Multiple sequence alignment - TraesCS1A01G380700

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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 TraesCS1A01G380700 chr1A 100.000 4154 0 0 1 4154 551743344 551747497 0.000000e+00 7672.0
1 TraesCS1A01G380700 chr1A 90.631 555 42 4 1952 2501 253946167 253946716 0.000000e+00 728.0
2 TraesCS1A01G380700 chr1A 83.103 290 33 6 3875 4154 551533989 551533706 2.480000e-62 250.0
3 TraesCS1A01G380700 chr1D 92.517 2352 110 33 1847 4154 460192191 460194520 0.000000e+00 3308.0
4 TraesCS1A01G380700 chr1D 87.664 916 60 22 943 1846 460190871 460191745 0.000000e+00 1016.0
5 TraesCS1A01G380700 chr1D 89.466 693 38 23 31 717 460189718 460190381 0.000000e+00 843.0
6 TraesCS1A01G380700 chr1D 90.982 499 35 4 2003 2496 90272087 90272580 0.000000e+00 664.0
7 TraesCS1A01G380700 chr1D 92.000 200 5 1 714 902 460190593 460190792 1.900000e-68 270.0
8 TraesCS1A01G380700 chr1D 85.897 156 16 6 3875 4027 459523736 459523584 1.200000e-35 161.0
9 TraesCS1A01G380700 chr1D 86.275 153 15 6 3875 4024 459624327 459624476 1.200000e-35 161.0
10 TraesCS1A01G380700 chr1B 91.115 1812 96 31 2392 4154 632718920 632720715 0.000000e+00 2394.0
11 TraesCS1A01G380700 chr1B 84.749 918 75 25 955 1839 632715680 632716565 0.000000e+00 859.0
12 TraesCS1A01G380700 chr1B 100.000 31 0 0 1 31 269041854 269041824 1.610000e-04 58.4
13 TraesCS1A01G380700 chr3A 90.758 660 45 9 1847 2501 439566051 439565403 0.000000e+00 867.0
14 TraesCS1A01G380700 chr3A 85.877 439 46 10 1417 1846 439566554 439566123 1.760000e-123 453.0
15 TraesCS1A01G380700 chr6A 89.910 555 45 9 1952 2501 493359952 493359404 0.000000e+00 704.0
16 TraesCS1A01G380700 chr6A 100.000 31 0 0 1 31 614983433 614983463 1.610000e-04 58.4
17 TraesCS1A01G380700 chr7D 91.348 497 33 4 2005 2496 105980780 105981271 0.000000e+00 671.0
18 TraesCS1A01G380700 chr7D 90.982 499 35 4 2003 2496 513238681 513238188 0.000000e+00 664.0
19 TraesCS1A01G380700 chr5A 90.982 499 35 4 2003 2496 267322730 267323223 0.000000e+00 664.0
20 TraesCS1A01G380700 chr5A 97.059 34 1 0 1 34 229487893 229487926 1.610000e-04 58.4
21 TraesCS1A01G380700 chr4D 90.982 499 35 4 2003 2496 189769091 189768598 0.000000e+00 664.0
22 TraesCS1A01G380700 chr3B 90.654 107 10 0 988 1094 479296741 479296847 4.330000e-30 143.0
23 TraesCS1A01G380700 chr3D 89.216 102 11 0 975 1076 367307002 367307103 1.210000e-25 128.0
24 TraesCS1A01G380700 chr3D 100.000 31 0 0 1 31 317405218 317405188 1.610000e-04 58.4
25 TraesCS1A01G380700 chr3D 100.000 31 0 0 1 31 422482025 422481995 1.610000e-04 58.4
26 TraesCS1A01G380700 chr3D 96.875 32 1 0 1 32 556072175 556072206 2.000000e-03 54.7
27 TraesCS1A01G380700 chr5B 100.000 32 0 0 1 32 350495547 350495578 4.480000e-05 60.2
28 TraesCS1A01G380700 chr5B 100.000 32 0 0 1 32 681819346 681819315 4.480000e-05 60.2
29 TraesCS1A01G380700 chr5B 92.105 38 3 0 1 38 561917068 561917105 2.000000e-03 54.7
30 TraesCS1A01G380700 chr7B 100.000 31 0 0 1 31 193955881 193955851 1.610000e-04 58.4
31 TraesCS1A01G380700 chr7A 100.000 31 0 0 1 31 217084359 217084389 1.610000e-04 58.4
32 TraesCS1A01G380700 chr6B 100.000 31 0 0 1 31 75982906 75982876 1.610000e-04 58.4
33 TraesCS1A01G380700 chr2A 97.059 34 0 1 2 35 733402536 733402568 5.800000e-04 56.5
34 TraesCS1A01G380700 chr2B 94.444 36 1 1 4 39 666632617 666632651 2.000000e-03 54.7


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 TraesCS1A01G380700 chr1A 551743344 551747497 4153 False 7672.00 7672 100.00000 1 4154 1 chr1A.!!$F2 4153
1 TraesCS1A01G380700 chr1A 253946167 253946716 549 False 728.00 728 90.63100 1952 2501 1 chr1A.!!$F1 549
2 TraesCS1A01G380700 chr1D 460189718 460194520 4802 False 1359.25 3308 90.41175 31 4154 4 chr1D.!!$F3 4123
3 TraesCS1A01G380700 chr1B 632715680 632720715 5035 False 1626.50 2394 87.93200 955 4154 2 chr1B.!!$F1 3199
4 TraesCS1A01G380700 chr3A 439565403 439566554 1151 True 660.00 867 88.31750 1417 2501 2 chr3A.!!$R1 1084
5 TraesCS1A01G380700 chr6A 493359404 493359952 548 True 704.00 704 89.91000 1952 2501 1 chr6A.!!$R1 549

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
798 1020 0.179000 AGTAGCCAGGATTTCAGCGG 59.821 55.0 0.00 0.0 0.00 5.52 F
1961 4245 0.252513 TGGTGCTACCTTCCTAGCCA 60.253 55.0 6.83 0.0 39.58 4.75 F
3021 5314 0.476771 TCAACTTCCACCCTGAACCC 59.523 55.0 0.00 0.0 0.00 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 4663 0.625091 CCCCCACCCCCTAACATACA 60.625 60.000 0.0 0.0 0.00 2.29 R
3141 5452 0.538584 ACTCTGATCATTGCTCGGCA 59.461 50.000 0.0 0.0 36.47 5.69 R
4066 6422 1.275291 ACGTTCAATGGTCGATGAGGT 59.725 47.619 0.0 0.0 0.00 3.85 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
22 23 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
23 24 3.007635 GAGACACTTATTTTGGGACGGG 58.992 50.000 0.00 0.00 0.00 5.28
24 25 2.089201 GACACTTATTTTGGGACGGGG 58.911 52.381 0.00 0.00 0.00 5.73
25 26 1.272258 ACACTTATTTTGGGACGGGGG 60.272 52.381 0.00 0.00 0.00 5.40
127 128 9.469807 TTCATACACATTTGTACATTTTTGGAC 57.530 29.630 0.00 0.00 41.12 4.02
260 262 7.548196 AATACACATGAAATACTTACACCCG 57.452 36.000 0.00 0.00 0.00 5.28
300 302 8.511465 AGAACATTTTTCGAAATCATGAACAG 57.489 30.769 26.00 12.03 0.00 3.16
451 453 5.504755 GTGAACAATATTGAAAAGACGCGAG 59.495 40.000 22.16 0.00 0.00 5.03
452 454 4.003519 ACAATATTGAAAAGACGCGAGC 57.996 40.909 22.16 3.96 0.00 5.03
453 455 3.435327 ACAATATTGAAAAGACGCGAGCA 59.565 39.130 22.16 0.00 0.00 4.26
454 456 4.094887 ACAATATTGAAAAGACGCGAGCAT 59.905 37.500 22.16 0.00 0.00 3.79
633 636 9.455847 CTTTAAGTTTCTGAGAATTTGTTGAGG 57.544 33.333 0.00 0.00 0.00 3.86
653 656 9.670719 GTTGAGGAATGAAAGAAAACTAAGAAG 57.329 33.333 0.00 0.00 0.00 2.85
657 660 7.667635 AGGAATGAAAGAAAACTAAGAAGAGGG 59.332 37.037 0.00 0.00 0.00 4.30
707 714 3.967326 AGGGAAAGAAACAGGGAAAAAGG 59.033 43.478 0.00 0.00 0.00 3.11
710 717 5.357257 GGAAAGAAACAGGGAAAAAGGAAC 58.643 41.667 0.00 0.00 0.00 3.62
713 720 3.704566 AGAAACAGGGAAAAAGGAACACC 59.295 43.478 0.00 0.00 0.00 4.16
798 1020 0.179000 AGTAGCCAGGATTTCAGCGG 59.821 55.000 0.00 0.00 0.00 5.52
858 1091 4.374584 CGCCAACCCCAATCCCCA 62.375 66.667 0.00 0.00 0.00 4.96
912 1161 2.354729 CCCCGCCTTGATTCACCA 59.645 61.111 0.00 0.00 0.00 4.17
913 1162 1.076777 CCCCGCCTTGATTCACCAT 60.077 57.895 0.00 0.00 0.00 3.55
914 1163 1.103398 CCCCGCCTTGATTCACCATC 61.103 60.000 0.00 0.00 0.00 3.51
917 1172 1.103398 CGCCTTGATTCACCATCCCC 61.103 60.000 0.00 0.00 0.00 4.81
941 1196 3.470888 CCCGGACCCGCAAGATCT 61.471 66.667 0.73 0.00 43.02 2.75
943 1198 2.107141 CGGACCCGCAAGATCTCC 59.893 66.667 0.00 0.00 43.02 3.71
1164 1441 2.363795 CCCCCTCTCTGCACCGTA 60.364 66.667 0.00 0.00 0.00 4.02
1173 1450 3.701604 CTGCACCGTACGCCCTCTC 62.702 68.421 10.49 0.00 0.00 3.20
1227 1513 2.450345 CGTTTTAGGAGGCGCCGTC 61.450 63.158 23.20 18.39 43.43 4.79
1275 1561 3.902162 TTCGGTTCGGCTCGGTTCG 62.902 63.158 0.00 0.00 0.00 3.95
1282 1568 3.119096 GGCTCGGTTCGGTTCTGC 61.119 66.667 0.00 0.00 0.00 4.26
1358 1644 6.091577 TGTGAATATCATGAAGTACGCGTTTT 59.908 34.615 20.78 13.22 0.00 2.43
1359 1645 6.623743 GTGAATATCATGAAGTACGCGTTTTC 59.376 38.462 20.78 21.59 0.00 2.29
1361 1647 2.070783 TCATGAAGTACGCGTTTTCCC 58.929 47.619 20.78 4.12 0.00 3.97
1376 1663 0.324460 TTCCCCCGAGTCTTCCTCTC 60.324 60.000 0.00 0.00 38.11 3.20
1403 1690 0.590732 GCATCTTGGCGATTTCTGCG 60.591 55.000 0.00 0.00 0.00 5.18
1484 1771 0.807667 CGTCTTGGATTCAGAGGCCG 60.808 60.000 0.00 0.00 0.00 6.13
1503 1796 1.937899 CGATTCATAAACCGGGTGGAC 59.062 52.381 6.32 0.00 39.21 4.02
1526 1819 5.066593 CCAATTTACTCCTCTGGATTAGCC 58.933 45.833 0.00 0.00 37.10 3.93
1527 1820 4.608948 ATTTACTCCTCTGGATTAGCCG 57.391 45.455 0.00 0.00 40.66 5.52
1528 1821 2.750141 TACTCCTCTGGATTAGCCGT 57.250 50.000 0.00 0.00 40.66 5.68
1529 1822 2.750141 ACTCCTCTGGATTAGCCGTA 57.250 50.000 0.00 0.00 40.66 4.02
1530 1823 2.308690 ACTCCTCTGGATTAGCCGTAC 58.691 52.381 0.00 0.00 40.66 3.67
1531 1824 2.091775 ACTCCTCTGGATTAGCCGTACT 60.092 50.000 0.00 0.00 40.66 2.73
1532 1825 3.137913 ACTCCTCTGGATTAGCCGTACTA 59.862 47.826 0.00 0.00 40.66 1.82
1533 1826 3.752665 TCCTCTGGATTAGCCGTACTAG 58.247 50.000 0.00 0.00 40.66 2.57
1534 1827 3.393609 TCCTCTGGATTAGCCGTACTAGA 59.606 47.826 0.00 0.00 40.66 2.43
1540 1837 8.087303 TCTGGATTAGCCGTACTAGATAGATA 57.913 38.462 0.00 0.00 40.66 1.98
1572 1870 2.026822 ACCAAGAGAACCGATTGCAGAT 60.027 45.455 0.00 0.00 0.00 2.90
1605 1903 1.155042 CAAGTCTGAAGCTGCTGTCC 58.845 55.000 1.35 0.00 0.00 4.02
1675 1980 6.258287 TGAAATTGCAGTGAACTTGGATTTTG 59.742 34.615 0.00 0.00 0.00 2.44
1680 1985 5.936956 TGCAGTGAACTTGGATTTTGTTTTT 59.063 32.000 0.00 0.00 0.00 1.94
1742 2047 8.488308 TTTCTAGAGTACTTTTACCCACTCTT 57.512 34.615 8.26 0.00 44.03 2.85
1749 2075 2.450609 TTTACCCACTCTTGAGCGTC 57.549 50.000 0.00 0.00 0.00 5.19
1757 2083 4.093556 CCCACTCTTGAGCGTCTAATTTTC 59.906 45.833 0.00 0.00 0.00 2.29
1835 2162 6.635030 AAAACAAAACTACCATCCTCACTC 57.365 37.500 0.00 0.00 0.00 3.51
1950 4234 1.826385 AGGCAGTTCATTGGTGCTAC 58.174 50.000 6.55 0.00 37.37 3.58
1961 4245 0.252513 TGGTGCTACCTTCCTAGCCA 60.253 55.000 6.83 0.00 39.58 4.75
1990 4277 3.515602 ATATGCATCCCTGTTCCTTCC 57.484 47.619 0.19 0.00 0.00 3.46
2119 4411 1.464997 GTGATCTGTTTCGGTTCTGCC 59.535 52.381 0.00 0.00 0.00 4.85
2201 4493 6.344500 TCAGACTTCAGAGATATTTGCCTTC 58.656 40.000 0.00 0.00 0.00 3.46
2203 4495 5.091261 ACTTCAGAGATATTTGCCTTCGT 57.909 39.130 0.00 0.00 0.00 3.85
2214 4506 3.897819 GCCTTCGTTTCAATAGGCG 57.102 52.632 0.00 0.00 43.24 5.52
2227 4519 2.866762 CAATAGGCGAGTAGTTTGCTCC 59.133 50.000 0.00 0.00 36.37 4.70
2242 4534 5.416952 AGTTTGCTCCCAATCAACATAGAAG 59.583 40.000 0.00 0.00 0.00 2.85
2328 4620 8.367911 TCTTTACGATATGTTCTATTCCATGCT 58.632 33.333 0.00 0.00 0.00 3.79
2333 4625 6.293571 CGATATGTTCTATTCCATGCTGCAAA 60.294 38.462 6.36 0.00 0.00 3.68
2356 4648 5.253330 AGGGCGATTTTCATCTAAGTTGAA 58.747 37.500 0.00 0.00 0.00 2.69
2385 4677 5.789574 TTGATTTCTGTATGTTAGGGGGT 57.210 39.130 0.00 0.00 0.00 4.95
2388 4680 1.887797 TCTGTATGTTAGGGGGTGGG 58.112 55.000 0.00 0.00 0.00 4.61
2389 4681 0.843984 CTGTATGTTAGGGGGTGGGG 59.156 60.000 0.00 0.00 0.00 4.96
2390 4682 0.625091 TGTATGTTAGGGGGTGGGGG 60.625 60.000 0.00 0.00 0.00 5.40
2393 4686 3.269632 GTTAGGGGGTGGGGGCAA 61.270 66.667 0.00 0.00 0.00 4.52
2442 4735 6.013639 AGGGTACTGACTTGCTAAACTATTGT 60.014 38.462 0.00 0.00 0.00 2.71
2515 4808 4.564782 TGGATCAGCTGAAGATGAAACT 57.435 40.909 22.50 0.00 44.14 2.66
2664 4957 4.640771 AACCTAGAATTCCTTGCACAGA 57.359 40.909 0.65 0.00 0.00 3.41
2675 4968 5.381174 TCCTTGCACAGATTCAAATCTTG 57.619 39.130 2.47 6.55 42.96 3.02
2680 4973 5.633927 TGCACAGATTCAAATCTTGATTCG 58.366 37.500 2.47 0.00 42.96 3.34
2693 4986 8.843733 CAAATCTTGATTCGTCACACTATTTTG 58.156 33.333 0.00 0.00 0.00 2.44
2707 5000 8.904834 TCACACTATTTTGCCTTTTGTTACTTA 58.095 29.630 0.00 0.00 0.00 2.24
2708 5001 9.691362 CACACTATTTTGCCTTTTGTTACTTAT 57.309 29.630 0.00 0.00 0.00 1.73
2796 5089 1.152074 TGACCCACCGGACCCTTTA 60.152 57.895 9.46 0.00 0.00 1.85
2802 5095 2.640184 CCACCGGACCCTTTAAAGATC 58.360 52.381 16.98 12.74 0.00 2.75
2805 5098 1.296727 CGGACCCTTTAAAGATCCGC 58.703 55.000 30.97 13.19 45.13 5.54
2904 5197 8.545420 GGTTATTATGTGAACAACGATTACGAT 58.455 33.333 0.00 0.00 42.66 3.73
3021 5314 0.476771 TCAACTTCCACCCTGAACCC 59.523 55.000 0.00 0.00 0.00 4.11
3092 5385 0.834612 ACTTCACCGGAACCACAGAA 59.165 50.000 9.46 0.00 0.00 3.02
3134 5445 1.880894 CGCCACTAGAGAACGTCCA 59.119 57.895 0.00 0.00 0.00 4.02
3141 5452 2.563179 ACTAGAGAACGTCCACATTGCT 59.437 45.455 0.00 0.00 0.00 3.91
3147 5458 2.743752 CGTCCACATTGCTGCCGAG 61.744 63.158 0.00 0.00 0.00 4.63
3170 5481 1.067295 TGATCAGAGTTGGGGTGCTT 58.933 50.000 0.00 0.00 0.00 3.91
3173 5484 1.429930 TCAGAGTTGGGGTGCTTACA 58.570 50.000 0.00 0.00 0.00 2.41
3243 5554 1.812571 GGTGGTTCTGCATTGTACTGG 59.187 52.381 0.00 0.00 0.00 4.00
3253 5564 3.314913 TGCATTGTACTGGTCTGTTGTTG 59.685 43.478 0.00 0.00 0.00 3.33
3261 5572 2.936498 CTGGTCTGTTGTTGACGTTTCT 59.064 45.455 0.00 0.00 35.45 2.52
3266 5577 5.235616 GGTCTGTTGTTGACGTTTCTCAATA 59.764 40.000 0.00 0.00 35.45 1.90
3271 5582 6.909895 TGTTGTTGACGTTTCTCAATATGTTG 59.090 34.615 0.00 0.00 32.78 3.33
3275 5586 6.612247 TGACGTTTCTCAATATGTTGTGTT 57.388 33.333 1.86 0.00 36.69 3.32
3277 5588 6.037720 TGACGTTTCTCAATATGTTGTGTTGT 59.962 34.615 1.86 0.00 36.69 3.32
3453 5769 1.331214 CACCAGGTTTTCCACTGCAT 58.669 50.000 0.00 0.00 43.73 3.96
3551 5888 5.316167 TGAGACAATATTTTGGTCTGCACT 58.684 37.500 10.70 0.00 37.15 4.40
3571 5910 3.565482 ACTGTGAATTGCTTACTGGTGTG 59.435 43.478 0.00 0.00 0.00 3.82
3576 5915 6.095580 TGTGAATTGCTTACTGGTGTGTTTAA 59.904 34.615 0.00 0.00 0.00 1.52
3580 5919 8.956533 AATTGCTTACTGGTGTGTTTAATTTT 57.043 26.923 0.00 0.00 0.00 1.82
3581 5920 7.995463 TTGCTTACTGGTGTGTTTAATTTTC 57.005 32.000 0.00 0.00 0.00 2.29
3584 5923 8.254508 TGCTTACTGGTGTGTTTAATTTTCTTT 58.745 29.630 0.00 0.00 0.00 2.52
3611 5950 8.475639 GTGTAGATTCTAACTGGGTCAAGAATA 58.524 37.037 0.00 0.00 38.47 1.75
3680 6019 8.911918 TTTGAAACTTAGCTAGTAATTGGTGA 57.088 30.769 0.00 0.00 35.54 4.02
3681 6020 8.911918 TTGAAACTTAGCTAGTAATTGGTGAA 57.088 30.769 0.00 0.00 35.54 3.18
3682 6021 9.515226 TTGAAACTTAGCTAGTAATTGGTGAAT 57.485 29.630 0.00 0.00 35.54 2.57
3687 6026 9.601217 ACTTAGCTAGTAATTGGTGAATAACTG 57.399 33.333 0.00 0.00 34.56 3.16
3699 6038 7.558161 TGGTGAATAACTGAATATTGCTCAG 57.442 36.000 0.00 0.00 44.90 3.35
3942 6283 4.888239 GTGTCCTAGACCATCTAAGCTACA 59.112 45.833 0.00 0.00 0.00 2.74
3970 6314 9.585099 TCAAAATGAAATAAACATGCTGATACC 57.415 29.630 0.00 0.00 0.00 2.73
4040 6396 5.269189 TCCAGAGTAGTACATCAATGGTCA 58.731 41.667 2.52 0.00 0.00 4.02
4066 6422 5.070313 GGCTTTATATTCCCTGATTGCCAAA 59.930 40.000 0.00 0.00 36.91 3.28
4094 6450 2.094258 CGACCATTGAACGTGGAATGAG 59.906 50.000 17.33 11.50 39.12 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
1 2 3.558321 CCCGTCCCAAAATAAGTGTCTCA 60.558 47.826 0.00 0.00 0.00 3.27
2 3 3.007635 CCCGTCCCAAAATAAGTGTCTC 58.992 50.000 0.00 0.00 0.00 3.36
3 4 2.290705 CCCCGTCCCAAAATAAGTGTCT 60.291 50.000 0.00 0.00 0.00 3.41
4 5 2.089201 CCCCGTCCCAAAATAAGTGTC 58.911 52.381 0.00 0.00 0.00 3.67
5 6 1.272258 CCCCCGTCCCAAAATAAGTGT 60.272 52.381 0.00 0.00 0.00 3.55
6 7 1.470051 CCCCCGTCCCAAAATAAGTG 58.530 55.000 0.00 0.00 0.00 3.16
7 8 3.991972 CCCCCGTCCCAAAATAAGT 57.008 52.632 0.00 0.00 0.00 2.24
69 70 6.945072 AGACACGTATTGAAGAAAAAGTGAC 58.055 36.000 0.00 0.00 33.18 3.67
102 103 8.855110 AGTCCAAAAATGTACAAATGTGTATGA 58.145 29.630 0.00 0.00 42.18 2.15
348 350 7.063191 GGAATTGCACAAAAATGTTTGCTTTTT 59.937 29.630 8.34 0.00 46.84 1.94
366 368 6.147492 GCAAAATCAAAGTACATGGAATTGCA 59.853 34.615 17.60 0.79 38.42 4.08
607 610 9.455847 CCTCAACAAATTCTCAGAAACTTAAAG 57.544 33.333 0.00 0.00 0.00 1.85
608 611 9.184523 TCCTCAACAAATTCTCAGAAACTTAAA 57.815 29.630 0.00 0.00 0.00 1.52
609 612 8.746052 TCCTCAACAAATTCTCAGAAACTTAA 57.254 30.769 0.00 0.00 0.00 1.85
610 613 8.746052 TTCCTCAACAAATTCTCAGAAACTTA 57.254 30.769 0.00 0.00 0.00 2.24
624 627 9.801873 CTTAGTTTTCTTTCATTCCTCAACAAA 57.198 29.630 0.00 0.00 0.00 2.83
633 636 8.622948 TCCCTCTTCTTAGTTTTCTTTCATTC 57.377 34.615 0.00 0.00 0.00 2.67
686 689 3.964688 TCCTTTTTCCCTGTTTCTTTCCC 59.035 43.478 0.00 0.00 0.00 3.97
688 691 5.810587 GTGTTCCTTTTTCCCTGTTTCTTTC 59.189 40.000 0.00 0.00 0.00 2.62
703 710 3.915346 ACCCCTATTTGGTGTTCCTTT 57.085 42.857 0.00 0.00 33.94 3.11
707 714 2.490509 CGGAAACCCCTATTTGGTGTTC 59.509 50.000 0.00 0.00 35.88 3.18
710 717 2.365582 CTCGGAAACCCCTATTTGGTG 58.634 52.381 0.00 0.00 35.88 4.17
713 720 1.389555 GGCTCGGAAACCCCTATTTG 58.610 55.000 0.00 0.00 0.00 2.32
737 959 3.798511 GCTCCCCTGCCCACCTAC 61.799 72.222 0.00 0.00 0.00 3.18
798 1020 4.168291 CGGGGAAGCAGAGCCCTC 62.168 72.222 0.00 0.00 44.10 4.30
873 1106 3.605749 TTTTGGAGGAGGGAGCGCG 62.606 63.158 0.00 0.00 0.00 6.86
941 1196 2.052782 TCAATCGATCGAGGAGTGGA 57.947 50.000 23.84 6.70 30.93 4.02
943 1198 5.123027 TCTGATATCAATCGATCGAGGAGTG 59.877 44.000 23.84 17.08 34.60 3.51
1095 1372 2.747855 GTACCGTCGTCGAGGGGT 60.748 66.667 31.26 24.89 41.34 4.95
1098 1375 2.397252 GACGTACCGTCGTCGAGG 59.603 66.667 7.96 7.96 46.56 4.63
1150 1427 2.202623 GCGTACGGTGCAGAGAGG 60.203 66.667 18.39 0.00 0.00 3.69
1158 1435 3.834799 GGGAGAGGGCGTACGGTG 61.835 72.222 18.39 0.00 0.00 4.94
1164 1441 3.155167 GAATCGGGGAGAGGGCGT 61.155 66.667 0.00 0.00 0.00 5.68
1267 1553 0.734253 CAGAGCAGAACCGAACCGAG 60.734 60.000 0.00 0.00 0.00 4.63
1275 1561 0.735632 CGACAGAGCAGAGCAGAACC 60.736 60.000 0.00 0.00 0.00 3.62
1282 1568 2.282147 CTGGAGGCGACAGAGCAGAG 62.282 65.000 5.69 0.00 38.20 3.35
1307 1593 3.049674 CGGCACACCAATCGCTGT 61.050 61.111 0.00 0.00 34.57 4.40
1344 1630 0.603439 GGGGGAAAACGCGTACTTCA 60.603 55.000 26.12 0.00 0.00 3.02
1348 1634 2.048316 TCGGGGGAAAACGCGTAC 60.048 61.111 14.46 7.37 45.53 3.67
1376 1663 0.735978 TCGCCAAGATGCACTGTACG 60.736 55.000 0.00 0.00 0.00 3.67
1403 1690 0.240145 GTTTTTACCCAGTCGCAGCC 59.760 55.000 0.00 0.00 0.00 4.85
1408 1695 1.796459 CCAGTCGTTTTTACCCAGTCG 59.204 52.381 0.00 0.00 0.00 4.18
1484 1771 2.294979 GGTCCACCCGGTTTATGAATC 58.705 52.381 0.00 0.00 0.00 2.52
1503 1796 5.066593 GGCTAATCCAGAGGAGTAAATTGG 58.933 45.833 0.00 0.00 31.75 3.16
1526 1819 8.832521 GTCAGGGATCAATATCTATCTAGTACG 58.167 40.741 0.00 0.00 32.29 3.67
1527 1820 9.127277 GGTCAGGGATCAATATCTATCTAGTAC 57.873 40.741 0.00 0.00 32.29 2.73
1528 1821 8.846804 TGGTCAGGGATCAATATCTATCTAGTA 58.153 37.037 0.00 0.00 32.29 1.82
1529 1822 7.713518 TGGTCAGGGATCAATATCTATCTAGT 58.286 38.462 0.00 0.00 32.29 2.57
1530 1823 8.601047 TTGGTCAGGGATCAATATCTATCTAG 57.399 38.462 0.00 0.00 26.67 2.43
1531 1824 8.401894 TCTTGGTCAGGGATCAATATCTATCTA 58.598 37.037 0.00 0.00 31.92 1.98
1532 1825 7.251936 TCTTGGTCAGGGATCAATATCTATCT 58.748 38.462 0.00 0.00 31.92 1.98
1533 1826 7.398618 TCTCTTGGTCAGGGATCAATATCTATC 59.601 40.741 0.00 0.00 31.92 2.08
1534 1827 7.251936 TCTCTTGGTCAGGGATCAATATCTAT 58.748 38.462 0.00 0.00 31.92 1.98
1540 1837 3.054065 GGTTCTCTTGGTCAGGGATCAAT 60.054 47.826 0.00 0.00 31.92 2.57
1572 1870 2.886523 CAGACTTGGCTCCACAAAATCA 59.113 45.455 0.00 0.00 0.00 2.57
1605 1903 2.569404 AGCTTCTGTCCTAGAACAAGGG 59.431 50.000 0.00 0.00 40.43 3.95
1646 1947 4.114073 CAAGTTCACTGCAATTTCAGCAA 58.886 39.130 4.91 0.00 42.17 3.91
1657 1962 6.313658 AGAAAAACAAAATCCAAGTTCACTGC 59.686 34.615 0.00 0.00 0.00 4.40
1660 1965 8.382875 CAGAAGAAAAACAAAATCCAAGTTCAC 58.617 33.333 0.00 0.00 0.00 3.18
1664 1969 9.936759 TTAACAGAAGAAAAACAAAATCCAAGT 57.063 25.926 0.00 0.00 0.00 3.16
1742 2047 7.410800 TTTCTTAACGAAAATTAGACGCTCA 57.589 32.000 0.00 0.00 38.62 4.26
1749 2075 9.015577 TGTTTGTGCTTTCTTAACGAAAATTAG 57.984 29.630 0.00 0.00 40.87 1.73
1757 2083 4.549599 CGCTATGTTTGTGCTTTCTTAACG 59.450 41.667 0.00 0.00 0.00 3.18
1771 2097 3.552604 ATTCACGTTTGCGCTATGTTT 57.447 38.095 9.73 0.00 42.83 2.83
1835 2162 9.903682 GTGAAGGATATGATAATTTGGTCATTG 57.096 33.333 6.14 0.00 36.53 2.82
1950 4234 6.599638 GCATATAATTAAGGTGGCTAGGAAGG 59.400 42.308 0.00 0.00 0.00 3.46
1961 4245 6.948309 GGAACAGGGATGCATATAATTAAGGT 59.052 38.462 0.00 0.00 0.00 3.50
1990 4277 2.229543 TGCAGGCTGCTTCACTATTTTG 59.770 45.455 36.50 0.00 45.31 2.44
2068 4355 2.344592 TCCCAGTGGACAAGTAATGGT 58.655 47.619 11.95 0.00 35.03 3.55
2119 4411 3.255642 CCCACACTACTGAATGGGTTTTG 59.744 47.826 0.00 0.00 45.89 2.44
2201 4493 4.724036 GCAAACTACTCGCCTATTGAAACG 60.724 45.833 0.00 0.00 0.00 3.60
2203 4495 4.575885 AGCAAACTACTCGCCTATTGAAA 58.424 39.130 0.00 0.00 0.00 2.69
2214 4506 4.072131 TGTTGATTGGGAGCAAACTACTC 58.928 43.478 0.00 0.00 32.18 2.59
2227 4519 9.459640 CAAATTATGCTCTTCTATGTTGATTGG 57.540 33.333 0.00 0.00 0.00 3.16
2242 4534 6.974622 CCAATACAGGACAACAAATTATGCTC 59.025 38.462 0.00 0.00 0.00 4.26
2299 4591 8.246430 TGGAATAGAACATATCGTAAAGACCT 57.754 34.615 0.00 0.00 0.00 3.85
2328 4620 2.170166 AGATGAAAATCGCCCTTTGCA 58.830 42.857 0.00 0.00 41.33 4.08
2333 4625 4.843728 TCAACTTAGATGAAAATCGCCCT 58.156 39.130 0.00 0.00 0.00 5.19
2356 4648 8.960591 CCCTAACATACAGAAATCAAAATCAGT 58.039 33.333 0.00 0.00 0.00 3.41
2371 4663 0.625091 CCCCCACCCCCTAACATACA 60.625 60.000 0.00 0.00 0.00 2.29
2380 4672 1.053835 CAATATTTGCCCCCACCCCC 61.054 60.000 0.00 0.00 0.00 5.40
2416 4709 4.273148 AGTTTAGCAAGTCAGTACCCTG 57.727 45.455 0.00 0.00 40.25 4.45
2442 4735 9.184523 CTAATAGGTCACCCAACAAAATATCAA 57.815 33.333 0.00 0.00 0.00 2.57
2447 4740 7.557719 CAGATCTAATAGGTCACCCAACAAAAT 59.442 37.037 3.11 0.00 0.00 1.82
2515 4808 3.867493 CGCTCTCAAGTTGCTGATCATAA 59.133 43.478 0.00 0.00 0.00 1.90
2664 4957 6.808008 AGTGTGACGAATCAAGATTTGAAT 57.192 33.333 15.20 0.00 43.95 2.57
2675 4968 4.946784 AGGCAAAATAGTGTGACGAATC 57.053 40.909 0.00 0.00 0.00 2.52
2680 4973 7.200455 AGTAACAAAAGGCAAAATAGTGTGAC 58.800 34.615 0.00 0.00 0.00 3.67
2752 5045 7.056006 GCCTGGAATGGAAATGGAAAATTAAT 58.944 34.615 0.00 0.00 0.00 1.40
2758 5051 2.833338 CAGCCTGGAATGGAAATGGAAA 59.167 45.455 0.00 0.00 0.00 3.13
2796 5089 2.163818 TGTCTTGTTCGCGGATCTTT 57.836 45.000 6.13 0.00 0.00 2.52
2802 5095 1.202065 CCAATGATGTCTTGTTCGCGG 60.202 52.381 6.13 0.00 0.00 6.46
2805 5098 3.498018 TGACACCAATGATGTCTTGTTCG 59.502 43.478 9.42 0.00 45.58 3.95
2904 5197 1.184431 CTTCTCTCAGCTGCTCCTCA 58.816 55.000 9.47 0.00 0.00 3.86
3141 5452 0.538584 ACTCTGATCATTGCTCGGCA 59.461 50.000 0.00 0.00 36.47 5.69
3147 5458 1.747355 CACCCCAACTCTGATCATTGC 59.253 52.381 0.00 0.00 0.00 3.56
3170 5481 2.540383 AGGCATGGAGAACAGACTGTA 58.460 47.619 8.91 0.00 0.00 2.74
3173 5484 2.264455 AGAAGGCATGGAGAACAGACT 58.736 47.619 0.00 0.00 0.00 3.24
3243 5554 4.593597 TTGAGAAACGTCAACAACAGAC 57.406 40.909 0.00 0.00 31.31 3.51
3253 5564 6.427150 ACAACACAACATATTGAGAAACGTC 58.573 36.000 0.00 0.00 39.30 4.34
3261 5572 7.869937 CCCAACATTTACAACACAACATATTGA 59.130 33.333 0.00 0.00 39.30 2.57
3266 5577 5.105146 ACACCCAACATTTACAACACAACAT 60.105 36.000 0.00 0.00 0.00 2.71
3271 5582 4.911514 AGACACCCAACATTTACAACAC 57.088 40.909 0.00 0.00 0.00 3.32
3275 5586 4.634012 AGCTAGACACCCAACATTTACA 57.366 40.909 0.00 0.00 0.00 2.41
3277 5588 7.630082 AGAAATAGCTAGACACCCAACATTTA 58.370 34.615 0.00 0.00 0.00 1.40
3350 5661 2.430465 GCTGAAGCATTCCAGTCTCAA 58.570 47.619 0.00 0.00 46.93 3.02
3426 5737 2.146073 GAAAACCTGGTGCAGCGCAT 62.146 55.000 11.47 0.00 41.91 4.73
3453 5769 2.874014 TGCCAGATTGTGAACCATCAA 58.126 42.857 0.00 0.00 37.30 2.57
3551 5888 3.550820 ACACACCAGTAAGCAATTCACA 58.449 40.909 0.00 0.00 0.00 3.58
3576 5915 9.014297 CCCAGTTAGAATCTACACAAAGAAAAT 57.986 33.333 0.00 0.00 0.00 1.82
3580 5919 6.269077 TGACCCAGTTAGAATCTACACAAAGA 59.731 38.462 0.00 0.00 0.00 2.52
3581 5920 6.464222 TGACCCAGTTAGAATCTACACAAAG 58.536 40.000 0.00 0.00 0.00 2.77
3584 5923 5.778241 TCTTGACCCAGTTAGAATCTACACA 59.222 40.000 0.00 0.00 0.00 3.72
3681 6020 9.553064 CCTACTTTCTGAGCAATATTCAGTTAT 57.447 33.333 3.43 0.00 42.11 1.89
3682 6021 7.495934 GCCTACTTTCTGAGCAATATTCAGTTA 59.504 37.037 3.43 0.00 42.11 2.24
3683 6022 6.317391 GCCTACTTTCTGAGCAATATTCAGTT 59.683 38.462 3.43 0.00 42.11 3.16
3684 6023 5.819901 GCCTACTTTCTGAGCAATATTCAGT 59.180 40.000 3.43 0.00 42.11 3.41
3685 6024 6.018098 CAGCCTACTTTCTGAGCAATATTCAG 60.018 42.308 0.00 0.00 42.68 3.02
3686 6025 5.819379 CAGCCTACTTTCTGAGCAATATTCA 59.181 40.000 0.00 0.00 32.26 2.57
3687 6026 6.051717 TCAGCCTACTTTCTGAGCAATATTC 58.948 40.000 0.00 0.00 34.69 1.75
3873 6214 2.426023 ACGCAAGGGACACCAGAC 59.574 61.111 0.00 0.00 46.39 3.51
3910 6251 2.438800 GTCTAGGACACTCTAGGCCA 57.561 55.000 5.01 0.00 36.31 5.36
4040 6396 4.835056 GGCAATCAGGGAATATAAAGCCTT 59.165 41.667 0.00 0.00 35.63 4.35
4066 6422 1.275291 ACGTTCAATGGTCGATGAGGT 59.725 47.619 0.00 0.00 0.00 3.85
4127 6483 4.222114 GCTAGTGCAGTGATGTTTTGTTC 58.778 43.478 3.69 0.00 39.41 3.18


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

AutoCloner maintained by Alex Coulton.