Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1337797 original size:30 final size:30
Alignment explanation
Indices: 1337763--1337829 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1337753 CTGCTGGAAA
* * * *
1337763 ACCGGTTTGACCGTTTTTGAACTGGTTTTG
1 ACCGGTTTAACCGGTTTTGAACCGGTTTCG
*
1337793 ACCGGTTTAATCGGTTTTGAACCGGTTTCG
1 ACCGGTTTAACCGGTTTTGAACCGGTTTCG
1337823 ACCGGTT
1 ACCGGTT
1337830 CGAACCAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (30 bp):
ACCGGTTTAACCGGTTTTGAACCGGTTTCG
Found at i:1337799 original size:10 final size:10
Alignment explanation
Indices: 1337763--1337829 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
1337753 CTGCTGGAAA
1337763 ACCGG-TTTG
1 ACCGGTTTTG
*
1337772 ACCGTTTTTG
1 ACCGGTTTTG
*
1337782 AACTGGTTTTG
1 -ACCGGTTTTG
*
1337793 ACCGG-TTTA
1 ACCGGTTTTG
*
1337802 ATCGGTTTTG
1 ACCGGTTTTG
*
1337812 AACCGGTTTCG
1 -ACCGGTTTTG
1337823 ACCGGTT
1 ACCGGTT
1337830 CGAACCAGTC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 11 0.24
10 18 0.40
11 16 0.36
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1337896 original size:17 final size:17
Alignment explanation
Indices: 1337874--1337911 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1337864 GGTCTGACCC
1337874 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1337891 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1337908 GACC
1 GACC
1337912 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1337911 original size:7 final size:7
Alignment explanation
Indices: 1337901--1337938 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1337891 GACCCGACCC
1337901 GACCGTT
1 GACCGTT
1337908 GACCGTT
1 GACCGTT
1337915 GACCGTT
1 GACCGTT
*
1337922 GATCG-T
1 GACCGTT
1337928 GACCGTT
1 GACCGTT
1337935 GACC
1 GACC
1337939 TCCTTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1337911 original size:24 final size:23
Alignment explanation
Indices: 1337858--1337918 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 23
1337848 CTGAATCGGT
1337858 TTGACCGGTCTGACCCGACCCGACC
1 TTGACC-GT-TGACCCGACCCGACC
*
1337883 -CGACCGTTGACCCGACCCGACC
1 TTGACCGTTGACCCGACCCGACC
1337905 GTTGACCGTTGACC
1 -TTGACCGTTGACC
1337919 GTTGATCGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.47
23 2 0.06
24 15 0.47
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (23 bp):
TTGACCGTTGACCCGACCCGACC
Found at i:1345136 original size:9 final size:9
Alignment explanation
Indices: 1345122--1345201 Score: 61
Period size: 10 Copynumber: 8.2 Consensus size: 9
1345112 AGCTGGAAAG
1345122 CCGGTTTGA
1 CCGGTTTGA
1345131 CCGGTTTTGAA
1 CCGG-TTTG-A
*
1345142 CCGATTTTGA
1 CCG-GTTTGA
1345152 CCGGTTTCGA
1 CCGGTTT-GA
*
1345162 CCGGTTCGAA
1 CCGGTTTG-A
*
1345172 CCGGTCTGA
1 CCGGTTTGA
* *
1345181 CCCGTCTGAA
1 CCGGTTTG-A
1345191 CCGGTTTGA
1 CCGGTTTGA
1345200 CC
1 CC
1345202 CGACCGACCC
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 19 0.33
10 30 0.53
11 8 0.14
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.29
Consensus pattern (9 bp):
CCGGTTTGA
Found at i:1347115 original size:14 final size:14
Alignment explanation
Indices: 1347081--1347121 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1347071 TTCGGTCTAA
1347081 ATACCCATAAATAT
1 ATACCCATAAATAT
1347095 ATA-CCATAAATAT
1 ATACCCATAAATAT
*
1347108 GTACCCATAAATAT
1 ATACCCATAAATAT
1347122 TAATGGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (14 bp):
ATACCCATAAATAT
Found at i:1351875 original size:70 final size:70
Alignment explanation
Indices: 1351801--1351972 Score: 263
Period size: 70 Copynumber: 2.4 Consensus size: 70
1351791 ACTGAACACG
*
1351801 AACACCTTAAAAATAAACAATCTAACATGAACATGAAAATAAAAAATTAAACGAAAATAAATTAA
1 AACACCTTAAAAATAAACAAACTAACATGAACATGAAAATAAAAAATTAAACGAAAATAAATTAA
1351866 ATATT
66 ATATT
* * * * * *
1351871 AACACCTTTAAAATAAACAAACTAACATGAGCATGATATTAAAAATTTACACGAAAATAAATTAA
1 AACACCTTAAAAATAAACAAACTAACATGAACATGAAAATAAAAAATTAAACGAAAATAAATTAA
1351936 ATATT
66 ATATT
*
1351941 AACACCTTTAAAAATAAACAAACTAAAATGAA
1 AACACC-TTAAAAATAAACAAACTAACATGAA
1351973 TAGGATATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 69 0.76
71 22 0.24
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (70 bp):
AACACCTTAAAAATAAACAAACTAACATGAACATGAAAATAAAAAATTAAACGAAAATAAATTAA
ATATT
Found at i:1352658 original size:22 final size:22
Alignment explanation
Indices: 1352628--1352673 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1352618 TTTTTTATTA
*
1352628 TAATATTTTTTCTTTAAAATTT
1 TAATATTTTTTCATTAAAATTT
*
1352650 TAATTTTTTTTCATTAAAATTT
1 TAATATTTTTTCATTAAAATTT
1352672 TA
1 TA
1352674 CATTCGTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATATTTTTTCATTAAAATTT
Found at i:1354504 original size:12 final size:12
Alignment explanation
Indices: 1354487--1354511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1354477 ACCATTGGCT
1354487 TAAAAAGTTAGA
1 TAAAAAGTTAGA
1354499 TAAAAAGTTAGA
1 TAAAAAGTTAGA
1354511 T
1 T
1354512 GAGGATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TAAAAAGTTAGA
Found at i:1355831 original size:109 final size:109
Alignment explanation
Indices: 1355715--1356022 Score: 334
Period size: 109 Copynumber: 2.8 Consensus size: 109
1355705 AAAATCATGT
*
1355715 CTTCTTCTTTATCCCATCCTCTCCTTCCTCAATCTTAAAACATCAAAT-TTCCATGTTTTGCTCT
1 CTTCTTCTTTATCCCATCCTCTCCTTCCCCAATCTT-AAACATCAAATCTT-CATGTTTTGCTCT
*
1355779 ACTTTTTCTTTAATCCACCATTAT-AATATAAATTAAAAATCACCA
64 ACTCTTTCTTTAATCCACCATTATAAATATAAATTAAAAATCACCA
* * ** *
1355824 CTTCTTCTTTATCTCATCCTTTCCTTCCCCAATCTTAAGTATTAAATCTTCATGTTTTGCTCTAC
1 CTTCTTCTTTATCCCATCCTCTCCTTCCCCAATCTTAAACATCAAATCTTCATGTTTTGCTCTAC
* **
1355889 TCTTTCTTTAATCCACCATTATAAATCTAAATTAAAAATTCAATA
66 TCTTTCTTTAATCCACCATTATAAATATAAATTAAAAA-TCACCA
* * * ** * * * * * *
1355934 CTTCTT-TTTGTCTCATCCTTTTATTTCCCAATCTTAAGCATTAAATCTCCATGCTTTTTCTATA
1 CTTCTTCTTTATCCCATCCTCTCCTTCCCCAATCTTAAACATCAAATCTTCATG-TTTTGCTCTA
* ** *
1355998 TTCTTTCTTTGGTTCACCATTATAA
65 CTCTTTCTTTAATCCACCATTATAA
1356023 TCCATCTTAA
Statistics
Matches: 173, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
108 44 0.25
109 90 0.52
110 39 0.23
ACGTcount: A:0.26, C:0.25, G:0.03, T:0.45
Consensus pattern (109 bp):
CTTCTTCTTTATCCCATCCTCTCCTTCCCCAATCTTAAACATCAAATCTTCATGTTTTGCTCTAC
TCTTTCTTTAATCCACCATTATAAATATAAATTAAAAATCACCA
Found at i:1356237 original size:13 final size:13
Alignment explanation
Indices: 1356219--1356244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1356209 TTGTTTTAAA
1356219 TCTTGATTATAAT
1 TCTTGATTATAAT
1356232 TCTTGATTATAAT
1 TCTTGATTATAAT
1356245 AGTGAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TCTTGATTATAAT
Found at i:1356659 original size:3 final size:3
Alignment explanation
Indices: 1356651--1356686 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1356641 GTCTGGGTCT
1356651 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1356687 AAAATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1357327 original size:22 final size:22
Alignment explanation
Indices: 1357285--1357328 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1357275 AACATTCGGT
1357285 GAGAAAAACGAACAAGAAAAAA
1 GAGAAAAACGAACAAGAAAAAA
* *
1357307 GAGAGAAATCGAACTAGAAAAA
1 GAGA-AAAACGAACAAGAAAAA
1357329 TTAAAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.66, C:0.09, G:0.20, T:0.05
Consensus pattern (22 bp):
GAGAAAAACGAACAAGAAAAAA
Found at i:1357940 original size:6 final size:6
Alignment explanation
Indices: 1357929--1358006 Score: 70
Period size: 6 Copynumber: 12.5 Consensus size: 6
1357919 AAGATACCAA
* * *
1357929 AAAAAG AAAAAG AAAGAG AAAATAA AAAAAGG AAAAA- AGAAAA- AAAGAG
1 AAAAAG AAAAAG AAAAAG AAAA-AG AAAAA-G AAAAAG A-AAAAG AAAAAG
1357978 AAAAGAG AAAAGAG AAAAAG AAAAAG AAA
1 AAAA-AG AAAA-AG AAAAAG AAAAAG AAA
1358007 TAAATAAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 4 0.07
6 34 0.56
7 23 0.38
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:1357958 original size:8 final size:8
Alignment explanation
Indices: 1357927--1358002 Score: 59
Period size: 8 Copynumber: 9.6 Consensus size: 8
1357917 TGAAGATACC
1357927 AAAAAAAG
1 AAAAAAAG
1357935 AAAAAGAA-
1 AAAAA-AAG
* *
1357943 AGAGAAAAT
1 A-AAAAAAG
1357952 AAAAAAAG
1 AAAAAAAG
*
1357960 GAAAAAAG
1 AAAAAAAG
1357968 AAAAAAAG
1 AAAAAAAG
*
1357976 -AGAAAAG
1 AAAAAAAG
*
1357983 -AGAAAAG
1 AAAAAAAG
*
1357990 AGAAAAAG
1 AAAAAAAG
1357998 AAAAA
1 AAAAA
1358003 GAAATAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
7 13 0.24
8 36 0.65
9 6 0.11
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1357966 original size:16 final size:16
Alignment explanation
Indices: 1357928--1357988 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
1357918 GAAGATACCA
*
1357928 AAAAAAGAAAAAGAAAG
1 AAAAAAGAAAAA-AAGG
* *
1357945 AGAAAATAAAAAAAGG
1 AAAAAAGAAAAAAAGG
1357961 AAAAAAGAAAAAAAGAG
1 AAAAAAGAAAAAAAG-G
*
1357978 AAAAGAGAAAA
1 AAAAAAGAAAA
1357989 GAGAAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGG
Found at i:1357979 original size:31 final size:29
Alignment explanation
Indices: 1357928--1358002 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 29
1357918 GAAGATACCA
1357928 AAAAAAGAAAAAGAAAGAGAAAATAAAAAAAGG
1 AAAAAAG-AAAA-AAAGAGAAAA-AAAAAAA-G
* *
1357961 AAAAAAGAAAAAAAGAGAAAAGAGAAAAG
1 AAAAAAGAAAAAAAGAGAAAAAAAAAAAG
1357990 AGAAAAAGAAAAA
1 A-AAAAAGAAAAA
1358003 GAAATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 2 0.05
30 16 0.41
31 10 0.26
32 4 0.10
33 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (29 bp):
AAAAAAGAAAAAAAGAGAAAAAAAAAAAG
Found at i:1357982 original size:15 final size:15
Alignment explanation
Indices: 1357930--1358002 Score: 76
Period size: 16 Copynumber: 4.7 Consensus size: 15
1357920 AGATACCAAA
1357930 AAAAGAAAAAGAAAGAG
1 AAAAG-AAAA-AAAGAG
* *
1357947 AAAATAAAAAAAGGAA
1 AAAAGAAAAAAA-GAG
1357963 AAAAGAAAAAAAGAG
1 AAAAGAAAAAAAGAG
*
1357978 AAAAG-AGAAAAGAG
1 AAAAGAAAAAAAGAG
1357992 AAAAAGAAAAA
1 -AAAAGAAAAA
1358003 GAAATAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.17
15 15 0.32
16 20 0.43
17 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAAAAGAG
Found at i:1359221 original size:108 final size:109
Alignment explanation
Indices: 1359032--1359243 Score: 268
Period size: 108 Copynumber: 2.0 Consensus size: 109
1359022 TAATCAGATG
* ** * *
1359032 TCCTCATCATGTAGGAATCTTGCTATTAATATTATCCCTAAAGATACCTAGCCATCCTCATCACA
1 TCCTCATCACGTAGGAATCGAGCTATCAACATTATCCCTAAAGATACCTAGCCATCCTCATCACA
* * *
1359097 TAGGAACTATGTCATCCA-CGACCATATCTCCTCATCACAACCA
66 TAGGAAATATGTCATCCACCAACCAGATCTCCTCATCACAACCA
* * *
1359140 TCCTCATCACGTAGGAATCGAGTTATCAACATTATCCCTAAAGATGGCC-AGCCATCCTCATCAG
1 TCCTCATCACGTAGGAATCGAGCTATCAACATTATCCCTAAAGAT-ACCTAGCCATCCTCATCAC
* *
1359204 GT-GGAAATCGTGTCATCCACCAACCAGATCTCCTCATCAC
65 ATAGGAAAT-ATGTCATCCACCAACCAGATCTCCTCATCAC
1359244 GTAGGAGTCG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 5 0.06
108 63 0.72
109 20 0.23
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.26
Consensus pattern (109 bp):
TCCTCATCACGTAGGAATCGAGCTATCAACATTATCCCTAAAGATACCTAGCCATCCTCATCACA
TAGGAAATATGTCATCCACCAACCAGATCTCCTCATCACAACCA
Found at i:1360680 original size:137 final size:137
Alignment explanation
Indices: 1360413--1360723 Score: 335
Period size: 137 Copynumber: 2.3 Consensus size: 137
1360403 AACTATGACT
* * * * *
1360413 AGATCTCATCATC-TGTAGGAGTCGCATCAACCTTAGATAACCAGATGTCCTCATCACGTAGGAA
1 AGATCTCCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGATGTCCGCATCACGTAGGAA
* * ** * ***
1360477 CTGTTCTATCAATATTATCCCTAAAGATGGATAGCTTTCCTCATCATATAGGAATTGTATCATCC
66 CCGTTCTATCAACATTATCCCTAAAGATGGATAGCCATCCTCATCAGATAGGAACCATATCATCC
*
1360542 ACCGACC
131 ACCAACC
* * *
1360549 ATATCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCA-ATCGTCCGCATCACGTAGGA
1 AGATCTCCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGAT-GTCCGCATCACGTAGGA
* * * *
1360613 ACCGTGT-TATCAACATTATCCCTAGAGATGG-TCAGCCATCCTTATCAGGT-GGAAACCATGTC
65 ACCGT-TCTATCAACATTATCCCTAAAGATGGAT-AGCCATCCTCATCAGATAGG-AACCATATC
*
1360675 TTCCACCAACC
127 ATCCACCAACC
* *
1360686 AGATCTCCTCATAACGTAGGAGCCGCGTCACCCTTAGA
1 AGATCTCCTCATCACGTAGGAGTCGCGTCACCCTTAGA
1360724 ATACTTCCTC
Statistics
Matches: 143, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
136 16 0.11
137 126 0.88
138 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (137 bp):
AGATCTCCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGATGTCCGCATCACGTAGGAA
CCGTTCTATCAACATTATCCCTAAAGATGGATAGCCATCCTCATCAGATAGGAACCATATCATCC
ACCAACC
Found at i:1367989 original size:3 final size:3
Alignment explanation
Indices: 1367981--1368086 Score: 158
Period size: 3 Copynumber: 34.7 Consensus size: 3
1367971 TCATTTAAAT
** *
1367981 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1368029 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T-TA
1368076 TTA TTA TTA TT
1 TTA TTA TTA TT
1368087 TAATAAATAA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
3 87 0.94
4 6 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1368494 original size:28 final size:31
Alignment explanation
Indices: 1368463--1368533 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
1368453 CGGATCCTGC
1368463 AAAACAAAAAAAAAAG-G-A-CGACGACAGAA
1 AAAACAAAAAAAAAAGAGAAGCGA-GACAGAA
* *
1368492 AAAA-AAAAGAAAAAGAGAAGGGAGACAGAA
1 AAAACAAAAAAAAAAGAGAAGCGAGACAGAA
1368522 AAAACAAAAAAA
1 AAAACAAAAAAA
1368534 GAGGAAGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 10 0.29
29 5 0.14
30 12 0.34
31 8 0.23
ACGTcount: A:0.73, C:0.08, G:0.18, T:0.00
Consensus pattern (31 bp):
AAAACAAAAAAAAAAGAGAAGCGAGACAGAA
Found at i:1369584 original size:140 final size:139
Alignment explanation
Indices: 1369440--1369735 Score: 307
Period size: 141 Copynumber: 2.1 Consensus size: 139
1369430 CTTAGTCTTA
** * *
1369440 TAAATATTTATAT-TAAATATTATAAAAATTATA-ATTTATTTAAATCTTTTTATGAAAAATTAT
1 TAAATATAAATATCTAAATATTATAAAAATTATATA-TTAATT--AT-TTTTTA-GAAAAA-AAT
**
1369503 -TATATTTTTA-ATATTTA-TTATTAATATCGAAGAAAAGAACTGTCTTAAAGCACCTAGAAGTT
60 GTATATTTTTAGATATTTATTTATTAATATCGAAGAAAAGAACTGTCTTAAAGCACCTAGAAGCC
1369565 CTTTTCTGATA-TTC
125 CTTTTCTGATATTTC
*** * * * *
1369579 TTAAATAAATAAATATCTTGTTTTTTTATAAATTATATATTAATTATTTTTTAGAAAAAAATGTT
1 -TAAAT--ATAAATATCTAAATATTATAAAAATTATATATTAATTATTTTTTAGAAAAAAATGTA
* * *
1369644 TTTTTTTAGTTATTTATTTATTAATATCGAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTT
63 TATTTTTAGATATTTATTTATTAATATCGAAGAAAAGAACTGTCTTAAAGCACCTAGAAGCCCTT
1369709 TTCTGATATTTC
128 TTCTGATATTTC
1369721 TAAATAAATAAATAT
1 TAAAT--ATAAATAT
1369736 TTTATACATA
Statistics
Matches: 132, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
138 2 0.02
139 14 0.11
140 17 0.13
141 70 0.53
142 9 0.07
143 19 0.14
144 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (139 bp):
TAAATATAAATATCTAAATATTATAAAAATTATATATTAATTATTTTTTAGAAAAAAATGTATAT
TTTTAGATATTTATTTATTAATATCGAAGAAAAGAACTGTCTTAAAGCACCTAGAAGCCCTTTTC
TGATATTTC
Found at i:1376718 original size:114 final size:114
Alignment explanation
Indices: 1376510--1376735 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
1376500 AAGTGCCATA
*
1376510 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
1376575 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
*
1376624 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
1376689 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
1376736 CTGCATGATC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
Found at i:1377642 original size:35 final size:34
Alignment explanation
Indices: 1377591--1377656 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
1377581 TTCAACCAGA
1377591 AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
1 AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
* *
1377625 AATATGAATATTTGGGCATTTTGAAGGTTCAT
1 AATA-GAATATTGGGGCATTTTGAAGGCTCAT
1377657 CTCAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (34 bp):
AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
Found at i:1377939 original size:75 final size:75
Alignment explanation
Indices: 1377779--1377948 Score: 209
Period size: 75 Copynumber: 2.3 Consensus size: 75
1377769 AACAAGAAGC
* * * *
1377779 AAATGCTGGGGCATGCTGAAAACCCTTTTTTAATCAGAATCAGAAATGTTGAAATATTCTGAATA
1 AAATGCTGGGGCATGCTGAAAACCCTATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACA
1377844 TTTATCAGCA
66 TTTATCAGCA
* ** *
1377854 AAATGCTGGGGCATGCTGAAAACCC-ATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACA
1 AAATGCTGGGGCATGCTGAAAACCCTATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACA
*
1377918 CTTGTATTAGC-
66 -TT-TATCAGCA
* *
1377929 CAATGTTGGGGCATGCTGAA
1 AAATGCTGGGGCATGCTGAA
1377949 GGCCCACAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 31 0.38
75 45 0.55
76 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (75 bp):
AAATGCTGGGGCATGCTGAAAACCCTATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACA
TTTATCAGCA
Found at i:1380082 original size:76 final size:76
Alignment explanation
Indices: 1379956--1380224 Score: 438
Period size: 76 Copynumber: 3.6 Consensus size: 76
1379946 ATTTCCCACG
1379956 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1380021 CCTCAGGGTCA
66 CCTCAGGGTCA
* * *
1380032 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTTAAAG
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
*
1380097 CCTTAGGGTCA
66 CCTCAGGGTCA
1380108 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1380172 CCTTC-GGGTCA
66 CC-TCAGGGTCA
* * *
1380183 TCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAGCCTTCGGG
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1380225 TCATCCGTAA
Statistics
Matches: 181, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
73 12 0.07
75 35 0.19
76 134 0.74
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
CCTCAGGGTCA
Found at i:1380207 original size:44 final size:45
Alignment explanation
Indices: 1380159--1380260 Score: 170
Period size: 45 Copynumber: 2.3 Consensus size: 45
1380149 GGGAGCTTTT
* *
1380159 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1380203 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
*
1380248 GGATGTTTTCAAA
1 TGATGTTTTCAAA
1380261 AAGCCTTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 13 0.24
45 41 0.76
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
Found at i:1380235 original size:120 final size:121
Alignment explanation
Indices: 1380083--1380348 Score: 408
Period size: 120 Copynumber: 2.2 Consensus size: 121
1380073 GGGAGCTTTT
* * * * *
1380083 TGATGTTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
** *
1380148 CGGGAGCTTTTTGATGTTTTC-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CAAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1380203 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
1380268 CAAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CAAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1380324 TGATGTTTTCCAAAAAGCCTTCGGG
1 TGATGTTTT-C--AAAGCCTTCGGG
1380349 AGCTTTTTGA
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
120 76 0.58
121 43 0.33
122 1 0.01
124 12 0.09
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (121 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTACAGTGCAGGATGTTTCCAAAAAGCCTT
CAAGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1380373 original size:76 final size:76
Alignment explanation
Indices: 1380203--1380786 Score: 908
Period size: 76 Copynumber: 7.7 Consensus size: 76
1380193 CTTCAGTGCA
* * * * *
1380203 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
**
1380268 CAAGAGCTTTT
66 CGGGAGCTTTT
* * * *
1380279 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATG-TTTCCAAAAAGCCT
1380344 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
1380356 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1380420 CGGGAGCTTTT
66 CGGGAGCTTTT
*
1380431 TGATGTTTTCAAAGCC-TCAGGGTCGTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
1380495 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* *
1380507 TGATGTTCTCAAAGCC-TCAGGGTCGTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
1380571 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
1380583 TGATGTTTTCAAAGCC-TCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTC-GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
*
1380647 TTGGGAGCTTTT
65 TCGGGAGCTTTT
* *
1380659 TGATGTTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1380724 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
1380735 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
1380787 TCAACATTTC
Statistics
Matches: 477, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
75 73 0.15
76 372 0.78
77 32 0.07
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:1380925 original size:3 final size:3
Alignment explanation
Indices: 1380917--1381013 Score: 131
Period size: 3 Copynumber: 31.7 Consensus size: 3
1380907 TCATTTAAAT
** *
1380917 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1380965 TTA TTA TTA TTA TTTA TTA TTA ATA TTA ATA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
1381012 TT
1 TT
1381014 TAATAAATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
3 76 0.93
4 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1381465 original size:29 final size:30
Alignment explanation
Indices: 1381389--1381466 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
1381379 CGGATCCTGC
1381389 AAAACAAAAAAAAAAGG-A-CGACGACAGAA
1 AAAAC-AAAAAAAAAGGAAGCGACGACAGAA
* * *
1381418 AAAA-AAAGAAAAAGAGAAGGGA-GATAGAA
1 AAAACAAAAAAAAAG-GAAGCGACGACAGAA
1381447 AAAACAAAAAAAAAGGAAGC
1 AAAACAAAAAAAAAGGAAGC
1381467 AACTAACGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
27 9 0.22
28 1 0.03
29 19 0.47
30 11 0.28
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.01
Consensus pattern (30 bp):
AAAACAAAAAAAAAGGAAGCGACGACAGAA
Found at i:1385373 original size:45 final size:46
Alignment explanation
Indices: 1385287--1385374 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 46
1385277 TAGTACACCG
* * *
1385287 TTATATATTTTCATTTGTGGCATCCATTCATTCTAATTATGCATTA
1 TTATACATTTTCATTTATGGCATCCATTCATTCTAACTATGCATTA
* *
1385333 TTATACATTTTTATTTAT-GCATCCTTTCATGTC-AACTATGCA
1 TTATACATTTTCATTTATGGCATCCATTCAT-TCTAACTATGCA
1385375 CTGTTTTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 19 0.53
46 17 0.47
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (46 bp):
TTATACATTTTCATTTATGGCATCCATTCATTCTAACTATGCATTA
Found at i:1385458 original size:45 final size:45
Alignment explanation
Indices: 1385394--1385525 Score: 160
Period size: 45 Copynumber: 2.9 Consensus size: 45
1385384 TCTAAAATGT
* *
1385394 ATTAGTGGCACCTTTCTGCCAAAAATGCACCGTTAGGCATCTAA-C
1 ATTAATGGCACCTTTCTGCCAAAAA-GCACAGTTAGGCATCTAATC
* *
1385439 ATTAATGGTACTTTTCTGCCCAAAAAGCACAGTTA-GCATCTAACTTGC
1 ATTAATGGCACCTTTCTG-CCAAAAAGCACAGTTAGGCATCTAA--T-C
*
1385487 ATTAATGGCACCTTTCTGCCAAAAAGCATAGTTAGGCAT
1 ATTAATGGCACCTTTCTGCCAAAAAGCACAGTTAGGCAT
1385526 TTAGTCTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
44 8 0.11
45 23 0.31
46 7 0.09
47 15 0.20
48 21 0.28
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (45 bp):
ATTAATGGCACCTTTCTGCCAAAAAGCACAGTTAGGCATCTAATC
Found at i:1385630 original size:82 final size:82
Alignment explanation
Indices: 1385475--1385692 Score: 310
Period size: 82 Copynumber: 2.6 Consensus size: 82
1385465 GCACAGTTAG
* * * * * * *
1385475 CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAAGCATAGTTAGGCATTTAGTCTTTTATCT
1 CATCTAACTGGCATTATTGGCACCTTTCTGCC-AAATGCACAGCTATGCATTTAGTCTTTAATCT
1385540 CAAAGGCATTTAACATTT
65 CAAAGGCATTTAACATTT
* * *
1385558 CATCTAACTGGTATTATTGGCACCTTTCTACCAAATGCACAGCCATGCATTTAGTCTTTAATCTC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTATGCATTTAGTCTTTAATCTC
*
1385623 AAAGGCATTTAACCTTT
66 AAAGGCATTTAACATTT
* *
1385640 CATCTAACTGGCATTATTGGCACTTTTTTGCCAAATGCACAGCTATGCATTTA
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTATGCATTTA
1385693 ATTTTTTGTT
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
82 91 0.76
83 28 0.24
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (82 bp):
CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTATGCATTTAGTCTTTAATCTC
AAAGGCATTTAACATTT
Found at i:1388781 original size:35 final size:35
Alignment explanation
Indices: 1388734--1388803 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1388724 TATATGCATG
*
1388734 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
*
1388769 GGGAACATATTCCCCCTAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
1388804 CTAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
Found at i:1388806 original size:20 final size:20
Alignment explanation
Indices: 1388741--1388806 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1388731 ATGGGGAACA
*
1388741 GATTCCCCCTGGGGGGTATC
1 GATTCCCCCTAGGGGGTATC
***
1388761 GATT-CCCC--GGGAACAT-
1 GATTCCCCCTAGGGGGTATC
1388777 -ATTCCCCCTAGGGGGTATC
1 GATTCCCCCTAGGGGGTATC
1388796 GATTCCCCCTA
1 GATTCCCCCTA
1388807 AATGAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
15 3 0.09
16 4 0.11
17 5 0.14
18 5 0.14
19 4 0.11
20 14 0.40
ACGTcount: A:0.17, C:0.33, G:0.26, T:0.24
Consensus pattern (20 bp):
GATTCCCCCTAGGGGGTATC
Found at i:1389196 original size:14 final size:15
Alignment explanation
Indices: 1389166--1389198 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1389156 TATACATGAT
*
1389166 TATATGCATATGTGA
1 TATATGCATATGAGA
1389181 TATATGC-TATGAGA
1 TATATGCATATGAGA
1389195 TATA
1 TATA
1389199 ACCAATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (15 bp):
TATATGCATATGAGA
Found at i:1401014 original size:21 final size:19
Alignment explanation
Indices: 1400971--1401015 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1400961 AATTGAAGAT
*
1400971 AAAAAATATAATTTTACCC
1 AAAAAATATAATTTTACCA
*
1400990 AAAAAATAATAACTTTTACGA
1 AAAAAAT-ATAA-TTTTACCA
1401011 AAAAA
1 AAAAA
1401016 CTACAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATATAATTTTACCA
Found at i:1408367 original size:16 final size:16
Alignment explanation
Indices: 1408346--1408385 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1408336 GATGGGAAAG
1408346 GGAAATGATAGATGAA
1 GGAAATGATAGATGAA
1408362 GGAAATGATAGATGAA
1 GGAAATGATAGATGAA
1408378 GGAAATGA
1 GGAAATGA
1408386 GAGCAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (16 bp):
GGAAATGATAGATGAA
Found at i:1412049 original size:20 final size:20
Alignment explanation
Indices: 1412017--1412054 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1412007 ACCAGCACAG
*
1412017 AGAAAAAACAGC-ATAAAAT
1 AGAAAAAAAAGCAATAAAAT
1412036 AGAAAAACAAAGCAATAAA
1 AGAAAAA-AAAGCAATAAA
1412055 TGGAGTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 4 0.25
21 5 0.31
ACGTcount: A:0.71, C:0.11, G:0.11, T:0.08
Consensus pattern (20 bp):
AGAAAAAAAAGCAATAAAAT
Found at i:1412416 original size:28 final size:28
Alignment explanation
Indices: 1412379--1412441 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1412369 CTTCAAGGTG
*
1412379 CAATTTGGTAACTAAAC-TATTTTTGGTC
1 CAATTAGGTAACTAAACAT-TTTTTGGTC
* *
1412407 CAATTAGGTACCTAAACATTTTTTGTTC
1 CAATTAGGTAACTAAACATTTTTTGGTC
1412435 CAATTAG
1 CAATTAG
1412442 ATACCTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (28 bp):
CAATTAGGTAACTAAACATTTTTTGGTC
Found at i:1412446 original size:28 final size:28
Alignment explanation
Indices: 1412390--1412452 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1412380 AATTTGGTAA
*
1412390 CTAAACTATTTTTGGTCCAATTAGGTAC
1 CTAAACTATTTTTGGTCCAATTAGATAC
*
1412418 CTAAAC-ATTTTTTGTTCCAATTAGATAC
1 CTAAACTA-TTTTTGGTCCAATTAGATAC
*
1412446 CTGAACT
1 CTAAACT
1412453 TGGCTTCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (28 bp):
CTAAACTATTTTTGGTCCAATTAGATAC
Found at i:1412656 original size:21 final size:21
Alignment explanation
Indices: 1412632--1412671 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1412622 CAGGTGAACC
*
1412632 GGTCCAGGAGGATTTGGAGTA
1 GGTCCAGGAGGAATTGGAGTA
1412653 GGTCCAGGAGGAATTGGAG
1 GGTCCAGGAGGAATTGGAG
1412672 CAGCCCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.45, T:0.20
Consensus pattern (21 bp):
GGTCCAGGAGGAATTGGAGTA
Found at i:1413747 original size:9 final size:9
Alignment explanation
Indices: 1413733--1413757 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1413723 AGCATAACAA
1413733 CTTCATCAT
1 CTTCATCAT
1413742 CTTCATCAT
1 CTTCATCAT
1413751 CTTCATC
1 CTTCATC
1413758 TATAAGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:1414359 original size:58 final size:59
Alignment explanation
Indices: 1414262--1414396 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 59
1414252 CTGTGATTAT
* **
1414262 CAAGAACAGACACATACGCAAACGAATAACTGCATACTTA-AAAA-AGGA-AAAAAAAA
1 CAAGAACAGACACATACGAAAACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAA
*
1414318 CAAGAACAGACACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAA
1 CAAGAACAGACACATACGAAA--ACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAA
*
1414379 CAAGAACAAACACATACG
1 CAAGAACAGACACATACG
1414397 CACGAATTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
56 20 0.29
58 18 0.26
59 4 0.06
60 2 0.03
61 25 0.36
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.12
Consensus pattern (59 bp):
CAAGAACAGACACATACGAAAACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAA
Found at i:1414886 original size:21 final size:21
Alignment explanation
Indices: 1414860--1414899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1414850 TATAATGTAA
* *
1414860 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
1414881 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
1414900 TAATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:1419957 original size:21 final size:21
Alignment explanation
Indices: 1419933--1419974 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1419923 AGGCTGAACC
*
1419933 GTCCAGGAGGATTTGGAGCAG
1 GTCCAGGAGGAATTGGAGCAG
1419954 GTCCAGGAGGAATTGGAGCAG
1 GTCCAGGAGGAATTGGAGCAG
1419975 CCCGAGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.43, T:0.17
Consensus pattern (21 bp):
GTCCAGGAGGAATTGGAGCAG
Found at i:1424403 original size:16 final size:16
Alignment explanation
Indices: 1424382--1424412 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1424372 TTCAAGATAG
*
1424382 AAATAATTAATAAAAC
1 AAATAATAAATAAAAC
1424398 AAATAATAAATAAAA
1 AAATAATAAATAAAA
1424413 AATAGATTTT
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:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAATAAATAAAAC
Found at i:1425732 original size:15 final size:15
Alignment explanation
Indices: 1425709--1425738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1425699 TTGAGATCTT
*
1425709 ACCCGCCCCACATCC
1 ACCCACCCCACATCC
1425724 ACCCACCCCACATCC
1 ACCCACCCCACATCC
1425739 GTCCGCCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.67, G:0.03, T:0.07
Consensus pattern (15 bp):
ACCCACCCCACATCC
Found at i:1431195 original size:13 final size:13
Alignment explanation
Indices: 1431177--1431208 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1431167 CGTATCGCAC
1431177 AAGGACCTACAGT
1 AAGGACCTACAGT
1431190 AAGGACCTACAGT
1 AAGGACCTACAGT
1431203 AAGGAC
1 AAGGAC
1431209 TTACCTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (13 bp):
AAGGACCTACAGT
Found at i:1432234 original size:21 final size:21
Alignment explanation
Indices: 1432185--1432227 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
1432175 GAGAATTCAA
*
1432185 TTTTATTTCATTTACGATTCT
1 TTTTATTTCATTTACAATTCT
1432206 TTTTATTT-ATTT-CAATTCT
1 TTTTATTTCATTTACAATTCT
1432225 TTT
1 TTT
1432228 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 4 0.19
21 8 0.38
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTTCATTTACAATTCT
Found at i:1446937 original size:21 final size:21
Alignment explanation
Indices: 1446881--1446940 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1446871 TATTTGGCAG
*
1446881 AGGGAATCGATACCCCC-ATA
1 AGGGAATCGATACCCCCTGTA
* *
1446901 AGGGAACCGATTCCCCCTGTA
1 AGGGAATCGATACCCCCTGTA
* *
1446922 GGGGAATAGATACCCCCTG
1 AGGGAATCGATACCCCCTG
1446941 GGGTTCTGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTGTA
Found at i:1449672 original size:20 final size:19
Alignment explanation
Indices: 1449643--1449681 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1449633 AATGCTCGGA
1449643 GGGAACCGATTCCCCCCAG
1 GGGAACCGATTCCCCCCAG
1449662 GGGATACCGATTCCCCCCAG
1 GGGA-ACCGATTCCCCCCAG
1449682 TTTAACGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:1450083 original size:14 final size:14
Alignment explanation
Indices: 1450061--1450094 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1450051 AAACAACCTA
*
1450061 CCTTATGAGGATTT
1 CCTTGTGAGGATTT
1450075 CCTTGTGAGGATTT
1 CCTTGTGAGGATTT
1450089 CCTTGT
1 CCTTGT
1450095 AAGTTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (14 bp):
CCTTGTGAGGATTT
Found at i:1453286 original size:85 final size:83
Alignment explanation
Indices: 1453126--1453424 Score: 409
Period size: 83 Copynumber: 3.6 Consensus size: 83
1453116 ATGGAATCTG
* * * * *
1453126 ACTCGACGGATTGATGACAGATAACTCTTCTCGCCTTTGAGTTATGCTGTAAATTTGATATGCCC
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCC-TTGAGCTATGCTGTAAATTTGATATGCCC
1453191 TTGAGCTGAATGTAATCAA
65 TTGAGCTGAATGTAATCAA
* * * *
1453210 ACTCGAAGGTTTTTATTAACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATGTGCC
1 ACTCGAAGG--TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCC
*
1453275 CTTGAGCTGAATGTAATCGA
64 CTTGAGCTGAATGTAATCAA
* * * * * * *
1453295 ACTCGAAGGTTTGTTGACATATAGCCCTTATTGCCTTGAGCTATACTATAAATTTGATATGTCCT
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCT
*
1453360 TGAGCTGAGTGTAATCAA
66 TGAGCTGAATGTAATCAA
1453378 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT
1453425 ATAATAGGCT
Statistics
Matches: 187, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
83 103 0.55
84 8 0.04
85 55 0.29
86 21 0.11
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (83 bp):
ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCT
TGAGCTGAATGTAATCAA
Found at i:1460408 original size:3 final size:3
Alignment explanation
Indices: 1460396--1460437 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1460386 TAAAGTGTTC
1460396 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1460438 AATGTCTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1460544 original size:15 final size:14
Alignment explanation
Indices: 1460526--1460599 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
1460516 GCAAACTAAA
1460526 AAAATAATAAAAAAT
1 AAAATAA-AAAAAAT
*
1460541 AAAAT-AAACAAAT
1 AAAATAAAAAAAAT
* *
1460554 AACATAAATAAAAT
1 AAAATAAAAAAAAT
**
1460568 AAACA-AAACCAAAT
1 AAA-ATAAAAAAAAT
1460582 AAAATAAAAAGAAAT
1 AAAATAAAAA-AAAT
1460597 AAA
1 AAA
1460600 CAAATAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
13 11 0.24
14 22 0.48
15 13 0.28
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:1460549 original size:28 final size:26
Alignment explanation
Indices: 1460534--1460599 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 26
1460524 AAAAAATAAT
*
1460534 AAAAAATAAAATAAACAAATAACATAA
1 AAAAAATAAAA-AAACAAATAAAATAA
*
1460561 ATAAAATAAACAAAACCAAATAAAATAA
1 AAAAAATAAA-AAAA-CAAATAAAATAA
1460589 AAAGAAATAAA
1 AAA-AAATAAA
1460600 CAAATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.36
28 14 0.42
29 7 0.21
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.14
Consensus pattern (26 bp):
AAAAAATAAAAAAACAAATAAAATAA
Found at i:1460564 original size:9 final size:9
Alignment explanation
Indices: 1460522--1460599 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
1460512 TAAAGCAAAC
1460522 TAAA-AAAA
1 TAAATAAAA
*
1460530 TAATAAAAAA
1 TAA-ATAAAA
1460540 TAAA-ATAAA
1 TAAATA-AAA
* *
1460549 CAAATAACA
1 TAAATAAAA
1460558 TAAATAAAA
1 TAAATAAAA
*
1460567 TAAACAAAA
1 TAAATAAAA
*
1460576 CCAAATAAAA
1 -TAAATAAAA
*
1460586 TAAAAAGAAA
1 TAAATA-AAA
1460596 TAAA
1 TAAA
1460600 CAAATAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.07
9 29 0.53
10 22 0.40
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (9 bp):
TAAATAAAA
Found at i:1460565 original size:22 final size:19
Alignment explanation
Indices: 1460537--1460589 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
1460527 AAATAATAAA
*
1460537 AAATAAAATAAACAAATAACAT
1 AAATAAAATAAAC-AA-AAC-C
1460559 AAATAAAATAAACAAAACC
1 AAATAAAATAAACAAAACC
1460578 AAATAAAATAAA
1 AAATAAAATAAA
1460590 AAGAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.40
20 3 0.10
21 2 0.07
22 13 0.43
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAATAAACAAAACC
Found at i:1460600 original size:51 final size:49
Alignment explanation
Indices: 1460501--1460614 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 49
1460491 AAAAAAACCA
*
1460501 AAATAACAAAATAAAGCAAACTAAAAAAATAATAAAAAATAAAATAAAC
1 AAATAACAAAATAAAACAAACTAAAAAAATAATAAAAAATAAAATAAAC
*
1460550 AAATAACATAAATAAAATAAAC-AAAACCAAATAA-AATAAAA-AGAAATAAAC
1 AAATAACA-AAATAAAACAAACTAAAA--AAATAATAA-AAAATA-AAATAAAC
*
1460601 AAATAA-AAAGTAAA
1 AAATAACAAAATAAA
1460615 TACCTGAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
49 18 0.32
50 15 0.26
51 24 0.42
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (49 bp):
AAATAACAAAATAAAACAAACTAAAAAAATAATAAAAAATAAAATAAAC
Found at i:1460818 original size:14 final size:13
Alignment explanation
Indices: 1460809--1460871 Score: 69
Period size: 14 Copynumber: 4.9 Consensus size: 13
1460799 GAAAAATAGT
1460809 AAAAATAAAAT-A
1 AAAAATAAAATAA
1460821 AAAAAT--AATAA
1 AAAAATAAAATAA
*
1460832 AAAAATAGAATAA
1 AAAAATAAAATAA
1460845 AGAAAATAAAATAA
1 A-AAAATAAAATAA
*
1460859 TAAAAATATAATA
1 -AAAAATAAAATA
1460872 TATAATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 3 0.07
11 7 0.16
12 6 0.14
13 6 0.14
14 21 0.48
15 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:1460843 original size:23 final size:22
Alignment explanation
Indices: 1460792--1460863 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
1460782 AAAAGGAAAC
* *
1460792 TAAAA-AAGAAAAATAGTAAAAA
1 TAAAATAAAAAAAATA-AAAAAA
1460814 TAAAATAAAAAATAATAAAAAAA
1 TAAAATAAAAAA-AATAAAAAAA
* * *
1460837 TAGAATAAAGAAAATAAAATAA
1 TAAAATAAAAAAAATAAAAAAA
1460859 TAAAA
1 TAAAA
1460864 ATATAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 18 0.43
23 20 0.48
24 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (22 bp):
TAAAATAAAAAAAATAAAAAAA
Found at i:1460851 original size:32 final size:30
Alignment explanation
Indices: 1460800--1460864 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
1460790 ACTAAAAAAG
*
1460800 AAAAATAGTAAAAATAAAATAAAAAATAATAA
1 AAAAATAGTAAAAAGAAAAT--AAAATAATAA
1460832 AAAAATAG-AATAAAGAAAATAAAATAATAA
1 AAAAATAGTAA-AAAGAAAATAAAATAATAA
1460862 AAA
1 AAA
1460865 TATAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 13 0.42
31 2 0.06
32 16 0.52
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAAATAGTAAAAAGAAAATAAAATAATAA
Found at i:1462762 original size:20 final size:20
Alignment explanation
Indices: 1462737--1462819 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 20
1462727 AAAGTGTTTT
*
1462737 ATAAATTAATAAAATAAAAA
1 ATAAAATAATAAAATAAAAA
1462757 AT-AAATAGATAAAAAATAAGAATA
1 ATAAAATA-AT--AAAATAA-AA-A
*
1462781 ATAAAATAA-ATAGATAAAAA
1 ATAAAATAATA-AAATAAAAA
1462801 ATAAAAATAATAAAATAAA
1 AT-AAAATAATAAAATAAA
1462820 TAAAATAGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
21 16 0.31
22 13 0.25
23 2 0.04
24 4 0.08
25 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
ATAAAATAATAAAATAAAAA
Found at i:1462770 original size:15 final size:14
Alignment explanation
Indices: 1462749--1462822 Score: 89
Period size: 15 Copynumber: 5.1 Consensus size: 14
1462739 AAATTAATAA
1462749 AATAAAAAATAAAT
1 AATAAAAAATAAAT
*
1462763 AGATAAAAAAT-AAG
1 A-ATAAAAAATAAAT
1462777 AATAATAAAATAAAT
1 AATAA-AAAATAAAT
1462792 AGATAAAAAATAAA-
1 A-ATAAAAAATAAAT
1462806 AATAATAAAATAAAT
1 AATAA-AAAATAAAT
1462821 AA
1 AA
1462823 AATAGAGGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
13 8 0.15
14 18 0.35
15 22 0.42
16 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AATAAAAAATAAAT
Found at i:1462792 original size:9 final size:9
Alignment explanation
Indices: 1462739--1462826 Score: 67
Period size: 9 Copynumber: 9.6 Consensus size: 9
1462729 AGTGTTTTAT
*
1462739 AAATTAATA
1 AAATAAATA
1462748 AAAT-AA-A
1 AAATAAATA
1462755 AAATAAATA
1 AAATAAATA
*
1462764 GATAAAAAATA
1 -A-AATAAATA
1462775 AGAAT-AATA
1 A-AATAAATA
1462784 AAATAAATA
1 AAATAAATA
*
1462793 GATAAAAAATA
1 -A-AATAAATA
1462804 AAA-ATAATA
1 AAATA-AATA
1462813 AAATAAATA
1 AAATAAATA
1462822 AAATA
1 AAATA
1462827 GAGGACCATG
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
7 5 0.08
8 8 0.12
9 32 0.48
10 7 0.11
11 14 0.21
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:1462792 original size:29 final size:28
Alignment explanation
Indices: 1462744--1462821 Score: 131
Period size: 29 Copynumber: 2.8 Consensus size: 28
1462734 TTTATAAATT
1462744 AATAAAATAA-AAAATAAATAGATAAAA
1 AATAAAATAATAAAATAAATAGATAAAA
1462771 AATAAGAATAATAAAATAAATAGATAAAA
1 AATAA-AATAATAAAATAAATAGATAAAA
1462800 AATAAAAATAATAAAATAAATA
1 AAT-AAAATAATAAAATAAATA
1462822 AAATAGAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 36 0.75
30 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.21
Consensus pattern (28 bp):
AATAAAATAATAAAATAAATAGATAAAA
Found at i:1463087 original size:25 final size:25
Alignment explanation
Indices: 1463000--1463080 Score: 153
Period size: 25 Copynumber: 3.2 Consensus size: 25
1462990 CGACTAAAAT
1463000 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
1463025 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
1463050 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
*
1463075 GAAATC
1 GTAATC
1463081 CAAACAATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (25 bp):
GTAATCATAACAAAATCTAAAGCTC
Found at i:1465140 original size:22 final size:22
Alignment explanation
Indices: 1465112--1465172 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
1465102 TTGGGAGCGT
*
1465112 AGGTGTATTGGTACACTATCAA
1 AGGTGTATCGGTACACTATCAA
1465134 AGGTGTATCGGTACACTATCAA
1 AGGTGTATCGGTACACTATCAA
1465156 AGGTGTATCGGTACACT
1 AGGTGTATCGGTACACT
1465173 CAAGTGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (22 bp):
AGGTGTATCGGTACACTATCAA
Found at i:1465699 original size:21 final size:21
Alignment explanation
Indices: 1465673--1465713 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1465663 TTTTTGAAAT
1465673 CAATTTCGAAAATTACTCCCC
1 CAATTTCGAAAATTACTCCCC
*
1465694 CAATTTTGAAAATTACTCCC
1 CAATTTCGAAAATTACTCCC
1465714 TCCCCTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (21 bp):
CAATTTCGAAAATTACTCCCC
Found at i:1465984 original size:2 final size:2
Alignment explanation
Indices: 1465977--1466088 Score: 224
Period size: 2 Copynumber: 56.0 Consensus size: 2
1465967 AACCATTCAA
1465977 AT AT AT AT AT 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
1466019 AT AT AT AT AT 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
1466061 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
1466089 CTAAACATCC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 110 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1467548 original size:12 final size:13
Alignment explanation
Indices: 1467531--1467563 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1467521 TGGGCAATAA
*
1467531 TTTGAAAACTAT-
1 TTTGAAAACAATG
1467543 TTTGAAAACAATG
1 TTTGAAAACAATG
1467556 TTTGAAAA
1 TTTGAAAA
1467564 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1467943 original size:21 final size:21
Alignment explanation
Indices: 1467892--1467949 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 21
1467882 GTTGAAGAAG
*
1467892 AGTGTATCAATACACATTCAA
1 AGTGTATCGATACACATTCAA
*
1467913 AGAATGTATCGATACACATTCAT
1 AG--TGTATCGATACACATTCAA
1467936 AGTGTATCGATACA
1 AGTGTATCGATACA
1467950 TAGCGAGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
23 19 0.58
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (21 bp):
AGTGTATCGATACACATTCAA
Found at i:1480292 original size:10 final size:10
Alignment explanation
Indices: 1480277--1480301 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1480267 CAACAAAAAC
1480277 AAAAATACAA
1 AAAAATACAA
1480287 AAAAATACAA
1 AAAAATACAA
1480297 AAAAA
1 AAAAA
1480302 GTGACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATACAA
Found at i:1480298 original size:18 final size:17
Alignment explanation
Indices: 1480266--1480299 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1480256 GCAACGTGCA
*
1480266 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
1480283 ACAAAAAAATACAAAAA
1 ACAAAAAAA-ACAAAAA
1480300 AAGTGACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:1481204 original size:26 final size:24
Alignment explanation
Indices: 1481167--1481216 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
1481157 AAGGTCAACT
*
1481167 AGAAAAAGAAAGTGTTTGCAAAAAGA
1 AGAAAAAGAAAGAG-TTG-AAAAAGA
1481193 AGAAGAAA-AAAGAGTTGAAAAAGA
1 AGAA-AAAGAAAGAGTTGAAAAAGA
1481217 CATTGAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 9 0.41
27 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.24, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAGAGTTGAAAAAGA
Found at i:1483720 original size:18 final size:17
Alignment explanation
Indices: 1483688--1483723 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1483678 ACGTGCAACA
*
1483688 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
1483705 ACAAAAAAATACAAAAAT
1 ACAAAAAAA-ACAAAAAT
1483723 A
1 A
1483724 AGTGACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.78, C:0.14, G:0.00, T:0.08
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:1484715 original size:21 final size:21
Alignment explanation
Indices: 1484691--1484740 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1484681 GAAAATTTGT
1484691 TTCCTACTAACCAATCTTTTC
1 TTCCTACTAACCAATCTTTTC
1484712 TTCCTACTAACCAATCTTTTC
1 TTCCTACTAACCAATCTTTTC
1484733 TTCCTACT
1 TTCCTACT
1484741 CATCCTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.34, G:0.00, T:0.44
Consensus pattern (21 bp):
TTCCTACTAACCAATCTTTTC
Found at i:1487139 original size:18 final size:17
Alignment explanation
Indices: 1487107--1487140 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1487097 ACGTGCAACA
*
1487107 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
1487124 ACAAAAAAATACAAAAA
1 ACAAAAAAA-ACAAAAA
1487141 GAAGTGACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:1488217 original size:26 final size:31
Alignment explanation
Indices: 1488187--1488259 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 31
1488177 ATTTATTAAT
*
1488187 TATATATTATATATTA-T-TAAAATAA-GAA
1 TATATATTATACATTATTATAAAATAATGAA
1488215 TATAATATTATACATTATTATAAAATAATTGAA
1 TAT-ATATTATACATTATTATAAAATAA-TGAA
1488248 TATATTATTATA
1 TATA-TATTATA
1488260 ATGTTAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 3 0.08
29 12 0.32
30 1 0.03
31 8 0.21
32 1 0.03
33 13 0.34
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (31 bp):
TATATATTATACATTATTATAAAATAATGAA
Found at i:1488222 original size:29 final size:28
Alignment explanation
Indices: 1488190--1488284 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
1488180 TATTAATTAT
1488190 ATATTATATATTATTAAAATAAGAATATA
1 ATATTATA-ATTATTAAAATAAGAATATA
1488219 ATATTATACATTATTATAAAATAATTGAATATA
1 ATATTATA-ATTA-T-TAAAATAA--GAATATA
* * * *
1488252 TTATTATAA-TGTTAAAA-AATAATATT
1 ATATTATAATTATTAAAATAAGAATATA
1488278 ATATTAT
1 ATATTAT
1488285 TACAATTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 11 0.20
28 2 0.04
29 17 0.30
30 2 0.04
31 9 0.16
32 1 0.02
33 14 0.25
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (28 bp):
ATATTATAATTATTAAAATAAGAATATA
Found at i:1488360 original size:19 final size:19
Alignment explanation
Indices: 1488324--1488361 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1488314 TTAATATTTG
*
1488324 TATTATATTCATATTAAAT
1 TATTATATTCATAGTAAAT
1488343 TATTATA-TCGATAGTAAAT
1 TATTATATTC-ATAGTAAAT
1488362 ACATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TATTATATTCATAGTAAAT
Found at i:1488628 original size:18 final size:19
Alignment explanation
Indices: 1488590--1488636 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
1488580 CCATAATATT
1488590 TTAATTAAAAATTAAATTAAA
1 TTAA-TAAAAATT-AATTAAA
1488611 TTAATAAAAATT-ATTAAA
1 TTAATAAAAATTAATTAAA
*
1488629 TTGATAAA
1 TTAATAAA
1488637 GATAAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
20 8 0.32
21 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAATAAAAATTAATTAAA
Found at i:1490620 original size:59 final size:60
Alignment explanation
Indices: 1490472--1490622 Score: 153
Period size: 59 Copynumber: 2.5 Consensus size: 60
1490462 TTTCTACAAA
* * * * ** *
1490472 GTACAGATCATGAAGTGCACCTTCGAG-GGTTCTGTCCGAGCTGGTGTCACGGTGGAAAG
1 GTACGGATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAG
* * * * *
1490531 GTACGGATCAAGAGGTGCGCCTCCGTGAGGTTCTGTCCGAGCTGACGCCACGTTGG-AAG
1 GTACGGATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAG
* * *
1490590 GTGCGGATCAAGAAGCGTGCCTTCGCGAGGTTC
1 GTACGGATCAAGAAGCGCGCCTTCGAGAGGTTC
1490623 CGTCATGATC
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 51 0.68
60 24 0.32
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.22
Consensus pattern (60 bp):
GTACGGATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAG
Found at i:1493466 original size:20 final size:21
Alignment explanation
Indices: 1493441--1493482 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1493431 TGGTCGTTTA
1493441 TAGCCG-TTGAGGATGATTTC
1 TAGCCGTTTGAGGATGATTTC
* *
1493461 TAGCCGTTTGGGGATGTTTTC
1 TAGCCGTTTGAGGATGATTTC
1493482 T
1 T
1493483 CTGCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (21 bp):
TAGCCGTTTGAGGATGATTTC
Found at i:1497962 original size:86 final size:86
Alignment explanation
Indices: 1497794--1497962 Score: 241
Period size: 86 Copynumber: 2.0 Consensus size: 86
1497784 CTACATATCA
* **
1497794 GACCGTACTAAAAGATACCTAGTGTGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGGCAC
1 GACCGTACTAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAAC
*
1497859 GACCTTATGTGTCATATTCGT
66 GACCTTACGTGTCATATTCGT
* * * *
1497880 GACCGTACTAAAGGATACCTAGTGCGGGTTAGTACTAAAGGATACCTAGTGTTGATGGTGGAAAT
1 GACCGTACTAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAAC
*
1497945 GACCTCT-CGTGTGATATT
66 GACCT-TACGTGTCATATT
1497963 GGTTTAGCAC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 72 0.99
87 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (86 bp):
GACCGTACTAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAAC
GACCTTACGTGTCATATTCGT
Found at i:1516704 original size:20 final size:20
Alignment explanation
Indices: 1516666--1516704 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1516656 AGATGAACTA
**
1516666 TGGCTTTGCAACAGGTTTCT
1 TGGCTTTGCAACAAATTTCT
*
1516686 TGGCTTTGTAACAAATTTC
1 TGGCTTTGCAACAAATTTC
1516705 CTTGATTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TGGCTTTGCAACAAATTTCT
Found at i:1522170 original size:25 final size:26
Alignment explanation
Indices: 1522133--1522181 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1522123 GTTAGGGTGA
*
1522133 TTTTTAGGTAAAAAATCCGCATATTT
1 TTTTTAGGTAAAAAAACCGCATATTT
* *
1522159 TTTTTTGG-AAAAAAAGCGCATAT
1 TTTTTAGGTAAAAAAACCGCATAT
1522182 AGCGAAGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (26 bp):
TTTTTAGGTAAAAAAACCGCATATTT
Found at i:1524408 original size:32 final size:32
Alignment explanation
Indices: 1524370--1524446 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
1524360 CGGGGCCACG
* *
1524370 GGGCCTACCTAAGAACAT-ATCTTAGGGTCGTA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGTA
*
1524402 GGGCCTACCTGAG-AATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGTA
**
1524433 TAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1524447 GTCACATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 23 0.62
32 12 0.32
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGTA
Found at i:1537217 original size:19 final size:21
Alignment explanation
Indices: 1537180--1537218 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1537170 AAAAGAAAAT
*
1537180 GTAGTCAACTTATTTCAACTG
1 GTAGTCAACTTATTCCAACTG
1537201 GTAGT-AAC-TATTCCAACT
1 GTAGTCAACTTATTCCAACT
1537219 ATCATCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (21 bp):
GTAGTCAACTTATTCCAACTG
Found at i:1541444 original size:32 final size:32
Alignment explanation
Indices: 1541408--1541553 Score: 107
Period size: 32 Copynumber: 4.6 Consensus size: 32
1541398 GTAACTGATG
* *
1541408 TGCATTATCTGAATGTGACACTAACACTACTA
1 TGCATTATCTGAATGCGACATTAACACTACTA
* * * * ** *
1541440 TGCATT-T-TGAATACGACATTGATATTGTTG
1 TGCATTATCTGAATGCGACATTAACACTACTA
** *
1541470 TATATTATCTGAATGGGACATTAACACTACTA
1 TGCATTATCTGAATGCGACATTAACACTACTA
* * * * * *
1541502 TGCATTATCTGAAAGCGAAAATGACACTATTG
1 TGCATTATCTGAATGCGACATTAACACTACTA
*
1541534 TGCATTATCTGGATGCGACA
1 TGCATTATCTGAATGCGACA
1541554 CACTGTTAGT
Statistics
Matches: 81, Mismatches: 31, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
30 18 0.22
31 2 0.02
32 61 0.75
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (32 bp):
TGCATTATCTGAATGCGACATTAACACTACTA
Found at i:1547494 original size:16 final size:16
Alignment explanation
Indices: 1547473--1547503 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1547463 ATTCTAAGCC
1547473 TCCACGAAATTACGTT
1 TCCACGAAATTACGTT
1547489 TCCACGAAATTACGT
1 TCCACGAAATTACGT
1547504 CTCGGCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
TCCACGAAATTACGTT
Found at i:1551735 original size:17 final size:17
Alignment explanation
Indices: 1551707--1551751 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
1551697 TAATCCATCT
1551707 ATATGTGT--CTCACTG
1 ATATGTGTGCCTCACTG
1551722 ATATGTGTGCCTCACTG
1 ATATGTGTGCCTCACTG
1551739 ATATGTGTGCCTC
1 ATATGTGTGCCTC
1551752 TAAATTCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.29
17 20 0.71
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGTGTGCCTCACTG
Found at i:1554826 original size:31 final size:30
Alignment explanation
Indices: 1554788--1555131 Score: 321
Period size: 31 Copynumber: 11.0 Consensus size: 30
1554778 GTCGAGGAAT
*
1554788 TACCTATGTCTTTTGGGACATATGGACAGTA
1 TACCTATGT-TTTCGGGACATATGGACAGTA
* * *
1554819 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTT-TTCGGGACATATGGACAGTA
*
1554850 TTACCTATGTCTTTCGGGACATATAGACAGTA
1 -TACCTATGT-TTTCGGGACATATGGACAGTA
* *
1554882 TACCTATGTTTTACGGAACATATGGACAGAA
1 TACCTATGTTTT-CGGGACATATGGACAGTA
1554913 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 -TACCTATGT-TTTCGGGACATATGGACAGTA
* * *
1554945 TACTTATGTTCTAT-GGAACATATGGACAGAA
1 TACCTATGTT-T-TCGGGACATATGGACAGTA
*
1554976 TTACCTATGTCTTTCGGGACATATGGATAGTA
1 -TACCTATGT-TTTCGGGACATATGGACAGTA
* * *
1555008 TACCTATGTTATACGGAACATATGGACAGAA
1 TACCTATGTT-TTCGGGACATATGGACAGTA
* * *
1555039 TTACCTATGTCTTTTGAGACATATGGACAATA
1 -TACCTATGT-TTTCGGGACATATGGACAGTA
** * *
1555071 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTT-TTCGGGACATATGGACAGTA
* * *
1555102 TACCTAGGTTTTTTGGGACCTATGGACAGT
1 TACCTATG-TTTTCGGGACATATGGACAGT
1555132 TGCCGAGGTT
Statistics
Matches: 256, Mismatches: 41, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
30 7 0.03
31 144 0.56
32 99 0.39
33 6 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (30 bp):
TACCTATGTTTTCGGGACATATGGACAGTA
Found at i:1554862 original size:63 final size:63
Alignment explanation
Indices: 1554784--1555131 Score: 545
Period size: 63 Copynumber: 5.5 Consensus size: 63
1554774 AAGAGTCGAG
*
1554784 GAATTACCTATGTCTTTTGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* *
1554847 GAATTACCTATGTCTTTCGGGACATATAGACAGTATACCTATGTTTTACGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* *
1554910 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACTTATGTTCTATGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* *
1554973 GAATTACCTATGTCTTTCGGGACATATGGATAGTATACCTATGTTATACGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* * * *
1555036 GAATTACCTATGTCTTTTGAGACATATGGACAATATACCTATGTTCTAAGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* * * * *
1555099 G-TTTACCTAGGTTTTTTGGGACCTATGGACAGT
1 GAATTACCTATGTCTTTCGGGACATATGGACAGT
1555132 TGCCGAGGTT
Statistics
Matches: 262, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
62 26 0.10
63 236 0.90
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (63 bp):
GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
Found at i:1555152 original size:30 final size:31
Alignment explanation
Indices: 1555091--1555152 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
1555081 CTAAGGAACA
* * *
1555091 TATGGACAGTTTACCTAGGTTTTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
1555122 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
1555152 T
1 T
1555153 CTAGATAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:1564821 original size:13 final size:13
Alignment explanation
Indices: 1564805--1564840 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1564795 TTCAGTTGTT
1564805 TGATTCATTTTCG
1 TGATTCATTTTCG
1564818 TGATTCATTTTCG
1 TGATTCATTTTCG
*
1564831 TGATTAATTT
1 TGATTCATTT
1564841 GTCGATGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (13 bp):
TGATTCATTTTCG
Found at i:1565821 original size:2 final size:2
Alignment explanation
Indices: 1565757--1565809 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1565747 ACGTAATCTC
1565757 AT AT AT AT AT 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
1565799 AT AT AT AT AT A
1 AT AT AT AT AT A
1565810 ATTAAAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1566643 original size:58 final size:58
Alignment explanation
Indices: 1566523--1566660 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 58
1566513 ATCAACCTTT
* * ** * **
1566523 AAACTTTAGAATATTCTAATTTCATCCAAACTATGACTCTTGTTTTAAATTAGTCATT
1 AAACTTTTGAATATTCTAATTTCATCCAAACTATGACCCTCATTCTAAATTAGTCACC
* *
1566581 AAACTTTTGAATATTCTAATTTCATCCTTAAACTTTGACCCTCATTCT-AATTGGTC-CC
1 AAACTTTTGAATATTCTAATTTCATCC--AAACTATGACCCTCATTCTAAATTAGTCACC
* *
1566639 AAACTTTTGAATCTTCCAATTT
1 AAACTTTTGAATATTCTAATTT
1566661 TGTCCCCTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 46 0.69
59 7 0.10
60 14 0.21
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.43
Consensus pattern (58 bp):
AAACTTTTGAATATTCTAATTTCATCCAAACTATGACCCTCATTCTAAATTAGTCACC
Found at i:1568122 original size:35 final size:35
Alignment explanation
Indices: 1568076--1568148 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
1568066 TTTAAATCTC
1568076 AACAAATCAATGTATATTAAATAAGAAAATATATA
1 AACAAATCAATGTATATTAAATAAGAAAATATATA
1568111 AACAAATCAATGTATATTAAATAAGAAAATATATA
1 AACAAATCAATGTATATTAAATAAGAAAATATATA
1568146 AAC
1 AAC
1568149 TTCAATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.27
Consensus pattern (35 bp):
AACAAATCAATGTATATTAAATAAGAAAATATATA
Found at i:1568145 original size:19 final size:19
Alignment explanation
Indices: 1568088--1568145 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
1568078 CAAATCAATG
1568088 TATATTAAATAAGAAAATA
1 TATATTAAATAAGAAAATA
** *
1568107 TATA--AACA-AA-TCAATG
1 TATATTAA-ATAAGAAAATA
1568123 TATATTAAATAAGAAAATA
1 TATATTAAATAAGAAAATA
1568142 TATA
1 TATA
1568146 AACTTCAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
16 7 0.25
17 5 0.18
18 5 0.18
19 11 0.39
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (19 bp):
TATATTAAATAAGAAAATA
Found at i:1568828 original size:9 final size:9
Alignment explanation
Indices: 1568816--1568870 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
1568806 CATAATTTCC
1568816 AATATTTTT
1 AATATTTTT
1568825 AATATTTTCTT
1 AATA-TTT-TT
*
1568836 AATTTTTTT
1 AATATTTTT
*
1568845 AATA-TTAT
1 AATATTTTT
1568853 AATATTTTT
1 AATATTTTT
1568862 --TATTTTT
1 AATATTTTT
1568869 AA
1 AA
1568871 AATTGTACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 12 0.32
10 6 0.16
11 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:1570433 original size:20 final size:21
Alignment explanation
Indices: 1570396--1570434 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1570386 CTTTCTTTAA
*
1570396 TGTAAATTAATCTTATATTTT
1 TGTAAATTAATCTAATATTTT
*
1570417 TGTAATTTAAT-TAATATT
1 TGTAAATTAATCTAATATT
1570435 ATTTAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
TGTAAATTAATCTAATATTTT
Found at i:1584284 original size:28 final size:28
Alignment explanation
Indices: 1584203--1584271 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
1584193 TCTATTTACA
*
1584203 TTATATCGTCAAGCCATTGTTTGAAACT
1 TTATGTCGTCAAGCCATTGTTTGAAACT
1584231 TTATGCTC-TCAAGCCATTGTTTGAAACT
1 TTATG-TCGTCAAGCCATTGTTTGAAACT
1584259 TTATGTCGTCAAG
1 TTATGTCGTCAAG
1584272 TCAATGCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 2 0.05
28 34 0.89
29 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (28 bp):
TTATGTCGTCAAGCCATTGTTTGAAACT
Found at i:1590306 original size:190 final size:192
Alignment explanation
Indices: 1590029--1590415 Score: 597
Period size: 191 Copynumber: 2.0 Consensus size: 192
1590019 TGTTTTAATT
1590029 TTCCCTTTTTACCATTTTCCATTTAAATTTAATTTAATATAAATTATATTTCCTTTTTTTACTTG
1 TTCCCTTTTTACCATTTTCCATTTAAATTTAATTTAATATAAATTATATTTCCTTTTTTTACTTG
1590094 TTTTCATTCACGTGTCTTTTATTTTCTTCTCATTTTG-AATTT-T-A-GTAACTTCCTTCATTTT
66 TTTTCATTCACGTGTCTTTTATTTTCTTCTCATTTTGCAATTTATAACGTAACTTCCTTCATTTT
*
1590155 CTCTCACTTTTTCCCAAACAATCTGATCAATTCTTTCTCTTTTTCTTCTTGATTTCTAAATTAG
131 CTCTC-CTTTTTCCCAAACAA-CTGATCAATTCTTTCTCTTTCTCTTCTTGATTTCTAAATTAG
*
1590219 TTCCCTTTTTTATCATTTTCCATTTAAATTTAATTTAATATAAATTATATTTCC-TTTTTTACTT
1 TTCCC-TTTTTACCATTTTCCATTTAAATTTAATTTAATATAAATTATATTTCCTTTTTTTACTT
* *
1590283 GTTTTCATTCACGTG-CTTTTTATTTTCTTCTTATTTTGCATTTTAGTAACTTCCCGTAACTTCC
65 GTTTTCATTCACGTGTC-TTTTATTTTCTTCTCATTTTGCAATTTA-TAA-----CGTAACTTCC
*
1590347 TTCATTTTCTCTCGTTTTTCCCAAACAACTGATCAATTCTTTCTCTTTCTCTTCTTGATTTCTAA
123 TTCATTTTCTCTCCTTTTTCCCAAACAACTGATCAATTCTTTCTCTTTCTCTTCTTGATTTCTAA
1590412 ATTA
188 ATTA
1590416 ACTCATCTCA
Statistics
Matches: 180, Mismatches: 5, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
189 1 0.01
190 50 0.28
191 51 0.28
193 1 0.01
194 1 0.01
198 40 0.22
199 14 0.08
200 22 0.12
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (192 bp):
TTCCCTTTTTACCATTTTCCATTTAAATTTAATTTAATATAAATTATATTTCCTTTTTTTACTTG
TTTTCATTCACGTGTCTTTTATTTTCTTCTCATTTTGCAATTTATAACGTAACTTCCTTCATTTT
CTCTCCTTTTTCCCAAACAACTGATCAATTCTTTCTCTTTCTCTTCTTGATTTCTAAATTAG
Found at i:1592476 original size:18 final size:18
Alignment explanation
Indices: 1592390--1592476 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
1592380 ACTTAAAATT
** *
1592390 TGTCCCGAAGGATAACTT
1 TGTCCCGAAGGACCACTA
*
1592408 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
1592426 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1592444 TATCCGGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1592462 TGTCCTGAAGCACCA
1 TGTCCCGAAGGACCA
1592477 GTTATAACCC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1599404 original size:18 final size:18
Alignment explanation
Indices: 1599381--1599454 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
1599371 GCACTTAAAA
*
1599381 TTTGTCCCGAAGGACAAC
1 TTTGTCCCGAAGGACCAC
* *
1599399 TTTGTCCCAAAGAACCAC
1 TTTGTCCCGAAGGACCAC
*
1599417 TATGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
* *
1599435 TATGTCCAGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
1599453 TT
1 TT
1599455 ATAACCCTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:1610852 original size:2 final size:2
Alignment explanation
Indices: 1610839--1610886 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1610829 TGCACCTTTC
*
1610839 AT AT AG AT AT 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
1610881 AT AT AT
1 AT AT AT
1610887 TCTTTCCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1611191 original size:30 final size:30
Alignment explanation
Indices: 1611135--1611257 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1611125 GAAGGACCTA
* * *
1611135 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1611164 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1611194 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1611224 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1611254 TCCA
1 TCCA
1611258 TATGTTCCTT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 16 0.18
30 74 0.82
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1611306 original size:31 final size:30
Alignment explanation
Indices: 1611246--1611311 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1611236 AAAGATCCTC
**
1611246 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCAAAGAACATA
*
1611276 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCAAAGAACATA
1611307 GGTAA
1 GGTAA
1611312 AACCCTCGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 22 0.71
32 4 0.13
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCAAAGAACATA
Found at i:1612052 original size:21 final size:21
Alignment explanation
Indices: 1612028--1612072 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1612018 CTATGTTCGT
* * *
1612028 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1612049 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1612070 TTG
1 TTG
1612073 CCCAGAAATC
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:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1615875 original size:2 final size:2
Alignment explanation
Indices: 1615862--1615896 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1615852 TGCACCTTTC
*
1615862 AT AT AG 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 AT AT A
1615897 ATTATCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1616210 original size:30 final size:30
Alignment explanation
Indices: 1616151--1616276 Score: 209
Period size: 30 Copynumber: 4.2 Consensus size: 30
1616141 CCCGAAGGAC
* *
1616151 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1616180 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1616210 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1616240 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1616270 CTGTCCA
1 CTATCCA
1616277 TATGTTCCTT
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 19 0.21
30 72 0.79
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1616325 original size:31 final size:30
Alignment explanation
Indices: 1616265--1616330 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1616255 AAAGATCCTC
**
1616265 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCAAAGAACATA
*
1616295 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCAAAGAACATA
1616326 GGTAA
1 GGTAA
1616331 AACCCTCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 22 0.71
32 4 0.13
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCAAAGAACATA
Found at i:1617080 original size:21 final size:21
Alignment explanation
Indices: 1617056--1617100 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1617046 CTATGTTCGT
* * *
1617056 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1617077 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1617098 TTG
1 TTG
1617101 CCCAAAAATC
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:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1619184 original size:2 final size:2
Alignment explanation
Indices: 1619173--1619203 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1619163 CACTCTCAAA
1619173 AT AT -T 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
1619204 TTACTAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1628636 original size:20 final size:20
Alignment explanation
Indices: 1628596--1628632 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1628586 ACCTCGTGCA
*
1628596 TTTGCATTTGCATTCTTATT
1 TTTGCATTTGCATTATTATT
1628616 TTTGCATTTGC-TTATTA
1 TTTGCATTTGCATTATTA
1628633 ATTTATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (20 bp):
TTTGCATTTGCATTATTATT
Done.