Multiple sequence alignment - TraesCS1B01G438200

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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 TraesCS1B01G438200 chr1B 100.000 3461 0 0 1 3461 660641377 660637917 0.000000e+00 6392
1 TraesCS1B01G438200 chr1B 87.646 1546 169 15 966 2498 660996739 660995203 0.000000e+00 1777
2 TraesCS1B01G438200 chr1B 86.034 1475 179 19 987 2446 660745864 660744402 0.000000e+00 1557
3 TraesCS1B01G438200 chr1B 91.017 1091 91 6 966 2051 661054678 661053590 0.000000e+00 1465
4 TraesCS1B01G438200 chr1B 84.023 1546 194 28 987 2498 660722727 660721201 0.000000e+00 1437
5 TraesCS1B01G438200 chr1B 88.089 1083 119 5 966 2045 660914432 660913357 0.000000e+00 1277
6 TraesCS1B01G438200 chr1B 87.338 1082 123 6 971 2045 660949908 660948834 0.000000e+00 1227
7 TraesCS1B01G438200 chr1B 86.937 1087 119 5 966 2051 661122004 661120940 0.000000e+00 1199
8 TraesCS1B01G438200 chr1B 86.661 1087 119 6 966 2051 660880262 660879201 0.000000e+00 1181
9 TraesCS1B01G438200 chr1B 85.316 1076 137 11 979 2045 660529683 660528620 0.000000e+00 1092
10 TraesCS1B01G438200 chr1B 89.809 628 40 10 2525 3139 660995103 660994487 0.000000e+00 784
11 TraesCS1B01G438200 chr1B 96.335 382 10 1 3060 3441 660701911 660701534 2.930000e-175 625
12 TraesCS1B01G438200 chr1B 92.457 411 25 3 2525 2932 660721105 660720698 1.790000e-162 582
13 TraesCS1B01G438200 chr1B 94.872 312 10 2 3135 3441 660971465 660971155 1.870000e-132 483
14 TraesCS1B01G438200 chr1B 90.749 227 15 3 3215 3441 660912013 660911793 7.260000e-77 298
15 TraesCS1B01G438200 chr1B 89.908 218 20 1 3215 3432 660795741 660795526 2.630000e-71 279
16 TraesCS1B01G438200 chr1B 80.120 332 62 4 2119 2448 660879166 660878837 9.600000e-61 244
17 TraesCS1B01G438200 chr1B 87.558 217 19 7 3222 3438 661051608 661051400 9.600000e-61 244
18 TraesCS1B01G438200 chr1D 86.976 1528 169 19 966 2473 475195595 475194078 0.000000e+00 1692
19 TraesCS1B01G438200 chr1D 92.872 477 28 4 2525 2999 475193968 475193496 0.000000e+00 688
20 TraesCS1B01G438200 chr1A 97.538 975 21 3 1 974 111595394 111594422 0.000000e+00 1664
21 TraesCS1B01G438200 chr1A 97.723 966 20 2 1 965 589664879 589665843 0.000000e+00 1661
22 TraesCS1B01G438200 chr1A 97.317 969 25 1 1 969 59604708 59605675 0.000000e+00 1644
23 TraesCS1B01G438200 chr1A 87.442 430 45 4 971 1400 570878013 570877593 1.440000e-133 486
24 TraesCS1B01G438200 chr2B 97.725 967 21 1 1 966 115228 114262 0.000000e+00 1663
25 TraesCS1B01G438200 chr2B 96.998 966 29 0 1 966 185877056 185876091 0.000000e+00 1624
26 TraesCS1B01G438200 chr6B 97.208 967 24 2 1 966 275776333 275777297 0.000000e+00 1633
27 TraesCS1B01G438200 chr5B 97.010 970 27 2 1 969 695708158 695707190 0.000000e+00 1629
28 TraesCS1B01G438200 chr7B 97.101 966 26 2 1 966 705354491 705353528 0.000000e+00 1628
29 TraesCS1B01G438200 chr4B 97.164 952 26 1 16 966 667849987 667849036 0.000000e+00 1607


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 TraesCS1B01G438200 chr1B 660637917 660641377 3460 True 6392.0 6392 100.0000 1 3461 1 chr1B.!!$R2 3460
1 TraesCS1B01G438200 chr1B 660744402 660745864 1462 True 1557.0 1557 86.0340 987 2446 1 chr1B.!!$R4 1459
2 TraesCS1B01G438200 chr1B 660994487 660996739 2252 True 1280.5 1777 88.7275 966 3139 2 chr1B.!!$R12 2173
3 TraesCS1B01G438200 chr1B 660948834 660949908 1074 True 1227.0 1227 87.3380 971 2045 1 chr1B.!!$R6 1074
4 TraesCS1B01G438200 chr1B 661120940 661122004 1064 True 1199.0 1199 86.9370 966 2051 1 chr1B.!!$R8 1085
5 TraesCS1B01G438200 chr1B 660528620 660529683 1063 True 1092.0 1092 85.3160 979 2045 1 chr1B.!!$R1 1066
6 TraesCS1B01G438200 chr1B 660720698 660722727 2029 True 1009.5 1437 88.2400 987 2932 2 chr1B.!!$R9 1945
7 TraesCS1B01G438200 chr1B 661051400 661054678 3278 True 854.5 1465 89.2875 966 3438 2 chr1B.!!$R13 2472
8 TraesCS1B01G438200 chr1B 660911793 660914432 2639 True 787.5 1277 89.4190 966 3441 2 chr1B.!!$R11 2475
9 TraesCS1B01G438200 chr1B 660878837 660880262 1425 True 712.5 1181 83.3905 966 2448 2 chr1B.!!$R10 1482
10 TraesCS1B01G438200 chr1D 475193496 475195595 2099 True 1190.0 1692 89.9240 966 2999 2 chr1D.!!$R1 2033
11 TraesCS1B01G438200 chr1A 111594422 111595394 972 True 1664.0 1664 97.5380 1 974 1 chr1A.!!$R1 973
12 TraesCS1B01G438200 chr1A 589664879 589665843 964 False 1661.0 1661 97.7230 1 965 1 chr1A.!!$F2 964
13 TraesCS1B01G438200 chr1A 59604708 59605675 967 False 1644.0 1644 97.3170 1 969 1 chr1A.!!$F1 968
14 TraesCS1B01G438200 chr2B 114262 115228 966 True 1663.0 1663 97.7250 1 966 1 chr2B.!!$R1 965
15 TraesCS1B01G438200 chr2B 185876091 185877056 965 True 1624.0 1624 96.9980 1 966 1 chr2B.!!$R2 965
16 TraesCS1B01G438200 chr6B 275776333 275777297 964 False 1633.0 1633 97.2080 1 966 1 chr6B.!!$F1 965
17 TraesCS1B01G438200 chr5B 695707190 695708158 968 True 1629.0 1629 97.0100 1 969 1 chr5B.!!$R1 968
18 TraesCS1B01G438200 chr7B 705353528 705354491 963 True 1628.0 1628 97.1010 1 966 1 chr7B.!!$R1 965
19 TraesCS1B01G438200 chr4B 667849036 667849987 951 True 1607.0 1607 97.1640 16 966 1 chr4B.!!$R1 950

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
79 80 0.181114 TGGGAAGAATGGCTCCATCG 59.819 55.0 1.31 0.0 35.31 3.84 F
1610 1631 0.307760 CGGAAATTGGTGCGCCTATC 59.692 55.0 18.96 9.9 35.27 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2112 0.038166 CAAAAGGAGTGGCTGGCCTA 59.962 55.0 13.05 0.0 36.94 3.93 R
3381 4602 0.037447 AGAGAACTTGCTTCCCAGCC 59.963 55.0 0.00 0.0 46.74 4.85 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
79 80 0.181114 TGGGAAGAATGGCTCCATCG 59.819 55.000 1.31 0.00 35.31 3.84
88 89 1.860641 TGGCTCCATCGAGTTAGGAA 58.139 50.000 0.00 0.00 38.49 3.36
119 120 3.152341 CATCCAGCTTTCTCAACAACCT 58.848 45.455 0.00 0.00 0.00 3.50
659 660 4.316823 ACCCAGACGGAGGCCAGA 62.317 66.667 5.01 0.00 34.64 3.86
742 743 4.365514 TTGGATGGCGGTCATGTAATAT 57.634 40.909 0.00 0.00 35.97 1.28
993 996 8.908786 AGATCAAGTGTAAAGAACTGAAATGA 57.091 30.769 0.00 0.00 0.00 2.57
1023 1026 3.137176 TGGCTGAAGGATTCCTTGATAGG 59.863 47.826 22.64 4.12 46.93 2.57
1211 1221 2.058057 CACTGTTTTAAATGGGCGTGC 58.942 47.619 0.00 0.00 0.00 5.34
1214 1224 3.508012 ACTGTTTTAAATGGGCGTGCATA 59.492 39.130 0.00 0.00 0.00 3.14
1455 1468 5.537300 AACATATAGGAAGCTCACGTCAT 57.463 39.130 0.00 0.00 0.00 3.06
1610 1631 0.307760 CGGAAATTGGTGCGCCTATC 59.692 55.000 18.96 9.90 35.27 2.08
1681 1714 1.550976 CCTTGGAGGAGTTACGCTTCT 59.449 52.381 0.00 0.00 37.67 2.85
1747 1780 1.737735 GGCAAATGCAACCTTCGCC 60.738 57.895 7.80 0.00 44.36 5.54
1757 1790 2.550978 CAACCTTCGCCATCTTCGTAT 58.449 47.619 0.00 0.00 0.00 3.06
1758 1791 2.936498 CAACCTTCGCCATCTTCGTATT 59.064 45.455 0.00 0.00 0.00 1.89
1759 1792 2.550978 ACCTTCGCCATCTTCGTATTG 58.449 47.619 0.00 0.00 0.00 1.90
1760 1793 1.867233 CCTTCGCCATCTTCGTATTGG 59.133 52.381 0.00 0.00 0.00 3.16
1796 1838 2.829720 AGCGTCTGTTCTGTAACCCATA 59.170 45.455 0.00 0.00 34.49 2.74
1798 1840 3.615592 GCGTCTGTTCTGTAACCCATACA 60.616 47.826 0.00 0.00 42.22 2.29
1832 1874 6.127730 CCGTGCCTCCAAGTTCTTAAAATTAT 60.128 38.462 0.00 0.00 0.00 1.28
1837 1879 8.303876 GCCTCCAAGTTCTTAAAATTATGTCAA 58.696 33.333 0.00 0.00 0.00 3.18
1969 2026 2.634940 TCTATGGCCCATCTTCAGCTAC 59.365 50.000 0.00 0.00 0.00 3.58
1970 2027 1.516110 ATGGCCCATCTTCAGCTACT 58.484 50.000 0.00 0.00 0.00 2.57
2045 2105 2.441750 TGCTAAAGGTGTTCCACTTCCT 59.558 45.455 0.00 0.00 34.40 3.36
2051 2111 8.208903 GCTAAAGGTGTTCCACTTCCTATATAA 58.791 37.037 0.00 0.00 34.40 0.98
2062 2125 5.189736 CACTTCCTATATAATAGGCCAGCCA 59.810 44.000 12.03 0.00 38.92 4.75
2077 2140 3.761752 GCCAGCCACTCCTTTTGTATTTA 59.238 43.478 0.00 0.00 0.00 1.40
2082 2145 7.378181 CAGCCACTCCTTTTGTATTTAAACAT 58.622 34.615 0.00 0.00 0.00 2.71
2115 2178 1.806542 GGACTGCGCATCTCAGAAAAA 59.193 47.619 12.24 0.00 35.61 1.94
2175 2241 2.030562 CCAGCACTCCGACGGTTT 59.969 61.111 14.79 0.00 0.00 3.27
2217 2283 6.350361 CCATGATTGTGGCATCAGACTTTTTA 60.350 38.462 0.00 0.00 31.43 1.52
2221 2287 6.554334 TTGTGGCATCAGACTTTTTAGTAC 57.446 37.500 0.00 0.00 0.00 2.73
2248 2314 0.674581 TGTGGAGCATCTTTCAGGCG 60.675 55.000 0.00 0.00 33.73 5.52
2288 2354 5.700832 TCAAAATCGATTGTTACAGAGCAGT 59.299 36.000 12.25 0.00 0.00 4.40
2360 2426 1.616159 CACCCCAACCGTGAAATCTT 58.384 50.000 0.00 0.00 32.77 2.40
2410 2476 5.947663 TGTTTAAGGATGAAAAGGAGTGGA 58.052 37.500 0.00 0.00 0.00 4.02
2418 2484 2.443255 TGAAAAGGAGTGGAAAGAGGCT 59.557 45.455 0.00 0.00 0.00 4.58
2448 2514 7.012607 TGAAGGAAAGAAAGGAGATGGAAAAT 58.987 34.615 0.00 0.00 0.00 1.82
2449 2515 7.510343 TGAAGGAAAGAAAGGAGATGGAAAATT 59.490 33.333 0.00 0.00 0.00 1.82
2453 2519 8.777413 GGAAAGAAAGGAGATGGAAAATTTTTG 58.223 33.333 4.63 0.00 0.00 2.44
2458 2524 7.855784 AAGGAGATGGAAAATTTTTGTAGGT 57.144 32.000 4.63 0.00 0.00 3.08
2500 2602 0.106149 ACGAAGAAACGGAACTGGCT 59.894 50.000 0.00 0.00 37.61 4.75
2625 2771 3.624861 GTGCTGACCCTGTATTCATCTTG 59.375 47.826 0.00 0.00 0.00 3.02
2687 2833 0.393537 CAGCTGTCCAATCCAGTCCC 60.394 60.000 5.25 0.00 32.41 4.46
2719 2866 3.996150 CAAGTCTGCAATTCAACTGGT 57.004 42.857 0.00 0.00 0.00 4.00
2759 2906 2.501261 TGATCTGCAGCCATATTCAGC 58.499 47.619 9.47 0.00 0.00 4.26
2762 2909 2.049372 TCTGCAGCCATATTCAGCCTA 58.951 47.619 9.47 0.00 0.00 3.93
2775 2922 7.147828 CCATATTCAGCCTATATTCCGAGAGAA 60.148 40.741 0.00 0.00 39.32 2.87
2836 2992 6.840527 TCAGATGAATTCATGGTGCCTTATA 58.159 36.000 25.37 3.47 36.57 0.98
2843 2999 4.972751 TCATGGTGCCTTATATGCAGTA 57.027 40.909 0.00 0.00 39.87 2.74
2847 3005 4.898320 TGGTGCCTTATATGCAGTATGAG 58.102 43.478 0.00 0.00 39.69 2.90
2850 3012 6.440328 TGGTGCCTTATATGCAGTATGAGATA 59.560 38.462 0.00 0.00 39.69 1.98
2885 3049 1.344953 ATGTTCGCCAGCCTCCCATA 61.345 55.000 0.00 0.00 0.00 2.74
2888 3052 0.550914 TTCGCCAGCCTCCCATATTT 59.449 50.000 0.00 0.00 0.00 1.40
2932 3096 2.668617 CAGTATGTGTGTGTGTGTGC 57.331 50.000 0.00 0.00 0.00 4.57
2935 3131 3.003585 CAGTATGTGTGTGTGTGTGCAAT 59.996 43.478 0.00 0.00 0.00 3.56
2952 3148 7.013559 TGTGTGCAATATCCCTGAATTCTATTG 59.986 37.037 15.17 15.17 34.45 1.90
3012 3208 4.835199 ATGATTTAAACGAACCGAGTCG 57.165 40.909 5.29 5.29 46.54 4.18
3141 3492 1.864565 ACGCGTGCATGCATTATCTA 58.135 45.000 29.23 0.00 34.15 1.98
3143 3494 1.127397 CGCGTGCATGCATTATCTAGG 59.873 52.381 29.23 5.44 34.15 3.02
3144 3495 1.135859 GCGTGCATGCATTATCTAGGC 60.136 52.381 25.64 12.12 34.15 3.93
3145 3496 2.420642 CGTGCATGCATTATCTAGGCT 58.579 47.619 25.64 0.00 0.00 4.58
3146 3497 3.588955 CGTGCATGCATTATCTAGGCTA 58.411 45.455 25.64 0.00 0.00 3.93
3148 3499 5.351458 CGTGCATGCATTATCTAGGCTATA 58.649 41.667 25.64 0.00 0.00 1.31
3149 3500 5.987953 CGTGCATGCATTATCTAGGCTATAT 59.012 40.000 25.64 0.00 0.00 0.86
3150 3501 6.481313 CGTGCATGCATTATCTAGGCTATATT 59.519 38.462 25.64 0.00 0.00 1.28
3151 3502 7.011763 CGTGCATGCATTATCTAGGCTATATTT 59.988 37.037 25.64 0.00 0.00 1.40
3152 3503 9.330063 GTGCATGCATTATCTAGGCTATATTTA 57.670 33.333 25.64 0.00 0.00 1.40
3202 3553 7.953158 TTGATAAGAGTTCTGACTGAGTTTG 57.047 36.000 0.00 0.00 35.88 2.93
3203 3554 6.459066 TGATAAGAGTTCTGACTGAGTTTGG 58.541 40.000 0.00 0.00 35.88 3.28
3204 3555 4.762289 AAGAGTTCTGACTGAGTTTGGT 57.238 40.909 0.00 0.00 35.88 3.67
3205 3556 4.329462 AGAGTTCTGACTGAGTTTGGTC 57.671 45.455 0.00 0.00 35.88 4.02
3206 3557 3.706594 AGAGTTCTGACTGAGTTTGGTCA 59.293 43.478 0.00 0.00 39.71 4.02
3208 3559 4.384056 AGTTCTGACTGAGTTTGGTCATG 58.616 43.478 0.00 0.00 40.90 3.07
3209 3560 4.130118 GTTCTGACTGAGTTTGGTCATGT 58.870 43.478 0.00 0.00 40.90 3.21
3210 3561 5.070446 AGTTCTGACTGAGTTTGGTCATGTA 59.930 40.000 0.00 0.00 40.90 2.29
3211 3562 5.745312 TCTGACTGAGTTTGGTCATGTAT 57.255 39.130 0.00 0.00 40.90 2.29
3212 3563 5.482006 TCTGACTGAGTTTGGTCATGTATG 58.518 41.667 0.00 0.00 40.90 2.39
3227 4448 1.149854 TATGCATCAGGCCCTGCTG 59.850 57.895 19.70 10.26 43.89 4.41
3242 4463 3.568538 CCTGCTGTTGCTTGTTTCATAC 58.431 45.455 0.00 0.00 40.48 2.39
3304 4525 0.033504 AGTCCGAAACTGCACACGAT 59.966 50.000 0.00 0.00 36.65 3.73
3338 4559 7.177216 TCTCAACTGAATTTTATGGAACTGCAT 59.823 33.333 0.00 0.00 0.00 3.96
3339 4560 7.092079 TCAACTGAATTTTATGGAACTGCATG 58.908 34.615 0.00 0.00 0.00 4.06
3340 4561 6.839124 ACTGAATTTTATGGAACTGCATGA 57.161 33.333 0.00 0.00 0.00 3.07
3346 4567 2.414994 ATGGAACTGCATGAGTCTGG 57.585 50.000 0.00 0.00 31.73 3.86
3359 4580 3.653344 TGAGTCTGGAGTGAAAACATCG 58.347 45.455 0.00 0.00 0.00 3.84
3381 4602 2.360553 ACGAGACACATGAGCTTCTG 57.639 50.000 0.00 0.00 0.00 3.02
3394 4615 2.564471 CTTCTGGCTGGGAAGCAAG 58.436 57.895 0.00 0.00 37.20 4.01
3400 4621 0.037447 GGCTGGGAAGCAAGTTCTCT 59.963 55.000 0.00 0.00 36.48 3.10
3433 4654 2.353011 GGTTGTTGGCATGTGGATTCAG 60.353 50.000 0.00 0.00 0.00 3.02
3435 4656 0.174162 GTTGGCATGTGGATTCAGCC 59.826 55.000 0.00 0.00 45.41 4.85
3436 4657 4.342427 GGCATGTGGATTCAGCCA 57.658 55.556 0.00 0.00 44.59 4.75
3438 4659 1.117150 GGCATGTGGATTCAGCCATT 58.883 50.000 0.00 0.00 44.59 3.16
3440 4661 1.202486 GCATGTGGATTCAGCCATTGG 60.202 52.381 0.00 0.00 40.68 3.16
3441 4662 2.380941 CATGTGGATTCAGCCATTGGA 58.619 47.619 6.95 0.00 40.68 3.53
3442 4663 1.838112 TGTGGATTCAGCCATTGGAC 58.162 50.000 6.95 0.00 40.68 4.02
3443 4664 1.075212 TGTGGATTCAGCCATTGGACA 59.925 47.619 6.95 0.00 40.68 4.02
3444 4665 2.291735 TGTGGATTCAGCCATTGGACAT 60.292 45.455 6.95 0.00 40.68 3.06
3445 4666 3.053768 TGTGGATTCAGCCATTGGACATA 60.054 43.478 6.95 0.00 40.68 2.29
3446 4667 3.567164 GTGGATTCAGCCATTGGACATAG 59.433 47.826 6.95 0.00 40.68 2.23
3447 4668 2.555757 GGATTCAGCCATTGGACATAGC 59.444 50.000 6.95 0.00 0.00 2.97
3448 4669 2.804986 TTCAGCCATTGGACATAGCA 57.195 45.000 6.95 0.00 0.00 3.49
3449 4670 2.042686 TCAGCCATTGGACATAGCAC 57.957 50.000 6.95 0.00 0.00 4.40
3450 4671 1.281577 TCAGCCATTGGACATAGCACA 59.718 47.619 6.95 0.00 0.00 4.57
3451 4672 2.092267 TCAGCCATTGGACATAGCACAT 60.092 45.455 6.95 0.00 0.00 3.21
3452 4673 2.292569 CAGCCATTGGACATAGCACATC 59.707 50.000 6.95 0.00 0.00 3.06
3453 4674 2.092267 AGCCATTGGACATAGCACATCA 60.092 45.455 6.95 0.00 0.00 3.07
3454 4675 2.889045 GCCATTGGACATAGCACATCAT 59.111 45.455 6.95 0.00 0.00 2.45
3455 4676 3.305131 GCCATTGGACATAGCACATCATG 60.305 47.826 6.95 0.00 0.00 3.07
3456 4677 3.887110 CCATTGGACATAGCACATCATGT 59.113 43.478 0.00 0.00 38.08 3.21
3457 4678 5.065235 CCATTGGACATAGCACATCATGTA 58.935 41.667 0.00 0.00 35.55 2.29
3458 4679 5.180680 CCATTGGACATAGCACATCATGTAG 59.819 44.000 0.00 0.00 35.55 2.74
3459 4680 5.612725 TTGGACATAGCACATCATGTAGA 57.387 39.130 0.00 0.00 35.55 2.59
3460 4681 4.948847 TGGACATAGCACATCATGTAGAC 58.051 43.478 0.00 0.00 35.55 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.119694 GGATGTCCATCAGTTTCCTAACTC 58.880 45.833 9.34 0.00 38.02 3.01
88 89 3.009916 AGAAAGCTGGATGTCCATCAGTT 59.990 43.478 9.34 0.00 46.46 3.16
119 120 1.825090 ACTTCCAGCGCAATTCATCA 58.175 45.000 11.47 0.00 0.00 3.07
659 660 2.644798 AGACCCAGTAACCAAATGCTCT 59.355 45.455 0.00 0.00 0.00 4.09
742 743 9.256228 CTAGGTAGGAATACTAAATGCCTATCA 57.744 37.037 5.32 0.00 35.30 2.15
819 820 0.108898 CTCACACAGAGCCCGAAGAG 60.109 60.000 0.00 0.00 37.59 2.85
993 996 3.708121 GGAATCCTTCAGCCATCCATTTT 59.292 43.478 0.00 0.00 0.00 1.82
1023 1026 0.173255 CATCCAAACGTCCCCATTGC 59.827 55.000 0.00 0.00 0.00 3.56
1084 1094 8.344446 TCATAAATATCAATTGGCTGGATCAG 57.656 34.615 5.42 0.00 34.12 2.90
1214 1224 7.382218 GTCGAATCTTGTTTGGAAATGAATTGT 59.618 33.333 0.00 0.00 0.00 2.71
1455 1468 5.178096 TGCCAATTCTCAAATACCTCAGA 57.822 39.130 0.00 0.00 0.00 3.27
1610 1631 2.495409 TTGTGTTGCATTGCTGACAG 57.505 45.000 15.46 0.00 0.00 3.51
1681 1714 0.834612 ACTGGGTCGTCAGTTTTCCA 59.165 50.000 3.72 0.00 44.74 3.53
1747 1780 4.655762 TCTCTCCACCAATACGAAGATG 57.344 45.455 0.00 0.00 0.00 2.90
1757 1790 1.403814 CTCGGCTATCTCTCCACCAA 58.596 55.000 0.00 0.00 0.00 3.67
1758 1791 1.109920 GCTCGGCTATCTCTCCACCA 61.110 60.000 0.00 0.00 0.00 4.17
1759 1792 1.663173 GCTCGGCTATCTCTCCACC 59.337 63.158 0.00 0.00 0.00 4.61
1760 1793 1.284408 CGCTCGGCTATCTCTCCAC 59.716 63.158 0.00 0.00 0.00 4.02
1969 2026 7.827819 TTTCTTTGATGTCCTGTATAACGAG 57.172 36.000 0.00 0.00 0.00 4.18
1970 2027 7.148474 GCTTTTCTTTGATGTCCTGTATAACGA 60.148 37.037 0.00 0.00 0.00 3.85
2045 2105 4.960332 AGGAGTGGCTGGCCTATTATATA 58.040 43.478 13.05 0.00 36.94 0.86
2051 2111 1.002857 AAAAGGAGTGGCTGGCCTAT 58.997 50.000 13.05 1.13 36.94 2.57
2052 2112 0.038166 CAAAAGGAGTGGCTGGCCTA 59.962 55.000 13.05 0.00 36.94 3.93
2053 2113 1.228675 CAAAAGGAGTGGCTGGCCT 60.229 57.895 13.05 0.00 36.94 5.19
2054 2114 0.251165 TACAAAAGGAGTGGCTGGCC 60.251 55.000 4.43 4.43 0.00 5.36
2062 2125 9.073475 TGCTGTATGTTTAAATACAAAAGGAGT 57.927 29.630 3.85 0.00 41.33 3.85
2077 2140 0.881118 CCACCGCTTGCTGTATGTTT 59.119 50.000 0.00 0.00 0.00 2.83
2082 2145 1.005037 CAGTCCACCGCTTGCTGTA 60.005 57.895 0.00 0.00 0.00 2.74
2115 2178 3.418684 AGCCGTAGTCCATCTGTTTTT 57.581 42.857 0.00 0.00 0.00 1.94
2130 2196 1.453155 CTGGAGCAAATGTTAGCCGT 58.547 50.000 0.00 0.00 0.00 5.68
2173 2239 3.702792 TGGGGTTCAAGTCAAGACAAAA 58.297 40.909 2.72 0.00 0.00 2.44
2175 2241 3.117701 TCATGGGGTTCAAGTCAAGACAA 60.118 43.478 2.72 0.00 0.00 3.18
2232 2298 0.449388 CAACGCCTGAAAGATGCTCC 59.551 55.000 0.00 0.00 34.07 4.70
2248 2314 0.880278 TTGACCTCGAGCTGTGCAAC 60.880 55.000 6.99 0.00 37.35 4.17
2360 2426 3.566351 TCTTCAGAGACTCTGTGGACAA 58.434 45.455 27.62 15.51 44.58 3.18
2385 2451 7.695055 TCCACTCCTTTTCATCCTTAAACATA 58.305 34.615 0.00 0.00 0.00 2.29
2410 2476 3.864789 TTCCTTCAAGACAGCCTCTTT 57.135 42.857 0.00 0.00 37.08 2.52
2418 2484 5.630415 TCTCCTTTCTTTCCTTCAAGACA 57.370 39.130 0.00 0.00 32.28 3.41
2449 2515 9.323985 CCTTTCATCAAAAATTCACCTACAAAA 57.676 29.630 0.00 0.00 0.00 2.44
2453 2519 6.691508 AGCCTTTCATCAAAAATTCACCTAC 58.308 36.000 0.00 0.00 0.00 3.18
2458 2524 4.236935 GCGAGCCTTTCATCAAAAATTCA 58.763 39.130 0.00 0.00 0.00 2.57
2464 2530 0.516877 CGTGCGAGCCTTTCATCAAA 59.483 50.000 0.00 0.00 0.00 2.69
2471 2537 0.586802 GTTTCTTCGTGCGAGCCTTT 59.413 50.000 0.00 0.00 0.00 3.11
2500 2602 7.328404 TCATATGAATTACCAGGATAAGGCA 57.672 36.000 1.98 0.00 0.00 4.75
2581 2727 4.811024 ACTCAGCACAATGTATATGGAACG 59.189 41.667 0.00 0.00 0.00 3.95
2582 2728 5.504665 GCACTCAGCACAATGTATATGGAAC 60.505 44.000 0.00 0.00 44.79 3.62
2583 2729 4.576053 GCACTCAGCACAATGTATATGGAA 59.424 41.667 0.00 0.00 44.79 3.53
2625 2771 3.141002 TCCACGTACGAACTGCTATTC 57.859 47.619 24.41 0.00 0.00 1.75
2628 2774 1.402968 GGATCCACGTACGAACTGCTA 59.597 52.381 24.41 1.35 0.00 3.49
2759 2906 4.991687 GGCTTGTTTCTCTCGGAATATAGG 59.008 45.833 0.00 0.00 33.53 2.57
2762 2909 4.446371 CTGGCTTGTTTCTCTCGGAATAT 58.554 43.478 0.00 0.00 33.53 1.28
2775 2922 1.986882 CTTCTGGAACCTGGCTTGTT 58.013 50.000 0.00 0.00 0.00 2.83
2850 3012 8.062065 TGGCGAACATATTTAGGAAAGAAAAT 57.938 30.769 0.00 0.00 0.00 1.82
2866 3028 1.344953 TATGGGAGGCTGGCGAACAT 61.345 55.000 0.00 10.94 0.00 2.71
2885 3049 8.232913 TGTTCTACTGAAGCAAACCTAAAAAT 57.767 30.769 0.00 0.00 32.15 1.82
2888 3052 7.934665 TGTATGTTCTACTGAAGCAAACCTAAA 59.065 33.333 0.00 0.00 32.15 1.85
2935 3131 7.310921 GCCAGAGATCAATAGAATTCAGGGATA 60.311 40.741 8.44 0.00 0.00 2.59
2952 3148 0.182061 TTCTGCCATGGCCAGAGATC 59.818 55.000 33.44 4.41 41.09 2.75
2959 3155 3.915575 CAGAGTTCTGCCATGGCC 58.084 61.111 33.44 18.09 41.09 5.36
3012 3208 6.428159 ACAAATATTTCCCAGATACATCGCTC 59.572 38.462 0.00 0.00 0.00 5.03
3176 3527 9.645059 CAAACTCAGTCAGAACTCTTATCAATA 57.355 33.333 0.00 0.00 31.71 1.90
3177 3528 7.605691 CCAAACTCAGTCAGAACTCTTATCAAT 59.394 37.037 0.00 0.00 31.71 2.57
3178 3529 6.931281 CCAAACTCAGTCAGAACTCTTATCAA 59.069 38.462 0.00 0.00 31.71 2.57
3179 3530 6.042093 ACCAAACTCAGTCAGAACTCTTATCA 59.958 38.462 0.00 0.00 31.71 2.15
3180 3531 6.459923 ACCAAACTCAGTCAGAACTCTTATC 58.540 40.000 0.00 0.00 31.71 1.75
3182 3533 5.362717 TGACCAAACTCAGTCAGAACTCTTA 59.637 40.000 0.00 0.00 38.07 2.10
3183 3534 4.162320 TGACCAAACTCAGTCAGAACTCTT 59.838 41.667 0.00 0.00 38.07 2.85
3184 3535 3.706594 TGACCAAACTCAGTCAGAACTCT 59.293 43.478 0.00 0.00 38.07 3.24
3185 3536 4.060038 TGACCAAACTCAGTCAGAACTC 57.940 45.455 0.00 0.00 38.07 3.01
3186 3537 4.141620 ACATGACCAAACTCAGTCAGAACT 60.142 41.667 0.00 0.00 45.60 3.01
3187 3538 4.130118 ACATGACCAAACTCAGTCAGAAC 58.870 43.478 0.00 0.00 45.60 3.01
3188 3539 4.422073 ACATGACCAAACTCAGTCAGAA 57.578 40.909 0.00 0.00 45.60 3.02
3189 3540 5.482006 CATACATGACCAAACTCAGTCAGA 58.518 41.667 0.00 0.00 45.60 3.27
3190 3541 4.093998 GCATACATGACCAAACTCAGTCAG 59.906 45.833 0.00 0.00 45.60 3.51
3191 3542 4.002982 GCATACATGACCAAACTCAGTCA 58.997 43.478 0.00 0.00 46.39 3.41
3192 3543 4.002982 TGCATACATGACCAAACTCAGTC 58.997 43.478 0.00 0.00 0.00 3.51
3193 3544 4.019792 TGCATACATGACCAAACTCAGT 57.980 40.909 0.00 0.00 0.00 3.41
3194 3545 4.637091 TGATGCATACATGACCAAACTCAG 59.363 41.667 0.00 0.00 36.35 3.35
3196 3547 4.036027 CCTGATGCATACATGACCAAACTC 59.964 45.833 0.00 0.00 36.35 3.01
3199 3550 2.689471 GCCTGATGCATACATGACCAAA 59.311 45.455 0.00 0.00 40.77 3.28
3200 3551 2.300433 GCCTGATGCATACATGACCAA 58.700 47.619 0.00 0.00 40.77 3.67
3201 3552 1.477377 GGCCTGATGCATACATGACCA 60.477 52.381 0.00 0.00 43.89 4.02
3202 3553 1.242076 GGCCTGATGCATACATGACC 58.758 55.000 0.00 0.00 43.89 4.02
3203 3554 1.202855 AGGGCCTGATGCATACATGAC 60.203 52.381 4.50 0.00 43.89 3.06
3204 3555 1.142936 AGGGCCTGATGCATACATGA 58.857 50.000 4.50 0.00 43.89 3.07
3205 3556 1.244816 CAGGGCCTGATGCATACATG 58.755 55.000 29.96 0.00 43.89 3.21
3206 3557 0.538977 GCAGGGCCTGATGCATACAT 60.539 55.000 37.07 0.00 43.89 2.29
3208 3559 1.150081 AGCAGGGCCTGATGCATAC 59.850 57.895 37.07 16.91 45.01 2.39
3209 3560 1.149854 CAGCAGGGCCTGATGCATA 59.850 57.895 35.86 0.00 40.91 3.14
3210 3561 2.123854 CAGCAGGGCCTGATGCAT 60.124 61.111 35.86 13.58 40.91 3.96
3227 4448 4.298332 CCAACCTGTATGAAACAAGCAAC 58.702 43.478 0.00 0.00 37.74 4.17
3242 4463 1.923356 ATAACCAACCAGCCAACCTG 58.077 50.000 0.00 0.00 41.41 4.00
3289 4510 1.460743 ACATCATCGTGTGCAGTTTCG 59.539 47.619 0.00 0.00 0.00 3.46
3304 4525 8.680001 CCATAAAATTCAGTTGAGATCACATCA 58.320 33.333 0.00 0.00 0.00 3.07
3338 4559 3.554960 CCGATGTTTTCACTCCAGACTCA 60.555 47.826 0.00 0.00 0.00 3.41
3339 4560 2.996621 CCGATGTTTTCACTCCAGACTC 59.003 50.000 0.00 0.00 0.00 3.36
3340 4561 2.632996 TCCGATGTTTTCACTCCAGACT 59.367 45.455 0.00 0.00 0.00 3.24
3346 4567 3.121445 GTCTCGTTCCGATGTTTTCACTC 59.879 47.826 0.00 0.00 34.61 3.51
3359 4580 1.996191 GAAGCTCATGTGTCTCGTTCC 59.004 52.381 0.00 0.00 0.00 3.62
3381 4602 0.037447 AGAGAACTTGCTTCCCAGCC 59.963 55.000 0.00 0.00 46.74 4.85
3400 4621 2.029290 GCCAACAACCTTCTACTCGAGA 60.029 50.000 21.68 1.61 0.00 4.04
3433 4654 2.300433 TGATGTGCTATGTCCAATGGC 58.700 47.619 0.00 0.00 0.00 4.40
3435 4656 5.993441 TCTACATGATGTGCTATGTCCAATG 59.007 40.000 8.61 0.00 38.41 2.82
3436 4657 5.994054 GTCTACATGATGTGCTATGTCCAAT 59.006 40.000 8.61 0.00 38.41 3.16
3438 4659 4.948847 GTCTACATGATGTGCTATGTCCA 58.051 43.478 8.61 0.00 38.41 4.02


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

AutoCloner maintained by Alex Coulton.