Multiple sequence alignment - TraesCS7A01G185200

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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 TraesCS7A01G185200 chr7A 100.000 3368 0 0 1 3368 139151468 139154835 0.000000e+00 6220
1 TraesCS7A01G185200 chr7A 86.283 452 46 10 1745 2193 139418044 139418482 8.450000e-131 477
2 TraesCS7A01G185200 chr7A 88.827 179 14 2 1598 1773 139153008 139153183 7.320000e-52 215
3 TraesCS7A01G185200 chr7A 88.827 179 14 2 1541 1716 139153065 139153240 7.320000e-52 215
4 TraesCS7A01G185200 chr7D 88.991 1853 152 23 1542 3368 139107242 139109068 0.000000e+00 2244
5 TraesCS7A01G185200 chr7D 88.312 1309 85 30 486 1773 139106044 139107305 0.000000e+00 1507
6 TraesCS7A01G185200 chr7D 86.301 511 34 12 1 479 139105491 139105997 1.070000e-144 523
7 TraesCS7A01G185200 chr7D 90.503 179 14 1 1541 1716 139107298 139107476 2.020000e-57 233
8 TraesCS7A01G185200 chr7D 88.623 167 8 3 2287 2448 139252049 139252209 3.430000e-45 193
9 TraesCS7A01G185200 chr7D 93.333 120 8 0 1654 1773 139107072 139107191 9.600000e-41 178
10 TraesCS7A01G185200 chr7D 91.270 126 11 0 1541 1666 139107355 139107480 4.470000e-39 172
11 TraesCS7A01G185200 chr7D 85.714 119 12 3 3231 3346 139186178 139186294 1.640000e-23 121
12 TraesCS7A01G185200 chr7B 89.055 1471 116 21 1543 3002 104518002 104519438 0.000000e+00 1783
13 TraesCS7A01G185200 chr7B 85.494 1165 98 32 588 1709 104516978 104518114 0.000000e+00 1149
14 TraesCS7A01G185200 chr7B 82.181 376 32 8 2998 3368 104522116 104522461 1.180000e-74 291
15 TraesCS7A01G185200 chr7B 87.179 234 13 5 273 490 104516618 104516850 2.010000e-62 250
16 TraesCS7A01G185200 chr7B 82.007 289 25 11 1 270 104510374 104510654 1.570000e-53 220
17 TraesCS7A01G185200 chr7B 92.683 123 6 1 1654 1773 104517942 104518064 1.240000e-39 174
18 TraesCS7A01G185200 chr7B 82.320 181 11 8 1541 1718 104518057 104518219 1.630000e-28 137
19 TraesCS7A01G185200 chr1A 80.159 630 112 9 2515 3141 548668192 548667573 3.060000e-125 459
20 TraesCS7A01G185200 chr5A 79.685 635 109 15 2520 3142 539071785 539071159 1.110000e-119 440
21 TraesCS7A01G185200 chr4B 79.466 599 117 5 2520 3114 128373950 128373354 1.450000e-113 420
22 TraesCS7A01G185200 chr1D 79.930 568 102 9 2562 3126 396886562 396886004 1.130000e-109 407
23 TraesCS7A01G185200 chr1D 79.232 573 111 7 2562 3129 396946884 396946315 3.150000e-105 392
24 TraesCS7A01G185200 chr1D 77.379 557 98 17 2558 3110 477505276 477504744 4.220000e-79 305
25 TraesCS7A01G185200 chr3D 79.417 583 97 7 2558 3138 485230623 485230062 1.130000e-104 390
26 TraesCS7A01G185200 chr2A 78.140 613 102 17 2518 3117 690720147 690720740 8.880000e-96 361
27 TraesCS7A01G185200 chr5D 78.030 528 103 6 2613 3128 530362272 530361746 1.510000e-83 320
28 TraesCS7A01G185200 chr4D 81.379 145 21 4 2518 2658 51922467 51922325 2.750000e-21 113


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 TraesCS7A01G185200 chr7A 139151468 139154835 3367 False 2216.666667 6220 92.551333 1 3368 3 chr7A.!!$F2 3367
1 TraesCS7A01G185200 chr7D 139105491 139109068 3577 False 809.500000 2244 89.785000 1 3368 6 chr7D.!!$F3 3367
2 TraesCS7A01G185200 chr7B 104516618 104522461 5843 False 630.666667 1783 86.485333 273 3368 6 chr7B.!!$F2 3095
3 TraesCS7A01G185200 chr1A 548667573 548668192 619 True 459.000000 459 80.159000 2515 3141 1 chr1A.!!$R1 626
4 TraesCS7A01G185200 chr5A 539071159 539071785 626 True 440.000000 440 79.685000 2520 3142 1 chr5A.!!$R1 622
5 TraesCS7A01G185200 chr4B 128373354 128373950 596 True 420.000000 420 79.466000 2520 3114 1 chr4B.!!$R1 594
6 TraesCS7A01G185200 chr1D 396886004 396886562 558 True 407.000000 407 79.930000 2562 3126 1 chr1D.!!$R1 564
7 TraesCS7A01G185200 chr1D 396946315 396946884 569 True 392.000000 392 79.232000 2562 3129 1 chr1D.!!$R2 567
8 TraesCS7A01G185200 chr1D 477504744 477505276 532 True 305.000000 305 77.379000 2558 3110 1 chr1D.!!$R3 552
9 TraesCS7A01G185200 chr3D 485230062 485230623 561 True 390.000000 390 79.417000 2558 3138 1 chr3D.!!$R1 580
10 TraesCS7A01G185200 chr2A 690720147 690720740 593 False 361.000000 361 78.140000 2518 3117 1 chr2A.!!$F1 599
11 TraesCS7A01G185200 chr5D 530361746 530362272 526 True 320.000000 320 78.030000 2613 3128 1 chr5D.!!$R1 515

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
352 380 0.107066 TACACTAGTCCCCGATCGCA 60.107 55.0 10.32 0.0 0.0 5.1 F
804 965 0.177836 GCAGCCTTTCCTCTCCTCTC 59.822 60.0 0.00 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1595 0.105913 ATTCCTCCTCCTCCTCGTCC 60.106 60.0 0.00 0.0 0.00 4.79 R
2794 3205 0.390340 CGCTTTGAGTAGCTGGCAGA 60.390 55.0 20.86 0.0 39.03 4.26 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
64 66 0.890996 AAACGGGCCAAAGCTCTGAG 60.891 55.000 4.39 0.00 37.33 3.35
86 88 3.084039 TGGCATCTGGCTTTAGACAAAG 58.916 45.455 5.30 0.00 43.46 2.77
96 98 4.290969 GCTTTAGACAAAGGAAGTGTTGC 58.709 43.478 0.00 0.00 41.33 4.17
126 129 7.339598 GCTCGGGCTACATAGAACTCTATGG 62.340 52.000 23.99 12.61 45.24 2.74
134 137 1.404843 AGAACTCTATGGGAGCGTCC 58.595 55.000 0.00 0.00 45.48 4.79
206 224 1.453762 GAGCTTGGATGCCTGATGCC 61.454 60.000 0.00 0.00 40.16 4.40
212 230 3.405093 GATGCCTGATGCCGGGACA 62.405 63.158 2.18 0.24 41.53 4.02
222 240 1.116308 TGCCGGGACATATCGAAGAA 58.884 50.000 2.18 0.00 43.58 2.52
223 241 1.068588 TGCCGGGACATATCGAAGAAG 59.931 52.381 2.18 0.00 43.58 2.85
224 242 1.784525 CCGGGACATATCGAAGAAGC 58.215 55.000 0.00 0.00 43.58 3.86
225 243 1.341531 CCGGGACATATCGAAGAAGCT 59.658 52.381 0.00 0.00 43.58 3.74
257 275 1.655597 CGTTGTCAGATGTCACATCCG 59.344 52.381 14.53 4.22 0.00 4.18
261 279 2.099756 TGTCAGATGTCACATCCGCTAG 59.900 50.000 14.53 0.29 0.00 3.42
271 295 5.183331 TGTCACATCCGCTAGATCTAATACC 59.817 44.000 3.57 0.00 30.59 2.73
278 302 9.088512 CATCCGCTAGATCTAATACCAATTAAC 57.911 37.037 3.57 0.00 30.59 2.01
285 309 7.639945 AGATCTAATACCAATTAACAAAGCGC 58.360 34.615 0.00 0.00 0.00 5.92
314 338 4.196626 TGGTTAACTGTAATCCAGGACG 57.803 45.455 5.42 0.00 46.06 4.79
337 361 3.019564 ACGTAGTACACCCTGGATACAC 58.980 50.000 0.00 0.00 41.29 2.90
351 379 1.199558 GATACACTAGTCCCCGATCGC 59.800 57.143 10.32 0.00 0.00 4.58
352 380 0.107066 TACACTAGTCCCCGATCGCA 60.107 55.000 10.32 0.00 0.00 5.10
353 381 1.360551 CACTAGTCCCCGATCGCAG 59.639 63.158 10.32 2.61 0.00 5.18
361 393 1.006805 CCCGATCGCAGAGTCATCC 60.007 63.158 10.32 0.00 43.63 3.51
414 446 1.060937 GCGAGCTGTAACCATTGCG 59.939 57.895 0.00 0.00 0.00 4.85
479 518 1.134694 GGTGCAAGAATTCGTCGCC 59.865 57.895 12.32 11.17 0.00 5.54
734 854 2.653130 GTTCGTACCCGCGATCCG 60.653 66.667 8.23 4.18 40.76 4.18
757 877 1.476833 CCCCTTTCATATGACCACCGG 60.477 57.143 4.48 0.00 0.00 5.28
801 962 2.985456 CGCAGCCTTTCCTCTCCT 59.015 61.111 0.00 0.00 0.00 3.69
802 963 1.153469 CGCAGCCTTTCCTCTCCTC 60.153 63.158 0.00 0.00 0.00 3.71
803 964 1.612395 CGCAGCCTTTCCTCTCCTCT 61.612 60.000 0.00 0.00 0.00 3.69
804 965 0.177836 GCAGCCTTTCCTCTCCTCTC 59.822 60.000 0.00 0.00 0.00 3.20
805 966 0.829990 CAGCCTTTCCTCTCCTCTCC 59.170 60.000 0.00 0.00 0.00 3.71
806 967 0.715987 AGCCTTTCCTCTCCTCTCCT 59.284 55.000 0.00 0.00 0.00 3.69
807 968 1.119684 GCCTTTCCTCTCCTCTCCTC 58.880 60.000 0.00 0.00 0.00 3.71
808 969 1.342975 GCCTTTCCTCTCCTCTCCTCT 60.343 57.143 0.00 0.00 0.00 3.69
809 970 2.666317 CCTTTCCTCTCCTCTCCTCTC 58.334 57.143 0.00 0.00 0.00 3.20
810 971 2.666317 CTTTCCTCTCCTCTCCTCTCC 58.334 57.143 0.00 0.00 0.00 3.71
811 972 0.930726 TTCCTCTCCTCTCCTCTCCC 59.069 60.000 0.00 0.00 0.00 4.30
812 973 0.996762 TCCTCTCCTCTCCTCTCCCC 60.997 65.000 0.00 0.00 0.00 4.81
813 974 0.998945 CCTCTCCTCTCCTCTCCCCT 60.999 65.000 0.00 0.00 0.00 4.79
814 975 0.478507 CTCTCCTCTCCTCTCCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
815 976 0.996762 TCTCCTCTCCTCTCCCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
816 977 2.015726 TCCTCTCCTCTCCCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
817 978 2.612251 CTCTCCTCTCCCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
818 979 2.018086 CTCTCCTCTCCCCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
819 980 2.015726 TCTCCTCTCCCCTCCCCTC 61.016 68.421 0.00 0.00 0.00 4.30
824 985 4.825679 CTCCCCTCCCCTCCCACC 62.826 77.778 0.00 0.00 0.00 4.61
969 1151 2.256461 GTTTTGCTCTGGCCGCAG 59.744 61.111 3.94 0.03 38.80 5.18
983 1165 1.078848 CGCAGGGGAGGTTCTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
984 1166 1.301293 GCAGGGGAGGTTCTCTTGG 59.699 63.158 0.00 0.00 0.00 3.61
985 1167 1.301293 CAGGGGAGGTTCTCTTGGC 59.699 63.158 0.00 0.00 0.00 4.52
1419 1610 1.152839 GGAGGACGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
1431 1622 2.559231 GGAGGAGGAGGAATACGATGAC 59.441 54.545 0.00 0.00 0.00 3.06
1435 1626 1.338337 AGGAGGAATACGATGACTGCG 59.662 52.381 0.00 0.00 0.00 5.18
1533 1724 4.200283 GAGCTGTCGCCTCCTCCG 62.200 72.222 0.00 0.00 36.60 4.63
1575 1766 4.452733 GGAGGGGCCGTCGTCAAG 62.453 72.222 19.16 0.00 0.00 3.02
1635 1826 2.240162 GAGGGGCCGTCGTCAAGAAT 62.240 60.000 10.92 0.00 0.00 2.40
1664 1969 4.988486 GGTGTTCGCCGACGTCGT 62.988 66.667 33.49 0.00 41.18 4.34
1709 2017 2.762535 GAGGAAATCCAGGTGTTCGA 57.237 50.000 1.67 0.00 38.89 3.71
1755 2120 4.265073 CCATCGTCAAGAAGGAGGAAATT 58.735 43.478 0.00 0.00 40.01 1.82
2384 2749 6.126409 TCTGTTAATGGAACCACTCTGTTTT 58.874 36.000 0.00 0.00 37.22 2.43
2387 2752 8.472007 TGTTAATGGAACCACTCTGTTTTAAT 57.528 30.769 0.00 0.00 37.22 1.40
2399 2770 7.442062 CCACTCTGTTTTAATTGCTTGGATTTT 59.558 33.333 0.00 0.00 0.00 1.82
2502 2873 0.582005 AACAGCGCGTCAGAAAAGAC 59.418 50.000 8.43 0.00 35.19 3.01
2531 2902 3.090037 GAGGTAGCTTTTTCTTTCCCCC 58.910 50.000 0.00 0.00 0.00 5.40
2552 2926 0.320374 TCTCGCACGACCAGGAAAAT 59.680 50.000 0.00 0.00 0.00 1.82
2667 3058 5.247084 GTGCCTCGACTTAGATAGATAGGA 58.753 45.833 0.00 0.00 0.00 2.94
2731 3142 4.557695 GCTTCTTCTTCGAGTCTGTCTTCA 60.558 45.833 0.00 0.00 0.00 3.02
2743 3154 1.757118 CTGTCTTCAGGGCTCCGATTA 59.243 52.381 0.00 0.00 37.97 1.75
2767 3178 2.886862 TAAGTTTGTTCGTCGGGACA 57.113 45.000 0.00 0.00 0.00 4.02
2770 3181 0.857287 GTTTGTTCGTCGGGACAGAC 59.143 55.000 0.00 7.29 37.76 3.51
2787 3198 1.654954 GACTAGACGGAGCTTCGGCA 61.655 60.000 25.32 7.68 44.74 5.69
2794 3205 1.139058 ACGGAGCTTCGGCATAGATTT 59.861 47.619 20.69 0.00 44.74 2.17
2809 3220 3.988976 AGATTTCTGCCAGCTACTCAA 57.011 42.857 0.00 0.00 0.00 3.02
2823 3234 0.249398 ACTCAAAGCGGCGAGGTTAT 59.751 50.000 12.98 0.00 40.06 1.89
2862 3280 3.513680 TGCAATGGTGAGATTTGATGC 57.486 42.857 0.00 0.00 0.00 3.91
2887 3305 5.466058 CAGATTCTTCAGATCGATTCAAGGG 59.534 44.000 0.00 0.00 0.00 3.95
2900 3318 3.806949 TTCAAGGGTTCAATGGCTACT 57.193 42.857 0.00 0.00 0.00 2.57
2937 3355 2.266279 GCTGGTCCTTAGGGGCATATA 58.734 52.381 0.00 0.00 39.39 0.86
2938 3356 2.846827 GCTGGTCCTTAGGGGCATATAT 59.153 50.000 0.00 0.00 39.39 0.86
2949 3367 7.341256 CCTTAGGGGCATATATACGAAGACTTA 59.659 40.741 0.00 0.00 0.00 2.24
3005 6105 1.520600 TTAGAGCGGTGACAGCGACA 61.521 55.000 29.64 8.52 42.41 4.35
3022 6122 1.737735 CATGTCGGCAGCTCGTTCA 60.738 57.895 0.00 0.20 0.00 3.18
3066 6166 3.520290 TGTCCACGGATCTCAATGTAC 57.480 47.619 0.00 0.00 0.00 2.90
3070 6171 4.567159 GTCCACGGATCTCAATGTACTTTC 59.433 45.833 0.00 0.00 0.00 2.62
3143 6245 4.260784 CGATATTTCCGCAGAAAAGAAGGG 60.261 45.833 0.00 0.00 44.91 3.95
3175 6277 2.529632 AGGGAGGAACAGAAATTTGCC 58.470 47.619 0.00 0.00 0.00 4.52
3176 6278 1.550524 GGGAGGAACAGAAATTTGCCC 59.449 52.381 0.00 0.00 0.00 5.36
3181 6283 2.029020 GGAACAGAAATTTGCCCTCCAC 60.029 50.000 0.00 0.00 0.00 4.02
3228 6334 1.444553 CGGGTCGAGCTGTGAAGAC 60.445 63.158 15.34 0.00 0.00 3.01
3265 6371 6.729187 AGAATAAACAGTTGCTTGTGAGAAC 58.271 36.000 0.00 0.00 0.00 3.01
3266 6372 3.782889 AAACAGTTGCTTGTGAGAACC 57.217 42.857 0.00 0.00 0.00 3.62
3269 6375 2.292267 CAGTTGCTTGTGAGAACCACT 58.708 47.619 0.00 0.00 45.86 4.00
3270 6376 2.032550 CAGTTGCTTGTGAGAACCACTG 59.967 50.000 0.00 0.00 45.86 3.66
3273 6388 0.590195 GCTTGTGAGAACCACTGCAG 59.410 55.000 13.48 13.48 45.86 4.41
3355 6470 4.084433 GCTACGACTCTAGTAGATGTTCGG 60.084 50.000 21.07 11.29 43.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.477975 GACGACAGCTCGACCGGG 62.478 72.222 6.32 0.00 43.06 5.73
64 66 2.113860 TGTCTAAAGCCAGATGCCAC 57.886 50.000 0.00 0.00 42.71 5.01
113 115 3.158676 GGACGCTCCCATAGAGTTCTAT 58.841 50.000 0.00 0.00 45.21 1.98
116 118 3.969995 GGACGCTCCCATAGAGTTC 57.030 57.895 0.00 0.00 45.21 3.01
134 137 3.192633 CCTTTAATCCAAAACCCGACAGG 59.807 47.826 0.00 0.00 43.78 4.00
142 145 3.334691 GGCCAAGCCTTTAATCCAAAAC 58.665 45.455 0.00 0.00 46.69 2.43
199 217 0.603065 TCGATATGTCCCGGCATCAG 59.397 55.000 0.00 0.00 0.00 2.90
206 224 2.802787 AGCTTCTTCGATATGTCCCG 57.197 50.000 0.00 0.00 0.00 5.14
224 242 2.663602 CTGACAACGTGTTGCTAGCTAG 59.336 50.000 16.84 16.84 44.03 3.42
225 243 2.295070 TCTGACAACGTGTTGCTAGCTA 59.705 45.455 17.23 5.31 44.03 3.32
261 279 7.639945 AGCGCTTTGTTAATTGGTATTAGATC 58.360 34.615 2.64 0.00 0.00 2.75
271 295 3.059166 AGCCAAAGCGCTTTGTTAATTG 58.941 40.909 43.76 33.06 46.19 2.32
278 302 0.530431 AACCAAGCCAAAGCGCTTTG 60.530 50.000 42.24 42.24 46.97 2.77
285 309 5.242838 TGGATTACAGTTAACCAAGCCAAAG 59.757 40.000 15.76 0.00 33.76 2.77
314 338 1.772836 ATCCAGGGTGTACTACGTCC 58.227 55.000 0.00 0.00 0.00 4.79
317 341 3.285484 AGTGTATCCAGGGTGTACTACG 58.715 50.000 0.00 0.00 0.00 3.51
337 361 0.820074 ACTCTGCGATCGGGGACTAG 60.820 60.000 18.30 4.84 0.00 2.57
351 379 3.303938 ACTAGTGGATGGGATGACTCTG 58.696 50.000 0.00 0.00 0.00 3.35
352 380 3.697190 ACTAGTGGATGGGATGACTCT 57.303 47.619 0.00 0.00 0.00 3.24
353 381 5.080337 TGATACTAGTGGATGGGATGACTC 58.920 45.833 5.39 0.00 0.00 3.36
361 393 4.227197 AGGAACCTGATACTAGTGGATGG 58.773 47.826 5.39 5.52 0.00 3.51
393 425 0.370273 CAATGGTTACAGCTCGCGTC 59.630 55.000 5.77 0.00 0.00 5.19
414 446 2.123468 ACCCAACACCCAACAGCC 60.123 61.111 0.00 0.00 0.00 4.85
479 518 2.030562 ACTGCCGGTTCGAAGTGG 59.969 61.111 1.90 10.55 0.00 4.00
534 636 4.779733 TGGACGCCTCCTCCTCCC 62.780 72.222 3.30 0.00 37.48 4.30
567 669 4.286320 CTCGATTCTCGGCCGGGG 62.286 72.222 28.04 18.66 40.88 5.73
569 671 0.249489 AATTCTCGATTCTCGGCCGG 60.249 55.000 27.83 16.54 40.88 6.13
570 672 1.132588 GAATTCTCGATTCTCGGCCG 58.867 55.000 22.12 22.12 40.83 6.13
571 673 1.202533 TGGAATTCTCGATTCTCGGCC 60.203 52.381 5.23 0.00 43.08 6.13
572 674 1.861575 GTGGAATTCTCGATTCTCGGC 59.138 52.381 5.23 0.00 43.08 5.54
573 675 3.119291 CTGTGGAATTCTCGATTCTCGG 58.881 50.000 5.23 0.00 43.08 4.63
574 676 2.537625 GCTGTGGAATTCTCGATTCTCG 59.462 50.000 5.23 0.00 43.08 4.04
575 677 2.869192 GGCTGTGGAATTCTCGATTCTC 59.131 50.000 5.23 0.00 43.08 2.87
576 678 2.237143 TGGCTGTGGAATTCTCGATTCT 59.763 45.455 5.23 0.00 43.08 2.40
577 679 2.352960 GTGGCTGTGGAATTCTCGATTC 59.647 50.000 5.23 0.00 42.84 2.52
578 680 2.359900 GTGGCTGTGGAATTCTCGATT 58.640 47.619 5.23 0.00 0.00 3.34
579 681 1.740380 CGTGGCTGTGGAATTCTCGAT 60.740 52.381 5.23 0.00 0.00 3.59
580 682 0.389817 CGTGGCTGTGGAATTCTCGA 60.390 55.000 5.23 0.00 0.00 4.04
684 804 0.310854 GTGCGGGTTGAAAGTTGGAG 59.689 55.000 0.00 0.00 0.00 3.86
714 834 4.197498 ATCGCGGGTACGAACGGG 62.197 66.667 6.13 12.01 46.59 5.28
797 958 1.541672 GGAGGGGAGAGGAGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
799 960 2.612251 GGGAGGGGAGAGGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
800 961 2.018086 AGGGGAGGGGAGAGGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
801 962 2.015726 GAGGGGAGGGGAGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
802 963 2.612251 GAGGGGAGGGGAGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
803 964 3.036959 GGAGGGGAGGGGAGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
804 965 4.179599 GGGAGGGGAGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
805 966 3.368501 TGGGAGGGGAGGGGAGAG 61.369 72.222 0.00 0.00 0.00 3.20
806 967 3.695825 GTGGGAGGGGAGGGGAGA 61.696 72.222 0.00 0.00 0.00 3.71
807 968 4.825679 GGTGGGAGGGGAGGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
915 1076 2.650163 GATCGGTGGAACGAACGAG 58.350 57.895 0.14 0.00 46.92 4.18
969 1151 2.269241 CGCCAAGAGAACCTCCCC 59.731 66.667 0.00 0.00 0.00 4.81
1317 1508 2.430367 GTCTTGGTGGGCGTCCTT 59.570 61.111 7.97 0.00 0.00 3.36
1318 1509 4.003788 CGTCTTGGTGGGCGTCCT 62.004 66.667 7.97 0.00 0.00 3.85
1401 1592 1.152839 CTCCTCCTCCTCGTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1402 1593 1.152839 CCTCCTCCTCCTCGTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1403 1594 1.215679 TTCCTCCTCCTCCTCGTCCT 61.216 60.000 0.00 0.00 0.00 3.85
1404 1595 0.105913 ATTCCTCCTCCTCCTCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
1405 1596 2.232399 GTATTCCTCCTCCTCCTCGTC 58.768 57.143 0.00 0.00 0.00 4.20
1406 1597 1.477195 CGTATTCCTCCTCCTCCTCGT 60.477 57.143 0.00 0.00 0.00 4.18
1407 1598 1.202782 TCGTATTCCTCCTCCTCCTCG 60.203 57.143 0.00 0.00 0.00 4.63
1408 1599 2.660670 TCGTATTCCTCCTCCTCCTC 57.339 55.000 0.00 0.00 0.00 3.71
1409 1600 2.447429 TCATCGTATTCCTCCTCCTCCT 59.553 50.000 0.00 0.00 0.00 3.69
1419 1610 1.202371 TCCACGCAGTCATCGTATTCC 60.202 52.381 0.00 0.00 41.61 3.01
1435 1626 4.394712 CTCCACCTGCCCGTCCAC 62.395 72.222 0.00 0.00 0.00 4.02
1563 1754 1.737008 GTCCTTCTTGACGACGGCC 60.737 63.158 0.00 0.00 31.32 6.13
1575 1766 2.365408 ACACCTCGATTTCGTCCTTC 57.635 50.000 0.00 0.00 40.80 3.46
1620 1811 1.084370 CCTCATTCTTGACGACGGCC 61.084 60.000 0.00 0.00 0.00 6.13
1635 1826 1.610624 GCGAACACCTGGATTTCCTCA 60.611 52.381 0.00 0.00 36.82 3.86
1677 1982 0.472471 TTTCCTCCTTGACAACGGCT 59.528 50.000 0.00 0.00 0.00 5.52
1683 1988 2.040278 CACCTGGATTTCCTCCTTGACA 59.960 50.000 0.00 0.00 45.21 3.58
1878 2243 3.111939 CGGAGGCTCGTCAGGTAG 58.888 66.667 8.69 0.00 0.00 3.18
1974 2339 3.188786 GCGTGCATCGACAGGTCC 61.189 66.667 11.94 0.00 42.86 4.46
2178 2543 4.129148 GGCCCATCTTTCCCGCCT 62.129 66.667 0.00 0.00 36.65 5.52
2399 2770 4.461081 AGAAGGCACACTAACAACAACAAA 59.539 37.500 0.00 0.00 0.00 2.83
2502 2873 2.474410 AAAAGCTACCTCCGGTTGAG 57.526 50.000 0.00 0.00 41.07 3.02
2531 2902 2.154798 TTTCCTGGTCGTGCGAGAGG 62.155 60.000 11.40 11.40 0.00 3.69
2535 2908 0.672401 GGATTTTCCTGGTCGTGCGA 60.672 55.000 0.00 0.00 32.53 5.10
2552 2926 2.099263 CGAAGATCGAAGGCAAGTAGGA 59.901 50.000 0.00 0.00 43.74 2.94
2556 2930 0.741221 GGCGAAGATCGAAGGCAAGT 60.741 55.000 3.61 0.00 43.74 3.16
2560 2934 2.962253 CCGGCGAAGATCGAAGGC 60.962 66.667 9.30 0.00 43.74 4.35
2621 3001 1.615424 AATACCCTCCTGCCACCGT 60.615 57.895 0.00 0.00 0.00 4.83
2731 3142 3.588569 ACTTAAGGATAATCGGAGCCCT 58.411 45.455 7.53 0.00 0.00 5.19
2743 3154 3.007182 TCCCGACGAACAAACTTAAGGAT 59.993 43.478 7.53 0.00 0.00 3.24
2767 3178 1.378124 GCCGAAGCTCCGTCTAGTCT 61.378 60.000 0.00 0.00 35.50 3.24
2770 3181 0.952280 TATGCCGAAGCTCCGTCTAG 59.048 55.000 0.00 0.00 40.80 2.43
2787 3198 5.620738 TTGAGTAGCTGGCAGAAATCTAT 57.379 39.130 20.86 0.00 0.00 1.98
2794 3205 0.390340 CGCTTTGAGTAGCTGGCAGA 60.390 55.000 20.86 0.00 39.03 4.26
2809 3220 0.322187 AAACCATAACCTCGCCGCTT 60.322 50.000 0.00 0.00 0.00 4.68
2862 3280 5.466058 CCTTGAATCGATCTGAAGAATCTGG 59.534 44.000 0.00 0.00 0.00 3.86
2887 3305 1.933853 CCGCAGTAGTAGCCATTGAAC 59.066 52.381 0.00 0.00 0.00 3.18
2900 3318 2.571757 CGTTCAGGAGCCGCAGTA 59.428 61.111 0.00 0.00 0.00 2.74
2937 3355 3.507233 TGACAACCGGTAAGTCTTCGTAT 59.493 43.478 29.32 1.81 33.56 3.06
2938 3356 2.884012 TGACAACCGGTAAGTCTTCGTA 59.116 45.455 29.32 14.20 33.56 3.43
2949 3367 0.320421 CCTTGTCGATGACAACCGGT 60.320 55.000 0.00 0.00 45.88 5.28
2987 3405 1.313091 ATGTCGCTGTCACCGCTCTA 61.313 55.000 0.00 0.00 0.00 2.43
3005 6105 1.446792 CTGAACGAGCTGCCGACAT 60.447 57.895 15.53 3.63 0.00 3.06
3039 6139 0.246635 AGATCCGTGGACAACCGAAG 59.753 55.000 0.00 0.00 39.42 3.79
3151 6253 4.281941 GCAAATTTCTGTTCCTCCCTTCTT 59.718 41.667 0.00 0.00 0.00 2.52
3152 6254 3.829026 GCAAATTTCTGTTCCTCCCTTCT 59.171 43.478 0.00 0.00 0.00 2.85
3175 6277 0.399454 CTAGCATGGATGGGTGGAGG 59.601 60.000 0.00 0.00 0.00 4.30
3176 6278 0.399454 CCTAGCATGGATGGGTGGAG 59.601 60.000 0.00 0.00 0.00 3.86
3181 6283 1.427809 TCAGTCCTAGCATGGATGGG 58.572 55.000 0.00 0.00 38.52 4.00
3228 6334 5.514914 ACTGTTTATTCTTTGCGTGTTTGTG 59.485 36.000 0.00 0.00 0.00 3.33
3289 6404 2.700371 TCACATGGTTCAGTCAGACAGT 59.300 45.455 2.66 0.00 0.00 3.55
3346 6461 1.691976 TGGTTCACACTCCGAACATCT 59.308 47.619 5.50 0.00 43.70 2.90
3347 6462 2.163818 TGGTTCACACTCCGAACATC 57.836 50.000 5.50 0.00 43.70 3.06


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

AutoCloner maintained by Alex Coulton.