Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008650.1 Hibiscus syriacus cultivar Beakdansim tig00111640_pilon, whole genome shotgun sequence
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: 1713193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1229589 original size:34 final size:34
Alignment explanation
Indices: 1229546--1229619 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
1229536 TCAGATCAGG
1229546 CAAGGGTAGTAGCACAAGGTGTGTGTCAATAGGT
1 CAAGGGTAGTAGCACAAGGTGTGTGTCAATAGGT
*
1229580 CAAGGGTAGTAGCACAAGGTGTGTGTCAATAGTT
1 CAAGGGTAGTAGCACAAGGTGTGTGTCAATAGGT
1229614 CAAGGG
1 CAAGGG
1229620 CAAGAAGCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (34 bp):
CAAGGGTAGTAGCACAAGGTGTGTGTCAATAGGT
Found at i:1238863 original size:15 final size:16
Alignment explanation
Indices: 1238845--1238877 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1238835 AATTTGATCA
*
1238845 AATAATTAAATA-AAT
1 AATAAATAAATATAAT
1238860 AATAAATAAATATAAT
1 AATAAATAAATATAAT
1238876 AA
1 AA
1238878 AAAAGTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATAAATATAAT
Found at i:1242866 original size:55 final size:55
Alignment explanation
Indices: 1242798--1242923 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 55
1242788 ATCGATCGTT
* * * *
1242798 AAACATCAGACATTTGCCATAAAGTTGATTGAGCAATCTCTATGTTAAAACTATA
1 AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
*
1242853 TAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
1 AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
1242908 AAACATGAGACATTTG
1 AAACATGAGACATTTG
1242924 ATGTGCCTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (55 bp):
AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
Found at i:1247768 original size:15 final size:15
Alignment explanation
Indices: 1247748--1247792 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1247738 TTATCTAAAA
*
1247748 ATAATTAAAAAATAT
1 ATAATTTAAAAATAT
*
1247763 ATAATTTTAAAATAT
1 ATAATTTAAAAATAT
* *
1247778 TTATTTTAAAAATAT
1 ATAATTTAAAAATAT
1247793 CAGAAAATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATTTAAAAATAT
Found at i:1247785 original size:14 final size:15
Alignment explanation
Indices: 1247756--1247792 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1247746 AAATAATTAA
1247756 AAAATATATAATTTT
1 AAAATATATAATTTT
*
1247771 AAAATAT-TTATTTT
1 AAAATATATAATTTT
1247785 AAAA-ATAT
1 AAAATATAT
1247793 CAGAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATATATAATTTT
Found at i:1247868 original size:119 final size:118
Alignment explanation
Indices: 1247658--1247883 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 118
1247648 ATAAGATATT
* * *
1247658 TATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATATAA
1 TATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCTTTAAGACAGCTCATTTCTTAATATAA
*
1247723 AAAATAAATAAACATTTATCTAAAAA-TAATTAAAAAATATATAATTTTAAAA
66 AAAATAAATAAACATTTATCTAAAAATTAATCAAAAAATATATAATTTTAAAA
* *
1247775 TATTTATTTTAAAAATATCAGAAAATGAACATCCAGTTGCTTTAAGACTGC-CATTTCTTAATAT
1 TATTTA-TTTAAAAATATCAGAAAATG-ACATCCAGGTGCTTTAAGACAGCTCATTTCTTAATA-
* * * *
1247839 TGAAAAATAAATAAATA-TTATTTATAAAATTAATCAAATAATATA
63 TAAAAAATAAATAAACATTTATCTA-AAAATTAATCAAAAAATATA
1247884 ATATTAATAT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
117 6 0.06
118 37 0.39
119 38 0.40
120 13 0.14
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (118 bp):
TATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCTTTAAGACAGCTCATTTCTTAATATAA
AAAATAAATAAACATTTATCTAAAAATTAATCAAAAAATATATAATTTTAAAA
Found at i:1247919 original size:118 final size:119
Alignment explanation
Indices: 1247669--1247906 Score: 270
Period size: 118 Copynumber: 2.0 Consensus size: 119
1247659 ATTTATTTAG
* * *
1247669 AAATATCAGAAAATG-ACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATATAAAAAATAAATA
1 AAATATCAGAAAATGAACATCCAGTTGCTTTAAGACAGCTCATTTCTTAATATAAAAAATAAATA
* * * **
1247733 AACATTTATCTAAAAATAATTAAAAAATATATAATTTTAAAATATTTATTTTAA
66 AACATTTATCTAAAAATAATTAAAAAATATATAATATTAAAATACTAAAATTAA
* *
1247787 AAATATCAGAAAATGAACATCCAGTTGCTTTAAGACTGC-CATTTCTTAATATTGAAAAATAAAT
1 AAATATCAGAAAATGAACATCCAGTTGCTTTAAGACAGCTCATTTCTTAATA-TAAAAAATAAAT
* * * * *
1247851 AAATA-TTAT-TTATAA-AATTAATCAAATAATATAATATTAATATGACTAAAATTAA
65 AAACATTTATCTAAAAATAATTAA-AAAAT-ATATAATATTAAAAT-ACTAAAATTAA
1247906 A
1 A
1247907 GAAATATAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
116 6 0.06
117 8 0.08
118 44 0.44
119 42 0.42
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (119 bp):
AAATATCAGAAAATGAACATCCAGTTGCTTTAAGACAGCTCATTTCTTAATATAAAAAATAAATA
AACATTTATCTAAAAATAATTAAAAAATATATAATATTAAAATACTAAAATTAA
Found at i:1249389 original size:3 final size:3
Alignment explanation
Indices: 1249383--1249448 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
1249373 TATTTTTTTA
* * * **
1249383 AAT AAT AAT ATT AAT AAT AAT ATAT AAT AAA AAT AAT AAA AAT TTT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
*
1249429 AAT AAT CAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1249449 CTATATGAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1263914 original size:22 final size:22
Alignment explanation
Indices: 1263886--1263928 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1263876 AAGAGTATGT
1263886 CTCTCTGTTTTGTGACAGTCAC
1 CTCTCTGTTTTGTGACAGTCAC
1263908 CTCTCTGTTTTGTGACAGTCA
1 CTCTCTGTTTTGTGACAGTCA
1263929 AAGCGCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (22 bp):
CTCTCTGTTTTGTGACAGTCAC
Found at i:1269391 original size:34 final size:34
Alignment explanation
Indices: 1269348--1269458 Score: 132
Period size: 35 Copynumber: 3.2 Consensus size: 34
1269338 AAAACATTCC
*
1269348 TCAATTTCATTCTAAACCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
*
1269382 TCAATTTCATTATAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * * * *
1269417 CCAATTACAATCTAAAACTCAAATTCTAAAATATT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1269452 TCAATTT
1 TCAATTT
1269459 AAGGAGGAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 18 0.28
35 41 0.64
36 5 0.08
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1270559 original size:35 final size:34
Alignment explanation
Indices: 1270518--1270630 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1270508 AAAAAAGACA
* *
1270518 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
1270553 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
1270588 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
1270623 GAAATTGA
1 GAAATTGA
1270631 GGATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:1279504 original size:16 final size:16
Alignment explanation
Indices: 1279485--1279534 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
1279475 GAGAATTTAA
1279485 AATATTTTATATTTTT
1 AATATTTTATATTTTT
* *
1279501 AATA-TTTA-ATATTC
1 AATATTTTATATTTTT
*
1279515 AATATTTTACTATTTAT
1 AATATTTTA-TATTTTT
1279532 AAT
1 AAT
1279535 TTTATGGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
14 8 0.31
15 8 0.31
16 4 0.15
17 6 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATTTTATATTTTT
Found at i:1279582 original size:16 final size:17
Alignment explanation
Indices: 1279547--1279583 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1279537 TATGGGATGA
1279547 AAAAATAGTATTATTAT
1 AAAAATAGTATTATTAT
1279564 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTAT
1279580 AAAA
1 AAAA
1279584 CAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTAT
Found at i:1279624 original size:17 final size:19
Alignment explanation
Indices: 1279602--1279638 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1279592 TACTACCATA
1279602 ATATTAT-TTTT-TATAAT
1 ATATTATATTTTATATAAT
1279619 ATATTATATTTTATATAAT
1 ATATTATATTTTATATAAT
1279638 A
1 A
1279639 AATATGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTATATTTTATATAAT
Found at i:1284906 original size:11 final size:11
Alignment explanation
Indices: 1284887--1284916 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1284877 ATATTACATA
1284887 TTAATTATAAAT
1 TTAA-TATAAAT
1284899 TTAATATAAAT
1 TTAATATAAAT
1284910 TTAATAT
1 TTAATAT
1284917 TTATCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAATATAAAT
Found at i:1293454 original size:27 final size:27
Alignment explanation
Indices: 1293399--1293453 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1293389 ATCTTAGAGG
*
1293399 TGCACAAAAAATTCGAATATCTGATTT
1 TGCACAAAAAATTCGAATATCGGATTT
*
1293426 TGCATAAAAAATATCCGAA-ATCGGATTT
1 TGCACAAAAAAT-T-CGAATATCGGATTT
1293454 GGAAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 9 0.38
29 4 0.17
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (27 bp):
TGCACAAAAAATTCGAATATCGGATTT
Found at i:1293973 original size:19 final size:19
Alignment explanation
Indices: 1293951--1293993 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1293941 GCCATGAATT
*
1293951 GTCATAGGCTGTCTTTACA
1 GTCAGAGGCTGTCTTTACA
*
1293970 GTCAGGGGCTGTCTTTACA
1 GTCAGAGGCTGTCTTTACA
1293989 GTCAG
1 GTCAG
1293994 GGGCAGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (19 bp):
GTCAGAGGCTGTCTTTACA
Found at i:1293994 original size:19 final size:19
Alignment explanation
Indices: 1293957--1293997 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1293947 AATTGTCATA
1293957 GGCTGTCTTTACAGTCAGG
1 GGCTGTCTTTACAGTCAGG
1293976 GGCTGTCTTTACAGTCAGG
1 GGCTGTCTTTACAGTCAGG
1293995 GGC
1 GGC
1293998 AGTCGGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.34, T:0.29
Consensus pattern (19 bp):
GGCTGTCTTTACAGTCAGG
Found at i:1302506 original size:24 final size:24
Alignment explanation
Indices: 1302456--1302568 Score: 113
Period size: 24 Copynumber: 4.8 Consensus size: 24
1302446 AAAATTTCAA
* * *
1302456 GAGCTTGATTAAA-CTCAAAACTT
1 GAGCTCGATTAAAGCTCGAAACTC
*
1302479 GAGCTTGATTAAAGCTCGAAACTC
1 GAGCTCGATTAAAGCTCGAAACTC
* *
1302503 GAGCTCGATTGAAGCTTGAAACTC
1 GAGCTCGATTAAAGCTCGAAACTC
* ** *
1302527 GAGCTCGATTGAAGCTCG-ATTTT
1 GAGCTCGATTAAAGCTCGAAACTC
*
1302550 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTAAAGCTCGA
1302569 TTTTAAGCTC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
23 32 0.41
24 46 0.59
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAAACTC
Found at i:1302544 original size:11 final size:11
Alignment explanation
Indices: 1302528--1302570 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1302518 TTGAAACTCG
1302528 AGCTCGATTGA
1 AGCTCGATTGA
1302539 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
1302551 AGCTCGATTCA
1 AGCTCGATTGA
1302562 AGCTCGATT
1 AGCTCGATT
1302571 TTAAGCTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:1302557 original size:23 final size:23
Alignment explanation
Indices: 1302503--1302578 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
1302493 CTCGAAACTC
* ** *
1302503 GAGCTCGATTGAAGCTTGAAACTC
1 GAGCTCGATTGAAGCTCG-ATTTT
1302527 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTT
*
1302550 GAGCTCGATTCAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTT
*
1302573 AAGCTC
1 GAGCTC
1302579 AATTCGGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 29 0.63
24 17 0.37
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTT
Found at i:1302576 original size:12 final size:11
Alignment explanation
Indices: 1302528--1302578 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
1302518 TTGAAACTCG
*
1302528 AGCTCGATTGA
1 AGCTCGATTTA
*
1302539 AGCTCGATTTTG
1 AGCTCGA-TTTA
*
1302551 AGCTCGATTCA
1 AGCTCGATTTA
1302562 AGCTCGATTTTA
1 AGCTCGA-TTTA
1302574 AGCTC
1 AGCTC
1302579 AATTCGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (11 bp):
AGCTCGATTTA
Found at i:1303972 original size:7 final size:7
Alignment explanation
Indices: 1303960--1304059 Score: 121
Period size: 7 Copynumber: 14.4 Consensus size: 7
1303950 TATCAGATTA
1303960 AGGGTTT
1 AGGGTTT
*
1303967 ATGGTTT
1 AGGGTTT
1303974 AGGGTTT
1 AGGGTTT
*
1303981 AGGATTT
1 AGGGTTT
*
1303988 AGGTTTT
1 AGGGTTT
1303995 AGGGTTT
1 AGGGTTT
1304002 AGGGTTT
1 AGGGTTT
1304009 A-GGTTT
1 AGGGTTT
1304015 AGGGTTT
1 AGGGTTT
1304022 AGGGTTT
1 AGGGTTT
*
1304029 AAGGTTT
1 AGGGTTT
*
1304036 AAGGTTT
1 AGGGTTT
***
1304043 ATAATTT
1 AGGGTTT
1304050 AGGGTTT
1 AGGGTTT
1304057 AGG
1 AGG
1304060 TTCATGGCTC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
6 6 0.08
7 74 0.93
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
AGGGTTT
Found at i:1304599 original size:14 final size:14
Alignment explanation
Indices: 1304580--1304609 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1304570 TATAATTATC
*
1304580 AATAATGTATTTTT
1 AATAATGTAATTTT
1304594 AATAATGTAATTTT
1 AATAATGTAATTTT
1304608 AA
1 AA
1304610 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:1305996 original size:20 final size:20
Alignment explanation
Indices: 1305971--1306019 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1305961 TTCGAGTTTG
* *
1305971 ACTCGAAAAGTTTGCAAGTA
1 ACTCGAAAAGCTTACAAGTA
* *
1305991 AGTCGAAAAGCTTACGAGTA
1 ACTCGAAAAGCTTACAAGTA
1306011 ACTCGAAAA
1 ACTCGAAAA
1306020 TATAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTCGAAAAGCTTACAAGTA
Found at i:1311941 original size:21 final size:21
Alignment explanation
Indices: 1311916--1311959 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1311906 AAGGGGAGGT
1311916 ATTCCAATACAAAAAAGTTAC
1 ATTCCAATACAAAAAAGTTAC
* *
1311937 ATTCCAATGCAATAAAGTTAC
1 ATTCCAATACAAAAAAGTTAC
1311958 AT
1 AT
1311960 AGTGTCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (21 bp):
ATTCCAATACAAAAAAGTTAC
Found at i:1313088 original size:38 final size:38
Alignment explanation
Indices: 1313031--1313105 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
1313021 TAACGTTAAG
*
1313031 TTTTGAACAAGGGTACTAAAATTAAACAAAAACTAAAC
1 TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAAC
* * * *
1313069 TTTTTAACAATGGTGCTAAAATGAAATAAAAACTAAA
1 TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAA
1313106 GTTTAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (38 bp):
TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAAC
Found at i:1313809 original size:21 final size:21
Alignment explanation
Indices: 1313785--1313844 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1313775 AATTACTTGA
1313785 TTTGTACTTAGCTTTAAGCAT
1 TTTGTACTTAGCTTTAAGCAT
* *
1313806 TTTG-AGTT--CATT--G-A-
1 TTTGTACTTAGCTTTAAGCAT
1313820 TTTGTACTTAGCTTTAAGCAT
1 TTTGTACTTAGCTTTAAGCAT
1313841 TTTG
1 TTTG
1313845 AGTTCATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 14
0.61 0.09 0.30
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 1 0.04
17 3 0.11
18 3 0.11
19 1 0.04
20 4 0.14
21 8 0.29
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTGTACTTAGCTTTAAGCAT
Found at i:1313827 original size:35 final size:35
Alignment explanation
Indices: 1313781--1313884 Score: 183
Period size: 35 Copynumber: 3.0 Consensus size: 35
1313771 ACATAATTAC
1313781 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
1 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
1313816 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
1 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
*
1313851 TTGATTTGTACTT-GTCTTTAAGCAATTTGAGTTC
1 TTGATTTGTACTTAG-CTTTAAGCATTTTGAGTTC
1313885 TTCGGCAATC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 1 0.01
35 66 0.99
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (35 bp):
TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
Found at i:1318986 original size:14 final size:14
Alignment explanation
Indices: 1318967--1318996 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1318957 GTAAAAGAAG
1318967 TTATGGCAACGAAA
1 TTATGGCAACGAAA
1318981 TTATGGCAACGAAA
1 TTATGGCAACGAAA
1318995 TT
1 TT
1318997 TGATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (14 bp):
TTATGGCAACGAAA
Found at i:1327646 original size:162 final size:162
Alignment explanation
Indices: 1327354--1327681 Score: 514
Period size: 162 Copynumber: 2.0 Consensus size: 162
1327344 GGATTTGGCA
* * *
1327354 AATGGGACTGATAGCAATCAAGTTGTGTTGGAGAAAGTTACTGCTGGACAGGGATCAGAATCTCA
1 AATGGGACTGATACCAATCAAGTTGTGTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCTCA
* * *
1327419 GCCTACAGACAATATGCAAAAGTCTGGGGATGTAGGTCAATCTCAATCAGCAAGTGGAAATCACA
66 GCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCACA
*
1327484 GTGATATTTCTTCTTCAGTCAAGAAGGATACT
131 GTGATATTTCTTCTTCAGTCAAGAAGGATACG
*
1327516 AATGGGGCTGATACCAATCAAGTTG-GCTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCTC
1 AATGGGACTGATACCAATCAAGTTGTG-TCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCTC
* * * * * *
1327580 AGCCTTCAGACAATATGCAGAAGTCTGGGGATATAGGTCAATCTTACCCAGTAAATGGAGATCAC
65 AGCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCAC
1327645 AGTGATATTTCTTCTTCAGTCAAGAAGGATACG
130 AGTGATATTTCTTCTTCAGTCAAGAAGGATACG
1327678 AATG
1 AATG
1327682 AATCGGGAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
161 1 0.01
162 150 0.99
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (162 bp):
AATGGGACTGATACCAATCAAGTTGTGTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCTCA
GCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCACA
GTGATATTTCTTCTTCAGTCAAGAAGGATACG
Found at i:1337526 original size:19 final size:20
Alignment explanation
Indices: 1337498--1337536 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1337488 CTTGTGATTA
*
1337498 TTATTTGAAATATT-ATTTT
1 TTATTGGAAATATTGATTTT
1337517 TTATTGGAAATATTGATTTT
1 TTATTGGAAATATTGATTTT
1337537 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (20 bp):
TTATTGGAAATATTGATTTT
Found at i:1338990 original size:45 final size:44
Alignment explanation
Indices: 1338935--1339039 Score: 129
Period size: 45 Copynumber: 2.4 Consensus size: 44
1338925 AATTGGTAGC
*** * *
1338935 AAAAAATAATATTTTAGATAGTGTATAATATTAATATTTTCGAT
1 AAAAAATAATATTTTAGATAGCACACAATATTAATATTTTCAAT
* *
1338979 AGAAAAATAATATTTTAGGTAGCACACAATATTAATATTTTTAAT
1 A-AAAAATAATATTTTAGATAGCACACAATATTAATATTTTCAAT
*
1339024 AAAAAATAATAATTTA
1 AAAAAATAATATTTTA
1339040 ATGAAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 15 0.29
45 37 0.71
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.39
Consensus pattern (44 bp):
AAAAAATAATATTTTAGATAGCACACAATATTAATATTTTCAAT
Found at i:1340236 original size:14 final size:15
Alignment explanation
Indices: 1340217--1340245 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1340207 TTAATAAAAT
1340217 TTTAATA-TAAATAA
1 TTTAATATTAAATAA
1340231 TTTAATATTAAATAA
1 TTTAATATTAAATAA
1340246 ATTATATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATATTAAATAA
Found at i:1340647 original size:93 final size:93
Alignment explanation
Indices: 1340503--1340672 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
1340493 CTTTGCAGTT
* *
1340503 GGAGTTTGGTCTACCTAAAACCTTTAATTTCAATTTACGTACAATTACAAATATACGATGTTTAA
1 GGAGTTTGGTCCACCTAAAACCTTTAATTTCAATTTACGTACAATTACAAATATACAATGTTTAA
1340568 TCTTTAGTATATATTTGCGTTGATTGAG
66 TCTTTAGTATATATTTGCGTTGATTGAG
* *
1340596 GGAGTTTGTTCCACCTAACACCTTTAATTTCAATTTACGTACAATTACAAATATACAATGTTTAA
1 GGAGTTTGGTCCACCTAAAACCTTTAATTTCAATTTACGTACAATTACAAATATACAATGTTTAA
*
1340661 TTTTTAGTATAT
66 TCTTTAGTATAT
1340673 TTTTAAAATA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (93 bp):
GGAGTTTGGTCCACCTAAAACCTTTAATTTCAATTTACGTACAATTACAAATATACAATGTTTAA
TCTTTAGTATATATTTGCGTTGATTGAG
Found at i:1348889 original size:31 final size:31
Alignment explanation
Indices: 1348854--1348924 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1348844 TTAAAAAAAC
*
1348854 TGGTCACTTACATTATTG-TTTTATTAAGTTT
1 TGGTCACTTACATTA-TGATTTTATTAAGATT
* ** *
1348885 TGGTCACTAATGTTATGATTTTATTCAGATT
1 TGGTCACTTACATTATGATTTTATTAAGATT
1348916 TGGTCACTT
1 TGGTCACTT
1348925 GAACGTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (31 bp):
TGGTCACTTACATTATGATTTTATTAAGATT
Found at i:1350157 original size:31 final size:31
Alignment explanation
Indices: 1350122--1350200 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1350112 ATTCAACGTC
* *
1350122 TAAGTGACCAAAATTTAATAAAACGATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
*
1350153 TAAGTGACTAAAACTTAATAAAACAATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
*
1350184 TAAGTGATCAAAACTTA
1 TAAGTGACCAAAACTTA
1350201 CTTTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACG
Found at i:1353567 original size:23 final size:23
Alignment explanation
Indices: 1353541--1353587 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1353531 ATATAGGATC
1353541 ATATTAAATCAAACATAGATGAA
1 ATATTAAATCAAACATAGATGAA
1353564 ATATTAAATCAAACATAGATGAA
1 ATATTAAATCAAACATAGATGAA
1353587 A
1 A
1353588 GAAATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
ATATTAAATCAAACATAGATGAA
Found at i:1355720 original size:17 final size:17
Alignment explanation
Indices: 1355698--1355732 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1355688 GAACGAGGCA
*
1355698 TATTTTAACATGCATTC
1 TATTTTAACAAGCATTC
1355715 TATTTTAACAAGCATTC
1 TATTTTAACAAGCATTC
1355732 T
1 T
1355733 TCATTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (17 bp):
TATTTTAACAAGCATTC
Found at i:1357459 original size:21 final size:22
Alignment explanation
Indices: 1357435--1357481 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1357425 ATGGCTGAGT
1357435 AACATA-AATTTTTT-ATATAAA
1 AACATATAATTTTTTCA-ATAAA
1357456 AACA-ATAATTTTTTCAATAAA
1 AACATATAATTTTTTCAATAAA
1357477 AACAT
1 AACAT
1357482 GTAAACATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
AACATATAATTTTTTCAATAAA
Found at i:1359078 original size:2 final size:2
Alignment explanation
Indices: 1359073--1359102 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1359063 GTGTGTGAGT
1359073 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
1359103 CCTGTGACAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1367364 original size:21 final size:20
Alignment explanation
Indices: 1367338--1367446 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 20
1367328 GTTTCCAGAT
*
1367338 TCGCAATGTGATTTTAGACTA
1 TCGCAATGTGACTTT-GACTA
*
1367359 TCGCAATGCGAACTTTGACTA
1 TCGCAATGTG-ACTTTGACTA
* * *
1367380 TCGCAATGTGAATATGTA-AA
1 TCGCAATGTGACTTTG-ACTA
* *
1367400 TCGCAATGCGAACTTGGACTA
1 TCGCAATGTG-ACTTTGACTA
* *
1367421 TCGCAATGCGAACTTCGACTA
1 TCGCAATGTG-ACTTTGACTA
1367442 TCGCA
1 TCGCA
1367447 TTGCGGTAGT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 15 0.21
21 53 0.74
22 4 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGTGACTTTGACTA
Found at i:1367451 original size:21 final size:20
Alignment explanation
Indices: 1367354--1367451 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
1367344 TGTGATTTTA
1367354 GACTATCGCAATGCGAACTTT
1 GACTATCGCAATGCGAAC-TT
*
1367375 GACTATCGCAATGTGAA-TAT
1 GACTATCGCAATGCGAACT-T
*
1367395 GTA-AATCGCAATGCGAACTT
1 G-ACTATCGCAATGCGAACTT
1367415 GGACTATCGCAATGCGAACTT
1 -GACTATCGCAATGCGAACTT
*
1367436 CGACTATCGCATTGCG
1 -GACTATCGCAATGCG
1367452 GTAGTCAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.02
20 16 0.24
21 49 0.74
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGAACTT
Found at i:1367609 original size:5 final size:5
Alignment explanation
Indices: 1367587--1367627 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
1367577 ACCATTACCA
1367587 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGAC
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGAC
1367628 TCGAGACGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1369818 original size:2 final size:2
Alignment explanation
Indices: 1369806--1369852 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1369796 TGATTCGTGC
* *
1369806 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1369848 TA TA T
1 TA TA T
1369853 TAAGATGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1370612 original size:14 final size:14
Alignment explanation
Indices: 1370593--1370620 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1370583 AAGTGAAAGA
1370593 ATAGTTATATAATT
1 ATAGTTATATAATT
1370607 ATAGTTATATAATT
1 ATAGTTATATAATT
1370621 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1390324 original size:33 final size:33
Alignment explanation
Indices: 1390227--1390423 Score: 174
Period size: 33 Copynumber: 6.2 Consensus size: 33
1390217 GGCGGATTTA
** *
1390227 ATGGTATTGGTGCAAATAATGGAGGTAGAGGTG
1 ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
** * * * * *
1390260 ATGGTGCTGTTGAAGG-AGATGAAGATGGAGATG
1 ATGGTATTGGTGCAGGTA-ATGGAGGTAGAGATG
*
1390293 ATGGTATTGGTTCAGGTAATGGAGGTAGAGATG
1 ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
* *
1390326 ATGGTATTGGTGCAGGTGATGGAGAT-GA-A-G
1 ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
* *
1390356 --GCT-TTGGTGCAGGTGATGGAGGTAGAGATG
1 ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
* * *
1390386 ATGGTATTCGTGCAGGTAATAGAGGTAGAGATA
1 ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
1390419 ATGGT
1 ATGGT
1390424 GCTGGTAAAG
Statistics
Matches: 128, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
27 19 0.15
28 4 0.03
29 1 0.01
30 2 0.02
31 1 0.01
32 5 0.04
33 95 0.74
34 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.41, T:0.27
Consensus pattern (33 bp):
ATGGTATTGGTGCAGGTAATGGAGGTAGAGATG
Found at i:1390350 original size:27 final size:27
Alignment explanation
Indices: 1390283--1390376 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
1390273 AGGAGATGAA
*
1390283 GATGGAGATGATGGTATTGGTTCAGGTAAT
1 GATGGAGATGATGGTATTGGTGCAGG---T
*
1390313 GGAGGTAGAGATGATGGTATTGGTGCAGGT
1 -GA--TGGAGATGATGGTATTGGTGCAGGT
*
1390343 GATGGAGATGAAGGCT-TTGGTGCAGGT
1 GATGGAGATGATGG-TATTGGTGCAGGT
1390370 GATGGAG
1 GATGGAG
1390377 GTAGAGATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
27 28 0.50
28 1 0.02
29 2 0.04
30 1 0.02
31 2 0.04
33 22 0.39
ACGTcount: A:0.24, C:0.04, G:0.44, T:0.28
Consensus pattern (27 bp):
GATGGAGATGATGGTATTGGTGCAGGT
Found at i:1390351 original size:60 final size:60
Alignment explanation
Indices: 1390283--1390402 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
1390273 AGGAGATGAA
* * *
1390283 GATGGAGATGATGG-TATTGGTTCAGGTAATGGAGGTAGAGATGATGGTATTGGTGCAGGT
1 GATGGAGATGAAGGCT-TTGGTGCAGGTAATGGAGGTAGAGATGATGGTATTCGTGCAGGT
*
1390343 GATGGAGATGAAGGCTTTGGTGCAGGTGATGGAGGTAGAGATGATGGTATTCGTGCAGGT
1 GATGGAGATGAAGGCTTTGGTGCAGGTAATGGAGGTAGAGATGATGGTATTCGTGCAGGT
1390403 AATAGAGGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.42, T:0.28
Consensus pattern (60 bp):
GATGGAGATGAAGGCTTTGGTGCAGGTAATGGAGGTAGAGATGATGGTATTCGTGCAGGT
Found at i:1390408 original size:27 final size:27
Alignment explanation
Indices: 1390318--1390409 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 27
1390308 GTAATGGAGG
*
1390318 TAGAGATGATGGTATTGGTGCAGGTGA
1 TAGAGATGATGGTATTGGTGCAGGTAA
* *
1390345 TGGAGATGAAGGCT-TTGGTGCAGGTGATGGA
1 TAGAGATGATGG-TATTGGTGCAGGT-A---A
*
1390376 GGTAGAGATGATGGTATTCGTGCAGGTAA
1 --TAGAGATGATGGTATTGGTGCAGGTAA
1390405 TAGAG
1 TAGAG
1390410 GTAGAGATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
27 26 0.51
28 1 0.02
29 1 0.02
31 1 0.02
32 2 0.04
33 20 0.39
ACGTcount: A:0.26, C:0.05, G:0.41, T:0.27
Consensus pattern (27 bp):
TAGAGATGATGGTATTGGTGCAGGTAA
Found at i:1390415 original size:93 final size:90
Alignment explanation
Indices: 1390287--1390468 Score: 247
Period size: 93 Copynumber: 2.0 Consensus size: 90
1390277 GATGAAGATG
* * * * * **
1390287 GAGATGATGGTATTGGTTCAGGTAATGGAGGTAGAGATGATGGTATTGGTGCAGGTGATGGAGAT
1 GAGATGATGGTATTCGTGCAGGTAATAGAGGTAGAGATAATGGTACTGGTAAAGGTGATGGAGAT
*
1390352 GAAGGCTTTGGTGCAGGTGATGGAGGTA
66 GAA-GC--TGGTGCAGATGATGGAGGTA
*
1390380 GAGATGATGGTATTCGTGCAGGTAATAGAGGTAGAGATAATGGTGCTGGTAAAGGTGATGGAGAT
1 GAGATGATGGTATTCGTGCAGGTAATAGAGGTAGAGATAATGGTACTGGTAAAGGTGATGGAGAT
*
1390445 GAAGCTGGTGTAGATGATGGAGGT
66 GAAGCTGGTGCAGATGATGGAGGT
1390469 TTTAGAAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 17 0.22
92 2 0.03
93 60 0.76
ACGTcount: A:0.27, C:0.04, G:0.42, T:0.27
Consensus pattern (90 bp):
GAGATGATGGTATTCGTGCAGGTAATAGAGGTAGAGATAATGGTACTGGTAAAGGTGATGGAGAT
GAAGCTGGTGCAGATGATGGAGGTA
Found at i:1390565 original size:39 final size:39
Alignment explanation
Indices: 1390451--1390566 Score: 187
Period size: 39 Copynumber: 3.0 Consensus size: 39
1390441 AGATGAAGCT
* * * * *
1390451 GGTGTAGATGATGGAGGTTTTAGAAATGGAGCCGGAACT
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
1390490 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
1390529 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGC
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGC
1390567 AGATGATGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.26
Consensus pattern (39 bp):
GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
Found at i:1406812 original size:12 final size:12
Alignment explanation
Indices: 1406795--1406821 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1406785 TAAAAAAATA
1406795 AAATATTATTTT
1 AAATATTATTTT
1406807 AAATATTATTTT
1 AAATATTATTTT
1406819 AAA
1 AAA
1406822 AAAATCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:1410867 original size:3 final size:3
Alignment explanation
Indices: 1410853--1410888 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1410843 ATTTGGTTTC
1410853 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1410889 AGTTAAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1411345 original size:15 final size:16
Alignment explanation
Indices: 1411325--1411369 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1411315 TGTCATGTCC
1411325 AGATTTTTTTTAAAT-
1 AGATTTTTTTTAAATA
1411340 AGA-TTTTTTTAAATA
1 AGATTTTTTTTAAATA
*
1411355 ATATTTTATTTTAAA
1 AGATTTT-TTTTAAA
1411370 AAAAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 3 0.12
17 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
AGATTTTTTTTAAATA
Found at i:1411643 original size:42 final size:42
Alignment explanation
Indices: 1411584--1411700 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
1411574 TTTTCCCGAA
* *
1411584 TTCCCGTATTTGTTTCACGTAATTCGTTTTCTGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
* *
1411626 TTCCCGTGTTTGTTTCACGTAATTCGTTTCCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
* * *
1411668 TTCCCATGTTTGTTTAACGTAATTGGTTTTCCG
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCG
1411701 GAATGTAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
Found at i:1411921 original size:22 final size:22
Alignment explanation
Indices: 1411893--1411973 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
1411883 ATTTATTTAT
1411893 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
1411915 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
1411939 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
1411962 TAAGATATTATA
1 TAATAT-TTATA
1411974 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 13 0.29
25 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:1412065 original size:32 final size:30
Alignment explanation
Indices: 1411875--1412066 Score: 96
Period size: 29 Copynumber: 6.3 Consensus size: 30
1411865 CATTTTCATC
* *
1411875 AAAATA-TTATTTATTTATTAATATTT-AT
1 AAAATATTTATATATTTAATAATATTTAAT
* *
1411903 AATAATATAATATAATATTT-TTAATA-TTATAT
1 AA-AATAT-TTAT-ATATTTAATAATATTTA-AT
** *
1411935 AAAATAATCAATTATATTATAATAATA-TAAGAT
1 AAAAT-ATTTA-TATATT-TAATAATATTTA-AT
** * *
1411968 ATTATATTTTTAT-TTTAATAATATATAAT
1 AAAATATTTATATATTTAATAATATTTAAT
* *
1411997 AAAAAATTTATATATTTAAT-A-A-TGAAT
1 AAAATATTTATATATTTAATAATATTTAAT
*
1412024 AATATTATTTATATATTTAAATAATATTTAAT
1 AA-AATATTTATATATTT-AATAATATTTAAT
1412056 AAAGATATTTA
1 AAA-ATATTTA
1412067 AAATATACTA
Statistics
Matches: 122, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.04
28 16 0.13
29 27 0.22
30 12 0.10
31 23 0.19
32 27 0.22
33 12 0.10
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (30 bp):
AAAATATTTATATATTTAATAATATTTAAT
Found at i:1412208 original size:29 final size:31
Alignment explanation
Indices: 1412148--1412214 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
1412138 TTTATTTCAC
* * *
1412148 TAAAA-TATACAAAATTATTATTTTTATTAA
1 TAAAATTATACAAAATTATTATTATAATAAA
1412178 TAAAATTATA-AAAATTA-TATTATAATAAA
1 TAAAATTATACAAAATTATTATTATAATAAA
1412207 T-AAATTAT
1 TAAAATTAT
1412215 TTTAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.21
29 10 0.30
30 12 0.36
31 4 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAAATTATACAAAATTATTATTATAATAAA
Found at i:1413254 original size:37 final size:37
Alignment explanation
Indices: 1413181--1413255 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
1413171 GTTGAAAAAT
* * *
1413181 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAACTGAAAATCATAAA
* *
1413218 ATTTATATAATTTTTTTTACAAAACTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAACTGAAAATCATAAA
1413255 A
1 A
1413256 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAACTGAAAATCATAAA
Found at i:1418878 original size:6 final size:7
Alignment explanation
Indices: 1418837--1418875 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
1418827 GATAGTTTTG
*
1418837 TTTTGCT
1 TTTTTCT
1418844 TTTTTCT
1 TTTTTCT
1418851 TTTTTCT
1 TTTTTCT
1418858 TTTTTCT
1 TTTTTCT
1418865 TTTTTCT
1 TTTTTCT
1418872 TTTT
1 TTTT
1418876 CTTCTTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:1429569 original size:20 final size:20
Alignment explanation
Indices: 1429544--1429590 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
1429534 TTTTAGGGTC
1429544 GAATTTTAAAAAAAATTATT
1 GAATTTTAAAAAAAATTATT
1429564 GAATTTT--AAAAAATTATT
1 GAATTTTAAAAAAAATTATT
1429582 GAATTTTAA
1 GAATTTTAA
1429591 TTTGATCCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.72
20 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
GAATTTTAAAAAAAATTATT
Found at i:1430121 original size:31 final size:31
Alignment explanation
Indices: 1430083--1430175 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
1430073 AAGTTTTTTA
1430083 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1430114 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
1430145 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1430176 ATGTACCATG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:1430208 original size:22 final size:22
Alignment explanation
Indices: 1430180--1430223 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1430170 CTTTGCATGT
1430180 ACCATGCACGTCGGAAGAGGTC
1 ACCATGCACGTCGGAAGAGGTC
*
1430202 ACCATGCACGTTGGAAGAGGTC
1 ACCATGCACGTCGGAAGAGGTC
1430224 GCCTGCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.32, T:0.16
Consensus pattern (22 bp):
ACCATGCACGTCGGAAGAGGTC
Found at i:1430783 original size:18 final size:18
Alignment explanation
Indices: 1430760--1430797 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1430750 TTAGGAGTGT
1430760 AAGGGTTAAATGTCAAAA
1 AAGGGTTAAATGTCAAAA
1430778 AAGGGTTAAATGTCAAAA
1 AAGGGTTAAATGTCAAAA
1430796 AA
1 AA
1430798 TTGAGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (18 bp):
AAGGGTTAAATGTCAAAA
Found at i:1431874 original size:21 final size:21
Alignment explanation
Indices: 1431845--1431889 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1431835 TCGGTAAAAA
**
1431845 TTTACCTAAATTATTATTATT
1 TTTACCTAAAACATTATTATT
* *
1431866 TTTATCTAAAACATTATTGTT
1 TTTACCTAAAACATTATTATT
1431887 TTT
1 TTT
1431890 TAATATTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTACCTAAAACATTATTATT
Found at i:1438483 original size:20 final size:21
Alignment explanation
Indices: 1438453--1438493 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1438443 GTTAAAATAA
*
1438453 CCGGTTTAAAAAAAATCCGAT
1 CCGGTTTAAAAAAAAACCGAT
1438474 CCGG-TTAAAAAAAAACCGAT
1 CCGGTTTAAAAAAAAACCGAT
1438494 TTTTCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (21 bp):
CCGGTTTAAAAAAAAACCGAT
Found at i:1441175 original size:30 final size:30
Alignment explanation
Indices: 1441139--1441195 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1441129 CATTATAATC
1441139 ACATCTT-AGTTAAATAAAAACAAAAGTGAT
1 ACATCTTCA-TTAAATAAAAACAAAAGTGAT
1441169 ACATCTTCATTAAATAAAAACAAAAGT
1 ACATCTTCATTAAATAAAAACAAAAGT
1441196 AATCATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.26
Consensus pattern (30 bp):
ACATCTTCATTAAATAAAAACAAAAGTGAT
Found at i:1451736 original size:15 final size:15
Alignment explanation
Indices: 1451716--1451753 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1451706 TTAAACAAAG
1451716 GAAACACATACGCAC
1 GAAACACATACGCAC
1451731 GAAACACATACGCAC
1 GAAACACATACGCAC
*
1451746 AAAACACA
1 GAAACACA
1451754 AAACCAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.32, G:0.11, T:0.05
Consensus pattern (15 bp):
GAAACACATACGCAC
Found at i:1480165 original size:19 final size:20
Alignment explanation
Indices: 1480124--1480165 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1480114 CCATTTACTC
* *
1480124 GATTATTTATTTTCAATTCA
1 GATTATGTATTTTCAATTAA
1480144 GATTATGTATTTT-AATTAA
1 GATTATGTATTTTCAATTAA
1480163 GAT
1 GAT
1480166 AATTAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (20 bp):
GATTATGTATTTTCAATTAA
Found at i:1488140 original size:33 final size:31
Alignment explanation
Indices: 1488103--1488169 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1488093 CAAACAAGCA
*
1488103 TAAGATAGGATCATTTTTTTGTTTTTATATAAT
1 TAAGATAGGATCA--CTTTTGTTTTTATATAAT
*
1488136 TAAGATATGATCACTTTTGTTTTTATATAAT
1 TAAGATAGGATCACTTTTGTTTTTATATAAT
1488167 TAA
1 TAA
1488170 TATATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.62
33 12 0.38
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (31 bp):
TAAGATAGGATCACTTTTGTTTTTATATAAT
Found at i:1489199 original size:21 final size:21
Alignment explanation
Indices: 1489173--1489222 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1489163 TAAAAATTTT
1489173 ATTATTTTTTAAAATTAAGTC
1 ATTATTTTTTAAAATTAAGTC
1489194 ATTATTTTTTAAAATTAAGTC
1 ATTATTTTTTAAAATTAAGTC
*
1489215 CTTATTTT
1 ATTATTTT
1489223 ATATCAGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTATTTTTTAAAATTAAGTC
Found at i:1494664 original size:28 final size:27
Alignment explanation
Indices: 1494594--1494655 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1494584 ACAACTATAA
1494594 ATTTTTTAGAAGTTGCCATGAACAATC
1 ATTTTTTAGAAGTTGCCATGAACAATC
1494621 ATTTTTTAGAAGTTGCCATGAACAATC
1 ATTTTTTAGAAGTTGCCATGAACAATC
*
1494648 CTTTTTTA
1 ATTTTTTA
1494656 TCGTTTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (27 bp):
ATTTTTTAGAAGTTGCCATGAACAATC
Found at i:1502909 original size:71 final size:71
Alignment explanation
Indices: 1502793--1502932 Score: 253
Period size: 71 Copynumber: 2.0 Consensus size: 71
1502783 AAATAATAGC
* *
1502793 ACGGACCTGCAACGTAAAATTGCCTGAGAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
1 ACGGACCTGCAAAGTAAAATTGCCTGAGAACTCAAATAATCAAGAAGACAATACGTCAAAAGAAG
1502858 TCTATT
66 TCTATT
*
1502864 ACGGACCTGCAAAGTAAAATTGCTTGAGAACTCAAATAATCAAGAAGACAATACGTCAAAAGAAG
1 ACGGACCTGCAAAGTAAAATTGCCTGAGAACTCAAATAATCAAGAAGACAATACGTCAAAAGAAG
1502929 TCTA
66 TCTA
1502933 CAGGAAAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (71 bp):
ACGGACCTGCAAAGTAAAATTGCCTGAGAACTCAAATAATCAAGAAGACAATACGTCAAAAGAAG
TCTATT
Found at i:1503999 original size:18 final size:19
Alignment explanation
Indices: 1503964--1504000 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1503954 CACGGAATGT
1503964 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1503984 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1504001 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1508795 original size:29 final size:29
Alignment explanation
Indices: 1508753--1508841 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
1508743 TACCGGGGGT
*
1508753 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
1508782 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
1508811 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
1508840 AG
1 AG
1508842 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:1508905 original size:3 final size:3
Alignment explanation
Indices: 1508899--1508976 Score: 86
Period size: 3 Copynumber: 25.7 Consensus size: 3
1508889 TTTTTTTGTA
** * *
1508899 TAT TAT TAT TAT CGT TAT TTT TAT TTT TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
1508945 TAT TAT TATT TAT TAT TA- TAT TAT TAA TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
1508977 CATTTTACAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 6 0.10
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1508954 original size:37 final size:37
Alignment explanation
Indices: 1508899--1508970 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1508889 TTTTTTTGTA
* *
1508899 TATTATTATTATCGTTATTT-TTATTTTTATTATTATT
1 TATTATTATTATCATTATTTATTA-TTATATTATTATT
*
1508936 TATTATTATTATTATTATTTATTATTATATTATTA
1 TATTATTATTATCATTATTTATTATTATATTATTA
1508971 ATATTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (37 bp):
TATTATTATTATCATTATTTATTATTATATTATTATT
Found at i:1509034 original size:11 final size:11
Alignment explanation
Indices: 1509013--1509043 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1509003 CCCAATACAA
1509013 CAAGG-CCAAC
1 CAAGGCCCAAC
1509023 CAAGGCCCAAC
1 CAAGGCCCAAC
1509034 CAAGGCCCAA
1 CAAGGCCCAA
1509044 ACACGAGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.39, C:0.42, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:1511202 original size:30 final size:30
Alignment explanation
Indices: 1511168--1511228 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1511158 TTATATTCGA
1511168 TTCATACTTTCCATCATTTACGACAATGTG
1 TTCATACTTTCCATCATTTACGACAATGTG
1511198 TTCATACTTTCCATCATTTACGACAATGTG
1 TTCATACTTTCCATCATTTACGACAATGTG
1511228 T
1 T
1511229 AAGCGACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (30 bp):
TTCATACTTTCCATCATTTACGACAATGTG
Found at i:1516553 original size:4 final size:4
Alignment explanation
Indices: 1516544--1516577 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1516534 AAAAGTATAC
1516544 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1516578 GATACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1516568 original size:22 final size:21
Alignment explanation
Indices: 1516540--1516585 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1516530 CGAGAAAAGT
1516540 ATACACATACATACATACATAC
1 ATACACATACATACAT-CATAC
*
1516562 ATACACATACATACATGATAC
1 ATACACATACATACATCATAC
1516583 ATA
1 ATA
1516586 AAATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ATACACATACATACATCATAC
Found at i:1516991 original size:38 final size:38
Alignment explanation
Indices: 1516933--1517069 Score: 123
Period size: 38 Copynumber: 3.8 Consensus size: 38
1516923 GAGACAGTTT
* *
1516933 TCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTC
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
1516971 TCTTTAAAACAAATTATGTCTCGCTTGAGAC-A--TT-
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
** ** *
1517005 T-TTT-CCACAAATT-T-T-GAGAATT-AGACAACTTTC
1 TCTTTAAAACAAATTATGTCTCG-CTTGAGACAACTTTC
*
1517038 TCTTTAAAACATATTATGTCTCGCTTGAGACA
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACA
1517070 TTTTTCCACA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
29 5 0.07
30 4 0.05
31 1 0.01
32 9 0.12
33 4 0.05
34 4 0.05
35 8 0.11
36 1 0.01
37 4 0.05
38 35 0.47
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (38 bp):
TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
Found at i:1517054 original size:67 final size:66
Alignment explanation
Indices: 1516960--1517092 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 66
1516950 GTCTCGCTTG
1516960 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTTCCACAAATTTTGAGAA
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACA-TTTTTCCACAAATTTTGAGAA
1517025 TT
65 TT
*
1517027 AGACAACTTTCTCTTTAAAACATATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAAT
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAAT
1517092 T
66 T
1517093 TTAAAACAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 23 0.35
67 42 0.65
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (66 bp):
AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAAT
T
Found at i:1517322 original size:35 final size:36
Alignment explanation
Indices: 1517278--1517358 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1517268 ACAAAGTTGA
*
1517278 TCTCACTTGAAATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAAA-CAATTTCTCTAAAAACAAACTTTG
* * *
1517313 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
*
1517349 TCTCATTTGA
1 TCTCACTTGA
1517359 GACTATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.03
35 16 0.42
36 21 0.55
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
Found at i:1517349 original size:36 final size:36
Alignment explanation
Indices: 1517293--1517396 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
1517283 CTTGAAATCG
*
1517293 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
1517328 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
1517364 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
1517397 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:1517681 original size:25 final size:26
Alignment explanation
Indices: 1517652--1517803 Score: 137
Period size: 29 Copynumber: 5.5 Consensus size: 26
1517642 TTGAGAAAAA
*
1517652 AAAAATCTTTGAGTTTGTTTCTCTTG
1 AAAAATCTTTGAGTTTGTTCCTCTTG
1517678 AAAAAAATCTTTGAGTTTGTTCCTCTTG
1 --AAAAATCTTTGAGTTTGTTCCTCTTG
* *
1517706 -AAAATCTTTGAGTTTGCTCCTTTTG
1 AAAAATCTTTGAGTTTGTTCCTCTTG
* *
1517731 AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 ---AAAAATCTTTGAGTTTGTTCCTCTTG
* *
1517760 AATAAAAATCTTTGAG-TTGTTTCTTTTG
1 ---AAAAATCTTTGAGTTTGTTCCTCTTG
1517788 AAAAATATCTTTGAGT
1 -AAAA-ATCTTTGAGT
1517804 CTATTTATTT
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
25 23 0.21
26 4 0.04
27 9 0.08
28 36 0.33
29 38 0.35
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (26 bp):
AAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:1517747 original size:29 final size:28
Alignment explanation
Indices: 1517650--1517803 Score: 199
Period size: 28 Copynumber: 5.6 Consensus size: 28
1517640 TTTTGAGAAA
* *
1517650 AAAAAAATCTTTGAGTTTGTTTCTCTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
*
1517678 AAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
*
1517706 ---AAAATCTTTGAGTTTGCTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
*
1517731 AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
*
1517760 AATAAAAATCTTTGAG-TTGTTTCTTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
*
1517788 AAAAATATCTTTGAGT
1 AAAAAAATCTTTGAGT
1517804 CTATTTATTT
Statistics
Matches: 113, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
25 23 0.20
27 12 0.11
28 40 0.35
29 38 0.34
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (28 bp):
AAAAAAATCTTTGAGTTTGTTCCTTTTG
Found at i:1517755 original size:54 final size:53
Alignment explanation
Indices: 1517653--1517761 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 53
1517643 TGAGAAAAAA
* * *
1517653 AAAATCTTTGAGTTTGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAATCTTTGAGTTTGCTCCTCTTGAAAAAAATCTTGGAGTTTGTTCCTCTTG
* *
1517706 AAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAATCTTTGAGTTTGCTCCTCTTGAA-AAAAATCTTGGAGTTTGTTCCTCTTG
1517760 AA
1 AA
1517762 TAAAAATCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 24 0.48
54 26 0.52
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (53 bp):
AAAATCTTTGAGTTTGCTCCTCTTGAAAAAAATCTTGGAGTTTGTTCCTCTTG
Found at i:1517892 original size:52 final size:53
Alignment explanation
Indices: 1517814--1517917 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
1517804 CTATTTATTT
1517814 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTA
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTA
*
1517866 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
1517918 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTA
Found at i:1517917 original size:26 final size:28
Alignment explanation
Indices: 1517887--1517945 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
1517877 TTTGTCTCTC
1517887 TTGAGA-CAATT-TTGTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
*** *
1517913 TTGAGATTGTTTCTTTTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
1517941 TTGAG
1 TTGAG
1517946 TTGGTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGAGATCAATTCTTGTGAAAAAAATCT
Found at i:1517957 original size:27 final size:28
Alignment explanation
Indices: 1517901--1517971 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
1517891 GACAATTTTG
1517901 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
1517929 TGAAAAAAATCTTTGAG-TTGGTTTCTTT
1 TGAAAAAAATCTTTGAGATT-GTTTCTTT
*
1517957 GGAAATAAAAT-TTTG
1 TGAAA-AAAATCTTTG
1517972 TCTCTCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 2 0.05
28 33 0.82
29 5 0.12
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.44
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTT
Found at i:1517991 original size:37 final size:37
Alignment explanation
Indices: 1517950--1518070 Score: 107
Period size: 37 Copynumber: 3.5 Consensus size: 37
1517940 TTTGAGTTGG
*
1517950 TTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAAAAAAATTTTGTCTCTCTTAAGATAA
* **
1517987 TTTCTTTTGAAACAAAAATCTTTG--AGTC-T--G----
1 TTTCTTTGGAAA-AAAAAT-TTTGTCTCTCTTAAGATAA
*
1518017 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAAAAAAATTTTGTCTCTCTTAAGATAA
*
1518054 TTTCTTTTGAAAAAAAA
1 TTTCTTTGGAAAAAAAA
1518071 ATCTTTGAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
28 4 0.06
29 5 0.08
30 13 0.21
31 1 0.02
33 1 0.02
34 1 0.02
36 1 0.02
37 28 0.44
38 5 0.08
39 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTCTTTGGAAAAAAAATTTTGTCTCTCTTAAGATAA
Found at i:1518011 original size:67 final size:66
Alignment explanation
Indices: 1517922--1518088 Score: 275
Period size: 67 Copynumber: 2.5 Consensus size: 66
1517912 TTTGAGATTG
*
1517922 TTTCTTTTG-AAAAAAATCTTTGAGT-TGGTTTCTTTGGAAATAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAAAAAAATCTTTGAGTCT-GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1517985 AA
65 AA
1517987 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAA-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1518052 AA
65 AA
*
1518054 TTTCTTTTGAAAAAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTG-AAAAAAAATCTTTGAGTCTGTTTCT
1518089 CTTAAAATGA
Statistics
Matches: 96, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
65 9 0.09
66 2 0.02
67 81 0.84
68 4 0.04
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (66 bp):
TTTCTTTTGAAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
A
Found at i:1518020 original size:95 final size:91
Alignment explanation
Indices: 1517867--1518038 Score: 222
Period size: 95 Copynumber: 1.8 Consensus size: 91
1517857 CTTTGAGTAT
* * *
1517867 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAGATTGTTTCTTTTGA
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAATCTTTGAGATTGTTTCTTTGGA
1517932 AA-AAAATCTTTGAGTTGGTTTCTTTG
66 AACAAAAT-TTTGAGTTGGTTTCTTTG
* * *
1517958 GAAATAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAG-TCTGTTTCT
1 GAAACAAAATTTTGTCTCTCTTAAGACAA-TT-TTGTG-AA-AAAAATCTTTGAGAT-TGTTTCT
1518022 TTGGAAACAAAATTTTG
61 TTGGAAACAAAATTTTG
1518039 TCTCTCTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
91 25 0.36
92 2 0.03
93 4 0.06
94 3 0.04
95 30 0.43
96 5 0.07
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (91 bp):
GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAATCTTTGAGATTGTTTCTTTGGA
AACAAAATTTTGAGTTGGTTTCTTTG
Found at i:1518611 original size:97 final size:97
Alignment explanation
Indices: 1518502--1518719 Score: 411
Period size: 97 Copynumber: 2.3 Consensus size: 97
1518492 TAAATATAAA
*
1518502 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATTTTTGAGTCGTTTCCCTTGAAACGAATTTTC
1 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTC
1518567 ACTCTTGAGACATTTTCTTTTAAAACAAGATC
66 ACTCTTGAGACATTTTCTTTTAAAACAAGATC
1518599 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTC
1 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTC
*
1518664 ACTCTTGAGACGTTTTCTTTTAAAACAAGATC
66 ACTCTTGAGACATTTTCTTTTAAAACAAGATC
1518696 ATCTTTGAGTTTGTTTCTC-TGAAA
1 ATCTTTGAGTTTGTTTCTCTTGAAA
1518720 AAATGTTTTA
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
96 5 0.04
97 114 0.96
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (97 bp):
ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTC
ACTCTTGAGACATTTTCTTTTAAAACAAGATC
Found at i:1518713 original size:32 final size:31
Alignment explanation
Indices: 1518580--1518720 Score: 95
Period size: 32 Copynumber: 4.4 Consensus size: 31
1518570 CTTGAGACAT
* *
1518580 TTTCTTTTAAAACAAGATCATCTTTGAGTTTG
1 TTTCTCTTAAAACAAGATCATCTTTGAG-TCG
* * * *
1518612 TTTCTCTTGAAATAAAACCATCTTTGAGTCG
1 TTTCTCTTAAAACAAGATCATCTTTGAGTCG
* * ** *
1518643 TTTCCCTTGAAACGAATTTTCA-CTCTTGAGACG
1 TTTCTCTTAAAAC-AA-GATCATCT-TTGAGTCG
* *
1518676 TTTTCTTTTAAAACAAGATCATCTTTGAGTTTG
1 -TTTCTCTTAAAACAAGATCATCTTTGAG-TCG
*
1518709 TTTCTCTGAAAA
1 TTTCTCTTAAAA
1518721 AATGTTTTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
31 13 0.16
32 45 0.55
33 14 0.17
34 10 0.12
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTCTCTTAAAACAAGATCATCTTTGAGTCG
Found at i:1518809 original size:36 final size:34
Alignment explanation
Indices: 1518758--1518836 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 34
1518748 TTTGAGAAAA
* * *
1518758 ATCTTTGAGTTTGTTT-CTTTGGGAACAAAATTCACC
1 ATCTTTGAGTCTGTTTCCTTT-GAAACAAAA--CAAC
1518794 ATCTTTGAGTCTGTTTCCTTTGAAACAAAACAAC
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAACAAC
1518828 ATCTTTGAG
1 ATCTTTGAG
1518837 ATCATTTCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
34 12 0.31
36 23 0.59
37 4 0.10
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (34 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAACAAC
Found at i:1518904 original size:36 final size:36
Alignment explanation
Indices: 1518831--1518905 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1518821 AAACAACATC
*
1518831 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
1518867 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
1518903 TTT
1 TTT
1518906 CCTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:1519088 original size:46 final size:46
Alignment explanation
Indices: 1519019--1519236 Score: 188
Period size: 46 Copynumber: 4.9 Consensus size: 46
1519009 AACCATAACT
* * *
1519019 TTTAGATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTTAGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC
* *
1519065 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC
1 TTTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCA-TCACC
* * *
1519111 --CAGA---CCAGATCTCCTCATCACGTAGGAGCCGTGCCA--ACC
1 TTTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
* ** * * *
1519150 -ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTTAGATGGCCAGAAC-TCCTCATCACGTAGGAGCCGTGTCATCACC
* *
1519195 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
1 TTTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCAT
1519237 TCCCCAGACC
Statistics
Matches: 137, Mismatches: 23, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 28 0.20
42 1 0.01
43 26 0.19
44 3 0.02
45 3 0.02
46 67 0.49
47 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (46 bp):
TTTAGATGGCCAGAACTCCTCATCACGTAGGAGCCGTGTCATCACC
Found at i:1519131 original size:41 final size:40
Alignment explanation
Indices: 1519074--1519304 Score: 178
Period size: 41 Copynumber: 5.5 Consensus size: 40
1519064 CTTTAGATGG
* *
1519074 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCA-TCCCCAGA
* * * **
1519115 CCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATCCCCAG---A
* * * * *
1519158 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGATC-TCCTCATCACGTATGAGCCGTGTCATC-CC--CAGA
* *
1519201 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGA
1 ---CCAGATCTCCTCATCACGTATGAGCCGTGTCA-TCCCCAGA
* *
1519245 CCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTC-GA
1 CCAGATCTCCTCATCACGTATGAGCCGTGTCATCCC-CAGA
*
1519285 CCAGATTTCCTCATCACGTA
1 CCAGATCTCCTCATCACGTA
1519305 GGAACCATGT
Statistics
Matches: 153, Mismatches: 24, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
40 28 0.18
41 58 0.38
42 1 0.01
43 29 0.19
44 4 0.03
46 30 0.20
47 3 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTATGAGCCGTGTCATCCCCAGA
Found at i:1519254 original size:130 final size:127
Alignment explanation
Indices: 1519028--1519352 Score: 494
Period size: 130 Copynumber: 2.6 Consensus size: 127
1519018 TTTTAGATGG
1519028 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
*
1519093 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGCCAACCATAGATAA
66 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCAGTGCCAACCATAG---A
1519158 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * * *
1519223 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTCGA
66 ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCAGTGCCAACCATAGA
*** * * * *
1519285 CCAGATTTCCTCATCACGTAGGAACCATG---TCACCCTTAGATGACCCGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1519347 ATGAGC
66 ATGAGC
1519353 AGTGGCGTCC
Statistics
Matches: 183, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
124 36 0.20
127 26 0.14
130 121 0.66
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (127 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCATCACGTAGGAGCAGTGCCAACCATAGA
Found at i:1519316 original size:40 final size:39
Alignment explanation
Indices: 1519204--1519320 Score: 105
Period size: 40 Copynumber: 2.9 Consensus size: 39
1519194 CTTTAGATGG
* * *
1519204 CCAGAACTCTTCATCACGTATGAGCC-GTGTCATTCCC-CAGA
1 CCAGATCTCCTCATCACGTAGGA-CCAGTGTCA--CCCTC-GA
* *
1519245 CCAGATCTCCTCATCACGTATGAGCAGTGTCAACCCTCGA
1 CCAGATCTCCTCATCACGTAGGACCAGTGTC-ACCCTCGA
*
1519285 CCAGATTTCCTCATCACGTAGGAACCA-TGTCACCCT
1 CCAGATCTCCTCATCACGTAGG-ACCAGTGTCACCCT
1519321 TAGATGACCC
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
39 5 0.08
40 30 0.45
41 30 0.45
42 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (39 bp):
CCAGATCTCCTCATCACGTAGGACCAGTGTCACCCTCGA
Found at i:1519522 original size:3 final size:3
Alignment explanation
Indices: 1519516--1519604 Score: 117
Period size: 3 Copynumber: 29.7 Consensus size: 3
1519506 TTTTTTTGTA
** * *
1519516 TAT TAT TAT TAT CGT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1519564 TAT TAT TAT TAT TAT TATT TAT TAT TA- TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
1519605 CATTTTACAT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1519657 original size:11 final size:11
Alignment explanation
Indices: 1519641--1519672 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1519631 CCCAATACAA
1519641 CAAGGCCCAAC
1 CAAGGCCCAAC
1519652 CAAGGCCCAAC
1 CAAGGCCCAAC
1519663 CAAGGCCCAA
1 CAAGGCCCAA
1519673 ACACGAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.44, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:1522122 original size:22 final size:23
Alignment explanation
Indices: 1522074--1522135 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
1522064 AATACTCAAT
*
1522074 TTTTCAAAATAAAATTCATAATCG
1 TTTTAAAAATAAAATT-ATAATCG
* *
1522098 TTTTAAAAATAATATT-TAATTG
1 TTTTAAAAATAAAATTATAATCG
*
1522120 TTTTACAAAAAAAAAT
1 TTTTA-AAAATAAAAT
1522136 GGTTATGACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 10 0.31
23 8 0.25
24 14 0.44
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTAAAAATAAAATTATAATCG
Found at i:1522161 original size:10 final size:10
Alignment explanation
Indices: 1522146--1522170 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1522136 GGTTATGACA
1522146 CCCATGCACG
1 CCCATGCACG
1522156 CCCATGCACG
1 CCCATGCACG
1522166 CCCAT
1 CCCAT
1522171 CTCGCCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.52, G:0.16, T:0.12
Consensus pattern (10 bp):
CCCATGCACG
Found at i:1522435 original size:12 final size:11
Alignment explanation
Indices: 1522415--1522450 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1522405 GAAATCAACT
1522415 GCATTATTGCA
1 GCATTATTGCA
*
1522426 GCACTTATTGCT
1 GCA-TTATTGCA
1522438 GCATTATTGCA
1 GCATTATTGCA
1522449 GC
1 GC
1522451 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:1522781 original size:28 final size:27
Alignment explanation
Indices: 1522742--1522794 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1522732 ATATTAAAAA
1522742 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1522770 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1522795 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1522800 original size:27 final size:29
Alignment explanation
Indices: 1522741--1522805 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1522731 TATATTAAAA
1522741 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1522770 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1522796 AAATAGTTAA
1 AAATAATTAA
1522806 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1522944 original size:18 final size:18
Alignment explanation
Indices: 1522921--1522975 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1522911 AATAATTATT
1522921 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1522939 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1522951 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1522968 TAAATTAG
1 TAAATTAG
1522976 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:1523028 original size:21 final size:21
Alignment explanation
Indices: 1523003--1523042 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1522993 GTTAATTAGT
1523003 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1523024 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1523043 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1525581 original size:14 final size:14
Alignment explanation
Indices: 1525562--1525654 Score: 68
Period size: 14 Copynumber: 6.6 Consensus size: 14
1525552 TTCAAGTCGT
1525562 AAATCATTACTATC
1 AAATCATTACTATC
1525576 AAATCATTAC--T-
1 AAATCATTACTATC
*
1525587 AAATCATTAATATC
1 AAATCATTACTATC
* *
1525601 -AATCATTAAATATTA
1 AAATCATT-ACTA-TC
* *
1525616 ATAATAAATTATTATC
1 A-AAT-CATTACTATC
*
1525632 TAATCATTACTATC
1 AAATCATTACTATC
1525646 AAATCATTA
1 AAATCATTA
1525655 AAAATTAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 8 0.13
14 30 0.48
15 4 0.06
16 1 0.02
17 6 0.10
18 3 0.05
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1525589 original size:25 final size:25
Alignment explanation
Indices: 1525561--1525654 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 25
1525551 GTTCAAGTCG
*
1525561 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
1525586 TAAATCATTAATATC-AATCA-T--
1 TAAATCATTAATATCAAATCATTAC
*
1525607 TAAAT-ATTAATAAT-AAATTATTATC
1 TAAATCATTAAT-ATCAAATCATTA-C
*
1525632 T-AATCATTACTATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
1525655 AAAATTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
20 6 0.11
21 11 0.19
22 1 0.02
23 1 0.02
24 10 0.18
25 28 0.49
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:1525629 original size:21 final size:21
Alignment explanation
Indices: 1525581--1525664 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 21
1525571 CTATCAAATC
* *
1525581 ATTACTAAATCATTAATATCA
1 ATTATTAAATCATTAATATAA
*
1525602 ATCATTAAAT-ATTAATAATAA
1 ATTATTAAATCATTAAT-ATAA
*
1525623 ATTATTATCTAATCATTACTATCAA
1 ATTATTA---AATCATTAATAT-AA
* *
1525648 ATCATTAAA-AATTAATA
1 ATTATTAAATCATTAATA
1525665 ATTTTCATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
20 6 0.12
21 23 0.47
22 2 0.04
24 5 0.10
25 13 0.27
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTATTAAATCATTAATATAA
Found at i:1525675 original size:45 final size:45
Alignment explanation
Indices: 1525579--1525686 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 45
1525569 TACTATCAAA
*
1525579 TCATTA-CTAAATCATTAATATCAATCATTAAATATTAATAATAAAT
1 TCATTATCT-AATCATTAATATCAATCATTAAAAATTAATAAT-AAT
* *
1525625 T-ATTATCTAATCATTACTATCAAATCATTAAAAATTAATAAT-TT
1 TCATTATCTAATCATTAATATC-AATCATTAAAAATTAATAATAAT
1525669 TCATTATTACTAATCATT
1 TCATTA-T-CTAATCATT
1525687 TCTAAATCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
44 2 0.04
45 20 0.37
46 23 0.43
47 9 0.17
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (45 bp):
TCATTATCTAATCATTAATATCAATCATTAAAAATTAATAATAAT
Found at i:1525757 original size:60 final size:60
Alignment explanation
Indices: 1525633--1526052 Score: 653
Period size: 60 Copynumber: 7.1 Consensus size: 60
1525623 ATTATTATCT
* *
1525633 AATCATTACTATCAAATCATTAAAAATTAATAAT--TTTCATTATTACTAATCATTTCTA
1 AATCATTACTATCAAATCATTAATAATTAATAATAATTTCATTATTACTAATCATTACTA
1525691 AATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTA-ATAATTAATAATAATTTCATTATTACTAATCATTACTA
*
1525751 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAATAATTAATAATAATTTCATTATTACTAATCATTACTA
*
1525811 AGTCATTACTATC-AATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTA-ATAATTAATAATAATTTCATTATTACTAATCATTACTA
*
1525870 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAATAATTAATAATAATTTCATTATTACTAATCATTACTA
1525930 AATCATTACTATCAAATCA-TACATAATTAAT-ATAATTTCATTATTACTAATCATTACT-
1 AATCATTACTATCAAATCATTA-ATAATTAATAATAATTTCATTATTACTAATCATTACTA
* *
1525988 -ATCAAATTACTATTAAATCATTAA-ATATTAATAATAATTTCATCATTACTAATCATTACTA
1 AATC--ATTACTATCAAATCATTAATA-ATTAATAATAATTTCATTATTACTAATCATTACTA
1526049 AATC
1 AATC
1526053 TTATAAATAC
Statistics
Matches: 337, Mismatches: 10, Indels: 26
0.90 0.03 0.07
Matches are distributed among these distances:
57 5 0.01
58 33 0.10
59 104 0.31
60 188 0.56
61 4 0.01
62 3 0.01
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTATCAAATCATTAATAATTAATAATAATTTCATTATTACTAATCATTACTA
Found at i:1525807 original size:10 final size:10
Alignment explanation
Indices: 1525794--1525880 Score: 56
Period size: 10 Copynumber: 8.7 Consensus size: 10
1525784 TAATTTCATT
1525794 ATTACTAATC
1 ATTACTAATC
1525804 ATTACTAAGTC
1 ATTACTAA-TC
1525815 ATTACT-ATC
1 ATTACTAATC
* *
1525824 AAT-CATACATA
1 ATTAC-TA-ATC
* *
1525835 ATTAATAATA
1 ATTACTAATC
* *
1525845 ATT--TCATT
1 ATTACTAATC
1525853 ATTACTAATC
1 ATTACTAATC
1525863 ATTACTAAATC
1 ATTACT-AATC
1525874 ATTACTA
1 ATTACTA
1525881 TCAAATCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 7 0.11
9 5 0.08
10 25 0.41
11 24 0.39
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.40
Consensus pattern (10 bp):
ATTACTAATC
Found at i:1525857 original size:119 final size:120
Alignment explanation
Indices: 1525633--1526052 Score: 735
Period size: 119 Copynumber: 3.5 Consensus size: 120
1525623 ATTATTATCT
*
1525633 AATCATTACTATCAAATCATTAAAAATTAATAAT--TTTCATTATTACTAATCATTTCTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1525696 TTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
66 TTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
*
1525751 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAGTCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1525816 TTACTATC-AATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
66 TTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
1525870 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1525935 TTACTATCAAATCATACATAATTAAT-ATAATTTCATTATTACTAATCATTACT-
66 TTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
* * *
1525988 -ATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAAT
1 AATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
1526052 C
64 C
1526053 TTATAAATAC
Statistics
Matches: 291, Mismatches: 6, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
117 3 0.01
118 34 0.12
119 202 0.69
120 52 0.18
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (120 bp):
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
TTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTA
Found at i:1525877 original size:179 final size:177
Alignment explanation
Indices: 1525626--1526052 Score: 652
Period size: 179 Copynumber: 2.4 Consensus size: 177
1525616 ATAATAAATT
* *
1525626 ATTATCTAATCATTACTATCAAATCATTAAAAATTAATAAT--TTTCATTATTACTAATCATTTC
1 ATTA-CTAATCATTACTATC-AATCATTAATAATTAATAATAATTTCATTATTACTAATCATTAC
*
1525689 TAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTACTAAA
64 TAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATCATTACTAAA
1525753 TCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
128 TCATTACTATCAAATCA-TACAAAATTAAT-ATAATTTCATTATTACTAATC
1525804 ATTACTAAGTCATTACTATCAATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAA-TCATTACTATCAATCATTA-ATAATTAATAATAATTTCATTATTACTAATCATTAC
1525868 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
64 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAAT
*
1525933 CATTACTATCAAATCATACATAATTAATATAATTTCATTATTACTAATC
129 CATTACTATCAAATCATACAAAATTAATATAATTTCATTATTACTAATC
* *
1525982 ATTACT-ATCAAATTACTATTAAATCATTAA-ATATTAATAATAATTTCATCATTACTAATCATT
1 ATTACTAATC--ATTACTA-TCAATCATTAATA-ATTAATAATAATTTCATTATTACTAATCATT
1526045 ACTAAATC
62 ACTAAATC
1526053 TTATAAATAC
Statistics
Matches: 232, Mismatches: 6, Indels: 21
0.90 0.02 0.08
Matches are distributed among these distances:
176 4 0.02
177 21 0.09
178 52 0.22
179 151 0.65
180 4 0.02
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (177 bp):
ATTACTAATCATTACTATCAATCATTAATAATTAATAATAATTTCATTATTACTAATCATTACTA
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
TTACTATCAAATCATACAAAATTAATATAATTTCATTATTACTAATC
Done.