Multiple sequence alignment - TraesCS7A01G400200

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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 TraesCS7A01G400200 chr7A 100.000 3342 0 0 1 3342 580468502 580471843 0.000000e+00 6172.0
1 TraesCS7A01G400200 chr7A 89.091 385 27 7 1978 2354 580506125 580506502 6.530000e-127 464.0
2 TraesCS7A01G400200 chr7A 81.797 423 37 16 273 666 580481328 580481739 5.380000e-83 318.0
3 TraesCS7A01G400200 chr7A 88.889 252 25 3 581 830 580481756 580482006 1.160000e-79 307.0
4 TraesCS7A01G400200 chr7B 92.894 1731 82 18 5 1708 537670892 537672608 0.000000e+00 2477.0
5 TraesCS7A01G400200 chr7B 94.062 943 34 7 1822 2745 537672656 537673595 0.000000e+00 1411.0
6 TraesCS7A01G400200 chr7B 93.813 598 31 6 2746 3340 537673629 537674223 0.000000e+00 894.0
7 TraesCS7A01G400200 chr7B 92.517 441 31 2 1914 2353 537826987 537827426 6.080000e-177 630.0
8 TraesCS7A01G400200 chr7B 90.909 242 13 4 2113 2354 537791857 537792089 1.940000e-82 316.0
9 TraesCS7A01G400200 chr7B 90.000 240 18 3 971 1204 576358339 576358100 4.190000e-79 305.0
10 TraesCS7A01G400200 chr7B 100.000 34 0 0 1790 1823 568110565 568110598 2.780000e-06 63.9
11 TraesCS7A01G400200 chr7B 100.000 33 0 0 1791 1823 568110564 568110532 1.000000e-05 62.1
12 TraesCS7A01G400200 chr7D 92.946 1531 68 19 272 1774 509554015 509555533 0.000000e+00 2193.0
13 TraesCS7A01G400200 chr7D 94.497 945 26 6 1822 2745 509555550 509556489 0.000000e+00 1434.0
14 TraesCS7A01G400200 chr7D 92.219 604 38 5 2746 3340 509556523 509557126 0.000000e+00 846.0
15 TraesCS7A01G400200 chr7D 90.716 377 34 1 1978 2354 509610953 509611328 4.980000e-138 501.0
16 TraesCS7A01G400200 chr7D 82.383 596 55 24 273 830 509571814 509572397 1.090000e-129 473.0
17 TraesCS7A01G400200 chr7D 91.566 83 5 2 3 85 509552995 509553075 2.730000e-21 113.0
18 TraesCS7A01G400200 chr5A 94.514 401 21 1 2746 3145 425485605 425486005 4.740000e-173 617.0
19 TraesCS7A01G400200 chr5A 91.022 401 35 1 2746 3145 44117004 44117404 1.050000e-149 540.0
20 TraesCS7A01G400200 chr3D 92.519 401 29 1 2746 3145 258275422 258275022 1.040000e-159 573.0
21 TraesCS7A01G400200 chr1A 92.663 368 26 1 2746 3112 13963229 13962862 2.280000e-146 529.0
22 TraesCS7A01G400200 chr1A 86.598 97 11 1 1823 1917 531824637 531824541 4.560000e-19 106.0
23 TraesCS7A01G400200 chr1A 94.872 39 2 0 1785 1823 588468065 588468027 1.000000e-05 62.1
24 TraesCS7A01G400200 chr2B 86.912 489 38 9 2224 2711 126731509 126731046 2.950000e-145 525.0
25 TraesCS7A01G400200 chr2B 85.405 370 37 15 1822 2187 126731865 126731509 5.270000e-98 368.0
26 TraesCS7A01G400200 chr2B 89.627 241 18 4 971 1204 529046309 529046549 1.950000e-77 300.0
27 TraesCS7A01G400200 chr2B 92.262 168 12 1 1615 1781 126732041 126731874 1.550000e-58 237.0
28 TraesCS7A01G400200 chr3B 91.250 240 15 3 971 1204 385853902 385853663 4.160000e-84 322.0
29 TraesCS7A01G400200 chr6B 91.139 237 15 3 973 1204 233933906 233933671 1.940000e-82 316.0
30 TraesCS7A01G400200 chr6D 90.377 239 18 2 971 1204 201584803 201585041 3.240000e-80 309.0
31 TraesCS7A01G400200 chr1B 87.952 249 22 4 962 1204 303874638 303874884 1.520000e-73 287.0
32 TraesCS7A01G400200 chr2A 88.333 240 21 4 971 1204 741426643 741426405 7.060000e-72 281.0
33 TraesCS7A01G400200 chr2A 89.500 200 18 2 2949 3145 186437545 186437744 1.990000e-62 250.0
34 TraesCS7A01G400200 chr2A 97.561 41 1 0 1786 1826 144858303 144858263 1.660000e-08 71.3
35 TraesCS7A01G400200 chr5B 86.992 246 32 0 1914 2159 667412697 667412452 9.130000e-71 278.0
36 TraesCS7A01G400200 chr3A 97.619 42 1 0 1782 1823 31434843 31434802 4.630000e-09 73.1
37 TraesCS7A01G400200 chr2D 90.385 52 5 0 1784 1835 23167415 23167364 5.980000e-08 69.4
38 TraesCS7A01G400200 chr4B 84.507 71 6 2 18 84 230638933 230639002 7.740000e-07 65.8


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 TraesCS7A01G400200 chr7A 580468502 580471843 3341 False 6172.000000 6172 100.000000 1 3342 1 chr7A.!!$F1 3341
1 TraesCS7A01G400200 chr7A 580481328 580482006 678 False 312.500000 318 85.343000 273 830 2 chr7A.!!$F3 557
2 TraesCS7A01G400200 chr7B 537670892 537674223 3331 False 1594.000000 2477 93.589667 5 3340 3 chr7B.!!$F4 3335
3 TraesCS7A01G400200 chr7D 509552995 509557126 4131 False 1146.500000 2193 92.807000 3 3340 4 chr7D.!!$F3 3337
4 TraesCS7A01G400200 chr7D 509571814 509572397 583 False 473.000000 473 82.383000 273 830 1 chr7D.!!$F1 557
5 TraesCS7A01G400200 chr2B 126731046 126732041 995 True 376.666667 525 88.193000 1615 2711 3 chr2B.!!$R1 1096

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
89 90 0.250513 CGGCTCCTAGGTTGCTTTCT 59.749 55.0 22.02 0.0 0.00 2.52 F
1373 2317 0.179081 GCATCGGGTAAGGACTGACC 60.179 60.0 0.00 0.0 39.35 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 2525 1.685803 CCCAAGGCATATCCAGCAACA 60.686 52.381 0.0 0.0 37.29 3.33 R
2884 3884 0.034337 GTCGGTGTGCTTCCTTGGTA 59.966 55.000 0.0 0.0 0.00 3.25 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
21 22 1.287425 GTGGTTAGTATCCTGTGCGC 58.713 55.000 0.00 0.00 0.00 6.09
28 29 2.030401 TATCCTGTGCGCGCGTTTT 61.030 52.632 32.35 11.30 0.00 2.43
30 31 4.605967 CCTGTGCGCGCGTTTTGT 62.606 61.111 32.35 0.00 0.00 2.83
31 32 3.085010 CTGTGCGCGCGTTTTGTC 61.085 61.111 32.35 14.02 0.00 3.18
89 90 0.250513 CGGCTCCTAGGTTGCTTTCT 59.749 55.000 22.02 0.00 0.00 2.52
130 405 2.478134 GCATAAGAGGCGATGTCATGTC 59.522 50.000 0.00 0.00 0.00 3.06
181 456 3.181489 CCGACTAGCCGAGTTACAAGATT 60.181 47.826 0.00 0.00 39.06 2.40
182 457 3.791887 CGACTAGCCGAGTTACAAGATTG 59.208 47.826 0.00 0.00 39.06 2.67
183 458 4.438336 CGACTAGCCGAGTTACAAGATTGA 60.438 45.833 0.00 0.00 39.06 2.57
184 459 5.593010 GACTAGCCGAGTTACAAGATTGAT 58.407 41.667 0.00 0.00 39.06 2.57
203 478 9.865321 AGATTGATGTAATTCAGGATTTGTTTG 57.135 29.630 0.00 0.00 0.00 2.93
254 538 6.371595 TGCATTTGAAATCTGGGGTATTTT 57.628 33.333 0.00 0.00 0.00 1.82
329 1121 3.797039 TCAGGTTGATCCTTCTAATGCG 58.203 45.455 0.00 0.00 45.67 4.73
341 1140 3.159353 TCTAATGCGTACGCTTCACAT 57.841 42.857 36.99 21.31 42.51 3.21
342 1141 2.857748 TCTAATGCGTACGCTTCACATG 59.142 45.455 36.99 20.88 42.51 3.21
422 1229 5.659463 TGTAAAGCTGTGCTGACAAAAATT 58.341 33.333 0.00 0.00 39.62 1.82
535 1354 0.773644 AAGGCCCTGTGTCTCAATGT 59.226 50.000 0.00 0.00 0.00 2.71
539 1358 3.010584 AGGCCCTGTGTCTCAATGTATTT 59.989 43.478 0.00 0.00 0.00 1.40
543 1362 6.204882 GGCCCTGTGTCTCAATGTATTTATAC 59.795 42.308 0.00 0.00 0.00 1.47
611 1543 3.487574 GCATCATTACTAGACACTGCGAC 59.512 47.826 0.00 0.00 0.00 5.19
647 1579 4.380531 GGGCTGATGAACGATGATAAGAA 58.619 43.478 0.00 0.00 0.00 2.52
683 1616 5.012328 TCCCTCTCTTTCGAATTAGCTTC 57.988 43.478 0.00 0.00 0.00 3.86
684 1617 4.712337 TCCCTCTCTTTCGAATTAGCTTCT 59.288 41.667 0.00 0.00 0.00 2.85
708 1641 6.166279 TCAGTACATGTTCTCTTCAACATCC 58.834 40.000 2.30 0.00 43.75 3.51
748 1681 2.107031 TGGCATATGGCTGCTAGTCATT 59.893 45.455 27.41 0.00 37.20 2.57
800 1740 9.730420 GTACTTTTTCTACAATGTTTGTGTCAT 57.270 29.630 3.22 0.00 45.03 3.06
838 1778 8.954950 AGATCGACATTATGAAATCAGTTTCT 57.045 30.769 0.00 0.00 43.30 2.52
843 1783 9.098355 CGACATTATGAAATCAGTTTCTTAGGA 57.902 33.333 0.00 0.00 43.30 2.94
914 1854 4.862641 AGGGATGCAGTTAAAGTGGTAT 57.137 40.909 0.00 0.00 0.00 2.73
947 1887 6.446781 AGATGACATGACCATTCACAATTC 57.553 37.500 0.00 0.00 33.38 2.17
953 1893 7.013559 TGACATGACCATTCACAATTCATATCC 59.986 37.037 0.00 0.00 33.38 2.59
1152 2092 5.531287 TGAGAAGTTTTTAGGTTCAAGCTCC 59.469 40.000 0.00 0.00 0.00 4.70
1181 2123 2.561858 TGCAAAGCAATGTAAGCATGGA 59.438 40.909 0.00 0.00 34.76 3.41
1255 2199 4.300189 TGTAAGTTTTGCTTGATTGCGT 57.700 36.364 0.00 0.00 38.05 5.24
1373 2317 0.179081 GCATCGGGTAAGGACTGACC 60.179 60.000 0.00 0.00 39.35 4.02
1407 2352 1.792949 CAAGAACCTCTTTCGTGTCGG 59.207 52.381 0.00 0.00 38.50 4.79
1580 2525 3.385193 GCTTTTGCCACCTACATTGTT 57.615 42.857 0.00 0.00 40.15 2.83
1775 2720 3.119137 AGGCAAGTGGTTCTGTTTGTTTC 60.119 43.478 0.00 0.00 0.00 2.78
1778 2723 5.393678 GGCAAGTGGTTCTGTTTGTTTCTTA 60.394 40.000 0.00 0.00 0.00 2.10
1780 2725 6.253512 GCAAGTGGTTCTGTTTGTTTCTTAAG 59.746 38.462 0.00 0.00 0.00 1.85
1781 2726 7.312899 CAAGTGGTTCTGTTTGTTTCTTAAGT 58.687 34.615 1.63 0.00 0.00 2.24
1782 2727 7.462571 AGTGGTTCTGTTTGTTTCTTAAGTT 57.537 32.000 1.63 0.00 0.00 2.66
1785 2730 9.285770 GTGGTTCTGTTTGTTTCTTAAGTTTAG 57.714 33.333 1.63 0.00 0.00 1.85
1787 2732 9.850628 GGTTCTGTTTGTTTCTTAAGTTTAGTT 57.149 29.630 1.63 0.00 0.00 2.24
1790 2735 8.680001 TCTGTTTGTTTCTTAAGTTTAGTTCCC 58.320 33.333 1.63 0.00 0.00 3.97
1791 2736 7.774134 TGTTTGTTTCTTAAGTTTAGTTCCCC 58.226 34.615 1.63 0.00 0.00 4.81
1792 2737 6.964807 TTGTTTCTTAAGTTTAGTTCCCCC 57.035 37.500 1.63 0.00 0.00 5.40
1793 2738 6.015991 TGTTTCTTAAGTTTAGTTCCCCCA 57.984 37.500 1.63 0.00 0.00 4.96
1794 2739 6.066032 TGTTTCTTAAGTTTAGTTCCCCCAG 58.934 40.000 1.63 0.00 0.00 4.45
1795 2740 4.296621 TCTTAAGTTTAGTTCCCCCAGC 57.703 45.455 1.63 0.00 0.00 4.85
1796 2741 3.914435 TCTTAAGTTTAGTTCCCCCAGCT 59.086 43.478 1.63 0.00 0.00 4.24
1797 2742 5.095809 TCTTAAGTTTAGTTCCCCCAGCTA 58.904 41.667 1.63 0.00 0.00 3.32
1798 2743 3.715638 AAGTTTAGTTCCCCCAGCTAC 57.284 47.619 0.00 0.00 0.00 3.58
1799 2744 2.627933 AGTTTAGTTCCCCCAGCTACA 58.372 47.619 0.00 0.00 0.00 2.74
1800 2745 2.983898 AGTTTAGTTCCCCCAGCTACAA 59.016 45.455 0.00 0.00 0.00 2.41
1801 2746 3.009143 AGTTTAGTTCCCCCAGCTACAAG 59.991 47.826 0.00 0.00 0.00 3.16
1802 2747 2.337359 TAGTTCCCCCAGCTACAAGT 57.663 50.000 0.00 0.00 0.00 3.16
1803 2748 2.337359 AGTTCCCCCAGCTACAAGTA 57.663 50.000 0.00 0.00 0.00 2.24
1804 2749 2.846950 AGTTCCCCCAGCTACAAGTAT 58.153 47.619 0.00 0.00 0.00 2.12
1805 2750 3.190439 AGTTCCCCCAGCTACAAGTATT 58.810 45.455 0.00 0.00 0.00 1.89
1819 2764 4.819105 CAAGTATTGTGGTACAGAGGGA 57.181 45.455 0.00 0.00 42.34 4.20
1820 2765 4.759782 CAAGTATTGTGGTACAGAGGGAG 58.240 47.826 0.00 0.00 42.34 4.30
1859 2804 3.586892 CGAAAGGTTGAAGGGTAGAGAC 58.413 50.000 0.00 0.00 0.00 3.36
2038 3002 4.334552 TGCAAGTCATCCTCATTAAAGCA 58.665 39.130 0.00 0.00 0.00 3.91
2296 3260 0.104304 TTCTTCTATTCCTCGCGGCC 59.896 55.000 6.13 0.00 0.00 6.13
2359 3323 4.900096 CTGATGTTTCAGTCTTGTCTCG 57.100 45.455 0.00 0.00 43.73 4.04
2569 3534 4.469657 TGGTCTGCAAAGGATGTTACTTT 58.530 39.130 0.00 0.00 38.62 2.66
2570 3535 4.518970 TGGTCTGCAAAGGATGTTACTTTC 59.481 41.667 0.00 0.00 36.09 2.62
2662 3629 9.003658 CCTAAAAGTACATCTTCAATTGTCACT 57.996 33.333 5.13 0.00 35.02 3.41
2678 3645 3.188254 TGTCACTGTTCATATTTGTGCCG 59.812 43.478 0.00 0.00 0.00 5.69
2738 3705 1.221021 GCTAAGGCCTGCGTAACCT 59.779 57.895 5.69 0.00 34.45 3.50
2761 3761 9.004231 ACCTGAATCTATCTTGGGTAACTAAAT 57.996 33.333 0.00 0.00 36.22 1.40
2822 3822 4.082081 TGTGGTTTGGCATCAATCTTGATC 60.082 41.667 2.45 0.00 45.62 2.92
2828 3828 7.315142 GTTTGGCATCAATCTTGATCAAGTTA 58.685 34.615 29.80 15.90 45.62 2.24
2850 3850 2.935955 CCACGTCACGGTGCTTTC 59.064 61.111 0.35 0.00 36.59 2.62
2899 3899 0.811281 GGCATACCAAGGAAGCACAC 59.189 55.000 0.00 0.00 35.26 3.82
2900 3900 0.811281 GCATACCAAGGAAGCACACC 59.189 55.000 0.00 0.00 0.00 4.16
2947 3947 5.124776 CGCCTTTATTTATTCACCCTTCACA 59.875 40.000 0.00 0.00 0.00 3.58
3032 4040 7.120726 TCTGTAGTATCTGTTCGACAAATGAGA 59.879 37.037 0.00 0.00 0.00 3.27
3067 4075 7.149569 TCTTTGCCTCTGATTTATGAACTTG 57.850 36.000 0.00 0.00 0.00 3.16
3069 4077 5.885230 TGCCTCTGATTTATGAACTTGTG 57.115 39.130 0.00 0.00 0.00 3.33
3086 4094 5.133221 ACTTGTGTTAGTTGATCTTTGGCT 58.867 37.500 0.00 0.00 0.00 4.75
3155 4163 3.548770 TGCTCTTATGAGAAATGCCCAG 58.451 45.455 9.72 0.00 42.73 4.45
3157 4165 3.548770 CTCTTATGAGAAATGCCCAGCA 58.451 45.455 0.00 0.00 42.13 4.41
3159 4167 4.539726 TCTTATGAGAAATGCCCAGCAAT 58.460 39.130 0.00 0.00 43.62 3.56
3174 4182 5.222631 CCCAGCAATGTTCAGTTTTAGTTC 58.777 41.667 0.00 0.00 0.00 3.01
3270 4279 2.098117 GCTCTTGCCATGTGGTATGTTC 59.902 50.000 0.35 0.00 37.57 3.18
3333 4342 6.784031 AGATATCCTGTGACTTCAAAAAGGT 58.216 36.000 0.00 0.00 36.78 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.011968 TCAGATCCCGACAAAACGCG 61.012 55.000 3.53 3.53 0.00 6.01
28 29 1.751351 GTGTCAGATCAGATCCCGACA 59.249 52.381 21.53 21.53 38.88 4.35
30 31 2.443958 AGTGTCAGATCAGATCCCGA 57.556 50.000 6.80 1.54 0.00 5.14
31 32 3.481453 TCTAGTGTCAGATCAGATCCCG 58.519 50.000 6.80 0.00 0.00 5.14
130 405 1.140375 GTGTAGGTCTAACGGCCCG 59.860 63.158 0.00 0.00 0.00 6.13
181 456 6.867816 GTGCAAACAAATCCTGAATTACATCA 59.132 34.615 0.00 0.00 0.00 3.07
182 457 6.867816 TGTGCAAACAAATCCTGAATTACATC 59.132 34.615 0.00 0.00 0.00 3.06
183 458 6.757237 TGTGCAAACAAATCCTGAATTACAT 58.243 32.000 0.00 0.00 0.00 2.29
184 459 6.154203 TGTGCAAACAAATCCTGAATTACA 57.846 33.333 0.00 0.00 0.00 2.41
203 478 2.223340 CGTCAGGAAGCCAATAATGTGC 60.223 50.000 0.00 0.00 0.00 4.57
229 513 2.181975 ACCCCAGATTTCAAATGCAGG 58.818 47.619 0.00 0.00 0.00 4.85
254 538 8.194104 TGCAACTGCTTTTTACTCAAATCTAAA 58.806 29.630 2.95 0.00 42.66 1.85
257 541 6.147864 TGCAACTGCTTTTTACTCAAATCT 57.852 33.333 2.95 0.00 42.66 2.40
258 542 6.826893 TTGCAACTGCTTTTTACTCAAATC 57.173 33.333 0.00 0.00 42.66 2.17
259 543 6.818142 AGTTTGCAACTGCTTTTTACTCAAAT 59.182 30.769 0.00 0.00 41.01 2.32
288 1080 0.390866 AGCTCACATGCGTTCCTCTG 60.391 55.000 0.00 0.00 38.13 3.35
341 1140 0.320683 AGCACACGATAAGCACTGCA 60.321 50.000 3.30 0.00 0.00 4.41
342 1141 0.371645 GAGCACACGATAAGCACTGC 59.628 55.000 0.00 0.00 0.00 4.40
543 1362 9.869844 CTAGTCTAGTTTCACACAAATTTCTTG 57.130 33.333 0.00 0.00 0.00 3.02
549 1368 7.897864 AGTAGCTAGTCTAGTTTCACACAAAT 58.102 34.615 8.68 0.00 0.00 2.32
647 1579 6.512514 AAGAGAGGGAGAAATAGCATGATT 57.487 37.500 0.00 0.00 0.00 2.57
683 1616 6.312426 GGATGTTGAAGAGAACATGTACTGAG 59.688 42.308 0.00 0.00 44.78 3.35
684 1617 6.014242 AGGATGTTGAAGAGAACATGTACTGA 60.014 38.462 0.00 0.00 44.78 3.41
708 1641 3.189287 GCCAACTTACACCAGAATGTGAG 59.811 47.826 0.00 0.00 40.94 3.51
748 1681 0.834261 TGGATCACCACGACCCAGAA 60.834 55.000 0.00 0.00 41.77 3.02
813 1753 8.954950 AGAAACTGATTTCATAATGTCGATCT 57.045 30.769 2.86 0.00 45.78 2.75
817 1757 9.098355 TCCTAAGAAACTGATTTCATAATGTCG 57.902 33.333 2.86 0.00 45.78 4.35
914 1854 6.353404 TGGTCATGTCATCTACAAACTACA 57.647 37.500 0.00 0.00 42.70 2.74
947 1887 6.586344 ACCAATAGTCAGACAACAGGATATG 58.414 40.000 2.66 0.00 0.00 1.78
953 1893 6.038161 TGTTCAAACCAATAGTCAGACAACAG 59.962 38.462 2.66 0.00 0.00 3.16
997 1937 3.449377 TCAATGTTCATTGCTGCCATCAT 59.551 39.130 17.48 0.00 0.00 2.45
1121 2061 7.332557 TGAACCTAAAAACTTCTCACTGTACA 58.667 34.615 0.00 0.00 0.00 2.90
1152 2092 5.003778 GCTTACATTGCTTTGCATAAAGTCG 59.996 40.000 0.36 0.00 44.11 4.18
1181 2123 9.970553 ACAGGTATATCTATGAATGAAATGCAT 57.029 29.630 0.00 0.00 46.79 3.96
1255 2199 8.040002 TGGACAAATATTGGGTGATCTGTATA 57.960 34.615 0.00 0.00 34.12 1.47
1373 2317 2.226674 GGTTCTTGAGAAAAAGGAGGCG 59.773 50.000 0.00 0.00 35.58 5.52
1407 2352 1.731720 GACCTCACAATCTGCAGGTC 58.268 55.000 15.13 7.84 46.26 3.85
1580 2525 1.685803 CCCAAGGCATATCCAGCAACA 60.686 52.381 0.00 0.00 37.29 3.33
1726 2671 5.230936 CAGCACTCACTATAATGAAGTGACG 59.769 44.000 14.05 2.57 46.38 4.35
1775 2720 4.302559 AGCTGGGGGAACTAAACTTAAG 57.697 45.455 0.00 0.00 0.00 1.85
1778 2723 2.983898 TGTAGCTGGGGGAACTAAACTT 59.016 45.455 0.00 0.00 0.00 2.66
1780 2725 3.244805 ACTTGTAGCTGGGGGAACTAAAC 60.245 47.826 0.00 0.00 0.00 2.01
1781 2726 2.983898 ACTTGTAGCTGGGGGAACTAAA 59.016 45.455 0.00 0.00 0.00 1.85
1782 2727 2.627933 ACTTGTAGCTGGGGGAACTAA 58.372 47.619 0.00 0.00 0.00 2.24
1785 2730 3.279434 CAATACTTGTAGCTGGGGGAAC 58.721 50.000 0.00 0.00 0.00 3.62
1787 2732 2.238646 CACAATACTTGTAGCTGGGGGA 59.761 50.000 0.00 0.00 43.23 4.81
1788 2733 2.643551 CACAATACTTGTAGCTGGGGG 58.356 52.381 0.00 0.00 43.23 5.40
1789 2734 2.026262 ACCACAATACTTGTAGCTGGGG 60.026 50.000 0.00 10.59 43.23 4.96
1790 2735 3.350219 ACCACAATACTTGTAGCTGGG 57.650 47.619 0.00 0.00 43.23 4.45
1791 2736 4.827692 TGTACCACAATACTTGTAGCTGG 58.172 43.478 0.00 0.00 43.23 4.85
1792 2737 5.720202 TCTGTACCACAATACTTGTAGCTG 58.280 41.667 0.00 0.00 43.23 4.24
1793 2738 5.105310 CCTCTGTACCACAATACTTGTAGCT 60.105 44.000 0.00 0.00 43.23 3.32
1794 2739 5.109903 CCTCTGTACCACAATACTTGTAGC 58.890 45.833 0.00 0.00 43.23 3.58
1795 2740 5.421056 TCCCTCTGTACCACAATACTTGTAG 59.579 44.000 0.00 0.00 43.23 2.74
1796 2741 5.335261 TCCCTCTGTACCACAATACTTGTA 58.665 41.667 0.00 0.00 43.23 2.41
1797 2742 4.164981 TCCCTCTGTACCACAATACTTGT 58.835 43.478 0.00 0.00 46.75 3.16
1798 2743 4.223032 ACTCCCTCTGTACCACAATACTTG 59.777 45.833 0.00 0.00 0.00 3.16
1799 2744 4.426704 ACTCCCTCTGTACCACAATACTT 58.573 43.478 0.00 0.00 0.00 2.24
1800 2745 4.062490 ACTCCCTCTGTACCACAATACT 57.938 45.455 0.00 0.00 0.00 2.12
1801 2746 5.927281 TTACTCCCTCTGTACCACAATAC 57.073 43.478 0.00 0.00 0.00 1.89
1802 2747 6.938698 TTTTACTCCCTCTGTACCACAATA 57.061 37.500 0.00 0.00 0.00 1.90
1803 2748 5.836024 TTTTACTCCCTCTGTACCACAAT 57.164 39.130 0.00 0.00 0.00 2.71
1804 2749 5.556915 CATTTTACTCCCTCTGTACCACAA 58.443 41.667 0.00 0.00 0.00 3.33
1805 2750 4.564821 GCATTTTACTCCCTCTGTACCACA 60.565 45.833 0.00 0.00 0.00 4.17
1806 2751 3.939592 GCATTTTACTCCCTCTGTACCAC 59.060 47.826 0.00 0.00 0.00 4.16
1807 2752 3.585289 TGCATTTTACTCCCTCTGTACCA 59.415 43.478 0.00 0.00 0.00 3.25
1808 2753 4.081087 TCTGCATTTTACTCCCTCTGTACC 60.081 45.833 0.00 0.00 0.00 3.34
1809 2754 5.086104 TCTGCATTTTACTCCCTCTGTAC 57.914 43.478 0.00 0.00 0.00 2.90
1810 2755 5.957771 ATCTGCATTTTACTCCCTCTGTA 57.042 39.130 0.00 0.00 0.00 2.74
1811 2756 4.851639 ATCTGCATTTTACTCCCTCTGT 57.148 40.909 0.00 0.00 0.00 3.41
1812 2757 5.923204 AGTATCTGCATTTTACTCCCTCTG 58.077 41.667 0.00 0.00 0.00 3.35
1813 2758 6.239458 GCTAGTATCTGCATTTTACTCCCTCT 60.239 42.308 6.62 0.00 0.00 3.69
1814 2759 5.929415 GCTAGTATCTGCATTTTACTCCCTC 59.071 44.000 6.62 0.00 0.00 4.30
1815 2760 5.509840 CGCTAGTATCTGCATTTTACTCCCT 60.510 44.000 6.62 0.00 0.00 4.20
1816 2761 4.686554 CGCTAGTATCTGCATTTTACTCCC 59.313 45.833 6.62 1.07 0.00 4.30
1817 2762 5.529791 TCGCTAGTATCTGCATTTTACTCC 58.470 41.667 6.62 1.33 0.00 3.85
1818 2763 7.306866 CCTTTCGCTAGTATCTGCATTTTACTC 60.307 40.741 6.62 0.00 0.00 2.59
1819 2764 6.480320 CCTTTCGCTAGTATCTGCATTTTACT 59.520 38.462 8.03 8.03 0.00 2.24
1820 2765 6.258068 ACCTTTCGCTAGTATCTGCATTTTAC 59.742 38.462 0.00 0.00 0.00 2.01
2296 3260 2.561549 AAAGCATGGGGAATTGCGCG 62.562 55.000 0.00 0.00 43.61 6.86
2354 3318 1.777941 AGGTATCCCTGTTCCGAGAC 58.222 55.000 0.00 0.00 40.58 3.36
2377 3341 6.439058 TCCACCTTGAAGAAAAGAAAAGGAAA 59.561 34.615 6.75 0.00 39.88 3.13
2378 3342 5.955355 TCCACCTTGAAGAAAAGAAAAGGAA 59.045 36.000 6.75 0.00 39.88 3.36
2529 3494 7.611467 TGCAGACCAATAAGATAACATTGACTT 59.389 33.333 0.00 0.00 34.69 3.01
2550 3515 5.620206 TGAGAAAGTAACATCCTTTGCAGA 58.380 37.500 0.00 0.00 32.47 4.26
2569 3534 8.140628 GTCTTCAGCTAGTCATAAATCATGAGA 58.859 37.037 0.09 0.00 44.42 3.27
2570 3535 7.924947 TGTCTTCAGCTAGTCATAAATCATGAG 59.075 37.037 0.09 0.00 44.42 2.90
2662 3629 2.161410 GCAGACGGCACAAATATGAACA 59.839 45.455 0.00 0.00 43.97 3.18
2732 3699 7.793036 AGTTACCCAAGATAGATTCAGGTTAC 58.207 38.462 0.00 0.00 30.30 2.50
2789 3789 1.818674 GCCAAACCACATGTTAGGGAG 59.181 52.381 7.66 0.00 35.67 4.30
2822 3822 2.570169 CGTGACGTGGCAAATAACTTG 58.430 47.619 0.00 0.00 38.15 3.16
2828 3828 2.903547 GCACCGTGACGTGGCAAAT 61.904 57.895 12.20 0.00 34.16 2.32
2884 3884 0.034337 GTCGGTGTGCTTCCTTGGTA 59.966 55.000 0.00 0.00 0.00 3.25
2899 3899 4.418013 TGTATGCAAATTTCACTGTCGG 57.582 40.909 0.00 0.00 0.00 4.79
2900 3900 5.164292 CGTTTGTATGCAAATTTCACTGTCG 60.164 40.000 12.26 4.30 45.11 4.35
3032 4040 5.503927 TCAGAGGCAAAGAAATGCTTATCT 58.496 37.500 0.00 0.00 45.68 1.98
3067 4075 5.689383 TTCAGCCAAAGATCAACTAACAC 57.311 39.130 0.00 0.00 0.00 3.32
3069 4077 8.443953 AGATATTCAGCCAAAGATCAACTAAC 57.556 34.615 0.00 0.00 30.91 2.34
3086 4094 8.105197 CCCATCTGGATGTTTCATAGATATTCA 58.895 37.037 9.35 0.00 37.11 2.57
3174 4182 3.199946 TGCCAGAGGGGAAAGTATTAGTG 59.800 47.826 0.00 0.00 40.01 2.74


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

AutoCloner maintained by Alex Coulton.