Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 15 of 144
Found at i:3689215 original size:99 final size:99
Alignment explanation
Indices: 3689045--3689269 Score: 317
Period size: 99 Copynumber: 2.3 Consensus size: 99
3689035 CATCGGGTTC
* * * * *
3689045 CCTCAACCTTTCCCATCACAT-TTGATGGTACCGAATTCGCCGTTGCGGCCTCAATCTTTCCCAT
1 CCTCAACCTTTCCCTTTACATCTTCATGGTACCGAATTCGCCGTTGCGACCTCAAACTTTCCCAT
* *
3689109 CTCATCTTCTAAGGTACCGGGTTCGCCGTTGCGG
66 CACATCTTCTAAGGTACCGGGTTCACCGTTGCGG
* ** *
3689143 CCTCAACCTTTCCCTTTACATCCTCATGGTACCGGGTTCGCCGTTGCGACCTTAAACTTTCCCAT
1 CCTCAACCTTTCCCTTTACATCTTCATGGTACCGAATTCGCCGTTGCGACCTCAAACTTTCCCAT
* *
3689208 CACATCTTCTTAGGTACCGGGTTCACCGTTGTGG
66 CACATCTTCTAAGGTACCGGGTTCACCGTTGCGG
*
3689242 TCTCAACCTTTCCCTTTACATCTTCATG
1 CCTCAACCTTTCCCTTTACATCTTCATG
3689270 TTTTTCTCAG
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 19 0.17
99 92 0.83
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.33
Consensus pattern (99 bp):
CCTCAACCTTTCCCTTTACATCTTCATGGTACCGAATTCGCCGTTGCGACCTCAAACTTTCCCAT
CACATCTTCTAAGGTACCGGGTTCACCGTTGCGG
Found at i:3690236 original size:20 final size:19
Alignment explanation
Indices: 3690213--3690296 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
3690203 TCGACCTCTC
3690213 CTTTTTTTTTCCTTTTTTTT
1 CTTTTTTTTT-CTTTTTTTT
* *
3690233 CTTTTTCCTTTT-TTATTTCT
1 CTTTTT--TTTTCTTTTTTTT
3690253 CTTTCTTTTTTTCTATTTTCTTT
1 C-TT-TTTTTTTCT-TTTT-TTT
* *
3690276 CTTTTTTTAT-TTATTTTT
1 CTTTTTTTTTCTTTTTTTT
3690294 CTT
1 CTT
3690297 CATTGAATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
18 6 0.12
19 3 0.06
20 18 0.35
21 9 0.18
22 12 0.24
23 3 0.06
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTTTTTCTTTTTTTT
Found at i:3690262 original size:25 final size:24
Alignment explanation
Indices: 3690230--3690277 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3690220 TTTCCTTTTT
*
3690230 TTTCTTTTTCCTTTTTTATTTCTC
1 TTTCTTTTTCCTATTTTATTTCTC
* *
3690254 TTTCTTTTTTTCTATTTTCTTTCT
1 TTTC-TTTTTCCTATTTTATTTCT
3690278 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTCTTTTTCCTATTTTATTTCTC
Found at i:3690264 original size:27 final size:27
Alignment explanation
Indices: 3690211--3690264 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3690201 CCTCGACCTC
*
3690211 TCCTTTTTTTTTCCTTTTTTTTCTTTT
1 TCCTTTTTTTTTCCTTTTCTTTCTTTT
3690238 TCCTTTTTTATTT-CTCTTTCTTT-TTTT
1 TCCTTTTTT-TTTCCT-TTTCTTTCTTTT
3690265 CTATTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (27 bp):
TCCTTTTTTTTTCCTTTTCTTTCTTTT
Found at i:3690274 original size:19 final size:19
Alignment explanation
Indices: 3690241--3690287 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
3690231 TTCTTTTTCC
3690241 TTTTTTATTTCTCTTTCTT
1 TTTTTTATTTCTCTTTCTT
3690260 TTTTTCTATTT-TCTTTC-T
1 TTTTT-TATTTCTCTTTCTT
3690278 TTTTTTATTT
1 TTTTTTATTT
3690288 ATTTTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 11 0.41
20 5 0.19
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTATTTCTCTTTCTT
Found at i:3690296 original size:18 final size:18
Alignment explanation
Indices: 3690225--3690287 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
3690215 TTTTTTTTCC
* *
3690225 TTTTT-TTTCTTTTTCCT
1 TTTTTATTTCTCTTTCTT
3690242 TTTTTATTTCTCTTTCTTT
1 TTTTTATTTCTCTTTC-TT
3690261 TTTTCTATTT-TCTTTCTT
1 TTTT-TATTTCTCTTTCTT
3690279 TTTTTATTT
1 TTTTTATTT
3690288 ATTTTTCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 10 0.24
18 15 0.37
19 11 0.27
20 5 0.12
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTATTTCTCTTTCTT
Found at i:3691151 original size:14 final size:15
Alignment explanation
Indices: 3691129--3691157 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3691119 CTTGACTTTC
3691129 CTTTCTTCTTTTTTT
1 CTTTCTTCTTTTTTT
3691144 CTTT-TTCTTTTTTT
1 CTTTCTTCTTTTTTT
3691158 TGCCCTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTCTTCTTTTTTT
Found at i:3691223 original size:16 final size:16
Alignment explanation
Indices: 3691204--3691242 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3691194 TCTTGGCCCC
3691204 TTTTTTATTTCTTT-TG
1 TTTTTTATTT-TTTCTG
*
3691220 TTTTTTATTTTTTCTT
1 TTTTTTATTTTTTCTG
3691236 TTTTTTA
1 TTTTTTA
3691243 ACACGTCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTTATTTTTTCTG
Found at i:3692817 original size:22 final size:22
Alignment explanation
Indices: 3692789--3692837 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3692779 ATTCAGGTAA
3692789 CCACTAAAGGTTTGGCATAGTT
1 CCACTAAAGGTTTGGCATAGTT
3692811 CCACTAAAGGTTTGGCATAGTT
1 CCACTAAAGGTTTGGCATAGTT
3692833 CCACT
1 CCACT
3692838 TATGGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (22 bp):
CCACTAAAGGTTTGGCATAGTT
Found at i:3695253 original size:59 final size:57
Alignment explanation
Indices: 3695131--3695442 Score: 265
Period size: 59 Copynumber: 5.3 Consensus size: 57
3695121 TGCTTGAGAG
* * * * * * *
3695131 TAAAATGGTGATTTTTGGAAGTTCGGGGG-GAAAATGTGATTTTTGGAAGTTTAAAGGC
1 TAAAAT-GTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTT-AGGGT
* * *
3695189 AAAAATGTGATTTTTGGAAGTTCGGGGGGTAAAAATGTAATTTTTGGAAAGTTTAGGGT
1 TAAAATGTAATTTTTGGAAGTT-TGGGGGTAAAAATGTAATTTTT-GAAAGTTTAGGGT
* * *
3695248 TAAAATGCAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTT-GAGGA
1 TAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGA-AAGTTTAG-GGT
* * * *
3695306 TAATAATGTAATTTTTGGAAATTTAGGGGCAAAAATGTAATTTTTGATAAG-TTCGAGG-
1 TAA-AATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGA-AAGTTTAG-GGT
* * * * * *
3695364 CAATAATGTAATTTTTGGAAAGTTTGGGGGTTAAAATATAATATCTAGAAAGTTTGGGGGT
1 TAA-AATGTAATTTTTGG-AAGTTTGGGGGTAAAAATGTAAT-TTTTGAAAGTTT-AGGGT
3695425 TAAAATGT-ATTTTTGGAA
1 TAAAATGTAATTTTTGGAA
3695443 TAGTTTAAGG
Statistics
Matches: 215, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
57 19 0.09
58 62 0.29
59 111 0.52
60 20 0.09
61 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (57 bp):
TAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGAAAGTTTAGGGT
Found at i:3695448 original size:30 final size:30
Alignment explanation
Indices: 3695131--3695482 Score: 244
Period size: 29 Copynumber: 11.9 Consensus size: 30
3695121 TGCTTGAGAG
* * *
3695131 TAAAATGGTGATTTTTGG-AAG-TTCGGGGG
1 TAAAAT-GTAATTTTTGGAAAGTTTAGGGGT
* * ** *
3695160 GAAAATGTGATTTTTGG-AAGTTTAAAGGC
1 TAAAATGTAATTTTTGGAAAGTTTAGGGGT
* * **
3695189 AAAAATGTGATTTTTGG-AAGTTCGGGGGGT
1 TAAAATGTAATTTTTGGAAAGTT-TAGGGGT
*
3695219 AAAAATGTAATTTTTGGAAAGTTTA-GGGT
1 TAAAATGTAATTTTTGGAAAGTTTAGGGGT
*
3695248 TAAAATGCAATTTTTGG-AAGTTTAGGGGT
1 TAAAATGTAATTTTTGGAAAGTTTAGGGGT
* * *
3695277 AAAAATGTAATTTTT-GAGAAGTTT-GAGGA
1 TAAAATGTAATTTTTGGA-AAGTTTAGGGGT
*
3695306 TAATAATGTAATTTTTGGAAA-TTTAGGGGC
1 TAA-AATGTAATTTTTGGAAAGTTTAGGGGT
* * *
3695336 AAAAATGTAATTTTT-GATAAG-TTCGAGG-
1 TAAAATGTAATTTTTGGA-AAGTTTAGGGGT
* *
3695364 CAATAATGTAATTTTTGGAAAGTTTGGGGGT
1 TAA-AATGTAATTTTTGGAAAGTTTAGGGGT
* * * * *
3695395 TAAAATATAATATCTAGAAAGTTTGGGGGT
1 TAAAATGTAATTTTTGGAAAGTTTAGGGGT
*
3695425 TAAAATGT-ATTTTTGGAATAGTTTAAGGGT
1 TAAAATGTAATTTTTGGAA-AGTTTAGGGGT
* * * * *
3695455 CAAAATATGATTTTTGGACAGTTCAGGG
1 TAAAATGTAATTTTTGGAAAGTTTAGGG
3695483 ACCTTTTGGG
Statistics
Matches: 261, Mismatches: 45, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
28 26 0.10
29 115 0.44
30 102 0.39
31 18 0.07
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
TAAAATGTAATTTTTGGAAAGTTTAGGGGT
Found at i:3697128 original size:6 final size:6
Alignment explanation
Indices: 3697119--3697207 Score: 87
Period size: 6 Copynumber: 15.2 Consensus size: 6
3697109 TTAGACTTTT
**
3697119 AATTTA AATTTA CAA--TA AATTTA AATTTA AAAATA AATTTA AATTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
3697166 AA-TTA AATTTA AATATAA AATTTA AACTTA AA-ATA AATTTA A
1 AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA A
3697208 CAAATGAGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
4 2 0.03
5 11 0.16
6 48 0.71
7 7 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:3697141 original size:17 final size:16
Alignment explanation
Indices: 3697119--3697207 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 16
3697109 TTAGACTTTT
3697119 AATTTAAATTTACAATA
1 AATTTAAATTTA-AATA
3697136 AATTTAAATTTAAAAATA
1 AATTTAAATTT--AAATA
3697154 AATTTAAATTTAAATTA
1 AATTTAAATTTAAA-TA
*
3697171 AATTTAAA--TATA-A
1 AATTTAAATTTAAATA
*
3697184 AATTTAAACTTAAAATA
1 AATTTAAA-TTTAAATA
3697201 AATTTAA
1 AATTTAA
3697208 CAAATGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
13 9 0.15
15 3 0.05
16 5 0.08
17 29 0.47
18 15 0.24
19 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:3697158 original size:35 final size:35
Alignment explanation
Indices: 3697119--3697185 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3697109 TTAGACTTTT
*
3697119 AATTTAAATTTACAA-TAAATTTAAATTTAAAAATA
1 AATTTAAATTTA-AATTAAATTTAAATATAAAAATA
3697154 AATTTAAATTTAAATTAAATTTAAATATAAAA
1 AATTTAAATTTAAATTAAATTTAAATATAAAA
3697186 TTTAAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AATTTAAATTTAAATTAAATTTAAATATAAAAATA
Found at i:3697168 original size:30 final size:30
Alignment explanation
Indices: 3697134--3697212 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
3697124 AAATTTACAA
*
3697134 TAAATTTAAATTTAAAAAT-AAATTTAAATT
1 TAAA-TTAAATTTAAAAATAAAATTTAAACT
*
3697164 TAAATTAAATTTAAATATAAAATTTAAACT
1 TAAATTAAATTTAAAAATAAAATTTAAACT
*
3697194 TAAAATAAATTTAACAAAT
1 TAAATTAAATTTAA-AAAT
3697213 GAGTTTAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.30
30 27 0.63
31 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATTAAATTTAAAAATAAAATTTAAACT
Found at i:3698862 original size:24 final size:24
Alignment explanation
Indices: 3698760--3699060 Score: 177
Period size: 24 Copynumber: 12.5 Consensus size: 24
3698750 CATATTTATG
* *
3698760 CGTTTACGCTCGCCAGCTT-AATA
1 CGTTTACGCTCGCCAGCTTGCACA
* * * *
3698783 TGCATTTACGTTCGTCAGCGTGCACA
1 --CGTTTACGCTCGCCAGCTTGCACA
* *
3698809 CGTTTACGCTGGTCAGCTT--A-A
1 CGTTTACGCTCGCCAGCTTGCACA
*
3698830 ---TTACGCTCACCAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
*
3698851 CGTTTACGCTCACCAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
* * * **
3698875 CGTTTATACACTCGTCAGCTTAGTTATG
1 CG-TT-TACGCTCGCCAGCTT-G-CACA
3698903 CGTTTACGCTCGCCAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
* * *
3698927 CGTTTACGCTCGTCAGCTT-AATA
1 CGTTTACGCTCGCCAGCTTGCACA
* *
3698950 TGCATTTACGCTCGCCAGCTTACACA
1 --CGTTTACGCTCGCCAGCTTGCACA
* ** * * **
3698976 CGTTTACGTTCATCAACTTAGTTATG
1 CGTTTACGCTCGCCAGCTT-G-CACA
* *
3699002 CGTTTATGCTTGCCAGCTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
* *
3699026 CGTTTACGCTTGCCAACTTGCACA
1 CGTTTACGCTCGCCAGCTTGCACA
3699050 CGTTTACGCTC
1 CGTTTACGCTC
3699061 ATTAGCTTAA
Statistics
Matches: 208, Mismatches: 52, Indels: 33
0.71 0.18 0.11
Matches are distributed among these distances:
18 13 0.06
20 1 0.00
21 2 0.01
22 1 0.00
23 2 0.01
24 104 0.50
25 36 0.17
26 43 0.21
27 3 0.01
28 3 0.01
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (24 bp):
CGTTTACGCTCGCCAGCTTGCACA
Found at i:3698966 original size:49 final size:50
Alignment explanation
Indices: 3698851--3699035 Score: 255
Period size: 50 Copynumber: 3.7 Consensus size: 50
3698841 AGCTTGCACA
* *
3698851 CGTTTACGCTCACCAGCTTGCACACGTTTATACACTCGTCAGCTTAGTTATG
1 CGTTTACGCTCGCCAGCTTGCACACG-TT-TACGCTCGTCAGCTTAGTTATG
*
3698903 CGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTA-ATATG
1 CGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAGTTATG
* * * * *
3698952 CATTTACGCTCGCCAGCTTACACACGTTTACGTTCATCAACTTAGTTATG
1 CGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAGTTATG
* *
3699002 CGTTTATGCTTGCCAGCTTGCACACGTTTACGCT
1 CGTTTACGCTCGCCAGCTTGCACACGTTTACGCT
3699036 TGCCAACTTG
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 43 0.36
50 48 0.41
51 2 0.02
52 25 0.21
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (50 bp):
CGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAGTTATG
Found at i:3699022 original size:99 final size:101
Alignment explanation
Indices: 3698853--3699035 Score: 280
Period size: 99 Copynumber: 1.8 Consensus size: 101
3698843 CTTGCACACG
* * *
3698853 TTTACGCTCACCAGCTTGCACACGTTTATACACTCGTCAGCTTAGTTATGCGTTTACGCTCGCCA
1 TTTACGCTCACCAGCTTACACACGTTTATACACTCATCAACTTAGTTATGCGTTTACGCTCGCCA
3698918 GCTTGCACACGTTTACGCTCGTCAGCTTAATATGCA
66 GCTTGCACACGTTTACGCTCGTCAGCTTAATATGCA
* ** * *
3698954 TTTACGCTCGCCAGCTTACACACG-TT-TACGTTCATCAACTTAGTTATGCGTTTATGCTTGCCA
1 TTTACGCTCACCAGCTTACACACGTTTATACACTCATCAACTTAGTTATGCGTTTACGCTCGCCA
3699017 GCTTGCACACGTTTACGCT
66 GCTTGCACACGTTTACGCT
3699036 TGCCAACTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 50 0.68
100 2 0.03
101 22 0.30
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.33
Consensus pattern (101 bp):
TTTACGCTCACCAGCTTACACACGTTTATACACTCATCAACTTAGTTATGCGTTTACGCTCGCCA
GCTTGCACACGTTTACGCTCGTCAGCTTAATATGCA
Found at i:3699050 original size:74 final size:74
Alignment explanation
Indices: 3698954--3699094 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 74
3698944 TTAATATGCA
* * * * *
3698954 TTTACGCTCGCCAGCTTACACACGTTTACGTTCATCAACTTAGTTATGCGTTTATGCTTGCCAGC
1 TTTACGCTCGCCAACTTACACACGTTTACGCTCATCAACTTAATTATGAGTTTACGCTTGCCAGC
3699019 TTGCACACG
66 TTGCACACG
* * * * * *
3699028 TTTACGCTTGCCAACTTGCACACGTTTACGCTCATTAGCTTAATTATGAGTTTGCGCTTTCCAGC
1 TTTACGCTCGCCAACTTACACACGTTTACGCTCATCAACTTAATTATGAGTTTACGCTTGCCAGC
3699093 TT
66 TT
3699095 ATTAATTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (74 bp):
TTTACGCTCGCCAACTTACACACGTTTACGCTCATCAACTTAATTATGAGTTTACGCTTGCCAGC
TTGCACACG
Found at i:3699172 original size:12 final size:12
Alignment explanation
Indices: 3699153--3699183 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3699143 AAATAAACTT
3699153 AAAAACATTAAA
1 AAAAACATTAAA
*
3699165 ACAAACATTAAA
1 AAAAACATTAAA
3699177 AAAAACA
1 AAAAACA
3699184 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAACATTAAA
Found at i:3699294 original size:22 final size:22
Alignment explanation
Indices: 3699269--3699312 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3699259 TAAGTTCTAC
* * *
3699269 AACATTCAAATAATATTAAAAA
1 AACAGTCAAAAAATAGTAAAAA
*
3699291 AACAGTGAAAAAATAGTAAAAA
1 AACAGTCAAAAAATAGTAAAAA
3699313 CGCTGTCGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (22 bp):
AACAGTCAAAAAATAGTAAAAA
Found at i:3700604 original size:59 final size:59
Alignment explanation
Indices: 3700435--3700804 Score: 321
Period size: 59 Copynumber: 6.4 Consensus size: 59
3700425 CTTTGGGAAC
* * ** * *
3700435 AAAATGGCAACTTTTGGAAAGTTCGAGGTCAAAAAT-GAAGTTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAA-TTTTTGGAAGTTTGGGGGT
* * * *
3700494 AAAATAGTAA-TTTTGGAAAAGTCGAGGTC-AAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
3700551 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * ** ** * *
3700610 AAAATGGTAATTTTTGGAAAAATTAGGGT-AAAAAAGGGTTTTTTTTAAGTTTAGGGGC
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
3700668 AAAATGGT-ATTTTTGGAAAGATCGAGGGTC-AAAATGTAATTTTTGGAAAGTTTGAGGGTT
1 AAAATGGTAATTTTTGGAAAAATC-AAGGTCAAAAATGGAATTTTTGG-AAGTTTG-GGGGT
** * * * * *
3700728 AAAAT-GTAA-TTTTGGAAAGTTTAGGGGTC-AAAATGTAATTTTTAGAAAGTTTGGGGTT
1 AAAATGGTAATTTTTGGAAAAATCA-AGGTCAAAAATGGAATTTTT-GGAAGTTTGGGGGT
3700786 AAAAT-GTAATTTTT-GAAAA
1 AAAATGGTAATTTTTGGAAAA
3700805 GTTTAGGGAT
Statistics
Matches: 264, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
57 44 0.17
58 99 0.38
59 111 0.42
60 10 0.04
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:3700701 original size:30 final size:31
Alignment explanation
Indices: 3700434--3700835 Score: 209
Period size: 29 Copynumber: 13.7 Consensus size: 31
3700424 GCTTTGGGAA
* * *
3700434 CAAAATGGCAACTTTTGGAAAGTTCGA-GGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
**
3700464 CAAAAAT-G-AAGTTTTTGG-AAG-TTTAGGGGT
1 C-AAAATGGTAA-TTTTTGGAAAGATCGA-GGGT
*
3700494 -AAAATAGTAA-TTTTGGAAA-AGTCGA-GGT
1 CAAAATGGTAATTTTTGGAAAGA-TCGAGGGT
* *
3700522 CAAAATGG-AATTTTTGG-AAGTTCGGGGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* *
3700551 -AAAATGGTAATTTTTGGAAAAATC-AAGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* * *
3700580 CAAAAATGG-AATTTTTGG-ATGTTCGGGGGT
1 C-AAAATGGTAATTTTTGGAAAGATCGAGGGT
* *
3700610 -AAAATGGTAATTTTTGGAAAAAT-TAGGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* * ** ** *
3700639 AAAAAAGGGT--TTTTT-TTAAG-TTTAGGGG
1 -CAAAATGGTAATTTTTGGAAAGATCGAGGGT
3700667 CAAAATGGT-ATTTTTGGAAAGATCGAGGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* *
3700697 CAAAAT-GTAATTTTTGGAAAGTTTGAGGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* **
3700727 TAAAAT-GTAA-TTTTGGAAAG-TTTAGGGGT
1 CAAAATGGTAATTTTTGGAAAGATCGA-GGGT
* * *
3700756 CAAAAT-GTAATTTTTAGAAAGTTTG-GGGT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGGT
* * **
3700785 TAAAAT-GTAATTTTTGAAAAG-TTTAGGGAT
1 CAAAATGGTAATTTTTGGAAAGATCGAGGG-T
3700815 CAAAAT-GTAATTTTTGGAAAG
1 CAAAATGGTAATTTTTGGAAAG
3700836 TTTAAGTGTC
Statistics
Matches: 293, Mismatches: 47, Indels: 64
0.73 0.12 0.16
Matches are distributed among these distances:
27 8 0.03
28 54 0.18
29 109 0.37
30 101 0.34
31 21 0.07
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (31 bp):
CAAAATGGTAATTTTTGGAAAGATCGAGGGT
Found at i:3700806 original size:59 final size:59
Alignment explanation
Indices: 3700693--3700838 Score: 249
Period size: 59 Copynumber: 2.5 Consensus size: 59
3700683 GAAAGATCGA
*
3700693 GGGTCAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAGTTTAG
*
3700752 GGGTCAAAATGTAATTTTTAGAAAGTTTG-GGGTTAAAATGTAATTTTTGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAA-TTTTGAAAAGTTTAG
*
3700811 GGATCAAAATGTAATTTTTGGAAAGTTT
1 GGGTCAAAATGTAATTTTTGGAAAGTTT
3700839 AAGTGTCAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
58 14 0.17
59 68 0.83
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTGAAAAGTTTAG
Found at i:3700836 original size:30 final size:29
Alignment explanation
Indices: 3700446--3700858 Score: 276
Period size: 30 Copynumber: 14.1 Consensus size: 29
3700436 AAATGGCAAC
*
3700446 TTTTGGAAAG-TTCGAGGTCAAAAATG-AAGT
1 TTTTGGAAAGTTTAG-GGTC-AAAATGTAA-T
3700476 TTTTGG-AAGTTTAGGGGT-AAAATAGTAA-
1 TTTTGGAAAGTTTA-GGGTCAAAAT-GTAAT
** *
3700504 TTTTGGAAAAGTCGA-GGTCAAAATGGAAT
1 TTTTGG-AAAGTTTAGGGTCAAAATGTAAT
**
3700533 TTTTGG-AAGTTCGGGGGT-AAAATGGTAAT
1 TTTTGGAAAGTT-TAGGGTCAAAAT-GTAAT
** * * *
3700562 TTTTGGAAAAATCAAGGTCAAAAATGGAAT
1 TTTTGGAAAGTTTAGGGTC-AAAATGTAAT
* **
3700592 TTTTGG-ATGTTCGGGGGT-AAAATGGTAAT
1 TTTTGGAAAGTT-TAGGGTCAAAAT-GTAAT
** * * **
3700621 TTTTGGAAAAATTAGGGTAAAAAAG-GGT
1 TTTTGGAAAGTTTAGGGTCAAAATGTAAT
*** *
3700649 TTTTTTTAAGTTTAGGGGCAAAATGGT-AT
1 TTTTGGAAAGTTTAGGGTCAAAAT-GTAAT
**
3700678 TTTTGGAAAGATCGAGGGTCAAAATGTAAT
1 TTTTGGAAAG-TTTAGGGTCAAAATGTAAT
*
3700708 TTTTGGAAAGTTTGAGGGTTAAAATGTAA-
1 TTTTGGAAAGTTT-AGGGTCAAAATGTAAT
3700737 TTTTGGAAAGTTTAGGGGTCAAAATGTAAT
1 TTTTGGAAAGTTTA-GGGTCAAAATGTAAT
* * *
3700767 TTTTAGAAAGTTTGGGGTTAAAATGTAAT
1 TTTTGGAAAGTTTAGGGTCAAAATGTAAT
*
3700796 TTTTGAAAAGTTTAGGGATCAAAATGTAAT
1 TTTTGGAAAGTTTAGGG-TCAAAATGTAAT
* **
3700826 TTTTGGAAAGTTTAAGTGTCAAAAAATAAT
1 TTTTGGAAAGTTT-AGGGTCAAAATGTAAT
3700856 TTT
1 TTT
3700859 CGGACAGATT
Statistics
Matches: 298, Mismatches: 58, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
27 4 0.01
28 46 0.15
29 114 0.38
30 125 0.42
31 9 0.03
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTCAAAATGTAAT
Found at i:3701315 original size:22 final size:22
Alignment explanation
Indices: 3701275--3701316 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3701265 TCGGTTCATG
*
3701275 CTCAAAACGACGCCGTTTTGGC
1 CTCAAAACGACGCCATTTTGGC
*
3701297 CTCAAAACGACGTCATTTTG
1 CTCAAAACGACGCCATTTTG
3701317 AGGGTCTTTA
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:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (22 bp):
CTCAAAACGACGCCATTTTGGC
Found at i:3702787 original size:17 final size:17
Alignment explanation
Indices: 3702761--3702849 Score: 88
Period size: 17 Copynumber: 5.2 Consensus size: 17
3702751 TTGGATTTTT
*
3702761 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
3702778 AATTTGAATTTAAAGTA
1 AATTTAAATTTAAAATA
* * *
3702795 AATTTAAACTCAAAATG
1 AATTTAAATTTAAAATA
*
3702812 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* * *
3702829 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAATA
3702846 AATT
1 AATT
3702850 AAAAAATAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:3702926 original size:21 final size:20
Alignment explanation
Indices: 3702911--3702976 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
3702901 ACAAACACAT
*
3702911 AAAAATAACATCCAAACAAC
1 AAAAATAACAACCAAACAAC
*
3702931 AAAAATAACAACCAAAATAGCAGC
1 AAAAATAACAACC--AA-A-CAAC
*
3702955 AAAAATAACAACTAAACAAC
1 AAAAATAACAACCAAACAAC
3702975 AA
1 AA
3702977 CAAAAATAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 17 0.45
21 1 0.03
22 4 0.11
23 1 0.03
24 15 0.39
ACGTcount: A:0.67, C:0.21, G:0.03, T:0.09
Consensus pattern (20 bp):
AAAAATAACAACCAAACAAC
Found at i:3702942 original size:12 final size:12
Alignment explanation
Indices: 3702925--3703023 Score: 119
Period size: 12 Copynumber: 8.3 Consensus size: 12
3702915 ATAACATCCA
3702925 AACAACAAAAAT
1 AACAACAAAAAT
*
3702937 AACAACCAAAAT
1 AACAACAAAAAT
* *
3702949 AGCAGCAAAAAT
1 AACAACAAAAAT
* *
3702961 AACAAC-TAAAC
1 AACAACAAAAAT
3702972 AACAACAAAAAT
1 AACAACAAAAAT
3702984 AACAACAAAAAT
1 AACAACAAAAAT
*
3702996 AACAGCAAAAAT
1 AACAACAAAAAT
**
3703008 TGCAACAAAAAT
1 AACAACAAAAAT
3703020 AACA
1 AACA
3703024 GTATCAAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
11 9 0.13
12 61 0.87
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:3703053 original size:22 final size:22
Alignment explanation
Indices: 3703028--3703146 Score: 134
Period size: 22 Copynumber: 5.3 Consensus size: 22
3703018 ATAACAGTAT
3703028 CAAAACAGTAAAAAAAAGCAAC
1 CAAAACAGTAAAAAAAAGCAAC
*
3703050 CAAAATAGTAAAAAAAAATAGCAAC
1 CAAAACAGT--AAAAAAA-AGCAAC
*
3703075 CAAAACAGTAAAAAAACAAC-AC
1 CAAAACAGTAAAAAAA-AGCAAC
* *
3703097 CAAAACAGTAAAAAACAGTAAC
1 CAAAACAGTAAAAAAAAGCAAC
* *
3703119 CAAAACAGTAAAAAACAG-TAC
1 CAAAACAGTAAAAAAAAGCAAC
3703140 CAAAACA
1 CAAAACA
3703147 ACAATATAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
21 10 0.12
22 45 0.53
23 9 0.11
24 7 0.08
25 14 0.16
ACGTcount: A:0.66, C:0.18, G:0.08, T:0.08
Consensus pattern (22 bp):
CAAAACAGTAAAAAAAAGCAAC
Found at i:3703065 original size:47 final size:47
Alignment explanation
Indices: 3703028--3703146 Score: 140
Period size: 47 Copynumber: 2.6 Consensus size: 47
3703018 ATAACAGTAT
* * *
3703028 CAAAACAGTAAAAAAA-AGCAACCAAAATAGTAAAAAAAAATAGCAAC
1 CAAAACAGTAAAAAAACAAC-ACCAAAACAGTAAAAAAAAACAGCAAC
*
3703075 CAAAACAGTAAAAAAACAACACCAAAACAGT---AAAAAACAGTAAC
1 CAAAACAGTAAAAAAACAACACCAAAACAGTAAAAAAAAACAGCAAC
**
3703119 CAAAACAGT-AAAAAACAGTACCAAAACA
1 CAAAACAGTAAAAAAACAACACCAAAACA
3703147 ACAATATAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 17 0.26
44 20 0.31
47 26 0.40
48 2 0.03
ACGTcount: A:0.66, C:0.18, G:0.08, T:0.08
Consensus pattern (47 bp):
CAAAACAGTAAAAAAACAACACCAAAACAGTAAAAAAAAACAGCAAC
Found at i:3703113 original size:10 final size:10
Alignment explanation
Indices: 3703098--3703138 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
3703088 AAACAACACC
3703098 AAAACAGTAA
1 AAAACAGTAA
3703108 AAAACAGTAA
1 AAAACAGTAA
3703118 CCAAAACAGTAA
1 --AAAACAGTAA
3703130 AAAACAGTA
1 AAAACAGTA
3703139 CCAAAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 19 0.66
12 10 0.34
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAACAGTAA
Found at i:3709940 original size:24 final size:24
Alignment explanation
Indices: 3709910--3710015 Score: 88
Period size: 24 Copynumber: 4.2 Consensus size: 24
3709900 TTAATTATGT
*
3709910 GTTTACGCTCGTCAGCTTGTACAC
1 GTTTACGCTCGTCAGCTTGCACAC
3709934 GTTTACGCTCG-CTAGCTTGCACAC
1 GTTTACGCTCGTC-AGCTTGCACAC
* * * *
3709958 GTTTATACGCTCGTCAACTTAGTTATAT
1 G-TT-TACGCTCGTCAGCTT-G-CACAC
* * *
3709986 ATTTACGATCGCCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTGCACAC
3710010 GTTTAC
1 GTTTAC
3710016 TCAATAACCA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
23 1 0.02
24 29 0.46
25 3 0.05
26 24 0.38
27 4 0.06
28 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTGCACAC
Found at i:3709951 original size:50 final size:49
Alignment explanation
Indices: 3709834--3709951 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 49
3709824 CATATTTATG
* * *
3709834 CGTTTACGCTCGCCAGTTTAATATGCGTTTACATTCCTCAGCTTGCACA
1 CGTTTACGCTCGCTAGCTTAATATGCGTTTACACTCCTCAGCTTGCACA
* * * * * *
3709883 CGTTTATGCT-GGTAAGCTTAATTATGTGTTTACGCTCGTCAGCTTGTACA
1 CGTTTACGCTCGCT-AGCTTAA-TATGCGTTTACACTCCTCAGCTTGCACA
3709933 CGTTTACGCTCGCTAGCTT
1 CGTTTACGCTCGCTAGCTT
3709952 GCACACGTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
48 1 0.02
49 15 0.27
50 37 0.67
51 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (49 bp):
CGTTTACGCTCGCTAGCTTAATATGCGTTTACACTCCTCAGCTTGCACA
Found at i:3710013 original size:76 final size:74
Alignment explanation
Indices: 3709873--3710015 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 74
3709863 TACATTCCTC
* * * * * *
3709873 AGCTTGCACACGTTTATGCTGGTAAGCTTAATTATGTGTTTACGCTCGTCAGCTTGTACACGTTT
1 AGCTTGCACACGTTTATGCTCGTAAGCTTAATTATATATTTACGATCGCCAGCTTGCACACGTTT
3709938 ACGCTCGCT
66 ACGCTCGCT
*
3709947 AGCTTGCACACGTTTATACGCTCGTCAA-CTTAGTTATATATTTACGATCGCCAGCTTGCACACG
1 AGCTTGCACACGTTTAT--GCTCGT-AAGCTTAATTATATATTTACGATCGCCAGCTTGCACACG
3710011 TTTAC
63 TTTAC
3710016 TCAATAACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 17 0.29
76 40 0.68
77 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (74 bp):
AGCTTGCACACGTTTATGCTCGTAAGCTTAATTATATATTTACGATCGCCAGCTTGCACACGTTT
ACGCTCGCT
Found at i:3713848 original size:18 final size:18
Alignment explanation
Indices: 3713745--3713850 Score: 79
Period size: 18 Copynumber: 5.9 Consensus size: 18
3713735 ACTTAGATCG
*
3713745 CAAAGCTGCAAGCTCATC
1 CAAAGCTGCAAGCTCATT
** *
3713763 CAAATTTGCGAGCTCATT
1 CAAAGCTGCAAGCTCATT
* * * **
3713781 CAAAGTTGCGAGCTGAAA
1 CAAAGCTGCAAGCTCATT
3713799 CATAA-CTGCAAGCTCATT
1 CA-AAGCTGCAAGCTCATT
* *
3713817 GAAAGCTACAAGCTCATT
1 CAAAGCTGCAAGCTCATT
* *
3713835 CAAAGTTGCGAGCTCA
1 CAAAGCTGCAAGCTCA
3713851 CGAAACATGC
Statistics
Matches: 67, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
17 2 0.03
18 63 0.94
19 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (18 bp):
CAAAGCTGCAAGCTCATT
Found at i:3713849 original size:36 final size:35
Alignment explanation
Indices: 3713745--3713850 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 35
3713735 ACTTAGATCG
*
3713745 CAAAGCTGCAAGCTCATCCAAATTTGCGAGCTCATT
1 CAAAGCTGCAAGCTCATACAAA-TTGCGAGCTCATT
* * * * * *
3713781 CAAAGTTGCGAGCTGAAACATAACTGCAAGCTCATT
1 CAAAGCTGCAAGCTCATACA-AATTGCGAGCTCATT
* * *
3713817 GAAAGCTACAAGCTCATTCAAAGTTGCGAGCTCA
1 CAAAGCTGCAAGCTCATACAAA-TTGCGAGCTCA
3713851 CGAAACATGC
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
35 2 0.04
36 48 0.92
37 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (35 bp):
CAAAGCTGCAAGCTCATACAAATTGCGAGCTCATT
Found at i:3722278 original size:58 final size:58
Alignment explanation
Indices: 3722207--3722325 Score: 204
Period size: 58 Copynumber: 2.1 Consensus size: 58
3722197 CCAAAACCCT
* *
3722207 AAAATTAACCTAAAAATAATAATAA-ATAATTCTTTAAAATATTTAAATTAAATCATAA
1 AAAAATAACCTAAAAATAATAA-AAGATAATTCTTGAAAATATTTAAATTAAATCATAA
3722265 AAAAATAACCTAAAAATAATAAAAGATAATTCTTGAAAATATTTAAATTAAATCATAA
1 AAAAATAACCTAAAAATAATAAAAGATAATTCTTGAAAATATTTAAATTAAATCATAA
3722323 AAA
1 AAA
3722326 CAAAAGATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 2 0.03
58 56 0.97
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (58 bp):
AAAAATAACCTAAAAATAATAAAAGATAATTCTTGAAAATATTTAAATTAAATCATAA
Found at i:3723194 original size:10 final size:10
Alignment explanation
Indices: 3723170--3723211 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
3723160 AGCAACCATG
3723170 TTTTTTTCT-
1 TTTTTTTCTC
*
3723179 TCTTTTTCTC
1 TTTTTTTCTC
3723189 TTTTTTT-TC
1 TTTTTTTCTC
*
3723198 TTTTTTTTTC
1 TTTTTTTCTC
3723208 TTTT
1 TTTT
3723212 CGAACCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 17 0.59
10 12 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:3723203 original size:9 final size:9
Alignment explanation
Indices: 3723170--3723211 Score: 57
Period size: 10 Copynumber: 4.3 Consensus size: 9
3723160 AGCAACCATG
3723170 TTTTTTTCT
1 TTTTTTTCT
3723179 TCTTTTTCTCT
1 T-TTTTT-TCT
3723190 TTTTTTTCTT
1 TTTTTTTC-T
3723200 TTTTTTTCT
1 TTTTTTTCT
3723209 TTT
1 TTT
3723212 CGAACCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.23
10 19 0.63
11 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:3732181 original size:13 final size:13
Alignment explanation
Indices: 3732163--3732189 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3732153 GATAAAAACT
3732163 TACATCATTATGA
1 TACATCATTATGA
3732176 TACATCATTATGA
1 TACATCATTATGA
3732189 T
1 T
3732190 GAGTGAAATG
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TACATCATTATGA
Found at i:3734297 original size:26 final size:25
Alignment explanation
Indices: 3734247--3734297 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
3734237 ATATTTAAGT
*
3734247 TTTTAAAATATTTTATGTATCATTAA
1 TTTTAAAATAATTTATGTA-CATTAA
3734273 TTTTACAAATAATTTATAGTA-ATTA
1 TTTTA-AAATAATTTAT-GTACATTA
3734298 CTTAGAAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
TTTTAAAATAATTTATGTACATTAA
Found at i:3737589 original size:19 final size:19
Alignment explanation
Indices: 3737562--3737598 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3737552 GCTTCTGTTT
* *
3737562 TGTTTCAAAACAAAATGAA
1 TGTTGCAAAAAAAAATGAA
3737581 TGTTGCAAAAAAAAATGA
1 TGTTGCAAAAAAAAATGA
3737599 TAGAACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (19 bp):
TGTTGCAAAAAAAAATGAA
Found at i:3748691 original size:30 final size:29
Alignment explanation
Indices: 3748651--3748961 Score: 196
Period size: 30 Copynumber: 10.4 Consensus size: 29
3748641 TATGGAATAC
3748651 GGGGTCAAAATGTAATTTTGAAAAAGTTT
1 GGGGTCAAAATGTAATTTTGAAAAAGTTT
* * **
3748680 AGGGGTAAAAATGTGATTTTGGGAAAGTTT
1 -GGGGTCAAAATGTAATTTTGAAAAAGTTT
* * * *
3748710 GGGGTTAAAATATGATTTT-AGAGAAGTTT
1 GGGGTCAAAATGTAATTTTGA-AAAAGTTT
* *
3748739 AGGGGTCAAAATGTGATTTTTGAGAAA-TTT
1 -GGGGTCAAAATGT-AATTTTGAAAAAGTTT
* * * * *
3748769 GAAGGTTAAAATATACTTTTGGAAAAGTTT
1 G-GGGTCAAAATGTAATTTTGAAAAAGTTT
* *
3748799 AGGGGTCAAAATGAAATTTT-AGAGAAGTTT
1 -GGGGTCAAAATGTAATTTTGA-AAAAGTTT
* * * *
3748829 GAGGGTCAAAATGCAATTTTGGATAGGTTT
1 G-GGGTCAAAATGTAATTTTGAAAAAGTTT
* * * *
3748859 GAGGGTCAAAATGTAATTTTGGAAAGGATG
1 G-GGGTCAAAATGTAATTTTGAAAAAGTTT
* * * * *
3748889 GGGAGTTAAAATGTGATTTTGGAGAAGTTC
1 GGG-GTCAAAATGTAATTTTGAAAAAGTTT
* *
3748919 GAGGGTCAAAATATAATTTTTGGAAAAGTTT
1 G-GGGTCAAAATGTAA-TTTTGAAAAAGTTT
3748950 GGAGGTCAAAAT
1 GG-GGTCAAAAT
3748962 ATGATTTTTA
Statistics
Matches: 220, Mismatches: 47, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
29 36 0.16
30 152 0.69
31 31 0.14
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGAAAAAGTTT
Found at i:3748797 original size:60 final size:60
Alignment explanation
Indices: 3748652--3748944 Score: 240
Period size: 60 Copynumber: 4.9 Consensus size: 60
3748642 ATGGAATACG
* * * * * *
3748652 GGGTCAAAATGTAATTTTGAAAAAGTTTAGGGGTAAAAATGTGA-TTTTGGGAAAGTTTG-
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTGAGAAA-TTTGA
* * * *
3748711 GGGTTAAAATATGATTTTAGAGAAGTTTAGGGGTCAAAATGTGATTTTTGAGAAATTTGA
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTGAGAAATTTGA
* * * * *
3748771 AGGTTAAAATATACTTTTGGAAAAGTTTAGGGGTCAAAATGAAATTTTAGAGAAGTTTGA
1 GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTGAGAAATTTGA
* ** * * ** *
3748831 GGGTCAAAATGCAATTTTGGATAGGTTT-GAGGGTCAAAATGTAA-TTTTG-GAAAGGATGG
1 GGGTTAAAATATAATTTTGGAAAAGTTTAG-GGGTCAAAATGTAATTTTTGAGAAA-TTTGA
* * * * *
3748890 GGAGTTAAAATGTGATTTTGGAGAAG-TTCGAGGGTCAAAATATAATTTTTG-GAAA
1 GG-GTTAAAATATAATTTTGGAAAAGTTTAG-GGGTCAAAATGTAATTTTTGAGAAA
3748945 AGTTTGGAGG
Statistics
Matches: 191, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
58 3 0.02
59 52 0.27
60 127 0.66
61 9 0.05
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (60 bp):
GGGTTAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTGAGAAATTTGA
Found at i:3748848 original size:90 final size:88
Alignment explanation
Indices: 3748652--3748969 Score: 277
Period size: 90 Copynumber: 3.5 Consensus size: 88
3748642 ATGGAATACG
* * * * *
3748652 GGGTCAAAATGTAA-TTTTGAAAAAGTTT-AGGGGTAAAAATGTGATTTTGGGAAAGTTTGGGGT
1 GGGTCAAAATGTAATTTTTGAGAAA-TTTGA-AGGTCAAAATATAATTTT-GGAAAGTTTGGGGT
3748715 TAAAAT-ATGATTTTAGAGAAGTTT-A
63 TAAAATGA-GATTTTAGAGAAGTTTGA
* * *
3748740 GGGGTCAAAATGTGATTTTTGAGAAATTTGAAGGTTAAAATATACTTTTGGAAAAGTTTAGGGGT
1 -GGGTCAAAATGTAATTTTTGAGAAATTTGAAGGTCAAAATATAATTTTGG-AAAGTTT-GGGGT
* *
3748805 CAAAATGAAATTTTAGAGAAGTTTGA
63 TAAAATGAGATTTTAGAGAAGTTTGA
* * * ** * * * *
3748831 GGGTCAAAATGCAATTTTGGATAGGTTTGAGGGTCAAAATGTAATTTTGGAAAGGATGGGGAGTT
1 GGGTCAAAATGTAATTTTTGAGAAATTTGAAGGTCAAAATATAATTTTGGAAA-GTTTGGG-GTT
* * *
3748896 AAAATGTGATTTTGGAGAAGTTCGA
64 AAAATGAGATTTTAGAGAAGTTTGA
* * *
3748921 GGGTCAAAATATAATTTTTG-GAAAAGTTTGGAGGTCAAAATATGATTTT
1 GGGTCAAAATGTAATTTTTGAG-AAA-TTTGAAGGTCAAAATATAATTTT
3748970 TAAATAAAAC
Statistics
Matches: 183, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
88 2 0.01
89 42 0.23
90 118 0.64
91 21 0.11
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (88 bp):
GGGTCAAAATGTAATTTTTGAGAAATTTGAAGGTCAAAATATAATTTTGGAAAGTTTGGGGTTAA
AATGAGATTTTAGAGAAGTTTGA
Found at i:3751243 original size:17 final size:17
Alignment explanation
Indices: 3751221--3751279 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
3751211 AAGAATATGA
3751221 AAGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
3751238 AAGGTTAAAGGTTAAG--GG
1 AAGGTT-AAGG--AAGATGG
3751256 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
3751272 AAGGTTAA
1 AAGGTTAA
3751280 AAGTCAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.08
16 6 0.17
17 18 0.50
18 6 0.17
20 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:3751265 original size:34 final size:34
Alignment explanation
Indices: 3751222--3751291 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
3751212 AGAATATGAA
* *
3751222 AGGTTAAGGAAGATGGAAGGTTAAAGGTTAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
3751256 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
3751290 AG
1 AG
3751292 ATGAAAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.40, C:0.01, G:0.40, T:0.19
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
Found at i:3755506 original size:12 final size:12
Alignment explanation
Indices: 3755489--3755527 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3755479 CCTCGATCGC
3755489 GACCACGACCAT
1 GACCACGACCAT
*
3755501 GACCACGGCCAT
1 GACCACGACCAT
* *
3755513 GTCCTCGACCAT
1 GACCACGACCAT
3755525 GAC
1 GAC
3755528 TACTAGTGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.41, G:0.21, T:0.13
Consensus pattern (12 bp):
GACCACGACCAT
Found at i:3758125 original size:10 final size:10
Alignment explanation
Indices: 3758091--3758170 Score: 51
Period size: 10 Copynumber: 8.0 Consensus size: 10
3758081 TAAAAAAAAT
3758091 TTTAAAATT-
1 TTTAAAATTA
*
3758100 TCTAAAATTA
1 TTTAAAATTA
**
3758110 AATAAAATTA
1 TTTAAAATTA
3758120 TTTAAAAATTA
1 TTT-AAAATTA
3758131 -TT-AAATT-
1 TTTAAAATTA
*
3758138 TTAATAAAAATA
1 TT--TAAAATTA
3758150 TTTTAAAATTA
1 -TTTAAAATTA
*
3758161 TTAAAAATTA
1 TTTAAAATTA
3758171 CATTCAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.11
9 8 0.15
10 21 0.38
11 18 0.33
13 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:3758135 original size:20 final size:19
Alignment explanation
Indices: 3758085--3758170 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
3758075 AATACCTAAA
*
3758085 AAAAATT-TTAAAATTTCT
1 AAAAATTATTAAAATTTTT
*
3758103 -AAAATTAAATAAAATTATTT
1 AAAAATT-ATTAAAATT-TTT
3758123 AAAAATTATT-AAATTTTAAT
1 AAAAATTATTAAAATTTT--T
* *
3758143 AAAAATATTTTAAAATTATT
1 AAAAAT-TATTAAAATTTTT
3758163 AAAAATTA
1 AAAAATTA
3758171 CATTCAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 13 0.24
20 18 0.33
21 9 0.17
22 6 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTATTAAAATTTTT
Found at i:3765020 original size:30 final size:30
Alignment explanation
Indices: 3764986--3765049 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
3764976 TTTTTTTCTA
3764986 CCAAAACGTCACTTACCTCTATGTTTTCAC
1 CCAAAACGTCACTTACCTCTATGTTTTCAC
*
3765016 CCAAAACGTCACTTACCTTTATGTTTTCAC
1 CCAAAACGTCACTTACCTCTATGTTTTCAC
3765046 CCAA
1 CCAA
3765050 TTTTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.33
Consensus pattern (30 bp):
CCAAAACGTCACTTACCTCTATGTTTTCAC
Found at i:3765815 original size:22 final size:22
Alignment explanation
Indices: 3765776--3765846 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
3765766 CTCTCCGTTA
* *
3765776 TTTAGCACGTATTGTGCTTTCTG
1 TTTAGCACGT-TTGTGCTCTCCG
3765799 TTTAGCACGTTTGTGCTCTCCG
1 TTTAGCACGTTTGTGCTCTCCG
* *
3765821 TTTAGCACCTTGGTGCTCTCCG
1 TTTAGCACGTTTGTGCTCTCCG
3765843 TTTA
1 TTTA
3765847 TTTGTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 34 0.77
23 10 0.23
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (22 bp):
TTTAGCACGTTTGTGCTCTCCG
Found at i:3770599 original size:15 final size:15
Alignment explanation
Indices: 3770581--3770623 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3770571 ACAAGAGCAG
*
3770581 CATCAATAGGGTCAA
1 CATCAATAGGATCAA
* *
3770596 CATCAACAAGATCAA
1 CATCAATAGGATCAA
3770611 CATCAATAGGATC
1 CATCAATAGGATC
3770624 TGGAGCTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (15 bp):
CATCAATAGGATCAA
Found at i:3776765 original size:23 final size:23
Alignment explanation
Indices: 3776739--3776789 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
3776729 AATTAATTAT
3776739 ATGTTATCTTCGTGACTTAAAGC
1 ATGTTATCTTCGTGACTTAAAGC
3776762 ATGTTATCTTCGTGACTTAAAGC
1 ATGTTATCTTCGTGACTTAAAGC
3776785 ATGTT
1 ATGTT
3776790 TGTTTATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (23 bp):
ATGTTATCTTCGTGACTTAAAGC
Found at i:3781118 original size:24 final size:24
Alignment explanation
Indices: 3781090--3781140 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3781080 AGGTTGACTC
3781090 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
*
3781114 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
3781138 AAA
1 AAA
3781141 GATTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:3785898 original size:23 final size:23
Alignment explanation
Indices: 3785866--3785909 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3785856 TCTGCCATTT
3785866 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
3785889 TCTAACTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
3785910 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:3785902 original size:13 final size:11
Alignment explanation
Indices: 3785870--3785912 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3785860 CCATTTTCTA
*
3785870 AATAAAATAAT
1 AATAAAATATT
3785881 AAT-AAATATCT
1 AATAAAATAT-T
3785892 AACTAAAATATT
1 AA-TAAAATATT
3785904 AATAAAATA
1 AATAAAATA
3785913 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:3787087 original size:13 final size:13
Alignment explanation
Indices: 3787056--3787098 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3787046 TATATTAGGT
3787056 ATAATAA-A-TAA
1 ATAATAATATTAA
3787067 ATAA-AATATTAA
1 ATAATAATATTAA
*
3787079 TTAATAATATTAA
1 ATAATAATATTAA
3787092 ATAATAA
1 ATAATAA
3787099 AAAGAGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.07
11 5 0.19
12 6 0.22
13 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAATATTAA
Found at i:3788188 original size:29 final size:29
Alignment explanation
Indices: 3788131--3788412 Score: 287
Period size: 30 Copynumber: 9.6 Consensus size: 29
3788121 AACTTTCAAG
* *
3788131 AAATCACATTTTGACCCCTAAACTTTTCTA
1 AAATTACATTTT-AACCCTAAACTTTTCTA
3788161 AAATTACATTTTAACCCTAAA-TTATTCTA
1 AAATTACATTTTAACCCTAAACTT-TTCTA
*
3788190 AAATTACATTTTAACTCCTAAACTTTTCCA
1 AAATTACATTTTAAC-CCTAAACTTTTCTA
*
3788220 AAATTACATTTTAACCCCTAAACTTTTCCA
1 AAATTACATTTTAA-CCCTAAACTTTTCTA
* * ** *
3788250 TAATTAGATTTTAATTCTAAACTTTTCCA
1 AAATTACATTTTAACCCTAAACTTTTCTA
* *
3788279 AAATTATATTTTAACCCTTAAACTTCTCTA
1 AAATTACATTTTAACCC-TAAACTTTTCTA
* * *
3788309 AAATTACATTTTAACCTTAAACTTCTCCA
1 AAATTACATTTTAACCCTAAACTTTTCTA
** * ** * *
3788338 AAATGGCATTTTGACCCCGAGCTTTCCTA
1 AAATTACATTTTAACCCTAAACTTTTCTA
*
3788367 AAATTACATTTTACCCCTAAACTTTTTCTA
1 AAATTACATTTTAACCCTAAAC-TTTTCTA
**
3788397 AAATTATGTTTTAACC
1 AAATTACATTTTAACC
3788413 TTGTATTCTC
Statistics
Matches: 209, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.01
29 99 0.47
30 105 0.50
31 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTAACCCTAAACTTTTCTA
Found at i:3788228 original size:59 final size:59
Alignment explanation
Indices: 3788131--3788412 Score: 293
Period size: 59 Copynumber: 4.8 Consensus size: 59
3788121 AACTTTCAAG
* * *
3788131 AAATCACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCCTAAA-TTATTCTA
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAACTT-TTCTA
* *
3788190 AAATTACATTTTAACTCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCA
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAA-CCCTAAACTTTTCTA
* * ** * *
3788250 TAATTAGATTTTAA-TTCTAAACTTTTCCAAAATTATATTTTAACCCTTAAACTTCTCTA
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCC-TAAACTTTTCTA
* * ** * ** * *
3788309 AAATTACATTTTAA-CCTTAAACTTCTCCAAAATGGCATTTTGACCCCGAGCTTTCCTA
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCTA
* **
3788367 AAATTACATTTT-ACCCCTAAACTTTTTCTAAAATTATGTTTTAACC
1 AAATTACATTTTAACCCCTAAAC-TTTTCCAAAATTACATTTTAACC
3788413 TTGTATTCTC
Statistics
Matches: 184, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
57 1 0.01
58 29 0.16
59 129 0.70
60 23 0.12
61 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCTA
Found at i:3788282 original size:89 final size:89
Alignment explanation
Indices: 3788131--3788390 Score: 269
Period size: 89 Copynumber: 2.9 Consensus size: 89
3788121 AACTTTCAAG
* * * *
3788131 AAATCACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCCTAAATTATTCTAAAATTA
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAATTATTCCAAAATTA
*
3788196 CATTTTAACTCC-TAAACTTTTCCA
66 CATTTTAAC-CCTTAAACTTCTCCA
* * **
3788220 AAATTACATTTTAACCCCTAAACTTTTCCATAATTAGATTTTAATTCTAAACTT-TTCCAAAATT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAA-TTATTCCAAAATT
* *
3788284 ATATTTTAACCCTTAAACTTCTCTA
65 ACATTTTAACCCTTAAACTTCTCCA
* * ** * ** **
3788309 AAATTACATTTTAA-CCTTAAACTTCTCCAAAATGGCATTTTGACCCCGAGCT-TTCCTAAAATT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAATTATTCC-AAAATT
*
3788372 ACATTTT-ACCCCTAAACTT
65 ACATTTTAACCCTTAAACTT
3788391 TTTCTAAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
87 16 0.11
88 38 0.27
89 86 0.61
90 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (89 bp):
AAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAATTATTCCAAAATTA
CATTTTAACCCTTAAACTTCTCCA
Found at i:3799710 original size:39 final size:39
Alignment explanation
Indices: 3799607--3800094 Score: 365
Period size: 39 Copynumber: 12.5 Consensus size: 39
3799597 AATTGAAGAT
* *
3799607 TCCAATCTCTTACCCCGATCATGGGGCAGATCA-CAGTCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCA
* * * **
3799646 TCCGATCTTTTACGCCGAGTTTGGGGCAGATCACCATCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* * * *
3799685 GCCAATCTCTTACCCCGATCATGGGGCAGATCA-CAGTAA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCA
* * *
3799724 TCCAATCTTTTACCCCGAGCCTAGAGCA-AGTCACCATCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGA-TCACCATCA
* * * ** * ** * *
3799763 GCCAATCTCTTATCCTGAGCCTAAGGCAAATTGCAACCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* * *
3799802 TCCGATCTCTTACCTCGAGCCTGGGGCAGATCGCCATCAA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATC-A
** * ** * *
3799842 T-CAATCTCTTACCCTAAGCCTGGGGTAGATTGCAACCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* * *
3799880 TTCGATCTCTTACCCCGAG-CTAGGGGCAGATCACCATTA
1 TCCAATCTCTTACCCCGAGCCT-GGGGCAGATCACCATCA
* * * ** * *
3799919 ACCAATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* *
3799958 TCCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* * *** * * * *
3799997 GCCAATCTCTTACCTCGAGCCAAAGGTAGATTACAACCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* *
3800036 TCCGATCTCTTACCCCGAGCCTGGGGTAGATCACCATCA
1 TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
* *
3800075 GCCAATCTCTTACCTCGAGC
1 TCCAATCTCTTACCCCGAGC
3800095 TTGAGAAAGA
Statistics
Matches: 341, Mismatches: 99, Indels: 18
0.74 0.22 0.04
Matches are distributed among these distances:
38 7 0.02
39 326 0.96
40 8 0.02
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.24
Consensus pattern (39 bp):
TCCAATCTCTTACCCCGAGCCTGGGGCAGATCACCATCA
Found at i:3799742 original size:78 final size:78
Alignment explanation
Indices: 3799608--3800204 Score: 554
Period size: 78 Copynumber: 7.7 Consensus size: 78
3799598 ATTGAAGATT
* ** ** * * *
3799608 CCAATCTCTTACCCCGATCATGGGGCAGATCACAGTCATCCGATCTTTTACGCCGAGTTTGGGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
3799673 AGATCACCATCAG
66 AGATCACCATCAG
* ** *** * * * * *
3799686 CCAATCTCTTACCCCGATCATGGGGCAGATCACAGTAATCCAATCTTTTACCCCGAGCCTAGAGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
3799751 A-AGTCACCATCAG
66 AGA-TCACCATCAG
* * * ** * * *
3799764 CCAATCTCTTATCCTGAGCCTAAGGCAAATTGCAACCATCCGATCTCTTACCTCGAGCCTGGGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
* *
3799829 AGATCGCCATCAA
66 AGATCACCATCAG
* ** * * * *
3799842 TCAATCTCTTACCCTAAGCCTGGGGTAGATTGCAACCATTCGATCTCTTACCCCGAGCTAGGGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
* *
3799907 AGATCACCATTAA
66 AGATCACCATCAG
* *
3799920 CCAATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
3799985 AGATCACCATCAG
66 AGATCACCATCAG
* ** * * *
3799998 CCAATCTCTTACCTCGAGCCA-AAGGTAGATTACAACCATCCGATCTCTTACCCCGAGCCTGGGG
1 CCAATCTCTTACCCCGAG-CATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGG
*
3800062 TAGATCACCATCAG
65 CAGATCACCATCAG
* * * ** **** **
3800076 CCAATCTCTTACCTCGAGCTTGAGAAAGATTGCAGTTGTCCGATCTCTTACCCCGAGCTTGGGAA
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
3800141 AGATCACCATCAG
66 AGATCACCATCAG
* * * * * *
3800154 CCAATTTTTTGCCCCGAGCCA-AGGGCA-AGTTGCAACCATCCAATATCTTAC
1 CCAATCTCTTACCCCGAG-CATGGGGCAGA-TTGCAACCATCCGATCTCTTAC
3800205 AAAAAAAATC
Statistics
Matches: 430, Mismatches: 83, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
77 3 0.01
78 424 0.99
79 3 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (78 bp):
CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTCTTACCCCGAGCTTGGGGC
AGATCACCATCAG
Found at i:3802529 original size:28 final size:29
Alignment explanation
Indices: 3802414--3802658 Score: 167
Period size: 29 Copynumber: 8.4 Consensus size: 29
3802404 TTTTCCAAAT
* *
3802414 TTTTCTAAAATTACATTTTAACCCTAAAT
1 TTTTCTAAAATTACATTTTGACCCTAAAC
*
3802443 TTTTCCAAAATTACATTTTGACTCCTAAAC
1 TTTTCTAAAATTACATTTTGAC-CCTAAAC
* * *
3802473 TTCTCTAAAATTGCA--TTAACCCCTAAAC
1 TTTTCTAAAATTACATTTTGA-CCCTAAAC
* *
3802501 TTTTCTAAAATTATATTTTGA-CCTTAAC
1 TTTTCTAAAATTACATTTTGACCCTAAAC
* **
3802529 TTCTCTAAAATCGCATTTTGACTCC-AAAC
1 TTTTCTAAAATTACATTTTGAC-CCTAAAC
** * * * * *
3802558 ACTACCAAGATTACGTTTTGACCCCAAAC
1 TTTTCTAAAATTACATTTTGACCCTAAAC
* * * * ** *
3802587 TTCTCCAAAATCATATTTTGACCCCGAGC
1 TTTTCTAAAATTACATTTTGACCCTAAAC
* *
3802616 TTTCCCAAAATTACATTTT-ACCCCTAAAC
1 TTTTCTAAAATTACATTTTGA-CCCTAAAC
3802645 TTTTTCTAAAATTA
1 -TTTTCTAAAATTA
3802659 TGTTTTAACC
Statistics
Matches: 162, Mismatches: 45, Indels: 17
0.72 0.20 0.08
Matches are distributed among these distances:
28 48 0.30
29 80 0.49
30 34 0.21
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTTCTAAAATTACATTTTGACCCTAAAC
Found at i:3805602 original size:22 final size:20
Alignment explanation
Indices: 3805569--3805608 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3805559 AATATATTGC
3805569 CTTTTTTTTTTCTTTCCCGG
1 CTTTTTTTTTTCTTTCCCGG
3805589 CTTTCTTTTCTTTCTTTCCC
1 CTTT-TTTT-TTTCTTTCCC
3805609 TCATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (20 bp):
CTTTTTTTTTTCTTTCCCGG
Found at i:3813488 original size:14 final size:14
Alignment explanation
Indices: 3813469--3813510 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
3813459 AAGTTAACGG
3813469 AAGATTGAATTGTT
1 AAGATTGAATTGTT
* *
3813483 AAGATTG-GTTGTA
1 AAGATTGAATTGTT
3813496 AAGATATGAATTGTT
1 AAGAT-TGAATTGTT
3813511 GTTTAAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (14 bp):
AAGATTGAATTGTT
Found at i:3815197 original size:31 final size:32
Alignment explanation
Indices: 3815161--3815238 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
3815151 TTTTGCCGTC
*
3815161 CATATTATTTTTATTTTTAT-TTTAA-AATATT
1 CATATTATTTTTATTTTAATATTTAATAAT-TT
* *
3815192 TATATTA-TATTATTTTAATATTTAATAATTT
1 CATATTATTTTTATTTTAATATTTAATAATTT
3815223 CATA-TATTTTTTATTT
1 CATATTA-TTTTTATTT
3815239 ATTGAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 12 0.32
31 16 0.42
32 10 0.26
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
CATATTATTTTTATTTTAATATTTAATAATTT
Found at i:3830157 original size:41 final size:41
Alignment explanation
Indices: 3830103--3830210 Score: 146
Period size: 41 Copynumber: 2.6 Consensus size: 41
3830093 GCTTATGAAA
* ** * *
3830103 AAAGTGCCGCTAATGACATGACCTTTAGCGGCGCTT-ATTGG
1 AAAGCGCCGCTAATGACCCGACCTTTAGCGGCACTTGA-GGG
3830144 AAAGCGCCGCTAATGACCCGACCTTTAGCGGCACTTGAGGG
1 AAAGCGCCGCTAATGACCCGACCTTTAGCGGCACTTGAGGG
*
3830185 AAAGCACCGCTAATGACCCGACCTTT
1 AAAGCGCCGCTAATGACCCGACCTTT
3830211 CTATTGCTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 59 0.98
42 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (41 bp):
AAAGCGCCGCTAATGACCCGACCTTTAGCGGCACTTGAGGG
Found at i:3831835 original size:4 final size:4
Alignment explanation
Indices: 3831826--3831875 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
3831816 CCCAGCAAGG
* *
3831826 TACA TACA TACA AACCA TACA TGCA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TA-CA TACA TACA TACA TACA TACA TACA TACA TACA
3831875 T
1 T
3831876 GTATATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:3856926 original size:35 final size:35
Alignment explanation
Indices: 3856850--3856951 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 35
3856840 ACTCCACTAG
* * *
3856850 ATCTTC-AGCCTCATCTTCATGTTCACGTCGGGGTTG
1 ATCTTCGA-CCTCATCTTCATGTGCAAGTC-GGGTTA
*
3856886 ATCTTCGATCTCATCTTCATGTGCAAGTCGGGTTA
1 ATCTTCGACCTCATCTTCATGTGCAAGTCGGGTTA
* * *
3856921 ATCTTCGGCCTCGTCTTCATGTGCATGTCGG
1 ATCTTCGACCTCATCTTCATGTGCAAGTCGG
3856952 AGTTGATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 32 0.56
36 24 0.42
37 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (35 bp):
ATCTTCGACCTCATCTTCATGTGCAAGTCGGGTTA
Found at i:3857267 original size:62 final size:63
Alignment explanation
Indices: 3857196--3857314 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
3857186 TGTGGAAAAG
* * *
3857196 GTGTCGATGCAAGAAATGATTATG-GTGTTGTGGTGCTT-GTGTAAAATAAATTGGTGATTACT
1 GTGTCGATGCAAGAAATGAATACGCGTGTTGTGGTG-TTAGTGTAAAATAAACTGGTGATTACT
* ** *
3857258 GTGTTGATGCTGGAAATGAATGCGCGTGTTGTGGTGTTAGTGTAAAATAAACTGGTG
1 GTGTCGATGCAAGAAATGAATACGCGTGTTGTGGTGTTAGTGTAAAATAAACTGGTG
3857315 CGTCTTGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 20 0.42
63 28 0.58
ACGTcount: A:0.26, C:0.07, G:0.32, T:0.35
Consensus pattern (63 bp):
GTGTCGATGCAAGAAATGAATACGCGTGTTGTGGTGTTAGTGTAAAATAAACTGGTGATTACT
Found at i:3858504 original size:19 final size:20
Alignment explanation
Indices: 3858440--3858513 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
3858430 CTTTTCGATA
* *
3858440 AAAAATTCAAGATAATTTTC
1 AAAAATTCAAAATAATTTTT
*
3858460 AAAAATTCAAAATAAATTTT
1 AAAAATTCAAAATAATTTTT
* *
3858480 -AGAATTCAAAAT-GTTTTT
1 AAAAATTCAAAATAATTTTT
3858498 AAAAATT-AAAA-AATTT
1 AAAAATTCAAAATAATTT
3858514 ATATATTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.25
19 16 0.36
20 17 0.39
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:3858826 original size:21 final size:21
Alignment explanation
Indices: 3858781--3858826 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3858771 ATTCGATCCG
* *
3858781 ATTTGACTCAACTCGAGTTTT
1 ATTTCACTCAACTCGAGTTTA
3858802 ATTTCACTCAACTCGA-TTTGA
1 ATTTCACTCAACTCGAGTTT-A
3858823 ATTT
1 ATTT
3858827 TTTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (21 bp):
ATTTCACTCAACTCGAGTTTA
Found at i:3859276 original size:11 final size:11
Alignment explanation
Indices: 3859260--3859318 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 11
3859250 AAAAATTAGC
*
3859260 TATTAAATTAA
1 TATTAAATAAA
3859271 TATTAAATCAAA
1 TATTAAAT-AAA
*
3859283 TTTTAATATAAA
1 TATTAA-ATAAA
* *
3859295 TTTTAAATTAA
1 TATTAAATAAA
3859306 -ATTAAA-AAA
1 TATTAAATAAA
3859315 TATT
1 TATT
3859319 TTTTCAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 2 0.05
10 8 0.20
11 12 0.30
12 16 0.40
13 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATAAA
Found at i:3859542 original size:32 final size:32
Alignment explanation
Indices: 3859506--3859567 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
3859496 AAAACATTCT
* *
3859506 ATTTTTTAATT-ATAATTTTTAAAACTTTTAGG
1 ATTTTTTAATTGA-AATTATAAAAACTTTTAGG
*
3859538 ATTTTTTTATTGAAATTATAAAAACTTTTA
1 ATTTTTTAATTGAAATTATAAAAACTTTTA
3859568 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (32 bp):
ATTTTTTAATTGAAATTATAAAAACTTTTAGG
Found at i:3869759 original size:70 final size:67
Alignment explanation
Indices: 3869633--3869765 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 67
3869623 ATAAACAATA
* *
3869633 TAATGGTTTTACCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTACCTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
3869698 CT
66 CT
* * *
3869700 TAATGGTTTTGA-CTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTATCTT
1 TAATGGTTTT-ACCTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTT
3869764 TT
62 TT
3869766 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
67 18 0.32
68 3 0.05
70 36 0.63
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTACCTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:3872947 original size:6 final size:6
Alignment explanation
Indices: 3872936--3872966 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3872926 GGTGAAATTA
*
3872936 TGGTTT TGGTTT TGGTTT TGTTTT TGGTTT T
1 TGGTTT TGGTTT TGGTTT TGGTTT TGGTTT T
3872967 AAAACAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TGGTTT
Found at i:3873105 original size:182 final size:183
Alignment explanation
Indices: 3872589--3873497 Score: 1525
Period size: 183 Copynumber: 5.1 Consensus size: 183
3872579 AAATTACGAA
* * * *
3872589 TGTTTTGGTTTTAAAACAAGTTAAATGTTGTTCAGATCAGTTTTTAGCGGTTTAAGATAAAAAAA
1 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
3872654 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTTCTTGGTTTCACATTTG
66 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTTCTTGGTTTCACATTTG
*
3872719 CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGTTTTTT
131 CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
3872772 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
1 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
*
3872837 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAAGTTCTTGGTTTCACGTTT
66 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATC-AAGTTCTTGGTTTCACATTT
* *
3872902 GCTTTTATTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTG
130 GCTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
3872956 T-TTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
1 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
*
3873020 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTACTTGGTTTCACATTTG
66 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTTCTTGGTTTCACATTTG
3873085 CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTT-GTTTTT
131 CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
3873137 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
1 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
3873202 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAA-------G-TT--C--TTG
66 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTTCTTGGTTTCACATTTG
*
3873255 -----GTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGTTTTTT
131 CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
* * *
3873303 TGTTTTGGTTTTTAAATAAGTTAAACGTTGTTCAAACCAGTTTTTAGAGGTTTAAGACAAAAAAA
1 TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
*
3873368 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAAGTTCTTGGTTTCACGTTT
66 AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATC-AAGTTCTTGGTTTCACATTT
*
3873433 GCTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTG
130 GCTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
3873487 T-TTTTGGTTTT
1 TGTTTTGGTTTT
3873498 TTTGAATTAT
Statistics
Matches: 687, Mismatches: 18, Indels: 42
0.92 0.02 0.06
Matches are distributed among these distances:
165 41 0.06
166 111 0.16
167 2 0.00
170 3 0.00
172 1 0.00
174 3 0.00
175 3 0.00
177 1 0.00
179 3 0.00
181 6 0.01
182 173 0.25
183 222 0.32
184 118 0.17
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (183 bp):
TGTTTTGGTTTTAAAACAAGTTAAACGTTGTTCAGACCAGTTTTTAGAGGTTTAAGACAAAAAAA
AGCTTTTAGTTGACCGACACAAATTTGAATCAATTATGACAATCAAGTTCTTGGTTTCACATTTG
CTTTTGTTTGCCTGTCTTGTTTCGGTGAAATTATGGTTTTGGTTTTGGTTTTT
Found at i:3873478 original size:6 final size:6
Alignment explanation
Indices: 3873467--3873497 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3873457 GGTGAAATTA
*
3873467 TGGTTT TGGTTT TGGTTT TGTTTT TGGTTT T
1 TGGTTT TGGTTT TGGTTT TGGTTT TGGTTT T
3873498 TTTGAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TGGTTT
Found at i:3879972 original size:15 final size:16
Alignment explanation
Indices: 3879954--3879983 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3879944 TCAAGAACTC
3879954 AATAAT-CAAATATTT
1 AATAATCCAAATATTT
3879969 AATAATCCAAATATT
1 AATAATCCAAATATT
3879984 ATGTATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAATCCAAATATTT
Found at i:3881138 original size:73 final size:73
Alignment explanation
Indices: 3881034--3881197 Score: 235
Period size: 73 Copynumber: 2.2 Consensus size: 73
3881024 ATTCACTGTC
* * * *
3881034 TCTGATTTCACAAAACAGAATATCCACACGGTCTGACACACT-CTCGTGTGTCCAAGCTGTGTAA
1 TCTGATTTCACAAAACAGAATAGCCACACGGTCTAACACA-TGCCCGTGTGTCCAAGCCGTGTAA
3881098 CTCACAATT
65 CTCACAATT
3881107 TCTGATTTCACAAAACAGAATAGCCACACGGTCTAACACATGCCCGTGTGTCCAAGCCGTGTAAC
1 TCTGATTTCACAAAACAGAATAGCCACACGGTCTAACACATGCCCGTGTGTCCAAGCCGTGTAAC
*
3881172 TCACTATT
66 TCACAATT
3881180 TGCT-AGTTTC-CAAAACAG
1 T-CTGA-TTTCACAAAACAG
3881198 TATGCTAACA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
72 1 0.01
73 76 0.92
74 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (73 bp):
TCTGATTTCACAAAACAGAATAGCCACACGGTCTAACACATGCCCGTGTGTCCAAGCCGTGTAAC
TCACAATT
Found at i:3884538 original size:25 final size:26
Alignment explanation
Indices: 3884500--3884557 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
3884490 AGTTTATAAT
*
3884500 TAATTTTAATTTTATAAT-AT-AAAA
1 TAATTTTAATTTTAAAATAATAAAAA
3884524 TATATTTT-ATATTTAAAATAATAAAAA
1 TA-ATTTTAAT-TTTAAAATAATAAAAA
3884551 TAATTTT
1 TAATTTT
3884558 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 4 0.14
25 12 0.41
26 7 0.24
27 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATTTTAATTTTAAAATAATAAAAA
Found at i:3884542 original size:18 final size:19
Alignment explanation
Indices: 3884508--3884543 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3884498 ATTAATTTTA
3884508 ATTTTATAATATAAAATAT
1 ATTTTATAATATAAAATAT
*
3884527 ATTTTAT-ATTTAAAATA
1 ATTTTATAATATAAAATA
3884544 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTATAATATAAAATAT
Found at i:3884613 original size:19 final size:18
Alignment explanation
Indices: 3884584--3884625 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
3884574 ACCATATACA
3884584 ATTTATTAATTATTTTT-T
1 ATTTATTAATT-TTTTTAT
3884602 ATTTACTTAATTTTTTTAT
1 ATTTA-TTAATTTTTTTAT
3884621 ATTTA
1 ATTTA
3884626 AAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTAATTTTTTTAT
Found at i:3886356 original size:18 final size:18
Alignment explanation
Indices: 3886335--3886407 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
3886325 ATAAAAAGAA
*
3886335 TAAATTTTAGAAAATTAT
1 TAAATATTAGAAAATTAT
* * *
3886353 TAAATTTTAATAAAAATAT
1 TAAATATT-AGAAAATTAT
* * *
3886372 AAAAAATT-GAAATTTAT
1 TAAATATTAGAAAATTAT
*
3886389 TAAATATTAGAAATTTAT
1 TAAATATTAGAAAATTAT
3886407 T
1 T
3886408 TTATAAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
17 12 0.28
18 18 0.42
19 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATATTAGAAAATTAT
Found at i:3886466 original size:20 final size:21
Alignment explanation
Indices: 3886438--3886482 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3886428 TAAAAATTGT
*
3886438 AAAATTTTATAGAAAT-CAT-A
1 AAAAATTTATA-AAATGCATCA
3886458 AAAAATTTATAAAATGCATCA
1 AAAAATTTATAAAATGCATCA
3886479 AAAA
1 AAAA
3886483 GTTCCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATTTATAAAATGCATCA
Found at i:3887477 original size:20 final size:19
Alignment explanation
Indices: 3887454--3887492 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3887444 TTTATAAAAA
3887454 TTTACAATTTTTATATATTT
1 TTTACAATTTTTA-ATATTT
*
3887474 TTTATAATTTTTAATATTT
1 TTTACAATTTTTAATATTT
3887493 AAATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTACAATTTTTAATATTT
Found at i:3887687 original size:88 final size:90
Alignment explanation
Indices: 3887574--3887778 Score: 267
Period size: 88 Copynumber: 2.3 Consensus size: 90
3887564 GCAGGGAATT
*
3887574 AATTGCTTTCTTTTGAAAAAATTTGAGGGTCTTGTTGATGCATTTTAAAAGTTCAAGTACCCAAT
1 AATTGCTTTCTTTTGAAAAAATTTGAGGGTCTTGTTGATGCATTTTAAAAGTTCAAGTACCCAAA
3887639 TGAGTGCAAAAAAAATTATGGATTC
66 TGAGTGCAAAAAAAATTATGGATTC
** * * * *
3887664 AATTGC-TT-TTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCTAAA
1 AATTGCTTTCTTTTGAAAAAATTTGAGGGTCTTGTTGATGCATTTTAAAAGTTCAAGTACCCAAA
* * *
3887727 TGAGTGCAAAAAAAA-GAGGGGCTT-
66 TGAGTGCAAAAAAAATTA-TGGATTC
*
3887751 AATTGCTTT-TTTTGAAAAAATTTAAGGG
1 AATTGCTTTCTTTTGAAAAAATTTGAGGG
3887779 CTTTTTACAC
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
87 7 0.07
88 85 0.85
89 2 0.02
90 6 0.06
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (90 bp):
AATTGCTTTCTTTTGAAAAAATTTGAGGGTCTTGTTGATGCATTTTAAAAGTTCAAGTACCCAAA
TGAGTGCAAAAAAAATTATGGATTC
Found at i:3888338 original size:31 final size:31
Alignment explanation
Indices: 3888290--3888348 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3888280 ATTTTTAAAA
*
3888290 AATTAAATTAAATTTTTATCATTT-TTAAGTG
1 AATTAAAGTAAATTTTTAT-ATTTATTAAGTG
3888321 AATTAAAGTATAA-TTTTATATTTATTAA
1 AATTAAAGTA-AATTTTTATATTTATTAA
3888349 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 19 0.76
32 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (31 bp):
AATTAAAGTAAATTTTTATATTTATTAAGTG
Found at i:3899060 original size:7 final size:7
Alignment explanation
Indices: 3899048--3899074 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3899038 ATTATTTGAT
3899048 AATTTTA
1 AATTTTA
3899055 AATTTTA
1 AATTTTA
3899062 AATTTTA
1 AATTTTA
3899069 AATTTT
1 AATTTT
3899075 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:3903250 original size:14 final size:13
Alignment explanation
Indices: 3903233--3903280 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
3903223 TCATAATGAC
3903233 TAATTAATTTAATT
1 TAATT-ATTTAATT
3903247 TAATT-TTTGAATT
1 TAATTATTT-AATT
3903260 TCAATTATTTAATT
1 T-AATTATTTAATT
3903274 ATAATTA
1 -TAATTA
3903281 ATAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.10
13 5 0.17
14 18 0.60
15 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:3903505 original size:28 final size:27
Alignment explanation
Indices: 3903474--3903528 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
3903464 ATTAAATCAA
3903474 AATTTAATCATT-TTAAAGATTAAAATTT
1 AATTTAATCATTATT-AA-ATTAAAATTT
* *
3903502 AATTTTATTATTATTAAATTAAAATTT
1 AATTTAATCATTATTAAATTAAAATTT
3903529 TATAAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 12 0.50
29 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
AATTTAATCATTATTAAATTAAAATTT
Found at i:3904421 original size:5 final size:5
Alignment explanation
Indices: 3904411--3904435 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3904401 GGCGATGGCA
3904411 CTAAG CTAAG CTAAG CTAAG CTAAG
1 CTAAG CTAAG CTAAG CTAAG CTAAG
3904436 GGGGGAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
CTAAG
Found at i:3908778 original size:14 final size:15
Alignment explanation
Indices: 3908759--3908790 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3908749 GACTCAGTAA
3908759 AAATAAATT-AAAAT
1 AAATAAATTCAAAAT
3908773 AAATAAATTCAAAAT
1 AAATAAATTCAAAAT
3908788 AAA
1 AAA
3908791 AATCCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAATTCAAAAT
Found at i:3910351 original size:6 final size:6
Alignment explanation
Indices: 3910340--3910364 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3910330 GATTTGATGG
3910340 GCTTTT GCTTTT GCTTTT GCTTTT G
1 GCTTTT GCTTTT GCTTTT GCTTTT G
3910365 AGAGGGGTTT
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:0.00, C:0.16, G:0.20, T:0.64
Consensus pattern (6 bp):
GCTTTT
Found at i:3911838 original size:15 final size:16
Alignment explanation
Indices: 3911803--3911837 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3911793 TTTTTTTAAA
3911803 AAAATTAAATCCTTTT
1 AAAATTAAATCCTTTT
* *
3911819 AAAATTTAATCTTTTT
1 AAAATTAAATCCTTTT
3911835 AAA
1 AAA
3911838 TCACCCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATTAAATCCTTTT
Found at i:3911869 original size:18 final size:17
Alignment explanation
Indices: 3911846--3911883 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3911836 AATCACCCTT
*
3911846 TTTTATTTATTTTTATCA
1 TTTTATTTAGTTTTAT-A
3911864 TTTTATTTAGTTTTATA
1 TTTTATTTAGTTTTATA
3911881 TTT
1 TTT
3911884 GATTCATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTTAGTTTTATA
Found at i:3913038 original size:26 final size:26
Alignment explanation
Indices: 3912988--3913038 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3912978 TAATCAACAC
**
3912988 AATTAATATTATACATAAATGTTTTG
1 AATTAATATTATACATAAACATTTTG
* *
3913014 AATTAATATTATTCATTAACATTTT
1 AATTAATATTATACATAAACATTTT
3913039 TATTGTTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (26 bp):
AATTAATATTATACATAAACATTTTG
Found at i:3913588 original size:25 final size:23
Alignment explanation
Indices: 3913547--3913592 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3913537 TCAATTAGGG
3913547 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
3913570 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
3913593 TGAATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:3918020 original size:26 final size:25
Alignment explanation
Indices: 3917960--3918020 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
3917950 GTAGTTGTTA
* *
3917960 AATAATAATTATTAAGTACTCAAAG
1 AATAATAATTATAAAGGACTCAAAG
* *
3917985 AAGACA-AATTAGTAAAGGACTTAAAG
1 AATA-ATAATTA-TAAAGGACTCAAAG
3918011 AATAATAATT
1 AATAATAATT
3918021 CATTTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (25 bp):
AATAATAATTATAAAGGACTCAAAG
Found at i:3919605 original size:17 final size:17
Alignment explanation
Indices: 3919583--3919652 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
3919573 AACCCATTTT
3919583 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
3919600 TTT-AA---A-TTTAAA
1 TTTAAATTTATTTTAAA
3919612 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
3919629 TTTAAAATTT-TTCTAAA
1 TTT-AAATTTATTTTAAA
3919646 TTTAAAT
1 TTTAAAT
3919653 AAATACATGC
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
12 9 0.20
13 3 0.07
16 7 0.15
17 21 0.46
18 6 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3919609 original size:23 final size:23
Alignment explanation
Indices: 3919583--3919652 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
3919573 AACCCATTTT
3919583 TTTAAATTTATTTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
* *
3919606 TTTAAATTTAAATTT-ATTTTAAA
1 TTTAAATTT-ATTTTAAATTTAAA
*
3919629 TTTAAAATTT-TTCTAAATTTAAA
1 TTT-AAATTTATTTTAAATTTAAA
3919652 T
1 T
3919653 AAATACATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.05
23 27 0.69
24 10 0.26
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:3919632 original size:11 final size:11
Alignment explanation
Indices: 3919578--3919615 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3919568 AACTAAACCC
3919578 ATTT-TTTTAA
1 ATTTATTTTAA
3919588 ATTTATTTTAA
1 ATTTATTTTAA
*
3919599 ATTTAAATTTAA
1 ATTT-ATTTTAA
3919611 ATTTA
1 ATTTA
3919616 AATTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:3919652 original size:6 final size:6
Alignment explanation
Indices: 3919583--3919634 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
3919573 AACCCATTTT
* *
3919583 TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3919629 TTTAAA
1 TTTAAA
3919635 ATTTTTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 8 0.20
6 32 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:3921533 original size:30 final size:30
Alignment explanation
Indices: 3921494--3921611 Score: 157
Period size: 30 Copynumber: 3.9 Consensus size: 30
3921484 CATATTTTAG
3921494 CCCCCAAAC-TTCTCAAAAATTACATTTTGA
1 CCCCCAAACTTTC-CAAAAATTACATTTTGA
* *
3921524 CCCCTAAACTTTCCAAAAATTACATTTTAA
1 CCCCCAAACTTTCCAAAAATTACATTTTGA
* * * * *
3921554 TCCCTAAACTTTTCAAAAATAATATTTTGA
1 CCCCCAAACTTTCCAAAAATTACATTTTGA
3921584 CCCCCAAACTTTCCAAAAATTACATTTT
1 CCCCCAAACTTTCCAAAAATTACATTTT
3921612 TGCTCTCGAG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
30 72 0.96
31 3 0.04
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
CCCCCAAACTTTCCAAAAATTACATTTTGA
Found at i:3921564 original size:60 final size:60
Alignment explanation
Indices: 3921499--3921611 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
3921489 TTTAGCCCCC
* *
3921499 AAACTTCTCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTACATTTTAATCCCT
1 AAACTTCTCAAAAATAACATTTTGACCCCCAAACTTTCCAAAAATTACATTTTAATCCCT
* *
3921559 AAACTTTTCAAAAATAATATTTTGACCCCCAAACTTTCCAAAAATTACATTTT
1 AAACTTCTCAAAAATAACATTTTGACCCCCAAACTTTCCAAAAATTACATTTT
3921612 TGCTCTCGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (60 bp):
AAACTTCTCAAAAATAACATTTTGACCCCCAAACTTTCCAAAAATTACATTTTAATCCCT
Found at i:3921672 original size:15 final size:15
Alignment explanation
Indices: 3921647--3921682 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3921637 TTAACCCCAA
*
3921647 ATTTCTCAAAAATTAC
1 ATTT-TCAAAAAATAC
3921663 ATTTTCAAAAAATAC
1 ATTTTCAAAAAATAC
3921678 ATTTT
1 ATTTT
3921683 TACCCTCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTTCAAAAAATAC
Found at i:3921710 original size:29 final size:30
Alignment explanation
Indices: 3921663--3921836 Score: 177
Period size: 29 Copynumber: 6.0 Consensus size: 30
3921653 CAAAAATTAC
* *
3921663 ATTTTCAAAAAATA-CATTTTTACCCTCGA
1 ATTTCCAAAAATTACCATTTTTACCCTCGA
* *
3921692 ATCTCCAAAAATT-CCATTTTTA-GCTCTGAA
1 ATTTCCAAAAATTACCATTTTTACCCTC-G-A
*
3921722 ATTTCC-AAAATTACCA-TTTTACCC-CCA
1 ATTTCCAAAAATTACCATTTTTACCCTCGA
3921749 ACTTTCCAAAAATT-CCATTTTTACCCTCGA
1 A-TTTCCAAAAATTACCATTTTTACCCTCGA
* *
3921779 GTTTCCAAAAATTACC-GTTTTACCCTCGA
1 ATTTCCAAAAATTACCATTTTTACCCTCGA
**
3921808 ACCTCCAAAAATTACCA-TTTTACCCTCGA
1 ATTTCCAAAAATTACCATTTTTACCCTCGA
3921837 GCATCCAAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.02
28 11 0.09
29 94 0.78
30 14 0.12
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
ATTTCCAAAAATTACCATTTTTACCCTCGA
Found at i:3921819 original size:87 final size:87
Alignment explanation
Indices: 3921668--3921832 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 87
3921658 ATTACATTTT
* * **
3921668 CAAAAAATACATTTTTACCCTCGAATCTCCAAAAATTCCATTTTTAGCTCTGAAATTTCCAAAAT
1 CAAAAAATACATTTTTACCCTCGAATCTCCAAAAATTCCAGTTTTACCTCTGAAACCTCCAAAAT
3921733 TACCATTTTACCCCCAACTTTC
66 TACCATTTTACCCCCAACTTTC
* * * *
3921755 CAAAAATTCCATTTTTACCCTCGAGTTTCCAAAAATTACC-GTTTTACC-CTCG-AACCTCCAAA
1 CAAAAAATACATTTTTACCCTCGAATCTCCAAAAATT-CCAGTTTTACCTCT-GAAACCTCC-AA
3921817 AATTACCATTTTACCC
63 AATTACCATTTTACCC
3921833 TCGAGCATCC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
86 7 0.10
87 58 0.87
88 2 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (87 bp):
CAAAAAATACATTTTTACCCTCGAATCTCCAAAAATTCCAGTTTTACCTCTGAAACCTCCAAAAT
TACCATTTTACCCCCAACTTTC
Found at i:3921837 original size:58 final size:58
Alignment explanation
Indices: 3921680--3921846 Score: 198
Period size: 58 Copynumber: 2.9 Consensus size: 58
3921670 AAAAATACAT
* * *
3921680 TTTTACCCTCGAATCTCCAAAAATTCCATTTTTA-GCTCTGAAATTTCC-AAAATTACCA
1 TTTTACCCTCGAACCTCCAAAAATTCCATTTTTACCCTC-G-AGTTTCCAAAAATTACCA
* * *
3921738 TTTTACCC-CCAACTTTCCAAAAATTCCATTTTTACCCTCGAGTTTCCAAAAATTACCG
1 TTTTACCCTCGAAC-CTCCAAAAATTCCATTTTTACCCTCGAGTTTCCAAAAATTACCA
**
3921796 TTTTACCCTCGAACCTCCAAAAATTACCA-TTTTACCCTCGAGCATCCAAAA
1 TTTTACCCTCGAACCTCCAAAAATT-CCATTTTTACCCTCGAGTTTCCAAAA
3921847 GTCGTATTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
57 9 0.10
58 75 0.80
59 10 0.11
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (58 bp):
TTTTACCCTCGAACCTCCAAAAATTCCATTTTTACCCTCGAGTTTCCAAAAATTACCA
Found at i:3923095 original size:16 final size:16
Alignment explanation
Indices: 3923074--3923131 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 16
3923064 CTAAAAATTC
3923074 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
* *
3923090 AGGCTTCGTGCCGGTGTATT
1 AGGCTTTGTGCC----TAGT
3923110 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
3923127 AGGCT
1 AGGCT
3923132 CCGTGCCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 16 0.48
17 3 0.09
20 3 0.09
21 11 0.33
ACGTcount: A:0.12, C:0.21, G:0.33, T:0.34
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:3923116 original size:21 final size:21
Alignment explanation
Indices: 3923090--3923159 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
3923080 TGTGCCTAGT
3923090 AGGCTTCGTGCCGGTGTATTC
1 AGGCTTCGTGCCGGTGTATTC
* *
3923111 AGGCTTTGTGCC----TAGT-
1 AGGCTTCGTGCCGGTGTATTC
*
3923127 AGGCTCCGTGCCGGTGTATTC
1 AGGCTTCGTGCCGGTGTATTC
*
3923148 AGGCTTTGTGCC
1 AGGCTTCGTGCC
3923160 AGTGATCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
16 10 0.27
17 3 0.08
20 3 0.08
21 21 0.57
ACGTcount: A:0.10, C:0.24, G:0.33, T:0.33
Consensus pattern (21 bp):
AGGCTTCGTGCCGGTGTATTC
Found at i:3923120 original size:37 final size:37
Alignment explanation
Indices: 3923070--3923159 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
3923060 ACATCTAAAA
*
3923070 ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGT
1 ATTCAGGCTTTGTGCCTAGTAGGCTCCGTGCCGGTGT
3923107 ATTCAGGCTTTGTGCCTAGTAGGCTCCGTGCCGGTGT
1 ATTCAGGCTTTGTGCCTAGTAGGCTCCGTGCCGGTGT
3923144 ATTCAGGCTTTGTGCC
1 ATTCAGGCTTTGTGCC
3923160 AGTGATCAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.34
Consensus pattern (37 bp):
ATTCAGGCTTTGTGCCTAGTAGGCTCCGTGCCGGTGT
Found at i:3928952 original size:26 final size:25
Alignment explanation
Indices: 3928892--3928952 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
3928882 GTAGTTGTTA
* *
3928892 AATAATAATTATTAAGTACTCAAAG
1 AATAATAATTATAAAGGACTCAAAG
* *
3928917 AAGACA-AATTAGTAAAGGACTTAAAG
1 AATA-ATAATTA-TAAAGGACTCAAAG
3928943 AATAATAATT
1 AATAATAATT
3928953 CATTTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (25 bp):
AATAATAATTATAAAGGACTCAAAG
Found at i:3933974 original size:20 final size:20
Alignment explanation
Indices: 3933949--3933989 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3933939 CAGAAGAAAG
3933949 ATTACCCGGCCTTATGCCAA
1 ATTACCCGGCCTTATGCCAA
3933969 ATTACCCGGCCTTATGCCAA
1 ATTACCCGGCCTTATGCCAA
3933989 A
1 A
3933990 GTTAAATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (20 bp):
ATTACCCGGCCTTATGCCAA
Found at i:3934262 original size:36 final size:36
Alignment explanation
Indices: 3934222--3934291 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
3934212 TTACTTTTGG
* * * *
3934222 GTTAATAGGGAGAAAAATGATCATAATGACCTTTAA
1 GTTAACAGAGAGAAAAACGAGCATAATGACCTTTAA
* *
3934258 GTTAACAGAGAGTAAAACGAGCATCATGACCTTT
1 GTTAACAGAGAGAAAAACGAGCATAATGACCTTT
3934292 GCGGTCAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
GTTAACAGAGAGAAAAACGAGCATAATGACCTTTAA
Found at i:3934814 original size:21 final size:21
Alignment explanation
Indices: 3934784--3934840 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3934774 ATTCTATACA
*
3934784 CTTGTTTCGGTAGAACTCATG
1 CTTGTATCGGTAGAACTCATG
3934805 CTTGTATCGGTAGAACTCATG
1 CTTGTATCGGTAGAACTCATG
3934826 CTTGTATCGGTAGAA
1 CTTGTATCGGTAGAA
3934841 GTACAGGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
CTTGTATCGGTAGAACTCATG
Found at i:3934908 original size:21 final size:24
Alignment explanation
Indices: 3934882--3934935 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3934872 TTGAGTTGTT
*
3934882 TCGGTAGTTGTATA-A-T-AGGTA
1 TCGGTAGTTCTATACATTGAGGTA
*
3934903 TCGGTAGTTCTTTACATTGAGGTA
1 TCGGTAGTTCTATACATTGAGGTA
3934927 TCGGTAGTT
1 TCGGTAGTT
3934936 TAAATACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
22 1 0.04
23 1 0.04
24 14 0.50
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (24 bp):
TCGGTAGTTCTATACATTGAGGTA
Found at i:3935012 original size:116 final size:116
Alignment explanation
Indices: 3934826--3935086 Score: 432
Period size: 116 Copynumber: 2.2 Consensus size: 116
3934816 AGAACTCATG
* *
3934826 CTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGATTGTTCTCTGACTTGAGTTGTTTCGGTAGTT
1 CTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
* * *
3934891 GTATAATAGGTATCGGTAGTTCTTTACATTGAGGTATCGGTAGTTTAAATA
66 GTATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
* *
3934942 CTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTATTTCGGTAGTT
1 CTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
*
3935007 GTATAACAGGTATCTATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
66 GTATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
*
3935058 CTTGTATCGGTAGAAATTACAGGGTAAGA
1 CTTGTATCGGTAG-AAGTACAGGGTAAGA
3935087 CTTCTCAGCT
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
116 121 0.90
117 13 0.10
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (116 bp):
CTTGTATCGGTAGAAGTACAGGGTAAGAGAGAGATTATTCTCTGACTTGAGTTATTTCGGTAGTT
GTATAACAGGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATA
Done.