Multiple sequence alignment - TraesCS6D01G331100

Loading Multiple Alignment...

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 TraesCS6D01G331100 chr6D 100.000 3733 0 0 1 3733 434023567 434019835 0.000000e+00 6894.0
1 TraesCS6D01G331100 chr6A 93.078 1098 70 3 1643 2736 580281866 580280771 0.000000e+00 1602.0
2 TraesCS6D01G331100 chr6A 94.884 860 29 6 2877 3733 580280529 580279682 0.000000e+00 1330.0
3 TraesCS6D01G331100 chr6A 93.146 642 30 7 774 1411 580282804 580282173 0.000000e+00 929.0
4 TraesCS6D01G331100 chr6A 91.575 546 31 12 12 551 580284136 580283600 0.000000e+00 739.0
5 TraesCS6D01G331100 chr6A 85.754 358 35 8 1293 1646 580282250 580281905 7.620000e-97 364.0
6 TraesCS6D01G331100 chr6A 93.750 64 1 2 679 742 580282853 580282793 3.970000e-15 93.5
7 TraesCS6D01G331100 chr6B 93.195 1014 40 17 2747 3733 656512460 656511449 0.000000e+00 1463.0
8 TraesCS6D01G331100 chr6B 95.607 865 32 3 1876 2736 656513363 656512501 0.000000e+00 1382.0
9 TraesCS6D01G331100 chr6B 89.197 1009 58 17 873 1865 656514317 656513344 0.000000e+00 1212.0
10 TraesCS6D01G331100 chr6B 81.693 437 53 16 124 548 656515504 656515083 4.620000e-89 339.0
11 TraesCS6D01G331100 chr6B 96.923 130 4 0 2828 2957 584612655 584612784 6.280000e-53 219.0
12 TraesCS6D01G331100 chr6B 95.385 130 6 0 2828 2957 692771537 692771408 1.360000e-49 207.0
13 TraesCS6D01G331100 chr4A 84.867 489 64 8 3238 3726 559946921 559946443 5.610000e-133 484.0
14 TraesCS6D01G331100 chr4B 84.254 489 67 8 3238 3726 58597947 58598425 5.650000e-128 468.0
15 TraesCS6D01G331100 chr4D 84.664 476 64 7 3251 3726 40123649 40124115 2.030000e-127 466.0
16 TraesCS6D01G331100 chr5A 82.834 501 74 9 3122 3615 597798684 597799179 4.430000e-119 438.0
17 TraesCS6D01G331100 chr5D 81.183 372 57 10 3122 3488 478965576 478965939 1.700000e-73 287.0
18 TraesCS6D01G331100 chr5D 96.154 130 5 0 2828 2957 240136088 240135959 2.920000e-51 213.0
19 TraesCS6D01G331100 chr5D 95.385 130 6 0 2828 2957 6202894 6203023 1.360000e-49 207.0
20 TraesCS6D01G331100 chr5D 96.875 32 1 0 3486 3517 479060731 479060762 2.000000e-03 54.7
21 TraesCS6D01G331100 chr3B 96.923 130 4 0 2828 2957 201511510 201511381 6.280000e-53 219.0
22 TraesCS6D01G331100 chrUn 96.154 130 5 0 2828 2957 440189663 440189534 2.920000e-51 213.0
23 TraesCS6D01G331100 chr7D 96.154 130 5 0 2828 2957 231553138 231553009 2.920000e-51 213.0
24 TraesCS6D01G331100 chr1D 95.385 130 6 0 2828 2957 483916220 483916349 1.360000e-49 207.0


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 TraesCS6D01G331100 chr6D 434019835 434023567 3732 True 6894.000000 6894 100.000000 1 3733 1 chr6D.!!$R1 3732
1 TraesCS6D01G331100 chr6A 580279682 580284136 4454 True 842.916667 1602 92.031167 12 3733 6 chr6A.!!$R1 3721
2 TraesCS6D01G331100 chr6B 656511449 656515504 4055 True 1099.000000 1463 89.923000 124 3733 4 chr6B.!!$R2 3609

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
558 574 0.038744 AGAGGCACCCACAAGATTGG 59.961 55.0 0.00 0.0 36.26 3.16 F
559 575 0.251341 GAGGCACCCACAAGATTGGT 60.251 55.0 0.00 0.0 34.44 3.67 F
743 1479 0.252375 AGGTGAATGCATGGGCCTTT 60.252 50.0 4.53 0.0 40.13 3.11 F
782 1518 0.405585 AGGGGTATGTATGCATGGGC 59.594 55.0 10.16 0.0 41.68 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 3243 1.153489 CATCTCCAGGCAGGTCACG 60.153 63.158 0.00 0.0 39.02 4.35 R
2400 3246 1.222936 CACCATCTCCAGGCAGGTC 59.777 63.158 0.00 0.0 39.02 3.85 R
2572 3421 1.466025 TACCGCGAAACCTCCTGTGT 61.466 55.000 8.23 0.0 0.00 3.72 R
2742 3595 1.816074 TACATTGGTTTGAGCGGGAC 58.184 50.000 0.00 0.0 0.00 4.46 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
28 29 5.480642 TTTTGCAAGCCATCCTAAATTCA 57.519 34.783 0.00 0.00 0.00 2.57
95 96 9.788960 AAGAAGAAGAAAATACTGTGACAAAAC 57.211 29.630 0.00 0.00 0.00 2.43
96 97 9.178758 AGAAGAAGAAAATACTGTGACAAAACT 57.821 29.630 0.00 0.00 0.00 2.66
152 153 4.199432 TGTGGAAATTGTTGCAACTGTT 57.801 36.364 28.61 19.73 36.77 3.16
164 165 2.614983 TGCAACTGTTAAAGGAACCGAC 59.385 45.455 0.00 0.00 37.22 4.79
253 254 4.444536 ACGACGATTCTAGTCTCTAAGCT 58.555 43.478 0.00 0.00 36.53 3.74
254 255 4.508861 ACGACGATTCTAGTCTCTAAGCTC 59.491 45.833 0.00 0.00 36.53 4.09
271 274 3.582444 GCTCTGTAGCGATGTTCAATG 57.418 47.619 0.00 0.00 39.39 2.82
314 317 2.512896 AGCCCACCATCAAGATCAAGAT 59.487 45.455 0.00 0.00 0.00 2.40
378 383 3.065648 GGAGAGTAAGAGAGTTGTAGCGG 59.934 52.174 0.00 0.00 0.00 5.52
399 411 3.119495 GGTGTGTTGCATGGATAAACTCC 60.119 47.826 0.00 0.00 45.19 3.85
428 440 6.542821 TGAGTGGAGGAGTTAATTGTTCATT 58.457 36.000 0.00 0.00 0.00 2.57
430 442 5.711976 AGTGGAGGAGTTAATTGTTCATTGG 59.288 40.000 0.00 0.00 0.00 3.16
453 465 7.411274 TGGTGTAGTGAATTGTTTTAGAAACG 58.589 34.615 0.00 0.00 0.00 3.60
540 556 8.555166 AAATACAACAAACACGAACAATACAG 57.445 30.769 0.00 0.00 0.00 2.74
551 567 1.064003 ACAATACAGAGGCACCCACA 58.936 50.000 0.00 0.00 0.00 4.17
553 569 2.086869 CAATACAGAGGCACCCACAAG 58.913 52.381 0.00 0.00 0.00 3.16
554 570 1.656587 ATACAGAGGCACCCACAAGA 58.343 50.000 0.00 0.00 0.00 3.02
556 572 0.773644 ACAGAGGCACCCACAAGATT 59.226 50.000 0.00 0.00 0.00 2.40
557 573 1.171308 CAGAGGCACCCACAAGATTG 58.829 55.000 0.00 0.00 0.00 2.67
558 574 0.038744 AGAGGCACCCACAAGATTGG 59.961 55.000 0.00 0.00 36.26 3.16
559 575 0.251341 GAGGCACCCACAAGATTGGT 60.251 55.000 0.00 0.00 34.44 3.67
566 582 2.091885 ACCCACAAGATTGGTGAACAGT 60.092 45.455 0.00 0.00 38.54 3.55
567 583 3.137544 ACCCACAAGATTGGTGAACAGTA 59.862 43.478 0.00 0.00 38.54 2.74
569 585 4.389374 CCACAAGATTGGTGAACAGTACT 58.611 43.478 0.00 0.00 38.54 2.73
570 586 4.821805 CCACAAGATTGGTGAACAGTACTT 59.178 41.667 0.00 0.00 38.54 2.24
582 1186 5.122869 GTGAACAGTACTTGCATGATGTCAT 59.877 40.000 6.60 0.00 36.96 3.06
604 1208 2.076863 AGACCAACACTAATCTTGCGC 58.923 47.619 0.00 0.00 0.00 6.09
639 1243 1.220529 TTGCAAGCTCTCTTCGTGTG 58.779 50.000 0.00 0.00 0.00 3.82
646 1250 5.435557 CAAGCTCTCTTCGTGTGTAAAAAG 58.564 41.667 0.00 0.00 0.00 2.27
659 1263 7.981225 TCGTGTGTAAAAAGTAAGTAGGACTTT 59.019 33.333 0.00 0.00 46.57 2.66
663 1267 8.554528 GTGTAAAAAGTAAGTAGGACTTTGGTC 58.445 37.037 1.78 0.00 44.43 4.02
710 1446 5.763204 GGAGTGGTGACAAGTGAAAAAGATA 59.237 40.000 0.00 0.00 46.06 1.98
711 1447 6.073003 GGAGTGGTGACAAGTGAAAAAGATAG 60.073 42.308 0.00 0.00 46.06 2.08
742 1478 0.974010 CAGGTGAATGCATGGGCCTT 60.974 55.000 4.53 0.00 40.13 4.35
743 1479 0.252375 AGGTGAATGCATGGGCCTTT 60.252 50.000 4.53 0.00 40.13 3.11
744 1480 0.614812 GGTGAATGCATGGGCCTTTT 59.385 50.000 4.53 0.00 40.13 2.27
745 1481 1.003464 GGTGAATGCATGGGCCTTTTT 59.997 47.619 4.53 0.00 40.13 1.94
767 1503 3.380471 TTTGAGAGAGAGAGAGAGGGG 57.620 52.381 0.00 0.00 0.00 4.79
768 1504 1.979809 TGAGAGAGAGAGAGAGGGGT 58.020 55.000 0.00 0.00 0.00 4.95
769 1505 3.138123 TGAGAGAGAGAGAGAGGGGTA 57.862 52.381 0.00 0.00 0.00 3.69
770 1506 3.675613 TGAGAGAGAGAGAGAGGGGTAT 58.324 50.000 0.00 0.00 0.00 2.73
771 1507 3.394274 TGAGAGAGAGAGAGAGGGGTATG 59.606 52.174 0.00 0.00 0.00 2.39
772 1508 3.394606 GAGAGAGAGAGAGAGGGGTATGT 59.605 52.174 0.00 0.00 0.00 2.29
773 1509 4.572978 AGAGAGAGAGAGAGGGGTATGTA 58.427 47.826 0.00 0.00 0.00 2.29
774 1510 5.170198 AGAGAGAGAGAGAGGGGTATGTAT 58.830 45.833 0.00 0.00 0.00 2.29
775 1511 5.014123 AGAGAGAGAGAGAGGGGTATGTATG 59.986 48.000 0.00 0.00 0.00 2.39
776 1512 3.761752 GAGAGAGAGAGGGGTATGTATGC 59.238 52.174 0.00 0.00 0.00 3.14
777 1513 3.141083 AGAGAGAGAGGGGTATGTATGCA 59.859 47.826 0.00 0.00 0.00 3.96
778 1514 4.093011 GAGAGAGAGGGGTATGTATGCAT 58.907 47.826 3.79 3.79 39.03 3.96
779 1515 3.837146 AGAGAGAGGGGTATGTATGCATG 59.163 47.826 10.16 0.00 36.58 4.06
780 1516 2.909006 AGAGAGGGGTATGTATGCATGG 59.091 50.000 10.16 0.00 36.58 3.66
781 1517 1.988107 AGAGGGGTATGTATGCATGGG 59.012 52.381 10.16 0.00 36.58 4.00
782 1518 0.405585 AGGGGTATGTATGCATGGGC 59.594 55.000 10.16 0.00 41.68 5.36
783 1519 0.611896 GGGGTATGTATGCATGGGCC 60.612 60.000 10.16 0.00 40.13 5.80
784 1520 0.405585 GGGTATGTATGCATGGGCCT 59.594 55.000 10.16 0.00 40.13 5.19
815 1552 7.944061 TGTATTTTGGGAGCATGAATGAATAG 58.056 34.615 0.00 0.00 0.00 1.73
861 1598 4.280677 CCAGTCACCACCACAACAAAATAT 59.719 41.667 0.00 0.00 0.00 1.28
871 1608 9.076781 CCACCACAACAAAATATCATCCATATA 57.923 33.333 0.00 0.00 0.00 0.86
906 1656 1.474143 GCCTAGCTAAGAGCCACCAAG 60.474 57.143 0.00 0.00 43.77 3.61
915 1665 3.373565 GCCACCAAGAAAGGCCCG 61.374 66.667 0.00 0.00 42.58 6.13
981 1732 3.690460 CAGAAAACCTTACCCTGATGCT 58.310 45.455 0.00 0.00 0.00 3.79
1004 1755 1.443407 CCGTCATGGCAGGACCTAG 59.557 63.158 24.73 12.02 40.22 3.02
1145 1899 2.993853 CTTGTGAGGCCTCTCCCC 59.006 66.667 32.28 17.72 39.23 4.81
1146 1900 1.614824 CTTGTGAGGCCTCTCCCCT 60.615 63.158 32.28 0.00 39.23 4.79
1187 1941 3.904800 TTCCATCTCCAATTAGTGCGA 57.095 42.857 0.00 0.00 0.00 5.10
1202 1956 3.829948 AGTGCGATGAATTGAGCAAAAG 58.170 40.909 0.00 0.00 41.56 2.27
1203 1957 2.343544 GTGCGATGAATTGAGCAAAAGC 59.656 45.455 0.00 0.00 41.56 3.51
1205 1959 2.988493 GCGATGAATTGAGCAAAAGCAA 59.012 40.909 0.00 0.00 0.00 3.91
1209 1963 5.801444 CGATGAATTGAGCAAAAGCAATACA 59.199 36.000 0.00 0.00 33.87 2.29
1216 1970 5.231702 TGAGCAAAAGCAATACAGTACGTA 58.768 37.500 0.00 0.00 0.00 3.57
1242 1997 6.535540 TGTAGTATTTTGGCAACTTAGGACA 58.464 36.000 0.00 0.00 37.61 4.02
1262 2017 3.122971 GGTTTGTCGGCCGGTAGC 61.123 66.667 27.83 13.71 42.60 3.58
1330 2088 3.486875 GCAGTTTGTCACACGCTTTACTT 60.487 43.478 0.00 0.00 0.00 2.24
1348 2106 3.350833 ACTTAATCTTGGCCTTCTGCAG 58.649 45.455 7.63 7.63 43.89 4.41
1349 2107 3.245052 ACTTAATCTTGGCCTTCTGCAGT 60.245 43.478 14.67 0.00 43.89 4.40
1350 2108 2.299326 AATCTTGGCCTTCTGCAGTT 57.701 45.000 14.67 0.00 43.89 3.16
1351 2109 1.542492 ATCTTGGCCTTCTGCAGTTG 58.458 50.000 14.67 7.64 43.89 3.16
1411 2206 5.756347 TGCAGTTAGTTACACACTTTACTGG 59.244 40.000 14.04 3.02 42.15 4.00
1415 2218 6.259387 AGTTAGTTACACACTTTACTGGCAAC 59.741 38.462 0.00 0.00 36.88 4.17
1429 2232 2.622942 CTGGCAACTGCTTTGGTTAAGA 59.377 45.455 1.06 0.00 41.70 2.10
1437 2240 8.244113 GCAACTGCTTTGGTTAAGACTAATTAT 58.756 33.333 0.00 0.00 35.80 1.28
1443 2246 7.067008 GCTTTGGTTAAGACTAATTATGCCAGA 59.933 37.037 0.00 0.00 35.80 3.86
1464 2267 6.989169 CCAGATACAGTTTTATTCTCCTCCTG 59.011 42.308 0.00 0.00 0.00 3.86
1498 2301 4.467795 TGAGCTCAAGTAGTAGGCAGAAAT 59.532 41.667 15.67 0.00 0.00 2.17
1540 2343 3.492102 TCTTTGACTGAACCTTGGGAG 57.508 47.619 0.00 0.00 0.00 4.30
1545 2348 3.976015 TGACTGAACCTTGGGAGTTTTT 58.024 40.909 0.00 0.00 0.00 1.94
1675 2520 2.952978 ACTGAGGTATGCTTAGTCCTCG 59.047 50.000 10.10 8.19 46.48 4.63
1682 2527 4.038883 GGTATGCTTAGTCCTCGGTGTAAT 59.961 45.833 0.00 0.00 0.00 1.89
1683 2528 4.755266 ATGCTTAGTCCTCGGTGTAATT 57.245 40.909 0.00 0.00 0.00 1.40
1699 2544 7.977293 TCGGTGTAATTTCTTCTTATTGATCGA 59.023 33.333 0.00 0.00 0.00 3.59
1735 2580 3.565307 TGGTTGAGTTGCTTCCTTTCAT 58.435 40.909 0.00 0.00 0.00 2.57
1736 2581 3.960102 TGGTTGAGTTGCTTCCTTTCATT 59.040 39.130 0.00 0.00 0.00 2.57
1780 2625 9.442047 CTCTTATTTCAAGTCTACTTCCACATT 57.558 33.333 0.00 0.00 33.11 2.71
1787 2632 8.722480 TCAAGTCTACTTCCACATTGATTATG 57.278 34.615 0.00 0.00 35.71 1.90
1830 2676 3.503363 TGTTGCCATGATCTCTGTTTGTC 59.497 43.478 0.00 0.00 0.00 3.18
1870 2716 3.907894 TTAATGTGCCGACCAAAGTTC 57.092 42.857 0.00 0.00 0.00 3.01
2397 3243 2.224450 CGTCAAGGGGGATATTGGGTAC 60.224 54.545 0.00 0.00 0.00 3.34
2400 3246 1.430992 AGGGGGATATTGGGTACGTG 58.569 55.000 0.00 0.00 0.00 4.49
2572 3421 1.905894 TGGATGATGACCAGGTTCGAA 59.094 47.619 0.00 0.00 33.22 3.71
2630 3483 2.504175 AGTTACAGGCCATACCATTCGT 59.496 45.455 5.01 0.00 43.14 3.85
2737 3590 9.965824 CAAATACATATCCTATTTTGTGGAACC 57.034 33.333 0.00 0.00 35.81 3.62
2738 3591 8.706322 AATACATATCCTATTTTGTGGAACCC 57.294 34.615 0.00 0.00 35.81 4.11
2740 3593 6.365520 ACATATCCTATTTTGTGGAACCCTC 58.634 40.000 0.00 0.00 35.81 4.30
2741 3594 3.732048 TCCTATTTTGTGGAACCCTCC 57.268 47.619 0.00 0.00 42.81 4.30
2742 3595 2.026636 TCCTATTTTGTGGAACCCTCCG 60.027 50.000 0.00 0.00 45.85 4.63
2743 3596 2.290705 CCTATTTTGTGGAACCCTCCGT 60.291 50.000 0.00 0.00 45.85 4.69
2744 3597 1.905637 ATTTTGTGGAACCCTCCGTC 58.094 50.000 0.00 0.00 45.85 4.79
2774 3709 7.981142 TCAAACCAATGTATAAGACGGATTTC 58.019 34.615 0.00 0.00 0.00 2.17
2776 3711 7.931578 AACCAATGTATAAGACGGATTTCAA 57.068 32.000 0.00 0.00 0.00 2.69
2862 3860 1.797025 GTATAGCATTCCCTCACGCC 58.203 55.000 0.00 0.00 0.00 5.68
2867 3865 1.450312 CATTCCCTCACGCCAGGAC 60.450 63.158 1.66 0.00 35.20 3.85
2871 3869 1.043116 TCCCTCACGCCAGGACTATG 61.043 60.000 1.66 0.00 35.20 2.23
2880 3878 1.340017 GCCAGGACTATGCTTCACCAA 60.340 52.381 0.00 0.00 0.00 3.67
2882 3880 2.359900 CAGGACTATGCTTCACCAACC 58.640 52.381 0.00 0.00 0.00 3.77
2890 3888 1.160137 GCTTCACCAACCTGCTAGTG 58.840 55.000 0.00 0.00 0.00 2.74
2922 3923 2.403259 GCAAGGACACCGGAATTTTTG 58.597 47.619 9.46 8.40 0.00 2.44
2952 3953 6.803642 AGTAGAAGAGTTACACAAAGTTCGT 58.196 36.000 0.00 0.00 0.00 3.85
2957 3958 6.730960 AGAGTTACACAAAGTTCGTGAAAA 57.269 33.333 0.00 0.00 37.80 2.29
3021 4034 2.766263 TGATCGTCCAGGTAGCAAAGAT 59.234 45.455 0.00 0.00 0.00 2.40
3022 4035 3.197766 TGATCGTCCAGGTAGCAAAGATT 59.802 43.478 0.00 0.00 0.00 2.40
3034 4047 4.292186 AGCAAAGATTAGCAAGTGGAGA 57.708 40.909 0.00 0.00 0.00 3.71
3092 4107 7.015226 TGATGAAATATAAACTCAAGTGCCG 57.985 36.000 0.00 0.00 0.00 5.69
3099 4115 2.165319 AACTCAAGTGCCGTCCTTAC 57.835 50.000 0.00 0.00 0.00 2.34
3153 4169 4.734398 ATTCTCAACAAGGCAAAACACA 57.266 36.364 0.00 0.00 0.00 3.72
3239 4255 4.444876 GGAAATCTGGATGCTTAGTAGGCA 60.445 45.833 9.63 9.63 44.05 4.75
3479 4495 0.608130 TGTCCTCCGACAGATTGGTG 59.392 55.000 0.00 0.00 44.20 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.710676 TTTAGGATGGCTTGCAAAATACTTA 57.289 32.000 0.00 0.00 0.00 2.24
1 2 6.603940 TTTAGGATGGCTTGCAAAATACTT 57.396 33.333 0.00 0.00 0.00 2.24
2 3 6.796785 ATTTAGGATGGCTTGCAAAATACT 57.203 33.333 0.00 3.59 0.00 2.12
3 4 7.041107 TGAATTTAGGATGGCTTGCAAAATAC 58.959 34.615 0.00 0.00 0.00 1.89
4 5 7.180322 TGAATTTAGGATGGCTTGCAAAATA 57.820 32.000 0.00 0.00 0.00 1.40
5 6 6.052405 TGAATTTAGGATGGCTTGCAAAAT 57.948 33.333 0.00 0.00 0.00 1.82
6 7 5.480642 TGAATTTAGGATGGCTTGCAAAA 57.519 34.783 0.00 0.00 0.00 2.44
7 8 5.680594 ATGAATTTAGGATGGCTTGCAAA 57.319 34.783 0.00 0.00 0.00 3.68
8 9 5.046448 ACAATGAATTTAGGATGGCTTGCAA 60.046 36.000 0.00 0.00 0.00 4.08
9 10 4.467082 ACAATGAATTTAGGATGGCTTGCA 59.533 37.500 0.00 0.00 0.00 4.08
10 11 5.014808 ACAATGAATTTAGGATGGCTTGC 57.985 39.130 0.00 0.00 0.00 4.01
73 74 9.573133 CAAAGTTTTGTCACAGTATTTTCTTCT 57.427 29.630 0.00 0.00 33.59 2.85
95 96 1.764851 TTTTGCGCGGATTCACAAAG 58.235 45.000 8.83 0.00 33.87 2.77
96 97 2.209838 TTTTTGCGCGGATTCACAAA 57.790 40.000 8.83 5.68 0.00 2.83
117 118 6.208402 ACAATTTCCACAAAGTTTTGCCTTTT 59.792 30.769 4.58 0.00 41.79 2.27
119 120 5.252547 ACAATTTCCACAAAGTTTTGCCTT 58.747 33.333 4.58 0.00 41.79 4.35
120 121 4.842574 ACAATTTCCACAAAGTTTTGCCT 58.157 34.783 4.58 0.00 41.79 4.75
121 122 5.331098 CAACAATTTCCACAAAGTTTTGCC 58.669 37.500 4.58 0.00 41.79 4.52
122 123 4.792702 GCAACAATTTCCACAAAGTTTTGC 59.207 37.500 4.58 3.83 42.58 3.68
152 153 5.419788 TCAAGCTATAGTGTCGGTTCCTTTA 59.580 40.000 0.84 0.00 0.00 1.85
164 165 6.625362 TGAAGAGTGAACTCAAGCTATAGTG 58.375 40.000 12.76 0.00 45.21 2.74
253 254 3.610040 ACCATTGAACATCGCTACAGA 57.390 42.857 0.00 0.00 0.00 3.41
254 255 4.034048 GGTTACCATTGAACATCGCTACAG 59.966 45.833 0.00 0.00 0.00 2.74
269 272 4.166144 CCTCAAGGATACAAGGGTTACCAT 59.834 45.833 2.98 0.00 36.83 3.55
270 273 3.521937 CCTCAAGGATACAAGGGTTACCA 59.478 47.826 2.98 0.00 36.83 3.25
271 274 3.778629 TCCTCAAGGATACAAGGGTTACC 59.221 47.826 0.00 0.00 39.78 2.85
314 317 9.767228 AATTGCAAGCAATATCATTATTAGCAA 57.233 25.926 19.45 0.00 44.86 3.91
345 350 8.989653 ACTCTCTTACTCTCCTTTTAAAATCG 57.010 34.615 0.09 0.00 0.00 3.34
352 357 6.570764 CGCTACAACTCTCTTACTCTCCTTTT 60.571 42.308 0.00 0.00 0.00 2.27
428 440 7.411274 CGTTTCTAAAACAATTCACTACACCA 58.589 34.615 3.72 0.00 0.00 4.17
430 442 6.854381 CCCGTTTCTAAAACAATTCACTACAC 59.146 38.462 3.72 0.00 0.00 2.90
540 556 0.251341 ACCAATCTTGTGGGTGCCTC 60.251 55.000 0.00 0.00 43.56 4.70
551 567 4.460263 TGCAAGTACTGTTCACCAATCTT 58.540 39.130 0.00 0.00 0.00 2.40
553 569 4.455533 TCATGCAAGTACTGTTCACCAATC 59.544 41.667 0.00 0.00 0.00 2.67
554 570 4.397420 TCATGCAAGTACTGTTCACCAAT 58.603 39.130 0.00 0.00 0.00 3.16
556 572 3.483808 TCATGCAAGTACTGTTCACCA 57.516 42.857 0.00 0.00 0.00 4.17
557 573 3.753272 ACATCATGCAAGTACTGTTCACC 59.247 43.478 0.00 0.00 0.00 4.02
558 574 4.452114 TGACATCATGCAAGTACTGTTCAC 59.548 41.667 0.00 0.00 0.00 3.18
559 575 4.640364 TGACATCATGCAAGTACTGTTCA 58.360 39.130 0.00 0.00 0.00 3.18
560 576 5.566623 CATGACATCATGCAAGTACTGTTC 58.433 41.667 8.86 0.00 45.92 3.18
561 577 5.556355 CATGACATCATGCAAGTACTGTT 57.444 39.130 8.86 0.00 45.92 3.16
582 1186 3.325870 CGCAAGATTAGTGTTGGTCTCA 58.674 45.455 0.00 0.00 43.02 3.27
620 1224 1.220529 CACACGAAGAGAGCTTGCAA 58.779 50.000 0.00 0.00 33.61 4.08
639 1243 8.899427 AGACCAAAGTCCTACTTACTTTTTAC 57.101 34.615 0.00 0.00 42.97 2.01
681 1285 2.891580 TCACTTGTCACCACTCCTACTC 59.108 50.000 0.00 0.00 0.00 2.59
710 1446 0.842030 TCACCTGCCACCAATCCTCT 60.842 55.000 0.00 0.00 0.00 3.69
711 1447 0.038166 TTCACCTGCCACCAATCCTC 59.962 55.000 0.00 0.00 0.00 3.71
745 1481 4.093011 CCCCTCTCTCTCTCTCTCAAAAA 58.907 47.826 0.00 0.00 0.00 1.94
746 1482 3.076785 ACCCCTCTCTCTCTCTCTCAAAA 59.923 47.826 0.00 0.00 0.00 2.44
747 1483 2.652348 ACCCCTCTCTCTCTCTCTCAAA 59.348 50.000 0.00 0.00 0.00 2.69
748 1484 2.283834 ACCCCTCTCTCTCTCTCTCAA 58.716 52.381 0.00 0.00 0.00 3.02
749 1485 1.979809 ACCCCTCTCTCTCTCTCTCA 58.020 55.000 0.00 0.00 0.00 3.27
750 1486 3.394606 ACATACCCCTCTCTCTCTCTCTC 59.605 52.174 0.00 0.00 0.00 3.20
751 1487 3.403322 ACATACCCCTCTCTCTCTCTCT 58.597 50.000 0.00 0.00 0.00 3.10
752 1488 3.876309 ACATACCCCTCTCTCTCTCTC 57.124 52.381 0.00 0.00 0.00 3.20
753 1489 4.508405 GCATACATACCCCTCTCTCTCTCT 60.508 50.000 0.00 0.00 0.00 3.10
754 1490 3.761752 GCATACATACCCCTCTCTCTCTC 59.238 52.174 0.00 0.00 0.00 3.20
755 1491 3.141083 TGCATACATACCCCTCTCTCTCT 59.859 47.826 0.00 0.00 0.00 3.10
756 1492 3.501349 TGCATACATACCCCTCTCTCTC 58.499 50.000 0.00 0.00 0.00 3.20
757 1493 3.619900 TGCATACATACCCCTCTCTCT 57.380 47.619 0.00 0.00 0.00 3.10
758 1494 3.055530 CCATGCATACATACCCCTCTCTC 60.056 52.174 0.00 0.00 33.67 3.20
759 1495 2.909006 CCATGCATACATACCCCTCTCT 59.091 50.000 0.00 0.00 33.67 3.10
760 1496 2.026822 CCCATGCATACATACCCCTCTC 60.027 54.545 0.00 0.00 33.67 3.20
761 1497 1.988107 CCCATGCATACATACCCCTCT 59.012 52.381 0.00 0.00 33.67 3.69
762 1498 1.614317 GCCCATGCATACATACCCCTC 60.614 57.143 0.00 0.00 33.67 4.30
763 1499 0.405585 GCCCATGCATACATACCCCT 59.594 55.000 0.00 0.00 33.67 4.79
764 1500 0.611896 GGCCCATGCATACATACCCC 60.612 60.000 0.00 0.00 40.13 4.95
765 1501 0.405585 AGGCCCATGCATACATACCC 59.594 55.000 0.00 0.00 40.13 3.69
766 1502 2.305927 ACTAGGCCCATGCATACATACC 59.694 50.000 0.00 0.00 40.13 2.73
767 1503 3.703001 ACTAGGCCCATGCATACATAC 57.297 47.619 0.00 0.00 40.13 2.39
768 1504 4.222810 CAGTACTAGGCCCATGCATACATA 59.777 45.833 0.00 0.00 40.13 2.29
769 1505 3.008375 CAGTACTAGGCCCATGCATACAT 59.992 47.826 0.00 0.00 40.13 2.29
770 1506 2.368548 CAGTACTAGGCCCATGCATACA 59.631 50.000 0.00 0.00 40.13 2.29
771 1507 2.368875 ACAGTACTAGGCCCATGCATAC 59.631 50.000 0.00 0.00 40.13 2.39
772 1508 2.689658 ACAGTACTAGGCCCATGCATA 58.310 47.619 0.00 0.00 40.13 3.14
773 1509 1.511613 ACAGTACTAGGCCCATGCAT 58.488 50.000 0.00 0.00 40.13 3.96
774 1510 2.168458 TACAGTACTAGGCCCATGCA 57.832 50.000 0.00 0.00 40.13 3.96
775 1511 3.771577 AATACAGTACTAGGCCCATGC 57.228 47.619 0.00 0.00 0.00 4.06
776 1512 4.821805 CCAAAATACAGTACTAGGCCCATG 59.178 45.833 0.00 0.00 0.00 3.66
777 1513 4.141251 CCCAAAATACAGTACTAGGCCCAT 60.141 45.833 0.00 0.00 0.00 4.00
778 1514 3.201266 CCCAAAATACAGTACTAGGCCCA 59.799 47.826 0.00 0.00 0.00 5.36
779 1515 3.457012 TCCCAAAATACAGTACTAGGCCC 59.543 47.826 0.00 0.00 0.00 5.80
780 1516 4.704965 CTCCCAAAATACAGTACTAGGCC 58.295 47.826 0.00 0.00 0.00 5.19
781 1517 4.127907 GCTCCCAAAATACAGTACTAGGC 58.872 47.826 0.00 0.00 0.00 3.93
782 1518 5.353394 TGCTCCCAAAATACAGTACTAGG 57.647 43.478 0.00 0.00 0.00 3.02
783 1519 6.582636 TCATGCTCCCAAAATACAGTACTAG 58.417 40.000 0.00 0.00 0.00 2.57
784 1520 6.553953 TCATGCTCCCAAAATACAGTACTA 57.446 37.500 0.00 0.00 0.00 1.82
815 1552 5.221601 GGGTAGTCTTAGGCCCAAATACTAC 60.222 48.000 23.05 23.05 40.76 2.73
871 1608 2.605299 GGCCCATCTGAAGCCCAT 59.395 61.111 0.00 0.00 41.00 4.00
878 1615 2.603021 CTCTTAGCTAGGCCCATCTGA 58.397 52.381 0.00 0.00 0.00 3.27
906 1656 0.601558 GTTCCTTTTCCGGGCCTTTC 59.398 55.000 0.84 0.00 0.00 2.62
915 1665 4.284746 TCTCCTCTCTTCTGTTCCTTTTCC 59.715 45.833 0.00 0.00 0.00 3.13
981 1732 0.468226 GTCCTGCCATGACGGGATTA 59.532 55.000 13.23 0.00 46.71 1.75
1004 1755 2.437897 CCATAGCTGGGGATGGGC 59.562 66.667 5.44 0.00 39.23 5.36
1145 1899 7.176690 TGGAAACCCTGAAATTAAAGCTTAGAG 59.823 37.037 0.00 0.00 0.00 2.43
1146 1900 7.007723 TGGAAACCCTGAAATTAAAGCTTAGA 58.992 34.615 0.00 0.00 0.00 2.10
1209 1963 6.271488 TGCCAAAATACTACAGTACGTACT 57.729 37.500 22.45 22.45 36.90 2.73
1216 1970 6.653740 GTCCTAAGTTGCCAAAATACTACAGT 59.346 38.462 0.00 0.00 0.00 3.55
1227 1982 1.349688 ACCGATGTCCTAAGTTGCCAA 59.650 47.619 0.00 0.00 0.00 4.52
1262 2017 4.202441 CAAGATCCCACCTTTACCTGATG 58.798 47.826 0.00 0.00 0.00 3.07
1330 2088 3.084039 CAACTGCAGAAGGCCAAGATTA 58.916 45.455 23.35 0.00 43.89 1.75
1348 2106 9.821662 GATTCAGTAAAGTGTGTAATAACCAAC 57.178 33.333 0.00 0.00 0.00 3.77
1349 2107 9.787435 AGATTCAGTAAAGTGTGTAATAACCAA 57.213 29.630 0.00 0.00 0.00 3.67
1350 2108 9.787435 AAGATTCAGTAAAGTGTGTAATAACCA 57.213 29.630 0.00 0.00 0.00 3.67
1411 2206 3.990318 AGTCTTAACCAAAGCAGTTGC 57.010 42.857 0.00 0.00 42.49 4.17
1415 2218 7.148086 TGGCATAATTAGTCTTAACCAAAGCAG 60.148 37.037 0.00 0.00 34.97 4.24
1437 2240 6.313519 AGGAGAATAAAACTGTATCTGGCA 57.686 37.500 0.00 0.00 0.00 4.92
1443 2246 6.313519 TGCAGGAGGAGAATAAAACTGTAT 57.686 37.500 0.00 0.00 0.00 2.29
1445 2248 4.640771 TGCAGGAGGAGAATAAAACTGT 57.359 40.909 0.00 0.00 0.00 3.55
1464 2267 4.698583 ACTTGAGCTCATTTTCTGATGC 57.301 40.909 19.04 0.00 32.10 3.91
1511 2314 5.941788 AGGTTCAGTCAAAGAAATGGTACT 58.058 37.500 0.00 0.00 0.00 2.73
1512 2315 6.438763 CAAGGTTCAGTCAAAGAAATGGTAC 58.561 40.000 0.00 0.00 0.00 3.34
1540 2343 4.457949 TCGAATTCCTTCCAGGCTAAAAAC 59.542 41.667 0.00 0.00 34.61 2.43
1545 2348 2.431057 GACTCGAATTCCTTCCAGGCTA 59.569 50.000 0.00 0.00 34.61 3.93
1699 2544 6.173427 ACTCAACCAAGTGGCAAAATAATT 57.827 33.333 0.00 0.00 39.32 1.40
1704 2549 2.676463 GCAACTCAACCAAGTGGCAAAA 60.676 45.455 0.00 0.00 44.29 2.44
1780 2625 6.430864 TCCAAATTGTAGAAGGGCATAATCA 58.569 36.000 0.00 0.00 0.00 2.57
1787 2632 4.220602 ACATGTTCCAAATTGTAGAAGGGC 59.779 41.667 0.00 0.00 0.00 5.19
1859 2705 8.977505 ACATTAATCATTTTTGAACTTTGGTCG 58.022 29.630 0.00 0.00 0.00 4.79
1870 2716 7.332430 ACATGGTCAGCACATTAATCATTTTTG 59.668 33.333 0.00 0.00 0.00 2.44
2065 2911 1.330655 ATCGCCGTCTCCAGGTCATT 61.331 55.000 0.00 0.00 0.00 2.57
2067 2913 2.362503 ATCGCCGTCTCCAGGTCA 60.363 61.111 0.00 0.00 0.00 4.02
2283 3129 1.298413 CATCACCGTCTCGTAGCCG 60.298 63.158 0.00 0.00 0.00 5.52
2397 3243 1.153489 CATCTCCAGGCAGGTCACG 60.153 63.158 0.00 0.00 39.02 4.35
2400 3246 1.222936 CACCATCTCCAGGCAGGTC 59.777 63.158 0.00 0.00 39.02 3.85
2572 3421 1.466025 TACCGCGAAACCTCCTGTGT 61.466 55.000 8.23 0.00 0.00 3.72
2630 3483 6.327279 TGATAAAACGTCTCTCAACTCTGA 57.673 37.500 0.00 0.00 0.00 3.27
2742 3595 1.816074 TACATTGGTTTGAGCGGGAC 58.184 50.000 0.00 0.00 0.00 4.46
2743 3596 2.799126 ATACATTGGTTTGAGCGGGA 57.201 45.000 0.00 0.00 0.00 5.14
2744 3597 4.035208 GTCTTATACATTGGTTTGAGCGGG 59.965 45.833 0.00 0.00 0.00 6.13
2774 3709 4.552166 AAACAACTTCCGTCACTCATTG 57.448 40.909 0.00 0.00 0.00 2.82
2776 3711 4.451900 AGAAAACAACTTCCGTCACTCAT 58.548 39.130 0.00 0.00 0.00 2.90
2855 3853 0.176680 AAGCATAGTCCTGGCGTGAG 59.823 55.000 0.00 0.00 0.00 3.51
2862 3860 2.026822 AGGTTGGTGAAGCATAGTCCTG 60.027 50.000 0.00 0.00 31.56 3.86
2867 3865 2.119801 AGCAGGTTGGTGAAGCATAG 57.880 50.000 0.00 0.00 31.56 2.23
2871 3869 1.160137 CACTAGCAGGTTGGTGAAGC 58.840 55.000 0.00 0.00 32.12 3.86
2880 3878 3.006967 CCCGATAATAAGCACTAGCAGGT 59.993 47.826 0.00 0.00 45.49 4.00
2882 3880 2.996621 GCCCGATAATAAGCACTAGCAG 59.003 50.000 0.00 0.00 45.49 4.24
2890 3888 2.548480 GTGTCCTTGCCCGATAATAAGC 59.452 50.000 0.00 0.00 0.00 3.09
2913 3914 8.554835 ACTCTTCTACTTCTAGCAAAAATTCC 57.445 34.615 0.00 0.00 0.00 3.01
2922 3923 8.083462 ACTTTGTGTAACTCTTCTACTTCTAGC 58.917 37.037 0.00 0.00 38.04 3.42
2980 3993 5.156608 TCAAGATCAGTTGAGAATCTGCA 57.843 39.130 0.00 0.00 34.92 4.41
3021 4034 4.967084 TGGTTACTTCTCCACTTGCTAA 57.033 40.909 0.00 0.00 0.00 3.09
3022 4035 4.967084 TTGGTTACTTCTCCACTTGCTA 57.033 40.909 0.00 0.00 33.12 3.49
3034 4047 4.649218 ACCTGTTGCTTCATTTGGTTACTT 59.351 37.500 0.00 0.00 0.00 2.24
3092 4107 6.635641 GGTGAAAAAGTGAATTTCGTAAGGAC 59.364 38.462 0.00 0.00 39.17 3.85
3099 4115 6.033341 TCTGTTGGTGAAAAAGTGAATTTCG 58.967 36.000 0.00 0.00 39.17 3.46
3153 4169 0.459899 TGTGTCGTGAGCTTGTGTCT 59.540 50.000 0.00 0.00 0.00 3.41
3239 4255 4.405036 GCACCTAGGCCTACTTAGTTACTT 59.595 45.833 8.91 0.00 0.00 2.24
3344 4360 3.691498 CTTTGGGTTCGTCAACTTTGTC 58.309 45.455 0.00 0.00 32.50 3.18
3479 4495 0.592148 ACGAGAACTCTGTCCGTGTC 59.408 55.000 0.00 0.00 31.85 3.67
3638 4654 3.382832 AAGGACCTCGCTCCACCG 61.383 66.667 0.00 0.00 31.94 4.94


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

AutoCloner maintained by Alex Coulton.