Multiple sequence alignment - TraesCS3A01G261400

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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 TraesCS3A01G261400 chr3A 100.000 5868 0 0 1 5868 484626506 484632373 0.000000e+00 10837.0
1 TraesCS3A01G261400 chr3A 100.000 33 0 0 4026 4058 484630449 484630481 1.770000e-05 62.1
2 TraesCS3A01G261400 chr3A 100.000 33 0 0 3944 3976 484630531 484630563 1.770000e-05 62.1
3 TraesCS3A01G261400 chr3B 96.296 4023 112 18 1855 5868 473685834 473689828 0.000000e+00 6569.0
4 TraesCS3A01G261400 chr3B 90.432 1066 46 21 740 1778 473684606 473685642 0.000000e+00 1352.0
5 TraesCS3A01G261400 chr3B 94.845 97 5 0 1763 1859 473685660 473685756 1.020000e-32 152.0
6 TraesCS3A01G261400 chr3B 95.122 41 1 1 3972 4011 37966839 37966879 4.910000e-06 63.9
7 TraesCS3A01G261400 chr3B 100.000 33 0 0 3944 3976 473687988 473688020 1.770000e-05 62.1
8 TraesCS3A01G261400 chr3D 94.537 3423 133 21 1955 5346 363589507 363592906 0.000000e+00 5236.0
9 TraesCS3A01G261400 chr3D 90.534 1162 60 23 740 1859 363588219 363589372 0.000000e+00 1491.0
10 TraesCS3A01G261400 chr3D 93.478 46 2 1 3974 4019 125763090 125763134 3.800000e-07 67.6
11 TraesCS3A01G261400 chr3D 93.182 44 1 2 3972 4013 157474348 157474305 4.910000e-06 63.9
12 TraesCS3A01G261400 chr3D 91.304 46 1 3 3931 3976 363591558 363591600 6.350000e-05 60.2
13 TraesCS3A01G261400 chr2A 95.135 740 34 2 1 739 559814092 559813354 0.000000e+00 1166.0
14 TraesCS3A01G261400 chr2A 94.758 744 37 2 1 743 566102999 566102257 0.000000e+00 1157.0
15 TraesCS3A01G261400 chr7A 94.993 739 36 1 1 739 645014012 645013275 0.000000e+00 1158.0
16 TraesCS3A01G261400 chr7B 94.858 739 36 2 1 739 434803 435539 0.000000e+00 1153.0
17 TraesCS3A01G261400 chr7B 94.723 739 36 3 1 739 542374 543109 0.000000e+00 1146.0
18 TraesCS3A01G261400 chr6A 94.858 739 37 1 1 739 454494411 454495148 0.000000e+00 1153.0
19 TraesCS3A01G261400 chr5D 94.587 739 39 1 1 739 459442071 459442808 0.000000e+00 1142.0
20 TraesCS3A01G261400 chr4A 94.587 739 36 3 1 739 115499754 115499020 0.000000e+00 1140.0
21 TraesCS3A01G261400 chr4A 95.122 41 1 1 3972 4011 3394718 3394758 4.910000e-06 63.9
22 TraesCS3A01G261400 chr7D 94.459 740 40 1 1 740 633546771 633546033 0.000000e+00 1138.0
23 TraesCS3A01G261400 chr2B 87.546 546 48 13 1170 1700 729633182 729633722 1.080000e-171 614.0
24 TraesCS3A01G261400 chr2B 97.436 39 1 0 3972 4010 232269449 232269411 3.800000e-07 67.6
25 TraesCS3A01G261400 chr6B 85.965 513 54 11 1187 1688 716951772 716951267 3.110000e-147 532.0
26 TraesCS3A01G261400 chr6B 95.122 41 1 1 3972 4011 100747843 100747883 4.910000e-06 63.9
27 TraesCS3A01G261400 chr5A 85.361 526 63 11 1187 1703 603994705 603994185 3.110000e-147 532.0
28 TraesCS3A01G261400 chr4B 95.122 41 1 1 3972 4011 476357560 476357600 4.910000e-06 63.9


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 TraesCS3A01G261400 chr3A 484626506 484632373 5867 False 3653.733333 10837 100.00000 1 5868 3 chr3A.!!$F1 5867
1 TraesCS3A01G261400 chr3B 473684606 473689828 5222 False 2033.775000 6569 95.39325 740 5868 4 chr3B.!!$F2 5128
2 TraesCS3A01G261400 chr3D 363588219 363592906 4687 False 2262.400000 5236 92.12500 740 5346 3 chr3D.!!$F2 4606
3 TraesCS3A01G261400 chr2A 559813354 559814092 738 True 1166.000000 1166 95.13500 1 739 1 chr2A.!!$R1 738
4 TraesCS3A01G261400 chr2A 566102257 566102999 742 True 1157.000000 1157 94.75800 1 743 1 chr2A.!!$R2 742
5 TraesCS3A01G261400 chr7A 645013275 645014012 737 True 1158.000000 1158 94.99300 1 739 1 chr7A.!!$R1 738
6 TraesCS3A01G261400 chr7B 434803 435539 736 False 1153.000000 1153 94.85800 1 739 1 chr7B.!!$F1 738
7 TraesCS3A01G261400 chr7B 542374 543109 735 False 1146.000000 1146 94.72300 1 739 1 chr7B.!!$F2 738
8 TraesCS3A01G261400 chr6A 454494411 454495148 737 False 1153.000000 1153 94.85800 1 739 1 chr6A.!!$F1 738
9 TraesCS3A01G261400 chr5D 459442071 459442808 737 False 1142.000000 1142 94.58700 1 739 1 chr5D.!!$F1 738
10 TraesCS3A01G261400 chr4A 115499020 115499754 734 True 1140.000000 1140 94.58700 1 739 1 chr4A.!!$R1 738
11 TraesCS3A01G261400 chr7D 633546033 633546771 738 True 1138.000000 1138 94.45900 1 740 1 chr7D.!!$R1 739
12 TraesCS3A01G261400 chr2B 729633182 729633722 540 False 614.000000 614 87.54600 1170 1700 1 chr2B.!!$F1 530
13 TraesCS3A01G261400 chr6B 716951267 716951772 505 True 532.000000 532 85.96500 1187 1688 1 chr6B.!!$R1 501
14 TraesCS3A01G261400 chr5A 603994185 603994705 520 True 532.000000 532 85.36100 1187 1703 1 chr5A.!!$R1 516

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
970 978 0.520827 CGTCGTCTCTTGGTAGCGAC 60.521 60.000 0.00 0.00 45.52 5.19 F
1144 1176 0.036010 ACTCGCCAGATTCCCAACTG 60.036 55.000 0.00 0.00 0.00 3.16 F
1146 1178 0.400213 TCGCCAGATTCCCAACTGTT 59.600 50.000 0.00 0.00 32.93 3.16 F
1147 1179 0.523072 CGCCAGATTCCCAACTGTTG 59.477 55.000 13.50 13.50 32.93 3.33 F
1466 1526 1.004080 CAGGTCTGTGCCTCTGTGG 60.004 63.158 0.00 0.00 36.58 4.17 F
1475 1535 1.004440 GCCTCTGTGGGTGTCTGTC 60.004 63.158 0.00 0.00 36.00 3.51 F
2516 2693 1.064952 CAATCGCAGATGCATGCAGAA 59.935 47.619 26.69 1.91 46.87 3.02 F
3437 3621 1.575419 TTTATCACGTGGCCTACCCT 58.425 50.000 17.00 0.00 33.59 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2175 3.073062 ACAAACTTAGATGCCCTGACACT 59.927 43.478 0.00 0.00 0.00 3.55 R
2516 2693 4.217118 GTCTGACTGAATGGTTGCAGAAAT 59.783 41.667 0.00 0.00 34.57 2.17 R
3089 3272 5.530915 TCAGTTTTCCATTAAGTCACCACTG 59.469 40.000 0.00 0.00 31.06 3.66 R
3126 3310 7.526608 TGCTACACAAACAGCTATATTGAAAC 58.473 34.615 11.08 0.00 38.63 2.78 R
3182 3366 2.166254 CTGTTTGTGGGCTTCAACAAGT 59.834 45.455 0.00 0.00 31.45 3.16 R
3332 3516 2.227388 ACCTGCTTTTCTGAATTGCTCG 59.773 45.455 13.52 7.88 0.00 5.03 R
3569 3759 1.446907 CTGTGTCCCAGAATCACTGC 58.553 55.000 0.00 0.00 44.49 4.40 R
4913 5128 1.238439 CAAAGCTTCGCCCAAGAGAA 58.762 50.000 0.00 0.00 33.29 2.87 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
32 33 7.541162 TCTACGAAGATCTTTATCGGTCAAAA 58.459 34.615 17.21 0.00 40.71 2.44
72 73 5.180271 GTTGTTCCCTTTGTCATCGGTATA 58.820 41.667 0.00 0.00 0.00 1.47
129 130 8.822805 TCAATACCTAGTTCAATCTTGTTACCT 58.177 33.333 0.00 0.00 0.00 3.08
161 162 6.194463 TCTTTACTCGTTCCGTAATACATCG 58.806 40.000 0.00 0.00 0.00 3.84
162 163 2.724349 ACTCGTTCCGTAATACATCGC 58.276 47.619 0.00 0.00 0.00 4.58
165 166 1.269413 CGTTCCGTAATACATCGCCCT 60.269 52.381 0.00 0.00 0.00 5.19
199 200 5.476599 TCATTAGTTACAATGCTTGCAAGGT 59.523 36.000 27.10 18.06 36.13 3.50
264 265 3.431912 CCGACAATCGAAGTGACAAATCA 59.568 43.478 6.48 0.00 43.74 2.57
300 301 3.146066 GCCAACTCAACAAGTACCATCA 58.854 45.455 0.00 0.00 37.17 3.07
377 378 0.944386 CACAAAGTGTTCCTCCGGTG 59.056 55.000 0.00 0.00 0.00 4.94
432 433 9.739276 AGGAACATGTATAAGTCATGAAGAAAA 57.261 29.630 0.00 0.00 43.47 2.29
506 509 9.551734 CAAGTCAATCACATCATTCTCCTAATA 57.448 33.333 0.00 0.00 0.00 0.98
515 518 8.654215 CACATCATTCTCCTAATAATGTGATCG 58.346 37.037 7.85 0.00 43.10 3.69
634 637 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
756 760 6.437928 TCCTTCACGATTTGTCATGAAAAAG 58.562 36.000 16.02 6.63 31.00 2.27
761 765 7.032580 TCACGATTTGTCATGAAAAAGTGTTT 58.967 30.769 21.34 6.04 34.09 2.83
763 767 6.255453 ACGATTTGTCATGAAAAAGTGTTTGG 59.745 34.615 16.02 3.80 0.00 3.28
783 787 4.804108 TGGTTTGACATGCCTAAAAATCG 58.196 39.130 0.00 0.00 0.00 3.34
815 819 6.986231 GGCTGGATATTCGGATTCAAAATTTT 59.014 34.615 0.00 0.00 0.00 1.82
841 845 5.308825 ACTGACCTGGTGAGATGTTTTAAG 58.691 41.667 20.45 0.00 0.00 1.85
868 876 1.282157 AGCCCTGGTGAGATTTACCAC 59.718 52.381 0.00 0.00 43.00 4.16
904 912 2.344500 CGGTTGGTACGGCTCCAA 59.656 61.111 4.54 4.54 41.84 3.53
930 938 4.722700 GCCGTGCCACAGACCCAT 62.723 66.667 0.00 0.00 0.00 4.00
931 939 2.747460 CCGTGCCACAGACCCATG 60.747 66.667 0.00 0.00 0.00 3.66
966 974 1.807886 CCCCGTCGTCTCTTGGTAG 59.192 63.158 0.00 0.00 0.00 3.18
967 975 1.139095 CCCGTCGTCTCTTGGTAGC 59.861 63.158 0.00 0.00 0.00 3.58
969 977 1.642037 CCGTCGTCTCTTGGTAGCGA 61.642 60.000 0.00 0.00 0.00 4.93
970 978 0.520827 CGTCGTCTCTTGGTAGCGAC 60.521 60.000 0.00 0.00 45.52 5.19
972 980 4.787999 GTCTCTTGGTAGCGACGG 57.212 61.111 0.00 0.00 0.00 4.79
974 982 2.202756 CTCTTGGTAGCGACGGGC 60.203 66.667 0.00 0.00 44.05 6.13
1006 1023 1.359117 GACCGAATCGCGATGGAGA 59.641 57.895 26.97 0.00 44.57 3.71
1101 1118 1.686110 CCAGGTACCGCCCTCTTCT 60.686 63.158 6.18 0.00 38.26 2.85
1139 1171 2.396590 TTTGTACTCGCCAGATTCCC 57.603 50.000 0.00 0.00 0.00 3.97
1141 1173 1.271856 TGTACTCGCCAGATTCCCAA 58.728 50.000 0.00 0.00 0.00 4.12
1143 1175 1.207329 GTACTCGCCAGATTCCCAACT 59.793 52.381 0.00 0.00 0.00 3.16
1144 1176 0.036010 ACTCGCCAGATTCCCAACTG 60.036 55.000 0.00 0.00 0.00 3.16
1146 1178 0.400213 TCGCCAGATTCCCAACTGTT 59.600 50.000 0.00 0.00 32.93 3.16
1147 1179 0.523072 CGCCAGATTCCCAACTGTTG 59.477 55.000 13.50 13.50 32.93 3.33
1311 1366 5.220605 CGAACTCGAACTCCTTTGAACTTTT 60.221 40.000 0.00 0.00 43.02 2.27
1325 1380 5.489792 TGAACTTTTCTAGGCACTCATCT 57.510 39.130 0.00 0.00 41.75 2.90
1338 1393 3.835779 CACTCATCTGACTGACTGACTG 58.164 50.000 0.00 0.00 0.00 3.51
1339 1394 3.505293 CACTCATCTGACTGACTGACTGA 59.495 47.826 0.00 0.00 0.00 3.41
1340 1395 3.505680 ACTCATCTGACTGACTGACTGAC 59.494 47.826 0.00 0.00 0.00 3.51
1341 1396 3.758023 CTCATCTGACTGACTGACTGACT 59.242 47.826 0.00 0.00 0.00 3.41
1342 1397 3.505293 TCATCTGACTGACTGACTGACTG 59.495 47.826 0.00 0.00 0.00 3.51
1343 1398 3.214696 TCTGACTGACTGACTGACTGA 57.785 47.619 0.00 0.00 0.00 3.41
1344 1399 2.881513 TCTGACTGACTGACTGACTGAC 59.118 50.000 0.00 0.00 0.00 3.51
1345 1400 1.957177 TGACTGACTGACTGACTGACC 59.043 52.381 0.00 0.00 0.00 4.02
1466 1526 1.004080 CAGGTCTGTGCCTCTGTGG 60.004 63.158 0.00 0.00 36.58 4.17
1472 1532 1.762522 CTGTGCCTCTGTGGGTGTCT 61.763 60.000 0.00 0.00 36.00 3.41
1473 1533 1.302033 GTGCCTCTGTGGGTGTCTG 60.302 63.158 0.00 0.00 36.00 3.51
1474 1534 1.766059 TGCCTCTGTGGGTGTCTGT 60.766 57.895 0.00 0.00 36.00 3.41
1475 1535 1.004440 GCCTCTGTGGGTGTCTGTC 60.004 63.158 0.00 0.00 36.00 3.51
1476 1536 1.476007 GCCTCTGTGGGTGTCTGTCT 61.476 60.000 0.00 0.00 36.00 3.41
1496 1557 6.323266 TGTCTTCTCTAACTTCATAACGCTC 58.677 40.000 0.00 0.00 0.00 5.03
1517 1578 3.070590 TCGATCTGTGGATCATTCTGCAT 59.929 43.478 0.00 0.00 46.30 3.96
1636 1697 1.374343 TACTGGGTCACTCGCTAGCG 61.374 60.000 30.91 30.91 41.35 4.26
1673 1735 2.238847 GACCACAGGTATGCCTCGCA 62.239 60.000 0.00 0.00 44.97 5.10
1683 1745 1.271840 ATGCCTCGCAAACTCCCCTA 61.272 55.000 0.00 0.00 43.62 3.53
1700 1762 8.967779 ACTCCCCTATACAGTAGCAATAATTA 57.032 34.615 0.00 0.00 0.00 1.40
1742 1804 6.553476 ACCAAAGCTTTTACAGTTATCCCTTT 59.447 34.615 9.53 0.00 0.00 3.11
1756 1818 7.764901 CAGTTATCCCTTTAGTGGTTCTACTTC 59.235 40.741 0.00 0.00 32.19 3.01
1773 1868 6.327934 TCTACTTCTCGGTAATGTTTACAGC 58.672 40.000 0.38 0.00 0.00 4.40
1838 1933 7.521509 TTTGCGAGAAGTTATTAGAGTTAGC 57.478 36.000 0.00 0.00 0.00 3.09
1872 2049 8.597662 TGAGTACAAGTTAACCTGTTATTGAC 57.402 34.615 14.78 7.05 0.00 3.18
1878 2055 7.227910 ACAAGTTAACCTGTTATTGACACGAAT 59.772 33.333 3.94 0.00 33.82 3.34
1880 2057 4.419522 AACCTGTTATTGACACGAATGC 57.580 40.909 0.00 0.00 33.82 3.56
1930 2107 6.649155 TGTGCCTATGTCATTTAGAGCTTTA 58.351 36.000 0.00 0.00 0.00 1.85
1933 2110 8.072567 GTGCCTATGTCATTTAGAGCTTTATTG 58.927 37.037 0.00 0.00 0.00 1.90
2145 2322 5.235516 ACATTGTCGAAGGTACTACCAAAG 58.764 41.667 8.01 0.00 41.95 2.77
2428 2605 1.204704 TGTGATCATCGTGTCAGGACC 59.795 52.381 0.00 0.00 0.00 4.46
2516 2693 1.064952 CAATCGCAGATGCATGCAGAA 59.935 47.619 26.69 1.91 46.87 3.02
2908 3087 7.713764 AAAAATTGGCAAGGCGAAATATATC 57.286 32.000 5.96 0.00 29.01 1.63
3126 3310 5.820131 TGGAAAACTGATAATGCAATAGCG 58.180 37.500 0.00 0.00 46.23 4.26
3208 3392 4.202101 TGTTGAAGCCCACAAACAGTAATG 60.202 41.667 0.00 0.00 0.00 1.90
3221 3405 9.541143 CACAAACAGTAATGGACCTTTTATTTT 57.459 29.630 0.00 0.00 0.00 1.82
3332 3516 1.790481 GCAGAAATTAAGCGCCGTGTC 60.790 52.381 2.29 0.00 0.00 3.67
3375 3559 5.178252 GGTATGCATATGACTAACTGCTGTG 59.822 44.000 10.16 0.00 35.66 3.66
3394 3578 5.289917 TGTGGTGCAAAATATTACAGTCG 57.710 39.130 0.00 0.00 0.00 4.18
3412 3596 6.518493 ACAGTCGTACTTGGATTTTCTTACA 58.482 36.000 0.00 0.00 0.00 2.41
3433 3617 5.736813 ACAAACTATTTATCACGTGGCCTA 58.263 37.500 17.00 2.51 0.00 3.93
3434 3618 5.583457 ACAAACTATTTATCACGTGGCCTAC 59.417 40.000 17.00 0.00 0.00 3.18
3435 3619 4.332428 ACTATTTATCACGTGGCCTACC 57.668 45.455 17.00 0.00 0.00 3.18
3436 3620 2.632987 ATTTATCACGTGGCCTACCC 57.367 50.000 17.00 0.00 33.59 3.69
3437 3621 1.575419 TTTATCACGTGGCCTACCCT 58.425 50.000 17.00 0.00 33.59 4.34
3450 3638 4.415512 TGGCCTACCCTCTATTTTGCTATT 59.584 41.667 3.32 0.00 33.59 1.73
3456 3644 7.229506 CCTACCCTCTATTTTGCTATTTTCCTG 59.770 40.741 0.00 0.00 0.00 3.86
3569 3759 9.416794 AGTCATCTTTGCTGATATATCGTTTAG 57.583 33.333 8.19 1.34 0.00 1.85
3614 3804 3.260884 TGTCCAGACATGTTCCTTACTCC 59.739 47.826 0.00 0.00 36.21 3.85
3621 3811 4.906618 ACATGTTCCTTACTCCGTTTCAT 58.093 39.130 0.00 0.00 0.00 2.57
3657 3847 5.937111 ACTACCTCTGTTTCTTTGGCTTTA 58.063 37.500 0.00 0.00 0.00 1.85
3889 4079 7.972832 TGAGTTGACCGTTAAATTACAGATT 57.027 32.000 0.00 0.00 0.00 2.40
3940 4130 9.810545 CTTAACAACTGTTCCCTTTTTCATTAA 57.189 29.630 0.00 0.00 39.31 1.40
4251 4466 1.843851 TCTATGAATGGACACACCCCC 59.156 52.381 0.00 0.00 38.00 5.40
4255 4470 2.075355 GAATGGACACACCCCCACCA 62.075 60.000 0.00 0.00 38.00 4.17
4256 4471 1.660019 AATGGACACACCCCCACCAA 61.660 55.000 0.00 0.00 38.00 3.67
4366 4581 6.200854 TCAGTGCAGCATTTAGTATAATCGTG 59.799 38.462 0.00 0.00 0.00 4.35
4458 4673 9.639563 TTGTTATTCAGGATATATTTGGCTGAA 57.360 29.630 0.00 0.00 34.52 3.02
4727 4942 5.564259 GCACTGAAATTCTTTGTCTGCTCAT 60.564 40.000 0.00 0.00 0.00 2.90
4913 5128 6.542821 TCCTACACCAGATTCAAGATGTTTT 58.457 36.000 0.00 0.00 0.00 2.43
4960 5175 3.058016 AGTCATGGCAGTGTTTGATTTCG 60.058 43.478 0.00 0.00 0.00 3.46
5053 5268 1.134580 AGATGTCAGAAGGCGATGGTG 60.135 52.381 0.00 0.00 0.00 4.17
5314 5530 1.606668 TGGTGTTTCATCAACTTCGCC 59.393 47.619 0.00 0.00 36.21 5.54
5384 5600 8.340618 TCATTTTTCTTGAAATCTACTCCAGG 57.659 34.615 0.00 0.00 0.00 4.45
5393 5609 5.488919 TGAAATCTACTCCAGGATCTTGGTT 59.511 40.000 22.17 13.47 39.35 3.67
5443 5659 9.508567 GCTTCATGGAGTTTATTTTATCTGAAC 57.491 33.333 2.16 0.00 0.00 3.18
5726 5942 9.018582 TCCTTTCTGTAGTTACTAGTTAGTTCC 57.981 37.037 0.00 0.00 37.73 3.62
5746 5962 6.040504 AGTTCCACCTTCTGTATTTGGTTTTC 59.959 38.462 0.00 0.00 0.00 2.29
5859 6075 7.237055 GGGATCCTACCACCTTATAACAATAGT 59.763 40.741 12.58 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.654414 GATCGAATCTCGGGCAAGTAAT 58.346 45.455 0.00 0.00 40.88 1.89
129 130 3.650139 GGAACGAGTAAAGAGACTTGCA 58.350 45.455 0.00 0.00 34.59 4.08
161 162 3.610911 ACTAATGAGTTAGTTGCAGGGC 58.389 45.455 0.00 0.00 46.40 5.19
199 200 6.478673 CACTCGGTAATGCACATCACTATAAA 59.521 38.462 0.00 0.00 0.00 1.40
264 265 8.970020 TGTTGAGTTGGCATAAATCAAGATTAT 58.030 29.630 13.68 0.00 30.99 1.28
300 301 1.076350 AGGTGCTCTACAGGTGTCTCT 59.924 52.381 0.00 0.00 0.00 3.10
377 378 6.870965 ACTATGAGATTATGCAACTTCCGATC 59.129 38.462 0.00 0.00 0.00 3.69
383 384 8.874156 TCCTATGACTATGAGATTATGCAACTT 58.126 33.333 0.00 0.00 0.00 2.66
452 454 7.284034 CCCATTCTGTTAGCTTATCACTTGATT 59.716 37.037 0.00 0.00 36.05 2.57
461 463 6.067217 ACTTGACCCATTCTGTTAGCTTAT 57.933 37.500 0.00 0.00 0.00 1.73
506 509 7.482474 TGTCATTTGATTAATGCGATCACATT 58.518 30.769 13.21 13.21 42.79 2.71
563 566 8.301720 TCTACTTGACTAGCTCGTTAATCAAAA 58.698 33.333 0.00 0.00 0.00 2.44
634 637 7.989416 AGAATTGTATTAACCGGAAACTTGA 57.011 32.000 9.46 0.00 0.00 3.02
635 638 7.908601 GCTAGAATTGTATTAACCGGAAACTTG 59.091 37.037 9.46 0.00 0.00 3.16
756 760 2.888834 AGGCATGTCAAACCAAACAC 57.111 45.000 0.00 0.00 0.00 3.32
761 765 4.321601 CCGATTTTTAGGCATGTCAAACCA 60.322 41.667 0.00 0.00 0.00 3.67
763 767 4.857037 GTCCGATTTTTAGGCATGTCAAAC 59.143 41.667 0.00 0.00 0.00 2.93
783 787 2.154462 CCGAATATCCAGCCAATGTCC 58.846 52.381 0.00 0.00 0.00 4.02
815 819 4.974645 AACATCTCACCAGGTCAGTAAA 57.025 40.909 0.00 0.00 0.00 2.01
841 845 2.568623 TCTCACCAGGGCTCTTTTTC 57.431 50.000 0.00 0.00 0.00 2.29
868 876 1.328680 CGGCATCAAAGATTGAGTCCG 59.671 52.381 16.04 16.04 45.27 4.79
930 938 2.032634 GCAATTCGTCCGGTCAGCA 61.033 57.895 0.00 0.00 0.00 4.41
931 939 2.750888 GGCAATTCGTCCGGTCAGC 61.751 63.158 0.00 0.00 0.00 4.26
966 974 3.039202 CTTGTTGGATGCCCGTCGC 62.039 63.158 0.00 0.00 38.31 5.19
967 975 1.375396 TCTTGTTGGATGCCCGTCG 60.375 57.895 0.00 0.00 34.29 5.12
969 977 1.303317 GGTCTTGTTGGATGCCCGT 60.303 57.895 0.00 0.00 34.29 5.28
970 978 2.398554 CGGTCTTGTTGGATGCCCG 61.399 63.158 0.00 0.00 34.29 6.13
971 979 1.002624 TCGGTCTTGTTGGATGCCC 60.003 57.895 0.00 0.00 0.00 5.36
972 980 1.305930 GGTCGGTCTTGTTGGATGCC 61.306 60.000 0.00 0.00 0.00 4.40
974 982 0.037697 TCGGTCGGTCTTGTTGGATG 60.038 55.000 0.00 0.00 0.00 3.51
975 983 0.682852 TTCGGTCGGTCTTGTTGGAT 59.317 50.000 0.00 0.00 0.00 3.41
976 984 0.682852 ATTCGGTCGGTCTTGTTGGA 59.317 50.000 0.00 0.00 0.00 3.53
977 985 1.076332 GATTCGGTCGGTCTTGTTGG 58.924 55.000 0.00 0.00 0.00 3.77
1139 1171 1.217882 GTCGAGGTGTCCAACAGTTG 58.782 55.000 6.28 6.28 0.00 3.16
1141 1173 1.746517 GGTCGAGGTGTCCAACAGT 59.253 57.895 0.00 0.00 0.00 3.55
1143 1175 2.732016 CGGTCGAGGTGTCCAACA 59.268 61.111 0.00 0.00 0.00 3.33
1144 1176 2.737376 GCGGTCGAGGTGTCCAAC 60.737 66.667 0.00 0.00 0.00 3.77
1305 1338 5.012561 AGTCAGATGAGTGCCTAGAAAAGTT 59.987 40.000 0.00 0.00 0.00 2.66
1311 1366 3.020274 GTCAGTCAGATGAGTGCCTAGA 58.980 50.000 11.98 0.00 43.40 2.43
1325 1380 1.957177 GGTCAGTCAGTCAGTCAGTCA 59.043 52.381 0.00 0.00 0.00 3.41
1338 1393 0.798776 CAAAGCATGGTCGGTCAGTC 59.201 55.000 0.00 0.00 0.00 3.51
1339 1394 0.606401 CCAAAGCATGGTCGGTCAGT 60.606 55.000 0.00 0.00 44.85 3.41
1340 1395 2.174334 CCAAAGCATGGTCGGTCAG 58.826 57.895 0.00 0.00 44.85 3.51
1341 1396 4.395519 CCAAAGCATGGTCGGTCA 57.604 55.556 0.00 0.00 44.85 4.02
1398 1458 2.439156 GCCAGTGCCATGTCCTCC 60.439 66.667 0.00 0.00 0.00 4.30
1446 1506 2.046507 CAGAGGCACAGACCTGGC 60.047 66.667 0.00 2.53 41.32 4.85
1466 1526 5.455056 TGAAGTTAGAGAAGACAGACACC 57.545 43.478 0.00 0.00 0.00 4.16
1472 1532 6.268825 AGCGTTATGAAGTTAGAGAAGACA 57.731 37.500 0.00 0.00 0.00 3.41
1473 1533 5.452944 CGAGCGTTATGAAGTTAGAGAAGAC 59.547 44.000 0.00 0.00 0.00 3.01
1474 1534 5.353400 TCGAGCGTTATGAAGTTAGAGAAGA 59.647 40.000 0.00 0.00 0.00 2.87
1475 1535 5.570344 TCGAGCGTTATGAAGTTAGAGAAG 58.430 41.667 0.00 0.00 0.00 2.85
1476 1536 5.556355 TCGAGCGTTATGAAGTTAGAGAA 57.444 39.130 0.00 0.00 0.00 2.87
1517 1578 2.798283 GTGTGCAAACTGTAAGCTCGTA 59.202 45.455 0.00 0.00 37.60 3.43
1588 1649 4.164981 ACACCCATTACTTGTAGACCTGA 58.835 43.478 0.00 0.00 0.00 3.86
1673 1735 7.685849 TTATTGCTACTGTATAGGGGAGTTT 57.314 36.000 0.00 0.00 0.00 2.66
1700 1762 3.662759 TGGTGGTTTCTTTGTTCCTCT 57.337 42.857 0.00 0.00 0.00 3.69
1707 1769 5.872070 TGTAAAAGCTTTGGTGGTTTCTTTG 59.128 36.000 13.54 0.00 36.75 2.77
1710 1772 4.709886 ACTGTAAAAGCTTTGGTGGTTTCT 59.290 37.500 13.54 0.00 36.75 2.52
1742 1804 5.948162 ACATTACCGAGAAGTAGAACCACTA 59.052 40.000 0.00 0.00 0.00 2.74
1756 1818 3.596214 AGGTGCTGTAAACATTACCGAG 58.404 45.455 9.11 0.00 37.05 4.63
1773 1868 4.589908 ACTGATAAGCTTTGGGTTAGGTG 58.410 43.478 3.20 0.00 38.55 4.00
1812 1907 8.111224 GCTAACTCTAATAACTTCTCGCAAAAG 58.889 37.037 0.00 0.00 0.00 2.27
1847 1942 8.205512 TGTCAATAACAGGTTAACTTGTACTCA 58.794 33.333 22.04 12.95 34.96 3.41
1930 2107 6.270927 TCCTATGCCATAGAAACTAGAGCAAT 59.729 38.462 13.35 0.00 34.77 3.56
1933 2110 5.719173 CTCCTATGCCATAGAAACTAGAGC 58.281 45.833 13.35 0.00 34.77 4.09
1998 2175 3.073062 ACAAACTTAGATGCCCTGACACT 59.927 43.478 0.00 0.00 0.00 3.55
2002 2179 5.876357 ACTTAACAAACTTAGATGCCCTGA 58.124 37.500 0.00 0.00 0.00 3.86
2056 2233 9.345517 CACATAAAACCTATTTGAACATGAGTG 57.654 33.333 0.00 0.00 0.00 3.51
2145 2322 8.293157 AGAAATGCTTTGTTAAGAGTAAAGAGC 58.707 33.333 0.00 0.00 34.23 4.09
2516 2693 4.217118 GTCTGACTGAATGGTTGCAGAAAT 59.783 41.667 0.00 0.00 34.57 2.17
2891 3069 8.986477 ATAATTTTGATATATTTCGCCTTGCC 57.014 30.769 0.00 0.00 0.00 4.52
3089 3272 5.530915 TCAGTTTTCCATTAAGTCACCACTG 59.469 40.000 0.00 0.00 31.06 3.66
3093 3276 7.702348 GCATTATCAGTTTTCCATTAAGTCACC 59.298 37.037 0.00 0.00 0.00 4.02
3126 3310 7.526608 TGCTACACAAACAGCTATATTGAAAC 58.473 34.615 11.08 0.00 38.63 2.78
3182 3366 2.166254 CTGTTTGTGGGCTTCAACAAGT 59.834 45.455 0.00 0.00 31.45 3.16
3208 3392 7.550712 AGCAGATTCATGAAAATAAAAGGTCC 58.449 34.615 13.09 0.00 0.00 4.46
3332 3516 2.227388 ACCTGCTTTTCTGAATTGCTCG 59.773 45.455 13.52 7.88 0.00 5.03
3375 3559 6.657836 AGTACGACTGTAATATTTTGCACC 57.342 37.500 0.00 0.00 30.94 5.01
3410 3594 4.585879 AGGCCACGTGATAAATAGTTTGT 58.414 39.130 19.30 0.00 0.00 2.83
3412 3596 5.121105 GGTAGGCCACGTGATAAATAGTTT 58.879 41.667 19.30 0.00 34.09 2.66
3433 3617 5.893824 CCAGGAAAATAGCAAAATAGAGGGT 59.106 40.000 0.00 0.00 0.00 4.34
3434 3618 5.893824 ACCAGGAAAATAGCAAAATAGAGGG 59.106 40.000 0.00 0.00 0.00 4.30
3435 3619 6.681368 GCACCAGGAAAATAGCAAAATAGAGG 60.681 42.308 0.00 0.00 0.00 3.69
3436 3620 6.096001 AGCACCAGGAAAATAGCAAAATAGAG 59.904 38.462 0.00 0.00 0.00 2.43
3437 3621 5.951747 AGCACCAGGAAAATAGCAAAATAGA 59.048 36.000 0.00 0.00 0.00 1.98
3450 3638 3.973206 TCGAATAAGAGCACCAGGAAA 57.027 42.857 0.00 0.00 0.00 3.13
3456 3644 4.377841 GCATAGCAATCGAATAAGAGCACC 60.378 45.833 0.00 0.00 0.00 5.01
3569 3759 1.446907 CTGTGTCCCAGAATCACTGC 58.553 55.000 0.00 0.00 44.49 4.40
3614 3804 6.201044 GGTAGTAGATGGTGATTGATGAAACG 59.799 42.308 0.00 0.00 0.00 3.60
3621 3811 5.519808 ACAGAGGTAGTAGATGGTGATTGA 58.480 41.667 0.00 0.00 0.00 2.57
3889 4079 8.314751 AGCTAATCTCAGAAAGCAAACTAACTA 58.685 33.333 13.39 0.00 37.44 2.24
4087 4278 6.732531 ATGGCATATCACACTTCATATTCG 57.267 37.500 0.00 0.00 0.00 3.34
4178 4371 7.736447 AATAGAGCTCAATACTGTAAATGCC 57.264 36.000 17.77 0.00 0.00 4.40
4235 4450 1.458486 GTGGGGGTGTGTCCATTCA 59.542 57.895 0.00 0.00 38.11 2.57
4308 4523 3.738830 AGCTGAAAAGATTTGCTTGCA 57.261 38.095 0.00 0.00 36.80 4.08
4366 4581 5.464389 AGCTGCACATGAAATTTCACTTTTC 59.536 36.000 22.71 11.51 40.49 2.29
4727 4942 8.514330 ACCTTCAAAACAAATAGTGAAGTACA 57.486 30.769 10.42 0.00 43.51 2.90
4913 5128 1.238439 CAAAGCTTCGCCCAAGAGAA 58.762 50.000 0.00 0.00 33.29 2.87
5006 5221 6.687604 AGTACTAATGGAATGTGTTTTTGCC 58.312 36.000 0.00 0.00 0.00 4.52
5314 5530 2.893637 CACGAACCAAGTCCCAGATAG 58.106 52.381 0.00 0.00 0.00 2.08
5393 5609 8.439971 AGCTGTCAGGACATAATAATAATTCCA 58.560 33.333 2.09 0.00 41.01 3.53
5443 5659 0.390472 GAGGCCCTGTCAAGACGAAG 60.390 60.000 0.00 0.00 0.00 3.79
5726 5942 7.038154 TCAAGAAAACCAAATACAGAAGGTG 57.962 36.000 0.00 0.00 33.93 4.00
5746 5962 9.408069 AGTAGAACAGAAATAGTAACGTTCAAG 57.592 33.333 2.82 0.00 36.16 3.02


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

AutoCloner maintained by Alex Coulton.