Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_pilon, whole genome shotgun sequence
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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:3514966 original size:17 final size:17
Alignment explanation
Indices: 3514946--3515039 Score: 64
Period size: 17 Copynumber: 5.2 Consensus size: 17
3514936 ATTTAACATT
3514946 TTTTTTATTTTTATTTA
1 TTTTTTATTTTTATTTA
*** *
3514963 TTTTTCCCTTTGATTTA
1 TTTTTTATTTTTATTTA
**
3514980 TTTAATATTTTTTATTTTA
1 TTTTTTA-TTTTTA-TTTA
*
3514999 TTTTATTTTTCCTTTGATTTA
1 TTTT-TTATT--TTT-ATTTA
3515020 TTTTTTATTTTTA-TTA
1 TTTTTTATTTTTATTTA
3515036 TTTT
1 TTTT
3515040 ATTTTTTCCT
Statistics
Matches: 57, Mismatches: 14, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
16 7 0.12
17 17 0.30
18 7 0.12
19 9 0.16
20 5 0.09
21 11 0.19
22 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTATTTTTATTTA
Found at i:3515041 original size:14 final size:13
Alignment explanation
Indices: 3515016--3515045 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3515006 TTTCCTTTGA
3515016 TTTATTTTTTATT
1 TTTATTTTTTATT
3515029 TTTATTATTTTATT
1 TTTATT-TTTTATT
3515043 TTT
1 TTT
3515046 TCCTTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:3515054 original size:78 final size:73
Alignment explanation
Indices: 3514943--3515108 Score: 219
Period size: 78 Copynumber: 2.2 Consensus size: 73
3514933 AACATTTAAC
*
3514943 ATTTTTT-TTATTT-TTATTTATTTTTCCCTTTGATTTATTTAATATTTTTTATTTTATTTTATT
1 ATTTTTTATT-TTTATTATTTATTTTTCCCTTTGATTTATTTAACA-TTTTT-TTTTA-TTT-TT
*
3515006 TTTCCTTTGATTT
61 TTCCCTTTGATTT
*
3515019 ATTTTTTATTTTTATTATTTTATTTTTTCCTTTGATTTATTTAACATTTTTTTTTATTTTTTTCC
1 ATTTTTTATTTTTATTA-TTTATTTTTCCCTTTGATTTATTTAACATTTTTTTTTATTTTTTTCC
3515084 CTTTGATTT
65 CTTTGATTT
*
3515093 ATTTATTATTTCTTAT
1 ATTTTTTATTT-TTAT
3515109 CTGATATTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
74 24 0.29
75 7 0.09
76 15 0.18
77 10 0.12
78 26 0.32
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (73 bp):
ATTTTTTATTTTTATTATTTATTTTTCCCTTTGATTTATTTAACATTTTTTTTTATTTTTTTCCC
TTTGATTT
Found at i:3515073 original size:42 final size:42
Alignment explanation
Indices: 3514936--3515081 Score: 171
Period size: 38 Copynumber: 3.6 Consensus size: 42
3514926 TACTTTTAAC
* *
3514936 ATTTAACA-TTTTTTTTATTTTTATTTATTTTTCCCTTTGATTT
1 ATTTAACATTTTTTTTTA-TTAT-TTTATTTTTTCCTTTGATTT
* *
3514979 ATTTAATATTTTTTATT-TTATTTTA-TTTTTCCTTTGATTT
1 ATTTAACATTTTTTTTTATTATTTTATTTTTTCCTTTGATTT
*
3515019 ATTT----TTTATTTTTATTATTTTATTTTTTCCTTTGATTT
1 ATTTAACATTTTTTTTTATTATTTTATTTTTTCCTTTGATTT
*
3515057 ATTTAACATTTTTTTTTATTTTTTT
1 ATTTAACATTTTTTTTTATTATTTT
3515082 CCCTTTGATT
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
36 7 0.08
37 8 0.09
38 19 0.22
40 18 0.20
41 4 0.05
42 18 0.20
43 7 0.08
44 7 0.08
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (42 bp):
ATTTAACATTTTTTTTTATTATTTTATTTTTTCCTTTGATTT
Found at i:3515117 original size:74 final size:78
Alignment explanation
Indices: 3514961--3515119 Score: 211
Period size: 74 Copynumber: 2.1 Consensus size: 78
3514951 TATTTTTATT
* * *
3514961 TATTTTTCCCTTTGATTTATTTAATATTTTTTATTTTATTTTATTTTTCCTTTGATTTATTTTTT
1 TATTTTTCCCTTTGATTTATTTAACATTTTTTATTTTATTTTATTTTCCCTTTGATTTATTTATT
**
3515026 ATTTTTATTATTT
66 ATTTTTATTATGA
*
3515039 TATTTTTTCCTTTGATTTATTTAACA-TTTTT-TTTTA-TTT-TTTTCCCTTTGATTTATTTATT
1 TATTTTTCCCTTTGATTTATTTAACATTTTTTATTTTATTTTATTTTCCCTTTGATTTATTTATT
*
3515100 ATTTCTTA-TCTGA
66 ATTT-TTATTATGA
3515113 TATTTTT
1 TATTTTT
3515120 GACTTTTTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
74 33 0.45
75 6 0.08
76 5 0.07
77 5 0.07
78 24 0.33
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (78 bp):
TATTTTTCCCTTTGATTTATTTAACATTTTTTATTTTATTTTATTTTCCCTTTGATTTATTTATT
ATTTTTATTATGA
Found at i:3518810 original size:23 final size:23
Alignment explanation
Indices: 3518767--3518812 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3518757 ATGTTTGTTT
*
3518767 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
3518790 TACATAAC-TACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
3518812 T
1 T
3518813 TCTATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:3521613 original size:28 final size:28
Alignment explanation
Indices: 3521581--3521667 Score: 147
Period size: 28 Copynumber: 3.1 Consensus size: 28
3521571 CTCATAGCTT
* *
3521581 GAAAATTTATTTGATTGAATGTTAAAAA
1 GAAAATTTATTTGACTGAATATTAAAAA
*
3521609 GAAAATTTATATGACTGAATATTAAAAA
1 GAAAATTTATTTGACTGAATATTAAAAA
3521637 GAAAATTTATTTGACTGAATATTAAAAA
1 GAAAATTTATTTGACTGAATATTAAAAA
3521665 GAA
1 GAA
3521668 GCTAATAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (28 bp):
GAAAATTTATTTGACTGAATATTAAAAA
Found at i:3525764 original size:21 final size:20
Alignment explanation
Indices: 3525740--3525792 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
3525730 TCTATATTTT
3525740 TTAAATTATTTCATCTTAATA
1 TTAAATTATTT-ATCTTAATA
* *
3525761 TTAAAATTATTTATTTTAATC
1 TT-AAATTATTTATCTTAATA
3525782 TTAAATTATTT
1 TTAAATTATTT
3525793 TAAATTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 11 0.38
22 9 0.31
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATTATTTATCTTAATA
Found at i:3525827 original size:13 final size:13
Alignment explanation
Indices: 3525809--3525834 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3525799 TAGTTATATT
3525809 TATTTTATTTTTA
1 TATTTTATTTTTA
3525822 TATTTTATTTTTA
1 TATTTTATTTTTA
3525835 GATTATATAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:3525950 original size:16 final size:16
Alignment explanation
Indices: 3525929--3525969 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3525919 ATTTTTCTTA
* *
3525929 AAAAATAACATAAATT
1 AAAAATAAAATAAAAT
3525945 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
*
3525961 AAATATAAA
1 AAAAATAAA
3525970 CCGGGTACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:3528404 original size:135 final size:135
Alignment explanation
Indices: 3528162--3528404 Score: 486
Period size: 135 Copynumber: 1.8 Consensus size: 135
3528152 CGCATATACA
3528162 ACTGATCTTGTTGTACCTCTTTTGGCGTCAAAGGCATCAAGGTTACCTTGCATCCATCATGCTTA
1 ACTGATCTTGTTGTACCTCTTTTGGCGTCAAAGGCATCAAGGTTACCTTGCATCCATCATGCTTA
3528227 AAAATGTATTGATTGTGATAACAATCATGAATGGCCCTTTTATCATACTGCCATGGTCTTCCAAG
66 AAAATGTATTGATTGTGATAACAATCATGAATGGCCCTTTTATCATACTGCCATGGTCTTCCAAG
3528292 TAAGC
131 TAAGC
3528297 ACTGATCTTGTTGTACCTCTTTTGGCGTCAAAGGCATCAAGGTTACCTTGCATCCATCATGCTTA
1 ACTGATCTTGTTGTACCTCTTTTGGCGTCAAAGGCATCAAGGTTACCTTGCATCCATCATGCTTA
3528362 AAAATGTATTGATTGTGATAACAATCATGAATGGCCCTTTTAT
66 AAAATGTATTGATTGTGATAACAATCATGAATGGCCCTTTTAT
3528405 GGAGTGGGAT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 108 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (135 bp):
ACTGATCTTGTTGTACCTCTTTTGGCGTCAAAGGCATCAAGGTTACCTTGCATCCATCATGCTTA
AAAATGTATTGATTGTGATAACAATCATGAATGGCCCTTTTATCATACTGCCATGGTCTTCCAAG
TAAGC
Found at i:3530130 original size:12 final size:13
Alignment explanation
Indices: 3530108--3530136 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3530098 TTCTTGATTT
3530108 CTTTGACTTTGCA
1 CTTTGACTTTGCA
3530121 CTTT-ACTTTGCA
1 CTTTGACTTTGCA
3530133 CTTT
1 CTTT
3530137 TTTTTGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (13 bp):
CTTTGACTTTGCA
Found at i:3534344 original size:23 final size:24
Alignment explanation
Indices: 3534295--3534347 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3534285 TTCTTTTCTT
* *
3534295 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
3534318 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
3534341 TTTCTTT
1 TTTCTTT
3534348 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:3538586 original size:23 final size:24
Alignment explanation
Indices: 3538537--3538589 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3538527 TTCTTTTCTT
* *
3538537 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
3538560 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
3538583 TTTCTTT
1 TTTCTTT
3538590 TATGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:3541264 original size:24 final size:25
Alignment explanation
Indices: 3541218--3541265 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3541208 CACCATGATA
* * *
3541218 TGCATTTTCTTCAGTTTCTTCGTCT
1 TGCATTGTCTTCAGGTTCCTCGTCT
3541243 TGCATTGT-TTCAGGTTCCTCGTC
1 TGCATTGTCTTCAGGTTCCTCGTC
3541266 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.08, C:0.25, G:0.17, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCGTCT
Found at i:3542831 original size:23 final size:23
Alignment explanation
Indices: 3542750--3542834 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
3542740 GACTTGTTGA
3542750 TGAGTGCTTCAAC-TTCTTTCTTT
1 TGAGTGCTTC-ACTTTCTTTCTTT
***
3542773 TTTTTGCTT---TTTC-TTCTTT
1 TGAGTGCTTCACTTTCTTTCTTT
** *
3542792 TGAGTGCTGGATTTTTCTTTCTTT
1 TGAGTGCTTCA-CTTTCTTTCTTT
3542816 TGAGTGCTTCACTTTCTTT
1 TGAGTGCTTCACTTTCTTT
3542835 TCTGATTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
19 11 0.24
20 3 0.07
23 17 0.37
24 15 0.33
ACGTcount: A:0.08, C:0.18, G:0.14, T:0.60
Consensus pattern (23 bp):
TGAGTGCTTCACTTTCTTTCTTT
Found at i:3542836 original size:24 final size:24
Alignment explanation
Indices: 3542786--3542837 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3542776 TTGCTTTTTC
* *
3542786 TTCTTTTGAGTGCTGGATTTTTCT
1 TTCTTTTGAGTGCTGCATTTCTCT
*
3542810 TTCTTTTGAGTGCTTCACTTTCT-T
1 TTCTTTTGAGTGCTGCA-TTTCTCT
3542834 TTCT
1 TTCT
3542838 GATTTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTCTTTTGAGTGCTGCATTTCTCT
Found at i:3544251 original size:20 final size:19
Alignment explanation
Indices: 3544209--3544253 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3544199 ATGTGTAAGA
*
3544209 TAATCATGAAGCTTAAGAGC
1 TAAT-ATGAAGCTTAAGAAC
*
3544229 TAATATGAATGCTTATGAAC
1 TAATATGAA-GCTTAAGAAC
3544249 TAATA
1 TAATA
3544254 AAAATGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (19 bp):
TAATATGAAGCTTAAGAAC
Found at i:3546913 original size:21 final size:21
Alignment explanation
Indices: 3546889--3546928 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3546879 AGGGATTTTA
3546889 TTATTTAAATTAA-TTAAATCT
1 TTATTT-AATTAATTTAAATCT
3546910 TTATTTAATTAATTTAAAT
1 TTATTTAATTAATTTAAAT
3546929 TAAATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTTAATTAATTTAAATCT
Found at i:3562704 original size:13 final size:13
Alignment explanation
Indices: 3562686--3562711 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3562676 GTGGCAAGCA
3562686 TTAGACATCCAAC
1 TTAGACATCCAAC
3562699 TTAGACATCCAAC
1 TTAGACATCCAAC
3562712 ATCTAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TTAGACATCCAAC
Found at i:3564754 original size:90 final size:88
Alignment explanation
Indices: 3564602--3564771 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
3564592 ACACACTCTT
* *
3564602 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTCTTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
*
3564667 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
*
3564691 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATATTT
3564756 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
3564772 ATATTACAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 37 0.49
90 39 0.51
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:3564761 original size:20 final size:21
Alignment explanation
Indices: 3564736--3564805 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
3564726 TATTATTTCA
3564736 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
3564756 AATTAATTGAAATTAAATATTAC
1 AATTAATT-AAAATATATATT-T
*
3564779 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAATATATATTT
3564800 AATTAA
1 AATTAA
3564806 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 18 0.47
23 4 0.11
24 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:3566651 original size:25 final size:25
Alignment explanation
Indices: 3566598--3566692 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
3566588 GAGGATAGAG
3566598 ATATAATAAA-ATAAAATAAATAATTATA
1 ATATAATAAAGA-AAAAT-AATAA--ATA
*
3566626 ATTTAA-AAAGAAAAATAATAAAATA
1 ATATAATAAAGAAAAATAAT-AAATA
* *
3566651 A-ATAATAAGGGAAAATAATAAATA
1 ATATAATAAAGAAAAATAATAAATA
*
3566675 ATAGTAGTAAAGATAAAA
1 ATA-TAATAAAGA-AAAA
3566693 AGGGTTTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
24 9 0.17
25 16 0.30
26 9 0.17
27 14 0.26
28 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (25 bp):
ATATAATAAAGAAAAATAATAAATA
Found at i:3566652 original size:20 final size:20
Alignment explanation
Indices: 3566600--3566652 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
3566590 GGATAGAGAT
*
3566600 ATAATAAAATAAAATAAATA
1 ATAATAAAATAAAATAAAAA
* **
3566620 ATTATAATTTAAAA-AGAAAA
1 ATAATAAAATAAAATA-AAAA
3566640 ATAATAAAATAAA
1 ATAATAAAATAAA
3566653 TAATAAGGGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAATAAAATAAAATAAAAA
Found at i:3567434 original size:19 final size:19
Alignment explanation
Indices: 3567407--3567514 Score: 64
Period size: 19 Copynumber: 5.8 Consensus size: 19
3567397 AATAATATCA
*
3567407 TAAACCCTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
*
3567426 TAAAACCT-ATTAAACTA-
1 TAAAACCTAATTAAAATAC
*
3567443 -AAATACCTAA-AACAAATA-
1 TAAA-ACCTAATTA-AAATAC
** * * *
3567461 TAAAATATAAAATAATATCC
1 TAAAACCT-AATTAAAATAC
*
3567481 TAAAACTTAATTAAAATAC
1 TAAAACCTAATTAAAATAC
*
3567500 TAAAACCTATTTAAA
1 TAAAACCTAATTAAA
3567515 CTAAAATACC
Statistics
Matches: 66, Mismatches: 16, Indels: 14
0.69 0.17 0.15
Matches are distributed among these distances:
16 3 0.05
17 5 0.08
18 15 0.23
19 36 0.55
20 7 0.11
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAACCTAATTAAAATAC
Found at i:3567485 original size:31 final size:31
Alignment explanation
Indices: 3567444--3567504 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3567434 ATTAAACTAA
3567444 AATACCTAAAAC-AAATATAAAATA-TAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAT
*
3567474 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
3567505 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 15 0.56
32 8 0.30
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (31 bp):
AATACCTAAAACTAAATTAAAATACTAAAAT
Found at i:3567496 original size:74 final size:75
Alignment explanation
Indices: 3567334--3567545 Score: 304
Period size: 73 Copynumber: 2.9 Consensus size: 75
3567324 TAAAACATCT
* * * * *
3567334 TAAATCCTAATTAAAACACTTAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TTA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
3567397 AATAATATCA
66 AATAATATCA
* *
3567407 TAAACCCTAATTAAAATACTAAAACCTA-TTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
*
3567471 AATAATATCC
66 AATAATATCA
* * *
3567481 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
3567546 TATTTAAAAT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
73 51 0.41
74 40 0.32
75 34 0.27
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
AATAATATCA
Found at i:3568504 original size:37 final size:38
Alignment explanation
Indices: 3568426--3568525 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 38
3568416 TCGAATTTCC
* * ** *
3568426 TTTTTTCTGTTGTTTGAAACAGTGAACATTTTTTCTCT
1 TTTTTTATGTTGTTCGAAACAGTGAACAACTTTTCTAT
3568464 TTTTTTATGTTGTTCGAAACAGTGAACAACTTTT-TAT
1 TTTTTTATGTTGTTCGAAACAGTGAACAACTTTTCTAT
* * *
3568501 TTTTTTATTTTTTTCAAAACA-TGAA
1 TTTTTTATGTTGTTCGAAACAGTGAA
3568526 TTTTTTTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
36 4 0.07
37 20 0.37
38 30 0.56
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (38 bp):
TTTTTTATGTTGTTCGAAACAGTGAACAACTTTTCTAT
Found at i:3569652 original size:19 final size:18
Alignment explanation
Indices: 3569617--3569668 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3569607 TAAGGTTCGC
3569617 AAAAAATAAAACGAAATA
1 AAAAAATAAAACGAAATA
* *
3569635 AAAAAATGAAATGAAA-A
1 AAAAAATAAAACGAAATA
* *
3569652 TAAAAATATAACGAAAT
1 AAAAAATAAAACGAAAT
3569669 GGGTTGCCTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAAAATAAAACGAAATA
Found at i:3573340 original size:44 final size:45
Alignment explanation
Indices: 3573220--3573345 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
3573210 TATAAAATCC
*
3573220 CTTACCATTTATTCCATAAGATCGTAAGCTTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * * *
3573265 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
3573312 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
3573346 GTATGCTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:3573556 original size:58 final size:59
Alignment explanation
Indices: 3573454--3573581 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 59
3573444 CGTAGTGCTA
* * *
3573454 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTATACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
3573513 TCCCGAATATGACACATAA-GTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
3573571 TCCCGAATATG
1 TCCCGAATATG
3573582 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 43 0.69
59 19 0.31
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:3584685 original size:46 final size:46
Alignment explanation
Indices: 3584634--3585320 Score: 564
Period size: 45 Copynumber: 14.8 Consensus size: 46
3584624 ATAAAAGTTA
* *
3584634 AATGCATAATTGGCATAAAAGGATGCCATAAATGAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
*
3584680 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTATAA-
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
3584725 AATGCATAGTTGGCATGAAAGGATTCCATAAATGAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
3584771 AATGCATAATTGGCATGAAAGGATGCCATAAATTAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
3584817 AATGCATAATTGGCATGAAAGGATGCCATAAATTAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
3584863 AATGCATAATTGACATGAAAGGATGCCAT--ATGAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
** * * * * * *
3584907 GGTATGTAATGCATAACGGTGCATTATATGCATG--A-AAGGATGCCATAAATGAAATGCAT
1 -------AATGCATAATTG-GCATGA-AAGGATGCCATAA--ATG--A-AAATG-CAT-AAC
* *
3584966 AATAGGGCATTATTGGCATGAAAGGATGCCATAAATG-AGATGCATAA-
1 AAT---GCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
3585013 AGGTG-ATTAA-CGACATGAAAGGATGCCATAAATG-AAATGCATAAC
1 A-ATGCA-TAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
3585058 GATGCATTATCGGCATGAAAGGATGCCATAAACG-AAATGCATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * * *
3585103 GA--CATTATCGACATGAAAGGATGCCATAAATG-AAATGCATAAT
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
** * * * *
3585146 GGTGCATTATTGGCATGAAAGGATGCCATAAATG-ATATTCATAGC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
** * *
3585191 GGTGCATTATCGGCATGAAAGGATGCCATAAATG-AAATGCATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
** * * *
3585236 GGTGCATTATTGGCATAAAAGGATGCCATAAATGAAAATGCATAGC
1 AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * ** *
3585282 -GTGCATTATAAGCATGAAAGGAATGCTATAAATGAAAAT
1 AATGCATAATTGGCATGAAAGG-ATGCCATAAATGAAAAT
3585321 AAAGTATAAT
Statistics
Matches: 550, Mismatches: 57, Indels: 68
0.81 0.08 0.10
Matches are distributed among these distances:
43 39 0.07
44 50 0.09
45 208 0.38
46 187 0.34
47 1 0.00
48 2 0.00
49 2 0.00
50 4 0.01
51 11 0.02
52 7 0.01
53 10 0.02
54 11 0.02
55 7 0.01
56 3 0.01
57 5 0.01
58 2 0.00
59 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (46 bp):
AATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
Found at i:3584804 original size:23 final size:23
Alignment explanation
Indices: 3584778--3584850 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
3584768 AACAATGCAT
3584778 AATTGGCATGAAAGGATGCCATA
1 AATTGGCATGAAAGGATGCCATA
*** **
3584801 AATTAAAATGTATAACAATG-CAT-
1 AATTGGCATG-A-AAGGATGCCATA
3584824 AATTGGCATGAAAGGATGCCATA
1 AATTGGCATGAAAGGATGCCATA
3584847 AATT
1 AATT
3584851 AAAATGTATA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
21 5 0.14
22 4 0.11
23 18 0.50
24 4 0.11
25 5 0.14
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (23 bp):
AATTGGCATGAAAGGATGCCATA
Found at i:3591983 original size:19 final size:19
Alignment explanation
Indices: 3591959--3592003 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3591949 ATATTGCTGC
*
3591959 ATGCCCTAGGAAACATCGT
1 ATGCCCTAGGAAACATCAT
*
3591978 ATGCCCTAGGAAACTTCAT
1 ATGCCCTAGGAAACATCAT
3591997 ATGCCCT
1 ATGCCCT
3592004 TTATAGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (19 bp):
ATGCCCTAGGAAACATCAT
Found at i:3592058 original size:15 final size:15
Alignment explanation
Indices: 3592038--3592078 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3592028 TCTCGATTAC
* *
3592038 ATCCACTTTGGCTTT
1 ATCCACTTCGACTTT
3592053 ATCCACTTCGACTTT
1 ATCCACTTCGACTTT
*
3592068 ATACACTTCGA
1 ATCCACTTCGA
3592079 TGCCTTGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (15 bp):
ATCCACTTCGACTTT
Found at i:3601205 original size:78 final size:75
Alignment explanation
Indices: 3601077--3601229 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 75
3601067 ACAATCTAAG
3601077 TGGCATTTTGATTGTTTTCGTAGGCCCATAGTTCTCGTCAAGCTTTGGTAACCAATCCTTATGTT
1 TGGCATTTTGATTGTTTTCGTAGGCCCATAGTTCTCGTCAAGCTTTGGTAACCAATCCTTATGTT
3601142 TAGGGTTGAC
66 TAGGGTTGAC
3601152 TGGCATTTTGATTGTTTTTCGGTAGGCCCATAGTTCCTCGTCAAGCTTTGGTAACCAATCCTTAT
1 TGGCATTTTGATTG-TTTTC-GTAGGCCCATAGTT-CTCGTCAAGCTTTGGTAACCAATCCTTAT
3601217 GTTTAGGGTTGAC
63 GTTTAGGGTTGAC
3601230 CACAAAATTC
Statistics
Matches: 75, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
75 14 0.19
76 5 0.07
77 14 0.19
78 42 0.56
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (75 bp):
TGGCATTTTGATTGTTTTCGTAGGCCCATAGTTCTCGTCAAGCTTTGGTAACCAATCCTTATGTT
TAGGGTTGAC
Found at i:3604029 original size:26 final size:26
Alignment explanation
Indices: 3603974--3604027 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3603964 TAATTATCCC
*
3603974 AAATATTTAATTTAAATTAATTAAAT
1 AAATATTTAATTTAAATTAAATAAAT
*
3604000 AAATATTTAA-TTAATTTGAAAT-AAT
1 AAATATTTAATTTAAATT-AAATAAAT
3604025 AAA
1 AAA
3604028 ATCCCTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATATTTAATTTAAATTAAATAAAT
Found at i:3610682 original size:26 final size:25
Alignment explanation
Indices: 3610653--3610702 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3610643 TTTCCCGAAT
3610653 ATTTAATTTAAATT-AAATAAATAAAG
1 ATTTAA-TTAAATTGAAAT-AATAAAG
*
3610679 ATTTAATTAATTTGAAATAATAAA
1 ATTTAATTAAATTGAAATAATAAA
3610703 ATTCCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTAATTAAATTGAAATAATAAAG
Found at i:3615738 original size:21 final size:21
Alignment explanation
Indices: 3615697--3615739 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3615687 ACTTCATTGC
*
3615697 AAGAATTCATGGCCTTGACAA
1 AAGAATTCATGGCCTTAACAA
*
3615718 AAGATTTCATGG-CTTCAACAA
1 AAGAATTCATGGCCTT-AACAA
3615739 A
1 A
3615740 GACTCTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (21 bp):
AAGAATTCATGGCCTTAACAA
Found at i:3618850 original size:15 final size:15
Alignment explanation
Indices: 3618830--3618858 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3618820 CAAATAATCC
3618830 AAAGATGTGTCCCAA
1 AAAGATGTGTCCCAA
3618845 AAAGATGTGTCCCA
1 AAAGATGTGTCCCA
3618859 GAAGAAGAAC
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:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (15 bp):
AAAGATGTGTCCCAA
Found at i:3626081 original size:50 final size:50
Alignment explanation
Indices: 3626027--3626134 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 50
3626017 ATTTCATTCC
3626027 CACCAACTTCCATTTCATTTTGCCACAACATTCTCATTTGTACATACCAT
1 CACCAACTTCCATTTCATTTTGCCACAACATTCTCATTTGTACATACCAT
3626077 CACCAACTTCCATTTCATTTTGCCACAACATTCTCATTTGTACATACCAT
1 CACCAACTTCCATTTCATTTTGCCACAACATTCTCATTTGTACATACCAT
*
3626127 CACTAACT
1 CACCAACT
3626135 GTACTTAGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.29, C:0.32, G:0.04, T:0.35
Consensus pattern (50 bp):
CACCAACTTCCATTTCATTTTGCCACAACATTCTCATTTGTACATACCAT
Found at i:3626400 original size:26 final size:26
Alignment explanation
Indices: 3626353--3626402 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3626343 AGCATTTTTA
* *
3626353 TTTTACTTGTTCATTTTTTTGTATAG
1 TTTTACTTATTCATTTTCTTGTATAG
3626379 TTTTACTTATT-ATTTTCCTTGTAT
1 TTTTACTTATTCATTTT-CTTGTAT
3626403 TTTTCATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.66
Consensus pattern (26 bp):
TTTTACTTATTCATTTTCTTGTATAG
Found at i:3630455 original size:20 final size:20
Alignment explanation
Indices: 3630427--3630464 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3630417 GTCTAAGAGC
*
3630427 GCATATAGGATCATATAGAT
1 GCATATAGGAGCATATAGAT
*
3630447 GCATTTAGGAGCATATAG
1 GCATATAGGAGCATATAG
3630465 TTTCATGTGG
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:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
GCATATAGGAGCATATAGAT
Found at i:3643535 original size:13 final size:13
Alignment explanation
Indices: 3643517--3643541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3643507 ATATAATATA
3643517 CATTATACTTATC
1 CATTATACTTATC
3643530 CATTATACTTAT
1 CATTATACTTAT
3643542 AATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
CATTATACTTATC
Found at i:3644463 original size:19 final size:20
Alignment explanation
Indices: 3644420--3644463 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
3644410 TCACACACAA
*
3644420 AAAAGGATCGATCCCTTGACT
1 AAAAGGATCAATCCCTT-ACT
3644441 AAAAGGATCAATCCCTT-CT
1 AAAAGGATCAATCCCTTACT
3644460 AAAA
1 AAAA
3644464 AAAAGGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
21 16 0.73
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (20 bp):
AAAAGGATCAATCCCTTACT
Found at i:3645846 original size:14 final size:14
Alignment explanation
Indices: 3645827--3645856 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3645817 CGCATTCATG
3645827 TATACTTATGCATA
1 TATACTTATGCATA
*
3645841 TATACTTATGTATA
1 TATACTTATGCATA
3645855 TA
1 TA
3645857 CAATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (14 bp):
TATACTTATGCATA
Found at i:3645867 original size:23 final size:24
Alignment explanation
Indices: 3645838--3645898 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
3645828 ATACTTATGC
3645838 ATATATACTTATG-TATATACAAT
1 ATATATACTTATGATATATACAAT
* *
3645861 ATATATA-TCTATGCATATGTATAAT
1 ATATATACT-TATG-ATATATACAAT
3645886 ATATATACTTATG
1 ATATATACTTATG
3645899 CACGCGCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
25 19 0.59
26 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (24 bp):
ATATATACTTATGATATATACAAT
Found at i:3650839 original size:15 final size:15
Alignment explanation
Indices: 3650819--3650852 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3650809 CATCATCTTC
3650819 CATCAAGTCCATCAA
1 CATCAAGTCCATCAA
3650834 CATCAAGTCCATCAA
1 CATCAAGTCCATCAA
3650849 CATC
1 CATC
3650853 TTCATAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.35, G:0.06, T:0.21
Consensus pattern (15 bp):
CATCAAGTCCATCAA
Found at i:3650920 original size:20 final size:20
Alignment explanation
Indices: 3650892--3650949 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
3650882 TTTTTCATTT
* *
3650892 CATTACTTATCTTATTTATC
1 CATTTCTTATCTTATTAATC
3650912 CATTTCTTATTCCATTATTAATC
1 CATTTCTTA-T-C-TTATTAATC
3650935 CTATTTCTT-TCTTAT
1 C-ATTTCTTATCTTAT
3650950 CTTTGTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 2 0.06
23 9 0.28
24 7 0.22
ACGTcount: A:0.22, C:0.21, G:0.00, T:0.57
Consensus pattern (20 bp):
CATTTCTTATCTTATTAATC
Found at i:3652911 original size:29 final size:30
Alignment explanation
Indices: 3652855--3652913 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3652845 CTATCATATC
* *
3652855 TATAACAATTAATGATATCATCTTTTTATT
1 TATAAAAATTAATGACATCATCTTTTTATT
3652885 TATAAAAATTAAT-ACATCATCTTTTTATT
1 TATAAAAATTAATGACATCATCTTTTTATT
3652914 AACTCTCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (30 bp):
TATAAAAATTAATGACATCATCTTTTTATT
Found at i:3653421 original size:14 final size:14
Alignment explanation
Indices: 3653404--3653438 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3653394 TATTTATATC
* *
3653404 AATATTATTATTAA
1 AATATTATAAATAA
3653418 AATATTATAAATAA
1 AATATTATAAATAA
3653432 AATATTA
1 AATATTA
3653439 AGACTAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATTATAAATAA
Found at i:3653580 original size:21 final size:20
Alignment explanation
Indices: 3653526--3653583 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
3653516 TTTTATGAAA
*
3653526 TATTAAAATAATTTTA-ATT
1 TATTAAAATAATATTATATT
*
3653545 TATTAATAAT-TTATTATATAT
1 TATTAA-AATAATATTATAT-T
3653566 TATTAAAATAATATTATA
1 TATTAAAATAATATTATA
3653584 ATATCATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 10 0.31
20 8 0.25
21 14 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAAATAATATTATATT
Found at i:3653726 original size:66 final size:66
Alignment explanation
Indices: 3653647--3653788 Score: 166
Period size: 66 Copynumber: 2.1 Consensus size: 66
3653637 ATATATACAC
* *
3653647 ATATATATGTAG-TTTGCAAATTGTTTTTGAAAATACATATAATATATAG-TTT-AAAAC-TTTT
1 ATATATATATAGTTTTGCAAA-TATTTTTGAAAAT--ATATAATATATAGTTTTGAAAACGTTTT
*
3653708 TGAA
63 TAAA
* *
3653712 ATAGTATATATAGTTTTTCAAATATTTTTGAAAATTTATAATATATAGTTTTTGAAAACGTTTTT
1 ATA-TATATATAGTTTTGCAAATATTTTTGAAAATATATAATATATAG-TTTTGAAAACGTTTTT
3653777 AAA
64 AAA
3653780 ATATATATA
1 ATATATATA
3653789 ATATACTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
64 12 0.18
65 3 0.05
66 23 0.35
67 18 0.27
68 10 0.15
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (66 bp):
ATATATATATAGTTTTGCAAATATTTTTGAAAATATATAATATATAGTTTTGAAAACGTTTTTAA
A
Found at i:3653781 original size:35 final size:37
Alignment explanation
Indices: 3653717--3653793 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 37
3653707 TTGAAATAGT
3653717 ATATATAGTTTTTCAAATATTTTTGAAAAT-T-TATA
1 ATATATAGTTTTTCAAATATTTTTGAAAATATATATA
*
3653752 ATATATAGTTTTTGAAA-ACGTTTTT-AAAATATATATA
1 ATATATAGTTTTTCAAATA--TTTTTGAAAATATATATA
3653789 ATATA
1 ATATA
3653794 CTTTTGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 1 0.03
35 21 0.57
36 6 0.16
37 9 0.24
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (37 bp):
ATATATAGTTTTTCAAATATTTTTGAAAATATATATA
Found at i:3653935 original size:115 final size:123
Alignment explanation
Indices: 3653736--3653969 Score: 353
Period size: 115 Copynumber: 2.0 Consensus size: 123
3653726 TTTTCAAATA
3653736 TTTTTGAAAATTTATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATACTTTTGA
1 TTTTTGAAAATTTATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATACTTTTGA
3653801 ACGTTATGAAAACATTTATAT-A-ATATAATTTTAAAAAAAACCATTTTGAAAATACATT
66 ACGTTATGAAAACATTTATATAATATATAATTTT--AAAAAACCATTTTGAAAATACATT
*
3653859 TTTTTGAAAA-TTAT-A-ATATAG-TTTTGAAAACG-TTTTAATATATA-AT-ATATA-TTTTGA
1 TTTTTGAAAATTTATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATACTTTTGA
* *
3653916 ATGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATA
66 ACGTTATGAAAACATTTATATAATATATAATTTTAAAAAACCATTTTGAAAATA
3653970 TATAATATAT
Statistics
Matches: 106, Mismatches: 3, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
115 45 0.42
116 6 0.06
117 12 0.11
118 11 0.10
119 11 0.10
120 6 0.06
121 1 0.01
122 4 0.04
123 10 0.09
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (123 bp):
TTTTTGAAAATTTATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATACTTTTGA
ACGTTATGAAAACATTTATATAATATATAATTTTAAAAAACCATTTTGAAAATACATT
Found at i:3653972 original size:36 final size:34
Alignment explanation
Indices: 3653932--3654012 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 34
3653922 TGAAAACATT
*
3653932 TATATAATATATAATTTTTAAAAACCATTTTGAAAA
1 TATATAATATATAATTTTT-AAAA-CATTTTAAAAA
*
3653968 TATATAATATATAGTTTTTAAAACATTTTAAAAA
1 TATATAATATATAATTTTTAAAACATTTTAAAAA
*
3654002 TTTAT-ATATAT
1 TATATAATATAT
3654013 GTTTTTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.14
34 14 0.33
35 4 0.10
36 18 0.43
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (34 bp):
TATATAATATATAATTTTTAAAACATTTTAAAAA
Found at i:3653978 original size:34 final size:35
Alignment explanation
Indices: 3653932--3654024 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 35
3653922 TGAAAACATT
* *
3653932 TATATA-ATATATAATTTTTAAAAACCATTTTGAAAA
1 TATATATATATATAGTTTTT-AAAA-CATTTTAAAAA
3653968 TATATA-ATATATAGTTTTTAAAACATTTTAAAAA
1 TATATATATATATAGTTTTTAAAACATTTTAAAAA
3654002 T-T-TATATATAT-GTTTTTGAAAAC
1 TATATATATATATAGTTTTT-AAAAC
3654025 GTTATATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
32 8 0.15
33 12 0.23
34 11 0.21
35 4 0.08
36 18 0.34
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATATATATAGTTTTTAAAACATTTTAAAAA
Found at i:3654017 original size:21 final size:23
Alignment explanation
Indices: 3653993--3654035 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3653983 TTTTAAAACA
*
3653993 TTTT-AAAAATTTATATATATGT
1 TTTTGAAAAAGTTATATATATGT
*
3654015 TTTTGAAAACGTTATATATAT
1 TTTTGAAAAAGTTATATATAT
3654036 ATATATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTTGAAAAAGTTATATATATGT
Found at i:3654024 original size:33 final size:32
Alignment explanation
Indices: 3653938--3654024 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 32
3653928 CATTTATATA
* *
3653938 ATATATA-AT-TTTTAAAAACCATTTTGAAAAT
1 ATATATATATGTTTTTAAAA-CATTTTAAAAAT
3653969 ATATAATATATAGTTTTTAAAACATTTTAAAAAT
1 ATAT-ATATAT-GTTTTTAAAACATTTTAAAAAT
*
3654003 TTATATATATGTTTTTGAAAAC
1 ATATATATATGTTTTT-AAAAC
3654025 GTTATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 4 0.08
32 9 0.19
33 13 0.27
34 14 0.29
35 8 0.17
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (32 bp):
ATATATATATGTTTTTAAAACATTTTAAAAAT
Found at i:3654041 original size:33 final size:31
Alignment explanation
Indices: 3653924--3654041 Score: 82
Period size: 33 Copynumber: 3.7 Consensus size: 31
3653914 GAATGTTATG
3653924 AAAACATT-TATATA-ATATATA-A-TTTTT
1 AAAACATTATATATATATATATATAGTTTTT
* *
3653951 AAAAACCATTTTGAAAATATATAATATATAGTTTTT
1 -AAAA-CATTAT--ATATATAT-ATATATAGTTTTT
* * * *
3653987 AAAACATTTTAAAAATTTATATATATGTTTTT
1 AAAACATTATATATATATATATATA-GTTTTT
*
3654019 GAAAACGTTATATATATATATAT
1 -AAAACATTATATATATATATAT
3654042 TACTATTTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
28 4 0.06
29 4 0.06
30 1 0.01
31 7 0.10
32 16 0.22
33 19 0.26
34 11 0.15
35 5 0.07
36 5 0.07
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
AAAACATTATATATATATATATATAGTTTTT
Found at i:3655329 original size:24 final size:23
Alignment explanation
Indices: 3655297--3655347 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
3655287 TTTTATCCCG
*
3655297 TTTTCATTT-TATTTCATTTATTTA
1 TTTTAATTTATATTTCA-TTA-TTA
*
3655321 TTTTAATTTATTTTTCATTATTA
1 TTTTAATTTATATTTCATTATTA
3655344 TTTT
1 TTTT
3655348 TTGATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 11 0.46
25 6 0.25
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTAATTTATATTTCATTATTA
Found at i:3655513 original size:14 final size:14
Alignment explanation
Indices: 3655490--3655523 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3655480 ATTAATTATC
3655490 ATTTTTTTTTG-AT
1 ATTTTTTTTTGAAT
3655503 ATTTCTTTTTTGAAT
1 ATTT-TTTTTTGAAT
3655518 ATTTTT
1 ATTTTT
3655524 AGTAATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (14 bp):
ATTTTTTTTTGAAT
Found at i:3657540 original size:19 final size:19
Alignment explanation
Indices: 3657506--3657550 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3657496 ATTTAGACAT
3657506 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
3657524 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
3657543 TTTGCATT
1 TTTGCATT
3657551 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:3660897 original size:84 final size:84
Alignment explanation
Indices: 3660786--3661330 Score: 608
Period size: 84 Copynumber: 6.6 Consensus size: 84
3660776 CAGCTTTGAG
3660786 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTT
*
3660851 CGACTATGCTCAGCTCCAA-
65 CGACTACGCTCAGCTCCAAC
* * * *
3660870 GGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACA-AAGACCTTCGAGTT
3660935 CGACTACGCTCAGCTCCAA-
65 CGACTACGCTCAGCTCCAAC
* * * *
3660954 GGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTT-AAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGA-CCTTCGAGTT
* * * *
3661015 CGATTACACTCAGCTTCAAG
65 CGACTACGCTCAGCTCCAAC
* * * * * * * ** * *
3661035 GGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTAGCTGTGATCAAAGACCTTTGAGTTC
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTC
3661100 GACTACGCTCAGCT-CAAC
66 GACTACGCTCAGCTCCAAC
* ** * * *
3661118 GGCACATCATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATATGCCAAC-AAGACCTTCGAGTTC
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTC
*
3661182 GACTATGCTCAGCTCCAA-
66 GACTACGCTCAGCTCCAAC
* * * * * * *
3661200 GGCATATC-TTTTCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTT
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTT
3661264 CGACTACGCTCAGCT-CAAC
65 CGACTACGCTCAGCTCCAAC
* * *
3661283 GGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAA
1 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
3661331 AGACCCCTGG
Statistics
Matches: 381, Mismatches: 68, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
80 24 0.06
81 72 0.19
82 37 0.10
83 79 0.21
84 169 0.44
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (84 bp):
GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTC
GACTACGCTCAGCTCCAAC
Found at i:3661154 original size:248 final size:244
Alignment explanation
Indices: 3660737--3661246 Score: 637
Period size: 248 Copynumber: 2.1 Consensus size: 244
3660727 GCTCAAGGCC
** ** * *
3660737 AGAAGGGCTATCTGCCAAAGACCCCCGTTCGATTACACTCAGCTTTGAGGGCACATCATTTGCAG
1 AGAAGGGCTATCTGCCAAAGACCCAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
* * * *
3660802 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTATGCTCAGCTC
66 CATAACTCAAGGCGAGAAGGGTTAGCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * * * *
3660867 CAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTCGA
131 CAAGGCACATCATTTCCAGCACAACTTAAGTCGAGAAGGGCTATATGCC-A-ACAAGACCTTCGA
* *
3660932 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCG
194 GTTCGACTACGCTCAGCTCCAAGGCACATC-TTTGCAGAACAACTTAAGTCG
*
3660984 AGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTAC
1 AGAAGGGCTATCTGCCAAAGACCC--AAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTAC
* ** * *
3661049 AGCATAACTCAAGGCTAGAAGGGTTAGCTGTGATC-AAAGACCTTTGAGTTCGACTACGCTCAGC
64 AGCATAACTCAAGGCGAGAAGGGTTAGCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
*** *
3661113 T-CAACGGCACATCATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATATGCCAACAAGACCTTCG
129 TCCAA-GGCACATCATTTCCAGCACAACTTAAGTCGAGAAGGGCTATATGCCAACAAGACCTTCG
* * * * *
3661177 AGTTCGACTATGCTCAGCTCCAAGGCATATCTTTTCAGTACAACTTAAGTCT
193 AGTTCGACTACGCTCAGCTCCAAGGCACATCTTTGCAGAACAACTTAAGTCG
* *
3661229 AGAAGGGTTGTCTGCCAA
1 AGAAGGGCTATCTGCCAA
3661247 CAAAAGACCT
Statistics
Matches: 225, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
245 32 0.14
246 41 0.18
247 28 0.12
248 64 0.28
249 60 0.27
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (244 bp):
AGAAGGGCTATCTGCCAAAGACCCAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAG
CATAACTCAAGGCGAGAAGGGTTAGCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCACATCATTTCCAGCACAACTTAAGTCGAGAAGGGCTATATGCCAACAAGACCTTCGAGT
TCGACTACGCTCAGCTCCAAGGCACATCTTTGCAGAACAACTTAAGTCG
Found at i:3661293 original size:165 final size:166
Alignment explanation
Indices: 3660786--3661330 Score: 753
Period size: 165 Copynumber: 3.3 Consensus size: 166
3660776 CAGCTTTGAG
* *
3660786 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC--AAGACCTTCGAGTT
*
3660851 CGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
64 CGACTATGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
* *
3660916 AACACAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-
129 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAC
* *
3660954 GGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCC-A-AAGACCCTT-AAGTTC
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAGA-CCTTCGAGTTC
* ** * * * * * *
3661016 GATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTAG-CTGT
65 GACTATGCTCAGCTCCAA-GGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTT-GTCTGC
* *
3661080 GATC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
128 CAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
* ** *
3661118 GGCACATCATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATATGCCAACAAGACCTTCGAGTTCG
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAGACCTTCGAGTTCG
* *
3661183 ACTATGCTCAGCTCCAAGGCATATC-TTTTCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
66 ACTATGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
3661247 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
131 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
* *
3661283 GGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAA
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
3661331 AGACCCCTGG
Statistics
Matches: 326, Mismatches: 42, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
163 4 0.01
164 123 0.38
165 131 0.40
166 24 0.07
167 1 0.00
168 43 0.13
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (166 bp):
GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAGACCTTCGAGTTCG
ACTATGCTCAGCTCCAAGGCATATCATTTACAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAC
Found at i:3661391 original size:329 final size:331
Alignment explanation
Indices: 3660786--3661398 Score: 964
Period size: 329 Copynumber: 1.9 Consensus size: 331
3660776 CAGCTTTGAG
* * *
3660786 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
1 GGCACATCATTTCCAGCATAACTTAAGTCGAGAAGGGCTATATGCCAAC-AAAGACCTTCGAGTT
3660851 CGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
65 CGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
* *
3660916 AACACAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAG
130 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGAATAGCTTAAG
* * * *
3660981 TCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATT
195 TCGAGAAGGGATATCTGCCAAAGACCCCTAAGATCGATTACACTCAACTTCAAGGGCATAACATT
* *
3661046 TACAGCATAACTCAAGGCTAGAAGGGTTAGCTGTGATCAAAGACCTTTGAGTTCGACTACGCTCA
260 TACAACATAACTCAAGGCAAGAAGGGTTAGCTGTGATCAAAGACCTTTGAGTTCGACTACGCTCA
3661111 GCTCAAC
325 GCTCAAC
** *
3661118 GGCACATCATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATATGCCAAC-AAGACCTTCGAGTTC
1 GGCACATCATTTCCAGCATAACTTAAGTCGAGAAGGGCTATATGCCAACAAAGACCTTCGAGTTC
* *
3661182 GACTATGCTCAGCTCCAAGGCATATC-TTTTCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCA
66 GACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCA
* *
3661246 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGAACATCATTTGCAGCATAGCTTAAG
131 ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGAACATCATTTGCAGAATAGCTTAAG
** * *
3661310 TCGAGAAGGGATATCTGCCAAAGACCCCTGGGATCGATTACACTCAACTTC-GGGGTCATATCAT
195 TCGAGAAGGGATATCTGCCAAAGACCCCTAAGATCGATTACACTCAACTTCAAGGG-CATAACAT
*
3661374 TTACAACATAGCTCAAGGCAAGAAG
259 TTACAACATAACTCAAGGCAAGAAG
3661399 AGCTATTTGT
Statistics
Matches: 256, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
328 6 0.02
329 166 0.65
330 41 0.16
332 43 0.17
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (331 bp):
GGCACATCATTTCCAGCATAACTTAAGTCGAGAAGGGCTATATGCCAACAAAGACCTTCGAGTTC
GACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCA
ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGAATAGCTTAAGT
CGAGAAGGGATATCTGCCAAAGACCCCTAAGATCGATTACACTCAACTTCAAGGGCATAACATTT
ACAACATAACTCAAGGCAAGAAGGGTTAGCTGTGATCAAAGACCTTTGAGTTCGACTACGCTCAG
CTCAAC
Found at i:3662021 original size:37 final size:34
Alignment explanation
Indices: 3661968--3662087 Score: 105
Period size: 37 Copynumber: 3.3 Consensus size: 34
3661958 ATATATACAC
* *
3661968 ATATATATTATGTAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATATAATATAGTTT-CAAA-T-TTTTTGAAAAT
* *
3662005 ACATATATAATATAGTTTAAAACATTTTTTGAAAAT
1 ATATATATAATATAGTTT-CAA-ATTTTTTGAAAAT
* *
3662041 ATGTATATTATATAGTTTTTCAAATATTTTTGAAAATT
1 ATATATATAATATAG--TTTCAAAT-TTTTTGAAAA-T
3662079 ATATATATA
1 ATATATATA
3662088 GTTTTGAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
36 25 0.37
37 30 0.45
38 12 0.18
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (34 bp):
ATATATATAATATAGTTTCAAATTTTTTGAAAAT
Found at i:3662084 original size:36 final size:36
Alignment explanation
Indices: 3661968--3662086 Score: 123
Period size: 36 Copynumber: 3.2 Consensus size: 36
3661958 ATATATACAC
* * *
3661968 ATATATATTATGTAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATATTATATAGTTTTCAAA-TATTTTTGAAAAT
* * * *
3662005 ACATATATAATATAG-TTTAAAACATTTTTTGAAAAT
1 ATATATATTATATAGTTTTCAAATA-TTTTTGAAAAT
*
3662041 ATGTATATTATATAGTTTTTCAAATATTTTTGAAAATT
1 ATATATATTATATAG-TTTTCAAATATTTTTGAAAA-T
3662079 ATATATAT
1 ATATATAT
3662087 AGTTTTGAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
36 28 0.43
37 22 0.34
38 15 0.23
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (36 bp):
ATATATATTATATAGTTTTCAAATATTTTTGAAAAT
Found at i:3662119 original size:36 final size:37
Alignment explanation
Indices: 3662078--3662167 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
3662068 TTTTGAAAAT
* *
3662078 TATATATATAGTTTTGAAAACGTT-TTAAAA-ATATA
1 TATATATATACTTTTGAAAACGTTATGAAAACATATA
*
3662113 TA-ATATATACTTTTGAAAACGTTATGAAAACATTTA
1 TATATATATACTTTTGAAAACGTTATGAAAACATATA
* *
3662149 TA-ATATATAATTTTTAAAA
1 TATATATATACTTTTGAAAA
3662168 AAACCATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 20 0.42
35 7 0.15
36 21 0.44
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (37 bp):
TATATATATACTTTTGAAAACGTTATGAAAACATATA
Found at i:3662235 original size:126 final size:119
Alignment explanation
Indices: 3662067--3662307 Score: 385
Period size: 126 Copynumber: 2.0 Consensus size: 119
3662057 TTTTCAAATA
3662067 TTTTTGAAAATTATATATATAGTTTTGAAAACGTTTTAAAAATATATAATATATACTTTTGAAAA
1 TTTTTGAAAATTATATATATAGTTTTGAAAACGTTTTAAAAATATATAATATATACTTTTGAAAA
3662132 CGTTATGAAAACATT-TATAATATATAATTTTTAAAAAAACCATTTTGAAAATACATT
66 CGTTATGAAAACATTATAT-A-ATATAATTTTT--AAAAACCATTTTGAAAATACATT
*
3662189 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATATACTTTTG
1 TTTTTGAAAA-T-TAT-ATATATAG-TTTTGAAAACGTTTTAAAAATATATAATATATACTTTTG
*
3662254 AAAATGTTATGAAAACATTATATAATATAATTTTTAAAAACCATTTTGAAAATA
62 AAAACGTTATGAAAACATTATATAATATAATTTTTAAAAACCATTTTGAAAATA
3662308 TATATAATAT
Statistics
Matches: 112, Mismatches: 2, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
122 10 0.09
123 20 0.18
124 3 0.03
125 19 0.17
126 57 0.51
127 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (119 bp):
TTTTTGAAAATTATATATATAGTTTTGAAAACGTTTTAAAAATATATAATATATACTTTTGAAAA
CGTTATGAAAACATTATATAATATAATTTTTAAAAACCATTTTGAAAATACATT
Found at i:3662239 original size:35 final size:36
Alignment explanation
Indices: 3662190--3662371 Score: 185
Period size: 36 Copynumber: 5.1 Consensus size: 36
3662180 AAATACATTT
*
3662190 TTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTAAAAATTATATAATATATAGTTTTTGAAAACG
* * *
3662226 TTTTTAAAA-TATATAATATATA-CTTTTGAAAATG
1 TTTTAAAAATTATATAATATATAGTTTTTGAAAACG
* * *
3662260 TTATGAAAACATTATATAATATA-A-TTTTTAAAAACCA
1 TT-TTAAAA-ATTATATAATATATAGTTTTTGAAAA-CG
* * *
3662297 TTTTGAAAATATATATAATATATAGTTTTTTAAAAACA
1 TTTTAAAAAT-TATATAATATATAG-TTTTTGAAAACG
*
3662335 TTTTAAAAATTATATATTATAT-GTTTTTGAAAACG
1 TTTTAAAAATTATATAATATATAGTTTTTGAAAACG
3662370 TT
1 TT
3662372 ATATATATAA
Statistics
Matches: 123, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
34 12 0.10
35 31 0.25
36 34 0.28
37 25 0.20
38 11 0.09
39 10 0.08
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTTAAAAATTATATAATATATAGTTTTTGAAAACG
Found at i:3662247 original size:37 final size:36
Alignment explanation
Indices: 3662190--3662371 Score: 169
Period size: 35 Copynumber: 5.1 Consensus size: 36
3662180 AAATACATTT
3662190 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATAT-ATATATAGTTTTTGAAAACG
* * *
3662226 TTTTTAAAATATATA-ATATATA-CTTTTGAAAATG
1 TTTTGAAAATATATATATATATAGTTTTTGAAAACG
* * * * *
3662260 TTATGAAAACAT-TATATAATATAATTTTTAAAAACCA
1 TTTTGAAAATATATATAT-ATATAGTTTTTGAAAA-CG
* *
3662297 TTTTGAAAATATATATAATATATAGTTTTTTAAAAACA
1 TTTTGAAAATATATAT-ATATATAG-TTTTTGAAAACG
*
3662335 TTTTAAAAAT-TATATAT-TATATGTTTTTGAAAACG
1 TTTTGAAAATATATATATATATA-GTTTTTGAAAACG
3662370 TT
1 TT
3662372 ATATATATAA
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.02
34 21 0.17
35 28 0.23
36 20 0.17
37 19 0.16
38 19 0.16
39 12 0.10
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATATATATAGTTTTTGAAAACG
Found at i:3662408 original size:26 final size:26
Alignment explanation
Indices: 3662379--3662430 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3662369 GTTATATATA
3662379 TAATATTATTAC-TA-TTTATTTTATTT
1 TAAT-TTATTACTTATTTTA-TTTATTT
3662405 TAATTTATTACTTATTTTATTTATTT
1 TAATTTATTACTTATTTTATTTATTT
3662431 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (26 bp):
TAATTTATTACTTATTTTATTTATTT
Found at i:3662422 original size:22 final size:20
Alignment explanation
Indices: 3662394--3662433 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3662384 TTATTACTAT
3662394 TTATTTTATTTTAATTTATTAC
1 TTATTTTA-TTT-ATTTATTAC
3662416 TTATTTTATTTATTTATT
1 TTATTTTATTTATTTATT
3662434 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTATTTATTTATTAC
Found at i:3663854 original size:15 final size:16
Alignment explanation
Indices: 3663834--3663863 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3663824 TAATTATCAT
3663834 TTTTTTTG-ATATTTC
1 TTTTTTTGAATATTTC
3663849 TTTTTTTGAATATTT
1 TTTTTTTGAATATTT
3663864 TTAGTAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTTTGAATATTTC
Found at i:3664230 original size:20 final size:23
Alignment explanation
Indices: 3664177--3664221 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3664167 TCCGACAATA
*
3664177 ATATAATTGAATATATTATTATG
1 ATATAATTGAATATATCATTATG
3664200 ATATAATTGAATATATCATTAT
1 ATATAATTGAATATATCATTAT
3664222 AGTATTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (23 bp):
ATATAATTGAATATATCATTATG
Found at i:3664624 original size:29 final size:30
Alignment explanation
Indices: 3664569--3664627 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
3664559 CTATCATATC
*
3664569 TATAAACATTAATGATATCATCTTTTTATT
1 TATAAAAATTAATGATATCATCTTTTTATT
*
3664599 TATAAAAATTAAT-ATATTATCTTTTTATT
1 TATAAAAATTAATGATATCATCTTTTTATT
3664628 AACTCTCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
TATAAAAATTAATGATATCATCTTTTTATT
Found at i:3665104 original size:23 final size:23
Alignment explanation
Indices: 3665061--3665105 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3665051 TATTATCATA
* *
3665061 ATATAATTGAATATATTATTATG
1 ATATAATTGAATAGATCATTATG
3665084 ATATAATTGAATAGATCATTAT
1 ATATAATTGAATAGATCATTAT
3665106 AGTATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (23 bp):
ATATAATTGAATAGATCATTATG
Found at i:3665105 original size:26 final size:23
Alignment explanation
Indices: 3665048--3665096 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3665038 ATATAATATC
3665048 ATATATTATCATAATATAATTGA
1 ATATATTATCATAATATAATTGA
* *
3665071 ATATATTATTATGATATAATTGA
1 ATATATTATCATAATATAATTGA
3665094 ATA
1 ATA
3665097 GATCATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
ATATATTATCATAATATAATTGA
Found at i:3665204 original size:27 final size:27
Alignment explanation
Indices: 3665156--3665217 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3665146 TTAGTAATTA
*
3665156 ATATTTTTTAAATAATAGTAAAATATT
1 ATATTTTTTAAATAATAGTAAAAGATT
3665183 ATATTATTATTAAAT-ATA-TAAAAGATT
1 ATATT-TT-TTAAATAATAGTAAAAGATT
3665210 ATTATTTT
1 A-TATTTT
3665218 GAGTATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 16 0.52
28 9 0.29
29 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (27 bp):
ATATTTTTTAAATAATAGTAAAAGATT
Found at i:3671786 original size:34 final size:34
Alignment explanation
Indices: 3671748--3671891 Score: 153
Period size: 34 Copynumber: 3.9 Consensus size: 34
3671738 TCATAGCTGA
*
3671748 AATGCATATGGGTGAATTATTGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
3671782 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATTGGCAT-AAA--A-G--A-A--T
*
3671825 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* *
3671861 AATGCAAATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGGCATAAAAG
3671892 GATCCCATAA
Statistics
Matches: 94, Mismatches: 5, Indels: 22
0.78 0.04 0.18
Matches are distributed among these distances:
34 53 0.56
35 3 0.03
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.03
45 25 0.27
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:3671833 original size:45 final size:41
Alignment explanation
Indices: 3671780--3671900 Score: 130
Period size: 45 Copynumber: 3.0 Consensus size: 41
3671770 GCATAAAAGA
3671780 ATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT
1 ATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT
*
3671821 AGCTGAAATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-
1 A--T--AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT
* *
3671859 ATAATGCAAATGGGTGCATTATTGGCATGAAAGGATCCCAT
1 ATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT
3671900 A
1 A
3671901 ATTGAAAATG
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
34 24 0.37
35 3 0.05
36 1 0.02
37 1 0.02
38 1 0.02
39 1 0.02
40 1 0.02
41 3 0.05
42 1 0.02
43 1 0.02
44 3 0.05
45 25 0.38
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (41 bp):
ATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT
Found at i:3671907 original size:79 final size:79
Alignment explanation
Indices: 3671642--3671900 Score: 428
Period size: 79 Copynumber: 3.3 Consensus size: 79
3671632 TCATAATTAA
* * * *
3671642 ATTGTCATGAAAGGATGCTATAGTTGAAATGCATATGGGTGCATTATTGGCATAAAATAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATG
3671707 CATATGGGTGCATT
66 CATATGGGTGCATT
* * *
3671721 ATTGGCTTGAAAGGATGTCATAGCTGAAATGCATATGGGTGAATTATTGGCATAAAAGAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATG
3671786 CATATGGGTGCATT
66 CATATGGGTGCATT
*
3671800 ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATG
1 ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATG
*
3671865 CAAATGGGTGCATT
66 CATATGGGTGCATT
*
3671879 ATTGGCATGAAAGGATCCCATA
1 ATTGGCATGAAAGGATGCCATA
3671901 ATTGAAAATG
Statistics
Matches: 167, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 167 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (79 bp):
ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATG
CATATGGGTGCATT
Found at i:3671933 original size:47 final size:46
Alignment explanation
Indices: 3671873--3672217 Score: 318
Period size: 47 Copynumber: 7.6 Consensus size: 46
3671863 TGCAAATGGG
* * * *
3671873 TGCATTATTGGCATGAAAGGATCCCATAATTGAAAATGCATGAACAGA
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAAC-GA
* *
3671921 TTCATTGAGGCATGAAAGGATGCCATAA-T-----TG-A--AA--A
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGA
*
3671956 TGCATTAAGGCATGAAAGGATGTCATAACTAAAAATGCATGAACGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAC-GA
** *
3672003 TGCATTAAGGCATGAAA-GATGAGATAAATAAAAATGCATGAACGAA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACG-A
* ** * * *
3672049 TGCATTAAGGCATGAAAGAATGTTAAAACTAAAAATGCATAAACAGG
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAC-GA
* * ** * *
3672096 TGAATTAAGGTATGAAAGGATATCATAACTAAAAGTACATGAACGAA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACG-A
* *
3672143 TGCATTAAGGCATGAAAGGATGCCATAATTAAAAATGCATGAACATA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAC-GA
*
3672190 TGCATCAAGGCATGAAAGGATGCCATAA
1 TGCATTAAGGCATGAAAGGATGCCATAA
3672218 GTGAAAATTA
Statistics
Matches: 244, Mismatches: 36, Indels: 35
0.77 0.11 0.11
Matches are distributed among these distances:
35 26 0.11
36 1 0.00
38 2 0.01
40 1 0.00
41 4 0.02
42 1 0.00
44 2 0.01
45 1 0.00
46 43 0.18
47 157 0.64
48 6 0.02
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGA
Found at i:3671974 original size:35 final size:35
Alignment explanation
Indices: 3671923--3671995 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3671913 TGAACAGATT
* * *
3671923 CATTGAGGCATGAAAGGATGCCATAATTGAAAATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATG
*
3671958 CATTAAGGCATGAAAGGATGTCATAACTAAAAATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATG
3671993 CAT
1 CAT
3671996 GAACGGATGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (35 bp):
CATTAAGGCATGAAAGGATGCCATAACTAAAAATG
Found at i:3672880 original size:2 final size:2
Alignment explanation
Indices: 3672873--3672947 Score: 129
Period size: 2 Copynumber: 39.0 Consensus size: 2
3672863 ATTAAGGGAT
3672873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3672915 TA TA TA -A TA TA TA TA TA -A TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3672948 AAGTACCATA
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 67 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3676960 original size:34 final size:34
Alignment explanation
Indices: 3676917--3677134 Score: 132
Period size: 34 Copynumber: 5.8 Consensus size: 34
3676907 AGCTAAAATT
3676917 CATATGGGTGCATTATCGGCATAAAATAATAATG
1 CATATGGGTGCATTATCGGCATAAAATAATAATG
* *
3676951 CATATGGGTGCATTATTGGCATGAAAGGATGGCATAAAAAATG
1 CATATGGGTGCATTATCGGCAT--AA--A----AT-AATAATG
*
3676994 CATATGGGTGCATTATCGGCATAAAATAATAATT
1 CATATGGGTGCATTATCGGCATAAAATAATAATG
* * * * *
3677028 CATATTGGTACATTATTGG-AAAGAATGGATGTCAAAACTGAAATT
1 CATATGGGTGCATTATCGGCATA-AA---A--T---AA-T--AATG
* *
3677073 CATATGGGTGCATTATCGACATAAAACAATAATG
1 CATATGGGTGCATTATCGGCATAAAATAATAATG
* *
3677107 CATATGGGTGCATTATTGGCATGAAATA
1 CATATGGGTGCATTATCGGCATAAAATA
3677135 TGCCATAATA
Statistics
Matches: 142, Mismatches: 20, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
33 2 0.01
34 71 0.50
35 2 0.01
36 3 0.02
37 3 0.02
38 1 0.01
39 2 0.01
41 2 0.01
42 5 0.04
43 28 0.20
45 21 0.15
46 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (34 bp):
CATATGGGTGCATTATCGGCATAAAATAATAATG
Found at i:3677202 original size:47 final size:47
Alignment explanation
Indices: 3677115--3677337 Score: 333
Period size: 47 Copynumber: 4.8 Consensus size: 47
3677105 TGCATATGGG
* * *
3677115 TGCATTATTGGCATGAAA-TATGCCATAA-TAAAAATGCATGAACGTA
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
* ** * *
3677161 TGCATTAAGGCATGAAAGAATTTCATAACTAAAAACGCATGAATGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
* *
3677208 TGCATTAAGGCATGAAATGATGTCATAACTAAAAATGCATGAACGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
3677255 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
3677302 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
3677338 TAACGAATAA
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
45 9 0.06
46 14 0.09
47 138 0.86
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (47 bp):
TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
Found at i:3677222 original size:20 final size:20
Alignment explanation
Indices: 3677197--3677324 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
3677187 AACTAAAAAC
*
3677197 GCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3677217 GCATGAAATGATGTCATAACTAAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
3677244 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
3677264 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
3677291 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
3677311 GCATGAAAGGATGC
1 GCATGAAAGGATGC
3677325 CATAACTAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
20 40 0.48
21 6 0.07
23 2 0.02
24 2 0.02
26 6 0.07
27 27 0.33
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:3677247 original size:27 final size:26
Alignment explanation
Indices: 3677217--3677337 Score: 86
Period size: 20 Copynumber: 5.0 Consensus size: 26
3677207 ATGCATTAAG
*
3677217 GCATGAAATGATGTCATAACTAAAAAT
1 GCATGAAAGGATG-CATAACTAAAAAT
* *
3677244 GCATGAACGGATGCAT---T---AAG
1 GCATGAAAGGATGCATAACTAAAAAT
3677264 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-CATAACTAAAAAT
* *
3677291 GCATGAACGGATGCAT---T---AAG
1 GCATGAAAGGATGCATAACTAAAAAT
3677311 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-CATAACTAAAAAT
3677338 TAACGAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 28
0.66 0.08 0.26
Matches are distributed among these distances:
20 28 0.39
21 6 0.08
23 2 0.03
24 2 0.03
26 6 0.08
27 27 0.38
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (26 bp):
GCATGAAAGGATGCATAACTAAAAAT
Found at i:3680461 original size:29 final size:31
Alignment explanation
Indices: 3680413--3680475 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
3680403 TTTTCTTCCC
* *
3680413 TTTAATTTTATTACA-TTTTATTTCTGT-TA
1 TTTAATTTTATTACACTTTAATTTATGTCTA
3680442 TTTAATTTTATT-CACCTTTAATTTATGTCTA
1 TTTAATTTTATTACA-CTTTAATTTATGTCTA
3680473 TTT
1 TTT
3680476 TAAGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 12 0.41
30 10 0.34
31 5 0.17
ACGTcount: A:0.24, C:0.10, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTAATTTTATTACACTTTAATTTATGTCTA
Found at i:3680505 original size:16 final size:16
Alignment explanation
Indices: 3680480--3680525 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3680470 CTATTTTAAG
3680480 TTTT-TTATTTATTGT
1 TTTTATTATTTATTGT
*
3680495 TTTTATTATTTTTTGT
1 TTTTATTATTTATTGT
3680511 TATTGTATT-TTTATT
1 T-TT-TATTATTTATT
3680526 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 7 0.27
18 4 0.15
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (16 bp):
TTTTATTATTTATTGT
Found at i:3680506 original size:22 final size:21
Alignment explanation
Indices: 3680481--3680532 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
3680471 TATTTTAAGT
*
3680481 TTTTTATTTATTGTTTTTATTA
1 TTTTTATTTATTGTATTT-TTA
3680503 TTTTT-TGTTATTGTATTTTTA
1 TTTTTAT-TTATTGTATTTTTA
3680524 TTTTTATTT
1 TTTTTATTT
3680533 TAAATAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTTATTTATTGTATTTTTA
Found at i:3682884 original size:149 final size:149
Alignment explanation
Indices: 3682601--3682896 Score: 351
Period size: 149 Copynumber: 2.0 Consensus size: 149
3682591 TAGCTTCAAA
*
3682601 AGGGAGTCTACCTACCAAGGAGACAATCCAAACCTTTACCTGATGAGGTAACAAGTAGGACTCAA
1 AGGGAGTCTACCTACCAAGGAGACAATCCAAACATTTACCTGATGAGGTAACAAGTAGGACTCAA
** * * * * * * * * *
3682666 GATTATTTGATGATGAATCCAACAATTGAAGATCACGAACTAGCTCAAAAGATTTCTAGAAATAG
66 GACGATTCGATGACGAAGCCAACAATTAAAGATCACGAACCAGATCAAAAGATTTATAGAAACAA
3682731 GAGATGAAGCAGAAGCTAG
131 GAGATGAAGCAGAAGCTAG
* * * * * * *
3682750 AGGGAGTCTATCTACTAATGAGACGATCCAGACATTTTCCTGCTGAGGTAACAAGTTA-GACTCA
1 AGGGAGTCTACCTACCAAGGAGACAATCCAAACATTTACCTGATGAGGTAACAAG-TAGGACTCA
* * * * *
3682814 AGACGATTCGATGCCGAAGCCAACAGTTAAAGATCATGAACCAGATCAAAAGATTTATGGAAGCA
65 AGACGATTCGATGACGAAGCCAACAATTAAAGATCACGAACCAGATCAAAAGATTTATAGAAACA
*
3682879 AGAGATGAAGTAGAAGCT
130 AGAGATGAAGCAGAAGCT
3682897 TTGAAGATGA
Statistics
Matches: 121, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
149 119 0.98
150 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (149 bp):
AGGGAGTCTACCTACCAAGGAGACAATCCAAACATTTACCTGATGAGGTAACAAGTAGGACTCAA
GACGATTCGATGACGAAGCCAACAATTAAAGATCACGAACCAGATCAAAAGATTTATAGAAACAA
GAGATGAAGCAGAAGCTAG
Found at i:3684292 original size:14 final size:13
Alignment explanation
Indices: 3684273--3684307 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3684263 TGCGAAAAAA
3684273 AAAGAAAAAAGAG
1 AAAGAAAAAAGAG
3684286 CAAAGAAAAAAGAG
1 -AAAGAAAAAAGAG
3684300 -AAGAAAAA
1 AAAGAAAAA
3684308 CAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
14 13 0.62
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAG
Found at i:3684294 original size:22 final size:20
Alignment explanation
Indices: 3684269--3684325 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 20
3684259 AGAGTGCGAA
3684269 AAAAAAAGAAAAAAGAGCAAAG
1 AAAAAAAGAAAAAA-A-CAAAG
3684291 AAAAAAGAGAAGAAAAACAAAG
1 AAAAAA-AGAA-AAAAACAAAG
*
3684313 AAAAAAATAAAAA
1 AAAAAAAGAAAAA
3684326 TTACAAGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 17 0.53
23 5 0.16
24 4 0.12
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAAAAACAAAG
Found at i:3685432 original size:9 final size:9
Alignment explanation
Indices: 3685418--3685450 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3685408 GGCTTAAAAA
3685418 TATTATATT
1 TATTATATT
3685427 TATTAT-TAT
1 TATTATAT-T
3685436 TATTATATT
1 TATTATATT
3685445 TATTAT
1 TATTAT
3685451 TATGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTATATT
Found at i:3685434 original size:3 final size:3
Alignment explanation
Indices: 3685426--3685473 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
3685416 AATATTATAT
3685426 TTA TTA TTA TTA TTA -TA TTTA TTA TTA TGT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA
3685471 TTA
1 TTA
3685474 GTAGTAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3685441 original size:18 final size:18
Alignment explanation
Indices: 3685418--3685473 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
3685408 GGCTTAAAAA
3685418 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
3685436 TATTATATTTATTATTA-
1 TATTATATTTATTATTAT
*
3685453 TGTT-TA-TTATTATTAT
1 TATTATATTTATTATTAT
3685469 TATTA
1 TATTA
3685474 GTAGTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.26
16 5 0.15
17 3 0.09
18 17 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:3699562 original size:105 final size:107
Alignment explanation
Indices: 3699365--3699655 Score: 340
Period size: 105 Copynumber: 2.7 Consensus size: 107
3699355 TGAGGGATTG
* * *
3699365 ACATTTCTAATGGAGAGTTCATAATGAGAAGAACACATCCTAAAAGG-GAAAGTTCATAATGAGA
1 ACATTTCCAA-GGAGAGTTCATAATGAGAAGAACTCATCCTTAAAGGAGAAAGTTCATAATGAGA
*
3699429 AGAACTTGTTCCTTTCAAATTCACCACAGAAGGA-AGTGAACCA
65 AGAACTTGTTCCTTTCAAATCCACCACAGAAGGAGA-TGAACCA
* *
3699472 ACATTTCC-A-GAGGAGTTCATAATGAGAAGAACTCGT-CTTAAAGGAGAAAGTTCATAATAAGA
1 ACATTTCCAAGGA-GAGTTCATAATGAGAAGAACTCATCCTTAAAGGAGAAAGTTCATAATGAGA
* * * **
3699534 AGAACTTGTTCCTTTCAAGTCCATCACAGAAGGAGATGGATTA
65 AGAACTTGTTCCTTTCAAATCCACCACAGAAGGAGATGAACCA
* * * *
3699577 ACATTTTCAATGGAGAGTTCATAATGAGAATAACTCATCCAATGAAGGAGAAGAAGTTCATAATG
1 ACATTTCCAA-GGAGAGTTCATAATGAGAAGAACTCATCC-TTAAAGGAG-A-AAGTTCATAATG
*
3699642 AGAATAACTTGTTC
62 AGAAGAACTTGTTC
3699656 AATCCAACGC
Statistics
Matches: 156, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
104 9 0.06
105 80 0.51
106 3 0.02
107 29 0.19
108 3 0.02
109 7 0.04
110 1 0.01
111 24 0.15
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (107 bp):
ACATTTCCAAGGAGAGTTCATAATGAGAAGAACTCATCCTTAAAGGAGAAAGTTCATAATGAGAA
GAACTTGTTCCTTTCAAATCCACCACAGAAGGAGATGAACCA
Found at i:3699831 original size:3 final size:3
Alignment explanation
Indices: 3699823--3699880 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
3699813 AATATTATAT
* * * *
3699823 TTA TTA TTA TTA TTA TTA TTTA TTT TTA TGA TGA TGA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3699869 TTA GTA TTA TTA
1 TTA TTA TTA TTA
3699881 GTAATATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3702949 original size:113 final size:113
Alignment explanation
Indices: 3702814--3703063 Score: 358
Period size: 113 Copynumber: 2.2 Consensus size: 113
3702804 GAAACTATGT
** *
3702814 TAATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAATTTTTATAAGAAACTAAGAGT-GAGGG
1 TAATTTTCAGGGGTTTCTTGATGACAATTTTCAATGAATTTTTATAAGAAACTAAG-CTCGAGGG
* *
3702878 ACCAACGTGATATCTAGGGGTTCCTTGATGATAACTAAGAAACTAAGCC
65 ACCAACATGATATCTAGGGGTTCCTTGATGACAACTAAGAAACTAAGCC
*
3702927 TAATTTTCCGGGGTTTCTTGATGACAATTTTCAATGAATTTTTATAAGAAACTAAGCTCGAGGGA
1 TAATTTTCAGGGGTTTCTTGATGACAATTTTCAATGAATTTTTATAAGAAACTAAGCTCGAGGGA
* * * * *
3702992 TCAGCATGATATGTAGGGGTTCTTTGATGACAACTAAGAAACTAAGCT
66 CCAACATGATATCTAGGGGTTCCTTGATGACAACTAAGAAACTAAGCC
* * *
3703040 TGATTTTCAAGGGTTTCTTAATGA
1 TAATTTTCAGGGGTTTCTTGATGA
3703064 GTAAGTCCTT
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
112 1 0.01
113 120 0.99
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (113 bp):
TAATTTTCAGGGGTTTCTTGATGACAATTTTCAATGAATTTTTATAAGAAACTAAGCTCGAGGGA
CCAACATGATATCTAGGGGTTCCTTGATGACAACTAAGAAACTAAGCC
Found at i:3703131 original size:42 final size:41
Alignment explanation
Indices: 3703079--3703188 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 41
3703069 TCCTTTGGTC
3703079 CATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGT
1 CATC-ATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGT
*
3703121 CATCAGTAAGTCTTTCGAACATGATGCTTAAATCCTTCGAGT
1 CATCA-TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGT
*
3703163 CATCTATAAGTCTTTCGAGCAAGATG
1 CATC-ATAAGTCTTTCGAGCATGATG
3703189 ATAAGTCCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
CATCATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGT
Found at i:3703403 original size:42 final size:40
Alignment explanation
Indices: 3703357--3703469 Score: 147
Period size: 42 Copynumber: 2.8 Consensus size: 40
3703347 AAGGGTTTCT
3703357 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGA-TAAGTCCTTCGGGCCATCTA-TAAGTCTTT-GAGCA
* * *
3703399 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTGAGCA
1 TGATG-ATAAGTCCTTCGGGCCATCTATAAGTCTTTGAGCA
*
3703440 AGATGATAAGTCCTTCGGGCCATCTATAAG
1 TGATGATAAGTCCTTCGGGCCATCTATAAG
3703470 ACCTTCGGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 22 0.35
41 9 0.15
42 30 0.48
43 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (40 bp):
TGATGATAAGTCCTTCGGGCCATCTATAAGTCTTTGAGCA
Found at i:3703468 original size:20 final size:20
Alignment explanation
Indices: 3703364--3703478 Score: 65
Period size: 20 Copynumber: 5.7 Consensus size: 20
3703354 TCTTGATGAG
3703364 TAAGTCCTTCGGGCCATC-A
1 TAAGTCCTTCGGGCCATCTA
* * *
3703383 GTAAGTCTTTCGAGCATGATGCT-
1 -TAAGTCCTTCGGGC--CAT-CTA
* *
3703406 TAAATCCTTCGGGTCATCTA
1 TAAGTCCTTCGGGCCATCTA
* * * **
3703426 TAAGT-CTTTGAGCAAGATGA
1 TAAGTCCTTCGGGCCATCT-A
3703446 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGGGCCATCTA
*
3703466 TAAGACCTTCGGG
1 TAAGTCCTTCGGG
3703479 AAGGATGTTT
Statistics
Matches: 67, Mismatches: 21, Indels: 14
0.66 0.21 0.14
Matches are distributed among these distances:
19 9 0.13
20 37 0.55
21 8 0.12
22 12 0.18
23 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCTA
Found at i:3705786 original size:11 final size:11
Alignment explanation
Indices: 3705772--3705813 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3705762 TTTTAAGTTT
3705772 TTTATTTATTG
1 TTTATTTATTG
3705783 TTTATTTATTG
1 TTTATTTATTG
* *
3705794 CTT-TTTACTG
1 TTTATTTATTG
*
3705804 TTTTTTTATT
1 TTTATTTATT
3705814 ATTTTGCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTATTTATTG
Found at i:3708465 original size:29 final size:30
Alignment explanation
Indices: 3708407--3708469 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3708397 TAGACTACAA
*
3708407 TATTTATAAAAATTAATGATATCATCTTTT
1 TATTTATAAAAATTAATGATATCATATTTT
* *
3708437 TATTTATAAAAGTTAAT-ATATTATATTTT
1 TATTTATAAAAATTAATGATATCATATTTT
3708466 TATT
1 TATT
3708470 AATTGTCCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (30 bp):
TATTTATAAAAATTAATGATATCATATTTT
Found at i:3714172 original size:15 final size:14
Alignment explanation
Indices: 3714151--3714195 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3714141 TTTACCCAAA
3714151 ATAAAATATTTAAAT
1 ATAAAA-ATTTAAAT
*
3714166 -TTAAAATTTAAAT
1 ATAAAAATTTAAAT
3714179 ATAAAAATATTAAAT
1 ATAAAAAT-TTAAAT
3714194 AT
1 AT
3714196 TCAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 8 0.31
14 10 0.38
15 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAAAATTTAAAT
Found at i:3714174 original size:13 final size:13
Alignment explanation
Indices: 3714149--3714195 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3714139 AGTTTACCCA
3714149 AAATA-AAATATTT
1 AAATATAAA-ATTT
*
3714162 AAATTTAAAATTT
1 AAATATAAAATTT
3714175 AAATATAAAAATATT
1 AAATAT-AAAAT-TT
3714190 AAATAT
1 AAATAT
3714196 TCAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 13 0.45
14 8 0.28
15 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAAAATTT
Found at i:3714787 original size:2 final size:2
Alignment explanation
Indices: 3714780--3714811 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3714770 TAGCTTATGG
3714780 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3714812 TAAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3714801 original size:13 final size:13
Alignment explanation
Indices: 3714783--3714808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3714773 CTTATGGTAT
3714783 ATATATATATATA
1 ATATATATATATA
3714796 ATATATATATATA
1 ATATATATATATA
3714809 TATTAAAATA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:3714801 original size:15 final size:15
Alignment explanation
Indices: 3714781--3714810 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3714771 AGCTTATGGT
3714781 ATATATATATATATA
1 ATATATATATATATA
3714796 ATATATATATATATA
1 ATATATATATATATA
3714811 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:3715539 original size:21 final size:21
Alignment explanation
Indices: 3715487--3715532 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
3715477 TTAAAAACAT
*
3715487 TTTTAAAATATTGAAATATGA
1 TTTTAGAATATTGAAATATGA
*
3715508 TTTTAGAATATT-AAATATTA
1 TTTTAGAATATTGAAATATGA
3715528 TTTTA
1 TTTTA
3715533 TTGATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTAGAATATTGAAATATGA
Found at i:3716790 original size:13 final size:14
Alignment explanation
Indices: 3716764--3716824 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 14
3716754 AGGTTACCCA
3716764 AAATA-AAATATTT
1 AAATATAAATATTT
*
3716777 AAATTTAAAT-TTT
1 AAATATAAATATTT
*
3716790 AAATATAAAAATATT
1 AAATATAAATAT-TT
*
3716805 -AATATTAAATATTA
1 AAATA-TAAATATTT
3716819 AAATAT
1 AAATAT
3716825 TCAAAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
13 15 0.39
14 11 0.29
15 12 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATAAATATTT
Found at i:3716793 original size:21 final size:21
Alignment explanation
Indices: 3716769--3716825 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3716759 ACCCAAAATA
* *
3716769 AAATATTTAAAT-TTAAATTTT
1 AAATATTAAAATATT-AATATT
*
3716790 AAATATAAAAATATTAATATT
1 AAATATTAAAATATTAATATT
3716811 AAATATTAAAATATT
1 AAATATTAAAATATT
3716826 CAAAAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATTAAAATATTAATATT
Found at i:3716822 original size:29 final size:29
Alignment explanation
Indices: 3716768--3716824 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3716758 TACCCAAAAT
*
3716768 AAAATATTTAAATTTAAATTTTAAATATA
1 AAAATATTTAAATTTAAATTTAAAATATA
3716797 AAAATA-TT-AATATTAAATATTAAAATAT
1 AAAATATTTAAAT-TTAAAT-TTAAAATAT
3716825 TCAAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 8 0.32
29 14 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATATTTAAATTTAAATTTAAAATATA
Found at i:3718122 original size:24 final size:24
Alignment explanation
Indices: 3718095--3718146 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3718085 AACGGATATA
*
3718095 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
3718119 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
3718143 TCAA
1 TCAA
3718147 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:3718147 original size:24 final size:25
Alignment explanation
Indices: 3718111--3718234 Score: 145
Period size: 24 Copynumber: 5.2 Consensus size: 25
3718101 ATCAAAACAT
*
3718111 AAAT-CAGGTCAAGTATCATATCAG
1 AAATCCAGGTCAAGTATCAGATCAG
*
3718135 AAAT-CAGGTCAAGTAACAGATCAG
1 AAATCCAGGTCAAGTATCAGATCAG
*
3718159 -AATCCAAGTCAAGTATCAGATC--
1 AAATCCAGGTCAAGTATCAGATCAG
*
3718181 AAATCCATGTC-AGATATCAGATCAG
1 AAATCCAGGTCAAG-TATCAGATCAG
*
3718206 -AATCCATGTCAAGTATCAGATCAG
1 AAATCCAGGTCAAGTATCAGATCAG
3718230 AAATC
1 AAATC
3718235 AAATCGAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
22 2 0.02
23 21 0.24
24 59 0.67
25 6 0.07
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (25 bp):
AAATCCAGGTCAAGTATCAGATCAG
Found at i:3721900 original size:2 final size:2
Alignment explanation
Indices: 3721893--3721920 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3721883 TTATGGATGG
3721893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3721921 TAAAAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.