Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 84 of 221
Found at i:25302016 original size:25 final size:25
Alignment explanation
Indices: 25301946--25302019 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
25301936 AAAGCTTACC
* *
25301946 GATTCTCAGCTCGTATGAGCTTACT
1 GATTCACAGCTCGTATGAGCATACT
* *
25301971 GATTTACAACTCGTGA-GAGCATACT
1 GATTCACAGCTCGT-ATGAGCATACT
*
25301996 GATTCATAGCTCGTATGAGCATAC
1 GATTCACAGCTCGTATGAGCATAC
25302020 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
26 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (25 bp):
GATTCACAGCTCGTATGAGCATACT
Found at i:25305163 original size:27 final size:26
Alignment explanation
Indices: 25305133--25305308 Score: 145
Period size: 27 Copynumber: 6.5 Consensus size: 26
25305123 AATTGTACAG
* *
25305133 CACTAAATGTGCGATCTGACTATGTTA
1 CACTAAGTGTGCGATTTGACTATG-TA
** * *
25305160 CACTAAGTGTGCGAAATGAATATGATG
1 CACTAAGTGTGCGATTTGACTATG-TA
* * **
25305187 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGATTTGACTATG-TA
25305214 CACTAAGTGTGCGAGTTTGACTATGTA
1 CACTAAGTGTGCGA-TTTGACTATGTA
* *
25305241 GCACTAAGTGTGCGATTTGATTACGTA
1 -CACTAAGTGTGCGATTTGACTATGTA
* * *
25305268 GCACTAAGTGTGCGAGTTGATTATATA
1 -CACTAAGTGTGCGATTTGACTATGTA
*
25305295 GCACTGAGTGTGCG
1 -CACTAAGTGTGCG
25305309 GACTCAATAG
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
27 104 0.83
28 22 0.17
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (26 bp):
CACTAAGTGTGCGATTTGACTATGTA
Found at i:25305246 original size:82 final size:81
Alignment explanation
Indices: 25305132--25305287 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
25305122 AAATTGTACA
*
25305132 GCACTAAATGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAATGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
25305196 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* * ** *
25305213 GCACTAAGTGTGCGAGTTTGACTATG-TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAATGTGCGA-TCTGACTATGTTA-CACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
25305277 GTGCGAGTTGA
64 GTGCGAATTGA
25305288 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 16 0.25
82 48 0.74
83 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
GCACTAAATGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:25305254 original size:55 final size:54
Alignment explanation
Indices: 25305160--25305308 Score: 165
Period size: 55 Copynumber: 2.7 Consensus size: 54
25305150 GACTATGTTA
** * *
25305160 CACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACGCAG
* * ** *
25305214 CACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCAG
* * *
25305269 CACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 CACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
25305309 GACTCAATAG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 36 0.44
55 44 0.54
56 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (54 bp):
CACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCAG
Found at i:25305299 original size:82 final size:81
Alignment explanation
Indices: 25305128--25305308 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
25305118 GATTAAATTG
* *
25305128 TACAGCACTAAATGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATACGATGCACTAA
25305193 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
25305209 TGCGGCACTAAGTGTGCGAGTTTGACTATG-TAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTTA-CACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
25305272 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
25305291 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
25305309 GACTCAATAG
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 19 0.23
82 63 0.77
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTTACACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:25323532 original size:14 final size:14
Alignment explanation
Indices: 25323513--25323563 Score: 79
Period size: 13 Copynumber: 3.8 Consensus size: 14
25323503 TATCAAGTTG
25323513 TGAAAAAAAAATTT
1 TGAAAAAAAAATTT
*
25323527 TGAAAAAAAAATTG
1 TGAAAAAAAAATTT
25323541 TG-AAAAAAAA-TT
1 TGAAAAAAAAATTT
25323553 TGAAAAAAAAA
1 TGAAAAAAAAA
25323564 GAGAGCTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 3 0.09
13 16 0.47
14 15 0.44
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (14 bp):
TGAAAAAAAAATTT
Found at i:25323534 original size:12 final size:12
Alignment explanation
Indices: 25323517--25323561 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
25323507 AAGTTGTGAA
25323517 AAAAAAATTTTG
1 AAAAAAATTTTG
*
25323529 AAAAAAAAATTGTG
1 --AAAAAAATTTTG
*
25323543 AAAAAAAATTTG
1 AAAAAAATTTTG
25323555 AAAAAAA
1 AAAAAAA
25323562 AAGAGAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (12 bp):
AAAAAAATTTTG
Found at i:25323534 original size:13 final size:13
Alignment explanation
Indices: 25323516--25323562 Score: 69
Period size: 14 Copynumber: 3.6 Consensus size: 13
25323506 CAAGTTGTGA
25323516 AAAAAAAATTTTG
1 AAAAAAAATTTTG
*
25323529 AAAAAAAAATTGTG
1 -AAAAAAAATTTTG
25323543 AAAAAAAA-TTTG
1 AAAAAAAATTTTG
25323555 AAAAAAAA
1 AAAAAAAA
25323563 AGAGAGCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 11 0.35
13 8 0.26
14 12 0.39
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTTG
Found at i:25323541 original size:28 final size:26
Alignment explanation
Indices: 25323510--25323563 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
25323500 GGATATCAAG
25323510 TTGTGAAAAAAAAATTTTGAAAAAAAAA
1 TTGTG-AAAAAAAA-TTTGAAAAAAAAA
25323538 TTGTGAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAATTTGAAAAAAAAA
25323564 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.50
27 8 0.31
28 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (26 bp):
TTGTGAAAAAAAATTTGAAAAAAAAA
Found at i:25325009 original size:22 final size:22
Alignment explanation
Indices: 25324958--25325023 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
25324948 GGTATTTGGG
* *
25324958 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
25324979 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
25325001 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
25325024 TGAAAAAGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:25330811 original size:18 final size:18
Alignment explanation
Indices: 25330790--25330824 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25330780 TTTTTCTTTT
25330790 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
25330808 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
25330825 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:25331782 original size:12 final size:12
Alignment explanation
Indices: 25331778--25331835 Score: 64
Period size: 12 Copynumber: 4.6 Consensus size: 12
25331768 TTTTTTTCAC
25331778 TTTTTTTTGAATT
1 TTTTTTTTGAA-T
*
25331791 TTTTTTTCAATCAAT
1 TTTTTTT---TGAAT
25331806 TTTTTTTTGAAT
1 TTTTTTTTGAAT
25331818 TTTTTTTTG-AT
1 TTTTTTTTGAAT
25331829 TTTTTTT
1 TTTTTTT
25331836 GTTACTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 9 0.22
12 13 0.32
13 7 0.17
15 8 0.20
16 3 0.08
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:25333605 original size:30 final size:29
Alignment explanation
Indices: 25333570--25333639 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
25333560 AGTTTTTCCC
25333570 AGCTCGATTTAGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTAGCTCA-ATTGAGCTTAATTT
* * *
25333600 AGCTCGTTTGAGCTTAATTTAGCTTACTTT
1 AGCTCGTTT-AGCTCAATTGAGCTTAATTT
25333630 AGCTCGTTTA
1 AGCTCGTTTA
25333640 AGCTTGGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (29 bp):
AGCTCGTTTAGCTCAATTGAGCTTAATTT
Found at i:25333633 original size:20 final size:20
Alignment explanation
Indices: 25333576--25333633 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
25333566 TCCCAGCTCG
* * *
25333576 ATTTAGCTCACATGAGCTTA
1 ATTTAGCTTACTTTAGCTTA
25333596 ATTTAGC-T-CGTTTGAGCTTA
1 ATTTAGCTTAC-TTT-AGCTTA
25333616 ATTTAGCTTACTTTAGCT
1 ATTTAGCTTACTTTAGCT
25333634 CGTTTAAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 24 0.77
21 4 0.13
22 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (20 bp):
ATTTAGCTTACTTTAGCTTA
Found at i:25335922 original size:13 final size:13
Alignment explanation
Indices: 25335890--25335959 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 13
25335880 TAGGAGTAAC
25335890 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
25335901 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
25335914 AAAAAAAATTTGA
1 AAAAAAAATTCGA
25335927 TTGAAAAAAAATTC-A
1 ---AAAAAAAATTCGA
* *
25335942 TAAAAAAAGT-GA
1 AAAAAAAATTCGA
25335954 AAAAAA
1 AAAAAA
25335960 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.17
12 16 0.33
13 13 0.27
15 1 0.02
16 10 0.21
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:25337067 original size:6 final size:6
Alignment explanation
Indices: 25337037--25337144 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
25337027 AAAGAAATTG
* ** *
25337037 AAAG-A AAACAA AAAGAA AACA-AA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
25337084 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
25337135 AAAGAA AAAG
1 AAAGAA AAAG
25337145 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:25337126 original size:14 final size:13
Alignment explanation
Indices: 25337105--25337142 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25337095 AAAAGTGAGA
25337105 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25337117 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
25337132 GAAAAAGAAAA
1 GAAAAAGAAAA
25337143 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:25337156 original size:21 final size:21
Alignment explanation
Indices: 25337049--25337156 Score: 51
Period size: 24 Copynumber: 4.9 Consensus size: 21
25337039 AGAAAACAAA
*
25337049 AAGAAAACAAAAAAGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
**
25337070 AAATTGCAAAAG-AAAAAGAAATCG
1 -AA--G-AAAAGAAAAAAGAAAAAG
*
25337094 AA-AAAGTGAGAGAAAAAGAAAATG
1 AAGAAA---AGA-AAAAAGAAAAAG
**
25337118 AAGAAAAGAAAATTGAAAAAG
1 AAGAAAAGAAAAAAGAAAAAG
*
25337139 AA-AAAGCGAAAAAAGAAA
1 AAGAAA-AGAAAAAAGAAA
25337157 TTGAAAGAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 20 0.31
22 7 0.11
23 2 0.03
24 23 0.35
25 7 0.11
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (21 bp):
AAGAAAAGAAAAAAGAAAAAG
Found at i:25337196 original size:33 final size:33
Alignment explanation
Indices: 25337159--25337221 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25337149 AAAAGAAATT
25337159 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
25337192 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
25337222 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:25349816 original size:24 final size:25
Alignment explanation
Indices: 25349763--25349816 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
25349753 AACAAATTCT
* *
25349763 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
25349788 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
25349811 TTTTTT
1 TTTTTT
25349817 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:25352128 original size:13 final size:13
Alignment explanation
Indices: 25352112--25352137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25352102 TTTTTTCCAA
25352112 AACTTTTTTTTTT
1 AACTTTTTTTTTT
25352125 AACTTTTTTTTTT
1 AACTTTTTTTTTT
25352138 CGAAGCTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
AACTTTTTTTTTT
Found at i:25360989 original size:12 final size:11
Alignment explanation
Indices: 25360969--25361026 Score: 107
Period size: 11 Copynumber: 5.2 Consensus size: 11
25360959 TAGTAGTTTC
25360969 TTCAAAAAAAA
1 TTCAAAAAAAA
25360980 TTCAAAAAAAA
1 TTCAAAAAAAA
25360991 TTCAAAAAAAAA
1 TTC-AAAAAAAA
25361003 TTCAAAAAAAA
1 TTCAAAAAAAA
25361014 TTCAAAAAAAA
1 TTCAAAAAAAA
25361025 TT
1 TT
25361027 TGGTTTCCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
11 35 0.76
12 11 0.24
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:25361002 original size:23 final size:23
Alignment explanation
Indices: 25360972--25361024 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
25360962 TAGTTTCTTC
25360972 AAAAAAAATTCAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAATTCA
25360995 AAAAAAAATTCAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAATTCA
25361018 AAAAAAA
1 AAAAAAA
25361025 TTTGGTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAATTCA
Found at i:25361087 original size:16 final size:17
Alignment explanation
Indices: 25361066--25361106 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
25361056 TATCAAGTTG
25361066 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
25361082 AAAAAAAAATTTTCGTGA
1 AAAAAAAAA-TTTCGTGA
25361100 AAAAAAA
1 AAAAAAA
25361107 GAAGCTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:25363411 original size:4 final size:4
Alignment explanation
Indices: 25363402--25363433 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25363392 TTAAACTAAG
25363402 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
25363434 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:25364839 original size:23 final size:22
Alignment explanation
Indices: 25364787--25364839 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25364777 TCCACGTCTT
*
25364787 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
25364809 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
25364832 TTTCTTTT
1 TTTCTTTT
25364840 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:25365465 original size:20 final size:20
Alignment explanation
Indices: 25365442--25365495 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25365432 AGTTTTTCCC
*
25365442 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25365462 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25365482 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25365496 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25365477 original size:30 final size:30
Alignment explanation
Indices: 25365442--25365515 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25365432 AGTTTTTCCC
25365442 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25365472 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25365502 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25365516 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:25365505 original size:20 final size:20
Alignment explanation
Indices: 25365442--25365506 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25365432 AGTTTTTCCC
* * * *
25365442 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25365462 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25365481 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25365502 AGCTC
1 AGCTC
25365507 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:25367133 original size:13 final size:13
Alignment explanation
Indices: 25367115--25367148 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25367105 TTGGAGTAAC
25367115 AAAAAAATCAAAA
1 AAAAAAATCAAAA
* *
25367128 AAAAAATTCGAAA
1 AAAAAAATCAAAA
25367141 AAAAAAAT
1 AAAAAAAT
25367149 TTGATTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAATCAAAA
Found at i:25367141 original size:14 final size:13
Alignment explanation
Indices: 25367115--25367149 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
25367105 TTGGAGTAAC
25367115 AAAAAAA-TCAAA
1 AAAAAAATTCAAA
25367127 AAAAAAATTCGAAA
1 AAAAAAATTC-AAA
25367141 AAAAAAATT
1 AAAAAAATT
25367150 TGATTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 2 0.10
14 12 0.57
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:25368262 original size:17 final size:18
Alignment explanation
Indices: 25368230--25368263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25368220 AAAAGAGAGT
*
25368230 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
25368248 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
25368264 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:25369552 original size:20 final size:20
Alignment explanation
Indices: 25369529--25369582 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25369519 AGTTTTTCCC
*
25369529 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25369549 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25369569 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25369583 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25369564 original size:30 final size:30
Alignment explanation
Indices: 25369529--25369602 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25369519 AGTTTTTCCC
25369529 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25369559 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25369589 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25369603 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:25369592 original size:20 final size:20
Alignment explanation
Indices: 25369529--25369593 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25369519 AGTTTTTCCC
* * * *
25369529 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25369549 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25369568 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25369589 AGCTC
1 AGCTC
25369594 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:25383161 original size:23 final size:23
Alignment explanation
Indices: 25383130--25383175 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25383120 TAGTAGTTTT
*
25383130 TTCAAAAAAAATTTCAAAAAAAA
1 TTCAAAAAAAAATTCAAAAAAAA
*
25383153 TTCAGAAAAAAATTCAAAAAAAA
1 TTCAAAAAAAAATTCAAAAAAAA
25383176 AATTTTGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (23 bp):
TTCAAAAAAAAATTCAAAAAAAA
Found at i:25383175 original size:11 final size:11
Alignment explanation
Indices: 25383130--25383175 Score: 74
Period size: 12 Copynumber: 4.0 Consensus size: 11
25383120 TAGTAGTTTT
25383130 TTCAAAAAAAA
1 TTCAAAAAAAA
25383141 TTTCAAAAAAAA
1 -TTCAAAAAAAA
25383153 TTCAGAAAAAAA
1 TTCA-AAAAAAA
25383165 TTCAAAAAAAA
1 TTCAAAAAAAA
25383176 AATTTTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.33
12 22 0.67
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:25383241 original size:16 final size:17
Alignment explanation
Indices: 25383220--25383258 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
25383210 TATCAAGTTG
25383220 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
25383236 AAAAAAAAATTTTCGTGA
1 AAAAAAAAA-TTTCGTGA
25383254 AAAAA
1 AAAAA
25383259 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
18 12 0.57
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:25385336 original size:16 final size:16
Alignment explanation
Indices: 25385315--25385346 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25385305 AGAAAAAATT
25385315 GAGGGAGTGGAGGTAA
1 GAGGGAGTGGAGGTAA
25385331 GAGGGAGTGGAGGTAA
1 GAGGGAGTGGAGGTAA
25385347 AAGTACGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.56, T:0.12
Consensus pattern (16 bp):
GAGGGAGTGGAGGTAA
Found at i:25388509 original size:11 final size:11
Alignment explanation
Indices: 25388493--25388522 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25388483 GGAGTAACAA
25388493 AAAAAAAATCG
1 AAAAAAAATCG
*
25388504 AAAAAAATTCG
1 AAAAAAAATCG
25388515 AAAAAAAA
1 AAAAAAAA
25388523 ATTTGATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:25389475 original size:25 final size:25
Alignment explanation
Indices: 25389440--25389501 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
25389430 TAGTGAAAAA
*
25389440 GAAAAAG-AAATCAAAATAGTGAGT
1 GAAAAAGAAAATCAAAATAGTGAGC
* *
25389464 GAAAAAGAAAATGAAGATAGTGAGC
1 GAAAAAGAAAATCAAAATAGTGAGC
25389489 GAGAACAAGAAAA
1 GA-AA-AAGAAAA
25389502 GGAGAACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 2 0.06
27 7 0.22
ACGTcount: A:0.60, C:0.05, G:0.24, T:0.11
Consensus pattern (25 bp):
GAAAAAGAAAATCAAAATAGTGAGC
Found at i:25394132 original size:13 final size:13
Alignment explanation
Indices: 25394114--25394186 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
25394104 TTGGAGTAAC
25394114 AAAAAAAA-TC-A
1 AAAAAAAATTCAA
25394125 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
* *
25394139 AAAAAATTGATTGAA
1 AAAAAA--AATTCAA
25394154 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* * *
25394167 AAAAATAAGTGAA
1 AAAAAAAATTCAA
25394180 AAAAAAA
1 AAAAAAA
25394187 TCGAGCAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 8 0.16
12 2 0.04
13 21 0.43
14 7 0.14
15 8 0.16
16 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:25394184 original size:29 final size:29
Alignment explanation
Indices: 25394124--25394186 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
25394114 AAAAAAAATC
* * **
25394124 AAAAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAAAATTCAAAAAAAAAGTGATAAA
25394153 AAAAAAAAATTCAAAAAAATAAGTGA-AAA
1 AAAAAAAAATTCAAAAAAA-AAGTGATAAA
25394182 AAAAA
1 AAAAA
25394187 TCGAGCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (29 bp):
AAAAAAAAATTCAAAAAAAAAGTGATAAA
Found at i:25395133 original size:18 final size:18
Alignment explanation
Indices: 25395112--25395146 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25395102 AGAAAAGAAA
25395112 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25395130 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25395147 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25399730 original size:11 final size:10
Alignment explanation
Indices: 25399705--25399765 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25399695 ACCAATAAAA
25399705 TAAA-TGAGC
1 TAAATTGAGC
*
25399714 TGAATTGTAGC
1 TAAATTG-AGC
25399725 TAAATTGAGC
1 TAAATTGAGC
**
25399735 TCGATTGAGC
1 TAAATTGAGC
25399745 TGAAA-TGAGC
1 T-AAATTGAGC
*
25399755 TCAATTGAGC
1 TAAATTGAGC
25399765 T
1 T
25399766 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25399766 original size:20 final size:20
Alignment explanation
Indices: 25399706--25399766 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25399696 CCAATAAAAT
*
25399706 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25399726 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25399747 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25399767 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25401854 original size:27 final size:27
Alignment explanation
Indices: 25401823--25401895 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
25401813 TCTTCTTCAA
25401823 CATCTTTTTCTTTTTCAATTTT-TTCT
1 CATCTTTTTCTTTTTCAATTTTCTTCT
* *
25401849 CAATCTCAATTTCTTTTTCAATTTTCTTTT
1 C-ATCT--TTTTCTTTTTCAATTTTCTTCT
* *
25401879 CTTCATTTTCTTTTTCA
1 CATCTTTTTCTTTTTCA
25401896 CTCACTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
29 18 0.47
30 4 0.11
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (27 bp):
CATCTTTTTCTTTTTCAATTTTCTTCT
Found at i:25401859 original size:17 final size:18
Alignment explanation
Indices: 25401837--25401870 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25401827 TTTTTCTTTT
25401837 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
25401854 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
25401871 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:25402784 original size:16 final size:16
Alignment explanation
Indices: 25402765--25402817 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 16
25402755 TTTAACTTGA
25402765 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCACCT
25402781 TTTTTTTTGCTCGA---
1 TTTTTTTTGCTC-ACCT
25402795 TTTTTTTT--TCACCT
1 TTTTTTTTGCTCACCT
25402809 TTTTTTTTG
1 TTTTTTTTG
25402818 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
11 1 0.03
12 2 0.06
14 16 0.50
16 12 0.38
17 1 0.03
ACGTcount: A:0.06, C:0.17, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTTTTTGCTCACCT
Found at i:25402785 original size:30 final size:28
Alignment explanation
Indices: 25402743--25402815 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 28
25402733 CTCGCAAGAC
*
25402743 TTTTCA-CTTTTTTTTAACTTGATTTTT
1 TTTTCACCTTTTTTTTAACTCGATTTTT
**
25402770 TTTGCTCACCTTTTTTTTTGCTCGATTTTT
1 TTT--TCACCTTTTTTTTAACTCGATTTTT
25402800 TTTTCACCTTTTTTTT
1 TTTTCACCTTTTTTTT
25402816 TGAATTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 3 0.08
28 13 0.32
29 3 0.08
30 21 0.52
ACGTcount: A:0.10, C:0.16, G:0.05, T:0.68
Consensus pattern (28 bp):
TTTTCACCTTTTTTTTAACTCGATTTTT
Found at i:25402853 original size:13 final size:13
Alignment explanation
Indices: 25402781--25402867 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 13
25402771 TTGCTCACCT
25402781 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
*
25402795 TTTTTTTTTC-ACC
1 TTTTTTTTTCGA-A
25402808 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
25402820 TTTTTTTTTTC-AA
1 -TTTTTTTTTCGAA
25402833 TCAATTTTTTTTCGAA
1 T---TTTTTTTTCGAA
25402849 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
25402860 TTTTTTTT
1 TTTTTTTT
25402868 GTTACTCCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 21
0.73 0.02 0.25
Matches are distributed among these distances:
11 9 0.15
12 4 0.06
13 29 0.47
14 8 0.13
15 9 0.15
16 3 0.05
ACGTcount: A:0.13, C:0.09, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:25402862 original size:11 final size:12
Alignment explanation
Indices: 25402835--25402867 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25402825 TTTTTCAATC
25402835 AATTTTTTTTCG
1 AATTTTTTTTCG
*
25402847 AATTTTTTTTTG
1 AATTTTTTTTCG
25402859 -ATTTTTTTT
1 AATTTTTTTT
25402868 GTTACTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTCG
Found at i:25404226 original size:11 final size:10
Alignment explanation
Indices: 25404201--25404261 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25404191 ACCAATAAAA
25404201 TAAA-TGAGC
1 TAAATTGAGC
*
25404210 TGAATTGTAGC
1 TAAATTG-AGC
25404221 TAAATTGAGC
1 TAAATTGAGC
**
25404231 TCGATTGAGC
1 TAAATTGAGC
25404241 TGAAA-TGAGC
1 T-AAATTGAGC
*
25404251 TCAATTGAGC
1 TAAATTGAGC
25404261 T
1 T
25404262 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25404262 original size:20 final size:20
Alignment explanation
Indices: 25404202--25404262 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25404192 CCAATAAAAT
*
25404202 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25404222 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25404243 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25404263 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25407345 original size:21 final size:23
Alignment explanation
Indices: 25407300--25407346 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25407290 TCACCTATAA
* *
25407300 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25407323 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25407344 TAA
1 TAA
25407347 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25409222 original size:22 final size:22
Alignment explanation
Indices: 25409194--25409259 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
25409184 TTTTGAACCA
25409194 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
25409216 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
25409238 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
25409260 AAATACCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:25410970 original size:14 final size:12
Alignment explanation
Indices: 25410951--25410992 Score: 52
Period size: 11 Copynumber: 3.5 Consensus size: 12
25410941 GAAATGAAGT
25410951 ATAAAAAAACCAAA
1 ATAAAAAAA--AAA
25410965 ATAAAAAAAAAA
1 ATAAAAAAAAAA
25410977 A-AAAAAAAAAA
1 ATAAAAAAAAAA
25410988 A-AAAA
1 ATAAAA
25410993 GATTTAGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 15 0.54
12 4 0.14
14 9 0.32
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (12 bp):
ATAAAAAAAAAA
Found at i:25410971 original size:1 final size:1
Alignment explanation
Indices: 25410962--25410992 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
25410952 TAAAAAAACC
*
25410962 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25410993 GATTTAGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:25413173 original size:17 final size:17
Alignment explanation
Indices: 25413128--25413175 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
25413118 AGAAAAGAGC
* *
25413128 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
25413145 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
25413162 GAAAATTCAAAAAA
1 GAAAATTCAAAAAA
25413176 GAGAATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:25417363 original size:11 final size:10
Alignment explanation
Indices: 25417338--25417398 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25417328 ACCAATAAAA
25417338 TAAA-TGAGC
1 TAAATTGAGC
*
25417347 TGAATTGTAGC
1 TAAATTG-AGC
25417358 TAAATTGAGC
1 TAAATTGAGC
**
25417368 TCGATTGAGC
1 TAAATTGAGC
25417378 TGAAA-TGAGC
1 T-AAATTGAGC
*
25417388 TCAATTGAGC
1 TAAATTGAGC
25417398 T
1 T
25417399 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25417399 original size:20 final size:20
Alignment explanation
Indices: 25417339--25417399 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25417329 CCAATAAAAT
*
25417339 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25417359 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25417380 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25417400 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25419455 original size:27 final size:27
Alignment explanation
Indices: 25419425--25419494 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
25419415 TCTTCTTCAA
25419425 CATCTTTTTCTTTTTCAATTTT-TTTCT
1 CATCTTTTTCTTTTTCAATTTTCTTT-T
*
25419452 CATCTCAATTTCTTTTTCAATTTTCTTTT
1 CATCT--TTTTCTTTTTCAATTTTCTTTT
* *
25419481 CTTCATTTTCTTTT
1 CATCTTTTTCTTTT
25419495 CTCTCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 13 0.36
29 20 0.56
30 3 0.08
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (27 bp):
CATCTTTTTCTTTTTCAATTTTCTTTT
Found at i:25420633 original size:12 final size:11
Alignment explanation
Indices: 25420609--25420650 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
25420599 TTGTCACTTC
*
25420609 TTTTTTTT-CT
1 TTTTTTTTGAT
25420619 TTTTTTTTGA-
1 TTTTTTTTGAT
25420629 TTTTTTTTGAAT
1 TTTTTTTTG-AT
25420641 TTTTTTTTGA
1 TTTTTTTTGA
25420651 ATTTCTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 9 0.32
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:25420651 original size:12 final size:12
Alignment explanation
Indices: 25420618--25420654 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
25420608 CTTTTTTTTC
25420618 TTTTTTTTTG-A
1 TTTTTTTTTGAA
25420629 -TTTTTTTTGAA
1 TTTTTTTTTGAA
25420640 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25420652 TTT
1 TTT
25420655 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25422026 original size:11 final size:10
Alignment explanation
Indices: 25422001--25422061 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
25421991 ACCAATAAAA
25422001 TAAA-TGAGC
1 TAAATTGAGC
*
25422010 TGAATTGTAGC
1 TAAATTG-AGC
25422021 TAAATTGAGC
1 TAAATTGAGC
**
25422031 TCGATTGAGC
1 TAAATTGAGC
25422041 TGAAA-TGAGC
1 T-AAATTGAGC
*
25422051 TCAATTGAGC
1 TAAATTGAGC
25422061 T
1 T
25422062 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:25422062 original size:20 final size:20
Alignment explanation
Indices: 25422002--25422062 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
25421992 CCAATAAAAT
*
25422002 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
25422022 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
25422043 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
25422063 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:25445628 original size:35 final size:35
Alignment explanation
Indices: 25445582--25445655 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
25445572 ATAAGTATTT
*
25445582 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTG
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTA
*
25445617 AGTTGTTGGAATAAATTACTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTA
25445652 AGTT
1 AGTT
25445656 CATCTTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (35 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTA
Found at i:25445660 original size:19 final size:19
Alignment explanation
Indices: 25445636--25445674 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
25445626 AATAAATTAC
25445636 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
25445655 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
25445674 T
1 T
25445675 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:25445806 original size:19 final size:18
Alignment explanation
Indices: 25445777--25445812 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
25445767 TAAGTCTAAT
25445777 ATGTGTTTAATGTGTTTA
1 ATGTGTTTAATGTGTTTA
25445795 ATGTGTTTTAATGTGTTT
1 ATGTG-TTTAATGTGTTT
25445813 TTTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
ATGTGTTTAATGTGTTTA
Found at i:25445813 original size:10 final size:9
Alignment explanation
Indices: 25445777--25445812 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
25445767 TAAGTCTAAT
25445777 ATGTGTTTA
1 ATGTGTTTA
25445786 ATGTGTTTA
1 ATGTGTTTA
25445795 ATGTGTTTTA
1 ATGTG-TTTA
25445805 ATGTGTTT
1 ATGTGTTT
25445813 TTTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:25445881 original size:74 final size:73
Alignment explanation
Indices: 25445781--25445919 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 73
25445771 TCTAATATGT
* *
25445781 GTTTAATGTGTTTAATGTGTTTTAATGTGTTTTTTAATAAATGCTTGCAGGTGACTATTTAGTTG
1 GTTTAATGTGTTTAATGTGTTTTAATGTGCTTGTTAATAAATGCTTGCAGGTGACTATTTAGTTG
25445846 CTTATTAA
66 CTTATTAA
* *
25445854 GTTTAGTGTGTTTAAATGTGTTTTAATGTGCTTGTTAATAAATGTTTGCAGGTGACTATTTAGTT
1 GTTTAATGTGTTT-AATGTGTTTTAATGTGCTTGTTAATAAATGCTTGCAGGTGACTATTTAGTT
25445919 G
65 G
25445920 GAATCAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
73 12 0.20
74 49 0.80
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.50
Consensus pattern (73 bp):
GTTTAATGTGTTTAATGTGTTTTAATGTGCTTGTTAATAAATGCTTGCAGGTGACTATTTAGTTG
CTTATTAA
Found at i:25446317 original size:24 final size:25
Alignment explanation
Indices: 25446271--25446317 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
25446261 AGGAATTTGG
*
25446271 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
25446296 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
25446318 TCGGCTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:25453292 original size:27 final size:27
Alignment explanation
Indices: 25453261--25453438 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
25453251 TAAATTGTAC
25453261 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
25453288 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
25453314 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
25453342 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
25453370 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
25453397 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
25453424 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25453439 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:25453375 original size:82 final size:81
Alignment explanation
Indices: 25453262--25453417 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
25453252 AAATTGTACA
* *
25453262 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
25453326 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
25453343 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
25453408 TGCGAGTTGA
65 TGCGAATTGA
25453418 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:25453429 original size:82 final size:81
Alignment explanation
Indices: 25453258--25453438 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
25453248 GATTAAATTG
* *
25453258 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
25453323 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
25453339 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
25453403 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
25453421 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
25453439 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:25453449 original size:27 final size:27
Alignment explanation
Indices: 25453343--25453449 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
25453333 TGACCATGCG
* * * *
25453343 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
25453371 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
25453398 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
25453425 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
25453450 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:25455200 original size:14 final size:14
Alignment explanation
Indices: 25455183--25455214 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
25455173 AAAACTAAGT
25455183 AAATAAAAAAATAA
1 AAATAAAAAAATAA
25455197 AAATAAAAAAATAA
1 AAATAAAAAAATAA
25455211 AAAT
1 AAAT
25455215 CATTAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:25456866 original size:40 final size:40
Alignment explanation
Indices: 25456775--25456943 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
25456765 TCCTCGTTCA
* * * * *
25456775 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
25456814 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
25456854 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
25456894 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCG-ACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
25456933 AAGGCCTTCGG
1 AATGCCTTCGG
25456944 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
39 43 0.39
40 68 0.61
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:25456876 original size:79 final size:80
Alignment explanation
Indices: 25456775--25456921 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
25456765 TCCTCGTTCA
* * * * *
25456775 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
25456839 TTAACAACTCGCACG
66 TTAACAACTCGCACG
* * *
25456854 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
25456919 TTA
66 TTA
25456922 GTATCTCGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 34 0.58
80 25 0.42
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGCACG
Found at i:25456940 original size:79 final size:79
Alignment explanation
Indices: 25456773--25456943 Score: 209
Period size: 79 Copynumber: 2.2 Consensus size: 79
25456763 GCTCCTCGTT
* * * * *
25456773 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACGTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
25456838 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * * *
25456852 CGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACAC-AATGCCCTCGGGACGTAACCCGG
** *
25456917 ATTTAGTATCTCG-A
65 ATTTAACAACTCGCA
*
25456931 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
25456944 ATCTTAGTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 47 0.61
80 30 0.39
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCCTCGGGACGTAACCCGGA
TTTAACAACTCGCA
Found at i:25464771 original size:40 final size:40
Alignment explanation
Indices: 25464680--25464849 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
25464670 TCCTCGTTCA
* * * * *
25464680 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
25464719 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
25464759 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
25464799 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
25464839 AAGGCCTTCGG
1 AATGCCTTCGG
25464850 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:25467082 original size:15 final size:16
Alignment explanation
Indices: 25467055--25467087 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
25467045 TTTGCATGCA
25467055 AAATATAGAAAGACAT
1 AAATATAGAAAGACAT
25467071 AAATAT-GAAAGACAT
1 AAATATAGAAAGACAT
25467086 AA
1 AA
25467088 TAGTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAATATAGAAAGACAT
Found at i:25473742 original size:24 final size:21
Alignment explanation
Indices: 25473714--25473757 Score: 52
Period size: 24 Copynumber: 2.0 Consensus size: 21
25473704 TTTATCAAGA
25473714 TAAATATTAGATTAAATATAATAT
1 TAAATATT--ATTAAA-ATAATAT
*
25473738 TAAATCTTATTAAAATAATA
1 TAAATATTATTAAAATAATA
25473758 GAATGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
24 7 0.37
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAATATTATTAAAATAATAT
Found at i:25473877 original size:97 final size:97
Alignment explanation
Indices: 25473681--25473877 Score: 218
Period size: 97 Copynumber: 2.0 Consensus size: 97
25473671 AACTTAATCT
* * * *
25473681 TTTAATATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATATAATATTAAATCTT
1 TTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATATAATATTAAATATT
* * * *
25473746 ATTAAAATAATAGAATGTTTATCTTAAATTAAA
66 ATT-AAATAATAGAATATTAATCTGAAATCAAA
* * * *
25473779 TTTAATATTCAATTAATAAAATA-CTATTAAGATAAGTATTAAATTAAATTTAATATTAAAATAT
1 TTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATATAATATT-AAATAT
* **
25473843 TATT-ATTTTTAGAATAATTAATCTGAAATCAAA
65 TATTAAATAATAGAAT-ATTAATCTGAAATCAAA
25473876 TT
1 TT
25473878 CTTTGGTAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
96 8 0.10
97 44 0.54
98 30 0.37
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (97 bp):
TTTAATATTAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATATAATATTAAATATT
ATTAAATAATAGAATATTAATCTGAAATCAAA
Found at i:25488105 original size:17 final size:16
Alignment explanation
Indices: 25488083--25488116 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25488073 AGGGATTGCA
25488083 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
25488100 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
25488116 T
1 T
25488117 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:25489548 original size:21 final size:21
Alignment explanation
Indices: 25489522--25489565 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25489512 AGCACACTCG
*
25489522 GATGCATCCACAACAAAGTCA
1 GATGCATCCACAACAAAATCA
*
25489543 GATGCATCCACACCAAAATCA
1 GATGCATCCACAACAAAATCA
25489564 GA
1 GA
25489566 CACAGCCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.14
Consensus pattern (21 bp):
GATGCATCCACAACAAAATCA
Found at i:25495470 original size:18 final size:19
Alignment explanation
Indices: 25495446--25495496 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
25495436 AATGTGATTG
25495446 GTATATATGTGCATGATCAA
1 GTATATATGTGCATGAT-AA
**
25495466 -T-TATATGCACATGATAA
1 GTATATATGTGCATGATAA
25495483 GTATATATGTGCAT
1 GTATATATGTGCAT
25495497 TCAGATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 10 0.40
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
GTATATATGTGCATGATAA
Found at i:25496638 original size:15 final size:15
Alignment explanation
Indices: 25496620--25496653 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25496610 AGGAAGACAA
25496620 TACTGAAAAAGAAGC
1 TACTGAAAAAGAAGC
* *
25496635 TACTGAGAAAGAATC
1 TACTGAAAAAGAAGC
25496650 TACT
1 TACT
25496654 AAGAACATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (15 bp):
TACTGAAAAAGAAGC
Found at i:25499109 original size:3 final size:3
Alignment explanation
Indices: 25499101--25499155 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
25499091 AAAGTTGTAG
** * * *
25499101 TAA TAA TAA TGG TAA TAA TAA TAA TAA TAA TAA GAA TGA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25499149 TATA TAA
1 TA-A TAA
25499156 AAAACGACAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25501915 original size:21 final size:23
Alignment explanation
Indices: 25501870--25501916 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25501860 TCACCTGCAA
* *
25501870 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25501893 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25501914 TAA
1 TAA
25501917 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25507272 original size:16 final size:16
Alignment explanation
Indices: 25507251--25507308 Score: 73
Period size: 15 Copynumber: 3.6 Consensus size: 16
25507241 CTTATTCTTC
25507251 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG-AAA-TT
* *
25507269 TTTTTTTCATGAATTT
1 TTTTTTTCACGAAATT
25507285 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
25507300 TTTTTTTCA
1 TTTTTTTCA
25507309 ACTTGATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 12 0.33
16 12 0.33
17 2 0.06
18 10 0.28
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:25507308 original size:15 final size:16
Alignment explanation
Indices: 25507251--25507306 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
25507241 CTTATTCTTC
25507251 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG--AATTT
*
25507269 TTTTTTTCATGAATTT
1 TTTTTTTCACGAATTT
25507285 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
25507301 TTTTTT
1 TTTTTT
25507307 CAACTTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 26 0.72
18 10 0.28
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTTTCACGAATTT
Found at i:25507370 original size:17 final size:17
Alignment explanation
Indices: 25507348--25507386 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
25507338 GGAAACCAAA
25507348 TTTTTTTTTTG--ATTT
1 TTTTTTTTTTGAAATTT
25507363 TTTTTTTTTTGAAATTT
1 TTTTTTTTTTGAAATTT
25507380 TTTTTTT
1 TTTTTTT
25507387 GAAAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.50
17 11 0.50
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTGAAATTT
Found at i:25507389 original size:14 final size:14
Alignment explanation
Indices: 25507345--25507390 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
25507335 AATGGAAACC
25507345 AAATTTTTTTTTTG
1 AAATTTTTTTTTTG
**
25507359 ATTTTTTTTTTTTTG
1 A-AATTTTTTTTTTG
25507374 AAATTTTTTTTTTG
1 AAATTTTTTTTTTG
25507388 AAA
1 AAA
25507391 AAACTACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
AAATTTTTTTTTTG
Found at i:25508424 original size:21 final size:23
Alignment explanation
Indices: 25508379--25508425 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25508369 TCACCTGTAA
* *
25508379 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
25508402 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
25508423 TAA
1 TAA
25508426 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25519787 original size:47 final size:47
Alignment explanation
Indices: 25519730--25519838 Score: 155
Period size: 47 Copynumber: 2.3 Consensus size: 47
25519720 ATGATGTGGT
* *
25519730 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * * *
25519777 TATATATGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
25519824 TATAAATGTGATAAG
1 TATATATGTGATAAG
25519839 TCCCGAAGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:25520011 original size:37 final size:37
Alignment explanation
Indices: 25519954--25520032 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 37
25519944 CCGAGCTCTA
*
25519954 AAGACCCGATGACTACGTGTGG-GAATT-TGGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTAT-GTCCGGGT
25519991 AAGACCCGATAACTTA-GTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAAC-TACGTGTGGAGATTATGTCCGGGT
25520028 AAGAC
1 AAGAC
25520033 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:25521925 original size:43 final size:43
Alignment explanation
Indices: 25521877--25521979 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
25521867 TTGGTTTTCA
*
25521877 GCACTAACTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
25521920 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
25521963 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
25521980 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:25521996 original size:29 final size:29
Alignment explanation
Indices: 25521961--25522034 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
25521951 GTTGTGAGAT
* *
25521961 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
25521990 TGGCACTAAGTGTGTGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
25522019 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
25522035 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:25522438 original size:40 final size:39
Alignment explanation
Indices: 25522355--25522482 Score: 170
Period size: 40 Copynumber: 3.3 Consensus size: 39
25522345 TTGAATGATG
*
25522355 TCCGGGCTAAGTCCGAAG-GC-TTTGTGCTAAGTGATATA
1 TCCGGGCTAAGTCCGAAGAGCATTCGTGCT-AGTGATATA
* *
25522393 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATATA
*
25522433 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATATA
1 TCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATATA
*
25522473 TCCGTGCTAA
1 TCCGGGCTAA
25522483 ACCTCGAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
38 12 0.15
39 5 0.06
40 54 0.68
41 8 0.10
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:25526270 original size:49 final size:47
Alignment explanation
Indices: 25526131--25526545 Score: 661
Period size: 47 Copynumber: 8.7 Consensus size: 47
25526121 TTAGGATTCT
* *
25526131 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
25526178 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
25526225 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
25526274 ATGTGATGAATGTGAAAGTGTATATATATGTGGTAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
25526323 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
25526370 ATGTGATAAATGTGAAAGTGTATATCTGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
25526417 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
25526464 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
25526511 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
25526546 TCCCGAAGGG
Statistics
Matches: 347, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 251 0.72
49 95 0.27
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:25526721 original size:37 final size:37
Alignment explanation
Indices: 25526664--25526742 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 37
25526654 CCGAGCTCTA
* *
25526664 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
25526701 AAGACCCGATAACTTA-GTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAAC-TACGTGTGGAGATTATGTCCGGGT
25526738 AAGAC
1 AAGAC
25526743 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 35 0.92
38 3 0.08
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:25534739 original size:11 final size:11
Alignment explanation
Indices: 25534725--25534750 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25534715 TTCTTTTAAC
25534725 TTTCTTTTTTT
1 TTTCTTTTTTT
25534736 TTTCTTTTTTT
1 TTTCTTTTTTT
25534747 TTTC
1 TTTC
25534751 AATTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:25542407 original size:51 final size:51
Alignment explanation
Indices: 25542331--25542428 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
25542321 CGTGGCGACA
* * * *
25542331 GTATATGGCATAAGACCATAGATGAAAGAGGCTATGATAGTTTGGTATAAG
1 GTATATGGCATAAGACCATAAATGAAAAAGGCTATGACAATTTGGTATAAG
* *
25542382 GTATATGGCGTAAGACTATAAATGAAAAAGGCTATGACAATTTGGTA
1 GTATATGGCATAAGACCATAAATGAAAAAGGCTATGACAATTTGGTA
25542429 AGTACGTAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.28
Consensus pattern (51 bp):
GTATATGGCATAAGACCATAAATGAAAAAGGCTATGACAATTTGGTATAAG
Found at i:25543586 original size:29 final size:29
Alignment explanation
Indices: 25543550--25543806 Score: 165
Period size: 29 Copynumber: 8.8 Consensus size: 29
25543540 CACGTAGGTG
* *
25543550 TCCTTTTAACAAAGATAGCCACAAGGGCA
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
* * *
25543579 TCCATTTAACTGAGATTGCCACAAAGGCA
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
** * * *
25543608 TCCTTTTAATTGAGATATCCATAAATGCA
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
* *
25543637 TCCTTTTAACAGAGATTGCCACAAAGGAA
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
* * * * * *
25543666 TTCATTTAATAAAGGTAGCCATAAAGGCA
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
** * *
25543695 TCCTTTTTAACAGAGATTTCCATAAAGGCT
1 TCC-TTTTAACAGAGATAGCCACAAAGGCA
* ** *
25543725 TCCTTATAGTAGAGATCGCCACAAAGGC-
1 TCCTTTTAACAGAGATAGCCACAAAGGCA
* * * * ***
25543753 TTCTTTATAACAAATATAGCTACAAAGATT
1 TCCTTT-TAACAGAGATAGCCACAAAGGCA
* * *
25543783 TCCTTATAACAGAAATTGCCACAA
1 TCCTTTTAACAGAGATAGCCACAA
25543807 GGGGTTCCTT
Statistics
Matches: 169, Mismatches: 56, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
28 4 0.02
29 139 0.82
30 26 0.15
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.28
Consensus pattern (29 bp):
TCCTTTTAACAGAGATAGCCACAAAGGCA
Found at i:25543624 original size:58 final size:58
Alignment explanation
Indices: 25543550--25543752 Score: 208
Period size: 58 Copynumber: 3.5 Consensus size: 58
25543540 CACGTAGGTG
* * * * *
25543550 TCCTTTTAACAAAGATAGCCACAAGGGCATCCATTTAACTGAGATTGCCACAAAGGCA
1 TCCTTTTAATAGAGATAGCCACAAAGGCATCCTTTTAACAGAGATTGCCACAAAGGCA
* * * * *
25543608 TCCTTTTAATTGAGATATCCATAAATGCATCCTTTTAACAGAGATTGCCACAAAGGAA
1 TCCTTTTAATAGAGATAGCCACAAAGGCATCCTTTTAACAGAGATTGCCACAAAGGCA
* * * * * * * *
25543666 TTCATTTAATAAAGGTAGCCATAAAGGCATCCTTTTTAACAGAGATTTCCATAAAGGCT
1 TCCTTTTAATAGAGATAGCCACAAAGGCATCC-TTTTAACAGAGATTGCCACAAAGGCA
* * *
25543725 TCCTTATAGTAGAGATCGCCACAAAGGC
1 TCCTTTTAATAGAGATAGCCACAAAGGC
25543753 TTCTTTATAA
Statistics
Matches: 115, Mismatches: 29, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
58 73 0.63
59 42 0.37
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (58 bp):
TCCTTTTAATAGAGATAGCCACAAAGGCATCCTTTTAACAGAGATTGCCACAAAGGCA
Found at i:25543658 original size:87 final size:88
Alignment explanation
Indices: 25543550--25543751 Score: 219
Period size: 87 Copynumber: 2.3 Consensus size: 88
25543540 CACGTAGGTG
* * * * *
25543550 TCCTTTTAACAAAGATAGCCACAAGGGCATCCATTTAACT-GAGATTGCCACAAAGGCATCC-TT
1 TCCTTTTAACAGAGATAGCCACAAAGGAATCCATTTAA-TAAAGATAGCCACAAAGGCATCCTTT
** *
25543613 TTAATTGAGATATCCATAAATGCA
65 TTAACAGAGATATCCATAAAGGCA
* * * *
25543637 TCCTTTTAACAGAGATTGCCACAAAGGAATTCATTTAATAAAGGTAGCCATAAAGGCATCCTTTT
1 TCCTTTTAACAGAGATAGCCACAAAGGAATCCATTTAATAAAGATAGCCACAAAGGCATCCTTTT
* *
25543702 TAACAGAGATTTCCATAAAGGCT
66 TAACAGAGATATCCATAAAGGCA
* ** *
25543725 TCCTTATAGTAGAGATCGCCACAAAGG
1 TCCTTTTAACAGAGATAGCCACAAAGG
25543752 CTTCTTTATA
Statistics
Matches: 95, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
86 1 0.01
87 50 0.53
88 44 0.46
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (88 bp):
TCCTTTTAACAGAGATAGCCACAAAGGAATCCATTTAATAAAGATAGCCACAAAGGCATCCTTTT
TAACAGAGATATCCATAAAGGCA
Found at i:25544281 original size:16 final size:17
Alignment explanation
Indices: 25544248--25544282 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
25544238 TTTAAATGTC
25544248 ATTATTAGATTGGTTTT
1 ATTATTAGATTGGTTTT
25544265 ATTATTAGATT-GTTTT
1 ATTATTAGATTGGTTTT
25544281 AT
1 AT
25544283 AGTAGTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTATTAGATTGGTTTT
Found at i:25547499 original size:26 final size:26
Alignment explanation
Indices: 25547427--25547502 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
25547417 AATTTCCATA
* *
25547427 AAAGGACACCTTTATGGCTAACTCTG
1 AAAGGACGCCTTTATGGCTATCTCTG
*
25547453 AAAGGACGCCTTTGTGGCTATCTCTG
1 AAAGGACGCCTTTATGGCTATCTCTG
** *
25547479 AAAGGATTCCTTTATGACTATCTC
1 AAAGGACGCCTTTATGGCTATCTC
25547503 AGTTAAAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (26 bp):
AAAGGACGCCTTTATGGCTATCTCTG
Found at i:25547528 original size:55 final size:56
Alignment explanation
Indices: 25547460--25547582 Score: 160
Period size: 58 Copynumber: 2.2 Consensus size: 56
25547450 CTGAAAGGAC
* * *
25547460 GCCTTTGTGGCTATCTC-TGAAAG-GATTCCTTTATGACTATCTCAGTTAAAAGTGA
1 GCCTTTGTGGCTATCTCATAAAAGTGA-GCATTTATGACTATCTCAGTTAAAAGTGA
* *
25547515 GCCTTTGTGGCTATCTCAGTTAAAAGTGAGCATTTGTGGCTATCTCAGTTAAAAGTGA
1 GCCTTTGTGGCTATCTCA--TAAAAGTGAGCATTTATGACTATCTCAGTTAAAAGTGA
25547573 GCCTTTGTGG
1 GCCTTTGTGG
25547583 TGATCTTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
55 17 0.29
58 40 0.68
59 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (56 bp):
GCCTTTGTGGCTATCTCATAAAAGTGAGCATTTATGACTATCTCAGTTAAAAGTGA
Found at i:25547594 original size:29 final size:29
Alignment explanation
Indices: 25547487--25547582 Score: 165
Period size: 29 Copynumber: 3.3 Consensus size: 29
25547477 TGAAAGGATT
* *
25547487 CCTTTATGACTATCTCAGTTAAAAGTGAG
1 CCTTTGTGGCTATCTCAGTTAAAAGTGAG
25547516 CCTTTGTGGCTATCTCAGTTAAAAGTGAG
1 CCTTTGTGGCTATCTCAGTTAAAAGTGAG
*
25547545 CATTTGTGGCTATCTCAGTTAAAAGTGAG
1 CCTTTGTGGCTATCTCAGTTAAAAGTGAG
25547574 CCTTTGTGG
1 CCTTTGTGG
25547583 TGATCTTTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (29 bp):
CCTTTGTGGCTATCTCAGTTAAAAGTGAG
Found at i:25547604 original size:29 final size:29
Alignment explanation
Indices: 25547572--25547637 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
25547562 GTTAAAAGTG
* * **
25547572 AGCCTTTGTGGTGATCTTTGTTATAAGAA
1 AGCCTTTGTAGAGATCTCCGTTATAAGAA
25547601 AGCCTTTGTAGAGATCTCCGTTATAAGAA
1 AGCCTTTGTAGAGATCTCCGTTATAAGAA
25547630 AGCCTTTG
1 AGCCTTTG
25547638 CGGCAATCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (29 bp):
AGCCTTTGTAGAGATCTCCGTTATAAGAA
Found at i:25547609 original size:58 final size:58
Alignment explanation
Indices: 25547487--25547609 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
25547477 TGAAAGGATT
* **
25547487 CCTTTATGACTATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGTGAG
1 CCTTTGTGACTATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGAAAG
* * ** *
25547545 CATTTGTGGCTATCTCAGTTAAAAGTGAGCCTTTGTGG-TGATCTTTGTTATAAGAAAG
1 CCTTTGTGACTATCTCAGTTAAAAGTGAGCCTTTGTGGCT-ATCTCAGTTAAAAGAAAG
25547603 CCTTTGT
1 CCTTTGT
25547610 AGAGATCTCC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 1 0.02
58 54 0.98
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (58 bp):
CCTTTGTGACTATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGAAAG
Found at i:25547618 original size:58 final size:58
Alignment explanation
Indices: 25547498--25547637 Score: 147
Period size: 58 Copynumber: 2.4 Consensus size: 58
25547488 CTTTATGACT
** * **
25547498 ATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGTGAGCATTTGTGGCT
1 ATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGAAAGCATTTGTAGAG
** * *
25547556 ATCTCAGTTAAAAGTGAGCCTTTGTGG-TGATCTTTGTTATAAGAAAGCCTTTGTAGAG
1 ATCTCAGTTAAAAGTGAGCCTTTGTGGCT-ATCTCAGTTAAAAGAAAGCATTTGTAGAG
* * **
25547614 ATCTCCGTTATAAGAAAGCCTTTG
1 ATCTCAGTTAAAAGTGAGCCTTTG
25547638 CGGCAATCCC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
57 1 0.01
58 67 0.99
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (58 bp):
ATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCTCAGTTAAAAGAAAGCATTTGTAGAG
Found at i:25547652 original size:29 final size:30
Alignment explanation
Indices: 25547590--25547655 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
25547580 TGGTGATCTT
*
25547590 TGTTATAAGAAAGCCTTTGTAGAGATCTCC
1 TGTTATAAGAAAGCCTTTGCAGAGATCTCC
*
25547620 -GTTATAAGAAAGCCTTTGCGGCA-ATC-CC
1 TGTTATAAGAAAGCCTTTGCAG-AGATCTCC
25547648 TGTTATAA
1 TGTTATAA
25547656 AGATGTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 2 0.06
29 29 0.91
30 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (30 bp):
TGTTATAAGAAAGCCTTTGCAGAGATCTCC
Found at i:25548128 original size:16 final size:16
Alignment explanation
Indices: 25548107--25548137 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25548097 AAAGAGATGT
*
25548107 TAAGTATGGTACGCCC
1 TAAGTACGGTACGCCC
25548123 TAAGTACGGTACGCC
1 TAAGTACGGTACGCC
25548138 AAAGAAAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (16 bp):
TAAGTACGGTACGCCC
Found at i:25548405 original size:26 final size:26
Alignment explanation
Indices: 25548369--25548424 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
25548359 ACGGTGCCAA
* *
25548369 GGCTACGCCAAGGCAGCTATGCACCG
1 GGCTACGCCAAGGAAGCGATGCACCG
* *
25548395 GGCTATGCCAAGGAAGCGATGCACTG
1 GGCTACGCCAAGGAAGCGATGCACCG
25548421 GGCT
1 GGCT
25548425 GTTATGCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.29, G:0.34, T:0.14
Consensus pattern (26 bp):
GGCTACGCCAAGGAAGCGATGCACCG
Found at i:25549254 original size:21 final size:21
Alignment explanation
Indices: 25549228--25549289 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
25549218 CGAACACGCC
* *
25549228 AACAGAAGCTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTA
25549249 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* *
25549270 AATAGAAGCTCAAAAGAGCT
1 AACAGAAGCTCATAAGAGCT
25549290 GACCACCAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:25557701 original size:17 final size:18
Alignment explanation
Indices: 25557675--25557711 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25557665 TATCCTAACC
*
25557675 TCCCATTAA-CCACTAAA
1 TCCCACTAACCCACTAAA
25557692 TCCCACTAACCCACTAAA
1 TCCCACTAACCCACTAAA
25557710 TC
1 TC
25557712 TCAACTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (18 bp):
TCCCACTAACCCACTAAA
Found at i:25563570 original size:18 final size:18
Alignment explanation
Indices: 25563547--25563583 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25563537 TAGAATTATA
*
25563547 GGCCCACATGTCCGTGTG
1 GGCCCACACGTCCGTGTG
25563565 GGCCCACACGTCCGTGTG
1 GGCCCACACGTCCGTGTG
25563583 G
1 G
25563584 TTCACTGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.35, G:0.35, T:0.19
Consensus pattern (18 bp):
GGCCCACACGTCCGTGTG
Done.