Multiple sequence alignment - TraesCS4A01G288700

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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 TraesCS4A01G288700 chr4A 100.000 4611 0 0 1 4611 593358505 593353895 0.000000e+00 8516.0
1 TraesCS4A01G288700 chr4A 83.687 1367 203 14 2242 3598 43233066 43231710 0.000000e+00 1271.0
2 TraesCS4A01G288700 chr4A 77.967 1348 261 30 2232 3563 550482520 550481193 0.000000e+00 811.0
3 TraesCS4A01G288700 chr4A 84.229 558 88 0 1676 2233 43233727 43233170 1.130000e-150 544.0
4 TraesCS4A01G288700 chr4A 83.186 452 73 2 1677 2125 550483260 550482809 1.190000e-110 411.0
5 TraesCS4A01G288700 chr4A 88.660 291 30 3 1121 1409 43235711 43235422 7.340000e-93 351.0
6 TraesCS4A01G288700 chr4A 96.791 187 6 0 115 301 624872445 624872259 3.460000e-81 313.0
7 TraesCS4A01G288700 chr4A 96.257 187 6 1 115 301 624896097 624895912 5.800000e-79 305.0
8 TraesCS4A01G288700 chr4A 95.722 187 8 0 115 301 8358485 8358299 7.500000e-78 302.0
9 TraesCS4A01G288700 chr4A 96.552 116 4 0 1 116 624872760 624872645 4.710000e-45 193.0
10 TraesCS4A01G288700 chr4A 96.552 116 4 0 1 116 624896412 624896297 4.710000e-45 193.0
11 TraesCS4A01G288700 chr4A 94.828 116 6 0 1 116 8358804 8358689 1.020000e-41 182.0
12 TraesCS4A01G288700 chr4D 94.657 2508 111 14 1529 4019 10250147 10252648 0.000000e+00 3868.0
13 TraesCS4A01G288700 chr4D 83.663 1365 201 16 2236 3589 420942842 420944195 0.000000e+00 1266.0
14 TraesCS4A01G288700 chr4D 85.068 1259 96 39 302 1528 10248769 10249967 0.000000e+00 1199.0
15 TraesCS4A01G288700 chr4D 78.561 1348 246 33 2236 3563 47535720 47534396 0.000000e+00 848.0
16 TraesCS4A01G288700 chr4D 83.498 606 78 16 4013 4610 10253016 10253607 3.140000e-151 545.0
17 TraesCS4A01G288700 chr4D 83.662 557 91 0 1677 2233 420942187 420942743 4.090000e-145 525.0
18 TraesCS4A01G288700 chr4D 83.628 452 71 1 1677 2125 47536520 47536069 5.520000e-114 422.0
19 TraesCS4A01G288700 chr4D 87.973 291 32 3 1121 1409 420940097 420940386 1.590000e-89 340.0
20 TraesCS4A01G288700 chr4D 87.000 100 4 3 607 706 10248778 10248868 2.270000e-18 104.0
21 TraesCS4A01G288700 chr4B 95.512 2362 83 12 1672 4019 19736095 19738447 0.000000e+00 3753.0
22 TraesCS4A01G288700 chr4B 83.798 1364 201 14 2236 3589 518098133 518099486 0.000000e+00 1277.0
23 TraesCS4A01G288700 chr4B 89.277 802 31 28 607 1401 19735143 19735896 0.000000e+00 953.0
24 TraesCS4A01G288700 chr4B 77.803 1347 252 35 2236 3560 69378927 69380248 0.000000e+00 787.0
25 TraesCS4A01G288700 chr4B 84.530 543 81 3 1672 2212 518097469 518098010 6.790000e-148 534.0
26 TraesCS4A01G288700 chr4B 88.811 429 35 12 4100 4525 19739144 19739562 8.850000e-142 514.0
27 TraesCS4A01G288700 chr4B 83.641 434 68 1 1677 2107 69378047 69378480 5.560000e-109 405.0
28 TraesCS4A01G288700 chr4B 84.571 350 41 10 1070 1409 518095347 518095693 7.390000e-88 335.0
29 TraesCS4A01G288700 chr4B 85.915 284 30 9 1121 1399 69375934 69376212 1.250000e-75 294.0
30 TraesCS4A01G288700 chr5A 99.003 301 3 0 1 301 559581286 559581586 1.460000e-149 540.0
31 TraesCS4A01G288700 chr7D 96.410 195 6 1 112 306 462069679 462069486 2.070000e-83 320.0
32 TraesCS4A01G288700 chr7D 97.414 116 3 0 1 116 462069992 462069877 1.010000e-46 198.0
33 TraesCS4A01G288700 chr7D 90.909 55 5 0 1574 1628 44291977 44291923 1.780000e-09 75.0
34 TraesCS4A01G288700 chr7A 95.312 192 9 0 112 303 35656840 35657031 5.800000e-79 305.0
35 TraesCS4A01G288700 chr7A 98.276 116 2 0 1 116 35656527 35656642 2.170000e-48 204.0
36 TraesCS4A01G288700 chr6D 77.532 543 99 22 3001 3533 389370151 389370680 5.800000e-79 305.0
37 TraesCS4A01G288700 chr6D 73.008 778 187 19 2232 2999 389369302 389370066 7.660000e-63 252.0
38 TraesCS4A01G288700 chr6D 80.645 341 50 13 1082 1418 389367204 389367532 2.750000e-62 250.0
39 TraesCS4A01G288700 chr1A 95.263 190 9 0 115 304 508553284 508553095 7.500000e-78 302.0
40 TraesCS4A01G288700 chr1A 95.263 190 8 1 112 301 570183874 570184062 2.700000e-77 300.0
41 TraesCS4A01G288700 chr1A 94.737 190 10 0 112 301 569195706 569195895 3.490000e-76 296.0
42 TraesCS4A01G288700 chr1A 95.690 116 3 1 1 116 569195397 569195510 7.880000e-43 185.0
43 TraesCS4A01G288700 chr1A 94.828 116 6 0 1 116 56446155 56446270 1.020000e-41 182.0
44 TraesCS4A01G288700 chr1A 93.966 116 7 0 1 116 508553591 508553476 4.740000e-40 176.0
45 TraesCS4A01G288700 chr6B 80.409 342 50 14 1082 1419 582397847 582398175 1.280000e-60 244.0
46 TraesCS4A01G288700 chr6B 79.612 103 11 10 4454 4554 290236501 290236595 1.070000e-06 65.8
47 TraesCS4A01G288700 chr3D 81.063 301 47 8 1123 1419 578422903 578422609 9.980000e-57 231.0
48 TraesCS4A01G288700 chr3B 84.694 196 22 2 2465 2653 104157461 104157655 6.090000e-44 189.0
49 TraesCS4A01G288700 chr3B 88.889 54 2 4 4500 4552 236176697 236176747 3.850000e-06 63.9
50 TraesCS4A01G288700 chr1D 93.617 47 0 1 4509 4552 474239002 474239048 2.980000e-07 67.6
51 TraesCS4A01G288700 chr1D 81.818 77 11 3 4478 4552 10511020 10510945 1.390000e-05 62.1
52 TraesCS4A01G288700 chr7B 83.784 74 7 5 4479 4552 389086399 389086467 1.070000e-06 65.8
53 TraesCS4A01G288700 chr7B 90.196 51 3 2 4502 4552 516462490 516462538 1.070000e-06 65.8
54 TraesCS4A01G288700 chr7B 91.667 48 2 2 4505 4552 718831218 718831263 1.070000e-06 65.8
55 TraesCS4A01G288700 chr1B 89.583 48 3 2 4505 4552 603565472 603565517 4.980000e-05 60.2


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 TraesCS4A01G288700 chr4A 593353895 593358505 4610 True 8516.000000 8516 100.000000 1 4611 1 chr4A.!!$R1 4610
1 TraesCS4A01G288700 chr4A 43231710 43235711 4001 True 722.000000 1271 85.525333 1121 3598 3 chr4A.!!$R3 2477
2 TraesCS4A01G288700 chr4A 550481193 550483260 2067 True 611.000000 811 80.576500 1677 3563 2 chr4A.!!$R4 1886
3 TraesCS4A01G288700 chr4A 624872259 624872760 501 True 253.000000 313 96.671500 1 301 2 chr4A.!!$R5 300
4 TraesCS4A01G288700 chr4A 624895912 624896412 500 True 249.000000 305 96.404500 1 301 2 chr4A.!!$R6 300
5 TraesCS4A01G288700 chr4A 8358299 8358804 505 True 242.000000 302 95.275000 1 301 2 chr4A.!!$R2 300
6 TraesCS4A01G288700 chr4D 10248769 10253607 4838 False 1429.000000 3868 87.555750 302 4610 4 chr4D.!!$F1 4308
7 TraesCS4A01G288700 chr4D 420940097 420944195 4098 False 710.333333 1266 85.099333 1121 3589 3 chr4D.!!$F2 2468
8 TraesCS4A01G288700 chr4D 47534396 47536520 2124 True 635.000000 848 81.094500 1677 3563 2 chr4D.!!$R1 1886
9 TraesCS4A01G288700 chr4B 19735143 19739562 4419 False 1740.000000 3753 91.200000 607 4525 3 chr4B.!!$F1 3918
10 TraesCS4A01G288700 chr4B 518095347 518099486 4139 False 715.333333 1277 84.299667 1070 3589 3 chr4B.!!$F3 2519
11 TraesCS4A01G288700 chr4B 69375934 69380248 4314 False 495.333333 787 82.453000 1121 3560 3 chr4B.!!$F2 2439
12 TraesCS4A01G288700 chr7D 462069486 462069992 506 True 259.000000 320 96.912000 1 306 2 chr7D.!!$R2 305
13 TraesCS4A01G288700 chr7A 35656527 35657031 504 False 254.500000 305 96.794000 1 303 2 chr7A.!!$F1 302
14 TraesCS4A01G288700 chr6D 389367204 389370680 3476 False 269.000000 305 77.061667 1082 3533 3 chr6D.!!$F1 2451

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
493 700 1.153086 ATGAGTTGCAGATCCGGCC 60.153 57.895 0.00 0.0 0.00 6.13 F
1043 1275 1.519234 TGCTCATGGCGACGATCAC 60.519 57.895 0.00 0.0 45.43 3.06 F
1428 1669 0.458889 TAGCCGCCGTTCATGTACAC 60.459 55.000 0.00 0.0 0.00 2.90 F
2146 5453 0.834687 TGAAAGGGTACGTGGCCTCT 60.835 55.000 3.32 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1650 0.458889 GTGTACATGAACGGCGGCTA 60.459 55.000 13.24 0.00 0.00 3.93 R
1987 5137 1.004679 GAACGGCGGGTTGAAGGTA 60.005 57.895 13.24 0.00 39.50 3.08 R
3355 7299 0.037326 GGAACATCAGCACCGAGTGA 60.037 55.000 8.04 0.00 35.23 3.41 R
4069 8414 1.590259 GATCGTCTGGCCTTCGCTC 60.590 63.158 3.32 3.66 34.44 5.03 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
70 71 2.196925 ATGCCTCCGCCTACTCGAG 61.197 63.158 11.84 11.84 0.00 4.04
388 595 9.947433 AAAAATGAAATCCTGCTATTCAAATCA 57.053 25.926 0.00 0.00 36.72 2.57
391 598 5.653330 TGAAATCCTGCTATTCAAATCAGCA 59.347 36.000 0.00 0.00 42.77 4.41
415 622 5.638596 ATCCCCGTGTAGAAATGAAAAAC 57.361 39.130 0.00 0.00 0.00 2.43
493 700 1.153086 ATGAGTTGCAGATCCGGCC 60.153 57.895 0.00 0.00 0.00 6.13
530 739 2.185004 ATGTAATAGATGTGCGGCCC 57.815 50.000 0.00 0.00 0.00 5.80
536 745 4.114997 GATGTGCGGCCCGGTTTG 62.115 66.667 4.77 0.00 0.00 2.93
581 790 8.571461 TTCAGATTTGAACATCTCATTTAGCT 57.429 30.769 0.00 0.00 38.37 3.32
586 795 7.509141 TTTGAACATCTCATTTAGCTTCACA 57.491 32.000 0.00 0.00 32.78 3.58
593 802 4.225942 TCTCATTTAGCTTCACATCACCCT 59.774 41.667 0.00 0.00 0.00 4.34
630 852 7.999450 TGGCAGAATATTAATGTCATGCATA 57.001 32.000 17.50 8.00 36.67 3.14
804 1031 9.988350 CAATTAATGTCCAGTAGAAATACACAC 57.012 33.333 0.00 0.00 0.00 3.82
805 1032 9.733556 AATTAATGTCCAGTAGAAATACACACA 57.266 29.630 0.00 0.00 0.00 3.72
812 1039 7.491696 GTCCAGTAGAAATACACACAATCCTAC 59.508 40.741 0.00 0.00 0.00 3.18
960 1191 4.871871 TCCCATCTTCTCTCTCTGTACT 57.128 45.455 0.00 0.00 0.00 2.73
961 1192 4.787551 TCCCATCTTCTCTCTCTGTACTC 58.212 47.826 0.00 0.00 0.00 2.59
962 1193 3.563808 CCCATCTTCTCTCTCTGTACTCG 59.436 52.174 0.00 0.00 0.00 4.18
963 1194 4.196193 CCATCTTCTCTCTCTGTACTCGT 58.804 47.826 0.00 0.00 0.00 4.18
964 1195 4.272504 CCATCTTCTCTCTCTGTACTCGTC 59.727 50.000 0.00 0.00 0.00 4.20
966 1197 3.261137 TCTTCTCTCTCTGTACTCGTCCA 59.739 47.826 0.00 0.00 0.00 4.02
967 1198 3.916359 TCTCTCTCTGTACTCGTCCAT 57.084 47.619 0.00 0.00 0.00 3.41
968 1199 4.223556 TCTCTCTCTGTACTCGTCCATT 57.776 45.455 0.00 0.00 0.00 3.16
969 1200 5.354842 TCTCTCTCTGTACTCGTCCATTA 57.645 43.478 0.00 0.00 0.00 1.90
970 1201 5.742063 TCTCTCTCTGTACTCGTCCATTAA 58.258 41.667 0.00 0.00 0.00 1.40
971 1202 5.585445 TCTCTCTCTGTACTCGTCCATTAAC 59.415 44.000 0.00 0.00 0.00 2.01
972 1203 5.250982 TCTCTCTGTACTCGTCCATTAACA 58.749 41.667 0.00 0.00 0.00 2.41
973 1204 5.708697 TCTCTCTGTACTCGTCCATTAACAA 59.291 40.000 0.00 0.00 0.00 2.83
974 1205 6.377429 TCTCTCTGTACTCGTCCATTAACAAT 59.623 38.462 0.00 0.00 0.00 2.71
975 1206 6.931838 TCTCTGTACTCGTCCATTAACAATT 58.068 36.000 0.00 0.00 0.00 2.32
1041 1273 2.580470 CGTGCTCATGGCGACGATC 61.580 63.158 17.40 0.00 43.02 3.69
1043 1275 1.519234 TGCTCATGGCGACGATCAC 60.519 57.895 0.00 0.00 45.43 3.06
1373 1614 2.405594 CGCCTCCTTCGACGAGAG 59.594 66.667 9.75 7.05 0.00 3.20
1409 1650 2.434185 CCAGGTATGCACGCACGT 60.434 61.111 0.00 0.00 0.00 4.49
1410 1651 1.153726 CCAGGTATGCACGCACGTA 60.154 57.895 0.00 0.00 0.00 3.57
1411 1652 1.145759 CCAGGTATGCACGCACGTAG 61.146 60.000 0.00 0.00 0.00 3.51
1412 1653 1.518572 AGGTATGCACGCACGTAGC 60.519 57.895 0.00 3.14 40.87 3.58
1414 1655 2.581138 TATGCACGCACGTAGCCG 60.581 61.111 12.62 0.00 41.38 5.52
1428 1669 0.458889 TAGCCGCCGTTCATGTACAC 60.459 55.000 0.00 0.00 0.00 2.90
1434 1675 2.029244 CGCCGTTCATGTACACTTCATC 59.971 50.000 0.00 0.00 0.00 2.92
1455 2332 3.877508 TCTTCGTATCTGCGAGATCTTCA 59.122 43.478 0.00 0.00 42.10 3.02
1466 2343 3.551863 GCGAGATCTTCATCGATCCAAGT 60.552 47.826 11.65 2.58 40.50 3.16
1469 2346 5.132897 AGATCTTCATCGATCCAAGTAGC 57.867 43.478 11.65 4.42 40.50 3.58
1567 3810 4.329256 GTGTTGCTAAATCTTAGTCGACCC 59.671 45.833 13.01 0.00 0.00 4.46
1615 4531 5.244785 TCTTGCGTAGAGATTCGTGTAAT 57.755 39.130 0.00 0.00 0.00 1.89
1661 4577 7.148306 GCGATAATTGGTCATCGGGTTATAATT 60.148 37.037 9.67 0.00 43.27 1.40
1666 4582 6.236558 TGGTCATCGGGTTATAATTGTACA 57.763 37.500 0.00 0.00 0.00 2.90
2089 5239 4.227134 CCTGCCTGCGCCGACTAT 62.227 66.667 4.18 0.00 0.00 2.12
2117 5267 2.359975 CCAAGACGTTCAGGGGGC 60.360 66.667 0.00 0.00 0.00 5.80
2131 5281 1.537643 GGGGCAATGGGGGTTGAAA 60.538 57.895 0.00 0.00 0.00 2.69
2146 5453 0.834687 TGAAAGGGTACGTGGCCTCT 60.835 55.000 3.32 0.00 0.00 3.69
2161 5468 1.515088 CTCTGACTGCGACGCGATT 60.515 57.895 15.93 0.76 0.00 3.34
2488 6334 0.888619 TCGTCCTGCTCAAGAACGAT 59.111 50.000 0.00 0.00 0.00 3.73
2528 6374 3.136123 GGTGGACGGTCGGATCGA 61.136 66.667 18.82 0.00 0.00 3.59
2616 6462 1.608717 GAGACCATCACGCCACTCCT 61.609 60.000 0.00 0.00 0.00 3.69
2653 6499 3.017265 GTCAAGGACGTAAGGTTCGAA 57.983 47.619 0.00 0.00 46.39 3.71
2866 6712 2.671070 CCGGTGATCCTGGTGCTT 59.329 61.111 0.00 0.00 0.00 3.91
3594 7542 0.593773 GAGATCAGCTTCGACGCCTC 60.594 60.000 10.66 6.23 0.00 4.70
3630 7584 4.673534 AGTTATTAGTCCGTTTTTGGCG 57.326 40.909 0.00 0.00 0.00 5.69
3668 7623 1.743623 CATAGCGGGTTGTTGCGGA 60.744 57.895 0.00 0.00 35.87 5.54
3684 7643 1.942586 GCGGAGACACAATTAACCGGT 60.943 52.381 0.00 0.00 40.55 5.28
3865 7833 1.382420 AAAACAGGCACAAGGGGCA 60.382 52.632 0.00 0.00 35.46 5.36
3868 7836 3.297620 CAGGCACAAGGGGCACAC 61.298 66.667 0.00 0.00 35.46 3.82
3890 7858 7.271223 CACACGTCTTTGAATTAATAAAGCCAG 59.729 37.037 6.01 3.59 34.67 4.85
3966 7934 6.740110 AGACAGAAATACATATCACGACTCC 58.260 40.000 0.00 0.00 0.00 3.85
3973 7941 2.230508 ACATATCACGACTCCAACACGT 59.769 45.455 0.00 0.00 40.87 4.49
3981 7949 1.219522 ACTCCAACACGTGCGCTAAC 61.220 55.000 17.22 0.00 0.00 2.34
4009 7977 1.335132 GGCCCCACAAGATCCGACTA 61.335 60.000 0.00 0.00 0.00 2.59
4019 8362 1.950909 AGATCCGACTAAAGAGCTCCG 59.049 52.381 10.93 5.41 0.00 4.63
4029 8372 2.338577 AAGAGCTCCGCATAAAGCAT 57.661 45.000 10.93 0.00 46.13 3.79
4054 8399 3.070576 GTTGCCCAGGCCATGACC 61.071 66.667 5.01 0.00 41.09 4.02
4090 8435 1.519455 CGAAGGCCAGACGATCCAC 60.519 63.158 5.01 0.00 0.00 4.02
4125 8716 6.038161 CCAAATGAATATACGCACTTTGAGGA 59.962 38.462 0.00 0.00 0.00 3.71
4126 8717 7.255242 CCAAATGAATATACGCACTTTGAGGAT 60.255 37.037 0.00 0.00 0.00 3.24
4127 8718 6.791887 ATGAATATACGCACTTTGAGGATG 57.208 37.500 0.00 0.00 0.00 3.51
4129 8720 1.668419 ATACGCACTTTGAGGATGGC 58.332 50.000 0.00 0.00 0.00 4.40
4130 8721 0.613260 TACGCACTTTGAGGATGGCT 59.387 50.000 0.00 0.00 0.00 4.75
4233 8825 7.651027 AATGTTTATGATTTCAGAGAAGGGG 57.349 36.000 0.00 0.00 0.00 4.79
4236 8828 3.967467 ATGATTTCAGAGAAGGGGCAT 57.033 42.857 0.00 0.00 0.00 4.40
4398 8994 9.825972 GAACATTTCTTTCTATTCGATGAACAA 57.174 29.630 0.00 0.00 0.00 2.83
4473 9069 9.574458 TTTGATGAACAAAAATTGTCTACGAAA 57.426 25.926 0.00 0.00 44.59 3.46
4532 9128 5.447624 AGAAAAACATAAACCGGTTCTGG 57.552 39.130 22.53 14.87 0.00 3.86
4560 9156 3.454858 TCTAGAACCTTCCAGCATTCCT 58.545 45.455 0.00 0.00 0.00 3.36
4564 9160 4.998051 AGAACCTTCCAGCATTCCTAAAA 58.002 39.130 0.00 0.00 0.00 1.52
4570 9166 3.364549 TCCAGCATTCCTAAAATGGGTG 58.635 45.455 0.45 0.00 0.00 4.61
4578 9174 2.307686 TCCTAAAATGGGTGTGGAGGAC 59.692 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 6.366604 GCTACCGAATCTAAATAGAAAGGCTC 59.633 42.308 0.00 0.00 35.69 4.70
167 374 9.271828 ACATTTTTGTCCATTTTAAGCCTTAAG 57.728 29.630 0.00 0.00 0.00 1.85
363 570 9.595823 CTGATTTGAATAGCAGGATTTCATTTT 57.404 29.630 0.00 0.00 0.00 1.82
376 583 4.095483 CGGGGATATGCTGATTTGAATAGC 59.905 45.833 0.00 0.00 37.93 2.97
388 595 3.646162 TCATTTCTACACGGGGATATGCT 59.354 43.478 0.00 0.00 0.00 3.79
391 598 6.887545 TGTTTTTCATTTCTACACGGGGATAT 59.112 34.615 0.00 0.00 0.00 1.63
432 639 9.567848 TGCGAATCTAAATGTTTTTCCTTTATC 57.432 29.630 0.00 0.00 0.00 1.75
437 644 8.655651 TTTTTGCGAATCTAAATGTTTTTCCT 57.344 26.923 0.00 0.00 0.00 3.36
488 695 2.595124 TATATGTGCATATCGGCCGG 57.405 50.000 27.83 10.44 35.71 6.13
489 696 3.982475 AGATATATGTGCATATCGGCCG 58.018 45.455 22.12 22.12 41.07 6.13
519 726 4.114997 CAAACCGGGCCGCACATC 62.115 66.667 23.20 0.00 0.00 3.06
581 790 2.885135 ATGCAAGAGGGTGATGTGAA 57.115 45.000 0.00 0.00 0.00 3.18
586 795 4.768968 GCCAAATATATGCAAGAGGGTGAT 59.231 41.667 0.00 0.00 0.00 3.06
665 887 8.555361 GCAGATTTGAATAGTACTGAGGATTTC 58.445 37.037 5.39 0.41 0.00 2.17
666 888 8.049117 TGCAGATTTGAATAGTACTGAGGATTT 58.951 33.333 5.39 0.00 0.00 2.17
667 889 7.568349 TGCAGATTTGAATAGTACTGAGGATT 58.432 34.615 5.39 0.00 0.00 3.01
669 891 6.544928 TGCAGATTTGAATAGTACTGAGGA 57.455 37.500 5.39 0.00 0.00 3.71
670 892 9.149225 GATATGCAGATTTGAATAGTACTGAGG 57.851 37.037 5.39 0.00 28.20 3.86
671 893 9.149225 GGATATGCAGATTTGAATAGTACTGAG 57.851 37.037 5.39 0.00 28.20 3.35
672 894 8.097038 GGGATATGCAGATTTGAATAGTACTGA 58.903 37.037 5.39 0.00 28.20 3.41
673 895 7.335422 GGGGATATGCAGATTTGAATAGTACTG 59.665 40.741 5.39 0.00 28.20 2.74
674 896 7.398024 GGGGATATGCAGATTTGAATAGTACT 58.602 38.462 0.00 0.00 28.20 2.73
675 897 6.313905 CGGGGATATGCAGATTTGAATAGTAC 59.686 42.308 0.00 0.00 28.20 2.73
676 898 6.406370 CGGGGATATGCAGATTTGAATAGTA 58.594 40.000 0.00 0.00 28.20 1.82
677 899 5.248640 CGGGGATATGCAGATTTGAATAGT 58.751 41.667 0.00 0.00 28.20 2.12
678 900 4.095483 GCGGGGATATGCAGATTTGAATAG 59.905 45.833 0.00 0.00 28.20 1.73
766 993 9.479549 ACTGGACATTAATTGGACATTATTTCT 57.520 29.630 0.00 0.00 0.00 2.52
775 1002 9.391006 TGTATTTCTACTGGACATTAATTGGAC 57.609 33.333 0.00 0.00 0.00 4.02
912 1142 2.054232 ATTCAGGAGAATGGCAGCTG 57.946 50.000 10.11 10.11 42.72 4.24
914 1144 2.617774 GAGAATTCAGGAGAATGGCAGC 59.382 50.000 8.44 0.00 43.52 5.25
960 1191 6.234920 TCAGGAGAAAATTGTTAATGGACGA 58.765 36.000 0.00 0.00 0.00 4.20
961 1192 6.494893 TCAGGAGAAAATTGTTAATGGACG 57.505 37.500 0.00 0.00 0.00 4.79
962 1193 7.329471 GCTTTCAGGAGAAAATTGTTAATGGAC 59.671 37.037 0.00 0.00 42.78 4.02
963 1194 7.233348 AGCTTTCAGGAGAAAATTGTTAATGGA 59.767 33.333 0.00 0.00 42.78 3.41
964 1195 7.330208 CAGCTTTCAGGAGAAAATTGTTAATGG 59.670 37.037 0.00 0.00 42.78 3.16
966 1197 8.181904 TCAGCTTTCAGGAGAAAATTGTTAAT 57.818 30.769 0.00 0.00 42.78 1.40
967 1198 7.581213 TCAGCTTTCAGGAGAAAATTGTTAA 57.419 32.000 0.00 0.00 42.78 2.01
968 1199 7.581213 TTCAGCTTTCAGGAGAAAATTGTTA 57.419 32.000 0.00 0.00 42.78 2.41
969 1200 6.469782 TTCAGCTTTCAGGAGAAAATTGTT 57.530 33.333 0.00 0.00 42.78 2.83
970 1201 5.508657 GCTTCAGCTTTCAGGAGAAAATTGT 60.509 40.000 0.00 0.00 42.78 2.71
971 1202 4.922103 GCTTCAGCTTTCAGGAGAAAATTG 59.078 41.667 0.00 0.00 42.78 2.32
972 1203 5.131594 GCTTCAGCTTTCAGGAGAAAATT 57.868 39.130 0.00 0.00 42.78 1.82
973 1204 4.780275 GCTTCAGCTTTCAGGAGAAAAT 57.220 40.909 0.00 0.00 42.78 1.82
1373 1614 1.270358 GGCCGATGAAGTACCAGATCC 60.270 57.143 0.00 0.00 0.00 3.36
1409 1650 0.458889 GTGTACATGAACGGCGGCTA 60.459 55.000 13.24 0.00 0.00 3.93
1410 1651 1.740296 GTGTACATGAACGGCGGCT 60.740 57.895 13.24 0.00 0.00 5.52
1411 1652 1.296056 AAGTGTACATGAACGGCGGC 61.296 55.000 13.24 0.00 0.00 6.53
1412 1653 0.719465 GAAGTGTACATGAACGGCGG 59.281 55.000 13.24 0.00 0.00 6.13
1414 1655 3.262420 AGATGAAGTGTACATGAACGGC 58.738 45.455 0.00 0.00 0.00 5.68
1428 1669 4.216366 TCTCGCAGATACGAAGATGAAG 57.784 45.455 0.00 0.00 42.39 3.02
1434 1675 4.216366 TGAAGATCTCGCAGATACGAAG 57.784 45.455 0.00 0.00 42.39 3.79
1455 2332 1.615883 AGATGCGCTACTTGGATCGAT 59.384 47.619 9.73 0.00 38.96 3.59
1466 2343 4.662468 AAATCAGAGAGAAGATGCGCTA 57.338 40.909 9.73 0.00 0.00 4.26
1622 4538 9.114952 TGACCAATTATCGCATCTACATAAAAA 57.885 29.630 0.00 0.00 0.00 1.94
1636 4552 7.843490 ATTATAACCCGATGACCAATTATCG 57.157 36.000 0.00 0.00 44.17 2.92
1637 4553 9.010029 ACAATTATAACCCGATGACCAATTATC 57.990 33.333 0.00 0.00 0.00 1.75
1643 4559 6.236558 TGTACAATTATAACCCGATGACCA 57.763 37.500 0.00 0.00 0.00 4.02
1661 4577 3.118555 GCCTACACACCATACCATGTACA 60.119 47.826 0.00 0.00 0.00 2.90
1666 4582 1.491668 TCGCCTACACACCATACCAT 58.508 50.000 0.00 0.00 0.00 3.55
1933 4893 3.617735 TTGTAGCGGACGGTGCCA 61.618 61.111 6.68 0.64 0.00 4.92
1987 5137 1.004679 GAACGGCGGGTTGAAGGTA 60.005 57.895 13.24 0.00 39.50 3.08
2089 5239 2.005370 ACGTCTTGGTGAGGAGGTTA 57.995 50.000 0.00 0.00 34.87 2.85
2117 5267 2.176045 GTACCCTTTCAACCCCCATTG 58.824 52.381 0.00 0.00 0.00 2.82
2131 5281 1.982938 GTCAGAGGCCACGTACCCT 60.983 63.158 5.01 5.92 0.00 4.34
2146 5453 3.478394 GCAATCGCGTCGCAGTCA 61.478 61.111 18.75 0.00 0.00 3.41
2410 6256 1.582968 GGGAGAGCACACGTCGTTA 59.417 57.895 0.00 0.00 0.00 3.18
2458 6304 1.448540 CAGGACGATGCCGCTCTTT 60.449 57.895 0.00 0.00 39.95 2.52
2611 6457 2.612115 CCCTTGAGCCCCAGGAGT 60.612 66.667 0.00 0.00 0.00 3.85
2616 6462 3.006728 CGTACCCCTTGAGCCCCA 61.007 66.667 0.00 0.00 0.00 4.96
2653 6499 2.819550 GTATCGATGCACCCGGGT 59.180 61.111 24.16 24.16 0.00 5.28
2800 6646 2.926779 AGGCTCTGCTGCTGTCCA 60.927 61.111 17.12 0.00 0.00 4.02
3355 7299 0.037326 GGAACATCAGCACCGAGTGA 60.037 55.000 8.04 0.00 35.23 3.41
3641 7595 3.550820 ACAACCCGCTATGCAATTCATA 58.449 40.909 0.00 0.00 36.63 2.15
3684 7643 4.495422 GGAACAATTAGCTCTTCGAGACA 58.505 43.478 0.00 0.00 0.00 3.41
3686 7645 3.428999 CCGGAACAATTAGCTCTTCGAGA 60.429 47.826 0.00 0.00 0.00 4.04
3707 7666 3.187022 GGCAAACATTTCTTGATGTTGCC 59.813 43.478 18.78 18.78 46.53 4.52
3796 7760 8.954950 TGGAGACAGAAATAAGAATCTCATTC 57.045 34.615 0.00 0.00 35.36 2.67
3865 7833 7.209471 TGGCTTTATTAATTCAAAGACGTGT 57.791 32.000 12.82 0.00 41.79 4.49
3868 7836 6.321717 TGCTGGCTTTATTAATTCAAAGACG 58.678 36.000 12.82 8.53 41.79 4.18
3942 7910 6.321435 TGGAGTCGTGATATGTATTTCTGTCT 59.679 38.462 0.00 0.00 0.00 3.41
3966 7934 2.156891 AGTTATGTTAGCGCACGTGTTG 59.843 45.455 18.38 11.40 0.00 3.33
3973 7941 2.557317 GGCCTTAGTTATGTTAGCGCA 58.443 47.619 11.47 0.00 0.00 6.09
3981 7949 3.644966 TCTTGTGGGGCCTTAGTTATG 57.355 47.619 0.84 0.00 0.00 1.90
4019 8362 3.859386 GCAACAGGTGTTATGCTTTATGC 59.141 43.478 0.00 0.00 38.19 3.14
4054 8399 5.452777 CCTTCGCTCTTAACCTTCAAAAAG 58.547 41.667 0.00 0.00 0.00 2.27
4069 8414 1.590259 GATCGTCTGGCCTTCGCTC 60.590 63.158 3.32 3.66 34.44 5.03
4092 8437 3.728718 CGTATATTCATTTGGCAAACGGC 59.271 43.478 16.00 0.00 43.74 5.68
4093 8438 3.728718 GCGTATATTCATTTGGCAAACGG 59.271 43.478 16.00 10.80 0.00 4.44
4096 8441 5.574891 AGTGCGTATATTCATTTGGCAAA 57.425 34.783 16.01 16.01 0.00 3.68
4102 8693 7.255242 CCATCCTCAAAGTGCGTATATTCATTT 60.255 37.037 0.00 0.00 0.00 2.32
4125 8716 5.220854 CGTAATTTTAGCTACTTGCAGCCAT 60.221 40.000 0.00 0.00 45.94 4.40
4126 8717 4.094294 CGTAATTTTAGCTACTTGCAGCCA 59.906 41.667 0.00 0.00 45.94 4.75
4127 8718 4.331717 TCGTAATTTTAGCTACTTGCAGCC 59.668 41.667 0.00 0.00 45.94 4.85
4129 8720 7.684670 TGATTCGTAATTTTAGCTACTTGCAG 58.315 34.615 0.00 0.00 45.94 4.41
4130 8721 7.603963 TGATTCGTAATTTTAGCTACTTGCA 57.396 32.000 0.00 0.00 45.94 4.08
4449 9045 9.179552 CATTTCGTAGACAATTTTTGTTCATCA 57.820 29.630 0.00 0.00 45.52 3.07
4553 9149 3.096092 TCCACACCCATTTTAGGAATGC 58.904 45.455 0.00 0.00 0.00 3.56
4555 9151 3.596046 TCCTCCACACCCATTTTAGGAAT 59.404 43.478 0.00 0.00 0.00 3.01
4570 9166 0.035056 CCCATTCAGGTGTCCTCCAC 60.035 60.000 0.00 0.00 43.74 4.02


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

AutoCloner maintained by Alex Coulton.