Multiple sequence alignment - TraesCS4D01G056200

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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 TraesCS4D01G056200 chr4D 100.000 2921 0 0 1 2921 31448513 31445593 0.000000e+00 5395.0
1 TraesCS4D01G056200 chr4D 90.226 266 25 1 497 762 108628766 108629030 2.570000e-91 346.0
2 TraesCS4D01G056200 chr4D 100.000 145 0 0 3329 3473 31445185 31445041 5.710000e-68 268.0
3 TraesCS4D01G056200 chr4D 91.892 74 6 0 2847 2920 338468437 338468510 1.710000e-18 104.0
4 TraesCS4D01G056200 chr4A 91.608 2562 155 20 22 2563 571485877 571483356 0.000000e+00 3485.0
5 TraesCS4D01G056200 chr4A 93.176 381 26 0 2541 2921 571467419 571467039 8.420000e-156 560.0
6 TraesCS4D01G056200 chr4A 86.595 373 26 2 2549 2921 571477149 571476801 1.170000e-104 390.0
7 TraesCS4D01G056200 chr4A 92.135 267 18 3 500 765 286747584 286747848 1.180000e-99 374.0
8 TraesCS4D01G056200 chr4A 90.226 266 24 2 497 762 467684115 467683852 2.570000e-91 346.0
9 TraesCS4D01G056200 chr4A 94.737 57 3 0 3366 3422 571466435 571466379 4.770000e-14 89.8
10 TraesCS4D01G056200 chr4B 93.230 1551 79 6 940 2482 44944433 44945965 0.000000e+00 2259.0
11 TraesCS4D01G056200 chr4B 89.218 371 33 3 2557 2920 44948812 44949182 1.140000e-124 457.0
12 TraesCS4D01G056200 chr4B 91.892 74 6 0 2847 2920 515038132 515038205 1.710000e-18 104.0
13 TraesCS4D01G056200 chr2D 76.944 1492 248 51 1022 2468 83157556 83156116 0.000000e+00 761.0
14 TraesCS4D01G056200 chr2B 76.950 1449 247 51 1052 2461 135026372 135024972 0.000000e+00 745.0
15 TraesCS4D01G056200 chr2B 74.174 1452 296 58 1051 2461 47417203 47418616 6.600000e-147 531.0
16 TraesCS4D01G056200 chr2B 76.418 899 161 32 1022 1875 135089991 135089099 4.120000e-119 438.0
17 TraesCS4D01G056200 chr2B 89.552 268 23 4 496 761 465133186 465132922 5.550000e-88 335.0
18 TraesCS4D01G056200 chr2B 76.599 594 94 22 1868 2461 135086647 135086099 5.670000e-73 285.0
19 TraesCS4D01G056200 chr2A 76.728 1461 244 52 1046 2461 83857329 83855920 0.000000e+00 726.0
20 TraesCS4D01G056200 chr2A 76.395 1487 268 47 1021 2461 85291723 85293172 0.000000e+00 725.0
21 TraesCS4D01G056200 chr2A 75.793 1450 254 51 1068 2461 85589897 85591305 0.000000e+00 643.0
22 TraesCS4D01G056200 chr6B 91.923 260 20 1 499 758 81010511 81010769 2.550000e-96 363.0
23 TraesCS4D01G056200 chr3A 91.120 259 22 1 500 758 721830158 721830415 1.980000e-92 350.0
24 TraesCS4D01G056200 chr3A 90.530 264 24 1 496 759 468323481 468323743 7.130000e-92 348.0
25 TraesCS4D01G056200 chr1D 89.552 268 25 3 495 762 285439490 285439754 1.540000e-88 337.0
26 TraesCS4D01G056200 chrUn 91.892 74 6 0 2847 2920 447134380 447134453 1.710000e-18 104.0
27 TraesCS4D01G056200 chr5D 91.892 74 6 0 2847 2920 128184400 128184327 1.710000e-18 104.0
28 TraesCS4D01G056200 chr5D 91.892 74 6 0 2847 2920 503249956 503250029 1.710000e-18 104.0
29 TraesCS4D01G056200 chr5D 91.892 74 6 0 2847 2920 503260091 503260018 1.710000e-18 104.0
30 TraesCS4D01G056200 chr3D 91.892 74 6 0 2847 2920 589258842 589258769 1.710000e-18 104.0


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 TraesCS4D01G056200 chr4D 31445041 31448513 3472 True 2831.5 5395 100.0000 1 3473 2 chr4D.!!$R1 3472
1 TraesCS4D01G056200 chr4A 571483356 571485877 2521 True 3485.0 3485 91.6080 22 2563 1 chr4A.!!$R3 2541
2 TraesCS4D01G056200 chr4A 571466379 571467419 1040 True 324.9 560 93.9565 2541 3422 2 chr4A.!!$R4 881
3 TraesCS4D01G056200 chr4B 44944433 44949182 4749 False 1358.0 2259 91.2240 940 2920 2 chr4B.!!$F2 1980
4 TraesCS4D01G056200 chr2D 83156116 83157556 1440 True 761.0 761 76.9440 1022 2468 1 chr2D.!!$R1 1446
5 TraesCS4D01G056200 chr2B 135024972 135026372 1400 True 745.0 745 76.9500 1052 2461 1 chr2B.!!$R1 1409
6 TraesCS4D01G056200 chr2B 47417203 47418616 1413 False 531.0 531 74.1740 1051 2461 1 chr2B.!!$F1 1410
7 TraesCS4D01G056200 chr2B 135086099 135089991 3892 True 361.5 438 76.5085 1022 2461 2 chr2B.!!$R3 1439
8 TraesCS4D01G056200 chr2A 83855920 83857329 1409 True 726.0 726 76.7280 1046 2461 1 chr2A.!!$R1 1415
9 TraesCS4D01G056200 chr2A 85291723 85293172 1449 False 725.0 725 76.3950 1021 2461 1 chr2A.!!$F1 1440
10 TraesCS4D01G056200 chr2A 85589897 85591305 1408 False 643.0 643 75.7930 1068 2461 1 chr2A.!!$F2 1393

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
75 76 0.319813 CACCACTCACGAGCACATCA 60.320 55.0 0.00 0.0 0.00 3.07 F
81 82 0.392706 TCACGAGCACATCACAGGTT 59.607 50.0 0.00 0.0 0.00 3.50 F
1299 1352 0.099968 TCGTGGAGCTTATTCGACGG 59.900 55.0 9.92 0.0 45.48 4.79 F
1782 1889 0.663568 CAAACTCCGACGACGAAGCT 60.664 55.0 9.28 0.0 42.66 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1027 0.735287 GGAGCCTACGTTCGTGAACC 60.735 60.000 8.14 1.68 38.03 3.62 R
1759 1863 1.008194 CGTCGTCGGAGTTTGACCA 60.008 57.895 0.00 0.00 32.68 4.02 R
2320 4934 1.225373 CCATTCTCCCCCTCCATGAA 58.775 55.000 0.00 0.00 0.00 2.57 R
3358 8751 1.202830 TCAACATGGTTTGCCTACGGT 60.203 47.619 0.00 0.00 35.27 4.83 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
17 18 3.808036 CCGTGGCCATTTACTCCG 58.192 61.111 9.72 5.55 0.00 4.63
18 19 1.219664 CCGTGGCCATTTACTCCGA 59.780 57.895 9.72 0.00 0.00 4.55
19 20 1.087771 CCGTGGCCATTTACTCCGAC 61.088 60.000 9.72 0.00 0.00 4.79
20 21 0.390603 CGTGGCCATTTACTCCGACA 60.391 55.000 9.72 0.00 0.00 4.35
21 22 1.816074 GTGGCCATTTACTCCGACAA 58.184 50.000 9.72 0.00 0.00 3.18
22 23 1.467342 GTGGCCATTTACTCCGACAAC 59.533 52.381 9.72 0.00 0.00 3.32
23 24 1.092348 GGCCATTTACTCCGACAACC 58.908 55.000 0.00 0.00 0.00 3.77
24 25 1.612199 GGCCATTTACTCCGACAACCA 60.612 52.381 0.00 0.00 0.00 3.67
25 26 2.365582 GCCATTTACTCCGACAACCAT 58.634 47.619 0.00 0.00 0.00 3.55
75 76 0.319813 CACCACTCACGAGCACATCA 60.320 55.000 0.00 0.00 0.00 3.07
81 82 0.392706 TCACGAGCACATCACAGGTT 59.607 50.000 0.00 0.00 0.00 3.50
83 84 1.995484 CACGAGCACATCACAGGTTAG 59.005 52.381 0.00 0.00 0.00 2.34
145 146 2.751436 GCCTCGAAATGGCCAGCA 60.751 61.111 13.05 0.00 44.32 4.41
146 147 3.056313 GCCTCGAAATGGCCAGCAC 62.056 63.158 13.05 3.52 44.32 4.40
152 153 1.660560 GAAATGGCCAGCACGAGCAT 61.661 55.000 13.05 0.00 45.49 3.79
155 156 2.515523 GGCCAGCACGAGCATGAT 60.516 61.111 7.77 0.00 45.49 2.45
156 157 1.227645 GGCCAGCACGAGCATGATA 60.228 57.895 7.77 0.00 45.49 2.15
176 177 2.946785 ACCTAGATCTGAACCTACCCG 58.053 52.381 5.18 0.00 0.00 5.28
190 191 4.710167 CCCGTCGGTCCAAACCCC 62.710 72.222 11.06 0.00 43.21 4.95
207 208 2.581354 CAGAGAAGGAGGCCACCG 59.419 66.667 14.10 0.00 34.73 4.94
241 242 3.740397 CCTGCACCACACCATGCG 61.740 66.667 0.00 0.00 45.13 4.73
266 267 4.340019 CAATGCACACCGCCGCAA 62.340 61.111 0.00 0.00 42.37 4.85
289 290 4.737346 CCACCAGGGAGCCTAGAT 57.263 61.111 0.00 0.00 40.01 1.98
307 308 3.647771 GGACCCACTCCACCACCC 61.648 72.222 0.00 0.00 39.21 4.61
308 309 3.647771 GACCCACTCCACCACCCC 61.648 72.222 0.00 0.00 0.00 4.95
330 331 1.910722 CCACCAGATGTCCTCCCAG 59.089 63.158 0.00 0.00 0.00 4.45
336 337 1.142748 GATGTCCTCCCAGCGACAG 59.857 63.158 0.00 0.00 42.01 3.51
370 371 4.715130 CCCGACCCCTCCCAGTCA 62.715 72.222 0.00 0.00 33.08 3.41
371 372 3.077556 CCGACCCCTCCCAGTCAG 61.078 72.222 0.00 0.00 33.08 3.51
372 373 3.775654 CGACCCCTCCCAGTCAGC 61.776 72.222 0.00 0.00 33.08 4.26
373 374 3.403558 GACCCCTCCCAGTCAGCC 61.404 72.222 0.00 0.00 33.08 4.85
374 375 4.270153 ACCCCTCCCAGTCAGCCA 62.270 66.667 0.00 0.00 0.00 4.75
412 413 9.909644 ATCCGACAGTACATAAACATTACTATC 57.090 33.333 0.00 0.00 0.00 2.08
442 443 8.855279 TCTTTTTGTACTCACAATTTTGTTTCG 58.145 29.630 0.00 0.00 44.01 3.46
524 525 4.575885 TCCATTCGGTCCTTTTTAGTCTG 58.424 43.478 0.00 0.00 0.00 3.51
550 551 9.750882 GTATATAAGTTTTGTCCGAAGTCAAAC 57.249 33.333 0.00 0.00 34.05 2.93
559 560 6.829229 TGTCCGAAGTCAAACTATCTCTAA 57.171 37.500 0.00 0.00 0.00 2.10
736 737 8.710835 TTGACTTGATACAAATCTAATACGCA 57.289 30.769 0.00 0.00 32.93 5.24
751 752 7.033791 TCTAATACGCAGAGTAAAAAGGACAG 58.966 38.462 0.00 0.00 39.04 3.51
758 759 4.041691 CAGAGTAAAAAGGACAGGAGGGAA 59.958 45.833 0.00 0.00 0.00 3.97
894 896 6.747280 CCTTTGTTCCTTTGTTCGCTAATATG 59.253 38.462 0.00 0.00 0.00 1.78
895 897 5.811399 TGTTCCTTTGTTCGCTAATATGG 57.189 39.130 0.00 0.00 0.00 2.74
901 903 6.314400 TCCTTTGTTCGCTAATATGGTTACAC 59.686 38.462 0.00 0.00 0.00 2.90
908 910 4.682401 CGCTAATATGGTTACACGCACATA 59.318 41.667 0.00 0.00 0.00 2.29
920 922 1.648165 GCACATAACATGCGACGCG 60.648 57.895 16.14 3.53 32.45 6.01
971 981 1.935199 CTTGTGTTAACAACCGGTCGT 59.065 47.619 8.04 0.00 41.41 4.34
1007 1027 1.153647 TGCCGCTAACGATGGAGTG 60.154 57.895 0.00 0.00 43.93 3.51
1019 1039 0.391597 ATGGAGTGGTTCACGAACGT 59.608 50.000 3.95 0.00 42.02 3.99
1256 1297 2.515523 GATCGACGACCTCCCCGA 60.516 66.667 0.00 0.00 35.43 5.14
1299 1352 0.099968 TCGTGGAGCTTATTCGACGG 59.900 55.000 9.92 0.00 45.48 4.79
1374 1439 4.752879 GCGCTGGTGCCGGACTTA 62.753 66.667 5.05 0.00 35.36 2.24
1782 1889 0.663568 CAAACTCCGACGACGAAGCT 60.664 55.000 9.28 0.00 42.66 3.74
1854 1970 1.441016 GTACGTCGCGTTCGGAAGT 60.441 57.895 23.64 9.36 41.54 3.01
2281 4895 4.717629 TCGTGGCGCGTGAGGAAG 62.718 66.667 20.88 0.00 42.13 3.46
2496 5110 2.087009 GTACGCTCGTGACTGCACC 61.087 63.158 5.05 0.00 42.09 5.01
2509 5123 4.679412 GCACCAACTGCAAATGGG 57.321 55.556 18.77 6.01 46.29 4.00
2611 7997 0.040157 CCCAACACACACGCATGAAG 60.040 55.000 0.00 0.00 0.00 3.02
2665 8051 2.221749 CGATGTCCATGTGAATTAGGCG 59.778 50.000 0.00 0.00 0.00 5.52
2693 8079 3.561313 GGTCTCAGAGCAAACCCCAAATA 60.561 47.826 0.00 0.00 0.00 1.40
2715 8106 3.627577 ACACGCTGAGACATTTGAAAAGT 59.372 39.130 0.00 0.00 0.00 2.66
2738 8129 0.661020 CGAGTGGTTGTTTTCGGCTT 59.339 50.000 0.00 0.00 0.00 4.35
2748 8141 7.010275 GTGGTTGTTTTCGGCTTTTATAAAACA 59.990 33.333 6.54 7.84 45.23 2.83
2758 8151 6.455647 GGCTTTTATAAAACAGACAAAGGCT 58.544 36.000 6.54 0.00 41.29 4.58
2793 8186 1.405526 CCTTTCCTTGAAGGCGATCGA 60.406 52.381 21.57 0.00 39.75 3.59
2811 8204 1.399440 CGATGGTCCAAACTCTGCATG 59.601 52.381 0.00 0.00 0.00 4.06
2824 8217 1.911357 TCTGCATGGAAGTGGAGTCAT 59.089 47.619 0.00 0.00 38.53 3.06
3347 8740 2.838386 CGTGAAGCATCATCCAAAGG 57.162 50.000 0.00 0.00 38.01 3.11
3348 8741 1.402968 CGTGAAGCATCATCCAAAGGG 59.597 52.381 0.00 0.00 38.01 3.95
3361 8754 4.216411 TCCAAAGGGAGAAGAATTACCG 57.784 45.455 0.00 0.00 38.64 4.02
3362 8755 3.585732 TCCAAAGGGAGAAGAATTACCGT 59.414 43.478 0.00 0.00 38.64 4.83
3363 8756 4.778958 TCCAAAGGGAGAAGAATTACCGTA 59.221 41.667 0.00 0.00 38.64 4.02
3364 8757 5.105064 TCCAAAGGGAGAAGAATTACCGTAG 60.105 44.000 0.00 0.00 38.64 3.51
3394 8946 7.811282 ACCATGTTGATTCCCATATAAGTGTA 58.189 34.615 0.00 0.00 0.00 2.90
3399 8951 9.693739 TGTTGATTCCCATATAAGTGTAAATGT 57.306 29.630 0.00 0.00 0.00 2.71
3446 8998 6.715347 GGCACCCTCTTAACATTATCATTT 57.285 37.500 0.00 0.00 0.00 2.32
3447 8999 6.507023 GGCACCCTCTTAACATTATCATTTG 58.493 40.000 0.00 0.00 0.00 2.32
3448 9000 6.096846 GGCACCCTCTTAACATTATCATTTGT 59.903 38.462 0.00 0.00 0.00 2.83
3449 9001 7.284489 GGCACCCTCTTAACATTATCATTTGTA 59.716 37.037 0.00 0.00 0.00 2.41
3450 9002 8.850156 GCACCCTCTTAACATTATCATTTGTAT 58.150 33.333 0.00 0.00 0.00 2.29
3452 9004 9.574516 ACCCTCTTAACATTATCATTTGTATCC 57.425 33.333 0.00 0.00 0.00 2.59
3453 9005 9.799106 CCCTCTTAACATTATCATTTGTATCCT 57.201 33.333 0.00 0.00 0.00 3.24
3470 9022 8.908786 TTGTATCCTTAGAGATAGCAAAATGG 57.091 34.615 0.00 0.00 29.40 3.16
3471 9023 8.034313 TGTATCCTTAGAGATAGCAAAATGGT 57.966 34.615 0.00 0.00 29.40 3.55
3472 9024 8.494433 TGTATCCTTAGAGATAGCAAAATGGTT 58.506 33.333 0.00 0.00 29.40 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.087771 GTCGGAGTAAATGGCCACGG 61.088 60.000 8.16 0.00 0.00 4.94
2 3 1.467342 GTTGTCGGAGTAAATGGCCAC 59.533 52.381 8.16 0.00 0.00 5.01
3 4 1.612199 GGTTGTCGGAGTAAATGGCCA 60.612 52.381 8.56 8.56 0.00 5.36
4 5 1.092348 GGTTGTCGGAGTAAATGGCC 58.908 55.000 0.00 0.00 0.00 5.36
5 6 1.816074 TGGTTGTCGGAGTAAATGGC 58.184 50.000 0.00 0.00 0.00 4.40
6 7 2.607635 CGATGGTTGTCGGAGTAAATGG 59.392 50.000 0.00 0.00 37.94 3.16
7 8 3.517602 TCGATGGTTGTCGGAGTAAATG 58.482 45.455 0.00 0.00 41.74 2.32
8 9 3.782046 CTCGATGGTTGTCGGAGTAAAT 58.218 45.455 0.00 0.00 41.74 1.40
9 10 2.673043 GCTCGATGGTTGTCGGAGTAAA 60.673 50.000 0.00 0.00 41.74 2.01
10 11 1.135199 GCTCGATGGTTGTCGGAGTAA 60.135 52.381 0.00 0.00 41.74 2.24
11 12 0.454600 GCTCGATGGTTGTCGGAGTA 59.545 55.000 0.00 0.00 41.74 2.59
12 13 1.215647 GCTCGATGGTTGTCGGAGT 59.784 57.895 0.00 0.00 41.74 3.85
13 14 1.078759 GTGCTCGATGGTTGTCGGAG 61.079 60.000 0.00 0.00 41.74 4.63
14 15 1.080093 GTGCTCGATGGTTGTCGGA 60.080 57.895 0.00 0.00 41.74 4.55
15 16 2.100631 GGTGCTCGATGGTTGTCGG 61.101 63.158 0.00 0.00 41.74 4.79
16 17 0.740868 ATGGTGCTCGATGGTTGTCG 60.741 55.000 0.00 0.00 42.74 4.35
17 18 1.933853 GTATGGTGCTCGATGGTTGTC 59.066 52.381 0.00 0.00 0.00 3.18
18 19 1.406887 GGTATGGTGCTCGATGGTTGT 60.407 52.381 0.00 0.00 0.00 3.32
19 20 1.299541 GGTATGGTGCTCGATGGTTG 58.700 55.000 0.00 0.00 0.00 3.77
20 21 0.180406 GGGTATGGTGCTCGATGGTT 59.820 55.000 0.00 0.00 0.00 3.67
21 22 0.980754 TGGGTATGGTGCTCGATGGT 60.981 55.000 0.00 0.00 0.00 3.55
22 23 0.532862 GTGGGTATGGTGCTCGATGG 60.533 60.000 0.00 0.00 0.00 3.51
23 24 0.875908 CGTGGGTATGGTGCTCGATG 60.876 60.000 0.00 0.00 0.00 3.84
24 25 1.040893 TCGTGGGTATGGTGCTCGAT 61.041 55.000 0.00 0.00 0.00 3.59
25 26 1.663379 CTCGTGGGTATGGTGCTCGA 61.663 60.000 0.00 0.00 0.00 4.04
83 84 1.457831 ATGTAGGAGAGGTCGGGCC 60.458 63.158 0.00 0.00 37.58 5.80
131 132 1.741401 CTCGTGCTGGCCATTTCGA 60.741 57.895 5.51 15.36 0.00 3.71
136 137 2.619941 ATCATGCTCGTGCTGGCCAT 62.620 55.000 5.51 0.00 40.48 4.40
143 144 3.192422 AGATCTAGGTATCATGCTCGTGC 59.808 47.826 1.71 1.71 40.20 5.34
145 146 4.657013 TCAGATCTAGGTATCATGCTCGT 58.343 43.478 0.00 0.00 0.00 4.18
146 147 5.398169 GTTCAGATCTAGGTATCATGCTCG 58.602 45.833 0.00 0.00 0.00 5.03
152 153 5.642165 GGGTAGGTTCAGATCTAGGTATCA 58.358 45.833 0.00 0.00 0.00 2.15
155 156 3.461085 ACGGGTAGGTTCAGATCTAGGTA 59.539 47.826 0.00 0.00 0.00 3.08
156 157 2.244252 ACGGGTAGGTTCAGATCTAGGT 59.756 50.000 0.00 0.00 0.00 3.08
190 191 2.581354 CGGTGGCCTCCTTCTCTG 59.419 66.667 21.24 1.07 0.00 3.35
227 228 1.746615 ATCTCGCATGGTGTGGTGC 60.747 57.895 0.00 0.00 37.97 5.01
230 231 3.104766 GCATCTCGCATGGTGTGG 58.895 61.111 0.00 0.00 41.79 4.17
308 309 4.457496 AGGACATCTGGTGGCGCG 62.457 66.667 0.00 0.00 36.36 6.86
310 311 2.187946 GGAGGACATCTGGTGGCG 59.812 66.667 0.00 0.00 36.36 5.69
330 331 3.825833 CTACGGCCGGATCTGTCGC 62.826 68.421 31.76 4.67 0.00 5.19
355 356 3.775654 GCTGACTGGGAGGGGTCG 61.776 72.222 0.00 0.00 35.45 4.79
372 373 2.202987 GGATCTGTCGCCAGCTGG 60.203 66.667 29.34 29.34 38.66 4.85
373 374 2.584418 CGGATCTGTCGCCAGCTG 60.584 66.667 6.78 6.78 38.66 4.24
374 375 2.755876 TCGGATCTGTCGCCAGCT 60.756 61.111 0.42 0.00 38.66 4.24
449 450 1.275573 ACTTCAGTCGACTTTAGGGCC 59.724 52.381 17.26 0.00 0.00 5.80
454 455 6.805271 CGAAGGAATAACTTCAGTCGACTTTA 59.195 38.462 17.26 12.47 45.54 1.85
455 456 5.634020 CGAAGGAATAACTTCAGTCGACTTT 59.366 40.000 17.26 10.46 45.54 2.66
463 464 1.933853 CCCGCGAAGGAATAACTTCAG 59.066 52.381 8.23 0.52 45.54 3.02
494 495 2.816411 AGGACCGAATGGAGTACTTGA 58.184 47.619 0.00 0.00 39.21 3.02
502 503 4.041198 ACAGACTAAAAAGGACCGAATGGA 59.959 41.667 0.00 0.00 39.21 3.41
524 525 9.750882 GTTTGACTTCGGACAAAACTTATATAC 57.249 33.333 0.00 0.00 40.09 1.47
582 583 3.872696 TGGCATTGTGAATGTCGATACT 58.127 40.909 0.00 0.00 46.30 2.12
583 584 4.614555 TTGGCATTGTGAATGTCGATAC 57.385 40.909 0.00 0.00 46.30 2.24
686 687 8.794335 AACTTTGTAAACTTTGGCCAAATTTA 57.206 26.923 30.46 27.37 0.00 1.40
695 696 8.702163 ATCAAGTCAAACTTTGTAAACTTTGG 57.298 30.769 1.44 0.00 36.03 3.28
727 728 6.255887 CCTGTCCTTTTTACTCTGCGTATTAG 59.744 42.308 0.00 0.00 0.00 1.73
733 734 2.996621 CTCCTGTCCTTTTTACTCTGCG 59.003 50.000 0.00 0.00 0.00 5.18
736 737 3.870559 TCCCTCCTGTCCTTTTTACTCT 58.129 45.455 0.00 0.00 0.00 3.24
751 752 8.196378 ACTTGATCTAGTGTTATATTCCCTCC 57.804 38.462 9.11 0.00 0.00 4.30
894 896 2.780993 GCATGTTATGTGCGTGTAACC 58.219 47.619 0.00 0.00 32.29 2.85
916 918 0.039256 TGGTCTAGTTAAACGCGCGT 60.039 50.000 32.73 32.73 0.00 6.01
918 920 1.986698 TCTGGTCTAGTTAAACGCGC 58.013 50.000 5.73 0.00 0.00 6.86
920 922 3.522553 AGCATCTGGTCTAGTTAAACGC 58.477 45.455 0.00 0.00 0.00 4.84
921 923 4.563184 GTGAGCATCTGGTCTAGTTAAACG 59.437 45.833 10.41 0.00 42.60 3.60
960 970 1.005394 GATGTGGACGACCGGTTGT 60.005 57.895 27.92 27.92 39.42 3.32
971 981 2.350895 CCGGTGGCAAGATGTGGA 59.649 61.111 0.00 0.00 0.00 4.02
993 1003 2.000447 GTGAACCACTCCATCGTTAGC 59.000 52.381 0.00 0.00 0.00 3.09
1007 1027 0.735287 GGAGCCTACGTTCGTGAACC 60.735 60.000 8.14 1.68 38.03 3.62
1177 1200 3.334054 GCTGGGGAGGGCTTCTGT 61.334 66.667 0.00 0.00 0.00 3.41
1519 1584 1.228003 GGATCTCGAGAGGCTCCGA 60.228 63.158 21.52 21.24 0.00 4.55
1759 1863 1.008194 CGTCGTCGGAGTTTGACCA 60.008 57.895 0.00 0.00 32.68 4.02
2266 4880 3.112709 GACTTCCTCACGCGCCAC 61.113 66.667 5.73 0.00 0.00 5.01
2267 4881 4.717629 CGACTTCCTCACGCGCCA 62.718 66.667 5.73 0.00 0.00 5.69
2268 4882 4.719369 ACGACTTCCTCACGCGCC 62.719 66.667 5.73 0.00 0.00 6.53
2269 4883 3.470567 CACGACTTCCTCACGCGC 61.471 66.667 5.73 0.00 0.00 6.86
2270 4884 2.805353 CCACGACTTCCTCACGCG 60.805 66.667 3.53 3.53 0.00 6.01
2272 4886 2.805353 CGCCACGACTTCCTCACG 60.805 66.667 0.00 0.00 0.00 4.35
2273 4887 3.112709 GCGCCACGACTTCCTCAC 61.113 66.667 0.00 0.00 0.00 3.51
2320 4934 1.225373 CCATTCTCCCCCTCCATGAA 58.775 55.000 0.00 0.00 0.00 2.57
2482 5096 1.595382 AGTTGGTGCAGTCACGAGC 60.595 57.895 0.00 0.00 44.03 5.03
2496 5110 1.543944 GGGGGTCCCATTTGCAGTTG 61.544 60.000 10.98 0.00 44.65 3.16
2611 7997 1.710013 TTTCCTCTCGTCACGCATTC 58.290 50.000 0.00 0.00 0.00 2.67
2665 8051 2.062519 GTTTGCTCTGAGACCGAGTTC 58.937 52.381 9.28 0.00 0.00 3.01
2693 8079 3.627577 ACTTTTCAAATGTCTCAGCGTGT 59.372 39.130 0.00 0.00 0.00 4.49
2715 8106 2.746269 CCGAAAACAACCACTCGTCTA 58.254 47.619 0.00 0.00 0.00 2.59
2748 8141 2.562738 GGCCAAATTGTAGCCTTTGTCT 59.437 45.455 0.00 0.00 43.62 3.41
2758 8151 2.635427 GGAAAGGGTTGGCCAAATTGTA 59.365 45.455 22.47 0.00 36.17 2.41
2793 8186 1.355381 TCCATGCAGAGTTTGGACCAT 59.645 47.619 1.73 0.00 34.65 3.55
3328 8721 1.402968 CCCTTTGGATGATGCTTCACG 59.597 52.381 4.14 0.00 33.85 4.35
3329 8722 2.686915 CTCCCTTTGGATGATGCTTCAC 59.313 50.000 4.14 0.00 40.80 3.18
3330 8723 2.577563 TCTCCCTTTGGATGATGCTTCA 59.422 45.455 4.57 4.57 40.80 3.02
3331 8724 3.287867 TCTCCCTTTGGATGATGCTTC 57.712 47.619 0.00 0.00 40.80 3.86
3332 8725 3.267812 TCTTCTCCCTTTGGATGATGCTT 59.732 43.478 0.00 0.00 40.80 3.91
3333 8726 2.848694 TCTTCTCCCTTTGGATGATGCT 59.151 45.455 0.00 0.00 40.80 3.79
3334 8727 3.287867 TCTTCTCCCTTTGGATGATGC 57.712 47.619 0.00 0.00 40.80 3.91
3335 8728 6.264067 GGTAATTCTTCTCCCTTTGGATGATG 59.736 42.308 0.00 0.00 40.80 3.07
3336 8729 6.368805 GGTAATTCTTCTCCCTTTGGATGAT 58.631 40.000 0.00 0.00 40.80 2.45
3337 8730 5.629133 CGGTAATTCTTCTCCCTTTGGATGA 60.629 44.000 0.00 0.00 40.80 2.92
3338 8731 4.576463 CGGTAATTCTTCTCCCTTTGGATG 59.424 45.833 0.00 0.00 40.80 3.51
3339 8732 4.227527 ACGGTAATTCTTCTCCCTTTGGAT 59.772 41.667 0.00 0.00 40.80 3.41
3340 8733 3.585732 ACGGTAATTCTTCTCCCTTTGGA 59.414 43.478 0.00 0.00 38.75 3.53
3341 8734 3.951663 ACGGTAATTCTTCTCCCTTTGG 58.048 45.455 0.00 0.00 0.00 3.28
3342 8735 5.116882 CCTACGGTAATTCTTCTCCCTTTG 58.883 45.833 0.00 0.00 0.00 2.77
3343 8736 4.383880 GCCTACGGTAATTCTTCTCCCTTT 60.384 45.833 0.00 0.00 0.00 3.11
3344 8737 3.134262 GCCTACGGTAATTCTTCTCCCTT 59.866 47.826 0.00 0.00 0.00 3.95
3345 8738 2.699321 GCCTACGGTAATTCTTCTCCCT 59.301 50.000 0.00 0.00 0.00 4.20
3346 8739 2.433239 TGCCTACGGTAATTCTTCTCCC 59.567 50.000 0.00 0.00 0.00 4.30
3347 8740 3.814005 TGCCTACGGTAATTCTTCTCC 57.186 47.619 0.00 0.00 0.00 3.71
3348 8741 4.331992 GGTTTGCCTACGGTAATTCTTCTC 59.668 45.833 0.00 0.00 0.00 2.87
3349 8742 4.259356 GGTTTGCCTACGGTAATTCTTCT 58.741 43.478 0.00 0.00 0.00 2.85
3350 8743 4.004982 TGGTTTGCCTACGGTAATTCTTC 58.995 43.478 0.00 0.00 35.27 2.87
3351 8744 4.023726 TGGTTTGCCTACGGTAATTCTT 57.976 40.909 0.00 0.00 35.27 2.52
3352 8745 3.706600 TGGTTTGCCTACGGTAATTCT 57.293 42.857 0.00 0.00 35.27 2.40
3353 8746 3.692593 ACATGGTTTGCCTACGGTAATTC 59.307 43.478 0.00 0.00 35.27 2.17
3354 8747 3.692690 ACATGGTTTGCCTACGGTAATT 58.307 40.909 0.00 0.00 35.27 1.40
3355 8748 3.359695 ACATGGTTTGCCTACGGTAAT 57.640 42.857 0.00 0.00 35.27 1.89
3356 8749 2.814919 CAACATGGTTTGCCTACGGTAA 59.185 45.455 0.00 0.00 35.27 2.85
3357 8750 2.038689 TCAACATGGTTTGCCTACGGTA 59.961 45.455 0.00 0.00 35.27 4.02
3358 8751 1.202830 TCAACATGGTTTGCCTACGGT 60.203 47.619 0.00 0.00 35.27 4.83
3359 8752 1.529226 TCAACATGGTTTGCCTACGG 58.471 50.000 0.00 0.00 35.27 4.02
3360 8753 3.427503 GGAATCAACATGGTTTGCCTACG 60.428 47.826 0.00 0.00 35.27 3.51
3361 8754 3.119137 GGGAATCAACATGGTTTGCCTAC 60.119 47.826 0.00 0.00 35.27 3.18
3362 8755 3.096092 GGGAATCAACATGGTTTGCCTA 58.904 45.455 0.00 0.00 35.27 3.93
3363 8756 1.901833 GGGAATCAACATGGTTTGCCT 59.098 47.619 0.00 0.00 35.27 4.75
3364 8757 1.622811 TGGGAATCAACATGGTTTGCC 59.377 47.619 0.00 0.00 0.00 4.52
3411 8963 1.308877 AGGGTGCCCTATGGACAATT 58.691 50.000 8.24 0.00 46.14 2.32
3422 8974 4.164843 TGATAATGTTAAGAGGGTGCCC 57.835 45.455 0.00 0.00 0.00 5.36
3423 8975 6.096846 ACAAATGATAATGTTAAGAGGGTGCC 59.903 38.462 0.00 0.00 0.00 5.01
3424 8976 7.100458 ACAAATGATAATGTTAAGAGGGTGC 57.900 36.000 0.00 0.00 0.00 5.01
3426 8978 9.574516 GGATACAAATGATAATGTTAAGAGGGT 57.425 33.333 0.00 0.00 0.00 4.34
3427 8979 9.799106 AGGATACAAATGATAATGTTAAGAGGG 57.201 33.333 0.00 0.00 41.41 4.30
3444 8996 9.342308 CCATTTTGCTATCTCTAAGGATACAAA 57.658 33.333 0.00 0.00 41.41 2.83
3445 8997 8.494433 ACCATTTTGCTATCTCTAAGGATACAA 58.506 33.333 0.00 0.00 41.41 2.41
3446 8998 8.034313 ACCATTTTGCTATCTCTAAGGATACA 57.966 34.615 0.00 0.00 41.41 2.29
3447 8999 8.910351 AACCATTTTGCTATCTCTAAGGATAC 57.090 34.615 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.