Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 23
Found at i:1751295 original size:19 final size:20
Alignment explanation
Indices: 1751256--1751305 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1751246 ATTATTAGTA
*
1751256 TATTATTATTTATTATTATTT
1 TATT-TTATTTACTATTATTT
1751277 TATTTTATTTACT-TTATTT
1 TATTTTATTTACTATTATTT
1751296 TATTTTATTT
1 TATTTTATTT
1751306 TTCTGGTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 16 0.57
20 8 0.29
21 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTTATTTACTATTATTT
Found at i:1752657 original size:30 final size:30
Alignment explanation
Indices: 1752617--1752689 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
1752607 TTTTATTTTA
* *
1752617 TTTGTTTTTATTTGTTT-TTCTATTTTTCTT
1 TTTGATTTTATTTGTTTATTCTATTTTTC-C
* *
1752647 TTTGATTTTATTATTTTTATTTTATTTTTCC
1 TTTGATTTTATT-TGTTTATTCTATTTTTCC
1752678 TTTGA-TTTATTT
1 TTTGATTTTATTT
1752690 ATTATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 1 0.03
30 17 0.46
31 9 0.24
32 10 0.27
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (30 bp):
TTTGATTTTATTTGTTTATTCTATTTTTCC
Found at i:1756952 original size:17 final size:17
Alignment explanation
Indices: 1756930--1756963 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1756920 TGTGAGCTTG
1756930 AGATGCAACCCCTCAGT
1 AGATGCAACCCCTCAGT
1756947 AGATGCAACCCCTCAGT
1 AGATGCAACCCCTCAGT
1756964 CGTACTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (17 bp):
AGATGCAACCCCTCAGT
Found at i:1765333 original size:17 final size:17
Alignment explanation
Indices: 1765313--1765355 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1765303 ACTACTTCCC
1765313 TAAATGAACTAG-ATGCT
1 TAAATGAACT-GCATGCT
1765330 TAAATGCAA-TGCATGCT
1 TAAATG-AACTGCATGCT
1765347 TAAATGAAC
1 TAAATGAAC
1765356 AACATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.13
17 18 0.78
18 2 0.09
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (17 bp):
TAAATGAACTGCATGCT
Found at i:1769951 original size:17 final size:16
Alignment explanation
Indices: 1769912--1769975 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 16
1769902 GCTAATTTAT
*
1769912 TCAATGAACTAGTTAAA
1 TCAATGAACTAATT-AA
*
1769929 TGAATGAACTAATGTAA
1 TCAATGAACTAAT-TAA
*
1769946 TCAATGAACTTAACTTTAT
1 TCAATGAAC-TAA--TTAA
1769965 TCAATGAACTA
1 TCAATGAACTA
1769976 GATGCATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 21 0.54
18 6 0.15
19 11 0.28
20 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (16 bp):
TCAATGAACTAATTAA
Found at i:1771296 original size:12 final size:12
Alignment explanation
Indices: 1771279--1771317 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1771269 TGTCACTAAG
1771279 TACCTAGCTAGC
1 TACCTAGCTAGC
1771291 TACCTA--TA-C
1 TACCTAGCTAGC
1771300 TACCTAGCTAGC
1 TACCTAGCTAGC
1771312 TACCTA
1 TACCTA
1771318 ACCTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 2 0.08
12 13 0.54
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.28
Consensus pattern (12 bp):
TACCTAGCTAGC
Found at i:1771305 original size:21 final size:21
Alignment explanation
Indices: 1771279--1771326 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1771269 TGTCACTAAG
1771279 TACCTAGCTAGCTACCTATA-C
1 TACCTAGCTAGCTACCTA-ACC
1771300 TACCTAGCTAGCTACCTAACC
1 TACCTAGCTAGCTACCTAACC
1771321 TACCTA
1 TACCTA
1771327 TGCATCCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.27
Consensus pattern (21 bp):
TACCTAGCTAGCTACCTAACC
Found at i:1775658 original size:16 final size:15
Alignment explanation
Indices: 1775637--1775717 Score: 51
Period size: 16 Copynumber: 5.4 Consensus size: 15
1775627 TGTAAGTGCA
1775637 ATACATGCATGACATT
1 ATACATGCATG-CATT
* **
1775653 ATACATGGATGTTTT
1 ATACATGCATGCATT
*
1775668 ATACAT-AAGTGCA--
1 ATACATGCA-TGCATT
1775681 ATACATGCATGACATT
1 ATACATGCATG-CATT
* **
1775697 ATACATGGATGTTTT
1 ATACATGCATGCATT
1775712 ATACAT
1 ATACAT
1775718 CATCAGGAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
13 8 0.16
14 4 0.08
15 18 0.36
16 20 0.40
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (15 bp):
ATACATGCATGCATT
Found at i:1775692 original size:44 final size:44
Alignment explanation
Indices: 1775629--1775717 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1775619 AGTGTCAATG
1775629 TAAGTGCAATACATGCATGACATTATACATGGATGTTTTATACA
1 TAAGTGCAATACATGCATGACATTATACATGGATGTTTTATACA
1775673 TAAGTGCAATACATGCATGACATTATACATGGATGTTTTATACA
1 TAAGTGCAATACATGCATGACATTATACATGGATGTTTTATACA
1775717 T
1 T
1775718 CATCAGGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (44 bp):
TAAGTGCAATACATGCATGACATTATACATGGATGTTTTATACA
Found at i:1783970 original size:2 final size:2
Alignment explanation
Indices: 1783963--1784019 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1783953 TGAGTTTTAC
1783963 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
1784005 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1784020 GTAATGAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1793659 original size:2 final size:2
Alignment explanation
Indices: 1793652--1793752 Score: 63
Period size: 2 Copynumber: 54.0 Consensus size: 2
1793642 TCGGGCCGGG
* * * *
1793652 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
1793692 TA T- TA -A TT TA AA T- TA AA T- TA AA TT TA T- TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1793729 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1793753 ATTATTTTTA
Statistics
Matches: 72, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
1 7 0.10
2 65 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1793726 original size:33 final size:38
Alignment explanation
Indices: 1793659--1793727 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1793649 GGGTATATAT
*
1793659 ATTTAAATTAAATATATAAATATTATATATATATATTA
1 ATTTAAATTAAATATATAAATATTATATAAATATATTA
1793697 ATTTAAATT-AA-AT-TAAAT-TTAT-TAAATATAT
1 ATTTAAATTAAATATATAAATATTATATAAATATAT
1793728 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 8 0.27
34 4 0.13
35 5 0.17
36 2 0.07
37 2 0.07
38 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATTTAAATTAAATATATAAATATTATATAAATATATTA
Found at i:1796234 original size:31 final size:31
Alignment explanation
Indices: 1796160--1796221 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1796150 CAGTTATGTC
* *
1796160 AGGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGACCATATTGCAAACGGACTAAATATTG
1796191 AGGGACCATATTGCAAACGGACTAAATATTG
1 AGGGACCATATTGCAAACGGACTAAATATTG
1796222 GGTGATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACCATATTGCAAACGGACTAAATATTG
Found at i:1798088 original size:31 final size:31
Alignment explanation
Indices: 1798011--1798088 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1798001 CTTTTAAAAC
* *
1798011 TTGCAATATAATCCCCCAACATTTAGTCCGT
1 TTGCAATATAGTCCCTCAACATTTAGTCCGT
* *
1798042 TTGCAATATGGTCCCTCAACATTTAGTCCTT
1 TTGCAATATAGTCCCTCAACATTTAGTCCGT
*
1798073 TTTCAATATAGTCCCT
1 TTGCAATATAGTCCCT
1798089 GACATAACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (31 bp):
TTGCAATATAGTCCCTCAACATTTAGTCCGT
Found at i:1802704 original size:41 final size:41
Alignment explanation
Indices: 1802658--1802830 Score: 220
Period size: 41 Copynumber: 4.2 Consensus size: 41
1802648 TTATATTTGC
*
1802658 TACATACTTTGCTCAGCTTATCCATGAGACACATGCATGCA
1 TACATACTTGGCTCAGCTTATCCATGAGACACATGCATGCA
* * * *
1802699 TACATACTTTGCTTAGCATATCCATGAGACACATGCTTGCA
1 TACATACTTGGCTCAGCTTATCCATGAGACACATGCATGCA
* * * *
1802740 TACATACTAGGCTCAGCTTATCCAAGAGACACATGAATGCG
1 TACATACTTGGCTCAGCTTATCCATGAGACACATGCATGCA
* *
1802781 TACTTTGCTCTGGCTCAGCTTATCCATGAGACACATGCATGCA
1 TAC-ATACT-TGGCTCAGCTTATCCATGAGACACATGCATGCA
*
1802824 AACATAC
1 TACATAC
1802831 ATTCCTAAGC
Statistics
Matches: 110, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
41 74 0.67
42 5 0.05
43 31 0.28
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (41 bp):
TACATACTTGGCTCAGCTTATCCATGAGACACATGCATGCA
Found at i:1804733 original size:2 final size:2
Alignment explanation
Indices: 1804699--1804752 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
1804689 AATTAAAATT
* * *
1804699 TA TA TA AA TA TA AA TA TA -A TT TA CTA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
1804740 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1804753 TAAAAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1805008 original size:108 final size:108
Alignment explanation
Indices: 1804819--1805031 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
1804809 ATCTTAAGGT
* * * *
1804819 GGCGTTTGGTTGGATGGAATCTCTTAGAATTTGGGGGAATTGAAATCCAATTTCATCAATTTCCC
1 GGCGTTTGGTTGCATGGAATCTCTTAGAATTAGGGGGAATTGAAATCCAATTCCACCAATTTCCC
*
1804884 ATGTTTGATTCAAGTTTTCCAAGGGAATTGGAATCCCTCAGAC
66 ATGTTTGATTCAAGTTTTCCAAGAGAATTGGAATCCCTCAGAC
* * *
1804927 GGCGTTTGGTTCGCAT-GAATCTCTTGGAATTAGGGGGAATTGGAATCCAATTCCACCACTTTCC
1 GGCGTTTGGTT-GCATGGAATCTCTTAGAATTAGGGGGAATTGAAATCCAATTCCACCAATTTCC
* *
1804991 CATGTTTGGTTCAAGTTTTCCAAGAGAATTTGAATCCCTCA
65 CATGTTTGATTCAAGTTTTCCAAGAGAATTGGAATCCCTCA
1805032 TGGCTTCAAC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 91 0.97
109 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (108 bp):
GGCGTTTGGTTGCATGGAATCTCTTAGAATTAGGGGGAATTGAAATCCAATTCCACCAATTTCCC
ATGTTTGATTCAAGTTTTCCAAGAGAATTGGAATCCCTCAGAC
Found at i:1805617 original size:250 final size:249
Alignment explanation
Indices: 1805171--1805729 Score: 765
Period size: 250 Copynumber: 2.2 Consensus size: 249
1805161 TGAATAAAAA
*
1805171 TTTTTTATTATTT-GGGTCGGGTAGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACT
1 TTTTTTATTATTTCGGGTC-GGTCGGGTTTCTAATTCATATA-T----TCGGGTC-GGTGAAACT
*
1805235 TTATTTTGGTCGGGTCGGGTCCGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTT
59 TTATTTT-GTC-GGTCAGGTCCGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTT
*
1805300 AGGGTGAAAAATACCCAACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACA
122 AGGGTGAAAAATACCCAACCCGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACA
1805365 ATAATACCACTCTATATATA-AT-TTTTTCAATT-AAGTCACTT-CTTTTATTGAATAAAAAT-A
187 ATAATACCACTCTATATATATATATTTTT--ATTCAAGTCA-TTGCTTTTATTGAATAAAAATAA
1805425 T
249 T
*
1805426 TTTTTTATTATTTCGGGTCAGTCGGGTTTCTAATTCATATATTCGGGTCGGTGAAACTTTATTTT
1 TTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTCGGTGAAACTTTATTTT
* ** * *
1805491 -T-GGTTAGGTTGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTTGAGTTCGGGTTTAGTG
66 GTCGGTCAGGTCCGTTTTTTTAAGTGTGATATTCGGGTC-----GGGTCGAGTTCGGGTTTAGGG
* * * *
1805554 TGAAATATACCCGACCCGAAAATATATATAATTTTACATTATATATTTATGAATAGTTACAATAA
126 TGAAAAATACCCAACCCGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAATAA
* * *
1805619 TACCCCTCTATATATATATATTTTTTTTCAAGTCATTGTTTTTATTGAATAAAAATAAT
191 TACCACTCTATATATATATATTTTTATTCAAGTCATTGCTTTTATTGAATAAAAATAAT
1805678 TTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTCGGT
1 TTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTCGGT
1805730 CGGGTGAAAC
Statistics
Matches: 276, Mismatches: 17, Indels: 25
0.87 0.05 0.08
Matches are distributed among these distances:
245 32 0.12
247 1 0.00
249 16 0.06
250 105 0.38
251 25 0.09
252 58 0.21
254 1 0.00
255 33 0.12
256 5 0.02
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (249 bp):
TTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTCGGTGAAACTTTATTTT
GTCGGTCAGGTCCGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAA
AATACCCAACCCGAAAATATATATAATTTTACATTATATATTTAGGAATAATTACAATAATACCA
CTCTATATATATATATTTTTATTCAAGTCATTGCTTTTATTGAATAAAAATAAT
Found at i:1806154 original size:18 final size:17
Alignment explanation
Indices: 1806111--1806156 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1806101 CATTAAATTG
* *
1806111 GATTCCAATTCTTGACG
1 GATTCCAATTCTTCACA
*
1806128 GATTTCAATTCTTTCACA
1 GATTCCAATTC-TTCACA
1806146 GATTCCAATTC
1 GATTCCAATTC
1806157 CCTCATAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (17 bp):
GATTCCAATTCTTCACA
Found at i:1806658 original size:36 final size:37
Alignment explanation
Indices: 1806618--1806702 Score: 138
Period size: 36 Copynumber: 2.3 Consensus size: 37
1806608 ATTCATATAT
1806618 TCGGGTCGGGTTTTTTAAGTGTGATATTC-GGTCGGA
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGA
*
1806654 TCGGGTCGGG-TTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGA
1806690 TCGGGTTCGGGTT
1 TCGGG-TCGGGTT
1806703 AGGGTGAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 18 0.40
36 21 0.47
37 5 0.11
38 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.40, T:0.38
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGA
Found at i:1807279 original size:18 final size:18
Alignment explanation
Indices: 1807242--1807288 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1807232 TATGAAATTG
* *
1807242 GATTCCAATT-CTTGACA
1 GATTTCAATTCCTTCACA
1807259 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
1807277 GATTTCAATTCC
1 GATTTCAATTCC
1807289 CACATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:1816805 original size:21 final size:21
Alignment explanation
Indices: 1816774--1816848 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
1816764 GTTTCCAGAT
* *
1816774 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1816795 TCGCATTGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1816816 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1816837 TCGCAATGCGAA
1 TCGCAATGCGAA
1816849 TATGTAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1817040 original size:6 final size:6
Alignment explanation
Indices: 1817029--1817059 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1817019 ACACGTATTA
1817029 CACGAC CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
1817060 CGAGACGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:1822161 original size:17 final size:16
Alignment explanation
Indices: 1822139--1822175 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1822129 TATAAGCATC
1822139 CAAATTCAAACAATCCA
1 CAAATTCAAAC-ATCCA
1822156 CAAATTCAAACATCCA
1 CAAATTCAAACATCCA
1822172 -AAAT
1 CAAAT
1822176 GTTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAATTCAAACATCCA
Found at i:1824908 original size:22 final size:22
Alignment explanation
Indices: 1824883--1824926 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1824873 CACCACAGCT
*
1824883 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
* *
1824905 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1824927 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:1825163 original size:148 final size:149
Alignment explanation
Indices: 1824905--1825207 Score: 599
Period size: 148 Copynumber: 2.0 Consensus size: 149
1824895 CCGAAGTGCC
1824905 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1824970 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1825035 CATATGTCCCGAAG-ACCG
131 CATATGTCCCGAAGAACCG
1825053 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1825118 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1825183 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1825202 CGTAGA
1 CGTAGA
1825208 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 144 0.94
149 10 0.06
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:1825842 original size:2 final size:2
Alignment explanation
Indices: 1825835--1825907 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1825825 TATCTATGTG
1825835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1825877 TA TA 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 TA TA T
1825908 CCTCAAGATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1826159 original size:18 final size:18
Alignment explanation
Indices: 1826138--1826172 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1826128 TCCCATCTAG
1826138 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1826156 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1826173 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1826776 original size:21 final size:21
Alignment explanation
Indices: 1826752--1826796 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1826742 TTCTTGTTCG
* *
1826752 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1826773 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1826794 TTG
1 TTG
1826797 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1829790 original size:22 final size:21
Alignment explanation
Indices: 1829748--1829787 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1829738 AAGACTATTT
1829748 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
1829769 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
1829788 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:1831107 original size:20 final size:22
Alignment explanation
Indices: 1831082--1831127 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1831072 GGTGGAAGCT
1831082 TTTGCAAA-AAAA-TGAAAATA
1 TTTGCAAAGAAAATTGAAAATA
1831102 TTTGCAAAGAAAATTGAAAATA
1 TTTGCAAAGAAAATTGAAAATA
1831124 TTTG
1 TTTG
1831128 AACAACTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
22 12 0.50
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (22 bp):
TTTGCAAAGAAAATTGAAAATA
Found at i:1833864 original size:13 final size:13
Alignment explanation
Indices: 1833848--1833910 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
1833838 GACTTATTAT
1833848 ATAAAATTATTTA
1 ATAAAATTATTTA
1833861 ATAAAATTATTTAA
1 ATAAAATTATTT-A
* *
1833875 ATGTAAATTATATA
1 AT-AAAATTATTTA
* *
1833889 A-AACATGA-TTA
1 ATAAAATTATTTA
1833900 ATAAAATTATT
1 ATAAAATTATT
1833911 GGCATTGAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 3 0.08
12 9 0.24
13 13 0.34
14 5 0.13
15 8 0.21
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1833970 original size:23 final size:24
Alignment explanation
Indices: 1833930--1833983 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1833920 CAATGATTAA
1833930 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
*
1833954 CTGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
1833977 ATGTAAA
1 ATGTAAA
1833984 GAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:1837332 original size:19 final size:17
Alignment explanation
Indices: 1837292--1837335 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1837282 ATCAGCTATG
*
1837292 CAAACAAACAATTATAA
1 CAAACAAACAATTAAAA
1837309 CAAACAAACAACATTAAAA
1 CAAACAAAC-A-ATTAAAA
*
1837328 TAAACAAA
1 CAAACAAA
1837336 ATGAATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
19 13 0.57
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAACAAACAATTAAAA
Found at i:1838395 original size:6 final size:6
Alignment explanation
Indices: 1838384--1838444 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
1838374 ATCATTTATA
*
1838384 ATTAAT ATTAAT A-TAA- ATTATAG ATT-AT AATTAAT ATTAAT A-T-A-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT
1838428 ATTAAT ATTAAT ATTAA
1 ATTAAT ATTAAT ATTAA
1838445 CTTATATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
3 1 0.02
4 3 0.07
5 8 0.17
6 29 0.63
7 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (6 bp):
ATTAAT
Found at i:1838396 original size:29 final size:28
Alignment explanation
Indices: 1838362--1838538 Score: 126
Period size: 29 Copynumber: 5.8 Consensus size: 28
1838352 CTTAATAGAG
1838362 TTAATATAAATAATCATTTATAATTAATA
1 TTAATATAAATAAT-ATTTATAATTAATA
* *
1838391 TTAATATAAATTATAGATTATAATTAATA
1 TTAATATAAATAATA-TTTATAATTAATA
*
1838420 TTAATATAATTAATATTAATATTAACTT-ATA
1 TTAATATAAATAATATT--TA-TAA-TTAATA
* *
1838451 TTATTATAATATAGTTTATAATTTGTAATTAATA
1 TTAATATAA-ATA----AT-ATTTATAATTAATA
1838485 TTAATATAAA-ATATAGTTTATAAAATTAATA
1 TTAATATAAATA-ATA-TTTAT--AATTAATA
1838516 TTAATATAAACT-ATATTTTATAA
1 TTAATATAAA-TAATA-TTTATAA
1838539 ATTATATAGT
Statistics
Matches: 120, Mismatches: 11, Indels: 34
0.73 0.07 0.21
Matches are distributed among these distances:
28 3 0.03
29 47 0.39
30 2 0.02
31 40 0.33
32 5 0.04
33 3 0.03
34 14 0.12
35 1 0.01
36 2 0.02
37 3 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAATATAAATAATATTTATAATTAATA
Found at i:1838410 original size:23 final size:22
Alignment explanation
Indices: 1838379--1838473 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
1838369 AAATAATCAT
1838379 TTATAATTAATATTAATATAAA
1 TTATAATTAATATTAATATAAA
*
1838401 TTATAGATT-ATAATTAATATTAA
1 TTATA-ATTAAT-ATTAATATAAA
*
1838424 -TATAATTAATATTAATATTAAC
1 TTATAATTAATATTAATA-TAAA
* **
1838446 TTAT-ATTATTA-TAATATAGT
1 TTATAATTAATATTAATATAAA
1838466 TTATAATT
1 TTATAATT
1838474 TGTAATTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.10
21 18 0.30
22 21 0.34
23 16 0.26
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATAATTAATATTAATATAAA
Found at i:1838512 original size:31 final size:31
Alignment explanation
Indices: 1838383--1838605 Score: 138
Period size: 31 Copynumber: 7.0 Consensus size: 31
1838373 AATCATTTAT
* *
1838383 AATTAATATTAATATAAATTATAGATTAT--
1 AATTAATATTAATATAAAATATAGTTTATAA
* *
1838412 AATTAATATTAATATAATTAATAT--TAATATTA
1 AATTAATATTAATATAA--AATATAGT-TTATAA
* *
1838444 ACTT-ATATT-AT-TATAATATAGTTTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
1838472 TTTGTAATTAATATTAATATAAAATATAGTTTATAA
1 -----AATTAATATTAATATAAAATATAGTTTATAA
* *
1838508 AATTAATATTAATATAAACTATATTTTAT-A
1 AATTAATATTAATATAAAATATAGTTTATAA
* * * *
1838538 AATTATATAGTAGAGTTTATAAACTATAGTTAATAT
1 AATTA-ATATTA-A---TATAAAATATAGTTTATAA
***
1838574 AATTAATATTAATATAGTTTATAGTTTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
1838605 A
1 A
1838606 CTATAATTAA
Statistics
Matches: 152, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
27 5 0.03
28 4 0.03
29 20 0.13
30 11 0.07
31 56 0.37
32 4 0.03
33 3 0.02
34 6 0.04
35 22 0.14
36 21 0.14
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAGTTTATAA
Found at i:1838754 original size:36 final size:35
Alignment explanation
Indices: 1838663--1838755 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 35
1838653 TAATGTGTTA
* *
1838663 ATATTAATACAAACTATACTTTATAAACTATCTACT
1 ATATTAATACAAA-TATAGTTTATAAACTATATACT
* *
1838699 ACATTAATACAAATTATAGTTTATAAACTATATATT
1 ATATTAATACAAA-TATAGTTTATAAACTATATACT
*
1838735 ATATTAATATAAATAATAGTT
1 ATATTAATACAAAT-ATAGTT
1838756 AAGATAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 1 0.02
36 48 0.98
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (35 bp):
ATATTAATACAAATATAGTTTATAAACTATATACT
Found at i:1838832 original size:21 final size:21
Alignment explanation
Indices: 1838808--1838847 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1838798 AAAGTATAGT
*
1838808 TTATAAATTATATACTACAGG
1 TTATAAACTATATACTACAGG
*
1838829 TTATAAACTATATAGTACA
1 TTATAAACTATATACTACA
1838848 CTAATATAAA
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:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
TTATAAACTATATACTACAGG
Found at i:1838960 original size:83 final size:80
Alignment explanation
Indices: 1838873--1839027 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 80
1838863 GTTTATAAAC
*
1838873 TATAGGTTACATATATATATATAGTT-TATATAAACAATATA-TAGATTGTATATATATATAA-T
1 TATAGGTTACATATA-A-ATAGA-TTGTATATAAAC-ATATACTAGA-TGT-TATATATATAATT
1838935 ACATATACTATAGGTTACATA
60 ACATATACTATAGGTTACATA
* * *
1838956 TATAGGTTACATATAAATAGATTGTATATATACATATACTATATGTTATATATATAATTTATATA
1 TATAGGTTACATATAAATAGATTGTATATAAACATATACTAGATGTTATATATATAA-TTACATA
1839021 TACTATA
65 TACTATA
1839028 CATAGTTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
79 11 0.17
80 10 0.16
81 27 0.42
82 1 0.02
83 15 0.23
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (80 bp):
TATAGGTTACATATAAATAGATTGTATATAAACATATACTAGATGTTATATATATAATTACATAT
ACTATAGGTTACATA
Found at i:1839027 original size:20 final size:20
Alignment explanation
Indices: 1839004--1839043 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1838994 CTATATGTTA
* *
1839004 TATATATAATTTATATATAC
1 TATACATAATTTATACATAC
*
1839024 TATACATAGTTTATACATAC
1 TATACATAATTTATACATAC
1839044 ATGTACTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
TATACATAATTTATACATAC
Found at i:1839264 original size:56 final size:56
Alignment explanation
Indices: 1839196--1839337 Score: 223
Period size: 56 Copynumber: 2.5 Consensus size: 56
1839186 CAACTGTGTC
* * * *
1839196 TATACATATATAGTTTGTATAAATTATATATAAATTATTGTTTATAGACTATAGGT
1 TATATATATATAGTTTATATAAATTATATATAAATTATTCTTTATACACTATAGGT
1839252 TATATATATATAGTTTATATAAATTATATATAAATTATTCTTTATACACTATAGGT
1 TATATATATATAGTTTATATAAATTATATATAAATTATTCTTTATACACTATAGGT
*
1839308 TACATATATATAGTTTATA-ATAATTATATA
1 TATATATATATAGTTTATATA-AATTATATA
1839338 GTTTATATAA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 1 0.01
56 79 0.99
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (56 bp):
TATATATATATAGTTTATATAAATTATATATAAATTATTCTTTATACACTATAGGT
Found at i:1839335 original size:20 final size:19
Alignment explanation
Indices: 1839311--1839450 Score: 82
Period size: 18 Copynumber: 7.4 Consensus size: 19
1839301 TATAGGTTAC
1839311 ATATATATAGTTTATA-ATA
1 ATATATATAGTTTATATA-A
1839330 AT-TATATAGTTTATATAA
1 ATATATATAGTTTATATAA
*
1839348 ACTATATATAG-TTA-ATAC
1 A-TATATATAGTTTATATAA
*
1839366 ATACATATA--TTATATTAA
1 ATATATATAGTTTATA-TAA
*
1839384 TATAAATTATA-TTTA-ATAA
1 -ATATA-TATAGTTTATATAA
* * *
1839403 A-CTATATACTTTATATAGTTT
1 ATATATATAGTTTATATA---A
1839424 ATATATATAGTTTATATAA
1 ATATATATAGTTTATATAA
1839443 ACTATATA
1 A-TATATA
1839451 GATTACATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 29
0.71 0.07 0.21
Matches are distributed among these distances:
16 7 0.07
17 13 0.14
18 25 0.26
19 15 0.16
20 18 0.19
21 4 0.04
22 14 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATATATAGTTTATATAA
Found at i:1839432 original size:13 final size:13
Alignment explanation
Indices: 1839414--1839614 Score: 141
Period size: 13 Copynumber: 14.1 Consensus size: 13
1839404 CTATATACTT
1839414 TATATAGTTTATA
1 TATATAGTTTATA
1839427 TATATAGTTTATATAAA
1 TATATAG-TT-TAT--A
* *
1839444 CTATATAGATTACA
1 -TATATAGTTTATA
1839458 TATATAGTTTATACA
1 TATATAGTTTAT--A
* *
1839473 TATGTAGCTTATA
1 TATATAGTTTATA
*
1839486 TATATAGATTATA
1 TATATAGTTTATA
1839499 TATATAGTTTATA
1 TATATAGTTTATA
*
1839512 TCTATATAGTTTATT
1 --TATATAGTTTATA
*
1839527 TATATAATTTATA
1 TATATAGTTTATA
*
1839540 TACATAGTTTATA
1 TATATAGTTTATA
*
1839553 CGTATGTAGTTTATATAAA
1 --TATATAG-TT-TAT--A
*
1839572 TTATATAGTTTATG
1 -TATATAGTTTATA
*
1839586 TATATAGTTCATACA
1 TATATAGTT--TATA
1839601 TATATAGTTTATA
1 TATATAGTTTATA
1839614 T
1 T
1839615 TTACATGTAT
Statistics
Matches: 149, Mismatches: 22, Indels: 34
0.73 0.11 0.17
Matches are distributed among these distances:
13 76 0.51
14 3 0.02
15 42 0.28
16 7 0.05
17 7 0.05
18 13 0.09
19 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:1839517 original size:28 final size:27
Alignment explanation
Indices: 1839443--1839613 Score: 123
Period size: 28 Copynumber: 6.0 Consensus size: 27
1839433 GTTTATATAA
* *
1839443 ACTATATAGATTACATATATAGTTTAT
1 ACTATATAGTTTATATATATAGTTTAT
* * *
1839470 ACATATGTAGCTTATATATATAGATTAT
1 AC-TATATAGTTTATATATATAGTTTAT
1839498 A-TATATAGTTTATATCTATATAGTTTAT
1 ACTATATAGTTTATA--TATATAGTTTAT
* * *
1839526 -TTATATAATTTATATACATAGTTTAT
1 ACTATATAGTTTATATATATAGTTTAT
*
1839552 ACGTATGTAGTTTATATAAATTATATAGTTTAT
1 AC-TATATAG-TT-TAT--A-TATATAGTTTAT
* *
1839585 -GTATATAGTTCATACATATATAGTTTAT
1 ACTATATAGTT--TATATATATAGTTTAT
1839613 A
1 A
1839614 TTTACATGTA
Statistics
Matches: 115, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
26 22 0.19
27 2 0.02
28 62 0.54
29 3 0.03
30 5 0.04
31 9 0.08
32 1 0.01
33 11 0.10
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (27 bp):
ACTATATAGTTTATATATATAGTTTAT
Found at i:1839748 original size:2 final size:2
Alignment explanation
Indices: 1839673--1839729 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1839663 CATAGATTAC
1839673 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
1839715 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1839730 ATCTATAGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1839847 original size:83 final size:83
Alignment explanation
Indices: 1839753--1840013 Score: 423
Period size: 83 Copynumber: 3.1 Consensus size: 83
1839743 ATATATCAGT
1839753 TATACATACATAAATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATATAGT
1 TATACATACATAAATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATATAGT
1839818 TTATACATAAATAGTTTA
66 TTATACATAAATAGTTTA
*
1839836 TATACATACATATATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATATAGT
1 TATACATACATAAATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATATAGT
1839901 TTATACATAAATAGTTTA
66 TTATACATAAATAGTTTA
* * * * *
1839919 TATACATACATATATATATATATTATATTAATATAAATTATAGTTTATAAACTATATATTTTTTA
1 TATACATAC--ATA-A-ATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATA
*
1839984 TAGTTTATACATATATAGTTTA
62 TAGTTTATACATAAATAGTTTA
1840006 TATACATA
1 TATACATA
1840014 GTTTATAAAT
Statistics
Matches: 166, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
83 91 0.55
85 3 0.02
87 72 0.43
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (83 bp):
TATACATACATAAATATACTATATTAATATAAATTATAATTTATAAACTATACACTTTATATAGT
TTATACATAAATAGTTTA
Found at i:1839851 original size:36 final size:36
Alignment explanation
Indices: 1839810--1839934 Score: 108
Period size: 40 Copynumber: 3.2 Consensus size: 36
1839800 CTATACACTT
1839810 TATATAGTTTATACATAAATAGTTTATATACATACA
1 TATATAGTTTATACATAAATAGTTTATATACATACA
* * *
1839846 TATATA-TACTATATTAATATAAATTATAATTTATAAACTATACA
1 TATATAGT--T-TA-T-ACAT-AA--ATAGTTTATATAC-ATACA
1839890 CTTTATATAGTTTATACATAAATAGTTTATATACATACA
1 ---TATATAGTTTATACATAAATAGTTTATATACATACA
1839929 TATATA
1 TATATA
1839935 TATATATTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
35 1 0.01
36 12 0.17
37 1 0.01
38 2 0.03
39 6 0.09
40 14 0.20
41 2 0.03
42 2 0.03
43 14 0.20
44 6 0.09
45 2 0.03
46 1 0.01
47 6 0.09
48 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATAGTTTATACATAAATAGTTTATATACATACA
Found at i:1840014 original size:13 final size:13
Alignment explanation
Indices: 1839982--1840114 Score: 78
Period size: 13 Copynumber: 10.2 Consensus size: 13
1839972 ATATATTTTT
1839982 TATAGTTTATACATA
1 TATAGTTTAT--ATA
1839997 TATAGTTTATATA
1 TATAGTTTATATA
* *
1840010 CATAGTTTATAAA
1 TATAGTTTATATA
*
1840023 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
1840038 CATAATTTATATA
1 TATAGTTTATATA
*
1840051 TATAGCTTATA-A
1 TATAGTTTATATA
1840063 TA-A--TTATATA
1 TATAGTTTATATA
* * *
1840073 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
*
1840087 TATAGTTTTTATA
1 TATAGTTTATATA
*
1840100 TATAGTTTTTATA
1 TATAGTTTATATA
1840113 TA
1 TA
1840115 AACTTATATT
Statistics
Matches: 94, Mismatches: 16, Indels: 18
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.05
10 1 0.01
11 2 0.02
12 4 0.04
13 55 0.59
14 6 0.06
15 21 0.22
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1840062 original size:26 final size:26
Alignment explanation
Indices: 1839994--1840062 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 26
1839984 TAGTTTATAC
* * *
1839994 ATATATAGTTTATATACATAGTTTAT
1 ATATATAGCTTATAAACATAATTTAT
* *
1840020 AAATATAGTTCATATAAACATAATTTAT
1 ATATATAG--CTTATAAACATAATTTAT
1840048 ATATATAGCTTATAA
1 ATATATAGCTTATAA
1840063 TAATTATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
26 13 0.38
28 21 0.62
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (26 bp):
ATATATAGCTTATAAACATAATTTAT
Found at i:1840073 original size:87 final size:82
Alignment explanation
Indices: 1839892--1840088 Score: 189
Period size: 87 Copynumber: 2.3 Consensus size: 82
1839882 ACTATACACT
* *
1839892 TTATATAGTTTATACATAAATAGTTTATATACATACATATATATATATATTATATTAATATAAAT
1 TTATATAGTTTATACATAAATAGTTTATATACATACATATATAAATATATTATATAAATAT-AAT
* *
1839957 TATAGTTTATAAACTATATATT
65 TATA---TATATACTATA-ATA
* * * * *
1839979 TTTTATAGTTTATACATATATAGTTTATATACATA-GTTTATAAATATAGTTCATATAAACATAA
1 TTATATAGTTTATACATAAATAGTTTATATACATACATATATAAATATA-TT-ATATAAATATAA
1840043 TTTATATATATAGCTTATAATAA
64 -TTATATATATA-C-TATAAT-A
*
1840066 TTATATAGTTTATAATATAAATA
1 TTATATAGTTTAT-ACATAAATA
1840089 TAGTTTTTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
85 5 0.05
86 13 0.14
87 53 0.58
88 20 0.22
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (82 bp):
TTATATAGTTTATACATAAATAGTTTATATACATACATATATAAATATATTATATAAATATAATT
ATATATATACTATAATA
Found at i:1840089 original size:18 final size:18
Alignment explanation
Indices: 1840045--1840103 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1840035 AAACATAATT
*
1840045 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
1840063 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
1840081 TATAAATATAGTTT-TTA
1 TATATATATAGTTTATAA
1840098 TATATA
1 TATATA
1840104 GTTTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 26 0.74
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:1840283 original size:11 final size:11
Alignment explanation
Indices: 1840266--1840301 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1840256 TAGTTTATTA
1840266 ATAAACTACAT
1 ATAAACTACAT
*
1840277 GTAAACTACAT
1 ATAAACTACAT
*
1840288 ATAAACTATAT
1 ATAAACTACAT
1840299 ATA
1 ATA
1840302 TTATATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:1840452 original size:16 final size:16
Alignment explanation
Indices: 1840431--1840480 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1840421 CTTTTGTGTT
1840431 TTTTAATTTATTTCAA
1 TTTTAATTTATTTCAA
* *
1840447 TTTTAAGTT-TTTCAC
1 TTTTAATTTATTTCAA
*
1840462 TTTTATATGTA-TTCAA
1 TTTTA-ATTTATTTCAA
1840478 TTT
1 TTT
1840481 AGTCTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTTAATTTATTTCAA
Found at i:1841389 original size:21 final size:21
Alignment explanation
Indices: 1841319--1841392 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
1841309 TATCAATTTT
* *
1841319 ATTATTATTTATATAATA-ATA
1 ATTATT-TTTATCTAAAATATA
*
1841340 ATTATTTTTAACTAAAATATA
1 ATTATTTTTATCTAAAATATA
1841361 ATTATTTTTATCTAAAATATTA
1 ATTATTTTTATCTAAAATA-TA
1841383 ATT-TTTTTAT
1 ATTATTTTTAT
1841393 TATTTCTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.17
21 34 0.72
22 5 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTTTTATCTAAAATATA
Found at i:1843613 original size:22 final size:23
Alignment explanation
Indices: 1843563--1843613 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1843553 GTACTCAACT
*
1843563 TATAATTGTATTTTAGTTGAAAA
1 TATAATTGTAATTTAGTTGAAAA
* *
1843586 TCTAATTGTAATTTA-TTTAAAA
1 TATAATTGTAATTTAGTTGAAAA
1843608 TATAAT
1 TATAAT
1843614 ATTAATTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (23 bp):
TATAATTGTAATTTAGTTGAAAA
Found at i:1844515 original size:21 final size:21
Alignment explanation
Indices: 1844476--1844515 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1844466 TTATAGTCAA
* *
1844476 GATGAAGATGGCCATAATAAG
1 GATGAAGATGGACACAATAAG
*
1844497 GATGAAGATGGATACAATA
1 GATGAAGATGGACACAATA
1844516 GTGAATCAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (21 bp):
GATGAAGATGGACACAATAAG
Found at i:1863991 original size:20 final size:20
Alignment explanation
Indices: 1863966--1864026 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1863956 TTTTTGTGCA
*
1863966 GAGGGAATCGATTCCCCCAT
1 GAGGGAACCGATTCCCCCAT
*
1863986 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-AT
*
1864007 AAAGGGGAACCGATTCCCCC
1 -GA-GGGAACCGATTCCCCC
1864027 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 1 0.03
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCAT
Found at i:1864035 original size:21 final size:21
Alignment explanation
Indices: 1863988--1864048 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1863978 TCCCCCATGA
*
1863988 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC--CAAAG
*
1864011 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCAAAG
* *
1864032 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
1864049 TGGGGTTCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCAAAG
Found at i:1868579 original size:22 final size:22
Alignment explanation
Indices: 1868509--1868579 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1868499 ACTTCAGTAT
1868509 CGATACTACTACACTATGGTAC
1 CGATACTACTACACTATGGTAC
* * *
1868531 CGATAC--CTTTCTCTCA--GTAT
1 CGATACTAC-TACACT-ATGGTAC
1868551 CGATACTACTACACTATGGTAC
1 CGATACTACTACACTATGGTAC
1868573 CGATACT
1 CGATACT
1868580 CCCTTTTGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 11 0.30
21 8 0.22
22 18 0.49
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (22 bp):
CGATACTACTACACTATGGTAC
Found at i:1875716 original size:15 final size:16
Alignment explanation
Indices: 1875696--1875725 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1875686 AAACATTTCT
1875696 TTCTCAAATT-TAAAA
1 TTCTCAAATTATAAAA
1875711 TTCTCAAATTATAAA
1 TTCTCAAATTATAAA
1875726 TTATTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (16 bp):
TTCTCAAATTATAAAA
Found at i:1876309 original size:127 final size:128
Alignment explanation
Indices: 1876081--1876339 Score: 421
Period size: 127 Copynumber: 2.0 Consensus size: 128
1876071 TGAAAATCCT
*
1876081 CAAGTTCTTAATCATGTATAGGCAATTTATGACAATTGAAAAGACCAACTTCATTGTGGTTACTT
1 CAAGTTCTTAATCATG-ATAGGCAATTTACGACAATTGAAAAGACCAACTTCATTGTGGTTACTT
* * *
1876146 GTGACAAGTTTTAACAAAATTCTCAGTCGTTCAACTCTCATCTCTTGCGTCATTCAATATCACA
65 GTGACAAGTTTTAACAAAATTCTCAATCGTTCAACTCTCATCTATTGCATCATTCAATATCACA
* * *
1876210 CAAGTTCTTAATCATG-TAGGCAGTTTACGACAATTGAAAAGATCAATTTCATTGTGGTTACTTG
1 CAAGTTCTTAATCATGATAGGCAATTTACGACAATTGAAAAGACCAACTTCATTGTGGTTACTTG
* *
1876274 TGACAAGTTTTACCAAAATTCTCAATCGTTCAACTCTCATCTATTGTATCATTCAATATCACA
66 TGACAAGTTTTAACAAAATTCTCAATCGTTCAACTCTCATCTATTGCATCATTCAATATCACA
1876337 CAA
1 CAA
1876340 TAGTTAAATG
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
127 105 0.87
129 16 0.13
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (128 bp):
CAAGTTCTTAATCATGATAGGCAATTTACGACAATTGAAAAGACCAACTTCATTGTGGTTACTTG
TGACAAGTTTTAACAAAATTCTCAATCGTTCAACTCTCATCTATTGCATCATTCAATATCACA
Found at i:1877629 original size:22 final size:23
Alignment explanation
Indices: 1877603--1877654 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
1877593 AATGAAAGTG
1877603 TTTTTCTAAGTTAAAGATTATTT
1 TTTTTCTAAGTTAAAGATTATTT
*
1877626 TTTTCTCATAAGTTAGAGATTATTT
1 TTTT-TC-TAAGTTAAAGATTATTT
1877651 TTTT
1 TTTT
1877655 CTCATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTCTAAGTTAAAGATTATTT
Found at i:1877640 original size:25 final size:25
Alignment explanation
Indices: 1877609--1877661 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1877599 AGTGTTTTTC
1877609 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
1877634 TAAGTTAGAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
1877659 TAA
1 TAA
1877662 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:1879487 original size:21 final size:20
Alignment explanation
Indices: 1879432--1879489 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1879422 ATATGCTCAC
1879432 TAATTTTTCAATTTGGCCATT
1 TAATTTTTCAA-TTGGCCATT
* * *
1879453 TAATATTTTAAATTGTCCTTT
1 TAAT-TTTTCAATTGGCCATT
1879474 TAATTTTTCGAATTGG
1 TAATTTTTC-AATTGG
1879490 TCATGCATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.13
21 20 0.67
22 6 0.20
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TAATTTTTCAATTGGCCATT
Found at i:1880479 original size:15 final size:15
Alignment explanation
Indices: 1880459--1880488 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1880449 AATTCAAAGC
*
1880459 TTTAAAACAAATTAG
1 TTTAAAAAAAATTAG
1880474 TTTAAAAAAAATTAG
1 TTTAAAAAAAATTAG
1880489 GTGTACTATT
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:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (15 bp):
TTTAAAAAAAATTAG
Found at i:1891601 original size:28 final size:28
Alignment explanation
Indices: 1891570--1891632 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
1891560 AGTTGATACA
*
1891570 ATATTTTAAAACAATAAATTTAAGATTTAT
1 ATATTTTAAAAC--TAAATTTAAGATATAT
* *
1891600 ATATTTTTAAACTAAATTTAATA-AT-T
1 ATATTTTAAAACTAAATTTAAGATATAT
1891626 ATATTTT
1 ATATTTT
1891633 TCATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.27
27 1 0.03
28 10 0.33
30 11 0.37
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (28 bp):
ATATTTTAAAACTAAATTTAAGATATAT
Found at i:1891733 original size:16 final size:18
Alignment explanation
Indices: 1891712--1891745 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1891702 ATTTCTTATT
1891712 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1891728 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1891746 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1895077 original size:132 final size:132
Alignment explanation
Indices: 1894840--1895103 Score: 528
Period size: 132 Copynumber: 2.0 Consensus size: 132
1894830 GCTTTGGAAG
1894840 TTCAGCCTCGGTATATCAGACACCTGAAGCATGGTATGTTAATTTTTCATTAGGTTCTAGTCAGA
1 TTCAGCCTCGGTATATCAGACACCTGAAGCATGGTATGTTAATTTTTCATTAGGTTCTAGTCAGA
1894905 GTTCATATAGTTTATGTAGTTCTGTATTTATGCCGTGTATATTCTGGATCAATTTGAAAGGATGA
66 GTTCATATAGTTTATGTAGTTCTGTATTTATGCCGTGTATATTCTGGATCAATTTGAAAGGATGA
1894970 TA
131 TA
1894972 TTCAGCCTCGGTATATCAGACACCTGAAGCATGGTATGTTAATTTTTCATTAGGTTCTAGTCAGA
1 TTCAGCCTCGGTATATCAGACACCTGAAGCATGGTATGTTAATTTTTCATTAGGTTCTAGTCAGA
1895037 GTTCATATAGTTTATGTAGTTCTGTATTTATGCCGTGTATATTCTGGATCAATTTGAAAGGATGA
66 GTTCATATAGTTTATGTAGTTCTGTATTTATGCCGTGTATATTCTGGATCAATTTGAAAGGATGA
1895102 TA
131 TA
1895104 CTTGCATAAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (132 bp):
TTCAGCCTCGGTATATCAGACACCTGAAGCATGGTATGTTAATTTTTCATTAGGTTCTAGTCAGA
GTTCATATAGTTTATGTAGTTCTGTATTTATGCCGTGTATATTCTGGATCAATTTGAAAGGATGA
TA
Found at i:1899558 original size:32 final size:32
Alignment explanation
Indices: 1899517--1899577 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1899507 AAAGATAAAT
*
1899517 TTATAATTTGAATCTTAAA-TATTATTTTATGA
1 TTATAATTTGAATATTAAATTATT-TTTTATGA
1899549 TTATAATTTGAATATTAAATTATTTTTTA
1 TTATAATTTGAATATTAAATTATTTTTTA
1899578 ATAATTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (32 bp):
TTATAATTTGAATATTAAATTATTTTTTATGA
Found at i:1899636 original size:17 final size:18
Alignment explanation
Indices: 1899614--1899649 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1899604 AAAATAAATA
1899614 TAAAAATA-TAAAGATTT
1 TAAAAATATTAAAGATTT
*
1899631 TAAAAATATTAAATATTT
1 TAAAAATATTAAAGATTT
1899649 T
1 T
1899650 TTTTATTAAA
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:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAAAATATTAAAGATTT
Found at i:1900775 original size:157 final size:155
Alignment explanation
Indices: 1900451--1901316 Score: 957
Period size: 157 Copynumber: 5.5 Consensus size: 155
1900441 CACACGATAG
* * * * *
1900451 CAAAATAAATTAAAAGC-AAAAATATTATGAATATTTATAATACATACAGTTGCACCCAAGAATG
1 CAAAATAAGTTAAAA-CTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAATG
* * * * *
1900515 TCACGGTTCATTAA-ATATTAGGTTGCGATTTGGAAAATTAATA-TTTTATTAATAAAATAGGTT
65 TCATGGTTCACTAAGAAATTAGGTTGCGATAT-GAACATTAATATTTTTATTAATAAAAT-GGTT
* *
1900578 GTGCCTAAAATATTACTTTAGCTTTAAA
128 GCGCCTAAAATATTACTTTAGCTTTGAA
* * * **
1900606 CAAATTAAGTTAAAAGC-AATAAGTGTTATGAATATCTCTAATAAATCGGGTTGCACCCAAGAAT
1 CAAAATAAGTTAAAA-CTAA-AAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAAT
*
1900670 GTCATGGTTCACTAAGAAATTAGGTTGCGATATGAACCATTTAATATTTTTATTAATAAAATGGG
64 GTCATGGTTCACTAAGAAATTAGGTTGCGATATGAA-CA-TTAATATTTTTATTAATAAAATGGT
* *
1900735 TG-GCCTAAAGTATTACTTTAGATTTGAA
127 TGCGCCTAAAATATTACTTTAGCTTTGAA
* * *
1900763 CAAAATATGTTAAACACTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCGA-CAAAAAAT
1 CAAAATAAGTTAAA-ACTAAAAATGTTATGAATATCTATAATAAATCCAGTTGC-ACCCAAGAAT
* * *
1900827 GTCATGGTTCACTAAGAAATTAGGTTACG-TCTAGAAAATTAATATTTTTATTAATAAAATGGTT
64 GTCATGGTTCACTAAGAAATTAGGTTGCGATAT-GAACATTAATATTTTTATTAATAAAATGG-T
* *
1900891 TGCGCCTAAAATATTACTTTATCTTTCAA
127 TGCGCCTAAAATATTACTTTAGCTTTGAA
* ** *** * *
1900920 CAAAATATA-TTAAAATATAAAAATGTTACAAATATCTATAATAAATTTGGTTGCGCCTAAGAAT
1 CAAAATA-AGTTAAAA-CTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAAT
* * * *
1900984 GCCATGGTTCACTAAGAAATTAGGTTGCAATCTGAAACATTCATATTTTTATTAATAAAATGGTT
64 GTCATGGTTCACTAAGAAATTAGGTTGCGATATG-AACATTAATATTTTTATTAATAAAATGGTT
*
1901049 GCGCCTAAAATATTACTTTAGCTTT-AGC
128 GCGCCTAAAATATTACTTTAGCTTTGA-A
* **
1901077 CAAAATAAGTAAAAAACTAAAAATGTTATGAATATCTAT-ATAAATCCAGTTGCATGCAAGAATG
1 CAAAATAAGT-TAAAACTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAATG
* * * *
1901141 TCATGCTTCACTAA-ACCATTGGGTTGCGATCAAGAACATTAATATTTTTATTAATAAAATGAGT
65 TCATGGTTCACTAAGA-AATTAGGTTGCGAT-ATGAACATTAATATTTTTATTAATAAAATG-GT
* * **
1901205 TGTGCCTAAAGTATTGGTTTAGCTTTGAA
127 TGCGCCTAAAATATTACTTTAGCTTTGAA
* **
1901234 CAAAATAGGTTAAAATCTAAAAATGTTAT-AATATCTATAATAAAT-TTGTTGCACCCAAGAATG
1 CAAAATAAGTTAAAA-CTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAATG
*
1901297 TCATGGTTCACTAATAAATT
65 TCATGGTTCACTAAGAAATT
1901317 GAGTTGTTTA
Statistics
Matches: 601, Mismatches: 84, Indels: 51
0.82 0.11 0.07
Matches are distributed among these distances:
155 42 0.07
156 170 0.28
157 326 0.54
158 48 0.08
159 15 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (155 bp):
CAAAATAAGTTAAAACTAAAAATGTTATGAATATCTATAATAAATCCAGTTGCACCCAAGAATGT
CATGGTTCACTAAGAAATTAGGTTGCGATATGAACATTAATATTTTTATTAATAAAATGGTTGCG
CCTAAAATATTACTTTAGCTTTGAA
Found at i:1904930 original size:19 final size:20
Alignment explanation
Indices: 1904890--1904983 Score: 102
Period size: 22 Copynumber: 4.5 Consensus size: 20
1904880 AGCAAATTTT
*
1904890 GGTATCGATACCGAAAG--GG
1 GGTATCGATACC-ATAGTAGG
1904909 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTAGG
1904929 GTAGTATCGATACCATAGTAGG
1 G--GTATCGATACCATAGTAGG
* *
1904951 GTAATATCGATACCATGGTAGG
1 G--GTATCGATACCATAGTAGG
1904973 GGTATCGATAC
1 GGTATCGATAC
1904984 TGAAGAGGCA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.04
19 12 0.18
20 12 0.18
22 40 0.60
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:1904937 original size:95 final size:95
Alignment explanation
Indices: 1904738--1904953 Score: 269
Period size: 95 Copynumber: 2.3 Consensus size: 95
1904728 GTACTGATGA
* * * *
1904738 GGTAGTATCCATACCATGGTGAGGGTATCGATACCAGGTAACATCAAACCTAATTTTGGTATCGA
1 GGTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCAAACCAAATTTTGGTATCGA
* *
1904803 TACCGGAAAGGGGTATCGTTACTCTAGCAT
66 TACCGGAAAGGGGTATCGATACTCTAGCAG
* * * *
1904833 AGTAATATCGATACCATGGTGAGGGTATCGATACCAAGCCACAT-AGAAGCAAATTTTGGTATCG
1 GGTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCA-AACCAAATTTTGGTATCG
*
1904897 ATACC-GAAAGGGGGTATCGATAC-CATAGTAG
65 ATACCGGAAA-GGGGTATCGATACTC-TAGCAG
*
1904928 GGTAGTATCGATACCATAGT-AGGGTA
1 GGTAGTATCGATACCATGGTGAGGGTA
1904954 ATATCGATAC
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
94 12 0.12
95 92 0.88
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCAAACCAAATTTTGGTATCGA
TACCGGAAAGGGGTATCGATACTCTAGCAG
Found at i:1904938 original size:22 final size:22
Alignment explanation
Indices: 1904910--1904983 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
1904900 CCGAAAGGGG
1904910 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
1904932 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
* *
1904954 ATATCGATACCATGGTAGGG--
1 GTATCGATACCATAGTAGGGTA
1904974 GTATCGATAC
1 GTATCGATAC
1904984 TGAAGAGGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 9 0.18
22 40 0.82
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:1905375 original size:59 final size:59
Alignment explanation
Indices: 1905310--1905765 Score: 632
Period size: 59 Copynumber: 7.8 Consensus size: 59
1905300 ATGACACTAA
*
1905310 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCA-TTGT
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTT-T
* * *
1905369 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTTCAGATA-GCCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* * * * *
1905427 ATGTGCTAAAAAGATAAGGAAATCATACCAAGTGTAAGGATTTCTAGATAGGGCACTTT
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* *
1905486 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* * *
1905545 GTGTGCTAAAAAGATAAGGAAATCTTACTAAGTGTATGGATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* * * **
1905604 ATGTGGTAAAAAGATAAGGAAATCATACTAACTGTATGAATTTCCAGATAGGGCACTAA
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* * **
1905663 GTGTGCTGAAACGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATA-GGCACTAA
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
* * *
1905721 GTGTGCTAAAATGATAAGGAAGTCGTACT-AGTTGTATGAATTTCC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAG-TGTATGAATTTCC
1905766 TATTGAATTT
Statistics
Matches: 360, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
57 2 0.01
58 93 0.26
59 265 0.74
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (59 bp):
GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
Found at i:1905727 original size:176 final size:176
Alignment explanation
Indices: 1905304--1905765 Score: 685
Period size: 176 Copynumber: 2.6 Consensus size: 176
1905294 TACCAAATGA
* **
1905304 CACTAAGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCATTGT
1 CACTAAGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTAA
*
1905369 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTTCAGATAGCCACTTCATGTGCT
66 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGCCACTTCATGTGCT
* * *
1905434 AAAAAGATAAGGAAATCATACCAAGTGTAAGGATTTCTAGATAGGG
131 AAAAAGATAAGGAAATCATACCAACTGTAAGAATTTCCAGATAGGG
** **
1905480 CACTTTGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTTC
1 CACTAAGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTAA
* * * *
1905545 GTGTGCTAAAAAGATAAGGAAATCTTACTAAGTGTATGGATTTCCAGATAGGGCACTTCATGTGG
66 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATA-GCCACTTCATGTGC
* *
1905610 TAAAAAGATAAGGAAATCATACTAACTGTATGAATTTCCAGATAGGG
130 TAAAAAGATAAGGAAATCATACCAACTGTAAGAATTTCCAGATAGGG
* * *
1905657 CACTAAGTGTGCTGAAACGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATA-GGCACTAA
1 CACTAAGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTAA
* * *
1905721 GTGTGCTAAAATGATAAGGAAGTCGTACT-AGTTGTATGAATTTCC
66 GTGTGCTAAAAAGATAAGGAAATCATACTAAG-TGTATGAATTTCC
1905766 TATTGAATTT
Statistics
Matches: 258, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
175 2 0.01
176 151 0.59
177 105 0.41
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (176 bp):
CACTAAGTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTAA
GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGCCACTTCATGTGCT
AAAAAGATAAGGAAATCATACCAACTGTAAGAATTTCCAGATAGGG
Found at i:1909496 original size:20 final size:21
Alignment explanation
Indices: 1909454--1909502 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1909444 ATTTTGAGGT
1909454 TTTAAAAATCAAAATCAATGA
1 TTTAAAAATCAAAATCAATGA
1909475 TTTAGAAAAT-AAAATC-ATGA
1 TTTA-AAAATCAAAATCAATGA
1909495 TTTAAAAA
1 TTTAAAAA
1909503 GTTAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 10 0.37
22 5 0.19
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (21 bp):
TTTAAAAATCAAAATCAATGA
Found at i:1909508 original size:21 final size:21
Alignment explanation
Indices: 1909454--1909508 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1909444 ATTTTGAGGT
*
1909454 TTTAAAAATCAAAATCAATGA
1 TTTAAAAATTAAAATCAATGA
1909475 TTTAGAAAA-TAAAATC-ATGA
1 TTTA-AAAATTAAAATCAATGA
1909495 TTTAAAAAGTTAAA
1 TTTAAAAA-TTAAA
1909509 TTTGAATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 8 0.27
21 14 0.47
22 4 0.13
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.31
Consensus pattern (21 bp):
TTTAAAAATTAAAATCAATGA
Found at i:1915262 original size:12 final size:12
Alignment explanation
Indices: 1915245--1915269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1915235 CCCCAAGAGA
1915245 AAATTTCTCTTC
1 AAATTTCTCTTC
1915257 AAATTTCTCTTC
1 AAATTTCTCTTC
1915269 A
1 A
1915270 TCCACGATAA
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:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTCTCTTC
Found at i:1923210 original size:18 final size:19
Alignment explanation
Indices: 1923184--1923221 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1923174 AAGTAAAAAT
1923184 AAGGAAATAAA-ATAAAAGA
1 AAGGAAATAAAGA-AAAAGA
1923203 AAGG-AATAAAGAAAAAGA
1 AAGGAAATAAAGAAAAAGA
1923221 A
1 A
1923222 TATTTTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAGGAAATAAAGAAAAAGA
Found at i:1932666 original size:161 final size:162
Alignment explanation
Indices: 1932355--1932678 Score: 641
Period size: 161 Copynumber: 2.0 Consensus size: 162
1932345 TATTTCTCAA
1932355 CTTTCCTTTTCTTGGTAACAATTTCCTTAAGAAATTTGGCATAAGTAGGCATTTATTCAACAACC
1 CTTTCCTTTTCTTGGTAACAATTTCCTTAAGAAATTTGGCATAAGTAGGCATTTATTCAACAACC
1932420 TCCAATAAAGATACATTAATATAAAGCTGATCAAGAATGTCAACAAACTTTTTAATTGAATTTTA
66 TCCAATAAAGATACATTAATATAAAGCTGATCAAGAATGTCAACAAACTTTTTAATTGAATTTTA
1932485 TCATTGTGCTTCTTCAATCTTTGCGAGAAGGG
131 TCATTGTGCTTCTTCAATCTTTGCGAGAAGGG
1932517 CTTTCCTTTTCTTGGTAACAATTTCCTTAAGAAATTTGGCATAAGTAGGCATTTATTCAACAACC
1 CTTTCCTTTTCTTGGTAACAATTTCCTTAAGAAATTTGGCATAAGTAGGCATTTATTCAACAACC
1932582 TCCAATAAAG-TACATTAATATAAAGCTGATCAAGAATGTCAACAAACTTTTTAATTGAATTTTA
66 TCCAATAAAGATACATTAATATAAAGCTGATCAAGAATGTCAACAAACTTTTTAATTGAATTTTA
1932646 TCATTGTGCTTCTTCAATCTTTGCGAGAAGGG
131 TCATTGTGCTTCTTCAATCTTTGCGAGAAGGG
1932678 C
1 C
1932679 GGTGGGGGTC
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 87 0.54
162 75 0.46
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (162 bp):
CTTTCCTTTTCTTGGTAACAATTTCCTTAAGAAATTTGGCATAAGTAGGCATTTATTCAACAACC
TCCAATAAAGATACATTAATATAAAGCTGATCAAGAATGTCAACAAACTTTTTAATTGAATTTTA
TCATTGTGCTTCTTCAATCTTTGCGAGAAGGG
Found at i:1939762 original size:3 final size:3
Alignment explanation
Indices: 1939756--1939849 Score: 86
Period size: 3 Copynumber: 32.0 Consensus size: 3
1939746 TATTATACTT
* * * **
1939756 TTA TTA TTA TTA ATA ATA -TA TTA TTA TTA TTA TTA TTA -AA TTA AAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
1939802 TTA AAA TTA TTA TTA TTA TTA TCA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1939847 TTA
1 TTA
1939850 AACAAATATT
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 5 0.07
3 66 0.89
4 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1939767 original size:17 final size:19
Alignment explanation
Indices: 1939756--1939844 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 19
1939746 TATTATACTT
1939756 TTATTATTATTAATAATATA
1 TTATTATTATT-ATAATATA
*
1939776 TTATTATTATTATTAT-TA
1 TTATTATTATTATAATATA
* ** *
1939794 -AATTAAAATTAAAAT-TA
1 TTATTATTATTATAATATA
*
1939811 TTATTATTATTATCATTATA
1 TTATTATTATTAT-AATATA
1939831 TATATTATTATTAT
1 T-TATTATTATTAT
1939845 TATTAAACAA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
17 12 0.22
18 10 0.19
19 6 0.11
20 14 0.26
21 12 0.22
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTATTATAATATA
Found at i:1939804 original size:23 final size:24
Alignment explanation
Indices: 1939756--1939816 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
1939746 TATTATACTT
* **
1939756 TTATTATTATTAAT-AATATATTA
1 TTATTATTATTATTAAATATAAAA
1939779 TTATTATTATTATTAAAT-TAAAA
1 TTATTATTATTATTAAATATAAAA
**
1939802 TTAAAATTATTATTA
1 TTATTATTATTATTA
1939817 TTATTATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTATTATTATTAAATATAAAA
Found at i:1941473 original size:2 final size:2
Alignment explanation
Indices: 1941466--1941492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1941456 ATATCCTTCT
1941466 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
1941493 TTACTTCATT
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:1942195 original size:18 final size:18
Alignment explanation
Indices: 1942139--1942184 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1942129 TTTTTGATTC
* *
1942139 TTTTTATTTCCTTCAATTA
1 TTTTTATATCCTT-TATTA
*
1942158 TTTTTTTATCCTTTATTA
1 TTTTTATATCCTTTATTA
1942176 TTTTTATAT
1 TTTTTATAT
1942185 TCTTATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATATCCTTTATTA
Found at i:1942209 original size:30 final size:31
Alignment explanation
Indices: 1942169--1942228 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1942159 TTTTTTATCC
*
1942169 TTTATTATTTTT-ATATTCTTATATATTAATG
1 TTTATTATTTTTGAT-TTCTTAGATATTAATG
*
1942200 TTTA-TATTTTTGATTTTTTAGATATTAAT
1 TTTATTATTTTTGATTTCTTAGATATTAAT
1942229 TTTTGTGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (31 bp):
TTTATTATTTTTGATTTCTTAGATATTAATG
Found at i:1944508 original size:33 final size:33
Alignment explanation
Indices: 1944466--1944543 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1944456 ACCTTTGTTG
*
1944466 CATTTGCATTTTGCATTCATATTTTTTTCATTA
1 CATTTGCATTTTGCATTCACATTTTTTTCATTA
*
1944499 CATTTGCATTTTGCATTCGCATTTTTTTCATTA
1 CATTTGCATTTTGCATTCACATTTTTTTCATTA
1944532 CATTTGCATTTT
1 CATTTGCATTTT
1944544 TTAAGTTTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (33 bp):
CATTTGCATTTTGCATTCACATTTTTTTCATTA
Found at i:1944509 original size:20 final size:20
Alignment explanation
Indices: 1944486--1944545 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
1944476 TTGCATTCAT
1944486 ATTTTTTTCATTACATTTGC
1 ATTTTTTTCATTACATTTGC
*
1944506 A--TTTTGCATT-C----GC
1 ATTTTTTTCATTACATTTGC
1944519 ATTTTTTTCATTACATTTGC
1 ATTTTTTTCATTACATTTGC
1944539 ATTTTTT
1 ATTTTTT
1944546 AAGTTTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 3 0.10
15 8 0.26
16 1 0.03
17 1 0.03
18 8 0.26
20 10 0.32
ACGTcount: A:0.18, C:0.15, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTTTTTCATTACATTTGC
Found at i:1944564 original size:20 final size:20
Alignment explanation
Indices: 1944508--1944644 Score: 73
Period size: 20 Copynumber: 6.7 Consensus size: 20
1944498 ACATTTGCAT
* *
1944508 TTTGCATTCGCATTTTTTTCA
1 TTTGCATTTGCATTTTTAT-A
*
1944529 -TTACATTTGCATTTTT-TAA
1 TTTGCATTTGCATTTTTAT-A
1944548 GTTTGCATTTGCATTTTTATA
1 -TTTGCATTTGCATTTTTATA
* * * *
1944569 TTTTCATTTACATTTTCATT
1 TTTGCATTTGCATTTTTATA
** * **
1944589 TTTATATTTGCATCTTTGCA
1 TTTGCATTTGCATTTTTATA
*
1944609 -TTGCACAGTTTGCATTCTTATA
1 TTTG--CA-TTTGCATTTTTATA
*
1944631 TTTGCATTTACATT
1 TTTGCATTTGCATT
1944645 ACATATTTAT
Statistics
Matches: 86, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.05
20 49 0.57
21 19 0.22
22 11 0.13
23 3 0.03
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (20 bp):
TTTGCATTTGCATTTTTATA
Found at i:1946799 original size:72 final size:72
Alignment explanation
Indices: 1946702--1946845 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
1946692 ATATAATAAA
*
1946702 GCTTGAGCTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTAGGGATAATATTCAGCTAGT
1 GCTTGAGCTATCCCCCTAAAGCAATTGGTTAATAGCCACGACTTTAGGGATAATATTCAGCTAGT
*
1946767 CTGTTAT
66 CCGTTAT
* * * * *
1946774 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCGCCACGCCTTTATGGATAATATTTAGCTAGT
1 GCTTGAGCTATCCCCCTAAAGCAATTGGTTAATAGCCACGACTTTAGGGATAATATTCAGCTAGT
1946839 CCGTTAT
66 CCGTTAT
1946846 ACTATTATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (72 bp):
GCTTGAGCTATCCCCCTAAAGCAATTGGTTAATAGCCACGACTTTAGGGATAATATTCAGCTAGT
CCGTTAT
Found at i:1949444 original size:54 final size:54
Alignment explanation
Indices: 1949355--1949516 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 54
1949345 TGATTGAGAA
* * * *
1949355 ATCTGAGCAGAAGCCACAGGAAAGGATGAACGTATTGTCAAATGCTTTACGAAC
1 ATCTAAGCAGAAGCCACAGGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
* ** *
1949409 ATTTGGGCAGAAGCCACAGGAAAGAATGAATGTATTGTCAAATGTTTTACGAGC
1 ATCTAAGCAGAAGCCACAGGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
* * * * * *
1949463 ATCTAACCAGAAACCACATGAGATAATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTAAGCAGAAGCCACAGGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
1949517 CTGCTACTCT
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (54 bp):
ATCTAAGCAGAAGCCACAGGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
Found at i:1949943 original size:22 final size:23
Alignment explanation
Indices: 1949882--1949943 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
1949872 ATCTACATTC
*
1949882 TTCAAAGATGATAGATTCTCTCT
1 TTCAAAGATGATAGATTTTCTCT
1949905 TT-AAAGATGATAGATTTTCT-T
1 TTCAAAGATGATAGATTTTCTCT
*
1949926 TTCAAAGATGAAAGATTT
1 TTCAAAGATGATAGATTT
1949944 ATTGGATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 3 0.08
22 31 0.86
23 2 0.06
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (23 bp):
TTCAAAGATGATAGATTTTCTCT
Found at i:1950644 original size:76 final size:76
Alignment explanation
Indices: 1950542--1950723 Score: 283
Period size: 76 Copynumber: 2.4 Consensus size: 76
1950532 CCCACATCTG
*
1950542 TAAGACCTACGGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTCAAAACCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTCAAAACCTT
1950607 CGGGTCATCCA
66 CGGGTCATCCA
* * * *
1950618 TAAGACTTACAGTGCAGGATGTTTTCAAAAAGCCTTTGGGAGTTTTTTGATGTTTTCAAAGCCTT
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTCAAAACCTT
* **
1950683 CGGGTCTTCTG
66 CGGGTCATCCA
*
1950694 TAAGACCTACAGTGCATGATGTTTTCAAAA
1 TAAGACCTACAGTGCAGGATGTTTTCAAAA
1950724 CCTTCGGGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 96 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (76 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTCAAAACCTT
CGGGTCATCCA
Found at i:1950729 original size:45 final size:45
Alignment explanation
Indices: 1950665--1950778 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
1950655 GGGAGTTTTT
* * **
1950665 TGATGTTTTCAAAGCCTTCGGGTCTTCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1950710 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1950755 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1950779 AGTTTTTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 51 0.81
46 4 0.06
47 8 0.13
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:1950751 original size:121 final size:121
Alignment explanation
Indices: 1950589--1950896 Score: 541
Period size: 121 Copynumber: 2.6 Consensus size: 121
1950579 GAGAGTTTTT
* *
1950589 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
* *
1950654 TGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCTTCTGTAAGACCTACAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1950710 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1950775 CGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
**
1950831 TGAT-TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1950893 CGGG
66 CGGG
1950897 TCATCCATAA
Statistics
Matches: 181, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
118 8 0.04
119 4 0.02
120 48 0.27
121 121 0.67
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
CGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:1950862 original size:165 final size:166
Alignment explanation
Indices: 1950665--1951054 Score: 701
Period size: 165 Copynumber: 2.4 Consensus size: 166
1950655 GGGAGTTTTT
* *
1950665 TGATGTTTTCAAAGCCTTCGGGTCTTCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
* * *
1950730 GGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTT
66 GGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
1950795 CAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
131 CAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1950831 TGAT-TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1950895 GGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
66 GGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
1950960 CAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
131 CAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
* * *
1950996 TGATGTTTTCAAAACCATCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAA
1951055 AGCCTTCGAG
Statistics
Matches: 215, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
165 160 0.74
166 55 0.26
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (166 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
CAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:1950899 original size:45 final size:45
Alignment explanation
Indices: 1950786--1950943 Score: 246
Period size: 45 Copynumber: 3.5 Consensus size: 45
1950776 GGGAGTTTTT
*
1950786 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1950831 TGAT-TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
**
1950875 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
* *
1950920 GGATGCTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1950944 AGCTTTTTGA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
44 43 0.41
45 50 0.48
46 4 0.04
47 8 0.08
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:1950986 original size:121 final size:120
Alignment explanation
Indices: 1950831--1951249 Score: 669
Period size: 121 Copynumber: 3.5 Consensus size: 120
1950821 CTACAGTGCA
*
1950831 TGATTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGG
1 TGATTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGG
* *
1950896 GTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTT
66 GTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
*
1950951 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCATCG
1 TGAT-TTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
* *
1951016 GGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTT
65 GGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* *
1951072 TAATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1 TGAT-TTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
* * *
1951137 GGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGTAGTTTTT
65 GGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* * * * *
1951193 TGA-TATTCAAAGCCTTTGGGTCATCTATAAGACCTACAATGCAGGATGTTTTCAAAA
1 TGATTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAA
1951250 ATCCTTAAGG
Statistics
Matches: 278, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
119 48 0.17
120 4 0.01
121 226 0.81
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (120 bp):
TGATTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGG
GTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:1951017 original size:45 final size:45
Alignment explanation
Indices: 1950951--1951054 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
1950941 GGGAGCTTTT
* * *
1950951 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCATCGGGTCATCTATAAGACCTACAGTGCA
1950996 TGATGTTTTCAAAACCATCGGGTCATCTATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCATCGGGTCATCTATAAGACCTACAGTGCA
*
1951041 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1951055 AGCCTTCGAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCATCGGGTCATCTATAAGACCTACAGTGCA
Found at i:1951101 original size:286 final size:287
Alignment explanation
Indices: 1950589--1951175 Score: 1032
Period size: 286 Copynumber: 2.0 Consensus size: 287
1950579 GAGAGTTTTT
* *
1950589 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACTTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTT
* * *
1950654 TGGGAGTTTTTTGATGTTTTCAAAGCCTTCGGGTCTTCTGTAAGACCTACAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT
* * * *
1950719 CAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTT
131 CAAAACCATCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTT
*
1950784 TTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGAT-TTTTCAAAACCTT
196 TTTAATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTT
**
1950848 CGGGTCATCTGTAAGACCTACAGTGCA
261 CGGGTCATCAATAAGACCTACAGTGCA
1950875 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTT
1950940 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT
*
1951005 CAAAACCATCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTT
131 CAAAACCATCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTT
*
1951070 TTTAATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTT
196 TTTAATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTT
1951135 CGGGTCATCAATAAGACCTACAGTGCA
261 CGGGTCATCAATAAGACCTACAGTGCA
*
1951162 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1951176 AGCCTTCAGT
Statistics
Matches: 285, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
286 234 0.82
287 51 0.18
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (287 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT
CAAAACCATCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTT
TTTAATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTT
CGGGTCATCAATAAGACCTACAGTGCA
Found at i:1951138 original size:45 final size:45
Alignment explanation
Indices: 1951074--1951175 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
1951064 GAGCTTTTTA
* ** *
1951074 ATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCAATAAGACCTACAGTGCAGG
1951119 ATGTTTTCAAAACCTTCGGGTCATCAATAAGACCTACAGTGCAGG
1 ATGTTTTCAAAACCTTCGGGTCATCAATAAGACCTACAGTGCAGG
1951164 ATGTTTTCAAAA
1 ATGTTTTCAAAA
1951176 AGCCTTCAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (45 bp):
ATGTTTTCAAAACCTTCGGGTCATCAATAAGACCTACAGTGCAGG
Found at i:1951305 original size:76 final size:76
Alignment explanation
Indices: 1951117--1951324 Score: 312
Period size: 74 Copynumber: 2.8 Consensus size: 76
1951107 CTACAGTGCA
* * *
1951117 TGATGTTTTCAAAACCTTCGGGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
* * *
1951182 CAGTAGTTTTT
66 AAGGAGCTTTT
* * *
1951193 TGATA--TTCAAAGCCTTTGGGTCATCTATAAGACCTACAATGCAGGATGTTTTCAAAAATCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1951256 AAGGAGCTTTT
66 AAGGAGCTTTT
*
1951267 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 TGATATTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAA
1951325 TGAGATTTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 66 0.56
76 52 0.44
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (76 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
AAGGAGCTTTT
Found at i:1951587 original size:3 final size:3
Alignment explanation
Indices: 1951579--1951671 Score: 125
Period size: 3 Copynumber: 31.0 Consensus size: 3
1951569 CATTTTACTT
* * * **
1951579 TTA TTA TTA TTA ATA ATA TATA TTA TTA TTT TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
1951625 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1951672 AACAAATATC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
3 75 0.94
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1965373 original size:14 final size:13
Alignment explanation
Indices: 1965354--1965393 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1965344 ACTGATTACA
1965354 ACATAACACTTATT
1 ACATAACACTTA-T
*
1965368 ACATAACACTGAT
1 ACATAACACTTAT
1965381 AGCATAACACTTA
1 A-CATAACACTTA
1965394 AACCAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (13 bp):
ACATAACACTTAT
Found at i:1965707 original size:3 final size:3
Alignment explanation
Indices: 1965690--1965748 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
1965680 TTGTCCCTTT
* * * * *
1965690 TTA TTT TTA -TA TTA TTA TTA TTA TAA ATA TCA TTA TTA TTA TTA TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1965737 TAA TTA -TA TTA T
1 TTA TTA TTA TTA T
1965749 AATATGTGCA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1967540 original size:2 final size:2
Alignment explanation
Indices: 1967533--1967558 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1967523 GATGTGCATA
1967533 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
1967559 GTACATGTAC
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:1970568 original size:6 final size:6
Alignment explanation
Indices: 1970557--1970597 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
1970547 ATCGATACCT
*
1970557 TTTGCA TTTGCA TATGCA TTTGCA TCTTCGCA TTTGCA TTT
1 TTTGCA TTTGCA TTTGCA TTTGCA T-TT-GCA TTTGCA TTT
1970598 ACCTTTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 23 0.74
7 4 0.13
8 4 0.13
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:1971236 original size:18 final size:18
Alignment explanation
Indices: 1971210--1971288 Score: 99
Period size: 18 Copynumber: 4.4 Consensus size: 18
1971200 TCCATCAAAC
1971210 AAAAGAAAAGAAAAAAAA
1 AAAAGAAAAGAAAAAAAA
1971228 AAAA-AAAA-AAAAAAGAA
1 AAAAGAAAAGAAAAAA-AA
*
1971245 AAAAGAAAAGAAAAAGAA
1 AAAAGAAAAGAAAAAAAA
* *
1971263 AAAAGAGAAGGAAAAAAA
1 AAAAGAAAAGAAAAAAAA
*
1971281 AAGAGAAA
1 AAAAGAAA
1971289 TTGAATCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
16 6 0.12
17 10 0.19
18 31 0.60
19 5 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAA
Found at i:1971282 original size:1 final size:1
Alignment explanation
Indices: 1971210--1971266 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
1971200 TCCATCAAAC
* * * * * *
1971210 AAAAGAAAAGAAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1971267 GAGAAGGAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:1971712 original size:20 final size:20
Alignment explanation
Indices: 1971687--1971734 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1971677 TTTCAAGATT
1971687 GATTTTTATTTAAAAAATTG
1 GATTTTTATTTAAAAAATTG
1971707 GATTTTTATTTAAAAAATTG
1 GATTTTTATTTAAAAAATTG
*
1971727 GTTTTTTA
1 GATTTTTA
1971735 AAATCTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
GATTTTTATTTAAAAAATTG
Found at i:1973432 original size:43 final size:43
Alignment explanation
Indices: 1973367--1973582 Score: 337
Period size: 43 Copynumber: 5.0 Consensus size: 43
1973357 ATATGGAACT
* *
1973367 AAGCTTGAGGAACCAACGTGATATGTAGGGGTTCCTTGATTAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* *
1973410 AAGATTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
* *
1973453 AAGCTTGAGGGACCAATGTGATATGTAGAGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
1973496 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCTTTGATGA-
1 AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
*
1973538 ACA-CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGGTGAC
1 A-AGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1973581 AA
1 AA
1973583 TTAAGAATCT
Statistics
Matches: 158, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
42 39 0.25
43 119 0.75
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAC
Found at i:1973646 original size:20 final size:20
Alignment explanation
Indices: 1973621--1973689 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1973611 TTTCTTGATG
1973621 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
1973641 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
* *
1973660 ATGCGTAAATCCTTCAGGCCATC
1 A---GTAAGTCCTTCGGGCCATC
1973683 AGTAAGT
1 AGTAAGT
1973690 ATTTCGAGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
22 10 0.28
23 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:1973680 original size:42 final size:42
Alignment explanation
Indices: 1973616--1973766 Score: 200
Period size: 42 Copynumber: 3.6 Consensus size: 42
1973606 AAGAGTTTCT
* *
1973616 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGCGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* *
1973658 TGATGCGTAAATCCTTCAGGCCATCAGTAAGTATTTCGAGCA
1 TGATGCGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1973700 TGATGCGTAAATCCTTCGGGCCATCTA-TAAGTCTTTTCGAGCA
1 TGATGCGTAAATCCTTCGGGCCATC-AGTAAGTC-TTTCGAGCA
* *
1973743 GGATG-ATAAGA-CCTTCGGGCCATC
1 TGATGCGTAA-ATCCTTCGGGCCATC
1973767 CATAAGACCT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
42 83 0.85
43 15 0.15
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (42 bp):
TGATGCGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
Found at i:1973717 original size:22 final size:22
Alignment explanation
Indices: 1973650--1973717 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
1973640 CAGTAAGTCT
1973650 TTCGAGCATGATGCGTAAATCC
1 TTCGAGCATGATGCGTAAATCC
* * **
1973672 TTC-AGGC--CAT-CAGTAAGTAT
1 TTCGA-GCATGATGC-GTAAATCC
1973692 TTCGAGCATGATGCGTAAATCC
1 TTCGAGCATGATGCGTAAATCC
1973714 TTCG
1 TTCG
1973718 GGCCATCTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 1 0.03
20 12 0.38
21 2 0.06
22 16 0.50
23 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
TTCGAGCATGATGCGTAAATCC
Found at i:1973914 original size:90 final size:90
Alignment explanation
Indices: 1973749--1974037 Score: 452
Period size: 90 Copynumber: 3.2 Consensus size: 90
1973739 AGCAGGATGA
* * *
1973749 TAAGACCTTCGGGCCATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATGAGATTTAAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACT
*
1973814 AAACCTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* *
1973839 TAAGTCTTTCGGGCCATCCATAACACCTTTAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACT
* *
1973904 AAGCCATCGGGGCTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
*
1973929 TAAGTCCTTCGGCCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAAC
1 TAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGA-TTTAAGAAAC
*
1973994 TAAGCCTTCGGGGGTTTCTTGATTTT
65 TAAGCCTTCGGGGGTTTCTTGATTTG
* * *
1974020 TAAATCCTTTGGGTCATC
1 TAAGTCCTTCGGGCCATC
1974038 TGTAAGCCTT
Statistics
Matches: 180, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 133 0.74
91 47 0.26
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (90 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTTAGTGCAGGATGTTTTCAAATGAGATTTAAGAAACT
AAGCCTTCGGGGGTTTCTTGATTTG
Found at i:1974486 original size:3 final size:3
Alignment explanation
Indices: 1974469--1974530 Score: 56
Period size: 3 Copynumber: 21.3 Consensus size: 3
1974459 TTGTCCCTTT
* * * *
1974469 TTA TTT TTA -TA TTA TTA TTA TTA TTA TAA ATA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1974516 TTC TAA TTA -TA TTA T
1 TTA TTA TTA TTA TTA T
1974531 AATATGTGTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1974506 original size:21 final size:21
Alignment explanation
Indices: 1974477--1974516 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1974467 TTTTATTTTT
*
1974477 ATATTATTATTATTATTATAA
1 ATATCATTATTATTATTATAA
1974498 ATATCATTATTATTATTAT
1 ATATCATTATTATTATTAT
1974517 TCTAATTATA
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATCATTATTATTATTATAA
Done.