Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 196 of 199
Found at i:61930371 original size:16 final size:17
Alignment explanation
Indices: 61930352--61930385 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61930342 ATTAATGTTT
61930352 TGGGCTA-TTTGGGCTG
1 TGGGCTAGTTTGGGCTG
*
61930368 TGGGTTAGTTTGGGCTG
1 TGGGCTAGTTTGGGCTG
61930385 T
1 T
61930386 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.44, T:0.41
Consensus pattern (17 bp):
TGGGCTAGTTTGGGCTG
Found at i:61931056 original size:44 final size:41
Alignment explanation
Indices: 61930868--61931107 Score: 157
Period size: 46 Copynumber: 5.7 Consensus size: 41
61930858 TTTTAATCCA
* * *
61930868 CTCCACTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATA--CTCTTTGATCTG
* * *
61930911 CTCCGCTGTAATCTCAGGGAGATAAGAT-CTCATGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATACTC-TTTGATCTG
* * * * *
61930952 CTCTACTGTAA-CTTTAGAGAGATAAGAT-C-CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATACTCTTTGATCTG
* * *
61930991 CTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TAC--TCTTTGATCTG
* * * *
61931035 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGA--T---ACTCTTTGATCTG
*
61931081 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
61931108 CCTGTATTAT
Statistics
Matches: 152, Mismatches: 32, Indels: 23
0.73 0.15 0.11
Matches are distributed among these distances:
39 24 0.16
40 6 0.04
41 30 0.20
43 24 0.16
44 32 0.21
45 1 0.01
46 34 0.22
48 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (41 bp):
CTCCACTGTAATCTCAGGGAGATAAGATACTCTTTGATCTG
Found at i:61943541 original size:42 final size:44
Alignment explanation
Indices: 61943454--61943546 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 44
61943444 ATAAATAAAG
* * ** *
61943454 ATATATATATATGAATTACAAAACATGAAAATATAAGTATTTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
* *
61943498 ATATATAAATA-GATTTAAAAAATAT-AAAATATAAACATGTAC
1 ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
61943540 AT-TATAA
1 ATATATAA
61943547 GAACGTAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.12
42 16 0.38
43 11 0.26
44 10 0.24
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (44 bp):
ATATATAAATATGAATTAAAAAACATGAAAATATAAACATGTAC
Found at i:61945028 original size:16 final size:17
Alignment explanation
Indices: 61945009--61945042 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61944999 ATTAATGTTT
61945009 TGGGCTA-TTTGGGCTG
1 TGGGCTAGTTTGGGCTG
*
61945025 TGGGTTAGTTTGGGCTG
1 TGGGCTAGTTTGGGCTG
61945042 T
1 T
61945043 TAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.44, T:0.41
Consensus pattern (17 bp):
TGGGCTAGTTTGGGCTG
Found at i:61952514 original size:16 final size:17
Alignment explanation
Indices: 61952493--61952526 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61952483 TTTGTATTTT
*
61952493 TATTTTT-ATATTTTAA
1 TATTTTTGAAATTTTAA
61952509 TATTTTTGAAATTTTAA
1 TATTTTTGAAATTTTAA
61952526 T
1 T
61952527 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTTTGAAATTTTAA
Found at i:61967859 original size:19 final size:19
Alignment explanation
Indices: 61967821--61967863 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
61967811 AGACAGAGAC
*
61967821 AGACAGTGACAGTGACAGG
1 AGACAGTGACAGTGAAAGG
61967840 AGACAGTGACAGCT-AAAGG
1 AGACAGTGACAG-TGAAAGG
61967859 AGACA
1 AGACA
61967864 ATATAGGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.42, C:0.16, G:0.33, T:0.09
Consensus pattern (19 bp):
AGACAGTGACAGTGAAAGG
Found at i:61968228 original size:3 final size:3
Alignment explanation
Indices: 61968222--61968247 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61968212 AACTTGTCGG
61968222 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
61968248 AAATCCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:61968317 original size:9 final size:9
Alignment explanation
Indices: 61968305--61968346 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
61968295 TTCTCTCACT
61968305 TTCCTCTTC
1 TTCCTCTTC
61968314 TTCCTCTTC
1 TTCCTCTTC
* *
61968323 CTCATCTTC
1 TTCCTCTTC
*
61968332 TTCTTCTTC
1 TTCCTCTTC
61968341 TTCCTC
1 TTCCTC
61968347 CTCCACTTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.55
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:61968355 original size:21 final size:21
Alignment explanation
Indices: 61968310--61968360 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
61968300 TCACTTTCCT
**
61968310 CTTCTTCCTCTTCCTCATCTT
1 CTTCTTCCTCTTCCTCATCCA
* *
61968331 CTTCTTCTTCTTCCTCCTCCA
1 CTTCTTCCTCTTCCTCATCCA
*
61968352 CTTCCTCCT
1 CTTCTTCCT
61968361 TCGCCGTTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (21 bp):
CTTCTTCCTCTTCCTCATCCA
Found at i:61968538 original size:15 final size:12
Alignment explanation
Indices: 61968502--61968530 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61968492 TTCTCTCTCC
61968502 TCCTC-TCTTCT
1 TCCTCGTCTTCT
61968513 TCCTCGTCTTCT
1 TCCTCGTCTTCT
61968525 TCCTCG
1 TCCTCG
61968531 AAGTCTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (12 bp):
TCCTCGTCTTCT
Found at i:61969399 original size:16 final size:16
Alignment explanation
Indices: 61969376--61969408 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61969366 TATGCTTATA
61969376 AAATTAA-TTAAAAAT
1 AAATTAATTTAAAAAT
61969391 AAATATAATTTAAAAAT
1 AAAT-TAATTTAAAAAT
61969408 A
1 A
61969409 TCATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAATTTAAAAAT
Found at i:61970073 original size:20 final size:18
Alignment explanation
Indices: 61970057--61970103 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
61970047 GGATTTTGAG
*
61970057 GTTTTTTTTTATTTTTTAA
1 GTTTTTTTATATTTTTT-A
*
61970076 GTTTATTATATATTTTTTA
1 GTTT-TTTTATATTTTTTA
61970095 GTTTTTTTA
1 GTTTTTTTA
61970104 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
GTTTTTTTATATTTTTTA
Found at i:61974003 original size:26 final size:24
Alignment explanation
Indices: 61973963--61974024 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
61973953 ATAAACAAAC
* * *
61973963 ATATTTTCTTCTTTTGCAAATTTTA
1 ATATTTT-TTTTTTTCCAAATGTTA
*
61973988 ATCATTTTATTTTTTTCCATATGTTA
1 AT-ATTTT-TTTTTTTCCAAATGTTA
61974014 ATATTTTTTTT
1 ATATTTTTTTT
61974025 ATTTTTGTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 4 0.13
25 7 0.23
26 20 0.65
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (24 bp):
ATATTTTTTTTTTTCCAAATGTTA
Found at i:61974170 original size:20 final size:21
Alignment explanation
Indices: 61974145--61974183 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
61974135 ATCCAAAATC
*
61974145 CTGAACCTTGAA-CTTGAACT
1 CTGAACCTTAAATCTTGAACT
61974165 CTGAACCTTAAATCTTGAA
1 CTGAACCTTAAATCTTGAA
61974184 TCATAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
CTGAACCTTAAATCTTGAACT
Found at i:61982155 original size:57 final size:56
Alignment explanation
Indices: 61982065--61982172 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 56
61982055 TAAAAATTAT
*
61982065 ATAAGGTCAAATTTCAATTTTAGTCTCCATGCTAAACTCAAATTTAAGATTATATA
1 ATAAGGTCAAATTTCAATTTTAGTCTCCATGCTAAACACAAATTTAAGATTATATA
* * *
61982121 ATAATGGTCAAATTTCAATTTT-GATC-CCTTTGCTACACACAGATTTAAGATT
1 ATAA-GGTCAAATTTCAATTTTAG-TCTCC-ATGCTAAACACAAATTTAAGATT
61982173 CAATCTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
56 7 0.16
57 38 0.84
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (56 bp):
ATAAGGTCAAATTTCAATTTTAGTCTCCATGCTAAACACAAATTTAAGATTATATA
Found at i:61983084 original size:2 final size:2
Alignment explanation
Indices: 61983077--61983103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61983067 AGTTTTTCAC
61983077 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 A
61983104 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61989553 original size:40 final size:40
Alignment explanation
Indices: 61989509--61989700 Score: 241
Period size: 40 Copynumber: 4.8 Consensus size: 40
61989499 ATAAATATAT
* *
61989509 TTTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAA
1 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
61989549 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TTTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAA
*
61989590 -TTTTTTTAATTTTAAAATA-TTTTAAAATATATTTTTTAA
1 TTTTTTTTAATTTTAAAATATTTTTAAAATA-CTTTTTTAA
* *
61989629 ATTTTTTTAATTTTAAAATA-TTTTAAAATA-TTTTTAAAA
1 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT-TAA
61989668 TACTTTTTTTAATTTTTAAAA-ATTTTTAAAATA
1 T--TTTTTTTAA-TTTTAAAATATTTTTAAAATA
61989701 AAAATGGGCC
Statistics
Matches: 137, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
38 5 0.04
39 20 0.15
40 76 0.55
41 18 0.13
42 18 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:61989600 original size:50 final size:49
Alignment explanation
Indices: 61989519--61989684 Score: 158
Period size: 50 Copynumber: 3.5 Consensus size: 49
61989509 TTTTTTTTAA
61989519 TTTTAAAATA-TTTTTTACATACTTTTTTAATTTTTTTAAATTTTAAAATAT
1 TTTTAAAATATTTTTTTA-AT--TTTTTTAATTTTTTTAAATTTTAAAATAT
*
61989570 TTTT-AAA-A------TACTTTTTTTAATTTTTTT-AATTTTAAAATA-
1 TTTTAAAATATTTTTTTAATTTTTTTAATTTTTTTAAATTTTAAAATAT
**
61989609 TTTTAAAATATATTTTTTAAATTTTTTTAA-TTTTAAAATATTTTAAAATAT
1 TTTTAAAATAT-TTTTTT-AATTTTTTTAATTTTTTTAA-ATTTTAAAATAT
61989660 TTTTAAAATACTTTTTTTAATTTTT
1 TTTTAAAATA-TTTTTTTAATTTTT
61989685 AAAAATTTTT
Statistics
Matches: 97, Mismatches: 4, Indels: 29
0.75 0.03 0.22
Matches are distributed among these distances:
39 4 0.04
40 15 0.15
41 16 0.16
43 1 0.01
44 2 0.02
48 5 0.05
49 12 0.12
50 21 0.22
51 20 0.21
52 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (49 bp):
TTTTAAAATATTTTTTTAATTTTTTTAATTTTTTTAAATTTTAAAATAT
Found at i:61989651 original size:10 final size:10
Alignment explanation
Indices: 61989598--61989700 Score: 63
Period size: 10 Copynumber: 10.1 Consensus size: 10
61989588 AATTTTTTTA
61989598 ATTTTAAAAT
1 ATTTTAAAAT
61989608 ATTTTAAAATAT
1 ATTTT-AAA-AT
*
61989620 ATTTTTTAAAT
1 A-TTTTAAAAT
**
61989631 -TTTT-TTA-
1 ATTTTAAAAT
61989638 ATTTTAAAAT
1 ATTTTAAAAT
61989648 ATTTTAAAAT
1 ATTTTAAAAT
61989658 ATTTTTAAAAT
1 A-TTTTAAAAT
**
61989669 ACTTTTTTTAAT
1 A--TTTTAAAAT
61989681 -TTTTAAAA-
1 ATTTTAAAAT
61989689 ATTTTTAAAAT
1 A-TTTTAAAAT
61989700 A
1 A
61989701 AAAATGGGCC
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
8 5 0.07
9 11 0.15
10 24 0.33
11 16 0.22
12 13 0.18
13 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:61989661 original size:90 final size:90
Alignment explanation
Indices: 61989518--61989684 Score: 259
Period size: 90 Copynumber: 1.9 Consensus size: 90
61989508 TTTTTTTTTA
**
61989518 ATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTAAATTTTAAAATATTTTTAAAATACTT
1 ATTTTAAAATATTTTTTACATACTTTTTTAATTTTTAAAAATTTTAAAATATTTTTAAAATACTT
61989583 TTTTTAATTTTTTTAATTTTAAAAT
66 TTTTTAATTTTTTTAATTTTAAAAT
*
61989608 ATTTTAAAATATATTTTTTA-A-ATTTTTTTAA-TTTTAAAATATTTTAAAATATTTTTAAAATA
1 ATTTT-AAA-ATATTTTTTACATACTTTTTTAATTTTTAAAA-ATTTTAAAATATTTTTAAAATA
61989670 CTTTTTTTAATTTTT
63 CTTTTTTTAATTTTT
61989685 AAAAATTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
89 6 0.08
90 51 0.72
91 4 0.06
92 10 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (90 bp):
ATTTTAAAATATTTTTTACATACTTTTTTAATTTTTAAAAATTTTAAAATATTTTTAAAATACTT
TTTTTAATTTTTTTAATTTTAAAAT
Found at i:61994167 original size:35 final size:35
Alignment explanation
Indices: 61994128--61994197 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
61994118 ACGATCTTCA
61994128 ATTAGTACTTTTAACAAATTTACTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
*
61994163 ATTAGTACTTTTAACAAATTTTCTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
61994198 TAACCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTAGTACTTTTAACAAATTTACTATGACATACTT
Found at i:61994865 original size:20 final size:20
Alignment explanation
Indices: 61994824--61994893 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
61994814 ATTTAAAAAT
**
61994824 ATTTTTATATTTATTTTGTA
1 ATTTTTATATTTATTTAATA
61994844 ATTTTTATATATT-TTTAATA
1 ATTTTTATAT-TTATTTAATA
*** * *
61994864 ATGTCAAAAATTAATTTAATA
1 AT-TTTTATATTTATTTAATA
61994885 ATTTTTATA
1 ATTTTTATA
61994894 ATTTTTGAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTTTATATTTATTTAATA
Found at i:61995977 original size:31 final size:31
Alignment explanation
Indices: 61995916--61995981 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
61995906 TTATTATACC
* **
61995916 ATTTGGTACATGAGTTTGGCTTTGAGGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
*
61995947 ATTTGGTACATGAATTTGGCTTCAATGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
61995978 ATTT
1 ATTT
61995982 AATACCTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (31 bp):
ATTTGGTACATGAATTTGGCTTCAAGGTTCA
Found at i:61998890 original size:20 final size:20
Alignment explanation
Indices: 61998854--61998893 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61998844 TCCTATTGTT
61998854 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
61998874 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
61998894 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:61999524 original size:44 final size:43
Alignment explanation
Indices: 61999428--61999544 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 43
61999418 TTTTAATCCA
* ** * *
61999428 CTCCACTGTAACTTCAGGGAGATAGGATAGCGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTCGGCTTCAATCTG
*
61999471 CTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTC-GGCTTCAATCTG
* *
61999515 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGAGATAAGATCT
61999545 GTAATTTCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
42 1 0.02
43 25 0.40
44 35 0.56
45 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (43 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCTCGGCTTCAATCTG
Found at i:61999973 original size:88 final size:88
Alignment explanation
Indices: 61999678--62000072 Score: 475
Period size: 88 Copynumber: 4.5 Consensus size: 88
61999668 AATCTGTAAC
* * * * *
61999678 CTTTAACCAGCTCCAATGCAACCGATG-GAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTT
1 CTTTAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTC
* **
61999740 AATGCAGGAAGGCAAGATCTGCT-T
64 AATGTAGGAAGGCAAGATCTTTTGT
* * * * * *
61999764 CTTTAACTAGCTCCACTGCAATCGATG-GATGTAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTT
1 CTTTAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTC
**
61999826 AATGTAGGAAGGCAAGATCTGCT-T
64 AATGTAGGAAGGCAAGATCTTTTGT
* *
61999850 CTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAA
1 CTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA
*
61999915 TGCAGGAAGGCAAGATCTTTTGT
66 TGTAGGAAGGCAAGATCTTTTGT
* * *
61999938 CTTCAACCAGCTCTA-TCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
1 CTTTAACCAGCTCCACT-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCA
62000002 ATGTAGGAAGGCAAGATCTTTTGT
65 ATGTAGGAAGGCAAGATCTTTTGT
*
62000026 CTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGACTTC
1 CTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTC
62000073 ATTGATCTGT
Statistics
Matches: 274, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
85 6 0.02
86 108 0.39
87 37 0.14
88 122 0.45
89 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
CTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA
TGTAGGAAGGCAAGATCTTTTGT
Found at i:62000058 original size:44 final size:45
Alignment explanation
Indices: 61999835--62000073 Score: 142
Period size: 44 Copynumber: 5.5 Consensus size: 45
61999825 TAATGTAGGA
*
61999835 AGGCAAGATC-TGCT-TCTTTAACCAGCTCCACT-ACAACCGAGAG
1 AGGCAAGATCTTG-TGTCTTCAACCAGCTCCACTGACAACCGAGAG
* * * * * *
61999878 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCACTGTCAA-TGCAG-G
1 AGGCAAGATCTTGTGTCTTCAACCAGCTCCACTGACAACCG-AGAG
* * * *
61999921 AAGGCAAGATCTTTTGTCTTCAACCAGCTCTA-TCACAACCGAAAG
1 -AGGCAAGATCTTGTGTCTTCAACCAGCTCCACTGACAACCGAGAG
* * * * * * * *
61999966 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAA-TGTAG-G
1 AGGCAAGATCTTGTGTCTTCAACCAGCTCCACTGACAACCG-AGAG
* *
62000009 AAGGCAAGATCTTTTGTCTTTAACCAGCTCCACT-ACAACCGAGAG
1 -AGGCAAGATCTTGTGTCTTCAACCAGCTCCACTGACAACCGAGAG
* *
62000054 AGGCAAGGT-TTGTGACTTCA
1 AGGCAAGATCTTGTGTCTTCA
62000074 TTGATCTGTC
Statistics
Matches: 139, Mismatches: 43, Indels: 28
0.66 0.20 0.13
Matches are distributed among these distances:
42 1 0.01
43 50 0.36
44 52 0.37
45 36 0.26
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (45 bp):
AGGCAAGATCTTGTGTCTTCAACCAGCTCCACTGACAACCGAGAG
Found at i:62001789 original size:27 final size:31
Alignment explanation
Indices: 62001727--62001791 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 31
62001717 GCTTTTCATA
*
62001727 TTTTTATTTTGACTTTGATTGATTTCTTTTTAT
1 TTTTTATTTTGAC-TT-ATTGATTTCTGTTTAT
62001760 TTTTTATTTTGA-TT-TTGATTT-TGTTT-T
1 TTTTTATTTTGACTTATTGATTTCTGTTTAT
62001787 TTTTT
1 TTTTT
62001792 CCCTTGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 6 0.19
28 4 0.13
29 7 0.23
31 2 0.06
33 12 0.39
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.75
Consensus pattern (31 bp):
TTTTTATTTTGACTTATTGATTTCTGTTTAT
Found at i:62009573 original size:20 final size:20
Alignment explanation
Indices: 62009537--62009576 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62009527 TCCTATTGTT
62009537 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
62009557 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
62009577 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:62013242 original size:20 final size:20
Alignment explanation
Indices: 62013206--62013245 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62013196 TCCTATTGTT
62013206 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
62013226 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
62013246 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:62013927 original size:15 final size:15
Alignment explanation
Indices: 62013889--62013929 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
62013879 TAAATAACTG
62013889 AATTTAATAAGT-CAA
1 AATTTAA-AAGTACAA
62013904 AATTT-AAAGTACAA
1 AATTTAAAAGTACAA
*
62013918 ATTTTAAAAGTA
1 AATTTAAAAGTA
62013930 AAGCGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTAAAAGTACAA
Found at i:62022601 original size:81 final size:82
Alignment explanation
Indices: 62022446--62022602 Score: 221
Period size: 82 Copynumber: 1.9 Consensus size: 82
62022436 AACCCTATAC
* **
62022446 TTCACACTTATTCTGTAAAAAAGTATAAAATGTAAAATATACATTTAAAAATTTTAAATTATTGA
1 TTCACACTTATTCTGTAAAAAAATATAAAATGTAAAATATACACATAAAAATTTTAAATTATTGA
62022511 TAGTTTTATTTTTTTTA
66 TAGTTTTATTTTTTTTA
* *
62022528 TTCACACTTATTTTGTAAAAAGAATATAAAATGT-AAATATACACAT-AAAATTTTATATTATTT
1 TTCACACTTATTCTGTAAAAA-AATATAAAATGTAAAATATACACATAAAAATTTTAAATTA-TT
*
62022591 G-TGGTTTTATTT
64 GATAGTTTTATTT
62022603 ATTTATTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 23 0.34
82 33 0.49
83 11 0.16
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (82 bp):
TTCACACTTATTCTGTAAAAAAATATAAAATGTAAAATATACACATAAAAATTTTAAATTATTGA
TAGTTTTATTTTTTTTA
Found at i:62025503 original size:20 final size:20
Alignment explanation
Indices: 62025480--62025521 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
62025470 TAATTCCATG
*
62025480 AAAAAATA-AATAAACTCAAA
1 AAAAAATATAAGAAA-TCAAA
*
62025500 AAAATATATAAGAAATCAAA
1 AAAAAATATAAGAAATCAAA
62025520 AA
1 AA
62025522 GAGAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAAATATAAGAAATCAAA
Found at i:62027316 original size:21 final size:19
Alignment explanation
Indices: 62027292--62027341 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
62027282 TTTAAACATT
62027292 TTTAAATATGTTATTATTATA
1 TTTAAATAT-TTATTATTA-A
62027313 TTT-AAT-TTTATTATTAA
1 TTTAAATATTTATTATTAA
*
62027330 TTAAAATATTTA
1 TTTAAATATTTA
62027342 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 12 0.46
19 5 0.19
20 3 0.12
21 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAAATATTTATTATTAA
Found at i:62029464 original size:58 final size:58
Alignment explanation
Indices: 62029391--62029557 Score: 282
Period size: 58 Copynumber: 2.9 Consensus size: 58
62029381 ATGTCTCATT
62029391 TCTATCGAGAGCTCAAAGGGTTCACGAAGGGACCCGAATGTAGAAGATATACCTCACC
1 TCTATCGAGAGCTCAAAGGGTTCACGAAGGGACCCGAATGTAGAAGATATACCTCACC
62029449 TCTATCGAGAGCTCAAAGGGTTCACGAAGGGACCCGAATGTAGAAGATATACCTCACC
1 TCTATCGAGAGCTCAAAGGGTTCACGAAGGGACCCGAATGTAGAAGATATACCTCACC
* ** *
62029507 TCTATCGAGAGCTCAAAGGGTTCAC-AGAGGGGCTTGAATGTAAAAGATATA
1 TCTATCGAGAGCTCAAAGGGTTCACGA-AGGGACCCGAATGTAGAAGATATA
62029558 TATATATATA
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
57 1 0.01
58 103 0.99
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (58 bp):
TCTATCGAGAGCTCAAAGGGTTCACGAAGGGACCCGAATGTAGAAGATATACCTCACC
Found at i:62035195 original size:23 final size:24
Alignment explanation
Indices: 62035169--62035213 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
62035159 TATAGCCCCT
*
62035169 TCAA-AAAATTATAAAATTACAAG
1 TCAATAAAATAATAAAATTACAAG
* *
62035192 TCAATATAATAATAAATTTACA
1 TCAATAAAATAATAAAATTACA
62035214 CTTTGACCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (24 bp):
TCAATAAAATAATAAAATTACAAG
Found at i:62042666 original size:21 final size:20
Alignment explanation
Indices: 62042634--62042691 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
62042624 ATTAATTGAC
*
62042634 AATTTGAGCTACAATATTAT
1 AATTTAAGCTACAATATTAT
62042654 GAATATTAA-CTACAATA-TAT
1 -AAT-TTAAGCTACAATATTAT
62042674 AATTTAAGCTAC-ATATTA
1 AATTTAAGCTACAATATTA
62042692 CAGTAATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 7 0.21
19 9 0.27
20 3 0.09
21 11 0.33
22 3 0.09
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
AATTTAAGCTACAATATTAT
Found at i:62043738 original size:39 final size:37
Alignment explanation
Indices: 62043632--62043752 Score: 109
Period size: 40 Copynumber: 3.1 Consensus size: 37
62043622 CGATTGGATA
* * *
62043632 AAAAACGCCGCTAAAAACCAAGCATTAGTGGCCCTTTTT-
1 AAAAATGCCGCTAAAAA-TAAGCATTAGCGG--CTTTTTG
* * *
62043671 AGAAAATGCAGCTAAAGATCAAGTATTAGCGGCGTTTTTTG
1 A-AAAATGCCGCTAAAAAT-AAGCATTAGCGGC--TTTTTG
*
62043712 AAAAATGCCGCTAAAAATGAGCATTAGCGGCTTTTTG
1 AAAAATGCCGCTAAAAATAAGCATTAGCGGCTTTTTG
62043749 AAAA
1 AAAA
62043753 TGCGCCGCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
37 10 0.15
38 1 0.01
39 12 0.18
40 43 0.64
41 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (37 bp):
AAAAATGCCGCTAAAAATAAGCATTAGCGGCTTTTTG
Found at i:62044444 original size:28 final size:29
Alignment explanation
Indices: 62044389--62044447 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
62044379 ATTTTTTAAT
* *
62044389 TAATAAACATGTTATTTATATAAATAAAA
1 TAATAAAAATGTTAATTATATAAATAAAA
*
62044418 TAATAAAAATG-TAATTATATAATTAAAA
1 TAATAAAAATGTTAATTATATAAATAAAA
62044446 TA
1 TA
62044448 TATCCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (29 bp):
TAATAAAAATGTTAATTATATAAATAAAA
Found at i:62047446 original size:30 final size:30
Alignment explanation
Indices: 62047412--62047471 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
62047402 GACTTGGGGG
* * *
62047412 TGGTGGTGGAGCTGGTGCCGGTGGTGGGTT
1 TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
*
62047442 TGGTGGAGGAGCTGGCGGAGGTGGTGGGTT
1 TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
62047472 AGGAGGTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.07, C:0.08, G:0.58, T:0.27
Consensus pattern (30 bp):
TGGTGGAGGAGCTGGCGCAGGTGGTGGGTT
Found at i:62047847 original size:22 final size:23
Alignment explanation
Indices: 62047796--62047850 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
62047786 TATTCAAGGT
*
62047796 CAAGTCTCGATACATAAGGTTAA
1 CAAGTCTCAATACATAAGGTTAA
* *
62047819 CAAGTCTCAATACATAATG-TAG
1 CAAGTCTCAATACATAAGGTTAA
62047841 CAAGTCTCAA
1 CAAGTCTCAA
62047851 GACTATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (23 bp):
CAAGTCTCAATACATAAGGTTAA
Found at i:62049183 original size:20 final size:20
Alignment explanation
Indices: 62049160--62049197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
62049150 TATATTTTTT
62049160 ATTTTTAAAATACATTTCCC
1 ATTTTTAAAATACATTTCCC
*
62049180 ATTTTTAAAATATATTTC
1 ATTTTTAAAATACATTTC
62049198 ATATGTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAATACATTTCCC
Found at i:62062959 original size:24 final size:25
Alignment explanation
Indices: 62062926--62063016 Score: 67
Period size: 25 Copynumber: 3.7 Consensus size: 25
62062916 AGCTCTGGGT
* *
62062926 CGGTATGCTCTTACGAGTTGTA-AA
1 CGGTAAGCTCTTACGAGTTGAATAA
* * *
62062950 TGGTAAGCTCTTCCTAGTTGAATAA
1 CGGTAAGCTCTTACGAGTTGAATAA
* * ** * *
62062975 CGGTAAGCTCATGCGAACTGAGTAT
1 CGGTAAGCTCTTACGAGTTGAATAA
*
62063000 CGGTAAGCTCATACGAG
1 CGGTAAGCTCTTACGAG
62063017 CTAAAATCGA
Statistics
Matches: 51, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
24 17 0.33
25 34 0.67
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (25 bp):
CGGTAAGCTCTTACGAGTTGAATAA
Found at i:62066390 original size:22 final size:22
Alignment explanation
Indices: 62066362--62066414 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
62066352 TTTTTTTTGC
62066362 TAAAATAGGAAATGAAAAATAA
1 TAAAATAGGAAATGAAAAATAA
*
62066384 TAAAATAGGAAGTGAAAAATAA
1 TAAAATAGGAAATGAAAAATAA
*
62066406 TATAATAGG
1 TAAAATAGG
62066415 TAAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (22 bp):
TAAAATAGGAAATGAAAAATAA
Found at i:62078783 original size:29 final size:29
Alignment explanation
Indices: 62078720--62078783 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
62078710 AGTACATTCA
*
62078720 AATAAATAATATTTTAAATGACCTATTTC
1 AATAAATAATATTTCAAATGACCTATTTC
**
62078749 CGTAAATAATATTTCAAATAGA-CT-TTTC
1 AATAAATAATATTTCAAAT-GACCTATTTC
62078777 TAATAAA
1 -AATAAA
62078784 ATACCCCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
28 4 0.14
29 22 0.79
30 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (29 bp):
AATAAATAATATTTCAAATGACCTATTTC
Found at i:62081118 original size:28 final size:32
Alignment explanation
Indices: 62081060--62081118 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 32
62081050 GTATAGTAAT
* *
62081060 TTAATAAATATATATAATTTATTATTGTAAAA
1 TTAATAAAAATATATAATTTATTAATGTAAAA
62081092 TTAATAAAAATA-AT-ATTTA-TAAT-TAAA
1 TTAATAAAAATATATAATTTATTAATGTAAA
62081119 TAATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.16
29 3 0.12
30 5 0.20
31 2 0.08
32 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
TTAATAAAAATATATAATTTATTAATGTAAAA
Found at i:62081318 original size:22 final size:23
Alignment explanation
Indices: 62081271--62081318 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
62081261 TATAAAAAAT
* **
62081271 ATAATTTTAACTATTTATTTTTA
1 ATAATTGTAACTATTTATTTAAA
62081294 ATAATTGTAA-TATTTATTTAAA
1 ATAATTGTAACTATTTATTTAAA
62081316 ATA
1 ATA
62081319 TTTTATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAATTGTAACTATTTATTTAAA
Found at i:62084925 original size:13 final size:13
Alignment explanation
Indices: 62084907--62084933 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62084897 AGGTGTTCCT
62084907 AAATCTAATGGGA
1 AAATCTAATGGGA
62084920 AAATCTAATGGGA
1 AAATCTAATGGGA
62084933 A
1 A
62084934 GAGTGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AAATCTAATGGGA
Found at i:62095789 original size:13 final size:13
Alignment explanation
Indices: 62095771--62095801 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62095761 AAATTCAGAA
62095771 TATAATTTATTTT
1 TATAATTTATTTT
62095784 TATAATTTATTTT
1 TATAATTTATTTT
*
62095797 GATAA
1 TATAA
62095802 AAATTACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TATAATTTATTTT
Found at i:62097449 original size:48 final size:48
Alignment explanation
Indices: 62097370--62097463 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
62097360 AGGGAATTCT
* * *
62097370 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCATTTTTACG
62097418 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCATTTTTA
62097464 AGCCAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCATTTTTACG
Found at i:62108524 original size:19 final size:20
Alignment explanation
Indices: 62108485--62108525 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
62108475 ATTTTTCTTT
62108485 AAATTAATTAATTATTTAAA
1 AAATTAATTAATTATTTAAA
62108505 AAATTAA-TAA-TATTTGAAA
1 AAATTAATTAATTATTT-AAA
62108524 AA
1 AA
62108526 CATATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 8 0.40
20 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTAATTAATTATTTAAA
Found at i:62111773 original size:18 final size:18
Alignment explanation
Indices: 62111747--62111784 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
62111737 ATTATTTTTA
*
62111747 TTTAATATTTTTATATTT
1 TTTAATATTTTCATATTT
*
62111765 TTTATTATTTTCATATTT
1 TTTAATATTTTCATATTT
62111783 TT
1 TT
62111785 CTTTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTAATATTTTCATATTT
Found at i:62118234 original size:16 final size:16
Alignment explanation
Indices: 62118210--62118255 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
62118200 TTATATTTAA
*
62118210 TAATATAATAAATTAT
1 TAATTTAATAAATTAT
*
62118226 TAATTTAATTAATTA-
1 TAATTTAATAAATTAT
62118241 T--TTTAATAAATTAT
1 TAATTTAATAAATTAT
62118255 T
1 T
62118256 TAATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 1 0.04
16 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTAATAAATTAT
Found at i:62118268 original size:29 final size:29
Alignment explanation
Indices: 62118215--62118281 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
62118205 TTTAATAATA
62118215 TAATAAATTATTAATTTAATTAA-TTATTT
1 TAATAAATTATTAATTTAA-TAATTTATTT
62118244 TAATAAATTATTTAATATTAA-AATTTTATTT
1 TAATAAATTA-TTAAT-TTAATAA-TTTATTT
62118275 TAA-AAAT
1 TAATAAAT
62118282 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 12 0.35
30 9 0.26
31 13 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAAATTATTAATTTAATAATTTATTT
Found at i:62118328 original size:6 final size:6
Alignment explanation
Indices: 62118317--62118346 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
62118307 ATTGTTGAAA
62118317 ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT
62118347 TAATAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:62118705 original size:16 final size:16
Alignment explanation
Indices: 62118668--62118707 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
62118658 TTAATAAAAT
* *
62118668 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
62118684 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
62118700 TAAAATTA
1 TAAAATTA
62118708 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:62118707 original size:22 final size:22
Alignment explanation
Indices: 62118640--62118692 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
62118630 TTATTAAAAT
* * *
62118640 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
62118662 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
62118684 TAAAATTAA
1 TAAAATTAA
62118693 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:62118759 original size:50 final size:50
Alignment explanation
Indices: 62118696--62118832 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 50
62118686 AAATTAATTG
*
62118696 TTAGTAAAATTATCAAATTATTAATTGTTGTAATAAAATCTAACATTTGA
1 TTAGTAAATTTATCAAATTATTAATTGTTGTAATAAAATCTAACATTTGA
62118746 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
1 TTAGTAAATTTATC-----A--AA-T-TATTAATTGTTGTAATAAAATCTAACATTTGA
62118805 TTAGTAAATTTATCAAATTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGT
62118833 ATTAATTGTT
Statistics
Matches: 77, Mismatches: 1, Indels: 18
0.80 0.01 0.19
Matches are distributed among these distances:
50 23 0.30
51 1 0.01
52 2 0.03
54 1 0.01
55 1 0.01
57 2 0.03
58 1 0.01
59 46 0.60
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (50 bp):
TTAGTAAATTTATCAAATTATTAATTGTTGTAATAAAATCTAACATTTGA
Found at i:62118779 original size:59 final size:59
Alignment explanation
Indices: 62118714--62118871 Score: 298
Period size: 59 Copynumber: 2.7 Consensus size: 59
62118704 ATTATCAAAT
62118714 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
62118773 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
**
62118832 TATTAATTGTTGTAGCAAAATCTAACATTTGATTAGTAAA
1 TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
62118872 ACAAACTTGA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 97 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (59 bp):
TATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG
Found at i:62118978 original size:22 final size:24
Alignment explanation
Indices: 62118938--62118981 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
62118928 AAATAAACTT
62118938 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
62118962 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
62118982 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:62119317 original size:24 final size:24
Alignment explanation
Indices: 62119288--62119334 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
62119278 GAAAAATATT
62119288 AAATATATATA-TTTTTTATTTTTA
1 AAATATA-ATAGTTTTTTATTTTTA
62119312 AAATATAATAGTTTTTTTATTTT
1 AAATATAATAG-TTTTTTATTTT
62119335 AAGTTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 7 0.33
25 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:62119464 original size:59 final size:59
Alignment explanation
Indices: 62119401--62119579 Score: 250
Period size: 68 Copynumber: 2.9 Consensus size: 59
62119391 TCAAGTTTGT
* *
62119401 TTTACTAATCAAATATTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
62119460 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
62119525 AAA
57 AAA
*
62119528 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
62119580 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 46 0.43
60 1 0.01
62 2 0.02
65 2 0.02
67 1 0.01
68 56 0.52
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:62119502 original size:9 final size:9
Alignment explanation
Indices: 62119490--62119517 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62119480 TTTTATTACA
62119490 ACAATTAAT
1 ACAATTAAT
62119499 ACAATTAAT
1 ACAATTAAT
62119508 ACAATTAAT
1 ACAATTAAT
62119517 A
1 A
62119518 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:62119508 original size:68 final size:68
Alignment explanation
Indices: 62119431--62119601 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
62119421 TTTTGTTACA
62119431 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
62119496 AAT
66 AAT
62119499 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
62119564 AAT
66 AAT
*
62119567 ACAATT-A-ACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAA
62119602 CAATTAGTTT
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 27 0.26
67 1 0.01
68 74 0.73
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:62119632 original size:16 final size:17
Alignment explanation
Indices: 62119611--62119642 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62119601 ACAATTAGTT
62119611 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
62119627 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
62119643 CAGGCCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:62119836 original size:28 final size:28
Alignment explanation
Indices: 62119797--62119862 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
62119787 GTAATATATG
*
62119797 TTAATTA-AATTAAGTTT-TA-ATTAGATA
1 TTAATTATTATTAAGTTTATATATT--ATA
*
62119824 TTATTTATTATTAAGTTTATATATTATA
1 TTAATTATTATTAAGTTTATATATTATA
62119852 TTAATTATTAT
1 TTAATTATTAT
62119863 AAAATATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 22 0.67
29 2 0.06
30 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
TTAATTATTATTAAGTTTATATATTATA
Found at i:62130796 original size:35 final size:35
Alignment explanation
Indices: 62130750--62130820 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
62130740 GGCATTCAAA
*
62130750 AGTGAGGATGATTTTTCTTTTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
62130785 AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
1 AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
62130820 A
1 A
62130821 CTTTGTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (35 bp):
AGTGAGGATGATTTTCCTTTTACTTTTCCTAGAAG
Found at i:62133669 original size:14 final size:15
Alignment explanation
Indices: 62133643--62133671 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62133633 TTTAATGTTT
62133643 TATATTATAGTATGA
1 TATATTATAGTATGA
62133658 TATATT-TAGTATGA
1 TATATTATAGTATGA
62133672 GTTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
TATATTATAGTATGA
Found at i:62135011 original size:11 final size:11
Alignment explanation
Indices: 62134995--62135020 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62134985 ATTTTTTTAA
62134995 TTTTAAAATAT
1 TTTTAAAATAT
62135006 TTTTAAAATAT
1 TTTTAAAATAT
62135017 TTTT
1 TTTT
62135021 TTATTTTTTT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:62139484 original size:234 final size:233
Alignment explanation
Indices: 62139066--62139809 Score: 1127
Period size: 234 Copynumber: 3.1 Consensus size: 233
62139056 TTTAGGACAA
* * *
62139066 ATCCAGGTTCGGAGTCTCGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
** *
62139131 AAATATGTGACATGATGCAGAGTTTTGAAGGACAAATCCGGGTTGCGAGTTCAGATTCCGTTCTC
66 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCC-TTCTC
* * *
62139196 GATACATATGTTCATGCTTTGCTTATCTTAAAATGTCTTCTGTTGTCGTTCTCAATACATATGTT
130 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTT
62139261 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
195 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
62139300 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
62139365 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCCATTCTC
66 AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCC-TTCTC
*
62139430 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCATTCTCAATGCATATGTT
130 GATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTT
62139495 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
195 CGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
*
62139534 ATCCGGGTTCGGAGTTTAGATACCGTTCTTGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
1 ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
62139599 AAATATCGAGTCTTTTTTTTTGACATGATGC--AGTTTCAAAGGACAAATCCAGGTTGCGAGTTC
66 AAATAT---G----------TGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTC
* * *
62139662 AGATT--TTCTCGATCCATATGTTCATTTGATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCG
118 AGATTCCTTCTCGATACATA---T--TTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCG
* * *
62139725 TTCTCGATGCATATGTTCGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGACGA
178 TTCTCAATGCATATGTTCGTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
62139781 ATCCGGGTTCGGAGTTTAGATACCGTTCT
1 ATCCGGGTTCGGAGTTTAGATACCGTTCT
62139810 TGATACATAT
Statistics
Matches: 473, Mismatches: 19, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
234 293 0.62
237 1 0.00
242 12 0.03
245 38 0.08
247 129 0.27
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (233 bp):
ATCCGGGTTCGGAGTTTAGATACCGTTCTCGATGCCTATGTTTGTTCCTTGTTTCTCCTATGTTA
AAATATGTGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCCTTCTCG
ATACATATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCGTTCTCAATGCATATGTTC
GTTCCTTGTTTCTCCTATGTTAAAATATTGAAGGATGG
Found at i:62139843 original size:247 final size:244
Alignment explanation
Indices: 62139372--62139848 Score: 710
Period size: 247 Copynumber: 1.9 Consensus size: 244
62139362 TTAAAATATG
62139372 TGACATGATGCAGAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCCATTCTCGATACAT
1 TGACATGATGCA-AGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATT-C-TTCTCGATACAT
*
62139437 ATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTGTTGTCATTCTCAATGCATATGTTCGTTCCT
63 ATTTTCATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCATTCTCAATGCATATGTTCGTTCCT
* *
62139502 TGTTTCTCCTATGTTAAAATATTGAAGGATGGATCCGGGTTCGGAGTTTAGATACCGTTCTTGAT
128 TGTTTCTCCTATGTTAAAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGATACCGTTCTTGAT
* * * ** *
62139567 GCCTATGTTTGTTCCTTGTTTCTCCTATGTTAAAATATCGAGTCTTTTTTTT
193 ACATATCTTCATTCCATGTTTCTCCTATGTTAAAATATCGAGTCTTTTTTTT
*
62139619 TGACATGATGC-AGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATT-TTCTCGATCCATATG
1 TGACATGATGCAAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCTTCTCGATACATA--
* * *
62139682 TTCATTTGATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCGTTCTCGATGCATATGTTCGTTC
64 -T--TTTCATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCATTCTCAATGCATATGTTCGTTC
62139747 CTTGTTTCTCCTATGTTAAAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGATACCGTTCTTG
126 CTTGTTTCTCCTATGTTAAAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGATACCGTTCTTG
*
62139812 ATACATATCTTCATAT-GATGTTT-TGCCTATGTTAAAA
191 ATACATATCTTCAT-TCCATGTTTCT-CCTATGTTAAAA
62139849 GATTTTATGT
Statistics
Matches: 209, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
242 12 0.06
245 38 0.18
246 1 0.00
247 157 0.75
248 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (244 bp):
TGACATGATGCAAGTTTCAAAGGACAAATCCAGGTTGCGAGTTCAGATTCTTCTCGATACATATT
TTCATGCTTTGCTTATCTTAAAATGTCTTGTATTGTCATTCTCAATGCATATGTTCGTTCCTTGT
TTCTCCTATGTTAAAATATTGAAGGACGAATCCGGGTTCGGAGTTTAGATACCGTTCTTGATACA
TATCTTCATTCCATGTTTCTCCTATGTTAAAATATCGAGTCTTTTTTTT
Found at i:62142683 original size:13 final size:13
Alignment explanation
Indices: 62142665--62142690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62142655 TTCAAGCTTT
62142665 TTTTTAATTAATA
1 TTTTTAATTAATA
62142678 TTTTTAATTAATA
1 TTTTTAATTAATA
62142691 AATATATTGA
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:62142789 original size:16 final size:16
Alignment explanation
Indices: 62142742--62142792 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
62142732 TTTTTAATTA
62142742 ATAAATATT-TTATTT
1 ATAAATATTATTATTT
*
62142757 ATTAAATTAAATAATTATTT
1 A-TAAA-T--ATTATTATTT
62142777 ATAAATATTATTATTT
1 ATAAATATTATTATTT
62142793 TTAGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 1 0.03
18 1 0.03
19 6 0.21
20 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAAATATTATTATTT
Found at i:62142806 original size:35 final size:34
Alignment explanation
Indices: 62142742--62142813 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
62142732 TTTTTAATTA
*
62142742 ATAAATATTTTATTTATTAAATTAAATAATTATTT
1 ATAAATATTTTATTTATTAAATAAAATAATT-TTT
*
62142777 ATAAATATTATTATTT-TT-AGTAAATATAATTTTT
1 ATAAATATT-TTATTTATTAAATAAA-ATAATTTTT
62142811 ATA
1 ATA
62142814 TGTGTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 10 0.30
35 17 0.52
36 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
ATAAATATTTTATTTATTAAATAAAATAATTTTT
Found at i:62144214 original size:20 final size:22
Alignment explanation
Indices: 62144189--62144247 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
62144179 ATTTAATATT
62144189 TTTGTAACTG-TAAAA-AACGG
1 TTTGTAACTGCTAAAATAACGG
* *
62144209 TTTGTAACTGTTGAAAATAATGG
1 TTTGTAACTGCT-AAAATAACGG
62144232 TTTGTAACTGCTAAAA
1 TTTGTAACTGCTAAAA
62144248 CAAATTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.29
21 1 0.03
22 8 0.24
23 15 0.44
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (22 bp):
TTTGTAACTGCTAAAATAACGG
Found at i:62145551 original size:39 final size:39
Alignment explanation
Indices: 62145305--62145550 Score: 278
Period size: 39 Copynumber: 6.3 Consensus size: 39
62145295 AGAAAATCTT
* * *
62145305 ATTCAGTATAATCAGTAGATAATGCTCGTTTGTGTAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* *
62145344 ATTCAGTATAATCAGTGGATAATGTTCGTTTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
62145383 ATTCGGTATAATCAGTGAATATTGCTCTTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * *
62145422 ATTCAGTATAATCAATGAATAATGCTCGTTTGAACAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * * *
62145461 ATTTAGTATGATTAATGGATATTGCTCGTTTGAGCAAGC
1 ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
* * * *
62145500 AATT-AATATAATTAGTGGATAATGCTCGTATGAGCAAAC
1 -ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
*
62145539 ATTTAGTATAAT
1 ATTCAGTATAAT
62145551 TGGTATTCCA
Statistics
Matches: 176, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
38 3 0.02
39 170 0.97
40 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (39 bp):
ATTCAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGC
Found at i:62150249 original size:66 final size:66
Alignment explanation
Indices: 62150143--62150273 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
62150133 CAAAAGGTTT
* *
62150143 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
62150208 G
66 G
* *
62150209 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATCTAATTTGAACTCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
62150274 CACATTTGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (66 bp):
TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
G
Found at i:62150541 original size:16 final size:16
Alignment explanation
Indices: 62150514--62150547 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
62150504 ATTTTAGTAA
62150514 ATTATATAAGAATATTT
1 ATTATATAAGAAT-TTT
62150531 ATTAT-TAAGAATTTT
1 ATTATATAAGAATTTT
62150546 AT
1 AT
62150548 GAAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTATATAAGAATTTT
Found at i:62150576 original size:47 final size:47
Alignment explanation
Indices: 62150525--62150669 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
62150515 TTATATAAGA
*
62150525 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
62150572 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * *
62150616 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
62150663 ATATTTA
1 ATATTTA
62150670 ATTAAAATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 32 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:62150636 original size:44 final size:43
Alignment explanation
Indices: 62150511--62150637 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 43
62150501 ATGATTTTAG
62150511 TAAATTATATAAGAATATTTATTATTAAGAATTTTATGAAATTATA
1 TAAATTATATAAGAATATTTATTATTAAGAA-TTT-T-AAATTATA
* * **
62150557 TATCATTAT-TAA-ATTATATTTAATATTAATTATTTTAAATTATA
1 TA-AATTATATAAGA--ATATTTATTATTAAGAATTTTAAATTATA
* *
62150601 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
1 TAAATT-ATATAAGAATATTTATTATTAAGAATTTTA
62150638 TGAAATTATA
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
45 5 0.08
46 9 0.14
47 19 0.29
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (43 bp):
TAAATTATATAAGAATATTTATTATTAAGAATTTTAAATTATA
Found at i:62150817 original size:57 final size:57
Alignment explanation
Indices: 62150755--62150937 Score: 179
Period size: 59 Copynumber: 3.1 Consensus size: 57
62150745 AATAATTATG
62150755 TTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATA
1 TTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATA
* * * * * * ** * * ** *
62150812 TTAATTATTAAGAATTTTATTA-AATTATATATTTTAATTAAAATATATTTAATAATAATTATG
1 TTAA-T-TT-A-TATTTTA-CAGTATCATATATTATGATTTCAGTA-AATTAAT-ATAAGAATA
62150875 TTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATA
1 TTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATA
62150932 TTAATT
1 TTAATT
62150938 ATTAAGAATT
Statistics
Matches: 92, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
57 16 0.17
58 8 0.09
59 24 0.26
60 2 0.02
61 24 0.26
62 8 0.09
63 10 0.11
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (57 bp):
TTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATA
Found at i:62150842 original size:120 final size:117
Alignment explanation
Indices: 62150718--62150996 Score: 468
Period size: 120 Copynumber: 2.3 Consensus size: 117
62150708 TTTATGCAGA
62150718 ATATAATTTTCAAGTTATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
1 ATAT-ATTTT-AA-TTATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
62150783 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
63 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
62150838 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
1 ATATATTTTAATT---ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATAT
62150903 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
63 TATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
*
62150958 ATATATTTTAATAAAAATATATTTAATAATAATTATGTT
1 ATATATTTTAAT---TATATATTTAATAATAATTATGTT
62150997 TAAATATGAT
Statistics
Matches: 152, Mismatches: 1, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
117 2 0.01
118 2 0.01
119 5 0.03
120 143 0.94
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (117 bp):
ATATATTTTAATTATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTAT
GATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:62150853 original size:18 final size:17
Alignment explanation
Indices: 62150825--62150859 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62150815 ATTATTAAGA
*
62150825 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62150842 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62150860 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:62150979 original size:16 final size:16
Alignment explanation
Indices: 62150958--62150999 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
62150948 TTATTAAATT
62150958 ATATATTTTAATAAAA
1 ATATATTTTAATAAAA
*
62150974 ATATA-TTTAATAATA
1 ATATATTTTAATAAAA
62150989 AT-TATGTTTAA
1 ATATAT-TTTAA
62151000 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATTTTAATAAAA
Found at i:62151209 original size:44 final size:45
Alignment explanation
Indices: 62151144--62151234 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
62151134 ACCTCTATTC
* * *
62151144 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
62151188 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
62151233 CA
1 CA
62151235 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:62151236 original size:16 final size:16
Alignment explanation
Indices: 62151215--62151283 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
62151205 GATTAGCTAT
62151215 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62151231 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
62151248 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
62151264 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
62151280 TACA
1 TACA
62151284 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:62151257 original size:33 final size:32
Alignment explanation
Indices: 62151215--62151283 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
62151205 GATTAGCTAT
62151215 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
62151248 TACACCTCTAATCCAATACATCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
62151280 TACA
1 TACA
62151284 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:62152014 original size:26 final size:26
Alignment explanation
Indices: 62151965--62152022 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
62151955 ATATACTTAC
* * *
62151965 ACTTTATTTTATTGTTTTCTATAGGA
1 ACTTTATTTTATTCTTTACAATAGGA
*
62151991 ACTTTCTTTTATTCTTTACAATAGG-
1 ACTTTATTTTATTCTTTACAATAGGA
62152016 -CTTTATT
1 ACTTTATT
62152023 AATGAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 6 0.22
26 21 0.78
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (26 bp):
ACTTTATTTTATTCTTTACAATAGGA
Found at i:62153656 original size:19 final size:20
Alignment explanation
Indices: 62153620--62153658 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
62153610 ACCCAACAAG
* *
62153620 AAAATCAATTTTATTATTTA
1 AAAATCAATATTACTATTTA
62153640 AAAATC-ATATTACTATTTA
1 AAAATCAATATTACTATTTA
62153659 CATATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCAATATTACTATTTA
Found at i:62161425 original size:12 final size:12
Alignment explanation
Indices: 62161408--62161438 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
62161398 GATCAATTGA
62161408 CTTGTTCTTCAT
1 CTTGTTCTTCAT
62161420 CTTGTTCTTCAT
1 CTTGTTCTTCAT
62161432 CTTGTTC
1 CTTGTTC
62161439 ATGTTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.58
Consensus pattern (12 bp):
CTTGTTCTTCAT
Found at i:62163694 original size:12 final size:13
Alignment explanation
Indices: 62163677--62163705 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
62163667 GAAGTTTTTG
62163677 TATACCC-AAAAT
1 TATACCCAAAAAT
62163689 TATACCCAAAAAT
1 TATACCCAAAAAT
62163702 TATA
1 TATA
62163706 ACAAAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (13 bp):
TATACCCAAAAAT
Found at i:62164175 original size:17 final size:18
Alignment explanation
Indices: 62164147--62164188 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
62164137 TAATCAAATG
* *
62164147 ATATAAAAAAAAATCTTA
1 ATATGAAAAAAATTCTTA
62164165 ATATGAAAAAAATTCTTA
1 ATATGAAAAAAATTCTTA
*
62164183 GTATGA
1 ATATGA
62164189 TTCAAATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (18 bp):
ATATGAAAAAAATTCTTA
Found at i:62170682 original size:29 final size:30
Alignment explanation
Indices: 62170648--62170717 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
62170638 TTATAGTGAC
* * *
62170648 TGGATCAAATTAGTTCTTCTATTATT-AAA
1 TGGATCAAATTAGTCCTTATACTATTCAAA
*
62170677 TGGATCAATTTAGTCCTTATACTATTCAAA
1 TGGATCAAATTAGTCCTTATACTATTCAAA
* *
62170707 AGAATCAAATT
1 TGGATCAAATT
62170718 CATCCAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (30 bp):
TGGATCAAATTAGTCCTTATACTATTCAAA
Found at i:62174910 original size:28 final size:26
Alignment explanation
Indices: 62174865--62174928 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
62174855 TAAGATAATT
62174865 ATATATAAAATTTTAATAAATAAAA-A
1 ATATATAAAATTTTAAT-AATAAAATA
*
62174891 ATATATAAAATTATTAAATATTAAAATA
1 ATATATAAAATT-TT-AATAATAAAATA
62174919 ATAATATAAA
1 AT-ATATAAA
62174929 TATATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 12 0.36
27 8 0.24
28 6 0.18
29 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATAAAATTTTAATAATAAAATA
Found at i:62174929 original size:28 final size:28
Alignment explanation
Indices: 62174849--62174928 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
62174839 AAACATTAAA
*
62174849 AAATATTAAGATAATTATATATAAAATTTT
1 AAATATTAAAATAA-TA-ATATAAAATTTT
*
62174879 -AATAAATAAAA-AAT-ATATAAAATTATT
1 AAAT-ATTAAAATAATAATATAAAATT-TT
62174906 AAATATTAAAATAATAATATAAA
1 AAATATTAAAATAATAATATAAA
62174929 TATATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
26 10 0.24
27 8 0.19
28 7 0.17
29 12 0.29
30 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAATATTAAAATAATAATATAAAATTTT
Found at i:62178512 original size:24 final size:23
Alignment explanation
Indices: 62178484--62178531 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
62178474 TTTATCTATG
62178484 ATTTTATATGTATTTTT-TTATAAA
1 ATTTT-TATGTATTTTTATTA-AAA
62178508 A-TTTTATGTATTTTTATTAAAA
1 ATTTTTATGTATTTTTATTAAAA
62178530 AT
1 AT
62178532 GAACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 15 0.68
23 6 0.27
24 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTTTTATGTATTTTTATTAAAA
Found at i:62178515 original size:22 final size:22
Alignment explanation
Indices: 62178490--62178531 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
62178480 TATGATTTTA
62178490 TATGTATTTTT-TTATAAAATTT
1 TATGTATTTTTATTA-AAAATTT
62178512 TATGTATTTTTATTAAAAAT
1 TATGTATTTTTATTAAAAAT
62178532 GAACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TATGTATTTTTATTAAAAATTT
Found at i:62178955 original size:21 final size:22
Alignment explanation
Indices: 62178931--62178978 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
62178921 GAAAATGTGC
*
62178931 AATTTAAACCCTTTA-AAAAAT
1 AATTTAAAACCTTTATAAAAAT
* **
62178952 AATTCAAAATGTTTATAAAAAT
1 AATTTAAAACCTTTATAAAAAT
62178974 AATTT
1 AATTT
62178979 TCCAAAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTTAAAACCTTTATAAAAAT
Found at i:62179563 original size:25 final size:25
Alignment explanation
Indices: 62179535--62179598 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
62179525 AGTATTTGTT
62179535 AACTTATAATCTTTAGACATTTGCC
1 AACTTATAATCTTTAGACATTTGCC
62179560 AACTTATAATCTTTAGACATTTGCC
1 AACTTATAATCTTTAGACATTTGCC
62179585 AACTTATAATCTTT
1 AACTTATAATCTTT
62179599 TTTGTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (25 bp):
AACTTATAATCTTTAGACATTTGCC
Found at i:62181919 original size:26 final size:26
Alignment explanation
Indices: 62181883--62181934 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
62181873 GAGCAGTTCT
62181883 AAGTATTGTATAAAAAATATTAACAA
1 AAGTATTGTATAAAAAATATTAACAA
62181909 AAGTATTGTATAAAAAATATTAACAA
1 AAGTATTGTATAAAAAATATTAACAA
62181935 TTAACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.31
Consensus pattern (26 bp):
AAGTATTGTATAAAAAATATTAACAA
Found at i:62183443 original size:20 final size:21
Alignment explanation
Indices: 62183418--62183469 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
62183408 GATATTTTTT
62183418 AATATATAAAAAA-ACA-ATAA
1 AATATATAAAAAAGACAGA-AA
*
62183438 AATATAAAGAAAAAGACAGAAA
1 AATATATA-AAAAAGACAGAAA
62183460 AATA-ATAAAA
1 AATATATAAAA
62183470 TATAAATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 10 0.37
21 7 0.26
22 9 0.33
23 1 0.04
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (21 bp):
AATATATAAAAAAGACAGAAA
Found at i:62184053 original size:19 final size:19
Alignment explanation
Indices: 62184029--62184091 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
62184019 TATTAGAAAC
*
62184029 CAAGGAACAACACATAAGA
1 CAAGGAACAACAAATAAGA
* * *
62184048 CAAGG-AC-A-TATTAGAAA
1 CAAGGAACAACAAATA-AGA
62184065 CCAAGGAACAACAAATAAGA
1 C-AAGGAACAACAAATAAGA
62184085 CAAGGAA
1 CAAGGAA
62184092 GAGAGGAGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 6 0.19
19 13 0.41
20 4 0.12
21 3 0.09
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.08
Consensus pattern (19 bp):
CAAGGAACAACAAATAAGA
Found at i:62184066 original size:37 final size:37
Alignment explanation
Indices: 62184016--62184090 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
62184006 CAACACAAAC
*
62184016 ACATATTAGAAACCAAGGAACAACACATAAGACAAGG
1 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
62184053 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
1 ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
62184090 A
1 A
62184091 AGAGAGGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.56, C:0.17, G:0.16, T:0.11
Consensus pattern (37 bp):
ACATATTAGAAACCAAGGAACAACAAATAAGACAAGG
Found at i:62188494 original size:27 final size:27
Alignment explanation
Indices: 62188456--62188507 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
62188446 AGCTAGTTAG
62188456 GCCATGGTACCACCAGTTTGATGCAAT
1 GCCATGGTACCACCAGTTTGATGCAAT
62188483 GCCATGGTACCACCAGTTTGATGCA
1 GCCATGGTACCACCAGTTTGATGCA
62188508 GCATTGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (27 bp):
GCCATGGTACCACCAGTTTGATGCAAT
Found at i:62189411 original size:25 final size:25
Alignment explanation
Indices: 62189356--62189413 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
62189346 TCAAGTAAAA
**
62189356 TAAAAAAATATAATAATTAAATTTT
1 TAAAAAAATATAATAATTAAATGAT
* *
62189381 TCAAAAAATATAATAATT-GATAGAT
1 TAAAAAAATATAATAATTAAAT-GAT
62189406 TAAAAAAA
1 TAAAAAAA
62189414 CATTCAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (25 bp):
TAAAAAAATATAATAATTAAATGAT
Found at i:62190540 original size:8 final size:7
Alignment explanation
Indices: 62190529--62190582 Score: 51
Period size: 8 Copynumber: 7.7 Consensus size: 7
62190519 TAAATAAAAA
62190529 TAAAATTC
1 TAAAA-TC
62190537 TAAAA-C
1 TAAAATC
62190543 TAAAA-C
1 TAAAATC
62190549 TAAAA-C
1 TAAAATC
*
62190555 TAAAGTC
1 TAAAATC
62190562 TAAAAGTC
1 TAAAA-TC
62190570 TAAAAGTC
1 TAAAA-TC
62190578 TAAAA
1 TAAAA
62190583 ATAATTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 17 0.40
7 5 0.12
8 20 0.48
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (7 bp):
TAAAATC
Found at i:62190620 original size:9 final size:9
Alignment explanation
Indices: 62190606--62190681 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
62190596 GTAGTGATTC
62190606 AATTCGGTT
1 AATTCGGTT
**
62190615 AATTCGGGC
1 AATTCGGTT
62190624 AATTCGGTT
1 AATTCGGTT
*
62190633 AATTCGGGT
1 AATTCGGTT
*
62190642 AATCCGGTT
1 AATTCGGTT
*
62190651 AATTCGGGT
1 AATTCGGTT
*
62190660 AATTTGGTT
1 AATTCGGTT
*
62190669 AATTCAGTT
1 AATTCGGTT
62190678 AATT
1 AATT
62190682 TTTAACCAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:62190682 original size:18 final size:18
Alignment explanation
Indices: 62190606--62190673 Score: 109
Period size: 18 Copynumber: 3.8 Consensus size: 18
62190596 GTAGTGATTC
*
62190606 AATTCGGTTAATTCGGGC
1 AATTCGGTTAATTCGGGT
62190624 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
62190642 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
62190660 AATTTGGTTAATTC
1 AATTCGGTTAATTC
62190674 AGTTAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:62197815 original size:13 final size:13
Alignment explanation
Indices: 62197797--62197826 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
62197787 TTAAGATTGG
*
62197797 ATTAAAATTTAAA
1 ATTAAAAATTAAA
62197810 ATTAAAAATTAAA
1 ATTAAAAATTAAA
62197823 ATTA
1 ATTA
62197827 TAAGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAAAATTAAA
Found at i:62202530 original size:17 final size:16
Alignment explanation
Indices: 62202504--62202535 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
62202494 GACAAACTTC
62202504 AAATTCATTTTTTAAT
1 AAATTCATTTTTTAAT
62202520 AAATGTCATTTTTTAA
1 AAAT-TCATTTTTTAA
62202536 AATATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
AAATTCATTTTTTAAT
Found at i:62204165 original size:23 final size:23
Alignment explanation
Indices: 62204139--62204202 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
62204129 AATGGAACAA
*
62204139 TAAACAAGCTTTGAATGAAT-TAT
1 TAAACAAGCTTTAAATG-ATCTAT
*
62204162 TAAACGAGCTTTAAATGATCTAT
1 TAAACAAGCTTTAAATGATCTAT
*
62204185 TAAACGAG-TTTCAAATGA
1 TAAACAAGCTTT-AAATGA
62204203 ACATAAACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (23 bp):
TAAACAAGCTTTAAATGATCTAT
Found at i:62206535 original size:15 final size:15
Alignment explanation
Indices: 62206487--62206540 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
62206477 TATATTATTC
62206487 ATATAAAATAATCAA
1 ATATAAAATAATCAA
* ** *
62206502 ATATATAATTTTTTTAA
1 ATATA-AA-ATAATCAA
62206519 ATATAAAATAATCAA
1 ATATAAAATAATCAA
62206534 ATATAAA
1 ATATAAA
62206541 TATTAATAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 16 0.55
16 4 0.14
17 9 0.31
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAAAATAATCAA
Found at i:62206643 original size:23 final size:23
Alignment explanation
Indices: 62206617--62206678 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
62206607 AATGGAACAA
* * *
62206617 TAAACAAGCTTTGAATGATTTAT
1 TAAACAAGCTTTAAATAATCTAT
*
62206640 TAAACGAGCTTTAAATAATCTAT
1 TAAACAAGCTTTAAATAATCTAT
62206663 TAAACAAG-TTTCAAAT
1 TAAACAAGCTTT-AAAT
62206679 GAACATAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (23 bp):
TAAACAAGCTTTAAATAATCTAT
Found at i:62207329 original size:5 final size:5
Alignment explanation
Indices: 62207319--62207358 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
62207309 TTCTTCGTGT
*
62207319 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
62207359 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:62207343 original size:19 final size:19
Alignment explanation
Indices: 62207319--62207355 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
62207309 TTCTTCGTGT
*
62207319 TTTTATTTTATTTTATTTA
1 TTTTATCTTATTTTATTTA
62207338 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
62207356 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTA
Found at i:62208244 original size:26 final size:25
Alignment explanation
Indices: 62208221--62208293 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
62208211 GGGAAGAAGG
*
62208221 AGAAGAAGAAAGAAAAAAATAGAAAA
1 AGAA-AAGAAAAAAAAAAATAGAAAA
*
62208247 AGAAAAGAAAAAAAAAAA-GGAAAA
1 AGAAAAGAAAAAAAAAAATAGAAAA
*
62208271 A-AAATA-AAAATAAAAAATTAGAA
1 AGAAA-AGAAAA-AAAAAAATAGAA
62208294 CAGTCGGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 7 0.17
24 13 0.32
25 16 0.40
26 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (25 bp):
AGAAAAGAAAAAAAAAAATAGAAAA
Found at i:62208249 original size:20 final size:21
Alignment explanation
Indices: 62208221--62208260 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62208211 GGGAAGAAGG
*
62208221 AGAAGAAG-AAAGAAAAAAAT
1 AGAAAAAGAAAAGAAAAAAAT
62208241 AGAAAAAGAAAAGAAAAAAA
1 AGAAAAAGAAAAGAAAAAAA
62208261 AAAAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (21 bp):
AGAAAAAGAAAAGAAAAAAAT
Found at i:62208274 original size:13 final size:12
Alignment explanation
Indices: 62208226--62208287 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
62208216 GAAGGAGAAG
62208226 AAGAAAGAAAAAA
1 AAGAAA-AAAAAA
*
62208239 ATAG-AAAAAGAA
1 A-AGAAAAAAAAA
62208251 AAGAAAAAAAAA
1 AAGAAAAAAAAA
62208263 AAGGAAAAAAAATA
1 AA-GAAAAAAAA-A
*
62208277 AA-AATAAAAAA
1 AAGAAAAAAAAA
62208288 TTAGAACAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 3 0.07
12 22 0.52
13 12 0.29
14 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:62208826 original size:4 final size:4
Alignment explanation
Indices: 62208817--62208843 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
62208807 TGCGTGTTTA
62208817 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
62208844 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:62208992 original size:20 final size:20
Alignment explanation
Indices: 62208967--62209004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62208957 AAAAATATTC
*
62208967 AAAAATCCTCGTATTTTAAT
1 AAAAATCATCGTATTTTAAT
*
62208987 AAAAATCATCGTGTTTTA
1 AAAAATCATCGTATTTTA
62209005 TTAGAATCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAAATCATCGTATTTTAAT
Done.