Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007565.1 Hibiscus syriacus cultivar Beakdansim tig00021513_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: 68608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:345 original size:192 final size:193
Alignment explanation
Indices: 1--401 Score: 713
Period size: 192 Copynumber: 2.1 Consensus size: 193
*
1 TTTAG-TTGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCG
1 TTTAGTTTGTGTCGATATTTTTGGTCAAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCG
65 ATCCATATATAAAGTGTCGATCCCAAAAACATCGAAACCAAAGTATAATGTAATAGTAATTTTCA
66 ATCCATATATAAAGTGTCGATCCCAAAAACATCGAAACCAAAGTATAATGTAATAGTAATTTTCA
130 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT-T-TCTAAATAATGTGTCGACACTTT
131 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC-TT
192 TTTAGTTTGTGTCGATATTTTTGGTCAAGAAT-AATGGAAAACAGGGTGCAACCATAAAGTGTCG
1 TTTAGTTTGTGTCGATATTTTTGGTCAAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCG
* *
256 ATCTATATA-AAAGTGTCGATCCCAAAAACATCGAACCCAAAGTATAATGTAATATGTAATTTTT
66 ATCCATATATAAAGTGTCGATCCCAAAAACATCGAAACCAAAGTATAATGTAATA-GTAA-TTTT
320 CAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT
129 CAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT
385 TTTAGTTTGTGTCGATA
1 TTTAGTTTGTGTCGATA
402 CTAATTTAAA
Statistics
Matches: 202, Mismatches: 3, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
190 44 0.22
191 49 0.24
192 69 0.34
193 20 0.10
194 20 0.10
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (193 bp):
TTTAGTTTGTGTCGATATTTTTGGTCAAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCG
ATCCATATATAAAGTGTCGATCCCAAAAACATCGAAACCAAAGTATAATGTAATAGTAATTTTCA
ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT
Found at i:1860 original size:6 final size:6
Alignment explanation
Indices: 1849--1930 Score: 83
Period size: 6 Copynumber: 13.7 Consensus size: 6
1839 CAAGCGGTCA
* * * * *
1849 ATGAAG ATGAAG CTGATG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * *
1897 CTGACG ATGAAG ATGATG ATGATG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1931 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:1934 original size:12 final size:12
Alignment explanation
Indices: 1849--1930 Score: 92
Period size: 12 Copynumber: 6.8 Consensus size: 12
1839 CAAGCGGTCA
*
1849 ATGAAGATGAAG
1 ATGACGATGAAG
* *
1861 CTGATGATGAAG
1 ATGACGATGAAG
*
1873 ATGACGATGATG
1 ATGACGATGAAG
1885 ATGACGATGAAG
1 ATGACGATGAAG
*
1897 CTGACGATGAAG
1 ATGACGATGAAG
* *
1909 ATGATGATGATG
1 ATGACGATGAAG
*
1921 ATGAAGATGA
1 ATGACGATGA
1931 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1934 original size:18 final size:18
Alignment explanation
Indices: 1849--1930 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1839 CAAGCGGTCA
*
1849 ATGAAGATGAAGCTGATG
1 ATGAAGATGAAGATGATG
*
1867 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGATG
* * *
1885 ATGACGATGAAGCTGACG
1 ATGAAGATGAAGATGATG
*
1903 ATGAAGATGATGATGATG
1 ATGAAGATGAAGATGATG
1921 ATGAAGATGA
1 ATGAAGATGA
1931 TGATCCAAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGATG
Found at i:3124 original size:16 final size:16
Alignment explanation
Indices: 3103--3136 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3093 TATCCACAAC
*
3103 AAAGTGTCGATTTAAA
1 AAAGTGTCGATTGAAA
3119 AAAGTGTCGATTGAAA
1 AAAGTGTCGATTGAAA
3135 AA
1 AA
3137 TGTAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (16 bp):
AAAGTGTCGATTGAAA
Found at i:3515 original size:23 final size:23
Alignment explanation
Indices: 3489--3561 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3479 AATAGGTAAA
*
3489 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3512 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3535 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3558 ATAT
1 ATAT
3562 TGTAAAGTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4263 original size:175 final size:179
Alignment explanation
Indices: 3938--4411 Score: 731
Period size: 175 Copynumber: 2.7 Consensus size: 179
3928 AATGCTATCA
* *
3938 GTAT-AATATACCGGTTTTATGAGCGAATAAATCTACAACCTATATCGACACTTTTTAATATT-T
1 GTATAAATATACCGGTTTTATGAGCGAAT-AGTCTACAACCTATATCGACACTTTCTAATATTGT
* *
4001 GTCGGTACTTTATGTCCAGATTGGAAAAAAATGTGTCGATA-CATTGTCAAAAA--GTCGACATT
65 GTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTC-ATACCATT-TAAAAAAGTGTCGACATT
*
4063 TACACATCGGAACCCATAATTATAATGTAATAGATAA-TTTGTAATATAA-CG
128 TACACATCGGAACCCAGAATTATAATGT-ATAGATAATTTTGTAATATAACCG
4114 G-ATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGT
1 GTATAAATATACCGGTTTTATGAGCGAATA-GTCTACAACCTATATCGACACTTTCTAATATTGT
4178 GTCGGTAC-TT-TGTCCAGATTGGAAGAAAATGTGTCA-ACCATTTAAAAAAGTGTCGACATTTA
65 GTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCATACCATTTAAAAAAGTGTCGACATTTA
*
4240 CACATCGGAACCCAGATTTATAATGTATAGATAATTTTGTAATATAACCG
130 CACATCGGAACCCAGAATTATAATGTATAGATAATTTTGTAATATAACCG
4290 GTATAAATATACCGG-TTT-TGAGCGAATAGTCTACAACCTATATCGACACTTTCTAATATTGTG
1 GTATAAATATACCGGTTTTATGAGCGAATAGTCTACAACCTATATCGACACTTTCTAATATTGTG
*
4353 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTTGATACCATTTAAAAAAGTGTCG
66 TCGGTACTTTATGTCCAGATTGGAAG-AAAATGTG-TCATACCATTTAAAAAAGTGTCG
4412 GTAATTTTAA
Statistics
Matches: 277, Mismatches: 7, Indels: 25
0.90 0.02 0.08
Matches are distributed among these distances:
173 7 0.03
174 55 0.20
175 86 0.31
176 78 0.28
177 30 0.11
178 2 0.01
179 19 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (179 bp):
GTATAAATATACCGGTTTTATGAGCGAATAGTCTACAACCTATATCGACACTTTCTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCATACCATTTAAAAAAGTGTCGACATTTAC
ACATCGGAACCCAGAATTATAATGTATAGATAATTTTGTAATATAACCG
Found at i:6904 original size:29 final size:31
Alignment explanation
Indices: 6853--6910 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
6843 AATTTAAGGC
*
6853 AAATGGTTTTTGGACTTGAATTGAATTTACA
1 AAATGGTTTTTGGACGTGAATTGAATTTACA
6884 AAAT-GTTTTTGGACGT-AATTGAATTTA
1 AAATGGTTTTTGGACGTGAATTGAATTTA
6911 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 11 0.42
31 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (31 bp):
AAATGGTTTTTGGACGTGAATTGAATTTACA
Found at i:7036 original size:22 final size:21
Alignment explanation
Indices: 7000--7077 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 21
6990 TTCAAGATTG
* *
7000 CCCAGGGGTATAGATTCCCCC
1 CCCAGGGGTACAGATACCCCC
7021 CCCAGGGGGTACAGATA----C
1 CCCA-GGGGTACAGATACCCCC
7039 CCC--GGGTACAGATA--CCC
1 CCCAGGGGTACAGATACCCCC
7056 CCCAGGGGGTACAGATACCCCC
1 CCCA-GGGGTACAGATACCCCC
7078 TGCAGGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
15 11 0.23
17 4 0.09
18 4 0.09
20 11 0.23
21 4 0.09
22 13 0.28
ACGTcount: A:0.23, C:0.37, G:0.27, T:0.13
Consensus pattern (21 bp):
CCCAGGGGTACAGATACCCCC
Found at i:7047 original size:15 final size:15
Alignment explanation
Indices: 7027--7056 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7017 CCCCCCCAGG
7027 GGGTACAGATACCCC
1 GGGTACAGATACCCC
7042 GGGTACAGATACCCC
1 GGGTACAGATACCCC
7057 CCAGGGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:7067 original size:20 final size:20
Alignment explanation
Indices: 7018--7077 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
7008 TATAGATTCC
7018 CCCCCCAGGGGGTACAGATA
1 CCCCCCAGGGGGTACAGATA
7038 --CCCC---GGGTACAGATA
1 CCCCCCAGGGGGTACAGATA
7053 CCCCCCAGGGGGTACAGATA
1 CCCCCCAGGGGGTACAGATA
7073 CCCCC
1 CCCCC
7078 TGCAGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 11 0.31
17 4 0.11
18 4 0.11
20 16 0.46
ACGTcount: A:0.23, C:0.40, G:0.27, T:0.10
Consensus pattern (20 bp):
CCCCCCAGGGGGTACAGATA
Found at i:7152 original size:20 final size:19
Alignment explanation
Indices: 7115--7151 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7105 GAATGTCCAG
7115 GGGGTACCGATTCCCCCCA
1 GGGGTACCGATTCCCCCCA
7134 GGGGTACCGATTCCCCCC
1 GGGGTACCGATTCCCCCC
7152 CTGTTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.43, G:0.27, T:0.16
Consensus pattern (19 bp):
GGGGTACCGATTCCCCCCA
Found at i:7214 original size:21 final size:21
Alignment explanation
Indices: 7188--7230 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
7178 ATTTGAATAT
*
7188 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
7209 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
7230 T
1 T
7231 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:7294 original size:20 final size:22
Alignment explanation
Indices: 7256--7295 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
7246 TTTGAGTATA
7256 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
7278 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
7296 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:7549 original size:34 final size:32
Alignment explanation
Indices: 7510--7579 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
7500 TTTTGTAAAG
*
7510 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
7544 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
7576 GGGA
1 GGGA
7580 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:8463 original size:19 final size:20
Alignment explanation
Indices: 8439--8486 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
8429 AACGATTTTC
*
8439 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
8458 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
8478 TTTTGAAAA
1 TTTTGAAAA
8487 AGGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:9794 original size:30 final size:30
Alignment explanation
Indices: 9751--9810 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
9741 CAATTTAAGG
*
9751 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACGT-AATTGAATTTA
9782 CAAAAT-GTTTTTGGACGTAATTGAATTTA
1 CAAAATAGTTTTTGGACGTAATTGAATTTA
9811 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACGTAATTGAATTTA
Found at i:9985 original size:21 final size:20
Alignment explanation
Indices: 9920--9979 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
9910 ATAGATTCCC
*
9920 CCCCCCCAGGGGGACAGATA
1 CCCCCCCAGGGGTACAGATA
9940 ---CCCC--GGGTACAGATA
1 CCCCCCCAGGGGTACAGATA
9955 CCCCCCCAGGGGTACAGATA
1 CCCCCCCAGGGGTACAGATA
9975 CCCCC
1 CCCCC
9980 TGCAGGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 10 0.29
17 4 0.12
18 4 0.12
20 16 0.47
ACGTcount: A:0.23, C:0.43, G:0.25, T:0.08
Consensus pattern (20 bp):
CCCCCCCAGGGGTACAGATA
Found at i:10119 original size:21 final size:21
Alignment explanation
Indices: 10093--10135 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
10083 ATTTGAATAT
*
10093 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
10114 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
10135 T
1 T
10136 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:10201 original size:20 final size:22
Alignment explanation
Indices: 10163--10202 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
10153 TTTGAGTATA
10163 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
10185 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
10203 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:10456 original size:34 final size:32
Alignment explanation
Indices: 10417--10486 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
10407 TTTTGTAAAG
* *
10417 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
10451 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
10483 GGGA
1 GGGA
10487 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:11123 original size:23 final size:23
Alignment explanation
Indices: 11092--11164 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
11082 ATATGTAAAA
*
11092 ATATGATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGTGCTT
11115 ATATAATGTAATAGGTA-T-CATTT
1 ATATAATGTAATAGGTAGTGC--TT
*
11138 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
11161 ATAT
1 ATAT
11165 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 41 0.93
24 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:11553 original size:23 final size:23
Alignment explanation
Indices: 11522--11594 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
11512 ATAGGTAAAA
*
11522 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
11545 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
11568 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
11591 ATAT
1 ATAT
11595 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:11984 original size:23 final size:23
Alignment explanation
Indices: 11953--12012 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11943 ATAGGTAAAA
* *
11953 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCACTT
* *
11976 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCACTT
11999 ATATAATGTAATAG
1 ATATAATGTAATAG
12013 CTAGTGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:12023 original size:23 final size:23
Alignment explanation
Indices: 11953--12025 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
11943 ATAGGTAAAA
* *
11953 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
11976 ATATAATGTAATAGGTA-T-CATTT
1 ATATAATGTAATAGGTAGTGC--TT
* *
11999 ATATAATGTAATAGCTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
12022 ATAT
1 ATAT
12026 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:12090 original size:431 final size:431
Alignment explanation
Indices: 10723--13050 Score: 4312
Period size: 431 Copynumber: 5.4 Consensus size: 431
10713 AATCCCAACA
*
10723 TAGTGGTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTCTATAC-TTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
10787 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
66 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
*
10852 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTTTAAATATTATTTTA
131 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
10917 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
196 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
10982 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
261 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
* *
11047 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATGTAAAAATATGATGTAATAGGTAGTG
326 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
*
11112 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGG
391 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
11153 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
* *
11218 AACATTAATTTAATGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCTTCT
66 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
11283 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
131 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
*
11348 TCAAATATTAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
196 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
11413 GAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAACA-AAGTATCG
261 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA-AGAAGTATCG
11476 ATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGC
325 ATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGC
11541 GCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
390 GCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
11583 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
*
11648 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAAGCGTCT
66 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
11713 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
131 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
* *
11778 TCAAATATCAAAACAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTG
196 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
11843 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
261 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
11908 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
326 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
* *
11973 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGC
391 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
12014 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
* * *
12079 AATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAGGATATTAATTTAGTAATTATAGACGTCT
66 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
12144 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
131 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
* *
12209 TAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTG
196 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
12274 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAACA-AAGTATCG
261 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA-AGAAGTATCG
* * *
12338 ATCATTTTTATAAAAAGTATGTATACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGC
325 ATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGC
12403 GCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
390 GCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
*
12445 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATATTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
*
12510 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCT
66 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
12575 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
131 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
* * *
12640 TAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTGGGTG
196 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
12705 GAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
261 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
*
12769 TCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
326 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
*
12834 CTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGG
391 CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
*
12875 TAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGT-TCATACTTTTTTCACTGTGGA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCT-ATACTTTTTTCACTGTGGA
12939 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
65 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
13004 TAATGATTTATTTTTTACGTTA--ATATATATTATTATTAAATTAAAAA
130 TAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAA
13051 CAATAAACAT
Statistics
Matches: 1850, Mismatches: 41, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
428 25 0.01
429 2 0.00
430 760 0.41
431 1062 0.57
432 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (431 bp):
TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
CTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGG
Found at i:12415 original size:23 final size:23
Alignment explanation
Indices: 12384--12456 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
12374 ATAGGTAAAA
*
12384 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
12407 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
12430 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
12453 ATAT
1 ATAT
12457 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:12730 original size:861 final size:860
Alignment explanation
Indices: 10723--13050 Score: 4340
Period size: 861 Copynumber: 2.7 Consensus size: 860
10713 AATCCCAACA
* *
10723 TAGTGGTTATATTGTAAAATATCTATCCTTTTTATAAAAGTGTCTATACTTTTTCACTGTGGAAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATATTTTTTCACTGTGGAAA
10788 ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTA
66 ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTA
*
10853 ATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTTTAAATATTATTTTAT
131 ATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTAT
10918 CAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG
196 CAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG
10983 AAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
261 AAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
* *
11048 CCTTTTTATAAAAAGTATGGACACTTTCAATATAATATGTAAAAATATGATGTAATAGGTAGTGC
326 CCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGC
11113 TTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTA
391 TTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTA
*
11178 TCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACATTAATTTAATGTTATCTTTTG
456 TCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
*
11243 AGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCTTCTAATGATTTATTTTTTACGTTACGAT
521 AGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGAT
* *
11308 ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATCAAATATTAAAACAATCAAATAAT
586 ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
*
11373 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
651 TTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
*
11438 ATTGAAACATAAATTACATAACTTTAAACAAAGTATCGATCCTTTTTATAAAAAGTATGGACACT
716 ATTGAAACATAAATTACATAACTTTAAACAAAGTATCGATCATTTTTATAAAAAGTATGGACACT
11503 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
781 TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
11568 ATATAATGTAATAGG
846 ATATAATGTAATAGG
11583 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATA-TTTTTTCACTGTGGAA
*
11648 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAAGCGTCT
65 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
11713 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
130 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
* *
11778 TCAAATATCAAAACAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTG
195 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
11843 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
260 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
11908 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
325 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
*
11973 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGCTAGTGGTTATATTGTAAAGTATCT
390 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCT
*
12038 ATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTT
455 ATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTT
* *
12103 GAGTGAGTTTTAGGATATTAATTTAGTAATTATAGACGTCTAATGATTTATTTTTTACGTTACGA
520 GAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
12168 TATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
585 TATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAA
12233 TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
650 TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAA
* *
12298 AAATTGAAACATAAATTACATAACTTTAAACAAAGTATCGATCATTTTTATAAAAAGTATGTATA
714 AAATTGAAACATAAATTACATAACTTTAAACAAAGTATCGATCATTTTTATAAAAAGTATGGACA
12363 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
779 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
12428 TTATATAATGTAATAGG
844 TTATATAATGTAATAGG
12445 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATATTTTTTTCACTGTGGAA
1 TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATA-TTTTTTCACTGTGGAA
*
12510 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCT
65 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
12575 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
130 AATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTA
* * *
12640 TAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTGGGTG
195 TCAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTG
12705 GAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
260 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
*
12769 TCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
325 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
* * *
12834 CTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCT
390 CTTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCT
12899 ATCCTTTTTATAAAAGTGT-TCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTT
455 ATCCTTTTTATAAAAGTGTCT-ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTT
12963 TGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA--
519 TGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACG
13026 ATATATATTATTATTAAATTAAAAA
584 ATATATATTATTATTAAATTAAAAA
13051 CAATAAACAT
Statistics
Matches: 1429, Mismatches: 36, Indels: 7
0.97 0.02 0.00
Matches are distributed among these distances:
859 25 0.02
860 48 0.03
861 937 0.66
862 419 0.29
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (860 bp):
TAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATATTTTTTCACTGTGGAAA
ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTA
ATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTAT
CAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG
AAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
CCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGC
TTATATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTATCTA
TCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
AGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGAT
ATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAT
TTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
ATTGAAACATAAATTACATAACTTTAAACAAAGTATCGATCATTTTTATAAAAAGTATGGACACT
TTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
ATATAATGTAATAGG
Found at i:12845 original size:23 final size:23
Alignment explanation
Indices: 12814--12886 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
12804 ATAGGTAAAA
*
12814 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
12837 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
12860 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
12883 ATAT
1 ATAT
12887 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:17401 original size:20 final size:20
Alignment explanation
Indices: 17376--17442 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
17366 AATTCTCAAT
17376 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
17396 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
17417 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
17437 GCGAAT
1 GCGAAT
17443 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:17412 original size:21 final size:21
Alignment explanation
Indices: 17386--17461 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
17376 GCGAATAAGT
17386 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
17407 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
17427 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
17448 AAATCGCAATGCGA
1 AAATCGCAACGCGA
17462 TACTTACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:17417 original size:41 final size:41
Alignment explanation
Indices: 17372--17461 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
17362 TCCCAATTCT
17372 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
17413 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
17454 CAATGCGA
1 CAATGCGA
17462 TACTTACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
Found at i:17474 original size:41 final size:41
Alignment explanation
Indices: 17388--17522 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
17378 GAATAAGTAA
** *
17388 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
17429 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
17470 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
17511 TTCGCAACGCGA
1 ATCGCAACGCGA
17523 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:17475 original size:20 final size:20
Alignment explanation
Indices: 17450--17543 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
17440 AATTGGGAAA
*
17450 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
17470 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
17491 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
17511 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
17531 TTCGCAACGCGAT
1 ATCGCAACGCGAT
17544 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:17759 original size:22 final size:21
Alignment explanation
Indices: 17731--17773 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
17721 CACTCTCTCA
17731 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAA-CCGTC
*
17753 CCCATCTCCGGCGAAACCGTC
1 CCCATCTCCGACGAAACCGTC
17774 TATCTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.16
Consensus pattern (21 bp):
CCCATCTCCGACGAAACCGTC
Found at i:19329 original size:18 final size:18
Alignment explanation
Indices: 19308--19352 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19298 TCCACTTCGG
* *
19308 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
19326 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
19344 GAGCCATCA
1 GAGCCATCA
19353 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:19859 original size:20 final size:19
Alignment explanation
Indices: 19825--19890 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
19815 TAGTTTACTT
*
19825 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
19844 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
19864 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
19883 TCGCAACG
1 TCGCAACG
19891 ACAAAATCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:19898 original size:14 final size:14
Alignment explanation
Indices: 19879--19936 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
19869 ATGCGAAATG
19879 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
19893 AAAATCTCAACGCGAA
1 AAAATCGCAA--CGAC
19909 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
19925 AAAATCGCAACG
1 AAAATCGCAACG
19937 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:19913 original size:33 final size:33
Alignment explanation
Indices: 19863--19950 Score: 151
Period size: 32 Copynumber: 2.7 Consensus size: 33
19853 GGAAATGGCT
*
19863 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
19896 ATCTCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
19928 ATCGCAACGCGAAATGAAAATCG
1 ATCGCAACGCGAAATGAAAATCG
19951 AGTTTTGTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 31 0.61
33 20 0.39
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:19947 original size:19 final size:19
Alignment explanation
Indices: 19825--19950 Score: 76
Period size: 19 Copynumber: 7.2 Consensus size: 19
19815 TAGTTTACTT
* **
19825 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
19844 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
19864 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
19883 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
19897 TCTCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
19915 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
19929 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
19948 TCG
1 TCG
19951 AGTTTTGTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 19 0.23
15 1 0.01
16 6 0.07
17 2 0.02
18 10 0.12
19 28 0.34
20 17 0.20
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:21010 original size:24 final size:24
Alignment explanation
Indices: 20983--21036 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
20973 GTATTCGAAA
* *
20983 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
21007 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
21031 TTTGAT
1 TTTGAT
21037 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:21228 original size:12 final size:12
Alignment explanation
Indices: 21211--21235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21201 ATATAATCCT
21211 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21223 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21235 G
1 G
21236 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:23547 original size:33 final size:33
Alignment explanation
Indices: 23505--23631 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
23495 CTTAATGTCC
23505 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
23538 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
23570 TTTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
23604 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
23632 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:23614 original size:66 final size:66
Alignment explanation
Indices: 23508--23638 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
23498 AATGTCCATC
*
23508 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
23573 T
66 T
*
23574 GCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
23639 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (66 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
T
Found at i:23653 original size:19 final size:20
Alignment explanation
Indices: 23631--23673 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
23621 AAATCGCAAC
23631 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
23650 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
23670 GCGA
1 GCGA
23674 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:23658 original size:14 final size:14
Alignment explanation
Indices: 23659--23692 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23649 TGCGATTTTC
23659 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
23673 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
23687 ATTTTC
1 ATTTTC
23693 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:23834 original size:14 final size:14
Alignment explanation
Indices: 23815--23851 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
23805 CATCAATTAA
23815 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
23829 ACAAATCACCTTTT
1 ACAAATCAACTTTT
23843 ACAAATCAA
1 ACAAATCAA
23852 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:25275 original size:21 final size:21
Alignment explanation
Indices: 25209--25275 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
25199 GTGAATCGGG
*
25209 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
25229 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
25251 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
25272 CTCT
1 CTCT
25276 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:25294 original size:42 final size:41
Alignment explanation
Indices: 25209--25330 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
25199 GTGAATCGGG
* * * * *
25209 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGAGGC
25251 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGAGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGAGGC
* * * * *
25293 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAG
25331 GCGAGTCGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGAGGC
Found at i:27378 original size:39 final size:37
Alignment explanation
Indices: 27335--27485 Score: 157
Period size: 39 Copynumber: 4.1 Consensus size: 37
27325 TCTTTTGGTT
*
27335 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAAAATCGCAACGC
** * * *
27374 GAAATGACTATCGCGAC---CA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
*
27407 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CG-GAAATGAAAATCGCAACGC
*
27446 GAAATGAAAATCGCAACGTGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACG-GAAATGAAAATCGCAACGC
27484 GA
1 GA
27486 TTTTGGTTTC
Statistics
Matches: 92, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
33 26 0.28
34 2 0.02
38 22 0.24
39 42 0.46
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
Found at i:27386 original size:19 final size:19
Alignment explanation
Indices: 27335--27485 Score: 168
Period size: 19 Copynumber: 8.1 Consensus size: 19
27325 TCTTTTGGTT
*
27335 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
27354 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
27374 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
27392 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
27407 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
27427 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
27446 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
*
27465 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
27484 GA
1 GA
27486 TTTTGGTTTC
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
18 2 0.02
19 63 0.56
20 35 0.31
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:27514 original size:19 final size:19
Alignment explanation
Indices: 27481--27561 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
27471 AAAATCGCAA
**
27481 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
27500 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
27519 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
27533 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
27553 TGCGATTTT
1 TGCGATTTT
27562 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:28086 original size:20 final size:20
Alignment explanation
Indices: 28063--28105 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28053 CGCGTTAATA
*
28063 CGAAAATCAGTATCGCGTTG
1 CGAAAATAAGTATCGCGTTG
* *
28083 CGAAAGTAAGTATCTCGTTG
1 CGAAAATAAGTATCGCGTTG
28103 CGA
1 CGA
28106 TTTTGTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
CGAAAATAAGTATCGCGTTG
Found at i:28139 original size:20 final size:20
Alignment explanation
Indices: 28071--28147 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
28061 TACGAAAATC
* *
28071 AGTATCGCGTTGCGAAAGTA
1 AGTATCGCATTGCGATAGTA
* * *
28091 AGTATCTCGTTGCGATTTTGT-
1 AGTATCGCATTGCGA--TAGTA
*
28112 ATTATCGCATTGCGATAGTA
1 AGTATCGCATTGCGATAGTA
28132 AGTATCGCATTGCGAT
1 AGTATCGCATTGCGAT
28148 TTTCCCAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.07
20 29 0.63
21 12 0.26
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (20 bp):
AGTATCGCATTGCGATAGTA
Found at i:28165 original size:21 final size:21
Alignment explanation
Indices: 28136--28228 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
28126 ATAGTAAGTA
28136 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28157 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28177 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28198 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28218 TCGCATTGCGA
1 TCGCATTGCGA
28229 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:28166 original size:41 final size:41
Alignment explanation
Indices: 28075--28209 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
28065 AAAATCAGTA
* * * ** *
28075 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
28115 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
28157 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
28198 TCGCGTTGCGAT
1 TCGCGTTGCGAT
28210 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:28210 original size:41 final size:41
Alignment explanation
Indices: 28136--28228 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28126 ATAGTAAGTA
28136 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28177 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28218 TCGCATTGCGA
1 TCGCATTGCGA
28229 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:34284 original size:105 final size:105
Alignment explanation
Indices: 34140--34983 Score: 1364
Period size: 105 Copynumber: 8.0 Consensus size: 105
34130 TCAAAACAAA
* * * *
34140 TCCAGACAACACATGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAAT
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
*
34205 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * * *
34245 TCCAGACAACGCAAGTTCAACTTCACGACAAATGGACCGCTGGTTGTCAACAAACATTTCTCAAA
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
*
34310 TCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
34350 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
*
34415 TCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
34455 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGAT
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
*
34520 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
34560 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
34625 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
34665 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA
*
34730 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * * *
34771 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCGA
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA
*
34836 TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
34877 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCAG
1 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA
* * ** * *
34942 TTCCATAGCCAATTTCAACTTCACGGCGGATGATATTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
34983 T
1 T
34984 TGGAACAATA
Statistics
Matches: 694, Mismatches: 44, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
105 454 0.65
106 240 0.35
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
Found at i:35335 original size:83 final size:84
Alignment explanation
Indices: 35174--35343 Score: 218
Period size: 83 Copynumber: 2.0 Consensus size: 84
35164 AGAAGGAGTG
* *
35174 TCTGCCAACAAAAGACCTTTGAATTCGACTACGCTCAGCTCAATGGCACATCATTTGCAGCATAA
1 TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTCAATGGCACATCATTTACAGCATAA
** * * *
35239 TTCAAGTCGAGAAGGGTTA
66 CCCAAGGCAAGAAGGGCTA
* * *
35258 TCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTTAGCTC-TTAGGCACATCATTTACAGCATA
1 TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTCAAT-GGCACATCATTTACAGCATA
*
35321 GCCCAAGGCAAGAAGGGCTA
65 ACCCAAGGCAAGAAGGGCTA
35341 TCT
1 TCT
35344 ATCAATAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
82 1 0.01
83 64 0.86
84 9 0.12
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (84 bp):
TCTGCCAACAAAAGACCTTCGAATTCGACTACGCTCAGCTCAATGGCACATCATTTACAGCATAA
CCCAAGGCAAGAAGGGCTA
Found at i:39118 original size:18 final size:18
Alignment explanation
Indices: 39090--39140 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
39080 AAATAATTAA
39090 AATAA-ATATAAAATTTT
1 AATAATATATAAAATTTT
*
39107 AATAATATATAAATAATTT
1 AATAATATATAAA-ATTTT
39126 -AT-ATGATATAAAATT
1 AATAAT-ATATAAAATT
39141 AAATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATATATAAAATTTT
Found at i:39124 original size:20 final size:19
Alignment explanation
Indices: 39080--39126 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
39070 ACTTAAATCA
*
39080 AAATAATTAAAATAAATAT
1 AAATAATTTAAATAAATAT
*
39099 -AA-AATTTTAATAATATAT
1 AAATAATTTAAATAA-ATAT
39117 AAATAATTTA
1 AAATAATTTA
39127 TATGATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 2 0.09
20 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAAATAAATAT
Found at i:39170 original size:25 final size:24
Alignment explanation
Indices: 39135--39196 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
39125 TATATGATAT
39135 AAAATTAAATATCTATAATATAATT-A
1 AAAATT-AATAT-T-TAATATAATTAA
* *
39161 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATATAATTAA
39185 AAAATTAATATT
1 AAAATTAATATT
39197 AAAATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 8 0.24
24 14 0.42
25 5 0.15
26 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTAATATTTAATATAATTAA
Found at i:39202 original size:12 final size:12
Alignment explanation
Indices: 39185--39290 Score: 85
Period size: 12 Copynumber: 8.7 Consensus size: 12
39175 ATTTATTTAA
39185 AAAATTAATATT
1 AAAATTAATATT
39197 AAAATTAATATCT
1 AAAATTAATAT-T
*
39210 ATAATATAATATT
1 AAAAT-TAATATT
39223 AAATATTAATATT
1 AAA-ATTAATATT
* *
39236 -TAATTTAT-TT
1 AAAATTAATATT
39246 AAAAAATTAATATT
1 --AAAATTAATATT
*
39260 AAAATTAA-AAT
1 AAAATTAATATT
*
39271 CAAATATAATA-T
1 AAAAT-TAATATT
39283 AAAATTAA
1 AAAATTAA
39291 ATAAAACCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
10 2 0.03
11 14 0.18
12 28 0.37
13 22 0.29
14 10 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:39237 original size:63 final size:62
Alignment explanation
Indices: 39134--39290 Score: 250
Period size: 63 Copynumber: 2.6 Consensus size: 62
39124 TTATATGATA
*
39134 TAAAATTAAATATCTATAATATAAT-TAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAATTAATATTTAATTTATTTAAAAAATTAATAT
39196 TAAAATTAATATCTATAATATAATATTAAATATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAA-ATTAATATTTAATTTATTTAAAAAATTAATAT
*
39259 TAAAATTAAAATC-A-AATATAATA-TAAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAATTAA
39291 ATAAAACCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
59 5 0.05
60 4 0.04
61 26 0.29
62 12 0.13
63 44 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (62 bp):
TAAAATTAATATCTATAATATAATATTAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:39621 original size:12 final size:13
Alignment explanation
Indices: 39594--39619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39584 GAAAAACATC
39594 TAAATTATATTTT
1 TAAATTATATTTT
39607 TAAATTATATTTT
1 TAAATTATATTTT
39620 AAGTTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATTATATTTT
Found at i:39646 original size:17 final size:17
Alignment explanation
Indices: 39624--39665 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
39614 TATTTTAAGT
*
39624 TAAATTTACGTGTTAAAA
1 TAAATTTACGT-TAAAAA
*
39642 T-AATTTTCGTTAAAAA
1 TAAATTTACGTTAAAAA
39658 TAAATTTA
1 TAAATTTA
39666 TAATATCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 6 0.30
17 13 0.65
18 1 0.05
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (17 bp):
TAAATTTACGTTAAAAA
Found at i:44206 original size:19 final size:20
Alignment explanation
Indices: 44142--44230 Score: 60
Period size: 20 Copynumber: 4.4 Consensus size: 20
44132 ATAAAAGTTC
* *
44142 AATAATATAATAATTATTTT
1 AATAATTTAATAAGTATTTT
*
44162 -ATAGTATTTAGATAAAT-TTATT
1 AATA--ATTTA-ATAAGTATT-TT
* *
44184 AATAATTTCATAA-TCTTTT
1 AATAATTTAATAAGTATTTT
44203 AATAAATTTAATAAGTATTTT
1 AAT-AATTTAATAAGTATTTT
44224 -ATAATTT
1 AATAATTT
44231 TTTAAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
19 14 0.25
20 17 0.30
21 15 0.27
22 7 0.12
23 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (20 bp):
AATAATTTAATAAGTATTTT
Found at i:44211 original size:31 final size:31
Alignment explanation
Indices: 44168--44235 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
44158 TTTTATAGTA
*
44168 TTTAGATAAATTTATTAA-TAATTTCATAATCT
1 TTTA-ATAAATTTAATAAGT-ATTTCATAATCT
* *
44200 TTTAATAAATTTAATAAGTATTTTATAATTT
1 TTTAATAAATTTAATAAGTATTTCATAATCT
44231 TTTAA
1 TTTAA
44236 ATTTTATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGTATTTCATAATCT
Found at i:45003 original size:31 final size:31
Alignment explanation
Indices: 44962--45046 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
44952 ATAAAGCTTA
44962 AAAAAATTATAAAATACTTATTAAATTTAT-T
1 AAAAAATTATAAAATA-TTATTAAATTTATCT
* *
44993 AAAAGATTATAAAATTATTAATAAATTTATCT
1 AAAAAATTATAAAA-TATTATTAAATTTATCT
* *
45025 -AAATACTATAAAATAATTATTA
1 AAAAAATTATAAAAT-ATTATTA
45047 TATTATTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAAATTATAAAATATTATTAAATTTATCT
Found at i:46199 original size:21 final size:21
Alignment explanation
Indices: 46175--46214 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
46165 AATAATGACG
46175 TGATATTACTTAATGATGAAA
1 TGATATTACTTAATGATGAAA
*
46196 TGATATTACTTTATGATGA
1 TGATATTACTTAATGATGA
46215 CACGCAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (21 bp):
TGATATTACTTAATGATGAAA
Found at i:58110 original size:13 final size:13
Alignment explanation
Indices: 58087--58133 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
58077 CGAGAAAGAA
58087 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
58099 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
58112 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
58126 AGATAAGG
1 AGA-AAGG
58134 CTCTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:58393 original size:45 final size:47
Alignment explanation
Indices: 58331--58420 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 47
58321 TTATATAGTT
* *
58331 AAAAATAATTAATTAGTTTGT-TTTGTT-ATTCGTT-AGTTATATAA
1 AAAAATAATTAATTAGTTTGTGTTAGTTAATTAGTTAAGTTATATAA
*
58375 AAAAATTATTTAATTAGTTTGTGTTAGTTAATTAGTTAAGTTATAT
1 AAAAA-TAATTAATTAGTTTGTGTTAGTTAATTAGTTAAGTTATAT
58421 TAGTTTGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 5 0.13
45 15 0.38
46 5 0.13
47 6 0.15
48 8 0.21
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (47 bp):
AAAAATAATTAATTAGTTTGTGTTAGTTAATTAGTTAAGTTATATAA
Found at i:58508 original size:39 final size:37
Alignment explanation
Indices: 58435--58514 Score: 88
Period size: 39 Copynumber: 2.1 Consensus size: 37
58425 TTGTTGAATT
* *
58435 TATATTATATAAAAAAATTAGTTAGTAATATTAGTAG
1 TATATTATATAAAAAAATAAGTTAATAATATTAGTAG
* * * *
58472 TATATTATAATGAAAAAAATAATTTAATAGTTTTAGTTG
1 TATATTAT-AT-AAAAAAATAAGTTAATAATATTAGTAG
58511 TATA
1 TATA
58515 AAAGAATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 8 0.23
38 2 0.06
39 25 0.71
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (37 bp):
TATATTATATAAAAAAATAAGTTAATAATATTAGTAG
Found at i:58611 original size:15 final size:16
Alignment explanation
Indices: 58583--58616 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
58573 AAAGTTTACT
58583 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
58599 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
58614 TTA
1 TTA
58617 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:60837 original size:17 final size:17
Alignment explanation
Indices: 60817--60858 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
60807 ATTAGTATCA
60817 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* * *
60834 AATAAATCATTATTAAT
1 AATAATTAAATATTAAT
60851 AATAATTA
1 AATAATTA
60859 GTACATCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:61007 original size:14 final size:13
Alignment explanation
Indices: 60988--61148 Score: 120
Period size: 14 Copynumber: 13.1 Consensus size: 13
60978 TAGTAATAAT
60988 TATTAAATCATTA
1 TATTAAATCATTA
61001 GTATTAAATCATTA
1 -TATTAAATCATTA
*
61015 TTATAAAATCA-T-
1 -TATTAAATCATTA
*
61027 TACTAAATCA-T-
1 TATTAAATCATTA
61038 TATTAAATCATTA
1 TATTAAATCATTA
61051 CTATTAAATCA-T-
1 -TATTAAATCATTA
61063 TATT--ATCATTA
1 TATTAAATCATTA
61074 TTATTAAATCA-T-
1 -TATTAAATCATTA
61086 TATTAAATCA-T-
1 TATTAAATCATTA
*
61097 TATTATAATGATTA
1 TATTA-AATCATTA
61111 TTATTAAATCA-T-
1 -TATTAAATCATTA
61123 TATT--ATCATTA
1 TATTAAATCATTA
61134 TTATTAAATCATTA
1 -TATTAAATCATTA
61148 T
1 T
61149 TATAATGATT
Statistics
Matches: 123, Mismatches: 7, Indels: 35
0.75 0.04 0.21
Matches are distributed among these distances:
9 8 0.07
10 2 0.02
11 42 0.34
12 13 0.11
13 6 0.05
14 47 0.38
15 5 0.04
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (13 bp):
TATTAAATCATTA
Found at i:61090 original size:26 final size:26
Alignment explanation
Indices: 60986--61394 Score: 170
Period size: 26 Copynumber: 16.3 Consensus size: 26
60976 ATTAGTAATA
* *
60986 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATTATCATTATTATTAAATC
** * *
61011 ATTATTA-TAAAATCATTACTAAATC
1 ATTATTATTATCATTATTATTAAATC
* *
61036 ATTATTA-AATCATTACTATTAAATC
1 ATTATTATTATCATTATTATTAAATC
61061 ---ATTATTATCATTATTATTAAATC
1 ATTATTATTATCATTATTATTAAATC
* *
61084 ATTATTA-AATCATTATTA-T-AATG
1 ATTATTATTATCATTATTATTAAATC
* *
61107 ATTATTATTA-AATCATTATT--ATC
1 ATTATTATTATCATTATTATTAAATC
*
61130 ATTATTATTAAATCATTATTA-T-AATG
1 ATTATTATT--ATCATTATTATTAAATC
** * *
61156 ATTATTAACA-AATCATTATT--ATC
1 ATTATTATTATCATTATTATTAAATC
* *
61179 ATTATTATTAAACATTATTA-T-AATG
1 ATTATTATT-ATCATTATTATTAAATC
* * *
61204 ATTATTACTAAACCATTATTA-T-AATG
1 ATTATTA-T-TATCATTATTATTAAATC
* * *
61230 ATTATTATCA-AATCATTATTAAATC
1 ATTATTATTATCATTATTATTAAATC
* *
61255 ATCA--A--ATCATTAAATATTAAAATC
1 ATTATTATTATCATT-ATTATT-AAATC
* * *
61279 ATTATTATAATGATTATTACTAAATC
1 ATTATTATTATCATTATTATTAAATC
* * * *
61305 ATTATTATAATGATTATTATCAAATT
1 ATTATTATTATCATTATTATTAAATC
* *
61331 ATTAATTATTATCAAATCATTACTAAATC
1 ATT-ATTATTATC--ATTATTATTAAATC
* *
61360 ATTAAATATTA-AATTCATTATTAAATC
1 ATT-ATTATTATCATT-ATTATTAAATC
*
61387 ATTTTTAT
1 ATTATTAT
61395 GGTTAATTGA
Statistics
Matches: 293, Mismatches: 62, Indels: 57
0.71 0.15 0.14
Matches are distributed among these distances:
21 1 0.00
22 6 0.02
23 70 0.24
24 17 0.06
25 72 0.25
26 78 0.27
27 24 0.08
28 5 0.02
29 20 0.07
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTATTATCATTATTATTAAATC
Found at i:61177 original size:3 final size:3
Alignment explanation
Indices: 61061--61162 Score: 50
Period size: 3 Copynumber: 35.3 Consensus size: 3
61051 CTATTAAATC
* * * * * * *
61061 ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT A-A ATC ATT ATT ATA ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
61107 ATT ATT ATT A-A ATC ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
61153 ATG ATT ATT A
1 ATT ATT ATT A
61163 ACAAATCATT
Statistics
Matches: 73, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
2 4 0.05
3 69 0.95
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (3 bp):
ATT
Found at i:61299 original size:87 final size:84
Alignment explanation
Indices: 61176--61352 Score: 268
Period size: 87 Copynumber: 2.1 Consensus size: 84
61166 AATCATTATT
*
61176 ATCATT-ATTATTAAACATTATTATAATGATTATTACTAAACCATTATTATAATGATTATTATCA
1 ATCATTAAATATTAAACATTATTATAATGATTATTACTAAACCATTATTATAATGATTATTATCA
61240 AATCATT-ATTAAATCATCAA
66 AATCATTAATT--ATCATCAA
*
61260 ATCATTAAATATTAAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTAT
1 ATCATTAAATATT-AAA-CATTATTATAATGATTATTACTAAACCATTATTATAATGATTATTAT
* *
61325 CAAATTATTAATTATTATCAA
64 CAAATCATTAATTATCATCAA
61346 ATCATTA
1 ATCATTA
61353 CTAAATCATT
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
84 6 0.07
85 5 0.06
86 17 0.20
87 54 0.64
88 3 0.04
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (84 bp):
ATCATTAAATATTAAACATTATTATAATGATTATTACTAAACCATTATTATAATGATTATTATCA
AATCATTAATTATCATCAA
Found at i:61340 original size:18 final size:18
Alignment explanation
Indices: 61317--61352 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61307 TATTATAATG
*
61317 ATTATTATCAAATTATTA
1 ATTATTATCAAATCATTA
61335 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
61353 CTAAATCATT
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:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTATCAAATCATTA
Found at i:61383 original size:12 final size:11
Alignment explanation
Indices: 60986--61389 Score: 201
Period size: 11 Copynumber: 33.3 Consensus size: 11
60976 ATTAGTAATA
60986 ATTATTAAATC
1 ATTATTAAATC
60997 ATTAGTATTAAATC
1 A-T--TATTAAATC
61011 ATTATTATAAAATC
1 ATTA-T-T-AAATC
*
61025 ATTACTAAATC
1 ATTATTAAATC
61036 ATTATTAAATC
1 ATTATTAAATC
61047 ATTACTATTAAATC
1 A-T--TATTAAATC
* *
61061 ATTATTATCATT
1 ATTATTA-AATC
61073 ATTATTAAATC
1 ATTATTAAATC
61084 ATTATTAAATC
1 ATTATTAAATC
*
61095 ATTATTATAATGATT
1 ATTA-T-TAA--ATC
61110 ATTATTAAATC
1 ATTATTAAATC
* *
61121 ATTATTATCATT
1 ATTATTA-AATC
61133 ATTATTAAATC
1 ATTATTAAATC
*
61144 ATTATTATAATG
1 ATTATTA-AATC
61156 ATTATTAACAAATC
1 ATTATT---AAATC
* *
61170 ATTATTATCATT
1 ATTATTA-AATC
61182 ATTATTAAA-C
1 ATTATTAAATC
*
61192 ATTATTATAATG
1 ATTATTA-AATC
*
61204 ATTATTACTAAACC
1 ATTA-T--TAAATC
*
61218 ATTATTATAATG
1 ATTATTA-AATC
61230 ATTATTATCAAATC
1 ATTA-T-T-AAATC
61244 ATTATTAAATC
1 ATTATTAAATC
61255 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
61270 ATTA--AAATC
1 ATTATTAAATC
*
61279 ATTATTATAATG
1 ATTATTA-AATC
61291 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
61305 ATTATTATAATG
1 ATTATTA-AATC
61317 ATTATT--ATC
1 ATTATTAAATC
*
61326 AAATTATT-AATT
1 --ATTATTAAATC
*
61338 ATTATCAAATC
1 ATTATTAAATC
*
61349 ATTACTAAATC
1 ATTATTAAATC
61360 ATTAAATATTAAATTC
1 A-T---TATTAAA-TC
61376 ATTATTAAATC
1 ATTATTAAATC
61387 ATT
1 ATT
61390 TTTATGGTTA
Statistics
Matches: 308, Mismatches: 34, Indels: 102
0.69 0.08 0.23
Matches are distributed among these distances:
8 4 0.01
9 6 0.02
10 13 0.04
11 100 0.32
12 78 0.25
13 15 0.05
14 60 0.19
15 22 0.07
16 10 0.03
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:61651 original size:49 final size:49
Alignment explanation
Indices: 61595--61782 Score: 324
Period size: 49 Copynumber: 3.8 Consensus size: 49
61585 ATTATTAATA
*
61595 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* * *
61644 ATTACTAATCATTATTATCAAATCATTAAAAATTGATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
61693 ATTACTAATCATTACTATCAAATCATTACAA-ATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTA-AATATTAATAATAATTTCATT
61742 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
61783 GATGGGTGCC
Statistics
Matches: 132, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
48 2 0.02
49 128 0.97
50 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:61657 original size:13 final size:14
Alignment explanation
Indices: 61639--61671 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61629 AATAATAATT
*
61639 TCATTATTA-CTAA
1 TCATTATTATCAAA
61652 TCATTATTATCAAA
1 TCATTATTATCAAA
61666 TCATTA
1 TCATTA
61672 AAAATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (14 bp):
TCATTATTATCAAA
Found at i:66202 original size:44 final size:44
Alignment explanation
Indices: 66152--66262 Score: 168
Period size: 44 Copynumber: 2.5 Consensus size: 44
66142 TGCAATAATG
* * *
66152 CAGCTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCC
1 CAGCTATGGATGCAACGCATGCAACTACGAATGCAAGAATCTCC
*
66196 CAGCTATGGATGCAACGCATACAACTACGAATGCAAGAATCTCC
1 CAGCTATGGATGCAACGCATGCAACTACGAATGCAAGAATCTCC
* *
66240 CATCTATGGATGAAACGCATGCA
1 CAGCTATGGATGCAACGCATGCA
66263 TGAGGCTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (44 bp):
CAGCTATGGATGCAACGCATGCAACTACGAATGCAAGAATCTCC
Found at i:66404 original size:26 final size:25
Alignment explanation
Indices: 66375--66461 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 25
66365 CCATTCGGCG
66375 TGCATGACCCATGCACAGCTCCCACA
1 TGCATG-CCCATGCACAGCTCCCACA
** * * *
66401 TGCAT-CCCAACCTACA-CTATTCGACG
1 TGCATGCCCATGC-ACAGC--TCCCACA
66427 TGCATGGCCCATGCACAGCTCCCACA
1 TGCAT-GCCCATGCACAGCTCCCACA
66453 TGCAT-CCCA
1 TGCATGCCCA
66462 AGCTCCCACA
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
24 10 0.22
25 3 0.07
26 23 0.51
27 3 0.07
28 6 0.13
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.18
Consensus pattern (25 bp):
TGCATGCCCATGCACAGCTCCCACA
Found at i:66438 original size:52 final size:52
Alignment explanation
Indices: 66356--66462 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
66346 GACTCCATGG
*
66356 CAACCTACACCATTCGGCGTGCATGACCCATGCACAGCTCCCACATGCATCC
1 CAACCTACACCATTCGACGTGCATGACCCATGCACAGCTCCCACATGCATCC
* *
66408 CAACCTACACTATTCGACGTGCATGGCCCATGCACAGCTCCCACATGCATCC
1 CAACCTACACCATTCGACGTGCATGACCCATGCACAGCTCCCACATGCATCC
66460 CAA
1 CAA
66463 GCTCCCACAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.26, C:0.41, G:0.15, T:0.18
Consensus pattern (52 bp):
CAACCTACACCATTCGACGTGCATGACCCATGCACAGCTCCCACATGCATCC
Found at i:68077 original size:24 final size:24
Alignment explanation
Indices: 68050--68100 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
68040 ATTTCATAAT
* *
68050 TTTAATTTAAATATATTTTA-TTTA
1 TTTAATTCAAACAT-TTTTATTTTA
68074 TTTAATTCAAACATTTTTATTTTA
1 TTTAATTCAAACATTTTTATTTTA
68098 TTT
1 TTT
68101 CTAGAATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATTCAAACATTTTTATTTTA
Done.