Multiple sequence alignment - TraesCS2A01G385900

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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 TraesCS2A01G385900 chr2A 100.000 4303 0 0 1 4303 631854136 631858438 0.000000e+00 7947.0
1 TraesCS2A01G385900 chr2A 85.159 1671 139 63 710 2341 632589795 632588195 0.000000e+00 1611.0
2 TraesCS2A01G385900 chr2A 82.511 1418 158 58 2375 3764 632588089 632586734 0.000000e+00 1162.0
3 TraesCS2A01G385900 chr2A 84.206 1089 118 36 2427 3487 46336704 46337766 0.000000e+00 1009.0
4 TraesCS2A01G385900 chr2A 82.018 228 34 7 1567 1790 632595219 632594995 2.040000e-43 187.0
5 TraesCS2A01G385900 chr2A 83.621 116 6 6 593 707 632590076 632589973 3.540000e-16 97.1
6 TraesCS2A01G385900 chr2D 91.354 2695 125 43 1634 4303 486390978 486393589 0.000000e+00 3587.0
7 TraesCS2A01G385900 chr2D 84.409 3098 286 101 706 3745 487935097 487932139 0.000000e+00 2863.0
8 TraesCS2A01G385900 chr2D 89.589 1556 76 37 1 1536 486389421 486390910 0.000000e+00 1897.0
9 TraesCS2A01G385900 chr2D 83.177 2027 207 68 1634 3644 487724708 487722800 0.000000e+00 1731.0
10 TraesCS2A01G385900 chr2D 81.235 1247 172 34 1634 2874 487593944 487592754 0.000000e+00 950.0
11 TraesCS2A01G385900 chr2D 82.642 651 59 28 906 1542 487725380 487724770 1.060000e-145 527.0
12 TraesCS2A01G385900 chr2D 79.548 753 98 32 1565 2310 488058577 488057874 1.800000e-133 486.0
13 TraesCS2A01G385900 chr2D 79.148 657 61 36 905 1548 487594595 487594002 6.750000e-103 385.0
14 TraesCS2A01G385900 chr2D 80.606 495 45 20 3064 3557 488056262 488055818 6.890000e-88 335.0
15 TraesCS2A01G385900 chr2D 76.393 377 45 19 352 689 487935673 487935302 3.440000e-36 163.0
16 TraesCS2A01G385900 chr2B 92.499 2293 107 37 2048 4303 571346558 571348822 0.000000e+00 3221.0
17 TraesCS2A01G385900 chr2B 84.193 2733 256 86 1087 3764 572314291 572311680 0.000000e+00 2492.0
18 TraesCS2A01G385900 chr2B 82.933 2121 247 60 1634 3735 572179518 572177494 0.000000e+00 1805.0
19 TraesCS2A01G385900 chr2B 91.892 1184 70 10 353 1536 571344951 571346108 0.000000e+00 1631.0
20 TraesCS2A01G385900 chr2B 92.268 388 24 3 1634 2016 571346171 571346557 2.930000e-151 545.0
21 TraesCS2A01G385900 chr2B 91.105 371 29 4 1 370 571343943 571344310 2.310000e-137 499.0
22 TraesCS2A01G385900 chr2B 82.309 537 41 26 1021 1542 572180077 572179580 2.390000e-112 416.0
23 TraesCS2A01G385900 chr2B 90.491 326 14 6 668 988 572314602 572314289 8.610000e-112 414.0
24 TraesCS2A01G385900 chr2B 80.168 358 35 20 905 1241 572326094 572325752 7.190000e-58 235.0
25 TraesCS2A01G385900 chr2B 84.795 171 18 4 3403 3567 548939694 548939526 9.570000e-37 165.0
26 TraesCS2A01G385900 chr2B 88.095 126 9 2 588 707 572314928 572314803 1.250000e-30 145.0
27 TraesCS2A01G385900 chr7D 84.573 1089 116 35 2427 3487 446551165 446550101 0.000000e+00 1033.0
28 TraesCS2A01G385900 chr7D 81.360 456 36 23 1884 2331 446551625 446551211 4.150000e-85 326.0
29 TraesCS2A01G385900 chr3B 83.693 1067 110 39 2427 3458 555550647 555549610 0.000000e+00 948.0
30 TraesCS2A01G385900 chr3B 96.226 53 2 0 3339 3391 454138767 454138715 2.130000e-13 87.9
31 TraesCS2A01G385900 chr3B 96.226 53 2 0 3339 3391 454346038 454345986 2.130000e-13 87.9
32 TraesCS2A01G385900 chr4B 83.599 1067 111 39 2427 3458 16787152 16788189 0.000000e+00 942.0
33 TraesCS2A01G385900 chr3D 84.694 882 91 28 2630 3487 16449275 16450136 0.000000e+00 841.0
34 TraesCS2A01G385900 chr6A 83.973 443 45 11 3339 3766 226334904 226334473 6.700000e-108 401.0
35 TraesCS2A01G385900 chr7A 89.451 237 20 4 2096 2331 321636924 321636692 1.170000e-75 294.0
36 TraesCS2A01G385900 chr6B 87.121 264 23 8 2427 2684 247035362 247035104 5.440000e-74 289.0
37 TraesCS2A01G385900 chr6B 96.226 53 2 0 3339 3391 699127372 699127320 2.130000e-13 87.9
38 TraesCS2A01G385900 chr7B 98.000 50 1 0 3339 3388 421245028 421244979 2.130000e-13 87.9
39 TraesCS2A01G385900 chr1B 98.000 50 1 0 3339 3388 665779399 665779448 2.130000e-13 87.9


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 TraesCS2A01G385900 chr2A 631854136 631858438 4302 False 7947.0 7947 100.000000 1 4303 1 chr2A.!!$F2 4302
1 TraesCS2A01G385900 chr2A 46336704 46337766 1062 False 1009.0 1009 84.206000 2427 3487 1 chr2A.!!$F1 1060
2 TraesCS2A01G385900 chr2A 632586734 632590076 3342 True 956.7 1611 83.763667 593 3764 3 chr2A.!!$R2 3171
3 TraesCS2A01G385900 chr2D 486389421 486393589 4168 False 2742.0 3587 90.471500 1 4303 2 chr2D.!!$F1 4302
4 TraesCS2A01G385900 chr2D 487932139 487935673 3534 True 1513.0 2863 80.401000 352 3745 2 chr2D.!!$R3 3393
5 TraesCS2A01G385900 chr2D 487722800 487725380 2580 True 1129.0 1731 82.909500 906 3644 2 chr2D.!!$R2 2738
6 TraesCS2A01G385900 chr2D 487592754 487594595 1841 True 667.5 950 80.191500 905 2874 2 chr2D.!!$R1 1969
7 TraesCS2A01G385900 chr2D 488055818 488058577 2759 True 410.5 486 80.077000 1565 3557 2 chr2D.!!$R4 1992
8 TraesCS2A01G385900 chr2B 571343943 571348822 4879 False 1474.0 3221 91.941000 1 4303 4 chr2B.!!$F1 4302
9 TraesCS2A01G385900 chr2B 572177494 572180077 2583 True 1110.5 1805 82.621000 1021 3735 2 chr2B.!!$R3 2714
10 TraesCS2A01G385900 chr2B 572311680 572314928 3248 True 1017.0 2492 87.593000 588 3764 3 chr2B.!!$R4 3176
11 TraesCS2A01G385900 chr7D 446550101 446551625 1524 True 679.5 1033 82.966500 1884 3487 2 chr7D.!!$R1 1603
12 TraesCS2A01G385900 chr3B 555549610 555550647 1037 True 948.0 948 83.693000 2427 3458 1 chr3B.!!$R3 1031
13 TraesCS2A01G385900 chr4B 16787152 16788189 1037 False 942.0 942 83.599000 2427 3458 1 chr4B.!!$F1 1031
14 TraesCS2A01G385900 chr3D 16449275 16450136 861 False 841.0 841 84.694000 2630 3487 1 chr3D.!!$F1 857

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
796 1943 0.031994 AAATGGGAAACTGTGCACGC 59.968 50.0 13.13 0.00 0.00 5.34 F
897 2056 0.191064 TCACACTTCACTCCCTCCCT 59.809 55.0 0.00 0.00 0.00 4.20 F
1657 2953 0.249398 AGGATTACACCGGTGAGCAC 59.751 55.0 40.21 25.07 34.73 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2609 4508 1.003118 ACGCTGCCTGAAATAACTGGA 59.997 47.619 0.0 0.0 0.00 3.86 R
2610 4509 1.453155 ACGCTGCCTGAAATAACTGG 58.547 50.000 0.0 0.0 0.00 4.00 R
3333 5682 0.676466 TGGAGCATTTGGTACAGGCG 60.676 55.000 0.0 0.0 42.39 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
34 35 5.065602 CAGTATCACACCAATTGACATCCAG 59.934 44.000 7.12 0.00 0.00 3.86
38 39 2.297033 ACACCAATTGACATCCAGCAAC 59.703 45.455 7.12 0.00 0.00 4.17
49 51 4.074970 ACATCCAGCAACGATTTTCTCTT 58.925 39.130 0.00 0.00 0.00 2.85
70 72 4.380841 TCATCAATGCTCCTTTGATTGC 57.619 40.909 4.26 0.00 40.84 3.56
81 83 2.415893 CCTTTGATTGCATCACGGAACC 60.416 50.000 0.00 0.00 39.39 3.62
82 84 1.902938 TTGATTGCATCACGGAACCA 58.097 45.000 0.00 0.00 39.39 3.67
106 108 9.793259 CCAAAAGTATTCTTAGCAAGGGATATA 57.207 33.333 0.00 0.00 33.09 0.86
159 161 8.786898 TGTAGTTGAAAGAATGATCTGGAAAAG 58.213 33.333 0.00 0.00 35.59 2.27
162 164 6.579666 TGAAAGAATGATCTGGAAAAGGTG 57.420 37.500 0.00 0.00 35.59 4.00
181 183 5.167845 AGGTGCCTTATAAAACAAATTGCG 58.832 37.500 0.00 0.00 0.00 4.85
189 191 8.311120 CCTTATAAAACAAATTGCGAACGAATC 58.689 33.333 0.00 0.00 0.00 2.52
423 1083 0.249238 GCATACGCTGTCCCTCTCAG 60.249 60.000 0.00 0.00 36.18 3.35
432 1092 4.180946 CCCTCTCAGGTCGTCGCG 62.181 72.222 0.00 0.00 31.93 5.87
446 1121 2.534349 TCGTCGCGCATTCTATTTTCTC 59.466 45.455 8.75 0.00 0.00 2.87
449 1124 4.049186 GTCGCGCATTCTATTTTCTCCTA 58.951 43.478 8.75 0.00 0.00 2.94
450 1125 4.506654 GTCGCGCATTCTATTTTCTCCTAA 59.493 41.667 8.75 0.00 0.00 2.69
628 1334 1.889105 CCTTCCGTGCGATGGATGG 60.889 63.158 12.02 12.02 40.75 3.51
768 1914 1.735700 GCAAGTTTAGGCGGGCATTTC 60.736 52.381 3.78 0.00 0.00 2.17
793 1940 2.744494 GCCAAAAATGGGAAACTGTGCA 60.744 45.455 0.00 0.00 0.00 4.57
794 1941 2.871633 CCAAAAATGGGAAACTGTGCAC 59.128 45.455 10.75 10.75 0.00 4.57
795 1942 2.507339 AAAATGGGAAACTGTGCACG 57.493 45.000 13.13 9.67 0.00 5.34
796 1943 0.031994 AAATGGGAAACTGTGCACGC 59.968 50.000 13.13 0.00 0.00 5.34
797 1944 1.805428 AATGGGAAACTGTGCACGCC 61.805 55.000 13.13 8.05 0.00 5.68
798 1945 2.904866 GGGAAACTGTGCACGCCA 60.905 61.111 13.13 0.00 0.00 5.69
799 1946 2.639286 GGAAACTGTGCACGCCAG 59.361 61.111 13.13 6.82 36.01 4.85
800 1947 2.186826 GGAAACTGTGCACGCCAGT 61.187 57.895 13.13 7.53 44.80 4.00
897 2056 0.191064 TCACACTTCACTCCCTCCCT 59.809 55.000 0.00 0.00 0.00 4.20
902 2061 2.513026 CTTCACTCCCTCCCTGCACG 62.513 65.000 0.00 0.00 0.00 5.34
903 2062 4.767255 CACTCCCTCCCTGCACGC 62.767 72.222 0.00 0.00 0.00 5.34
1056 2245 1.415672 TTTGTGGACTCCTCCCGCTT 61.416 55.000 0.00 0.00 35.34 4.68
1244 2473 2.262915 GCACCAGGTGAGACGAGG 59.737 66.667 24.96 0.00 35.23 4.63
1252 2481 1.596895 GGTGAGACGAGGGTCCTCAC 61.597 65.000 16.31 11.93 44.54 3.51
1253 2482 0.609681 GTGAGACGAGGGTCCTCACT 60.610 60.000 16.31 13.67 44.54 3.41
1254 2483 0.989602 TGAGACGAGGGTCCTCACTA 59.010 55.000 16.31 3.39 44.54 2.74
1255 2484 1.353358 TGAGACGAGGGTCCTCACTAA 59.647 52.381 16.31 6.11 44.54 2.24
1256 2485 2.018515 GAGACGAGGGTCCTCACTAAG 58.981 57.143 16.31 3.11 44.54 2.18
1257 2486 1.634459 AGACGAGGGTCCTCACTAAGA 59.366 52.381 16.31 0.00 44.54 2.10
1328 2586 1.459209 CGTGTGCTTGCTCAACGATTA 59.541 47.619 0.00 0.00 0.00 1.75
1338 2596 3.171277 GCTCAACGATTATTTGTGGTGC 58.829 45.455 0.00 0.00 0.00 5.01
1353 2611 3.243128 TGCTGTTGATGCACGACG 58.757 55.556 0.00 0.00 35.31 5.12
1373 2631 1.026182 ACGACGTACAGGCCGATGTA 61.026 55.000 0.00 0.00 34.56 2.29
1376 2634 1.108776 ACGTACAGGCCGATGTATGT 58.891 50.000 19.39 19.39 46.26 2.29
1442 2700 8.248117 AGAACATAGTGGTTTTTATGTACGAC 57.752 34.615 0.00 0.00 39.04 4.34
1599 2892 8.601845 ATGTAAAGAATGCATAGCGTTGTATA 57.398 30.769 0.00 0.00 37.94 1.47
1604 2897 6.390721 AGAATGCATAGCGTTGTATACCTAG 58.609 40.000 0.00 0.00 37.94 3.02
1605 2898 5.723672 ATGCATAGCGTTGTATACCTAGT 57.276 39.130 0.00 0.00 0.00 2.57
1628 2924 7.571919 AGTTTCCTACAATGACTGATGATCAT 58.428 34.615 8.25 8.25 38.47 2.45
1642 2938 9.941325 GACTGATGATCATCTTTATTACAGGAT 57.059 33.333 30.65 8.04 38.60 3.24
1657 2953 0.249398 AGGATTACACCGGTGAGCAC 59.751 55.000 40.21 25.07 34.73 4.40
1849 3156 6.638468 CCTTGTACTTCAGCTGATTTGTTTTC 59.362 38.462 19.04 10.88 0.00 2.29
1855 3162 8.089115 ACTTCAGCTGATTTGTTTTCTAGTAC 57.911 34.615 19.04 0.00 0.00 2.73
1992 3303 6.473455 CGAAAATGGTATGCATCCTTTCTTTC 59.527 38.462 0.19 9.39 0.00 2.62
2319 3643 5.041940 GGAAGACAGGTACGTAATAAGCAG 58.958 45.833 0.00 0.00 0.00 4.24
2337 3976 4.458951 GCAGCAGCTGTAATACATGTAC 57.541 45.455 23.60 0.00 37.91 2.90
2338 3977 4.122776 GCAGCAGCTGTAATACATGTACT 58.877 43.478 23.60 0.00 37.91 2.73
2339 3978 5.289595 GCAGCAGCTGTAATACATGTACTA 58.710 41.667 23.60 0.00 37.91 1.82
2340 3979 5.175856 GCAGCAGCTGTAATACATGTACTAC 59.824 44.000 23.60 15.81 37.91 2.73
2341 3980 6.273071 CAGCAGCTGTAATACATGTACTACA 58.727 40.000 22.06 22.06 0.00 2.74
2342 3981 6.925718 CAGCAGCTGTAATACATGTACTACAT 59.074 38.462 23.25 10.37 39.91 2.29
2343 3982 7.439356 CAGCAGCTGTAATACATGTACTACATT 59.561 37.037 23.25 14.10 36.53 2.71
2344 3983 8.638873 AGCAGCTGTAATACATGTACTACATTA 58.361 33.333 23.25 10.07 36.53 1.90
2345 3984 8.700644 GCAGCTGTAATACATGTACTACATTAC 58.299 37.037 23.25 19.56 36.53 1.89
2370 4172 9.877178 ACTTCAAGTTTGTATCTGTTATCTAGG 57.123 33.333 0.00 0.00 0.00 3.02
2384 4186 9.072375 TCTGTTATCTAGGAGTACAATCATGAG 57.928 37.037 0.09 0.00 0.00 2.90
2388 4190 6.716934 TCTAGGAGTACAATCATGAGGTTC 57.283 41.667 0.09 0.30 0.00 3.62
2404 4206 5.734720 TGAGGTTCGCTTTCTATTCTGAAT 58.265 37.500 8.14 8.14 0.00 2.57
2408 4210 6.481644 AGGTTCGCTTTCTATTCTGAATCATC 59.518 38.462 6.10 0.00 0.00 2.92
2410 4212 4.984785 TCGCTTTCTATTCTGAATCATCGG 59.015 41.667 6.10 0.00 0.00 4.18
2411 4213 4.984785 CGCTTTCTATTCTGAATCATCGGA 59.015 41.667 6.10 0.00 39.22 4.55
2412 4214 5.636965 CGCTTTCTATTCTGAATCATCGGAT 59.363 40.000 6.10 0.00 40.61 4.18
2413 4215 6.183360 CGCTTTCTATTCTGAATCATCGGATC 60.183 42.308 6.10 0.00 40.61 3.36
2414 4216 6.183360 GCTTTCTATTCTGAATCATCGGATCG 60.183 42.308 6.10 0.00 40.61 3.69
2521 4420 1.280998 CCCCCAAACGAGTCCAGTATT 59.719 52.381 0.00 0.00 0.00 1.89
2524 4423 1.737793 CCAAACGAGTCCAGTATTGGC 59.262 52.381 0.00 0.00 44.63 4.52
2609 4508 4.471904 TTCGATCCTGCAAAGTCATACT 57.528 40.909 0.00 0.00 0.00 2.12
2610 4509 4.046938 TCGATCCTGCAAAGTCATACTC 57.953 45.455 0.00 0.00 0.00 2.59
2614 4513 2.906389 TCCTGCAAAGTCATACTCCAGT 59.094 45.455 0.00 0.00 0.00 4.00
2615 4514 3.327757 TCCTGCAAAGTCATACTCCAGTT 59.672 43.478 0.00 0.00 0.00 3.16
2617 4516 5.189736 TCCTGCAAAGTCATACTCCAGTTAT 59.810 40.000 0.00 0.00 0.00 1.89
2618 4517 5.882557 CCTGCAAAGTCATACTCCAGTTATT 59.117 40.000 0.00 0.00 0.00 1.40
2619 4518 6.375455 CCTGCAAAGTCATACTCCAGTTATTT 59.625 38.462 0.00 0.00 0.00 1.40
2778 5033 8.553459 TTTGTTTTTCCAAATTTGTCTGCTAA 57.447 26.923 16.73 1.98 29.67 3.09
2779 5034 7.532682 TGTTTTTCCAAATTTGTCTGCTAAC 57.467 32.000 16.73 12.26 0.00 2.34
2780 5035 7.327214 TGTTTTTCCAAATTTGTCTGCTAACT 58.673 30.769 16.73 0.00 0.00 2.24
2781 5036 8.470805 TGTTTTTCCAAATTTGTCTGCTAACTA 58.529 29.630 16.73 3.24 0.00 2.24
3062 5331 4.644234 TCACATAAATATGCAACACCCTGG 59.356 41.667 0.00 0.00 37.19 4.45
3126 5452 2.594303 CCAACTGCCAGGTGCGAA 60.594 61.111 3.60 0.00 45.60 4.70
3329 5678 0.251354 CACTGCAGTACATGGGAGCT 59.749 55.000 21.20 0.00 0.00 4.09
3330 5679 0.251354 ACTGCAGTACATGGGAGCTG 59.749 55.000 20.16 2.60 0.00 4.24
3331 5680 0.251354 CTGCAGTACATGGGAGCTGT 59.749 55.000 5.25 0.00 0.00 4.40
3332 5681 1.482182 CTGCAGTACATGGGAGCTGTA 59.518 52.381 5.25 0.00 0.00 2.74
3333 5682 1.207089 TGCAGTACATGGGAGCTGTAC 59.793 52.381 0.00 0.00 45.99 2.90
3335 5684 2.973420 GTACATGGGAGCTGTACGC 58.027 57.895 0.00 2.08 39.51 4.42
3336 5685 0.529992 GTACATGGGAGCTGTACGCC 60.530 60.000 0.00 0.00 39.51 5.68
3337 5686 0.686441 TACATGGGAGCTGTACGCCT 60.686 55.000 0.00 0.00 40.39 5.52
3391 5742 8.721133 AGACCTCATATATGGTGTACATACAA 57.279 34.615 12.78 0.00 44.41 2.41
3505 5876 6.073819 GCTCGTGCCTTTGTAAATCAAATTTT 60.074 34.615 0.00 0.00 43.78 1.82
3574 5949 3.884693 TGAATGTCTTTGCATGACAGTGT 59.115 39.130 21.94 12.93 45.88 3.55
3667 6054 0.541392 GGGCCAAAATTGATGACCCC 59.459 55.000 4.39 5.09 0.00 4.95
3727 6125 4.677378 CCAAGATCACTTCGTAAGCTATCG 59.323 45.833 0.00 4.42 33.70 2.92
3757 6155 9.282247 CTAACAAGATGAGAATACAATGTTTGC 57.718 33.333 0.00 0.00 32.20 3.68
4049 6448 3.034635 CAGGAATAGCCAGTACCAGTCT 58.965 50.000 0.00 0.00 40.02 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.201950 GCTGGATGTCAATTGGTGTGATAC 60.202 45.833 5.42 0.00 0.00 2.24
34 35 5.004156 GCATTGATGAAGAGAAAATCGTTGC 59.996 40.000 0.00 0.00 0.00 4.17
38 39 5.296283 AGGAGCATTGATGAAGAGAAAATCG 59.704 40.000 0.00 0.00 0.00 3.34
49 51 3.764972 TGCAATCAAAGGAGCATTGATGA 59.235 39.130 2.81 0.00 44.53 2.92
70 72 5.880054 AGAATACTTTTGGTTCCGTGATG 57.120 39.130 0.00 0.00 0.00 3.07
130 132 8.327941 TCCAGATCATTCTTTCAACTACAAAG 57.672 34.615 0.00 0.00 32.89 2.77
140 142 5.405797 GCACCTTTTCCAGATCATTCTTTC 58.594 41.667 0.00 0.00 0.00 2.62
153 155 8.503196 CAATTTGTTTTATAAGGCACCTTTTCC 58.497 33.333 7.35 0.00 37.47 3.13
159 161 5.164954 TCGCAATTTGTTTTATAAGGCACC 58.835 37.500 0.00 0.00 0.00 5.01
162 164 5.569823 TCGTTCGCAATTTGTTTTATAAGGC 59.430 36.000 0.00 0.00 0.00 4.35
327 329 5.522456 TCACTAGCAACTGAAAAATGCAAG 58.478 37.500 0.00 0.00 42.45 4.01
423 1083 0.928229 AAATAGAATGCGCGACGACC 59.072 50.000 12.10 0.00 0.00 4.79
465 1140 4.799473 CACGCAAGCGCACGATGG 62.799 66.667 21.60 8.71 44.19 3.51
470 1145 0.865639 AAAAACTCACGCAAGCGCAC 60.866 50.000 15.09 0.00 44.19 5.34
643 1360 2.117941 GACACAGCTCCGTGGTTTGC 62.118 60.000 8.85 0.00 41.38 3.68
768 1914 3.059166 CAGTTTCCCATTTTTGGCTTCG 58.941 45.455 0.00 0.00 0.00 3.79
795 1942 3.350612 TTTGCGTGGCGTACTGGC 61.351 61.111 4.70 4.70 45.12 4.85
796 1943 2.554272 GTTTGCGTGGCGTACTGG 59.446 61.111 0.00 0.00 0.00 4.00
797 1944 2.554272 GGTTTGCGTGGCGTACTG 59.446 61.111 0.00 0.00 0.00 2.74
798 1945 2.667199 GGGTTTGCGTGGCGTACT 60.667 61.111 0.00 0.00 0.00 2.73
799 1946 3.729698 GGGGTTTGCGTGGCGTAC 61.730 66.667 0.00 0.00 0.00 3.67
800 1947 4.251771 TGGGGTTTGCGTGGCGTA 62.252 61.111 0.00 0.00 0.00 4.42
848 1995 3.764466 AGTTCTCGCTCGGGCAGG 61.764 66.667 8.62 0.00 38.60 4.85
849 1996 2.507992 CAGTTCTCGCTCGGGCAG 60.508 66.667 8.62 3.99 38.60 4.85
850 1997 4.742201 GCAGTTCTCGCTCGGGCA 62.742 66.667 8.62 0.00 38.60 5.36
851 1998 2.945398 CTAGCAGTTCTCGCTCGGGC 62.945 65.000 0.00 0.00 40.96 6.13
852 1999 1.064946 CTAGCAGTTCTCGCTCGGG 59.935 63.158 0.00 0.00 40.96 5.14
853 2000 1.064946 CCTAGCAGTTCTCGCTCGG 59.935 63.158 0.00 0.00 40.96 4.63
868 2023 1.135489 GTGAAGTGTGATCGTCGCCTA 60.135 52.381 0.00 0.00 0.00 3.93
1244 2473 4.081642 TGCATTAGTGTCTTAGTGAGGACC 60.082 45.833 0.00 0.00 0.00 4.46
1252 2481 3.775202 ACGAGCTGCATTAGTGTCTTAG 58.225 45.455 1.02 0.00 0.00 2.18
1253 2482 3.868757 ACGAGCTGCATTAGTGTCTTA 57.131 42.857 1.02 0.00 0.00 2.10
1254 2483 2.751166 ACGAGCTGCATTAGTGTCTT 57.249 45.000 1.02 0.00 0.00 3.01
1255 2484 5.241728 TGATATACGAGCTGCATTAGTGTCT 59.758 40.000 1.02 0.00 0.00 3.41
1256 2485 5.461526 TGATATACGAGCTGCATTAGTGTC 58.538 41.667 1.02 0.00 0.00 3.67
1257 2486 5.453567 TGATATACGAGCTGCATTAGTGT 57.546 39.130 1.02 0.00 0.00 3.55
1328 2586 1.687660 TGCATCAACAGCACCACAAAT 59.312 42.857 0.00 0.00 37.02 2.32
1338 2596 1.001745 TCGTCGTCGTGCATCAACAG 61.002 55.000 1.33 0.00 38.33 3.16
1353 2611 1.585521 CATCGGCCTGTACGTCGTC 60.586 63.158 0.00 0.00 0.00 4.20
1373 2631 0.102481 GGATCTGGTACGCGTGACAT 59.898 55.000 24.59 6.41 0.00 3.06
1376 2634 0.678684 TCAGGATCTGGTACGCGTGA 60.679 55.000 24.59 11.18 31.51 4.35
1442 2700 1.069765 AGGGCTGTTGGCGATATCG 59.930 57.895 20.79 20.79 42.94 2.92
1569 2862 6.489675 ACGCTATGCATTCTTTACATCAAAG 58.510 36.000 3.54 0.00 44.36 2.77
1589 2882 5.653769 TGTAGGAAACTAGGTATACAACGCT 59.346 40.000 5.01 0.00 45.49 5.07
1599 2892 6.440647 TCATCAGTCATTGTAGGAAACTAGGT 59.559 38.462 0.00 0.00 45.49 3.08
1604 2897 7.714377 AGATGATCATCAGTCATTGTAGGAAAC 59.286 37.037 31.99 4.61 40.22 2.78
1605 2898 7.799081 AGATGATCATCAGTCATTGTAGGAAA 58.201 34.615 31.99 0.00 40.22 3.13
1628 2924 6.154877 TCACCGGTGTAATCCTGTAATAAAGA 59.845 38.462 32.74 5.12 0.00 2.52
1642 2938 1.007038 GACGTGCTCACCGGTGTAA 60.007 57.895 32.74 17.31 0.00 2.41
1657 2953 4.846137 GCATACAAGTTTTTAGCAGTGACG 59.154 41.667 0.00 0.00 0.00 4.35
2022 3337 9.948964 TCAGATTCAAAAACAATAGAGATCTCA 57.051 29.630 24.39 10.95 0.00 3.27
2028 3343 8.909671 GCTGTTTCAGATTCAAAAACAATAGAG 58.090 33.333 13.95 6.79 41.04 2.43
2029 3344 8.412456 TGCTGTTTCAGATTCAAAAACAATAGA 58.588 29.630 13.95 1.79 41.04 1.98
2030 3345 8.578308 TGCTGTTTCAGATTCAAAAACAATAG 57.422 30.769 13.95 7.27 41.04 1.73
2319 3643 7.715265 AATGTAGTACATGTATTACAGCTGC 57.285 36.000 31.91 18.31 40.13 5.25
2344 3983 9.877178 CCTAGATAACAGATACAAACTTGAAGT 57.123 33.333 0.00 0.00 0.00 3.01
2347 3986 9.256228 ACTCCTAGATAACAGATACAAACTTGA 57.744 33.333 0.00 0.00 0.00 3.02
2360 4162 7.785028 ACCTCATGATTGTACTCCTAGATAACA 59.215 37.037 0.00 0.00 0.00 2.41
2367 4169 4.202121 GCGAACCTCATGATTGTACTCCTA 60.202 45.833 0.00 0.00 0.00 2.94
2368 4170 3.430929 GCGAACCTCATGATTGTACTCCT 60.431 47.826 0.00 0.00 0.00 3.69
2369 4171 2.866762 GCGAACCTCATGATTGTACTCC 59.133 50.000 0.00 0.00 0.00 3.85
2370 4172 3.786635 AGCGAACCTCATGATTGTACTC 58.213 45.455 0.00 0.00 0.00 2.59
2371 4173 3.895232 AGCGAACCTCATGATTGTACT 57.105 42.857 0.00 0.00 0.00 2.73
2372 4174 4.631813 AGAAAGCGAACCTCATGATTGTAC 59.368 41.667 0.00 0.00 0.00 2.90
2384 4186 6.563010 CGATGATTCAGAATAGAAAGCGAACC 60.563 42.308 0.00 0.00 0.00 3.62
2388 4190 4.984785 TCCGATGATTCAGAATAGAAAGCG 59.015 41.667 0.00 0.00 0.00 4.68
2410 4212 2.545946 GCAAGTTAAGCAGGATCCGATC 59.454 50.000 5.98 0.00 0.00 3.69
2411 4213 2.092968 TGCAAGTTAAGCAGGATCCGAT 60.093 45.455 5.98 0.00 37.02 4.18
2412 4214 1.277842 TGCAAGTTAAGCAGGATCCGA 59.722 47.619 5.98 0.00 37.02 4.55
2413 4215 1.737838 TGCAAGTTAAGCAGGATCCG 58.262 50.000 5.98 2.47 37.02 4.18
2521 4420 1.576577 ACTCCATGACATGAGAGCCA 58.423 50.000 23.17 2.24 33.57 4.75
2524 4423 4.343239 TCACCATACTCCATGACATGAGAG 59.657 45.833 22.29 22.29 36.69 3.20
2609 4508 1.003118 ACGCTGCCTGAAATAACTGGA 59.997 47.619 0.00 0.00 0.00 3.86
2610 4509 1.453155 ACGCTGCCTGAAATAACTGG 58.547 50.000 0.00 0.00 0.00 4.00
2614 4513 2.346099 GCAAACGCTGCCTGAAATAA 57.654 45.000 0.00 0.00 46.13 1.40
2778 5033 7.492524 TGAAAGCGAGAAGATACATCATTAGT 58.507 34.615 0.00 0.00 0.00 2.24
2779 5034 7.651304 ACTGAAAGCGAGAAGATACATCATTAG 59.349 37.037 0.00 0.00 37.60 1.73
2780 5035 7.492524 ACTGAAAGCGAGAAGATACATCATTA 58.507 34.615 0.00 0.00 37.60 1.90
2781 5036 6.344500 ACTGAAAGCGAGAAGATACATCATT 58.656 36.000 0.00 0.00 37.60 2.57
2851 5120 3.070018 AGCACAGTTTCTTTGATCTCCG 58.930 45.455 0.00 0.00 0.00 4.63
3062 5331 1.801178 CAACCGGAAGCAGAAAGAGTC 59.199 52.381 9.46 0.00 0.00 3.36
3126 5452 1.272490 TCCGCACTGAGACTCGAAAAT 59.728 47.619 0.00 0.00 0.00 1.82
3330 5679 1.664151 GAGCATTTGGTACAGGCGTAC 59.336 52.381 9.98 9.98 46.18 3.67
3331 5680 1.406341 GGAGCATTTGGTACAGGCGTA 60.406 52.381 0.00 0.00 42.39 4.42
3332 5681 0.676782 GGAGCATTTGGTACAGGCGT 60.677 55.000 0.00 0.00 42.39 5.68
3333 5682 0.676466 TGGAGCATTTGGTACAGGCG 60.676 55.000 0.00 0.00 42.39 5.52
3334 5683 3.264574 TGGAGCATTTGGTACAGGC 57.735 52.632 0.00 0.00 42.39 4.85
3337 5686 1.985159 ACCTCTGGAGCATTTGGTACA 59.015 47.619 0.00 0.00 34.79 2.90
3505 5876 5.465532 TTGCCTTTCAATTGATTGCAGTA 57.534 34.783 19.73 9.48 37.68 2.74
3667 6054 4.653341 AGGAGGATCACTACCAAATCAGAG 59.347 45.833 0.00 0.00 36.25 3.35
3727 6125 6.668541 TTGTATTCTCATCTTGTTAGCAGC 57.331 37.500 0.00 0.00 0.00 5.25
3757 6155 1.594862 GCATGGTCCGAAGAAGATTCG 59.405 52.381 3.13 3.13 41.21 3.34
4027 6426 3.031736 GACTGGTACTGGCTATTCCTGA 58.968 50.000 0.00 0.00 37.25 3.86
4140 6539 6.068461 TGGAGGCAAGTAAAATATACACCA 57.932 37.500 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.