Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_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: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:3754653 original size:37 final size:37
Alignment explanation
Indices: 3754580--3754654 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
3754570 GTTGAAAAAT
* *
3754580 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
3754617 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
3754654 A
1 A
3754655 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:3755112 original size:22 final size:23
Alignment explanation
Indices: 3755084--3755127 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3755074 CTAAGATTAA
*
3755084 AGATTTTA-AGATTTTTTTTTTG
1 AGATTTTAGAGAATTTTTTTTTG
3755106 AGATTTTAGAGAATTTTTTTTT
1 AGATTTTAGAGAATTTTTTTTT
3755128 CAAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (23 bp):
AGATTTTAGAGAATTTTTTTTTG
Found at i:3758237 original size:278 final size:279
Alignment explanation
Indices: 3757440--3758548 Score: 2103
Period size: 279 Copynumber: 4.0 Consensus size: 279
3757430 CGTTCCCACA
* * *
3757440 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAATCCCGTGGCAAATTCAACACAAAAAAAG
1 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAAGCCCGAGGAAAATTCAACACAAAAAAAG
3757505 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
66 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
*
3757570 TGGAGCAGAGTTTAAAACCCAGATTCTTTTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
131 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
3757635 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
196 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
3757700 TAAGAAGGTCTTTAACGTT
261 TAAGAAGGTCTTTAACGTT
*
3757719 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATACGCCCGAGGAAAATTCAACACAAAAAAAG
1 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAAGCCCGAGGAAAATTCAACACAAAAAAAG
3757784 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
66 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
3757849 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
131 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
3757914 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
196 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
3757979 TAAGAAGGTCTTTAACGTT
261 TAAGAAGGTCTTTAACGTT
*
3757998 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATACGCCCGAGGAAAATTCAACAC-AAAAAAG
1 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAAGCCCGAGGAAAATTCAACACAAAAAAAG
3758062 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
66 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
3758127 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
131 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
3758192 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
196 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
3758257 TAAGAAGGTCTTTAACGTT
261 TAAGAAGGTCTTTAACGTT
* *
3758276 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGAATAAGCCCGGGGAAAATTCAACACAAAAAAAG
1 TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAAGCCCGAGGAAAATTCAACACAAAAAAAG
*
3758341 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTCTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
66 CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
*
3758406 TGGAGCAGAGTTTAAAACCCAGATTCTTATGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
131 TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
* *
3758471 GAGAAGTGAGGGGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
196 GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
3758536 TAAGAAGGTCTTT
261 TAAGAAGGTCTTT
3758549 GGGGAAGAAG
Statistics
Matches: 817, Mismatches: 12, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
278 275 0.34
279 542 0.66
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (279 bp):
TTGGGAAAAGAGGTCTTTGATATCAGCAACCGTATAAGCCCGAGGAAAATTCAACACAAAAAAAG
CTTTCTTTTCACATTTGATTTCTGGGTTTTCTGTGTTGCAGCTTCTACGCTTAGTTCTTGCAAAG
TGGAGCAGAGTTTAAAACCCAGATTCTTCTGGGTGCTGATTAATGGAGGGATGGAGAAATTTTGG
GAGAAGAGAGGAGTAGATATGGATATTTGAAAAGTTAAGGAAGATAACCTTTGGGATTTTGGACT
TAAGAAGGTCTTTAACGTT
Found at i:3758734 original size:18 final size:18
Alignment explanation
Indices: 3758711--3758748 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3758701 TGGTTTTAAA
3758711 TATAAATTATAA-ATATTT
1 TATAAATT-TAATATATTT
3758729 TATAAATTTAATATATTT
1 TATAAATTTAATATATTT
3758747 TA
1 TA
3758749 ATTGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAAATTTAATATATTT
Found at i:3758890 original size:22 final size:22
Alignment explanation
Indices: 3758865--3758915 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
3758855 AGAATATTTT
*
3758865 TTATTTCAATAATCATATACT-A
1 TTATTTCAAAAATCATATA-TGA
3758887 TTATTTCAAAAATCATATATGA
1 TTATTTCAAAAATCATATATGA
3758909 TTATTTC
1 TTATTTC
3758916 TTGGATGCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATTTCAAAAATCATATATGA
Found at i:3761581 original size:42 final size:42
Alignment explanation
Indices: 3761524--3761607 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
3761514 GAAAAATTCA
* * *
3761524 ATTTCTTAATGAAAAAGGGGGAGCTGAA-AGTTTTCACATATT
1 ATTTCTTAATAAAAAAGGAGGAGCTGAACA-TTTTAACATATT
3761566 ATTTCTTAATAAAAAAGGAGGAGCTGAACATTTTAACATATT
1 ATTTCTTAATAAAAAAGGAGGAGCTGAACATTTTAACATATT
3761608 TTCCAACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (42 bp):
ATTTCTTAATAAAAAAGGAGGAGCTGAACATTTTAACATATT
Found at i:3762899 original size:82 final size:79
Alignment explanation
Indices: 3762801--3762961 Score: 196
Period size: 82 Copynumber: 2.0 Consensus size: 79
3762791 TATGTTCTAT
* * *
3762801 ATATATATAATTTTTCTCTTTCCATAATCCTTCTTAGACGAGTAAATAATTTTTTTCTGATTTTT
1 ATATATATAATTTTTCTCTTTCCATAATCCTTCATAGACGAGTAAACAA--TTTTT-TGATTATT
3762866 AAGATGATTATAAAGTA
63 AAGATGATTATAAAGTA
** * * * **
3762883 ATATATATGTTTTTTCTCTTTTCATAATCTTTCATGGGTGAGTAAACAATTTTTTGATTATTAAG
1 ATATATATAATTTTTCTCTTTCCATAATCCTTCATAGACGAGTAAACAATTTTTTGATTATTAAG
*
3762948 GTGATTATAAAGTA
66 ATGATTATAAAGTA
3762962 GTATTCTAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
79 23 0.34
80 5 0.07
82 40 0.59
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (79 bp):
ATATATATAATTTTTCTCTTTCCATAATCCTTCATAGACGAGTAAACAATTTTTTGATTATTAAG
ATGATTATAAAGTA
Found at i:3763169 original size:21 final size:22
Alignment explanation
Indices: 3763128--3763172 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3763118 TACACTTTAT
3763128 TTTTATAATATAAAAATATAAA
1 TTTTATAATATAAAAATATAAA
*
3763150 TTTTATAATAAAAATAATA-AAA
1 TTTTATAATATAAA-AATATAAA
3763172 T
1 T
3763173 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTATAATATAAAAATATAAA
Found at i:3768026 original size:33 final size:34
Alignment explanation
Indices: 3767964--3768076 Score: 133
Period size: 33 Copynumber: 3.3 Consensus size: 34
3767954 TTCAAATGTA
* *
3767964 ATTTTTGAAAACATATAGTATATGGTTTTGAAAACG
1 ATTTTTGAAAACGTATA--ATATGATTTTGAAAACG
* *
3768000 -TTTTGGAAAACGTATAATATGATTTTGAAAATG
1 ATTTTTGAAAACGTATAATATGATTTTGAAAACG
*
3768033 ATTTTTG--AACGTATAATATGTTTTTTGAAAACG
1 ATTTTTGAAAACGTATAATATG-ATTTTGAAAACG
3768066 ATTTTTGAAAA
1 ATTTTTGAAAA
3768077 TATATTAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 13 0.20
33 32 0.48
34 5 0.08
35 16 0.24
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (34 bp):
ATTTTTGAAAACGTATAATATGATTTTGAAAACG
Found at i:3768112 original size:22 final size:22
Alignment explanation
Indices: 3768086--3768142 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
3768076 ATATATTAAT
*
3768086 ATATATAATTTTTGAAAACATA
1 ATATATAGTTTTTGAAAACATA
* * *
3768108 TTATATAGTTTTTGGAAATATA
1 ATATATAGTTTTTGAAAACATA
3768130 ATATATAGTTTTT
1 ATATATAGTTTTT
3768143 TATTATTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
ATATATAGTTTTTGAAAACATA
Found at i:3768160 original size:12 final size:10
Alignment explanation
Indices: 3768141--3768200 Score: 68
Period size: 10 Copynumber: 5.6 Consensus size: 10
3768131 TATATAGTTT
3768141 TTTATTATTA
1 TTTATTATTA
3768151 TTTA-TATTA
1 TTTATTATTA
3768160 TTTATTATTA
1 TTTATTATTA
3768170 TTTTATGTATTA
1 -TTTAT-TATTA
3768182 GGTTATATTATTA
1 --TT-TATTATTA
3768195 TTTATT
1 TTTATT
3768201 TATTTAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
9 9 0.20
10 13 0.30
11 7 0.16
12 5 0.11
13 7 0.16
14 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (10 bp):
TTTATTATTA
Found at i:3768180 original size:22 final size:21
Alignment explanation
Indices: 3768141--3768216 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 21
3768131 TATATAGTTT
3768141 TTTATTATTA-TTTATATTA-
1 TTTATTATTATTTTATATTAG
3768160 TTTATTATTATTTTATGTATTAGG
1 TTTATTATTATTTTA--TATTA-G
3768184 TTATATTATTA-TTTAT-TTA-
1 TT-TATTATTATTTTATATTAG
3768203 TTTAATT-TTATTTT
1 TTT-ATTATTATTTT
3768217 TAACAGGTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
18 4 0.08
19 18 0.37
20 4 0.08
21 3 0.06
22 6 0.12
24 6 0.12
25 8 0.16
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTATTATTATTTTATATTAG
Found at i:3769314 original size:73 final size:73
Alignment explanation
Indices: 3769234--3769395 Score: 263
Period size: 73 Copynumber: 2.2 Consensus size: 73
3769224 TTAAATGACT
*
3769234 AAGGGTATCGATACCTCTAGGAGGTATCAGTACCCATTGGG-ACTTCTATTTTTCTCGGAGCCAA
1 AAGGGTATCGGTACCTCTAGGAGGTATCAGTACCCATTGGGCA-TTCTATTTTTCTCGGAGCCAA
3769298 AATTAACAC
65 AATTAACAC
* * * *
3769307 AAGGGTATCGGTACCTCTAGGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTTGGAGCCAAA
1 AAGGGTATCGGTACCTCTAGGAGGTATCAGTACCCATTGGGCATTCTATTTTTCTCGGAGCCAAA
3769372 ATTAACAC
66 ATTAACAC
3769380 AAGGGTATCGGTACCT
1 AAGGGTATCGGTACCT
3769396 ATGACTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 82 0.99
74 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (73 bp):
AAGGGTATCGGTACCTCTAGGAGGTATCAGTACCCATTGGGCATTCTATTTTTCTCGGAGCCAAA
ATTAACAC
Found at i:3769736 original size:13 final size:14
Alignment explanation
Indices: 3769718--3769751 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3769708 GATTTTCTTA
3769718 TTGAAAATC-ATTT
1 TTGAAAATCAATTT
3769731 TTG-AAATCAATTT
1 TTGAAAATCAATTT
3769744 TTGAAAAT
1 TTGAAAAT
3769752 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 10 0.53
14 4 0.21
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (14 bp):
TTGAAAATCAATTT
Found at i:3770076 original size:14 final size:16
Alignment explanation
Indices: 3770057--3770088 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3770047 TCAAACATCC
3770057 ATATC-ATCCAAA-AT
1 ATATCAATCCAAACAT
3770071 ATATCAATCCAAACAT
1 ATATCAATCCAAACAT
3770087 AT
1 AT
3770089 CCAAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATCAATCCAAACAT
Found at i:3772069 original size:23 final size:23
Alignment explanation
Indices: 3772022--3772101 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
3772012 AACTTGACGG
* *
3772022 GGGTATCGATAC-C-CTTATAG-
1 GGGTATCGATACACATTTAAAGA
*
3772042 GGGTATTGATACACATTTAAAGA
1 GGGTATCGATACACATTTAAAGA
3772065 GGGTATCGATACACATTTAAAGA
1 GGGTATCGATACACATTTAAAGA
3772088 GGGTATCGATACAC
1 GGGTATCGATACAC
3772102 GTTGAAGGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 11 0.21
21 1 0.02
22 5 0.09
23 36 0.68
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (23 bp):
GGGTATCGATACACATTTAAAGA
Found at i:3772116 original size:21 final size:21
Alignment explanation
Indices: 3772021--3772164 Score: 98
Period size: 21 Copynumber: 6.7 Consensus size: 21
3772011 AAACTTGACG
*
3772021 GGGGTATCGATAC-CCTT-ATA
1 GGGGTATCGATACACGTTGA-A
* * *
3772041 GGGGTATTGATACACATTTAAA
1 GGGGTATCGATACAC-GTTGAA
* *
3772063 GAGGGTATCGATACACATTTAAA
1 G-GGGTATCGATACAC-GTTGAA
3772086 GAGGGTATCGATACACGTTGAA
1 G-GGGTATCGATACACGTTGAA
* *
3772108 GGAGTATCGATAC-C-TAGTAA
1 GGGGTATCGATACACGTTG-AA
* **
3772128 GGGGGTATCGATACATGTTTTA
1 -GGGGTATCGATACACGTTGAA
3772150 GGGGTATCGATACAC
1 GGGGTATCGATACAC
3772165 TATGCACAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
19 2 0.02
20 15 0.15
21 38 0.37
22 10 0.10
23 38 0.37
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (21 bp):
GGGGTATCGATACACGTTGAA
Found at i:3777863 original size:73 final size:73
Alignment explanation
Indices: 3777744--3777884 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 73
3777734 AAATGAATAA
* *
3777744 GGGTATCGGTACCCATTGGGCATTCTATTTTTCTCAGAGCCAAAATTAACACAAGGGTATCGGTA
1 GGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCCAAAATTAACACAAGGGTATCAGTA
3777809 CCTCTAGG
66 CCTCTAGG
* *
3777817 GGGTATCGGTACCCATTAGGCATTCTGTTTTTCTCAGAGCCAAAATTAGCACAAGGGTATCAGTA
1 GGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCCAAAATTAACACAAGGGTATCAGTA
3777882 CCT
66 CCT
3777885 ATGACTTAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (73 bp):
GGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCCAAAATTAACACAAGGGTATCAGTA
CCTCTAGG
Found at i:3779334 original size:2 final size:2
Alignment explanation
Indices: 3779327--3779354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3779317 TATTTATTGG
3779327 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
3779355 GTTTTATGTA
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):
TA
Found at i:3781297 original size:13 final size:12
Alignment explanation
Indices: 3781279--3781322 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
3781269 CTTTTCTTCG
3781279 ATATTAAAAATAA
1 ATATT-AAAATAA
3781292 ATATTAAAATAA
1 ATATTAAAATAA
*
3781304 TTTATTTAAAATAA
1 -ATA-TTAAAATAA
3781318 ATATT
1 ATATT
3781323 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:3781323 original size:13 final size:13
Alignment explanation
Indices: 3781279--3781324 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3781269 CTTTTCTTCG
*
3781279 ATATTAAAAATAA
1 ATATTTAAAATAA
3781292 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
3781304 TTTATTTAAAATAA
1 -ATATTTAAAATAA
3781318 ATATTTA
1 ATATTTA
3781325 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:3782202 original size:15 final size:15
Alignment explanation
Indices: 3782178--3782209 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3782168 TGACAGTAAG
3782178 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
3782193 TTTCTTTTCTTTCTT
1 TTTCTCTTCTTTCTT
3782208 TT
1 TT
3782210 CTTGGTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:3782321 original size:18 final size:19
Alignment explanation
Indices: 3782252--3782338 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 19
3782242 GTTTAGTAGT
* **
3782252 TTTTTTTTTCCTTTCTCTGT
1 TTTTTTTTT-CTGTCTCTCC
3782272 TTTTTTTTTCTGTCT-TCC
1 TTTTTTTTTCTGTCTCTCC
*
3782290 TTCTCTTCTTTCTGTCTCT-C
1 TT-T-TTTTTTCTGTCTCTCC
3782310 TTTTTTTTTCTGTCTC-CC
1 TTTTTTTTTCTGTCTCTCC
3782328 TTTTTTTTTCT
1 TTTTTTTTTCT
3782339 TCAGGTTCGG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
18 27 0.47
19 7 0.12
20 23 0.40
21 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTCTGTCTCTCC
Found at i:3782814 original size:3 final size:3
Alignment explanation
Indices: 3782806--3782909 Score: 181
Period size: 3 Copynumber: 34.7 Consensus size: 3
3782796 AATATATATT
*
3782806 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3782854 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3782902 TAA TAA TA
1 TAA TAA TA
3782910 TGGATAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3783785 original size:113 final size:113
Alignment explanation
Indices: 3783232--3783770 Score: 927
Period size: 113 Copynumber: 4.8 Consensus size: 113
3783222 AGAATTATGC
* * * *
3783232 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
3783297 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
* *
3783344 AAAAGGTAGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
3783409 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
* *
3783457 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3783522 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
3783570 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3783635 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
3783683 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3783748 TATGAACTTTCTCTGGAAAAGCT
66 TATGAACTTTCTCTGGAAAAGCT
3783771 AACCTTTCAA
Statistics
Matches: 407, Mismatches: 19, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
112 66 0.16
113 341 0.84
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:3784722 original size:83 final size:83
Alignment explanation
Indices: 3784583--3784841 Score: 482
Period size: 83 Copynumber: 3.1 Consensus size: 83
3784573 TTTACTATGA
3784583 GCAAATTCATCTTCCAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
3784648 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
3784666 GCAAATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
3784731 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* * *
3784749 GCAAATTCATCTTCTAAACTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
3784814 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
3784832 GCAAATTCAT
1 GCAAATTCAT
3784842 TTGTTCTATT
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 171 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:3785983 original size:1 final size:1
Alignment explanation
Indices: 3785973--3786009 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
3785963 TTGACCTTCC
* *
3785973 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3786010 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:3797343 original size:13 final size:12
Alignment explanation
Indices: 3797325--3797368 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
3797315 CTTTTCTTCG
3797325 ATATTAAAAATAA
1 ATATT-AAAATAA
3797338 ATATTAAAATAA
1 ATATTAAAATAA
*
3797350 TTTATTTAAAATAA
1 -ATA-TTAAAATAA
3797364 ATATT
1 ATATT
3797369 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:3797369 original size:13 final size:13
Alignment explanation
Indices: 3797325--3797370 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3797315 CTTTTCTTCG
*
3797325 ATATTAAAAATAA
1 ATATTTAAAATAA
3797338 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
3797350 TTTATTTAAAATAA
1 -ATATTTAAAATAA
3797364 ATATTTA
1 ATATTTA
3797371 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:3798248 original size:5 final size:5
Alignment explanation
Indices: 3798226--3798275 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
3798216 TGACAGTAAG
*
3798226 TTTCT CTTC- TTTCTT TTTCT TTTC- TTTCTT TTTCT TTTC- TTTCT TTTCT
1 TTTCT TTTCT TTTC-T TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT
3798275 T
1 T
3798276 GGTTGCTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 11 0.29
5 19 0.50
6 8 0.21
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:3798250 original size:15 final size:15
Alignment explanation
Indices: 3798226--3798272 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
3798216 TGACAGTAAG
*
3798226 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTCTT
3798241 TTTCTTTTCTTTCTT
1 TTTCTTTTCTTTCTT
3798256 TTTCTTTTCTTTCTT
1 TTTCTTTTCTTTCTT
3798271 TT
1 TT
3798273 CTTGGTTGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:3798253 original size:9 final size:9
Alignment explanation
Indices: 3798226--3798275 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
3798216 TGACAGTAAG
*
3798226 TTTCTCTTC
1 TTTCTTTTC
3798235 TTTCTTTTTC
1 TTTC-TTTTC
*
3798245 TTTTCTTTCTT
1 -TTTCTTT-TC
3798256 TTTCTTTTC
1 TTTCTTTTC
3798265 TTTCTTTTC
1 TTTCTTTTC
3798274 TT
1 TT
3798276 GGTTGCTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 16 0.46
10 14 0.40
11 5 0.14
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:3798379 original size:16 final size:17
Alignment explanation
Indices: 3798334--3798396 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 17
3798324 CTTTCTCTGT
3798334 TTTTTTTTTCTGTCTTCC
1 TTTTTTTTTCTGTC-TCC
*
3798352 TTCTCTTCTTTCTGTCT-C
1 TT-T-TTTTTTCTGTCTCC
3798370 TTTTTTTTTCTGTCTCCC
1 TTTTTTTTTCTGTCT-CC
3798388 TTTTTTTTT
1 TTTTTTTTT
3798397 TCAGGTTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.28
17 1 0.03
18 15 0.38
19 2 0.05
20 10 0.26
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTTTTTTCTGTCTCC
Found at i:3798380 original size:20 final size:19
Alignment explanation
Indices: 3798333--3798398 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
3798323 CCTTTCTCTG
*
3798333 TTTTTTT-TTTCTGTCTTCC
1 TTTTTTTCTTTCTGTCTT-T
* *
3798352 TTCTCTTCTTTCTGTCTCTT
1 TTTTTTTCTTTCTGTCT-TT
* **
3798372 TTTTTTTCTGTCTCCCTTT
1 TTTTTTTCTTTCTGTCTTT
3798391 TTTTTTTC
1 TTTTTTTC
3798399 AGGTTCGGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.41
20 21 0.57
21 1 0.03
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTTTCTTTCTGTCTTT
Found at i:3798860 original size:13 final size:13
Alignment explanation
Indices: 3798835--3798870 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
3798825 CTGTAATTAT
3798835 TATTTATATATATA
1 TATTTA-ATATATA
*
3798849 TGTTTAATATATA
1 TATTTAATATATA
3798862 TATTTAATA
1 TATTTAATA
3798871 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TATTTAATATATA
Found at i:3798874 original size:3 final size:3
Alignment explanation
Indices: 3798866--3798978 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
3798856 TATATATATT
* *
3798866 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3798914 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3798962 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
3798979 TAGATAAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3804296 original size:19 final size:20
Alignment explanation
Indices: 3804268--3804308 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3804258 GTTGAAAATG
*
3804268 ATTTGGTTTTGA-AAGCAAA
1 ATTTGATTTTGAGAAGCAAA
*
3804287 ATTTGATTTTGAGAATCAAA
1 ATTTGATTTTGAGAAGCAAA
3804307 AT
1 AT
3804309 GAAATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTTGATTTTGAGAAGCAAA
Found at i:3805869 original size:20 final size:20
Alignment explanation
Indices: 3805844--3805898 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3805834 CTCTACATAG
3805844 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
* *
3805864 TAGTATCGATACTATTGGCA
1 TAGTATCGATACCATAGGCA
3805884 TAGTATCGATACCAT
1 TAGTATCGATACCAT
3805899 CAGACCCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCA
Found at i:3814388 original size:35 final size:34
Alignment explanation
Indices: 3814313--3814436 Score: 128
Period size: 33 Copynumber: 3.6 Consensus size: 34
3814303 TTCAAATGTA
*
3814313 ATTTTTGAAAATATATAGTATATGCTTTTGAAAACG
1 ATTTTTGAAAATATATA--ATATGATTTTGAAAACG
* *
3814349 -TTTTGGAAAATGTATAATATGATTTTGAAAACG
1 ATTTTTGAAAATATATAATATGATTTTGAAAACG
** * *
3814382 ATTTTTG--AACGTATAATATGGTTTTTGAAAACA
1 ATTTTTGAAAATATATAATAT-GATTTTGAAAACG
3814415 ATTTTTGAAAATATATTAATAT
1 ATTTTTGAAAATATA-TAATAT
3814437 ATATAATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
32 11 0.15
33 34 0.46
34 5 0.07
35 18 0.24
36 6 0.08
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.43
Consensus pattern (34 bp):
ATTTTTGAAAATATATAATATGATTTTGAAAACG
Found at i:3814461 original size:22 final size:22
Alignment explanation
Indices: 3814435--3814484 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
3814425 ATATATTAAT
3814435 ATATATAATTTTTGAAAACATA
1 ATATATAATTTTTGAAAACATA
* * * *
3814457 TTATATAGTTTTTGGAAATATA
1 ATATATAATTTTTGAAAACATA
3814479 ATATAT
1 ATATAT
3814485 GTTATATAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
ATATATAATTTTTGAAAACATA
Found at i:3814525 original size:17 final size:17
Alignment explanation
Indices: 3814495--3814559 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 17
3814485 GTTATATAGT
3814495 TTTTTATTATTTTTATTA
1 TTTTTATTA-TTTTATTA
3814513 TTTTTATTATTTTATGTA
1 TTTTTATTATTTTAT-TA
3814531 TTAGGTTATATTA-TTTATTTA
1 TT---TT-TATTATTTTA-TTA
3814552 TTTTTATT
1 TTTTTATT
3814560 TTTAACAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
17 10 0.24
18 15 0.37
21 10 0.24
22 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTTTATTATTTTATTA
Found at i:3814532 original size:9 final size:9
Alignment explanation
Indices: 3814495--3814525 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
3814485 GTTATATAGT
3814495 TTTTTATTA
1 TTTTTATTA
3814504 TTTTTATTA
1 TTTTTATTA
3814513 TTTTTATTA
1 TTTTTATTA
3814522 TTTT
1 TTTT
3814526 ATGTATTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3817086 original size:21 final size:18
Alignment explanation
Indices: 3817060--3817099 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
3817050 AATATTTTAA
3817060 ATTTAAATTATTCTGAAATTT
1 ATTTAAA-TATT-T-AAATTT
3817081 ATTTAAATATTTAAATTT
1 ATTTAAATATTTAAATTT
3817099 A
1 A
3817100 AGTTATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 4 0.21
21 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATTTAAATTT
Found at i:3819215 original size:20 final size:20
Alignment explanation
Indices: 3819190--3819236 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3819180 TAGAGGTAAT
3819190 TAATTTGAAGGTAAATTATG
1 TAATTTGAAGGTAAATTATG
3819210 TAATTTGAAGGTAAATTATG
1 TAATTTGAAGGTAAATTATG
*
3819230 TATTTTG
1 TAATTTG
3819237 TCATCTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (20 bp):
TAATTTGAAGGTAAATTATG
Found at i:3820225 original size:18 final size:18
Alignment explanation
Indices: 3820199--3820235 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3820189 ATCCTCTTTA
*
3820199 TTTCTTCTTCTTTCTCTT
1 TTTCCTCTTCTTTCTCTT
3820217 TTTCCTCTTCTTTCTCTT
1 TTTCCTCTTCTTTCTCTT
3820235 T
1 T
3820236 AAGTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCCTCTTCTTTCTCTT
Found at i:3821131 original size:724 final size:725
Alignment explanation
Indices: 3819661--3821147 Score: 2525
Period size: 723 Copynumber: 2.0 Consensus size: 725
3819651 AACATAAATA
* *
3819661 TAAAAGTATTTTTTGAAA-GAAAATTAGATCTATAGATGTTTTTATTTTAATTAAATTTCAATTT
1 TAAAAGTATTTTTTTAAACGAAAATTAGATCTATA-A-----ATATTTTAATTAAATTTCAATTT
*
3819725 TTTCTTTATAAAATTTTAATAGTCACTTAACTTTTCTTTATCGTTGGTTAATAGACGACGACATC
60 TTTCTTTATAAAATTTTAATAGTCACTTAACTTTTCTTTATCGATGGTTAATAGACGACGACATC
3819790 AATTTTAATATTGGTTGTCATCATCGATTTTTCTTATTTTCCTTTTATTTCATTCTATCACATCT
125 AATTTTAATATTGGTTGTCATCATCGATTTTTCTTATTTTCCTTTTATTTCATTCTATCACATCT
* * *
3819855 TTAAGTTTTCTTTGATTTTGAATAATCATGCTTTTATAACACTTTTTTTTCTACCTTTTGGGGTG
190 TTAAGTTTTCTTTGATTTTGAATAATCATGCCTTTATAACACTTTTTTCTCTACCTTTTGGCGTG
3819920 TTTTCGGTCGTTTGATCATTTTTTTTGTTTATCCTTTTTAGCATGGTTTGTAACACCCCAAATTC
255 TTTTCGGTCGTTTGATCATTTTTTTTGTTTATCCTTTTTAGCATGGTTTGTAACACCCCAAATTC
3819985 CGGACTAATAATTTCGAGTTTATCCGAGAGACTTATGGACCCCATGAATTGTTTAATCCAAGTCG
320 CGGACTAATAATTTCGAGTTTATCCGAGAGACTTATGGACCCCATGAATTGTTTAATCCAAGTCG
* *
3820050 TTGGGCTTAATTGGTTTGAACTTGGGCTCGATTAGCCATAAAAAATGGATTTTTATTTAACAGAA
385 TTGGGCTTAATTGGTTTGAACTTGGGCTCAATTAGCCATAAAAAAGGGATTTTTATTTAACAGAA
* * *
3820115 AAATGAGGAAGAACCAATTGAGTAATTTCCCCATTTTTGAAAAGGTTAAGACTTTATTATCTCTT
450 AAATGAGGAAGAACCAATTGAGTAATTTCCCCATTTTTAAAAAGATGAAGACTTTATTATCTCTT
* * *
3820180 TATTTTCTCATCCTCTTTATTTCTTCTTCTTTCTCTTTTTCCTCTTCTTTCTCTTTAAGTTCATA
515 TATTTTCTCATCCTCTCTATTTATTCTTCTTTCTCTTTTTCCTCTTCTTTCTCTTCAAGTTCATA
*
3820245 TTACAAATCCGTCCTTAATCACTCCAGCACCATCATTTATGGATTTAAAGCTTTGGGTTTTTATT
580 TTACAAATCCGTCCATAATCACTCCAGCACCATCATTTATGGATTTAAAGCTTTGGGTTTTTATT
* *
3820310 TTTGTAAGAAAAAAGGGGTTTTATCATCCAAGCCTAGAGGAGAGTGTTTGCTGGCTAAAGGAGCT
645 TTTGTAAGAAAAAAGGGGTTTTATCATCCAAGCCTAGAGGAAAGTGTTTGATGGCTAAAGGAGCT
*
3820375 TCATTTTGGGATTCTT
710 TCATTCTGGGATTCTT
*
3820391 TAAAAGTATTTTTTTAAAC-AAAATTATATCTATAAATATTTTAATTAAATTTCAATTTTTTCTT
1 TAAAAGTATTTTTTTAAACGAAAATTAGATCTATAAATATTTTAATTAAATTTCAATTTTTTCTT
* *
3820455 TCTAAAATTTTAATAGTCACTTAACTTTTCTTTATCGATGGTTGATAGACGACGACATCAATTTT
66 TATAAAATTTTAATAGTCACTTAACTTTTCTTTATCGATGGTTAATAGACGACGACATCAATTTT
* * * *
3820520 AGTGTTGGTTGTCGTCATCGATTTTTCTTATTTTCCTTTTATTTTC-TTCTATCACATCTTTAAT
131 AATATTGGTTGTCATCATCGATTTTTCTTATTTTCCTTTTA-TTTCATTCTATCACATCTTTAAG
*
3820584 TTTTCTTTGATTTTGAATAATCATGCCTTTATGACAC-TTTTTCTCTACCTTTTGGCGTGTTTTC
195 TTTTCTTTGATTTTGAATAATCATGCCTTTATAACACTTTTTTCTCTACCTTTTGGCGTGTTTTC
* *
3820648 GGTCGTTTGATCATTTTTTTTGTTTATCCTTTTTAGCATGGTTTGTAACACCCCAAATTTCGGGC
260 GGTCGTTTGATCATTTTTTTTGTTTATCCTTTTTAGCATGGTTTGTAACACCCCAAATTCCGGAC
* * *
3820713 TAATAATTTCGAGTTTATCCGAGAGACTTGTGGACCCCATGAATTGTTTAATCCAATTTGTTGGG
325 TAATAATTTCGAGTTTATCCGAGAGACTTATGGACCCCATGAATTGTTTAATCCAAGTCGTTGGG
* * *
3820778 CTTAATTGGTTTGGACTTGGGCTCAATTAGCCATACAAAGGGGATTTTTATTTAACAGAAAAATG
390 CTTAATTGGTTTGAACTTGGGCTCAATTAGCCATAAAAAAGGGATTTTTATTTAACAGAAAAATG
*
3820843 AGGAAGTACCAATTGAGTAATTTCCCCATTTTTAAAAAGATGAAGACTTTATTATCTCTTTATTT
455 AGGAAGAACCAATTGAGTAATTTCCCCATTTTTAAAAAGATGAAGACTTTATTATCTCTTTATTT
3820908 TCTCATCCTCTCTATTTATTCTTCTTTCTCTTTTTCCTCTTC-TTCATCTTCAAGTTCATATTAC
520 TCTCATCCTCTCTATTTATTCTTCTTTCTCTTTTTCCTCTTCTTTC-TCTTCAAGTTCATATTAC
*
3820972 AAATCCGTCCATAATCCCTCCAGCACCATCATTTATGGATTTAAAGCTTTGGGTTTTTATTTTTG
584 AAATCCGTCCATAATCACTCCAGCACCATCATTTATGGATTTAAAGCTTTGGGTTTTTATTTTTG
*
3821037 TAAGAAAAAAAGGGGTTTTATCATCCAAGCCTAGAGGAAAGTGTTTGATGGCTAAATGAGCTTCA
649 TAAG-AAAAAAGGGGTTTTATCATCCAAGCCTAGAGGAAAGTGTTTGATGGCTAAAGGAGCTTCA
3821102 TTCTGGGATTCTT
713 TTCTGGGATTCTT
3821115 TAAAAGTATTTTTTTAAACGAAAATTAGATCTA
1 TAAAAGTATTTTTTTAAACGAAAATTAGATCTA
3821148 AAAGAAAATT
Statistics
Matches: 714, Mismatches: 38, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
722 3 0.00
723 395 0.55
724 268 0.38
725 16 0.02
729 1 0.00
730 31 0.04
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (725 bp):
TAAAAGTATTTTTTTAAACGAAAATTAGATCTATAAATATTTTAATTAAATTTCAATTTTTTCTT
TATAAAATTTTAATAGTCACTTAACTTTTCTTTATCGATGGTTAATAGACGACGACATCAATTTT
AATATTGGTTGTCATCATCGATTTTTCTTATTTTCCTTTTATTTCATTCTATCACATCTTTAAGT
TTTCTTTGATTTTGAATAATCATGCCTTTATAACACTTTTTTCTCTACCTTTTGGCGTGTTTTCG
GTCGTTTGATCATTTTTTTTGTTTATCCTTTTTAGCATGGTTTGTAACACCCCAAATTCCGGACT
AATAATTTCGAGTTTATCCGAGAGACTTATGGACCCCATGAATTGTTTAATCCAAGTCGTTGGGC
TTAATTGGTTTGAACTTGGGCTCAATTAGCCATAAAAAAGGGATTTTTATTTAACAGAAAAATGA
GGAAGAACCAATTGAGTAATTTCCCCATTTTTAAAAAGATGAAGACTTTATTATCTCTTTATTTT
CTCATCCTCTCTATTTATTCTTCTTTCTCTTTTTCCTCTTCTTTCTCTTCAAGTTCATATTACAA
ATCCGTCCATAATCACTCCAGCACCATCATTTATGGATTTAAAGCTTTGGGTTTTTATTTTTGTA
AGAAAAAAGGGGTTTTATCATCCAAGCCTAGAGGAAAGTGTTTGATGGCTAAAGGAGCTTCATTC
TGGGATTCTT
Found at i:3821154 original size:17 final size:17
Alignment explanation
Indices: 3821129--3821164 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3821119 AGTATTTTTT
*
3821129 TAAACGAAAATTAGATC
1 TAAAAGAAAATTAGATC
3821146 TAAAAGAAAATTAGATC
1 TAAAAGAAAATTAGATC
3821163 TA
1 TA
3821165 TAGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (17 bp):
TAAAAGAAAATTAGATC
Found at i:3821367 original size:17 final size:17
Alignment explanation
Indices: 3821345--3821397 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3821335 TTTGGGCTCG
*
3821345 GCCTGGCCTATTTAAAA
1 GCCTGGCCTGTTTAAAA
3821362 GCCTGGCCTGTTTAAAA
1 GCCTGGCCTGTTTAAAA
* * *
3821379 ACATGGCATGTTTAAAA
1 GCCTGGCCTGTTTAAAA
3821396 GC
1 GC
3821398 ATGTTTCCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (17 bp):
GCCTGGCCTGTTTAAAA
Found at i:3821611 original size:40 final size:41
Alignment explanation
Indices: 3821529--3821613 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
3821519 CAGGCTTATA
* * *
3821529 AGGCTTTTTAATAAGCCTAAGCCTGGCCTATTTAATTTAAT
1 AGGCTTTTTAAAAAGCCCAAGCCTGGCCTATTTAATTAAAT
*
3821570 AGGC-TTTTAAAAAGGCCCAAGCCTGGCCT-TTTTATTAAAT
1 AGGCTTTTTAAAAA-GCCCAAGCCTGGCCTATTTAATTAAAT
3821610 AGGC
1 AGGC
3821614 CAGGCCAGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 21 0.54
41 18 0.46
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
AGGCTTTTTAAAAAGCCCAAGCCTGGCCTATTTAATTAAAT
Found at i:3822476 original size:11 final size:11
Alignment explanation
Indices: 3822460--3822487 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3822450 TCAATTTTTC
3822460 TTATTTTCTTT
1 TTATTTTCTTT
3822471 TTATTTTCTTT
1 TTATTTTCTTT
3822482 TTATTT
1 TTATTT
3822488 CCTTCTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (11 bp):
TTATTTTCTTT
Found at i:3823342 original size:20 final size:21
Alignment explanation
Indices: 3823303--3823343 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3823293 CCAGGGGTTG
*
3823303 AGTATCGATACTGGGATGAAT
1 AGTATCGATACTGAGATGAAT
3823324 AGTATCGATACT-AGATGAAT
1 AGTATCGATACTGAGATGAAT
3823344 TGGGGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
AGTATCGATACTGAGATGAAT
Found at i:3824721 original size:32 final size:32
Alignment explanation
Indices: 3824568--3824721 Score: 105
Period size: 32 Copynumber: 4.8 Consensus size: 32
3824558 TACATAGCAT
* ** * *
3824568 AGTCAATGTTGCATTCAGGCAATGCGCATCAA-
1 AGTCAGTGTTGCATTCAGATAATGCACA-GAAG
* * * * *
3824600 AGTTAGTATTGCATTTAGATAATGTATAGAAG
1 AGTCAGTGTTGCATTCAGATAATGCACAGAAG
* * * *
3824632 AGTCATTATTACATTTAGATAATGC-CTAGAAG
1 AGTCAGTGTTGCATTCAGATAATGCAC-AGAAG
** **
3824664 AGTCAGTGTTTTATTCAGATAATGCACATCAG
1 AGTCAGTGTTGCATTCAGATAATGCACAGAAG
*
3824696 AGTTAGTGTTGCATTCAGATAATGCA
1 AGTCAGTGTTGCATTCAGATAATGCA
3824722 TAGGAGCACC
Statistics
Matches: 94, Mismatches: 25, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
31 2 0.02
32 91 0.97
33 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (32 bp):
AGTCAGTGTTGCATTCAGATAATGCACAGAAG
Found at i:3826278 original size:2 final size:2
Alignment explanation
Indices: 3826273--3826299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3826263 TCTCTCTCTC
3826273 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3826300 TCGTTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3840221 original size:12 final size:12
Alignment explanation
Indices: 3840204--3840234 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3840194 CTATTGCTTG
*
3840204 AAAATAATAATA
1 AAAATAACAATA
3840216 AAAATAACAATA
1 AAAATAACAATA
3840228 AAAATAA
1 AAAATAA
3840235 ACTAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:3841597 original size:41 final size:41
Alignment explanation
Indices: 3841536--3841657 Score: 199
Period size: 41 Copynumber: 3.0 Consensus size: 41
3841526 CCAACGATGT
*
3841536 TGAACATTGATACATGAATGTACCAAAGTTGAACTGATAAC
1 TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAAC
* ** *
3841577 TGGACATTGATACACAAATGTACCAAAGCTGAACTGATAAT
1 TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAAC
3841618 TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAA
1 TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAA
3841658 GCACTCACTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (41 bp):
TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAAC
Found at i:3841789 original size:17 final size:18
Alignment explanation
Indices: 3841752--3841786 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3841742 TATTAAACTT
*
3841752 TATCTTATAACTGTAAAA
1 TATCTGATAACTGTAAAA
3841770 TATCTGATAACTGTAAA
1 TATCTGATAACTGTAAA
3841787 TATTTAGAAT
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:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
TATCTGATAACTGTAAAA
Found at i:3846634 original size:64 final size:65
Alignment explanation
Indices: 3846502--3846657 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 65
3846492 TACACTAGGG
* * * * *
3846502 GTGCATCGATGCATAAAATACATTCGATGTTTCAAATGAGCCTGGGGTGCATCGATGCATGGTCT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAAATGAGCCAGGAGTGCATCGATGCATGCTCT
* **
3846567 GTGCATCGGTACATAAAATTCATTCGATG-TTCAAAAT-ATTCAGGAGTGCATCGATGCATGC-C
1 GTGCATCGGTACATAAAATACATTCGATGTTTC-AAATGAGCCAGGAGTGCATCGATGCATGCTC
3846629 TT
65 -T
* * *
3846631 GTGCATTGGTACACAAAATGCATTCGA
1 GTGCATCGGTACATAAAATACATTCGA
3846658 AATTTAATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 47 0.60
65 30 0.38
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAAATGAGCCAGGAGTGCATCGATGCATGCTCT
Found at i:3846671 original size:64 final size:64
Alignment explanation
Indices: 3846546--3846689 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
3846536 AATGAGCCTG
* * * **
3846546 GGGTGCATCGATGCATGGTCTGTGCATCGGTACATAAAATTCATTCGATGTTCAAAATATTC-A
1 GGGTGCATCGATGCATGCTCTGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCAA
* * **
3846609 GGAGTGCATCGATGCATGC-CTTGTGCATTGGTACACAAAATGCATTCGAAATTTAATTTATTCA
1 GG-GTGCATCGATGCATGCTC-TGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCA
3846673 A
64 A
*
3846674 GGGTACATCGATGCAT
1 GGGTGCATCGATGCAT
3846690 TAGATGGTGC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.04
64 62 0.91
65 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GGGTGCATCGATGCATGCTCTGTGCATCGGTACACAAAATGCATTCGAAATTCAAAATATTCAA
Found at i:3849390 original size:21 final size:21
Alignment explanation
Indices: 3849361--3849434 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
3849351 AGTGCATCGG
*
3849361 ATCGGTGCACCTTCATGGTGA
1 ATCGATGCACCTTCATGGTGA
* * *
3849382 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACCTTC-ATGG-TGA
* * *
3849405 ATTGGTTCACCTTCATGGTGA
1 ATCGATGCACCTTCATGGTGA
3849426 ATCGATGCA
1 ATCGATGCA
3849435 TATTCAAGGG
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
21 20 0.53
22 6 0.16
23 12 0.32
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGA
Found at i:3849390 original size:49 final size:46
Alignment explanation
Indices: 3849333--3849452 Score: 165
Period size: 44 Copynumber: 2.6 Consensus size: 46
3849323 AACATAGTGC
3849333 ATCGATGCACATTCAA-GGAGTGCATCGGATCGGTGCACCTTCATGGTGA
1 ATCGATGCACATTCAAGGGA-TGCATC-G-T-GGTGCACCTTCATGGTGA
*
3849382 ATCGATGCACATTCAAGGGATGCAT--TGGTTCACCTTCATGGTGA
1 ATCGATGCACATTCAAGGGATGCATCGTGGTGCACCTTCATGGTGA
*
3849426 ATCGATGCATATTCAAGGGATGCATCG
1 ATCGATGCACATTCAAGGGATGCATCG
3849453 ATGCACTAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
44 41 0.62
45 1 0.02
49 21 0.32
50 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (46 bp):
ATCGATGCACATTCAAGGGATGCATCGTGGTGCACCTTCATGGTGA
Found at i:3850664 original size:46 final size:45
Alignment explanation
Indices: 3850613--3850713 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
3850603 TACCATGAAC
* *
3850613 CGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCAT
1 CGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCAT
* *
3850659 CGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCAT
3850704 CGATGCACTC
1 CGATGCACTC
3850714 TTAGTGCACC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 33 0.66
46 14 0.28
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
CGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCAT
Found at i:3850711 original size:17 final size:19
Alignment explanation
Indices: 3850683--3850731 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3850673 TATTTTGAAA
3850683 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3850701 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3850720 CACCGATGCACT
1 CATCGATGCACT
3850732 GAGAGACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3857793 original size:21 final size:21
Alignment explanation
Indices: 3857751--3857794 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3857741 ACTCTGGGAG
* *
3857751 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
3857772 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
3857793 CT
1 CT
3857795 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:3858509 original size:14 final size:14
Alignment explanation
Indices: 3858490--3858519 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3858480 AAAGGGGGAG
3858490 AAGTGTTAGGTGTT
1 AAGTGTTAGGTGTT
3858504 AAGTGTTAGGTGTT
1 AAGTGTTAGGTGTT
3858518 AA
1 AA
3858520 AAGTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (14 bp):
AAGTGTTAGGTGTT
Found at i:3859007 original size:65 final size:64
Alignment explanation
Indices: 3858938--3859120 Score: 212
Period size: 65 Copynumber: 2.8 Consensus size: 64
3858928 AATTAAATTG
*
3858938 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTGAGGATATTT-TG-
3859002 A
64 A
* ** *
3859003 AACATCGAATGCATTTGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATATTTTGA
* * * *
3859067 AACATTGACTGCACTTGATGCATCGATGCAC-T-CTTAGTGCACCGATGCACTGAG
1 AACATCGAATGCATTTGATGCATCGATGCACATAC-CA-TGCACCGATGCACTGAG
3859121 AGACCAACGG
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 42 0.42
65 51 0.50
66 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:3859098 original size:17 final size:19
Alignment explanation
Indices: 3859076--3859117 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3859066 AAACATTGAC
*
3859076 TGCACT-TGA-TGCATCGA
1 TGCACTCTGAGTGCACCGA
*
3859093 TGCACTCTTAGTGCACCGA
1 TGCACTCTGAGTGCACCGA
3859112 TGCACT
1 TGCACT
3859118 GAGAGACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (19 bp):
TGCACTCTGAGTGCACCGA
Found at i:3864829 original size:64 final size:65
Alignment explanation
Indices: 3864697--3864850 Score: 188
Period size: 64 Copynumber: 2.4 Consensus size: 65
3864687 TACACTAGGG
* * * * * *
3864697 GTGCATCGATGCATAAAATACATTCGATGTTTCAAATGAGTCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAAATGAGTCAGGAATGCATCGATGCATGCTCT
* *
3864762 GTGCATCGGTACATAAAATGCATTCGATG-TTCAAAAT-ATTCAGGAATGCATTGATGCATGC-C
1 GTGCATCGGTACATAAAATGCATTCGATGTTTC-AAATGAGTCAGGAATGCATCGATGCATGCTC
3864824 TT
65 -T
*
3864826 GTGCATCGGTACACAAAATGCATTC
1 GTGCATCGGTACATAAAATGCATTC
3864851 AAAATTTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 47 0.60
65 30 0.38
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAATGAGTCAGGAATGCATCGATGCATGCTCT
Found at i:3865287 original size:13 final size:13
Alignment explanation
Indices: 3865269--3865328 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
3865259 AGGGACATAT
3865269 TTTTAAAAGTGAC
1 TTTTAAAAGTGAC
**
3865282 TTTTAAAAGTGGT
1 TTTTAAAAGTGAC
*
3865295 TTTTTAAAGTGA-
1 TTTTAAAAGTGAC
3865307 TTTTCAAAAGTGTAC
1 TTTT-AAAAGTG-AC
3865322 -TTTAAAA
1 TTTTAAAA
3865329 TTTAACTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 4 0.10
13 31 0.79
14 4 0.10
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (13 bp):
TTTTAAAAGTGAC
Found at i:3865299 original size:14 final size:13
Alignment explanation
Indices: 3865267--3865318 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
3865257 TTAGGGACAT
3865267 ATTTTTAAAAGTG
1 ATTTTTAAAAGTG
*
3865280 ACTTTTAAAAGTG
1 ATTTTTAAAAGTG
* *
3865293 GTTTTTTAAAGTG
1 ATTTTTAAAAGTG
*
3865306 ATTTTCAAAAGTG
1 ATTTTTAAAAGTG
3865319 TACTTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (13 bp):
ATTTTTAAAAGTG
Found at i:3865304 original size:26 final size:26
Alignment explanation
Indices: 3865268--3865318 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3865258 TAGGGACATA
3865268 TTTTTAAAAGTGACTTTT-AAAAGTGG
1 TTTTTAAAAGTGA-TTTTCAAAAGTGG
*
3865294 TTTTTTAAAGTGATTTTCAAAAGTG
1 TTTTTAAAAGTGATTTTCAAAAGTG
3865319 TACTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (26 bp):
TTTTTAAAAGTGATTTTCAAAAGTGG
Found at i:3865989 original size:2 final size:2
Alignment explanation
Indices: 3865984--3866017 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3865974 TTAAAAAACG
3865984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3866018 CAATTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3866547 original size:42 final size:42
Alignment explanation
Indices: 3866480--3866621 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 42
3866470 ATCGACAATA
* * * * *
3866480 GAAAGTGTAATGCTTCCTTCTGTTCTAATTTAGACGAGAATC
1 GAAAGTGTGATGCCTCATTCCGTTCTACTTTAGACGAGAATC
* * *
3866522 GAAAGTGTTATGCCTCTTTTCGTTCTACTTTAGACGAGAATC
1 GAAAGTGTGATGCCTCATTCCGTTCTACTTTAGACGAGAATC
*
3866564 GAAAGTGTGATGCTTCATTCCGTTCTACTTTAGACGAGAATC
1 GAAAGTGTGATGCCTCATTCCGTTCTACTTTAGACGAGAATC
3866606 GAAAGTGTGATGCCTC
1 GAAAGTGTGATGCCTC
3866622 CAGTATAACC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (42 bp):
GAAAGTGTGATGCCTCATTCCGTTCTACTTTAGACGAGAATC
Found at i:3869234 original size:21 final size:22
Alignment explanation
Indices: 3869210--3869250 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3869200 TGATTGTTGC
3869210 ATATGA-TGTTATCATGAATAT
1 ATATGATTGTTATCATGAATAT
*
3869231 ATATGATTTTTATCATGAAT
1 ATATGATTGTTATCATGAAT
3869251 GTTATTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
ATATGATTGTTATCATGAATAT
Found at i:3869495 original size:60 final size:59
Alignment explanation
Indices: 3869395--3869524 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 59
3869385 CAGCAGGCTG
** * * *
3869395 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGT
** *
3869454 CATATTCGGGAACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGT
3869514 CATATTCGGGA
1 CATATTCGGGA
3869525 TTGCACTACG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
59 12 0.19
60 50 0.81
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGT
Found at i:3869684 original size:21 final size:21
Alignment explanation
Indices: 3869659--3869733 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
3869649 TACGAGCTTA
3869659 TGGTACAAATGGTAAGTATTT
1 TGGTACAAATGGTAAGTATTT
* * * * *
3869680 TGGTAAAACAAGCTTACGAG-CTTA
1 TGGTACAA-ATG-GTA--AGTATTT
3869704 TGGTACAAATGGTAAGTATTT
1 TGGTACAAATGGTAAGTATTT
3869725 TGGTA-AAAT
1 TGGTACAAAT
3869734 AAGCTTACAA
Statistics
Matches: 39, Mismatches: 10, Indels: 11
0.65 0.17 0.18
Matches are distributed among these distances:
20 6 0.15
21 14 0.36
22 4 0.10
23 4 0.10
24 9 0.23
25 2 0.05
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (21 bp):
TGGTACAAATGGTAAGTATTT
Found at i:3869685 original size:45 final size:45
Alignment explanation
Indices: 3869634--3869752 Score: 220
Period size: 45 Copynumber: 2.6 Consensus size: 45
3869624 GGCAAGTGTA
3869634 TTGGTAAAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATT
1 TTGGTAAAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATT
*
3869679 TTGGTAAAACAAGCTTACGAGCTTATGGTACAAATGGTAAGTATT
1 TTGGTAAAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATT
*
3869724 TTGGTAAAATAAGCTTACAAGCTTATGGT
1 TTGGTAAAATAAGCTTACGAGCTTATGGT
3869753 TAATAAATGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (45 bp):
TTGGTAAAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATT
Found at i:3872601 original size:11 final size:11
Alignment explanation
Indices: 3872585--3872609 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3872575 TACAACTGAC
3872585 GTTACATTGTA
1 GTTACATTGTA
3872596 GTTACATTGTA
1 GTTACATTGTA
3872607 GTT
1 GTT
3872610 GCGCTACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (11 bp):
GTTACATTGTA
Found at i:3872985 original size:16 final size:16
Alignment explanation
Indices: 3872960--3872993 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3872950 ATATTTGTAA
3872960 AATTAATATTAT-AAT
1 AATTAATATTATGAAT
3872975 AATTAAATATTATGAAT
1 AATT-AATATTATGAAT
3872992 AA
1 AA
3872994 AGTAGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATATTATGAAT
Found at i:3878040 original size:25 final size:25
Alignment explanation
Indices: 3877993--3878041 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3877983 CCATAGGCGA
** *
3877993 AAAAGAAAAGCCCAATGAGATGAAG
1 AAAAGAAAAGCCCAACAAAATGAAG
*
3878018 AAAAGAAAGGCCCAACAAAATGAA
1 AAAAGAAAAGCCCAACAAAATGAA
3878042 TACAAGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAGCCCAACAAAATGAAG
Found at i:3880173 original size:18 final size:18
Alignment explanation
Indices: 3880152--3880198 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3880142 AAGCCAAAGG
3880152 AAAAAATAAAATA-ACAAT
1 AAAAAATAAAATACA-AAT
3880170 -AAAAATACAAATACAAAT
1 AAAAAATA-AAATACAAAT
*
3880188 ACAAAATAAAA
1 AAAAAATAAAA
3880199 GAAATAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.28
18 11 0.44
19 7 0.28
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAATAAAATACAAAT
Found at i:3880214 original size:18 final size:18
Alignment explanation
Indices: 3880191--3880225 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3880181 TACAAATACA
3880191 AAATAAAAGAAATAAAAG
1 AAATAAAAGAAATAAAAG
3880209 AAATAAAAGAAATAAAA
1 AAATAAAAGAAATAAAA
3880226 AATATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (18 bp):
AAATAAAAGAAATAAAAG
Found at i:3881332 original size:3 final size:3
Alignment explanation
Indices: 3881324--3881359 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
3881314 CTGAAACAAA
3881324 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
3881360 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3881495 original size:30 final size:30
Alignment explanation
Indices: 3881438--3881534 Score: 151
Period size: 30 Copynumber: 3.2 Consensus size: 30
3881428 TTATATATTA
3881438 TATATAAATTTTCAAAAATGTTTTTTAAAAAC
1 TATAT-AATTTTCAAAAATG-TTTTTAAAAAC
*
3881470 TATATAATTTCCAAAAATGTTTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
*
3881500 TATATAATTTTCAAAAATG-TTTTAAAAAT
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
3881529 TATATA
1 TATATA
3881535 TTATATATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
29 15 0.24
30 29 0.47
31 13 0.21
32 5 0.08
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAC
Found at i:3881765 original size:37 final size:35
Alignment explanation
Indices: 3881500--3881764 Score: 305
Period size: 37 Copynumber: 7.2 Consensus size: 35
3881490 TTTTAAAAAC
*
3881500 TATATAATTTTCAAAAATGTTTTAAAAATTATATATT
1 TATATAATTTTC-AAAATGTTTTAAAAACTATATA-T
*
3881537 ATATATAAGTTTTTAAAAATGTTTTCAAAAACTATATAT
1 -TATATAA--TTTTCAAAATGTTTT-AAAAACTATATAT
* *
3881576 TATATAAGTTTCAAAAATGTTTTCAAAAATTATATAT
1 TATATAATTTTC-AAAATGTTTT-AAAAACTATATAT
*
3881613 TATATAAGATTTCAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAATG-TTTTAAAAACTATATAT
* *
3881650 TATATATATTTTTAAAATGTTTTAAGAACTATATAT
1 TATATA-ATTTTCAAAATGTTTTAAAAACTATATAT
* *
3881686 TATATAGTTTTCAAAAGTGTCTTAAAAACTATATAT
1 TATATAATTTTCAAAA-TGTTTTAAAAACTATATAT
* *
3881722 TATATACATTTTCACAATGTTTTAAAAAACTAAATAT
1 TATATA-ATTTTCAAAATGTTTT-AAAAACTATATAT
3881759 TATATA
1 TATATA
3881765 CGTATTTTCA
Statistics
Matches: 199, Mismatches: 18, Indels: 21
0.84 0.08 0.09
Matches are distributed among these distances:
35 8 0.04
36 53 0.27
37 89 0.45
38 23 0.12
39 11 0.06
40 15 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATAATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:3881813 original size:2 final size:2
Alignment explanation
Indices: 3881808--3881840 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3881798 TATATATATA
3881808 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3881841 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3882668 original size:84 final size:84
Alignment explanation
Indices: 3882427--3883589 Score: 1364
Period size: 84 Copynumber: 13.8 Consensus size: 84
3882417 GATTTTCCTC
* * * * * ** * * *
3882427 TGAGCTGAGTGTAATCGAACACGAAGGTCTTT-GTTGGTAAATAGTCTTTCTTGCCTTGAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*** *
3882491 GCTGCAAATGATGCACCAT
66 GCTGCAAATGATATGCCTT
* * * * *
3882510 TGAGCTGAGTGTAATCGAACTCAAAGGTCTTT-GTTGACAGATAACCGTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
**
3882574 GCTGCAAATGATATGTTTT
66 GCTGCAAATGATATGCCTT
* * * *
3882593 TGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
3882658 GCTGCAAATGATATGCCTT
66 GCTGCAAATGATATGCCTT
*
3882677 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*
3882742 GCTACAAATGATATGCCTT
66 GCTGCAAATGATATGCCTT
* * * * * * *
3882761 TGAGTTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGCAAACAACCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* * *
3882826 GTTGCAAATGATGTGCATT
66 GCTGCAAATGATATGCCTT
* * *
3882845 GGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* *
3882910 GCTACAAATGGTATGCCTT
66 GCTGCAAATGATATGCCTT
* * * * * * **
3882929 TGAGCTAAGCGTAGTTGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTA-CCTTGAACTA
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-TAGCCTTGAGTTA
* *
3882993 TGCTGCAAATGATGTGTCTT
65 TGCTGCAAATGATATGCCTT
* * * *
3883013 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGTAGATAACCCTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*
3883078 GCTGCAAATAATATGCCTT
66 GCTGCAAATGATATGCCTT
* * * *
3883097 TGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTTA-CCTTGAGCTA
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-TAGCCTTGAGTTA
* *
3883161 TGTTGCAAATGATGTGCCTT
65 TGCTGCAAATGATATGCCTT
* *
3883181 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
*
3883246 GCTACAAATGATATATGCCTT
66 GCTGCAAATG--ATATGCCTT
* ** * * * *
3883267 TGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTTTTTTGCAAATAGCCCTTCTTA-CCTTGAGCT
1 TGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTTGGCAGATAACCCTTC-TAGCCTTGAGTT
* *
3883331 ATGTTGCAAATGATGTGCCTT
64 ATGCTGCAAATGATATGCCTT
* * * *
3883352 GGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCGTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
* *
3883417 GCTACAAATGATATGTCTT
66 GCTGCAAATGATATGCCTT
* * * * * * *
3883436 GGAGCTGAGCATAGTCGAACTTGAAGGTCTTTTGTTGGCAAATATCCCTTCTTGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
** * *
3883501 ATTGCAAATTATGTGCCTT
66 GCTGCAAATGATATGCCTT
* * * * *
3883520 AGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
3883585 GCTGC
66 GCTGC
3883590 CAATAGTTTC
Statistics
Matches: 914, Mismatches: 156, Indels: 19
0.84 0.14 0.02
Matches are distributed among these distances:
83 103 0.11
84 703 0.77
85 37 0.04
86 34 0.04
87 35 0.04
88 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
GCTGCAAATGATATGCCTT
Found at i:3882789 original size:168 final size:168
Alignment explanation
Indices: 3882427--3883587 Score: 1551
Period size: 168 Copynumber: 6.9 Consensus size: 168
3882417 GATTTTCCTC
* * * * ** * *
3882427 TGAGCTGAGTGTAATCGAACACGAAGGTC-TTTGTTGGTAAATAGTCTTTCTTGCCTTGAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
* ** * * * *
3882491 GCTGCAAATGATGCACCATT-GAGCTGAGTGTAATCGAACTCAAAGGTCTTT-GTTGACAGATAA
66 GTTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
* * **
3882554 CCGTTCTAGCCTTGAGTTATGCTGCAAATGATATGTTTT
130 CCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
* * * * * * *
3882593 TGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTAGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
* * *
3882658 GCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAC
66 GTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAC
*
3882723 TCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
131 CCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
* * * *
3882761 TGAGTTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGCAAACAACCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
* *
3882826 GTTGCAAATGATGTGCATTGGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTGGTTGGCAGATAAC
66 GTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAC
* *
3882891 CCTTATAGCCTTGAGTTATGCTACAAATGGTATGCCTT
131 CCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
* * * * *
3882929 TGAGCTAAGCGTAGTTGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTA-CCTTGAACTA
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTC-TAGCCTTGAGCTA
* * * * *
3882993 TGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGTAGATAA
65 TGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
* *
3883058 CCCTTCTAGCCTTGAGTTATGCTGCAAATAATATGCCTT
130 CCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
* *
3883097 TGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCTTA-CCTTGAGCTA
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTC-TAGCCTTGAGCTA
*
3883161 TGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAA
65 TGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
3883226 CCCTTCTAGCCTTGAGTTATGCTACAAATGATATATGCCTT
130 CCCTTCTAGCCTTGAGTTATGCTACAAATG--ATATGCCTT
* * * *
3883267 TGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTTTTTTGCAAATAGCCCTTCTTA-CCTTGAGCT
1 TGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTTGTTGGCAAATAACCCTTC-TAGCCTTGAGCT
* *
3883331 ATGTTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATA
64 ATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA
* *
3883396 ACCGTTCTAGCCTTGAGTTATGCTACAAATGATATGTCTT
129 ACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
* * * * * *
3883436 GGAGCTGAGCATAGTCGAACTTGAAGGTCTTTTGTTGGCAAATATCCCTTCTTGCCTTGAGTTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
* * * * * * *
3883501 ATTGCAAATTATGTGCCTTAGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGCAGATAAC
66 GTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAC
3883566 CCTTCTAGCCTTGAGTTATGCT
131 CCTTCTAGCCTTGAGTTATGCT
3883588 GCCAATAGTT
Statistics
Matches: 886, Mismatches: 101, Indels: 14
0.89 0.10 0.01
Matches are distributed among these distances:
166 29 0.03
167 71 0.08
168 593 0.67
169 33 0.04
170 35 0.04
171 125 0.14
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (168 bp):
TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTAT
GTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAAC
CCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTT
Found at i:3884895 original size:94 final size:95
Alignment explanation
Indices: 3884770--3884969 Score: 303
Period size: 95 Copynumber: 2.1 Consensus size: 95
3884760 CATTGTATAG
* *
3884770 ATATTATAATCACCTTTATCAGGTTACCTGAATATTATTCATAAAGC-CGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGCTCGGGCGTTTAACCAATT
3884834 TCTCTAGAGGGACAACTCAAGCTTTATTGT
66 TCTCTAGAGGGACAACTCAAGCTTTATTGT
* * * * *
3884864 ATATTATAATCACCTTTTTCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGTGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGCTCGGGCGTTTAACCAATT
* *
3884929 TCTTTAGAGGGACACCTCAAGCTTTATTGT
66 TCTCTAGAGGGACAACTCAAGCTTTATTGT
3884959 ATATATATAAT
1 ATAT-TATAAT
3884970 ATTATAATCT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 42 0.44
95 47 0.49
96 6 0.06
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGCTCGGGCGTTTAACCAATT
TCTCTAGAGGGACAACTCAAGCTTTATTGT
Found at i:3884954 original size:95 final size:94
Alignment explanation
Indices: 3884708--3884969 Score: 301
Period size: 95 Copynumber: 2.7 Consensus size: 94
3884698 GGCTAGTTGA
* * * * * * * *
3884708 ATCCATAGAGCCAGGACGTTTAACCAATTGCTCTAGAGGGATAGCTTAATATCATTGTATAG-AT
1 ATCCATAAAGCC-GGGCGTTTAACCAATTTCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
3884772 ATTATAATCACCTTTATCAGGTTACCTGAATATT
61 ATTATAATCACCTTTATCAGGCTACCTGAATATT
*
3884806 ATTCATAAAGCCGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTAT
1 ATCCATAAAGCCGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTAT
* * *
3884871 AATCACCTTTTTCAGGCTAGCTGAATCTT
66 AATCACCTTTATCAGGCTACCTGAATATT
* * * *
3884900 ATCCATAAAGCTGGGGTGTTTAACCAATTTCTTTAGAGGGACACCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGC-CGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
3884965 ATAAT
64 ATAAT
3884970 ATTATAATCT
Statistics
Matches: 143, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
93 4 0.03
94 44 0.31
95 49 0.34
96 8 0.06
97 28 0.20
98 10 0.07
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (94 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTAT
AATCACCTTTATCAGGCTACCTGAATATT
Found at i:3887559 original size:15 final size:15
Alignment explanation
Indices: 3887523--3887690 Score: 94
Period size: 16 Copynumber: 10.9 Consensus size: 15
3887513 AAGACTAAGT
3887523 AAATCAAAAGAAAA-AA
1 AAAT-AAAA-AAAATAA
3887539 ATAATAAAAAAAATAA
1 A-AATAAAAAAAATAA
* *
3887555 AAATAAAGTAAAATGA
1 AAATAAA-AAAAATAA
* *
3887571 AAAGAGAAAAAAT--
1 AAATAAAAAAAATAA
* *
3887584 --ATAAAAAAATTTA
1 AAATAAAAAAAATAA
*
3887597 AAATAAACAAAATAA
1 AAATAAAAAAAATAA
*
3887612 AAATAAATAAACAAAGAA
1 AAAT-AA-AAA-AAATAA
** *
3887630 AAATAAACCAAAGAA
1 AAATAAAAAAAATAA
*
3887645 AAATAAAAGAAATAAA
1 AAATAAAAAAAAT-AA
*
3887661 AAATAAAAGAAATAAA
1 AAATAAAAAAAAT-AA
*
3887677 AAATAATAAAAATA
1 AAATAAAAAAAATA
3887691 TTAAATAAAC
Statistics
Matches: 121, Mismatches: 20, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.07
15 46 0.38
16 51 0.42
17 7 0.06
18 9 0.07
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.14
Consensus pattern (15 bp):
AAATAAAAAAAATAA
Found at i:3887574 original size:42 final size:40
Alignment explanation
Indices: 3887519--3887678 Score: 139
Period size: 42 Copynumber: 4.0 Consensus size: 40
3887509 AATAAAGACT
3887519 AAGT-AAATCAAAAGAAAAAAATAATAAAAAAAATAAAAATA
1 AAGTAAAAT-AAAAGAAAAAAA-AATAAAAAAAATAAAAATA
* * *
3887560 AAGTAAAATGAAAAGAGAAAAAATATAAAAAAATTTAAAATA
1 AAGTAAAAT-AAAAGA-AAAAAAAATAAAAAAAATAAAAATA
* * * * **
3887602 AA-CAAAATAAAA-ATAAATAAACAAAGAAAAAT-AAACCA
1 AAGTAAAATAAAAGAAAAAAAAATAAA-AAAAATAAAAATA
* *
3887640 AAGAAAAATAAAAGAAATAAAAAATAAAAGAAATAAAAA
1 AAGTAAAATAAAAGAAA-AAAAAATAAAAAAAATAAAAA
3887679 ATAATAAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
38 14 0.15
39 15 0.16
40 11 0.12
41 20 0.21
42 28 0.30
43 6 0.06
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (40 bp):
AAGTAAAATAAAAGAAAAAAAAATAAAAAAAATAAAAATA
Found at i:3887592 original size:10 final size:9
Alignment explanation
Indices: 3887534--3887688 Score: 86
Period size: 9 Copynumber: 16.6 Consensus size: 9
3887524 AATCAAAAGA
3887534 AAAAAATAAT
1 AAAAAA-AAT
3887544 AAAAAAAAT
1 AAAAAAAAT
3887553 AAAAATAAAGT
1 AAAAA-AAA-T
*
3887564 AAAATGAAAAG
1 AAAA--AAAAT
*
3887575 AGAAAAAAT
1 AAAAAAAAT
3887584 ATAAAAAAAT
1 A-AAAAAAAT
**
3887594 --TTAAAAT
1 AAAAAAAAT
*
3887601 AAACAAAAT
1 AAAAAAAAT
3887610 AAAAATAAAT
1 AAAAA-AAAT
3887620 AAACAAAGAA-
1 AAA-AAA-AAT
* **
3887630 AAATAAACC
1 AAAAAAAAT
3887639 AAAGAAAAAT
1 AAA-AAAAAT
*
3887649 AAAAGAAAT
1 AAAAAAAAT
3887658 --AAAAAAT
1 AAAAAAAAT
*
3887665 AAAAGAAAT
1 AAAAAAAAT
3887674 AAAAAATAAT
1 AAAAAA-AAT
3887684 AAAAA
1 AAAAA
3887689 TATTAAATAA
Statistics
Matches: 112, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
7 11 0.10
8 1 0.01
9 43 0.38
10 41 0.37
11 12 0.11
12 3 0.03
13 1 0.01
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:3888940 original size:18 final size:18
Alignment explanation
Indices: 3888917--3888952 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3888907 AACAAAAAAT
*
3888917 AAAAATAAGTAATAATAA
1 AAAAATAAATAATAATAA
3888935 AAAAATAAATAATAATAA
1 AAAAATAAATAATAATAA
3888953 TAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATAAATAATAATAA
Found at i:3888941 original size:24 final size:24
Alignment explanation
Indices: 3888910--3888959 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3888900 GACCTGAAAC
3888910 AAAAAATAAA-AATAAGTAATAATA
1 AAAAAATAAATAATAA-TAATAATA
3888934 AAAAAATAAATAATAATAATAATA
1 AAAAAATAAATAATAATAATAATA
3888958 AA
1 AA
3888960 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAAATAAATAATAATAATAATA
Found at i:3888964 original size:18 final size:20
Alignment explanation
Indices: 3888913--3888964 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
3888903 CTGAAACAAA
*
3888913 AAATAAAAATAAGTAATAAT
1 AAATAAATATAAGTAATAAT
*
3888933 AAA-AAA-ATAAATAATAAT
1 AAATAAATATAAGTAATAAT
3888951 AATAATAAATATAA
1 -A-AATAAATATAA
3888965 AAAAAAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.41
19 4 0.15
20 5 0.19
21 3 0.11
22 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATAAATATAAGTAATAAT
Found at i:3889058 original size:41 final size:40
Alignment explanation
Indices: 3888964--3889071 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 40
3888954 AATAAATATA
*
3888964 AAAAAAAGTATTTTTTTAAAAC--TATATAATATAAATTTTT
1 AAAAAAA-TA-TTTTTTAAAACTATATATAATATAAATTTTC
* **
3889004 TAAAATGT-TTTTTTAAAACTATATATTATATATAAATTTTC
1 AAAAAAATATTTTTTAAAACTATATA-TA-ATATAAATTTTC
3889045 AAAAAAATATTTTTTAAAAACTATATA
1 AAAAAAATATTTTTT-AAAACTATATA
3889072 ATTTTCAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
37 11 0.20
39 5 0.09
40 6 0.11
41 16 0.29
42 6 0.11
43 11 0.20
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (40 bp):
AAAAAAATATTTTTTAAAACTATATATAATATAAATTTTC
Found at i:3889111 original size:29 final size:30
Alignment explanation
Indices: 3889032--3889130 Score: 137
Period size: 30 Copynumber: 3.2 Consensus size: 30
3889022 CTATATATTA
3889032 TATATAAATTTTCAAAAAAATATTTTTTAAAAAC
1 TATAT-AATTTTC--AAAAATA-TTTTTAAAAAC
3889066 TATATAATTTTCAAAAATATTTTTAAAAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
* *
3889096 TATATAATTTTCAAAAAT-GTTTTAAAAAT
1 TATATAATTTTCAAAAATATTTTTAAAAAC
3889125 TATATA
1 TATATA
3889131 TTATATAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.24
30 29 0.46
31 7 0.11
33 7 0.11
34 5 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:3889150 original size:37 final size:37
Alignment explanation
Indices: 3889096--3889368 Score: 273
Period size: 37 Copynumber: 7.5 Consensus size: 37
3889086 TTTTAAAAAC
*
3889096 TATATAA-TTTTCAAAAATGTTTTAAAAATTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
*
3889132 TATATAATTTTTCAAAAATGTTTTTCAAAAACTATATAT
1 TATATAAGTTTTCAAAAATG-TTTT-AAAAACTATATAT
*** *
3889171 TATATAAGTTTTCAAAAA--AAAT-CAAA--AT-TAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
* *
3889202 TATATAAGTTTTC-AAAATAATTTTAAAAGCTATATAT
1 TATATAAGTTTTCAAAAAT-GTTTTAAAAACTATATAT
*
3889239 TATATATA-TTTTCTAAAATGTTTTAAAAACTATATAT
1 TATATA-AGTTTTCAAAAATGTTTTAAAAACTATATAT
* *
3889276 TATAT-AGTTTTCAAAAGTGTCTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
*
3889312 TATATACA-TTTTC-ACAATGTTTTTAAAAACTATATAT
1 TATATA-AGTTTTCAAAAATG-TTTTAAAAACTATATAT
*
3889349 TATATATGTATTTTCAAAAA
1 TATATAAG--TTTTCAAAAA
3889369 CCGTTTGCAA
Statistics
Matches: 196, Mismatches: 21, Indels: 36
0.77 0.08 0.14
Matches are distributed among these distances:
30 4 0.02
31 16 0.08
32 2 0.01
33 1 0.01
34 5 0.03
35 1 0.01
36 45 0.23
37 74 0.38
38 11 0.06
39 34 0.17
40 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:3889152 original size:141 final size:142
Alignment explanation
Indices: 3888976--3889317 Score: 368
Period size: 141 Copynumber: 2.4 Consensus size: 142
3888966 AAAAAGTATT
* * * *
3888976 TTTTTAAAACTATATAATATA-AATTTTTTAAAATGTTTTTTTAAAACTATATATTATATATAAA
1 TTTTAAAAACTATATATTATATAATTTTTCAAAATGTTTTTTAAAAACTATATATTATATATAAA
* *
3889040 TTTTCAAAAAAATATTTTTTAAAA-ACTATATAA-TTTTCAAAA-ATATTTT-TAA-A-A-ACTA
66 TTTTCAAAAAAA-A----TCAAAATACTATATAAGTTTTCAAAATA-ATTTTAAAACATATACTA
3889098 TATA-ATTTTCAAAAATG
125 TATATATTTTCAAAAATG
* *
3889115 TTTTAAAAATTATATATTATATAATTTTTCAAAAATGTTTTTCAAAAACTATATA-T-TATATAA
1 TTTTAAAAACTATATATTATATAATTTTTC-AAAATGTTTTTTAAAAACTATATATTATATATAA
* * *
3889178 GTTTTCAAAAAAAATCAAAATTATTATATAAGTTTTCAAAATAATTTTAAAAGCTATATATTATA
65 ATTTTCAAAAAAAATCAAAA-TACTATATAAGTTTTCAAAATAATTTTAAAA-C-ATATACTATA
*
3889243 TATATTTTCTAAAATG
127 TATATTTTCAAAAATG
* * *
3889259 TTTTAAAAACTATATATTATAT-AGTTTTCAAAA-GTGTCTTAAAAACTATATATTATATA
1 TTTTAAAAACTATATATTATATAATTTTTCAAAATGTTTTTTAAAAACTATATATTATATA
3889318 CATTTTCACA
Statistics
Matches: 171, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
134 5 0.03
136 8 0.05
137 14 0.08
138 4 0.02
139 37 0.22
140 8 0.05
141 39 0.23
142 6 0.04
143 17 0.10
144 33 0.19
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (142 bp):
TTTTAAAAACTATATATTATATAATTTTTCAAAATGTTTTTTAAAAACTATATATTATATATAAA
TTTTCAAAAAAAATCAAAATACTATATAAGTTTTCAAAATAATTTTAAAACATATACTATATATA
TTTTCAAAAATG
Found at i:3889229 original size:107 final size:103
Alignment explanation
Indices: 3889096--3889291 Score: 288
Period size: 107 Copynumber: 1.9 Consensus size: 103
3889086 TTTTAAAAAC
* *
3889096 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTATATA-ATTTTTCAAAAATGTTTTTCAA
1 TATATAATTTTCAAAAATATTTTAAAAACTATATATTATATATA-TTTTCAAAAATG-TTTT-AA
3889160 AAACTATATATTATATAAGTTTTCAAAAAAAATCAAAATTAT
63 AAACTATATATTATAT-AGTTTTCAAAAAAAATCAAAATTAT
* *
3889202 TATATAAGTTTTC-AAAATAATTTTAAAAGCTATATATTATATATATTTTCTAAAATGTTTTAAA
1 TATATAA-TTTTCAAAAAT-ATTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAA
3889266 AACTATATATTATATAGTTTTCAAAA
64 AACTATATATTATATAGTTTTCAAAA
3889292 GTGTCTTAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
104 11 0.13
105 18 0.22
106 16 0.19
107 37 0.45
108 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (103 bp):
TATATAATTTTCAAAAATATTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAA
CTATATATTATATAGTTTTCAAAAAAAATCAAAATTAT
Found at i:3889301 original size:73 final size:73
Alignment explanation
Indices: 3889199--3889354 Score: 226
Period size: 73 Copynumber: 2.1 Consensus size: 73
3889189 AAATCAAAAT
* * *
3889199 TATTATATAAGTTTTCAAAATAATTTTAAAAGCTATATATTATATATATTTTCTAAAATG-TTTT
1 TATTATAT-AGTTTTCAAAATAATCTTAAAAACTATATATTATATACATTTTC-AAAATGTTTTT
3889263 AAAAACTATA
64 AAAAACTATA
* *
3889273 TATTATATAGTTTTCAAAAGT-GTCTTAAAAACTATATATTATATACATTTTCACAATGTTTTTA
1 TATTATATAGTTTTCAAAA-TAATCTTAAAAACTATATATTATATACATTTTCAAAATGTTTTTA
3889337 AAAACTATA
65 AAAACTATA
3889346 TATTATATA
1 TATTATATA
3889355 TGTATTTTCA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
72 5 0.07
73 61 0.81
74 9 0.12
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (73 bp):
TATTATATAGTTTTCAAAATAATCTTAAAAACTATATATTATATACATTTTCAAAATGTTTTTAA
AAACTATA
Found at i:3889392 original size:2 final size:2
Alignment explanation
Indices: 3889381--3889463 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
3889371 GTTTGCAAAC
3889381 TA TA -A 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
*
3889422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3889464 AAATAAAATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3890122 original size:25 final size:25
Alignment explanation
Indices: 3890088--3890136 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3890078 TTAAAAAAGA
3890088 CTTATATAACAAATAAGTACCTAGG
1 CTTATATAACAAATAAGTACCTAGG
*
3890113 CTTATCTAACAAATAAGTACCTAG
1 CTTATATAACAAATAAGTACCTAG
3890137 AGTATACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (25 bp):
CTTATATAACAAATAAGTACCTAGG
Found at i:3890262 original size:31 final size:30
Alignment explanation
Indices: 3890162--3890263 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 30
3890152 TCATTTAAAT
* * *
3890162 ACCTAAAGTA--TTTTTGGTCAAAATAAGT
1 ACCTAAAGTATTTTTTTGGTTAAAATAGGC
* * *
3890190 GCCTAAACTTATCTTTTTGGTTAAAATAGGC
1 ACCTAAA-GTATTTTTTTGGTTAAAATAGGC
* * *
3890221 ATCTAAAGTATTTTTTTTGTTCAAAATAGGT
1 ACCTAAAGTATTTTTTTGGTT-AAAATAGGC
*
3890252 ACCTAGAGTATT
1 ACCTAAAGTATT
3890264 CAAATTTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
28 6 0.11
29 2 0.04
30 11 0.19
31 38 0.67
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (30 bp):
ACCTAAAGTATTTTTTTGGTTAAAATAGGC
Found at i:3890424 original size:29 final size:29
Alignment explanation
Indices: 3890348--3890424 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 29
3890338 AAAATGTTTG
* * *
3890348 AATAGTTTAGGTACCTATTTTGACCAAAA
1 AATACTTTAAGTACTTATTTTGACCAAAA
*
3890377 AGATAACTTTAAGTACTTATTTTGACTAAAA
1 A-AT-ACTTTAAGTACTTATTTTGACCAAAA
*
3890408 AATACTTTATGTACTTA
1 AATACTTTAAGTACTTA
3890425 AATGAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.34
30 4 0.10
31 23 0.56
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
AATACTTTAAGTACTTATTTTGACCAAAA
Found at i:3893481 original size:16 final size:16
Alignment explanation
Indices: 3893460--3893490 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3893450 AGAATCTGTG
3893460 AAGGAATTGGAATCTA
1 AAGGAATTGGAATCTA
3893476 AAGGAATTGGAATCT
1 AAGGAATTGGAATCT
3893491 GAATCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGGAATTGGAATCTA
Found at i:3894130 original size:31 final size:31
Alignment explanation
Indices: 3894064--3894138 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
3894054 AACCCGAATT
* * ** *
3894064 TTTTTTTAAAAAATCCGACCCCGATCCTGAT
1 TTTTTTTAAAAAACCCGACCCCGACCCAAAA
3894095 TTTTTTTAAAAAACCCGA-CCCGACCCCAAAA
1 TTTTTTTAAAAAACCCGACCCCGA-CCCAAAA
*
3894126 TTTTTATAAAAAA
1 TTTTTTTAAAAAA
3894139 TCCAATACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (31 bp):
TTTTTTTAAAAAACCCGACCCCGACCCAAAA
Found at i:3895563 original size:55 final size:56
Alignment explanation
Indices: 3895503--3895613 Score: 190
Period size: 55 Copynumber: 2.0 Consensus size: 56
3895493 ATTAAAAACA
3895503 TATTTAATATGGG-TCTATTAAAACTAGAATTTTAAC-TTTTAATCAACATTGAAAG
1 TATTTAATA-GGGATCTATTAAAACTAGAATTTTAACTTTTTAATCAACATTGAAAG
*
3895558 TATTTAATAGGGATCTATTAAAACTAGAATTTTAACTTTTTAATCCACATTGAAAG
1 TATTTAATAGGGATCTATTAAAACTAGAATTTTAACTTTTTAATCAACATTGAAAG
3895614 ATATACTTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
54 3 0.06
55 32 0.60
56 18 0.34
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (56 bp):
TATTTAATAGGGATCTATTAAAACTAGAATTTTAACTTTTTAATCAACATTGAAAG
Found at i:3897546 original size:40 final size:40
Alignment explanation
Indices: 3897486--3897563 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
3897476 ATATAAGCAA
*
3897486 ATAAAAGCTAGTAGTACAGCTAATAAAACATCAATTTTCT
1 ATAAAAGCAAGTAGTACAGCTAATAAAACATCAATTTTCT
* * * *
3897526 ATAAATGCAAGTAGTTCAGCTAATCAAACATCAGTTTT
1 ATAAAAGCAAGTAGTACAGCTAATAAAACATCAATTTT
3897564 TCTCTTGCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (40 bp):
ATAAAAGCAAGTAGTACAGCTAATAAAACATCAATTTTCT
Found at i:3901021 original size:73 final size:69
Alignment explanation
Indices: 3900906--3901053 Score: 242
Period size: 73 Copynumber: 2.1 Consensus size: 69
3900896 TTGTCTAAGT
* *
3900906 GATCAAGTTGAAGAAAGACATTCGACTGCTATAGTGCCTTATGATGAGCCATTGTTTCAAACACT
1 GATCAAGTTGAAGAAAGACATTCGACTGCCATAGTGCCTTATGATGAGCCATCGTTTCAAACACT
3900971 TATC
66 TATC
3900975 GATCAAGTTGAAGAGAGACAGACATTCGACTGCCATAGTGCCTTATGATGAGCCATCGTTTCAAA
1 GATCAAGTTG-A-AGA-A-AGACATTCGACTGCCATAGTGCCTTATGATGAGCCATCGTTTCAAA
3901040 CACTTATC
62 CACTTATC
3901048 GATCAA
1 GATCAA
3901054 TCCATGGAAC
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
69 10 0.14
70 1 0.01
71 3 0.04
72 1 0.01
73 58 0.79
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (69 bp):
GATCAAGTTGAAGAAAGACATTCGACTGCCATAGTGCCTTATGATGAGCCATCGTTTCAAACACT
TATC
Found at i:3902128 original size:157 final size:156
Alignment explanation
Indices: 3901945--3902473 Score: 690
Period size: 156 Copynumber: 3.4 Consensus size: 156
3901935 CCCGATTTCA
* * * * *
3901945 TTATTTCTTCAATTCCTCCTTCATTTTAAGTCCATTGTTTACCAAATTTTAACCACATGCTCCTA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGT-CATTTTTTACCAAATTTGAACCACATGCTCCTA
* * *
3902010 AACCATAGTAGAATACATGTTTACTTTCAATTTCTCTTTTTGATAATACTTTTTTATTTTTCAAT
65 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTATTTTTCAAT
*
3902075 TTAGTCTTTCTATTTTTCATAATCTTC
130 TTAGTCATTCTATTTTTCATAATCTTC
* * ** *
3902102 TTATTTCTTCAATTCATCATTTATTTTAAGTC-TGTTTTTACTAAATTTGAGTCACATGCTCCTT
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCAT-TTTTTACCAAATTTGAACCACATGCTCCTA
* * *
3902166 AACCATAGTAGAATACATATGTACTTCCAATTCCTCTTTTTGATAACAATTTTTTATTTTTCAAT
65 AACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTATTTTTCAAT
3902231 TTAGTCATTC-ATTTTTTCATAAT-TTCC
130 TTAGTCATTCTA-TTTTTCATAATCTT-C
* * *
3902258 TTATTTCTTCAATTCGTCATTTATTTTAAATCATTTTTTACCAAATTTGAGCCATATGCTCCTAA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTTACCAAATTTGAACCACATGCTCCTAA
* * * * *
3902323 ATCATAATAGAATACATGTGCACATTCAATTCCTCTTTTTGATAATAATTTTTTATTTTTCCATT
66 ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTATTTTTCAATT
* * * *
3902388 TAATCCTTGTATTTTTCATAATCTCC
131 TAGTCATTCTATTTTTCATAATCTTC
* * *
3902414 TTA-TTCATTCAATTTGTCATTTATTTTAAGT-TTTTTTTACCAAATTTAAACCACATGCTC
1 TTATTTC-TTCAATTCGTCATTTATTTTAAGTCATTTTTTACCAAATTTGAACCACATGCTC
3902474 ATATACTACA
Statistics
Matches: 325, Mismatches: 40, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
155 32 0.10
156 262 0.81
157 31 0.10
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (156 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTTACCAAATTTGAACCACATGCTCCTAA
ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAATTTTTTATTTTTCAATT
TAGTCATTCTATTTTTCATAATCTTC
Found at i:3906109 original size:14 final size:14
Alignment explanation
Indices: 3906090--3906116 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3906080 CCCTCTGTTC
3906090 GAACATAAATGAAT
1 GAACATAAATGAAT
3906104 GAACATAAATGAA
1 GAACATAAATGAA
3906117 CATAAACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (14 bp):
GAACATAAATGAAT
Found at i:3906116 original size:10 final size:10
Alignment explanation
Indices: 3906101--3906130 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3906091 AACATAAATG
3906101 AATGAACATA
1 AATGAACATA
3906111 AATGAACATA
1 AATGAACATA
*
3906121 AACGAACATA
1 AATGAACATA
3906131 TAATCGAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.13, G:0.10, T:0.17
Consensus pattern (10 bp):
AATGAACATA
Found at i:3906217 original size:30 final size:30
Alignment explanation
Indices: 3906181--3906283 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 30
3906171 TTGTTCGTGT
3906181 TTGTTCATTTAATTAAACGAACACAAAATC
1 TTGTTCATTTAATTAAACGAACACAAAATC
** * * *
3906211 TTGTTCATGTTCGTTCATTAA-TAATA-AAAGTTC
1 TTGTTCAT-TTAATT-A--AACGAACACAAA-ATC
3906244 GTTTGTTCATTTAATTAAACGAACACAAAATC
1 --TTGTTCATTTAATTAAACGAACACAAAATC
3906276 TTGTTCAT
1 TTGTTCAT
3906284 GTTCGTTCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
30 16 0.30
31 6 0.11
32 9 0.17
33 9 0.17
34 6 0.11
35 8 0.15
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (30 bp):
TTGTTCATTTAATTAAACGAACACAAAATC
Found at i:3906231 original size:35 final size:35
Alignment explanation
Indices: 3906192--3906294 Score: 101
Period size: 35 Copynumber: 3.1 Consensus size: 35
3906182 TGTTCATTTA
3906192 ATTAAACGAACACAAAATCTTGTTCATGTTCGTTC
1 ATTAAACGAACACAAAATCTTGTTCATGTTCGTTC
* * * * * *
3906227 ATT-AA-TAATA-AAAGT-TCGTT--TGTTCATTTA
1 ATTAAACGAACACAAAATCTTGTTCATGTTC-GTTC
3906257 ATTAAACGAACACAAAATCTTGTTCATGTTCGTTC
1 ATTAAACGAACACAAAATCTTGTTCATGTTCGTTC
3906292 ATT
1 ATT
3906295 TAATAAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
29 5 0.10
30 5 0.10
31 6 0.12
32 7 0.14
33 7 0.14
34 6 0.12
35 8 0.16
36 5 0.10
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (35 bp):
ATTAAACGAACACAAAATCTTGTTCATGTTCGTTC
Found at i:3906254 original size:65 final size:67
Alignment explanation
Indices: 3906179--3906307 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 67
3906169 CTTTGTTCGT
3906179 GTTTGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCA-TTAAT-AATAAAAGT
1 GTTTGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAATAAATAAAAGT
3906242 TC
66 TC
3906244 GTTTGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAATAAATAAAAG
1 GTTTGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAATAAATAAAAG
3906308 AACATAAACG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 49 0.79
66 5 0.08
67 8 0.13
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (67 bp):
GTTTGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAATAAATAAAAGT
TC
Found at i:3908343 original size:19 final size:18
Alignment explanation
Indices: 3908290--3908343 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
3908280 CCAATCTAAG
3908290 AACAAATTATAAA-AAAAT
1 AACAAATTA-AAATAAAAT
3908308 AACTAAA-TAAAACTAAAAT
1 AAC-AAATTAAAA-TAAAAT
3908327 AACAAATTTAAAATAAA
1 AACAAA-TTAAAATAAA
3908344 CAATAAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 3 0.10
18 8 0.26
19 15 0.48
20 5 0.16
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (18 bp):
AACAAATTAAAATAAAAT
Found at i:3908434 original size:40 final size:40
Alignment explanation
Indices: 3908384--3908464 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3908374 AGCAAAGTAT
3908384 ATATGGATTAATTTGTAATAAATTAAAAATACAAAGCCAA
1 ATATGGATTAATTTGTAATAAATTAAAAATACAAAGCCAA
3908424 ATATGGATTAATTTGTAATAAATTAAAAATACAAAGCCAA
1 ATATGGATTAATTTGTAATAAATTAAAAATACAAAGCCAA
3908464 A
1 A
3908465 ATTAAAGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (40 bp):
ATATGGATTAATTTGTAATAAATTAAAAATACAAAGCCAA
Found at i:3910459 original size:17 final size:18
Alignment explanation
Indices: 3910431--3910464 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3910421 AATAAAATAA
*
3910431 ACAAAGAAAGACTAAATT
1 ACAAAGAAAGACAAAATT
3910449 ACAAA-AAAGACAAAAT
1 ACAAAGAAAGACAAAAT
3910465 AATAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.12, G:0.09, T:0.12
Consensus pattern (18 bp):
ACAAAGAAAGACAAAATT
Found at i:3910471 original size:17 final size:17
Alignment explanation
Indices: 3910424--3910471 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3910414 GAATTAAAAT
3910424 AAAATAAACAAAGAAAGAC
1 AAAAT-AACAAA-AAAGAC
* *
3910443 TAAATTACAAAAAAGAC
1 AAAATAACAAAAAAGAC
*
3910460 AAAATAATAAAA
1 AAAATAACAAAA
3910472 TCTAATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 15 0.62
18 5 0.21
19 4 0.17
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAATAACAAAAAAGAC
Done.