Multiple sequence alignment - TraesCS6A01G325900

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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 TraesCS6A01G325900 chr6A 100.000 3235 0 0 1 3235 559400455 559403689 0.000000e+00 5975.0
1 TraesCS6A01G325900 chr6D 85.763 1749 146 43 17 1702 414463880 414465588 0.000000e+00 1755.0
2 TraesCS6A01G325900 chr6D 87.828 953 66 18 1727 2644 414466073 414467010 0.000000e+00 1072.0
3 TraesCS6A01G325900 chr6D 92.522 575 27 6 2661 3228 414466994 414467559 0.000000e+00 809.0
4 TraesCS6A01G325900 chr6B 84.063 1644 117 58 147 1703 624780494 624782079 0.000000e+00 1450.0
5 TraesCS6A01G325900 chr6B 86.247 1287 93 41 1977 3235 624785067 624786297 0.000000e+00 1319.0
6 TraesCS6A01G325900 chr6B 80.156 257 23 14 1726 1959 624784744 624784995 2.000000e-37 167.0
7 TraesCS6A01G325900 chr4D 75.776 161 26 3 1 161 129768543 129768396 5.790000e-08 69.4
8 TraesCS6A01G325900 chr7D 89.362 47 5 0 123 169 106922044 106921998 3.490000e-05 60.2
9 TraesCS6A01G325900 chr7A 89.362 47 5 0 123 169 112340284 112340238 3.490000e-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 TraesCS6A01G325900 chr6A 559400455 559403689 3234 False 5975.000000 5975 100.000000 1 3235 1 chr6A.!!$F1 3234
1 TraesCS6A01G325900 chr6D 414463880 414467559 3679 False 1212.000000 1755 88.704333 17 3228 3 chr6D.!!$F1 3211
2 TraesCS6A01G325900 chr6B 624780494 624786297 5803 False 978.666667 1450 83.488667 147 3235 3 chr6B.!!$F1 3088

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
90 91 0.033504 GTGTTGTCTTCCTCTCGCCA 59.966 55.0 0.00 0.0 0.00 5.69 F
381 406 0.040067 GGAAGTTCTTGGCTTGCACG 60.040 55.0 2.25 0.0 34.95 5.34 F
1336 1438 0.176219 TGTTGCTTGCTTGCTTGCTT 59.824 45.0 10.35 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 4629 0.031857 TGTGTGATTTTGCGGCCTTG 59.968 50.0 0.00 0.00 0.0 3.61 R
2140 5016 0.173481 TCGAAGAGCTCCATGAACCG 59.827 55.0 10.93 4.05 0.0 4.44 R
3063 5991 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.0 0.00 0.00 0.0 3.71 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
43 44 2.631160 ACGAAAGTGTGGGATTGTCA 57.369 45.000 0.00 0.00 46.97 3.58
44 45 3.140325 ACGAAAGTGTGGGATTGTCAT 57.860 42.857 0.00 0.00 46.97 3.06
51 52 3.131396 GTGTGGGATTGTCATATCGTCC 58.869 50.000 0.00 0.00 0.00 4.79
74 75 1.203001 ACGGTGGGATTTTGATGGTGT 60.203 47.619 0.00 0.00 0.00 4.16
81 82 4.280677 TGGGATTTTGATGGTGTTGTCTTC 59.719 41.667 0.00 0.00 0.00 2.87
90 91 0.033504 GTGTTGTCTTCCTCTCGCCA 59.966 55.000 0.00 0.00 0.00 5.69
91 92 0.976641 TGTTGTCTTCCTCTCGCCAT 59.023 50.000 0.00 0.00 0.00 4.40
105 106 2.440796 CCATGCGGTCAATGGCCT 60.441 61.111 3.32 0.00 0.00 5.19
121 122 1.596934 CCTCGCTCAGCTTTGGGTA 59.403 57.895 0.00 0.00 0.00 3.69
125 126 0.798776 CGCTCAGCTTTGGGTAACTG 59.201 55.000 0.00 0.00 0.00 3.16
151 153 2.197283 TGCTTGGTGTGTGCATGATA 57.803 45.000 0.00 0.00 0.00 2.15
162 164 1.869132 GTGCATGATATTCAGCTCGCA 59.131 47.619 0.00 0.00 0.00 5.10
163 165 1.869132 TGCATGATATTCAGCTCGCAC 59.131 47.619 0.00 0.00 0.00 5.34
183 185 5.166398 GCACGGCTAAACTTCTACTCTTTA 58.834 41.667 0.00 0.00 0.00 1.85
197 199 9.868277 CTTCTACTCTTTATATCAATGCCTAGG 57.132 37.037 3.67 3.67 0.00 3.02
215 218 2.108970 AGGATTTCTAGGTCACCGGAC 58.891 52.381 9.46 0.00 43.55 4.79
260 271 1.144503 AGGCCTGGATCTATTGGCAAG 59.855 52.381 3.11 0.00 46.53 4.01
312 325 2.287457 TTAACATCGCCTCCCCGTCG 62.287 60.000 0.00 0.00 0.00 5.12
315 328 4.816984 ATCGCCTCCCCGTCGTCT 62.817 66.667 0.00 0.00 0.00 4.18
353 366 3.496131 CGCCATCGTTGAACCGGG 61.496 66.667 6.32 0.00 0.00 5.73
381 406 0.040067 GGAAGTTCTTGGCTTGCACG 60.040 55.000 2.25 0.00 34.95 5.34
383 408 1.103398 AAGTTCTTGGCTTGCACGCT 61.103 50.000 15.41 0.00 0.00 5.07
408 433 1.339438 ACATTGACCTGCTTGCTCGAT 60.339 47.619 0.00 0.00 0.00 3.59
423 448 3.007290 TGCTCGATGGGATCATTTCCTAG 59.993 47.826 0.00 0.00 44.75 3.02
425 450 4.620332 GCTCGATGGGATCATTTCCTAGAG 60.620 50.000 0.00 0.00 44.75 2.43
443 473 0.610232 AGTACGTGCTCCCCGTTACT 60.610 55.000 0.00 0.00 39.60 2.24
444 474 0.457337 GTACGTGCTCCCCGTTACTG 60.457 60.000 0.00 0.00 39.60 2.74
466 496 1.878522 CAGGGCACGTATGTCGCTC 60.879 63.158 0.00 5.66 44.19 5.03
539 569 2.377628 ATCGACCACGCCACAACAGT 62.378 55.000 0.00 0.00 39.58 3.55
559 589 0.831288 ATCCAGAGCCCCAGATCGAG 60.831 60.000 0.00 0.00 32.16 4.04
569 599 3.440415 AGATCGAGCACGCCACGA 61.440 61.111 2.38 10.37 40.18 4.35
610 640 2.520069 AGTCTCGAGTGTCACTCCATT 58.480 47.619 24.15 5.61 42.12 3.16
611 641 3.687125 AGTCTCGAGTGTCACTCCATTA 58.313 45.455 24.15 9.01 42.12 1.90
612 642 4.274147 AGTCTCGAGTGTCACTCCATTAT 58.726 43.478 24.15 7.88 42.12 1.28
613 643 4.097135 AGTCTCGAGTGTCACTCCATTATG 59.903 45.833 24.15 11.25 42.12 1.90
614 644 3.119291 CTCGAGTGTCACTCCATTATGC 58.881 50.000 24.15 1.15 42.12 3.14
615 645 2.495669 TCGAGTGTCACTCCATTATGCA 59.504 45.455 24.15 0.00 42.12 3.96
616 646 3.132824 TCGAGTGTCACTCCATTATGCAT 59.867 43.478 24.15 3.79 42.12 3.96
617 647 4.340950 TCGAGTGTCACTCCATTATGCATA 59.659 41.667 24.15 1.16 42.12 3.14
618 648 4.445718 CGAGTGTCACTCCATTATGCATAC 59.554 45.833 24.15 0.00 42.12 2.39
887 947 2.394632 TGCTCCTCGCCCTCTATAAAA 58.605 47.619 0.00 0.00 38.05 1.52
925 985 3.276091 CCTTCCACACGCGCACAA 61.276 61.111 5.73 0.00 0.00 3.33
926 986 2.616330 CCTTCCACACGCGCACAAT 61.616 57.895 5.73 0.00 0.00 2.71
927 987 1.295357 CCTTCCACACGCGCACAATA 61.295 55.000 5.73 0.00 0.00 1.90
928 988 0.179225 CTTCCACACGCGCACAATAC 60.179 55.000 5.73 0.00 0.00 1.89
929 989 0.880718 TTCCACACGCGCACAATACA 60.881 50.000 5.73 0.00 0.00 2.29
930 990 1.154488 CCACACGCGCACAATACAC 60.154 57.895 5.73 0.00 0.00 2.90
931 991 1.506891 CACACGCGCACAATACACG 60.507 57.895 5.73 0.00 0.00 4.49
955 1015 2.179517 GGGACACTCTCGCACTCG 59.820 66.667 0.00 0.00 0.00 4.18
958 1033 1.510204 GACACTCTCGCACTCGACG 60.510 63.158 0.00 0.00 40.21 5.12
960 1035 4.104417 ACTCTCGCACTCGACGGC 62.104 66.667 0.00 0.00 40.21 5.68
961 1036 4.103103 CTCTCGCACTCGACGGCA 62.103 66.667 0.00 0.00 40.21 5.69
963 1038 4.103103 CTCGCACTCGACGGCAGA 62.103 66.667 0.00 2.43 40.21 4.26
964 1039 4.103103 TCGCACTCGACGGCAGAG 62.103 66.667 8.32 8.32 40.21 3.35
968 1043 2.955402 ACTCGACGGCAGAGTGAC 59.045 61.111 13.74 0.00 46.12 3.67
969 1044 1.897137 ACTCGACGGCAGAGTGACA 60.897 57.895 13.74 0.00 46.12 3.58
970 1045 1.442857 CTCGACGGCAGAGTGACAC 60.443 63.158 0.00 0.00 0.00 3.67
971 1046 1.857318 CTCGACGGCAGAGTGACACT 61.857 60.000 8.12 8.12 0.00 3.55
972 1047 1.007271 CGACGGCAGAGTGACACTT 60.007 57.895 10.01 0.00 0.00 3.16
973 1048 1.278172 CGACGGCAGAGTGACACTTG 61.278 60.000 10.01 10.80 0.00 3.16
1057 1137 2.507992 CAGAGCAGAACGAGGGCG 60.508 66.667 0.00 0.00 44.79 6.13
1124 1204 2.522193 CTACGGGGAGGAGGAGGC 60.522 72.222 0.00 0.00 0.00 4.70
1161 1250 1.796796 GCTCAACTTCGGCATGGTC 59.203 57.895 0.00 0.00 0.00 4.02
1253 1342 2.126307 CGTCGTGTGAGCTCCCTG 60.126 66.667 12.15 0.00 0.00 4.45
1275 1367 3.127533 GTGCCACGCCCACATCTC 61.128 66.667 0.00 0.00 33.50 2.75
1298 1390 1.246056 CCACCATGCACCCAGACTTG 61.246 60.000 0.00 0.00 0.00 3.16
1330 1432 2.355009 CCCGTGTTGCTTGCTTGC 60.355 61.111 0.00 0.00 0.00 4.01
1336 1438 0.176219 TGTTGCTTGCTTGCTTGCTT 59.824 45.000 10.35 0.00 0.00 3.91
1337 1439 0.580104 GTTGCTTGCTTGCTTGCTTG 59.420 50.000 10.35 0.00 0.00 4.01
1338 1440 1.155424 TTGCTTGCTTGCTTGCTTGC 61.155 50.000 10.35 7.41 34.50 4.01
1339 1441 1.300697 GCTTGCTTGCTTGCTTGCT 60.301 52.632 10.35 0.00 0.00 3.91
1340 1442 0.878961 GCTTGCTTGCTTGCTTGCTT 60.879 50.000 10.35 0.00 0.00 3.91
1341 1443 0.859232 CTTGCTTGCTTGCTTGCTTG 59.141 50.000 10.35 0.00 0.00 4.01
1479 1581 2.162208 TCAGCCTTTGATTCGTGCATTC 59.838 45.455 0.00 0.00 0.00 2.67
1482 1584 1.202177 CCTTTGATTCGTGCATTCCCG 60.202 52.381 0.00 0.00 0.00 5.14
1528 1630 2.219216 CGACCTGCATTTTTGCTTGTTG 59.781 45.455 0.00 0.00 35.49 3.33
1531 1633 2.563702 CTGCATTTTTGCTTGTTGGGT 58.436 42.857 0.00 0.00 35.49 4.51
1553 1675 2.095869 GCGCTCTGCATATGATCTTTGG 60.096 50.000 6.97 0.00 45.45 3.28
1565 1687 5.690464 ATGATCTTTGGTTCAGAGTAGCT 57.310 39.130 0.00 0.00 0.00 3.32
1717 4513 9.712305 AACAGTATATACATATCTGAAACCTGC 57.288 33.333 15.18 0.00 0.00 4.85
1718 4514 8.029522 ACAGTATATACATATCTGAAACCTGCG 58.970 37.037 15.18 0.00 0.00 5.18
1719 4515 7.009631 CAGTATATACATATCTGAAACCTGCGC 59.990 40.741 15.18 0.00 0.00 6.09
1722 4518 0.461870 ATATCTGAAACCTGCGCGCA 60.462 50.000 34.12 34.12 0.00 6.09
1723 4519 0.461870 TATCTGAAACCTGCGCGCAT 60.462 50.000 36.48 20.97 0.00 4.73
1724 4520 1.985447 ATCTGAAACCTGCGCGCATG 61.985 55.000 36.48 33.25 0.00 4.06
1744 4540 1.144276 TGCAGGAACCGTTTGTCGA 59.856 52.632 0.00 0.00 42.86 4.20
1759 4555 1.337447 TGTCGACATCCCCGAAGAAAC 60.337 52.381 15.76 0.00 37.81 2.78
1795 4591 4.870991 GCTCAAAGTCATCCTTGGTACTAC 59.129 45.833 0.00 0.00 32.32 2.73
1796 4592 5.337652 GCTCAAAGTCATCCTTGGTACTACT 60.338 44.000 0.00 0.00 32.32 2.57
1797 4593 6.127423 GCTCAAAGTCATCCTTGGTACTACTA 60.127 42.308 0.00 0.00 32.32 1.82
1833 4629 4.935808 ACTTACAAACATCTTCACCGATCC 59.064 41.667 0.00 0.00 0.00 3.36
1854 4652 0.244450 AGGCCGCAAAATCACACATG 59.756 50.000 0.00 0.00 0.00 3.21
1861 4659 3.568538 GCAAAATCACACATGACCACTC 58.431 45.455 0.00 0.00 37.79 3.51
1867 4665 3.738982 TCACACATGACCACTCGAAATT 58.261 40.909 0.00 0.00 0.00 1.82
1872 4670 4.003648 ACATGACCACTCGAAATTTCTCC 58.996 43.478 15.92 0.00 0.00 3.71
1887 4685 9.372369 CGAAATTTCTCCTTCTCTAACTAACAT 57.628 33.333 15.92 0.00 0.00 2.71
1916 4736 3.073678 TGTTTCCATGGATTCAGACGTG 58.926 45.455 17.06 0.00 0.00 4.49
1973 4818 4.263506 GGCAAGGTATATTCTGCACCCTAT 60.264 45.833 0.00 0.00 32.43 2.57
1976 4821 6.520061 GCAAGGTATATTCTGCACCCTATACA 60.520 42.308 13.02 0.00 31.58 2.29
1977 4822 6.607004 AGGTATATTCTGCACCCTATACAC 57.393 41.667 13.02 6.35 31.58 2.90
1986 4862 3.641436 TGCACCCTATACACCTCATACAG 59.359 47.826 0.00 0.00 0.00 2.74
1993 4869 5.986135 CCTATACACCTCATACAGCACTTTC 59.014 44.000 0.00 0.00 0.00 2.62
2021 4897 6.855836 TGAAAATCATAACCATGTGCTTCTC 58.144 36.000 0.00 0.00 33.57 2.87
2067 4943 2.033141 TGCCTGAGGAAGCTGCAC 59.967 61.111 0.65 0.00 0.00 4.57
2140 5016 2.677979 GCGAGGAAAACCGACCAGC 61.678 63.158 0.00 0.00 0.00 4.85
2170 5046 1.618640 GCTCTTCGACACGTCAAGCC 61.619 60.000 0.00 0.00 0.00 4.35
2184 5060 1.378250 AAGCCTGGTGCATCTGCTC 60.378 57.895 13.76 0.00 44.83 4.26
2222 5098 2.171489 AAGCGAGCGAGCGTTTTTCC 62.171 55.000 0.00 0.00 43.00 3.13
2233 5109 5.744490 CGAGCGTTTTTCCTTTCTCTTTTA 58.256 37.500 0.00 0.00 0.00 1.52
2279 5155 1.853319 CTGCGACGACCTGTGTTTC 59.147 57.895 0.00 0.00 0.00 2.78
2293 5169 0.672401 TGTTTCTCCCGCGGTGATTC 60.672 55.000 26.12 16.18 0.00 2.52
2356 5235 9.599056 ATCTATGAGAGATAGAAGACCAATGAA 57.401 33.333 0.00 0.00 43.54 2.57
2358 5237 9.474920 CTATGAGAGATAGAAGACCAATGAAAC 57.525 37.037 0.00 0.00 0.00 2.78
2463 5350 4.245660 ACAACGTTGAATGATCGATCTGT 58.754 39.130 33.66 14.69 0.00 3.41
2464 5351 4.327357 ACAACGTTGAATGATCGATCTGTC 59.673 41.667 33.66 20.55 0.00 3.51
2473 5361 3.969899 TGATCGATCTGTCAGGATTTCG 58.030 45.455 25.02 4.81 0.00 3.46
2518 5413 2.749621 GGCTGGACTGAATGTTTACTGG 59.250 50.000 0.00 0.00 0.00 4.00
2522 5417 3.181445 TGGACTGAATGTTTACTGGTGCT 60.181 43.478 0.00 0.00 0.00 4.40
2523 5418 3.821033 GGACTGAATGTTTACTGGTGCTT 59.179 43.478 0.00 0.00 0.00 3.91
2559 5454 2.435805 ACTTCTCCAGCTTGTGAGTGAA 59.564 45.455 4.97 0.00 0.00 3.18
2565 5460 2.935201 CCAGCTTGTGAGTGAATCTAGC 59.065 50.000 0.00 0.00 0.00 3.42
2638 5551 2.441410 CTGTGAGTGAGTCTAGCCAGA 58.559 52.381 0.00 0.00 0.00 3.86
2639 5552 2.822561 CTGTGAGTGAGTCTAGCCAGAA 59.177 50.000 0.00 0.00 30.85 3.02
2640 5553 3.230976 TGTGAGTGAGTCTAGCCAGAAA 58.769 45.455 0.00 0.00 30.85 2.52
2641 5554 3.256879 TGTGAGTGAGTCTAGCCAGAAAG 59.743 47.826 0.00 0.00 30.85 2.62
2642 5555 3.508012 GTGAGTGAGTCTAGCCAGAAAGA 59.492 47.826 0.00 0.00 30.85 2.52
2643 5556 4.159506 GTGAGTGAGTCTAGCCAGAAAGAT 59.840 45.833 0.00 0.00 30.85 2.40
2644 5557 4.774726 TGAGTGAGTCTAGCCAGAAAGATT 59.225 41.667 0.00 0.00 30.85 2.40
2645 5558 5.247110 TGAGTGAGTCTAGCCAGAAAGATTT 59.753 40.000 0.00 0.00 30.85 2.17
2646 5559 6.120507 AGTGAGTCTAGCCAGAAAGATTTT 57.879 37.500 0.00 0.00 30.85 1.82
2647 5560 6.538263 AGTGAGTCTAGCCAGAAAGATTTTT 58.462 36.000 0.00 0.00 30.85 1.94
2680 5593 5.241662 ACAAGTCTAGCCAGAAAGATGAAC 58.758 41.667 0.00 0.00 30.85 3.18
2691 5604 2.010145 AAGATGAACGATGGACCGTG 57.990 50.000 0.00 0.00 42.54 4.94
2728 5641 1.224592 GTGGACATGGGCCTGGTAG 59.775 63.158 4.53 0.00 0.00 3.18
2784 5702 1.279271 AGGGAGTACGCTGATGCTTTT 59.721 47.619 0.00 0.00 37.89 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.801699 CGCAAGTGTCTGTCAGTGGTAA 60.802 50.000 0.00 0.00 0.00 2.85
3 4 1.269569 CGCAAGTGTCTGTCAGTGGTA 60.270 52.381 0.00 0.00 0.00 3.25
4 5 0.530650 CGCAAGTGTCTGTCAGTGGT 60.531 55.000 0.00 0.00 0.00 4.16
5 6 0.249447 TCGCAAGTGTCTGTCAGTGG 60.249 55.000 0.00 0.00 39.48 4.00
6 7 0.855349 GTCGCAAGTGTCTGTCAGTG 59.145 55.000 0.00 0.00 39.48 3.66
7 8 0.595053 CGTCGCAAGTGTCTGTCAGT 60.595 55.000 0.00 0.00 39.48 3.41
8 9 0.317854 TCGTCGCAAGTGTCTGTCAG 60.318 55.000 0.00 0.00 39.48 3.51
9 10 0.101579 TTCGTCGCAAGTGTCTGTCA 59.898 50.000 0.00 0.00 39.48 3.58
10 11 1.190323 CTTTCGTCGCAAGTGTCTGTC 59.810 52.381 0.00 0.00 39.48 3.51
11 12 1.209128 CTTTCGTCGCAAGTGTCTGT 58.791 50.000 0.00 0.00 39.48 3.41
12 13 1.071239 CACTTTCGTCGCAAGTGTCTG 60.071 52.381 23.99 4.48 44.18 3.51
13 14 1.209128 CACTTTCGTCGCAAGTGTCT 58.791 50.000 23.99 0.00 44.18 3.41
14 15 3.710233 CACTTTCGTCGCAAGTGTC 57.290 52.632 23.99 0.00 44.18 3.67
39 40 0.685131 ACCGTGGGGACGATATGACA 60.685 55.000 0.00 0.00 36.97 3.58
41 42 1.396607 CCACCGTGGGGACGATATGA 61.397 60.000 9.99 0.00 36.97 2.15
43 44 3.546009 CCACCGTGGGGACGATAT 58.454 61.111 9.99 0.00 36.97 1.63
56 57 2.632512 ACAACACCATCAAAATCCCACC 59.367 45.455 0.00 0.00 0.00 4.61
66 67 2.029020 CGAGAGGAAGACAACACCATCA 60.029 50.000 0.00 0.00 0.00 3.07
70 71 0.670854 GGCGAGAGGAAGACAACACC 60.671 60.000 0.00 0.00 0.00 4.16
74 75 0.391661 GCATGGCGAGAGGAAGACAA 60.392 55.000 0.00 0.00 0.00 3.18
90 91 2.514592 CGAGGCCATTGACCGCAT 60.515 61.111 5.01 0.00 0.00 4.73
95 96 2.467826 GCTGAGCGAGGCCATTGAC 61.468 63.158 5.01 0.00 0.00 3.18
102 103 2.521958 TACCCAAAGCTGAGCGAGGC 62.522 60.000 0.00 0.00 0.00 4.70
104 105 1.079503 GTTACCCAAAGCTGAGCGAG 58.920 55.000 0.00 0.00 0.00 5.03
105 106 0.685097 AGTTACCCAAAGCTGAGCGA 59.315 50.000 0.00 0.00 0.00 4.93
151 153 0.391130 TTTAGCCGTGCGAGCTGAAT 60.391 50.000 14.49 0.00 41.71 2.57
162 164 8.910944 TGATATAAAGAGTAGAAGTTTAGCCGT 58.089 33.333 0.00 0.00 0.00 5.68
163 165 9.745880 TTGATATAAAGAGTAGAAGTTTAGCCG 57.254 33.333 0.00 0.00 0.00 5.52
195 197 2.108970 GTCCGGTGACCTAGAAATCCT 58.891 52.381 0.00 0.00 35.34 3.24
197 199 3.447944 AGAAGTCCGGTGACCTAGAAATC 59.552 47.826 0.00 0.00 42.81 2.17
312 325 0.520847 GCAAGAGCAGCCAAGAAGAC 59.479 55.000 0.00 0.00 41.58 3.01
353 366 2.289565 CCAAGAACTTCCGGATAAGGC 58.710 52.381 4.15 0.00 0.00 4.35
381 406 1.818642 AGCAGGTCAATGTTCTCAGC 58.181 50.000 0.00 0.00 0.00 4.26
383 408 1.881973 GCAAGCAGGTCAATGTTCTCA 59.118 47.619 0.00 0.00 0.00 3.27
423 448 0.179153 GTAACGGGGAGCACGTACTC 60.179 60.000 7.29 7.29 44.83 2.59
425 450 0.457337 CAGTAACGGGGAGCACGTAC 60.457 60.000 0.00 0.00 44.83 3.67
466 496 3.527434 GGTTTGGTACCGACAGGAG 57.473 57.895 17.11 0.00 41.02 3.69
539 569 0.482887 TCGATCTGGGGCTCTGGATA 59.517 55.000 0.00 0.00 0.00 2.59
569 599 3.221389 GCCCATCATGCATGCCGT 61.221 61.111 22.25 7.49 0.00 5.68
611 641 8.874156 TCAGAAAATGTAGGATCTAGTATGCAT 58.126 33.333 3.79 3.79 0.00 3.96
612 642 8.250143 TCAGAAAATGTAGGATCTAGTATGCA 57.750 34.615 0.00 0.00 0.00 3.96
613 643 8.580720 TCTCAGAAAATGTAGGATCTAGTATGC 58.419 37.037 0.00 0.00 0.00 3.14
617 647 9.432982 AAGATCTCAGAAAATGTAGGATCTAGT 57.567 33.333 0.00 0.00 38.51 2.57
618 648 9.695526 CAAGATCTCAGAAAATGTAGGATCTAG 57.304 37.037 0.00 0.00 38.51 2.43
673 709 0.108585 TTTGACTGTCAGTGAGGCCC 59.891 55.000 11.04 0.00 0.00 5.80
674 710 1.230324 GTTTGACTGTCAGTGAGGCC 58.770 55.000 11.04 0.00 0.00 5.19
675 711 1.953559 TGTTTGACTGTCAGTGAGGC 58.046 50.000 11.04 0.00 0.00 4.70
925 985 0.171903 GTGTCCCGTGTAGCGTGTAT 59.828 55.000 0.00 0.00 39.32 2.29
926 986 0.890542 AGTGTCCCGTGTAGCGTGTA 60.891 55.000 0.00 0.00 39.32 2.90
927 987 2.138656 GAGTGTCCCGTGTAGCGTGT 62.139 60.000 0.00 0.00 39.32 4.49
928 988 1.443872 GAGTGTCCCGTGTAGCGTG 60.444 63.158 0.00 0.00 39.32 5.34
929 989 1.584380 GAGAGTGTCCCGTGTAGCGT 61.584 60.000 0.00 0.00 39.32 5.07
930 990 1.136984 GAGAGTGTCCCGTGTAGCG 59.863 63.158 0.00 0.00 40.95 4.26
931 991 1.136984 CGAGAGTGTCCCGTGTAGC 59.863 63.158 0.00 0.00 0.00 3.58
932 992 1.136984 GCGAGAGTGTCCCGTGTAG 59.863 63.158 0.00 0.00 0.00 2.74
933 993 1.601477 TGCGAGAGTGTCCCGTGTA 60.601 57.895 0.00 0.00 0.00 2.90
934 994 2.910479 TGCGAGAGTGTCCCGTGT 60.910 61.111 0.00 0.00 0.00 4.49
935 995 2.430921 GTGCGAGAGTGTCCCGTG 60.431 66.667 0.00 0.00 0.00 4.94
936 996 2.597805 AGTGCGAGAGTGTCCCGT 60.598 61.111 0.00 0.00 0.00 5.28
955 1015 1.560860 GCAAGTGTCACTCTGCCGTC 61.561 60.000 20.49 3.44 31.05 4.79
958 1033 2.320587 CGGCAAGTGTCACTCTGCC 61.321 63.158 30.00 30.00 43.03 4.85
960 1035 2.320587 GGCGGCAAGTGTCACTCTG 61.321 63.158 5.82 8.16 0.00 3.35
961 1036 2.031163 GGCGGCAAGTGTCACTCT 59.969 61.111 5.82 0.00 0.00 3.24
963 1038 2.031163 GAGGCGGCAAGTGTCACT 59.969 61.111 13.08 0.00 0.00 3.41
964 1039 2.031163 AGAGGCGGCAAGTGTCAC 59.969 61.111 13.08 0.00 0.00 3.67
965 1040 2.031012 CAGAGGCGGCAAGTGTCA 59.969 61.111 13.08 0.00 0.00 3.58
966 1041 3.426568 GCAGAGGCGGCAAGTGTC 61.427 66.667 13.08 0.00 0.00 3.67
1060 1140 2.825836 CTTCCATGGCTCCACGGC 60.826 66.667 6.96 0.00 38.97 5.68
1061 1141 2.825836 GCTTCCATGGCTCCACGG 60.826 66.667 6.96 0.00 0.00 4.94
1062 1142 2.046023 TGCTTCCATGGCTCCACG 60.046 61.111 6.96 0.00 0.00 4.94
1063 1143 2.048603 GGTGCTTCCATGGCTCCAC 61.049 63.158 6.96 12.76 41.35 4.02
1064 1144 2.356278 GGTGCTTCCATGGCTCCA 59.644 61.111 6.96 0.00 41.35 3.86
1065 1145 2.440980 GGGTGCTTCCATGGCTCC 60.441 66.667 6.96 5.93 41.09 4.70
1069 1149 2.409870 GCTTCGGGTGCTTCCATGG 61.410 63.158 4.97 4.97 38.11 3.66
1101 1181 4.475444 TCCTCCCCGTAGCCCAGG 62.475 72.222 0.00 0.00 0.00 4.45
1255 1344 3.899981 GATGTGGGCGTGGCACAGA 62.900 63.158 19.09 0.00 45.08 3.41
1258 1347 3.127533 GAGATGTGGGCGTGGCAC 61.128 66.667 7.79 7.79 0.00 5.01
1259 1348 4.408821 GGAGATGTGGGCGTGGCA 62.409 66.667 0.00 0.00 0.00 4.92
1261 1350 4.838152 CCGGAGATGTGGGCGTGG 62.838 72.222 0.00 0.00 0.00 4.94
1268 1360 1.820906 CATGGTGGCCGGAGATGTG 60.821 63.158 5.05 0.00 0.00 3.21
1270 1362 2.903855 GCATGGTGGCCGGAGATG 60.904 66.667 5.05 0.00 0.00 2.90
1293 1385 2.062519 GGCGTCAAGAAGAGACAAGTC 58.937 52.381 0.00 0.00 35.77 3.01
1298 1390 1.446272 CGGGGCGTCAAGAAGAGAC 60.446 63.158 0.00 0.00 0.00 3.36
1446 1548 4.071423 TCAAAGGCTGAATTGTTCATCGA 58.929 39.130 0.00 0.00 39.30 3.59
1448 1550 5.514204 CGAATCAAAGGCTGAATTGTTCATC 59.486 40.000 0.00 0.00 39.30 2.92
1449 1551 5.047802 ACGAATCAAAGGCTGAATTGTTCAT 60.048 36.000 0.00 0.00 39.30 2.57
1482 1584 3.795638 GATGGTTTCGCCGTCCTC 58.204 61.111 0.00 0.00 45.47 3.71
1553 1675 3.145228 GCCCACAGCTACTCTGAAC 57.855 57.895 0.00 0.00 45.72 3.18
1575 1697 1.665679 AGCAAGTTATTCATCCACGCG 59.334 47.619 3.53 3.53 0.00 6.01
1622 1744 4.531351 GCCCAAGCAAAGGGGTAA 57.469 55.556 9.79 0.00 46.86 2.85
1705 1832 1.746615 ATGCGCGCAGGTTTCAGAT 60.747 52.632 38.44 16.48 0.00 2.90
1706 1833 2.358615 ATGCGCGCAGGTTTCAGA 60.359 55.556 38.44 12.65 0.00 3.27
1722 4518 0.467290 ACAAACGGTTCCTGCACCAT 60.467 50.000 0.00 0.00 36.49 3.55
1723 4519 1.077357 ACAAACGGTTCCTGCACCA 60.077 52.632 0.00 0.00 36.49 4.17
1724 4520 1.652563 GACAAACGGTTCCTGCACC 59.347 57.895 0.00 0.00 0.00 5.01
1744 4540 1.134491 GGATCGTTTCTTCGGGGATGT 60.134 52.381 0.00 0.00 0.00 3.06
1795 4591 9.897744 ATGTTTGTAAGTGAATGTGTGAAATAG 57.102 29.630 0.00 0.00 0.00 1.73
1796 4592 9.891828 GATGTTTGTAAGTGAATGTGTGAAATA 57.108 29.630 0.00 0.00 0.00 1.40
1797 4593 8.632679 AGATGTTTGTAAGTGAATGTGTGAAAT 58.367 29.630 0.00 0.00 0.00 2.17
1833 4629 0.031857 TGTGTGATTTTGCGGCCTTG 59.968 50.000 0.00 0.00 0.00 3.61
1854 4652 4.570930 AGAAGGAGAAATTTCGAGTGGTC 58.429 43.478 12.42 3.71 0.00 4.02
1861 4659 8.758633 TGTTAGTTAGAGAAGGAGAAATTTCG 57.241 34.615 12.42 0.00 0.00 3.46
1867 4665 8.532819 GGAGAAATGTTAGTTAGAGAAGGAGAA 58.467 37.037 0.00 0.00 0.00 2.87
1872 4670 7.616313 ACAGGGAGAAATGTTAGTTAGAGAAG 58.384 38.462 0.00 0.00 0.00 2.85
1973 4818 6.599356 TTAGAAAGTGCTGTATGAGGTGTA 57.401 37.500 0.00 0.00 0.00 2.90
1976 4821 6.299805 TCATTAGAAAGTGCTGTATGAGGT 57.700 37.500 0.00 0.00 0.00 3.85
1977 4822 7.615582 TTTCATTAGAAAGTGCTGTATGAGG 57.384 36.000 0.00 0.00 38.76 3.86
1986 4862 9.807649 ATGGTTATGATTTTCATTAGAAAGTGC 57.192 29.630 0.00 0.00 44.03 4.40
1993 4869 9.241317 GAAGCACATGGTTATGATTTTCATTAG 57.759 33.333 0.00 0.00 38.26 1.73
2067 4943 2.743928 GAGGACAGGCGCCACTTG 60.744 66.667 31.54 21.18 0.00 3.16
2140 5016 0.173481 TCGAAGAGCTCCATGAACCG 59.827 55.000 10.93 4.05 0.00 4.44
2170 5046 3.200593 GGCGAGCAGATGCACCAG 61.201 66.667 7.68 0.00 45.16 4.00
2184 5060 1.291184 TTCATCAACACTGCGAGGCG 61.291 55.000 0.00 0.00 0.00 5.52
2222 5098 3.003480 CGGGACAGGCTAAAAGAGAAAG 58.997 50.000 0.00 0.00 0.00 2.62
2233 5109 3.474570 GCAGGATCGGGACAGGCT 61.475 66.667 0.00 0.00 0.00 4.58
2279 5155 1.811266 CTGTGAATCACCGCGGGAG 60.811 63.158 31.76 21.75 32.73 4.30
2344 5220 5.940470 AGGAGTACATGTTTCATTGGTCTTC 59.060 40.000 2.30 0.00 0.00 2.87
2356 5235 8.408043 TTTTGATCATTCAAGGAGTACATGTT 57.592 30.769 2.30 0.00 42.60 2.71
2400 5283 5.231357 TGCGAGAATAACGATAATGTGTCAC 59.769 40.000 0.00 0.00 0.00 3.67
2429 5316 7.484975 TCATTCAACGTTGTTCTACCATTTTT 58.515 30.769 26.47 0.00 0.00 1.94
2430 5317 7.033530 TCATTCAACGTTGTTCTACCATTTT 57.966 32.000 26.47 0.00 0.00 1.82
2431 5318 6.627395 TCATTCAACGTTGTTCTACCATTT 57.373 33.333 26.47 0.00 0.00 2.32
2432 5319 6.402118 CGATCATTCAACGTTGTTCTACCATT 60.402 38.462 26.47 5.52 0.00 3.16
2433 5320 5.063438 CGATCATTCAACGTTGTTCTACCAT 59.937 40.000 26.47 11.27 0.00 3.55
2444 5331 4.108336 CTGACAGATCGATCATTCAACGT 58.892 43.478 26.47 11.34 0.00 3.99
2446 5333 4.686972 TCCTGACAGATCGATCATTCAAC 58.313 43.478 26.47 11.81 0.00 3.18
2463 5350 5.753438 CGAAATAACATCTCCGAAATCCTGA 59.247 40.000 0.00 0.00 0.00 3.86
2464 5351 5.753438 TCGAAATAACATCTCCGAAATCCTG 59.247 40.000 0.00 0.00 0.00 3.86
2473 5361 5.973565 CCAGCATTTTCGAAATAACATCTCC 59.026 40.000 12.12 0.00 0.00 3.71
2518 5413 7.694886 AGAAGTAGTTAGTTGTCAAAAAGCAC 58.305 34.615 0.00 0.00 0.00 4.40
2522 5417 7.012044 GCTGGAGAAGTAGTTAGTTGTCAAAAA 59.988 37.037 6.30 0.00 32.34 1.94
2523 5418 6.482308 GCTGGAGAAGTAGTTAGTTGTCAAAA 59.518 38.462 6.30 0.00 32.34 2.44
2614 5527 2.357637 GGCTAGACTCACTCACAGCTAG 59.642 54.545 0.00 0.00 32.37 3.42
2615 5528 2.290960 TGGCTAGACTCACTCACAGCTA 60.291 50.000 0.00 0.00 32.37 3.32
2649 5562 5.290493 TCTGGCTAGACTTGTCTCAAAAA 57.710 39.130 6.55 0.00 0.00 1.94
2650 5563 4.955811 TCTGGCTAGACTTGTCTCAAAA 57.044 40.909 6.55 0.00 0.00 2.44
2651 5564 4.955811 TTCTGGCTAGACTTGTCTCAAA 57.044 40.909 6.55 0.00 31.21 2.69
2652 5565 4.588951 TCTTTCTGGCTAGACTTGTCTCAA 59.411 41.667 6.55 0.00 31.21 3.02
2653 5566 4.152647 TCTTTCTGGCTAGACTTGTCTCA 58.847 43.478 6.55 0.00 31.21 3.27
2654 5567 4.792521 TCTTTCTGGCTAGACTTGTCTC 57.207 45.455 6.55 0.00 31.21 3.36
2655 5568 4.774726 TCATCTTTCTGGCTAGACTTGTCT 59.225 41.667 0.00 8.41 31.21 3.41
2656 5569 5.078411 TCATCTTTCTGGCTAGACTTGTC 57.922 43.478 0.00 0.00 31.21 3.18
2657 5570 5.241662 GTTCATCTTTCTGGCTAGACTTGT 58.758 41.667 0.00 0.00 31.21 3.16
2658 5571 4.328440 CGTTCATCTTTCTGGCTAGACTTG 59.672 45.833 0.00 0.00 31.21 3.16
2659 5572 4.220821 TCGTTCATCTTTCTGGCTAGACTT 59.779 41.667 0.00 0.00 31.21 3.01
2660 5573 3.764434 TCGTTCATCTTTCTGGCTAGACT 59.236 43.478 0.00 0.00 31.21 3.24
2661 5574 4.111375 TCGTTCATCTTTCTGGCTAGAC 57.889 45.455 0.00 0.00 31.21 2.59
2662 5575 4.442052 CCATCGTTCATCTTTCTGGCTAGA 60.442 45.833 0.00 0.00 0.00 2.43
2663 5576 3.806521 CCATCGTTCATCTTTCTGGCTAG 59.193 47.826 0.00 0.00 0.00 3.42
2664 5577 3.450817 TCCATCGTTCATCTTTCTGGCTA 59.549 43.478 0.00 0.00 0.00 3.93
2665 5578 2.237143 TCCATCGTTCATCTTTCTGGCT 59.763 45.455 0.00 0.00 0.00 4.75
2666 5579 2.352960 GTCCATCGTTCATCTTTCTGGC 59.647 50.000 0.00 0.00 0.00 4.85
2667 5580 2.939103 GGTCCATCGTTCATCTTTCTGG 59.061 50.000 0.00 0.00 0.00 3.86
2668 5581 2.604914 CGGTCCATCGTTCATCTTTCTG 59.395 50.000 0.00 0.00 0.00 3.02
2669 5582 2.233922 ACGGTCCATCGTTCATCTTTCT 59.766 45.455 0.00 0.00 40.85 2.52
2670 5583 2.348666 CACGGTCCATCGTTCATCTTTC 59.651 50.000 0.00 0.00 41.86 2.62
2680 5593 1.520787 GGCCTTACACGGTCCATCG 60.521 63.158 0.00 0.00 0.00 3.84
2751 5669 4.844998 GTACTCCCTACGATAACCCTTC 57.155 50.000 0.00 0.00 0.00 3.46
2779 5697 4.404715 GGGGTTTATTAGGGGAAGAAAAGC 59.595 45.833 0.00 0.00 30.31 3.51
2784 5702 3.239508 TGGGGGTTTATTAGGGGAAGA 57.760 47.619 0.00 0.00 0.00 2.87
2854 5773 2.192263 AGCTAGGGTTTGGGAGAAGAG 58.808 52.381 0.00 0.00 0.00 2.85
2982 5907 2.490685 GGCGTCTTCGTCCTCCTC 59.509 66.667 0.00 0.00 39.49 3.71
2983 5908 3.441290 CGGCGTCTTCGTCCTCCT 61.441 66.667 0.00 0.00 38.56 3.69
2984 5909 3.398353 CTCGGCGTCTTCGTCCTCC 62.398 68.421 6.85 0.00 38.56 4.30
2985 5910 2.100603 CTCGGCGTCTTCGTCCTC 59.899 66.667 6.85 0.00 38.56 3.71
2986 5911 2.672307 ACTCGGCGTCTTCGTCCT 60.672 61.111 6.85 0.00 38.56 3.85
3063 5991 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
3064 5992 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
3065 5993 1.293683 ACTCCTCCTCCTCCTCCTCC 61.294 65.000 0.00 0.00 0.00 4.30
3200 6128 1.098712 CCTCCTCCTCGTCGGAAGAG 61.099 65.000 13.15 13.15 46.03 2.85


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

AutoCloner maintained by Alex Coulton.