Multiple sequence alignment - TraesCS7B01G399300

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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 TraesCS7B01G399300 chr7B 100.000 2738 0 0 1 2738 665522094 665524831 0.000000e+00 5057.0
1 TraesCS7B01G399300 chr7B 86.533 2094 200 37 692 2731 23318279 23316214 0.000000e+00 2230.0
2 TraesCS7B01G399300 chr7B 86.953 1349 138 23 1315 2646 665531654 665532981 0.000000e+00 1482.0
3 TraesCS7B01G399300 chr7B 93.299 970 61 2 1215 2180 665539204 665540173 0.000000e+00 1428.0
4 TraesCS7B01G399300 chr7B 84.929 982 88 32 822 1770 665534602 665535556 0.000000e+00 939.0
5 TraesCS7B01G399300 chr7B 80.707 1244 189 37 923 2139 23325672 23324453 0.000000e+00 920.0
6 TraesCS7B01G399300 chr7B 81.103 979 158 18 790 1746 33956105 33957078 0.000000e+00 758.0
7 TraesCS7B01G399300 chr7B 91.691 349 23 5 584 931 23326036 23325693 1.910000e-131 479.0
8 TraesCS7B01G399300 chr7B 80.273 659 105 16 790 1427 34140716 34141370 8.870000e-130 473.0
9 TraesCS7B01G399300 chr7B 93.213 221 11 3 1 220 23332623 23332406 3.400000e-84 322.0
10 TraesCS7B01G399300 chr7B 84.195 348 32 8 223 554 23332349 23332009 1.580000e-82 316.0
11 TraesCS7B01G399300 chr7B 97.778 90 2 0 2642 2731 665533256 665533345 3.650000e-34 156.0
12 TraesCS7B01G399300 chr7B 74.426 305 55 17 1852 2139 665535727 665536025 2.880000e-20 110.0
13 TraesCS7B01G399300 chr7D 90.481 1828 140 21 915 2731 590647662 590649466 0.000000e+00 2381.0
14 TraesCS7B01G399300 chr7D 85.378 1744 165 44 707 2405 590731824 590733522 0.000000e+00 1725.0
15 TraesCS7B01G399300 chr7D 86.070 1084 110 20 760 1808 590651936 590653013 0.000000e+00 1127.0
16 TraesCS7B01G399300 chr7D 81.393 876 136 19 790 1642 84406597 84407468 0.000000e+00 689.0
17 TraesCS7B01G399300 chr7D 85.621 306 29 9 2432 2731 590733516 590733812 9.520000e-80 307.0
18 TraesCS7B01G399300 chr7D 86.328 256 18 5 682 931 590647405 590647649 2.090000e-66 263.0
19 TraesCS7B01G399300 chr7D 74.900 251 43 13 1905 2139 590653142 590653388 2.240000e-16 97.1
20 TraesCS7B01G399300 chr7A 82.645 1066 139 28 704 1746 85693512 85694554 0.000000e+00 902.0
21 TraesCS7B01G399300 chr5B 83.511 564 65 16 2098 2646 93470961 93470411 4.070000e-138 501.0
22 TraesCS7B01G399300 chr6B 82.495 537 90 4 1189 1723 696080013 696080547 4.130000e-128 468.0
23 TraesCS7B01G399300 chr1A 88.235 68 6 2 77 144 584968847 584968912 2.260000e-11 80.5
24 TraesCS7B01G399300 chr1D 87.879 66 8 0 72 137 427869062 427868997 8.130000e-11 78.7


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 TraesCS7B01G399300 chr7B 665522094 665524831 2737 False 5057.000 5057 100.00000 1 2738 1 chr7B.!!$F3 2737
1 TraesCS7B01G399300 chr7B 23316214 23318279 2065 True 2230.000 2230 86.53300 692 2731 1 chr7B.!!$R1 2039
2 TraesCS7B01G399300 chr7B 665531654 665540173 8519 False 823.000 1482 87.47700 822 2731 5 chr7B.!!$F4 1909
3 TraesCS7B01G399300 chr7B 33956105 33957078 973 False 758.000 758 81.10300 790 1746 1 chr7B.!!$F1 956
4 TraesCS7B01G399300 chr7B 23324453 23326036 1583 True 699.500 920 86.19900 584 2139 2 chr7B.!!$R2 1555
5 TraesCS7B01G399300 chr7B 34140716 34141370 654 False 473.000 473 80.27300 790 1427 1 chr7B.!!$F2 637
6 TraesCS7B01G399300 chr7B 23332009 23332623 614 True 319.000 322 88.70400 1 554 2 chr7B.!!$R3 553
7 TraesCS7B01G399300 chr7D 590731824 590733812 1988 False 1016.000 1725 85.49950 707 2731 2 chr7D.!!$F3 2024
8 TraesCS7B01G399300 chr7D 590647405 590653388 5983 False 967.025 2381 84.44475 682 2731 4 chr7D.!!$F2 2049
9 TraesCS7B01G399300 chr7D 84406597 84407468 871 False 689.000 689 81.39300 790 1642 1 chr7D.!!$F1 852
10 TraesCS7B01G399300 chr7A 85693512 85694554 1042 False 902.000 902 82.64500 704 1746 1 chr7A.!!$F1 1042
11 TraesCS7B01G399300 chr5B 93470411 93470961 550 True 501.000 501 83.51100 2098 2646 1 chr5B.!!$R1 548
12 TraesCS7B01G399300 chr6B 696080013 696080547 534 False 468.000 468 82.49500 1189 1723 1 chr6B.!!$F1 534

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
775 856 0.030235 GGACGACCTTTTGTTGCCAC 59.97 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 8986 0.109272 TCTGCACGTCGAGGAATGAC 60.109 55.0 12.85 0.0 0.0 3.06 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
45 46 7.236019 TGAAGGGTAAGTTCATAGGTTTCTACA 59.764 37.037 0.00 0.00 0.00 2.74
50 51 7.711339 GGTAAGTTCATAGGTTTCTACATGGAG 59.289 40.741 0.00 0.00 0.00 3.86
202 203 6.207691 ACAAGTACAGCAAAACACTGAAAT 57.792 33.333 0.00 0.00 38.55 2.17
282 338 3.187227 GCGTCATCTCTTTCTGCTCAAAA 59.813 43.478 0.00 0.00 0.00 2.44
285 341 5.456265 GTCATCTCTTTCTGCTCAAAAACC 58.544 41.667 0.00 0.00 0.00 3.27
286 342 5.009010 GTCATCTCTTTCTGCTCAAAAACCA 59.991 40.000 0.00 0.00 0.00 3.67
290 346 6.061441 TCTCTTTCTGCTCAAAAACCATGTA 58.939 36.000 0.00 0.00 0.00 2.29
347 403 2.022240 GCGAGGGTGATCTCCTCCAC 62.022 65.000 21.72 14.38 46.01 4.02
348 404 0.684479 CGAGGGTGATCTCCTCCACA 60.684 60.000 21.72 0.00 46.01 4.17
351 407 2.998493 GGTGATCTCCTCCACACCT 58.002 57.895 6.56 0.00 46.14 4.00
352 408 1.280457 GGTGATCTCCTCCACACCTT 58.720 55.000 6.56 0.00 46.14 3.50
364 436 3.052082 CACCTTGGCCGAGCACAG 61.052 66.667 15.36 3.34 0.00 3.66
405 477 3.823281 TGGAAGTTGTCGAGTAAACCA 57.177 42.857 0.00 0.00 0.00 3.67
406 478 3.460103 TGGAAGTTGTCGAGTAAACCAC 58.540 45.455 0.00 0.00 0.00 4.16
408 480 3.493503 GGAAGTTGTCGAGTAAACCACAG 59.506 47.826 0.00 0.00 0.00 3.66
409 481 2.480845 AGTTGTCGAGTAAACCACAGC 58.519 47.619 0.00 0.00 0.00 4.40
428 500 4.828296 CACAGCCCCCATCCTGCC 62.828 72.222 0.00 0.00 32.37 4.85
434 506 1.228675 CCCCCATCCTGCCATTAGC 60.229 63.158 0.00 0.00 44.14 3.09
469 541 4.624452 GCATCCAGACTTCTTTTGCAAATC 59.376 41.667 13.65 7.16 0.00 2.17
472 544 4.279169 TCCAGACTTCTTTTGCAAATCAGG 59.721 41.667 13.65 12.97 0.00 3.86
488 560 6.294731 GCAAATCAGGAGGTCAAAGTAATGTT 60.295 38.462 0.00 0.00 0.00 2.71
489 561 7.308435 CAAATCAGGAGGTCAAAGTAATGTTC 58.692 38.462 0.00 0.00 0.00 3.18
519 591 5.564848 CGTCTCAAGTTCTTGGTCACATAGA 60.565 44.000 11.82 3.94 0.00 1.98
520 592 6.223852 GTCTCAAGTTCTTGGTCACATAGAA 58.776 40.000 11.82 0.00 0.00 2.10
525 597 4.757149 AGTTCTTGGTCACATAGAAAGCAC 59.243 41.667 0.00 0.00 30.88 4.40
526 598 4.350368 TCTTGGTCACATAGAAAGCACA 57.650 40.909 0.00 0.00 0.00 4.57
548 620 2.390599 CGTTGTGTGGCCATCCTCG 61.391 63.158 9.72 7.32 0.00 4.63
551 623 3.127533 GTGTGGCCATCCTCGTGC 61.128 66.667 9.72 0.00 0.00 5.34
554 626 2.046023 TGGCCATCCTCGTGCTTG 60.046 61.111 0.00 0.00 0.00 4.01
555 627 3.512516 GGCCATCCTCGTGCTTGC 61.513 66.667 0.00 0.00 0.00 4.01
556 628 2.747460 GCCATCCTCGTGCTTGCA 60.747 61.111 0.00 0.00 0.00 4.08
558 630 1.503542 CCATCCTCGTGCTTGCAAC 59.496 57.895 0.00 0.00 0.00 4.17
559 631 1.236616 CCATCCTCGTGCTTGCAACA 61.237 55.000 0.00 0.00 0.00 3.33
560 632 0.167470 CATCCTCGTGCTTGCAACAG 59.833 55.000 0.00 0.00 0.00 3.16
561 633 0.035317 ATCCTCGTGCTTGCAACAGA 59.965 50.000 0.00 0.00 0.00 3.41
563 635 0.445436 CCTCGTGCTTGCAACAGATC 59.555 55.000 0.00 0.00 0.00 2.75
564 636 0.445436 CTCGTGCTTGCAACAGATCC 59.555 55.000 0.00 0.00 0.00 3.36
566 638 1.154150 GTGCTTGCAACAGATCCGC 60.154 57.895 0.00 0.00 0.00 5.54
567 639 2.334946 TGCTTGCAACAGATCCGCC 61.335 57.895 0.00 0.00 0.00 6.13
568 640 2.787249 CTTGCAACAGATCCGCCG 59.213 61.111 0.00 0.00 0.00 6.46
569 641 2.031919 TTGCAACAGATCCGCCGT 59.968 55.556 0.00 0.00 0.00 5.68
570 642 1.970917 CTTGCAACAGATCCGCCGTC 61.971 60.000 0.00 0.00 0.00 4.79
571 643 3.195698 GCAACAGATCCGCCGTCC 61.196 66.667 0.00 0.00 0.00 4.79
572 644 2.264480 CAACAGATCCGCCGTCCA 59.736 61.111 0.00 0.00 0.00 4.02
573 645 1.375396 CAACAGATCCGCCGTCCAA 60.375 57.895 0.00 0.00 0.00 3.53
574 646 0.744414 CAACAGATCCGCCGTCCAAT 60.744 55.000 0.00 0.00 0.00 3.16
575 647 0.035439 AACAGATCCGCCGTCCAATT 60.035 50.000 0.00 0.00 0.00 2.32
576 648 0.035439 ACAGATCCGCCGTCCAATTT 60.035 50.000 0.00 0.00 0.00 1.82
577 649 0.657840 CAGATCCGCCGTCCAATTTC 59.342 55.000 0.00 0.00 0.00 2.17
612 684 8.571336 AGCAACAGCCATACATAGAATTTAATC 58.429 33.333 0.00 0.00 0.00 1.75
627 699 2.489528 TAATCTTCCCCTCCATCCGT 57.510 50.000 0.00 0.00 0.00 4.69
646 718 1.697754 CCCCTCCATACCTTGGCCT 60.698 63.158 3.32 0.00 46.01 5.19
647 719 1.533711 CCCTCCATACCTTGGCCTG 59.466 63.158 3.32 0.00 46.01 4.85
723 795 7.339482 AGACTAACTAATTCCATTTCCTCACC 58.661 38.462 0.00 0.00 0.00 4.02
736 808 2.600790 TCCTCACCTTCGTGGAAGTAA 58.399 47.619 4.82 0.00 40.65 2.24
775 856 0.030235 GGACGACCTTTTGTTGCCAC 59.970 55.000 0.00 0.00 0.00 5.01
872 3007 2.666862 AAACGAATGTCCGCGCCA 60.667 55.556 0.00 0.00 0.00 5.69
913 3059 3.052082 CAGCCTTCAGCCACACCG 61.052 66.667 0.00 0.00 45.47 4.94
914 3060 3.241530 AGCCTTCAGCCACACCGA 61.242 61.111 0.00 0.00 45.47 4.69
915 3061 2.743928 GCCTTCAGCCACACCGAG 60.744 66.667 0.00 0.00 34.35 4.63
916 3062 3.059982 CCTTCAGCCACACCGAGA 58.940 61.111 0.00 0.00 0.00 4.04
917 3063 1.371183 CCTTCAGCCACACCGAGAA 59.629 57.895 0.00 0.00 0.00 2.87
918 3064 0.671781 CCTTCAGCCACACCGAGAAG 60.672 60.000 0.00 0.00 36.38 2.85
981 3186 7.907214 GGATTCGCCTATATAACACTTCAAT 57.093 36.000 0.00 0.00 0.00 2.57
1008 3215 4.449075 CGTTGCCACACGAATGGAACAA 62.449 50.000 12.96 6.35 42.64 2.83
1066 3276 0.459899 TCCATCTTCCACCGTGATCG 59.540 55.000 0.00 0.00 0.00 3.69
1076 3286 1.037579 ACCGTGATCGAGATGCCTCA 61.038 55.000 0.00 0.00 39.39 3.86
1087 3297 1.134580 AGATGCCTCAATCTCCACACG 60.135 52.381 0.00 0.00 30.91 4.49
1094 3304 2.325082 AATCTCCACACGCCAACGC 61.325 57.895 0.00 0.00 45.53 4.84
1162 3387 3.142162 CCATGGCATCCGCAGCAA 61.142 61.111 0.00 0.00 41.24 3.91
1236 3461 2.184579 GCACAGCTCCTACCGACC 59.815 66.667 0.00 0.00 0.00 4.79
1284 3509 0.336048 CCCCATCCTTCACCAACCAT 59.664 55.000 0.00 0.00 0.00 3.55
1307 3532 0.035458 AAGTGCTTCTCCTCCAACCG 59.965 55.000 0.00 0.00 0.00 4.44
1524 3749 2.525248 GCTCGATTTCATCCGCGCA 61.525 57.895 8.75 0.00 36.63 6.09
1746 8181 6.145535 CCAAAAGCTCACTTGATGTTTAGAC 58.854 40.000 5.05 0.00 35.85 2.59
2030 8516 3.444916 AGAGAAACGGCATGTATGTACG 58.555 45.455 0.00 8.69 36.73 3.67
2091 8577 7.504238 TCCTGAAAGTCTATCTAAGCTCCTAAG 59.496 40.741 0.00 0.00 0.00 2.18
2105 8592 3.100671 CTCCTAAGTACTGAAGCCTGGT 58.899 50.000 0.00 0.00 0.00 4.00
2309 8807 3.323751 TCCTTACAAGGGAAACTACGC 57.676 47.619 8.14 0.00 46.47 4.42
2323 8821 1.203994 ACTACGCCGAGCACAATAGTT 59.796 47.619 0.00 0.00 0.00 2.24
2454 8952 6.670695 AAAAATACTCTTGCTCCACCAATT 57.329 33.333 0.00 0.00 0.00 2.32
2458 8956 3.837355 ACTCTTGCTCCACCAATTTTCT 58.163 40.909 0.00 0.00 0.00 2.52
2472 8976 5.903010 ACCAATTTTCTAAAGGGGTGAAGTT 59.097 36.000 0.00 0.00 0.00 2.66
2475 8984 7.014808 CCAATTTTCTAAAGGGGTGAAGTTGTA 59.985 37.037 0.00 0.00 0.00 2.41
2476 8985 8.585018 CAATTTTCTAAAGGGGTGAAGTTGTAT 58.415 33.333 0.00 0.00 0.00 2.29
2477 8986 7.519032 TTTTCTAAAGGGGTGAAGTTGTATG 57.481 36.000 0.00 0.00 0.00 2.39
2478 8987 5.836024 TCTAAAGGGGTGAAGTTGTATGT 57.164 39.130 0.00 0.00 0.00 2.29
2479 8988 5.801380 TCTAAAGGGGTGAAGTTGTATGTC 58.199 41.667 0.00 0.00 0.00 3.06
2480 8989 4.447138 AAAGGGGTGAAGTTGTATGTCA 57.553 40.909 0.00 0.00 0.00 3.58
2488 8997 5.168569 GTGAAGTTGTATGTCATTCCTCGA 58.831 41.667 0.00 0.00 0.00 4.04
2489 8998 5.062308 GTGAAGTTGTATGTCATTCCTCGAC 59.938 44.000 0.00 0.00 0.00 4.20
2491 9000 3.192844 AGTTGTATGTCATTCCTCGACGT 59.807 43.478 0.00 0.00 36.11 4.34
2492 9001 3.145212 TGTATGTCATTCCTCGACGTG 57.855 47.619 0.00 0.00 36.11 4.49
2499 9008 1.391485 CATTCCTCGACGTGCAGAAAG 59.609 52.381 0.00 0.00 0.00 2.62
2506 9015 0.235926 GACGTGCAGAAAGCCAAGTC 59.764 55.000 0.00 0.00 44.83 3.01
2517 9026 2.789409 AGCCAAGTCCATACAACTCC 57.211 50.000 0.00 0.00 0.00 3.85
2519 9028 2.644798 AGCCAAGTCCATACAACTCCTT 59.355 45.455 0.00 0.00 0.00 3.36
2521 9030 4.288626 AGCCAAGTCCATACAACTCCTTAA 59.711 41.667 0.00 0.00 0.00 1.85
2529 9038 6.884836 GTCCATACAACTCCTTAAATTCCACT 59.115 38.462 0.00 0.00 0.00 4.00
2550 9059 0.454196 GTGAACAGGGTTTGCAACGT 59.546 50.000 0.00 0.00 0.00 3.99
2621 9130 1.611491 GGATTGTTTGGCACTCCGAAA 59.389 47.619 0.00 0.00 37.22 3.46
2649 9164 8.082852 GGATATCGAGCTTCAAGAAGTACATAA 58.917 37.037 11.14 0.00 40.45 1.90
2674 9189 1.604278 GGTCGCTTTTGTTTCTGCTCT 59.396 47.619 0.00 0.00 0.00 4.09
2686 9201 1.351076 TCTGCTCTGTTGGTCCATGA 58.649 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.263462 ACCCTTCACACTATCTTCAATGCA 60.263 41.667 0.00 0.00 0.00 3.96
78 79 6.155221 AGCAGAACTCCTACTATTCATGTCAA 59.845 38.462 0.00 0.00 0.00 3.18
79 80 5.658634 AGCAGAACTCCTACTATTCATGTCA 59.341 40.000 0.00 0.00 0.00 3.58
94 95 4.863491 TCTTCAATGCAAAAGCAGAACTC 58.137 39.130 0.00 0.00 0.00 3.01
97 98 5.518848 TCTTCTTCAATGCAAAAGCAGAA 57.481 34.783 0.00 0.00 0.00 3.02
120 121 6.238759 GGCTGAGTGTCTTGTAAAACTTCAAT 60.239 38.462 0.00 0.00 0.00 2.57
173 174 3.876914 TGTTTTGCTGTACTTGTCCTCTG 59.123 43.478 0.00 0.00 0.00 3.35
262 318 5.009010 TGGTTTTTGAGCAGAAAGAGATGAC 59.991 40.000 0.00 0.00 0.00 3.06
282 338 7.610580 TTGGAAGGAAAGAAATTACATGGTT 57.389 32.000 0.00 0.00 0.00 3.67
290 346 7.761249 CGCAGAATATTTGGAAGGAAAGAAATT 59.239 33.333 0.00 0.00 0.00 1.82
347 403 3.052082 CTGTGCTCGGCCAAGGTG 61.052 66.667 2.24 0.00 0.00 4.00
364 436 2.048127 GTGACTGGTGGTCTCGGC 60.048 66.667 0.00 0.00 44.74 5.54
365 437 2.657237 GGTGACTGGTGGTCTCGG 59.343 66.667 0.00 0.00 44.74 4.63
381 453 2.933495 TACTCGACAACTTCCATCGG 57.067 50.000 0.00 0.00 36.51 4.18
406 478 4.828296 GATGGGGGCTGTGGGCTG 62.828 72.222 0.00 0.00 41.46 4.85
409 481 4.133373 CAGGATGGGGGCTGTGGG 62.133 72.222 0.00 0.00 0.00 4.61
424 496 3.066342 CAGTTCCATCAAGCTAATGGCAG 59.934 47.826 18.91 8.12 42.89 4.85
428 500 4.261489 GGATGCAGTTCCATCAAGCTAATG 60.261 45.833 1.24 0.00 42.63 1.90
434 506 2.681848 GTCTGGATGCAGTTCCATCAAG 59.318 50.000 14.43 0.00 44.66 3.02
469 541 4.627467 CGAGAACATTACTTTGACCTCCTG 59.373 45.833 0.00 0.00 0.00 3.86
472 544 3.371285 GCCGAGAACATTACTTTGACCTC 59.629 47.826 0.00 0.00 0.00 3.85
488 560 0.894184 AGAACTTGAGACGGCCGAGA 60.894 55.000 35.90 9.29 0.00 4.04
489 561 0.038159 AAGAACTTGAGACGGCCGAG 60.038 55.000 35.90 21.20 0.00 4.63
525 597 1.577328 GATGGCCACACAACGACCTG 61.577 60.000 8.16 0.00 0.00 4.00
526 598 1.302511 GATGGCCACACAACGACCT 60.303 57.895 8.16 0.00 0.00 3.85
548 620 1.154150 GCGGATCTGTTGCAAGCAC 60.154 57.895 0.00 0.00 0.00 4.40
551 623 1.970917 GACGGCGGATCTGTTGCAAG 61.971 60.000 13.24 0.00 33.57 4.01
554 626 3.195698 GGACGGCGGATCTGTTGC 61.196 66.667 13.24 0.00 33.57 4.17
555 627 0.744414 ATTGGACGGCGGATCTGTTG 60.744 55.000 13.24 0.00 33.57 3.33
556 628 0.035439 AATTGGACGGCGGATCTGTT 60.035 50.000 13.24 0.00 33.57 3.16
558 630 0.657840 GAAATTGGACGGCGGATCTG 59.342 55.000 13.24 0.00 0.00 2.90
559 631 0.541863 AGAAATTGGACGGCGGATCT 59.458 50.000 13.24 0.67 0.00 2.75
560 632 0.657840 CAGAAATTGGACGGCGGATC 59.342 55.000 13.24 0.00 0.00 3.36
561 633 0.035439 ACAGAAATTGGACGGCGGAT 60.035 50.000 13.24 0.00 0.00 4.18
563 635 0.168128 GAACAGAAATTGGACGGCGG 59.832 55.000 13.24 0.00 0.00 6.13
564 636 1.135972 CAGAACAGAAATTGGACGGCG 60.136 52.381 4.80 4.80 0.00 6.46
566 638 2.744202 CTCCAGAACAGAAATTGGACGG 59.256 50.000 0.00 0.00 34.90 4.79
567 639 2.160417 GCTCCAGAACAGAAATTGGACG 59.840 50.000 0.00 0.00 34.90 4.79
568 640 3.149196 TGCTCCAGAACAGAAATTGGAC 58.851 45.455 0.00 0.00 34.90 4.02
569 641 3.507162 TGCTCCAGAACAGAAATTGGA 57.493 42.857 0.00 0.00 37.38 3.53
570 642 3.318839 TGTTGCTCCAGAACAGAAATTGG 59.681 43.478 0.00 0.00 0.00 3.16
571 643 4.572985 TGTTGCTCCAGAACAGAAATTG 57.427 40.909 0.00 0.00 0.00 2.32
612 684 2.444256 GGGACGGATGGAGGGGAAG 61.444 68.421 0.00 0.00 0.00 3.46
646 718 1.971167 GAATTGACACGCCTGGCCA 60.971 57.895 14.12 4.71 0.00 5.36
647 719 0.392461 TAGAATTGACACGCCTGGCC 60.392 55.000 14.12 0.00 0.00 5.36
655 727 5.163513 CCAATTTGTGGCTAGAATTGACAC 58.836 41.667 15.95 0.00 41.72 3.67
723 795 2.132762 ACGCAGTTTACTTCCACGAAG 58.867 47.619 0.00 0.00 37.78 3.79
861 2996 0.889186 ACTTTTCTTGGCGCGGACAT 60.889 50.000 8.83 0.00 0.00 3.06
864 2999 0.816018 TCAACTTTTCTTGGCGCGGA 60.816 50.000 8.83 0.00 0.00 5.54
867 3002 2.223479 TGACTTCAACTTTTCTTGGCGC 60.223 45.455 0.00 0.00 0.00 6.53
913 3059 4.467735 GCCGTGTTGATTTTTCTCTTCTC 58.532 43.478 0.00 0.00 0.00 2.87
914 3060 3.253432 GGCCGTGTTGATTTTTCTCTTCT 59.747 43.478 0.00 0.00 0.00 2.85
915 3061 3.004315 TGGCCGTGTTGATTTTTCTCTTC 59.996 43.478 0.00 0.00 0.00 2.87
916 3062 2.955660 TGGCCGTGTTGATTTTTCTCTT 59.044 40.909 0.00 0.00 0.00 2.85
917 3063 2.582052 TGGCCGTGTTGATTTTTCTCT 58.418 42.857 0.00 0.00 0.00 3.10
918 3064 3.308530 CTTGGCCGTGTTGATTTTTCTC 58.691 45.455 0.00 0.00 0.00 2.87
976 3181 2.025719 TGGCAACGCAACGATTGAA 58.974 47.368 0.00 0.00 42.51 2.69
977 3182 3.737824 TGGCAACGCAACGATTGA 58.262 50.000 0.00 0.00 42.51 2.57
1066 3276 2.559440 GTGTGGAGATTGAGGCATCTC 58.441 52.381 0.00 1.38 41.81 2.75
1076 3286 2.325082 GCGTTGGCGTGTGGAGATT 61.325 57.895 0.00 0.00 40.81 2.40
1162 3387 0.977395 GTGGGTTCTAGTCCTGCAGT 59.023 55.000 13.81 0.00 0.00 4.40
1167 3392 2.348888 CGCCGTGGGTTCTAGTCCT 61.349 63.158 6.66 0.00 0.00 3.85
1172 3397 3.751246 CCGTCGCCGTGGGTTCTA 61.751 66.667 0.00 0.00 0.00 2.10
1284 3509 1.376466 GGAGGAGAAGCACTTGCCA 59.624 57.895 0.00 0.00 43.38 4.92
1329 3554 1.947456 CACGAGATGGTGAGGACGATA 59.053 52.381 0.00 0.00 40.38 2.92
1512 3737 0.320334 TGAAGACTGCGCGGATGAAA 60.320 50.000 25.98 2.09 0.00 2.69
1524 3749 2.526873 ACCAGGGCCGTGAAGACT 60.527 61.111 26.78 0.00 0.00 3.24
1842 8282 4.423732 ACCGCGATTACACTACGTTTTAT 58.576 39.130 8.23 0.00 0.00 1.40
1848 8288 3.532892 AGATACCGCGATTACACTACG 57.467 47.619 8.23 0.00 0.00 3.51
1968 8443 1.101049 CAACTGCACCGAACAAGGGT 61.101 55.000 0.00 0.00 38.65 4.34
2016 8498 2.927477 ACAAGAACGTACATACATGCCG 59.073 45.455 0.00 1.64 0.00 5.69
2078 8564 4.645588 GGCTTCAGTACTTAGGAGCTTAGA 59.354 45.833 12.07 0.00 0.00 2.10
2083 8569 2.159028 CCAGGCTTCAGTACTTAGGAGC 60.159 54.545 5.13 5.13 0.00 4.70
2091 8577 4.575885 TCAAATACACCAGGCTTCAGTAC 58.424 43.478 0.00 0.00 0.00 2.73
2262 8752 3.627732 TGACGAAAGACTCTCACACTC 57.372 47.619 0.00 0.00 0.00 3.51
2309 8807 2.550978 CACCCTAACTATTGTGCTCGG 58.449 52.381 0.00 0.00 0.00 4.63
2323 8821 4.320870 GAATCTTCAACGAAACCACCCTA 58.679 43.478 0.00 0.00 0.00 3.53
2454 8952 6.607019 ACATACAACTTCACCCCTTTAGAAA 58.393 36.000 0.00 0.00 0.00 2.52
2458 8956 5.570205 TGACATACAACTTCACCCCTTTA 57.430 39.130 0.00 0.00 0.00 1.85
2472 8976 2.734175 GCACGTCGAGGAATGACATACA 60.734 50.000 12.85 0.00 36.11 2.29
2475 8984 0.246360 TGCACGTCGAGGAATGACAT 59.754 50.000 12.85 0.00 36.11 3.06
2476 8985 0.388520 CTGCACGTCGAGGAATGACA 60.389 55.000 12.85 3.07 36.11 3.58
2477 8986 0.109272 TCTGCACGTCGAGGAATGAC 60.109 55.000 12.85 0.00 0.00 3.06
2478 8987 0.601057 TTCTGCACGTCGAGGAATGA 59.399 50.000 12.85 1.91 0.00 2.57
2479 8988 1.391485 CTTTCTGCACGTCGAGGAATG 59.609 52.381 12.85 1.57 0.00 2.67
2480 8989 1.714794 CTTTCTGCACGTCGAGGAAT 58.285 50.000 12.85 0.00 0.00 3.01
2488 8997 1.166531 GGACTTGGCTTTCTGCACGT 61.167 55.000 0.00 0.00 45.15 4.49
2489 8998 1.165907 TGGACTTGGCTTTCTGCACG 61.166 55.000 0.00 0.00 45.15 5.34
2491 9000 2.224744 TGTATGGACTTGGCTTTCTGCA 60.225 45.455 0.00 0.00 45.15 4.41
2492 9001 2.436417 TGTATGGACTTGGCTTTCTGC 58.564 47.619 0.00 0.00 41.94 4.26
2499 9008 2.789409 AGGAGTTGTATGGACTTGGC 57.211 50.000 0.00 0.00 0.00 4.52
2506 9015 8.047310 ACTAGTGGAATTTAAGGAGTTGTATGG 58.953 37.037 0.00 0.00 0.00 2.74
2517 9026 6.238648 ACCCTGTTCACTAGTGGAATTTAAG 58.761 40.000 22.48 10.35 0.00 1.85
2519 9028 5.836024 ACCCTGTTCACTAGTGGAATTTA 57.164 39.130 22.48 0.00 0.00 1.40
2521 9030 4.724279 AACCCTGTTCACTAGTGGAATT 57.276 40.909 22.48 5.51 0.00 2.17
2529 9038 1.944024 CGTTGCAAACCCTGTTCACTA 59.056 47.619 0.00 0.00 46.28 2.74
2550 9059 2.642311 TCCTGGACATCAGCTAAACCAA 59.358 45.455 0.00 0.00 42.05 3.67
2621 9130 5.606348 ACTTCTTGAAGCTCGATATCCTT 57.394 39.130 9.98 0.00 0.00 3.36
2630 9139 7.173390 ACCTTTGTTATGTACTTCTTGAAGCTC 59.827 37.037 9.98 4.81 0.00 4.09
2649 9164 3.769536 CAGAAACAAAAGCGACCTTTGT 58.230 40.909 4.65 4.65 40.30 2.83
2669 9184 1.352017 ACATCATGGACCAACAGAGCA 59.648 47.619 0.00 0.00 0.00 4.26
2674 9189 1.807139 CGACACATCATGGACCAACA 58.193 50.000 0.00 0.00 0.00 3.33
2686 9201 1.072505 AACCCCGAAAGCGACACAT 59.927 52.632 0.00 0.00 40.82 3.21


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

AutoCloner maintained by Alex Coulton.