Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 1 of 45
Found at i:25 original size:7 final size:7
Alignment explanation
Indices: 10--2834 Score: 1433
Period size: 7 Copynumber: 401.6 Consensus size: 7
1 CAACCCGGC
10 ACCCG-A
1 ACCCGAA
16 ACCCGAA
1 ACCCGAA
23 ACCCGAA
1 ACCCGAA
30 ACCCGAA
1 ACCCGAA
*
37 TCCCGAA
1 ACCCGAA
44 ACCCG-A
1 ACCCGAA
50 ACCCGAA
1 ACCCGAA
57 A-CCGAA
1 ACCCGAA
*
63 ACCCGCA
1 ACCCGAA
70 ACCCG-A
1 ACCCGAA
76 ACCCGGAA
1 ACCC-GAA
84 ACCTCGAA
1 ACC-CGAA
92 ACCCGACA
1 ACCCGA-A
100 ACCCGAA
1 ACCCGAA
* *
107 CCCCGCA
1 ACCCGAA
114 ACCCGAA
1 ACCCGAA
*
121 A-CCGCA
1 ACCCGAA
127 ACCCGAA
1 ACCCGAA
134 ACCCGAAA
1 ACCCG-AA
*
142 ATCCGCAA
1 ACCCG-AA
150 ACCCGATA
1 ACCCGA-A
158 ACTCCG--
1 AC-CCGAA
164 ACCCGAA
1 ACCCGAA
171 ACCCGAA
1 ACCCGAA
178 ACCCG-A
1 ACCCGAA
184 ACCCGAA
1 ACCCGAA
191 ACCCG-A
1 ACCCGAA
197 ACCCGAA
1 ACCCGAA
204 TACCCGAA
1 -ACCCGAA
212 TACCCGAA
1 -ACCCGAA
220 ACCCGAGAA
1 ACCC--GAA
*
229 ACCCGGA
1 ACCCGAA
236 ACCC--A
1 ACCCGAA
*
241 ACCCGGA
1 ACCCGAA
248 ACCC-AA
1 ACCCGAA
254 ACCCGAA
1 ACCCGAA
261 ACCCGAA
1 ACCCGAA
268 ACCCTGAA
1 ACCC-GAA
276 ACCCGAA
1 ACCCGAA
283 ACCCGAAA
1 ACCCG-AA
291 ACCCGGAA
1 ACCC-GAA
299 ACCCGAA
1 ACCCGAA
* *
306 AACCTAA
1 ACCCGAA
313 A-CCGAA
1 ACCCGAA
319 TACCCGAA
1 -ACCCGAA
327 ACCCGAA
1 ACCCGAA
334 A-CCGAA
1 ACCCGAA
*
340 ACCCGGCA
1 ACCC-GAA
* *
348 ATCCGCA
1 ACCCGAA
*
355 ACCCGCA
1 ACCCGAA
362 ACCCGAA
1 ACCCGAA
369 ACCCGATA
1 ACCCGA-A
377 ACCCGGAA
1 ACCC-GAA
385 ACCCGAA
1 ACCCGAA
392 ACCCGAA
1 ACCCGAA
* *
399 ACCGGAC
1 ACCCGAA
406 A-CCGAA
1 ACCCGAA
*
412 ACCCGAC
1 ACCCGAA
419 ACCCGAA
1 ACCCGAA
426 ACCTCTGAA
1 ACC-C-GAA
435 ACCCGAA
1 ACCCGAA
442 ACCCGAA
1 ACCCGAA
449 ACCCGAA
1 ACCCGAA
*
456 ACCCTAA
1 ACCCGAA
463 ACCCGAAA
1 ACCCG-AA
*
471 ACCCTAA
1 ACCCGAA
**
478 ACCCGTC
1 ACCCGAA
485 A-CCGAA
1 ACCCGAA
491 ACCCGAA
1 ACCCGAA
498 ACCCGGAA
1 ACCC-GAA
*
506 ACCC-TA
1 ACCCGAA
*
512 ACACCTAA
1 AC-CCGAA
*
520 ACCCTAA
1 ACCCGAA
*
527 ACTC-AA
1 ACCCGAA
*
533 ACCC-CA
1 ACCCGAA
*
539 ACCCTAA
1 ACCCGAA
*
546 A-CCTAA
1 ACCCGAA
552 ACCCGAA
1 ACCCGAA
*
559 ACCCTAA
1 ACCCGAA
*
566 ACCTCTAA
1 ACC-CGAA
* *
574 CCCCTAA
1 ACCCGAA
* *
581 CCCCTAA
1 ACCCGAA
*
588 ACCCTAA
1 ACCCGAA
*
595 ACCAGAA
1 ACCCGAA
*
602 A-CCTAA
1 ACCCGAA
*
608 ACCCGCA
1 ACCCGAA
*
615 ACCCTAA
1 ACCCGAA
622 ACCCGACA
1 ACCCGA-A
*
630 CCCCGAAA
1 ACCCG-AA
638 ACCCGAA
1 ACCCGAA
645 ACCTC---
1 ACC-CGAA
*
650 ACCTGAA
1 ACCCGAA
*
657 ACCCCTAAA
1 A-CCC-GAA
*
666 ACCCTAA
1 ACCCGAA
*
673 ACCCTAA
1 ACCCGAA
*
680 ACCCTAA
1 ACCCGAA
*
687 ACCCTAA
1 ACCCGAA
*
694 ACCCTAA
1 ACCCGAA
*
701 ACCCTAA
1 ACCCGAA
*
708 ACCCTAA
1 ACCCGAA
**
715 ACCCTTA
1 ACCCGAA
*
722 ACCCGAC
1 ACCCGAA
729 ACCCG-A
1 ACCCGAA
*
735 A-CC-TA
1 ACCCGAA
740 ACCACGAA
1 ACC-CGAA
748 A-CCGAA
1 ACCCGAA
754 A-CCGAA
1 ACCCGAA
*
760 CCCCGAA
1 ACCCGAA
767 ACCCG-A
1 ACCCGAA
773 ACCCGAA
1 ACCCGAA
780 ACCCG-A
1 ACCCGAA
*
786 A-CCTAA
1 ACCCGAA
*
792 ACCCTAA
1 ACCCGAA
*
799 ACCCTAA
1 ACCCGAA
*
806 ACCCGAC
1 ACCCGAA
*
813 ACCCTTAA
1 ACCC-GAA
*
821 ACCCTAA
1 ACCCGAA
*
828 ACCCTAA
1 ACCCGAA
**
835 AAACGAA
1 ACCCGAA
842 ACCCGCTAA
1 ACCCG--AA
851 A-CCG-A
1 ACCCGAA
** *
856 ACCTTAC
1 ACCCGAA
863 ACCCGAAA
1 ACCCG-AA
*
871 ACCCTAA
1 ACCCGAA
878 ACCCGAA
1 ACCCGAA
885 ACCCGCGAAA
1 A-CC-CG-AA
*
895 ACCCTAA
1 ACCCGAA
*
902 ACCCTAA
1 ACCCGAA
*
909 ACCCTAA
1 ACCCGAA
* *
916 CCCCTAA
1 ACCCGAA
923 ACCCGAA
1 ACCCGAA
*
930 ACCCTAA
1 ACCCGAA
*
937 ACCCTCTATAA
1 A-CC-C--GAA
948 ACCCGTAA
1 ACCCG-AA
956 A-CCGAA
1 ACCCGAA
962 ACCC-AA
1 ACCCGAA
*
968 ACCCTAA
1 ACCCGAA
975 ACCCGCAA
1 ACCCG-AA
983 ACCCGAA
1 ACCCGAA
*
990 ACCCTAA
1 ACCCGAA
*
997 ACCCTTAA
1 ACCC-GAA
*
1005 ACCCTAA
1 ACCCGAA
*
1012 A-CCTAA
1 ACCCGAA
1018 ACCCGAA
1 ACCCGAA
1025 A-CCGTAA
1 ACCCG-AA
1032 ACCCGAA
1 ACCCGAA
1039 ACCCCGAA
1 A-CCCGAA
*
1047 ACCCGCA
1 ACCCGAA
1054 A-CCGAA
1 ACCCGAA
*
1060 A-CCTAA
1 ACCCGAA
**
1066 ACACTTAA
1 AC-CCGAA
1074 ACCCGAA
1 ACCCGAA
**
1081 ACCCTTCA
1 ACCC-GAA
1089 A-CCGAAA
1 ACCCG-AA
1096 ACCCCGAA
1 A-CCCGAA
*
1104 A-CCTAA
1 ACCCGAA
1110 A-CCGAA
1 ACCCGAA
*
1116 ACCCTAAA
1 ACCC-GAA
1124 ACCCG-A
1 ACCCGAA
*
1130 A-CCTAA
1 ACCCGAA
1136 ACCCGTAA
1 ACCCG-AA
1144 ACCCGAA
1 ACCCGAA
*
1151 CCCCGAA
1 ACCCGAA
*
1158 ACCCTAA
1 ACCCGAA
*
1165 ACCCTAA
1 ACCCGAA
*
1172 ACTCGAA
1 ACCCGAA
*
1179 ACCCGAC
1 ACCCGAA
*
1186 ACCC-TA
1 ACCCGAA
1192 ACCCGAA
1 ACCCGAA
1199 ACCCGAA
1 ACCCGAA
*
1206 CCCCGAA
1 ACCCGAA
1213 ACCCGGGTAA
1 ACCC--G-AA
1223 ACCC-AA
1 ACCCGAA
1229 ACTCCCGAA
1 A--CCCGAA
1238 ACCCGAA
1 ACCCGAA
*
1245 A-CCTAA
1 ACCCGAA
1251 ACCCGAA
1 ACCCGAA
1258 ACCCGAA
1 ACCCGAA
1265 A-CCGAA
1 ACCCGAA
1271 A-CCGAA
1 ACCCGAA
1277 ACCCGAA
1 ACCCGAA
1284 ACCCGAA
1 ACCCGAA
1291 ACCCGAAA
1 ACCCG-AA
1299 ACCCGAA
1 ACCCGAA
*
1306 A-CCTAA
1 ACCCGAA
*
1312 ACCCTAA
1 ACCCGAA
1319 ACCCGAA
1 ACCCGAA
*
1326 ACCCTAA
1 ACCCGAA
*
1333 ACCCTAAA
1 ACCC-GAA
*
1341 ACCCCTAA
1 A-CCCGAA
**
1349 ACCTTAA
1 ACCCGAA
1356 ACCCGAA
1 ACCCGAA
**
1363 A-CTTAA
1 ACCCGAA
*
1369 ACCCTAA
1 ACCCGAA
*
1376 ACCCTAA
1 ACCCGAA
**
1383 ACCCTCA
1 ACCCGAA
1390 ACCCGGAA
1 ACCC-GAA
* *
1398 CCCCTAA
1 ACCCGAA
* *
1405 ACCCTAC
1 ACCCGAA
*
1412 A-CCTAA
1 ACCCGAA
*
1418 ACCCGCA
1 ACCCGAA
*
1425 ACCC-TA
1 ACCCGAA
*
1431 ACCCTAA
1 ACCCGAA
*
1438 ACCC-TA
1 ACCCGAA
1444 ACCCGAA
1 ACCCGAA
*
1451 ACCCTAAA
1 ACCC-GAA
1459 ACCCGAATGA
1 ACCCG-A--A
*
1469 ACCTGAA
1 ACCCGAA
*
1476 A-CCTATA
1 ACCCGA-A
*
1483 ACCCTAA
1 ACCCGAA
1490 ACCCTAGAAA
1 ACCC--G-AA
*
1500 ACCCTAA
1 ACCCGAA
1507 ACCCGAA
1 ACCCGAA
1514 A-CCGACA
1 ACCCGA-A
1521 ACCCGAA
1 ACCCGAA
1528 ACCCGAA
1 ACCCGAA
*
1535 ACCCTAA
1 ACCCGAA
* *
1542 ACCTAGCA
1 ACC-CGAA
*
1550 ACCCTAA
1 ACCCGAA
*
1557 ACCCTAA
1 ACCCGAA
1564 ACCCGTAA
1 ACCCG-AA
*
1572 ACCCTCAA
1 ACCC-GAA
*
1580 ACCCTAA
1 ACCCGAA
*
1587 A-CCTAA
1 ACCCGAA
*
1593 ACCCTAA
1 ACCCGAA
*
1600 TCCC-AA
1 ACCCGAA
1606 ACCCGAAA
1 ACCCG-AA
**
1614 ACCCTTA
1 ACCCGAA
1621 ACCCGAA
1 ACCCGAA
1628 ACCCGAA
1 ACCCGAA
* *
1635 TCCCTAA
1 ACCCGAA
*
1642 AACCGAA
1 ACCCGAA
* **
1649 A-ACGGT
1 ACCCGAA
*
1655 GCCCGAAAA
1 ACCCG--AA
1664 ACCCGAA
1 ACCCGAA
*
1671 ACCCTAA
1 ACCCGAA
*
1678 ACCCTAA
1 ACCCGAA
1685 ACCCGGAGAA
1 ACCC---GAA
1695 ACCC-AA
1 ACCCGAA
1701 ACCCGAA
1 ACCCGAA
1708 A-CCGTAA
1 ACCCG-AA
* *
1715 CCCCCTAA
1 -ACCCGAA
**
1723 ACCATAA
1 ACCCGAA
1730 ACCCGAA
1 ACCCGAA
1737 ACCCGAA
1 ACCCGAA
1744 ACCCGAA
1 ACCCGAA
** *
1751 AAACAAA
1 ACCCGAA
***
1758 ACAAAAAA
1 AC-CCGAA
*
1766 ACCTGAAA
1 ACCCG-AA
*
1774 ACCCGAC
1 ACCCGAA
*
1781 ACCCTAA
1 ACCCGAA
1788 ACCCGAA
1 ACCCGAA
1795 ACCCGAAA
1 ACCCG-AA
*
1803 ACCCGGTGA
1 ACCC-G-AA
1812 ACCCGAA
1 ACCCGAA
*
1819 ACCTGAA
1 ACCCGAA
1826 ACCCGAA
1 ACCCGAA
1833 ACTCCGAA
1 AC-CCGAA
*
1841 AGCCCGAC
1 A-CCCGAA
1849 ACCCGAA
1 ACCCGAA
*
1856 ACCCCTAA
1 A-CCCGAA
1864 A-CCGAA
1 ACCCGAA
1870 ACCCGAA
1 ACCCGAA
1877 ACCCGAA
1 ACCCGAA
*
1884 ACCCTAA
1 ACCCGAA
1891 ACCCG-A
1 ACCCGAA
*
1897 ACCCTAAA
1 ACCC-GAA
1905 ACCCGAA
1 ACCCGAA
*
1912 A-CC-TA
1 ACCCGAA
1917 ACCCGAA
1 ACCCGAA
1924 ACCCGAA
1 ACCCGAA
1931 ACCCGAA
1 ACCCGAA
*
1938 ACCCTAA
1 ACCCGAA
1945 ACCCGAA
1 ACCCGAA
1952 ACCCGAA
1 ACCCGAA
*
1959 ACACGAA
1 ACCCGAA
*
1966 ACCCTAA
1 ACCCGAA
*
1973 ACCCTAA
1 ACCCGAA
*
1980 ACCCTAA
1 ACCCGAA
* *
1987 CCCCTTAA
1 ACCC-GAA
*
1995 ACCCTAA
1 ACCCGAA
*
2002 ACCCAAA
1 ACCCGAA
* *
2009 AACCGCA
1 ACCCGAA
*
2016 ACCCTAA
1 ACCCGAA
*
2023 ACCCTAAA
1 ACCC-GAA
2031 ACCCGAA
1 ACCCGAA
*
2038 A-CC-TA
1 ACCCGAA
2043 ACCCGAA
1 ACCCGAA
**
2050 ACCATAA
1 ACCCGAA
2057 ACCCGAA
1 ACCCGAA
2064 ACCCGAA
1 ACCCGAA
2071 ACCCGAA
1 ACCCGAA
*
2078 AACCGAA
1 ACCCGAA
**
2085 ACCCCTA
1 ACCCGAA
2092 ACCCGAA
1 ACCCGAA
2099 ACCCGAA
1 ACCCGAA
2106 ACCCGAA
1 ACCCGAA
2113 ACCCGAA
1 ACCCGAA
2120 ACCCGAAA
1 ACCCG-AA
**
2128 ACCCTCA
1 ACCCGAA
2135 ACCCGAA
1 ACCCGAA
*
2142 ACCC-TA
1 ACCCGAA
*
2148 ACCCTAA
1 ACCCGAA
*
2155 ACCCTAA
1 ACCCGAA
*
2162 ACCCTAAAA
1 ACCC--GAA
*
2171 ACCCTAA
1 ACCCGAA
*
2178 ACCCTAA
1 ACCCGAA
*
2185 ACCCTATA
1 ACCCGA-A
* *
2193 AACCTAA
1 ACCCGAA
*
2200 ACCCTAA
1 ACCCGAA
*
2207 ACCCTAAA
1 ACCC-GAA
*
2215 ACCCTAA
1 ACCCGAA
**
2222 ACCCCTTA
1 A-CCCGAA
*
2230 ACCCTAAA
1 ACCC-GAA
**
2238 ACCC-TC
1 ACCCGAA
*
2244 A-CCTAA
1 ACCCGAA
*
2250 ACCCTAAAA
1 ACCC--GAA
*
2259 ACCCTAA
1 ACCCGAA
*
2266 ACCCTAA
1 ACCCGAA
*
2273 ACCCTAA
1 ACCCGAA
*
2280 ACCC-TA
1 ACCCGAA
*
2286 ACCCTAA
1 ACCCGAA
*
2293 A-CCTAA
1 ACCCGAA
2299 ACCCGAA
1 ACCCGAA
*
2306 ACCCTAA
1 ACCCGAA
*
2313 ACCCTAA
1 ACCCGAA
*
2320 ACCCTAA
1 ACCCGAA
*
2327 A-CC-TA
1 ACCCGAA
*
2332 ACCCTAA
1 ACCCGAA
*
2339 ACCCTAA
1 ACCCGAA
*
2346 ACCCTAA
1 ACCCGAA
*
2353 A-CCTAA
1 ACCCGAA
*
2359 A-CCTAA
1 ACCCGAA
*
2365 ACCCTTAAA
1 ACCC--GAA
* *
2374 AACCTAA
1 ACCCGAA
*
2381 ACCCTAA
1 ACCCGAA
*
2388 ACCCTAA
1 ACCCGAA
* *
2395 CCCCAAA
1 ACCCGAA
**
2402 ACCCTCA
1 ACCCGAA
*
2409 A-CCTAA
1 ACCCGAA
**
2415 ACCTAAA
1 ACCCGAA
**
2422 ACCCTCA
1 ACCCGAA
*
2429 ACCCTAA
1 ACCCGAA
*
2436 A-CCTAA
1 ACCCGAA
*
2442 ACCCTTAA
1 ACCC-GAA
**
2450 ACCTAAA
1 ACCCGAA
**
2457 ACCC-TC
1 ACCCGAA
*
2463 ACCC-TA
1 ACCCGAA
*
2469 ACCCTAA
1 ACCCGAA
*
2476 ACCCTAA
1 ACCCGAA
**
2483 ACCCTCA
1 ACCCGAA
2490 ACCC-AA
1 ACCCGAA
*
2496 ACCCTAA
1 ACCCGAA
*
2503 ACCCTAA
1 ACCCGAA
*
2510 ACCCTAA
1 ACCCGAA
*
2517 ACCCTAA
1 ACCCGAA
*
2524 ACCC-TA
1 ACCCGAA
*
2530 ACCC-TA
1 ACCCGAA
*
2536 A-CCTAA
1 ACCCGAA
*
2542 ACCC-TA
1 ACCCGAA
*
2548 A-CCTAA
1 ACCCGAA
*
2554 ACCC-TA
1 ACCCGAA
*
2560 ACCCAAA
1 ACCCGAA
*
2567 ACCCAAA
1 ACCCGAA
*
2574 ACCCAAA
1 ACCCGAA
*
2581 ACCCTAA
1 ACCCGAA
*
2588 ACCCTAA
1 ACCCGAA
*
2595 ACCCTAA
1 ACCCGAA
*
2602 ACCCTAAA
1 ACCC-GAA
*
2610 ACCCTAA
1 ACCCGAA
*
2617 ACCCTAA
1 ACCCGAA
*
2624 ACCCTAA
1 ACCCGAA
*
2631 ACCCTAA
1 ACCCGAA
*
2638 ACCCTAA
1 ACCCGAA
*
2645 ACCCTAA
1 ACCCGAA
*
2652 ACCCTAA
1 ACCCGAA
*
2659 ACCCTAA
1 ACCCGAA
*
2666 ACCCTAA
1 ACCCGAA
*
2673 ACCCTAA
1 ACCCGAA
* *
2680 ACGCTAA
1 ACCCGAA
2687 ACCCCGAA
1 A-CCCGAA
*
2695 CCCCGAA
1 ACCCGAA
*
2702 CCCCG-A
1 ACCCGAA
2708 ACCCGAA
1 ACCCGAA
*
2715 CCCCGAA
1 ACCCGAA
*
2722 CCCCGAA
1 ACCCGAA
*
2729 CCCCGAA
1 ACCCGAA
*
2736 CCCCGAA
1 ACCCGAA
*
2743 CCCCGAA
1 ACCCGAA
*
2750 CCCCG-A
1 ACCCGAA
2756 ACCCGAA
1 ACCCGAA
*
2763 CCCCGAA
1 ACCCGAA
*
2770 CCCCGAA
1 ACCCGAA
*
2777 CCCCG-A
1 ACCCGAA
2783 ACCCGAA
1 ACCCGAA
*
2790 CCCCGAA
1 ACCCGAA
*
2797 CCCCGAA
1 ACCCGAA
*
2804 CCCCGAA
1 ACCCGAA
*
2811 CCCCG-A
1 ACCCGAA
*
2817 ACCCCAA
1 ACCCGAA
*
2824 ACCCCAA
1 ACCCGAA
2831 ACCC
1 ACCC
2835 TAATTCCCAA
Statistics
Matches: 2308, Mismatches: 324, Indels: 373
0.77 0.11 0.12
Matches are distributed among these distances:
5 33 0.01
6 343 0.15
7 1472 0.64
8 354 0.15
9 74 0.03
10 28 0.01
11 4 0.00
ACGTcount: A:0.41, C:0.43, G:0.08, T:0.08
Consensus pattern (7 bp):
ACCCGAA
Found at i:175 original size:57 final size:54
Alignment explanation
Indices: 15--2145 Score: 814
Period size: 57 Copynumber: 37.9 Consensus size: 54
5 CCGGCACCCG
*
15 AACCCGAAACCCGAAACCCGAATCCCGAAACCCGAACCCGAAA-CCGAAACCCGC
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCGAAA-CCGC
*
69 AACCCG-AACCCGGAAACCTCGAAACCCGACAACCCGAACCCCGCAACCCGAAACCGC
1 AACCCGAAACCC-GAAACC-CGAAACCCGA-AACCCGAA-CCCGAAACCCGAAACCGC
*
126 AACCCGAAACCCGAAAATCCGCAAACCCGATAACTCCG-ACCCGAAACCCGAAACC-C
1 AACCCGAAACCCG-AAACCCG-AAACCCGA-AAC-CCGAACCCGAAACCCGAAACCGC
*
182 GAACCCGAAACCCG-AACCCGAATACCCGAATACCCGAAACCCGAGAAACCCGGAACC-C
1 -AACCCGAAACCCGAAACCCGAA-ACCCGAA-ACCCG-AACCC--GAAACCCGAAACCGC
* *
240 AACCCGGAACCC-AAACCCGAAACCCGAAACCCTGAAACCCGAAACCCGAAAACCCGGA
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCC-G-AACCCGAAACCCG-AAA-CC-GC
* * * *
298 AACCCGAAAACCTAAA-CCGAATACCCGAAACCCGAAACCGAAACCCGGCAATCCGC
1 AACCCGAAACCCGAAACCCGAA-ACCCGAAACCCGAACCCGAAACCC-G-AAACCGC
* * * *
354 AACCCGCAACCCGAAACCCGATAACCCGGAAACCCGAAACCCGAAACCGGACACCGA
1 AACCCGAAACCCGAAACCCGA-AACCC-GAAACCCG-AACCCGAAACCCGAAACCGC
* *
411 AACCCGACACCCGAAACCTCTGAAACCCGAAACCCGAAACCCGAAACCCTAAACC-C
1 AACCCGAAACCCGAAACC-C-GAAACCCGAAACCCG-AACCCGAAACCCGAAACCGC
* * ** * **
467 GA----AAACCCTAAACCCGTCA-CCGAAACCCGAAACCCGGAAACCCTAACACCTA
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCG-AACCC-GAAACCCGAA-ACCGC
* * * * ** * *
519 AACCCTAAACTC-AAACCC-CAACCCTAAACCTAAACCCGAAACCCTAAACCTC
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCGAAACCGC
* * * * * ** * *
571 TAACCCCTAACCCCTAAACCCTAAACCAGAAACCTAAACCCGCAACCCTAAACCCGAC
1 -AA-CCCGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCGAAA-CCG-C
* * * * *
629 ACCCCGAAAACCCGAAACCTC---ACCTGAAACCCCTAAAACCCTAAACCCTAAACC-C
1 AACCCG-AAACCCGAAACC-CGAAACCCGAAA-CCC--GAACCCGAAACCCGAAACCGC
* * * * * * *
684 TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTTAACCCGACACCCG-AACC-T
1 --AACCCGAAACCCGAAACCCGAAACCCGAAACCC-GAACCCGAAACCCGAAACCGC
* **
739 AACCACGAAA-CCGAAA-CCGAACCCCGAAACCCGAACCCGAAACCCG-AACCTA
1 AACC-CGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCGAAACCGC
* * * * * * **
791 AACCCTAAACCCTAAACCCGACACCCTTAAACCCTAAACCCTAAAAACGAAACCCGC
1 AACCCGAAACCCGAAACCCGAAACCC-GAAACCC-GAACCCGAAACCCGAAA-CCGC
* ** * * *
848 TAAACCG-AACCTTACACCCGAAAACCCTAAACCCGAAACCCGCGAAAACCCTAAACC-C
1 -AACCCGAAACCCGAAACCCG-AAACCCGAAACCCG-AA-CC-CG-AAACCCGAAACCGC
* * * * * *** *
906 TAAACCCTAACCCCTAAACCCGAAACCCTAAACCC--TCTATAAACCCGTAAACCGA
1 --AACCCGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCG-AAACCGC
* * * * **
961 AACCC-AAACCCTAAACCCGCAAACCCGAAACCCTAAACCCTTAAACCCTAAACCTA
1 AACCCGAAACCCGAAACCCG-AAACCCGAAACCC-GAACCC-GAAACCCGAAACCGC
* **
1017 AACCCGAAA-CCGTAAACCCGAAACCCCGAAACCCGCAA-CCGAAA-CCTAAACACTTA
1 AACCCGAAACCCG-AAACCCGAAA-CCCGAAACCCG-AACCCGAAACCCGAAAC-C-GC
** * **
1073 AACCCGAAACCCTTCAA-CCGAAAACCCCGAAACCTAAACCGAAACCCTAAAACCCG-AACCTA
1 AACCCGAAACCC-GAAACCCG-AAA-CCCGAAA-C----CCG-AACCC-GAAACCCGAAACCGC
* * * * *
1135 AACCCGTAAACCCGAACCCCGAAACCCTAAACCCTAAACTCGAAACCCGACACC-C
1 AACCCG-AAACCCGAAACCCGAAACCCGAAACCC-GAACCCGAAACCCGAAACCGC
* * **
1190 TAACCCGAAACCCGAACCCCGAAACCCGGGTAAACCCAAACTCCCGAAACCCGAAACCTA
1 -AACCCGAAACCCGAAACCCGAAACCC--G-AAACCCGAA--CCCGAAACCCGAAACCGC
1250 AACCCGAAACCCGAAA-CCGAAA-CCGAAACCCGAAACCCGAAACCCGAAAACC-C
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCG-AACCCGAAACCCG-AAACCGC
* * * * * * **
1303 GAAACCTAAACCCTAAACCCGAAACCCTAAACCCTAAAACCCCTAAACCTTAAACC-C
1 -AACCCGAAACCCGAAACCCGAAACCCGAAACCC--GAA-CCCGAAACCCGAAACCGC
* ** * * ** * * * **
1360 GAAACTTAAACCCTAAACCCTAAACCCTCAACCCGGAACCCCTAAACCCTACACCTA
1 -AACCCGAAACCCGAAACCCGAAACCCGAAACCC-GAA-CCCGAAACCCGAAACCGC
* * * * *
1417 AACCCGCAACCC-TAACCCTAAACCC-TAACCCGAAACCCTAAAACCCGAATGAACCTG-
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCG-AACCC-GAAACCCG-A--AACC-GC
* * * * * *
1474 AAACCTATAACCCTAAACCCTAGAAAACCCTAAACCCGAAACCGACAACCCGAAACCCGA
1 AACCCGA-AACCCGAAACCC--G-AAACCCGAAACCCGAACCCGA-AACCCGAAA-CCGC
* * * * * * * **
1534 AACCCTAAACCTAGCAACCCTAAACCCTAAACCCGTAAACCCTCAAACCCTAAACCTA
1 AACCCGAAACC-CGAAACCCGAAACCCGAAACCCG--AACCC-GAAACCCGAAACCGC
* * ** * * *
1592 AACCCTAATCCC-AAACCCGAAAACCCTTAACCCGAAACCCGAATCCCTAAAACCGAA
1 AACCCGAAACCCGAAACCCG-AAACCCGAAACCCG-AACCCGAAACCC-GAAACCG-C
* * *
1649 AACGGTGCCCGAAAAACCCGAAACCCTAAACCCTAAACCCGGAGAAACCC-AAACCCGAAACCGT
1 AA-----CCCG--AAACCCGAAACCCGAAACCCGAAACCC---G-AACCCGAAACCCGAAACCGC
* ** ** * **
1713 AACCCCCTAAACCATAAACCCGAAACCCGAAACCCGAAAAAC-AAA-AC-AAA--AA
1 AA--CCCGAAACCCGAAACCCGAAACCCGAAACCCG-AACCCGAAACCCGAAACCGC
* * * * *
1765 AACCTGAAAACCCGACACCCTAAACCCGAAACCCGAAAACCCGGTGAACCCGAAACCTGA
1 AACCCG-AAACCCGAAACCCGAAACCCGAAACCCG--AACCC-G-AAACCCGAAACC-GC
* * * *
1825 AACCCGAAACTCCGAAAGCCCGACACCCGAAACCCCTAAACCGAAACCCGAAACCCGA
1 AACCCGAAAC-CCGAAA-CCCGAAACCCGAAA-CCCGAACCCGAAACCCGAAA-CCGC
* * * *
1883 AACCCTAAACCCG-AACCCTAAAACCCGAAA-CCTAACCCGAAACCCGAAACCCGA
1 AACCCGAAACCCGAAACCC-GAAACCCGAAACCCGAACCCGAAACCCGAAA-CCGC
* * * * *
1937 AACCCTAAACCCGAAACCCGAAACACGAAACCCTAAACCCTAAACCC-TAA-C-C
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCC-GAACCCGAAACCCGAAACCGC
** * * * * * * *
1989 --CCTTAAACCCTAAACCCAAAAACCGCAACCCTAAACCCTAAAACCCGAAACC-T
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCC-GAACCC-GAAACCCGAAACCGC
** * * * *
2042 AACCCGAAACCATAAACCCGAAACCCGAAACCCGAAAACCGAAACCCCTAACCCGA
1 AACCCGAAACCCGAAACCCGAAACCCGAAACCCG-AACCCGAAA-CCCGAAACCGC
*
2098 AACCCGAAACCCGAAACCCGAAACCCGAAAACCCTCAACCCGAAACCC
1 AACCCGAAACCCGAAACCCGAAACCCG-AAACCC-GAACCCGAAACCC
2146 TAACCCTAAA
Statistics
Matches: 1635, Mismatches: 266, Indels: 350
0.73 0.12 0.16
Matches are distributed among these distances:
49 16 0.01
50 46 0.03
51 54 0.03
52 58 0.04
53 73 0.04
54 150 0.09
55 180 0.11
56 259 0.16
57 320 0.20
58 169 0.10
59 132 0.08
60 47 0.03
61 23 0.01
62 39 0.02
63 18 0.01
64 25 0.02
65 14 0.01
66 5 0.00
67 7 0.00
ACGTcount: A:0.41, C:0.42, G:0.10, T:0.07
Consensus pattern (54 bp):
AACCCGAAACCCGAAACCCGAAACCCGAAACCCGAACCCGAAACCCGAAACCGC
Found at i:788 original size:6 final size:6
Alignment explanation
Indices: 721--788 Score: 57
Period size: 6 Copynumber: 10.7 Consensus size: 6
711 CTAAACCCTT
* * *
721 AACCCG ACACCCG AA-CCT AACCACG AAACCG AAACCG AACCCCG AAACCCG
1 AACCCG A-ACCCG AACCCG AACC-CG AACCCG AACCCG AA-CCCG -AACCCG
772 AACCCG AAACCCG AACC
1 AACCCG -AACCCG AACC
789 TAAACCCTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 4 0.08
6 23 0.44
7 23 0.44
8 2 0.04
ACGTcount: A:0.40, C:0.46, G:0.13, T:0.01
Consensus pattern (6 bp):
AACCCG
Found at i:2724 original size:27 final size:28
Alignment explanation
Indices: 2686--2834 Score: 259
Period size: 27 Copynumber: 5.4 Consensus size: 28
2676 CTAAACGCTA
2686 AACCCCGAACCCCGAACCCCGAA-CCCG
1 AACCCCGAACCCCGAACCCCGAACCCCG
2713 AACCCCGAACCCCGAACCCCGAACCCCG
1 AACCCCGAACCCCGAACCCCGAACCCCG
2741 AACCCCGAACCCCGAA-CCCGAACCCCG
1 AACCCCGAACCCCGAACCCCGAACCCCG
2768 AACCCCGAACCCCGAA-CCCGAACCCCG
1 AACCCCGAACCCCGAACCCCGAACCCCG
*
2795 AACCCCGAACCCCGAACCCCGAACCCCA
1 AACCCCGAACCCCGAACCCCGAACCCCG
*
2823 AACCCCAAACCC
1 AACCCCGAACCC
2835 TAATTCCCAA
Statistics
Matches: 118, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
27 77 0.65
28 41 0.35
ACGTcount: A:0.31, C:0.56, G:0.13, T:0.00
Consensus pattern (28 bp):
AACCCCGAACCCCGAACCCCGAACCCCG
Found at i:2853 original size:7 final size:7
Alignment explanation
Indices: 2816--2914 Score: 67
Period size: 7 Copynumber: 14.3 Consensus size: 7
2806 CCGAACCCCG
*
2816 AACCCCA
1 AACCCTA
*
2823 AACCCCA
1 AACCCTA
2830 AACCCTA
1 AACCCTA
*
2837 ATTCCC-A
1 A-ACCCTA
2844 AACCCTA
1 AACCCTA
*
2851 AACTCTA
1 AACCCTA
2858 AACCCTA
1 AACCCTA
*
2865 AA-CCTC
1 AACCCTA
*
2871 AACCCAA
1 AACCCTA
* *
2878 AATCTTA
1 AACCCTA
*
2885 AACCCGA
1 AACCCTA
2892 AACCCTA
1 AACCCTA
* *
2899 AATCTTA
1 AACCCTA
*
2906 AACCTTA
1 AACCCTA
2913 AA
1 AA
2915 TCTTTAAATT
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
6 8 0.11
7 60 0.85
8 3 0.04
ACGTcount: A:0.43, C:0.38, G:0.01, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:2901 original size:21 final size:21
Alignment explanation
Indices: 2822--2914 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 21
2812 CCCGAACCCC
* * *
2822 AAACCCCAAACCCTAATTCCC
1 AAACCCTAAACCCTAAATCCT
* *
2843 AAACCCTAAACTCTAAACCCT
1 AAACCCTAAACCCTAAATCCT
* * *
2864 AAA-CCTCAACCCAAAATCTT
1 AAACCCTAAACCCTAAATCCT
* *
2884 AAACCCGAAACCCTAAATCTT
1 AAACCCTAAACCCTAAATCCT
*
2905 AAACCTTAAA
1 AAACCCTAAA
2915 TCTTTAAATT
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
20 15 0.27
21 41 0.73
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCCTAAATCCT
Found at i:2980 original size:14 final size:14
Alignment explanation
Indices: 2963--3084 Score: 70
Period size: 14 Copynumber: 8.8 Consensus size: 14
2953 CCTAACCTTT
* *
2963 ATCCCTAAACCTCA
1 ATCCCTAATCCCCA
*
2977 ATCCCCAATCCCCA
1 ATCCCTAATCCCCA
*
2991 ATCCC-AAGCCCCTA
1 ATCCCTAATCCCC-A
* * *
3005 ATCCTTAATTCCTA
1 ATCCCTAATCCCCA
* * *
3019 AACCC-AAACCTCA
1 ATCCCTAATCCCCA
*
3032 ATCCCTCATCCCCA
1 ATCCCTAATCCCCA
*
3046 ATCCCTAATTCCCGA
1 ATCCCTAA-TCCCCA
** *
3061 A-CCGAAAACCCCA
1 ATCCCTAATCCCCA
3074 ATCCCTAATCC
1 ATCCCTAATCC
3085 TCAAACTTTA
Statistics
Matches: 76, Mismatches: 27, Indels: 10
0.67 0.24 0.09
Matches are distributed among these distances:
13 19 0.25
14 47 0.62
15 10 0.13
ACGTcount: A:0.32, C:0.46, G:0.02, T:0.20
Consensus pattern (14 bp):
ATCCCTAATCCCCA
Found at i:3090 original size:21 final size:21
Alignment explanation
Indices: 3066--3113 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
3056 CCCGAACCGA
*
3066 AAACCCCAATCCCTAATCCTC
1 AAACCCCAATCCCTAAACCTC
*** *
3087 AAACTTTAATCCCTAAACCTT
1 AAACCCCAATCCCTAAACCTC
3108 AAACCC
1 AAACCC
3114 TAAACTCTAA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCCAATCCCTAAACCTC
Found at i:3112 original size:7 final size:7
Alignment explanation
Indices: 3097--3220 Score: 55
Period size: 7 Copynumber: 18.1 Consensus size: 7
3087 AAACTTTAAT
3097 CCCTAAA
1 CCCTAAA
*
3104 CCTTAAA
1 CCCTAAA
3111 CCCTAAA
1 CCCTAAA
*
3118 CTCTAAA
1 CCCTAAA
* *
3125 -TCAAAA
1 CCCTAAA
3131 TCCCTAAA
1 -CCCTAAA
3139 CTCC-AAA
1 C-CCTAAA
*
3146 TCCTAAA
1 CCCTAAA
3153 CCCTAAA
1 CCCTAAA
*
3160 -CCTTAA
1 CCCTAAA
* * *
3166 TCTTCAAT
1 CCCT-AAA
*
3174 CCTTAAA
1 CCCTAAA
*
3181 -CTTCAAA
1 CCCT-AAA
3188 CCCTAAA
1 CCCTAAA
3195 CCC-AAA
1 CCCTAAA
*
3201 CCCCAAA
1 CCCTAAA
3208 CCC-AAA
1 CCCTAAA
3214 -CCTAAA
1 CCCTAAA
3220 C
1 C
3221 TTAAACCTCG
Statistics
Matches: 91, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
5 2 0.02
6 27 0.30
7 50 0.55
8 12 0.13
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:3153 original size:42 final size:42
Alignment explanation
Indices: 3101--3202 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
3091 TTTAATCCCT
*
3101 AAACCTTAAACCCTAAACTCTAAATC-AAAATCCCTAAACTCC
1 AAACCCTAAACCCTAAAC-CTAAATCTAAAATCCCTAAACTCC
* * ** * *
3143 AAATCCTAAACCCTAAACCTTAATCTTCAATCCTTAAACTTC
1 AAACCCTAAACCCTAAACCTAAATCTAAAATCCCTAAACTCC
3185 AAACCCTAAACCC-AAACC
1 AAACCCTAAACCCTAAACC
3203 CCAAACCCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 11 0.22
42 40 0.78
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (42 bp):
AAACCCTAAACCCTAAACCTAAATCTAAAATCCCTAAACTCC
Found at i:3194 original size:14 final size:14
Alignment explanation
Indices: 3101--3221 Score: 74
Period size: 14 Copynumber: 8.9 Consensus size: 14
3091 TTTAATCCCT
*
3101 AAACCTTAAAC-CC
1 AAACCCTAAACTCC
* *
3114 TAAACTCTAAA-TCA
1 -AAACCCTAAACTCC
3128 AAATCCCTAAACTCC
1 AAA-CCCTAAACTCC
*
3143 AAATCCTAAAC-CC
1 AAACCCTAAACTCC
* * *
3156 TAAACCTTAATCTTC
1 -AAACCCTAAACTCC
* * *
3171 AATCCTTAAACTTC
1 AAACCCTAAACTCC
3185 AAACCCTAAAC-CC
1 AAACCCTAAACTCC
*
3198 AAACCCCAAAC-CC
1 AAACCCTAAACTCC
3211 AAA-CCTAAACT
1 AAACCCTAAACT
3222 TAAACCTCGA
Statistics
Matches: 84, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
12 6 0.07
13 21 0.25
14 51 0.61
15 6 0.07
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCCTAAACTCC
Found at i:3241 original size:7 final size:7
Alignment explanation
Indices: 3149--3368 Score: 57
Period size: 7 Copynumber: 31.7 Consensus size: 7
3139 CTCCAAATCC
*
3149 TAAACCC
1 TAAACCT
3156 TAAACCT
1 TAAACCT
*
3163 T-AATCT
1 TAAACCT
*
3169 TCAATCCT
1 T-AAACCT
3177 TAAA-CT
1 TAAACCT
*
3183 TCAAACCC
1 T-AAACCT
3191 TAAACC-
1 TAAACCT
* *
3197 CAAACCC
1 TAAACCT
*
3204 CAAACC-
1 TAAACCT
*
3210 CAAACC-
1 TAAACCT
3216 TAAA-CT
1 TAAACCT
3222 TAAACCT
1 TAAACCT
**
3229 CGAACCT
1 TAAACCT
*
3236 TAAACCC
1 TAAACCT
*
3243 TCAACC-
1 TAAACCT
*
3249 TGAA-CT
1 TAAACCT
3255 TCAAACCCT
1 T-AAA-CCT
*
3264 TAATCCT
1 TAAACCT
*
3271 TAACCCT
1 TAAACCT
*
3278 T-GACCT
1 TAAACCT
3284 TAAAACCT
1 T-AAACCT
*
3292 TAAGCCT
1 TAAACCT
*
3299 TAAACTTT
1 TAAAC-CT
*
3307 TAAAACT
1 TAAACCT
3314 TAAAACCT
1 T-AAACCT
*
3322 TAAGCC-
1 TAAACCT
* *
3328 TCAAGCT
1 TAAACCT
*
3335 CTAATCC-
1 -TAAACCT
3342 TAAACCT
1 TAAACCT
*
3349 TAAACCC
1 TAAACCT
*
3356 CAAACCTT
1 TAAACC-T
3364 TAAAC
1 TAAAC
3369 ACTGAATTAA
Statistics
Matches: 155, Mismatches: 39, Indels: 37
0.67 0.17 0.16
Matches are distributed among these distances:
5 2 0.01
6 42 0.27
7 77 0.50
8 31 0.20
9 3 0.02
ACGTcount: A:0.39, C:0.34, G:0.03, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:3253 original size:20 final size:21
Alignment explanation
Indices: 3224--3263 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3214 CCTAAACTTA
3224 AACCTCGAACCTT-AAACCCTC
1 AACCTCGAA-CTTCAAACCCTC
3245 AACCT-GAACTTCAAACCCT
1 AACCTCGAACTTCAAACCCT
3264 TAATCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.35, C:0.40, G:0.05, T:0.20
Consensus pattern (21 bp):
AACCTCGAACTTCAAACCCTC
Found at i:3299 original size:15 final size:15
Alignment explanation
Indices: 3281--3328 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3271 TAACCCTTGA
3281 CCTTAAAACCTTAAG
1 CCTTAAAACCTTAAG
* *
3296 CCTT-AAACTTTTAAA
1 CCTTAAAAC-CTTAAG
*
3311 ACTTAAAACCTTAAG
1 CCTTAAAACCTTAAG
3326 CCT
1 CCT
3329 CAAGCTCTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (15 bp):
CCTTAAAACCTTAAG
Found at i:4989 original size:14 final size:14
Alignment explanation
Indices: 4971--5004 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4961 ATTTTTTTTG
*
4971 AATTTTAAATAATT
1 AATTTAAAATAATT
*
4985 TATTTAAAATAATT
1 AATTTAAAATAATT
4999 AATTTA
1 AATTTA
5005 TATGTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAAATAATT
Found at i:7695 original size:25 final size:24
Alignment explanation
Indices: 7632--7705 Score: 139
Period size: 24 Copynumber: 3.0 Consensus size: 24
7622 TTTGTTAAGG
7632 ATTCTAAATGATTAACTTTTTTAA
1 ATTCTAAATGATTAACTTTTTTAA
7656 ATTCTAAATGATTAACTTTTTTAA
1 ATTCTAAATGATTAACTTTTTTAA
7680 ATTCTAAATGATTTAACTTTTTTAA
1 ATTCTAAATGA-TTAACTTTTTTAA
7705 A
1 A
7706 ATCATTAACT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 35 0.71
25 14 0.29
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTCTAAATGATTAACTTTTTTAA
Found at i:10749 original size:2 final size:2
Alignment explanation
Indices: 10742--10806 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
10732 AATAATTAAA
10742 AG 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 AG
*
10784 AG AG AG AG AG AG AG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
10807 AAAGGTTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13019 original size:20 final size:21
Alignment explanation
Indices: 12994--13036 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
12984 CTCAATCTCG
12994 AAACTCCAAAC-CCAAAACTA
1 AAACTCCAAACTCCAAAACTA
*
13014 AAACTCCAAACTCCAAACCTA
1 AAACTCCAAACTCCAAAACTA
13035 AA
1 AA
13037 CCTTAATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACTCCAAACTCCAAAACTA
Found at i:13050 original size:27 final size:26
Alignment explanation
Indices: 12980--13066 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 26
12970 CTAAATCTCG
*
12980 AAACCTCAATCTCGAAACTCCAAACCC
1 AAACCTTAATCTC-AAACTCCAAACCC
* * * *
13007 AAAACTAAAACTCCAAACTCCAAACCT
1 AAACCTTAATCT-CAAACTCCAAACCC
13034 AAACCTTAATCCTCAAAC-CTCAAACCC
1 AAACCTTAAT-CTCAAACTC-CAAACCC
*
13061 CAACCT
1 AAACCT
13067 AACCCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.02
27 44 0.92
28 3 0.06
ACGTcount: A:0.44, C:0.39, G:0.01, T:0.16
Consensus pattern (26 bp):
AAACCTTAATCTCAAACTCCAAACCC
Found at i:13144 original size:20 final size:20
Alignment explanation
Indices: 13121--13190 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
13111 ACCAAACTTG
13121 AAACCTTAACCTTAAACCTT
1 AAACCTTAACCTTAAACCTT
* * *
13141 AAA-CTCCAACCTTAATCCCT
1 AAACCT-TAACCTTAAACCTT
* * *
13161 AAACTCTAAATCTAAAACCTT
1 AAAC-CTTAACCTTAAACCTT
*
13182 AAACTTTAA
1 AAACCTTAA
13191 ATTCTAAATC
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.05
20 20 0.54
21 13 0.35
22 2 0.05
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (20 bp):
AAACCTTAACCTTAAACCTT
Found at i:13186 original size:21 final size:21
Alignment explanation
Indices: 13134--13225 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
13124 CCTTAACCTT
* * *
13134 AAACCTTAAACTC-CAACCTT
1 AAACCTTAAACTCTAAATCTA
* *
13154 AATCCCTAAACTCTAAATCTA
1 AAACCTTAAACTCTAAATCTA
*
13175 AAACCTTAAACTTTAAATTCT-
1 AAACCTTAAACTCTAAA-TCTA
* * *
13196 AAATCTCAAACTCTAAATCCA
1 AAACCTTAAACTCTAAATCTA
13217 AAA-CTTAAA
1 AAACCTTAAA
13226 ACCCTAAACC
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 18 0.32
21 35 0.62
22 3 0.05
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACCTTAAACTCTAAATCTA
Found at i:13221 original size:14 final size:14
Alignment explanation
Indices: 13161--13218 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
13151 CTTAATCCCT
*
13161 AAACTCTAAATCTA
1 AAACTCTAAATCTC
*
13175 AAAC-CTTAAA-CTTT
1 AAACTC-TAAATC-TC
*
13189 AAATTCTAAATCTC
1 AAACTCTAAATCTC
13203 AAACTCTAAATC-C
1 AAACTCTAAATCTC
13216 AAA
1 AAA
13219 ACTTAAAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 6 0.17
14 28 0.78
15 2 0.06
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.29
Consensus pattern (14 bp):
AAACTCTAAATCTC
Found at i:13263 original size:14 final size:14
Alignment explanation
Indices: 13231--13289 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
13221 TTAAAACCCT
*
13231 AAACCTCGATCGC-C
1 AAACCTCGAAC-CTC
*
13245 AAACCTCGAACCTT
1 AAACCTCGAACCTC
* *
13259 GAACCTCGAAACTC
1 AAACCTCGAACCTC
*
13273 AAACCTCGAACTTC
1 AAACCTCGAACCTC
13287 AAA
1 AAA
13290 ACTCAAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.37, C:0.36, G:0.10, T:0.17
Consensus pattern (14 bp):
AAACCTCGAACCTC
Found at i:13277 original size:21 final size:21
Alignment explanation
Indices: 13231--13296 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
13221 TTAAAACCCT
* *
13231 AAACCTCGATCGC-CAAACCTC
1 AAACCTCGAAC-CTCAAAACTC
* * *
13252 GAACCTTGAACCTCGAAACTC
1 AAACCTCGAACCTCAAAACTC
*
13273 AAACCTCGAACTTCAAAACTC
1 AAACCTCGAACCTCAAAACTC
13294 AAA
1 AAA
13297 ATCTAAAACC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.17
Consensus pattern (21 bp):
AAACCTCGAACCTCAAAACTC
Found at i:13572 original size:20 final size:20
Alignment explanation
Indices: 13529--13572 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13519 TTGAACCTTA
*
13529 AAACTCTAACTCTAAACCCC
1 AAACTCTAACTCTAAAACCC
*
13549 AAACTCTAAC-CTTAAAACCT
1 AAACTCTAACTC-TAAAACCC
13569 AAAC
1 AAAC
13573 CTCGAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (20 bp):
AAACTCTAACTCTAAAACCC
Found at i:13617 original size:22 final size:22
Alignment explanation
Indices: 13592--13661 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
13582 CTGACCCCCG
13592 AACCCTTGAACCTCAAAACCCT
1 AACCCTTGAACCTCAAAACCCT
* *
13614 AACCCTTGAAACTTAAAACCCT
1 AACCCTTGAACCTCAAAACCCT
* * *
13636 AA-CCTCGAACC-CTAAACCCC
1 AACCCTTGAACCTCAAAACCCT
13656 AACCCT
1 AACCCT
13662 CAGCTTCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 8 0.20
21 10 0.25
22 22 0.55
ACGTcount: A:0.37, C:0.41, G:0.04, T:0.17
Consensus pattern (22 bp):
AACCCTTGAACCTCAAAACCCT
Found at i:13703 original size:21 final size:21
Alignment explanation
Indices: 13677--13726 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13667 TCAAATCCTT
13677 AACCTTAAAACTCATA-CCTCA
1 AACCTTAAAACTCATACCCT-A
* *
13698 AACCTTAAATCTCATGCCCTA
1 AACCTTAAAACTCATACCCTA
13719 AACCTTAA
1 AACCTTAA
13727 GCCCTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (21 bp):
AACCTTAAAACTCATACCCTA
Found at i:13776 original size:14 final size:14
Alignment explanation
Indices: 13759--13807 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
13749 CTCAAAATGC
13759 TAAACCTAAAACCT
1 TAAACCTAAAACCT
13773 TAAA-CTCAAAACCT
1 TAAACCT-AAAACCT
*
13787 TATACCCT-AAACCT
1 TA-AACCTAAAACCT
13801 T-AACCTA
1 TAAACCTA
13808 TCTTTAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 20 0.69
15 1 0.03
16 2 0.07
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTAAAACCT
Found at i:14420 original size:18 final size:18
Alignment explanation
Indices: 14397--14434 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
14387 CCTTCTCGTC
14397 ATACAACATCCTGATTGA
1 ATACAACATCCTGATTGA
14415 ATACAACATCCTGATTGA
1 ATACAACATCCTGATTGA
14433 AT
1 AT
14435 TCTTGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (18 bp):
ATACAACATCCTGATTGA
Found at i:21625 original size:19 final size:19
Alignment explanation
Indices: 21603--21640 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21593 CACAGTAACC
*
21603 GTATGTATGAACAGTGCCT
1 GTATATATGAACAGTGCCT
*
21622 GTATATGTGAACAGTGCCT
1 GTATATATGAACAGTGCCT
21641 CGACAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
GTATATATGAACAGTGCCT
Found at i:24449 original size:33 final size:34
Alignment explanation
Indices: 24384--24455 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
24374 TAAGTCATGG
*
24384 AACTTGTATATAATGAATAGCTGAGCAAAATATA
1 AACTTGTATATAATGAACAGCTGAGCAAAATATA
* * * * *
24418 CACTT-TATATAATGAGCAGTTGGGCACAATATA
1 AACTTGTATATAATGAACAGCTGAGCAAAATATA
24451 AACTT
1 AACTT
24456 CTAAATCTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (34 bp):
AACTTGTATATAATGAACAGCTGAGCAAAATATA
Found at i:26034 original size:73 final size:75
Alignment explanation
Indices: 25949--26090 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 75
25939 AATTAAAAAA
* * ** *
25949 TAATTAAATTAAAAAATTTATGTT-A-AAA-TCACGTATTAATTATTAT-TTTTTATTAAAATAA
1 TAATTAAATTAAAAAATTTATATTAATAAATTAAAATATTAATTATTATATTTTTA-AAAAATAA
26010 AAAATAATATT
65 AAAATAATATT
*
26021 TAATTAAATTTAAAAACTTTATATTAATAAATTAAAATATTAATTATTATATTTTTAAAAAATAA
1 TAATTAAA-TTAAAAAATTTATATTAATAAATTAAAATATTAATTATTATATTTTTAAAAAATAA
26086 AAAAT
65 AAAAT
26091 TTTAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
72 8 0.14
73 14 0.24
74 1 0.02
75 3 0.05
76 27 0.46
77 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (75 bp):
TAATTAAATTAAAAAATTTATATTAATAAATTAAAATATTAATTATTATATTTTTAAAAAATAAA
AAATAATATT
Found at i:26107 original size:23 final size:23
Alignment explanation
Indices: 26077--26121 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
26067 TTATATTTTT
26077 AAAAAATAAAAAATTTTAAATTA
1 AAAAAATAAAAAATTTTAAATTA
26100 AAAAAATAAAAAATTTTAAATT
1 AAAAAATAAAAAATTTTAAATT
26122 GAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATAAAAAATTTTAAATTA
Found at i:26539 original size:14 final size:15
Alignment explanation
Indices: 26511--26539 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26501 GATATTATTA
26511 ATTTTTTTATGATAT
1 ATTTTTTTATGATAT
26526 ATTTTTTTAT-ATAT
1 ATTTTTTTATGATAT
26540 CAAAATACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATTTTTTTATGATAT
Found at i:34297 original size:14 final size:13
Alignment explanation
Indices: 34280--34316 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
34270 GGTTATCCAC
34280 TACTTATTATATTA
1 TACTTATTAT-TTA
34294 TACTTA-T-TTTA
1 TACTTATTATTTA
34305 TACTTATTATTT
1 TACTTATTATTT
34317 TACCCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 4 0.19
14 6 0.29
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TACTTATTATTTA
Found at i:34308 original size:25 final size:24
Alignment explanation
Indices: 34280--34342 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
34270 GGTTATCCAC
34280 TACTTATTATATTATACTTATTTTA
1 TACTTATTATATTATACTTA-TTTA
* **
34305 TACTTATTATTTTACCCTTATTTA
1 TACTTATTATATTATACTTATTTA
*
34329 -ACTTATTTTATTAT
1 TACTTATTATATTAT
34343 TTTACCTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 11 0.34
24 4 0.12
25 17 0.53
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (24 bp):
TACTTATTATATTATACTTATTTA
Found at i:34456 original size:8 final size:7
Alignment explanation
Indices: 34407--34452 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
34397 TCAAATCTCC
34407 AAACCCA
1 AAACCCA
*
34414 AAACCCT
1 AAACCCA
*
34421 TAACCCAA
1 AAACCC-A
34429 AAACCCA
1 AAACCCA
*
34436 AAACTCA
1 AAACCCA
34443 AAACCCA
1 AAACCCA
34450 AAA
1 AAA
34453 ACCCTAAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.57, C:0.37, G:0.00, T:0.07
Consensus pattern (7 bp):
AAACCCA
Found at i:34468 original size:21 final size:22
Alignment explanation
Indices: 34407--34472 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
34397 TCAAATCTCC
* **
34407 AAACCCAAAACCCTTAACCCAA
1 AAACCCAAAACTCAAAACCCAA
34429 AAACCCAAAACTCAAAACCCAA
1 AAACCCAAAACTCAAAACCCAA
* *
34451 AAACCCTAAA-TCAGAACCCAA
1 AAACCCAAAACTCAAAACCCAA
34472 A
1 A
34473 CCTTAGATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 11 0.28
22 28 0.72
ACGTcount: A:0.55, C:0.36, G:0.02, T:0.08
Consensus pattern (22 bp):
AAACCCAAAACTCAAAACCCAA
Found at i:34522 original size:7 final size:7
Alignment explanation
Indices: 34512--34686 Score: 87
Period size: 7 Copynumber: 25.1 Consensus size: 7
34502 AAGCCCCATG
34512 CCTTAAA
1 CCTTAAA
34519 CCTTAAA
1 CCTTAAA
34526 -CTCTAAA
1 CCT-TAAA
*
34533 CTTTAAA
1 CCTTAAA
34540 CCTT-AA
1 CCTTAAA
34546 -CTCTAAA
1 CCT-TAAA
*
34553 TCC-TAAC
1 -CCTTAAA
34560 CCTTAAAA
1 CCTT-AAA
*
34568 CTTTAAA
1 CCTTAAA
*
34575 CCCTAAA
1 CCTTAAA
*
34582 CTTTAAA
1 CCTTAAA
34589 CCTTTAAA
1 CC-TTAAA
* *
34597 TCTTAAC
1 CCTTAAA
34604 CCTTAAA
1 CCTTAAA
*
34611 CCCT-AA
1 CCTTAAA
34617 CCTCT-AA
1 CCT-TAAA
**
34624 CCCCAAA
1 CCTTAAA
*
34631 CTCCT-AA
1 C-CTTAAA
*
34638 CCCTAAA
1 CCTTAAA
*
34645 CCTCAAA
1 CCTTAAA
*
34652 CATT-AA
1 CCTTAAA
34658 CCTTAAA
1 CCTTAAA
*
34665 CTTTAAA
1 CCTTAAA
34672 CCTTAAA
1 CCTTAAA
*
34679 TCTTAAA
1 CCTTAAA
34686 C
1 C
34687 TCTAATTTTA
Statistics
Matches: 126, Mismatches: 28, Indels: 28
0.69 0.15 0.15
Matches are distributed among these distances:
5 2 0.02
6 19 0.15
7 90 0.71
8 14 0.11
9 1 0.01
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (7 bp):
CCTTAAA
Found at i:34538 original size:21 final size:20
Alignment explanation
Indices: 34514--34552 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34504 GCCCCATGCC
34514 TTAAACCTTAAACTCTAAACT
1 TTAAACCTT-AACTCTAAACT
34535 TTAAACCTTAACTCTAAA
1 TTAAACCTTAACTCTAAA
34553 TCCTAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAACCTTAACTCTAAACT
Found at i:34611 original size:22 final size:22
Alignment explanation
Indices: 34549--34612 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
34539 ACCTTAACTC
*
34549 TAAATCCTAACCCTTAAAACTT
1 TAAATCCTAACCCTTAAACCTT
* * *
34571 TAAACCCTAAACTTTAAACCTT
1 TAAATCCTAACCCTTAAACCTT
*
34593 TAAATCTTAACCCTTAAACC
1 TAAATCCTAACCCTTAAACC
34613 CTAACCTCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATCCTAACCCTTAAACCTT
Found at i:34672 original size:20 final size:20
Alignment explanation
Indices: 34635--34687 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
34625 CCCAAACTCC
* *
34635 TAACCCTAAACCTCAAACAT
1 TAACCTTAAACTTCAAACAT
* *
34655 TAACCTTAAACTTTAAACCT
1 TAACCTTAAACTTCAAACAT
*
34675 TAAATCTTAAACT
1 T-AACCTTAAACT
34688 CTAATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (20 bp):
TAACCTTAAACTTCAAACAT
Found at i:34686 original size:14 final size:14
Alignment explanation
Indices: 34641--34678 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
34631 CTCCTAACCC
* *
34641 TAAACCTCAAACAT
1 TAAACCTTAAACTT
34655 T-AACCTTAAACTT
1 TAAACCTTAAACTT
34668 TAAACCTTAAA
1 TAAACCTTAAA
34679 TCTTAAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCTTAAACTT
Found at i:34755 original size:21 final size:21
Alignment explanation
Indices: 34729--34774 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
34719 TTCGACCCCA
* *
34729 AACCTCGAATCCCCAACCTTT
1 AACCTCCAAACCCCAACCTTT
*
34750 AACCTCCAAACCCTAACCTTT
1 AACCTCCAAACCCCAACCTTT
34771 AACC
1 AACC
34775 CTAAGCCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.22
Consensus pattern (21 bp):
AACCTCCAAACCCCAACCTTT
Found at i:35680 original size:37 final size:34
Alignment explanation
Indices: 35613--35681 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 34
35603 TCGACTGGAA
35613 GGAAAAGAAAGAAAAAAAAATAAGAAAAAAGACG
1 GGAAAAGAAAGAAAAAAAAATAAGAAAAAAGACG
* *
35647 GGAAAGGAAAGAAAAAGAAAAACTAAGAGAAAAGA
1 GGAAAAGAAAG-AAAA-AAAAA-TAAGAAAAAAGA
35682 AAGAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 10 0.33
35 4 0.13
36 5 0.17
37 11 0.37
ACGTcount: A:0.71, C:0.03, G:0.23, T:0.03
Consensus pattern (34 bp):
GGAAAAGAAAGAAAAAAAAATAAGAAAAAAGACG
Found at i:35700 original size:21 final size:20
Alignment explanation
Indices: 35660--35710 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
35650 AAGGAAAGAA
35660 AAAGAAAAACTAAGAGAAAAG
1 AAAGAAAAA-TAAGAGAAAAG
35681 AAAGAAAAAT-AGACGAAAA-
1 AAAGAAAAATAAGA-GAAAAG
*
35700 AGAGAAAAATA
1 AAAGAAAAATA
35711 CAAGAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 9 0.33
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.06
Consensus pattern (20 bp):
AAAGAAAAATAAGAGAAAAG
Found at i:35717 original size:19 final size:18
Alignment explanation
Indices: 35654--35718 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
35644 ACGGGAAAGG
*
35654 AAAGAAAAAGA-AAAACT
1 AAAGAAAAAGAGAAAAAT
*
35671 AAGAGAAAAGAAAGAAAAAT
1 AA-AGAAAA-AGAGAAAAAT
*
35691 AGACGAAAAAGAGAAAAAT
1 A-AAGAAAAAGAGAAAAAT
35710 ACAAGAAAA
1 A-AAGAAAA
35719 TTTTGTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 6 0.16
19 18 0.47
20 11 0.29
21 1 0.03
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAGAGAAAAAT
Found at i:43539 original size:2 final size:2
Alignment explanation
Indices: 43532--43560 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43522 CAATTAAGAA
43532 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
43561 CTATTCATCT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:44464 original size:1 final size:1
Alignment explanation
Indices: 44460--44486 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
44450 TTTTTTTTTT
44460 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
44487 TTGGGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:47037 original size:20 final size:22
Alignment explanation
Indices: 46998--47039 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
46988 AGTCAATTTA
*
46998 TTTAAATAAAATTTTAAATATT
1 TTTAAATAAAAATTTAAATATT
47020 TTTAAA-AAAAATTT-AATATT
1 TTTAAATAAAAATTTAAATATT
47040 AAATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATAAAAATTTAAATATT
Found at i:49283 original size:91 final size:91
Alignment explanation
Indices: 49123--49305 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
49113 AGATTATCGT
* * *
49123 TATCAGAACAGACTAAATACCGAGGGGAGTGCATTTCAGGTGCAATTAACCTATAAAATAAGTCC
1 TATCAGAACAGACTAAACACCGAAGGGAGTGCATTTCAGGTGCAATTAACCTATAAAAGAAGTCC
49188 TGAGTATCCATAAATATGAAAGGCTA
66 TGAGTATCCATAAATATGAAAGGCTA
* * * *
49214 TATCAGAACAGACTAAGCACCTAATGGAGTGCATTTCAGGTGCAATTAACCTATAAAAGAAGTCT
1 TATCAGAACAGACTAAACACCGAAGGGAGTGCATTTCAGGTGCAATTAACCTATAAAAGAAGTCC
49279 TGAGTATCCATAAATATGAAAGGCTA
66 TGAGTATCCATAAATATGAAAGGCTA
49305 T
1 T
49306 GTAATGCAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (91 bp):
TATCAGAACAGACTAAACACCGAAGGGAGTGCATTTCAGGTGCAATTAACCTATAAAAGAAGTCC
TGAGTATCCATAAATATGAAAGGCTA
Found at i:52476 original size:21 final size:22
Alignment explanation
Indices: 52437--52482 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
52427 ATCTATTGAA
***
52437 ACTCCACCTGCTTTGGAGTA-T
1 ACTCCACCTGCTGCAGAGTACT
52458 ACTCCACCTGCTGCAGAGTACT
1 ACTCCACCTGCTGCAGAGTACT
52480 ACT
1 ACT
52483 TGTCTAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (22 bp):
ACTCCACCTGCTGCAGAGTACT
Found at i:54967 original size:13 final size:13
Alignment explanation
Indices: 54934--54958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54924 AAATGAATTG
54934 AAGAGGGATACAA
1 AAGAGGGATACAA
54947 AAGAGGGATACA
1 AAGAGGGATACA
54959 TGAGAGGGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (13 bp):
AAGAGGGATACAA
Found at i:56557 original size:20 final size:19
Alignment explanation
Indices: 56526--56632 Score: 61
Period size: 19 Copynumber: 6.1 Consensus size: 19
56516 TGATCCATTT
56526 AAAATATGAATTTAAATTA
1 AAAATATGAATTTAAATTA
*
56545 AAAATATTGAATTTGAATT-
1 AAAATA-TGAATTTAAATTA
* *
56564 ----TATAAATTTAAATTT
1 AAAATATGAATTTAAATTA
*** *
56579 TTTATTTGAATTTAAATTA
1 AAAATATGAATTTAAATTA
*
56598 AAAA-ATAAATTTAAATT-
1 AAAATATGAATTTAAATTA
*
56615 TAAATA--AATTTAAATTA
1 AAAATATGAATTTAAATTA
56632 A
1 A
56633 TTTTGAACAA
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 10 0.15
17 3 0.04
18 12 0.18
19 19 0.28
20 11 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
AAAATATGAATTTAAATTA
Found at i:56575 original size:6 final size:6
Alignment explanation
Indices: 56534--56630 Score: 54
Period size: 6 Copynumber: 15.7 Consensus size: 6
56524 TTAAAATATG
* * * * * *
56534 AATTTA AATTAAA AATATTG AATTTGA ATTTATA AATTTA AATTTTT TATTTG
1 AATTTA AATT-TA AAT-TTA AATTT-A AATT-TA AATTTA AA-TTTA AATTTA
* **
56587 AATTTA AATTAA AAAATA AATTTA AATTTA AA--TA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT
56631 AATTTTGAAC
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
4 4 0.06
6 43 0.64
7 18 0.27
8 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:56603 original size:27 final size:26
Alignment explanation
Indices: 56532--56619 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
56522 ATTTAAAATA
56532 TGAATTTAAATTAAAAATATTGAATT
1 TGAATTTAAATTAAAAATATTGAATT
* * **
56558 TGAATTTATAAATT-TAAATTTTTTATT
1 TGAA-TT-TAAATTAAAAATATTGAATT
*
56585 TGAATTTAAATTAAAAA-A-TAAATT
1 TGAATTTAAATTAAAAATATTGAATT
*
56609 TAAATTTAAAT
1 TGAATTTAAAT
56620 AAATTTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 14 0.28
25 6 0.12
26 9 0.18
27 15 0.30
28 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TGAATTTAAATTAAAAATATTGAATT
Found at i:56621 original size:16 final size:16
Alignment explanation
Indices: 56600--56630 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56590 TTAAATTAAA
56600 AAATAAATTTAAATTT
1 AAATAAATTTAAATTT
56616 AAATAAATTTAAATT
1 AAATAAATTTAAATT
56631 AATTTTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAAATTTAAATTT
Found at i:56772 original size:14 final size:14
Alignment explanation
Indices: 56753--56816 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
56743 ATCTTAATTA
56753 TTTAAATAAAAAAT
1 TTTAAATAAAAAAT
* *
56767 TTTAAATTTATAAAT
1 TTTAAA-TAAAAAAT
* * *
56782 TTAAAAATCATAAAT
1 TT-TAAATAAAAAAT
*
56797 TTTAAATATAAAAT
1 TTTAAATAAAAAAT
56811 TTTAAA
1 TTTAAA
56817 ATTCAAAACC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 20 0.50
15 17 0.43
16 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAATAAAAAAT
Found at i:56783 original size:15 final size:15
Alignment explanation
Indices: 56763--56816 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
56753 TTTAAATAAA
56763 AAATTTTAAATTTAT
1 AAATTTTAAATTTAT
* * *
56778 AAATTTAAAAATCAT
1 AAATTTTAAATTTAT
*
56793 AAATTTTAAATATA-
1 AAATTTTAAATTTAT
56807 AAATTTTAAA
1 AAATTTTAAA
56817 ATTCAAAACC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTTTAAATTTAT
Found at i:56824 original size:15 final size:14
Alignment explanation
Indices: 56762--56824 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
56752 ATTTAAATAA
*
56762 AAAATTTTAAATTT
1 AAAATTTTAAATTC
* *
56776 ATAAATTTAAAAATC
1 A-AAATTTTAAATTC
56791 ATAAATTTTAAATAT-
1 A-AAATTTTAAAT-TC
56806 AAAATTTTAAAATTC
1 AAAATTTT-AAATTC
56821 AAAA
1 AAAA
56825 CCAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.22
15 30 0.75
16 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTTTAAATTC
Found at i:57050 original size:20 final size:20
Alignment explanation
Indices: 56984--57040 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
56974 AAATTAACTT
56984 TAAATAAA-TTT-ATTTTT-
1 TAAATAAATTTTAATTTTTA
* * *
57001 TTAAGAATTTTTAATTTTTA
1 TAAATAAATTTTAATTTTTA
57021 TAAATAAATTTTAATTTTTA
1 TAAATAAATTTTAATTTTTA
57041 ATCATTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 5 0.16
18 3 0.10
19 6 0.19
20 17 0.55
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TAAATAAATTTTAATTTTTA
Found at i:57577 original size:14 final size:15
Alignment explanation
Indices: 57513--57589 Score: 61
Period size: 14 Copynumber: 5.1 Consensus size: 15
57503 ATCAATTTTA
57513 TATATTATATAATA-
1 TATATTATATAATAT
*
57527 TATATTATATAATTT
1 TATATTATATAATAT
* *
57542 TA-ATAATATAAAAAT
1 TATATTATAT-AATAT
*
57557 ACATATATATATAATAT
1 -TATAT-TATATAATAT
*
57574 TATAGTATA-AATAT
1 TATATTATATAATAT
57588 TA
1 TA
57590 AAAATTAAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
14 26 0.53
15 9 0.18
16 4 0.08
17 6 0.12
18 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
TATATTATATAATAT
Found at i:57672 original size:15 final size:14
Alignment explanation
Indices: 57654--57698 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
57644 TAAAGGTTAA
57654 ATTTTAAAAATATAT
1 ATTTTAAAAA-ATAT
*
57669 ATTTTAAAAAAATAA
1 ATTTT-AAAAAATAT
*
57684 ATTATAAAAAATAT
1 ATTTTAAAAAATAT
57698 A
1 A
57699 ATATGAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 9 0.35
15 12 0.46
16 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:57934 original size:19 final size:19
Alignment explanation
Indices: 57910--57946 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57900 ATTTTGACAT
*
57910 TAACTATATTCTTCTATTA
1 TAACTAGATTCTTCTATTA
*
57929 TAACTAGATTCTTGTATT
1 TAACTAGATTCTTCTATT
57947 GTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (19 bp):
TAACTAGATTCTTCTATTA
Found at i:58871 original size:14 final size:14
Alignment explanation
Indices: 58852--58889 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
58842 ACAGCTTACC
58852 AAAAGATATAATCA
1 AAAAGATATAATCA
58866 AAAAGATATAATCA
1 AAAAGATATAATCA
58880 AAAAGATATA
1 AAAAGATATA
58890 TCATAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (14 bp):
AAAAGATATAATCA
Found at i:59537 original size:14 final size:15
Alignment explanation
Indices: 59511--59554 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
59501 TTTAATTCTC
*
59511 AAAATAGATTTTTTT
1 AAAATATATTTTTTT
*
59526 AAAA-ATA-TTTTTC
1 AAAATATATTTTTTT
59539 AAAATATATTTTTTT
1 AAAATATATTTTTTT
59554 A
1 A
59555 CGAATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.38
14 5 0.21
15 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
AAAATATATTTTTTT
Found at i:59921 original size:73 final size:73
Alignment explanation
Indices: 59724--60054 Score: 338
Period size: 74 Copynumber: 4.6 Consensus size: 73
59714 TTGTATTAAA
* * *
59724 AAATTTTTAAGATATTATTTATCTTTT-TTTGTAGAAGTTTAAATTTA-TTTTTAGGTATGATTA
1 AAATTTTTAAGGTATAATTTAT-TTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
*
59787 TACGAGTTA
65 TACGAGTTT
* * * *
59796 AAATTTTTAAGGTATAATTTATCTTTATTTATAAAAGTTTAAATGTGTTTTTTAGGTAT-ACTTA
1 AAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGA-TTA
*
59860 TATGAGTTT
65 TACGAGTTT
* * *
59869 AAATTTTTGATGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTGTTTTTTGGGTATGATTA
1 AAATTTTT-AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
*
59934 TACGAATTT
65 TACGAGTTT
* ** * * * ** *
59943 ATATTTTTGATCGTATAATTCATTTTTATTTGTAGAAATTTAAATTTA-TTTTT-GGGCTGA-CA
1 AAATTTTT-AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTA
60005 TA--AGTTT
65 TACGAGTTT
* * *
60012 AAA-TTTTAAGGTATTATTTATCTTTATTTGTATAAGTTTAAAT
1 AAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTAAAT
60055 TCTTATTTAA
Statistics
Matches: 220, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
67 29 0.13
68 4 0.02
69 6 0.03
71 6 0.03
72 42 0.19
73 34 0.15
74 98 0.45
75 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (73 bp):
AAATTTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTATTTTTTAGGTATGATTAT
ACGAGTTT
Found at i:59995 original size:147 final size:140
Alignment explanation
Indices: 59728--60055 Score: 344
Period size: 147 Copynumber: 2.3 Consensus size: 140
59718 ATTAAAAAAT
* *
59728 TTTTAAGATATTATTTATCTTTT-TTTGTAGAAGTTTAAATTTATTTTTAGGTATGATTATACGA
1 TTTTAAGGTATAATTTAT-TTTTATTTGTAGAAGTTTAAATTTATTTTTAGGTATGATTATACGA
* * * *
59792 GTTAAAATTTTTAAGGTATAATTTATCTTTATTTATAAAAGTTTAAATGTGTTTTTTAGG-TATA
65 ATTAAAATTTTTAACGTATAATTCATCTTTATTTATAAAAGTTTAAATGTGTTTTTTAGGCT-GA
59856 CTTATATGAGTTTAAA
129 C--ATA--AGTTTAAA
* *
59872 TTTTTGATGGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTGT-TTTTTGGGTATGATTATA
1 -TTTT-AAGGTATAATTTATTTTTATTTGTAGAAGTTTAAAT-T-TATTTTTAGGTATGATTATA
* * * * * *
59936 CGAATTTATATTTTTGATCGTATAATTCATTTTTATTTGTAGAAA-TTTAAAT-T-TATTTTTGG
62 CGAATTAAAATTTTT-AACGTATAATTCATCTTTATTTATA-AAAGTTTAAATGTGT-TTTTTAG
59998 GCTGACATAAGTTTAAA
124 GCTGACATAAGTTTAAA
* * *
60015 TTTTAAGGTATTATTTATCTTTATTTGTATAAGTTTAAATT
1 TTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATT
60056 CTTATTTAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
140 1 0.01
141 32 0.20
142 4 0.03
143 8 0.05
145 11 0.07
146 29 0.18
147 40 0.25
148 29 0.18
149 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (140 bp):
TTTTAAGGTATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTAGGTATGATTATACGAA
TTAAAATTTTTAACGTATAATTCATCTTTATTTATAAAAGTTTAAATGTGTTTTTTAGGCTGACA
TAAGTTTAAA
Found at i:61624 original size:147 final size:140
Alignment explanation
Indices: 61291--61623 Score: 368
Period size: 147 Copynumber: 2.3 Consensus size: 140
61281 ATCTTTAAAT
* * *
61291 AAAAATTTAAACTTATACAAATAAAGATAAATAATACCCTAAAAATTTAAACTTATGTCAACCCA
1 AAAAATTTAAACTTCTACAAATAAAGATAAATAATACCATAAAAATTAAAACTTATGTCAACCCA
* * * * *
61356 AAAATAAATTTAAATTGCTACAAATAAAAATGAATTATACGGTCACAAATATAAACTCGTATAAT
66 AAAATAAATTTAAATTGCTACAAATAAAAATAAATTATACCGTAAAAAATATAAACTCATATAAT
*
61421 CATACTCAAA
131 CATACCCAAA
* *
61431 AAACACATTTAAACTTCTACAAA-AAAAATAAATTATACCATCAAAAATTAAAACTCATATAAGT
1 AAA-A-ATTTAAACTTCTACAAATAAAGATAAATAATACCAT-AAAAATTAAAACT--TAT--GT
* * * * *
61495 -ATACCTAAAAA-ACATATTTAAACTT-TTATAAATAAAAATAAATTATACCGTAAAAAATTTTA
59 CA-ACCCAAAAATA-A-ATTTAAA-TTGCTACAAATAAAAATAAATTATACCGTAAAAAATATAA
61557 ACTCATATAATCATACCCAAA
120 ACTCATATAATCATACCCAAA
* *
61578 AATAAATTTAAACTTCTACAAATAAAGATAAATAATATCTTAAAAA
1 AA-AAATTTAAACTTCTACAAATAAAGATAAATAATACCATAAAAA
61624 AATTTTAATA
Statistics
Matches: 160, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
140 3 0.02
141 16 0.10
142 28 0.17
144 3 0.02
145 2 0.01
146 33 0.21
147 72 0.45
148 3 0.02
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (140 bp):
AAAAATTTAAACTTCTACAAATAAAGATAAATAATACCATAAAAATTAAAACTTATGTCAACCCA
AAAATAAATTTAAATTGCTACAAATAAAAATAAATTATACCGTAAAAAATATAAACTCATATAAT
CATACCCAAA
Found at i:61631 original size:74 final size:72
Alignment explanation
Indices: 61291--61624 Score: 333
Period size: 73 Copynumber: 4.6 Consensus size: 72
61281 ATCTTTAAAT
* * * * *
61291 AAAAATTTAAACTTATACAAATAAAGATAAATAATACCCT-AAAAATTTAAACT--TAT-GTCA-
1 AAAAATTTAAACTTCTACAAATAAAAATAAATTATACCGTAAAAAATTTAAACTCATATAATCAT
61351 ACCCAAA
66 ACCCAAA
* * * * * *
61358 AATAAATTTAAA-TTGCTACAAATAAAAATGAATTATACGGTCACAAATATAAACTCGTATAATC
1 AA-AAATTTAAACTT-CTACAAATAAAAATAAATTATACCGTAAAAAATTTAAACTCATATAATC
*
61422 ATACTCAAA
64 ATACCCAAA
* * *
61431 AAACACATTTAAACTTCTACAAA-AAAAATAAATTATACCATCAAAAATTAAAACTCATATAAGT
1 AAA-A-ATTTAAACTTCTACAAATAAAAATAAATTATACCGTAAAAAATTTAAACTCATATAA-T
*
61495 -ATACCTAAA
63 CATACCCAAA
* * *
61504 AAACATATTTAAACTTTTATAAATAAAAATAAATTATACCGTAAAAAATTTTAACTCATATAATC
1 AAA-A-ATTTAAACTTCTACAAATAAAAATAAATTATACCGTAAAAAATTTAAACTCATATAATC
61569 ATACCCAAA
64 ATACCCAAA
* * * *
61578 AATAAATTTAAACTTCTACAAATAAAGATAAATAATATCTTAAAAAA
1 AA-AAATTTAAACTTCTACAAATAAAAATAAATTATACCGTAAAAAA
61625 ATTTTAATAC
Statistics
Matches: 220, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
67 4 0.02
68 29 0.13
69 11 0.05
71 3 0.01
72 4 0.02
73 105 0.48
74 61 0.28
75 3 0.01
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (72 bp):
AAAAATTTAAACTTCTACAAATAAAAATAAATTATACCGTAAAAAATTTAAACTCATATAATCAT
ACCCAAA
Found at i:66246 original size:23 final size:22
Alignment explanation
Indices: 66220--66267 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
66210 CTTAATTCAA
**
66220 AATAATGAGGTGATTACAAATTT
1 AATAATGAGACGATTAC-AATTT
*
66243 AATAATTAGACGATTACAATTT
1 AATAATGAGACGATTACAATTT
66265 AAT
1 AAT
66268 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (22 bp):
AATAATGAGACGATTACAATTT
Found at i:66305 original size:31 final size:30
Alignment explanation
Indices: 66243--66302 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
66233 TTACAAATTT
*
66243 AATAATTAGACGATTACAATTTAATTTTTAA
1 AATAATTAGACGATTACAATCTAA-TTTTAA
*
66274 AATAATTTGACGATTACAACTCCTAATTT
1 AATAATTAGACGATTACAA-T-CTAATTT
66303 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 4 0.16
33 3 0.12
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (30 bp):
AATAATTAGACGATTACAATCTAATTTTAA
Found at i:66489 original size:19 final size:19
Alignment explanation
Indices: 66454--66506 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
66444 TAAAAACTAT
66454 TATTATC-TTTA-TAATAA
1 TATTATCTTTTATTAATAA
66471 TATTATCTTTTATTAATAA
1 TATTATCTTTTATTAATAA
*
66490 TATAATCTTTTATTAAT
1 TATTATCTTTTATTAAT
66507 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 22 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATCTTTTATTAATAA
Found at i:66803 original size:13 final size:13
Alignment explanation
Indices: 66785--66831 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
66775 AAAATGATTA
66785 TATTTTGATAATT
1 TATTTTGATAATT
*
66798 TATTTTAAATTAATAT
1 TATTTT-GA-TAAT-T
66814 TATTTTGATAATT
1 TATTTTGATAATT
66827 TATTT
1 TATTT
66832 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 12 0.41
14 5 0.17
15 5 0.17
16 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TATTTTGATAATT
Found at i:66806 original size:29 final size:30
Alignment explanation
Indices: 66773--66842 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
66763 TTCTCGTGAG
*
66773 TTAAAATGATTA-TATTTTGATAATTTATT
1 TTAAAATGAATATTATTTTGATAATTTATT
*
66802 TT-AAATTAATATTATTTTGATAATTTATT
1 TTAAAATGAATATTATTTTGATAATTTATT
* *
66831 TAAAAATTAATA
1 TTAAAATGAATA
66843 GCACTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.19
29 20 0.56
30 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
TTAAAATGAATATTATTTTGATAATTTATT
Found at i:66840 original size:30 final size:29
Alignment explanation
Indices: 66785--66842 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
66775 AAAATGATTA
*
66785 TATTTTGATAATTTATTTTAAATTAATAT
1 TATTTTGATAATTTATTTAAAATTAATAT
66814 TATTTTGATAATTTATTTAAAAATTAATA
1 TATTTTGATAATTTATTT-AAAATTAATA
66843 GCACTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TATTTTGATAATTTATTTAAAATTAATAT
Found at i:66851 original size:30 final size:29
Alignment explanation
Indices: 66788--66852 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
66778 ATGATTATAT
* ** *
66788 TTTGATAATTTATTTTAAATTAATATTAT
1 TTTGATAATTTATTTAAAATTAATAGCAC
66817 TTTGATAATTTATTTAAAAATTAATAGCAC
1 TTTGATAATTTATTT-AAAATTAATAGCAC
66847 TTTGAT
1 TTTGAT
66853 CAAGACCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (29 bp):
TTTGATAATTTATTTAAAATTAATAGCAC
Found at i:70236 original size:18 final size:18
Alignment explanation
Indices: 70193--70236 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
70183 GCCCGACCTC
70193 CTTCCC-TCTCTTTCTCT
1 CTTCCCTTCTCTTTCTCT
** *
70210 CTTTTCTTCTCTTTGTCT
1 CTTCCCTTCTCTTTCTCT
70228 CTTCCCTTC
1 CTTCCCTTC
70237 CGGTGCCTAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (18 bp):
CTTCCCTTCTCTTTCTCT
Found at i:71853 original size:2 final size:2
Alignment explanation
Indices: 71846--71883 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
71836 AGGAGAATGC
71846 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
71884 GGTTTGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72787 original size:2 final size:2
Alignment explanation
Indices: 72780--72813 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
72770 TGCTGGACTC
72780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
72814 TTTGTTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75149 original size:2 final size:2
Alignment explanation
Indices: 75142--75172 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
75132 CTAATCTATC
75142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75173 TTACACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80149 original size:18 final size:19
Alignment explanation
Indices: 80121--80167 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
80111 AAATATAATT
80121 ATTTTTATTTGATTTTATG
1 ATTTTTATTTGATTTTATG
* *
80140 ATTTTT-TTTGTTTTTATTT
1 ATTTTTATTTGATTTTA-TG
80159 ATTTTTATT
1 ATTTTTATT
80168 AGTAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 13 0.54
20 2 0.08
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (19 bp):
ATTTTTATTTGATTTTATG
Found at i:80164 original size:10 final size:10
Alignment explanation
Indices: 80119--80167 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
80109 AAAAATATAA
80119 TTATTTTTAT
1 TTATTTTTAT
80129 TTGA-TTTTA-
1 TT-ATTTTTAT
*
80138 TGATTTTT-T
1 TTATTTTTAT
*
80147 TTGTTTTTAT
1 TTATTTTTAT
80157 TTATTTTTAT
1 TTATTTTTAT
80167 T
1 T
80168 AGTAAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
8 1 0.03
9 11 0.35
10 18 0.58
11 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:85011 original size:5 final size:5
Alignment explanation
Indices: 84998--85029 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
84988 TTTGGAGACA
84998 TTTGAT TTTGT TTTGT TTTGT TTTGT TTTGT T
1 TTTG-T TTTGT TTTGT TTTGT TTTGT TTTGT T
85030 GTGGTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.03, C:0.00, G:0.19, T:0.78
Consensus pattern (5 bp):
TTTGT
Found at i:85486 original size:3 final size:3
Alignment explanation
Indices: 85478--85513 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
85468 CTTGTTACTT
*
85478 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
85514 CCGTCAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:87595 original size:4 final size:4
Alignment explanation
Indices: 87586--87619 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
87576 GTTGATCCAT
87586 TATC TATC TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TATC TATC TA
87620 AGATCTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:91551 original size:2 final size:2
Alignment explanation
Indices: 91544--91575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91534 GCTGGCTGCA
91544 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
91576 TGTTTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97408 original size:13 final size:13
Alignment explanation
Indices: 97390--97414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97380 ATATATATAT
97390 TATTTTTTATTTA
1 TATTTTTTATTTA
97403 TATTTTTTATTT
1 TATTTTTTATTT
97415 TAATAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:97437 original size:17 final size:19
Alignment explanation
Indices: 97402--97438 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
97392 TTTTTTATTT
*
97402 ATATTTTTTATTTTAATAA
1 ATATTTTTTATATTAATAA
97421 ATATTTTTTA-ATT-ATAA
1 ATATTTTTTATATTAATAA
97438 A
1 A
97439 ATAATTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 2 0.12
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTTTTATATTAATAA
Found at i:103229 original size:84 final size:84
Alignment explanation
Indices: 103088--103253 Score: 269
Period size: 84 Copynumber: 2.0 Consensus size: 84
103078 TGAAAATTGG
* * * * *
103088 ACTTGGACCATTTGCGAGTTGAGGTATCCCTCTTTCTCTGAAAGGATGGGATGGAGGTATCCTGG
1 ACTTGGACCATCTGCGAGTTGAGGTATCCCACTTTCTCAGAAAGAATGGGATGGAGGTAGCCTGG
103153 AATCAGTGAGTTTCAGGAA
66 AATCAGTGAGTTTCAGGAA
*
103172 ACTTGGACCATCTGGGAGTTGAGGTATCCCACTTTCTCAGAAAGAATGGGATGGAGGTAGCCTGG
1 ACTTGGACCATCTGCGAGTTGAGGTATCCCACTTTCTCAGAAAGAATGGGATGGAGGTAGCCTGG
*
103237 AATCGGTGAGTTTCAGG
66 AATCAGTGAGTTTCAGG
103254 TTTCTGTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (84 bp):
ACTTGGACCATCTGCGAGTTGAGGTATCCCACTTTCTCAGAAAGAATGGGATGGAGGTAGCCTGG
AATCAGTGAGTTTCAGGAA
Found at i:105449 original size:2 final size:2
Alignment explanation
Indices: 105444--105470 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105434 TCTCTCTCTC
105444 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
105471 TAATAACAAG
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:105498 original size:3 final size:3
Alignment explanation
Indices: 105490--105518 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
105480 GATTTCCTTT
105490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
105519 TGAAGTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:107580 original size:2 final size:2
Alignment explanation
Indices: 107575--107617 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
107565 GATATATATA
* *
107575 TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
107617 T
1 T
107618 ACAAAAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.05, G:0.49, T:0.47
Consensus pattern (2 bp):
TG
Found at i:107890 original size:5 final size:5
Alignment explanation
Indices: 107880--107906 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
107870 AGAGAACTGA
107880 ATCTC ATCTC ATCTC ATCTC ATCTC AT
1 ATCTC ATCTC ATCTC ATCTC ATCTC AT
107907 GCAGTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCTC
Found at i:108168 original size:40 final size:40
Alignment explanation
Indices: 108117--108196 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
108107 ATGCATCCAG
*
108117 CTGTTTTAAATAACAATAATTAAAGATGCATGGTTTTCAT
1 CTGTTTGAAATAACAATAATTAAAGATGCATGGTTTTCAT
108157 CTGTTTGAAATAACAATAATTAAAGATGCATGGTTTTCAT
1 CTGTTTGAAATAACAATAATTAAAGATGCATGGTTTTCAT
108197 ACATACATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (40 bp):
CTGTTTGAAATAACAATAATTAAAGATGCATGGTTTTCAT
Found at i:108315 original size:4 final size:4
Alignment explanation
Indices: 108306--108336 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
108296 TCATATTCGT
108306 CAGC CAGC CAGC CAGC CAGC CAGC CAGC CAG
1 CAGC CAGC CAGC CAGC CAGC CAGC CAGC CAG
108337 TCATTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.26, T:0.00
Consensus pattern (4 bp):
CAGC
Found at i:108384 original size:3 final size:3
Alignment explanation
Indices: 108376--108419 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
108366 CCTTCCTAAT
108376 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
108420 TATCATCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:110467 original size:3 final size:3
Alignment explanation
Indices: 110459--110485 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
110449 TCAGTCTATG
110459 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
110486 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:110700 original size:2 final size:2
Alignment explanation
Indices: 110693--110735 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
110683 TCATCCTGCT
*
110693 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
110735 T
1 T
110736 TTGTTTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:111217 original size:3 final size:3
Alignment explanation
Indices: 111209--111251 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
111199 TTCTATTTAT
*
111209 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
111252 CATTCATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:111459 original size:2 final size:2
Alignment explanation
Indices: 111452--111487 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
111442 TCGATTTCAA
111452 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
111488 TTACATGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111591 original size:2 final size:2
Alignment explanation
Indices: 111584--111610 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
111574 TGCAATAAAT
111584 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
111611 GCTGCTTCAT
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:118060 original size:6 final size:6
Alignment explanation
Indices: 118049--118078 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
118039 TCACTCTTGA
118049 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC
1 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC
118079 GACCGCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
TGCCAC
Found at i:124074 original size:10 final size:11
Alignment explanation
Indices: 124054--124078 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
124044 GTTTTATATA
124054 TTTCTTTTTTT
1 TTTCTTTTTTT
124065 TTTCTTTTTTT
1 TTTCTTTTTTT
124076 TTT
1 TTT
124079 TTACTTCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:124745 original size:38 final size:38
Alignment explanation
Indices: 124694--124770 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
124684 TGGTTCCCTT
* *
124694 AAAACAGATATTATGTGATTCAGTACAGGCAAAGTTTC
1 AAAACAGATATTATCTGATACAGTACAGGCAAAGTTTC
124732 AAAACAGATATTATCTGATACAGTACAGGCAAAGTTTC
1 AAAACAGATATTATCTGATACAGTACAGGCAAAGTTTC
124770 A
1 A
124771 GAAATAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (38 bp):
AAAACAGATATTATCTGATACAGTACAGGCAAAGTTTC
Found at i:129413 original size:29 final size:30
Alignment explanation
Indices: 129381--129442 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
129371 TTATTCAAGT
*
129381 ATTTTCATC-CGCTTTATTATTTGAGATTA
1 ATTTTCATCACGCTTTACTATTTGAGATTA
** * *
129410 ATTTTGTTCAGGTTTTACTATTTGAGATTA
1 ATTTTCATCACGCTTTACTATTTGAGATTA
129440 ATT
1 ATT
129443 CTATTCAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (30 bp):
ATTTTCATCACGCTTTACTATTTGAGATTA
Found at i:129450 original size:30 final size:30
Alignment explanation
Indices: 129393--129450 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
129383 TTTCATCCGC
* * *
129393 TTTATTATTTGAGATTAATTTTGTTCAGGT
1 TTTACTATTTGAGATTAATTCTATTCAGGT
129423 TTTACTATTTGAGATTAATTCTATTCAG
1 TTTACTATTTGAGATTAATTCTATTCAG
129451 AAAATTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (30 bp):
TTTACTATTTGAGATTAATTCTATTCAGGT
Found at i:143262 original size:13 final size:13
Alignment explanation
Indices: 143246--143270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
143236 AGTTTGATTC
143246 ATAAATTTAATTT
1 ATAAATTTAATTT
143259 ATAAATTTAATT
1 ATAAATTTAATT
143271 CATTAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAATTTAATTT
Found at i:143825 original size:2 final size:2
Alignment explanation
Indices: 143820--143858 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
143810 ATAAACTACA
* *
143820 AT AT AT AC AT AT AA 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 AT AT AT A
143859 AAGAGAAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:145563 original size:6 final size:6
Alignment explanation
Indices: 145552--145585 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
145542 TTGATTCTAG
145552 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCC
145586 GTCGCATCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCCCT
Found at i:149234 original size:16 final size:16
Alignment explanation
Indices: 149213--149246 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
149203 ATAATAGATT
*
149213 ATAATGAGGATCGAAA
1 ATAATGAGGACCGAAA
149229 ATAATGAGGACCGAAA
1 ATAATGAGGACCGAAA
149245 AT
1 AT
149247 TAAGCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.18
Consensus pattern (16 bp):
ATAATGAGGACCGAAA
Found at i:155836 original size:5 final size:5
Alignment explanation
Indices: 155826--155850 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
155816 AAAGTCAGGC
155826 CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT
155851 ATTTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:157834 original size:5 final size:5
Alignment explanation
Indices: 157824--157874 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
157814 ATAACTGCCA
*
157824 TCTTC TCTTC TCTTC TCTTC TCTTC TCTT- TC-CC TCTTC TTCTTC TTCTTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC -TCTTC -TCTTC
157874 T
1 T
157875 TCTTTTTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 26 0.63
6 11 0.27
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTTC
Found at i:157865 original size:3 final size:3
Alignment explanation
Indices: 157824--157878 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
157814 ATAACTGCCA
* *
157824 TCT TC- TCT TC- TCT TC- TCT TC- TCT TC- TCT T-T CCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
157866 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
157879 TTTTCTTACA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
2 11 0.26
3 31 0.74
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:157877 original size:15 final size:15
Alignment explanation
Indices: 157824--157878 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 15
157814 ATAACTGCCA
157824 TCTTC-TCTTC-TCT
1 TCTTCTTCTTCTTCT
157837 TC-TCTTC-TCTTC-
1 TCTTCTTCTTCTTCT
* *
157849 TCTT-TCCCTCTTCT
1 TCTTCTTCTTCTTCT
157863 TCTTCTTCTTCTTCT
1 TCTTCTTCTTCTTCT
157878 T
1 T
157879 TTTTCTTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
12 8 0.24
13 12 0.36
14 4 0.12
15 9 0.27
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTCTTCT
Found at i:163154 original size:16 final size:14
Alignment explanation
Indices: 163127--163238 Score: 73
Period size: 16 Copynumber: 7.2 Consensus size: 14
163117 TTCAGCTAAA
*
163127 TTTAAATTAAATTAT
1 TTTAATTTAAATT-T
163142 TTTATATTTAAATTAT
1 TTTA-ATTTAAATT-T
163158 TTTAAATTTAAATTT
1 TTT-AATTTAAATTT
*
163173 ATTTAAGTTT-TATTAT
1 -TTTAA-TTTAAATT-T
* *
163189 TTTAGGTTTGAATTT
1 TTTA-ATTTAAATTT
163204 ATTTAGATTTAAATTTT
1 -TTTA-ATTTAAA-TTT
163221 TTTGAATTTAAATTT
1 TTT-AATTTAAATTT
163236 TTT
1 TTT
163239 CGAGTTTGAG
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
15 24 0.30
16 52 0.64
17 5 0.06
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
TTTAATTTAAATTT
Found at i:163188 original size:31 final size:32
Alignment explanation
Indices: 163127--163235 Score: 109
Period size: 31 Copynumber: 3.5 Consensus size: 32
163117 TTCAGCTAAA
*
163127 TTTAAA-TTAAA-TTATTTTATATTTAAATTAT
1 TTTAAATTTAAATTTA-TTTAGATTTAAATTAT
*
163158 TTTAAATTTAAATTTATTTA-AGTTT-TATTAT
1 TTTAAATTTAAATTTATTTAGA-TTTAAATTAT
** * *
163189 TTTAGGTTTGAATTTATTTAGATTTAAATTTT
1 TTTAAATTTAAATTTATTTAGATTTAAATTAT
*
163221 TTTGAATTTAAATTT
1 TTTAAATTTAAATTT
163236 TTTCGAGTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
31 32 0.51
32 28 0.44
33 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (32 bp):
TTTAAATTTAAATTTATTTAGATTTAAATTAT
Found at i:175089 original size:2 final size:2
Alignment explanation
Indices: 175082--175113 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
175072 GGTATCAATC
175082 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
175114 TAAACTACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178923 original size:5 final size:5
Alignment explanation
Indices: 178906--178936 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
178896 TTGTAAATTA
178906 GCTTG GCCTTG GCTTG GCTTG GCTTG GCTTG
1 GCTTG G-CTTG GCTTG GCTTG GCTTG GCTTG
178937 TGAAAGACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.23, G:0.39, T:0.39
Consensus pattern (5 bp):
GCTTG
Found at i:179329 original size:23 final size:23
Alignment explanation
Indices: 179273--179317 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
179263 TATTATTAAT
179273 AAATAAAATAATATTATTTATTA
1 AAATAAAATAATATTATTTATTA
*
179296 AAATAAAATAATTTTATTTATT
1 AAATAAAATAATATTATTTATT
179318 TTTAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATAAAATAATATTATTTATTA
Done.