Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 1 of 320
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--2328 Score: 1805
Period size: 7 Copynumber: 325.3 Consensus size: 7
1 CCCTAAA
1 CCCTAAA
8 CCCTAAA
1 CCCTAAA
15 CCCTAAA
1 CCCTAAA
22 CCCTAAAA
1 CCCT-AAA
30 CCCTAAA
1 CCCTAAA
37 CCCTAAA
1 CCCTAAA
44 CCCTAAA
1 CCCTAAA
51 CCCTAAA
1 CCCTAAA
*
58 ---AAAA
1 CCCTAAA
*
62 ACCTAAA
1 CCCTAAA
69 CCCTAAA
1 CCCTAAA
76 CCCTAAA
1 CCCTAAA
**
83 --AAAAA
1 CCCTAAA
*
88 ACCTAAA
1 CCCTAAA
95 CCCTAAAAAA
1 CCCT---AAA
105 CCCTAAA
1 CCCTAAA
112 CCCTAAAA
1 CCCT-AAA
120 CCCTAAA
1 CCCTAAA
127 CCCTAAA
1 CCCTAAA
134 CCCTAAA
1 CCCTAAA
141 CCCCTAAA
1 -CCCTAAA
149 CCCTAAA
1 CCCTAAA
156 CCCTAAAA
1 CCCT-AAA
****
164 AAAAAAA
1 CCCTAAA
****
171 AAAAAAA
1 CCCTAAA
178 CCCTAAAA
1 CCCT-AAA
186 CCCTAAA
1 CCCTAAA
193 CCCTAAA
1 CCCTAAA
200 CCCTAAAA
1 CCCT-AAA
208 CCCTCCTAAA
1 --C-CCTAAA
218 CCCCCCT-AA
1 ---CCCTAAA
**
227 CCC--CC
1 CCCTAAA
232 CCCTAAA
1 CCCTAAA
239 CCCTAAA
1 CCCTAAA
246 CCCTAAA
1 CCCTAAA
253 CCCCTAAA
1 -CCCTAAA
261 CCCTAAAA
1 CCCT-AAA
269 CCCCCCTAAAAA
1 ---CCCT--AAA
281 CCCTAAA
1 CCCTAAA
288 CCCTAAAA
1 CCCT-AAA
296 CCCTAAA
1 CCCTAAA
303 CCCTAAA
1 CCCTAAA
310 CCCTAAAA
1 CCCT-AAA
318 CCCTAAA
1 CCCTAAA
325 CCCTAAA
1 CCCTAAA
332 CCCTAAA
1 CCCTAAA
339 CCCTAAA
1 CCCTAAA
*
346 -CCAAAA
1 CCCTAAA
*
352 ACCTAAAAA
1 CCCT--AAA
361 CCCTAAA
1 CCCTAAA
368 CCCTAAA
1 CCCTAAA
375 CCCTAAA
1 CCCTAAA
382 CCCTAAA
1 CCCTAAA
389 CCCTAAAAA
1 CCCT--AAA
398 CCCTAAAA
1 CCCT-AAA
406 CCCTAAA
1 CCCTAAA
413 CCCTAAA
1 CCCTAAA
420 CCCTAAAAA
1 CCCT--AAA
429 CCCTAAA
1 CCCTAAA
436 CCCTAAA
1 CCCTAAA
443 CCCTAAA
1 CCCTAAA
450 ---TAAA
1 CCCTAAA
454 CCCTAAA
1 CCCTAAA
461 CCCTAAA
1 CCCTAAA
468 ---TAAA
1 CCCTAAA
472 CCCTAAAA
1 CCCT-AAA
480 CCCTAAA
1 CCCTAAA
487 CCCTAAATAA
1 CCCT--A-AA
497 CCCTAAA
1 CCCTAAA
504 CCCTAAA
1 CCCTAAA
511 CCCCCCTAAA
1 ---CCCTAAA
521 CCCTAAA
1 CCCTAAA
528 CCCTAAA
1 CCCTAAA
535 CCCTAAAAAA
1 CCCT---AAA
545 CCCTAAA
1 CCCTAAA
552 CCCTAAA
1 CCCTAAA
559 CCCTAAA
1 CCCTAAA
566 ---TAAA
1 CCCTAAA
**
570 --AAAAA
1 CCCTAAA
575 CCCTAAA
1 CCCTAAA
582 CCCTAAA
1 CCCTAAA
589 -CCTAAAAA
1 CCCT--AAA
597 CCCTAAA
1 CCCTAAA
604 CCCTAAA
1 CCCTAAA
611 CCCTAAAA
1 CCCT-AAA
619 CCCTAAA
1 CCCTAAA
626 CCCTAAA
1 CCCTAAA
*
633 -AC-AAA
1 CCCTAAA
638 CCCTAAA
1 CCCTAAA
645 CCCTAAA
1 CCCTAAA
652 CCCTAAA
1 CCCTAAA
659 CCCTAAA
1 CCCTAAA
666 CCCTAAAA
1 CCCT-AAA
674 CCCTAAA
1 CCCTAAA
681 CCCTAAA
1 CCCTAAA
*
688 ---AAAA
1 CCCTAAA
692 CCCTAAA
1 CCCTAAA
699 CCCTAAA
1 CCCTAAA
706 CCCTAAA
1 CCCTAAA
713 -CCTAAA
1 CCCTAAA
****
719 AAAAAAA
1 CCCTAAA
*
726 ACC-AAA
1 CCCTAAA
732 CCCTAAAAAA
1 CCCT---AAA
742 CCCTAAAA
1 CCCT-AAA
750 CCCTAAA
1 CCCTAAA
757 CCCTAAA
1 CCCTAAA
764 CCCTAAAA
1 CCCT-AAA
772 CCCTAAA
1 CCCTAAA
779 CCCTAAA
1 CCCTAAA
786 CCCTAAA
1 CCCTAAA
793 CCCTAAA
1 CCCTAAA
800 CCCTAAAA
1 CCCT-AAA
808 CCCTAAA
1 CCCTAAA
815 CCCTAAA
1 CCCTAAA
822 CCCTAAA
1 CCCTAAA
829 CCCTAAA
1 CCCTAAA
****
836 AAAAAAA
1 CCCTAAA
843 CCCTAAA
1 CCCTAAA
850 CCCTAAAAA
1 CCCT--AAA
859 CCCTAAA
1 CCCTAAA
**
866 --AAAAA
1 CCCTAAA
****
871 AAAAAAA
1 CCCTAAA
878 CCCTAAAAA
1 CCCT--AAA
887 CCCTAAA
1 CCCTAAA
894 CCCTAAA
1 CCCTAAA
901 CCCTAAAA
1 CCCT-AAA
909 CCCTAAA
1 CCCTAAA
916 CCCTAAA
1 CCCTAAA
923 CCCTAAA
1 CCCTAAA
930 CCCTAAAA
1 CCCT-AAA
938 CCCTAAA
1 CCCTAAA
945 CCCTAAA
1 CCCTAAA
952 CCCCTAAA
1 -CCCTAAA
960 CCCTAAA
1 CCCTAAA
967 CCCTAAA
1 CCCTAAA
974 CCCTAAA
1 CCCTAAA
981 CCCTAAA
1 CCCTAAA
988 CCCTAAA
1 CCCTAAA
995 CCCTAAA
1 CCCTAAA
1002 CCCTAAA
1 CCCTAAA
1009 CCCTAAAA
1 CCCT-AAA
1017 CCCTAAA
1 CCCTAAA
1024 CCCTAAAAAA
1 CCCT---AAA
1034 CCCTAAA
1 CCCTAAA
1041 CCCTAAAAA
1 CCCT--AAA
*
1050 ACCTAAAA
1 CCCT-AAA
****
1058 AAAAAAA
1 CCCTAAA
*
1065 ACCTAAAAA
1 CCCT--AAA
*
1074 ACCTAAA
1 CCCTAAA
1081 CCCTAAAAAA
1 CCCT---AAA
****
1091 AAAAAAA
1 CCCTAAA
1098 CCCTAAA
1 CCCTAAA
1105 CCCTAAA
1 CCCTAAA
1112 CCCTAAA
1 CCCTAAA
1119 CCCTAAAAA
1 CCCT--AAA
1128 CCCTAAA
1 CCCTAAA
1135 CCCTAAA
1 CCCTAAA
1142 CCCTAAA
1 CCCTAAA
1149 CCCTAAA
1 CCCTAAA
1156 CCCTAAA
1 CCCTAAA
1163 CCCTAAA
1 CCCTAAA
1170 CCCTAAAA
1 CCCT-AAA
1178 CCCTAAA
1 CCCTAAA
1185 CCCTAAA
1 CCCTAAA
1192 CCCTAAA
1 CCCTAAA
1199 ---TAAA
1 CCCTAAA
1203 CCCTAAA
1 CCCTAAA
1210 CCCTAAA
1 CCCTAAA
1217 CCCTAAA
1 CCCTAAA
1224 CCCTAAAA
1 CCCT-AAA
1232 CCCTAAA
1 CCCTAAA
1239 -CCTAAA
1 CCCTAAA
**
1245 --AAAAA
1 CCCTAAA
1250 CCCTAAA
1 CCCTAAA
1257 -CCTAAA
1 CCCTAAA
1263 CCCTAAA
1 CCCTAAA
**
1270 --AAAAA
1 CCCTAAA
1275 CCCTAAA
1 CCCTAAA
1282 CCCTAAA
1 CCCTAAA
1289 CCCTAAA
1 CCCTAAA
1296 CCCTAAA
1 CCCTAAA
1303 CCCTAAA
1 CCCTAAA
1310 CCCTAAA
1 CCCTAAA
1317 CCCTAAAA
1 CCCT-AAA
1325 CCCTAAA
1 CCCTAAA
**
1332 --AAAAA
1 CCCTAAA
****
1337 AAAAAAA
1 CCCTAAA
****
1344 AAAAAAA
1 CCCTAAA
1351 CCCTAAAA
1 CCCT-AAA
1359 CCCTAAA
1 CCCTAAA
1366 CCCTAAA
1 CCCTAAA
1373 CCCTAAA
1 CCCTAAA
1380 CCCTAAA
1 CCCTAAA
1387 CCCTAAAAA
1 CCCT--AAA
*
1396 ACCTAAA
1 CCCTAAA
1403 CCCTAAAA
1 CCCT-AAA
1411 CCCTAAA
1 CCCTAAA
1418 CCCTAAA
1 CCCTAAA
1425 CCCTAAA
1 CCCTAAA
1432 CCCTAAA
1 CCCTAAA
**
1439 --AAAAA
1 CCCTAAA
1444 CCCTAAA
1 CCCTAAA
1451 CCCTAAAAAA
1 CCCT---AAA
1461 CCCTAAA
1 CCCTAAA
1468 CCCTAAA
1 CCCTAAA
1475 -CCTAAAAAA
1 CCCT---AAA
1484 CCCTAAA
1 CCCTAAA
1491 CCCTAAAA
1 CCCT-AAA
1499 CCCTAAA
1 CCCTAAA
1506 CCCTAAAAAA
1 CCCT---AAA
*
1516 ACCTAAA
1 CCCTAAA
1523 CCCTAAA
1 CCCTAAA
***
1530 -AAAAAA
1 CCCTAAA
****
1536 AAAAAAA
1 CCCTAAA
****
1543 AAAAAAA
1 CCCTAAA
1550 CCCTAAAA
1 CCCT-AAA
1558 CCCTAAA
1 CCCTAAA
****
1565 AAAAAAA
1 CCCTAAA
****
1572 AAAAAAA
1 CCCTAAA
*
1579 ACCTAAA
1 CCCTAAA
1586 CCCTAAA
1 CCCTAAA
1593 CCCTAAAA
1 CCCT-AAA
1601 CCCTAAA
1 CCCTAAA
1608 CCCTAAA
1 CCCTAAA
1615 CCCTAAAA
1 CCCT-AAA
1623 CCCTAAA
1 CCCTAAA
1630 CCCTAAA
1 CCCTAAA
1637 CCCTAAA
1 CCCTAAA
1644 CCCTAAAAA
1 CCCT--AAA
1653 CCCTAAAA
1 CCCT-AAA
1661 CCCTAAA
1 CCCTAAA
1668 CCCTAAA
1 CCCTAAA
1675 CCCTAAA
1 CCCTAAA
1682 CCCTAAA
1 CCCTAAA
1689 CCCTAAAA
1 CCCT-AAA
1697 CCCTAAA
1 CCCTAAA
1704 CCCTAAA
1 CCCTAAA
**
1711 --AAAAA
1 CCCTAAA
1716 CCCTAAAAAA
1 CCCT---AAA
1726 CCCTAAA
1 CCCTAAA
*
1733 ---AAAA
1 CCCTAAA
1737 CCCTAAAAA
1 CCCT--AAA
1746 CCCTAAA
1 CCCTAAA
1753 CCCTAAA
1 CCCTAAA
1760 CCCTAAA
1 CCCTAAA
1767 CCCTAAAA
1 CCCT-AAA
1775 CCCTAAA
1 CCCTAAA
1782 CCCTAAA
1 CCCTAAA
***
1789 -AAAAAA
1 CCCTAAA
1795 CCCTAAA
1 CCCTAAA
1802 -CCTAAAAA
1 CCCT--AAA
*
1810 ACCTAAA
1 CCCTAAA
*
1817 ---AAAA
1 CCCTAAA
1821 CCCTAAA
1 CCCTAAA
1828 CCCTAAA
1 CCCTAAA
*
1835 ---AAAA
1 CCCTAAA
1839 CCCTAAA
1 CCCTAAA
1846 CCCTAAA
1 CCCTAAA
1853 -CCTAAA
1 CCCTAAA
1859 CCCTAAA
1 CCCTAAA
1866 CCCTAAAA
1 CCCT-AAA
1874 CCCTAAA
1 CCCTAAA
1881 CCCTAAA
1 CCCTAAA
1888 CCCTAAAA
1 CCCT-AAA
1896 CCCTAAA
1 CCCTAAA
1903 CCCTAAA
1 CCCTAAA
1910 CCCTAAA
1 CCCTAAA
1917 CCCTAAAA
1 CCCT-AAA
1925 CCCTAAA
1 CCCTAAA
1932 CCCTAAA
1 CCCTAAA
1939 CCCTAAAA
1 CCCT-AAA
1947 CCCTAAA
1 CCCTAAA
1954 CCCTAAA
1 CCCTAAA
1961 CCCTAAA
1 CCCTAAA
1968 CCCTAAA
1 CCCTAAA
1975 CCCCCTAAA
1 --CCCTAAA
1984 CCC-AAA
1 CCCTAAA
*
1990 CCCCCCAAA
1 --CCCTAAA
*
1999 CCC-CAA
1 CCCTAAA
*
2005 CCCCAAA
1 CCCTAAA
*
2012 CCCGAAA
1 CCCTAAA
*
2019 CCCTAAC
1 CCCTAAA
2026 CCCTAAA
1 CCCTAAA
*
2033 CCC-AAC
1 CCCTAAA
2039 CCCTAAA
1 CCCTAAA
2046 CCC-AAA
1 CCCTAAA
2052 -CCTAAAAA
1 CCCT--AAA
2060 CCCTAAAA
1 CCCT-AAA
2068 CCCTAAA
1 CCCTAAA
2075 CCCT-AA
1 CCCTAAA
*
2081 CCCTAACC
1 CCCTAA-A
2089 CCCTAAA
1 CCCTAAA
2096 CCCCTAAA
1 -CCCTAAA
**
2104 CCC-CGA
1 CCCTAAA
*
2110 CCCTATAC
1 CCCTA-AA
2118 CCCTAAA
1 CCCTAAA
*
2125 CCC--GA
1 CCCTAAA
2130 CCCT-AA
1 CCCTAAA
**
2136 CCCCGAA
1 CCCTAAA
**
2143 CCC-CGA
1 CCCTAAA
** *
2149 CCCCGAC
1 CCCTAAA
* *
2156 CCCCAAC
1 CCCTAAA
** *
2163 CCCGGAC
1 CCCTAAA
** *
2170 CCCCGAC
1 CCCTAAA
2177 CCCTAAA
1 CCCTAAA
* *
2184 CCCCAAC
1 CCCTAAA
**
2191 CCCCCAA
1 CCCTAAA
* *
2198 CCCCAAC
1 CCCTAAA
**
2205 CCCCCAA
1 CCCTAAA
2212 CCCTAAA
1 CCCTAAA
*
2219 GCCTAAA
1 CCCTAAA
**
2226 CCCCCAA
1 CCCTAAA
*
2233 CCCCAAA
1 CCCTAAA
*
2240 CCCCCAAA
1 -CCCTAAA
2248 CCCTAAA
1 CCCTAAA
*
2255 CCCCCAAA
1 -CCCTAAA
2263 CCCTAAA
1 CCCTAAA
2270 CCCCTAAAA
1 -CCCT-AAA
2279 CCC--AA
1 CCCTAAA
2284 CCCTTAAA
1 CCC-TAAA
2292 CCCTAAA
1 CCCTAAA
*
2299 CCCCAAA
1 CCCTAAA
*
2306 CCCTAAC
1 CCCTAAA
2313 CCCTAAAA
1 CCCT-AAA
2321 CCC-AAA
1 CCCTAAA
2327 CC
1 CC
2329 GATGTCCAAA
Statistics
Matches: 1966, Mismatches: 172, Indels: 367
0.78 0.07 0.15
Matches are distributed among these distances:
4 31 0.02
5 41 0.02
6 93 0.05
7 1283 0.65
8 324 0.16
9 106 0.05
10 74 0.04
11 10 0.01
12 4 0.00
ACGTcount: A:0.49, C:0.39, G:0.00, T:0.12
Consensus pattern (7 bp):
CCCTAAA
Found at i:33 original size:22 final size:21
Alignment explanation
Indices: 1--2328 Score: 1805
Period size: 22 Copynumber: 108.4 Consensus size: 21
1 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
22 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
*
44 CCCTAAACCCTAAA---AAAA
1 CCCTAAACCCTAAACCCTAAA
*
62 ACCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
** *
83 --AAAAAACCTAAACCCTAAAAAA
1 CCCTAAACCCTAAACCCT---AAA
105 CCCTAAACCCTAAAACCCTAAA
1 CCCTAAACCCT-AAACCCTAAA
127 CCCTAAACCCTAAACCCCTAAA
1 CCCTAAACCCTAAA-CCCTAAA
****
149 CCCTAAACCCTAAAAAAAAAAA
1 CCCTAAACCCT-AAACCCTAAA
****
171 AAAAAAACCCTAAAACCCTAAA
1 CCCTAAACCCT-AAACCCTAAA
193 CCCTAAACCCTAAAACCCTCCTAAA
1 CCCTAAACCCT-AAA--C-CCTAAA
**
218 CCCCCCT-AACCC--CCCCCTAAA
1 ---CCCTAAACCCTAAACCCTAAA
239 CCCTAAACCCTAAACCCCTAAA
1 CCCTAAACCCTAAA-CCCTAAA
261 CCCTAAAACCCCCCTAAAAACCCTAAA
1 CCCT-AAA---CCCT--AAACCCTAAA
288 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
310 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
*
332 CCCTAAACCCTAAA-CCAAAA
1 CCCTAAACCCTAAACCCTAAA
*
352 ACCTAAAAACCCTAAACCCTAAA
1 CCCT--AAACCCTAAACCCTAAA
375 CCCTAAACCCTAAACCCTAAAAA
1 CCCTAAACCCTAAACCCT--AAA
398 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
420 CCCTAAAAACCCTAAACCCTAAA
1 CCCT--AAACCCTAAACCCTAAA
443 CCCTAAA---TAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
461 CCCTAAA---TAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
480 CCCTAAACCCTAAATAACCCTAAA
1 CCCTAAACCCT--A-AACCCTAAA
504 CCCTAAACCCCCCTAAACCCTAAA
1 CCCTAAA---CCCTAAACCCTAAA
528 CCCTAAACCCTAAAAAACCCTAAA
1 CCCTAAACCCT---AAACCCTAAA
552 CCCTAAACCCTAAA---TAAA
1 CCCTAAACCCTAAACCCTAAA
**
570 --AAAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
589 -CCTAAAAACCCTAAACCCTAAA
1 CCCT--AAACCCTAAACCCTAAA
611 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
*
633 -AC-AAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
652 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
*
674 CCCTAAACCCTAAA---AAAA
1 CCCTAAACCCTAAACCCTAAA
692 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
**** *
713 -CCTAAAAAAAAAAACC-AAA
1 CCCTAAACCCTAAACCCTAAA
732 CCCTAAAAAACCCTAAAACCCTAAA
1 CCCT---AAACCCT-AAACCCTAAA
757 CCCTAAACCCTAAAACCCTAAA
1 CCCTAAACCCT-AAACCCTAAA
779 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
800 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
****
822 CCCTAAACCCTAAAAAAAAAA
1 CCCTAAACCCTAAACCCTAAA
843 CCCTAAACCCTAAAAACCCTAAA
1 CCCTAAACCCT--AAACCCTAAA
** ****
866 --AAAAAAAAAAAACCCTAAAAA
1 CCCTAAACCCTAAACCCT--AAA
887 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
909 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
930 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
952 CCCCTAAACCCTAAACCCTAAA
1 -CCCTAAACCCTAAACCCTAAA
974 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
995 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1017 CCCTAAACCCTAAAAAACCCTAAA
1 CCCTAAACCCT---AAACCCTAAA
* ****
1041 CCCTAAAAAACCTAAAAAAAAAAA
1 CCCT--AAACCCT-AAACCCTAAA
* *
1065 ACCTAAAAAACCTAAACCCTAAAAAA
1 CCCT--AAACCCTAAACCCT---AAA
****
1091 AAAAAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1112 CCCTAAACCCTAAAAACCCTAAA
1 CCCTAAACCCT--AAACCCTAAA
1135 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1156 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1178 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1199 ---TAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1217 CCCTAAACCCTAAAACCCTAAA
1 CCCTAAACCCT-AAACCCTAAA
**
1239 -CCTAAA--AAAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
**
1257 -CCTAAACCCTAAA--AAAAA
1 CCCTAAACCCTAAACCCTAAA
1275 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1296 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
**
1317 CCCTAAAACCCTAAA--AAAAA
1 CCCT-AAACCCTAAACCCTAAA
**** ****
1337 AAAAAAAAAAAAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1359 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
*
1380 CCCTAAACCCTAAAAAACCTAAA
1 CCCTAAACCCT--AAACCCTAAA
1403 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
**
1425 CCCTAAACCCTAAA--AAAAA
1 CCCTAAACCCTAAACCCTAAA
1444 CCCTAAACCCTAAAAAACCCTAAA
1 CCCTAAACCCT---AAACCCTAAA
1468 CCCTAAA-CCTAAAAAACCCTAAA
1 CCCTAAACCCT---AAACCCTAAA
1491 CCCTAAAACCCTAAACCCTAAAAAA
1 CCCT-AAACCCTAAACCCT---AAA
* ***
1516 ACCTAAACCCTAAA-AAAAAA
1 CCCTAAACCCTAAACCCTAAA
**** ****
1536 AAAAAAAAAAAAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
**** ****
1558 CCCTAAAAAAAAAAAAAAAAA
1 CCCTAAACCCTAAACCCTAAA
*
1579 ACCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1601 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1623 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1644 CCCTAAAAACCCTAAAACCCTAAA
1 CCCT--AAACCCT-AAACCCTAAA
1668 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1689 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
**
1711 --AAAAACCCTAAAAAACCCTAAA
1 CCCTAAACCCT---AAACCCTAAA
*
1733 ---AAAACCCTAAAAACCCTAAA
1 CCCTAAACCCT--AAACCCTAAA
1753 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
***
1775 CCCTAAACCCTAAA-AAAAAA
1 CCCTAAACCCTAAACCCTAAA
*
1795 CCCTAAA-CCTAAAAAACCTAAA
1 CCCTAAACCCT--AAACCCTAAA
*
1817 ---AAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
*
1835 ---AAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1853 -CCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1874 CCCTAAACCCTAAACCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
1896 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCTAAACCCTAAA
1917 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
1939 CCCTAAAACCCTAAACCCTAAA
1 CCCT-AAACCCTAAACCCTAAA
1961 CCCTAAACCCTAAACCCCCTAAA
1 CCCTAAACCCTAAA--CCCTAAA
* *
1984 CCC-AAACCCCCCAAACCC-CAA
1 CCCTAAA--CCCTAAACCCTAAA
* * *
2005 CCCCAAACCCGAAACCCTAAC
1 CCCTAAACCCTAAACCCTAAA
*
2026 CCCTAAACCC-AACCCCTAAA
1 CCCTAAACCCTAAACCCTAAA
2046 CCC-AAA-CCTAAAAACCCTAAAA
1 CCCTAAACCCT--AAACCCT-AAA
*
2068 CCCTAAACCCT-AACCCTAACC
1 CCCTAAACCCTAAACCCTAA-A
**
2089 CCCTAAACCCCTAAACCC-CGA
1 CCCTAAA-CCCTAAACCCTAAA
* *
2110 CCCTATACCCCTAAACCC--GA
1 CCCTA-AACCCTAAACCCTAAA
** **
2130 CCCT-AACCCCGAACCC-CGA
1 CCCTAAACCCTAAACCCTAAA
** * * * ** *
2149 CCCCGACCCCCAACCCCGGAC
1 CCCTAAACCCTAAACCCTAAA
** * * *
2170 CCCCGACCCCTAAACCCCAAC
1 CCCTAAACCCTAAACCCTAAA
** * * **
2191 CCCCCAACCCCAACCCCCCAA
1 CCCTAAACCCTAAACCCTAAA
* **
2212 CCCTAAAGCCTAAACCCCCAA
1 CCCTAAACCCTAAACCCTAAA
* *
2233 CCCCAAACCCCCAAACCCTAAA
1 CCCTAAA-CCCTAAACCCTAAA
*
2255 CCCCCAAACCCTAAACCCCTAAAA
1 -CCCTAAACCCTAAA-CCCT-AAA
2279 CCC--AACCCTTAAACCCTAAA
1 CCCTAAACCC-TAAACCCTAAA
* *
2299 CCCCAAACCCTAACCCCTAAAA
1 CCCTAAACCCTAAACCCT-AAA
2321 CCC-AAACC
1 CCCTAAACC
2329 GATGTCCAAA
Statistics
Matches: 1930, Mismatches: 213, Indels: 328
0.78 0.09 0.13
Matches are distributed among these distances:
16 10 0.01
18 142 0.07
19 113 0.06
20 121 0.06
21 470 0.24
22 641 0.33
23 172 0.09
24 173 0.09
25 43 0.02
26 14 0.01
27 24 0.01
28 7 0.00
ACGTcount: A:0.49, C:0.39, G:0.00, T:0.12
Consensus pattern (21 bp):
CCCTAAACCCTAAACCCTAAA
Found at i:1036 original size:10 final size:10
Alignment explanation
Indices: 1021--1059 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1011 CTAAAACCCT
1021 AAACCCTAAA
1 AAACCCTAAA
1031 AAACCCT---
1 AAACCCTAAA
1038 AAACCCTAAA
1 AAACCCTAAA
1048 AAA-CCTAAA
1 AAACCCTAAA
1057 AAA
1 AAA
1060 AAAAAACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.27
9 9 0.35
10 10 0.38
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (10 bp):
AAACCCTAAA
Found at i:1256 original size:12 final size:12
Alignment explanation
Indices: 1239--1281 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1229 AAACCCTAAA
1239 CCTAAAAAAAAC
1 CCTAAAAAAAAC
**
1251 CCTAAACCTAAAC
1 CCTAAA-AAAAAC
1264 CCTAAAAAAAAC
1 CCTAAAAAAAAC
1276 CCTAAA
1 CCTAAA
1282 CCCTAAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.58, C:0.30, G:0.00, T:0.12
Consensus pattern (12 bp):
CCTAAAAAAAAC
Found at i:1725 original size:10 final size:10
Alignment explanation
Indices: 1710--1752 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
1700 TAAACCCTAA
1710 AAAAAACCCT
1 AAAAAACCCT
1720 AAAAAACCCT
1 AAAAAACCCT
1730 AAAAAAACCCT
1 -AAAAAACCCT
1741 -AAAAACCCT
1 AAAAAACCCT
1750 AAA
1 AAA
1753 CCCTAAACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.29
10 12 0.39
11 10 0.32
ACGTcount: A:0.63, C:0.28, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAACCCT
Found at i:1725 original size:11 final size:11
Alignment explanation
Indices: 1701--1745 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
1691 CTAAAACCCT
1701 AAACCCTAAAAA
1 AAACCCT-AAAA
1713 AAACCCT-AAA
1 AAACCCTAAAA
1723 AAACCCTAAAA
1 AAACCCTAAAA
1734 AAACCCTAAAA
1 AAACCCTAAAA
1745 A
1 A
1746 CCCTAAACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.31
11 15 0.47
12 7 0.22
ACGTcount: A:0.64, C:0.27, G:0.00, T:0.09
Consensus pattern (11 bp):
AAACCCTAAAA
Found at i:2112 original size:29 final size:29
Alignment explanation
Indices: 1839--2127 Score: 149
Period size: 29 Copynumber: 10.1 Consensus size: 29
1829 CCTAAAAAAA
* * *
1839 CCCTAAACCCTAAACCTA-AACCCTAAA-
1 CCCTAAACCCCAACCCTATACCCCTAAAC
* * *
1866 CCCTAAAACCCTAAACCCTA-AACCCTAAAA
1 CCCT-AAACCC-CAACCCTATACCCCTAAAC
* * *
1896 CCCTAAACCCTAAACCCTA-AACCCTAAAA
1 CCCTAAACCC-CAACCCTATACCCCTAAAC
* * *
1925 CCCTAAACCCTAAACCCTAAAACCCTAAA-
1 CCCTAAACCC-CAACCCTATACCCCTAAAC
* *
1954 CCCTAAACCCTAAACCCTAAACCCCCTAAA-
1 CCCTAAACCC-CAACCCTATA-CCCCTAAAC
*
1984 CCC-AAACCCCCCAAACCCCA-ACCCC-AAA-
1 CCCTAAA--CCCC-AACCCTATACCCCTAAAC
* * *
2012 CCCGAAACCCTAACCCCTA-AACCC--AAC
1 CCCTAAACCCCAA-CCCTATACCCCTAAAC
* * * *
2039 CCCTAAA-CCCAAACCTAAAAACCCTAAAA
1 CCCTAAACCCCAACCCT-ATACCCCTAAAC
*
2068 CCCTAAACCCTAACCCTA-ACCCCCTAAAC
1 CCCTAAACCCCAACCCTATA-CCCCTAAAC
*
2097 CCCTAAACCCCGACCCTATACCCCTAAAC
1 CCCTAAACCCCAACCCTATACCCCTAAAC
2126 CC
1 CC
2128 GACCCTAACC
Statistics
Matches: 226, Mismatches: 18, Indels: 34
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.01
26 9 0.04
27 26 0.12
28 13 0.06
29 134 0.59
30 32 0.14
31 9 0.04
ACGTcount: A:0.41, C:0.47, G:0.01, T:0.11
Consensus pattern (29 bp):
CCCTAAACCCCAACCCTATACCCCTAAAC
Found at i:2201 original size:36 final size:35
Alignment explanation
Indices: 2154--2328 Score: 147
Period size: 36 Copynumber: 4.9 Consensus size: 35
2144 CCCGACCCCG
* * *
2154 ACCCCCAACCCCGGACCCCCGACCCCTAAACCCCAA
1 ACCCCCAACCCC-AACCCCCAAACCCTAAACCCCAA
* * * *
2190 CCCCCCAACCCCAACCCCCCAACCCTAAAGCCTAA
1 ACCCCCAACCCCAACCCCCAAACCCTAAACCCCAA
2225 ACCCCCAACCCCAAACCCCCAAACCCTAAACCCCCAA
1 ACCCCCAACCCC-AACCCCCAAACCCTAAA-CCCCAA
** ** *
2262 ACCCTAAACCCCTAAAACCC-AACCCTTAAACCCTAA
1 ACCCCCAACCCC-AACCCCCAAACCC-TAAACCCCAA
* * *
2298 ACCCCAAACCCTAACCCCTAAAACCC-AAACC
1 ACCCCCAACCCCAACCCC-CAAACCCTAAACC
2329 GATGTCCAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
35 38 0.34
36 47 0.42
37 28 0.25
ACGTcount: A:0.36, C:0.55, G:0.02, T:0.06
Consensus pattern (35 bp):
ACCCCCAACCCCAACCCCCAAACCCTAAACCCCAA
Found at i:2355 original size:20 final size:20
Alignment explanation
Indices: 2332--2566 Score: 80
Period size: 22 Copynumber: 11.4 Consensus size: 20
2322 CCAAACCGAT
2332 GTCCAAAAAACTGAACCGGG
1 GTCCAAAAAACTGAACCGGG
**
2352 GTCCTAAAAAAAGC-GAACCTTG
1 GTCC--AAAAAA-CTGAACCGGG
*
2374 GT-CATAAAAAATCGAACCGGG
1 GTCCA-AAAAACT-GAACCGGG
* * *
2395 CTCATAAAAAACCGAACCGGG
1 GTC-CAAAAAACTGAACCGGG
* *
2416 ATCCTAAAAAAATCGAACC-GG
1 GTCC-AAAAAACT-GAACCGGG
**
2437 GT-CATAAAAACCT-AACTAGG
1 GTCCA-AAAAA-CTGAACCGGG
* *
2457 GTCATAAAAAAATTCGAACC-GG
1 GTC--CAAAAAACT-GAACCGGG
2479 GTCCAAAAAAAAC-GAACC-GG
1 GTCC--AAAAAACTGAACCGGG
*
2499 G--CATAAGAAACAGAACCGGG
1 GTCCA-AA-AAACTGAACCGGG
* *
2519 TTCCAAAAAAATCGAACC-GG
1 GTCCAAAAAACT-GAACCGGG
*
2539 GT-CAAAAAACCGAACCGGG
1 GTCCAAAAAACTGAACCGGG
2558 GTCCAAAAA
1 GTCCAAAAA
2567 CCCAAACCGG
Statistics
Matches: 159, Mismatches: 27, Indels: 58
0.65 0.11 0.24
Matches are distributed among these distances:
16 1 0.01
17 2 0.01
18 10 0.06
19 21 0.13
20 41 0.26
21 36 0.23
22 42 0.26
23 6 0.04
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (20 bp):
GTCCAAAAAACTGAACCGGG
Found at i:2360 original size:21 final size:21
Alignment explanation
Indices: 2332--2566 Score: 111
Period size: 21 Copynumber: 11.5 Consensus size: 21
2322 CCAAACCGAT
2332 GTCC-AAAAAACTGAACCGGG
1 GTCCTAAAAAACTGAACCGGG
**
2352 GTCCTAAAAAAAGC-GAACCTTG
1 GTCCT-AAAAAA-CTGAACCGGG
*
2374 GTCATAAAAAA-TCGAACCGGG
1 GTCCTAAAAAACT-GAACCGGG
* * *
2395 CTCATAAAAAACCGAACCGGG
1 GTCCTAAAAAACTGAACCGGG
* *
2416 ATCCTAAAAAAATCGAACC-GG
1 GTCCTAAAAAACT-GAACCGGG
* * **
2437 GTCATAAAAACCT-AACTAGG
1 GTCCTAAAAAACTGAACCGGG
* *
2457 GTCATAAAAAAATTCGAACC-GG
1 GTCCT-AAAAAACT-GAACCGGG
*
2479 GTCCAAAAAAAAC-GAACC-GG
1 GTCC-TAAAAAACTGAACCGGG
* * *
2499 G-CATAAGAAACAGAACCGGG
1 GTCCTAAAAAACTGAACCGGG
* *
2519 TTCC-AAAAAAATCGAACC-GG
1 GTCCTAAAAAACT-GAACCGGG
*
2539 GT-C-AAAAAACCGAACCGGG
1 GTCCTAAAAAACTGAACCGGG
2558 GTCC-AAAAA
1 GTCCTAAAAA
2567 CCCAAACCGG
Statistics
Matches: 164, Mismatches: 33, Indels: 36
0.70 0.14 0.15
Matches are distributed among these distances:
18 11 0.07
19 20 0.12
20 35 0.21
21 62 0.38
22 32 0.20
23 4 0.02
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (21 bp):
GTCCTAAAAAACTGAACCGGG
Found at i:2405 original size:42 final size:40
Alignment explanation
Indices: 2336--2557 Score: 172
Period size: 43 Copynumber: 5.4 Consensus size: 40
2326 ACCGATGTCC
* * *
2336 AAAAAA-CTGAACCGGGGTCCTAAAAAAAGCGAACCTTGGTCAT
1 AAAAAATC-GAACC-GGGTCAT-AAAAAACCGAACC-GGGTCAT
*
2379 AAAAAATCGAACCGGGCTCATAAAAAACCGAACCGGGATCCT
1 AAAAAATCGAACCGGG-TCATAAAAAACCGAACCGGG-TCAT
* *
2421 AAAAAAATCGAACCGGGTCAT-AAAAACCTAACTAGGGTCAT
1 -AAAAAATCGAACCGGGTCATAAAAAACCGAAC-CGGGTCAT
*
2462 AAAAAAATTCGAACCGGGTCCA-AAAAAAACGAACCGGG-CAT
1 -AAAAAA-TCGAACCGGGT-CATAAAAAACCGAACCGGGTCAT
* *
2503 AAGAAA-CAGAACCGGGTTCCA-AAAAAATCGAACCGGGTC--
1 AAAAAATC-GAACCGGG-T-CATAAAAAACCGAACCGGGTCAT
*
2542 AAAAAACCGAACCGGG
1 AAAAAATCGAACCGGG
2558 GTCCAAAAAC
Statistics
Matches: 154, Mismatches: 13, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
38 1 0.01
39 21 0.14
40 25 0.16
41 26 0.17
42 39 0.25
43 41 0.27
44 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (40 bp):
AAAAAATCGAACCGGGTCATAAAAAACCGAACCGGGTCAT
Found at i:2412 original size:64 final size:60
Alignment explanation
Indices: 2336--2539 Score: 189
Period size: 64 Copynumber: 3.3 Consensus size: 60
2326 ACCGATGTCC
* *
2336 AAAAAACTGAACCGGGGTCCTAAAAAAAGCGAACCTTGGTCATAAAAAATCGAACCGGGCTCAT
1 AAAAAACCGAACCGGGGTCCTAAAAAAAACGAACC--GGTCATAAAAAA-CGAACCGGG-TCAT
* * * * *
2400 AAAAAACCGAACCGGGATCCTAAAAAAATCGAACCGGGTCATAAAAACCTAACTAGGGTCAT
1 AAAAAACCGAACCGGGGTCCTAAAAAAAACGAACC-GGTCATAAAAAACGAAC-CGGGTCAT
* * *
2462 AAAAAAATTCGAACC-GGGTCC-AAAAAAAACGAACCGGGCATAAGAAACAGAACCGGGTTCCA-
1 -AAAAAA-CCGAACCGGGGTCCTAAAAAAAACGAACCGGTCATAAAAAAC-GAACCGGG-T-CAT
*
2524 AAAAAATCGAACCGGG
1 AAAAAACCGAACCGGG
2540 TCAAAAAACC
Statistics
Matches: 118, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
60 7 0.06
61 21 0.18
62 25 0.21
63 27 0.23
64 38 0.32
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (60 bp):
AAAAAACCGAACCGGGGTCCTAAAAAAAACGAACCGGTCATAAAAAACGAACCGGGTCAT
Found at i:2535 original size:40 final size:38
Alignment explanation
Indices: 2335--2566 Score: 132
Period size: 42 Copynumber: 5.7 Consensus size: 38
2325 AACCGATGTC
* * *
2335 CAAAAAACTGAACCGGGGTCCTAAAAAAAGCGAACCTTGGT
1 CAAAAAACAGAACC-GGGTCC-AAAAAAAACGAACC-GGGT
*
2376 CATAAAAA-ATCGAACCGGG-CTCATAAAAAACCGAACCGGGAT
1 CA-AAAAACA--GAACCGGGTC-CA-AAAAAAACGAACCGGG-T
* * * *
2418 CCTAAAAAA-ATCGAACCGGGT-CATAAAAACCTAACTAGGGT
1 -C-AAAAAACA--GAACCGGGTCCAAAAAAAACGAAC-CGGGT
*
2459 CATAAAAAAATTCGAACCGGGTCCAAAAAAAACGAACCGGG-
1 CA-AAAAACA---GAACCGGGTCCAAAAAAAACGAACCGGGT
*
2500 CATAAGAAACAGAACCGGGTTCCAAAAAAATCGAACCGGGT
1 CA-AA-AAACAGAACCGGG-TCCAAAAAAAACGAACCGGGT
*
2541 CAAAAAACCGAACCGGGGTCCAAAAA
1 CAAAAAACAGAACC-GGGTCCAAAAA
2567 CCCAAACCGG
Statistics
Matches: 160, Mismatches: 13, Indels: 38
0.76 0.06 0.18
Matches are distributed among these distances:
39 26 0.16
40 30 0.19
41 25 0.16
42 45 0.28
43 33 0.21
44 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (38 bp):
CAAAAAACAGAACCGGGTCCAAAAAAAACGAACCGGGT
Found at i:2574 original size:20 final size:19
Alignment explanation
Indices: 2533--2577 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2523 AAAAAAATCG
*
2533 AACC-GGGTCAAAAAACCG
1 AACCGGGGTCAAAAAACCA
*
2551 AACCGGGGTCCAAAAACCCA
1 AACCGGGGT-CAAAAAACCA
2571 AACCGGG
1 AACCGGG
2578 ATATCAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.40, C:0.31, G:0.24, T:0.04
Consensus pattern (19 bp):
AACCGGGGTCAAAAAACCA
Found at i:3417 original size:19 final size:19
Alignment explanation
Indices: 3393--3432 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3383 GAGAAGATAG
* *
3393 AAAAATAATAATAAATGGT
1 AAAAATAAGAATAAAAGGT
*
3412 AAAAATCAGAATAAAAGGT
1 AAAAATAAGAATAAAAGGT
3431 AA
1 AA
3433 CAACTAACAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (19 bp):
AAAAATAAGAATAAAAGGT
Found at i:4762 original size:2 final size:2
Alignment explanation
Indices: 4755--4783 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4745 CTGAAAAGGC
4755 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
4784 TTAAGCTATG
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:13799 original size:31 final size:31
Alignment explanation
Indices: 13761--13826 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
13751 AAGAAAGAAA
*
13761 GAAACTTGTATAGGTGCTCTCCTCTACTGAT
1 GAAACTTGTATAGGTGCTCTCATCTACTGAT
13792 GAAACTTGTATAGGTGCTCTCATCTACTGAT
1 GAAACTTGTATAGGTGCTCTCATCTACTGAT
13823 GAAA
1 GAAA
13827 GTTGGAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
GAAACTTGTATAGGTGCTCTCATCTACTGAT
Found at i:17142 original size:33 final size:33
Alignment explanation
Indices: 17100--17190 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
17090 TTTCTTCTTG
*
17100 ACATTCCAGCTACTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
17133 ACATTCCAGCTCCCGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
17166 ACATTCCAGCTCCTGTCCAACAACC
1 ACATTCCAGCTCCTGTCCAGCAACC
17191 TGAAACAGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.31, C:0.43, G:0.09, T:0.18
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:25301 original size:16 final size:16
Alignment explanation
Indices: 25280--25311 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25270 TTAATATATA
25280 AAAAAGAGGAAAACAG
1 AAAAAGAGGAAAACAG
25296 AAAAAGAGGAAAACAG
1 AAAAAGAGGAAAACAG
25312 TAAGCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAAGAGGAAAACAG
Found at i:29579 original size:78 final size:78
Alignment explanation
Indices: 29449--29599 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 78
29439 GTACACAAAG
* * * * *
29449 TCCATGGTGATCGCTATCAACATGATCACCAACTCTCCTAGCTGATGCGATCAAGGGATCAGGGT
1 TCCATAGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATGAGATCAAGGGATCACGGT
29514 TTAATGGTCGAAC
66 TTAATGGTCGAAC
* * * *
29527 TCCATAGTGATCATTATCAACATGATCACCGACTCTCCCAGTTGGTGAGATCAAGGGATCACGGT
1 TCCATAGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATGAGATCAAGGGATCACGGT
29592 TTAATGGT
66 TTAATGGT
29600 AGAATATGAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (78 bp):
TCCATAGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATGAGATCAAGGGATCACGGT
TTAATGGTCGAAC
Found at i:32814 original size:16 final size:15
Alignment explanation
Indices: 32774--32819 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
32764 AGATAAACCT
*
32774 AAGCCGGGATATCCT
1 AAGCCGGGATATCCA
* *
32789 TAGGCGGGATATCACA
1 AAGCCGGGATATC-CA
32805 AAGCCGGGATATCCA
1 AAGCCGGGATATCCA
32820 TAGAATAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.17
Consensus pattern (15 bp):
AAGCCGGGATATCCA
Found at i:33963 original size:341 final size:338
Alignment explanation
Indices: 33473--34142 Score: 1304
Period size: 341 Copynumber: 2.0 Consensus size: 338
33463 CTTCTCTTTG
33473 ACGATACGATACCCTCTCCGATCTTTCATTTCATTTCCATTTCATTCCAGAATTTTTTTTTCTTT
1 ACGATACGATACCCTCTCCGATCTTTCATTTCATTTCCATTTCATTCCAGAATTTTTTTTTCTTT
33538 GATATTACCACTTGGGCTTTTTTTAAAAAAAACTCAGTATGATTTAATTAGTGTTTTCTTATTCC
66 GATATTACCACTTGGGCTTTTTTTAAAAAAAACTCAGTATGATTTAATTAGTGTTTTCTTATTCC
*
33603 CTCAACAAATATAATGTTTTTACTAGTTGAAAAAGGGAAAACCAGGAGACAATAAAAGGGAAAGA
131 CTCAACAAATATAATGTTTTTACTAGTTGAAAAAGGGAAAACCAGCAGACAATAAAAGGGAAAGA
33668 AACAAGAAAATGTTTCCATTTACCTTCTGCTAATCAGTTATGGTTTTAGGGTGGATACCTACATA
196 AACAAGAAAATGTTTCCATTTACCTTCTGCTAATCAGTTATGGTTTTAGGGTGGATACCTACATA
33733 GTTGTTAGAAACATATCTTCGCTATAAAATCTCATAGGACTGAAAGATTTATAAGAAAATGTCCT
261 GTTGTTAGAAACATATCTTCGCTATAAAATCTCATAGGACTGAAAGATTTATAAGAAAATGTCCT
33798 TAAACATATACCT
326 TAAACATATACCT
33811 ACGATACGATACCCTCTCCGATCTTTCATTTCATTTCCATTTCATTCCAGAATTTTTTTTTTCTT
1 ACGATACGATACCCTCTCCGATCTTTCATTTCATTTCCATTTCATTCCAGAA-TTTTTTTTTCTT
33876 TGATATTACCACTTGGGCTTTTTTTTAAAAAAAAACTCAGTATGATTTAATTAGTGTTTTCTTAT
65 TGATATTACCACTTGGGC-TTTTTTT-AAAAAAAACTCAGTATGATTTAATTAGTGTTTTCTTAT
33941 TCCCTCAACAAATATAATGTTTTTACTAGTTGAAAAAGGGAAAACCAGCAGACAATAAAAGGGAA
128 TCCCTCAACAAATATAATGTTTTTACTAGTTGAAAAAGGGAAAACCAGCAGACAATAAAAGGGAA
34006 AGAAACAAGAAAATGTTTCCATTTACCTTCTGCTAATCAGTTATGGTTTTAGGGTGGATACCTAC
193 AGAAACAAGAAAATGTTTCCATTTACCTTCTGCTAATCAGTTATGGTTTTAGGGTGGATACCTAC
34071 ATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAGGACTGAAAGATTTATAAGAAAATGT
258 ATAGTTGTTAGAAACATATCTTCGCTATAAAATCTCATAGGACTGAAAGATTTATAAGAAAATGT
34136 CCTTAAA
323 CCTTAAA
34143 TAAGGAGGGA
Statistics
Matches: 328, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
338 52 0.16
339 30 0.09
340 7 0.02
341 239 0.73
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (338 bp):
ACGATACGATACCCTCTCCGATCTTTCATTTCATTTCCATTTCATTCCAGAATTTTTTTTTCTTT
GATATTACCACTTGGGCTTTTTTTAAAAAAAACTCAGTATGATTTAATTAGTGTTTTCTTATTCC
CTCAACAAATATAATGTTTTTACTAGTTGAAAAAGGGAAAACCAGCAGACAATAAAAGGGAAAGA
AACAAGAAAATGTTTCCATTTACCTTCTGCTAATCAGTTATGGTTTTAGGGTGGATACCTACATA
GTTGTTAGAAACATATCTTCGCTATAAAATCTCATAGGACTGAAAGATTTATAAGAAAATGTCCT
TAAACATATACCT
Found at i:47286 original size:20 final size:20
Alignment explanation
Indices: 47248--47286 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47238 TCATTTAAGC
* *
47248 TAAAAAATTTCCTTTTTTTT
1 TAAAAAATTTCATTCTTTTT
*
47268 TAAAAGATTTCATTCTTTT
1 TAAAAAATTTCATTCTTTT
47287 ACTGCTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (20 bp):
TAAAAAATTTCATTCTTTTT
Found at i:47857 original size:17 final size:17
Alignment explanation
Indices: 47817--47861 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
47807 TATCTATTTT
*
47817 TTCTTTCTTGTTTTTTGC
1 TTCTTT-TTGTTTTCTGC
47835 -TC--TTTGTTTTCTGC
1 TTCTTTTTGTTTTCTGC
47849 TTCTTTTTGTTTT
1 TTCTTTTTGTTTT
47862 TTTGCTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 10 0.43
15 3 0.13
17 10 0.43
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (17 bp):
TTCTTTTTGTTTTCTGC
Found at i:54029 original size:14 final size:14
Alignment explanation
Indices: 54012--54042 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54002 TTAGATTAAT
54012 CTATTTAGGACTGC
1 CTATTTAGGACTGC
54026 CTATTTAGGACTGC
1 CTATTTAGGACTGC
54040 CTA
1 CTA
54043 GAACTGCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (14 bp):
CTATTTAGGACTGC
Found at i:56127 original size:13 final size:13
Alignment explanation
Indices: 56111--56140 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56101 AGTGCTGCAA
56111 AAAAATGCTTATG
1 AAAAATGCTTATG
*
56124 AAAAATGCTTTTG
1 AAAAATGCTTATG
56137 AAAA
1 AAAA
56141 GCTTGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (13 bp):
AAAAATGCTTATG
Found at i:57727 original size:16 final size:18
Alignment explanation
Indices: 57690--57724 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
57680 AATACTAAGA
57690 ATTT-TATTAAATTATAT
1 ATTTATATTAAATTATAT
57707 ATTTATATTAAATTATAT
1 ATTTATATTAAATTATAT
57725 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTAAATTATAT
Found at i:57738 original size:26 final size:26
Alignment explanation
Indices: 57709--57765 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
57699 AATTATATAT
57709 TTATATT-AAATTATATTTAATAATAA
1 TTATATTCAAATTATATTTAATAAT-A
* * *
57735 TTAT-TTCAGATTATATTTTATAGTA
1 TTATATTCAAATTATATTTAATAATA
57760 TTATAT
1 TTATAT
57766 ATTATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (26 bp):
TTATATTCAAATTATATTTAATAATA
Found at i:57833 original size:18 final size:18
Alignment explanation
Indices: 57812--57847 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
57802 ATATTAAGAA
57812 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
57830 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
57848 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTATATTT
Found at i:57854 original size:13 final size:13
Alignment explanation
Indices: 57838--57895 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
57828 TTTTTTATTA
*
57838 AATTATATTTAAT
1 AATTATATTTTAT
57851 AATTATTATTTTA-
1 AATTA-TATTTTAT
57864 AATTATATTTTAT
1 AATTATATTTTAT
*
57877 ACTATTATATATTAT
1 A--ATTATATTTTAT
57892 AATT
1 AATT
57896 TTAGTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.18
13 14 0.36
14 6 0.15
15 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATTTTAT
Found at i:57855 original size:18 final size:18
Alignment explanation
Indices: 57816--57855 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57806 TAAGAATTTT
** *
57816 ATTAAATTATATTTTTTT
1 ATTAAATTATATTTAATA
57834 ATTAAATTATATTTAATA
1 ATTAAATTATATTTAATA
57852 ATTA
1 ATTA
57856 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTAAATTATATTTAATA
Found at i:57861 original size:121 final size:120
Alignment explanation
Indices: 57613--57920 Score: 519
Period size: 121 Copynumber: 2.6 Consensus size: 120
57603 CCACAAAATC
*
57613 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCGTATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
57678 TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
66 TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
*
57733 AATTATTTCAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-
* * *
57798 TTTAATATTAAGAATTTTATTAAATTATATTTTTTTATTAAATTATATTTAATAAT
65 TTTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
* * * *
57854 TATTATTTTAAATTATATTTTATACTATTATATATTATAATTTTAGTAAATTCATATAAGAAT-T
1 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
57918 TTA
66 TTA
57921 TTAAATTATA
Statistics
Matches: 177, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
119 4 0.02
120 62 0.35
121 111 0.63
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (120 bp):
AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
TTAATACTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAAT
Found at i:58187 original size:45 final size:44
Alignment explanation
Indices: 58101--58191 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
58091 ACCTCTATTC
* *
58101 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
*** *
58145 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCATTA
58190 CA
1 CA
58192 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
Found at i:58191 original size:16 final size:16
Alignment explanation
Indices: 58170--58239 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
58160 TTGATTTGCT
58170 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
58186 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
58202 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
58218 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
58234 AATACA
1 ATTACA
58240 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.31, C:0.36, G:0.01, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:59076 original size:115 final size:115
Alignment explanation
Indices: 58874--59104 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
58864 GACTTGAATG
58874 TTTTTAATATCTTAAAGGGGGAATCAAAATAAAATACTAAGTGACCGTTAAAATGGCCCAAAACT
1 TTTTTAATATCTTAAAGGGGGAATCAAAATAAAATACTAAGTGACCGTTAAAATGGCCCAAAACT
*
58939 GATTTGTTAGCCGTTTATCAAATATCTCTTCAATCTTTGCACATTTATTA
66 GATTTGTTAGCCGTTTATCAAATATCTCTTCAATCTATGCACATTTATTA
58989 TTTTTAATATCTTAAAGGGGGAATCAAAATAAAATACTAAGTGACCGTTAAAATGGCCCAAAACT
1 TTTTTAATATCTTAAAGGGGGAATCAAAATAAAATACTAAGTGACCGTTAAAATGGCCCAAAACT
59054 GATTTGTTAGCCGTTTATCAAATATCTCTTCAATCTATGCACATTTATTA
66 GATTTGTTAGCCGTTTATCAAATATCTCTTCAATCTATGCACATTTATTA
59104 T
1 T
59105 CCGTTTCTTT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (115 bp):
TTTTTAATATCTTAAAGGGGGAATCAAAATAAAATACTAAGTGACCGTTAAAATGGCCCAAAACT
GATTTGTTAGCCGTTTATCAAATATCTCTTCAATCTATGCACATTTATTA
Found at i:60703 original size:7 final size:7
Alignment explanation
Indices: 60691--60738 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
60681 GACCATTTCA
60691 TTTAGGG
1 TTTAGGG
60698 TTTAGGG
1 TTTAGGG
60705 TTTAGGG
1 TTTAGGG
60712 TTTAGGG
1 TTTAGGG
* *
60719 CTTAAGG
1 TTTAGGG
60726 TTTAGGG
1 TTTAGGG
*
60733 CTTAGG
1 TTTAGG
60739 CCCCAAGCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.17, C:0.04, G:0.40, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:60710 original size:14 final size:14
Alignment explanation
Indices: 60692--60738 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
60682 ACCATTTCAT
*
60692 TTAGGGTTTAGGGT
1 TTAGGGTTTAGGGC
60706 TTAGGGTTTAGGGC
1 TTAGGGTTTAGGGC
*
60720 TTAAGGTTTAGGGC
1 TTAGGGTTTAGGGC
60734 TTAGG
1 TTAGG
60739 CCCCAAGCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.40, T:0.38
Consensus pattern (14 bp):
TTAGGGTTTAGGGC
Found at i:60748 original size:7 final size:7
Alignment explanation
Indices: 60738--60776 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
60728 TAGGGCTTAG
60738 GCCCCAA
1 GCCCCAA
60745 GCCCCAA
1 GCCCCAA
60752 GCCCCAA
1 GCCCCAA
60759 GCCCCAA
1 GCCCCAA
60766 GCCCCAA
1 GCCCCAA
60773 GCCC
1 GCCC
60777 ATGACCGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.26, C:0.59, G:0.15, T:0.00
Consensus pattern (7 bp):
GCCCCAA
Found at i:61248 original size:15 final size:16
Alignment explanation
Indices: 61222--61251 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61212 AGTTTAGGGG
61222 CAAAATTATAATTTTC
1 CAAAATTATAATTTTC
61238 CAAAA-TATAATTTT
1 CAAAATTATAATTTT
61252 GGGTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
CAAAATTATAATTTTC
Found at i:61718 original size:46 final size:46
Alignment explanation
Indices: 61665--61933 Score: 280
Period size: 46 Copynumber: 5.8 Consensus size: 46
61655 TATTTGAGCA
* *
61665 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
61711 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
61756 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * * *
61804 TCCGAACTCGTTAAGTTGAGTCCGAGTT-AGTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
* * *
61849 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * *
61897 CCCGAGCTCGTTGAGTTAAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
61934 GCGGGTTACA
Statistics
Matches: 185, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
43 12 0.06
45 9 0.05
46 88 0.48
47 56 0.30
48 9 0.05
50 11 0.06
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
Found at i:61779 original size:47 final size:47
Alignment explanation
Indices: 61711--61879 Score: 229
Period size: 47 Copynumber: 3.6 Consensus size: 47
61701 GATGCAAATG
61711 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * *
61758 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
* *
61804 TCCGAACTCGTTAAGTTGAGTCCGAGTTAGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
61851 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
61880 ACTCATGGAT
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 27 0.26
47 56 0.54
48 4 0.04
50 6 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:61799 original size:93 final size:93
Alignment explanation
Indices: 61662--61925 Score: 447
Period size: 93 Copynumber: 2.8 Consensus size: 93
61652 GGATATTTGA
*
61662 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
61727 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
61755 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTAAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
*
61820 TGAGTCCGAGTTAGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * *
61848 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
*
61913 TAAGTCCGAGTTC
66 TGAGTCCGAGTTC
61926 ACTTATGGGC
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:78506 original size:16 final size:16
Alignment explanation
Indices: 78437--78504 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
78427 TTTGGTTCGC
78437 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
78453 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
78469 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
78485 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
78501 TGTA
1 TGTA
78505 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:78536 original size:45 final size:44
Alignment explanation
Indices: 78485--78579 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
78475 GGATTAGAGG
*** *
78485 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAACGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
78530 TGTAATGGAATAGAAACGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAACGTAATAGCAAAACACTGTTTGGTTGAA
78574 TGTAAT
1 TGTAAT
78580 AGAGGTGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAAACGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:78762 original size:18 final size:17
Alignment explanation
Indices: 78741--78775 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
78731 TTATTATTTA
*
78741 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
78759 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
78776 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:78769 original size:28 final size:27
Alignment explanation
Indices: 78699--78771 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
78689 TTTATTATCA
*
78699 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
78727 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
78754 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
78772 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:78909 original size:18 final size:17
Alignment explanation
Indices: 78888--78922 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
78878 TTATTATTAA
*
78888 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
78906 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
78923 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:78934 original size:147 final size:149
Alignment explanation
Indices: 78660--78934 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
78650 ATGATTATTG
*
78660 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
78725 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
78790 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
78809 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
78872 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
78935 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:79030 original size:18 final size:17
Alignment explanation
Indices: 78990--79042 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
78980 AAATATAAAT
78990 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
79004 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
79019 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
79037 TAAAAT
1 TAAAAT
79043 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:79100 original size:60 final size:59
Alignment explanation
Indices: 78916--79102 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
78906 ATATAATTTA
*
78916 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
78977 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
79035 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
79096 ATAAAAT
1 ATAAAAT
79103 ATAATTTAAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:79101 original size:119 final size:120
Alignment explanation
Indices: 78868--79162 Score: 504
Period size: 119 Copynumber: 2.5 Consensus size: 120
78858 TTACTCATAT
*
78868 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
78933 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
78989 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
79053 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
*
79108 TTAAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
79163 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 109 0.65
120 53 0.32
121 5 0.03
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:84931 original size:256 final size:257
Alignment explanation
Indices: 84436--84950 Score: 987
Period size: 256 Copynumber: 2.0 Consensus size: 257
84426 GATTCTCTAA
84436 AGGTGAAACAGAAAACCGTGACAAAAACACACTGAAAATAGAAGTAAAAAGAAGCATACATCTTA
1 AGGTGAAACAGAAAACCGTGACAAAAACACACTGAAAATAGAAGTAAAAAGAAGCATACATCTTA
84501 AACTAAAAACAGAGATGAAAAGGCAAAGACAAAGGATTTATAAAGCAGAAAAAAAAAATCATAAA
66 AACTAAAAACAGAGATGAAAAGGCAAAGACAAAGGATTTATAAAGCAG-AAAAAAAAATCATAAA
84566 AATACCCACTGACATACAAGTAAAAAAGCATCAACCAATAAGCAAATTAAAATTATGTTAATCTA
130 AATACCCACTGACATACAAGTAAAAAAGCATCAACCAATAAGCAAATTAAAATTATGTTAATCTA
84631 AGGATTGCGACTAGAACCTATTCATTTAAAAGATTACAACTCAATTTCCCTTCATGTAAGGCT
195 AGGATTGCGACTAGAACCTATTCATTTAAAAGATTACAACTCAATTTCCCTTCATGTAAGGCT
84694 AGGTGAAACAGAAAACCGTGACAAAAACACACTGAAAATAGAAGTAAAAAGAAGCATACATCTTA
1 AGGTGAAACAGAAAACCGTGACAAAAACACACTGAAAATAGAAGTAAAAAGAAGCATACATCTTA
84759 AACTAAAAACAGAGATGAAAAGGCAAAGACAAAGGATTTATAAAGCAG-AAAAAAAATCATAAAA
66 AACTAAAAACAGAGATGAAAAGGCAAAGACAAAGGATTTATAAAGCAGAAAAAAAAATCATAAAA
84823 ATACCCACTGACATACAAGTAAAAAAGCATCAACCAATAAGCAAATTAAAATTATGTTAATCTAA
131 ATACCCACTGACATACAAGTAAAAAAGCATCAACCAATAAGCAAATTAAAATTATGTTAATCTAA
* * *
84888 GGATTGCGACTAGAACCTATTCATTTAAAAGGTTGCAACTCAATTTCCCTTCATGTGAGGCT
196 GGATTGCGACTAGAACCTATTCATTTAAAAGATTACAACTCAATTTCCCTTCATGTAAGGCT
84950 A
1 A
84951 AGTAACACAG
Statistics
Matches: 254, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
256 141 0.56
258 113 0.44
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (257 bp):
AGGTGAAACAGAAAACCGTGACAAAAACACACTGAAAATAGAAGTAAAAAGAAGCATACATCTTA
AACTAAAAACAGAGATGAAAAGGCAAAGACAAAGGATTTATAAAGCAGAAAAAAAAATCATAAAA
ATACCCACTGACATACAAGTAAAAAAGCATCAACCAATAAGCAAATTAAAATTATGTTAATCTAA
GGATTGCGACTAGAACCTATTCATTTAAAAGATTACAACTCAATTTCCCTTCATGTAAGGCT
Found at i:85007 original size:20 final size:20
Alignment explanation
Indices: 84982--85027 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
84972 TCTATCTTTA
84982 ACCAAAATCAGAGTATTTTC
1 ACCAAAATCAGAGTATTTTC
85002 ACCAAAATCAGAGTATTTTC
1 ACCAAAATCAGAGTATTTTC
85022 ACCAAA
1 ACCAAA
85028 TGGATATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (20 bp):
ACCAAAATCAGAGTATTTTC
Found at i:86021 original size:89 final size:89
Alignment explanation
Indices: 85925--86098 Score: 321
Period size: 89 Copynumber: 2.0 Consensus size: 89
85915 AAAAGGGCCC
85925 ATCTAACTAATTAAATGAAGACCCAAAACAAGTTTAGTACATGGGGTATAAAATAAGCTCAAAAA
1 ATCTAACTAATTAAATGAAGACCCAAAACAAGTTTAGTACATGGGGTATAAAATAAGCTCAAAAA
*
85990 TTTAGTAACTAAAATTTAAGGTCT
66 TTCAGTAACTAAAATTTAAGGTCT
**
86014 ATCTAACTAATTAAATGAAGACCCAAAACAAGTTTAGTACATGGGGTATAACGTAAGCTCAAAAA
1 ATCTAACTAATTAAATGAAGACCCAAAACAAGTTTAGTACATGGGGTATAAAATAAGCTCAAAAA
86079 TTCAGTAACTAAAATTTAAG
66 TTCAGTAACTAAAATTTAAG
86099 AGGTTCACAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (89 bp):
ATCTAACTAATTAAATGAAGACCCAAAACAAGTTTAGTACATGGGGTATAAAATAAGCTCAAAAA
TTCAGTAACTAAAATTTAAGGTCT
Found at i:92372 original size:53 final size:53
Alignment explanation
Indices: 92292--92397 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
92282 ATCCCGTTCC
*
92292 GGTTCAATATTTTTATTGCTCGGTTCAGCTGATTTGGTAACCGGTTTAGAGTT
1 GGTTCAATATTTTTATTGCTCGGTTCAGCTGATTTCGTAACCGGTTTAGAGTT
92345 GGTTCAATATTTTTATTGCTCGGTTCAGCTGATTTCGTAACCGGTTTAGAGTT
1 GGTTCAATATTTTTATTGCTCGGTTCAGCTGATTTCGTAACCGGTTTAGAGTT
92398 TTTTGCGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (53 bp):
GGTTCAATATTTTTATTGCTCGGTTCAGCTGATTTCGTAACCGGTTTAGAGTT
Found at i:103550 original size:46 final size:46
Alignment explanation
Indices: 103500--103675 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
103490 TGGTTGAGCA
103500 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
103546 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
103591 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
103639 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
103676 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 30 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:103656 original size:93 final size:93
Alignment explanation
Indices: 103497--103667 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
103487 GGATGGTTGA
* *
103497 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
103562 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
*
103590 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
103655 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
103668 GCTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:110637 original size:30 final size:30
Alignment explanation
Indices: 110581--110637 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
110571 ATCCCGAGCC
*
110581 TAGGGGCAAAAATGTAAATATGCAAAAGTT
1 TAGGGGCAAAAATGTAAATATCCAAAAGTT
* * *
110611 TAGGGGCAAAATTGTAATTTTCCAAAA
1 TAGGGGCAAAAATGTAAATATCCAAAA
110638 TTTGAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATCCAAAAGTT
Found at i:111108 original size:46 final size:46
Alignment explanation
Indices: 111058--111233 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
111048 TGGTTGAGCA
111058 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
111104 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
111149 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
111197 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
111234 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:111214 original size:93 final size:93
Alignment explanation
Indices: 111055--111226 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
111045 GGATGGTTGA
* *
111055 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
111120 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
111148 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
111213 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
111227 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:114940 original size:38 final size:38
Alignment explanation
Indices: 114898--115001 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 38
114888 AAATAGGGTA
*
114898 TTATTCAGGCTTAGTGCCTAGCAAGCTTAGTGCCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
* * ** ** * *
114936 TTATTTAGGCTTACTTTCTAATAGGCTTAATGTCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
* *
114974 TTGA-TCAAGCTTAGTGCTTAGCAAGCTT
1 TT-ATTCAGGCTTAGTGCCTAGCAAGCTT
115002 TAAGTCGGTG
Statistics
Matches: 47, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
38 46 0.98
39 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (38 bp):
TTATTCAGGCTTAGTGCCTAGCAAGCTTAATGCCGGTG
Found at i:118456 original size:48 final size:49
Alignment explanation
Indices: 118394--118528 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 49
118384 AAATTATGAG
* *
118394 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG-AGA-CGAGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGTAGATC-A-T
* * *
118443 -GCCAGTGTAAGACCATGTCTGGGACATGACATTGGCCTCGTTGATCAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGTAGATCAT
* *
118491 AGCTAGTGTAAGACCATGTTTGGGACATGGCATTGGCA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA
118529 CACTTACCCC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 37 0.50
49 36 0.49
50 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (49 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGTAGATCAT
Found at i:131948 original size:6 final size:6
Alignment explanation
Indices: 131937--131961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
131927 TAAAATTTTG
131937 ATAATC ATAATC ATAATC ATAATC A
1 ATAATC ATAATC ATAATC ATAATC A
131962 CCCTTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAATC
Found at i:133730 original size:18 final size:17
Alignment explanation
Indices: 133694--133742 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
133684 AAATAGATAG
*
133694 AATAAAAATTAATAAAAA
1 AATAAAAATT-ATATAAA
133712 AATAAGAAATTATATAAA
1 AATAA-AAATTATATAAA
133730 AATATAAAATTAT
1 AATA-AAAATTAT
133743 TAATAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATAAAAATTATATAAA
Found at i:133759 original size:19 final size:18
Alignment explanation
Indices: 133694--133759 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
133684 AAATAGATAG
*
133694 AATA-AAAATTAATAAAAA
1 AATAGAAAATT-ATATAAA
133712 AATA-AGAAATTATATAAA
1 AATAGA-AAATTATATAAA
*
133730 AATATAAAATTAT-TAATA
1 AATAGAAAATTATATAA-A
133748 AATTAGAAAATT
1 AA-TAGAAAATT
133760 GTAACAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.07
18 25 0.60
19 14 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AATAGAAAATTATATAAA
Found at i:134160 original size:64 final size:64
Alignment explanation
Indices: 134081--134205 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
134071 ACACTGGAGT
* * * *
134081 ATACAAATTCAAATATTAGAGTAGACATTGTTGAGAGAGATAACCATGAACTTCGAAGGGGAAG
1 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGGAAG
134145 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGG
1 ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGG
134206 TTAAGTAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (64 bp):
ATACAAATTCAAATATTAGAGTAAACATTGATGAGAGAGACAACCATGAACTCCGAAGGGGAAG
Found at i:135150 original size:40 final size:41
Alignment explanation
Indices: 135070--135150 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
135060 TTTATATTAT
135070 TATTTATATTATGACATTAGTATTATTATTATTATAAAAGA
1 TATTTATATTATGACATTAGTATTATTATTATTATAAAAGA
* * * *
135111 TATTTATATT-TTATATTATTATTATTATTATTATTAAAGA
1 TATTTATATTATGACATTAGTATTATTATTATTATAAAAGA
135151 AAGATAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 26 0.72
41 10 0.28
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (41 bp):
TATTTATATTATGACATTAGTATTATTATTATTATAAAAGA
Found at i:136640 original size:25 final size:25
Alignment explanation
Indices: 136612--136673 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
136602 ACCTTAGCGC
136612 GCTATCTGATTATTAGCACGTCAGT
1 GCTATCTGATTATTAGCACGTCAGT
136637 GCTATCTGATTATTAGCACGTCAGT
1 GCTATCTGATTATTAGCACGTCAGT
*
136662 GCTCTCTGATTA
1 GCTATCTGATTA
136674 GCACATCCGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTATCTGATTATTAGCACGTCAGT
Found at i:136676 original size:22 final size:23
Alignment explanation
Indices: 136622--136690 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 23
136612 GCTATCTGAT
*
136622 TATTAGCACGTCAGTGCTATCTG
1 TATTAGCACGTCAGTGCTCTCTG
136645 ATTATTAGCACGTCAGTGCTCTCTG
1 --TATTAGCACGTCAGTGCTCTCTG
* *
136670 -ATTAGCACATCCGTGCTCTCT
1 TATTAGCACGTCAGTGCTCTCT
136691 ATTCATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
22 19 0.46
25 22 0.54
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (23 bp):
TATTAGCACGTCAGTGCTCTCTG
Found at i:146426 original size:39 final size:42
Alignment explanation
Indices: 146372--146469 Score: 162
Period size: 44 Copynumber: 2.3 Consensus size: 42
146362 TTTCTGCATT
*
146372 TATTTA-TTTTAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
146413 TATTTAGTTATAAAATAAAATAAGATATCATATTTTAATGATAA
1 TATTTAGTTAT--AATAAAATAAGATATCATATTTTAATGATAA
146457 TATTTAGTTATAA
1 TATTTAGTTATAA
146470 AATTATTAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
41 6 0.11
42 5 0.09
44 42 0.79
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (42 bp):
TATTTAGTTATAATAAAATAAGATATCATATTTTAATGATAA
Found at i:146430 original size:44 final size:44
Alignment explanation
Indices: 146382--146472 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
146372 TATTTATTTT
146382 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
146426 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
1 AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
146470 AAT
1 AAT
146473 TATTAGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (44 bp):
AATAAAATAAGATATCATATTTTAATGATAATATTTAGTTATAA
Found at i:146607 original size:19 final size:19
Alignment explanation
Indices: 146567--146612 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
146557 TTTTTCAAAA
*
146567 TTTAGAGAAATAAGCTATT
1 TTTAGAGAAATAAGCGATT
*
146586 TTTAGAGAAATACATCGA-T
1 TTTAGAGAAATA-AGCGATT
146605 TTTAGAGA
1 TTTAGAGA
146613 TAGAGTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (19 bp):
TTTAGAGAAATAAGCGATT
Found at i:146783 original size:18 final size:19
Alignment explanation
Indices: 146737--146783 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
146727 TCTTAAATTT
*
146737 AACTCTCTCTATTCTCTCTA
1 AACT-TCTCAATTCTCTCTA
146757 AACTT-TCAATTCTCTC-A
1 AACTTCTCAATTCTCTCTA
*
146774 AATTTCTCAA
1 AACTTCTCAA
146784 GATTTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 1 0.04
20 4 0.17
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
AACTTCTCAATTCTCTCTA
Found at i:150325 original size:14 final size:14
Alignment explanation
Indices: 150306--150332 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
150296 TCAGAAAAAT
150306 AAAAATATTTTTAG
1 AAAAATATTTTTAG
150320 AAAAATATTTTTA
1 AAAAATATTTTTA
150333 ACGTAATTAA
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:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAAATATTTTTAG
Found at i:150386 original size:17 final size:18
Alignment explanation
Indices: 150341--150388 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
150331 TAACGTAATT
*
150341 AAATAATTATTAGTGAAAG
1 AAATAATT-TTAGTCAAAG
*
150360 TAATTAATTTTAGTCAAA-
1 -AAATAATTTTAGTCAAAG
150378 AAATAATTTTA
1 AAATAATTTTA
150389 AAATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
19 8 0.32
20 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (18 bp):
AAATAATTTTAGTCAAAG
Found at i:152310 original size:18 final size:18
Alignment explanation
Indices: 152287--152327 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
152277 TACTTTTCTC
152287 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
152305 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
152323 TTTCT
1 TTTCT
152328 TTTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:153893 original size:23 final size:23
Alignment explanation
Indices: 153850--153908 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
153840 AACTTAATTT
153850 AAAAAAATAATAATAATTTAATA
1 AAAAAAATAATAATAATTTAATA
*
153873 AAAAAACATACTAATAA-TTAATA
1 AAAAAA-ATAATAATAATTTAATA
* *
153896 ATAATAATAATAA
1 AAAAAAATAATAA
153909 AATCTTAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 6 0.19
23 16 0.52
24 9 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAATAATAATAATTTAATA
Found at i:159491 original size:94 final size:94
Alignment explanation
Indices: 159330--159534 Score: 365
Period size: 94 Copynumber: 2.2 Consensus size: 94
159320 TGGAAGCTTA
* *
159330 GCACACGCCCATGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCTATTTGGT
1 GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
*
159395 CATGAGCAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
* *
159424 GCACACGCCCGTGTGCTAAGGACACGCCTGTGTCCCGTGCCCATAGAGCTCTTTGTCCATTTGGT
1 GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
159489 CATGAACAAGTTAGGGTCACATGGCCAAG
66 CATGAACAAGTTAGGGTCACATGGCCAAG
159518 GCACACGCCCGTGTGCT
1 GCACACGCCCGTGTGCT
159535 TAAGCCATAT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 106 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.22
Consensus pattern (94 bp):
GCACACGCCCGTGTGCTAAGGACACGCCCGTGTCCCGTGCCCATAGAGCTCTCTGTCCATTTGGT
CATGAACAAGTTAGGGTCACATGGCCAAG
Found at i:161358 original size:22 final size:22
Alignment explanation
Indices: 161330--161403 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
161320 TGTACCTGTC
*
161330 CACACGGGCCTATTAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
161352 CACACGGGCCTATGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
*
161374 CACACGGGCCTGTGAGGGGTTG
1 CACACGGGCCTATGAGGGGTTG
161396 CACACGGG
1 CACACGGG
161404 TGTGTGGGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (22 bp):
CACACGGGCCTATGAGGGGTTG
Found at i:161452 original size:30 final size:30
Alignment explanation
Indices: 161418--161482 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
161408 TGGGTAAGTA
* *
161418 ACACGGGCATGTGGAAACTAGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
** * *
161448 ACACGGGTGTATGAAAATTGGAGCTATCAC
1 ACACGGGCATATGAAAACTAGAGCTATCAC
161478 ACACG
1 ACACG
161483 AGTGTATGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (30 bp):
ACACGGGCATATGAAAACTAGAGCTATCAC
Found at i:163806 original size:18 final size:18
Alignment explanation
Indices: 163783--163839 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
163773 ACACTAAGAT
163783 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
** *
163801 AAATGCTTC-TAA-AA-T
1 AAATGCAACTTAACAAGC
163816 AAATGCAACTTAACAAGC
1 AAATGCAACTTAACAAGC
163834 AAATGC
1 AAATGC
163840 TTCTAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 5 0.17
18 13 0.43
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATGCAACTTAACAAGC
Found at i:163821 original size:33 final size:33
Alignment explanation
Indices: 163776--163850 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
163766 TTAAATAACA
*
163776 CTAAGATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
163809 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
1 CTAAAATAAATGCAACTTAACAAGCAAATGCTT
163842 CTAAAATAA
1 CTAAAATAA
163851 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.24
Consensus pattern (33 bp):
CTAAAATAAATGCAACTTAACAAGCAAATGCTT
Found at i:163892 original size:30 final size:31
Alignment explanation
Indices: 163833--163893 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
163823 ACTTAACAAG
163833 CAAATGCTTCTAAAATAATAAAAAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAAATTAA
*
163864 CAAATGCCTT-TAAAATAAT-AAGAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAAATTAA
163894 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.36
31 15 0.54
32 3 0.11
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAAAAAAAATTAA
Found at i:164794 original size:19 final size:19
Alignment explanation
Indices: 164770--164817 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
164760 TTCTCTTTTT
164770 TTTCTATTCATTCTATCCA
1 TTTCTATTCATTCTATCCA
*
164789 TTTCTATTCATTCTATTCA
1 TTTCTATTCATTCTATCCA
164808 TTTCTATTCA
1 TTTCTATTCA
164818 AACACACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTCTATTCATTCTATCCA
Found at i:164795 original size:10 final size:10
Alignment explanation
Indices: 164770--164817 Score: 73
Period size: 9 Copynumber: 5.0 Consensus size: 10
164760 TTCTCTTTTT
164770 TTTCTATTCA
1 TTTCTATTCA
*
164780 -TTCTATCCA
1 TTTCTATTCA
164789 TTTCTATTCA
1 TTTCTATTCA
164799 -TTCTATTCA
1 TTTCTATTCA
164808 TTTCTATTCA
1 TTTCTATTCA
164818 AACACACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:167528 original size:39 final size:39
Alignment explanation
Indices: 167482--167660 Score: 286
Period size: 39 Copynumber: 4.6 Consensus size: 39
167472 GCTCTGATGA
* *
167482 GCTTCAGTTAGCCTTCGGGCTTCCGTATAGTACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
167521 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
167560 GCTTCACTTAGCCTTCGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
167599 GCTTCACTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
167638 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
167661 AGATCACGAT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:169692 original size:13 final size:13
Alignment explanation
Indices: 169674--169698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169664 TATTTTAATA
169674 TTATTTTGTGTGT
1 TTATTTTGTGTGT
169687 TTATTTTGTGTG
1 TTATTTTGTGTG
169699 AATTCGATGG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:171440 original size:41 final size:41
Alignment explanation
Indices: 171233--171429 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
171223 TTTATCGTTA
* * * *
171233 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
171274 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
171315 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
171356 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
171397 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
171430 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:171698 original size:33 final size:32
Alignment explanation
Indices: 171643--171705 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
171633 GATAGATATG
171643 TATATATATATGTTGCATTCGGCATAGGTGGA
1 TATATATATATGTTGCATTCGGCATAGGTGGA
* *
171675 TATATTTATGTGTATGCATTCGGCATAGGTG
1 TATATATATATGT-TGCATTCGGCATAGGTG
171706 AAAATAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (32 bp):
TATATATATATGTTGCATTCGGCATAGGTGGA
Found at i:171722 original size:33 final size:33
Alignment explanation
Indices: 171649--171722 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
171639 TATGTATATA
* * **
171649 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
171681 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
171714 TGTATGTAT
1 TATATGTAT
171723 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:176455 original size:30 final size:30
Alignment explanation
Indices: 176421--176481 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
176411 TTCTCGAGAC
176421 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
176451 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
176481 T
1 T
176482 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:188309 original size:21 final size:21
Alignment explanation
Indices: 188283--188325 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
188273 TATCATTATC
188283 TAAATCCTCAAAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
*
188304 TAAATCCTCAGAGAAAGTAAT
1 TAAATCCTCAAAGAAAGTAAT
188325 T
1 T
188326 TGAACCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (21 bp):
TAAATCCTCAAAGAAAGTAAT
Found at i:190476 original size:20 final size:20
Alignment explanation
Indices: 190451--190492 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
190441 TTCTGCTGCC
*
190451 AACTTTTCTAATGTTTTGCA
1 AACTTTTCTAATATTTTGCA
190471 AACTTTTCTAATATTTTGCA
1 AACTTTTCTAATATTTTGCA
190491 AA
1 AA
190493 TTCTTGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (20 bp):
AACTTTTCTAATATTTTGCA
Found at i:197309 original size:51 final size:51
Alignment explanation
Indices: 197233--197334 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
197223 TTGGAGATAG
197233 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
197284 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
1 GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
197335 ACCATATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (51 bp):
GACAGAATCACCTCCCAATATATAGCAGCTATAGCTCAAGTCCAGTGGACC
Found at i:197587 original size:25 final size:25
Alignment explanation
Indices: 197559--197609 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
197549 AGTTTCCAGC
197559 ATGCTGATCTGGGTTGTTTGTTCTT
1 ATGCTGATCTGGGTTGTTTGTTCTT
197584 ATGCTGATCTGGGTTGTTTGTTCTT
1 ATGCTGATCTGGGTTGTTTGTTCTT
197609 A
1 A
197610 GTCCCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.27, T:0.51
Consensus pattern (25 bp):
ATGCTGATCTGGGTTGTTTGTTCTT
Found at i:208847 original size:23 final size:23
Alignment explanation
Indices: 208798--208847 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
208788 GATTTTTTCT
* *
208798 AAATATTATTACTAAATATTCCT
1 AAATATTATCACTAAATATTCCA
*
208821 AAATGTTATCACTAAATAATT-CA
1 AAATATTATCACTAAAT-ATTCCA
208844 AAAT
1 AAAT
208848 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATATTCCA
Found at i:210561 original size:33 final size:33
Alignment explanation
Indices: 210524--210597 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
210514 GAGTCAAATC
*
210524 TAATAGGAAAATTCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
210557 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
1 TAATAGGAAAATCCATAAATCGAGTTAATGTGA
210590 TAATAGGA
1 TAATAGGA
210598 GTTTTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (33 bp):
TAATAGGAAAATCCATAAATCGAGTTAATGTGA
Found at i:211873 original size:15 final size:15
Alignment explanation
Indices: 211850--211884 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
211840 CATTATCCTA
* *
211850 AATATATTATAATTT
1 AATAAATTATAATAT
211865 AATAAATTATAATAT
1 AATAAATTATAATAT
211880 AATAA
1 AATAA
211885 TTAATCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATAATAT
Found at i:212804 original size:14 final size:14
Alignment explanation
Indices: 212767--212809 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
212757 TTAATTCTTA
*
212767 AATATAAAAAATTT
1 AATATAAAATATTT
*
212781 ATTA-ATAAATATTT
1 AATATA-AAATATTT
212795 AATATAAAATATTT
1 AATATAAAATATTT
212809 A
1 A
212810 TCAGTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATAAAATATTT
Found at i:216317 original size:26 final size:27
Alignment explanation
Indices: 216287--216352 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
216277 TTTTTAATGG
*
216287 TGCTCACACGAGCTA-TGAAATGGGTC
1 TGCTCACACGAGCTAGTGAAATGGGCC
*
216313 TGCTCATACGAGC-AGTGAAATGGGCC
1 TGCTCACACGAGCTAGTGAAATGGGCC
216339 TGCTCACACGAGCT
1 TGCTCACACGAGCT
216353 GTAGGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (27 bp):
TGCTCACACGAGCTAGTGAAATGGGCC
Found at i:226682 original size:503 final size:503
Alignment explanation
Indices: 225735--226744 Score: 2020
Period size: 503 Copynumber: 2.0 Consensus size: 503
225725 TCCATTGCTG
225735 GAGACTGATTAACGATCTGCTGCCCCATTTTGGTAATCTGGCACGACGGAAGTTGAGTGTGGATG
1 GAGACTGATTAACGATCTGCTGCCCCATTTTGGTAATCTGGCACGACGGAAGTTGAGTGTGGATG
225800 TTGCTTGCCCTCTGTGTAAGACAGATCTGGAGGATACAGCTCATTTGGTATGGTCTTGTGATACT
66 TTGCTTGCCCTCTGTGTAAGACAGATCTGGAGGATACAGCTCATTTGGTATGGTCTTGTGATACT
225865 CAATAGCGTGTTTGGGCTTCATTACAAGTAAAGGTTCCTCCACTAGAAGCTTCGTTGTGCTGTAA
131 CAATAGCGTGTTTGGGCTTCATTACAAGTAAAGGTTCCTCCACTAGAAGCTTCGTTGTGCTGTAA
225930 GAGGCGTTTTGTTAGAATGTTTCTGCAACAGATGAGCAAACAGAGATGAATCATTACTTTGTCAG
196 GAGGCGTTTTGTTAGAATGTTTCTGCAACAGATGAGCAAACAGAGATGAATCATTACTTTGTCAG
225995 TTTGGGGACTTTGGCATCGCAGAAATAAGCTAATCCACAAAGGGGTCAAATTTTTTATGCAAGAA
261 TTTGGGGACTTTGGCATCGCAGAAATAAGCTAATCCACAAAGGGGTCAAATTTTTTATGCAAGAA
226060 TTTTTAGGGTTTATTCGAGGGTATGAACTAGAGATCTGCCTAAACCAAGAGAATCTCCGTCCTCC
326 TTTTTAGGGTTTATTCGAGGGTATGAACTAGAGATCTGCCTAAACCAAGAGAATCTCCGTCCTCC
226125 CATTAAAATTATGGTGAAGGATCTGTGAAGACCCCCAGATGATGTTATCAAGTTAAACTTTGATG
391 CATTAAAATTATGGTGAAGGATCTGTGAAGACCCCCAGATGATGTTATCAAGTTAAACTTTGATG
226190 CATCCTTCCAAAAAGATGTCAAAATCGCTACAACTGCAGTTATAGTCA
456 CATCCTTCCAAAAAGATGTCAAAATCGCTACAACTGCAGTTATAGTCA
226238 GAGACTGATTAACGATCTGCTGCCCCATTTTGGTAATCTGGCACGACGGAAGTTGAGTGTGGATG
1 GAGACTGATTAACGATCTGCTGCCCCATTTTGGTAATCTGGCACGACGGAAGTTGAGTGTGGATG
226303 TTGCTTGCCCTCTGTGTAAGACAGATCTGGAGGATACAGCTCATTTGGTATGGTCTTGTGATACT
66 TTGCTTGCCCTCTGTGTAAGACAGATCTGGAGGATACAGCTCATTTGGTATGGTCTTGTGATACT
226368 CAATAGCGTGTTTGGGCTTCATTACAAGTAAAGGTTCCTCCACTAGAAGCTTCGTTGTGCTGTAA
131 CAATAGCGTGTTTGGGCTTCATTACAAGTAAAGGTTCCTCCACTAGAAGCTTCGTTGTGCTGTAA
226433 GAGGCGTTTTGTTAGAATGTTTCTGCAACAGATGAGCAAACAGAGATGAATCATTACTTTGTCAG
196 GAGGCGTTTTGTTAGAATGTTTCTGCAACAGATGAGCAAACAGAGATGAATCATTACTTTGTCAG
226498 TTTGGGGACTTTGGCATCGCAGAAATAAGCTAATCCACAAAGGGGTCAAATTTTTTATGCAAGAA
261 TTTGGGGACTTTGGCATCGCAGAAATAAGCTAATCCACAAAGGGGTCAAATTTTTTATGCAAGAA
226563 TTTTTAGGGTTTATTCGAGGGTATGAACTAGAGATCTGCCTAAACCAAGAGAATCTCCGTCCTCC
326 TTTTTAGGGTTTATTCGAGGGTATGAACTAGAGATCTGCCTAAACCAAGAGAATCTCCGTCCTCC
226628 CATTAAAATTATGGTGAAGGATCTGTGAAGACCCCCAGATGATGTTATCAAGTTAAACTTTGATG
391 CATTAAAATTATGGTGAAGGATCTGTGAAGACCCCCAGATGATGTTATCAAGTTAAACTTTGATG
226693 CATCCTTCCAAAAAGATGTCAAAATCGCTACAACTGCAGTTATAGTCA
456 CATCCTTCCAAAAAGATGTCAAAATCGCTACAACTGCAGTTATAGTCA
226741 GAGA
1 GAGA
226745 TTCTACAGGA
Statistics
Matches: 507, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
503 507 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (503 bp):
GAGACTGATTAACGATCTGCTGCCCCATTTTGGTAATCTGGCACGACGGAAGTTGAGTGTGGATG
TTGCTTGCCCTCTGTGTAAGACAGATCTGGAGGATACAGCTCATTTGGTATGGTCTTGTGATACT
CAATAGCGTGTTTGGGCTTCATTACAAGTAAAGGTTCCTCCACTAGAAGCTTCGTTGTGCTGTAA
GAGGCGTTTTGTTAGAATGTTTCTGCAACAGATGAGCAAACAGAGATGAATCATTACTTTGTCAG
TTTGGGGACTTTGGCATCGCAGAAATAAGCTAATCCACAAAGGGGTCAAATTTTTTATGCAAGAA
TTTTTAGGGTTTATTCGAGGGTATGAACTAGAGATCTGCCTAAACCAAGAGAATCTCCGTCCTCC
CATTAAAATTATGGTGAAGGATCTGTGAAGACCCCCAGATGATGTTATCAAGTTAAACTTTGATG
CATCCTTCCAAAAAGATGTCAAAATCGCTACAACTGCAGTTATAGTCA
Found at i:227578 original size:18 final size:17
Alignment explanation
Indices: 227547--227582 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
227537 AGGCCTTCCT
227547 TTTATATAATAGTAGTA
1 TTTATATAATAGTAGTA
227564 TTTATATATATAGTAGTA
1 TTTATATA-ATAGTAGTA
227582 T
1 T
227583 AGATACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATATAATAGTAGTA
Found at i:227775 original size:28 final size:28
Alignment explanation
Indices: 227713--227777 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
227703 TCATATACAT
*
227713 AAGTAAATTATATAAAATATTCAAAAAA
1 AAGTAAATTATATAAAAAATTCAAAAAA
* *
227741 AAGTAAATTATATAAAAGAATTCACATAA
1 AAGTAAATTATATAAAA-AATTCAAAAAA
227770 AA-TAAATT
1 AAGTAAATT
227778 CAACAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (28 bp):
AAGTAAATTATATAAAAAATTCAAAAAA
Found at i:228463 original size:164 final size:169
Alignment explanation
Indices: 228191--228527 Score: 576
Period size: 164 Copynumber: 2.0 Consensus size: 169
228181 ATAGTCTACC
* *
228191 ATCAATCTCTTTTGTCTCCTCTATCTTCTAATCTCTTCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
*
228256 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTGCCATTGTTGTGTCG-C-CA-AA-TTTCAA
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
228317 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
131 TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
228356 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATC-CTCCCCATCCAGATTCTGTCATGCCAAAATT
1 ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
228420 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCAAATCACAACTTT
66 CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCC--A-CACAACTTT
*
228485 CAATCTTATGTCGCCAAAACTAGAAACACATATTGCAACCTA
128 CAATCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
228527 A
1 A
228528 CTGCTTGTGA
Statistics
Matches: 161, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
164 79 0.49
165 33 0.20
169 2 0.01
170 2 0.01
171 45 0.28
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (169 bp):
ATCAATCTCTTTTGTCTCCTCTATCTTCCAATCTCTCCCCATCCAGATTCTGTCATGCCAAAATT
CAAAACCACAACTTCCAATCTATGCCCTCGTGTCTACCATTGTTGTGTCGCCACACAACTTTCAA
TCTTATGTCGCCAAAACTAAAAACACATATTGCAACCTA
Found at i:228914 original size:9 final size:9
Alignment explanation
Indices: 228895--228938 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
228885 ACTCTAGAAG
228895 TTTTCTCTTC
1 TTTT-TCTTC
228905 TTTTTCTTC
1 TTTTTCTTC
*
228914 TTCTTCTTC
1 TTTTTCTTC
*
228923 -TTTGCTTC
1 TTTTTCTTC
228931 TTTTTCTT
1 TTTTTCTT
228939 TTACTGTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 6 0.21
9 19 0.66
10 4 0.14
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:229318 original size:22 final size:22
Alignment explanation
Indices: 229274--229319 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
229264 ACCGTGGGAC
** * *
229274 AATCCAAAAAATCAAGAATGAA
1 AATCCAAAAAAGAAAAAAAGAA
229296 AATCCAAAAAAGAAAAAAAGAA
1 AATCCAAAAAAGAAAAAAAGAA
229318 AA
1 AA
229320 GAAAAGAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.72, C:0.11, G:0.09, T:0.09
Consensus pattern (22 bp):
AATCCAAAAAAGAAAAAAAGAA
Found at i:233454 original size:28 final size:28
Alignment explanation
Indices: 233414--233471 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
233404 AGGCCAACAG
233414 ATAACACTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
*
233442 ATAACCCTTCTATTGCAGCATGATTCTT
1 ATAACACTTCTATTGCAGCATGATTCTT
233470 AT
1 AT
233472 CCAAAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (28 bp):
ATAACACTTCTATTGCAGCATGATTCTT
Found at i:244672 original size:134 final size:133
Alignment explanation
Indices: 244412--244735 Score: 436
Period size: 134 Copynumber: 2.4 Consensus size: 133
244402 CATTCTAACA
* * * *
244412 GCTCATTGATTTACGATCACAACCTAAGTTTATTGATTTATGATCATGAATAATTTCTTTAAGTT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
* * *
244477 AGCTGATTTACGATTGCAACTCCATTTTAACAACTCACTGATTTACGATCACGATTGATATTATT
66 AGCTGATTTACGATTGCAACTCCATTCTAACAACTCAATGATTTACAATCACGATTGATATTATT
244542 AAG
131 AAG
* * * * *
244545 GCTTATTGATTTATGATCATAGCCTAAGTTCATTGATTTACGATCACGAACAATTTCTTTTGAGT
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC-TTTAAGT
* *** *
244610 TAGCTGATTTATGATTGCAACTCCATTCTAATTGC-CTAATGATTTACAATGAC-ATTTGATATT
65 TAGCTGATTTACGATTGCAACTCCATTCTAACAACTC-AATGATTTACAATCACGA-TTGATATT
244673 ATTAAG
128 ATTAAG
* *
244679 GCTCACTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACGATTTC
1 GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTC
244736 ATCTGTTAAA
Statistics
Matches: 165, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
133 51 0.31
134 114 0.69
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (133 bp):
GCTCATTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTTAAGTT
AGCTGATTTACGATTGCAACTCCATTCTAACAACTCAATGATTTACAATCACGATTGATATTATT
AAG
Found at i:244890 original size:19 final size:20
Alignment explanation
Indices: 244854--244896 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
244844 AATTAAATTT
*
244854 TTTTCAATTGAGTTAAAC-A
1 TTTTCAATTCAGTTAAACTA
244873 TTTTCAA-TCAGTTAAAACTA
1 TTTTCAATTCAGTT-AAACTA
244893 TTTT
1 TTTT
244897 TAAACAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTCAATTCAGTTAAACTA
Found at i:245049 original size:21 final size:21
Alignment explanation
Indices: 245023--245062 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
245013 CAATCAACAT
*
245023 AAAAAGTATTGATACCTTTCC
1 AAAAAGTATCGATACCTTTCC
*
245044 AAAAAGTCTCGATACCTTT
1 AAAAAGTATCGATACCTTT
245063 TAGCAGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGTATCGATACCTTTCC
Found at i:257415 original size:48 final size:48
Alignment explanation
Indices: 257360--257461 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
257350 TTCAAGAGGG
* *
257360 GATAAATAGTGATAATAGTATAGACAGTGGAAAACCAAATTTAACAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
* * * *
257408 GATAAATAGTGATGAGAGTGTAGACAGTGGAAGACCAAGTTTAAAAAT
1 GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
257456 GCATAA
1 G-ATAA
257462 CATAATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 43 0.91
49 4 0.09
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.24
Consensus pattern (48 bp):
GATAAATAGTGATAAGAGTATAGACAGTGGAAAACCAAATTTAAAAAT
Found at i:261054 original size:3 final size:3
Alignment explanation
Indices: 261046--261077 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
261036 TGTTGTATCT
261046 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
261078 TTTTATAAAA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:272121 original size:14 final size:14
Alignment explanation
Indices: 272104--272133 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
272094 ATTCAACTAA
*
272104 ACTAAAATGATTAT
1 ACTAAAATGATCAT
272118 ACTAAAATGATCAT
1 ACTAAAATGATCAT
272132 AC
1 AC
272134 ATACTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
ACTAAAATGATCAT
Found at i:272510 original size:12 final size:11
Alignment explanation
Indices: 272491--272523 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
272481 ATTTACCTAC
272491 TGAAAAAAATT
1 TGAAAAAAATT
272502 TGAAAAAAATT
1 TGAAAAAAATT
272513 TGAAAAAAATT
1 TGAAAAAAATT
272524 CTTAGGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (11 bp):
TGAAAAAAATT
Found at i:282239 original size:52 final size:52
Alignment explanation
Indices: 282177--282279 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
282167 TGCTGGTTAG
*
282177 TTGTTTTCTATGCATTAAAAATATTCCAACTTTGTCTATTTTCGCTTCTATA
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
282229 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
1 TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTAT
282280 GTCAATGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (52 bp):
TTGTTTTCTATGCATTAAAAATATCCCAACTTTGTCTATTTTCGCTTCTATA
Found at i:286756 original size:21 final size:21
Alignment explanation
Indices: 286732--286786 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
286722 ATTTTACTTT
* * *
286732 TAAAATTTTTAATAGTATTTA
1 TAAAATTTTAAAAAGTATATA
*
286753 TAAAAATTTAAAAAGTATATA
1 TAAAATTTTAAAAAGTATATA
286774 -AAAATTTTAAAAA
1 TAAAATTTTAAAAA
286787 ATTAAATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATTTTAAAAAGTATATA
Found at i:288609 original size:26 final size:25
Alignment explanation
Indices: 288580--288666 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
288570 ATCTGGGAAG
*
288580 CCTTTCTGGCTAATCTTGTGGAAAAA
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
*
288606 CCTTTGTGG-TGAATTCTCTGGAAAAA
1 CCTTTGTGGCT-AATT-TGTGGAAAAA
* * *
288632 CCTATGTGACTAATATTGTGG-AAAG
1 CCTTTGTGGCTAAT-TTGTGGAAAAA
288657 CCTTTGTGGC
1 CCTTTGTGGC
288667 ATGTTATTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
25 13 0.27
26 34 0.69
27 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (25 bp):
CCTTTGTGGCTAATTTGTGGAAAAA
Found at i:291775 original size:24 final size:21
Alignment explanation
Indices: 291716--291775 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
291706 GGATCAAAAT
291716 TAAATTATAATTTTTACTATAA
1 TAAATTAT-ATTTTTACTATAA
* * *
291738 AAAAATATAATTTTACTATTTTAA
1 TAAATTATATTTTTACTA---TAA
291762 TAAATTATATTTTT
1 TAAATTATATTTTT
291776 TAAAAGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 9 0.31
22 6 0.21
24 14 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATTATATTTTTACTATAA
Found at i:304536 original size:84 final size:84
Alignment explanation
Indices: 304390--304559 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
304380 TGAGGGAGGT
*
304390 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCTCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
304455 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
*
304474 AGTTTACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
1 AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
304539 GGAGAGATCTCAGTTAAAC
66 GGAGAGATCTCAGTTAAAC
304558 AG
1 AG
304560 GGGTGTGCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (84 bp):
AGTTCACTCTCATTCCCTAATTAAATCCTGCCCTGCTCTCCCCTAGATTGACTTGACATATCTTG
GGAGAGATCTCAGTTAAAC
Found at i:308501 original size:16 final size:15
Alignment explanation
Indices: 308476--308508 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
308466 ATTCGGTTAC
308476 TTTTTTTTGTTATTT
1 TTTTTTTTGTTATTT
308491 TTTTTTCTTGTTATTT
1 TTTTTT-TTGTTATTT
308507 TT
1 TT
308509 CACTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTTTTGTTATTT
Done.