Multiple sequence alignment - TraesCS7D01G146300

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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 TraesCS7D01G146300 chr7D 100.000 2874 0 0 1 2874 93686704 93683831 0.000000e+00 5308
1 TraesCS7D01G146300 chr7B 90.530 1246 62 31 232 1456 46889538 46888328 0.000000e+00 1596
2 TraesCS7D01G146300 chr7B 84.397 1128 83 45 1488 2604 46888333 46887288 0.000000e+00 1022
3 TraesCS7D01G146300 chr7B 83.784 148 17 3 2610 2752 46887240 46887095 1.800000e-27 134
4 TraesCS7D01G146300 chr7B 87.395 119 10 4 2757 2874 46887128 46887014 6.460000e-27 132
5 TraesCS7D01G146300 chr7A 90.920 837 39 14 1487 2300 96192623 96191801 0.000000e+00 1090
6 TraesCS7D01G146300 chr7A 87.789 606 39 13 617 1195 96193496 96192899 0.000000e+00 676
7 TraesCS7D01G146300 chr7A 89.418 378 19 7 232 588 96193873 96193496 9.390000e-125 457
8 TraesCS7D01G146300 chr7A 88.435 294 28 4 2467 2757 96191409 96191119 1.640000e-92 350
9 TraesCS7D01G146300 chr7A 89.655 203 10 6 5 197 96194150 96193949 6.150000e-62 248
10 TraesCS7D01G146300 chr7A 97.163 141 4 0 1259 1399 96192799 96192659 3.700000e-59 239
11 TraesCS7D01G146300 chr7A 94.958 119 6 0 2756 2874 96191158 96191040 1.360000e-43 187
12 TraesCS7D01G146300 chr3B 83.942 548 41 18 1632 2176 52788223 52787720 5.570000e-132 481
13 TraesCS7D01G146300 chr6D 84.921 126 18 1 1684 1808 445159288 445159163 3.010000e-25 126
14 TraesCS7D01G146300 chrUn 84.252 127 17 3 1684 1808 163384008 163383883 1.400000e-23 121
15 TraesCS7D01G146300 chr6A 84.127 126 19 1 1684 1808 591950975 591950850 1.400000e-23 121


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 TraesCS7D01G146300 chr7D 93683831 93686704 2873 True 5308.000000 5308 100.000000 1 2874 1 chr7D.!!$R1 2873
1 TraesCS7D01G146300 chr7B 46887014 46889538 2524 True 721.000000 1596 86.526500 232 2874 4 chr7B.!!$R1 2642
2 TraesCS7D01G146300 chr7A 96191040 96194150 3110 True 463.857143 1090 91.191143 5 2874 7 chr7A.!!$R1 2869
3 TraesCS7D01G146300 chr3B 52787720 52788223 503 True 481.000000 481 83.942000 1632 2176 1 chr3B.!!$R1 544

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
992 1099 0.111001 CGGCGTCTTTACCAACGTTG 60.111 55.0 21.47 21.47 40.87 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2582 3093 0.102481 CCTCCTTATGACGTGACCCG 59.898 60.0 0.0 0.0 44.03 5.28 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
30 31 4.103103 CTCGACGACGCAGGAGCA 62.103 66.667 1.48 0.00 42.27 4.26
44 45 4.947147 AGCAAGCGAAACCGGCCA 62.947 61.111 0.00 0.00 0.00 5.36
53 54 0.808453 GAAACCGGCCAATCGATCGA 60.808 55.000 21.86 21.86 0.00 3.59
54 55 0.179056 AAACCGGCCAATCGATCGAT 60.179 50.000 24.60 24.60 36.23 3.59
75 76 2.421739 GTGTCGTGTCCAGCACCT 59.578 61.111 0.00 0.00 44.97 4.00
132 138 2.035442 GTGGAAGCCAGCGGAAGAC 61.035 63.158 0.00 0.00 32.34 3.01
134 140 2.815647 GAAGCCAGCGGAAGACGG 60.816 66.667 0.00 0.00 44.51 4.79
148 154 0.602905 AGACGGAGAAGGCAAAACGG 60.603 55.000 0.00 0.00 0.00 4.44
157 163 4.337060 GCAAAACGGTGCCGGGTC 62.337 66.667 15.44 0.00 44.69 4.46
158 164 2.593436 CAAAACGGTGCCGGGTCT 60.593 61.111 15.44 0.00 44.69 3.85
168 179 2.890766 GCCGGGTCTGGACTTTGGA 61.891 63.158 2.18 0.00 0.00 3.53
198 209 4.139420 CAACAAGGCGAGCGCGAG 62.139 66.667 15.92 0.19 43.06 5.03
279 340 0.391793 GGAAAGAGGCCTCGTCCTTG 60.392 60.000 34.53 0.00 36.38 3.61
417 491 2.885113 CCACTGTCGCTCCGATCA 59.115 61.111 0.00 0.00 38.42 2.92
419 493 1.869574 CACTGTCGCTCCGATCACG 60.870 63.158 0.00 0.00 38.42 4.35
433 507 2.507110 ATCACGGCACTGTTCTCCCG 62.507 60.000 0.00 0.00 45.80 5.14
614 696 2.504519 GATTTCCCTCCCGTCCCG 59.495 66.667 0.00 0.00 0.00 5.14
615 697 2.285144 ATTTCCCTCCCGTCCCGT 60.285 61.111 0.00 0.00 0.00 5.28
616 698 2.307611 GATTTCCCTCCCGTCCCGTC 62.308 65.000 0.00 0.00 0.00 4.79
700 782 2.409948 ATTAAGCTGGCTGTGGACTC 57.590 50.000 0.00 0.00 0.00 3.36
790 879 4.947147 CCCCCACCACACACCACG 62.947 72.222 0.00 0.00 0.00 4.94
837 926 2.762745 TCGATCGATCACCATACGAGA 58.237 47.619 24.40 7.85 39.31 4.04
838 927 2.479275 TCGATCGATCACCATACGAGAC 59.521 50.000 24.40 0.00 39.31 3.36
931 1023 2.897350 GCCCGTATGAGCAGTGCC 60.897 66.667 12.58 3.92 0.00 5.01
970 1077 1.876453 GCTCACGTACGTGCACAGTG 61.876 60.000 37.13 23.18 45.04 3.66
985 1092 1.012486 CAGTGGTCGGCGTCTTTACC 61.012 60.000 6.85 7.34 0.00 2.85
992 1099 0.111001 CGGCGTCTTTACCAACGTTG 60.111 55.000 21.47 21.47 40.87 4.10
1197 1304 2.956964 CGGCGAGCTTGATCGGTC 60.957 66.667 4.70 0.00 42.94 4.79
1202 1309 1.586564 GAGCTTGATCGGTCGGTCG 60.587 63.158 0.00 0.00 0.00 4.79
1223 1330 3.059044 CGATCGTCTCGTAGGTTGTTTTG 59.941 47.826 7.03 0.00 42.56 2.44
1224 1331 3.441496 TCGTCTCGTAGGTTGTTTTGT 57.559 42.857 0.00 0.00 0.00 2.83
1243 1350 7.540400 TGTTTTGTGTGTGTAATTCAGAGTTTG 59.460 33.333 0.00 0.00 0.00 2.93
1247 1354 6.257849 TGTGTGTGTAATTCAGAGTTTGAGAC 59.742 38.462 0.00 0.00 37.07 3.36
1250 1357 4.389077 GTGTAATTCAGAGTTTGAGACGGG 59.611 45.833 0.00 0.00 37.07 5.28
1257 1408 0.249741 AGTTTGAGACGGGGTGAACG 60.250 55.000 0.00 0.00 37.36 3.95
1351 1502 6.910925 CTGGACCAGAAGCTCAAGAGCAAT 62.911 50.000 22.68 11.80 44.65 3.56
1388 1539 2.028385 ACCGTCATCAAGAGGTGGTTAC 60.028 50.000 0.00 0.00 35.36 2.50
1404 1555 3.932710 TGGTTACTCAAGTTGATCGATGC 59.067 43.478 0.54 0.00 0.00 3.91
1424 1575 1.560923 CGATGCGAGATTCGGTTTCT 58.439 50.000 0.34 0.00 40.84 2.52
1444 1595 2.755836 TTTTGTTCTGCTTCACTCGC 57.244 45.000 0.00 0.00 0.00 5.03
1447 1598 0.601046 TGTTCTGCTTCACTCGCCAG 60.601 55.000 0.00 0.00 0.00 4.85
1455 1606 3.772636 CACTCGCCAGTGTGATCG 58.227 61.111 2.94 0.00 44.63 3.69
1456 1607 1.212751 CACTCGCCAGTGTGATCGA 59.787 57.895 2.94 0.00 44.63 3.59
1457 1608 1.073216 CACTCGCCAGTGTGATCGAC 61.073 60.000 2.94 0.00 44.63 4.20
1458 1609 1.869574 CTCGCCAGTGTGATCGACG 60.870 63.158 0.00 0.00 0.00 5.12
1459 1610 2.126463 CGCCAGTGTGATCGACGT 60.126 61.111 0.00 0.00 0.00 4.34
1460 1611 2.436539 CGCCAGTGTGATCGACGTG 61.437 63.158 0.00 0.00 0.00 4.49
1461 1612 2.730672 GCCAGTGTGATCGACGTGC 61.731 63.158 0.00 0.00 0.00 5.34
1462 1613 2.436539 CCAGTGTGATCGACGTGCG 61.437 63.158 0.00 0.00 42.69 5.34
1483 1634 5.720261 CGAAGCAAAGGGATTAGTTAGAC 57.280 43.478 0.00 0.00 0.00 2.59
1484 1635 4.267928 CGAAGCAAAGGGATTAGTTAGACG 59.732 45.833 0.00 0.00 0.00 4.18
1485 1636 4.820894 AGCAAAGGGATTAGTTAGACGT 57.179 40.909 0.00 0.00 0.00 4.34
1531 1682 2.599645 ATCACAGCACGGGGAGCATC 62.600 60.000 0.00 0.00 0.00 3.91
1535 1686 2.825836 GCACGGGGAGCATCAAGG 60.826 66.667 0.00 0.00 36.25 3.61
1537 1688 1.002134 CACGGGGAGCATCAAGGTT 60.002 57.895 0.00 0.00 36.25 3.50
1545 1696 2.559440 GAGCATCAAGGTTAGCAGAGG 58.441 52.381 0.00 0.00 33.17 3.69
2013 2189 3.531538 ACCACTTGTATTGTAGGATGCG 58.468 45.455 0.00 0.00 0.00 4.73
2043 2219 1.168714 GATGGCAGACACTTGGGAAC 58.831 55.000 0.00 0.00 0.00 3.62
2079 2255 0.447801 CGGCCGTGAAAGAAATCCTG 59.552 55.000 19.50 0.00 0.00 3.86
2082 2258 0.811281 CCGTGAAAGAAATCCTGGCC 59.189 55.000 0.00 0.00 0.00 5.36
2084 2260 0.811281 GTGAAAGAAATCCTGGCCGG 59.189 55.000 3.88 3.88 0.00 6.13
2143 2319 1.200020 CCGGTTCTGCCATTTCAGTTC 59.800 52.381 0.00 0.00 36.97 3.01
2144 2320 2.154462 CGGTTCTGCCATTTCAGTTCT 58.846 47.619 0.00 0.00 36.97 3.01
2230 2408 1.394917 GCAATGTCAGTCCGATGTGTC 59.605 52.381 0.00 0.00 0.00 3.67
2241 2422 1.339055 CCGATGTGTCACACCATCCTT 60.339 52.381 8.08 0.00 32.73 3.36
2300 2545 1.145571 AGCAAGGGTGGGACTTTGTA 58.854 50.000 0.00 0.00 0.00 2.41
2301 2546 1.497286 AGCAAGGGTGGGACTTTGTAA 59.503 47.619 0.00 0.00 0.00 2.41
2302 2547 1.886542 GCAAGGGTGGGACTTTGTAAG 59.113 52.381 0.00 0.00 0.00 2.34
2303 2548 2.488347 GCAAGGGTGGGACTTTGTAAGA 60.488 50.000 0.00 0.00 0.00 2.10
2304 2549 3.412386 CAAGGGTGGGACTTTGTAAGAG 58.588 50.000 0.00 0.00 0.00 2.85
2305 2550 1.985895 AGGGTGGGACTTTGTAAGAGG 59.014 52.381 0.00 0.00 0.00 3.69
2306 2551 1.613520 GGGTGGGACTTTGTAAGAGGC 60.614 57.143 0.00 0.00 0.00 4.70
2307 2552 1.439679 GTGGGACTTTGTAAGAGGCG 58.560 55.000 0.00 0.00 0.00 5.52
2308 2553 0.321298 TGGGACTTTGTAAGAGGCGC 60.321 55.000 0.00 0.00 35.77 6.53
2309 2554 1.359459 GGGACTTTGTAAGAGGCGCG 61.359 60.000 0.00 0.00 0.00 6.86
2310 2555 0.389426 GGACTTTGTAAGAGGCGCGA 60.389 55.000 12.10 0.00 0.00 5.87
2311 2556 1.641577 GACTTTGTAAGAGGCGCGAT 58.358 50.000 12.10 0.00 0.00 4.58
2312 2557 1.588861 GACTTTGTAAGAGGCGCGATC 59.411 52.381 12.10 7.03 0.00 3.69
2313 2558 1.067142 ACTTTGTAAGAGGCGCGATCA 60.067 47.619 12.10 0.00 0.00 2.92
2314 2559 2.205074 CTTTGTAAGAGGCGCGATCAT 58.795 47.619 12.10 1.97 0.00 2.45
2315 2560 1.570813 TTGTAAGAGGCGCGATCATG 58.429 50.000 12.10 0.00 0.00 3.07
2316 2561 0.875908 TGTAAGAGGCGCGATCATGC 60.876 55.000 12.10 4.08 0.00 4.06
2317 2562 0.598680 GTAAGAGGCGCGATCATGCT 60.599 55.000 12.10 0.00 0.00 3.79
2318 2563 0.104855 TAAGAGGCGCGATCATGCTT 59.895 50.000 12.10 6.31 0.00 3.91
2319 2564 0.745845 AAGAGGCGCGATCATGCTTT 60.746 50.000 12.10 0.00 0.00 3.51
2320 2565 1.156645 AGAGGCGCGATCATGCTTTC 61.157 55.000 12.10 5.10 0.00 2.62
2321 2566 2.052766 GGCGCGATCATGCTTTCG 60.053 61.111 12.10 7.81 38.37 3.46
2326 2571 3.521534 CGATCATGCTTTCGCCAAG 57.478 52.632 0.00 0.00 35.29 3.61
2397 2642 3.460857 AGCTGACGAAACTGAAGAAGT 57.539 42.857 0.00 0.00 42.60 3.01
2405 2650 3.650139 GAAACTGAAGAAGTCGTGGCTA 58.350 45.455 0.00 0.00 38.56 3.93
2417 2662 1.816835 TCGTGGCTACTACTGAACCTG 59.183 52.381 0.00 0.00 0.00 4.00
2420 2665 1.816835 TGGCTACTACTGAACCTGACG 59.183 52.381 0.00 0.00 0.00 4.35
2425 2670 3.382048 ACTACTGAACCTGACGAAACC 57.618 47.619 0.00 0.00 0.00 3.27
2428 2673 1.137479 ACTGAACCTGACGAAACCGAA 59.863 47.619 0.00 0.00 0.00 4.30
2442 2950 2.556287 CGAAGAAGGCGTGGTTGC 59.444 61.111 0.00 0.00 0.00 4.17
2491 2999 1.757699 GAAGGGTGCTCTACTCCGAAT 59.242 52.381 0.00 0.00 32.34 3.34
2582 3093 3.366374 GCACAAGTATGCTGGGAAAGAAC 60.366 47.826 0.00 0.00 42.62 3.01
2617 3170 0.811616 GAGGGACCTACATGCAAGCG 60.812 60.000 0.00 0.00 0.00 4.68
2618 3171 1.220749 GGGACCTACATGCAAGCGA 59.779 57.895 0.00 0.00 0.00 4.93
2686 3240 1.823899 GGGCATTGGGTGGATCGTC 60.824 63.158 0.00 0.00 0.00 4.20
2699 3253 3.079578 TGGATCGTCGAACTGTAGAACT 58.920 45.455 0.00 0.00 0.00 3.01
2708 3262 4.974275 TCGAACTGTAGAACTCTTGAAACG 59.026 41.667 0.00 0.00 0.00 3.60
2730 3288 1.457303 GCTCACGCCTCGCTTTATATG 59.543 52.381 0.00 0.00 0.00 1.78
2731 3289 2.743938 CTCACGCCTCGCTTTATATGT 58.256 47.619 0.00 0.00 0.00 2.29
2732 3290 3.855895 GCTCACGCCTCGCTTTATATGTA 60.856 47.826 0.00 0.00 0.00 2.29
2733 3291 4.295870 CTCACGCCTCGCTTTATATGTAA 58.704 43.478 0.00 0.00 0.00 2.41
2734 3292 4.684877 TCACGCCTCGCTTTATATGTAAA 58.315 39.130 0.00 0.00 0.00 2.01
2735 3293 4.743151 TCACGCCTCGCTTTATATGTAAAG 59.257 41.667 15.53 15.53 46.20 1.85
2749 3307 9.838975 TTTATATGTAAAGCAAACATCACAGTG 57.161 29.630 0.00 0.00 38.49 3.66
2750 3308 3.963665 TGTAAAGCAAACATCACAGTGC 58.036 40.909 0.00 0.00 37.26 4.40
2751 3309 3.379688 TGTAAAGCAAACATCACAGTGCA 59.620 39.130 0.00 0.00 39.50 4.57
2752 3310 2.497107 AAGCAAACATCACAGTGCAC 57.503 45.000 9.40 9.40 39.50 4.57
2753 3311 0.308684 AGCAAACATCACAGTGCACG 59.691 50.000 12.01 9.15 39.50 5.34
2754 3312 0.661187 GCAAACATCACAGTGCACGG 60.661 55.000 15.82 15.82 36.97 4.94
2755 3313 0.661187 CAAACATCACAGTGCACGGC 60.661 55.000 17.33 0.00 0.00 5.68
2756 3314 1.795170 AAACATCACAGTGCACGGCC 61.795 55.000 17.33 0.00 0.00 6.13
2757 3315 3.434319 CATCACAGTGCACGGCCC 61.434 66.667 17.33 0.00 0.00 5.80
2758 3316 4.722700 ATCACAGTGCACGGCCCC 62.723 66.667 17.33 0.00 0.00 5.80
2765 3323 4.418328 TGCACGGCCCCGCTTTAT 62.418 61.111 12.00 0.00 44.19 1.40
2766 3324 3.583086 GCACGGCCCCGCTTTATC 61.583 66.667 6.63 0.00 44.19 1.75
2767 3325 2.189521 CACGGCCCCGCTTTATCT 59.810 61.111 6.63 0.00 44.19 1.98
2768 3326 2.180204 CACGGCCCCGCTTTATCTG 61.180 63.158 6.63 0.00 44.19 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.358737 CCGGTTTCGCTTGCTCCT 60.359 61.111 0.00 0.00 34.56 3.69
30 31 2.686816 CGATTGGCCGGTTTCGCTT 61.687 57.895 1.90 0.00 34.56 4.68
44 45 0.040336 CGACACGGGATCGATCGATT 60.040 55.000 29.89 14.35 44.59 3.34
53 54 2.970639 CTGGACACGACACGGGAT 59.029 61.111 0.00 0.00 32.98 3.85
54 55 3.986006 GCTGGACACGACACGGGA 61.986 66.667 0.00 0.00 32.98 5.14
132 138 1.574428 CACCGTTTTGCCTTCTCCG 59.426 57.895 0.00 0.00 0.00 4.63
134 140 4.944249 GCACCGTTTTGCCTTCTC 57.056 55.556 0.00 0.00 36.42 2.87
148 154 1.966451 CAAAGTCCAGACCCGGCAC 60.966 63.158 0.00 0.00 0.00 5.01
157 163 2.328099 GCCGCTGTCCAAAGTCCAG 61.328 63.158 0.00 0.00 0.00 3.86
158 164 2.281484 GCCGCTGTCCAAAGTCCA 60.281 61.111 0.00 0.00 0.00 4.02
201 212 4.265056 AGTTGTCCCACCACCCGC 62.265 66.667 0.00 0.00 0.00 6.13
202 213 2.124507 ATCAGTTGTCCCACCACCCG 62.125 60.000 0.00 0.00 0.00 5.28
203 214 0.609131 CATCAGTTGTCCCACCACCC 60.609 60.000 0.00 0.00 0.00 4.61
204 215 0.400213 TCATCAGTTGTCCCACCACC 59.600 55.000 0.00 0.00 0.00 4.61
213 224 1.203523 GACCTCGCTCTCATCAGTTGT 59.796 52.381 0.00 0.00 0.00 3.32
216 227 1.040339 GGGACCTCGCTCTCATCAGT 61.040 60.000 0.00 0.00 0.00 3.41
419 493 1.519455 CGATCGGGAGAACAGTGCC 60.519 63.158 7.38 0.00 45.37 5.01
433 507 2.436087 ATCGGCCCGGTTGATCGATC 62.436 60.000 18.72 18.72 36.01 3.69
476 554 4.383602 CCAAAACCGTCGCTGGCG 62.384 66.667 8.80 8.80 41.35 5.69
588 670 4.796495 AGGGAAATCCACCGGCGC 62.796 66.667 0.00 0.00 38.24 6.53
589 671 2.513897 GAGGGAAATCCACCGGCG 60.514 66.667 0.00 0.00 38.24 6.46
590 672 2.124278 GGAGGGAAATCCACCGGC 60.124 66.667 0.00 0.00 39.34 6.13
591 673 2.595655 GGGAGGGAAATCCACCGG 59.404 66.667 0.00 0.00 45.89 5.28
823 912 2.219458 TCCTCGTCTCGTATGGTGATC 58.781 52.381 0.00 0.00 0.00 2.92
824 913 2.158798 TCTCCTCGTCTCGTATGGTGAT 60.159 50.000 0.00 0.00 0.00 3.06
825 914 1.208776 TCTCCTCGTCTCGTATGGTGA 59.791 52.381 0.00 0.00 0.00 4.02
826 915 1.600013 CTCTCCTCGTCTCGTATGGTG 59.400 57.143 0.00 0.00 0.00 4.17
837 926 2.765807 CCATGGGCCTCTCCTCGT 60.766 66.667 2.85 0.00 34.39 4.18
838 927 2.444706 TCCATGGGCCTCTCCTCG 60.445 66.667 13.02 0.00 34.39 4.63
865 957 2.748058 TTTGAGGAAGCGGGACAGCC 62.748 60.000 0.00 0.00 38.01 4.85
866 958 0.678048 ATTTGAGGAAGCGGGACAGC 60.678 55.000 0.00 0.00 37.41 4.40
870 962 1.378514 GCCATTTGAGGAAGCGGGA 60.379 57.895 0.00 0.00 0.00 5.14
907 999 2.279517 CTCATACGGGCGCAGGAC 60.280 66.667 10.83 0.00 0.00 3.85
970 1077 1.620413 CGTTGGTAAAGACGCCGACC 61.620 60.000 0.00 0.00 36.12 4.79
985 1092 0.171007 GCCATGATGGACCAACGTTG 59.829 55.000 21.47 21.47 40.96 4.10
992 1099 2.833913 ATCCCGGCCATGATGGACC 61.834 63.158 17.22 14.66 44.91 4.46
994 1101 2.838360 CATCCCGGCCATGATGGA 59.162 61.111 17.22 9.78 40.96 3.41
995 1102 2.987547 GCATCCCGGCCATGATGG 60.988 66.667 25.07 7.21 39.00 3.51
1157 1264 2.098293 CATACCTTGCTGCCGGAAC 58.902 57.895 5.05 0.00 0.00 3.62
1202 1309 3.985925 ACAAAACAACCTACGAGACGATC 59.014 43.478 0.00 0.00 0.00 3.69
1215 1322 7.027161 ACTCTGAATTACACACACAAAACAAC 58.973 34.615 0.00 0.00 0.00 3.32
1223 1330 6.562270 CGTCTCAAACTCTGAATTACACACAC 60.562 42.308 0.00 0.00 32.17 3.82
1224 1331 5.462068 CGTCTCAAACTCTGAATTACACACA 59.538 40.000 0.00 0.00 32.17 3.72
1243 1350 1.731969 CGAACGTTCACCCCGTCTC 60.732 63.158 26.71 0.00 37.61 3.36
1247 1354 3.411351 CTGCGAACGTTCACCCCG 61.411 66.667 26.71 14.74 0.00 5.73
1250 1357 1.891060 CTCTGCTGCGAACGTTCACC 61.891 60.000 26.71 17.17 0.00 4.02
1388 1539 1.926561 TCGGCATCGATCAACTTGAG 58.073 50.000 0.00 0.00 40.88 3.02
1411 1562 5.399596 GCAGAACAAAAAGAAACCGAATCTC 59.600 40.000 0.00 0.00 0.00 2.75
1419 1570 5.228012 CGAGTGAAGCAGAACAAAAAGAAAC 59.772 40.000 0.00 0.00 0.00 2.78
1424 1575 2.223479 GGCGAGTGAAGCAGAACAAAAA 60.223 45.455 0.00 0.00 36.08 1.94
1444 1595 2.436539 CGCACGTCGATCACACTGG 61.437 63.158 0.00 0.00 41.67 4.00
1453 1604 2.307309 CCTTTGCTTCGCACGTCGA 61.307 57.895 0.00 6.09 46.88 4.20
1454 1605 2.170985 CCTTTGCTTCGCACGTCG 59.829 61.111 0.00 0.00 38.71 5.12
1455 1606 1.298859 ATCCCTTTGCTTCGCACGTC 61.299 55.000 0.00 0.00 38.71 4.34
1456 1607 0.889186 AATCCCTTTGCTTCGCACGT 60.889 50.000 0.00 0.00 38.71 4.49
1457 1608 1.062587 CTAATCCCTTTGCTTCGCACG 59.937 52.381 0.00 0.00 38.71 5.34
1458 1609 2.084546 ACTAATCCCTTTGCTTCGCAC 58.915 47.619 0.00 0.00 38.71 5.34
1459 1610 2.489938 ACTAATCCCTTTGCTTCGCA 57.510 45.000 0.00 0.00 36.47 5.10
1460 1611 4.034163 GTCTAACTAATCCCTTTGCTTCGC 59.966 45.833 0.00 0.00 0.00 4.70
1461 1612 4.267928 CGTCTAACTAATCCCTTTGCTTCG 59.732 45.833 0.00 0.00 0.00 3.79
1462 1613 5.176592 ACGTCTAACTAATCCCTTTGCTTC 58.823 41.667 0.00 0.00 0.00 3.86
1463 1614 5.046520 AGACGTCTAACTAATCCCTTTGCTT 60.047 40.000 18.46 0.00 0.00 3.91
1464 1615 4.466726 AGACGTCTAACTAATCCCTTTGCT 59.533 41.667 18.46 0.00 0.00 3.91
1465 1616 4.567159 CAGACGTCTAACTAATCCCTTTGC 59.433 45.833 19.57 0.00 0.00 3.68
1466 1617 5.962433 TCAGACGTCTAACTAATCCCTTTG 58.038 41.667 19.57 1.30 0.00 2.77
1467 1618 6.459848 CGATCAGACGTCTAACTAATCCCTTT 60.460 42.308 19.57 0.00 0.00 3.11
1468 1619 5.008811 CGATCAGACGTCTAACTAATCCCTT 59.991 44.000 19.57 0.00 0.00 3.95
1469 1620 4.515944 CGATCAGACGTCTAACTAATCCCT 59.484 45.833 19.57 0.00 0.00 4.20
1470 1621 4.320348 CCGATCAGACGTCTAACTAATCCC 60.320 50.000 19.57 0.00 0.00 3.85
1471 1622 4.275443 ACCGATCAGACGTCTAACTAATCC 59.725 45.833 19.57 1.26 0.00 3.01
1472 1623 5.421212 ACCGATCAGACGTCTAACTAATC 57.579 43.478 19.57 14.12 0.00 1.75
1473 1624 4.025061 CGACCGATCAGACGTCTAACTAAT 60.025 45.833 19.57 6.99 0.00 1.73
1474 1625 3.308053 CGACCGATCAGACGTCTAACTAA 59.692 47.826 19.57 2.00 0.00 2.24
1475 1626 2.862536 CGACCGATCAGACGTCTAACTA 59.137 50.000 19.57 4.63 0.00 2.24
1476 1627 1.664659 CGACCGATCAGACGTCTAACT 59.335 52.381 19.57 5.53 0.00 2.24
1477 1628 1.662629 TCGACCGATCAGACGTCTAAC 59.337 52.381 19.57 11.30 0.00 2.34
1478 1629 2.014335 TCGACCGATCAGACGTCTAA 57.986 50.000 19.57 3.55 0.00 2.10
1479 1630 1.662629 GTTCGACCGATCAGACGTCTA 59.337 52.381 19.57 7.46 0.00 2.59
1480 1631 0.447011 GTTCGACCGATCAGACGTCT 59.553 55.000 13.58 13.58 0.00 4.18
1481 1632 0.167470 TGTTCGACCGATCAGACGTC 59.833 55.000 7.70 7.70 0.00 4.34
1482 1633 0.109873 GTGTTCGACCGATCAGACGT 60.110 55.000 3.72 0.00 0.00 4.34
1483 1634 0.168348 AGTGTTCGACCGATCAGACG 59.832 55.000 3.72 0.00 0.00 4.18
1484 1635 2.251893 GAAGTGTTCGACCGATCAGAC 58.748 52.381 3.72 0.00 0.00 3.51
1485 1636 1.201647 GGAAGTGTTCGACCGATCAGA 59.798 52.381 3.72 0.00 0.00 3.27
1531 1682 2.076863 CCGTTTCCTCTGCTAACCTTG 58.923 52.381 0.00 0.00 0.00 3.61
1535 1686 1.732809 GCTTCCGTTTCCTCTGCTAAC 59.267 52.381 0.00 0.00 0.00 2.34
1537 1688 0.108804 CGCTTCCGTTTCCTCTGCTA 60.109 55.000 0.00 0.00 0.00 3.49
1975 2151 3.936203 TTCTTCGCCGTGGCAGGT 61.936 61.111 12.06 0.00 42.06 4.00
2043 2219 1.296722 CGTCTTCTCTCCGTACGCG 60.297 63.158 10.49 3.53 37.95 6.01
2084 2260 2.747507 AAAACCATGCAACTCGGCGC 62.748 55.000 0.00 0.00 36.28 6.53
2196 2374 1.527380 ATTGCCAACCGACAACCGT 60.527 52.632 0.00 0.00 36.31 4.83
2241 2422 8.974060 AATCTACAGTTTTTACTCTTGACCAA 57.026 30.769 0.00 0.00 0.00 3.67
2300 2545 0.745845 AAAGCATGATCGCGCCTCTT 60.746 50.000 0.00 0.00 36.85 2.85
2301 2546 1.153289 AAAGCATGATCGCGCCTCT 60.153 52.632 0.00 0.00 36.85 3.69
2302 2547 1.278038 GAAAGCATGATCGCGCCTC 59.722 57.895 0.00 0.60 36.85 4.70
2303 2548 2.528743 CGAAAGCATGATCGCGCCT 61.529 57.895 0.00 0.00 36.85 5.52
2304 2549 2.052766 CGAAAGCATGATCGCGCC 60.053 61.111 0.00 0.00 36.85 6.53
2321 2566 3.740397 TGCTGATGCACGCTTGGC 61.740 61.111 0.00 0.00 45.31 4.52
2397 2642 1.816835 CAGGTTCAGTAGTAGCCACGA 59.183 52.381 0.00 0.00 0.00 4.35
2405 2650 2.288030 CGGTTTCGTCAGGTTCAGTAGT 60.288 50.000 0.00 0.00 0.00 2.73
2417 2662 0.942884 ACGCCTTCTTCGGTTTCGTC 60.943 55.000 0.00 0.00 37.69 4.20
2420 2665 0.883370 ACCACGCCTTCTTCGGTTTC 60.883 55.000 0.00 0.00 0.00 2.78
2425 2670 1.961277 AGCAACCACGCCTTCTTCG 60.961 57.895 0.00 0.00 0.00 3.79
2428 2673 2.980233 GCAGCAACCACGCCTTCT 60.980 61.111 0.00 0.00 0.00 2.85
2442 2950 0.600255 AGTTTCGTCCGGTTCAGCAG 60.600 55.000 0.00 0.00 0.00 4.24
2582 3093 0.102481 CCTCCTTATGACGTGACCCG 59.898 60.000 0.00 0.00 44.03 5.28
2617 3170 4.965200 AGCAGGGACCAATTATACTCTC 57.035 45.455 0.00 0.00 0.00 3.20
2618 3171 9.203163 GTATATAGCAGGGACCAATTATACTCT 57.797 37.037 0.00 0.00 0.00 3.24
2686 3240 4.148348 CCGTTTCAAGAGTTCTACAGTTCG 59.852 45.833 0.00 0.00 0.00 3.95
2699 3253 4.354155 CGTGAGCCCGTTTCAAGA 57.646 55.556 0.00 0.00 0.00 3.02
2730 3288 3.730715 GTGCACTGTGATGTTTGCTTTAC 59.269 43.478 12.86 0.00 35.91 2.01
2731 3289 3.547813 CGTGCACTGTGATGTTTGCTTTA 60.548 43.478 16.19 0.00 35.91 1.85
2732 3290 2.795681 CGTGCACTGTGATGTTTGCTTT 60.796 45.455 16.19 0.00 35.91 3.51
2733 3291 1.268692 CGTGCACTGTGATGTTTGCTT 60.269 47.619 16.19 0.00 35.91 3.91
2734 3292 0.308684 CGTGCACTGTGATGTTTGCT 59.691 50.000 16.19 0.00 35.91 3.91
2735 3293 0.661187 CCGTGCACTGTGATGTTTGC 60.661 55.000 16.19 0.00 35.45 3.68
2736 3294 0.661187 GCCGTGCACTGTGATGTTTG 60.661 55.000 16.19 0.00 0.00 2.93
2737 3295 1.654220 GCCGTGCACTGTGATGTTT 59.346 52.632 16.19 0.00 0.00 2.83
2738 3296 2.260869 GGCCGTGCACTGTGATGTT 61.261 57.895 16.19 0.00 0.00 2.71
2739 3297 2.669569 GGCCGTGCACTGTGATGT 60.670 61.111 16.19 0.00 0.00 3.06
2740 3298 3.434319 GGGCCGTGCACTGTGATG 61.434 66.667 16.19 0.00 0.00 3.07
2741 3299 4.722700 GGGGCCGTGCACTGTGAT 62.723 66.667 16.19 0.00 29.71 3.06
2748 3306 4.418328 ATAAAGCGGGGCCGTGCA 62.418 61.111 19.75 1.70 42.09 4.57
2749 3307 3.583086 GATAAAGCGGGGCCGTGC 61.583 66.667 11.08 11.08 42.09 5.34
2750 3308 2.180204 CAGATAAAGCGGGGCCGTG 61.180 63.158 0.00 0.00 42.09 4.94
2751 3309 1.332144 TACAGATAAAGCGGGGCCGT 61.332 55.000 0.00 0.00 42.09 5.68
2752 3310 0.179067 TTACAGATAAAGCGGGGCCG 60.179 55.000 0.00 0.00 43.09 6.13
2753 3311 1.947456 CTTTACAGATAAAGCGGGGCC 59.053 52.381 0.00 0.00 40.60 5.80
2760 3318 8.292448 ACTGTGATGTTTGCTTTACAGATAAAG 58.708 33.333 8.94 2.99 46.95 1.85
2761 3319 8.165239 ACTGTGATGTTTGCTTTACAGATAAA 57.835 30.769 8.94 0.00 38.07 1.40
2762 3320 7.744087 ACTGTGATGTTTGCTTTACAGATAA 57.256 32.000 8.94 0.00 38.07 1.75
2763 3321 7.875554 TGTACTGTGATGTTTGCTTTACAGATA 59.124 33.333 8.94 0.00 38.07 1.98
2764 3322 6.710295 TGTACTGTGATGTTTGCTTTACAGAT 59.290 34.615 8.94 0.00 38.07 2.90
2765 3323 6.018262 GTGTACTGTGATGTTTGCTTTACAGA 60.018 38.462 8.94 0.00 38.07 3.41
2766 3324 6.136071 GTGTACTGTGATGTTTGCTTTACAG 58.864 40.000 0.00 0.00 40.11 2.74
2767 3325 5.277106 CGTGTACTGTGATGTTTGCTTTACA 60.277 40.000 0.00 0.00 0.00 2.41
2768 3326 5.137403 CGTGTACTGTGATGTTTGCTTTAC 58.863 41.667 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.