Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 142 of 206
Found at i:43498050 original size:17 final size:17
Alignment explanation
Indices: 43498028--43498061 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43498018 AATTGTAATT
43498028 TCATTAAATAAATGGTC
1 TCATTAAATAAATGGTC
43498045 TCATTAAATAAATGGTC
1 TCATTAAATAAATGGTC
43498062 ATTATTGTCA
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:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TCATTAAATAAATGGTC
Found at i:43511675 original size:25 final size:25
Alignment explanation
Indices: 43511642--43511761 Score: 159
Period size: 25 Copynumber: 4.8 Consensus size: 25
43511632 CTTACCAATT
*
43511642 CTCAACTCGTATGAGTTTACCGTTA
1 CTCAGCTCGTATGAGTTTACCGTTA
* *
43511667 TTCAGCTCGCATGAGTTTACCGTTA
1 CTCAGCTCGTATGAGTTTACCGTTA
* *
43511692 CTCAACTCGTATGAGCTTACCGTTA
1 CTCAGCTCGTATGAGTTTACCGTTA
* *
43511717 TTCAGCTCGCATGAGTTTACCGTTA
1 CTCAGCTCGTATGAGTTTACCGTTA
* *
43511742 CTCATCTCGTATGAGCTTAC
1 CTCAGCTCGTATGAGTTTAC
43511762 TAATTACAGA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 80 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (25 bp):
CTCAGCTCGTATGAGTTTACCGTTA
Found at i:43511700 original size:50 final size:50
Alignment explanation
Indices: 43511642--43511761 Score: 222
Period size: 50 Copynumber: 2.4 Consensus size: 50
43511632 CTTACCAATT
*
43511642 CTCAACTCGTATGAGTTTACCGTTATTCAGCTCGCATGAGTTTACCGTTA
1 CTCAACTCGTATGAGCTTACCGTTATTCAGCTCGCATGAGTTTACCGTTA
43511692 CTCAACTCGTATGAGCTTACCGTTATTCAGCTCGCATGAGTTTACCGTTA
1 CTCAACTCGTATGAGCTTACCGTTATTCAGCTCGCATGAGTTTACCGTTA
*
43511742 CTCATCTCGTATGAGCTTAC
1 CTCAACTCGTATGAGCTTAC
43511762 TAATTACAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (50 bp):
CTCAACTCGTATGAGCTTACCGTTATTCAGCTCGCATGAGTTTACCGTTA
Found at i:43514076 original size:20 final size:18
Alignment explanation
Indices: 43514029--43514077 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
43514019 CAAGATAAAC
43514029 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43514046 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
43514066 ATTAAATTAATA
1 ATTAAATTAATA
43514078 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:43514093 original size:39 final size:36
Alignment explanation
Indices: 43514042--43514124 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 36
43514032 AAATTAAATT
43514042 TAATATTAAGATAA-TCACTTTAATATTAAATTAATAAAA
1 TAATATTAAGATAAGT-A--TTAA-ATTAAATTAATAAAA
* *
43514081 TACTATTAAGATAAGTATTAAATTAAATTATTAAAA
1 TAATATTAAGATAAGTATTAAATTAAATTAATAAAA
43514117 TAATATTA
1 TAATATTA
43514125 TTTTTGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 21 0.52
37 4 0.10
39 14 0.35
40 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (36 bp):
TAATATTAAGATAAGTATTAAATTAAATTAATAAAA
Found at i:43514570 original size:19 final size:19
Alignment explanation
Indices: 43514537--43514576 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43514527 AAAATATCAT
*
43514537 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
43514556 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
43514575 AT
1 AT
43514577 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:43515731 original size:16 final size:16
Alignment explanation
Indices: 43515710--43515740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43515700 CTATGCATGC
*
43515710 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
43515726 AAAATACAAAAGACA
1 AAAATACAAAAGACA
43515741 TAATAGTGAA
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:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:43519904 original size:19 final size:19
Alignment explanation
Indices: 43519870--43519918 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
43519860 ATTTCTCATG
*
43519870 TTATTAT-TAATTAATT-T
1 TTATTATATATTTAATTAT
43519887 CTTATTATATATTTAATTAT
1 -TTATTATATATTTAATTAT
*
43519907 TTATTGTATATT
1 TTATTATATATT
43519919 ATTTTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATTATATATTTAATTAT
Found at i:43520381 original size:29 final size:29
Alignment explanation
Indices: 43520326--43520381 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
43520316 TATAATATTA
* * *
43520326 TAATATTATATATATAGTTTAGTTTTGTG
1 TAATATTATATATAAAATTTAGATTTGTG
* *
43520355 TAATTTTATATATAAAATTTTGATTTG
1 TAATATTATATATAAAATTTAGATTTG
43520382 ATTCAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (29 bp):
TAATATTATATATAAAATTTAGATTTGTG
Found at i:43523222 original size:41 final size:43
Alignment explanation
Indices: 43523159--43523276 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 43
43523149 TTTCGGGGAA
* * *
43523159 ATTAGTGGCG-TTTTTAGTGAAGCGCCGCTAATGCTCTG-GTT
1 ATTAGCGGCGTTTTTTAGAGAAGCGCCGCTAATGCTCAGTGTT
* * *
43523200 ATTAGCGGCGTTTTTTA-AGAAGCACCGCTAATGTTGAGTGTT
1 ATTAGCGGCGTTTTTTAGAGAAGCGCCGCTAATGCTCAGTGTT
* * *
43523242 TTTAGCGGCGTTTTTTATA-TAGCGCCGCTAATGCT
1 ATTAGCGGCGTTTTTTAGAGAAGCGCCGCTAATGCT
43523277 AAGACTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 25 0.39
42 38 0.59
43 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (43 bp):
ATTAGCGGCGTTTTTTAGAGAAGCGCCGCTAATGCTCAGTGTT
Found at i:43523270 original size:42 final size:41
Alignment explanation
Indices: 43523159--43523350 Score: 128
Period size: 41 Copynumber: 4.7 Consensus size: 41
43523149 TTTCGGGGAA
* * *
43523159 ATTAGTGGCG-TTTTTAGTGAAGCGCCGCTAATGCTCTGGTT
1 ATTAGCGGCGTTTTTTA-AGAAGCGCCGCTAATGCTCAGGTT
* * *
43523200 ATTAGCGGCGTTTTTTAAGAAGCACCGCTAATGTTGAGTGTT
1 ATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCAG-GTT
* * * *
43523242 TTTAGCGGCGTTTTTTATA-TAGCGCCGCTAATGCTAAGACTT
1 ATTAGCGGCGTTTTTTA-AGAAGCGCCGCTAATGCTCAG-GTT
* * *
43523284 -TTAGTGGCGTTTTGTTAA-AATCTCCGCTAAT-CT-AGGTGT
1 ATTAGCGGCGTTTT-TTAAGAAGCGCCGCTAATGCTCAGGT-T
* * *
43523323 TTTAGCGGTGTTTTTGT-TGAAGCGCCGC
1 ATTAGCGGCGTTTTT-TAAGAAGCGCCGC
43523351 AAAAACAATT
Statistics
Matches: 120, Mismatches: 23, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 21 0.17
41 48 0.40
42 45 0.38
43 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
ATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCAGGTT
Found at i:43523311 original size:83 final size:81
Alignment explanation
Indices: 43523179--43523337 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 81
43523169 TTTTTAGTGA
** * * *
43523179 AGCGCCGCTAATGCTCTGGTTATTAGCGGCGTTTTTTAAGAAGCACCGCTAATGTTGAGTGTTTT
1 AGCGCCGCTAATGCTAAGCTTATTAGCGGCGTTTTTTAAGAAGCACCGCTAATCTAG-GTG-TTT
43523244 TAGCGGCGTTTTTTATAT
64 TAGCGGCGTTTTTTATAT
* * *
43523262 AGCGCCGCTAATGCTAAGACTT-TTAGTGGCGTTTTGTTAA-AATCTCCGCTAATCTAGGTGTTT
1 AGCGCCGCTAATGCTAAG-CTTATTAGCGGCGTTTT-TTAAGAAGCACCGCTAATCTAGGTGTTT
*
43523325 TAGCGGTGTTTTT
64 TAGCGGCGTTTTT
43523338 GTTGAAGCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
81 15 0.23
82 3 0.05
83 41 0.63
84 6 0.09
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (81 bp):
AGCGCCGCTAATGCTAAGCTTATTAGCGGCGTTTTTTAAGAAGCACCGCTAATCTAGGTGTTTTA
GCGGCGTTTTTTATAT
Found at i:43523759 original size:2 final size:2
Alignment explanation
Indices: 43523752--43523784 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
43523742 TGATCAAGAG
*
43523752 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43523785 TGGATTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43524960 original size:15 final size:15
Alignment explanation
Indices: 43524940--43524969 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43524930 ATATTAAACG
43524940 CCGCAAAAGAGTTTT
1 CCGCAAAAGAGTTTT
43524955 CCGCAAAAGAGTTTT
1 CCGCAAAAGAGTTTT
43524970 AAAATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
CCGCAAAAGAGTTTT
Found at i:43526103 original size:13 final size:13
Alignment explanation
Indices: 43526079--43526119 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
43526069 ATTTTGCCAG
*
43526079 ATTTTCTAAATGA
1 ATTTTCTTAATGA
43526092 ATTTT-TTGAATGA
1 ATTTTCTT-AATGA
43526105 ATTTTCTTAATGA
1 ATTTTCTTAATGA
43526118 AT
1 AT
43526120 ATAGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (13 bp):
ATTTTCTTAATGA
Found at i:43527836 original size:9 final size:9
Alignment explanation
Indices: 43527818--43527925 Score: 73
Period size: 9 Copynumber: 12.2 Consensus size: 9
43527808 CTTATATATA
*
43527818 AACTTGCAT
1 AACTTACAT
43527827 AACTTACAT
1 AACTTACAT
*
43527836 AA-TAACATACT
1 AACTTAC--A-T
43527847 AACTTACAT
1 AACTTACAT
43527856 AA--TACAT
1 AACTTACAT
* *
43527863 AGCATACAT
1 AACTTACAT
43527872 AACTTACAT
1 AACTTACAT
* * *
43527881 AA--GATAG
1 AACTTACAT
43527888 AACTTACAT
1 AACTTACAT
*
43527897 AACTTAAAT
1 AACTTACAT
43527906 AACTTACAT
1 AACTTACAT
*
43527915 AATTTACAT
1 AACTTACAT
43527924 AA
1 AA
43527926 AACATAACTC
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
7 10 0.13
8 3 0.04
9 55 0.72
10 2 0.03
11 3 0.04
12 3 0.04
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:43527851 original size:20 final size:19
Alignment explanation
Indices: 43527826--43527863 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
43527816 TAAACTTGCA
43527826 TAACTTACATAATAACATAC
1 TAACTTACATAAT-ACATAC
43527846 TAACTTACATAATACATA
1 TAACTTACATAATACATA
43527864 GCATACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (19 bp):
TAACTTACATAATACATAC
Found at i:43527895 original size:25 final size:23
Alignment explanation
Indices: 43527815--43527907 Score: 77
Period size: 25 Copynumber: 4.0 Consensus size: 23
43527805 AAGCTTATAT
* *
43527815 ATAAACTTGCATAACTTACAT-A
1 ATAAACATACATAACTTACATAA
43527837 AT-AACATAC-TAACTTACAT-A
1 ATAAACATACATAACTTACATAA
43527857 ATACATAGCATACATAACTTACATAA
1 ATA-A-A-CATACATAACTTACATAA
* *
43527883 GATAGAACTTACATAACTTAAATAA
1 -ATA-AACATACATAACTTACATAA
43527908 CTTACATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
20 13 0.22
21 5 0.08
22 3 0.05
23 1 0.02
24 5 0.08
25 26 0.44
26 2 0.03
27 4 0.07
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.29
Consensus pattern (23 bp):
ATAAACATACATAACTTACATAA
Found at i:43527925 original size:18 final size:17
Alignment explanation
Indices: 43527824--43527934 Score: 66
Period size: 16 Copynumber: 6.4 Consensus size: 17
43527814 TATAAACTTG
*
43527824 CATAACTTACATAATAA
1 CATAACTTACATAATTA
43527841 CATACTAACTTACATAA-TA
1 C--A-TAACTTACATAATTA
* *
43527860 CATAGCATACATAACTTA
1 CATAACTTACATAA-TTA
** * *
43527878 CATAAGATAGA-ACTTA
1 CATAACTTACATAATTA
*
43527894 CATAACTTAAATAACTTA
1 CATAACTTACATAA-TTA
* *
43527912 CATAATTTACATAA-AA
1 CATAACTTACATAATTA
43527928 CATAACT
1 CATAACT
43527935 CTGATAACTA
Statistics
Matches: 72, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
16 28 0.39
17 4 0.06
18 25 0.35
19 3 0.04
20 12 0.17
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.30
Consensus pattern (17 bp):
CATAACTTACATAATTA
Found at i:43527949 original size:18 final size:18
Alignment explanation
Indices: 43527926--43527964 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
43527916 ATTTACATAA
*
43527926 AACATAACTCTGATAACT
1 AACATAACTCTGATAAAT
43527944 AACATAACTCTGATAAAT
1 AACATAACTCTGATAAAT
43527962 AAC
1 AAC
43527965 CCTGATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (18 bp):
AACATAACTCTGATAAAT
Found at i:43529943 original size:23 final size:23
Alignment explanation
Indices: 43529913--43529957 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
43529903 GTTTGTGAGG
*
43529913 AAAGCGCCGTTAAAGAACATGTA
1 AAAGCGCCGCTAAAGAACATGTA
43529936 AAAGCGCCGCTAAAGAACATGT
1 AAAGCGCCGCTAAAGAACATGT
43529958 TCTTTAGCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (23 bp):
AAAGCGCCGCTAAAGAACATGTA
Found at i:43530873 original size:19 final size:19
Alignment explanation
Indices: 43530835--43530881 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
43530825 TTCGTATTAT
* *
43530835 TTATGTTATGTTAATTTTG
1 TTATATTATGTTAATATTG
*
43530854 TTATATTATGTTGATATTG
1 TTATATTATGTTAATATTG
*
43530873 TGATATTAT
1 TTATATTAT
43530882 ACAATTTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.60
Consensus pattern (19 bp):
TTATATTATGTTAATATTG
Found at i:43534043 original size:17 final size:17
Alignment explanation
Indices: 43534023--43534071 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
43534013 TCGTTTGGCG
43534023 GATAGTATCGCCTAGCA
1 GATAGTATCGCCTAGCA
**
43534040 GATAGTATTACCTAGCA
1 GATAGTATCGCCTAGCA
*
43534057 AATAGTATCGCCTAG
1 GATAGTATCGCCTAG
43534072 GGAATACAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (17 bp):
GATAGTATCGCCTAGCA
Found at i:43534077 original size:17 final size:17
Alignment explanation
Indices: 43534024--43534077 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
43534014 CGTTTGGCGG
* *
43534024 ATAGTATCGCCTAGCAG
1 ATAGTATCGCCTAGGAA
** *
43534041 ATAGTATTACCTAGCAA
1 ATAGTATCGCCTAGGAA
*
43534058 ATAGTATCGCCTAGGGA
1 ATAGTATCGCCTAGGAA
43534075 ATA
1 ATA
43534078 CAATTCGCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (17 bp):
ATAGTATCGCCTAGGAA
Found at i:43534914 original size:43 final size:43
Alignment explanation
Indices: 43534866--43535191 Score: 390
Period size: 43 Copynumber: 7.6 Consensus size: 43
43534856 TTTTAGAAAT
* * *
43534866 AAACGCCGCTAAA-AGTCATGACCTTTAGCGGCGCTTTTCCTAA
1 AAACGCCGCTAAAGA-CCATGACCTTTAGCGGCGCTTTTCCCAC
*
43534909 AAACGCCGCTATAA-ACCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTA-AAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
43534952 AAACGCCGCTACAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
43534995 AAACGCCGCTATAGACCACGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
43535038 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * **
43535081 AAAAGCCGCTACAGACCATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
43535124 AAACGCCGCTAAAGAACA-AACCTTTAGCGGCACTTCTCGCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
43535166 AAACGCCACTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGACCATGACCTTTA
43535192 AAAAAATATT
Statistics
Matches: 253, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
41 4 0.02
42 39 0.15
43 207 0.82
44 3 0.01
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:43535364 original size:35 final size:35
Alignment explanation
Indices: 43535328--43535395 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
43535318 CTATGAAAAT
43535328 TTTAACTTTAAAA-CTAAATATAA-AAATTAATAAA
1 TTTAACTTTAAAATCTAAA-ATAATAAATTAATAAA
** *
43535362 TTTAGTTTTAAAATTTAAAATAATAAATTAATAA
1 TTTAACTTTAAAATCTAAAATAATAAATTAATAA
43535396 CACAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
TTTAACTTTAAAATCTAAAATAATAAATTAATAAA
Found at i:43539222 original size:82 final size:87
Alignment explanation
Indices: 43539061--43539253 Score: 243
Period size: 89 Copynumber: 2.3 Consensus size: 87
43539051 CTAACTTTTA
* * * * *
43539061 ACCCCAAACCCCTAACCACTAACCCCTAAGCCTTATTTAATATATAAATTAAAAAACACTAATTA
1 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATT-AAAAACAC-AACTA
43539126 ATCTAAATCATAAACCCTAACCAG
64 ATCTAAATCATAAACCCTAACCAG
43539150 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATT-AAAACAC-ACTAAT
1 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAACACAACTAAT
*
43539213 -T-AATC-TAAACCCTAACCTG
66 CTAAATCATAAACCCTAACCAG
* * * *
43539232 ACACCGAATCCATAAACCCTAA
1 ACCCCAAATCCCTAACCCCTAA
43539254 ATCCCTAACT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
82 31 0.33
83 4 0.04
84 1 0.01
85 5 0.05
87 7 0.07
89 46 0.49
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (87 bp):
ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAACACAACTAAT
CTAAATCATAAACCCTAACCAG
Found at i:43539282 original size:7 final size:7
Alignment explanation
Indices: 43539272--43539306 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
43539262 CTCTTAATCT
*
43539272 CTAACCT
1 CTAACCC
43539279 CTAACCC
1 CTAACCC
43539286 CTAACCC
1 CTAACCC
43539293 CTAACCC
1 CTAACCC
43539300 CTAACCC
1 CTAACCC
43539307 ATAAACCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAACCC
Found at i:43539843 original size:41 final size:41
Alignment explanation
Indices: 43539776--43539968 Score: 233
Period size: 41 Copynumber: 4.7 Consensus size: 41
43539766 AATGTTTTTA
** *
43539776 CGGCGCTTTTTCAAAAACGTCACTAAAGATCTGAGCATTAG
1 CGGCGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
* * ** *
43539817 CGGTGCTTTTCCAAAAATGCTGCTAAAGATCTGAGCATTAG
1 CGGCGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
* * * *
43539858 CAGCGCTTTTTCAAAAACCCCGCTAAAGATATGTGCATTAG
1 CGGCGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
*
43539899 CGGTGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
1 CGGCGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
* * *
43539940 CGGCGCTTTTTTTAAAAACGCCACTAAAG
1 CGGCGC-TTTTTCAAAAACACCGCTAAAG
43539969 CCCCAAAAGG
Statistics
Matches: 128, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 109 0.85
42 19 0.15
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
CGGCGCTTTTTCAAAAACACCGCTAAAGATCTGAGCATTAG
Found at i:43539915 original size:82 final size:82
Alignment explanation
Indices: 43539778--43539968 Score: 274
Period size: 82 Copynumber: 2.3 Consensus size: 82
43539768 TGTTTTTACG
* * ** *
43539778 GCGCTTTTTCAAAAACGTCACTAAAGATCTGAGCATTAGCGGTGCTTTTCCAAAAATGCTGCTAA
1 GCGCTTTTTCAAAAACGCCACTAAAGATATGAGCATTAGCGGTGCTTTTCCAAAAACACCGCTAA
43539843 AGATCTGAGCATTAGCA
66 AGATCTGAGCATTAGCA
* * * *
43539860 GCGCTTTTTCAAAAACCCCGCTAAAGATATGTGCATTAGCGGTGCTTTTTCAAAAACACCGCTAA
1 GCGCTTTTTCAAAAACGCCACTAAAGATATGAGCATTAGCGGTGCTTTTCCAAAAACACCGCTAA
*
43539925 AGATCTGAGCATTAGCG
66 AGATCTGAGCATTAGCA
*
43539942 GCGCTTTTTTTAAAAACGCCACTAAAG
1 GCGC-TTTTTCAAAAACGCCACTAAAG
43539969 CCCCAAAAGG
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
82 76 0.80
83 19 0.20
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (82 bp):
GCGCTTTTTCAAAAACGCCACTAAAGATATGAGCATTAGCGGTGCTTTTCCAAAAACACCGCTAA
AGATCTGAGCATTAGCA
Found at i:43550461 original size:28 final size:28
Alignment explanation
Indices: 43550394--43550470 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
43550384 AGCACTATTC
*
43550394 TTGATGGATACCTCTTACTTATCATACTT
1 TTGATGGATACCT-TTACTAATCATACTT
**
43550423 TTGGCGGATACCTTTACTAATCATACTT
1 TTGATGGATACCTTTACTAATCATACTT
* *
43550451 TTGATGAATACCTTTGCTAA
1 TTGATGGATACCTTTACTAA
43550471 GCTTGATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 30 0.73
29 11 0.27
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (28 bp):
TTGATGGATACCTTTACTAATCATACTT
Found at i:43550985 original size:20 final size:19
Alignment explanation
Indices: 43550960--43551029 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
43550950 AAAGCCATAT
*
43550960 CAAATGCCATAAAGGCTAA
1 CAAATGCCACAAAGGCTAA
*
43550979 CATAATGCCACAAAGGCCATAT
1 CA-AATGCCACAAAGG-C-TAA
*
43551001 CAGATGCCACAAAGGCTAA
1 CAAATGCCACAAAGGCTAA
43551020 CAGAATGCCA
1 CA-AATGCCA
43551030 GAAGGGCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.14
20 19 0.45
21 13 0.31
22 4 0.10
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (19 bp):
CAAATGCCACAAAGGCTAA
Found at i:43551014 original size:21 final size:21
Alignment explanation
Indices: 43550941--43551016 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
43550931 GGGCTAGCAG
* *
43550941 AATGCTACAAAAGCCATATCA
1 AATGCCACAAAGGCCATATCA
* *
43550962 AATGCCATAAAGG-C-TAACA
1 AATGCCACAAAGGCCATATCA
43550981 TAATGCCACAAAGGCCATATCA
1 -AATGCCACAAAGGCCATATCA
*
43551003 GATGCCACAAAGGC
1 AATGCCACAAAGGC
43551017 TAACAGAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.09
20 13 0.29
21 24 0.53
22 4 0.09
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (21 bp):
AATGCCACAAAGGCCATATCA
Found at i:43551042 original size:41 final size:41
Alignment explanation
Indices: 43550925--43551029 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
43550915 ACAGATTACA
* * * *
43550925 CCACAAGGGCTAGCAGAATGCTACAAAAGCCATATCAAATG
1 CCACAAAGGCTAACAGAATGCCACAAAGGCCATATCAAATG
* * *
43550966 CCATAAAGGCTAACATAATGCCACAAAGGCCATATCAGATG
1 CCACAAAGGCTAACAGAATGCCACAAAGGCCATATCAAATG
43551007 CCACAAAGGCTAACAGAATGCCA
1 CCACAAAGGCTAACAGAATGCCA
43551030 GAAGGGCTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (41 bp):
CCACAAAGGCTAACAGAATGCCACAAAGGCCATATCAAATG
Found at i:43552640 original size:43 final size:43
Alignment explanation
Indices: 43552572--43552780 Score: 212
Period size: 43 Copynumber: 4.9 Consensus size: 43
43552562 TACCGTAACA
* * * * ***
43552572 ATGCC-ATATCCCAGATATGGCCTTACATGTAATCTTGTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCG
*
43552614 ATGCCAATAG-CCCAGCCATGGTCTTACATGAAATCACATATCG
1 ATGCCAAT-GTCCCAGACATGGTCTTACATGAAATCACATATCG
43552657 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCG
* * * * * * *
43552700 ATGTCAATTTCCTAGACATGGTTTTACACGAAGTCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCG
* *
43552743 ATGCC-ATATCCCAGATATGGTCTTAC-TGGAAA-CACATA
1 ATGCCAATGTCCCAGACATGGTCTTACAT-GAAATCACATA
43552781 AATTTACACA
Statistics
Matches: 139, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.04
42 26 0.19
43 108 0.78
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCG
Found at i:43552727 original size:86 final size:85
Alignment explanation
Indices: 43552572--43552780 Score: 242
Period size: 86 Copynumber: 2.5 Consensus size: 85
43552562 TACCGTAACA
* * *** *
43552572 ATGCCATATCCCAGATATGGCCTTACATGTAATCTTGTATCGATGCCAATAGCCCAGCCATGGTC
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAGCCCAGACATGGTC
*
43552637 TTACATGAAATCACATATCG
66 TTACACGAAATCACATATCG
* * * ** *
43552657 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCACATATCGATGTCAATTTCCTAGACATGGT
1 ATGCC-ATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAGCCCAGACATGGT
* * *
43552722 TTTACACGAAGTCTCATATCG
65 CTTACACGAAATCACATATCG
43552743 ATGCCATATCCCAGATATGGTCTTAC-TGGAAA-CACATA
1 ATGCCATATCCCAGATATGGTCTTACAT-GAAATCACATA
43552781 AATTTACACA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
84 7 0.07
85 28 0.27
86 69 0.66
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (85 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAATCACATATCGATGCCAATAGCCCAGACATGGTC
TTACACGAAATCACATATCG
Found at i:43559879 original size:27 final size:27
Alignment explanation
Indices: 43559832--43559885 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
43559822 TTTTTCGTGT
* *
43559832 ATTATTTTTAATTATTTTATA-CATTA
1 ATTATTTTAAATTATTATATATCATTA
43559858 ATTATTTTAAAATTATTATATATCATTA
1 ATTATTTT-AAATTATTATATATCATTA
43559886 TCTTTATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 11 0.46
28 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTTTAAATTATTATATATCATTA
Found at i:43559886 original size:40 final size:42
Alignment explanation
Indices: 43559842--43559927 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 42
43559832 ATTATTTTTA
*
43559842 ATTAT-TTTATACAT-TA-ATTATTTTAAAATTATTATATATC
1 ATTATCTTTAT-CATGTACATTATTTTAAAATTATTATACATC
* *
43559882 ATTATCTTTATCATGTACTATTTTTTTTAAATTATTATACATC
1 ATTATCTTTATCATGTAC-ATTATTTTAAAATTATTATACATC
43559925 ATT
1 ATT
43559928 GCTTAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
40 8 0.21
41 7 0.18
43 24 0.62
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (42 bp):
ATTATCTTTATCATGTACATTATTTTAAAATTATTATACATC
Found at i:43563428 original size:27 final size:27
Alignment explanation
Indices: 43563388--43563583 Score: 202
Period size: 27 Copynumber: 7.3 Consensus size: 27
43563378 CAAAATAGGC
* * * **
43563388 AAAATGACCAAAATACCCTTATAACGT
1 AAAATGATCGAAATACCCCTATAGGGT
43563415 AAAATGATCGAAATACCCCTATAGGGT
1 AAAATGATCGAAATACCCCTATAGGGT
**
43563442 AAAATGA-CTGAAATACCCCTATAATGT
1 AAAATGATC-GAAATACCCCTATAGGGT
* *
43563469 AAAATGAACGAAATACCCCCATAGGGT
1 AAAATGATCGAAATACCCCTATAGGGT
*
43563496 -AAAT-AACTGAAATA-CCCTCATAGGGT
1 AAAATGATC-GAAATACCCCT-ATAGGGT
* *
43563522 AGAATGATCGAAATACCCCAATAGGGT
1 AAAATGATCGAAATACCCCTATAGGGT
* * *
43563549 AAAATGACCGAAATACCCTTATAGAGT
1 AAAATGATCGAAATACCCCTATAGGGT
43563576 AAAATGAT
1 AAAATGAT
43563584 TGTTATACCC
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
25 6 0.04
26 18 0.13
27 112 0.79
28 6 0.04
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATGATCGAAATACCCCTATAGGGT
Found at i:43563594 original size:54 final size:54
Alignment explanation
Indices: 43563388--43563583 Score: 252
Period size: 54 Copynumber: 3.6 Consensus size: 54
43563378 CAAAATAGGC
* *
43563388 AAAATGACCAAAATACCCTTATAACGTAAAATGATCGAAATACCCCTATAGGGT
1 AAAATGACCGAAATACCCTTATAACGTAAAATGATCGAAATACCCCAATAGGGT
* * * * *
43563442 AAAATGACTGAAATACCCCTATAATGTAAAATGAACGAAATACCCCCATAGGGT
1 AAAATGACCGAAATACCCTTATAACGTAAAATGATCGAAATACCCCAATAGGGT
* * * ** *
43563496 -AAATAACTGAAATACCCTCATAGGGTAGAATGATCGAAATACCCCAATAGGGT
1 AAAATGACCGAAATACCCTTATAACGTAAAATGATCGAAATACCCCAATAGGGT
43563549 AAAATGACCGAAATACCCTTATAGA-GTAAAATGAT
1 AAAATGACCGAAATACCCTTATA-ACGTAAAATGAT
43563584 TGTTATACCC
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 45 0.37
54 76 0.63
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (54 bp):
AAAATGACCGAAATACCCTTATAACGTAAAATGATCGAAATACCCCAATAGGGT
Found at i:43566021 original size:25 final size:25
Alignment explanation
Indices: 43565986--43566046 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
43565976 CTCCTAAATT
* *
43565986 TTAATTTAATTATCTACT-TTTTATA
1 TTAATTAAATTAT-TAATATTTTATA
*
43566011 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
43566036 TTAATTAAATT
1 TTAATTAAATT
43566047 TTTGAGAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 3 0.10
25 28 0.90
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:43580100 original size:25 final size:24
Alignment explanation
Indices: 43580056--43580153 Score: 90
Period size: 25 Copynumber: 4.0 Consensus size: 24
43580046 TACGAGCCAT
* * *
43580056 AATCGATAAGCTCTTCCGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
*
43580080 ACAACGGTAAGCTCATACGAGCTGA
1 A-ATCGGTAAGCTCATACGAGCTGA
* * *
43580105 GATTCGGTAAACTC-TCACGAGTTGTA
1 -AATCGGTAAGCTCAT-ACGAGCTG-A
43580131 AATCGGTAAGCTCATACGAGCTG
1 AATCGGTAAGCTCATACGAGCTG
43580154 TGGTGGGTCC
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
24 2 0.03
25 53 0.91
26 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:43582930 original size:11 final size:13
Alignment explanation
Indices: 43582910--43582941 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
43582900 AATAAAATAA
43582910 TAAAATATC-ATT
1 TAAAATATCAATT
43582922 TAAAA-ATCAATT
1 TAAAATATCAATT
43582934 TAAAATAT
1 TAAAATAT
43582942 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCAATT
Found at i:43587032 original size:17 final size:17
Alignment explanation
Indices: 43587006--43587042 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43586996 CCAAAAAATT
43587006 GTTGTCAATAGGGGGTC
1 GTTGTCAATAGGGGGTC
*
43587023 GTTGTTAATAGGGGGTC
1 GTTGTCAATAGGGGGTC
43587040 GTT
1 GTT
43587043 CTACTACCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.08, G:0.41, T:0.35
Consensus pattern (17 bp):
GTTGTCAATAGGGGGTC
Found at i:43593185 original size:31 final size:31
Alignment explanation
Indices: 43593150--43593211 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
43593140 CGATTTGGTT
*
43593150 ACTGAATTATTC-AAAAATTTCCATTTAAGTC
1 ACTGAACTATTCAAAAAATTT-CATTTAAGTC
*
43593181 ACTGAACTATTCAAAAAATTTTATTTAAGTC
1 ACTGAACTATTCAAAAAATTTCATTTAAGTC
43593212 CCTGGTCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (31 bp):
ACTGAACTATTCAAAAAATTTCATTTAAGTC
Found at i:43600566 original size:69 final size:69
Alignment explanation
Indices: 43600428--43600567 Score: 167
Period size: 69 Copynumber: 2.0 Consensus size: 69
43600418 TCTATTTTGA
* * * * * *
43600428 TTGCGCTAATAATTCCAGAATCGATTAGATTACTAATTACTTAGCTAGTAATTAATTTGGCAAAT
1 TTGCACTAATAATTCCAGAATCAATTAGACTACTAATTACTTAGCTAGTAATTAAGTTGACAAAC
43600493 ATGT
66 ATGT
* *
43600497 TTGCACTAATAATTCCTA-AATCAATTTGACTAGTAATTGA-TTAGCTAGTAATTAAGTTGACAA
1 TTGCACTAATAATTCC-AGAATCAATTAGACTACTAATT-ACTTAGCTAGTAATTAAGTTGACAA
*
43600560 GCATGT
64 ACATGT
43600566 TT
1 TT
43600568 AGCAATTAAC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
69 58 0.97
70 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (69 bp):
TTGCACTAATAATTCCAGAATCAATTAGACTACTAATTACTTAGCTAGTAATTAAGTTGACAAAC
ATGT
Found at i:43602021 original size:18 final size:18
Alignment explanation
Indices: 43601998--43602032 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43601988 TGATGAAATA
43601998 TGGATATGTATG-TATGTC
1 TGGATA-GTATGTTATGTC
43602016 TGGATAGTATGTTATGT
1 TGGATAGTATGTTATGT
43602033 GATGTGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.46
Consensus pattern (18 bp):
TGGATAGTATGTTATGTC
Found at i:43602378 original size:27 final size:27
Alignment explanation
Indices: 43602340--43602495 Score: 143
Period size: 27 Copynumber: 5.8 Consensus size: 27
43602330 AACACATCGA
* * * *
43602340 AAAAGGATAGCCTTTGTGACGAAGTCT
1 AAAAGAATAGCCTTTGTGGCGTATTCT
*
43602367 AAAAGAATAGCCTTTGTGGTGTATTAC-
1 AAAAGAATAGCCTTTGTGGCGTATT-CT
* *** *
43602394 AAAATAATAGCCTTTGTGGTAAAGTCT
1 AAAAGAATAGCCTTTGTGGCGTATTCT
** * *
43602421 AAAAGAATAAACTTTATGGCGTATTAT
1 AAAAGAATAGCCTTTGTGGCGTATTCT
* *
43602448 GAAAGAATAACCTTTGTGGCGTATTCT
1 AAAAGAATAGCCTTTGTGGCGTATTCT
*
43602475 AAAAGAATAGGCTTTGTGGCG
1 AAAAGAATAGCCTTTGTGGCG
43602496 CACTTTGAAT
Statistics
Matches: 102, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
26 1 0.01
27 100 0.98
28 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (27 bp):
AAAAGAATAGCCTTTGTGGCGTATTCT
Found at i:43602428 original size:54 final size:54
Alignment explanation
Indices: 43602340--43602495 Score: 177
Period size: 54 Copynumber: 2.9 Consensus size: 54
43602330 AACACATCGA
* * * *
43602340 AAAAGGATAGCCTTTGTGACGAAGTCTAAAAGAATAGCCTTTGTGGTGTATTAC
1 AAAAGAATAGCCTTTGTGGCGAAGTCTAAAAGAATAGACTTTGTGGCGTATTAC
* ** * * *
43602394 AAAATAATAGCCTTTGTGGTAAAGTCTAAAAGAATAAACTTTATGGCGTATTAT
1 AAAAGAATAGCCTTTGTGGCGAAGTCTAAAAGAATAGACTTTGTGGCGTATTAC
* * * * *
43602448 GAAAGAATAACCTTTGTGGCGTATTCTAAAAGAATAGGCTTTGTGGCG
1 AAAAGAATAGCCTTTGTGGCGAAGTCTAAAAGAATAGACTTTGTGGCG
43602496 CACTTTGAAT
Statistics
Matches: 82, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (54 bp):
AAAAGAATAGCCTTTGTGGCGAAGTCTAAAAGAATAGACTTTGTGGCGTATTAC
Found at i:43603686 original size:43 final size:43
Alignment explanation
Indices: 43603625--43603710 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
43603615 TTATCCTATA
* * * *
43603625 AAAAAATAATTTAAAAAGAGGAGAATATAATA-TTGGGTTGTTG
1 AAAAAAGAATTTAAAAAGAGAAGAAGATAA-ACATGGGTTGTTG
43603668 AAAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTG
1 AAAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTG
43603711 GATTTACCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.51, C:0.01, G:0.22, T:0.26
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGAGAAGAAGATAAACATGGGTTGTTG
Found at i:43604644 original size:17 final size:17
Alignment explanation
Indices: 43604600--43604638 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
43604590 GCCATAACAT
43604600 TTCCAAGTATTCATTAA
1 TTCCAAGTATTCATTAA
*
43604617 TTTCAAGTATTCATTAA
1 TTCCAAGTATTCATTAA
43604634 TTCCA
1 TTCCA
43604639 CATATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (17 bp):
TTCCAAGTATTCATTAA
Found at i:43605724 original size:36 final size:36
Alignment explanation
Indices: 43605670--43605771 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
43605660 TATGATTATC
43605670 GATATTCTGATTTGCATGTTAAACATGCCATATTCT
1 GATATTCTGATTTGCATGTTAAACATGCCATATTCT
* * * *
43605706 GATATTCTAATTTACATGTTAAGCATGTCATATTCT
1 GATATTCTGATTTGCATGTTAAACATGCCATATTCT
* *
43605742 AATATTCTGATTTGCGTG-TAAAGCATGCCA
1 GATATTCTGATTTGCATGTTAAA-CATGCCA
43605772 CTAAAAATCC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 3 0.05
36 52 0.95
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (36 bp):
GATATTCTGATTTGCATGTTAAACATGCCATATTCT
Found at i:43619390 original size:18 final size:19
Alignment explanation
Indices: 43619367--43619415 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
43619357 GTTGTAAAGT
*
43619367 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
43619385 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
43619404 TTTAATTTTTAT
1 TTT-ATTTTTAT
43619416 GTAAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:43619395 original size:22 final size:22
Alignment explanation
Indices: 43619366--43619415 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43619356 AGTTGTAAAG
* *
43619366 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
43619387 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
43619410 TTTTAT
1 TTTTAT
43619416 GTAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:43619943 original size:18 final size:18
Alignment explanation
Indices: 43619920--43619960 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
43619910 CCCAAAAATC
43619920 CCCAATTTCTAGGGTTCT
1 CCCAATTTCTAGGGTTCT
43619938 CCCAATTTCTAGGGTTCT
1 CCCAATTTCTAGGGTTCT
*
43619956 TCCAA
1 CCCAA
43619961 ACTCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.37
Consensus pattern (18 bp):
CCCAATTTCTAGGGTTCT
Found at i:43626512 original size:18 final size:18
Alignment explanation
Indices: 43626489--43626524 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43626479 CCCAAAAATC
43626489 CCCAATTTCTAGGGTTCT
1 CCCAATTTCTAGGGTTCT
43626507 CCCAATTTCTAGGGTTCT
1 CCCAATTTCTAGGGTTCT
43626525 TCCATACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
CCCAATTTCTAGGGTTCT
Found at i:43630652 original size:21 final size:19
Alignment explanation
Indices: 43630622--43630665 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
43630612 ATTTATATGA
43630622 ATGGTAAAATTCAAGGAAAAT
1 ATGGTAAAA-T-AAGGAAAAT
* *
43630643 ATGGTGAAATAATGAAAAT
1 ATGGTAAAATAAGGAAAAT
43630662 ATGG
1 ATGG
43630666 ACTGTATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.25
Consensus pattern (19 bp):
ATGGTAAAATAAGGAAAAT
Found at i:43645810 original size:22 final size:22
Alignment explanation
Indices: 43645785--43645828 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43645775 AATTATGAAC
* *
43645785 ATATTTAATTTTAATTAATTTT
1 ATATTAAATTTTAATAAATTTT
*
43645807 ATATTAAATTTTCATAAATTTT
1 ATATTAAATTTTAATAAATTTT
43645829 GATTTACTTT
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:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTAAATTTTAATAAATTTT
Found at i:43647334 original size:28 final size:28
Alignment explanation
Indices: 43647298--43647353 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
43647288 TTATTTTACT
*
43647298 TAGTTAAATTTTAGTTTTTAATCTCTTC
1 TAGTTAAATTTTAGTTTTTAATCACTTC
43647326 TAGTTAAATTTTAGTTTTTAATCACTTC
1 TAGTTAAATTTTAGTTTTTAATCACTTC
43647354 ATCAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (28 bp):
TAGTTAAATTTTAGTTTTTAATCACTTC
Found at i:43649729 original size:20 final size:20
Alignment explanation
Indices: 43649704--43649745 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
43649694 TGATGCTACC
43649704 TAAGTTTCCACACTTTTAAA
1 TAAGTTTCCACACTTTTAAA
43649724 TAAGTTTCCACACTTTTAAA
1 TAAGTTTCCACACTTTTAAA
43649744 TA
1 TA
43649746 TTTTATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAGTTTCCACACTTTTAAA
Found at i:43658661 original size:42 final size:41
Alignment explanation
Indices: 43658602--43658730 Score: 123
Period size: 42 Copynumber: 3.1 Consensus size: 41
43658592 TTTATAGAGG
* ** *
43658602 ATGCCATAAATGCCATATCAGGATAACACAGATGCTAACAGA
1 ATGCCACAAA-GCCATATCAAAATAACACAGAGGCTAACAGA
* ** *
43658644 ATGCCACAAAGGCCATATCAAAATACCATGGAGGCTAATAGA
1 ATGCCACAAA-GCCATATCAAAATAACACAGAGGCTAACAGA
* * * * *
43658686 ATGCCACAAAGCCATACCAAAGTACCACAAAGGTTAACAGA
1 ATGCCACAAAGCCATATCAAAATAACACAGAGGCTAACAGA
43658727 ATGC
1 ATGC
43658731 AAAAAGGCTA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 28 0.39
42 43 0.61
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (41 bp):
ATGCCACAAAGCCATATCAAAATAACACAGAGGCTAACAGA
Found at i:43658728 original size:41 final size:42
Alignment explanation
Indices: 43658635--43658738 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
43658625 TAACACAGAT
* ***
43658635 GCTAACAGAATGCCACAAAGGCCATATCAAAATACCATGGAG
1 GCTAACAGAATGCCACAAAGGCCATACCAAAATACCACAAAG
* *
43658677 GCTAATAGAATGCCACAAA-GCCATACCAAAGTACCACAAAG
1 GCTAACAGAATGCCACAAAGGCCATACCAAAATACCACAAAG
* *
43658718 GTTAACAGAATG-CAAAAAGGC
1 GCTAACAGAATGCCACAAAGGC
43658739 TATGTAAAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.10
41 29 0.56
42 18 0.35
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.13
Consensus pattern (42 bp):
GCTAACAGAATGCCACAAAGGCCATACCAAAATACCACAAAG
Found at i:43659699 original size:38 final size:38
Alignment explanation
Indices: 43659657--43659733 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
43659647 AATTAAAGAA
43659657 TTAATCTGAAGAAAGAAGAAAACCTTCTCACGAACCTT
1 TTAATCTGAAGAAAGAAGAAAACCTTCTCACGAACCTT
43659695 TTAATCTGAAGAAAGAAGAAAACCTTCTCACGAACCTT
1 TTAATCTGAAGAAAGAAGAAAACCTTCTCACGAACCTT
43659733 T
1 T
43659734 CTCACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (38 bp):
TTAATCTGAAGAAAGAAGAAAACCTTCTCACGAACCTT
Found at i:43668473 original size:24 final size:24
Alignment explanation
Indices: 43668446--43668493 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
43668436 TAACACTACA
*
43668446 CAGCCTAATTCGCATTCAATTGCT
1 CAGCCTAATTCGCAGTCAATTGCT
43668470 CAGCCTAATTCGCAGTCAATTGCT
1 CAGCCTAATTCGCAGTCAATTGCT
43668494 AAATTATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (24 bp):
CAGCCTAATTCGCAGTCAATTGCT
Found at i:43670390 original size:50 final size:48
Alignment explanation
Indices: 43670335--43670471 Score: 132
Period size: 50 Copynumber: 2.8 Consensus size: 48
43670325 TATTGAGATT
* *
43670335 ATGAGAGGTCCCACGTAAGACTATGTCTGGGACATGGTGTTGGCACCGAG
1 ATGAGAGATCCCACGTAAGACTATATCTGGGACATGGTG-T-GCACCGAG
* * * * * *
43670385 ATGAGAGATCCCCCGTAAGACCATCTCTAGGACATGACATGTGCACCGAT
1 ATGAGAGATCCCACGTAAGACTATATCTGGGACATG--GTGTGCACCGAG
* *
43670435 ATGAGA-ACTCCCATGTAAGACTATATCTGGGATATGG
1 ATGAGAGA-TCCCACGTAAGACTATATCTGGGACATGG
43670472 CATTGGTAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
49 1 0.01
50 66 0.94
51 1 0.01
52 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (48 bp):
ATGAGAGATCCCACGTAAGACTATATCTGGGACATGGTGTGCACCGAG
Found at i:43676055 original size:23 final size:22
Alignment explanation
Indices: 43676029--43676084 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
43676019 ATATTTTTTT
43676029 CATTTTTACATGTGTTTTTCA-TG
1 CATTTTTACAT-TG-TTTTCATTG
**
43676052 CATTCATA-ATTGTTTTCATTG
1 CATTTTTACATTGTTTTCATTG
43676073 CATTTTCTACAT
1 CATTTT-TACAT
43676085 ATCTATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 4 0.15
23 8 0.31
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (22 bp):
CATTTTTACATTGTTTTCATTG
Found at i:43678620 original size:44 final size:46
Alignment explanation
Indices: 43678520--43678621 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 46
43678510 GAATGAATAG
* *
43678520 AAAAATGGAAATGGAAAACATTTAGAAATGATTATGGTTTTCCCGA
1 AAAAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
* * * *
43678566 AATAAA--GAAATGG-AATCATTTGGAAATGAATGTGGGTTTCTC-A
1 AA-AAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
43678609 AAAAATGGAAATG
1 AAAAATGGAAATG
43678622 ATAATGGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.06
43 3 0.06
44 29 0.62
45 7 0.15
46 2 0.04
47 3 0.06
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAATGGAAATGGAAAACATTTAGAAATGAATATGGGTTTCCCGA
Found at i:43678629 original size:12 final size:12
Alignment explanation
Indices: 43678612--43678658 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
43678602 TTTCTCAAAA
43678612 AATGGAAATGAT
1 AATGGAAATGAT
43678624 AATGGAAATGAT
1 AATGGAAATGAT
43678636 AATGGAAATGAT
1 AATGGAAATGAT
43678648 AATGGAAATGA
1 AATGGAAATGA
43678659 AATTAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (12 bp):
AATGGAAATGAT
Found at i:43679874 original size:27 final size:27
Alignment explanation
Indices: 43679828--43679900 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 27
43679818 AGGTTCGCTA
*
43679828 ATGTGTTGATGAGCTAGGGCTTCACTAGT
1 ATGT-TTGGTGAGCT-GGGCTTCACTAGT
43679857 ATGTTTGGTGAGCTGGGCTTCACTAGT
1 ATGTTTGGTGAGCTGGGCTTCACTAGT
* *
43679884 CTGTGTGGTGAGCTGGG
1 ATGTTTGGTGAGCTGGG
43679901 TTGGCCAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 28 0.68
28 9 0.22
29 4 0.10
ACGTcount: A:0.15, C:0.14, G:0.37, T:0.34
Consensus pattern (27 bp):
ATGTTTGGTGAGCTGGGCTTCACTAGT
Found at i:43680899 original size:13 final size:13
Alignment explanation
Indices: 43680881--43680907 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43680871 ATGCAAGTCC
43680881 TTTTTAAAAGAAA
1 TTTTTAAAAGAAA
43680894 TTTTTAAAAGAAA
1 TTTTTAAAAGAAA
43680907 T
1 T
43680908 GATTTCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTTAAAAGAAA
Found at i:43681092 original size:12 final size:12
Alignment explanation
Indices: 43681075--43681100 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43681065 TGGTTTCCGA
43681075 TTATTCACTGAG
1 TTATTCACTGAG
43681087 TTATTCACTGAG
1 TTATTCACTGAG
43681099 TT
1 TT
43681101 CTCCTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (12 bp):
TTATTCACTGAG
Found at i:43682474 original size:45 final size:45
Alignment explanation
Indices: 43682425--43682596 Score: 229
Period size: 45 Copynumber: 3.8 Consensus size: 45
43682415 ATACTAGAAA
*
43682425 TGAGTAAGACTATGACTGAAAGACGTTATGGCATCACTATTCTAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
* *
43682470 TGAGTAAGACCATGACTGAAAAACGTTATGGCATTACTATTCTAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
* * * *
43682515 CGAGTAAGACCATGACTGAAAGACATTATGACATCACGATTCTAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
* * * *
43682560 TGAGTAAGTCCAT-AGTTGAAAGATGCTATGGCATCAC
1 TGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCAC
43682597 GAATCAAAGG
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 109 0.99
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (45 bp):
TGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
Found at i:43682629 original size:90 final size:90
Alignment explanation
Indices: 43682429--43682618 Score: 220
Period size: 90 Copynumber: 2.1 Consensus size: 90
43682419 TAGAAATGAG
* * * *
43682429 TAAGACTATGACTGAAAGACGTTATGGCATCACTATTCTATTGAGTAAGACCATGACTGAAAAAC
1 TAAGACCATGACTGAAAGACATTATGACATCACGATTCTATTGAGTAAGACCATGACTGAAAAAC
* * * * * * *
43682494 GTTATGGCATTACTATTCTATCGAG
66 GCTATGGCATCACGAATCAAACGAA
* * *
43682519 TAAGACCATGACTGAAAGACATTATGACATCACGATTCTATTGAGTAAGTCCAT-AGTTGAAAGA
1 TAAGACCATGACTGAAAGACATTATGACATCACGATTCTATTGAGTAAGACCATGA-CTGAAAAA
* *
43682583 TGCTATGGCATCACGAATCAAAGGAA
65 CGCTATGGCATCACGAATCAAACGAA
43682609 TAAGACCATG
1 TAAGACCATG
43682619 GTTTAAAGAC
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
89 1 0.01
90 82 0.99
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (90 bp):
TAAGACCATGACTGAAAGACATTATGACATCACGATTCTATTGAGTAAGACCATGACTGAAAAAC
GCTATGGCATCACGAATCAAACGAA
Found at i:43682685 original size:48 final size:45
Alignment explanation
Indices: 43682606--43682722 Score: 128
Period size: 48 Copynumber: 2.5 Consensus size: 45
43682596 CGAATCAAAG
* *
43682606 GAATAAGACCATGGTTTAAAGACACTATGGCAACGCAATGGA-AAAAAT
1 GAATAAGACCATGGTTGAAAGACAATATGGC-A-GCAA--GATAAAAAT
* * * *
43682654 GAATAAGACCATGGTTGAAAGACAATGTGGCATCAAGATGAGAAT
1 GAATAAGACCATGGTTGAAAGACAATATGGCAGCAAGATAAAAAT
*
43682699 AAATAAGACCATGGTTGAAAGACA
1 GAATAAGACCATGGTTGAAAGACA
43682723 CCATGGCACA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
44 2 0.03
45 27 0.44
46 3 0.05
47 1 0.02
48 28 0.46
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (45 bp):
GAATAAGACCATGGTTGAAAGACAATATGGCAGCAAGATAAAAAT
Found at i:43683046 original size:49 final size:49
Alignment explanation
Indices: 43682977--43683074 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
43682967 ACGGGCATGA
* *
43682977 AAAGGAAAGGTATGTGTTCGAATGAACTATGTCATGAAGTTATAAAAAG
1 AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAAG
* *
43683026 AAAGTAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATGAAAAG
1 AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAAG
43683075 GATTAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (49 bp):
AAAGGAAAGGTATGTATTCGAATGAACTATGTCATGAAATTATAAAAAG
Found at i:43683503 original size:42 final size:43
Alignment explanation
Indices: 43683420--43683505 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
43683410 TACCTATATC
* ** *
43683420 ATAGAACAGATCTTTAGCGACGCTTTTTCGTACAAATGCCGCT
1 ATAGAACAGACCTTTAGCGACGCTTTTTCACACAAACGCCGCT
*
43683463 ATAGAACAGACCTTTAGCGGCGC-TTTTCACACAAACGCCGCT
1 ATAGAACAGACCTTTAGCGACGCTTTTTCACACAAACGCCGCT
43683505 A
1 A
43683506 AAAATATATC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 17 0.45
43 21 0.55
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
ATAGAACAGACCTTTAGCGACGCTTTTTCACACAAACGCCGCT
Found at i:43683838 original size:43 final size:43
Alignment explanation
Indices: 43683776--43683858 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
43683766 GTGCAAGGTA
* *
43683776 ATAAAACATACAATGCATTTTCTTAATCAA-GTAAATCTTGGTG
1 ATAAAACATACAATACATTTACTTAATCAATG-AAATCTTGGTG
* *
43683819 ATAAAAGATATAATACATTTACTTAATCAATGAAATCTTG
1 ATAAAACATACAATACATTTACTTAATCAATGAAATCTTG
43683859 TAATGAACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 34 0.97
44 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (43 bp):
ATAAAACATACAATACATTTACTTAATCAATGAAATCTTGGTG
Found at i:43688038 original size:10 final size:10
Alignment explanation
Indices: 43688023--43688047 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43688013 TAGTTATACC
43688023 TATTTTGGAA
1 TATTTTGGAA
43688033 TATTTTGGAA
1 TATTTTGGAA
43688043 TATTT
1 TATTT
43688048 CTATTTTTCT
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (10 bp):
TATTTTGGAA
Found at i:43692880 original size:41 final size:41
Alignment explanation
Indices: 43692586--43692873 Score: 341
Period size: 41 Copynumber: 7.0 Consensus size: 41
43692576 AATATTTTTT
* * * *
43692586 GCGGCGCTTTCAT-AAAAAAGCCACTAAAAACCCGAGCATTA
1 GCGGCGCTTT-TTCAAAAACGCCGCTAAAACCCCGAGCATTA
*
43692627 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCTAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* *
43692668 GTGGCGC-TTTTCTAAAAACGCCACTAAAACCCCGAGCATTA
1 GCGGCGCTTTTTC-AAAAACGCCGCTAAAACCCCGAGCATTA
*
43692709 GCGGCGC-TTTTCTAAAAACGCCGGTAAAACCCCGAGCATTA
1 GCGGCGCTTTTTC-AAAAACGCCGCTAAAACCCCGAGCATTA
* ** * * *
43692750 GCGGTGCTTAATCATAAACGCCCCTAAAACCCCAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* *
43692791 GCGGCGCTTTATCAAAAACGCTGCTAAAACCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
* * *
43692832 GCGGTGCTTTTTTAAAAACACCGCTAAAACCCAC-AGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCC-CGAGCATTA
43692873 G
1 G
43692874 TGGTGCTACT
Statistics
Matches: 214, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
40 6 0.03
41 204 0.95
42 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTA
Found at i:43692892 original size:123 final size:123
Alignment explanation
Indices: 43692586--43692894 Score: 385
Period size: 123 Copynumber: 2.5 Consensus size: 123
43692576 AATATTTTTT
* * * **
43692586 GCGGCGC-TTTCATAAAAA-AGCCACTAAAAACCCGAGCATTAGCGGCGCTTTTTCAAAAACGCC
1 GCGGCGCTTTTC-TAAAAACA-CCGCTAAAACCCCGAGCATTAGCGGTGCTTAATCAAAAACGCC
* * *
43692649 GCTAAAACCCCTAGCATTAGTGGCGCTTTTCTAAAAACGCCACTAAAACCCCGAGCATTA
64 CCTAAAACCCCAAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAAACCCCGAGCATTA
* * *
43692709 GCGGCGCTTTTCTAAAAACGCCGGTAAAACCCCGAGCATTAGCGGTGCTTAATCATAAACGCCCC
1 GCGGCGCTTTTCTAAAAACACCGCTAAAACCCCGAGCATTAGCGGTGCTTAATCAAAAACGCCCC
**
43692774 TAAAACCCCAAGCATTAGCGGCGCTTTATC-AAAAACGCTGCTAAAACCCCGAGCATTA
66 TAAAACCCCAAGCATTAGCGGCGCTTT-TCTAAAAACGCCACTAAAACCCCGAGCATTA
* * * *
43692832 GCGGTGCTTTTTTAAAAACACCGCTAAAACCCAC-AGCATTAGTGGTGC-TACTCCAAAAACGCC
1 GCGGCGCTTTTCTAAAAACACCGCTAAAACCC-CGAGCATTAGCGGTGCTTAAT-CAAAAACGCC
43692895 ACTATCACCA
Statistics
Matches: 161, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
122 3 0.02
123 151 0.94
124 7 0.04
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.20
Consensus pattern (123 bp):
GCGGCGCTTTTCTAAAAACACCGCTAAAACCCCGAGCATTAGCGGTGCTTAATCAAAAACGCCCC
TAAAACCCCAAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAAACCCCGAGCATTA
Found at i:43692969 original size:40 final size:40
Alignment explanation
Indices: 43692925--43693001 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
43692915 TTGGGTTTGG
43692925 TTTTTT-GAGGAGTTTTCCCAAAAAACGCCGCTAATGCTTT
1 TTTTTTAGAGGAGTTTT-CCAAAAAACGCCGCTAATGCTTT
* ** *
43692965 TTTTTTAGAGGCGTTTTCTTAAAAACGCCGGTAATGC
1 TTTTTTAGAGGAGTTTTCCAAAAAACGCCGCTAATGC
43693002 ACAATCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
TTTTTTAGAGGAGTTTTCCAAAAAACGCCGCTAATGCTTT
Found at i:43701711 original size:16 final size:16
Alignment explanation
Indices: 43701690--43701723 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43701680 CATACCATCA
43701690 TTCTTTTTCTC-TTTTT
1 TTCTTTTTC-CATTTTT
43701706 TTCTTTTTCCATTTTT
1 TTCTTTTTCCATTTTT
43701722 TT
1 TT
43701724 ATCCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTTTCCATTTTT
Found at i:43705836 original size:27 final size:27
Alignment explanation
Indices: 43705761--43705828 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
43705751 CAGTATTGGA
*
43705761 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
43705788 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
43705815 GCCTATCTGGGAGG
1 GCCTATCTGGGAGG
43705829 TGTCAATGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.24
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:43705876 original size:19 final size:19
Alignment explanation
Indices: 43705852--43705892 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
43705842 ATTTTTCAGG
*
43705852 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
43705871 TTTAGGATTATGTTATAAA
1 TTTAGGATTATGTTATAAA
43705890 TTT
1 TTT
43705893 TTGTGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:43706135 original size:19 final size:19
Alignment explanation
Indices: 43706103--43706154 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
43706093 ATTCATACAA
43706103 ATTAT-TTA-AAATTTAAG
1 ATTATGTTATAAATTTAAG
*
43706120 ATTATGTTATAAATTTAGG
1 ATTATGTTATAAATTTAAG
43706139 ATTATGTTATAAATTT
1 ATTATGTTATAAATTT
43706155 TTGTGTTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 5 0.16
18 3 0.09
19 24 0.75
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTATGTTATAAATTTAAG
Found at i:43706322 original size:260 final size:262
Alignment explanation
Indices: 43705859--43706359 Score: 934
Period size: 260 Copynumber: 1.9 Consensus size: 262
43705849 AGGTTTAGGG
43705859 TTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTA
1 TTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTA
43705924 TTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTA
66 TTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTA
* *
43705989 CTAATAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATCC
131 CTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATCA
*
43706054 CGACATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAATTATTTAAAATTTAA
196 CGACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAAAATTTAA
43706119 GA
261 GA
*
43706121 TTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTTAATTTA
1 TTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTA
43706186 TTAGTAATAAATTACAAAATTACTAATAAG-T-TACTAATAAATTTATAACATAATCCTAAATTA
66 TTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTA
* *
43706249 CTAACAAATTAATTATAAAATAATTTCAATATTCATACAAAAAATTACAATATTATAATATATCA
131 CTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATCA
43706314 CGACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
196 CGACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
43706360 TAAAATTGCA
Statistics
Matches: 233, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
260 138 0.59
261 1 0.00
262 94 0.40
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (262 bp):
TTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTA
TTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTA
CTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATCA
CGACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAAAATTTAA
GA
Found at i:43706356 original size:27 final size:27
Alignment explanation
Indices: 43706318--43706374 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
43706308 ATATCACGAC
43706318 ATTACAATATTCACACAAAATTACAAT
1 ATTACAATATTCACACAAAATTACAAT
* * *
43706345 ATTACAATATTCATATAAAATTGCAAT
1 ATTACAATATTCACACAAAATTACAAT
43706372 ATT
1 ATT
43706375 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCACACAAAATTACAAT
Found at i:43706455 original size:8 final size:8
Alignment explanation
Indices: 43706442--43706562 Score: 57
Period size: 8 Copynumber: 14.4 Consensus size: 8
43706432 TTTTTGTATG
43706442 AATATTGT
1 AATATTGT
*
43706450 AATATTAT
1 AATATTGT
*
43706458 AATTTTGTAT
1 AATATTG--T
*
43706468 GAATATTGC
1 -AATATTGT
*
43706477 AATATTTT
1 AATATTGT
**
43706485 TGTA-TG-
1 AATATTGT
43706491 AATATTGT
1 AATATTGT
43706499 AATATTGT
1 AATATTGT
*
43706507 AATATTAT
1 AATATTGT
*
43706515 AATTTTGTAT
1 AATATTG--T
43706525 GAATATTGT
1 -AATATTGT
* * *
43706534 AATGTCAGG
1 AATAT-TGT
43706543 ATATATTGT
1 A-ATATTGT
43706552 AATATTGT
1 AATATTGT
43706560 AAT
1 AAT
43706563 TTTTTGTATG
Statistics
Matches: 81, Mismatches: 22, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
6 2 0.02
7 3 0.04
8 54 0.67
9 5 0.06
10 5 0.06
11 12 0.15
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (8 bp):
AATATTGT
Found at i:43706469 original size:49 final size:49
Alignment explanation
Indices: 43706410--43706589 Score: 170
Period size: 57 Copynumber: 3.6 Consensus size: 49
43706400 GATTATCTAT
*
43706410 ATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
43706459 ATTTTGTATGAATATTGCAATATTTTTGTATGAATATTGTAATATTGTAATATTATA
1 ATTTTGTATGAATATTG-TA-ATTTTT-T-TG--TA-TG-AATATTGTAATATTATA
* ** * *
43706516 ATTTTGTATGAATATTGTAA--TGTCAGGAT--ATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
*
43706561 ATTTTTTGTATGAATATTGTAATTATTTT
1 A--TTTTGTATGAATATTGTAATTTTTTT
43706590 ATAATTAATT
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
45 16 0.15
47 19 0.18
48 1 0.01
49 18 0.17
50 1 0.01
51 7 0.07
52 1 0.01
53 4 0.04
55 3 0.03
56 3 0.03
57 34 0.32
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (49 bp):
ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATA
Found at i:43706502 original size:22 final size:22
Alignment explanation
Indices: 43706415--43706504 Score: 117
Period size: 22 Copynumber: 3.9 Consensus size: 22
43706405 TCTATATTTA
*
43706415 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATATTTTT
43706437 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-A-TAT--TTTT
*
43706464 GTATGAATATTGCAATATTTTT
1 GTATGAATATTGTAATATTTTT
43706486 GTATGAATATTGTAATATT
1 GTATGAATATTGTAATATT
43706505 GTAATATTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
22 35 0.58
23 1 0.02
24 4 0.07
25 3 0.05
26 1 0.02
27 16 0.27
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (22 bp):
GTATGAATATTGTAATATTTTT
Found at i:43706736 original size:28 final size:27
Alignment explanation
Indices: 43706705--43706762 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43706695 CACAAAAATT
*
43706705 TATAACATAAATTTCATTGGCGCCTCTC
1 TATAACA-AAACTTCATTGGCGCCTCTC
* * *
43706733 TATAAGACACCTTCATTGGCGCCTCTC
1 TATAACAAAACTTCATTGGCGCCTCTC
43706760 TAT
1 TAT
43706763 GAGGCACCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (27 bp):
TATAACAAAACTTCATTGGCGCCTCTC
Found at i:43706794 original size:27 final size:27
Alignment explanation
Indices: 43706717--43706783 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
43706707 TAACATAAAT
*
43706717 TTCATTGGCGCCTCTCTATAAGACACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
*
43706744 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
43706771 TTCATTGGCGCCT
1 TTCATTGGCGCCT
43706784 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGGCACC
Found at i:43706861 original size:12 final size:12
Alignment explanation
Indices: 43706846--43706895 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
43706836 GTATTTTTTA
43706846 AAAAAAATTATT
1 AAAAAAATTATT
43706858 AAAAAAA-TA-T
1 AAAAAAATTATT
43706868 AAAAAATATTTTATT
1 AAAAAA-A--TTATT
43706883 AAAAAAATTATT
1 AAAAAAATTATT
43706895 A
1 A
43706896 TTTTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
12 13 0.39
14 3 0.09
15 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAAAAATTATT
Found at i:43706887 original size:15 final size:15
Alignment explanation
Indices: 43706843--43706897 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 15
43706833 CTCGTATTTT
43706843 TTAAAAAAA--ATTA
1 TTAAAAAAATTATTA
43706856 TTAAAAAAA-TA-TA
1 TTAAAAAAATTATTA
*
43706869 --AAAAATATT-TTA
1 TTAAAAAAATTATTA
43706881 TTAAAAAAATTATTA
1 TTAAAAAAATTATTA
43706896 TT
1 TT
43706898 TTTTTATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 11 0.32
14 9 0.26
15 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAAAAATTATTA
Found at i:43717392 original size:12 final size:13
Alignment explanation
Indices: 43717367--43717414 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
43717357 TTTTCTGAGG
43717367 TAAAAATAATTAT
1 TAAAAATAATTAT
*
43717380 TAAAAGTAA-TAT
1 TAAAAATAATTAT
*
43717392 TAAAAATAAATCAT
1 TAAAAAT-AATTAT
43717406 ATAAAAATA
1 -TAAAAATA
43717415 CAAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 3 0.10
15 7 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAAATAATTAT
Found at i:43720192 original size:23 final size:24
Alignment explanation
Indices: 43720145--43720190 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
43720135 GAAAAATATT
43720145 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
43720169 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTTTATTTT
43720191 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:43720320 original size:59 final size:59
Alignment explanation
Indices: 43720257--43720435 Score: 259
Period size: 68 Copynumber: 2.9 Consensus size: 59
43720247 TCAAGTTTGT
*
43720257 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
43720316 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
43720381 AAA
57 AAA
*
43720384 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
43720436 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 47 0.43
60 1 0.01
62 2 0.02
65 2 0.02
67 1 0.01
68 56 0.51
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:43720358 original size:9 final size:9
Alignment explanation
Indices: 43720346--43720373 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43720336 TTTTATTACA
43720346 ACAATTAAT
1 ACAATTAAT
43720355 ACAATTAAT
1 ACAATTAAT
43720364 ACAATTAAT
1 ACAATTAAT
43720373 A
1 A
43720374 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:43720479 original size:68 final size:68
Alignment explanation
Indices: 43720287--43720460 Score: 318
Period size: 68 Copynumber: 2.6 Consensus size: 68
43720277 TTTTGTTACA
43720287 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
43720352 AAT
66 AAT
43720355 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
43720420 AAT
66 AAT
*
43720423 ACAATT-A-ACAATTAATAATTTGATAATTTTACT-ATCAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAA
43720461 TTAATTTTAA
Statistics
Matches: 105, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
65 5 0.05
66 25 0.24
67 1 0.01
68 74 0.70
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:43720486 original size:22 final size:22
Alignment explanation
Indices: 43720461--43720521 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
43720451 TTACTATCAA
** * *
43720461 TTAATTTTAATAACTATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
43720483 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
43720505 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
43720522 CGGGCCGGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:43721935 original size:2 final size:2
Alignment explanation
Indices: 43721928--43721970 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
43721918 GAATGGTATA
* *
43721928 TG TG TG TG TG TG TG TG TG TG TG TA TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43721970 T
1 T
43721971 CTAGTTGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:43724182 original size:19 final size:20
Alignment explanation
Indices: 43724160--43724197 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
43724150 CTGCTAAACC
43724160 ATTTCATTGCAT-TTAGTTT
1 ATTTCATTGCATATTAGTTT
43724179 ATTTCATTGCATATTAGTT
1 ATTTCATTGCATATTAGTT
43724198 GTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTTCATTGCATATTAGTTT
Found at i:43728999 original size:29 final size:30
Alignment explanation
Indices: 43728956--43729022 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
43728946 GTATGAATAT
*
43728956 ACTTTTGGAGTAGATATCTTGTTTGATGGA
1 ACTTTTAGAGTAGATATCTTGTTTGATGGA
43728986 ACTTTTAG-GTAGATATCTTGTTTGATGGA
1 ACTTTTAGAGTAGATATCTTGTTTGATGGA
43729015 ACTTTTAG
1 ACTTTTAG
43729023 TGCTTTGGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (30 bp):
ACTTTTAGAGTAGATATCTTGTTTGATGGA
Found at i:43735996 original size:11 final size:12
Alignment explanation
Indices: 43735966--43736002 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43735956 CTCACACAAA
43735966 TTCTT-TTCTTTT
1 TTCTTCTTC-TTT
43735978 TTCTTCTTCTTT
1 TTCTTCTTCTTT
43735990 TTC-TCTTCTTT
1 TTCTTCTTCTTT
43736001 TT
1 TT
43736003 TGGGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 11 0.46
13 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:43758637 original size:15 final size:16
Alignment explanation
Indices: 43758611--43758641 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
43758601 CAAAGGCACC
43758611 ACAATATATAAAAACA
1 ACAATATATAAAAACA
43758627 ACAAT-TATAAAAACA
1 ACAATATATAAAAACA
43758642 TGTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (16 bp):
ACAATATATAAAAACA
Found at i:43760588 original size:18 final size:16
Alignment explanation
Indices: 43760554--43760589 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
43760544 TAATATAATA
43760554 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
43760570 TATTTTGTAATATACTTT
1 TATTTT-TAATA-ACTTT
43760588 TA
1 TA
43760590 AAAACCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:43764441 original size:57 final size:57
Alignment explanation
Indices: 43764371--43764479 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
43764361 AATTCGGATT
*
43764371 ACCCGTCCGGGCTAAATCCA-TTTTC-CACATATTCTTCAGGAGGGCTATATCAAGATC
1 ACCCGTCCAGGCTAAAT--ATTTTTCACACATATTCTTCAGGAGGGCTATATCAAGATC
* *
43764428 ACCCGTCCAGGCTAGATATTTTTCACACATATTCTTCGGGAGGGCTATATCA
1 ACCCGTCCAGGCTAAATATTTTTCACACATATTCTTCAGGAGGGCTATATCA
43764480 GGATAGGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
55 1 0.02
56 5 0.11
57 41 0.87
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (57 bp):
ACCCGTCCAGGCTAAATATTTTTCACACATATTCTTCAGGAGGGCTATATCAAGATC
Found at i:43765342 original size:15 final size:17
Alignment explanation
Indices: 43765324--43765358 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
43765314 ATTATTAAGG
43765324 ATTATAA-TCAT-ATAA
1 ATTATAACTCATAATAA
43765339 ATTATAACTCATAATAA
1 ATTATAACTCATAATAA
43765356 ATT
1 ATT
43765359 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 4 0.22
17 7 0.39
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTATAACTCATAATAA
Found at i:43770085 original size:50 final size:50
Alignment explanation
Indices: 43770005--43770197 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
43769995 ATTTGGGTAA
*
43770005 AGAGGTCTCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
* * *
43770055 AGAGGTCCCATGTTAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
** * * * *
43770105 AGAGGTCCCCCGTAAGACCATGTCTAGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
** * *
43770155 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA
43770198 TGTTGTTATC
Statistics
Matches: 121, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
50 89 0.74
51 32 0.26
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
Found at i:43779662 original size:31 final size:31
Alignment explanation
Indices: 43779625--43779686 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
43779615 AGATAATTTT
43779625 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
43779656 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
43779687 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:43783675 original size:12 final size:13
Alignment explanation
Indices: 43783644--43783676 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
43783634 AATGTGGTTT
43783644 TTTAAAATATATG
1 TTTAAAATATATG
*
43783657 CTTAAAATAT-TG
1 TTTAAAATATATG
43783669 TTTAAAAT
1 TTTAAAAT
43783677 TTATAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTAAAATATATG
Found at i:43789373 original size:28 final size:26
Alignment explanation
Indices: 43789340--43789403 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 26
43789330 TCTCATTCCT
43789340 ATTTTACCCTCAG-CAAAATTTTACGATG
1 ATTTTACCC-CAGACAAAATTTT--GATG
* *
43789368 ATTTTACCCCTGATAAAATTTTGATG
1 ATTTTACCCCAGACAAAATTTTGATG
43789394 ATTTTACCCC
1 ATTTTACCCC
43789404 TGGTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 14 0.42
27 2 0.06
28 17 0.52
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCAGACAAAATTTTGATG
Found at i:43789400 original size:26 final size:27
Alignment explanation
Indices: 43789354--43789414 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 27
43789344 TACCCTCAGC
43789354 AAAATTTTACGATGATTTTACCCCTGAT
1 AAAATTTTA-GATGATTTTACCCCTGAT
*
43789382 AAAATTTT-GATGATTTTACCCCTGGT
1 AAAATTTTAGATGATTTTACCCCTGAT
43789408 AAAATTT
1 AAAATTT
43789415 CAAGAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 24 0.75
28 8 0.25
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (27 bp):
AAAATTTTAGATGATTTTACCCCTGAT
Found at i:43791233 original size:36 final size:36
Alignment explanation
Indices: 43791186--43791257 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
43791176 CATGAGTTAA
43791186 TTCATAAACCATTCATGACATTACTTCATGCCAAAT
1 TTCATAAACCATTCATGACATTACTTCATGCCAAAT
43791222 TTCATAAACCATTCATGACATTACTTCATGCCAAAT
1 TTCATAAACCATTCATGACATTACTTCATGCCAAAT
43791258 CATATACCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (36 bp):
TTCATAAACCATTCATGACATTACTTCATGCCAAAT
Found at i:43792286 original size:41 final size:44
Alignment explanation
Indices: 43792237--43792386 Score: 127
Period size: 43 Copynumber: 3.5 Consensus size: 44
43792227 AACCGTTACT
* *
43792237 CGGTGGAATCAGCACTTAGCAACCAAC-TT-ATATTC-AGTGATA
1 CGGTGGAATCAGCACTTAGCAACCAACTTTCACAATCAAG-GATA
* *
43792279 CTG-GGAATCAGCA-TATAGCAACC-CCTTTCACAATCAAGGATA
1 CGGTGGAATCAGCACT-TAGCAACCAACTTTCACAATCAAGGATA
* * ** *
43792321 CGGTGGAATCAGCACTTAGCAACC-ACCTTCAGAATCAATAATT
1 CGGTGGAATCAGCACTTAGCAACCAACTTTCACAATCAAGGATA
* *
43792364 TGG-GGAATCAACACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
43792387 CCTCGGGGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
40 2 0.02
41 20 0.22
42 31 0.35
43 35 0.39
44 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCAACTTTCACAATCAAGGATA
Found at i:43792404 original size:26 final size:26
Alignment explanation
Indices: 43792365--43792441 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 26
43792355 TCAATAATTT
**
43792365 GGGGAATCAACACTTAGCAACCCCTC
1 GGGGAATCTGCACTTAGCAACCCCTC
*
43792391 GGGGAATCTGCACTTAGCAACCGCTC
1 GGGGAATCTGCACTTAGCAACCCCTC
43792417 GGGGAATCTGCACTTAGCAACCCCT
1 GGGGAATCTGCACTTAGCAACCCCT
43792442 TTTTGATCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.18
Consensus pattern (26 bp):
GGGGAATCTGCACTTAGCAACCCCTC
Found at i:43794911 original size:14 final size:14
Alignment explanation
Indices: 43794892--43794918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43794882 GCGTCCGTAT
43794892 TTAAATTAGATTAG
1 TTAAATTAGATTAG
43794906 TTAAATTAGATTA
1 TTAAATTAGATTA
43794919 AAAACAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TTAAATTAGATTAG
Found at i:43795866 original size:119 final size:119
Alignment explanation
Indices: 43795650--43795867 Score: 312
Period size: 119 Copynumber: 1.8 Consensus size: 119
43795640 AGAAAAAATA
* * **
43795650 GGGTGTTGTGATTAGGGATTAATACGATGACTTAAGATTTAACATATCTTGCGGATTCTCTGAAG
1 GGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTCTGAAG
**
43795715 CTAGTGTTAGCAAACTTGATCTGAAGCTAGTGTTGTCATTTTGCAAAAACAAAC
66 CTAGTGTTAGCAAACTTGATCCAAAGCTAGTGTTGTCATTTTGCAAAAACAAAC
* * * * *
43795769 GGGTTTTGTGATCAGGGACTAATTCGATTACTTGAGATCCAACATATGTTGCGGATTCTCTGAAG
1 GGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTCTGAAG
*
43795834 CTAGTGTTAGC-AACTCTGATCCAAAGTTAGTGTT
66 CTAGTGTTAGCAAACT-TGATCCAAAGCTAGTGTT
43795868 AGCAGCTCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 4 0.05
119 82 0.95
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (119 bp):
GGGTGTTGTGATCAGGGACTAATACGATGACTTAAGATCCAACATATCTTGCGGATTCTCTGAAG
CTAGTGTTAGCAAACTTGATCCAAAGCTAGTGTTGTCATTTTGCAAAAACAAAC
Found at i:43797224 original size:9 final size:9
Alignment explanation
Indices: 43797210--43797240 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43797200 GTTAAACGAA
43797210 TCGAGTTAT
1 TCGAGTTAT
*
43797219 TCGAGTTAA
1 TCGAGTTAT
43797228 TCGAGTTAT
1 TCGAGTTAT
43797237 TCGA
1 TCGA
43797241 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:43797310 original size:9 final size:9
Alignment explanation
Indices: 43797293--43797329 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43797283 TGAGTTTTCG
43797293 AATTCGAAT
1 AATTCGAAT
*
43797302 AACTCGAAT
1 AATTCGAAT
43797311 AATTCGAAT
1 AATTCGAAT
43797320 AATTCGAAT
1 AATTCGAAT
43797329 A
1 A
43797330 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.