Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 15 of 333
Found at i:4359787 original size:35 final size:35
Alignment explanation
Indices: 4359741--4359812 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4359731 AAGTTTGGTG
4359741 CATAATTGCACAATCTTACCCGCATAAAATCATCC
1 CATAATTGCACAATCTTACCCGCATAAAATCATCC
4359776 CATAATTGCACAATCTTACCCGCATAAAATCATCC
1 CATAATTGCACAATCTTACCCGCATAAAATCATCC
4359811 CA
1 CA
4359813 AACACATACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.25
Consensus pattern (35 bp):
CATAATTGCACAATCTTACCCGCATAAAATCATCC
Found at i:4361385 original size:52 final size:52
Alignment explanation
Indices: 4361323--4361479 Score: 296
Period size: 52 Copynumber: 3.0 Consensus size: 52
4361313 GTTGTTACAT
4361323 AGTTGCTTTGGCTTTCCTCTGTTGTTACGATCAATCACCTTTGCCATACGAA
1 AGTTGCTTTGGCTTTCCTCTGTTGTTACGATCAATCACCTTTGCCATACGAA
*
4361375 AGTTGCTTTGGCTTTCCTTTGTTGTTACGATCAATCACCTTTGCCATACGAA
1 AGTTGCTTTGGCTTTCCTCTGTTGTTACGATCAATCACCTTTGCCATACGAA
*
4361427 AGTTGCTTTGGCTTTCCTCTGTTGTTATGATCAATCACCTTTGCCATACGAA
1 AGTTGCTTTGGCTTTCCTCTGTTGTTACGATCAATCACCTTTGCCATACGAA
4361479 A
1 A
4361480 TAGGAGGTTC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (52 bp):
AGTTGCTTTGGCTTTCCTCTGTTGTTACGATCAATCACCTTTGCCATACGAA
Found at i:4374742 original size:22 final size:22
Alignment explanation
Indices: 4374709--4374764 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
4374699 TAATTTGAAC
* *
4374709 TATAATGATAATTCTAAACAATT
1 TATAATAATAATTCTAAA-AATA
4374732 TATAA-AATAATTCTAAAAATA
1 TATAATAATAATTCTAAAAATA
4374753 TATAATAATAAT
1 TATAATAATAAT
4374765 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 8 0.27
22 17 0.57
23 5 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
TATAATAATAATTCTAAAAATA
Found at i:4377001 original size:15 final size:15
Alignment explanation
Indices: 4376981--4377010 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4376971 TTCGATTTCC
*
4376981 TTTTTATTTTTTATT
1 TTTTTATGTTTTATT
4376996 TTTTTATGTTTTATT
1 TTTTTATGTTTTATT
4377011 ATAAATCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTATGTTTTATT
Found at i:4377973 original size:24 final size:26
Alignment explanation
Indices: 4377946--4378008 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
4377936 AAACTTTCAC
*
4377946 ATATTATTTATTTCAAA-TA-TATAT
1 ATATTATTTATTTAAAACTATTATAT
* *
4377970 ATATTATTTGTTTAAAACTATTTTAT
1 ATATTATTTATTTAAAACTATTATAT
*
4377996 ATATTATCTATTT
1 ATATTATTTATTT
4378009 TAGATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 15 0.47
25 2 0.06
26 15 0.47
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (26 bp):
ATATTATTTATTTAAAACTATTATAT
Found at i:4381292 original size:51 final size:51
Alignment explanation
Indices: 4381229--4381336 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
4381219 TTGGAAAATG
* * * * *
4381229 GGTGTCATGACACTGAGGGTAGAATACTCCAATGTCATGATACTAACTTTT
1 GGTGTCACGACACTGAGAGTAGAATACTCCAATGTCACGACACTAACTTGT
*
4381280 GGTGTCACGACACTGAGAGTAGAATACTCCAATGTCGCGACACTAACTTGT
1 GGTGTCACGACACTGAGAGTAGAATACTCCAATGTCACGACACTAACTTGT
4381331 GGTGTC
1 GGTGTC
4381337 GTGACAACAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (51 bp):
GGTGTCACGACACTGAGAGTAGAATACTCCAATGTCACGACACTAACTTGT
Found at i:4384054 original size:21 final size:21
Alignment explanation
Indices: 4384028--4384070 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4384018 ACCATATTTA
4384028 TCTTAAAATGTTGAATTCACT
1 TCTTAAAATGTTGAATTCACT
*
4384049 TCTTAAAATTTTGAATTCACT
1 TCTTAAAATGTTGAATTCACT
4384070 T
1 T
4384071 TTTAGGACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (21 bp):
TCTTAAAATGTTGAATTCACT
Found at i:4387509 original size:6 final size:6
Alignment explanation
Indices: 4387498--4387522 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4387488 GGCTAGGAAG
4387498 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
4387523 GGGGAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:4390644 original size:54 final size:54
Alignment explanation
Indices: 4390557--4390659 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
4390547 ATTGCATAAA
*
4390557 ATGATAAATTTAAGGGTTAATGTATAAGGGCCAAATTATGATTGTTTTTATATT
1 ATGAAAAATTTAAGGGTTAATGTATAAGGGCCAAATTATGATTGTTTTTATATT
4390611 ATGAAAAATTTAAGGGTTAATGTATAAGGGCCAAATTATGATTGTTTTT
1 ATGAAAAATTTAAGGGTTAATGTATAAGGGCCAAATTATGATTGTTTTT
4390660 TGCAATTTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (54 bp):
ATGAAAAATTTAAGGGTTAATGTATAAGGGCCAAATTATGATTGTTTTTATATT
Found at i:4401180 original size:13 final size:13
Alignment explanation
Indices: 4401162--4401187 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4401152 GCTCGGCAGG
4401162 GACACGCCCGTGT
1 GACACGCCCGTGT
4401175 GACACGCCCGTGT
1 GACACGCCCGTGT
4401188 TCGATTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:4403985 original size:29 final size:29
Alignment explanation
Indices: 4403951--4404016 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
4403941 TGGAAAAAGG
*
4403951 AAGTCCACTGAGGATTGGCCCCATCATGA
1 AAGTCCACTAAGGATTGGCCCCATCATGA
* * *
4403980 AAGTCCGCTAAGGATTGGCCCGATCATGG
1 AAGTCCACTAAGGATTGGCCCCATCATGA
4404009 AAGTCCAC
1 AAGTCCAC
4404017 CAGGAAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (29 bp):
AAGTCCACTAAGGATTGGCCCCATCATGA
Found at i:4407058 original size:30 final size:30
Alignment explanation
Indices: 4407022--4407083 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
4407012 AAATTTACCA
4407022 TAGTATCATAATTCATTTCATCACAAAACT
1 TAGTATCATAATTCATTTCATCACAAAACT
4407052 TAGTATCATAATTCATTTCATCACAAAACT
1 TAGTATCATAATTCATTTCATCACAAAACT
4407082 TA
1 TA
4407084 CCCTATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.37
Consensus pattern (30 bp):
TAGTATCATAATTCATTTCATCACAAAACT
Found at i:4410829 original size:16 final size:16
Alignment explanation
Indices: 4410808--4410838 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4410798 GTAAGTTGTG
4410808 AACTTTGAGCAGTTAA
1 AACTTTGAGCAGTTAA
*
4410824 AACTTTGATCAGTTA
1 AACTTTGAGCAGTTA
4410839 CAAGCACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (16 bp):
AACTTTGAGCAGTTAA
Found at i:4412772 original size:3 final size:3
Alignment explanation
Indices: 4412764--4412790 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4412754 TTTAAAGTTG
4412764 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
4412791 TTGTGTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:4418014 original size:3 final size:3
Alignment explanation
Indices: 4418006--4418071 Score: 98
Period size: 3 Copynumber: 21.7 Consensus size: 3
4417996 AAAATTCTTC
*
4418006 ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4418054 ATT ATGT CATT ATT -TT AT
1 ATT AT-T -ATT ATT ATT AT
4418072 GTTAGTTACT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.90
4 2 0.03
5 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4418886 original size:23 final size:21
Alignment explanation
Indices: 4418845--4418888 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
4418835 TGGTTTCGAC
4418845 AAATAATTATATAAACAAATA
1 AAATAATTATATAAACAAATA
*
4418866 AAATAAATTAATATAAGCAAATA
1 AAAT-AATT-ATATAAACAAATA
4418889 TTTATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 12 0.60
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATTATATAAACAAATA
Found at i:4422701 original size:23 final size:19
Alignment explanation
Indices: 4422652--4422688 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4422642 TCCTGTTTTA
*
4422652 CCCTCTGCCTCTTCTGTTC
1 CCCTTTGCCTCTTCTGTTC
4422671 CCCTTTGCCTCTTCTGTT
1 CCCTTTGCCTCTTCTGTT
4422689 TCGCCCGATT
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:0.00, C:0.43, G:0.11, T:0.46
Consensus pattern (19 bp):
CCCTTTGCCTCTTCTGTTC
Found at i:4422730 original size:15 final size:15
Alignment explanation
Indices: 4422710--4422771 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
4422700 GCTCCCTCCA
* *
4422710 TTTCTTTTCTTTTCT
1 TTTCTTTGCTTTGCT
4422725 TTTCTTTGCTTTGCT
1 TTTCTTTGCTTTGCT
4422740 TTCTCCTTTGCTTT-C-
1 TT-T-CTTTGCTTTGCT
*
4422755 TTCCTTTGCTTTGCT
1 TTTCTTTGCTTTGCT
4422770 TT
1 TT
4422772 CTCCAGTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 19 0.47
16 2 0.05
17 9 0.22
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (15 bp):
TTTCTTTGCTTTGCT
Found at i:4422750 original size:12 final size:13
Alignment explanation
Indices: 4422733--4422766 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4422723 CTTTTCTTTG
4422733 CTTTGCTTTC-TC
1 CTTTGCTTTCTTC
4422745 CTTTGCTTTCTTC
1 CTTTGCTTTCTTC
4422758 CTTTGCTTT
1 CTTTGCTTT
4422767 GCTTTCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.29, G:0.09, T:0.62
Consensus pattern (13 bp):
CTTTGCTTTCTTC
Found at i:4425082 original size:18 final size:18
Alignment explanation
Indices: 4425036--4425083 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4425026 TATAAGAATA
*
4425036 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
4425052 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
4425069 TTAATTATAATATAT
1 TTAATTATAATATAT
4425084 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:4425088 original size:15 final size:15
Alignment explanation
Indices: 4425053--4425104 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4425043 TTAATAATTT
*
4425053 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4425067 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4425081 TATTTAATAATAAT-
1 TATTTAATTATAATA
4425095 TATGTTAATT
1 TAT-TTAATT
4425105 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4425171 original size:66 final size:65
Alignment explanation
Indices: 4425101--4425295 Score: 182
Period size: 56 Copynumber: 3.1 Consensus size: 65
4425091 TAATTATGTT
4425101 AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
1 AATTT-TATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
4425166 G
65 G
* * * * * *
4425167 AATTTTA--TTA-A--ATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATT-ATGTTA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTAATTTTA
*
4425221 AT
64 AG
* *
4425223 T--TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-TTAA
4425286 G
65 G
4425287 AATTTTATT
1 AATTTTATT
4425296 AAATTATATA
Statistics
Matches: 95, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
54 3 0.03
56 20 0.21
57 6 0.06
58 1 0.01
59 13 0.14
60 13 0.14
61 1 0.01
62 6 0.06
63 16 0.17
64 4 0.04
65 2 0.02
66 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAAG
Found at i:4425201 original size:119 final size:120
Alignment explanation
Indices: 4425019--4425339 Score: 619
Period size: 119 Copynumber: 2.7 Consensus size: 120
4425009 ATTGTTTTAT
*
4425019 TAAATT-ATATAAGAATATTAATTATTAATAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
4425083 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
4425138 TAAATTCATATAAGAATATTAATT-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
4425202 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
4425257 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
4425322 TTTAATAATAATTATGTT
66 TTTAATAATAATTATGTT
4425340 TAAATATGAT
Statistics
Matches: 199, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
119 124 0.62
120 75 0.38
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (120 bp):
TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
Found at i:4425207 original size:15 final size:15
Alignment explanation
Indices: 4425172--4425223 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4425162 TTAAGAATTT
*
4425172 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4425186 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4425200 TATTTAATAATAAT-
1 TATTTAATTATAATA
4425214 TATGTTAATT
1 TAT-TTAATT
4425224 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4425322 original size:16 final size:16
Alignment explanation
Indices: 4425301--4425342 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
4425291 TTATTAAATT
*
4425301 ATATATTTTAATTATA
1 ATATATTTTAATAATA
4425317 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
4425332 AT-TATGTTTAA
1 ATATAT-TTTAA
4425343 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:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:4425327 original size:15 final size:15
Alignment explanation
Indices: 4425292--4425333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4425282 TTAAGAATTT
*
4425292 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4425306 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4425320 TATTTAATAATAAT
1 TATTTAATTATAAT
4425334 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4425580 original size:16 final size:16
Alignment explanation
Indices: 4425559--4425626 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
4425549 GATTTGCTAT
4425559 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
4425575 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
4425591 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
4425607 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
4425623 TACA
1 TACA
4425627 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:4425982 original size:18 final size:18
Alignment explanation
Indices: 4425948--4425982 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4425938 TAGCCTATTT
4425948 TTATAAAAACCATATTAG
1 TTATAAAAACCATATTAG
4425966 TTATCAAAAACCA-ATTA
1 TTAT-AAAAACCATATTA
4425983 ATTGTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
TTATAAAAACCATATTAG
Found at i:4426487 original size:45 final size:44
Alignment explanation
Indices: 4426303--4427069 Score: 436
Period size: 45 Copynumber: 16.7 Consensus size: 44
4426293 AGCCACCAGC
* * * *
4426303 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAATTTCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACAAAT
* ** * * * *
4426348 ATTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAAT
* * * * * * ** *
4426392 ATTATCTTCCC-GAGGTAGTAGGGGAGCAGATTTAAGCCACAAGT
1 CTTATC-TCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAAT
* *
4426436 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAAT
* * * * *
4426481 CTTATCTCCCTAAAGTTGCAGTGGGGCAGATTAAAGCTACAAACCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G--A-AGA-TACAAAT
* *
4426532 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACAAAT
* * * *
4426576 CTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAAT
* *
4426621 CTTATCTCCTTGAAGTTGCAGTTGG-GCAGATTGAAGCTACAAATCACAAAC
1 CTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTGAAG------AT-ACAAAT
* * * **
4426672 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAAT
* *
4426717 CTTATCTCCCTGAAGTTGCAGTGGGGCAGATTGAAGCTACAAATCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG------AT-ACAAAT
*
4426768 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAAT
* * * * * *
4426813 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCTATAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAAT
* * * * * *
4426857 CCTATAC-CTCTAAAGTTGCAGTAGG-TC-GAATCAA-ACTACCATGGTGAAT
1 CTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGA-TA-CA-----AAT
* * ** *
4426906 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAAT
* * * *
4426950 CTTATCCCCCTGAAGTTGCAGTGGGGCA-AGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATACAAAT
* * * * * * *
4426994 CTTATCTCTCTGAAGTCGCGGTGGAGCAAACTCAAGATAATAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAAT
** *
4427039 CTTATCTCATTGAAGTTGCAATGGAGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
4427070 CAAGCTACAA
Statistics
Matches: 548, Mismatches: 128, Indels: 92
0.71 0.17 0.12
Matches are distributed among these distances:
43 13 0.02
44 182 0.33
45 205 0.37
46 4 0.01
48 5 0.01
49 21 0.04
50 10 0.02
51 106 0.19
52 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAAT
Found at i:4426648 original size:140 final size:141
Alignment explanation
Indices: 4426430--4426752 Score: 488
Period size: 140 Copynumber: 2.3 Consensus size: 141
4426420 GATTTAAGCC
4426430 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAA
*
4426495 GTTGCAGTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA
66 GTTGCAGTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCA
** *
4426560 GGTTGAA-ATT
131 GACTGAAGATA
* * * *
4426570 ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATCTTATCTCCTTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAA
* * * *
4426635 GTTGCAGTTGGGCAGATTGAAGCTACAAATCACAAACCTTATCTCTCTAAAGTTGCAGTGGAGCA
66 GTTGCAGTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCA
4426700 GACTGAAGATA
131 GACTGAAGATA
* * *
4426711 AC-GGATCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTGAAG
1 ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
4426753 CTACAAATCA
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
140 127 0.77
141 37 0.23
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (141 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAA
GTTGCAGTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCA
GACTGAAGATA
Found at i:4426704 original size:96 final size:96
Alignment explanation
Indices: 4426576--4426857 Score: 431
Period size: 96 Copynumber: 2.9 Consensus size: 96
4426566 AATTACAAGT
*
4426576 CTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATCTTATCTCCTTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCTTGAAGTTGCA
*
4426641 GTTGGGCAGATTGAAGCTACAAATCACAAAC
66 GTAGGGCAGATTGAAGCTACAAATCACAAAC
* * * *
4426672 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGGATCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCTTGAAGTTGCA
*
4426737 GTGGGGCAGATTGAAGCTACAAATCACAAAC
66 GTAGGGCAGATTGAAGCTACAAATCACAAAC
* * *
4426768 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCT-CTCTGAAGTTGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCT-TGAAGTTGC
* * *
4426832 AGTAGAGCAGATTAAAGCTATAAATC
65 AGTAGGGCAGATTGAAGCTACAAATC
4426858 CTATACCTCT
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 1 0.01
96 167 0.99
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (96 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCTTGAAGTTGCA
GTAGGGCAGATTGAAGCTACAAATCACAAAC
Found at i:4426875 original size:236 final size:236
Alignment explanation
Indices: 4426436--4426878 Score: 631
Period size: 236 Copynumber: 1.9 Consensus size: 236
4426426 AGCCACAAGT
* *
4426436 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCTTATCTCCCTAAAGTTGCA
**
4426501 GTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGA
66 GTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
* * * * * * *
4426566 AATTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATCTTATCTCCT
131 AATTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGATAGCAAATCCTATCACCT
*
4426631 TGAAGTTGCAGTTGGGCAGATTGAAGCTACAAATCACAAAC
196 TAAAGTTGCAGTTGGGCAGATTGAAGCTACAAATCACAAAC
* * *
4426672 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGGATCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCTTATCTCCCTAAAGTTGCA
* *
4426737 GTGGGGCAGATTGAAGCTACAAATCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
66 GTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
* * * * * *
4426802 AGA-TAGCAAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCTA-TAAATCCTAT-AC
131 A-ATTA-CAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGATAGCAAATCCTATCAC
4426864 CTCTAAAGTTGCAGT
194 CT-TAAAGTTGCAGT
4426879 AGGTCGAATC
Statistics
Matches: 181, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
235 3 0.02
236 142 0.78
237 36 0.20
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (236 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAACGAATCTTATCTCCCTAAAGTTGCA
GTGGGGCAGATTAAAGCTACAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
AATTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAAGATAGCAAATCCTATCACCT
TAAAGTTGCAGTTGGGCAGATTGAAGCTACAAATCACAAAC
Found at i:4430009 original size:50 final size:50
Alignment explanation
Indices: 4429890--4430138 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
4429880 GATAATAACA
* * * ** * *
4429890 TGCCAAAGCCATGTCCCAGACATGGACTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
4429941 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4429991 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
4430041 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
4430096 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4430139 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:4430067 original size:100 final size:104
Alignment explanation
Indices: 4429889--4430138 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
4429879 TGATAATAAC
* **
4429889 ATGCCAAAGCCATGTCCCAGACATGGACTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
4429954 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
4429991 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
4430054 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
4430096 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4430139 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:4430254 original size:13 final size:13
Alignment explanation
Indices: 4430233--4430264 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4430223 GCTTGGATCA
*
4430233 TCATCAAATAAAT
1 TCATAAAATAAAT
4430246 TCATAAAATAAAT
1 TCATAAAATAAAT
4430259 TCATAA
1 TCATAA
4430265 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4430511 original size:30 final size:30
Alignment explanation
Indices: 4430476--4430533 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4430466 CCTCGACTCT
*
4430476 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4430506 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4430534 AAGACTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4435281 original size:18 final size:18
Alignment explanation
Indices: 4435258--4435343 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
4435248 GAATGATTAT
* *
4435258 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
4435276 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
4435294 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
4435312 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
4435331 TTATTCAGTAACA
1 TTATTCAGTAACA
4435344 GTCGATCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
18 41 0.73
19 15 0.27
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:4435299 original size:36 final size:37
Alignment explanation
Indices: 4435258--4435346 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 37
4435248 GAATGATTAT
* *
4435258 TTATTCAGTAACAGTCAGTTATTCGGTAACAA-TCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
* * *
4435294 TTATTCAATAATAATCAGTTATTCAGTAACAATTAAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
4435331 TTATTCAGTAACAGTC
1 TTATTCAGTAACAGTC
4435347 GATCTTTCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 28 0.64
37 16 0.36
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (37 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
Found at i:4435547 original size:47 final size:46
Alignment explanation
Indices: 4435477--4435593 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 46
4435467 CAGTAACAAT
* * * *
4435477 AACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCTGG
1 AACAGTAACAGTACGGTA-ACAGAGTACCTCATCGGAACAAATCCGA
4435524 AACAGTAACAGTACGGTATACAGAGTACCTCATCGGAACAAATCCGA
1 AACAGTAACAGTACGGTA-ACAGAGTACCTCATCGGAACAAATCCGA
4435571 AACAGTAACAGTAACGGTAACAG
1 AACAGTAACAGT-ACGGTAACAG
4435594 TAACAATATC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 58 0.91
48 6 0.09
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (46 bp):
AACAGTAACAGTACGGTAACAGAGTACCTCATCGGAACAAATCCGA
Found at i:4435641 original size:12 final size:12
Alignment explanation
Indices: 4435624--4435648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4435614 AGTGCCGAAT
4435624 CGGTAACAGTAA
1 CGGTAACAGTAA
4435636 CGGTAACAGTAA
1 CGGTAACAGTAA
4435648 C
1 C
4435649 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:4435822 original size:20 final size:21
Alignment explanation
Indices: 4435774--4435822 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4435764 CACTTTTCAG
4435774 TTTTCAATTAATTCATATTTT
1 TTTTCAATTAATTCATATTTT
**
4435795 AATT-AATTAATT-ATATTTT
1 TTTTCAATTAATTCATATTTT
4435814 TTTTCAATT
1 TTTTCAATT
4435823 CAATATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTCAATTAATTCATATTTT
Found at i:4436592 original size:6 final size:6
Alignment explanation
Indices: 4436571--4436602 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4436561 ATTTATTTCA
4436571 TAATA- TAATA- TAATAT TAATAT TAATAT TAAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAAT
4436603 TAATAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:4436598 original size:12 final size:11
Alignment explanation
Indices: 4436570--4436607 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
4436560 AATTTATTTC
4436570 ATAATA-TAAT
1 ATAATATTAAT
4436580 ATAATATTAAT
1 ATAATATTAAT
4436591 ATTAATATTAAT
1 A-TAATATTAAT
4436603 -TAATA
1 ATAATA
4436608 ATTATAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.42
11 5 0.19
12 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:4441139 original size:18 final size:18
Alignment explanation
Indices: 4441118--4441183 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
4441108 TAACAGCTAG
*
4441118 TTATTCGGTAATAATCAA
1 TTATTCAGTAATAATCAA
** *
4441136 TTATTCAACAATAATCAG
1 TTATTCAGTAATAATCAA
* *
4441154 TTATTCAGTAACAATTAAA
1 TTATTCAGTAATAA-TCAA
4441173 TTATTCAGTAA
1 TTATTCAGTAA
4441184 CAGTCGATCT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 25 0.66
19 13 0.34
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAATAATCAA
Found at i:4441390 original size:47 final size:46
Alignment explanation
Indices: 4441318--4441434 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 46
4441308 CAGTAATAGT
* * * * *
4441318 AACAGTAGCAATACGGTACATAGAGTACCTCATCGGAAGAAATCCGG
1 AACAGTAACAGTACGGTA-ACAGAGTACCTCATCGGAACAAATCCGA
*
4441365 AACAGTAACAGTACGGTATACAGAGTACCTCATCGGAACAAATCTGA
1 AACAGTAACAGTACGGTA-ACAGAGTACCTCATCGGAACAAATCCGA
4441412 AACAGTAACAGTAACGGTAACAG
1 AACAGTAACAGT-ACGGTAACAG
4441435 TAACAATATC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 56 0.90
48 6 0.10
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (46 bp):
AACAGTAACAGTACGGTAACAGAGTACCTCATCGGAACAAATCCGA
Found at i:4442285 original size:31 final size:32
Alignment explanation
Indices: 4442229--4442291 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
4442219 CACACTTGTC
*
4442229 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
4442261 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
4442292 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:4444749 original size:46 final size:46
Alignment explanation
Indices: 4444380--4444745 Score: 491
Period size: 46 Copynumber: 8.0 Consensus size: 46
4444370 TTATCTTCGA
* * * * *
4444380 CATGATGCCATAGTGTCTTTCAACAATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
* **
4444426 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
4444472 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* *
4444518 CATGTTGCCATGGTATCTTTCAACCATGATCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * * *
4444564 CACGTTGCCATGGTATCTTTCCACCATGATCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * * *
4444610 CACGTTGCCATGGTATATTTCAACCATGGTCTTATTCTTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* ** *
4444656 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* **
4444702 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
4444746 TTCAGTAAGC
Statistics
Matches: 294, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 4 0.01
46 290 0.99
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:4447188 original size:40 final size:40
Alignment explanation
Indices: 4447118--4447295 Score: 261
Period size: 40 Copynumber: 4.5 Consensus size: 40
4447108 AAACCAAGTA
* * * *
4447118 CCTTCGAGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
4447157 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4447197 CCTTCGGGACTTAGCCCGGATATAGTATCTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4447237 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4447277 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
4447296 TTATTATCCG
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 13 0.10
40 114 0.90
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:4455059 original size:40 final size:40
Alignment explanation
Indices: 4454969--4455187 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
4454959 ACCCAAGTAT
* ** * *
4454969 CTTCGGGATTTAG-CCGGATATAACCACTCGCAT-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
* *
4455007 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
* * *
4455047 CTTCGGGACTTAGCCCGGATATAGTCGCTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
* * * * *
4455087 CTTCGGGTCTTAGCCCAGATATAG-CAACTCGTACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCATAAATGC
* *
4455127 CTTC-GGATCTTAG-TCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCATAAATGC
4455166 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
4455188 CATTCGAATA
Statistics
Matches: 149, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
38 11 0.07
39 46 0.31
40 92 0.62
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
Found at i:4455187 original size:79 final size:80
Alignment explanation
Indices: 4454969--4455187 Score: 250
Period size: 79 Copynumber: 2.8 Consensus size: 80
4454959 ACCCAAGTAT
** * * *
4454969 CTTCGGGAT-TTAGCCGGATATAACCACTCGCAT-AAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGATCTTAGCCGGATATAGTCACTAGCATAAAAGCCTTCGGGTCTTAGCCCGGATATAGT
*
4455032 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * * * *
4455047 CTTCGGGA-CTTAGCCCGGATATAGTCGCTTGCACAAATGCCTTCGGGTCTTAGCCCAGATATAG
1 CTTCGGGATCTTAG-CCGGATATAGTCACTAGCATAAAAGCCTTCGGGTCTTAGCCCGGATATAG
* *
4455111 -CAACTCGTACAAATGC
65 TC-ACTAGCACAAATGC
* *
4455127 CTTC-GGATCTTAGTCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGATCTTAGCCGGATATAGTCACTAGCATAAAAGCCTTCGGGTCTTAGCCCGGATAT
4455188 CATTCGAATA
Statistics
Matches: 118, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
78 12 0.10
79 60 0.51
80 46 0.39
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
CTTCGGGATCTTAGCCGGATATAGTCACTAGCATAAAAGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:4459361 original size:25 final size:23
Alignment explanation
Indices: 4459309--4459363 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
4459299 TATAAATAGT
4459309 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
4459332 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
4459357 AATAGTG
1 AATAGTG
4459364 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:4459464 original size:25 final size:25
Alignment explanation
Indices: 4459428--4459575 Score: 113
Period size: 25 Copynumber: 5.8 Consensus size: 25
4459418 GATATAAAAG
* *
4459428 AAAATATGTACATAATATAGTGTAA
1 AAAATATATACATAATATAGTATAA
* *
4459453 AAAATACATACATAATATA--AT-T
1 AAAATATATACATAATATAGTATAA
* *
4459475 AAAATATATACATAAGATAACATGTAGAAAA
1 AAAATATATACAT-A-AT-ATA-GT--ATAA
* *
4459506 AAAATATATAAATAATATAGTATTA
1 AAAATATATACATAATATAGTATAA
* *
4459531 AAGATATATACATAAAATAGTATAA
1 AAAATATATACATAATATAGTATAA
* *
4459556 TATATATATACATAATATAG
1 AAAATATATACATAATATAG
4459576 AATTTAGAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
22 12 0.13
23 2 0.02
24 2 0.02
25 59 0.62
27 2 0.02
28 2 0.02
29 2 0.02
30 2 0.02
31 12 0.13
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAATATATACATAATATAGTATAA
Found at i:4459505 original size:27 final size:28
Alignment explanation
Indices: 4459475--4459546 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
4459465 TAATATAATT
4459475 AAAATATATACATAAGATAACAT-GTA-G
1 AAAATATATACATAA-ATAACATAGTATG
* * * * *
4459502 AAAAAAAATATATAAATAATATAGTATT
1 AAAATATATACATAAATAACATAGTATG
4459530 AAAGATATATACATAAA
1 AAA-ATATATACATAAA
4459547 ATAGTATAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 6 0.18
27 15 0.44
28 3 0.09
29 10 0.29
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATATATACATAAATAACATAGTATG
Found at i:4459512 original size:78 final size:82
Alignment explanation
Indices: 4459423--4459570 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 82
4459413 AAATAGATAT
* * * *
4459423 AAAAGAAAATATGTACATAATATAGTGTAAAAAATACATACATAATATAAT-TAA-A-ATATATA
1 AAAAGAAAATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAATATATATATA
4459485 CATAAGATAACATGTAG
66 CATAAGATAACATGTAG
* * * *
4459502 AAAA-AAAATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTATAATATATATATA
1 AAAAGAAAATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAATATATATATA
4459566 CATAA
66 CATAA
4459571 TATAGAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
78 38 0.66
79 7 0.12
80 1 0.02
81 12 0.21
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (82 bp):
AAAAGAAAATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAATATATATATA
CATAAGATAACATGTAG
Found at i:4459587 original size:25 final size:24
Alignment explanation
Indices: 4459507--4459597 Score: 85
Period size: 25 Copynumber: 3.8 Consensus size: 24
4459497 TGTAGAAAAA
* *
4459507 AAATATATAAATAATATAGTATTA
1 AAATATATACATAATATAGTATTT
* *
4459531 AAGATATATACATAAAATAGTATAAT
1 AA-ATATATACATAATATAGTAT-TT
* *
4459557 ATATATATACATAATATAGAATTT
1 AAATATATACATAATATAGTATTT
* *
4459581 AGA-ATATACCTAATATA
1 AAATATATACATAATATA
4459598 TTAAAAGAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 13 0.24
24 5 0.09
25 36 0.65
26 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (24 bp):
AAATATATACATAATATAGTATTT
Found at i:4459960 original size:16 final size:16
Alignment explanation
Indices: 4459922--4459960 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4459912 CTCCAAAAAA
*
4459922 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
4459938 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
4459954 AATAACT
1 AAAAACT
4459961 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:4460155 original size:30 final size:30
Alignment explanation
Indices: 4460119--4460246 Score: 220
Period size: 30 Copynumber: 4.3 Consensus size: 30
4460109 AGGTACAAGT
*
4460119 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
4460149 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
* *
4460179 GGTGGTAGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
4460209 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
4460239 GGTGGTGG
1 GGTGGTGG
4460247 CAAAGGCTAG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 94 1.00
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.25
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:4461154 original size:161 final size:162
Alignment explanation
Indices: 4460965--4461324 Score: 659
Period size: 161 Copynumber: 2.2 Consensus size: 162
4460955 ACGTGAACCA
* *
4460965 AGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGA
*
4461030 AAATACCTTGGTATGTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAATTG-AAAAAA
66 AAATACCTCGGTATGTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAATTGAAAAAAA
4461094 AATCAATTGAAAATACATCGGCGTGTGATCTG
131 AATCAATTGAAAATACATCGGCGTGTGATCTG
4461126 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGA
4461191 AAATACCTCGGTATGTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAATTGAAAAAAA
66 AAATACCTCGGTATGTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAATTGAAAAAAA
*
4461256 AATCAATTGAAAATACCTCGGCGTGTGATCTG
131 AATCAATTGAAAATACATCGGCGTGTGATCTG
* *
4461288 AGGCTCAACTCACCTTTCGTAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4461325 TTGACAAACA
Statistics
Matches: 192, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
161 120 0.62
162 72 0.38
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (162 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAAAATTTGTAAAACAGATTTTGA
AAATACCTCGGTATGTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAATTGAAAAAAA
AATCAATTGAAAATACATCGGCGTGTGATCTG
Found at i:4461363 original size:93 final size:91
Alignment explanation
Indices: 4461206--4461614 Score: 394
Period size: 91 Copynumber: 4.5 Consensus size: 91
4461196 CCTCGGTATG
* * * **
4461206 TCACCTCTCGTAATATGAGTTGA--TTTTTGCAAAGCATAAATTGAAAAAAAAATCAATTGAAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTGAAAAAAAAAGAAATTGAAAA
*
4461269 TACCTCGGCGTGTGATCTGAGGCTCAAC
65 TACCTCAGCGTGT-ATCTGAGGCTCAAC
* * *
4461297 TCACCTTTCGTAATATGAGTTGATTTTTTTGACAAACATAAATTGAAAAAAAAAGAAATTGAAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAACAGAAATTGAAAAAAAAAGAAATTGAAAA
* * * *
4461362 TATCTCAGCGTGT-CCTGAGGTTGAAC
65 TACCTCAGCGTGTATCTGAGGCTCAAC
* * *
4461388 TCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACA-AAATTTG--AAAAACAGAATTTGAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAA-TTGAAAAAAAAAGAAATTGAAA
*
4461450 ATACCTCAGCGTGTGAGTC-AAGGCTCAAC
64 ATACCTCAGCGTGT-A-TCTGAGGCTCAAC
* * * * * *
4461479 TCACCACTCGCAATATGAGATGACTTTTTTGAAACACAGAAATTG--AAGAACAGAAATGGAAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAAAAAAAGAAATTGAAAA
* *
4461542 CACCTCAGC----ATCTTGAGGTTCAAC
65 TACCTCAGCGTGTATC-TGAGGCTCAAC
* *
4461566 TCACCTCTCGCAATATGAGCTGATTTTTTTTAAAGACAGAAATTGAAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAA
4461615 TACCTCAACG
Statistics
Matches: 270, Mismatches: 34, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
85 2 0.01
86 1 0.00
87 48 0.18
89 30 0.11
90 6 0.02
91 131 0.49
92 6 0.02
93 46 0.17
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (91 bp):
TCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAAAAAAAGAAATTGAAAAT
ACCTCAGCGTGTATCTGAGGCTCAAC
Found at i:4461450 original size:13 final size:14
Alignment explanation
Indices: 4461418--4461450 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4461408 TGATTTTTTG
4461418 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
4461432 GAAAAACAGAATTT
1 GAAAAACAAAATTT
4461446 GAAAA
1 GAAAA
4461451 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:4461524 original size:182 final size:177
Alignment explanation
Indices: 4461206--4461614 Score: 459
Period size: 182 Copynumber: 2.3 Consensus size: 177
4461196 CCTCGGTATG
* * *
4461206 TCACCTCTCGTAATATGAGTTGA-TTTTTGCAAAGCATAAATTGAAAAAAAAATCAATTGAAAAT
1 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTGAAAAAAAAAT--ATTGAAAAT
* * ** * * *
4461270 ACCTCGGCGTGTGATCTGAGGCTCAACTCACCTTTCGTAATATGAGTTGATTTTTTTGACAAACA
64 ACCTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGATGACTTTTTTGACAAACA
* * * * * *
4461335 TAAATTGAAAAAAAAAGAAATTGAAAATATCTCAGCGTGTCCTGAGGTTGAAC
129 GAAATTG--AAAAAAAGAAATGGAAAACACCTCAGC--ATCCTGAGGTTCAAC
*
4461388 TCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACA-AAATTTGAAAAACAGAAT-TTGAAAA
1 TCACCTCTCGCAATATGAGTTGATTTTTT-GAAAAACATAAA-TTGAAAAA-AAAATATTGAAAA
4461451 TACCTCAGCGTGTGAGTC-AAGGCTCAACTCACCACTCGCAATATGAGATGACTTTTTTGA-AAC
63 TACCTCAGCGTGTGA-TCTAAGGCTCAACTCACCACTCGCAATATGAGATGACTTTTTTGACAA-
* * *
4461514 ACAGAAATTGAAGAACAGAAATGGAAAACACCTCAGCATCTTGAGGTTCAAC
126 ACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCATCCTGAGGTTCAAC
* * * *
4461566 TCACCTCTCGCAATATGAGCTGATTTTTTTTAAAGACAGAAATTGAAAA
1 TCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACATAAATTGAAAA
4461615 TACCTCAACG
Statistics
Matches: 196, Mismatches: 23, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
178 47 0.24
179 9 0.05
180 22 0.11
181 2 0.01
182 88 0.45
183 10 0.05
184 14 0.07
185 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (177 bp):
TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTGAAAAAAAAATATTGAAAATAC
CTCAGCGTGTGATCTAAGGCTCAACTCACCACTCGCAATATGAGATGACTTTTTTGACAAACAGA
AATTGAAAAAAAGAAATGGAAAACACCTCAGCATCCTGAGGTTCAAC
Found at i:4461686 original size:73 final size:73
Alignment explanation
Indices: 4461527--4462108 Score: 726
Period size: 73 Copynumber: 7.9 Consensus size: 73
4461517 GAAATTGAAG
* * ** * *
4461527 AACAGAAATGGAAAACACCTC-A-GCATCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
4461590 TTTTTTTA-A
65 -TTTTTGACA
*
4461599 AGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
4461664 TTTTTGACA
65 TTTTTGACA
* * * * *
4461673 AACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
4461736 TTTTTTGAAA
65 -TTTTTGACA
* *
4461746 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
4461811 TTTTTA-A
66 TTTTGACA
*
4461818 AGACAGAAATTGAAAATACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
4461883 TTTTTGACA
65 TTTTTGACA
* * * * * * * *
4461892 AAAAAAAATTGAAATTACCTCAGCGTGTCCTGAGGGTCAACTCACCTATCACAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
4461957 TTCTTTGAAA
65 TT-TTTGACA
* *
4461967 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGAG
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
4462032 TTTTGACA
66 TTTTGACA
* * * * * **
4462040 AACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCATAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
4462105 TTTT
66 TTTT
4462109 TTAGAAACAT
Statistics
Matches: 443, Mismatches: 55, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
71 36 0.08
72 4 0.01
73 261 0.59
74 9 0.02
75 133 0.30
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGACA
Found at i:4461951 original size:221 final size:219
Alignment explanation
Indices: 4461521--4462108 Score: 903
Period size: 221 Copynumber: 2.7 Consensus size: 219
4461511 AACACAGAAA
* * * **
4461521 TTGAAGAACAGAAATGGAAAACACCTC-A-GCATCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
4461584 GCTGATTTTTTTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
66 GCTGA--TTTTTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
* * *
4461649 CACAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTC
129 CACAATATGAGTTGATTTTTGACAAAAAAAAATTGAAATTACCTCAGCGTCCTGAGGGTCAACTC
* *
4461714 ACCTATCGCAATATGAGTTGATTTTT
194 ACCTATCACAATATGAGTTGATTTCT
4461740 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
* *
4461805 GCTGATTTTTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCG
66 GCTGATTTTTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCA
4461870 CAATATGAGTTGATTTTTGACAAAAAAAAATTGAAATTACCTCAGCGTGTCCTGAGGGTCAACTC
131 CAATATGAGTTGATTTTTGACAAAAAAAAATTGAAATTACCTCAGC--GTCCTGAGGGTCAACTC
4461935 ACCTATCACAATATGAGTTGATTTCT
194 ACCTATCACAATATGAGTTGATTTCT
* *
4461961 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
* * * * * * * *
4462026 GTTGAGTTTTGACAA-ACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTC
66 GCTGATTTTTTA-AAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
*
4462090 ATAATATGAGTTGATTTTT
130 ACAATATGAGTTGATTTTT
4462109 TTAGAAACAT
Statistics
Matches: 339, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
219 127 0.37
220 1 0.00
221 209 0.62
222 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (219 bp):
TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
GCTGATTTTTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCA
CAATATGAGTTGATTTTTGACAAAAAAAAATTGAAATTACCTCAGCGTCCTGAGGGTCAACTCAC
CTATCACAATATGAGTTGATTTCT
Found at i:4462330 original size:13 final size:14
Alignment explanation
Indices: 4462297--4462328 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4462287 TTGATTTTTG
4462297 AAAAATAGAAATTA
1 AAAAATAGAAATTA
4462311 AAAAATAGAAATTA
1 AAAAATAGAAATTA
4462325 AAAA
1 AAAA
4462329 TACCTCGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAATAGAAATTA
Found at i:4462364 original size:87 final size:87
Alignment explanation
Indices: 4462219--4462402 Score: 282
Period size: 87 Copynumber: 2.1 Consensus size: 87
4462209 TGTAAGGCAA
* *
4462219 AAATTGAAAAACAGAAATTAAAAATCCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAAACAGAAATTAAAAATCCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATAT
4462284 GAGTTGA-TTTTTGAAAAATAG
66 GAGTTGATTTTTTGAAAAATAG
* * *
4462305 AAATTAAAAAATAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATA
1 AAATTAAAAAACAGAAATTAAAAAT-CCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
*
4462370 TGAGTTGATTTTTTTGAAAGATAG
65 TGAGTTGA-TTTTTTGAAAAATAG
4462394 AAA-TAAAAA
1 AAATTAAAAA
4462403 CATCAAAATA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
86 23 0.26
87 44 0.49
88 6 0.07
89 16 0.18
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (87 bp):
AAATTAAAAAACAGAAATTAAAAATCCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTGAAAAATAG
Found at i:4462380 original size:185 final size:188
Alignment explanation
Indices: 4462034--4462380 Score: 486
Period size: 185 Copynumber: 1.9 Consensus size: 188
4462024 GAGTTGAGTT
* * * * * *
4462034 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCATAATATGA
1 TTGAAAAACAAAAATTAAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGA
* * * * * **
4462099 GTTGATTTTTTTAGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCTTGAGG
66 GTTGATTTTTTGAAAAACAGAAATTAAAAAAACGAAAATTAAAAATACCTCAGCGTGCCCCGAGG
4462164 CTCAACTCACCTCTCACAATATGAGTTGATTTGAAAAGCAGAATTTGTAAGGCAAAAA
131 CTCAACTCACCTCTCACAATATGAGTTGATTTGAAAAGCAGAATTTGTAAGGCAAAAA
* *
4462222 TTGAAAAACAGAAATTAAAAAT-CCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAAAAATTAAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGA
* *
4462286 GTTGA-TTTTTGAAAAATAGAAATTAAAAAATA-G-AAATTAAAAATACCTCGGCGTGCCCCGAG
66 GTTGATTTTTTGAAAAACAGAAATTAAAAAA-ACGAAAATTAAAAATACCTCAGCGTGCCCCGAG
* *
4462348 GCTCAGCTCACCTCTCGCAATATGAGTTGATTT
130 GCTCAACTCACCTCTCACAATATGAGTTGATTT
4462381 TTTTGAAAGA
Statistics
Matches: 139, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
185 55 0.40
186 22 0.16
187 44 0.32
188 18 0.13
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (188 bp):
TTGAAAAACAAAAATTAAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATTTTTTGAAAAACAGAAATTAAAAAAACGAAAATTAAAAATACCTCAGCGTGCCCCGAGG
CTCAACTCACCTCTCACAATATGAGTTGATTTGAAAAGCAGAATTTGTAAGGCAAAAA
Found at i:4464434 original size:37 final size:37
Alignment explanation
Indices: 4464384--4464462 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
4464374 TTATTACGAA
* *
4464384 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
** *
4464421 GTCTTACTTGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
4464458 GTCTT
1 GTCTT
4464463 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:4464659 original size:47 final size:47
Alignment explanation
Indices: 4464581--4465105 Score: 843
Period size: 47 Copynumber: 11.1 Consensus size: 47
4464571 CCCTTCGGGA
* * * * * * *
4464581 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
4464628 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4464675 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4464722 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4464769 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4464816 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4464865 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4464912 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4464959 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4465006 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
4465055 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4465102 CTTA
1 CTTA
4465106 CTATCATTTC
Statistics
Matches: 449, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 359 0.80
49 90 0.20
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4464902 original size:190 final size:190
Alignment explanation
Indices: 4464636--4465105 Score: 886
Period size: 190 Copynumber: 2.5 Consensus size: 190
4464626 GCCCCGTCAC
4464636 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
* *
4464701 TCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
*
4464766 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACAT
131 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
4464826 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
4464891 TCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
4464956 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
131 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
4465016 GTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
4465081 TCATCACATCGGCCATTAGGCCTTA
66 TCATCACATCGGCCATTAGGCCTTA
4465106 CTATCATTTC
Statistics
Matches: 272, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
190 272 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (190 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:4470267 original size:40 final size:40
Alignment explanation
Indices: 4470197--4470372 Score: 248
Period size: 40 Copynumber: 4.4 Consensus size: 40
4470187 AAACCAAGTA
* * * *
4470197 CCTTCGAGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
4470236 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4470276 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4470316 CCTTCAGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4470356 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
4470373 AGTTATCATT
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 12 0.10
40 111 0.90
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:4492772 original size:21 final size:21
Alignment explanation
Indices: 4492748--4492792 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4492738 GCTAGCTCAT
*
4492748 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
* *
4492769 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
4492790 CAT
1 CAT
4492793 TTGATCCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:4499758 original size:26 final size:26
Alignment explanation
Indices: 4499722--4499825 Score: 172
Period size: 26 Copynumber: 4.0 Consensus size: 26
4499712 ACAAATTGAC
*
4499722 AATGGGTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
*
4499748 AATGGATTAGGTAAATATTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
4499774 AATGGGTTAGGTAAATATTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
* *
4499800 AATGGTTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
4499826 GGACATTTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
AATGGGTTAGGTAAATATTCCATGAT
Found at i:4505751 original size:46 final size:47
Alignment explanation
Indices: 4505693--4505912 Score: 245
Period size: 46 Copynumber: 4.8 Consensus size: 47
4505683 TTTGGGCATT
*
4505693 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* * * *** * * * * *
4505739 TGAA-ATCGTTGAGTTGAGTCTGAGTTCGAGAGATGTA-ACTAGGCATC
1 CGAAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-ACGTC
4505786 CG-AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-C
1 CGAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
*
4505831 CCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-C
1 CGAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* *
4505877 CTAAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4505913 GCGGGTTACA
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
45 2 0.01
46 110 0.77
47 31 0.22
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (47 bp):
CGAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
Found at i:4505846 original size:93 final size:93
Alignment explanation
Indices: 4505687--4505858 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 93
4505677 AGGATATTTG
* * **
4505687 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAAATCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAAATCGTTGAG
*
4505752 TTGAGTCTGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
4505780 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-ATCGTTGA
4505844 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
4505859 ACTTATGGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 3 0.04
93 68 0.96
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAAATCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:4508655 original size:15 final size:15
Alignment explanation
Indices: 4508635--4508703 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
4508625 ATATCTTGGG
4508635 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
4508650 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
*
4508665 TTTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
4508680 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
4508695 TTTCTTTAT
1 TTTCTTTAT
4508704 TCGGTTTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:4508704 original size:30 final size:30
Alignment explanation
Indices: 4508626--4508713 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
4508616 CATAGTATCA
* * * *
4508626 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
4508656 TAT-TCTGGATTTCTTTATTCTGGATTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
4508686 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
4508714 TGTTATCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.16
30 42 0.82
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:4524046 original size:26 final size:27
Alignment explanation
Indices: 4523999--4524050 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4523989 CAAGTTTCTA
*
4523999 TTTGATTTGTTTTTTTTAAATTTAGTT
1 TTTGATTTGTTTTGTTTAAATTTAGTT
4524026 TTTGATTT-TTTTGGTTT-AATTTAGT
1 TTTGATTTGTTTT-GTTTAAATTTAGT
4524051 CTCATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.69
Consensus pattern (27 bp):
TTTGATTTGTTTTGTTTAAATTTAGTT
Found at i:4524196 original size:22 final size:24
Alignment explanation
Indices: 4524171--4524230 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
4524161 TATAACATAT
*
4524171 AAAATTAAAAAAATGT-A-TTTGA
1 AAAATTAAAAAAATGTAATTTTAA
* * *
4524193 AAAAGTATAAAAATTTAATTTTAA
1 AAAATTAAAAAAATGTAATTTTAA
4524217 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
4524231 AAATTTATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 13 0.43
23 1 0.03
24 16 0.53
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (24 bp):
AAAATTAAAAAAATGTAATTTTAA
Found at i:4524237 original size:22 final size:22
Alignment explanation
Indices: 4524171--4524237 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
4524161 TATAACATAT
**
4524171 AAAATTAAAAAAATGTATTTGAA
1 AAAATTAAAAAAATAAATTT-AA
* ** *
4524194 AAAGTATAAAAATTTAATTTTAA
1 AAAAT-TAAAAAAATAAATTTAA
4524217 AAAATTAAAAAAATAAATTTA
1 AAAATTAAAAAAATAAATTTA
4524238 TGAAGTGACA
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
22 13 0.39
23 10 0.30
24 10 0.30
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATTAAAAAAATAAATTTAA
Found at i:4526439 original size:19 final size:18
Alignment explanation
Indices: 4526415--4526450 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4526405 TCCTCAAATT
*
4526415 TTTTTTTTGTATTTCCTTG
1 TTTTTTTGGTA-TTCCTTG
4526434 TTTTTTTGGTATTCCTT
1 TTTTTTTGGTATTCCTT
4526451 TATAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTTTGGTATTCCTTG
Found at i:4526902 original size:20 final size:20
Alignment explanation
Indices: 4526879--4526944 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
4526869 TTTCCTAAGA
*
4526879 ATTTTTTGTACTCTCTCATG
1 ATTTTTGGTACTCTCTCATG
* * *
4526899 ATTTTTGGTTCTCTCTCGTA
1 ATTTTTGGTACTCTCTCATG
* *
4526919 ATTTTTGGTATTTTCTCATG
1 ATTTTTGGTACTCTCTCATG
4526939 ATTTTT
1 ATTTTT
4526945 TTTTGGTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.15, G:0.12, T:0.59
Consensus pattern (20 bp):
ATTTTTGGTACTCTCTCATG
Found at i:4526967 original size:24 final size:24
Alignment explanation
Indices: 4526920--4526977 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4526910 TCTCTCGTAA
*
4526920 TTTTTGGTATTTTCTCATGATTTT
1 TTTTTGGTATTTTCTCATCATTTT
*
4526944 TTTTTGGTATTTTCTCTTC-TTTT
1 TTTTTGGTATTTTCTCATCATTTT
4526967 TTTCTT-GTATT
1 TTT-TTGGTATT
4526978 CCTCGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.09, C:0.10, G:0.10, T:0.71
Consensus pattern (24 bp):
TTTTTGGTATTTTCTCATCATTTT
Found at i:4527214 original size:20 final size:20
Alignment explanation
Indices: 4527178--4527294 Score: 74
Period size: 20 Copynumber: 5.5 Consensus size: 20
4527168 GGTATTCCCT
*
4527178 CTCCCTCGTATATTTTTGGTA
1 CTCCCTCATA-ATTTTTGGTA
4527199 CTCCCTCATAATTTTTGGTA
1 CTCCCTCATAATTTTTGGTA
* * *
4527219 CTTCATCATATTTTTTAGTTTGGTA
1 CTCCCTCATA---ATT--TTTGGTA
* **
4527244 TTCCCTCATAATTTTTAATA
1 CTCCCTCATAATTTTTGGTA
** *
4527264 CTCCCTCATTCTTTTTTGTA
1 CTCCCTCATAATTTTTGGTA
4527284 -TCCCTTCATAA
1 CTCCC-TCATAA
4527295 ATTTAGGTAT
Statistics
Matches: 73, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
19 4 0.05
20 42 0.58
21 9 0.12
22 2 0.03
23 2 0.03
25 14 0.19
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.50
Consensus pattern (20 bp):
CTCCCTCATAATTTTTGGTA
Found at i:4529788 original size:40 final size:40
Alignment explanation
Indices: 4529705--4529967 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
4529695 TTGAATGCTG
* * * * * *
4529705 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
4529745 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
4529785 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
4529825 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
4529865 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
4529905 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
4529944 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4529968 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:4529987 original size:79 final size:80
Alignment explanation
Indices: 4529744--4530002 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
4529734 AAGTGAATAT
* * * * * *
4529744 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
4529808 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
4529824 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
4529889 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
4529904 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
4529968 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
4529983 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
4530003 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:4533873 original size:16 final size:17
Alignment explanation
Indices: 4533852--4533886 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4533842 TTTCTACACT
4533852 AAAGACAAA-GAGGAAA
1 AAAGACAAAGGAGGAAA
4533868 AAAGACAAATGGAGGAAA
1 AAAGACAAA-GGAGGAAA
4533886 A
1 A
4533887 TTTTATGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAGACAAAGGAGGAAA
Found at i:4536113 original size:60 final size:60
Alignment explanation
Indices: 4536018--4536139 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
4536008 TTTGCAGATG
*
4536018 ATTGCATTTTATTCGCAGAAGCTACTGAAAAAGGAGTGCATTCCTTAAAACGGATTTTGA
1 ATTGCATTTTATTCGCAGAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
* *
4536078 ATTGCATTTTATTCGCAGAAGCTACTGAAAGAGGAGTACATTCCTTAAAATGGATTTTGA
1 ATTGCATTTTATTCGCAGAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
4536138 AT
1 AT
4536140 GAATATGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (60 bp):
ATTGCATTTTATTCGCAGAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
Found at i:4538462 original size:15 final size:15
Alignment explanation
Indices: 4538442--4538484 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
4538432 TATTTTAAGC
4538442 TTAATAATTAAATAT
1 TTAATAATTAAATAT
*
4538457 TTAATAATTTTAATAT
1 TTAATAA-TTAAATAT
4538473 TATAAT-ATTAAA
1 T-TAATAATTAAA
4538485 AAATATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATAATTAAATAT
Found at i:4540501 original size:24 final size:24
Alignment explanation
Indices: 4540474--4540525 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4540464 TTAGTAAGTC
*
4540474 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4540498 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4540522 AAAT
1 AAAT
4540526 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4542472 original size:24 final size:24
Alignment explanation
Indices: 4542445--4542496 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4542435 TTAGTAAGTC
*
4542445 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4542469 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4542493 AAAT
1 AAAT
4542497 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4543997 original size:22 final size:22
Alignment explanation
Indices: 4543966--4544007 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4543956 AATACATGAT
*
4543966 AAAATCTATAATTCACATTTCA
1 AAAATCTATAATTCAAATTTCA
*
4543988 AAAATTTATAATTCAAATTT
1 AAAATCTATAATTCAAATTT
4544008 GGCCCCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATCTATAATTCAAATTTCA
Found at i:4547216 original size:27 final size:26
Alignment explanation
Indices: 4547162--4547216 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
4547152 TCCTCAAATG
* * *
4547162 AATAATTTTAAAGAAAATATATATAT
1 AATAAATTTAAAAAAAATATATACAT
*
4547188 AATAAATTTAGAAAAAAATATTTACAT
1 AATAAATTTA-AAAAAAATATATACAT
4547215 AA
1 AA
4547217 AATATTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
AATAAATTTAAAAAAAATATATACAT
Found at i:4548092 original size:6 final size:6
Alignment explanation
Indices: 4548081--4548114 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
4548071 TCGTGGACTC
4548081 AAATAA AAATAA AAATAA AAATAACA AAATAA AA
1 AAATAA AAATAA AAATAA AAAT-A-A AAATAA AA
4548115 TAATGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.73
7 2 0.08
8 5 0.19
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:4548818 original size:14 final size:14
Alignment explanation
Indices: 4548799--4548826 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4548789 ATTGATTTTT
4548799 ATAATATTATAAAA
1 ATAATATTATAAAA
4548813 ATAATATTATAAAA
1 ATAATATTATAAAA
4548827 TCTTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATATTATAAAA
Found at i:4554166 original size:31 final size:31
Alignment explanation
Indices: 4554128--4554187 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4554118 ATTAATTTAC
4554128 TCGAAAATTTTCATTCAAGTCACTAAACTAT
1 TCGAAAATTTTCATTCAAGTCACTAAACTAT
* * * *
4554159 TCGAAAATTTTTATTTAAGTTATTAAACT
1 TCGAAAATTTTCATTCAAGTCACTAAACT
4554188 GTTAAGGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (31 bp):
TCGAAAATTTTCATTCAAGTCACTAAACTAT
Found at i:4558641 original size:13 final size:12
Alignment explanation
Indices: 4558625--4558652 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4558615 TAGAAAAATT
4558625 AAAAAAAAAAAG
1 AAAAAAAAAAAG
4558637 AAAAAAAAAAAG
1 AAAAAAAAAAAG
4558649 AAAA
1 AAAA
4558653 GGAGAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:4566335 original size:20 final size:20
Alignment explanation
Indices: 4566310--4566347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4566300 TAAATTTTTA
*
4566310 TATATAAAATTTTAAAAAAT
1 TATATAAAATATTAAAAAAT
*
4566330 TATATAATATATTAAAAA
1 TATATAAAATATTAAAAA
4566348 TACTAAAAAC
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAAAATATTAAAAAAT
Found at i:4566961 original size:24 final size:24
Alignment explanation
Indices: 4566934--4566982 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4566924 TTAATTCATA
*
4566934 ATAT-AACATATACATTTTGATTTT
1 ATATAAACATATA-ATTTTAATTTT
*
4566958 ATATAAACATTTAATTTTAATTTT
1 ATATAAACATATAATTTTAATTTT
4566982 A
1 A
4566983 ATTTACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATAAACATATAATTTTAATTTT
Found at i:4567370 original size:22 final size:21
Alignment explanation
Indices: 4567330--4567370 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4567320 TTCTTTTCTG
*
4567330 TTATTTTTTGTTGTCATTTTA
1 TTATTTTTTGTTATCATTTTA
*
4567351 TTATTTTATTGTTATGATTT
1 TTATTTT-TTGTTATCATTT
4567371 GAATATTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (21 bp):
TTATTTTTTGTTATCATTTTA
Found at i:4570160 original size:20 final size:20
Alignment explanation
Indices: 4570128--4570165 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4570118 ATTTTTATAT
4570128 ATTTTCTTATTAAAATTTAC
1 ATTTTCTTATTAAAATTTAC
*
4570148 ATTTT-TTAGTTAATATTT
1 ATTTTCTTA-TTAAAATTT
4570166 TTATATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTCTTATTAAAATTTAC
Found at i:4572961 original size:9 final size:10
Alignment explanation
Indices: 4572930--4572959 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
4572920 AAAAAAAAAC
4572930 CCTTTTTAGAA
1 CCTTTTTA-AA
4572941 CCTTTTTAAA
1 CCTTTTTAAA
4572951 CCTTTTTAA
1 CCTTTTTAA
4572960 CCCCGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (10 bp):
CCTTTTTAAA
Found at i:4575177 original size:11 final size:11
Alignment explanation
Indices: 4575163--4575187 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4575153 TTGGGTTTTA
4575163 TTTATTTTATT
1 TTTATTTTATT
4575174 TTTATTTTATT
1 TTTATTTTATT
4575185 TTT
1 TTT
4575188 GTTTGGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:4598656 original size:16 final size:17
Alignment explanation
Indices: 4598635--4598687 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
4598625 TAGAGTGAAA
4598635 AAAAATTGAAAAGAT-G
1 AAAAATTGAAAAGATGG
* *
4598651 AAAAATT-AAATGGCTGG
1 AAAAATTGAAA-AGATGG
4598668 AAAAA-TGAAAAGATGG
1 AAAAATTGAAAAGATGG
4598684 AAAA
1 AAAA
4598688 CATAATTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 18 0.60
17 9 0.30
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (17 bp):
AAAAATTGAAAAGATGG
Found at i:4599729 original size:15 final size:15
Alignment explanation
Indices: 4599709--4599737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4599699 ATGGTGACAG
4599709 TCAAAAAAATTTAGC
1 TCAAAAAAATTTAGC
4599724 TCAAAAAAATTTAG
1 TCAAAAAAATTTAG
4599738 GATACCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (15 bp):
TCAAAAAAATTTAGC
Found at i:4602287 original size:60 final size:59
Alignment explanation
Indices: 4602221--4602334 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
4602211 ACTAGGTGAT
* *
4602221 AAAAAAGACACAATT-TAATAGTTGGGTGACCATTTTGTAACTTTTCATAGTTGGATGACC
1 AAAAAAGA-A-AATTATAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGGATGACC
* *
4602281 AAAAAAGAAATTTACTAATAGTTGGGTGAACACTTTGTAACTTTTTATAGTTGG
1 AAAAAAGAAAATTA-TAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGG
4602335 GTGATTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 3 0.06
59 1 0.02
60 44 0.92
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAAAAGAAAATTATAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGGATGACC
Found at i:4604126 original size:17 final size:16
Alignment explanation
Indices: 4604103--4604149 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
4604093 TTTTATTAAC
4604103 TTTTTTTTATAATT-T
1 TTTTTTTTATAATTCT
*
4604118 TTATTTTTTGATTATTCT
1 TT-TTTTTT-ATAATTCT
*
4604136 TTTTTTTTAAAATT
1 TTTTTTTTATAATT
4604150 ATTTGTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 10 0.38
17 11 0.42
18 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTTTTATAATTCT
Found at i:4606845 original size:22 final size:23
Alignment explanation
Indices: 4606820--4606879 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
4606810 TGGACTGAAT
4606820 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
4606842 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
4606864 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
4606880 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:4606847 original size:4 final size:4
Alignment explanation
Indices: 4606829--4606862 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
4606819 TATAAAAATT
4606829 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
4606863 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:4608262 original size:23 final size:22
Alignment explanation
Indices: 4608211--4608262 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
4608201 CCTCGTCTTT
* * *
4608211 TTCTTTTGTTTCTTTTTTTAAC
1 TTCTTTTCTTTCTTTCTTCAAC
4608233 -TCATTTTCTCTTCTTTCTTCAAC
1 TTC-TTTTCT-TTCTTTCTTCAAC
4608256 TTCTTTT
1 TTCTTTT
4608263 TCAATTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.08
22 5 0.21
23 15 0.62
24 2 0.08
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTCTTCAAC
Found at i:4610665 original size:22 final size:23
Alignment explanation
Indices: 4610640--4610699 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
4610630 TGGACTGAAT
4610640 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
4610662 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
4610684 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
4610700 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:4610667 original size:4 final size:4
Alignment explanation
Indices: 4610649--4610682 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
4610639 TATAAAAATT
4610649 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
4610683 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:4616489 original size:24 final size:26
Alignment explanation
Indices: 4616460--4616522 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
4616450 ATATACGAAG
*
4616460 CAATTTAAAGTAGA-TAATATA-AA-A
1 CAATTTAAAATA-ATTAATATATAACA
4616484 CAATTTAAAATAATTAATATATAACA
1 CAATTTAAAATAATTAATATATAACA
*
4616510 TAATTTAAAATAA
1 CAATTTAAAATAA
4616523 AATAAAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 18 0.53
25 2 0.06
26 13 0.38
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (26 bp):
CAATTTAAAATAATTAATATATAACA
Found at i:4616782 original size:29 final size:28
Alignment explanation
Indices: 4616752--4616807 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4616742 AAGAATTTTA
*
4616752 AAATAACAGTATGT-AAAGACTTAAAAAT
1 AAATAA-AGTATATGAAAGACTTAAAAAT
* *
4616780 AAATAATGTATATGAAAGATTTAAAAAT
1 AAATAAAGTATATGAAAGACTTAAAAAT
4616808 GATAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.29
Consensus pattern (28 bp):
AAATAAAGTATATGAAAGACTTAAAAAT
Found at i:4616805 original size:27 final size:27
Alignment explanation
Indices: 4616761--4616846 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
4616751 AAAATAACAG
*
4616761 TATGTAAAGACTTAAAAATAAATAATGTA
1 TATG-AAAGA-TTTAAAATAAATAATGTA
* *
4616790 TATGAAAGATTTAAAAATGATAGTAA-ATA
1 TATGAAAGATTT-AAAAT-A-AATAATGTA
*
4616819 TAT-AAA-ATTTAAAACAAATAATGTA
1 TATGAAAGATTTAAAATAAATAATGTA
4616844 TAT
1 TAT
4616847 ATGTATAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
24 4 0.09
25 6 0.13
26 4 0.09
27 6 0.13
28 13 0.28
29 10 0.21
30 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (27 bp):
TATGAAAGATTTAAAATAAATAATGTA
Found at i:4619365 original size:7 final size:7
Alignment explanation
Indices: 4619353--4619383 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4619343 ATGAATTTTT
4619353 TTTATAA
1 TTTATAA
4619360 TTTATAA
1 TTTATAA
*
4619367 TTTATCA
1 TTTATAA
4619374 TTTATAA
1 TTTATAA
4619381 TTT
1 TTT
4619384 TCTATTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTATAA
Found at i:4619534 original size:17 final size:18
Alignment explanation
Indices: 4619512--4619545 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4619502 CAAAAATTAA
4619512 TGTTTTTTTAAT-ATTTC
1 TGTTTTTTTAATGATTTC
4619529 TGTTTTTTTAATGATTT
1 TGTTTTTTTAATGATTT
4619546 TTTACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (18 bp):
TGTTTTTTTAATGATTTC
Found at i:4632915 original size:27 final size:27
Alignment explanation
Indices: 4632885--4632939 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4632875 ACAATATTGG
*
4632885 TAATTAAAGCAT-TATATACTATTAGAA
1 TAATT-AAGCATATATATACTAGTAGAA
*
4632912 TAATTAATCATATATATACTAGTAGAA
1 TAATTAAGCATATATATACTAGTAGAA
4632939 T
1 T
4632940 GCGAGTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (27 bp):
TAATTAAGCATATATATACTAGTAGAA
Found at i:4636686 original size:135 final size:135
Alignment explanation
Indices: 4636523--4636854 Score: 423
Period size: 135 Copynumber: 2.5 Consensus size: 135
4636513 CAATATTTGA
*
4636523 TATATTTAGCCTGCTTCACTCCTGCTCAGTGAAGATAAGTCTGATGATTGGAATCTGCTCCATCG
1 TATATTTAGCCTGCTTCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCG
* * * *
4636588 CTAG-TACAGGGAGATAAGATTCACCAAAATTCGATCTGCTCCGCTCCTGCTCAGCGAAGATAAG
66 -TAGATACAGGGAGATAAAACTCACCAAAATTCGATCTGCTCCACTCCTGCTCAGCGAAGAAAAG
*
4636652 ATCTGC
130 ATCAGC
* * * *
4636658 TATACTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGAATCTGCTCCATTG
1 TATATTTAGCCTGCTTCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCG
* * * * * * *
4636723 TCGATACATGGAGATAAAACTCGCCAAAATTTGATCTGCTTCACTCTTGCTCAGTGAAGAAAAGA
66 TAGATACAGGGAGATAAAACTCACCAAAATTCGATCTGCTCCACTCCTGCTCAGCGAAGAAAAGA
*
4636788 TCAGG
131 TCAGC
* * * * ** *
4636793 TATGTTTAGCCTGCTCCACTTCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCA
1 TATATTTAGCCTGCTTCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCA
4636855 CTCCTATTCA
Statistics
Matches: 168, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
134 2 0.01
135 166 0.99
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (135 bp):
TATATTTAGCCTGCTTCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCG
TAGATACAGGGAGATAAAACTCACCAAAATTCGATCTGCTCCACTCCTGCTCAGCGAAGAAAAGA
TCAGC
Found at i:4636866 original size:44 final size:44
Alignment explanation
Indices: 4636803--4636922 Score: 195
Period size: 44 Copynumber: 2.7 Consensus size: 44
4636793 TATGTTTAGC
* * * *
4636803 CTGCTCCACTTCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAAT
1 CTGCTCCACTCCTACTCAGTGAAGATAAGACTGGTGGCTGAAAG
*
4636847 CTGCTCCACTCCTATTCAGTGAAGATAAGACTGGTGGCTGAAAG
1 CTGCTCCACTCCTACTCAGTGAAGATAAGACTGGTGGCTGAAAG
4636891 CTGCTCCACTCCTACTCAGTGAAGATAAGACT
1 CTGCTCCACTCCTACTCAGTGAAGATAAGACT
4636923 TCGCCAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (44 bp):
CTGCTCCACTCCTACTCAGTGAAGATAAGACTGGTGGCTGAAAG
Found at i:4644702 original size:20 final size:21
Alignment explanation
Indices: 4644666--4644709 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4644656 TTAGCTGGCT
*
4644666 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
4644687 CATGTT-TTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
4644707 CAT
1 CAT
4644710 TTGATCATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Done.