Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 1 of 144
Found at i:16 original size:7 final size:7
Alignment explanation
Indices: 5--3244 Score: 5104
Period size: 7 Copynumber: 468.4 Consensus size: 7
1 CTAA
5 CCTAAAC
1 CCTAAAC
12 CCTAAAC
1 CCTAAAC
19 CCTAAAC
1 CCTAAAC
26 CCTAAAC
1 CCTAAAC
33 CCTAAAC
1 CCTAAAC
40 CCTAAAC
1 CCTAAAC
47 CCTAAA-
1 CCTAAAC
53 CCTAAAC
1 CCTAAAC
60 CCTAAAC
1 CCTAAAC
*
67 CCTAAAA
1 CCTAAAC
74 CCTAAAC
1 CCTAAAC
81 CCTAAAC
1 CCTAAAC
88 CCTAAAC
1 CCTAAAC
95 CCT-AAC
1 CCTAAAC
101 CCTAAA-
1 CCTAAAC
107 CCTAAAC
1 CCTAAAC
114 CCTAAAC
1 CCTAAAC
121 CCTAAAC
1 CCTAAAC
128 CCTTAAAC
1 CC-TAAAC
136 CCTAAAC
1 CCTAAAC
143 CCTAAAC
1 CCTAAAC
150 CCTAAAC
1 CCTAAAC
157 CCTAAAC
1 CCTAAAC
164 CCT-AAC
1 CCTAAAC
170 CCTAAA-
1 CCTAAAC
176 CCTAAAC
1 CCTAAAC
183 CCTAAAC
1 CCTAAAC
190 CCTAAAC
1 CCTAAAC
197 CCTAAAC
1 CCTAAAC
204 CCTAAAC
1 CCTAAAC
211 CCTAAAC
1 CCTAAAC
218 CCTAAAC
1 CCTAAAC
225 CCTAAAC
1 CCTAAAC
232 CCTAAA-
1 CCTAAAC
238 CCTAAA-
1 CCTAAAC
244 CCTAAAC
1 CCTAAAC
251 CCTAAAC
1 CCTAAAC
258 CCTAAAC
1 CCTAAAC
265 CCTAAAC
1 CCTAAAC
272 CCTAAAC
1 CCTAAAC
279 CCT-AAC
1 CCTAAAC
285 CCTAAA-
1 CCTAAAC
291 CCTAAAC
1 CCTAAAC
298 CCTAAAC
1 CCTAAAC
305 CCTAAAC
1 CCTAAAC
312 CCT-AAC
1 CCTAAAC
318 CCTAAAC
1 CCTAAAC
325 CCTAAAC
1 CCTAAAC
332 CCTAAAC
1 CCTAAAC
339 CCTAAAC
1 CCTAAAC
346 CCTAAAC
1 CCTAAAC
353 CCTAAAC
1 CCTAAAC
360 CCTAAAC
1 CCTAAAC
367 CCTAAAC
1 CCTAAAC
374 CCTAAAC
1 CCTAAAC
381 CCTAAAC
1 CCTAAAC
388 CCTAAAC
1 CCTAAAC
395 CCTAAAC
1 CCTAAAC
402 CCTAAA-
1 CCTAAAC
*
408 CCAAAAC
1 CCTAAAC
415 CCTAAA-
1 CCTAAAC
421 CCTAAAC
1 CCTAAAC
428 CCTAAAC
1 CCTAAAC
435 CCTAAACC
1 CCTAAA-C
443 CCTAAAC
1 CCTAAAC
450 CCTAAAC
1 CCTAAAC
457 CCTAAAC
1 CCTAAAC
464 CCTAAAC
1 CCTAAAC
471 CCTAAAC
1 CCTAAAC
478 CCT-AAC
1 CCTAAAC
484 CCTAAAC
1 CCTAAAC
491 CCTAAAC
1 CCTAAAC
498 CCTAAAC
1 CCTAAAC
505 CCTAAAC
1 CCTAAAC
512 CCTAAAC
1 CCTAAAC
519 CCTAAAC
1 CCTAAAC
526 CCTAAAC
1 CCTAAAC
533 CCT-AA-
1 CCTAAAC
538 CCTAAACC
1 CCTAAA-C
546 CCTAAAC
1 CCTAAAC
553 CCTAAA-
1 CCTAAAC
559 CCT-AAC
1 CCTAAAC
565 CCTAAAC
1 CCTAAAC
572 CCTAAAC
1 CCTAAAC
579 CCTAAAAC
1 CCT-AAAC
587 CCTAAAC
1 CCTAAAC
594 CCTAAAC
1 CCTAAAC
601 CCTAAAC
1 CCTAAAC
608 CCTAAAC
1 CCTAAAC
615 CCTTAAA-
1 CC-TAAAC
622 CCTAAAC
1 CCTAAAC
629 CCTAAAC
1 CCTAAAC
636 CCTAAA-
1 CCTAAAC
642 CCTAAAC
1 CCTAAAC
649 CCTAAAC
1 CCTAAAC
656 CCTAAAC
1 CCTAAAC
663 CCTAAAC
1 CCTAAAC
670 CCTAAAAC
1 CCT-AAAC
678 CCTAAAC
1 CCTAAAC
685 CCTAAAC
1 CCTAAAC
692 CCTAAAC
1 CCTAAAC
699 CCT-AAC
1 CCTAAAC
705 CCTAAAC
1 CCTAAAC
712 CCTAAAC
1 CCTAAAC
719 CCTAAAC
1 CCTAAAC
726 CCTAAAC
1 CCTAAAC
733 CCTAAAC
1 CCTAAAC
740 CCTAAAC
1 CCTAAAC
747 CCTAAA-
1 CCTAAAC
753 CCTAAAAC
1 CCT-AAAC
761 CCTAAAC
1 CCTAAAC
768 CCT-AAC
1 CCTAAAC
774 CCTAAAC
1 CCTAAAC
781 CCTAAAC
1 CCTAAAC
788 CCTAAAC
1 CCTAAAC
795 CCTAAAC
1 CCTAAAC
802 CCT-AAC
1 CCTAAAC
808 CCTAAAC
1 CCTAAAC
815 CCTAAAC
1 CCTAAAC
822 CCTAAAAC
1 CCT-AAAC
830 CCTAAA-
1 CCTAAAC
836 CCT-AAC
1 CCTAAAC
842 CCTAAAC
1 CCTAAAC
849 CCTAAAC
1 CCTAAAC
856 CCTAAAC
1 CCTAAAC
863 CCTAAAC
1 CCTAAAC
870 CCT-AAC
1 CCTAAAC
876 CCTAAAC
1 CCTAAAC
883 CCTTAAAC
1 CC-TAAAC
*
891 CCTAAAA
1 CCTAAAC
898 CCTAAAC
1 CCTAAAC
905 CCTAAAC
1 CCTAAAC
912 CCTAAAC
1 CCTAAAC
919 CCTAAAC
1 CCTAAAC
926 CCTAAAC
1 CCTAAAC
933 CCTAAAC
1 CCTAAAC
940 CCTAAAC
1 CCTAAAC
947 CCTAAA-
1 CCTAAAC
953 CCTAAAC
1 CCTAAAC
960 CCTAAAC
1 CCTAAAC
967 CCTAAA-
1 CCTAAAC
973 CCTAAAC
1 CCTAAAC
980 CCTAAAC
1 CCTAAAC
*
987 CCTAAAA
1 CCTAAAC
994 CCTAAAC
1 CCTAAAC
1001 CCTAAAC
1 CCTAAAC
1008 CCTAAAC
1 CCTAAAC
1015 CCTAAAC
1 CCTAAAC
1022 CCTAAAC
1 CCTAAAC
1029 CCTAAAC
1 CCTAAAC
1036 CCTAAAC
1 CCTAAAC
1043 CCTAAAC
1 CCTAAAC
1050 CCTAAAC
1 CCTAAAC
1057 CCTAAAC
1 CCTAAAC
1064 CCTAAAAC
1 CCT-AAAC
1072 CCTAAAC
1 CCTAAAC
1079 CCTAAAC
1 CCTAAAC
1086 CCTAAA-
1 CCTAAAC
1092 CCT-AAC
1 CCTAAAC
1098 CCTAAAC
1 CCTAAAC
1105 CCTAAAC
1 CCTAAAC
1112 CCTAAAC
1 CCTAAAC
1119 CCTAAACCC
1 CCTAAA--C
1128 CCTAAAC
1 CCTAAAC
1135 CCTAAAC
1 CCTAAAC
1142 CCTAAAC
1 CCTAAAC
1149 CCTAAAC
1 CCTAAAC
1156 CCTAAA-
1 CCTAAAC
1162 CCTAAAC
1 CCTAAAC
1169 CCTAAAC
1 CCTAAAC
1176 CCTAAAC
1 CCTAAAC
1183 CCTAAAC
1 CCTAAAC
1190 CCTAAAC
1 CCTAAAC
1197 CCTAAA-
1 CCTAAAC
1203 CCTAAAC
1 CCTAAAC
1210 CCTAAA-
1 CCTAAAC
1216 CCTAAAAC
1 CCT-AAAC
1224 CCT-AAC
1 CCTAAAC
1230 CCT-AAC
1 CCTAAAC
1236 CCTAAAC
1 CCTAAAC
1243 CCTAAAC
1 CCTAAAC
1250 CCTAAACC
1 CCTAAA-C
1258 CCTAAAC
1 CCTAAAC
1265 CCTAAAC
1 CCTAAAC
1272 CCTAAAC
1 CCTAAAC
1279 CCTAAAC
1 CCTAAAC
1286 CCTAAAC
1 CCTAAAC
1293 CCTAAAC
1 CCTAAAC
1300 CCTAAAC
1 CCTAAAC
1307 CCTAAAC
1 CCTAAAC
1314 CCTAAA-
1 CCTAAAC
1320 CCTAAAC
1 CCTAAAC
1327 CCTAAAC
1 CCTAAAC
1334 CCTAAAC
1 CCTAAAC
1341 CCTAAAC
1 CCTAAAC
1348 CCTAAAC
1 CCTAAAC
1355 CCT-AAC
1 CCTAAAC
1361 CCTAAAC
1 CCTAAAC
1368 CCTAAA-
1 CCTAAAC
1374 CCTAAA-
1 CCTAAAC
1380 CCTAAAC
1 CCTAAAC
1387 CCTAAAC
1 CCTAAAC
1394 CCTAAAC
1 CCTAAAC
1401 CCTAAAC
1 CCTAAAC
1408 CCT-AAC
1 CCTAAAC
1414 CCTAAAC
1 CCTAAAC
1421 CCTAAAC
1 CCTAAAC
1428 CCTAAACC
1 CCTAAA-C
1436 CCTAAAC
1 CCTAAAC
1443 CC-AAAC
1 CCTAAAC
1449 CCT-AAC
1 CCTAAAC
1455 CCTAAAC
1 CCTAAAC
1462 CCTAAAC
1 CCTAAAC
1469 CCTAAAC
1 CCTAAAC
1476 CCT-AA-
1 CCTAAAC
1481 CCTAAAC
1 CCTAAAC
1488 CCTAAA-
1 CCTAAAC
1494 CCTAAAC
1 CCTAAAC
1501 CCTAAAC
1 CCTAAAC
1508 CCTAAAC
1 CCTAAAC
1515 CCTAAAC
1 CCTAAAC
1522 CCT-AAC
1 CCTAAAC
1528 CCTAAAC
1 CCTAAAC
1535 CCTAAAC
1 CCTAAAC
1542 CCTAAAC
1 CCTAAAC
1549 CCTAAAC
1 CCTAAAC
1556 CCTAAA-
1 CCTAAAC
1562 CCTAAAC
1 CCTAAAC
1569 CCTAAAC
1 CCTAAAC
1576 CCT-AAC
1 CCTAAAC
1582 CCTAAAC
1 CCTAAAC
1589 CCTAAAC
1 CCTAAAC
1596 CCTAAAC
1 CCTAAAC
1603 CCTAAAC
1 CCTAAAC
1610 CCTAAAC
1 CCTAAAC
1617 CCTAAA-
1 CCTAAAC
1623 CCTAAAC
1 CCTAAAC
1630 CCTAAA-
1 CCTAAAC
1636 CCTAAAC
1 CCTAAAC
1643 CCTAAAC
1 CCTAAAC
1650 CCTAAAC
1 CCTAAAC
1657 CCTAAAC
1 CCTAAAC
1664 CCTAAAC
1 CCTAAAC
1671 CCTAAA-
1 CCTAAAC
1677 CCTAAACCC
1 CCTAAA--C
1686 CCTAAAC
1 CCTAAAC
1693 CCTAAAC
1 CCTAAAC
1700 CCTAAAC
1 CCTAAAC
1707 CCTAAA-
1 CCTAAAC
1713 CCTAAAC
1 CCTAAAC
1720 CCTAAAC
1 CCTAAAC
1727 CCTAAAC
1 CCTAAAC
1734 CCTAAAC
1 CCTAAAC
1741 CCTAAAC
1 CCTAAAC
1748 CCTAAAC
1 CCTAAAC
1755 CCTAAAC
1 CCTAAAC
1762 CCTAAAC
1 CCTAAAC
1769 CCTAAAC
1 CCTAAAC
1776 CCTAAAC
1 CCTAAAC
1783 CCTAAAC
1 CCTAAAC
1790 CCTAAAC
1 CCTAAAC
1797 CCTAAAC
1 CCTAAAC
1804 CCTAAAC
1 CCTAAAC
1811 CCTAAAC
1 CCTAAAC
1818 CCTAAAC
1 CCTAAAC
1825 CCTAAAC
1 CCTAAAC
1832 CCTAAAC
1 CCTAAAC
1839 CCTAAAC
1 CCTAAAC
1846 CCTAAAC
1 CCTAAAC
1853 CCTAAAC
1 CCTAAAC
1860 CCTAAAC
1 CCTAAAC
1867 CCTAAAC
1 CCTAAAC
1874 CCTAAAC
1 CCTAAAC
1881 CCTAAAC
1 CCTAAAC
1888 CCTAAAC
1 CCTAAAC
1895 CCTAAAC
1 CCTAAAC
1902 CCTAAAC
1 CCTAAAC
1909 CCTAAAC
1 CCTAAAC
1916 CCTAAAC
1 CCTAAAC
1923 CCTAAAC
1 CCTAAAC
1930 CCTAAAC
1 CCTAAAC
1937 CCTAAAC
1 CCTAAAC
1944 CCTAAAC
1 CCTAAAC
1951 CCTAAAC
1 CCTAAAC
1958 CCTAAAC
1 CCTAAAC
1965 CCTAAAC
1 CCTAAAC
1972 CCTAAAC
1 CCTAAAC
1979 CCTAAAC
1 CCTAAAC
1986 CCTAAAC
1 CCTAAAC
1993 CCTAAAC
1 CCTAAAC
2000 CCTAAAC
1 CCTAAAC
2007 CCTAAAC
1 CCTAAAC
2014 CCTAAAC
1 CCTAAAC
2021 CCTAAAC
1 CCTAAAC
2028 CCTAAAC
1 CCTAAAC
2035 CCTAAA-
1 CCTAAAC
2041 CCTAAAC
1 CCTAAAC
2048 CCTAAAC
1 CCTAAAC
2055 CCTAAAC
1 CCTAAAC
2062 CCTAAAC
1 CCTAAAC
2069 CCTAAAC
1 CCTAAAC
2076 CCTAAAC
1 CCTAAAC
2083 CCTAAAC
1 CCTAAAC
2090 CCTAAAC
1 CCTAAAC
2097 CCTAAAC
1 CCTAAAC
2104 CCTAAAC
1 CCTAAAC
2111 CCTAAAAAAC
1 CCT---AAAC
2121 CCTAAAC
1 CCTAAAC
2128 CCTAAAC
1 CCTAAAC
2135 CCTAAAC
1 CCTAAAC
2142 CCTAAAC
1 CCTAAAC
2149 CCTAAAC
1 CCTAAAC
2156 CCTAAA-
1 CCTAAAC
2162 CCTAAAC
1 CCTAAAC
2169 CCTAAA-
1 CCTAAAC
2175 CCTAAAC
1 CCTAAAC
2182 CCTAAAC
1 CCTAAAC
2189 CCTAAAC
1 CCTAAAC
2196 CCTAAAC
1 CCTAAAC
2203 CCTAAAC
1 CCTAAAC
2210 CCTAAAC
1 CCTAAAC
2217 CCTAAAC
1 CCTAAAC
2224 CCTAAAC
1 CCTAAAC
2231 CCTAAAC
1 CCTAAAC
2238 CCTAAAC
1 CCTAAAC
2245 CCTAAAC
1 CCTAAAC
2252 CCT-AAC
1 CCTAAAC
2258 CCTAAAC
1 CCTAAAC
2265 CCTAAAC
1 CCTAAAC
2272 CCTAAAC
1 CCTAAAC
2279 CCTAAAC
1 CCTAAAC
2286 CCTAAAC
1 CCTAAAC
2293 CCTAAAC
1 CCTAAAC
2300 CCTAAAC
1 CCTAAAC
2307 CCTAAAC
1 CCTAAAC
2314 CCTAAAC
1 CCTAAAC
2321 CCTAAAC
1 CCTAAAC
2328 CCTAAAC
1 CCTAAAC
2335 CCTAAAC
1 CCTAAAC
2342 CCTAAAC
1 CCTAAAC
2349 CCTAAAC
1 CCTAAAC
2356 CCTAAAC
1 CCTAAAC
2363 CCTAAAC
1 CCTAAAC
2370 CCT-AAC
1 CCTAAAC
2376 CCTAAAC
1 CCTAAAC
2383 CCTAAAC
1 CCTAAAC
2390 CCT-AAC
1 CCTAAAC
2396 CCTAAAC
1 CCTAAAC
2403 CCTAAAC
1 CCTAAAC
2410 CCTAAAC
1 CCTAAAC
2417 CCTAAAC
1 CCTAAAC
2424 CCTAAAC
1 CCTAAAC
2431 CCTAAAC
1 CCTAAAC
2438 CCTAAAC
1 CCTAAAC
2445 CCTAAAC
1 CCTAAAC
2452 CCTAAAC
1 CCTAAAC
2459 CCTAAAC
1 CCTAAAC
2466 CCTAAAC
1 CCTAAAC
2473 CCTAAAC
1 CCTAAAC
2480 CCTAAAC
1 CCTAAAC
2487 CCTAAAC
1 CCTAAAC
2494 CCTAAAC
1 CCTAAAC
2501 CCTAAAC
1 CCTAAAC
2508 CCTAAAC
1 CCTAAAC
2515 CCTAAAC
1 CCTAAAC
2522 CCT-AAC
1 CCTAAAC
2528 CCTAAAC
1 CCTAAAC
*
2535 CCTAAAA
1 CCTAAAC
2542 CCTAAAC
1 CCTAAAC
2549 CCTAAAC
1 CCTAAAC
2556 CCTAAAC
1 CCTAAAC
2563 CCTAAAC
1 CCTAAAC
2570 CCTAAAC
1 CCTAAAC
2577 CCTAAAC
1 CCTAAAC
2584 CCTAAAC
1 CCTAAAC
2591 CCTAAAC
1 CCTAAAC
2598 CCTAAAC
1 CCTAAAC
2605 CCTAAAC
1 CCTAAAC
2612 CCTAAAC
1 CCTAAAC
2619 CCTAAAC
1 CCTAAAC
2626 CCTAAAC
1 CCTAAAC
2633 CCTAAAC
1 CCTAAAC
2640 CCTAAAC
1 CCTAAAC
2647 CCTAAAC
1 CCTAAAC
2654 CCTAAAC
1 CCTAAAC
2661 CCTAAAC
1 CCTAAAC
*
2668 CCTAAGC
1 CCTAAAC
*
2675 CCTAAGC
1 CCTAAAC
*
2682 CCTAAGC
1 CCTAAAC
*
2689 CCTAAGC
1 CCTAAAC
*
2696 CCTAAGC
1 CCTAAAC
*
2703 CCTAAGC
1 CCTAAAC
*
2710 CCTAAGC
1 CCTAAAC
*
2717 CCTAAGC
1 CCTAAAC
*
2724 CCTAAGC
1 CCTAAAC
*
2731 CCTAAGC
1 CCTAAAC
*
2738 CCTAAGC
1 CCTAAAC
*
2745 CCTAAGC
1 CCTAAAC
*
2752 CCTAAGC
1 CCTAAAC
*
2759 CCTAAGC
1 CCTAAAC
*
2766 CCTAAGC
1 CCTAAAC
*
2773 CCTAAGC
1 CCTAAAC
*
2780 CCTAAGC
1 CCTAAAC
*
2787 CCTAAGC
1 CCTAAAC
*
2794 CCTAAGC
1 CCTAAAC
*
2801 CCTAAGC
1 CCTAAAC
*
2808 CCTAAGC
1 CCTAAAC
*
2815 CCTAAGC
1 CCTAAAC
*
2822 CCTAAGC
1 CCTAAAC
*
2829 CCTAAGC
1 CCTAAAC
*
2836 CCTAAGC
1 CCTAAAC
*
2843 CCTAAGC
1 CCTAAAC
*
2850 CCTAAGC
1 CCTAAAC
*
2857 CCTAAGC
1 CCTAAAC
*
2864 CCTAAGC
1 CCTAAAC
*
2871 CCTAAGC
1 CCTAAAC
*
2878 CCTAAGC
1 CCTAAAC
*
2885 CCTAAGC
1 CCTAAAC
*
2892 CCTAAGC
1 CCTAAAC
*
2899 CCTAAGC
1 CCTAAAC
*
2906 CCTAAGC
1 CCTAAAC
*
2913 CCTAAGC
1 CCTAAAC
*
2920 CCTAAGC
1 CCTAAAC
*
2927 CCTAAGC
1 CCTAAAC
*
2934 CCTAAGC
1 CCTAAAC
*
2941 CCTAAGC
1 CCTAAAC
*
2948 CCTAAGC
1 CCTAAAC
*
2955 CCTAAGC
1 CCTAAAC
*
2962 CCTAAGC
1 CCTAAAC
*
2969 CCTAAGC
1 CCTAAAC
*
2976 CCTAAGC
1 CCTAAAC
*
2983 CCTAAGC
1 CCTAAAC
*
2990 CCTAAGC
1 CCTAAAC
*
2997 CCTAAGC
1 CCTAAAC
*
3004 CCTAAGC
1 CCTAAAC
*
3011 CCTAAGC
1 CCTAAAC
*
3018 CCTAAGC
1 CCTAAAC
*
3025 CCTAAGC
1 CCTAAAC
*
3032 CCTAAGC
1 CCTAAAC
*
3039 CCTAAGC
1 CCTAAAC
*
3046 CCTAAGC
1 CCTAAAC
*
3053 CCTAAGC
1 CCTAAAC
*
3060 CCTAAGC
1 CCTAAAC
*
3067 CCTAAGC
1 CCTAAAC
*
3074 CCTAAGC
1 CCTAAAC
*
3081 CCTAAGC
1 CCTAAAC
*
3088 CCTAAGC
1 CCTAAAC
*
3095 CCTAAGC
1 CCTAAAC
*
3102 CCTAAGC
1 CCTAAAC
*
3109 CCTAAGC
1 CCTAAAC
*
3116 CCTAAGC
1 CCTAAAC
*
3123 CCTAAGC
1 CCTAAAC
*
3130 CCTAAGC
1 CCTAAAC
*
3137 CCTAAGC
1 CCTAAAC
*
3144 CCTAAGC
1 CCTAAAC
*
3151 CCTAAGC
1 CCTAAAC
*
3158 CCTAAGC
1 CCTAAAC
*
3165 CCTAAGC
1 CCTAAAC
*
3172 CCTAAGC
1 CCTAAAC
*
3179 CCTAAGC
1 CCTAAAC
*
3186 CCTAAGC
1 CCTAAAC
*
3193 CCTAAGC
1 CCTAAAC
*
3200 CCTAAGC
1 CCTAAAC
*
3207 CCTAAGC
1 CCTAAAC
*
3214 CCTAAGC
1 CCTAAAC
*
3221 CCTAAGC
1 CCTAAAC
*
3228 CCTAAGC
1 CCTAAAC
*
3235 CCTAAGC
1 CCTAAAC
3242 CCT
1 CCT
3245 GAGCCCTGAG
Statistics
Matches: 3146, Mismatches: 11, Indels: 152
0.95 0.00 0.05
Matches are distributed among these distances:
5 12 0.00
6 311 0.10
7 2724 0.87
8 79 0.03
9 13 0.00
10 7 0.00
ACGTcount: A:0.40, C:0.42, G:0.03, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:3440 original size:7 final size:7
Alignment explanation
Indices: 2667--3582 Score: 905
Period size: 7 Copynumber: 130.9 Consensus size: 7
2657 AAACCCTAAA
*
2667 CCCTAAG
1 CCCTGAG
*
2674 CCCTAAG
1 CCCTGAG
*
2681 CCCTAAG
1 CCCTGAG
*
2688 CCCTAAG
1 CCCTGAG
*
2695 CCCTAAG
1 CCCTGAG
*
2702 CCCTAAG
1 CCCTGAG
*
2709 CCCTAAG
1 CCCTGAG
*
2716 CCCTAAG
1 CCCTGAG
*
2723 CCCTAAG
1 CCCTGAG
*
2730 CCCTAAG
1 CCCTGAG
*
2737 CCCTAAG
1 CCCTGAG
*
2744 CCCTAAG
1 CCCTGAG
*
2751 CCCTAAG
1 CCCTGAG
*
2758 CCCTAAG
1 CCCTGAG
*
2765 CCCTAAG
1 CCCTGAG
*
2772 CCCTAAG
1 CCCTGAG
*
2779 CCCTAAG
1 CCCTGAG
*
2786 CCCTAAG
1 CCCTGAG
*
2793 CCCTAAG
1 CCCTGAG
*
2800 CCCTAAG
1 CCCTGAG
*
2807 CCCTAAG
1 CCCTGAG
*
2814 CCCTAAG
1 CCCTGAG
*
2821 CCCTAAG
1 CCCTGAG
*
2828 CCCTAAG
1 CCCTGAG
*
2835 CCCTAAG
1 CCCTGAG
*
2842 CCCTAAG
1 CCCTGAG
*
2849 CCCTAAG
1 CCCTGAG
*
2856 CCCTAAG
1 CCCTGAG
*
2863 CCCTAAG
1 CCCTGAG
*
2870 CCCTAAG
1 CCCTGAG
*
2877 CCCTAAG
1 CCCTGAG
*
2884 CCCTAAG
1 CCCTGAG
*
2891 CCCTAAG
1 CCCTGAG
*
2898 CCCTAAG
1 CCCTGAG
*
2905 CCCTAAG
1 CCCTGAG
*
2912 CCCTAAG
1 CCCTGAG
*
2919 CCCTAAG
1 CCCTGAG
*
2926 CCCTAAG
1 CCCTGAG
*
2933 CCCTAAG
1 CCCTGAG
*
2940 CCCTAAG
1 CCCTGAG
*
2947 CCCTAAG
1 CCCTGAG
*
2954 CCCTAAG
1 CCCTGAG
*
2961 CCCTAAG
1 CCCTGAG
*
2968 CCCTAAG
1 CCCTGAG
*
2975 CCCTAAG
1 CCCTGAG
*
2982 CCCTAAG
1 CCCTGAG
*
2989 CCCTAAG
1 CCCTGAG
*
2996 CCCTAAG
1 CCCTGAG
*
3003 CCCTAAG
1 CCCTGAG
*
3010 CCCTAAG
1 CCCTGAG
*
3017 CCCTAAG
1 CCCTGAG
*
3024 CCCTAAG
1 CCCTGAG
*
3031 CCCTAAG
1 CCCTGAG
*
3038 CCCTAAG
1 CCCTGAG
*
3045 CCCTAAG
1 CCCTGAG
*
3052 CCCTAAG
1 CCCTGAG
*
3059 CCCTAAG
1 CCCTGAG
*
3066 CCCTAAG
1 CCCTGAG
*
3073 CCCTAAG
1 CCCTGAG
*
3080 CCCTAAG
1 CCCTGAG
*
3087 CCCTAAG
1 CCCTGAG
*
3094 CCCTAAG
1 CCCTGAG
*
3101 CCCTAAG
1 CCCTGAG
*
3108 CCCTAAG
1 CCCTGAG
*
3115 CCCTAAG
1 CCCTGAG
*
3122 CCCTAAG
1 CCCTGAG
*
3129 CCCTAAG
1 CCCTGAG
*
3136 CCCTAAG
1 CCCTGAG
*
3143 CCCTAAG
1 CCCTGAG
*
3150 CCCTAAG
1 CCCTGAG
*
3157 CCCTAAG
1 CCCTGAG
*
3164 CCCTAAG
1 CCCTGAG
*
3171 CCCTAAG
1 CCCTGAG
*
3178 CCCTAAG
1 CCCTGAG
*
3185 CCCTAAG
1 CCCTGAG
*
3192 CCCTAAG
1 CCCTGAG
*
3199 CCCTAAG
1 CCCTGAG
*
3206 CCCTAAG
1 CCCTGAG
*
3213 CCCTAAG
1 CCCTGAG
*
3220 CCCTAAG
1 CCCTGAG
*
3227 CCCTAAG
1 CCCTGAG
*
3234 CCCTAAG
1 CCCTGAG
3241 CCCTGAG
1 CCCTGAG
3248 CCCTGAG
1 CCCTGAG
3255 CCCTGAG
1 CCCTGAG
3262 CCCTGAG
1 CCCTGAG
3269 CCCTGAG
1 CCCTGAG
3276 CCCTGAG
1 CCCTGAG
3283 CCCTGAG
1 CCCTGAG
3290 CCCTGAG
1 CCCTGAG
3297 CCCTGAG
1 CCCTGAG
3304 CCCTGAG
1 CCCTGAG
3311 CCCTGAG
1 CCCTGAG
3318 CCCTGAG
1 CCCTGAG
3325 CCCTGAG
1 CCCTGAG
3332 CCCTGAG
1 CCCTGAG
3339 CCCTGAG
1 CCCTGAG
3346 CCCTGAG
1 CCCTGAG
3353 CCCTGAG
1 CCCTGAG
3360 CCCTGAG
1 CCCTGAG
3367 CCCTGAG
1 CCCTGAG
3374 CCCTGAG
1 CCCTGAG
3381 CCCTGAG
1 CCCTGAG
3388 CCCTGAG
1 CCCTGAG
3395 CCCTGAG
1 CCCTGAG
3402 CCCTGAG
1 CCCTGAG
3409 CCCTGAG
1 CCCTGAG
3416 CCCTGAG
1 CCCTGAG
3423 CCCTGAG
1 CCCTGAG
*
3430 CCCTGAA
1 CCCTGAG
*
3437 CCCTGAA
1 CCCTGAG
*
3444 CCCTGAA
1 CCCTGAG
*
3451 CCCTGAA
1 CCCTGAG
*
3458 CCCTGAA
1 CCCTGAG
*
3465 CCCTGAA
1 CCCTGAG
*
3472 CCCTGAA
1 CCCTGAG
*
3479 CCCTGAA
1 CCCTGAG
*
3486 CCCTGAA
1 CCCTGAG
*
3493 CCCTGAA
1 CCCTGAG
*
3500 CCCTGAA
1 CCCTGAG
*
3507 CCCTGAA
1 CCCTGAG
*
3514 CCCTGAA
1 CCCTGAG
*
3521 CCCTGAA
1 CCCTGAG
*
3528 CCCTGAA
1 CCCTGAG
*
3535 CCCTGAA
1 CCCTGAG
*
3542 CCCTGAA
1 CCCTGAG
*
3549 CCCTGAA
1 CCCTGAG
*
3556 CCCTGAA
1 CCCTGAG
*
3563 CCCTGAA
1 CCCTGAG
*
3570 CCCTGAA
1 CCCTGAG
3577 CCCTGA
1 CCCTGA
3583 ACCCCAGACC
Statistics
Matches: 907, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 907 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.14
Consensus pattern (7 bp):
CCCTGAG
Found at i:3593 original size:7 final size:7
Alignment explanation
Indices: 3583--3695 Score: 154
Period size: 7 Copynumber: 15.6 Consensus size: 7
3573 TGAACCCTGA
3583 ACCCCAG
1 ACCCCAG
3590 ACCCCAG
1 ACCCCAG
3597 ACCCCAG
1 ACCCCAG
3604 ACCCCAG
1 ACCCCAG
3611 ACCCCAG
1 ACCCCAG
3618 ACCCCAG
1 ACCCCAG
3625 ACCCCAG
1 ACCCCAG
3632 ACCCCAG
1 ACCCCAG
*
3639 ACCCCGG
1 ACCCCAG
*
3646 AACCCCGG
1 -ACCCCAG
*
3654 AACCCCGG
1 -ACCCCAG
*
3662 AACCCCGAA
1 -ACCCC-AG
3671 ACCCCAG
1 ACCCCAG
3678 ACCCCAG
1 ACCCCAG
3685 ACCCCAG
1 ACCCCAG
3692 ACCC
1 ACCC
3696 GAAACCCGAG
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
7 74 0.74
8 26 0.26
ACGTcount: A:0.28, C:0.56, G:0.16, T:0.00
Consensus pattern (7 bp):
ACCCCAG
Found at i:3652 original size:8 final size:8
Alignment explanation
Indices: 3639--3675 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
3629 CAGACCCCAG
3639 ACCCCGGA
1 ACCCCGGA
3647 ACCCCGGA
1 ACCCCGGA
3655 ACCCCGGA
1 ACCCCGGA
*
3663 ACCCCGAA
1 ACCCCGGA
3671 ACCCC
1 ACCCC
3676 AGACCCCAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (8 bp):
ACCCCGGA
Found at i:3702 original size:21 final size:21
Alignment explanation
Indices: 3583--3723 Score: 124
Period size: 21 Copynumber: 6.6 Consensus size: 21
3573 TGAACCCTGA
*
3583 ACCCCAGACCCCAGACCCCAG
1 ACCCCAAACCCCAGACCCCAG
*
3604 ACCCCAGACCCCAGACCCCAG
1 ACCCCAAACCCCAGACCCCAG
* *
3625 ACCCCAGACCCCAGACCCCGG
1 ACCCCAAACCCCAGACCCCAG
* * *
3646 AACCCCGGAACCCCGGAACCCCGAA
1 -ACCCC-AAACCCCAG-ACCCC-AG
*
3671 ACCCCAGACCCCAGACCCCAG
1 ACCCCAAACCCCAGACCCCAG
* *
3692 ACCCGAAACCCGAG-CCCC-G
1 ACCCCAAACCCCAGACCCCAG
*
3711 AGCCCCGAACCCC
1 A-CCCCAAACCCC
3724 GAGCAAAACA
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 12 0.12
21 53 0.54
22 10 0.10
23 12 0.12
24 10 0.10
ACGTcount: A:0.28, C:0.55, G:0.17, T:0.00
Consensus pattern (21 bp):
ACCCCAAACCCCAGACCCCAG
Found at i:3717 original size:14 final size:14
Alignment explanation
Indices: 3245--3727 Score: 54
Period size: 14 Copynumber: 34.3 Consensus size: 14
3235 CCTAAGCCCT
* * *
3245 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3259 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3273 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3287 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3301 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3315 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3329 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3343 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3357 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3371 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3385 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3399 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* * *
3413 GAGCCCTGAGCCCT
1 GAGCCCCGAACCCC
* *
3427 GAGCCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3441 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3455 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3469 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3483 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3497 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3511 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3525 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3539 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3553 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
* * *
3567 GAACCCTGAACCCT
1 GAGCCCCGAACCCC
*
3581 GAACCCC-AGACCCC
1 GAGCCCCGA-ACCCC
3595 -AGACCCC-AGACCCC
1 GAG-CCCCGA-ACCCC
3609 -AGACCCC-AGACCCC
1 GAG-CCCCGA-ACCCC
3623 -AGACCCC-AGACCCC
1 GAG-CCCCGA-ACCCC
3637 -AGACCCCGGAACCCC
1 GAG-CCCC-GAACCCC
*
3652 GGAACCCCGGAACCCC
1 -GAGCCCC-GAACCCC
*
3668 GAAACCCC-AGACCCC
1 G-AGCCCCGA-ACCCC
3683 -AGACCCC-AGA-CCC
1 GAG-CCCCGA-ACCCC
** *
3696 GAAACCCGAGCCCC
1 GAGCCCCGAACCCC
3710 GAGCCCCGAACCCC
1 GAGCCCCGAACCCC
3724 GAGC
1 GAGC
3728 AAAACATCCT
Statistics
Matches: 444, Mismatches: 13, Indels: 24
0.92 0.03 0.05
Matches are distributed among these distances:
13 9 0.02
14 404 0.91
15 11 0.02
16 19 0.04
17 1 0.00
ACGTcount: A:0.23, C:0.46, G:0.21, T:0.10
Consensus pattern (14 bp):
GAGCCCCGAACCCC
Found at i:3770 original size:14 final size:14
Alignment explanation
Indices: 3751--3786 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3741 CTTTTTATTT
3751 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
*
3765 CCTAAACCTTAAAT
1 CCTAAACCTTAAAC
3779 CCTAAACC
1 CCTAAACC
3787 CTAACCCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:3789 original size:7 final size:7
Alignment explanation
Indices: 3751--3790 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3741 CTTTTTATTT
3751 CCTAAAC
1 CCTAAAC
*
3758 CTTAAAC
1 CCTAAAC
3765 CCTAAAC
1 CCTAAAC
* *
3772 CTTAAAT
1 CCTAAAC
3779 CCTAAAC
1 CCTAAAC
3786 CCTAA
1 CCTAA
3791 CCCCGAGCCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:7111 original size:27 final size:26
Alignment explanation
Indices: 7081--7152 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
7071 ATCGAGTGTC
7081 TAGGGTTTAAGG-TCGGGGTCGGGGGTT
1 TAGGGTTTAAGGTTCGGGGT--GGGGTT
* * *
7108 TAGGTTTTAAGGTTTGGGGTTGGGTT
1 TAGGGTTTAAGGTTCGGGGTGGGGTT
*
7134 TAGGGTTTATGGGTTCGGG
1 TAGGGTTTA-AGGTTCGGG
7153 TTCGGGTTCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 13 0.35
27 18 0.49
28 6 0.16
ACGTcount: A:0.11, C:0.04, G:0.47, T:0.38
Consensus pattern (26 bp):
TAGGGTTTAAGGTTCGGGGTGGGGTT
Found at i:7132 original size:26 final size:27
Alignment explanation
Indices: 7081--7160 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 27
7071 ATCGAGTGTC
*
7081 TAGGGTTTAA-GG-TCGGGGTCGGGGGTT
1 TAGGGTTTAAGGGTTCGGGTTC--GGGTT
* * *
7108 TAGGTTTTAAGGTTTGGGGTT-GGGTT
1 TAGGGTTTAAGGGTTCGGGTTCGGGTT
*
7134 TAGGGTTTATGGGTTCGGGTTCGGGTT
1 TAGGGTTTAAGGGTTCGGGTTCGGGTT
7161 CGGGGCTTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 22 0.52
27 14 0.33
28 1 0.02
29 5 0.12
ACGTcount: A:0.10, C:0.05, G:0.46, T:0.39
Consensus pattern (27 bp):
TAGGGTTTAAGGGTTCGGGTTCGGGTT
Found at i:15193 original size:21 final size:21
Alignment explanation
Indices: 15167--15211 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
15157 GTATTTACAG
15167 ACTCCCCACTTTCTACTTCTT
1 ACTCCCCACTTTCTACTTCTT
15188 ACTCCCCACTTTCTACTTCTT
1 ACTCCCCACTTTCTACTTCTT
15209 ACT
1 ACT
15212 TTAAAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (21 bp):
ACTCCCCACTTTCTACTTCTT
Found at i:16162 original size:38 final size:38
Alignment explanation
Indices: 16114--16228 Score: 212
Period size: 38 Copynumber: 3.0 Consensus size: 38
16104 TCTTGACAAA
*
16114 TATAGCATGCATGAGAAAGGGAAACTACTCAAACTTTG
1 TATAGGATGCATGAGAAAGGGAAACTACTCAAACTTTG
16152 TATAGGATGCATGAGAAAGGGAAACTACTCAAACTTTG
1 TATAGGATGCATGAGAAAGGGAAACTACTCAAACTTTG
*
16190 TATAGGATGCATGAGAAAGGGAAACTACTCAACCTTTG
1 TATAGGATGCATGAGAAAGGGAAACTACTCAAACTTTG
16228 T
1 T
16229 GCTGCTATTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (38 bp):
TATAGGATGCATGAGAAAGGGAAACTACTCAAACTTTG
Found at i:22706 original size:18 final size:17
Alignment explanation
Indices: 22680--22713 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22670 TCTTTTTTTT
22680 AATTATAATTAAATTAAA
1 AATTATAATT-AATTAAA
*
22698 AATTTTAATTAATTAA
1 AATTATAATTAATTAA
22714 TGATCACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATAATTAATTAAA
Found at i:41603 original size:45 final size:45
Alignment explanation
Indices: 41552--41642 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
41542 TCAGCAATAA
41552 AGGCAAATAAGTTGATTAATCAGGGTTGTAAAGCGTTTCTTGCTT
1 AGGCAAATAAGTTGATTAATCAGGGTTGTAAAGCGTTTCTTGCTT
*
41597 AGGCAAATAAGTTGATTAATCAGGGTTGTGAAGCGTTTCTTGCTT
1 AGGCAAATAAGTTGATTAATCAGGGTTGTAAAGCGTTTCTTGCTT
41642 A
1 A
41643 TGTTATGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (45 bp):
AGGCAAATAAGTTGATTAATCAGGGTTGTAAAGCGTTTCTTGCTT
Found at i:50565 original size:21 final size:19
Alignment explanation
Indices: 50515--50570 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
50505 TCATGTAAGA
50515 AATTTTTAATTTTTAATAT
1 AATTTTTAATTTTTAATAT
*
50534 AATTTTAAATTTTTAATAT
1 AATTTTTAATTTTTAATAT
50553 AATTTTTTGAATTTTTAA
1 AA-TTTTT-AATTTTTAA
50571 ATCTAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.61
20 4 0.12
21 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTTTTAATTTTTAATAT
Found at i:53330 original size:6 final size:6
Alignment explanation
Indices: 53320--53349 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
53310 TATAGTTGTG
*
53320 CCTGCG CCTGCA CCTGCA CCTGCA CCTGCA
1 CCTGCA CCTGCA CCTGCA CCTGCA CCTGCA
53350 ACTTTAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.50, G:0.20, T:0.17
Consensus pattern (6 bp):
CCTGCA
Found at i:65670 original size:13 final size:13
Alignment explanation
Indices: 65647--65686 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
65637 ATAATTTAAA
65647 TAAAAATATAAATT
1 TAAAAA-ATAAATT
65661 TAAAAAATAAATT
1 TAAAAAATAAATT
65674 TGAATAAAATAAA
1 T-AA-AAAATAAA
65687 ATTTGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
TAAAAAATAAATT
Found at i:71290 original size:23 final size:23
Alignment explanation
Indices: 71264--71365 Score: 109
Period size: 23 Copynumber: 4.3 Consensus size: 23
71254 ACACTAGCGC
*
71264 GCTCTCTGATTAGCACTGTGTAT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
71287 GCTCTTTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
71310 GCTCTCTGTTATTAGCACT-TCGTGT
1 GCTCTCTG--ATTAGCACTGT-GTGT
*
71335 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
71358 GCTCTCTG
1 GCTCTCTG
71366 TTACCTAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.05
23 43 0.65
24 1 0.02
25 18 0.27
26 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:71324 original size:25 final size:23
Alignment explanation
Indices: 71264--71392 Score: 72
Period size: 23 Copynumber: 5.4 Consensus size: 23
71254 ACACTAGCGC
*
71264 GCTCTCTG--ATTAGCACTGTGTAT
1 GCTCTCTGTTATTAGCACTCTG--T
*
71287 GCTCTTTG-T-TTAGCACGTCTCGT
1 GCTCTCTGTTATTAGCAC-TCT-GT
71310 GCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTGTTATTAGCAC-TC-TGT
*
71335 GCTCTCTG--ATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCAC--TCTGT
* *
71358 GCTCTCTGTTACCTAGCACTTATGT
1 GCTCTCTGTTA-TTAGCAC-TCTGT
*
71383 GCTCTTTGTT
1 GCTCTCTGTT
71393 TAGTACTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
23 41 0.47
24 5 0.06
25 35 0.40
26 7 0.08
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTATTAGCACTCTGT
Found at i:71338 original size:48 final size:47
Alignment explanation
Indices: 71264--71395 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 47
71254 ACACTAGCGC
*
71264 GCTCTCTG--ATTAGCACTGTGTATGCTCTTTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTATTAGCACT-TGTGTGCTCTTTGTTTAGCAC-TCTGCGT
* * * *
71310 GCTCTCTGTTATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCACTT-GTGTGCTCTTTGTTTAGCACTCTGCGT
* *
71358 GCTCTCTGTTACCTAGCACTTATGTGCTCTTTGTTTAG
1 GCTCTCTGTTA-TTAGCACTTGTGTGCTCTTTGTTTAG
71396 TACTTTAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
46 8 0.11
47 3 0.04
48 53 0.74
49 8 0.11
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (47 bp):
GCTCTCTGTTATTAGCACTTGTGTGCTCTTTGTTTAGCACTCTGCGT
Found at i:71401 original size:48 final size:47
Alignment explanation
Indices: 71286--71410 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 47
71276 GCACTGTGTA
* * *
71286 TGCTCTTTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTTCGTG
1 TGCTCTTTGTTTAGCAC-TTTCGTGCTCTCTGTTACTAGCACTTCATG
* * *
71334 TGCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTACCTAGCACTT-ATG
1 TGCTCTTTGTTTAGCACTTT-CGTGCTCTCTGTTA-CTAGCACTTCATG
* * *
71382 TGCTCTTTGTTTAGTACTTTAGTACTCTC
1 TGCTCTTTGTTTAGCACTTTCGTGCTCTC
71411 CATTTGTTCC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 9 0.14
48 47 0.73
49 8 0.12
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (47 bp):
TGCTCTTTGTTTAGCACTTTCGTGCTCTCTGTTACTAGCACTTCATG
Found at i:72316 original size:92 final size:94
Alignment explanation
Indices: 72138--72338 Score: 212
Period size: 92 Copynumber: 2.2 Consensus size: 94
72128 AAAATTGATG
* * *
72138 AAAATTATCGATACCTTTTAAGATGGTATCGATACCCAATTGACAGAATGCCCTCTTGGTCTCGA
1 AAAATTATCGATACCTTCTAAAAAGGTATCGATACCCAATTGACAGAATGCCCTCTTGGTCTCGA
* *
72203 TTTTGAAGAAAAGTACCGATATTTT-TGA
66 TTTTGAAGAAAAGTACAGATATTTTATAA
* * *
72231 GAAATTATCGATACC-TCTAAAAAGGTATCGATA-CCAATTTGACAGAATGCCTTGGTT-GTCTC
1 AAAATTATCGATACCTTCTAAAAAGGTATCGATACCCAA-TTGACAGAATGCCCT-CTTGGTCTC
* ******
72293 GATTTTTACTTTTGGTACAGATATTTTATAA
64 GATTTTGAAGAAAAGTACAGATATTTTATAA
*
72324 AAAAGTATCGATACC
1 AAAATTATCGATACC
72339 AATTATTTGG
Statistics
Matches: 88, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
91 4 0.05
92 53 0.60
93 31 0.35
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (94 bp):
AAAATTATCGATACCTTCTAAAAAGGTATCGATACCCAATTGACAGAATGCCCTCTTGGTCTCGA
TTTTGAAGAAAAGTACAGATATTTTATAA
Found at i:74833 original size:23 final size:23
Alignment explanation
Indices: 74790--74889 Score: 112
Period size: 23 Copynumber: 4.4 Consensus size: 23
74780 ATTTAAAATA
* *
74790 AAACATTATGGTAGGAAAGTTAC
1 AAACATAATGGTAGGAGAGTTAC
* * *
74813 AAATATAATGGCAAGAGAGTTAC
1 AAACATAATGGTAGGAGAGTTAC
**
74836 AAACATAATAATAGGAGAGTTAC
1 AAACATAATGGTAGGAGAGTTAC
* *
74859 GAACACAATGGTAGGAGAGTTAC
1 AAACATAATGGTAGGAGAGTTAC
74882 AAA-ATAAT
1 AAACATAAT
74890 AATAATTGGT
Statistics
Matches: 61, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 4 0.07
23 57 0.93
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (23 bp):
AAACATAATGGTAGGAGAGTTAC
Found at i:75474 original size:22 final size:24
Alignment explanation
Indices: 75429--75483 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 24
75419 GAACAATCAA
* *
75429 ATAACTCTAGCAAGAGTTTTTTAT
1 ATAACTCTTGCAAGAGTTTGTTAT
75453 ATAACTCTTG-AA-AGTTTGTTAT
1 ATAACTCTTGCAAGAGTTTGTTAT
75475 ATAACTCTT
1 ATAACTCTT
75484 TTTCAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.62
23 2 0.07
24 9 0.31
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (24 bp):
ATAACTCTTGCAAGAGTTTGTTAT
Found at i:75656 original size:3 final size:3
Alignment explanation
Indices: 75648--75672 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
75638 AATTAAAAAG
75648 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
75673 AAGAAACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:76566 original size:16 final size:16
Alignment explanation
Indices: 76521--76596 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
76511 GTTTGGTTCA
*
76521 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
**
76537 CTACAATGGAATAGAG
1 CTGTAATGGAATAGAG
76553 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
* *
76569 TTGTAATAGAATA-AGG
1 CTGTAATGGAATAGA-G
76585 CTGTAAT-GAATA
1 CTGTAATGGAATA
76597 ATTCAGTTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
15 6 0.12
16 45 0.88
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:76825 original size:58 final size:58
Alignment explanation
Indices: 76763--76881 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 58
76753 TTTTAATAAG
* * *
76763 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAACATTTTTAACATA
* *
76821 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
76879 ATT
1 ATT
76882 TAATTATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 21 0.38
58 34 0.62
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:76880 original size:22 final size:21
Alignment explanation
Indices: 76852--76898 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
76842 ATAAAATAAT
76852 ATATAATTTAATAACATTTTTA
1 ATATAATTTAATAACA-TTTTA
* *
76874 ATATAATTTAATTATATTTTA
1 ATATAATTTAATAACATTTTA
76895 ATAT
1 ATAT
76899 TATAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAATTTAATAACATTTTA
Found at i:76883 original size:10 final size:10
Alignment explanation
Indices: 76773--76898 Score: 50
Period size: 10 Copynumber: 12.5 Consensus size: 10
76763 ATTATTATTA
76773 AATATAATTT
1 AATATAATTT
**
76783 AATA-AAAAT
1 AATATAATTT
76792 AATAAATAATTT
1 AAT--ATAATTT
*
76804 AATTATATTTT
1 AA-TATAATTT
*
76815 AACATAA-TT
1 AATATAATTT
*
76824 -AT-T-ATTA
1 AATATAATTT
*
76831 AATACAATTT
1 AATATAATTT
* *
76841 AATA-AAATA
1 AATATAATTT
76850 ATATATAATTT
1 A-ATATAATTT
76861 AATA-ACATTTTT
1 AATATA-A--TTT
76873 AATATAATTT
1 AATATAATTT
*
76883 AATTATATTTT
1 AA-TATAATTT
76894 AATAT
1 AATAT
76899 TATAATATAT
Statistics
Matches: 85, Mismatches: 16, Indels: 30
0.65 0.12 0.23
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 3 0.04
9 13 0.15
10 29 0.34
11 22 0.26
12 13 0.15
13 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
AATATAATTT
Found at i:82416 original size:16 final size:16
Alignment explanation
Indices: 82395--82428 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
82385 CGTAACTATT
82395 AATTATTAATATTTAC
1 AATTATTAATATTTAC
82411 AATTATTAATATTTAC
1 AATTATTAATATTTAC
82427 AA
1 AA
82429 GGTCATTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATTAATATTTAC
Found at i:84130 original size:52 final size:52
Alignment explanation
Indices: 84027--84413 Score: 566
Period size: 52 Copynumber: 7.5 Consensus size: 52
84017 AAAAGGTCTG
*
84027 ATGACTTTGTGTCATCGTGAGTTATATGAATCCTTTACGGATTATGAGGTCCA
1 ATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACGGATTATGAGGTCCA
* ** *
84080 ATGACTATGTGTCATCTTGAGTATACAAATCCATTACGGATTATGAGGTCCA
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
* ** *
84132 ATGACTATGTGTCATCTTGAGTATACAAATCCTTTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
84184 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
* *
84236 ATGAC--TGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
* *
84286 ATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATGAGGTCTA
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
* * *
84338 ATGACTATGTGTCATCGTGAGCATAT-AGATCCTTTTACGGATT-TAAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGA-ATCC-TTTACGGATTATGAGGTCCA
*
84390 ATGACTATGTGTCATCGTAAGTAT
1 ATGACTATGTGTCATCGTGAGTAT
84414 TAAATGGGAA
Statistics
Matches: 306, Mismatches: 24, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
50 48 0.16
51 1 0.00
52 228 0.75
53 29 0.09
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCA
Found at i:84389 original size:206 final size:207
Alignment explanation
Indices: 84034--84413 Score: 611
Period size: 206 Copynumber: 1.8 Consensus size: 207
84024 CTGATGACTT
* *
84034 TGTGTCATCGTGAGTTATATGAATCCTTTACGGATTATGAGGTCCAATGACTATGTGTCATCTTG
1 TGTGTCATCGTGAGTTATACGAATCCTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTG
* *
84099 AGTATACAAATCCATTACGGATTATGAGGTCCAATGACTATGTGTCATCTTGAGTATACAAATCC
66 AGTATACAAATCCATTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAGCATACAAATCC
* *
84164 TTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
131 TTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
84229 AGGTCCAATGAC
196 AGGTCCAATGAC
*
84241 TGTGTCATCGTGAG-TATACGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTG
1 TGTGTCATCGTGAGTTATACGAATCCTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTG
** * * * * *
84305 AGTATATGAATTCTTTACGGATTATGAGGTCTAATGACTATGTGTCATCGTGAGCATATAGATCC
66 AGTATACAAATCCATTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAGCATACAAATCC
84370 TTTTACGGATT-TAAGGTCCGATGACTATGTGTCATCGTAAGTAT
131 -TTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTAAGTAT
84414 TAAATGGGAA
Statistics
Matches: 158, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
206 134 0.85
207 24 0.15
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (207 bp):
TGTGTCATCGTGAGTTATACGAATCCTTTACGGATTATGAGGTCCAATGACTATGTGTCATCGTG
AGTATACAAATCCATTACGGATTATGAGGTCCAATGACTATGTGTCATCGTGAGCATACAAATCC
TTTACGGATTATAAGGTCCGATGACTATGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
AGGTCCAATGAC
Found at i:90847 original size:4 final size:4
Alignment explanation
Indices: 90800--90856 Score: 64
Period size: 4 Copynumber: 14.5 Consensus size: 4
90790 CACTATTTAA
* * *
90800 TATT TATT TTTT TATT TTTT TA-T TATT TAAT TAGTT TA-T TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TATT
90847 TATT TATT TA
1 TATT TATT TA
90857 AGTTTTTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 6 0.14
4 35 0.80
5 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:91199 original size:29 final size:30
Alignment explanation
Indices: 91167--91225 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
91157 TCACGTGTAT
*
91167 AATTGCAC-CAAATTAAAGTTCATGTATAC
1 AATTGCACACAAATCAAAGTTCATGTATAC
*
91196 AATTGCACATTAAATCAAAGTTCATGTATA
1 AATTGCACA-CAAATCAAAGTTCATGTATA
91226 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
AATTGCACACAAATCAAAGTTCATGTATAC
Found at i:91228 original size:29 final size:27
Alignment explanation
Indices: 91162--91228 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
91152 GAGTTTCACG
*
91162 TGTATAATTGCACCAAATTAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
*
91189 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTGCAC--CAAATCAAAGTTCA
91220 TGTATAATT
1 TGTATAATT
91229 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.35
31 17 0.50
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Found at i:92709 original size:30 final size:30
Alignment explanation
Indices: 92675--92769 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
92665 ACTTATTTTA
*
92675 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
92705 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
*
92735 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
92765 TTGTT
1 TTGTT
92770 TGTTAAGTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGGCAT
Found at i:93137 original size:2 final size:2
Alignment explanation
Indices: 93130--93158 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
93120 TCATTTATTT
93130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93159 TACATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96069 original size:6 final size:6
Alignment explanation
Indices: 96058--96084 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
96048 GGGGCGTCGC
96058 CGGTGG CGGTGG CGGTGG CGGTGG CGG
1 CGGTGG CGGTGG CGGTGG CGGTGG CGG
96085 ATGAAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.67, T:0.15
Consensus pattern (6 bp):
CGGTGG
Found at i:104930 original size:19 final size:19
Alignment explanation
Indices: 104893--104935 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
104883 ATCGCATAGG
* *
104893 GTGGAGGCATGTGGGTTTT
1 GTGGAGGAATGTGGATTTT
* *
104912 TTGGAGGAATTTGGATTTT
1 GTGGAGGAATGTGGATTTT
104931 GTGGA
1 GTGGA
104936 AGGACCCAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.02, G:0.42, T:0.40
Consensus pattern (19 bp):
GTGGAGGAATGTGGATTTT
Found at i:108995 original size:18 final size:18
Alignment explanation
Indices: 108974--109012 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
108964 ATTTTGAAAA
* *
108974 TATTTTTTAAATTTATAT
1 TATTTTTGAAATTTAAAT
*
108992 TATTTTTGAAGTTTAAAT
1 TATTTTTGAAATTTAAAT
109010 TAT
1 TAT
109013 ATATTCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTTTTGAAATTTAAAT
Found at i:120661 original size:22 final size:22
Alignment explanation
Indices: 120613--120661 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
120603 TAATTATTTT
*
120613 ATTTAAAATAAAATCAATCCTA
1 ATTTAAAATAAAATCAATCATA
* *
120635 TTTTAAAATAAACATGAAT-ATA
1 ATTTAAAATAAA-ATCAATCATA
120657 ATTTA
1 ATTTA
120662 TCCAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTTAAAATAAAATCAATCATA
Found at i:129599 original size:24 final size:24
Alignment explanation
Indices: 129559--129605 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
129549 TACAATAAGC
*
129559 ACTTTACTTATTTTATATAAAATA
1 ACTTTACTTATTATATATAAAATA
129583 ACTTTA-TTATATATATATAAAAT
1 ACTTTACTTAT-TATATATAAAAT
129606 TTATGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (24 bp):
ACTTTACTTATTATATATAAAATA
Found at i:143378 original size:34 final size:34
Alignment explanation
Indices: 143313--143390 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
143303 TATTATCAGT
* * * *
143313 AAAGAGCAAGAATGGATAGATAATCAGATCTCTAA
1 AAAGAACAAGAATAGATAAATAATCAAATCTC-AA
143348 AAAGAACAA-AATAGATAAATAATCAAATCTCAA
1 AAAGAACAAGAATAGATAAATAATCAAATCTCAA
143381 AAAGAA-AAGA
1 AAAGAACAAGA
143391 GAATAAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 2 0.05
33 9 0.24
34 19 0.50
35 8 0.21
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.17
Consensus pattern (34 bp):
AAAGAACAAGAATAGATAAATAATCAAATCTCAA
Found at i:146383 original size:2 final size:2
Alignment explanation
Indices: 146370--146409 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
146360 CTTCACATCC
*
146370 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146410 TAGACATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:156571 original size:6 final size:6
Alignment explanation
Indices: 156560--156588 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
156550 TATTAAAAGT
156560 ATTAAC ATTAAC ATTAAC ATTAAC ATTAA
1 ATTAAC ATTAAC ATTAAC ATTAAC ATTAA
156589 AAACTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAC
Found at i:160293 original size:138 final size:138
Alignment explanation
Indices: 160045--160322 Score: 520
Period size: 138 Copynumber: 2.0 Consensus size: 138
160035 TTTATGTTTG
*
160045 AAGAAAAATTGCACCCAACATGTTAGAGCACTATTTTTCGAAGTCCTTAAAATAAACGAGCATCA
1 AAGAAAAATTGCACCCAACACGTTAGAGCACTATTTTTCGAAGTCCTTAAAATAAACGAGCATCA
160110 CTTCCCTTTTTCAAAATCATTTCATTCATCAAAATATACAATCATTAACATTTTTATGCACAAAA
66 CTTCCCTTTTTCAAAATCATTTCATTCATCAAAATATACAATCATTAACATTTTTATGCACAAAA
160175 AATGGGAA
131 AATGGGAA
* *
160183 AAGAAAAATTGCACCCAACACGTTAGATCATTATTTTTCGAAGTCCTTAAAATAAACGAGCATCA
1 AAGAAAAATTGCACCCAACACGTTAGAGCACTATTTTTCGAAGTCCTTAAAATAAACGAGCATCA
*
160248 CTTCCCTTTTTCAAAATGATTTCATTCATCAAAATATACAATCATTAACATTTTTATGCACAAAA
66 CTTCCCTTTTTCAAAATCATTTCATTCATCAAAATATACAATCATTAACATTTTTATGCACAAAA
160313 AATGGGAA
131 AATGGGAA
160321 AA
1 AA
160323 TACACATATG
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (138 bp):
AAGAAAAATTGCACCCAACACGTTAGAGCACTATTTTTCGAAGTCCTTAAAATAAACGAGCATCA
CTTCCCTTTTTCAAAATCATTTCATTCATCAAAATATACAATCATTAACATTTTTATGCACAAAA
AATGGGAA
Found at i:160951 original size:30 final size:30
Alignment explanation
Indices: 160696--160926 Score: 284
Period size: 30 Copynumber: 7.7 Consensus size: 30
160686 GTTTACGATC
* * *
160696 AAAATGTAATTTTTAAAAAGTTTG-GGGTCA
1 AAAATG-AAATTTTAGAAAGTTCGAGGGTCA
* *
160726 AAAATAAAATTTTAGAAAGTTCGAGGGTTA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
* *
160756 AAAATGAAATTTTATAAAGTTCAAGGGTCA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
* *
160786 AAAATGAAGTTTTAGAAAGTTCGAGAGTCA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
*
160816 AAAATGAAACTTTAGAAAGTTCGAGGGTCA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
* * * *
160846 AAAATAAAATTTTAGAAAGTTTGGGGGTTA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
* * *
160876 AAAATGAAGTTTTATAAAGTTCGAGGGTTA
1 AAAATGAAATTTTAGAAAGTTCGAGGGTCA
*
160906 AAAATGAAATTTTAAAAAGTT
1 AAAATGAAATTTTAGAAAGTT
160927 TTAGGGTTAA
Statistics
Matches: 172, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
29 14 0.08
30 158 0.92
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (30 bp):
AAAATGAAATTTTAGAAAGTTCGAGGGTCA
Found at i:161892 original size:2 final size:2
Alignment explanation
Indices: 161885--161915 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
161875 CTTTTCCTTT
161885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
161916 TTCCAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:161997 original size:22 final size:23
Alignment explanation
Indices: 161970--162015 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
161960 TCTTTGGATT
161970 TCTATTGCTAGTATTCAAT-TTC
1 TCTATTGCTAGTATTCAATCTTC
** *
161992 TCTATTTTTTGTATTCAATCTTC
1 TCTATTGCTAGTATTCAATCTTC
162015 T
1 T
162016 GTAAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (23 bp):
TCTATTGCTAGTATTCAATCTTC
Found at i:162988 original size:23 final size:23
Alignment explanation
Indices: 162939--163111 Score: 172
Period size: 23 Copynumber: 7.5 Consensus size: 23
162929 TAAACGGAAC
* *
162939 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACGAAGTGCT
* *
162961 GAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
* *
162984 AAACAGAGAGTACACAAAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
*
163007 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
* *
163030 AATCGGAGAGCACAC-ACAGTGCT
1 AAACAGAGAGCACACGA-AGTGCT
*
163053 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACGAAGTGCT
*
163078 AAACAGAGAGCACACGCAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
**
163101 AATTAGAGAGC
1 AAACAGAGAGC
163112 GCGCTAGTGT
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
22 13 0.10
23 95 0.75
24 2 0.02
25 15 0.12
26 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACGAAGTGCT
Found at i:163066 original size:48 final size:48
Alignment explanation
Indices: 162962--163103 Score: 191
Period size: 46 Copynumber: 3.0 Consensus size: 48
162952 CGAAGTACTG
* * *
162962 AACAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTAAT
1 AACAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
* *
163010 --CAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 AACAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
* *
163056 AACAGAGAGCACGA-GACGTGCTAAACAGAGAGCACACGCAGTGCTAAT
1 AACAGAGAGCAC-ACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
163104 TAGAGAGCGC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 41 0.50
48 40 0.49
49 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (48 bp):
AACAGAGAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAAT
Found at i:163110 original size:71 final size:68
Alignment explanation
Indices: 162939--163111 Score: 199
Period size: 71 Copynumber: 2.5 Consensus size: 68
162929 TAAACGGAAC
* *
162939 AAACAGAGAGTAC-CGAAGTACTGAA-CAGAGAGCACACAAAGTGCTAAACAGAGAGTACACAAA
1 AAACAGAGAGCACACGAAGTGCT-AATCAGAGAGCACACAAAGTGCTAAACAGAGAG-ACACAAA
163002 GTGCT
64 GTGCT
* * *
163007 AATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAATAACAGAGAG-CACGAG
1 AAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACACAAAGTGCT-A-AACAGAGAGACAC-A-
*
163071 ACGTGCT
62 AAGTGCT
* *
163078 AAACAGAGAGCACACGCAGTGCTAATTAGAGAGC
1 AAACAGAGAGCACACGAAGTGCTAATCAGAGAGC
163112 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
68 13 0.15
69 29 0.33
70 2 0.02
71 45 0.51
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (68 bp):
AAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACACAAAGTGCTAAACAGAGAGACACAAAGT
GCT
Found at i:165553 original size:38 final size:38
Alignment explanation
Indices: 165480--166084 Score: 212
Period size: 38 Copynumber: 16.1 Consensus size: 38
165470 TTGCCCCACA
* * *
165480 ATTGCATGTCTTCAATCTGCC-CTCTGAT-TAGGGTAAAAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGA-GGTAAGAG
165519 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
* *
165557 GTT-GATGTCTTCAATCT--ATCTT--T-----T--GA-
1 ATTGGATG-CTTCAATCTGCCTCTTGATCGAGGTAAGAG
* ** * * *
165583 TTTGGATTTTTCAATCTGCCCCATGATCGGGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
* **
165621 ATTGCATGTCTTCAATCTGCCT-TCTGATTAAGGTAAGAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* * * *
165660 ATTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
* * * * ** *
165698 ACTGCATGTCTTCAATCTACCT-TCTAATTAAGGTAAAAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* * * * *
165737 ATTGAATTCTTCAATCAGCCCCATGATCGAGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
* * * **
165775 ATCGCATGGTTTCAATCTGCCT-TCTGATTAAGGTAAGAG
1 ATTGGAT-GCTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* * * * *
165814 ATTGGATTCTTTAATTTGTCC-CATGATCGGGGTAAGAG
1 ATTGGATGCTTCAATCTG-CCTCTTGATCGAGGTAAGAG
*** * **
165852 ATCACATGTCTTCAATCTACCT-TCTGATTAAGGTAAGAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* * * * *
165891 ATTGGATTCTTTAATCTGCCTCATGATTGGGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
* * * ** * **
165929 ATCGCATGTCTTTAATCTATCT-TCTAATTAAGGTAAGAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGAGGTAAGAG
** ** *
165968 ATCAGATTTTTCAATCTGCCT-TATGATCGGGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* ** * **
166006 ACTACATGTCTTCAATCTTCCT-TCTGATTAAGGTAAGAG
1 ATTGGATG-CTTCAATCTGCCTCT-TGATCGAGGTAAGAG
* * * * *
166045 ATTCGATTCTTAAATCTGCCTCATGATCGGGGTAAGAG
1 ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
166083 AT
1 AT
166085 CGGCTGTCTT
Statistics
Matches: 403, Mismatches: 129, Indels: 69
0.67 0.21 0.11
Matches are distributed among these distances:
26 10 0.02
27 5 0.01
28 2 0.00
29 1 0.00
30 1 0.00
34 1 0.00
35 1 0.00
36 4 0.01
37 6 0.01
38 198 0.49
39 174 0.43
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (38 bp):
ATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAGAG
Found at i:165673 original size:103 final size:102
Alignment explanation
Indices: 165490--165676 Score: 254
Period size: 103 Copynumber: 1.8 Consensus size: 102
165480 ATTGCATGTC
* * *
165490 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCTCTTGATCGAGGTAAG
1 TTCAATCTGCCCTCTGATCAGGGTAAAAGATTGCATGCTTCAATCTGCCTCTTGATCAAGGTAAG
*
165555 AGGTTGATGTCTTCAATCTATCTTTTGATTTGGATTT
66 AGATTGATGTCTTCAATCTATCTTTTGATTTGGATTT
* * *
165592 TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGCATGTCTTCAATCTGCCT-TCTGATTAAGGT
1 TTCAATCTGCCCTC-TGATCAGGGTAAAAGATTGCATG-CTTCAATCTGCCTCT-TGATCAAGGT
165655 AAGAGATTGGAT-TCTTCAATCT
63 AAGAGATT-GATGTCTTCAATCT
165677 GCCCCATGAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 1 0.01
102 32 0.43
103 38 0.51
104 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (102 bp):
TTCAATCTGCCCTCTGATCAGGGTAAAAGATTGCATGCTTCAATCTGCCTCTTGATCAAGGTAAG
AGATTGATGTCTTCAATCTATCTTTTGATTTGGATTT
Found at i:165711 original size:77 final size:77
Alignment explanation
Indices: 165584--166163 Score: 720
Period size: 77 Copynumber: 7.5 Consensus size: 77
165574 ATCTTTTGAT
* * *
165584 TTGGATTTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGCATGTCTTCAATCTGCCTTCTGAT
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTACCTTCTGAT
165649 TAAGGTAAGAGA
66 TAAGGTAAGAGA
*
165661 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTACCTTCTAAT
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTACCTTCTGAT
*
165726 TAAGGTAAAAGA
66 TAAGGTAAGAGA
* * * *
165738 TTGAATTCTTCAATCAGCCCCATGATCGAGGTAAGAGA-TCGCATGGT-TTCAATCTGCCTTCTG
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACT-GCAT-GTCTTCAATCTACCTTCTG
165801 ATTAAGGTAAGAGA
64 ATTAAGGTAAGAGA
* * * *
165815 TTGGATTCTTTAATTTGTCCCATGATCGGGGTAAGAGA-TCACATGTCTTCAATCTACCTTCTGA
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACT-GCATGTCTTCAATCTACCTTCTGA
165879 TTAAGGTAAGAGA
65 TTAAGGTAAGAGA
* * * * * *
165892 TTGGATTCTTTAATCTGCCTCATGATTGGGGTAAGAGA-TCGCATGTCTTTAATCTATCTTCTAA
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACT-GCATGTCTTCAATCTACCTTCTGA
165956 TTAAGGTAAGAGA
65 TTAAGGTAAGAGA
** * ** * *
165969 TCAGATTTTTCAATCTGCCTTATGATCGGGGTAAGAGACTACATGTCTTCAATCTTCCTTCTGAT
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTACCTTCTGAT
166034 TAAGGTAAGAGA
66 TAAGGTAAGAGA
* * * * * * * *
166046 TTCGATTCTTAAATCTGCCTCATGATCGGGGTAAGAGATCGGC-TGTCTTCAAATTTGCCCTCTA
1 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGA-CTGCATGTCTTC-AATCTACCTTCTG
* *
166110 ATTAGGGTGAGAGA
64 ATTAAGGTAAGAGA
* *
166124 TTTGGATACTTCGATCTGCCCCATGATCGGGGTAAGAGAC
1 -TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGAC
166164 CTGTAAAATA
Statistics
Matches: 440, Mismatches: 56, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
76 3 0.01
77 377 0.86
78 27 0.06
79 33 0.08
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (77 bp):
TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTACCTTCTGAT
TAAGGTAAGAGA
Found at i:178097 original size:59 final size:59
Alignment explanation
Indices: 178022--178240 Score: 273
Period size: 59 Copynumber: 3.7 Consensus size: 59
178012 AAATGTAATT
178022 TTTAGAAAGTTTGAGGGTCAAAAATGAAATTTTAGAAAGTTTAGGGTTTAAAAATGAAA
1 TTTAGAAAGTTTGAGGGTCAAAAATGAAATTTTAGAAAGTTTAGGGTTTAAAAATGAAA
* * * * *
178081 TTTAGAAAGCTTGAGGGTTAAAAATGAAATTTCAAAAAGTTTGGGGTTTAAAAATGAAA
1 TTTAGAAAGTTTGAGGGTCAAAAATGAAATTTTAGAAAGTTTAGGGTTTAAAAATGAAA
* * *
178140 TTTTATAAAGTTT-AGGGGTC-AAAATGAAATTTTAGAAAGTTTGAGGG-TCAAAAATGAAG
1 -TTTAGAAAGTTTGA-GGGTCAAAAATGAAATTTTAGAAAGTTT-AGGGTTTAAAAATGAAA
* * * * *
178199 TTTATAAAGTTTAAAGGTTAAAAATAAAATTTTAGAAAGTTT
1 TTTAGAAAGTTTGAGGGTCAAAAATGAAATTTTAGAAAGTTT
178241 TAGGATTAAA
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
58 15 0.11
59 107 0.77
60 17 0.12
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (59 bp):
TTTAGAAAGTTTGAGGGTCAAAAATGAAATTTTAGAAAGTTTAGGGTTTAAAAATGAAA
Found at i:178250 original size:30 final size:30
Alignment explanation
Indices: 177956--178251 Score: 300
Period size: 30 Copynumber: 9.9 Consensus size: 30
177946 GGTAAAAACA
* *
177956 AAATTTTGGAAAGTTTTAGAGGGCT-AAAATG
1 AAATTTTAGAAAG-TTT-GAGGGTTAAAAATG
* * *
177987 TAATTTTTAAAAAGTTTGAGGG-TCAAAATG
1 -AAATTTTAGAAAGTTTGAGGGTTAAAAATG
* *
178017 TAATTTTTAGAAAGTTTGAGGGTCAAAAATG
1 -AAATTTTAGAAAGTTTGAGGGTTAAAAATG
178048 AAATTTTAGAAAGTTT-AGGGTTTAAAAATG
1 AAATTTTAGAAAGTTTGAGGG-TTAAAAATG
*
178078 AAA-TTTAGAAAGCTTGAGGGTTAAAAATG
1 AAATTTTAGAAAGTTTGAGGGTTAAAAATG
* *
178107 AAATTTCAAAAAGTTTG-GGGTTTAAAAATG
1 AAATTTTAGAAAGTTTGAGGG-TTAAAAATG
* * *
178137 AAATTTTATAAAGTTT-AGGGGTCAAAATG
1 AAATTTTAGAAAGTTTGAGGGTTAAAAATG
*
178166 AAATTTTAGAAAGTTTGAGGGTCAAAAATG
1 AAATTTTAGAAAGTTTGAGGGTTAAAAATG
* * * * *
178196 -AAGTTTATAAAGTTTAAAGGTTAAAAATA
1 AAATTTTAGAAAGTTTGAGGGTTAAAAATG
* *
178225 AAATTTTAGAAAGTTTTAGGATTAAAA
1 AAATTTTAGAAAGTTTGAGGGTTAAAA
178252 TATAATTTTT
Statistics
Matches: 224, Mismatches: 31, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
29 76 0.34
30 129 0.58
31 9 0.04
32 10 0.04
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (30 bp):
AAATTTTAGAAAGTTTGAGGGTTAAAAATG
Found at i:189613 original size:6 final size:6
Alignment explanation
Indices: 189602--189631 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
189592 CACAATCATA
*
189602 CCTATT CCTATT CCTATT CCTATT GCTATT
1 CCTATT CCTATT CCTATT CCTATT CCTATT
189632 ATATAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.03, T:0.50
Consensus pattern (6 bp):
CCTATT
Found at i:193656 original size:28 final size:31
Alignment explanation
Indices: 193585--193657 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 31
193575 TTTATTATAT
*
193585 ATTAATATATTAATTTATTATTTTTAAACAAG
1 ATTAAAATA-TAATTTATTATTTTTAAACAAG
*
193617 ATT-AAATA-AATTTCTTA-TTTTAAA-AA-
1 ATTAAAATATAATTTATTATTTTTAAACAAG
193643 ATTAAAATATAATTT
1 ATTAAAATATAATTT
193658 TACCATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 3 0.08
27 7 0.19
28 12 0.32
29 8 0.22
31 4 0.11
32 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (31 bp):
ATTAAAATATAATTTATTATTTTTAAACAAG
Found at i:198134 original size:19 final size:19
Alignment explanation
Indices: 198112--198156 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
198102 TTATATTAAG
*
198112 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAAAAT-TGT
*
198131 ATTTATTATTTAAAATTGT
1 ATTTAATATTTAAAATTGT
198150 ATTTAAT
1 ATTTAAT
198157 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAAATTGT
Found at i:198982 original size:22 final size:22
Alignment explanation
Indices: 198956--198998 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
198946 TCAACTTCCT
198956 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
198978 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
198999 CTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:210435 original size:21 final size:23
Alignment explanation
Indices: 210402--210451 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
210392 TTACTAATAC
* *
210402 ATTT-TTGTTAAACTAAATT-A-
1 ATTTGTTGTCAAACAAAATTGAT
210422 ATTTGTTGTCAAACAAAATTGAT
1 ATTTGTTGTCAAACAAAATTGAT
210445 ATTTGTT
1 ATTTGTT
210452 TTCTACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 1 0.04
23 7 0.28
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (23 bp):
ATTTGTTGTCAAACAAAATTGAT
Found at i:212536 original size:11 final size:12
Alignment explanation
Indices: 212504--212574 Score: 67
Period size: 12 Copynumber: 6.0 Consensus size: 12
212494 GATTTATTTC
212504 TAAATTTAAATT
1 TAAATTTAAATT
212516 TAAATTTAAATT
1 TAAATTTAAATT
*
212528 T-AGTTTAAATT
1 TAAATTTAAATT
*
212539 TGAAA--TAATTT
1 T-AAATTTAAATT
*
212550 TAAACTTAAACTT
1 TAAATTTAAA-TT
*
212563 TAAAATTAAATT
1 TAAATTTAAATT
212575 CAAAGTCCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
10 3 0.06
11 16 0.33
12 18 0.37
13 12 0.24
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:214486 original size:30 final size:30
Alignment explanation
Indices: 214442--214562 Score: 97
Period size: 29 Copynumber: 4.0 Consensus size: 30
214432 CCTTACAGGT
*
214442 CCCTAAACTATCCAAAAATTATATTTTGAC
1 CCCTAAACTTTCCAAAAATTATATTTTGAC
* * *
214472 CCCCAAACTTTCC-AAAATT-TCATTTTTAA
1 CCCTAAACTTTCCAAAAATTAT-ATTTTGAC
** *
214501 CCCTAATTTTTCCCAAAAATTACCATTTT-AC
1 CCCTAAACTTT-CCAAAAATTA-TATTTTGAC
* *
214532 CCTTAAACTTTCCAAAATTTCAT-TTTTGAC
1 CCCTAAACTTTCCAAAAATT-ATATTTTGAC
214562 C
1 C
214563 TTGATTTTTC
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
28 1 0.01
29 24 0.34
30 24 0.34
31 16 0.23
32 5 0.07
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTATATTTTGAC
Found at i:214512 original size:29 final size:29
Alignment explanation
Indices: 214480--214629 Score: 103
Period size: 29 Copynumber: 5.1 Consensus size: 29
214470 ACCCCCAAAC
*
214480 TTTCCAAAATTTCATTTTTAACCCTAATT
1 TTTCCAAAATTCCATTTTTAACCCTAATT
**
214509 TTTCCCAAAAATTACCA-TTTT-ACCCTTAAAC
1 TTT-CC-AAAATT-CCATTTTTAACCC-TAATT
* * * *
214540 TTTCCAAAATTTCATTTTTGACCTTGATT
1 TTTCCAAAATTCCATTTTTAACCCTAATT
* *
214569 TTTCCAAAATGACCA-TTTTACCCCTTAA--
1 TTTCCAAAAT-TCCATTTTTAACCC-TAATT
* *
214597 CTTCCAAAAATTCCATTTTTGACCCTAATT
1 TTTCC-AAAATTCCATTTTTAACCCTAATT
214627 TTT
1 TTT
214630 TTTCAAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 23
0.68 0.14 0.17
Matches are distributed among these distances:
28 12 0.13
29 43 0.48
30 17 0.19
31 16 0.18
32 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTAACCCTAATT
Found at i:214540 original size:60 final size:59
Alignment explanation
Indices: 214452--214629 Score: 220
Period size: 60 Copynumber: 3.0 Consensus size: 59
214442 CCCTAAACTA
* ** *
214452 TCCAAAAATTA-TATTTTGACCCCCAAACTTTCCAAAATTTCATTTTTAACCCTAATTTT
1 TCCAAAAATTACCATTTT-ACCCTTAAACTTTCCAAAATTTCATTTTTGACCCTAATTTT
* *
214511 TCCCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTTCATTTTTGACCTTGATTTT
1 T-CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTTCATTTTTGACCCTAATTTT
* *
214571 TCC-AAAATGACCATTTTACCCCTT-AAC-TTCCAAAAATTCCATTTTTGACCCTAATTTT
1 TCCAAAAATTACCATTTTA-CCCTTAAACTTTCC-AAAATTTCATTTTTGACCCTAATTTT
214629 T
1 T
214630 TTTCAAAATT
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.04
58 41 0.39
59 8 0.08
60 47 0.45
61 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTTCATTTTTGACCCTAATTTT
Found at i:214607 original size:58 final size:60
Alignment explanation
Indices: 214476--214629 Score: 217
Period size: 58 Copynumber: 2.6 Consensus size: 60
214466 TTTGACCCCC
* *
214476 AAACTTTCCAAAATTTCATTTTTAACCCTAATTTTTCCCAAAAATTACCATTTTACCCTT
1 AAACTTTCCAAAATTTCATTTTTGACCCTAATTTTTCCCAAAAATGACCATTTTACCCTT
* *
214536 AAACTTTCCAAAATTTCATTTTTGACCTTGATTTTT-CC-AAAATGACCATTTTACCCCTT
1 AAACTTTCCAAAATTTCATTTTTGACCCTAATTTTTCCCAAAAATGACCATTTTA-CCCTT
*
214595 -AAC-TTCCAAAAATTCCATTTTTGACCCTAATTTTT
1 AAACTTTCC-AAAATTTCATTTTTGACCCTAATTTTT
214630 TTTCAAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
57 4 0.05
58 41 0.48
59 7 0.08
60 33 0.39
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (60 bp):
AAACTTTCCAAAATTTCATTTTTGACCCTAATTTTTCCCAAAAATGACCATTTTACCCTT
Found at i:216235 original size:22 final size:21
Alignment explanation
Indices: 216210--216258 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
216200 AAAACTCATC
216210 AACCCAAATCCCATTTAAACCA
1 AACCCAAAT-CCATTTAAACCA
* *
216232 AACCCACATTCATTTAAACCA
1 AACCCAAATCCATTTAAACCA
216253 AACCCA
1 AACCCA
216259 TTTAAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (21 bp):
AACCCAAATCCATTTAAACCA
Found at i:216272 original size:20 final size:20
Alignment explanation
Indices: 216247--216308 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
216237 ACATTCATTT
216247 AAACCAAACCCATTTAAACC
1 AAACCAAACCCATTTAAACC
216267 AAACCAAACCCATTTAAACC
1 AAACCAAACCCATTTAAACC
* * *
216287 TAACCAAACCCTTTTGAACC
1 AAACCAAACCCATTTAAACC
216307 AA
1 AA
216309 GTACAACCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.18
Consensus pattern (20 bp):
AAACCAAACCCATTTAAACC
Found at i:216291 original size:15 final size:15
Alignment explanation
Indices: 216242--216271 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
216232 AACCCACATT
216242 CATTTAAACCAAACC
1 CATTTAAACCAAACC
216257 CATTTAAACCAAACC
1 CATTTAAACCAAACC
216272 AAACCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:216376 original size:7 final size:7
Alignment explanation
Indices: 216364--216429 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
216354 TTGACCGACT
216364 GTTGACC
1 GTTGACC
216371 GTTGA-C
1 GTTGACC
*
216377 TTTGACC
1 GTTGACC
216384 GTTGACC
1 GTTGACC
**
216391 ACTGACC
1 GTTGACC
*
216398 TTTGA-C
1 GTTGACC
*
216404 TTTGACC
1 GTTGACC
216411 GTTGA-C
1 GTTGACC
*
216417 TTTGACC
1 GTTGACC
216424 GTTGAC
1 GTTGAC
216430 TTTTTTTCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
6 16 0.34
7 31 0.66
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.35
Consensus pattern (7 bp):
GTTGACC
Found at i:216383 original size:13 final size:13
Alignment explanation
Indices: 216360--216432 Score: 101
Period size: 13 Copynumber: 5.5 Consensus size: 13
216350 GGTGTTGACC
216360 GACTGTTGACCGTT
1 GACT-TTGACCGTT
216374 GACTTTGACCGTT
1 GACTTTGACCGTT
** *
216387 GACCACTGACCTTT
1 GA-CTTTGACCGTT
216401 GACTTTGACCGTT
1 GACTTTGACCGTT
216414 GACTTTGACCGTT
1 GACTTTGACCGTT
216427 GACTTT
1 GACTTT
216433 TTTTCGAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
13 38 0.73
14 14 0.27
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (13 bp):
GACTTTGACCGTT
Found at i:223582 original size:20 final size:20
Alignment explanation
Indices: 223553--223677 Score: 83
Period size: 20 Copynumber: 6.2 Consensus size: 20
223543 GACCGTTGAC
* *
223553 TGACCATTGACTTTGACTGT
1 TGACCGTTGACTTTGACCGT
* *
223573 TGACCGTTGACCATTGA-CTT
1 TGACCGTTGA-CTTTGACCGT
** * *
223593 TGATTGTTGACCATTGACCAT
1 TGACCGTTGA-CTTTGACCGT
* * **
223614 TGA-CTTTGACCGTTGACCAC
1 TGACCGTTGA-CTTTGACCGT
* *
223634 TGATCGTTGACTTTGACCAT
1 TGACCGTTGACTTTGACCGT
223654 TGACCGTTGACTTTGACCGT
1 TGACCGTTGACTTTGACCGT
223674 TGAC
1 TGAC
223678 TTTTTTCGAA
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
20 71 0.83
21 15 0.17
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (20 bp):
TGACCGTTGACTTTGACCGT
Found at i:223585 original size:27 final size:27
Alignment explanation
Indices: 223553--223664 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
223543 GACCGTTGAC
* *
223553 TGACCATTGACTTTGACTGTTGACCGT
1 TGACCATTGACTTTGACCGTTGACCAT
**
223580 TGACCATTGACTTTGATTGTTGACCAT
1 TGACCATTGACTTTGACCGTTGACCAT
*
223607 TGACCATTGACTTTGACCGTTGACCAC
1 TGACCATTGACTTTGACCGTTGACCAT
* * * *
223634 TGATCGTTGACTTTGACCATTGACCGT
1 TGACCATTGACTTTGACCGTTGACCAT
223661 TGAC
1 TGAC
223665 TTTGACCGTT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (27 bp):
TGACCATTGACTTTGACCGTTGACCAT
Found at i:223606 original size:47 final size:47
Alignment explanation
Indices: 223565--223677 Score: 84
Period size: 47 Copynumber: 2.4 Consensus size: 47
223555 ACCATTGACT
* ** * * *
223565 TTGACTGTTGACCGTTGACCATTGACTTTGATTGTTGACCATTGACCA
1 TTGACT-TTGACCATTGACCATTGACTTTGACCGTTGACCACTGATCG
* * * * * *
223613 TTGACTTTGACCGTTGACCACTGATCGTTGA-CTTTGACCATTGACCG
1 TTGACTTTGACCATTGACCATTGA-CTTTGACCGTTGACCACTGATCG
*
223660 TTGACTTTGACCGTTGAC
1 TTGACTTTGACCATTGAC
223678 TTTTTTCGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 48 0.81
48 11 0.19
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (47 bp):
TTGACTTTGACCATTGACCATTGACTTTGACCGTTGACCACTGATCG
Found at i:224633 original size:3 final size:3
Alignment explanation
Indices: 224625--224688 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
224615 TATTTTATTC
*
224625 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
224673 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
224689 TTGGGATGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:227956 original size:24 final size:24
Alignment explanation
Indices: 227896--227956 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
227886 AATTTGTATC
*
227896 TTTCTTGCGAGCCTAGTTCGCAAT
1 TTTCTTGCGACCCTAGTTCGCAAT
*
227920 TTTCTTGCAACCCTAGTTCGC-AT
1 TTTCTTGCGACCCTAGTTCGCAAT
*
227943 TTGTCTTACGACCC
1 TT-TCTTGCGACCC
227957 CAATTTGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (24 bp):
TTTCTTGCGACCCTAGTTCGCAAT
Found at i:230533 original size:28 final size:28
Alignment explanation
Indices: 230489--230543 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
230479 TTTTATCATA
*
230489 CATATATATATATAAAAACTAGAAAAAG
1 CATATAAATATATAAAAACTAGAAAAAG
* *
230517 CATATAAACTATA-AAAAATTATAAAAA
1 CATATAAA-TATATAAAAACTAGAAAAA
230544 TAAAAATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.25
Consensus pattern (28 bp):
CATATAAATATATAAAAACTAGAAAAAG
Found at i:230726 original size:11 final size:11
Alignment explanation
Indices: 230703--230740 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
230693 AATTTAAACA
230703 TTTTAAATATT
1 TTTTAAATATT
*
230714 TTTTACA-ATT
1 TTTTAAATATT
*
230724 TTTTATATATT
1 TTTTAAATATT
230735 TTTTAA
1 TTTTAA
230741 GTTTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:230745 original size:19 final size:20
Alignment explanation
Indices: 230703--230748 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
230693 AATTTAAACA
*
230703 TTTTAAATATTTTTTACAATT
1 TTTTAAATATTTTTTA-AAGT
*
230724 TTTTATATATTTTTT-AAGT
1 TTTTAAATATTTTTTAAAGT
230743 TTTTAA
1 TTTTAA
230749 TTTTTATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTAAATATTTTTTAAAGT
Found at i:230873 original size:21 final size:19
Alignment explanation
Indices: 230848--230896 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
230838 ATCTAAACTT
230848 TATATTTTTCTCAATTTTTCA
1 TATATTTTT-TCAATTTTT-A
*
230869 TATATTTATTTCTATTTTTA
1 TATATTT-TTTCAATTTTTA
230889 TAT-TTTTT
1 TATATTTTT
230897 ATATTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 4 0.15
21 15 0.58
22 2 0.08
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATTTTTTCAATTTTTA
Found at i:242911 original size:23 final size:23
Alignment explanation
Indices: 242861--243035 Score: 124
Period size: 23 Copynumber: 7.4 Consensus size: 23
242851 AAGCTAGCGC
242861 GCTTACTGTTTCGCACTTTGTGTGT
1 GCTTACTGTTTCGCAC-TT-TGTGT
242886 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
*
242909 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTTGTGT
** * * *
242932 GCCCACTGATTT-GCGCTATGTGC
1 GCTTACTG-TTTCGCACTTTGTGT
* * * *
242955 GCCTACTGATT-ACACTGTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
* * * *
242977 GCCTACTGGATT-ACACTGTGTGT
1 GCTTACT-GTTTCGCACTTTGTGT
243000 GCTTACTGTTTCCCCAGCAC-TTGTGT
1 GCTTACTGTTT---C-GCACTTTGTGT
243026 GCTTACTGTT
1 GCTTACTGTT
243036 AAGTACTTCG
Statistics
Matches: 126, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
22 19 0.15
23 68 0.54
24 5 0.04
25 16 0.13
26 15 0.12
27 3 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:247024 original size:31 final size:32
Alignment explanation
Indices: 246989--247066 Score: 122
Period size: 31 Copynumber: 2.4 Consensus size: 32
246979 ACTCTATTTT
246989 TTTAATTTTAATTTATTTTTTAGGGTTTAT-A
1 TTTAATTTTAATTTATTTTTTAGGGTTTATAA
*
247020 TTTAATTTTAATTTATTTTTTAGGTTTTATAA
1 TTTAATTTTAATTTATTTTTTAGGGTTTATAA
*
247052 TTTAGAGTTTAATTT
1 TTTA-ATTTTAATTT
247067 GGATCCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 29 0.67
32 5 0.12
33 9 0.21
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (32 bp):
TTTAATTTTAATTTATTTTTTAGGGTTTATAA
Found at i:253246 original size:17 final size:16
Alignment explanation
Indices: 253226--253340 Score: 113
Period size: 17 Copynumber: 6.7 Consensus size: 16
253216 TGATTTTAAA
*
253226 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
253243 TTAAATTTAAATTTAT
1 TTAAATTTAAATTTAT
253259 CTTAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
** *
253276 TTAAATTTATCTTAAAT
1 TTAAATTTAAATT-TAT
253293 TTAAATTTATTTAAATTTAT
1 TT-AA---ATTTAAATTTAT
*
253313 CTTAAATTTAAATTTAA
1 -TTAAATTTAAATTTAT
253330 TTAAATTTAAA
1 TTAAATTTAAA
253341 AGGATATTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
16 27 0.33
17 41 0.49
18 2 0.02
20 4 0.05
21 9 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:253257 original size:6 final size:6
Alignment explanation
Indices: 253220--253340 Score: 99
Period size: 6 Copynumber: 22.0 Consensus size: 6
253210 AGCTTTTGAT
* *
253220 TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
253265 TTTAAA TTT--A TTTAAA TTT--A TCTTAAA TTTAAA TTT--A TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA
253308 TTT--A TCTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
253341 AGGATATTAA
Statistics
Matches: 94, Mismatches: 4, Indels: 34
0.71 0.03 0.26
Matches are distributed among these distances:
4 16 0.17
5 18 0.19
6 54 0.57
7 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:253277 original size:27 final size:27
Alignment explanation
Indices: 253220--253338 Score: 177
Period size: 27 Copynumber: 4.4 Consensus size: 27
253210 AGCTTTTGAT
* * *
253220 TTTAAATTAATTTTAAATTT-TATTTAAA
1 TTTAAATTTATCTTAAATTTAAATTT--A
253248 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTTATCTTAAATTTAAATTTA
253275 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTTATCTTAAATTTAAATTTA
253302 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTTATCTTAAATTTAAATTTA
*
253329 ATTAAATTTA
1 TTTAAATTTA
253339 AAAGGATATT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
27 64 0.74
28 18 0.21
29 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTAAATTTATCTTAAATTTAAATTTA
Found at i:253290 original size:21 final size:20
Alignment explanation
Indices: 253220--253322 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 20
253210 AGCTTTTGAT
*
253220 TTTAAATTAATTTTAAATTTTA
1 TTTAAATTTA-TTTAAA-TTTA
** *
253242 TTTAAATTTAAATTTATCTTAAA
1 TTTAAATTT--ATTTAAATT-TA
253265 TTTAAATTTATTTAAATTTA
1 TTTAAATTTATTTAAATTTA
253285 TCTT-AA---ATTTAAATTTA
1 T-TTAAATTTATTTAAATTTA
253302 TTTAAATTTATCTTAAATTTA
1 TTTAAATTTAT-TTAAATTTA
253323 AATTTAATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.03
17 14 0.22
20 6 0.09
21 18 0.28
22 10 0.15
23 14 0.22
24 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATTTATTTAAATTTA
Found at i:254072 original size:15 final size:15
Alignment explanation
Indices: 254052--254081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
254042 ATAATTTCAT
254052 AAATATCATTAATAA
1 AAATATCATTAATAA
*
254067 AAATATTATTAATAA
1 AAATATCATTAATAA
254082 TCATAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATCATTAATAA
Found at i:254104 original size:16 final size:15
Alignment explanation
Indices: 254074--254145 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
254064 TAAAAATATT
254074 ATTAATAATCATAATA
1 ATTAATAAT-ATAATA
254090 ATTAATAATAGTAATAA
1 ATTAATAATA-TAAT-A
*
254107 ATGTTTATAAT-T-ATA
1 A--TTAATAATATAATA
254122 ATTAAT-AT-TAATA
1 ATTAATAATATAATA
254135 ATTAATAATAT
1 ATTAATAATAT
254146 CAACCATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
12 3 0.06
13 13 0.28
14 2 0.04
15 4 0.09
16 15 0.32
17 3 0.06
19 7 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (15 bp):
ATTAATAATATAATA
Found at i:254123 original size:19 final size:20
Alignment explanation
Indices: 254059--254144 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
254049 CATAAATATC
*
254059 ATTAATAA-AAATATTATTA
1 ATTAATAATAAATATTAATA
*
254078 A-TAATCAT-AATAATTAATA
1 ATTAATAATAAAT-ATTAATA
* * *
254097 A-TAGTAATAAATGTTTATA
1 ATTAATAATAAATATTAATA
*
254116 ATT-ATAATTAATATTAATA
1 ATTAATAATAAATATTAATA
254135 ATTAATAATA
1 ATTAATAATA
254145 TCAACCATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
18 8 0.16
19 34 0.67
20 9 0.18
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTAATAATAAATATTAATA
Found at i:254222 original size:22 final size:22
Alignment explanation
Indices: 254194--254244 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
254184 CTGCGTCCCT
* *
254194 GTCTCGCACCGCCATCGCCGGA
1 GTCTCGCACCACCACCGCCGGA
*
254216 GTCTCGCACCACCACCGTCGGA
1 GTCTCGCACCACCACCGCCGGA
*
254238 GTTTCGC
1 GTCTCGC
254245 TCGTACGTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.25, T:0.18
Consensus pattern (22 bp):
GTCTCGCACCACCACCGCCGGA
Found at i:255199 original size:29 final size:28
Alignment explanation
Indices: 255167--255357 Score: 135
Period size: 29 Copynumber: 6.7 Consensus size: 28
255157 AAACAGTCCA
255167 AAAATTACCATTTTACCCCTAAACTTT-CC
1 AAAATTACCATTTTACCCC--AACTTTACC
*
255196 AAAATT-CCATTTTAACCCCGA-TTTCACC
1 AAAATTACCATTTT-ACCCCAACTTT-ACC
*
255224 AAAAATTATCATTTTACCCCTAAACTTT-CC
1 -AAAATTACCATTTTACCCC--AACTTTACC
* *
255254 AAAATT-CCATTTTAACCCCGATTTTACC
1 AAAATTACCATTTT-ACCCCAACTTTACC
** *
255282 AAAATTACCATTTTACCCCCGAACCCT-CT
1 AAAATTACCATTTTA-CCCC-AACTTTACC
* * * *
255311 AAAATT-CCTTTTTTAACCCGATTTTACC
1 AAAATTACC-ATTTTACCCCAACTTTACC
255339 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
255358 CGGGTATCCA
Statistics
Matches: 126, Mismatches: 20, Indels: 33
0.70 0.11 0.18
Matches are distributed among these distances:
26 3 0.02
27 7 0.06
28 44 0.35
29 58 0.46
30 10 0.08
31 1 0.01
32 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAACTTTACC
Found at i:255229 original size:58 final size:57
Alignment explanation
Indices: 255167--255357 Score: 285
Period size: 57 Copynumber: 3.3 Consensus size: 57
255157 AAACAGTCCA
*
255167 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTACC
*
255224 AAAAATTATCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTACC
1 -AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTACC
** ** * *
255282 AAAATTACCATTTTACCCCCGAACCCTCTAAAATTCCTTTTTTAA-CCCGATTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-ATTTTAACCCCGATTTTACC
255339 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
255358 CGGGTATCCA
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
57 62 0.50
58 61 0.50
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTACC
Found at i:263269 original size:21 final size:22
Alignment explanation
Indices: 263226--263270 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
263216 AGAGCGATTA
**
263226 AAATATTTAAATTTTAAAAATT
1 AAATATTTAAATTAAAAAAATT
*
263248 AAATA-TTAAATTAAAAATATT
1 AAATATTTAAATTAAAAAAATT
263269 AA
1 AA
263271 TAAGGATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTTAAATTAAAAAAATT
Found at i:263433 original size:6 final size:6
Alignment explanation
Indices: 263422--263467 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
263412 TAGAGAGCCA
* *
263422 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TATCTG TTCCTG TTTC
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTC
263468 AGTGAGCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.02, C:0.20, G:0.15, T:0.63
Consensus pattern (6 bp):
TTTCTG
Found at i:270673 original size:20 final size:21
Alignment explanation
Indices: 270645--270692 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
270635 ATTTTAAAGT
*
270645 TTTAAAGTTG-GTATCGATAC
1 TTTATAGTTGTGTATCGATAC
270665 TTTATAGTTGTGTATCGATAC
1 TTTATAGTTGTGTATCGATAC
*
270686 TGTATAG
1 TTTATAG
270693 ATACCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (21 bp):
TTTATAGTTGTGTATCGATAC
Found at i:275699 original size:37 final size:37
Alignment explanation
Indices: 275654--275746 Score: 150
Period size: 37 Copynumber: 2.5 Consensus size: 37
275644 CAGTAAGTAT
*
275654 CGAAGTAATATGTGCCCAACACTCATCAGTTTATAAC
1 CGAAGTAATATGTGCCCAACACCCATCAGTTTATAAC
* *
275691 CGAAGTAATATGTGCCCAACACCCATCGGTTTATAAT
1 CGAAGTAATATGTGCCCAACACCCATCAGTTTATAAC
*
275728 CGAAGTAATATGTGACCAA
1 CGAAGTAATATGTGCCCAA
275747 TGCTAAGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (37 bp):
CGAAGTAATATGTGCCCAACACCCATCAGTTTATAAC
Found at i:276353 original size:2 final size:2
Alignment explanation
Indices: 276346--276375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
276336 AGCAGTCAAG
276346 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
276376 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:276380 original size:2 final size:2
Alignment explanation
Indices: 276375--276406 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
276365 TCTCTCTCTC
276375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
276407 AATAATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:286306 original size:6 final size:6
Alignment explanation
Indices: 286281--286325 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
286271 ACAATTCATA
* * *
286281 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
286326 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:293370 original size:205 final size:203
Alignment explanation
Indices: 293012--293392 Score: 462
Period size: 205 Copynumber: 1.9 Consensus size: 203
293002 TTGTATACGC
* * ** * * *
293012 AAAATCATGTTCACATTATGTTTACACTTCATTTTGGCCATTCAATTTTTAGGTCCCTATCATTT
1 AAAATCATGTCCACATTATGTTTACACTTCATTTTGACCACCCAACTTCTAGATCCCTATCATTT
* * * *
293077 TGGTCACTAAAAAAAATCCTTTTTAATTCTTATCTATGTAAAAAAAAAAAAAACCTCTAATGTTA
66 TAGTCACTAAAAAAAATCATTTCTAATTCTTATCTATGT-AAAAAAAAAAAAACCTCTAAAGTTA
* *
293142 AAGTGAAAAAACAATAGAAACTAAAACAATGCATAAATAAATTTGTAAAATTGTACTTATTTATC
130 AAGTGAAAAAACAATAAAAACTAAAACAATGCATAAACAAATTTGTAAAATTGTACTTATTTATC
293207 CCATTACTG
195 CCATTACTG
* * * * *
293216 AAAATCATGTCCACATTATGTTTACAATTTCATTTTGATCACCCAACTTCTAGATCGCTTTTATT
1 AAAATCATGTCCACATTATGTTTAC-ACTTCATTTTGACCACCCAACTTCTAGATCCCTATCATT
* * *
293281 TTAGTCACTCAAAAAAATCATTTCTAAGTT-TTGATCTATGT-AAAGAAAAAAAA-CTTTAAGAG
65 TTAGTCACTAAAAAAAATCATTTCTAA-TTCTT-ATCTATGTAAAAAAAAAAAAACCTCTAA-AG
* * * *
293343 TTAAAAGTGAAAAAGCGATAAAAACTAAAATAATGCATTAACAAATTTGT
127 TT-AAAGTGAAAAAACAATAAAAACTAAAACAATGCATAAACAAATTTGT
293393 CGATGCTGAA
Statistics
Matches: 147, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
203 5 0.03
204 38 0.26
205 94 0.64
206 10 0.07
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (203 bp):
AAAATCATGTCCACATTATGTTTACACTTCATTTTGACCACCCAACTTCTAGATCCCTATCATTT
TAGTCACTAAAAAAAATCATTTCTAATTCTTATCTATGTAAAAAAAAAAAAACCTCTAAAGTTAA
AGTGAAAAAACAATAAAAACTAAAACAATGCATAAACAAATTTGTAAAATTGTACTTATTTATCC
CATTACTG
Found at i:302311 original size:6 final size:6
Alignment explanation
Indices: 302302--302333 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
302292 GAAACTGAAT
302302 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TG
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TG
302334 AAGAAGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
TGGAGA
Found at i:302956 original size:6 final size:6
Alignment explanation
Indices: 302945--302986 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
302935 AGGAAACGGT
* *
302945 AGAGGC AGAGGC GGAGGC GGAGGC AGAGGC AGAGGC AGAGGC
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC
302987 TCAGAGCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.55, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:315990 original size:6 final size:6
Alignment explanation
Indices: 315979--316017 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
315969 TGATCAAAAT
* * *
315979 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
316018 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:316165 original size:41 final size:40
Alignment explanation
Indices: 316119--316219 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
316109 TTGACCTTGA
** *
316119 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
316159 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
316197 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
316220 TTTATTACTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:322919 original size:37 final size:37
Alignment explanation
Indices: 322856--322995 Score: 190
Period size: 37 Copynumber: 3.8 Consensus size: 37
322846 ATCACCAGCT
* * * * *
322856 CGAAGCTTACTAGGCACACAGTCTGAAAACACTGGCA
1 CGAAGCCTGCTAGGCACACAGCCTGAATACACCGGCA
* * * *
322893 CAAAGCCAGTTAGGCACACAGCCTGAATACACCAGCA
1 CGAAGCCTGCTAGGCACACAGCCTGAATACACCGGCA
*
322930 CGAAGCCTGCTAGGCACACAGCCTGAATACACCGGTA
1 CGAAGCCTGCTAGGCACACAGCCTGAATACACCGGCA
322967 CGAAGCCTGCTAGGCACACAGCCTGAATA
1 CGAAGCCTGCTAGGCACACAGCCTGAATA
322996 TTGTGCAAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 89 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.14
Consensus pattern (37 bp):
CGAAGCCTGCTAGGCACACAGCCTGAATACACCGGCA
Found at i:323311 original size:19 final size:19
Alignment explanation
Indices: 323287--323324 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
323277 CTTATACCCT
323287 TTATTTATGAAAAATTACA
1 TTATTTATGAAAAATTACA
323306 TTATTTATGAAAAATTACA
1 TTATTTATGAAAAATTACA
323325 AAAATTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TTATTTATGAAAAATTACA
Found at i:334440 original size:17 final size:17
Alignment explanation
Indices: 334418--334456 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
334408 CTCCACCTTG
*
334418 ACAAGAA-TTCTCTACGA
1 ACAAGAACTT-TCAACGA
334435 ACAAGAACTTTCAACGA
1 ACAAGAACTTTCAACGA
334452 ACAAG
1 ACAAG
334457 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTTTCAACGA
Found at i:344243 original size:24 final size:24
Alignment explanation
Indices: 344216--344263 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
344206 CTAATGCTCA
344216 CTTTCTCTGCCACTGTACTAGTAG
1 CTTTCTCTGCCACTGTACTAGTAG
344240 CTTTCTCTGCCACTGTACTAGTAG
1 CTTTCTCTGCCACTGTACTAGTAG
344264 TAGCTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (24 bp):
CTTTCTCTGCCACTGTACTAGTAG
Found at i:364809 original size:29 final size:29
Alignment explanation
Indices: 364742--364809 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
364732 AAAAGATAAT
*
364742 TTGAGTGATCATTTTGTAACATTTCATAG
1 TTGAGTGACCATTTTGTAACATTTCATAG
* **
364771 TTGAGAGACCATTTTGTAATGTTTCATAG
1 TTGAGTGACCATTTTGTAACATTTCATAG
*
364800 TTGGGTGACC
1 TTGAGTGACC
364810 TTTACCGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (29 bp):
TTGAGTGACCATTTTGTAACATTTCATAG
Found at i:368482 original size:17 final size:16
Alignment explanation
Indices: 368460--368493 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
368450 TGTATACTTC
*
368460 ATTTTTTTTAATTATTT
1 ATTTTTTATAATT-TTT
368477 ATTTTTTATAATTTTT
1 ATTTTTTATAATTTTT
368493 A
1 A
368494 AATTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTTATAATTTTT
Found at i:375612 original size:52 final size:52
Alignment explanation
Indices: 375527--375868 Score: 535
Period size: 52 Copynumber: 6.6 Consensus size: 52
375517 TTCTCATTTG
* *
375527 ATACTCACGATGACACATAGTCATCTGACCTCATAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
375579 ATGCTCACGATGACACATGGTCATCGGATCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
375631 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
375683 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
** * * * *
375735 ATACTCGTGATGACACTTAGTCATCGAACCTCATAATCCATAAAGCATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
375787 ATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
375838 ATACTCACAATGACACTTAGTCATC-GACCTC
1 ATACTCACGATGACACATAGTCATCGGACCTC
375869 TTTCATTTAC
Statistics
Matches: 268, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
50 5 0.02
51 41 0.15
52 222 0.83
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:379216 original size:20 final size:21
Alignment explanation
Indices: 379168--379216 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
379158 AATAAATCCA
*
379168 AAAATAAAATAAAATGGATTTT
1 AAAAT-AAATAAAATGAATTTT
*
379190 -AATTAAATAAAAT-AATTTT
1 AAAATAAATAAAATGAATTTT
379209 AAAATAAA
1 AAAATAAA
379217 AATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.22
20 15 0.65
21 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATAAATAAAATGAATTTT
Found at i:380974 original size:18 final size:19
Alignment explanation
Indices: 380935--380985 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
380925 TTCAATTACA
*
380935 ATTTTGTGTATTTTTATATT
1 ATTTTATGTA-TTTTATATT
380955 ATTTTATGTATTTT-TATT
1 ATTTTATGTATTTTATATT
*
380973 ATTTTATTTATTT
1 ATTTTATGTATTT
380986 ACTTGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.55
19 4 0.14
20 9 0.31
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTATGTATTTTATATT
Found at i:380986 original size:8 final size:10
Alignment explanation
Indices: 380946--380985 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
380936 TTTTGTGTAT
380946 TTTTATATTA
1 TTTTATATTA
*
380956 TTTTAT-GTA
1 TTTTATATTA
380965 TTTT-TATTA
1 TTTTATATTA
380974 TTTTAT-TTA
1 TTTTATATTA
380983 TTT
1 TTT
380986 ACTTGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 1 0.04
9 18 0.69
10 7 0.27
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTATATTA
Found at i:382767 original size:11 final size:11
Alignment explanation
Indices: 382737--382801 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
382727 AGAACTACAC
*
382737 CGGTCAACAGT
1 CGGTCAACGGT
382748 CGGTCAACGGT
1 CGGTCAACGGT
* **
382759 CGATCAACGAC
1 CGGTCAACGGT
*
382770 CGGTCAACGGC
1 CGGTCAACGGT
* *
382781 CGATCAAAGGT
1 CGGTCAACGGT
382792 CGGTCAACGG
1 CGGTCAACGG
382802 CTGGTCAATG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (11 bp):
CGGTCAACGGT
Found at i:382773 original size:22 final size:22
Alignment explanation
Indices: 382748--382802 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
382738 GGTCAACAGT
* *
382748 CGGTCAACGGTCGATCAACGAC
1 CGGTCAACGGCCGATCAAAGAC
**
382770 CGGTCAACGGCCGATCAAAGGT
1 CGGTCAACGGCCGATCAAAGAC
382792 CGGTCAACGGC
1 CGGTCAACGGC
382803 TGGTCAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (22 bp):
CGGTCAACGGCCGATCAAAGAC
Found at i:382777 original size:33 final size:33
Alignment explanation
Indices: 382735--382809 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
382725 ATAGAACTAC
* * *
382735 ACCGGTCAACAGTCGGTCAACGGTCGATCAACG
1 ACCGGTCAACAGCCGATCAAAGGTCGATCAACG
* *
382768 ACCGGTCAACGGCCGATCAAAGGTCGGTCAACG
1 ACCGGTCAACAGCCGATCAAAGGTCGATCAACG
* *
382801 GCTGGTCAA
1 ACCGGTCAA
382810 TGATTTGACT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (33 bp):
ACCGGTCAACAGCCGATCAAAGGTCGATCAACG
Found at i:382850 original size:21 final size:20
Alignment explanation
Indices: 382824--382862 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
382814 TTGACTTGGT
382824 TTGGGTTTGGTCTTGGTTTAA
1 TTGGGTTTGGT-TTGGTTTAA
382845 TTGGGTTTGGTTTGGTTT
1 TTGGGTTTGGTTTGGTTT
382863 TTTAAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.05, C:0.03, G:0.36, T:0.56
Consensus pattern (20 bp):
TTGGGTTTGGTTTGGTTTAA
Found at i:385286 original size:49 final size:48
Alignment explanation
Indices: 385175--385796 Score: 367
Period size: 49 Copynumber: 12.7 Consensus size: 48
385165 CATTAGCACG
* ** * *
385175 AAGATATGGAGGGAAAGGTTTAAGTCGCAACAACGAA-CCTTGTACCTAA
1 AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTA-CTCA
* * * * *
385224 AAAACATGAAGGGAAATATTTAAGTCGCAACGGCGAATCCAATACTGCA
1 AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACT-CA
* ** * * **
385273 AAGATATGGAGGGAAAGGTTTAAGTCGTGATGGTGAA-CCTTTTACCTCA
1 AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTA-CTCA
* * * *
385322 TAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA
1 -AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTA-CTCA
* * **
385371 AAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAA-CTTTGTACCTCA
1 AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATC-CAGTA-CTCA
* * * *
385420 GAA-ACATGAAGGGAAAGATTTAAGTCGCAATGGTGAATCCAGTAC-CA
1 -AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACTCA
* * * * * *
385467 CGAGGATATAGAGGGAAAGGTTTAAGTTGCAATGGCGAA-CCTTGTACCTCA
1 --AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTA-CTCA
* * * *
385518 GAAGCATA--AAGGGAAAGATTTAAGTCGCAATGGTGAATCTAGTAC-CA
1 -AAG-ATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACTCA
* * * *
385565 CGAAGATATTGAGGGAAAGGTTTAAGTCGCAACGGCG-AGCCTTGTACCTCA
1 --AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTA-CTCA
* * *
385616 GAA-ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAC-CA
1 -AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACTCA
* * * * *
385663 CGAGGATATAGAGGGAAAGATTTAAGTCGCAACAGTGAA-CCTTGTACCTCA
1 --AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTA-CTCA
* * * * *
385714 GAA-ACATGAAGGGAAAGATTTAAGCCGCAACGTCGAATCCAATAC-CA
1 -AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACTCA
*
385761 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGC
1 --AAGATATGGAGGGAAAGATTTAAGTCGCAACGGC
385797 AAACCTTGTA
Statistics
Matches: 443, Mismatches: 98, Indels: 64
0.73 0.16 0.11
Matches are distributed among these distances:
47 11 0.02
48 29 0.07
49 365 0.82
50 29 0.07
51 9 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (48 bp):
AAGATATGGAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACTCA
Done.