Multiple sequence alignment - TraesCS7A01G025900

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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 TraesCS7A01G025900 chr7A 100.000 3532 0 0 1 3532 10256179 10252648 0.000000e+00 6523
1 TraesCS7A01G025900 chr7A 90.574 3119 228 44 77 3165 10354044 10350962 0.000000e+00 4071
2 TraesCS7A01G025900 chr7A 91.449 1567 102 17 844 2402 10608851 10610393 0.000000e+00 2122
3 TraesCS7A01G025900 chr7A 91.712 1110 85 5 1765 2868 10279844 10278736 0.000000e+00 1533
4 TraesCS7A01G025900 chr7A 87.587 1289 132 16 2026 3301 10208388 10207115 0.000000e+00 1469
5 TraesCS7A01G025900 chr7A 91.299 770 49 11 92 853 10607923 10608682 0.000000e+00 1035
6 TraesCS7A01G025900 chr7A 92.635 706 46 5 1063 1763 10280632 10279928 0.000000e+00 1011
7 TraesCS7A01G025900 chr7A 89.134 543 38 10 322 853 641529942 641529410 0.000000e+00 656
8 TraesCS7A01G025900 chr7A 88.950 543 39 10 322 853 646921436 646920904 0.000000e+00 651
9 TraesCS7A01G025900 chr7A 92.035 226 15 1 3310 3532 10278013 10277788 7.360000e-82 315
10 TraesCS7A01G025900 chr7A 85.590 229 28 4 3074 3299 10278393 10278167 5.890000e-58 235
11 TraesCS7A01G025900 chr7A 90.217 184 9 6 3311 3487 10206968 10206787 7.630000e-57 231
12 TraesCS7A01G025900 chr7A 86.636 217 12 9 200 415 10286780 10286580 1.280000e-54 224
13 TraesCS7A01G025900 chr7D 90.281 2706 213 28 611 3299 11072213 11069541 0.000000e+00 3494
14 TraesCS7A01G025900 chr4A 92.582 2049 141 9 569 2608 726978473 726980519 0.000000e+00 2931
15 TraesCS7A01G025900 chr4A 92.484 1610 105 11 1063 2658 727054991 727056598 0.000000e+00 2289
16 TraesCS7A01G025900 chr4A 93.342 736 41 3 2801 3529 727056640 727057374 0.000000e+00 1081
17 TraesCS7A01G025900 chr4A 87.544 851 50 26 36 853 726977622 726978449 0.000000e+00 933
18 TraesCS7A01G025900 chr4A 89.948 388 32 6 2919 3301 726980517 726980902 8.810000e-136 494
19 TraesCS7A01G025900 chr4A 81.538 390 35 23 40 412 727048492 727048861 1.600000e-73 287
20 TraesCS7A01G025900 chr6A 88.645 546 41 10 319 853 409920133 409920668 0.000000e+00 645
21 TraesCS7A01G025900 chr5A 88.582 543 41 10 322 853 579649715 579649183 1.070000e-179 640
22 TraesCS7A01G025900 chr3A 88.214 543 43 10 322 853 19077743 19077211 2.310000e-176 628


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 TraesCS7A01G025900 chr7A 10252648 10256179 3531 True 6523.000000 6523 100.000000 1 3532 1 chr7A.!!$R1 3531
1 TraesCS7A01G025900 chr7A 10350962 10354044 3082 True 4071.000000 4071 90.574000 77 3165 1 chr7A.!!$R3 3088
2 TraesCS7A01G025900 chr7A 10607923 10610393 2470 False 1578.500000 2122 91.374000 92 2402 2 chr7A.!!$F1 2310
3 TraesCS7A01G025900 chr7A 10206787 10208388 1601 True 850.000000 1469 88.902000 2026 3487 2 chr7A.!!$R6 1461
4 TraesCS7A01G025900 chr7A 10277788 10280632 2844 True 773.500000 1533 90.493000 1063 3532 4 chr7A.!!$R7 2469
5 TraesCS7A01G025900 chr7A 641529410 641529942 532 True 656.000000 656 89.134000 322 853 1 chr7A.!!$R4 531
6 TraesCS7A01G025900 chr7A 646920904 646921436 532 True 651.000000 651 88.950000 322 853 1 chr7A.!!$R5 531
7 TraesCS7A01G025900 chr7D 11069541 11072213 2672 True 3494.000000 3494 90.281000 611 3299 1 chr7D.!!$R1 2688
8 TraesCS7A01G025900 chr4A 727054991 727057374 2383 False 1685.000000 2289 92.913000 1063 3529 2 chr4A.!!$F3 2466
9 TraesCS7A01G025900 chr4A 726977622 726980902 3280 False 1452.666667 2931 90.024667 36 3301 3 chr4A.!!$F2 3265
10 TraesCS7A01G025900 chr6A 409920133 409920668 535 False 645.000000 645 88.645000 319 853 1 chr6A.!!$F1 534
11 TraesCS7A01G025900 chr5A 579649183 579649715 532 True 640.000000 640 88.582000 322 853 1 chr5A.!!$R1 531
12 TraesCS7A01G025900 chr3A 19077211 19077743 532 True 628.000000 628 88.214000 322 853 1 chr3A.!!$R1 531

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
36 37 0.107831 TAGCACCACACCAACCAGAC 59.892 55.0 0.0 0.0 0.00 3.51 F
1457 2005 0.323302 TCACCGCTGGTATGCTCAAA 59.677 50.0 0.0 0.0 32.11 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2450 1.018226 AGATGCACGCTCAGCTTCAC 61.018 55.0 0.00 0.0 38.28 3.18 R
3029 3771 0.754587 CTGTACCGGTAGACCCCTCC 60.755 65.0 16.41 0.6 0.00 4.30 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
19 20 2.021355 ACCCTGTCGACTCGTACTAG 57.979 55.000 17.92 3.40 0.00 2.57
20 21 0.656785 CCCTGTCGACTCGTACTAGC 59.343 60.000 17.92 0.00 0.00 3.42
21 22 1.366679 CCTGTCGACTCGTACTAGCA 58.633 55.000 17.92 0.00 0.00 3.49
22 23 1.062294 CCTGTCGACTCGTACTAGCAC 59.938 57.143 17.92 0.00 0.00 4.40
23 24 1.062294 CTGTCGACTCGTACTAGCACC 59.938 57.143 17.92 0.00 0.00 5.01
24 25 1.081892 GTCGACTCGTACTAGCACCA 58.918 55.000 8.70 0.00 0.00 4.17
25 26 1.081892 TCGACTCGTACTAGCACCAC 58.918 55.000 0.00 0.00 0.00 4.16
26 27 0.800631 CGACTCGTACTAGCACCACA 59.199 55.000 0.00 0.00 0.00 4.17
27 28 1.465354 CGACTCGTACTAGCACCACAC 60.465 57.143 0.00 0.00 0.00 3.82
28 29 0.886563 ACTCGTACTAGCACCACACC 59.113 55.000 0.00 0.00 0.00 4.16
29 30 0.885879 CTCGTACTAGCACCACACCA 59.114 55.000 0.00 0.00 0.00 4.17
30 31 1.271379 CTCGTACTAGCACCACACCAA 59.729 52.381 0.00 0.00 0.00 3.67
31 32 1.000060 TCGTACTAGCACCACACCAAC 60.000 52.381 0.00 0.00 0.00 3.77
32 33 1.804601 GTACTAGCACCACACCAACC 58.195 55.000 0.00 0.00 0.00 3.77
33 34 1.071071 GTACTAGCACCACACCAACCA 59.929 52.381 0.00 0.00 0.00 3.67
34 35 0.108585 ACTAGCACCACACCAACCAG 59.891 55.000 0.00 0.00 0.00 4.00
35 36 0.396435 CTAGCACCACACCAACCAGA 59.604 55.000 0.00 0.00 0.00 3.86
36 37 0.107831 TAGCACCACACCAACCAGAC 59.892 55.000 0.00 0.00 0.00 3.51
37 38 2.193536 GCACCACACCAACCAGACC 61.194 63.158 0.00 0.00 0.00 3.85
38 39 1.225983 CACCACACCAACCAGACCA 59.774 57.895 0.00 0.00 0.00 4.02
39 40 0.395036 CACCACACCAACCAGACCAA 60.395 55.000 0.00 0.00 0.00 3.67
53 54 4.366684 CCAACCAGACCCAGGCCC 62.367 72.222 0.00 0.00 0.00 5.80
78 82 4.475135 GACCCTCTTCCCTGCCGC 62.475 72.222 0.00 0.00 0.00 6.53
94 98 3.986006 GCCGTCACCCGTCAGTGA 61.986 66.667 0.00 0.00 44.38 3.41
98 102 2.520020 TCACCCGTCAGTGACCGT 60.520 61.111 17.57 10.87 41.78 4.83
274 302 3.003173 CCAAGACCTCCTCCGCCA 61.003 66.667 0.00 0.00 0.00 5.69
312 340 2.415010 CGCCGAGGACCTCATCAG 59.585 66.667 21.49 7.75 0.00 2.90
359 387 7.222872 GTCATCCTCTGGTAATCAATCATTCT 58.777 38.462 0.00 0.00 0.00 2.40
417 453 4.695455 CCTGTACCTGAAAATGTACCACTG 59.305 45.833 0.00 0.00 37.19 3.66
418 454 4.647611 TGTACCTGAAAATGTACCACTGG 58.352 43.478 0.00 0.00 37.19 4.00
419 455 3.876309 ACCTGAAAATGTACCACTGGT 57.124 42.857 5.88 5.88 40.16 4.00
420 456 4.986054 ACCTGAAAATGTACCACTGGTA 57.014 40.909 3.57 3.57 37.09 3.25
439 477 3.181479 GGTACACGATGGAGCTCATTGTA 60.181 47.826 17.19 11.28 46.05 2.41
440 478 3.827008 ACACGATGGAGCTCATTGTAT 57.173 42.857 17.19 3.96 46.05 2.29
441 479 3.722147 ACACGATGGAGCTCATTGTATC 58.278 45.455 17.19 9.55 46.05 2.24
442 480 3.132824 ACACGATGGAGCTCATTGTATCA 59.867 43.478 17.19 2.25 46.05 2.15
572 612 3.438434 CCTGTTTGGTTTGGTTTGGTTTG 59.562 43.478 0.00 0.00 0.00 2.93
573 613 3.412386 TGTTTGGTTTGGTTTGGTTTGG 58.588 40.909 0.00 0.00 0.00 3.28
574 614 3.181443 TGTTTGGTTTGGTTTGGTTTGGT 60.181 39.130 0.00 0.00 0.00 3.67
575 615 3.790089 TTGGTTTGGTTTGGTTTGGTT 57.210 38.095 0.00 0.00 0.00 3.67
576 616 3.790089 TGGTTTGGTTTGGTTTGGTTT 57.210 38.095 0.00 0.00 0.00 3.27
632 677 0.757935 ATGCTTGGGTGGATGATGGC 60.758 55.000 0.00 0.00 0.00 4.40
734 779 6.470278 TCATGTTGCTGCTATATATGCTCTT 58.530 36.000 0.00 0.00 0.00 2.85
741 786 5.642919 GCTGCTATATATGCTCTTTCTGCTT 59.357 40.000 0.00 0.00 0.00 3.91
748 793 1.000736 GCTCTTTCTGCTTTGTGCGC 61.001 55.000 0.00 0.00 46.63 6.09
769 1125 4.384247 CGCTTTCTCCGATATCATTCTCAC 59.616 45.833 3.12 0.00 0.00 3.51
840 1202 6.480763 TCACTCTCATCTATGGACCTCTATC 58.519 44.000 0.00 0.00 0.00 2.08
883 1423 4.600012 TGCGAGATTTAAGCTTAGCAAC 57.400 40.909 12.01 4.32 0.00 4.17
928 1468 7.382110 CCTTACTTTCTGATTCTGTTCTCTGA 58.618 38.462 0.00 0.00 0.00 3.27
956 1497 2.126965 CGCTGCTGTTCTTGCTGC 60.127 61.111 0.00 7.37 46.83 5.25
972 1513 2.290832 TGCTGCAGAATATTCCACCACA 60.291 45.455 20.43 0.00 0.00 4.17
993 1534 1.406069 GCTGCTTCGATTTCCTCTCCA 60.406 52.381 0.00 0.00 0.00 3.86
1140 1682 1.451387 CGGGCGCCATTTCTACCTT 60.451 57.895 30.85 0.00 0.00 3.50
1218 1760 4.335416 CATTTTTGGGTTCCTCTCAGCTA 58.665 43.478 0.00 0.00 0.00 3.32
1250 1797 2.616256 CCAGTTAAGCAGCCACAGATCA 60.616 50.000 0.00 0.00 0.00 2.92
1262 1809 2.034179 CCACAGATCATGCGCATTGAAT 59.966 45.455 22.81 14.59 0.00 2.57
1292 1840 3.576078 ATCTTGTGAACCTGTGGTTGA 57.424 42.857 6.72 0.00 46.95 3.18
1457 2005 0.323302 TCACCGCTGGTATGCTCAAA 59.677 50.000 0.00 0.00 32.11 2.69
1512 2061 6.658816 TCTGTGATATACTTTGTGGTTGCATT 59.341 34.615 0.00 0.00 0.00 3.56
1710 2266 9.420551 GTTACCCTGCTATAGTAATATGAACAC 57.579 37.037 0.84 0.00 0.00 3.32
1763 2402 6.707290 TCCTTGCTATGAGTACTTTTGCTAA 58.293 36.000 0.00 0.00 0.00 3.09
1811 2450 2.370281 ACACAGTACAGCGATCAAGG 57.630 50.000 0.00 0.00 0.00 3.61
1935 2574 7.617041 AAGTGTGGTCTTGAAGCTAAATATC 57.383 36.000 0.00 0.00 0.00 1.63
2004 2645 1.471676 CCCCTTATGTCTCGTGTGCTC 60.472 57.143 0.00 0.00 0.00 4.26
2082 2723 0.689623 CCTTCAGGACTTCTGTGGCT 59.310 55.000 0.00 0.00 43.76 4.75
2103 2744 4.571176 GCTCACATACCCTTAGCTGTTTAC 59.429 45.833 0.00 0.00 0.00 2.01
2167 2808 1.541147 CATCGTGCACCATTGGTTCTT 59.459 47.619 12.15 0.00 31.02 2.52
2174 2815 5.296748 GTGCACCATTGGTTCTTATTTGTT 58.703 37.500 5.34 0.00 31.02 2.83
2176 2817 4.690280 GCACCATTGGTTCTTATTTGTTGG 59.310 41.667 5.34 0.00 31.02 3.77
2177 2818 4.690280 CACCATTGGTTCTTATTTGTTGGC 59.310 41.667 5.34 0.00 31.02 4.52
2186 2827 6.262049 GGTTCTTATTTGTTGGCCATTTTGTT 59.738 34.615 6.09 0.00 0.00 2.83
2191 2832 8.738645 TTATTTGTTGGCCATTTTGTTTTACT 57.261 26.923 6.09 0.00 0.00 2.24
2201 2842 6.632434 GCCATTTTGTTTTACTTGATGTTTGC 59.368 34.615 0.00 0.00 0.00 3.68
2219 2861 6.580788 TGTTTGCATCTCAATTTTTCAGGAA 58.419 32.000 0.00 0.00 34.12 3.36
2225 2867 7.093640 TGCATCTCAATTTTTCAGGAAGCTTAT 60.094 33.333 0.00 0.00 0.00 1.73
2253 2895 1.065102 GTGTATCAGCATGCTTGGCAG 59.935 52.381 19.98 6.55 43.65 4.85
2286 2932 5.002464 AGAAAATTCAATTGATCCGCCTG 57.998 39.130 9.40 0.00 0.00 4.85
2298 2944 1.898574 CCGCCTGTTGGAAGTGCTT 60.899 57.895 0.00 0.00 34.57 3.91
2313 2959 9.461312 TTGGAAGTGCTTATTTAGTTGATGTAT 57.539 29.630 0.00 0.00 0.00 2.29
2382 3028 5.429109 TGAGGTAGCTCTTCTAAGGTCTCTA 59.571 44.000 21.80 0.00 0.00 2.43
2534 3193 7.512130 TGCAGGTTTCTGAGATATTATGACAT 58.488 34.615 0.00 0.00 43.49 3.06
2541 3200 9.993454 TTTCTGAGATATTATGACATCCTCAAG 57.007 33.333 0.00 0.00 30.60 3.02
2551 3210 1.895798 ACATCCTCAAGTCGCTTCAGA 59.104 47.619 0.00 0.00 0.00 3.27
2652 3311 5.439721 TCCTTCATATGTGGATTGGTCTTG 58.560 41.667 13.49 0.00 0.00 3.02
2713 3374 6.006449 ACTTCTATTTGCTGTGAAATGGACT 58.994 36.000 0.00 0.00 33.86 3.85
2715 3376 6.500684 TCTATTTGCTGTGAAATGGACTTC 57.499 37.500 0.00 0.00 30.39 3.01
2720 3381 5.186996 TGCTGTGAAATGGACTTCTTTTC 57.813 39.130 0.00 0.00 38.94 2.29
2754 3417 8.458573 AGTCCTTATCTGAGTATGTACTTCTG 57.541 38.462 0.00 0.00 36.50 3.02
2795 3458 9.627123 TCTATGTTCTTGTCAATTATTAAGGGG 57.373 33.333 0.00 0.00 0.00 4.79
2846 3509 3.933861 AACCTATTCCTAAGCAGTGGG 57.066 47.619 0.00 0.00 0.00 4.61
2868 3531 4.802039 GGAAATTACTCGCACGAACATCTA 59.198 41.667 0.00 0.00 0.00 1.98
2871 3534 7.328737 GGAAATTACTCGCACGAACATCTATAT 59.671 37.037 0.00 0.00 0.00 0.86
2876 3539 5.687730 ACTCGCACGAACATCTATATTTCTG 59.312 40.000 0.00 0.00 0.00 3.02
2877 3540 5.588240 TCGCACGAACATCTATATTTCTGT 58.412 37.500 0.00 0.00 0.00 3.41
2887 3550 7.385267 ACATCTATATTTCTGTCAGGATCAGC 58.615 38.462 0.00 0.00 33.48 4.26
2931 3595 0.970640 TTGCCATGAAATGCTGCAGT 59.029 45.000 16.64 1.48 44.97 4.40
3174 4026 5.919141 GCATCCATCTTTTATGTCTGCATTC 59.081 40.000 0.00 0.00 36.58 2.67
3177 4029 4.336433 CCATCTTTTATGTCTGCATTCGGT 59.664 41.667 0.00 0.00 36.58 4.69
3209 4075 1.276138 TGCATACTCTGGAGGTGTGTG 59.724 52.381 2.58 0.00 34.94 3.82
3273 4140 1.615392 CTGCTTCCACCCTTTCTTTGG 59.385 52.381 0.00 0.00 0.00 3.28
3396 4413 5.639931 TGTTGCACAAACGATATGCTACTTA 59.360 36.000 13.91 0.00 42.90 2.24
3398 4415 5.656480 TGCACAAACGATATGCTACTTAGA 58.344 37.500 0.00 0.00 40.13 2.10
3399 4416 6.280643 TGCACAAACGATATGCTACTTAGAT 58.719 36.000 0.00 0.00 40.13 1.98
3404 4424 9.250624 ACAAACGATATGCTACTTAGATCTTTC 57.749 33.333 0.00 0.00 0.00 2.62
3436 4458 5.276270 CAAGGAGCCATTCAATACAAATCG 58.724 41.667 0.00 0.00 0.00 3.34
3442 4464 5.415701 AGCCATTCAATACAAATCGACACTT 59.584 36.000 0.00 0.00 0.00 3.16
3489 4513 7.836842 TCAACTAAGTCACATACTATCTGCAA 58.163 34.615 0.00 0.00 37.50 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.081892 TGGTGCTAGTACGAGTCGAC 58.918 55.000 21.50 7.70 0.00 4.20
6 7 1.081892 GTGGTGCTAGTACGAGTCGA 58.918 55.000 21.50 0.00 0.00 4.20
7 8 0.800631 TGTGGTGCTAGTACGAGTCG 59.199 55.000 11.85 11.85 0.00 4.18
8 9 1.135460 GGTGTGGTGCTAGTACGAGTC 60.135 57.143 4.80 0.00 0.00 3.36
9 10 0.886563 GGTGTGGTGCTAGTACGAGT 59.113 55.000 4.80 0.00 0.00 4.18
10 11 0.885879 TGGTGTGGTGCTAGTACGAG 59.114 55.000 4.80 0.00 0.00 4.18
11 12 1.000060 GTTGGTGTGGTGCTAGTACGA 60.000 52.381 4.80 0.00 0.00 3.43
13 14 1.071071 TGGTTGGTGTGGTGCTAGTAC 59.929 52.381 1.77 1.77 0.00 2.73
14 15 1.346395 CTGGTTGGTGTGGTGCTAGTA 59.654 52.381 0.00 0.00 0.00 1.82
15 16 0.108585 CTGGTTGGTGTGGTGCTAGT 59.891 55.000 0.00 0.00 0.00 2.57
16 17 0.396435 TCTGGTTGGTGTGGTGCTAG 59.604 55.000 0.00 0.00 0.00 3.42
17 18 0.107831 GTCTGGTTGGTGTGGTGCTA 59.892 55.000 0.00 0.00 0.00 3.49
18 19 1.152963 GTCTGGTTGGTGTGGTGCT 60.153 57.895 0.00 0.00 0.00 4.40
19 20 2.193536 GGTCTGGTTGGTGTGGTGC 61.194 63.158 0.00 0.00 0.00 5.01
20 21 0.395036 TTGGTCTGGTTGGTGTGGTG 60.395 55.000 0.00 0.00 0.00 4.17
21 22 0.395173 GTTGGTCTGGTTGGTGTGGT 60.395 55.000 0.00 0.00 0.00 4.16
22 23 1.106944 GGTTGGTCTGGTTGGTGTGG 61.107 60.000 0.00 0.00 0.00 4.17
23 24 0.395036 TGGTTGGTCTGGTTGGTGTG 60.395 55.000 0.00 0.00 0.00 3.82
24 25 0.106719 CTGGTTGGTCTGGTTGGTGT 60.107 55.000 0.00 0.00 0.00 4.16
25 26 0.182537 TCTGGTTGGTCTGGTTGGTG 59.817 55.000 0.00 0.00 0.00 4.17
26 27 0.182775 GTCTGGTTGGTCTGGTTGGT 59.817 55.000 0.00 0.00 0.00 3.67
27 28 0.537371 GGTCTGGTTGGTCTGGTTGG 60.537 60.000 0.00 0.00 0.00 3.77
28 29 0.537371 GGGTCTGGTTGGTCTGGTTG 60.537 60.000 0.00 0.00 0.00 3.77
29 30 0.991355 TGGGTCTGGTTGGTCTGGTT 60.991 55.000 0.00 0.00 0.00 3.67
30 31 1.385347 TGGGTCTGGTTGGTCTGGT 60.385 57.895 0.00 0.00 0.00 4.00
31 32 1.376466 CTGGGTCTGGTTGGTCTGG 59.624 63.158 0.00 0.00 0.00 3.86
32 33 1.376466 CCTGGGTCTGGTTGGTCTG 59.624 63.158 0.00 0.00 0.00 3.51
33 34 2.529744 GCCTGGGTCTGGTTGGTCT 61.530 63.158 0.00 0.00 0.00 3.85
34 35 2.034221 GCCTGGGTCTGGTTGGTC 59.966 66.667 0.00 0.00 0.00 4.02
35 36 3.580319 GGCCTGGGTCTGGTTGGT 61.580 66.667 0.00 0.00 0.00 3.67
36 37 4.366684 GGGCCTGGGTCTGGTTGG 62.367 72.222 0.84 0.00 0.00 3.77
37 38 3.574074 CTGGGCCTGGGTCTGGTTG 62.574 68.421 4.53 0.00 0.00 3.77
38 39 3.260100 CTGGGCCTGGGTCTGGTT 61.260 66.667 4.53 0.00 0.00 3.67
65 66 4.821589 GACGGCGGCAGGGAAGAG 62.822 72.222 8.47 0.00 0.00 2.85
146 174 1.683418 GGGCGACGAGGAAATAGGGT 61.683 60.000 0.00 0.00 0.00 4.34
198 226 3.542676 AAGCCGTCGTGGTGGTCA 61.543 61.111 0.00 0.00 41.21 4.02
312 340 3.706373 TCGAAGAGGGTGGCCTGC 61.706 66.667 3.32 0.00 0.00 4.85
417 453 2.205074 CAATGAGCTCCATCGTGTACC 58.795 52.381 12.15 0.00 33.53 3.34
418 454 2.893637 ACAATGAGCTCCATCGTGTAC 58.106 47.619 12.15 0.00 33.53 2.90
419 455 4.340950 TGATACAATGAGCTCCATCGTGTA 59.659 41.667 12.15 11.96 34.67 2.90
420 456 3.132824 TGATACAATGAGCTCCATCGTGT 59.867 43.478 12.15 10.19 33.53 4.49
438 476 8.695456 TGTTGAGCTAGTACAGATTGATTGATA 58.305 33.333 0.00 0.00 0.00 2.15
439 477 7.493971 GTGTTGAGCTAGTACAGATTGATTGAT 59.506 37.037 0.00 0.00 0.00 2.57
440 478 6.813649 GTGTTGAGCTAGTACAGATTGATTGA 59.186 38.462 0.00 0.00 0.00 2.57
441 479 6.036517 GGTGTTGAGCTAGTACAGATTGATTG 59.963 42.308 0.00 0.00 0.00 2.67
442 480 6.070538 AGGTGTTGAGCTAGTACAGATTGATT 60.071 38.462 0.00 0.00 0.00 2.57
572 612 4.826733 TGATGCATATATGGTGACCAAACC 59.173 41.667 9.06 0.00 36.95 3.27
573 613 6.389830 TTGATGCATATATGGTGACCAAAC 57.610 37.500 9.06 0.00 36.95 2.93
574 614 6.461370 GCTTTGATGCATATATGGTGACCAAA 60.461 38.462 9.06 0.00 36.95 3.28
575 615 5.009911 GCTTTGATGCATATATGGTGACCAA 59.990 40.000 9.06 0.00 36.95 3.67
576 616 4.520111 GCTTTGATGCATATATGGTGACCA 59.480 41.667 6.84 6.84 38.19 4.02
632 677 3.470709 TCTCTGTTTCTGAAAGCCTGTG 58.529 45.455 2.48 0.00 0.00 3.66
734 779 1.002468 GAGAAAGCGCACAAAGCAGAA 60.002 47.619 11.47 0.00 46.13 3.02
741 786 2.201732 GATATCGGAGAAAGCGCACAA 58.798 47.619 11.47 0.00 43.58 3.33
748 793 6.095432 AGGTGAGAATGATATCGGAGAAAG 57.905 41.667 0.00 0.00 43.58 2.62
769 1125 2.928334 AGCTGAATGGAAGTGCATAGG 58.072 47.619 0.00 0.00 0.00 2.57
840 1202 6.690098 CGCAATGATCTTCTGGAAATAACTTG 59.310 38.462 0.00 0.00 0.00 3.16
883 1423 2.743664 GGGGCTGCAGCTTTAATTTTTG 59.256 45.455 35.82 0.00 41.70 2.44
892 1432 0.113190 AAAGTAAGGGGCTGCAGCTT 59.887 50.000 35.82 24.93 41.70 3.74
928 1468 1.811266 CAGCAGCGCAACCGTCTAT 60.811 57.895 11.47 0.00 36.67 1.98
956 1497 2.357009 GCAGCTGTGGTGGAATATTCTG 59.643 50.000 16.64 3.69 0.00 3.02
957 1498 2.240667 AGCAGCTGTGGTGGAATATTCT 59.759 45.455 16.64 0.00 31.51 2.40
972 1513 1.134551 GGAGAGGAAATCGAAGCAGCT 60.135 52.381 0.00 0.00 0.00 4.24
1055 1596 2.683465 GGCAGGAAGATCAGGGCCA 61.683 63.158 6.18 0.00 41.02 5.36
1250 1797 7.431249 AGATAAAAATCTGATTCAATGCGCAT 58.569 30.769 19.28 19.28 0.00 4.73
1262 1809 7.040478 CCACAGGTTCACAAGATAAAAATCTGA 60.040 37.037 1.03 0.00 0.00 3.27
1292 1840 1.956477 GTGTCCTCTGCACACCAAAAT 59.044 47.619 0.00 0.00 38.61 1.82
1512 2061 8.902806 CACTTAGCTATCCCAAAATTGTCAATA 58.097 33.333 0.00 0.00 0.00 1.90
1560 2113 9.825972 TTCTCTTGAAGAATTAAGCAATTAACG 57.174 29.630 0.00 0.00 39.12 3.18
1617 2170 5.297527 TCTGCAATCGCACAATCATAATTCT 59.702 36.000 0.00 0.00 45.36 2.40
1710 2266 6.038603 TGAACAATCAAGAGAACCTGAAACAG 59.961 38.462 0.00 0.00 30.99 3.16
1789 2428 2.933495 TGATCGCTGTACTGTGTACC 57.067 50.000 12.33 4.86 0.00 3.34
1811 2450 1.018226 AGATGCACGCTCAGCTTCAC 61.018 55.000 0.00 0.00 38.28 3.18
1935 2574 3.251729 AGCAAGCATCTGTTACAACTGTG 59.748 43.478 0.00 0.00 0.00 3.66
2082 2723 4.382254 CCGTAAACAGCTAAGGGTATGTGA 60.382 45.833 0.00 0.00 0.00 3.58
2103 2744 6.009115 AGCACTGAAAGGTAAAATTTACCG 57.991 37.500 24.29 14.69 42.26 4.02
2150 2791 3.848272 AATAAGAACCAATGGTGCACG 57.152 42.857 13.82 0.00 35.34 5.34
2167 2808 8.616076 CAAGTAAAACAAAATGGCCAACAAATA 58.384 29.630 10.96 0.00 0.00 1.40
2174 2815 5.923204 ACATCAAGTAAAACAAAATGGCCA 58.077 33.333 8.56 8.56 0.00 5.36
2176 2817 6.632434 GCAAACATCAAGTAAAACAAAATGGC 59.368 34.615 0.00 0.00 0.00 4.40
2177 2818 7.692088 TGCAAACATCAAGTAAAACAAAATGG 58.308 30.769 0.00 0.00 0.00 3.16
2201 2842 9.649167 AAATAAGCTTCCTGAAAAATTGAGATG 57.351 29.630 0.00 0.00 0.00 2.90
2219 2861 6.338146 TGCTGATACACGTCTTAAATAAGCT 58.662 36.000 0.00 0.00 33.40 3.74
2225 2867 4.503910 AGCATGCTGATACACGTCTTAAA 58.496 39.130 21.98 0.00 0.00 1.52
2253 2895 9.860898 ATCAATTGAATTTTCTTAGTTACCTGC 57.139 29.630 13.09 0.00 0.00 4.85
2265 2910 4.747810 ACAGGCGGATCAATTGAATTTTC 58.252 39.130 13.09 5.22 0.00 2.29
2270 2916 1.818060 CCAACAGGCGGATCAATTGAA 59.182 47.619 13.09 0.00 0.00 2.69
2286 2932 7.593825 ACATCAACTAAATAAGCACTTCCAAC 58.406 34.615 0.00 0.00 0.00 3.77
2313 2959 5.007921 CACGATTCCATCTGCACAATCATAA 59.992 40.000 0.00 0.00 0.00 1.90
2382 3028 3.071023 TGACGAATCCACTGGTTTCTTCT 59.929 43.478 19.01 4.58 33.58 2.85
2534 3193 3.469008 TTTTCTGAAGCGACTTGAGGA 57.531 42.857 6.31 0.00 0.00 3.71
2541 3200 6.790825 GTGTAACAGTAATTTTCTGAAGCGAC 59.209 38.462 9.68 2.03 36.32 5.19
2551 3210 9.841295 TTAGTCCTGAAGTGTAACAGTAATTTT 57.159 29.630 0.00 0.00 41.43 1.82
2652 3311 7.645058 TCCCATCATTCTGAAACCTAATTTC 57.355 36.000 0.00 0.00 46.07 2.17
2699 3359 5.444663 AGAAAAGAAGTCCATTTCACAGC 57.555 39.130 8.86 0.00 35.91 4.40
2741 3404 8.958119 TGTTGAAAGAAACAGAAGTACATACT 57.042 30.769 0.00 0.00 35.16 2.12
2795 3458 9.784680 TGTCGTACTAGTCTAAAAATCTTCATC 57.215 33.333 0.00 0.00 0.00 2.92
2824 3487 4.291249 TCCCACTGCTTAGGAATAGGTTTT 59.709 41.667 0.00 0.00 0.00 2.43
2846 3509 4.842139 AGATGTTCGTGCGAGTAATTTC 57.158 40.909 0.00 0.00 0.00 2.17
2868 3531 4.141551 TGCAGCTGATCCTGACAGAAATAT 60.142 41.667 20.43 0.00 37.54 1.28
2871 3534 1.348696 TGCAGCTGATCCTGACAGAAA 59.651 47.619 20.43 0.00 37.54 2.52
2876 3539 2.008329 CTCTTTGCAGCTGATCCTGAC 58.992 52.381 20.43 0.00 34.77 3.51
2877 3540 1.904537 TCTCTTTGCAGCTGATCCTGA 59.095 47.619 20.43 7.26 34.77 3.86
2887 3550 1.542492 ATTGGGCTGTCTCTTTGCAG 58.458 50.000 0.00 0.00 35.93 4.41
2931 3595 3.616219 AGGCGCACCAATTCTAACATAA 58.384 40.909 10.83 0.00 39.06 1.90
2986 3650 7.776933 AGTGTAACAGACAATAGCATGTATG 57.223 36.000 9.48 9.48 45.57 2.39
3029 3771 0.754587 CTGTACCGGTAGACCCCTCC 60.755 65.000 16.41 0.60 0.00 4.30
3132 3981 2.566952 GCATGGGCACACTCATTTAC 57.433 50.000 0.00 0.00 40.72 2.01
3174 4026 7.307396 CCAGAGTATGCAAAATGAAGTATACCG 60.307 40.741 0.00 0.00 34.96 4.02
3177 4029 7.933577 CCTCCAGAGTATGCAAAATGAAGTATA 59.066 37.037 0.00 0.00 0.00 1.47
3209 4075 7.367285 TCAGTTATAACATTTCAACCAACAGC 58.633 34.615 17.65 0.00 0.00 4.40
3414 4436 5.066505 GTCGATTTGTATTGAATGGCTCCTT 59.933 40.000 0.00 0.00 0.00 3.36
3436 4458 1.940613 GTCAAGTGTGGACCAAGTGTC 59.059 52.381 0.00 0.00 43.67 3.67
3489 4513 1.528309 CTGGCGGAAAGGGTGTTGT 60.528 57.895 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.