Multiple sequence alignment - TraesCS4B01G141800

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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 TraesCS4B01G141800 chr4B 100.000 3450 0 0 1 3450 187366361 187362912 0.000000e+00 6372.0
1 TraesCS4B01G141800 chr4B 79.474 570 91 19 325 874 17070841 17070278 6.990000e-102 381.0
2 TraesCS4B01G141800 chr4B 88.889 81 9 0 883 963 551054230 551054150 2.190000e-17 100.0
3 TraesCS4B01G141800 chr4B 92.647 68 5 0 883 950 39903673 39903606 7.880000e-17 99.0
4 TraesCS4B01G141800 chr6B 98.434 1341 18 2 2113 3450 62118915 62117575 0.000000e+00 2357.0
5 TraesCS4B01G141800 chr5B 86.050 2086 265 19 1106 3188 670111993 670109931 0.000000e+00 2217.0
6 TraesCS4B01G141800 chr5B 89.744 78 7 1 883 960 398075049 398075125 7.880000e-17 99.0
7 TraesCS4B01G141800 chr5D 86.785 1748 183 17 1124 2867 530869697 530867994 0.000000e+00 1905.0
8 TraesCS4B01G141800 chr5D 89.815 324 29 4 2865 3188 530859038 530858719 2.480000e-111 412.0
9 TraesCS4B01G141800 chr5D 78.292 562 85 22 343 874 538625373 538625927 9.230000e-86 327.0
10 TraesCS4B01G141800 chr4D 87.838 1110 93 17 1 1093 122718636 122717552 0.000000e+00 1264.0
11 TraesCS4B01G141800 chr4D 79.152 566 97 15 322 874 414043881 414044438 4.210000e-99 372.0
12 TraesCS4B01G141800 chr4A 86.319 1111 111 22 1 1094 447043555 447044641 0.000000e+00 1171.0
13 TraesCS4B01G141800 chr4A 96.721 61 2 0 883 943 77093603 77093663 6.090000e-18 102.0
14 TraesCS4B01G141800 chr4A 88.608 79 7 2 883 961 358184552 358184476 1.020000e-15 95.3
15 TraesCS4B01G141800 chr1B 81.262 1046 171 19 1462 2498 570851441 570852470 0.000000e+00 822.0
16 TraesCS4B01G141800 chr1B 80.736 815 139 17 2645 3450 570852695 570853500 1.360000e-173 619.0
17 TraesCS4B01G141800 chr7A 80.261 613 85 20 285 874 142951037 142950438 2.460000e-116 429.0
18 TraesCS4B01G141800 chr6A 82.150 493 84 4 2959 3450 573844667 573845156 1.480000e-113 420.0
19 TraesCS4B01G141800 chr6A 79.268 328 52 15 2645 2963 573836491 573836811 7.500000e-52 215.0
20 TraesCS4B01G141800 chr3B 79.652 575 86 19 325 874 821758707 821758139 5.400000e-103 385.0
21 TraesCS4B01G141800 chr2D 79.673 551 81 21 345 874 61450279 61450819 5.440000e-98 368.0
22 TraesCS4B01G141800 chr2D 75.446 505 113 10 2916 3415 168931336 168930838 5.760000e-58 235.0
23 TraesCS4B01G141800 chr1D 78.435 575 94 17 323 874 359640519 359641086 7.090000e-92 348.0
24 TraesCS4B01G141800 chr1D 78.182 440 76 14 449 874 457087766 457087333 2.640000e-66 263.0
25 TraesCS4B01G141800 chr7D 77.487 573 104 20 320 874 4154689 4154124 1.540000e-83 320.0
26 TraesCS4B01G141800 chr7D 79.303 459 79 11 428 874 189258365 189258819 1.200000e-79 307.0
27 TraesCS4B01G141800 chr3A 80.000 360 59 11 279 632 672445064 672444712 1.590000e-63 254.0
28 TraesCS4B01G141800 chr3A 90.123 81 7 1 883 963 469147865 469147786 1.690000e-18 104.0
29 TraesCS4B01G141800 chr7B 76.180 466 89 18 424 874 591203140 591202682 3.460000e-55 226.0
30 TraesCS4B01G141800 chr5A 93.846 65 4 0 883 947 537122568 537122632 7.880000e-17 99.0
31 TraesCS4B01G141800 chr6D 90.411 73 7 0 871 943 356601315 356601387 2.830000e-16 97.1


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 TraesCS4B01G141800 chr4B 187362912 187366361 3449 True 6372.0 6372 100.000 1 3450 1 chr4B.!!$R3 3449
1 TraesCS4B01G141800 chr4B 17070278 17070841 563 True 381.0 381 79.474 325 874 1 chr4B.!!$R1 549
2 TraesCS4B01G141800 chr6B 62117575 62118915 1340 True 2357.0 2357 98.434 2113 3450 1 chr6B.!!$R1 1337
3 TraesCS4B01G141800 chr5B 670109931 670111993 2062 True 2217.0 2217 86.050 1106 3188 1 chr5B.!!$R1 2082
4 TraesCS4B01G141800 chr5D 530867994 530869697 1703 True 1905.0 1905 86.785 1124 2867 1 chr5D.!!$R2 1743
5 TraesCS4B01G141800 chr5D 538625373 538625927 554 False 327.0 327 78.292 343 874 1 chr5D.!!$F1 531
6 TraesCS4B01G141800 chr4D 122717552 122718636 1084 True 1264.0 1264 87.838 1 1093 1 chr4D.!!$R1 1092
7 TraesCS4B01G141800 chr4D 414043881 414044438 557 False 372.0 372 79.152 322 874 1 chr4D.!!$F1 552
8 TraesCS4B01G141800 chr4A 447043555 447044641 1086 False 1171.0 1171 86.319 1 1094 1 chr4A.!!$F2 1093
9 TraesCS4B01G141800 chr1B 570851441 570853500 2059 False 720.5 822 80.999 1462 3450 2 chr1B.!!$F1 1988
10 TraesCS4B01G141800 chr7A 142950438 142951037 599 True 429.0 429 80.261 285 874 1 chr7A.!!$R1 589
11 TraesCS4B01G141800 chr3B 821758139 821758707 568 True 385.0 385 79.652 325 874 1 chr3B.!!$R1 549
12 TraesCS4B01G141800 chr2D 61450279 61450819 540 False 368.0 368 79.673 345 874 1 chr2D.!!$F1 529
13 TraesCS4B01G141800 chr1D 359640519 359641086 567 False 348.0 348 78.435 323 874 1 chr1D.!!$F1 551
14 TraesCS4B01G141800 chr7D 4154124 4154689 565 True 320.0 320 77.487 320 874 1 chr7D.!!$R1 554

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
293 294 0.902531 CGGGTAGCCTTCTCTTTCCA 59.097 55.0 9.73 0.0 0.00 3.53 F
1252 1291 0.179000 CCTGATTCTCCTTCCCACCG 59.821 60.0 0.00 0.0 0.00 4.94 F
1460 1499 0.181114 GGACCTGATGGCAGCATACA 59.819 55.0 5.64 0.0 40.91 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1352 0.107831 TTCCTCACCAGGTTGTTCCG 59.892 55.000 0.0 0.0 41.28 4.30 R
2336 2382 0.469892 CCCTGTTTGCTCCCCTTGTT 60.470 55.000 0.0 0.0 0.00 2.83 R
2544 2675 3.394606 AGCCTTACTTGGTTCTCTTTCCA 59.605 43.478 0.0 0.0 0.00 3.53 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
159 160 3.376546 GCCATGTTCATCTTCTTCCTCAC 59.623 47.826 0.00 0.00 0.00 3.51
235 236 3.760151 CTCTTTCATTTGCACCAGGATGA 59.240 43.478 0.00 0.00 39.69 2.92
293 294 0.902531 CGGGTAGCCTTCTCTTTCCA 59.097 55.000 9.73 0.00 0.00 3.53
321 323 5.166398 CACAAGAAAGATTCCATGCTTTCC 58.834 41.667 15.66 3.79 46.92 3.13
454 461 6.421501 TCTCGTTCTTGTTAAATTTAGCGTCA 59.578 34.615 7.44 0.55 0.00 4.35
500 514 3.871594 CGATGTCCCTCAGTTGGAATAAC 59.128 47.826 0.00 0.00 32.59 1.89
542 559 2.932261 TCCTAGTGCATCTAGCTTCGA 58.068 47.619 14.35 0.00 43.36 3.71
549 566 1.936547 GCATCTAGCTTCGACAAAGGG 59.063 52.381 0.00 0.00 41.15 3.95
550 567 2.678190 GCATCTAGCTTCGACAAAGGGT 60.678 50.000 0.00 0.00 41.15 4.34
633 650 5.476091 GATCTATTTGGATCCGGTCTTCT 57.524 43.478 7.39 0.00 36.91 2.85
648 665 4.033587 CGGTCTTCTTTCGTCTTTGTTTGA 59.966 41.667 0.00 0.00 0.00 2.69
694 723 1.590238 CTTCATCGACGATGGTTGCTC 59.410 52.381 31.58 0.00 40.15 4.26
716 747 1.214673 TCTAGTGCGGGTCCTATGAGT 59.785 52.381 0.00 0.00 0.00 3.41
746 781 2.163815 CGACAACTTCCCGACTGTCTAT 59.836 50.000 6.21 0.00 36.80 1.98
814 853 1.768870 ACCTTTGGCTCACACTAGTGT 59.231 47.619 22.95 22.95 46.01 3.55
897 936 3.054655 GGTGTTCCTATAGACCCAAAGCA 60.055 47.826 0.00 0.00 0.00 3.91
922 961 2.935481 CCTTCCCTGGACCCTGCA 60.935 66.667 0.00 0.00 0.00 4.41
947 986 1.292223 GGAGCTACGTGCACAAGGA 59.708 57.895 18.64 0.00 45.94 3.36
951 990 1.548719 AGCTACGTGCACAAGGATGTA 59.451 47.619 18.64 8.62 45.94 2.29
955 994 3.671008 ACGTGCACAAGGATGTACTTA 57.329 42.857 18.64 0.00 37.82 2.24
989 1028 6.092259 GTGTTTAGTGTTCCTTATACTGCCAG 59.908 42.308 0.00 0.00 30.13 4.85
1010 1049 7.094075 TGCCAGGATTGAAGATGAATATATTGC 60.094 37.037 1.78 0.00 0.00 3.56
1020 1059 9.890352 GAAGATGAATATATTGCAAGTTTCTCC 57.110 33.333 4.94 2.54 0.00 3.71
1094 1133 6.507023 TGCATGGAAAAGAAAGAGAGAAAAC 58.493 36.000 0.00 0.00 0.00 2.43
1095 1134 6.096705 TGCATGGAAAAGAAAGAGAGAAAACA 59.903 34.615 0.00 0.00 0.00 2.83
1096 1135 7.150640 GCATGGAAAAGAAAGAGAGAAAACAT 58.849 34.615 0.00 0.00 0.00 2.71
1097 1136 8.299570 GCATGGAAAAGAAAGAGAGAAAACATA 58.700 33.333 0.00 0.00 0.00 2.29
1141 1180 2.677199 CAGTGTTTCTCGCTGCTTCTA 58.323 47.619 0.00 0.00 45.63 2.10
1187 1226 1.750341 TTCTCGTCGGCAACCCTTCA 61.750 55.000 0.00 0.00 0.00 3.02
1190 1229 2.280592 GTCGGCAACCCTTCACGT 60.281 61.111 0.00 0.00 0.00 4.49
1203 1242 2.356125 CCTTCACGTTCAATCCCCATCT 60.356 50.000 0.00 0.00 0.00 2.90
1212 1251 4.125124 TCAATCCCCATCTGTTTTCCAA 57.875 40.909 0.00 0.00 0.00 3.53
1213 1252 4.487804 TCAATCCCCATCTGTTTTCCAAA 58.512 39.130 0.00 0.00 0.00 3.28
1214 1253 4.904251 TCAATCCCCATCTGTTTTCCAAAA 59.096 37.500 0.00 0.00 0.00 2.44
1252 1291 0.179000 CCTGATTCTCCTTCCCACCG 59.821 60.000 0.00 0.00 0.00 4.94
1253 1292 0.462759 CTGATTCTCCTTCCCACCGC 60.463 60.000 0.00 0.00 0.00 5.68
1255 1294 2.610532 GATTCTCCTTCCCACCGCCC 62.611 65.000 0.00 0.00 0.00 6.13
1259 1298 3.093835 CCTTCCCACCGCCCCATA 61.094 66.667 0.00 0.00 0.00 2.74
1262 1301 2.608970 CTTCCCACCGCCCCATACAG 62.609 65.000 0.00 0.00 0.00 2.74
1270 1309 1.051812 CGCCCCATACAGAGATTCCT 58.948 55.000 0.00 0.00 0.00 3.36
1271 1310 2.248248 CGCCCCATACAGAGATTCCTA 58.752 52.381 0.00 0.00 0.00 2.94
1298 1337 1.374190 CAGCAAGTGTGAGAGCCCT 59.626 57.895 0.00 0.00 0.00 5.19
1313 1352 4.095946 AGAGCCCTATCCAGATCTGATTC 58.904 47.826 24.62 9.24 0.00 2.52
1314 1353 2.830923 AGCCCTATCCAGATCTGATTCG 59.169 50.000 24.62 7.33 0.00 3.34
1351 1390 4.662650 AGGAATAGAGAGGATTTTGGGAGG 59.337 45.833 0.00 0.00 0.00 4.30
1361 1400 0.187361 TTTTGGGAGGAGGTTGTGGG 59.813 55.000 0.00 0.00 0.00 4.61
1408 1447 3.248248 AAGGGGGCTACGGTGGAGA 62.248 63.158 0.00 0.00 0.00 3.71
1412 1451 4.208686 GGCTACGGTGGAGAGGCG 62.209 72.222 0.00 0.00 0.00 5.52
1413 1452 3.138798 GCTACGGTGGAGAGGCGA 61.139 66.667 0.00 0.00 0.00 5.54
1417 1456 4.452733 CGGTGGAGAGGCGAACCC 62.453 72.222 0.00 0.00 36.11 4.11
1422 1461 2.125350 GAGAGGCGAACCCAGCAG 60.125 66.667 0.00 0.00 36.11 4.24
1429 1468 2.401766 CGAACCCAGCAGCCATCAC 61.402 63.158 0.00 0.00 0.00 3.06
1460 1499 0.181114 GGACCTGATGGCAGCATACA 59.819 55.000 5.64 0.00 40.91 2.29
1475 1514 2.435805 GCATACATGGAAGGAGTGGAGA 59.564 50.000 0.00 0.00 0.00 3.71
1476 1515 3.072184 GCATACATGGAAGGAGTGGAGAT 59.928 47.826 0.00 0.00 0.00 2.75
1477 1516 4.445448 GCATACATGGAAGGAGTGGAGATT 60.445 45.833 0.00 0.00 0.00 2.40
1480 1519 5.365021 ACATGGAAGGAGTGGAGATTAAG 57.635 43.478 0.00 0.00 0.00 1.85
1481 1520 4.785376 ACATGGAAGGAGTGGAGATTAAGT 59.215 41.667 0.00 0.00 0.00 2.24
1500 1539 1.534595 GTTCAAGAACCTGCAGCTCTG 59.465 52.381 8.66 7.48 35.36 3.35
1516 1555 2.290641 GCTCTGTGAAGCGGAAAAGAAA 59.709 45.455 0.00 0.00 31.56 2.52
1561 1600 1.193323 CATGCTCCTCTCAGGTGAGT 58.807 55.000 6.87 0.00 42.60 3.41
1565 1604 2.041755 TGCTCCTCTCAGGTGAGTAAGA 59.958 50.000 6.87 2.46 42.60 2.10
1630 1670 4.563580 GCTGAACATGTGGGAAGAACTCTA 60.564 45.833 0.00 0.00 0.00 2.43
1649 1689 2.367512 GGGGAGTCTGGAGCCCAT 60.368 66.667 0.00 0.00 43.89 4.00
1650 1690 2.003548 GGGGAGTCTGGAGCCCATT 61.004 63.158 0.00 0.00 43.89 3.16
1651 1691 1.225704 GGGAGTCTGGAGCCCATTG 59.774 63.158 0.00 0.00 41.64 2.82
1672 1712 1.337118 TTGGGGTGGATTGCAAAGAC 58.663 50.000 1.71 0.00 0.00 3.01
1861 1901 4.344890 AGCTTACGGCATCCCAATTGGA 62.345 50.000 26.60 12.25 44.79 3.53
1930 1971 7.202047 GGAGAAGTTATTGATGTAGACCCAGAT 60.202 40.741 0.00 0.00 0.00 2.90
2023 2064 8.596271 TGAGATTTATAACAACGTTCACTGAA 57.404 30.769 0.00 0.00 0.00 3.02
2031 2072 3.181465 ACAACGTTCACTGAAGATGAGGT 60.181 43.478 0.00 0.00 0.00 3.85
2059 2100 9.688592 GAACAAGAACAGAAAGATGAAATGATT 57.311 29.630 0.00 0.00 0.00 2.57
2060 2101 9.688592 AACAAGAACAGAAAGATGAAATGATTC 57.311 29.630 0.00 0.00 36.04 2.52
2078 2121 7.966339 ATGATTCTTTTGGGAGATGATGAAA 57.034 32.000 0.00 0.00 0.00 2.69
2079 2122 7.966339 TGATTCTTTTGGGAGATGATGAAAT 57.034 32.000 0.00 0.00 0.00 2.17
2194 2240 9.450807 GGAATTATTGGACATACTGAAAAATCG 57.549 33.333 0.00 0.00 0.00 3.34
2237 2283 1.133792 CGGGGTCTAGGCAATTTGGAT 60.134 52.381 0.00 0.00 0.00 3.41
2268 2314 3.882888 CGTGCAAATATGTACAAGGGGAT 59.117 43.478 0.00 0.00 41.68 3.85
2336 2382 2.104967 AGCCACGCAATAGTACAGGTA 58.895 47.619 0.00 0.00 0.00 3.08
2544 2675 4.832823 CCCCACTGAAAAGGTACAAAGAAT 59.167 41.667 0.00 0.00 0.00 2.40
2747 2878 1.889170 GGAAGGAAAGAAACCAGCAGG 59.111 52.381 0.00 0.00 42.21 4.85
2775 2906 9.239002 CCAATTAAGTACGACAGAATAGAAGAG 57.761 37.037 0.00 0.00 0.00 2.85
2778 2909 9.616156 ATTAAGTACGACAGAATAGAAGAGAGA 57.384 33.333 0.00 0.00 0.00 3.10
2780 2911 7.925043 AGTACGACAGAATAGAAGAGAGAAA 57.075 36.000 0.00 0.00 0.00 2.52
2781 2912 7.981142 AGTACGACAGAATAGAAGAGAGAAAG 58.019 38.462 0.00 0.00 0.00 2.62
2782 2913 6.202516 ACGACAGAATAGAAGAGAGAAAGG 57.797 41.667 0.00 0.00 0.00 3.11
2783 2914 5.712917 ACGACAGAATAGAAGAGAGAAAGGT 59.287 40.000 0.00 0.00 0.00 3.50
2952 3100 3.140814 GGAACTGCCGGGGATTGC 61.141 66.667 2.18 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.952335 CCCCAGAAAGAAGTATTGCTCATT 59.048 41.667 0.00 0.00 0.00 2.57
159 160 2.486636 TAGGTCGGCTGTCAACTGCG 62.487 60.000 6.02 2.79 41.04 5.18
255 256 4.407945 ACCCGCTGTCAAAGGTACTATAAT 59.592 41.667 0.00 0.00 38.49 1.28
274 275 0.902531 TGGAAAGAGAAGGCTACCCG 59.097 55.000 0.00 0.00 35.76 5.28
293 294 4.338879 CATGGAATCTTTCTTGTGGAGGT 58.661 43.478 0.00 0.00 0.00 3.85
321 323 2.851071 GCATCGACGGGAGGAGGAG 61.851 68.421 0.00 0.00 0.00 3.69
358 360 4.743018 CCCAAAGGCCATCGAAGT 57.257 55.556 5.01 0.00 0.00 3.01
454 461 0.758685 CACCACACAACCCCAACCAT 60.759 55.000 0.00 0.00 0.00 3.55
500 514 2.903784 TGGGGATAGAATGTGGGATACG 59.096 50.000 0.00 0.00 37.60 3.06
542 559 2.062636 ACCTCCACACATACCCTTTGT 58.937 47.619 0.00 0.00 0.00 2.83
549 566 2.960819 GAGACACACCTCCACACATAC 58.039 52.381 0.00 0.00 0.00 2.39
633 650 7.136289 AGTAAACACTCAAACAAAGACGAAA 57.864 32.000 0.00 0.00 0.00 3.46
648 665 6.821031 AGTCGTAGATCAGAAGTAAACACT 57.179 37.500 0.00 0.00 40.67 3.55
694 723 0.962489 CATAGGACCCGCACTAGAGG 59.038 60.000 0.00 0.00 0.00 3.69
716 747 1.001633 GGGAAGTTGTCGTGCTAAGGA 59.998 52.381 0.00 0.00 0.00 3.36
746 781 0.891904 GGAGCGGGCAAACCTTGTAA 60.892 55.000 0.00 0.00 36.97 2.41
778 817 0.877071 AGGTGTGTCGTCGTTATCGT 59.123 50.000 0.00 0.00 38.33 3.73
876 915 4.192317 CTGCTTTGGGTCTATAGGAACAC 58.808 47.826 0.00 0.00 32.19 3.32
897 936 2.284699 CCAGGGAAGGGTCCGACT 60.285 66.667 0.00 0.00 46.04 4.18
922 961 2.261671 CACGTAGCTCCCGCTTGT 59.738 61.111 5.69 0.00 46.47 3.16
961 1000 6.428771 GCAGTATAAGGAACACTAAACACCAA 59.571 38.462 0.00 0.00 0.00 3.67
1055 1094 3.645212 TCCATGCAATCCAAAACAAGGAA 59.355 39.130 0.00 0.00 38.93 3.36
1061 1100 6.482973 TCTTTCTTTTCCATGCAATCCAAAAC 59.517 34.615 0.00 0.00 0.00 2.43
1094 1133 1.597663 GCGGACGGACCTCAAAATATG 59.402 52.381 0.00 0.00 36.31 1.78
1095 1134 1.805120 CGCGGACGGACCTCAAAATAT 60.805 52.381 0.00 0.00 36.31 1.28
1096 1135 0.458889 CGCGGACGGACCTCAAAATA 60.459 55.000 0.00 0.00 36.31 1.40
1097 1136 1.740296 CGCGGACGGACCTCAAAAT 60.740 57.895 0.00 0.00 36.31 1.82
1098 1137 2.356553 CGCGGACGGACCTCAAAA 60.357 61.111 0.00 0.00 36.31 2.44
1119 1158 1.599542 GAAGCAGCGAGAAACACTGTT 59.400 47.619 0.00 0.00 33.87 3.16
1122 1161 2.928731 GCTAGAAGCAGCGAGAAACACT 60.929 50.000 0.00 0.00 41.89 3.55
1141 1180 3.559657 GAGTCGCCACACAGTCGCT 62.560 63.158 0.00 0.00 0.00 4.93
1169 1208 2.204461 TGAAGGGTTGCCGACGAGA 61.204 57.895 0.00 0.00 0.00 4.04
1187 1226 2.879103 AACAGATGGGGATTGAACGT 57.121 45.000 0.00 0.00 0.00 3.99
1190 1229 4.125124 TGGAAAACAGATGGGGATTGAA 57.875 40.909 0.00 0.00 0.00 2.69
1213 1252 4.987912 CAGGGCGATTTTGTGTATGTTTTT 59.012 37.500 0.00 0.00 0.00 1.94
1214 1253 4.279671 TCAGGGCGATTTTGTGTATGTTTT 59.720 37.500 0.00 0.00 0.00 2.43
1220 1259 3.938963 GAGAATCAGGGCGATTTTGTGTA 59.061 43.478 0.00 0.00 44.65 2.90
1252 1291 3.198853 GGATAGGAATCTCTGTATGGGGC 59.801 52.174 0.00 0.00 32.29 5.80
1253 1292 4.693420 AGGATAGGAATCTCTGTATGGGG 58.307 47.826 0.00 0.00 32.29 4.96
1255 1294 5.588845 AGGAGGATAGGAATCTCTGTATGG 58.411 45.833 0.00 0.00 32.29 2.74
1257 1296 5.317262 TGGAGGAGGATAGGAATCTCTGTAT 59.683 44.000 0.00 0.00 32.29 2.29
1259 1298 3.469006 TGGAGGAGGATAGGAATCTCTGT 59.531 47.826 0.00 0.00 32.29 3.41
1262 1301 2.831526 GCTGGAGGAGGATAGGAATCTC 59.168 54.545 0.00 0.00 32.29 2.75
1270 1309 1.833630 CACACTTGCTGGAGGAGGATA 59.166 52.381 0.00 0.00 0.00 2.59
1271 1310 0.617413 CACACTTGCTGGAGGAGGAT 59.383 55.000 0.00 0.00 0.00 3.24
1298 1337 5.453339 GGTTGTTCCGAATCAGATCTGGATA 60.453 44.000 22.42 3.84 0.00 2.59
1313 1352 0.107831 TTCCTCACCAGGTTGTTCCG 59.892 55.000 0.00 0.00 41.28 4.30
1314 1353 2.586648 ATTCCTCACCAGGTTGTTCC 57.413 50.000 0.00 0.00 41.28 3.62
1351 1390 2.597510 GCCACACCCCACAACCTC 60.598 66.667 0.00 0.00 0.00 3.85
1373 1412 1.334869 CCTTCACGCCTCCAAATATGC 59.665 52.381 0.00 0.00 0.00 3.14
1376 1415 0.254747 CCCCTTCACGCCTCCAAATA 59.745 55.000 0.00 0.00 0.00 1.40
1412 1451 2.048603 GGTGATGGCTGCTGGGTTC 61.049 63.158 0.00 0.00 0.00 3.62
1413 1452 2.036256 GGTGATGGCTGCTGGGTT 59.964 61.111 0.00 0.00 0.00 4.11
1417 1456 1.320344 AATGCAGGTGATGGCTGCTG 61.320 55.000 0.00 0.00 43.74 4.41
1422 1461 2.428925 CCCCAATGCAGGTGATGGC 61.429 63.158 1.78 0.00 0.00 4.40
1424 1463 3.944123 CCCCCAATGCAGGTGATG 58.056 61.111 1.78 0.00 0.00 3.07
1449 1488 0.918258 TCCTTCCATGTATGCTGCCA 59.082 50.000 0.00 0.00 0.00 4.92
1451 1490 1.945394 CACTCCTTCCATGTATGCTGC 59.055 52.381 0.00 0.00 0.00 5.25
1453 1492 2.437281 CTCCACTCCTTCCATGTATGCT 59.563 50.000 0.00 0.00 0.00 3.79
1460 1499 5.488919 TGAACTTAATCTCCACTCCTTCCAT 59.511 40.000 0.00 0.00 0.00 3.41
1475 1514 4.401925 AGCTGCAGGTTCTTGAACTTAAT 58.598 39.130 13.85 0.00 0.00 1.40
1476 1515 3.815401 GAGCTGCAGGTTCTTGAACTTAA 59.185 43.478 21.18 0.00 0.00 1.85
1477 1516 3.071602 AGAGCTGCAGGTTCTTGAACTTA 59.928 43.478 21.18 0.00 31.35 2.24
1480 1519 1.534595 CAGAGCTGCAGGTTCTTGAAC 59.465 52.381 21.18 5.08 33.17 3.18
1481 1520 1.141657 ACAGAGCTGCAGGTTCTTGAA 59.858 47.619 21.18 0.00 33.17 2.69
1500 1539 2.227194 TCCCTTTCTTTTCCGCTTCAC 58.773 47.619 0.00 0.00 0.00 3.18
1516 1555 3.321950 CTTCCTACCAATCCTGATCCCT 58.678 50.000 0.00 0.00 0.00 4.20
1552 1591 3.173151 TGCCTGAATCTTACTCACCTGA 58.827 45.455 0.00 0.00 0.00 3.86
1561 1600 3.682718 GCTTGCCTACTGCCTGAATCTTA 60.683 47.826 0.00 0.00 40.16 2.10
1565 1604 0.622665 AGCTTGCCTACTGCCTGAAT 59.377 50.000 0.00 0.00 40.16 2.57
1608 1648 4.013267 AGAGTTCTTCCCACATGTTCAG 57.987 45.455 0.00 0.00 0.00 3.02
1630 1670 4.423209 GGGCTCCAGACTCCCCCT 62.423 72.222 0.00 0.00 33.91 4.79
1649 1689 1.500474 TTGCAATCCACCCCAAACAA 58.500 45.000 0.00 0.00 0.00 2.83
1650 1690 1.415659 CTTTGCAATCCACCCCAAACA 59.584 47.619 0.00 0.00 0.00 2.83
1651 1691 1.691434 TCTTTGCAATCCACCCCAAAC 59.309 47.619 0.00 0.00 0.00 2.93
1699 1739 5.144100 TCCTTATCAGCCTTTTGTTGGAAA 58.856 37.500 0.00 0.00 0.00 3.13
1827 1867 3.808174 GCCGTAAGCTCTAACCCAAATAG 59.192 47.826 0.00 0.00 38.99 1.73
1861 1901 5.022122 TCTCCTGTCTCTCTGTTCATCATT 58.978 41.667 0.00 0.00 0.00 2.57
1869 1910 4.650972 ACTAAGTCTCCTGTCTCTCTGT 57.349 45.455 0.00 0.00 0.00 3.41
1930 1971 4.029520 CCCCCATTGAATCACCATTAACA 58.970 43.478 0.00 0.00 0.00 2.41
2014 2055 5.784177 TGTTCTACCTCATCTTCAGTGAAC 58.216 41.667 0.08 0.00 33.94 3.18
2019 2060 6.459066 TGTTCTTGTTCTACCTCATCTTCAG 58.541 40.000 0.00 0.00 0.00 3.02
2023 2064 6.672266 TTCTGTTCTTGTTCTACCTCATCT 57.328 37.500 0.00 0.00 0.00 2.90
2031 2072 9.559732 TCATTTCATCTTTCTGTTCTTGTTCTA 57.440 29.630 0.00 0.00 0.00 2.10
2059 2100 7.670979 TCTTTCATTTCATCATCTCCCAAAAGA 59.329 33.333 0.00 0.00 0.00 2.52
2060 2101 7.833786 TCTTTCATTTCATCATCTCCCAAAAG 58.166 34.615 0.00 0.00 0.00 2.27
2095 2138 3.275848 TCCTCCCCTTCTTTCTTCTCA 57.724 47.619 0.00 0.00 0.00 3.27
2096 2139 4.642466 TTTCCTCCCCTTCTTTCTTCTC 57.358 45.455 0.00 0.00 0.00 2.87
2097 2140 4.665483 TCTTTTCCTCCCCTTCTTTCTTCT 59.335 41.667 0.00 0.00 0.00 2.85
2108 2151 3.721087 TGAGACAATCTTTTCCTCCCC 57.279 47.619 0.00 0.00 0.00 4.81
2194 2240 5.353111 GTTCTTCTAGATCTAGTTGGGCAC 58.647 45.833 25.54 13.91 34.84 5.01
2237 2283 1.065851 CATATTTGCACGCAGCCATGA 59.934 47.619 0.00 0.00 44.83 3.07
2268 2314 4.322049 CCCTACTTCTTTCTTCGCTTGAGA 60.322 45.833 0.00 0.00 0.00 3.27
2316 2362 0.902531 ACCTGTACTATTGCGTGGCT 59.097 50.000 0.00 0.00 0.00 4.75
2321 2367 3.869246 CCCTTGTTACCTGTACTATTGCG 59.131 47.826 0.00 0.00 0.00 4.85
2336 2382 0.469892 CCCTGTTTGCTCCCCTTGTT 60.470 55.000 0.00 0.00 0.00 2.83
2544 2675 3.394606 AGCCTTACTTGGTTCTCTTTCCA 59.605 43.478 0.00 0.00 0.00 3.53
2747 2878 8.922058 TTCTATTCTGTCGTACTTAATTGGTC 57.078 34.615 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.