Multiple sequence alignment - TraesCS3D01G191400

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 TraesCS3D01G191400 chr3D 100.000 3659 0 0 1 3659 180472317 180468659 0.000000e+00 6758.0
1 TraesCS3D01G191400 chr3D 84.255 235 37 0 1573 1807 546198933 546198699 2.840000e-56 230.0
2 TraesCS3D01G191400 chr3D 83.333 108 14 4 1179 1284 546199112 546199007 3.010000e-16 97.1
3 TraesCS3D01G191400 chr3A 90.030 3039 116 62 712 3659 225895450 225892508 0.000000e+00 3760.0
4 TraesCS3D01G191400 chr3A 88.595 605 32 16 2 580 225896160 225895567 0.000000e+00 701.0
5 TraesCS3D01G191400 chr3A 85.470 234 34 0 1574 1807 682479242 682479009 1.010000e-60 244.0
6 TraesCS3D01G191400 chr3A 95.745 94 3 1 558 650 225895557 225895464 2.280000e-32 150.0
7 TraesCS3D01G191400 chr3A 85.185 108 12 4 1179 1284 682479422 682479317 1.390000e-19 108.0
8 TraesCS3D01G191400 chr3B 89.194 2989 96 78 749 3659 258722102 258719263 0.000000e+00 3520.0
9 TraesCS3D01G191400 chr3B 88.501 487 24 6 209 682 258722580 258722113 8.870000e-156 560.0
10 TraesCS3D01G191400 chr3B 85.106 235 35 0 1573 1807 722590913 722590679 1.310000e-59 241.0
11 TraesCS3D01G191400 chr3B 85.185 108 12 4 1179 1284 722591094 722590989 1.390000e-19 108.0
12 TraesCS3D01G191400 chr4D 88.095 210 23 2 1575 1783 80836572 80836780 7.850000e-62 248.0
13 TraesCS3D01G191400 chr4D 84.834 211 30 2 1574 1783 28881790 28881999 1.030000e-50 211.0
14 TraesCS3D01G191400 chr4B 87.143 210 25 2 1575 1783 112921626 112921834 1.700000e-58 237.0
15 TraesCS3D01G191400 chr4B 84.360 211 31 2 1574 1783 41197714 41197923 4.790000e-49 206.0


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 TraesCS3D01G191400 chr3D 180468659 180472317 3658 True 6758 6758 100.000000 1 3659 1 chr3D.!!$R1 3658
1 TraesCS3D01G191400 chr3A 225892508 225896160 3652 True 1537 3760 91.456667 2 3659 3 chr3A.!!$R1 3657
2 TraesCS3D01G191400 chr3B 258719263 258722580 3317 True 2040 3520 88.847500 209 3659 2 chr3B.!!$R1 3450

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
464 478 0.467290 GTCAAGGTGGCAAGGGACAA 60.467 55.0 0.0 0.0 30.25 3.18 F
1544 1665 0.165944 GGTTGTGCCTGATTCGTTCG 59.834 55.0 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 2365 0.106369 CTGGCCATGTCCATGTCCAT 60.106 55.0 5.51 0.0 44.68 3.41 R
2981 3162 0.183252 GGTCCGCTCCTAGTCCTAGT 59.817 60.0 0.96 0.0 0.00 2.57 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
34 35 7.328737 CACGGTTACTATACTTATCTGAATGGC 59.671 40.741 0.00 0.00 0.00 4.40
36 37 7.870954 CGGTTACTATACTTATCTGAATGGCAA 59.129 37.037 0.00 0.00 0.00 4.52
38 39 8.713271 GTTACTATACTTATCTGAATGGCAAGC 58.287 37.037 0.00 0.00 0.00 4.01
55 56 1.668826 AGCAATCCCCTGGTCTTACA 58.331 50.000 0.00 0.00 0.00 2.41
69 70 7.993183 CCCTGGTCTTACATAAATGTGTAGATT 59.007 37.037 5.85 0.00 41.89 2.40
98 100 1.209747 GTGGGGGAAGGTGTAGATGAC 59.790 57.143 0.00 0.00 0.00 3.06
143 145 2.430332 TGCTTGCTTTGCTTAGGTGTTT 59.570 40.909 0.00 0.00 0.00 2.83
158 160 7.481798 GCTTAGGTGTTTCAAATATTTGACTCG 59.518 37.037 26.69 15.88 45.99 4.18
164 166 3.342719 TCAAATATTTGACTCGGCAGCA 58.657 40.909 23.86 1.34 41.88 4.41
172 174 0.514691 GACTCGGCAGCACTGAAAAG 59.485 55.000 0.81 0.00 31.65 2.27
178 180 3.374988 TCGGCAGCACTGAAAAGATATTG 59.625 43.478 0.81 0.00 0.00 1.90
183 185 7.483307 GGCAGCACTGAAAAGATATTGAAATA 58.517 34.615 0.81 0.00 0.00 1.40
185 187 9.525409 GCAGCACTGAAAAGATATTGAAATATT 57.475 29.630 0.81 0.00 31.96 1.28
237 239 2.762327 CAAAAGTGCAGCCTTGGGATAT 59.238 45.455 0.00 0.00 0.00 1.63
238 240 3.951563 AAAGTGCAGCCTTGGGATATA 57.048 42.857 0.00 0.00 0.00 0.86
239 241 4.459852 AAAGTGCAGCCTTGGGATATAT 57.540 40.909 0.00 0.00 0.00 0.86
240 242 5.582950 AAAGTGCAGCCTTGGGATATATA 57.417 39.130 0.00 0.00 0.00 0.86
260 262 2.224606 AGCAATTGTCAGCCATATCCG 58.775 47.619 7.40 0.00 0.00 4.18
368 371 8.883954 AAATGCATGAGATGGATATAGATACG 57.116 34.615 0.00 0.00 40.66 3.06
369 372 7.830099 ATGCATGAGATGGATATAGATACGA 57.170 36.000 0.00 0.00 39.69 3.43
370 373 7.032377 TGCATGAGATGGATATAGATACGAC 57.968 40.000 0.00 0.00 0.00 4.34
371 374 6.139435 GCATGAGATGGATATAGATACGACG 58.861 44.000 0.00 0.00 0.00 5.12
416 430 3.462678 TATGCTACGGGGTGCGCA 61.463 61.111 5.66 5.66 36.75 6.09
464 478 0.467290 GTCAAGGTGGCAAGGGACAA 60.467 55.000 0.00 0.00 30.25 3.18
567 626 7.734942 AGAATCATAAAACCATCTCTCTCTCC 58.265 38.462 0.00 0.00 0.00 3.71
667 727 1.153229 GTATCCGACCCAAGCACCC 60.153 63.158 0.00 0.00 0.00 4.61
676 736 1.133325 ACCCAAGCACCCAACAATACA 60.133 47.619 0.00 0.00 0.00 2.29
682 742 1.613437 GCACCCAACAATACAACTGCT 59.387 47.619 0.00 0.00 0.00 4.24
683 743 2.607771 GCACCCAACAATACAACTGCTG 60.608 50.000 0.00 0.00 0.00 4.41
684 744 2.622942 CACCCAACAATACAACTGCTGT 59.377 45.455 0.00 0.00 42.47 4.40
685 745 3.818210 CACCCAACAATACAACTGCTGTA 59.182 43.478 0.00 0.00 44.65 2.74
686 746 3.818773 ACCCAACAATACAACTGCTGTAC 59.181 43.478 0.00 0.00 43.35 2.90
687 747 3.818210 CCCAACAATACAACTGCTGTACA 59.182 43.478 0.00 0.00 43.35 2.90
688 748 4.277174 CCCAACAATACAACTGCTGTACAA 59.723 41.667 0.00 0.00 43.35 2.41
689 749 5.221145 CCCAACAATACAACTGCTGTACAAA 60.221 40.000 0.00 0.00 43.35 2.83
690 750 6.269315 CCAACAATACAACTGCTGTACAAAA 58.731 36.000 0.00 0.00 43.35 2.44
691 751 6.198216 CCAACAATACAACTGCTGTACAAAAC 59.802 38.462 0.00 0.00 43.35 2.43
692 752 6.443934 ACAATACAACTGCTGTACAAAACA 57.556 33.333 0.00 0.00 43.35 2.83
693 753 6.857956 ACAATACAACTGCTGTACAAAACAA 58.142 32.000 0.00 0.00 43.35 2.83
694 754 6.972328 ACAATACAACTGCTGTACAAAACAAG 59.028 34.615 0.00 0.00 43.35 3.16
695 755 4.370364 ACAACTGCTGTACAAAACAAGG 57.630 40.909 0.00 0.00 37.74 3.61
696 756 3.761752 ACAACTGCTGTACAAAACAAGGT 59.238 39.130 0.00 0.00 37.74 3.50
697 757 4.219725 ACAACTGCTGTACAAAACAAGGTT 59.780 37.500 0.00 0.00 37.74 3.50
700 760 4.337274 ACTGCTGTACAAAACAAGGTTACC 59.663 41.667 0.00 0.00 37.74 2.85
705 765 4.866068 TGTACAAAACAAGGTTACCACCGT 60.866 41.667 3.51 0.00 39.86 4.83
725 785 8.592155 CCACCGTAAAAGAAAAGAAAAGAAAAG 58.408 33.333 0.00 0.00 0.00 2.27
726 786 8.592155 CACCGTAAAAGAAAAGAAAAGAAAAGG 58.408 33.333 0.00 0.00 0.00 3.11
727 787 8.525316 ACCGTAAAAGAAAAGAAAAGAAAAGGA 58.475 29.630 0.00 0.00 0.00 3.36
728 788 9.361315 CCGTAAAAGAAAAGAAAAGAAAAGGAA 57.639 29.630 0.00 0.00 0.00 3.36
820 880 1.068921 GCATTTTGTTGCGGGTGGT 59.931 52.632 0.00 0.00 32.06 4.16
1013 1080 0.423544 ACCCCTCTCCAATCCTCCTT 59.576 55.000 0.00 0.00 0.00 3.36
1014 1081 0.842635 CCCCTCTCCAATCCTCCTTG 59.157 60.000 0.00 0.00 0.00 3.61
1015 1082 1.626350 CCCCTCTCCAATCCTCCTTGA 60.626 57.143 0.00 0.00 0.00 3.02
1016 1083 2.200081 CCCTCTCCAATCCTCCTTGAA 58.800 52.381 0.00 0.00 0.00 2.69
1018 1085 2.092699 CCTCTCCAATCCTCCTTGAACC 60.093 54.545 0.00 0.00 0.00 3.62
1019 1086 2.843113 CTCTCCAATCCTCCTTGAACCT 59.157 50.000 0.00 0.00 0.00 3.50
1020 1087 3.260205 TCTCCAATCCTCCTTGAACCTT 58.740 45.455 0.00 0.00 0.00 3.50
1062 1138 1.069204 GGCTCGTGAGATGAATGGCTA 59.931 52.381 0.00 0.00 40.84 3.93
1385 1475 0.947180 TGCGCAAACGGAACTACTCC 60.947 55.000 8.16 0.00 41.40 3.85
1386 1476 0.669625 GCGCAAACGGAACTACTCCT 60.670 55.000 0.30 0.00 42.85 3.69
1387 1477 1.403249 GCGCAAACGGAACTACTCCTA 60.403 52.381 0.30 0.00 42.85 2.94
1540 1659 1.875963 GTGGGTTGTGCCTGATTCG 59.124 57.895 0.00 0.00 37.43 3.34
1544 1665 0.165944 GGTTGTGCCTGATTCGTTCG 59.834 55.000 0.00 0.00 0.00 3.95
1559 1680 4.212213 TCGTTCGTGGTTTATTTTGTGG 57.788 40.909 0.00 0.00 0.00 4.17
1866 1996 3.760035 CGCACTACCCAGGCGTCT 61.760 66.667 0.00 0.00 45.27 4.18
1898 2028 3.289834 CACCAGCACCAGCACCAC 61.290 66.667 0.00 0.00 45.49 4.16
1967 2097 2.699554 ATGGGGGTGGCCATAGCA 60.700 61.111 9.72 0.00 42.56 3.49
2227 2368 1.491754 TCCACATGGACATGGAGATGG 59.508 52.381 15.94 13.44 40.17 3.51
2228 2369 1.491754 CCACATGGACATGGAGATGGA 59.508 52.381 15.94 0.00 42.91 3.41
2415 2559 4.756458 AGCAGCAGCACGAGGAGC 62.756 66.667 3.17 0.00 45.49 4.70
2524 2678 3.379240 GAGGCCGATATCATCATCATCG 58.621 50.000 3.12 0.00 40.88 3.84
2527 2681 2.786027 GCCGATATCATCATCATCGTCG 59.214 50.000 3.12 0.00 39.86 5.12
2530 2684 3.716433 CGATATCATCATCATCGTCGTCG 59.284 47.826 3.12 0.00 37.40 5.12
2590 2749 6.275494 AGCAAGGTTAGAGTCTAGAAGAAC 57.725 41.667 0.00 0.00 0.00 3.01
2628 2787 5.467668 TGAGGAGGATGAGGAGTTAAGTA 57.532 43.478 0.00 0.00 0.00 2.24
2728 2891 3.686726 AGATGGAAAAGAAGTCGCATGTC 59.313 43.478 0.00 0.00 0.00 3.06
2732 2895 3.189287 GGAAAAGAAGTCGCATGTCATGT 59.811 43.478 14.26 0.00 0.00 3.21
2766 2929 1.601166 GTGGCAACCCGAACTTAGTT 58.399 50.000 0.00 0.00 0.00 2.24
2767 2930 1.951602 GTGGCAACCCGAACTTAGTTT 59.048 47.619 0.00 0.00 0.00 2.66
2768 2931 2.031420 GTGGCAACCCGAACTTAGTTTC 60.031 50.000 0.00 0.00 0.00 2.78
2769 2932 2.158726 TGGCAACCCGAACTTAGTTTCT 60.159 45.455 0.00 0.00 0.00 2.52
2826 3005 4.166523 GCCGAAGAAGCAAGAAAATAACC 58.833 43.478 0.00 0.00 0.00 2.85
2828 3007 5.768317 CCGAAGAAGCAAGAAAATAACCAA 58.232 37.500 0.00 0.00 0.00 3.67
2829 3008 6.212955 CCGAAGAAGCAAGAAAATAACCAAA 58.787 36.000 0.00 0.00 0.00 3.28
2832 3011 8.764287 CGAAGAAGCAAGAAAATAACCAAAAAT 58.236 29.630 0.00 0.00 0.00 1.82
2835 3014 8.344831 AGAAGCAAGAAAATAACCAAAAATTGC 58.655 29.630 0.00 0.00 40.50 3.56
2877 3058 2.612604 TGATATGTCCGTTGTTGTCCG 58.387 47.619 0.00 0.00 0.00 4.79
2979 3160 1.822990 CCGGTGCACTAGGAGTAAGAA 59.177 52.381 21.86 0.00 0.00 2.52
2980 3161 2.159226 CCGGTGCACTAGGAGTAAGAAG 60.159 54.545 21.86 0.00 0.00 2.85
2981 3162 2.753452 CGGTGCACTAGGAGTAAGAAGA 59.247 50.000 17.98 0.00 0.00 2.87
3155 3342 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3156 3343 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
3166 3355 0.323908 CTCTCTCTCAAGGGTCGGGT 60.324 60.000 0.00 0.00 0.00 5.28
3260 3463 4.974721 GCCTGGTGGTGGTGGTGG 62.975 72.222 0.00 0.00 35.27 4.61
3289 3492 1.524621 GACGGATGGATGGTGCCTG 60.525 63.158 0.00 0.00 0.00 4.85
3326 3529 2.242572 CGCCTCATGCATCCTCACG 61.243 63.158 0.00 0.00 41.33 4.35
3327 3530 2.541120 GCCTCATGCATCCTCACGC 61.541 63.158 0.00 0.00 40.77 5.34
3328 3531 1.153309 CCTCATGCATCCTCACGCA 60.153 57.895 0.00 0.00 43.45 5.24
3329 3532 1.434622 CCTCATGCATCCTCACGCAC 61.435 60.000 0.00 0.00 41.79 5.34
3330 3533 1.759293 CTCATGCATCCTCACGCACG 61.759 60.000 0.00 0.00 41.79 5.34
3415 3621 1.000506 TGACTCCGTTACCAGTTGCTC 59.999 52.381 0.00 0.00 0.00 4.26
3416 3622 1.000506 GACTCCGTTACCAGTTGCTCA 59.999 52.381 0.00 0.00 0.00 4.26
3417 3623 1.623811 ACTCCGTTACCAGTTGCTCAT 59.376 47.619 0.00 0.00 0.00 2.90
3418 3624 2.271800 CTCCGTTACCAGTTGCTCATC 58.728 52.381 0.00 0.00 0.00 2.92
3494 3706 0.460109 CTCATCACCGGCGACAATCA 60.460 55.000 9.30 0.00 0.00 2.57
3587 3811 1.282875 GACCAAGAAACCGTGCAGC 59.717 57.895 0.00 0.00 0.00 5.25
3615 3839 3.807553 TCACTGCAATGTGAGTTTCTCA 58.192 40.909 4.76 0.00 41.43 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.990120 AGTATAGTAACCGTGGTCAAAGT 57.010 39.130 0.00 0.00 0.00 2.66
34 35 2.290896 TGTAAGACCAGGGGATTGCTTG 60.291 50.000 0.00 0.00 0.00 4.01
36 37 1.668826 TGTAAGACCAGGGGATTGCT 58.331 50.000 0.00 0.00 0.00 3.91
38 39 6.039717 CACATTTATGTAAGACCAGGGGATTG 59.960 42.308 0.00 0.00 39.39 2.67
74 75 0.768622 CTACACCTTCCCCCACACAA 59.231 55.000 0.00 0.00 0.00 3.33
76 77 1.065418 CATCTACACCTTCCCCCACAC 60.065 57.143 0.00 0.00 0.00 3.82
98 100 6.619801 AGCTACCAAGTTTTTGTAACTCAG 57.380 37.500 0.00 0.00 32.21 3.35
143 145 3.126858 GTGCTGCCGAGTCAAATATTTGA 59.873 43.478 23.86 23.86 44.31 2.69
158 160 4.970662 TCAATATCTTTTCAGTGCTGCC 57.029 40.909 0.00 0.00 0.00 4.85
237 239 5.178061 CGGATATGGCTGACAATTGCTATA 58.822 41.667 5.05 0.00 37.13 1.31
238 240 4.005650 CGGATATGGCTGACAATTGCTAT 58.994 43.478 5.05 0.00 34.80 2.97
239 241 3.402110 CGGATATGGCTGACAATTGCTA 58.598 45.455 5.05 0.00 0.00 3.49
240 242 2.224606 CGGATATGGCTGACAATTGCT 58.775 47.619 5.05 0.00 0.00 3.91
327 330 3.206964 GCATTTACTACTTCTGCTCCCC 58.793 50.000 0.00 0.00 0.00 4.81
368 371 6.828502 TTCTTCATCACATTACTATGCGTC 57.171 37.500 0.00 0.00 35.03 5.19
369 372 7.280876 ACATTTCTTCATCACATTACTATGCGT 59.719 33.333 0.00 0.00 35.03 5.24
370 373 7.585210 CACATTTCTTCATCACATTACTATGCG 59.415 37.037 0.00 0.00 35.03 4.73
371 374 7.859377 CCACATTTCTTCATCACATTACTATGC 59.141 37.037 0.00 0.00 35.03 3.14
416 430 2.043941 AACGCCCCTTCCCCCTAT 59.956 61.111 0.00 0.00 0.00 2.57
567 626 1.063717 AGAAGGGCAGAGAGAGAGAGG 60.064 57.143 0.00 0.00 0.00 3.69
667 727 6.749578 TGTTTTGTACAGCAGTTGTATTGTTG 59.250 34.615 0.00 0.00 43.79 3.33
676 736 5.163591 GGTAACCTTGTTTTGTACAGCAGTT 60.164 40.000 0.00 2.29 38.19 3.16
682 742 3.626670 CGGTGGTAACCTTGTTTTGTACA 59.373 43.478 0.00 0.00 45.17 2.90
683 743 3.627123 ACGGTGGTAACCTTGTTTTGTAC 59.373 43.478 0.00 0.00 45.17 2.90
684 744 3.883669 ACGGTGGTAACCTTGTTTTGTA 58.116 40.909 0.00 0.00 45.17 2.41
685 745 2.725637 ACGGTGGTAACCTTGTTTTGT 58.274 42.857 0.00 0.00 45.17 2.83
686 746 4.897025 TTACGGTGGTAACCTTGTTTTG 57.103 40.909 0.00 0.00 45.17 2.44
687 747 5.651576 TCTTTTACGGTGGTAACCTTGTTTT 59.348 36.000 0.00 0.00 45.17 2.43
688 748 5.192176 TCTTTTACGGTGGTAACCTTGTTT 58.808 37.500 0.00 0.00 45.17 2.83
689 749 4.779696 TCTTTTACGGTGGTAACCTTGTT 58.220 39.130 0.00 0.00 45.17 2.83
690 750 4.420522 TCTTTTACGGTGGTAACCTTGT 57.579 40.909 0.00 0.00 45.17 3.16
691 751 5.754543 TTTCTTTTACGGTGGTAACCTTG 57.245 39.130 0.00 0.00 45.17 3.61
692 752 6.121590 TCTTTTCTTTTACGGTGGTAACCTT 58.878 36.000 0.00 0.00 45.17 3.50
693 753 5.683681 TCTTTTCTTTTACGGTGGTAACCT 58.316 37.500 0.00 0.00 45.17 3.50
694 754 6.375945 TTCTTTTCTTTTACGGTGGTAACC 57.624 37.500 0.00 0.00 43.76 2.85
695 755 8.183536 TCTTTTCTTTTCTTTTACGGTGGTAAC 58.816 33.333 0.00 0.00 38.31 2.50
696 756 8.278729 TCTTTTCTTTTCTTTTACGGTGGTAA 57.721 30.769 0.00 0.00 36.86 2.85
697 757 7.862512 TCTTTTCTTTTCTTTTACGGTGGTA 57.137 32.000 0.00 0.00 0.00 3.25
700 760 8.592155 CCTTTTCTTTTCTTTTCTTTTACGGTG 58.408 33.333 0.00 0.00 0.00 4.94
741 801 6.512342 TTATATCTCTCGGCTAAGCTTACC 57.488 41.667 0.86 8.36 0.00 2.85
742 802 7.595604 ACTTTATATCTCTCGGCTAAGCTTAC 58.404 38.462 0.86 0.00 0.00 2.34
744 804 6.658188 ACTTTATATCTCTCGGCTAAGCTT 57.342 37.500 3.48 3.48 0.00 3.74
820 880 5.282055 TCTCTTCTCTTGTTCTTGCTTCA 57.718 39.130 0.00 0.00 0.00 3.02
864 925 4.936802 TCTCTAATATAGGAGGTGGAGGC 58.063 47.826 5.41 0.00 0.00 4.70
865 926 5.515106 CCTCTCTAATATAGGAGGTGGAGG 58.485 50.000 11.02 0.00 37.93 4.30
983 1048 2.777692 TGGAGAGGGGTATGCCTTAAAG 59.222 50.000 0.00 0.00 34.45 1.85
996 1061 1.885049 TCAAGGAGGATTGGAGAGGG 58.115 55.000 0.00 0.00 0.00 4.30
999 1064 2.921221 AGGTTCAAGGAGGATTGGAGA 58.079 47.619 0.00 0.00 0.00 3.71
1013 1080 4.289934 TGGTCTCTCTCTCTCTAAGGTTCA 59.710 45.833 0.00 0.00 0.00 3.18
1014 1081 4.850680 TGGTCTCTCTCTCTCTAAGGTTC 58.149 47.826 0.00 0.00 0.00 3.62
1015 1082 4.938575 TGGTCTCTCTCTCTCTAAGGTT 57.061 45.455 0.00 0.00 0.00 3.50
1016 1083 4.538490 TCTTGGTCTCTCTCTCTCTAAGGT 59.462 45.833 0.00 0.00 0.00 3.50
1018 1085 6.039717 CCATTCTTGGTCTCTCTCTCTCTAAG 59.960 46.154 0.00 0.00 38.30 2.18
1019 1086 5.890985 CCATTCTTGGTCTCTCTCTCTCTAA 59.109 44.000 0.00 0.00 38.30 2.10
1020 1087 5.445069 CCATTCTTGGTCTCTCTCTCTCTA 58.555 45.833 0.00 0.00 38.30 2.43
1062 1138 4.021925 GCGGAGGGTGGCTGAAGT 62.022 66.667 0.00 0.00 0.00 3.01
1097 1173 4.208686 CTCCTCCTGGTACGGCGC 62.209 72.222 6.90 0.00 34.23 6.53
1205 1284 1.587054 CGACGAGTTCCTTGAGCCT 59.413 57.895 0.00 0.00 0.00 4.58
1385 1475 7.307811 GGTTGCAGTAAAAGAAACCAGTAGTAG 60.308 40.741 0.00 0.00 43.10 2.57
1386 1476 6.484308 GGTTGCAGTAAAAGAAACCAGTAGTA 59.516 38.462 0.00 0.00 43.10 1.82
1387 1477 5.298527 GGTTGCAGTAAAAGAAACCAGTAGT 59.701 40.000 0.00 0.00 43.10 2.73
1481 1593 5.092781 CCGCAACACACTCCAAATTAATAC 58.907 41.667 0.00 0.00 0.00 1.89
1484 1596 2.952978 ACCGCAACACACTCCAAATTAA 59.047 40.909 0.00 0.00 0.00 1.40
1540 1659 4.922719 TCACCACAAAATAAACCACGAAC 58.077 39.130 0.00 0.00 0.00 3.95
1544 1665 4.915085 CGACATCACCACAAAATAAACCAC 59.085 41.667 0.00 0.00 0.00 4.16
1559 1680 2.040544 CCCTGTTGGCCGACATCAC 61.041 63.158 26.36 0.00 0.00 3.06
1634 1755 1.324005 CCTCCTCCTCCTCCGTGAAC 61.324 65.000 0.00 0.00 0.00 3.18
1823 1947 2.206536 GGCGATGGAGGAGGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
1859 1983 2.604686 TGCTGGAGGAAGACGCCT 60.605 61.111 0.00 0.00 40.14 5.52
1866 1996 2.431683 GTGCTGGTGCTGGAGGAA 59.568 61.111 0.00 0.00 40.48 3.36
1897 2027 3.319198 CCCCGTGGTGCTGGTAGT 61.319 66.667 0.00 0.00 0.00 2.73
1898 2028 4.778143 GCCCCGTGGTGCTGGTAG 62.778 72.222 0.00 0.00 0.00 3.18
1916 2046 1.227102 CGGCATGGGAATGGGAGAA 59.773 57.895 0.00 0.00 0.00 2.87
1967 2097 1.072505 CTTGCTGTACACCCCGGTT 59.927 57.895 0.00 0.00 0.00 4.44
2090 2226 1.299976 GTGGTGGTAGAAGCAGGGG 59.700 63.158 0.00 0.00 0.00 4.79
2163 2299 0.829990 AAACAACAACAGCTTGGGGG 59.170 50.000 0.00 0.00 0.00 5.40
2223 2364 0.106569 TGGCCATGTCCATGTCCATC 60.107 55.000 0.00 0.00 41.39 3.51
2224 2365 0.106369 CTGGCCATGTCCATGTCCAT 60.106 55.000 5.51 0.00 44.68 3.41
2225 2366 1.303948 CTGGCCATGTCCATGTCCA 59.696 57.895 5.51 9.47 43.72 4.02
2226 2367 2.123428 GCTGGCCATGTCCATGTCC 61.123 63.158 5.51 3.60 37.36 4.02
2227 2368 2.475466 CGCTGGCCATGTCCATGTC 61.475 63.158 5.51 0.00 37.11 3.06
2228 2369 2.438975 CGCTGGCCATGTCCATGT 60.439 61.111 5.51 0.00 37.11 3.21
2271 2412 0.698238 TAGCCTGCACCAAAGACCAT 59.302 50.000 0.00 0.00 0.00 3.55
2415 2559 1.078918 TGAGCTTGTCGCCATCCTG 60.079 57.895 0.00 0.00 40.39 3.86
2590 2749 4.144297 CTCCTCATCTTCTCCTAGTCTGG 58.856 52.174 0.00 0.00 0.00 3.86
2628 2787 7.915397 GTCACATTCATCGCCATAAATAAAACT 59.085 33.333 0.00 0.00 0.00 2.66
2716 2879 4.864916 ACATTACATGACATGCGACTTC 57.135 40.909 15.49 0.00 0.00 3.01
2728 2891 7.036996 TGCCACCATTACATTACATTACATG 57.963 36.000 0.00 0.00 0.00 3.21
2732 2895 5.361285 GGGTTGCCACCATTACATTACATTA 59.639 40.000 9.52 0.00 46.43 1.90
2766 2929 5.815233 AGAGACAAGAGGACATGAAAGAA 57.185 39.130 0.00 0.00 0.00 2.52
2767 2930 7.364232 GGAATAGAGACAAGAGGACATGAAAGA 60.364 40.741 0.00 0.00 0.00 2.52
2768 2931 6.760770 GGAATAGAGACAAGAGGACATGAAAG 59.239 42.308 0.00 0.00 0.00 2.62
2769 2932 6.213397 TGGAATAGAGACAAGAGGACATGAAA 59.787 38.462 0.00 0.00 0.00 2.69
2877 3058 1.135402 GCACCGACAATGGAATGGAAC 60.135 52.381 0.00 0.00 0.00 3.62
2910 3091 2.702751 TTTTTCTCTCGCCGTCGCCA 62.703 55.000 0.00 0.00 35.26 5.69
2979 3160 1.141455 GTCCGCTCCTAGTCCTAGTCT 59.859 57.143 0.96 0.00 0.00 3.24
2980 3161 1.596603 GTCCGCTCCTAGTCCTAGTC 58.403 60.000 0.96 0.00 0.00 2.59
2981 3162 0.183252 GGTCCGCTCCTAGTCCTAGT 59.817 60.000 0.96 0.00 0.00 2.57
3242 3443 4.974721 CACCACCACCACCAGGCC 62.975 72.222 0.00 0.00 39.06 5.19
3244 3445 4.974721 GCCACCACCACCACCAGG 62.975 72.222 0.00 0.00 42.21 4.45
3245 3446 4.974721 GGCCACCACCACCACCAG 62.975 72.222 0.00 0.00 0.00 4.00
3415 3621 1.936880 GCGAGCGAGTGACGAGATG 60.937 63.158 0.00 0.00 45.77 2.90
3416 3622 2.042520 GAGCGAGCGAGTGACGAGAT 62.043 60.000 0.00 0.00 45.77 2.75
3417 3623 2.741726 GAGCGAGCGAGTGACGAGA 61.742 63.158 0.00 0.00 45.77 4.04
3418 3624 2.276994 GAGCGAGCGAGTGACGAG 60.277 66.667 0.00 0.00 45.77 4.18
3494 3706 5.052693 TGCAGAGGCCATAATTAAGACAT 57.947 39.130 5.01 0.00 40.13 3.06
3530 3753 3.741249 TGGTTTTAGCATTGACCGTGTA 58.259 40.909 0.00 0.00 34.90 2.90
3615 3839 2.024751 ACTGTGGGTGGTAAAAACTGGT 60.025 45.455 0.00 0.00 0.00 4.00
3616 3840 2.360801 CACTGTGGGTGGTAAAAACTGG 59.639 50.000 0.00 0.00 41.90 4.00


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

AutoCloner maintained by Alex Coulton.