Multiple sequence alignment - TraesCS3D01G086800

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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 TraesCS3D01G086800 chr3D 100.000 2579 0 0 1 2579 43808498 43811076 0.000000e+00 4763.0
1 TraesCS3D01G086800 chr3B 92.974 854 51 5 978 1827 68593338 68594186 0.000000e+00 1236.0
2 TraesCS3D01G086800 chr3B 93.510 755 46 1 1825 2579 68626657 68627408 0.000000e+00 1120.0
3 TraesCS3D01G086800 chr3B 91.111 675 50 8 270 939 68592674 68593343 0.000000e+00 905.0
4 TraesCS3D01G086800 chr3B 83.784 222 31 4 406 627 332011176 332010960 3.360000e-49 206.0
5 TraesCS3D01G086800 chr3B 77.636 313 65 4 1 310 730781104 730780794 4.380000e-43 185.0
6 TraesCS3D01G086800 chr3A 90.160 813 61 8 1 797 55742202 55743011 0.000000e+00 1040.0
7 TraesCS3D01G086800 chr3A 91.126 755 48 5 1825 2579 55776777 55777512 0.000000e+00 1005.0
8 TraesCS3D01G086800 chr3A 88.133 750 56 12 970 1716 55743103 55743822 0.000000e+00 861.0
9 TraesCS3D01G086800 chr3A 93.750 112 7 0 839 950 55743008 55743119 4.410000e-38 169.0
10 TraesCS3D01G086800 chr3A 90.909 110 7 2 1715 1823 55743951 55744058 7.440000e-31 145.0
11 TraesCS3D01G086800 chr1A 89.163 203 20 2 400 602 349363026 349363226 4.260000e-63 252.0
12 TraesCS3D01G086800 chr1A 74.227 582 103 29 61 627 164454837 164455386 1.570000e-47 200.0
13 TraesCS3D01G086800 chr6D 74.560 625 131 22 20 627 57993387 57994000 5.510000e-62 248.0
14 TraesCS3D01G086800 chr5D 85.957 235 28 5 396 629 322176321 322176551 1.980000e-61 246.0
15 TraesCS3D01G086800 chr5B 86.026 229 28 3 401 627 122455473 122455699 2.560000e-60 243.0
16 TraesCS3D01G086800 chr1D 84.454 238 30 6 395 628 111087975 111088209 7.180000e-56 228.0
17 TraesCS3D01G086800 chr1D 81.183 186 24 5 1 183 339382991 339383168 3.460000e-29 139.0
18 TraesCS3D01G086800 chr2A 84.444 225 28 4 406 629 778635311 778635093 5.590000e-52 215.0
19 TraesCS3D01G086800 chr2A 85.366 123 16 2 19 140 527778191 527778312 2.690000e-25 126.0
20 TraesCS3D01G086800 chr2B 81.579 190 34 1 1 189 142976694 142976505 3.440000e-34 156.0
21 TraesCS3D01G086800 chr7B 86.957 138 17 1 1 137 4144349 4144486 1.240000e-33 154.0
22 TraesCS3D01G086800 chr7B 84.247 146 21 1 1828 1973 228015072 228014929 9.620000e-30 141.0
23 TraesCS3D01G086800 chr7D 84.932 146 20 1 1828 1973 251039497 251039354 2.070000e-31 147.0
24 TraesCS3D01G086800 chr7D 84.892 139 21 0 1828 1966 162820320 162820182 9.620000e-30 141.0
25 TraesCS3D01G086800 chr6B 84.106 151 24 0 1828 1978 613531616 613531466 2.070000e-31 147.0
26 TraesCS3D01G086800 chr6A 85.417 144 18 3 1825 1966 543401702 543401844 2.070000e-31 147.0
27 TraesCS3D01G086800 chr6A 83.453 139 23 0 1828 1966 554622458 554622320 2.080000e-26 130.0
28 TraesCS3D01G086800 chr6A 84.615 117 16 2 25 140 407495078 407494963 5.830000e-22 115.0
29 TraesCS3D01G086800 chr7A 75.908 303 59 12 19 320 18550662 18550951 2.680000e-30 143.0
30 TraesCS3D01G086800 chr7A 83.562 146 24 0 1828 1973 163613668 163613523 1.240000e-28 137.0
31 TraesCS3D01G086800 chr4A 85.366 123 16 2 19 140 100956286 100956407 2.690000e-25 126.0
32 TraesCS3D01G086800 chr2D 93.333 60 2 2 339 397 85864947 85864889 1.270000e-13 87.9


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 TraesCS3D01G086800 chr3D 43808498 43811076 2578 False 4763.00 4763 100.0000 1 2579 1 chr3D.!!$F1 2578
1 TraesCS3D01G086800 chr3B 68626657 68627408 751 False 1120.00 1120 93.5100 1825 2579 1 chr3B.!!$F1 754
2 TraesCS3D01G086800 chr3B 68592674 68594186 1512 False 1070.50 1236 92.0425 270 1827 2 chr3B.!!$F2 1557
3 TraesCS3D01G086800 chr3A 55776777 55777512 735 False 1005.00 1005 91.1260 1825 2579 1 chr3A.!!$F1 754
4 TraesCS3D01G086800 chr3A 55742202 55744058 1856 False 553.75 1040 90.7380 1 1823 4 chr3A.!!$F2 1822
5 TraesCS3D01G086800 chr6D 57993387 57994000 613 False 248.00 248 74.5600 20 627 1 chr6D.!!$F1 607

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
845 941 1.206132 CAATGCATGCTGGACCACATT 59.794 47.619 20.33 4.49 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2577 0.818938 TCTGCGCCAATTGATGCAAT 59.181 45.0 20.21 0.0 36.82 3.56 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
36 37 2.202566 GCCTGCCGAGTATTGTAGAAC 58.797 52.381 0.00 0.00 0.00 3.01
77 79 8.585471 ATTTCTTGACATTTAGATGGACACAT 57.415 30.769 0.00 0.00 40.85 3.21
108 110 3.963374 AGAATGTAGCATGTCTGGCTCTA 59.037 43.478 0.00 0.00 42.62 2.43
114 116 6.010219 TGTAGCATGTCTGGCTCTATGTATA 58.990 40.000 0.00 0.00 42.62 1.47
142 145 9.897744 CTGACAAAAATATAATATGACCGCATT 57.102 29.630 0.00 0.00 35.94 3.56
165 168 3.173668 TGAATGTCTATACGTGGTGGC 57.826 47.619 0.00 0.00 0.00 5.01
212 215 4.498520 CTCGACGCCGTGCTCCAT 62.499 66.667 0.00 0.00 37.05 3.41
213 216 4.794439 TCGACGCCGTGCTCCATG 62.794 66.667 0.00 0.00 37.05 3.66
219 222 2.821366 CCGTGCTCCATGTCCTGC 60.821 66.667 0.00 0.00 0.00 4.85
277 280 1.374125 CGTCCTTCATGGTGTCGCA 60.374 57.895 0.00 0.00 37.07 5.10
594 641 2.832129 AGCACGAAACAAGATCTCCCTA 59.168 45.455 0.00 0.00 0.00 3.53
723 773 3.497332 GGAAGCTACCAACTCCCTTTTT 58.503 45.455 0.00 0.00 0.00 1.94
725 775 3.156288 AGCTACCAACTCCCTTTTTCC 57.844 47.619 0.00 0.00 0.00 3.13
728 778 1.704641 ACCAACTCCCTTTTTCCAGC 58.295 50.000 0.00 0.00 0.00 4.85
729 779 1.217942 ACCAACTCCCTTTTTCCAGCT 59.782 47.619 0.00 0.00 0.00 4.24
730 780 2.445525 ACCAACTCCCTTTTTCCAGCTA 59.554 45.455 0.00 0.00 0.00 3.32
821 917 9.694520 CATATATACTTATCACTTTTCATGCGC 57.305 33.333 0.00 0.00 0.00 6.09
822 918 7.728847 ATATACTTATCACTTTTCATGCGCA 57.271 32.000 14.96 14.96 0.00 6.09
823 919 4.970662 ACTTATCACTTTTCATGCGCAT 57.029 36.364 19.28 19.28 0.00 4.73
824 920 7.728847 ATACTTATCACTTTTCATGCGCATA 57.271 32.000 24.84 5.48 0.00 3.14
825 921 5.810525 ACTTATCACTTTTCATGCGCATAC 58.189 37.500 24.84 0.00 0.00 2.39
826 922 5.353956 ACTTATCACTTTTCATGCGCATACA 59.646 36.000 24.84 10.08 0.00 2.29
827 923 4.700268 ATCACTTTTCATGCGCATACAA 57.300 36.364 24.84 15.94 0.00 2.41
828 924 4.700268 TCACTTTTCATGCGCATACAAT 57.300 36.364 24.84 0.00 0.00 2.71
829 925 4.413969 TCACTTTTCATGCGCATACAATG 58.586 39.130 24.84 20.41 0.00 2.82
840 936 2.787601 CATACAATGCATGCTGGACC 57.212 50.000 20.33 0.00 0.00 4.46
841 937 2.025898 CATACAATGCATGCTGGACCA 58.974 47.619 20.33 0.00 0.00 4.02
845 941 1.206132 CAATGCATGCTGGACCACATT 59.794 47.619 20.33 4.49 0.00 2.71
909 1007 7.383843 CCAACGATGTGTATATATACTTGCACA 59.616 37.037 20.80 16.80 40.42 4.57
918 1016 9.673454 TGTATATATACTTGCACACGTAAAGAG 57.327 33.333 20.80 0.00 34.41 2.85
950 1048 4.115516 CACGAAGAGAGAGAGAGAGAGAG 58.884 52.174 0.00 0.00 0.00 3.20
951 1049 4.023980 ACGAAGAGAGAGAGAGAGAGAGA 58.976 47.826 0.00 0.00 0.00 3.10
952 1050 4.098654 ACGAAGAGAGAGAGAGAGAGAGAG 59.901 50.000 0.00 0.00 0.00 3.20
954 1052 5.507149 CGAAGAGAGAGAGAGAGAGAGAGAG 60.507 52.000 0.00 0.00 0.00 3.20
956 1054 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
957 1055 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
958 1056 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
959 1057 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
960 1058 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
961 1059 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
962 1060 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
963 1061 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
964 1062 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
965 1063 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
966 1064 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
967 1065 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
968 1066 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
969 1067 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
970 1068 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
971 1069 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
972 1070 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
973 1071 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
974 1072 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
975 1073 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
976 1074 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
977 1075 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
978 1076 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
979 1077 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
980 1078 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
981 1079 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
982 1080 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
983 1081 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
984 1082 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
985 1083 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
986 1084 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
987 1085 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
988 1086 4.100808 AGAGAGAGAGAGAGAGAGAGAAGC 59.899 50.000 0.00 0.00 0.00 3.86
989 1087 3.776969 AGAGAGAGAGAGAGAGAGAAGCA 59.223 47.826 0.00 0.00 0.00 3.91
990 1088 3.873952 GAGAGAGAGAGAGAGAGAAGCAC 59.126 52.174 0.00 0.00 0.00 4.40
991 1089 2.609459 GAGAGAGAGAGAGAGAAGCACG 59.391 54.545 0.00 0.00 0.00 5.34
1014 1112 6.183360 ACGCACTCTCTATGACTATGTCAAAT 60.183 38.462 4.46 0.00 45.96 2.32
1018 1116 9.553418 CACTCTCTATGACTATGTCAAATATCG 57.447 37.037 4.46 0.00 45.96 2.92
1032 1130 4.585162 TCAAATATCGTTCTCCTCCTCCTC 59.415 45.833 0.00 0.00 0.00 3.71
1033 1131 2.257691 TATCGTTCTCCTCCTCCTCG 57.742 55.000 0.00 0.00 0.00 4.63
1034 1132 0.256464 ATCGTTCTCCTCCTCCTCGT 59.744 55.000 0.00 0.00 0.00 4.18
1110 1211 0.250901 ACATGGAGGCGTCTTTTGCT 60.251 50.000 6.34 0.00 0.00 3.91
1137 1238 0.107643 TGATGTGGTTGTCGAAGCCA 59.892 50.000 0.00 0.00 0.00 4.75
1206 1307 2.022129 CGTGTCGCACAAGGAGGAC 61.022 63.158 9.95 0.00 33.40 3.85
1207 1308 1.668151 GTGTCGCACAAGGAGGACC 60.668 63.158 5.30 0.00 34.08 4.46
1233 1334 1.301401 GTACGTGACCCTTGCTGCA 60.301 57.895 0.00 0.00 0.00 4.41
1251 1352 1.602237 ATGGTTCGCCGTGGAATCT 59.398 52.632 0.00 0.00 41.18 2.40
1436 1537 1.816835 CCTCAGCTACGAGTACAACCA 59.183 52.381 0.00 0.00 0.00 3.67
1497 1598 0.249447 CGCTGACTCAGGTGAACACA 60.249 55.000 8.17 0.00 31.21 3.72
1561 1662 1.136305 TGGCGTACCATCTTGCTACTC 59.864 52.381 0.00 0.00 42.67 2.59
1584 1685 7.446931 ACTCTGATAGGTGTAGTGTGATAGATG 59.553 40.741 0.00 0.00 0.00 2.90
1592 1693 4.956075 TGTAGTGTGATAGATGAAGAGGCA 59.044 41.667 0.00 0.00 0.00 4.75
1616 1717 1.398451 CGTACGCCAAAGAGCAAACAG 60.398 52.381 0.52 0.00 0.00 3.16
1624 1725 5.918011 CGCCAAAGAGCAAACAGTAAAATAA 59.082 36.000 0.00 0.00 0.00 1.40
1634 1735 8.643324 AGCAAACAGTAAAATAAACATTGGGTA 58.357 29.630 0.00 0.00 0.00 3.69
1648 1749 2.148446 TGGGTACACCGCTACATAGT 57.852 50.000 0.00 0.00 44.64 2.12
1689 1791 5.183530 TGTCAGAGTTGGATCCATGATTT 57.816 39.130 17.06 0.00 0.00 2.17
1700 1802 0.819582 CCATGATTTGGTGCCAGGTC 59.180 55.000 0.00 0.00 40.99 3.85
1701 1803 1.617804 CCATGATTTGGTGCCAGGTCT 60.618 52.381 0.00 0.00 40.99 3.85
1718 1820 5.954752 CCAGGTCTGGCTAATCTATCTATCA 59.045 44.000 3.86 0.00 44.73 2.15
1720 1822 7.363705 CCAGGTCTGGCTAATCTATCTATCAAG 60.364 44.444 3.86 0.00 44.73 3.02
1722 1824 7.732593 AGGTCTGGCTAATCTATCTATCAAGTT 59.267 37.037 0.00 0.00 0.00 2.66
1723 1825 9.026121 GGTCTGGCTAATCTATCTATCAAGTTA 57.974 37.037 0.00 0.00 0.00 2.24
1805 2036 0.538746 ACCCGCAAAAATTCTCCCGT 60.539 50.000 0.00 0.00 0.00 5.28
1815 2046 0.466922 ATTCTCCCGTATCCGTCCGT 60.467 55.000 0.00 0.00 0.00 4.69
1846 2077 3.432378 ACGGGTAGTTCTTCAGAGTGAT 58.568 45.455 0.00 0.00 0.00 3.06
1881 2112 2.359900 AGGTTCAATCTTGCGGTGATC 58.640 47.619 0.00 0.00 0.00 2.92
1976 2207 5.241403 TCACACTTGGATTGTAGTTCCAT 57.759 39.130 0.00 0.00 42.69 3.41
1981 2212 7.390440 CACACTTGGATTGTAGTTCCATTAAGA 59.610 37.037 0.00 0.00 42.69 2.10
2030 2261 3.778629 AGGGTGATGTAACGGAGGTAAAT 59.221 43.478 0.00 0.00 0.00 1.40
2061 2292 7.534723 AGGTAACAGATATATAGCAACGGAA 57.465 36.000 0.07 0.00 41.41 4.30
2084 2315 6.482898 AGATGAGAGAGTATGAAAGCATGT 57.517 37.500 0.00 0.00 35.94 3.21
2123 2354 1.312815 GATGAGCCAAGAAATCCCCG 58.687 55.000 0.00 0.00 0.00 5.73
2197 2428 4.368874 TGGAAAATCATGTATTGCACGG 57.631 40.909 0.00 0.00 0.00 4.94
2264 2495 2.949451 AAATTGTTGCACGACACCAA 57.051 40.000 0.00 0.00 34.91 3.67
2362 2593 2.780065 TCTATTGCATCAATTGGCGC 57.220 45.000 5.42 0.00 35.54 6.53
2378 2609 1.891060 GCGCAGAGACCAACTTGTCG 61.891 60.000 0.30 0.00 40.26 4.35
2380 2611 1.140816 GCAGAGACCAACTTGTCGAC 58.859 55.000 9.11 9.11 40.26 4.20
2385 2616 1.480954 AGACCAACTTGTCGACACAGT 59.519 47.619 19.90 20.30 40.26 3.55
2408 2639 8.702438 CAGTCCGAAAGTAAAACGAACTATTTA 58.298 33.333 0.00 0.00 0.00 1.40
2471 2702 7.394016 TCATACTGAGTTTCTATTTGCCTCAA 58.606 34.615 0.00 0.00 32.23 3.02
2472 2703 5.948992 ACTGAGTTTCTATTTGCCTCAAC 57.051 39.130 0.00 0.00 32.23 3.18
2473 2704 4.452455 ACTGAGTTTCTATTTGCCTCAACG 59.548 41.667 0.00 0.00 32.23 4.10
2489 2720 5.446473 GCCTCAACGACAACATGATAGAAAG 60.446 44.000 0.00 0.00 0.00 2.62
2512 2743 1.742761 ATGTGAACGATGGGCTTCTG 58.257 50.000 0.00 0.00 0.00 3.02
2533 2764 4.393834 TGTTGCTTGTGTTCTATTAGGCA 58.606 39.130 0.00 0.00 0.00 4.75
2534 2765 4.824537 TGTTGCTTGTGTTCTATTAGGCAA 59.175 37.500 0.00 0.00 36.34 4.52
2545 2776 7.532884 GTGTTCTATTAGGCAAGTTTTTGTACG 59.467 37.037 0.00 0.00 36.65 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.202566 GTTCTACAATACTCGGCAGGC 58.797 52.381 0.00 0.00 0.00 4.85
67 68 7.318141 ACATTCTCAAATCAAATGTGTCCATC 58.682 34.615 0.00 0.00 40.95 3.51
77 79 7.362315 CCAGACATGCTACATTCTCAAATCAAA 60.362 37.037 0.00 0.00 0.00 2.69
114 116 8.898761 TGCGGTCATATTATATTTTTGTCAGTT 58.101 29.630 0.00 0.00 0.00 3.16
142 145 4.739436 GCCACCACGTATAGACATTCATGA 60.739 45.833 0.00 0.00 0.00 3.07
212 215 1.219124 GCTCGAGAATGGCAGGACA 59.781 57.895 18.75 0.00 0.00 4.02
213 216 0.179062 ATGCTCGAGAATGGCAGGAC 60.179 55.000 18.75 0.00 39.38 3.85
214 217 0.543277 AATGCTCGAGAATGGCAGGA 59.457 50.000 18.75 0.00 39.38 3.86
219 222 0.942962 GGCTCAATGCTCGAGAATGG 59.057 55.000 18.75 9.49 42.39 3.16
254 257 1.671054 CACCATGAAGGACGCCGTT 60.671 57.895 0.00 0.00 41.22 4.44
277 280 0.461339 CTTGCGTAGGGGCGTTGTAT 60.461 55.000 0.00 0.00 35.06 2.29
300 303 4.954933 GGGTGTATGCATCCGTGT 57.045 55.556 0.19 0.00 35.96 4.49
380 384 7.140705 CGGTGCACATATTAAATGACAATCAT 58.859 34.615 20.43 0.00 39.09 2.45
594 641 9.473007 CCCATTAAAAACCAAATCCCATTAAAT 57.527 29.630 0.00 0.00 0.00 1.40
797 893 8.825667 TGCGCATGAAAAGTGATAAGTATATA 57.174 30.769 5.66 0.00 0.00 0.86
798 894 7.728847 TGCGCATGAAAAGTGATAAGTATAT 57.271 32.000 5.66 0.00 0.00 0.86
799 895 7.728847 ATGCGCATGAAAAGTGATAAGTATA 57.271 32.000 24.69 0.00 0.00 1.47
800 896 6.624352 ATGCGCATGAAAAGTGATAAGTAT 57.376 33.333 24.69 0.00 0.00 2.12
801 897 6.536941 TGTATGCGCATGAAAAGTGATAAGTA 59.463 34.615 32.48 3.50 0.00 2.24
802 898 4.970662 ATGCGCATGAAAAGTGATAAGT 57.029 36.364 24.69 0.00 0.00 2.24
803 899 5.809464 TGTATGCGCATGAAAAGTGATAAG 58.191 37.500 32.48 0.00 0.00 1.73
804 900 5.809719 TGTATGCGCATGAAAAGTGATAA 57.190 34.783 32.48 4.95 0.00 1.75
805 901 5.809719 TTGTATGCGCATGAAAAGTGATA 57.190 34.783 32.48 5.53 0.00 2.15
806 902 4.700268 TTGTATGCGCATGAAAAGTGAT 57.300 36.364 32.48 5.52 0.00 3.06
807 903 4.413969 CATTGTATGCGCATGAAAAGTGA 58.586 39.130 32.48 7.18 0.00 3.41
808 904 4.748503 CATTGTATGCGCATGAAAAGTG 57.251 40.909 32.48 18.06 0.00 3.16
821 917 2.025898 TGGTCCAGCATGCATTGTATG 58.974 47.619 21.98 10.06 31.97 2.39
822 918 2.026641 GTGGTCCAGCATGCATTGTAT 58.973 47.619 21.98 0.00 31.97 2.29
823 919 1.271817 TGTGGTCCAGCATGCATTGTA 60.272 47.619 21.98 0.00 31.97 2.41
824 920 0.540133 TGTGGTCCAGCATGCATTGT 60.540 50.000 21.98 0.00 31.97 2.71
825 921 0.821517 ATGTGGTCCAGCATGCATTG 59.178 50.000 21.98 10.38 31.97 2.82
826 922 1.563924 AATGTGGTCCAGCATGCATT 58.436 45.000 21.98 5.09 31.97 3.56
827 923 2.440517 TAATGTGGTCCAGCATGCAT 57.559 45.000 21.98 1.69 31.97 3.96
828 924 2.440517 ATAATGTGGTCCAGCATGCA 57.559 45.000 21.98 0.00 31.97 3.96
829 925 2.689471 TGAATAATGTGGTCCAGCATGC 59.311 45.455 10.51 10.51 31.97 4.06
830 926 5.524971 AATGAATAATGTGGTCCAGCATG 57.475 39.130 0.00 0.00 0.00 4.06
831 927 7.658525 TTTAATGAATAATGTGGTCCAGCAT 57.341 32.000 0.00 0.00 0.00 3.79
832 928 7.341512 TGATTTAATGAATAATGTGGTCCAGCA 59.658 33.333 0.00 0.00 0.00 4.41
833 929 7.715657 TGATTTAATGAATAATGTGGTCCAGC 58.284 34.615 0.00 0.00 0.00 4.85
909 1007 3.568853 CGTGGGGAGATATCTCTTTACGT 59.431 47.826 27.65 0.00 42.48 3.57
918 1016 3.756434 CTCTCTCTTCGTGGGGAGATATC 59.244 52.174 9.57 0.00 37.85 1.63
950 1048 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
951 1049 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
952 1050 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
954 1052 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
956 1054 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
957 1055 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
958 1056 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
959 1057 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
960 1058 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
961 1059 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
962 1060 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
963 1061 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
964 1062 5.738783 GCTTCTCTCTCTCTCTCTCTCTCTC 60.739 52.000 0.00 0.00 0.00 3.20
965 1063 4.100808 GCTTCTCTCTCTCTCTCTCTCTCT 59.899 50.000 0.00 0.00 0.00 3.10
966 1064 4.141846 TGCTTCTCTCTCTCTCTCTCTCTC 60.142 50.000 0.00 0.00 0.00 3.20
967 1065 3.776969 TGCTTCTCTCTCTCTCTCTCTCT 59.223 47.826 0.00 0.00 0.00 3.10
968 1066 3.873952 GTGCTTCTCTCTCTCTCTCTCTC 59.126 52.174 0.00 0.00 0.00 3.20
969 1067 3.679917 CGTGCTTCTCTCTCTCTCTCTCT 60.680 52.174 0.00 0.00 0.00 3.10
970 1068 2.609459 CGTGCTTCTCTCTCTCTCTCTC 59.391 54.545 0.00 0.00 0.00 3.20
971 1069 2.632377 CGTGCTTCTCTCTCTCTCTCT 58.368 52.381 0.00 0.00 0.00 3.10
972 1070 1.064060 GCGTGCTTCTCTCTCTCTCTC 59.936 57.143 0.00 0.00 0.00 3.20
973 1071 1.094785 GCGTGCTTCTCTCTCTCTCT 58.905 55.000 0.00 0.00 0.00 3.10
974 1072 0.808125 TGCGTGCTTCTCTCTCTCTC 59.192 55.000 0.00 0.00 0.00 3.20
975 1073 0.525761 GTGCGTGCTTCTCTCTCTCT 59.474 55.000 0.00 0.00 0.00 3.10
976 1074 0.525761 AGTGCGTGCTTCTCTCTCTC 59.474 55.000 0.00 0.00 0.00 3.20
977 1075 0.525761 GAGTGCGTGCTTCTCTCTCT 59.474 55.000 9.21 0.00 0.00 3.10
978 1076 0.525761 AGAGTGCGTGCTTCTCTCTC 59.474 55.000 11.95 0.00 33.98 3.20
979 1077 0.525761 GAGAGTGCGTGCTTCTCTCT 59.474 55.000 25.13 17.55 45.96 3.10
980 1078 3.028760 GAGAGTGCGTGCTTCTCTC 57.971 57.895 21.50 21.50 44.34 3.20
981 1079 1.827681 TAGAGAGTGCGTGCTTCTCT 58.172 50.000 23.11 23.11 40.62 3.10
982 1080 2.098280 TCATAGAGAGTGCGTGCTTCTC 59.902 50.000 14.80 14.80 0.00 2.87
983 1081 2.095461 TCATAGAGAGTGCGTGCTTCT 58.905 47.619 0.00 0.00 0.00 2.85
984 1082 2.159310 AGTCATAGAGAGTGCGTGCTTC 60.159 50.000 0.00 0.00 0.00 3.86
985 1083 1.821753 AGTCATAGAGAGTGCGTGCTT 59.178 47.619 0.00 0.00 0.00 3.91
986 1084 1.468985 AGTCATAGAGAGTGCGTGCT 58.531 50.000 0.00 0.00 0.00 4.40
987 1085 3.243234 ACATAGTCATAGAGAGTGCGTGC 60.243 47.826 0.00 0.00 0.00 5.34
988 1086 4.035675 TGACATAGTCATAGAGAGTGCGTG 59.964 45.833 0.00 0.00 37.67 5.34
989 1087 4.200092 TGACATAGTCATAGAGAGTGCGT 58.800 43.478 0.00 0.00 37.67 5.24
990 1088 4.820284 TGACATAGTCATAGAGAGTGCG 57.180 45.455 0.00 0.00 37.67 5.34
991 1089 9.352784 GATATTTGACATAGTCATAGAGAGTGC 57.647 37.037 0.12 0.00 42.40 4.40
1014 1112 1.489649 ACGAGGAGGAGGAGAACGATA 59.510 52.381 0.00 0.00 0.00 2.92
1018 1116 0.033894 AGGACGAGGAGGAGGAGAAC 60.034 60.000 0.00 0.00 0.00 3.01
1032 1130 4.760047 CGAAGGGGTGCCAGGACG 62.760 72.222 0.00 0.00 0.00 4.79
1110 1211 2.741517 CGACAACCACATCATGCTACAA 59.258 45.455 0.00 0.00 0.00 2.41
1137 1238 1.670087 CGGACGCAGAGATCTTGTTGT 60.670 52.381 0.00 1.38 0.00 3.32
1206 1307 1.668793 GGTCACGTACCCGGTTTGG 60.669 63.158 0.00 0.00 43.16 3.28
1207 1308 3.955775 GGTCACGTACCCGGTTTG 58.044 61.111 0.00 0.00 43.16 2.93
1233 1334 0.035439 AAGATTCCACGGCGAACCAT 60.035 50.000 16.62 0.00 34.57 3.55
1251 1352 0.787787 CGATCCGCGTGACTTCAAAA 59.212 50.000 4.92 0.00 34.64 2.44
1414 1515 2.415625 GGTTGTACTCGTAGCTGAGGTG 60.416 54.545 0.00 0.00 40.39 4.00
1521 1622 0.819259 GCACTGCTTTGTCCTGGTCA 60.819 55.000 0.00 0.00 0.00 4.02
1561 1662 7.751768 TCATCTATCACACTACACCTATCAG 57.248 40.000 0.00 0.00 0.00 2.90
1584 1685 0.525029 GGCGTACGTACTGCCTCTTC 60.525 60.000 34.17 19.23 40.32 2.87
1592 1693 0.599558 TGCTCTTTGGCGTACGTACT 59.400 50.000 22.55 0.00 34.52 2.73
1616 1717 5.801444 GCGGTGTACCCAATGTTTATTTTAC 59.199 40.000 0.00 0.00 0.00 2.01
1624 1725 1.348366 TGTAGCGGTGTACCCAATGTT 59.652 47.619 0.00 0.00 0.00 2.71
1634 1735 5.350365 CACATGTAAAACTATGTAGCGGTGT 59.650 40.000 0.00 0.00 35.86 4.16
1648 1749 8.614469 TCTGACAATACATCACACATGTAAAA 57.386 30.769 0.00 0.00 37.93 1.52
1718 1820 7.711339 CGAATTTGAGGGAGCTTATAGTAACTT 59.289 37.037 0.00 0.00 0.00 2.66
1720 1822 7.208080 TCGAATTTGAGGGAGCTTATAGTAAC 58.792 38.462 0.00 0.00 0.00 2.50
1722 1824 6.971726 TCGAATTTGAGGGAGCTTATAGTA 57.028 37.500 0.00 0.00 0.00 1.82
1723 1825 5.848406 CTCGAATTTGAGGGAGCTTATAGT 58.152 41.667 14.18 0.00 32.18 2.12
1750 1981 4.122776 CCCTAACACTATGACACATCAGC 58.877 47.826 0.00 0.00 38.57 4.26
1815 2046 2.038329 CTACCCGTCCCCTGTCCA 59.962 66.667 0.00 0.00 0.00 4.02
1846 2077 6.952358 AGATTGAACCTACTACTCTACACCAA 59.048 38.462 0.00 0.00 0.00 3.67
1881 2112 4.226427 TCCCTTTCTGTCATTGAGATGG 57.774 45.455 0.00 0.00 33.93 3.51
1981 2212 8.739972 AGGTTGTTTTATCGCAAAGAATTCTAT 58.260 29.630 8.75 0.46 0.00 1.98
2050 2281 3.957497 ACTCTCTCATCTTCCGTTGCTAT 59.043 43.478 0.00 0.00 0.00 2.97
2061 2292 6.482898 ACATGCTTTCATACTCTCTCATCT 57.517 37.500 0.00 0.00 0.00 2.90
2084 2315 7.066307 TCATCATGCTATTGCTCTAGGTTTA 57.934 36.000 0.00 0.00 40.48 2.01
2177 2408 3.115554 GCCGTGCAATACATGATTTTCC 58.884 45.455 0.00 0.00 37.49 3.13
2197 2428 8.780249 ACGTATTCCATTTTTATAGTATGGTGC 58.220 33.333 0.00 0.00 39.81 5.01
2346 2577 0.818938 TCTGCGCCAATTGATGCAAT 59.181 45.000 20.21 0.00 36.82 3.56
2362 2593 2.128035 GTGTCGACAAGTTGGTCTCTG 58.872 52.381 21.95 0.00 35.63 3.35
2378 2609 3.798337 TCGTTTTACTTTCGGACTGTGTC 59.202 43.478 0.00 0.00 0.00 3.67
2380 2611 4.269363 AGTTCGTTTTACTTTCGGACTGTG 59.731 41.667 0.00 0.00 41.08 3.66
2471 2702 3.937814 TGCCTTTCTATCATGTTGTCGT 58.062 40.909 0.00 0.00 0.00 4.34
2472 2703 4.944962 TTGCCTTTCTATCATGTTGTCG 57.055 40.909 0.00 0.00 0.00 4.35
2473 2704 6.032094 CACATTGCCTTTCTATCATGTTGTC 58.968 40.000 0.00 0.00 0.00 3.18
2489 2720 1.139520 GCCCATCGTTCACATTGCC 59.860 57.895 0.00 0.00 0.00 4.52
2512 2743 5.048713 ACTTGCCTAATAGAACACAAGCAAC 60.049 40.000 0.00 0.00 38.41 4.17
2533 2764 4.879545 AGTCATGACACCGTACAAAAACTT 59.120 37.500 27.02 0.00 0.00 2.66
2534 2765 4.448210 AGTCATGACACCGTACAAAAACT 58.552 39.130 27.02 0.00 0.00 2.66
2545 2776 1.078759 CGGCGAGAAGTCATGACACC 61.079 60.000 27.02 17.26 0.00 4.16


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

AutoCloner maintained by Alex Coulton.