Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 19
Found at i:3628169 original size:71 final size:71
Alignment explanation
Indices: 3628037--3628171 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 71
3628027 TCTCTACAAG
* * * * * *
3628037 TTCAGCTCGATCAAACTGGTAATTCCTTATATAGGTTCAGACTGATCAAATTGGTATTTCCTTAT
1 TTCAACTCGATCAAACTGGTAATTCCTTATATAGCTTCAGACCGATCAAACTGATAATTCCTTAT
3628102 GGCAAA
66 GGCAAA
* * * * *
3628108 TTCAACTCGATGAAATTGGTAATTCCTTATATAGCTTTAGACCGATCGAGCTGATAATTCCTTA
1 TTCAACTCGATCAAACTGGTAATTCCTTATATAGCTTCAGACCGATCAAACTGATAATTCCTTA
3628172 CAGATCTAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (71 bp):
TTCAACTCGATCAAACTGGTAATTCCTTATATAGCTTCAGACCGATCAAACTGATAATTCCTTAT
GGCAAA
Found at i:3630028 original size:217 final size:218
Alignment explanation
Indices: 3629645--3630079 Score: 863
Period size: 217 Copynumber: 2.0 Consensus size: 218
3629635 ATTAATGTCA
3629645 AAGCTTGAAAAAGAATGGTTCTCCTTCCATCATGTTCTACAGTTATCGTTGCATCATGTCCCTGA
1 AAGCTTGAAAAAGAATGGTTCTCCTTCCATCATGTTCTACAGTTATCGTTGCATCATGTCCCTGA
3629710 AATGTGTATAAATTGATAAAATATTAAATATTGTTTTTTGTTTTTCAACACAATTTTGTGTGGTC
66 AATGTGTATAAATTGATAAAATATTAAATATTGTTTTTTGTTTTTCAACACAATTTTGTGTGGTC
3629775 AATTAATAATGAATATGATTTGCGCATCAATGGAGAGACTCATTTGTGTGTAATTTTTTTACTCG
131 AATTAATAATGAATATGATTTGCGCATCAATGGAGAGACTCATTTGTGTGTAATTTTTTTACTCG
3629840 ACAAAATAATAATTTACTAAAGG
196 ACAAAATAATAATTTACTAAAGG
3629863 AAGCTTG-AAAAGAATGGTTCTCCTTCCATCATGTTCTACAGTTATCGTTGCATCATGTCCCTGA
1 AAGCTTGAAAAAGAATGGTTCTCCTTCCATCATGTTCTACAGTTATCGTTGCATCATGTCCCTGA
3629927 AATGTGTATAAATTGATAAAATATTAAATATTGTTTTTTGTTTTTCAACACAATTTTGTGTGGTC
66 AATGTGTATAAATTGATAAAATATTAAATATTGTTTTTTGTTTTTCAACACAATTTTGTGTGGTC
3629992 AATTAATAATGAATATGATTTGCGCATCAATGGAGAGACTCATTTGTGTGTAATTTTTTTACTCG
131 AATTAATAATGAATATGATTTGCGCATCAATGGAGAGACTCATTTGTGTGTAATTTTTTTACTCG
3630057 ACAAAATAATAATTTACTAAAGG
196 ACAAAATAATAATTTACTAAAGG
3630080 CGATCCGAAC
Statistics
Matches: 217, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
217 210 0.97
218 7 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (218 bp):
AAGCTTGAAAAAGAATGGTTCTCCTTCCATCATGTTCTACAGTTATCGTTGCATCATGTCCCTGA
AATGTGTATAAATTGATAAAATATTAAATATTGTTTTTTGTTTTTCAACACAATTTTGTGTGGTC
AATTAATAATGAATATGATTTGCGCATCAATGGAGAGACTCATTTGTGTGTAATTTTTTTACTCG
ACAAAATAATAATTTACTAAAGG
Found at i:3634263 original size:15 final size:16
Alignment explanation
Indices: 3634233--3634265 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3634223 TTATAATTAC
3634233 AACTAGAAATGACATA
1 AACTAGAAATGACATA
*
3634249 AACTAGGAA-GACATA
1 AACTAGAAATGACATA
3634264 AA
1 AA
3634266 TTATCCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (16 bp):
AACTAGAAATGACATA
Found at i:3635197 original size:20 final size:19
Alignment explanation
Indices: 3635158--3635222 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
3635148 GAGGGTGCCA
*
3635158 ATACTGAGCCCTTCAATATCG
1 ATACTGA-CCCTT-AGTATCG
3635179 ATACTGACCCTTGAGTATCG
1 ATACTGACCCTT-AGTATCG
** *
3635199 ATACCCACCCATAGTATCG
1 ATACTGACCCTTAGTATCG
3635218 ATACT
1 ATACT
3635223 AAAAATGGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.29
20 20 0.53
21 7 0.18
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (19 bp):
ATACTGACCCTTAGTATCG
Found at i:3635304 original size:22 final size:21
Alignment explanation
Indices: 3635256--3635314 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
3635246 AGAACTAGGT
*
3635256 AGTATCAATACTCCTAGCTAG
1 AGTATCGATACTCCTAGCTAG
*
3635277 AATATCGATACTACTCTA-CTAG
1 AGTATCGATACT-C-CTAGCTAG
3635299 AGTATCGATACTCCTA
1 AGTATCGATACTCCTA
3635315 TAATGGGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 11 0.33
22 16 0.48
23 3 0.09
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTCCTAGCTAG
Found at i:3637788 original size:7 final size:7
Alignment explanation
Indices: 3637776--3637822 Score: 76
Period size: 7 Copynumber: 6.6 Consensus size: 7
3637766 TTTAAACTTT
3637776 TTTTTCC
1 TTTTTCC
3637783 TTTTTCC
1 TTTTTCC
3637790 TTTTTCC
1 TTTTTCC
3637797 TTTTTCC
1 TTTTTCC
*
3637804 TTTTTCTT
1 TTTTTC-C
3637812 TTTTTCC
1 TTTTTCC
3637819 TTTT
1 TTTT
3637823 CTCTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:3637802 original size:21 final size:22
Alignment explanation
Indices: 3637777--3637828 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
3637767 TTAAACTTTT
3637777 TTTTCCTTTTTCCTTTTTC-CT
1 TTTTCCTTTTTCCTTTTTCTCT
* *
3637798 TTTTCCTTTTT-CTTTTTTTCC
1 TTTTCCTTTTTCCTTTTTCTCT
3637819 TTTTCTCTTT
1 TTTTC-CTTT
3637829 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 17 0.63
22 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTCCTTTTTCCTTTTTCTCT
Found at i:3637858 original size:24 final size:25
Alignment explanation
Indices: 3637813--3637872 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
3637803 CTTTTTCTTT
* *
3637813 TTTTCCTTTTCTCTTTATTTTTTCA
1 TTTTCTTTTTCTCATTATTTTTTCA
3637838 TTTTCTTTTTCTCATTA-TTTTTCA
1 TTTTCTTTTTCTCATTATTTTTTCA
3637862 TTTTCTATTTT
1 TTTTCT-TTTT
3637873 TTTTCCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTCTTTTTCTCATTATTTTTTCA
Found at i:3637875 original size:17 final size:18
Alignment explanation
Indices: 3637838--3637901 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
3637828 TATTTTTTCA
*
3637838 TTTTCTTTTTCTCATTAT
1 TTTTCATTTTCTCATTAT
*
3637856 TTTTCATTTTCT-ATTTT
1 TTTTCATTTTCTCATTAT
3637873 TTTTCCATTTCTCTC-TATAT
1 TTTT-CATTT-TCTCAT-TAT
3637893 TTTTC-TTTT
1 TTTTCATTTT
3637902 TTTTCTTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 9 0.23
18 19 0.49
19 5 0.13
20 6 0.15
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTCATTTTCTCATTAT
Found at i:3647656 original size:22 final size:21
Alignment explanation
Indices: 3647625--3647676 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3647615 AAAACAAATT
3647625 GATCC-TTTTGACAAAGGGATC
1 GATCCTTTTTG-CAAAGGGATC
* * *
3647646 GATTCTTTTTGTAAAGGGATT
1 GATCCTTTTTGCAAAGGGATC
3647667 GATCCTTTTT
1 GATCCTTTTT
3647677 ATGAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.42
Consensus pattern (21 bp):
GATCCTTTTTGCAAAGGGATC
Found at i:3647661 original size:21 final size:21
Alignment explanation
Indices: 3647637--3647676 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3647627 TCCTTTTGAC
*
3647637 AAAGGGATCGATTCTTTTTGT
1 AAAGGGATCGATCCTTTTTGT
*
3647658 AAAGGGATTGATCCTTTTT
1 AAAGGGATCGATCCTTTTT
3647677 ATGAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
AAAGGGATCGATCCTTTTTGT
Found at i:3650578 original size:21 final size:21
Alignment explanation
Indices: 3650554--3650593 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3650544 GTATCGATCA
*
3650554 TTTTAATCGAGGGATCAATTC
1 TTTTAATCAAGGGATCAATTC
**
3650575 TTTTCCTCAAGGGATCAAT
1 TTTTAATCAAGGGATCAAT
3650594 CATTTTTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTTAATCAAGGGATCAATTC
Found at i:3656112 original size:95 final size:94
Alignment explanation
Indices: 3655988--3656187 Score: 276
Period size: 95 Copynumber: 2.1 Consensus size: 94
3655978 TTATGATGTG
* * *
3655988 AGTATCGATACTAAGAGAAAGGTATCGATACCTTGCAATCCAAAATGTTAAAAAGTTATCGATAT
1 AGTATCGATACTAAGAGAAAGATATCGATACCATGCAATCCAAAATGTTAAAAAGGTATCGATAT
3656053 TGAAAGGGAGTATCGGTACCATAATATAGA
66 TG-AAGGGAGTATCGGTACCATAATATAGA
* * * * * * *
3656083 AGTATCGGTAC-AAGGAGAAATATATCGATACCATGGATTCCATAATGTTGAAATGGTATCGATA
1 AGTATCGATACTAA-GAGAAAGATATCGATACCATGCAATCCAAAATGTTAAAAAGGTATCGATA
*
3656147 TTGAAGGGAGTATCGGTACCATAGTATAGA
65 TTGAAGGGAGTATCGGTACCATAATATAGA
3656177 AGTATCGATAC
1 AGTATCGATAC
3656188 CATGGTATGG
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 38 0.41
95 54 0.59
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (94 bp):
AGTATCGATACTAAGAGAAAGATATCGATACCATGCAATCCAAAATGTTAAAAAGGTATCGATAT
TGAAGGGAGTATCGGTACCATAATATAGA
Found at i:3657117 original size:81 final size:81
Alignment explanation
Indices: 3656604--3657099 Score: 787
Period size: 81 Copynumber: 6.1 Consensus size: 81
3656594 GTTCTTAAAA
* * * * *
3656604 TAAAAAATTAAATGTCTAGTTGTGCATTTGGCAGAAAGGTGCCAATATTACAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* *
3656669 GCTAATTTCCTTTGAG
66 GCTAAATGCCTTTGAG
* * *
3656685 TAAAAGATTAATTGCCTAGCTGTGTATTTGGCAGAAAGGTGTCAGTATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* **
3656750 GTTAAATGTATTTGAG
66 GCTAAATGCCTTTGAG
3656766 TAAAAGATTAATTGCCTA-CTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
3656830 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
3656846 TAATAGATTAATTGCCTAGTTGCGCATTTGGCAGAAATGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
3656911 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
3656927 TAAAAGATTAATTGCCTAGCTTTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATAAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
3656992 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * *
3657008 TAAATGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTACCAATATTGTAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
3657073 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
3657089 TAAAAGATTAA
1 TAAAAGATTAA
3657100 ATGATTAACA
Statistics
Matches: 379, Mismatches: 35, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
80 73 0.19
81 306 0.81
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:3663348 original size:95 final size:95
Alignment explanation
Indices: 3663200--3663400 Score: 253
Period size: 95 Copynumber: 2.1 Consensus size: 95
3663190 TATTTATGTG
* * * * * *
3663200 AGTATCGATACTAAGAGAAATGTATTGATACCTTGGAATCCATAATGTAGAAATGGTATTGATAC
1 AGTATCGATACTAAGAAAAAGGTATCGATACCATGGAATCCAAAATGTAGAAATGGTATCGATAC
3663265 TGAAA-ATGAGTATCAGTACCATAATATAGA
66 TGAAAGA-GAGTATCAGTACCATAATATAGA
* * * *
3663295 TGTATCGGTACTAGGAAAAAGGTATCGATACCATGGATTCCAAAATG-ATGAAATGGTATCGATA
1 AGTATCGATACTAAGAAAAAGGTATCGATACCATGGAATCCAAAATGTA-GAAATGGTATCGATA
* * *
3663359 TTGAAAGAGAGTATCGGTACCATAGTATAGA
65 CTGAAAGAGAGTATCAGTACCATAATATAGA
3663390 AGTATCGATAC
1 AGTATCGATAC
3663401 CATGGTATGA
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 87 0.98
96 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (95 bp):
AGTATCGATACTAAGAAAAAGGTATCGATACCATGGAATCCAAAATGTAGAAATGGTATCGATAC
TGAAAGAGAGTATCAGTACCATAATATAGA
Found at i:3663415 original size:20 final size:21
Alignment explanation
Indices: 3663366--3663420 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
3663356 ATATTGAAAG
*
3663366 AGAGTATCGGTACCATAGTAT
1 AGAGTATCGATACCATAGTAT
*
3663387 AGAAGTATCGATACCATGGTAT
1 AG-AGTATCGATACCATAGTAT
3663409 -GAGTATCGATAC
1 AGAGTATCGATAC
3663421 TATTGAGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
22 17 0.55
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (21 bp):
AGAGTATCGATACCATAGTAT
Found at i:3663954 original size:81 final size:80
Alignment explanation
Indices: 3663818--3664315 Score: 645
Period size: 81 Copynumber: 6.1 Consensus size: 80
3663808 GTTCTTAAAA
3663818 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAG-TGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
*
3663883 ACTAAATGCCTTTGAG
65 GCTAAATGCCTTTGAG
* * * * * * *
3663899 AAAAAGATTAATTGCCTATCTTTGTATTTGGTAGAAATGTACCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTA-GTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
*
3663964 GCTAAATGCCTTTAAG
65 GCTAAATGCCTTTGAG
* * * * * **
3663980 CAAATGATAAATTGCCTAGGTGTGCATTTGGAAAAAAGGTAACAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTA-GTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* *
3664045 GCTAAATACATTTGAG
65 GCTAAATGCCTTTGAG
** * * *
3664061 TAAAAGATTAATTTTCAAGTTGTGCATTTGGCATAAAGGTGCCAATATTTCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAG-TGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
3664126 GCTAAATGCCTTTGAG
65 GCTAAATGCCTTTGAG
* * *
3664142 TAAAAGATTAATTGCCTAGATGTGCATTTGCCAGAAAAGGTGTCAATATTGCAAGTTATATGAAA
1 TAAAAGATTAATTGCCTAG-TGTGCATTTGGCAG-AAAGGTGCCAATATTGCAAGTTAGATGAAA
3664207 GGCTAAATGCCTTTGAG
64 GGCTAAATGCCTTTGAG
** *
3664224 TAAAATTTTAATTGCCTAGTTGTGAATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAG-TGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
* *
3664289 GATAAATTCCTTTGAG
65 GCTAAATGCCTTTGAG
*
3664305 TAAAATATTAA
1 TAAAAGATTAA
3664316 ATGATTAACA
Statistics
Matches: 359, Mismatches: 55, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
80 1 0.00
81 285 0.79
82 73 0.20
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (80 bp):
TAAAAGATTAATTGCCTAGTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGG
CTAAATGCCTTTGAG
Found at i:3676706 original size:35 final size:35
Alignment explanation
Indices: 3676643--3676742 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
3676633 TTTCGTCCTA
*
3676643 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
3676680 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
3676715 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
3676743 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:3677062 original size:24 final size:24
Alignment explanation
Indices: 3677033--3677089 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
3677023 TTTCATGTAA
*
3677033 TATTTTTTTACATTT-TATGTATTT
1 TATTTTTTTAC-TTTATATATATTT
*
3677057 T-CTTTTTTACTTTAGTATATATTT
1 TATTTTTTTACTTTA-TATATATTT
3677081 TATTTTTTT
1 TATTTTTTT
3677090 TGATTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 8 0.30
24 10 0.37
25 6 0.22
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (24 bp):
TATTTTTTTACTTTATATATATTT
Found at i:3677118 original size:36 final size:37
Alignment explanation
Indices: 3677072--3677166 Score: 95
Period size: 40 Copynumber: 2.5 Consensus size: 37
3677062 TTTACTTTAG
*
3677072 TATATATTTTATTTTTTTTGATT-A-TATATATAAATA
1 TATATTTTTTATTTTTTTT-ATTAATTATATATAAATA
* *
3677108 TATATTTTTTATTATCAGTTTTATTAATTATATATATATA
1 TATATTTTTTATT-T--TTTTTATTAATTATATATAAATA
*
3677148 TTTACTTTTTTATTTTTTT
1 TATA-TTTTTTATTTTTTT
3677167 ATTTTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
36 12 0.25
37 1 0.02
38 6 0.12
39 5 0.10
40 15 0.31
41 9 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (37 bp):
TATATTTTTTATTTTTTTTATTAATTATATATAAATA
Found at i:3677158 original size:42 final size:40
Alignment explanation
Indices: 3677080--3677204 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 40
3677070 AGTATATATT
* * *
3677080 TTATTTTT-TTTGATTATATATATAAATATA-TATTTTTTA
1 TTATTTTTATTTAATTATATATATATATTTACT-TTTTTTA
3677119 TTATCAGTTTTA-TTAATTATATATATATATTTAC-TTTTTTA
1 TTAT---TTTTATTTAATTATATATATATATTTACTTTTTTTA
*
3677160 TT-TTTTTATTTTATTA-ATAT-TAT-TTTACTTTTTTTA
1 TTATTTTTATTTAATTATATATATATATTTACTTTTTTTA
3677196 TTATATTTT
1 TTAT-TTTT
3677205 TTATTTGTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
35 5 0.07
36 12 0.16
37 10 0.14
38 10 0.14
39 4 0.05
40 1 0.01
41 9 0.12
42 22 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (40 bp):
TTATTTTTATTTAATTATATATATATATTTACTTTTTTTA
Found at i:3677185 original size:21 final size:20
Alignment explanation
Indices: 3677161--3677229 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
3677151 ACTTTTTTAT
3677161 TTTTTTATTTTATTAATATTA
1 TTTTTTATTTTATT-ATATTA
* *
3677182 TTTTACTTTTTTTATTATATTT
1 TTTT--TTATTTTATTATATTA
* *
3677204 TTTATTTGTTTTATTCTA-TA
1 TTT-TTTATTTTATTATATTA
3677224 TTTTTT
1 TTTTTT
3677230 CTTCTTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 15 0.38
22 8 0.20
23 10 0.25
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTTATTATATTA
Found at i:3677207 original size:35 final size:37
Alignment explanation
Indices: 3677080--3677209 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 37
3677070 AGTATATATT
* *
3677080 TTATTTTTTTTGATTATATATATAAATATATA-TTTTTTA
1 TTATATTTTTT-ATTATATATAT--ATATTTACTTTTTTA
3677119 TTATCAGTTTTATTAATTATATATATATATTTACTTTTTTA
1 TTAT-A-TTTT-TT-ATTATATATATATATTTACTTTTTTA
* *
3677160 TTTTTTTATTTTATTA-ATAT-TAT-TTTACTTTTTTTA
1 TTATATT-TTTTATTATATATATATATTTAC-TTTTTTA
3677196 TTATATTTTTTATT
1 TTATATTTTTTATT
3677210 TGTTTTATTC
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
35 12 0.15
36 15 0.19
37 4 0.05
38 4 0.05
39 8 0.10
40 8 0.10
41 14 0.18
42 13 0.17
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (37 bp):
TTATATTTTTTATTATATATATATATTTACTTTTTTA
Found at i:3677223 original size:23 final size:21
Alignment explanation
Indices: 3677160--3677298 Score: 79
Period size: 23 Copynumber: 6.4 Consensus size: 21
3677150 TACTTTTTTA
* *
3677160 TTTTT-TTATTTTATTAATAT
1 TTTTTATTTTTTTATTTATAT
3677180 TATTTTACTTTTTTTA-TTATAT
1 T-TTTTA-TTTTTTTATTTATAT
3677202 TTTTTATTTGTTTTATTCTATAT
1 TTTTTATTT-TTTTATT-TATAT
* *
3677225 TTTTTCTTCTTTTT-CTT-TAT
1 TTTTTATT-TTTTTATTTATAT
* *
3677245 TTTATATTTATTTTACTTACTAT
1 TTTTTATTT-TTTTATTTA-TAT
* * * *
3677268 TTTATCTTGTTTTCTTTATTAT
1 TTTTTATTTTTTTATTTA-TAT
*
3677290 CTTTTATTT
1 TTTTTATTT
3677299 AATTTGTTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
19 1 0.01
20 17 0.18
21 18 0.19
22 23 0.25
23 33 0.35
24 1 0.01
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTTTTATTTATAT
Found at i:3677254 original size:6 final size:5
Alignment explanation
Indices: 3677155--3677325 Score: 52
Period size: 5 Copynumber: 34.0 Consensus size: 5
3677145 ATATTTACTT
* * * *
3677155 TTTTA -TTT- TTTTA TTTTA -TTAA TATTA TTTTA CTTT- TTTTA TTATA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
3677201 TTTTT TATTTG TTTTA TTCTATA TTTT- TTCTTC TTTT- TCTTTA TTTTA
1 TTTTA T-TTTA TTTTA TT-T-TA TTTTA TT-TTA TTTTA T-TTTA TTTTA
* * * * * *
3677249 TATTTA TTTTA CTTACTA TTTTA TCTTG TTTT- CTTTA TTATC TTTTA
1 T-TTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * *
3677296 -TTTA ATTTG TTTTC TCTTTA TTTTA ATTTA
1 TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
3677326 ATTAATTATT
Statistics
Matches: 122, Mismatches: 27, Indels: 34
0.67 0.15 0.19
Matches are distributed among these distances:
4 22 0.18
5 72 0.59
6 22 0.18
7 6 0.05
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:3677259 original size:43 final size:41
Alignment explanation
Indices: 3677164--3677287 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 41
3677154 TTTTTATTTT
* * *
3677164 TTTATTTTATTAATATTATTTTACTTTTTTTATTATATTTTTTA
1 TTTATTTTATTTATATT-TTTT-CTTTTTTTCTT-TATTTTATA
*
3677208 TTTGTTTTATTCTATATTTTTTCTTCTTTTTCTTTATTTTATA
1 TTTATTTTATT-TATATTTTTTCTT-TTTTTCTTTATTTTATA
* * *
3677251 TTTATTTTACTTACTATTTTATCTTGTTTTCTTTATT
1 TTTATTTTATTTA-TATTTTTTCTTTTTTTCTTTATT
3677288 ATCTTTTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
42 13 0.19
43 30 0.43
44 21 0.30
45 5 0.07
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.73
Consensus pattern (41 bp):
TTTATTTTATTTATATTTTTTCTTTTTTTCTTTATTTTATA
Found at i:3677361 original size:15 final size:15
Alignment explanation
Indices: 3677341--3677370 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3677331 TTATTTATTC
3677341 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3677356 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3677371 ACATGGTTTT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:3680364 original size:8 final size:8
Alignment explanation
Indices: 3680353--3680421 Score: 61
Period size: 8 Copynumber: 8.5 Consensus size: 8
3680343 CAAAAAGGGC
3680353 AAAAAG-A
1 AAAAAGAA
3680360 AAAAAGAA
1 AAAAAGAA
3680368 AAAAAGAA
1 AAAAAGAA
*
3680376 AAAAAGGA
1 AAAAAGAA
*
3680384 AAAAACAA
1 AAAAAGAA
3680392 GAACAAA-AA
1 -AA-AAAGAA
*
3680401 AGAAAGAA
1 AAAAAGAA
*
3680409 TAAAAATAA
1 -AAAAAGAA
3680418 AAAA
1 AAAA
3680422 GGGGACAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
7 9 0.18
8 29 0.57
9 10 0.20
10 3 0.06
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3680393 original size:19 final size:19
Alignment explanation
Indices: 3680359--3680405 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3680349 GGGCAAAAAG
3680359 AAAAAAG-AAAAAAAGAA-
1 AAAAAAGAAAAAAAAGAAC
*
3680376 AAAAAGGAAAAAACAAGAAC
1 AAAAAAGAAAAAA-AAGAAC
3680396 AAAAAAGAAA
1 AAAAAAGAAA
3680406 GAATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 5 0.20
20 9 0.36
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAGAAC
Found at i:3681053 original size:22 final size:22
Alignment explanation
Indices: 3681025--3681075 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3681015 CCCCATCAAT
3681025 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
3681047 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
3681069 CCTTTGA
1 CCTTTGA
3681076 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:3682002 original size:37 final size:36
Alignment explanation
Indices: 3681906--3682021 Score: 162
Period size: 36 Copynumber: 3.1 Consensus size: 36
3681896 TCGTGCTCAC
3681906 CATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 CATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
3681942 CATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 CATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
3681978 -ATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CA--TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AAA
3682017 CATTG
1 CATTG
3682022 AAAACATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
35 1 0.01
36 36 0.51
37 28 0.39
38 2 0.03
39 3 0.04
40 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (36 bp):
CATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:3682103 original size:37 final size:37
Alignment explanation
Indices: 3682044--3682114 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
3682034 TTGAAATGAG
* *
3682044 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
3682081 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
3682115 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:3682106 original size:102 final size:102
Alignment explanation
Indices: 3681926--3682317 Score: 660
Period size: 102 Copynumber: 3.9 Consensus size: 102
3681916 CTTGAGACAG
** ** * *
3681926 TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3681991 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
3682028 TTTTCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3682093 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
3682130 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3682195 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
3682232 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3682296 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
3682318 CAAAACCTTT
Statistics
Matches: 274, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
101 36 0.13
102 238 0.87
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3682197 original size:37 final size:37
Alignment explanation
Indices: 3682130--3682216 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
3682120 ATTGGAAACA
** * *
3682130 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3682166 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3682203 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
3682217 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3682276 original size:204 final size:203
Alignment explanation
Indices: 3681926--3682384 Score: 675
Period size: 204 Copynumber: 2.2 Consensus size: 203
3681916 CTTGAGACAG
*
3681926 TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * *
3681991 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTGAAATGAGTTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
* *
3682056 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
3682121 TTGGAAACA
195 TTGGAAACA
** ** *
3682130 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3682195 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
* *
3682260 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAACA
* ***
3682325 TTTGAGATTG
195 TTGGA-AACA
* ** * * *
3682335 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
3682385 CAAAATCTTT
Statistics
Matches: 228, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 36 0.16
204 148 0.65
205 44 0.19
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:3682278 original size:36 final size:36
Alignment explanation
Indices: 3682231--3682317 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
3682221 CATTGAAAAC
** * *
3682231 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
3682267 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
3682303 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
3682318 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:3682350 original size:67 final size:67
Alignment explanation
Indices: 3682259--3682396 Score: 231
Period size: 67 Copynumber: 2.1 Consensus size: 67
3682249 TTCGTCTCTC
* *
3682259 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
3682324 CT
66 CT
** *
3682326 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
3682391 CT
66 CT
3682393 TTGA
1 TTGA
3682397 ATTTATCCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (67 bp):
TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:3682448 original size:67 final size:67
Alignment explanation
Indices: 3682277--3682449 Score: 181
Period size: 67 Copynumber: 2.6 Consensus size: 67
3682267 ATTTCCCTTG
* * * * *
3682277 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCT
1 AAACAAATTTCGTCTCCCATGAAACAGTATCTCTTGAAACACAAAACCTTTGAGATTGTATCCCT
*
3682342 CG
66 CA
* * * *
3682344 AAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-ATT-TATCCCT
1 AAACAAATTTCGTCTCCCATGAAACAGTATCTCTTGAAACACAAAACCTTTGAGATTGTATCCCT
*
3682407 TA
66 CA
* *
3682409 AAACAAAATTTCGTTTCTCATGAAAACAGATATCT-TTGAAA
1 AAAC-AAATTTCGTCTCCCATG-AAACAG-TATCTCTTGAAA
3682450 TCATTTCCCT
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 10 0.11
66 17 0.18
67 62 0.67
68 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (67 bp):
AAACAAATTTCGTCTCCCATGAAACAGTATCTCTTGAAACACAAAACCTTTGAGATTGTATCCCT
CA
Found at i:3682630 original size:36 final size:36
Alignment explanation
Indices: 3682547--3682642 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
3682537 CATCTCCCCG
* * * *
3682547 TGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTATCT
*
3682584 TGAGATAGTTTCTCTTGAAACAA-TTTTCGTCTATCT
1 TGAGACAGTTTCTCTTGAAACAAGTTTT-GTCTATCT
*
3682620 TGAGACAGTTTCCCTTGAAACAA
1 TGAGACAGTTTCTCTTGAAACAA
3682643 AATCTTTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.08
36 30 0.59
37 17 0.33
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (36 bp):
TGAGACAGTTTCTCTTGAAACAAGTTTTGTCTATCT
Found at i:3682705 original size:65 final size:67
Alignment explanation
Indices: 3682601--3682758 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
3682591 GTTTCTCTTG
** * * **
3682601 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
3682663 CTA
65 CTA
* *
3682666 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
3682731 TA
66 TA
*
3682733 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
3682759 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:3682735 original size:67 final size:65
Alignment explanation
Indices: 3682592--3682758 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
3682582 CTTGAGATAG
* * ** * * **
3682592 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
3682656 A
65 A
* *
3682657 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
3682722 TA
64 TA
*
3682724 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
3682759 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:3683538 original size:106 final size:105
Alignment explanation
Indices: 3683378--3684153 Score: 821
Period size: 105 Copynumber: 7.3 Consensus size: 105
3683368 GCCATCTGCG
* *
3683378 ATTTCAACTCCACGACGAAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
*
3683443 GGGACGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * * * **
3683487 ATTTCAACTTCACAACGAAGAATTTTGGACTCCAGACAACCCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** *
3683552 ACCGCTGCCTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
3683592 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
3683657 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * * * *
3683697 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCATAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAACGAA
* * ** *
3683762 GGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TTCGCG
63 GGGACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGC-CA
* *
3683806 ATTTCAAC-TCTACGACGGAGGATATTGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTC-ACAACGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTTCACAACGA
* *
3683870 AGGGACGGCTGGTTGTCAACAA-ACATTTTTCAAATTTCAGAGCCA
62 AGGGACGGCTGGTTGTCAACAACA-ACTTCTC-AATTTCAGAGCCA
* * * *
3683915 ATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCATAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
3683980 ACGGCTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
66 ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * * * *
3684015 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** * * * * *
3684080 GCGGCTGACTGTCAACAAACAATTTCCCAGTTTTAGAACCA
66 ACGGCTGGTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
** *
3684121 ATTTCAACTTCACAGTGGAGGATATTGGACTCG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCG
3684154 GAACAATATT
Statistics
Matches: 574, Mismatches: 75, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
100 80 0.14
101 2 0.00
102 1 0.00
103 4 0.01
104 3 0.01
105 146 0.25
106 133 0.23
107 8 0.01
108 57 0.10
109 137 0.24
110 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:3684687 original size:35 final size:34
Alignment explanation
Indices: 3684614--3684712 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 34
3684604 TTTCGTCCTA
*
3684614 CTAGGATTCAAACTCTCAAAAATAGGATAAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAAATTCTG
*
3684650 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATA-AATTCTG
** *
3684685 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
3684713 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
34 12 0.22
35 14 0.25
36 22 0.40
37 7 0.13
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (34 bp):
CTAGGATTCAACTCCTAAAATAGGATAAATTCTG
Found at i:3685068 original size:24 final size:24
Alignment explanation
Indices: 3685001--3685071 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
3684991 TTTCATGTAA
* *
3685001 TATTTTTTTTACATTTTATGTATTTT
1 TATTTTTTTTAGA--TTATATATTTT
*
3685027 CATTTTTACTTTAG--TATATATTTT
1 TATTTTT--TTTAGATTATATATTTT
3685051 TATTTTTTTTAGATTATATAT
1 TATTTTTTTTAGATTATATAT
3685072 ATAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
22 5 0.14
24 22 0.59
26 6 0.16
28 4 0.11
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (24 bp):
TATTTTTTTTAGATTATATATTTT
Found at i:3685132 original size:8 final size:8
Alignment explanation
Indices: 3685121--3685224 Score: 79
Period size: 8 Copynumber: 12.1 Consensus size: 8
3685111 TATATATATA
*
3685121 TTTACTTT
1 TTTATTTT
3685129 TTTATTTT
1 TTTATTTT
3685137 TTTATTTT
1 TTTATTTT
3685145 ATATATATTATT
1 -T-T-TATT-TT
3685157 TTTACTTTTT
1 TTTA--TTTT
*
3685167 TATTATTAT
1 T-TTATTTT
3685176 TTTATTTTT
1 TTTA-TTTT
3685185 TGTTATTTT
1 T-TTATTTT
3685194 TTT-TTTT
1 TTTATTTT
3685201 TCTT-TTTT
1 T-TTATTTT
3685209 TTT-TTTT
1 TTTATTTT
3685216 TTTATTTT
1 TTTATTTT
3685224 T
1 T
3685225 ATTTTACTAC
Statistics
Matches: 82, Mismatches: 3, Indels: 22
0.77 0.03 0.21
Matches are distributed among these distances:
7 14 0.17
8 32 0.39
9 16 0.20
10 8 0.10
11 10 0.12
12 2 0.02
ACGTcount: A:0.14, C:0.03, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTATTTT
Found at i:3685136 original size:6 final size:6
Alignment explanation
Indices: 3685135--3685229 Score: 65
Period size: 6 Copynumber: 15.7 Consensus size: 6
3685125 CTTTTTTATT
* *
3685135 TTTTTA TTTTATA TATATTA TTTTTA CTTTTTTA TTATTA -TTTTA TTTTT-
1 TTTTTA TTTT-TA T-TTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTTTTA
* *
3685185 TGTTATT- TTTTT- TTTTTC TTTTT- TTTTTT TTTTTA TTTTTA TTTT
1 T-TT-TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
3685230 ACTACTATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
5 17 0.23
6 41 0.55
7 9 0.12
8 8 0.11
ACGTcount: A:0.15, C:0.02, G:0.01, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:3685138 original size:7 final size:7
Alignment explanation
Indices: 3685121--3685229 Score: 66
Period size: 7 Copynumber: 15.1 Consensus size: 7
3685111 TATATATATA
3685121 TTTACTTT
1 TTTA-TTT
3685129 TTTATTTT
1 TTTA-TTT
3685137 TTTATTT
1 TTTATTT
* *
3685144 TATATAT
1 TTTATTT
*
3685151 ATTATTT
1 TTTATTT
*
3685158 TTACTTTTT
1 TT--TATTT
3685167 TATTATTAT
1 T-TTATT-T
3685176 TTTATTT
1 TTTATTT
*
3685183 TTTGTTAT
1 TTTATT-T
3685191 TTT-TTT
1 TTTATTT
3685197 TTT-TTCT
1 TTTATT-T
3685204 TTT-TTT
1 TTTATTT
3685210 TTT-TTT
1 TTTATTT
3685216 TTTA-TT
1 TTTATTT
3685222 TTTATTT
1 TTTATTT
3685229 T
1 T
3685230 ACTACTATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
6 22 0.27
7 30 0.36
8 23 0.28
9 7 0.08
10 1 0.01
ACGTcount: A:0.15, C:0.03, G:0.01, T:0.82
Consensus pattern (7 bp):
TTTATTT
Found at i:3685148 original size:29 final size:26
Alignment explanation
Indices: 3685121--3685270 Score: 103
Period size: 25 Copynumber: 5.5 Consensus size: 26
3685111 TATATATATA
3685121 TTTACTTTTTTATTTTTTTATTTTATAT
1 TTTA-TTTTTTATTTTTTTATTTT-TAT
* *
3685149 ATATTA-TTTTTACTTTTTTATTATTAT
1 -T-TTATTTTTTATTTTTTTATTTTTAT
*
3685176 TTTATTTTTTGTTATTTTT-TTTTT-T
1 TTTATTTTTTATT-TTTTTATTTTTAT
*
3685201 TCTT-TTTTTTTTTTTTTTATTTTTAT
1 T-TTATTTTTTATTTTTTTATTTTTAT
*
3685227 TTTACTACTATTTTATCTTTTTT-TCTTTAT
1 TTTA-T--T-TTTTAT-TTTTTTATTTTTAT
* *
3685257 CTTATCTTTTATTT
1 TTTATTTTTTATTT
3685271 AATTTGTTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
24 5 0.05
25 22 0.22
26 21 0.21
27 9 0.09
28 16 0.16
29 3 0.03
30 17 0.17
31 6 0.06
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTATTTTTTATTTTTTTATTTTTAT
Found at i:3685158 original size:21 final size:21
Alignment explanation
Indices: 3685134--3685178 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3685124 ACTTTTTTAT
3685134 TTTTTTA-TTTTATATATATTA
1 TTTTTTACTTTTATAT-TATTA
*
3685155 -TTTTTACTTTTTTATTATTA
1 TTTTTTACTTTTATATTATTA
3685175 TTTT
1 TTTT
3685179 ATTTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTACTTTTATATTATTA
Found at i:3685166 original size:35 final size:35
Alignment explanation
Indices: 3685076--3685180 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 35
3685066 ATATATATAA
* * *
3685076 ATATATTATTTTTTA-TTATCAGTTTTATTAATTTAT
1 ATATATTA-TTTTTACTTTTTA-TTTTATTATTTTAT
* *
3685112 ATATA-TATATTTACTTTTTTATTTTTTTATTTTAT
1 ATATATTATTTTTAC-TTTTTATTTTATTATTTTAT
*
3685147 ATATATTATTTTTACTTTTT-TATTATTATTTTAT
1 ATATATTATTTTTACTTTTTATTTTATTATTTTAT
3685181 TTTTTGTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
34 17 0.29
35 24 0.41
36 17 0.29
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.69
Consensus pattern (35 bp):
ATATATTATTTTTACTTTTTATTTTATTATTTTAT
Found at i:3685176 original size:34 final size:34
Alignment explanation
Indices: 3685099--3685180 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 34
3685089 TATTATCAGT
*
3685099 TTTATTAATTTATATATATATATTTACTTTTTTA
1 TTTATTATTTTATATATATATATTTACTTTTTTA
* *
3685133 TTTTTTTATTTTATATATATTATTTTTACTTTTTTA
1 -TTTATTATTTTATATATA-TATATTTACTTTTTTA
3685169 -TTATTATTTTAT
1 TTTATTATTTTAT
3685181 TTTTTGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 11 0.26
35 16 0.38
36 15 0.36
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTATTATTTTATATATATATATTTACTTTTTTA
Found at i:3685184 original size:1 final size:1
Alignment explanation
Indices: 3685175--3685229 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
3685165 TTTATTATTA
* * * * * *
3685175 TTTTATTTTTTGTTATTTTTTTTTTTTCTTTTTTTTTTTTTTTTATTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3685230 ACTACTATTT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.07, C:0.02, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:3685192 original size:15 final size:13
Alignment explanation
Indices: 3685126--3685230 Score: 84
Period size: 14 Copynumber: 7.5 Consensus size: 13
3685116 ATATATTTAC
3685126 TTTTTTATTTTTT
1 TTTTTTATTTTTT
* *
3685139 TATTTTATATATATT
1 T-TTTT-TATTTTTT
*
3685154 ATTTTTACTTTTTT
1 TTTTTTA-TTTTTT
* *
3685168 ATTATTATTTTATT
1 TTTTTTATTTT-TT
3685182 TTTTGTTATTTTTT
1 TTTT-TTATTTTTT
*
3685196 TTTTTTCTTTTTT
1 TTTTTTATTTTTT
*
3685209 TTTTTTTTTTATTT
1 TTTTTTATTT-TTT
3685223 TTATTTTA
1 TT-TTTTA
3685231 CTACTATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
13 24 0.32
14 33 0.45
15 17 0.23
ACGTcount: A:0.15, C:0.02, G:0.01, T:0.82
Consensus pattern (13 bp):
TTTTTTATTTTTT
Found at i:3685206 original size:28 final size:27
Alignment explanation
Indices: 3685126--3685292 Score: 99
Period size: 28 Copynumber: 5.9 Consensus size: 27
3685116 ATATATTTAC
* *
3685126 TTTTTTATTTTTTTATTTTATATATATT
1 TTTTTTATTTTTTTTTTTTAT-TTTATT
* * *
3685154 ATTTTTACTTTTTTATTATTATTTTATT
1 TTTTTTA-TTTTTTTTTTTTATTTTATT
*
3685182 TTTTGTTA-TTTTTTTTTTT-TCTT-TT
1 TTTT-TTATTTTTTTTTTTTATTTTATT
* *
3685207 TTTTTT-TTTTTTATTTTTATTTTACTAC
1 TTTTTTATTTTTTTTTTTTATTTTA-T-T
* * *
3685235 TATTTTATCTTTTTTTCTTTATCTTATCT
1 TTTTTTAT-TTTTTTTTTTTATTTTAT-T
*
3685264 TTTATTTAATTTGTTTTCTCTTTATTTTA
1 TTT-TTT-ATTT-TTTT-TTTTTATTTTA
3685293 ATTTAATTAA
Statistics
Matches: 106, Mismatches: 20, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
24 12 0.11
25 9 0.08
26 3 0.03
27 10 0.09
28 19 0.18
29 18 0.17
30 19 0.18
31 6 0.06
32 10 0.09
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (27 bp):
TTTTTTATTTTTTTTTTTTATTTTATT
Found at i:3685333 original size:15 final size:15
Alignment explanation
Indices: 3685313--3685342 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3685303 TTATTTATTT
3685313 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3685328 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
3685343 ACATGGTTTT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:3690870 original size:20 final size:20
Alignment explanation
Indices: 3690801--3690860 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 20
3690791 TTTTTTAAAA
*
3690801 TTTTGGCTTTTTTG-TTTTT
1 TTTTGCCTTTTTTGTTTTTT
**
3690820 TTTTG---TTTTTG-GGTTT
1 TTTTGCCTTTTTTGTTTTTT
3690836 TTTTGCCTTTTTTGTTTTTT
1 TTTTGCCTTTTTTGTTTTTT
3690856 TTTTG
1 TTTTG
3690861 TTTTATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 14 0.42
19 11 0.33
20 8 0.24
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.78
Consensus pattern (20 bp):
TTTTGCCTTTTTTGTTTTTT
Found at i:3692846 original size:153 final size:153
Alignment explanation
Indices: 3692568--3692874 Score: 614
Period size: 153 Copynumber: 2.0 Consensus size: 153
3692558 TTTCTTGTTA
3692568 ATGTTCTCTGTTTTTGGTGGTGTTTCTCTTTTTCTTTACGAGAATTGTGTGTTGTTTATAAGAAA
1 ATGTTCTCTGTTTTTGGTGGTGTTTCTCTTTTTCTTTACGAGAATTGTGTGTTGTTTATAAGAAA
3692633 TGGGAAATCGAATAGAAATTGGGAGACCCTTGTTTTACTATTACTTTCGAATGGGAGGGAAAGAA
66 TGGGAAATCGAATAGAAATTGGGAGACCCTTGTTTTACTATTACTTTCGAATGGGAGGGAAAGAA
3692698 AATCCATTACACTGCTTCTCTCG
131 AATCCATTACACTGCTTCTCTCG
3692721 ATGTTCTCTGTTTTTGGTGGTGTTTCTCTTTTTCTTTACGAGAATTGTGTGTTGTTTATAAGAAA
1 ATGTTCTCTGTTTTTGGTGGTGTTTCTCTTTTTCTTTACGAGAATTGTGTGTTGTTTATAAGAAA
3692786 TGGGAAATCGAATAGAAATTGGGAGACCCTTGTTTTACTATTACTTTCGAATGGGAGGGAAAGAA
66 TGGGAAATCGAATAGAAATTGGGAGACCCTTGTTTTACTATTACTTTCGAATGGGAGGGAAAGAA
3692851 AATCCATTACACTGCTTCTCTCG
131 AATCCATTACACTGCTTCTCTCG
3692874 A
1 A
3692875 ATCAACAAAA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (153 bp):
ATGTTCTCTGTTTTTGGTGGTGTTTCTCTTTTTCTTTACGAGAATTGTGTGTTGTTTATAAGAAA
TGGGAAATCGAATAGAAATTGGGAGACCCTTGTTTTACTATTACTTTCGAATGGGAGGGAAAGAA
AATCCATTACACTGCTTCTCTCG
Found at i:3698859 original size:2 final size:2
Alignment explanation
Indices: 3698852--3698876 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3698842 ATTTCTGGTC
3698852 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3698877 ACTTTTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3705121 original size:9 final size:9
Alignment explanation
Indices: 3705107--3705138 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3705097 ATAAGTGAAT
*
3705107 TATAATCTA
1 TATAATCAA
3705116 TATAATCAA
1 TATAATCAA
3705125 TATAATCAA
1 TATAATCAA
3705134 TATAA
1 TATAA
3705139 GTAACTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (9 bp):
TATAATCAA
Found at i:3706089 original size:3 final size:3
Alignment explanation
Indices: 3706083--3706173 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
3706073 ATAAAAATCG
3706083 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3706131 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3706174 TGAAAACTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3706302 original size:105 final size:105
Alignment explanation
Indices: 3706146--3706343 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 105
3706136 AAGAAGAAGA
* * * * *
3706146 AGAAGAAGAAGAAGAAGAAGAAGAAGAATGAAAACTTACCATTCTACCATAGCAAATGACTCGAA
1 AGAAGAAGAAGAAGAAGAAGAAAAAAAATGAAAACTTACCATTCGACCATAGCAAACGAATCGAA
* *
3706211 GAGAGGGATGAAAAGAATACAAGTAATAGCATGGAATTTG
66 GAGAGGGATGAAAAAAATAAAAGTAATAGCATGGAATTTG
* * * * * *
3706251 AGAAGAATAAGAAGAAGATGAAAAAAAATGAAGACTTACCAATTCGA-CATAGTAAACGAATTGC
1 AGAAGAAGAAGAAGAAGAAGAAAAAAAATGAAAACTTACC-ATTCGACCATAGCAAACGAATCGA
*
3706315 AGAGAGGGGTGAAAAAAATAAAAGTAATA
65 AGAGAGGGATGAAAAAAATAAAAGTAATA
3706344 TATGAAAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
105 73 0.94
106 5 0.06
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (105 bp):
AGAAGAAGAAGAAGAAGAAGAAAAAAAATGAAAACTTACCATTCGACCATAGCAAACGAATCGAA
GAGAGGGATGAAAAAAATAAAAGTAATAGCATGGAATTTG
Found at i:3706985 original size:104 final size:104
Alignment explanation
Indices: 3706862--3707239 Score: 407
Period size: 104 Copynumber: 3.6 Consensus size: 104
3706852 CTTAACTATG
*
3706862 TTGAATGCAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATTCTTT
1 TTGAATGAAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATTCTTT
*
3706927 TTCAATGATATATCACTTCAAATAAGAACTTATTTCATA
66 TTCAGTGATATATCACTTCAAATAAGAACTTATTTCATA
*
3706966 TTGAATGTAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTA-T-TTT
1 TTGAATGAAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATTCTTT
** *
3707029 TTCAGTGATATATCACCTT-AAATCTG-ACTTATTACATA
66 TTCAGTGATATATCA-CTTCAAATAAGAACTTATTTCATA
* * *
3707067 TTGAATGAAAAGAT-TTA----GTACAATAATAATTTCAAATGATAAAGTACCTTAACTATTCAC
1 TTGAATGAAAA-ATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATT--C
* *
3707127 ATCCTTTTCCTTTTAGTGATATATTACCTCAAATCAA-AACTTTATTTCATA
63 -T--TTTT-C----AGTGATATATCACTTCAAAT-AAGAAC-TTATTTCATA
*** * * *
3707178 TTGAATGAAAAATCTTATATAGTACAATAATAATTTTAAATGACAGAGAATCTTAAATATTC
1 TTGAATGAAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATTC
3707240 ACGTTCTTTT
Statistics
Matches: 231, Mismatches: 20, Indels: 37
0.80 0.07 0.13
Matches are distributed among these distances:
97 35 0.15
98 1 0.00
101 24 0.10
102 25 0.11
103 4 0.02
104 62 0.27
105 1 0.00
108 2 0.01
109 15 0.06
110 4 0.02
111 23 0.10
113 1 0.00
115 34 0.15
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (104 bp):
TTGAATGAAAAATCTTATCCGGTACAATAATAATTTCAAATGACAAAGAATCTTAACTATTCTTT
TTCAGTGATATATCACTTCAAATAAGAACTTATTTCATA
Found at i:3707233 original size:115 final size:118
Alignment explanation
Indices: 3707032--3707364 Score: 384
Period size: 123 Copynumber: 2.8 Consensus size: 118
3707022 CTATTTTTTC
* ** *
3707032 AGTGATATATCACCTTAAATC-TGACTTATTACATATTGAATGAAAAGA---T-T-TAGTACAAT
1 AGTGATATATCACCTCAAATCAAAACTTATTTCATATTGAATGAAAA-ATCTTATATAGTACAAT
* *
3707091 AATAATTTCAAATGATAAAGTACCTTAACTATTCACATCCTTTTCCTTTT-AGTG-
65 AATAATTTCAAATGACAAAG-AACTTAACTATTCACATCCTTTT-CTTTTAAGTGT
3707145 A-T-ATAT-T-ACCTCAAATCAAAACTTTATTTCATATTGAATGAAAAATCTTATATAGTACAAT
1 AGTGATATATCACCTCAAATCAAAAC-TTATTTCATATTGAATGAAAAATCTTATATAGTACAAT
* * * * *
3707206 AATAATTTTAAATGACAGAGAATCTTAAATATTCACGTTCTTTTCTTTTAAGTGATTT
65 AATAATTTCAAATGACAAAGAA-CTTAACTATTCACATCCTTTTCTTTTAAGTG---T
*
3707264 CAGTGATATATCACCTCAAATCAAAACTTATTTCATATTGAATGAAAAATCTTATATGGTACAAT
1 -AGTGATATATCACCTCAAATCAAAACTTATTTCATATTGAATGAAAAATCTTATATAGTACAAT
3707329 AATAATTTCAAATGACAAAGAACATTAACTATTCAC
65 AATAATTTCAAATGACAAAGAAC-TTAACTATTCAC
3707365 GTCATTCCAT
Statistics
Matches: 186, Mismatches: 15, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
109 9 0.05
110 4 0.02
111 24 0.13
112 1 0.01
113 2 0.01
114 7 0.04
115 48 0.26
120 1 0.01
121 1 0.01
122 5 0.03
123 69 0.37
124 15 0.08
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (118 bp):
AGTGATATATCACCTCAAATCAAAACTTATTTCATATTGAATGAAAAATCTTATATAGTACAATA
ATAATTTCAAATGACAAAGAACTTAACTATTCACATCCTTTTCTTTTAAGTGT
Found at i:3709667 original size:3 final size:3
Alignment explanation
Indices: 3709661--3709685 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3709651 TTCTTCTTCT
3709661 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
3709686 GTTCATCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:3710128 original size:25 final size:26
Alignment explanation
Indices: 3710095--3710146 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
3710085 TATTTTCATA
** *
3710095 TATTAATTTTTTAATAAA-ACTATAT
1 TATTAATTTCATAATAAATAATATAT
*
3710120 TATTTATTTCATAATAAATAATATAT
1 TATTAATTTCATAATAAATAATATAT
3710146 T
1 T
3710147 TGAAAGGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTAATTTCATAATAAATAATATAT
Found at i:3712979 original size:24 final size:24
Alignment explanation
Indices: 3712952--3713000 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3712942 TATTAATTTT
3712952 TTTATTATTTAAAAATAAAAATAA
1 TTTATTATTTAAAAATAAAAATAA
* * *
3712976 TTTATTATTTATATATTAAAATAA
1 TTTATTATTTAAAAATAAAAATAA
3713000 T
1 T
3713001 ACTAATGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTATTATTTAAAAATAAAAATAA
Found at i:3714545 original size:30 final size:32
Alignment explanation
Indices: 3714511--3714586 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
3714501 ATAATTGTTA
3714511 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* * *
3714541 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
3714574 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
3714587 TTATTAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.36
31 2 0.05
32 7 0.18
33 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:3714575 original size:33 final size:30
Alignment explanation
Indices: 3714496--3714583 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 30
3714486 AGTATTTGTT
* *
3714496 TTTAAATAATTGTTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAATATA
* *
3714528 ATTATATAAATATTATTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTATT--AAT-ATA
3714561 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
3714584 AATTTATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 15 0.33
33 19 0.41
34 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAATATA
Found at i:3716387 original size:21 final size:21
Alignment explanation
Indices: 3716361--3716401 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3716351 GCCATCTCTG
3716361 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
3716382 CAGGGTTACATTCCTAGCCC
1 CAGGGTTACATTCCTAGCCC
3716402 GCCAAGTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.27
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCT
Found at i:3716410 original size:21 final size:21
Alignment explanation
Indices: 3716365--3716420 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3716355 TCTCTGCAGG
* *
3716365 GTTACATTCCTAGCCCTCAGG
1 GTTACATTCCTAGCCCCCAGA
3716386 GTTACATTCCTAGCCCGCCA-A
1 GTTACATTCCTAGCCC-CCAGA
*
3716407 GTTACATGCCTAGC
1 GTTACATTCCTAGC
3716421 ATGCAGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.27
Consensus pattern (21 bp):
GTTACATTCCTAGCCCCCAGA
Found at i:3716983 original size:34 final size:34
Alignment explanation
Indices: 3716945--3717017 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
3716935 TTAAATATGT
3716945 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
*
3716979 TTAAAATACAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
3717013 TTAAA
1 TTAAA
3717018 TTCAACTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:3717144 original size:14 final size:14
Alignment explanation
Indices: 3717125--3717155 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3717115 TTTTATCCTT
3717125 AACATATACATTAA
1 AACATATACATTAA
3717139 AACATATACATTAA
1 AACATATACATTAA
3717153 AAC
1 AAC
3717156 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:3717305 original size:63 final size:63
Alignment explanation
Indices: 3717221--3717348 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
3717211 TTTCAATGTC
* * *
3717221 ACAACCAACTTATTACTTCACATTTGTTCAATTTATCCATAACATTTTATACAATTTATTCAA
1 ACAACCAACTCATCACTTCACATTTATTCAATTTATCCATAACATTTTATACAATTTATTCAA
* *
3717284 ACAACCAACTCATCACTTCACATTTATTCAATTTATCCATAACATTTTTTCCAATTTATTCAA
1 ACAACCAACTCATCACTTCACATTTATTCAATTTATCCATAACATTTTATACAATTTATTCAA
3717347 AC
1 AC
3717349 TTCACATAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (63 bp):
ACAACCAACTCATCACTTCACATTTATTCAATTTATCCATAACATTTTATACAATTTATTCAA
Found at i:3717953 original size:127 final size:126
Alignment explanation
Indices: 3717478--3718338 Score: 1021
Period size: 127 Copynumber: 6.7 Consensus size: 126
3717468 CCATCCATCT
* *
3717478 ATAGTTTCCCGGGGGACGTGAGTGACATAATAGGGCAATGATAACATATTCTCTGGCAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
3717543 AGAAGGCGCGCCCCCGGGAACGCGA-TTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
66 GGAAGGCGC-CCCCCGGGAACGC-ACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
3717605 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
3717670 GGAAAGCACCCCCCCCCCGGGAACGCACTTTCACCACTTTGCCAAGCCCCCTTCAAAAATAATAG
66 GG-AAG---GCGCCCCCCGGGAACG---------CACTTT--CAAGTCCCC-TCAGAAATAATAG
*
3717735 GTACTGACATGA
115 GTACTGCCATGA
* *
3717747 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
3717812 AGAAGGCGTGCCCCCGGGAACGCACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATTA
66 GGAAGGCG-CCCCCCGGGAACGCACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
*
3717874 ATAGTTTCCTGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
** * * *
3717939 GGAAGGCGTCCCCCCGGGAATACGCTTTCAAGCCCCCTCAGAAATAATAGGTACTACCATGA
66 GGAAGGCG-CCCCCCGGGAACGCACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
*
3718001 ATAG-TTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
1 ATAGTTTCC-CGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
* * *
3718065 TGGAAGGCGCACCCCCGGGAACGCGCTTTCAAGTCCCCAT-AGAAATAATAGTTACTTCCATGA
65 TGGAAGGCGC-CCCCCGGGAACGCACTTTCAAGTCCCC-TCAGAAATAATAGGTACTGCCATGA
* * *
3718128 ATAGTTCCCCGGGGGACATGAATGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * **
3718193 GGAAGGCACGCCCCCGGGAACGCGCTTTC-A--CCACT------T--TGGGTACTGATATGA
66 GGAAGGCGC-CCCCCGGGAACGCACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
* ** *** * *
3718244 ATAATGCCCATAGGGACATGAGTGACATAATAAGGCAATGATAACATATTATCTGACAAAATAAT
1 ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
3718309 GGAAGGCGCCCCTCCAGGAACGCACCTTCA
66 GGAAGGCGCCCC-CCGGGAACGCACTTTCA
3718339 CATGAATAGT
Statistics
Matches: 649, Mismatches: 61, Indels: 58
0.85 0.08 0.08
Matches are distributed among these distances:
115 3 0.00
116 87 0.13
118 1 0.00
123 1 0.00
124 3 0.00
126 6 0.01
127 397 0.61
128 15 0.02
130 18 0.03
131 2 0.00
138 2 0.00
139 16 0.02
141 11 0.02
142 87 0.13
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (126 bp):
ATAGTTTCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCCCCCCGGGAACGCACTTTCAAGTCCCCTCAGAAATAATAGGTACTGCCATGA
Found at i:3721471 original size:22 final size:23
Alignment explanation
Indices: 3721443--3721490 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3721433 TTTATGATAT
*
3721443 TTATTTAATATAATAATTAA-TA
1 TTATTTAATATAAAAATTAATTA
*
3721465 TTATTTATTATAAAAATTAATTA
1 TTATTTAATATAAAAATTAATTA
3721488 TTA
1 TTA
3721491 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAATATAAAAATTAATTA
Found at i:3726502 original size:21 final size:20
Alignment explanation
Indices: 3726456--3726574 Score: 75
Period size: 20 Copynumber: 5.8 Consensus size: 20
3726446 CAGTCTCCAG
*
3726456 ATTCGCAATGCGA-TTTTGA
1 ATTCGCAATGCGATTTTTAA
*
3726475 CTATCGCAATGCGATTTTTCAA
1 AT-TCGCAATGCGATTTTT-AA
*
3726497 ATTCGC-GTAGCGATTTTGTAA
1 ATTCGCAAT-GCGATTTT-TAA
* * *
3726518 AATCGCAATGCGAATATGTAA
1 ATTCGCAATGCG-ATTTTTAA
* *
3726539 A-TCGCAATGCGAATATGTAA
1 ATTCGCAATGCG-ATTTTTAA
*
3726559 A-TCGCAACGCGATTTT
1 ATTCGCAATGCGATTTT
3726575 CAAAGCGCCA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.05
20 41 0.50
21 30 0.37
22 7 0.09
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (20 bp):
ATTCGCAATGCGATTTTTAA
Found at i:3726542 original size:20 final size:20
Alignment explanation
Indices: 3726517--3726570 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3726507 CGATTTTGTA
3726517 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
3726537 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
*
3726557 AAATCGCAACGCGA
1 AAATCGCAATGCGA
3726571 TTTTCAAAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGT
Found at i:3726734 original size:22 final size:22
Alignment explanation
Indices: 3726709--3726766 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
3726699 TCACTCTCTA
*
3726709 CGGTGACATCCGTCCCCATCTC
1 CGGTGAAATCCGTCCCCATCTC
3726731 CGGTGAAATCCGTCCCCATCTC
1 CGGTGAAATCCGTCCCCATCTC
*
3726753 CGGCGAAATCCGTC
1 CGGTGAAATCCGTC
3726767 TATCTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.41, G:0.21, T:0.21
Consensus pattern (22 bp):
CGGTGAAATCCGTCCCCATCTC
Found at i:3727169 original size:20 final size:20
Alignment explanation
Indices: 3727144--3727243 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
3727134 AAAATCGCAA
3727144 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** * *
3727164 CGATAGTCATTTTTGTGTTG
1 CGATAGTCAAATTCGCGTTG
** *
3727184 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
3727203 CGAT--T---A-TCTCGTTG
1 CGATAGTCAAATTCGCGTTG
3727217 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
3727237 CGATAGT
1 CGATAGT
3727244 AATTTTCGTG
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
14 11 0.18
16 1 0.02
17 1 0.02
19 13 0.21
20 36 0.58
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:3727251 original size:20 final size:19
Alignment explanation
Indices: 3727144--3727260 Score: 73
Period size: 20 Copynumber: 6.2 Consensus size: 19
3727134 AAAATCGCAA
*
3727144 CGATAGTCAAATTCGCGTTG
1 CGATAGT-AATTTCGCGTTG
* * *
3727164 CGATAGTCATTTTTGTGTTG
1 CGATAGT-AATTTCGCGTTG
** *
3727184 CGATTTTCATTTCGCGTTG
1 CGATAGTAATTTCGCGTTG
*
3727203 CGAT--T-A--TCTCGTTG
1 CGATAGTAATTTCGCGTTG
*
3727217 CGATAGTCAAATTCGCGTTG
1 CGATAGT-AATTTCGCGTTG
*
3727237 CGATAGTAATTTTCGTGTTG
1 CGATAGTAA-TTTCGCGTTG
3727257 CGAT
1 CGAT
3727261 TTTAAGTTTC
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
14 11 0.14
16 2 0.03
17 1 0.01
18 1 0.01
19 14 0.18
20 47 0.62
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (19 bp):
CGATAGTAATTTCGCGTTG
Found at i:3727270 original size:20 final size:20
Alignment explanation
Indices: 3727212--3727270 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
3727202 GCGATTATCT
*
3727212 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
*
3727232 CGTTGCGATAGTAATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* **
3727252 TGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
3727271 AGAAACTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:3727282 original size:73 final size:73
Alignment explanation
Indices: 3727144--3727282 Score: 190
Period size: 73 Copynumber: 1.9 Consensus size: 73
3727134 AAAATCGCAA
* * * * ***
3727144 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTTGTGTTGCGATTTTCATTTCGCGTTGCGATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTAATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
3727209 TCTCGTTG
66 TCTCGTTG
*
3727217 CGATAGTCAAATTCGCGTTGCGATAGTAATTTTCGTGTTGCGATTTTAAGTTTC-AGAAACTATT
1 CGATAGTCAAATTCGCGTTGCGATAGTAATTTTCGTGTTGCGATTTTAA-TTTCGAGAAACGATT
3727281 AT
65 AT
3727283 TCTTCTGCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 53 0.93
74 4 0.07
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTAATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
TCTCGTTG
Found at i:3729156 original size:33 final size:33
Alignment explanation
Indices: 3729119--3729181 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
3729109 CACGAAACTT
* *
3729119 AAATCGCAACGGGATAATCGCAATACGAAATAA
1 AAATCGCAACGGGAAAATCACAATACGAAATAA
* *
3729152 AAATCGCAACGTGAAAATCACAATGCGAAA
1 AAATCGCAACGGGAAAATCACAATACGAAA
3729182 ATGACTATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.14
Consensus pattern (33 bp):
AAATCGCAACGGGAAAATCACAATACGAAATAA
Found at i:3729240 original size:34 final size:39
Alignment explanation
Indices: 3729202--3729288 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
3729192 CAATTTTGGT
3729202 TTCGCGTTGCGA-A-T-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATTCCGCGTTGCGATAGTCAAA
**
3729236 TTCGCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCA-TTCCGCGTTGCGATAGTCAAA
3729276 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3729289 TTAAGTTTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 12 0.27
35 1 0.02
36 1 0.02
37 1 0.02
39 3 0.07
40 27 0.60
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (39 bp):
TTCGCGTTGCGATAGTCATTCCGCGTTGCGATAGTCAAA
Found at i:3729245 original size:20 final size:20
Alignment explanation
Indices: 3729220--3729288 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3729210 GCGAATATCC
*
3729220 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
3729240 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
3729260 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
3729280 CGTTGCGAT
1 CGTTGCGAT
3729289 TTAAGTTTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:3729303 original size:19 final size:20
Alignment explanation
Indices: 3729275--3729317 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
3729265 CGATAGTCAT
3729275 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
3729294 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
3729314 TTTC
1 TTTC
3729318 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:3729869 original size:42 final size:42
Alignment explanation
Indices: 3729823--3729914 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
3729813 TCTCCTATTT
*
3729823 TTCAAGAGG-CCTCTATCATCCCTCAAGA-GTCTCCTCCCACCG
1 TTCAAGAGGCCCT-TATCATCCCTCAAGAGGTC-CCTCCCACCA
* ** *
3729865 TTCAAGAGGCCCTTGTCATCGTTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCTTATCATCCCTCAAGAGGTCCCTCCCACCA
3729907 TTCAAGAG
1 TTCAAGAG
3729915 CCCGATTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
42 37 0.86
43 6 0.14
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCCTTATCATCCCTCAAGAGGTCCCTCCCACCA
Found at i:3729913 original size:21 final size:21
Alignment explanation
Indices: 3729845--3729914 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
3729835 CTATCATCCC
3729845 TCAAGA-GTCTCCTCCCACCGT
1 TCAAGAGGTC-CCTCCCACCGT
** *
3729866 TCAAGAGG-CCCTTGTCATCGT
1 TCAAGAGGTCCC-TCCCACCGT
* *
3729887 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCACCGT
3729908 TCAAGAG
1 TCAAGAG
3729915 CCCGATTCAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGGTCCCTCCCACCGT
Found at i:3731335 original size:15 final size:14
Alignment explanation
Indices: 3731300--3731347 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
3731290 TTTCTTGTTT
3731300 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3731314 AATTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
3731329 TATTGATGTGTAAA
1 AATTGATTTGTAAA
3731343 TAATT
1 -AATT
3731348 CTTATTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3731568 original size:34 final size:34
Alignment explanation
Indices: 3731508--3731629 Score: 100
Period size: 34 Copynumber: 3.4 Consensus size: 34
3731498 AGTCAATTCG
* **
3731508 CATTGCGATAGTCTAATACGTTTTGCGATTTTCT
1 CATTGCGATAGTCAAATACGCATTGCGATTTTCT
* * *
3731542 CATTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATACGCATTGCGAT--T----TTCT
* * * *
3731582 CGTTGTGATAGTCAAATTCGCATTGCGATTTTTT
1 CATTGCGATAGTCAAATACGCATTGCGATTTTCT
3731616 CATTGCGATAGTCA
1 CATTGCGATAGTCA
3731630 TATTCGCGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
34 39 0.57
36 1 0.01
38 1 0.01
40 27 0.40
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.37
Consensus pattern (34 bp):
CATTGCGATAGTCAAATACGCATTGCGATTTTCT
Found at i:3731599 original size:20 final size:20
Alignment explanation
Indices: 3731544--3731726 Score: 138
Period size: 20 Copynumber: 9.8 Consensus size: 20
3731534 GATTTTCTCA
* *
3731544 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATTCGCG
3731564 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
3731584 TTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
** *
3731604 TTGCGAT--T----TTTTCA
1 TTGCGATAGTCAAATTCGCG
*
3731618 TTGCGATAGTCATATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
3731638 TTACGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
3731658 TTGCGAT--T----TTTGAG
1 TTGCGATAGTCAAATTCGCG
* * *
3731672 TTGCGATAATCAAATTCACC
1 TTGCGATAGTCAAATTCGCG
*
3731692 TTGCGATAGTCAATTTCGCG
1 TTGCGATAGTCAAATTCGCG
*
3731712 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
3731727 GAGTGATAAC
Statistics
Matches: 126, Mismatches: 25, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
14 22 0.17
16 2 0.02
18 2 0.02
20 100 0.79
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:3731608 original size:74 final size:74
Alignment explanation
Indices: 3731493--3731664 Score: 229
Period size: 74 Copynumber: 2.3 Consensus size: 74
3731483 AAATTGCAAC
* * * **
3731493 ACGAAAGTC-AATTCGCATTGCGATAGTCTAATACGTTTTGCGATTTTCTCATTGCGATAGTCAA
1 ACGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCATTGCGATTTTCTCATTGCGATAGTCAA
3731557 ATACCCGTT
66 ATACCCGTT
* * * * *
3731566 GCGATAGTCAAATTCGCGTTGTGATAGTCAAATTCGCATTGCGATTTTTTCATTGCGATAGTCAT
1 ACGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCATTGCGATTTTCTCATTGCGATAGTCAA
* *
3731631 ATTCGCGTT
66 ATACCCGTT
3731640 ACGATAGTCAAATTCGCGTTGCGAT
1 ACGATAGTCAAATTCGCGTTGCGAT
3731665 TTTTGAGTTG
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
73 7 0.08
74 77 0.92
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (74 bp):
ACGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCATTGCGATTTTCTCATTGCGATAGTCAA
ATACCCGTT
Found at i:3731622 original size:54 final size:55
Alignment explanation
Indices: 3731563--3731718 Score: 217
Period size: 54 Copynumber: 2.9 Consensus size: 55
3731553 TCAAATACCC
* *
3731563 GTTGCGATAGTCAAATTCGCGTTGTGATAGTCAAATTCGCATTGCGATTTTTTCA
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTTCA
* * *
3731618 -TTGCGATAGTCATATTCGCGTTACGATAGTCAAATTCGCGTTGCGA-TTTTTGA
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTTCA
* * * *
3731671 GTTGCGATAATCAAATTCACCTTGCGATAGTCAATTTCGCGTTGCGAT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
3731719 ATTCAAATGA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 6 0.07
54 82 0.93
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (55 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTTCA
Found at i:3732049 original size:18 final size:18
Alignment explanation
Indices: 3732026--3732060 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3732016 AAGCCGGTTG
*
3732026 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3732044 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
3732061 GCCTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3734355 original size:24 final size:24
Alignment explanation
Indices: 3734321--3734374 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3734311 CTGAAACATC
*
3734321 ATCAAAATCTGAGTATTGACTAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
3734345 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
3734369 ATCAAA
1 ATCAAA
3734375 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:3735255 original size:41 final size:41
Alignment explanation
Indices: 3735210--3735304 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
3735200 GACAGTCAGA
3735210 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
3735251 ATCGCGTTGCGATAGTCAGAATCGTGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
3735292 ATTGCGTTGCGAT
1 ATCGCGTTGCGAT
3735305 TATGTATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:3735256 original size:21 final size:21
Alignment explanation
Indices: 3735230--3735325 Score: 133
Period size: 21 Copynumber: 4.6 Consensus size: 21
3735220 GATAGTCAGA
3735230 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
3735251 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
3735271 ATCGTGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
*
3735292 ATTGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
3735313 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
3735326 AGTCAGAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 46 0.72
22 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.40
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:3735313 original size:62 final size:61
Alignment explanation
Indices: 3735203--3735344 Score: 214
Period size: 62 Copynumber: 2.3 Consensus size: 61
3735193 GTGTTGAGAC
3735203 AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGAT
* ** *
3735264 AGTCAGAATCGTGTTGCGATTATGT-ATTATTGCGTTGCGATTATGTATTATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGAT
*
3735326 AGTCAGAATCGCATTGCGA
1 AGTCAGAATCGCGTTGCGA
3735345 ATCTGGAAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 18 0.25
62 53 0.73
63 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (61 bp):
AGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGAT
Found at i:3735394 original size:19 final size:19
Alignment explanation
Indices: 3735370--3735406 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3735360 TGTGATACTG
*
3735370 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
3735389 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3735407 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:3737827 original size:3 final size:3
Alignment explanation
Indices: 3737821--3737851 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3737811 AATTATTATT
*
3737821 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3737852 TATCGGGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3738338 original size:41 final size:42
Alignment explanation
Indices: 3738279--3738371 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
3738269 ACCCGAAGGT
* * *
3738279 CTTACGGATGGCCCGAAGGACTT-ACCATCTTGCTCGAAAGA
1 CTTACAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
* * * * *
3738320 CTTACAGATGACCTGAAGGATTTAATCATCATGTTTGAAAGA
1 CTTACAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
*
3738362 CTTACTGATG
1 CTTACAGATG
3738372 GCCCAAATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 19 0.45
42 23 0.55
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CTTACAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
Found at i:3738578 original size:21 final size:21
Alignment explanation
Indices: 3738554--3738646 Score: 100
Period size: 21 Copynumber: 4.4 Consensus size: 21
3738544 GGATGGCCCA
*
3738554 AAGGACTTATCATCTTGCTCG
1 AAGGACTTATCATCATGCTCG
*
3738575 AAGGACTTATCATCTTGCTCG
1 AAGGACTTATCATCATGCTCG
* *
3738596 AAAGACTTA-CAT-ATGACCCG
1 AAGGACTTATCATCATG-CTCG
* *
3738616 AAGGATTTATTCATCATGCTTG
1 AAGGACTTA-TCATCATGCTCG
3738638 AAGGACTTA
1 AAGGACTTA
3738647 CTGATGGCCC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 29 0.48
22 13 0.22
23 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
AAGGACTTATCATCATGCTCG
Found at i:3738618 original size:41 final size:42
Alignment explanation
Indices: 3738573--3738665 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
3738563 TCATCTTGCT
*
3738573 CGAAGGACTTA-TCATCTTGCTCGAAAGACTTACAT-ATGACC
1 CGAAGGACTTATTCATCATGCTCGAAAGACTTAC-TGATGACC
* * * *
3738614 CGAAGGATTTATTCATCATGCTTGAAGGACTTACTGATGGCC
1 CGAAGGACTTATTCATCATGCTCGAAAGACTTACTGATGACC
3738656 CGAAGGACTT
1 CGAAGGACTT
3738666 GCCAATTTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 11 0.25
42 33 0.75
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (42 bp):
CGAAGGACTTATTCATCATGCTCGAAAGACTTACTGATGACC
Found at i:3751797 original size:22 final size:23
Alignment explanation
Indices: 3751742--3751798 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 23
3751732 GATCAGATCT
*
3751742 TTGTAATTAGGTCTGGGTTTGGGT
1 TTGTAATTAGGTCTGGGTTT-GGC
3751766 TGGCTGTAATTAGGTCTGGGTTT-GC
1 T---TGTAATTAGGTCTGGGTTTGGC
3751791 TTGTAATT
1 TTGTAATT
3751799 GGGCCTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
22 7 0.24
24 1 0.03
25 2 0.07
27 19 0.66
ACGTcount: A:0.14, C:0.07, G:0.33, T:0.46
Consensus pattern (23 bp):
TTGTAATTAGGTCTGGGTTTGGC
Found at i:3751853 original size:3 final size:3
Alignment explanation
Indices: 3751847--3751872 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3751837 AATAATAATA
3751847 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3751873 CGGGACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3753928 original size:24 final size:24
Alignment explanation
Indices: 3753881--3753955 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
3753871 CGAAGGTGTT
3753881 CGTGTTCGTTTATTTAATGTTCGTGAA
1 CGTGTTCGTTTA---AATGTTCGTGAA
*
3753908 CGTGTTCGTTTAAATGTTCGTGAG
1 CGTGTTCGTTTAAATGTTCGTGAA
* * *
3753932 CTTGTTCGTTTATACGTTCGTGAA
1 CGTGTTCGTTTAAATGTTCGTGAA
3753956 TATGTTTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 31 0.72
27 12 0.28
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.45
Consensus pattern (24 bp):
CGTGTTCGTTTAAATGTTCGTGAA
Found at i:3753961 original size:24 final size:24
Alignment explanation
Indices: 3753899--3754036 Score: 129
Period size: 23 Copynumber: 5.9 Consensus size: 24
3753889 TTTATTTAAT
* * *
3753899 GTTCGTGAACGTGTTCGTTTAAAT
1 GTTCGTGAACATGTTCGTTTAGAC
* * *
3753923 GTTCGTGAGCTTGTTCGTTTATAC
1 GTTCGTGAACATGTTCGTTTAGAC
* *
3753947 GTTCGTGAATATGTTTGTTTAG-C
1 GTTCGTGAACATGTTCGTTTAGAC
* * *
3753970 GTTCGCGAACATGTTAGTTT-GGC
1 GTTCGTGAACATGTTCGTTTAGAC
*
3753993 GTTCGTGAACATGTTCGTTT-GGC
1 GTTCGTGAACATGTTCGTTTAGAC
* *
3754016 GTTCATGAACATGCTCGTTTA
1 GTTCGTGAACATGTTCGTTTA
3754037 TATATGTTCA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
22 1 0.01
23 58 0.60
24 37 0.39
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.41
Consensus pattern (24 bp):
GTTCGTGAACATGTTCGTTTAGAC
Found at i:3761322 original size:20 final size:20
Alignment explanation
Indices: 3761297--3761343 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3761287 AATTTCAGTA
* *
3761297 TCATCGCCTGCATAAACTGT
1 TCATCGACTGCATAAACTAT
*
3761317 TCATCGATTGCATAAACTAT
1 TCATCGACTGCATAAACTAT
3761337 TCATCGA
1 TCATCGA
3761344 TGTACTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (20 bp):
TCATCGACTGCATAAACTAT
Found at i:3761344 original size:20 final size:20
Alignment explanation
Indices: 3761305--3761344 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3761295 TATCATCGCC
*
3761305 TGCATAAACTGTTCATCGAT
1 TGCATAAACTATTCATCGAT
3761325 TGCATAAACTATTCATCGAT
1 TGCATAAACTATTCATCGAT
3761345 GTACTTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TGCATAAACTATTCATCGAT
Found at i:3762725 original size:17 final size:17
Alignment explanation
Indices: 3762703--3762745 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3762693 CTATCATTGC
*
3762703 ACACAAATTGAAATAAT
1 ACACAAAGTGAAATAAT
3762720 ACACAAAGTGAAATAAT
1 ACACAAAGTGAAATAAT
3762737 ACACAAAGT
1 ACACAAAGT
3762746 ACACTTACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.58, C:0.14, G:0.09, T:0.19
Consensus pattern (17 bp):
ACACAAAGTGAAATAAT
Found at i:3776624 original size:25 final size:23
Alignment explanation
Indices: 3776591--3776637 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
3776581 TTCAACTATA
3776591 ATAACATGAGTTATCAATAATAATC
1 ATAACATGAG-TAT-AATAATAATC
3776616 ATAACATGAGTATAATAATAAT
1 ATAACATGAGTATAATAATAAT
3776638 TAGCACTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.41
24 3 0.14
25 10 0.45
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (23 bp):
ATAACATGAGTATAATAATAATC
Found at i:3776776 original size:16 final size:16
Alignment explanation
Indices: 3776752--3776782 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3776742 AACTAAACAA
*
3776752 ATTATATAAACAAAAC
1 ATTAAATAAACAAAAC
3776768 ATTAAATAAACAAAA
1 ATTAAATAAACAAAA
3776783 TAAATGTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
ATTAAATAAACAAAAC
Found at i:3778471 original size:14 final size:14
Alignment explanation
Indices: 3778448--3778540 Score: 87
Period size: 14 Copynumber: 6.6 Consensus size: 14
3778438 GCTTGGTCTG
*
3778448 GTCCGGGTCAACTC
1 GTCCGAGTCAACTC
*
3778462 ATCCGAGTCAACTC
1 GTCCGAGTCAACTC
* *
3778476 GTTCTGAGTCAACCC
1 G-TCCGAGTCAACTC
**
3778491 GTCTAAGTCAACTC
1 GTCCGAGTCAACTC
* *
3778505 GTCCGAGTAAACCC
1 GTCCGAGTCAACTC
**
3778519 GTCTAAGTCAACTC
1 GTCCGAGTCAACTC
3778533 GTCCGAGT
1 GTCCGAGT
3778541 AAACCCGTTG
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 49 0.80
15 12 0.20
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (14 bp):
GTCCGAGTCAACTC
Found at i:3778520 original size:28 final size:28
Alignment explanation
Indices: 3778467--3778548 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
3778457 AACTCATCCG
* *
3778467 AGTCAACTCGTTCTGAGTCAACCCGTCTA
1 AGTCAACTCG-TCCGAGTAAACCCGTCTA
3778496 AGTCAACTCGTCCGAGTAAACCCGTCTA
1 AGTCAACTCGTCCGAGTAAACCCGTCTA
3778524 AGTCAACTCGTCCGAGTAAACCCGT
1 AGTCAACTCGTCCGAGTAAACCCGT
3778549 TGACTTTGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 41 0.80
29 10 0.20
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
AGTCAACTCGTCCGAGTAAACCCGTCTA
Found at i:3784598 original size:36 final size:36
Alignment explanation
Indices: 3784546--3784620 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
3784536 TATAAAAAAT
*
3784546 TAAGCGAGCTTATAAACAAGCATGTTCATGAACATA
1 TAAGCGAGCTTATAAACAAGCATGTTAATGAACATA
* *
3784582 TAAGCGAGCTTCTAAACAAGCTTGTTAATGAACATA
1 TAAGCGAGCTTATAAACAAGCATGTTAATGAACATA
3784618 TAA
1 TAA
3784621 ATAAGCTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (36 bp):
TAAGCGAGCTTATAAACAAGCATGTTAATGAACATA
Found at i:3784626 original size:24 final size:24
Alignment explanation
Indices: 3784594--3784641 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3784584 AGCGAGCTTC
3784594 TAAACAAGCTTGTTAATGAACATA
1 TAAACAAGCTTGTTAATGAACATA
* **
3784618 TAAATAAGCTTGTTCGTGAACATA
1 TAAACAAGCTTGTTAATGAACATA
3784642 AACGAACCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (24 bp):
TAAACAAGCTTGTTAATGAACATA
Found at i:3784628 original size:36 final size:36
Alignment explanation
Indices: 3784552--3784628 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
3784542 AAATTAAGCG
* * *
3784552 AGCTTATAAACAAGCATGTTCATGAACATATAAGCG
1 AGCTTATAAACAAGCATGTTAATGAACATATAAACA
* * *
3784588 AGCTTCTAAACAAGCTTGTTAATGAACATATAAATA
1 AGCTTATAAACAAGCATGTTAATGAACATATAAACA
3784624 AGCTT
1 AGCTT
3784629 GTTCGTGAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (36 bp):
AGCTTATAAACAAGCATGTTAATGAACATATAAACA
Found at i:3791028 original size:19 final size:19
Alignment explanation
Indices: 3790981--3791031 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3790971 ATTGAGCTTT
3790981 TTGGTATC-AGTACTGACCC
1 TTGGTATCGA-TACTGACCC
* *
3791000 TTGAGTATCGATACTTACTC
1 TTG-GTATCGATACTGACCC
3791020 TTGGTATCGATA
1 TTGGTATCGATA
3791032 TTGAAATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 15 0.54
21 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGGTATCGATACTGACCC
Found at i:3791112 original size:22 final size:22
Alignment explanation
Indices: 3791086--3791142 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
3791076 CCCTTAGACC
3791086 GAGTATCGATACTTCTATACTA
1 GAGTATCGATACTTCTATACTA
* *
3791108 GAGTATTGATACTTTTATACTA
1 GAGTATCGATACTTCTATACTA
*
3791130 GATTATCGATACT
1 GAGTATCGATACT
3791143 CTCCTGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
GAGTATCGATACTTCTATACTA
Found at i:3791571 original size:2 final size:2
Alignment explanation
Indices: 3791564--3791630 Score: 88
Period size: 2 Copynumber: 35.0 Consensus size: 2
3791554 TTTCATATGC
3791564 TA TA TA TA -A T- TA T- TA TCA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
*
3791604 TA TA TA TA TA TA TA TA T- TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3791631 GTTATTATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
1 4 0.07
2 52 0.90
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.