Multiple sequence alignment - TraesCS2B01G599500

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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 TraesCS2B01G599500 chr2B 100.000 6220 0 0 1 6220 782143086 782149305 0.000000e+00 11487.0
1 TraesCS2B01G599500 chr2B 94.118 408 23 1 1 408 781711441 781711035 2.460000e-173 619.0
2 TraesCS2B01G599500 chr2B 92.162 421 25 5 484 903 781710994 781710581 6.950000e-164 588.0
3 TraesCS2B01G599500 chr2B 86.344 454 58 4 3096 3548 781778565 781778115 5.600000e-135 492.0
4 TraesCS2B01G599500 chr2B 92.222 180 13 1 2918 3097 781778905 781778727 2.880000e-63 254.0
5 TraesCS2B01G599500 chr2B 83.456 272 25 13 1917 2183 781779824 781779568 1.040000e-57 235.0
6 TraesCS2B01G599500 chr2B 88.060 67 7 1 18 84 782136158 782136223 1.860000e-10 78.7
7 TraesCS2B01G599500 chr2B 86.567 67 7 2 18 84 781712157 781712093 8.650000e-09 73.1
8 TraesCS2B01G599500 chr2D 93.570 4246 222 27 1361 5589 648204561 648208772 0.000000e+00 6281.0
9 TraesCS2B01G599500 chr2D 90.164 488 15 12 902 1361 648204045 648204527 6.900000e-169 604.0
10 TraesCS2B01G599500 chr2D 78.806 1005 116 63 1466 2418 648158886 648159845 2.500000e-163 586.0
11 TraesCS2B01G599500 chr2D 88.740 373 36 5 2550 2917 648159893 648160264 9.510000e-123 451.0
12 TraesCS2B01G599500 chr2D 83.889 360 26 11 3189 3548 648162493 648162820 1.300000e-81 315.0
13 TraesCS2B01G599500 chr2D 82.651 415 15 27 5744 6133 648209443 648209825 1.300000e-81 315.0
14 TraesCS2B01G599500 chr2D 86.802 197 19 7 2971 3163 648161783 648161976 4.880000e-51 213.0
15 TraesCS2B01G599500 chr2D 96.226 53 1 1 6167 6219 648209889 648209940 1.110000e-12 86.1
16 TraesCS2B01G599500 chrUn 94.085 1251 63 8 3279 4527 31219700 31218459 0.000000e+00 1890.0
17 TraesCS2B01G599500 chrUn 92.213 1053 65 11 1373 2416 31221700 31220656 0.000000e+00 1474.0
18 TraesCS2B01G599500 chrUn 90.564 816 41 12 2423 3230 31220489 31219702 0.000000e+00 1048.0
19 TraesCS2B01G599500 chrUn 91.051 771 47 12 4550 5312 31218465 31217709 0.000000e+00 1022.0
20 TraesCS2B01G599500 chrUn 86.706 504 27 14 902 1365 31222242 31221739 1.990000e-144 523.0
21 TraesCS2B01G599500 chrUn 81.373 510 48 27 5745 6219 31216986 31216489 7.610000e-99 372.0
22 TraesCS2B01G599500 chrUn 82.880 368 37 16 2057 2416 31233719 31233370 2.180000e-79 307.0
23 TraesCS2B01G599500 chrUn 92.920 113 7 1 5478 5589 31217478 31217366 4.990000e-36 163.0
24 TraesCS2B01G599500 chr5D 84.492 187 27 2 277 462 438974709 438974524 3.830000e-42 183.0
25 TraesCS2B01G599500 chr6B 76.923 104 22 2 359 462 719775600 719775701 2.420000e-04 58.4


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 TraesCS2B01G599500 chr2B 782143086 782149305 6219 False 11487.000000 11487 100.000000 1 6220 1 chr2B.!!$F2 6219
1 TraesCS2B01G599500 chr2B 781710581 781712157 1576 True 426.700000 619 90.949000 1 903 3 chr2B.!!$R1 902
2 TraesCS2B01G599500 chr2B 781778115 781779824 1709 True 327.000000 492 87.340667 1917 3548 3 chr2B.!!$R2 1631
3 TraesCS2B01G599500 chr2D 648204045 648209940 5895 False 1821.525000 6281 90.652750 902 6219 4 chr2D.!!$F2 5317
4 TraesCS2B01G599500 chr2D 648158886 648162820 3934 False 391.250000 586 84.559250 1466 3548 4 chr2D.!!$F1 2082
5 TraesCS2B01G599500 chrUn 31216489 31222242 5753 True 927.428571 1890 89.844571 902 6219 7 chrUn.!!$R2 5317

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
570 1317 0.038159 AAAGCTCTGAGTTCGGTCCG 60.038 55.000 4.39 4.39 0.0 4.79 F
1382 2237 2.040278 CCACCAGATCAACCCTCAGAAA 59.960 50.000 0.00 0.00 0.0 2.52 F
1707 2572 1.663643 GTTTCGTTATCATCTGCGGCA 59.336 47.619 1.29 1.29 0.0 5.69 F
3351 6655 0.106268 TGTGCCCATGTGACAACCTT 60.106 50.000 0.00 0.00 0.0 3.50 F
3618 6925 0.730265 GAACAGCACAACGTCCAACA 59.270 50.000 0.00 0.00 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 2320 0.539051 CATGGGAGGTGGACAGAGAC 59.461 60.0 0.0 0.0 0.00 3.36 R
3166 5978 0.041312 GTGCGAAACATCGTGCAACT 60.041 50.0 0.0 0.0 39.34 3.16 R
3420 6724 0.320771 GCATATCGGGTACTGCCTGG 60.321 60.0 0.0 0.0 43.94 4.45 R
4947 8259 0.099082 CGGCTTCGAGTAGAGGTGAC 59.901 60.0 0.0 0.0 35.61 3.67 R
5353 8669 0.037975 CTTTGTCAGCAATGGGGCAC 60.038 55.0 0.0 0.0 34.18 5.01 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
85 802 9.447040 CTTACAAAAACTGGCTTAAGTAAGAAC 57.553 33.333 4.02 0.00 39.45 3.01
148 865 5.869579 ACTGAGAGTAAAAAGATCAAGCCA 58.130 37.500 0.00 0.00 0.00 4.75
149 866 6.299141 ACTGAGAGTAAAAAGATCAAGCCAA 58.701 36.000 0.00 0.00 0.00 4.52
189 906 6.768078 ACCACGCTTTATTAAAATAGTGTCG 58.232 36.000 12.89 0.00 33.56 4.35
217 934 7.996644 GGTTTACATGAATAACTAGGGGATCAA 59.003 37.037 0.00 0.00 0.00 2.57
251 968 2.094182 TGGCGTCCAACATCTAGAGAAC 60.094 50.000 0.00 0.00 0.00 3.01
295 1012 3.821033 GGAGTAAAATGCACAGAACCACT 59.179 43.478 0.00 0.00 0.00 4.00
304 1021 2.348666 GCACAGAACCACTACATTAGCG 59.651 50.000 0.00 0.00 0.00 4.26
306 1023 3.994392 CACAGAACCACTACATTAGCGTT 59.006 43.478 0.00 0.00 0.00 4.84
314 1031 7.344095 ACCACTACATTAGCGTTATAACTCT 57.656 36.000 12.48 12.48 0.00 3.24
315 1032 7.424001 ACCACTACATTAGCGTTATAACTCTC 58.576 38.462 11.28 1.96 0.00 3.20
327 1044 5.863397 CGTTATAACTCTCGTAAAACCACCA 59.137 40.000 13.56 0.00 0.00 4.17
349 1066 5.257108 CAGTTTACAAAACGTGACGCTTTA 58.743 37.500 4.25 0.00 0.00 1.85
401 1118 7.452880 AAAAACACTGATGCTAGATGCTAAA 57.547 32.000 0.00 0.00 43.37 1.85
408 1125 4.811024 TGATGCTAGATGCTAAAGGTTTCG 59.189 41.667 0.00 0.00 43.37 3.46
409 1126 4.465632 TGCTAGATGCTAAAGGTTTCGA 57.534 40.909 0.00 0.00 43.37 3.71
410 1127 5.023533 TGCTAGATGCTAAAGGTTTCGAT 57.976 39.130 0.00 0.00 43.37 3.59
411 1128 4.811024 TGCTAGATGCTAAAGGTTTCGATG 59.189 41.667 0.00 0.00 43.37 3.84
412 1129 5.050490 GCTAGATGCTAAAGGTTTCGATGA 58.950 41.667 0.00 0.00 38.95 2.92
413 1130 5.050702 GCTAGATGCTAAAGGTTTCGATGAC 60.051 44.000 0.00 0.00 38.95 3.06
414 1131 4.832248 AGATGCTAAAGGTTTCGATGACA 58.168 39.130 0.00 0.00 0.00 3.58
415 1132 5.431765 AGATGCTAAAGGTTTCGATGACAT 58.568 37.500 0.00 0.00 0.00 3.06
416 1133 5.525378 AGATGCTAAAGGTTTCGATGACATC 59.475 40.000 5.28 5.28 0.00 3.06
417 1134 4.574892 TGCTAAAGGTTTCGATGACATCA 58.425 39.130 15.58 0.35 0.00 3.07
418 1135 4.391830 TGCTAAAGGTTTCGATGACATCAC 59.608 41.667 15.58 6.10 0.00 3.06
419 1136 4.631813 GCTAAAGGTTTCGATGACATCACT 59.368 41.667 15.58 2.67 0.00 3.41
420 1137 5.810587 GCTAAAGGTTTCGATGACATCACTA 59.189 40.000 15.58 0.00 0.00 2.74
421 1138 6.312918 GCTAAAGGTTTCGATGACATCACTAA 59.687 38.462 15.58 3.87 0.00 2.24
422 1139 7.011482 GCTAAAGGTTTCGATGACATCACTAAT 59.989 37.037 15.58 0.00 0.00 1.73
423 1140 7.687941 AAAGGTTTCGATGACATCACTAATT 57.312 32.000 15.58 0.50 0.00 1.40
424 1141 6.668541 AGGTTTCGATGACATCACTAATTG 57.331 37.500 15.58 0.00 0.00 2.32
425 1142 5.586243 AGGTTTCGATGACATCACTAATTGG 59.414 40.000 15.58 0.00 0.00 3.16
426 1143 5.266242 GTTTCGATGACATCACTAATTGGC 58.734 41.667 15.58 0.00 0.00 4.52
427 1144 3.466836 TCGATGACATCACTAATTGGCC 58.533 45.455 15.58 0.00 0.00 5.36
428 1145 2.221749 CGATGACATCACTAATTGGCCG 59.778 50.000 15.58 0.00 0.00 6.13
429 1146 2.036958 TGACATCACTAATTGGCCGG 57.963 50.000 0.00 0.00 0.00 6.13
430 1147 1.308998 GACATCACTAATTGGCCGGG 58.691 55.000 2.18 0.00 0.00 5.73
431 1148 0.916086 ACATCACTAATTGGCCGGGA 59.084 50.000 2.18 0.00 0.00 5.14
432 1149 1.308998 CATCACTAATTGGCCGGGAC 58.691 55.000 2.18 0.00 0.00 4.46
433 1150 0.182775 ATCACTAATTGGCCGGGACC 59.817 55.000 2.18 0.00 0.00 4.46
434 1151 1.817941 CACTAATTGGCCGGGACCG 60.818 63.158 2.18 3.25 39.44 4.79
435 1152 2.900337 CTAATTGGCCGGGACCGC 60.900 66.667 2.18 0.91 38.24 5.68
436 1153 4.493049 TAATTGGCCGGGACCGCC 62.493 66.667 2.18 14.51 38.24 6.13
452 1169 4.760047 CCTGTCGGGCCGAGTTGG 62.760 72.222 31.98 25.71 36.23 3.77
463 1180 0.598065 CCGAGTTGGCAGGAAAAAGG 59.402 55.000 0.00 0.00 0.00 3.11
464 1181 1.318576 CGAGTTGGCAGGAAAAAGGT 58.681 50.000 0.00 0.00 0.00 3.50
465 1182 1.001378 CGAGTTGGCAGGAAAAAGGTG 60.001 52.381 0.00 0.00 0.00 4.00
466 1183 0.752658 AGTTGGCAGGAAAAAGGTGC 59.247 50.000 0.00 0.00 36.42 5.01
470 1187 2.123409 GCAGGAAAAAGGTGCCACA 58.877 52.632 0.00 0.00 0.00 4.17
471 1188 0.681175 GCAGGAAAAAGGTGCCACAT 59.319 50.000 0.00 0.00 0.00 3.21
472 1189 1.892474 GCAGGAAAAAGGTGCCACATA 59.108 47.619 0.00 0.00 0.00 2.29
481 1198 3.874392 AGGTGCCACATAAGCAAATTC 57.126 42.857 0.00 0.00 43.02 2.17
490 1207 6.095377 CCACATAAGCAAATTCACTTCTTCC 58.905 40.000 0.00 0.00 0.00 3.46
496 1213 4.764308 AGCAAATTCACTTCTTCCTCTTCC 59.236 41.667 0.00 0.00 0.00 3.46
547 1294 7.172757 CGAACTTCAAATCCAAACAAAACTTG 58.827 34.615 0.00 0.00 0.00 3.16
559 1306 6.401367 CCAAACAAAACTTGAACAAAGCTCTG 60.401 38.462 0.00 0.00 39.76 3.35
566 1313 2.483876 TGAACAAAGCTCTGAGTTCGG 58.516 47.619 6.53 0.00 42.35 4.30
570 1317 0.038159 AAAGCTCTGAGTTCGGTCCG 60.038 55.000 4.39 4.39 0.00 4.79
585 1332 4.183101 TCGGTCCGTCCATAAACAATTAC 58.817 43.478 11.88 0.00 35.57 1.89
648 1395 8.014070 TGCCAGTATAACATTAGCTACAGTAA 57.986 34.615 0.00 0.00 0.00 2.24
682 1429 3.113191 AGGCTCTCTTGATGAAGGAGA 57.887 47.619 12.31 4.87 32.41 3.71
700 1447 6.670695 AGGAGAAACCAAAAACTATGCAAT 57.329 33.333 0.00 0.00 42.04 3.56
702 1449 7.830739 AGGAGAAACCAAAAACTATGCAATAG 58.169 34.615 0.00 0.00 46.28 1.73
736 1483 7.615582 TGCACAAGAATCTACCAAAATAGAG 57.384 36.000 0.00 0.00 34.68 2.43
821 1568 9.780186 AAATAAAATACTAGACATACCTGGCTC 57.220 33.333 0.00 0.00 41.02 4.70
822 1569 8.728596 ATAAAATACTAGACATACCTGGCTCT 57.271 34.615 0.00 0.00 41.02 4.09
823 1570 9.824216 ATAAAATACTAGACATACCTGGCTCTA 57.176 33.333 0.00 0.00 41.02 2.43
824 1571 7.768807 AAATACTAGACATACCTGGCTCTAG 57.231 40.000 0.00 13.02 41.02 2.43
825 1572 3.492337 ACTAGACATACCTGGCTCTAGC 58.508 50.000 13.94 0.00 41.02 3.42
826 1573 2.461300 AGACATACCTGGCTCTAGCA 57.539 50.000 4.07 0.00 34.92 3.49
827 1574 2.969628 AGACATACCTGGCTCTAGCAT 58.030 47.619 4.07 0.00 34.92 3.79
828 1575 2.632028 AGACATACCTGGCTCTAGCATG 59.368 50.000 4.07 1.38 34.92 4.06
829 1576 2.366916 GACATACCTGGCTCTAGCATGT 59.633 50.000 4.07 4.59 44.36 3.21
830 1577 2.774234 ACATACCTGGCTCTAGCATGTT 59.226 45.455 4.07 0.00 44.36 2.71
831 1578 3.967326 ACATACCTGGCTCTAGCATGTTA 59.033 43.478 4.07 0.00 44.36 2.41
832 1579 4.408921 ACATACCTGGCTCTAGCATGTTAA 59.591 41.667 4.07 0.00 44.36 2.01
833 1580 5.072329 ACATACCTGGCTCTAGCATGTTAAT 59.928 40.000 4.07 0.00 44.36 1.40
834 1581 4.510167 ACCTGGCTCTAGCATGTTAATT 57.490 40.909 4.07 0.00 44.36 1.40
835 1582 4.860022 ACCTGGCTCTAGCATGTTAATTT 58.140 39.130 4.07 0.00 44.36 1.82
836 1583 5.264395 ACCTGGCTCTAGCATGTTAATTTT 58.736 37.500 4.07 0.00 44.36 1.82
837 1584 5.716703 ACCTGGCTCTAGCATGTTAATTTTT 59.283 36.000 4.07 0.00 44.36 1.94
838 1585 6.127619 ACCTGGCTCTAGCATGTTAATTTTTC 60.128 38.462 4.07 0.00 44.36 2.29
839 1586 6.096001 CCTGGCTCTAGCATGTTAATTTTTCT 59.904 38.462 4.07 0.00 44.36 2.52
840 1587 6.855836 TGGCTCTAGCATGTTAATTTTTCTG 58.144 36.000 4.07 0.00 44.36 3.02
841 1588 6.127647 TGGCTCTAGCATGTTAATTTTTCTGG 60.128 38.462 4.07 0.00 44.36 3.86
842 1589 6.095440 GGCTCTAGCATGTTAATTTTTCTGGA 59.905 38.462 4.07 0.00 44.36 3.86
843 1590 7.201857 GGCTCTAGCATGTTAATTTTTCTGGAT 60.202 37.037 4.07 0.00 44.36 3.41
844 1591 8.193438 GCTCTAGCATGTTAATTTTTCTGGATT 58.807 33.333 0.00 0.00 41.59 3.01
849 1596 9.558396 AGCATGTTAATTTTTCTGGATTTTCAA 57.442 25.926 0.00 0.00 0.00 2.69
885 1632 9.760926 ATTATCTCCAGCTCACAAGTATATAGA 57.239 33.333 0.00 0.00 0.00 1.98
886 1633 7.701539 ATCTCCAGCTCACAAGTATATAGAG 57.298 40.000 0.00 0.00 0.00 2.43
1010 1784 4.802051 CCCAGACATGGCCACCGG 62.802 72.222 8.16 0.00 46.19 5.28
1238 2028 2.287427 TCCCCTCCTCCTCCCGTA 60.287 66.667 0.00 0.00 0.00 4.02
1240 2030 2.123382 CCCTCCTCCTCCCGTACC 60.123 72.222 0.00 0.00 0.00 3.34
1250 2040 4.894203 CCCGTACCGTAGCGCGTC 62.894 72.222 8.43 0.00 39.32 5.19
1297 2087 2.695314 GGATTCATCCGTGCTGTCC 58.305 57.895 0.00 0.00 37.19 4.02
1326 2116 2.922740 TATGTAGCGTGGGGGATTTC 57.077 50.000 0.00 0.00 0.00 2.17
1354 2144 7.226128 GGATTTTACCCCTAGATTAGAACAACG 59.774 40.741 0.00 0.00 0.00 4.10
1382 2237 2.040278 CCACCAGATCAACCCTCAGAAA 59.960 50.000 0.00 0.00 0.00 2.52
1395 2250 3.012518 CCTCAGAAATTACAGTGGCCTG 58.987 50.000 3.32 0.00 44.68 4.85
1408 2263 4.142093 ACAGTGGCCTGATTAATTTGATGC 60.142 41.667 3.32 0.00 41.50 3.91
1412 2270 4.098349 TGGCCTGATTAATTTGATGCACTC 59.902 41.667 3.32 0.00 0.00 3.51
1421 2279 3.574284 TTTGATGCACTCGATTTTGGG 57.426 42.857 0.00 0.00 0.00 4.12
1462 2320 4.631131 TGTGGTTACTGATGTCTGAAGTG 58.369 43.478 0.00 0.00 0.00 3.16
1503 2365 3.255642 GGTGTGTGCCATACTTTGATGTT 59.744 43.478 0.00 0.00 0.00 2.71
1514 2376 2.622942 ACTTTGATGTTGACAATGGCGT 59.377 40.909 0.00 0.00 0.00 5.68
1552 2416 5.354767 CATGTAGCTCTGCTCTTGTGAATA 58.645 41.667 0.00 0.00 40.44 1.75
1696 2561 9.136952 GTCTGTCTGTATACTTTGTTTCGTTAT 57.863 33.333 4.17 0.00 0.00 1.89
1707 2572 1.663643 GTTTCGTTATCATCTGCGGCA 59.336 47.619 1.29 1.29 0.00 5.69
1747 2612 3.855689 AAGCAATTGTCTGGTGTATGC 57.144 42.857 7.40 0.00 0.00 3.14
1810 2686 9.780186 GGGAAAGTAGAAGCATTAGTTGTATAT 57.220 33.333 0.00 0.00 0.00 0.86
1846 2723 4.130857 GACCCTCCTAGATTTAAGCAAGC 58.869 47.826 0.00 0.00 0.00 4.01
1870 2760 6.338146 CCTCTGGTGTTTTAGTTCGATGATA 58.662 40.000 0.00 0.00 0.00 2.15
1873 2763 7.033791 TCTGGTGTTTTAGTTCGATGATAGTC 58.966 38.462 0.00 0.00 0.00 2.59
1875 2765 7.383687 TGGTGTTTTAGTTCGATGATAGTCTT 58.616 34.615 0.00 0.00 0.00 3.01
2067 2971 3.477530 GGAGCTGTGAAAGGTAGTTGTT 58.522 45.455 0.00 0.00 36.52 2.83
2309 3215 6.429624 CCCATGTATGTAATCACACAATTCG 58.570 40.000 0.00 0.00 34.57 3.34
2312 3218 6.902224 TGTATGTAATCACACAATTCGAGG 57.098 37.500 0.00 0.00 37.54 4.63
2419 3488 8.056571 CGATTCCGTTGTGTTATCTTCTAATTC 58.943 37.037 0.00 0.00 0.00 2.17
2420 3489 7.605410 TTCCGTTGTGTTATCTTCTAATTCC 57.395 36.000 0.00 0.00 0.00 3.01
2421 3490 6.703319 TCCGTTGTGTTATCTTCTAATTCCA 58.297 36.000 0.00 0.00 0.00 3.53
2587 3656 4.223953 TCCATCCTACCAGTAATCCTGAC 58.776 47.826 0.00 0.00 44.49 3.51
2605 3674 7.898014 TCCTGACTTGCTGAGTTATTCTATA 57.102 36.000 0.00 0.00 39.19 1.31
2637 3707 4.162690 GGTCGGCGAGGGAGCATT 62.163 66.667 11.20 0.00 39.27 3.56
2662 3732 5.354792 CCAATGGGCAAAATGTAAAGGAATG 59.645 40.000 0.00 0.00 0.00 2.67
2675 3745 8.746052 ATGTAAAGGAATGGACATAATCGAAA 57.254 30.769 0.00 0.00 30.83 3.46
2705 3775 8.668353 CATCGGAGGATAATAATGTAAACCATG 58.332 37.037 0.00 0.00 32.82 3.66
2818 3891 2.100584 TGCAAAAGCACAGTGGGTAAAG 59.899 45.455 1.84 0.00 0.00 1.85
2860 3933 3.938963 GTGCCAAGGAATCTGTTAATCGA 59.061 43.478 0.00 0.00 0.00 3.59
2951 4142 9.713740 CATATCTCACTTGTGCTTTAATTCTTC 57.286 33.333 0.00 0.00 0.00 2.87
2956 4147 5.691754 CACTTGTGCTTTAATTCTTCCCAAC 59.308 40.000 0.00 0.00 0.00 3.77
2958 4149 3.242518 GTGCTTTAATTCTTCCCAACGC 58.757 45.455 0.00 0.00 0.00 4.84
3087 5733 8.398665 CAATAGGAAGTTTACCATGAGCTTAAC 58.601 37.037 0.00 0.00 0.00 2.01
3089 5735 4.694037 GGAAGTTTACCATGAGCTTAACGT 59.306 41.667 0.00 0.00 0.00 3.99
3094 5742 6.707161 AGTTTACCATGAGCTTAACGTTTACA 59.293 34.615 5.91 0.62 0.00 2.41
3139 5951 1.780025 GCTGCGCTCAGGCCTATTTC 61.780 60.000 3.98 0.00 40.65 2.17
3191 6494 2.527671 CGATGTTTCGCACCTGTGA 58.472 52.632 0.51 0.00 38.75 3.58
3274 6578 7.987458 CACCACTTAGTTGTATCCAGTGATATT 59.013 37.037 0.00 0.00 37.63 1.28
3275 6579 8.548877 ACCACTTAGTTGTATCCAGTGATATTT 58.451 33.333 0.00 0.00 37.63 1.40
3290 6594 9.424319 CCAGTGATATTTATTACGATGCTTAGT 57.576 33.333 0.00 0.00 0.00 2.24
3326 6630 8.630037 CGGTGACATACATATCAGCCTATATAA 58.370 37.037 0.00 0.00 39.62 0.98
3351 6655 0.106268 TGTGCCCATGTGACAACCTT 60.106 50.000 0.00 0.00 0.00 3.50
3364 6668 5.472137 TGTGACAACCTTTTATGTTAGAGCC 59.528 40.000 0.00 0.00 0.00 4.70
3420 6724 1.831286 CCTGGATGCCATTCTGCCC 60.831 63.158 0.00 0.00 30.82 5.36
3618 6925 0.730265 GAACAGCACAACGTCCAACA 59.270 50.000 0.00 0.00 0.00 3.33
3619 6926 1.333619 GAACAGCACAACGTCCAACAT 59.666 47.619 0.00 0.00 0.00 2.71
3770 7080 8.461249 AATATCTTCTGCTGCATGTTATCTTT 57.539 30.769 1.31 0.00 0.00 2.52
3783 7094 7.809331 TGCATGTTATCTTTGATTCACTGTTTC 59.191 33.333 0.00 0.00 0.00 2.78
3924 7235 5.390356 GCACTAGTGATTCAACTCTGCTTTC 60.390 44.000 27.08 0.00 33.86 2.62
4173 7484 9.643693 GTCATTTGGTCATTTTATTCATCAGTT 57.356 29.630 0.00 0.00 0.00 3.16
4246 7557 7.601856 TCATATAAGCCCTTTGTTTGTTTCAG 58.398 34.615 0.00 0.00 0.00 3.02
4276 7587 3.238597 TCTGTTTGGGGCAAATTAAGCT 58.761 40.909 3.22 0.00 35.74 3.74
4302 7613 8.558973 AGATTTTTATGCCTATAGATGCTGAC 57.441 34.615 0.00 0.00 0.00 3.51
4336 7647 2.505982 CAGGTAGATGGCCGGGTG 59.494 66.667 2.18 0.00 0.00 4.61
4529 7840 7.174426 TCAGCTCTTTCCATATATCATTTGCAG 59.826 37.037 0.00 0.00 0.00 4.41
4537 7848 9.797642 TTCCATATATCATTTGCAGTCTACAAT 57.202 29.630 0.00 0.00 0.00 2.71
4722 8033 7.448588 TCATTACGTTTGCAATTCAATATGC 57.551 32.000 0.00 0.00 42.86 3.14
4872 8183 4.701956 AAGGTTATCATCTGCAAAACCG 57.298 40.909 0.00 0.00 43.49 4.44
4892 8203 2.987821 CGTCTCCTTTCCTTCGACTTTC 59.012 50.000 0.00 0.00 0.00 2.62
5054 8366 2.486727 GCCCAAAGGTAGGTAGTATGCC 60.487 54.545 0.00 0.00 36.82 4.40
5075 8387 2.265683 GTAGTCTCCGCTAAAAACCCG 58.734 52.381 0.00 0.00 0.00 5.28
5119 8435 2.541762 GTCTTCTCACGCTGGATAATGC 59.458 50.000 0.00 0.00 0.00 3.56
5232 8548 1.047596 AGGATGACGATCAGCTGCCT 61.048 55.000 9.47 3.95 32.54 4.75
5244 8560 2.282462 CTGCCTGTGTGGTTCCCC 60.282 66.667 0.00 0.00 38.35 4.81
5249 8565 1.479757 GCCTGTGTGGTTCCCCTTTTA 60.480 52.381 0.00 0.00 38.35 1.52
5253 8569 4.262420 CCTGTGTGGTTCCCCTTTTATTTG 60.262 45.833 0.00 0.00 0.00 2.32
5258 8574 4.591498 GTGGTTCCCCTTTTATTTGTCCTT 59.409 41.667 0.00 0.00 0.00 3.36
5261 8577 3.785364 TCCCCTTTTATTTGTCCTTGGG 58.215 45.455 0.00 0.00 0.00 4.12
5262 8578 2.236146 CCCCTTTTATTTGTCCTTGGGC 59.764 50.000 0.00 0.00 32.48 5.36
5267 8583 4.864704 TTTATTTGTCCTTGGGCACTTC 57.135 40.909 0.00 0.00 0.00 3.01
5291 8607 4.042809 TCTGTTATGTTGAGGGGTGAACAT 59.957 41.667 0.00 0.00 39.06 2.71
5353 8669 9.305555 GATAAATATGATATCCCCCATCCATTG 57.694 37.037 0.00 0.00 0.00 2.82
5403 8719 1.290203 CGACACATCGGCAAATAGCT 58.710 50.000 0.00 0.00 44.99 3.32
5452 8768 6.697019 ACTCGAAATTGAAGATGTTTGTTTGG 59.303 34.615 0.00 0.00 0.00 3.28
5455 8771 6.344936 CGAAATTGAAGATGTTTGTTTGGACG 60.345 38.462 0.00 0.00 0.00 4.79
5456 8772 5.766150 ATTGAAGATGTTTGTTTGGACGA 57.234 34.783 0.00 0.00 0.00 4.20
5460 8776 3.399330 AGATGTTTGTTTGGACGATCGT 58.601 40.909 22.97 22.97 0.00 3.73
5537 9012 6.291164 GCACGAAGAATCTTACATAACTCGTC 60.291 42.308 0.00 0.00 0.00 4.20
5563 9038 9.810545 CCTAAGTTTGACCAAATTTGTAGAAAA 57.189 29.630 16.73 8.88 33.31 2.29
5597 9072 6.519679 TCTACACTACCAAATTCTTAGCGA 57.480 37.500 0.00 0.00 0.00 4.93
5598 9073 6.561614 TCTACACTACCAAATTCTTAGCGAG 58.438 40.000 0.00 0.00 0.00 5.03
5611 9086 1.123077 TAGCGAGTACTCCCTCCGTA 58.877 55.000 17.23 0.00 0.00 4.02
5612 9087 0.254178 AGCGAGTACTCCCTCCGTAA 59.746 55.000 17.23 0.00 0.00 3.18
5613 9088 1.133853 AGCGAGTACTCCCTCCGTAAT 60.134 52.381 17.23 0.00 0.00 1.89
5615 9090 2.569059 CGAGTACTCCCTCCGTAATGA 58.431 52.381 17.23 0.00 0.00 2.57
5616 9091 2.947652 CGAGTACTCCCTCCGTAATGAA 59.052 50.000 17.23 0.00 0.00 2.57
5617 9092 3.379372 CGAGTACTCCCTCCGTAATGAAA 59.621 47.826 17.23 0.00 0.00 2.69
5618 9093 4.142315 CGAGTACTCCCTCCGTAATGAAAA 60.142 45.833 17.23 0.00 0.00 2.29
5619 9094 5.622914 CGAGTACTCCCTCCGTAATGAAAAA 60.623 44.000 17.23 0.00 0.00 1.94
5657 9687 8.959734 ACTTATGTTTCTTTAATACGGTTTGC 57.040 30.769 0.00 0.00 0.00 3.68
5660 9690 6.394025 TGTTTCTTTAATACGGTTTGCCTT 57.606 33.333 0.00 0.00 0.00 4.35
5661 9691 6.807789 TGTTTCTTTAATACGGTTTGCCTTT 58.192 32.000 0.00 0.00 0.00 3.11
5662 9692 7.266400 TGTTTCTTTAATACGGTTTGCCTTTT 58.734 30.769 0.00 0.00 0.00 2.27
5663 9693 7.764901 TGTTTCTTTAATACGGTTTGCCTTTTT 59.235 29.630 0.00 0.00 0.00 1.94
5687 9717 8.785329 TTTTTGAGGGAATTTATATGGTTTGC 57.215 30.769 0.00 0.00 0.00 3.68
5688 9718 6.478512 TTGAGGGAATTTATATGGTTTGCC 57.521 37.500 0.00 0.00 0.00 4.52
5689 9719 5.776358 TGAGGGAATTTATATGGTTTGCCT 58.224 37.500 6.24 6.24 41.87 4.75
5690 9720 6.201591 TGAGGGAATTTATATGGTTTGCCTT 58.798 36.000 7.50 0.00 39.64 4.35
5691 9721 6.671779 TGAGGGAATTTATATGGTTTGCCTTT 59.328 34.615 7.50 0.00 39.64 3.11
5692 9722 7.181845 TGAGGGAATTTATATGGTTTGCCTTTT 59.818 33.333 7.50 0.00 39.64 2.27
5693 9723 7.927788 AGGGAATTTATATGGTTTGCCTTTTT 58.072 30.769 0.00 0.00 36.63 1.94
5715 9745 4.866327 TTTTGAGGGGGATTTATACGGT 57.134 40.909 0.00 0.00 0.00 4.83
5716 9746 4.866327 TTTGAGGGGGATTTATACGGTT 57.134 40.909 0.00 0.00 0.00 4.44
5717 9747 4.866327 TTGAGGGGGATTTATACGGTTT 57.134 40.909 0.00 0.00 0.00 3.27
5718 9748 4.159244 TGAGGGGGATTTATACGGTTTG 57.841 45.455 0.00 0.00 0.00 2.93
5719 9749 2.882761 GAGGGGGATTTATACGGTTTGC 59.117 50.000 0.00 0.00 0.00 3.68
5720 9750 1.958579 GGGGGATTTATACGGTTTGCC 59.041 52.381 0.00 0.00 0.00 4.52
5721 9751 2.423803 GGGGGATTTATACGGTTTGCCT 60.424 50.000 0.00 0.00 0.00 4.75
5722 9752 2.621526 GGGGATTTATACGGTTTGCCTG 59.378 50.000 0.00 0.00 0.00 4.85
5723 9753 3.547746 GGGATTTATACGGTTTGCCTGA 58.452 45.455 0.00 0.00 0.00 3.86
5724 9754 3.949113 GGGATTTATACGGTTTGCCTGAA 59.051 43.478 0.00 0.00 0.00 3.02
5725 9755 4.399934 GGGATTTATACGGTTTGCCTGAAA 59.600 41.667 0.00 0.00 0.00 2.69
5726 9756 5.105675 GGGATTTATACGGTTTGCCTGAAAA 60.106 40.000 0.00 0.00 0.00 2.29
5727 9757 6.033966 GGATTTATACGGTTTGCCTGAAAAG 58.966 40.000 0.00 0.00 0.00 2.27
5728 9758 6.127842 GGATTTATACGGTTTGCCTGAAAAGA 60.128 38.462 0.00 0.00 0.00 2.52
5729 9759 5.873179 TTATACGGTTTGCCTGAAAAGAG 57.127 39.130 0.00 0.00 0.00 2.85
5764 9831 1.076339 TCCGGGCCCAATCAAATCC 60.076 57.895 24.92 0.00 0.00 3.01
5771 9839 1.269413 GCCCAATCAAATCCGATGCAG 60.269 52.381 0.00 0.00 0.00 4.41
5839 9907 0.473755 ACATCACCAGTTCACCAGCA 59.526 50.000 0.00 0.00 0.00 4.41
5871 9939 1.809547 GCCCAAACAAAGCTCTCTCTC 59.190 52.381 0.00 0.00 0.00 3.20
5872 9940 2.551938 GCCCAAACAAAGCTCTCTCTCT 60.552 50.000 0.00 0.00 0.00 3.10
5873 9941 3.072944 CCCAAACAAAGCTCTCTCTCTG 58.927 50.000 0.00 0.00 0.00 3.35
5919 10002 4.477975 CCGGTGTCTCGTCTCGCC 62.478 72.222 0.00 0.00 0.00 5.54
6066 10161 1.522580 CTTTCGCTGGGCTAGGAGC 60.523 63.158 0.00 0.00 41.46 4.70
6205 10330 1.461268 TGTGTGCTCTTCTCCCCCA 60.461 57.895 0.00 0.00 0.00 4.96
6219 10344 2.398554 CCCCACTTGCGTGATTCGG 61.399 63.158 0.00 0.00 43.97 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.809331 TGAAATTTTGCACACATGATCTCTTAC 59.191 33.333 0.00 0.00 0.00 2.34
1 2 7.884257 TGAAATTTTGCACACATGATCTCTTA 58.116 30.769 0.00 0.00 0.00 2.10
4 5 6.154445 ACTGAAATTTTGCACACATGATCTC 58.846 36.000 0.00 0.00 0.00 2.75
12 729 6.036953 TCCAAATCAACTGAAATTTTGCACAC 59.963 34.615 0.00 0.00 0.00 3.82
16 733 5.990996 TCCTCCAAATCAACTGAAATTTTGC 59.009 36.000 0.00 0.00 0.00 3.68
49 766 5.519722 CCAGTTTTTGTAAGCGAGTGATTT 58.480 37.500 0.00 0.00 0.00 2.17
59 776 9.447040 GTTCTTACTTAAGCCAGTTTTTGTAAG 57.553 33.333 1.29 0.00 37.81 2.34
119 836 8.731275 TTGATCTTTTTACTCTCAGTTTGACA 57.269 30.769 0.00 0.00 0.00 3.58
148 865 3.613299 CGTGGTTTAAAAACAAAGCGGTT 59.387 39.130 7.80 0.00 40.63 4.44
149 866 3.180613 CGTGGTTTAAAAACAAAGCGGT 58.819 40.909 7.80 0.00 40.63 5.68
181 898 8.475639 AGTTATTCATGTAAACCTCGACACTAT 58.524 33.333 0.00 0.00 0.00 2.12
182 899 7.833786 AGTTATTCATGTAAACCTCGACACTA 58.166 34.615 0.00 0.00 0.00 2.74
189 906 7.133133 TCCCCTAGTTATTCATGTAAACCTC 57.867 40.000 0.00 0.00 0.00 3.85
199 916 4.903149 TCCCTTGATCCCCTAGTTATTCA 58.097 43.478 0.00 0.00 0.00 2.57
227 944 0.940126 CTAGATGTTGGACGCCATGC 59.060 55.000 0.00 0.00 31.53 4.06
264 981 8.347004 TCTGTGCATTTTACTCCATAATTTCA 57.653 30.769 0.00 0.00 0.00 2.69
304 1021 6.870439 ACTGGTGGTTTTACGAGAGTTATAAC 59.130 38.462 7.57 7.57 46.40 1.89
306 1023 6.594788 ACTGGTGGTTTTACGAGAGTTATA 57.405 37.500 0.00 0.00 46.40 0.98
314 1031 6.320944 GTTTTGTAAACTGGTGGTTTTACGA 58.679 36.000 0.00 0.00 44.77 3.43
315 1032 5.227598 CGTTTTGTAAACTGGTGGTTTTACG 59.772 40.000 0.00 0.00 44.77 3.18
327 1044 4.345271 AAAGCGTCACGTTTTGTAAACT 57.655 36.364 11.55 0.00 38.67 2.66
349 1066 1.025812 TCAATTTTTCGGTGCGGTGT 58.974 45.000 0.00 0.00 0.00 4.16
401 1118 5.586243 CCAATTAGTGATGTCATCGAAACCT 59.414 40.000 8.29 2.16 0.00 3.50
408 1125 2.549754 CCGGCCAATTAGTGATGTCATC 59.450 50.000 2.24 5.83 0.00 2.92
409 1126 2.575532 CCGGCCAATTAGTGATGTCAT 58.424 47.619 2.24 0.00 0.00 3.06
410 1127 1.408127 CCCGGCCAATTAGTGATGTCA 60.408 52.381 2.24 0.00 0.00 3.58
411 1128 1.134220 TCCCGGCCAATTAGTGATGTC 60.134 52.381 2.24 0.00 0.00 3.06
412 1129 0.916086 TCCCGGCCAATTAGTGATGT 59.084 50.000 2.24 0.00 0.00 3.06
413 1130 1.308998 GTCCCGGCCAATTAGTGATG 58.691 55.000 2.24 0.00 0.00 3.07
414 1131 0.182775 GGTCCCGGCCAATTAGTGAT 59.817 55.000 2.24 0.00 0.00 3.06
415 1132 1.605453 GGTCCCGGCCAATTAGTGA 59.395 57.895 2.24 0.00 0.00 3.41
416 1133 1.817941 CGGTCCCGGCCAATTAGTG 60.818 63.158 2.24 0.00 35.56 2.74
417 1134 2.587889 CGGTCCCGGCCAATTAGT 59.412 61.111 2.24 0.00 35.56 2.24
418 1135 2.900337 GCGGTCCCGGCCAATTAG 60.900 66.667 2.24 0.00 40.19 1.73
435 1152 4.760047 CCAACTCGGCCCGACAGG 62.760 72.222 0.00 0.00 39.47 4.00
444 1161 0.598065 CCTTTTTCCTGCCAACTCGG 59.402 55.000 0.00 0.00 38.11 4.63
445 1162 1.001378 CACCTTTTTCCTGCCAACTCG 60.001 52.381 0.00 0.00 0.00 4.18
446 1163 1.269778 GCACCTTTTTCCTGCCAACTC 60.270 52.381 0.00 0.00 0.00 3.01
447 1164 0.752658 GCACCTTTTTCCTGCCAACT 59.247 50.000 0.00 0.00 0.00 3.16
448 1165 3.289128 GCACCTTTTTCCTGCCAAC 57.711 52.632 0.00 0.00 0.00 3.77
452 1169 0.681175 ATGTGGCACCTTTTTCCTGC 59.319 50.000 16.26 0.00 0.00 4.85
453 1170 3.614870 GCTTATGTGGCACCTTTTTCCTG 60.615 47.826 16.26 0.00 0.00 3.86
454 1171 2.562738 GCTTATGTGGCACCTTTTTCCT 59.437 45.455 16.26 0.00 0.00 3.36
455 1172 2.298729 TGCTTATGTGGCACCTTTTTCC 59.701 45.455 16.26 0.00 34.56 3.13
456 1173 3.658757 TGCTTATGTGGCACCTTTTTC 57.341 42.857 16.26 0.69 34.56 2.29
457 1174 4.414337 TTTGCTTATGTGGCACCTTTTT 57.586 36.364 16.26 0.00 39.55 1.94
458 1175 4.622260 ATTTGCTTATGTGGCACCTTTT 57.378 36.364 16.26 0.00 39.55 2.27
459 1176 4.040217 TGAATTTGCTTATGTGGCACCTTT 59.960 37.500 16.26 2.51 39.55 3.11
460 1177 3.577848 TGAATTTGCTTATGTGGCACCTT 59.422 39.130 16.26 5.25 39.55 3.50
461 1178 3.056607 GTGAATTTGCTTATGTGGCACCT 60.057 43.478 16.26 8.06 39.55 4.00
462 1179 3.056607 AGTGAATTTGCTTATGTGGCACC 60.057 43.478 16.26 0.00 39.55 5.01
463 1180 4.178545 AGTGAATTTGCTTATGTGGCAC 57.821 40.909 11.55 11.55 39.55 5.01
464 1181 4.523943 AGAAGTGAATTTGCTTATGTGGCA 59.476 37.500 0.00 0.00 37.97 4.92
465 1182 5.064441 AGAAGTGAATTTGCTTATGTGGC 57.936 39.130 0.00 0.00 0.00 5.01
466 1183 6.071728 AGGAAGAAGTGAATTTGCTTATGTGG 60.072 38.462 0.00 0.00 0.00 4.17
467 1184 6.917533 AGGAAGAAGTGAATTTGCTTATGTG 58.082 36.000 0.00 0.00 0.00 3.21
468 1185 6.944862 AGAGGAAGAAGTGAATTTGCTTATGT 59.055 34.615 0.00 0.00 0.00 2.29
469 1186 7.388460 AGAGGAAGAAGTGAATTTGCTTATG 57.612 36.000 0.00 0.00 0.00 1.90
470 1187 7.121907 GGAAGAGGAAGAAGTGAATTTGCTTAT 59.878 37.037 0.00 0.00 0.00 1.73
471 1188 6.431234 GGAAGAGGAAGAAGTGAATTTGCTTA 59.569 38.462 0.00 0.00 0.00 3.09
472 1189 5.242615 GGAAGAGGAAGAAGTGAATTTGCTT 59.757 40.000 0.00 0.00 0.00 3.91
481 1198 4.287326 AGGGTTTAGGAAGAGGAAGAAGTG 59.713 45.833 0.00 0.00 0.00 3.16
490 1207 3.590182 TGGGGTTTAGGGTTTAGGAAGAG 59.410 47.826 0.00 0.00 0.00 2.85
496 1213 6.673839 TCATTTTTGGGGTTTAGGGTTTAG 57.326 37.500 0.00 0.00 0.00 1.85
529 1276 7.271008 GCTTTGTTCAAGTTTTGTTTGGATTTG 59.729 33.333 0.00 0.00 34.56 2.32
547 1294 2.476997 GACCGAACTCAGAGCTTTGTTC 59.523 50.000 3.90 7.82 36.44 3.18
559 1306 2.265683 GTTTATGGACGGACCGAACTC 58.734 52.381 23.38 7.75 42.61 3.01
566 1313 8.493547 GCTATTAGTAATTGTTTATGGACGGAC 58.506 37.037 0.00 0.00 0.00 4.79
648 1395 6.609212 TCAAGAGAGCCTATGATAGTGTTTCT 59.391 38.462 0.00 0.00 0.00 2.52
658 1405 4.550669 TCCTTCATCAAGAGAGCCTATGA 58.449 43.478 0.00 0.00 0.00 2.15
700 1447 9.582431 GTAGATTCTTGTGCAACTTGTATACTA 57.418 33.333 4.17 0.00 38.04 1.82
702 1449 7.333423 TGGTAGATTCTTGTGCAACTTGTATAC 59.667 37.037 0.00 0.00 38.04 1.47
795 1542 9.780186 GAGCCAGGTATGTCTAGTATTTTATTT 57.220 33.333 0.00 0.00 0.00 1.40
796 1543 9.160412 AGAGCCAGGTATGTCTAGTATTTTATT 57.840 33.333 0.00 0.00 0.00 1.40
797 1544 8.728596 AGAGCCAGGTATGTCTAGTATTTTAT 57.271 34.615 0.00 0.00 0.00 1.40
798 1545 9.298250 CTAGAGCCAGGTATGTCTAGTATTTTA 57.702 37.037 8.25 0.00 35.67 1.52
799 1546 7.256012 GCTAGAGCCAGGTATGTCTAGTATTTT 60.256 40.741 14.17 0.00 40.40 1.82
800 1547 6.209788 GCTAGAGCCAGGTATGTCTAGTATTT 59.790 42.308 14.17 0.00 40.40 1.40
801 1548 5.712917 GCTAGAGCCAGGTATGTCTAGTATT 59.287 44.000 14.17 0.00 40.40 1.89
802 1549 5.222151 TGCTAGAGCCAGGTATGTCTAGTAT 60.222 44.000 14.17 0.00 40.40 2.12
803 1550 4.104261 TGCTAGAGCCAGGTATGTCTAGTA 59.896 45.833 14.17 9.75 40.40 1.82
804 1551 3.117474 TGCTAGAGCCAGGTATGTCTAGT 60.117 47.826 14.17 0.00 40.40 2.57
805 1552 3.491342 TGCTAGAGCCAGGTATGTCTAG 58.509 50.000 0.00 10.69 40.97 2.43
806 1553 3.595190 TGCTAGAGCCAGGTATGTCTA 57.405 47.619 0.00 0.00 41.18 2.59
807 1554 2.461300 TGCTAGAGCCAGGTATGTCT 57.539 50.000 0.00 0.00 41.18 3.41
808 1555 2.366916 ACATGCTAGAGCCAGGTATGTC 59.633 50.000 0.00 0.00 41.18 3.06
809 1556 2.402564 ACATGCTAGAGCCAGGTATGT 58.597 47.619 0.00 0.00 41.18 2.29
810 1557 3.482156 AACATGCTAGAGCCAGGTATG 57.518 47.619 0.00 0.00 41.18 2.39
811 1558 5.832539 ATTAACATGCTAGAGCCAGGTAT 57.167 39.130 0.00 0.00 41.18 2.73
812 1559 5.630415 AATTAACATGCTAGAGCCAGGTA 57.370 39.130 0.00 0.00 41.18 3.08
813 1560 4.510167 AATTAACATGCTAGAGCCAGGT 57.490 40.909 0.00 0.00 41.18 4.00
814 1561 5.841957 AAAATTAACATGCTAGAGCCAGG 57.158 39.130 0.00 0.00 41.18 4.45
815 1562 6.971184 CAGAAAAATTAACATGCTAGAGCCAG 59.029 38.462 0.00 0.00 41.18 4.85
816 1563 6.127647 CCAGAAAAATTAACATGCTAGAGCCA 60.128 38.462 0.00 0.00 41.18 4.75
817 1564 6.095440 TCCAGAAAAATTAACATGCTAGAGCC 59.905 38.462 0.00 0.00 41.18 4.70
818 1565 7.088589 TCCAGAAAAATTAACATGCTAGAGC 57.911 36.000 0.00 0.00 42.50 4.09
823 1570 9.558396 TTGAAAATCCAGAAAAATTAACATGCT 57.442 25.926 0.00 0.00 0.00 3.79
859 1606 9.760926 TCTATATACTTGTGAGCTGGAGATAAT 57.239 33.333 0.00 0.00 0.00 1.28
860 1607 9.237187 CTCTATATACTTGTGAGCTGGAGATAA 57.763 37.037 0.00 0.00 0.00 1.75
861 1608 7.338196 GCTCTATATACTTGTGAGCTGGAGATA 59.662 40.741 11.70 0.00 44.52 1.98
862 1609 6.152661 GCTCTATATACTTGTGAGCTGGAGAT 59.847 42.308 11.70 0.00 44.52 2.75
863 1610 5.475220 GCTCTATATACTTGTGAGCTGGAGA 59.525 44.000 11.70 0.00 44.52 3.71
864 1611 5.708948 GCTCTATATACTTGTGAGCTGGAG 58.291 45.833 11.70 0.00 44.52 3.86
865 1612 5.713792 GCTCTATATACTTGTGAGCTGGA 57.286 43.478 11.70 0.00 44.52 3.86
898 1645 8.687824 ACTTAACAGTAAAATAATGCACATGC 57.312 30.769 0.00 0.00 42.50 4.06
899 1646 9.838975 TGACTTAACAGTAAAATAATGCACATG 57.161 29.630 0.00 0.00 31.22 3.21
1270 2060 2.892305 GGATGAATCCGAGCTGACG 58.108 57.895 0.00 0.00 37.19 4.35
1297 2087 2.088763 CGCTACATATGCTCGGCGG 61.089 63.158 7.21 0.00 39.12 6.13
1326 2116 7.802117 TGTTCTAATCTAGGGGTAAAATCCTG 58.198 38.462 0.00 0.00 34.75 3.86
1354 2144 2.224402 GGGTTGATCTGGTGGCTCTATC 60.224 54.545 0.00 0.00 0.00 2.08
1382 2237 7.685155 GCATCAAATTAATCAGGCCACTGTAAT 60.685 37.037 5.01 0.44 45.14 1.89
1395 2250 7.043192 CCCAAAATCGAGTGCATCAAATTAATC 60.043 37.037 0.00 0.00 0.00 1.75
1408 2263 1.032114 GCCCCTCCCAAAATCGAGTG 61.032 60.000 0.00 0.00 0.00 3.51
1412 2270 1.754234 CAGGCCCCTCCCAAAATCG 60.754 63.158 0.00 0.00 34.51 3.34
1421 2279 2.054453 GTGGAAATGCAGGCCCCTC 61.054 63.158 0.00 0.00 0.00 4.30
1462 2320 0.539051 CATGGGAGGTGGACAGAGAC 59.461 60.000 0.00 0.00 0.00 3.36
1503 2365 1.737735 CTCGAGCACGCCATTGTCA 60.738 57.895 0.00 0.00 39.58 3.58
1552 2416 6.018433 ACACAAGGAGCATTAGGGATTATT 57.982 37.500 0.00 0.00 0.00 1.40
1678 2543 7.787935 CGCAGATGATAACGAAACAAAGTATAC 59.212 37.037 0.00 0.00 0.00 1.47
1683 2548 4.334443 CCGCAGATGATAACGAAACAAAG 58.666 43.478 0.00 0.00 0.00 2.77
1696 2561 1.667236 CCATAACTTGCCGCAGATGA 58.333 50.000 0.00 0.00 0.00 2.92
1707 2572 6.717289 TGCTTACTCATACAACCCATAACTT 58.283 36.000 0.00 0.00 0.00 2.66
1846 2723 4.566004 TCATCGAACTAAAACACCAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
1870 2760 6.770785 TGAAACAAGCAAGTACCAATAAGACT 59.229 34.615 0.00 0.00 0.00 3.24
1873 2763 8.641499 TTTTGAAACAAGCAAGTACCAATAAG 57.359 30.769 0.00 0.00 0.00 1.73
1875 2765 7.147811 ACCTTTTGAAACAAGCAAGTACCAATA 60.148 33.333 0.00 0.00 0.00 1.90
1878 2768 4.464597 ACCTTTTGAAACAAGCAAGTACCA 59.535 37.500 0.00 0.00 0.00 3.25
2055 2959 7.777095 TCAGTAAATTTGCAACAACTACCTTT 58.223 30.769 9.04 0.00 0.00 3.11
2303 3209 4.256920 ACATGGAGAAGAACCTCGAATTG 58.743 43.478 0.00 0.00 34.08 2.32
2309 3215 4.065789 ACGAAAACATGGAGAAGAACCTC 58.934 43.478 0.00 0.00 0.00 3.85
2312 3218 5.237779 TGGTAACGAAAACATGGAGAAGAAC 59.762 40.000 0.00 0.00 42.51 3.01
2352 3259 3.709653 ACACAAGGACAGGAAACTACTGA 59.290 43.478 0.00 0.00 40.21 3.41
2389 3296 1.700523 TAACACAACGGAATCGGTCG 58.299 50.000 0.00 0.00 41.39 4.79
2419 3488 3.640029 AGCATGAGCCAGGATTAATTTGG 59.360 43.478 13.05 13.05 43.56 3.28
2420 3489 4.340097 TCAGCATGAGCCAGGATTAATTTG 59.660 41.667 0.00 0.00 42.56 2.32
2421 3490 4.539726 TCAGCATGAGCCAGGATTAATTT 58.460 39.130 0.00 0.00 42.56 1.82
2498 3567 3.891422 TCATGCAATGGTTCAATTCCC 57.109 42.857 0.00 0.00 46.73 3.97
2605 3674 3.057806 CGCCGACCAAAAACCTAAGAAAT 60.058 43.478 0.00 0.00 0.00 2.17
2637 3707 4.163427 TCCTTTACATTTTGCCCATTGGA 58.837 39.130 3.62 0.00 0.00 3.53
2662 3732 3.247648 CCGATGTGGTTTCGATTATGTCC 59.752 47.826 0.00 0.00 38.88 4.02
2675 3745 5.825593 ACATTATTATCCTCCGATGTGGT 57.174 39.130 0.00 0.00 39.52 4.16
2705 3775 9.780413 GAATTGGATGAAAGAATTCTACAGAAC 57.220 33.333 8.75 7.44 36.80 3.01
2818 3891 1.126846 CTAGCAAGCAACGCACTGTAC 59.873 52.381 0.00 0.00 0.00 2.90
2860 3933 1.627329 TCTGAAGCAGAAGCAGTGGAT 59.373 47.619 0.00 0.00 45.49 3.41
3061 5707 8.398665 GTTAAGCTCATGGTAAACTTCCTATTG 58.601 37.037 0.00 0.00 0.00 1.90
3124 5935 2.315925 TTCAGAAATAGGCCTGAGCG 57.684 50.000 17.99 0.00 40.13 5.03
3157 5969 4.060038 ACATCGTGCAACTCCTAATAGG 57.940 45.455 0.00 0.00 36.46 2.57
3165 5977 0.234625 TGCGAAACATCGTGCAACTC 59.765 50.000 0.00 0.00 33.80 3.01
3166 5978 0.041312 GTGCGAAACATCGTGCAACT 60.041 50.000 0.00 0.00 39.34 3.16
3191 6494 8.629158 TGTACAATTGCAACTAAATCTTCTGTT 58.371 29.630 0.00 0.00 0.00 3.16
3234 6537 6.586344 ACTAAGTGGTGTCAATATCATCAGG 58.414 40.000 0.00 0.00 0.00 3.86
3301 6605 9.751542 GTTATATAGGCTGATATGTATGTCACC 57.248 37.037 0.00 0.00 0.00 4.02
3326 6630 4.199310 GTTGTCACATGGGCACATATAGT 58.801 43.478 0.00 0.00 34.99 2.12
3351 6655 8.514330 AAAATAACATCGGGCTCTAACATAAA 57.486 30.769 0.00 0.00 0.00 1.40
3364 6668 8.904099 AGAAATACCTCCTAAAATAACATCGG 57.096 34.615 0.00 0.00 0.00 4.18
3420 6724 0.320771 GCATATCGGGTACTGCCTGG 60.321 60.000 0.00 0.00 43.94 4.45
3476 6782 1.002502 GGTTGGGCTACAGGTGGAC 60.003 63.158 0.00 0.00 0.00 4.02
3727 7037 9.485206 GAAGATATTAAGCCAAAATGCATGAAT 57.515 29.630 0.00 0.00 0.00 2.57
3770 7080 6.419413 GCCAAAAATAACGAAACAGTGAATCA 59.581 34.615 0.00 0.00 0.00 2.57
3783 7094 6.826893 CATTTATGGAGGCCAAAAATAACG 57.173 37.500 5.01 0.00 36.95 3.18
3859 7170 9.791801 AGCTAAATATTTGGGTGTTGAAAATTT 57.208 25.926 14.53 0.00 0.00 1.82
3905 7216 3.070018 CCGAAAGCAGAGTTGAATCACT 58.930 45.455 0.00 0.00 0.00 3.41
4019 7330 8.566260 CCATGATTGATCTACTGAATTCTTTCC 58.434 37.037 7.05 0.00 0.00 3.13
4199 7510 1.399727 GGAACGACAATTCCAAGTGCG 60.400 52.381 0.00 0.00 46.49 5.34
4246 7557 4.156455 TGCCCCAAACAGATATCTTCTC 57.844 45.455 1.33 0.00 29.93 2.87
4276 7587 9.658799 GTCAGCATCTATAGGCATAAAAATCTA 57.341 33.333 0.00 0.00 33.96 1.98
4302 7613 2.230508 ACCTGCAAGAACATCATGCTTG 59.769 45.455 8.74 5.84 41.23 4.01
4336 7647 2.931320 GCCGTACATAGCAGCTAATCCC 60.931 54.545 6.13 0.00 0.00 3.85
4495 7806 3.393089 TGGAAAGAGCTGACTGAAGAC 57.607 47.619 0.00 0.00 0.00 3.01
4529 7840 7.391148 AATAACATGGTGACCAATTGTAGAC 57.609 36.000 9.06 0.00 36.95 2.59
4537 7848 4.397730 CGATCCAAATAACATGGTGACCAA 59.602 41.667 9.06 0.00 36.95 3.67
4603 7914 2.956333 GTTAGCAAAAGGTCCTTGGTGT 59.044 45.455 4.45 1.42 36.08 4.16
4713 8024 6.433716 TGTGACCTGAAAAGATGCATATTGAA 59.566 34.615 7.44 0.00 0.00 2.69
4722 8033 3.750130 CCAGACTGTGACCTGAAAAGATG 59.250 47.826 0.93 0.00 32.37 2.90
4872 8183 2.987821 CGAAAGTCGAAGGAAAGGAGAC 59.012 50.000 0.00 0.00 43.74 3.36
4892 8203 2.032860 AATGGAGGGGTCGCTCATCG 62.033 60.000 15.27 0.00 40.15 3.84
4947 8259 0.099082 CGGCTTCGAGTAGAGGTGAC 59.901 60.000 0.00 0.00 35.61 3.67
4950 8262 2.480100 GACGGCTTCGAGTAGAGGT 58.520 57.895 0.00 0.00 37.63 3.85
5054 8366 2.265683 GGGTTTTTAGCGGAGACTACG 58.734 52.381 1.58 1.58 0.00 3.51
5075 8387 4.326826 TGATCCAAACAATCAGGTGAGAC 58.673 43.478 0.00 0.00 0.00 3.36
5119 8435 5.710099 TCCCTAAGCATTGAAACCTACAAAG 59.290 40.000 0.00 0.00 0.00 2.77
5209 8525 2.471818 CAGCTGATCGTCATCCTTCAG 58.528 52.381 8.42 0.00 38.86 3.02
5210 8526 1.472201 GCAGCTGATCGTCATCCTTCA 60.472 52.381 20.43 0.00 0.00 3.02
5244 8560 4.871933 AGTGCCCAAGGACAAATAAAAG 57.128 40.909 0.00 0.00 0.00 2.27
5249 8565 2.108952 AGAGAAGTGCCCAAGGACAAAT 59.891 45.455 0.00 0.00 0.00 2.32
5253 8569 0.398318 ACAGAGAAGTGCCCAAGGAC 59.602 55.000 0.00 0.00 0.00 3.85
5258 8574 3.072330 TCAACATAACAGAGAAGTGCCCA 59.928 43.478 0.00 0.00 0.00 5.36
5261 8577 3.686726 CCCTCAACATAACAGAGAAGTGC 59.313 47.826 0.00 0.00 0.00 4.40
5262 8578 4.256920 CCCCTCAACATAACAGAGAAGTG 58.743 47.826 0.00 0.00 0.00 3.16
5267 8583 3.981071 TCACCCCTCAACATAACAGAG 57.019 47.619 0.00 0.00 0.00 3.35
5330 8646 6.899075 CACAATGGATGGGGGATATCATATTT 59.101 38.462 4.83 0.00 0.00 1.40
5353 8669 0.037975 CTTTGTCAGCAATGGGGCAC 60.038 55.000 0.00 0.00 34.18 5.01
5401 8717 9.638239 TTCAACATATATTCAAAGTTTGGAAGC 57.362 29.630 15.47 0.00 0.00 3.86
5421 8737 6.618287 ACATCTTCAATTTCGAGTTCAACA 57.382 33.333 0.00 0.00 0.00 3.33
5424 8740 7.026631 ACAAACATCTTCAATTTCGAGTTCA 57.973 32.000 0.00 0.00 0.00 3.18
5432 8748 6.568869 TCGTCCAAACAAACATCTTCAATTT 58.431 32.000 0.00 0.00 0.00 1.82
5455 8771 5.751990 ACTTAATAAACCGATCACCACGATC 59.248 40.000 0.00 0.00 46.19 3.69
5456 8772 5.522460 CACTTAATAAACCGATCACCACGAT 59.478 40.000 0.00 0.00 36.91 3.73
5460 8776 6.231951 TCAACACTTAATAAACCGATCACCA 58.768 36.000 0.00 0.00 0.00 4.17
5476 8792 4.877378 ATCCATGCAACAATCAACACTT 57.123 36.364 0.00 0.00 0.00 3.16
5537 9012 9.810545 TTTTCTACAAATTTGGTCAAACTTAGG 57.189 29.630 21.74 0.00 32.51 2.69
5594 9069 1.001597 CATTACGGAGGGAGTACTCGC 60.002 57.143 27.68 27.68 42.14 5.03
5595 9070 2.569059 TCATTACGGAGGGAGTACTCG 58.431 52.381 16.56 8.02 38.39 4.18
5596 9071 4.996788 TTTCATTACGGAGGGAGTACTC 57.003 45.455 14.87 14.87 36.76 2.59
5597 9072 5.750352 TTTTTCATTACGGAGGGAGTACT 57.250 39.130 0.00 0.00 0.00 2.73
5662 9692 7.826744 GGCAAACCATATAAATTCCCTCAAAAA 59.173 33.333 0.00 0.00 35.26 1.94
5663 9693 7.181845 AGGCAAACCATATAAATTCCCTCAAAA 59.818 33.333 0.00 0.00 39.06 2.44
5664 9694 6.671779 AGGCAAACCATATAAATTCCCTCAAA 59.328 34.615 0.00 0.00 39.06 2.69
5665 9695 6.201591 AGGCAAACCATATAAATTCCCTCAA 58.798 36.000 0.00 0.00 39.06 3.02
5666 9696 5.776358 AGGCAAACCATATAAATTCCCTCA 58.224 37.500 0.00 0.00 39.06 3.86
5667 9697 6.731292 AAGGCAAACCATATAAATTCCCTC 57.269 37.500 0.00 0.00 39.06 4.30
5693 9723 5.195848 ACCGTATAAATCCCCCTCAAAAA 57.804 39.130 0.00 0.00 0.00 1.94
5696 9726 4.528920 CAAACCGTATAAATCCCCCTCAA 58.471 43.478 0.00 0.00 0.00 3.02
5697 9727 3.686120 GCAAACCGTATAAATCCCCCTCA 60.686 47.826 0.00 0.00 0.00 3.86
5698 9728 2.882761 GCAAACCGTATAAATCCCCCTC 59.117 50.000 0.00 0.00 0.00 4.30
5699 9729 2.423803 GGCAAACCGTATAAATCCCCCT 60.424 50.000 0.00 0.00 0.00 4.79
5700 9730 1.958579 GGCAAACCGTATAAATCCCCC 59.041 52.381 0.00 0.00 0.00 5.40
5701 9731 2.621526 CAGGCAAACCGTATAAATCCCC 59.378 50.000 0.00 0.00 42.76 4.81
5702 9732 3.547746 TCAGGCAAACCGTATAAATCCC 58.452 45.455 0.00 0.00 42.76 3.85
5703 9733 5.570234 TTTCAGGCAAACCGTATAAATCC 57.430 39.130 0.00 0.00 42.76 3.01
5704 9734 6.848451 TCTTTTCAGGCAAACCGTATAAATC 58.152 36.000 0.00 0.00 42.76 2.17
5705 9735 6.657541 TCTCTTTTCAGGCAAACCGTATAAAT 59.342 34.615 0.00 0.00 42.76 1.40
5706 9736 5.998981 TCTCTTTTCAGGCAAACCGTATAAA 59.001 36.000 0.00 0.00 42.76 1.40
5707 9737 5.553123 TCTCTTTTCAGGCAAACCGTATAA 58.447 37.500 0.00 0.00 42.76 0.98
5708 9738 5.155278 TCTCTTTTCAGGCAAACCGTATA 57.845 39.130 0.00 0.00 42.76 1.47
5709 9739 4.015872 TCTCTTTTCAGGCAAACCGTAT 57.984 40.909 0.00 0.00 42.76 3.06
5710 9740 3.478857 TCTCTTTTCAGGCAAACCGTA 57.521 42.857 0.00 0.00 42.76 4.02
5711 9741 2.341846 TCTCTTTTCAGGCAAACCGT 57.658 45.000 0.00 0.00 42.76 4.83
5712 9742 3.708563 TTTCTCTTTTCAGGCAAACCG 57.291 42.857 0.00 0.00 42.76 4.44
5749 9779 0.675633 CATCGGATTTGATTGGGCCC 59.324 55.000 17.59 17.59 0.00 5.80
5753 9783 1.598676 CGCTGCATCGGATTTGATTGG 60.599 52.381 1.09 0.00 0.00 3.16
5813 9881 3.605749 AACTGGTGATGTCGGGCCG 62.606 63.158 22.51 22.51 0.00 6.13
5858 9926 2.008045 GCAGCCAGAGAGAGAGCTTTG 61.008 57.143 0.00 0.00 31.93 2.77


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

AutoCloner maintained by Alex Coulton.