Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1304
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: 180634
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
File 1 of 2
Found at i:3669 original size:12 final size:12
Alignment explanation
Indices: 3652--3690 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
3642 CCGCATATCC
3652 CGAAACCCGAAA
1 CGAAACCCGAAA
*
3664 CGAAACCCGAACC
1 CGAAACCCGAA-A
3677 CGAAAACCCGAAA
1 CG-AAACCCGAAA
3690 C
1 C
3691 CCTAAACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 3 0.13
14 9 0.39
ACGTcount: A:0.46, C:0.38, G:0.15, T:0.00
Consensus pattern (12 bp):
CGAAACCCGAAA
Found at i:4356 original size:10 final size:9
Alignment explanation
Indices: 4340--4420 Score: 53
Period size: 8 Copynumber: 10.3 Consensus size: 9
4330 AACTCCGTAT
4340 AAAACCCTG
1 AAAACCCTG
4349 ATAAACCC-G
1 A-AAACCCTG
4358 AAAACCCT-
1 AAAACCCTG
4366 AAAACCC-G
1 AAAACCCTG
*
4374 --AACCCCG
1 AAAACCCTG
4381 -AAACCCTG
1 AAAACCCTG
4389 -AAACCC-G
1 AAAACCCTG
4396 -AAACCC-G
1 AAAACCCTG
4403 -AAACCC-G
1 AAAACCCTG
4410 AAAACCC-G
1 AAAACCCTG
4418 AAA
1 AAA
4421 CCGAAACCGA
Statistics
Matches: 65, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
6 5 0.08
7 16 0.25
8 35 0.54
9 3 0.05
10 6 0.09
ACGTcount: A:0.46, C:0.38, G:0.11, T:0.05
Consensus pattern (9 bp):
AAAACCCTG
Found at i:5331 original size:8 final size:8
Alignment explanation
Indices: 5217--5351 Score: 108
Period size: 7 Copynumber: 19.1 Consensus size: 8
5207 ATAACCCAAA
5217 CCCAAA-C
1 CCCAAACC
5224 CCCAAA-C
1 CCCAAACC
*
5231 CCC-AATC
1 CCCAAACC
5238 CCCAAA--
1 CCCAAACC
5244 CCCAAA-C
1 CCCAAACC
*
5251 CCCAAAAC
1 CCCAAACC
5259 CCCAAA-C
1 CCCAAACC
5266 CCCAAA-C
1 CCCAAACC
5273 CCCAAA-C
1 CCCAAACC
5280 CCC-AACC
1 CCCAAACC
5287 CCCAAA-C
1 CCCAAACC
5294 CCCAAA-C
1 CCCAAACC
5301 CCCAAA-C
1 CCCAAACC
5308 CCCAAA-C
1 CCCAAACC
5315 CCCAAACC
1 CCCAAACC
*
5323 CCCATA--
1 CCCAAACC
5329 CCCAAA-C
1 CCCAAACC
*
5336 CCC-AAGC
1 CCCAAACC
5343 CCCAAACC
1 CCCAAACC
5351 C
1 C
5352 TAAAACCAAG
Statistics
Matches: 115, Mismatches: 3, Indels: 19
0.84 0.02 0.14
Matches are distributed among these distances:
6 17 0.15
7 77 0.67
8 21 0.18
ACGTcount: A:0.40, C:0.58, G:0.01, T:0.01
Consensus pattern (8 bp):
CCCAAACC
Found at i:5340 original size:7 final size:7
Alignment explanation
Indices: 4--5323 Score: 4729
Period size: 7 Copynumber: 735.9 Consensus size: 7
1 CGA
4 AAACCCG
1 AAACCCG
11 AAACCCG
1 AAACCCG
18 AAACCCG
1 AAACCCG
25 -AA-CCG
1 AAACCCG
30 AAACCCG
1 AAACCCG
37 ATAACCCG
1 A-AACCCG
45 AAACCCG
1 AAACCCG
*
52 AAACCTCT
1 AAACC-CG
60 AAA-CCG
1 AAACCCG
66 AAACCCG
1 AAACCCG
73 TAAA--CG
1 -AAACCCG
79 AAACCCG
1 AAACCCG
86 AAACCTCG
1 AAACC-CG
*
94 AAA-CCT
1 AAACCCG
100 ATAACCCG
1 A-AACCCG
108 TAAACCCG
1 -AAACCCG
116 AATATCCTCCG
1 AA-A--C-CCG
127 AAACCCG
1 AAACCCG
134 AAACCCTG
1 AAACCC-G
*
142 AACCCCCCCG
1 AA---ACCCG
152 AAACCCG
1 AAACCCG
159 AAACCCG
1 AAACCCG
166 AAACCC-
1 AAACCCG
172 AAACCCG
1 AAACCCG
*
179 AAACCGCT
1 AAACC-CG
*
187 AACCCCG
1 AAACCCG
194 AAACCCTG
1 AAACCC-G
202 AAACCCG
1 AAACCCG
209 -AACCCG
1 AAACCCG
215 AATACCCG
1 AA-ACCCG
223 TAAAACCCG
1 --AAACCCG
232 AAACCCG
1 AAACCCG
239 AAA-CCG
1 AAACCCG
245 AAACCCG
1 AAACCCG
252 AAACCCG
1 AAACCCG
259 -AACCCG
1 AAACCCG
265 AATAGCCCG
1 AA-A-CCCG
274 AAAACCCG
1 -AAACCCG
*
282 -AACTCGCT
1 AAAC-C-CG
*
290 ACACCCG
1 AAACCCG
297 AAACCCG
1 AAACCCG
304 AAA-CCG
1 AAACCCG
310 AAA-CCG
1 AAACCCG
316 AAACTCCGG
1 AAAC-CC-G
325 AAACCCG
1 AAACCCG
332 AAACCCCG
1 AAA-CCCG
340 AAAACCTCG
1 -AAACC-CG
349 AAACCCG
1 AAACCCG
356 AAGACCCTG
1 AA-ACCC-G
*
365 TAAACCCT
1 -AAACCCG
373 AATACTCCGG
1 AA-AC-CC-G
383 AAACCCG
1 AAACCCG
390 AAAATCCCG
1 -AAA-CCCG
399 AAACCCG
1 AAACCCG
*
406 AAAATCCG
1 -AAACCCG
*
414 ACACCCG
1 AAACCCG
421 AAACCCG
1 AAACCCG
428 AAACCCGG
1 AAACCC-G
436 AAACCCG
1 AAACCCG
*
443 TCAACCTCG
1 -AAACC-CG
452 AAAACCCG
1 -AAACCCG
460 AAATCCCG
1 AAA-CCCG
468 AAACCCG
1 AAACCCG
475 AAACCCG
1 AAACCCG
482 AAATCCCG
1 AAA-CCCG
490 AAACCCG
1 AAACCCG
497 AAACCCG
1 AAACCCG
504 -AACCCG
1 AAACCCG
510 AAA-CCG
1 AAACCCG
516 AAACCCG
1 AAACCCG
523 AAACCCG
1 AAACCCG
530 TAAACCCG
1 -AAACCCG
538 AAACCCG
1 AAACCCG
*
545 TAAACCCT
1 -AAACCCG
553 AAACCCG
1 AAACCCG
560 TAAACCTCG
1 -AAACC-CG
*
569 AAATCCG
1 AAACCCG
576 AAACCTCG
1 AAACC-CG
*
584 AAACCGG
1 AAACCCG
591 AAACCCG
1 AAACCCG
*
598 AACCCCG
1 AAACCCG
**
605 AATAAAAAAC-
1 ----AAACCCG
615 AAACCC-
1 AAACCCG
*
621 --CCCCAG
1 AAACCC-G
627 AAAACCCG
1 -AAACCCG
635 AAACCCG
1 AAACCCG
642 AAACCCG
1 AAACCCG
649 AAAACTCCG
1 -AAAC-CCG
658 AAACCCG
1 AAACCCG
665 AAACCCG
1 AAACCCG
672 TAAACCCG
1 -AAACCCG
680 AAACCCG
1 AAACCCG
687 AAAACCCG
1 -AAACCCG
*
695 CACACCCG
1 -AAACCCG
703 AAACCCG
1 AAACCCG
710 AAACCCG
1 AAACCCG
717 AAACCCG
1 AAACCCG
724 AAATCCCG
1 AAA-CCCG
732 AAACCCTG
1 AAACCC-G
*
740 AAACCCCC
1 AAA-CCCG
*
748 ATACCCG
1 AAACCCG
755 AAA-CCG
1 AAACCCG
761 AAACCCG
1 AAACCCG
*
768 CAACCCG
1 AAACCCG
775 AAACCCG
1 AAACCCG
*
782 ACACCCG
1 AAACCCG
789 AAACCCG
1 AAACCCG
*
796 AAAACCCT
1 -AAACCCG
804 AAACCCG
1 AAACCCG
811 AAATGCCCG
1 AAA--CCCG
820 AAAAACCCG
1 --AAACCCG
*
829 CAACCCG
1 AAACCCG
836 -AA-CCG
1 AAACCCG
841 AAA-CCG
1 AAACCCG
847 AATACCCG
1 AA-ACCCG
855 -AACTCCG
1 AAAC-CCG
862 ACATACTCCG
1 A-A-AC-CCG
*
872 CAACCCG
1 AAACCCG
879 TAAA-CCG
1 -AAACCCG
886 AAACCCG
1 AAACCCG
893 AAACCCG
1 AAACCCG
900 AAACCCG
1 AAACCCG
907 AATACCC-
1 AA-ACCCG
914 AAA-CCG
1 AAACCCG
920 AATACCCG
1 AA-ACCCG
*
928 CAACCC-
1 AAACCCG
934 AAACTCCCG
1 AAA--CCCG
943 -AA-CCG
1 AAACCCG
948 AAACTCCG
1 AAAC-CCG
956 AATA-CCG
1 AA-ACCCG
*
963 CAA-CCG
1 AAACCCG
969 AAACCCG
1 AAACCCG
976 ATAACCCG
1 A-AACCCG
984 -AACCCG
1 AAACCCG
990 AAACCCG
1 AAACCCG
*
997 AAACCCA
1 AAACCCG
1004 AAACTCCG
1 AAAC-CCG
1012 AAAACCCG
1 -AAACCCG
**
1020 -CCCCCTG
1 AAACCC-G
1027 AAACCCG
1 AAACCCG
1034 AAA-CCG
1 AAACCCG
*
1040 CAACCCG
1 AAACCCG
1047 AACACCCTG
1 AA-ACCC-G
1056 AAACCCG
1 AAACCCG
1063 --ACCCG
1 AAACCCG
1068 AAAACCCGG
1 -AAACCC-G
1077 AAACTCTCG
1 AAAC-C-CG
1086 AAA-CCG
1 AAACCCG
1092 AAACCCG
1 AAACCCG
*
1099 CAACCCG
1 AAACCCG
1106 AAACCCG
1 AAACCCG
*
1113 AAA-CTG
1 AAACCCG
1119 AAACCCG
1 AAACCCG
*
1126 AACCCCG
1 AAACCCG
1133 AAACCCG
1 AAACCCG
1140 AAACCCG
1 AAACCCG
1147 AAACCTCG
1 AAACC-CG
*
1155 TAACCCTG
1 AAACCC-G
1163 AAA-CCG
1 AAACCCG
1169 TAAATCCTGGCG
1 -AAA-CC---CG
*
1181 ACACCTCG
1 AAACC-CG
1189 AAACTCCG
1 AAAC-CCG
1197 AAATCCCG
1 AAA-CCCG
1205 AATACCCTG
1 AA-ACCC-G
1214 AAACCCG
1 AAACCCG
1221 AAACCCG
1 AAACCCG
1228 AAACCCG
1 AAACCCG
*
1235 AAACTCCTAA
1 AAAC-CC--G
1245 AAACCCG
1 AAACCCG
1252 AAACCCG
1 AAACCCG
1259 TAAAGCCCG
1 -AAA-CCCG
1268 AAACCC-
1 AAACCCG
**
1274 TCACCCG
1 AAACCCG
1281 -AACCCG
1 AAACCCG
*
1287 AAACCCT
1 AAACCCG
1294 AAA-CCG
1 AAACCCG
1300 AAACCCG
1 AAACCCG
1307 AAACCCG
1 AAACCCG
1314 AAACCCG
1 AAACCCG
1321 AAAACCCG
1 -AAACCCG
*
1329 AAAAACCG
1 -AAACCCG
1337 AAACCTCG
1 AAACC-CG
1345 AAA-CCG
1 AAACCCG
1351 AAACCCCG
1 AAA-CCCG
*
1359 AAAACCG
1 AAACCCG
1366 AAA-CCG
1 AAACCCG
1372 -AACCTCG
1 AAACC-CG
1379 AAACCCG
1 AAACCCG
1386 AAACCCG
1 AAACCCG
1393 AAACCCG
1 AAACCCG
1400 AAACCCG
1 AAACCCG
1407 AAAACCCG
1 -AAACCCG
1415 AAACCCTG
1 AAACCC-G
1423 AAACCCTG
1 AAACCC-G
1431 AGAACCCG
1 A-AACCCG
1439 AAACCCTG
1 AAACCC-G
1447 AAAACCCG
1 -AAACCCG
1455 AAA-CCG
1 AAACCCG
1461 AAAATCCCG
1 -AAA-CCCG
*
1470 TAGACCCG
1 -AAACCCG
* *
1478 AACCCCTT
1 AAACCC-G
1486 AAACCCG
1 AAACCCG
1493 AAACCCG
1 AAACCCG
1500 AAAACCCG
1 -AAACCCG
*
1508 CAACCCG
1 AAACCCG
1515 TAATACCCG
1 -AA-ACCCG
*
1524 CAACCCG
1 AAACCCG
1531 AAACCC-
1 AAACCCG
*
1537 CAACCCG
1 AAACCCG
*
1544 AAATCCCC
1 AAA-CCCG
1552 AAACCCG
1 AAACCCG
1559 AAAACCC-
1 -AAACCCG
**
1566 -TCCCCG
1 AAACCCG
***
1572 TCCCCCCCCAG
1 ---AAACCC-G
1583 AAA--CG
1 AAACCCG
1588 AAACCCG
1 AAACCCG
1595 AAACCCG
1 AAACCCG
1602 AAACCCG
1 AAACCCG
1609 -AACCCG
1 AAACCCG
1615 AAACCCG
1 AAACCCG
1622 AAACTCCG
1 AAAC-CCG
1630 AAACCCG
1 AAACCCG
*
1637 TAACCCTG
1 AAACCC-G
1645 TAAACCTCG
1 -AAACC-CG
1654 AAACCCG
1 AAACCCG
1661 -AACCCG
1 AAACCCG
*
1667 AAAGACCGG
1 -AA-ACCCG
*
1676 CAACCCG
1 AAACCCG
1683 AAACCCG
1 AAACCCG
1690 AAACCC-
1 AAACCCG
*
1696 TAACCCG
1 AAACCCG
1703 AAA-CCG
1 AAACCCG
1709 ATAGAACCCG
1 --A-AACCCG
1719 AAACCCG
1 AAACCCG
1726 AAACCCG
1 AAACCCG
1733 AAAACCCCG
1 -AAA-CCCG
1742 -AACCCG
1 AAACCCG
1748 AAA-CCG
1 AAACCCG
1754 AAACCC-
1 AAACCCG
1760 AAACCCG
1 AAACCCG
1767 AAACCCG
1 AAACCCG
1774 AAACCCG
1 AAACCCG
1781 AAACCCG
1 AAACCCG
1788 AAA-CCG
1 AAACCCG
*
1794 AAAACCAG
1 -AAACCCG
1802 AAACCCG
1 AAACCCG
1809 AACACTCCG
1 AA-AC-CCG
1818 AAACCCTG
1 AAACCC-G
1826 -AACCCG
1 AAACCCG
*
1832 AACCCCG
1 AAACCCG
1839 AAACCCG
1 AAACCCG
*
1846 AACCCCG
1 AAACCCG
1853 AAACCCG
1 AAACCCG
1860 AAACCCGG
1 AAACCC-G
1868 AAACCCG
1 AAACCCG
1875 AAACCCG
1 AAACCCG
1882 AAACCCTG
1 AAACCC-G
*
1890 AAACTCG
1 AAACCCG
1897 AAA-CCG
1 AAACCCG
1903 AAACCCG
1 AAACCCG
1910 AAACCCG
1 AAACCCG
*
1917 ACACCCG
1 AAACCCG
1924 AAAACCCG
1 -AAACCCG
1932 AAACCCG
1 AAACCCG
1939 AAACCCG
1 AAACCCG
1946 -AACCCG
1 AAACCCG
1952 AAA-CCG
1 AAACCCG
1958 AAACCCG
1 AAACCCG
1965 AAACCCG
1 AAACCCG
1972 AAACCCG
1 AAACCCG
1979 AAACCCG
1 AAACCCG
*
1986 AAACCCT
1 AAACCCG
1993 AAACCTCG
1 AAACC-CG
2001 AAA-CCG
1 AAACCCG
2007 TAAACCGCG
1 -AAACC-CG
2016 -AACCCG
1 AAACCCG
2022 AATACCCG
1 AA-ACCCG
2030 ACAACCCG
1 A-AACCCG
2038 AAAACCCG
1 -AAACCCG
2046 AAA-CCG
1 AAACCCG
2052 AAACCCG
1 AAACCCG
2059 TAAACCTCG
1 -AAACC-CG
2068 AAAACCCG
1 -AAACCCG
*
2076 AACCCCG
1 AAACCCG
2083 -AA-CCG
1 AAACCCG
2088 AAACCCG
1 AAACCCG
*
2095 ACACCCG
1 AAACCCG
2102 AAACCC-
1 AAACCCG
*
2108 TAACCCG
1 AAACCCG
2115 AAACCCG
1 AAACCCG
2122 AAACCCG
1 AAACCCG
2129 AAACCCG
1 AAACCCG
*
2136 ACACCCG
1 AAACCCG
2143 AAA--CG
1 AAACCCG
2148 AAAACCCG
1 -AAACCCG
2156 AATACCCGG
1 AA-ACCC-G
2165 TAAACCCG
1 -AAACCCG
2173 AAACCCG
1 AAACCCG
2180 CAACAGACCTCG
1 --A-A-ACC-CG
2192 AAACCCG
1 AAACCCG
2199 AAACCCG
1 AAACCCG
2206 AAACCCG
1 AAACCCG
*
2213 CAACCCG
1 AAACCCG
2220 AAA-CCG
1 AAACCCG
*
2226 AACCCCG
1 AAACCCG
*
2233 CAACCCCG
1 -AAACCCG
2241 -AACCCG
1 AAACCCG
*
2247 AAACTCG
1 AAACCCG
*
2254 ACACCCG
1 AAACCCG
2261 AAACCCG
1 AAACCCG
2268 AAACCCAG
1 AAACCC-G
2276 AAACCCG
1 AAACCCG
*
2283 GAACCCG
1 AAACCCG
2290 AAACCCG
1 AAACCCG
2297 AAACCCG
1 AAACCCG
2304 AAACCCG
1 AAACCCG
2311 ACAACCCG
1 A-AACCCG
*
2319 CAACCCCG
1 -AAACCCG
2327 AAACCCG
1 AAACCCG
2334 AAAACCCG
1 -AAACCCG
*
2342 CAATCCCG
1 -AAACCCG
2350 -AACCCG
1 AAACCCG
2356 AAACCCG
1 AAACCCG
2363 AAA-CCG
1 AAACCCG
2369 AAA-CCG
1 AAACCCG
2375 AAACCC-
1 AAACCCG
2381 AAA-CCG
1 AAACCCG
2387 AAACCCG
1 AAACCCG
2394 AAACCCG
1 AAACCCG
2401 AATAACCCG
1 -A-AACCCG
*
2410 AAAACCG
1 AAACCCG
2417 -AACCCG
1 AAACCCG
2423 AAATCCTCG
1 AAA-CC-CG
2432 AAACCCG
1 AAACCCG
2439 AAACCCG
1 AAACCCG
2446 AAACCCG
1 AAACCCG
* *
2453 CAACGCG
1 AAACCCG
2460 AAA-CCG
1 AAACCCG
2466 AAACCCG
1 AAACCCG
2473 CAAACCGCGCTGG
1 -AAA-C-C-C--G
2486 AAATCCCG
1 AAA-CCCG
2494 TAAAACCCG
1 --AAACCCG
2503 AAACCCG
1 AAACCCG
2510 AAACCCG
1 AAACCCG
2517 -AACCCG
1 AAACCCG
2523 AAACCCG
1 AAACCCG
2530 AAAACCCG
1 -AAACCCG
2538 -AACCCG
1 AAACCCG
2544 AAACCCG
1 AAACCCG
2551 ATAAACCCG
1 --AAACCCG
2560 -AACCCAG
1 AAACCC-G
2567 AAACCCG
1 AAACCCG
2574 AAACCCG
1 AAACCCG
*
2581 AAACCAG
1 AAACCCG
2588 AAACCCG
1 AAACCCG
*
2595 AACCCCG
1 AAACCCG
2602 AAACCTCG
1 AAACC-CG
2610 -AACCCG
1 AAACCCG
2616 AAACCCG
1 AAACCCG
2623 AAA-CCG
1 AAACCCG
2629 AAA--CG
1 AAACCCG
2634 AAACCCG
1 AAACCCG
2641 AAACCCG
1 AAACCCG
2648 -AACCCG
1 AAACCCG
2654 AAACCCG
1 AAACCCG
2661 AAACCCG
1 AAACCCG
2668 AAA-CCG
1 AAACCCG
2674 AAACCCG
1 AAACCCG
2681 --A-CCG
1 AAACCCG
*
2685 AACCCCG
1 AAACCCG
2692 AAACCCG
1 AAACCCG
2699 -AACCCG
1 AAACCCG
2705 AAACCCG
1 AAACCCG
2712 AAACCCG
1 AAACCCG
2719 AATAACCCG
1 -A-AACCCG
2728 AAACCCG
1 AAACCCG
2735 AAACCCG
1 AAACCCG
2742 AAACCCG
1 AAACCCG
2749 AAACCCG
1 AAACCCG
2756 AAACCCG
1 AAACCCG
2763 -AACCCG
1 AAACCCG
*
2769 AACCCCTG
1 AAACCC-G
2777 AAACCCG
1 AAACCCG
2784 AAACCCG
1 AAACCCG
2791 AAA-CCG
1 AAACCCG
2797 -AACCCG
1 AAACCCG
*
2803 TAACCCG
1 AAACCCG
*
2810 AACCCCG
1 AAACCCG
2817 AAA-CCG
1 AAACCCG
2823 AAACCCG
1 AAACCCG
2830 AAACCCG
1 AAACCCG
2837 AAACCCG
1 AAACCCG
2844 -AACCCG
1 AAACCCG
2850 AAACCC-
1 AAACCCG
2856 AAACCCG
1 AAACCCG
2863 AAACCCG
1 AAACCCG
2870 AAACCCG
1 AAACCCG
2877 AAACCCG
1 AAACCCG
2884 AAACCCG
1 AAACCCG
2891 AAACCCG
1 AAACCCG
2898 -AACCCG
1 AAACCCG
2904 AAACCCG
1 AAACCCG
2911 ACAACCCG
1 A-AACCCG
2919 AAACCCG
1 AAACCCG
2926 AAACCCG
1 AAACCCG
2933 AAACCCTG
1 AAACCC-G
2941 AAACCCG
1 AAACCCG
*
2948 AACCCCG
1 AAACCCG
2955 AAACCCG
1 AAACCCG
2962 AAACCCG
1 AAACCCG
2969 -AACCCG
1 AAACCCG
2975 -AACCCG
1 AAACCCG
*
2981 CAACCTCCG
1 -AAAC-CCG
2990 AAA-CCG
1 AAACCCG
2996 AAAACCCG
1 -AAACCCG
3004 AAACCCG
1 AAACCCG
*
3011 CAACCCG
1 AAACCCG
3018 AAACCCG
1 AAACCCG
3025 AAACCCG
1 AAACCCG
3032 AAACCCG
1 AAACCCG
*
3039 AAATCCG
1 AAACCCG
3046 AAACCCG
1 AAACCCG
3053 AAA-CCG
1 AAACCCG
3059 ATAACCCGG
1 A-AACCC-G
3068 AAACCCG
1 AAACCCG
3075 AAA-CCG
1 AAACCCG
3081 AATACCCG
1 AA-ACCCG
3089 AAACCCG
1 AAACCCG
3096 AAACCCG
1 AAACCCG
*
3103 CAACCCG
1 AAACCCG
*
3110 CTAACCCG
1 -AAACCCG
3118 AAACCCG
1 AAACCCG
3125 AAACCCG
1 AAACCCG
*
3132 CAA-CCG
1 AAACCCG
3138 AAACCCG
1 AAACCCG
3145 ATAACCCG
1 A-AACCCG
3153 AAACCCG
1 AAACCCG
3160 AAA-CCG
1 AAACCCG
3166 AAACCCG
1 AAACCCG
3173 AAACCCG
1 AAACCCG
3180 AAACCCG
1 AAACCCG
3187 AAACCCG
1 AAACCCG
3194 TAAACCCG
1 -AAACCCG
3202 AAA-CCG
1 AAACCCG
3208 AAACCCG
1 AAACCCG
3215 AAAACCCG
1 -AAACCCG
* *
3223 ACACCCCT
1 A-AACCCG
*
3231 CAACCCG
1 AAACCCG
3238 AAACCCG
1 AAACCCG
3245 -AACTCCG
1 AAAC-CCG
3252 ATAACCCG
1 A-AACCCG
3260 AAACCCG
1 AAACCCG
*
3267 AAA-CCT
1 AAACCCG
3273 AAACCCG
1 AAACCCG
3280 AAACCCG
1 AAACCCG
3287 AATACCCG
1 AA-ACCCG
3295 AAA-CCG
1 AAACCCG
*
3301 CTAACCCG
1 -AAACCCG
3309 AAACCCG
1 AAACCCG
3316 ATAACCCG
1 A-AACCCG
3324 ATAACCCG
1 A-AACCCG
3332 AAACCCG
1 AAACCCG
3339 AAACCCTG
1 AAACCC-G
3347 -AACCCG
1 AAACCCG
*
3353 AAAACCGG
1 -AAACCCG
3361 AAACCCG
1 AAACCCG
3368 AAACCCG
1 AAACCCG
3375 -AACCCG
1 AAACCCG
3381 AAACCCG
1 AAACCCG
3388 CAAA-CCG
1 -AAACCCG
3395 ATATACCTCG
1 A-A-ACC-CG
3405 AAACCCG
1 AAACCCG
*
3412 AAACACG
1 AAACCCG
3419 -AACCCG
1 AAACCCG
3425 CAAAACCCG
1 --AAACCCG
*
3434 TACTACCCG
1 -A-AACCCG
3443 AAACCCG
1 AAACCCG
3450 AAACCCG
1 AAACCCG
3457 AAA-CCG
1 AAACCCG
3463 AAACCC-
1 AAACCCG
3469 AAACCCG
1 AAACCCG
3476 AAAAAACCCG
1 ---AAACCCG
3486 AAACCTTCGG
1 AAACC--C-G
3496 AAAACGGTCCG
1 -AAAC---CCG
3507 -AACCCG
1 AAACCCG
*
3513 TATCACCCG
1 -A-AACCCG
3522 AAACCCG
1 AAACCCG
*
3529 CAACTCCG
1 AAAC-CCG
3537 AAGACCCG
1 AA-ACCCG
3545 AAACCCG
1 AAACCCG
*
3552 AACCCCG
1 AAACCCG
*
3559 -CACCCG
1 AAACCCG
3565 AAACCCG
1 AAACCCG
3572 AAACAACCCG
1 --A-AACCCG
**
3582 CCACCCG
1 AAACCCG
*
3589 GAACCCG
1 AAACCCG
3596 AAACCCG
1 AAACCCG
3603 AAAAACCCG
1 --AAACCCG
3612 AAACCACG
1 AAACC-CG
3620 AATACCCCG
1 AA-A-CCCG
3629 TAAACCCG
1 -AAACCCG
3637 TAAACCCG
1 -AAACCCG
*
3645 CATATCCCG
1 -A-AACCCG
3654 AAACCCG
1 AAACCCG
3661 AAA--CG
1 AAACCCG
3666 AAACCCG
1 AAACCCG
3673 -AACCCG
1 AAACCCG
3679 AAAACCCG
1 -AAACCCG
*
3687 AAACCCT
1 AAACCCG
3694 AAACCCTG
1 AAACCC-G
3702 TAAACCCGG
1 -AAACCC-G
* *
3711 CACCTCCAG
1 AAAC-CC-G
3720 AAACCCG
1 AAACCCG
*
3727 AAACCCT
1 AAACCCG
*
3734 AACCCCG
1 AAACCCG
3741 -AACCCGG
1 AAACCC-G
*
3748 AAAACCG
1 AAACCCG
3755 ATAACCCG
1 A-AACCCG
3763 ACAACCCG
1 A-AACCCG
3771 AAACCCG
1 AAACCCG
3778 AAAAATCCCG
1 --AAA-CCCG
3788 AAAACCCG
1 -AAACCCG
*
3796 ATA-CCG
1 AAACCCG
3802 -AACCCG
1 AAACCCG
3808 -AACCCG
1 AAACCCG
3814 AAACCCG
1 AAACCCG
*
3821 CAACCCG
1 AAACCCG
3828 AAACCCG
1 AAACCCG
3835 AAA-CCG
1 AAACCCG
3841 ATAACCCG
1 A-AACCCG
3849 AAACCCGG
1 AAACCC-G
3857 AAA-CCG
1 AAACCCG
3863 ATTAACCCG
1 A--AACCCG
3872 AAACCCG
1 AAACCCG
3879 AAACCCTG
1 AAACCC-G
* *
3887 AAGCCCTA
1 AAACCC-G
3895 AAACCCG
1 AAACCCG
3902 AAACCCCG
1 AAA-CCCG
3910 AAACCCG
1 AAACCCG
3917 AAACCCG
1 AAACCCG
*
3924 -ATCACCG
1 AAAC-CCG
3931 -AA-CCG
1 AAACCCG
3936 -AACCCG
1 AAACCCG
3942 AAACCCG
1 AAACCCG
3949 AAACCCG
1 AAACCCG
3956 AAACCCG
1 AAACCCG
3963 AAACCCG
1 AAACCCG
3970 -AA-CCG
1 AAACCCG
3975 AAACCCGG
1 AAACCC-G
3983 AAACCCG
1 AAACCCG
3990 -AACCCG
1 AAACCCG
3996 AAACCCGG
1 AAACCC-G
4004 AAACCCG
1 AAACCCG
*
4011 AAAAACAAC-
1 --AAAC-CCG
4020 AAACCCCCG
1 AAA--CCCG
4029 AAACCCG
1 AAACCCG
*
4036 AACCCCG
1 AAACCCG
4043 AAACCCG
1 AAACCCG
4050 AAACCCG
1 AAACCCG
4057 AAACCCG
1 AAACCCG
4064 -AA-CCG
1 AAACCCG
*
4069 ACACCCG
1 AAACCCG
4076 ATCAACCCGG
1 A--AACCC-G
4086 AAACCCG
1 AAACCCG
4093 AAAACCCG
1 -AAACCCG
4101 AAACCCG
1 AAACCCG
*
4108 AAGCCCG
1 AAACCCG
*
4115 AAGCCCG
1 AAACCCG
*
4122 AAGCCCG
1 AAACCCG
*
4129 AAGCCCG
1 AAACCCG
*
4136 ATACCCCGG
1 A-AACCC-G
4145 AAAACCCG
1 -AAACCCG
*
4153 AAATTACTCCTAA
1 -AA--AC-CC--G
4166 AAACCCG
1 AAACCCG
4173 AAAACCCG
1 -AAACCCG
4181 ACAACCCG
1 A-AACCCG
*
4189 TACACCCG
1 -AAACCCG
4197 AAACCCG
1 AAACCCG
4204 AAACCTCG
1 AAACC-CG
4212 AAACCCG
1 AAACCCG
4219 AAACCCG
1 AAACCCG
*
4226 AAA-CCT
1 AAACCCG
4232 AAACCCGG
1 AAACCC-G
4240 AAACTCCG
1 AAAC-CCG
4248 AAAACCCG
1 -AAACCCG
4256 AAACCCG
1 AAACCCG
4263 AAACCCG
1 AAACCCG
4270 AAACCCG
1 AAACCCG
4277 AAACCCG
1 AAACCCG
4284 ATAACCCG
1 A-AACCCG
4292 AAACCCG
1 AAACCCG
4299 AAACCCG
1 AAACCCG
4306 AAACCCG
1 AAACCCG
*
4313 AACCCCG
1 AAACCCG
*
4320 AAAATCCTG
1 -AAA-CCCG
4329 AAACTCCG
1 AAAC-CCG
4337 TATAAAACCCTG
1 ----AAACCC-G
4349 ATAAACCCG
1 --AAACCCG
*
4358 AAAACCCTA
1 -AAACCC-G
4367 AAACCCG
1 AAACCCG
*
4374 AACCCCG
1 AAACCCG
4381 AAACCCTG
1 AAACCC-G
4389 AAACCCG
1 AAACCCG
4396 AAACCCG
1 AAACCCG
4403 AAACCCG
1 AAACCCG
4410 AAAACCCG
1 -AAACCCG
4418 AAA-CCG
1 AAACCCG
4424 AAA-CCG
1 AAACCCG
4430 AAA-CCG
1 AAACCCG
*
4436 ACACCCG
1 AAACCCG
4443 AAACCCG
1 AAACCCG
*
4450 AAACCTTGG
1 AAACC--CG
4459 AAA-CCG
1 AAACCCG
4465 AAACCCG
1 AAACCCG
4472 AAACCCG
1 AAACCCG
4479 AAACCCG
1 AAACCCG
4486 AAA-CCG
1 AAACCCG
4492 AAACCCG
1 AAACCCG
4499 AAACCCG
1 AAACCCG
4506 AAACCCG
1 AAACCCG
*
4513 TAACCCTG
1 AAACCC-G
4521 AAACCCG
1 AAACCCG
4528 -AACCCG
1 AAACCCG
4534 AAAACCCG
1 -AAACCCG
4542 AAAACCCG
1 -AAACCCG
4550 -AACCCG
1 AAACCCG
4556 AAACCCG
1 AAACCCG
4563 AAACCCG
1 AAACCCG
4570 AAACCCG
1 AAACCCG
4577 AAACCCG
1 AAACCCG
4584 AAACCCG
1 AAACCCG
4591 AAACCCG
1 AAACCCG
4598 TAAACCCG
1 -AAACCCG
*
4606 AAACCCT
1 AAACCCG
*
4613 AAACCCT
1 AAACCCG
4620 AAACCCG
1 AAACCCG
4627 AAACCCCG
1 AAA-CCCG
4635 ACAA-CCG
1 A-AACCCG
*
4642 GAACCCTG
1 AAACCC-G
*
4650 AAACCCT
1 AAACCCG
4657 AAACCCG
1 AAACCCG
4664 AAACCGCG
1 AAACC-CG
4672 AAACCCG
1 AAACCCG
4679 AAACCCG
1 AAACCCG
4686 --A-CCG
1 AAACCCG
4690 AAACCCG
1 AAACCCG
*
4697 AAACCCA
1 AAACCCG
4704 AAACCCG
1 AAACCCG
4711 AAACCCG
1 AAACCCG
4718 AAACCCG
1 AAACCCG
*
4725 AAACACG
1 AAACCCG
4732 AAACCCG
1 AAACCCG
4739 AAACCCGG
1 AAACCC-G
4747 AAACCCG
1 AAACCCG
4754 AAACCTCG
1 AAACC-CG
4762 -AACCC-
1 AAACCCG
*
4767 -ACCCCG
1 AAACCCG
4773 AAACCCG
1 AAACCCG
4780 AAACCCG
1 AAACCCG
*
4787 AACCCCG
1 AAACCCG
4794 AAACCCG
1 AAACCCG
4801 AAACCC-
1 AAACCCG
*
4807 TAACCCGG
1 AAACCC-G
4815 AAACCCG
1 AAACCCG
4822 -AACCCG
1 AAACCCG
4828 AAACCCG
1 AAACCCG
4835 AATACCCG
1 AA-ACCCG
4843 AAACCCG
1 AAACCCG
4850 AAA-CCG
1 AAACCCG
4856 -AACCCG
1 AAACCCG
4862 AAACCCG
1 AAACCCG
4869 AAACCCG
1 AAACCCG
4876 AAACCCG
1 AAACCCG
4883 AAACCCG
1 AAACCCG
4890 AAACCCCG
1 AAA-CCCG
4898 AAACCCG
1 AAACCCG
4905 AAAACCCG
1 -AAACCCG
4913 AAACCC-
1 AAACCCG
*
4919 AACCCTCG
1 AAACC-CG
*
4927 AACCCCG
1 AAACCCG
4934 AAATCCCG
1 AAA-CCCG
4942 AAACCCG
1 AAACCCG
4949 TAAACCCG
1 -AAACCCG
4957 AAATCCCG
1 AAA-CCCG
4965 AAACCCG
1 AAACCCG
*
4972 AACCCCG
1 AAACCCG
4979 AAACCCG
1 AAACCCG
4986 AAA-CCG
1 AAACCCG
4992 AAACCCG
1 AAACCCG
4999 AAACCCG
1 AAACCCG
5006 AAACCCG
1 AAACCCG
5013 AAACCCG
1 AAACCCG
5020 AAAACCCG
1 -AAACCCG
5028 -AACCCG
1 AAACCCG
5034 AAACCCG
1 AAACCCG
*
5041 CAAACCCT
1 -AAACCCG
5049 AATACTCCG
1 AA-AC-CCG
5058 ATAA-CCG
1 A-AACCCG
5065 AAA-CCG
1 AAACCCG
5071 AAACCC-
1 AAACCCG
5077 AAACCCG
1 AAACCCG
5084 -AACCCG
1 AAACCCG
*
5090 AACCCCG
1 AAACCCG
*
5097 AAAACCCT
1 -AAACCCG
*
5105 AAATCCCT
1 AAA-CCCG
*
5113 CAA-CCG
1 AAACCCG
5119 AAA-CCG
1 AAACCCG
5125 -AACCCG
1 AAACCCG
*
5131 AAACCCT
1 AAACCCG
*
5138 AAACCCT
1 AAACCCG
*
5145 AAACCCT
1 AAACCCG
*
5152 AAACCCT
1 AAACCCG
*
5159 AAACCCT
1 AAACCCG
*
5166 AACCCCG
1 AAACCCG
*
5173 AAACCCT
1 AAACCCG
*
5180 AAACCCT
1 AAACCCG
*
5187 AAACCCT
1 AAACCCG
5194 AAACCC-
1 AAACCCG
** *
5200 TCACCCC
1 AAACCCG
5207 ATAACCC-
1 A-AACCCG
5214 AAACCC-
1 AAACCCG
*
5220 AAACCCC
1 AAACCCG
*
5227 AAACCCC
1 AAACCCG
* *
5234 AATCCCC
1 AAACCCG
5241 AAACCC-
1 AAACCCG
*
5247 AAACCCCA
1 AAA-CCCG
*
5255 AAACCCC
1 AAACCCG
*
5262 AAACCCC
1 AAACCCG
*
5269 AAACCCC
1 AAACCCG
*
5276 AAACCCC
1 AAACCCG
* *
5283 AACCCCC
1 AAACCCG
*
5290 AAACCCC
1 AAACCCG
*
5297 AAACCCC
1 AAACCCG
*
5304 AAACCCC
1 AAACCCG
*
5311 AAACCCC
1 AAACCCG
5318 AAACCC
1 AAACCC
5324 CCATACCCAA
Statistics
Matches: 4526, Mismatches: 314, Indels: 946
0.78 0.05 0.16
Matches are distributed among these distances:
4 9 0.00
5 69 0.02
6 616 0.14
7 2441 0.54
8 968 0.21
9 291 0.06
10 83 0.02
11 31 0.01
12 16 0.00
13 1 0.00
14 1 0.00
ACGTcount: A:0.40, C:0.42, G:0.13, T:0.04
Consensus pattern (7 bp):
AAACCCG
Found at i:5543 original size:21 final size:21
Alignment explanation
Indices: 5518--5584 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5508 CTTAAACTCA
*
5518 AACCCCTAAACCCCAACCCCG
1 AACCCCTAACCCCCAACCCCG
5539 AA-CCCTCAACCCCCAAGCCCCG
1 AACCCCT-AACCCCCAA-CCCCG
* * *
5561 AGCCTC-AACCCCCAACCCCT
1 AACCCCTAACCCCCAACCCCG
5581 AACC
1 AACC
5585 TCTACCCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.29
21 19 0.50
22 6 0.16
23 2 0.05
ACGTcount: A:0.30, C:0.58, G:0.06, T:0.06
Consensus pattern (21 bp):
AACCCCTAACCCCCAACCCCG
Found at i:5584 original size:14 final size:14
Alignment explanation
Indices: 5518--5584 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
5508 CTTAAACTCA
*
5518 AACCCCTAAACCCC
1 AACCCCTAACCCCC
* *
5532 AACCCCGAACCCTC
1 AACCCCTAACCCCC
* *
5546 AACCCCCAAGCCCC
1 AACCCCTAACCCCC
* *
5560 GA-GCCTCAACCCCC
1 AACCCCT-AACCCCC
5574 AACCCCTAACC
1 AACCCCTAACC
5585 TCTACCCGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
13 2 0.05
14 34 0.87
15 3 0.08
ACGTcount: A:0.30, C:0.58, G:0.06, T:0.06
Consensus pattern (14 bp):
AACCCCTAACCCCC
Found at i:6831 original size:2 final size:2
Alignment explanation
Indices: 6824--6881 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
6814 TATCTTAGTC
6824 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6866 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
6882 TTGTTGACTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8781 original size:56 final size:53
Alignment explanation
Indices: 8709--8818 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 53
8699 TGGCTAGAAA
*
8709 AATGCATGGGTTTGACTATCATCGCCCTCTTTTTCATTTTGCCTTTGGACTAATAT
1 AATGCATGGCTTTGACTATCATCGCCCTCTTTTTCATTTT---TTTGGACTAATAT
* *
8765 AATGCATGGCTTTGACTATCATCGCTCTTTTTTTCATTTTTTTGGACTAATAT
1 AATGCATGGCTTTGACTATCATCGCCCTCTTTTTCATTTTTTTGGACTAATAT
8818 A
1 A
8819 TTATATTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
53 14 0.27
56 37 0.73
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (53 bp):
AATGCATGGCTTTGACTATCATCGCCCTCTTTTTCATTTTTTTGGACTAATAT
Found at i:9419 original size:2 final size:2
Alignment explanation
Indices: 9412--9456 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
9402 TTTGCTTGTT
9412 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9453 TA TA
1 TA TA
9457 GTGGAAGTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14643 original size:18 final size:19
Alignment explanation
Indices: 14602--14643 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
14592 CTCATGCTTT
* *
14602 ATTTTAAAATATTTTGATT
1 ATTTTAAAATATTTTAATA
*
14621 TTTTTAAAA-ATTTTAATA
1 ATTTTAAAATATTTTAATA
14639 ATTTT
1 ATTTT
14644 TCGATGACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAAAATATTTTAATA
Found at i:14643 original size:19 final size:19
Alignment explanation
Indices: 14603--14644 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
14593 TCATGCTTTA
* *
14603 TTTTAAAATATTTTGATTT
1 TTTTAAAATATTTTAATAT
14622 TTTTAAAA-ATTTTAATAAT
1 TTTTAAAATATTTTAAT-AT
14641 TTTT
1 TTTT
14645 CGATGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAAAATATTTTAATAT
Found at i:15675 original size:38 final size:38
Alignment explanation
Indices: 15653--15754 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 38
15643 ATATCACTGG
*
15653 TTAAAAATAATAATTTTTATTTTGAATTATACTACCAA
1 TTAAAAATAATAATTTTTATTTTAAATTATACTACCAA
* ** * * * *
15691 TTAACAATAATAATTTTTATTTCGAATAATATTATCTA
1 TTAAAAATAATAATTTTTATTTTAAATTATACTACCAA
* *
15729 TTAAAATTAATGATTTTTATATTTAA
1 TTAAAAATAATAATTTTTAT-TTTAA
15755 CGGTGCAACA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 49 0.94
39 3 0.06
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (38 bp):
TTAAAAATAATAATTTTTATTTTAAATTATACTACCAA
Found at i:20545 original size:2 final size:2
Alignment explanation
Indices: 20538--20586 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
20528 TATTTGTACT
* *
20538 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20580 TA CA TA T
1 TA TA TA T
20587 TAATTATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:21341 original size:2 final size:2
Alignment explanation
Indices: 21334--21375 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21324 AACTCTACTA
21334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21376 TCTAAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23791 original size:3 final size:3
Alignment explanation
Indices: 23783--23838 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
23773 AAGTGGGTGA
23783 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23831 AAT AAT AA
1 AAT AAT AA
23839 AATTGGATAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:24242 original size:3 final size:3
Alignment explanation
Indices: 24234--24277 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
24224 CCTTAGTTGC
24234 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24278 GCTGCTAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26830 original size:25 final size:25
Alignment explanation
Indices: 26796--26849 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
26786 GAGTTATTTA
26796 TCTACAAACAAAGTTTGCTAATAGG
1 TCTACAAACAAAGTTTGCTAATAGG
*
26821 TCTACAAACAAAGTTTGCTAATATG
1 TCTACAAACAAAGTTTGCTAATAGG
26846 TCTA
1 TCTA
26850 AGCAATAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (25 bp):
TCTACAAACAAAGTTTGCTAATAGG
Found at i:34752 original size:19 final size:19
Alignment explanation
Indices: 34725--34768 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34715 GCAGTAAATA
* *
34725 AATAGTCAACTATGATTAG
1 AATAATCAACTATAATTAG
*
34744 AATAATCAACTGTAATTAG
1 AATAATCAACTATAATTAG
34763 AATAAT
1 AATAAT
34769 AATACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (19 bp):
AATAATCAACTATAATTAG
Found at i:35464 original size:20 final size:20
Alignment explanation
Indices: 35435--35473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35425 TTAAAAAAAT
35435 TTAAAATTTTATAATTTTAC
1 TTAAAATTTTATAATTTTAC
* *
35455 TTAAATTTTTATATTTTTA
1 TTAAAATTTTATAATTTTA
35474 TTATATTCAA
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:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTATAATTTTAC
Found at i:35550 original size:18 final size:18
Alignment explanation
Indices: 35527--35570 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35517 TATTTTAATT
35527 AAATAAATATTAATTTAA
1 AAATAAATATTAATTTAA
* *
35545 AAATAAAAATTTATTTAA
1 AAATAAATATTAATTTAA
*
35563 ACATAAAT
1 AAATAAAT
35571 TAAAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAAATATTAATTTAA
Found at i:35603 original size:30 final size:30
Alignment explanation
Indices: 35541--35610 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
35531 AAATATTAAT
35541 TTAAAAA-TAAAAATTTATTTAAACATAAA
1 TTAAAAATTAAAAATTTATTTAAACATAAA
* **
35570 TTAAAAGTTAAAAATTTATTTAATTA-AACA
1 TTAAAAATTAAAAATTTATTTAAACATAA-A
35600 TTAAAAATTAA
1 TTAAAAATTAA
35611 GAGTTCGACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.23
30 27 0.77
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
TTAAAAATTAAAAATTTATTTAAACATAAA
Found at i:36550 original size:2 final size:2
Alignment explanation
Indices: 36543--36570 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36533 TTCATGTGAA
36543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36571 GAAATTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39386 original size:26 final size:25
Alignment explanation
Indices: 39343--39393 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
39333 TTAATTAGTA
39343 AAAAGTTTAAATTTAGATTTAATTT
1 AAAAGTTTAAATTTAGATTTAATTT
39368 AAAA-TTTAAGATTTAAGATTTAATTT
1 AAAAGTTTAA-ATTT-AGATTTAATTT
39394 TAAGTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.21
25 8 0.33
26 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
AAAAGTTTAAATTTAGATTTAATTT
Found at i:42267 original size:18 final size:19
Alignment explanation
Indices: 42210--42267 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 19
42200 AAAATAAAGT
42210 TATAAATATTATTATAAAAA
1 TATAAATATTATTAT-AAAA
42230 TATATAAT-TATATTATAAAA
1 TATA-AATAT-TATTATAAAA
*
42250 TA-AAATATTATGATAAAA
1 TATAAATATTATTATAAAA
42268 AATATGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 12 0.35
19 2 0.06
20 11 0.32
21 9 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAATATTATTATAAAA
Found at i:44726 original size:2 final size:2
Alignment explanation
Indices: 44719--44748 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44709 CTTTAATTAG
44719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44749 TGTAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47269 original size:3 final size:3
Alignment explanation
Indices: 47261--47291 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
47251 TTTCATGTAA
47261 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
47292 CACCACTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:53212 original size:27 final size:29
Alignment explanation
Indices: 53178--53245 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
53168 TATCTTTAAA
53178 AAATAAA-TTATTAGATTATTA-ATTTTT
1 AAATAAATTTATTAGATTATTATATTTTT
*
53205 AAATAAATTTTTATTATATTATTATATTTTT
1 AAATAAA--TTTATTAGATTATTATATTTTT
*
53236 -AATATATTTA
1 AAATAAATTTA
53246 ATTATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
30 18 0.51
31 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
AAATAAATTTATTAGATTATTATATTTTT
Found at i:53251 original size:19 final size:19
Alignment explanation
Indices: 53206--53252 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
53196 TTAATTTTTA
* *
53206 AATAAATTTTTATTATATT
1 AATATATTTTTAATATATT
*
53225 ATTATATTTTTAATATATTT
1 AATATATTTTTAATATA-TT
53245 AAT-TATTT
1 AATATATTT
53253 ATTTATTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATATTTTTAATATATT
Found at i:53454 original size:9 final size:10
Alignment explanation
Indices: 53436--53480 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
53426 ATATCAAATT
53436 AATATTTAAA
1 AATATTTAAA
53446 AAT-TTTAAA
1 AATATTTAAA
53455 ATATATTTAATAA
1 A-ATATTT-A-AA
53468 AATATTTAAA
1 AATATTTAAA
53478 AAT
1 AAT
53481 TTATTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 4 0.13
12 7 0.23
13 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATTTAAA
Found at i:53472 original size:12 final size:11
Alignment explanation
Indices: 53436--53479 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
53426 ATATCAAATT
53436 AATATTT-AAA
1 AATATTTAAAA
53446 AAT-TTTAAAA
1 AATATTTAAAA
*
53456 TATATTTAATAA
1 AATATTTAA-AA
53468 AATATTTAAAA
1 AATATTTAAAA
53479 A
1 A
53480 TTTATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 3 0.10
10 8 0.28
11 8 0.28
12 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:53479 original size:24 final size:23
Alignment explanation
Indices: 53442--53489 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
53432 AATTAATATT
*
53442 TAAAAATTTTAAAATATATTTAA
1 TAAAAATTTAAAAATATATTTAA
*
53465 TAAAATATTTAAAAATTTATTTAA
1 TAAAA-ATTTAAAAATATATTTAA
53489 T
1 T
53490 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAATTTAAAAATATATTTAA
Found at i:58763 original size:24 final size:24
Alignment explanation
Indices: 58731--58782 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
58721 CTAAGGATAC
58731 GTGAAAATTACAAGTAATATTTAG
1 GTGAAAATTACAAGTAATATTTAG
58755 GTGAAAATTACAAGTAATATTTAG
1 GTGAAAATTACAAGTAATATTTAG
58779 GTGA
1 GTGA
58783 TTTGGTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (24 bp):
GTGAAAATTACAAGTAATATTTAG
Found at i:58908 original size:44 final size:44
Alignment explanation
Indices: 58858--58947 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
58848 CAATTAGTTG
58858 ATTATGTCAAATCACATAAATGTAAATAAAAGATAACATCGAAT
1 ATTATGTCAAATCACATAAATGTAAATAAAAGATAACATCGAAT
58902 ATTATGTCAAATCACATAAATGTAAATAAAAGATAACATCGAAT
1 ATTATGTCAAATCACATAAATGTAAATAAAAGATAACATCGAAT
58946 AT
1 AT
58948 AAGGTGTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (44 bp):
ATTATGTCAAATCACATAAATGTAAATAAAAGATAACATCGAAT
Found at i:58995 original size:18 final size:18
Alignment explanation
Indices: 58956--58998 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58946 ATAAGGTGTT
***
58956 AAAACCTTCAGGATGGGT
1 AAAACCTTCAGGATGAAA
58974 AAAACCTTCAGGATGAAA
1 AAAACCTTCAGGATGAAA
58992 AAAACCT
1 AAAACCT
58999 CCACGAGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (18 bp):
AAAACCTTCAGGATGAAA
Found at i:67342 original size:16 final size:16
Alignment explanation
Indices: 67318--67406 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 16
67308 CAAATATTTA
67318 AATTCTAAATTATTTTT
1 AATT-TAAATTATTTTT
* **
67335 AAATTAAAAAATTATTTCG
1 -AATT--TAAATTATTTTT
67354 AATTTAAATTA-TTTT
1 AATTTAAATTATTTTT
67369 AATTTTAAATTA-TTTT
1 AA-TTTAAATTATTTTT
*
67385 AATTTAAATTTATTTTA
1 AATTTAAA-TTATTTTT
67402 AATTT
1 AATTT
67407 TGATCAATTG
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
15 10 0.17
16 24 0.41
17 8 0.14
18 8 0.14
19 9 0.15
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
AATTTAAATTATTTTT
Found at i:67398 original size:32 final size:33
Alignment explanation
Indices: 67318--67407 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 33
67308 CAAATATTTA
**
67318 AATTCTAAATTATTTTTAAATTAAAAAATTATTTCG
1 AATT-TAAATTA-TTTTAAATT-TTAAATTATTTCG
*
67354 AATTTAAATTATTTT-AATTTTAAATTATTT-T
1 AATTTAAATTATTTTAAATTTTAAATTATTTCG
67385 AATTTAAATTTATTTTAAATTTT
1 AATTTAAA-TTATTTTAAATTTT
67408 GATCAATTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 8 0.16
32 16 0.33
33 10 0.20
34 4 0.08
35 7 0.14
36 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (33 bp):
AATTTAAATTATTTTAAATTTTAAATTATTTCG
Found at i:76258 original size:30 final size:30
Alignment explanation
Indices: 76223--76281 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
76213 CAGTTGGAGC
* *
76223 TGGAGCTGGAGCTAGGAGTTGTAACAGAAT
1 TGGAGCTAGAGCTAGGAATTGTAACAGAAT
*
76253 TGGAGCTAGAGCTGGGAATTGTAACAGAA
1 TGGAGCTAGAGCTAGGAATTGTAACAGAA
76282 AGATTAGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.36, T:0.22
Consensus pattern (30 bp):
TGGAGCTAGAGCTAGGAATTGTAACAGAAT
Found at i:77065 original size:2 final size:2
Alignment explanation
Indices: 77058--77082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77048 TTGGGCAGGA
77058 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
77083 AAATAAAAAA
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:84293 original size:3 final size:3
Alignment explanation
Indices: 84285--84313 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
84275 ACTAACGCCG
84285 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
84314 AACAACCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:86871 original size:22 final size:24
Alignment explanation
Indices: 86810--86872 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
86800 ATTAAATAAG
*
86810 TTATATTTTAA-TATTTAATTTTTA
1 TTAT-TTTTAATTAATTAATTTTTA
*
86834 TTAGTTTATAATTTAATTAA-TTTT-
1 TTA-TTTTTAA-TTAATTAATTTTTA
86858 TTATTTTTAATTAAT
1 TTATTTTTAATTAAT
86873 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.15
23 6 0.18
24 11 0.33
25 5 0.15
26 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTTTTAATTAATTAATTTTTA
Found at i:86904 original size:20 final size:20
Alignment explanation
Indices: 86875--86922 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
86865 TAATTAATAT
86875 TATAAA-ATTTAAATTTAAA
1 TATAAATATTTAAATTTAAA
86894 TATAAATATTTAAATTTAAA
1 TATAAATATTTAAATTTAAA
86914 -ATTAAATAT
1 TA-TAAATAT
86923 AAAAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAATATTTAAATTTAAA
Found at i:86912 original size:26 final size:26
Alignment explanation
Indices: 86870--86931 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
86860 ATTTTTAATT
*
86870 AATATTATAAAATTTAAATTTAAATATA
1 AATATT-T-AAATTTAAAATTAAATATA
86898 AATATTTAAATTTAAAATTAAATATA
1 AATATTTAAATTTAAAATTAAATATA
*
86924 AAAATTTA
1 AATATTTA
86932 TTTTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 25 0.78
27 1 0.03
28 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATTTAAATTTAAAATTAAATATA
Found at i:86928 original size:20 final size:21
Alignment explanation
Indices: 86885--86931 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
86875 TATAAAATTT
**
86885 AAATTT-AAATATAAATATTT
1 AAATTTAAAATATAAATATAA
86905 AAATTTAAAAT-TAAATATAA
1 AAATTTAAAATATAAATATAA
86925 AAATTTA
1 AAATTTA
86932 TTTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTAAAATATAAATATAA
Found at i:86992 original size:20 final size:23
Alignment explanation
Indices: 86969--87010 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
86959 TTCAAATAAA
86969 CTCAAAT-A-ATTTA-ATTTTAT
1 CTCAAATCATATTTATATTTTAT
86989 CTCAAATCATATTTATATTTTA
1 CTCAAATCATATTTATATTTTA
87011 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 5 0.26
23 6 0.32
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (23 bp):
CTCAAATCATATTTATATTTTAT
Found at i:88237 original size:18 final size:17
Alignment explanation
Indices: 88208--88243 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
88198 ATAAATTTTT
*
88208 TTTAAAAATATATAAAA
1 TTTAAAAATATACAAAA
88225 TTTAAATAATATACAAAA
1 TTTAAA-AATATACAAAA
88243 T
1 T
88244 ATTTTTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAAATATACAAAA
Found at i:88692 original size:24 final size:24
Alignment explanation
Indices: 88652--88698 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
88642 TTATAATAAT
*
88652 AAATAATAACTTGATATAAATATA
1 AAATAATAAATTGATATAAATATA
*
88676 AAATAATTAAATT-ATATATATAT
1 AAATAA-TAAATTGATATAAATAT
88699 TATATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATAATAAATTGATATAAATATA
Found at i:88710 original size:27 final size:27
Alignment explanation
Indices: 88671--88727 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 27
88661 CTTGATATAA
*
88671 ATATAAAATAATTAAATTATATATATATT
1 ATATAAAATAATT--ATTATAAATATATT
*
88700 ATAT-AAA-AATTATTTTAAATATATT
1 ATATAAAATAATTATTATAAATATATT
88725 ATA
1 ATA
88728 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 15 0.58
27 4 0.15
28 3 0.12
29 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATAAAATAATTATTATAAATATATT
Found at i:88735 original size:27 final size:27
Alignment explanation
Indices: 88693--88759 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
88683 TAAATTATAT
** *
88693 ATATATTAT--ATAAAAATTATTTTAA
1 ATATATTATAAATAAAAAAAATATTAA
*
88718 ATATATTATAAATTAAAAAAATATTAA
1 ATATATTATAAATAAAAAAAATATTAA
*
88745 ATTTATATATAAATA
1 ATATAT-TATAAATA
88760 TGTAAATGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 9 0.27
27 17 0.52
28 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATATTATAAATAAAAAAAATATTAA
Found at i:89684 original size:7 final size:7
Alignment explanation
Indices: 89672--89699 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
89662 TTAATTAATT
89672 AAATTAA
1 AAATTAA
89679 AAATTAA
1 AAATTAA
89686 AAATTAA
1 AAATTAA
89693 AAATTAA
1 AAATTAA
89700 TTTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:90187 original size:27 final size:27
Alignment explanation
Indices: 90126--90213 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
90116 TGCGTGGTTA
* *
90126 GTCAACAAA-AATTATT-TTTTGTGTTT
1 GTCAA-AAATAATAATTATTTTGTATTT
* *
90152 GTC-ACAATAGTAATTATTTTGTATTT
1 GTCAAAAATAATAATTATTTTGTATTT
* * *
90178 GTCAAAAATAATGATTCTTTTTTATTT
1 GTCAAAAATAATAATTATTTTGTATTT
90205 GTCAAAAAT
1 GTCAAAAAT
90214 TATGATTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 2 0.04
25 6 0.12
26 15 0.30
27 27 0.54
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (27 bp):
GTCAAAAATAATAATTATTTTGTATTT
Found at i:90218 original size:27 final size:24
Alignment explanation
Indices: 90162--90235 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 24
90152 GTCACAATAG
* *
90162 TAATTATTTTGTATTTGTCAAAAA
1 TAATGATTTTTTATTTGTCAAAAA
90186 TAATGATTCTTTTTTATTTGTCAAAAA
1 TAATGA---TTTTTTATTTGTCAAAAA
* *
90213 TTATGATTTATTATTTGTCAAAA
1 TAATGATTTTTTATTTGTCAAAA
90236 TTGGTGGCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
24 21 0.49
27 22 0.51
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (24 bp):
TAATGATTTTTTATTTGTCAAAAA
Found at i:94768 original size:27 final size:27
Alignment explanation
Indices: 94731--94803 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
94721 AAAAACTACC
* * * *
94731 CTTTGTGTTTGTCAACAATGGTGGTTA
1 CTTTGTATTTGTCAAAAATGATAGTTA
* *
94758 CTTTGTATTTGTAAAAAATGATAGTTC
1 CTTTGTATTTGTCAAAAATGATAGTTA
*
94785 CTTTTTATTTGTCAAAAAT
1 CTTTGTATTTGTCAAAAAT
94804 TATGGCTGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (27 bp):
CTTTGTATTTGTCAAAAATGATAGTTA
Found at i:95332 original size:18 final size:18
Alignment explanation
Indices: 95309--95348 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
95299 ATTATTTAAA
95309 TTTAATTTAAT-TTTAATT
1 TTTAA-TTAATATTTAATT
95327 TTTAATTAATATTTAATT
1 TTTAATTAATATTTAATT
95345 TTTA
1 TTTA
95349 TAATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTAATTAATATTTAATT
Found at i:95407 original size:18 final size:18
Alignment explanation
Indices: 95372--95409 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
95362 AATATTTTAT
*
95372 TTTTAAAATATTTAAAAA
1 TTTTAAAATATATAAAAA
95390 TTTTAAAATATCATAAAAA
1 TTTTAAAATAT-ATAAAAA
95409 T
1 T
95410 ATCTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAATATATAAAAA
Found at i:95893 original size:8 final size:9
Alignment explanation
Indices: 95878--95924 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
95868 TCATTTTCGC
95878 ATATTATAT
1 ATATTATAT
95887 A-ATTATAT
1 ATATTATAT
95895 ATATATATAT
1 ATAT-TATAT
*
95905 ATATTTATGT
1 ATA-TTATAT
95915 ATATGTATAT
1 ATAT-TATAT
95925 CTTGGCACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 8 0.25
9 4 0.12
10 19 0.59
11 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (9 bp):
ATATTATAT
Found at i:96397 original size:23 final size:23
Alignment explanation
Indices: 96369--96414 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
96359 CATTTAAATT
* *
96369 AAATAAATTTATTTATGAATATA
1 AAATAAATATATTTATAAATATA
96392 AAATAAATATATTTATAAATATA
1 AAATAAATATATTTATAAATATA
96415 TAATTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATAAATATATTTATAAATATA
Found at i:97217 original size:12 final size:13
Alignment explanation
Indices: 97199--97259 Score: 56
Period size: 12 Copynumber: 4.9 Consensus size: 13
97189 AATAGATTGA
97199 ATATTTATATTTT
1 ATATTTATATTTT
97212 AT-TTTAT-TTTT
1 ATATTTATATTTT
*
97223 ATATTTA-AATTT
1 ATATTTATATTTT
**
97235 ATATAAATATTTT
1 ATATTTATATTTT
* *
97248 AAATTTAAATTT
1 ATATTTATATTT
97260 GTATGAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 6 0.16
12 17 0.46
13 14 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTATATTTT
Found at i:97235 original size:18 final size:18
Alignment explanation
Indices: 97202--97236 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
97192 AGATTGAATA
* *
97202 TTTATATTTTATTTTATT
1 TTTATATTTAAATTTATT
97220 TTTATATTTAAATTTAT
1 TTTATATTTAAATTTAT
97237 ATAAATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATTTAAATTTATT
Found at i:97274 original size:25 final size:25
Alignment explanation
Indices: 97225--97275 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
97215 TTATTTTTAT
*
97225 ATTTAAATTTATATAAATATTTTAA
1 ATTTAAATTTATATAAATATCTTAA
* * *
97250 ATTTAAATTTGTATGAGTATCTTAA
1 ATTTAAATTTATATAAATATCTTAA
97275 A
1 A
97276 CTTTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTAAATTTATATAAATATCTTAA
Found at i:97646 original size:2 final size:2
Alignment explanation
Indices: 97639--97666 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
97629 TTATAACATT
97639 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
97667 ACCACTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:98355 original size:13 final size:13
Alignment explanation
Indices: 98337--98361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
98327 AAATTTATGA
98337 TAATTTTTTTAAT
1 TAATTTTTTTAAT
98350 TAATTTTTTTAA
1 TAATTTTTTTAA
98362 AGTGTAAATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTTTTAAT
Found at i:100208 original size:6 final size:6
Alignment explanation
Indices: 100197--100225 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
100187 TTCACAATTT
100197 CATTAC CATTAC CATTAC CATTAC CATTA
1 CATTAC CATTAC CATTAC CATTAC CATTA
100226 TATAAGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
CATTAC
Found at i:100345 original size:25 final size:25
Alignment explanation
Indices: 100304--100352 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
100294 ATATAAATTT
*
100304 AAAAATAGACATAATTTTTTTTTAA
1 AAAAATAGACATAATTTTGTTTTAA
*
100329 AAAAATTGATCAT-ATTTTGTTTTA
1 AAAAATAGA-CATAATTTTGTTTTA
100353 TATATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (25 bp):
AAAAATAGACATAATTTTGTTTTAA
Found at i:101668 original size:12 final size:12
Alignment explanation
Indices: 101613--101676 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
101603 TTTATTATTA
101613 TTAAATATTAAT
1 TTAAATATTAAT
101625 TT-AAT-TTAATT
1 TTAAATATTAA-T
101636 TATAAATATTTTAAT
1 T-TAAATA--TTAAT
** *
101651 AAAAATATTTAT
1 TTAAATATTAAT
101663 TTAAATATTAAT
1 TTAAATATTAAT
101675 TT
1 TT
101677 TAAAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
12 18 0.45
13 3 0.08
14 5 0.12
15 1 0.03
16 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATATTAAT
Found at i:101760 original size:17 final size:17
Alignment explanation
Indices: 101727--101762 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
101717 TAATTTGAAT
101727 AATATATTTTAAATAAA
1 AATATATTTTAAATAAA
*
101744 AATAT-TTTTAAATTAA
1 AATATATTTTAAATAAA
101760 AAT
1 AAT
101763 TTTAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATATTTTAAATAAA
Found at i:101871 original size:21 final size:21
Alignment explanation
Indices: 101828--101891 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 21
101818 ATGAGTACGA
* * *
101828 ATTTTTTATATTATTTTTTATT
1 ATTTTTAATA-TAATTTTAATT
101850 ATTTTTAATATAATTTTAATT
1 ATTTTTAATATAATTTTAATT
101871 ATTACTTATAAATATAATTTT
1 ATT--TT-T-AATATAATTTT
101892 TATAATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 9 0.26
23 2 0.06
24 1 0.03
25 11 0.31
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATATAATTTTAATT
Found at i:102230 original size:7 final size:7
Alignment explanation
Indices: 102218--102242 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
102208 GGGAAGAAGT
102218 GTGGGTG
1 GTGGGTG
102225 GTGGGTG
1 GTGGGTG
102232 GTGGGTG
1 GTGGGTG
102239 GTGG
1 GTGG
102243 TGGGGGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.72, T:0.28
Consensus pattern (7 bp):
GTGGGTG
Found at i:104472 original size:3 final size:3
Alignment explanation
Indices: 104464--104498 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
104454 TAAAAGAACC
104464 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
104499 CTCTCGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:106222 original size:24 final size:24
Alignment explanation
Indices: 106185--106234 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
106175 AAAATCAACA
106185 TATATCTAGATAATTAAAGTTTGTT
1 TATATCTAGATAATTAAAGTTT-TT
*
106210 TATATTTA-ATAATTAAAGTTTTT
1 TATATCTAGATAATTAAAGTTTTT
106233 TA
1 TA
106235 CATTAAGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 13 0.54
25 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
TATATCTAGATAATTAAAGTTTTT
Found at i:106377 original size:10 final size:10
Alignment explanation
Indices: 106371--106396 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
106361 AATAAAAACA
106371 AAAAAAAAAG
1 AAAAAAAAAG
106381 AAAAAAAAAG
1 AAAAAAAAAG
106391 AAAAAA
1 AAAAAA
106397 GAGAAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:106397 original size:17 final size:17
Alignment explanation
Indices: 106349--106398 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
106339 TTTGAGAGAC
*
106349 ACAATAAAATAAAATAAAA
1 ACAA-AAAA-AAAAGAAAA
106368 ACAAAAAAAAAAGAAAA
1 ACAAAAAAAAAAGAAAA
106385 A-AAAAGAAAAAAGA
1 ACAAAA-AAAAAAGA
106399 GAAGAGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
18 4 0.14
19 4 0.14
ACGTcount: A:0.84, C:0.04, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAAAAGAAAA
Found at i:106675 original size:2 final size:2
Alignment explanation
Indices: 106670--106702 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
106660 ATATATGTAT
*
106670 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
106703 TCATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:107450 original size:20 final size:17
Alignment explanation
Indices: 107409--107462 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
107399 AGCTTAAAAT
107409 TTATATTTATATTTTTA
1 TTATATTTATATTTTTA
107426 TTATATTTGATATATTTTA
1 TTATATTT-ATAT-TTTTA
* *
107445 TGTATATATAAATTTTTA
1 T-TATATTTATATTTTTA
107463 ATAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 8 0.25
18 9 0.28
19 9 0.28
20 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTATATTTATATTTTTA
Found at i:113152 original size:18 final size:18
Alignment explanation
Indices: 113112--113153 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
113102 AAGTATAAAG
*
113112 TTAATTATTTTTTAATTAT
1 TTAA-TATTTTTTAATTAA
113131 TTAATATTTTTT-ATCTAA
1 TTAATATTTTTTAAT-TAA
113149 TTAAT
1 TTAAT
113154 TTAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 15 0.71
19 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATATTTTTTAATTAA
Found at i:113187 original size:24 final size:24
Alignment explanation
Indices: 113155--113208 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
113145 CTAATTAATT
113155 TAAATTATT-TTTAAATATATTTAAA
1 TAAA-TATTATTTAAAT-TATTTAAA
*
113180 TAAATATTATTTAACTTATTTAAA
1 TAAATATTATTTAAATTATTTAAA
113204 -AAATA
1 TAAATA
113209 AGTGTATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 5 0.19
24 12 0.44
25 10 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAATATTATTTAAATTATTTAAA
Found at i:122612 original size:26 final size:26
Alignment explanation
Indices: 122582--122632 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
122572 GGAAAACAAA
122582 ACTTAGATCATCCAGGATCATAACAG
1 ACTTAGATCATCCAGGATCATAACAG
122608 ACTTAGATCATCCAGGATCATAACA
1 ACTTAGATCATCCAGGATCATAACA
122633 AAAAGACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (26 bp):
ACTTAGATCATCCAGGATCATAACAG
Found at i:126824 original size:2 final size:2
Alignment explanation
Indices: 126817--126841 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
126807 TAGAAGGAAC
126817 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
126842 GAAAAAAAAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:127794 original size:21 final size:20
Alignment explanation
Indices: 127757--127795 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
127747 CGTTTCTTAA
* *
127757 CAAATTTTTTTTAATATTAT
1 CAAAATTTTTTCAATATTAT
127777 CAAAATTTTTTCAGATATT
1 CAAAATTTTTTCA-ATATT
127796 TCCACATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (20 bp):
CAAAATTTTTTCAATATTAT
Found at i:127927 original size:26 final size:26
Alignment explanation
Indices: 127891--127970 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
127881 AGAAAGAAAA
127891 TTGCAGCCAAGAAGATGTTAAATATT
1 TTGCAGCCAAGAAGATGTTAAATATT
127917 TTGCAGCCAAGAAGATGTTAAATATT
1 TTGCAGCCAAGAAGATGTTAAATATT
*
127943 TTGCAGCCAAGATGATGTTAAATATT
1 TTGCAGCCAAGAAGATGTTAAATATT
127969 TT
1 TT
127971 AATCATAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (26 bp):
TTGCAGCCAAGAAGATGTTAAATATT
Found at i:129402 original size:112 final size:114
Alignment explanation
Indices: 129246--129471 Score: 309
Period size: 112 Copynumber: 2.0 Consensus size: 114
129236 AGACTCCCCT
*
129246 TTCGCTTTACTTAAGAGTCTACTACTTTGAAATTACTAATAGATTTTGCTTAAGTAGACCATTCT
1 TTCGCCTTACTTAAGAGTCTACTACTTTGAAATTACTAATAGATTTTGCTTAAGTAGACCATTCT
* * * *
129311 TGATGTTTT-TGG-AGATATTTTGATGGTGAA-TTTTCTATAGGGATAAGG
66 TGATGTTTTGGGGCAGAT-TTCTGATGGAGAACTTTT-TATAAGGATAAGG
* * * *
129359 TTCGCCTTACTTAA-A-TGCTACTGCTTTGAAATTACTGATAGATTTTGCTTAAGTGGATCATTC
1 TTCGCCTTACTTAAGAGT-CTACTACTTTGAAATTACTAATAGATTTTGCTTAAGTAGACCATTC
129422 TTGATGTTTTGGGGCAGATTTCTGATGGAGAACTTTTTATAAGGATAAGG
65 TTGATGTTTTGGGGCAGATTTCTGATGGAGAACTTTTTATAAGGATAAGG
129472 CTATTTTGAA
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
111 1 0.01
112 53 0.53
113 38 0.38
114 8 0.08
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.41
Consensus pattern (114 bp):
TTCGCCTTACTTAAGAGTCTACTACTTTGAAATTACTAATAGATTTTGCTTAAGTAGACCATTCT
TGATGTTTTGGGGCAGATTTCTGATGGAGAACTTTTTATAAGGATAAGG
Found at i:130109 original size:2 final size:2
Alignment explanation
Indices: 130102--130144 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
130092 TTTATAAGGT
130102 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
130144 T
1 T
130145 GTAGTTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:134863 original size:2 final size:2
Alignment explanation
Indices: 134856--134886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
134846 AACAGCAGTA
134856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
134887 AGTTTACCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:140578 original size:21 final size:21
Alignment explanation
Indices: 140554--140594 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
140544 TTTTAAAATT
*
140554 TAAAT-TTAATTAATAAATATA
1 TAAATATTAA-TAAAAAATATA
140575 TAAATATTAATAAAAAATAT
1 TAAATATTAATAAAAAATAT
140595 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:140971 original size:10 final size:10
Alignment explanation
Indices: 140929--140962 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
140919 TTTTTTAATT
*
140929 TTTATATCAA
1 TTTATATTAA
140939 TTTTATATTAA
1 -TTTATATTAA
140950 TTTATATTAA
1 TTTATATTAA
140960 TTT
1 TTT
140963 GTCTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATATTAA
Found at i:141210 original size:23 final size:23
Alignment explanation
Indices: 141176--141221 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
141166 ATTAATTAAT
*
141176 TCAAAAATTTAATCCCAAAAATC
1 TCAAAAAATTAATCCCAAAAATC
141199 TCAAAAAATTAATCCCAAAAATC
1 TCAAAAAATTAATCCCAAAAATC
141222 CCATTTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (23 bp):
TCAAAAAATTAATCCCAAAAATC
Found at i:141541 original size:2 final size:2
Alignment explanation
Indices: 141534--141560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
141524 CACATGTGCA
141534 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
141561 GGATTTAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141714 original size:11 final size:11
Alignment explanation
Indices: 141694--141731 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
141684 TTTTTATATT
141694 TATA-TTTAAA
1 TATATTTTAAA
141704 TATATTTTAAA
1 TATATTTTAAA
141715 TATAATTATTAAA
1 TAT-ATT-TTAAA
141728 TATA
1 TATA
141732 AATATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 9 0.36
12 4 0.16
13 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATTTTAAA
Found at i:141728 original size:13 final size:13
Alignment explanation
Indices: 141699--141737 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
141689 ATATTTATAT
141699 TTAAATAT-ATT-
1 TTAAATATAATTA
141710 TTAAATATAATTA
1 TTAAATATAATTA
*
141723 TTAAATATAAATA
1 TTAAATATAATTA
141736 TT
1 TT
141738 TTATATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
12 3 0.12
13 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAAATATAATTA
Found at i:142391 original size:2 final size:2
Alignment explanation
Indices: 142384--142413 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
142374 TATGTATTAC
142384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
142414 CATCTTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:145732 original size:14 final size:14
Alignment explanation
Indices: 145713--145749 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
145703 TTTTCTACAA
145713 TATATATATGTATG
1 TATATATATGTATG
*
145727 TATATAAATGTATG
1 TATATATATGTATG
145741 TATATATAT
1 TATATATAT
145750 ATATATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:145760 original size:14 final size:14
Alignment explanation
Indices: 145712--145762 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
145702 TTTTTCTACA
145712 ATATATATATGTAT
1 ATATATATATGTAT
* *
145726 GTATATAAATGTAT
1 ATATATATATGTAT
* *
145740 GTATATATATATAT
1 ATATATATATGTAT
*
145754 ATGTATATA
1 ATATATATA
145763 GAATTATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:145770 original size:16 final size:15
Alignment explanation
Indices: 145723--145771 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
145713 TATATATATG
*
145723 TATGTATATAAA-TG
1 TATGTATATAAATTA
*
145737 TATGTATATATATATA
1 TATGTATATAAAT-TA
145753 TATGTATATAGAATTA
1 TATGTATATA-AATTA
145769 TAT
1 TAT
145772 ATTTGGCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 11 0.38
16 16 0.55
17 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (15 bp):
TATGTATATAAATTA
Found at i:146237 original size:105 final size:103
Alignment explanation
Indices: 145936--146320 Score: 328
Period size: 105 Copynumber: 3.6 Consensus size: 103
145926 AATGTTATCA
* * * * * * *
145936 TATTTAATTATGTAATCTTATTAAATTT-TTTTAATTAAAATTAATAAATATTTAAAAATAGAGT
1 TATTTAAATATATAATTTTATT-AATTTGTTTAAATTTAAATAAATAAATATTTAAAAATAAAGT
* * * ***
146000 CCATATGATATTAATCTATTTTAAAATTTATAAAAAAAAT-T
65 CCAAATGATATTAA--TACTTTAAAATTAAT-AAAATTTTCT
* * * * *
146041 TATTTAAATATATAATTTTATTATTTTAAAATTTAAATCTAAATTAATAAATATTTAAAAATAGA
1 TATTTAAATATATAATTTTATTAATTT---GTTTAAATTTAAATAAATAAATATTTAAAAATAAA
* * * *
146106 GTTCACATTATATTAATCCATATTAAAATTAATAAAATTTTCT
63 GTCCAAATGATATTAATAC-T-TTAAAATTAATAAAATTTTCT
* * * *
146149 TATTTTAATATGTAATTTTATTAATTTGTTTAAATTTAAATAAATAAATATGTAAAACTAAAGTC
1 TATTTAAATATATAATTTTATTAATTTGTTTAAATTTAAATAAATAAATATTTAAAAATAAAGTC
* * *
146214 CAAATGATATTAAATGACTTTAAAATTAATGAACTTTCCCT
66 CAAATGATATT-AAT-ACTTTAAAATTAATAAAATTT-TCT
* * *
146255 T-TTTAAATATATAATTTTTATTAA-TTGTTTGAATTTAAATGAACTAAATTTTTAAAAATAAAG
1 TATTTAAATATATAA-TTTTATTAATTTGTTTAAATTTAAAT-AAATAAATATTTAAAAATAAAG
146318 TCC
64 TCC
146321 TTATAAATAT
Statistics
Matches: 229, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
104 4 0.02
105 101 0.44
106 38 0.17
107 7 0.03
108 79 0.34
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (103 bp):
TATTTAAATATATAATTTTATTAATTTGTTTAAATTTAAATAAATAAATATTTAAAAATAAAGTC
CAAATGATATTAATACTTTAAAATTAATAAAATTTTCT
Found at i:148059 original size:15 final size:15
Alignment explanation
Indices: 148031--148064 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
148021 AAGTTTTTTC
*
148031 ATATTCCTAATTATT
1 ATATTACTAATTATT
*
148046 ATATTACTATTTATT
1 ATATTACTAATTATT
148061 ATAT
1 ATAT
148065 GAAAGATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTACTAATTATT
Found at i:148902 original size:22 final size:22
Alignment explanation
Indices: 148859--148902 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
148849 AGATTCAAAC
*
148859 CATAATAATAAACACTTAATAA
1 CATAATAATAAACAATTAATAA
* * *
148881 CATAGTAATAAATAATTTATAA
1 CATAATAATAAACAATTAATAA
148903 TATATAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (22 bp):
CATAATAATAAACAATTAATAA
Found at i:149219 original size:2 final size:2
Alignment explanation
Indices: 149209--149246 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
149199 CAAAAAAAAC
*
149209 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
149247 AAGATGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:151944 original size:16 final size:16
Alignment explanation
Indices: 151925--151970 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
151915 TTAAAATTTT
151925 TTAATATATTTATGTA
1 TTAATATATTTATGTA
151941 TTAA-A-A-TT-T-T-
1 TTAATATATTTATGTA
151951 TTAATATATTTATGTA
1 TTAATATATTTATGTA
151967 TTAA
1 TTAA
151971 AATTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 4 0.17
11 2 0.08
12 2 0.08
13 4 0.17
14 2 0.08
15 2 0.08
16 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TTAATATATTTATGTA
Found at i:151985 original size:26 final size:26
Alignment explanation
Indices: 151913--151975 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
151903 GTGTTTAAAA
151913 TATTAAAATTTTTTAATATATTTATG
1 TATTAAAATTTTTTAATATATTTATG
151939 TATTAAAATTTTTTAATATATTTATG
1 TATTAAAATTTTTTAATATATTTATG
151965 TATTAAAATTT
1 TATTAAAATTT
151976 ATATAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (26 bp):
TATTAAAATTTTTTAATATATTTATG
Found at i:152305 original size:2 final size:2
Alignment explanation
Indices: 152298--152334 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
152288 GATAATATTA
152298 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A
152335 AATAAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:152360 original size:29 final size:28
Alignment explanation
Indices: 152328--152395 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
152318 ATATATGATA
152328 TATTATAAATAAAATATAAAAT-ATTATTT
1 TATTATAAATAAAA-ATAAAATGA-TATTT
* **
152357 TATTAAAAATTTTAAATAAAATGATATTT
1 TATTATAAA-TAAAAATAAAATGATATTT
152386 TA-TATAAATA
1 TATTATAAATA
152396 TTTAATAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.03
28 5 0.16
29 22 0.69
30 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TATTATAAATAAAAATAAAATGATATTT
Found at i:153461 original size:17 final size:18
Alignment explanation
Indices: 153436--153501 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
153426 GTTAATAATT
*
153436 TATTTTATTA-ATTTTAA
1 TATTATATTATATTTTAA
153453 TATTATATTATATTTTAA
1 TATTATATTATATTTTAA
153471 TTATT-T-TTATATTATATAA
1 -TATTATATTATATT-T-TAA
*
153490 TATTACATTATA
1 TATTATATTATA
153502 AAAAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 16 0.39
18 13 0.32
19 7 0.17
20 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATATTATATTTTAA
Found at i:153466 original size:27 final size:27
Alignment explanation
Indices: 153436--153493 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
153426 GTTAATAATT
*
153436 TATTTT-ATTAATTTTAATATTATATTA
1 TATTTTAATT-ATTTTAATATTATATAA
*
153463 TATTTTAATTATTTTTATATTATATAA
1 TATTTTAATTATTTTAATATTATATAA
153490 TATT
1 TATT
153494 ACATTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTAATTATTTTAATATTATATAA
Found at i:153484 original size:11 final size:12
Alignment explanation
Indices: 153455--153487 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
153445 AATTTTAATA
153455 TTATATTATATT
1 TTATATTATATT
153467 TTA-ATTAT-TT
1 TTATATTATATT
153477 TTATATTATAT
1 TTATATTATAT
153488 AATATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.26
11 10 0.53
12 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTATATT
Found at i:156280 original size:26 final size:27
Alignment explanation
Indices: 156230--156297 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
156220 TAAGATAATT
*
156230 AAATATTTTTATATT-ATATATA-TTTA
1 AAATA-TTTTATATTAATATAAATTTTA
156256 AAATATTTTATATTAATATAAATTTTTA
1 AAATATTTTATATTAATATAAA-TTTTA
*
156284 AAA-AATTTATATTA
1 AAATATTTTATATTA
156298 TATTTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.24
26 11 0.30
27 10 0.27
28 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATATTTTATATTAATATAAATTTTA
Found at i:156315 original size:31 final size:30
Alignment explanation
Indices: 156240--156345 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 30
156230 AAATATTTTT
* *
156240 ATATTATATATATTTAAAAT-ATTTTATATTA
1 ATATTAT-TATTTTTAAAATAATTATAT-TTA
*
156271 ATA-TA-AATTTTTAAAA-AATT-TATATTA
1 ATATTATTATTTTTAAAATAATTATAT-TTA
*
156298 TATTTTAATTATTTTTAAAATAATTATATTTA
1 -ATATT-ATTATTTTTAAAATAATTATATTTA
156330 ATATTATTATTTTTAA
1 ATATTATTATTTTTAA
156346 TTTATAATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
27 7 0.11
28 14 0.22
29 1 0.02
30 14 0.22
31 17 0.27
32 7 0.11
33 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATTATTATTTTTAAAATAATTATATTTA
Found at i:156323 original size:15 final size:15
Alignment explanation
Indices: 156303--156345 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
156293 TATTATATTT
156303 TAATTATTTTTAAAA
1 TAATTATTTTTAAAA
* *
156318 TAATTATATTTAATA
1 TAATTATTTTTAAAA
*
156333 TTATTATTTTTAA
1 TAATTATTTTTAA
156346 TTTATAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTATTTTTAAAA
Found at i:156346 original size:15 final size:15
Alignment explanation
Indices: 156305--156350 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
156295 TTATATTTTA
* *
156305 ATTATTTTTAAAATA
1 ATTATTTTTAATATT
*
156320 ATTATATTTAATATT
1 ATTATTTTTAATATT
156335 ATTATTTTTAAT-TT
1 ATTATTTTTAATATT
156349 AT
1 AT
156351 AATATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTTTTAATATT
Found at i:161055 original size:15 final size:14
Alignment explanation
Indices: 161035--161077 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
161025 TCAAAAATTT
*
161035 AAATTATTATTCAAA
1 AAATTAATATT-AAA
161050 AAATTAAATATTAAA
1 AAATT-AATATTAAA
*
161065 AAATTAATTTTAA
1 AAATTAATATTAA
161078 TTAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTAATATTAAA
Found at i:161061 original size:19 final size:20
Alignment explanation
Indices: 161025--161062 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
161015 GTGGACTAAC
*
161025 TCAAAAATTTAAATTATTAT
1 TCAAAAAATTAAATTATTAT
161045 TCAAAAAATTAAA-TATTA
1 TCAAAAAATTAAATTATTA
161063 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAAAATTAAATTATTAT
Found at i:161077 original size:14 final size:15
Alignment explanation
Indices: 161042--161071 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
161032 TTTAAATTAT
161042 TATTCAAAAAATTAAA
1 TATT-AAAAAATTAAA
161058 TATTAAAAAATTAA
1 TATTAAAAAATTAA
161072 TTTTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTAAAAAATTAAA
Found at i:163053 original size:3 final size:3
Alignment explanation
Indices: 163045--163079 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
163035 TTAAATAAAT
163045 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
163080 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:163332 original size:31 final size:31
Alignment explanation
Indices: 163263--163333 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
163253 TTTATTTTGA
* *
163263 TTAATATTTATAATTATAATTTTAGATTAAG
1 TTAAAATTTACAATTATAATTTTAGATTAAG
163294 -TACAAATTTACAATTATAA-TTTA-ACTTAATG
1 TTA-AAATTTACAATTATAATTTTAGA-TTAA-G
163325 TTAAAATTT
1 TTAAAATTT
163334 GCCAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
29 1 0.03
30 10 0.29
31 21 0.62
32 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
TTAAAATTTACAATTATAATTTTAGATTAAG
Found at i:163517 original size:34 final size:34
Alignment explanation
Indices: 163474--163539 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
163464 ATTAGTTTTT
163474 AATAAATTAATTAATAAAAAATGATAAAAATAAA
1 AATAAATTAATTAATAAAAAATGATAAAAATAAA
* ** *
163508 AATAAATTAATTAGTAAAGGATGATCAAAATA
1 AATAAATTAATTAATAAAAAATGATAAAAATA
163540 TTTAAGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.27
Consensus pattern (34 bp):
AATAAATTAATTAATAAAAAATGATAAAAATAAA
Found at i:166471 original size:2 final size:2
Alignment explanation
Indices: 166458--166496 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
166448 TATCTATTAC
*
166458 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
166497 GTCACAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:171012 original size:16 final size:16
Alignment explanation
Indices: 170991--171024 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
170981 ACGGAACACA
170991 TAAAATATTATATATT
1 TAAAATATTATATATT
171007 TAAAATATTATATATT
1 TAAAATATTATATATT
171023 TA
1 TA
171025 TTTATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATTATATATT
Found at i:173306 original size:22 final size:21
Alignment explanation
Indices: 173271--173311 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
173261 CGATTCGAAT
173271 AAAATTTAAAGTATTACTAAAC
1 AAAATTTAAAGTA-TACTAAAC
**
173293 AAAATTTATTGTATACTAA
1 AAAATTTAAAGTATACTAA
173312 CTTGACCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAATTTAAAGTATACTAAAC
Found at i:177604 original size:11 final size:11
Alignment explanation
Indices: 177588--177625 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
177578 ATATGAAGTG
177588 AAAAGAAGAAA
1 AAAAGAAGAAA
*
177599 AAAAGAACAAAA
1 AAAAGAA-GAAA
177611 AAAAGAAGAAA
1 AAAAGAAGAAA
177622 AAAA
1 AAAA
177626 TTATATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:177613 original size:12 final size:12
Alignment explanation
Indices: 177596--177625 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
177586 TGAAAAGAAG
177596 AAAAAAAGAACA
1 AAAAAAAGAACA
*
177608 AAAAAAAGAAGA
1 AAAAAAAGAACA
177620 AAAAAA
1 AAAAAA
177626 TTATATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAACA
Found at i:179187 original size:11 final size:11
Alignment explanation
Indices: 179171--179210 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
179161 TACTCAGGTG
179171 AAAAAGAAAAA
1 AAAAAGAAAAA
*
179182 AAAAAGAAACA
1 AAAAAGAAAAA
179193 AAAAAGCAAAAA
1 AAAAAG-AAAAA
179205 GAAAAA
1 -AAAAA
179211 AAAGGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.64
12 4 0.16
13 5 0.20
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:179205 original size:7 final size:6
Alignment explanation
Indices: 179170--179210 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
179160 TTACTCAGGT
*
179170 GAAAAA GAAAAA -AAAAA GAAACA -AAAAA GCAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-AAAAA GAAAAA
179211 AAAGGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (6 bp):
GAAAAA
Done.