Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009459.1 Hibiscus syriacus cultivar Beakdansim tig00113721_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: 1147073
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 4
Found at i:1003 original size:19 final size:18
Alignment explanation
Indices: 964--1075 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
954 GTTGAAATGA
964 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
979 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
996 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1012 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1029 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
1044 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1061 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1076 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 18 0.23
17 8 0.10
18 8 0.10
19 20 0.25
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1003 original size:33 final size:33
Alignment explanation
Indices: 957--1070 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
947 TCTTTTGGTT
957 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
990 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1023 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1055 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1071 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1106 original size:14 final size:14
Alignment explanation
Indices: 1087--1140 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
1077 TTTGGTTTCG
1087 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1101 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
1119 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1133 CGTTGCGA
1 CGTTGCGA
1141 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 18 0.53
15 3 0.09
17 3 0.09
18 10 0.29
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1124 original size:18 final size:17
Alignment explanation
Indices: 1082--1128 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
1072 GCGATTTTGG
1082 TTTCGCGTTGCGA-TTC
1 TTTCGCGTTGCGATTTC
*
1098 --TCTCGTTGCGATTTC
1 TTTCGCGTTGCGATTTC
1113 ATTTCGCGTTGCGATT
1 -TTTCGCGTTGCGATT
1129 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
18 12 0.48
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTTC
Found at i:1302 original size:33 final size:33
Alignment explanation
Indices: 1260--1330 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1250 AATACTAACT
*
1260 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1293 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1326 TGAAA
1 TGAAA
1331 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1563 original size:22 final size:22
Alignment explanation
Indices: 1511--1565 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1501 TGGTTGTGAG
**
1511 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1533 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1555 GGATTTCTTCG
1 GGATTTCTTCG
1566 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1732 original size:20 final size:20
Alignment explanation
Indices: 1707--1899 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1697 CTTTAAATAT
1707 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1727 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1749 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1768 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1788 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1808 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1828 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1848 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1868 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1888 CGCGTTGCGATT
1 CGCGTTGCGATT
1900 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1894 original size:60 final size:60
Alignment explanation
Indices: 1707--1899 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1697 CTTTAAATAT
**
1707 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1768 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1828 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1888 CGCGTTGCGATT
1 CGCGTTGCGATT
1900 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1980 original size:20 final size:20
Alignment explanation
Indices: 1955--2006 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1945 AAGAATCGCG
*
1955 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1975 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1995 TTGCGATTCTGG
1 TTGCGATTCTGG
2007 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:7267 original size:61 final size:61
Alignment explanation
Indices: 7172--7298 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
7162 ACTGAACATT
7172 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
1 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
* *
7233 AACATGTTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACTATTCA
1 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
7294 AACAT
1 AACAT
7299 TTCTGAGATC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (61 bp):
AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
Found at i:9180 original size:14 final size:14
Alignment explanation
Indices: 9161--9187 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9151 GGACGGAGGG
9161 TTGTTTTCATGGCA
1 TTGTTTTCATGGCA
9175 TTGTTTTCATGGC
1 TTGTTTTCATGGC
9188 TTGGCAGGAA
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:0.11, C:0.15, G:0.22, T:0.52
Consensus pattern (14 bp):
TTGTTTTCATGGCA
Found at i:10875 original size:21 final size:21
Alignment explanation
Indices: 10831--10875 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10821 AAATTACGTA
*
10831 TTTAGTACCTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
* * *
10852 TTTAGTACTTAAACTTTTAAT
1 TTTAGTACCTAAACTATCAAT
10873 TTT
1 TTT
10876 TTTAAAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:12467 original size:6 final size:5
Alignment explanation
Indices: 12389--12466 Score: 68
Period size: 5 Copynumber: 14.6 Consensus size: 5
12379 GAATAATTAT
* * *
12389 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TGTTGCGA TTGCTT- TGTTG
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TT--TA TT--TTA TTTTA
12438 TTTTA TTTTA TTTTA TTTTA TTTATA TTT
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTT
12467 AGATAATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
4 2 0.03
5 47 0.77
6 8 0.13
7 1 0.02
8 2 0.03
9 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:14120 original size:2 final size:2
Alignment explanation
Indices: 14113--14166 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
14103 TTAGTGTACG
14113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14155 TA TA TA TA TA TA
1 TA TA TA TA TA TA
14167 GACATGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19280 original size:38 final size:38
Alignment explanation
Indices: 19231--19308 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
19221 CTGATTATGC
*
19231 ATGATCCATCCTCCTTTCCCATCTTGATTCGAGTATTT
1 ATGATCCATCCTCCTTTCCAATCTTGATTCGAGTATTT
19269 ATGATCCATCCTCCTTTCCAATCTTGATTCGAGTATTT
1 ATGATCCATCCTCCTTTCCAATCTTGATTCGAGTATTT
19307 AT
1 AT
19309 AACGACCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (38 bp):
ATGATCCATCCTCCTTTCCAATCTTGATTCGAGTATTT
Found at i:21005 original size:71 final size:70
Alignment explanation
Indices: 20897--21076 Score: 229
Period size: 71 Copynumber: 2.5 Consensus size: 70
20887 TAAACAAGAT
* *
20897 AACGGAAGGAAACGTCGCACTTCCGATTCAAAGTGAACGGAAGAAAGCATCGACACTTCCGATTC
1 AACGGAAGGAAGCGTCGCACTTCCGATTC-AACTGAACGGAAGAAAGCATCGACACTTCCGATTC
20962 AAACT-G
65 -AACTCG
* * *
20968 AACGGAAGGAAGCATCGACACTTCCGATTCAACTGAACGGAAGGAAGCATCGACACTTTCGATTC
1 AACGGAAGGAAGCGTCG-CACTTCCGATTCAACTGAACGGAAGAAAGCATCGACACTTCCGATTC
*
21033 AAGTCG
65 AACTCG
* *
21039 ACCGGAAGGAGGCGTCTGCACTT-CGATTCAACTAGAAC
1 AACGGAAGGAAGCGTC-GCACTTCCGATTCAACT-GAAC
21077 AGATAGTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
70 13 0.14
71 70 0.73
72 13 0.14
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (70 bp):
AACGGAAGGAAGCGTCGCACTTCCGATTCAACTGAACGGAAGAAAGCATCGACACTTCCGATTCA
ACTCG
Found at i:21009 original size:35 final size:35
Alignment explanation
Indices: 20897--21076 Score: 213
Period size: 36 Copynumber: 5.1 Consensus size: 35
20887 TAAACAAGAT
* * *
20897 AACGGAAGGAAACGTCG-CACTTCCGATTCAAAGTG
1 AACGGAAGGAAGCATCGACACTTCCGATTC-AACTG
*
20932 AACGGAAGAAAGCATCGACACTTCCGATTCAAACTG
1 AACGGAAGGAAGCATCGACACTTCCGATTC-AACTG
20968 AACGGAAGGAAGCATCGACACTTCCGATTCAACTG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAACTG
* *
21003 AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAACT-G
* * *
21039 ACCGGAAGGAGGCGTCTG-CACTT-CGATTCAACTAG
1 AACGGAAGGAAGCATC-GACACTTCCGATTCAACT-G
21074 AAC
1 AAC
21077 AGATAGTTTA
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
35 63 0.49
36 65 0.50
37 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (35 bp):
AACGGAAGGAAGCATCGACACTTCCGATTCAACTG
Found at i:21061 original size:36 final size:35
Alignment explanation
Indices: 20897--21076 Score: 195
Period size: 35 Copynumber: 5.1 Consensus size: 35
20887 TAAACAAGAT
* * * *
20897 AACGGAAGGAAACGTCG-CACTTCCGATTCAAAGTG
1 AACGGAAGGAAGCATCGACACTTTCGATTC-AACTG
* *
20932 AACGGAAGAAAGCATCGACACTTCCGATTCAAACTG
1 AACGGAAGGAAGCATCGACACTTTCGATTC-AACTG
*
20968 AACGGAAGGAAGCATCGACACTTCCGATTCAACTG
1 AACGGAAGGAAGCATCGACACTTTCGATTCAACTG
*
21003 AACGGAAGGAAGCATCGACACTTTCGATTCAAGTCG
1 AACGGAAGGAAGCATCGACACTTTCGATTCAACT-G
* * *
21039 ACCGGAAGGAGGCGTCTG-CAC-TTCGATTCAACTAG
1 AACGGAAGGAAGCATC-GACACTTTCGATTCAACT-G
21074 AAC
1 AAC
21077 AGATAGTTTA
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
35 65 0.50
36 63 0.49
37 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (35 bp):
AACGGAAGGAAGCATCGACACTTTCGATTCAACTG
Found at i:22095 original size:32 final size:31
Alignment explanation
Indices: 22032--22130 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 31
22022 TGTATAATAA
* *
22032 TTGTAAAAATTCGATAAATTTAATGACCATT
1 TTGTAACAATTCGATAAATTTAATAACCATT
* *
22063 TTGTAACATTTCGATAAAATTTAATAATCATT
1 TTGTAACAATTCGAT-AAATTTAATAACCATT
* *
22095 TTGTAACAGTTCGATAAATTTAATTACCATT
1 TTGTAACAATTCGATAAATTTAATAACCATT
22126 TTGTA
1 TTGTA
22131 TTGTTTGAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (31 bp):
TTGTAACAATTCGATAAATTTAATAACCATT
Found at i:24816 original size:150 final size:149
Alignment explanation
Indices: 24546--24844 Score: 589
Period size: 150 Copynumber: 2.0 Consensus size: 149
24536 AATAGAAAAT
24546 TACAAGCAAGAAAAGCACTATTTATTAGAATAGCCTTTAAAATACTGGAAGGAATTAAAAACCTT
1 TACAAGCAAGAAAAGCACTATTTATTAGAATAGCCTTTAAAATACTGGAAGGAATTAAAAACCTT
24611 CATTCTCTAAATGGAATTTTCTTAAAAAATAATGCAAAACTTAGTCACCTGCTAATTGCACTTGG
66 CATTCTCTAAATGGAATTTTCTTAAAAAATAATGCAAAACTTAGTCACCTGCTAATTGCACTTGG
24676 TACATCTTCACGCCGTTCA
131 TACATCTTCACGCCGTTCA
24695 TACAAGCAAGAAAAGCACTATTTATTAGAATAGCCTTTAAAATACTGGAAAGGAATTAAAAACCT
1 TACAAGCAAGAAAAGCACTATTTATTAGAATAGCCTTTAAAATACTGG-AAGGAATTAAAAACCT
24760 TCATTCTCTAAATGGAATTTTCTTAAAAAATAATGCAAAACTTAGTCACCTGCTAATTGCACTTG
65 TCATTCTCTAAATGGAATTTTCTTAAAAAATAATGCAAAACTTAGTCACCTGCTAATTGCACTTG
24825 GTACATCTTCACGCCGTTCA
130 GTACATCTTCACGCCGTTCA
24845 GATTCGGTCT
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 48 0.32
150 101 0.68
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (149 bp):
TACAAGCAAGAAAAGCACTATTTATTAGAATAGCCTTTAAAATACTGGAAGGAATTAAAAACCTT
CATTCTCTAAATGGAATTTTCTTAAAAAATAATGCAAAACTTAGTCACCTGCTAATTGCACTTGG
TACATCTTCACGCCGTTCA
Found at i:30214 original size:20 final size:22
Alignment explanation
Indices: 30175--30216 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
30165 TAATATGTAT
30175 ATTATTATTTTATATTGATTTAC
1 ATTATTATTTTATA-TGATTTAC
30198 ATTATTATTTT-TA-GATTTA
1 ATTATTATTTTATATGATTTA
30217 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTATTATTTTATATGATTTAC
Found at i:30480 original size:25 final size:25
Alignment explanation
Indices: 30424--30481 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
30414 TTAATTATTT
30424 ATATTATTATAAAATTAAAATTAAA
1 ATATTATTATAAAATTAAAATTAAA
* *
30449 ATCTTATTCT-AAATT-AAATTAAA
1 ATATTATTATAAAATTAAAATTAAA
30472 TATAATTATT
1 -AT-ATTATT
30482 TTTGTTATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 8 0.29
24 7 0.25
25 13 0.46
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTATTATAAAATTAAAATTAAA
Found at i:42072 original size:23 final size:24
Alignment explanation
Indices: 42040--42084 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
42030 AATTTAACGG
*
42040 TAAGTTTTAAAAAAT-TGAAAATT
1 TAAGTATTAAAAAATATGAAAATT
*
42063 TAAGTATTAAAACATATGAAAA
1 TAAGTATTAAAAAATATGAAAA
42085 CTAATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (24 bp):
TAAGTATTAAAAAATATGAAAATT
Found at i:42953 original size:8 final size:8
Alignment explanation
Indices: 42940--42964 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42930 ATATCTTAGT
42940 TATTTTTA
1 TATTTTTA
42948 TATTTTTA
1 TATTTTTA
42956 TATTTTTA
1 TATTTTTA
42964 T
1 T
42965 TTCGATCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTTA
Found at i:43564 original size:24 final size:24
Alignment explanation
Indices: 43532--43577 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43522 TTACCTGACT
*
43532 GAAGCTGTCGGGGTTTCCCGAACC
1 GAAGATGTCGGGGTTTCCCGAACC
* *
43556 GAAGATGTCGGTGTTTCTCGAA
1 GAAGATGTCGGGGTTTCCCGAA
43578 TTGTTGCTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.26
Consensus pattern (24 bp):
GAAGATGTCGGGGTTTCCCGAACC
Found at i:46326 original size:18 final size:19
Alignment explanation
Indices: 46303--46346 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
46293 TCAGTAATCC
*
46303 TATTCC-CTGGTAATCTTA
1 TATTCCACTAGTAATCTTA
46321 TATTCCCACTAGTAATCTTA
1 TATT-CCACTAGTAATCTTA
*
46341 CATTCC
1 TATTCC
46347 GTGAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (19 bp):
TATTCCACTAGTAATCTTA
Found at i:47746 original size:14 final size:14
Alignment explanation
Indices: 47723--47752 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47713 TGAATATAAG
47723 CAAATATAAACGAA
1 CAAATATAAACGAA
*
47737 CAAATGTAAACGAA
1 CAAATATAAACGAA
47751 CA
1 CA
47753 TGAATGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (14 bp):
CAAATATAAACGAA
Found at i:49961 original size:31 final size:31
Alignment explanation
Indices: 49925--49984 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
49915 AACTTAAAAA
* *
49925 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
49956 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
49985 AATATAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:50034 original size:22 final size:22
Alignment explanation
Indices: 50008--50050 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
49998 TAATAAATTA
50008 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
50030 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
50051 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:50059 original size:22 final size:22
Alignment explanation
Indices: 50010--50058 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
50000 ATAAATTATT
**
50010 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
50032 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
50055 TAAA
1 TAAA
50059 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:50103 original size:80 final size:79
Alignment explanation
Indices: 50013--50323 Score: 471
Period size: 80 Copynumber: 3.8 Consensus size: 79
50003 AATTATTTAA
* *
50013 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
50078 TCATACAACTACAAT
66 TCATACAA-TACAAT
**
50093 AATAAATCAATATATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
50158 AT-ATACAAATACAAT
66 -TCATAC-AATACAAT
*
50173 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
*
50238 TCATACTAATAAATTATTT
66 TCATAC-AATACA--A--T
50257 AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
50322 AT
64 AT
50324 CTATGTTTTA
Statistics
Matches: 214, Mismatches: 8, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
79 1 0.00
80 144 0.67
81 3 0.01
82 1 0.00
84 1 0.00
86 64 0.30
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (79 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
TCATACAATACAAT
Found at i:50216 original size:18 final size:18
Alignment explanation
Indices: 50195--50305 Score: 76
Period size: 18 Copynumber: 6.4 Consensus size: 18
50185 TATATTTTAA
50195 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
50213 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
50227 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
50245 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
* *
50259 AATAAATCAATCCATATTTT
1 AATAAATCAATTCATA--CT
50279 AAAATAAATCAATTCATACT
1 --AATAAATCAATTCATACT
50299 AATAAAT
1 AATAAAT
50306 TATTTAAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
14 14 0.20
15 9 0.13
17 10 0.14
18 21 0.30
20 1 0.01
22 15 0.21
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:50230 original size:14 final size:14
Alignment explanation
Indices: 50213--50265 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
50203 AATTCATACT
50213 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
50227 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
50245 AATAAATTATTTAA
1 AATAAATTATTTAA
50259 AATAAAT
1 AATAAAT
50266 CAATCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:50280 original size:22 final size:22
Alignment explanation
Indices: 50254--50296 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
50244 TAATAAATTA
50254 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
50276 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
50297 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:50280 original size:54 final size:54
Alignment explanation
Indices: 50222--50482 Score: 425
Period size: 54 Copynumber: 4.8 Consensus size: 54
50212 TAATAAATTA
50222 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
50276 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATGT
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
50330 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
50384 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATTCGTAT
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
50438 TTTAAAATAAATCAA-TCTATACTAATAAATTATTTTATAATAAAT
1 TTTAAAATAAATCAATTC-ATACTAATAAATTA-TTTAAAATAAAT
50483 TATTTTAAAA
Statistics
Matches: 194, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
53 2 0.01
54 181 0.93
55 11 0.06
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (54 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:50305 original size:22 final size:22
Alignment explanation
Indices: 50256--50304 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
50246 ATAAATTATT
**
50256 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
50278 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
50301 TAAA
1 TAAA
50305 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:50378 original size:32 final size:32
Alignment explanation
Indices: 50190--50377 Score: 218
Period size: 32 Copynumber: 6.5 Consensus size: 32
50180 CAATCTATAT
50190 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
50222 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
50254 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
50276 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
50308 TTTAAAATAAATC-A---AT-CT-AT---GT-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
50330 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
50362 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
50378 CTATATTTTA
Statistics
Matches: 134, Mismatches: 2, Indels: 40
0.76 0.01 0.23
Matches are distributed among these distances:
22 28 0.21
23 5 0.04
24 1 0.01
26 7 0.05
27 4 0.03
28 7 0.05
30 1 0.01
31 5 0.04
32 76 0.57
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:50480 original size:15 final size:15
Alignment explanation
Indices: 50460--50607 Score: 242
Period size: 15 Copynumber: 9.9 Consensus size: 15
50450 CAATCTATAC
50460 TAATAAATTATTTTA
1 TAATAAATTATTTTA
50475 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
50490 AAATAAATTATTTTA
1 TAATAAATTATTTTA
*
50505 TAATAAATTAGTTTA
1 TAATAAATTATTTTA
50520 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
50535 AAATAAATTATTTTA
1 TAATAAATTATTTTA
50550 TAATAAATTATTTTA
1 TAATAAATTATTTTA
50565 TAATAAATTATTTTA
1 TAATAAATTATTTTA
* *
50580 AAATAAATTAGTTTA
1 TAATAAATTATTTTA
*
50595 AAATAAATTATTT
1 TAATAAATTATTT
50608 AAAATTATTT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 124 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TAATAAATTATTTTA
Found at i:50520 original size:45 final size:45
Alignment explanation
Indices: 50381--50607 Score: 274
Period size: 45 Copynumber: 4.8 Consensus size: 45
50371 AATCAATCTA
* * *
50381 TATTTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATT
1 TATTTTAAAATAAATT-ATT-TTA-TAATAAATTATTT--TAT-AAT-AAAT
* *
50433 CGTATTTTAAAATAAATCAATCTATACTAATAAATTATTTTATAATAAAT
1 --TATTTTAAAATAAAT-TAT-TTTA-TAATAAATTATTTTATAATAAAT
*
50483 TATTTTAAAATAAATTATTTTATAATAAATTAGTTTATAATAAAT
1 TATTTTAAAATAAATTATTTTATAATAAATTATTTTATAATAAAT
50528 TATTTTAAAATAAATTATTTTATAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATTATTTTATAATAAATTATTTTATAATAAAT
* *
50573 TATTTTAAAATAAATTAGTTTAAAATAAATTATTT
1 TATTTTAAAATAAATTATTTTATAATAAATTATTT
50608 AAAATTATTT
Statistics
Matches: 162, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
45 99 0.61
46 3 0.02
47 2 0.01
48 15 0.09
50 3 0.02
51 3 0.02
52 2 0.01
54 34 0.21
55 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (45 bp):
TATTTTAAAATAAATTATTTTATAATAAATTATTTTATAATAAAT
Found at i:51529 original size:18 final size:17
Alignment explanation
Indices: 51488--51520 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51478 TTAAGAAAAA
51488 AATTAATATGATTTTTT
1 AATTAATATGATTTTTT
51505 AATTAATATGATTTTT
1 AATTAATATGATTTTT
51521 GTAGTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTAATATGATTTTTT
Found at i:55417 original size:2 final size:2
Alignment explanation
Indices: 55410--55507 Score: 59
Period size: 2 Copynumber: 53.0 Consensus size: 2
55400 TCGGACCGAG
* * * *
55410 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
55450 TA T- TT TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- 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
55486 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
55508 ATAATTATTT
Statistics
Matches: 71, Mismatches: 17, Indels: 16
0.68 0.16 0.15
Matches are distributed among these distances:
1 8 0.11
2 63 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57817 original size:34 final size:34
Alignment explanation
Indices: 57774--57842 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
57764 GTTATTGGGG
**
57774 CCATGTAAACAATGTAAGCCTCGCCTTCAATGAT
1 CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
57808 CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
1 CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
57842 C
1 C
57843 GGAGTTCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (34 bp):
CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
Found at i:63618 original size:34 final size:34
Alignment explanation
Indices: 63575--63643 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
63565 GTTATTGGGG
**
63575 CCATGTAAACAATGTAAACCTCGCCTTCAATGAT
1 CCATGTAAACAACATAAACCTCGCCTTCAATGAT
*
63609 CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
1 CCATGTAAACAACATAAACCTCGCCTTCAATGAT
63643 C
1 C
63644 GGAGTTCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (34 bp):
CCATGTAAACAACATAAACCTCGCCTTCAATGAT
Found at i:66379 original size:46 final size:46
Alignment explanation
Indices: 66303--66394 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
66293 TATAGTTCAT
*
66303 GAATACTTCGATTTCTGTTTGTTTATCTCCATTAATAAGAATTCGA
1 GAATACTTCGATTTATGTTTGTTTATCTCCATTAATAAGAATTCGA
* *
66349 GAATCCTTTGATTTATGTTTGTTTATCTCCATTAATAAGAATTCGA
1 GAATACTTCGATTTATGTTTGTTTATCTCCATTAATAAGAATTCGA
66395 TAATTGTATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (46 bp):
GAATACTTCGATTTATGTTTGTTTATCTCCATTAATAAGAATTCGA
Found at i:69545 original size:34 final size:34
Alignment explanation
Indices: 69502--69604 Score: 188
Period size: 34 Copynumber: 3.0 Consensus size: 34
69492 GTTATTGGGG
69502 CCATGTAAACAACGTAAGCCTCGCCTTCAATGAT
1 CCATGTAAACAACGTAAGCCTCGCCTTCAATGAT
*
69536 CCATGTAAACAACGTAAGCCTCTCCTTCAATGAT
1 CCATGTAAACAACGTAAGCCTCGCCTTCAATGAT
*
69570 CCATGTAAACAACATAAGCCTCGCCTTCAATGAT
1 CCATGTAAACAACGTAAGCCTCGCCTTCAATGAT
69604 C
1 C
69605 GGAGTTCAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (34 bp):
CCATGTAAACAACGTAAGCCTCGCCTTCAATGAT
Found at i:70432 original size:7 final size:7
Alignment explanation
Indices: 70422--70454 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
70412 ATTTGAGGGT
70422 TGAAGGC
1 TGAAGGC
70429 TGAAGGC
1 TGAAGGC
70436 TGAAGGC
1 TGAAGGC
70443 TGAAGGC
1 TGAAGGC
70450 TGAAG
1 TGAAG
70455 AGCAACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.42, T:0.15
Consensus pattern (7 bp):
TGAAGGC
Found at i:87409 original size:44 final size:44
Alignment explanation
Indices: 87346--87433 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
87336 TCGAGAAAGA
87346 AAAAAATTAAAGAGAAAAGAACGAAGTAATTAGGTGCTTCTTAC
1 AAAAAATTAAAGAGAAAAGAACGAAGTAATTAGGTGCTTCTTAC
87390 AAAAAATTAAAGAGAAAAGAACGAAGTAATTAGGTGCTTCTTAC
1 AAAAAATTAAAGAGAAAAGAACGAAGTAATTAGGTGCTTCTTAC
87434 CATAAAGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (44 bp):
AAAAAATTAAAGAGAAAAGAACGAAGTAATTAGGTGCTTCTTAC
Found at i:93285 original size:13 final size:13
Alignment explanation
Indices: 93263--93295 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
93253 GACTGGTAAG
*
93263 TGGTTAGTGGGTT
1 TGGTTTGTGGGTT
93276 TGGTTTGTGGGTT
1 TGGTTTGTGGGTT
93289 TGGTTTG
1 TGGTTTG
93296 GGTCGTGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (13 bp):
TGGTTTGTGGGTT
Found at i:96184 original size:16 final size:17
Alignment explanation
Indices: 96134--96185 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
96124 AAAACAATTA
96134 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
96151 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
96166 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
96182 AATT
1 AATT
96186 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:96703 original size:30 final size:28
Alignment explanation
Indices: 96662--96719 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
96652 GTTAAAAGTA
* *
96662 TTTTTTTTTTTGTAATT-TTAGGTCCAT
1 TTTTTTTTTTTTTGATTATTAGGTCCAT
96689 TTTTTTTATTTTTTGATTAGTTAGGTCCAT
1 TTTTTTT-TTTTTTGATTA-TTAGGTCCAT
96719 T
1 T
96720 CTTAATCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 8 0.31
30 11 0.42
ACGTcount: A:0.16, C:0.07, G:0.12, T:0.66
Consensus pattern (28 bp):
TTTTTTTTTTTTTGATTATTAGGTCCAT
Found at i:101219 original size:29 final size:29
Alignment explanation
Indices: 101178--101246 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
101168 TTTTTATTGA
* * *
101178 AAATATAATTTTACCTCA-AAAAATTTTAT
1 AAATTTAAATTTA-CTCACAAAAATATTAT
* *
101207 AAATTTAAATTTATTCACTAAAATATTAT
1 AAATTTAAATTTACTCACAAAAATATTAT
101236 AAATTTAAATT
1 AAATTTAAATT
101247 CATTTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATTTAAATTTACTCACAAAAATATTAT
Found at i:103999 original size:6 final size:6
Alignment explanation
Indices: 103988--104017 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
103978 TTCCAGCTGT
103988 CTCCGC CTCCGC CTCCGC CTCCGC CTCCGC
1 CTCCGC CTCCGC CTCCGC CTCCGC CTCCGC
104018 TCCTGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.17, T:0.17
Consensus pattern (6 bp):
CTCCGC
Found at i:105139 original size:19 final size:20
Alignment explanation
Indices: 105090--105139 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
105080 TGTATATATT
105090 TATTTATTTGAGTATATAAA
1 TATTTATTTGAGTATATAAA
**
105110 -ATTTAAGTGAGT-TA-AATA
1 TATTTATTTGAGTATATAA-A
105128 TATTTATTTGAG
1 TATTTATTTGAG
105140 CTTACGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
19 19 0.79
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (20 bp):
TATTTATTTGAGTATATAAA
Found at i:105359 original size:28 final size:28
Alignment explanation
Indices: 105325--105379 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
105315 TTACTAAAAA
*
105325 AATATTAAAA-ATATTATTTCTTAATACT
1 AATATTAAAAGATATTA-ATCTTAATACT
105353 AATATTAAAATGATATTAATCTTAATA
1 AATATTAAAA-GATATTAATCTTAATA
105380 TTGGTTGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 8 0.33
30 6 0.25
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AATATTAAAAGATATTAATCTTAATACT
Found at i:112193 original size:15 final size:15
Alignment explanation
Indices: 112173--112203 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
112163 TAGTTATGTT
112173 CCAGTGGTTCAGCGG
1 CCAGTGGTTCAGCGG
112188 CCAGTGGTTCAGCGG
1 CCAGTGGTTCAGCGG
112203 C
1 C
112204 TTTCATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.39, T:0.19
Consensus pattern (15 bp):
CCAGTGGTTCAGCGG
Found at i:114729 original size:23 final size:23
Alignment explanation
Indices: 114698--114781 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
114688 TTTACGTTAA
*
114698 TTTATGTTCATTTATTGTGTTCG
1 TTTACGTTCATTTATTGTGTTCG
* *
114721 TTTACGTTCATTCATTTGTGTTCA
1 TTTACGTTCATTTA-TTGTGTTCG
**
114745 TTTACGTTTGTTTATTGTGTTCG
1 TTTACGTTCATTTATTGTGTTCG
* * *
114768 ATTATGTTCGTTTA
1 TTTACGTTCATTTA
114782 CATACGTTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 31 0.62
24 19 0.38
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (23 bp):
TTTACGTTCATTTATTGTGTTCG
Found at i:114805 original size:47 final size:47
Alignment explanation
Indices: 114690--114807 Score: 119
Period size: 47 Copynumber: 2.5 Consensus size: 47
114680 TTATTTTGTT
* * * **
114690 TACGTTAATTTATGTTCATTTATTGTGTTCGTTTACGTTCATTCATT
1 TACGTTCATTTATGTTCGTTTATTGTGTTCGATTACGTTCATTCACA
** * * * * *
114737 TGTGTTCATTTACGTTTGTTTATTGTGTTCGATTATGTTCGTTTACA
1 TACGTTCATTTATGTTCGTTTATTGTGTTCGATTACGTTCATTCACA
*
114784 TACGTTCGTTTATGTTCGTTTATT
1 TACGTTCATTTATGTTCGTTTATT
114808 TATGTTCGTG
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (47 bp):
TACGTTCATTTATGTTCGTTTATTGTGTTCGATTACGTTCATTCACA
Found at i:114814 original size:24 final size:23
Alignment explanation
Indices: 114698--114816 Score: 103
Period size: 24 Copynumber: 5.0 Consensus size: 23
114688 TTTACGTTAA
*
114698 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
* * * *
114721 TTTACGTTCATTCATTTGTGTTCA
1 TTTATGTTCGTTTA-TTGTGTTCG
* *
114745 TTTACGTTTGTTTATTGTGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
* * **
114768 ATTATGTTCGTTTACATACGTTCG
1 TTTATGTTCGTTTA-TTGTGTTCG
*
114792 TTTATGTTCGTTTATTTATGTTCG
1 TTTATGTTCGTTTA-TTGTGTTCG
114816 T
1 T
114817 GTATCATTTA
Statistics
Matches: 77, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 31 0.40
24 46 0.60
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTATGTTCGTTTATTGTGTTCG
Found at i:116812 original size:83 final size:83
Alignment explanation
Indices: 116649--116812 Score: 220
Period size: 83 Copynumber: 2.0 Consensus size: 83
116639 GTGTATATCT
* * * * *
116649 GTTTATTATTTAAAATTTAAAAGATATTATTATCTATTTAAATTTATATATTAAAAGATATATGG
1 GTTTAATATTTAAAATTTAAAAGATATTATTATATATTTAAATTTAGATATTAAAAGAGATATAG
* *
116714 TTGAAGTAAATCTCTCAG
66 TTGAAGAAAAACTCTCAG
* * * *
116732 GTTTAATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGAGGTTTAG
1 GTTTAATATTTAAAATTTAAAAGATATTATTATATATTTAAATTTAGATATTAAAAGAGATATAG
*
116797 TTGGAGAAAAACTCTC
66 TTGAAGAAAAACTCTC
116813 TCGAAATTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (83 bp):
GTTTAATATTTAAAATTTAAAAGATATTATTATATATTTAAATTTAGATATTAAAAGAGATATAG
TTGAAGAAAAACTCTCAG
Found at i:117857 original size:18 final size:18
Alignment explanation
Indices: 117834--117870 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
117824 TTTCTCTCCA
117834 CGTTTCCCCAGGTCGGAG
1 CGTTTCCCCAGGTCGGAG
117852 CGTTTCCCCAGGTCGGAG
1 CGTTTCCCCAGGTCGGAG
117870 C
1 C
117871 CGCCCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.35, G:0.32, T:0.22
Consensus pattern (18 bp):
CGTTTCCCCAGGTCGGAG
Found at i:119945 original size:30 final size:27
Alignment explanation
Indices: 119888--119945 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
119878 CCCAAAACAT
**
119888 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
119915 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
119945 T
1 T
119946 TAATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:119981 original size:36 final size:38
Alignment explanation
Indices: 119893--119982 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 38
119883 AACATTATTA
* *
119893 TTTTATATATTTAATATTAATATATTATTTTAGTATCAT
1 TTTTATA-ATATAATATTAATATATTATTTTAGTATAAT
* *
119932 TTTAATAA-A-AATATTAAT-TA-TA-TTTATTGATAAT
1 TTTTATAATATAATATTAATATATTATTTTAGT-ATAAT
119966 TTTTATAATATAATATT
1 TTTTATAATATAATATT
119983 TTTATTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
33 5 0.12
34 13 0.30
35 3 0.07
36 15 0.35
38 1 0.02
39 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (38 bp):
TTTTATAATATAATATTAATATATTATTTTAGTATAAT
Found at i:124172 original size:17 final size:18
Alignment explanation
Indices: 124140--124173 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
124130 TATTTAAATA
124140 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
124158 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
124174 ACCTTAACGA
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:130625 original size:20 final size:20
Alignment explanation
Indices: 130600--130638 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
130590 TTTTGGTGCA
*
130600 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
130620 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
130639 GGGGTTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:135647 original size:29 final size:29
Alignment explanation
Indices: 135598--135653 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
135588 TTTTTTATTT
* *
135598 TTTTATTAAAATAATTATTTAACATTTTA
1 TTTTATAAAAATAAGTATTTAACATTTTA
* *
135627 TTTTATAAAAATAAGTGTTTAATATTT
1 TTTTATAAAAATAAGTATTTAACATTT
135654 GAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTATAAAAATAAGTATTTAACATTTTA
Found at i:138500 original size:46 final size:47
Alignment explanation
Indices: 138430--138521 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 47
138420 ATAAATAGAT
* *
138430 AATTCTCGATATCCTCTCCAAATTCACTC-GAATCAATTAAAGAACC
1 AATTCTCGAGATCCTCTCCAAATTCACTCAAAATCAATTAAAGAACC
* *
138476 AATTCTCGAGATCCTCTCCCAATTCACTCAAAATCAATTGAAGAAC
1 AATTCTCGAGATCCTCTCCAAATTCACTCAAAATCAATTAAAGAAC
138522 TAAGGATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 27 0.66
47 14 0.34
ACGTcount: A:0.37, C:0.28, G:0.08, T:0.27
Consensus pattern (47 bp):
AATTCTCGAGATCCTCTCCAAATTCACTCAAAATCAATTAAAGAACC
Found at i:144827 original size:20 final size:19
Alignment explanation
Indices: 144774--144827 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
144764 ACACAAGCTT
*
144774 TTTTTTAATAGAGCATGATA
1 TTTTTTAATAGA-CATGAAA
144794 TTTTCTT-ATA-ACATGAAA
1 TTTT-TTAATAGACATGAAA
144812 TTTTTTAATATGACAT
1 TTTTTTAATA-GACAT
144828 TGTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 2 0.07
18 13 0.45
19 1 0.03
20 11 0.38
21 2 0.07
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (19 bp):
TTTTTTAATAGACATGAAA
Found at i:148491 original size:13 final size:13
Alignment explanation
Indices: 148449--148493 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
148439 GTCATAAATC
148449 TATGACGCGCATT
1 TATGACGCGCATT
* *
148462 TACGACGTGCATT
1 TATGACGCGCATT
*
148475 TATGACGCGCATG
1 TATGACGCGCATT
148488 TATGAC
1 TATGAC
148494 TTACATTACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:148500 original size:26 final size:26
Alignment explanation
Indices: 148449--148500 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
148439 GTCATAAATC
* *
148449 TATGACGCGCATTTACGACGTGCATT
1 TATGACGCGCATGTACGACGTACATT
* *
148475 TATGACGCGCATGTATGACTTACATT
1 TATGACGCGCATGTACGACGTACATT
148501 ACGCGTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (26 bp):
TATGACGCGCATGTACGACGTACATT
Found at i:148578 original size:85 final size:85
Alignment explanation
Indices: 148472--148779 Score: 431
Period size: 85 Copynumber: 3.6 Consensus size: 85
148462 TACGACGTGC
* * *
148472 ATTTATGACGCGCATGTATGACTTACATTACGCGTCATTGAAGCCTCCGTCATAAATTAATATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCTCCGTCATAAATTAATATGA
148537 CACACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* * *
148557 ATTTATGACACGCATGTATGACTTACATTGTGCGTCATTAAAGCCCCCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCTCCGTCATAAATTAATATGA
*
148622 CACACATTTGTGCGTCATAA
66 CACACATTTGTGTGTCATAA
* * *
148642 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCC-CTCGTCATAAATCT-GTTT
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCTC-CGTCATAAAT-TAATAT
*
148705 GACATACATTTGTGTGTCATAA
64 GACACACATTTGTGTGTCATAA
** * * * *
148727 ATTTATGACACATATATATGACTTACATTGCGTGTCATTAAAGCATACGTCAT
1 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCTCCGTCAT
148780 TTAAAAAGAC
Statistics
Matches: 199, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
84 1 0.01
85 197 0.99
86 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCTCCGTCATAAATTAATATGA
CACACATTTGTGTGTCATAA
Found at i:150269 original size:12 final size:12
Alignment explanation
Indices: 150252--150282 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
150242 ATATATTGAT
150252 AATCAAATGAAA
1 AATCAAATGAAA
150264 AATCAAATGAAA
1 AATCAAATGAAA
*
150276 AAACAAA
1 AATCAAA
150283 CCCGAGATTA
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:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:151964 original size:15 final size:15
Alignment explanation
Indices: 151939--151994 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
151929 GATGCTTTCT
151939 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTTGACG
*
151955 TTTTCTTCTTTGACA
1 TTTTCTTCTTTGACG
*
151970 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
151985 TTGTCTTCTT
1 TTTTCTTCTT
151995 ACCTCATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.21, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:159405 original size:18 final size:18
Alignment explanation
Indices: 159382--159417 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
159372 GATAATTCAC
159382 ATTCTGAATAACTGATGA
1 ATTCTGAATAACTGATGA
159400 ATTCTGAATAACTGATGA
1 ATTCTGAATAACTGATGA
159418 TTTCACCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
ATTCTGAATAACTGATGA
Found at i:159626 original size:12 final size:12
Alignment explanation
Indices: 159588--159680 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
159578 ATTTCTGACT
159588 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
159600 TG-ATACATGACC
1 TGAATTC-TGTTC
159612 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
159624 TGATTTCTGATC
1 TGAATTCTGTTC
*
159636 TGGATTCTGTTC
1 TGAATTCTGTTC
159648 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
* *
159660 TGAATTCCGTTT
1 TGAATTCTGTTC
*
159672 TGATTTCTG
1 TGAATTCTG
159681 ATATCTCCGT
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
11 5 0.08
12 52 0.84
13 5 0.08
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:159643 original size:48 final size:49
Alignment explanation
Indices: 159578--159682 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 49
159568 ATTTTATCTA
*
159578 ATTTCTGA-CTTGAATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTG
1 ATTTCTGATCTTGAATTCTGTTCTGATATC-TGACCTGAATTCCGTTCTG
* ** *
159626 ATTTCTGATC-TGGATTCTGTTCTGATATCTGTTCTGAATTCCGTTTTG
1 ATTTCTGATCTTGAATTCTGTTCTGATATCTGACCTGAATTCCGTTCTG
159674 ATTTCTGAT
1 ATTTCTGAT
159683 ATCTCCGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 48 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTCTGTTCTGATATCTGACCTGAATTCCGTTCTG
Found at i:159680 original size:24 final size:24
Alignment explanation
Indices: 159578--159682 Score: 115
Period size: 24 Copynumber: 4.4 Consensus size: 24
159568 ATTTTATCTA
159578 ATTTCTGA-CTTGAATTCTGTTCTG
1 ATTTCTGATC-TGAATTCTGTTCTG
* *
159602 A-TACATGACCTGAATTCTGTTCTG
1 ATTTC-TGATCTGAATTCTGTTCTG
*
159626 ATTTCTGATCTGGATTCTGTTCTG
1 ATTTCTGATCTGAATTCTGTTCTG
* * * *
159650 ATATCTGTTCTGAATTCCGTTTTG
1 ATTTCTGATCTGAATTCTGTTCTG
159674 ATTTCTGAT
1 ATTTCTGAT
159683 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.03
24 62 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
ATTTCTGATCTGAATTCTGTTCTG
Found at i:159849 original size:2 final size:2
Alignment explanation
Indices: 159842--159866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
159832 GATGGGGGTG
159842 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 T
159867 GTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:163720 original size:18 final size:18
Alignment explanation
Indices: 163694--163745 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
163684 GAGAAAGAAC
* * *
163694 ATGACGACGACGATGAGG
1 ATGATGACGAAGATGACG
163712 ATGATGACGAAGATGACG
1 ATGATGACGAAGATGACG
* *
163730 ATGATAAGGAAGATGA
1 ATGATGACGAAGATGA
163746 TGCCCAAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (18 bp):
ATGATGACGAAGATGACG
Found at i:172278 original size:16 final size:16
Alignment explanation
Indices: 172257--172287 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
172247 CTAAAGGTTT
*
172257 CGGGTTCGAGTACCAA
1 CGGGTTCGAATACCAA
172273 CGGGTTCGAATACCA
1 CGGGTTCGAATACCA
172288 GCGATTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (16 bp):
CGGGTTCGAATACCAA
Found at i:178051 original size:70 final size:70
Alignment explanation
Indices: 177977--178109 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 70
177967 TTTTCATGAA
* * * *
177977 CATGTTTATTTAGCGTTTGTTTAATGTTTGCGAACGTGTTCGTTTATATGTTCACGTACGTGTTT
1 CATGTTCATTTAGCATTCGTTTAATGTTTGCGAACGTGTTCGTTTATATGTTCACGAACGTGTTT
178042 ATAAT
66 ATAAT
* * *
178047 CATGTTCGTTTAGCATTCGTTTAATGTTTGTGAACGTGTTTGTTTATATGTTCACGAACGTGT
1 CATGTTCATTTAGCATTCGTTTAATGTTTGCGAACGTGTTCGTTTATATGTTCACGAACGTGT
178110 CTATGTTCGT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (70 bp):
CATGTTCATTTAGCATTCGTTTAATGTTTGCGAACGTGTTCGTTTATATGTTCACGAACGTGTTT
ATAAT
Found at i:180378 original size:21 final size:20
Alignment explanation
Indices: 180354--180463 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 20
180344 TATTCGCAAC
180354 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGC-TT
* * *
180375 GCGATTCATTCCAAATTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
180396 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGC-TT
* * *
180417 GCGATTCATTCCAAATTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
180438 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
180459 GCGAT
1 GCGAT
180464 TCATTCCAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
19 18 0.26
20 2 0.03
21 29 0.42
22 2 0.03
23 18 0.26
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (20 bp):
GCGATAGTCGAAGTTCGCTT
Found at i:180405 original size:42 final size:42
Alignment explanation
Indices: 180354--180660 Score: 395
Period size: 42 Copynumber: 7.2 Consensus size: 42
180344 TATTCGCAAC
*
180354 GCGATAGTCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
*
180396 GCGATAGTCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* *
180438 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* * *
180479 GCGACAGGCAAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* *
180520 GAGACAGGCGAAGTTCGCATTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
* *
180561 GCGACAGGCGAAGTTCGCGTTTCGCCTGTCGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAA------G-TTCGCAT-T-GCGATTCATTCCAAATTCGTT
* *
180612 GCGATAGGCGAATTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
180654 GCGATAG
1 GCGATAG
180661 TCCAAATATT
Statistics
Matches: 242, Mismatches: 12, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
40 2 0.01
41 89 0.37
42 105 0.43
43 1 0.00
44 6 0.02
47 1 0.00
48 6 0.02
49 1 0.00
50 12 0.05
51 19 0.08
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (42 bp):
GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
Found at i:180615 original size:21 final size:21
Alignment explanation
Indices: 180591--180658 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
180581 TTCGCCTGTC
180591 GCGATTCATTCCAAATTCGTT
1 GCGATTCATTCCAAATTCGTT
** * *
180612 GCGA-T-AGGCGAATTTCGCGTT
1 GCGATTCATTCCAAATT--CGTT
180633 GCGATTCATTCCAAATTCGTT
1 GCGATTCATTCCAAATTCGTT
180654 GCGAT
1 GCGAT
180659 AGTCCAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 6 0.17
20 1 0.03
21 21 0.60
22 1 0.03
23 6 0.17
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (21 bp):
GCGATTCATTCCAAATTCGTT
Found at i:180666 original size:19 final size:19
Alignment explanation
Indices: 180600--180667 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
180590 CGCGATTCAT
180600 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * * *
180619 GCGAATTTCGCGTTGCGATTCAT
1 TCCAAATT--CGTTGCGA-T-AG
180642 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
180661 TCCAAAT
1 TCCAAAT
180668 ATTGCATTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 13 0.35
20 1 0.03
21 16 0.43
22 1 0.03
23 6 0.16
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:181503 original size:21 final size:21
Alignment explanation
Indices: 181479--181549 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
181469 TTGGAATGAA
181479 TCGCAACGCGAACTTCGCATG
1 TCGCAACGCGAACTTCGCATG
* *
181500 TCGCAA--CGAA-TTTGGACTG
1 TCGCAACGCGAACTTCGCA-TG
*
181519 AATCGCAACGCGAACTTCGCCTG
1 --TCGCAACGCGAACTTCGCATG
181542 TCGCAACG
1 TCGCAACG
181550 AATTGGAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 4 0.10
19 6 0.15
21 20 0.51
23 6 0.15
24 3 0.08
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGCATG
Found at i:181608 original size:83 final size:84
Alignment explanation
Indices: 181464--181620 Score: 253
Period size: 83 Copynumber: 1.9 Consensus size: 84
181454 TATATGTCTT
* * *
181464 CGAATTTGGAATGAATCGCAACGCGAACTTCGCATGTCGCAACGAATTTGGACTGAATCGCAACG
1 CGAATTTGGAATGAATCACAACGCGAACTTCGCATGTCGCAACGAATTGGGAATGAATCGCAACG
181529 CGAACTTCGCCTGTCGCAA
66 CGAACTTCGCCTGTCGCAA
* * *
181548 CGAA-TTGGAATGAATCACAATGCGAACTTCGCCTGTCGCGACGAATTGGGAATGAATCGCAACG
1 CGAATTTGGAATGAATCACAACGCGAACTTCGCATGTCGCAACGAATTGGGAATGAATCGCAACG
181612 CGAACTTCG
66 CGAACTTCG
181621 ACTATCGCGT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 63 0.94
84 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (84 bp):
CGAATTTGGAATGAATCACAACGCGAACTTCGCATGTCGCAACGAATTGGGAATGAATCGCAACG
CGAACTTCGCCTGTCGCAA
Found at i:181629 original size:42 final size:42
Alignment explanation
Indices: 181464--181620 Score: 253
Period size: 42 Copynumber: 3.8 Consensus size: 42
181454 TATATGTCTT
*
181464 CGAATTTGGAATGAATCGCAACGCGAACTTCGCATGTCGCAA
1 CGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAA
*
181506 CGAATTTGGACTGAATCGCAACGCGAACTTCGCCTGTCGCAA
1 CGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAA
* * *
181548 CGAA-TTGGAATGAATCACAATGCGAACTTCGCCTGTCGCGA
1 CGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAA
*
181589 CGAATTGGGAATGAATCGCAACGCGAACTTCG
1 CGAATTTGGAATGAATCGCAACGCGAACTTCG
181621 ACTATCGCGT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
41 37 0.35
42 68 0.65
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAA
Found at i:181710 original size:19 final size:19
Alignment explanation
Indices: 181663--181713 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
181653 CGATTTCGGA
* *
181663 GATCGCGTTACGAATTATC
1 GATCGCATTGCGAATTATC
181682 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
181701 GATCGCATTGCGA
1 GATCGCATTGCGA
181714 TTTACTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:191160 original size:16 final size:16
Alignment explanation
Indices: 191136--191169 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
191126 TATCGCCGAC
*
191136 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
191152 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
191168 CG
1 CG
191170 TGAATAGTAA
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:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:197261 original size:77 final size:77
Alignment explanation
Indices: 197126--197272 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
197116 TTGTGTTATT
* * * * *
197126 AACATATTGGCCTTTTCTCATTCTAATCTTTTTGCTTATATGAAAGTTTTGTTAACTTGTATTTA
1 AACATATTGGCCTTTTCTCAATCTAAGCTTTTTGCTTATAAGAAAGTTGTGTTAACTTGTATGTA
197191 TGCCAAATAATA
66 TGCCAAATAATA
* *
197203 AACATATTGGCTTTTTCTCAATCTAAGCTTTTTGCTTATACAG-AAGTTGTGTTTACTTGTATGT
1 AACATATTGGCCTTTTCTCAATCTAAGCTTTTTGCTTATA-AGAAAGTTGTGTTAACTTGTATGT
197267 ATGCCA
65 ATGCCA
197273 GGTTAATCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 61 0.98
78 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (77 bp):
AACATATTGGCCTTTTCTCAATCTAAGCTTTTTGCTTATAAGAAAGTTGTGTTAACTTGTATGTA
TGCCAAATAATA
Found at i:208376 original size:13 final size:13
Alignment explanation
Indices: 208358--208382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208348 AAAATCTTAA
208358 AATCATTAATCGT
1 AATCATTAATCGT
208371 AATCATTAATCG
1 AATCATTAATCG
208383 ATATAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
AATCATTAATCGT
Found at i:219687 original size:263 final size:250
Alignment explanation
Indices: 219284--219809 Score: 761
Period size: 263 Copynumber: 2.0 Consensus size: 250
219274 ATCCGAGACT
* *
219284 CGACCCGATCAAAATAAAGTTTCACCCGATCCGAATATATGAATTAGAAACCCGACCCGACCCGA
1 CGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCGA
* *
219349 AATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAAATATATATAGAGA
66 AATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAATATATATAGAAA
*
219414 GGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATATTTTTTGAGTCGGGTCGG
131 GGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATA-TATTT---TCGGGTCGG
*
219479 GTATTTTTCACCCTAAACCCG-AC-CCCGACCCGAATATCACACTTAAAAAAAATCGACC
192 GTATTTTTCACCCTAAACCCGAACACCCGACCCAAATATCACACTTAAAAAAAAT-GACC
219537 CGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGA
1 CGACCCGACCAAAATAAAGTTT----C-ACCCGACCCGAATATATGAATTAG-AA----ACCCGA
*
219602 CCCGACCCGAAATAATACAAAAAATATTTTTATTCAATAAAAACAATGACTTAATT-GAAAATAT
56 CCCGACCCGAAATAATA-AAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAT
* *
219666 ATATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
120 ATATATAGAAAGGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATATATTTTC
*
219731 GGGTCGGGTATTTTTCACCCTAAACCCGAACTAGACCCGACCCAAATATCACACTTAAAAAAACT
185 GGGTCGGGTATTTTTCACCCTAAACCCGAAC---ACCCGACCCAAATATCACACTTAAAAAAAAT
219796 GACC
247 GACC
*
219800 CGACCTGACC
1 CGACCCGACC
219810 CGGATATATG
Statistics
Matches: 246, Mismatches: 11, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
253 21 0.09
257 1 0.00
258 23 0.09
259 32 0.13
260 2 0.01
262 4 0.02
263 98 0.40
264 65 0.26
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (250 bp):
CGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCGA
AATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAATATATATAGAAA
GGGGTATTATTGTAATTATTCCTAAATATATAAAGTAAAATTATATATATTTTCGGGTCGGGTAT
TTTTCACCCTAAACCCGAACACCCGACCCAAATATCACACTTAAAAAAAATGACC
Found at i:220193 original size:18 final size:19
Alignment explanation
Indices: 220153--220194 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
220143 TAAAATTTTA
220153 AAAATATTATAGAAATATG
1 AAAATATTATAGAAATATG
*
220172 AAAA-ATTAT-GAAACTATT
1 AAAATATTATAGAAA-TATG
220190 AAAAT
1 AAAAT
220195 GTTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (19 bp):
AAAATATTATAGAAATATG
Found at i:224176 original size:12 final size:13
Alignment explanation
Indices: 224151--224180 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
224141 GCATTATATA
224151 TTTCTTTATGGTT
1 TTTCTTTATGGTT
224164 TTTCTTTAT-GTT
1 TTTCTTTATGGTT
224176 TTTCT
1 TTTCT
224181 AGCAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (13 bp):
TTTCTTTATGGTT
Found at i:227101 original size:37 final size:38
Alignment explanation
Indices: 227015--227103 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
227005 TTTTCACCCT
227015 AAACCCGAACCCGACCCGACCCAAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCAAATATCACACTTAAAA
* * *
227054 AAACCCGACCCGACTCGACCCGAATATTACACTT-AAA
1 AAACCCGACCCGACCCGACCCAAATATCACACTTAAAA
227091 AAACCCGACCCGA
1 AAACCCGACCCGA
227104 ACAAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 16 0.34
38 24 0.51
39 7 0.15
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCAAATATCACACTTAAAA
Found at i:227692 original size:4 final size:4
Alignment explanation
Indices: 227683--228393 Score: 1394
Period size: 4 Copynumber: 178.8 Consensus size: 4
227673 TCTTGCCCCA
227683 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227731 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227779 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227827 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227875 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227923 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
227971 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228019 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228067 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228115 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228163 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228211 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228259 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228305 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
228351 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
228394 AAAATCATTA
Statistics
Matches: 703, Mismatches: 0, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.01
4 699 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:229825 original size:4 final size:4
Alignment explanation
Indices: 229816--229846 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
229806 GTTAATTGTT
229816 AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
229847 CGATAGTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:230066 original size:27 final size:27
Alignment explanation
Indices: 230036--230096 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
230026 ATAATACATC
*
230036 TTATTTTATTATATATATA-TATATAAA-
1 TTATTTTA-TATATAGATAGTATA-AAAT
*
230063 TTATTTGATATATAGATAGTATAAAAT
1 TTATTTTATATATAGATAGTATAAAAT
230090 TTATTTT
1 TTATTTT
230097 GCATAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
TTATTTTATATATAGATAGTATAAAAT
Found at i:230140 original size:22 final size:21
Alignment explanation
Indices: 230115--230160 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
230105 TATTTATATT
* * *
230115 AATCTTAAAATTTAAAATCTTA
1 AATCATAAAATCT-AAACCTTA
230137 AATCATAAAATCTAAACCTTA
1 AATCATAAAATCTAAACCTTA
230158 AAT
1 AAT
230161 AAGACTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (21 bp):
AATCATAAAATCTAAACCTTA
Found at i:231442 original size:3 final size:3
Alignment explanation
Indices: 231434--231462 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
231424 TGTATATTAA
231434 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
231463 GGACAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:232832 original size:54 final size:55
Alignment explanation
Indices: 232756--232861 Score: 187
Period size: 54 Copynumber: 1.9 Consensus size: 55
232746 GTTAACACTA
232756 AAATGTCACATTATTTGATTGATAATAATATAA-AGTTCATTGATAAAAAAAATT
1 AAATGTCACATTATTTGATTGATAATAATATAACAGTTCATTGATAAAAAAAATT
* *
232810 AAATGTTACATTATTTGATTGATTATAATATAACAGTTCATTGATAAAAAAA
1 AAATGTCACATTATTTGATTGATAATAATATAACAGTTCATTGATAAAAAAA
232862 TCAATTCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 31 0.63
55 18 0.37
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (55 bp):
AAATGTCACATTATTTGATTGATAATAATATAACAGTTCATTGATAAAAAAAATT
Found at i:236468 original size:144 final size:141
Alignment explanation
Indices: 236208--236494 Score: 495
Period size: 144 Copynumber: 2.0 Consensus size: 141
236198 GCACTGAATC
* *
236208 CATCAATGAACAGCAATCTGAAATTACAGAATTCCCGAGCATGGAAATCAATCATCAAATGGTGA
1 CATCAATGAAAAGCAATCTGAAATTACAGAAATCCCGAGCATGGAAATCAATCATCAAATGGTGA
* *
236273 AAAATTCTGAGGATAAGAAAGATTTTGGTTTGAGAGCTGCACCAGTTGAACATTTACATGAAGCA
66 AAAATTCTGAGGATAAGAAAGATTTTGGTTTGAGACCTGCACCAGTTGAACACTTACATG-A--A
236338 GCAAATGGAAGTTT
128 GCAAATGGAAGTTT
236352 CATCAATGAAAAGCAATCTGAAATTAC-GAAATCCACGAGCATGGAAATCAATCATCAAATGGTG
1 CATCAATGAAAAGCAATCTGAAATTACAGAAATCC-CGAGCATGGAAATCAATCATCAAATGGTG
236416 AAAAATTCTGAGGATAAGAAAGATTTTGGTTTGAGACCTGCACCAGTTGAACACTTACATGAAGC
65 AAAAATTCTGAGGATAAGAAAGATTTTGGTTTGAGACCTGCACCAGTTGAACACTTACATGAAGC
236481 AAATGGAAGTTT
130 AAATGGAAGTTT
236493 CA
1 CA
236495 AGCATTTTGA
Statistics
Matches: 138, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
141 17 0.12
143 7 0.05
144 114 0.83
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (141 bp):
CATCAATGAAAAGCAATCTGAAATTACAGAAATCCCGAGCATGGAAATCAATCATCAAATGGTGA
AAAATTCTGAGGATAAGAAAGATTTTGGTTTGAGACCTGCACCAGTTGAACACTTACATGAAGCA
AATGGAAGTTT
Found at i:237632 original size:108 final size:108
Alignment explanation
Indices: 237499--237693 Score: 266
Period size: 108 Copynumber: 1.8 Consensus size: 108
237489 AAAGCAGTGG
* * * * *
237499 TCCTCGACATATGAATCATAATGAAGATGCAAAAAAACCTCAAGATATAAACTGGAATGAGGATA
1 TCCTCAACATATAAAGCATAATGAAGATGCAAAAAAACCTCAACATATAAACTGGAATGAAGATA
*
237564 CACAAAGTCC-TCAAAAGATAAGCCATGATGCAAACATGAATAA
66 AACAAAG-CCATCAAAAGATAAGCCATGATGCAAACATGAATAA
* * * * *
237607 TCCTCAACATATAAAGCATGATGAAGATGCACAAAAAGCTCAACCTATAAGCTGGAATGAAGATA
1 TCCTCAACATATAAAGCATAATGAAGATGCAAAAAAACCTCAACATATAAACTGGAATGAAGATA
*
237672 AACCAAGCCATCAAAAGATAAG
66 AACAAAGCCATCAAAAGATAAG
237694 TCGCGATGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
107 2 0.03
108 72 0.97
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (108 bp):
TCCTCAACATATAAAGCATAATGAAGATGCAAAAAAACCTCAACATATAAACTGGAATGAAGATA
AACAAAGCCATCAAAAGATAAGCCATGATGCAAACATGAATAA
Found at i:240318 original size:17 final size:15
Alignment explanation
Indices: 240288--240336 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 15
240278 ATATTCTAAG
240288 TTGATATTTTTATTT
1 TTGATATTTTTATTT
240303 TTGATATTAATTTATTT
1 TTGATATT--TTTATTT
*
240320 TTGAATATTTTAATTT
1 TTG-ATATTTTTATTT
240336 T
1 T
240337 ATCCTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 10 0.33
18 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTGATATTTTTATTT
Found at i:241720 original size:20 final size:18
Alignment explanation
Indices: 241697--241737 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
241687 ATAAAAATTA
241697 ATAATTTAGATACTAAATAC
1 ATAATTTA-A-ACTAAATAC
*
241717 ATAATTTAACCTAAATAC
1 ATAATTTAAACTAAATAC
241735 ATA
1 ATA
241738 GTCTGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (18 bp):
ATAATTTAAACTAAATAC
Found at i:244703 original size:9 final size:9
Alignment explanation
Indices: 244675--244708 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
244665 ATATTATTCT
244675 TTAATTAAA
1 TTAATTAAA
*
244684 TT-ATAAAA
1 TTAATTAAA
244692 TTAATTAAA
1 TTAATTAAA
244701 TTAATTAA
1 TTAATTAA
244709 CATAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:245293 original size:2 final size:2
Alignment explanation
Indices: 245278--245328 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
245268 AATATTCGAA
245278 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245318 AT AT AT AT AT A
1 AT AT AT AT AT A
245329 ATAATGTGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252852 original size:22 final size:20
Alignment explanation
Indices: 252805--252858 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
252795 TAAAAGGGGT
252805 TGGTATTGATACTCGATCTG
1 TGGTATTGATACTCGATCTG
*
252825 -GAGTATTGATACTTCTGGTCTG
1 TG-GTATTGATAC-TC-GATCTG
*
252847 TGGTATCGATAC
1 TGGTATTGATAC
252859 AGTCCTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 10 0.36
21 2 0.07
22 14 0.50
23 1 0.04
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (20 bp):
TGGTATTGATACTCGATCTG
Found at i:259730 original size:21 final size:21
Alignment explanation
Indices: 259706--259787 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
259696 CCTTCGACTA
*
259706 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
259727 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * *
259748 TCGTGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
259771 T--CGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
259788 AATCACAACG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 7 0.14
21 36 0.71
23 8 0.16
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:260614 original size:21 final size:21
Alignment explanation
Indices: 260585--261080 Score: 292
Period size: 21 Copynumber: 23.8 Consensus size: 21
260575 ATTTTGGACT
*
260585 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
260606 ATCGTAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260627 ATCGCAATGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
260648 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260669 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
260690 ATCGCAACAAGAAATTCGACT--
1 ATCGCAAC--GAACTTGGAATAA
*
260711 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
260732 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
260753 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
260774 ATCACAACAAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
260795 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
* *
260818 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260839 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
260860 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260881 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
*
260900 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260921 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
260942 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
* *
260961 ATCGCATTGCGAACTTGGACT--
1 ATCGCA--ACGAACTTGGAATAA
*
260982 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
* *
261001 ATCGCATTGCGAACTTGGACT--
1 ATCGCA--ACGAACTTGGAATAA
*
261022 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
261043 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
261064 ATCGCAACGAACTTGGA
1 ATCGCAACGAACTTGGA
261081 CTATCGCATT
Statistics
Matches: 397, Mismatches: 46, Indels: 66
0.78 0.09 0.13
Matches are distributed among these distances:
19 117 0.29
21 196 0.49
23 84 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:260628 original size:42 final size:42
Alignment explanation
Indices: 260581--261006 Score: 507
Period size: 42 Copynumber: 10.2 Consensus size: 42
260571 TGCGATTTTG
* *
260581 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
260623 GACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* ** *
260665 GACTATCGCAACGAATTTGGAATAAATCGCAACAAGAAATTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
260707 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
260749 GACTATCGCAACGAACTTGGAATAAATCACAA--CAAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
260789 GAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* *
260835 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
260877 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
260917 GACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
260957 GACTATCGCATTGCGAACTTGGACT--ATCGCAA--CGAACTTG
1 GACTATCGCA--ACGAACTTGGAATAAATCGCAACGCGAACTTC
260997 GACTATCGCA
1 GACTATCGCA
261007 TTGCGAACTT
Statistics
Matches: 349, Mismatches: 25, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
40 92 0.26
42 221 0.63
44 27 0.08
46 9 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:260925 original size:61 final size:60
Alignment explanation
Indices: 260578--261088 Score: 514
Period size: 61 Copynumber: 8.2 Consensus size: 60
260568 CGTTGCGATT
* * * *
260578 TTGGACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTCGACTATCGCAATGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * * * *
260639 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAA--CGAATTTGGAATAAATCGCAACAAG
1 TTGGACT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTGGACT--ATCGCAAC--G
*
260701 AAA
58 AAC
* * *
260704 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * * *
260765 TTGGAATAAATCACAACAAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGA
1 TTGGACT--ATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACT--ATCGCAA--CGA
260830 AC
59 AC
* *
260832 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
*
260893 TTGGACTATCGCAACGCGAACTTGGACT-ATCGCAACGCGAACTTGGACTATCGCAACGAAC
1 TTGGACTATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCAACGAAC
* * *
260954 TTGGACTATCGCATTGCGAACTTGGACT-ATCGCAA--CGAACTTGGACTATCGCATTGCGAAC
1 TTGGACTATCGCA--ACGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCA--ACGAAC
* * *
261015 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAAC
261076 TTGGACTATCGCA
1 TTGGACTATCGCA
261089 TTGCGATAGT
Statistics
Matches: 379, Mismatches: 43, Indels: 56
0.79 0.09 0.12
Matches are distributed among these distances:
59 28 0.07
61 158 0.42
63 112 0.30
65 71 0.19
67 10 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (60 bp):
TTGGACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCAACGAAC
Found at i:262397 original size:22 final size:23
Alignment explanation
Indices: 262367--262413 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
262357 AAACTATATT
262367 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
262390 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
262412 TA
1 TA
262414 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:266678 original size:2 final size:2
Alignment explanation
Indices: 266671--266704 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
266661 GTTGTTCTTT
266671 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
266705 AATCTGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:267011 original size:2 final size:2
Alignment explanation
Indices: 267004--267030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
266994 GTATAGATGC
267004 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
267031 ATTTCTTGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:283770 original size:2 final size:2
Alignment explanation
Indices: 283765--283791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
283755 ATATATATAT
283765 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
283792 AACTTTTGTC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:284273 original size:21 final size:21
Alignment explanation
Indices: 284249--284293 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
284239 AATTTTGAAA
*
284249 AAAACTGAAAGTTTAGGTATT
1 AAAACTGAAAGTTTAGGTAGT
**
284270 AAAACTGATGGTTTAGGTAGT
1 AAAACTGAAAGTTTAGGTAGT
284291 AAA
1 AAA
284294 CTCGTTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGGTAGT
Found at i:294464 original size:13 final size:13
Alignment explanation
Indices: 294446--294470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294436 AAGAGTTAAA
294446 ATAAAATTTTATT
1 ATAAAATTTTATT
294459 ATAAAATTTTAT
1 ATAAAATTTTAT
294471 CCTTTTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAAATTTTATT
Found at i:298309 original size:18 final size:18
Alignment explanation
Indices: 298286--298333 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
298276 TACAGGACAA
298286 ACTTTTAGCTCTTACGAG
1 ACTTTTAGCTCTTACGAG
298304 ACTTTTAGCTCTTACGAG
1 ACTTTTAGCTCTTACGAG
*
298322 ACTTCTAGCTCT
1 ACTTTTAGCTCT
298334 GATGAGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (18 bp):
ACTTTTAGCTCTTACGAG
Found at i:298953 original size:268 final size:270
Alignment explanation
Indices: 298322--299226 Score: 1019
Period size: 269 Copynumber: 3.4 Consensus size: 270
298312 CTCTTACGAG
* *
298322 ACTTCTAGCTCTGATGAGTCAGAGAAAGAGAATGAGTTACTCAAGTTTGATGGCACTGGGGATAT
1 ACTTCTAGCTCTGATGAGTCAGAGAAAGAGGATGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
* * * * * *
298387 TGCTGATGAATCTAGTACAAAACCAAGTCTGGAGGTGGATTAACTAGGAAAAGTTAATTTTTAGC
66 TGTTGATGAATCTAGTACAAAACCAAGGCAGAAGGTAGATTAACTAGGAAAAGATAATTTTTAGC
* * * * * *
298452 GCTGTATTTA-T-TGTACCTTCCATTTTGTTTTGGCAGAGGTCAAAGTATCATATTAG--CATGC
131 ACTGT-TTTACTGTGTACCTTCCATTTTGTTTTGGCAAAGTTCAAAGTATAATATTAGTATATAC
* *
298513 TCGAGTATATTTCA-AAAAGTGAACTATATCTTTCAATGATTTTGAATGCAGGTCACAGAAGCTG
195 T-GAGTACATTT-ATAAAAGTGAACAATATCTTTCAATGA-TTTGAATGCAGGTCACAGAAGCTG
* *
298577 AAGCTGCGGGCCAA
257 AAGCTACAGGCCAA
* * *
298591 ACTTCTAGCTCTGATGAGTCAGAGAAAGAAGATGAGTTACTCAAGCTTGATGGCAGCGGGGATAT
1 ACTTCTAGCTCTGATGAGTCAGAGAAAGAGGATGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
* * * *
298656 TGTTGATGAATCTTGTTCAAAACCAAGGCAGAAGGTAGATTAACTAGGACAAGATGA-TTTTAGC
66 TGTTGATGAATCTAGTACAAAACCAAGGCAGAAGGTAGATTAACTAGGAAAAGATAATTTTTAGC
* *
298720 ACTGTGTTTACTGTGTACCTTCCGTTTTGTTTTCGCAAAGTTCAAAGTATAATATTAGTATATAC
131 ACTGT-TTTACTGTGTACCTTCCATTTTGTTTTGGCAAAGTTCAAAGTATAATATTAGTATATAC
* * * *
298785 TGTAGTACATTTATTATAGTGAACAATGTCTTTCAATGATTTGAATGCAGATCACAGAAGCTGAA
195 TG-AGTACATTTATAAAAGTGAACAATATCTTTCAATGATTTGAATGCAGGTCACAGAAGCTGAA
298850 GCTACAGGCCAA
259 GCTACAGGCCAA
* * *
298862 ACTTCTAGCTCTGATGAGT-TG-G-AGGAGGAGGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
1 ACTTCTAGCTCTGATGAGTCAGAGAAAGAGGATGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
* * *
298924 TGTTGATGAATCTAGTACAAAATCAAGGCAGAAGGTTGATTAACTAGGAAAAGCTAATTTTTAAC
66 TGTTGATGAATCTAGTACAAAACCAAGGCAGAAGGTAGATTAACTAGGAAAAGATAATTTTT-A-
* * * *
298989 GCACTGTTTAACATGCGT--CTTCTATTTTGTTTTGGCAAA-TGCCAAAGTATAATATTAGTATA
129 GCACTGTTTTAC-TGTGTACCTTCCATTTTGTTTTGGCAAAGT-TCAAAGTATAATATTAGTATA
* * ** *
299051 TACTGAAGTACATTTCTGAAAGTGAACAATATCTTTCAATTCTTTG-ATGCAGGT-AGCTGAAGC
192 TACTG-AGTACATTTATAAAAGTGAACAATATCTTTCAATGATTTGAATGCAGGTCA-CAGAAGC
* **
299114 TGAAACTACAGTACAA
255 TGAAGCTACAGGCCAA
* * * ** ** ** **
299130 ACTTCTAGTTCTGATGAGTCGGAGAAAGAGAACAAGTCGCTCAAGCCTGATGGCAGCAGGGATAT
1 ACTTCTAGCTCTGATGAGTCAGAGAAAGAGGATGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
* ** * *
299195 TGCTGATGAATCTTTTACAGAGCCAAGGCAGA
66 TGTTGATGAATCTAGTACAAAACCAAGGCAGA
299227 GGGTGAAGCA
Statistics
Matches: 540, Mismatches: 81, Indels: 28
0.83 0.12 0.04
Matches are distributed among these distances:
267 1 0.00
268 145 0.27
269 191 0.35
270 47 0.09
271 123 0.23
272 33 0.06
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (270 bp):
ACTTCTAGCTCTGATGAGTCAGAGAAAGAGGATGAGTTACTCAAGTTTGATGGCAGTGGGGATAT
TGTTGATGAATCTAGTACAAAACCAAGGCAGAAGGTAGATTAACTAGGAAAAGATAATTTTTAGC
ACTGTTTTACTGTGTACCTTCCATTTTGTTTTGGCAAAGTTCAAAGTATAATATTAGTATATACT
GAGTACATTTATAAAAGTGAACAATATCTTTCAATGATTTGAATGCAGGTCACAGAAGCTGAAGC
TACAGGCCAA
Done.