Multiple sequence alignment - TraesCS3B01G158800

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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 TraesCS3B01G158800 chr3B 100.000 3038 0 0 1 3038 154194711 154197748 0.000000e+00 5611
1 TraesCS3B01G158800 chr3D 93.054 2073 82 28 987 3038 103621046 103623077 0.000000e+00 2974
2 TraesCS3B01G158800 chr3D 89.619 472 30 12 224 690 103620325 103620782 1.570000e-162 582
3 TraesCS3B01G158800 chr3D 93.333 210 10 3 1 207 103620132 103620340 1.060000e-79 307
4 TraesCS3B01G158800 chr3D 92.268 194 10 3 784 974 103620773 103620964 1.390000e-68 270
5 TraesCS3B01G158800 chr3A 88.378 1566 103 32 931 2434 552641827 552640279 0.000000e+00 1810
6 TraesCS3B01G158800 chr3A 89.574 470 32 5 224 689 552642566 552642110 5.650000e-162 580
7 TraesCS3B01G158800 chr3A 93.333 75 5 0 1 75 552642725 552642651 8.900000e-21 111
8 TraesCS3B01G158800 chr2D 83.858 254 27 10 1476 1722 527272546 527272300 2.360000e-56 230
9 TraesCS3B01G158800 chr2A 83.399 253 30 9 1476 1722 672265664 672265418 1.100000e-54 224
10 TraesCS3B01G158800 chr2B 81.781 247 33 11 1483 1723 623869945 623869705 2.390000e-46 196
11 TraesCS3B01G158800 chr4A 77.626 219 33 16 1477 1684 703941884 703941671 5.320000e-23 119
12 TraesCS3B01G158800 chr4A 77.670 206 27 18 1477 1673 704153888 704153693 1.150000e-19 108
13 TraesCS3B01G158800 chr4A 76.471 221 33 19 1510 1717 703932300 703932514 5.360000e-18 102
14 TraesCS3B01G158800 chr7D 77.720 193 26 16 1537 1717 27453334 27453521 5.360000e-18 102


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 TraesCS3B01G158800 chr3B 154194711 154197748 3037 False 5611.000000 5611 100.000000 1 3038 1 chr3B.!!$F1 3037
1 TraesCS3B01G158800 chr3D 103620132 103623077 2945 False 1033.250000 2974 92.068500 1 3038 4 chr3D.!!$F1 3037
2 TraesCS3B01G158800 chr3A 552640279 552642725 2446 True 833.666667 1810 90.428333 1 2434 3 chr3A.!!$R1 2433

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
387 395 0.988678 AAGGGATGGGTCCTACCTGC 60.989 60.0 0.0 0.0 44.44 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2439 0.8794 CAAACCCAAGCATGCGCAAA 60.879 50.0 17.11 0.0 42.27 3.68 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
184 188 5.518848 TTACCTCTTAGTGTCACGTTTGA 57.481 39.130 0.00 0.00 0.00 2.69
196 200 2.543848 TCACGTTTGAGACATCAACTGC 59.456 45.455 0.00 0.00 45.07 4.40
197 201 2.545526 CACGTTTGAGACATCAACTGCT 59.454 45.455 0.00 0.00 45.07 4.24
198 202 3.740832 CACGTTTGAGACATCAACTGCTA 59.259 43.478 0.00 0.00 45.07 3.49
199 203 4.389992 CACGTTTGAGACATCAACTGCTAT 59.610 41.667 0.00 0.00 45.07 2.97
200 204 5.576774 CACGTTTGAGACATCAACTGCTATA 59.423 40.000 0.00 0.00 45.07 1.31
201 205 6.256539 CACGTTTGAGACATCAACTGCTATAT 59.743 38.462 0.00 0.00 45.07 0.86
202 206 6.818644 ACGTTTGAGACATCAACTGCTATATT 59.181 34.615 0.00 0.00 45.07 1.28
203 207 7.334421 ACGTTTGAGACATCAACTGCTATATTT 59.666 33.333 0.00 0.00 45.07 1.40
204 208 8.817100 CGTTTGAGACATCAACTGCTATATTTA 58.183 33.333 0.00 0.00 45.07 1.40
207 211 9.890629 TTGAGACATCAACTGCTATATTTAACT 57.109 29.630 0.00 0.00 40.54 2.24
208 212 9.890629 TGAGACATCAACTGCTATATTTAACTT 57.109 29.630 0.00 0.00 30.61 2.66
210 214 9.331282 AGACATCAACTGCTATATTTAACTTCC 57.669 33.333 0.00 0.00 0.00 3.46
211 215 8.451908 ACATCAACTGCTATATTTAACTTCCC 57.548 34.615 0.00 0.00 0.00 3.97
212 216 7.226720 ACATCAACTGCTATATTTAACTTCCCG 59.773 37.037 0.00 0.00 0.00 5.14
213 217 5.526111 TCAACTGCTATATTTAACTTCCCGC 59.474 40.000 0.00 0.00 0.00 6.13
214 218 5.031066 ACTGCTATATTTAACTTCCCGCA 57.969 39.130 0.00 0.00 0.00 5.69
215 219 5.433526 ACTGCTATATTTAACTTCCCGCAA 58.566 37.500 0.00 0.00 0.00 4.85
216 220 5.883673 ACTGCTATATTTAACTTCCCGCAAA 59.116 36.000 0.00 0.00 0.00 3.68
217 221 6.376018 ACTGCTATATTTAACTTCCCGCAAAA 59.624 34.615 0.00 0.00 0.00 2.44
218 222 7.094118 ACTGCTATATTTAACTTCCCGCAAAAA 60.094 33.333 0.00 0.00 0.00 1.94
387 395 0.988678 AAGGGATGGGTCCTACCTGC 60.989 60.000 0.00 0.00 44.44 4.85
390 398 1.700042 GGATGGGTCCTACCTGCCAG 61.700 65.000 0.00 0.00 41.60 4.85
430 438 3.500680 TGAGTGAAAAATTGGAGTACGGC 59.499 43.478 0.00 0.00 0.00 5.68
432 440 3.502211 AGTGAAAAATTGGAGTACGGCTG 59.498 43.478 0.00 0.00 0.00 4.85
438 446 3.975168 ATTGGAGTACGGCTGTAGTTT 57.025 42.857 14.27 0.00 34.34 2.66
454 462 2.791655 AGTTTGAACCCGAAATCTCCC 58.208 47.619 0.00 0.00 0.00 4.30
481 489 1.763545 GACAGGTAAGACTCATCCCCC 59.236 57.143 0.00 0.00 0.00 5.40
522 530 6.160684 ACCAGACAAAACCAAACAGTAAAAC 58.839 36.000 0.00 0.00 0.00 2.43
534 542 5.351948 AACAGTAAAACAAACCAGCCAAT 57.648 34.783 0.00 0.00 0.00 3.16
621 629 8.281893 CACAATTTTGCTTACATTGGGTAAAAG 58.718 33.333 0.00 0.00 41.27 2.27
624 632 9.483916 AATTTTGCTTACATTGGGTAAAAGTAC 57.516 29.630 0.00 0.00 41.27 2.73
638 646 7.231115 TGGGTAAAAGTACATGGAAAAACTACC 59.769 37.037 0.00 0.00 31.21 3.18
647 655 5.011635 ACATGGAAAAACTACCAAATGGGAC 59.988 40.000 4.17 0.00 39.69 4.46
690 698 7.119553 GTGAAACGTGGGGTACAAATAGAATTA 59.880 37.037 0.00 0.00 0.00 1.40
691 699 7.664731 TGAAACGTGGGGTACAAATAGAATTAA 59.335 33.333 0.00 0.00 0.00 1.40
692 700 6.990341 ACGTGGGGTACAAATAGAATTAAC 57.010 37.500 0.00 0.00 0.00 2.01
693 701 5.882000 ACGTGGGGTACAAATAGAATTAACC 59.118 40.000 0.00 0.00 0.00 2.85
694 702 5.297527 CGTGGGGTACAAATAGAATTAACCC 59.702 44.000 0.00 0.00 43.62 4.11
695 703 6.429151 GTGGGGTACAAATAGAATTAACCCT 58.571 40.000 7.51 0.00 43.79 4.34
696 704 6.320418 GTGGGGTACAAATAGAATTAACCCTG 59.680 42.308 7.51 0.00 43.79 4.45
697 705 6.217900 TGGGGTACAAATAGAATTAACCCTGA 59.782 38.462 7.51 0.00 43.79 3.86
698 706 7.091720 TGGGGTACAAATAGAATTAACCCTGAT 60.092 37.037 7.51 0.00 43.79 2.90
699 707 7.230712 GGGGTACAAATAGAATTAACCCTGATG 59.769 40.741 7.51 0.00 43.79 3.07
700 708 7.778382 GGGTACAAATAGAATTAACCCTGATGT 59.222 37.037 0.00 0.00 41.57 3.06
701 709 9.841295 GGTACAAATAGAATTAACCCTGATGTA 57.159 33.333 0.00 0.00 0.00 2.29
710 718 9.492730 AGAATTAACCCTGATGTAATTCCATTT 57.507 29.630 10.31 0.00 37.67 2.32
711 719 9.533253 GAATTAACCCTGATGTAATTCCATTTG 57.467 33.333 0.00 0.00 33.44 2.32
712 720 8.608185 ATTAACCCTGATGTAATTCCATTTGT 57.392 30.769 0.00 0.00 0.00 2.83
713 721 9.707957 ATTAACCCTGATGTAATTCCATTTGTA 57.292 29.630 0.00 0.00 0.00 2.41
714 722 7.404671 AACCCTGATGTAATTCCATTTGTAC 57.595 36.000 0.00 0.00 0.00 2.90
715 723 6.489603 ACCCTGATGTAATTCCATTTGTACA 58.510 36.000 0.00 0.00 0.00 2.90
716 724 7.125391 ACCCTGATGTAATTCCATTTGTACAT 58.875 34.615 0.00 0.00 39.33 2.29
717 725 7.619302 ACCCTGATGTAATTCCATTTGTACATT 59.381 33.333 0.00 0.00 37.32 2.71
718 726 8.477256 CCCTGATGTAATTCCATTTGTACATTT 58.523 33.333 0.00 0.00 37.32 2.32
719 727 9.874205 CCTGATGTAATTCCATTTGTACATTTT 57.126 29.630 0.00 0.00 37.32 1.82
721 729 9.868277 TGATGTAATTCCATTTGTACATTTTCC 57.132 29.630 0.00 0.00 37.32 3.13
724 732 9.308000 TGTAATTCCATTTGTACATTTTCCTCT 57.692 29.630 0.00 0.00 0.00 3.69
725 733 9.573133 GTAATTCCATTTGTACATTTTCCTCTG 57.427 33.333 0.00 0.00 0.00 3.35
726 734 8.421249 AATTCCATTTGTACATTTTCCTCTGA 57.579 30.769 0.00 0.00 0.00 3.27
727 735 6.817765 TCCATTTGTACATTTTCCTCTGAC 57.182 37.500 0.00 0.00 0.00 3.51
728 736 6.303054 TCCATTTGTACATTTTCCTCTGACA 58.697 36.000 0.00 0.00 0.00 3.58
729 737 6.775142 TCCATTTGTACATTTTCCTCTGACAA 59.225 34.615 0.00 0.00 0.00 3.18
730 738 7.451255 TCCATTTGTACATTTTCCTCTGACAAT 59.549 33.333 0.00 0.00 0.00 2.71
731 739 8.090214 CCATTTGTACATTTTCCTCTGACAATT 58.910 33.333 0.00 0.00 0.00 2.32
736 744 9.513906 TGTACATTTTCCTCTGACAATTATTGA 57.486 29.630 12.28 0.00 0.00 2.57
758 766 7.607615 TGAAAAAGTAGAGTTACAGTAGGGT 57.392 36.000 0.00 0.00 31.96 4.34
759 767 8.026396 TGAAAAAGTAGAGTTACAGTAGGGTT 57.974 34.615 0.00 0.00 31.96 4.11
760 768 8.488668 TGAAAAAGTAGAGTTACAGTAGGGTTT 58.511 33.333 0.00 0.00 31.96 3.27
761 769 9.334947 GAAAAAGTAGAGTTACAGTAGGGTTTT 57.665 33.333 0.00 0.00 31.96 2.43
763 771 9.770097 AAAAGTAGAGTTACAGTAGGGTTTTAC 57.230 33.333 0.00 0.00 31.96 2.01
764 772 7.473735 AGTAGAGTTACAGTAGGGTTTTACC 57.526 40.000 0.00 0.00 32.89 2.85
765 773 6.438741 AGTAGAGTTACAGTAGGGTTTTACCC 59.561 42.308 6.79 6.79 44.44 3.69
875 886 9.663904 CAAAAGAAAAATGTCGAGTGAGAAATA 57.336 29.630 0.00 0.00 0.00 1.40
982 1140 4.398988 TGAATCGTTGGGAGGAATTGAATG 59.601 41.667 0.00 0.00 0.00 2.67
1052 1286 4.083862 GGTCCTGTCCGACCCTGC 62.084 72.222 0.00 0.00 45.72 4.85
1274 1518 0.102300 CGTGTCATCTCATACGGGCA 59.898 55.000 0.00 0.00 33.27 5.36
1403 1653 3.479269 GGCCGACGACAAGAAGCG 61.479 66.667 0.00 0.00 0.00 4.68
1878 2155 2.273449 CAGCCGAGCCAGGGAAAT 59.727 61.111 0.00 0.00 0.00 2.17
1956 2233 1.677552 GGTGGAGAACGTGGTGGAT 59.322 57.895 0.00 0.00 0.00 3.41
2040 2317 2.868964 TCCTGTGGGAGTATTAGGCT 57.131 50.000 0.00 0.00 36.57 4.58
2043 2320 2.158755 CCTGTGGGAGTATTAGGCTTGG 60.159 54.545 0.00 0.00 33.58 3.61
2084 2374 7.718334 TTCCTTTCTTCTTCTTTTCTTGGTT 57.282 32.000 0.00 0.00 0.00 3.67
2149 2439 2.200899 GCTTTGTCATTTGGTTTGCGT 58.799 42.857 0.00 0.00 0.00 5.24
2150 2440 2.607180 GCTTTGTCATTTGGTTTGCGTT 59.393 40.909 0.00 0.00 0.00 4.84
2151 2441 3.063316 GCTTTGTCATTTGGTTTGCGTTT 59.937 39.130 0.00 0.00 0.00 3.60
2153 2443 1.929836 TGTCATTTGGTTTGCGTTTGC 59.070 42.857 0.00 0.00 43.20 3.68
2262 2567 6.989759 TCTAATGTACATGTGAATTATGCGGT 59.010 34.615 9.63 0.00 0.00 5.68
2285 2590 6.762661 GGTCTTTAGGTTACCGCAATATTACA 59.237 38.462 0.00 0.00 0.00 2.41
2297 2602 6.094464 ACCGCAATATTACAGGTTTTCTTACC 59.906 38.462 3.62 0.00 38.53 2.85
2394 2699 4.607293 TGACATACCACCTCAGATATGC 57.393 45.455 0.00 0.00 0.00 3.14
2400 2705 1.008424 ACCTCAGATATGCGACGCG 60.008 57.895 16.14 3.53 0.00 6.01
2410 2715 1.431488 ATGCGACGCGATTGCTTGAT 61.431 50.000 15.93 0.20 38.71 2.57
2443 2749 0.457851 TGCTTGTTTTCAACACGGGG 59.542 50.000 0.00 0.00 41.97 5.73
2445 2751 1.339929 GCTTGTTTTCAACACGGGGAT 59.660 47.619 0.00 0.00 41.97 3.85
2447 2753 2.350057 TGTTTTCAACACGGGGATCA 57.650 45.000 0.00 0.00 36.25 2.92
2455 2761 2.874701 CAACACGGGGATCATCATCTTC 59.125 50.000 0.00 0.00 0.00 2.87
2459 2765 1.973515 CGGGGATCATCATCTTCCTCA 59.026 52.381 0.00 0.00 29.89 3.86
2466 2772 6.409695 GGGATCATCATCTTCCTCAAACCTAA 60.410 42.308 0.00 0.00 0.00 2.69
2468 2774 6.627087 TCATCATCTTCCTCAAACCTAACT 57.373 37.500 0.00 0.00 0.00 2.24
2469 2775 7.733773 TCATCATCTTCCTCAAACCTAACTA 57.266 36.000 0.00 0.00 0.00 2.24
2470 2776 8.324191 TCATCATCTTCCTCAAACCTAACTAT 57.676 34.615 0.00 0.00 0.00 2.12
2471 2777 8.206867 TCATCATCTTCCTCAAACCTAACTATG 58.793 37.037 0.00 0.00 0.00 2.23
2499 2805 7.851822 TTTCAACAACAGAGATTAAATTCGC 57.148 32.000 0.00 0.00 0.00 4.70
2500 2806 6.552859 TCAACAACAGAGATTAAATTCGCA 57.447 33.333 0.00 0.00 0.00 5.10
2501 2807 6.964908 TCAACAACAGAGATTAAATTCGCAA 58.035 32.000 0.00 0.00 0.00 4.85
2502 2808 7.421599 TCAACAACAGAGATTAAATTCGCAAA 58.578 30.769 0.00 0.00 0.00 3.68
2503 2809 7.918033 TCAACAACAGAGATTAAATTCGCAAAA 59.082 29.630 0.00 0.00 0.00 2.44
2504 2810 8.538856 CAACAACAGAGATTAAATTCGCAAAAA 58.461 29.630 0.00 0.00 0.00 1.94
2625 2931 5.121298 CGTGATGAGTTGATGACATGACTTT 59.879 40.000 0.00 0.00 0.00 2.66
2630 2936 3.254166 AGTTGATGACATGACTTTGGTGC 59.746 43.478 0.00 0.00 0.00 5.01
2647 2953 1.226603 GCGGTCGCGATTAGTCTGT 60.227 57.895 14.06 0.00 0.00 3.41
2694 3000 1.812571 GTCGTTTGCATGGATCTTGGT 59.187 47.619 0.00 0.00 0.00 3.67
2787 3093 9.393512 CATGATTATCTTCTTAATGATCCCCTC 57.606 37.037 0.00 0.00 0.00 4.30
2824 3130 9.139734 TCCCTGTGTAGAAACGATATAAACTAT 57.860 33.333 0.00 0.00 0.00 2.12
2830 3139 9.903682 TGTAGAAACGATATAAACTATGTAGCC 57.096 33.333 0.00 0.00 0.00 3.93
2873 3182 7.771927 AATAATTGATATTTCAGGCTGGAGG 57.228 36.000 15.73 0.00 29.67 4.30
2874 3183 4.803329 ATTGATATTTCAGGCTGGAGGT 57.197 40.909 15.73 1.07 32.27 3.85
2904 3213 8.603242 AGTCTTTCTTCTTCTTTTATGCGTTA 57.397 30.769 0.00 0.00 0.00 3.18
2969 3279 1.603931 GCAAAGCTGAAGAACCTTGGC 60.604 52.381 0.00 0.00 0.00 4.52
2981 3291 4.898320 AGAACCTTGGCAATCATTTTTCC 58.102 39.130 0.00 0.00 0.00 3.13
2991 3301 6.713903 TGGCAATCATTTTTCCTTGCATTAAA 59.286 30.769 8.21 0.00 44.41 1.52
3027 3337 1.306141 CACCTCAGAGGCCCTACCA 60.306 63.158 17.31 0.00 39.63 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 7.847096 TCAACAAATGACTACAGATAAGCCTA 58.153 34.615 0.00 0.00 31.50 3.93
158 160 7.496591 TCAAACGTGACACTAAGAGGTAAAAAT 59.503 33.333 3.68 0.00 0.00 1.82
174 176 3.604772 GCAGTTGATGTCTCAAACGTGAC 60.605 47.826 0.00 0.00 42.85 3.67
184 188 9.331282 GGAAGTTAAATATAGCAGTTGATGTCT 57.669 33.333 0.00 0.00 0.00 3.41
221 225 9.515226 TGAAAACCTGTTAAATATAGCAGTTCT 57.485 29.630 0.00 0.00 38.34 3.01
222 226 9.556030 GTGAAAACCTGTTAAATATAGCAGTTC 57.444 33.333 0.00 0.00 38.34 3.01
223 227 9.073475 TGTGAAAACCTGTTAAATATAGCAGTT 57.927 29.630 0.00 0.00 38.34 3.16
224 228 8.630054 TGTGAAAACCTGTTAAATATAGCAGT 57.370 30.769 0.00 0.00 38.34 4.40
305 309 7.094720 CCAAAATGGCATGTACAATCAACATTT 60.095 33.333 0.00 15.47 38.49 2.32
387 395 1.928868 ATTTCTTGCTCCCCAACTGG 58.071 50.000 0.00 0.00 0.00 4.00
390 398 4.096984 CACTCATATTTCTTGCTCCCCAAC 59.903 45.833 0.00 0.00 0.00 3.77
426 434 0.601841 CGGGTTCAAACTACAGCCGT 60.602 55.000 0.92 0.00 44.69 5.68
430 438 4.392138 GGAGATTTCGGGTTCAAACTACAG 59.608 45.833 0.00 0.00 0.00 2.74
432 440 3.688185 GGGAGATTTCGGGTTCAAACTAC 59.312 47.826 0.00 0.00 0.00 2.73
438 446 1.996086 GGGGGAGATTTCGGGTTCA 59.004 57.895 0.00 0.00 0.00 3.18
454 462 1.218316 GTCTTACCTGTCTGCGGGG 59.782 63.158 0.00 0.00 45.50 5.73
481 489 4.735132 TTTGCTCTCGGTCCGGCG 62.735 66.667 12.29 0.00 0.00 6.46
489 497 2.287009 GGTTTTGTCTGGTTTGCTCTCG 60.287 50.000 0.00 0.00 0.00 4.04
534 542 1.811965 GTGTTGACTGTGCATGCCATA 59.188 47.619 16.68 0.00 0.00 2.74
570 578 8.943085 TGCCACAAATTATCCCCATTTATTTAT 58.057 29.630 0.00 0.00 0.00 1.40
580 588 4.486125 AATTGTGCCACAAATTATCCCC 57.514 40.909 15.17 0.00 41.96 4.81
621 629 6.209788 TCCCATTTGGTAGTTTTTCCATGTAC 59.790 38.462 0.00 0.00 33.50 2.90
624 632 5.011533 TGTCCCATTTGGTAGTTTTTCCATG 59.988 40.000 0.00 0.00 33.50 3.66
671 679 6.320418 CAGGGTTAATTCTATTTGTACCCCAC 59.680 42.308 0.00 0.00 43.81 4.61
690 698 6.951198 TGTACAAATGGAATTACATCAGGGTT 59.049 34.615 2.92 0.00 33.67 4.11
691 699 6.489603 TGTACAAATGGAATTACATCAGGGT 58.510 36.000 2.92 3.03 33.67 4.34
692 700 7.587037 ATGTACAAATGGAATTACATCAGGG 57.413 36.000 2.92 0.00 33.67 4.45
693 701 9.874205 AAAATGTACAAATGGAATTACATCAGG 57.126 29.630 2.92 0.00 33.24 3.86
695 703 9.868277 GGAAAATGTACAAATGGAATTACATCA 57.132 29.630 2.92 0.00 33.24 3.07
698 706 9.308000 AGAGGAAAATGTACAAATGGAATTACA 57.692 29.630 0.00 0.00 33.67 2.41
699 707 9.573133 CAGAGGAAAATGTACAAATGGAATTAC 57.427 33.333 0.00 0.00 33.67 1.89
700 708 9.527157 TCAGAGGAAAATGTACAAATGGAATTA 57.473 29.630 0.00 0.00 33.67 1.40
701 709 8.306761 GTCAGAGGAAAATGTACAAATGGAATT 58.693 33.333 0.00 0.00 38.98 2.17
702 710 7.451255 TGTCAGAGGAAAATGTACAAATGGAAT 59.549 33.333 0.00 0.00 0.00 3.01
703 711 6.775142 TGTCAGAGGAAAATGTACAAATGGAA 59.225 34.615 0.00 0.00 0.00 3.53
704 712 6.303054 TGTCAGAGGAAAATGTACAAATGGA 58.697 36.000 0.00 0.00 0.00 3.41
705 713 6.573664 TGTCAGAGGAAAATGTACAAATGG 57.426 37.500 0.00 0.00 0.00 3.16
710 718 9.513906 TCAATAATTGTCAGAGGAAAATGTACA 57.486 29.630 0.00 0.00 31.20 2.90
732 740 8.657712 ACCCTACTGTAACTCTACTTTTTCAAT 58.342 33.333 0.00 0.00 0.00 2.57
733 741 8.026396 ACCCTACTGTAACTCTACTTTTTCAA 57.974 34.615 0.00 0.00 0.00 2.69
734 742 7.607615 ACCCTACTGTAACTCTACTTTTTCA 57.392 36.000 0.00 0.00 0.00 2.69
735 743 8.899427 AAACCCTACTGTAACTCTACTTTTTC 57.101 34.615 0.00 0.00 0.00 2.29
737 745 9.770097 GTAAAACCCTACTGTAACTCTACTTTT 57.230 33.333 0.00 0.00 0.00 2.27
738 746 8.370940 GGTAAAACCCTACTGTAACTCTACTTT 58.629 37.037 0.00 0.00 30.04 2.66
739 747 7.901029 GGTAAAACCCTACTGTAACTCTACTT 58.099 38.462 0.00 0.00 30.04 2.24
740 748 7.473735 GGTAAAACCCTACTGTAACTCTACT 57.526 40.000 0.00 0.00 30.04 2.57
819 830 4.411013 ACGGTAGGATAATACCCCACTAC 58.589 47.826 0.00 0.00 41.98 2.73
829 840 2.775384 TGAAGGGCAACGGTAGGATAAT 59.225 45.455 0.00 0.00 37.60 1.28
875 886 6.920569 AGCACGGTCGAATTAGAAATAATT 57.079 33.333 0.00 0.00 32.81 1.40
893 904 9.831054 CTTAGAAATAAAAACGTCTATAGCACG 57.169 33.333 17.54 17.54 43.13 5.34
954 1112 1.003118 TCCTCCCAACGATTCACTTGG 59.997 52.381 0.00 3.92 37.30 3.61
982 1140 1.123928 ATGCCCTGCTACACCTAGAC 58.876 55.000 0.00 0.00 0.00 2.59
1038 1269 4.135153 CTCGCAGGGTCGGACAGG 62.135 72.222 10.76 0.00 0.00 4.00
1040 1271 3.062466 CTCTCGCAGGGTCGGACA 61.062 66.667 10.76 0.00 0.00 4.02
1046 1278 3.023949 GCATGGTCTCTCGCAGGGT 62.024 63.158 0.00 0.00 0.00 4.34
1052 1286 1.101635 TAGGGTCGCATGGTCTCTCG 61.102 60.000 0.00 0.00 0.00 4.04
1282 1526 1.515088 CGCAGAGAGCACCACGTAG 60.515 63.158 0.00 0.00 46.13 3.51
1638 1906 3.291611 GCGAGGTCCGGGAAGTTA 58.708 61.111 0.00 0.00 39.04 2.24
1945 2222 2.961669 GCGCGAAATCCACCACGTT 61.962 57.895 12.10 0.00 0.00 3.99
1956 2233 4.423022 TGATCGGACGGCGCGAAA 62.423 61.111 12.10 3.16 0.00 3.46
2043 2320 2.812011 AGGAAATCAAGGTGTTGTACGC 59.188 45.455 0.00 0.00 34.98 4.42
2084 2374 4.676723 GCAGCACTAGAAAACCACACAAAA 60.677 41.667 0.00 0.00 0.00 2.44
2149 2439 0.879400 CAAACCCAAGCATGCGCAAA 60.879 50.000 17.11 0.00 42.27 3.68
2150 2440 1.300775 CAAACCCAAGCATGCGCAA 60.301 52.632 17.11 0.00 42.27 4.85
2151 2441 2.339348 CAAACCCAAGCATGCGCA 59.661 55.556 14.96 14.96 42.27 6.09
2153 2443 1.080569 GTCCAAACCCAAGCATGCG 60.081 57.895 13.01 0.00 0.00 4.73
2154 2444 1.202348 GTAGTCCAAACCCAAGCATGC 59.798 52.381 10.51 10.51 0.00 4.06
2262 2567 6.987992 CCTGTAATATTGCGGTAACCTAAAGA 59.012 38.462 10.94 0.00 0.00 2.52
2279 2584 6.357579 TCACCGGTAAGAAAACCTGTAATA 57.642 37.500 6.87 0.00 35.06 0.98
2285 2590 4.721132 TCATTTCACCGGTAAGAAAACCT 58.279 39.130 20.26 5.45 37.30 3.50
2297 2602 2.226330 TGAGGTTGGTTCATTTCACCG 58.774 47.619 0.00 0.00 37.07 4.94
2394 2699 1.650961 CGTTATCAAGCAATCGCGTCG 60.651 52.381 5.77 0.00 45.49 5.12
2400 2705 4.037690 GCCAACATCGTTATCAAGCAATC 58.962 43.478 0.00 0.00 0.00 2.67
2410 2715 2.226330 ACAAGCAAGCCAACATCGTTA 58.774 42.857 0.00 0.00 0.00 3.18
2443 2749 7.278875 AGTTAGGTTTGAGGAAGATGATGATC 58.721 38.462 0.00 0.00 0.00 2.92
2445 2751 6.627087 AGTTAGGTTTGAGGAAGATGATGA 57.373 37.500 0.00 0.00 0.00 2.92
2447 2753 8.095452 ACATAGTTAGGTTTGAGGAAGATGAT 57.905 34.615 0.00 0.00 0.00 2.45
2506 2812 9.574516 ACCACATAGAGTTTTAATCTCTGTTTT 57.425 29.630 13.93 0.00 41.57 2.43
2555 2861 7.394816 ACCTGTTGAGCAATATAAGTTACTGT 58.605 34.615 0.00 0.00 0.00 3.55
2625 2931 2.202690 CTAATCGCGACCGCACCA 60.203 61.111 12.93 0.00 42.06 4.17
2630 2936 0.179171 ACACAGACTAATCGCGACCG 60.179 55.000 12.93 5.11 0.00 4.79
2647 2953 1.536072 GGCGTGCTCTATCGATCAACA 60.536 52.381 0.00 0.00 0.00 3.33
2665 2971 0.674895 ATGCAAACGACAGAGGAGGC 60.675 55.000 0.00 0.00 0.00 4.70
2727 3033 7.828717 ACATGTTGTGGTTGAATACATGAGATA 59.171 33.333 17.43 0.00 45.46 1.98
2787 3093 7.435488 CGTTTCTACACAGGGATAGAGTAATTG 59.565 40.741 0.00 0.00 0.00 2.32
2791 3097 5.748402 TCGTTTCTACACAGGGATAGAGTA 58.252 41.667 0.00 0.00 0.00 2.59
2824 3130 5.073008 TCATGCCCTGAATAATTAGGCTACA 59.927 40.000 12.41 0.44 44.19 2.74
2904 3213 4.003648 GGAAGTTCTCACCATCGTTTCAT 58.996 43.478 2.25 0.00 0.00 2.57
2920 3229 1.481871 TCGATTAGAGGCCGGAAGTT 58.518 50.000 5.05 0.00 0.00 2.66
2969 3279 9.815936 GTCTTTTAATGCAAGGAAAAATGATTG 57.184 29.630 0.00 0.00 0.00 2.67
2991 3301 7.505585 TCTGAGGTGTCAAAAATAATTGGTCTT 59.494 33.333 0.00 0.00 30.14 3.01


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

AutoCloner maintained by Alex Coulton.