Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold420
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: 186816
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
File 1 of 2
Found at i:14 original size:7 final size:7
Alignment explanation
Indices: 3--6105 Score: 5184
Period size: 7 Copynumber: 878.7 Consensus size: 7
1 AT
3 AACCCTA
1 AACCCTA
10 AACCCTA
1 AACCCTA
17 AACCCCTA
1 AA-CCCTA
*
25 CA-CCTA
1 AACCCTA
31 AACCCTA
1 AACCCTA
38 AACCCTA
1 AACCCTA
45 AACCCT-
1 AACCCTA
51 AACCCT-
1 AACCCTA
57 AA-CCTA
1 AACCCTA
63 AA-CCTA
1 AACCCTA
69 AACCCTA
1 AACCCTA
76 AACCCTA
1 AACCCTA
83 AACCCTA
1 AACCCTA
90 AA-CCT-
1 AACCCTA
95 AACCCTA
1 AACCCTA
102 AA-CCTAAAA
1 AACCCT---A
111 AACCC-A
1 AACCCTA
*
117 AA-ACT-
1 AACCCTA
122 AACCCTAA
1 AACCCT-A
130 AACCCTAA
1 AACCCT-A
*
138 AACCCAA
1 AACCCTA
145 AACCCTA
1 AACCCTA
**
152 AACAATA
1 AACCCTA
*
159 AACCCGA
1 AACCCTA
166 AACCCTA
1 AACCCTA
173 AACCCTA
1 AACCCTA
* *
180 AAACATA
1 AACCCTA
187 AACCAACCTA
1 AA-C--CCTA
197 AACCCTA
1 AACCCTA
204 AACCCTA
1 AACCCTA
211 AACCGCCTA
1 AA-C-CCTA
220 AA-CC-A
1 AACCCTA
225 AACCCTA
1 AACCCTA
*
232 AACGCTA
1 AACCCTA
*
239 AA---AA
1 AACCCTA
243 AACCCTA
1 AACCCTA
250 AACCCTA
1 AACCCTA
*
257 ACCCACT-
1 AACC-CTA
264 AACCCTAA
1 AACCCT-A
272 AACCC-A
1 AACCCTA
278 AACCCTA
1 AACCCTA
*
285 CA-CCTAA
1 AACCCT-A
292 AACCCTA
1 AACCCTA
299 AA-CCTA
1 AACCCTA
305 AAGCCCTAA
1 AA-CCCT-A
314 AACCCTA
1 AACCCTA
321 AACCCTA
1 AACCCTA
328 AACGCCTA
1 AAC-CCTA
*
336 ACCCCT-
1 AACCCTA
342 AACCCTA
1 AACCCTA
*
349 AACCCGA
1 AACCCTA
356 AACCCTA
1 AACCCTA
363 AA-CC-A
1 AACCCTA
368 AACCCTA
1 AACCCTA
375 AACACC-A
1 AAC-CCTA
*
382 AACACCGA
1 AAC-CCTA
390 AACCCTATA
1 AACCC--TA
399 AACCCT-
1 AACCCTA
405 AACCCTA
1 AACCCTA
412 AACAAACCTAA
1 AAC---CCT-A
423 AACCCTA
1 AACCCTA
430 AACCCTA
1 AACCCTA
*
437 ACCCCTA
1 AACCCTA
***
444 AA-GAAA
1 AACCCTA
450 AACCCTA
1 AACCCTA
457 AACCCTAAAA
1 AACCCT---A
467 AACCCT-
1 AACCCTA
*
473 AACCCGA
1 AACCCTA
*
480 ACGCCCTA
1 A-ACCCTA
488 AACCCTA
1 AACCCTA
495 AACACCT-
1 AAC-CCTA
502 AACCCTAA
1 AACCCT-A
*
510 AACCATA
1 AACCCTA
517 AACCCTAA
1 AACCCT-A
525 AACCCT-
1 AACCCTA
531 AA-CCTA
1 AACCCTA
537 AACCCTAA
1 AACCCT-A
545 AACCCT-
1 AACCCTA
551 AACCCTA
1 AACCCTA
*
558 AACCCAA
1 AACCCTA
565 ACCACCCT-
1 A--ACCCTA
573 -ACCCTA
1 AACCCTA
579 AACCCTA
1 AACCCTA
586 AACCCTA
1 AACCCTA
593 AACCCTA
1 AACCCTA
600 AACCCTA
1 AACCCTA
607 AACCCTA
1 AACCCTA
*
614 AACACTA
1 AACCCTA
621 AACCCTA
1 AACCCTA
*
628 ACCCCTA
1 AACCCTA
635 AACCC-A
1 AACCCTA
641 CAACCCTA
1 -AACCCTA
*
649 AACCCGA
1 AACCCTA
*
656 ACCCCTA
1 AACCCTA
*
663 AACCCTC
1 AACCCTA
670 AA-CC-A
1 AACCCTA
675 AACCCTA
1 AACCCTA
682 AACCCTAA
1 AACCCT-A
690 AACCCTAA
1 AACCCT-A
*
698 AAACCTA
1 AACCCTA
705 AA-CCTA
1 AACCCTA
*
711 AAACCTA
1 AACCCTA
718 AA--CTAA
1 AACCCT-A
724 AACCCCTA
1 AA-CCCTA
*
732 AACACTA
1 AACCCTA
739 AACCCTA
1 AACCCTA
746 AACCCTA
1 AACCCTA
*
753 AA-ACTA
1 AACCCTA
759 AACCCTA
1 AACCCTA
*
766 AACCCGAAAA
1 AACCC---TA
*
776 AACCCTC
1 AACCCTA
783 AACCCTAA
1 AACCCT-A
791 AACCCTA
1 AACCCTA
798 AACCCTA
1 AACCCTA
805 AACCCTA
1 AACCCTA
812 AACCCTA
1 AACCCTA
819 AACCCTAA
1 AACCCT-A
827 AACCCTA
1 AACCCTA
834 AACCCT-
1 AACCCTA
840 AACCCTA
1 AACCCTA
*
847 AA-CATA
1 AACCCTA
853 AACCCTA
1 AACCCTA
860 AACCCTA
1 AACCCTA
* *
867 ACCCCTC
1 AACCCTA
874 AACCCTA
1 AACCCTA
881 AA-CCT-
1 AACCCTA
886 AACCCT-
1 AACCCTA
892 AACCCTAAAA
1 AACCCT---A
902 AACCCTA
1 AACCCTA
909 AACCCTA
1 AACCCTA
*
916 AACCC-G
1 AACCCTA
922 AACCCTA
1 AACCCTA
*
929 AGCCCGCTA
1 A-ACC-CTA
938 AACCCTA
1 AACCCTA
*
945 AACCCAA
1 AACCCTA
*
952 AAACCTA
1 AACCCTA
959 AACCCTA
1 AACCCTA
966 AACCC-A
1 AACCCTA
*
972 AACCCCA
1 AACCCTA
979 AACACC-A
1 AAC-CCTA
*
986 AACCCCA
1 AACCCTA
993 AACCCTA
1 AACCCTA
*
1000 AACACT-
1 AACCCTA
*
1006 AACACTA
1 AACCCTA
1013 AACCCATA
1 AACCC-TA
1021 AACCCT-
1 AACCCTA
1027 AACCCT-
1 AACCCTA
1033 AACCCTA
1 AACCCTA
*
1040 AAACCTA
1 AACCCTA
1047 AACCCT-
1 AACCCTA
1053 AACCCTA
1 AACCCTA
1060 AA-CCTA
1 AACCCTA
1066 AACCCTA
1 AACCCTA
1073 AA-CCTA
1 AACCCTA
1079 AACCCTA
1 AACCCTA
*
1086 AACCCGA
1 AACCCTA
1093 AACCCTAA
1 AACCCT-A
1101 AACCC-A
1 AACCCTA
* *
1107 ACCCCCA
1 AACCCTA
1114 AA-CCT-
1 AACCCTA
1119 AACCC-A
1 AACCCTA
1125 AACCCTGA
1 AACCCT-A
1133 AACCCCTA
1 AA-CCCTA
*
1141 AACCCCA
1 AACCCTA
*
1148 AACCCCA
1 AACCCTA
1155 AACCCTA
1 AACCCTA
1162 AACCC-A
1 AACCCTA
1168 AA-CCT-
1 AACCCTA
*
1173 AACACTA
1 AACCCTA
1180 AACCCTA
1 AACCCTA
1187 AACCCTA
1 AACCCTA
1194 AA-CC-A
1 AACCCTA
*
1199 AAACCTA
1 AACCCTA
1206 AACCCTAAAA
1 AACCCT---A
**
1216 AAAACTA
1 AACCCTA
1223 AA-CCTAA
1 AACCCT-A
1230 AACCCTA
1 AACCCTA
1237 AACCCTA
1 AACCCTA
1244 AACCCTA
1 AACCCTA
*
1251 AAACCTA
1 AACCCTA
*
1258 AACACTAAAA
1 AACCCT---A
1268 AACCCTAA
1 AACCCT-A
*
1276 AACCCAA
1 AACCCTA
1283 AACCCTAAA
1 AACCCT--A
1292 AACCCT-
1 AACCCTA
1298 AACCCTAAAA
1 AACCCT---A
1308 AACCCTA
1 AACCCTA
1315 AACCCTA
1 AACCCTA
*
1322 AACCCCA
1 AACCCTA
1329 AACCCTA
1 AACCCTA
1336 AACCCTA
1 AACCCTA
1343 AACCCTA
1 AACCCTA
*
1350 AAACC-A
1 AACCCTA
1356 TAA-CCTA
1 -AACCCTA
*
1363 AA-CC-G
1 AACCCTA
1368 AACCCTA
1 AACCCTA
1375 AACCCTA
1 AACCCTA
1382 AACCCCTA
1 AA-CCCTA
*
1390 AACCCCA
1 AACCCTA
1397 AACCCTA
1 AACCCTA
*
1404 AACCCCA
1 AACCCTA
1411 AACCCTA
1 AACCCTA
1418 AACCCTA
1 AACCCTA
1425 AACCCTA
1 AACCCTA
*
1432 AACCCCA
1 AACCCTA
*
1439 AACCCGA
1 AACCCTA
*
1446 AACCCCA
1 AACCCTA
1453 AACCCT-
1 AACCCTA
1459 AACGCCTA
1 AAC-CCTA
1467 AACCCTA
1 AACCCTA
1474 AACCCTA
1 AACCCTA
1481 AACCCT-
1 AACCCTA
1487 AACCCTA
1 AACCCTA
1494 AA-CCTAA
1 AACCCT-A
1501 AACCCTA
1 AACCCTA
*
1508 AACCC-C
1 AACCCTA
1514 AACCC--
1 AACCCTA
1519 AA-CCTA
1 AACCCTA
*
1525 AACCCCA
1 AACCCTA
*
1532 AACCCCA
1 AACCCTA
*
1539 AACCCCA
1 AACCCTA
*
1546 AACCCCA
1 AACCCTA
1553 AACCGC-A
1 AACC-CTA
1560 AACCCTAAA
1 AACCCT--A
1569 AACCCTA
1 AACCCTA
1576 AACCCT-
1 AACCCTA
1582 AACCCTA
1 AACCCTA
1589 AACCCTA
1 AACCCTA
1596 AACCCT-
1 AACCCTA
*
1602 AACCCCA
1 AACCCTA
1609 AACCC-A
1 AACCCTA
1615 AACCCTA
1 AACCCTA
1622 AACCCTA
1 AACCCTA
1629 AA-CCT-
1 AACCCTA
1634 AA-CC-A
1 AACCCTA
1639 AACCCTA
1 AACCCTA
*
1646 AACACTA
1 AACCCTA
*
1653 AACCCCA
1 AACCCTA
*
1660 AACCCCA
1 AACCCTA
*
1667 AACCCGA
1 AACCCTA
1674 AACCCTA
1 AACCCTA
*
1681 AACCCCA
1 AACCCTA
*
1688 AACCC-C
1 AACCCTA
1694 AACCCTA
1 AACCCTA
* *
1701 CACCATA
1 AACCCTA
1708 AACCCTA
1 AACCCTA
1715 AACCCTA
1 AACCCTA
1722 AACCCT-
1 AACCCTA
1728 AACCCT-
1 AACCCTA
1734 AACCCTA
1 AACCCTA
1741 AACCCT-
1 AACCCTA
1747 AACACCTA
1 AAC-CCTA
1755 AACCCTA
1 AACCCTA
*
1762 AAACCT-
1 AACCCTA
1768 AA-CCTAA
1 AACCCT-A
*
1775 AACCCGA
1 AACCCTA
*
1782 AA-CAT-
1 AACCCTA
1787 AACCCTAA
1 AACCCT-A
1795 AACCCTA
1 AACCCTA
1802 AA-CCTA
1 AACCCTA
1808 AACCCTA
1 AACCCTA
1815 AACCCTAAA
1 AACCCT--A
1824 AACCCT-
1 AACCCTA
1830 AACCC-A
1 AACCCTA
1836 AACACCTA
1 AAC-CCTA
1844 AACCCTA
1 AACCCTA
1851 AACCCTA
1 AACCCTA
*
1858 AACACTA
1 AACCCTA
1865 AACCCTA
1 AACCCTA
1872 AACCCTAAA
1 AACCCT--A
*
1881 AACCC-G
1 AACCCTA
*
1887 AACCC-G
1 AACCCTA
1893 AACCCTA
1 AACCCTA
1900 AA-CCTA
1 AACCCTA
*
1906 AACCCGA
1 AACCCTA
1913 AACCCTAAA
1 AACCCT--A
1922 AACCCTAAA
1 AACCCT--A
1931 AACCCTA
1 AACCCTA
1938 AACCCTA
1 AACCCTA
1945 AA-CCTA
1 AACCCTA
1951 AACCCGT-
1 AACCC-TA
*
1958 AACACT-
1 AACCCTA
1964 AACCCTA
1 AACCCTA
1971 AA-CCTAAA
1 AACCCT--A
1979 AGACCCTA
1 A-ACCCTA
1987 AACCCTAA
1 AACCCT-A
*
1995 AACCCGA
1 AACCCTA
*
2002 ACCCCTA
1 AACCCTA
2009 AACCCTA
1 AACCCTA
2016 AACCCTA
1 AACCCTA
2023 AA-CC--
1 AACCCTA
2027 AACCCTA
1 AACCCTA
2034 AACCCT-
1 AACCCTA
2040 AACCCTA
1 AACCCTA
2047 AACCCTA
1 AACCCTA
2054 AACCCTA
1 AACCCTA
2061 AACCCTA
1 AACCCTA
2068 AACCCTA
1 AACCCTA
2075 AACCCTA
1 AACCCTA
2082 AACCCT-
1 AACCCTA
2088 AACCCTA
1 AACCCTA
2095 AACCCTAAA
1 AACCCT--A
2104 AACCCT-
1 AACCCTA
2110 AACCCT-
1 AACCCTA
2116 AACCCTA
1 AACCCTA
2123 AACCCTA
1 AACCCTA
2130 AACCCTAA
1 AACCCT-A
2138 AACCCTA
1 AACCCTA
2145 AACCCTA
1 AACCCTA
2152 AACCCTA
1 AACCCTA
2159 AACCCTA
1 AACCCTA
2166 AACCCTA
1 AACCCTA
2173 AACCCTA
1 AACCCTA
2180 AACCCTA
1 AACCCTA
2187 AACCCTA
1 AACCCTA
2194 AACCCT-
1 AACCCTA
2200 AACCCTA
1 AACCCTA
2207 AACCCTA
1 AACCCTA
2214 AA-CCTAA
1 AACCCT-A
2221 AACCCTA
1 AACCCTA
2228 AACCCTA
1 AACCCTA
2235 AACCCTA
1 AACCCTA
2242 AACCCTA
1 AACCCTA
2249 AACCCTA
1 AACCCTA
2256 AACCCTA
1 AACCCTA
2263 AACCCTAA
1 AACCCT-A
2271 AACCCTA
1 AACCCTA
2278 AACCCTA
1 AACCCTA
2285 AACCCTA
1 AACCCTA
2292 AACCCTA
1 AACCCTA
2299 AACCCT-
1 AACCCTA
2305 AACCCTA
1 AACCCTA
2312 AACCCTA
1 AACCCTA
2319 AACCCTA
1 AACCCTA
2326 AACCCTA
1 AACCCTA
2333 AACCCTA
1 AACCCTA
2340 AA-CCTA
1 AACCCTA
2346 AACCCTA
1 AACCCTA
2353 AACCCTA
1 AACCCTA
2360 AACCCTA
1 AACCCTA
2367 AACCCTA
1 AACCCTA
2374 AACCCTA
1 AACCCTA
2381 AACCCTA
1 AACCCTA
2388 AACCCTA
1 AACCCTA
2395 AACCCTA
1 AACCCTA
2402 AACCCTA
1 AACCCTA
2409 AACCCTA
1 AACCCTA
2416 AACCCTA
1 AACCCTA
2423 AACCCTAA
1 AACCCT-A
2431 AACCCTA
1 AACCCTA
2438 AACCCTA
1 AACCCTA
2445 AACCCTA
1 AACCCTA
2452 AACCCTAA
1 AACCCT-A
2460 AACCCTA
1 AACCCTA
2467 AA-CCT-
1 AACCCTA
2472 AACCCTA
1 AACCCTA
2479 AACCCTA
1 AACCCTA
2486 AACCCTA
1 AACCCTA
2493 AACCCTA
1 AACCCTA
2500 AACCCTA
1 AACCCTA
2507 AACCCTA
1 AACCCTA
2514 AACCCT-
1 AACCCTA
*
2520 AACCATA
1 AACCCTA
2527 AACCCTA
1 AACCCTA
2534 AA-CCTAAAA
1 AACCCT---A
*
2543 AAACCTA
1 AACCCTA
2550 AACCCCTA
1 AA-CCCTA
2558 AACACCTA
1 AAC-CCTA
2566 AACCCTA
1 AACCCTA
2573 AACCCTA
1 AACCCTA
2580 AACCCT-
1 AACCCTA
2586 AACCCTA
1 AACCCTA
2593 AACCCT-
1 AACCCTA
2599 AACCCTA
1 AACCCTA
2606 AACCCTA
1 AACCCTA
*
2613 AACCCGAA
1 AACCC-TA
2621 AACCC--
1 AACCCTA
2626 AACCCTA
1 AACCCTA
2633 AGACCCTA
1 A-ACCCTA
2641 AACCCCTA
1 AA-CCCTA
2649 AACCCTA
1 AACCCTA
2656 AACCCTA
1 AACCCTA
*
2663 AAACCTA
1 AACCCTA
2670 AACCCTAA
1 AACCCT-A
2678 AACCCTA
1 AACCCTA
2685 AA-CCTA
1 AACCCTA
2691 AACCCTA
1 AACCCTA
*
2698 AACCATA
1 AACCCTA
2705 AACCCTA
1 AACCCTA
2712 AACCCTAA
1 AACCCT-A
2720 AACCCTA
1 AACCCTA
2727 AA-CCTA
1 AACCCTA
2733 AACCCTA
1 AACCCTA
2740 AACCCTAAA
1 AACCCT--A
2749 AACCACT-
1 AACC-CTA
2756 AACCCTA
1 AACCCTA
2763 AACCCTA
1 AACCCTA
2770 AACCCTAA
1 AACCCT-A
2778 AACCCT-
1 AACCCTA
2784 AACCCTA
1 AACCCTA
2791 AA-CCT-
1 AACCCTA
*
2796 AACCC-G
1 AACCCTA
2802 AACCCTAA
1 AACCCT-A
2810 AACCCTA
1 AACCCTA
*
2817 AACCCGA
1 AACCCTA
2824 AA-CCTA
1 AACCCTA
2830 AACGCCTA
1 AAC-CCTA
2838 AACCCTA
1 AACCCTA
2845 AACCCTA
1 AACCCTA
2852 AACCCTA
1 AACCCTA
*
2859 AACCCAAA
1 AACCC-TA
2867 AACCCTA
1 AACCCTA
*
2874 AACCCGA
1 AACCCTA
2881 AACCCTA
1 AACCCTA
2888 AACCCT-
1 AACCCTA
2894 AACCCTAAA
1 AACCCT--A
2903 AACCCTA
1 AACCCTA
2910 AACCCTAAA
1 AACCCT--A
*
2919 AACCATAAA
1 AACCCT--A
2928 AACCCTA
1 AACCCTA
2935 AACCCTA
1 AACCCTA
2942 AACCCTA
1 AACCCTA
2949 AA-CCTA
1 AACCCTA
2955 AACCCTA
1 AACCCTA
2962 AACCC-A
1 AACCCTA
*
2968 AACCCGA
1 AACCCTA
*
2975 AACCCCGGA
1 AA-CCC-TA
2984 AACCCGTAA
1 AACCC-T-A
*
2993 AACCCGA
1 AACCCTA
*
3000 AACCCGA
1 AACCCTA
*
3007 TAACCC-G
1 -AACCCTA
*
3014 AACCC-G
1 AACCCTA
3020 AACCCT-
1 AACCCTA
3026 AACCCT-
1 AACCCTA
3032 AACCCTA
1 AACCCTA
3039 AA-CCTA
1 AACCCTA
3045 AA-CCTAA
1 AACCCT-A
3052 AACCCT-
1 AACCCTA
3058 -ACCCT-
1 AACCCTA
3063 AACCCTA
1 AACCCTA
3070 AACCCTA
1 AACCCTA
3077 AACCCTA
1 AACCCTA
3084 AA-CCT-
1 AACCCTA
*
3089 ACCCCT-
1 AACCCTA
3095 AACCCTA
1 AACCCTA
3102 AACCCTA
1 AACCCTA
3109 AA-CCT-
1 AACCCTA
3114 -ACCCT-
1 AACCCTA
3119 -A-CCTAA
1 AACCCT-A
3125 AACCCTA
1 AACCCTA
3132 AACCCTA
1 AACCCTA
*
3139 AA--CTC
1 AACCCTA
3144 AACCCTA
1 AACCCTA
*
3151 TACCCCTAA
1 -AACCCT-A
3160 AACCCTGA
1 AACCCT-A
3168 AACCCTA
1 AACCCTA
3175 AACCCTAAA
1 AACCCT--A
3184 AACCCTA
1 AACCCTA
3191 AA-CCTA
1 AACCCTA
*
3197 AAACCTA
1 AACCCTA
3204 AACCCTAAA
1 AACCCT--A
3213 AACCCTA
1 AACCCTA
3220 AACCCTA
1 AACCCTA
3227 AACCCTA
1 AACCCTA
3234 AACCCTA
1 AACCCTA
3241 AACCCTA
1 AACCCTA
3248 AACCCTA
1 AACCCTA
3255 AACCCTA
1 AACCCTA
3262 AACCCTA
1 AACCCTA
3269 AACCCTA
1 AACCCTA
3276 AACCCT-
1 AACCCTA
3282 AACCCTA
1 AACCCTA
3289 AACCCTA
1 AACCCTA
3296 AACCCTAA
1 AACCCT-A
3304 AACCCTA
1 AACCCTA
3311 AACCCTA
1 AACCCTA
3318 AA-CCTA
1 AACCCTA
3324 AA-CCTA
1 AACCCTA
3330 AACCCTA
1 AACCCTA
3337 AA-CCTA
1 AACCCTA
3343 AACCCTA
1 AACCCTA
3350 AACCCTA
1 AACCCTA
3357 AACCCTA
1 AACCCTA
3364 AACCCTA
1 AACCCTA
3371 AACCCTA
1 AACCCTA
3378 AACCCTA
1 AACCCTA
3385 AACCCTA
1 AACCCTA
3392 AACCCTA
1 AACCCTA
3399 AA-CCT-
1 AACCCTA
3404 AACCCTA
1 AACCCTA
3411 AACCCTA
1 AACCCTA
3418 AACCCTA
1 AACCCTA
3425 AA-CCTA
1 AACCCTA
3431 AACCCTA
1 AACCCTA
3438 AACCCTA
1 AACCCTA
3445 AACCCTA
1 AACCCTA
3452 AACCCTA
1 AACCCTA
3459 AACCCTA
1 AACCCTA
3466 AACCCTA
1 AACCCTA
3473 AACCCTA
1 AACCCTA
*
3480 ACCCCTA
1 AACCCTA
3487 AACCCTA
1 AACCCTA
3494 AACCCTA
1 AACCCTA
3501 AACCCTA
1 AACCCTA
3508 AACCCTA
1 AACCCTA
3515 AACCCTA
1 AACCCTA
3522 AACCCTA
1 AACCCTA
3529 AACCCT-
1 AACCCTA
3535 AACCCTA
1 AACCCTA
3542 AACCCTA
1 AACCCTA
3549 AACCCTA
1 AACCCTA
3556 AACCCTA
1 AACCCTA
3563 AA-CCTA
1 AACCCTA
3569 AACCCTA
1 AACCCTA
3576 AACCCTA
1 AACCCTA
3583 AACCCTA
1 AACCCTA
3590 AACCCTAA
1 AACCCT-A
3598 AACCCTA
1 AACCCTA
3605 AACCCTA
1 AACCCTA
3612 AACCCTA
1 AACCCTA
3619 AACCCTA
1 AACCCTA
3626 AACCCT-
1 AACCCTA
3632 AACCCTAA
1 AACCCT-A
3640 AACCCTA
1 AACCCTA
3647 AACCCTA
1 AACCCTA
3654 AACCCTA
1 AACCCTA
3661 AACCCTA
1 AACCCTA
3668 AACCCTAA
1 AACCCT-A
3676 AACCCTA
1 AACCCTA
3683 AACCCTA
1 AACCCTA
3690 AACCCTA
1 AACCCTA
3697 AACCCTA
1 AACCCTA
3704 AACCCTA
1 AACCCTA
3711 AACCCT-
1 AACCCTA
3717 AACCCTA
1 AACCCTA
3724 AACCCTA
1 AACCCTA
3731 AACCCTA
1 AACCCTA
3738 AACCCTA
1 AACCCTA
3745 AACCCTA
1 AACCCTA
3752 AACCCT-
1 AACCCTA
3758 AACCCTA
1 AACCCTA
3765 AACCCTA
1 AACCCTA
3772 AACCCT-
1 AACCCTA
3778 AACCCTA
1 AACCCTA
3785 AACCCTA
1 AACCCTA
3792 AACCCTA
1 AACCCTA
3799 AACCCTA
1 AACCCTA
3806 AACCCTA
1 AACCCTA
3813 AACCCTA
1 AACCCTA
3820 AACCCTA
1 AACCCTA
3827 AACCCTA
1 AACCCTA
3834 AACCCTA
1 AACCCTA
3841 AACCCTA
1 AACCCTA
3848 AACCCTA
1 AACCCTA
3855 AACCCTA
1 AACCCTA
3862 AA-CCT-
1 AACCCTA
3867 AACCCTA
1 AACCCTA
3874 AACCCTA
1 AACCCTA
3881 AACCCTA
1 AACCCTA
3888 AACCCTA
1 AACCCTA
3895 AACCCTA
1 AACCCTA
3902 AACCCTA
1 AACCCTA
3909 AACCCTA
1 AACCCTA
3916 AACCCTA
1 AACCCTA
3923 AACCCTA
1 AACCCTA
3930 AACCCT-
1 AACCCTA
3936 AACCCTA
1 AACCCTA
3943 AACCCTA
1 AACCCTA
3950 AACCCTA
1 AACCCTA
3957 AACCCTA
1 AACCCTA
3964 AACCCTA
1 AACCCTA
3971 AACCCTA
1 AACCCTA
3978 AACCCTAA
1 AACCCT-A
3986 AACCCTA
1 AACCCTA
3993 AACCCTA
1 AACCCTA
4000 AACCCTA
1 AACCCTA
4007 AACCCTA
1 AACCCTA
*
4014 AACCCGA
1 AACCCTA
*
4021 AACCCGA
1 AACCCTA
*
4028 AACCCGA
1 AACCCTA
*
4035 AACCCGA
1 AACCCTA
*
4042 AACCCGA
1 AACCCTA
*
4049 AACCCGA
1 AACCCTA
*
4056 AACCCGA
1 AACCCTA
*
4063 AACCCGA
1 AACCCTA
*
4070 AACCCGA
1 AACCCTA
*
4077 AACCCGA
1 AACCCTA
*
4084 AACCC-G
1 AACCCTA
*
4090 AACCCGA
1 AACCCTA
*
4097 AA-CC-G
1 AACCCTA
*
4102 AACCC-G
1 AACCCTA
**
4108 AACCCCG
1 AACCCTA
**
4115 AACCCCG
1 AACCCTA
**
4122 AACCCCG
1 AACCCTA
**
4129 AACCCCG
1 AACCCTA
**
4136 AACCCCG
1 AACCCTA
**
4143 AACCCCG
1 AACCCTA
**
4150 AACCCCG
1 AACCCTA
**
4157 AACCCCG
1 AACCCTA
**
4164 AACCCCG
1 AACCCTA
**
4171 AACCCCG
1 AACCCTA
**
4178 AACCCCG
1 AACCCTA
**
4185 AACCCCG
1 AACCCTA
**
4192 AACCCCG
1 AACCCTA
**
4199 AACCCCG
1 AACCCTA
**
4206 AACCCCG
1 AACCCTA
**
4213 AACCCCG
1 AACCCTA
**
4220 AACCCCG
1 AACCCTA
*
4227 AACCCCA
1 AACCCTA
* *
4234 AACTCGA
1 AACCCTA
*
4241 AACCCCA
1 AACCCTA
*
4248 AACCCCA
1 AACCCTA
4255 AACCCTA
1 AACCCTA
*
4262 AACCCCA
1 AACCCTA
*
4269 AACCCCA
1 AACCCTA
*
4276 AACCCCA
1 AACCCTA
*
4283 AACCCCA
1 AACCCTA
*
4290 AACCCCCCA
1 AA--CCCTA
*
4299 AACCCCA
1 AACCCTA
*
4306 AACCC-C
1 AACCCTA
*
4312 AACCC-C
1 AACCCTA
**
4318 AACCCCC
1 AACCCTA
**
4325 AACCCCC
1 AACCCTA
*
4332 AACCCCA
1 AACCCTA
*
4339 AACCCCA
1 AACCCTA
* *
4346 ACCCCCCA
1 A-ACCCTA
*
4354 ACCCCT-
1 AACCCTA
*
4360 AACCCCA
1 AACCCTA
*
4367 AACCCCA
1 AACCCTA
*
4374 AACCCCA
1 AACCCTA
4381 AACCCTA
1 AACCCTA
*
4388 AACCCCA
1 AACCCTA
4395 AACCC-A
1 AACCCTA
*
4401 AACCCCA
1 AACCCTA
*
4408 AACCCCA
1 AACCCTA
*
4415 AACCCCA
1 AACCCTA
*
4422 AACCCCA
1 AACCCTA
*
4429 AACCCCA
1 AACCCTA
*
4436 AACCCCA
1 AACCCTA
*
4443 AACCCCA
1 AACCCTA
*
4450 AACCCCA
1 AACCCTA
*
4457 AACCCCA
1 AACCCTA
*
4464 AACCCCA
1 AACCCTA
*
4471 AACCCCA
1 AACCCTA
* *
4478 ACCCCCA
1 AACCCTA
*
4485 ACCCCTA
1 AACCCTA
*
4492 ACCCCTA
1 AACCCTA
*
4499 ACCCCCTA
1 A-ACCCTA
4507 AACCCCTA
1 AA-CCCTA
*
4515 ACCCCCT-
1 A-ACCCTA
4522 -A-CCTA
1 AACCCTA
4527 AACCCCTA
1 AA-CCCTA
4535 AACCCCTA
1 AA-CCCTA
*
4543 ACCCCTA
1 AACCCTA
*
4550 ACCCCT-
1 AACCCTA
4556 AACCCTA
1 AACCCTA
*
4563 ACCCCT-
1 AACCCTA
*
4569 AACCCCA
1 AACCCTA
*
4576 AACCCCA
1 AACCCTA
4583 AACCCTA
1 AACCCTA
*
4590 AACCCCA
1 AACCCTA
*
4597 AACCCCA
1 AACCCTA
*
4604 AACCCCA
1 AACCCTA
*
4611 AACCCGA
1 AACCCTA
*
4618 AACCCCA
1 AACCCTA
4625 AACCCTA
1 AACCCTA
4632 AACCCTA
1 AACCCTA
*
4639 AACCCCA
1 AACCCTA
*
4646 AACCCCA
1 AACCCTA
*
4653 AACCCCA
1 AACCCTA
4660 AACCCTA
1 AACCCTA
4667 AACCCTA
1 AACCCTA
4674 AACCCTA
1 AACCCTA
4681 AACCCTA
1 AACCCTA
4688 AACCCTAA
1 AACCCT-A
4696 AACCCTAA
1 AACCCT-A
4704 AACCCTA
1 AACCCTA
4711 AACCCTAA
1 AACCCT-A
4719 AACCCTA
1 AACCCTA
4726 AACCCTA
1 AACCCTA
4733 AACCCTA
1 AACCCTA
4740 AACCCTA
1 AACCCTA
4747 AACCCTA
1 AACCCTA
4754 AACCCTA
1 AACCCTA
*
4761 AGCCCTA
1 AACCCTA
*
4768 AGCCCTA
1 AACCCTA
*
4775 AGCCCTA
1 AACCCTA
*
4782 AGCCCTA
1 AACCCTA
*
4789 AGCCCTA
1 AACCCTA
*
4796 AGCCCTA
1 AACCCTA
*
4803 AGCCCTA
1 AACCCTA
*
4810 AGCCCTA
1 AACCCTA
*
4817 AGCCCTA
1 AACCCTA
*
4824 AGCCCTA
1 AACCCTA
*
4831 AGCCCTA
1 AACCCTA
*
4838 AGCCCTA
1 AACCCTA
*
4845 AGCCCTA
1 AACCCTA
*
4852 AGCCCTA
1 AACCCTA
*
4859 AGCCCTA
1 AACCCTA
*
4866 AGCCCTA
1 AACCCTA
4873 AACCCTA
1 AACCCTA
*
4880 AGCCCTA
1 AACCCTA
4887 AACCCTA
1 AACCCTA
4894 AACCCTA
1 AACCCTA
4901 AACCCTA
1 AACCCTA
*
4908 AACCCCA
1 AACCCTA
4915 AACCCTA
1 AACCCTA
*
4922 AACCCCA
1 AACCCTA
*
4929 AACCCCA
1 AACCCTA
*
4936 AACCCCA
1 AACCCTA
4943 AACCCTA
1 AACCCTA
* *
4950 CACCCCA
1 AACCCTA
*
4957 AACCCCA
1 AACCCTA
* *
4964 GACCCCA
1 AACCCTA
* *
4971 GACCCCA
1 AACCCTA
* *
4978 GACCCCA
1 AACCCTA
* *
4985 GACCCCA
1 AACCCTA
*
4992 GA-CCTA
1 AACCCTA
* *
4998 ACCCCGA
1 AACCCTA
* *
5005 ACCCCGA
1 AACCCTA
* *
5012 ACCCCGA
1 AACCCTA
* *
5019 ACCCCCA
1 AACCCTA
*
5026 AACCCCA
1 AACCCTA
*
5033 ACCCCTA
1 AACCCTA
*
5040 AACCCCA
1 AACCCTA
* *
5047 ACCCCCA
1 AACCCTA
5054 AA-CCTCA
1 AACCCT-A
*
5061 AACCCCA
1 AACCCTA
*
5068 AACCCCA
1 AACCCTA
*
5075 AACCCCA
1 AACCCTA
5082 AACCCTA
1 AACCCTA
5089 AA-CCTCA
1 AACCCT-A
5096 AACCCTA
1 AACCCTA
*
5103 AACCCCA
1 AACCCTA
*
5110 AACCCCA
1 AACCCTA
*
5117 AACCCCA
1 AACCCTA
* *
5124 GACCCCA
1 AACCCTA
* *
5131 GACCCCA
1 AACCCTA
* *
5138 GACCCCA
1 AACCCTA
*
5145 GACCCTA
1 AACCCTA
5152 AA-CCT-
1 AACCCTA
**
5157 AACCCCG
1 AACCCTA
**
5164 AACCCCG
1 AACCCTA
**
5171 AACCCCG
1 AACCCTA
**
5178 AACCCCC
1 AACCCTA
**
5185 AACCCCG
1 AACCCTA
**
5192 AACCCCC
1 AACCCTA
*
5199 AACCTCCA
1 AACC-CTA
* *
5207 ACCCCCA
1 AACCCTA
*
5214 AACCCCA
1 AACCCTA
*
5221 AACCCCA
1 AACCCTA
*
5228 AACCC-C
1 AACCCTA
**
5234 AACCCCC
1 AACCCTA
*
5241 AACCC-C
1 AACCCTA
**
5247 AACCCCC
1 AACCCTA
**
5254 AACCCCC
1 AACCCTA
*
5261 AACCCCA
1 AACCCTA
*
5268 AACCCCA
1 AACCCTA
*
5275 AACCCCA
1 AACCCTA
*
5282 AACCCCA
1 AACCCTA
*
5289 AACCCCA
1 AACCCTA
5296 AACCCTA
1 AACCCTA
* *
5303 CACCCCA
1 AACCCTA
*
5310 AACCCCA
1 AACCCTA
* *
5317 GACCCCA
1 AACCCTA
* *
5324 GACCCCA
1 AACCCTA
* *
5331 GACCCCA
1 AACCCTA
*
5338 GA-CCT-
1 AACCCTA
**
5343 AACCCCG
1 AACCCTA
**
5350 AACCCCG
1 AACCCTA
*
5357 AA-CCTCG
1 AACCCT-A
5364 AACCCTGA
1 AACCCT-A
* *
5372 ACCCCGA
1 AACCCTA
* *
5379 ACCCCCA
1 AACCCTA
*
5386 AACCCCA
1 AACCCTA
*
5393 ACCCCTA
1 AACCCTA
*
5400 AACCCCA
1 AACCCTA
* *
5407 ACCCCCA
1 AACCCTA
*
5414 AACCCCA
1 AACCCTA
5421 AATCCC-A
1 AA-CCCTA
*
5428 AACCCCA
1 AACCCTA
*
5435 AACCCCA
1 AACCCTA
*
5442 AACCCCA
1 AACCCTA
*
5449 AACCCCA
1 AACCCTA
* *
5456 GACCCCA
1 AACCCTA
* *
5463 GACCCCA
1 AACCCTA
* *
5470 GACCCCA
1 AACCCTA
* *
5477 GACCCCA
1 AACCCTA
* *
5484 GACCCCA
1 AACCCTA
* *
5491 GACCCCA
1 AACCCTA
*
5498 GACCC-A
1 AACCCTA
*
5504 GACCCTA
1 AACCCTA
5511 AA-CCT-
1 AACCCTA
**
5516 AACCCCG
1 AACCCTA
**
5523 AACCCCG
1 AACCCTA
**
5530 AACCCCG
1 AACCCTA
**
5537 AACCCCG
1 AACCCTA
**
5544 AACCCCC
1 AACCCTA
**
5551 AACCCCG
1 AACCCTA
**
5558 AACCCCG
1 AACCCTA
**
5565 AACCCCC
1 AACCCTA
*
5572 AACCTCCA
1 AACC-CTA
* *
5580 ACCCCCA
1 AACCCTA
*
5587 AACCCCA
1 AACCCTA
*
5594 AACCCCA
1 AACCCTA
*
5601 AACCC-C
1 AACCCTA
**
5607 AACCCCC
1 AACCCTA
**
5614 AACCCCC
1 AACCCTA
**
5621 AACCCCC
1 AACCCTA
*
5628 AACCCCA
1 AACCCTA
*
5635 AACCCCA
1 AACCCTA
*
5642 AACCCCA
1 AACCCTA
*
5649 AACCCCA
1 AACCCTA
* *
5656 ACCCCCA
1 AACCCTA
*
5663 AA-CCTC
1 AACCCTA
**
5669 AACCCCC
1 AACCCTA
**
5676 AACCCCC
1 AACCCTA
*
5683 AACCCCA
1 AACCCTA
*
5690 AACCCCA
1 AACCCTA
*
5697 AACCCCA
1 AACCCTA
*
5704 AACCCCA
1 AACCCTA
* *
5711 GACCCCA
1 AACCCTA
*
5718 AACCCCA
1 AACCCTA
*
5725 AACCCCA
1 AACCCTA
* *
5732 GACCCCA
1 AACCCTA
*
5739 GACCCTA
1 AACCCTA
* *
5746 GACCCCA
1 AACCCTA
*
5753 AACCCCA
1 AACCCTA
* *
5760 GACCCCA
1 AACCCTA
5767 AA---TA
1 AACCCTA
***
5771 AA-AAAA
1 AACCCTA
5777 AACCCTA
1 AACCCTA
5784 AACCCTA
1 AACCCTA
*
5791 AACCTTA
1 AACCCTA
*
5798 AACCCCA
1 AACCCTA
5805 AACCCTA
1 AACCCTA
5812 AA-CC-A
1 AACCCTA
5817 AA-CCT-
1 AACCCTA
5822 AACCTCTA
1 AACC-CTA
5830 AACCCTA
1 AACCCTA
**
5837 AACCCCG
1 AACCCTA
5844 AA-CCTCA
1 AACCCT-A
**
5851 AACCCCG
1 AACCCTA
**
5858 AACCCCG
1 AACCCTA
*
5865 AA-CCTCG
1 AACCCT-A
5872 AA-CCTA
1 AACCCTA
*
5878 ACCCCTA
1 AACCCTA
5885 AACCCTA
1 AACCCTA
5892 AACCCTA
1 AACCCTA
*
5899 ACCCCTA
1 AACCCTA
*
5906 ATCCCTA
1 AACCCTA
*
5913 ACCCCTA
1 AACCCTA
5920 AACCCCTA
1 AA-CCCTA
* *
5928 AACTCAA
1 AACCCTA
*
5935 AACCCAA
1 AACCCTA
**
5942 AACCCCG
1 AACCCTA
*
5949 AA-CCTCG
1 AACCCT-A
**
5956 AACCCCG
1 AACCCTA
*
5963 AACCCCA
1 AACCCTA
*
5970 AACCC-G
1 AACCCTA
**
5976 AACCCCG
1 AACCCTA
*
5983 AACCC-G
1 AACCCTA
* *
5989 AACTCTG
1 AACCCTA
*
5996 AA-CCTCG
1 AACCCT-A
*
6003 AA-CCTCG
1 AACCCT-A
6010 AA-CCTA
1 AACCCTA
*
6016 ACCCCTA
1 AACCCTA
6023 AACCCTA
1 AACCCTA
6030 AACCCTA
1 AACCCTA
6037 AACCCTA
1 AACCCTA
*
6044 ACCCCTA
1 AACCCTA
6051 AACCCCTA
1 AA-CCCTA
* *
6059 AACTCGA
1 AACCCTA
*
6066 AACCCAA
1 AACCCTA
**
6073 AACCCGG
1 AACCCTA
*
6080 AACCCCA
1 AACCCTA
**
6087 AACCCCG
1 AACCCTA
*
6094 AACCCCA
1 AACCCTA
6101 AACCC
1 AACCC
6106 GAACCCCGAA
Statistics
Matches: 5407, Mismatches: 347, Indels: 684
0.84 0.05 0.11
Matches are distributed among these distances:
4 17 0.00
5 95 0.02
6 728 0.13
7 3902 0.72
8 463 0.09
9 144 0.03
10 54 0.01
11 4 0.00
ACGTcount: A:0.42, C:0.46, G:0.03, T:0.10
Consensus pattern (7 bp):
AACCCTA
Found at i:126 original size:39 final size:43
Alignment explanation
Indices: 27--4016 Score: 1368
Period size: 48 Copynumber: 86.9 Consensus size: 43
17 AACCCCTACA
*
27 CCTAAACCCTAAACCCTAAACCCTAACCCTAACCTAAACCTAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCTAACCTAAA-C-AAAC
*
72 CCTAAACCCTAAACCCTAAA-CCTAACCCTAAACCTAAA-AAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AACCTAAACAAAC
*
114 CC-AAA-ACT-AACCCTAAAACCCTAA----AACC--CA-AAAC
1 CCTAAACACTAAACCCT-AAACCCTAACCCTAACCTAAACAAAC
* * *
148 CCTAAACAATAAACCCGAAACCCTAAACCCT-A---AAACATAAA
1 CCTAAACACTAAACCCTAAACCCT-AACCCTAACCTAAACA-AAC
* *
189 CC--AAC-CTAAACCCTAAACCCTAAACC--GCCTAAACCAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCTAACCTAAA-CAAAC
*
228 CCTAAACGCTAAAAAAACCCTAAACCCTAACCCACTAACCCTAAAACCCAAAC
1 CCTAAACACT----AAACCCTAAACCCTAA-CC-CTAA-CCT-AAA--CAAAC
* *
281 CCTACAC-CTAAAACCCTAAA-CCTAAAGCCCTAA---AACCCTAAAC
1 CCTAAACACT-AAACCCTAAACCCT-AA-CCCTAACCTAA-AC-AAAC
* * *
324 CCTAAACGCCTAACCCCT-AACCCTAAACCCGAAACCCTAAACCAAAC
1 CCTAAAC-ACTAAACCCTAAACCCT-AACCC-TAA-CCTAAA-CAAAC
* *
371 CCTAAACACCAAACACCGAAACCCTATAAACCCTAACCCTAAACAAA-
1 CCTAAACACTAAAC-CCTAAACCC--T-AACCCTAA-CCTAAACAAAC
418 CCT----A--AAACCCTAAACCCTAACCCCTAA---AGAA-AAAC
1 CCTAAACACTAAACCCTAAACCCTAA-CCCTAACCTA-AACAAAC
* * *
453 CCTAAACCCTAAA----AAACCCTAACCCGAACGC---CCTAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCTAAC-CTAAAC-AAAC
* *
491 CCTAAACACCT-AACCCTAAAACCATAAACCCTAAAACCCTAACCTAAAC
1 CCTAAACA-CTAAACCCT-AAACCCT-AACCCT--AA-CCTAAAC-AAAC
* * * **
540 CCTAAAACCCT-AACCCTAAACCC-AAACC-ACCCTACCCTAAAC
1 CCT-AAACACTAAACCCTAAACCCTAACCCTAACCTAAAC-AAAC
* *
582 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACACTAAACCCTAACC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AAC-CTAAA--C-AAAC
* * *
631 CCTAAAC-CCACAACCCTAAACCCGAACCCCTAAACCCTCAACCAAAC
1 CCTAAACACTA-AACCCTAAACCCTAA-CCCT-AA-CCT-AAACAAAC
* * *
678 CCTAAACCCTAAAACCCTAAAAACCTAAACCTAAAACCTAAACTAAAACC
1 CCTAAACACT-AAACCCT-AAACCCTAACCCT--AACCTAAAC--AAA-C
**
728 CCTAAACACTAAACCCTAAACCCTAAAACTAAACCCTAAACCCGAAAAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAA--C----AAAC
* *
779 CCTCAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAA--C--AAAC
* *
830 CCTAAACCCT-AACCCTAAA-CATAAACCCTAAACCCT-AAC---C
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAACAAAC
* *
870 CCTCAACCCTAAA-CCT-AACCCTAA--C---CCTAAA-AAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCTAACCTAAACAAAC
* * *
905 CCTAAACCCTAAACCC-GAACCCTAAGCCCGCTAAACCCTAAACCCAAAAA
1 CCTAAACACTAAACCCTAAACCCTAA--CC-CT-AA-CCTAAA--C-AAAC
* * * *
955 CCTAAACCCTAAACCC-AAACCCCAAACACCAAACC---CCAAAC
1 CCTAAACACTAAACCCTAAA-CCCTAAC-CCTAACCTAAACAAAC
* *
996 CCTAAACACT-AACACTAAACCCATAAACCCTAACC----CTAAC
1 CCTAAACACTAAACCCTAAACCC-T-AACCCTAACCTAAACAAAC
*
1036 CCTAAA-ACCTAAACCCT-AACCCTAAACCTAAACCCTAAACCTAAAC
1 CCTAAACA-CTAAACCCTAAACCCTAACCCT-AA-CCTAAA-C-AAAC
* * * *
1082 CCTAAACCCGAAACCCTAAAACCC-AACCCCCAAACCTAACCCAAAC
1 CCTAAACACTAAACCCT-AAACCCTAA--CCCTAACCTAA-ACAAAC
* * * * *
1128 CCTGAAACCCCTAAACCCCAAACCCCAAACCCTAAACCCAAACCTAAC
1 CCT-AAA-CACTAAACCCTAAA-CCCTAACCCT-AACCTAAA-CAAAC
* * * * *
1176 ACTAAACCCTAAACCCTAAA-CCAAAACCTAAACCCTAAA-AAAA
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAACAAAC
*
1219 ACTAAAC-CTAAAACCCTAAACCCTAAACCCTAAAACCTAAACACTAA-
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT--AACCTAAACA--AAC
* * *
1266 --AAAACCCTAAAACCCAAAACCCTAAAAACCCTAACCCTAAA-AAAC
1 CCTAAACACT-AAACCCTAAACCCT---AACCCTAA-CCTAAACAAAC
* *
1311 CCTAAACCCTAAACCCCAAACCCTAAACCCTAAACCCTAAAACCATAA-
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCT-AAA-CA-AAC
* *
1359 CCTAAAC-C-GAACCCTAAACCCTAAACCCCTAAACC---CCAAAC
1 CCTAAACACTAAACCCTAAACCCT-AA-CCCT-AACCTAAACAAAC
* * *
1400 CCTAAACCCCAAACCCTAAACCCTAAACCCTAAACC---CCAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AACCTAAACAAAC
* * * *
1442 CCGAAACCCCAAACCCT-AACGCCTAAACCCTAAACCCTAAACCCTAAC
1 CCTAAACACTAAACCCTAAAC-CCT-AACCCT-AA-CCTAAA--CAAAC
*
1490 CCTAAAC-CTAAAACCCTAAACCCCAACCC-AACCTAAAC---C
1 CCTAAACACT-AAACCCTAAACCCTAACCCTAACCTAAACAAAC
* * * * *
1529 CC-AAACCCCAAACCCCAAACCCCAAACCGCAAACCCT-AA-AAAC
1 CCTAAACACTAAACCCTAAA-CCCTAACC-CTAA-CCTAAACAAAC
* *
1572 CCTAAACCCT-AACCCTAAACCCTAAACCCTAACCCCAAACCCAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCTAA-CCTAAA--CAAAC
* *
1618 CCTAAACCCTAAA-CCT-AA-CCAAACCCTAAACACTAAACCCCAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AAC-CTAAA---CAAAC
* * * * * *
1663 CCCAAACCCGAAACCCTAAACCCCAAACCCCAACCCTACACCATAAAC
1 CCTAAACACTAAACCCTAAA-CCCTAACCCTAA-CCTA-A--ACAAAC
*
1711 CCTAAACCCTAAACCCT-AACCCTAACCCTAAACCCTAACACCTAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAA-A-C-AAAC
* * *
1758 CCTAAA-ACCT-AA-CCTAAAACCCGAAACATAACCCT--A-AAAC
1 CCTAAACA-CTAAACCCT-AAACCCTAACCCTAA-CCTAAACAAAC
*
1798 CCTAAAC-CTAAACCCTAAACCCTAAAAACCCTAACCCAAAC--A-
1 CCTAAACACTAAACCCTAAACCCT---AACCCTAACCTAAACAAAC
* * *
1840 CCTAAACCCTAAACCCTAAACACTAAACCCTAAACCCTAAAAACCCGAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCT--AAA--CAAAC
* * *
1890 CC-GAACCCTAAA-CCTAAACCCGAAACCCTAAAAACCCT-AA-AAAC
1 CCTAAACACTAAACCCTAAACCC-TAACCCT---AA-CCTAAACAAAC
* *
1934 CCTAAACCCTAAA-CCTAAACCCGTAACACTAACCCTAAACCTAAAAGAC
1 CCTAAACACTAAACCCTAAACCC-TAACCCTAA-CCTAAA-C---AA-AC
* * * *
1983 CCTAAACCCTAAAACCCGAACCCCTAAACCCTAAACCCTAAACCAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAACAAAC
*
2030 CCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
* *
2078 CCTAAACCCT-AACCCTAAACCCTAAAAACCCTAACCCTAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT---AACCCTAA-CCTAA-AC-AAAC
*
2126 CCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
2176 CCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAACCTAAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAA-C--AAAC
*
2224 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C--AAAC
*
2274 CCTAAACCCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCTAA-CCTAAA--C-AAAC
*
2322 CCTAAACCCTAAACCCTAAA-CCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
2370 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
2419 CCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCT--A-AAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAACAAAC
2463 CCTAAAC-CT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
* * * **
2510 CCTAAACCCT-AACCATAAACCCTAAACCTAA-AAAAACCTAAACC
1 CCTAAACACTAAACCCTAAACCCTAACCCTAACCTAAA-C-AAA-C
*
2554 CCTAAACACCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAC
1 CCTAAACA-CTAAACCCTAAACCCT-AACCCTAA-CCTAAA--CAAAC
* *
2602 CCTAAACCCTAAACCCGAAAACCC-AACCCTAAGACCCTAAAC---C
1 CCTAAACACTAAACCC-TAAACCCTAACCCT-A-A-CCTAAACAAAC
* *
2645 CCTAAACCCTAAACCCTAAAACCTAAACCCTAAAACCCTAAACCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT--AA-CCTAAA-C-AAAC
2694 CCTAAAC-CATAAACCCTAAACCCTAAAACCCTAAACCTAAACCCTAAAC
1 CCTAAACAC-TAAACCCTAAACCCT--AACCCT-AACCTAAA--C-AAAC
* *
2743 CCTAAAAACCACT-AACCCTAAACCCTAAACCCTAA---AACCCTAAC
1 CCT--AAA-CACTAAACCCTAAACCCT-AACCCTAACCTAA-ACAAAC
* *
2787 CCTAAAC-CT-AACCC-GAACCCTAAAACCCTAAACCCGAAACCTAAAC
1 CCTAAACACTAAACCCTAAACCCT--AACCCT-AA-CCTAAA-C-AAAC
* *
2833 GCCTAAACCCTAAACCCTAAACCCTAAACCCAAAAACCCTAAACCCGAAAC
1 -CCTAAACACTAAACCCTAAACCCT-AACCC--TAA-CCTAAA--C-AAAC
*
2884 CCTAAACCCT-AACCCTAAAAACCCTAAACCCTAAAAACC-ATAA-AAAC
1 CCTAAACACTAAACCCT--AAACCCT-AACCCT---AACCTA-AACAAAC
* *
2931 CCTAAACCCTAAACCCTAAA-CCTAAACCCTAAACCCAAACCCGAAACC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AACCTAAA--C-AAA-C
* * * * * * *
2979 CCGGAAACCCGTAAAACCCGAAACCCGATAACCCGAACCCGAACCCTAAC
1 CC-TAAACAC-T-AAACCCTAAACCC--TAACCCTAA-CCTAA-ACAAAC
* * *
3029 CCT-AACCCTAAA-CCTAAA-CCTAAAACCCTACCCTAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT--AACCCTAACCTAA-AC-AAAC
* * **
3073 CCTAAACCCTAAA-CCT-ACCCCTAACCCTAAACCCTAAACCTAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAACAAAC
* *
3116 CCT--AC-CTAAAACCCTAAACCCTAA-ACTCAACCCTATAC---C
1 CCTAAACACT-AAACCCTAAACCCTAACCCT-AA-CCTAAACAAAC
*
3155 CCTAAAACCCTGAAACCCTAAACCCTAAAAACCCTAAACCT--A-AAA-
1 CCT-AAACACT-AAACCCTAAACCCT---AACCCT-AACCTAAACAAAC
*
3200 CCTAAACCCTAAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACT--AAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
3251 CCTAAACCCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCTAA-CCTAAA--C-AAAC
* *
3299 CCTAAAACCCTAAACCCTAAA-CCTAAACCTAAACCCTAAACCTAAAC
1 CCT-AAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAA-C-AAAC
*
3346 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
3395 CCTAAAC-CT-AACCCTAAACCCTAAACCCTAAACCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AACCTAAA--C-AAAC
* *
3441 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAACCCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAA--AC-AAAC
* *
3490 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--CAAAC
* *
3538 CCTAAACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAA--C-AAAC
* *
3586 CCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAA--CAAAC
*
3635 CCTAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAACCCTAAAC
1 CCT-AAACACTAAACCCTAAACCCT-AACCCT-AA-CCT-AAA--C-AAAC
*
3686 CCTAAACCCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCTAA-CCTAAA--C-AAAC
* *
3734 CCTAAACCCTAAACCCTAAACCCTAACCCTAAACCCTAAACCCTAAC
1 CCTAAACACTAAACCCTAAACCCTAACCCT-AA-CCTAAA--CAAAC
*
3781 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
* *
3830 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCTAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AACCTAA-AC-AAAC
*
3877 CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
3926 CCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAACCCTAAACCCT-AACCCT-AA-CCTAAA--C-AAAC
*
3974 CCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTAAAC
1 CCTAAACACT-AAACCCTAAACCCT-AACCCT-AA-CCTAAAC
4017 CCGAAACCCG
Statistics
Matches: 3329, Mismatches: 223, Indels: 783
0.77 0.05 0.18
Matches are distributed among these distances:
32 3 0.00
33 2 0.00
34 11 0.00
35 21 0.01
36 28 0.01
37 23 0.01
38 52 0.02
39 50 0.02
40 95 0.03
41 119 0.04
42 141 0.04
43 197 0.06
44 151 0.05
45 201 0.06
46 241 0.07
47 345 0.10
48 637 0.19
49 520 0.16
50 300 0.09
51 111 0.03
52 41 0.01
53 39 0.01
54 1 0.00
ACGTcount: A:0.44, C:0.42, G:0.01, T:0.13
Consensus pattern (43 bp):
CCTAAACACTAAACCCTAAACCCTAACCCTAACCTAAACAAAC
Found at i:1926 original size:9 final size:9
Alignment explanation
Indices: 1912--1939 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1902 CCTAAACCCG
1912 AAACCCTAA
1 AAACCCTAA
1921 AAACCCTAA
1 AAACCCTAA
1930 AAACCCTAA
1 AAACCCTAA
1939 A
1 A
1940 CCCTAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.32, G:0.00, T:0.11
Consensus pattern (9 bp):
AAACCCTAA
Found at i:2908 original size:9 final size:9
Alignment explanation
Indices: 2894--2936 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
2884 CCTAAACCCT
2894 AACCCTAAA
1 AACCCTAAA
2903 AACCCT--A
1 AACCCTAAA
2910 AACCCTAAA
1 AACCCTAAA
*
2919 AACCATAAA
1 AACCCTAAA
2928 AACCCTAAA
1 AACCCTAAA
2937 CCCTAAACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 7 0.23
9 23 0.77
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.12
Consensus pattern (9 bp):
AACCCTAAA
Found at i:6113 original size:7 final size:7
Alignment explanation
Indices: 5837--6135 Score: 110
Period size: 7 Copynumber: 43.3 Consensus size: 7
5827 CTAAACCCTA
5837 AACCCCG
1 AACCCCG
* *
5844 AACCTCA
1 AACCCCG
5851 AACCCCG
1 AACCCCG
5858 AACCCCG
1 AACCCCG
*
5865 AACCTCG
1 AACCCCG
*
5872 AA--CCT
1 AACCCCG
*
5877 AACCCCT
1 AACCCCG
* *
5884 AAACCCT
1 AACCCCG
* *
5891 AAACCCT
1 AACCCCG
*
5898 AACCCCT
1 AACCCCG
* *
5905 AATCCCT
1 AACCCCG
*
5912 AACCCCTA
1 AACCCC-G
*
5920 AACCCCTA
1 AACCCC-G
* **
5928 AACTCAA
1 AACCCCG
**
5935 AACCCAA
1 AACCCCG
5942 AACCCCG
1 AACCCCG
*
5949 AACCTCG
1 AACCCCG
5956 AACCCCG
1 AACCCCG
5963 AACCCC-
1 AACCCCG
*
5969 AAACCCG
1 AACCCCG
5976 AACCCCG
1 AACCCCG
5983 AA-CCCG
1 AACCCCG
* *
5989 AACTCTG
1 AACCCCG
*
5996 AACCTCG
1 AACCCCG
*
6003 AACCTCG
1 AACCCCG
*
6010 AA--CCT
1 AACCCCG
*
6015 AACCCCT
1 AACCCCG
* *
6022 AAACCCT
1 AACCCCG
* *
6029 AAACCCT
1 AACCCCG
* *
6036 AAACCCT
1 AACCCCG
*
6043 AACCCCTA
1 AACCCC-G
*
6051 AACCCCT
1 AACCCCG
* *
6058 AAACTCG
1 AACCCCG
**
6065 AAACCCAA
1 -AACCCCG
*
6073 AACCCGG
1 AACCCCG
*
6080 AACCCCA
1 AACCCCG
6087 AACCCCG
1 AACCCCG
6094 AACCCC-
1 AACCCCG
*
6100 AAACCCG
1 AACCCCG
6107 AACCCCG
1 AACCCCG
*
6114 AA-CCTG
1 AACCCCG
*
6120 AACCCCT
1 AACCCCG
6127 AACCCCG
1 AACCCCG
6134 AA
1 AA
6136 ACTCGAGCCC
Statistics
Matches: 231, Mismatches: 50, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
5 6 0.03
6 21 0.09
7 183 0.79
8 21 0.09
ACGTcount: A:0.36, C:0.48, G:0.07, T:0.09
Consensus pattern (7 bp):
AACCCCG
Found at i:6218 original size:15 final size:14
Alignment explanation
Indices: 6196--6230 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
6186 CCCCAGCCCC
6196 AAACCCCAAACCCT
1 AAACCCCAAACCCT
*
6210 AACACCCCAGACCCT
1 AA-ACCCCAAACCCT
6225 AAACCC
1 AAACCC
6231 TGAACCTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.51, G:0.03, T:0.06
Consensus pattern (14 bp):
AAACCCCAAACCCT
Found at i:6244 original size:28 final size:28
Alignment explanation
Indices: 6213--6283 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
6203 AAACCCTAAC
* *
6213 ACCCCAG-ACCCTAAACCCTGAACCTCGA
1 ACCCCAGAACCCAAAACCCCGAACCTC-A
6241 ACCCC-GAACCCAAAACCCCGAACCTCA
1 ACCCCAGAACCCAAAACCCCGAACCTCA
* *
6268 AGCCCCAAAACTCAAA
1 A-CCCCAGAACCCAAA
6284 GCCTGAACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 26 0.72
29 7 0.19
ACGTcount: A:0.38, C:0.46, G:0.08, T:0.07
Consensus pattern (28 bp):
ACCCCAGAACCCAAAACCCCGAACCTCA
Found at i:6273 original size:14 final size:14
Alignment explanation
Indices: 6195--6283 Score: 58
Period size: 14 Copynumber: 6.3 Consensus size: 14
6185 TCCCCAGCCC
*
6195 CAAACCCCAAACC-
1 CAAACCCCGAACCT
*
6208 CTAACACCCCAGACCCT
1 C-AA-ACCCC-GAACCT
*
6225 -AAACCCTGAACCT
1 CAAACCCCGAACCT
*
6238 CGAACCCCGAACC-
1 CAAACCCCGAACCT
6251 CAAAACCCCGAACCT
1 C-AAACCCCGAACCT
* * *
6266 CAAGCCCCAAAACT
1 CAAACCCCGAACCT
6280 CAAA
1 CAAA
6284 GCCTGAACCC
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
13 7 0.12
14 40 0.69
15 8 0.14
16 3 0.05
ACGTcount: A:0.39, C:0.47, G:0.07, T:0.07
Consensus pattern (14 bp):
CAAACCCCGAACCT
Found at i:11368 original size:22 final size:20
Alignment explanation
Indices: 11327--11451 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
11317 TTTTAACTAG
*
11327 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
11347 ATGTATCGATACATATGAAAAAAAA
1 ATGTATCGATACAT-TG----AAAA
*
11372 GATAGAATGTATCGATACATTGAAGA
1 -AT-G--T--ATCGATACATTGAAAA
* * * *
11398 ATATATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
11418 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
11438 ATATATCGATACAT
1 ATGTATCGATACAT
11452 CTAGGTAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 54 0.66
21 2 0.02
22 1 0.01
25 6 0.07
26 5 0.06
27 1 0.01
29 1 0.01
30 2 0.02
31 10 0.12
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:11404 original size:20 final size:20
Alignment explanation
Indices: 11375--11451 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
11365 AAAAAAAGAT
*
11375 AGAATGTATCGATACATTGA
1 AGAATATATCGATACATTGA
*
11395 AGAATATATCGATACATTCA
1 AGAATATATCGATACATTGA
* *
11415 TA-CATGTATCGATACATTGA
1 -AGAATATATCGATACATTGA
*
11435 AAAATATATCGATACAT
1 AGAATATATCGATACAT
11452 CTAGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
AGAATATATCGATACATTGA
Found at i:13132 original size:22 final size:21
Alignment explanation
Indices: 13106--13147 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
13096 AATTAAAAAA
13106 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
13126 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
13147 A
1 A
13148 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:13307 original size:2 final size:2
Alignment explanation
Indices: 13302--13335 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13292 ATACACACAC
*
13302 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13336 TGAGAAATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15558 original size:2 final size:2
Alignment explanation
Indices: 15551--15579 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15541 TGACAGAATT
15551 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
15580 AGACAAGAAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17762 original size:2 final size:2
Alignment explanation
Indices: 17757--17803 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
17747 ATATATTTTG
17757 AT AT AT AT AT 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 AT
17799 GAT AT
1 -AT AT
17804 GCATACAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21182 original size:8 final size:8
Alignment explanation
Indices: 21171--21195 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21161 ATTCTCCCAT
21171 AGGCAGTG
1 AGGCAGTG
21179 AGGCAGTG
1 AGGCAGTG
21187 AGGCAGTG
1 AGGCAGTG
21195 A
1 A
21196 ACAAACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.48, T:0.12
Consensus pattern (8 bp):
AGGCAGTG
Found at i:21843 original size:42 final size:42
Alignment explanation
Indices: 21797--21881 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
21787 AAAACACTTA
21797 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
1 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
21839 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
1 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
21881 A
1 A
21882 AGATAACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
Found at i:26566 original size:8 final size:8
Alignment explanation
Indices: 26555--26579 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
26545 ATTCTCCCAT
26555 AGGCAGTG
1 AGGCAGTG
26563 AGGCAGTG
1 AGGCAGTG
26571 AGGCAGTG
1 AGGCAGTG
26579 A
1 A
26580 ACAAACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.48, T:0.12
Consensus pattern (8 bp):
AGGCAGTG
Found at i:27227 original size:42 final size:42
Alignment explanation
Indices: 27181--27265 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
27171 AAAACACTTA
27181 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
1 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
27223 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
1 ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
27265 A
1 A
27266 AGATAACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
ATTTGCCACAAAAATCTGGTGGCATATGAGCATGTCCATTTT
Found at i:31262 original size:192 final size:185
Alignment explanation
Indices: 30923--31297 Score: 457
Period size: 192 Copynumber: 2.0 Consensus size: 185
30913 ATGGACACTC
* *
30923 AGAGGATGAAATTAATTATACAAGCATGCAAAGAAATATCATAAGTTCAGTATCCATCATTACTT
1 AGAGGATGAAATTAATGATACAAGCATGCAAAGAAATATCATAAGTTCAGTATCCATCATAACTT
** * * * *
30988 TTGCTGTCTGATAAACTAACTTGTATCATATAGCATTCACCATGATAAGAAACTTACCCATCACT
66 TTGCCATCTCATAAACTAACATGTATCATATAGCATTCACCATAATAACAAACTTACCCATCACT
* *
31053 ACTCCCTTAACATATCCTA-TTCAATTCATGGCTCCAGGTCACAGTTAGAGCACAT
131 ACTCCCTGAACATATCCTATTTCAA-TCATGGCTCCAGGTCACACTTAGAGCACAT
** *
31108 AGAGGATGAAATTAATGATACAAGCATGCCCAGAAATATCATAAGTAT-AGTATGCTGTATGCAT
1 AGAGGATGAAATTAATGATACAAGCATGCAAAGAAATATCATAAGT-TCAGTAT-C--CAT-CAT
* * * ** *
31172 CAACAGTTTTGCCATCTCATAAACTTACATGTATCATATGGTATTCACTTTAATGACAAACTTAC
61 -AAC--TTTTGCCATCTCATAAACTAACATGTATCATATAGCATTCACCATAATAACAAACTTAC
* * *
31237 CCGTCACTACTCCCTGAATATATCCTATTTGAATCATGGCTCCAGGTCACACTTAGAGCAC
123 CCATCACTACTCCCTGAACATATCCTATTTCAATCATGGCTCCAGGTCACACTTAGAGCAC
31298 GTCCTGCAGA
Statistics
Matches: 159, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
185 48 0.30
186 2 0.01
188 2 0.01
189 3 0.02
190 2 0.01
192 98 0.62
193 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (185 bp):
AGAGGATGAAATTAATGATACAAGCATGCAAAGAAATATCATAAGTTCAGTATCCATCATAACTT
TTGCCATCTCATAAACTAACATGTATCATATAGCATTCACCATAATAACAAACTTACCCATCACT
ACTCCCTGAACATATCCTATTTCAATCATGGCTCCAGGTCACACTTAGAGCACAT
Found at i:32317 original size:12 final size:12
Alignment explanation
Indices: 32300--32338 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
32290 ACTGACACTA
32300 ATACATACATAT
1 ATACATACATAT
32312 ATACATACATAT
1 ATACATACATAT
* *
32324 ATATATATATAT
1 ATACATACATAT
32336 ATA
1 ATA
32339 TATAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (12 bp):
ATACATACATAT
Found at i:32325 original size:2 final size:2
Alignment explanation
Indices: 32308--32342 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
32298 TAATACATAC
* *
32308 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32343 ACACAACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:34550 original size:45 final size:45
Alignment explanation
Indices: 34490--34579 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
34480 AACAGATGAG
*
34490 GGAGCAGCCGTTGCGATTTCATGGGTTCAGCCTAGACACTGAGAT
1 GGAGCACCCGTTGCGATTTCATGGGTTCAGCCTAGACACTGAGAT
34535 GGAGCACCCGTTGCGATTTCATGGGTTCAGCCTAGACACTGAGAT
1 GGAGCACCCGTTGCGATTTCATGGGTTCAGCCTAGACACTGAGAT
34580 TTTGCCAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (45 bp):
GGAGCACCCGTTGCGATTTCATGGGTTCAGCCTAGACACTGAGAT
Found at i:37870 original size:3 final size:3
Alignment explanation
Indices: 37864--37895 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
37854 TTCTTTTTCT
37864 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
37896 TGGTTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38711 original size:2 final size:2
Alignment explanation
Indices: 38665--38694 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38655 TTCCGAAACA
38665 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
38695 TGGAACTAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43147 original size:2 final size:2
Alignment explanation
Indices: 43130--43171 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
43120 TGATCATTTT
*
43130 TA TA AA TA TA -A 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 TA TA TA TA TA
43171 T
1 T
43172 GGCCATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:43920 original size:82 final size:82
Alignment explanation
Indices: 43754--44002 Score: 304
Period size: 81 Copynumber: 3.0 Consensus size: 82
43744 CTAAATCGGG
* * * *
43754 TGGATTATATTTTGAGCCTTGAATTACATGGCTTTCTTCTTTAATCTTCTTCAACTTAGACAGAC
1 TGGATTATATTTTGAGCCTTGAATTACAT-GTTTTTTTCTTTGATCTTCTTCAGCTTAGACAGAC
*
43819 GCTTGGCCACATTAC-AA
65 ACTTGGCCACATTACAAA
* * *
43836 TGGATTATATTTTGAGCCTTGAATTGCATGTTTTTTTCTTCGATCTTCTTCAGCTTAGACGGACA
1 TGGATTATATTTTGAGCCTTGAATTACATGTTTTTTTCTTTGATCTTCTTCAGCTTAGACAGACA
* *
43901 CTTGGCTAGATTACAAA
66 CTTGGCCACATTACAAA
* * * * ** *
43918 TGGATTGTATTTTAAGCCTCGAATTACAT-TTTTTTTCTTTGATCATCTTCAGCTTAGATTGACT
1 TGGATTATATTTTGAGCCTTGAATTACATGTTTTTTTCTTTGATCTTCTTCAGCTTAGACAGACA
* *
43982 CTTGGCCATATTAAAAA
66 CTTGGCCACATTACAAA
43999 TGGA
1 TGGA
44003 AGAAAATTAA
Statistics
Matches: 144, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
81 89 0.62
82 55 0.38
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (82 bp):
TGGATTATATTTTGAGCCTTGAATTACATGTTTTTTTCTTTGATCTTCTTCAGCTTAGACAGACA
CTTGGCCACATTACAAA
Found at i:47092 original size:18 final size:18
Alignment explanation
Indices: 47069--47146 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
47059 TTATAAAATC
47069 AATAAATAATTAAAATTA
1 AATAAATAATTAAAATTA
* **
47087 AATAAAACTATATTTATGTTA
1 AAT-AAA-TA-ATTAAAATTA
**
47108 AAT-AATAATT-TTATT-
1 AATAAATAATTAAAATTA
*
47123 AATAAATAATTAAAATTT
1 AATAAATAATTAAAATTA
47141 AATAAA
1 AATAAA
47147 AATAACGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.06
16 10 0.21
17 6 0.13
18 11 0.23
19 5 0.11
20 2 0.04
21 10 0.21
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
AATAAATAATTAAAATTA
Found at i:47176 original size:12 final size:12
Alignment explanation
Indices: 47159--47201 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
47149 TAACGATTAA
*
47159 TATTTTAGTATT
1 TATTTTATTATT
47171 TATTTTTATTATT
1 TA-TTTTATTATT
*
47184 TATATTATTATT
1 TATTTTATTATT
47196 TATTTT
1 TATTTT
47202 TAATTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:47189 original size:27 final size:29
Alignment explanation
Indices: 47158--47216 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 29
47148 ATAACGATTA
47158 ATATTTTAGTATTTATTTTT-ATT-ATTT
1 ATATTTTAGTATTTATTTTTAATTAATTT
*
47185 ATA--TTATTATTTATTTTTAATTAATTT
1 ATATTTTAGTATTTATTTTTAATTAATTT
47212 ATATT
1 ATATT
47217 AATTTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 14 0.52
26 3 0.11
27 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (29 bp):
ATATTTTAGTATTTATTTTTAATTAATTT
Found at i:47196 original size:25 final size:27
Alignment explanation
Indices: 47167--47217 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
47157 AATATTTTAG
47167 TATTTATTTTT-ATT-ATTTATATTAT
1 TATTTATTTTTAATTAATTTATATTAT
47192 TATTTATTTTTAATTAATTTATATTA
1 TATTTATTTTTAATTAATTTATATTA
47218 ATTTCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 11 0.46
26 3 0.12
27 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TATTTATTTTTAATTAATTTATATTAT
Found at i:47279 original size:23 final size:24
Alignment explanation
Indices: 47253--47299 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47243 TTTATTATAG
47253 TATTACATAA-AATAAAATATATT
1 TATTACATAATAATAAAATATATT
* *
47276 TATTGCATAATAATAAAATTTATT
1 TATTACATAATAATAAAATATATT
47300 ATTTTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TATTACATAATAATAAAATATATT
Found at i:49080 original size:4 final size:4
Alignment explanation
Indices: 49071--49100 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
49061 CCTGCTTAAC
*
49071 CTAT CTAT CTAT CTAT CTAT TTAT CTAT CT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CT
49101 TTAGGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (4 bp):
CTAT
Found at i:53504 original size:2 final size:2
Alignment explanation
Indices: 53497--53527 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53487 AATTTAACTT
53497 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
53528 GAAGGAAATA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56674 original size:6 final size:6
Alignment explanation
Indices: 56658--56696 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
56648 AGAATCCATC
* *
56658 GGCAGT GGCAAT CGCAAT GGCAAT GGCAAT GGCAAT GGC
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGC
56697 GGGCCAGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.15
Consensus pattern (6 bp):
GGCAAT
Found at i:58897 original size:2 final size:2
Alignment explanation
Indices: 58890--58927 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58880 TTATTTTGAA
*
58890 TG TG TG TG TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58928 AACATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:68624 original size:3 final size:3
Alignment explanation
Indices: 68616--68653 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
68606 ATTCAATTGA
68616 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
68654 AAGGATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:76720 original size:2 final size:2
Alignment explanation
Indices: 76713--76752 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
76703 GAAATGAAAC
76713 AT AT AT AT 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
76753 TCCGACTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78564 original size:1 final size:1
Alignment explanation
Indices: 78560--78584 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
78550 TAAAAATATG
78560 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
78585 AAAACCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:81773 original size:5 final size:5
Alignment explanation
Indices: 81736--81771 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
81726 GAGTGAGAGT
* *
81736 TGGTC TTGTC TGGTC TGGTC TGGTC TGGTC TAGTC T
1 TGGTC TGGTC TGGTC TGGTC TGGTC TGGTC TGGTC T
81772 AGCAACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.19, G:0.33, T:0.44
Consensus pattern (5 bp):
TGGTC
Found at i:90160 original size:3 final size:3
Alignment explanation
Indices: 90152--90183 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
90142 AGCATGGCCA
*
90152 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
90184 ATATGTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:90524 original size:2 final size:2
Alignment explanation
Indices: 90507--90546 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
90497 GGATTGATGC
* *
90507 AT AT AT GT AT AC 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
90547 CCCGACTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:92185 original size:2 final size:2
Alignment explanation
Indices: 92178--92210 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
92168 GTACCAATTA
92178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
92211 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92215 original size:2 final size:2
Alignment explanation
Indices: 92210--92238 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
92200 ATATATATAT
92210 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
92239 AGGATAGTTG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:92434 original size:14 final size:14
Alignment explanation
Indices: 92415--92460 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
92405 TGTTTGAATT
92415 AATATTTTTATAAA
1 AATATTTTTATAAA
*
92429 AATATTTTTATTAA
1 AATATTTTTATAAA
*
92443 AAT-TTAATTATAAA
1 AATATT-TTTATAAA
92457 AATA
1 AATA
92461 GTAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 25 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTTTATAAA
Found at i:93811 original size:3 final size:3
Alignment explanation
Indices: 93805--93853 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
93795 CAACAACAAC
93805 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
93852 AA
1 AA
93854 ATAAAACTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:95004 original size:26 final size:26
Alignment explanation
Indices: 94949--95004 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
94939 TTAATTAATG
* ***
94949 TAATAAAAAATAAGTTATCTTTATTT
1 TAATAAAAAATAAGTAATCTTTAAAA
94975 TAATAAAAAATAA-TAATCTCTTAAAA
1 TAATAAAAAATAAGTAATCT-TTAAAA
95001 TAAT
1 TAAT
95005 TATTTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (26 bp):
TAATAAAAAATAAGTAATCTTTAAAA
Found at i:96133 original size:20 final size:20
Alignment explanation
Indices: 96085--96122 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
96075 TTTTATTACT
96085 ATTT-ATAATATGTAATTAA
1 ATTTAATAATATGTAATTAA
96104 ATTTAATAATATG-AATTAA
1 ATTTAATAATATGTAATTAA
96123 TTATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTAATAATATGTAATTAA
Found at i:96159 original size:14 final size:14
Alignment explanation
Indices: 96140--96166 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
96130 TAATTTATTT
96140 AATAAAAATATAAA
1 AATAAAAATATAAA
96154 AATAAAAATATAA
1 AATAAAAATATAA
96167 TTATTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAATATAAA
Found at i:96199 original size:22 final size:24
Alignment explanation
Indices: 96171--96220 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
96161 ATATAATTAT
96171 TTTATTAAAATT-AATAAAAAT-A
1 TTTATTAAAATTAAATAAAAATAA
**
96193 TTTATTATTATTAAATAAAAATAA
1 TTTATTAAAATTAAATAAAAATAA
96217 TTTA
1 TTTA
96221 CTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 9 0.38
24 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATTAAAATTAAATAAAAATAA
Found at i:97834 original size:2 final size:2
Alignment explanation
Indices: 97827--97856 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
97817 ATTTTTATTC
*
97827 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97857 CACTCGCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:102677 original size:23 final size:23
Alignment explanation
Indices: 102651--102718 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
102641 ACATAATAAA
102651 ATATAAAAAATAATATAAATATT
1 ATATAAAAAATAATATAAATATT
**
102674 ATATAATACGA-AATATAAATATT
1 ATATAA-AAAATAATATAAATATT
* *
102697 TTA-ATAAAAATTATATAAATAT
1 ATATA-AAAAATAATATAAATAT
102719 ATAATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 3 0.08
23 31 0.86
24 2 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (23 bp):
ATATAAAAAATAATATAAATATT
Found at i:103752 original size:24 final size:23
Alignment explanation
Indices: 103720--103764 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
103710 AAAATCATAA
*
103720 AAAATAATATAAATTAAATAATTTT
1 AAAATAATA-AAAATAAA-AATTTT
103745 AAAA-AATAAAAATAAAAATT
1 AAAATAATAAAAATAAAAATT
103765 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 4 0.21
25 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATAAAAATAAAAATTTT
Found at i:111641 original size:2 final size:2
Alignment explanation
Indices: 111634--111663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
111624 ATTATCCTAA
111634 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
111664 TTGAATGCAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112540 original size:2 final size:2
Alignment explanation
Indices: 112535--112574 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
112525 ATATATATAT
112535 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
112575 CACATTCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:113910 original size:12 final size:11
Alignment explanation
Indices: 113867--113918 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
113857 ATTTAAAAAA
*
113867 ATTAAATTTAT
1 ATTAAATATAT
113878 ATT-AATATAT
1 ATTAAATATAT
* *
113888 -TTATATTTAT
1 ATTAAATATAT
113898 ATTCAAATATAT
1 ATT-AAATATAT
113910 ATTAAATAT
1 ATTAAATAT
113919 GAATTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 2 0.06
10 11 0.33
11 11 0.33
12 9 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTAAATATAT
Found at i:118087 original size:19 final size:18
Alignment explanation
Indices: 118051--118089 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
118041 AAAAGTGAAC
**
118051 TATTTTTTGATTAAAAAA
1 TATTTTTTGAAAAAAAAA
118069 TATTTTTTGAAAAAGAAAA
1 TATTTTTTGAAAAA-AAAA
118088 TA
1 TA
118090 AGATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
TATTTTTTGAAAAAAAAA
Found at i:118250 original size:20 final size:20
Alignment explanation
Indices: 118225--118271 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
118215 AAAAATTTAA
118225 TTTTAGCTTCAAGGAATGAG
1 TTTTAGCTTCAAGGAATGAG
118245 TTTTAGCTTCAAGGAATGAG
1 TTTTAGCTTCAAGGAATGAG
118265 TTATTAG
1 TT-TTAG
118272 TGTAACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (20 bp):
TTTTAGCTTCAAGGAATGAG
Found at i:118310 original size:27 final size:25
Alignment explanation
Indices: 118280--118349 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 25
118270 AGTGTAACTC
*
118280 TTAATTATGATTTGAATTTAAAAAAAT
1 TTAATTA--ATTTAAATTTAAAAAAAT
118307 TTAATTAATTTAAATTTAAAAAAA-
1 TTAATTAATTTAAATTTAAAAAAAT
118331 -TAA-TAATTTAAATTTAAAA
1 TTAATTAATTTAAATTTAAAA
118350 TGATTTAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
22 16 0.38
23 3 0.07
25 16 0.38
27 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
TTAATTAATTTAAATTTAAAAAAAT
Found at i:118355 original size:16 final size:16
Alignment explanation
Indices: 118336--118366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118326 AAAAATAATA
*
118336 ATTTAAATTTAAAATG
1 ATTTAAATATAAAATG
118352 ATTTAAATATAAAAT
1 ATTTAAATATAAAAT
118367 AATAAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTAAATATAAAATG
Found at i:118448 original size:16 final size:16
Alignment explanation
Indices: 118427--118481 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
118417 TTTCAATATG
118427 AAATGATTCGAATTTA
1 AAATGATTCGAATTTA
*
118443 AAATGA-TCTAAATTTA
1 AAATGATTC-GAATTTA
* *
118459 AAATTATAT-GAATATA
1 AAATGAT-TCGAATTTA
118475 AAATGAT
1 AAATGAT
118482 CAACCTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 28 0.90
18 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (16 bp):
AAATGATTCGAATTTA
Found at i:119103 original size:97 final size:97
Alignment explanation
Indices: 118933--119127 Score: 327
Period size: 97 Copynumber: 2.0 Consensus size: 97
118923 TTTCATCAAG
* * *
118933 ATGCTTAATTTCTAAATATCTTTCATTTTAATAATTATTTAAATTAATAATAACATAATTTTAAG
1 ATGCTTAATTTCTAAATATCTTTCATTTTAATAATTAGTTAAATTAATAATAACATAAATTTAAA
118998 TTAAATTATATTAAATAATTATTATTTATTTA
66 TTAAATTATATTAAATAATTATTATTTATTTA
* * *
119030 ATGCTTAATTTCTAAATATTTTTCATTTTAATAATTAGTTAAATTAATAATCATATAAATTTAAA
1 ATGCTTAATTTCTAAATATCTTTCATTTTAATAATTAGTTAAATTAATAATAACATAAATTTAAA
*
119095 TTATATTATATTAAATAATTATTATTTATTTA
66 TTAAATTATATTAAATAATTATTATTTATTTA
119127 A
1 A
119128 ATAATTTTCG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (97 bp):
ATGCTTAATTTCTAAATATCTTTCATTTTAATAATTAGTTAAATTAATAATAACATAAATTTAAA
TTAAATTATATTAAATAATTATTATTTATTTA
Found at i:119112 original size:49 final size:48
Alignment explanation
Indices: 118962--119118 Score: 135
Period size: 49 Copynumber: 3.2 Consensus size: 48
118952 CTTTCATTTT
* * * *
118962 AATAATTATTTAAATTAATAATAACATAATTTTAAGTTAAATTATATTA
1 AATAATTA-TTAAATTAATAATCATATAATTTTAAATTATATTATATTA
* * * *
119011 AATAATTATT-ATTTATTTAATGC-T-TAATTTCTAAA-TAT-TTTTCATTTT
1 AATAATTATTAAATTA-ATAAT-CATATAATTT-TAAATTATATTAT-A-TTA
*
119059 AATAATTAGTTAAATTAATAATCATATAAATTTAAATTATATTATATTA
1 AATAATTA-TTAAATTAATAATCATATAATTTTAAATTATATTATATTA
119108 AATAATTATTA
1 AATAATTATTA
119119 TTTATTTAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
46 3 0.04
47 13 0.15
48 23 0.27
49 29 0.35
50 13 0.15
51 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (48 bp):
AATAATTATTAAATTAATAATCATATAATTTTAAATTATATTATATTA
Found at i:119127 original size:19 final size:21
Alignment explanation
Indices: 119094--119133 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
119084 ATAAATTTAA
119094 ATTATATTATATTAAATAATT
1 ATTATATTATATTAAATAATT
119115 ATTAT-TTAT-TTAAATAATT
1 ATTATATTATATTAAATAATT
119134 TTCGTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATATTATATTAAATAATT
Found at i:120039 original size:24 final size:24
Alignment explanation
Indices: 120007--120080 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 24
119997 ACGTAGACGT
120007 AAAAA-AAATTAAAACATAATATA
1 AAAAATAAATTAAAACATAATATA
* *
120030 AAAAATAAATATGACACA-AATAT-
1 AAAAATAAAT-TAAAACATAATATA
* * *
120053 AAAAATACATAAAAATATAAGTATA
1 AAAAATAAATTAAAACATAA-TATA
120078 AAA
1 AAA
120081 TATTATATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 3 0.08
23 16 0.41
24 12 0.31
25 8 0.21
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAAATAAATTAAAACATAATATA
Found at i:122716 original size:2 final size:2
Alignment explanation
Indices: 122709--122752 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
122699 ATCTCTGTTA
122709 AT AT AT AT AT 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 AT
122751 AT
1 AT
122753 TTGGCAATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130069 original size:47 final size:46
Alignment explanation
Indices: 129999--130096 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 46
129989 CTTTGAATAG
*
129999 CTAGGTGCAACACAGATTTATGATTTAG-CCACTTGACGTCTGCATA
1 CTAGGTGCAACACAGATTTATGATTT-GTCCACTAGACGTCTGCATA
*
130045 CGTAGGTGCAGCACAGATTTATGATTTGTCCACTAGACGTCTGCATA
1 C-TAGGTGCAACACAGATTTATGATTTGTCCACTAGACGTCTGCATA
130092 CTAGG
1 CTAGG
130097 GCTTCGAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
46 6 0.12
47 42 0.88
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (46 bp):
CTAGGTGCAACACAGATTTATGATTTGTCCACTAGACGTCTGCATA
Found at i:131256 original size:32 final size:36
Alignment explanation
Indices: 131211--131278 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 36
131201 AAATATATTT
*
131211 TTAAAATTTATAT-AATATA-AA-TTATT-AATATA
1 TTAAAATTAATATAAATATATAATTTATTAAATATA
131243 TTAAAATTAATATAAATATATAATTTATTAAATATA
1 TTAAAATTAATATAAATATATAATTTATTAAATATA
131279 ATTATAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 12 0.39
33 6 0.19
34 2 0.06
35 5 0.16
36 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
TTAAAATTAATATAAATATATAATTTATTAAATATA
Found at i:131280 original size:27 final size:27
Alignment explanation
Indices: 131220--131280 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
131210 TTTAAAATTT
131220 ATATAATATAAATTATTAATATATTAA
1 ATATAATATAAATTATTAATATATTAA
*
131247 A-ATTAATATAAA-TATATAATTTATTAA
1 ATA-TAATATAAATTAT-TAATATATTAA
131274 ATATAAT
1 ATATAAT
131281 TATAGTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 25 0.83
28 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAATATAAATTATTAATATATTAA
Found at i:131725 original size:19 final size:17
Alignment explanation
Indices: 131681--131746 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
131671 ATTTAATTTG
131681 ATTTTAAATTAAACTTA
1 ATTTTAAATTAAACTTA
131698 ATTAATTAAATTAAACTTTAA
1 ATT--TTAAATTAAAC-TT-A
131719 ATTTTAAATTTTAAA-TTA
1 ATTTTAAA--TTAAACTTA
*
131737 AATTTAAATT
1 ATTTTAAATT
131747 CAACCCTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 2 0.05
17 3 0.07
18 8 0.19
19 18 0.43
20 2 0.05
21 9 0.21
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTAAATTAAACTTA
Found at i:136743 original size:30 final size:30
Alignment explanation
Indices: 136709--136768 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
136699 TCCTGCTAAT
136709 AGGTGCATGCATCCTTCGTTTTGTGTCCTA
1 AGGTGCATGCATCCTTCGTTTTGTGTCCTA
136739 AGGTGCATGCATCCTTCGTTTTGTGTCCTA
1 AGGTGCATGCATCCTTCGTTTTGTGTCCTA
136769 TTTGACCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (30 bp):
AGGTGCATGCATCCTTCGTTTTGTGTCCTA
Found at i:137779 original size:2 final size:2
Alignment explanation
Indices: 137772--137796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
137762 GTTTGTGTAG
137772 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
137797 TTAGATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:138269 original size:15 final size:15
Alignment explanation
Indices: 138213--138268 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
138203 TTTCAAAAAT
138213 AATATATATATATATA
1 AATATAT-TATATATA
* *
138229 AATATATGAAATATGA
1 AATATATTATATAT-A
*
138245 ATATATATTTTATATA
1 A-ATATATTATATATA
138261 AATATATT
1 AATATATT
138269 TAAAATTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 12 0.36
16 11 0.33
17 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (15 bp):
AATATATTATATATA
Found at i:139096 original size:14 final size:13
Alignment explanation
Indices: 139070--139095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139060 TTTAATTTAT
139070 TTATTTTATAAAA
1 TTATTTTATAAAA
139083 TTATTTTATAAAA
1 TTATTTTATAAAA
139096 AATAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTTATAAAA
Found at i:139363 original size:16 final size:16
Alignment explanation
Indices: 139344--139394 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
139334 TCTAAACTCG
*
139344 AAATGATTCAAATTTA
1 AAATAATTCAAATTTA
*
139360 AAATAATCCAAATTTA
1 AAATAATTCAAATTTA
* *
139376 AAATAATTTAAAATTA
1 AAATAATTCAAATTTA
139392 AAA
1 AAA
139395 AGATCCAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATAATTCAAATTTA
Found at i:139441 original size:15 final size:15
Alignment explanation
Indices: 139408--139480 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
139398 TCCAATCGAG
*
139408 TAATTTAAACACAAAA
1 TAATTTAAA-ATAAAA
*
139424 TAATTTAAAATTAAA
1 TAATTTAAAATAAAA
* *
139439 TAATCGTAAACTAAAA
1 TAAT-TTAAAATAAAA
*
139455 TAATTCAAAATCAAAA
1 TAATTTAAAAT-AAAA
139471 TAA-TTAAAAT
1 TAATTTAAAAT
139481 TTTAAATTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
15 18 0.39
16 28 0.61
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.30
Consensus pattern (15 bp):
TAATTTAAAATAAAA
Found at i:139449 original size:32 final size:32
Alignment explanation
Indices: 139413--139474 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
139403 TCGAGTAATT
* *
139413 TAAACACAAAATAATTTAAAAT-TAAATAATCG
1 TAAAC-CAAAATAATTCAAAATCAAAATAATCG
*
139445 TAAACTAAAATAATTCAAAATCAAAATAAT
1 TAAACCAAAATAATTCAAAATCAAAATAAT
139475 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (32 bp):
TAAACCAAAATAATTCAAAATCAAAATAATCG
Found at i:140212 original size:27 final size:30
Alignment explanation
Indices: 140164--140218 Score: 89
Period size: 27 Copynumber: 1.9 Consensus size: 30
140154 TAAATTTAAT
140164 AAAAATAATATATTAAATATAATTTTTTTA
1 AAAAATAATATATTAAATATAATTTTTTTA
140194 AAAAATAATA-ATT-AA-ATAATTTTTT
1 AAAAATAATATATTAAATATAATTTTTT
140219 ATCATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 2 0.08
29 3 0.12
30 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAAATAATATATTAAATATAATTTTTTTA
Found at i:146605 original size:3 final size:3
Alignment explanation
Indices: 146597--146635 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
146587 TAGACAAATC
146597 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
146636 GTTGTTTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:146705 original size:3 final size:3
Alignment explanation
Indices: 146697--146735 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
146687 AGAAATCTGT
146697 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
146736 GTCTTAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:153400 original size:5 final size:5
Alignment explanation
Indices: 153355--153494 Score: 54
Period size: 5 Copynumber: 26.8 Consensus size: 5
153345 AACTTAAAAT
* * *
153355 AATTA AATTT AA-TA AATATA AGTATTA AA-TA TAATTG AATTA AATTT
1 AATTA AATTA AATTA AAT-TA A--ATTA AATTA -AATTA AATTA AATTA
* * * * * *
153402 AATTA ATTTA TGTATTA AATTA AATTA ATTTTA ATTTA AAATA ATTTA
1 AATTA AATTA --AATTA AATTA AATTA A-ATTA AATTA AATTA AATTA
* * *
153450 AATTTA AA-T- AATTAA ATATTA AATTT AATTA ATTTA ATTTA AATT
1 AA-TTA AATTA AATT-A A-ATTA AATTA AATTA AATTA AATTA AATT
153495 TAAAGTGATT
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
3 2 0.02
4 7 0.07
5 65 0.64
6 16 0.16
7 9 0.09
8 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (5 bp):
AATTA
Found at i:153435 original size:16 final size:16
Alignment explanation
Indices: 153416--153462 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
153406 AATTTATGTA
*
153416 TTAAATTAAATTAATT
1 TTAAATTAAAATAATT
*
153432 TTAATTTAAAATAA-T
1 TTAAATTAAAATAATT
*
153447 TTAAATTTAAATAATT
1 TTAAATTAAAATAATT
153463 AAATATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTAAAATAATT
Found at i:153438 original size:37 final size:36
Alignment explanation
Indices: 153355--153493 Score: 133
Period size: 37 Copynumber: 3.8 Consensus size: 36
153345 AACTTAAAAT
* * *
153355 AATTAAATTTAATAAATATAAGTATTAAATATAATTG
1 AATTAAATTTAATTAATTTAAGTATTAAATA-AATTA
*
153392 AATTAAATTTAATTAATTTATGTATTAAATTAAATTA
1 AATTAAATTTAATTAATTTAAGTATTAAA-TAAATTA
* * * *
153429 ATTTTAATTTAAAATAATTTAAAT-TTAAAT-AATTAA
1 AATTAAATTT-AATTAATTTAAGTATTAAATAAATT-A
153465 ATATTAAATTTAATTAATTTAA-T-TTAAAT
1 A-ATTAAATTTAATTAATTTAAGTATTAAAT
153494 TTAAAGTGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
35 11 0.13
36 13 0.15
37 50 0.58
38 12 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (36 bp):
AATTAAATTTAATTAATTTAAGTATTAAATAAATTA
Found at i:153494 original size:15 final size:15
Alignment explanation
Indices: 153416--153497 Score: 69
Period size: 16 Copynumber: 5.3 Consensus size: 15
153406 AATTTATGTA
*
153416 TTAAATTAAATTAATT
1 TTAATTTAAATTAA-T
*
153432 TTAATTTAAAATAAT
1 TTAATTTAAATTAAT
153447 TTAAATTTAAA-TAAT
1 TT-AATTTAAATTAAT
*
153462 TAAATATTAAATTTAA-
1 TTAAT-TTAAA-TTAAT
*
153478 TTAATTTAATTTAAAT
1 TTAATTTAAATT-AAT
153494 TTAA
1 TTAA
153498 AGTGATTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.09
15 19 0.35
16 28 0.51
17 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATTTAAATTAAT
Found at i:153505 original size:16 final size:16
Alignment explanation
Indices: 153486--153521 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
153476 AATTAATTTA
* *
153486 ATTTAAATTTAAAGTG
1 ATTTAAAATTAAAATG
153502 ATTTAAAATTAAAATG
1 ATTTAAAATTAAAATG
153518 ATTT
1 ATTT
153522 GAGTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
ATTTAAAATTAAAATG
Found at i:153507 original size:21 final size:20
Alignment explanation
Indices: 153443--153498 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
153433 TAATTTAAAA
153443 TAATTTAAATTTAAATAATT
1 TAATTTAAATTTAAATAATT
* *
153463 AAATATTAAATTTAATTAATT
1 TAAT-TTAAATTTAAATAATT
153484 TAATTTAAATTTAAA
1 TAATTTAAATTTAAA
153499 GTGATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTTAAATTTAAATAATT
Found at i:153567 original size:16 final size:16
Alignment explanation
Indices: 153546--153622 Score: 93
Period size: 16 Copynumber: 4.8 Consensus size: 16
153536 ACATCCGTAA
153546 TTAAAATAATTTTAAT
1 TTAAAATAATTTTAAT
*
153562 TTAAAATAATTTTAAA
1 TTAAAATAATTTTAAT
**
153578 TTAAAATAATATAAAAAT
1 TTAAAATAAT-T-TTAAT
153596 TTAAAATAA-TTTAAT
1 TTAAAATAATTTTAAT
*
153611 TTAAATTAATTT
1 TTAAAATAATTT
153623 GATTCAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
15 11 0.22
16 28 0.55
17 1 0.02
18 11 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATAATTTTAAT
Found at i:153895 original size:16 final size:17
Alignment explanation
Indices: 153874--153905 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
153864 TTTGTTACGT
153874 AAAAAATAAT-TTTTTA
1 AAAAAATAATATTTTTA
153890 AAAAAATAATATTTTT
1 AAAAAATAATATTTTT
153906 GGTAGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAAATAATATTTTTA
Found at i:154259 original size:19 final size:19
Alignment explanation
Indices: 154235--154273 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
154225 ATAACCTGAT
*
154235 TAAAAT-TATTATATATTAA
1 TAAAATATATT-TAAATTAA
154254 TAAAATATATTTAAATTAA
1 TAAAATATATTTAAATTAA
154273 T
1 T
154274 TATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAATATATTTAAATTAA
Found at i:155029 original size:23 final size:21
Alignment explanation
Indices: 154994--155043 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
154984 TATATCATTT
* *
154994 ATATTATATAAAAAATATATA
1 ATATTATATAAAAAATAAAAA
155015 ATATTATAATAAAAACATAAAAA
1 ATATTAT-ATAAAAA-ATAAAAA
155038 ATATTA
1 ATATTA
155044 AGTTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 7 0.28
23 11 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATTATATAAAAAATAAAAA
Found at i:155229 original size:2 final size:2
Alignment explanation
Indices: 155224--155278 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
155214 GCATACATAC
155224 AT AT AT AT AT 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 AT
*
155266 A- AA AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
155279 AAATGAAACA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:155659 original size:21 final size:23
Alignment explanation
Indices: 155635--155679 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
155625 TAATATAGTT
*
155635 TAAATAT-TAT-ATTTTTCAAAA
1 TAAATATATATGATTATTCAAAA
155656 TAAATATATATGATTATTCAAAA
1 TAAATATATATGATTATTCAAAA
155679 T
1 T
155680 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATATATATGATTATTCAAAA
Found at i:155684 original size:25 final size:23
Alignment explanation
Indices: 155633--155684 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
155623 TTTAATATAG
*
155633 TTTAAATATTATATTTTTCAAAA
1 TTTAAATATTATATTATTCAAAA
155656 --TAAATATATATGATTATTCAAAA
1 TTTAAATAT-TAT-ATTATTCAAAA
155679 TTTAAA
1 TTTAAA
155685 AATTTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 7 0.29
22 3 0.12
23 10 0.42
25 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTAAATATTATATTATTCAAAA
Found at i:155770 original size:21 final size:22
Alignment explanation
Indices: 155732--155773 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
155722 TAATCTTTTT
*
155732 GATATTTTTATCCGTCTAAAAG
1 GATATTTTTATCCATCTAAAAG
155754 GATATTTTTAT-CATCTAAAA
1 GATATTTTTATCCATCTAAAA
155774 TTAAGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
GATATTTTTATCCATCTAAAAG
Found at i:160387 original size:15 final size:16
Alignment explanation
Indices: 160361--160488 Score: 118
Period size: 16 Copynumber: 7.7 Consensus size: 16
160351 ATTTATATTA
160361 ATTTTAATTTTAAATT
1 ATTTTAATTTTAAATT
160377 ATTTT-ATTTTAAATT
1 ATTTTAATTTTAAATT
*
160392 ATTTTAAATTTAAATT
1 ATTTTAATTTTAAATT
160408 ATTTTAATTTTGAATTAATT
1 ATTTTAATTTT--A--AATT
*
160428 AAATTTAATATTTAAATT
1 -ATTTTAAT-TTTAAATT
* *
160446 A-ATTAGA-TTTATATT
1 ATTTTA-ATTTTAAATT
*
160461 ATTTTAAATTTAAATT
1 ATTTTAATTTTAAATT
160477 ATTTTAAATTTT
1 ATTTT-AATTTT
160489 GATCAATCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
15 24 0.26
16 42 0.45
17 7 0.08
18 5 0.05
20 5 0.05
21 7 0.08
22 3 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTTAATTTTAAATT
Found at i:160404 original size:31 final size:32
Alignment explanation
Indices: 160352--160482 Score: 124
Period size: 31 Copynumber: 4.0 Consensus size: 32
160342 TTTTAAAAAA
* *
160352 TTTATATTAATTTTAATTTTAAATTATTTTAT
1 TTTAAATTAATTTTAAATTTAAATTATTTTAT
160384 TTTAAATT-ATTTTAAATTTAAATTATTTTAAT
1 TTTAAATTAATTTTAAATTTAAATTATTTT-AT
* * *
160416 TTTGAATTAATTAAATTTAATATTTAAATTA-ATTAGA
1 TTT--A--AATTAATTTTAA-ATTTAAATTATTTTA-T
*
160453 TTTATATT-ATTTTAAATTTAAATTATTTTA
1 TTTAAATTAATTTTAAATTTAAATTATTTTA
160483 AATTTTGATC
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
31 30 0.37
32 21 0.26
33 3 0.04
34 1 0.01
35 1 0.01
36 5 0.06
37 11 0.13
38 10 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTAAATTAATTTTAAATTTAAATTATTTTAT
Found at i:160443 original size:69 final size:69
Alignment explanation
Indices: 160357--160507 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 69
160347 AAAAATTTAT
* * *
160357 ATTAATTTTAAT-TTTAAATTATTTTA-TTTTAAATTATTTTAAATTTAAATTATTTT-AATTTT
1 ATTAAATTTAATATTTAAATTA-ATTAGATTTAAATTATTTTAAATTTAAATTATTTTAAATTTT
*
160419 GAATTA
65 G-ATCA
*
160425 ATTAAATTTAATATTTAAATTAATTAGATTTATATTATTTTAAATTTAAATTATTTTAAATTTTG
1 ATTAAATTTAATATTTAAATTAATTAGATTTAAATTATTTTAAATTTAAATTATTTTAAATTTTG
160490 ATCA
66 ATCA
*
160494 ATCAAATTTAATAT
1 ATTAAATTTAATAT
160508 AGATTAATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
68 14 0.19
69 53 0.72
70 7 0.09
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (69 bp):
ATTAAATTTAATATTTAAATTAATTAGATTTAAATTATTTTAAATTTAAATTATTTTAAATTTTG
ATCA
Found at i:160477 original size:53 final size:55
Alignment explanation
Indices: 160384--160487 Score: 140
Period size: 53 Copynumber: 1.9 Consensus size: 55
160374 ATTATTTTAT
* * *
160384 TTTAAATTATTTTAAATTTAAATTATTTTAATTTTGAATTA-ATTAAATTTAATA
1 TTTAAATTATATTAAATTTAAATTATTTTAAATTTAAATTATATTAAATTTAATA
* * *
160438 TTTAAATTA-ATTAGATTTATATTATTTTAAATTTAAATTATTTTAAATTT
1 TTTAAATTATATTAAATTTAAATTATTTTAAATTTAAATTATATTAAATTT
160488 TGATCAATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 26 0.60
54 17 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (55 bp):
TTTAAATTATATTAAATTTAAATTATTTTAAATTTAAATTATATTAAATTTAATA
Found at i:161464 original size:22 final size:22
Alignment explanation
Indices: 161420--161477 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
161410 GTTTATTGAA
*
161420 TTAAATTT--ATTTATTATATGC
1 TTAAATTTAAATTTAAT-TATGC
*
161441 TTAATTTTAAATTTAATTATGC
1 TTAAATTTAAATTTAATTATGC
*
161463 TTAAATTTGAATTTA
1 TTAAATTTAAATTTA
161478 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 18 0.58
23 6 0.19
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (22 bp):
TTAAATTTAAATTTAATTATGC
Found at i:161799 original size:21 final size:21
Alignment explanation
Indices: 161751--161799 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
161741 TAATAAAAAA
* * *
161751 TAAAAAATTTATATTTATATT
1 TAAATAATTTATAATTAAATT
**
161772 TTTATAATTTATAATTAAATT
1 TAAATAATTTATAATTAAATT
161793 TAAATAA
1 TAAATAA
161800 AAATAATTTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATAATTTATAATTAAATT
Found at i:162210 original size:2 final size:2
Alignment explanation
Indices: 162203--162229 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
162193 ACCCATTTTC
162203 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 T
162230 GCACTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:163861 original size:16 final size:16
Alignment explanation
Indices: 163840--163945 Score: 88
Period size: 16 Copynumber: 6.6 Consensus size: 16
163830 AACTTAATTG
163840 ATTTAAAATTAAAATA
1 ATTTAAAATTAAAATA
*
163856 ATTTAAATTTAAAATA
1 ATTTAAAATTAAAATA
* *
163872 ATATT-AAATTAAAGTG
1 AT-TTAAAATTAAAATA
** * *
163888 ACATAAATTTGAAATA
1 ATTTAAAATTAAAATA
* *
163904 ATCTAAAATCAAAATA
1 ATTTAAAATTAAAATA
* * *
163920 ACTTAAATTTTAAATA
1 ATTTAAAATTAAAATA
163936 ATTTAAAATT
1 ATTTAAAATT
163946 TTAAAAATTC
Statistics
Matches: 66, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
15 1 0.02
16 63 0.95
17 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTTAAAATTAAAATA
Found at i:163883 original size:22 final size:22
Alignment explanation
Indices: 163840--163884 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
163830 AACTTAATTG
*
163840 ATTTAAAATTAAAATAATTTAA
1 ATTTAAAATTAAAATAAATTAA
*
163862 ATTTAAAA-TAATATTAAATTAA
1 ATTTAAAATTAA-AATAAATTAA
163884 A
1 A
163885 GTGACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAAATTAAAATAAATTAA
Found at i:163943 original size:32 final size:32
Alignment explanation
Indices: 163840--163945 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
163830 AACTTAATTG
*
163840 ATTTAAAATTAAAATAATTTAAATTTAAAATA
1 ATTTAAAATTAAAATAACTTAAATTTAAAATA
* * * *
163872 ATATT-AAATTAAAGTGACATAAATTTGAAATA
1 AT-TTAAAATTAAAATAACTTAAATTTAAAATA
* * *
163904 ATCTAAAATCAAAATAACTTAAATTTTAAATA
1 ATTTAAAATTAAAATAACTTAAATTTAAAATA
163936 ATTTAAAATT
1 ATTTAAAATT
163946 TTAAAAATTC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
31 1 0.02
32 56 0.95
33 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (32 bp):
ATTTAAAATTAAAATAACTTAAATTTAAAATA
Found at i:163961 original size:16 final size:17
Alignment explanation
Indices: 163924--163961 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
163914 AAAATAACTT
*
163924 AAATTTTAAATAATTTA
1 AAATTTTAAATAATTCA
163941 AAATTTTAAA-AATTCA
1 AAATTTTAAATAATTCA
*
163957 TAATT
1 AAATT
163962 ATCCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTAAATAATTCA
Found at i:164419 original size:17 final size:18
Alignment explanation
Indices: 164388--164436 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
164378 AAAAAATTTA
164388 ATTTTATTAAA-AAATATT
1 ATTTTA-TAAATAAATATT
164406 -TTTTATAAATAAAT-TT
1 ATTTTATAAATAAATATT
*
164422 ATTTCAT-AATAAATA
1 ATTTTATAAATAAATA
164437 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTATAAATAAATATT
Found at i:166066 original size:3 final size:3
Alignment explanation
Indices: 166058--166093 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
166048 ACACCTAAAT
166058 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
166094 CAAAACCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:168134 original size:2 final size:2
Alignment explanation
Indices: 168127--168158 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
168117 ATCTATAGGT
*
168127 TA TA TA TA CA 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
168159 AGATTTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:170344 original size:24 final size:25
Alignment explanation
Indices: 170317--170371 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
170307 CATAATAAAT
* * *
170317 ATAAATTAAAAACAATTTATAA-TA
1 ATAAATAAAAAAAAATTTACAATTA
170341 AT-AATAAAAAAAAATTTACAATTA
1 ATAAATAAAAAAAAATTTACAATTA
170365 ATAAATA
1 ATAAATA
170372 TTATGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 16 0.62
24 6 0.23
25 4 0.15
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
ATAAATAAAAAAAAATTTACAATTA
Found at i:170609 original size:2 final size:2
Alignment explanation
Indices: 170602--170644 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
170592 CTTTCATTTC
170602 AT AT AT AT AT 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 AT
170644 A
1 A
170645 GATTACAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:170790 original size:2 final size:2
Alignment explanation
Indices: 170783--170813 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
170773 TCGTCTCTTT
*
170783 TA TA TA TA TA TA TA CA 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
170814 TACATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:172141 original size:22 final size:21
Alignment explanation
Indices: 172105--172159 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
172095 TTAAAAAATA
172105 TAAAA-ATTT-AATTAAAC-T
1 TAAAATATTTGAATTAAACAT
*
172123 CATAAATTATTTGAATTAAACAT
1 --TAAAATATTTGAATTAAACAT
172146 TAAAATATTTGAAT
1 TAAAATATTTGAAT
172160 CTAACTCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 17 0.57
22 8 0.27
23 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATATTTGAATTAAACAT
Found at i:174061 original size:16 final size:15
Alignment explanation
Indices: 174040--174085 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 15
174030 TGATCATGTT
174040 ATTTTATATATTATTA
1 ATTTTAT-TATTATTA
174056 ATTTTATT-TT-TTA
1 ATTTTATTATTATTA
*
174069 ATTTTTTTATTATTA
1 ATTTTATTATTATTA
174084 AT
1 AT
174086 AAGATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.37
14 4 0.15
15 6 0.22
16 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTATTATTA
Found at i:174116 original size:20 final size:19
Alignment explanation
Indices: 174093--174139 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
174083 AATAAGATTT
174093 ATTTAA-TTTATAAATAAAAA
1 ATTTAATTTTAT-AA-AAAAA
*
174113 ATTTAATTTTATCAAAAAA
1 ATTTAATTTTATAAAAAAA
174132 ATTTAATT
1 ATTTAATT
174140 AAATAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 7 0.28
21 5 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAATTTTATAAAAAAA
Found at i:174382 original size:30 final size:31
Alignment explanation
Indices: 174346--174405 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
174336 CTCACTGTTC
* *
174346 CCATTAATGTCTG-TACTAACTACAAAGTTA
1 CCATTAATGCCTGCAACTAACTACAAAGTTA
*
174376 CCATTAATGCCTGCAATTAACTACAAAGTT
1 CCATTAATGCCTGCAACTAACTACAAAGTT
174406 GCCGTAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (31 bp):
CCATTAATGCCTGCAACTAACTACAAAGTTA
Found at i:174754 original size:2 final size:2
Alignment explanation
Indices: 174742--174792 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
174732 GTTTACAGCT
* *
174742 TA TA TA CA TA TA TA CA 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 TA TA TA TA TA
*
174784 TA TA CA TA T
1 TA TA TA TA T
174793 GTATGAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:174965 original size:26 final size:27
Alignment explanation
Indices: 174918--174976 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
174908 CTTTAAATTT
* *
174918 TTAATTAATAATTAAAGTTTAAT-AAA
1 TTAATTAATAAATAAAGATTAATAAAA
* *
174944 TTAATTAATAAATGATGATTAATAAAA
1 TTAATTAATAAATAAAGATTAATAAAA
174971 TTAATT
1 TTAATT
174977 TTTAGTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAATTAATAAATAAAGATTAATAAAA
Found at i:175198 original size:139 final size:136
Alignment explanation
Indices: 174911--175186 Score: 362
Period size: 139 Copynumber: 2.0 Consensus size: 136
174901 ATAACTCCTT
* *
174911 TAAATTTTTAATTAATAATTAAAGTTTAATAAATTAATTAATAAATGATGATTAATAAAATTAAT
1 TAAATTTTT--TTAATAATTAAAGTCTAATAAATTAATTAATAAATGATGATTAATAAAATTAAG
* * *
174976 TTTTAGTCTTTTATAAAATAAAAATTCTATATTAATTTTTTTATAAAATACTTAGGGTTAAATAA
64 TTTTAGTCTTTTATAAAATAAAAATTCTATATTAATTTATATATAAAATA-TTA-GATT-AATAA
*
175041 AAATTATAATG
126 AAATTATAAAG
* *
175052 TTAATTTTTTTAATAATTATAGTCTAATAAATTAATTAATAAATGATGATTTAA-AAAATTAAGT
1 TAAATTTTTTTAATAATTAAAGTCTAATAAATTAATTAATAAATGATGA-TTAATAAAATTAAGT
*
175116 TTTAGTCTTTTATAAAATAAAAATTCTATGTTAACTTTATATATATAAAT-TTA-ATT-ATAAAA
65 TTTAGTCTTTTATAAAATAAAAATTCTATATTAA-TTTATATATA-AAATATTAGATTAATAAAA
175178 ATATATAAA
128 AT-TATAAA
175187 AAGTAATATT
Statistics
Matches: 122, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
135 8 0.07
136 5 0.04
137 2 0.02
139 83 0.68
140 12 0.10
141 12 0.10
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (136 bp):
TAAATTTTTTTAATAATTAAAGTCTAATAAATTAATTAATAAATGATGATTAATAAAATTAAGTT
TTAGTCTTTTATAAAATAAAAATTCTATATTAATTTATATATAAAATATTAGATTAATAAAAATT
ATAAAG
Found at i:175566 original size:10 final size:10
Alignment explanation
Indices: 175546--175581 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
175536 TTCAACAGAT
175546 AGAACAACAAA
1 AGAA-AACAAA
175557 AGAAAACAAA
1 AGAAAACAAA
*
175567 AGAAAAGAAA
1 AGAAAACAAA
175577 AGAAA
1 AGAAA
175582 CCAAGACAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (10 bp):
AGAAAACAAA
Found at i:176155 original size:27 final size:27
Alignment explanation
Indices: 176117--176168 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
176107 AAAAATTATA
*
176117 ACAAGAAGTTACTAAACCCTTTGTTTC
1 ACAACAAGTTACTAAACCCTTTGTTTC
176144 ACAACAAGTTACTAAACCCTTTGTT
1 ACAACAAGTTACTAAACCCTTTGTT
176169 ATCTTTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (27 bp):
ACAACAAGTTACTAAACCCTTTGTTTC
Found at i:177541 original size:2 final size:2
Alignment explanation
Indices: 177534--177599 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
177524 TTTCGTCTCT
177534 TA TA TA TA TA 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 TA TA TA TA TA
177576 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
177600 CAGACTACAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.