Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 15 of 24
Found at i:1959793 original size:32 final size:32
Alignment explanation
Indices: 1959747--1959822 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
1959737 GCAGTAGCTT
* *
1959747 TGTAGCGATACATTGTATCGATACAACATTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1959779 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
1959811 TATATCGATACA
1 TGTATCGATACA
1959823 GTTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1960813 original size:48 final size:48
Alignment explanation
Indices: 1960596--1961133 Score: 309
Period size: 48 Copynumber: 11.4 Consensus size: 48
1960586 CGAAGAATGA
* * *** * *
1960596 CAATGTGCTGATTCATGGCCAGCGACATTAAACTTGAAG--AAGAATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAG-GTGC
* ** * * *
1960643 CAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGGATGTTA-AAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA---AAG--ACAAGGTGC
* * * * ** * **
1960695 CAATATGCTGATTCAACGCCAACGATATCGAACTTAAAGATGAAAATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
*
1960744 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * * * *
1960792 CAACATGCCGATTCAAAGCCAGCGATATTGGGCTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * * * *
1960831 CAATGTGTTGATTCAAGGCCAACAACATTGGTCTTAAAGATGC-CGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA--CAAGGTGC
* * *
1960880 CGATATGCTGATTCAAGGCCAGCGACATT-GACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
* *
1960928 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
*
1960976 CAATATGCTGATTCAAGGCCAGCGATATTAGG-CTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGACAAGGTGC
* * * * * * *
1961015 CAATGTGTTGATTCAAGGCCAAC-AGCATTAGTCTTAATGACAAAGTGT
1 CAATATGCTGATTCAAGGCCAGCGA-CATTGGTCTTAAAGACAAGGTGC
* * * *
1961063 CAGTATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGA-CAAGGTGC
1961113 CAATATGCT-AGTTCAAGGCCA
1 CAATATGCTGA-TTCAAGGCCA
1961134 ACGATATTAA
Statistics
Matches: 377, Mismatches: 78, Indels: 69
0.72 0.15 0.13
Matches are distributed among these distances:
38 2 0.01
39 58 0.15
41 2 0.01
46 1 0.00
47 30 0.08
48 136 0.36
49 89 0.24
50 25 0.07
52 31 0.08
53 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
Found at i:1960952 original size:184 final size:182
Alignment explanation
Indices: 1960687--1961133 Score: 601
Period size: 184 Copynumber: 2.4 Consensus size: 182
1960677 TAGGGATGTT
* * * **
1960687 AAAGATGCCAATATGCTGATTCAACGCCAACGATATCGAACTTAAAGATGAAAATGCCAATGTGC
1 AAAG-TGCC-ATATGCTGATTCAAGGCCAGCGATATTG-ACTTAAAGATGAAGGTGCCAATGTGC
1960752 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACATGCCGATTCAAAGCCAGCGA
63 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACATGCCGATTCAAAGCCAGCGA
* *
1960817 TATTGGGCTTATGCCAATGTGTTGATTCAAGGCCAACAACATTGGTCTTAAAGATGC
128 TATTAGGCTTATGCCAATGTGTTGATTCAAGGCCAACAACATTAGTCTTAAAGA--C
** *
1960874 -CGGTGCCGATATGCTGATTCAAGGCCAGCGACATTGACTTAAAGATGAAGGTGCCAATGTGCTG
1 AAAGTGCC-ATATGCTGATTCAAGGCCAGCGATATTGACTTAAAGATGAAGGTGCCAATGTGCTG
* * * *
1960938 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
65 ATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACATGCCGATTCAAAGCCAGCGATA
* *
1961003 TTAGGCTTATGCCAATGTGTTGATTCAAGGCCAACAGCATTAGTCTTAATGAC
130 TTAGGCTTATGCCAATGTGTTGATTCAAGGCCAACAACATTAGTCTTAAAGAC
* ** * *
1961056 AAAGTGTCAGTATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGCCAATATGC
1 AAAGTGCCA-TATGCTGATTCAAGGCCAGCGATATT--GACTTAAAGATGAAGGTGCCAATGTGC
1961121 T-AGTTCAAGGCCA
63 TGA-TTCAAGGCCA
1961134 ACGATATTAA
Statistics
Matches: 230, Mismatches: 25, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
182 2 0.01
183 29 0.13
184 136 0.59
185 62 0.27
186 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (182 bp):
AAAGTGCCATATGCTGATTCAAGGCCAGCGATATTGACTTAAAGATGAAGGTGCCAATGTGCTGA
TTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACATGCCGATTCAAAGCCAGCGATAT
TAGGCTTATGCCAATGTGTTGATTCAAGGCCAACAACATTAGTCTTAAAGAC
Found at i:1961045 original size:39 final size:39
Alignment explanation
Indices: 1960973--1961050 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1960963 AAAGATAAGG
* *
1960973 TGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGACATTAGGCTTA
* * *
1961012 TGCCAATGTGTTGATTCAAGGCCAAC-AGCATTAGTCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGA-CATTAGGCTTA
1961051 ATGACAAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTAGGCTTA
Found at i:1961071 original size:87 final size:87
Alignment explanation
Indices: 1960925--1961091 Score: 246
Period size: 87 Copynumber: 1.9 Consensus size: 87
1960915 AAGATGAAGG
* * * *
1960925 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTAGTCTTAAAGACAAAGTGCCAATATGCTGATTC
1960990 AAGGCCAGCGATATTAGGCTTA
66 AAGGCCAGCGATATTAGGCTTA
* * * *
1961012 TGCCAATGTGTTGATTCAAGGCCAAC-AGCATTAGTCTTAATGACAAAGTGTCAGTATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAACGA-CATTAGTCTTAAAGACAAAGTGCCAATATGCTGATT
1961076 CAAGGCCAGCGATATT
65 CAAGGCCAGCGATATT
1961092 GGGTTTTAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 70 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTAGTCTTAAAGACAAAGTGCCAATATGCTGATTC
AAGGCCAGCGATATTAGGCTTA
Found at i:1961228 original size:28 final size:29
Alignment explanation
Indices: 1961170--1961524 Score: 349
Period size: 28 Copynumber: 12.5 Consensus size: 29
1961160 CACCAACTTG
*
1961170 TGTGGGCTTTTGAAAGGGTTG-CA-TCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACT-GACT
*
1961199 TGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1961227 TGTGGGC-TTTGAAAGGATACCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1961255 TGTGGGC--TTGAAAGGGGTGCCATTGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
1961283 TGTGGGCTTTTG-AAGATTGCCATTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1961311 TGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1961340 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1961368 TGTGGGC-TTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
*
1961397 TGTGGGCTTTTG-AAGATTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1961425 TATGGGC-TTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
* *
1961454 TATGGGTTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * ** *
1961482 TGTGGGCTTTGGAAAAGATATCATTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1961511 TGTGGGC-TTTGAAA
1 TGTGGGCTTTTGAAA
1961525 ATGTGATGAA
Statistics
Matches: 273, Mismatches: 39, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
27 23 0.08
28 143 0.52
29 96 0.35
30 11 0.04
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:1961255 original size:56 final size:57
Alignment explanation
Indices: 1961170--1961492 Score: 331
Period size: 57 Copynumber: 5.7 Consensus size: 57
1961160 CACCAACTTG
* * *
1961170 TGTGGGCTTTTGAAAGGGTTG-CA-TCAACTTGTGTGCTTTTG-AA-GGTTGCCACTGACT
1 TGTGGGCTTTTG-AA-GGATGCCACT-AACTTGTGGGC-TTTGAAAGGGGTGCCACTGACT
* *
1961227 TGTGGGC-TTTGAAAGGATACCACTAACTTGTGGGC-TTGAAAGGGGTGCCATTGACT
1 TGTGGGCTTTTG-AAGGATGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
* * * *
1961283 TGTGGGCTTTTGAA-GATTGCCATTGACTTGTGGGCTTTGGAAA-AGATGCCACTGACT
1 TGTGGGCTTTTGAAGGA-TGCCACTAACTTGTGGGCTTT-GAAAGGGGTGCCACTGACT
* *
1961340 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTTGAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
* * ** *
1961397 TGTGGGCTTTTGAA-GATTGCCACTGACTTATGGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAGGA-TGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
* * * *
1961454 TATGGGTTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
1 TGTGGGCTTTTGAAGGATGCCACTAACTTGTGGGCTTTG
1961493 GAAAAGATAT
Statistics
Matches: 230, Mismatches: 24, Indels: 24
0.83 0.09 0.09
Matches are distributed among these distances:
54 3 0.01
55 7 0.03
56 60 0.26
57 154 0.67
58 6 0.03
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (57 bp):
TGTGGGCTTTTGAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGGTGCCACTGACT
Found at i:1961341 original size:57 final size:57
Alignment explanation
Indices: 1961216--1961520 Score: 386
Period size: 57 Copynumber: 5.4 Consensus size: 57
1961206 TTTTGAAGGT
* * * *
1961216 TGCCACTGACTTGTGGGC-TTTGAAAGGA-TACCACTAACTTGTGGGC-TT-GAAAGGGG
1 TGCCACTGACTTGTGGGCTTTTG-AA-GATTGCCACTGACTTGTGGGCTTTGGAAA-AGA
* *
1961272 TGCCATTGACTTGTGGGCTTTTGAAGATTGCCATTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAAAGA
* * *
1961329 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT-GAAAGGGG
1 TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAA-AGA
* *
1961386 TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTATGGGCTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAAAGA
* * *
1961443 TGCCACTGACTTATGGGTTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAAAGA
** *
1961500 TATCATTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1961521 GAAAATGTGA
Statistics
Matches: 217, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
55 2 0.01
56 38 0.18
57 170 0.78
58 7 0.03
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (57 bp):
TGCCACTGACTTGTGGGCTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:1961415 original size:114 final size:114
Alignment explanation
Indices: 1961216--1961492 Score: 450
Period size: 114 Copynumber: 2.4 Consensus size: 114
1961206 TTTTGAAGGT
* * * *
1961216 TGCCACTGACTTGTGGGC-TTTGAAAGGATACCACTAACTTGTGGGC-TTGAAAGGGGTGCCATT
1 TGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACT
* * *
1961279 GACTTGTGGGCTTTTGAAGATTGCCATTGACTTGTGGGCTTTGGAAAAGA
65 GACTTGTGGGCTTTTGAAGATTGCCACTGACTTATGGGCTTTGAAAAAGA
1961329 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTG
1961394 ACTTGTGGGCTTTTGAAGATTGCCACTGACTTATGGGCTTTGAAAAAGA
66 ACTTGTGGGCTTTTGAAGATTGCCACTGACTTATGGGCTTTGAAAAAGA
* *
1961443 TGCCACTGACTTATGGGTTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
1 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
1961493 GAAAAGATAT
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
113 38 0.25
114 115 0.75
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (114 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTG
ACTTGTGGGCTTTTGAAGATTGCCACTGACTTATGGGCTTTGAAAAAGA
Found at i:1962976 original size:16 final size:16
Alignment explanation
Indices: 1962957--1962989 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
1962947 ATCCGGACCC
1962957 TTTTTGTTGTTGTTTTT
1 TTTTTGTT-TTGTTTTT
1962974 TTTTTGTTTTGTTTTT
1 TTTTTGTTTTGTTTTT
1962990 GTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (16 bp):
TTTTTGTTTTGTTTTT
Found at i:1962980 original size:11 final size:11
Alignment explanation
Indices: 1962966--1963001 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1962956 CTTTTTGTTG
1962966 TTGTTTTTTTT
1 TTGTTTTTTTT
*
1962977 TTGTTTTGTTT
1 TTGTTTTTTTT
1962988 TTGTTTATTTTT
1 TTGTTT-TTTTT
1963000 TT
1 TT
1963002 ACGGAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:1962986 original size:22 final size:23
Alignment explanation
Indices: 1962958--1963001 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1962948 TCCGGACCCT
1962958 TTTTGTTGTTGTTT-TTTTTTTG
1 TTTTGTTGTTGTTTATTTTTTTG
*
1962980 TTTTGTTTTTGTTTATTTTTTT
1 TTTTGTTGTTGTTTATTTTTTT
1963002 ACGGAGGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (23 bp):
TTTTGTTGTTGTTTATTTTTTTG
Found at i:1966236 original size:21 final size:21
Alignment explanation
Indices: 1966203--1966243 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1966193 CTAAGTAAAA
1966203 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1966224 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1966244 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1966308 original size:20 final size:21
Alignment explanation
Indices: 1966282--1966335 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1966272 AACCCTGAAA
*
1966282 AGTATCGATACACATTTAAAT
1 AGTATCGATACACAATTAAAT
**
1966303 -GTATCGATACA-AATTGCAT
1 AGTATCGATACACAATTAAAT
1966322 AGTATCGATACACA
1 AGTATCGATACACA
1966336 CAAATATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
20 22 0.79
21 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (21 bp):
AGTATCGATACACAATTAAAT
Found at i:1968629 original size:84 final size:84
Alignment explanation
Indices: 1968469--1968633 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
1968459 ACTCAAAGAA
* * *
1968469 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTAAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
1968534 TATGAAAGAGTTGCAAAAT
66 TAAGAAAGAGTTGCAAAAT
* * * *
1968553 GAAAGTAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
1968616 AA-AAGAAATGAGTTGCAA
64 AATAAGAAA-GAGTTGCAA
1968634 GTGGAAAATG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 60 0.86
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTGCAAAAT
Found at i:1971086 original size:21 final size:21
Alignment explanation
Indices: 1971062--1971102 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1971052 CTAAGTAAAA
1971062 ATACGTATT-GTATCAATACAT
1 ATAC-TATTGGTATCAATACAT
*
1971083 ATACTATTGGTATTAATACA
1 ATACTATTGGTATCAATACA
1971103 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACTATTGGTATCAATACAT
Found at i:1971265 original size:53 final size:53
Alignment explanation
Indices: 1971182--1971318 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1971172 AAATTGCATA
1971182 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1971236 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1971289 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1971319 TTGGTAGTGG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:1971361 original size:10 final size:10
Alignment explanation
Indices: 1971342--1971380 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1971332 AATCTCATTT
*
1971342 TCACTGTTCA
1 TCACTATTCA
1971352 TCACTATTCA
1 TCACTATTCA
*
1971362 TCACTGTTCA
1 TCACTATTCA
1971372 -CACTATTCA
1 TCACTATTCA
1971381 CGTATCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (10 bp):
TCACTATTCA
Found at i:1971377 original size:19 final size:20
Alignment explanation
Indices: 1971342--1971380 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1971332 AATCTCATTT
1971342 TCACTGTTCATCACTATTCA
1 TCACTGTTCATCACTATTCA
1971362 TCACTGTTCA-CACTATTCA
1 TCACTGTTCATCACTATTCA
1971381 CGTATCACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (20 bp):
TCACTGTTCATCACTATTCA
Found at i:1972659 original size:13 final size:13
Alignment explanation
Indices: 1972641--1972666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1972631 ACAAAGATCC
1972641 ATGTATCGATACA
1 ATGTATCGATACA
1972654 ATGTATCGATACA
1 ATGTATCGATACA
1972667 TTTGAGTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1972745 original size:19 final size:19
Alignment explanation
Indices: 1972719--1972768 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1972709 AGCGATACAT
*
1972719 TATATCGATACAACATTTA
1 TATATCGATACAACACTTA
*
1972738 TGTATCGATACAACACTTA
1 TATATCGATACAACACTTA
1972757 TATATCGATACA
1 TATATCGATACA
1972769 GTTACTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (19 bp):
TATATCGATACAACACTTA
Found at i:1974876 original size:21 final size:20
Alignment explanation
Indices: 1974859--1974942 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 20
1974849 TCCTTATCTC
1974859 TTTTT-TTTTTTAATTTATT
1 TTTTTATTTTTTAATTTATT
1974878 TTTTTAATTTTTTAATTT-TT
1 TTTTT-ATTTTTTAATTTATT
*
1974898 ATATTTTATTTGATTTTTAACTTTAAT
1 -T-TTTTA--T--TTTTTAA-TTTATT
*
1974925 TTTTTAGTTTTTAATTTA
1 TTTTTATTTTTTAATTTA
1974943 AAAAAATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
19 5 0.09
20 6 0.11
21 20 0.38
22 4 0.08
23 1 0.02
25 12 0.23
26 4 0.08
27 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTTTAATTTATT
Found at i:1974881 original size:13 final size:13
Alignment explanation
Indices: 1974863--1974887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1974853 TATCTCTTTT
1974863 TTTTTTTAATTTA
1 TTTTTTTAATTTA
1974876 TTTTTTTAATTT
1 TTTTTTTAATTT
1974888 TTTAATTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTAATTTA
Found at i:1976952 original size:21 final size:21
Alignment explanation
Indices: 1976919--1976959 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1976909 ATATAAGTTG
*
1976919 ATTTAATTTTATGTTGGATAT
1 ATTTAATTATATGTTGGATAT
*
1976940 ATTTTATTATATGTTGGATA
1 ATTTAATTATATGTTGGATA
1976960 ATTGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (21 bp):
ATTTAATTATATGTTGGATAT
Found at i:1977353 original size:2 final size:2
Alignment explanation
Indices: 1977346--1977386 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1977336 CTTTTTCTTC
*
1977346 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1977387 GGAATCTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1977442 original size:6 final size:6
Alignment explanation
Indices: 1977431--1977467 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
1977421 CGTATCAGTT
1977431 ATATAA ATATAA ATATAA ATATAA ATTATTAA ATATA
1 ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATA
1977468 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.72
7 4 0.14
8 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:1978150 original size:26 final size:28
Alignment explanation
Indices: 1978067--1978164 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 28
1978057 ATTTTGCAAT
* * *
1978067 AAAAATTAGCCACCAATTTTGACAAAC-
1 AAAAAGTAACCACCATTTTTGACAAACA
* *
1978094 AACAAG---CCACAATTTTTGACAAACA
1 AAAAAGTAACCACCATTTTTGACAAACA
* *
1978119 AAAAAG-AACCATCATTTTTGACAAA-T
1 AAAAAGTAACCACCATTTTTGACAAACA
* *
1978145 ACAAAGTAACTACCATTTTT
1 AAAAAGTAACCACCATTTTT
1978165 TATAAACACA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
24 16 0.29
25 5 0.09
26 5 0.09
27 30 0.54
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (28 bp):
AAAAAGTAACCACCATTTTTGACAAACA
Found at i:1978164 original size:27 final size:27
Alignment explanation
Indices: 1978076--1978143 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 27
1978066 TAAAAATTAG
* *
1978076 CCACCAATTTTGACAAAC-AACAAG--
1 CCACCATTTTTGACAAACAAAAAAGAA
*
1978100 CCACAATTTTTGACAAACAAAAAAGAA
1 CCACCATTTTTGACAAACAAAAAAGAA
*
1978127 CCATCATTTTTGACAAA
1 CCACCATTTTTGACAAA
1978144 TACAAAGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 16 0.44
25 5 0.14
27 15 0.42
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAAGAA
Found at i:1982666 original size:24 final size:24
Alignment explanation
Indices: 1982639--1982684 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1982629 CAATAAAATT
1982639 AGCCACCAA-TTTTGACAAACAACA
1 AGCCA-CAATTTTTGACAAACAACA
1982663 AGCCACAATTTTTGACAAACAA
1 AGCCACAATTTTTGACAAACAA
1982685 AAAGAAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.20
Consensus pattern (24 bp):
AGCCACAATTTTTGACAAACAACA
Found at i:1982708 original size:27 final size:27
Alignment explanation
Indices: 1982641--1982737 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 27
1982631 ATAAAATTAG
* *
1982641 CCACCAATTTTGACAAACAACAAG---
1 CCACCATTTTTGACAAACAAAAAGAAA
*
1982665 CCACAATTTTTGACAAACAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
** * * *
1982692 CCATTATTTTTGACAAATATAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
*
1982719 TCACCATTTTTGACAAACA
1 CCACCATTTTTGACAAACA
1982738 CAAACGATGA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 21 0.36
27 37 0.64
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:1984118 original size:6 final size:6
Alignment explanation
Indices: 1984107--1984138 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1984097 CAATGTGGGC
1984107 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AA
1984139 TGATGGAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:1991588 original size:15 final size:16
Alignment explanation
Indices: 1991554--1991588 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1991544 GAATTATAAT
1991554 TTAACTTAATTAGAAA
1 TTAACTTAATTAGAAA
*
1991570 TTAACTTAA-TAGTAA
1 TTAACTTAATTAGAAA
1991585 TTAA
1 TTAA
1991589 ACATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (16 bp):
TTAACTTAATTAGAAA
Found at i:1994058 original size:5 final size:6
Alignment explanation
Indices: 1994042--1994071 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1994032 TTGTCTAATG
1994042 TAAAAA TAAAAA T-AAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1994072 GTACAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:1994060 original size:11 final size:11
Alignment explanation
Indices: 1994044--1994069 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1994034 GTCTAATGTA
1994044 AAAATAAAAAT
1 AAAATAAAAAT
1994055 AAAATAAAAAT
1 AAAATAAAAAT
1994066 AAAA
1 AAAA
1994070 ATGTACAACT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1995090 original size:34 final size:34
Alignment explanation
Indices: 1995047--1995124 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
1995037 TTAATTTCTT
1995047 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
*
1995081 TGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
*
1995115 TGTTAAGTGA
1 TGTTAGGTGA
1995125 GAATGTTAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (34 bp):
TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
Found at i:1995124 original size:22 final size:22
Alignment explanation
Indices: 1995099--1995236 Score: 113
Period size: 22 Copynumber: 6.2 Consensus size: 22
1995089 GATGTGTTTG
1995099 GTGAGAATGTTAGGTGTGTTAA
1 GTGAGAATGTTAGGTGTGTTAA
*
1995121 GTGAGAATGTTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAA
* *
1995143 GTGATGTAT-TT-GGTGAG--AA
1 GTGA-GAATGTTAGGTGTGTTAA
* ** *
1995162 TGTTAGGTGTGTTAGGTGATGTGTTTA
1 -GTGA-GAATGTTA-G-G-TGTGTTAA
*
1995189 GTGAGAATGTTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAA
*
1995211 GTGAGAATGTTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAA
1995233 GTGA
1 GTGA
1995237 TGTATTTGGT
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 6 0.06
21 7 0.08
22 59 0.63
23 5 0.05
24 2 0.02
25 9 0.10
26 3 0.03
27 1 0.01
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.38
Consensus pattern (22 bp):
GTGAGAATGTTAGGTGTGTTAA
Found at i:1995136 original size:56 final size:56
Alignment explanation
Indices: 1995064--1995236 Score: 230
Period size: 56 Copynumber: 3.1 Consensus size: 56
1995054 TGATGTATTT
1995064 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
* *
1995120 AGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
* *
1995176 GGTGATG--TGTTTAGTGAGAATGTTA-G-G-TGTGTTAGGTGAGAATGTTAGGTGTGTTA
1 GGTGA-GAATG-TTAG-GTG--TGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1995232 GGTGA
1 GGTGA
1995237 TGTATTTGGT
Statistics
Matches: 106, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
55 2 0.02
56 94 0.89
57 4 0.04
58 1 0.01
59 5 0.05
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
Found at i:1995163 original size:34 final size:34
Alignment explanation
Indices: 1995120--1995214 Score: 172
Period size: 34 Copynumber: 2.8 Consensus size: 34
1995110 AGGTGTGTTA
1995120 AGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1 AGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
* *
1995154 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTT
1 AGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1995188 AGTGAGAATGTTAGGTGTGTTAGGTGA
1 AGTGAGAATGTTAGGTGTGTTAGGTGA
1995215 GAATGTTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (34 bp):
AGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
Found at i:1995200 original size:90 final size:90
Alignment explanation
Indices: 1995047--1995265 Score: 420
Period size: 90 Copynumber: 2.4 Consensus size: 90
1995037 TTAATTTCTT
*
1995047 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAG
1995112 GTGTGTTAAGTGAGAATGTTAGGTG
66 GTGTGTTAAGTGAGAATGTTAGGTG
1995137 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAG
*
1995202 GTGTGTTAGGTGAGAATGTTAGGTG
66 GTGTGTTAAGTGAGAATGTTAGGTG
1995227 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1995266 ACATGTATAT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 127 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (90 bp):
TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAG
GTGTGTTAAGTGAGAATGTTAGGTG
Found at i:1995237 original size:56 final size:56
Alignment explanation
Indices: 1995091--1995265 Score: 216
Period size: 56 Copynumber: 3.1 Consensus size: 56
1995081 TGTTAGGTGA
* * *
1995091 TGTGTTTGGTGAGAATGTTAGGTGTGTTAAGTGA-GAATG-TTAG-GTG--TGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATG--TGTTTAGTGAGAATGTTAGG
*
1995144 TGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAGG
1 TG-TG--TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAGG
* *
1995203 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAGG
1995259 TGTGTTA
1 TGTGTTA
1995266 ACATGTATAT
Statistics
Matches: 109, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
53 2 0.02
54 2 0.02
55 2 0.02
56 89 0.82
57 3 0.03
58 2 0.02
59 9 0.08
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (56 bp):
TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTAGTGAGAATGTTAGG
Found at i:1999964 original size:34 final size:34
Alignment explanation
Indices: 1999921--1999998 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
1999911 TTAATTTCTT
1999921 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
*
1999955 TGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
1999989 TGTTAGGTGA
1 TGTTAGGTGA
1999999 GAATGTTAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (34 bp):
TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTG
Found at i:1999994 original size:9 final size:9
Alignment explanation
Indices: 1999980--2000041 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 9
1999970 TTGGTGAGAA
1999980 TGTTAGGTG
1 TGTTAGGTG
1999989 TGTTAGGTGAG
1 TGTTAGGT--G
2000000 AATGTTAGGTG
1 --TGTTAGGTG
2000011 TGTTAGGTGAG
1 TGTTAGGT--G
2000022 AATGTTAGGTG
1 --TGTTAGGTG
2000033 TGTTAGGTG
1 TGTTAGGTG
2000042 ATGTATTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
9 25 0.56
11 4 0.09
13 16 0.36
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (9 bp):
TGTTAGGTG
Found at i:1999997 original size:22 final size:22
Alignment explanation
Indices: 1999965--2000042 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
1999955 TGTTAGGTGA
*
1999965 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1999987 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2000009 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2000031 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2000043 TGTATTTGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:2000010 original size:56 final size:54
Alignment explanation
Indices: 1999921--2000071 Score: 182
Period size: 56 Copynumber: 2.7 Consensus size: 54
1999911 TTAATTTCTT
* *
1999921 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATG-TGTTTGGTGAG
1 TGTTAGGTGATG-ATTAGGTGAGAATGTTAGGTGTGTTAGGTGA-GATGTTAGGT--G
1999978 AATGTTAGGTG-TG-TTAGGTGAGAATGTTAGGTGTGTTAGGTGAGAATGTTAGGTG
1 --TGTTAGGTGATGATTAGGTGAGAATGTTAGGTGTGTTAGGTGAG-ATGTTAGGTG
*
2000033 TGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTTAGGTGATG-ATTAGGTGAGAATGTTAGGTGTGTTA
2000072 ACATGTATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
53 9 0.11
54 2 0.02
55 2 0.02
56 53 0.63
57 7 0.08
58 2 0.02
59 9 0.11
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (54 bp):
TGTTAGGTGATGATTAGGTGAGAATGTTAGGTGTGTTAGGTGAGATGTTAGGTG
Found at i:2001062 original size:26 final size:25
Alignment explanation
Indices: 2000994--2001067 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 25
2000984 ACGCATGTTA
2000994 ATTTATTTATTTTTAAATTTATTTGT
1 ATTTATTTA-TTTTAAATTTATTTGT
2001020 ATTTATTAATAATTTTAAATTTTTATTTGT
1 ATTTATT--T-ATTTTAAA--TTTATTTGT
*
2001050 ATTTATTTATTTAAAATT
1 ATTTATTTATTTTAAATT
2001068 AAGTGTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 7 0.17
28 9 0.21
29 1 0.02
30 16 0.38
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (25 bp):
ATTTATTTATTTTAAATTTATTTGT
Found at i:2001163 original size:12 final size:12
Alignment explanation
Indices: 2001148--2001187 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2001138 AATATATAAT
2001148 TAAATATATTTA
1 TAAATATATTTA
2001160 TAAATA-A-TTA
1 TAAATATATTTA
*
2001170 AAAATATATTTA
1 TAAATATATTTA
2001182 TAAATA
1 TAAATA
2001188 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATATATTTA
Found at i:2001177 original size:22 final size:23
Alignment explanation
Indices: 2001138--2001204 Score: 91
Period size: 22 Copynumber: 2.9 Consensus size: 23
2001128 CATGTTCATT
*
2001138 AATATATAATTAAATATATTTATA
1 AATA-ATAAATAAATATATTTATA
*
2001162 AATAATTAA-AAATATATTTATA
1 AATAATAAATAAATATATTTATA
*
2001184 AATAATAAATAAATAAATTTA
1 AATAATAAATAAATATATTTA
2001205 AATAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 21 0.55
23 13 0.34
24 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAATAAATAAATATATTTATA
Found at i:2001314 original size:37 final size:40
Alignment explanation
Indices: 2001261--2001359 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 40
2001251 AGTTTTCAAC
*
2001261 ATAAAT-AATAAGACATAAAT-AT-TATTA-AATTATATT
1 ATAAATAAATAAAACATAAATAATATATTATAATTATATT
2001297 ATAAATAAATAAAACATAAATAATAATATTATTAATTATATT
1 ATAAATAAATAAAACATAAATAAT-ATATTA-TAATTATATT
*
2001339 ATAATTAAATAATAA-ATAAAT
1 ATAAATAAATAA-AACATAAAT
2001360 TTTAAATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
36 6 0.11
37 13 0.24
38 2 0.04
40 5 0.09
42 26 0.48
43 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (40 bp):
ATAAATAAATAAAACATAAATAATATATTATAATTATATT
Found at i:2001342 original size:42 final size:43
Alignment explanation
Indices: 2001278--2001359 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 43
2001268 ATAAGACATA
2001278 AATATTATTAAATTATATTATAAATAAATAA-AACATAAATAAT
1 AATATTATTAAATTATATTATAAATAAATAATAA-ATAAATAAT
*
2001321 AATATTATT-AATTATATTATAATTAAATAATAAATAAAT
1 AATATTATTAAATTATATTATAAATAAATAATAAATAAAT
2001360 TTTAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 26 0.70
43 11 0.30
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (43 bp):
AATATTATTAAATTATATTATAAATAAATAATAAATAAATAAT
Found at i:2004410 original size:6 final size:7
Alignment explanation
Indices: 2004392--2004416 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2004382 TAAAAAAATT
2004392 ATTTTTA
1 ATTTTTA
2004399 ATTTTTA
1 ATTTTTA
2004406 ATTTTTA
1 ATTTTTA
2004413 ATTT
1 ATTT
2004417 ACTTTTTGAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:2006664 original size:21 final size:22
Alignment explanation
Indices: 2006631--2006679 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
2006621 ATATAAATTG
* *
2006631 ATTTAATTTTATGTTGGAT-TT
1 ATTTTATTATATGTTGGATATT
2006652 ATTTTATTATATGTTGGATAATT
1 ATTTTATTATATGTTGGAT-ATT
2006675 ATTTT
1 ATTTT
2006680 TATTTGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (22 bp):
ATTTTATTATATGTTGGATATT
Found at i:2007159 original size:17 final size:19
Alignment explanation
Indices: 2007121--2007159 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2007111 CGTGTAAATA
2007121 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
*
2007140 TAAATATATTA-AAATT-T
1 TAAATATAATATAAATTAT
2007157 TAA
1 TAA
2007160 CACGAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:2007289 original size:24 final size:24
Alignment explanation
Indices: 2007237--2007283 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2007227 CATGTTTATT
* * *
2007237 ATATTATTTTTATATTTATTAAAC
1 ATATTATATTTAAAATTATTAAAC
2007261 ATATTATATTTAAAATTATTAAA
1 ATATTATATTTAAAATTATTAAA
2007284 TTTATTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTATATTTAAAATTATTAAAC
Found at i:2009467 original size:88 final size:89
Alignment explanation
Indices: 2009311--2009474 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 89
2009301 TATTGATTTG
* * *
2009311 TCTTTATATTTTCAATTTTATTGATATTTTAAAAATACATAATGAAATTAAAACATTTCAGAAAA
1 TCTTTACATTTTCAATTTCATTGATATTTTAAAAATACATAATGAAATTAAAACATTTCACAAAA
2009376 TATTCTATTAATGCAAATGATAAT
66 TATTCTATTAATGCAAATGATAAT
* *
2009400 TCTTTACACTTTT-AATTTCATTGAT-TTTTGAAGAAA-AC-TAATGAAATTCAAATATTTCACA
1 TCTTTACA-TTTTCAATTTCATTGATATTTT-AA-AAATACATAATGAAATTAAAACATTTCACA
* *
2009461 AGATATTTTATTAA
63 AAATATTCTATTAA
2009475 GTTTTTTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
88 36 0.55
89 22 0.34
90 7 0.11
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.43
Consensus pattern (89 bp):
TCTTTACATTTTCAATTTCATTGATATTTTAAAAATACATAATGAAATTAAAACATTTCACAAAA
TATTCTATTAATGCAAATGATAAT
Found at i:2012009 original size:18 final size:18
Alignment explanation
Indices: 2011986--2012025 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2011976 TAAAAAGGAG
* * *
2011986 ATAAAATTAATTTGTTAT
1 ATAAAATCAATATGTTAA
2012004 ATAAAATCAATATGTTAA
1 ATAAAATCAATATGTTAA
2012022 ATAA
1 ATAA
2012026 TTTATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAAATCAATATGTTAA
Found at i:2012877 original size:8 final size:8
Alignment explanation
Indices: 2012864--2012889 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2012854 TATATATTAT
2012864 ATAATTTA
1 ATAATTTA
2012872 ATAATTTA
1 ATAATTTA
2012880 ATAATTTA
1 ATAATTTA
2012888 AT
1 AT
2012890 TTTTAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATAATTTA
Found at i:2013765 original size:24 final size:23
Alignment explanation
Indices: 2013738--2013783 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
2013728 TTTATTATTT
*
2013738 TTTATATTAAATTTAAATCTTAAG
1 TTTAGATTAAATTTAAAT-TTAAG
* *
2013762 TTTAGATTGATTTTAAATTTAA
1 TTTAGATTAAATTTAAATTTAA
2013784 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTAGATTAAATTTAAATTTAAG
Found at i:2014957 original size:16 final size:16
Alignment explanation
Indices: 2014917--2014957 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2014907 AGGAAAAGTT
2014917 ATATTTA-TTTGATTG
1 ATATTTATTTTGATTG
*
2014932 ATATTCATTTTGA-TG
1 ATATTTATTTTGATTG
2014947 ATTATTTATTT
1 A-TATTTATTT
2014958 AATAGTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (16 bp):
ATATTTATTTTGATTG
Found at i:2015061 original size:54 final size:56
Alignment explanation
Indices: 2014957--2015106 Score: 189
Period size: 54 Copynumber: 2.7 Consensus size: 56
2014947 ATTATTTATT
* * * *
2014957 TAATAGTTGATTTTTTATAAAAAAATTATTTATTTTGAAAGTAATTATTTTTCATC
1 TAATAATTGACTTTTTATAAAAAAATTATTTATTTTAAAAGTAATAATTTTTCATC
** *
2015013 TAATAATTGA-TTTTTATTCAAAAA-TATTTATTTTAAAAGTAATAATTTTTTATC
1 TAATAATTGACTTTTTATAAAAAAATTATTTATTTTAAAAGTAATAATTTTTCATC
* *
2015067 TAATAATTAACTTTTTATGAAAAAAATTATTT-TTTAAAAA
1 TAATAATTGACTTTTTAT-AAAAAAATTATTTATTTTAAAA
2015107 AATATTTTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
54 36 0.44
55 19 0.23
56 21 0.26
57 5 0.06
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (56 bp):
TAATAATTGACTTTTTATAAAAAAATTATTTATTTTAAAAGTAATAATTTTTCATC
Found at i:2015918 original size:24 final size:24
Alignment explanation
Indices: 2015890--2015935 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2015880 ATAAAAAATT
2015890 AGCCACCAA-TTTTAACAAACAACA
1 AGCCA-CAATTTTTAACAAACAACA
*
2015914 AGCCACAATTTTTTACAAACAA
1 AGCCACAATTTTTAACAAACAA
2015936 AAGGAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (24 bp):
AGCCACAATTTTTAACAAACAACA
Found at i:2015958 original size:27 final size:27
Alignment explanation
Indices: 2015892--2015988 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 27
2015882 AAAAAATTAG
* * *
2015892 CCACCAATTTTAACAAACAACAAG---
1 CCACCATTTTTTACAAACAAAAAGAAA
* *
2015916 CCACAATTTTTTACAAACAAAAGGAAA
1 CCACCATTTTTTACAAACAAAAAGAAA
* * *
2015943 CCATCATTTTTTACAAATAAAAAGTAA
1 CCACCATTTTTTACAAACAAAAAGAAA
*
2015970 CCACCATTTTTGACAAACA
1 CCACCATTTTTTACAAACA
2015989 CAAATGGTGG
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 19 0.33
27 38 0.67
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (27 bp):
CCACCATTTTTTACAAACAAAAAGAAA
Found at i:2017910 original size:21 final size:22
Alignment explanation
Indices: 2017872--2017917 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2017862 ATCTGTTGAA
* **
2017872 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2017893 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2017915 ACT
1 ACT
2017918 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2020561 original size:29 final size:27
Alignment explanation
Indices: 2020482--2020561 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
2020472 ATAAGCCACA
* * *
2020482 ATTTTTGACAAA-CAAAAATGAACCATC
1 ATTTTTGATAAATAAAAAAT-AACTATC
* *
2020509 ATTTTTGATAAATATAAAGTAACTATC
1 ATTTTTGATAAATAAAAAATAACTATC
*
2020536 ATTTTTTATAAATACAAAAAATAACT
1 ATTTTTGATAAAT--AAAAAATAACT
2020562 TTTGTTGACT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 29 0.69
28 4 0.10
29 9 0.21
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (27 bp):
ATTTTTGATAAATAAAAAATAACTATC
Found at i:2021273 original size:23 final size:22
Alignment explanation
Indices: 2021212--2021276 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
2021202 ATTTTATAAC
*
2021212 TTAA-ATTATTTTTTAAATTTTA
1 TTAATATTATTTTTT-TATTTTA
* *
2021234 TTATTATTATATTTTTTATTTTT
1 TTAATATTAT-TTTTTTATTTTA
2021257 TTAATATTATCTTTTTTATT
1 TTAATATTAT-TTTTTTATT
2021277 ATAATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.08
23 28 0.78
24 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTAATATTATTTTTTTATTTTA
Found at i:2022902 original size:16 final size:15
Alignment explanation
Indices: 2022877--2022919 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2022867 TTTAAAAATT
*
2022877 AATAAATTAAATTCAA
1 AATAATTTAAATT-AA
*
2022893 AATAATTTAAATTTA
1 AATAATTTAAATTAA
*
2022908 AATAATGTAAAT
1 AATAATTTAAAT
2022920 ATTAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AATAATTTAAATTAA
Found at i:2022924 original size:22 final size:22
Alignment explanation
Indices: 2022899--2022942 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2022889 TCAAAATAAT
*
2022899 TTAAATTTAAATAATGTAAATA
1 TTAAATATAAATAATGTAAATA
* *
2022921 TTAAATATAAATTATTTAAATA
1 TTAAATATAAATAATGTAAATA
2022943 ATTCAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAATATAAATAATGTAAATA
Found at i:2029644 original size:6 final size:6
Alignment explanation
Indices: 2029633--2029663 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2029623 ATTATCACTG
2029633 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
2029664 TAAAGCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2029985 original size:84 final size:84
Alignment explanation
Indices: 2029844--2030014 Score: 342
Period size: 84 Copynumber: 2.0 Consensus size: 84
2029834 CTTTTGAACA
2029844 TACCCTGAAGCATATATTTGTTAGTTCAAAGTAGCAAGAAAATGATAGGGTATTATGCATGCATT
1 TACCCTGAAGCATATATTTGTTAGTTCAAAGTAGCAAGAAAATGATAGGGTATTATGCATGCATT
2029909 AATAGGCTATAAGTGGGCT
66 AATAGGCTATAAGTGGGCT
2029928 TACCCTGAAGCATATATTTGTTAGTTCAAAGTAGCAAGAAAATGATAGGGTATTATGCATGCATT
1 TACCCTGAAGCATATATTTGTTAGTTCAAAGTAGCAAGAAAATGATAGGGTATTATGCATGCATT
2029993 AATAGGCTATAAGTGGGCT
66 AATAGGCTATAAGTGGGCT
2030012 TAC
1 TAC
2030015 TTCTATTTAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (84 bp):
TACCCTGAAGCATATATTTGTTAGTTCAAAGTAGCAAGAAAATGATAGGGTATTATGCATGCATT
AATAGGCTATAAGTGGGCT
Found at i:2037464 original size:22 final size:22
Alignment explanation
Indices: 2037436--2037481 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2037426 CTATAGAGAT
2037436 ACTCATGAAGTGTTTTCATGCC
1 ACTCATGAAGTGTTTTCATGCC
*
2037458 ACTCATGAAGTGTTTTGATGCC
1 ACTCATGAAGTGTTTTCATGCC
2037480 AC
1 AC
2037482 CTAAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (22 bp):
ACTCATGAAGTGTTTTCATGCC
Found at i:2042395 original size:17 final size:17
Alignment explanation
Indices: 2042363--2042424 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 17
2042353 TAAATCTAAC
2042363 AATATTAAATATAATTTAA
1 AATA-TAAA-ATAATTTAA
*
2042382 AATATAAAATAA-TTCA
1 AATATAAAATAATTTAA
*
2042398 AATATAAAA-AATATAA
1 AATATAAAATAATTTAA
2042414 ATATGATAAAA
1 A-AT-ATAAAA
2042425 ATAGAGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.05
16 15 0.41
17 6 0.16
18 10 0.27
19 4 0.11
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AATATAAAATAATTTAA
Found at i:2042408 original size:18 final size:18
Alignment explanation
Indices: 2042363--2042410 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2042353 TAAATCTAAC
* * *
2042363 AATATTAAATATAATTTA
1 AATATAAAAAATAATTCA
*
2042381 AA-ATATAAAATAATTCA
1 AATATAAAAAATAATTCA
2042398 AATATAAAAAATA
1 AATATAAAAAATA
2042411 TAAATATGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAAAAAATAATTCA
Found at i:2042507 original size:22 final size:21
Alignment explanation
Indices: 2042461--2042521 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
2042451 AATATAATTT
*
2042461 AAATAAAAAATTATTTATTAA
1 AAATAAAAAATTATTTAGTAA
*
2042482 AAAT-AAAAATATATTTAAGTAC
1 AAATAAAAAAT-TATTT-AGTAA
* *
2042504 AAATTAATAATTAATTTA
1 AAATAAAAAATT-ATTTA
2042522 TTTGAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 9 0.27
23 9 0.27
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATAAAAAATTATTTAGTAA
Found at i:2042535 original size:23 final size:23
Alignment explanation
Indices: 2042461--2042557 Score: 65
Period size: 23 Copynumber: 4.2 Consensus size: 23
2042451 AATATAATTT
* *
2042461 AAATAAA-AAATTATTT-ATTAA
1 AAATAAATAATTTATTTAAATAA
* *
2042482 AAATAAA-AATATATTTAAGTACAA
1 AAATAAATAATTTATTTAA--ATAA
* *
2042506 ATTAATAATTAATTTATTTGAATAA
1 A--AATAAATAATTTATTTAAATAA
* *
2042531 AAATAAATATTTTATTTAAATAT
1 AAATAAATAATTTATTTAAATAA
2042554 AAAT
1 AAAT
2042558 TAAAGATTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
21 14 0.24
22 1 0.02
23 22 0.38
24 3 0.05
25 4 0.07
26 5 0.09
27 9 0.16
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAAATAATTTATTTAAATAA
Found at i:2042567 original size:50 final size:48
Alignment explanation
Indices: 2042471--2042595 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 48
2042461 AAATAAAAAA
* *
2042471 TTATTTATTAAAAATAAAAATATATTTAAGTACAAATTAATAATTAAT
1 TTATTTAATAAAAATAAAAATATATTTAAATACAAATTAATAATTAAT
* * *
2042519 TTATTTGAATAAAAATAAATATTTTATTTAAATATAAATTAA-AGATTAAAAAT
1 TTATTT-AATAAAAATAAA-AATATATTTAAATACAAATTAATA-ATT---AAT
*
2042572 TTATTTAA-ATATAATAAAAATATA
1 TTATTTAATA-AAAATAAAAATATA
2042596 AAAATTTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
48 6 0.10
49 12 0.19
50 21 0.34
51 5 0.08
52 9 0.15
53 9 0.15
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (48 bp):
TTATTTAATAAAAATAAAAATATATTTAAATACAAATTAATAATTAAT
Found at i:2042608 original size:29 final size:30
Alignment explanation
Indices: 2042526--2042609 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
2042516 AATTTATTTG
* *
2042526 AATAAAAATA-AATATTTTATTTAAATATA
1 AATAAAAATATAAAAATTTATTTAAATATA
*
2042555 AATTAAAGAT-TAAAAATTTATTTAAATAT-
1 AA-TAAAAATATAAAAATTTATTTAAATATA
*
2042584 AATAAAAATATAAAAATTTAATTAAA
1 AATAAAAATATAAAAATTTATTTAAA
2042610 AACTTATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 6 0.13
29 19 0.40
30 22 0.47
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
AATAAAAATATAAAAATTTATTTAAATATA
Found at i:2043975 original size:21 final size:22
Alignment explanation
Indices: 2043949--2044002 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2043939 TAGAACACAC
*
2043949 CTAATTAAATTTTAATTTAT-A
1 CTAATTAAATTTAAATTTATAA
**
2043970 CTAATTAAAAATAAATTTATAA
1 CTAATTAAATTTAAATTTATAA
*
2043992 TTAATTAAATT
1 CTAATTAAATT
2044003 ATAGTAATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
CTAATTAAATTTAAATTTATAA
Found at i:2045813 original size:20 final size:19
Alignment explanation
Indices: 2045760--2045818 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
2045750 ATAAAACATA
* *
2045760 ATATAAATATATTAAATGAT
1 ATATAAATATATTATAT-TT
2045780 ATATCAAA-AT-TTATATTT
1 ATAT-AAATATATTATATTT
*
2045798 ATATAAAATATATTATCTTT
1 ATAT-AAATATATTATATTT
2045818 A
1 A
2045819 AATATGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 14 0.44
21 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATAAATATATTATATTT
Found at i:2047481 original size:24 final size:25
Alignment explanation
Indices: 2047454--2047500 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2047444 TTAAAATTTA
*
2047454 TATAATA-AAAATTATAAAAATAAT
1 TATAATATAAAAGTATAAAAATAAT
2047478 TATAATATAAAAGTATAAAAATA
1 TATAATATAAAAGTATAAAAATA
2047501 TAATGAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TATAATATAAAAGTATAAAAATAAT
Found at i:2048068 original size:34 final size:34
Alignment explanation
Indices: 2048025--2048111 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
2048015 TTAATTTCTT
*
2048025 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
*
2048059 TGTTAGGTGTGTTAGGTGATGTGTTTGGTAAGAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
2048093 TGTTAGGTGTGTTAGGTGA
1 TGTTAGGTGTGTTAGGTGA
2048112 GAATGTTAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
Found at i:2048114 original size:22 final size:22
Alignment explanation
Indices: 2048078--2048223 Score: 142
Period size: 22 Copynumber: 6.5 Consensus size: 22
2048068 TGTTAGGTGA
* *
2048078 TGTGTTTGGTAAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2048100 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
*
2048122 TGTGTTAGGTGATGTAT-TT-GG
1 TGTGTTAGGTGA-GAATGTTAGG
2048143 TGAGAATGTTAGGT--G--TGTTAGGTG
1 T--G--TGTTAGGTGAGAATGTTA-G-G
*
2048167 ATGTGTTTGGTGAGAATGTTAGG
1 -TGTGTTAGGTGAGAATGTTAGG
2048190 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2048212 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2048224 TGTATTTGGT
Statistics
Matches: 105, Mismatches: 5, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.01
21 12 0.11
22 68 0.65
23 8 0.08
24 2 0.02
25 14 0.13
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:2048123 original size:56 final size:56
Alignment explanation
Indices: 2048051--2048223 Score: 230
Period size: 56 Copynumber: 3.1 Consensus size: 56
2048041 TGATGTATTT
*
2048051 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
*
2048107 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
* *
2048163 GGTGATG--TGTTTGGTGAGAATGTTA-G-G-TGTGTTAGGTGAGAATGTTAGGTGTGTTA
1 GGTGA-GAATGTTAGGT--G--TGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
2048219 GGTGA
1 GGTGA
2048224 TGTATTTGGT
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
55 7 0.07
56 91 0.85
57 3 0.03
58 1 0.01
59 5 0.05
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
Found at i:2048149 original size:34 final size:34
Alignment explanation
Indices: 2048107--2048201 Score: 181
Period size: 34 Copynumber: 2.8 Consensus size: 34
2048097 AGGTGTGTTA
2048107 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
*
2048141 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
2048175 GGTGAGAATGTTAGGTGTGTTAGGTGA
1 GGTGAGAATGTTAGGTGTGTTAGGTGA
2048202 GAATGTTAGG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (34 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
Found at i:2048183 original size:90 final size:90
Alignment explanation
Indices: 2048025--2048252 Score: 447
Period size: 90 Copynumber: 2.5 Consensus size: 90
2048015 TTAATTTCTT
2048025 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
2048090 GAATGTTAGGTGTGTTAGGTGAGAA
66 GAATGTTAGGTGTGTTAGGTGAGAA
*
2048115 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
2048180 GAATGTTAGGTGTGTTAGGTGAGAA
66 GAATGTTAGGTGTGTTAGGTGAGAA
2048205 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
2048253 ACATGTATAT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 137 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (90 bp):
TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
GAATGTTAGGTGTGTTAGGTGAGAA
Found at i:2048224 original size:56 final size:56
Alignment explanation
Indices: 2048078--2048252 Score: 225
Period size: 56 Copynumber: 3.1 Consensus size: 56
2048068 TGTTAGGTGA
* * *
2048078 TGTGTTTGGTAAGAATGTTAGGTGTGTTAGGTGA-GAATGTTAGGT--G--TGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATG--TGTTTGGTGAGAATGTTAGG
*
2048131 TGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
1 TG-TG--TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
*
2048190 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
2048246 TGTGTTA
1 TGTGTTA
2048253 ACATGTATAT
Statistics
Matches: 110, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
53 2 0.02
54 2 0.02
55 7 0.06
56 86 0.78
57 2 0.02
58 2 0.02
59 9 0.08
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.41
Consensus pattern (56 bp):
TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
Found at i:2052961 original size:34 final size:34
Alignment explanation
Indices: 2052918--2053004 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
2052908 TTAATTTCTT
*
2052918 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
*
2052952 TGTTAGGTGTGTTAGGTGATGTGTTTGGTAAGAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
2052986 TGTTAGGTGTGTTAGGTGA
1 TGTTAGGTGTGTTAGGTGA
2053005 GAATGTTAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTTAGGTGTGTTAGGTGATGTATTTGGTAAGAA
Found at i:2053007 original size:22 final size:22
Alignment explanation
Indices: 2052971--2053116 Score: 142
Period size: 22 Copynumber: 6.5 Consensus size: 22
2052961 TGTTAGGTGA
* *
2052971 TGTGTTTGGTAAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2052993 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
*
2053015 TGTGTTAGGTGATGTAT-TT-GG
1 TGTGTTAGGTGA-GAATGTTAGG
2053036 TGAGAATGTTAGGT--G--TGTTAGGTG
1 T--G--TGTTAGGTGAGAATGTTA-G-G
*
2053060 ATGTGTTTGGTGAGAATGTTAGG
1 -TGTGTTAGGTGAGAATGTTAGG
2053083 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2053105 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2053117 TGTATTTGGT
Statistics
Matches: 105, Mismatches: 5, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.01
21 12 0.11
22 68 0.65
23 8 0.08
24 2 0.02
25 14 0.13
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:2053016 original size:56 final size:56
Alignment explanation
Indices: 2052944--2053116 Score: 230
Period size: 56 Copynumber: 3.1 Consensus size: 56
2052934 TGATGTATTT
*
2052944 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
*
2053000 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
* *
2053056 GGTGATG--TGTTTGGTGAGAATGTTA-G-G-TGTGTTAGGTGAGAATGTTAGGTGTGTTA
1 GGTGA-GAATGTTAGGT--G--TGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
2053112 GGTGA
1 GGTGA
2053117 TGTATTTGGT
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
55 7 0.07
56 91 0.85
57 3 0.03
58 1 0.01
59 5 0.05
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
Found at i:2053042 original size:34 final size:34
Alignment explanation
Indices: 2053000--2053094 Score: 181
Period size: 34 Copynumber: 2.8 Consensus size: 34
2052990 AGGTGTGTTA
2053000 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
*
2053034 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
2053068 GGTGAGAATGTTAGGTGTGTTAGGTGA
1 GGTGAGAATGTTAGGTGTGTTAGGTGA
2053095 GAATGTTAGG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (34 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
Found at i:2053076 original size:90 final size:90
Alignment explanation
Indices: 2052918--2053145 Score: 447
Period size: 90 Copynumber: 2.5 Consensus size: 90
2052908 TTAATTTCTT
2052918 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
2052983 GAATGTTAGGTGTGTTAGGTGAGAA
66 GAATGTTAGGTGTGTTAGGTGAGAA
*
2053008 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
2053073 GAATGTTAGGTGTGTTAGGTGAGAA
66 GAATGTTAGGTGTGTTAGGTGAGAA
2053098 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
2053146 ACATGTATAT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 137 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (90 bp):
TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAA
GAATGTTAGGTGTGTTAGGTGAGAA
Found at i:2053117 original size:56 final size:56
Alignment explanation
Indices: 2052971--2053145 Score: 225
Period size: 56 Copynumber: 3.1 Consensus size: 56
2052961 TGTTAGGTGA
* * *
2052971 TGTGTTTGGTAAGAATGTTAGGTGTGTTAGGTGA-GAATGTTAGGT--G--TGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATG--TGTTTGGTGAGAATGTTAGG
*
2053024 TGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
1 TG-TG--TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
*
2053083 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
2053139 TGTGTTA
1 TGTGTTA
2053146 ACATGTATAT
Statistics
Matches: 110, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
53 2 0.02
54 2 0.02
55 7 0.06
56 86 0.78
57 2 0.02
58 2 0.02
59 9 0.08
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.41
Consensus pattern (56 bp):
TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGG
Found at i:2054307 original size:2 final size:2
Alignment explanation
Indices: 2054300--2054324 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2054290 TATAGAATAC
2054300 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2054325 ATTATCCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2054416 original size:58 final size:58
Alignment explanation
Indices: 2054326--2054444 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 58
2054316 ATATATATAA
* *
2054326 TTATCCATACATATACCAACAATTCCATATGTATAAGAAAGAGTTACCTGATTTCATT
1 TTATCCACACATATACCAACAATTCCATATGTATAAGAAAGAATTACCTGATTTCATT
** * *
2054384 TTATCCACACATATATGAACGATTCCATATGTATAAGAGAGAATTACCTGATTTCATT
1 TTATCCACACATATACCAACAATTCCATATGTATAAGAAAGAATTACCTGATTTCATT
2054442 TTA
1 TTA
2054445 CAAAGTTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (58 bp):
TTATCCACACATATACCAACAATTCCATATGTATAAGAAAGAATTACCTGATTTCATT
Found at i:2056410 original size:19 final size:17
Alignment explanation
Indices: 2056386--2056422 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
2056376 CCTCCGTTGT
2056386 AATATGATCATATAAAATA
1 AATATGAT-ATA-AAAATA
2056405 AATATGATATAAAAATA
1 AATATGATATAAAAATA
2056422 A
1 A
2056423 TTAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (17 bp):
AATATGATATAAAAATA
Found at i:2056442 original size:27 final size:28
Alignment explanation
Indices: 2056412--2056493 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
2056402 ATAAATATGA
2056412 TATAAAAATAATTAATAATATATAAAT-
1 TATAAAAATAATTAATAATATATAAATG
*
2056439 TATAATAATAATAATAATAATATATAAATG
1 TATAAAAATAAT--TAATAATATATAAATG
*
2056469 TATTAAAAT--TTATATAATATA-AAAT
1 TATAAAAATAATTA-ATAATATATAAAT
2056494 ATTAATGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.12
27 19 0.40
28 1 0.02
29 15 0.31
30 7 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
TATAAAAATAATTAATAATATATAAATG
Found at i:2056446 original size:3 final size:3
Alignment explanation
Indices: 2056413--2056465 Score: 52
Period size: 3 Copynumber: 16.3 Consensus size: 3
2056403 TAAATATGAT
* *
2056413 ATA AAA ATA ATTA ATA ATA TATAA ATT ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA ATA
2056461 TATA A
1 -ATA A
2056466 ATGTATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 31 0.74
4 10 0.24
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2056486 original size:33 final size:33
Alignment explanation
Indices: 2056419--2056516 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 33
2056409 TGATATAAAA
2056419 ATAATTAATAATATATAAAT-TA-TAATAA--TA-
1 ATAA-TAATAATATATAAATGTATTAA-AATTTAT
2056449 ATAATAATAATATATAAATGTATTAAAATTTAT
1 ATAATAATAATATATAAATGTATTAAAATTTAT
* * *
2056482 ATAAT-ATAAAATATTAATGTATCAAAATTTAT
1 ATAATAATAATATATAAATGTATTAAAATTTAT
2056514 ATA
1 ATA
2056517 TCATAAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
29 15 0.25
30 8 0.13
31 3 0.05
32 29 0.48
33 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (33 bp):
ATAATAATAATATATAAATGTATTAAAATTTAT
Found at i:2056502 original size:32 final size:33
Alignment explanation
Indices: 2056449--2056524 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 33
2056439 TATAATAATA
* *
2056449 ATAATAATAATATATAAATGTATTAAAATTTAT
1 ATAATAATAAAATATAAATGTATCAAAATTTAT
*
2056482 ATAAT-ATAAAATATTAATGTATCAAAATTTAT
1 ATAATAATAAAATATAAATGTATCAAAATTTAT
*
2056514 AT-ATCATAAAA
1 ATAATAATAAAA
2056525 ATAGTGATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.05
32 32 0.82
33 5 0.13
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (33 bp):
ATAATAATAAAATATAAATGTATCAAAATTTAT
Found at i:2056524 original size:16 final size:15
Alignment explanation
Indices: 2056472--2056524 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2056462 ATAAATGTAT
2056472 TAAAATTTATATAATA
1 TAAAATTTATAT-ATA
*
2056488 TAAAATATTA-ATGTA
1 TAAAAT-TTATATATA
2056503 TCAAAATTTATATATCA
1 T-AAAATTTATATAT-A
2056520 TAAAA
1 TAAAA
2056525 ATAGTGATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 6 0.19
16 20 0.65
17 5 0.16
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (15 bp):
TAAAATTTATATATA
Found at i:2056939 original size:21 final size:22
Alignment explanation
Indices: 2056914--2056968 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2056904 TAATTCAAAT
*
2056914 TTTAAATATTAT-ATAAAATAA
1 TTTAAATATTATAAAAAAATAA
*
2056935 TTTAAATATAATAAAAAAATAA
1 TTTAAATATTATAAAAAAATAA
2056957 TTCT-AATATTAT
1 TT-TAAATATTAT
2056969 GCAAATACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.38
22 17 0.59
23 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAATATTATAAAAAAATAA
Found at i:2057794 original size:25 final size:25
Alignment explanation
Indices: 2057766--2057814 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2057756 TATTATTTTT
*
2057766 TATTAAATTAAATTATTATTATAAC
1 TATTAAATTAAATTATAATTATAAC
** *
2057791 TATTTTATTCAATTATAATTATAA
1 TATTAAATTAAATTATAATTATAA
2057815 TATATTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTAAATTAAATTATAATTATAAC
Found at i:2061099 original size:13 final size:13
Alignment explanation
Indices: 2061063--2061099 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2061053 TAATTGATAA
2061063 TATTTCATATT-T
1 TATTTCATATTAT
*
2061075 TA-TTCGTATTAT
1 TATTTCATATTAT
2061087 TATTTCATATTAT
1 TATTTCATATTAT
2061100 AATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 7 0.33
12 5 0.24
13 9 0.43
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (13 bp):
TATTTCATATTAT
Found at i:2061204 original size:28 final size:27
Alignment explanation
Indices: 2061154--2061208 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2061144 ACGTAAATAA
2061154 TTTATATTTTATTAATTTTATCATATT
1 TTTATATTTTATTAATTTTATCATATT
*
2061181 TTTATATTTATATT-TTTTATATCATATT
1 TTTATATTT-TATTAATTT-TATCATATT
2061209 ATATATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATATTTTATTAATTTTATCATATT
Found at i:2061207 original size:14 final size:14
Alignment explanation
Indices: 2061172--2061227 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 14
2061162 TTATTAATTT
2061172 TATCATA-TTTTTA
1 TATCATATTTTTTA
*
2061185 TATTTATATTTTTTA
1 TA-TCATATTTTTTA
2061200 TATCATATTATATATTA
1 TATCATATT-T-T-TTA
*
2061217 TATCTTATTTT
1 TATCATATTTT
2061228 AATTATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.06
14 10 0.29
15 10 0.29
16 2 0.06
17 11 0.31
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (14 bp):
TATCATATTTTTTA
Found at i:2061209 original size:42 final size:41
Alignment explanation
Indices: 2061172--2061258 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 41
2061162 TTATTAATTT
*
2061172 TATCATATTTTTATATTTATATTTTTTATATCATATTATATATTA
1 TATCATA-TTTTA-A-TTAT-TTTTTTATATAATATTATATATTA
* *
2061217 TATCTTATTTTAATTATTTTTGTTATATAATATT-TTTATTA
1 TATCATATTTTAATTATTTTT-TTATATAATATTATATATTA
2061258 T
1 T
2061259 GTTTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
41 11 0.29
42 15 0.39
43 1 0.03
44 5 0.13
45 6 0.16
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (41 bp):
TATCATATTTTAATTATTTTTTTATATAATATTATATATTA
Found at i:2061639 original size:24 final size:25
Alignment explanation
Indices: 2061607--2061658 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2061597 GTTATTATTA
*
2061607 AAAAAAATTAT-AATTTAAAAATAT
1 AAAAAAATTATAAATATAAAAATAT
*
2061631 AAAAAAATTATAAATATAAAAATTT
1 AAAAAAATTATAAATATAAAAATAT
2061656 AAA
1 AAA
2061659 CATCGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAAATTATAAATATAAAAATAT
Found at i:2063042 original size:5 final size:5
Alignment explanation
Indices: 2063007--2063175 Score: 52
Period size: 5 Copynumber: 34.0 Consensus size: 5
2062997 ATATTATTGC
* * * *
2063007 ATTAT ATTTT ATTAT TTTAT A-AAT ATATAT ATTAT A-TAT ACTAT ATT-T
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT
* * *
2063055 ATATAA ATTTT AATT-T ATTA- ATAAT -TTAT ATTAT A-TATT ATT-T
1 AT-TAT ATTAT -ATTAT ATTAT ATTAT ATTAT ATTAT ATTA-T ATTAT
** * * *
2063098 AAAAT ATTTAT ATCATT TTTAT ATTAT A-TA- ATTAT ATCATAT TTTAT
1 ATTAT A-TTAT ATTA-T ATTAT ATTAT ATTAT ATTAT AT--TAT ATTAT
* * *
2063145 ATTAT ATTTT AATTTT TTTAT ATTAT ATTAT
1 ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT
2063176 TAATTTCACA
Statistics
Matches: 119, Mismatches: 26, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
3 1 0.01
4 27 0.23
5 66 0.55
6 21 0.18
7 4 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:2063058 original size:15 final size:14
Alignment explanation
Indices: 2063022--2063155 Score: 62
Period size: 12 Copynumber: 10.3 Consensus size: 14
2063012 ATTTTATTAT
*
2063022 TTTATAAATATATA
1 TTTATATATATATA
2063036 TATTATATATACTATA
1 T-TTATATATA-TATA
* *
2063052 TTTATATAAATTTTAA
1 TTTATATATA-TAT-A
2063068 TTTAT-TA-ATA-A
1 TTTATATATATATA
2063079 TTTATAT-TATATA
1 TTTATATATATATA
* *
2063092 -TTATTTA-AAATA
1 TTTATATATATATA
*
2063104 TTTATAT-CAT-T-
1 TTTATATATATATA
2063115 TTTATAT-TATATA
1 TTTATATATATATA
* *
2063128 ATTATAT-CATAT-
1 TTTATATATATATA
2063140 TTTATAT-TATAT-
1 TTTATATATATATA
2063152 TTTA
1 TTTA
2063156 ATTTTTTTAT
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
11 15 0.16
12 29 0.31
13 18 0.19
14 2 0.02
15 20 0.21
16 11 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:2063094 original size:54 final size:55
Alignment explanation
Indices: 2063032--2063152 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 55
2063022 TTTATAAATA
** *
2063032 TATATATTATATATACTATATTTATATAAATTTTAAT-TTAT-TAATAAT-TTATAT
1 TATATATTATAT-TAAAATATTTATAT-AATTTTAATATTATATAATAATATCATAT
* * *
2063086 TATATATTAT-TTAAAATATTTATATCATTTTTATATTATATAATTATATCATAT
1 TATATATTATATTAAAATATTTATATAATTTTAATATTATATAATAATATCATAT
*
2063140 TTTATATTATATT
1 TATATATTATATT
2063153 TTAATTTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
51 7 0.12
52 16 0.29
53 7 0.12
54 24 0.43
55 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (55 bp):
TATATATTATATTAAAATATTTATATAATTTTAATATTATATAATAATATCATAT
Found at i:2063144 original size:36 final size:37
Alignment explanation
Indices: 2063079--2063155 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
2063069 TTATTAATAA
*
2063079 TTTATATTATATATTATTTAAAATATTTATATCAT-T
1 TTTATATTATATATTATATAAAATATTTATATCATAT
* * *
2063115 TTTATATTATATAATTATATCATAT-TTTATATTATAT
1 TTTATATTATAT-ATTATATAAAATATTTATATCATAT
2063152 TTTA
1 TTTA
2063156 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (37 bp):
TTTATATTATATATTATATAAAATATTTATATCATAT
Found at i:2063165 original size:21 final size:22
Alignment explanation
Indices: 2063113--2063181 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 22
2063103 ATTTATATCA
*
2063113 TTTTTATATTATATAATTATATCAT
1 TTTTTATATTATATTATTA-AT--T
*
2063138 ATTTTATATTATATT-TTAATT
1 TTTTTATATTATATTATTAATT
2063159 TTTTTATATTATATTATTAATT
1 TTTTTATATTATATTATTAATT
2063181 T
1 T
2063182 CACATAATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 15 0.38
22 7 0.17
23 2 0.05
24 3 0.08
25 13 0.32
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATATTATATTATTAATT
Found at i:2064989 original size:5 final size:5
Alignment explanation
Indices: 2064973--2065043 Score: 60
Period size: 5 Copynumber: 14.6 Consensus size: 5
2064963 GTTTAAAAAA
* * *
2064973 TAATT T-ATT TAATT TAA-T AAATT TAAATT TAAATA TAATT T--TT TATTT
1 TAATT TAATT TAATT TAATT TAATT T-AATT T-AATT TAATT TAATT TAATT
*
2065021 TAAAT TAATT TAATT TAATT TAA
1 TAATT TAATT TAATT TAATT TAA
2065044 AATATATATT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
3 3 0.06
4 7 0.13
5 34 0.63
6 10 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TAATT
Found at i:2065012 original size:35 final size:34
Alignment explanation
Indices: 2064972--2065038 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
2064962 TGTTTAAAAA
2064972 ATAATTTATTTAATTT-AATAAATTTAAATTTAAAT
1 ATAATTT-TTTAATTTAAATAAATTT-AATTTAAAT
* *
2065007 ATAATTTTTTATTTTAAATTAATTTAATTTAA
1 ATAATTTTTTAATTTAAATAAATTTAATTTAA
2065039 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
ATAATTTTTTAATTTAAATAAATTTAATTTAAAT
Found at i:2065152 original size:18 final size:18
Alignment explanation
Indices: 2065129--2065164 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2065119 TTTAATAAAA
* *
2065129 TAAATAATAATTTAAATT
1 TAAATAAAAAATTAAATT
2065147 TAAATAAAAAATTAAATT
1 TAAATAAAAAATTAAATT
2065165 AAACTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATAAAAAATTAAATT
Found at i:2065872 original size:24 final size:21
Alignment explanation
Indices: 2065829--2065873 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
2065819 AGTTTATAAA
2065829 TTTAATTAATTTTTTTTAATT
1 TTTAATTAATTTTTTTTAATT
2065850 TTTAATATATATTTATTTTTAATT
1 TTTAAT-TA-ATTT-TTTTTAATT
2065874 AATATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 4 0.19
24 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTAATTTTTTTTAATT
Found at i:2066100 original size:25 final size:26
Alignment explanation
Indices: 2066049--2066098 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
2066039 TATTGATCTC
2066049 AAATCAAATTTTAAATCTTAAATTTT
1 AAATCAAATTTTAAATCTTAAATTTT
2066075 AAAT-AAA-TTTAAA-CTTAAAATTTT
1 AAATCAAATTTTAAATCTT-AAATTTT
2066099 TATAACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.13
24 13 0.57
25 3 0.13
26 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATCAAATTTTAAATCTTAAATTTT
Found at i:2070591 original size:19 final size:17
Alignment explanation
Indices: 2070563--2070600 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
2070553 TACTTAAAAA
2070563 CTTTCTCTTCTCTTCTTT
1 CTTTCTCTTCTCTT-TTT
2070581 CTTTACTCTTCTCTTTTT
1 CTTT-CTCTTCTCTTTTT
2070599 CT
1 CT
2070601 CCTTAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCTCTTCTCTTTTT
Found at i:2074510 original size:3 final size:3
Alignment explanation
Indices: 2074502--2074543 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2074492 CTAATCCATA
* *
2074502 CAT CAT CAT CAT CAT CAT CAT CAT CAT CGT CGT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2074544 TATAAATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.29, C:0.33, G:0.05, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2075517 original size:41 final size:42
Alignment explanation
Indices: 2075444--2075530 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
2075434 CAGAATATAA
* * * *
2075444 TTAATTTTAAATTAAATTTAAGTATAATATTTTTATTTTTAT
1 TTAAGTTTAAATTAAATTTAAATATAATATTTTAAATTTTAT
2075486 TTAAGTTTAAATT-AATTTAAAATATAA-ATTTTAAATTTTAT
1 TTAAGTTTAAATTAAATTT-AAATATAATATTTTAAATTTTAT
2075527 TTAA
1 TTAA
2075531 ATATTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (42 bp):
TTAAGTTTAAATTAAATTTAAATATAATATTTTAAATTTTAT
Found at i:2075810 original size:18 final size:18
Alignment explanation
Indices: 2075783--2075817 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2075773 ATTAAAAACA
* *
2075783 AAATATAATTTATTTTTT
1 AAATAAAATTAATTTTTT
2075801 AAATAAAATTAATTTTT
1 AAATAAAATTAATTTTT
2075818 ATACTTAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATAAAATTAATTTTTT
Found at i:2077136 original size:9 final size:9
Alignment explanation
Indices: 2077122--2077146 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2077112 TTAATTATTC
2077122 ATATTTTTT
1 ATATTTTTT
2077131 ATATTTTTT
1 ATATTTTTT
2077140 ATATTTT
1 ATATTTT
2077147 ATATTATATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATATTTTTT
Done.