Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 1 of 216
Found at i:31 original size:7 final size:7
Alignment explanation
Indices: 19--2583 Score: 3237
Period size: 7 Copynumber: 363.1 Consensus size: 7
9 CCTAACCTTA
19 AAACCCT
1 AAACCCT
26 AAACCCT
1 AAACCCT
33 AAACCCT
1 AAACCCT
40 -AA-CCT
1 AAACCCT
45 -AACCCT
1 AAACCCT
51 AAACCCT
1 AAACCCT
58 AAACCCT
1 AAACCCT
65 AAACCCT
1 AAACCCT
72 AAACCCT
1 AAACCCT
79 AAACCCT
1 AAACCCT
86 AAAACCCT
1 -AAACCCT
94 AAACCCT
1 AAACCCT
101 AAACCCT
1 AAACCCT
108 AAACCCT
1 AAACCCT
115 AAACCCT
1 AAACCCT
122 -AACCCT
1 AAACCCT
128 AAACCCT
1 AAACCCT
135 AAACCCT
1 AAACCCT
142 AAACCCT
1 AAACCCT
149 AAAACCCT
1 -AAACCCT
157 AAACCCT
1 AAACCCT
164 AAACCCT
1 AAACCCT
171 AAACCCT
1 AAACCCT
178 AAACCCT
1 AAACCCT
185 AAACCCT
1 AAACCCT
192 AAACCCT
1 AAACCCT
199 AAACCCT
1 AAACCCT
206 AAAACCCT
1 -AAACCCT
214 AAA-CCT
1 AAACCCT
*
220 AAACCCC
1 AAACCCT
227 AAACCCTT
1 AAACCC-T
235 AAACCCT
1 AAACCCT
242 -AACCC-
1 AAACCCT
247 AAACCCT
1 AAACCCT
254 -AACCCT
1 AAACCCT
260 AAACCCT
1 AAACCCT
267 AAACCCT
1 AAACCCT
274 AAACCCT
1 AAACCCT
281 AAAACCCT
1 -AAACCCT
289 -AACCCT
1 AAACCCT
295 AAACCCT
1 AAACCCT
302 AAACCCT
1 AAACCCT
309 AAACCCT
1 AAACCCT
316 AAACCCT
1 AAACCCT
323 AAAAACCCT
1 --AAACCCT
332 AAACCCT
1 AAACCCT
339 AAACCCT
1 AAACCCT
346 AAACCCT
1 AAACCCT
353 AAAACCCT
1 -AAACCCT
361 AAA-CCT
1 AAACCCT
367 AAACCCT
1 AAACCCT
374 AAACCCT
1 AAACCCT
381 AAAACCCT
1 -AAACCCT
389 AAAACCCT
1 -AAACCCT
397 AAACCCT
1 AAACCCT
404 AAAACCCT
1 -AAACCCT
412 AAACCCT
1 AAACCCT
419 AAACCCT
1 AAACCCT
426 AAACCCT
1 AAACCCT
433 AAACCCT
1 AAACCCT
440 AAACCCT
1 AAACCCT
447 AAACCCT
1 AAACCCT
454 AAACCCT
1 AAACCCT
461 AAACCCT
1 AAACCCT
468 AAACCCT
1 AAACCCT
475 AAACCCT
1 AAACCCT
482 AAACCCT
1 AAACCCT
489 AAACCCT
1 AAACCCT
496 AAACCCT
1 AAACCCT
503 AAACCCT
1 AAACCCT
510 AAACCCT
1 AAACCCT
517 AAACCCT
1 AAACCCT
524 AAACCCT
1 AAACCCT
531 AAACCCT
1 AAACCCT
538 AAACCCT
1 AAACCCT
545 AAACCCT
1 AAACCCT
552 AAACCCT
1 AAACCCT
559 AAACCCT
1 AAACCCT
566 AAACCCT
1 AAACCCT
573 AAACCCT
1 AAACCCT
580 AAACCCT
1 AAACCCT
587 -AACCC-
1 AAACCCT
592 -AACCCT
1 AAACCCT
598 AAACCCT
1 AAACCCT
605 AAACCCT
1 AAACCCT
612 AAACCCT
1 AAACCCT
619 AAACCCT
1 AAACCCT
626 AAACCCT
1 AAACCCT
633 AAACCCT
1 AAACCCT
640 AAACCCT
1 AAACCCT
647 AAA-CCT
1 AAACCCT
653 AAACCCT
1 AAACCCT
660 AAACCCT
1 AAACCCT
667 AAACCCT
1 AAACCCT
674 AAAACCCT
1 -AAACCCT
682 AAACCCT
1 AAACCCT
689 AAACCCT
1 AAACCCT
696 AAACCCT
1 AAACCCT
703 AAACCCT
1 AAACCCT
710 AAACCCT
1 AAACCCT
717 AAACCCT
1 AAACCCT
724 AAACCCT
1 AAACCCT
731 AAACCCT
1 AAACCCT
738 AAACCCT
1 AAACCCT
745 AAACCCT
1 AAACCCT
752 AAAACCCT
1 -AAACCCT
760 AAACCCT
1 AAACCCT
767 AAACCCT
1 AAACCCT
774 AAACCCT
1 AAACCCT
781 AAACCCT
1 AAACCCT
788 AAACCCT
1 AAACCCT
795 AAACCCT
1 AAACCCT
*
802 -AACCCC
1 AAACCCT
*
808 AAACCCCA
1 AAA-CCCT
816 AAACCCT
1 AAACCCT
823 AAACCCT
1 AAACCCT
830 AAACCCT
1 AAACCCT
837 AAACCCT
1 AAACCCT
844 AAACCCT
1 AAACCCT
851 AAACCCT
1 AAACCCT
858 AAACCCT
1 AAACCCT
865 AAACCCT
1 AAACCCT
872 AAACCCT
1 AAACCCT
879 AAACCCT
1 AAACCCT
886 AAACCCT
1 AAACCCT
893 AAACCCT
1 AAACCCT
900 AAACCCT
1 AAACCCT
907 AAACCCT
1 AAACCCT
914 AAACCCT
1 AAACCCT
921 AAACCCT
1 AAACCCT
928 AAACCCT
1 AAACCCT
935 AAACCCT
1 AAACCCT
942 AAACCC-
1 AAACCCT
948 AAACCCT
1 AAACCCT
955 AAACCCT
1 AAACCCT
962 AAACCCT
1 AAACCCT
969 AAACCCT
1 AAACCCT
976 AAACCCT
1 AAACCCT
983 AAACCCT
1 AAACCCT
* *
990 -AACACA
1 AAACCCT
996 AAACCCT
1 AAACCCT
1003 AAACCCT
1 AAACCCT
*
1010 AAACCCA
1 AAACCCT
1017 AAACCCT
1 AAACCCT
1024 AAACCCT
1 AAACCCT
1031 AAACCCT
1 AAACCCT
1038 -AA-CCT
1 AAACCCT
1043 AAACCCT
1 AAACCCT
1050 -AACCCT
1 AAACCCT
1056 AAACCCT
1 AAACCCT
1063 AAACCCT
1 AAACCCT
1070 AAACCCT
1 AAACCCT
1077 AAACCCT
1 AAACCCT
1084 AAACCCT
1 AAACCCT
1091 AAACCCT
1 AAACCCT
1098 AAAACCCT
1 -AAACCCT
1106 AAACCCT
1 AAACCCT
1113 AAACCCT
1 AAACCCT
1120 AAACCCT
1 AAACCCT
1127 AAACCCT
1 AAACCCT
1134 AAACCCT
1 AAACCCT
1141 AAACCCT
1 AAACCCT
1148 AAACCCT
1 AAACCCT
1155 AAACCCT
1 AAACCCT
1162 AAACCCT
1 AAACCCT
1169 AAACCCT
1 AAACCCT
1176 AAACCCCT
1 AAA-CCCT
1184 AAACCCT
1 AAACCCT
1191 AAACCCT
1 AAACCCT
1198 AAACCCT
1 AAACCCT
1205 AAAACCCT
1 -AAACCCT
1213 AAACCCT
1 AAACCCT
1220 AAACCCT
1 AAACCCT
1227 AAACCCT
1 AAACCCT
1234 AAACCCT
1 AAACCCT
1241 AAACCCT
1 AAACCCT
1248 AAACCCT
1 AAACCCT
1255 AAACCCT
1 AAACCCT
1262 AAACCCT
1 AAACCCT
1269 AAACCCT
1 AAACCCT
1276 AAACCCT
1 AAACCCT
1283 AAACCCT
1 AAACCCT
1290 AAAACCCT
1 -AAACCCT
1298 AAACCCT
1 AAACCCT
1305 AAACCCT
1 AAACCCT
1312 AAACCCT
1 AAACCCT
1319 AAACCCT
1 AAACCCT
1326 AAAACCCT
1 -AAACCCT
*
1334 AAACACT
1 AAACCCT
1341 AAACCCT
1 AAACCCT
1348 AAACCCT
1 AAACCCT
*
1355 AACCCCT
1 AAACCCT
*
1362 AACCCCT
1 AAACCCT
1369 AAAACCCT
1 -AAACCCT
1377 AAAACCCT
1 -AAACCCT
1385 AAACCCT
1 AAACCCT
1392 AAAACCCT
1 -AAACCCT
1400 AAACCCT
1 AAACCCT
1407 AAAACCC-
1 -AAACCCT
*
1414 AAACCCC
1 AAACCCT
*
1421 AAACCCC
1 AAACCCT
*
1428 AAACCCC
1 AAACCCT
*
1435 AAACCCC
1 AAACCCT
1442 AAACCC-
1 AAACCCT
*
1448 AAACCCC
1 AAACCCT
*
1455 AAACCCC
1 AAACCCT
*
1462 AAACCCC
1 AAACCCT
*
1469 AAACCCC
1 AAACCCT
*
1476 AAACCCC
1 AAACCCT
*
1483 AAACCCC
1 AAACCCT
*
1490 AAACCCC
1 AAACCCT
1497 AAACCC-
1 AAACCCT
*
1503 AAACCCC
1 AAACCCT
*
1510 AAACCCCA
1 AAA-CCCT
1518 AAACCC-
1 AAACCCT
1524 AAACCCT
1 AAACCCT
1531 AAACCCT
1 AAACCCT
1538 AAACCCT
1 AAACCCT
1545 AAACCCT
1 AAACCCT
1552 AAACCCT
1 AAACCCT
1559 AAAACCCT
1 -AAACCCT
*
1567 GGAA-CCT
1 -AAACCCT
1574 AAACCCT
1 AAACCCT
1581 AAACCCT
1 AAACCCT
*
1588 AGACCCT
1 AAACCCT
*
1595 GGAACCCT
1 -AAACCCT
*
1603 -GACCCT
1 AAACCCT
*
1609 AGACCCT
1 AAACCCT
*
1616 AGA-CCT
1 AAACCCT
*
1622 -AGCCCT
1 AAACCCT
1628 AAAACCCT
1 -AAACCCT
1636 AAACCCT
1 AAACCCT
1643 AAACCCT
1 AAACCCT
1650 AAAACCCT
1 -AAACCCT
1658 -AACCCT
1 AAACCCT
1664 AAACCCT
1 AAACCCT
1671 AAACCCT
1 AAACCCT
1678 AAACCCT
1 AAACCCT
1685 AAAACCCT
1 -AAACCCT
1693 AAAACCCT
1 -AAACCCT
1701 AAAACCCT
1 -AAACCCT
1709 AAACCCT
1 AAACCCT
1716 AAACCCT
1 AAACCCT
1723 AAAACCCT
1 -AAACCCT
1731 AAACCCCT
1 AAA-CCCT
1739 AAA-CCT
1 AAACCCT
*
1745 GAACCCT
1 AAACCCT
*
1752 GAACCCT
1 AAACCCT
1759 AAAACCCT
1 -AAACCCT
1767 AAACCCT
1 AAACCCT
1774 AAACCCT
1 AAACCCT
1781 AAACCCT
1 AAACCCT
1788 AAACCCT
1 AAACCCT
1795 AAACCCT
1 AAACCCT
1802 AAACCCT
1 AAACCCT
*
1809 AACCCCT
1 AAACCCT
1816 AAACCCT
1 AAACCCT
1823 AAACCCT
1 AAACCCT
1830 AAACCCCT
1 AAA-CCCT
*
1838 AACCCCT
1 AAACCCT
*
1845 AACCCCT
1 AAACCCT
1852 AAACCCT
1 AAACCCT
1859 AAACCCT
1 AAACCCT
1866 AAAACCCT
1 -AAACCCT
1874 AAACCCT
1 AAACCCT
1881 AAAACCCT
1 -AAACCCT
1889 AAAACCCT
1 -AAACCCT
1897 AAAACCCT
1 -AAACCCT
1905 AAAACCCT
1 -AAACCCT
1913 AAAACCC-
1 -AAACCCT
*
1920 AAACCCC
1 AAACCCT
*
1927 AAACCCC
1 AAACCCT
*
1934 AAACCCC
1 AAACCCT
*
1941 AAACCCC
1 AAACCCT
*
1948 AAACCCC
1 AAACCCT
1955 AAACCC-
1 AAACCCT
*
1961 AAACCCCCC
1 AAA--CCCT
*
1970 AAACCCC
1 AAACCCT
*
1977 AAACCCC
1 AAACCCT
*
1984 AAACCCC
1 AAACCCT
*
1991 AAACCCC
1 AAACCCT
*
1998 AAACCCC
1 AAACCCT
*
2005 AAACCCC
1 AAACCCT
2012 AAACCC-
1 AAACCCT
*
2018 AAACCCC
1 AAACCCT
*
2025 AAACCCC
1 AAACCCT
2032 AAACCC-
1 AAACCCT
2038 AAACCC-
1 AAACCCT
*
2044 AAACCCC
1 AAACCCT
*
2051 AAACCCC
1 AAACCCT
*
2058 AAACCCC
1 AAACCCT
*
2065 AAACCCC
1 AAACCCT
*
2072 AAACCCC
1 AAACCCT
*
2079 AAACCCC
1 AAACCCT
*
2086 AAACCCC
1 AAACCCT
2093 AAACCCT
1 AAACCCT
2100 AAACCCT
1 AAACCCT
2107 AAACCCT
1 AAACCCT
2114 AAACCCT
1 AAACCCT
*
2121 AAACCTT
1 AAACCCT
2128 AAAACCCT
1 -AAACCCT
*
2136 GGAA-CCT
1 -AAACCCT
2143 AAACCCT
1 AAACCCT
2150 AAACCCT
1 AAACCCT
*
2157 AGACCCT
1 AAACCCT
*
2164 GGAACCCT
1 -AAACCCT
*
2172 AGACCCT
1 AAACCCT
*
2179 AGACCCT
1 AAACCCT
*
2186 AGACCCT
1 AAACCCT
*
2193 AGACCCT
1 AAACCCT
2200 AAAACCCT
1 -AAACCCT
2208 AAAACCCT
1 -AAACCCT
2216 AAAACCCT
1 -AAACCCT
2224 AAAACCCT
1 -AAACCCT
2232 AAAACCCT
1 -AAACCCT
2240 AAACCCT
1 AAACCCT
2247 AAACCCCT
1 AAA-CCCT
2255 AAACCCCT
1 AAA-CCCT
2263 AAA-CCT
1 AAACCCT
*
2269 GAACCCT
1 AAACCCT
*
2276 GAACCCT
1 AAACCCT
*
2283 GAACCCT
1 AAACCCT
*
2290 GAACCCT
1 AAACCCT
*
2297 GAACCCT
1 AAACCCT
*
2304 GAACCCT
1 AAACCCT
* *
2311 GAACCCC
1 AAACCCT
* *
2318 AGACCCC
1 AAACCCT
* *
2325 AGACCCC
1 AAACCCT
* *
2332 AGACCCC
1 AAACCCT
* *
2339 AGACCCC
1 AAACCCT
*
2346 AGACCC-
1 AAACCCT
* *
2352 AGACCCC
1 AAACCCT
* *
2359 AGACCCC
1 AAACCCT
* *
2366 AGACCCC
1 AAACCCT
*
2373 AGACCCAT
1 AAACCC-T
*
2381 AAACCCC
1 AAACCCT
2388 AAACCCT
1 AAACCCT
2395 AAAACCCT
1 -AAACCCT
2403 AAAACCCCT
1 -AAA-CCCT
*
2412 AACCCCT
1 AAACCCT
* *
2419 AACCCCC
1 AAACCCT
2426 AAACCC-
1 AAACCCT
* *
2432 AAGCCCC
1 AAACCCT
*
2439 AAGCCCT
1 AAACCCT
*
2446 AAACCCC
1 AAACCCT
*
2453 AAACCCCC
1 AAA-CCCT
* *
2461 AAGCCCC
1 AAACCCT
* *
2468 AGACCCC
1 AAACCCT
*
2475 AAACCCC
1 AAACCCT
*
2482 AAACCCC
1 AAACCCT
** *
2489 AGTCCCC
1 AAACCCT
* *
2496 AGACCCC
1 AAACCCT
*
2503 AAACCCC
1 AAACCCT
** *
2510 AGGCCCC
1 AAACCCT
* *
2517 AGACCCC
1 AAACCCT
2524 AAACCCT
1 AAACCCT
2531 AAACCCTT
1 AAACCC-T
* *
2539 AAAGCAT
1 AAACCCT
*
2546 AATCCCCT
1 AA-ACCCT
*
2554 AACCCCT
1 AAACCCT
2561 AAACCCT
1 AAACCCT
*
2568 AAAACCCC
1 -AAACCCT
2576 AAACCCT
1 AAACCCT
2583 A
1 A
2584 CATCCTAAAT
Statistics
Matches: 2396, Mismatches: 80, Indels: 164
0.91 0.03 0.06
Matches are distributed among these distances:
5 13 0.01
6 174 0.07
7 1816 0.76
8 379 0.16
9 14 0.01
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (7 bp):
AAACCCT
Found at i:2581 original size:15 final size:16
Alignment explanation
Indices: 2554--2583 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2544 ATAATCCCCT
2554 AACCCCTAAACCCTAA
1 AACCCCTAAACCCTAA
2570 AACCCC-AAACCCTA
1 AACCCCTAAACCCTA
2584 CATCCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.47, G:0.00, T:0.10
Consensus pattern (16 bp):
AACCCCTAAACCCTAA
Found at i:3300 original size:32 final size:32
Alignment explanation
Indices: 3235--3305 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
3225 ATCCTTCGAG
*
3235 TGGGATAAATCTAAACCGGGATAACCGCCGAA
1 TGGGATAAATCTAAACCGGGATAACCGCAGAA
*
3267 TGGGATAAATCTAAACCGGGAT-ATCGACAGAA
1 TGGGATAAATCTAAACCGGGATAACCG-CAGAA
3299 TGGGATA
1 TGGGATA
3306 TCCCTACCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (32 bp):
TGGGATAAATCTAAACCGGGATAACCGCAGAA
Found at i:4343 original size:2 final size:2
Alignment explanation
Indices: 4338--4373 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4328 AAAGGATACT
4338 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4374 CGGCGAACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9717 original size:20 final size:19
Alignment explanation
Indices: 9692--9731 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9682 AACCTTAAAA
9692 TTTTAAA-TTATATTAAATTT
1 TTTTAAACTTAT-TT-AATTT
9712 TTTTAAACTTATTTAATTT
1 TTTTAAACTTATTTAATTT
9731 T
1 T
9732 AAAACAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAACTTATTTAATTT
Found at i:9724 original size:19 final size:20
Alignment explanation
Indices: 9692--9731 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9682 AACCTTAAAA
*
9692 TTTTAAATTATATTAAATTT
1 TTTTAAACTATATTAAATTT
*
9712 TTTTAAACT-TATTTAATTT
1 TTTTAAACTATATTAAATTT
9731 T
1 T
9732 AAAACAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAACTATATTAAATTT
Found at i:13938 original size:16 final size:16
Alignment explanation
Indices: 13918--13962 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
13908 ACCATTGAGC
13918 CGGGATACCCTAAGAA
1 CGGGATACCCTAAGAA
* *
13934 TGGGATATCCTAAGAA
1 CGGGATACCCTAAGAA
13950 CGGGATATCCCTA
1 CGGGATA-CCCTA
13963 TCCGGGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (16 bp):
CGGGATACCCTAAGAA
Found at i:18227 original size:3 final size:3
Alignment explanation
Indices: 18219--18255 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
18209 TAATCTATTG
* *
18219 TCT TCT TCT TCT TCT TCT TCT TCT TAT TCT TAT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
18256 TATAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:18813 original size:15 final size:15
Alignment explanation
Indices: 18760--18813 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
18750 ACCAACCCCG
18760 GGATATCCTTGGAATC
1 GGATATCC-TGGAATC
** *
18776 GGATATCCCCGAACC
1 GGATATCCTGGAATC
* *
18791 GGACATCCTGGAATG
1 GGATATCCTGGAATC
18806 GGATATCC
1 GGATATCC
18814 CAGATCGGCA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
15 21 0.72
16 8 0.28
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (15 bp):
GGATATCCTGGAATC
Found at i:19947 original size:47 final size:47
Alignment explanation
Indices: 19878--19976 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
19868 TTCAATACAG
* *
19878 TTACATTCAATATCTTTACCTGATTCAAAC-CACCTAATCAAGCTTTA
1 TTACATACAATATCTCTACCTGATTC-AACTCACCTAATCAAGCTTTA
*
19925 TTACATACAATATCTCTACCTGATTCAGCTCACCTAATCAAGCTTTA
1 TTACATACAATATCTCTACCTGATTCAACTCACCTAATCAAGCTTTA
19972 -TACAT
1 TTACAT
19977 TAGGTCTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
46 7 0.15
47 41 0.85
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.35
Consensus pattern (47 bp):
TTACATACAATATCTCTACCTGATTCAACTCACCTAATCAAGCTTTA
Found at i:21841 original size:23 final size:23
Alignment explanation
Indices: 21815--22104 Score: 180
Period size: 23 Copynumber: 12.7 Consensus size: 23
21805 TTGTACACCA
*
21815 CAATTTGCAGCACTTAAACACTT
1 CAATTTACAGCACTTAAACACTT
* * * * *
21838 CAATTTACATCATTTGAGCACCT
1 CAATTTACAGCACTTAAACACTT
*
21861 CAATTTACAGCAATTAAACACTT
1 CAATTTACAGCACTTAAACACTT
* *
21884 CAATTTACAGCATTTAAACACCT
1 CAATTTACAGCACTTAAACACTT
* * * *
21907 CAACTTACAACACTTTAACA-TCC
1 CAATTTACAGCACTTAAACACT-T
* * * * *
21930 CAATTAACAACATTTATACACCT
1 CAATTTACAGCACTTAAACACTT
21953 CAA-TTACAGCGA--TAAACA-TCT
1 CAATTTACAGC-ACTTAAACACT-T
* * *
21974 CAATTTCCAACAAC-TAAACAATT
1 CAATTTACAGC-ACTTAAACACTT
* *
21997 CAATTTGCAGTACTTAAAACACTT
1 CAATTTACAGCACTT-AAACACTT
* *
22021 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCACTTAAACACTT
*
22044 CAATTTGCAGCACGTT-AACACTT
1 CAATTTACAGCAC-TTAAACACTT
* * * **
22067 AAATTCACAGCATTTAAATTCTT
1 CAATTTACAGCACTTAAACACTT
* *
22090 CAATTTGCAACACTT
1 CAATTTACAGCACTT
22105 GAATAGGGCT
Statistics
Matches: 201, Mismatches: 55, Indels: 22
0.72 0.20 0.08
Matches are distributed among these distances:
21 9 0.04
22 15 0.07
23 156 0.78
24 21 0.10
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (23 bp):
CAATTTACAGCACTTAAACACTT
Found at i:21851 original size:46 final size:46
Alignment explanation
Indices: 21809--22084 Score: 240
Period size: 46 Copynumber: 6.0 Consensus size: 46
21799 ACTCATTTGT
* * * *
21809 ACACCACAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGA
1 ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAACATTTAA
* * *
21855 GCACCTCAATTTACAGCAATTAAACACTTCAATTTACAGCATTTAA
1 ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAACATTTAA
* * * * * *
21901 ACACCTCAACTTACAACACTTTAACA-TCCCAATTAACAACATTTAT
1 ACACCTCAATTTACAGCACTTAAACACT-TCAATTTACAACATTTAA
* **
21947 ACACCTCAA-TTACAGCGA--TAAACA-TCTCAATTTCCAACAACTAA
1 ACACCTCAATTTACAGC-ACTTAAACACT-TCAATTTACAACATTTAA
** * *
21991 ACAATTCAATTTGCAGTACTTAAAACACTTCAATTTACAACATTTAA
1 ACACCTCAATTTACAGCACTT-AAACACTTCAATTTACAACATTTAA
* * * * *
22038 ACACTTCAATTTGCAGCACGTT-AACACTTAAATTCACAGCATTTAA
1 ACACCTCAATTTACAGCAC-TTAAACACTTCAATTTACAACATTTAA
22084 A
1 A
22085 TTCTTCAATT
Statistics
Matches: 187, Mismatches: 35, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
44 27 0.14
45 12 0.06
46 108 0.58
47 37 0.20
48 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.29
Consensus pattern (46 bp):
ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAACATTTAA
Found at i:33785 original size:40 final size:40
Alignment explanation
Indices: 33730--33813 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
33720 CTACGTGCGT
33730 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
33770 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
33810 CACA
1 CACA
33814 GATGCAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (40 bp):
CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:35116 original size:15 final size:15
Alignment explanation
Indices: 35093--35128 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
35083 CTTTTATTCC
*
35093 TTTCCTTACACTGTA
1 TTTCTTTACACTGTA
*
35108 TTTCTTTACACTTTA
1 TTTCTTTACACTGTA
35123 TTTCTT
1 TTTCTT
35129 CCTCCTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTCTTTACACTGTA
Found at i:37751 original size:22 final size:23
Alignment explanation
Indices: 37725--37767 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
37715 ATTTAGAATT
*
37725 TAAAC-TAAAATGATAAATTTTG
1 TAAACATAAAAGGATAAATTTTG
*
37747 TAAACATTAAAGGATAAATTT
1 TAAACATAAAAGGATAAATTT
37768 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAACATAAAAGGATAAATTTTG
Found at i:48318 original size:2 final size:2
Alignment explanation
Indices: 48311--48337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48301 ACTTCATATG
48311 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
48338 ACTCACGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:55863 original size:30 final size:28
Alignment explanation
Indices: 55829--55888 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
55819 CCTTTAGATA
55829 ATTTTTAAAATTCAAAAAAATATAAAAATT
1 ATTTTTAAAATT--AAAAAATATAAAAATT
* *
55859 ATTTTTAAAATTAAAAATTATTAAAATT
1 ATTTTTAAAATTAAAAAATATAAAAATT
55887 AT
1 AT
55889 AAAATGTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 16 0.57
30 12 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTTTAAAATTAAAAAATATAAAAATT
Found at i:56384 original size:16 final size:18
Alignment explanation
Indices: 56360--56396 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56350 TTTATATTAT
56360 ATATGCTTTAT-TTTTTA
1 ATATGCTTTATATTTTTA
56377 ATAT-CTTTATAATTTTTA
1 ATATGCTTTAT-ATTTTTA
56395 AT
1 AT
56397 TTTTCTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
ATATGCTTTATATTTTTA
Found at i:57735 original size:17 final size:17
Alignment explanation
Indices: 57713--57746 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57703 TATTCTTATC
*
57713 ATTAATATTTATTTTTA
1 ATTAATATTTATATTTA
*
57730 ATTAATTTTTATATTTA
1 ATTAATATTTATATTTA
57747 TCCTAGCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTAATATTTATATTTA
Found at i:60818 original size:25 final size:25
Alignment explanation
Indices: 60784--60836 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
60774 TTTTCACTAG
60784 TTGTGAAGGGCTCCAAATTAAGCCT
1 TTGTGAAGGGCTCCAAATTAAGCCT
*
60809 TTGTGAAGGGCTCCAAATTATGCCT
1 TTGTGAAGGGCTCCAAATTAAGCCT
60834 TTG
1 TTG
60837 AAAATAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (25 bp):
TTGTGAAGGGCTCCAAATTAAGCCT
Found at i:61219 original size:17 final size:17
Alignment explanation
Indices: 61197--61246 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
61187 AAAGCAAGAC
61197 GATAGTTATTTTTGGA-T
1 GATAGTTATTTTT-GACT
* *
61214 GATAGTTGTTCTTGACT
1 GATAGTTATTTTTGACT
*
61231 GAGAGTTA-TTTTGACT
1 GATAGTTATTTTTGACT
61247 TGTTTCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (17 bp):
GATAGTTATTTTTGACT
Found at i:73944 original size:205 final size:207
Alignment explanation
Indices: 73415--74042 Score: 911
Period size: 211 Copynumber: 3.0 Consensus size: 207
73405 TAAAGCACAT
* * *
73415 GTTGAGGTTTGAGTCCATAAGTAGCGTCAAAAGGTATCTTCTTAATTGTTCTATTCAAAGGGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCAAAGAGTTG
* *
73480 TATGTAAACTCATCTTGAGGGATAACCAAATCCTAACTCTTCATATGATTCCAAA-CAGGACACC
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCA-GACACC
73544 TAAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
130 TAAGCATATTTCCTAAAC--T--TTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
*
73609 CTAGAAAATTTCAATTG
191 CTAGAAAATTTCAATCG
* *
73626 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTTACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCAAAGAGTTG
* *
73691 AATGTAAACTCATCTTGAGGACTAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* * * * * * * *
73756 GAGCATATTTCCTGAAC-TTAACAACCTCTATTTTCCCATATATTTCTGGATGAAAAGTGCCATA
131 AAGCATATTTCCTAAACTTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGCTAGA
73820 AAATTTCAATCG
196 AAATTTCAATCG
* * * * *
73832 GTTGAGGTCTAAGTCCATAAATAGCTTCAAAAGGTGTATT-TTAATTGTTCTATTCATAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCAAAGAGTTG
*
73896 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACAAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* *
73961 AAGAATAATTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
131 AAGCATATTTCCTAAAC--T--TTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
*
74026 TAGGAAATTTCAATCG
192 TAGAAAATTTCAATCG
74042 G
1 G
74043 GTTCCCATTT
Statistics
Matches: 373, Mismatches: 38, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
205 97 0.26
206 88 0.24
210 53 0.14
211 133 0.36
212 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (207 bp):
GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCAAAGAGTTG
TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
AAGCATATTTCCTAAACTTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGCTAGA
AAATTTCAATCG
Found at i:78434 original size:95 final size:97
Alignment explanation
Indices: 78267--78463 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 97
78257 GAAATTGAAT
* *
78267 ATATAATTATAATTATTTAAATGCTCGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTGCTTGT
1 ATATAATTATAATTATTTAAA--CTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGT
*
78332 GTTATAAAGTTATATATATAATT-TTTTTTCCAAA
64 GTTATAAACTTATATATA-AATTATTTTTTCCAAA
*
78366 ATATAATTATAATTATTTAAA-T-GCTCCTAGATTTTATTACCATTGTAAAAGTTTTACTTGTGT
1 ATATAATTATAATTATTTAAACTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGT
*
78429 TATAAACTTATATATAATTTATTTTTTCCAAA
66 TATAAACTTATATATAAATTATTTTTTCCAAA
78461 ATA
1 ATA
78464 AGTTTTTTAA
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
94 3 0.03
95 67 0.73
96 1 0.01
99 21 0.23
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (97 bp):
ATATAATTATAATTATTTAAACTCGCTCCTAGATCTTATTACCATTGTAAAAGTTTTACTTGTGT
TATAAACTTATATATAAATTATTTTTTCCAAA
Found at i:81164 original size:19 final size:19
Alignment explanation
Indices: 81131--81174 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
81121 TTTATTCTTG
*
81131 AAATATTAATTAATTAAAAT
1 AAAT-TTAATAAATTAAAAT
81151 AAATTTAATAAATTAAAAT
1 AAATTTAATAAATTAAAAT
81170 AAATT
1 AAATT
81175 AAATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTTAATAAATTAAAAT
Found at i:81170 original size:10 final size:10
Alignment explanation
Indices: 81142--81177 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
81132 AATATTAATT
81142 AATTAAAATA
1 AATTAAAATA
*
81152 AATT-TAATA
1 AATTAAAATA
81161 AATTAAAATA
1 AATTAAAATA
81171 AATTAAA
1 AATTAAA
81178 TTAATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATTAAAATA
Found at i:81183 original size:19 final size:19
Alignment explanation
Indices: 81138--81183 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
81128 TTGAAATATT
*
81138 AATTAATTAAAATAAATTT
1 AATTAATTAAAATAAATTA
*
81157 AATAAATTAAAATAAATTA
1 AATTAATTAAAATAAATTA
81176 AATTAATT
1 AATTAATT
81184 TTCTCAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATTAAAATAAATTA
Found at i:82730 original size:34 final size:34
Alignment explanation
Indices: 82687--82753 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
82677 TATTCGAATG
* *
82687 CATAAGACATTTCAACCCAGAAATGCCTGAATCC
1 CATAAGACATCTCAACCCAGAAATGCCTAAATCC
82721 CATAAGACATCTCAACCCAGAAATGCCTAAATC
1 CATAAGACATCTCAACCCAGAAATGCCTAAATC
82754 TCATCCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.19
Consensus pattern (34 bp):
CATAAGACATCTCAACCCAGAAATGCCTAAATCC
Found at i:90824 original size:20 final size:20
Alignment explanation
Indices: 90776--90830 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
90766 AACACTATTA
* *
90776 AAATAATTAAAATGCAACGC
1 AAATAAATAAAATGCAACAC
90796 AAA-AAATAAAAT-CAACAC
1 AAATAAATAAAATGCAACAC
90814 AACATAAAT-AAATGCAA
1 AA-ATAAATAAAATGCAA
90831 ATATAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.23
19 13 0.43
20 10 0.33
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAATAAAATGCAACAC
Found at i:92117 original size:14 final size:15
Alignment explanation
Indices: 92100--92138 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
92090 TAATAGTAAA
92100 ATAATATTTAGA-AT
1 ATAATATTTAGAGAT
92114 ATAATATTTAGAGAT
1 ATAATATTTAGAGAT
*
92129 TTAATATTTA
1 ATAATATTTA
92139 TCATTTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (15 bp):
ATAATATTTAGAGAT
Found at i:92199 original size:15 final size:15
Alignment explanation
Indices: 92167--92206 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
92157 AGAATTAGAA
92167 TTAAAATTTAG-AGTT
1 TTAAAATTTAGAAG-T
*
92182 TTAGAATTTAGAAGT
1 TTAAAATTTAGAAGT
92197 TTAAAATTTA
1 TTAAAATTTA
92207 AGGATTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAATTTAGAAGT
Found at i:94234 original size:22 final size:22
Alignment explanation
Indices: 94202--94247 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
94192 AACTTCTATT
94202 TTCAAGCGTTTAATAATATAGG
1 TTCAAGCGTTTAATAATATAGG
* *
94224 TTCAAGTGTTTAATAATGTAGG
1 TTCAAGCGTTTAATAATATAGG
94246 TT
1 TT
94248 GGGTGACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (22 bp):
TTCAAGCGTTTAATAATATAGG
Found at i:99734 original size:6 final size:6
Alignment explanation
Indices: 99723--99776 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
99713 AAGGTACGGA
* *
99723 TGCGGG TGCGGG TGCGGG TGCGGA TACGGG TGCGGG TGCGGG TGCGGG
1 TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG TGCGGG
99771 TGCGGG
1 TGCGGG
99777 CGGAAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.04, C:0.17, G:0.63, T:0.17
Consensus pattern (6 bp):
TGCGGG
Found at i:106194 original size:4 final size:4
Alignment explanation
Indices: 106185--106211 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
106175 TGATTTTAAT
106185 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
106212 TTCGACGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:112399 original size:36 final size:36
Alignment explanation
Indices: 112261--112403 Score: 232
Period size: 36 Copynumber: 4.0 Consensus size: 36
112251 TTGGCGGCAT
*
112261 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGATTC
1 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACTC
*
112297 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACTT
1 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACTC
* *
112333 GGGCTGGGGCTGCGAATTCGAGGCTGACTTGGACTG
1 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACTC
* *
112369 GGGCTGGGGCTGCGAATTCGAGGCTTACTTGGACT
1 GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACT
112404 AGAAGAAGGG
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 102 1.00
ACGTcount: A:0.15, C:0.20, G:0.41, T:0.24
Consensus pattern (36 bp):
GGGCTGGGGCTGCGAATTCGAGGCTGACTTAGACTC
Found at i:118221 original size:9 final size:9
Alignment explanation
Indices: 118207--118236 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
118197 CGCGACTCAC
118207 TCTTCTTCA
1 TCTTCTTCA
118216 TCTTCTTCA
1 TCTTCTTCA
118225 TCTTCTTCA
1 TCTTCTTCA
118234 TCT
1 TCT
118237 GCCCACATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.57
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:119780 original size:18 final size:18
Alignment explanation
Indices: 119756--119798 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
119746 GGATGAACCA
119756 GAAGAAGATGATGAAGGG
1 GAAGAAGATGATGAAGGG
* * *
119774 GATGAAGATGGTGAATGG
1 GAAGAAGATGATGAAGGG
119792 GAAGAAG
1 GAAGAAG
119799 CAGATGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (18 bp):
GAAGAAGATGATGAAGGG
Found at i:121303 original size:74 final size:74
Alignment explanation
Indices: 121182--121329 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
121172 CTATTAAAAA
121182 AACCAAATTTAAATAGATTTAATATTTGTTATTTAACATAATTAATATTCTTGTTTAACCAAAAG
1 AACCAAATTTAAATAGATTTAATATTTGTTATTTAACATAATTAATATTCTTGTTTAACCAAAAG
121247 CGAAGTCTT
66 CGAAGTCTT
121256 AACCAAATTTAAATAGATTTAATATTTGTTATTTAACATAATTAATATTCTTGTTTAACCAAAAG
1 AACCAAATTTAAATAGATTTAATATTTGTTATTTAACATAATTAATATTCTTGTTTAACCAAAAG
121321 CGAAGTCTT
66 CGAAGTCTT
121330 TCATTTTATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (74 bp):
AACCAAATTTAAATAGATTTAATATTTGTTATTTAACATAATTAATATTCTTGTTTAACCAAAAG
CGAAGTCTT
Found at i:123018 original size:4 final size:4
Alignment explanation
Indices: 123009--123120 Score: 134
Period size: 4 Copynumber: 27.5 Consensus size: 4
122999 TTTCTTAATA
* * * * * *
123009 ACAT ACAT ACAT ACAT GCAT GCAT GCAT GCAT ACAT ACAC ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
123057 ACAC ACAC ACGCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT A--CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
123107 ACAT ACAT ACAT AC
1 ACAT ACAT ACAT AC
123121 CCACTGTCCA
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
4 97 0.97
6 3 0.03
ACGTcount: A:0.46, C:0.29, G:0.04, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:126284 original size:26 final size:27
Alignment explanation
Indices: 126232--126286 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
126222 TATACAGATC
*
126232 AAAGACAGTGAGCCCAATTATGAAAAA
1 AAAGACACTGAGCCCAATTATGAAAAA
126259 AAAGACACTGAGCCC-ATTATGAAAAA
1 AAAGACACTGAGCCCAATTATGAAAAA
126285 AA
1 AA
126287 TGGTAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.15
Consensus pattern (27 bp):
AAAGACACTGAGCCCAATTATGAAAAA
Found at i:135387 original size:57 final size:57
Alignment explanation
Indices: 135318--135431 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
135308 GCTCGATGTT
135318 TTAAAATTTTGGAAAAGACCAACTTGATCTGTATCGAAATTGCTAAGGACTGGAGAG
1 TTAAAATTTTGGAAAAGACCAACTTGATCTGTATCGAAATTGCTAAGGACTGGAGAG
135375 TTAAAATTTTGGAAAAGACCAACTTGATCTGTATCGAAATTGCTAAGGACTGGAGAG
1 TTAAAATTTTGGAAAAGACCAACTTGATCTGTATCGAAATTGCTAAGGACTGGAGAG
135432 GTATTTTCAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (57 bp):
TTAAAATTTTGGAAAAGACCAACTTGATCTGTATCGAAATTGCTAAGGACTGGAGAG
Found at i:146755 original size:31 final size:31
Alignment explanation
Indices: 146720--146780 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
146710 TAGCCCAATG
*
146720 ACTTAAAT-AAAATCTTTCAAATAGTTTAGTA
1 ACTTAAATGAAAA-CTTTCAAATAATTTAGTA
146751 ACTTAAATGAAAACTTTCAAATAATTTAGT
1 ACTTAAATGAAAACTTTCAAATAATTTAGT
146781 GAATATTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAATTTAGTA
Found at i:154471 original size:129 final size:126
Alignment explanation
Indices: 154088--154491 Score: 546
Period size: 129 Copynumber: 3.2 Consensus size: 126
154078 GCTAGCATGG
* * * * *
154088 ATATAATTCATGTTGTGGACAACTAGGAATCTTAAAAGATGTAGCTTTAGATCAATTTGTGGTGT
1 ATATAATTCATGGTGTGAACAACTAAGAACCTT-AAAGATGTAGCTTTAGATCAATTTGGGGTGT
*
154153 AATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAAACATAT--AT-AC
65 AATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATAAC
* * * *
154212 ATATAATTCATGGCGTGAACAA-TAGGAACCTTAAAGATGGAGCTTTAGATCTATTTGGGGTGTA
1 ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
* * * *
154276 ATATAACATTCAATCAAGATAAGCTAGCATGAAAAAGTGTCGATATAGACACACATACATAAAC
66 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAG--ACATATAAAT-AAC
* * ***
154340 ATATAATTCAAGGTTTGAACAACTAAGAGTGTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
1 ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
*
154405 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAAAATAC
66 ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATA-AC
*
154467 ACATAATTCATGGTGTGAACAACTA
1 ATATAATTCATGGTGTGAACAACTA
154492 GGAATCTGAA
Statistics
Matches: 244, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
122 74 0.30
123 9 0.04
124 24 0.10
126 3 0.01
127 31 0.13
128 21 0.09
129 82 0.34
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (126 bp):
ATATAATTCATGGTGTGAACAACTAAGAACCTTAAAGATGTAGCTTTAGATCAATTTGGGGTGTA
ATATAACATTCAATCAAGATGAGCTAGCATGAAAAAGTGTTGATATAGACATATAAATAAC
Found at i:160751 original size:4 final size:4
Alignment explanation
Indices: 160744--160776 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
160734 AGGTAGAAGA
160744 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
160777 AGGAGTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:163271 original size:3 final size:3
Alignment explanation
Indices: 163263--163287 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
163253 AGTATACGAC
163263 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
163288 AGAAGCGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:175302 original size:23 final size:23
Alignment explanation
Indices: 175259--175303 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
175249 ACCTGAATCC
*
175259 AATTTTAAAAATTATTTTTATAT
1 AATTTTAAAAATTATTATTATAT
175282 AATTTATAAAAATTA-TATTATA
1 AATTT-TAAAAATTATTATTATA
175304 AGAATCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTAAAAATTATTATTATAT
Found at i:175536 original size:13 final size:13
Alignment explanation
Indices: 175518--175543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175508 TTATAAAAAT
175518 TTATGATCAATAA
1 TTATGATCAATAA
175531 TTATGATCAATAA
1 TTATGATCAATAA
175544 ATTTGGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TTATGATCAATAA
Found at i:179196 original size:36 final size:36
Alignment explanation
Indices: 179144--179214 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
179134 AGCTTCTGTG
*
179144 TCATCTTATACGAGACCATCCTCTCCCATTACTCGA
1 TCATCTTATACCAGACCATCCTCTCCCATTACTCGA
*
179180 TCATCTTATACCAGACCATCCTCTCCTATTACTCG
1 TCATCTTATACCAGACCATCCTCTCCCATTACTCG
179215 CTCGCCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.37, G:0.07, T:0.32
Consensus pattern (36 bp):
TCATCTTATACCAGACCATCCTCTCCCATTACTCGA
Found at i:192290 original size:25 final size:22
Alignment explanation
Indices: 192249--192306 Score: 55
Period size: 25 Copynumber: 2.5 Consensus size: 22
192239 TTTATTTAAT
*
192249 TTTAAAATA-TTATAAAATATCA
1 TTTAAATTATTTA-AAAATATCA
*
192271 CTAATTAAATTATTTAAAAATTTCA
1 -T--TTAAATTATTTAAAAATATCA
192296 TTTAAATTATT
1 TTTAAATTATT
192307 AATTTGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 10 0.33
23 1 0.03
24 1 0.03
25 15 0.50
26 3 0.10
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAATTATTTAAAAATATCA
Found at i:200865 original size:12 final size:12
Alignment explanation
Indices: 200848--200873 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
200838 ACTTATTTTT
200848 AAAAAATTATTA
1 AAAAAATTATTA
200860 AAAAAATTATTA
1 AAAAAATTATTA
200872 AA
1 AA
200874 TTATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAAATTATTA
Found at i:206477 original size:12 final size:13
Alignment explanation
Indices: 206453--206484 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
206443 AAAAAGAAAG
206453 TTTCTCTCTTTCT
1 TTTCTCTCTTTCT
206466 TTTCTC-CTTTCT
1 TTTCTCTCTTTCT
206478 TTTCTCT
1 TTTCTCT
206485 TCATACGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTCTCTTTCT
Found at i:208508 original size:20 final size:19
Alignment explanation
Indices: 208467--208512 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
208457 GTATTATATT
*
208467 AAATATTTATCTAATGTTC
1 AAATATTTATCCAATGTTC
*
208486 AAATATTTATCCCAATTTTC
1 AAATATTTAT-CCAATGTTC
208506 AAA-ATTT
1 AAATATTT
208513 TGTATGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (19 bp):
AAATATTTATCCAATGTTC
Found at i:209567 original size:19 final size:19
Alignment explanation
Indices: 209536--209575 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
209526 ATATGTCATA
*
209536 TTAATAAATAATTTAAAAT
1 TTAATAAATAATTCAAAAT
209555 TTAA-AAATAAATTCAAAAT
1 TTAATAAAT-AATTCAAAAT
209574 TT
1 TT
209576 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAAATAATTCAAAAT
Found at i:218922 original size:21 final size:22
Alignment explanation
Indices: 218883--218924 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
218873 TTAATAGTTC
218883 AATAATTTGAATAAATTTTTTA
1 AATAATTTGAATAAATTTTTTA
218905 AATAATTT-AAT-AATTTTTTA
1 AATAATTTGAATAAATTTTTTA
218925 TACTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATAATTTGAATAAATTTTTTA
Found at i:222491 original size:7 final size:7
Alignment explanation
Indices: 222481--222512 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
222471 CTAAATGTCT
222481 AATGGGA
1 AATGGGA
222488 AATGGGA
1 AATGGGA
222495 AATGGGA
1 AATGGGA
222502 AATGGGA
1 AATGGGA
222509 AATG
1 AATG
222513 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.16
Consensus pattern (7 bp):
AATGGGA
Found at i:228021 original size:16 final size:16
Alignment explanation
Indices: 228000--228031 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
227990 ACAAGGTTAA
*
228000 GAAAAGGACTGTATAT
1 GAAAAGGACCGTATAT
228016 GAAAAGGACCGTATAT
1 GAAAAGGACCGTATAT
228032 ATAATAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (16 bp):
GAAAAGGACCGTATAT
Found at i:229572 original size:13 final size:13
Alignment explanation
Indices: 229554--229578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229544 CAAGTATTCA
229554 ACCCAACCCAATT
1 ACCCAACCCAATT
229567 ACCCAACCCAAT
1 ACCCAACCCAAT
229579 CCAATCATAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:229700 original size:9 final size:9
Alignment explanation
Indices: 229686--229743 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
229676 GTAGTGATTC
229686 AATTCGGGT
1 AATTCGGGT
229695 AATTCGGGT
1 AATTCGGGT
* *
229704 AATCCGGTT
1 AATTCGGGT
229713 AATTCGGGT
1 AATTCGGGT
229722 AATTCGGGT
1 AATTCGGGT
*
229731 AATTCGGTT
1 AATTCGGGT
229740 AATT
1 AATT
229744 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (9 bp):
AATTCGGGT
Found at i:229717 original size:27 final size:27
Alignment explanation
Indices: 229686--229743 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
229676 GTAGTGATTC
229686 AATTCGGGTAATTCGGGTAATCCGGTT
1 AATTCGGGTAATTCGGGTAATCCGGTT
*
229713 AATTCGGGTAATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGGTAATCCGGTT
229740 AATT
1 AATT
229744 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (27 bp):
AATTCGGGTAATTCGGGTAATCCGGTT
Found at i:239010 original size:19 final size:20
Alignment explanation
Indices: 238986--239026 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
238976 GGGATTAAAT
* *
238986 TGAAAAGTTATTAAA-TTCA
1 TGAAAAATTATAAAATTTCA
239005 TGAAAAATTATAAAATTTCA
1 TGAAAAATTATAAAATTTCA
239025 TG
1 TG
239027 GAATTCATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAAATTATAAAATTTCA
Found at i:239400 original size:15 final size:15
Alignment explanation
Indices: 239380--239412 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
239370 ATGTAAATTG
239380 TGTAAATGACATATA
1 TGTAAATGACATATA
239395 TGTAAATGACATATA
1 TGTAAATGACATATA
239410 TGT
1 TGT
239413 GTATGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (15 bp):
TGTAAATGACATATA
Found at i:239415 original size:17 final size:17
Alignment explanation
Indices: 239378--239415 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
239368 ATATGTAAAT
239378 TGTGTAAATGACATATA
1 TGTGTAAATGACATATA
239395 --TGTAAATGACATATA
1 TGTGTAAATGACATATA
239410 TGTGTA
1 TGTGTA
239416 TGTAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 15 0.79
17 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (17 bp):
TGTGTAAATGACATATA
Found at i:239800 original size:24 final size:24
Alignment explanation
Indices: 239759--239837 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
239749 CTAGAACTTT
* * *
239759 CCGTTATATGGCTATTCGGTGCTTC
1 CCGTTA-ATTGCTATTCGGAGCTGC
*
239784 CCGTTAATTGCTCTTCGGAGCTGC
1 CCGTTAATTGCTATTCGGAGCTGC
* * * * *
239808 CCATTAATTGTTTTTTGGAGCTAC
1 CCGTTAATTGCTATTCGGAGCTGC
239832 CCGTTA
1 CCGTTA
239838 TAGGCTCTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 38 0.86
25 6 0.14
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (24 bp):
CCGTTAATTGCTATTCGGAGCTGC
Found at i:271814 original size:20 final size:20
Alignment explanation
Indices: 271779--271822 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
271769 AAAATATAAA
*
271779 TTTTAGAAATATTTTGAAT-
1 TTTTAAAAATATTTTGAATC
271798 TTTTAAAAATCATTTTGAATC
1 TTTTAAAAAT-ATTTTGAATC
271819 TTTT
1 TTTT
271823 TTGTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 9 0.41
21 4 0.18
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATATTTTGAATC
Found at i:272496 original size:24 final size:24
Alignment explanation
Indices: 272469--272514 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
272459 TTATAAAAGT
*
272469 AAGAGATCAATTTGTTAAATTTCA
1 AAGAGAACAATTTGTTAAATTTCA
*
272493 AAGATAACAATTTGTTAAATTT
1 AAGAGAACAATTTGTTAAATTT
272515 GAATATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (24 bp):
AAGAGAACAATTTGTTAAATTTCA
Found at i:278729 original size:26 final size:25
Alignment explanation
Indices: 278687--278735 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
278677 TTTTAAAAAG
*
278687 TAATTTTTATAGCATGAGATTTTTA
1 TAATTTTTATAGCATGAAATTTTTA
*
278712 TAATTTTTATAGTTATGAAATTTT
1 TAATTTTTATAG-CATGAAATTTT
278736 GAAAAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (25 bp):
TAATTTTTATAGCATGAAATTTTTA
Found at i:278971 original size:13 final size:13
Alignment explanation
Indices: 278953--279016 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
278943 TGTCATTTCG
278953 AAATTTCTATCTA
1 AAATTTCTATCTA
*
278966 AAATTTC-A---G
1 AAATTTCTATCTA
278975 AAATTTCTATCTA
1 AAATTTCTATCTA
*
278988 AAATTTC-A---G
1 AAATTTCTATCTA
278997 AAATTTCTATCTA
1 AAATTTCTATCTA
279010 AAATTTC
1 AAATTTC
279017 GGCACATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
9 14 0.36
10 2 0.05
12 2 0.05
13 21 0.54
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (13 bp):
AAATTTCTATCTA
Found at i:278978 original size:22 final size:22
Alignment explanation
Indices: 278947--279016 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
278937 ATTTAATGTC
278947 ATTTC-GAAATTTCTATCTAAA
1 ATTTCAGAAATTTCTATCTAAA
278968 ATTTCAGAAATTTCTATCTAAA
1 ATTTCAGAAATTTCTATCTAAA
278990 ATTTCAGAAATTTCTATCTAAA
1 ATTTCAGAAATTTCTATCTAAA
279012 ATTTC
1 ATTTC
279017 GGCACATCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 5 0.10
22 43 0.90
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTCAGAAATTTCTATCTAAA
Found at i:279089 original size:12 final size:12
Alignment explanation
Indices: 279072--279097 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
279062 AAATAGAATT
279072 AAATTATTGAAG
1 AAATTATTGAAG
279084 AAATTATTGAAG
1 AAATTATTGAAG
279096 AA
1 AA
279098 TGATACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AAATTATTGAAG
Found at i:293296 original size:29 final size:30
Alignment explanation
Indices: 293242--293322 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
293232 TTTTATAGAA
* *
293242 TTTCAATATATTTTTATAAAAATTTA-AA-AT
1 TTTCAA-ATATTTTTAT-TAATTTTATAATAT
293272 TTTCAAATATGTTTTATTAATTTTATAATAT
1 TTTCAAATAT-TTTTATTAATTTTATAATAT
*
293303 TTT-AAATTTTTTTA-TAATTT
1 TTTCAAATATTTTTATTAATTT
293323 ATTAGTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 6 0.13
29 15 0.33
30 19 0.42
31 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTCAAATATTTTTATTAATTTTATAATAT
Found at i:295015 original size:17 final size:17
Alignment explanation
Indices: 294993--295028 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
294983 AAATGTATGC
294993 ATTTAA-AAATAATTATA
1 ATTTAATAAA-AATTATA
295010 ATTTAATAAAAATTATA
1 ATTTAATAAAAATTATA
295027 AT
1 AT
295029 AATTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAATAAAAATTATA
Found at i:295021 original size:20 final size:19
Alignment explanation
Indices: 294996--295036 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
294986 TGTATGCATT
*
294996 TAAAAATAATTATAATTTAA
1 TAAAAATAATAATAA-TTAA
*
295016 TAAAAATTATAATAATTAA
1 TAAAAATAATAATAATTAA
295035 TA
1 TA
295037 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAATAATAATAATTAA
Found at i:298363 original size:29 final size:29
Alignment explanation
Indices: 298330--298388 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
298320 GAAGGAATGG
298330 TCTAATTGCGTTCACAAGTATACTATTCT
1 TCTAATTGCGTTCACAAGTATACTATTCT
298359 TCTAATTGCGTTCACAAGTATACTATTCT
1 TCTAATTGCGTTCACAAGTATACTATTCT
298388 T
1 T
298389 TCTCATCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (29 bp):
TCTAATTGCGTTCACAAGTATACTATTCT
Found at i:304605 original size:6 final size:6
Alignment explanation
Indices: 304594--304625 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
304584 TGATAAAAGT
304594 ATATAA ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT
304626 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:306492 original size:49 final size:49
Alignment explanation
Indices: 306420--306519 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
306410 TTGTCATTTT
*
306420 GCTGTCTTGGTTTTCATAGCTATCGATTGGTGTGATCATCAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
* *
306469 GCTGTCTTGGTTTTTATAGCTATCAATTGGTGTGATCATTAACCTAAGA
1 GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
306518 GC
1 GC
306520 ATTCATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (49 bp):
GCTGTCTTGGTTTTCATAGCTATCAATTGGTGTGATCATCAACCTAAGA
Found at i:332193 original size:29 final size:29
Alignment explanation
Indices: 332161--332237 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
332151 ATTTTAAAAT
*
332161 ATTTTTAAAATATATTTTTTTATTTTTTA
1 ATTTTTAAAATATATTTTTTTACTTTTTA
**
332190 A-TTTTAAAATAT-TTTTAAAATACTTTTTA
1 ATTTTTAAAATATATTTT--TTTACTTTTTA
332219 ATTTTTAAAATA-ATTTTTT
1 ATTTTTAAAATATATTTTTT
332238 GGTATTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 10 0.26
30 14 0.36
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTTAAAATATATTTTTTTACTTTTTA
Found at i:332222 original size:19 final size:19
Alignment explanation
Indices: 332200--332236 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
332190 ATTTTAAAAT
*
332200 ATTTTTAAAATACTTTTTA
1 ATTTTTAAAATAATTTTTA
332219 ATTTTTAAAATAATTTTT
1 ATTTTTAAAATAATTTTT
332237 TGGTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTAAAATAATTTTTA
Found at i:335586 original size:28 final size:26
Alignment explanation
Indices: 335537--335591 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
335527 ATAAATAATT
*
335537 TAAAAATTATAAATATTCAAAAAAAA
1 TAAAAATTATAAACATTCAAAAAAAA
*
335563 TAAAAAGTTCATAAACATTTAAAAAAAA
1 TAAAAA-TT-ATAAACATTCAAAAAAAA
335591 T
1 T
335592 CATGAAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 2 0.08
28 17 0.68
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAAAATTATAAACATTCAAAAAAAA
Found at i:339043 original size:24 final size:24
Alignment explanation
Indices: 339016--339066 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
339006 CGTTCCCATG
339016 TAAATATTAAAATATAAATTAG-TA
1 TAAATATTAAAATA-AAATTAGATA
*
339040 TAAATATTAATATAAAATTAGATA
1 TAAATATTAAAATAAAATTAGATA
339064 TAA
1 TAA
339067 TGATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAATATTAAAATAAAATTAGATA
Found at i:348354 original size:24 final size:24
Alignment explanation
Indices: 348321--348367 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
348311 TACCCAAAAA
*
348321 TTTACGATATTCCATATATTTAAT
1 TTTACAATATTCCATATATTTAAT
348345 TTTACAATATTCCATATATTTAA
1 TTTACAATATTCCATATATTTAA
348368 GATTATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTACAATATTCCATATATTTAAT
Found at i:367797 original size:20 final size:20
Alignment explanation
Indices: 367772--367818 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
367762 CGAAAAATGA
367772 TTTTTGGAAAATGGAATAGT
1 TTTTTGGAAAATGGAATAGT
* ** *
367792 TTTTTGAAAAATGTTATATT
1 TTTTTGGAAAATGGAATAGT
367812 TTTTTGG
1 TTTTTGG
367819 TGTTTGATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTTTGGAAAATGGAATAGT
Found at i:370416 original size:14 final size:14
Alignment explanation
Indices: 370379--370416 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
370369 AAAGGGGAAG
370379 AACTTTCAAATAAA
1 AACTTTCAAATAAA
370393 AAC-TT-AAATAAA
1 AACTTTCAAATAAA
*
370405 AACTTTCGAATA
1 AACTTTCAAATA
370417 GTTCAGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.48
13 4 0.19
14 7 0.33
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (14 bp):
AACTTTCAAATAAA
Found at i:370942 original size:41 final size:40
Alignment explanation
Indices: 370890--370993 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
370880 AATTTATTTT
*
370890 AAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
* *
370930 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
1 AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
*
370970 AAATTTTAAAAAAGTATTTTAAAA
1 AAAATTTAAAAAAGTATTTTAAAA
370994 TTAATAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
AAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAATTAAA
Found at i:370971 original size:29 final size:28
Alignment explanation
Indices: 370945--371004 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
370935 TTAAAAAAGT
370945 ATTTTAAAAAA-ATTTTAAAATTTAAAA
1 ATTTTAAAAAAGATTTTAAAATTTAAAA
370972 ATTTTAAAAAAGTATTTTAAAATTAATAAAA
1 ATTTTAAAAAAG-ATTTTAAAATT--TAAAA
371003 AT
1 AT
371005 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 11 0.38
29 11 0.38
31 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAAAGATTTTAAAATTTAAAA
Found at i:375893 original size:4 final size:4
Alignment explanation
Indices: 375884--375918 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
375874 GTAAACAATG
* *
375884 ATAC ATAC ATAC ATAC ATTC AAAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
375919 ATGTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:404744 original size:17 final size:17
Alignment explanation
Indices: 404724--404759 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
404714 TAGAAAATTG
404724 AAAGAATAGAAAA-ATAA
1 AAAG-ATAGAAAATATAA
404741 AAAGATAGAAAATATAA
1 AAAGATAGAAAATATAA
404758 AA
1 AA
404760 TTTCTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAGATAGAAAATATAA
Found at i:404748 original size:16 final size:18
Alignment explanation
Indices: 404712--404759 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
404702 ATATTGCAAA
*
404712 AATAGAAAAT-T-GAAAG
1 AATAGAAAATATAAAAAG
404728 AATAGAAAA-ATAAAAAG
1 AATAGAAAATATAAAAAG
404745 -ATAGAAAATATAAAA
1 AATAGAAAATATAAAA
404760 TTTCTTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (18 bp):
AATAGAAAATATAAAAAG
Found at i:410430 original size:29 final size:29
Alignment explanation
Indices: 410379--410461 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
410369 ACACTCCCAC
* *
410379 AAAATTTTTATAAAATTTTATTAAGCCC-CTT
1 AAAAATTTTA-AAAATTTAATTAA-CCCTC-T
**
410410 AATTATTTTAAAAA-TTAATTATACCCTCT
1 AAAAATTTTAAAAATTTAATTA-ACCCTCT
410439 AAAAATTTTAAAAATTTAATTAA
1 AAAAATTTTAAAAATTTAATTAA
410462 ATTTCCAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
29 23 0.53
30 13 0.30
31 7 0.16
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (29 bp):
AAAAATTTTAAAAATTTAATTAACCCTCT
Found at i:411030 original size:20 final size:20
Alignment explanation
Indices: 411001--411039 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
410991 ATACCCTTCA
*
411001 AAATTTTTAAAAATTAAATT
1 AAATTCTTAAAAATTAAATT
*
411021 AAATTCTTAAAACTTAAAT
1 AAATTCTTAAAAATTAAAT
411040 AGCAAGATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTCTTAAAAATTAAATT
Found at i:414188 original size:15 final size:17
Alignment explanation
Indices: 414158--414190 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
414148 TCATGACATA
414158 ATATCATTGAGGAATGC
1 ATATCATTGAGGAATGC
414175 ATATCA-TG-GGAATGC
1 ATATCATTGAGGAATGC
414190 A
1 A
414191 GCAGGGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
ATATCATTGAGGAATGC
Found at i:434713 original size:69 final size:70
Alignment explanation
Indices: 434528--434715 Score: 227
Period size: 69 Copynumber: 2.7 Consensus size: 70
434518 ATCAGTAAAA
* * * *
434528 CTAGCTAAATCTTACATTAATTTACAAAACATTAATCGACAAAACCCCAAAAAAAAGTAGTAAAT
1 CTAGCTAAATATTACATTAATTTCCGAAACATTAATCGA-TAAACCCC-AAAAAAAGTAGTAAAT
434593 CGAGCTC
64 CGAGCTC
* * * * * *
434600 GTAGCTAAATATTCCATTAATTACAG-AACATTAGTCGATCAAACCCC-AGAAAAGTAGTAAATC
1 CTAGCTAAATATTACATTAATTTCCGAAACATTAATCGAT-AAACCCCAAAAAAAGTAGTAAATC
434663 GAGCTC
65 GAGCTC
* *
434669 CTAGCTAAATTTTACATTAATTTCCGAAACATTAATTGATAAACCCC
1 CTAGCTAAATATTACATTAATTTCCGAAACATTAATCGATAAACCCC
434716 CCCAAAAAAA
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
69 49 0.51
70 11 0.11
71 18 0.19
72 19 0.20
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (70 bp):
CTAGCTAAATATTACATTAATTTCCGAAACATTAATCGATAAACCCCAAAAAAAGTAGTAAATCG
AGCTC
Found at i:443398 original size:31 final size:31
Alignment explanation
Indices: 443362--443420 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
443352 ATTTGGTCAT
*
443362 TGAACTATTCGAAAGTTTTCATTTAAGTTGC
1 TGAACTATTCAAAAGTTTTCATTTAAGTTGC
*
443393 TGAACTATTCAAAAGTTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTCATTTAAGT
443421 CATTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTTGC
Found at i:445311 original size:11 final size:12
Alignment explanation
Indices: 445295--445323 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
445285 ATTCTAAAAG
445295 TTTAATTTTTT-
1 TTTAATTTTTTA
445306 TTTAATTTTTTA
1 TTTAATTTTTTA
445318 TTTAAT
1 TTTAAT
445324 AACATTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTAATTTTTTA
Found at i:448439 original size:31 final size:30
Alignment explanation
Indices: 448396--448462 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
448386 AAACATTTTG
* ** *
448396 AAAATTTGATTAAGTTTCTTAAAATTTTCT
1 AAAATTTCATTAAGCCTCTCAAAATTTTCT
448426 AAAATTCTCATTAAGCCTCTCAAAATTTT-T
1 AAAATT-TCATTAAGCCTCTCAAAATTTTCT
*
448456 GAAATTT
1 AAAATTT
448463 TTATTGAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.03
30 12 0.39
31 18 0.58
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (30 bp):
AAAATTTCATTAAGCCTCTCAAAATTTTCT
Found at i:452176 original size:21 final size:19
Alignment explanation
Indices: 452151--452195 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
452141 AATTTTAATC
*
452151 TAATTTTAGATTAAAGTTATT
1 TAATTATAGATTAAA-TT-TT
*
452172 TAATTATGGATTAAATTTT
1 TAATTATAGATTAAATTTT
452191 TAATT
1 TAATT
452196 GGTTTGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (19 bp):
TAATTATAGATTAAATTTT
Found at i:454999 original size:31 final size:31
Alignment explanation
Indices: 454963--455021 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
454953 ATTTGGTCAT
*
454963 TGAACTATTCGAAAGTTTTCATTTAAGTTGC
1 TGAACTATTCAAAAGTTTTCATTTAAGTTGC
*
454994 TGAACTATTCAAAAGTTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTCATTTAAGT
455022 CATTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTTGC
Found at i:459767 original size:43 final size:42
Alignment explanation
Indices: 459671--459870 Score: 187
Period size: 43 Copynumber: 4.7 Consensus size: 42
459661 TAACCGTTAC
* *
459671 ACGGTGGAATCAGCACTTAGCAACCACCTTAT-A-A-TCAATGAT
1 ACGGTGGAATCAACACATAGCAACC-CCTT-TCACAGTCAA-GAT
459713 ACGG-GGAATCAACACATAGCAACCCCTTTCACAGTCAAGAAT
1 ACGGTGGAATCAACACATAGCAACCCCTTTCACAGTCAAG-AT
* * * * *
459755 ATGGTGGAATCAACACTTAGCAACTACCTTT-ATATTCAATGAT
1 ACGGTGGAATCAACACATAGCAAC-CCCTTTCACAGTCAA-GAT
* *
459798 ACGG-GGAATCAGCACATAGCAACCCCTTTCACAGTTAAGGAT
1 ACGGTGGAATCAACACATAGCAACCCCTTTCACAGTCAA-GAT
* *
459840 ACGGTGGAATCAGCACTTAGCAACCACCTTT
1 ACGGTGGAATCAACACATAGCAACC-CCTTT
459871 ATATTCAATG
Statistics
Matches: 132, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
40 5 0.04
41 25 0.19
42 42 0.32
43 48 0.36
44 11 0.08
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
ACGGTGGAATCAACACATAGCAACCCCTTTCACAGTCAAGAT
Found at i:459815 original size:85 final size:85
Alignment explanation
Indices: 459671--459882 Score: 354
Period size: 85 Copynumber: 2.5 Consensus size: 85
459661 TAACCGTTAC
*
459671 ACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGATACGGGGAATCAACACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAACACATAGCAA
459735 CCCCTTTCACAGTCAAGAAT
66 CCCCTTTCACAGTCAAGAAT
* * * *
459755 ATGGTGGAATCAACACTTAGCAACTACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAACACATAGCAA
* *
459820 CCCCTTTCACAGTTAAGGAT
66 CCCCTTTCACAGTCAAGAAT
459840 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
459883 GCGGATTCAC
Statistics
Matches: 117, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 25 0.21
85 92 0.79
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (85 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAACACATAGCAA
CCCCTTTCACAGTCAAGAAT
Found at i:459970 original size:51 final size:51
Alignment explanation
Indices: 459894--460084 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 51
459884 CGGATTCACA
* * * *
459894 TAGTAGCATGCATATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * *
459945 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * *
459996 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
*
460046 TAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
460085 TTCACTTTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.35
51 70 0.59
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:460068 original size:101 final size:102
Alignment explanation
Indices: 459892--460076 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
459882 TGCGGATTCA
* * *
459892 CATAGTAGCATGCATATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
459957 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
459994 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTAC
460057 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
460077 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.51
102 33 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:476988 original size:28 final size:28
Alignment explanation
Indices: 476936--476994 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
476926 TTTTGGTCCT
*
476936 TCTATTATTTTCAATTTTGAAAA-TTAA
1 TCTATTATTTTCAATTTGGAAAATTTAA
*
476963 TCTATGTATTTT-AATTTGGTATAATTTAA
1 TCTAT-TATTTTCAATTTGG-AAAATTTAA
476992 TCT
1 TCT
476995 TCGTAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.41
28 9 0.33
29 7 0.26
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (28 bp):
TCTATTATTTTCAATTTGGAAAATTTAA
Found at i:477809 original size:11 final size:11
Alignment explanation
Indices: 477793--477830 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
477783 ATTTTTTTAA
477793 TTTTAAAATAT
1 TTTTAAAATAT
477804 TTTTAAAATAT
1 TTTTAAAATAT
477815 TTTTAAAATACT
1 TTTTAAAATA-T
477827 TTTT
1 TTTT
477831 TTGTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:477844 original size:26 final size:27
Alignment explanation
Indices: 477812--477878 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
477802 ATTTTTAAAA
* * * *
477812 TATTTTTAAAATACTTTTTTTGTTTTT
1 TATTTTAAAAATAATTTTTTGGTGTTT
477839 TATTTTAAAAATAATTTTTTGGTGTTT
1 TATTTTAAAAATAATTTTTTGGTGTTT
**
477866 TATTAAAAAAATA
1 TATTTTAAAAATA
477879 GGCCGGGCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (27 bp):
TATTTTAAAAATAATTTTTTGGTGTTT
Found at i:480237 original size:18 final size:17
Alignment explanation
Indices: 480204--480242 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
480194 TTGTATAAAT
480204 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
480222 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
480239 TGTG
1 TGTG
480243 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:480495 original size:23 final size:23
Alignment explanation
Indices: 480468--480565 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
480458 AGTGTTATTG
480468 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
480491 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
480514 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
480536 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
480559 ATCAGTG
1 ATCAGTG
480566 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:480534 original size:45 final size:45
Alignment explanation
Indices: 480470--480558 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
480460 TGTTATTGAT
* *
480470 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
480515 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
480559 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:487790 original size:18 final size:17
Alignment explanation
Indices: 487768--487826 Score: 84
Period size: 18 Copynumber: 3.4 Consensus size: 17
487758 CAACTTCAAT
487768 TGAGCTTGCA-CTTTTGG
1 TGAGCTTGCAGC-TTTGG
487785 TAGAGCTTGCAGCTTTGG
1 T-GAGCTTGCAGCTTTGG
487803 TGGAGCTTGCAGCTTTGG
1 T-GAGCTTGCAGCTTTGG
487821 TGAGCT
1 TGAGCT
487827 CACAATTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 6 0.15
18 32 0.82
19 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.36
Consensus pattern (17 bp):
TGAGCTTGCAGCTTTGG
Found at i:488698 original size:129 final size:128
Alignment explanation
Indices: 488395--488753 Score: 306
Period size: 129 Copynumber: 2.8 Consensus size: 128
488385 CATTTCAAAA
* * * * * * *
488395 TTGATCATTTTAGACTAATATTGAATGGTGTTGGGTTA-TTTTTTTAGTCAAATCGGGTTTTGAA
1 TTGATCATTTTGGGCTCATATTGAATGGTGTTGGATTACTTTTTTTAGTCAAATCGAGTATTAAA
* * * * * *
488459 ATTTTTGAATCATTTTGGTTCGGGTTAGTTTCAAGTTCAAATCATTTTAGGTTCAAGTCATTGGT
66 ATTTCTAAATCATTTTGGTTCAGGTTAGGTTCAAGTT--AA-CATTTCAGGTTCAAATCATTGGT
488524 C
128 C
* * ** * * *
488525 TCGGATAATTCCGGGCTCATATTGAACGATGTTGGATAAC--TTTTTAGTCAAATCGAG-ATTAA
1 T-TGATCATTTTGGGCTCATATTGAATGGTGTTGGATTACTTTTTTTAGTCAAATCGAGTATTAA
*
488587 AATTTCTAAATCATTTTGGTTCAGGTTAGGTTCAAGTT-A-GTTTCAGGTTCAAATCAATTTCGG
65 AATTTCTAAATCATTTTGGTTCAGGTTAGGTTCAAGTTAACATTTCAGGTTCAAATC-A-TT-GG
488650 AT-
127 -TC
*
488652 TTGATCATTTTGGGCTCATATTGAATGGTGTTGGATTATCTTTTTTT-GTCAAATC-AGGTTTTA
1 TTGATCATTTTGGGCTCATATTGAATGGTGTTGGATTA-CTTTTTTTAGTCAAATCGA-GTATTA
* * * * *
488715 AATTTTCCAGATCATTTTGATTCCA-GTTAGTTTCAAGTT
64 AAATTTCTAAATCATTTTGGTT-CAGGTTAGGTTCAAGTT
488754 TAAATCAATT
Statistics
Matches: 183, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
124 13 0.07
125 1 0.01
126 33 0.18
127 5 0.03
128 10 0.05
129 76 0.42
130 19 0.10
131 26 0.14
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (128 bp):
TTGATCATTTTGGGCTCATATTGAATGGTGTTGGATTACTTTTTTTAGTCAAATCGAGTATTAAA
ATTTCTAAATCATTTTGGTTCAGGTTAGGTTCAAGTTAACATTTCAGGTTCAAATCATTGGTC
Found at i:488881 original size:122 final size:123
Alignment explanation
Indices: 488635--488895 Score: 305
Period size: 122 Copynumber: 2.1 Consensus size: 123
488625 AGTTTCAGGT
* * *** * *
488635 TCAAA-TCAATTTCGGATTTGATCATTTTGGGCTCATATTGAATGGTGTTGGATTATCTTTTTTT
1 TCAAATTCGATTTCAGATTTGATCATTTCAAGCTCATATAGAATGGTGTTGGATTA-CTTTTTTA
* * * *
488699 GTCAAATCAGGTTTTAAATTTTCCAGATCATTTTGATTCCAGTTAGTTTCAAGTTTAAA
65 ATCAAATCAGGTTTTAAATTTTCCAGATCATTTTGATTCCAGTTAATTCCAAGTTCAAA
* * *
488758 TCAATTTTGATTTCAGATTTGATCATTTCAAGTTCATATAGAATGGTGTTGGATTA-TTTTTTAA
1 TCAAATTCGATTTCAGATTTGATCATTTCAAGCTCATATAGAATGGTGTTGGATTACTTTTTTAA
* * **
488822 TCAAATCGGGTTTTAAGATTTT-CAGATCATTTTCG-TTCGAGTTAATTCCCGGTTCAAA
66 TCAAATCAGGTTTTAA-ATTTTCCAGATCATTTT-GATTCCAGTTAATTCCAAGTTCAAA
488880 TCAAATTCGATTTCAG
1 TCAAATTCGATTTCAG
488896 TTCATTTTGA
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
122 63 0.55
123 10 0.09
124 42 0.37
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (123 bp):
TCAAATTCGATTTCAGATTTGATCATTTCAAGCTCATATAGAATGGTGTTGGATTACTTTTTTAA
TCAAATCAGGTTTTAAATTTTCCAGATCATTTTGATTCCAGTTAATTCCAAGTTCAAA
Found at i:496820 original size:200 final size:200
Alignment explanation
Indices: 496477--496882 Score: 794
Period size: 200 Copynumber: 2.0 Consensus size: 200
496467 AATTTGATAA
*
496477 TAATAGCAACACTTGAAGAATTCAAAAACAAATTAGAGATGTATCACATTGATCAAACCGTTGAA
1 TAATAGCAACACTTGAAGAATTCAAAAACAAATCAGAGATGTATCACATTGATCAAACCGTTGAA
*
496542 ATTTGCATACTAACCTTGCCATCATCAGACCTAGTTGACGATGAACTTTAGCCAACCAATAAACC
66 ATTTGCATACTAACCTTGCCATCATCAGACCTAGTTGACGATGAACTTTAGCCAACCAAGAAACC
496607 ATTGTCAAGAACCTTAAGAGATCCACCACATCAACGATGCATAAAAAAGCACTACAGCAAAATGT
131 ATTGTCAAGAACCTTAAGAGATCCACCACATCAACGATGCATAAAAAAGCACTACAGCAAAATGT
496672 AGAAT
196 AGAAT
496677 TAATAGCAACACTTGAAGAATTCAAAAACAAATCAGAGATGTATCACATTGATCAAACCGTTGAA
1 TAATAGCAACACTTGAAGAATTCAAAAACAAATCAGAGATGTATCACATTGATCAAACCGTTGAA
496742 ATTTGCATACTAACCTTGCCATCATCAGACCTAGTTGACGATGAACTTTAGCCAACCAAGAAACC
66 ATTTGCATACTAACCTTGCCATCATCAGACCTAGTTGACGATGAACTTTAGCCAACCAAGAAACC
496807 ATTGTCAAGAACCTTAAGAGATCCACCACATCAACGATGCATAAAAAAGCACTACAGCAAAATGT
131 ATTGTCAAGAACCTTAAGAGATCCACCACATCAACGATGCATAAAAAAGCACTACAGCAAAATGT
496872 AGAAT
196 AGAAT
496877 TAATAG
1 TAATAG
496883 TGATTTACAG
Statistics
Matches: 204, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 204 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (200 bp):
TAATAGCAACACTTGAAGAATTCAAAAACAAATCAGAGATGTATCACATTGATCAAACCGTTGAA
ATTTGCATACTAACCTTGCCATCATCAGACCTAGTTGACGATGAACTTTAGCCAACCAAGAAACC
ATTGTCAAGAACCTTAAGAGATCCACCACATCAACGATGCATAAAAAAGCACTACAGCAAAATGT
AGAAT
Found at i:499718 original size:21 final size:21
Alignment explanation
Indices: 499686--499728 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
499676 TGAAGTTAGG
*
499686 AATATATTATTTATCTTTTAAAA
1 AATATAAT-TTTAT-TTTTAAAA
499709 AATATAATTTTATTTTTAAA
1 AATATAATTTTATTTTTAAA
499729 TGAATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATAATTTTATTTTTAAAA
Found at i:509819 original size:7 final size:7
Alignment explanation
Indices: 509809--509841 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
509799 ACAAAAACCC
509809 AAAACGT
1 AAAACGT
509816 AAAACGT
1 AAAACGT
509823 AAAACGT
1 AAAACGT
509830 AAAACGT
1 AAAACGT
509837 AAAAC
1 AAAAC
509842 AAAGAGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAACGT
Found at i:509819 original size:21 final size:20
Alignment explanation
Indices: 509796--509844 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
509786 AACTGAAACA
509796 AAAACAAAAACCCAAAACGT
1 AAAACAAAAACCCAAAACGT
* **
509816 AAAACGTAAAACGTAAAACGT
1 AAAAC-AAAAACCCAAAACGT
509837 AAAACAAA
1 AAAACAAA
509845 GAGGTTAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.65, C:0.18, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAACAAAAACCCAAAACGT
Found at i:512921 original size:27 final size:25
Alignment explanation
Indices: 512888--512956 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
512878 TACTTTATGC
512888 TATTTTTTAAAATTTTTATGAACTTTA
1 TATTTTTTAAAATTTTT-T-AACTTTA
** * *
512915 TATTTTTTTGAATTTTTTTATTTTA
1 TATTTTTTAAAATTTTTTAACTTTA
512940 TATGTTTTTATAAATTT
1 TAT-TTTTTA-AAATTT
512957 AAAATTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 8 0.24
26 6 0.18
27 20 0.59
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (25 bp):
TATTTTTTAAAATTTTTTAACTTTA
Found at i:517313 original size:2 final size:2
Alignment explanation
Indices: 517306--517330 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
517296 AGCCTAAAGC
517306 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
517331 AACAAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:519422 original size:29 final size:29
Alignment explanation
Indices: 519388--519445 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
519378 ATTTGATTTT
*
519388 TTTAATAATATAGAGACTAAATTGATACA
1 TTTAATAATAGAGAGACTAAATTGATACA
* * *
519417 TTTAATAGTAGAGGGACTAATTTGATACA
1 TTTAATAATAGAGAGACTAAATTGATACA
519446 ATCTATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAATAATAGAGAGACTAAATTGATACA
Found at i:524237 original size:15 final size:16
Alignment explanation
Indices: 524198--524247 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
524188 ATTCGATTAA
524198 ATAAATTATT-AAAAAT
1 ATAAA-TATTAAAAAAT
524214 CATAAATA-TAAAAAAT
1 -ATAAATATTAAAAAAT
*
524230 ATATATATTTAAAAAAT
1 ATAAATA-TTAAAAAAT
524247 A
1 A
524248 AAAAAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 14 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATATTAAAAAAT
Found at i:524548 original size:28 final size:28
Alignment explanation
Indices: 524506--524563 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
524496 GATATTAATT
*
524506 ATTTTAATTAATTAATAACATTATA-AA
1 ATTTTAACTAATTAATAACATTATATAA
*
524533 ATTTTAAACTAATTAATAATATTATATAA
1 ATTTT-AACTAATTAATAACATTATATAA
524562 AT
1 AT
524564 ATAGATACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 18 0.67
29 4 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTTAACTAATTAATAACATTATATAA
Found at i:525703 original size:2 final size:2
Alignment explanation
Indices: 525696--525726 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
525686 CGATCCCTTT
525696 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
525727 TTTTGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:540673 original size:28 final size:30
Alignment explanation
Indices: 540603--540680 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
540593 GTCGTTTGGT
* *
540603 TTAAATACCAAATTGAATATTGAAATTAAAC
1 TTAAATACCAAATTGAA-ATAGAAATAAAAC
*
540634 TTAAATATCAAATTGAAA-AGAAA-AAAAC
1 TTAAATACCAAATTGAAATAGAAATAAAAC
540662 TTAAATACCAAATTTGAAA
1 TTAAATACCAAA-TTGAAA
540681 CTAAACTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.36
29 10 0.24
30 1 0.02
31 16 0.38
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (30 bp):
TTAAATACCAAATTGAAATAGAAATAAAAC
Found at i:540680 original size:24 final size:24
Alignment explanation
Indices: 540653--540698 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
540643 AAATTGAAAA
540653 GAAA-AAAACTTAAATACCAAATTT
1 GAAACAAAACTT-AATACCAAATTT
* *
540677 GAAACTAAACTTAATACTAAAT
1 GAAACAAAACTTAATACCAAAT
540699 GATATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (24 bp):
GAAACAAAACTTAATACCAAATTT
Done.