Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 122 of 250
Found at i:39178697 original size:17 final size:17
Alignment explanation
Indices: 39178675--39178707 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39178665 TCAAGAGTAG
39178675 ACCAAAATATCATCTAA
1 ACCAAAATATCATCTAA
39178692 ACCAAAATATCATCTA
1 ACCAAAATATCATCTA
39178708 TAAATACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (17 bp):
ACCAAAATATCATCTAA
Found at i:39182133 original size:24 final size:24
Alignment explanation
Indices: 39182101--39182159 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
39182091 ACATGCCATT
39182101 ATACCCAAAATGACTCTACTATAA
1 ATACCCAAAATGACTCTACTATAA
39182125 ATACCCAAAATGACTCTACTATAA
1 ATACCCAAAATGACTCTACTATAA
39182149 ATACCCAAAAT
1 ATACCCAAAAT
39182160 AGCTAGGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.24
Consensus pattern (24 bp):
ATACCCAAAATGACTCTACTATAA
Found at i:39195516 original size:51 final size:49
Alignment explanation
Indices: 39195461--39195603 Score: 138
Period size: 51 Copynumber: 3.0 Consensus size: 49
39195451 CTACCACATA
39195461 ACATGTAACACATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATG
1 ACATGTAACACATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATG
* * * * * * *
39195510 TTACATG-AATCGCATCCATTATGGAGTTAGACCTCTCAACGAGCCCGGATG
1 --ACATGTAA-CACATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATG
*
39195561 -C---T--CACATCCATAATAAACTCAGACCTCTCAATGAGCTCGGATG
1 ACATGTAACACATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATG
39195604 CCACATATCT
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
43 33 0.44
48 1 0.01
50 2 0.03
51 39 0.52
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (49 bp):
ACATGTAACACATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATG
Found at i:39200665 original size:27 final size:27
Alignment explanation
Indices: 39200631--39200683 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39200621 TATGGGCTTT
*
39200631 CCTGTGTTTACTGTCTCAGTGGACTAC
1 CCTGTGTTTACTGTCCCAGTGGACTAC
* *
39200658 CCTGTGTTTATTGTCCCGGTGGACTA
1 CCTGTGTTTACTGTCCCAGTGGACTA
39200684 TACTAGATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.25, G:0.25, T:0.38
Consensus pattern (27 bp):
CCTGTGTTTACTGTCCCAGTGGACTAC
Found at i:39200830 original size:31 final size:31
Alignment explanation
Indices: 39200792--39200854 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
39200782 CCTCCAGACC
*
39200792 ACCATTGCGGTGTTGTTCTATGAAACCTATA
1 ACCATTGCGATGTTGTTCTATGAAACCTATA
39200823 ACCATTGCGATGTTGTTCTATGAAACCTATA
1 ACCATTGCGATGTTGTTCTATGAAACCTATA
39200854 A
1 A
39200855 ACTGTTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (31 bp):
ACCATTGCGATGTTGTTCTATGAAACCTATA
Found at i:39203477 original size:8 final size:7
Alignment explanation
Indices: 39203459--39203623 Score: 80
Period size: 7 Copynumber: 23.0 Consensus size: 7
39203449 ACTAATTAAT
39203459 CTAAACC
1 CTAAACC
39203466 CTAAATCC
1 CTAAA-CC
*
39203474 CTAACCC
1 CTAAACC
39203481 CTAAACC
1 CTAAACC
*
39203488 TTAAACC
1 CTAAACC
* *
39203495 ATAAAAC
1 CTAAACC
* **
39203502 ATAAATA
1 CTAAACC
*
39203509 CTTAACC
1 CTAAACC
*
39203516 CTTAACC
1 CTAAACC
*
39203523 CTTAACCC
1 C-TAAACC
39203531 CTAAACC
1 CTAAACC
*
39203538 TTAAACC
1 CTAAACC
* *
39203545 CCAACCC
1 CTAAACC
*
39203552 CTTAAAAC
1 C-TAAACC
*
39203560 TTAAACC
1 CTAAACC
39203567 CT-AACC
1 CTAAACC
*
39203573 CTTAACC
1 CTAAACC
39203580 CATAAACC
1 C-TAAACC
*
39203588 ATAAACC
1 CTAAACC
* *
39203595 ATAATCC
1 CTAAACC
*
39203602 TTAAACC
1 CTAAACC
*
39203609 CATAATCC
1 C-TAAACC
*
39203617 GTAAACC
1 CTAAACC
39203624 TTACAATAGT
Statistics
Matches: 119, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
6 6 0.05
7 89 0.75
8 24 0.20
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:39203544 original size:22 final size:21
Alignment explanation
Indices: 39203515--39203626 Score: 91
Period size: 21 Copynumber: 5.2 Consensus size: 21
39203505 AATACTTAAC
39203515 CCTT-AACCCTTAACCCCTAAA
1 CCTTAAACCC-TAACCCCTAAA
*
39203536 CCTTAAACCCCAACCCCTTAAA
1 CCTTAAACCCTAACCCC-TAAA
* * *
39203558 ACTTAAACCCTAACCCTTAAC
1 CCTTAAACCCTAACCCCTAAA
* * * * *
39203579 CCATAAACCATAAACCATAAT
1 CCTTAAACCCTAACCCCTAAA
* *
39203600 CCTTAAACCCATAATCCGTAAA
1 CCTTAAACCC-TAACCCCTAAA
39203622 CCTTA
1 CCTTA
39203627 CAATAGTAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
21 36 0.50
22 36 0.50
ACGTcount: A:0.39, C:0.38, G:0.01, T:0.22
Consensus pattern (21 bp):
CCTTAAACCCTAACCCCTAAA
Found at i:39203562 original size:50 final size:51
Alignment explanation
Indices: 39203460--39203595 Score: 154
Period size: 50 Copynumber: 2.7 Consensus size: 51
39203450 CTAATTAATC
* *
39203460 TAAACCCTAAATCCC-TAACCCCTAAACCTTAAACCATAAAACATAAATACT
1 TAAACCCTTAA-CCCTTAACCCCTAAACCTTAAACCACAAAACATAAATACT
* ** *
39203511 T-AACCCTTAACCCTTAACCCCTAAACCTTAAACCCCAACCCCTTAAA-ACT
1 TAAACCCTTAACCCTTAACCCCTAAACCTTAAACCACAA-AACATAAATACT
* *
39203561 TAAACCC-TAACCCTTAACCCATAAACCATAAACCA
1 TAAACCCTTAACCCTTAACCCCTAAACCTTAAACCA
39203596 TAATCCTTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
49 3 0.04
50 59 0.81
51 11 0.15
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.21
Consensus pattern (51 bp):
TAAACCCTTAACCCTTAACCCCTAAACCTTAAACCACAAAACATAAATACT
Found at i:39203576 original size:21 final size:21
Alignment explanation
Indices: 39203519--39203577 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
39203509 CTTAACCCTT
* *
39203519 AACCCTTAACCCCTAAACCTTA
1 AACCC-TAACCCTTAAAACTTA
*
39203541 AACCCCAACCCCTTAAAACTTA
1 AACCCTAA-CCCTTAAAACTTA
39203563 AACCCTAACCCTTAA
1 AACCCTAACCCTTAA
39203578 CCCATAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAACCCTTAAAACTTA
Found at i:39203899 original size:41 final size:41
Alignment explanation
Indices: 39203836--39203945 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 41
39203826 TTCATTTTTT
* *
39203836 GTGGCGTTTTTCAAAAAA-CGCCGCTAAAGGT-GTATATATA
1 GTGGCGTTTTTTAAAAAAGCGCCGCTAAAGCTCG-ATATATA
* *
39203876 GTGGCGTTTTTTAAAAAAGCGCCGCTAATA-CTCGATCTTTA
1 GTGGCGTTTTTTAAAAAAGCGCCGCTAA-AGCTCGATATATA
*
39203917 GTGGAG-TTTTT-AAAAAGCGCCGCTAAAGC
1 GTGGCGTTTTTTAAAAAAGCGCCGCTAAAGC
39203946 CACTAAAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 1 0.02
39 16 0.26
40 22 0.36
41 20 0.33
42 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (41 bp):
GTGGCGTTTTTTAAAAAAGCGCCGCTAAAGCTCGATATATA
Found at i:39204076 original size:40 final size:40
Alignment explanation
Indices: 39203979--39204076 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
39203969 AAATTATTTT
* * *
39203979 GCGGCGTTTTAAAAAAAACGCCGCTAAAGATCAAGCATTA
1 GCGGCGTTTTTAAAAAAGCGCCACTAAAGATCAAGCATTA
* **
39204019 GCGGCGTTTTCT-AAAAAGCGCCACTAAAGGTGGA-CATATA
1 GCGGCGTTTT-TAAAAAAGCGCCACTAAAGATCAAGCAT-TA
39204059 GCGGCGTTTTTAAAAAAG
1 GCGGCGTTTTTAAAAAAG
39204077 ACCTGCTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.08
40 45 0.92
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (40 bp):
GCGGCGTTTTTAAAAAAGCGCCACTAAAGATCAAGCATTA
Found at i:39204222 original size:186 final size:180
Alignment explanation
Indices: 39203842--39204310 Score: 573
Period size: 186 Copynumber: 2.5 Consensus size: 180
39203832 TTTTGTGGCG
* * *
39203842 TTTTTC-AAAAAACGCCGCTAAAGGTGTATATATAGTGGCGTTTTTTAAAAAAGCGCCGCTAATA
1 TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCG-TTTTTAAAAAA--GCCGCTAATA
* * * ** *****
39203906 CTCGATCTTTAGTGG-AGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAATCTCGGCGTTTTACAA
63 CTCAATCTTTAGTGGCA-TTTTTAAAAAGCGCCGCTAAAGCCACCAAAAGCTCAACACAAAACAA
39203970 AATTATTTTGCGGCGTTTTAAAAAAAACGCCGCTAAAGATCAAGCATTAGCGGC
127 AATTATTTTGCGGCGTTTTAAAAAAAACGCCGCTAAAGATCAAGCATTAGCGGC
* * *
39204024 GTTTTCTAAAAAGCGCCACTAAAGGTGGACATATAGCGGCGTTTTTAAAAAAGACCTGCTAATAC
1 TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCGTTTTTAAAAAAG-CC-GCTAATAC
* * *
39204089 TCAATCTTTAGTGGCATTTTTAAAAAGTGCCGCTAAAGCCACCAAAGGCTCAATACAAAACGATG
64 TCAATCTTTAGTGGCATTTTTAAAAAGCGCCGCTAAAGCCACCAAAAGCTCAACACAAAAC-A--
* * ***
39204154 TTAATTTTTTTGCGGCGTTTTTTGAAAAACGCCGCTAAAGATCAAGCATTAGCGGC
126 -AAATTATTTTGCGGCGTTTTAAAAAAAACGCCGCTAAAGATCAAGCATTAGCGGC
39204210 TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCGTTTTTAAAAAAGTGCCGCTAATAC
1 TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCGTTTTTAAAAAA--GCCGCTAATAC
** *
39204275 TCAATCTTTAACGGCGTTTTTAAAAAGCGCCGCTAA
64 TCAATCTTTAGTGGCATTTTTAAAAAGCGCCGCTAA
39204311 TGCTTGTTCT
Statistics
Matches: 246, Mismatches: 31, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
180 1 0.00
181 2 0.01
182 70 0.28
183 31 0.13
186 139 0.57
187 2 0.01
188 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (180 bp):
TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCGTTTTTAAAAAAGCCGCTAATACTC
AATCTTTAGTGGCATTTTTAAAAAGCGCCGCTAAAGCCACCAAAAGCTCAACACAAAACAAAATT
ATTTTGCGGCGTTTTAAAAAAAACGCCGCTAAAGATCAAGCATTAGCGGC
Found at i:39204227 original size:40 final size:39
Alignment explanation
Indices: 39204165--39204310 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 39
39204155 TAATTTTTTT
39204165 GCGGCGTTTTTTGAAAAA-CGCCGCTAAAGATCAAGCATTA
1 GCGGCGTTTTTT-AAAAAGCGCCGCTAAAGATCAA-CATTA
* **
39204205 GCGGC-TTTTTCTAAAAAGCGCCGCTAAAGGTGTACATATA
1 GCGGCGTTTTT-TAAAAAGCGCCGCTAAAGATCAACAT-TA
* * * *
39204245 GCGGCGTTTTTAAAAAAGTGCCGCTAATA-CTCAATCTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAA-AGATCAA-CATTA
*
39204285 ACGGCG-TTTTTAAAAAGCGCCGCTAA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAA
39204311 TGCTTGTTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
39 31 0.35
40 49 0.56
41 8 0.09
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (39 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAAAGATCAACATTA
Found at i:39204322 original size:39 final size:39
Alignment explanation
Indices: 39204206--39204323 Score: 103
Period size: 40 Copynumber: 3.0 Consensus size: 39
39204196 CAAGCATTAG
* * * * * *
39204206 CGGCTTTTTCTAAAAAGCGCCGCTAAAG-GTGTACATATAG
1 CGGCGTTTT-TAAAAAGCGCCGCTAATGCTTGTTC-TTTAA
* * ***
39204246 CGGCGTTTTTAAAAAAGTGCCGCTAATACTCAATCTTTAA
1 CGGCGTTTTT-AAAAAGCGCCGCTAATGCTTGTTCTTTAA
39204286 CGGCGTTTTTAAAAAGCGCCGCTAATGCTTGTTCTTTA
1 CGGCGTTTTTAAAAAGCGCCGCTAATGCTTGTTCTTTA
39204324 GCGGAACGCT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
39 24 0.40
40 35 0.58
41 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (39 bp):
CGGCGTTTTTAAAAAGCGCCGCTAATGCTTGTTCTTTAA
Found at i:39212583 original size:12 final size:12
Alignment explanation
Indices: 39212566--39212677 Score: 63
Period size: 12 Copynumber: 10.1 Consensus size: 12
39212556 AATAATTTTA
39212566 TATTAAAATTAT
1 TATTAAAATTAT
39212578 TATT-AAA-TAT
1 TATTAAAATTAT
39212588 TATTAATAATTA-
1 TATTAA-AATTAT
*
39212600 TATTAATAA-TGT
1 TATTAA-AATTAT
39212612 TATTAAAA-TAT
1 TATTAAAATTAT
39212623 ATATT---ATT-T
1 -TATTAAAATTAT
39212632 TATT-AAATTA-
1 TATTAAAATTAT
39212642 TATTTAATAATTA-
1 TA-TTAA-AATTAT
39212655 TATTAAAA-TAT
1 TATTAAAATTAT
*
39212666 GATT-AAATTAT
1 TATTAAAATTAT
39212677 T
1 T
39212678 TATTTTTATT
Statistics
Matches: 82, Mismatches: 4, Indels: 29
0.71 0.03 0.25
Matches are distributed among these distances:
8 4 0.05
9 2 0.02
10 18 0.22
11 19 0.23
12 30 0.37
13 9 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TATTAAAATTAT
Found at i:39212635 original size:54 final size:51
Alignment explanation
Indices: 39212577--39212683 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 51
39212567 ATTAAAATTA
* *
39212577 TTATTAAA-TAT-TATTAATAATTATATTAATAATGTTATTAAAATATATATTATT
1 TTATTAAATTATAT-TTAATAATTATATTAA-AATATGATT-AAAT-TAT-TTATT
39212631 TTATTAAATTATATTTAATAATTATATTAAAATATGATTAAATTATTTATT
1 TTATTAAATTATATTTAATAATTATATTAAAATATGATTAAATTATTTATT
39212682 TT
1 TT
39212684 TATTTTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
51 7 0.14
52 3 0.06
53 4 0.08
54 15 0.31
55 19 0.39
56 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (51 bp):
TTATTAAATTATATTTAATAATTATATTAAAATATGATTAAATTATTTATT
Found at i:39212880 original size:44 final size:46
Alignment explanation
Indices: 39212810--39212903 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
39212800 GTTACAACAT
39212810 CATTCCATTCAACCAAACATAAGAATT-CT-ATTACAGCTCTATTC
1 CATTCCATTCAACCAAACATAAGAATTACTGATTACAGCTCTATTC
* *
39212854 CATTCCATTCAATCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACATA-AGAATTACTGATTACAGCTCTATTC
39212900 CATT
1 CATT
39212904 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 2 0.04
46 19 0.42
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (46 bp):
CATTCCATTCAACCAAACATAAGAATTACTGATTACAGCTCTATTC
Found at i:39212906 original size:16 final size:16
Alignment explanation
Indices: 39212885--39212939 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
39212875 TGAATTACTG
39212885 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
39212901 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
39212917 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
39212933 ATTACAG
1 ATTACAG
39212940 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:39216534 original size:16 final size:17
Alignment explanation
Indices: 39216508--39216540 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39216498 TTTTTATTTG
39216508 TTATAAAAAATAATTAA
1 TTATAAAAAATAATTAA
39216525 TTAT-AAAAATAATTAA
1 TTATAAAAAATAATTAA
39216541 AAATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTATAAAAAATAATTAA
Found at i:39216546 original size:16 final size:16
Alignment explanation
Indices: 39216513--39216546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39216503 ATTTGTTATA
**
39216513 AAAAATAATTAATTAT
1 AAAAATAATTAAAAAT
39216529 AAAAATAATTAAAAAT
1 AAAAATAATTAAAAAT
39216545 AA
1 AA
39216547 TTATCATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAATTAAAAAT
Found at i:39217430 original size:16 final size:17
Alignment explanation
Indices: 39217409--39217441 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39217399 AATTTAAAAA
*
39217409 ATTTCTATTAT-ATATC
1 ATTTCTAATATAATATC
39217425 ATTTCTAATATAATATC
1 ATTTCTAATATAATATC
39217442 CTTAATAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTCTAATATAATATC
Found at i:39222729 original size:7 final size:7
Alignment explanation
Indices: 39222717--39222742 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39222707 TTGAAAAACA
39222717 AAACCAT
1 AAACCAT
39222724 AAACCAT
1 AAACCAT
39222731 AAACCAT
1 AAACCAT
39222738 AAACC
1 AAACC
39222743 TTACATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.31, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCAT
Found at i:39224533 original size:63 final size:63
Alignment explanation
Indices: 39224443--39224566 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
39224433 ATTATGTGAG
** *
39224443 AATACTACTAATGAGAACTTGTTAGAGAATTTGTTTTAACTTTTCATGCTTCAAATGTGCTCC
1 AATACTACTAATGAGAACTTAATAGAGAATTTGTTCTAACTTTTCATGCTTCAAATGTGCTCC
* * *
39224506 AATATTACTGATGAGAACTTAATAGAGAATTTGTTCTAACTTTTCATGTTTCAAATGTGCT
1 AATACTACTAATGAGAACTTAATAGAGAATTTGTTCTAACTTTTCATGCTTCAAATGTGCT
39224567 ATTGCAGTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (63 bp):
AATACTACTAATGAGAACTTAATAGAGAATTTGTTCTAACTTTTCATGCTTCAAATGTGCTCC
Found at i:39225877 original size:26 final size:26
Alignment explanation
Indices: 39225848--39225929 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
39225838 TGATACAAAT
39225848 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39225874 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39225900 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
39225926 TGAT
1 TGAT
39225930 GGGAATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39230300 original size:7 final size:7
Alignment explanation
Indices: 39230288--39230320 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
39230278 TTTTGCAAAA
39230288 ATGAAAT
1 ATGAAAT
39230295 ATGAAAT
1 ATGAAAT
39230302 ATGAAAT
1 ATGAAAT
39230309 ATGAAAT
1 ATGAAAT
39230316 ATGAA
1 ATGAA
39230321 TTTTTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (7 bp):
ATGAAAT
Found at i:39238598 original size:31 final size:31
Alignment explanation
Indices: 39238540--39238600 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39238530 TTAGCAGCCG
*
39238540 AGTGACTTAAATAAAAACTTTTGAATAGTTA
1 AGTGACTTAAATAAAAACTTTTAAATAGTTA
* *
39238571 AGTGACTTACATTAAAA-TTTTCAAATAGTT
1 AGTGACTTAAATAAAAACTTTT-AAATAGTT
39238601 CAAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTAAATAGTTA
Found at i:39239089 original size:16 final size:16
Alignment explanation
Indices: 39239066--39239110 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
39239056 AATTTGGTTC
39239066 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
* *
39239082 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAAA
*
39239098 GCTGTAATAGAAT
1 GCTGTAATGGAAT
39239111 TGAACTGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:39239158 original size:19 final size:19
Alignment explanation
Indices: 39239134--39239171 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39239124 ATAATTCAAT
39239134 TGTTTGGTTGAATGAAATG
1 TGTTTGGTTGAATGAAATG
39239153 TGTTTGGTTGAATGAAATG
1 TGTTTGGTTGAATGAAATG
39239172 GAATAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TGTTTGGTTGAATGAAATG
Found at i:39239453 original size:63 final size:61
Alignment explanation
Indices: 39239335--39239455 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
39239325 ATTTAATAAT
* * *
39239335 AATAAATAATTTAATCATATTTTAATATAATTATTACCAAATATAATTTAATAAAAATGAA
1 AATAAATAATTTAATAACATTTTAATATAATTATTACAAAATATAATTTAATAAAAATGAA
* *
39239396 AATATATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TTAATAAAAAT
1 AATAAATAATTTAATAACATT-TTAATATAATTATTA-CAAAATAT-AATTTAATAAAAAT
39239456 CATAACATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 18 0.35
62 15 0.29
63 17 0.33
64 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (61 bp):
AATAAATAATTTAATAACATTTTAATATAATTATTACAAAATATAATTTAATAAAAATGAA
Found at i:39245387 original size:40 final size:40
Alignment explanation
Indices: 39245332--39245548 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
39245322 TATTCGAATG
39245332 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* * *
39245372 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
* *
39245412 ATATCCGGGCTATGTCCCGAAGGCATTTGTGCTA-TTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
39245452 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* * *
39245492 ATATCCGGGCCAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
*
39245532 ATATCC-GGCTAAATCCC
1 ATATCCGGGCTAAGTCCC
39245549 AAAGATGCTT
Statistics
Matches: 160, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 10 0.06
40 147 0.92
41 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
Found at i:39258235 original size:48 final size:48
Alignment explanation
Indices: 39257994--39258267 Score: 199
Period size: 48 Copynumber: 5.8 Consensus size: 48
39257984 GGGTTGATGA
* * ** * * * * *
39257994 GATCCCGTATAAGACCATACCTGGAATATGGCATCGGCATCGATGTGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * ** * *
39258042 GATCCCATGTAAGAGCATGTTTGGGACACAGCTTTGGCATCGTTATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * * *
39258090 GATCCCATG-AA-ACCATGTCTGGGACATGGTATTGGTATCGGTATGAG
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG-T
* * *
39258137 GCAT--CGTGTAAGACCATAG-CTAGG-C-T---ATTGGCTTCAGTATATGT
1 G-ATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATC-G-ATATGT
39258181 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * **
39258229 GGTCCCATGTAAGACCATATCTGGGTTATGGCATTGGCA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39258268 CCTTACTATG
Statistics
Matches: 174, Mismatches: 37, Indels: 30
0.72 0.15 0.12
Matches are distributed among these distances:
43 9 0.05
44 3 0.02
45 20 0.11
46 31 0.18
47 7 0.04
48 94 0.54
49 2 0.01
50 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:39266267 original size:27 final size:26
Alignment explanation
Indices: 39266232--39266343 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
39266222 AGCATGGCTG
*
39266232 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
** *
39266258 CCAGATACAGATAATCGTGGTAGAACCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
*
39266286 CCAGAACAGATATATATGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * *
39266313 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGACAGAGCCA
39266340 CCAG
1 CCAG
39266344 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 49 0.70
28 15 0.21
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:39266341 original size:54 final size:54
Alignment explanation
Indices: 39266232--39266343 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
39266222 AGCATGGCTG
* * *
39266232 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAACCA
1 CCAGAACAGATAATATGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
* * *
39266286 CCAGAACAGATATATATGACAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATATGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
39266340 CCAG
1 CCAG
39266344 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATATGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
Found at i:39274089 original size:23 final size:23
Alignment explanation
Indices: 39274063--39274109 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
39274053 ATAGTCGATG
*
39274063 CTGATACAACATGGCCCAGAAAA
1 CTGATACAACATGACCCAGAAAA
39274086 CTGATACAACATGACCCAGAAAA
1 CTGATACAACATGACCCAGAAAA
39274109 C
1 C
39274110 AGACTTCACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.13
Consensus pattern (23 bp):
CTGATACAACATGACCCAGAAAA
Found at i:39279589 original size:40 final size:40
Alignment explanation
Indices: 39279521--39279697 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
39279511 ACCCAAGTAT
*
39279521 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAATAACTCGCACAAATGC
* *
39279560 CTTCTGGTCTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATAACTCGCACAAATGC
* * *
39279600 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAATAACTCGCACAAATGC
* * *
39279640 CTTCGGGACATAGCCCGGATAT-ATCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAAT-AACTCGCACAAATGC
* *
39279680 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
39279698 TTATCATCCG
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 12 0.10
40 104 0.89
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAATAACTCGCACAAATGC
Found at i:39292171 original size:28 final size:29
Alignment explanation
Indices: 39292112--39292171 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
39292102 ATTTATTTCA
* *
39292112 CAATTTAACCCTTCAATTTACACTTTTCT
1 CAATTTAACCCTTCAATTGACACTTTTAT
*
39292141 CAATTTAATCCC-T-AATTGACATTTTTAT
1 CAATTTAA-CCCTTCAATTGACACTTTTAT
39292169 CAA
1 CAA
39292172 AAATTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.56
29 9 0.33
30 3 0.11
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (29 bp):
CAATTTAACCCTTCAATTGACACTTTTAT
Found at i:39298592 original size:55 final size:55
Alignment explanation
Indices: 39298508--39298622 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
39298498 ATGAAGTAAG
39298508 TTGATATACAAATAAGCTTGTTTGAATTAAATTATTATTCATTTGATATTGAATT
1 TTGATATACAAATAAGCTTGTTTGAATTAAATTATTATTCATTTGATATTGAATT
39298563 TTGATATACAAATAAGCTTGTTTGAATTAAATTATTATTCATTTGATATTGAATT
1 TTGATATACAAATAAGCTTGTTTGAATTAAATTATTATTCATTTGATATTGAATT
*
39298618 GTGAT
1 TTGAT
39298623 GAATGAATGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (55 bp):
TTGATATACAAATAAGCTTGTTTGAATTAAATTATTATTCATTTGATATTGAATT
Found at i:39298617 original size:27 final size:27
Alignment explanation
Indices: 39298529--39298617 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
39298519 ATAAGCTTGT
39298529 TTGAATTAAATTATTATTCATTTGATA
1 TTGAATTAAATTATTATTCATTTGATA
** ** * * *
39298556 TTGAATTTTGATATACAAATAAGCTTG-T-
1 TTGAA-TTAAAT-TATTATTCA-TTTGATA
39298584 TTGAATTAAATTATTATTCATTTGATA
1 TTGAATTAAATTATTATTCATTTGATA
39298611 TTGAATT
1 TTGAATT
39298618 GTGATGAATG
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
25 3 0.07
26 6 0.14
27 16 0.37
28 9 0.21
29 6 0.14
30 3 0.07
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.49
Consensus pattern (27 bp):
TTGAATTAAATTATTATTCATTTGATA
Found at i:39301430 original size:46 final size:46
Alignment explanation
Indices: 39301377--39301545 Score: 189
Period size: 46 Copynumber: 3.7 Consensus size: 46
39301367 TGGTTGAGCA
*
39301377 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
* * * ** *
39301423 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATAC-AAACG
* * *
39301470 TCCGAACTCGTTGAGTTGAGTCCGAGGTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
* *
39301516 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA
39301546 TTTAGGGGCG
Statistics
Matches: 100, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 64 0.64
47 34 0.34
48 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
Found at i:39301533 original size:93 final size:93
Alignment explanation
Indices: 39301374--39301544 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
39301364 GGATGGTTGA
* * *
39301374 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGGTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
39301439 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
39301467 GCATCCGAACTCGTTGAGTTGAGTCCGAGGTCATTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGGTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
39301532 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39301545 ATTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGGTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:39301811 original size:19 final size:20
Alignment explanation
Indices: 39301774--39301811 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39301764 ATAAGGTGGT
39301774 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
39301794 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
39301812 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:39305298 original size:228 final size:228
Alignment explanation
Indices: 39304901--39305327 Score: 827
Period size: 228 Copynumber: 1.9 Consensus size: 228
39304891 CGAGGTTTCG
39304901 GTCATGGGTAGAAAAACTATAGATTTTGAGATTTATGATAGAAGTTAATGAGTGAGAGTTGGATA
1 GTCATGGGTAGAAAAACTATAGATTTTGAGATTTATGATAGAAGTTAATGAGTGAGAGTTGGATA
39304966 GATATTATGATGTTAAAATTCATGGGATTATAAGCTTGTAAGTTTGATGGTGAAATTTATGCTTT
66 GATATTATGATGTTAAAATTCATGGGATTATAAGCTTGTAAGTTTGATGGTGAAATTTATGCTTT
*
39305031 GTGAGGGTAAATGGTTTAAAAGGAGCATTCGGCCATGATGTAAAATTATGATGAAGTGATGTTAA
131 GTGAGGGTAAATGGTTTAAAAGGAGCATTCGGCCATGATGTAAAATTATGATGAAGTCATGTTAA
39305096 ATGCTTTTAATATTGAGTATATATTGTTAAATT
196 ATGCTTTTAATATTGAGTATATATTGTTAAATT
39305129 GTCATGGGTAGAAAAACTATAGATTTTGAGATTTATGATAGAAGTTAATGAGTGAGAGTTGGATA
1 GTCATGGGTAGAAAAACTATAGATTTTGAGATTTATGATAGAAGTTAATGAGTGAGAGTTGGATA
*
39305194 GATATTATGATGTTAAGATTCATGGGATTATAAGCTTGTAAGTTTGATGGTGAAATTTATGCTTT
66 GATATTATGATGTTAAAATTCATGGGATTATAAGCTTGTAAGTTTGATGGTGAAATTTATGCTTT
*
39305259 GTGAGGGTAAATTGTTTAAAAGGAGCATTCGGCCATGATGTAAAATTATGATGAAGTCATGTTAA
131 GTGAGGGTAAATGGTTTAAAAGGAGCATTCGGCCATGATGTAAAATTATGATGAAGTCATGTTAA
39305324 ATGC
196 ATGC
39305328 CATGATGTAT
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 196 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (228 bp):
GTCATGGGTAGAAAAACTATAGATTTTGAGATTTATGATAGAAGTTAATGAGTGAGAGTTGGATA
GATATTATGATGTTAAAATTCATGGGATTATAAGCTTGTAAGTTTGATGGTGAAATTTATGCTTT
GTGAGGGTAAATGGTTTAAAAGGAGCATTCGGCCATGATGTAAAATTATGATGAAGTCATGTTAA
ATGCTTTTAATATTGAGTATATATTGTTAAATT
Found at i:39306526 original size:45 final size:45
Alignment explanation
Indices: 39306462--39306594 Score: 221
Period size: 45 Copynumber: 3.0 Consensus size: 45
39306452 TACCGTATGG
*
39306462 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
39306507 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
39306552 TACTATTTGGGCCTTCGAGCCTAGCAAGCTATAATGCCGGTGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
39306595 AATGATATCA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:39317095 original size:17 final size:19
Alignment explanation
Indices: 39317055--39317095 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
39317045 AATTAAGTTC
*
39317055 GAGATTCACCGGGCAGTAT
1 GAGATTCACCGAGCAGTAT
39317074 GAGATT-ACCGAGC-GTAT
1 GAGATTCACCGAGCAGTAT
*
39317091 TAGAT
1 GAGAT
39317096 CGGTAGCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGATTCACCGAGCAGTAT
Found at i:39318779 original size:43 final size:42
Alignment explanation
Indices: 39318705--39318807 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
39318695 GATCATGTCC
* * * *
39318705 GGGACATTAGCATCGTATTTGATTTCGTGTAAGACC-CTGTCT
1 GGGACAGTGGCATCGTATTTGATTACATGTAAGACCAC-GTCT
* *
39318747 TGGACAGTGGCATCGATGTTTGATTACATGTAAGACCACGTCT
1 GGGACAGTGGCATCG-TATTTGATTACATGTAAGACCACGTCT
* *
39318790 GGGACATTGGCATTGTAT
1 GGGACAGTGGCATCGTAT
39318808 ATGCTTTCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 14 0.29
43 34 0.69
44 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (42 bp):
GGGACAGTGGCATCGTATTTGATTACATGTAAGACCACGTCT
Found at i:39320565 original size:29 final size:30
Alignment explanation
Indices: 39320532--39320590 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
39320522 TCCAATTAAA
* *
39320532 TCATCAAGCATACATAACCA-CAACACATC
1 TCATCAAGCACACACAACCACCAACACATC
* *
39320561 TCATCACGTACACACAACCACCAACACATC
1 TCATCAAGCACACACAACCACCAACACATC
39320591 ACAATTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.15
Consensus pattern (30 bp):
TCATCAAGCACACACAACCACCAACACATC
Found at i:39323122 original size:11 final size:11
Alignment explanation
Indices: 39323106--39323141 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39323096 AAAAGTGCAG
39323106 AGAAAAACTAA
1 AGAAAAACTAA
39323117 AG-AAAACT--
1 AGAAAAACTAA
39323125 AGAAAAACTAA
1 AGAAAAACTAA
39323136 AGAAAA
1 AGAAAA
39323142 CTAGACCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.09
9 6 0.27
10 6 0.27
11 8 0.36
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08
Consensus pattern (11 bp):
AGAAAAACTAA
Found at i:39323124 original size:10 final size:10
Alignment explanation
Indices: 39323109--39323144 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
39323099 AGTGCAGAGA
39323109 AAAACTAAAG
1 AAAACTAAAG
*
39323119 AAAACTAGA-
1 AAAACTAAAG
39323128 AAAACTAAAG
1 AAAACTAAAG
39323138 AAAACTA
1 AAAACTA
39323145 GACCTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.69, C:0.11, G:0.08, T:0.11
Consensus pattern (10 bp):
AAAACTAAAG
Found at i:39323130 original size:19 final size:19
Alignment explanation
Indices: 39323106--39323146 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
39323096 AAAAGTGCAG
39323106 AGAAAAACTAAAGAAAACT
1 AGAAAAACTAAAGAAAACT
39323125 AGAAAAACTAAAGAAAACT
1 AGAAAAACTAAAGAAAACT
39323144 AGA
1 AGA
39323147 CCTAAAACTA
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:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (19 bp):
AGAAAAACTAAAGAAAACT
Found at i:39327148 original size:6 final size:7
Alignment explanation
Indices: 39327132--39327156 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39327122 TCTTTATTGG
39327132 TTTTAAT
1 TTTTAAT
39327139 TTTTAAT
1 TTTTAAT
39327146 TTTTAAT
1 TTTTAAT
39327153 TTTT
1 TTTT
39327157 TCTGGTCTGT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:39333021 original size:27 final size:28
Alignment explanation
Indices: 39332991--39333060 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
39332981 TGAATATGAT
*
39332991 GCACTAAGTGTGCGA-ATTGACCATGCG
1 GCACTAAGTGTGCGAGATTGACCATGCA
* * *
39333018 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGATTGACCATGCA
39333046 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
39333061 TTTAGATTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 15 0.39
28 23 0.61
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGATTGACCATGCA
Found at i:39333054 original size:55 final size:54
Alignment explanation
Indices: 39332991--39333109 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 54
39332981 TGAATATGAT
* *
39332991 GCACTAAGTGTGCGAATT-GACCATGCG-GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAATTAGA--ATACGTGCACTAAGTGTGCGAG-TTGACTATATA
* * *
39333046 GCACTAAGTGTGCGATTTAGATTACGTGCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTAGAATACGTGCACTAAGTGTGCGAGTTGACTATATA
*
39333100 GCACTGAGTG
1 GCACTAAGTG
39333110 GCGGACTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
54 21 0.38
55 33 0.59
56 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAATTAGAATACGTGCACTAAGTGTGCGAGTTGACTATATA
Found at i:39333084 original size:27 final size:27
Alignment explanation
Indices: 39332991--39333109 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 27
39332981 TGAATATGAT
* ** * **
39332991 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGATTACGTA
* *
39333018 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGATTACGTA
39333046 GCACTAAGTGTGCGATTTAGATTACGT-
1 GCACTAAGTGTGCGATTT-GATTACGTA
* **
39333073 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGATTACGTA
*
39333100 GCACTGAGTG
1 GCACTAAGTG
39333110 GCGGACTCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.08
27 44 0.56
28 29 0.37
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGATTACGTA
Found at i:39347189 original size:27 final size:27
Alignment explanation
Indices: 39347154--39347328 Score: 147
Period size: 27 Copynumber: 6.4 Consensus size: 27
39347144 TTGAGTCCGC
* *
39347154 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAATCAACTCGCA
* *
39347181 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAATCAACTCGCA
*
39347208 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAATC-AACTCGCA
** ** *
39347236 CACTTAGTGCCGCCATGGTCAATTCGCA
1 CACTTAGTG-CTACATAATCAACTCGCA
* **
39347264 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAATCAACTCGCA
* * * *
39347291 CACTTTTGTGCAACATAGTCAAATCGCA
1 CAC-TTAGTGCTACATAATCAACTCGCA
39347319 CA-TTAGTGCT
1 CACTTAGTGCT
39347329 GTACAATTTA
Statistics
Matches: 122, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
26 6 0.05
27 56 0.46
28 52 0.43
29 8 0.07
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (27 bp):
CACTTAGTGCTACATAATCAACTCGCA
Found at i:39347242 original size:55 final size:54
Alignment explanation
Indices: 39347154--39347328 Score: 174
Period size: 55 Copynumber: 3.2 Consensus size: 54
39347144 TTGAGTCCGC
* * * * *
39347154 CACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
* ** * *
39347208 CACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCCATGGTCAATTCGCA
1 CACTTAGTGCTACATAATC-AACTCGCACACTTAGTG-CAACATAGTCAAATCGCA
* ** *
39347264 CACTTAGTGC-ATCATATTCATTTCGCACACTTTTGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTA-CATAATCAACTCGCACAC-TTAGTGCAACATAGTCAAATCGCA
39347319 CA-TTAGTGCT
1 CACTTAGTGCT
39347329 GTACAATTTA
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
54 23 0.23
55 43 0.43
56 33 0.33
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (54 bp):
CACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
Found at i:39347318 original size:83 final size:82
Alignment explanation
Indices: 39347171--39347327 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 82
39347161 TGCTATATAA
* *
39347171 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACTCGCA
39347236 CACTTAGTGCCGCCATGG
66 CA-TTAGTGCCGCCATGG
* * ** *
39347254 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTTTGTGCAACATAGTCAAA-TCG
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC-TTAGTGCAACATAGTCAAACTCG
39347317 CACATTAGTGC
64 CACATTAGTGC
39347328 TGTACAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
82 8 0.12
83 40 0.62
84 17 0.26
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACTCGCA
CATTAGTGCCGCCATGG
Found at i:39349790 original size:81 final size:81
Alignment explanation
Indices: 39349696--39349924 Score: 270
Period size: 81 Copynumber: 2.8 Consensus size: 81
39349686 GCTCCTCGTT
* *
39349696 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
39349761 ATTTAGTAACTC-GCA
66 AATTAGTAACTCGGCA
* *
39349776 CAAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTTAGCC
1 C-AAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGAC-TTAGCC
*
39349839 CGGAATTAGTATCTCGGCA
63 CGGAATTAGTAACTCGGCA
* * * * *
39349858 CAAATGCCTT-GGGTATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGG-A-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
39349921 CGGA
63 CGGA
39349925 CATCATTCAA
Statistics
Matches: 127, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
80 5 0.04
81 76 0.60
82 38 0.30
83 8 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGGCA
Found at i:39349794 original size:41 final size:40
Alignment explanation
Indices: 39349696--39349924 Score: 268
Period size: 40 Copynumber: 5.7 Consensus size: 40
39349686 GCTCCTCGTT
*
39349696 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
39349736 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
39349776 CAAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 C-AAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
39349817 CCAATGCCTTCGGG-CTTTAGCCCGGAATTAGTATCTCGGCA
1 CAAATGCCTTCGGGAC-TTAGCCCGGATTTAGTAACTC-GCA
* * * * *
39349858 CAAATGCCTT-GGGTATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGG-A-CTTAGCCCGGATTTAGTAAC-TCGCA
39349900 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39349925 CATCATTCAA
Statistics
Matches: 165, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
39 1 0.01
40 79 0.48
41 60 0.36
42 23 0.14
43 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39357788 original size:104 final size:104
Alignment explanation
Indices: 39357608--39357831 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
39357598 TGTATATAAA
** * *
39357608 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
39357673 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
39357712 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
39357776 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
39357816 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
39357832 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:39357881 original size:73 final size:72
Alignment explanation
Indices: 39357750--39357903 Score: 247
Period size: 73 Copynumber: 2.1 Consensus size: 72
39357740 TCATTGGTGG
* *
39357750 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39357815 GAGGGGT
66 GAGGGGT
**
39357822 TGCTAAGTGCGATATCCATTGTATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCC
1 TGCTAAGTGCGATATCCA--CCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCC
39357886 CCGAGGGGT
64 CCGAGGGGT
39357895 TGCTAAGTG
1 TGCTAAGTG
39357904 ATGATTCCCC
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
72 18 0.24
73 45 0.59
74 13 0.17
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:39365341 original size:104 final size:104
Alignment explanation
Indices: 39365161--39365384 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
39365151 TGTATATAAA
** * *
39365161 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
39365226 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
39365265 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
39365329 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
39365369 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
39365385 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:39365434 original size:70 final size:71
Alignment explanation
Indices: 39365303--39365453 Score: 241
Period size: 70 Copynumber: 2.1 Consensus size: 71
39365293 TCATTGGTGG
* *
39365303 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAA-GTGAAAAGGGGTTGCTATGTGCTGATTCCCCC
39365368 GAGGGGT
65 GAGGGGT
***
39365375 TGCTAAGTGCGATATCCATTGTATATTTGAAA-TGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
39365439 AGGGGT
66 AGGGGT
39365445 TGCTAAGTG
1 TGCTAAGTG
39365454 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 46 0.62
72 28 0.38
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:39365458 original size:27 final size:27
Alignment explanation
Indices: 39365412--39365463 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
39365402 TGAAATGAAA
* *
39365412 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGATGATTCCCCCG
39365439 AGGGGTTGCTAAGTGATGATTCCCC
1 AGGGGTTGCTAAGTGATGATTCCCC
39365464 GATTCAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGATGATTCCCCCG
Found at i:39367872 original size:44 final size:42
Alignment explanation
Indices: 39367824--39367941 Score: 109
Period size: 44 Copynumber: 2.8 Consensus size: 42
39367814 CAATAGTTAG
*
39367824 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCTTAACTAA
1 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCAT-A-TAA
* *
39367868 CCGAAGCTA-AGTCGATATC-GCACACTTAGTGCC-TCATATAG
1 CCGAAGCTAGAAT-GAT-TCTGCACACTTAGTGCCATCATATAA
** * *
39367909 CCGAAGCTAGTTTAAATCT-CACACTTAGTGCCA
1 CCGAAGCTAGAATGATTCTGCACACTTAGTGCCA
39367942 ATTACCATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
40 15 0.24
41 12 0.19
42 2 0.03
43 5 0.08
44 26 0.42
45 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
CCGAAGCTAGAATGATTCTGCACACTTAGTGCCATCATATAA
Found at i:39389210 original size:13 final size:13
Alignment explanation
Indices: 39389194--39389233 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
39389184 TTTAAGCTAA
39389194 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
39389207 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
39389220 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39389233 A
1 A
39389234 TTGCCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39390422 original size:13 final size:13
Alignment explanation
Indices: 39390401--39390471 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
39390391 AAATTTTTTC
39390401 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
39390414 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
39390427 AAAGCAC-TCTTCC
1 AAAGCACTTC-TCA
* *
39390440 ACAGCACTTTTCA
1 AAAGCACTTCTCA
*
39390453 AAAGCACTTTTCA
1 AAAGCACTTCTCA
39390466 AAAGCA
1 AAAGCA
39390472 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
12 2 0.04
13 46 0.94
14 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:39392402 original size:81 final size:81
Alignment explanation
Indices: 39392264--39392589 Score: 494
Period size: 81 Copynumber: 4.0 Consensus size: 81
39392254 AAGTCGTTAT
*
39392264 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTATAGAGTAAAATGACCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
39392329 GCCCCTATAGAGTAAA
66 GCCCCTATAGAGTAAA
** * *
39392345 ACGACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCTCTGTAGACTAAAATGACCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
* *
39392410 GCCCTTGTAGAGTAAA
66 GCCCCTATAGAGTAAA
* * *
39392426 ATAAGCATAATGCCCCTATAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
1 ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
*
39392491 GCCCCTATAGGGTAAA
66 GCCCCTATAGAGTAAA
*
39392507 ATAACCGTAATGCCCCTGTACGA-TAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCTTAA
1 ATAACCGTAATGCCCCTGTA-GAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAA
**
39392571 TATCCCTATATG-GTAAA
65 TGCCCCTATA-GAGTAAA
39392588 AT
1 AT
39392590 GACGATTTTT
Statistics
Matches: 220, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
81 217 0.99
82 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (81 bp):
ATAACCGTAATGCCCCTGTAGAGTAAAATGACTGTAATGCCCCTGTAGAGTAAAATGACCGTAAT
GCCCCTATAGAGTAAA
Found at i:39392577 original size:27 final size:27
Alignment explanation
Indices: 39392267--39392571 Score: 432
Period size: 27 Copynumber: 11.3 Consensus size: 27
39392257 TCGTTATATA
39392267 ACCGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
39392294 ACTGTAATGCCCCTATAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
39392321 ACCGTAATGCCCCTATAGAGTAAAACG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
39392348 ACCGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * *
39392375 ACTGTAATGCCTCTGTAGACTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* *
39392402 ACCGTAATGCCCTTGTAGAGTAAAATA
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * *
39392429 AGCATAATGCCCCTATAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
*
39392456 ACTGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
* * *
39392483 ACCGTAATGCCCCTATAGGGTAAAATA
1 ACCGTAATGCCCCTGTAGAGTAAAATG
39392510 ACCGTAATGCCCCTGTACGA-TAAAATG
1 ACCGTAATGCCCCTGTA-GAGTAAAATG
*
39392537 ACTGTAATGCCCCTGTAGAGTAAAATG
1 ACCGTAATGCCCCTGTAGAGTAAAATG
*
39392564 ACCTTAAT
1 ACCGTAAT
39392572 ATCCCTATAT
Statistics
Matches: 243, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 240 0.99
28 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
ACCGTAATGCCCCTGTAGAGTAAAATG
Found at i:39392993 original size:28 final size:28
Alignment explanation
Indices: 39392959--39393022 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
39392949 TGTACCGTAT
*
39392959 TGTTACTGCATTA-GGCGTAGGCCCACAC
1 TGTTACTG-AATAGGGCGTAGGCCCACAC
* *
39392987 TGTTACTGAATAGGGCTTAGGCCCAGAC
1 TGTTACTGAATAGGGCGTAGGCCCACAC
39393015 TG-TACTGA
1 TGTTACTGA
39393023 TACTGAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (28 bp):
TGTTACTGAATAGGGCGTAGGCCCACAC
Found at i:39393028 original size:33 final size:33
Alignment explanation
Indices: 39392985--39393047 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
39392975 GTAGGCCCAC
* *
39392985 ACTGTTACTGAATAGGGCTTAGGCCCAGACTGT
1 ACTGATACTGAATAAGGCTTAGGCCCAGACTGT
39393018 ACTGATACTGAATAAGGCTTAGGCCCAGAC
1 ACTGATACTGAATAAGGCTTAGGCCCAGAC
39393048 CGTGTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (33 bp):
ACTGATACTGAATAAGGCTTAGGCCCAGACTGT
Found at i:39403107 original size:49 final size:50
Alignment explanation
Indices: 39403027--39403272 Score: 298
Period size: 49 Copynumber: 4.9 Consensus size: 50
39403017 AGCTATTGTG
*
39403027 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * **
39403077 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * **
39403127 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
39403177 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
** * * *
39403227 -GGTCGTATTTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
39403273 GCTTTGGCTA
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
49 80 0.48
50 48 0.29
51 37 0.22
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:39403163 original size:28 final size:28
Alignment explanation
Indices: 39403132--39403215 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
39403122 AACTTCGATC
39403132 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
39403160 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
39403182 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
39403210 ACGTGT
1 ACGTGT
39403216 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:39409325 original size:27 final size:27
Alignment explanation
Indices: 39409287--39409593 Score: 409
Period size: 27 Copynumber: 11.4 Consensus size: 27
39409277 AGGTCGTTAT
*
39409287 ATGACCATAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
** *
39409314 ATGATTGTAATG-CCCTGTAGAGTTAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
39409340 ATGGCCGTAATGCCCTTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
39409367 ATGACCATAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
39409394 ATGATCGTAATGCCCCTATAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* * *
39409421 ATAACTGTAATGCCCCTATAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
39409448 ATAATCGTAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
39409475 ATGACTGTAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* *
39409502 ATGATCGTAATGCCCCTGTAGGGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
* * * *
39409529 ATAATCGTAATGCCCCTATAGGGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
*
39409556 ATGACCATAATGCCCCTGTAGAGTAAA
1 ATGACCGTAATGCCCCTGTAGAGTAAA
39409583 ATGACCGTAAT
1 ATGACCGTAAT
39409594 ACCTATGGTA
Statistics
Matches: 244, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 22 0.09
27 222 0.91
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
ATGACCGTAATGCCCCTGTAGAGTAAA
Found at i:39409828 original size:27 final size:27
Alignment explanation
Indices: 39409773--39409829 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
39409763 TGTCACATGC
*
39409773 ACTGTTACTGGTGGCTATGCCACAATT
1 ACTGATACTGGTGGCTATGCCACAATT
*
39409800 ACTGATACTGGTGGCT-TCGCCACATTT
1 ACTGATACTGGTGGCTAT-GCCACAATT
39409827 ACT
1 ACT
39409830 ATTTATGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
ACTGATACTGGTGGCTATGCCACAATT
Found at i:39415503 original size:43 final size:43
Alignment explanation
Indices: 39415370--39415503 Score: 180
Period size: 43 Copynumber: 3.1 Consensus size: 43
39415360 TATTTGAAAA
* *
39415370 AAATGTCGCTAAAGAA-CATGACCTTTAGCAGCGCTTTTCCCAC
1 AAATGCCGCTAAA-AATCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
39415413 AAACGCCGCTAAAGATCATGACCTTTAGCGGTGCTTTTCCAAA
1 AAATGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTTCCCAC
*
39415456 AAATGCCGCTAAAAATCATTACCTTTAGCGGCGCTTTTCCCAC
1 AAATGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTTCCCAC
39415499 AAATG
1 AAATG
39415504 TCGTTAAAGG
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 76 0.99
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
AAATGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:39421227 original size:42 final size:41
Alignment explanation
Indices: 39421169--39421298 Score: 154
Period size: 41 Copynumber: 3.1 Consensus size: 41
39421159 GATTTAAAGT
* * *
39421169 TTTTTGCGGCATTTTTTGCAAAAATGGCACTATATCTCAAC
1 TTTTTGCGGCATTTTTTGCAAAAACGCCACTATAACTCAAC
* * *
39421210 TTTTTGTGGCATTTTTTTGTAAAAACGCCACTATAACTCAAG
1 TTTTTGCGGCA-TTTTTTGCAAAAACGCCACTATAACTCAAC
* * *
39421252 TTTTTGCGGC-GTTTTCGCTAAAAACGCCACTATAGCTCAAC
1 TTTTTGCGGCATTTTTTGC-AAAAACGCCACTATAACTCAAC
39421293 TTTTTG
1 TTTTTG
39421299 AAGCGTTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 5 0.07
41 36 0.48
42 34 0.45
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (41 bp):
TTTTTGCGGCATTTTTTGCAAAAACGCCACTATAACTCAAC
Found at i:39421305 original size:41 final size:42
Alignment explanation
Indices: 39421196--39421326 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 42
39421186 GCAAAAATGG
* ** * ***
39421196 CACTATATCTCAACTTTTTGTGGCATTTTTTTGTAAAAACGC
1 CACTATAACTCAACTTTTTGAAGCGTTTTTCCCTAAAAACGC
* ** *
39421238 CACTATAACTCAAGTTTTTGCGGCG-TTTTCGCTAAAAACGC
1 CACTATAACTCAACTTTTTGAAGCGTTTTTCCCTAAAAACGC
* * *
39421279 CACTATAGCTCAACTTTTTGAAGCGTTTTTCCCAAAAAACAC
1 CACTATAACTCAACTTTTTGAAGCGTTTTTCCCTAAAAACGC
39421321 CACTAT
1 CACTAT
39421327 TGTTCAATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 34 0.46
42 40 0.54
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (42 bp):
CACTATAACTCAACTTTTTGAAGCGTTTTTCCCTAAAAACGC
Found at i:39421324 original size:42 final size:41
Alignment explanation
Indices: 39421230--39421326 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
39421220 ATTTTTTTGT
* ** * *
39421230 AAAAACGCCACTATAACTCAAGTTTTTGCGGCGTTTTCGCT
1 AAAAACGCCACTATAACTCAACTTTTTGAAGCGTTTTCCCA
*
39421271 AAAAACGCCACTATAGCTCAACTTTTTGAAGCGTTTTTCCCA
1 AAAAACGCCACTATAACTCAACTTTTTGAAGCG-TTTTCCCA
*
39421313 AAAAACACCACTAT
1 AAAAACGCCACTAT
39421327 TGTTCAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 29 0.60
42 19 0.40
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (41 bp):
AAAAACGCCACTATAACTCAACTTTTTGAAGCGTTTTCCCA
Found at i:39421494 original size:7 final size:8
Alignment explanation
Indices: 39421484--39421517 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
39421474 AATATTAAAA
39421484 TTTTAAGT
1 TTTTAAGT
39421492 TTTTAAGT
1 TTTTAAGT
39421500 TTTTAA-T
1 TTTTAAGT
39421507 TTTTAA-T
1 TTTTAAGT
39421514 TTTT
1 TTTT
39421518 TTATCTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 12 0.46
8 14 0.54
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (8 bp):
TTTTAAGT
Found at i:39421502 original size:15 final size:14
Alignment explanation
Indices: 39421484--39421547 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 14
39421474 AATATTAAAA
39421484 TTTTAAGTTTTTAAGT
1 TTTTAA-TTTTTAA-T
39421500 TTTTAATTTTTAATT
1 TTTTAATTTTTAA-T
* *
39421515 TTTTTATCTTTCAAT
1 TTTTAAT-TTTTAAT
*
39421530 TTTCAATTTTTAAT
1 TTTTAATTTTTAAT
39421544 TTTT
1 TTTT
39421548 TTGAAGATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 9 0.22
15 20 0.50
16 11 0.28
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTAATTTTTAAT
Found at i:39421548 original size:8 final size:7
Alignment explanation
Indices: 39421484--39421547 Score: 65
Period size: 7 Copynumber: 8.6 Consensus size: 7
39421474 AATATTAAAA
39421484 TTTTAAGT
1 TTTTAA-T
39421492 TTTTAAGT
1 TTTTAA-T
39421500 TTTTAAT
1 TTTTAAT
39421507 TTTTAATT
1 TTTTAA-T
*
39421515 TTTTTAT
1 TTTTAAT
*
39421522 CTTTCAAT
1 -TTTTAAT
*
39421530 TTTCAAT
1 TTTTAAT
39421537 TTTTAAT
1 TTTTAAT
39421544 TTTT
1 TTTT
39421548 TTGAAGATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
7 25 0.50
8 25 0.50
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:39422136 original size:14 final size:14
Alignment explanation
Indices: 39422117--39422184 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
39422107 ATCCTAAAAA
39422117 ATAAACCCTAAACC
1 ATAAACCCTAAACC
*
39422131 ACAAACACC-AAACC
1 ATAAAC-CCTAAACC
**
39422145 -TAAAAACTCAAACC
1 ATAAACCCT-AAACC
*
39422159 ATAAACCCTAAATC
1 ATAAACCCTAAACC
*
39422173 ATAAACCATAAA
1 ATAAACCCTAAA
39422185 ACTTACATCC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 1 0.02
13 3 0.07
14 30 0.71
15 8 0.19
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (14 bp):
ATAAACCCTAAACC
Found at i:39422198 original size:21 final size:21
Alignment explanation
Indices: 39422154--39422205 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
39422144 CTAAAAACTC
*
39422154 AAACCATAAACCCTAAATCAT
1 AAACCATAAAACCTAAATCAT
* * *
39422175 AAACCATAAAACTTACATCCT
1 AAACCATAAAACCTAAATCAT
*
39422196 AAACCCTAAA
1 AAACCATAAA
39422206 TATATATTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCATAAAACCTAAATCAT
Found at i:39422611 original size:40 final size:40
Alignment explanation
Indices: 39422553--39422668 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 40
39422543 TTTTTGCGGT
*
39422553 GTTTTTCAAAAAGCGCCGCTAATACTCGATCTTTAGC-AGC
1 GTTTTTAAAAAAGCGCCGCTAATACTCGATCTTTAGCGA-C
* *
39422593 GTTTTTAAAAAAGAGCCGCTAATGCTCGATCTTTAGCGAC
1 GTTTTTAAAAAAGCGCCGCTAATACTCGATCTTTAGCGAC
* *
39422633 GTTTTTAAAAAAGCGCCACTAATGA-TTGATCTTTAG
1 GTTTTTAAAAAAGCGCCGCTAAT-ACTCGATCTTTAG
39422669 TGGCATTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 66 0.99
41 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (40 bp):
GTTTTTAAAAAAGCGCCGCTAATACTCGATCTTTAGCGAC
Found at i:39424607 original size:42 final size:42
Alignment explanation
Indices: 39424550--39424652 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 42
39424540 TGAGATTTAT
*
39424550 GTGTAAGACCATGTCTAGGACA-TCGACATTG-TATTTGATTTC
1 GTGTAAGACCATGTCT-GGACAGT-GACATTGATATTTGATTAC
* *
39424592 GTGTAAGACCCTGTCTGAGACAGTGGCATTGATATTTGATTAC
1 GTGTAAGACCATGTCTG-GACAGTGACATTGATATTTGATTAC
*
39424635 ATGTAAGACCATGTCTGG
1 GTGTAAGACCATGTCTGG
39424653 GACGTTGGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.02
42 26 0.49
43 26 0.49
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGACAGTGACATTGATATTTGATTAC
Found at i:39424629 original size:43 final size:43
Alignment explanation
Indices: 39424500--39424665 Score: 160
Period size: 43 Copynumber: 3.9 Consensus size: 43
39424490 TTCGATATAC
* * * *
39424500 GATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGA
1 GATTTCGTGTAAGACCATGTCTGAGACGTTGGCATTGATATT-T
* * * *
39424543 GATTTATGTGTAAGACCATGTCT-AGGACATCGACATTG-TATTT
1 GATTT-CGTGTAAGACCATGTCTGA-GACGTTGGCATTGATATTT
*
39424586 GATTTCGTGTAAGACCCTGTCTGAGACAG-TGGCATTGATATTT
1 GATTTCGTGTAAGACCATGTCTGAGAC-GTTGGCATTGATATTT
* * *
39424629 GATTACATGTAAGACCATGTCTGGGACGTTGGCATTG
1 GATTTCGTGTAAGACCATGTCTGAGACGTTGGCATTG
39424666 TACAAGCTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
42 25 0.25
43 48 0.48
44 26 0.26
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGAGACGTTGGCATTGATATTT
Found at i:39429609 original size:25 final size:25
Alignment explanation
Indices: 39429570--39429627 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
39429560 CGTGTGGTTG
39429570 ACACGGCCCTAGACACGGACGTGTT
1 ACACGGCCCTAGACACGGACGTGTT
* *
39429595 ATACGGCCCTGGACACGGACGTGTT
1 ACACGGCCCTAGACACGGACGTGTT
39429620 ACACGGCC
1 ACACGGCC
39429628 GTGTGTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (25 bp):
ACACGGCCCTAGACACGGACGTGTT
Found at i:39432680 original size:5 final size:5
Alignment explanation
Indices: 39432656--39432732 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
39432646 TTTTTATAAA
* *
39432656 TATAT TAT-T TA-AT TAGAT TATAT TAT-T ATATTAT TATATT GTAAAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT TATA-T -TATAT
39432702 TATAT TA-AT TATAT TATA- -ATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
39432733 AAATAAATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
3 3 0.05
4 11 0.19
5 36 0.61
6 5 0.08
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:39432683 original size:8 final size:8
Alignment explanation
Indices: 39432672--39432726 Score: 56
Period size: 8 Copynumber: 6.2 Consensus size: 8
39432662 ATTTAATTAG
39432672 ATTATATT
1 ATTATATT
39432680 ATTATATT
1 ATTATATT
39432688 ATTATATTGT
1 ATTATA-T-T
39432698 AAATTATATT
1 --ATTATATT
39432708 AATTATATT
1 -ATTATATT
*
39432717 ATAATATT
1 ATTATATT
39432725 AT
1 AT
39432727 ATTATAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
8 23 0.55
9 10 0.24
10 2 0.05
11 1 0.02
12 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
ATTATATT
Found at i:39432867 original size:13 final size:14
Alignment explanation
Indices: 39432841--39432880 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
39432831 AATATAAGAA
39432841 ATTATTAT-TATAT
1 ATTATTATATATAT
39432854 ATTATTATAT-TAT
1 ATTATTATATATAT
39432867 A-TA-TATATATAT
1 ATTATTATATATAT
39432879 AT
1 AT
39432881 AAAGTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 12 0.50
14 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATTATATATAT
Found at i:39432881 original size:10 final size:9
Alignment explanation
Indices: 39432843--39432880 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
39432833 TATAAGAAAT
39432843 TATTATTATA
1 TATTA-TATA
39432853 TATTAT-TA
1 TATTATATA
39432861 TATTATATA
1 TATTATATA
39432870 TA-TATATA
1 TATTATATA
39432878 TAT
1 TAT
39432881 AAAGTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.62
9 5 0.19
10 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATATA
Found at i:39432981 original size:16 final size:15
Alignment explanation
Indices: 39432935--39432982 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
39432925 GGGACAAAAC
*
39432935 AGAAAGAAAAAGAAA
1 AGAAAGAAAAGGAAA
* *
39432950 GGAAAGAAGAGAGAAA
1 AGAAAGAAAAG-GAAA
39432966 AGAAAGAATAAGGAAA
1 AGAAAGAA-AAGGAAA
39432982 A
1 A
39432983 TAAGGTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.31
16 16 0.62
17 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAAGAAAAGGAAA
Found at i:39436116 original size:18 final size:18
Alignment explanation
Indices: 39436093--39436136 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
39436083 ATACACACAA
*
39436093 AGTAAGCTAACTTAGCTT
1 AGTAAGCCAACTTAGCTT
39436111 AGTAAGCCAACTTAGCTT
1 AGTAAGCCAACTTAGCTT
39436129 AGTAAGCC
1 AGTAAGCC
39436137 TTAAGCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (18 bp):
AGTAAGCCAACTTAGCTT
Found at i:39438594 original size:10 final size:10
Alignment explanation
Indices: 39438575--39438624 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
39438565 TTAAATTCTA
39438575 AAAGATAAAT
1 AAAGATAAAT
39438585 ACAA-ATAAAT
1 A-AAGATAAAT
*
39438595 AAAGATAATT
1 AAAGATAAAT
39438605 AAAGATAAAT
1 AAAGATAAAT
*
39438615 AAAAATAAAT
1 AAAGATAAAT
39438625 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:39439423 original size:96 final size:97
Alignment explanation
Indices: 39439293--39439476 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 97
39439283 ATTTAATTTA
* * ** * *
39439293 TTTATTTTTACTTAGGAATATATTGAACCTTTTGATGCGAAGAGATATGACAGCCAAGCA-CTCC
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCT-C
39439357 ACCCCAGTTACTCAGCCCAACATACTCCTTATT
65 ACCCCAGTTACTCAGCCCAACATACTCCTTATT
*
39439390 TTTATTTTT-CTTAAGAACATATCAAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCA
* *
39439454 CCCCGGTTACTCAGCCTAACATA
66 CCCCAGTTACTCAGCCCAACATA
39439477 TTCTTAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 66 0.86
97 11 0.14
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCA
CCCCAGTTACTCAGCCCAACATACTCCTTATT
Found at i:39440569 original size:4 final size:4
Alignment explanation
Indices: 39440555--39440623 Score: 52
Period size: 4 Copynumber: 16.8 Consensus size: 4
39440545 TTAATAACCA
* *
39440555 AAAT AAAAT AAAT AATT AAAT -AAT AAAT AATT AAAAT AAA- ATAAT AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT AAAT
* *
39440604 AATT AAAAT AAAA AAAT AAA
1 AAAT -AAAT AAAT AAAT AAA
39440624 GAGAAACATA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
3 4 0.08
4 36 0.71
5 11 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:39440576 original size:8 final size:8
Alignment explanation
Indices: 39440563--39440610 Score: 59
Period size: 7 Copynumber: 6.5 Consensus size: 8
39440553 CAAAATAAAA
39440563 TAAATAAT
1 TAAATAAT
39440571 TAAATAA-
1 TAAATAAT
39440578 TAAATAAT
1 TAAATAAT
39440586 T-AA-AAT
1 TAAATAAT
*
39440592 AAAATAA-
1 TAAATAAT
39440599 TAAATAAT
1 TAAATAAT
39440607 TAAA
1 TAAA
39440611 ATAAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 3 0.09
7 17 0.50
8 14 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAATAAT
Found at i:39440581 original size:15 final size:15
Alignment explanation
Indices: 39440561--39440606 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
39440551 ACCAAAATAA
39440561 AATAAATAATTAAAT
1 AATAAATAATTAAAT
39440576 AATAAATAATT-AA-
1 AATAAATAATTAAAT
39440589 AATAAAATAA-TAAAT
1 AAT-AAATAATTAAAT
39440604 AAT
1 AAT
39440607 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.14
14 10 0.36
15 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAATAATTAAAT
Found at i:39440591 original size:28 final size:25
Alignment explanation
Indices: 39440571--39440622 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 25
39440561 AATAAATAAT
39440571 TAAATAATAAATAATTAAAATAAAATAA
1 TAAATAATAAA-AA-TAAAAT-AAATAA
*
39440599 TAAATAATTAAAATAAAA-AAATAA
1 TAAATAATAAAAATAAAATAAATAA
39440623 AGAGAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 6 0.26
26 5 0.22
27 2 0.09
28 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAATAATAAAAATAAAATAAATAA
Found at i:39440598 original size:21 final size:21
Alignment explanation
Indices: 39440572--39440623 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
39440562 ATAAATAATT
39440572 AAATAATAAATAATTAAAATA
1 AAATAATAAATAATTAAAATA
39440593 AAATAATAAATAATTAAAATA
1 AAATAATAAATAATTAAAATA
*
39440614 AAAAAATAAA
1 AAATAATAAA
39440624 GAGAAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATAATAAATAATTAAAATA
Found at i:39440636 original size:12 final size:12
Alignment explanation
Indices: 39440619--39440643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39440609 AAATAAAAAA
39440619 ATAAAGAGAAAC
1 ATAAAGAGAAAC
39440631 ATAAAGAGAAAC
1 ATAAAGAGAAAC
39440643 A
1 A
39440644 AAAATTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
ATAAAGAGAAAC
Found at i:39448459 original size:10 final size:10
Alignment explanation
Indices: 39448440--39448489 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
39448430 TTAAATTCTA
39448440 AAAGATAAAT
1 AAAGATAAAT
39448450 ACAA-ATAAAT
1 A-AAGATAAAT
* *
39448460 AAATATAATT
1 AAAGATAAAT
39448470 AAAGATAAAT
1 AAAGATAAAT
*
39448480 AAAAATAAAT
1 AAAGATAAAT
39448490 CCTAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:39454122 original size:54 final size:54
Alignment explanation
Indices: 39453915--39454122 Score: 215
Period size: 53 Copynumber: 3.9 Consensus size: 54
39453905 TTTACTTTTT
* * * * * * *
39453915 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTTCCTTATA
* **
39453968 GAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC-TTTCCTTATA
* * *
39454022 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGACT-TCCTTTCCTTATA
1 G-AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA-TATCCTTTCCTTATA
* * * *
39454077 GAACTTATCAATTCCACGCCTTGGCTTGTTCTTACATGATATCCTT
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
39454123 ATCTTACCAA
Statistics
Matches: 130, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 45 0.35
54 37 0.28
55 44 0.34
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (54 bp):
GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTTCCTTATA
Found at i:39454159 original size:47 final size:47
Alignment explanation
Indices: 39454106--39454222 Score: 189
Period size: 47 Copynumber: 2.5 Consensus size: 47
39454096 CTTGGCTTGT
* *
39454106 TCTTACATGATATCCTTATCTTACCAAATGACATGTTCCAAACATTG
1 TCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACATGG
* *
39454153 TCTTACATGGTATCCTTTTCTTACCAAATGCCATGTTCCAAACATGG
1 TCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACATGG
*
39454200 TCTTACATGGTATCCTTGTCTTA
1 TCTTACATGGTATCCTTATCTTA
39454223 GTGCTAACGC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.38
Consensus pattern (47 bp):
TCTTACATGGTATCCTTATCTTACCAAATGACATGTTCCAAACATGG
Found at i:39454445 original size:44 final size:44
Alignment explanation
Indices: 39454361--39454445 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
39454351 ATCCTTAACC
* *
39454361 GTCAATTCCTCCTTAAATGCCATGTTATGAACATGGACTTTTCT
1 GTCAATTCCTCCTTAAATGCCATGGTATCAACATGGACTTTTCT
* *
39454405 GTCAATTCCTCCTTAATTGCCATGGTA-CAACCATGTACTTT
1 GTCAATTCCTCCTTAAATGCCATGGTATCAA-CATGGACTTT
39454446 GAGATATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (44 bp):
GTCAATTCCTCCTTAAATGCCATGGTATCAACATGGACTTTTCT
Found at i:39458812 original size:24 final size:24
Alignment explanation
Indices: 39458780--39458860 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 24
39458770 GATTAAGCTG
* *
39458780 AAACGGTAAGCTCTGACGAGCTAA
1 AAACAGTAAGCTCTAACGAGCTAA
* * * * *
39458804 AAACAGTAAGCTTTTATGGGCT-G
1 AAACAGTAAGCTCTAACGAGCTAA
* * *
39458827 AAACAGAAAGCTCCAACAAGCTAA
1 AAACAGTAAGCTCTAACGAGCTAA
39458851 AAACAGTAAG
1 AAACAGTAAG
39458861 TTCTTATGAG
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
23 15 0.37
24 26 0.63
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (24 bp):
AAACAGTAAGCTCTAACGAGCTAA
Found at i:39458827 original size:47 final size:47
Alignment explanation
Indices: 39458775--39458874 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 47
39458765 AGCTCGATTA
* * ** *
39458775 AGCTGAAACGGTAAGCTCTGACGAGCTAAAAACAGTAAGCTT-TTATG
1 AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAG-TTCTTATG
*
39458822 GGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
1 AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
39458869 AGCTGA
1 AGCTGA
39458875 TATATCAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 2 0.04
47 43 0.96
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (47 bp):
AGCTGAAACAGAAAGCTCCAACAAGCTAAAAACAGTAAGTTCTTATG
Found at i:39458872 original size:24 final size:24
Alignment explanation
Indices: 39458797--39458872 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
39458787 AAGCTCTGAC
39458797 GAGCTAAAAACAGTAAGCTT-TTAT
1 GAGCTAAAAACAGTAAG-TTCTTAT
* * * * ** *
39458821 GGGCT-GAAACAGAAAGCTCCAAC
1 GAGCTAAAAACAGTAAGTTCTTAT
*
39458844 AAGCTAAAAACAGTAAGTTCTTAT
1 GAGCTAAAAACAGTAAGTTCTTAT
39458868 GAGCT
1 GAGCT
39458873 GATATATCAG
Statistics
Matches: 34, Mismatches: 16, Indels: 4
0.63 0.30 0.07
Matches are distributed among these distances:
22 1 0.03
23 13 0.38
24 20 0.59
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (24 bp):
GAGCTAAAAACAGTAAGTTCTTAT
Found at i:39467975 original size:141 final size:141
Alignment explanation
Indices: 39467717--39467985 Score: 432
Period size: 141 Copynumber: 1.9 Consensus size: 141
39467707 AATTTGCATC
* *
39467717 ATATATCAAATGGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATATTC
1 ATATATCAAATAGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATAGTC
* * *
39467782 TTAGCTTATTTTACACCATTGTTCACAACTTATCATTGCCCGTTGAACCATTCGTAATTGAATAG
66 TTAGCTCATTTTACACCATCGTTCACAACTTATCATTGCCCGTTGAACCATTCGGAATTGAATAG
39467847 AATACTCAGAT
131 AATACTCAGAT
*
39467858 ATATATCAAATAGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATCGTC
1 ATATATCAAATAGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATAGTC
* * * *
39467923 TTAGCTCGTTTTACACCATCGTTCA-AATTTTATCATTTCCCGTTGAATCATTCGGAATTGAAT
66 TTAGCTCATTTTACACCATCGTTCACAA-CTTATCATTGCCCGTTGAACCATTCGGAATTGAAT
39467986 CATATATCAA
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
140 2 0.02
141 115 0.98
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (141 bp):
ATATATCAAATAGCCAACTTACCTTATTTTCGAATAGGTAATCAACTAACTCATACCTGATAGTC
TTAGCTCATTTTACACCATCGTTCACAACTTATCATTGCCCGTTGAACCATTCGGAATTGAATAG
AATACTCAGAT
Found at i:39468106 original size:40 final size:43
Alignment explanation
Indices: 39467997--39468108 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
39467987 ATATATCAAA
* * * **
39467997 CAATGCCAATGTCCTAGACGTGGTCTTACATGCTATCTCATAT
1 CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
* *
39468040 CAATGCCACTGTCCTAGACAGGGTCTTACACG-AATCAAATA-
1 CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
*
39468081 CGATGCCAATGTCC-AGACATGGTCTTAC
1 CAATGCCAATGTCCTAGACATGGTCTTAC
39468109 TCATAACGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 13 0.22
41 12 0.20
42 6 0.10
43 28 0.47
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
CAATGCCAATGTCCTAGACATGGTCTTACACGCAATCAAATAT
Found at i:39468166 original size:45 final size:44
Alignment explanation
Indices: 39468036--39468167 Score: 123
Period size: 45 Copynumber: 3.0 Consensus size: 44
39468026 ATGCTATCTC
* * *
39468036 ATATCAATGCCACTGTCCTAGACAGGGTCTTACAC-GAATC-A-A-
1 ATATCGATGCCAATGTCC-AGACATGGTCTTACACAGAA-CGACAT
* *
39468078 ATA-CGATGCCAATGTCCAGACATGGTCTTACTCATAACGACAT
1 ATATCGATGCCAATGTCCAGACATGGTCTTACACAGAACGACAT
* *
39468121 ATATCGATGTCAATGTCCCAGACGTGGTCTTACACAAGAAC-ACAT
1 ATATCGATGCCAATGT-CCAGACATGGTCTTACAC-AGAACGACAT
39468166 AT
1 AT
39468168 CAAAAATCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
40 15 0.20
41 15 0.20
42 4 0.05
43 3 0.04
44 11 0.15
45 22 0.30
46 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCAGACATGGTCTTACACAGAACGACAT
Found at i:39469919 original size:48 final size:48
Alignment explanation
Indices: 39469848--39470082 Score: 287
Period size: 48 Copynumber: 4.9 Consensus size: 48
39469838 AGGTTAAATT
* * *
39469848 GCCGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACAT-GTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAAT-GAG
*
39469896 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-ATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGA-G
* * * *
39469944 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT-ATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAAT-GAG
* * * *
39469992 ACCGATTCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
* * *
39470040 GCCAATGTCATGTCCCAGACATGGTCTTACACTAGCACACATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
39470083 TCAACCAAAT
Statistics
Matches: 160, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
47 3 0.02
48 153 0.96
49 4 0.03
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATGAG
Found at i:39470015 original size:96 final size:96
Alignment explanation
Indices: 39469848--39470087 Score: 372
Period size: 96 Copynumber: 2.5 Consensus size: 96
39469838 AGGTTAAATT
* * * * * **
39469848 GCCGATGCCATGTCCCAGACATGGTCTTATACTGGCTCACATGTCGAGGCCGATGCCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACACCGATGCCATGTCCCA
39469913 GACATGGTCTTACACTAGCTCTCATAATATG
66 GACATGGTCTTACACTAGCTCTCATAATATG
* *
39469944 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACACCGATTCCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACACCGATGCCATGTCCCA
*
39470009 GACATGGTCTTACACTAGCTCTCATAATGTG
66 GACATGGTCTTACACTAGCTCTCATAATATG
* *
39470040 GCCAATGTCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
39470088 CAAATGTTGT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 131 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACACCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCTCATAATATG
Found at i:39480592 original size:34 final size:34
Alignment explanation
Indices: 39480549--39480618 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
39480539 ACTTCATACT
39480549 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
1 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
39480583 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
1 TATCAAAGAACATAAATCTTAACCAGATTTCCAA
39480617 TA
1 TA
39480619 CCCATGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (34 bp):
TATCAAAGAACATAAATCTTAACCAGATTTCCAA
Found at i:39486253 original size:48 final size:47
Alignment explanation
Indices: 39486178--39486501 Score: 279
Period size: 48 Copynumber: 6.8 Consensus size: 47
39486168 AGGTTAAATT
* * * * *
39486178 GCCGATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-GAG
* * * *
39486226 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATTTTAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-TATGAG
* * * * * * *
39486274 ACCGATACCATGTCCCAGACATGGTCTTACATTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-GAG
* * * * * * *
39486322 ACCGATTCCATATCCTAGACATGGTCTTATACTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGAG
* * *
39486370 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATTGAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA-TGAG
* * * * * *
39486418 GCTGATGCCATGACCTAGACATGCTCTTACACTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGAG
* * *
39486466 GCCAATGCCATGTCCCACACATGGTCTTACGCTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
39486502 ACACATATCA
Statistics
Matches: 219, Mismatches: 52, Indels: 10
0.78 0.19 0.04
Matches are distributed among these distances:
47 3 0.01
48 212 0.97
49 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATGAG
Found at i:39486435 original size:96 final size:96
Alignment explanation
Indices: 39486178--39486510 Score: 355
Period size: 96 Copynumber: 3.5 Consensus size: 96
39486168 AGGTTAAATT
* * * * * * * * *
39486178 GCCGATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAGGCCAATGCCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGACCTA
* ** *
39486243 GACATGGTCTTACACTAGCTCTCATTTTAAT-
66 GACATGGTCTTACACTGGCTCTCATAAT-GTG
* * * * * * * * ** *
39486274 ACCGATACCATGTCCCAGACATGGTCTTACATTAGCTCTCGTCTCAATACCGATTCCAT-ATCCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGA-CCT
*
39486338 AGACATGGTCTTATACTGGCTCTCATAATGTG
65 AGACATGGTCTTACACTGGCTCTCATAATGTG
* *
39486370 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATTGACGCTGATGCCATGACCTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGACCTA
*
39486435 GACATGCTCTTACACTGGCTCTCATAATGTG
66 GACATGGTCTTACACTGGCTCTCATAATGTG
* * *
39486466 GCCAATGCCATGTCCCACACATGGTCTTACGCTAGCACACATATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC
39486511 AACCAAATGT
Statistics
Matches: 194, Mismatches: 40, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
95 1 0.01
96 192 0.99
97 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCGACGCCGATGCCATGACCTA
GACATGGTCTTACACTGGCTCTCATAATGTG
Found at i:39486439 original size:144 final size:144
Alignment explanation
Indices: 39486179--39486457 Score: 371
Period size: 144 Copynumber: 1.9 Consensus size: 144
39486169 GGTTAAATTG
* *
39486179 CCGATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAGGCCAATGCCATGTCCCAG
1 CCGATGCCATATCCTAGACATGGTCTTATACTGGCTCACATATCGAGGCCAATGCCATGTCCCAG
* * * * * * *
39486244 ACATGGTCTTACACTAGCTCTCATTTTAATACCGATACCATGTCCCAGACATGGTCTTACATTAG
66 ACATGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTAG
39486309 CTCTCGTCTCAATA
131 CTCTCGTCTCAATA
* * * *
39486323 CCGATTCCATATCCTAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCCGATGCCATGTCCCA
1 CCGATGCCATATCCTAGACATGGTCTTATACTGGCTCACAT-ATCGAGGCCAATGCCATGTCCCA
* * * * * *
39486387 GACATGGTCTTACACTAGCACACATATTGACGCTGATGCCATGACCTAGACATGCTCTTACACTG
65 GACATGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTA
39486452 GCTCTC
130 GCTCTC
39486458 ATAATGTGGC
Statistics
Matches: 115, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
144 114 0.99
145 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (144 bp):
CCGATGCCATATCCTAGACATGGTCTTATACTGGCTCACATATCGAGGCCAATGCCATGTCCCAG
ACATGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTAG
CTCTCGTCTCAATA
Found at i:39486488 original size:144 final size:143
Alignment explanation
Indices: 39486182--39486494 Score: 344
Period size: 144 Copynumber: 2.2 Consensus size: 143
39486172 TAAATTGCCG
*
39486182 ATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATGTCGAGGCCAATGCCATGTCCCAGACA
1 ATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATATCGAGGCCAATGCCATGTCCCAGACA
* * * * * * *
39486247 TGGTCTTACACTAGCTCTCATTTTAATACCGATACCATGTCCCAGACATGGTCTTACATTAGCTC
66 TGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTAGCTC
* *
39486312 TCGTCTCAATACCG
131 TCG-ATCAATACCA
* * * * *
39486326 ATTCCATATCCTAGACATGGTCTTATACTGGCTCTCATAAT-GTGGCCGATGCCATGTCCCAGAC
1 ATGCCATGTCCTAGACATGGTCTTATACTGGCTCACAT-ATCGAGGCCAATGCCATGTCCCAGAC
* * * * * *
39486390 ATGGTCTTACACTAGCACACATATTGACGCTGATGCCATGACCTAGACATGCTCTTACACTGGCT
65 ATGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTAGCT
*
39486455 CTC-AT-AATGTGGCCA
130 CTCGATCAA--T-ACCA
* *
39486470 ATGCCATGTCCCACACATGGTCTTA
1 ATGCCATGTCCTAGACATGGTCTTA
39486495 CGCTAGCACA
Statistics
Matches: 139, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
141 2 0.01
142 1 0.01
143 1 0.01
144 134 0.96
145 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (143 bp):
ATGCCATGTCCTAGACATGGTCTTATACTGGCTCACATATCGAGGCCAATGCCATGTCCCAGACA
TGGTCTTACACTAGCACACATATTAACACCGATACCATGACCCAGACATGCTCTTACACTAGCTC
TCGATCAATACCA
Found at i:39491383 original size:49 final size:49
Alignment explanation
Indices: 39491245--39491388 Score: 135
Period size: 49 Copynumber: 3.0 Consensus size: 49
39491235 GTAGGGGTAG
* *
39491245 TTATTGAGATAGCTTCAGC--TA--TGTATTGGCACTT-TGTGTGC--G-
1 TTATTGAGATAGCTTCGGCTATATTTATATTGGCACTTAT-TGTGCAAGA
* * *
39491287 TTATCGAGATAGCTTTGGCTATATATATATATTGGCACTTCA-GGTGCAAGA
1 TTATTGAGATAGCTTCGGCTATAT-T-TATATTGGCACTT-ATTGTGCAAGA
*
39491338 TTATTGAGATAGCTTCGGCTATATTTTTATTGGCACTTATTGTGCAAGA
1 TTATTGAGATAGCTTCGGCTATATTTATATTGGCACTTATTGTGCAAGA
39491387 TT
1 TT
39491389 CCAAGGTATC
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
42 16 0.20
44 2 0.02
48 17 0.21
49 22 0.27
50 2 0.02
51 22 0.27
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (49 bp):
TTATTGAGATAGCTTCGGCTATATTTATATTGGCACTTATTGTGCAAGA
Found at i:39492427 original size:12 final size:12
Alignment explanation
Indices: 39492410--39492435 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39492400 GGTTTGGCAT
39492410 GGCCTAGCACAC
1 GGCCTAGCACAC
39492422 GGCCTAGCACAC
1 GGCCTAGCACAC
39492434 GG
1 GG
39492436 GCGTGTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Done.