Multiple sequence alignment - TraesCS3B01G040600

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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 TraesCS3B01G040600 chr3B 100.000 3566 0 0 1 3566 20056260 20052695 0.000000e+00 6586.0
1 TraesCS3B01G040600 chr3B 90.278 144 14 0 1751 1894 20002078 20001935 4.700000e-44 189.0
2 TraesCS3B01G040600 chr3A 89.147 2801 205 38 798 3566 23274180 23276913 0.000000e+00 3397.0
3 TraesCS3B01G040600 chr3A 91.324 219 15 3 51 268 23271932 23272147 2.690000e-76 296.0
4 TraesCS3B01G040600 chr3A 89.316 234 23 2 332 563 23272582 23272815 3.480000e-75 292.0
5 TraesCS3B01G040600 chr3A 90.863 197 13 3 1 195 23246520 23246713 3.530000e-65 259.0
6 TraesCS3B01G040600 chr3A 89.423 208 19 3 1 206 23273967 23274173 3.530000e-65 259.0
7 TraesCS3B01G040600 chr3A 93.750 144 9 0 1751 1894 23319999 23320142 2.160000e-52 217.0
8 TraesCS3B01G040600 chr3A 97.674 43 1 0 1 43 23259185 23259227 1.370000e-09 75.0
9 TraesCS3B01G040600 chr3D 90.218 2341 152 34 783 3107 13664969 13662690 0.000000e+00 2983.0
10 TraesCS3B01G040600 chr3D 88.931 533 49 2 3040 3566 13662690 13662162 0.000000e+00 649.0
11 TraesCS3B01G040600 chr3D 81.765 680 74 24 1 654 13699779 13699124 1.130000e-144 523.0
12 TraesCS3B01G040600 chr3D 89.231 260 24 4 1 258 13687769 13687512 4.440000e-84 322.0
13 TraesCS3B01G040600 chr1A 92.000 50 3 1 162 211 448979294 448979342 6.390000e-08 69.4
14 TraesCS3B01G040600 chr6A 96.970 33 0 1 538 569 481027078 481027110 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 TraesCS3B01G040600 chr3B 20052695 20056260 3565 True 6586 6586 100.0000 1 3566 1 chr3B.!!$R2 3565
1 TraesCS3B01G040600 chr3A 23271932 23276913 4981 False 1061 3397 89.8025 1 3566 4 chr3A.!!$F4 3565
2 TraesCS3B01G040600 chr3D 13662162 13664969 2807 True 1816 2983 89.5745 783 3566 2 chr3D.!!$R3 2783
3 TraesCS3B01G040600 chr3D 13699124 13699779 655 True 523 523 81.7650 1 654 1 chr3D.!!$R2 653

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
733 1131 0.039708 GGTTGAGCAAGCAAGTGAGC 60.040 55.0 7.47 0.0 38.57 4.26 F
941 2585 0.106419 TTTCCACTCCCACCCAACAC 60.106 55.0 0.00 0.0 0.00 3.32 F
1359 3003 0.110010 GCAAGGACAAGAAGAAGCGC 60.110 55.0 0.00 0.0 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 3201 0.030101 GGATCTTGAGCTCGTCCTCG 59.970 60.0 9.64 0.0 34.56 4.63 R
2267 3932 0.253044 TTCATGAGCTTCCCCTTCCG 59.747 55.0 0.00 0.0 0.00 4.30 R
2828 4498 0.374758 CATGAATTCACGGTGCCTCG 59.625 55.0 11.07 0.0 0.00 4.63 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
43 44 6.771749 AGTAGTACCAAGCGACATAGTAAGAT 59.228 38.462 0.00 0.00 0.00 2.40
44 45 6.466885 AGTACCAAGCGACATAGTAAGATT 57.533 37.500 0.00 0.00 0.00 2.40
45 46 6.875076 AGTACCAAGCGACATAGTAAGATTT 58.125 36.000 0.00 0.00 0.00 2.17
48 49 7.073342 ACCAAGCGACATAGTAAGATTTTTC 57.927 36.000 0.00 0.00 0.00 2.29
49 50 6.879458 ACCAAGCGACATAGTAAGATTTTTCT 59.121 34.615 0.00 0.00 0.00 2.52
106 107 8.521059 CGTGCTTAAGTTTTACTTTGAAGTTTC 58.479 33.333 4.02 0.00 39.51 2.78
136 137 6.483640 AGCTTACTTGACTACTTTTTGTCCAG 59.516 38.462 0.00 0.00 33.75 3.86
211 213 4.733542 GCCCCGGGCTTGCTACAA 62.734 66.667 22.31 0.00 46.69 2.41
212 214 2.750237 CCCCGGGCTTGCTACAAC 60.750 66.667 17.73 0.00 0.00 3.32
255 257 9.278978 TGATGCTACAGTGAACAAAGTATTTAA 57.721 29.630 0.00 0.00 35.03 1.52
268 270 6.091713 ACAAAGTATTTAATCTTCACGTCCCG 59.908 38.462 0.00 0.00 35.03 5.14
305 343 2.212327 CCGCTCTGGGTCCTGTATT 58.788 57.895 0.00 0.00 0.00 1.89
309 347 0.105039 CTCTGGGTCCTGTATTCGCC 59.895 60.000 0.00 0.00 0.00 5.54
312 350 1.153229 GGGTCCTGTATTCGCCACC 60.153 63.158 0.00 0.00 0.00 4.61
327 365 3.311110 ACCGGCGAGGAGAAAGCA 61.311 61.111 9.30 0.00 45.00 3.91
328 366 2.047274 CCGGCGAGGAGAAAGCAA 60.047 61.111 9.30 0.00 45.00 3.91
367 740 3.376546 GTCAGGCAAGGCTAAGAAGAATG 59.623 47.826 0.00 0.00 0.00 2.67
377 750 4.944317 GGCTAAGAAGAATGCTAAGGTTGT 59.056 41.667 0.00 0.00 0.00 3.32
466 839 2.652590 AGGCATCTCCTGAGCATTTTC 58.347 47.619 0.00 0.00 45.54 2.29
472 845 5.472478 GCATCTCCTGAGCATTTTCATATCA 59.528 40.000 0.00 0.00 0.00 2.15
496 869 8.077991 TCACAAACATGTTTTCAAATTTGCAAA 58.922 25.926 21.10 15.44 39.85 3.68
497 870 8.697067 CACAAACATGTTTTCAAATTTGCAAAA 58.303 25.926 21.10 16.71 39.85 2.44
498 871 9.420551 ACAAACATGTTTTCAAATTTGCAAAAT 57.579 22.222 21.10 4.62 39.85 1.82
669 1067 6.904954 TTTTTAATCAGTGTTCGCGATTTC 57.095 33.333 10.88 4.47 31.94 2.17
670 1068 5.856126 TTTAATCAGTGTTCGCGATTTCT 57.144 34.783 10.88 5.59 31.94 2.52
671 1069 5.856126 TTAATCAGTGTTCGCGATTTCTT 57.144 34.783 10.88 0.33 31.94 2.52
672 1070 4.749245 AATCAGTGTTCGCGATTTCTTT 57.251 36.364 10.88 0.00 0.00 2.52
673 1071 3.788434 TCAGTGTTCGCGATTTCTTTC 57.212 42.857 10.88 0.00 0.00 2.62
674 1072 3.127589 TCAGTGTTCGCGATTTCTTTCA 58.872 40.909 10.88 0.00 0.00 2.69
675 1073 3.558006 TCAGTGTTCGCGATTTCTTTCAA 59.442 39.130 10.88 0.00 0.00 2.69
676 1074 4.034626 TCAGTGTTCGCGATTTCTTTCAAA 59.965 37.500 10.88 0.00 0.00 2.69
677 1075 4.144731 CAGTGTTCGCGATTTCTTTCAAAC 59.855 41.667 10.88 0.71 0.00 2.93
678 1076 3.420904 GTGTTCGCGATTTCTTTCAAACC 59.579 43.478 10.88 0.00 0.00 3.27
679 1077 3.314080 TGTTCGCGATTTCTTTCAAACCT 59.686 39.130 10.88 0.00 0.00 3.50
680 1078 3.536158 TCGCGATTTCTTTCAAACCTG 57.464 42.857 3.71 0.00 0.00 4.00
681 1079 3.135225 TCGCGATTTCTTTCAAACCTGA 58.865 40.909 3.71 0.00 0.00 3.86
682 1080 3.562141 TCGCGATTTCTTTCAAACCTGAA 59.438 39.130 3.71 0.00 39.87 3.02
683 1081 4.035792 TCGCGATTTCTTTCAAACCTGAAA 59.964 37.500 3.71 0.77 46.88 2.69
719 1117 9.179909 ACGTATATTTTTGGAACATATGGTTGA 57.820 29.630 7.80 0.00 40.63 3.18
720 1118 9.663904 CGTATATTTTTGGAACATATGGTTGAG 57.336 33.333 7.80 0.00 40.63 3.02
721 1119 9.463443 GTATATTTTTGGAACATATGGTTGAGC 57.537 33.333 7.80 0.00 40.63 4.26
722 1120 5.798125 TTTTTGGAACATATGGTTGAGCA 57.202 34.783 7.80 0.00 40.63 4.26
723 1121 5.798125 TTTTGGAACATATGGTTGAGCAA 57.202 34.783 7.80 0.00 40.63 3.91
724 1122 5.389859 TTTGGAACATATGGTTGAGCAAG 57.610 39.130 7.80 0.00 40.63 4.01
725 1123 2.754552 TGGAACATATGGTTGAGCAAGC 59.245 45.455 7.80 5.52 40.63 4.01
726 1124 5.292911 TTGGAACATATGGTTGAGCAAGCA 61.293 41.667 16.23 16.23 45.76 3.91
727 1125 6.733971 TTGGAACATATGGTTGAGCAAGCAA 61.734 40.000 17.57 8.82 45.19 3.91
728 1126 8.455080 TTGGAACATATGGTTGAGCAAGCAAG 62.455 42.308 17.57 13.01 45.19 4.01
731 1129 3.493028 TGGTTGAGCAAGCAAGTGA 57.507 47.368 12.17 0.00 44.63 3.41
732 1130 1.311859 TGGTTGAGCAAGCAAGTGAG 58.688 50.000 12.17 0.00 44.63 3.51
733 1131 0.039708 GGTTGAGCAAGCAAGTGAGC 60.040 55.000 7.47 0.00 38.57 4.26
734 1132 0.385223 GTTGAGCAAGCAAGTGAGCG 60.385 55.000 0.00 0.00 40.15 5.03
735 1133 0.532640 TTGAGCAAGCAAGTGAGCGA 60.533 50.000 0.00 0.00 40.15 4.93
736 1134 0.947660 TGAGCAAGCAAGTGAGCGAG 60.948 55.000 0.00 0.00 40.15 5.03
737 1135 2.175322 GCAAGCAAGTGAGCGAGC 59.825 61.111 0.00 0.00 40.15 5.03
738 1136 2.610694 GCAAGCAAGTGAGCGAGCA 61.611 57.895 0.00 0.00 40.15 4.26
739 1137 1.496393 CAAGCAAGTGAGCGAGCAG 59.504 57.895 0.00 0.00 40.15 4.24
740 1138 1.670406 AAGCAAGTGAGCGAGCAGG 60.670 57.895 0.00 0.00 40.15 4.85
741 1139 3.797546 GCAAGTGAGCGAGCAGGC 61.798 66.667 0.00 0.00 0.00 4.85
742 1140 3.123620 CAAGTGAGCGAGCAGGCC 61.124 66.667 0.00 0.00 0.00 5.19
743 1141 3.317571 AAGTGAGCGAGCAGGCCT 61.318 61.111 0.00 0.00 0.00 5.19
744 1142 2.888447 AAGTGAGCGAGCAGGCCTT 61.888 57.895 0.00 0.00 0.00 4.35
745 1143 1.544825 AAGTGAGCGAGCAGGCCTTA 61.545 55.000 0.00 0.00 0.00 2.69
746 1144 1.144936 GTGAGCGAGCAGGCCTTAT 59.855 57.895 0.00 0.00 0.00 1.73
747 1145 0.462759 GTGAGCGAGCAGGCCTTATT 60.463 55.000 0.00 0.00 0.00 1.40
748 1146 0.462581 TGAGCGAGCAGGCCTTATTG 60.463 55.000 0.00 0.00 0.00 1.90
749 1147 1.153086 AGCGAGCAGGCCTTATTGG 60.153 57.895 0.00 0.00 39.35 3.16
750 1148 2.189499 GCGAGCAGGCCTTATTGGG 61.189 63.158 0.00 0.00 36.00 4.12
825 2468 2.091541 TCGGCAGCATTTCCTAAAAGG 58.908 47.619 0.00 0.00 36.46 3.11
941 2585 0.106419 TTTCCACTCCCACCCAACAC 60.106 55.000 0.00 0.00 0.00 3.32
942 2586 2.002018 TTCCACTCCCACCCAACACC 62.002 60.000 0.00 0.00 0.00 4.16
950 2594 4.875301 ACCCAACACCCCCACCCT 62.875 66.667 0.00 0.00 0.00 4.34
1149 2793 0.894835 CGACCCAAAATTCCCCCAAG 59.105 55.000 0.00 0.00 0.00 3.61
1281 2925 1.144936 CCAGATCGCCTCCTCCAAC 59.855 63.158 0.00 0.00 0.00 3.77
1282 2926 1.144936 CAGATCGCCTCCTCCAACC 59.855 63.158 0.00 0.00 0.00 3.77
1283 2927 2.066999 AGATCGCCTCCTCCAACCC 61.067 63.158 0.00 0.00 0.00 4.11
1284 2928 3.447025 GATCGCCTCCTCCAACCCG 62.447 68.421 0.00 0.00 0.00 5.28
1319 2963 2.183300 CAAGCCCGAATCCGACGA 59.817 61.111 0.00 0.00 38.22 4.20
1321 2965 3.366739 AAGCCCGAATCCGACGACC 62.367 63.158 0.00 0.00 38.22 4.79
1322 2966 4.137872 GCCCGAATCCGACGACCA 62.138 66.667 0.00 0.00 38.22 4.02
1323 2967 2.104331 CCCGAATCCGACGACCAG 59.896 66.667 0.00 0.00 38.22 4.00
1357 3001 0.884514 GGGCAAGGACAAGAAGAAGC 59.115 55.000 0.00 0.00 0.00 3.86
1359 3003 0.110010 GCAAGGACAAGAAGAAGCGC 60.110 55.000 0.00 0.00 0.00 5.92
1363 3007 0.519077 GGACAAGAAGAAGCGCAAGG 59.481 55.000 11.47 0.00 38.28 3.61
1365 3009 1.211190 CAAGAAGAAGCGCAAGGCC 59.789 57.895 11.47 0.00 45.17 5.19
1366 3010 2.328099 AAGAAGAAGCGCAAGGCCG 61.328 57.895 11.47 0.00 45.17 6.13
1367 3011 3.804193 GAAGAAGCGCAAGGCCGG 61.804 66.667 11.47 0.00 45.17 6.13
1452 3117 2.685380 ACTCCTTCCAGCGAGGGG 60.685 66.667 0.00 0.00 40.79 4.79
1620 3285 1.723870 CGCTGGTGAGCTTATTGCC 59.276 57.895 0.00 0.00 43.77 4.52
1622 3287 1.026718 GCTGGTGAGCTTATTGCCGT 61.027 55.000 0.00 0.00 42.52 5.68
1641 3306 2.743928 GTTGGTGGCAGCCTCGAG 60.744 66.667 14.15 5.13 0.00 4.04
1686 3351 2.380084 TGTATGAGAAGGTGCGGAAC 57.620 50.000 0.00 0.00 0.00 3.62
1698 3363 3.197790 CGGAACATCAGGCAGCGG 61.198 66.667 0.00 0.00 0.00 5.52
1784 3449 2.270527 GGAGCAAGTCTGGGGAGC 59.729 66.667 0.00 0.00 0.00 4.70
1785 3450 2.596851 GGAGCAAGTCTGGGGAGCA 61.597 63.158 0.00 0.00 0.00 4.26
1800 3465 1.425412 GAGCAAATGCAAAGCAGGTG 58.575 50.000 8.28 0.00 43.65 4.00
1900 3565 1.543944 GGGCCATTCAAAGGGTGGTG 61.544 60.000 4.39 0.00 35.44 4.17
1914 3579 2.598394 GGTGCAGCAAAGGAGGCA 60.598 61.111 11.86 0.00 0.00 4.75
1955 3620 1.064389 AGAGGGCTATTCAAAGGGTGC 60.064 52.381 0.00 0.00 0.00 5.01
1996 3661 5.126384 ACCGAAGAGAAGGTAGAAGAAGATG 59.874 44.000 0.00 0.00 39.30 2.90
2022 3687 0.813821 GCAGGTCATCAAAGAAGGCC 59.186 55.000 0.00 0.00 0.00 5.19
2199 3864 0.835941 AGAAAGCGGATGGAGATGCT 59.164 50.000 0.00 0.00 39.89 3.79
2211 3876 1.614525 AGATGCTGAGAGCCCCACA 60.615 57.895 0.00 0.00 41.51 4.17
2216 3881 1.302832 CTGAGAGCCCCACACCAAC 60.303 63.158 0.00 0.00 0.00 3.77
2222 3887 3.246112 CCCCACACCAACGGAGGA 61.246 66.667 2.13 0.00 0.00 3.71
2267 3932 3.198872 GCACCCTTGCTCTGTATAAGAC 58.801 50.000 0.00 0.00 46.17 3.01
2278 3943 3.958798 TCTGTATAAGACGGAAGGGGAAG 59.041 47.826 0.00 0.00 40.68 3.46
2455 4120 4.409901 TCATTCCTGATGAGAAGGCATGTA 59.590 41.667 0.00 0.00 39.83 2.29
2701 4366 9.810545 ATGCATCTTACTTCTCTAGTTTACTTC 57.189 33.333 0.00 0.00 38.33 3.01
2737 4407 6.655078 ATATATCTGCAACCAAATTCCACC 57.345 37.500 0.00 0.00 0.00 4.61
2738 4408 1.337118 TCTGCAACCAAATTCCACCC 58.663 50.000 0.00 0.00 0.00 4.61
2739 4409 1.047002 CTGCAACCAAATTCCACCCA 58.953 50.000 0.00 0.00 0.00 4.51
2752 4422 0.774908 CCACCCACCACCCTAAAAGA 59.225 55.000 0.00 0.00 0.00 2.52
2786 4456 0.321564 CGGATGCAGGTGAGTTGGAA 60.322 55.000 0.00 0.00 0.00 3.53
2828 4498 4.107622 CAGTATAATTTTGTGCAGGCAGC 58.892 43.478 0.00 0.00 45.96 5.25
2845 4515 2.032634 GCGAGGCACCGTGAATTCA 61.033 57.895 3.38 3.38 0.00 2.57
2876 4546 1.692411 AGTCTGAAACAAGGGCCAAC 58.308 50.000 6.18 0.00 0.00 3.77
2895 4565 5.793817 CCAACGGACATGAGATGGATTATA 58.206 41.667 0.00 0.00 33.60 0.98
2896 4566 6.409704 CCAACGGACATGAGATGGATTATAT 58.590 40.000 0.00 0.00 33.60 0.86
2954 4632 4.940463 TCCACCGTATTTAGATACACAGC 58.060 43.478 4.47 0.00 38.42 4.40
3044 4723 6.211184 TGGCTGTCAAAATATTGTTCAGGATT 59.789 34.615 8.69 0.00 38.57 3.01
3056 4735 4.469657 TGTTCAGGATTAAACTGCTGGTT 58.530 39.130 0.00 0.00 40.28 3.67
3173 4926 6.862090 AGACAACGATTGACTAGTTAACTGAC 59.138 38.462 18.56 9.48 34.04 3.51
3221 4978 0.656785 GTAACACGGCGTTTTGGACA 59.343 50.000 20.58 0.00 39.14 4.02
3222 4979 1.063764 GTAACACGGCGTTTTGGACAA 59.936 47.619 20.58 0.00 39.14 3.18
3223 4980 0.526662 AACACGGCGTTTTGGACAAA 59.473 45.000 11.19 0.00 32.35 2.83
3224 4981 0.099791 ACACGGCGTTTTGGACAAAG 59.900 50.000 11.19 0.00 0.00 2.77
3292 5049 1.691196 TTGTTGCTTCCCCTTCAGTG 58.309 50.000 0.00 0.00 0.00 3.66
3330 5087 6.109320 ACTGTTGCATTTTTGTTCATGTTG 57.891 33.333 0.00 0.00 0.00 3.33
3331 5088 5.064962 ACTGTTGCATTTTTGTTCATGTTGG 59.935 36.000 0.00 0.00 0.00 3.77
3332 5089 4.201891 TGTTGCATTTTTGTTCATGTTGGC 60.202 37.500 0.00 0.00 0.00 4.52
3333 5090 3.538591 TGCATTTTTGTTCATGTTGGCA 58.461 36.364 0.00 0.00 0.00 4.92
3334 5091 4.135306 TGCATTTTTGTTCATGTTGGCAT 58.865 34.783 0.00 0.00 35.32 4.40
3407 5171 4.914983 TGATTTCCTGAAAGTCAGCAGAT 58.085 39.130 0.00 0.00 42.98 2.90
3459 5223 5.702670 ACAGAGAATGACAAAGTATGGTGTG 59.297 40.000 0.00 0.00 0.00 3.82
3463 5227 7.387948 AGAGAATGACAAAGTATGGTGTGTTAC 59.612 37.037 0.00 0.00 0.00 2.50
3464 5228 6.995686 AGAATGACAAAGTATGGTGTGTTACA 59.004 34.615 0.00 0.00 0.00 2.41
3505 5275 3.875727 GTGCTGTCATTGCAGAGATGTAT 59.124 43.478 10.89 0.00 41.41 2.29
3506 5276 4.025061 GTGCTGTCATTGCAGAGATGTATC 60.025 45.833 10.89 0.00 41.41 2.24
3512 5282 5.407995 GTCATTGCAGAGATGTATCCTAAGC 59.592 44.000 0.00 0.00 0.00 3.09
3560 5330 3.935828 TGTCGTTCACACAAATTGACAGA 59.064 39.130 0.00 0.00 31.81 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.919621 GTCGCTTGGTACTACTAAATATGAAGT 59.080 37.037 0.00 0.00 0.00 3.01
8 9 7.919091 TGTCGCTTGGTACTACTAAATATGAAG 59.081 37.037 0.00 0.00 0.00 3.02
43 44 7.093509 GGCCCCACTTGATCTATTAAAGAAAAA 60.094 37.037 0.00 0.00 37.89 1.94
44 45 6.379988 GGCCCCACTTGATCTATTAAAGAAAA 59.620 38.462 0.00 0.00 37.89 2.29
45 46 5.891551 GGCCCCACTTGATCTATTAAAGAAA 59.108 40.000 0.00 0.00 37.89 2.52
48 49 5.053978 AGGCCCCACTTGATCTATTAAAG 57.946 43.478 0.00 0.00 0.00 1.85
49 50 5.466127 AAGGCCCCACTTGATCTATTAAA 57.534 39.130 0.00 0.00 0.00 1.52
54 55 6.780198 AAATATAAGGCCCCACTTGATCTA 57.220 37.500 0.00 0.00 32.02 1.98
106 107 7.042658 ACAAAAAGTAGTCAAGTAAGCTCTTCG 60.043 37.037 0.00 0.00 0.00 3.79
136 137 1.087501 CGCAACCTTAGCCTTCTTCC 58.912 55.000 0.00 0.00 0.00 3.46
199 200 1.804601 AGTAACGTTGTAGCAAGCCC 58.195 50.000 11.99 0.00 0.00 5.19
211 213 4.570772 GCATCATGGACAATGTAGTAACGT 59.429 41.667 0.00 0.00 37.56 3.99
212 214 4.811024 AGCATCATGGACAATGTAGTAACG 59.189 41.667 0.00 0.00 37.56 3.18
288 326 0.249073 CGAATACAGGACCCAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
291 329 0.616395 TGGCGAATACAGGACCCAGA 60.616 55.000 0.00 0.00 0.00 3.86
309 347 2.815647 GCTTTCTCCTCGCCGGTG 60.816 66.667 9.28 9.28 0.00 4.94
312 350 1.497722 GTTTGCTTTCTCCTCGCCG 59.502 57.895 0.00 0.00 0.00 6.46
316 354 2.227626 GCTCAAGGTTTGCTTTCTCCTC 59.772 50.000 0.00 0.00 0.00 3.71
327 365 0.846693 ACAGAGTGGGCTCAAGGTTT 59.153 50.000 0.00 0.00 44.00 3.27
328 366 0.398318 GACAGAGTGGGCTCAAGGTT 59.602 55.000 0.00 0.00 44.00 3.50
367 740 0.321298 TTCTCCGCCACAACCTTAGC 60.321 55.000 0.00 0.00 0.00 3.09
377 750 4.415332 GCGTCGTCTTCTCCGCCA 62.415 66.667 0.00 0.00 40.25 5.69
431 804 2.593956 GCCTTCTCCGTCCCAACCT 61.594 63.158 0.00 0.00 0.00 3.50
432 805 2.046217 GCCTTCTCCGTCCCAACC 60.046 66.667 0.00 0.00 0.00 3.77
472 845 8.807667 TTTTGCAAATTTGAAAACATGTTTGT 57.192 23.077 23.93 13.90 35.50 2.83
650 1048 5.407084 TGAAAGAAATCGCGAACACTGATTA 59.593 36.000 15.24 0.29 32.32 1.75
652 1050 3.745975 TGAAAGAAATCGCGAACACTGAT 59.254 39.130 15.24 5.57 0.00 2.90
653 1051 3.127589 TGAAAGAAATCGCGAACACTGA 58.872 40.909 15.24 0.00 0.00 3.41
654 1052 3.519908 TGAAAGAAATCGCGAACACTG 57.480 42.857 15.24 0.00 0.00 3.66
655 1053 4.279659 GTTTGAAAGAAATCGCGAACACT 58.720 39.130 15.24 9.77 0.00 3.55
656 1054 3.420904 GGTTTGAAAGAAATCGCGAACAC 59.579 43.478 15.24 7.32 0.00 3.32
657 1055 3.314080 AGGTTTGAAAGAAATCGCGAACA 59.686 39.130 15.24 2.28 0.00 3.18
658 1056 3.664025 CAGGTTTGAAAGAAATCGCGAAC 59.336 43.478 15.24 8.13 0.00 3.95
659 1057 3.562141 TCAGGTTTGAAAGAAATCGCGAA 59.438 39.130 15.24 0.00 0.00 4.70
660 1058 3.135225 TCAGGTTTGAAAGAAATCGCGA 58.865 40.909 13.09 13.09 0.00 5.87
661 1059 3.536158 TCAGGTTTGAAAGAAATCGCG 57.464 42.857 0.00 0.00 0.00 5.87
693 1091 9.179909 TCAACCATATGTTCCAAAAATATACGT 57.820 29.630 1.24 0.00 34.00 3.57
694 1092 9.663904 CTCAACCATATGTTCCAAAAATATACG 57.336 33.333 1.24 0.00 34.00 3.06
695 1093 9.463443 GCTCAACCATATGTTCCAAAAATATAC 57.537 33.333 1.24 0.00 34.00 1.47
696 1094 9.194972 TGCTCAACCATATGTTCCAAAAATATA 57.805 29.630 1.24 0.00 34.00 0.86
697 1095 8.076910 TGCTCAACCATATGTTCCAAAAATAT 57.923 30.769 1.24 0.00 34.00 1.28
698 1096 7.473735 TGCTCAACCATATGTTCCAAAAATA 57.526 32.000 1.24 0.00 34.00 1.40
699 1097 6.357579 TGCTCAACCATATGTTCCAAAAAT 57.642 33.333 1.24 0.00 34.00 1.82
700 1098 5.798125 TGCTCAACCATATGTTCCAAAAA 57.202 34.783 1.24 0.00 34.00 1.94
701 1099 5.782047 CTTGCTCAACCATATGTTCCAAAA 58.218 37.500 1.24 0.00 34.00 2.44
702 1100 4.321899 GCTTGCTCAACCATATGTTCCAAA 60.322 41.667 1.24 0.00 34.00 3.28
703 1101 3.193267 GCTTGCTCAACCATATGTTCCAA 59.807 43.478 1.24 0.00 34.00 3.53
704 1102 2.754552 GCTTGCTCAACCATATGTTCCA 59.245 45.455 1.24 0.00 34.00 3.53
705 1103 2.754552 TGCTTGCTCAACCATATGTTCC 59.245 45.455 1.24 0.00 34.00 3.62
706 1104 4.082571 ACTTGCTTGCTCAACCATATGTTC 60.083 41.667 1.24 0.00 34.00 3.18
707 1105 3.828451 ACTTGCTTGCTCAACCATATGTT 59.172 39.130 1.24 0.00 37.80 2.71
708 1106 3.192001 CACTTGCTTGCTCAACCATATGT 59.808 43.478 1.24 0.00 0.00 2.29
709 1107 3.441222 TCACTTGCTTGCTCAACCATATG 59.559 43.478 0.00 0.00 0.00 1.78
710 1108 3.689347 TCACTTGCTTGCTCAACCATAT 58.311 40.909 0.00 0.00 0.00 1.78
711 1109 3.076621 CTCACTTGCTTGCTCAACCATA 58.923 45.455 0.00 0.00 0.00 2.74
712 1110 1.884579 CTCACTTGCTTGCTCAACCAT 59.115 47.619 0.00 0.00 0.00 3.55
713 1111 1.311859 CTCACTTGCTTGCTCAACCA 58.688 50.000 0.00 0.00 0.00 3.67
714 1112 0.039708 GCTCACTTGCTTGCTCAACC 60.040 55.000 0.00 0.00 0.00 3.77
715 1113 0.385223 CGCTCACTTGCTTGCTCAAC 60.385 55.000 0.00 0.00 0.00 3.18
716 1114 0.532640 TCGCTCACTTGCTTGCTCAA 60.533 50.000 0.00 0.00 0.00 3.02
717 1115 0.947660 CTCGCTCACTTGCTTGCTCA 60.948 55.000 0.00 0.00 0.00 4.26
718 1116 1.786582 CTCGCTCACTTGCTTGCTC 59.213 57.895 0.00 0.00 0.00 4.26
719 1117 2.323580 GCTCGCTCACTTGCTTGCT 61.324 57.895 0.00 0.00 0.00 3.91
720 1118 2.175322 GCTCGCTCACTTGCTTGC 59.825 61.111 0.00 0.00 0.00 4.01
721 1119 1.496393 CTGCTCGCTCACTTGCTTG 59.504 57.895 0.00 0.00 0.00 4.01
722 1120 1.670406 CCTGCTCGCTCACTTGCTT 60.670 57.895 0.00 0.00 0.00 3.91
723 1121 2.047465 CCTGCTCGCTCACTTGCT 60.047 61.111 0.00 0.00 0.00 3.91
724 1122 3.797546 GCCTGCTCGCTCACTTGC 61.798 66.667 0.00 0.00 0.00 4.01
725 1123 3.123620 GGCCTGCTCGCTCACTTG 61.124 66.667 0.00 0.00 0.00 3.16
726 1124 1.544825 TAAGGCCTGCTCGCTCACTT 61.545 55.000 5.69 0.00 0.00 3.16
727 1125 1.333636 ATAAGGCCTGCTCGCTCACT 61.334 55.000 5.69 0.00 0.00 3.41
728 1126 0.462759 AATAAGGCCTGCTCGCTCAC 60.463 55.000 5.69 0.00 0.00 3.51
729 1127 0.462581 CAATAAGGCCTGCTCGCTCA 60.463 55.000 5.69 0.00 0.00 4.26
730 1128 1.162800 CCAATAAGGCCTGCTCGCTC 61.163 60.000 5.69 0.00 0.00 5.03
731 1129 1.153086 CCAATAAGGCCTGCTCGCT 60.153 57.895 5.69 0.00 0.00 4.93
732 1130 2.189499 CCCAATAAGGCCTGCTCGC 61.189 63.158 5.69 0.00 35.39 5.03
733 1131 4.147701 CCCAATAAGGCCTGCTCG 57.852 61.111 5.69 0.00 35.39 5.03
751 1149 2.815647 GAGGTTCAAGCGGCGAGG 60.816 66.667 12.98 0.00 0.00 4.63
752 1150 3.181967 CGAGGTTCAAGCGGCGAG 61.182 66.667 12.98 0.00 0.00 5.03
753 1151 4.735132 CCGAGGTTCAAGCGGCGA 62.735 66.667 12.98 0.00 38.46 5.54
754 1152 4.735132 TCCGAGGTTCAAGCGGCG 62.735 66.667 0.51 0.51 44.45 6.46
755 1153 2.781595 TTCTCCGAGGTTCAAGCGGC 62.782 60.000 0.00 0.00 44.45 6.53
756 1154 0.737715 CTTCTCCGAGGTTCAAGCGG 60.738 60.000 0.00 0.00 46.08 5.52
757 1155 1.355066 GCTTCTCCGAGGTTCAAGCG 61.355 60.000 4.35 0.00 30.84 4.68
758 1156 1.021920 GGCTTCTCCGAGGTTCAAGC 61.022 60.000 9.90 9.90 39.02 4.01
759 1157 0.321671 TGGCTTCTCCGAGGTTCAAG 59.678 55.000 0.00 0.00 37.80 3.02
760 1158 0.762418 TTGGCTTCTCCGAGGTTCAA 59.238 50.000 0.00 0.00 37.80 2.69
761 1159 0.984230 ATTGGCTTCTCCGAGGTTCA 59.016 50.000 0.00 0.00 37.80 3.18
762 1160 1.208293 AGATTGGCTTCTCCGAGGTTC 59.792 52.381 0.00 0.00 37.80 3.62
763 1161 1.208293 GAGATTGGCTTCTCCGAGGTT 59.792 52.381 6.73 0.00 36.87 3.50
764 1162 0.827368 GAGATTGGCTTCTCCGAGGT 59.173 55.000 6.73 0.00 36.87 3.85
765 1163 0.249238 CGAGATTGGCTTCTCCGAGG 60.249 60.000 10.94 0.00 39.19 4.63
766 1164 0.741326 TCGAGATTGGCTTCTCCGAG 59.259 55.000 10.94 0.00 39.19 4.63
802 2445 4.381932 CCTTTTAGGAAATGCTGCCGATTT 60.382 41.667 0.00 0.00 37.67 2.17
825 2468 1.205820 GCCTACGCCACGTTGTTTC 59.794 57.895 0.00 0.00 41.54 2.78
1056 2700 2.348888 GGACTCCTCGGCGGAAGAA 61.349 63.158 7.21 0.00 42.53 2.52
1080 2724 4.507916 TCCTCCTCCTCCTCGGCG 62.508 72.222 0.00 0.00 0.00 6.46
1083 2727 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1084 2728 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1085 2729 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1203 2847 2.100603 GACTCCTCGTCGCTTCCG 59.899 66.667 0.00 0.00 32.04 4.30
1230 2874 3.417275 CTCGGCGTCGATCTTGCCT 62.417 63.158 14.65 0.00 46.67 4.75
1297 2941 2.869503 TCGGATTCGGGCTTGGAAGC 62.870 60.000 2.56 2.56 42.31 3.86
1298 2942 1.090052 GTCGGATTCGGGCTTGGAAG 61.090 60.000 0.00 0.00 36.95 3.46
1299 2943 1.078708 GTCGGATTCGGGCTTGGAA 60.079 57.895 0.00 0.00 36.95 3.53
1300 2944 2.582436 GTCGGATTCGGGCTTGGA 59.418 61.111 0.00 0.00 36.95 3.53
1301 2945 2.890474 CGTCGGATTCGGGCTTGG 60.890 66.667 0.00 0.00 36.95 3.61
1302 2946 2.165301 GTCGTCGGATTCGGGCTTG 61.165 63.158 0.00 0.00 36.95 4.01
1303 2947 2.183555 GTCGTCGGATTCGGGCTT 59.816 61.111 0.00 0.00 36.95 4.35
1304 2948 3.834799 GGTCGTCGGATTCGGGCT 61.835 66.667 0.00 0.00 36.95 5.19
1307 2951 2.104331 CCTGGTCGTCGGATTCGG 59.896 66.667 0.00 0.00 36.95 4.30
1340 2984 0.110010 GCGCTTCTTCTTGTCCTTGC 60.110 55.000 0.00 0.00 0.00 4.01
1383 3027 3.844090 GACGGAGAGGGCTCAGGC 61.844 72.222 0.00 0.00 43.14 4.85
1384 3028 3.151022 GGACGGAGAGGGCTCAGG 61.151 72.222 0.00 0.00 43.14 3.86
1385 3029 3.522731 CGGACGGAGAGGGCTCAG 61.523 72.222 0.00 0.00 43.14 3.35
1452 3117 0.884514 GGGCCTTGTGCTTCTTCTTC 59.115 55.000 0.84 0.00 40.92 2.87
1534 3199 0.736053 ATCTTGAGCTCGTCCTCGAC 59.264 55.000 9.64 0.00 41.35 4.20
1535 3200 1.018148 GATCTTGAGCTCGTCCTCGA 58.982 55.000 9.64 0.00 44.12 4.04
1536 3201 0.030101 GGATCTTGAGCTCGTCCTCG 59.970 60.000 9.64 0.00 34.56 4.63
1606 3271 0.676782 ACCACGGCAATAAGCTCACC 60.677 55.000 0.00 0.00 44.79 4.02
1620 3285 4.954970 AGGCTGCCACCAACCACG 62.955 66.667 22.65 0.00 29.30 4.94
1622 3287 4.641645 CGAGGCTGCCACCAACCA 62.642 66.667 22.65 0.00 29.30 3.67
1641 3306 2.147150 GTCTTGGTGCAGTTCTTCCTC 58.853 52.381 0.00 0.00 0.00 3.71
1651 3316 2.552599 TACATTTCCGTCTTGGTGCA 57.447 45.000 0.00 0.00 39.52 4.57
1652 3317 3.006940 TCATACATTTCCGTCTTGGTGC 58.993 45.455 0.00 0.00 39.52 5.01
1686 3351 0.390492 TCTCATACCGCTGCCTGATG 59.610 55.000 0.00 0.00 0.00 3.07
1698 3363 1.661112 GTGCTCACCGCTTTCTCATAC 59.339 52.381 0.00 0.00 40.11 2.39
1784 3449 2.535588 GCCACCTGCTTTGCATTTG 58.464 52.632 0.00 0.00 38.13 2.32
1900 3565 2.653115 GGTTGCCTCCTTTGCTGC 59.347 61.111 0.00 0.00 0.00 5.25
1914 3579 2.845752 TTTCATCGGCGCTAGCGGTT 62.846 55.000 35.86 14.37 46.35 4.44
1955 3620 1.589716 GGTGGCCTGCTTTGCTGTAG 61.590 60.000 3.32 0.00 0.00 2.74
1996 3661 0.899717 TTTGATGACCTGCCCTTGCC 60.900 55.000 0.00 0.00 36.33 4.52
2070 3735 2.018644 GCATCGCCTTCCAATTCCTCA 61.019 52.381 0.00 0.00 0.00 3.86
2099 3764 1.337823 CCACGGTCTCCTTTGTAGTGG 60.338 57.143 0.00 0.00 41.09 4.00
2199 3864 2.836154 GTTGGTGTGGGGCTCTCA 59.164 61.111 0.00 0.00 0.00 3.27
2211 3876 0.469917 CAGCCATATCCTCCGTTGGT 59.530 55.000 0.00 0.00 0.00 3.67
2216 3881 1.373497 GCGTCAGCCATATCCTCCG 60.373 63.158 0.00 0.00 37.42 4.63
2222 3887 2.620115 CCATTTTGAGCGTCAGCCATAT 59.380 45.455 0.00 0.00 46.67 1.78
2261 3926 1.763545 GAGCTTCCCCTTCCGTCTTAT 59.236 52.381 0.00 0.00 0.00 1.73
2267 3932 0.253044 TTCATGAGCTTCCCCTTCCG 59.747 55.000 0.00 0.00 0.00 4.30
2278 3943 4.456911 TGTGTCCATTTTCTCTTCATGAGC 59.543 41.667 0.00 0.00 42.38 4.26
2301 3966 2.679837 CGTGCCTTTCACATTAGCATCT 59.320 45.455 0.00 0.00 45.92 2.90
2394 4059 0.749454 GTGTCTCCCCACATGGATGC 60.749 60.000 0.00 0.00 37.39 3.91
2455 4120 5.184671 GCTTCTTGATCTTGGATTCCAAAGT 59.815 40.000 18.49 10.23 43.44 2.66
2701 4366 8.930760 GGTTGCAGATATATAAAGCTAGACTTG 58.069 37.037 0.00 0.00 39.09 3.16
2737 4407 6.481643 TCTTTCTAATCTTTTAGGGTGGTGG 58.518 40.000 0.00 0.00 36.30 4.61
2738 4408 8.581253 AATCTTTCTAATCTTTTAGGGTGGTG 57.419 34.615 0.00 0.00 36.30 4.17
2739 4409 9.907229 CTAATCTTTCTAATCTTTTAGGGTGGT 57.093 33.333 0.00 0.00 36.30 4.16
2752 4422 4.973168 TGCATCCGCCTAATCTTTCTAAT 58.027 39.130 0.00 0.00 37.32 1.73
2810 4480 1.818060 TCGCTGCCTGCACAAAATTAT 59.182 42.857 0.00 0.00 43.06 1.28
2828 4498 0.374758 CATGAATTCACGGTGCCTCG 59.625 55.000 11.07 0.00 0.00 4.63
2834 4504 1.541147 CAGTTGCCATGAATTCACGGT 59.459 47.619 20.90 0.00 30.68 4.83
2836 4506 3.557577 TTCAGTTGCCATGAATTCACG 57.442 42.857 11.07 1.48 31.86 4.35
2845 4515 3.953612 TGTTTCAGACTTTCAGTTGCCAT 59.046 39.130 0.00 0.00 0.00 4.40
2876 4546 5.422145 TGCATATAATCCATCTCATGTCCG 58.578 41.667 0.00 0.00 0.00 4.79
2895 4565 9.682465 AATATAAGCATAAGACATGAGATGCAT 57.318 29.630 19.96 0.00 45.72 3.96
2896 4566 9.159364 GAATATAAGCATAAGACATGAGATGCA 57.841 33.333 19.96 0.00 45.72 3.96
3056 4735 9.391006 ACAAACTCTACAGTAACAATCAAAGAA 57.609 29.630 0.00 0.00 30.14 2.52
3150 4903 6.746120 AGTCAGTTAACTAGTCAATCGTTGT 58.254 36.000 8.04 0.00 0.00 3.32
3152 4905 9.754382 TTAAAGTCAGTTAACTAGTCAATCGTT 57.246 29.630 8.04 2.19 0.00 3.85
3153 4906 9.924650 ATTAAAGTCAGTTAACTAGTCAATCGT 57.075 29.630 8.04 0.00 0.00 3.73
3169 4922 8.018677 AGTTGTCAACACGATATTAAAGTCAG 57.981 34.615 17.78 0.00 0.00 3.51
3209 4966 2.159296 ACTGTTCTTTGTCCAAAACGCC 60.159 45.455 0.00 0.00 0.00 5.68
3211 4968 5.224562 TGTACTGTTCTTTGTCCAAAACG 57.775 39.130 0.00 0.00 0.00 3.60
3221 4978 8.837389 GTTTCCTGAAACTATGTACTGTTCTTT 58.163 33.333 14.02 0.00 45.26 2.52
3222 4979 8.379457 GTTTCCTGAAACTATGTACTGTTCTT 57.621 34.615 14.02 0.00 45.26 2.52
3223 4980 7.964604 GTTTCCTGAAACTATGTACTGTTCT 57.035 36.000 14.02 0.00 45.26 3.01
3292 5049 4.574828 TGCAACAGTTGTTCTTTCTAGGAC 59.425 41.667 14.88 0.00 35.83 3.85
3330 5087 2.497675 TCAGACCTCAGAACTACATGCC 59.502 50.000 0.00 0.00 0.00 4.40
3331 5088 3.056536 TGTCAGACCTCAGAACTACATGC 60.057 47.826 0.00 0.00 0.00 4.06
3332 5089 4.790765 TGTCAGACCTCAGAACTACATG 57.209 45.455 0.00 0.00 0.00 3.21
3333 5090 6.014242 TCAAATGTCAGACCTCAGAACTACAT 60.014 38.462 0.00 0.00 0.00 2.29
3334 5091 5.304357 TCAAATGTCAGACCTCAGAACTACA 59.696 40.000 0.00 0.00 0.00 2.74
3335 5092 5.635700 GTCAAATGTCAGACCTCAGAACTAC 59.364 44.000 0.00 0.00 0.00 2.73
3336 5093 5.304357 TGTCAAATGTCAGACCTCAGAACTA 59.696 40.000 0.00 0.00 33.89 2.24
3343 5107 4.935885 GACATGTCAAATGTCAGACCTC 57.064 45.455 21.07 0.00 45.61 3.85
3365 5129 2.363359 CAGCCCTTTTTGAGCAAGACTT 59.637 45.455 0.00 0.00 0.00 3.01
3366 5130 1.959282 CAGCCCTTTTTGAGCAAGACT 59.041 47.619 0.00 0.00 0.00 3.24
3374 5138 3.843422 TCAGGAAATCAGCCCTTTTTGA 58.157 40.909 0.00 0.00 0.00 2.69
3375 5139 4.605640 TTCAGGAAATCAGCCCTTTTTG 57.394 40.909 0.00 0.00 0.00 2.44
3407 5171 6.489700 TCAGAACTTCCAACTGAATTTGCATA 59.510 34.615 0.00 0.00 37.66 3.14
3445 5209 5.298276 CAGGTTGTAACACACCATACTTTGT 59.702 40.000 0.00 0.00 0.00 2.83
3446 5210 5.529430 TCAGGTTGTAACACACCATACTTTG 59.471 40.000 0.00 0.00 0.00 2.77
3459 5223 4.911514 TTTCAGCCTTTCAGGTTGTAAC 57.088 40.909 6.54 0.00 45.52 2.50
3463 5227 4.053295 CACAATTTCAGCCTTTCAGGTTG 58.947 43.478 0.31 0.31 46.54 3.77
3464 5228 3.493176 GCACAATTTCAGCCTTTCAGGTT 60.493 43.478 0.00 0.00 37.80 3.50
3486 5250 4.958509 AGGATACATCTCTGCAATGACAG 58.041 43.478 3.89 0.00 37.92 3.51
3505 5275 4.568072 TGCTGAAATAACAGGCTTAGGA 57.432 40.909 0.00 0.00 38.22 2.94
3506 5276 4.702131 AGTTGCTGAAATAACAGGCTTAGG 59.298 41.667 0.00 0.00 38.22 2.69
3512 5282 8.866140 AACTTCCAGAGTTGCTGAAATAACAGG 61.866 40.741 0.00 0.00 46.66 4.00


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

AutoCloner maintained by Alex Coulton.