Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 94 of 199
Found at i:28831015 original size:38 final size:38
Alignment explanation
Indices: 28830968--28831079 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
28830958 GTTATATTTC
* * * *
28830968 TTTACATTTTGTATAATTTTCTTATGACTTTATAAAAT
1 TTTAAATTTTATATAATTTTTTTATGATTTTATAAAAT
* *
28831006 TTTATATTTTATA-AATTTTTTTACGATTTTTATAAAAT
1 TTTAAATTTTATATAATTTTTTTATGA-TTTTATAAAAT
*
28831044 TTTACAATTTTTTATATATTTTTTTATGATTTTATA
1 TTTA-AATTTTATATA-ATTTTTTTATGATTTTATA
28831080 TTTTTTCTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
37 11 0.18
38 25 0.40
39 7 0.11
40 8 0.13
41 11 0.18
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (38 bp):
TTTAAATTTTATATAATTTTTTTATGATTTTATAAAAT
Found at i:28831046 original size:19 final size:19
Alignment explanation
Indices: 28830996--28831055 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
28830986 TTCTTATGAC
*
28830996 TTTATAAAATTTTA-TA-T
1 TTTATAAAATTTTACAATT
* *
28831013 TTTATAAATTTTTTTACGATT
1 TTTATAAA--ATTTTACAATT
28831034 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTACAATT
28831053 TTT
1 TTT
28831056 TATATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.23
19 17 0.49
20 1 0.03
21 9 0.26
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTTACAATT
Found at i:28831067 original size:41 final size:38
Alignment explanation
Indices: 28830996--28831076 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 38
28830986 TTCTTATGAC
28830996 TTTATAAAATTTTATATTTTATAAATTTTTTTACGATT
1 TTTATAAAATTTTATATTTTATAAATTTTTTTACGATT
* * *
28831034 TTTATAAAATTTTACAATTTTTTATATATTTTTTTATGATT
1 TTTATAAAATTTT---ATATTTTATAAATTTTTTTACGATT
28831075 TT
1 TT
28831077 ATATTTTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 13 0.35
41 24 0.65
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (38 bp):
TTTATAAAATTTTATATTTTATAAATTTTTTTACGATT
Found at i:28831092 original size:10 final size:10
Alignment explanation
Indices: 28831032--28831135 Score: 53
Period size: 10 Copynumber: 10.9 Consensus size: 10
28831022 TTTTTTACGA
*
28831032 TTTTTATAAA
1 TTTTTATAAT
* *
28831042 ATTTTACAAT
1 TTTTTATAAT
28831052 TTTTTATATAT
1 TTTTTATA-AT
28831063 TTTTT-T-AT
1 TTTTTATAAT
*
28831071 GATTTTAT-AT
1 -TTTTTATAAT
*
28831081 TTTTTCTAA-
1 TTTTTATAAT
28831090 -TTTT-TAAT
1 TTTTTATAAT
*
28831098 ATTTTATAA-
1 TTTTTATAAT
28831107 -TTTTATAATT
1 TTTTTATAA-T
*
28831117 TTTTTCTAAT
1 TTTTTATAAT
*
28831127 TTTTAATAA
1 TTTTTATAA
28831136 AAGAAGGGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.04
8 14 0.19
9 13 0.18
10 29 0.40
11 14 0.19
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:28831119 original size:9 final size:9
Alignment explanation
Indices: 28831012--28831119 Score: 53
Period size: 10 Copynumber: 11.4 Consensus size: 9
28831002 AAATTTTATA
28831012 TTTTATAAAT
1 TTTTAT-AAT
*
28831022 TTTTTTACGAT
1 TTTTATA--AT
*
28831033 TTTTATAAAA
1 TTTTAT-AAT
*
28831043 TTTTACAATT
1 TTTTATAA-T
28831053 TTTTATATAT
1 TTTTATA-AT
*
28831063 TTTT-TTAT
1 TTTTATAAT
*
28831071 GATTTTATATT
1 --TTTTATAAT
*
28831082 TTTTCTAA-
1 TTTTATAAT
28831090 TTTT-TAAT
1 TTTTATAAT
28831098 ATTTTATAA-
1 -TTTTATAAT
28831107 TTTTATAAT
1 TTTTATAAT
28831116 TTTT
1 TTTT
28831120 TTCTAATTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 25
0.68 0.10 0.23
Matches are distributed among these distances:
7 3 0.04
8 14 0.19
9 18 0.24
10 29 0.39
11 10 0.13
12 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:28831127 original size:36 final size:34
Alignment explanation
Indices: 28831065--28831134 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 34
28831055 TTATATATTT
*
28831065 TTTTATGATTTTATATTTTTTCTAATTTTTAATA
1 TTTTATAATTTTATATTTTTTCTAATTTTTAATA
28831099 TTTTATAATTTTATAATTTTTTTCTAATTTTTAATA
1 TTTTATAATTTTAT-A-TTTTTTCTAATTTTTAATA
28831135 AAAGAAGGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 13 0.39
35 1 0.03
36 19 0.58
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (34 bp):
TTTTATAATTTTATATTTTTTCTAATTTTTAATA
Found at i:28831252 original size:85 final size:83
Alignment explanation
Indices: 28831142--28831320 Score: 245
Period size: 86 Copynumber: 2.1 Consensus size: 83
28831132 ATAAAAGAAG
* * **
28831142 GGGCTTAATTGTTTTTTTTAAAGG-TTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACTG
1 GGGCTTAATTGTTTTTTTAAAAGGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCA
*
28831206 AATTGAGTGA-AAAAAATAA
66 AAATGAGT-ACAAAAAA-AA
*
28831225 GGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGTTTTTTTGATGCATTTTAAAAGTTCAAGTAC
1 GGGCTTAATTG-TTTTTTT-AAAAGGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTAC
28831290 CAAAATGAGTACAAAAAAAA
64 CAAAATGAGTACAAAAAAAA
28831310 GGGACTTAATT
1 GGG-CTTAATT
28831321 TATTTTATTT
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
83 11 0.13
84 7 0.08
85 11 0.13
86 56 0.66
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (83 bp):
GGGCTTAATTGTTTTTTTAAAAGGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCA
AAATGAGTACAAAAAAAA
Found at i:28833153 original size:23 final size:24
Alignment explanation
Indices: 28833123--28833169 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
28833113 TTTTAAAAAA
*
28833123 TAAAAATTATGAAAAA-AAAATTT
1 TAAAAATTATAAAAAATAAAATTT
*
28833146 TAAAAATTTTAAAAAATAAAATTT
1 TAAAAATTATAAAAAATAAAATTT
28833170 ATTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAAAATTATAAAAAATAAAATTT
Found at i:28834266 original size:34 final size:34
Alignment explanation
Indices: 28834223--28834291 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
28834213 TGGAAGAGTG
*
28834223 ACCAAAATACT-AAGTTTCGACAACAATAATAACT
1 ACCAAAATACTAAAATTT-GACAACAATAATAACT
*
28834257 ACCAAAATACTAAAATTTGATAACAATAATAACT
1 ACCAAAATACTAAAATTTGACAACAATAATAACT
28834291 A
1 A
28834292 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (34 bp):
ACCAAAATACTAAAATTTGACAACAATAATAACT
Found at i:28835246 original size:120 final size:120
Alignment explanation
Indices: 28835033--28835552 Score: 958
Period size: 120 Copynumber: 4.4 Consensus size: 120
28835023 TTTTAGGTAG
* *
28835033 ATGAATTTACTAAAATCATAATATATAACACTATAAAATATCATTTAAAATAATTATTATTAAAT
1 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
*
28835098 ATAACTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
66 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
28835153 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
1 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
*
28835218 ATACTTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
66 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
28835273 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
1 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
28835338 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
66 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
28835393 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
1 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
* *
28835458 ATAATTTAATAATAATATATAATTTAATAAAATTC--AATA-TAATTATTCTTAT
66 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
28835510 ATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAAT
1 ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
28835553 ATATAATCTA
Statistics
Matches: 393, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
116 5 0.01
117 50 0.13
118 4 0.01
120 334 0.85
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (120 bp):
ATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAT
ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAT
Found at i:28837018 original size:49 final size:49
Alignment explanation
Indices: 28836946--28837049 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
28836936 GAAAAAAAAC
* * *
28836946 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
28836995 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
28837044 AAATTA
1 AAATTA
28837050 TAACACATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:28839690 original size:36 final size:36
Alignment explanation
Indices: 28839653--28839723 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
28839643 AATTAAAAAT
*
28839653 AATAA-AAAT-AAAA-TGTTTTGCACTAACTATTAC
1 AATAATAAATCAAAACTGATTTGCACTAACTATTAC
* *
28839686 AATAATCACTCAAAACTGATTTGCACTAACTATTAC
1 AATAATAAATCAAAACTGATTTGCACTAACTATTAC
28839722 AA
1 AA
28839724 CCACCTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.16
34 2 0.06
35 4 0.12
36 21 0.66
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (36 bp):
AATAATAAATCAAAACTGATTTGCACTAACTATTAC
Found at i:28841080 original size:78 final size:78
Alignment explanation
Indices: 28840936--28841080 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 78
28840926 GGGGTTAACA
* * * * ***
28840936 AGGAGTGAATTTGCAATTGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGGCAGTGACA
1 AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAACAACA
28841001 CTCGAGGTTAATG
66 CTCGAGGTTAATG
* * * *
28841014 AGGACTGAATTCGCAATGGTGATTCTATCTTATTTGGCTTAGCTTCCTTTGGTAAGACAACAACA
1 AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAACAACA
28841079 CT
66 CT
28841081 TGAAACTTGC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 56 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (78 bp):
AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAACAACA
CTCGAGGTTAATG
Found at i:28842036 original size:20 final size:20
Alignment explanation
Indices: 28841988--28842038 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
28841978 AAATAGAGAA
*
28841988 AAGAAAAGAAACGTAAATAG
1 AAGAAAAGAAACGTAAAGAG
*
28842008 AAGAAAAGAAACGT-ACGAG
1 AAGAAAAGAAACGTAAAGAG
28842027 AAGAAGAAGAAA
1 AAGAA-AAGAAA
28842039 AAATTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.65, C:0.06, G:0.24, T:0.06
Consensus pattern (20 bp):
AAGAAAAGAAACGTAAAGAG
Found at i:28843633 original size:69 final size:70
Alignment explanation
Indices: 28843545--28843712 Score: 205
Period size: 70 Copynumber: 2.4 Consensus size: 70
28843535 ATCGTTTTAT
* *
28843545 AGGTTTAGCCCAGACGGGTAACCTTACAGGTATA-TACAACTTTGGCCAAACTATCTAATGTGTA
1 AGGTTTAGCCC-GACGGGTAACCTAACAGGTACATTACAACTTTGGCCAAACTATCTAATGTGTA
28843609 GAT-AA
65 GATAAA
** * * * *
28843614 AGGTTTAGCCCGTACGGGTAACCTAACTTGTACATTACAACTTTGGCCAAGCTATTTGATGTGTC
1 AGGTTTAGCCCG-ACGGGTAACCTAACAGGTACATTACAACTTTGGCCAAACTATCTAATGTGTA
28843679 GATAAA
65 GATAAA
* *
28843685 AAGTTTAGCCCGGACAGGTAACCTAACA
1 AGGTTTAGCCC-GACGGGTAACCTAACA
28843713 CAAATGAATA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
68 1 0.01
69 28 0.33
70 29 0.35
71 25 0.30
72 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (70 bp):
AGGTTTAGCCCGACGGGTAACCTAACAGGTACATTACAACTTTGGCCAAACTATCTAATGTGTAG
ATAAA
Found at i:28845208 original size:53 final size:54
Alignment explanation
Indices: 28845130--28845232 Score: 181
Period size: 53 Copynumber: 1.9 Consensus size: 54
28845120 TTCTTAAATT
*
28845130 TTTCTTATATGATGCCATAACCCACTAGTTACGGTCTTACACGATATGGTCTTC
1 TTTCTTATATGATGCCATAACCCACTAGTTACAGTCTTACACGATATGGTCTTC
*
28845184 TTTC-TATATGATGTCATAACCCACTAGTTACAGTCTTACACGATATGGT
1 TTTCTTATATGATGCCATAACCCACTAGTTACAGTCTTACACGATATGGT
28845233 TTTCAGCGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 43 0.91
54 4 0.09
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
TTTCTTATATGATGCCATAACCCACTAGTTACAGTCTTACACGATATGGTCTTC
Found at i:28846897 original size:17 final size:17
Alignment explanation
Indices: 28846875--28846910 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28846865 GATTAAGGGG
* *
28846875 AACAAAAATAACTAAAT
1 AACAAAAAGAAATAAAT
28846892 AACAAAAAGAAATAAAT
1 AACAAAAAGAAATAAAT
28846909 AA
1 AA
28846911 AGAGAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (17 bp):
AACAAAAAGAAATAAAT
Found at i:28848047 original size:13 final size:13
Alignment explanation
Indices: 28848016--28848090 Score: 80
Period size: 14 Copynumber: 5.5 Consensus size: 13
28848006 ACAAACTAAG
*
28848016 AAAGAAAAACAAA
1 AAAGAAAAAGAAA
28848029 GAAAGAAAAAGAAA
1 -AAAGAAAAAGAAA
*
28848043 GAAG-AAAAGAAGA
1 AAAGAAAAAGAA-A
28848056 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
*
28848069 AAAGAAAGAACAAA
1 AAAGAAA-AAGAAA
28848083 CAAAGAAA
1 -AAAGAAA
28848091 TTTCAATTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.13
13 15 0.28
14 24 0.45
15 7 0.13
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:28848053 original size:8 final size:7
Alignment explanation
Indices: 28848013--28848090 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
28848003 AATACAAACT
28848013 AAGAAAGA
1 AAGAAA-A
*
28848021 AA-AACA
1 AAGAAAA
28848027 AAGAAAGA
1 AAGAAA-A
*
28848035 AA-AAGA
1 AAGAAAA
28848041 AAGAAGAA
1 AAGAA-AA
28848049 AAGAAGAA
1 AAGAA-AA
28848057 AAG-AAA
1 AAGAAAA
28848063 AAGAAAA
1 AAGAAAA
*
28848070 AAGAAAG
1 AAGAAAA
*
28848077 AACAAACA
1 AAGAAA-A
28848085 AAGAAA
1 AAGAAA
28848091 TTTCAATTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
6 11 0.20
7 23 0.41
8 22 0.39
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:28848059 original size:26 final size:25
Alignment explanation
Indices: 28848013--28848075 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
28848003 AATACAAACT
28848013 AAGAAAGAA-AAACAAAGAAAGAAA
1 AAGAAAGAAGAAACAAAGAAAGAAA
28848037 AAGAAAGAAGAAA-AGAAGAAAAGAAA
1 AAGAAAGAAGAAACA-AAG-AAAGAAA
*
28848063 AAGAAAAAAGAAA
1 AAGAAAGAAGAAA
28848076 GAACAAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 10 0.29
25 6 0.17
26 19 0.54
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (25 bp):
AAGAAAGAAGAAACAAAGAAAGAAA
Found at i:28848087 original size:11 final size:10
Alignment explanation
Indices: 28848016--28848090 Score: 64
Period size: 11 Copynumber: 7.1 Consensus size: 10
28848006 ACAAACTAAG
28848016 AAAGAAA-AA
1 AAAGAAAGAA
28848025 CAAAGAAAGAA
1 -AAAGAAAGAA
28848036 AAAGAAAGAA
1 AAAGAAAGAA
28848046 GAAA-AGAAGAA
1 -AAAGA-AAGAA
*
28848057 AAGAAAAAGAAA
1 AA-AGAAAG-AA
28848069 AAAGAAAGAA
1 AAAGAAAGAA
*
28848079 CAAACAAAGAA
1 -AAAGAAAGAA
28848090 A
1 A
28848091 TTTCAATTGG
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 23 0.41
11 28 0.50
12 5 0.09
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:28848087 original size:22 final size:21
Alignment explanation
Indices: 28848026--28848090 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
28848016 AAAGAAAAAC
*
28848026 AAAGAAAGAAAAAGAAAGAAGA
1 AAAGAAAGAAAAAAAAAGAA-A
28848048 AAAG-AAGAAAAGAAAAAGAAA
1 AAAGAAAGAAAA-AAAAAGAAA
*
28848069 AAAGAAAGAACAAACAAAGAAA
1 AAAGAAAGAA-AAAAAAAGAAA
28848091 TTTCAATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.32
22 24 0.63
23 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAGAAA
Found at i:28850270 original size:22 final size:22
Alignment explanation
Indices: 28850240--28850281 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28850230 AACAAAAATC
* *
28850240 TGCTTTTTTTTTGTTGTTTTAA
1 TGCTATTTTCTTGTTGTTTTAA
28850262 TGCTATTTTCTTGTTGTTTT
1 TGCTATTTTCTTGTTGTTTT
28850282 CTTCCTATTT
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:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (22 bp):
TGCTATTTTCTTGTTGTTTTAA
Found at i:28850289 original size:22 final size:22
Alignment explanation
Indices: 28850245--28850292 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
28850235 AAATCTGCTT
* *
28850245 TTTTTTTGTTGTTTTAATGCTA
1 TTTTCTTGTTGTTTTAATCCTA
**
28850267 TTTTCTTGTTGTTTTCTTCCTA
1 TTTTCTTGTTGTTTTAATCCTA
28850289 TTTT
1 TTTT
28850293 GTTACCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTTCTTGTTGTTTTAATCCTA
Found at i:28856215 original size:38 final size:38
Alignment explanation
Indices: 28856172--28856253 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
28856162 TAAAACAATT
* *
28856172 GATAAACCAAACTTTGTGAGATAAACATGTAAAAAACA
1 GATAAAACAAACTTTGTGAGATAAACATATAAAAAACA
* * *
28856210 GATAAAAGATATTTTGTGAGATAAACATATAAAAAACA
1 GATAAAACAAACTTTGTGAGATAAACATATAAAAAACA
28856248 GATAAA
1 GATAAA
28856254 GTTTGTAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (38 bp):
GATAAAACAAACTTTGTGAGATAAACATATAAAAAACA
Found at i:28857121 original size:39 final size:39
Alignment explanation
Indices: 28857078--28857165 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
28857068 TGGGCTTAGG
* *
28857078 TTTTTTGCGGCGCTTTTCTAAAAA-CGCCACTAATGCTCA
1 TTTTTAGCGGCG-TTTTCCAAAAAGCGCCACTAATGCTCA
* * *
28857117 TTTTTAGCGGTGTTTTCCAAAAAGCGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTCCAAAAAGCGCCACTAATGCTCA
28857156 TTTTTAGCGG
1 TTTTTAGCGG
28857166 TTAAGGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 10 0.23
39 33 0.77
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCCAAAAAGCGCCACTAATGCTCA
Found at i:28857133 original size:38 final size:39
Alignment explanation
Indices: 28857091--28857166 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
28857081 TTTGCGGCGC
*
28857091 TTTTCTAAAAA-CGCCACTAATGCTCATTTTTAGCGGTG
1 TTTTCCAAAAAGCGCCACTAATGCTCATTTTTAGCGGTG
* *
28857129 TTTTCCAAAAAGCGCCGCTAATGCTTATTTTTAGCGGT
1 TTTTCCAAAAAGCGCCACTAATGCTCATTTTTAGCGGT
28857167 TAAGGAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 10 0.29
39 24 0.71
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (39 bp):
TTTTCCAAAAAGCGCCACTAATGCTCATTTTTAGCGGTG
Found at i:28857743 original size:6 final size:7
Alignment explanation
Indices: 28857717--28857753 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
28857707 CACTAACTCT
*
28857717 TAACCTC
1 TAACCCC
28857724 TAACCCC
1 TAACCCC
28857731 TAACCCC
1 TAACCCC
28857738 -AACCCC
1 TAACCCC
28857744 TAACCCC
1 TAACCCC
28857751 TAA
1 TAA
28857754 ACCTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:28857743 original size:13 final size:13
Alignment explanation
Indices: 28857725--28857750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28857715 CTTAACCTCT
28857725 AACCCCTAACCCC
1 AACCCCTAACCCC
28857738 AACCCCTAACCCC
1 AACCCCTAACCCC
28857751 TAAACCTTAT
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:0.31, C:0.62, G:0.00, T:0.08
Consensus pattern (13 bp):
AACCCCTAACCCC
Found at i:28857868 original size:14 final size:15
Alignment explanation
Indices: 28857849--28857881 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28857839 ATTAAACCAG
28857849 AATCCCT-ATTCCAT
1 AATCCCTAATTCCAT
28857863 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
28857878 AATC
1 AATC
28857882 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:28858194 original size:41 final size:41
Alignment explanation
Indices: 28858136--28858285 Score: 223
Period size: 41 Copynumber: 3.7 Consensus size: 41
28858126 CAATGTTTTT
*
28858136 GCGGCACTTTTTCAAAAACGCCGCTAAAAGCCAGAACATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAAGCCAGAGCATTA
* *
28858177 GCGGCGCTTCTTT-AAAAACGCCGCTAAAAG-CATGAGCAATA
1 GCGGCACTT-TTTCAAAAACGCCGCTAAAAGCCA-GAGCATTA
* *
28858218 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAAGCCAGAGCATTA
28858259 GCGGCACTTTTTCAAAAACGCCGCTAA
1 GCGGCACTTTTTCAAAAACGCCGCTAA
28858286 TGCCCCGAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
40 5 0.05
41 90 0.91
42 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (41 bp):
GCGGCACTTTTTCAAAAACGCCGCTAAAAGCCAGAGCATTA
Found at i:28858369 original size:40 final size:41
Alignment explanation
Indices: 28858325--28858461 Score: 149
Period size: 40 Copynumber: 3.4 Consensus size: 41
28858315 TGGGCTTAGG
* *
28858325 TTTTTTGCGGCGCTTTTCCAAGAAACGCCGCCAATGCTC-A
1 TTTTTAGCGGCGCTTTTCCAAGAAACGCCGCTAATGCTCAA
* ** *
28858365 TTTTTAGCGGCAC-TTTCCTGGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGCTTTTCCAAGAAACGCCGCTAATGCTCAA
* *
28858405 TCTTTAGCGGCG-TTTT--ATGTAAAGCGCCGCTAATGCTCAA
1 TTTTTAGCGGCGCTTTTCCAAG-AAA-CGCCGCTAATGCTCAA
28858445 TTTTTAGCGGCGCTTTT
1 TTTTTAGCGGCGCTTTT
28858462 TGTCCAAACG
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 25 0.31
40 51 0.63
41 4 0.05
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (41 bp):
TTTTTAGCGGCGCTTTTCCAAGAAACGCCGCTAATGCTCAA
Found at i:28860008 original size:23 final size:23
Alignment explanation
Indices: 28859977--28860031 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28859967 AAACTAATCC
**
28859977 TCTCTCAAATTTCC-TCCCAATT
1 TCTCTCAAATTTCCTTCAAAATT
28859999 TCCTCTCAAA-TTCCTTCAAAATT
1 T-CTCTCAAATTTCCTTCAAAATT
28860022 TCTCTCAAAT
1 TCTCTCAAAT
28860032 CCATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (23 bp):
TCTCTCAAATTTCCTTCAAAATT
Found at i:28860031 original size:11 final size:11
Alignment explanation
Indices: 28859977--28860031 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
28859967 AAACTAATCC
28859977 TCTCTCAAATT
1 TCTCTCAAATT
*
28859988 TC-CTCCCAATT
1 TCTCT-CAAATT
28859999 TCCTCTCAAATT
1 T-CTCTCAAATT
*
28860011 CCT-TCAAAATT
1 TCTCTC-AAATT
28860022 TCTCTCAAAT
1 TCTCTCAAAT
28860032 CCATATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
10 4 0.11
11 21 0.60
12 8 0.23
13 2 0.06
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:28860056 original size:51 final size:50
Alignment explanation
Indices: 28859994--28860090 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
28859984 AATTTCCTCC
28859994 CAATTTCCTCTCAAATTCCTTCA-AAATTTCTCTCAAATCCATATTTAATTT
1 CAATTTCCTCTCAAATT-CTT-ATAAATTTCTCTCAAATCCATATTTAATTT
* * * *
28860045 CAATTTGCTCTCAAGTTCTTATTAAATTTCTCTTAAATCCCTATTT
1 CAATTTCCTCTCAAATTCTTA-TAAATTTCTCTCAAATCCATATTT
28860091 TTAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 1 0.03
50 3 0.08
51 36 0.90
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (50 bp):
CAATTTCCTCTCAAATTCTTATAAATTTCTCTCAAATCCATATTTAATTT
Found at i:28860067 original size:29 final size:28
Alignment explanation
Indices: 28860018--28860074 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
28860008 ATTCCTTCAA
*
28860018 AATTTCTCTCAAATCCATATTTAATTTC
1 AATTTCTCTCAAATCCATATTAAATTTC
* * *
28860046 AATTTGCTCTCAAGTTCTTATTAAATTTC
1 AATTT-CTCTCAAATCCATATTAAATTTC
28860075 TCTTAAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (28 bp):
AATTTCTCTCAAATCCATATTAAATTTC
Found at i:28862398 original size:45 final size:45
Alignment explanation
Indices: 28862348--28862435 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
28862338 ATATTTTGAA
* *
28862348 TATTTTGATATTATTTTATGTAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
** *
28862393 TATTTTGATATTATTTGATGTAATTTAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
28862436 TGTAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:28862431 original size:25 final size:25
Alignment explanation
Indices: 28862403--28862460 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
28862393 TATTTTGATA
** *
28862403 TTATTTGATGTAATTTAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
28862428 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
*
28862453 TTTTTTGA
1 TTATTTGA
28862461 GTTATTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:28865897 original size:125 final size:125
Alignment explanation
Indices: 28865653--28866072 Score: 621
Period size: 125 Copynumber: 3.4 Consensus size: 125
28865643 AACATACTAT
* * *
28865653 TGTAGCAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGGTAGA
* *
28865718 AGCGATTTTATACTATTTTCTTAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
66 AGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * *
28865778 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCA-AATAGCATCTTGCTTG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAA-AGCATCCTGGTAG
* * * * *
28865842 AAGTGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTTCAGGACCTAC
65 AAGCG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* *
28865903 TGTAGCAAAAGCGCGTCCATGTGGGCGCGATTT-AACAAATTCTTCTCATAAAGCATCCTGGTAG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAA-AAATTCTTCTCATAAAGCATCCTGGTAG
*
28865967 AAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCAAC
65 AAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * *
28866028 TGTAGCAAAAGCGCGTTCAGGAGGGCGCGATTTCACAAATTCTTC
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTC
28866073 GCGTCCACGT
Statistics
Matches: 261, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
124 43 0.16
125 177 0.68
126 41 0.16
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (125 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGGTAGA
AGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
Found at i:28866709 original size:20 final size:21
Alignment explanation
Indices: 28866679--28866745 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 21
28866669 AAAATTACAA
28866679 AAAAAGATTCAAAATAATTT-T
1 AAAAAG-TTCAAAATAATTTAT
*
28866700 CAAAAGTTCAAAAT-ATTTAT
1 AAAAAGTTCAAAATAATTTAT
* *
28866720 AAAAATTTCAAAAAAATTTAT
1 AAAAAGTTCAAAATAATTTAT
28866741 AAAAA
1 AAAAA
28866746 ATCTAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.10
20 20 0.50
21 16 0.40
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAAAGTTCAAAATAATTTAT
Found at i:28866739 original size:21 final size:21
Alignment explanation
Indices: 28866679--28866745 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
28866669 AAAATTACAA
*
28866679 AAAAAGATTCAAAATAATTT-T
1 AAAAAG-TTCAAAAAAATTTAT
* *
28866700 CAAAAGTTC-AAAATATTTAT
1 AAAAAGTTCAAAAAAATTTAT
*
28866720 AAAAATTTCAAAAAAATTTAT
1 AAAAAGTTCAAAAAAATTTAT
28866741 AAAAA
1 AAAAA
28866746 ATCTAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 7 0.18
20 11 0.29
21 20 0.53
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAAAGTTCAAAAAAATTTAT
Found at i:28866753 original size:20 final size:21
Alignment explanation
Indices: 28866709--28866763 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28866699 TCAAAAGTTC
* *
28866709 AAAATATTTATAAAAATTTCA
1 AAAAAATTTATAAAAATATCA
28866730 AAAAAATTTATAAAAA-ATC-
1 AAAAAATTTATAAAAATATCA
*
28866749 TAAAAATTATATAAA
1 AAAAAATT-TATAAA
28866764 GAAAGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 8 0.27
21 15 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATTTATAAAAATATCA
Found at i:28871244 original size:62 final size:62
Alignment explanation
Indices: 28871168--28871293 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
28871158 GAGCAATACT
* * * *
28871168 TTCCTAGAATCTACTGGTATTAATATATGGTTCTTATGTCTAAATAGTATATCTTCGAGTTC
1 TTCCTAGAATCTACTAGTATTAATATATGATTCTTACGTCTAAATAGTAGATCTTCGAGTTC
* * * *
28871230 TTCCTAGAATCTACTATTATTGATATATGATTCTTCCGTCTAAATTGTAGATCTTCGAGTTC
1 TTCCTAGAATCTACTAGTATTAATATATGATTCTTACGTCTAAATAGTAGATCTTCGAGTTC
28871292 TT
1 TT
28871294 TTTAAAATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (62 bp):
TTCCTAGAATCTACTAGTATTAATATATGATTCTTACGTCTAAATAGTAGATCTTCGAGTTC
Found at i:28873502 original size:51 final size:51
Alignment explanation
Indices: 28873426--28873628 Score: 237
Period size: 51 Copynumber: 4.0 Consensus size: 51
28873416 TTATTGCTTA
* *
28873426 GCCCTTGCGGTTGAGCCCCCGGTGTGGTAGCATAGATCCCACCGTGAAACT
1 GCCCTAGCGGTTGAGCCCCCGGTGTGGAAGCATAGATCCCACCGTGAAACT
* * *
28873477 GCCCTTGCGGTTGAGCCCCCGGTGTGGAAGCATAGATCCTACCGCGAAACT
1 GCCCTAGCGGTTGAGCCCCCGGTGTGGAAGCATAGATCCCACCGTGAAACT
* * * * * *
28873528 GCCCCAGTGGTTGAGTCCCCAGTGTGGAAGCATAGATCCCACCATGAAATT
1 GCCCTAGCGGTTGAGCCCCCGGTGTGGAAGCATAGATCCCACCGTGAAACT
* * * * * *
28873579 GGCCTAGTGGTTGAGTCCCCGGAGTGAAAGCAT-GAATCCCACCCTGAAAC
1 GCCCTAGCGGTTGAGCCCCCGGTGTGGAAGCATAG-ATCCCACCGTGAAAC
28873629 CGCCGTTGAG
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
50 1 0.01
51 131 0.99
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (51 bp):
GCCCTAGCGGTTGAGCCCCCGGTGTGGAAGCATAGATCCCACCGTGAAACT
Found at i:28879057 original size:10 final size:9
Alignment explanation
Indices: 28879034--28879110 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 9
28879024 ATTATTATAC
28879034 TTTTTAATA
1 TTTTTAATA
*
28879043 ATTTTAATGA
1 TTTTTAAT-A
28879053 TTTTTAAT-
1 TTTTTAATA
*
28879061 TTTTAAAAATA
1 TTTT--TAATA
*
28879072 TTTTTTATA
1 TTTTTAATA
28879081 TTTTTAA-A
1 TTTTTAATA
28879089 -TTTTAA-A
1 TTTTTAATA
*
28879096 TTTTAAAT-
1 TTTTTAATA
28879104 TTTTTAA
1 TTTTTAA
28879111 AAATTAATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
7 7 0.13
8 16 0.30
9 16 0.30
10 11 0.20
11 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTTAATA
Found at i:28879076 original size:29 final size:28
Alignment explanation
Indices: 28879039--28879095 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28879029 TATACTTTTT
*
28879039 AATAATTTTAATGATTTTTAATTTTTAAA
1 AATAATTTTAAT-ATTTTTAAATTTTAAA
* *
28879068 AATATTTTTTATATTTTTAAATTTTAAA
1 AATAATTTTAATATTTTTAAATTTTAAA
28879096 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
AATAATTTTAATATTTTTAAATTTTAAA
Found at i:28879084 original size:7 final size:7
Alignment explanation
Indices: 28879082--28879106 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28879072 TTTTTTATAT
28879082 TTTTAAA
1 TTTTAAA
28879089 TTTTAAA
1 TTTTAAA
28879096 TTTTAAA
1 TTTTAAA
28879103 TTTT
1 TTTT
28879107 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:28879711 original size:19 final size:20
Alignment explanation
Indices: 28879683--28879721 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
28879673 TAATATATAT
*
28879683 AAATACATAA-ATATTTTAA
1 AAATACATAATAAATTTTAA
*
28879702 AAATATATAATAAATTTTAA
1 AAATACATAATAAATTTTAA
28879722 TTTTATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATACATAATAAATTTTAA
Found at i:28885525 original size:77 final size:77
Alignment explanation
Indices: 28885398--28885548 Score: 275
Period size: 77 Copynumber: 2.0 Consensus size: 77
28885388 TACTGGGGAC
*
28885398 CTGTACTTTTTGAAGAAAGAAATGGAAAAAGAAAGTTGTGTGGCTATAAAAGTGGAAGATTCACC
1 CTGTACTTTTTGAAGAAAGAAATGAAAAAAGAAAGTTGTGTGGCTATAAAAGTGGAAGATTCACC
*
28885463 GATGCTGAGGAG
66 AATGCTGAGGAG
*
28885475 CTGTACTTTTTGAAGAAAGAAATGAAAAAAGATAGTTGTGTGGCTATAAAAGTGGAAGATTCACC
1 CTGTACTTTTTGAAGAAAGAAATGAAAAAAGAAAGTTGTGTGGCTATAAAAGTGGAAGATTCACC
28885540 AATGCTGAG
66 AATGCTGAG
28885549 ATCCATTACC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (77 bp):
CTGTACTTTTTGAAGAAAGAAATGAAAAAAGAAAGTTGTGTGGCTATAAAAGTGGAAGATTCACC
AATGCTGAGGAG
Found at i:28888414 original size:11 final size:12
Alignment explanation
Indices: 28888379--28888419 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
28888369 AACTCCCTTC
*
28888379 TTTT-AAATAAT
1 TTTTAAAATATT
*
28888390 TTTAAAAATATT
1 TTTTAAAATATT
28888402 TTTTAAAAT-TT
1 TTTTAAAATATT
28888413 TTTTAAA
1 TTTTAAA
28888420 CCTAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTAAAATATT
Found at i:28890687 original size:35 final size:34
Alignment explanation
Indices: 28890648--28890755 Score: 87
Period size: 35 Copynumber: 3.2 Consensus size: 34
28890638 TTTTGAATAT
28890648 TTTGATATTATTTGATGTACTAAAATAGAAGTTTA
1 TTTGATATTATTTGATGTA-TAAAATAGAAGTTTA
* * * ** * * **
28890683 TTTGAT-GTA-ATAAAATAAAAAAAATTAG-TTA
1 TTTGATATTATTTGATGTATAAAATAGAAGTTTA
28890714 TTTTGATATTATTTGATGTATTAAAATAGAAGTTTA
1 -TTTGATATTATTTGATGTA-TAAAATAGAAGTTTA
28890750 TTTGAT
1 TTTGAT
28890756 GTAATAAAAT
Statistics
Matches: 50, Mismatches: 18, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
31 3 0.06
32 13 0.26
33 6 0.12
34 6 0.12
35 19 0.38
36 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (34 bp):
TTTGATATTATTTGATGTATAAAATAGAAGTTTA
Found at i:28890750 original size:25 final size:25
Alignment explanation
Indices: 28890722--28890769 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
28890712 TATTTTGATA
*
28890722 TTATTTGATGTATTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
28890747 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
28890770 ATTTTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:28890783 original size:67 final size:67
Alignment explanation
Indices: 28890633--28890784 Score: 225
Period size: 67 Copynumber: 2.3 Consensus size: 67
28890623 TTATTTGTAC
28890633 AAATATTTTGAATATTTTGATATTATTTGATGTACTAAAATAGAAGTTTATTTGATGTAATAAAA
1 AAAT-TTTTGAATATTTTGATATTATTTGATGTACTAAAATAGAAGTTTATTTGATGTAATAAAA
28890698 TAA
65 TAA
*** * *
28890701 AAAAAATT-AGTTATTTTGATATTATTTGATGTATTAAAATAGAAGTTTATTTGATGTAATAAAA
1 AAATTTTTGA-ATATTTTGATATTATTTGATGTACTAAAATAGAAGTTTATTTGATGTAATAAAA
*
28890765 TAG
65 TAA
28890768 AAATTTTTGAATATTTT
1 AAATTTTTGAATATTTT
28890785 AAATATTTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
66 1 0.01
67 67 0.93
68 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (67 bp):
AAATTTTTGAATATTTTGATATTATTTGATGTACTAAAATAGAAGTTTATTTGATGTAATAAAAT
AA
Found at i:28890941 original size:66 final size:67
Alignment explanation
Indices: 28890830--28891290 Score: 571
Period size: 66 Copynumber: 6.9 Consensus size: 67
28890820 ATTAATACTC
* * *
28890830 TTAACTTAAAAATCCTAACCTAATTAAATT-AAAACCCTAACCCTTAACTTAAAAACACTAACCT
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
28890894 AA
66 AA
* *
28890896 TTAAGTT-AAAACCCTAATCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
28890960 AA
66 AA
* * * * * * *
28890962 TTTAATTAAAAACCCTAAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTAG
1 TTAAATTAAAAACCCT-AACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA
*
28891025 CC--C
63 CCTAA
* * * **
28891028 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTTAAAACATTAACC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACC
*
28891093 --C
65 TAA
* * * *
28891094 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTTAAAACCCTGACC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACC
28891159 TAA
65 TAA
* *
28891162 TTAAATTAAAAATCCTGACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
28891227 AA
66 AA
* *
28891229 TTAAATTAAAAACCCTAACCTAATTAAATT-AAAACTCTAACCCTTAACTTTAAAACCCTAAC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC
28891291 NNNNNNNNNN
Statistics
Matches: 347, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
65 24 0.07
66 188 0.54
67 76 0.22
68 59 0.17
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.28
Consensus pattern (67 bp):
TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCT
AA
Found at i:28890998 original size:45 final size:44
Alignment explanation
Indices: 28890860--28891248 Score: 416
Period size: 44 Copynumber: 8.8 Consensus size: 44
28890850 TAATTAAATT
* * * * *
28890860 AAAACCCTAACC--CTTAACTTAAAAACACTAACCTAATTAAGTT-
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTA
*
28890903 AAAACCCTAATCTAATTAAATTAAAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTA
*
28890947 AAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTA
* *
28890992 AAAACCCTAACCTAATTAAATTAAAAACCTTAGCCCTTAACTTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTA
* *
28891036 AAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTT
1 AAAACCCTAACCTAATTAAATTAAAAACCCT-AACCCTTAACTTA
** * * *
28891081 AAAACATTAACC--CTTAACTTAAAAACCCTAACCTAATTTAA-TTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC---CTTAACTTA
* * * * * *
28891125 AAAACCCTAAACC--CTTAACTTTAAAACCCTGACCTAATTAAATTA
1 AAAACCCT-AACCTAATTAAATTAAAAACCCTAACC--CTTAACTTA
* *
28891170 AAAATCCTGACCTAATTAAATTAAAAACCCTAACCCTTAACTTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTA
28891214 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC
28891249 TAATTAAATT
Statistics
Matches: 296, Mismatches: 38, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
42 4 0.01
43 31 0.10
44 126 0.43
45 118 0.40
46 17 0.06
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.27
Consensus pattern (44 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTA
Found at i:28891007 original size:89 final size:89
Alignment explanation
Indices: 28890903--28891246 Score: 423
Period size: 89 Copynumber: 3.9 Consensus size: 89
28890893 TAATTAAGTT
*
28890903 AAAACCCTAATCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTTAAT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTTAAT
28890968 TAAAAACCCTAAACCCTTAACTTA
66 TAAAAACCCTAAACCCTTAACTTA
* *
28890992 AAAACCCTAACCTAATTAAATTAAAAACCTTAGCCCTTAACTTAAAAACCCTAACCTAATTTAAT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTTAAT
*
28891057 TAAAAACCCTAAACCCTTAACTTT
66 TAAAAACCCTAAACCCTTAACTTA
** * * * *
28891081 AAAACATTAACC--CTTAACTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAAACC---CT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC---CTTAACTTAAAAACCCT-AACCTAATT
* * * *
28891140 TAACTTTAAAACCCT-GACCTAATTAAATTA
62 TAA-TTAAAAACCCTAAACC--CTTAACTTA
* * *
28891170 AAAATCCTGACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAAT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTTAAT
28891235 TAAAAACCCTAA
66 TAAAAACCCTAA
28891247 CCTAATTAAA
Statistics
Matches: 213, Mismatches: 28, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
87 24 0.11
88 18 0.08
89 131 0.62
90 18 0.08
91 22 0.10
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (89 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTTAAT
TAAAAACCCTAAACCCTTAACTTA
Found at i:28891048 original size:155 final size:154
Alignment explanation
Indices: 28890829--28891248 Score: 587
Period size: 155 Copynumber: 2.7 Consensus size: 154
28890819 CATTAATACT
* * * *
28890829 CTTAACTTAAAAATCCTAACCTAATTAAATTAAAACCCTAACCCTTAACTTAAAAACACTAACCT
1 CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTACCCTTAACTTAAAAACCCTAACCT
*
28890894 AATTAAGTT-AAAACCCTAATCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC
66 AATTAA-TTAAAAACCCTAAACTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC
28890958 CTAATTTAATTAAAAACCCTAAACC
130 CTAATTTAATTAAAAACCCTAAACC
28890983 CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTAGCCCTTAACTTAAAAACCCTAACC
1 CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTA-CCCTTAACTTAAAAACCCTAACC
** * * **
28891048 TAATTTAATTAAAAACCCTAAAC-CCTTAACTTTAAAACATTAACCCTTAACTTAAAAACCCTAA
65 TAA-TTAATTAAAAACCCTAAACTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAA
28891112 CCTAATTTAATTAAAAACCCTAAACC
129 CCTAATTTAATTAAAAACCCTAAACC
* * * * *
28891138 CTTAACTTTAAAACCCTGACCTAATTAAATTAAAAATCCTGACCTAATTAAATTAAAAACCCTAA
1 CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAA-CCTTACC--CTTAACTTAAAAACCCTAA
* *
28891203 CC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
63 CCTAATTAA-TTAAAAACCCTAAACTAATTAAATTAAAAACCCTAACC
28891249 TAATTAAATT
Statistics
Matches: 234, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
154 42 0.18
155 138 0.59
156 35 0.15
157 19 0.08
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.27
Consensus pattern (154 bp):
CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTACCCTTAACTTAAAAACCCTAACCT
AATTAATTAAAAACCCTAAACTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACC
TAATTTAATTAAAAACCCTAAACC
Found at i:28891272 original size:28 final size:23
Alignment explanation
Indices: 28890830--28891270 Score: 416
Period size: 23 Copynumber: 19.9 Consensus size: 23
28890820 ATTAATACTC
* *
28890830 TTAACTTAAAAATCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28890853 TTAAATT-AAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
* *
28890873 TTAACTTAAAAACACTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28890896 TTAAGTT-AAAACCCTAATCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28890918 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28890939 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28890962 TTTAATTAAAAACCCTAAACC--C
1 TTAAATTAAAAACCCT-AACCTAA
*
28890984 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* * *
28891007 TTAAATTAAAAACCTTAGCC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28891028 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28891051 TTTAATTAAAAACCCTAAACC--C
1 TTAAATTAAAAACCCT-AACCTAA
* * ** *
28891073 TTAACTTTAAAACATTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28891094 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28891117 TTTAATTAAAAACCCTAAACC--C
1 TTAAATTAAAAACCCT-AACCTAA
* * *
28891139 TTAACTTTAAAACCCTGACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28891162 TTAAATTAAAAATCCTGACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28891185 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28891206 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
28891229 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28891252 TTAAATT-AAAACTCTAACC
1 TTAAATTAAAAACCCTAACC
28891271 CTTAACTTTA
Statistics
Matches: 341, Mismatches: 58, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
20 6 0.02
21 95 0.28
22 79 0.23
23 149 0.44
24 12 0.04
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.28
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:28891662 original size:21 final size:20
Alignment explanation
Indices: 28891638--28891762 Score: 115
Period size: 21 Copynumber: 5.8 Consensus size: 20
28891628 GATAAATGTG
*
28891638 TACTTAAAAACCCTAATCTGT
1 TACTTAAAAACCCTAACCT-T
28891659 TACTTAAAAACCCTAACCCTT
1 TACTTAAAAACCCTAA-CCTT
*
28891680 AACTTAAAAACCCTAACCCCCTT
1 TACTTAAAAACCCTAA---CCTT
*
28891703 AACTTAAAAACCCTAACCTT
1 TACTTAAAAACCCTAACCTT
* *
28891723 TAACTTTAAAACCCTAAACTAATT
1 T-ACTTAAAAACCCT-AAC--CTT
*
28891747 TAATTAAAAACCCTAA
1 TACTTAAAAACCCTAA
28891763 TCTAAATTAA
Statistics
Matches: 90, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.04
21 44 0.49
22 7 0.08
23 32 0.36
24 3 0.03
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.28
Consensus pattern (20 bp):
TACTTAAAAACCCTAACCTT
Found at i:28891718 original size:44 final size:42
Alignment explanation
Indices: 28891639--28891739 Score: 139
Period size: 44 Copynumber: 2.4 Consensus size: 42
28891629 ATAAATGTGT
* **
28891639 ACTTAAAAACCCTAATCTGTTACTTAAAAACCCTAACCCTTA
1 ACTTAAAAACCCTAACCCCTTACTTAAAAACCCTAACCCTTA
*
28891681 ACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTAACCTTTA
1 ACTTAAAAACCCTAA-CCCCTT-ACTTAAAAACCCTAACCCTTA
*
28891725 ACTTTAAAACCCTAA
1 ACTTAAAAACCCTAA
28891740 ACTAATTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 15 0.29
43 3 0.06
44 34 0.65
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.27
Consensus pattern (42 bp):
ACTTAAAAACCCTAACCCCTTACTTAAAAACCCTAACCCTTA
Found at i:28891754 original size:44 final size:44
Alignment explanation
Indices: 28891639--28891762 Score: 137
Period size: 44 Copynumber: 2.9 Consensus size: 44
28891629 ATAAATGTGT
* **
28891639 ACTTAAAAACCCTAATC-TGTT-ACTTAAAAACCCTAACCCTTA
1 ACTTAAAAACCCTAACCAACTTAACTTAAAAACCCTAACCCTTA
** *
28891681 ACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTAACCTTTA
1 ACTTAAAAACCCTAACCAACTTAACTTAAAAACCCTAACCCTTA
* * *
28891725 ACTTTAAAACCCTAAACTAATTTAA-TTAAAAACCCTAA
1 ACTTAAAAACCCT-AACCAACTTAACTTAAAAACCCTAA
28891763 TCTAAATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 16 0.23
43 2 0.03
44 45 0.64
45 7 0.10
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (44 bp):
ACTTAAAAACCCTAACCAACTTAACTTAAAAACCCTAACCCTTA
Found at i:28891975 original size:115 final size:116
Alignment explanation
Indices: 28891767--28892009 Score: 400
Period size: 115 Copynumber: 2.1 Consensus size: 116
28891757 CCCTAATCTA
* * * **
28891767 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAAAGTTAGATTTGAAAAAATGTTTTTGACTGGTACTAACAAT
*
28891832 TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATATAATTTATC
66 TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
28891883 AATTAATAATTTTACATTCACATAAAGTTAGATTTGAAAAAATG-TTTTGACTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAAAGTTAGATTTGAAAAAATGTTTTTGACTGGTACTAACAAT
28891947 TAATAATTTTATATAATTTGA-AATTTTTACTAATCATTAATACAATTTATC
66 TAATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
*
28891998 AAGTAATAATTT
1 AATTAATAATTT
28892010 CACAAACTTA
Statistics
Matches: 119, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
114 2 0.02
115 76 0.64
116 41 0.34
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAAAGTTAGATTTGAAAAAATGTTTTTGACTGGTACTAACAAT
TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
Found at i:28895244 original size:124 final size:125
Alignment explanation
Indices: 28895018--28895244 Score: 321
Period size: 124 Copynumber: 1.8 Consensus size: 125
28895008 CCCAAACATG
* ** *
28895018 CTACTGTAGCAAAAGCGCGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATATTATCCTG
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
* * * * *
28895083 CTAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTATTTATTCCATGAC
66 CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAAAAAAAATTATTTATTCCATGAC
* **
28895143 CTACTGTAGCATAAGCACGTCCACGAGGGCGTGA-TTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
* *
28895207 CTAAAAGCGATTTTATACTATTTGATAAAAAATGTCAA
66 CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAA
28895245 CTCGAAATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
124 58 0.66
125 30 0.34
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAAAAAAAATTATTTATTCCATGAC
Found at i:28895269 original size:125 final size:125
Alignment explanation
Indices: 28895018--28895270 Score: 319
Period size: 124 Copynumber: 2.0 Consensus size: 125
28895008 CCCAAACATG
* ** *
28895018 CTACTGTAGCAAAAGCGCGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATATTATCCTG
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
* * * * * *
28895083 CTAGAAGCAATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTATTTATTCCATGAC
66 CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAAAAAAAATTATTTATTCCAGGAC
* **
28895143 CTACTGTAGCATAAGCACGTCCACGAGGGCGTGA-TTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
* * *** *
28895207 CTAAAAGCGATTTTATACTATTTGATAAAAAATGTCAACTCGAAATTATTTCTTCCAGGAC
66 CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAA-AAAAAATTATTTATTCCAGGAC
28895268 CTA
1 CTA
28895271 AAATCCCTAA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
124 58 0.54
125 50 0.46
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTA
CTAAAAGCAATTTTATACTATTTGATAAAAAACGTCAAAAAAAATTATTTATTCCAGGAC
Found at i:28901237 original size:54 final size:54
Alignment explanation
Indices: 28901134--28901238 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
28901124 TGGGACACAC
*
28901134 GGCCGTGTCTCAGCCCGTGTAACTCACTGACTTGAGACACACAGTCGTGTCGTA
1 GGCCGTGTCTCAGCCCGTGTAACTCACTGACTTGAGACACACAGCCGTGTCGTA
* * * ** *
28901188 GGCCGTGTGTCAGGCTGTGTAACTCTTTGACTTGATACACAC-GACCGTGTC
1 GGCCGTGTCTCAGCCCGTGTAACTCACTGACTTGAGACACACAG-CCGTGTC
28901239 ACAGACCGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (54 bp):
GGCCGTGTCTCAGCCCGTGTAACTCACTGACTTGAGACACACAGCCGTGTCGTA
Found at i:28919729 original size:23 final size:23
Alignment explanation
Indices: 28919700--28919821 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
28919690 ATAAGTGCCA
28919700 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28919723 CAATGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28919746 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28919769 CACTGATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
28919792 AATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28919815 CACTGAT
1 CACTGAT
28919822 CAATAACACT
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28919776 original size:46 final size:46
Alignment explanation
Indices: 28919707--28919821 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
28919697 CCACACTGAT
* *
28919707 ATGTAGCCGAAGCTACCAATGATATGTAGCCGTAGCTACCACTAAA
1 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACAACTAAA
* * *
28919753 ATGTAGCCGAAGCTACCACTGATATGTAGTCGTAGCTACAATTGAA
1 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACAACTAAA
28919799 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
28919822 CAATAACACT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACAACTAAA
Found at i:28933491 original size:42 final size:42
Alignment explanation
Indices: 28933459--28933539 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
28933449 TAGCCCAGCT
*
28933459 ATAGTCTTACACGAATCTCGTATCGATGCCAATGTCCCAAAC
1 ATAGTCTTACACGAATATCGTATCGATGCCAATGTCCCAAAC
* * *
28933501 ATGGTCTTACACGAATATCATATCGATGTCAATGTCCCA
1 ATAGTCTTACACGAATATCGTATCGATGCCAATGTCCCA
28933540 GACACGAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
ATAGTCTTACACGAATATCGTATCGATGCCAATGTCCCAAAC
Found at i:28935931 original size:24 final size:24
Alignment explanation
Indices: 28935894--28935948 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
28935884 AGGATCAATA
*
28935894 GGAGGTGCAGCTGGAGGTGCCTCC
1 GGAGGTGCAACTGGAGGTGCCTCC
* *
28935918 GGAGGTGTAACTGGATGTGCCTCC
1 GGAGGTGCAACTGGAGGTGCCTCC
28935942 GGAGGTG
1 GGAGGTG
28935949 ATACCAGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.20, G:0.45, T:0.20
Consensus pattern (24 bp):
GGAGGTGCAACTGGAGGTGCCTCC
Found at i:28938333 original size:33 final size:33
Alignment explanation
Indices: 28938271--28938333 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
28938261 TTTCATGATC
* *
28938271 CATTTCAATTCAATTCCATTTTCATATCATTTT
1 CATTTCAATTCAATTCCATGTTCAAATCATTTT
*
28938304 CATTTCAATTTC-ATTTCATGTTCAAATCAT
1 CATTTCAA-TTCAATTCCATGTTCAAATCAT
28938334 ATATCCCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.29, C:0.21, G:0.02, T:0.49
Consensus pattern (33 bp):
CATTTCAATTCAATTCCATGTTCAAATCATTTT
Found at i:28939429 original size:18 final size:18
Alignment explanation
Indices: 28939406--28939461 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
28939396 ATTATATATT
28939406 ATAATATTAATTATTAAA
1 ATAATATTAATTATTAAA
* *
28939424 ATAATATTATTTAATAAA
1 ATAATATTAATTATTAAA
** *
28939442 A-AAGGTAAATTATTAAA
1 ATAATATTAATTATTAAA
28939459 ATA
1 ATA
28939462 GTCACTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
ATAATATTAATTATTAAA
Found at i:28942011 original size:21 final size:21
Alignment explanation
Indices: 28941987--28942089 Score: 129
Period size: 21 Copynumber: 5.0 Consensus size: 21
28941977 TAGTTTTTTT
*
28941987 AGCTCTTTTGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* *
28942008 AGCTCTTACGAGCTTCTGTTA
1 AGCTCTTATGAGCTTCTGTTC
* * *
28942029 AACTCTTATGAGTTTCTGTTG
1 AGCTCTTATGAGCTTCTGTTC
28942050 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
28942071 AGCT-TT-CGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
28942090 GCATGTTCGG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
19 12 0.17
20 2 0.03
21 57 0.80
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:28963394 original size:31 final size:30
Alignment explanation
Indices: 28963359--28963461 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
28963349 TACACCATTA
*
28963359 GTCACTAAACTATGCGTAAGTTTTCATTTTG
1 GTCACTAAACTAT-CGAAAGTTTTCATTTTG
* * ** * *
28963390 GTCACTTAACTA--AAAAAATTACAATTTG
1 GTCACTAAACTATCGAAAGTTTTCATTTTG
**
28963418 GTCACTAAACTATTCGAAAGTTTTCATTTAA
1 GTCACTAAACTA-TCGAAAGTTTTCATTTTG
28963449 GTCACTAAACTAT
1 GTCACTAAACTAT
28963462 TTAGAAGTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
28 21 0.39
30 1 0.02
31 32 0.59
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (30 bp):
GTCACTAAACTATCGAAAGTTTTCATTTTG
Found at i:28963470 original size:31 final size:31
Alignment explanation
Indices: 28963418--28963483 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
28963408 TTACAATTTG
*
28963418 GTCACTAAACTATTCGAAAGTTTTCATTTAA
1 GTCACTAAACTATTAGAAAGTTTTCATTTAA
* *
28963449 GTCACTAAACTATTTAG-AAGTTTTTATTTTA
1 GTCACTAAACTA-TTAGAAAGTTTTCATTTAA
28963480 GTCA
1 GTCA
28963484 TTAGATTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTAGAAAGTTTTCATTTAA
Found at i:28964604 original size:18 final size:18
Alignment explanation
Indices: 28964548--28964604 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 18
28964538 GTGAATGATG
*
28964548 ATGAGAGAAAAACAAAGAG
1 ATGAGAGAAAAACAAAG-T
28964567 ATAGATGAAGAAAAAC-AAGT
1 AT-GA-G-AGAAAAACAAAGT
28964587 ATGAGAGAAAAACAAAGT
1 ATGAGAGAAAAACAAAGT
28964605 GAAGGAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 4 0.12
20 4 0.12
21 4 0.12
22 8 0.24
ACGTcount: A:0.61, C:0.05, G:0.23, T:0.11
Consensus pattern (18 bp):
ATGAGAGAAAAACAAAGT
Found at i:28966125 original size:165 final size:165
Alignment explanation
Indices: 28965853--28966347 Score: 927
Period size: 165 Copynumber: 3.0 Consensus size: 165
28965843 TACCATTAAG
* *
28965853 GAATGATTCAATATACGAACTTACTTGAACTCATAACAACTTCTAACACGATTAGACCACTATTT
1 GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACACGATTAGACCACTATTC
* *
28965918 CGCTACTTCGACTTTTTCGTGATTTGTGTTCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
66 CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
28965983 TATTCAATTAAACTCATTCCAGCATTTAAAATAAT
131 TATTCAATTAAACTCATTCCAGCATTTAAAATAAT
28966018 GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACACGATTAGACCACTATTC
1 GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACACGATTAGACCACTATTC
28966083 CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
66 CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
*
28966148 TGTTCAATTAAACTCATTCCAGCATTTAAAATAAT
131 TATTCAATTAAACTCATTCCAGCATTTAAAATAAT
*
28966183 GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACGCGATTAGACCACTATTC
1 GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACACGATTAGACCACTATTC
28966248 CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
66 CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
*
28966313 TATTCAACTAAACTCATTCCAGCATTTAAAATAAT
131 TATTCAATTAAACTCATTCCAGCATTTAAAATAAT
28966348 CAATTTAACT
Statistics
Matches: 322, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 322 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (165 bp):
GAATGATTCAATATACGAACTTACTTTAACTCATAACAACTTCTAACACGATTAGACCACTATTC
CGCTACTTTGACTTTTTCGTGATTTGTGTCCGTTCGAGTTGTTTCTTGATCTAGATAAATAATTT
TATTCAATTAAACTCATTCCAGCATTTAAAATAAT
Found at i:28968327 original size:19 final size:20
Alignment explanation
Indices: 28968303--28968340 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28968293 CACTTATCTA
28968303 ACTTTA-AGACAATTTAAAC
1 ACTTTAGAGACAATTTAAAC
*
28968322 ACTTTAGAGAGAATTTAAA
1 ACTTTAGAGACAATTTAAA
28968341 ATCATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
ACTTTAGAGACAATTTAAAC
Found at i:28968495 original size:22 final size:22
Alignment explanation
Indices: 28968442--28968484 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28968432 GGACTTGGGA
28968442 CAGTTGT-TGTGTCACAAGTCCT
1 CAGTTGTGT-TGTCACAAGTCCT
28968464 CAGTTGTGTTGTCACAAGTCC
1 CAGTTGTGTTGTCACAAGTCC
28968485 CTGTTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (22 bp):
CAGTTGTGTTGTCACAAGTCCT
Found at i:28969983 original size:11 final size:11
Alignment explanation
Indices: 28969967--28969999 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28969957 TATGTTATTT
28969967 TATAATAAAAA
1 TATAATAAAAA
28969978 TATAATAAATAA
1 TATAATAAA-AA
28969990 -ATAATAAAAA
1 TATAATAAAAA
28970000 GTAAGTGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:28972885 original size:2 final size:2
Alignment explanation
Indices: 28972880--28972926 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
28972870 ACACACACAA
28972880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28972922 AT AT A
1 AT AT A
28972927 AAAGAGCACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28973439 original size:18 final size:19
Alignment explanation
Indices: 28973399--28973446 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
28973389 TATTTTAAAT
*
28973399 AAAAATAT-AAAAATTATG
1 AAAAATATAAAAAATCATG
*
28973417 AAAAATATAAAAAATCCTG
1 AAAAATATAAAAAATCATG
28973436 AAAAATA-AAAA
1 AAAAATATAAAA
28973447 TAAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAAATATAAAAAATCATG
Found at i:28974036 original size:18 final size:18
Alignment explanation
Indices: 28973995--28974029 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28973985 TCTAAAATAA
*
28973995 AAAAAAATAATAATAAAG
1 AAAAAAATAATAAAAAAG
28974013 AAAAAAAT-ATAAAAAAG
1 AAAAAAATAATAAAAAAG
28974030 TACAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAAAAATAATAAAAAAG
Found at i:28985737 original size:7 final size:7
Alignment explanation
Indices: 28985725--28985761 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
28985715 CGGATTCCGT
28985725 TTTTAAA
1 TTTTAAA
28985732 TTTTAAA
1 TTTTAAA
28985739 TTTTAAA
1 TTTTAAA
28985746 TTTTAAA
1 TTTTAAA
28985753 TTTTAAA
1 TTTTAAA
28985760 TT
1 TT
28985762 AAATATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:28985769 original size:21 final size:21
Alignment explanation
Indices: 28985725--28985769 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
28985715 CGGATTCCGT
*
28985725 TTTTAAATTTTAAATTTTAAA
1 TTTTAAATTTTAAATTTAAAA
28985746 TTTTAAATTTTAAA-TTAAATA
1 TTTTAAATTTTAAATTTAAA-A
28985767 TTT
1 TTT
28985770 AGAAGTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAAATTTTAAATTTAAAA
Found at i:28991726 original size:13 final size:13
Alignment explanation
Indices: 28991708--28991732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28991698 ACTAAAAAAA
28991708 TTCTAAAATAATT
1 TTCTAAAATAATT
28991721 TTCTAAAATAAT
1 TTCTAAAATAAT
28991733 AATTTTGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTCTAAAATAATT
Found at i:28991800 original size:3 final size:3
Alignment explanation
Indices: 28991792--28991832 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28991782 AAAGTATCTT
28991792 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28991833 TTGCTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28992012 original size:145 final size:145
Alignment explanation
Indices: 28991843--28992133 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 145
28991833 TTGCTTTAAA
28991843 TTTTTTTTCAAATATATATGATTTCAAATTTATGTGCTCTAACATAAAATTAGTTATACTGTAAC
1 TTTTTTTTCAAATATATATGATTTCAAATTTATGTGCTCTAACATAAAATTAGTTATACTGTAAC
28991908 AAAATTTAAATTTAACATGTTTAATTTTTTTTAATTTAACTTGAACAATTGCACTTGATTCGACT
66 AAAATTTAAATTTAACATGTTTAATTTTTTTTAATTTAACTTGAACAATTGCACTTGATTCGACT
28991973 CAAATTTCATTTCAC
131 CAAATTTCATTTCAC
28991988 TTTTTTTTCAAATATATATGATTTCAAATTTATGTGCTCTAACATAAAATTAGTTATACTGTAAC
1 TTTTTTTTCAAATATATATGATTTCAAATTTATGTGCTCTAACATAAAATTAGTTATACTGTAAC
*
28992053 AAAATTTTAATTTAACATGTTTAATTTTTTTTAATTTAACTTGAACAATTGCACTTGATTCGACT
66 AAAATTTAAATTTAACATGTTTAATTTTTTTTAATTTAACTTGAACAATTGCACTTGATTCGACT
28992118 CAAATTTCATTTCAC
131 CAAATTTCATTTCAC
28992133 T
1 T
28992134 CGACTCAATT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (145 bp):
TTTTTTTTCAAATATATATGATTTCAAATTTATGTGCTCTAACATAAAATTAGTTATACTGTAAC
AAAATTTAAATTTAACATGTTTAATTTTTTTTAATTTAACTTGAACAATTGCACTTGATTCGACT
CAAATTTCATTTCAC
Found at i:28992102 original size:24 final size:24
Alignment explanation
Indices: 28992057--28992102 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28992047 TGTAACAAAA
***
28992057 TTTTAATTTAACATGTTTAATTTT
1 TTTTAATTTAACATGAACAATTTT
*
28992081 TTTTAATTTAACTTGAACAATT
1 TTTTAATTTAACATGAACAATT
28992103 GCACTTGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAATTTAACATGAACAATTTT
Found at i:28992123 original size:21 final size:21
Alignment explanation
Indices: 28992099--28992141 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28992089 TAACTTGAAC
* *
28992099 AATTGCACTTGATTCGACTCA
1 AATTGCACTTCACTCGACTCA
* *
28992120 AATTTCATTTCACTCGACTCA
1 AATTGCACTTCACTCGACTCA
28992141 A
1 A
28992142 TTAGAAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (21 bp):
AATTGCACTTCACTCGACTCA
Found at i:28993235 original size:2 final size:2
Alignment explanation
Indices: 28993228--28993253 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28993218 AAATGCATAC
28993228 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28993254 GATCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28995602 original size:15 final size:15
Alignment explanation
Indices: 28995561--28995606 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
28995551 AGTGATTGAA
*
28995561 AAAAAACAGAAAAAAG
1 AAAAAACA-AAAAAAT
*
28995577 AAAATACAAAAAAAT
1 AAAAAACAAAAAAAT
*
28995592 AAAAAATAAAAAAAT
1 AAAAAACAAAAAAAT
28995607 TATTATGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (15 bp):
AAAAAACAAAAAAAT
Found at i:29009463 original size:15 final size:15
Alignment explanation
Indices: 29009438--29009473 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
29009428 AAATTAACAA
29009438 TAATATTAATATAAAT
1 TAAT-TTAATATAAAT
*
29009454 TAATTTAATATAATT
1 TAATTTAATATAAAT
29009469 TAATT
1 TAATT
29009474 ATAGAAGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTTAATATAAAT
Found at i:29009656 original size:20 final size:20
Alignment explanation
Indices: 29009633--29009671 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29009623 TAGAAATTAC
29009633 AAAAAAAATATAAAAATATG
1 AAAAAAAATATAAAAATATG
* *
29009653 AAAAAATATTTAAAAATAT
1 AAAAAAAATATAAAAATAT
29009672 AGAACCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAAAATATAAAAATATG
Found at i:29009930 original size:10 final size:9
Alignment explanation
Indices: 29009905--29009929 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29009895 ATTTTAAAAT
29009905 AATTTTTAC
1 AATTTTTAC
29009914 AATTTTTAC
1 AATTTTTAC
29009923 AATTTTT
1 AATTTTT
29009930 TCGTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (9 bp):
AATTTTTAC
Found at i:29013866 original size:42 final size:42
Alignment explanation
Indices: 29013810--29013896 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
29013800 TGTTTTAACC
29013810 AATTGGGCTACTACCCATTCTTGGTATGTTATAAAACTATTT
1 AATTGGGCTACTACCCATTCTTGGTATGTTATAAAACTATTT
29013852 AATTGGGCTACTACCCATTCTTGGTATGTTATAAAACTATTT
1 AATTGGGCTACTACCCATTCTTGGTATGTTATAAAACTATTT
29013894 AAT
1 AAT
29013897 ATATATCCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (42 bp):
AATTGGGCTACTACCCATTCTTGGTATGTTATAAAACTATTT
Found at i:29014719 original size:27 final size:28
Alignment explanation
Indices: 29014689--29014763 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
29014679 GTATCGTGAA
*
29014689 AGGGTACTCATGGGAA-GGTACT-ATTGG
1 AGGGTACTCAT-GGAAGGGTACTCATGGG
* *
29014716 AGGGTAC-CGTGGAAGGGTACTCGTGGG
1 AGGGTACTCATGGAAGGGTACTCATGGG
29014743 AGGGTA-TCATGGAAGGGTACT
1 AGGGTACTCATGGAAGGGTACT
29014764 TGCAAGAGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.10
26 8 0.20
27 29 0.71
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.23
Consensus pattern (28 bp):
AGGGTACTCATGGAAGGGTACTCATGGG
Found at i:29014732 original size:13 final size:13
Alignment explanation
Indices: 29014716--29014762 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
29014706 GTACTATTGG
29014716 AGGGTACCGTGGA
1 AGGGTACCGTGGA
*
29014729 AGGGTACTCGTGGG
1 AGGGTAC-CGTGGA
* *
29014743 AGGGTATCATGGA
1 AGGGTACCGTGGA
29014756 AGGGTAC
1 AGGGTAC
29014763 TTGCAAGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.23, C:0.13, G:0.45, T:0.19
Consensus pattern (13 bp):
AGGGTACCGTGGA
Found at i:29014772 original size:27 final size:27
Alignment explanation
Indices: 29014715--29014776 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
29014705 GGTACTATTG
* ***
29014715 GAGGGTACCGTGGAAGGGTACTCGTGG
1 GAGGGTACCATGGAAGGGTACTCGCAA
* *
29014742 GAGGGTATCATGGAAGGGTACTTGCAA
1 GAGGGTACCATGGAAGGGTACTCGCAA
29014769 GAGGGTAC
1 GAGGGTAC
29014777 TCTCGTAAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.44, T:0.19
Consensus pattern (27 bp):
GAGGGTACCATGGAAGGGTACTCGCAA
Found at i:29014818 original size:14 final size:14
Alignment explanation
Indices: 29014756--29014821 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
29014746 GTATCATGGA
* *
29014756 AGGGTACTTGCAAG
1 AGGGTACTCGTAAG
29014770 AGGGTACTCTCGTAAG
1 AGGGTA--CTCGTAAG
* *
29014786 AAGGTA-TCATGAA-
1 AGGGTACTCGT-AAG
29014799 AGGGTACTCGTAAG
1 AGGGTACTCGTAAG
29014813 AGGGTACTC
1 AGGGTACTC
29014822 TGTATTGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 10 0.24
14 20 0.49
16 11 0.27
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (14 bp):
AGGGTACTCGTAAG
Found at i:29016103 original size:56 final size:55
Alignment explanation
Indices: 29016041--29016147 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 55
29016031 CCTTCTTTCG
* * *
29016041 CGTCCACAACTTGTCTTTTCCCGCGTCCAC-AATTGACCATCCCCTTGTCCGCTTGA
1 CGTCCACAACTCGCCTTTTCCCACGTCCACGAATTG-CCAT-CCCTTGTCCGCTTGA
* *
29016097 CGTCCACAACTCGCCTTTTCCCACGTCCACGACTTGTCATCCCTTGTCCGC
1 CGTCCACAACTCGCCTTTTCCCACGTCCACGAATTGCCATCCCTTGTCCGC
29016148 CGAATGGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 11 0.24
56 30 0.67
57 4 0.09
ACGTcount: A:0.15, C:0.42, G:0.14, T:0.29
Consensus pattern (55 bp):
CGTCCACAACTCGCCTTTTCCCACGTCCACGAATTGCCATCCCTTGTCCGCTTGA
Found at i:29016187 original size:16 final size:15
Alignment explanation
Indices: 29016162--29016192 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
29016152 TGGTTACATC
29016162 TCGTCATCTCATTAT
1 TCGTCATCTCATTAT
29016177 TCGTACATCTCATTAT
1 TCGT-CATCTCATTAT
29016193 CCGTTAGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (15 bp):
TCGTCATCTCATTAT
Found at i:29021380 original size:2 final size:2
Alignment explanation
Indices: 29021373--29021400 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29021363 TGAACAAACC
29021373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29021401 GACATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29022561 original size:8 final size:8
Alignment explanation
Indices: 29022530--29022577 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
29022520 TTTAATACGA
29022530 TAAAATAAT
1 TAAAAT-AT
*
29022539 TTAAATA-
1 TAAAATAT
29022546 TAATAATAT
1 TAA-AATAT
29022555 TAAAATAT
1 TAAAATAT
*
29022563 TAAAAAAT
1 TAAAATAT
29022571 TAAAATA
1 TAAAATA
29022578 AATATAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 2 0.06
8 23 0.70
9 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAAATAT
Found at i:29022899 original size:31 final size:30
Alignment explanation
Indices: 29022856--29022918 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29022846 TAATAAAAAT
29022856 AAAATTGTATTTAACTTCCCTAAAAATAATA
1 AAAATTGTATTTAA-TTCCCTAAAAATAATA
** *
29022887 AAAATT-TGATTTAATTCTTTAAAAATTATA
1 AAAATTGT-ATTTAATTCCCTAAAAATAATA
29022917 AA
1 AA
29022919 GGTATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTGTATTTAATTCCCTAAAAATAATA
Found at i:29040409 original size:6 final size:6
Alignment explanation
Indices: 29040379--29040412 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
29040369 TACTTCTTAA
*
29040379 TTATTA TTATTAT TTATTT TTATTT TTATTT TTA
1 TTATTT TTATT-T TTATTT TTATTT TTATTT TTA
29040413 ATACTCTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:29045341 original size:17 final size:16
Alignment explanation
Indices: 29045318--29045376 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
29045308 TCAGTTCTCA
29045318 ATTTAAATTTTATTTT
1 ATTTAAATTTTATTTT
*
29045334 AGTTTAAATCTTA--TT
1 A-TTTAAATTTTATTTT
*
29045349 ATTTAAA-TTTATTCTA
1 ATTTAAATTTTATT-TT
*
29045365 ATTTAAAGTTTA
1 ATTTAAATTTTA
29045377 GATATATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 3 0.09
14 6 0.17
15 3 0.09
16 9 0.26
17 14 0.40
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTAAATTTTATTTT
Found at i:29045397 original size:23 final size:23
Alignment explanation
Indices: 29045344--29045400 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
29045334 AGTTTAAATC
*
29045344 TTATTA-TTTAAATTTATTCTAA
1 TTATTAGTTTAAATATATTCTAA
* *
29045366 TT-TAAAGTTTAGATATATTCTAA
1 TTAT-TAGTTTAAATATATTCTAA
29045389 TTATTAGTTTAA
1 TTATTAGTTTAA
29045401 GTATTTATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 22 0.81
24 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (23 bp):
TTATTAGTTTAAATATATTCTAA
Found at i:29045749 original size:27 final size:26
Alignment explanation
Indices: 29045706--29045757 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
29045696 AAGAATTAAG
*
29045706 TTTTTTATTAAATATAAAGTTATTTAC
1 TTTTTTATTAAATAT-AACTTATTTAC
*
29045733 TTTTTATATTATA-ATAACTTATTTA
1 TTTTT-TATTAAATATAACTTATTTA
29045758 TTATTAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.41
27 7 0.32
28 6 0.27
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTTATTAAATATAACTTATTTAC
Found at i:29046226 original size:3 final size:3
Alignment explanation
Indices: 29046218--29046251 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29046208 ATTCAAGCTC
29046218 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29046252 TGCACGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29050502 original size:7 final size:7
Alignment explanation
Indices: 29050488--29050521 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
29050478 ATTTGGGATT
29050488 ACAAAAA
1 ACAAAAA
*
29050495 AAAAAAA
1 ACAAAAA
29050502 ACAAAAA
1 ACAAAAA
29050509 ACAAAAA
1 ACAAAAA
29050516 ACAAAA
1 ACAAAA
29050522 CAAAATCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:29050507 original size:14 final size:14
Alignment explanation
Indices: 29050488--29050526 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
29050478 ATTTGGGATT
29050488 ACAAAAAAAAAAAA
1 ACAAAAAAAAAAAA
*
29050502 ACAAAAAACAAAAA
1 ACAAAAAAAAAAAA
29050516 ACAAAACAAAA
1 ACAAAA-AAAA
29050527 TCAACATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAAAAAA
Found at i:29051570 original size:43 final size:43
Alignment explanation
Indices: 29051521--29051773 Score: 303
Period size: 43 Copynumber: 5.9 Consensus size: 43
29051511 GCGCCGCAAA
** **
29051521 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
29051564 AAACGCCACTAAAGACCATGACTTTTAGCGGCGC-TTTCCCGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC-AC
* * * * *
29051607 AAACACCGCTAAAGACCATTACCTTTAGCGGCACTTTTTCGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* **
29051650 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCAAAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
29051693 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
29051736 AAACGCCGC-AACAGACCATGACCTTTAGTGGCGTTTTT
1 AAACGCCGCTAA-AGACCATGACCTTTAGCGGCGCTTTT
29051774 TAAAAACGCC
Statistics
Matches: 177, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 8 0.05
43 165 0.93
44 4 0.02
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:29052187 original size:65 final size:65
Alignment explanation
Indices: 29052112--29052252 Score: 176
Period size: 65 Copynumber: 2.2 Consensus size: 65
29052102 ACGCTGCTCT
* *
29052112 GCTTCCCTCGCTGCAACCTCTGCTTTAAGCTGCAGCTGGAGTTCTTC-ATCTTTCATTGAACCTC
1 GCTTCTCTCGCTGCAACATCTGCTTTAAGCTGCAGCTGGAGTTCTTCAATCTTT-ATTGAACCTC
29052176 A
65 A
** * * ** *
29052177 GCTTCTCTCGCTGCTGCATTTGCTTTAAGTTTTAGCTGGAGTTCTTCATATCTTTTTTGAACCTC
1 GCTTCTCTCGCTGCAACATCTGCTTTAAGCTGCAGCTGGAGTTCTTCA-ATCTTTATTGAACCTC
29052242 A
65 A
29052243 GCTTCTCTCG
1 GCTTCTCTCG
29052253 ATGTTGCCTC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 39 0.60
66 20 0.31
67 6 0.09
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (65 bp):
GCTTCTCTCGCTGCAACATCTGCTTTAAGCTGCAGCTGGAGTTCTTCAATCTTTATTGAACCTCA
Found at i:29052268 original size:66 final size:65
Alignment explanation
Indices: 29052145--29052273 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 65
29052135 TTTAAGCTGC
* **
29052145 AGCTGGAGTTCTTCATCTTTCATTGAACCTCAGCTTCTCTCGCTGCTGCATTTGCTTTAAGTTTT
1 AGCTGGAGTTCTTCATCTTTCATTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTTT
* * *
29052210 AGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 AGCTGGAGTTCTTC--ATCTTTCATTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTT
29052274 GTGTAATTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
65 14 0.25
66 36 0.64
67 6 0.11
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.43
Consensus pattern (65 bp):
AGCTGGAGTTCTTCATCTTTCATTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTTT
Found at i:29057693 original size:9 final size:9
Alignment explanation
Indices: 29057676--29057927 Score: 91
Period size: 9 Copynumber: 28.7 Consensus size: 9
29057666 AATTTATGTA
*
29057676 TTATATAAG
1 TTATGTAAG
29057685 TTATGTAAG
1 TTATGTAAG
*
29057694 TTACGT-A-
1 TTATGTAAG
29057701 TTATGTAAG
1 TTATGTAAG
*
29057710 CTATGTAAG
1 TTATGTAAG
**
29057719 -T-TGTATT
1 TTATGTAAG
*
29057726 TTATGTTAG
1 TTATGTAAG
* *
29057735 CTAT-TTA-
1 TTATGTAAG
29057742 TTATGTAAG
1 TTATGTAAG
*
29057751 CTATGTAAG
1 TTATGTAAG
*
29057760 TTGTGT-A-
1 TTATGTAAG
29057767 TTATGTAAG
1 TTATGTAAG
*
29057776 CTATGTAAG
1 TTATGTAAG
*
29057785 TTATGTGAG
1 TTATGTAAG
*
29057794 TTATATATAAG
1 -T-TATGTAAG
* *
29057805 TTATCTTAATAA
1 TTAT-GT-A-AG
*
29057817 TTATATAAG
1 TTATGTAAG
* *
29057826 TTATCTTAATAA
1 TTAT-GT-A-AG
*
29057838 TTATATAAG
1 TTATGTAAG
*
29057847 CTATGT-A-
1 TTATGTAAG
*
29057854 TTATGTTAG
1 TTATGTAAG
**
29057863 TTATGCCAG
1 TTATGTAAG
29057872 TTATGT-A-
1 TTATGTAAG
*
29057879 TTATGTATG
1 TTATGTAAG
29057888 TTATGTAAG
1 TTATGTAAG
*
29057897 TTGTGT-AG
1 TTATGTAAG
*
29057905 -AATGTAAG
1 TTATGTAAG
*
29057913 CTATGTAAG
1 TTATGTAAG
29057922 TTATGT
1 TTATGT
29057928 TAGAAATTTT
Statistics
Matches: 179, Mismatches: 42, Indels: 44
0.68 0.16 0.17
Matches are distributed among these distances:
7 31 0.17
8 18 0.10
9 104 0.58
10 6 0.03
11 10 0.06
12 10 0.06
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29057709 original size:25 final size:23
Alignment explanation
Indices: 29057672--29057786 Score: 107
Period size: 25 Copynumber: 5.0 Consensus size: 23
29057662 TGAAAATTTA
* *
29057672 TGTATTATATAAGTTATGTAAGT
1 TGTATTATGTAAGCTATGTAAGT
29057695 TACGTATTATGTAAGCTATGTAAGT
1 T--GTATTATGTAAGCTATGTAAGT
* *
29057720 TGTATT-T-TATGTTA-GCT-A-T
1 TGTATTATGTAAGCTATG-TAAGT
29057739 T-TATTATGTAAGCTATGTAAGTT
1 TGTATTATGTAAGCTATGTAAG-T
29057762 GTGTATTATGTAAGCTATGTAAGT
1 -TGTATTATGTAAGCTATGTAAGT
29057786 T
1 T
29057787 ATGTGAGTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.05
19 3 0.04
20 8 0.11
21 8 0.11
22 1 0.01
23 8 0.11
24 2 0.03
25 41 0.55
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (23 bp):
TGTATTATGTAAGCTATGTAAGT
Found at i:29057779 original size:41 final size:41
Alignment explanation
Indices: 29057685--29057782 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
29057675 ATTATATAAG
* * *
29057685 TTATGTAAGTTACGTATTATGTAAGCTATGTAAGTTGTATT
1 TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
* * *
29057726 TTATGTTAGCTATTTATTATGTAAGCTATGTAAGTTGTGTA
1 TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
29057767 TTATGTAAGCTATGTA
1 TTATGTAAGCTATGTA
29057783 AGTTATGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (41 bp):
TTATGTAAGCTATGTATTATGTAAGCTATGTAAGTTGTATA
Found at i:29057823 original size:21 final size:21
Alignment explanation
Indices: 29057797--29057846 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
29057787 ATGTGAGTTA
29057797 TATATAAGTTATCTTAATAAT
1 TATATAAGTTATCTTAATAAT
29057818 TATATAAGTTATCTTAATAAT
1 TATATAAGTTATCTTAATAAT
29057839 TATATAAG
1 TATATAAG
29057847 CTATGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAAGTTATCTTAATAAT
Found at i:29057898 original size:25 final size:25
Alignment explanation
Indices: 29057838--29057927 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
29057828 ATCTTAATAA
* *
29057838 TTATATAAGCTATGTATTATGT-TAG
1 TTATGTAAGTTATGTATTATGTAT-G
**
29057863 TTATGCCAGTTATGTATTATGTATG
1 TTATGTAAGTTATGTATTATGTATG
* ** *
29057888 TTATGTAAGTTGTGTAGAATGTAAG
1 TTATGTAAGTTATGTATTATGTATG
*
29057913 CTATGTAAGTTATGT
1 TTATGTAAGTTATGT
29057928 TAGAAATTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 51 0.98
26 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTATG
Found at i:29057964 original size:20 final size:20
Alignment explanation
Indices: 29057936--29058046 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
29057926 GTTAGAAATT
*
29057936 TTATATTAATATTATATAAG
1 TTATCTTAATATTATATAAG
29057956 TTATCTTAATAATTATATAAG
1 TTATCTTAAT-ATTATATAAG
* *
29057977 TTAT-GT-A-ATTAGA-AA-
1 TTATCTTAATATTATATAAG
* *
29057992 TTGTCTTAATACTATATAAG
1 TTATCTTAATATTATATAAG
*
29058012 TAATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
29058032 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
29058047 GTAATTAGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.04
16 3 0.04
17 6 0.08
18 4 0.05
19 3 0.04
20 40 0.55
21 14 0.19
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Done.