAGAATACTAT 59.579 44.000 0.00 0.00 0.00 2.12
913 936 6.604795 GGGGGTACTGCGATAAGAATACTATA 59.395 42.308 0.00 0.00 0.00 1.31
914 937 7.123247 GGGGGTACTGCGATAAGAATACTATAA 59.877 40.741 0.00 0.00 0.00 0.98
953 976 3.953612 TCTGCACAGTTTCAAAATCACCT 59.046 39.130 0.00 0.00 0.00 4.00
1171 1194 3.222603 CCATGGGATTTACCTGGTAAGC 58.777 50.000 18.02 14.14 38.98 3.09
1175 1198 3.785887 TGGGATTTACCTGGTAAGCTGAT 59.214 43.478 18.02 9.83 38.98 2.90
1217 1240 6.889177 TGCCTGTGATTATTTTGGTTCATAGA 59.111 34.615 0.00 0.00 31.30 1.98
1241 1264 9.232473 AGAAAAATACAGTATGGAGGAGAAAAC 57.768 33.333 0.00 0.00 43.62 2.43
1242 1265 8.934023 AAAAATACAGTATGGAGGAGAAAACA 57.066 30.769 0.00 0.00 43.62 2.83
1248 1271 7.162082 ACAGTATGGAGGAGAAAACAGTTTAG 58.838 38.462 0.00 0.00 43.62 1.85
1255 1302 7.282450 TGGAGGAGAAAACAGTTTAGTTTCTTC 59.718 37.037 0.00 0.00 40.60 2.87
1284 1331 0.032130 TGAGCCTTCTCGTGTCACAC 59.968 55.000 0.00 0.00 42.26 3.82
1288 1335 1.461127 GCCTTCTCGTGTCACACAATC 59.539 52.381 9.06 0.00 33.40 2.67
1297 1344 8.130307 TCTCGTGTCACACAATCATAATTATG 57.870 34.615 17.82 17.82 33.40 1.90
1366 1414 6.704310 ACGTGACATATACCCTTGTTTAACT 58.296 36.000 0.00 0.00 0.00 2.24
1406 1723 9.490379 AATCTTAATACTGTTTGTCTTTCGTCT 57.510 29.630 0.00 0.00 0.00 4.18
1454 1772 7.907214 ATGATGTAGTTTCTTTGTCAGTACC 57.093 36.000 0.00 0.00 0.00 3.34
1455 1773 5.924254 TGATGTAGTTTCTTTGTCAGTACCG 59.076 40.000 0.00 0.00 0.00 4.02
1456 1774 4.624015 TGTAGTTTCTTTGTCAGTACCGG 58.376 43.478 0.00 0.00 0.00 5.28
1463 1781 3.896888 TCTTTGTCAGTACCGGTCCTTTA 59.103 43.478 12.40 0.00 0.00 1.85
1471 1789 4.750098 CAGTACCGGTCCTTTAGCATTATG 59.250 45.833 12.40 0.00 0.00 1.90
1488 1806 6.264067 AGCATTATGGAGGATTTACTTTCTGC 59.736 38.462 0.00 0.00 0.00 4.26
1513 1831 7.385205 GCTTTTAGTATCCGATGCATTCTAGAA 59.615 37.037 7.82 7.82 0.00 2.10
1520 1838 7.856145 ATCCGATGCATTCTAGAATTTATCC 57.144 36.000 15.49 3.90 0.00 2.59
1523 1841 5.349817 CGATGCATTCTAGAATTTATCCGCT 59.650 40.000 15.49 5.36 0.00 5.52
1540 1858 2.554032 CCGCTGTGTTCTTCAAATCCTT 59.446 45.455 0.00 0.00 0.00 3.36
1547 1870 8.178313 GCTGTGTTCTTCAAATCCTTATCTAAC 58.822 37.037 0.00 0.00 0.00 2.34
1560 1883 9.796242 AATCCTTATCTAACCCTCTGATGATAT 57.204 33.333 0.00 0.00 0.00 1.63
1562 1885 9.261035 TCCTTATCTAACCCTCTGATGATATTC 57.739 37.037 0.00 0.00 0.00 1.75
1574 1897 5.928264 TCTGATGATATTCCATGTTACAGCG 59.072 40.000 0.00 0.00 0.00 5.18
1592 1915 1.268999 GCGAAGTGCAATGTTCCAACA 60.269 47.619 0.00 0.00 45.45 3.33
1722 2045 2.105821 CGGGCCATTAAGGTGGATAAGA 59.894 50.000 4.39 0.00 42.02 2.10
1833 2156 8.417106 ACTACATAGATGAGAACGAATGTCAAT 58.583 33.333 0.00 0.00 34.60 2.57
1922 2245 6.094719 CAGCATGAGAGAGCTAGATACATTC 58.905 44.000 0.00 0.00 39.50 2.67
2172 2495 5.484173 TTTTAGCTGTCAGTGTTGAACAG 57.516 39.130 0.00 5.53 36.44 3.16
2249 2572 1.615883 CGTAGCTATCCCTGCTCACAT 59.384 52.381 0.00 0.00 41.46 3.21
2250 2573 2.608998 CGTAGCTATCCCTGCTCACATG 60.609 54.545 0.00 0.00 41.46 3.21
2384 2707 5.808540 CGGATGAACAAAATGCTGAATCATT 59.191 36.000 0.00 0.00 38.23 2.57
2396 2719 8.467963 AATGCTGAATCATTGGTATGTTATCA 57.532 30.769 0.00 0.00 35.52 2.15
2539 2862 2.836479 TTTGATCTCATGCATGTGCG 57.164 45.000 25.43 15.11 45.83 5.34
2674 2997 7.795431 ACAAATGAGTTTATTTATGCACACG 57.205 32.000 0.00 0.00 0.00 4.49
2809 3132 1.207329 CTGGACCTGGTGTTAGTAGCC 59.793 57.143 2.82 0.00 0.00 3.93
3520 3857 6.775088 AGAAACATGTGCGTGATATTACTTG 58.225 36.000 0.00 0.00 0.00 3.16
3573 3910 5.395214 GGAAGTCACAACAACCAAGGATTTT 60.395 40.000 0.00 0.00 0.00 1.82
3904 4254 7.175641 GGACATTGATTCCCTTATATCTGGTTG 59.824 40.741 0.00 0.00 0.00 3.77
4078 4429 5.245531 TCTGAACCATAGTTAACAGCTTGG 58.754 41.667 8.61 10.76 35.94 3.61
4110 4461 7.355778 GTCATCTTTTTCATTCGAGTTGAACT 58.644 34.615 11.18 0.00 40.00 3.01
4118 4469 9.667107 TTTTCATTCGAGTTGAACTAAGGATAT 57.333 29.630 11.18 0.00 40.00 1.63
4175 4528 9.107177 CTCTATGGATTACAGCATTATTGGATC 57.893 37.037 0.00 0.00 0.00 3.36
4232 4585 6.785488 TTGCTTGAGTACTACTGTCATTTG 57.215 37.500 0.00 0.00 0.00 2.32
4233 4586 6.096673 TGCTTGAGTACTACTGTCATTTGA 57.903 37.500 0.00 0.00 0.00 2.69
4234 4587 6.521162 TGCTTGAGTACTACTGTCATTTGAA 58.479 36.000 0.00 0.00 0.00 2.69
4235 4588 6.646653 TGCTTGAGTACTACTGTCATTTGAAG 59.353 38.462 0.00 0.00 0.00 3.02
4236 4589 6.401581 GCTTGAGTACTACTGTCATTTGAAGC 60.402 42.308 0.00 0.00 0.00 3.86
4237 4590 5.161358 TGAGTACTACTGTCATTTGAAGCG 58.839 41.667 0.00 0.00 0.00 4.68
4238 4591 5.048294 TGAGTACTACTGTCATTTGAAGCGA 60.048 40.000 0.00 0.00 0.00 4.93
4239 4592 5.967088 AGTACTACTGTCATTTGAAGCGAT 58.033 37.500 0.00 0.00 0.00 4.58
4240 4593 5.807520 AGTACTACTGTCATTTGAAGCGATG 59.192 40.000 0.00 0.00 0.00 3.84
4241 4594 4.820897 ACTACTGTCATTTGAAGCGATGA 58.179 39.130 0.00 0.00 0.00 2.92
4245 4598 3.395858 GTCATTTGAAGCGATGACCTG 57.604 47.619 5.41 0.00 43.92 4.00
4246 4599 2.744202 GTCATTTGAAGCGATGACCTGT 59.256 45.455 5.41 0.00 43.92 4.00
4247 4600 3.189287 GTCATTTGAAGCGATGACCTGTT 59.811 43.478 5.41 0.00 43.92 3.16
4248 4601 3.820467 TCATTTGAAGCGATGACCTGTTT 59.180 39.130 0.00 0.00 0.00 2.83
4249 4602 3.624326 TTTGAAGCGATGACCTGTTTG 57.376 42.857 0.00 0.00 0.00 2.93
4250 4603 0.874390 TGAAGCGATGACCTGTTTGC 59.126 50.000 0.00 0.00 0.00 3.68
4251 4604 1.160137 GAAGCGATGACCTGTTTGCT 58.840 50.000 0.00 0.00 0.00 3.91
4252 4605 1.537202 GAAGCGATGACCTGTTTGCTT 59.463 47.619 0.00 0.00 44.59 3.91
4253 4606 0.877071 AGCGATGACCTGTTTGCTTG 59.123 50.000 0.00 0.00 0.00 4.01
4254 4607 0.874390 GCGATGACCTGTTTGCTTGA 59.126 50.000 0.00 0.00 0.00 3.02
4255 4608 1.135859 GCGATGACCTGTTTGCTTGAG 60.136 52.381 0.00 0.00 0.00 3.02
4256 4609 2.146342 CGATGACCTGTTTGCTTGAGT 58.854 47.619 0.00 0.00 0.00 3.41
4257 4610 3.325870 CGATGACCTGTTTGCTTGAGTA 58.674 45.455 0.00 0.00 0.00 2.59
4258 4611 3.123621 CGATGACCTGTTTGCTTGAGTAC 59.876 47.826 0.00 0.00 0.00 2.73
4259 4612 3.838244 TGACCTGTTTGCTTGAGTACT 57.162 42.857 0.00 0.00 0.00 2.73
4260 4613 4.948341 TGACCTGTTTGCTTGAGTACTA 57.052 40.909 0.00 0.00 0.00 1.82
4261 4614 4.628074 TGACCTGTTTGCTTGAGTACTAC 58.372 43.478 0.00 0.00 0.00 2.73
4262 4615 4.344102 TGACCTGTTTGCTTGAGTACTACT 59.656 41.667 0.00 0.00 0.00 2.57
4263 4616 4.632153 ACCTGTTTGCTTGAGTACTACTG 58.368 43.478 0.00 0.00 0.00 2.74
4264 4617 4.101119 ACCTGTTTGCTTGAGTACTACTGT 59.899 41.667 0.00 0.00 0.00 3.55
4265 4618 4.686554 CCTGTTTGCTTGAGTACTACTGTC 59.313 45.833 0.00 0.00 0.00 3.51
4266 4619 5.270893 TGTTTGCTTGAGTACTACTGTCA 57.729 39.130 0.00 0.00 0.00 3.58
4267 4620 5.853936 TGTTTGCTTGAGTACTACTGTCAT 58.146 37.500 0.00 0.00 0.00 3.06
4268 4621 6.288294 TGTTTGCTTGAGTACTACTGTCATT 58.712 36.000 0.00 0.00 0.00 2.57
4269 4622 6.765989 TGTTTGCTTGAGTACTACTGTCATTT 59.234 34.615 0.00 0.00 0.00 2.32
4352 4705 8.964150 GTATGACAGCTAAAACAACGAAAATTT 58.036 29.630 0.00 0.00 0.00 1.82
4399 4752 5.030295 GTCTATTGATTTGCACGGTGATTG 58.970 41.667 13.29 0.00 0.00 2.67
4413 4766 2.630580 GGTGATTGGGGCACTTGTTTTA 59.369 45.455 0.00 0.00 36.53 1.52
4416 4769 3.706594 TGATTGGGGCACTTGTTTTAACA 59.293 39.130 0.00 0.00 37.08 2.41
4583 4995 8.782339 TTAATTCCCTCTTTACTCTTAAACCG 57.218 34.615 0.00 0.00 0.00 4.44
4635 5047 7.811117 TCAAATCCTTCTTTCTTAAACCGAA 57.189 32.000 0.00 0.00 0.00 4.30
4655 5067 6.127897 ACCGAATCTTCTTTTCAATCATGTCC 60.128 38.462 0.00 0.00 0.00 4.02
4688 5100 9.667107 TTGATATTGTTTACCTTCTTACTCTGG 57.333 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 198 3.738745 AAGGGAATGGGATGCGGGC 62.739 63.158 0.00 0.00 0.00 6.13
191 200 0.746659 GAAAAGGGAATGGGATGCGG 59.253 55.000 0.00 0.00 0.00 5.69
586 608 1.758440 AACCAACGAGAGCTCTGCCA 61.758 55.000 23.91 0.00 0.00 4.92
707 730 1.153784 CTCCGCATGCGCCAAAATT 60.154 52.632 34.00 0.00 38.24 1.82
837 860 3.477530 GGGATCCATTAGTACTGCAACC 58.522 50.000 15.23 0.17 0.00 3.77
911 934 8.947115 GTGCAGAGTAATTAGAACCACTTTTAT 58.053 33.333 0.00 0.00 0.00 1.40
912 935 7.934665 TGTGCAGAGTAATTAGAACCACTTTTA 59.065 33.333 0.00 0.00 0.00 1.52
913 936 6.770785 TGTGCAGAGTAATTAGAACCACTTTT 59.229 34.615 0.00 0.00 0.00 2.27
914 937 6.296026 TGTGCAGAGTAATTAGAACCACTTT 58.704 36.000 0.00 0.00 0.00 2.66
968 991 4.002982 TCTGCGCAAGAATAACAGAACAT 58.997 39.130 13.05 0.00 43.02 2.71
1050 1073 2.364324 AGCAACGAGTTCAGTGTCCTTA 59.636 45.455 0.00 0.00 0.00 2.69
1171 1194 5.123502 GGCAACCATATAGAAGCATCATCAG 59.876 44.000 0.00 0.00 0.00 2.90
1175 1198 4.141413 ACAGGCAACCATATAGAAGCATCA 60.141 41.667 0.00 0.00 37.17 3.07
1217 1240 8.934023 TGTTTTCTCCTCCATACTGTATTTTT 57.066 30.769 0.00 0.00 0.00 1.94
1241 1264 8.405531 TCAATTTGTGGAGAAGAAACTAAACTG 58.594 33.333 0.00 0.00 0.00 3.16
1242 1265 8.519799 TCAATTTGTGGAGAAGAAACTAAACT 57.480 30.769 0.00 0.00 0.00 2.66
1248 1271 4.279420 AGGCTCAATTTGTGGAGAAGAAAC 59.721 41.667 0.00 0.00 32.87 2.78
1255 1302 2.417933 CGAGAAGGCTCAATTTGTGGAG 59.582 50.000 0.00 0.00 41.36 3.86
1297 1344 9.574516 AAATGTCTAGTTATGATTCATTACCCC 57.425 33.333 11.19 0.45 0.00 4.95
1324 1372 7.934457 TGTCACGTTCTTTAGTTACTCTTACT 58.066 34.615 0.00 0.00 0.00 2.24
1433 1751 5.221581 ACCGGTACTGACAAAGAAACTACAT 60.222 40.000 4.49 0.00 0.00 2.29
1438 1756 2.804527 GGACCGGTACTGACAAAGAAAC 59.195 50.000 10.47 0.00 0.00 2.78
1454 1772 3.071023 TCCTCCATAATGCTAAAGGACCG 59.929 47.826 0.00 0.00 0.00 4.79
1455 1773 4.706842 TCCTCCATAATGCTAAAGGACC 57.293 45.455 0.00 0.00 0.00 4.46
1456 1774 7.939588 AGTAAATCCTCCATAATGCTAAAGGAC 59.060 37.037 0.00 0.00 35.84 3.85
1463 1781 6.264067 GCAGAAAGTAAATCCTCCATAATGCT 59.736 38.462 0.00 0.00 0.00 3.79
1471 1789 7.689446 ACTAAAAGCAGAAAGTAAATCCTCC 57.311 36.000 0.00 0.00 0.00 4.30
1488 1806 8.818141 TTCTAGAATGCATCGGATACTAAAAG 57.182 34.615 0.00 0.00 0.00 2.27
1513 1831 5.957842 TTTGAAGAACACAGCGGATAAAT 57.042 34.783 0.00 0.00 0.00 1.40
1520 1838 3.904136 AAGGATTTGAAGAACACAGCG 57.096 42.857 0.00 0.00 0.00 5.18
1523 1841 7.610305 GGGTTAGATAAGGATTTGAAGAACACA 59.390 37.037 0.00 0.00 0.00 3.72
1540 1858 8.985922 CATGGAATATCATCAGAGGGTTAGATA 58.014 37.037 0.00 0.00 0.00 1.98
1547 1870 6.772605 TGTAACATGGAATATCATCAGAGGG 58.227 40.000 0.00 0.00 0.00 4.30
1560 1883 1.804151 GCACTTCGCTGTAACATGGAA 59.196 47.619 0.00 0.00 37.77 3.53
1562 1885 1.155889 TGCACTTCGCTGTAACATGG 58.844 50.000 0.00 0.00 43.06 3.66
1574 1897 3.374745 CTGTGTTGGAACATTGCACTTC 58.625 45.455 0.00 0.00 41.59 3.01
1592 1915 4.666512 AGAAATGCCACTTGTTATCCTGT 58.333 39.130 0.00 0.00 0.00 4.00
1722 2045 5.953571 AGTTTTCTTTGTTCCTATGGTCCT 58.046 37.500 0.00 0.00 0.00 3.85
1833 2156 2.196742 ACCTTCATATCAGGGCAGGA 57.803 50.000 3.03 0.00 35.46 3.86
1922 2245 6.321717 ACATAACATGTAAAAGATGCAACGG 58.678 36.000 0.00 0.00 42.78 4.44
2172 2495 1.805345 GATGATGCAGCAGTATCTGGC 59.195 52.381 11.66 0.00 37.69 4.85
2249 2572 3.135348 GTCATCATTCCCATCTGGAGTCA 59.865 47.826 0.00 0.00 46.24 3.41
2250 2573 3.495806 GGTCATCATTCCCATCTGGAGTC 60.496 52.174 0.00 0.00 46.24 3.36
2384 2707 4.222810 ACTGCTGTGAGTGATAACATACCA 59.777 41.667 0.00 0.00 0.00 3.25
2396 2719 4.543590 AATACTAAGCACTGCTGTGAGT 57.456 40.909 25.94 20.78 46.55 3.41
2476 2799 6.942532 TGGCTTGCAAAATCTACCTAATAG 57.057 37.500 0.00 0.00 0.00 1.73
2539 2862 2.846193 TCAACTACCACCAAGCAACTC 58.154 47.619 0.00 0.00 0.00 3.01
2674 2997 7.854534 AGCACTGCAATTTAGATTTTGTTTTC 58.145 30.769 3.30 0.00 0.00 2.29
2809 3132 9.167311 ACATAAGCTAGTTTAAGGAATTGACAG 57.833 33.333 2.95 0.00 0.00 3.51
2965 3301 0.034670 ATGCCCAGCAGAAAGGAGAC 60.035 55.000 0.00 0.00 43.65 3.36
3455 3792 5.360999 AGTCATGAGATCAAGATGACCGTTA 59.639 40.000 19.98 0.00 44.74 3.18
3520 3857 2.404995 GCATCAGACTGCCTGGCAC 61.405 63.158 19.30 9.44 43.12 5.01
3573 3910 2.434331 CCTTTGGACGCCCCTGAA 59.566 61.111 0.00 0.00 35.38 3.02
3689 4026 3.508012 CCCTCTACTACAATCTGATCCCG 59.492 52.174 0.00 0.00 0.00 5.14
3698 4035 4.834406 TCTGATCCCCCTCTACTACAAT 57.166 45.455 0.00 0.00 0.00 2.71
3867 4217 1.256812 TCAATGTCCTGCACGAGAGA 58.743 50.000 0.00 0.00 0.00 3.10
3872 4222 0.734889 GGGAATCAATGTCCTGCACG 59.265 55.000 0.00 0.00 35.33 5.34
3904 4254 4.096231 TCATATGTACAAACACCATGCAGC 59.904 41.667 0.00 0.00 38.78 5.25
3947 4297 5.190528 CCATCACCATAATACCTAGCCAGAT 59.809 44.000 0.00 0.00 0.00 2.90
4024 4374 9.979578 CAAATCTAGCATGTAGTAAGAGAGAAT 57.020 33.333 0.00 0.00 0.00 2.40
4037 4388 6.595716 GGTTCAGAGTTACAAATCTAGCATGT 59.404 38.462 0.00 0.00 31.29 3.21
4078 4429 6.106673 TCGAATGAAAAAGATGACCCTACTC 58.893 40.000 0.00 0.00 0.00 2.59
4147 4498 8.097038 TCCAATAATGCTGTAATCCATAGAGAC 58.903 37.037 0.00 0.00 0.00 3.36
4232 4585 1.160137 AGCAAACAGGTCATCGCTTC 58.840 50.000 0.00 0.00 0.00 3.86
4233 4586 1.267806 CAAGCAAACAGGTCATCGCTT 59.732 47.619 0.00 0.00 40.16 4.68
4234 4587 0.877071 CAAGCAAACAGGTCATCGCT 59.123 50.000 0.00 0.00 0.00 4.93
4235 4588 0.874390 TCAAGCAAACAGGTCATCGC 59.126 50.000 0.00 0.00 0.00 4.58
4236 4589 2.146342 ACTCAAGCAAACAGGTCATCG 58.854 47.619 0.00 0.00 0.00 3.84
4237 4590 4.319177 AGTACTCAAGCAAACAGGTCATC 58.681 43.478 0.00 0.00 0.00 2.92
4238 4591 4.357918 AGTACTCAAGCAAACAGGTCAT 57.642 40.909 0.00 0.00 0.00 3.06
4239 4592 3.838244 AGTACTCAAGCAAACAGGTCA 57.162 42.857 0.00 0.00 0.00 4.02
4240 4593 4.686554 CAGTAGTACTCAAGCAAACAGGTC 59.313 45.833 0.00 0.00 0.00 3.85
4241 4594 4.101119 ACAGTAGTACTCAAGCAAACAGGT 59.899 41.667 0.00 0.00 0.00 4.00
4242 4595 4.632153 ACAGTAGTACTCAAGCAAACAGG 58.368 43.478 0.00 0.00 0.00 4.00
4243 4596 5.289595 TGACAGTAGTACTCAAGCAAACAG 58.710 41.667 0.00 0.00 0.00 3.16
4244 4597 5.270893 TGACAGTAGTACTCAAGCAAACA 57.729 39.130 0.00 0.00 0.00 2.83
4245 4598 6.787085 AATGACAGTAGTACTCAAGCAAAC 57.213 37.500 0.00 0.00 0.00 2.93
4246 4599 6.989759 TCAAATGACAGTAGTACTCAAGCAAA 59.010 34.615 0.00 0.00 0.00 3.68
4247 4600 6.521162 TCAAATGACAGTAGTACTCAAGCAA 58.479 36.000 0.00 0.00 0.00 3.91
4248 4601 6.096673 TCAAATGACAGTAGTACTCAAGCA 57.903 37.500 0.00 0.00 0.00 3.91
4249 4602 6.401581 GCTTCAAATGACAGTAGTACTCAAGC 60.402 42.308 0.00 0.00 0.00 4.01
4250 4603 6.183360 CGCTTCAAATGACAGTAGTACTCAAG 60.183 42.308 0.00 0.00 0.00 3.02
4251 4604 5.633601 CGCTTCAAATGACAGTAGTACTCAA 59.366 40.000 0.00 0.00 0.00 3.02
4252 4605 5.048294 TCGCTTCAAATGACAGTAGTACTCA 60.048 40.000 0.00 0.00 0.00 3.41
4253 4606 5.399858 TCGCTTCAAATGACAGTAGTACTC 58.600 41.667 0.00 0.00 0.00 2.59
4254 4607 5.386958 TCGCTTCAAATGACAGTAGTACT 57.613 39.130 0.00 0.00 0.00 2.73
4255 4608 5.805486 TCATCGCTTCAAATGACAGTAGTAC 59.195 40.000 0.00 0.00 0.00 2.73
4256 4609 5.961272 TCATCGCTTCAAATGACAGTAGTA 58.039 37.500 0.00 0.00 0.00 1.82
4257 4610 4.820897 TCATCGCTTCAAATGACAGTAGT 58.179 39.130 0.00 0.00 0.00 2.73
4264 4617 3.057969 ACAGGTCATCGCTTCAAATGA 57.942 42.857 0.00 0.00 0.00 2.57
4265 4618 3.837213 AACAGGTCATCGCTTCAAATG 57.163 42.857 0.00 0.00 0.00 2.32
4266 4619 3.612479 GCAAACAGGTCATCGCTTCAAAT 60.612 43.478 0.00 0.00 0.00 2.32
4267 4620 2.287547 GCAAACAGGTCATCGCTTCAAA 60.288 45.455 0.00 0.00 0.00 2.69
4268 4621 1.266718 GCAAACAGGTCATCGCTTCAA 59.733 47.619 0.00 0.00 0.00 2.69
4269 4622 0.874390 GCAAACAGGTCATCGCTTCA 59.126 50.000 0.00 0.00 0.00 3.02
4327 4680 8.963130 CAAATTTTCGTTGTTTTAGCTGTCATA 58.037 29.630 0.00 0.00 0.00 2.15
4399 4752 4.394439 TTTCTGTTAAAACAAGTGCCCC 57.606 40.909 0.00 0.00 38.66 5.80
4413 4766 8.776376 TTTCTCTTTTTCAAGCAATTTCTGTT 57.224 26.923 0.00 0.00 0.00 3.16
4475 4884 8.108172 CGAAGTAGTACAAGATAAACGTACGTA 58.892 37.037 23.12 7.43 40.32 3.57
4476 4885 6.955963 CGAAGTAGTACAAGATAAACGTACGT 59.044 38.462 16.72 16.72 40.32 3.57
4583 4995 4.072839 ACGGAGGATTGAAAAGAAGAACC 58.927 43.478 0.00 0.00 0.00 3.62
4655 5067 8.469309 AGAAGGTAAACAATATCAATGGATGG 57.531 34.615 0.00 0.00 34.89 3.51


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

AutoCloner maintained by Alex Coulton.