Multiple sequence alignment - TraesCS7D01G320100

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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 TraesCS7D01G320100 chr7D 100.000 3857 0 0 1 3857 409612011 409608155 0.000000e+00 7123
1 TraesCS7D01G320100 chr7A 92.786 2495 132 22 1174 3635 470801327 470798848 0.000000e+00 3567
2 TraesCS7D01G320100 chr7A 93.617 423 21 1 2 424 470844365 470843949 9.100000e-176 627
3 TraesCS7D01G320100 chr7A 85.766 548 32 22 614 1147 470815109 470814594 4.380000e-149 538
4 TraesCS7D01G320100 chr7B 93.969 1973 79 10 962 2903 424154443 424152480 0.000000e+00 2948
5 TraesCS7D01G320100 chr7B 95.688 603 15 1 2972 3574 424152483 424151892 0.000000e+00 959
6 TraesCS7D01G320100 chr7B 92.231 399 29 1 1 399 424155457 424155061 7.230000e-157 564
7 TraesCS7D01G320100 chr7B 96.262 214 7 1 3645 3857 424151884 424151671 2.210000e-92 350
8 TraesCS7D01G320100 chr7B 84.078 358 24 11 614 965 424154817 424154487 8.040000e-82 315
9 TraesCS7D01G320100 chr7B 86.935 199 12 6 403 596 424154994 424154805 1.090000e-50 211


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 TraesCS7D01G320100 chr7D 409608155 409612011 3856 True 7123.000000 7123 100.000000 1 3857 1 chr7D.!!$R1 3856
1 TraesCS7D01G320100 chr7A 470798848 470801327 2479 True 3567.000000 3567 92.786000 1174 3635 1 chr7A.!!$R1 2461
2 TraesCS7D01G320100 chr7A 470814594 470815109 515 True 538.000000 538 85.766000 614 1147 1 chr7A.!!$R2 533
3 TraesCS7D01G320100 chr7B 424151671 424155457 3786 True 891.166667 2948 91.527167 1 3857 6 chr7B.!!$R1 3856

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
158 159 0.169009 GAACAGACGCTTGGGATTGC 59.831 55.0 0.00 0.0 0.00 3.56 F
261 262 0.172352 CTCTCCTGGAGCGTCTTCAC 59.828 60.0 19.08 0.0 35.08 3.18 F
365 366 0.249911 GCCCGCTATAACTGGGACTG 60.250 60.0 0.00 0.0 46.41 3.51 F
1950 2081 0.036952 CAGAGTGCTACCACACCCTG 60.037 60.0 0.00 0.0 44.53 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1834 0.033011 AGACCTGACGTATGGAGGCT 60.033 55.0 12.54 0.0 0.00 4.58 R
1761 1892 1.002366 GTGATGATGAGACACACGGC 58.998 55.0 0.00 0.0 35.06 5.68 R
1984 2115 1.179814 ACCTGAAAGCGAGAGGACGT 61.180 55.0 0.00 0.0 35.59 4.34 R
3651 3842 0.388907 CAAAATCCACCAGCAAGGCG 60.389 55.0 0.00 0.0 43.14 5.52 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
21 22 2.307686 TGAGGTGATACCAAGGTTTCCC 59.692 50.000 0.00 3.47 41.95 3.97
33 34 0.322906 GGTTTCCCCTGCTGGAGAAG 60.323 60.000 11.88 0.00 35.37 2.85
42 43 0.610174 TGCTGGAGAAGATCGTGCTT 59.390 50.000 0.00 0.00 0.00 3.91
66 67 2.224113 GGGTTACCGAAGAAGTGTCACA 60.224 50.000 5.62 0.00 0.00 3.58
73 74 2.289694 CGAAGAAGTGTCACAGGGGATT 60.290 50.000 5.62 0.00 0.00 3.01
75 76 3.146104 AGAAGTGTCACAGGGGATTTG 57.854 47.619 5.62 0.00 0.00 2.32
92 93 6.263168 GGGGATTTGTATCAAGTCATTGGTAG 59.737 42.308 7.16 0.00 32.63 3.18
132 133 1.004080 CCTCGAGCTATGCCATGGG 60.004 63.158 15.13 0.00 0.00 4.00
135 136 1.670406 CGAGCTATGCCATGGGAGC 60.670 63.158 15.13 11.83 35.07 4.70
147 148 1.903877 ATGGGAGCAGGGAACAGACG 61.904 60.000 0.00 0.00 0.00 4.18
156 157 0.322546 GGGAACAGACGCTTGGGATT 60.323 55.000 0.00 0.00 0.00 3.01
158 159 0.169009 GAACAGACGCTTGGGATTGC 59.831 55.000 0.00 0.00 0.00 3.56
165 166 1.519898 GCTTGGGATTGCGGCATTG 60.520 57.895 2.28 0.00 0.00 2.82
199 200 2.796193 ATCGCCCTCATACGCTGCA 61.796 57.895 0.00 0.00 0.00 4.41
210 211 0.787787 TACGCTGCAATGTGAACGAC 59.212 50.000 0.00 0.00 0.00 4.34
261 262 0.172352 CTCTCCTGGAGCGTCTTCAC 59.828 60.000 19.08 0.00 35.08 3.18
273 274 1.070786 TCTTCACGTGAGGGGTTGC 59.929 57.895 25.30 0.00 33.12 4.17
283 284 0.528684 GAGGGGTTGCTTCGAGATCG 60.529 60.000 0.00 0.00 41.45 3.69
284 285 2.174319 GGGGTTGCTTCGAGATCGC 61.174 63.158 0.00 0.00 39.60 4.58
347 348 4.037690 GCAATGTCGGTTCAAATCTATGC 58.962 43.478 0.00 0.00 0.00 3.14
349 350 2.639065 TGTCGGTTCAAATCTATGCCC 58.361 47.619 0.00 0.00 0.00 5.36
365 366 0.249911 GCCCGCTATAACTGGGACTG 60.250 60.000 0.00 0.00 46.41 3.51
370 371 2.223829 CGCTATAACTGGGACTGAGTGG 60.224 54.545 0.00 0.00 0.00 4.00
386 387 5.222130 ACTGAGTGGTTGGTATTTCTCCATT 60.222 40.000 0.00 0.00 34.75 3.16
387 388 5.640147 TGAGTGGTTGGTATTTCTCCATTT 58.360 37.500 0.00 0.00 34.75 2.32
436 500 7.533561 GGCAACCAAATTTTTATCAAATTGTCG 59.466 33.333 0.00 0.00 30.94 4.35
451 515 8.334016 TCAAATTGTCGTTGTTAATCAGTTTG 57.666 30.769 0.00 0.00 37.20 2.93
453 517 5.821516 TTGTCGTTGTTAATCAGTTTGGT 57.178 34.783 0.00 0.00 0.00 3.67
454 518 5.163302 TGTCGTTGTTAATCAGTTTGGTG 57.837 39.130 0.00 0.00 0.00 4.17
455 519 4.876679 TGTCGTTGTTAATCAGTTTGGTGA 59.123 37.500 0.00 0.00 0.00 4.02
456 520 5.202640 GTCGTTGTTAATCAGTTTGGTGAC 58.797 41.667 0.00 0.00 0.00 3.67
457 521 4.025563 TCGTTGTTAATCAGTTTGGTGACG 60.026 41.667 0.00 0.00 0.00 4.35
458 522 4.025563 CGTTGTTAATCAGTTTGGTGACGA 60.026 41.667 0.00 0.00 0.00 4.20
459 523 5.502706 CGTTGTTAATCAGTTTGGTGACGAA 60.503 40.000 0.00 0.00 0.00 3.85
460 524 6.435428 GTTGTTAATCAGTTTGGTGACGAAT 58.565 36.000 0.00 0.00 35.78 3.34
461 525 6.236017 TGTTAATCAGTTTGGTGACGAATC 57.764 37.500 0.00 0.00 35.78 2.52
462 526 5.760743 TGTTAATCAGTTTGGTGACGAATCA 59.239 36.000 0.00 0.00 35.78 2.57
466 530 5.400066 TCAGTTTGGTGACGAATCAGATA 57.600 39.130 0.00 0.00 34.75 1.98
487 551 1.222936 CGGATTCTGAGGGCAGCTT 59.777 57.895 0.00 0.00 42.01 3.74
508 577 5.741040 GCTTTGTACATATTTCAGAAGCTGC 59.259 40.000 14.45 0.00 36.31 5.25
528 597 1.618343 CCATTTTCTTTTCCAGGCGGT 59.382 47.619 0.00 0.00 0.00 5.68
590 659 6.861065 TTATTATTCATCTGCCGACCTTTC 57.139 37.500 0.00 0.00 0.00 2.62
591 660 2.044123 ATTCATCTGCCGACCTTTCC 57.956 50.000 0.00 0.00 0.00 3.13
592 661 0.984230 TTCATCTGCCGACCTTTCCT 59.016 50.000 0.00 0.00 0.00 3.36
593 662 0.984230 TCATCTGCCGACCTTTCCTT 59.016 50.000 0.00 0.00 0.00 3.36
594 663 1.351017 TCATCTGCCGACCTTTCCTTT 59.649 47.619 0.00 0.00 0.00 3.11
595 664 1.740025 CATCTGCCGACCTTTCCTTTC 59.260 52.381 0.00 0.00 0.00 2.62
596 665 1.056660 TCTGCCGACCTTTCCTTTCT 58.943 50.000 0.00 0.00 0.00 2.52
597 666 1.420138 TCTGCCGACCTTTCCTTTCTT 59.580 47.619 0.00 0.00 0.00 2.52
598 667 2.158667 TCTGCCGACCTTTCCTTTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
599 668 2.623416 CTGCCGACCTTTCCTTTCTTTT 59.377 45.455 0.00 0.00 0.00 2.27
600 669 3.028130 TGCCGACCTTTCCTTTCTTTTT 58.972 40.909 0.00 0.00 0.00 1.94
644 713 5.757320 CCTTTCTACAGCAGAATCATTCGAT 59.243 40.000 0.00 0.00 42.88 3.59
772 842 1.544314 GGTGAAGCTGAGTTTGCTCCT 60.544 52.381 0.00 0.00 40.22 3.69
777 847 3.988976 AGCTGAGTTTGCTCCTCAATA 57.011 42.857 0.00 0.00 40.95 1.90
796 866 2.632987 AACAGTAGAAGCACGGGTTT 57.367 45.000 0.00 0.00 0.00 3.27
805 875 3.611674 CACGGGTTTGGTTGGGCC 61.612 66.667 0.00 0.00 37.90 5.80
806 876 3.828023 ACGGGTTTGGTTGGGCCT 61.828 61.111 4.53 0.00 38.35 5.19
807 877 3.302344 CGGGTTTGGTTGGGCCTG 61.302 66.667 4.53 0.00 38.35 4.85
808 878 2.922503 GGGTTTGGTTGGGCCTGG 60.923 66.667 4.53 0.00 38.35 4.45
809 879 2.922503 GGTTTGGTTGGGCCTGGG 60.923 66.667 4.53 0.00 38.35 4.45
810 880 3.625897 GTTTGGTTGGGCCTGGGC 61.626 66.667 12.58 12.58 38.35 5.36
838 908 3.086600 GGGCCCTGGTGGAGAGAG 61.087 72.222 17.04 0.00 35.39 3.20
895 970 1.059942 GGCGCCAAAAACTCAATTCG 58.940 50.000 24.80 0.00 0.00 3.34
916 991 3.202706 GGAGGGCGCGCTAAAAGG 61.203 66.667 32.29 0.00 0.00 3.11
965 1088 2.990479 CGGGGAAACAGAGGGAGG 59.010 66.667 0.00 0.00 0.00 4.30
1089 1214 2.671070 CACCGCTTCCTCACCCAT 59.329 61.111 0.00 0.00 0.00 4.00
1171 1296 2.418910 CGCCTCACCGTCCTCATCT 61.419 63.158 0.00 0.00 0.00 2.90
1185 1310 0.911769 TCATCTCCCGCCACATCTTT 59.088 50.000 0.00 0.00 0.00 2.52
1196 1321 3.274288 GCCACATCTTTCCTCAGGTAAG 58.726 50.000 3.62 3.62 32.48 2.34
1198 1323 3.307691 CCACATCTTTCCTCAGGTAAGCA 60.308 47.826 5.17 0.00 31.50 3.91
1199 1324 3.937706 CACATCTTTCCTCAGGTAAGCAG 59.062 47.826 5.17 3.14 31.50 4.24
1206 1331 1.555075 CCTCAGGTAAGCAGCAACCTA 59.445 52.381 16.90 7.28 44.43 3.08
1209 1334 2.571653 TCAGGTAAGCAGCAACCTACAT 59.428 45.455 16.90 0.00 44.43 2.29
1211 1336 2.840651 AGGTAAGCAGCAACCTACATCT 59.159 45.455 16.03 0.00 44.40 2.90
1220 1345 3.640967 AGCAACCTACATCTCATCTCTCC 59.359 47.826 0.00 0.00 0.00 3.71
1222 1347 3.252554 ACCTACATCTCATCTCTCCCC 57.747 52.381 0.00 0.00 0.00 4.81
1226 1352 0.831288 CATCTCATCTCTCCCCGCCT 60.831 60.000 0.00 0.00 0.00 5.52
1227 1353 0.831288 ATCTCATCTCTCCCCGCCTG 60.831 60.000 0.00 0.00 0.00 4.85
1228 1354 1.760086 CTCATCTCTCCCCGCCTGT 60.760 63.158 0.00 0.00 0.00 4.00
1229 1355 0.468214 CTCATCTCTCCCCGCCTGTA 60.468 60.000 0.00 0.00 0.00 2.74
1230 1356 0.755698 TCATCTCTCCCCGCCTGTAC 60.756 60.000 0.00 0.00 0.00 2.90
1231 1357 1.457831 ATCTCTCCCCGCCTGTACC 60.458 63.158 0.00 0.00 0.00 3.34
1232 1358 1.950748 ATCTCTCCCCGCCTGTACCT 61.951 60.000 0.00 0.00 0.00 3.08
1233 1359 1.686110 CTCTCCCCGCCTGTACCTT 60.686 63.158 0.00 0.00 0.00 3.50
1234 1360 1.961180 CTCTCCCCGCCTGTACCTTG 61.961 65.000 0.00 0.00 0.00 3.61
1238 1364 1.740296 CCCGCCTGTACCTTGTTCG 60.740 63.158 0.00 0.00 0.00 3.95
1249 1375 5.871539 TGTACCTTGTTCGTTTCTTTTCAC 58.128 37.500 0.00 0.00 0.00 3.18
1256 1382 5.123227 TGTTCGTTTCTTTTCACCTCATCT 58.877 37.500 0.00 0.00 0.00 2.90
1267 1393 0.833287 ACCTCATCTCCATTCCCGTG 59.167 55.000 0.00 0.00 0.00 4.94
1269 1395 1.210478 CCTCATCTCCATTCCCGTGTT 59.790 52.381 0.00 0.00 0.00 3.32
1270 1396 2.356125 CCTCATCTCCATTCCCGTGTTT 60.356 50.000 0.00 0.00 0.00 2.83
1271 1397 2.939103 CTCATCTCCATTCCCGTGTTTC 59.061 50.000 0.00 0.00 0.00 2.78
1329 1458 2.026879 GTGGAGATCGAGCTCGGC 59.973 66.667 33.98 25.33 40.29 5.54
1374 1503 2.338984 GGCGACTTCACCGTCACT 59.661 61.111 0.00 0.00 33.54 3.41
1442 1572 3.454447 TCTTCCCATTCTCGCTAATTCCA 59.546 43.478 0.00 0.00 0.00 3.53
1541 1672 2.591715 GGCAACGTCCTGCACACT 60.592 61.111 13.82 0.00 44.52 3.55
1618 1749 2.922503 TGAGGCACCAGGAGCGAA 60.923 61.111 2.39 0.00 0.00 4.70
1744 1875 3.250762 TGTGTGCTGCTTCATCAGTAAAC 59.749 43.478 0.00 0.00 37.41 2.01
1761 1892 1.238439 AACCAGACCAGCAATTGACG 58.762 50.000 10.34 0.00 0.00 4.35
1803 1934 8.081633 TCACATTGTATTTTTCAGGTGATCAAC 58.918 33.333 1.26 1.26 31.34 3.18
1915 2046 2.837498 TCGGGTCGAAGATATACGTCA 58.163 47.619 0.00 0.00 40.67 4.35
1950 2081 0.036952 CAGAGTGCTACCACACCCTG 60.037 60.000 0.00 0.00 44.53 4.45
1953 2084 0.762842 AGTGCTACCACACCCTGTCA 60.763 55.000 0.00 0.00 44.53 3.58
2109 2241 1.009675 AGGCCTTCTACCCAGTGGTAT 59.990 52.381 8.74 0.00 46.04 2.73
2151 2283 1.375268 GTCGCTGAAGCAGAAGCCT 60.375 57.895 2.79 0.00 43.56 4.58
2178 2310 1.294780 GGAGCCTATGCGGGATGAG 59.705 63.158 0.00 0.00 44.33 2.90
2193 2325 1.852157 ATGAGTTCGGGGTGTGGCAT 61.852 55.000 0.00 0.00 0.00 4.40
2338 2470 2.303549 CTGCTTCCTGTCCCGGCTAG 62.304 65.000 0.00 0.00 0.00 3.42
2375 2507 4.890158 TCTGGAAGTTGCTCAGAATACA 57.110 40.909 0.00 0.00 34.97 2.29
2386 2518 6.628919 TGCTCAGAATACATCATGGAAATG 57.371 37.500 0.00 0.00 0.00 2.32
2519 2693 4.101430 ACAAGATTTTGCAATTGAGGTGGT 59.899 37.500 15.53 0.00 37.85 4.16
2651 2825 5.482878 AGGAGGAATTGCAGAATTCAAATGT 59.517 36.000 8.44 0.00 46.52 2.71
3077 3256 4.933330 TCTATCCGACATTAGCAACAGAC 58.067 43.478 0.00 0.00 0.00 3.51
3127 3306 1.607801 CTGCTGGAGTCGGGTCATCA 61.608 60.000 0.00 0.00 0.00 3.07
3238 3417 0.179001 CCTCCAAACGACCAAGGGTT 60.179 55.000 0.00 0.00 35.25 4.11
3264 3443 5.011090 TCCCAGTTTCGTCATCTATGAAG 57.989 43.478 0.00 0.00 38.75 3.02
3291 3470 6.914757 GCCTTTTGTTATCATAGCACAAGATC 59.085 38.462 8.55 0.00 31.09 2.75
3341 3532 2.557924 TCCCTGTGCAGCTACAAATTTG 59.442 45.455 16.67 16.67 0.00 2.32
3342 3533 2.297033 CCCTGTGCAGCTACAAATTTGT 59.703 45.455 25.99 25.99 44.86 2.83
3343 3534 3.243839 CCCTGTGCAGCTACAAATTTGTT 60.244 43.478 27.66 8.62 42.35 2.83
3344 3535 3.737266 CCTGTGCAGCTACAAATTTGTTG 59.263 43.478 27.66 25.16 42.35 3.33
3408 3599 6.721571 AGTGATTTAGTGGTTGTGAATACG 57.278 37.500 0.00 0.00 0.00 3.06
3475 3666 6.549364 TGATCCAAGTCCATGTTTACTTTTGT 59.451 34.615 3.35 0.00 33.72 2.83
3550 3741 5.127845 TGTTTTTATCAGTTTGGGCTCACAA 59.872 36.000 0.00 0.00 0.00 3.33
3575 3766 2.027192 GTGCCAAGTTCAGATAGGTGGA 60.027 50.000 0.00 0.00 0.00 4.02
3579 3770 3.369892 CCAAGTTCAGATAGGTGGACTGG 60.370 52.174 0.00 0.00 36.32 4.00
3586 3777 0.547712 ATAGGTGGACTGGGCTGTGT 60.548 55.000 0.00 0.00 0.00 3.72
3588 3779 2.520536 GGTGGACTGGGCTGTGTCT 61.521 63.158 0.00 0.00 34.01 3.41
3608 3799 6.096987 GTGTCTGGTATCTAGATTTCAGTCCA 59.903 42.308 23.01 19.39 0.00 4.02
3632 3823 5.595542 AGATTGTTACATTACATGCCATGCT 59.404 36.000 4.17 0.00 0.00 3.79
3635 3826 4.142425 TGTTACATTACATGCCATGCTGTG 60.142 41.667 14.75 9.32 0.00 3.66
3636 3827 1.135527 ACATTACATGCCATGCTGTGC 59.864 47.619 4.17 0.00 0.00 4.57
3637 3828 1.135333 CATTACATGCCATGCTGTGCA 59.865 47.619 4.17 0.00 44.86 4.57
3638 3829 1.254954 TTACATGCCATGCTGTGCAA 58.745 45.000 4.17 0.00 43.62 4.08
3639 3830 0.812549 TACATGCCATGCTGTGCAAG 59.187 50.000 4.17 0.00 43.62 4.01
3643 3834 4.124351 CCATGCTGTGCAAGGCCG 62.124 66.667 0.00 1.87 40.46 6.13
3669 3860 1.966762 CGCCTTGCTGGTGGATTTT 59.033 52.632 2.58 0.00 42.43 1.82
3673 3864 1.001181 CCTTGCTGGTGGATTTTGGTG 59.999 52.381 0.00 0.00 0.00 4.17
3815 4007 4.881920 TGAATGTTCGAGAAGATGTGACA 58.118 39.130 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.809241 GCACGATCTTCTCCAGCAGG 60.809 60.000 0.00 0.00 0.00 4.85
33 34 1.092348 GGTAACCCCAAAGCACGATC 58.908 55.000 0.00 0.00 0.00 3.69
42 43 1.770061 ACACTTCTTCGGTAACCCCAA 59.230 47.619 0.00 0.00 0.00 4.12
66 67 5.203528 CCAATGACTTGATACAAATCCCCT 58.796 41.667 0.00 0.00 34.04 4.79
73 74 7.148255 GCATGTTCTACCAATGACTTGATACAA 60.148 37.037 0.00 0.00 34.04 2.41
75 76 6.316140 TGCATGTTCTACCAATGACTTGATAC 59.684 38.462 0.00 0.00 34.04 2.24
92 93 3.740590 CACTCGAGTTGATTGCATGTTC 58.259 45.455 17.26 0.00 0.00 3.18
132 133 1.004440 AAGCGTCTGTTCCCTGCTC 60.004 57.895 0.00 0.00 34.19 4.26
135 136 1.672356 CCCAAGCGTCTGTTCCCTG 60.672 63.158 0.00 0.00 0.00 4.45
147 148 1.519898 CAATGCCGCAATCCCAAGC 60.520 57.895 0.00 0.00 0.00 4.01
181 182 2.029666 GCAGCGTATGAGGGCGAT 59.970 61.111 0.00 0.00 0.00 4.58
184 185 1.097547 ACATTGCAGCGTATGAGGGC 61.098 55.000 12.85 0.00 0.00 5.19
199 200 2.061773 CAGCTCTTCGTCGTTCACATT 58.938 47.619 0.00 0.00 0.00 2.71
210 211 4.274214 TCAATGATAAATGCCAGCTCTTCG 59.726 41.667 0.00 0.00 0.00 3.79
261 262 1.738099 CTCGAAGCAACCCCTCACG 60.738 63.158 0.00 0.00 0.00 4.35
273 274 4.251843 TCGCCGGCGATCTCGAAG 62.252 66.667 45.37 16.92 44.01 3.79
284 285 3.466791 ATCAGGATTGGCTCGCCGG 62.467 63.158 0.00 0.00 39.42 6.13
295 296 1.452651 CACGCTTGGCCATCAGGAT 60.453 57.895 6.09 0.00 36.89 3.24
347 348 1.341531 CTCAGTCCCAGTTATAGCGGG 59.658 57.143 9.26 9.26 41.76 6.13
349 350 2.223829 CCACTCAGTCCCAGTTATAGCG 60.224 54.545 0.00 0.00 0.00 4.26
365 366 7.610305 TCTTAAATGGAGAAATACCAACCACTC 59.390 37.037 0.00 0.00 40.93 3.51
399 400 1.122632 TTGGTTGCCCCTCTCGTGTA 61.123 55.000 0.00 0.00 0.00 2.90
400 401 1.990160 TTTGGTTGCCCCTCTCGTGT 61.990 55.000 0.00 0.00 0.00 4.49
401 402 0.609131 ATTTGGTTGCCCCTCTCGTG 60.609 55.000 0.00 0.00 0.00 4.35
410 474 7.533561 CGACAATTTGATAAAAATTTGGTTGCC 59.466 33.333 2.79 0.00 0.00 4.52
428 492 7.221838 CACCAAACTGATTAACAACGACAATTT 59.778 33.333 0.00 0.00 0.00 1.82
429 493 6.695278 CACCAAACTGATTAACAACGACAATT 59.305 34.615 0.00 0.00 0.00 2.32
436 500 5.412526 TCGTCACCAAACTGATTAACAAC 57.587 39.130 0.00 0.00 0.00 3.32
442 506 4.641396 TCTGATTCGTCACCAAACTGATT 58.359 39.130 0.00 0.00 0.00 2.57
451 515 4.238761 TCCGATTATCTGATTCGTCACC 57.761 45.455 9.98 0.00 30.58 4.02
453 517 6.016276 TCAGAATCCGATTATCTGATTCGTCA 60.016 38.462 23.62 14.17 45.63 4.35
454 518 6.382608 TCAGAATCCGATTATCTGATTCGTC 58.617 40.000 23.62 9.80 45.63 4.20
455 519 6.332735 TCAGAATCCGATTATCTGATTCGT 57.667 37.500 23.62 14.61 45.63 3.85
456 520 5.804473 CCTCAGAATCCGATTATCTGATTCG 59.196 44.000 23.62 19.75 45.63 3.34
457 521 6.105333 CCCTCAGAATCCGATTATCTGATTC 58.895 44.000 22.98 22.98 46.07 2.52
458 522 5.570439 GCCCTCAGAATCCGATTATCTGATT 60.570 44.000 10.81 10.81 46.07 2.57
459 523 4.081198 GCCCTCAGAATCCGATTATCTGAT 60.081 45.833 11.53 0.00 46.07 2.90
460 524 3.259374 GCCCTCAGAATCCGATTATCTGA 59.741 47.826 10.88 10.88 45.34 3.27
461 525 3.007290 TGCCCTCAGAATCCGATTATCTG 59.993 47.826 4.31 4.31 41.49 2.90
462 526 3.242867 TGCCCTCAGAATCCGATTATCT 58.757 45.455 0.00 0.00 0.00 1.98
466 530 0.179034 GCTGCCCTCAGAATCCGATT 60.179 55.000 0.00 0.00 42.95 3.34
479 543 4.640201 TCTGAAATATGTACAAAGCTGCCC 59.360 41.667 0.00 0.00 0.00 5.36
487 551 5.252547 TGGCAGCTTCTGAAATATGTACAA 58.747 37.500 0.00 0.00 32.44 2.41
508 577 1.618343 ACCGCCTGGAAAAGAAAATGG 59.382 47.619 0.00 0.00 39.21 3.16
612 681 3.008049 TCTGCTGTAGAAAGGAAAGGTCC 59.992 47.826 0.00 0.00 36.97 4.46
740 810 5.084818 TCAGCTTCACCGATGATTCTAAA 57.915 39.130 0.00 0.00 33.85 1.85
746 816 3.005554 CAAACTCAGCTTCACCGATGAT 58.994 45.455 0.00 0.00 33.85 2.45
750 820 0.106708 AGCAAACTCAGCTTCACCGA 59.893 50.000 0.00 0.00 39.87 4.69
772 842 3.259876 ACCCGTGCTTCTACTGTTATTGA 59.740 43.478 0.00 0.00 0.00 2.57
777 847 2.218603 CAAACCCGTGCTTCTACTGTT 58.781 47.619 0.00 0.00 0.00 3.16
831 901 0.818938 GTTCCCTTCGTCCTCTCTCC 59.181 60.000 0.00 0.00 0.00 3.71
838 908 2.152016 CCTTTCAAGTTCCCTTCGTCC 58.848 52.381 0.00 0.00 0.00 4.79
895 970 1.858372 TTTTAGCGCGCCCTCCAAAC 61.858 55.000 30.33 0.00 0.00 2.93
1171 1296 1.198094 TGAGGAAAGATGTGGCGGGA 61.198 55.000 0.00 0.00 0.00 5.14
1185 1310 0.324943 GGTTGCTGCTTACCTGAGGA 59.675 55.000 4.99 0.00 0.00 3.71
1196 1321 3.129871 GAGATGAGATGTAGGTTGCTGC 58.870 50.000 0.00 0.00 0.00 5.25
1198 1323 3.640967 GGAGAGATGAGATGTAGGTTGCT 59.359 47.826 0.00 0.00 0.00 3.91
1199 1324 3.244044 GGGAGAGATGAGATGTAGGTTGC 60.244 52.174 0.00 0.00 0.00 4.17
1206 1331 1.118356 GGCGGGGAGAGATGAGATGT 61.118 60.000 0.00 0.00 0.00 3.06
1209 1334 1.456518 CAGGCGGGGAGAGATGAGA 60.457 63.158 0.00 0.00 0.00 3.27
1211 1336 0.755698 GTACAGGCGGGGAGAGATGA 60.756 60.000 0.00 0.00 0.00 2.92
1220 1345 1.740296 CGAACAAGGTACAGGCGGG 60.740 63.158 0.00 0.00 0.00 6.13
1222 1347 1.193874 GAAACGAACAAGGTACAGGCG 59.806 52.381 0.00 0.00 0.00 5.52
1226 1352 5.163733 GGTGAAAAGAAACGAACAAGGTACA 60.164 40.000 0.00 0.00 0.00 2.90
1227 1353 5.065602 AGGTGAAAAGAAACGAACAAGGTAC 59.934 40.000 0.00 0.00 0.00 3.34
1228 1354 5.187687 AGGTGAAAAGAAACGAACAAGGTA 58.812 37.500 0.00 0.00 0.00 3.08
1229 1355 4.014406 AGGTGAAAAGAAACGAACAAGGT 58.986 39.130 0.00 0.00 0.00 3.50
1230 1356 4.095782 TGAGGTGAAAAGAAACGAACAAGG 59.904 41.667 0.00 0.00 0.00 3.61
1231 1357 5.229921 TGAGGTGAAAAGAAACGAACAAG 57.770 39.130 0.00 0.00 0.00 3.16
1232 1358 5.588648 AGATGAGGTGAAAAGAAACGAACAA 59.411 36.000 0.00 0.00 0.00 2.83
1233 1359 5.123227 AGATGAGGTGAAAAGAAACGAACA 58.877 37.500 0.00 0.00 0.00 3.18
1234 1360 5.334182 GGAGATGAGGTGAAAAGAAACGAAC 60.334 44.000 0.00 0.00 0.00 3.95
1238 1364 6.349694 GGAATGGAGATGAGGTGAAAAGAAAC 60.350 42.308 0.00 0.00 0.00 2.78
1249 1375 0.833287 ACACGGGAATGGAGATGAGG 59.167 55.000 0.00 0.00 0.00 3.86
1278 1404 2.292828 CAAGCTTTGGAGAGGGGAAA 57.707 50.000 0.00 0.00 0.00 3.13
1347 1476 2.754658 AAGTCGCCGTCGGGATCT 60.755 61.111 14.38 6.29 36.13 2.75
1374 1503 4.243008 TGGTTGGCGTCGAAGGCA 62.243 61.111 22.87 22.87 45.22 4.75
1442 1572 3.284197 GCGGTGGCGTACTAATGAT 57.716 52.632 0.00 0.00 0.00 2.45
1562 1693 2.110967 CAGGCCCTGAATGCAGTCG 61.111 63.158 4.15 4.45 40.63 4.18
1601 1732 2.922503 TTCGCTCCTGGTGCCTCA 60.923 61.111 14.57 0.00 0.00 3.86
1703 1834 0.033011 AGACCTGACGTATGGAGGCT 60.033 55.000 12.54 0.00 0.00 4.58
1744 1875 1.503542 GCGTCAATTGCTGGTCTGG 59.496 57.895 0.00 0.00 0.00 3.86
1761 1892 1.002366 GTGATGATGAGACACACGGC 58.998 55.000 0.00 0.00 35.06 5.68
1915 2046 4.392940 CACTCTGAATTCTTGTCCCTGTT 58.607 43.478 7.05 0.00 0.00 3.16
1950 2081 3.547249 TTCCGGTGCGACGAGTGAC 62.547 63.158 0.00 0.00 35.47 3.67
1953 2084 1.445582 GATTTCCGGTGCGACGAGT 60.446 57.895 0.00 0.00 35.47 4.18
1984 2115 1.179814 ACCTGAAAGCGAGAGGACGT 61.180 55.000 0.00 0.00 35.59 4.34
2178 2310 2.282180 ACATGCCACACCCCGAAC 60.282 61.111 0.00 0.00 0.00 3.95
2193 2325 1.197492 GAATGCATCGTCAAGCACACA 59.803 47.619 0.00 0.00 44.49 3.72
2338 2470 2.352805 GATGGGATCATCGGGGCC 59.647 66.667 0.00 0.00 40.15 5.80
2375 2507 4.847198 TGTGACAGTAGCATTTCCATGAT 58.153 39.130 0.00 0.00 32.40 2.45
2386 2518 0.390472 GGTGAGCCTGTGACAGTAGC 60.390 60.000 12.15 8.73 0.00 3.58
2519 2693 1.106351 AAACAATGTCACCGGCTGCA 61.106 50.000 0.00 0.00 0.00 4.41
3077 3256 1.002868 CAGTGTCAGGGCCTTCAGG 60.003 63.158 1.32 0.00 38.53 3.86
3127 3306 3.068024 TCAGCTTCGCATTCAAAACCTTT 59.932 39.130 0.00 0.00 0.00 3.11
3238 3417 2.257207 AGATGACGAAACTGGGAGGAA 58.743 47.619 0.00 0.00 0.00 3.36
3264 3443 3.699038 TGTGCTATGATAACAAAAGGCCC 59.301 43.478 0.00 0.00 0.00 5.80
3291 3470 6.514947 AGACAAATCTAGAGCTCTAGCAATG 58.485 40.000 36.18 31.87 44.24 2.82
3341 3532 8.223100 GGAATCACTTCAATACAAATTTGCAAC 58.777 33.333 18.12 0.00 32.70 4.17
3342 3533 8.149647 AGGAATCACTTCAATACAAATTTGCAA 58.850 29.630 18.12 7.17 32.70 4.08
3343 3534 7.669427 AGGAATCACTTCAATACAAATTTGCA 58.331 30.769 18.12 5.75 32.70 4.08
3344 3535 8.538409 AAGGAATCACTTCAATACAAATTTGC 57.462 30.769 18.12 0.00 32.70 3.68
3346 3537 8.992073 GCAAAGGAATCACTTCAATACAAATTT 58.008 29.630 0.00 0.00 32.70 1.82
3347 3538 8.370182 AGCAAAGGAATCACTTCAATACAAATT 58.630 29.630 0.00 0.00 32.70 1.82
3348 3539 7.899973 AGCAAAGGAATCACTTCAATACAAAT 58.100 30.769 0.00 0.00 32.70 2.32
3349 3540 7.288810 AGCAAAGGAATCACTTCAATACAAA 57.711 32.000 0.00 0.00 32.70 2.83
3350 3541 6.899393 AGCAAAGGAATCACTTCAATACAA 57.101 33.333 0.00 0.00 32.70 2.41
3351 3542 6.939730 TGTAGCAAAGGAATCACTTCAATACA 59.060 34.615 0.00 0.00 32.70 2.29
3408 3599 4.333926 GCCAAGACCATATCAAGAACTGAC 59.666 45.833 0.00 0.00 36.69 3.51
3575 3766 0.905357 GATACCAGACACAGCCCAGT 59.095 55.000 0.00 0.00 0.00 4.00
3579 3770 4.946478 AATCTAGATACCAGACACAGCC 57.054 45.455 5.46 0.00 0.00 4.85
3586 3777 6.673583 TCTGGACTGAAATCTAGATACCAGA 58.326 40.000 27.50 24.88 45.57 3.86
3588 3779 7.345653 ACAATCTGGACTGAAATCTAGATACCA 59.654 37.037 5.46 6.26 43.82 3.25
3608 3799 8.767438 ACAGCATGGCATGTAATGTAACAATCT 61.767 37.037 26.94 9.13 43.81 2.40
3651 3842 0.388907 CAAAATCCACCAGCAAGGCG 60.389 55.000 0.00 0.00 43.14 5.52
3815 4007 5.864418 ACATACAACCGTCATACACCTAT 57.136 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.