Multiple sequence alignment - TraesCS2A01G377900

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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 TraesCS2A01G377900 chr2A 100.000 2846 0 0 1 2846 620214453 620211608 0.000000e+00 5256.0
1 TraesCS2A01G377900 chr2D 89.811 2856 129 68 8 2780 477629343 477626567 0.000000e+00 3513.0
2 TraesCS2A01G377900 chr2B 90.020 1503 75 33 13 1485 559555683 559554226 0.000000e+00 1875.0
3 TraesCS2A01G377900 chr2B 89.846 1103 65 21 1522 2605 559554028 559552954 0.000000e+00 1373.0
4 TraesCS2A01G377900 chr2B 84.000 150 4 2 2650 2780 559552431 559552283 2.980000e-25 126.0
5 TraesCS2A01G377900 chr5B 80.537 298 22 21 1375 1648 119412057 119411772 2.240000e-46 196.0
6 TraesCS2A01G377900 chr6D 91.026 78 7 0 1557 1634 303981864 303981787 3.880000e-19 106.0
7 TraesCS2A01G377900 chr6D 86.517 89 10 2 1049 1135 303982470 303982382 2.330000e-16 97.1
8 TraesCS2A01G377900 chr6B 91.026 78 7 0 1557 1634 469707366 469707289 3.880000e-19 106.0
9 TraesCS2A01G377900 chr6B 86.517 89 10 2 1049 1135 469707876 469707788 2.330000e-16 97.1
10 TraesCS2A01G377900 chrUn 87.640 89 9 2 1049 1135 453558167 453558255 5.020000e-18 102.0
11 TraesCS2A01G377900 chr6A 88.462 78 9 0 1557 1634 412849100 412849023 8.390000e-16 95.3


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 TraesCS2A01G377900 chr2A 620211608 620214453 2845 True 5256.000000 5256 100.000000 1 2846 1 chr2A.!!$R1 2845
1 TraesCS2A01G377900 chr2D 477626567 477629343 2776 True 3513.000000 3513 89.811000 8 2780 1 chr2D.!!$R1 2772
2 TraesCS2A01G377900 chr2B 559552283 559555683 3400 True 1124.666667 1875 87.955333 13 2780 3 chr2B.!!$R1 2767

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
71 72 0.672711 GGGAGTAAAGGTGGACGTGC 60.673 60.0 0.00 0.0 0.0 5.34 F
1216 1254 0.169451 ATGTGTGCGTGCATGTGATG 59.831 50.0 7.93 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1380 0.393808 ACGCCCAAGAACACACAGTT 60.394 50.0 0.00 0.0 44.93 3.16 R
2191 2463 0.031994 AAAATGGCCAACGCTGTGAC 59.968 50.0 10.96 0.0 34.44 3.67 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
71 72 0.672711 GGGAGTAAAGGTGGACGTGC 60.673 60.000 0.00 0.00 0.00 5.34
145 148 6.039717 TCCACGTAAATGGAGTAGTACCATAC 59.960 42.308 0.00 0.00 45.89 2.39
265 268 3.181513 CGTGAATCCACTCTTTGATGCTG 60.182 47.826 0.00 0.00 41.06 4.41
320 323 4.914420 CTCGCGCCAGCTAGTCGG 62.914 72.222 0.00 0.00 42.32 4.79
389 393 5.105635 CCACTTCCATTACGGTACTACTGAA 60.106 44.000 1.79 0.00 35.57 3.02
426 430 6.691818 CGTAGTTATACTGTTGTCATCTCACC 59.308 42.308 0.00 0.00 0.00 4.02
516 525 2.755542 AAGCGAGACAGACAGGCACG 62.756 60.000 0.00 0.00 42.69 5.34
525 534 1.078848 GACAGGCACGAAGGATGCT 60.079 57.895 0.00 0.00 42.93 3.79
526 535 1.364626 GACAGGCACGAAGGATGCTG 61.365 60.000 0.00 0.00 42.93 4.41
527 536 2.437359 AGGCACGAAGGATGCTGC 60.437 61.111 0.00 0.00 42.93 5.25
528 537 3.512516 GGCACGAAGGATGCTGCC 61.513 66.667 0.00 0.00 42.93 4.85
529 538 2.747460 GCACGAAGGATGCTGCCA 60.747 61.111 0.00 0.00 40.08 4.92
530 539 2.334946 GCACGAAGGATGCTGCCAA 61.335 57.895 0.00 0.00 40.08 4.52
816 828 2.203998 ATATCCCTCGGGGCCAGG 60.204 66.667 4.39 4.01 43.94 4.45
944 956 4.373116 GGTGGCGACGCTCTCCAA 62.373 66.667 20.77 0.00 41.78 3.53
945 957 2.357034 GTGGCGACGCTCTCCAAA 60.357 61.111 20.77 0.00 32.38 3.28
947 959 2.815647 GGCGACGCTCTCCAAAGG 60.816 66.667 20.77 0.00 0.00 3.11
948 960 3.491652 GCGACGCTCTCCAAAGGC 61.492 66.667 13.73 0.00 0.00 4.35
950 962 2.665603 GACGCTCTCCAAAGGCCT 59.334 61.111 0.00 0.00 0.00 5.19
970 1004 4.082845 CCTTTTCTTTCCCTTTCTCTCCC 58.917 47.826 0.00 0.00 0.00 4.30
975 1009 1.657804 TTCCCTTTCTCTCCCCAGTC 58.342 55.000 0.00 0.00 0.00 3.51
980 1014 1.258445 TTTCTCTCCCCAGTCCGAGC 61.258 60.000 0.00 0.00 0.00 5.03
982 1016 1.760086 CTCTCCCCAGTCCGAGCAT 60.760 63.158 0.00 0.00 0.00 3.79
1077 1115 2.126424 GTGGACGACAGCTCGGTC 60.126 66.667 0.18 0.48 44.80 4.79
1129 1167 3.423154 CCAAGTTCCGCGGTGAGC 61.423 66.667 27.15 9.05 43.95 4.26
1165 1203 3.195825 ACATCCCGTTTCGATCTCTTCTT 59.804 43.478 0.00 0.00 0.00 2.52
1170 1208 4.238514 CCGTTTCGATCTCTTCTTCTTGT 58.761 43.478 0.00 0.00 0.00 3.16
1172 1210 5.164041 CCGTTTCGATCTCTTCTTCTTGTTC 60.164 44.000 0.00 0.00 0.00 3.18
1179 1217 6.644592 CGATCTCTTCTTCTTGTTCTTCTTGT 59.355 38.462 0.00 0.00 0.00 3.16
1214 1252 0.603439 AGATGTGTGCGTGCATGTGA 60.603 50.000 7.93 0.00 0.00 3.58
1215 1253 0.448990 GATGTGTGCGTGCATGTGAT 59.551 50.000 7.93 0.00 0.00 3.06
1216 1254 0.169451 ATGTGTGCGTGCATGTGATG 59.831 50.000 7.93 0.00 0.00 3.07
1331 1370 5.837586 TCGGATATTTTTGTGCTTTTTGC 57.162 34.783 0.00 0.00 43.25 3.68
1358 1403 3.003378 GTCTTAACTGTGTGTTCTTGGGC 59.997 47.826 0.00 0.00 39.89 5.36
1463 1511 6.312918 GTCAAGGTAATACATCACACGACATT 59.687 38.462 0.00 0.00 0.00 2.71
1469 1517 8.875803 GGTAATACATCACACGACATTCTTTTA 58.124 33.333 0.00 0.00 0.00 1.52
1472 1520 9.988350 AATACATCACACGACATTCTTTTATTC 57.012 29.630 0.00 0.00 0.00 1.75
1640 1876 4.780021 ACAAGGATCAACAGGTCAGTATCT 59.220 41.667 0.00 0.00 0.00 1.98
1649 1885 5.220710 ACAGGTCAGTATCTATTCCATGC 57.779 43.478 0.00 0.00 0.00 4.06
1653 1889 6.025539 AGGTCAGTATCTATTCCATGCCATA 58.974 40.000 0.00 0.00 0.00 2.74
1654 1890 6.675746 AGGTCAGTATCTATTCCATGCCATAT 59.324 38.462 0.00 0.00 0.00 1.78
1657 1893 7.497249 GTCAGTATCTATTCCATGCCATATTCC 59.503 40.741 0.00 0.00 0.00 3.01
1658 1894 6.769822 CAGTATCTATTCCATGCCATATTCCC 59.230 42.308 0.00 0.00 0.00 3.97
1681 1917 3.575256 TCCCATGCATGCCATATTCTTTC 59.425 43.478 21.69 0.00 31.47 2.62
1682 1918 3.306502 CCCATGCATGCCATATTCTTTCC 60.307 47.826 21.69 0.00 31.47 3.13
1688 1924 5.181811 TGCATGCCATATTCTTTCCTATTCG 59.818 40.000 16.68 0.00 0.00 3.34
1886 2131 4.754667 GTCGGACGCCCCTGAACC 62.755 72.222 0.00 0.00 0.00 3.62
1892 2137 4.077184 CGCCCCTGAACCGCACTA 62.077 66.667 0.00 0.00 0.00 2.74
1911 2156 3.204827 ATGGCGTGCGGATTCAGC 61.205 61.111 1.49 1.49 0.00 4.26
1927 2172 1.150536 AGCGTTTTGGCCTTCTGGA 59.849 52.632 3.32 0.00 34.57 3.86
1941 2190 1.026182 TCTGGAACATGGACGCATGC 61.026 55.000 7.91 7.91 38.20 4.06
1954 2203 2.176273 GCATGCGTGGCAGTAGAGG 61.176 63.158 8.27 0.00 43.65 3.69
1955 2204 1.517361 CATGCGTGGCAGTAGAGGA 59.483 57.895 0.00 0.00 43.65 3.71
1969 2218 4.461081 CAGTAGAGGAGTAGTATGATGGCC 59.539 50.000 0.00 0.00 0.00 5.36
1978 2232 1.134699 AGTATGATGGCCGTCAGTGTG 60.135 52.381 30.43 0.00 0.00 3.82
2063 2317 6.426025 TGTTATGTAGCAGTCGACGTATATCT 59.574 38.462 10.46 4.92 0.00 1.98
2066 2320 4.685165 TGTAGCAGTCGACGTATATCTCTC 59.315 45.833 10.46 1.45 0.00 3.20
2072 2326 4.986034 AGTCGACGTATATCTCTCTCAGTG 59.014 45.833 10.46 0.00 0.00 3.66
2073 2327 4.746115 GTCGACGTATATCTCTCTCAGTGT 59.254 45.833 0.00 0.00 0.00 3.55
2074 2328 5.234757 GTCGACGTATATCTCTCTCAGTGTT 59.765 44.000 0.00 0.00 0.00 3.32
2075 2329 5.462729 TCGACGTATATCTCTCTCAGTGTTC 59.537 44.000 0.00 0.00 0.00 3.18
2076 2330 5.464057 CGACGTATATCTCTCTCAGTGTTCT 59.536 44.000 0.00 0.00 0.00 3.01
2077 2331 6.563196 CGACGTATATCTCTCTCAGTGTTCTG 60.563 46.154 0.00 0.00 42.54 3.02
2078 2332 6.116806 ACGTATATCTCTCTCAGTGTTCTGT 58.883 40.000 0.00 0.00 41.91 3.41
2079 2333 6.037720 ACGTATATCTCTCTCAGTGTTCTGTG 59.962 42.308 0.00 0.00 41.91 3.66
2080 2334 6.037720 CGTATATCTCTCTCAGTGTTCTGTGT 59.962 42.308 0.00 0.00 41.91 3.72
2081 2335 6.849085 ATATCTCTCTCAGTGTTCTGTGTT 57.151 37.500 0.00 0.00 41.91 3.32
2082 2336 5.543507 ATCTCTCTCAGTGTTCTGTGTTT 57.456 39.130 0.00 0.00 41.91 2.83
2083 2337 4.938080 TCTCTCTCAGTGTTCTGTGTTTC 58.062 43.478 0.00 0.00 41.91 2.78
2084 2338 4.402474 TCTCTCTCAGTGTTCTGTGTTTCA 59.598 41.667 0.00 0.00 41.91 2.69
2140 2411 7.038154 AGTTTGCTTCAAGCTATTGTTTGTA 57.962 32.000 11.57 0.00 42.97 2.41
2165 2437 5.189928 TGGTACATGTTGAAGTTCACTTGT 58.810 37.500 20.18 20.18 36.11 3.16
2169 2441 6.515272 ACATGTTGAAGTTCACTTGTTCTT 57.485 33.333 4.68 0.00 36.11 2.52
2177 2449 5.841957 AGTTCACTTGTTCTTGCTGAAAT 57.158 34.783 0.00 0.00 36.30 2.17
2178 2450 6.212888 AGTTCACTTGTTCTTGCTGAAATT 57.787 33.333 0.00 0.00 36.30 1.82
2204 2476 2.476051 CATCGTCACAGCGTTGGC 59.524 61.111 3.74 0.00 40.37 4.52
2212 2484 0.031857 CACAGCGTTGGCCATTTTCA 59.968 50.000 6.09 0.00 41.24 2.69
2234 2506 1.559368 TGTGCCCTTTGGATGGATTG 58.441 50.000 0.00 0.00 0.00 2.67
2239 2511 1.832998 CCCTTTGGATGGATTGTTGGG 59.167 52.381 0.00 0.00 0.00 4.12
2259 2531 2.376956 GGAGATCGTCGATCAAACTCG 58.623 52.381 31.17 0.00 41.12 4.18
2269 2541 3.442625 TCGATCAAACTCGGTACTGTCAT 59.557 43.478 0.64 0.00 39.13 3.06
2298 2571 3.241458 CGTGCGAGCATATTCATACGATG 60.241 47.826 0.00 0.00 31.65 3.84
2327 2600 4.981806 TCTAAATGGCGAATGAAAAGGG 57.018 40.909 0.00 0.00 0.00 3.95
2475 2751 2.094182 TGTGCTGTTACGGAAGAGGATC 60.094 50.000 6.67 0.00 28.88 3.36
2597 2873 3.242673 CGTTAACGAGCAGGAGTACTAGG 60.243 52.174 23.35 0.00 43.02 3.02
2615 2891 1.666872 GGTACCACTGTGACGGCAC 60.667 63.158 16.50 16.50 45.35 5.01
2628 2904 5.004448 TGTGACGGCACCTTATCATTTTTA 58.996 37.500 21.02 0.00 44.51 1.52
2629 2905 5.650266 TGTGACGGCACCTTATCATTTTTAT 59.350 36.000 21.02 0.00 44.51 1.40
2632 2908 7.544217 GTGACGGCACCTTATCATTTTTATTTT 59.456 33.333 11.38 0.00 39.14 1.82
2633 2909 8.740906 TGACGGCACCTTATCATTTTTATTTTA 58.259 29.630 0.00 0.00 0.00 1.52
2694 3448 5.634020 GGTATACAAAGCGTGTCAGGATATC 59.366 44.000 5.01 0.00 41.98 1.63
2794 3570 3.936585 TTTTTCCACTCGCTTGTGC 57.063 47.368 1.10 0.00 36.68 4.57
2795 3571 1.098869 TTTTTCCACTCGCTTGTGCA 58.901 45.000 1.10 0.00 39.64 4.57
2796 3572 1.098869 TTTTCCACTCGCTTGTGCAA 58.901 45.000 0.00 0.00 39.64 4.08
2797 3573 0.380378 TTTCCACTCGCTTGTGCAAC 59.620 50.000 0.00 0.00 39.64 4.17
2798 3574 1.771073 TTCCACTCGCTTGTGCAACG 61.771 55.000 0.00 0.00 42.39 4.10
2799 3575 2.243957 CCACTCGCTTGTGCAACGA 61.244 57.895 0.00 0.00 42.39 3.85
2805 3581 2.949106 CTTGTGCAACGAGGGCTG 59.051 61.111 0.00 0.00 44.89 4.85
2806 3582 1.597854 CTTGTGCAACGAGGGCTGA 60.598 57.895 0.00 0.00 44.89 4.26
2807 3583 0.957395 CTTGTGCAACGAGGGCTGAT 60.957 55.000 0.00 0.00 44.89 2.90
2808 3584 0.537143 TTGTGCAACGAGGGCTGATT 60.537 50.000 0.00 0.00 42.39 2.57
2809 3585 0.955428 TGTGCAACGAGGGCTGATTC 60.955 55.000 0.00 0.00 42.39 2.52
2810 3586 0.674895 GTGCAACGAGGGCTGATTCT 60.675 55.000 0.00 0.00 0.00 2.40
2811 3587 0.674581 TGCAACGAGGGCTGATTCTG 60.675 55.000 0.00 0.00 0.00 3.02
2812 3588 0.674895 GCAACGAGGGCTGATTCTGT 60.675 55.000 0.00 0.00 0.00 3.41
2813 3589 1.081892 CAACGAGGGCTGATTCTGTG 58.918 55.000 0.00 0.00 0.00 3.66
2814 3590 0.687354 AACGAGGGCTGATTCTGTGT 59.313 50.000 0.00 0.00 0.00 3.72
2815 3591 0.247736 ACGAGGGCTGATTCTGTGTC 59.752 55.000 0.00 0.00 0.00 3.67
2816 3592 0.247460 CGAGGGCTGATTCTGTGTCA 59.753 55.000 0.00 0.00 0.00 3.58
2817 3593 1.731720 GAGGGCTGATTCTGTGTCAC 58.268 55.000 0.00 0.00 0.00 3.67
2818 3594 1.002430 GAGGGCTGATTCTGTGTCACA 59.998 52.381 5.36 5.36 0.00 3.58
2819 3595 1.421268 AGGGCTGATTCTGTGTCACAA 59.579 47.619 7.18 0.00 0.00 3.33
2820 3596 1.537202 GGGCTGATTCTGTGTCACAAC 59.463 52.381 7.18 0.36 0.00 3.32
2821 3597 2.221169 GGCTGATTCTGTGTCACAACA 58.779 47.619 7.18 4.72 0.00 3.33
2831 3607 3.304382 GTGTCACAACACGAAGTTCTG 57.696 47.619 0.56 1.45 45.84 3.02
2832 3608 2.030457 GTGTCACAACACGAAGTTCTGG 59.970 50.000 0.56 0.00 45.84 3.86
2833 3609 2.093921 TGTCACAACACGAAGTTCTGGA 60.094 45.455 0.56 0.00 41.61 3.86
2834 3610 3.131396 GTCACAACACGAAGTTCTGGAT 58.869 45.455 0.56 0.00 41.61 3.41
2835 3611 3.560068 GTCACAACACGAAGTTCTGGATT 59.440 43.478 0.56 0.00 41.61 3.01
2836 3612 4.748102 GTCACAACACGAAGTTCTGGATTA 59.252 41.667 0.56 0.00 41.61 1.75
2837 3613 5.235616 GTCACAACACGAAGTTCTGGATTAA 59.764 40.000 0.56 0.00 41.61 1.40
2838 3614 5.818336 TCACAACACGAAGTTCTGGATTAAA 59.182 36.000 0.56 0.00 41.61 1.52
2839 3615 6.485313 TCACAACACGAAGTTCTGGATTAAAT 59.515 34.615 0.56 0.00 41.61 1.40
2840 3616 6.578545 CACAACACGAAGTTCTGGATTAAATG 59.421 38.462 0.56 0.00 41.61 2.32
2841 3617 6.485313 ACAACACGAAGTTCTGGATTAAATGA 59.515 34.615 0.56 0.00 41.61 2.57
2842 3618 7.012894 ACAACACGAAGTTCTGGATTAAATGAA 59.987 33.333 0.56 0.00 41.61 2.57
2843 3619 7.504924 ACACGAAGTTCTGGATTAAATGAAA 57.495 32.000 0.56 0.00 41.61 2.69
2844 3620 7.360361 ACACGAAGTTCTGGATTAAATGAAAC 58.640 34.615 0.56 0.00 41.61 2.78
2845 3621 6.519761 CACGAAGTTCTGGATTAAATGAAACG 59.480 38.462 0.56 0.00 41.61 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 2.221169 TGTGTCCTGAAATGCACTCAC 58.779 47.619 0.00 0.00 33.44 3.51
89 90 2.636647 TGTGTCCTGAAATGCACTCA 57.363 45.000 0.00 0.00 33.44 3.41
90 91 3.254166 ACAATGTGTCCTGAAATGCACTC 59.746 43.478 0.00 0.00 33.44 3.51
91 92 3.225104 ACAATGTGTCCTGAAATGCACT 58.775 40.909 0.00 0.00 33.44 4.40
136 137 3.111853 CATCGGTGCATGTATGGTACT 57.888 47.619 0.00 0.00 0.00 2.73
161 164 3.425577 AAGTGGAATAACGCATGCATG 57.574 42.857 22.70 22.70 0.00 4.06
170 173 7.057894 TGGATGGTGGTAATAAGTGGAATAAC 58.942 38.462 0.00 0.00 0.00 1.89
320 323 0.110147 CGAGATACGGCGTGATCTCC 60.110 60.000 30.82 21.68 43.47 3.71
516 525 1.324740 TGGCATTGGCAGCATCCTTC 61.325 55.000 9.11 0.00 43.71 3.46
525 534 1.761784 GGGTTATTCATGGCATTGGCA 59.238 47.619 15.86 15.86 43.71 4.92
526 535 1.761784 TGGGTTATTCATGGCATTGGC 59.238 47.619 0.00 2.73 40.13 4.52
527 536 4.693042 AATGGGTTATTCATGGCATTGG 57.307 40.909 0.00 0.00 0.00 3.16
528 537 7.499292 TCTTAAATGGGTTATTCATGGCATTG 58.501 34.615 0.00 0.00 0.00 2.82
529 538 7.564660 TCTCTTAAATGGGTTATTCATGGCATT 59.435 33.333 0.00 0.00 0.00 3.56
530 539 7.068702 TCTCTTAAATGGGTTATTCATGGCAT 58.931 34.615 0.00 0.00 0.00 4.40
673 682 4.704833 CACCAGCACCACGAGGGG 62.705 72.222 3.29 0.00 42.91 4.79
943 955 4.298626 AGAAAGGGAAAGAAAAGGCCTTT 58.701 39.130 25.47 25.47 36.63 3.11
944 956 3.898123 GAGAAAGGGAAAGAAAAGGCCTT 59.102 43.478 13.78 13.78 0.00 4.35
945 957 3.141083 AGAGAAAGGGAAAGAAAAGGCCT 59.859 43.478 0.00 0.00 0.00 5.19
947 959 3.508012 GGAGAGAAAGGGAAAGAAAAGGC 59.492 47.826 0.00 0.00 0.00 4.35
948 960 4.082845 GGGAGAGAAAGGGAAAGAAAAGG 58.917 47.826 0.00 0.00 0.00 3.11
950 962 3.465588 TGGGGAGAGAAAGGGAAAGAAAA 59.534 43.478 0.00 0.00 0.00 2.29
970 1004 1.609555 GGACTACTATGCTCGGACTGG 59.390 57.143 0.00 0.00 0.00 4.00
975 1009 3.143211 ACCTAGGACTACTATGCTCGG 57.857 52.381 17.98 0.00 0.00 4.63
980 1014 5.883673 GCCATCTCTACCTAGGACTACTATG 59.116 48.000 17.98 11.08 0.00 2.23
982 1016 4.020396 CGCCATCTCTACCTAGGACTACTA 60.020 50.000 17.98 0.00 0.00 1.82
1129 1167 2.398498 GGGATGTGATCTCGTCGATTG 58.602 52.381 10.13 0.00 30.84 2.67
1165 1203 3.812156 TCCACGACAAGAAGAACAAGA 57.188 42.857 0.00 0.00 0.00 3.02
1170 1208 4.272504 GTCACAAATCCACGACAAGAAGAA 59.727 41.667 0.00 0.00 0.00 2.52
1172 1210 3.362986 CGTCACAAATCCACGACAAGAAG 60.363 47.826 0.00 0.00 35.49 2.85
1179 1217 2.029380 ACATCTCGTCACAAATCCACGA 60.029 45.455 0.00 0.00 40.14 4.35
1214 1252 4.314440 ACGGCGGTCACTGCACAT 62.314 61.111 11.68 0.00 0.00 3.21
1328 1367 3.944650 ACACACAGTTAAGACACATGCAA 59.055 39.130 0.00 0.00 0.00 4.08
1329 1368 3.540617 ACACACAGTTAAGACACATGCA 58.459 40.909 0.00 0.00 0.00 3.96
1330 1369 4.273480 AGAACACACAGTTAAGACACATGC 59.727 41.667 0.00 0.00 41.51 4.06
1331 1370 5.991328 AGAACACACAGTTAAGACACATG 57.009 39.130 0.00 0.00 41.51 3.21
1332 1371 5.296780 CCAAGAACACACAGTTAAGACACAT 59.703 40.000 0.00 0.00 41.51 3.21
1336 1375 3.003378 GCCCAAGAACACACAGTTAAGAC 59.997 47.826 0.00 0.00 41.51 3.01
1337 1376 3.211045 GCCCAAGAACACACAGTTAAGA 58.789 45.455 0.00 0.00 41.51 2.10
1338 1377 2.032030 CGCCCAAGAACACACAGTTAAG 60.032 50.000 0.00 0.00 41.51 1.85
1341 1380 0.393808 ACGCCCAAGAACACACAGTT 60.394 50.000 0.00 0.00 44.93 3.16
1358 1403 3.197790 CATTGGCCTCCTGCGACG 61.198 66.667 3.32 0.00 42.61 5.12
1463 1511 5.144100 TGGAGTTTGGCAAGGAATAAAAGA 58.856 37.500 0.00 0.00 0.00 2.52
1469 1517 3.173953 TCATGGAGTTTGGCAAGGAAT 57.826 42.857 0.00 0.00 0.00 3.01
1472 1520 5.127519 TGATTTATCATGGAGTTTGGCAAGG 59.872 40.000 0.00 0.00 0.00 3.61
1514 1750 6.535150 TCCATCGTCATCTCAAACAAGTATTC 59.465 38.462 0.00 0.00 0.00 1.75
1640 1876 3.269381 GGGAGGGAATATGGCATGGAATA 59.731 47.826 10.98 0.00 0.00 1.75
1649 1885 2.453521 CATGCATGGGAGGGAATATGG 58.546 52.381 19.40 0.00 0.00 2.74
1653 1889 1.152398 GGCATGCATGGGAGGGAAT 60.152 57.895 27.34 0.00 0.00 3.01
1654 1890 1.951923 ATGGCATGCATGGGAGGGAA 61.952 55.000 27.34 0.00 0.00 3.97
1657 1893 1.822990 GAATATGGCATGCATGGGAGG 59.177 52.381 27.34 2.48 0.00 4.30
1658 1894 2.803956 AGAATATGGCATGCATGGGAG 58.196 47.619 27.34 2.89 0.00 4.30
1682 1918 1.683917 AGAGCTGCTACCACCGAATAG 59.316 52.381 0.15 0.00 0.00 1.73
1892 2137 2.046411 TGAATCCGCACGCCATGT 60.046 55.556 0.00 0.00 0.00 3.21
1911 2156 1.028905 TGTTCCAGAAGGCCAAAACG 58.971 50.000 5.01 0.00 33.74 3.60
1941 2190 1.752683 ACTACTCCTCTACTGCCACG 58.247 55.000 0.00 0.00 0.00 4.94
1954 2203 2.623889 ACTGACGGCCATCATACTACTC 59.376 50.000 0.00 0.00 0.00 2.59
1955 2204 2.362397 CACTGACGGCCATCATACTACT 59.638 50.000 0.00 0.00 0.00 2.57
1969 2218 4.757554 CATGCATGCACACTGACG 57.242 55.556 25.37 1.67 0.00 4.35
2063 2317 4.736126 TGAAACACAGAACACTGAGAGA 57.264 40.909 0.00 0.00 35.80 3.10
2076 2330 2.364002 TGATCCACGAGACTGAAACACA 59.636 45.455 0.00 0.00 0.00 3.72
2077 2331 2.989840 CTGATCCACGAGACTGAAACAC 59.010 50.000 0.00 0.00 0.00 3.32
2078 2332 2.628178 ACTGATCCACGAGACTGAAACA 59.372 45.455 0.00 0.00 0.00 2.83
2079 2333 2.989840 CACTGATCCACGAGACTGAAAC 59.010 50.000 0.00 0.00 0.00 2.78
2080 2334 2.628178 ACACTGATCCACGAGACTGAAA 59.372 45.455 0.00 0.00 0.00 2.69
2081 2335 2.239400 ACACTGATCCACGAGACTGAA 58.761 47.619 0.00 0.00 0.00 3.02
2082 2336 1.911057 ACACTGATCCACGAGACTGA 58.089 50.000 0.00 0.00 0.00 3.41
2083 2337 2.029918 TGAACACTGATCCACGAGACTG 60.030 50.000 0.00 0.00 0.00 3.51
2084 2338 2.230025 CTGAACACTGATCCACGAGACT 59.770 50.000 0.00 0.00 0.00 3.24
2123 2390 8.397575 TGTACCATTACAAACAATAGCTTGAA 57.602 30.769 0.00 0.00 35.14 2.69
2134 2401 8.132362 TGAACTTCAACATGTACCATTACAAAC 58.868 33.333 0.00 0.00 41.64 2.93
2136 2403 7.500892 AGTGAACTTCAACATGTACCATTACAA 59.499 33.333 0.00 0.00 41.64 2.41
2140 2411 6.321181 ACAAGTGAACTTCAACATGTACCATT 59.679 34.615 0.00 0.00 33.11 3.16
2178 2450 2.734606 CGCTGTGACGATGGAGTAAAAA 59.265 45.455 0.00 0.00 34.06 1.94
2182 2454 0.885879 AACGCTGTGACGATGGAGTA 59.114 50.000 0.00 0.00 36.70 2.59
2183 2455 0.667487 CAACGCTGTGACGATGGAGT 60.667 55.000 0.00 0.00 32.81 3.85
2184 2456 2.073307 CAACGCTGTGACGATGGAG 58.927 57.895 0.00 0.00 32.81 3.86
2185 2457 4.260194 CAACGCTGTGACGATGGA 57.740 55.556 0.00 0.00 32.81 3.41
2187 2459 2.476051 GCCAACGCTGTGACGATG 59.524 61.111 0.00 0.00 35.81 3.84
2188 2460 2.742372 GGCCAACGCTGTGACGAT 60.742 61.111 0.00 0.00 36.70 3.73
2189 2461 3.529341 ATGGCCAACGCTGTGACGA 62.529 57.895 10.96 0.00 36.70 4.20
2190 2462 2.128853 AAATGGCCAACGCTGTGACG 62.129 55.000 10.96 0.00 39.50 4.35
2191 2463 0.031994 AAAATGGCCAACGCTGTGAC 59.968 50.000 10.96 0.00 34.44 3.67
2204 2476 3.502979 CCAAAGGGCACAAATGAAAATGG 59.497 43.478 0.00 0.00 0.00 3.16
2212 2484 2.323999 TCCATCCAAAGGGCACAAAT 57.676 45.000 0.00 0.00 0.00 2.32
2234 2506 0.744874 TGATCGACGATCTCCCCAAC 59.255 55.000 31.65 10.07 39.56 3.77
2239 2511 2.376956 CGAGTTTGATCGACGATCTCC 58.623 52.381 31.65 20.95 45.56 3.71
2259 2531 0.246635 ACGTGAGCCATGACAGTACC 59.753 55.000 0.00 0.00 0.00 3.34
2298 2571 5.300752 TCATTCGCCATTTAGATCTCTTCC 58.699 41.667 0.00 0.00 0.00 3.46
2475 2751 1.860950 CAAATGCACGATCCTACGGAG 59.139 52.381 0.00 0.00 34.05 4.63
2576 2852 3.066481 CCCTAGTACTCCTGCTCGTTAAC 59.934 52.174 0.00 0.00 0.00 2.01
2597 2873 1.666872 GTGCCGTCACAGTGGTACC 60.667 63.158 4.43 4.43 42.66 3.34
2632 2908 8.367660 TGTCACCCCTGCAATAAAATAAAATA 57.632 30.769 0.00 0.00 0.00 1.40
2633 2909 7.251321 TGTCACCCCTGCAATAAAATAAAAT 57.749 32.000 0.00 0.00 0.00 1.82
2643 3397 1.604593 GTGCTGTCACCCCTGCAAT 60.605 57.895 0.00 0.00 40.34 3.56
2694 3448 2.678336 GGAGAACTATGGAACGCTTTGG 59.322 50.000 0.00 0.00 0.00 3.28
2780 3556 2.243957 CGTTGCACAAGCGAGTGGA 61.244 57.895 12.44 7.56 46.23 4.02
2781 3557 2.162921 CTCGTTGCACAAGCGAGTGG 62.163 60.000 18.65 0.00 44.69 4.00
2782 3558 1.202568 CTCGTTGCACAAGCGAGTG 59.797 57.895 18.65 7.14 44.69 3.51
2783 3559 3.630204 CTCGTTGCACAAGCGAGT 58.370 55.556 18.65 0.00 44.69 4.18
2785 3561 2.664851 CCCTCGTTGCACAAGCGA 60.665 61.111 0.00 0.00 46.23 4.93
2786 3562 4.389576 GCCCTCGTTGCACAAGCG 62.390 66.667 0.00 0.00 46.23 4.68
2787 3563 2.980233 AGCCCTCGTTGCACAAGC 60.980 61.111 0.00 0.00 42.57 4.01
2788 3564 0.957395 ATCAGCCCTCGTTGCACAAG 60.957 55.000 0.00 0.00 0.00 3.16
2789 3565 0.537143 AATCAGCCCTCGTTGCACAA 60.537 50.000 0.00 0.00 0.00 3.33
2790 3566 0.955428 GAATCAGCCCTCGTTGCACA 60.955 55.000 0.00 0.00 0.00 4.57
2791 3567 0.674895 AGAATCAGCCCTCGTTGCAC 60.675 55.000 0.00 0.00 0.00 4.57
2792 3568 0.674581 CAGAATCAGCCCTCGTTGCA 60.675 55.000 0.00 0.00 0.00 4.08
2793 3569 0.674895 ACAGAATCAGCCCTCGTTGC 60.675 55.000 0.00 0.00 0.00 4.17
2794 3570 1.081892 CACAGAATCAGCCCTCGTTG 58.918 55.000 0.00 0.00 0.00 4.10
2795 3571 0.687354 ACACAGAATCAGCCCTCGTT 59.313 50.000 0.00 0.00 0.00 3.85
2796 3572 0.247736 GACACAGAATCAGCCCTCGT 59.752 55.000 0.00 0.00 0.00 4.18
2797 3573 0.247460 TGACACAGAATCAGCCCTCG 59.753 55.000 0.00 0.00 0.00 4.63
2798 3574 1.002430 TGTGACACAGAATCAGCCCTC 59.998 52.381 3.56 0.00 0.00 4.30
2799 3575 1.059098 TGTGACACAGAATCAGCCCT 58.941 50.000 3.56 0.00 0.00 5.19
2800 3576 1.537202 GTTGTGACACAGAATCAGCCC 59.463 52.381 8.55 0.00 0.00 5.19
2801 3577 2.221169 TGTTGTGACACAGAATCAGCC 58.779 47.619 8.55 0.00 0.00 4.85
2815 3591 5.666969 TTAATCCAGAACTTCGTGTTGTG 57.333 39.130 11.79 11.79 45.92 3.33
2816 3592 6.485313 TCATTTAATCCAGAACTTCGTGTTGT 59.515 34.615 1.75 0.00 39.30 3.32
2817 3593 6.898041 TCATTTAATCCAGAACTTCGTGTTG 58.102 36.000 1.75 0.00 39.30 3.33
2818 3594 7.504924 TTCATTTAATCCAGAACTTCGTGTT 57.495 32.000 0.00 0.00 42.38 3.32
2819 3595 7.360361 GTTTCATTTAATCCAGAACTTCGTGT 58.640 34.615 0.00 0.00 0.00 4.49
2820 3596 6.519761 CGTTTCATTTAATCCAGAACTTCGTG 59.480 38.462 0.00 0.00 0.00 4.35
2821 3597 6.599437 CGTTTCATTTAATCCAGAACTTCGT 58.401 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.