Multiple sequence alignment - TraesCS2D01G129500

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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 TraesCS2D01G129500 chr2D 100.000 1778 0 0 782 2559 75389467 75391244 0.000000e+00 3284
1 TraesCS2D01G129500 chr2D 100.000 604 0 0 1 604 75388686 75389289 0.000000e+00 1116
2 TraesCS2D01G129500 chr2A 90.051 1568 83 36 947 2478 75134953 75136483 0.000000e+00 1964
3 TraesCS2D01G129500 chr2A 84.032 620 45 19 15 596 75133812 75134415 4.810000e-152 547
4 TraesCS2D01G129500 chr2B 91.365 1077 46 32 782 1840 115378032 115379079 0.000000e+00 1430
5 TraesCS2D01G129500 chr2B 90.065 614 40 6 3 603 115376882 115377487 0.000000e+00 776
6 TraesCS2D01G129500 chr2B 89.109 404 20 8 1831 2212 115379198 115379599 4.950000e-132 481
7 TraesCS2D01G129500 chr2B 84.848 165 16 2 2304 2467 115379707 115379863 9.480000e-35 158


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 TraesCS2D01G129500 chr2D 75388686 75391244 2558 False 2200.00 3284 100.00000 1 2559 2 chr2D.!!$F1 2558
1 TraesCS2D01G129500 chr2A 75133812 75136483 2671 False 1255.50 1964 87.04150 15 2478 2 chr2A.!!$F1 2463
2 TraesCS2D01G129500 chr2B 115376882 115379863 2981 False 711.25 1430 88.84675 3 2467 4 chr2B.!!$F1 2464

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
344 372 0.368907 CAAATTACGACCGACAGGCG 59.631 55.0 0.0 0.0 42.76 5.52 F
932 1624 0.546122 TGATCCAGTACCACATGGCC 59.454 55.0 0.0 0.0 39.32 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 2146 0.320247 AGTTCAGGCTCAGCGTCTTG 60.320 55.0 0.00 0.00 0.00 3.02 R
2365 3304 0.183014 ATGGAGAATGCAGGGCTCTG 59.817 55.0 10.01 10.01 42.42 3.35 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
123 124 2.801631 GCCGACCCTGATGCTAGCT 61.802 63.158 17.23 0.83 0.00 3.32
126 127 1.412710 CCGACCCTGATGCTAGCTTAA 59.587 52.381 17.23 1.35 0.00 1.85
132 133 5.076873 ACCCTGATGCTAGCTTAAAAACAA 58.923 37.500 17.23 0.00 0.00 2.83
133 134 5.716703 ACCCTGATGCTAGCTTAAAAACAAT 59.283 36.000 17.23 0.00 0.00 2.71
134 135 6.038356 CCCTGATGCTAGCTTAAAAACAATG 58.962 40.000 17.23 0.00 0.00 2.82
135 136 5.517770 CCTGATGCTAGCTTAAAAACAATGC 59.482 40.000 17.23 0.00 0.00 3.56
138 145 5.964958 TGCTAGCTTAAAAACAATGCTCT 57.035 34.783 17.23 0.00 35.47 4.09
140 147 7.447374 TGCTAGCTTAAAAACAATGCTCTTA 57.553 32.000 17.23 0.00 35.47 2.10
143 157 8.801913 GCTAGCTTAAAAACAATGCTCTTATTG 58.198 33.333 7.70 0.00 42.38 1.90
275 297 2.863346 AAGCGGTGCGTACTCCACA 61.863 57.895 3.01 0.00 34.94 4.17
284 306 4.189231 GTGCGTACTCCACAGGATTATTT 58.811 43.478 0.00 0.00 33.50 1.40
344 372 0.368907 CAAATTACGACCGACAGGCG 59.631 55.000 0.00 0.00 42.76 5.52
828 1520 4.029186 CCGACGACCGACCGACAA 62.029 66.667 0.00 0.00 41.76 3.18
829 1521 2.051076 CGACGACCGACCGACAAA 60.051 61.111 3.56 0.00 41.76 2.83
830 1522 2.359791 CGACGACCGACCGACAAAC 61.360 63.158 3.56 0.00 41.76 2.93
831 1523 1.299316 GACGACCGACCGACAAACA 60.299 57.895 3.56 0.00 0.00 2.83
832 1524 1.273455 GACGACCGACCGACAAACAG 61.273 60.000 3.56 0.00 0.00 3.16
833 1525 2.654912 CGACCGACCGACAAACAGC 61.655 63.158 0.00 0.00 0.00 4.40
834 1526 2.654912 GACCGACCGACAAACAGCG 61.655 63.158 0.00 0.00 0.00 5.18
835 1527 4.072088 CCGACCGACAAACAGCGC 62.072 66.667 0.00 0.00 0.00 5.92
889 1581 3.888323 GTGATGCTCTCTCCACAGATCTA 59.112 47.826 0.00 0.00 0.00 1.98
905 1597 1.753930 TCTATGGCGACCTTGACGTA 58.246 50.000 0.00 0.00 0.00 3.57
931 1623 1.210478 ACTGATCCAGTACCACATGGC 59.790 52.381 0.00 0.00 43.46 4.40
932 1624 0.546122 TGATCCAGTACCACATGGCC 59.454 55.000 0.00 0.00 39.32 5.36
934 1626 1.983119 ATCCAGTACCACATGGCCGG 61.983 60.000 0.00 0.00 39.32 6.13
935 1627 2.665089 CCAGTACCACATGGCCGGA 61.665 63.158 5.05 0.00 39.32 5.14
936 1628 1.153369 CAGTACCACATGGCCGGAG 60.153 63.158 5.05 0.00 39.32 4.63
937 1629 2.513897 GTACCACATGGCCGGAGC 60.514 66.667 5.05 0.00 39.32 4.70
938 1630 2.687200 TACCACATGGCCGGAGCT 60.687 61.111 5.05 0.00 39.73 4.09
939 1631 3.030168 TACCACATGGCCGGAGCTG 62.030 63.158 5.05 0.00 39.73 4.24
940 1632 4.100084 CCACATGGCCGGAGCTGA 62.100 66.667 5.05 0.00 39.73 4.26
941 1633 2.513204 CACATGGCCGGAGCTGAG 60.513 66.667 5.05 0.00 39.73 3.35
942 1634 3.005539 ACATGGCCGGAGCTGAGT 61.006 61.111 5.05 0.00 39.73 3.41
956 1648 2.932498 GCTGAGTAGCTGATGATCGAG 58.068 52.381 0.00 0.00 46.57 4.04
957 1649 2.351641 GCTGAGTAGCTGATGATCGAGG 60.352 54.545 0.00 0.00 46.57 4.63
958 1650 1.611006 TGAGTAGCTGATGATCGAGGC 59.389 52.381 0.00 0.00 0.00 4.70
961 1658 1.611006 GTAGCTGATGATCGAGGCTGA 59.389 52.381 14.40 0.00 34.88 4.26
985 1682 2.598589 GCTTTTGCTTTGCGATGATCA 58.401 42.857 0.00 0.00 43.35 2.92
986 1683 2.597305 GCTTTTGCTTTGCGATGATCAG 59.403 45.455 0.09 0.00 43.35 2.90
988 1685 4.672542 GCTTTTGCTTTGCGATGATCAGTA 60.673 41.667 0.09 0.00 43.35 2.74
989 1686 4.604843 TTTGCTTTGCGATGATCAGTAG 57.395 40.909 0.09 0.00 0.00 2.57
990 1687 2.554142 TGCTTTGCGATGATCAGTAGG 58.446 47.619 0.09 0.00 0.00 3.18
991 1688 2.168313 TGCTTTGCGATGATCAGTAGGA 59.832 45.455 0.09 0.00 0.00 2.94
992 1689 2.799412 GCTTTGCGATGATCAGTAGGAG 59.201 50.000 0.09 0.00 0.00 3.69
993 1690 3.388308 CTTTGCGATGATCAGTAGGAGG 58.612 50.000 0.09 0.00 0.00 4.30
994 1691 1.332195 TGCGATGATCAGTAGGAGGG 58.668 55.000 0.09 0.00 0.00 4.30
995 1692 1.133482 TGCGATGATCAGTAGGAGGGA 60.133 52.381 0.09 0.00 0.00 4.20
996 1693 1.543802 GCGATGATCAGTAGGAGGGAG 59.456 57.143 0.09 0.00 0.00 4.30
997 1694 2.815963 GCGATGATCAGTAGGAGGGAGA 60.816 54.545 0.09 0.00 0.00 3.71
998 1695 3.081061 CGATGATCAGTAGGAGGGAGAG 58.919 54.545 0.09 0.00 0.00 3.20
999 1696 3.430453 GATGATCAGTAGGAGGGAGAGG 58.570 54.545 0.09 0.00 0.00 3.69
1176 1873 3.103911 GACCTCGCCGACAACGTG 61.104 66.667 0.00 0.00 37.88 4.49
1177 1874 4.657824 ACCTCGCCGACAACGTGG 62.658 66.667 0.00 3.00 46.68 4.94
1178 1875 4.351938 CCTCGCCGACAACGTGGA 62.352 66.667 0.00 0.00 44.73 4.02
1179 1876 3.103911 CTCGCCGACAACGTGGAC 61.104 66.667 0.00 0.00 37.88 4.02
1180 1877 4.986587 TCGCCGACAACGTGGACG 62.987 66.667 7.87 7.87 46.33 4.79
1339 2050 2.115911 CACCGTCTCCTCCTCCTCG 61.116 68.421 0.00 0.00 0.00 4.63
1346 2068 1.076923 TCCTCCTCCTCGCCAGTAC 60.077 63.158 0.00 0.00 0.00 2.73
1417 2146 3.188786 GACATGGACGCGGTGCTC 61.189 66.667 12.47 0.00 0.00 4.26
1570 2300 1.671845 CCTCGCTAGAGCTAAACGAGT 59.328 52.381 19.98 0.00 46.58 4.18
1571 2301 2.539953 CCTCGCTAGAGCTAAACGAGTG 60.540 54.545 19.98 11.69 46.58 3.51
1572 2302 1.192793 CGCTAGAGCTAAACGAGTGC 58.807 55.000 0.00 0.00 39.32 4.40
1573 2303 1.202200 CGCTAGAGCTAAACGAGTGCT 60.202 52.381 0.00 0.00 40.02 4.40
1574 2304 2.189342 GCTAGAGCTAAACGAGTGCTG 58.811 52.381 0.00 0.00 37.16 4.41
1576 2306 0.605589 AGAGCTAAACGAGTGCTGCT 59.394 50.000 0.00 0.00 37.16 4.24
1731 2467 3.333680 TGATTTCCCTTCCCTTGTAGCTT 59.666 43.478 0.00 0.00 0.00 3.74
1855 2723 4.101585 TCTCAAGTGCTTCTCTCTTTTGGA 59.898 41.667 0.00 0.00 0.00 3.53
1903 2773 2.524569 TGTGCACGATTCTTCACTGA 57.475 45.000 13.13 0.00 0.00 3.41
1948 2820 7.381139 GCTTAAAATAGAAGGTGAGAGAGATCG 59.619 40.741 0.00 0.00 0.00 3.69
2051 2923 4.989279 TTGGCCATCAAGAGCTTAAATC 57.011 40.909 6.09 0.00 0.00 2.17
2162 3052 2.751259 TGTACAACAGGTAGTAGAGGCG 59.249 50.000 0.00 0.00 31.13 5.52
2199 3089 6.811170 GCTTTTAGATTCATCTCCGATAGAGG 59.189 42.308 0.00 0.00 43.44 3.69
2200 3090 5.906113 TTAGATTCATCTCCGATAGAGGC 57.094 43.478 0.00 0.00 43.44 4.70
2201 3091 3.096092 AGATTCATCTCCGATAGAGGCC 58.904 50.000 0.00 0.00 43.44 5.19
2202 3092 2.685106 TTCATCTCCGATAGAGGCCT 57.315 50.000 3.86 3.86 43.44 5.19
2203 3093 3.808834 TTCATCTCCGATAGAGGCCTA 57.191 47.619 4.42 0.00 43.44 3.93
2204 3094 3.358111 TCATCTCCGATAGAGGCCTAG 57.642 52.381 4.42 0.00 43.44 3.02
2205 3095 2.025793 TCATCTCCGATAGAGGCCTAGG 60.026 54.545 4.42 3.67 43.44 3.02
2226 3116 5.891451 AGGTTGTTTGTTTCAGCTTTAGAC 58.109 37.500 0.00 0.00 0.00 2.59
2227 3117 4.733405 GGTTGTTTGTTTCAGCTTTAGACG 59.267 41.667 0.00 0.00 0.00 4.18
2228 3118 5.448089 GGTTGTTTGTTTCAGCTTTAGACGA 60.448 40.000 0.00 0.00 0.00 4.20
2239 3129 7.392494 TCAGCTTTAGACGAAAGATTCTAGA 57.608 36.000 11.73 0.00 46.57 2.43
2272 3211 5.598417 TCAATCTAGATTCGGACCATTCTCA 59.402 40.000 15.24 0.00 0.00 3.27
2273 3212 6.098266 TCAATCTAGATTCGGACCATTCTCAA 59.902 38.462 15.24 0.00 0.00 3.02
2310 3249 3.059800 GCACGTCCAAGTTTACTTCAGTC 60.060 47.826 0.00 0.00 33.11 3.51
2318 3257 6.067834 CAAGTTTACTTCAGTCGCGAAGCA 62.068 45.833 12.06 0.00 45.14 3.91
2365 3304 0.752658 AAGCTGAAACAAACAGGGCC 59.247 50.000 0.00 0.00 36.09 5.80
2366 3305 0.396974 AGCTGAAACAAACAGGGCCA 60.397 50.000 6.18 0.00 36.09 5.36
2367 3306 0.032540 GCTGAAACAAACAGGGCCAG 59.967 55.000 6.18 0.00 36.09 4.85
2455 3395 6.995091 GGAAATACAGGCATTCTACTTGATCT 59.005 38.462 0.00 0.00 0.00 2.75
2459 3399 6.798427 ACAGGCATTCTACTTGATCTTCTA 57.202 37.500 0.00 0.00 0.00 2.10
2463 3403 7.550551 CAGGCATTCTACTTGATCTTCTAACAA 59.449 37.037 0.00 0.00 0.00 2.83
2478 3418 6.877322 TCTTCTAACAACATTAGGCCTTGTAC 59.123 38.462 12.58 0.00 0.00 2.90
2479 3419 6.116711 TCTAACAACATTAGGCCTTGTACA 57.883 37.500 12.58 0.00 0.00 2.90
2480 3420 6.535540 TCTAACAACATTAGGCCTTGTACAA 58.464 36.000 12.58 8.28 0.00 2.41
2481 3421 7.172342 TCTAACAACATTAGGCCTTGTACAAT 58.828 34.615 12.58 0.00 0.00 2.71
2482 3422 5.643379 ACAACATTAGGCCTTGTACAATG 57.357 39.130 12.58 17.11 33.75 2.82
2483 3423 5.076873 ACAACATTAGGCCTTGTACAATGT 58.923 37.500 20.47 20.47 40.56 2.71
2484 3424 5.538433 ACAACATTAGGCCTTGTACAATGTT 59.462 36.000 27.08 27.08 45.74 2.71
2485 3425 5.643379 ACATTAGGCCTTGTACAATGTTG 57.357 39.130 20.47 4.39 36.66 3.33
2486 3426 4.462483 ACATTAGGCCTTGTACAATGTTGG 59.538 41.667 20.47 7.97 36.66 3.77
2487 3427 1.923356 AGGCCTTGTACAATGTTGGG 58.077 50.000 9.13 7.59 0.00 4.12
2488 3428 1.146982 AGGCCTTGTACAATGTTGGGT 59.853 47.619 9.13 0.00 0.00 4.51
2489 3429 1.272212 GGCCTTGTACAATGTTGGGTG 59.728 52.381 9.13 0.00 0.00 4.61
2490 3430 1.336795 GCCTTGTACAATGTTGGGTGC 60.337 52.381 9.13 0.00 0.00 5.01
2491 3431 2.238521 CCTTGTACAATGTTGGGTGCT 58.761 47.619 9.13 0.00 0.00 4.40
2492 3432 2.627699 CCTTGTACAATGTTGGGTGCTT 59.372 45.455 9.13 0.00 0.00 3.91
2493 3433 3.823873 CCTTGTACAATGTTGGGTGCTTA 59.176 43.478 9.13 0.00 0.00 3.09
2494 3434 4.082787 CCTTGTACAATGTTGGGTGCTTAG 60.083 45.833 9.13 0.00 0.00 2.18
2495 3435 4.359434 TGTACAATGTTGGGTGCTTAGA 57.641 40.909 0.00 0.00 0.00 2.10
2496 3436 4.720046 TGTACAATGTTGGGTGCTTAGAA 58.280 39.130 0.00 0.00 0.00 2.10
2497 3437 5.133941 TGTACAATGTTGGGTGCTTAGAAA 58.866 37.500 0.00 0.00 0.00 2.52
2498 3438 5.594725 TGTACAATGTTGGGTGCTTAGAAAA 59.405 36.000 0.00 0.00 0.00 2.29
2499 3439 5.606348 ACAATGTTGGGTGCTTAGAAAAA 57.394 34.783 0.00 0.00 0.00 1.94
2500 3440 5.356426 ACAATGTTGGGTGCTTAGAAAAAC 58.644 37.500 0.00 0.00 0.00 2.43
2501 3441 5.105146 ACAATGTTGGGTGCTTAGAAAAACA 60.105 36.000 0.00 0.00 0.00 2.83
2502 3442 5.606348 ATGTTGGGTGCTTAGAAAAACAA 57.394 34.783 0.00 0.00 30.64 2.83
2503 3443 5.407407 TGTTGGGTGCTTAGAAAAACAAA 57.593 34.783 0.00 0.00 0.00 2.83
2504 3444 5.172205 TGTTGGGTGCTTAGAAAAACAAAC 58.828 37.500 0.00 0.00 0.00 2.93
2505 3445 4.394439 TGGGTGCTTAGAAAAACAAACC 57.606 40.909 0.00 0.00 0.00 3.27
2506 3446 3.181485 TGGGTGCTTAGAAAAACAAACCG 60.181 43.478 0.00 0.00 0.00 4.44
2507 3447 3.377439 GGTGCTTAGAAAAACAAACCGG 58.623 45.455 0.00 0.00 0.00 5.28
2508 3448 3.377439 GTGCTTAGAAAAACAAACCGGG 58.623 45.455 6.32 0.00 0.00 5.73
2509 3449 3.025262 TGCTTAGAAAAACAAACCGGGT 58.975 40.909 6.32 0.00 0.00 5.28
2510 3450 3.447944 TGCTTAGAAAAACAAACCGGGTT 59.552 39.130 6.59 6.59 0.00 4.11
2511 3451 4.081586 TGCTTAGAAAAACAAACCGGGTTT 60.082 37.500 19.22 19.22 39.99 3.27
2517 3457 2.971660 AACAAACCGGGTTTTTCTGG 57.028 45.000 22.13 13.04 33.10 3.86
2518 3458 0.462375 ACAAACCGGGTTTTTCTGGC 59.538 50.000 22.13 0.00 36.66 4.85
2519 3459 0.461961 CAAACCGGGTTTTTCTGGCA 59.538 50.000 22.13 0.00 36.66 4.92
2520 3460 0.462375 AAACCGGGTTTTTCTGGCAC 59.538 50.000 19.22 0.00 36.66 5.01
2521 3461 1.396607 AACCGGGTTTTTCTGGCACC 61.397 55.000 6.59 0.00 36.66 5.01
2522 3462 1.830408 CCGGGTTTTTCTGGCACCA 60.830 57.895 0.00 0.00 31.50 4.17
2523 3463 1.659794 CGGGTTTTTCTGGCACCAG 59.340 57.895 10.60 10.60 44.86 4.00
2524 3464 1.106944 CGGGTTTTTCTGGCACCAGT 61.107 55.000 16.12 0.00 43.96 4.00
2525 3465 0.389025 GGGTTTTTCTGGCACCAGTG 59.611 55.000 16.12 0.00 43.96 3.66
2540 3480 4.832248 CACCAGTGCCTAATTCTACTTGA 58.168 43.478 0.00 0.00 0.00 3.02
2541 3481 4.872691 CACCAGTGCCTAATTCTACTTGAG 59.127 45.833 0.00 0.00 0.00 3.02
2542 3482 4.777896 ACCAGTGCCTAATTCTACTTGAGA 59.222 41.667 0.00 0.00 0.00 3.27
2543 3483 5.105146 ACCAGTGCCTAATTCTACTTGAGAG 60.105 44.000 0.00 0.00 34.93 3.20
2544 3484 5.127845 CCAGTGCCTAATTCTACTTGAGAGA 59.872 44.000 0.00 0.00 34.93 3.10
2545 3485 6.039616 CAGTGCCTAATTCTACTTGAGAGAC 58.960 44.000 0.00 0.00 34.93 3.36
2546 3486 5.128008 AGTGCCTAATTCTACTTGAGAGACC 59.872 44.000 0.00 0.00 34.93 3.85
2547 3487 5.023452 TGCCTAATTCTACTTGAGAGACCA 58.977 41.667 0.00 0.00 34.93 4.02
2548 3488 5.483937 TGCCTAATTCTACTTGAGAGACCAA 59.516 40.000 0.00 0.00 34.93 3.67
2549 3489 6.013725 TGCCTAATTCTACTTGAGAGACCAAA 60.014 38.462 0.00 0.00 34.93 3.28
2550 3490 7.051000 GCCTAATTCTACTTGAGAGACCAAAT 58.949 38.462 0.00 0.00 34.93 2.32
2551 3491 8.204836 GCCTAATTCTACTTGAGAGACCAAATA 58.795 37.037 0.00 0.00 34.93 1.40
2554 3494 8.499403 AATTCTACTTGAGAGACCAAATAAGC 57.501 34.615 0.00 0.00 34.93 3.09
2555 3495 6.605471 TCTACTTGAGAGACCAAATAAGCA 57.395 37.500 0.00 0.00 0.00 3.91
2556 3496 6.398918 TCTACTTGAGAGACCAAATAAGCAC 58.601 40.000 0.00 0.00 0.00 4.40
2557 3497 4.327680 ACTTGAGAGACCAAATAAGCACC 58.672 43.478 0.00 0.00 0.00 5.01
2558 3498 2.972625 TGAGAGACCAAATAAGCACCG 58.027 47.619 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 7.553881 ACGCATACTTTAACAATAAGAGCAT 57.446 32.000 0.00 0.00 0.00 3.79
133 134 6.978343 ACGCATACTTTAACAATAAGAGCA 57.022 33.333 0.00 0.00 0.00 4.26
134 135 7.902032 TGTACGCATACTTTAACAATAAGAGC 58.098 34.615 0.00 0.00 32.00 4.09
169 183 8.975439 CGACCTTTGTTATTATGTATGTACTCC 58.025 37.037 0.00 0.00 0.00 3.85
170 184 9.525409 ACGACCTTTGTTATTATGTATGTACTC 57.475 33.333 0.00 0.00 0.00 2.59
171 185 9.309516 CACGACCTTTGTTATTATGTATGTACT 57.690 33.333 0.00 0.00 0.00 2.73
172 186 9.090692 ACACGACCTTTGTTATTATGTATGTAC 57.909 33.333 0.00 0.00 0.00 2.90
173 187 9.656040 AACACGACCTTTGTTATTATGTATGTA 57.344 29.630 0.00 0.00 35.38 2.29
219 233 1.421410 CGAGGAGTTCGGCGGATTTG 61.421 60.000 7.21 0.00 45.54 2.32
284 306 6.422400 GCGTCAAAACCTTTTGGAAATAATCA 59.578 34.615 9.99 0.00 45.68 2.57
326 354 2.745728 CGCCTGTCGGTCGTAATTT 58.254 52.632 0.00 0.00 33.78 1.82
344 372 1.282930 GAGTCAAACGCACTCGACCC 61.283 60.000 0.00 0.00 39.41 4.46
425 453 3.064324 GCGCTCATGGGTTTGGCT 61.064 61.111 0.00 0.00 0.00 4.75
426 454 3.056313 GAGCGCTCATGGGTTTGGC 62.056 63.158 31.91 0.00 0.00 4.52
427 455 2.409870 GGAGCGCTCATGGGTTTGG 61.410 63.158 36.27 0.00 0.00 3.28
428 456 1.675310 TGGAGCGCTCATGGGTTTG 60.675 57.895 36.27 0.00 0.00 2.93
429 457 1.675641 GTGGAGCGCTCATGGGTTT 60.676 57.895 36.27 0.00 0.00 3.27
823 1515 0.248458 ACCTTTTGCGCTGTTTGTCG 60.248 50.000 9.73 0.00 0.00 4.35
824 1516 2.766970 TACCTTTTGCGCTGTTTGTC 57.233 45.000 9.73 0.00 0.00 3.18
828 1520 1.028905 TGCTTACCTTTTGCGCTGTT 58.971 45.000 9.73 0.00 0.00 3.16
829 1521 1.001378 CTTGCTTACCTTTTGCGCTGT 60.001 47.619 9.73 0.45 0.00 4.40
830 1522 1.266718 TCTTGCTTACCTTTTGCGCTG 59.733 47.619 9.73 0.00 0.00 5.18
831 1523 1.604604 TCTTGCTTACCTTTTGCGCT 58.395 45.000 9.73 0.00 0.00 5.92
832 1524 2.051423 GTTCTTGCTTACCTTTTGCGC 58.949 47.619 0.00 0.00 0.00 6.09
833 1525 2.307049 CGTTCTTGCTTACCTTTTGCG 58.693 47.619 0.00 0.00 0.00 4.85
834 1526 2.051423 GCGTTCTTGCTTACCTTTTGC 58.949 47.619 0.00 0.00 0.00 3.68
835 1527 2.661594 GGCGTTCTTGCTTACCTTTTG 58.338 47.619 0.00 0.00 34.52 2.44
868 1560 3.029483 AGATCTGTGGAGAGAGCATCA 57.971 47.619 0.00 0.00 37.82 3.07
889 1581 0.606604 AACTACGTCAAGGTCGCCAT 59.393 50.000 0.00 0.00 0.00 4.40
912 1604 1.475751 GGCCATGTGGTACTGGATCAG 60.476 57.143 0.00 0.00 37.57 2.90
918 1610 1.153369 CTCCGGCCATGTGGTACTG 60.153 63.158 2.24 0.00 37.57 2.74
921 1613 2.687200 AGCTCCGGCCATGTGGTA 60.687 61.111 2.24 0.00 39.73 3.25
924 1616 1.960040 TACTCAGCTCCGGCCATGTG 61.960 60.000 2.24 0.00 39.73 3.21
925 1617 1.680522 CTACTCAGCTCCGGCCATGT 61.681 60.000 2.24 0.00 39.73 3.21
926 1618 1.068753 CTACTCAGCTCCGGCCATG 59.931 63.158 2.24 0.00 39.73 3.66
927 1619 2.801631 GCTACTCAGCTCCGGCCAT 61.802 63.158 2.24 0.00 44.93 4.40
928 1620 3.461773 GCTACTCAGCTCCGGCCA 61.462 66.667 2.24 0.00 44.93 5.36
937 1629 2.351641 GCCTCGATCATCAGCTACTCAG 60.352 54.545 0.00 0.00 0.00 3.35
938 1630 1.611006 GCCTCGATCATCAGCTACTCA 59.389 52.381 0.00 0.00 0.00 3.41
939 1631 1.885887 AGCCTCGATCATCAGCTACTC 59.114 52.381 0.00 0.00 30.46 2.59
940 1632 1.612950 CAGCCTCGATCATCAGCTACT 59.387 52.381 0.00 0.00 31.23 2.57
941 1633 1.611006 TCAGCCTCGATCATCAGCTAC 59.389 52.381 0.00 0.00 31.23 3.58
942 1634 1.986882 TCAGCCTCGATCATCAGCTA 58.013 50.000 0.00 0.00 31.23 3.32
955 1647 3.135994 CAAAGCAAAAGCAAATCAGCCT 58.864 40.909 0.00 0.00 34.23 4.58
956 1648 2.350102 GCAAAGCAAAAGCAAATCAGCC 60.350 45.455 0.00 0.00 34.23 4.85
957 1649 2.660900 CGCAAAGCAAAAGCAAATCAGC 60.661 45.455 0.00 0.00 0.00 4.26
958 1650 2.796031 TCGCAAAGCAAAAGCAAATCAG 59.204 40.909 0.00 0.00 0.00 2.90
961 1658 3.391965 TCATCGCAAAGCAAAAGCAAAT 58.608 36.364 0.00 0.00 0.00 2.32
973 1670 2.103094 CCCTCCTACTGATCATCGCAAA 59.897 50.000 0.00 0.00 0.00 3.68
975 1672 1.133482 TCCCTCCTACTGATCATCGCA 60.133 52.381 0.00 0.00 0.00 5.10
976 1673 1.543802 CTCCCTCCTACTGATCATCGC 59.456 57.143 0.00 0.00 0.00 4.58
977 1674 3.081061 CTCTCCCTCCTACTGATCATCG 58.919 54.545 0.00 0.00 0.00 3.84
979 1676 3.067470 TCCTCTCCCTCCTACTGATCAT 58.933 50.000 0.00 0.00 0.00 2.45
980 1677 2.503824 TCCTCTCCCTCCTACTGATCA 58.496 52.381 0.00 0.00 0.00 2.92
981 1678 3.075283 TCATCCTCTCCCTCCTACTGATC 59.925 52.174 0.00 0.00 0.00 2.92
982 1679 3.067470 TCATCCTCTCCCTCCTACTGAT 58.933 50.000 0.00 0.00 0.00 2.90
983 1680 2.445145 CTCATCCTCTCCCTCCTACTGA 59.555 54.545 0.00 0.00 0.00 3.41
984 1681 2.875296 CTCATCCTCTCCCTCCTACTG 58.125 57.143 0.00 0.00 0.00 2.74
985 1682 1.146982 GCTCATCCTCTCCCTCCTACT 59.853 57.143 0.00 0.00 0.00 2.57
986 1683 1.133325 TGCTCATCCTCTCCCTCCTAC 60.133 57.143 0.00 0.00 0.00 3.18
988 1685 0.398381 GTGCTCATCCTCTCCCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
989 1686 1.406860 GGTGCTCATCCTCTCCCTCC 61.407 65.000 0.00 0.00 0.00 4.30
990 1687 0.689080 TGGTGCTCATCCTCTCCCTC 60.689 60.000 0.00 0.00 0.00 4.30
991 1688 0.030297 ATGGTGCTCATCCTCTCCCT 60.030 55.000 0.00 0.00 0.00 4.20
992 1689 0.108207 CATGGTGCTCATCCTCTCCC 59.892 60.000 0.00 0.00 32.92 4.30
993 1690 0.108207 CCATGGTGCTCATCCTCTCC 59.892 60.000 2.57 0.00 32.92 3.71
994 1691 0.534652 GCCATGGTGCTCATCCTCTC 60.535 60.000 14.67 0.00 32.92 3.20
995 1692 1.530771 GCCATGGTGCTCATCCTCT 59.469 57.895 14.67 0.00 32.92 3.69
996 1693 1.890979 CGCCATGGTGCTCATCCTC 60.891 63.158 13.39 0.00 32.92 3.71
997 1694 1.703014 ATCGCCATGGTGCTCATCCT 61.703 55.000 20.97 0.00 32.92 3.24
998 1695 1.228063 ATCGCCATGGTGCTCATCC 60.228 57.895 20.97 0.00 32.92 3.51
999 1696 0.816825 ACATCGCCATGGTGCTCATC 60.817 55.000 20.97 0.00 33.82 2.92
1101 1798 2.738521 CAGGCGGTGGTCTTGACG 60.739 66.667 0.00 0.00 0.00 4.35
1305 2008 1.469335 GGTGAGAGGTGTCCGGAACA 61.469 60.000 5.23 3.83 34.78 3.18
1310 2013 1.924320 GAGACGGTGAGAGGTGTCCG 61.924 65.000 0.00 0.00 46.98 4.79
1312 2015 0.609681 AGGAGACGGTGAGAGGTGTC 60.610 60.000 0.00 0.00 0.00 3.67
1339 2050 3.494336 CGCTGCTGCTGTACTGGC 61.494 66.667 14.03 3.41 36.97 4.85
1417 2146 0.320247 AGTTCAGGCTCAGCGTCTTG 60.320 55.000 0.00 0.00 0.00 3.02
1713 2449 1.633945 GGAAGCTACAAGGGAAGGGAA 59.366 52.381 0.00 0.00 0.00 3.97
1731 2467 1.003118 CATTTCTGAACACGGGAGGGA 59.997 52.381 0.00 0.00 36.77 4.20
1903 2773 1.843368 CCCTTCATGGCAATCACAGT 58.157 50.000 0.00 0.00 0.00 3.55
1948 2820 2.231964 TGATGGCAGAATCAACCAAAGC 59.768 45.455 0.00 0.00 36.94 3.51
2051 2923 4.697352 ACCTTCTTGATCAATTCACTTCCG 59.303 41.667 8.96 0.00 32.84 4.30
2162 3052 6.672147 TGAATCTAAAAGCAGCTTCTTGTTC 58.328 36.000 8.48 10.02 0.00 3.18
2199 3089 2.623416 AGCTGAAACAAACAACCTAGGC 59.377 45.455 9.30 0.00 0.00 3.93
2200 3090 4.918810 AAGCTGAAACAAACAACCTAGG 57.081 40.909 7.41 7.41 0.00 3.02
2201 3091 7.132863 GTCTAAAGCTGAAACAAACAACCTAG 58.867 38.462 0.00 0.00 0.00 3.02
2202 3092 6.238266 CGTCTAAAGCTGAAACAAACAACCTA 60.238 38.462 0.00 0.00 0.00 3.08
2203 3093 5.448632 CGTCTAAAGCTGAAACAAACAACCT 60.449 40.000 0.00 0.00 0.00 3.50
2204 3094 4.733405 CGTCTAAAGCTGAAACAAACAACC 59.267 41.667 0.00 0.00 0.00 3.77
2205 3095 5.565695 TCGTCTAAAGCTGAAACAAACAAC 58.434 37.500 0.00 0.00 0.00 3.32
2239 3129 7.283354 GGTCCGAATCTAGATTGATTTTTCCTT 59.717 37.037 22.61 0.00 36.86 3.36
2285 3224 3.942748 TGAAGTAAACTTGGACGTGCTTT 59.057 39.130 8.99 3.27 36.11 3.51
2291 3230 2.155155 GCGACTGAAGTAAACTTGGACG 59.845 50.000 0.00 6.53 36.11 4.79
2310 3249 0.738389 ATATGGGGTTTTGCTTCGCG 59.262 50.000 0.00 0.00 0.00 5.87
2318 3257 3.636764 GGCTTCGAATCATATGGGGTTTT 59.363 43.478 0.00 0.00 0.00 2.43
2321 3260 1.774254 TGGCTTCGAATCATATGGGGT 59.226 47.619 0.00 0.00 0.00 4.95
2324 3263 5.694231 TCAATTGGCTTCGAATCATATGG 57.306 39.130 5.42 0.00 0.00 2.74
2365 3304 0.183014 ATGGAGAATGCAGGGCTCTG 59.817 55.000 10.01 10.01 42.42 3.35
2366 3305 0.183014 CATGGAGAATGCAGGGCTCT 59.817 55.000 11.51 2.45 42.42 4.09
2367 3306 2.716814 CATGGAGAATGCAGGGCTC 58.283 57.895 0.00 0.00 42.42 4.70
2455 3395 6.535540 TGTACAAGGCCTAATGTTGTTAGAA 58.464 36.000 15.18 0.00 35.95 2.10
2459 3399 5.538433 ACATTGTACAAGGCCTAATGTTGTT 59.462 36.000 20.47 3.40 38.42 2.83
2463 3403 4.462483 CCAACATTGTACAAGGCCTAATGT 59.538 41.667 20.47 20.47 42.03 2.71
2478 3418 5.355596 TGTTTTTCTAAGCACCCAACATTG 58.644 37.500 0.00 0.00 0.00 2.82
2479 3419 5.606348 TGTTTTTCTAAGCACCCAACATT 57.394 34.783 0.00 0.00 0.00 2.71
2480 3420 5.606348 TTGTTTTTCTAAGCACCCAACAT 57.394 34.783 0.00 0.00 0.00 2.71
2481 3421 5.172205 GTTTGTTTTTCTAAGCACCCAACA 58.828 37.500 0.00 0.00 0.00 3.33
2482 3422 4.569162 GGTTTGTTTTTCTAAGCACCCAAC 59.431 41.667 0.00 0.00 31.70 3.77
2483 3423 4.678309 CGGTTTGTTTTTCTAAGCACCCAA 60.678 41.667 0.00 0.00 31.70 4.12
2484 3424 3.181485 CGGTTTGTTTTTCTAAGCACCCA 60.181 43.478 0.00 0.00 31.70 4.51
2485 3425 3.377439 CGGTTTGTTTTTCTAAGCACCC 58.623 45.455 0.00 0.00 31.70 4.61
2486 3426 3.377439 CCGGTTTGTTTTTCTAAGCACC 58.623 45.455 0.00 0.00 31.70 5.01
2487 3427 3.181484 ACCCGGTTTGTTTTTCTAAGCAC 60.181 43.478 0.00 0.00 31.70 4.40
2488 3428 3.025262 ACCCGGTTTGTTTTTCTAAGCA 58.975 40.909 0.00 0.00 31.70 3.91
2489 3429 3.720949 ACCCGGTTTGTTTTTCTAAGC 57.279 42.857 0.00 0.00 0.00 3.09
2496 3436 3.601435 CCAGAAAAACCCGGTTTGTTTT 58.399 40.909 16.42 12.57 45.23 2.43
2497 3437 2.678479 GCCAGAAAAACCCGGTTTGTTT 60.678 45.455 16.42 7.92 35.80 2.83
2498 3438 1.134640 GCCAGAAAAACCCGGTTTGTT 60.135 47.619 16.42 12.04 35.80 2.83
2499 3439 0.462375 GCCAGAAAAACCCGGTTTGT 59.538 50.000 16.42 11.08 35.80 2.83
2500 3440 0.461961 TGCCAGAAAAACCCGGTTTG 59.538 50.000 16.42 4.60 35.80 2.93
2501 3441 0.462375 GTGCCAGAAAAACCCGGTTT 59.538 50.000 9.92 9.92 37.34 3.27
2502 3442 1.396607 GGTGCCAGAAAAACCCGGTT 61.397 55.000 0.00 0.00 0.00 4.44
2503 3443 1.830847 GGTGCCAGAAAAACCCGGT 60.831 57.895 0.00 0.00 0.00 5.28
2504 3444 1.805428 CTGGTGCCAGAAAAACCCGG 61.805 60.000 12.66 0.00 46.30 5.73
2505 3445 1.106944 ACTGGTGCCAGAAAAACCCG 61.107 55.000 23.55 0.00 46.30 5.28
2506 3446 0.389025 CACTGGTGCCAGAAAAACCC 59.611 55.000 23.55 0.00 46.30 4.11
2507 3447 3.965780 CACTGGTGCCAGAAAAACC 57.034 52.632 23.55 0.00 46.30 3.27
2518 3458 4.832248 TCAAGTAGAATTAGGCACTGGTG 58.168 43.478 0.00 0.00 41.52 4.17
2519 3459 4.777896 TCTCAAGTAGAATTAGGCACTGGT 59.222 41.667 0.00 0.00 41.52 4.00
2520 3460 5.127845 TCTCTCAAGTAGAATTAGGCACTGG 59.872 44.000 0.00 0.00 34.59 4.00
2521 3461 6.039616 GTCTCTCAAGTAGAATTAGGCACTG 58.960 44.000 0.00 0.00 34.59 3.66
2522 3462 5.128008 GGTCTCTCAAGTAGAATTAGGCACT 59.872 44.000 0.00 0.00 36.55 4.40
2523 3463 5.105310 TGGTCTCTCAAGTAGAATTAGGCAC 60.105 44.000 0.00 0.00 32.46 5.01
2524 3464 5.023452 TGGTCTCTCAAGTAGAATTAGGCA 58.977 41.667 0.00 0.00 32.46 4.75
2525 3465 5.599999 TGGTCTCTCAAGTAGAATTAGGC 57.400 43.478 0.00 0.00 32.46 3.93
2528 3468 9.601217 GCTTATTTGGTCTCTCAAGTAGAATTA 57.399 33.333 0.00 0.00 32.46 1.40
2529 3469 8.103305 TGCTTATTTGGTCTCTCAAGTAGAATT 58.897 33.333 0.00 0.00 32.46 2.17
2530 3470 7.550906 GTGCTTATTTGGTCTCTCAAGTAGAAT 59.449 37.037 0.00 0.00 32.46 2.40
2531 3471 6.874134 GTGCTTATTTGGTCTCTCAAGTAGAA 59.126 38.462 0.00 0.00 32.46 2.10
2532 3472 6.398918 GTGCTTATTTGGTCTCTCAAGTAGA 58.601 40.000 0.00 0.00 0.00 2.59
2533 3473 5.582665 GGTGCTTATTTGGTCTCTCAAGTAG 59.417 44.000 0.00 0.00 0.00 2.57
2534 3474 5.488341 GGTGCTTATTTGGTCTCTCAAGTA 58.512 41.667 0.00 0.00 0.00 2.24
2535 3475 4.327680 GGTGCTTATTTGGTCTCTCAAGT 58.672 43.478 0.00 0.00 0.00 3.16
2536 3476 3.372206 CGGTGCTTATTTGGTCTCTCAAG 59.628 47.826 0.00 0.00 0.00 3.02
2537 3477 3.334691 CGGTGCTTATTTGGTCTCTCAA 58.665 45.455 0.00 0.00 0.00 3.02
2538 3478 2.972625 CGGTGCTTATTTGGTCTCTCA 58.027 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.