Multiple sequence alignment - TraesCS5A01G445600

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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 TraesCS5A01G445600 chr5A 100.000 2462 0 0 1 2462 625714442 625716903 0.000000e+00 4547.0
1 TraesCS5A01G445600 chr5A 83.835 1163 123 43 706 1854 644310197 644311308 0.000000e+00 1046.0
2 TraesCS5A01G445600 chr5A 85.124 968 80 40 924 1856 619344167 619345105 0.000000e+00 931.0
3 TraesCS5A01G445600 chr5A 86.397 272 28 6 1966 2230 644312259 644312528 3.100000e-74 289.0
4 TraesCS5A01G445600 chr5A 99.315 146 1 0 2317 2462 606490454 606490309 5.220000e-67 265.0
5 TraesCS5A01G445600 chr5B 89.968 2213 136 43 7 2189 633170460 633172616 0.000000e+00 2778.0
6 TraesCS5A01G445600 chr5B 84.561 1263 105 44 706 1947 629953399 629952206 0.000000e+00 1170.0
7 TraesCS5A01G445600 chr5B 88.073 981 62 34 916 1878 628724436 628723493 0.000000e+00 1112.0
8 TraesCS5A01G445600 chr5B 86.106 1022 95 23 945 1934 649498496 649499502 0.000000e+00 1057.0
9 TraesCS5A01G445600 chr5B 86.667 945 66 32 937 1870 629926357 629925462 0.000000e+00 992.0
10 TraesCS5A01G445600 chr5B 86.277 940 81 27 924 1852 611677676 611678578 0.000000e+00 977.0
11 TraesCS5A01G445600 chr5B 91.480 716 45 9 1 708 625134708 625134001 0.000000e+00 970.0
12 TraesCS5A01G445600 chr5B 91.061 716 48 8 1 708 628725362 628724655 0.000000e+00 953.0
13 TraesCS5A01G445600 chr5B 85.411 754 55 30 1143 1878 625131203 625130487 0.000000e+00 732.0
14 TraesCS5A01G445600 chr5B 89.474 456 32 9 1881 2324 629925422 629924971 1.650000e-156 562.0
15 TraesCS5A01G445600 chr5B 90.299 268 22 4 1965 2230 629951832 629951567 5.040000e-92 348.0
16 TraesCS5A01G445600 chr5B 92.511 227 16 1 483 708 629953675 629953449 8.490000e-85 324.0
17 TraesCS5A01G445600 chr5B 87.912 273 22 6 1965 2230 649506051 649506319 6.610000e-81 311.0
18 TraesCS5A01G445600 chr5B 87.179 273 23 8 1965 2230 649696243 649696510 1.430000e-77 300.0
19 TraesCS5A01G445600 chr5B 89.806 206 10 4 2119 2313 625130439 625130234 1.130000e-63 254.0
20 TraesCS5A01G445600 chr5B 76.289 582 76 27 1394 1934 649694845 649695405 1.130000e-63 254.0
21 TraesCS5A01G445600 chr5B 91.908 173 14 0 706 878 625133952 625133780 2.450000e-60 243.0
22 TraesCS5A01G445600 chr5B 91.908 173 13 1 706 878 628724606 628724435 8.800000e-60 241.0
23 TraesCS5A01G445600 chr5B 90.000 130 6 2 2119 2242 628723445 628723317 7.050000e-36 161.0
24 TraesCS5A01G445600 chr5B 95.714 70 2 1 2245 2313 628722677 628722608 7.200000e-21 111.0
25 TraesCS5A01G445600 chr5B 98.305 59 1 0 2255 2313 633172612 633172670 1.200000e-18 104.0
26 TraesCS5A01G445600 chr5B 94.595 37 2 0 1799 1835 611678751 611678787 9.510000e-05 58.4
27 TraesCS5A01G445600 chr5D 94.248 678 25 9 902 1572 296965032 296965702 0.000000e+00 1024.0
28 TraesCS5A01G445600 chr5D 88.721 860 61 20 937 1780 501450074 501449235 0.000000e+00 1018.0
29 TraesCS5A01G445600 chr5D 84.481 1089 102 49 775 1852 495199783 495200815 0.000000e+00 1013.0
30 TraesCS5A01G445600 chr5D 92.937 623 38 4 989 1611 517213457 517214073 0.000000e+00 902.0
31 TraesCS5A01G445600 chr5D 92.290 441 30 3 166 604 296959685 296960123 7.480000e-175 623.0
32 TraesCS5A01G445600 chr5D 91.544 272 10 5 1 264 501450782 501450516 1.800000e-96 363.0
33 TraesCS5A01G445600 chr5D 94.500 200 10 1 510 708 501450511 501450312 8.550000e-80 307.0
34 TraesCS5A01G445600 chr5D 87.823 271 22 6 1965 2228 517215142 517215408 8.550000e-80 307.0
35 TraesCS5A01G445600 chr5D 94.624 186 9 1 706 891 501450263 501450079 1.110000e-73 287.0
36 TraesCS5A01G445600 chr5D 92.000 200 15 1 706 905 296963445 296963643 1.860000e-71 279.0
37 TraesCS5A01G445600 chr5D 89.732 224 14 4 1971 2187 296998079 296998300 6.710000e-71 278.0
38 TraesCS5A01G445600 chr5D 85.926 270 12 11 1687 1947 296965771 296966023 5.220000e-67 265.0
39 TraesCS5A01G445600 chr5D 87.168 226 20 5 1966 2184 517307078 517307301 5.260000e-62 248.0
40 TraesCS5A01G445600 chr6A 99.320 147 1 0 2316 2462 2915750 2915896 1.450000e-67 267.0
41 TraesCS5A01G445600 chr6A 99.315 146 1 0 2317 2462 494642266 494642121 5.220000e-67 265.0
42 TraesCS5A01G445600 chr1A 99.320 147 1 0 2316 2462 489607762 489607908 1.450000e-67 267.0
43 TraesCS5A01G445600 chr4A 99.315 146 1 0 2317 2462 352157075 352156930 5.220000e-67 265.0
44 TraesCS5A01G445600 chr4A 99.315 146 1 0 2317 2462 352159506 352159361 5.220000e-67 265.0
45 TraesCS5A01G445600 chr4A 99.315 146 1 0 2317 2462 453035193 453035048 5.220000e-67 265.0
46 TraesCS5A01G445600 chr4A 99.315 146 1 0 2317 2462 454713642 454713787 5.220000e-67 265.0
47 TraesCS5A01G445600 chr2A 99.315 146 1 0 2317 2462 705888443 705888298 5.220000e-67 265.0
48 TraesCS5A01G445600 chr2A 78.030 264 32 14 1444 1700 60619151 60618907 2.550000e-30 143.0


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 TraesCS5A01G445600 chr5A 625714442 625716903 2461 False 4547.00 4547 100.000000 1 2462 1 chr5A.!!$F2 2461
1 TraesCS5A01G445600 chr5A 619344167 619345105 938 False 931.00 931 85.124000 924 1856 1 chr5A.!!$F1 932
2 TraesCS5A01G445600 chr5A 644310197 644312528 2331 False 667.50 1046 85.116000 706 2230 2 chr5A.!!$F3 1524
3 TraesCS5A01G445600 chr5B 633170460 633172670 2210 False 1441.00 2778 94.136500 7 2313 2 chr5B.!!$F4 2306
4 TraesCS5A01G445600 chr5B 649498496 649499502 1006 False 1057.00 1057 86.106000 945 1934 1 chr5B.!!$F1 989
5 TraesCS5A01G445600 chr5B 629924971 629926357 1386 True 777.00 992 88.070500 937 2324 2 chr5B.!!$R3 1387
6 TraesCS5A01G445600 chr5B 629951567 629953675 2108 True 614.00 1170 89.123667 483 2230 3 chr5B.!!$R4 1747
7 TraesCS5A01G445600 chr5B 625130234 625134708 4474 True 549.75 970 89.651250 1 2313 4 chr5B.!!$R1 2312
8 TraesCS5A01G445600 chr5B 611677676 611678787 1111 False 517.70 977 90.436000 924 1852 2 chr5B.!!$F3 928
9 TraesCS5A01G445600 chr5B 628722608 628725362 2754 True 515.60 1112 91.351200 1 2313 5 chr5B.!!$R2 2312
10 TraesCS5A01G445600 chr5B 649694845 649696510 1665 False 277.00 300 81.734000 1394 2230 2 chr5B.!!$F5 836
11 TraesCS5A01G445600 chr5D 495199783 495200815 1032 False 1013.00 1013 84.481000 775 1852 1 chr5D.!!$F2 1077
12 TraesCS5A01G445600 chr5D 517213457 517215408 1951 False 604.50 902 90.380000 989 2228 2 chr5D.!!$F5 1239
13 TraesCS5A01G445600 chr5D 296959685 296966023 6338 False 547.75 1024 91.116000 166 1947 4 chr5D.!!$F4 1781
14 TraesCS5A01G445600 chr5D 501449235 501450782 1547 True 493.75 1018 92.347250 1 1780 4 chr5D.!!$R1 1779
15 TraesCS5A01G445600 chr4A 352156930 352159506 2576 True 265.00 265 99.315000 2317 2462 2 chr4A.!!$R2 145

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
885 4130 0.034477 AATACTCTGCCCAAACCCCG 60.034 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 13599 0.031585 CGAGTGTCTTGAACCCGTCA 59.968 55.0 0.0 0.0 0.0 4.35 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
26 27 7.375834 TGGTAACGATGCCTTATCTTATGTAG 58.624 38.462 0.86 0.00 42.51 2.74
27 28 7.014905 TGGTAACGATGCCTTATCTTATGTAGT 59.985 37.037 0.86 0.00 42.51 2.73
28 29 8.517878 GGTAACGATGCCTTATCTTATGTAGTA 58.482 37.037 0.00 0.00 33.44 1.82
50 51 4.752661 TTTTGGATTTTCGGGTAAGACG 57.247 40.909 0.00 0.00 0.00 4.18
61 62 2.798499 CGGGTAAGACGATGGATCACAC 60.798 54.545 0.00 0.00 0.00 3.82
66 67 4.478206 AAGACGATGGATCACACAGATT 57.522 40.909 0.00 0.00 37.00 2.40
121 122 1.168714 AAAGCAAGCATTCCGACTCC 58.831 50.000 0.00 0.00 0.00 3.85
133 134 4.351874 TTCCGACTCCTTCTTGTTTGAT 57.648 40.909 0.00 0.00 0.00 2.57
185 194 8.487313 TTCGTATAGTTTATTGTGCATGAAGT 57.513 30.769 0.00 0.00 0.00 3.01
317 326 1.210545 ACACTTGCCGTAACGTCACG 61.211 55.000 3.66 3.66 41.59 4.35
344 355 3.622612 TCGTGTTGCCATCATAGTGAATG 59.377 43.478 0.00 0.00 36.88 2.67
385 396 2.251642 GGCGTGTTCCTGTCACACC 61.252 63.158 0.00 0.00 41.39 4.16
429 441 7.816411 AGATACAAAAGGCTTATGTAATCCCT 58.184 34.615 0.00 0.00 33.63 4.20
451 463 8.147704 TCCCTCAAGAAACATAATTTTGGAAAC 58.852 33.333 0.89 0.00 0.00 2.78
496 508 6.449448 TTCACACGGTTTTTACAACAAAAC 57.551 33.333 1.20 1.20 43.26 2.43
505 517 7.218204 CGGTTTTTACAACAAAACTCAAGAGAG 59.782 37.037 3.73 0.00 43.44 3.20
506 518 8.241367 GGTTTTTACAACAAAACTCAAGAGAGA 58.759 33.333 3.73 0.00 44.98 3.10
595 610 9.673454 CATGTCATATGGATTTGAGTTTACATG 57.327 33.333 2.13 7.04 0.00 3.21
885 4130 0.034477 AATACTCTGCCCAAACCCCG 60.034 55.000 0.00 0.00 0.00 5.73
928 5565 1.134946 CTCAAATCCCCATCGCCAAAC 59.865 52.381 0.00 0.00 0.00 2.93
949 5588 3.231889 CTCCGCACCAGCACACTCT 62.232 63.158 0.00 0.00 42.27 3.24
966 5605 1.208052 CTCTCGCCTTCTCAAATCCCA 59.792 52.381 0.00 0.00 0.00 4.37
1158 8164 3.900888 TTCCTCAAGAAGGGCCGT 58.099 55.556 0.00 0.00 46.23 5.68
1480 8515 6.193761 GCTTAGTCGATTACTGTCTAGTGAC 58.806 44.000 0.00 0.00 39.39 3.67
1483 8518 5.736813 AGTCGATTACTGTCTAGTGACTCT 58.263 41.667 0.00 0.00 43.29 3.24
1484 8519 5.813672 AGTCGATTACTGTCTAGTGACTCTC 59.186 44.000 0.00 0.00 43.29 3.20
1485 8520 5.006941 GTCGATTACTGTCTAGTGACTCTCC 59.993 48.000 0.00 0.00 43.29 3.71
1506 8541 5.348986 TCCATAGAATTAGTGTTCGCTGTC 58.651 41.667 0.00 0.00 33.36 3.51
1515 8550 3.786635 AGTGTTCGCTGTCTGGATAATC 58.213 45.455 0.00 0.00 0.00 1.75
1549 8591 8.798859 ATAGTAATGTTCTGTTCTGCTTTGAT 57.201 30.769 0.00 0.00 0.00 2.57
1555 8597 8.807667 ATGTTCTGTTCTGCTTTGATAAAAAG 57.192 30.769 0.00 0.00 0.00 2.27
1559 8601 9.467258 TTCTGTTCTGCTTTGATAAAAAGAATG 57.533 29.630 2.10 0.00 30.50 2.67
1560 8602 8.632679 TCTGTTCTGCTTTGATAAAAAGAATGT 58.367 29.630 2.10 0.00 30.50 2.71
1564 8606 7.086376 TCTGCTTTGATAAAAAGAATGTCAGC 58.914 34.615 2.10 0.00 0.00 4.26
1578 8620 5.642919 AGAATGTCAGCAATCTCTTTGACTC 59.357 40.000 5.25 0.00 40.36 3.36
1580 8622 4.313282 TGTCAGCAATCTCTTTGACTCTG 58.687 43.478 5.25 0.00 40.36 3.35
1581 8623 3.124976 GTCAGCAATCTCTTTGACTCTGC 59.875 47.826 0.00 0.00 37.53 4.26
1582 8624 3.072211 CAGCAATCTCTTTGACTCTGCA 58.928 45.455 0.00 0.00 37.53 4.41
1585 8628 4.765856 AGCAATCTCTTTGACTCTGCAAAT 59.234 37.500 0.00 0.00 37.16 2.32
1587 8630 6.432162 AGCAATCTCTTTGACTCTGCAAATTA 59.568 34.615 0.00 0.00 37.16 1.40
1588 8631 7.122353 AGCAATCTCTTTGACTCTGCAAATTAT 59.878 33.333 0.00 0.00 37.16 1.28
1591 8634 9.635520 AATCTCTTTGACTCTGCAAATTATTTG 57.364 29.630 12.84 12.84 43.44 2.32
1606 8650 7.649306 GCAAATTATTTGTTCTGTTGTCTGTCT 59.351 33.333 17.51 0.00 42.56 3.41
1609 8653 7.624360 TTATTTGTTCTGTTGTCTGTCTGTT 57.376 32.000 0.00 0.00 0.00 3.16
1610 8654 5.545658 TTTGTTCTGTTGTCTGTCTGTTC 57.454 39.130 0.00 0.00 0.00 3.18
1617 8661 2.509052 TGTCTGTCTGTTCCTGTTCG 57.491 50.000 0.00 0.00 0.00 3.95
1638 8685 2.599973 GTGATTTTGCAATGCCATCGAC 59.400 45.455 1.53 0.59 0.00 4.20
1646 8693 3.119884 TGCAATGCCATCGACTTTTACAG 60.120 43.478 1.53 0.00 0.00 2.74
1649 8696 5.391523 GCAATGCCATCGACTTTTACAGTTA 60.392 40.000 0.00 0.00 35.01 2.24
1650 8697 6.250819 CAATGCCATCGACTTTTACAGTTAG 58.749 40.000 0.00 0.00 35.01 2.34
1655 8702 4.261578 TCGACTTTTACAGTTAGGTGGG 57.738 45.455 0.00 0.00 35.01 4.61
1657 8704 4.529377 TCGACTTTTACAGTTAGGTGGGAT 59.471 41.667 0.00 0.00 35.01 3.85
1658 8705 5.716228 TCGACTTTTACAGTTAGGTGGGATA 59.284 40.000 0.00 0.00 35.01 2.59
1659 8706 6.381994 TCGACTTTTACAGTTAGGTGGGATAT 59.618 38.462 0.00 0.00 35.01 1.63
1660 8707 7.560991 TCGACTTTTACAGTTAGGTGGGATATA 59.439 37.037 0.00 0.00 35.01 0.86
1661 8708 8.365647 CGACTTTTACAGTTAGGTGGGATATAT 58.634 37.037 0.00 0.00 35.01 0.86
1662 8709 9.490379 GACTTTTACAGTTAGGTGGGATATATG 57.510 37.037 0.00 0.00 35.01 1.78
1663 8710 8.437575 ACTTTTACAGTTAGGTGGGATATATGG 58.562 37.037 0.00 0.00 27.32 2.74
1666 8713 6.930068 ACAGTTAGGTGGGATATATGGTAC 57.070 41.667 0.00 0.00 0.00 3.34
1667 8714 6.631107 ACAGTTAGGTGGGATATATGGTACT 58.369 40.000 0.00 0.00 0.00 2.73
1668 8715 6.724905 ACAGTTAGGTGGGATATATGGTACTC 59.275 42.308 0.00 0.00 0.00 2.59
1669 8716 6.154706 CAGTTAGGTGGGATATATGGTACTCC 59.845 46.154 0.00 0.00 0.00 3.85
1670 8717 6.048080 AGTTAGGTGGGATATATGGTACTCCT 59.952 42.308 0.00 0.00 34.23 3.69
1671 8718 4.689062 AGGTGGGATATATGGTACTCCTG 58.311 47.826 0.00 0.00 34.23 3.86
1672 8719 4.360140 AGGTGGGATATATGGTACTCCTGA 59.640 45.833 0.00 0.00 34.23 3.86
1685 8732 6.346096 TGGTACTCCTGATTGTATTTAGTGC 58.654 40.000 0.00 0.00 34.23 4.40
1688 8735 6.299805 ACTCCTGATTGTATTTAGTGCTCA 57.700 37.500 0.00 0.00 0.00 4.26
1752 8817 1.534595 GAAGTCAGAGTTGCAAGCTGG 59.465 52.381 22.25 5.78 0.00 4.85
1767 8848 0.612744 GCTGGAGAAACAGAGGAGCT 59.387 55.000 0.00 0.00 40.97 4.09
1768 8849 1.405391 GCTGGAGAAACAGAGGAGCTC 60.405 57.143 4.71 4.71 40.97 4.09
1769 8850 1.206849 CTGGAGAAACAGAGGAGCTCC 59.793 57.143 26.22 26.22 44.18 4.70
1785 8879 4.640647 GGAGCTCCCAAACCTGTATTTTAG 59.359 45.833 23.19 0.00 34.14 1.85
1786 8880 4.600062 AGCTCCCAAACCTGTATTTTAGG 58.400 43.478 0.00 0.00 41.22 2.69
2154 10261 7.905604 TCACTACATTCTAGAACCATGTTTG 57.094 36.000 13.85 11.73 33.19 2.93
2220 10328 7.716799 AGCAGACAAAACCCATTATTGATAA 57.283 32.000 0.00 0.00 0.00 1.75
2234 10342 3.517296 TTGATAACCTGCAGTTTGGGA 57.483 42.857 13.81 0.00 40.05 4.37
2236 10344 2.642311 TGATAACCTGCAGTTTGGGAGA 59.358 45.455 13.81 0.00 40.05 3.71
2241 10349 2.356667 GCAGTTTGGGAGAGGGGG 59.643 66.667 0.00 0.00 0.00 5.40
2242 10350 2.539081 GCAGTTTGGGAGAGGGGGT 61.539 63.158 0.00 0.00 0.00 4.95
2247 10991 1.002242 TTTGGGAGAGGGGGTTTGGT 61.002 55.000 0.00 0.00 0.00 3.67
2299 11044 1.137872 CGGGAAGACTGCTAGCAAGAT 59.862 52.381 19.86 7.21 0.00 2.40
2313 11058 1.674221 GCAAGATCACCGAGAGCACTT 60.674 52.381 0.00 0.00 34.30 3.16
2314 11059 2.266554 CAAGATCACCGAGAGCACTTC 58.733 52.381 0.00 0.00 34.30 3.01
2423 13599 3.170717 TCGACTTGAAGGTATCCCACTT 58.829 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.092533 TCGTCTTACCCGAAAATCCAAAATAC 59.907 38.462 0.00 0.00 0.00 1.89
27 28 6.171921 TCGTCTTACCCGAAAATCCAAAATA 58.828 36.000 0.00 0.00 0.00 1.40
28 29 5.005094 TCGTCTTACCCGAAAATCCAAAAT 58.995 37.500 0.00 0.00 0.00 1.82
29 30 4.387598 TCGTCTTACCCGAAAATCCAAAA 58.612 39.130 0.00 0.00 0.00 2.44
50 51 6.485648 TCATTCATCAATCTGTGTGATCCATC 59.514 38.462 0.00 0.00 33.37 3.51
61 62 7.584122 AAATTCTCCCTCATTCATCAATCTG 57.416 36.000 0.00 0.00 0.00 2.90
66 67 7.987458 GTGTAGTAAATTCTCCCTCATTCATCA 59.013 37.037 0.00 0.00 0.00 3.07
121 122 4.520492 AGTGTAAGCCCATCAAACAAGAAG 59.480 41.667 0.00 0.00 0.00 2.85
133 134 1.989586 ACCATGGTTAGTGTAAGCCCA 59.010 47.619 13.00 0.00 35.40 5.36
185 194 6.103330 GGAAATAAAAAGGCGGAATAAGCAA 58.897 36.000 0.00 0.00 36.08 3.91
335 346 7.682741 GCAATTAACATGCTGGACATTCACTAT 60.683 37.037 7.62 0.00 40.64 2.12
344 355 2.925563 GCTTGCAATTAACATGCTGGAC 59.074 45.455 14.21 1.35 44.14 4.02
380 391 6.222389 TCAAATGGCTTTCAAATAAGGTGTG 58.778 36.000 0.00 0.00 0.00 3.82
385 396 9.859427 TTGTATCTCAAATGGCTTTCAAATAAG 57.141 29.630 0.00 0.00 32.64 1.73
451 463 9.303537 GTGAAACACTAAGAGCTAGTTTATAGG 57.696 37.037 0.00 0.00 38.92 2.57
505 517 8.880750 GGGCGTAATATGACTATAAATTTCCTC 58.119 37.037 0.00 0.00 0.00 3.71
506 518 7.548075 CGGGCGTAATATGACTATAAATTTCCT 59.452 37.037 0.00 0.00 0.00 3.36
518 532 4.329528 TGTTTTGTACGGGCGTAATATGAC 59.670 41.667 0.00 0.00 31.86 3.06
800 4044 1.003355 CAGGCAATGGACGGTCTGT 60.003 57.895 8.23 0.00 0.00 3.41
802 4046 1.003355 CACAGGCAATGGACGGTCT 60.003 57.895 8.23 0.00 0.00 3.85
885 4130 3.236618 GAGTGTTGCGTTGGACGGC 62.237 63.158 2.48 0.00 42.82 5.68
895 4140 4.488879 GGGATTTGAGATTTGAGTGTTGC 58.511 43.478 0.00 0.00 0.00 4.17
928 5565 4.007644 TGTGCTGGTGCGGAGAGG 62.008 66.667 0.00 0.00 43.34 3.69
949 5588 0.690192 TGTGGGATTTGAGAAGGCGA 59.310 50.000 0.00 0.00 0.00 5.54
966 5605 1.164411 TTTGAGATTTGGCGCGATGT 58.836 45.000 12.10 0.00 0.00 3.06
1480 8515 5.689514 CAGCGAACACTAATTCTATGGAGAG 59.310 44.000 0.00 0.00 31.77 3.20
1483 8518 5.127194 AGACAGCGAACACTAATTCTATGGA 59.873 40.000 0.00 0.00 0.00 3.41
1484 8519 5.233050 CAGACAGCGAACACTAATTCTATGG 59.767 44.000 0.00 0.00 0.00 2.74
1485 8520 5.233050 CCAGACAGCGAACACTAATTCTATG 59.767 44.000 0.00 0.00 0.00 2.23
1506 8541 9.439537 CATTACTATATCGACACGATTATCCAG 57.560 37.037 11.65 5.63 44.59 3.86
1515 8550 7.856398 AGAACAGAACATTACTATATCGACACG 59.144 37.037 0.00 0.00 0.00 4.49
1549 8591 8.849168 TCAAAGAGATTGCTGACATTCTTTTTA 58.151 29.630 6.30 0.00 37.97 1.52
1555 8597 5.642919 AGAGTCAAAGAGATTGCTGACATTC 59.357 40.000 4.09 0.00 40.53 2.67
1559 8601 3.124976 GCAGAGTCAAAGAGATTGCTGAC 59.875 47.826 0.00 0.00 38.98 3.51
1560 8602 3.244318 TGCAGAGTCAAAGAGATTGCTGA 60.244 43.478 0.00 0.00 38.98 4.26
1564 8606 9.635520 AAATAATTTGCAGAGTCAAAGAGATTG 57.364 29.630 0.00 0.00 39.06 2.67
1578 8620 7.436080 ACAGACAACAGAACAAATAATTTGCAG 59.564 33.333 0.00 0.00 44.39 4.41
1580 8622 7.649306 AGACAGACAACAGAACAAATAATTTGC 59.351 33.333 0.00 0.00 44.39 3.68
1581 8623 8.961092 CAGACAGACAACAGAACAAATAATTTG 58.039 33.333 0.00 0.00 45.95 2.32
1582 8624 8.686334 ACAGACAGACAACAGAACAAATAATTT 58.314 29.630 0.00 0.00 0.00 1.82
1585 8628 7.201696 GGAACAGACAGACAACAGAACAAATAA 60.202 37.037 0.00 0.00 0.00 1.40
1587 8630 5.066505 GGAACAGACAGACAACAGAACAAAT 59.933 40.000 0.00 0.00 0.00 2.32
1588 8631 4.394920 GGAACAGACAGACAACAGAACAAA 59.605 41.667 0.00 0.00 0.00 2.83
1591 8634 3.557595 CAGGAACAGACAGACAACAGAAC 59.442 47.826 0.00 0.00 0.00 3.01
1606 8650 2.685388 TGCAAAATCACGAACAGGAACA 59.315 40.909 0.00 0.00 0.00 3.18
1609 8653 3.856638 GCATTGCAAAATCACGAACAGGA 60.857 43.478 1.71 0.00 0.00 3.86
1610 8654 2.409378 GCATTGCAAAATCACGAACAGG 59.591 45.455 1.71 0.00 0.00 4.00
1617 8661 2.599973 GTCGATGGCATTGCAAAATCAC 59.400 45.455 11.39 7.63 0.00 3.06
1638 8685 8.437575 ACCATATATCCCACCTAACTGTAAAAG 58.562 37.037 0.00 0.00 0.00 2.27
1646 8693 6.154706 CAGGAGTACCATATATCCCACCTAAC 59.845 46.154 0.00 0.00 38.94 2.34
1649 8696 4.360140 TCAGGAGTACCATATATCCCACCT 59.640 45.833 0.00 0.00 38.94 4.00
1650 8697 4.684724 TCAGGAGTACCATATATCCCACC 58.315 47.826 0.00 0.00 38.94 4.61
1659 8706 8.148351 GCACTAAATACAATCAGGAGTACCATA 58.852 37.037 0.00 0.00 38.94 2.74
1660 8707 6.992715 GCACTAAATACAATCAGGAGTACCAT 59.007 38.462 0.00 0.00 38.94 3.55
1661 8708 6.156256 AGCACTAAATACAATCAGGAGTACCA 59.844 38.462 0.00 0.00 38.94 3.25
1662 8709 6.583562 AGCACTAAATACAATCAGGAGTACC 58.416 40.000 0.00 0.00 0.00 3.34
1663 8710 7.265673 TGAGCACTAAATACAATCAGGAGTAC 58.734 38.462 0.00 0.00 0.00 2.73
1666 8713 7.171167 CAGATGAGCACTAAATACAATCAGGAG 59.829 40.741 0.00 0.00 0.00 3.69
1667 8714 6.988580 CAGATGAGCACTAAATACAATCAGGA 59.011 38.462 0.00 0.00 0.00 3.86
1668 8715 6.988580 TCAGATGAGCACTAAATACAATCAGG 59.011 38.462 0.00 0.00 0.00 3.86
1669 8716 8.429493 TTCAGATGAGCACTAAATACAATCAG 57.571 34.615 0.00 0.00 0.00 2.90
1670 8717 8.969260 ATTCAGATGAGCACTAAATACAATCA 57.031 30.769 0.00 0.00 0.00 2.57
1671 8718 9.270640 AGATTCAGATGAGCACTAAATACAATC 57.729 33.333 0.00 0.00 0.00 2.67
1672 8719 9.053840 CAGATTCAGATGAGCACTAAATACAAT 57.946 33.333 0.00 0.00 0.00 2.71
1682 8729 9.875675 GTTAATTTATCAGATTCAGATGAGCAC 57.124 33.333 2.07 0.00 0.00 4.40
1683 8730 9.842775 AGTTAATTTATCAGATTCAGATGAGCA 57.157 29.630 2.07 0.00 0.00 4.26
1752 8817 1.270907 TGGGAGCTCCTCTGTTTCTC 58.729 55.000 31.36 12.45 36.20 2.87
1767 8848 5.318630 GACACCTAAAATACAGGTTTGGGA 58.681 41.667 6.33 0.00 44.18 4.37
1768 8849 4.461431 GGACACCTAAAATACAGGTTTGGG 59.539 45.833 0.00 0.00 44.18 4.12
1769 8850 4.461431 GGGACACCTAAAATACAGGTTTGG 59.539 45.833 0.00 0.00 44.18 3.28
1785 8879 0.249398 AACTCATGCTACGGGACACC 59.751 55.000 0.00 0.00 0.00 4.16
1786 8880 1.067142 TGAACTCATGCTACGGGACAC 60.067 52.381 0.00 0.00 0.00 3.67
1960 9484 9.921637 CTGACTTTCACTAGTCTTTCTAGAAAT 57.078 33.333 18.02 6.70 46.53 2.17
1963 10058 8.353684 CAACTGACTTTCACTAGTCTTTCTAGA 58.646 37.037 8.58 0.00 46.53 2.43
2034 10129 8.310382 CCTAAATTCCAGTGTATCCTCATAGAG 58.690 40.741 0.00 0.00 0.00 2.43
2035 10130 7.789831 ACCTAAATTCCAGTGTATCCTCATAGA 59.210 37.037 0.00 0.00 0.00 1.98
2036 10131 7.967908 ACCTAAATTCCAGTGTATCCTCATAG 58.032 38.462 0.00 0.00 0.00 2.23
2037 10132 7.931015 ACCTAAATTCCAGTGTATCCTCATA 57.069 36.000 0.00 0.00 0.00 2.15
2038 10133 6.831664 ACCTAAATTCCAGTGTATCCTCAT 57.168 37.500 0.00 0.00 0.00 2.90
2040 10135 6.650120 TGAACCTAAATTCCAGTGTATCCTC 58.350 40.000 0.00 0.00 0.00 3.71
2100 10201 1.035139 CATAACCCATTGCTCCTGCC 58.965 55.000 0.00 0.00 38.71 4.85
2220 10328 1.763770 CCTCTCCCAAACTGCAGGT 59.236 57.895 19.93 9.19 0.00 4.00
2234 10342 1.072930 ACTCCACCAAACCCCCTCT 60.073 57.895 0.00 0.00 0.00 3.69
2236 10344 3.146828 GCACTCCACCAAACCCCCT 62.147 63.158 0.00 0.00 0.00 4.79
2241 10349 1.680338 AACAGAGCACTCCACCAAAC 58.320 50.000 0.00 0.00 0.00 2.93
2242 10350 2.297701 GAAACAGAGCACTCCACCAAA 58.702 47.619 0.00 0.00 0.00 3.28
2247 10991 1.762370 TCACTGAAACAGAGCACTCCA 59.238 47.619 5.76 0.00 35.18 3.86
2299 11044 0.539669 TCAGGAAGTGCTCTCGGTGA 60.540 55.000 0.00 0.00 0.00 4.02
2313 11058 5.080337 CCTAGGTACATAGCTTCATCAGGA 58.920 45.833 9.07 0.00 35.39 3.86
2314 11059 4.221703 CCCTAGGTACATAGCTTCATCAGG 59.778 50.000 9.07 0.00 35.39 3.86
2423 13599 0.031585 CGAGTGTCTTGAACCCGTCA 59.968 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.