Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 80 of 153
Found at i:25507569 original size:42 final size:41
Alignment explanation
Indices: 25507522--25507611 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 41
25507512 TCACTTATAA
* *
25507522 GTATTATTTC-ACTATGTAAGTTATCATATGATATATATTTAT
1 GTATTATGTCGACTATGTAAGTTAT-ATATGATATA-AGTTAT
* * *
25507564 GTATTATGTCGTATTATGTAAGTTATGTATTATATAAGTTAT
1 GTATTATGTCG-ACTATGTAAGTTATATATGATATAAGTTAT
25507606 GTATTA
1 GTATTA
25507612 ATAAGTTATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 20 0.49
43 8 0.20
44 13 0.32
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.50
Consensus pattern (41 bp):
GTATTATGTCGACTATGTAAGTTATATATGATATAAGTTAT
Found at i:25507591 original size:9 final size:9
Alignment explanation
Indices: 25507577--25507632 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
25507567 TTATGTCGTA
25507577 TTATGTAAG
1 TTATGTAAG
25507586 TTATGT-A-
1 TTATGTAAG
*
25507593 TTATATAAG
1 TTATGTAAG
25507602 TTATGT-A-
1 TTATGTAAG
*
25507609 TTA-ATAAG
1 TTATGTAAG
25507617 TTATGTAAG
1 TTATGTAAG
25507626 TTATGTA
1 TTATGTA
25507633 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 6 0.16
9 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:25507617 original size:15 final size:16
Alignment explanation
Indices: 25507574--25507623 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
25507564 GTATTATGTC
*
25507574 GTATTATGTAAGTTAT
1 GTATTATATAAGTTAT
25507590 GTATTATATAAGTTAT
1 GTATTATATAAGTTAT
25507606 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
25507621 GTA
1 GTA
25507624 AGTTATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTATTATATAAGTTAT
Found at i:25507666 original size:43 final size:40
Alignment explanation
Indices: 25507577--25507683 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 40
25507567 TTATGTCGTA
* * *
25507577 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
*
25507617 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAG
1 TTATGTAAGTTATGTATCA-TAT-AAAT-TATATATTAATAAG
25507660 TTATGTAA-TATATGTAT--TATAAAT
1 TTATGTAAGT-TATGTATCATATAAAT
25507684 GGGTAATTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.07
40 20 0.34
41 2 0.03
42 4 0.07
43 28 0.48
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
Found at i:25507677 original size:24 final size:24
Alignment explanation
Indices: 25507603--25507678 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 24
25507593 TTATATAAGT
25507603 TATGTATTAATAAGTTATGTAAGT-
1 TATGTATTAATAAGTTATGTAA-TA
* **
25507627 TATGTA-TCAT---TT-TAAAATA
1 TATGTATTAATAAGTTATGTAATA
*
25507646 TATATATTAATAAGTTATGTAATA
1 TATGTATTAATAAGTTATGTAATA
25507670 TATGTATTA
1 TATGTATTA
25507679 TAAATGGGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
18 1 0.03
19 8 0.21
20 5 0.13
23 5 0.13
24 19 0.50
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (24 bp):
TATGTATTAATAAGTTATGTAATA
Found at i:25508303 original size:15 final size:15
Alignment explanation
Indices: 25508278--25508313 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
25508268 TTAATAAAAG
25508278 GAAAA-AGTAGAAAT
1 GAAAACAGTAGAAAT
25508292 GAAAACAGTAGAAAT
1 GAAAACAGTAGAAAT
25508307 GAAAACA
1 GAAAACA
25508314 AATTGGTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.64, C:0.06, G:0.19, T:0.11
Consensus pattern (15 bp):
GAAAACAGTAGAAAT
Found at i:25512825 original size:41 final size:41
Alignment explanation
Indices: 25512759--25512851 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
25512749 AAACGCCGCT
* *
25512759 AACGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTTTCTAAGA
1 AACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTT-TAAGA
** *
25512800 TGCGCCGCTAATGCTCAGGTATTTAGCGGTGCTTTTTAAGA
1 AACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTTTAAGA
25512841 AACGCCGCTAA
1 AACGCCGCTAA
25512852 AAACCGGAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (41 bp):
AACGCCGCTAATGCTCAGGTATTTAGCGGCGCTTTTTAAGA
Found at i:25512867 original size:41 final size:40
Alignment explanation
Indices: 25512822--25513015 Score: 219
Period size: 41 Copynumber: 4.7 Consensus size: 40
25512812 GCTCAGGTAT
* *
25512822 TTAGCGGTGCTTTTTAAGAAACGCCGCTAAAAACCGGAGCA
1 TTAGCGGCGCTTTTTAA-AAACGCCGCTAAAGACCGGAGCA
* *
25512863 TTAGCGGCGCTTTCTAATAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTTTAA-AAACGCCGCTAAAGACCGGAGCA
* * * *
25512904 TTAGCGGCGCATCTTAGAAAATGCCGCTAAAGATCGGAGCA
1 TTAGCGGCGCTTTTTA-AAAACGCCGCTAAAGACCGGAGCA
* * *
25512945 TTAGCGGCGATTATTCAAAAACGCCGCTAAAGACAGGAGCA
1 TTAGCGGCGCTT-TTTAAAAACGCCGCTAAAGACCGGAGCA
*
25512986 TTAGTGGCG-TGTTTTAAAAAGCGCCGCTAA
1 TTAGCGGCGCT-TTTTAAAAA-CGCCGCTAA
25513016 GGGCCCCAAA
Statistics
Matches: 129, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
40 8 0.06
41 118 0.91
42 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTTTAAAAACGCCGCTAAAGACCGGAGCA
Found at i:25513144 original size:40 final size:40
Alignment explanation
Indices: 25513076--25513175 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
25513066 TTTGAAAACA
* * *
25513076 CCGCTAATGCTTG-TTTTTAGCGGTGTTTTACA-AATAGCG
1 CCGCTAATGCTTGTTTTTTGGCAGCGTTTTACATAAT-GCG
*
25513115 CCGCTAATGCTTGTTTTTTGGCAGCGTTTTACATAATTCG
1 CCGCTAATGCTTGTTTTTTGGCAGCGTTTTACATAATGCG
25513155 CCGCTAATGCTTGATTTTTTG
1 CCGCTAATGCTTG-TTTTTTG
25513176 TGGCGTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
39 13 0.24
40 31 0.57
41 10 0.19
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (40 bp):
CCGCTAATGCTTGTTTTTTGGCAGCGTTTTACATAATGCG
Found at i:25517539 original size:12 final size:12
Alignment explanation
Indices: 25517508--25517553 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
25517498 CCGTGTCCCA
25517508 GCCCGTGTGTCC
1 GCCCGTGTGTCC
* * *
25517520 TCTCGTGTGTCT
1 GCCCGTGTGTCC
*
25517532 GCCTGTGTGTCC
1 GCCCGTGTGTCC
25517544 GCCCGTGTGT
1 GCCCGTGTGT
25517554 ATATTCGAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.35
Consensus pattern (12 bp):
GCCCGTGTGTCC
Found at i:25518609 original size:33 final size:33
Alignment explanation
Indices: 25518572--25518656 Score: 80
Period size: 35 Copynumber: 2.5 Consensus size: 33
25518562 CGCCTAGTGT
* * **
25518572 TAGTCAGATAACCGAAATAGTTGTGCCCTGCAC
1 TAGTCAGATAACCGAAATAATTGTACCCAACAC
* * *
25518605 TAGTCAAATAATCGACAAATAATTGTACCCAACGC
1 TAGTCAGATAACCG--AAATAATTGTACCCAACAC
*
25518640 TAGTCGGATAACCGAAA
1 TAGTCAGATAACCGAAA
25518657 ATATCAATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
33 15 0.38
35 25 0.62
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (33 bp):
TAGTCAGATAACCGAAATAATTGTACCCAACAC
Found at i:25519276 original size:85 final size:83
Alignment explanation
Indices: 25519159--25519384 Score: 287
Period size: 85 Copynumber: 2.7 Consensus size: 83
25519149 ATGTCGCTAA
* *
25519159 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATA
1 CTTTAGCGGCGCTTA-TGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAG-AAA-A
*
25519224 AACGCCGCTAAAGATCGTGA-T
63 AACGCCGCTAAAGATCAT-ATT
* *
25519245 CTTTAGCGGCGCTTATGAAAAAACACCGCTAAAGATCACGTTCTTTAGCGGCGCTTAAGAAAAAA
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TAAGAAAAAA
25519310 CGCCGCTAAAGATCATATT
65 CGCCGCTAAAGATCATATT
* * *
25519329 CTTTAGCGGCGCTT-TGGGATAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCT
1 CTTTAGCGGCGCTTAT--GAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCT
25519385 TGTTCAAAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
83 2 0.02
84 35 0.28
85 70 0.56
86 18 0.14
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (83 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAC
GCCGCTAAAGATCATATT
Found at i:25519290 original size:42 final size:42
Alignment explanation
Indices: 25519159--25519429 Score: 289
Period size: 42 Copynumber: 6.4 Consensus size: 42
25519149 ATGTCGCTAA
* *
25519159 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-TGAAAAAACGCCGCTAAAGATCATGTT
* * *
25519202 CTTTAGCGGCGC-TAAGAAAATAAACGCCGCTAAAGATCGTGAT
1 CTTTAGCGGCGCTTATG-AAA-AAACGCCGCTAAAGATCATGTT
* *
25519245 CTTTAGCGGCGCTTATGAAAAAACACCGCTAAAGATCACGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
25519287 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATATT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
25519329 CTTTAGCGGCGCTT-TGGGATAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT--GAAAAAACGCCGCTAAAGA-TCATGTT
* * ** * *
25519372 CTATAGCGGCGCTTGTTCAAAAACGCTGCTAATAG-TAATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCATGTT
*
25519414 ATTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
25519430 TTCACAAACG
Statistics
Matches: 195, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.01
42 108 0.55
43 81 0.42
44 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:25519394 original size:85 final size:83
Alignment explanation
Indices: 25519159--25519429 Score: 280
Period size: 85 Copynumber: 3.2 Consensus size: 83
25519149 ATGTCGCTAA
* * *
25519159 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATA
1 CTTTAGCGGCGCTTA-TGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCT-TGAAAA-A
*
25519224 AACGCCGCTAAAGATCGTGA-T
63 AACGCCGCTAAAGATCAT-ATT
* * *
25519245 CTTTAGCGGCGCTTATGAAAAAACACCGCTAAAGATCACGTTCTTTAGCGGCGCTTAAGAAAAAA
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGA-AAAAAA
25519310 CGCCGCTAAAGATCATATT
65 CGCCGCTAAAGATCATATT
* * * **
25519329 CTTTAGCGGCGCTT-TGGGATAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTGTTCAA
1 CTTTAGCGGCGCTTAT--GAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG-AAAA
* * *
25519392 AAACGCTGCTAATAG-TAATGTT
62 AAACGCCGCTAA-AGATCATATT
*
25519414 ATTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
25519430 TTCACAAACG
Statistics
Matches: 158, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
83 2 0.01
84 35 0.22
85 104 0.66
86 17 0.11
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (83 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGAAAAAAAC
GCCGCTAAAGATCATATT
Found at i:25519395 original size:127 final size:128
Alignment explanation
Indices: 25519159--25519428 Score: 323
Period size: 127 Copynumber: 2.1 Consensus size: 128
25519149 ATGTCGCTAA
* *
25519159 CTTTTGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATA
1 CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTAAGAAAATA
** * *
25519224 AACGCCGCTAAAGATCGTGATCTTTAGCGGCGCTTATGAAAAAACACCGCTAA-AGATCACGTT
66 AACGCCGCTAAAGATAATGATCTATAGCGGCGCTTATGAAAAAACACCGCTAATAG-TAACGTT
** **
25519287 CTTTAGCGGCGCTTA-AGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTTG-GGATA
1 CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTAAGAAAAT-
* * ** * * *
25519350 AAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTGTTCAAAAACGCTGCTAATAGTAATGTT
65 AAACGCCGCTAAAGA-TAATGATCTATAGCGGCGCTTATGAAAAAACACCGCTAATAGTAACGTT
*
25519414 ATTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
25519429 TTTCACAAAC
Statistics
Matches: 121, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
126 3 0.02
127 102 0.84
128 16 0.13
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (128 bp):
CTTTAGCGGCGCTTACAGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTAAGAAAATA
AACGCCGCTAAAGATAATGATCTATAGCGGCGCTTATGAAAAAACACCGCTAATAGTAACGTT
Found at i:25519891 original size:21 final size:22
Alignment explanation
Indices: 25519867--25519935 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 22
25519857 GCTTCTATCG
*
25519867 CTGCTTCTCCT-GCTGTGGCCT
1 CTGCTTCTCCTCGCTGTAGCCT
*
25519888 CTGCTTCT-CTCGCTGTAGCAT
1 CTGCTTCTCCTCGCTGTAGCCT
**
25519909 CTGCTTC-CCTCGCTGCCGCCT
1 CTGCTTCTCCTCGCTGTAGCCT
25519930 CTGCTT
1 CTGCTT
25519936 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.95
ACGTcount: A:0.03, C:0.41, G:0.20, T:0.36
Consensus pattern (22 bp):
CTGCTTCTCCTCGCTGTAGCCT
Found at i:25525062 original size:95 final size:93
Alignment explanation
Indices: 25524901--25525072 Score: 308
Period size: 95 Copynumber: 1.8 Consensus size: 93
25524891 TAAGTTATAC
25524901 ATTATGTAAGTTGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTACGGTATG
1 ATTATGTAAGTTGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTACGGTATG
25524966 TATTATTATGTAAGTAGGGATGTAGGAT
66 TATTATTATGTAAGTAGGGATGTAGGAT
* *
25524994 ATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGTTA
1 ATTATGTAAG-T-TGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTACGGTA
25525059 TGTATTATTATGTA
64 TGTATTATTATGTA
25525073 TTATTATGTA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
93 10 0.13
94 1 0.01
95 64 0.85
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.53
Consensus pattern (93 bp):
ATTATGTAAGTTGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTACGGTATG
TATTATTATGTAAGTAGGGATGTAGGAT
Found at i:25525063 original size:34 final size:34
Alignment explanation
Indices: 25524993--25525066 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
25524983 GGATGTAGGA
* * * *
25524993 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTG
1 TATTATGTAACTTATGTAAGTTTATGTTGTTATG
*
25525027 TATTATGTAACTTATTTAA-TTTATGTATGTTATG
1 TATTATGTAACTTATGTAAGTTTATGT-TGTTATG
25525061 TATTAT
1 TATTAT
25525067 TATGTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.15, T:0.58
Consensus pattern (34 bp):
TATTATGTAACTTATGTAAGTTTATGTTGTTATG
Found at i:25525071 original size:10 final size:10
Alignment explanation
Indices: 25525047--25525106 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 10
25525037 CTTATTTAAT
*
25525047 TTATGTA-TG
1 TTATGTATTA
25525056 TTATGTATTA
1 TTATGTATTA
25525066 TTATGTATTA
1 TTATGTATTA
25525076 TTATGTAAGTTA
1 TTATGT-A-TTA
25525088 TTATGTAGGTTA
1 TTATGTA--TTA
25525100 TTATGTA
1 TTATGTA
25525107 AGTCATTATG
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
9 7 0.15
10 17 0.37
11 2 0.04
12 20 0.43
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (10 bp):
TTATGTATTA
Found at i:25525090 original size:12 final size:12
Alignment explanation
Indices: 25525063--25525117 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
25525053 ATGTTATGTA
25525063 TTATTATGT-A-
1 TTATTATGTAAG
25525073 TTATTATGTAAG
1 TTATTATGTAAG
*
25525085 TTATTATGTAGG
1 TTATTATGTAAG
25525097 TTATTATGTAAG
1 TTATTATGTAAG
*
25525109 TCATTATGT
1 TTATTATGT
25525118 TGGTTATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 30 0.75
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:25525105 original size:24 final size:24
Alignment explanation
Indices: 25525056--25525124 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
25525046 TTTATGTATG
25525056 TTATGT-A-TTATTATGTA--TTA
1 TTATGTAAGTTATTATGTAGGTTA
25525076 TTATGTAAGTTATTATGTAGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
* *
25525100 TTATGTAAGTCATTATGTTGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
25525124 T
1 T
25525125 GTAAGTTGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 10 0.23
24 26 0.60
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (24 bp):
TTATGTAAGTTATTATGTAGGTTA
Found at i:25525126 original size:21 final size:22
Alignment explanation
Indices: 25525076--25525130 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
25525066 TTATGTATTA
*
25525076 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
25525099 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
25525121 TTATGTAAGT
1 TTATGTAAGT
25525131 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:25525324 original size:9 final size:9
Alignment explanation
Indices: 25525310--25525390 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 9
25525300 TAAATATTAA
25525310 TAAGTTATG
1 TAAGTTATG
25525319 TAAGTTATG
1 TAAGTTATG
* *
25525328 TATTA-TAAATT
1 TA--AGT-TATG
* *
25525339 TAAATTACG
1 TAAGTTATG
25525348 TAAGTTATG
1 TAAGTTATG
25525357 -AA-TTATG
1 TAAGTTATG
*
25525364 TAAGATATG
1 TAAGTTATG
* *
25525373 TAAATTACG
1 TAAGTTATG
25525382 TAAGTTATG
1 TAAGTTATG
25525391 AAATTTGAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.08
9 37 0.70
10 2 0.04
11 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25525361 original size:29 final size:33
Alignment explanation
Indices: 25525318--25525392 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
25525308 AATAAGTTAT
*
25525318 GTAAGTTATGTATTA-TAA-AT-T-TAAATTAC
1 GTAAGTTATGAATTAGTAAGATATGTAAATTAC
25525347 GTAAGTTATGAATTATGTAAGATATGTAAATTAC
1 GTAAGTTATGAATTA-GTAAGATATGTAAATTAC
25525381 GTAAGTTATGAA
1 GTAAGTTATGAA
25525393 ATTTGAACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 14 0.35
31 3 0.08
32 2 0.05
33 1 0.03
34 20 0.50
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (33 bp):
GTAAGTTATGAATTAGTAAGATATGTAAATTAC
Found at i:25525384 original size:18 final size:17
Alignment explanation
Indices: 25525340--25525395 Score: 78
Period size: 16 Copynumber: 3.3 Consensus size: 17
25525330 TTATAAATTT
25525340 AAATTACGTAAGTTATG
1 AAATTACGTAAGTTATG
* *
25525357 -AATTATGTAAGATATG
1 AAATTACGTAAGTTATG
25525373 TAAATTACGTAAGTTATG
1 -AAATTACGTAAGTTATG
25525391 AAATT
1 AAATT
25525396 TGAACTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 14 0.42
17 5 0.15
18 14 0.42
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (17 bp):
AAATTACGTAAGTTATG
Found at i:25525484 original size:35 final size:35
Alignment explanation
Indices: 25525402--25525492 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 35
25525392 AATTTGAACT
** * *
25525402 TTAAAA-AAAATTTAATATTTAAAAATATTCGTGA
1 TTAAAATAAAATAAAATATTTAAAAAAATTCATGA
25525436 TT---ATAAAATAAAATATTTAAAAAAATTCATGA
1 TTAAAATAAAATAAAATATTTAAAAAAATTCATGA
25525468 TTAAAATAAAATAAAATATTTAAAA
1 TTAAAATAAAATAAAATATTTAAAA
25525493 TATAACTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 26 0.53
34 2 0.04
35 20 0.41
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (35 bp):
TTAAAATAAAATAAAATATTTAAAAAAATTCATGA
Found at i:25527133 original size:44 final size:44
Alignment explanation
Indices: 25527069--25527162 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
25527059 CTGGAAGGAG
* * *
25527069 GAAGGAGTCGATTTAGGGATTTCGGATTTCAAGAAATTCGGCAA
1 GAAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTCGGCAA
* *
25527113 GAAGGAGGCGATTTACGGATTTGGGAATTCAAGAAATTGGGCAA
1 GAAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTCGGCAA
25527157 GAAGGA
1 GAAGGA
25527163 CGCAAGAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.10, G:0.33, T:0.23
Consensus pattern (44 bp):
GAAGGAGGCGATTTACGGATTTCGGAATTCAAGAAATTCGGCAA
Found at i:25527248 original size:20 final size:20
Alignment explanation
Indices: 25527223--25527261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25527213 TTTGGGGCTG
25527223 GGGGAAGATTGCTTCGGGGA
1 GGGGAAGATTGCTTCGGGGA
*
25527243 GGGGAAGATTGCTTTGGGG
1 GGGGAAGATTGCTTCGGGG
25527262 GTATACCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.51, T:0.23
Consensus pattern (20 bp):
GGGGAAGATTGCTTCGGGGA
Found at i:25528342 original size:7 final size:7
Alignment explanation
Indices: 25528330--25528400 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
25528320 AAAGCAGTCT
25528330 AAACCCC
1 AAACCCC
25528337 AAACCCC
1 AAACCCC
* **
25528344 AAATCTT
1 AAACCCC
25528351 AAACCCC
1 AAACCCC
*
25528358 AAACTCCT
1 AAAC-CCC
*
25528366 AAACCCT
1 AAACCCC
*
25528373 AAACCCT
1 AAACCCC
*
25528380 AAACCCA
1 AAACCCC
*
25528387 AAACACC
1 AAACCCC
25528394 ATAACCC
1 A-AACCC
25528401 ACATCATAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
7 41 0.80
8 10 0.20
ACGTcount: A:0.45, C:0.44, G:0.00, T:0.11
Consensus pattern (7 bp):
AAACCCC
Found at i:25528355 original size:21 final size:21
Alignment explanation
Indices: 25528328--25528390 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
25528318 CTAAAGCAGT
*
25528328 CTAAACCCCAAACCCCAAATC
1 CTAAACCCCAAACCCCAAACC
* *
25528349 TTAAACCCCAAACTCCTAAACC
1 CTAAACCCCAAAC-CCCAAACC
* *
25528371 CTAAACCCTAAACCCAAAAC
1 CTAAACCCCAAACCCCAAAC
25528391 ACCATAACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.44, C:0.43, G:0.00, T:0.13
Consensus pattern (21 bp):
CTAAACCCCAAACCCCAAACC
Found at i:25528371 original size:29 final size:28
Alignment explanation
Indices: 25528330--25528420 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
25528320 AAAGCAGTCT
* * *
25528330 AAACCCCAAACCCCAAATCTTAAACCCC
1 AAACTCCAAACCCCAAATCATAAACCCA
* * *
25528358 AAACTCCTAAACCCTAAACCCTAAACCCA
1 AAACTCC-AAACCCCAAATCATAAACCCA
* * *
25528387 AAACACCATAA-CCCACATCATAAACCCT
1 AAACTCCA-AACCCCAAATCATAAACCCA
25528415 AAACTC
1 AAACTC
25528421 AATACTCTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
28 24 0.49
29 25 0.51
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.13
Consensus pattern (28 bp):
AAACTCCAAACCCCAAATCATAAACCCA
Found at i:25528390 original size:14 final size:14
Alignment explanation
Indices: 25528330--25528390 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
25528320 AAAGCAGTCT
*
25528330 AAACCCCAAACCCC
1 AAACCCTAAACCCC
* *
25528344 AAATCTTAAACCCC
1 AAACCCTAAACCCC
*
25528358 AAACTCCTAAACCCT
1 AAAC-CCTAAACCCC
*
25528373 AAACCCTAAACCCA
1 AAACCCTAAACCCC
25528387 AAAC
1 AAAC
25528391 ACCATAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.46, C:0.43, G:0.00, T:0.11
Consensus pattern (14 bp):
AAACCCTAAACCCC
Found at i:25528915 original size:115 final size:113
Alignment explanation
Indices: 25528713--25529203 Score: 363
Period size: 115 Copynumber: 4.3 Consensus size: 113
25528703 CCAAAACTGT
* * * * * * * *
25528713 GCGTTTTGGTAAAGATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATAATATGATTTAGTGGC
1 GCGTTTTGGTTAACATATCTTGCGGCGCTTCTAAGAAAGCGCCGCTAATAGTAT-ATTTAGCGGC
* * * ***
25528778 GATTTCTCGTGAA-CGCCACTAATTCCAGTATACATCAAGTTTTAAACACA
65 GTTTTC-CGT-AAGCGCCACTAATTCTAATATACATCAAGTACAAAACACA
* *
25528828 GCGTTTCGGTTAATATATCTTGCGGCGCTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGC
1 GCGTTTTGGTTAACATATCTTGCGGCGCTTCTAAGAAAGCGCCGCTAATAGTATA-TTTAGCGGC
* * * * * * *
25528893 GTTTTCCAATAAGGGCCACTAATTCTAATATACCTTAA-TACCAAACTCT
65 GTTTTCC-GTAAGCGCCACTAATTCTAATATACATCAAGTACAAAACACA
* *
25528942 GCGTTTTGGTGT-GCATATCTTGCGGCGC-T-TAACTGAAAGCGCCGCTAATACTGATATTTAGC
1 GCGTTTTGGT-TAACATATCTTGCGGCGCTTCTAA--GAAAGCGCCGCTAATAGT-ATATTTAGC
** * * **
25529004 GGCGTTTTATTGTAAGCGCCACTAATTATATTATACATCAAG-ACCAAAACGTA
62 GGCGTTTT-CCGTAAGCGCCACTAATTCTAATATACATCAAGTA-CAAAACACA
* * * * * * * * *
25529057 GAGTTTTGGTTAAGAAATATAGCGGCGCTTCTCCA-AACGCGCTGCTAATAGTACTCTTTAGCGG
1 GCGTTTTGGTTAACATATCTTGCGGCGCTTCT-AAGAAAGCGCCGCTAATAGTA-TATTTAGCGG
* * *
25529121 CGTTTTCCGTAAGCGCCACTAATTCTAATATACCTCAAG-ACCAAACTCTA
64 CGTTTTCCGTAAGCGCCACTAATTCTAATATACATCAAGTACAAAACAC-A
* * *
25529171 -CGTTTTGGTGT-GCATATCTTGTGGCGATTCTAA
1 GCGTTTTGGT-TAACATATCTTGCGGCGCTTCTAA
25529204 AAAATCGTAT
Statistics
Matches: 294, Mismatches: 65, Indels: 37
0.74 0.16 0.09
Matches are distributed among these distances:
112 4 0.01
113 27 0.09
114 122 0.41
115 138 0.47
116 1 0.00
117 1 0.00
118 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (113 bp):
GCGTTTTGGTTAACATATCTTGCGGCGCTTCTAAGAAAGCGCCGCTAATAGTATATTTAGCGGCG
TTTTCCGTAAGCGCCACTAATTCTAATATACATCAAGTACAAAACACA
Found at i:25528989 original size:114 final size:112
Alignment explanation
Indices: 25528732--25529202 Score: 384
Period size: 114 Copynumber: 4.1 Consensus size: 112
25528722 TAAAGATCTT
* * * * *
25528732 TTGCGGCGCTTATAAAAAAGCGCCGCTAATAATATGA-TTTAGTGGCGATTTCTCGTGAA-CGCC
1 TTGCGGCGCTTCT-AGAAAGCGCCGCTAATAGTAT-ACTTTAGCGGCGTTTTC-CGT-AAGCGCC
* * * *** * * * **
25528795 ACTAATTCCAGTATACATCAAGTTTTAAACACAGCGTTTCGGT-TAATATATC
62 ACTAATTCTAATATACCTCAAG-ACCAAACTCTGCGTTTTGGTGT-GCATATC
* *
25528847 TTGCGGCGCTTCTAAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGGGCCAC
1 TTGCGGCGCTTCT-AGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCC-GTAAGCGCCAC
* *
25528912 TAATTCTAATATACCTTAATACCAAACTCTGCGTTTTGGTGTGCATATC
64 TAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGCATATC
* **
25528961 TTGCGGCGCTTAACT-GAAAGCGCCGCTAATACTGATA-TTTAGCGGCGTTTTATTGTAAGCGCC
1 TTGCGGCGCTT--CTAGAAAGCGCCGCTAATAGT-ATACTTTAGCGGCGTTTT-CCGTAAGCGCC
* * * * * * *
25529024 ACTAATTATATTATACATCAAGACCAAAACGT-AGAGTTTTGGT-TAAG-AAATA
62 ACTAATTCTAATATACCTCAAGACC-AAAC-TCTGCGTTTTGGTGT--GCATATC
* ** *
25529076 TAGCGGCGCTTCTCCAAACGCGCTGCTAATAGTACT-CTTTAGCGGCGTTTTCCGTAAGCGCCAC
1 TTGCGGCGCTTCTAGAAA-GCGCCGCTAATAGTA-TACTTTAGCGGCGTTTTCCGTAAGCGCCAC
*
25529140 TAATTCTAATATACCTCAAGACCAAACTCTACGTTTTGGTGTGCATATC
64 TAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGCATATC
* *
25529189 TTGTGGCGATTCTA
1 TTGCGGCGCTTCTA
25529203 AAAAATCGTA
Statistics
Matches: 285, Mismatches: 52, Indels: 40
0.76 0.14 0.11
Matches are distributed among these distances:
112 2 0.01
113 27 0.09
114 129 0.45
115 123 0.43
116 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (112 bp):
TTGCGGCGCTTCTAGAAAGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCGTAAGCGCCACTA
ATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGCATATC
Found at i:25529338 original size:75 final size:74
Alignment explanation
Indices: 25529210--25529411 Score: 296
Period size: 75 Copynumber: 2.7 Consensus size: 74
25529200 CTAAAAAATC
25529210 GTATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGCACTTCTATTAAGC
1 GTATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGCACTTCTATTAAGC
25529275 GCCACTAATT
66 GCCACTAA-T
*
25529285 GTATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGTGGCACTTCTATTAAGC
1 GTATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGCACTTCTATTAAGC
*
25529350 GCGACTAAT
66 GCCACTAAT
* * * * * * * *
25529359 GCTAATATAGATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCGGC
1 G-TATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGC
25529412 GCTTTTAGTA
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
74 2 0.02
75 113 0.98
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (74 bp):
GTATTATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGCACTTCTATTAAGC
GCCACTAAT
Found at i:25529699 original size:115 final size:113
Alignment explanation
Indices: 25529421--25529699 Score: 275
Period size: 113 Copynumber: 2.5 Consensus size: 113
25529411 CGCTTTTAGT
* *
25529421 AAACGCCGCTAATACTTG-TTTTACTGGCGTTTTT-TTGTAAGCGCCACTAATTCTAATATACAT
1 AAACGCCGCTATTACTTGCTTTTAC-GGCGTTTTTCTTG-AAGCGCCACTAATTATAATATACAT
* * **
25529484 CGATACCAAAACGATGCATTTTCGTTAAGATTTTTGCCGCGCTTCCCACA
64 CAATACAAAAACGATGCATTTTCGTTAAGATTTTTGCCGCGCTAACCACA
** * * **
25529534 ATGCGCCGCTATTACTTGC-TTTAGCGGCGTTTTATCAT-AATCGCCACTAATTATTGTATACAT
1 AAACGCCGCTATTACTTGCTTTTA-CGGCGTTTT-TCTTGAAGCGCCACTAATTATAATATACAT
* * *
25529597 CAATACAAAAACGATGCGTTTTGGTCTTAAGA-TTTTGCGGCGCATAACCA-A
64 CAATACAAAAACGATGCATTTTCG--TTAAGATTTTTGCCGCGC-TAACCACA
* *
25529648 AAACGCCGCTACTTA-TGTTCTTTTACGGCGTTTTTCTTGAAGCGCCGCTAAT
1 AAACGCCGCTA-TTACT-TGCTTTTACGGCGTTTTTCTTGAAGCGCCACTAAT
25529700 GCCAGATATT
Statistics
Matches: 134, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
113 68 0.51
114 26 0.19
115 36 0.27
116 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (113 bp):
AAACGCCGCTATTACTTGCTTTTACGGCGTTTTTCTTGAAGCGCCACTAATTATAATATACATCA
ATACAAAAACGATGCATTTTCGTTAAGATTTTTGCCGCGCTAACCACA
Found at i:25531452 original size:71 final size:71
Alignment explanation
Indices: 25531368--25531511 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
25531358 TTCCCATAGA
25531368 TAGATTAAGAAAAAGTAATATATTATTCCATCCTAATTAAGCATGTAAATATAATGTGCTATAAA
1 TAGATTAAGAAAAAGTAATATATTATTCCATCCTAATTAAGCATGTAAATATAATGTGCTATAAA
*
25531433 CTTTAT
66 ATTTAT
25531439 TAGATTAAGAAAAAGTAATATATTATTCCATCCTAATTAAGCATGTAAATATAATGTGCTATAAA
1 TAGATTAAGAAAAAGTAATATATTATTCCATCCTAATTAAGCATGTAAATATAATGTGCTATAAA
25531504 ATTTAT
66 ATTTAT
25531510 TA
1 TA
25531512 TATTTCATAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (71 bp):
TAGATTAAGAAAAAGTAATATATTATTCCATCCTAATTAAGCATGTAAATATAATGTGCTATAAA
ATTTAT
Found at i:25533351 original size:21 final size:23
Alignment explanation
Indices: 25533297--25533351 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 23
25533287 GTAAACATTA
25533297 AAAATTTTA-AGATAACATTATAT
1 AAAATTTTAGA-ATAACATTATAT
25533320 AAAA-TTT-GAATAA-A-TATAT
1 AAAATTTTAGAATAACATTATAT
25533339 AAAATTTTAGAAT
1 AAAATTTTAGAAT
25533352 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
21 8 0.28
22 4 0.14
23 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
AAAATTTTAGAATAACATTATAT
Found at i:25537552 original size:25 final size:24
Alignment explanation
Indices: 25537524--25537575 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
25537514 AGGCCGTACA
25537524 GTGCTGACGTGGA-AGACTGGCGGTG
1 GTGCTGACGTGGAGAG-C-GGCGGTG
25537549 GTGCTGACGTGGAGAGCGGCGGTG
1 GTGCTGACGTGGAGAGCGGCGGTG
25537573 GTG
1 GTG
25537576 GCTAGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 10 0.38
25 14 0.54
26 2 0.08
ACGTcount: A:0.13, C:0.15, G:0.52, T:0.19
Consensus pattern (24 bp):
GTGCTGACGTGGAGAGCGGCGGTG
Found at i:25537574 original size:24 final size:25
Alignment explanation
Indices: 25537524--25537575 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
25537514 AGGCCGTACA
25537524 GTGCTGACGTGGAAGACTGGCGGTG
1 GTGCTGACGTGGAAGACTGGCGGTG
25537549 GTGCTGACGTGG-AGAGC-GGCGGTG
1 GTGCTGACGTGGAAGA-CTGGCGGTG
25537573 GTG
1 GTG
25537576 GCTAGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.13, C:0.15, G:0.52, T:0.19
Consensus pattern (25 bp):
GTGCTGACGTGGAAGACTGGCGGTG
Found at i:25537745 original size:20 final size:19
Alignment explanation
Indices: 25537704--25537764 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
25537694 AAAAAATGAG
25537704 TTTTGTATTTATTATATTT
1 TTTTGTATTTATTATATTT
25537723 TTTTGTATTTTATTAT-TTGT
1 TTTTGTA-TTTATTATATT-T
*
25537743 TTTTACGAATTTATT-TATTT
1 TTTT--GTATTTATTATATTT
25537763 TT
1 TT
25537765 ATTTGGGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 9 0.25
20 17 0.47
21 8 0.22
22 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTGTATTTATTATATTT
Found at i:25538223 original size:44 final size:41
Alignment explanation
Indices: 25538157--25538269 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 41
25538147 TATCTTCAGC
* * *
25538157 CTGCTCCACTGCAATTTTAGGGAGATAAAACTAGTAGCC-TCAAT
1 CTGCTCCACTACAACTTCAGGGAGATAAAA-T--TAGCCAT-AAT
* * *
25538201 CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATGAT
1 CTGCTCCACTACAACTTCAGGGAGATAAAATTAGCCATAAT
* *
25538242 CTGCTCTACTACAACTTCAGAGAGATAA
1 CTGCTCCACTACAACTTCAGGGAGATAA
25538270 GATATGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 32 0.53
42 1 0.02
43 1 0.02
44 26 0.43
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (41 bp):
CTGCTCCACTACAACTTCAGGGAGATAAAATTAGCCATAAT
Found at i:25538360 original size:179 final size:181
Alignment explanation
Indices: 25538020--25538425 Score: 514
Period size: 179 Copynumber: 2.3 Consensus size: 181
25538010 TACCTTCAGC
* * * * * * *
25538020 CTACTCCACTGCAACCTCAGAGAGATAGGGTTTGCTATGATCTACTCTACTAGAACTTCAGAGAG
1 CTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATCTGCTCTACTACAACTTCAGAGAG
* *
25538085 ATAAGATCTATAATTTATAGCCTCAACCTGTTCCACTACAACTTTAGGGAAATAGGATTCGCTAT
66 ATAAGATATATAATTTATAGCCTCAACCTGTTCCACTACAACTTTAGGGAAATAAGATTCGCTAT
* * *
25538150 CTTCAGCCTGCTCCACTGCAATTTTAGGGAGATAAAACTAGTAGCCTCAAT
131 CTTCAGCCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTAACCTCAAT
* * *
25538201 CTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTACAACTTCAGAGAG
1 CTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATCTGCTCTACTACAACTTCAGAGAG
* * * * *
25538266 ATAAGATATGTTA-TT-TAGCTTCAA-TTCGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTA
66 ATAAGATATATAATTTATAGCCTCAACCT-GTTCCACTACAACTTTAGGGAAATAAGATTCGCTA
* * * * * *
25538328 TCTGT-AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGACTTGTAACTTTAAT
130 TCT-TCAGCCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTAACCTCAAT
* *
25538380 CTACTCCGCTGCAACTTTAGGGAGATAAGATTTGCCATGATCTGCT
1 CTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATCTGCT
25538426 TGTTCATTAA
Statistics
Matches: 192, Mismatches: 31, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
178 1 0.01
179 123 0.64
180 3 0.02
181 65 0.34
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (181 bp):
CTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATCTGCTCTACTACAACTTCAGAGAG
ATAAGATATATAATTTATAGCCTCAACCTGTTCCACTACAACTTTAGGGAAATAAGATTCGCTAT
CTTCAGCCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTAACCTCAAT
Found at i:25538402 original size:44 final size:45
Alignment explanation
Indices: 25538299--25538411 Score: 149
Period size: 44 Copynumber: 2.5 Consensus size: 45
25538289 ATTCGTTCCA
* * * *
25538299 CTGCAACTTTAGGGAAATAAGATTCGCTATCTGTAGTCTGCTCCG
1 CTGCAACTTTAGGGAGATAAGATTCGCTAACTGTAATCTACTCCG
* *
25538344 CTGCAACTTCAGGGAGATAAGACTT-G-TAACTTTAATCTACTCCG
1 CTGCAACTTTAGGGAGATAAGA-TTCGCTAACTGTAATCTACTCCG
25538388 CTGCAACTTTAGGGAGATAAGATT
1 CTGCAACTTTAGGGAGATAAGATT
25538412 TGCCATGATC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 2 0.03
44 35 0.58
45 21 0.35
46 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (45 bp):
CTGCAACTTTAGGGAGATAAGATTCGCTAACTGTAATCTACTCCG
Found at i:25538408 original size:89 final size:88
Alignment explanation
Indices: 25538116--25538411 Score: 264
Period size: 89 Copynumber: 3.3 Consensus size: 88
25538106 CTCAACCTGT
* * * * *
25538116 TCCACTACAACTTTAGGGAAATAGGATTCGCTATCT-TCAGCCTGCTCCACTGCAATTTTAGGGA
1 TCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTGT-AGTCTGCTCCACTGCAACTTCAGGGA
* * * *
25538180 GATAAAACTAGTAGCCTCAATCTGC
65 GATAAGACTTGTAACTTCAATCT-C
* * * * * * *
25538205 TCCACTACAACTTCAGGGAGATAAGATTCGCCA--TG-A-TCTGCTCTACTACAACTTCAGAGAG
1 TCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTGTAGTCTGCTCCACTGCAACTTCAGGGAG
25538266 ATAAGA-TATGTTATTTAGCTTCAAT-TC
66 ATAAGACT-TG-TA---A-CTTCAATCTC
*
25538293 GTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTGTAGTCTGCTCCGCTGCAACTTCAGGG
1 --TCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTGTAGTCTGCTCCACTGCAACTTCAGGG
*
25538358 AGATAAGACTTGTAACTTTAATCTAC
64 AGATAAGACTTGTAACTTCAATCT-C
* *
25538384 TCCGCTGCAACTTTAGGGAGATAAGATT
1 TCCACTGCAACTTTAGGGAAATAAGATT
25538412 TGCCATGATC
Statistics
Matches: 166, Mismatches: 25, Indels: 32
0.74 0.11 0.14
Matches are distributed among these distances:
84 1 0.01
85 25 0.15
86 3 0.02
87 1 0.01
88 1 0.01
89 62 0.37
90 37 0.22
91 1 0.01
92 2 0.01
93 3 0.02
94 29 0.17
95 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (88 bp):
TCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTGTAGTCTGCTCCACTGCAACTTCAGGGAG
ATAAGACTTGTAACTTCAATCTC
Found at i:25540125 original size:12 final size:12
Alignment explanation
Indices: 25540108--25540154 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
25540098 CCTTGGCCTC
25540108 TCCTTTTTCTTT
1 TCCTTTTTCTTT
*
25540120 TCCTTTTTTTTT
1 TCCTTTTTCTTT
*
25540132 TCCTTCTT-TTT
1 TCCTTTTTCTTT
25540143 T-C-TTTTCTTT
1 TCCTTTTTCTTT
25540153 TC
1 TC
25540155 TCATCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 3 0.10
10 5 0.17
11 4 0.13
12 18 0.60
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TCCTTTTTCTTT
Found at i:25541024 original size:4 final size:4
Alignment explanation
Indices: 25541015--25541042 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25541005 CAATATGATT
25541015 ATGA ATGA ATGA ATGA ATGA ATGA ATGA
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA
25541043 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATGA
Found at i:25545552 original size:30 final size:30
Alignment explanation
Indices: 25545517--25545576 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
25545507 GATGCAAGTA
25545517 TGATACACAATCAAAA-TCGAGTCTCAGTCG
1 TGATACACAATCAAAACT-GAGTCTCAGTCG
25545547 TGATACACAATCAAAACTGAGTCTCAGTCG
1 TGATACACAATCAAAACTGAGTCTCAGTCG
25545577 AGCTTACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (30 bp):
TGATACACAATCAAAACTGAGTCTCAGTCG
Found at i:25546879 original size:22 final size:23
Alignment explanation
Indices: 25546853--25546936 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 23
25546843 ACCCTACCAA
25546853 AGAGCAAC-GAAGTGCTAAACAG
1 AGAGCAACAGAAGTGCTAAACAG
* *
25546875 AGAGC-ACAAAAGTGCTAATCAG
1 AGAGCAACAGAAGTGCTAAACAG
* * *
25546897 AGAGC-ACCGAAGTGCTGAACAA
1 AGAGCAACAGAAGTGCTAAACAG
*
25546919 AGAG-TACAGAAGTGCTAA
1 AGAGCAACAGAAGTGCTAA
25546937 TCAATTAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.04
22 49 0.96
ACGTcount: A:0.44, C:0.18, G:0.26, T:0.12
Consensus pattern (23 bp):
AGAGCAACAGAAGTGCTAAACAG
Found at i:25546932 original size:44 final size:44
Alignment explanation
Indices: 25546853--25546939 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
25546843 ACCCTACCAA
*
25546853 AGAGCAACGAAGTGCTAAACAGAGAGCACAAAAGTGCTAATCAG
1 AGAGCAACGAAGTGCTAAACAAAGAGCACAAAAGTGCTAATCAG
* * * *
25546897 AGAGCACCGAAGTGCTGAACAAAGAGTACAGAAGTGCTAATCA
1 AGAGCAACGAAGTGCTAAACAAAGAGCACAAAAGTGCTAATCA
25546940 ATTAATAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (44 bp):
AGAGCAACGAAGTGCTAAACAAAGAGCACAAAAGTGCTAATCAG
Found at i:25554256 original size:17 final size:17
Alignment explanation
Indices: 25554228--25554267 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25554218 TAAAAACTTG
*
25554228 AAATAA-AAAAATATCA
1 AAATAATAAAAATAACA
25554244 AAATAATAAAAATAACA
1 AAATAATAAAAATAACA
*
25554261 ACATAAT
1 AAATAAT
25554268 TCAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAATAAAAATAACA
Found at i:25555750 original size:3 final size:3
Alignment explanation
Indices: 25555744--25555769 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25555734 TAATAGTAGT
25555744 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
25555770 TACTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:25555825 original size:27 final size:26
Alignment explanation
Indices: 25555795--25555852 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
25555785 AACCTAATGT
* *
25555795 TAATAACAATAATCAAAATAACTATGA
1 TAATAAAAATAATCAAAATAAATAT-A
**
25555822 TAATAAAAATAATCCTAATAAATATA
1 TAATAAAAATAATCAAAATAAATATA
25555848 TAATA
1 TAATA
25555853 CTAATAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (26 bp):
TAATAAAAATAATCAAAATAAATATA
Found at i:25555856 original size:17 final size:15
Alignment explanation
Indices: 25555822--25555865 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
25555812 ATAACTATGA
*
25555822 TAATAAAAATAATCC
1 TAATAAAAATAATAC
25555837 TAATAAATATATAATAC
1 TAATAAA-A-ATAATAC
25555854 TAATAAACAATA
1 TAATAAA-AATA
25555866 TAGTAGTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 4 0.16
17 14 0.56
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAAAAATAATAC
Found at i:25563342 original size:15 final size:15
Alignment explanation
Indices: 25563322--25563350 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25563312 CCCTTGACAG
25563322 TTCATACTCCACACC
1 TTCATACTCCACACC
25563337 TTCATACTCCACAC
1 TTCATACTCCACAC
25563351 GTTGAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCATACTCCACACC
Found at i:25571166 original size:18 final size:20
Alignment explanation
Indices: 25571125--25571166 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
25571115 AAAATGGAAT
* *
25571125 ATTTAATATAAATAATATAT
1 ATTTAATATAAATAATAGAA
25571145 ATTT-ATAT-AATAATAGAA
1 ATTTAATATAAATAATAGAA
25571163 ATTT
1 ATTT
25571167 TAAAAGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTTAATATAAATAATAGAA
Found at i:25573134 original size:100 final size:100
Alignment explanation
Indices: 25572961--25573734 Score: 901
Period size: 100 Copynumber: 8.0 Consensus size: 100
25572951 AACTTTTGGA
** * * ** *
25572961 AAGTAAGATTCGCCATTGTGGCCTTAATCTTTTTAACTGCAATGTCCAGGAATCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* *
25573026 ATGTGGCTTTAATCTGTTCCACTGCACCACCAAGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * * *
25573061 AAGTAGGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGG-AGCCAAGATTCACC
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAG-CAAGATTCACC
* * * * *
25573125 GTTGTGGCTTTAATCTGCTCTACTGCATCGCCAGAG
65 GATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * * * * * *
25573161 AGGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAATATCGGGGAAGC--GATTCACCA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * *
25573224 ATGTGGCTTTAATCCGTTCCACTGCATCGCCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * *
25573259 GAGATAAGATTTGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC
1 AAG-TAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACC
* * * *
25573324 GATTTGGCTTTAATCTGTTCTACTGCATCGCCATGG
65 GATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * * *
25573360 AAGTATGATTCGATGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAG--TGATTCACCA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
25573423 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* *
25573458 AAGTAAGATTCACTGTTGTAGCTTTAA------T--CTGCAATGTTGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
25573515 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * *
25573550 AAGTAAGATTTGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC-A-ATTCACCA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* *
25573613 ATGTGGCTTTAATCTCTTCCAATGCACCGCCAGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * *
25573648 AAGTAAAACTCGCTGTTGTAGCTTTAA------T--CTGCAATGTCGGGGAAGCAAGATTCGCCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * *
25573705 TTGTGGCTTTAATCTGTTTCACTACACCGC
66 ATGTGGCTTTAATCTGTTCCACTGCACCGC
25573735 TTGGGAGATA
Statistics
Matches: 576, Mismatches: 81, Indels: 42
0.82 0.12 0.06
Matches are distributed among these distances:
90 34 0.06
91 1 0.00
92 100 0.17
98 165 0.29
99 46 0.08
100 188 0.33
101 42 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
Found at i:25573488 original size:50 final size:50
Alignment explanation
Indices: 25572961--25573678 Score: 349
Period size: 50 Copynumber: 14.6 Consensus size: 50
25572951 AACTTTTGGA
* * * * ** *
25572961 AAGTAAGATTCGCCATTGTGGCCTTAATCTTTTTAACTGCAATGTCCA-GG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACG-CCAGGG
* * * *
25573011 AA-TCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCACCAAGG
1 AAGT-AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * * ** * * *
25573061 AAGTAGGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * * *
25573111 -AGCCAAGATTCACCGTTGTGGCTTTAATCTGCTCTACTGCATCGCCAGAG
1 AAG-TAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * * * ** *** *
25573161 AGGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAATATCGGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* ** * * *
25573211 AAG--CGATTCACCAATGTGGCTTTAATCCGTTCCACTGCATCGCCTGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* **** * * ** * * *
25573259 GAGATAAGATTTGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG
1 AAG-TAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * *
25573310 AAGCAAGATTCACCGATT-TGGCTTTAATCTGTTCTACTGCATCGCCATGG
1 AAGTAAGATTCACCG-TTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * * ** * * *
25573360 AAGTATGATTCGA-TGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG
1 AAGTAAGATTC-ACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
** *
25573410 AAGT--GATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * **
25573458 AAGTAAGATTCACTGTTGTAGCTTTAATCTG---CAATG--TTG---GGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * *
25573500 AAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
** ** * * ** * * *
25573550 AAGTAAGATTTGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* ** * * *
25573600 AAG-CA-ATTCACCAATGTGGCTTTAATCTCTTCCAATGCACCGCCAGGG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
* * * * *
25573648 AAGTAAAACTCGCTGTTGTAGCTTTAATCTG
1 AAGTAAGATTCACCGTTGTGGCTTTAATCTG
25573679 CAATGTCGGG
Statistics
Matches: 474, Mismatches: 170, Indels: 48
0.68 0.25 0.07
Matches are distributed among these distances:
42 30 0.06
45 5 0.01
47 6 0.01
48 102 0.22
49 10 0.02
50 285 0.60
51 36 0.08
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (50 bp):
AAGTAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCAACGCCAGGG
Found at i:25573546 original size:92 final size:91
Alignment explanation
Indices: 25573391--25573734 Score: 442
Period size: 92 Copynumber: 3.7 Consensus size: 91
25573381 CTTTAATCTT
*
25573391 TTTAA-CTGCAATGTCGGGGAAG-TGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCC
1 TTTAATCTGCAATGTCGGGGAAGCAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCC
*
25573454 AGGGAAGTAAGATTCACTGTTGTAGC
66 AGGGAAGTAAGATTCGCTGTTGTAGC
* *
25573480 TTTAATCTGCAATGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGC
1 TTTAATCTGCAATGTCGGGGAAGC-AGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGC
* *
25573545 CAGGGAAGTAAGATTTGCTATTGTAGC
65 CAGGGAAGTAAGATTCGCTGTTGTAGC
* *
25573572 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCA-ATTCACCAATGTGGCTTTAATCTCTTCCAAT
1 TTTAA------T--CTGCAATGTCGGGGAAGCAGATTCACCAATGTGGCTTTAATCTGTTCCACT
* *
25573636 GCACCGCCAGGGAAGTAAAACTCGCTGTTGTAGC
58 GCACCGCCAGGGAAGTAAGATTCGCTGTTGTAGC
* ** * *
25573670 TTTAATCTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTTCACTACACCGC
1 TTTAATCTGCAATGTCGGGGAAGC-AGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGC
25573735 TTGGGAGATA
Statistics
Matches: 221, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
89 5 0.02
90 34 0.15
91 1 0.00
92 99 0.45
98 64 0.29
99 1 0.00
100 17 0.08
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (91 bp):
TTTAATCTGCAATGTCGGGGAAGCAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCC
AGGGAAGTAAGATTCGCTGTTGTAGC
Found at i:25573577 original size:190 final size:190
Alignment explanation
Indices: 25572961--25573734 Score: 911
Period size: 190 Copynumber: 4.0 Consensus size: 190
25572951 AACTTTTGGA
* * ** * *
25572961 AAGTAAGATTCGCCATTGTGGCCTTAATCTTTTTAACTGCAATGTCCAGGAATCAAGATTCACCG
1 AAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC--GATTCACCA
* * *
25573026 ATGTGGCTTTAATCTGTTCCACTGCACCACCAAGGAAGTAGGATTCACTGTTGTAGCTTTAATCT
64 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATC-
* * * * *
25573091 TTTTAACCGCAATGTCAGGG-AGCCAAGATTCACCGTTGTGGCTTTAATCTGCTCTACTGCATCG
128 ---T----GCAATGTCGGGGAAG-CAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCG
*
25573155 CCAGAG
185 CCAGGG
* * ** * *
25573161 AGGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAATATCGGGGAAGCGATTCACCAAT
1 AAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCAAT
* * * * ***
25573226 GTGGCTTTAATCCGTTCCACTGCATCGCCTGGGGAGATAAGATTTGTTGTTGTAGCTTTAATCTT
66 GTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAG-TAAGATTCACTGTTGTAGCTTTAA----
* * *
25573291 TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATTTGGCTTTAATCTGTTCTACTGCATCGCC
126 --T--CTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCC
*
25573356 ATGG
187 AGGG
* *** *
25573360 AAGTATGATTCGATGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTGATTCACCAAT
1 AAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCAAT
25573425 GTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGC
66 GTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGC
*
25573490 AATGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
131 AATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
* * *
25573550 AAGTAAGATTTGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAATTCACCAAT
1 AAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCAAT
* * * * *
25573615 GTGGCTTTAATCTCTTCCAATGCACCGCCAGGGAAGTAAAACTCGCTGTTGTAGCTTTAATCTGC
66 GTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGC
* * * *
25573680 AATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTTCACTACACCGC
131 AATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGC
25573735 TTGGGAGATA
Statistics
Matches: 502, Mismatches: 62, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
190 228 0.45
192 1 0.00
198 61 0.12
199 162 0.32
200 47 0.09
203 1 0.00
205 1 0.00
207 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (190 bp):
AAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGATTCACCAAT
GTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGC
AATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGG
Found at i:25573651 original size:98 final size:101
Alignment explanation
Indices: 25573480--25573677 Score: 303
Period size: 98 Copynumber: 2.0 Consensus size: 101
25573470 CTGTTGTAGC
* * * *
25573480 TTTAATCTGCAATGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGC
1 TTTAATCTGCAATGTCGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTCTTCCAATGCACCGC
* * *
25573545 CAGGGAAGTAAGATTTGCTATTGTAGCTTTAATCTT
66 CAGGGAAGTAAAACTCGCTATTGTAGCTTTAATCTT
25573581 TTTAA-CTGCAATGTCGGGGAAGC-A-ATTCACCAATGTGGCTTTAATCTCTTCCAATGCACCGC
1 TTTAATCTGCAATGTCGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTCTTCCAATGCACCGC
*
25573643 CAGGGAAGTAAAACTCGCTGTTGTAGCTTTAATCT
66 CAGGGAAGTAAAACTCGCTATTGTAGCTTTAATCT
25573678 GCAATGTCGG
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
98 66 0.74
99 1 0.01
100 17 0.19
101 5 0.06
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (101 bp):
TTTAATCTGCAATGTCGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTCTTCCAATGCACCGC
CAGGGAAGTAAAACTCGCTATTGTAGCTTTAATCTT
Found at i:25573964 original size:98 final size:96
Alignment explanation
Indices: 25573798--25574175 Score: 463
Period size: 98 Copynumber: 4.0 Consensus size: 96
25573788 ATAAGACCTG
* *
25573798 ATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAA
1 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTTTATTTTAATCCGCTCCACTGTAA
* *
25573863 TCTCAGGGAAATAGGATTACTGGCTTCAATCT
65 TCTCAGGGAGATAGGATTACTAGCTTCAATCT
25573895 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTA
1 -ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTTTATTTTAATCCGCTCCACTGTA
25573960 ATCTCAGGGAGATAGGATTACTAGCTTCAATC-
64 ATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * ** * *
25573992 -T--G-----CTCTGCTGTAA-TCTCAGGGAGATAAGAT-TTCTGGCTTCAATCTGCTCCACTGT
1 ATGCGATCTACTCTACTGTAACT-TCAGAGAGATAAGATCTT-T-ATTTTAATCCGCTCCACTGT
* ** *
25574047 AATCTCAGGGAGATAAGATTTTTGGCTTCAATCT
63 AATCTCAGGGAGATAGGATTACTAGCTTCAATCT
* * *
25574081 ATTGCGATCTACTCTACTGTAACTTCAGAGAGATAAAATCATTATTTTAATCTGCTCCACTGTAA
1 A-TGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTATTTTAATCCGCTCCACTGTAA
25574146 TCTCAGGGAGATAGGATTACTAGCTTCAAT
65 TCTCAGGGAGATAGGATTACTAGCTTCAAT
25574176 TTGCTCCACT
Statistics
Matches: 240, Mismatches: 25, Indels: 31
0.81 0.08 0.10
Matches are distributed among these distances:
86 2 0.01
87 2 0.01
88 69 0.29
91 1 0.00
93 2 0.01
95 1 0.00
97 45 0.19
98 116 0.48
99 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (96 bp):
ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTATTTTAATCCGCTCCACTGTAAT
CTCAGGGAGATAGGATTACTAGCTTCAATCT
Found at i:25573973 original size:44 final size:42
Alignment explanation
Indices: 25573901--25574251 Score: 240
Period size: 44 Copynumber: 7.8 Consensus size: 42
25573891 ATCTGATGCG
* * * * *
25573901 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTACTTCA
* * *
25573945 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTCA
** *
25573989 ATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT-T-ACTTCA
*
25574033 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TTTT-ACTTCA
* * * * *
25574077 ATCTATTGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAAATCATTATTTTA
1 ATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT-TTTACTTCA
* *
25574130 ATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTCA
* * *
25574174 ATTTGCTCCACTGTAATCTCAGGAAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT-T-ACTTCA
*
25574218 ATCTGCTCCACTGTAA-CATCAGAGAGATAAGATT
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
25574252 CACCATTTCT
Statistics
Matches: 246, Mismatches: 37, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
42 1 0.00
43 24 0.10
44 177 0.72
45 5 0.02
46 2 0.01
47 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 2 0.01
52 1 0.00
53 9 0.04
54 21 0.09
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTACTTCA
Found at i:25574204 original size:185 final size:186
Alignment explanation
Indices: 25573846--25574251 Score: 647
Period size: 185 Copynumber: 2.2 Consensus size: 186
25573836 CCTTTATTTT
* * * *
25573846 AATCCGCTCTACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGATGCGATCTACTCTA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGATGCGATCTACTCTA
* *
25573911 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTGTAACTTCAGAGAGATAAAATCCATTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
** *
25573976 ATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
131 ATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGAAGATAAGATTTCTGGCTTC
**
25574032 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTTGGCTTCAATCT-ATTGCGATCTACTCT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGA-TGCGATCTACTCT
*
25574096 ACTGTAACTTCAGAGAGATAAAAT-CATTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAG
65 ACTGTAACTTCAGAGAGATAAAATCCATTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
*
25574160 GATTACTAGCTTCAATTTGCTCCACTGTAATCTCAGGAAGATAAGATTTCTGGCTTC
130 GATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGAAGATAAGATTTCTGGCTTC
*
25574217 AATCTGCTCCACTGTAA-CATCAGAGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
25574252 CACCATTTCT
Statistics
Matches: 204, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
184 1 0.00
185 124 0.61
186 79 0.39
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (186 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGATGCGATCTACTCTA
CTGTAACTTCAGAGAGATAAAATCCATTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
ATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGAAGATAAGATTTCTGGCTTC
Found at i:25575661 original size:14 final size:14
Alignment explanation
Indices: 25575642--25575697 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
25575632 TTAGCATCTC
*
25575642 CATTTTTACTTTTT
1 CATTTTCACTTTTT
25575656 CATTTTCA-TTTTT
1 CATTTTCACTTTTT
* * *
25575669 TATATTCATTTTTT
1 CATTTTCACTTTTT
*
25575683 AATTTTTCACTTTTT
1 CA-TTTTCACTTTTT
25575698 TTTGAGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.32
14 13 0.38
15 10 0.29
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTCACTTTTT
Found at i:25576565 original size:22 final size:22
Alignment explanation
Indices: 25576522--25576567 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25576512 CTTTGGCCTC
* *
25576522 TCCTTTTTTCTTTTTTTCCTTT
1 TCCTTTTTTCTTTCTCTCCTTT
*
25576544 TCCTTTTTTCTCTTCTCTCTTTT
1 TCCTTTTTTCT-TTCTCTCCTTT
25576567 T
1 T
25576568 TCATTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TCCTTTTTTCTTTCTCTCCTTT
Found at i:25576631 original size:33 final size:37
Alignment explanation
Indices: 25576585--25576657 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 37
25576575 CATTTTGACC
25576585 TTGACTTTGA-TTTTTCTTTTT-CTT-CT-TTTTGTT
1 TTGACTTTGATTTTTTCTTTTTGCTTGCTCTTTTGTT
* *
25576618 TTGATTTTGATTTTTTCTTTTTGCTTGCTCTTTTTTT
1 TTGACTTTGATTTTTTCTTTTTGCTTGCTCTTTTGTT
25576655 TTG
1 TTG
25576658 GATCTGAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 9 0.26
34 11 0.32
35 3 0.09
36 2 0.06
37 9 0.26
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (37 bp):
TTGACTTTGATTTTTTCTTTTTGCTTGCTCTTTTGTT
Found at i:25581380 original size:3 final size:3
Alignment explanation
Indices: 25581372--25581416 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
25581362 TAGTGACCAG
25581372 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25581417 ACCCGTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25585584 original size:17 final size:17
Alignment explanation
Indices: 25585529--25585600 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
25585519 ATATTATTTT
25585529 TTTAAAAA-AT-AAAAA
1 TTTAAAAATATAAAAAA
*
25585544 TTATGAAAAA-ATAAAAACTC
1 TT-T-AAAAATATAAAAA--A
25585564 TTTAAAAATA-AAATAAA
1 TTTAAAAATATAAA-AAA
25585581 TTTAAAAATATAAAAAA
1 TTTAAAAATATAAAAAA
25585598 TTT
1 TTT
25585601 CAAACTTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.04
16 1 0.02
17 23 0.49
18 15 0.32
19 4 0.09
20 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
TTTAAAAATATAAAAAA
Found at i:25595411 original size:282 final size:282
Alignment explanation
Indices: 25594907--25595469 Score: 1108
Period size: 282 Copynumber: 2.0 Consensus size: 282
25594897 CATACTTTGC
* *
25594907 CCTTTTTCAATAAGTCCGTCAAGGGTGTAGTGATCTTGGAGTAGCCTTCAATGAAACGTCGATAG
1 CCTTTTTCAACAAGTCCGTCAAGGGTGTAGTGATCTTGGAATAGCCTTCAATGAAACGTCGATAG
25594972 TAGTTTGCTAAACCAAGAAAGGACCGCAATTCCGTTACCTTGGTTGGTGGCTCCCAATCGGAAAT
66 TAGTTTGCTAAACCAAGAAAGGACCGCAATTCCGTTACCTTGGTTGGTGGCTCCCAATCGGAAAT
25595037 TGCTCGGACTTTGCTTGCATCCATTCGGATCATGCCACCTCCTACAATATGGCCAAGAAAAGGCA
131 TGCTCGGACTTTGCTTGCATCCATTCGGATCATGCCACCTCCTACAATATGGCCAAGAAAAGGCA
25595102 CCTCTCGTTGGGCAAATGAGCATTTTTCCTCTTTGACATACAGCTCATTTTCCCGTAGGACTTGG
196 CCTCTCGTTGGGCAAATGAGCATTTTTCCTCTTTGACATACAGCTCATTTTCCCGTAGGACTTGG
25595167 AACACCTCTCTCAGATGTCCAT
261 AACACCTCTCTCAGATGTCCAT
25595189 CCTTTTTCAACAAGTCCGTCAAGGGTGTAGTGATCTTGGAATAGCCTTCAATGAAACGTCGATAG
1 CCTTTTTCAACAAGTCCGTCAAGGGTGTAGTGATCTTGGAATAGCCTTCAATGAAACGTCGATAG
25595254 TAGTTTGCTAAACCAAGAAAGGACCGCAATTCCGTTACCTTGGTTGGTGGCTCCCAATCGGAAAT
66 TAGTTTGCTAAACCAAGAAAGGACCGCAATTCCGTTACCTTGGTTGGTGGCTCCCAATCGGAAAT
25595319 TGCTCGGACTTTGCTTGCATCCATTCGGATCATGCCACCTCCTACAATATGGCCAAGAAAAGGCA
131 TGCTCGGACTTTGCTTGCATCCATTCGGATCATGCCACCTCCTACAATATGGCCAAGAAAAGGCA
25595384 CCTCTCGTTGGGCAAATGAGCATTTTTCCTCTTTGACATACAGCTCATTTTCCCGTAGGACTTGG
196 CCTCTCGTTGGGCAAATGAGCATTTTTCCTCTTTGACATACAGCTCATTTTCCCGTAGGACTTGG
25595449 AACACCTCTCTCAGATGTCCA
261 AACACCTCTCTCAGATGTCCA
25595470 ACATGCTCCT
Statistics
Matches: 279, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
282 279 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (282 bp):
CCTTTTTCAACAAGTCCGTCAAGGGTGTAGTGATCTTGGAATAGCCTTCAATGAAACGTCGATAG
TAGTTTGCTAAACCAAGAAAGGACCGCAATTCCGTTACCTTGGTTGGTGGCTCCCAATCGGAAAT
TGCTCGGACTTTGCTTGCATCCATTCGGATCATGCCACCTCCTACAATATGGCCAAGAAAAGGCA
CCTCTCGTTGGGCAAATGAGCATTTTTCCTCTTTGACATACAGCTCATTTTCCCGTAGGACTTGG
AACACCTCTCTCAGATGTCCAT
Found at i:25597073 original size:105 final size:105
Alignment explanation
Indices: 25596891--25597099 Score: 400
Period size: 105 Copynumber: 2.0 Consensus size: 105
25596881 CGTAGAAGTT
*
25596891 CTCTGCCTCAGCCATAGCTACAGTCAAATCGGTGATGCCTAGGCGGCGCAACTCTTGCTTAGCCC
1 CTCTGCCTCAGCCATAGCTACAGTCAAATCGGTGATACCTAGGCGGCGCAACTCTTGCTTAGCCC
25596956 ACATTCTTAGCCCATCCTCAAACATATAAAATGCTTCCTC
66 ACATTCTTAGCCCATCCTCAAACATATAAAATGCTTCCTC
*
25596996 CTCTGCCTCAGCCATAGCTACGGTCAAATCGGTGATACCTAGGCGGCGCAACTCTTGCTTAGCCC
1 CTCTGCCTCAGCCATAGCTACAGTCAAATCGGTGATACCTAGGCGGCGCAACTCTTGCTTAGCCC
25597061 ACATTCTTAGCCCATCCTCAAACATATAAAATGCTTCCT
66 ACATTCTTAGCCCATCCTCAAACATATAAAATGCTTCCT
25597100 TCTCATTCAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (105 bp):
CTCTGCCTCAGCCATAGCTACAGTCAAATCGGTGATACCTAGGCGGCGCAACTCTTGCTTAGCCC
ACATTCTTAGCCCATCCTCAAACATATAAAATGCTTCCTC
Found at i:25597985 original size:22 final size:22
Alignment explanation
Indices: 25597927--25597985 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
25597917 GAATGGTATC
25597927 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
25597949 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
25597972 TACATATCAAATCT
1 TACAAATCAAATCT
25597986 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:25606195 original size:12 final size:12
Alignment explanation
Indices: 25606178--25606203 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25606168 TTCATCATGG
25606178 TATCTGATTTTT
1 TATCTGATTTTT
25606190 TATCTGATTTTT
1 TATCTGATTTTT
25606202 TA
1 TA
25606204 GAATAAATTT
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:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (12 bp):
TATCTGATTTTT
Found at i:25629582 original size:12 final size:12
Alignment explanation
Indices: 25629565--25629589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25629555 GGTGTTCAGT
25629565 CGGTTAACCGAC
1 CGGTTAACCGAC
25629577 CGGTTAACCGAC
1 CGGTTAACCGAC
25629589 C
1 C
25629590 CGAAATTCTT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:25629764 original size:9 final size:9
Alignment explanation
Indices: 25629750--25629875 Score: 189
Period size: 9 Copynumber: 13.6 Consensus size: 9
25629740 TTTGGTTAAA
25629750 AATTACCCG
1 AATTACCCG
25629759 AATTACCCG
1 AATTACCCG
25629768 AATTACCCG
1 AATTACCCG
*
25629777 ACTTACCCG
1 AATTACCCG
25629786 AATTACCCG
1 AATTACCCG
*
25629795 ACTTACCCG
1 AATTACCCG
25629804 AATTACCCG
1 AATTACCCG
25629813 AATTACCCG
1 AATTACCCG
*
25629822 AAAATTACCCA
1 --AATTACCCG
25629833 AATTACCCG
1 AATTACCCG
25629842 AATTACCCG
1 AATTACCCG
25629851 AAAATTACCCG
1 --AATTACCCG
25629862 AATTACCCG
1 AATTACCCG
25629871 AATTA
1 AATTA
25629876 AATCACTACA
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
9 90 0.84
11 17 0.16
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:25629839 original size:29 final size:28
Alignment explanation
Indices: 25629751--25629875 Score: 191
Period size: 29 Copynumber: 4.5 Consensus size: 28
25629741 TTGGTTAAAA
25629751 ATTACCCGAATTACCCG-AATTACCCGA
1 ATTACCCGAATTACCCGAAATTACCCGA
* *
25629778 CTTACCCGAATTACCCG-ACTTACCCGA
1 ATTACCCGAATTACCCGAAATTACCCGA
*
25629805 ATTACCCGAATTACCCGAAAATTACCCAA
1 ATTACCCGAATTACCCG-AAATTACCCGA
25629834 ATTACCCGAATTACCCGAAAATTACCCGA
1 ATTACCCGAATTACCCG-AAATTACCCGA
25629863 ATTACCCGAATTA
1 ATTACCCGAATTA
25629876 AATCACTACA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 41 0.46
29 49 0.54
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (28 bp):
ATTACCCGAATTACCCGAAATTACCCGA
Found at i:25629904 original size:17 final size:17
Alignment explanation
Indices: 25629882--25629942 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
25629872 ATTAAATCAC
25629882 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
25629899 TACATAAATCTTTTAATCAC
1 TACAT-AA--TTAAAAACAT
*
25629919 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
25629936 TACATAA
1 TACATAA
25629943 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:25629982 original size:37 final size:37
Alignment explanation
Indices: 25629876--25629988 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
25629866 ACCCGAATTA
* * *
25629876 AATCACTACATAATTAAAAACATTACATAAATCTTTT
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
25629913 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
25629950 AATCACTACATAATTAAAAATATTACACAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
25629986 AAT
1 AAT
25629989 TAAAACATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 6 0.08
37 66 0.92
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.34
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:25630056 original size:24 final size:24
Alignment explanation
Indices: 25630029--25630087 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
25630019 ATTCTCCATT
*
25630029 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
25630053 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
25630077 TATCTCCATTT
1 TATATCCATTT
25630088 GCATTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:25633575 original size:9 final size:9
Alignment explanation
Indices: 25633561--25633624 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
25633551 TTTGGTTAAA
25633561 AATTACCCG
1 AATTACCCG
25633570 AATTACCCG
1 AATTACCCG
25633579 AATTACCCG
1 AATTACCCG
*
25633588 -ATTAACCG
1 AATTACCCG
*
25633596 AATTAACCG
1 AATTACCCG
*
25633605 AATTAACCG
1 AATTACCCG
25633614 AATTACCCG
1 AATTACCCG
25633623 AA
1 AA
25633625 AATTACCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
8 7 0.13
9 45 0.87
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:25634306 original size:112 final size:106
Alignment explanation
Indices: 25634082--25634286 Score: 259
Period size: 106 Copynumber: 1.9 Consensus size: 106
25634072 TTTTTATTGT
* * *
25634082 AATTTTTATGTCGTTTTTAATTTATTTTAAAATTATTTTGTTAGTAACTATTATAAATTGTTTGT
1 AATTTTTATGTCGTTTTTAATTTATTTTAAAATTATTTTGTTAGTAAATATTATAAAGTATTTGT
*
25634147 TTAATTTAATGTTTATTGTGATTTGTTAGGTTATGAATGGA
66 TTAATTTAATGTTTATTGTGATTTGTTAGGTAATGAATGGA
* * *
25634188 AATTTTTATGT-TTTTTTAAATTTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTAAG
1 AATTTTTATGTCGTTTTT-AATTTATTTTAAAATTATTTTGTTAGTAA---AT-ATTA--TAAAG
* *
25634252 TATTTGTTTAGTTTAATGTTTATTGTTATTTGTTA
59 TATTTGTTTAATTTAATGTTTATTGTGATTTGTTA
25634287 TGAATGTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
105 5 0.06
106 39 0.46
109 1 0.01
110 4 0.05
112 35 0.42
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (106 bp):
AATTTTTATGTCGTTTTTAATTTATTTTAAAATTATTTTGTTAGTAAATATTATAAAGTATTTGT
TTAATTTAATGTTTATTGTGATTTGTTAGGTAATGAATGGA
Found at i:25634567 original size:22 final size:21
Alignment explanation
Indices: 25634542--25634585 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
25634532 ATTTTTTGAT
25634542 TATAATTATATTATTATTGTAC
1 TATAATTATATTATTATT-TAC
* *
25634564 TATATTTATCTTATTATTTAC
1 TATAATTATATTATTATTTAC
25634585 T
1 T
25634586 GTATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TATAATTATATTATTATTTAC
Found at i:25636314 original size:22 final size:23
Alignment explanation
Indices: 25636284--25636327 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
25636274 GTATTTATTT
*
25636284 AATTGAGATTCACTGGAACAAAG
1 AATTGAGATTCACTGCAACAAAG
*
25636307 AATT-AGATTCATTGCAACAAA
1 AATTGAGATTCACTGCAACAAA
25636328 CTTGGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (23 bp):
AATTGAGATTCACTGCAACAAAG
Found at i:25639376 original size:29 final size:31
Alignment explanation
Indices: 25639318--25639376 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
25639308 CCCTTCTATT
*
25639318 AAAAAAAAACATACTTTATGCTGCCTCTTTA
1 AAAAAAAAACATACTTTATGCTGCCCCTTTA
*
25639349 AAAAAACAAACA-A-TTTAT-CTTCCCCTTT
1 AAAAAA-AAACATACTTTATGCTGCCCCTTT
25639377 CTTTCTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.32
30 5 0.20
31 7 0.28
32 5 0.20
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAAAAAACATACTTTATGCTGCCCCTTTA
Found at i:25639380 original size:4 final size:4
Alignment explanation
Indices: 25639373--25639428 Score: 51
Period size: 4 Copynumber: 13.0 Consensus size: 4
25639363 TTATCTTCCC
*
25639373 CTTT CTTT CTTT CTTCT CCTT CTCTT CTTCT CTATT GCTTT CTTT -TTT
1 CTTT CTTT CTTT CTT-T CTTT CT-TT CTT-T CT-TT -CTTT CTTT CTTT
25639421 CTTT CTTT
1 CTTT CTTT
25639429 TTTTTACCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
3 3 0.07
4 25 0.57
5 13 0.30
6 3 0.07
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:25639386 original size:8 final size:8
Alignment explanation
Indices: 25639373--25639428 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 8
25639363 TTATCTTCCC
25639373 CTTTCTTT
1 CTTTCTTT
25639381 CTTTCTTCT
1 CTTTCTT-T
*
25639390 CCTTCTCTT
1 CTTTCT-TT
25639399 CTTCTCTATT
1 CTT-TCT-TT
25639409 GCTTTCTTT
1 -CTTTCTTT
25639418 -TTTCTTT
1 CTTTCTTT
25639425 CTTT
1 CTTT
25639429 TTTTTACCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
7 7 0.17
8 10 0.25
9 11 0.28
10 9 0.22
11 3 0.08
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.68
Consensus pattern (8 bp):
CTTTCTTT
Found at i:25639393 original size:18 final size:18
Alignment explanation
Indices: 25639366--25639423 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
25639356 AAACAATTTA
*
25639366 TCTTCCCCTTTCTTTCTT
1 TCTTCTCCTTTCTTTCTT
25639384 TCTTCTCC-TTCTCTTCTT
1 TCTTCTCCTTTCT-TTCTT
*
25639402 CTCTAT-TGCTTTCTTT-TT
1 -TCT-TCTCCTTTCTTTCTT
25639420 TCTT
1 TCTT
25639424 TCTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 7 0.21
18 14 0.41
19 7 0.21
20 5 0.15
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.64
Consensus pattern (18 bp):
TCTTCTCCTTTCTTTCTT
Found at i:25642772 original size:23 final size:25
Alignment explanation
Indices: 25642723--25642773 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
25642713 AAAGTATGGA
25642723 GAATAAATTTGTGTACAATAAAAAT
1 GAATAAATTTGTGTACAATAAAAAT
*
25642748 GAATAAATTTGTGT-TAA-AAAAAT
1 GAATAAATTTGTGTACAATAAAAAT
25642771 GAA
1 GAA
25642774 AAAAATAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
24 2 0.08
25 14 0.56
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (25 bp):
GAATAAATTTGTGTACAATAAAAAT
Found at i:25642785 original size:22 final size:23
Alignment explanation
Indices: 25642742--25642786 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25642732 TGTGTACAAT
* * *
25642742 AAAAATGAATAAATTTGTGTTAA
1 AAAAATGAAAAAAATAGTGTTAA
25642765 AAAAATGAAAAAAATAG-GTTAA
1 AAAAATGAAAAAAATAGTGTTAA
25642787 CGAGGTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (23 bp):
AAAAATGAAAAAAATAGTGTTAA
Found at i:25657408 original size:60 final size:60
Alignment explanation
Indices: 25657315--25657435 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
25657305 AATGGAAGGG
25657315 TAGTTTTATGTACAACAACTCTGTGTTGTTTAAGCTTTTGTAGGCCAATATTGCCAAAAA
1 TAGTTTTATGTACAACAACTCTGTGTTGTTTAAGCTTTTGTAGGCCAATATTGCCAAAAA
*
25657375 TAGTTTTATGTACAACAATTCTGTGTTGTTTAAGCTTTTGTAGGCCAATATTGCCAAAAA
1 TAGTTTTATGTACAACAACTCTGTGTTGTTTAAGCTTTTGTAGGCCAATATTGCCAAAAA
25657435 T
1 T
25657436 TGAGCCACAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (60 bp):
TAGTTTTATGTACAACAACTCTGTGTTGTTTAAGCTTTTGTAGGCCAATATTGCCAAAAA
Found at i:25659899 original size:12 final size:13
Alignment explanation
Indices: 25659877--25659910 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
25659867 TACTGATTTA
*
25659877 ATTTTTCTTTTTC
1 ATTTTTTTTTTTC
25659890 -TTTTTTTTTTTC
1 ATTTTTTTTTTTC
25659902 ATTTTTTTT
1 ATTTTTTTT
25659911 CGTTTTGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTTTTTTTTC
Found at i:25663815 original size:21 final size:22
Alignment explanation
Indices: 25663773--25663816 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
25663763 TCTTTAGGGT
* **
25663773 ATCTTCAAGGGTGTGTTGCGAC
1 ATCTTCAAGGCTGTGTCACGAC
25663795 ATCTTC-AGGCTGTGTCACGAC
1 ATCTTCAAGGCTGTGTCACGAC
25663816 A
1 A
25663817 CTGAAAGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (22 bp):
ATCTTCAAGGCTGTGTCACGAC
Found at i:25674040 original size:10 final size:10
Alignment explanation
Indices: 25674025--25674058 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
25674015 AATATATTAT
*
25674025 ATATGATATG
1 ATATGATATA
25674035 ATATGATATA
1 ATATGATATA
*
25674045 ATATTATATA
1 ATATGATATA
25674055 ATAT
1 ATAT
25674059 ATTTAGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (10 bp):
ATATGATATA
Found at i:25677718 original size:21 final size:20
Alignment explanation
Indices: 25677690--25677732 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
25677680 ATAGAGTACA
25677690 TTCTTGTTT-AATTATCATAT
1 TTCTTGTTTGAATTAT-ATAT
25677710 TTCTATGTTTGAATTATATAT
1 TTCT-TGTTTGAATTATATAT
25677731 TT
1 TT
25677733 AATGGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (20 bp):
TTCTTGTTTGAATTATATAT
Found at i:25681686 original size:43 final size:43
Alignment explanation
Indices: 25681639--25681724 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
25681629 TATGTGATTG
* *
25681639 ATATTGAAATGGA-AAATATGATAAATGAATATGAGATGAGAAA
1 ATATTG-AATGAACAAATATGAGAAATGAATATGAGATGAGAAA
* * *
25681682 ATATTGAATTAACAAATATGAGAAATGATTGTGAGATGAGAAA
1 ATATTGAATGAACAAATATGAGAAATGAATATGAGATGAGAAA
25681725 TGAAATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 4 0.11
43 33 0.89
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.27
Consensus pattern (43 bp):
ATATTGAATGAACAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:25682754 original size:49 final size:49
Alignment explanation
Indices: 25682675--25682771 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
25682665 TCTAGAAGGG
* * * *
25682675 ATAAATAGTAATAAGAGTGTAGATAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTAATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATGT
* *
25682724 ATAAATAGTGATAAGAGTGTAGACATTGGAAGACCAAATTTAGAAATG
1 ATAAATAGTAATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATG
25682772 CATAGCATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (49 bp):
ATAAATAGTAATAAGAGTGTAGACAGTGGAAGACCAAATTTAGAAATGT
Found at i:25689267 original size:43 final size:43
Alignment explanation
Indices: 25689206--25689291 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
25689196 TAAGTGATTG
* *
25689206 ATATTGAAATGGCAAATATGATAAATGAATATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
* * * *
25689249 ATATTGAATTGACAAATATGGGAAATGATTGTGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
25689292 TGAAATATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (43 bp):
ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:25690627 original size:49 final size:49
Alignment explanation
Indices: 25690550--25690646 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
25690540 TCTAGAAGGG
* * *
25690550 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
*
25690599 ATAAATAGTGATAAGAGAGTAGATAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATG
25690647 CATAGCATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGAGTAGACAGTGGAAGACCAAGTTTAGAAATGT
Found at i:25696666 original size:49 final size:49
Alignment explanation
Indices: 25696609--25696705 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
25696599 TCCATATAAA
* * *
25696609 ACTATACTTCTTTTATTTTACATTAATTAGAATAAGGTTTTTCAACCTT
1 ACTATACTTCATCTATTTGACATTAATTAGAATAAGGTTTTTCAACCTT
*
25696658 ACTATACTTCATCTATTTGACATTTATTAGAATAAGGTTTTTCAACCT
1 ACTATACTTCATCTATTTGACATTAATTAGAATAAGGTTTTTCAACCT
25696706 ATAAATATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.46
Consensus pattern (49 bp):
ACTATACTTCATCTATTTGACATTAATTAGAATAAGGTTTTTCAACCTT
Found at i:25698524 original size:14 final size:14
Alignment explanation
Indices: 25698505--25698532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25698495 AGACTCGGGT
25698505 TAGTTTTGATTTGG
1 TAGTTTTGATTTGG
25698519 TAGTTTTGATTTGG
1 TAGTTTTGATTTGG
25698533 CAGTGTACAA
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:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (14 bp):
TAGTTTTGATTTGG
Found at i:25702864 original size:45 final size:45
Alignment explanation
Indices: 25702800--25702889 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
25702790 GAGTCATTGG
*
25702800 GTATGTTGATTCTGATTTTGCTAGGGACCTTGATAAAAGAAAATC
1 GTATGTTGATTCTGATTTTGCTAGAGACCTTGATAAAAGAAAATC
25702845 GTATGTTGATTCTGATTTTGCTAGAGACCTTGATAAAAGAAAATC
1 GTATGTTGATTCTGATTTTGCTAGAGACCTTGATAAAAGAAAATC
25702890 TTTAATAGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (45 bp):
GTATGTTGATTCTGATTTTGCTAGAGACCTTGATAAAAGAAAATC
Found at i:25707165 original size:82 final size:83
Alignment explanation
Indices: 25707024--25707189 Score: 325
Period size: 82 Copynumber: 2.0 Consensus size: 83
25707014 AAAAAATACT
25707024 TTTTACATATGATTTAGAATATTTTAACAAAATTAATAATAGCTTCTACAACGATAAGCAAAAAC
1 TTTTACATATGATTTAGAATATTTTAACAAAATTAATAATAGCTTCTACAACGATAAGCAAAAAC
25707089 AATACCACAACTTCATCA
66 AATACCACAACTTCATCA
25707107 TTTTACATATGATTTAGAATATTTTAAC-AAATTAATAATAGCTTCTACAACGATAAGCAAAAAC
1 TTTTACATATGATTTAGAATATTTTAACAAAATTAATAATAGCTTCTACAACGATAAGCAAAAAC
25707171 AATACCACAACTTCATCA
66 AATACCACAACTTCATCA
25707189 T
1 T
25707190 AGCATACATA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 55 0.66
83 28 0.34
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (83 bp):
TTTTACATATGATTTAGAATATTTTAACAAAATTAATAATAGCTTCTACAACGATAAGCAAAAAC
AATACCACAACTTCATCA
Found at i:25710646 original size:22 final size:22
Alignment explanation
Indices: 25710619--25710660 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25710609 CAATAATTTA
25710619 AAAAATAAGATATTTTTTGTAT
1 AAAAATAAGATATTTTTTGTAT
**
25710641 AAAAATTTGATATTTTTTGT
1 AAAAATAAGATATTTTTTGT
25710661 GGTGACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
AAAAATAAGATATTTTTTGTAT
Found at i:25712747 original size:35 final size:34
Alignment explanation
Indices: 25712667--25712750 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
25712657 CAGGGCTTGG
* * * *
25712667 GATTTAAGGTTTATGGTTTGGAGTTTAATGTTTA
1 GATTTAAGGTTTAAGATTTGGAGTTTAAGGTTAA
* *
25712701 GATTTAGGGTTTAAGTATTTGGAGTTTAGGGTTCAA
1 GATTTAAGGTTTAAG-ATTTGGAGTTTAAGGTT-AA
25712737 G-TTTAAGGTTTAAG
1 GATTTAAGGTTTAAG
25712751 GGTTTAGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 13 0.32
35 26 0.63
36 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (34 bp):
GATTTAAGGTTTAAGATTTGGAGTTTAAGGTTAA
Found at i:25713197 original size:59 final size:55
Alignment explanation
Indices: 25713105--25713222 Score: 191
Period size: 59 Copynumber: 2.1 Consensus size: 55
25713095 GTTAAATTTT
*
25713105 TTTAAAATATTCTAAAATAATGATTTCGGGGACCTAAATAAGTTAATTAATGATTCAAG
1 TTTAAAATATTCTAAAATAATGATTTCGGGGACC----TAAGTTAATTAACGATTCAAG
25713164 TTTAAAATATTCTAAAATAATGATTTCGGGGACCTAAGTTAATTAACGATTCAAG
1 TTTAAAATATTCTAAAATAATGATTTCGGGGACCTAAGTTAATTAACGATTCAAG
25713219 TTTA
1 TTTA
25713223 TCATACTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
55 24 0.41
59 34 0.59
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (55 bp):
TTTAAAATATTCTAAAATAATGATTTCGGGGACCTAAGTTAATTAACGATTCAAG
Found at i:25715747 original size:20 final size:20
Alignment explanation
Indices: 25715713--25715754 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25715703 AACTATTTAA
** *
25715713 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
25715733 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
25715753 AT
1 AT
25715755 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:25719172 original size:11 final size:12
Alignment explanation
Indices: 25719149--25719179 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
25719139 CTTTAAAAAC
25719149 TATATATACAAA
1 TATATATACAAA
25719161 TATATA-ACAAA
1 TATATATACAAA
25719172 TATATATA
1 TATATATA
25719180 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATATACAAA
Found at i:25719821 original size:3 final size:3
Alignment explanation
Indices: 25719813--25719884 Score: 53
Period size: 3 Copynumber: 23.7 Consensus size: 3
25719803 ATAAATTTAA
* *
25719813 TAT TAT TAT TATT TAT TAT TAT TAGT TTT TAT T-T TCCT T-T TAT CTAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT -TAT
25719860 TCAT TAT TAT TA- TAT TAT TA- TAT TA
1 T-AT TAT TAT TAT TAT TAT TAT TAT TA
25719885 ATTAGTTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
2 8 0.14
3 37 0.64
4 13 0.22
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25719831 original size:13 final size:13
Alignment explanation
Indices: 25719813--25719984 Score: 54
Period size: 13 Copynumber: 13.5 Consensus size: 13
25719803 ATAAATTTAA
25719813 TATTATTATTATT
1 TATTATTATTATT
25719826 TATTATTATTAGTT
1 TATTATTATTA-TT
*
25719840 T-TTATT-TTCCTTT
1 TATTATTATT--ATT
25719853 TATCTATTCATTA-T
1 TAT-TATT-ATTATT
25719867 TATTA-TATTATT
1 TATTATTATTATT
25719879 ATATTAATTAGTT-TT
1 -TATT-ATTA-TTATT
*
25719894 GCATTATT-TT-TT
1 -TATTATTATTATT
25719906 TA-TATT-TTATT
1 TATTATTATTATT
*
25719917 T-GT-TTATT-TT
1 TATTATTATTATT
*
25719927 TAATTTTTAATT-TT
1 T-ATTATT-ATTATT
25719941 T-TTA-TATATATT
1 TATTATTAT-TATT
*
25719953 TA-TCTTATTATAT
1 TATTATTATTAT-T
*
25719966 CATT-TTATTATT
1 TATTATTATTATT
25719978 TATTATT
1 TATTATT
25719985 CACTTTTAGC
Statistics
Matches: 123, Mismatches: 10, Indels: 52
0.66 0.05 0.28
Matches are distributed among these distances:
10 13 0.11
11 13 0.11
12 22 0.18
13 41 0.33
14 19 0.15
15 11 0.09
16 2 0.02
17 2 0.02
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:25719915 original size:15 final size:14
Alignment explanation
Indices: 25719897--25719941 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
25719887 TAGTTTTGCA
25719897 TTATTTTTTTATATT
1 TTATTTTTTTAT-TT
*
25719912 TTATTTGTTTATTT
1 TTATTTTTTTATTT
* *
25719926 TTAATTTTTAATTT
1 TTATTTTTTTATTT
25719940 TT
1 TT
25719942 TTATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (14 bp):
TTATTTTTTTATTT
Found at i:25719939 original size:22 final size:22
Alignment explanation
Indices: 25719901--25719945 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25719891 TTTGCATTAT
*
25719901 TTTTTTATATTTTATTTGTTTA
1 TTTTTAATATTTTATTTGTTTA
*
25719923 TTTTTAAT-TTTTAATTTTTTTA
1 TTTTTAATATTTT-ATTTGTTTA
25719945 T
1 T
25719946 ATATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTAATATTTTATTTGTTTA
Found at i:25719982 original size:20 final size:21
Alignment explanation
Indices: 25719952--25719992 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
25719942 TTATATATAT
25719952 TTATCTTATTATATCA-TTTTA
1 TTATCTTATTAT-TCACTTTTA
25719973 TTAT-TTATTATTCACTTTTA
1 TTATCTTATTATTCACTTTTA
25719993 GCTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATCTTATTATTCACTTTTA
Found at i:25722343 original size:19 final size:19
Alignment explanation
Indices: 25722319--25722365 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
25722309 ATGTCTCTTT
*
25722319 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
25722338 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
25722357 TATGCATTA
1 TTTGCATTA
25722366 AAGTCCATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:25726801 original size:44 final size:45
Alignment explanation
Indices: 25726693--25726806 Score: 140
Period size: 45 Copynumber: 2.6 Consensus size: 45
25726683 TTACAAGTCT
* *** *
25726693 TATCTCCCTGAAGTTGCAGCGGAGCAGACTAAAGATGGTGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAATGAATCC
* * * *
25726738 TATTTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAATGAATCC
25726782 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
25726807 GAATTGAAGT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 27 0.47
45 31 0.53
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAATGAATCC
Found at i:25726830 original size:44 final size:44
Alignment explanation
Indices: 25726673--25726859 Score: 148
Period size: 44 Copynumber: 4.2 Consensus size: 44
25726663 CCCCAGAGAA
* *
25726673 CAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
1 CAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* * * *
25726717 CAGACTAAAGATGGT-GAA-TCTTATTTCCCTAAAGTTGCAGTGGAG
1 CAGATTAAAG-T--TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
** * *
25726762 CAGATTAAAGCCA-ATAATCCTATCTCCCTGAAGTTGCAGTGGAG
1 CAGATTAAAGTTACA-AGTCTTATCTCCCTGAAGTTGCAGTGGAG
* ** * * *
25726806 C-GAATTGAAGTTACAAGTCTTATCTATCTAAAGTTACAGCGGAG
1 CAG-ATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
*
25726850 CAGACTAAAG
1 CAGATTAAAG
25726860 CGAAGCAGAT
Statistics
Matches: 110, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 68 0.62
45 36 0.33
46 2 0.02
47 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
CAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
Found at i:25727083 original size:44 final size:44
Alignment explanation
Indices: 25727014--25727605 Score: 356
Period size: 44 Copynumber: 13.0 Consensus size: 44
25727004 AGATCAAGAC
* * * *
25727014 TGAAGATAACCAACCTTGTCTCCCTGAAGTTGCAGTGGAGCAGGT
1 TGAAGAT-ACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
25727059 TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * *
25727103 TGAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
1 TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * * *
25727147 T-AAAATGA-TCAATCCTATAC-CTCTGAAGTTACAGTAGATCGGAT
1 TGAAGAT-ACT-AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGAT
* ** * *
25727191 TAAATCTACCATAATGAACCTTAACTCCCTGAAGTTGCAGTGGAGCAGAC
1 TGAAGATA-C-TAAT----CTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * *
25727241 TGAAAATAGCGAATCTTATTTCCCTGAAGTTGCAGTAGAACAGAT
1 TGAAGATA-CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * ** * *
25727286 TAAAGCTATAAATTATCGATCTTATCTATCTGAAGTTGCAGTAGAGCA-AA
1 TGAAG--AT--ACTA---ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * * *
25727336 T-CATAT-CAAACCTTATCTCCTTGAAGTTGCAGTGGAGCAGGT
1 TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * * *
25727378 TAAAAATAAAC-AATCTTATCTCCTTAAAGTTACAGTGGAGCAGAT
1 TGAAGAT--ACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * *
25727423 TGAAGACAGGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
1 TGAAG--A---TACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* ** * * * *
25727472 TAAAGCCACAAACCTTATCTCCCTGAAGTTGCAGTAGG-GTAGGT
1 TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGAT
*
25727516 TGAAGATAC-AAGTATTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 TGAAGATACTAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* * * *
25727560 TGAAGATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGAT
1 TGAAGATA-CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
25727605 T
1 T
25727606 AAAGCTATAA
Statistics
Matches: 428, Mismatches: 84, Indels: 70
0.74 0.14 0.12
Matches are distributed among these distances:
41 25 0.06
42 1 0.00
43 11 0.03
44 174 0.41
45 105 0.25
46 6 0.01
47 6 0.01
48 3 0.01
49 41 0.10
50 30 0.07
51 26 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TGAAGATACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
Found at i:25729094 original size:3 final size:3
Alignment explanation
Indices: 25729086--25729161 Score: 52
Period size: 3 Copynumber: 24.7 Consensus size: 3
25729076 ATAAATTTGA
* *
25729086 TAT TAT TAT TATT TAT TAT TAT TAGT TTT TAT T-T TCCT T-T TAT CTAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT -TAT
25729133 CTAT TCAT TAT TAT TA- TAT TAT TA- TAT TA
1 -TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
25729162 ATTAGTTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
2 8 0.13
3 37 0.60
4 17 0.27
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:25729104 original size:13 final size:13
Alignment explanation
Indices: 25729086--25729161 Score: 61
Period size: 13 Copynumber: 5.8 Consensus size: 13
25729076 ATAAATTTGA
25729086 TATTATTATTATT
1 TATTATTATTATT
25729099 TATTATTATTAGTT
1 TATTATTATTA-TT
**
25729113 T-TTATT-TTCCT
1 TATTATTATTATT
25729124 T-TTATCTATCTATT
1 TATTAT-TAT-TATT
*
25729138 CATTATTATTATAT
1 TATTATTATTAT-T
25729152 TATTA-TATTA
1 TATTATTATTA
25729162 ATTAGTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
11 6 0.12
12 3 0.06
13 25 0.49
14 13 0.25
15 4 0.08
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:25729258 original size:20 final size:21
Alignment explanation
Indices: 25729228--25729268 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
25729218 TTATATATAT
25729228 TTATCTTATTATATCA-TTTTA
1 TTATCTTATTAT-TCACTTTTA
25729249 TTAT-TTATTATTCACTTTTA
1 TTATCTTATTATTCACTTTTA
25729269 GCTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATCTTATTATTCACTTTTA
Found at i:25729432 original size:19 final size:20
Alignment explanation
Indices: 25729380--25729432 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
25729370 TTTTTATAAT
*
25729380 TTTATTCATTTTCTTTATTA
1 TTTATTCATTTACTTTATTA
**
25729400 TCATTATTGTTTTACTTTA-TA
1 T--TTATTCATTTACTTTATTA
25729421 TTTATTCATTTA
1 TTTATTCATTTA
25729433 TCCATTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 9 0.35
20 1 0.04
21 3 0.12
22 13 0.50
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATTCATTTACTTTATTA
Done.