Multiple sequence alignment - TraesCS6B01G321100

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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 TraesCS6B01G321100 chr6B 100.000 3465 0 0 1 3465 568260128 568256664 0.000000e+00 6399
1 TraesCS6B01G321100 chr6D 93.981 2891 101 36 139 2991 380801680 380798825 0.000000e+00 4307
2 TraesCS6B01G321100 chr6D 88.671 459 37 5 2978 3428 380797420 380796969 2.350000e-151 545
3 TraesCS6B01G321100 chr6A 91.826 2251 80 38 1244 3465 522227314 522225139 0.000000e+00 3042
4 TraesCS6B01G321100 chr6A 92.522 1003 61 10 216 1212 522228308 522227314 0.000000e+00 1424
5 TraesCS6B01G321100 chr4D 83.010 206 33 2 1530 1734 457075140 457075344 5.910000e-43 185
6 TraesCS6B01G321100 chr4D 80.556 216 36 5 1530 1742 471961691 471961903 9.950000e-36 161
7 TraesCS6B01G321100 chr4B 83.010 206 33 2 1530 1734 571049182 571048978 5.910000e-43 185
8 TraesCS6B01G321100 chr4B 81.481 216 34 5 1530 1742 593422904 593423116 4.600000e-39 172
9 TraesCS6B01G321100 chr4B 83.916 143 13 6 3 137 16879426 16879286 1.010000e-25 128
10 TraesCS6B01G321100 chr4A 83.010 206 33 2 1530 1734 11297792 11297996 5.910000e-43 185
11 TraesCS6B01G321100 chr4A 81.106 217 33 7 1530 1742 678872435 678872647 2.140000e-37 167
12 TraesCS6B01G321100 chr4A 83.571 140 13 8 9 140 704150044 704149907 4.700000e-24 122
13 TraesCS6B01G321100 chr1B 87.143 140 17 1 3 141 183262544 183262405 1.290000e-34 158
14 TraesCS6B01G321100 chr2B 87.500 136 11 3 3 138 769955435 769955564 5.990000e-33 152
15 TraesCS6B01G321100 chr2B 86.525 141 11 7 3 139 756671640 756671504 7.750000e-32 148
16 TraesCS6B01G321100 chr5B 86.029 136 16 3 2 136 120303549 120303682 3.600000e-30 143
17 TraesCS6B01G321100 chr5A 87.023 131 12 4 13 140 640684250 640684122 3.600000e-30 143
18 TraesCS6B01G321100 chr2D 84.783 138 13 4 3 138 118470089 118470220 7.800000e-27 132
19 TraesCS6B01G321100 chr3D 84.848 132 15 4 11 137 46491114 46490983 1.010000e-25 128


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 TraesCS6B01G321100 chr6B 568256664 568260128 3464 True 6399 6399 100.000 1 3465 1 chr6B.!!$R1 3464
1 TraesCS6B01G321100 chr6D 380796969 380801680 4711 True 2426 4307 91.326 139 3428 2 chr6D.!!$R1 3289
2 TraesCS6B01G321100 chr6A 522225139 522228308 3169 True 2233 3042 92.174 216 3465 2 chr6A.!!$R1 3249

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
755 767 0.105401 AGGAAGTAGCTAGGCCTCCC 60.105 60.0 9.68 0.22 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 2552 0.03582 GACCCAACATTACAGCGGGA 60.036 55.0 0.0 0.0 39.44 5.14 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
17 18 4.717313 GAAGGTCCGGCGGGCTTT 62.717 66.667 28.46 28.46 0.00 3.51
18 19 4.280019 AAGGTCCGGCGGGCTTTT 62.280 61.111 31.34 21.41 0.00 2.27
19 20 3.802852 AAGGTCCGGCGGGCTTTTT 62.803 57.895 31.34 18.85 0.00 1.94
20 21 4.050934 GGTCCGGCGGGCTTTTTG 62.051 66.667 31.34 0.00 0.00 2.44
21 22 4.717629 GTCCGGCGGGCTTTTTGC 62.718 66.667 25.70 1.27 41.94 3.68
25 26 3.972276 GGCGGGCTTTTTGCGTGA 61.972 61.111 0.00 0.00 44.05 4.35
26 27 2.258286 GCGGGCTTTTTGCGTGAT 59.742 55.556 0.00 0.00 44.05 3.06
27 28 2.088178 GCGGGCTTTTTGCGTGATG 61.088 57.895 0.00 0.00 44.05 3.07
28 29 1.444212 CGGGCTTTTTGCGTGATGG 60.444 57.895 0.00 0.00 44.05 3.51
29 30 1.079888 GGGCTTTTTGCGTGATGGG 60.080 57.895 0.00 0.00 44.05 4.00
30 31 1.737735 GGCTTTTTGCGTGATGGGC 60.738 57.895 0.00 0.00 44.05 5.36
31 32 1.737735 GCTTTTTGCGTGATGGGCC 60.738 57.895 0.00 0.00 0.00 5.80
32 33 1.664873 CTTTTTGCGTGATGGGCCA 59.335 52.632 9.61 9.61 0.00 5.36
33 34 0.388907 CTTTTTGCGTGATGGGCCAG 60.389 55.000 13.78 0.00 0.00 4.85
34 35 1.814772 TTTTTGCGTGATGGGCCAGG 61.815 55.000 13.78 2.06 0.00 4.45
38 39 3.136123 CGTGATGGGCCAGGCTTG 61.136 66.667 13.78 0.00 0.00 4.01
40 41 4.064768 TGATGGGCCAGGCTTGGG 62.065 66.667 17.71 0.34 45.16 4.12
54 55 3.510388 GCTTGGGCCTGATTTTTAGAC 57.490 47.619 4.53 0.00 0.00 2.59
55 56 2.166459 GCTTGGGCCTGATTTTTAGACC 59.834 50.000 4.53 0.00 0.00 3.85
56 57 2.525105 TGGGCCTGATTTTTAGACCC 57.475 50.000 4.53 0.00 36.36 4.46
57 58 1.340600 TGGGCCTGATTTTTAGACCCG 60.341 52.381 4.53 0.00 38.79 5.28
58 59 1.064979 GGGCCTGATTTTTAGACCCGA 60.065 52.381 0.84 0.00 0.00 5.14
59 60 2.422945 GGGCCTGATTTTTAGACCCGAT 60.423 50.000 0.84 0.00 0.00 4.18
60 61 2.618709 GGCCTGATTTTTAGACCCGATG 59.381 50.000 0.00 0.00 0.00 3.84
61 62 2.618709 GCCTGATTTTTAGACCCGATGG 59.381 50.000 0.00 0.00 37.80 3.51
62 63 2.618709 CCTGATTTTTAGACCCGATGGC 59.381 50.000 0.00 0.00 33.59 4.40
63 64 2.618709 CTGATTTTTAGACCCGATGGCC 59.381 50.000 0.00 0.00 33.59 5.36
64 65 1.602377 GATTTTTAGACCCGATGGCCG 59.398 52.381 0.00 0.00 38.18 6.13
65 66 0.614294 TTTTTAGACCCGATGGCCGA 59.386 50.000 0.00 0.00 41.76 5.54
66 67 0.177141 TTTTAGACCCGATGGCCGAG 59.823 55.000 0.00 0.00 41.76 4.63
67 68 2.306255 TTTAGACCCGATGGCCGAGC 62.306 60.000 0.00 0.00 41.76 5.03
85 86 3.148279 CGAGCTCGGGCCTAGGTT 61.148 66.667 28.40 0.00 39.73 3.50
86 87 2.722201 CGAGCTCGGGCCTAGGTTT 61.722 63.158 28.40 0.00 39.73 3.27
87 88 1.389609 CGAGCTCGGGCCTAGGTTTA 61.390 60.000 28.40 0.00 39.73 2.01
88 89 1.049402 GAGCTCGGGCCTAGGTTTAT 58.951 55.000 11.37 0.00 39.73 1.40
89 90 1.416772 GAGCTCGGGCCTAGGTTTATT 59.583 52.381 11.37 0.00 39.73 1.40
90 91 1.141053 AGCTCGGGCCTAGGTTTATTG 59.859 52.381 11.31 0.00 39.73 1.90
91 92 1.134189 GCTCGGGCCTAGGTTTATTGT 60.134 52.381 11.31 0.00 0.00 2.71
92 93 2.561569 CTCGGGCCTAGGTTTATTGTG 58.438 52.381 11.31 0.00 0.00 3.33
93 94 1.021968 CGGGCCTAGGTTTATTGTGC 58.978 55.000 11.31 0.00 0.00 4.57
94 95 1.399714 GGGCCTAGGTTTATTGTGCC 58.600 55.000 11.31 1.23 36.68 5.01
95 96 1.021968 GGCCTAGGTTTATTGTGCCG 58.978 55.000 11.31 0.00 0.00 5.69
96 97 1.021968 GCCTAGGTTTATTGTGCCGG 58.978 55.000 11.31 0.00 0.00 6.13
97 98 1.675552 CCTAGGTTTATTGTGCCGGG 58.324 55.000 2.18 0.00 0.00 5.73
98 99 1.021968 CTAGGTTTATTGTGCCGGGC 58.978 55.000 13.32 13.32 0.00 6.13
99 100 0.621609 TAGGTTTATTGTGCCGGGCT 59.378 50.000 21.46 1.61 0.00 5.19
100 101 0.251608 AGGTTTATTGTGCCGGGCTT 60.252 50.000 21.46 5.14 0.00 4.35
101 102 0.606096 GGTTTATTGTGCCGGGCTTT 59.394 50.000 21.46 4.77 0.00 3.51
102 103 1.671556 GGTTTATTGTGCCGGGCTTTG 60.672 52.381 21.46 0.00 0.00 2.77
103 104 0.605589 TTTATTGTGCCGGGCTTTGG 59.394 50.000 21.46 0.00 0.00 3.28
104 105 0.540830 TTATTGTGCCGGGCTTTGGT 60.541 50.000 21.46 5.24 0.00 3.67
105 106 0.328592 TATTGTGCCGGGCTTTGGTA 59.671 50.000 21.46 4.25 0.00 3.25
106 107 0.965363 ATTGTGCCGGGCTTTGGTAG 60.965 55.000 21.46 0.00 0.00 3.18
107 108 2.750237 GTGCCGGGCTTTGGTAGG 60.750 66.667 21.46 0.00 0.00 3.18
133 134 4.864334 GCCCGACAGATGGCCAGG 62.864 72.222 13.05 6.01 41.97 4.45
134 135 3.402681 CCCGACAGATGGCCAGGT 61.403 66.667 13.05 9.65 0.00 4.00
135 136 2.063979 CCCGACAGATGGCCAGGTA 61.064 63.158 13.05 0.00 0.00 3.08
136 137 1.410850 CCCGACAGATGGCCAGGTAT 61.411 60.000 13.05 0.00 0.00 2.73
137 138 1.338107 CCGACAGATGGCCAGGTATA 58.662 55.000 13.05 0.00 0.00 1.47
142 143 0.681733 AGATGGCCAGGTATAGTGCG 59.318 55.000 13.05 0.00 0.00 5.34
225 227 5.242393 ACATGAGAAAAGAACATGGTTCCAG 59.758 40.000 0.00 0.00 43.55 3.86
256 258 5.331906 AGATCTTGATAGCATAGAGAGCCA 58.668 41.667 0.00 0.00 0.00 4.75
270 272 0.842635 GAGCCATCTCCAACCTCCAT 59.157 55.000 0.00 0.00 33.19 3.41
273 275 1.771255 GCCATCTCCAACCTCCATACT 59.229 52.381 0.00 0.00 0.00 2.12
284 286 5.365605 CCAACCTCCATACTATGTAAGGTCA 59.634 44.000 15.72 0.00 41.16 4.02
511 519 3.138304 CAAGGGACAAACTCGTCAATCA 58.862 45.455 0.00 0.00 37.66 2.57
521 529 1.671054 CGTCAATCAACACCGCCCT 60.671 57.895 0.00 0.00 0.00 5.19
626 635 5.640732 CAATAGAAAATTGGTTGTCCCTCG 58.359 41.667 0.00 0.00 0.00 4.63
627 636 3.223674 AGAAAATTGGTTGTCCCTCGT 57.776 42.857 0.00 0.00 0.00 4.18
641 650 5.860611 TGTCCCTCGTTAAGAAAATCAAGA 58.139 37.500 0.00 0.00 0.00 3.02
715 725 2.125106 GCCGAATTGTCCCGCTCT 60.125 61.111 0.00 0.00 0.00 4.09
718 728 1.079127 CGAATTGTCCCGCTCTGGT 60.079 57.895 0.00 0.00 35.15 4.00
719 729 0.673644 CGAATTGTCCCGCTCTGGTT 60.674 55.000 0.00 0.00 35.15 3.67
738 748 4.856607 GCGTCTTCTCCGGCGAGG 62.857 72.222 9.30 0.00 42.97 4.63
750 762 1.364536 GGCGAGGAAGTAGCTAGGC 59.635 63.158 0.00 0.00 0.00 3.93
751 763 1.364536 GCGAGGAAGTAGCTAGGCC 59.635 63.158 0.00 0.00 0.00 5.19
752 764 1.110518 GCGAGGAAGTAGCTAGGCCT 61.111 60.000 11.78 11.78 0.00 5.19
755 767 0.105401 AGGAAGTAGCTAGGCCTCCC 60.105 60.000 9.68 0.22 0.00 4.30
756 768 0.398664 GGAAGTAGCTAGGCCTCCCA 60.399 60.000 9.68 0.00 0.00 4.37
760 772 1.116536 GTAGCTAGGCCTCCCACTCC 61.117 65.000 9.68 0.00 0.00 3.85
765 777 2.243774 TAGGCCTCCCACTCCTCCTG 62.244 65.000 9.68 0.00 0.00 3.86
770 782 0.252012 CTCCCACTCCTCCTGTGAGT 60.252 60.000 0.00 0.00 43.70 3.41
782 794 1.229209 TGTGAGTGGTCTCCTCCCC 60.229 63.158 0.00 0.00 39.75 4.81
1112 1128 2.570752 ACAGATGCTCTTCATGGACTGT 59.429 45.455 0.00 0.00 34.70 3.55
1173 1189 6.462207 CCATCGAGGTATCATATTCTCATCCC 60.462 46.154 0.00 0.00 0.00 3.85
1212 1228 1.264826 CCGGTTGTTTGGTTCGTTAGG 59.735 52.381 0.00 0.00 0.00 2.69
1213 1229 1.334329 CGGTTGTTTGGTTCGTTAGGC 60.334 52.381 0.00 0.00 0.00 3.93
1214 1230 1.677052 GGTTGTTTGGTTCGTTAGGCA 59.323 47.619 0.00 0.00 0.00 4.75
1215 1231 2.099427 GGTTGTTTGGTTCGTTAGGCAA 59.901 45.455 0.00 0.00 0.00 4.52
1216 1232 3.368495 GTTGTTTGGTTCGTTAGGCAAG 58.632 45.455 0.00 0.00 0.00 4.01
1217 1233 2.645802 TGTTTGGTTCGTTAGGCAAGT 58.354 42.857 0.00 0.00 0.00 3.16
1218 1234 3.806380 TGTTTGGTTCGTTAGGCAAGTA 58.194 40.909 0.00 0.00 0.00 2.24
1219 1235 3.810941 TGTTTGGTTCGTTAGGCAAGTAG 59.189 43.478 0.00 0.00 0.00 2.57
1221 1237 2.250031 TGGTTCGTTAGGCAAGTAGGA 58.750 47.619 0.00 0.00 0.00 2.94
1222 1238 2.232941 TGGTTCGTTAGGCAAGTAGGAG 59.767 50.000 0.00 0.00 0.00 3.69
1224 1240 3.445096 GGTTCGTTAGGCAAGTAGGAGTA 59.555 47.826 0.00 0.00 0.00 2.59
1225 1241 4.439837 GGTTCGTTAGGCAAGTAGGAGTAG 60.440 50.000 0.00 0.00 0.00 2.57
1226 1242 2.686915 TCGTTAGGCAAGTAGGAGTAGC 59.313 50.000 0.00 0.00 0.00 3.58
1228 1244 3.130693 CGTTAGGCAAGTAGGAGTAGCTT 59.869 47.826 0.00 0.00 0.00 3.74
1240 1257 3.067833 GGAGTAGCTTTTGTGTGGAGAC 58.932 50.000 0.00 0.00 0.00 3.36
1442 1459 0.670546 CGGAGCAGGTGACAATTCGT 60.671 55.000 0.00 0.00 0.00 3.85
1765 1795 1.905512 GGCTCCGGTCACAGGTAAT 59.094 57.895 0.00 0.00 0.00 1.89
1779 1816 4.578516 CACAGGTAATCAAAGTCAACCACA 59.421 41.667 0.00 0.00 32.43 4.17
2061 2102 0.624254 TGAAGGACGAGGAGAGGCTA 59.376 55.000 0.00 0.00 0.00 3.93
2499 2552 6.959639 TTGTTTTCTCTCCTTGTATGCTTT 57.040 33.333 0.00 0.00 0.00 3.51
2519 2572 1.366111 CCCGCTGTAATGTTGGGTCG 61.366 60.000 0.00 0.00 35.05 4.79
2520 2573 1.366111 CCGCTGTAATGTTGGGTCGG 61.366 60.000 0.00 0.00 0.00 4.79
2543 2596 1.255342 CGATCGACCAAGTTGTATGCG 59.745 52.381 10.26 0.33 0.00 4.73
2658 2714 3.632643 TGGCACAGTACATCATGTCAT 57.367 42.857 0.00 0.00 0.00 3.06
2659 2715 3.272581 TGGCACAGTACATCATGTCATG 58.727 45.455 6.47 6.47 0.00 3.07
2661 2717 3.310774 GGCACAGTACATCATGTCATGTC 59.689 47.826 12.54 0.00 38.07 3.06
2663 2719 4.392754 GCACAGTACATCATGTCATGTCAA 59.607 41.667 12.54 0.00 38.07 3.18
2664 2720 5.106594 GCACAGTACATCATGTCATGTCAAA 60.107 40.000 12.54 0.00 38.07 2.69
2665 2721 6.403964 GCACAGTACATCATGTCATGTCAAAT 60.404 38.462 12.54 0.00 38.07 2.32
2666 2722 6.964934 CACAGTACATCATGTCATGTCAAATG 59.035 38.462 12.54 10.83 38.07 2.32
2667 2723 6.880529 ACAGTACATCATGTCATGTCAAATGA 59.119 34.615 18.60 10.65 38.07 2.57
2668 2724 7.065443 ACAGTACATCATGTCATGTCAAATGAG 59.935 37.037 18.60 11.12 38.07 2.90
2669 2725 7.279313 CAGTACATCATGTCATGTCAAATGAGA 59.721 37.037 18.60 8.57 38.07 3.27
2670 2726 7.991460 AGTACATCATGTCATGTCAAATGAGAT 59.009 33.333 18.60 7.22 38.07 2.75
2671 2727 7.640597 ACATCATGTCATGTCAAATGAGATT 57.359 32.000 18.60 1.97 30.76 2.40
2672 2728 8.063200 ACATCATGTCATGTCAAATGAGATTT 57.937 30.769 18.60 0.00 30.76 2.17
2702 2759 4.775058 ATCATCTACTGCTATGTCGTCC 57.225 45.455 0.00 0.00 0.00 4.79
2762 2821 0.515127 TACGTGCGCTCATGGTTTTG 59.485 50.000 9.73 0.00 33.54 2.44
2764 2823 0.317770 CGTGCGCTCATGGTTTTGTT 60.318 50.000 9.73 0.00 0.00 2.83
2779 2838 4.513692 GGTTTTGTTGTATTTTTGGCCTCC 59.486 41.667 3.32 0.00 0.00 4.30
2881 2940 8.568676 TTATGTCATATTTTTCGGACCTTTCA 57.431 30.769 0.00 0.00 0.00 2.69
2883 2942 6.674066 TGTCATATTTTTCGGACCTTTCAAC 58.326 36.000 0.00 0.00 0.00 3.18
3005 4484 4.564769 TGAACCTTGCGAATTCAACAAAAC 59.435 37.500 6.22 2.69 29.56 2.43
3035 4522 2.019984 GGCAACCTATCTCAAAGCCTG 58.980 52.381 0.00 0.00 37.67 4.85
3066 4553 9.410556 CAACAGAAAATACTATTGAAACTTGGG 57.589 33.333 0.00 0.00 0.00 4.12
3087 4574 4.696402 GGGTATATTGTTGTTGTTGACCGA 59.304 41.667 0.00 0.00 0.00 4.69
3094 4581 5.176407 TGTTGTTGTTGACCGATTTTAGG 57.824 39.130 0.00 0.00 0.00 2.69
3154 4641 0.787787 TCAAATCGAACTTGGCGTCG 59.212 50.000 9.89 0.00 0.00 5.12
3174 4661 1.254313 GCGGTTCAGCGTTTTGAAAAC 59.746 47.619 10.62 10.62 38.69 2.43
3176 4663 3.112580 CGGTTCAGCGTTTTGAAAACAT 58.887 40.909 19.46 5.75 38.69 2.71
3199 4686 9.023962 ACATTTTCTTTATTCACTTATGGAGCA 57.976 29.630 0.00 0.00 0.00 4.26
3209 4696 4.070716 CACTTATGGAGCAATCATCCTCC 58.929 47.826 0.00 0.00 46.25 4.30
3238 4725 8.840321 ACCTAATTTTGTCTATGCATCATACAC 58.160 33.333 0.19 0.00 0.00 2.90
3319 4806 6.894682 AGATATTCAGGAAAAGGAGAGGTTC 58.105 40.000 0.00 0.00 0.00 3.62
3356 4843 7.657336 ACATTCATAATTGAGAAACAACCGTT 58.343 30.769 0.00 0.00 41.52 4.44
3357 4844 7.594758 ACATTCATAATTGAGAAACAACCGTTG 59.405 33.333 9.80 9.80 41.52 4.10
3358 4845 6.007936 TCATAATTGAGAAACAACCGTTGG 57.992 37.500 15.60 0.00 41.52 3.77
3359 4846 5.533154 TCATAATTGAGAAACAACCGTTGGT 59.467 36.000 15.60 6.05 41.52 3.67
3360 4847 7.416890 TTCATAATTGAGAAACAACCGTTGGTT 60.417 33.333 14.45 14.45 44.75 3.67
3361 4848 5.838531 AATTGAGAAACAACCGTTGGTTA 57.161 34.783 14.52 0.00 45.01 2.85
3362 4849 4.886247 TTGAGAAACAACCGTTGGTTAG 57.114 40.909 14.52 0.00 45.01 2.34
3363 4850 4.139859 TGAGAAACAACCGTTGGTTAGA 57.860 40.909 14.52 0.00 45.01 2.10
3410 4905 7.733608 AGAGCGATGATATTTTTACGCAATAG 58.266 34.615 0.00 0.00 46.65 1.73
3428 4923 9.953697 ACGCAATAGTTTTACAAAAATCTTACA 57.046 25.926 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.717313 AAAGCCCGCCGGACCTTC 62.717 66.667 5.05 0.00 0.00 3.46
1 2 3.802852 AAAAAGCCCGCCGGACCTT 62.803 57.895 5.05 3.65 0.00 3.50
2 3 4.280019 AAAAAGCCCGCCGGACCT 62.280 61.111 5.05 0.00 0.00 3.85
3 4 4.050934 CAAAAAGCCCGCCGGACC 62.051 66.667 5.05 0.00 0.00 4.46
4 5 4.717629 GCAAAAAGCCCGCCGGAC 62.718 66.667 5.05 0.00 37.23 4.79
8 9 3.281359 ATCACGCAAAAAGCCCGCC 62.281 57.895 0.00 0.00 41.38 6.13
9 10 2.088178 CATCACGCAAAAAGCCCGC 61.088 57.895 0.00 0.00 41.38 6.13
10 11 1.444212 CCATCACGCAAAAAGCCCG 60.444 57.895 0.00 0.00 41.38 6.13
11 12 1.079888 CCCATCACGCAAAAAGCCC 60.080 57.895 0.00 0.00 41.38 5.19
12 13 1.737735 GCCCATCACGCAAAAAGCC 60.738 57.895 0.00 0.00 41.38 4.35
13 14 1.737735 GGCCCATCACGCAAAAAGC 60.738 57.895 0.00 0.00 40.87 3.51
14 15 0.388907 CTGGCCCATCACGCAAAAAG 60.389 55.000 0.00 0.00 0.00 2.27
15 16 1.664873 CTGGCCCATCACGCAAAAA 59.335 52.632 0.00 0.00 0.00 1.94
16 17 2.274645 CCTGGCCCATCACGCAAAA 61.275 57.895 0.00 0.00 0.00 2.44
17 18 2.676121 CCTGGCCCATCACGCAAA 60.676 61.111 0.00 0.00 0.00 3.68
21 22 3.136123 CAAGCCTGGCCCATCACG 61.136 66.667 16.57 0.00 0.00 4.35
22 23 2.757099 CCAAGCCTGGCCCATCAC 60.757 66.667 16.57 0.00 35.39 3.06
23 24 4.064768 CCCAAGCCTGGCCCATCA 62.065 66.667 16.57 0.00 41.99 3.07
34 35 2.166459 GGTCTAAAAATCAGGCCCAAGC 59.834 50.000 0.00 0.00 31.16 4.01
39 40 2.413310 TCGGGTCTAAAAATCAGGCC 57.587 50.000 0.00 0.00 37.04 5.19
40 41 2.618709 CCATCGGGTCTAAAAATCAGGC 59.381 50.000 0.00 0.00 0.00 4.85
41 42 2.618709 GCCATCGGGTCTAAAAATCAGG 59.381 50.000 0.00 0.00 36.17 3.86
42 43 2.618709 GGCCATCGGGTCTAAAAATCAG 59.381 50.000 0.00 0.00 35.27 2.90
43 44 2.650322 GGCCATCGGGTCTAAAAATCA 58.350 47.619 0.00 0.00 35.27 2.57
44 45 1.602377 CGGCCATCGGGTCTAAAAATC 59.398 52.381 2.24 0.00 36.31 2.17
45 46 1.210967 TCGGCCATCGGGTCTAAAAAT 59.789 47.619 2.24 0.00 36.31 1.82
46 47 0.614294 TCGGCCATCGGGTCTAAAAA 59.386 50.000 2.24 0.00 36.31 1.94
47 48 0.177141 CTCGGCCATCGGGTCTAAAA 59.823 55.000 2.24 0.00 36.31 1.52
48 49 1.820581 CTCGGCCATCGGGTCTAAA 59.179 57.895 2.24 0.00 36.31 1.85
49 50 2.792947 GCTCGGCCATCGGGTCTAA 61.793 63.158 2.24 0.00 42.39 2.10
50 51 3.224324 GCTCGGCCATCGGGTCTA 61.224 66.667 2.24 0.00 42.39 2.59
68 69 1.389609 TAAACCTAGGCCCGAGCTCG 61.390 60.000 29.06 29.06 39.73 5.03
69 70 1.049402 ATAAACCTAGGCCCGAGCTC 58.951 55.000 9.30 2.73 39.73 4.09
70 71 1.141053 CAATAAACCTAGGCCCGAGCT 59.859 52.381 9.30 0.00 39.73 4.09
71 72 1.134189 ACAATAAACCTAGGCCCGAGC 60.134 52.381 9.30 0.00 38.76 5.03
72 73 2.561569 CACAATAAACCTAGGCCCGAG 58.438 52.381 9.30 0.00 0.00 4.63
73 74 1.407712 GCACAATAAACCTAGGCCCGA 60.408 52.381 9.30 0.00 0.00 5.14
74 75 1.021968 GCACAATAAACCTAGGCCCG 58.978 55.000 9.30 0.00 0.00 6.13
75 76 1.399714 GGCACAATAAACCTAGGCCC 58.600 55.000 9.30 0.00 33.93 5.80
76 77 1.021968 CGGCACAATAAACCTAGGCC 58.978 55.000 9.30 0.00 36.62 5.19
77 78 1.021968 CCGGCACAATAAACCTAGGC 58.978 55.000 9.30 0.00 0.00 3.93
78 79 1.675552 CCCGGCACAATAAACCTAGG 58.324 55.000 7.41 7.41 0.00 3.02
79 80 1.021968 GCCCGGCACAATAAACCTAG 58.978 55.000 3.91 0.00 0.00 3.02
80 81 0.621609 AGCCCGGCACAATAAACCTA 59.378 50.000 13.15 0.00 0.00 3.08
81 82 0.251608 AAGCCCGGCACAATAAACCT 60.252 50.000 13.15 0.00 0.00 3.50
82 83 0.606096 AAAGCCCGGCACAATAAACC 59.394 50.000 13.15 0.00 0.00 3.27
83 84 1.671556 CCAAAGCCCGGCACAATAAAC 60.672 52.381 13.15 0.00 0.00 2.01
84 85 0.605589 CCAAAGCCCGGCACAATAAA 59.394 50.000 13.15 0.00 0.00 1.40
85 86 0.540830 ACCAAAGCCCGGCACAATAA 60.541 50.000 13.15 0.00 0.00 1.40
86 87 0.328592 TACCAAAGCCCGGCACAATA 59.671 50.000 13.15 0.00 0.00 1.90
87 88 0.965363 CTACCAAAGCCCGGCACAAT 60.965 55.000 13.15 0.00 0.00 2.71
88 89 1.602323 CTACCAAAGCCCGGCACAA 60.602 57.895 13.15 0.00 0.00 3.33
89 90 2.033448 CTACCAAAGCCCGGCACA 59.967 61.111 13.15 0.00 0.00 4.57
90 91 2.750237 CCTACCAAAGCCCGGCAC 60.750 66.667 13.15 0.00 0.00 5.01
91 92 4.733542 GCCTACCAAAGCCCGGCA 62.734 66.667 13.15 0.00 40.41 5.69
117 118 1.410850 ATACCTGGCCATCTGTCGGG 61.411 60.000 5.51 4.26 0.00 5.14
118 119 1.273606 CTATACCTGGCCATCTGTCGG 59.726 57.143 5.51 5.16 0.00 4.79
119 120 1.964223 ACTATACCTGGCCATCTGTCG 59.036 52.381 5.51 0.00 0.00 4.35
120 121 2.548920 GCACTATACCTGGCCATCTGTC 60.549 54.545 5.51 0.00 0.00 3.51
121 122 1.417890 GCACTATACCTGGCCATCTGT 59.582 52.381 5.51 6.94 0.00 3.41
122 123 1.606480 CGCACTATACCTGGCCATCTG 60.606 57.143 5.51 0.00 0.00 2.90
123 124 0.681733 CGCACTATACCTGGCCATCT 59.318 55.000 5.51 0.00 0.00 2.90
124 125 0.951040 GCGCACTATACCTGGCCATC 60.951 60.000 5.51 0.00 0.00 3.51
125 126 1.071471 GCGCACTATACCTGGCCAT 59.929 57.895 5.51 0.00 0.00 4.40
126 127 1.695114 ATGCGCACTATACCTGGCCA 61.695 55.000 14.90 4.71 0.00 5.36
127 128 0.320374 TATGCGCACTATACCTGGCC 59.680 55.000 14.90 0.00 0.00 5.36
128 129 2.386661 ATATGCGCACTATACCTGGC 57.613 50.000 14.90 0.00 0.00 4.85
129 130 4.720649 AGTATATGCGCACTATACCTGG 57.279 45.455 27.68 0.00 34.13 4.45
130 131 4.327357 GCAAGTATATGCGCACTATACCTG 59.673 45.833 27.68 26.38 36.45 4.00
131 132 4.495422 GCAAGTATATGCGCACTATACCT 58.505 43.478 27.68 20.30 36.45 3.08
132 133 4.842139 GCAAGTATATGCGCACTATACC 57.158 45.455 27.68 17.95 36.45 2.73
212 214 1.327303 TTGTGGCTGGAACCATGTTC 58.673 50.000 0.00 0.00 43.01 3.18
225 227 4.970662 TGCTATCAAGATCTTTTGTGGC 57.029 40.909 4.86 8.78 0.00 5.01
256 258 6.498651 CCTTACATAGTATGGAGGTTGGAGAT 59.501 42.308 19.36 0.00 34.76 2.75
270 272 7.147549 CCCTTCTGGAAATGACCTTACATAGTA 60.148 40.741 0.00 0.00 35.39 1.82
273 275 5.729229 TCCCTTCTGGAAATGACCTTACATA 59.271 40.000 0.00 0.00 41.40 2.29
437 445 2.221906 ATCGAGACGGAACCAACGGG 62.222 60.000 0.00 0.00 41.29 5.28
613 622 3.842007 TTCTTAACGAGGGACAACCAA 57.158 42.857 0.00 0.00 43.89 3.67
615 624 4.758165 TGATTTTCTTAACGAGGGACAACC 59.242 41.667 0.00 0.00 40.67 3.77
618 627 5.860611 TCTTGATTTTCTTAACGAGGGACA 58.139 37.500 0.00 0.00 0.00 4.02
619 628 6.796705 TTCTTGATTTTCTTAACGAGGGAC 57.203 37.500 0.00 0.00 0.00 4.46
641 650 8.427276 AGCTCAAGAAGAAATGGAAATCTTTTT 58.573 29.630 0.00 0.00 36.08 1.94
653 663 3.331889 TGGAAGGGAGCTCAAGAAGAAAT 59.668 43.478 17.19 0.00 0.00 2.17
664 674 1.774217 TTGGTGGTGGAAGGGAGCT 60.774 57.895 0.00 0.00 0.00 4.09
703 713 1.244019 GCAAACCAGAGCGGGACAAT 61.244 55.000 0.00 0.00 40.22 2.71
715 725 1.301401 CCGGAGAAGACGCAAACCA 60.301 57.895 0.00 0.00 0.00 3.67
718 728 2.736995 CGCCGGAGAAGACGCAAA 60.737 61.111 5.05 0.00 0.00 3.68
719 729 3.626680 CTCGCCGGAGAAGACGCAA 62.627 63.158 9.83 0.00 43.27 4.85
738 748 0.753867 GTGGGAGGCCTAGCTACTTC 59.246 60.000 4.42 0.00 0.00 3.01
739 749 0.340208 AGTGGGAGGCCTAGCTACTT 59.660 55.000 4.42 0.00 0.00 2.24
740 750 0.105913 GAGTGGGAGGCCTAGCTACT 60.106 60.000 4.42 8.30 0.00 2.57
750 762 0.975040 CTCACAGGAGGAGTGGGAGG 60.975 65.000 0.00 0.00 41.13 4.30
751 763 2.589494 CTCACAGGAGGAGTGGGAG 58.411 63.158 0.00 0.00 39.88 4.30
752 764 1.861429 ACTCACAGGAGGAGTGGGA 59.139 57.895 0.00 0.00 45.81 4.37
756 768 0.485099 AGACCACTCACAGGAGGAGT 59.515 55.000 0.00 0.00 46.11 3.85
760 772 1.181786 GAGGAGACCACTCACAGGAG 58.818 60.000 0.00 0.00 46.96 3.69
765 777 2.352032 CGGGGAGGAGACCACTCAC 61.352 68.421 0.00 0.00 44.22 3.51
782 794 2.086251 GAGATCTCCTCAGGCCTGCG 62.086 65.000 28.91 22.52 41.58 5.18
788 800 0.476338 TCCCGAGAGATCTCCTCAGG 59.524 60.000 19.30 16.00 44.40 3.86
1173 1189 3.004524 CCGGGATCGAGAAAACTAGTAGG 59.995 52.174 0.00 0.00 39.00 3.18
1212 1228 4.065789 ACACAAAAGCTACTCCTACTTGC 58.934 43.478 0.00 0.00 0.00 4.01
1213 1229 4.452455 CCACACAAAAGCTACTCCTACTTG 59.548 45.833 0.00 0.00 0.00 3.16
1214 1230 4.347000 TCCACACAAAAGCTACTCCTACTT 59.653 41.667 0.00 0.00 0.00 2.24
1215 1231 3.901844 TCCACACAAAAGCTACTCCTACT 59.098 43.478 0.00 0.00 0.00 2.57
1216 1232 4.021368 TCTCCACACAAAAGCTACTCCTAC 60.021 45.833 0.00 0.00 0.00 3.18
1217 1233 4.021368 GTCTCCACACAAAAGCTACTCCTA 60.021 45.833 0.00 0.00 0.00 2.94
1218 1234 2.972713 TCTCCACACAAAAGCTACTCCT 59.027 45.455 0.00 0.00 0.00 3.69
1219 1235 3.067833 GTCTCCACACAAAAGCTACTCC 58.932 50.000 0.00 0.00 0.00 3.85
1221 1237 3.495100 CCAGTCTCCACACAAAAGCTACT 60.495 47.826 0.00 0.00 0.00 2.57
1222 1238 2.808543 CCAGTCTCCACACAAAAGCTAC 59.191 50.000 0.00 0.00 0.00 3.58
1224 1240 1.490490 TCCAGTCTCCACACAAAAGCT 59.510 47.619 0.00 0.00 0.00 3.74
1225 1241 1.876156 CTCCAGTCTCCACACAAAAGC 59.124 52.381 0.00 0.00 0.00 3.51
1226 1242 3.181461 ACTCTCCAGTCTCCACACAAAAG 60.181 47.826 0.00 0.00 0.00 2.27
1228 1244 2.103094 CACTCTCCAGTCTCCACACAAA 59.897 50.000 0.00 0.00 0.00 2.83
1240 1257 3.511540 TCAGTACACCAATCACTCTCCAG 59.488 47.826 0.00 0.00 0.00 3.86
1454 1474 4.712191 GATGAACAGAGCATCATCTTCG 57.288 45.455 8.17 0.00 45.41 3.79
1765 1795 3.013921 GGTGAAGTGTGGTTGACTTTGA 58.986 45.455 0.00 0.00 33.71 2.69
1812 1849 3.507162 TCTCCCAAATCAAACTCAGCA 57.493 42.857 0.00 0.00 0.00 4.41
1954 1995 1.021920 GCCAAGGAAGTCTTCGCCTC 61.022 60.000 6.50 0.00 34.21 4.70
1955 1996 1.003233 GCCAAGGAAGTCTTCGCCT 60.003 57.895 6.50 0.00 34.21 5.52
1956 1997 3.579685 GCCAAGGAAGTCTTCGCC 58.420 61.111 6.50 0.00 34.21 5.54
1957 1998 2.391389 CGGCCAAGGAAGTCTTCGC 61.391 63.158 2.24 4.33 38.59 4.70
1958 1999 1.014564 GTCGGCCAAGGAAGTCTTCG 61.015 60.000 2.24 0.00 32.41 3.79
1959 2000 1.014564 CGTCGGCCAAGGAAGTCTTC 61.015 60.000 2.24 3.80 32.41 2.87
2028 2069 1.241990 CCTTCACATGCAGCTGCTGT 61.242 55.000 36.61 31.36 42.66 4.40
2029 2070 0.958876 TCCTTCACATGCAGCTGCTG 60.959 55.000 36.61 30.76 42.66 4.41
2030 2071 0.959372 GTCCTTCACATGCAGCTGCT 60.959 55.000 36.61 20.88 42.66 4.24
2031 2072 1.505353 GTCCTTCACATGCAGCTGC 59.495 57.895 31.89 31.89 42.50 5.25
2032 2073 0.671472 TCGTCCTTCACATGCAGCTG 60.671 55.000 10.11 10.11 0.00 4.24
2033 2074 0.390866 CTCGTCCTTCACATGCAGCT 60.391 55.000 0.00 0.00 0.00 4.24
2229 2270 0.179026 CGTCCTCCTCCGACTGGATA 60.179 60.000 0.00 0.00 45.33 2.59
2326 2367 2.347490 GTCCGTGTGATGGTGGCT 59.653 61.111 0.00 0.00 0.00 4.75
2432 2481 8.088365 ACTGATATACGAAATTGATCGATTCCA 58.912 33.333 8.68 0.00 45.48 3.53
2433 2482 8.467402 ACTGATATACGAAATTGATCGATTCC 57.533 34.615 8.68 0.00 45.48 3.01
2499 2552 0.035820 GACCCAACATTACAGCGGGA 60.036 55.000 0.00 0.00 39.44 5.14
2519 2572 2.358939 ACAACTTGGTCGATCGTACC 57.641 50.000 22.20 22.20 37.53 3.34
2520 2573 3.242248 GCATACAACTTGGTCGATCGTAC 59.758 47.826 15.94 11.61 0.00 3.67
2543 2596 5.919141 CCCTAACTCGTACTACAATGCATAC 59.081 44.000 0.00 0.00 0.00 2.39
2555 2611 7.414540 CCACCGATATATTACCCTAACTCGTAC 60.415 44.444 0.00 0.00 0.00 3.67
2702 2759 3.181520 CCGGCTTGATCTTACAAAACTCG 60.182 47.826 0.00 0.00 0.00 4.18
2762 2821 2.252714 TGGGGAGGCCAAAAATACAAC 58.747 47.619 5.01 0.00 0.00 3.32
2764 2823 2.704190 TTGGGGAGGCCAAAAATACA 57.296 45.000 5.01 0.00 0.00 2.29
2779 2838 7.123355 TCTATGGCCTTTTCATATTTTTGGG 57.877 36.000 3.32 0.00 0.00 4.12
2880 2939 2.383855 TGGAGGGTGGTTTCTTTGTTG 58.616 47.619 0.00 0.00 0.00 3.33
2881 2940 2.838637 TGGAGGGTGGTTTCTTTGTT 57.161 45.000 0.00 0.00 0.00 2.83
2883 2942 2.102420 GGTTTGGAGGGTGGTTTCTTTG 59.898 50.000 0.00 0.00 0.00 2.77
2952 3013 5.874093 TCCATAAACCCAATTGTTTGCAAT 58.126 33.333 0.00 0.00 46.38 3.56
2956 3017 7.661027 ACAATTCTCCATAAACCCAATTGTTTG 59.339 33.333 4.43 0.00 40.04 2.93
3005 4484 1.037030 ATAGGTTGCCGCCCATGTTG 61.037 55.000 0.00 0.00 0.00 3.33
3066 4553 8.736751 AAAATCGGTCAACAACAACAATATAC 57.263 30.769 0.00 0.00 0.00 1.47
3072 4559 4.882427 TCCTAAAATCGGTCAACAACAACA 59.118 37.500 0.00 0.00 0.00 3.33
3094 4581 9.191995 CATTGTCCACATTAAACCTAAAACTTC 57.808 33.333 0.00 0.00 0.00 3.01
3154 4641 1.254313 GTTTTCAAAACGCTGAACCGC 59.746 47.619 0.00 0.00 35.07 5.68
3174 4661 9.859427 TTGCTCCATAAGTGAATAAAGAAAATG 57.141 29.630 0.00 0.00 0.00 2.32
3199 4686 6.735556 ACAAAATTAGGTGAGGAGGATGATT 58.264 36.000 0.00 0.00 0.00 2.57
3209 4696 7.558161 TGATGCATAGACAAAATTAGGTGAG 57.442 36.000 0.00 0.00 0.00 3.51
3238 4725 1.269166 GTCGTAGTGCAGATTCGTGG 58.731 55.000 0.00 0.00 0.00 4.94
3299 4786 4.308526 GGAACCTCTCCTTTTCCTGAAT 57.691 45.455 0.00 0.00 41.61 2.57
3300 4787 3.790089 GGAACCTCTCCTTTTCCTGAA 57.210 47.619 0.00 0.00 41.61 3.02
3348 4835 2.943036 ACCATCTAACCAACGGTTGT 57.057 45.000 18.73 4.81 46.35 3.32
3356 4843 4.431378 TCAACCTCCTAACCATCTAACCA 58.569 43.478 0.00 0.00 0.00 3.67
3357 4844 5.632034 ATCAACCTCCTAACCATCTAACC 57.368 43.478 0.00 0.00 0.00 2.85
3358 4845 7.120923 TGTATCAACCTCCTAACCATCTAAC 57.879 40.000 0.00 0.00 0.00 2.34
3359 4846 7.931015 ATGTATCAACCTCCTAACCATCTAA 57.069 36.000 0.00 0.00 0.00 2.10
3360 4847 7.931015 AATGTATCAACCTCCTAACCATCTA 57.069 36.000 0.00 0.00 0.00 1.98
3361 4848 6.831664 AATGTATCAACCTCCTAACCATCT 57.168 37.500 0.00 0.00 0.00 2.90
3362 4849 7.963532 TCTAATGTATCAACCTCCTAACCATC 58.036 38.462 0.00 0.00 0.00 3.51
3363 4850 7.473511 GCTCTAATGTATCAACCTCCTAACCAT 60.474 40.741 0.00 0.00 0.00 3.55
3421 4916 5.411669 GTCACCGGATTGAACTTTGTAAGAT 59.588 40.000 9.46 0.00 0.00 2.40
3439 4934 3.697439 ATGGGAATGGCCGTCACCG 62.697 63.158 0.00 0.00 37.63 4.94


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

AutoCloner maintained by Alex Coulton.