Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007930.1 Hibiscus syriacus cultivar Beakdansim tig00110338_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: 2280901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:1266 original size:11 final size:11
Alignment explanation
Indices: 1252--1325 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
1242 AAAATTCAAG
1252 AGCTCGATTGA
1 AGCTCGATTGA
*
1263 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
1276 AGCTCGATTGA
1 AGCTCGATTGA
1287 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
1299 AGCTCGATTCA
1 AGCTCGATTGA
*
1310 AGCTCGATTCA
1 AGCTCGATTGA
1321 AGCTC
1 AGCTC
1326 AAACTCGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.08
11 30 0.57
12 7 0.13
13 10 0.19
14 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:1305 original size:23 final size:23
Alignment explanation
Indices: 1251--1318 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
1241 AAAAATTCAA
**
1251 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-TTTC
*
1275 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTC
*
1298 GAGCTCGATTCAAGCTCGATT
1 GAGCTCGATTGAAGCTCGATT
1319 CAAGCTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTC
Found at i:1332 original size:17 final size:17
Alignment explanation
Indices: 1307--1348 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1297 TGAGCTCGAT
* *
1307 TCAAGCTCGATTCAAGC
1 TCAAACTCGATTAAAGC
1324 TCAAACTCGATTAAAGC
1 TCAAACTCGATTAAAGC
*
1341 TCGAACTC
1 TCAAACTC
1349 AAACTCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (17 bp):
TCAAACTCGATTAAAGC
Found at i:1648 original size:21 final size:21
Alignment explanation
Indices: 1623--1744 Score: 104
Period size: 21 Copynumber: 5.8 Consensus size: 21
1613 TGGCATAACT
1623 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
**
1644 TAAACTTTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* * *
1665 TAAACTCTAA-ACTTTAAACCT
1 TAAACCCTAACAC-ATAAACCC
* * *
1686 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
* *
1707 TAAACTCTAA-ACCCTAAACCC
1 TAAACCCTAACA-CATAAACCC
* *
1728 TAAACCTTATCACATAA
1 TAAACCCTAACACATAA
1745 TTAGTTATGA
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
20 3 0.04
21 71 0.92
22 3 0.04
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:1675 original size:14 final size:13
Alignment explanation
Indices: 1658--1733 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
1648 CTTTAACACA
1658 TAAACCCTAAACTC
1 TAAACCCTAAAC-C
**
1672 TAAACTTTAAACC
1 TAAACCCTAAACC
* * *
1685 TTAAATCCTATCACA
1 -TAAACCCTA-AACC
*
1700 TAAACTCTAAACTC
1 TAAACCCTAAAC-C
1714 TAAACCCTAAACCC
1 TAAACCCTAAA-CC
1728 TAAACC
1 TAAACC
1734 TTATCACATA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
13 3 0.07
14 40 0.87
15 3 0.07
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAACCCTAAACC
Found at i:1683 original size:42 final size:42
Alignment explanation
Indices: 1637--1744 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
1627 CCCTAACACA
* **
1637 TAAACCCTAAACTTTAACACATAAACCCTAAACTCTAAACTT
1 TAAACCCTAAACTTTATCACATAAACCCTAAACTCTAAACCC
* * *
1679 TAAACCTTAAA-TCCTATCACATAAACTCTAAACTCTAAACCC
1 TAAACCCTAAACT-TTATCACATAAACCCTAAACTCTAAACCC
*
1721 TAAACCCTAAACCTTATCACATAA
1 TAAACCCTAAACTTTATCACATAA
1745 TTAGTTATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 54 0.98
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (42 bp):
TAAACCCTAAACTTTATCACATAAACCCTAAACTCTAAACCC
Found at i:1712 original size:7 final size:7
Alignment explanation
Indices: 1700--1733 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1690 TCCTATCACA
*
1700 TAAACTC
1 TAAACCC
*
1707 TAAACTC
1 TAAACCC
1714 TAAACCC
1 TAAACCC
1721 TAAACCC
1 TAAACCC
1728 TAAACC
1 TAAACC
1734 TTATCACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:2747 original size:13 final size:13
Alignment explanation
Indices: 2729--2753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2719 AATTGAAAAG
2729 AAATATTAATTTC
1 AAATATTAATTTC
2742 AAATATTAATTT
1 AAATATTAATTT
2754 GGATTAAAAT
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:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTAATTTC
Found at i:4224 original size:24 final size:24
Alignment explanation
Indices: 4197--4245 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4187 ATTTAAAAAG
*
4197 TTTTTTAATAGTTTAAGATGATTA
1 TTTTTTAATAGTTCAAGATGATTA
* *
4221 TTTTTTTATAGTTCAAGATGGTTA
1 TTTTTTAATAGTTCAAGATGATTA
4245 T
1 T
4246 AAGATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (24 bp):
TTTTTTAATAGTTCAAGATGATTA
Found at i:4955 original size:20 final size:21
Alignment explanation
Indices: 4930--5022 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
4920 TTTTCCCAAT
*
4930 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4950 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
4971 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4991 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5012 TCGCAATGCGA
1 TCGCAATGCGA
5023 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4975 original size:41 final size:41
Alignment explanation
Indices: 4930--5022 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
4920 TTTTCCCAAT
4930 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4971 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
5012 TCGCAATGCGA
1 TCGCAATGCGA
5023 TACTTACTAT
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:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:5035 original size:41 final size:41
Alignment explanation
Indices: 4949--5083 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
4939 GAATAAGTAA
** *
4949 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
4990 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
5031 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
5072 TTCGCAACGCGA
1 ATCGCAACGCGA
5084 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:5036 original size:20 final size:20
Alignment explanation
Indices: 5011--5104 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
5001 AATTGGGAAA
* *
5011 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
5031 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
5052 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5072 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5092 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5105 TTACATAGCG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5658 original size:19 final size:19
Alignment explanation
Indices: 5620--5687 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
5610 TTCGAGAATG
5620 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
5640 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
5659 AAAATTCGCAACGCGAAACC
1 AAAA-TCGCAACGCGAAATA
5679 AAAATCGCA
1 AAAATCGCA
5688 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:5729 original size:20 final size:19
Alignment explanation
Indices: 5683--5847 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
5673 GAAACCAAAA
*
5683 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5702 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
5721 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
5741 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
5757 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
5774 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
5788 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5807 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5827 ATCTCGTTGCGATTTT-ATT
1 -TCGCGTTGCGATTTTCATT
5846 TC
1 TC
5848 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 3 0.03
19 42 0.36
20 45 0.38
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5764 original size:39 final size:39
Alignment explanation
Indices: 5688--5764 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
5678 CAAAATCGCA
* **
5688 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
5727 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
5765 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:5773 original size:33 final size:33
Alignment explanation
Indices: 5736--5823 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
5726 GTTGCGATTT
* *
5736 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
5769 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
5802 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5824 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:7908 original size:42 final size:42
Alignment explanation
Indices: 7848--7970 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
7838 GCCCGACTCG
* * *
7848 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
7890 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
7932 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
7971 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:7928 original size:21 final size:21
Alignment explanation
Indices: 7904--7970 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
7894 TCATTCCTCG
7904 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
7925 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
7946 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
7967 AGAG
1 AGAG
7971 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9342 original size:14 final size:14
Alignment explanation
Indices: 9323--9358 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
9313 ATTGTTTAAT
9323 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
9337 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
9351 TGATTTGT
1 TGATTTGT
9359 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:9560 original size:19 final size:19
Alignment explanation
Indices: 9538--9655 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
9528 CGAAATTAAA
9538 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9557 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
9572 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9590 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
9605 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
9623 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
9642 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
9656 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:9584 original size:33 final size:33
Alignment explanation
Indices: 9542--9635 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
9532 ATTAAATTCG
9542 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
9575 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
9608 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
9636 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:12157 original size:24 final size:24
Alignment explanation
Indices: 12123--12176 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12113 CTGAAACATC
* *
12123 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
12147 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
12171 ATCAAA
1 ATCAAA
12177 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:13235 original size:20 final size:20
Alignment explanation
Indices: 13210--13267 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
13200 ATTCATTTGA
13210 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
13230 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
13250 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
13268 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:13329 original size:19 final size:19
Alignment explanation
Indices: 13286--13387 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
13276 GAAATGAAAA
13286 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
13302 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
13319 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
13338 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
13357 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
13376 TCGCGTTGCGAT
1 TCGCATTGCGAT
13388 AGTCTGTTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
14 11 0.14
16 3 0.04
17 2 0.03
19 61 0.79
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:15304 original size:20 final size:19
Alignment explanation
Indices: 15269--15335 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
15259 GAAACTTAAA
15269 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
15288 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
15308 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
15327 ATCGCAACG
1 ATCGCAACG
15336 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:15343 original size:14 final size:14
Alignment explanation
Indices: 15324--15381 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
15314 ATGCGAAATG
15324 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
15338 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
15354 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
15370 AAAATCGCAACG
1 AAAATCGCAACG
15382 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:15366 original size:32 final size:33
Alignment explanation
Indices: 15308--15386 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
15298 GGAAATGGCT
*
15308 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
15341 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
15373 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
15387 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:15425 original size:19 final size:19
Alignment explanation
Indices: 15403--15526 Score: 63
Period size: 19 Copynumber: 7.1 Consensus size: 19
15393 TCGCATTCCA
15403 ATTTTCATTTCGCGTTGCG
1 ATTTTCATTTCGCGTTGCG
*
15422 A-TTT--TGT--CGTTGCG
1 ATTTTCATTTCGCGTTGCG
*
15436 A-TTTCATTTCGTGTTGCG
1 ATTTTCATTTCGCGTTGCG
*
15454 A-TTT--TGT--CGTTGCG
1 ATTTTCATTTCGCGTTGCG
* *
15468 ATTTTTATTTCGCATTGCG
1 ATTTTCATTTCGCGTTGCG
***
15487 ATAGCCATTTCCGCGTTGCG
1 ATTTTCATTT-CGCGTTGCG
** *
15507 ATAGTCATTTCGTGTTGCG
1 ATTTTCATTTCGCGTTGCG
15526 A
1 A
15527 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 14, Indels: 20
0.70 0.12 0.17
Matches are distributed among these distances:
14 18 0.22
15 3 0.04
16 6 0.07
17 2 0.02
18 13 0.16
19 22 0.27
20 17 0.21
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (19 bp):
ATTTTCATTTCGCGTTGCG
Found at i:15434 original size:14 final size:14
Alignment explanation
Indices: 15415--15472 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
15405 TTTCATTTCG
15415 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
15429 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
15445 CGTGTTGCGATTTTGT
1 C--GTTGCGATTTTGT
15461 CGTTGCGATTTT
1 CGTTGCGATTTT
15473 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:15446 original size:32 final size:33
Alignment explanation
Indices: 15403--15488 Score: 138
Period size: 32 Copynumber: 2.6 Consensus size: 33
15393 TCGCATTCCA
15403 ATTTTCATTTCGCGTTGCGATTTTGTCGTTGCG
1 ATTTTCATTTCGCGTTGCGATTTTGTCGTTGCG
*
15436 A-TTTCATTTCGTGTTGCGATTTTGTCGTTGCG
1 ATTTTCATTTCGCGTTGCGATTTTGTCGTTGCG
* *
15468 ATTTTTATTTCGCATTGCGAT
1 ATTTTCATTTCGCGTTGCGAT
15489 AGCCATTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 31 0.65
33 17 0.35
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (33 bp):
ATTTTCATTTCGCGTTGCGATTTTGTCGTTGCG
Found at i:15507 original size:20 final size:19
Alignment explanation
Indices: 15474--15526 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
15464 TGCGATTTTT
*
15474 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGATAGCC
*
15493 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGCC
*
15513 ATTTCGTGTTGCGA
1 ATTTCGCGTTGCGA
15527 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.36
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGCC
Found at i:16025 original size:18 final size:18
Alignment explanation
Indices: 15999--16043 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
15989 GTCGATCAGA
* *
15999 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
16017 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
16035 TGATGGCTC
1 TGATGGCTC
16044 CCGAAGTGGA
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:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:17583 original size:22 final size:22
Alignment explanation
Indices: 17558--17601 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17548 GATTTAGATA
17558 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
17580 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
17602 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:17882 original size:20 final size:20
Alignment explanation
Indices: 17769--17882 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
17759 CGCTTTGAAA
17769 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
17789 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
17809 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
** * * *
17829 ATATCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
17850 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
17870 ATCGCATTGCGAT
1 ATCGCATTGCGAT
17883 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 55 0.73
21 11 0.15
22 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:17900 original size:21 final size:21
Alignment explanation
Indices: 17871--17963 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
17861 ATAGTAAGTA
17871 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
17892 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
17912 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
17933 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
17953 TCGCATTGCGA
1 TCGCATTGCGA
17964 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:17901 original size:41 final size:41
Alignment explanation
Indices: 17810--17944 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
17800 AAAGTCAGTA
* ** * ** *
17810 TCGCGTTGCGAAAGTAAGTATATCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
17850 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
17892 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
17933 TCGCGTTGCGAT
1 TCGCGTTGCGAT
17945 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:17945 original size:41 final size:41
Alignment explanation
Indices: 17871--17963 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
17861 ATAGTAAGTA
17871 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
17912 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
17953 TCGCATTGCGA
1 TCGCATTGCGA
17964 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:19440 original size:17 final size:15
Alignment explanation
Indices: 19404--19438 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
19394 TATAATATAT
19404 TATATTTTCAAAAAA
1 TATATTTTCAAAAAA
*
19419 TATATTTTCAAAAAT
1 TATATTTTCAAAAAA
19434 TATAT
1 TATAT
19439 ATATATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATTTTCAAAAAA
Found at i:19478 original size:38 final size:40
Alignment explanation
Indices: 19386--19486 Score: 118
Period size: 38 Copynumber: 2.6 Consensus size: 40
19376 TAATATATAA
* * *
19386 TAAAAAACTATA-ATATATTATATTTTCAAAAAATATATTT
1 TAAAAAACTATATATATA-TGTGTTTTCAAAAAATACATTT
* * *
19426 TCAAAAATTATATATATATGTGTTTTC-AAAAAT-CGTTT
1 TAAAAAACTATATATATATGTGTTTTCAAAAAATACATTT
19464 TAAAAAACTATATATATATGTGT
1 TAAAAAACTATATATATATGTGT
19487 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
38 24 0.46
39 6 0.12
40 17 0.33
41 5 0.10
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (40 bp):
TAAAAAACTATATATATATGTGTTTTCAAAAAATACATTT
Found at i:19487 original size:2 final size:2
Alignment explanation
Indices: 19482--19506 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19472 TATATATATA
19482 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
19507 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:19488 original size:40 final size:41
Alignment explanation
Indices: 19386--19488 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
19376 TAATATATAA
* * *
19386 TAAAAAACTATA-ATATATTATATTTTCAAAAAATATATTT
1 TAAAAAACTATATATATATTGTGTTTTCAAAAAATACATTT
* * *
19426 TCAAAAATTATATATATA-TGTGTTTTC-AAAAAT-CGTTT
1 TAAAAAACTATATATATATTGTGTTTTCAAAAAATACATTT
19464 TAAAAAACTATATATATATGTGTGT
1 TAAAAAACTATATATATAT-TGTGT
19489 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
38 19 0.37
39 6 0.12
40 22 0.42
41 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (41 bp):
TAAAAAACTATATATATATTGTGTTTTCAAAAAATACATTT
Found at i:19566 original size:37 final size:37
Alignment explanation
Indices: 19512--19779 Score: 283
Period size: 37 Copynumber: 7.1 Consensus size: 37
19502 TGTGTTTTTT
* *
19512 AAAATATGTTTTCAAAACTATAT-TATATACGTTTTCA
1 AAAATGTGTTTTCAAAACTATATAT-TATATGTTTTCA
* * **
19549 AAAACCGT-TTTTTAAAACTATATATTATACATTTTCA
1 AAAA-TGTGTTTTCAAAACTATATATTATATGTTTTCA
*
19586 AAAATGTGTTTTCAAAACTATATAGTATATGTTTTCA
1 AAAATGTGTTTTCAAAACTATATATTATATGTTTTCA
**
19623 AAAATGTGTTTTCAAAACTATATATTATACATTTTCA
1 AAAATGTGTTTTCAAAACTATATATTATATGTTTTCA
* * *
19660 AAAAAGTGTTTTCAAAACCATAT-TATATATATTTTCA
1 AAAATGTGTTTTCAAAACTATATAT-TATATGTTTTCA
* * *
19697 AAAACTGATTTTTTAAAAAACTATATATTATATGCTTTCA
1 AAAA-TG-TGTTTT-CAAAACTATATATTATATGTTTTCA
* *
19737 AAAATCAT-TTTCTAAAAACTATATATTATATGTTTTCA
1 AAAAT-GTGTTT-TCAAAACTATATATTATATGTTTTCA
19775 AAAAT
1 AAAAT
19780 ATTTTCAAAA
Statistics
Matches: 198, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
36 3 0.02
37 128 0.65
38 35 0.18
39 8 0.04
40 23 0.12
41 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (37 bp):
AAAATGTGTTTTCAAAACTATATATTATATGTTTTCA
Found at i:19640 original size:74 final size:74
Alignment explanation
Indices: 19512--19778 Score: 319
Period size: 74 Copynumber: 3.6 Consensus size: 74
19502 TGTGTTTTTT
* * *
19512 AAAATATGTTTTCAAAACTATATTATATACGTTTTCAAAAACCGTTTTTTAAAACTATATATTAT
1 AAAATATGTTTTCAAAACTATATTATATATGTTTTCAAAAACTGTTTTTAAAAACTATATATTAT
19577 ACATTTTCA
66 ACATTTTCA
* *
19586 AAAATGTGTTTTCAAAACTATA-TAGTATATGTTTTCAAAAA-TGTGTTTTCAAAACTATATATT
1 AAAATATGTTTTCAAAACTATATTA-TATATGTTTTCAAAAACTGT-TTTTAAAAACTATATATT
19649 ATACATTTTCA
64 ATACATTTTCA
* *
19660 AAAA-AGTGTTTTCAAAACCATATTATATATATTTTCAAAAACTGATTTTTTAAAAAACTATATA
1 AAAATA-TGTTTTCAAAACTATATTATATATGTTTTCAAAAACTG--TTTTT-AAAAACTATATA
***
19724 TTATATGCTTTCA
62 TTATACATTTTCA
*
19737 AAAATCAT-TTTCTAAAAACTATA-TATTATATGTTTTCAAAAA
1 AAAAT-ATGTTT-TCAAAACTATATTA-TATATGTTTTCAAAAA
19779 TATTTTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
73 4 0.02
74 98 0.59
75 4 0.02
76 4 0.02
77 31 0.19
78 25 0.15
79 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (74 bp):
AAAATATGTTTTCAAAACTATATTATATATGTTTTCAAAAACTGTTTTTAAAAACTATATATTAT
ACATTTTCA
Found at i:27506 original size:22 final size:22
Alignment explanation
Indices: 27481--27524 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27471 GTATGAAGCT
27481 TTCATTATGTTTATTCTCCATA
1 TTCATTATGTTTATTCTCCATA
27503 TTCATTATGTTTATTCTCCATA
1 TTCATTATGTTTATTCTCCATA
27525 CTTTGTAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (22 bp):
TTCATTATGTTTATTCTCCATA
Found at i:32875 original size:26 final size:26
Alignment explanation
Indices: 32846--32896 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
32836 TTCTGTTGAG
32846 CTTCACTCTGGATCGATTTATTTGGA
1 CTTCACTCTGGATCGATTTATTTGGA
** *
32872 CTTCGTTCTGGATCGGTTTATTTGG
1 CTTCACTCTGGATCGATTTATTTGG
32897 GCTGGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.45
Consensus pattern (26 bp):
CTTCACTCTGGATCGATTTATTTGGA
Found at i:32943 original size:16 final size:15
Alignment explanation
Indices: 32924--32979 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 15
32914 TTGGACCTGA
32924 AAAAAATTAAATAAAT
1 AAAAAA-TAAATAAAT
32940 AAAATAATAAAT-AAT
1 AAAA-AATAAATAAAT
32955 AATATAAATAATATATAAT
1 AA-A-AAATAA-ATA-AAT
32974 AAAAAA
1 AAAAAA
32980 ATATATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.15
16 15 0.44
17 8 0.24
18 1 0.03
19 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:32950 original size:12 final size:13
Alignment explanation
Indices: 32933--32976 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
32923 AAAAAAATTA
32933 AATAAATAA-AAT
1 AATAAATAATAAT
32945 AATAAATAATAAT
1 AATAAATAATAAT
32958 -ATAAATAATATAT
1 AATAAATAATA-AT
32971 AATAAA
1 AATAAA
32977 AAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.66
13 5 0.17
14 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:32963 original size:19 final size:18
Alignment explanation
Indices: 32937--32987 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
32927 AAATTAAATA
32937 AATAAAATAATAAATAAT
1 AATAAAATAATAAATAAT
*
32955 AATATAAATAATATATAAT
1 AATA-AAATAATAAATAAT
*
32974 AAAAAAATATATAA
1 AATAAAATA-ATAA
32988 CATATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATAATAAATAAT
Found at i:32974 original size:22 final size:22
Alignment explanation
Indices: 32932--32993 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
32922 GAAAAAAATT
*
32932 AAATAAATAAAATAATAAATAATA
1 AAATAAATAAAAT-AT-AATAAAA
* *
32956 ATATAAATAATATATAATAAAA
1 AAATAAATAAAATATAATAAAA
* *
32978 AAATATATAACATATA
1 AAATAAATAAAATATA
32994 TTATATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 19 0.59
23 2 0.06
24 11 0.34
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATAAATAAAATATAATAAAA
Found at i:32982 original size:15 final size:16
Alignment explanation
Indices: 32932--32987 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
32922 GAAAAAAATT
* * *
32932 AAATAAATAAAATAAT
1 AAATATATAATATAAA
32948 AAATA-ATAATATAAA
1 AAATATATAATATAAA
*
32963 TAATATATAATA-AAA
1 AAATATATAATATAAA
32978 AAATATATAA
1 AAATATATAA
32988 CATATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATATAATATAAA
Found at i:32994 original size:26 final size:26
Alignment explanation
Indices: 32924--32987 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
32914 TTGGACCTGA
32924 AAAAAATTAA-ATAAATAA-A-ATAAT
1 AAAAAA-TAATATAAATAATATATAAT
*
32948 AAATAATAATATAAATAATATATAAT
1 AAAAAATAATATAAATAATATATAAT
32974 AAAAAA-ATATATAA
1 AAAAAATA-ATATAA
32988 CATATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.09
24 13 0.38
25 2 0.06
26 16 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAATAATATAAATAATATATAAT
Found at i:33103 original size:23 final size:23
Alignment explanation
Indices: 33077--33121 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33067 TATATATATA
*
33077 TATATTAAATATGTTTTCAAAAC
1 TATATTAAATACGTTTTCAAAAC
*
33100 TATATTATATACGTTTTCAAAA
1 TATATTAAATACGTTTTCAAAA
33122 ACCGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (23 bp):
TATATTAAATACGTTTTCAAAAC
Found at i:33180 original size:37 final size:37
Alignment explanation
Indices: 32989--33369 Score: 239
Period size: 37 Copynumber: 10.1 Consensus size: 37
32979 AATATATAAC
* * *
32989 ATATATTATAT-TTTTAAAAAAATATGTTTTCCAAAATTAT
1 ATATATTATATGTTTT-CAAAAACATGTTTT-CAAAA--CT
*
33029 ATATATTATATATGTTTTC-AAAA-ATCGTTTTAAAAAACT
1 ATATA-T-TATATGTTTTCAAAAACAT-GTTTT-CAAAACT
* * *
33068 ATATA-TATATATATT---AAATATGTTTTCAAAACT
1 ATATATTATATGTTTTCAAAAACATGTTTTCAAAACT
* * * *
33101 ATAT-TATATACGTTTTCAAAAACCGTTTTTTTAAAACT
1 ATATAT-TATATGTTTTCAAAAA-CATGTTTTCAAAACT
* * *
33139 ATATATTATATGTTTTCGAAAATATATTTTCAAAACT
1 ATATATTATATGTTTTCAAAAACATGTTTTCAAAACT
** *
33176 ATATATTATACATTTTCAAAAACGTGTTTTCAAAACT
1 ATATATTATATGTTTTCAAAAACATGTTTTCAAAACT
* ** * *
33213 ATATATTAAACATTTTCAAAAACGTGTTTTCAAAACC
1 ATATATTATATGTTTTCAAAAACATGTTTTCAAAACT
* * *
33250 ATAT-TATATATATATTCAAAAAC-TGATTTTTAAAAAAAAACT
1 ATATAT-TATATGTTTTCAAAAACATG--TTTT----CAAAACT
* *
33292 ATATATTATATGCTTTCAAAAAC-CGTTTTCTAAAAACT
1 ATATATTATATGTTTTCAAAAACATGTTTTC--AAAACT
*
33330 ATATATTATATGTTTTC-AAAA-ATATTTTCAAAAACT
1 ATATATTATATGTTTTCAAAAACATGTTTTC-AAAACT
33366 ATAT
1 ATAT
33370 TATATTATTA
Statistics
Matches: 277, Mismatches: 41, Indels: 50
0.75 0.11 0.14
Matches are distributed among these distances:
33 10 0.04
34 15 0.05
35 2 0.01
36 22 0.08
37 107 0.39
38 55 0.20
39 7 0.03
40 11 0.04
41 14 0.05
42 29 0.10
43 5 0.02
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (37 bp):
ATATATTATATGTTTTCAAAAACATGTTTTCAAAACT
Found at i:34941 original size:121 final size:124
Alignment explanation
Indices: 34660--34944 Score: 346
Period size: 121 Copynumber: 2.3 Consensus size: 124
34650 TATTTTATTA
* *
34660 AAAATGAAGAGATATCATTATTTCGTCTTAAAATTCAATATTGATTCGAGAGAAAACGATAATAT
1 AAAATGAAGAGATATCACTA-TT--T-TTAATATT-AATATTGATTCGAGAGAAAACGATAATAT
* *
34725 CTAATTATTTCCAATCGATAATAAATAACCTCTCATGCCTTAAAGCAATCCTTTATTACTCCAAT
61 CTAATTATTTCCAATC-A-AATAAATAACATCTCATGCCTTAAAGCAAGCCTTTATTACTCCAAT
34790 C
124 C
* * *
34791 GAAATGAAGAGTTATCACTATTTTCAATATTAATATTGATTCGAGAGAAAATC-ATAATATCTAA
1 AAAATGAAGAGATATCACTATTTTTAATATTAATATTGATTCGAGAGAAAA-CGATAATATCTAA
* * * *
34855 TTATTTTCAATC-AA-GAATAA-ATCTCATGTCTTAAAGC-AGCCATTTATTACTTCAATC
65 TTATTTCCAATCAAATAAATAACATCTCATGCCTTAAAGCAAGCC-TTTATTACTCCAATC
*
34912 AAAATGAAGAGATATTACTATTTTTAATATTAA
1 AAAATGAAGAGATATCACTATTTTTAATATTAA
34945 CTCGAGTGTT
Statistics
Matches: 137, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
120 3 0.02
121 58 0.42
122 5 0.04
123 2 0.01
126 42 0.31
127 7 0.05
128 1 0.01
130 2 0.01
131 17 0.12
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.35
Consensus pattern (124 bp):
AAAATGAAGAGATATCACTATTTTTAATATTAATATTGATTCGAGAGAAAACGATAATATCTAAT
TATTTCCAATCAAATAAATAACATCTCATGCCTTAAAGCAAGCCTTTATTACTCCAATC
Found at i:36910 original size:3 final size:3
Alignment explanation
Indices: 36882--36933 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
36872 GAAAATAAAT
* *
36882 TAA TAA -AA TAA -AA TAAA TAT TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
36926 CAA TAA TA
1 TAA TAA TA
36934 GTGTCCGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:37515 original size:27 final size:26
Alignment explanation
Indices: 37485--37540 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
37475 AAATATTAAC
37485 TTATA-CACAAAACCATAAATCCCCAAA
1 TTATACCACAAAA-CATAAA-CCCCAAA
* *
37512 TTATACCCCAAAACATAAACCCTAAA
1 TTATACCACAAAACATAAACCCCAAA
37538 TTA
1 TTA
37541 AAATCCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.35
27 11 0.42
28 6 0.23
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (26 bp):
TTATACCACAAAACATAAACCCCAAA
Found at i:37716 original size:26 final size:26
Alignment explanation
Indices: 37666--37716 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
37656 GGCATTGATA
* *
37666 ATTTGGGGATTAGGGTTTGGGATATT
1 ATTTGGGAATTAGGGTTTGGAATATT
37692 ATTTGGGAACTTAGGGTTT-GAATAT
1 ATTTGGGAA-TTAGGGTTTGGAATAT
37717 AAAATTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.41
Consensus pattern (26 bp):
ATTTGGGAATTAGGGTTTGGAATATT
Found at i:52396 original size:27 final size:27
Alignment explanation
Indices: 52358--52411 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
52348 AACAGAAAGA
52358 GAAGCCTAGGTTCGTCATAGCCACAGC
1 GAAGCCTAGGTTCGTCATAGCCACAGC
52385 GAAGCCTAGGTTCGTCATAGCCACAGC
1 GAAGCCTAGGTTCGTCATAGCCACAGC
52412 CACGGCAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (27 bp):
GAAGCCTAGGTTCGTCATAGCCACAGC
Found at i:61097 original size:19 final size:19
Alignment explanation
Indices: 61050--61097 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
61040 ACGCCACTAG
*
61050 CCACCAATGCCGAGCCATC
1 CCACCAACGCCGAGCCATC
* * * *
61069 TCATCGACGCCGAGCTATC
1 CCACCAACGCCGAGCCATC
61088 CCACCAACGC
1 CCACCAACGC
61098 GATGAGCCAT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.46, G:0.17, T:0.12
Consensus pattern (19 bp):
CCACCAACGCCGAGCCATC
Found at i:62120 original size:34 final size:35
Alignment explanation
Indices: 62060--62125 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
62050 ATGTTTTAAT
*
62060 TTCATTATATTTTAGTCCCTATTTTAT-ATTTTGG
1 TTCATTATAATTTAGTCCCTATTTTATGATTTTGG
62094 TTCATTATAATTTAG--CCTCATATTTATGATTT
1 TTCATTATAATTTAGTCCCT-AT-TTTATGATTT
62126 ATTGCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 3 0.11
33 2 0.07
34 19 0.68
35 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (35 bp):
TTCATTATAATTTAGTCCCTATTTTATGATTTTGG
Found at i:62470 original size:30 final size:30
Alignment explanation
Indices: 62417--62473 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
62407 CATTTTGGTC
* *
62417 TTTTAAATTTCTATTTGTGCTATTTTATTA
1 TTTTAAATTTCCATTTGTACTATTTTATTA
* *
62447 TTTTAAATTTCCGTTTTTACTATTTTA
1 TTTTAAATTTCCATTTGTACTATTTTA
62474 GTCTCTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTCCATTTGTACTATTTTATTA
Found at i:67998 original size:5 final size:5
Alignment explanation
Indices: 67978--68012 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
67968 TTCATAACGC
* *
67978 TAAAA TAAAC TAAAA TGAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
68013 GTGAAATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:68003 original size:20 final size:21
Alignment explanation
Indices: 67978--68020 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
67968 TTCATAACGC
*
67978 TAAAATAAACTAAAA-TGAAA
1 TAAAATAAAATAAAAGTGAAA
67998 TAAAATAAAATAAAAGTGAAA
1 TAAAATAAAATAAAAGTGAAA
68019 TA
1 TA
68021 GATTATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (21 bp):
TAAAATAAAATAAAAGTGAAA
Found at i:69167 original size:20 final size:22
Alignment explanation
Indices: 69114--69169 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
69104 AATTAATTAG
69114 TAATA-AGATTAATAATAATAA
1 TAATATAGATTAATAATAATAA
*
69135 TAATATAGA-TAATAA-AATAC
1 TAATATAGATTAATAATAATAA
69155 TAATATA-ATTAATAA
1 TAATATAGATTAATAA
69170 CGTTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.53
21 11 0.34
22 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (22 bp):
TAATATAGATTAATAATAATAA
Found at i:69905 original size:91 final size:90
Alignment explanation
Indices: 69751--69919 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 90
69741 AAGTGTTGAA
* *
69751 TTGAACAAGTTCTCTCATTATGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAACT
1 TTGAACAAGTTCTCTCATTATGAACTTCTTCTCTCTCGTTAGATGAGTTCTTCTCATTATGAACT
69816 CTCCACTGGAAATGTTAATGCAAGG
66 CTCCACTGGAAATGTTAATGCAAGG
*
69841 TTGAACGAGTTCTTCTCATTATGAACTTCTTCT-TCCTCGTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTC-TCTCATTATGAACTTCTTCTCT-CTCGTTAGATGAGTTCTTCTCATTATGAA
*
69905 CTCTTCACTGGAAAT
64 CTCTCCACTGGAAAT
69920 ATTGATCCAC
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 12 0.16
91 61 0.84
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (90 bp):
TTGAACAAGTTCTCTCATTATGAACTTCTTCTCTCTCGTTAGATGAGTTCTTCTCATTATGAACT
CTCCACTGGAAATGTTAATGCAAGG
Found at i:70042 original size:117 final size:117
Alignment explanation
Indices: 69836--70223 Score: 611
Period size: 117 Copynumber: 3.3 Consensus size: 117
69826 AATGTTAATG
* * *
69836 CAAGGTTGAACGAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
*
69901 TGAACTCTT-CACTGGAAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
66 TGAACT-TTCCACTGAAAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
69953 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * *
70018 TGAACTTTCCACTAAAAATATTGATCCACCT-CTTTTTTGATGGAATCAAAC
66 TGAACTTTCCACTGAAAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
* *
70069 CAATGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCATTAGGATGAGTTCTTCTCATT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATT
* * * *
70134 ATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAAC
65 ATGAACTTTCCACTGAAAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
*
70187 CAATGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
70224 GGAAATGTTG
Statistics
Matches: 251, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
116 64 0.25
117 139 0.55
118 48 0.19
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (117 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
TGAACTTTCCACTGAAAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
Found at i:70294 original size:18 final size:18
Alignment explanation
Indices: 70271--70325 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
70261 AAGGAACAAG
70271 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
*
70289 TTCTTCCTCATTGGATG-AGT
1 TTCTT-CTCATT--ATGAACT
70309 TT-TTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
70326 CTCCACTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.10
17 2 0.06
18 11 0.35
19 8 0.26
20 4 0.13
21 3 0.10
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:70569 original size:105 final size:106
Alignment explanation
Indices: 70199--70584 Score: 481
Period size: 105 Copynumber: 3.5 Consensus size: 106
70189 ATGTTGAACA
* *
70199 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCATCTCCTTCTATGGTGGACTTGAAAG
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGACTTGAAAG
70264 GAACAAGTTCTTCTCATTATGAACTTTCTTCCTCATTGGATG
66 GAACAAGTTCTTCTCATTATGAACTTTCTTCCT-ATTGGATG
* * * * * * * * **
70306 AGTTTTTCTCATTATGAACTCTCCACTGAAAATGTT-GATCCACATCTTTCTGTGATGGAATCAA
1 AGTTCTTCTCATTATGAACTCT--TCTGGAAATGTTGGGT-CACCTCCTTCTGTGGTGGACT-TG
70370 ACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATG
62 A--AA-G--GAACAAGTTCTTCTCATTATGAAC-T-TTCTTCCT-ATTGGATG
70423 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGACTTGAAAG
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGACTTGAAAG
*
70488 GAACAAGTTCTTCTCATTATGAACTTTC-TCCT-TTAGGACG
66 GAACAAGTTCTTCTCATTATGAACTTTCTTCCTATT-GGATG
* * *
70528 AGTTCTTTTCATTATGAACTCTTCTGTAAATGTTGGTTCACCTCCTTCTGTGGTGGA
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGA
70585 TCATGATCTT
Statistics
Matches: 240, Mismatches: 26, Indels: 28
0.82 0.09 0.10
Matches are distributed among these distances:
104 2 0.01
105 58 0.24
106 4 0.02
107 24 0.10
108 3 0.01
109 49 0.20
110 1 0.00
111 1 0.00
112 4 0.02
113 1 0.00
114 1 0.00
115 51 0.21
116 3 0.01
117 38 0.16
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (106 bp):
AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGACTTGAAAG
GAACAAGTTCTTCTCATTATGAACTTTCTTCCTATTGGATG
Found at i:71974 original size:51 final size:52
Alignment explanation
Indices: 71917--72065 Score: 196
Period size: 51 Copynumber: 2.9 Consensus size: 52
71907 ATATCCCAAC
* * *
71917 CTTTTCATGTTGGTGTGAGCCTTCAAGATTCCCCACATGGATAATATT-TGT
1 CTTTTCATGTTGATGTGAGCCTTCAAGATACCCCACATAGATAATATTCTGT
* * *
71968 CTTTTCATGTTGATGTGAACCTTCAAGATGCCTCACATAGAT--TACTTCTGT
1 CTTTTCATGTTGATGTGAGCCTTCAAGATACCCCACATAGATAATA-TTCTGT
* *
72019 CTTTTTATGCTGATGTGAGCCTTCAAGATACCCCACATAGATAATAT
1 CTTTTCATGTTGATGTGAGCCTTCAAGATACCCCACATAGATAATAT
72066 AGACCTCTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
49 2 0.02
50 2 0.02
51 77 0.92
52 1 0.01
53 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (52 bp):
CTTTTCATGTTGATGTGAGCCTTCAAGATACCCCACATAGATAATATTCTGT
Found at i:77918 original size:17 final size:18
Alignment explanation
Indices: 77896--77936 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
77886 AAATGTCTTT
77896 AAAAAA-CAATTTTAAGA
1 AAAAAATCAATTTTAAGA
*
77913 AAAAAATCATTTTTAAGA
1 AAAAAATCAATTTTAAGA
77931 AAAAAA
1 AAAAAA
77937 ACTAATCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAAATCAATTTTAAGA
Found at i:78236 original size:5 final size:5
Alignment explanation
Indices: 78222--78257 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
78212 TTTCATAACG
* *
78222 ATAAA ATAAA CTAAA ATGAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
78258 AGTGAAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:79373 original size:3 final size:3
Alignment explanation
Indices: 79365--79414 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
79355 GTAATAAGAT
*
79365 TAA TAA TAA TAA TAA TAA T-A TAGA TAA TAA -AA TAC TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
79408 TTAA TAA
1 -TAA TAA
79415 CATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:79412 original size:20 final size:21
Alignment explanation
Indices: 79367--79414 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
79357 AATAAGATTA
79367 ATAATAATAATAATAATATAG
1 ATAATAATAATAATAATATAG
*
79388 ATAATAA-AATACTAATATA-
1 ATAATAATAATAATAATATAG
79407 ATTAATAA
1 A-TAATAA
79415 CATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATAATAATAATAATATAG
Found at i:80051 original size:91 final size:91
Alignment explanation
Indices: 79943--80115 Score: 303
Period size: 91 Copynumber: 1.9 Consensus size: 91
79933 AAGTGTTGAA
*
79943 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTTGTTAGATGAGTTCTTCTCATTATGAA
80007 CTCTCCACTGGAAATGTTAATGCAAGG
65 CTCTCCACTGGAAATGTTAATGCAAGG
*
80034 TTGAACGAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTAGATGAGTTCTTCTCATTATGAAC
*
80099 TCTTCACTGGAAATGTT
66 TCTCCACTGGAAATGTT
80116 GATCCACCTC
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 76 0.97
92 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.42
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTAGATGAGTTCTTCTCATTATGAAC
TCTCCACTGGAAATGTTAATGCAAGG
Found at i:80239 original size:117 final size:117
Alignment explanation
Indices: 80033--80454 Score: 657
Period size: 117 Copynumber: 3.6 Consensus size: 117
80023 TTAATGCAAG
* **
80033 GTTGAACGAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTT-AGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGA-ATGAGTTCTTCTCATTATGA
* * *
80097 ACTCTTCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAACCAAT
65 ACTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGGAATCAAACCAAT
* *
80150 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCAATATTAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCATTATGAA
* * *
80215 CTTTTCACTGAAAATGTTGATCCACCTCTTTTTTTGATGGAATCAAACCAAT
66 CTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGGAATCAAACCAAT
* * *
80267 GTTGAACAAGTTCTTCTCATTATGAAATTTTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCATTATGAA
* * * *
80332 CTCTCCACTGAAAATGTTGATCCACATATTTCTGTGATGGAATCAAACCAAG
66 CTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGGAATCAAACCAAT
*
80384 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCATTATGAA
80449 CTCTTC
66 CTCTTC
80455 TGGAAATGTT
Statistics
Matches: 278, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
117 277 1.00
118 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (117 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCATTATGAA
CTCTTCACTGAAAATGTTGATCCACCTCTTTCTGTGATGGAATCAAACCAAT
Found at i:80535 original size:187 final size:187
Alignment explanation
Indices: 80314--80894 Score: 1056
Period size: 187 Copynumber: 3.1 Consensus size: 187
80304 TCATTGGATG
*
80314 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATATTTCTGTGATGGAATCAAA
1 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
80379 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
66 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
*
80444 ATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTTTGTGGTGGACTTGAAAGCAACA
131 ATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTTTGTGGTGGACTTGAAAGGAACA
80501 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
1 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
*
80566 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCTTCTCATT
66 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
* *
80631 ATGAACTCTTCTGGAAATATTGGGCCACCTCCTTCTT-TGGTGGACTTGAAAGGAACA
131 ATGAACTCTTCTGGAAATGTTGGGTCACCTCCTT-TTGTGGTGGACTTGAAAGGAACA
80688 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
1 AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
80753 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
66 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
* * * *
80818 ATGAACTCTTCTAGAAATGTTGGATCACCTCCTTCTGTGGTGGACTTAAAAGGAACA
131 ATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTTTGTGGTGGACTTGAAAGGAACA
*
80875 AGTTTTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
80895 TTCTCCTTTA
Statistics
Matches: 379, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
186 1 0.00
187 376 0.99
188 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (187 bp):
AGTTCTTCTCATTATGAACTCTCCACTGAAAATGTTGATCCACATCTTTCTGTGATGGAATCAAA
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTTTGTGGTGGACTTGAAAGGAACA
Found at i:80642 original size:19 final size:19
Alignment explanation
Indices: 80581--80642 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
80571 GTTGAACAAG
80581 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAAC-TC
*
80601 TTCTTCCTCA-T-TGAA-TGAG
1 TTCTT-CTCATTATGAACT--C
80620 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
80639 TTCT
1 TTCT
80643 GGAAATATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 14 0.41
20 10 0.29
21 5 0.15
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.48
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:80951 original size:105 final size:108
Alignment explanation
Indices: 80761--80964 Score: 310
Period size: 105 Copynumber: 1.9 Consensus size: 108
80751 AACCAAGGTT
* *
80761 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT-ATTGGACGAGTTCGTCTCATTATGAACTC
80826 TTCTAGAAATGTTGGATCACCTCCTTCTGTGGTGGACTTAAAAG
65 TTCTAGAAATGTTGGATCACCTCCTTCTGTGGTGGACTTAAAAG
*
80870 GAACAAGTTTTTCTCATTATGAAC-T-TTC-TCCT-TTAGGACGAGTTCGTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATT-GGACGAGTTCGTCTCATTATGAACTC
*
80931 TTCT-GTAAATGTTGGTTCACCTCCTTCTGTGGTG
65 TTCTAG-AAATGTTGGATCACCTCCTTCTGTGGTG
80965 AATCATGATC
Statistics
Matches: 89, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
104 3 0.03
105 55 0.62
106 4 0.04
107 3 0.03
108 1 0.01
109 23 0.26
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (108 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTGGACGAGTTCGTCTCATTATGAACTCT
TCTAGAAATGTTGGATCACCTCCTTCTGTGGTGGACTTAAAAG
Found at i:82445 original size:51 final size:52
Alignment explanation
Indices: 82306--82455 Score: 187
Period size: 52 Copynumber: 2.9 Consensus size: 52
82296 TATCCCAACC
* * *
82306 TTTTCATGTTGGTGTGAGCCTTCAAGATGCCCCACATGGATAATATATGTCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATATGTAT
* * * *
82358 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACT-TCTGTAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGA-TAATATATGTAT
** *
82410 TTTT-ATGCTGATGTGAGCCTTCAAGAAACCCCACATAGATAATATA
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATA
82456 AACCTCCAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.04
51 31 0.38
52 45 0.55
53 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (52 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATAATATATGTAT
Found at i:86769 original size:21 final size:22
Alignment explanation
Indices: 86743--86783 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
86733 CATGTTGAAG
86743 AATTCAAGA-TCAAGAATCATA
1 AATTCAAGATTCAAGAATCATA
*
86764 AATTCAAGATTCCAGAATCA
1 AATTCAAGATTCAAGAATCA
86784 AGAGTCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (22 bp):
AATTCAAGATTCAAGAATCATA
Found at i:87117 original size:60 final size:57
Alignment explanation
Indices: 86977--87149 Score: 211
Period size: 58 Copynumber: 2.9 Consensus size: 57
86967 GCAACACAAC
* * **
86977 ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTTAAAGTCAATTCAATGAA
1 ACAA-ATTGGATTTCAACTTCACAACGAA-GATATCCAACTCAAAGCCAATTTGATGAA
* * *
87036 GCAAATTGGATTTCAACTTCACAATGAATGATATCCAACTCAAAGCCAATTTGGTGAA
1 ACAAATTGGATTTCAACTTCACAACGAA-GATATCCAACTCAAAGCCAATTTGATGAA
* *
87094 ACAGTACTTGGATTTCAACTTCACAACGAAGTATATCCAATTCAAAGCCAATTTGA
1 ACA--AATTGGATTTCAACTTCACAACGAAG-ATATCCAACTCAAAGCCAATTTGA
87150 CGAAGTACTA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
58 49 0.50
59 4 0.04
60 45 0.46
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (57 bp):
ACAAATTGGATTTCAACTTCACAACGAAGATATCCAACTCAAAGCCAATTTGATGAA
Found at i:87537 original size:124 final size:124
Alignment explanation
Indices: 87397--87703 Score: 403
Period size: 124 Copynumber: 2.5 Consensus size: 124
87387 GCAATTTACA
* * *
87397 AGATTAAATTTTAACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAATGAAC
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAAC
* ** * *
87462 CATTCATGATTTCAACATCACGACAAAGGATATTGTGCCCACCAGCAGTATCCATCTCT
66 CATTCACGATTTCAACATCACGACAAAGGATATCATGCCCACCACCAGCATCCATCTCT
*
87521 AGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAACGAAT-AAG
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAA-
* * *
87585 CCATTCACGATTTTAACTTCACGACGAAGGATATCATGCCCACCACCAGCATCCATCTCT
65 CCATTCACGATTTCAACATCACGACAAAGGATATCATGCCCACCACCAGCATCCATCTCT
* ** * *
87645 AGATTGGATTTC-A----A-AACGAATTATATCCAATTCAAAGCTCAACTTCACAATGAAGGAAC
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAAC
87704 AATCCTTGGA
Statistics
Matches: 163, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
118 37 0.23
119 3 0.02
123 3 0.02
124 120 0.74
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (124 bp):
AGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAAC
CATTCACGATTTCAACATCACGACAAAGGATATCATGCCCACCACCAGCATCCATCTCT
Found at i:87795 original size:32 final size:32
Alignment explanation
Indices: 87750--87832 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
87740 AACTCAAAGC
*
87750 TCAACTTCACGACGAAGGAGCCATCCACGATT
1 TCAATTTCACGACGAAGGAGCCATCCACGATT
*
87782 TCAATTTCACGACGAATGAGCCATCCACGATT
1 TCAATTTCACGACGAAGGAGCCATCCACGATT
87814 TCAATTTCACGACGAAGGA
1 TCAATTTCACGACGAAGGA
87833 TATCGTGCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (32 bp):
TCAATTTCACGACGAAGGAGCCATCCACGATT
Found at i:88586 original size:19 final size:19
Alignment explanation
Indices: 88541--88587 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
88531 TGCCATTGAG
88541 CCACCAACGTCGAGCCATC
1 CCACCAACGTCGAGCCATC
* *
88560 TCATCAACGTCGAGCCATC
1 CCACCAACGTCGAGCCATC
88579 CCACCAACG
1 CCACCAACG
88588 CCGATGAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.45, G:0.15, T:0.13
Consensus pattern (19 bp):
CCACCAACGTCGAGCCATC
Found at i:94590 original size:33 final size:33
Alignment explanation
Indices: 94529--94591 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
94519 TAAAAAGTTA
***
94529 AAATTTTATATATTTCGATCATTTTGGTTACTC
1 AAATTTTATATATTTCGATCACAATGGTTACTC
94562 AAATTTTATATATTTCGATCACAATGGTTA
1 AAATTTTATATATTTCGATCACAATGGTTA
94592 GTGTTGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (33 bp):
AAATTTTATATATTTCGATCACAATGGTTACTC
Found at i:96817 original size:2 final size:2
Alignment explanation
Indices: 96810--96836 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96800 GTCAACTCTG
96810 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
96837 GGGACACGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103050 original size:11 final size:11
Alignment explanation
Indices: 103034--103058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
103024 ACTCTAAACT
103034 AAATTAATATA
1 AAATTAATATA
103045 AAATTAATATA
1 AAATTAATATA
103056 AAA
1 AAA
103059 CATACCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAATATA
Found at i:104544 original size:36 final size:36
Alignment explanation
Indices: 104460--104601 Score: 176
Period size: 36 Copynumber: 3.9 Consensus size: 36
104450 GACCCGATCT
* * * * **
104460 TGATTTGATTCACTACTCTTCCATAAAGTCTTGGGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
104496 TTGATTTGCTTCACTACTCTTTCGTGAAGACTTAAGA
1 -TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
104533 TGATTAGCTTCACTACTCTTCCGTGAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
104569 TGGTTTGCTTCACTATTCTTCCGTGAAGGCTTA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
104602 CAAATTACCC
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 63 0.68
37 29 0.32
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (36 bp):
TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:104660 original size:42 final size:42
Alignment explanation
Indices: 104613--104693 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
104603 AAATTACCCG
*
104613 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCA
*
104655 AAGGATTTCATCATCATGCTCGAAAGACTTACTAATGGC
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGC
104694 ACTTACTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (42 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCA
Found at i:111687 original size:11 final size:11
Alignment explanation
Indices: 111671--111695 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
111661 ACTCTAAACC
111671 AAATTAATATA
1 AAATTAATATA
111682 AAATTAATATA
1 AAATTAATATA
111693 AAA
1 AAA
111696 CATACCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAATATA
Found at i:112840 original size:16 final size:16
Alignment explanation
Indices: 112821--112851 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
112811 ATTAATTATA
*
112821 AAAATAAAAATAAAAT
1 AAAATAAAAACAAAAT
112837 AAAATAAAAACAAAA
1 AAAATAAAAACAAAA
112852 ATCCCGGACA
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:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAAACAAAAT
Found at i:116274 original size:35 final size:35
Alignment explanation
Indices: 116228--116297 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
116218 TTGAATTTAT
116228 TAAGAGTTTAACAAACTTAACCTTTCTGTTGGTAA
1 TAAGAGTTTAACAAACTTAACCTTTCTGTTGGTAA
116263 TAAGAGTTTAACAAACTTAACCTTTCTGTTGGTAA
1 TAAGAGTTTAACAAACTTAACCTTTCTGTTGGTAA
116298 GTTCATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (35 bp):
TAAGAGTTTAACAAACTTAACCTTTCTGTTGGTAA
Found at i:121934 original size:16 final size:18
Alignment explanation
Indices: 121888--121937 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
121878 TTGGCTTATA
121888 AAATATAAGATTATCTCT
1 AAATATAAGATTATCTCT
121906 AGAA-ATAAGATTATC-C-
1 A-AATATAAGATTATCTCT
*
121922 AAATATAATATTATCT
1 AAATATAAGATTATCT
121938 TACATGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 1 0.04
18 12 0.43
19 2 0.07
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (18 bp):
AAATATAAGATTATCTCT
Found at i:126995 original size:18 final size:18
Alignment explanation
Indices: 126970--127023 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
126960 ATGCTCGTAT
126970 GCATGTAGTTAGTTGTTA
1 GCATGTAGTTAGTTGTTA
* *
126988 GTATGTAGGTAGTTGTTA
1 GCATGTAGTTAGTTGTTA
*
127006 GCATGCAGTTAGTTGTTA
1 GCATGTAGTTAGTTGTTA
127024 AACTAGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.06, G:0.30, T:0.43
Consensus pattern (18 bp):
GCATGTAGTTAGTTGTTA
Found at i:135437 original size:2 final size:2
Alignment explanation
Indices: 135430--135454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
135420 TGAAATATTA
135430 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 A
135455 AATGAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:135521 original size:18 final size:18
Alignment explanation
Indices: 135472--135525 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
135462 AAAATAGAAA
*
135472 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
135493 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
135512 AATA-TAATATAAAA
1 AATAGTAATATAAAA
135526 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:135526 original size:18 final size:19
Alignment explanation
Indices: 135476--135526 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
135466 TAGAAAAATA
*
135476 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
135496 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
135515 ATAATATAAAAA
1 ATAATATAAAAA
135527 AACCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:135543 original size:33 final size:33
Alignment explanation
Indices: 135505--135587 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 33
135495 TAGTAATATG
135505 AAAATATAATATAATATAAAAAAACCAAAAACA
1 AAAATATAATATAATATAAAAAAACCAAAAACA
* * *
135538 AAAATA-AATA-AATAT--ATAAACCAAATATA
1 AAAATATAATATAATATAAAAAAACCAAAAACA
*
135567 AAAGTATACATATAATGATAA
1 AAAATATA-ATATAAT-ATAA
135588 TTGGCTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
29 16 0.40
30 1 0.03
31 8 0.20
32 7 0.17
33 8 0.20
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (33 bp):
AAAATATAATATAATATAAAAAAACCAAAAACA
Found at i:136352 original size:37 final size:37
Alignment explanation
Indices: 136311--136404 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
136301 TCCTATCTTT
* *
136311 AGGAGTTTAAATCATAGTAGAACTCTATCATATTTTA
1 AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
* * * * *
136348 AGGAGTTTGAATCCTAGCAAAATTCTATCCTATTTTT
1 AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
136385 AGGAGTTTGAATCCTAGTAG
1 AGGAGTTTGAATCCTAGTAG
136405 GACGAAAAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (37 bp):
AGGAGTTTGAATCCTAGTAGAACTCTATCATATTTTA
Found at i:137453 original size:106 final size:106
Alignment explanation
Indices: 137135--138827 Score: 2468
Period size: 106 Copynumber: 16.0 Consensus size: 106
137125 GCATTGTTCT
* * * ** * * * *
137135 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTAGCTCTGGAACCGAGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
137199 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
137241 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
137300 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
137342 G-GTCCAAGATCCTTCACTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
137406 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
137447 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTATTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
137512 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * * *
137553 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGATCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
137618 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
137659 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
137724 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
137765 GATTACAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
137830 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
137871 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
137936 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
137977 GAGTCCAATATCCTTCACTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
138042 CTAGCGATCCCTTCGTCGTGAAGTTG-ACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
138082 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
138147 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
138188 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
138253 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
138294 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
138359 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
138400 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
138465 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
138506 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
138571 CCAGCGGTCTCTTCGTTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
138612 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
138677 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
138718 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
138783 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
138824 GAGT
1 GAGT
138828 GGCACGATAT
Statistics
Matches: 1431, Mismatches: 146, Indels: 20
0.90 0.09 0.01
Matches are distributed among these distances:
100 80 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 102 0.07
106 1236 0.86
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:139655 original size:22 final size:22
Alignment explanation
Indices: 139629--139749 Score: 206
Period size: 22 Copynumber: 5.5 Consensus size: 22
139619 TTATGTTTGG
139629 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
139651 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
139673 TTAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
139695 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
139717 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
139739 TCAACGGTTTG
1 TCAAAGGTTTG
139750 ATGGGGTAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 92 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:140435 original size:172 final size:173
Alignment explanation
Indices: 140144--140490 Score: 583
Period size: 172 Copynumber: 2.0 Consensus size: 173
140134 TAAATAGGCC
* * *
140144 CAAACAAGTGTTTCAGGGTGTTGAACCTAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGAGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
*
140209 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTTGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
140274 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* *
140319 CAAACAAGTGTTTCAGAGTGTTGAACCAATGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGAGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
140381 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
140446 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
140491 TTTTAGGGAT
Statistics
Matches: 164, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 14 0.09
172 101 0.62
174 1 0.01
175 48 0.29
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGAGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:140578 original size:16 final size:15
Alignment explanation
Indices: 140537--140594 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
140527 TTCTTTTTGA
140537 TTTTTGTTCTTGTTTCT
1 TTTTTGTTC-T-TTTCT
*
140554 CTTTT-TTCTTTAT-T
1 TTTTTGTTCTTT-TCT
140568 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
140584 TTTTTGTTCTT
1 TTTTTGTTCTT
140595 GATTGGATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 7 0.20
15 8 0.23
16 16 0.46
17 4 0.11
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:145115 original size:12 final size:12
Alignment explanation
Indices: 145098--145170 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
145088 GGAAAAAATG
145098 AATAAATGAAAA
1 AATAAATGAAAA
145110 AATAAA-GAATAAA
1 AATAAATG-A-AAA
* *
145123 AATAAGTAAAATA
1 AATAAATGAAA-A
* *
145136 AATAAAAGGAAA
1 AATAAATGAAAA
145148 AATAAAT-AAATA
1 AATAAATGAAA-A
145160 AATAAATGAAA
1 AATAAATGAAA
145171 TATTAATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.06
12 24 0.51
13 20 0.43
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (12 bp):
AATAAATGAAAA
Found at i:145183 original size:2 final size:2
Alignment explanation
Indices: 145176--145206 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
145166 TGAAATATTA
145176 AT AT 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 AT AT A
145207 AATGAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:145279 original size:18 final size:19
Alignment explanation
Indices: 145229--145279 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
145219 TAGAAAATTA
*
145229 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
145249 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
145268 ATAATATAAAAA
1 ATAATATAAAAA
145280 AACCAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:145296 original size:33 final size:33
Alignment explanation
Indices: 145252--145340 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 33
145242 TAATAATAGT
*
145252 AATATGAAAATATAATATAATATAAAAAAACCA
1 AATATAAAAATATAATATAATATAAAAAAACCA
*
145285 AA-ATCAAAAATA-AATA-AATAT--ATAAACCA
1 AATAT-AAAAATATAATATAATATAAAAAAACCA
*
145314 AATATAAAAGTATACATATAATGATAA
1 AATATAAAAATATA-ATATAAT-ATAA
145341 TTGGCTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
29 15 0.33
30 3 0.07
31 8 0.18
32 9 0.20
33 10 0.22
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (33 bp):
AATATAAAAATATAATATAATATAAAAAAACCA
Found at i:145506 original size:19 final size:19
Alignment explanation
Indices: 145475--145512 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
145465 AAAAGTATAT
*
145475 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
145494 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
145513 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:146077 original size:37 final size:36
Alignment explanation
Indices: 146036--146140 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 36
146026 GTGCTTGTGG
* * *
146036 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAACTAT
* * *
146073 ATCCTATTTTAAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAACTAT
146110 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
146141 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.05
37 51 0.88
38 4 0.07
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTAT
Found at i:152917 original size:18 final size:19
Alignment explanation
Indices: 152894--152931 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
152884 AAAGTTCGAG
152894 ATTTTAATTTT-AAATATT
1 ATTTTAATTTTAAAATATT
152912 ATTTTAATTTTAAAATATT
1 ATTTTAATTTTAAAATATT
152931 A
1 A
152932 ATTCTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTAATTTTAAAATATT
Found at i:155269 original size:17 final size:17
Alignment explanation
Indices: 155247--155279 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
155237 GTTTAAATTG
155247 AAAATGTTACATTCTTC
1 AAAATGTTACATTCTTC
*
155264 AAAATGTTATATTCTT
1 AAAATGTTACATTCTT
155280 TGTAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (17 bp):
AAAATGTTACATTCTTC
Found at i:160939 original size:28 final size:30
Alignment explanation
Indices: 160895--160952 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
160885 ATTCAACAAA
160895 ATAATATTTTATAAATA-AAAGATCATTTT
1 ATAATATTTTATAAATAGAAAGATCATTTT
*
160924 ATAAT-TTTTA-ATAATAGAACGATCATTTT
1 ATAATATTTTATA-AATAGAAAGATCATTTT
160953 CAGGCTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 9 0.35
29 16 0.62
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (30 bp):
ATAATATTTTATAAATAGAAAGATCATTTT
Found at i:170038 original size:30 final size:30
Alignment explanation
Indices: 170002--170066 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
169992 GTCTTTTTAG
*
170002 TTTTTATTAATACTATTTTAATCCTTTAAT
1 TTTTTATTAATACTATTTTAATACTTTAAT
** ** *
170032 TTTTTATTTGTGTTATTTTAGTACTTTAAT
1 TTTTTATTAATACTATTTTAATACTTTAAT
170062 TTTTT
1 TTTTT
170067 TCCTTTTACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTTTATTAATACTATTTTAATACTTTAAT
Found at i:173041 original size:2 final size:2
Alignment explanation
Indices: 173034--173059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
173024 TCATTTATCC
173034 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
173060 CCCTTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:174303 original size:32 final size:32
Alignment explanation
Indices: 174267--174340 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
174257 GTATCTTTAA
*
174267 AGATTCAATAGTAAATATTGGGGCATATTTGG
1 AGATTCAACAGTAAATATTGGGGCATATTTGG
* *
174299 AGATTCAACATTGAATATTGGGGCATATTTGG
1 AGATTCAACAGTAAATATTGGGGCATATTTGG
*
174331 GGATTCAACA
1 AGATTCAACA
174341 TCCTGATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.32
Consensus pattern (32 bp):
AGATTCAACAGTAAATATTGGGGCATATTTGG
Found at i:174341 original size:32 final size:32
Alignment explanation
Indices: 174280--174341 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
174270 TTCAATAGTA
174280 AATATTGGGGCATATTTGGAGATTCAACATTG
1 AATATTGGGGCATATTTGGAGATTCAACATTG
*
174312 AATATTGGGGCATATTTGGGGATTCAACAT
1 AATATTGGGGCATATTTGGAGATTCAACAT
174342 CCTGATGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.34
Consensus pattern (32 bp):
AATATTGGGGCATATTTGGAGATTCAACATTG
Found at i:174678 original size:64 final size:65
Alignment explanation
Indices: 174598--174722 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
174588 TGAGCTTCTG
*
174598 TCAACAAATAACTTTCC-AATTTCATTAAGAGTCAACTTCAACTTCACAGCAAAGGATATTTTAC
1 TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCAAAGGATATTTTAC
* * * *
174662 TCAACAAACAATTTTCCAAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
1 TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCAAAGGATATT
174723 GAACTCGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 15 0.27
65 40 0.73
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (65 bp):
TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCAAAGGATATTTTAC
Found at i:174988 original size:43 final size:43
Alignment explanation
Indices: 174934--175143 Score: 233
Period size: 43 Copynumber: 4.9 Consensus size: 43
174924 ACGAATGGGC
* *
174934 CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
174977 GATCCACGATTTCAACTCCACGACGGAGGATATCATGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * * *
175020 CATCTACTATTTAAACTCCACGACAGAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
175063 GATCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
175106 CAACCACGGTTTCAACTTCACGACGAAGAGA-ATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAG-GATATCGTAC
175144 ACACAAGCAG
Statistics
Matches: 135, Mismatches: 31, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
43 133 0.99
44 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:175128 original size:86 final size:86
Alignment explanation
Indices: 174941--175129 Score: 279
Period size: 86 Copynumber: 2.2 Consensus size: 86
174931 GGCCATCCAT
* *
174941 GATTTCAACTCCATGACGGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
1 GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
* *
175006 ATATCATGCCCACACATCTAC
66 ATATCATGCCCACACAACCAC
* * * *
175027 TATTTAAACTCCACGACAGAGGATATCGTACCAACGGATCCACGATTTCAACTCCACGATGGAGG
1 GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
*
175092 ATATCGTGCCCACACAACCAC
66 ATATCATGCCCACACAACCAC
* *
175113 GGTTTCAACTTCACGAC
1 GATTTCAACTCCACGAC
175130 GAAGAGAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (86 bp):
GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
ATATCATGCCCACACAACCAC
Done.