Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 19
Found at i:1836151 original size:21 final size:21
Alignment explanation
Indices: 1836098--1836158 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1836088 GATGTTGATG
* * *
1836098 TGGCAGTCCACGATGCTAACG
1 TGGCAGTCTACGATGCTGACA
* * *
1836119 TGACACTTTACGATGCTGACA
1 TGGCAGTCTACGATGCTGACA
1836140 TGGCAGTCTACGATGCTGA
1 TGGCAGTCTACGATGCTGA
1836159 TGAGGCAATC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (21 bp):
TGGCAGTCTACGATGCTGACA
Found at i:1836165 original size:21 final size:21
Alignment explanation
Indices: 1836086--1836172 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
1836076 TTGACCGTTC
* * *
1836086 ACGATGTTGATGTGGCAGTCC
1 ACGATGCTGATGAGGCAGTCT
* * * * * *
1836107 ACGATGCTAACGTGACACTTT
1 ACGATGCTGATGAGGCAGTCT
*
1836128 ACGATGCTGA-CATGGCAGTCT
1 ACGATGCTGATGA-GGCAGTCT
*
1836149 ACGATGCTGATGAGGCAATCT
1 ACGATGCTGATGAGGCAGTCT
1836170 ACG
1 ACG
1836173 GTGGCTAGTG
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
21 48 0.98
22 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (21 bp):
ACGATGCTGATGAGGCAGTCT
Found at i:1836762 original size:31 final size:31
Alignment explanation
Indices: 1836710--1836771 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1836700 AGGAGGAATG
* *
1836710 GTCTCTAACGTTATCGGTCCATTCGATTTTA
1 GTCTCTAACATTATCGATCCATTCGATTTTA
*
1836741 GTCTTTAACATTATCGATCCATTCGATTTTA
1 GTCTCTAACATTATCGATCCATTCGATTTTA
1836772 ATCACTCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (31 bp):
GTCTCTAACATTATCGATCCATTCGATTTTA
Found at i:1836928 original size:21 final size:21
Alignment explanation
Indices: 1836904--1836947 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1836894 TTAGATAATG
1836904 TTAGGGATCATTTC-CTCTTAA
1 TTAGGGATCATTTCTC-CTTAA
1836925 TTAGGGATCATTTCTCCTTAA
1 TTAGGGATCATTTCTCCTTAA
1836946 TT
1 TT
1836948 TTTAAATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (21 bp):
TTAGGGATCATTTCTCCTTAA
Found at i:1837527 original size:15 final size:15
Alignment explanation
Indices: 1837489--1837535 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1837479 AAATATTTGA
*
1837489 TAATATTTTTATATT
1 TAATATTTTAATATT
1837504 TAACT-TTTTAATATT
1 TAA-TATTTTAATATT
*
1837519 TTATATTTTAA-ATT
1 TAATATTTTAATATT
1837533 TAA
1 TAA
1837536 AATATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.22
15 20 0.74
16 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATATTTTAATATT
Found at i:1837528 original size:23 final size:23
Alignment explanation
Indices: 1837483--1837553 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
1837473 ATATAAAAAT
1837483 ATTTGATAATATTTT-TATATTTAA
1 ATTT-ATAATATTTTATAT-TTTAA
* *
1837507 CTTTTTAATATTTTATATTTTAA
1 ATTTATAATATTTTATATTTTAA
* *
1837530 ATTTAAAATATGTTTATTTTTTAA
1 ATTTATAATAT-TTTATATTTTAA
1837554 GAAAAGCCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (23 bp):
ATTTATAATATTTTATATTTTAA
Found at i:1842567 original size:2 final size:2
Alignment explanation
Indices: 1842560--1842585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1842550 CTGCAAATTG
1842560 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1842586 TTTATTCCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1843727 original size:19 final size:19
Alignment explanation
Indices: 1843703--1843772 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
1843693 ATGCAATTAG
*
1843703 TGCATCAATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
*
1843722 TGCATCTATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
1843741 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
1843760 TGCATCGATGCAT
1 TGCATCGATGCAT
1843773 CCCAGTGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:1844901 original size:30 final size:30
Alignment explanation
Indices: 1844861--1844933 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1844851 GGTTATTCGG
* *
1844861 GACCTATGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
1844891 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
1844921 GACCTCTAGATAG
1 GACCTCTGGATAG
1844934 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:1846525 original size:13 final size:14
Alignment explanation
Indices: 1846490--1846526 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1846480 ATTTTCTATA
1846490 TTAATTAT-AATCC
1 TTAATTATAAATCC
1846503 TTATATTATAAAT-C
1 TTA-ATTATAAATCC
1846517 TTAATTATAA
1 TTAATTATAA
1846527 TAATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTATAAATCC
Found at i:1847045 original size:2 final size:2
Alignment explanation
Indices: 1847040--1847091 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
1847030 TATAAACTTT
* * * *
1847040 TA TA TA TC TA TA TA TC TA TA TC TA TA TA TA CA CTA -A 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
1847082 TA TA TA TA TA
1 TA TA TA TA TA
1847092 CTCACACACA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.03
2 38 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1847207 original size:2 final size:2
Alignment explanation
Indices: 1847202--1847436 Score: 136
Period size: 2 Copynumber: 118.0 Consensus size: 2
1847192 ACTTTACACT
*
1847202 TA TA TA TA TA TA TA TA GT- TA TA TA GT- TA TA TA TA CT- TA TG
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
1847242 TA CA TA TA GTA TA CA TA CA TA CA TA T- TCA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* *
1847285 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA CTCA TG CA TCA T- TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -T-A TA TA T-A TA T-A
* * * *
1847329 TCA TA CA TA -A T- TA CA TA TA TA CT- TA TT TA TG TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
1847370 TA TA TA TA T- TA -A TA T- TA TA TG CA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1847408 TA TA AA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1847437 AGTATAATGG
Statistics
Matches: 178, Mismatches: 31, Indels: 48
0.69 0.12 0.19
Matches are distributed among these distances:
1 13 0.07
2 148 0.83
3 16 0.09
4 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1854692 original size:26 final size:25
Alignment explanation
Indices: 1854661--1854731 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 25
1854651 ACTATATAAA
1854661 TTTGTAATTCATAAATATTATTATC
1 TTTGTAATTCATAAATATTATTATC
* *
1854686 TTATGT-A-T-A-AACTA-TATATAAC
1 TT-TGTAATTCATAAATATTAT-TATC
*
1854708 TTTATAATTCATAAATATTATTAT
1 TTTGTAATTCATAAATATTATTAT
1854732 AAAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
21 5 0.15
22 10 0.29
23 2 0.06
24 2 0.06
25 9 0.26
26 6 0.18
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (25 bp):
TTTGTAATTCATAAATATTATTATC
Found at i:1854704 original size:47 final size:45
Alignment explanation
Indices: 1854563--1854731 Score: 178
Period size: 47 Copynumber: 3.7 Consensus size: 45
1854553 GAATAGACTG
1854563 TATAAATTTGTAATTCATAAATATTATTATCTTATGTATATACTA
1 TATAAATTTGTAATTCATAAATATTATTATCTTATGTATATACTA
** ** ** ** * *
1854608 TATAAATTTGT-ATAAATTGATGGTAGAAACATGAAGTGTATATACTA
1 TATAAATTTGTAATTCATAAATATTATTATC-T-TA-TGTATATACTA
*
1854655 TATAAATTTGTAATTCATAAATATTATTATCTTATGTATAAACTA
1 TATAAATTTGTAATTCATAAATATTATTATCTTATGTATATACTA
*
1854700 TATATAACTTTATAATTCATAAATATTATTAT
1 TATA-AA-TTTGTAATTCATAAATATTATTAT
1854732 AAAATAAATT
Statistics
Matches: 96, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
44 10 0.10
45 26 0.27
46 4 0.04
47 46 0.48
48 10 0.10
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (45 bp):
TATAAATTTGTAATTCATAAATATTATTATCTTATGTATATACTA
Found at i:1854808 original size:25 final size:25
Alignment explanation
Indices: 1854774--1854825 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1854764 CACTAGATAC
1854774 AATTAAAATATAAGGTAA-AGTATAT
1 AATTAAAATATAAGGTAACA-TATAT
*
1854799 AATTAAAATATAGGGTAACATATAT
1 AATTAAAATATAAGGTAACATATAT
1854824 AA
1 AA
1854826 ACCGTCTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.31
Consensus pattern (25 bp):
AATTAAAATATAAGGTAACATATAT
Found at i:1855124 original size:21 final size:21
Alignment explanation
Indices: 1855061--1855126 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1855051 CAAACTTTAA
1855061 CCCATTTTATTATAGAAATTT
1 CCCATTTTATTATAGAAATTT
* * *
1855082 AACCAATATATCTA-AGGAAATTT
1 -CCCATTTTAT-TATA-GAAATTT
1855105 CCCATTTTATTATAGAAATTT
1 CCCATTTTATTATAGAAATTT
1855126 C
1 C
1855127 AAAGAAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 10 0.29
22 16 0.46
23 9 0.26
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (21 bp):
CCCATTTTATTATAGAAATTT
Found at i:1855883 original size:21 final size:20
Alignment explanation
Indices: 1855851--1855890 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1855841 CTGAAAATAA
*
1855851 ATTAAAAGTTCAATAATTGT
1 ATTAAAAGTTCAAAAATTGT
*
1855871 ATTATAAATTTCAAAAATTG
1 ATTA-AAAGTTCAAAAATTG
1855891 AGTAATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTAAAAGTTCAAAAATTGT
Found at i:1858232 original size:26 final size:26
Alignment explanation
Indices: 1858196--1858248 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1858186 TTGAGGCTTA
1858196 GGGAGTTGGGACAGAGCGTGAAGTAT
1 GGGAGTTGGGACAGAGCGTGAAGTAT
1858222 GGGAGTTGGGACAGAGCGTGAAGTAT
1 GGGAGTTGGGACAGAGCGTGAAGTAT
1858248 G
1 G
1858249 CAAGGAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.47, T:0.19
Consensus pattern (26 bp):
GGGAGTTGGGACAGAGCGTGAAGTAT
Found at i:1858581 original size:15 final size:16
Alignment explanation
Indices: 1858543--1858575 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1858533 TGTATTTGGT
*
1858543 AGGAAGGAAAAGTGAG
1 AGGAAAGAAAAGTGAG
1858559 AGGAAAGAAAA-TGAG
1 AGGAAAGAAAAGTGAG
1858574 AG
1 AG
1858576 AGAAGATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
AGGAAAGAAAAGTGAG
Found at i:1859662 original size:2 final size:2
Alignment explanation
Indices: 1859655--1859683 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1859645 ATTTATTTAT
1859655 TA TA TA TA -A 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
1859684 ATTTGACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1860968 original size:21 final size:20
Alignment explanation
Indices: 1860938--1861001 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1860928 TAAAATAAGG
*
1860938 AAAATAAAATGAAATGAGTAGA
1 AAAAT-AAAT-AAATGAGTAAA
*
1860960 AAAATAAATAAA-AAGGTAAA
1 AAAATAAATAAATGA-GTAAA
1860980 AGAAATAAATAAATGAGATAAA
1 A-AAATAAATAAATGAG-TAAA
1861002 TATAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 16 0.46
22 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (20 bp):
AAAATAAATAAATGAGTAAA
Found at i:1862985 original size:102 final size:100
Alignment explanation
Indices: 1862844--1863277 Score: 372
Period size: 102 Copynumber: 4.3 Consensus size: 100
1862834 GTGTTTCAAG
* * *
1862844 AGAAACTGTCTCGAGTGAGGCGAAATTTGTTTAATGGAAAACAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAG-GAGACGAAATTTGTTTAA-GGAAAACATATTCAAAGATTTTGTTTCAAG
* *
1862909 AGAAATTGTCTCAAGAGAGA-AAAACTTTAGTTCCAAA
64 AGAAACTGTCTCAAGAGAGACAAAA-TTTAGTTACAAA
* *
1862946 AGAAACTGTCTCAAGGGAGACGCAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAA-GGAGACGAAATTTGTTT-AAGGAAAACATATTCAAAGATTTTGTTTCAAG
* *
1863011 AGAAACTGTCTAAAGAGAGACAAAATTT-GTTTC-AA
64 AGAAACTGTCTCAAGAGAGACAAAATTTAGTTACAAA
* * * *
1863046 GGAAAACAGAT-TC----AGA--AATTTTGTTTTAA-GAGAAAC-TGTCTCAAGAGAGATAAAAT
1 AG-AAACTG-TCTCAAGGAGACGAAATTTG-TTTAAGGA-AAACATAT-TC-A-A-AGAT----T
* * * *
1863102 TTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTTAGTTATAAA
54 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTACAAA
*
1863149 AGAAACTGTCTCAAGAGAGATGAAATTTGTTTAAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAG-GAGACGAAATTTGTTT-AAGGAAAACATATTCAAAGATTTTGTTTCAAG
* ** **
1863214 GGAAACTGTCTCAAGAGAGACAAAATTT-GTTTTACG
64 AGAAACTGTCTCAAGAGAGACAAAATTTAGTTACAAA
* *
1863250 AGAAAATGTCTCAAAAGAGACGAAATTT
1 AGAAACTGTCTC-AAGGAGACGAAATTT
1863278 AGTTCTAAAA
Statistics
Matches: 270, Mismatches: 33, Indels: 59
0.75 0.09 0.16
Matches are distributed among these distances:
93 3 0.01
94 13 0.05
95 4 0.01
96 4 0.01
97 4 0.01
100 3 0.01
101 74 0.27
102 125 0.46
103 10 0.04
106 4 0.01
107 4 0.01
108 4 0.01
109 14 0.05
110 4 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (100 bp):
AGAAACTGTCTCAAGGAGACGAAATTTGTTTAAGGAAAACATATTCAAAGATTTTGTTTCAAGAG
AAACTGTCTCAAGAGAGACAAAATTTAGTTACAAA
Found at i:1863050 original size:65 final size:65
Alignment explanation
Indices: 1862946--1863394 Score: 379
Period size: 65 Copynumber: 6.6 Consensus size: 65
1862936 TAGTTCCAAA
* **
1862946 AGAAACTGTCTCAAGGGAGACGCAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
* *
1863011 AGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCAGAA-ATTTTGTTTTAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCA-AAGATTTTGTTTCAA
1863075 G
65 G
* * * **
1863076 AGAAACTGTCTCAAGAGAGATAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAA-ATTT
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAAA-----C---AGATTCAAAGATTT
* *
1863140 AGTTAT-AAA
57 TGTT-TCAAG
** * *
1863149 AGAAACTGTCTCAAGAGAGATGAAATTTGTTTAAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
* * * *
1863214 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAA-TG-TCTCAAAAGAGACGAAATT
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAAACAGAT-TC---A-A-A-G--ATT
* *
1863277 TAG-TTCTAAA
56 TTGTTTC-AAG
* * * *
1863287 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTGTTTAAA
1 AGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAA
1863352 G
65 G
* * *
1863353 GGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GGAAAA
1863395 TGTCTCAAGA
Statistics
Matches: 311, Mismatches: 44, Indels: 57
0.75 0.11 0.14
Matches are distributed among these distances:
64 8 0.03
65 140 0.45
66 46 0.15
67 3 0.01
68 2 0.01
69 2 0.01
70 2 0.01
71 3 0.01
72 8 0.03
73 79 0.25
74 17 0.05
75 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (65 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
Found at i:1863162 original size:37 final size:36
Alignment explanation
Indices: 1863065--1863456 Score: 275
Period size: 36 Copynumber: 11.2 Consensus size: 36
1863055 ATTCAGAAAT
*
1863065 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1863101 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * **
1863137 TTTAGTTATAAAAGAAACTGTCTCAAGAGAGATGAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1863174 TTTGTTTAAAG-GAAAACATAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* *
1863203 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1863239 TTTGTTTTACGAGAAAATGTCTCAAAAGAGACGAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1863275 TTTAGTTCTAAAAGAAATTGTCTCAAGAGAGACAAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* ** **
1863312 CTTTGTTTCAAG-GAAAACAAAT-TC-A-A-AG----TT
1 -TTTGTTTTAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* * *
1863342 TTTGTTTAAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1863378 TTTGTTTTAAGGGAAAATGTCTCAAGAGAGA-TAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1863413 TTT-TTTTAAGAGAAATTATCTCAAGAGAGACGAAAC
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1863449 TTTGTTTT
1 TTTGTTTT
1863457 GAGTAAATTA
Statistics
Matches: 277, Mismatches: 51, Indels: 55
0.72 0.13 0.14
Matches are distributed among these distances:
28 3 0.01
29 33 0.12
30 4 0.01
31 2 0.01
32 4 0.01
33 2 0.01
34 27 0.10
35 9 0.03
36 116 0.42
37 73 0.26
38 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1863385 original size:139 final size:138
Alignment explanation
Indices: 1863011--1863455 Score: 619
Period size: 138 Copynumber: 3.2 Consensus size: 138
1863001 TTGTTTCAAG
* * *
1863011 AGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGAAAACAGATTCAGAA-ATTTTGTTTTAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAAATTCA-AAGATTTTGTTTAAA
* *
1863075 GAGAAACTGTCTCAAGAGAGATAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTT
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTT
1863140 AGTTATAAA
130 AGTTATAAA
** * * *
1863149 AGAAACTGTCTCAAGAGAGATGAAATTTGTTTAAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTAAAG
* *
1863214 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAAAGAGACGAAATTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTTA
*
1863279 GTTCTAAA
131 GTTATAAA
* *
1863287 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTGTTTAAA
1 AGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTAAA
* * * *
1863352 GGGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAATGTCTCAAGAGAGA-TAAATTT
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTT
* *
1863416 --TTTTAAG
130 AGTTATAAA
* * *
1863423 AGAAATTATCTCAAGAGAGACGAAACTTTGTTT
1 AGAAACTGTCTCAAGAGAGAC-AAAATTTGTTT
1863456 TGAGTAAATT
Statistics
Matches: 277, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
136 32 0.12
137 5 0.02
138 152 0.55
139 88 0.32
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (138 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTAAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAATTTA
GTTATAAA
Found at i:1863465 original size:36 final size:33
Alignment explanation
Indices: 1863361--1863466 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 33
1863351 AGGGAAACCG
* * *
1863361 TCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAATG
1 TCTCAAGAGAGAC-AAATTTGTTTT--GAGAAATTA
*
1863397 TCTCAAGAGAGATAAATTT-TTTTAAGAGAAATTA
1 TCTCAAGAGAGACAAATTTGTTTT--GAGAAATTA
1863431 TCTCAAGAGAGACGAAACTTTGTTTTGAGTAAATTA
1 TCTCAAGAGAGAC-AAA-TTTGTTTTGAG-AAATTA
1863467 GTCTTGAGCG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
34 24 0.39
35 12 0.20
36 21 0.34
37 4 0.07
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (33 bp):
TCTCAAGAGAGACAAATTTGTTTTGAGAAATTA
Found at i:1868379 original size:18 final size:18
Alignment explanation
Indices: 1868356--1868398 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1868346 GATCGGAAAA
1868356 TTACCTTAAAATTTAAAC
1 TTACCTTAAAATTTAAAC
1868374 TTACCTTAAAATTTAAAC
1 TTACCTTAAAATTTAAAC
1868392 TTACCTT
1 TTACCTT
1868399 TTTCGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (18 bp):
TTACCTTAAAATTTAAAC
Found at i:1880492 original size:18 final size:18
Alignment explanation
Indices: 1880471--1880505 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1880461 TATAATATTT
1880471 ATATATAATATAC-TTAAC
1 ATATAT-ATATACATTAAC
1880489 ATATATATATACATTAA
1 ATATATATATACATTAA
1880506 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATATACATTAAC
Found at i:1884132 original size:42 final size:42
Alignment explanation
Indices: 1884065--1884161 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
1884055 CCCCACTTCG
* * * * *
1884065 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
* * *
1884107 AGAGTCATCACCTGATCAAGTCGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
1884149 AGAGCCATCACCT
1 AGAGCCATCACCT
1884162 ATTCCATCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (42 bp):
AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
Found at i:1884303 original size:21 final size:21
Alignment explanation
Indices: 1884276--1884325 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1884266 GTTAGGGGAG
1884276 TTACGTGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
* *
1884297 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
1884318 TTACGTGA
1 TTACGTGA
1884326 CGACAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1884750 original size:21 final size:21
Alignment explanation
Indices: 1884725--1884885 Score: 223
Period size: 21 Copynumber: 7.6 Consensus size: 21
1884715 ATTCAACTGT
*
1884725 CATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
1884746 CATCGTTCAAGAGACCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
1884767 CATCGTTTAAGAGACCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
1884788 CATCGTTTAAGAGACCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
1884809 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
1884830 CACCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
1884851 CATCGTTCAAGAGGGCTCCTCC
1 CATCGTTCAAGA-GGCCCCTCC
*
1884873 CACCGTTCAAGAG
1 CATCGTTCAAGAG
1884886 CCCGATTCAC
Statistics
Matches: 128, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
21 110 0.86
22 18 0.14
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1885417 original size:20 final size:20
Alignment explanation
Indices: 1885392--1885449 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1885382 AATAAAACTT
1885392 GTTGCGAATTCGAAATTCGA
1 GTTGCGAATTCGAAATTCGA
** * *
1885412 GTTGCGAAAACAAAATTCGC
1 GTTGCGAATTCGAAATTCGA
*
1885432 GTTGCGAATTTGAAATTC
1 GTTGCGAATTCGAAATTC
1885450 AGCGTTGTGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
GTTGCGAATTCGAAATTCGA
Found at i:1885974 original size:18 final size:18
Alignment explanation
Indices: 1885950--1886015 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
1885940 TTGTTTTTCC
*
1885950 TTTTTTTATTTATTTATTA
1 TTTTTTCATTT-TTTATTA
* *
1885969 TTTTTTCCTTTTTTTTTA
1 TTTTTTCATTTTTTATTA
*
1885987 TTTTTTTCA-TTCTTATT-
1 -TTTTTTCATTTTTTATTA
1886004 TTTTTTC-TTTTT
1 TTTTTTCATTTTT
1886016 ACTCAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 10 0.26
18 12 0.32
19 16 0.42
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTCATTTTTTATTA
Found at i:1886005 original size:21 final size:20
Alignment explanation
Indices: 1885950--1886006 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
1885940 TTGTTTTTCC
1885950 TTTTTTT-A-TTTATTTATTA
1 TTTTTTTCATTTTATTT-TTA
*
1885969 -TTTTTTCCTTTT-TTTTTA
1 TTTTTTTCATTTTATTTTTA
1885987 TTTTTTTCATTCTTATTTTT
1 TTTTTTTCATT-TTATTTTT
1886007 TTTCTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 9 0.29
19 12 0.39
20 5 0.16
21 5 0.16
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTCATTTTATTTTTA
Found at i:1886051 original size:17 final size:17
Alignment explanation
Indices: 1886026--1886058 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1886016 ACTCAATTTA
*
1886026 TTTATTTTTTAATTTTT
1 TTTAATTTTTAATTTTT
1886043 TTTAATTTTTAATTTT
1 TTTAATTTTTAATTTT
1886059 ATTATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTAATTTTTAATTTTT
Found at i:1890036 original size:110 final size:110
Alignment explanation
Indices: 1889847--1890591 Score: 1006
Period size: 110 Copynumber: 6.9 Consensus size: 110
1889837 GGTTGCCCAG
* *
1889847 CTTCACAGCGAAGGGGCG---G-CTGTCAACAAATAACTTTCCAGTTTCATTCAGAGTCAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* *
1889908 AACTTCACAACGAAGGATATTAGACTCGAGATAACACAAGCTCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* * *
1889953 CTTCACAGTGAAGGGGCGACTGACTGTCAACAAAAAACTTTTCAGTTTCATTCAAAGTCAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* * *
1890018 AACTTCATAGCGAAGGATATTGGACTCGAGACAACACAAACTCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* * *
1890063 ATTCACAACGAA-----G---G---GTCAACAAACAACTTTTTAGTTTCATTCAGAGTCAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* * *
1890117 AACTTCACAATGAAGGATATTAGACTCGAGACATCACAAGCTCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* * *
1890162 CTTCACAGCAAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTTAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* * *
1890227 AACTTCACAGCAAAAGATATTGGACTCGAGACAACACAAGCTCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* * * * *
1890272 CTTCACAGCGAAGGGGTGGCTGACTGTCAACAAACAACTTTTTAGTTTCATTCAAAGTCAATTTT
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* * *
1890337 AACTTCACAATGAAGGATATTGAACTCGAGACAACACAAGATCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* *
1890382 CTTCACAGCGAAGGGGCGACTGACAGTCAACAAACAAATTTTCAGTTTCATTCAGAGTCAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
1890447 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
* * *
1890492 CTTCACAGTGAAGGGGCGACTGGCTGTCAACAAACAACTTTCCAG-TT--TT-AGAGTCAATTTC
1 CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
* * * *
1890553 AACTTCATAATGAAGGATATTGGCCTCGAAACAACACAA
66 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAA
1890592 ATATTTGGAT
Statistics
Matches: 558, Mismatches: 66, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
99 85 0.15
102 1 0.00
104 1 0.00
105 1 0.00
106 64 0.11
107 3 0.01
109 3 0.01
110 400 0.72
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
CTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTC
AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAA
Found at i:1890797 original size:84 final size:84
Alignment explanation
Indices: 1890704--1891195 Score: 551
Period size: 84 Copynumber: 5.9 Consensus size: 84
1890694 CCCACCATGG
* * * *
1890704 CCTTCGAGTTCGATTACGCTTAGCGT-TAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
1 CCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1890768 GGTTATCTGCCAACCAAAGA
65 GGTTATCTGCCAACCAAAGA
* * *
1890788 CCTTCGAGTTCGACTATGCTCAGCTCAAAGGTACATCATTTGCAGTATAGCTTAAGTCGAGAAGG
1 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* * *
1890853 GCTATCTGTC-ATCAAAGA
66 GTTATCTGCCAACCAAAGA
* * * * * * *
1890871 CCTTCGAGTTCGACTATGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGG
1 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
*
1890936 GTTATCTGCCAACCAAATA
66 GTTATCTGCCAACCAAAGA
* * * * * * * *
1890955 CCTTCAAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGCAAGAAGT
1 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* * *
1891020 ATTATTTGCCAACAAAAGA
66 GTTATCTGCCAACCAAAGA
* * * *
1891039 CCTTCGAGTTCGACTACGCTCAACTCAAAGACACATCATTTGCATCATAGCTTAATTCGAGAAGG
1 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
* *
1891104 GTTATCTGTC-ATCAAAGA
66 GTTATCTGCCAACCAAAGA
* * * * *
1891122 CCTTTGAGTTCGATTACACTCAGCTCAGAGGCAAATCAAATTTGCAGCATAGCTTAAGGT-GAGA
1 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTTAA-GTCGAGA
*
1891186 AGGGCTATCT
63 AGGGTTATCT
1891196 ATCAATAAAA
Statistics
Matches: 341, Mismatches: 62, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
83 109 0.32
84 201 0.59
85 30 0.09
86 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGA
Found at i:1890980 original size:167 final size:168
Alignment explanation
Indices: 1890704--1891195 Score: 587
Period size: 167 Copynumber: 2.9 Consensus size: 168
1890694 CCCACCATGG
* * * * *
1890704 CCTTCGAGTTCGATTACGCTTAGCGT-TAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
1 CCTTCGAGTTCGACTACGCTCAAC-TCAAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAG
*
1890768 GGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCAAAGGTACATCATTTGCAG
65 GGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGTACATCATTTGCAG
* * *
1890833 TATAGCTTAAGTCGAGAAGGGCTATCTGTCATC-AAAGA
130 CATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGA
* * * * * *
1890871 CCTTCGAGTTCGACTATGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGG
1 CCTTCGAGTTCGACTACGCTCAACTCAAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * * *
1890936 GTTATCTGCCAACCAAATACCTTCAAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAAC
66 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGTACATCATTTGCAGC
* * * *** *
1891001 ATAGCTCAAGGCAAGAAGTATTATTTGCCAACAAAAGA
131 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGA
* * *
1891039 CCTTCGAGTTCGACTACGCTCAACTCAAAGACACATCATTTGCATCATAGCTTAATTCGAGAAGG
1 CCTTCGAGTTCGACTACGCTCAACTCAAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * * * * * * *
1891104 GTTATCTGTC-ATCAAAGACCTTTGAGTTCGATTACACTCAGCTCAGAGGCAAATCAAATTTGCA
66 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGTACATC--ATTTGCA
1891168 GCATAGCTTAAGGT-GAGAAGGGCTATCT
129 GCATAGCTTAA-GTCGAGAAGGGCTATCT
1891196 ATCAATAAAA
Statistics
Matches: 268, Mismatches: 52, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
166 1 0.00
167 171 0.64
168 70 0.26
169 25 0.09
170 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (168 bp):
CCTTCGAGTTCGACTACGCTCAACTCAAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGTACATCATTTGCAGC
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGA
Found at i:1891764 original size:18 final size:18
Alignment explanation
Indices: 1891743--1891777 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1891733 TATAATATTT
1891743 ATATATAATATAC-TTAAC
1 ATATAT-ATATACATTAAC
1891761 ATATATATATACATTAA
1 ATATATATATACATTAA
1891778 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATATACATTAAC
Found at i:1893427 original size:17 final size:16
Alignment explanation
Indices: 1893394--1893507 Score: 60
Period size: 17 Copynumber: 7.0 Consensus size: 16
1893384 CCTCTCTTCA
1893394 TTTTA-TTTTA-TA-T
1 TTTTATTTTTATTATT
1893407 TTTTATTTTTATTATT
1 TTTTATTTTTATTATT
*
1893423 CTTTT-TCCTTTT-TTCCTTT
1 -TTTTAT--TTTTATT--ATT
*
1893442 TTTTCATTCTTATTA-T
1 TTTT-ATTTTTATTATT
*
1893458 TTTTAATTTTATTTATT
1 TTTTATTTTTA-TTATT
*
1893475 TTTTAATTTTATTTATT
1 TTTTATTTTTA-TTATT
* *
1893492 TATTATTATTATTATT
1 TTTTATTTTTATTATT
1893508 ATTATATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.06
14 5 0.06
15 7 0.09
16 15 0.19
17 32 0.40
18 11 0.14
19 4 0.05
20 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTTATTATT
Found at i:1893460 original size:16 final size:16
Alignment explanation
Indices: 1893441--1893492 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
1893431 TTTTTTCCTT
*
1893441 TTTTTCATTCTTA-TTA
1 TTTTTAATT-TTATTTA
1893457 TTTTTAATTTTATTTA
1 TTTTTAATTTTATTTA
1893473 TTTTTTAATTTTATTTA
1 -TTTTTAATTTTATTTA
1893490 TTT
1 TTT
1893493 ATTATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 3 0.09
16 14 0.42
17 16 0.48
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTAATTTTATTTA
Found at i:1894405 original size:31 final size:31
Alignment explanation
Indices: 1894369--1894427 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1894359 AACTTAAAAG
* * *
1894369 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1894400 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1894428 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1894478 original size:22 final size:22
Alignment explanation
Indices: 1894452--1894494 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1894442 TAATAAATTA
1894452 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1894474 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1894495 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1894503 original size:22 final size:22
Alignment explanation
Indices: 1894454--1894502 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1894444 ATAAATTATT
**
1894454 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1894476 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1894499 TAAA
1 TAAA
1894503 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1894506 original size:54 final size:54
Alignment explanation
Indices: 1894442--1894844 Score: 440
Period size: 54 Copynumber: 7.6 Consensus size: 54
1894432 ACAACTACAA
1894442 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1894496 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1894550 TAATAAGTTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * ** *
1894604 TAATAAGTTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * *
1894664 TAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAAT-C---C
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
1894712 --AT--A-T-TTTAAAATAAATCATTCCATATTTTAAAATAAATAAATTTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
**
1894760 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1894814 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1894845 CTAATAAATT
Statistics
Matches: 299, Mismatches: 26, Indels: 48
0.80 0.07 0.13
Matches are distributed among these distances:
39 5 0.02
40 5 0.02
42 1 0.00
43 2 0.01
44 17 0.06
48 1 0.00
50 2 0.01
52 1 0.00
53 2 0.01
54 219 0.73
55 3 0.01
56 1 0.00
57 4 0.01
58 16 0.05
59 1 0.00
60 1 0.00
62 12 0.04
63 6 0.02
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1894512 original size:32 final size:32
Alignment explanation
Indices: 1894474--1894920 Score: 193
Period size: 32 Copynumber: 15.4 Consensus size: 32
1894464 CAATCCATAT
1894474 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1894506 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1894528 TTTAAAATAAATCAATCCATACTAATAAGTTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1894560 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1894582 TTTAAAATAAATCAATCCATACTAATAAGTTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1894614 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
1894644 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1894662 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1894694 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
1894716 TTTAAAATAAATCATTCCATATTTTAAAATAAATAAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* ** * * *
1894753 TTTATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 TTTA-A--AATAAATCAATCCATACT-AATAAAT---TA
**
1894791 TTTTAAAATAAATCAATATATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
1894824 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1894856 TTTAAAATAAAT-AA---AT-C-CAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1894878 TTTAAAATAAATCAATCCATA-AAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1894909 TTTAAAATAAAT
1 TTTAAAATAAAT
1894921 TATTTTAAAA
Statistics
Matches: 319, Mismatches: 28, Indels: 137
0.66 0.06 0.28
Matches are distributed among these distances:
20 1 0.00
22 66 0.21
23 10 0.03
24 5 0.02
25 1 0.00
26 28 0.09
27 11 0.03
28 12 0.04
29 1 0.00
30 2 0.01
31 21 0.07
32 109 0.34
33 2 0.01
34 1 0.00
36 20 0.06
37 11 0.03
38 4 0.01
39 7 0.02
40 7 0.02
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1894720 original size:22 final size:22
Alignment explanation
Indices: 1894694--1894749 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1894684 TAATAAATTA
1894694 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1894716 TTTAAAATAAATCATTCCATAT
1 TTTAAAATAAATCAATCCATAT
1894738 TTTAAAATAAAT
1 TTTAAAATAAAT
1894750 AAATTTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1894882 original size:22 final size:22
Alignment explanation
Indices: 1894856--1894956 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
1894846 TAATAAATTA
1894856 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATAAATCCATAT
* *
1894878 TTTAAAATAAATCAATCCATAA
1 TTTAAAATAAATAAATCCATAT
** * ** **
1894900 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-AAATCCA-TAT
*
1894924 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
1894946 TTT-TAATAAAT
1 TTTAAAATAAAT
1894957 TATTTTAAAA
Statistics
Matches: 57, Mismatches: 20, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
21 7 0.12
22 33 0.58
23 8 0.14
24 9 0.16
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1894882 original size:54 final size:50
Alignment explanation
Indices: 1894659--1895009 Score: 271
Period size: 54 Copynumber: 6.8 Consensus size: 50
1894649 AATCAATCCA
* *
1894659 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 TATTTTAAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATAAAT
* * * *
1894710 CCATATTTTAAAATAAATCATTCCATATTTTAAAATAAATAAATTTATACT-AATAAAT
1 ---TATTTTAAAATAAATCAATCCATA---T--AATAAAT-TATTTAAAATAAATAAAT
** * * *
1894768 TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATATAAT-AAATTATTTAA-A-ATA--AATAAAT
1894822 TA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAAT
1 TATTTTAAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATAAAT
*
1894872 CCATATTTTAAAATAAATCAATCCATAAAATAAATTATTT---A-AAATAAAT
1 ---TATTTTAAAATAAATCAATCCATATAATAAATTATTTAAAATAAATAAAT
*
1894921 TATTTTAAAATAAATCAATCCATATTTTTAATAAATTATTT--TA-AAATAAAT
1 TATTTTAAAATAAATCAATCCATA----TAATAAATTATTTAAAATAAATAAAT
*
1894972 TATTTTAAAATAAAT-AA-CC-T-TATTAAATTATTTAAAAT
1 TATTTTAAAATAAATCAATCCATATAATAAATTATTTAAAAT
1895010 TATTTTAATA
Statistics
Matches: 250, Mismatches: 23, Indels: 56
0.76 0.07 0.17
Matches are distributed among these distances:
43 12 0.05
45 1 0.00
46 24 0.10
48 1 0.00
49 15 0.06
50 27 0.11
51 26 0.10
52 3 0.01
53 15 0.06
54 101 0.40
55 4 0.02
56 1 0.00
58 13 0.05
59 7 0.03
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (50 bp):
TATTTTAAAATAAATCAATCCATATAATAAATTATTTAAAATAAATAAAT
Found at i:1894882 original size:108 final size:104
Alignment explanation
Indices: 1894443--1894986 Score: 376
Period size: 108 Copynumber: 5.2 Consensus size: 104
1894433 CAACTACAAT
**
1894443 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTATT
* ** * * *
1894508 TAAAATAAATCAATCTATA-TTTTAAAATAAATCAATCCATA
66 TAAAATAAATCAATCCATACTAAT-AAATAATTTAA--AATA
* * ** *
1894549 CTAATAAGTTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAGTTA
1 --AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTA
* *
1894614 TTTAAAATAAATCAATCTATAC-AACTACAATAA--T-AAATC
64 TTTAAAATAAATCAATCCATACTAA-TA-AATAATTTAAAATA
** * * * * * * * * **
1894653 AATCCA-TATTTTAAAATAAATCAATTCATA-CTAATAAATTATTTAAAATA-AATCAATCCA-T
1 AATAAATTA-TTTAAAATAAATCAATCCATATTTTA-AAATAAATCAATATATACT-AATAAATT
* * * *
1894714 ATTTTAAAATAAATCATTCCATATTTTAAAATAAATAAATTTATACT-
63 A-TTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTAAAATA
1894761 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTATT
*
1894826 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
66 TAAAATAAATCAATCCATACTAATAAATAATTTAAAATA
* *
1894865 AATAAATCCATATTTTAAAATAAATCAATCC--A---TAAAATAAAT---TATTTA-AAATAAAT
1 AATAAAT---TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAAT
* * *
1894921 TATTTTAAAATAAATCAATCCATATTTTTAATAAATTATTT--TA-A
62 TA-TTTAAAATAAATCAATCCATA---CTAATAAATAATTTAAAATA
1894965 AATAAATTATTTTAAAATAAAT
1 AATAAATTA-TTTAAAATAAAT
1894987 AACCTTATTA
Statistics
Matches: 356, Mismatches: 51, Indels: 69
0.75 0.11 0.14
Matches are distributed among these distances:
97 15 0.04
99 9 0.03
100 34 0.10
101 9 0.03
102 53 0.15
103 30 0.08
104 16 0.04
105 3 0.01
106 7 0.02
107 4 0.01
108 160 0.45
109 16 0.04
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (104 bp):
AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTATT
TAAAATAAATCAATCCATACTAATAAATAATTTAAAATA
Found at i:1894883 original size:86 final size:85
Alignment explanation
Indices: 1894738--1894920 Score: 294
Period size: 86 Copynumber: 2.1 Consensus size: 85
1894728 CATTCCATAT
** *
1894738 TTTAAAATAAATAAATTTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAA
* *
1894803 TCAATATATACTAATAAATTA
66 TCAATACATA-AAATAAATTA
*
1894824 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAA
1 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAA
*
1894889 TCAATCCATAAAATAAATTA
66 TCAATACATAAAATAAATTA
1894909 TTTAAAATAAAT
1 TTTAAAATAAAT
1894921 TATTTTAAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 21 0.23
86 69 0.77
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (85 bp):
TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATAAATCCATATTTTAAAATAAA
TCAATACATAAAATAAATTA
Found at i:1894887 original size:36 final size:34
Alignment explanation
Indices: 1894796--1894971 Score: 139
Period size: 36 Copynumber: 5.1 Consensus size: 34
1894786 CCATATTTTA
* *
1894796 AAATAAATCAATATATACTAATAAATTATTTAAAAT
1 AAATAAATCCATATTTA--AATAAATTATTTAAAAT
* *
1894832 AAATCAATCCATA-CT-AATAAATTATTTAAAAT
1 AAATAAATCCATATTTAAATAAATTATTTAAAAT
* * ** *
1894864 AAATAAATCCATATTTTAAAATAAATCAATCCATA-
1 AAATAAATCCATA-TTT-AAATAAATTATTTAAAAT
1894899 AAATAAAT---TATTTAAAATAAATTATTTTAAAAT
1 AAATAAATCCATATTT-AAATAAATTA-TTTAAAAT
* *
1894932 AAATCAATCCATATTTTTAATAAATTATTTTAAAAT
1 AAATAAATCCATA-TTTAAATAAATTA-TTTAAAAT
1894968 AAAT
1 AAAT
1894972 TATTTTAAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 20
0.75 0.11 0.13
Matches are distributed among these distances:
31 13 0.12
32 34 0.30
33 7 0.06
34 1 0.01
35 9 0.08
36 46 0.41
37 3 0.03
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATAAATCCATATTTAAATAAATTATTTAAAAT
Found at i:1894929 original size:15 final size:15
Alignment explanation
Indices: 1894897--1894986 Score: 101
Period size: 15 Copynumber: 5.7 Consensus size: 15
1894887 AATCAATCCA
1894897 TAAAATAAATTA-TT
1 TAAAATAAATTATTT
1894911 TAAAATAAATTATTT
1 TAAAATAAATTATTT
1894926 TAAAATAAATCAATCCATATT
1 TAAAATAAAT---T--AT-TT
**
1894947 TTTAATAAATTATTT
1 TAAAATAAATTATTT
1894962 TAAAATAAATTATTT
1 TAAAATAAATTATTT
1894977 TAAAATAAAT
1 TAAAATAAAT
1894987 AACCTTATTA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.18
15 37 0.57
16 2 0.03
18 2 0.03
20 2 0.03
21 10 0.15
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATAAATTATTT
Found at i:1905206 original size:20 final size:22
Alignment explanation
Indices: 1905166--1905206 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1905156 AGGATGGATT
1905166 TTAATGATCAATAATCTATGAA
1 TTAATGATCAATAATCTATGAA
1905188 TTAATG-TCAATAA-CTATGA
1 TTAATGATCAATAATCTATGA
1905207 TTATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (22 bp):
TTAATGATCAATAATCTATGAA
Found at i:1905213 original size:21 final size:22
Alignment explanation
Indices: 1905165--1905213 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1905155 AAGGATGGAT
1905165 TTTAATGATCAATAATCTATGA
1 TTTAATGATCAATAATCTATGA
*
1905187 ATTAATG-TCAATAA-CTATGA
1 TTTAATGATCAATAATCTATGA
1905207 TTATAAT
1 TT-TAAT
1905214 TATTATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 11 0.46
22 6 0.25
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (22 bp):
TTTAATGATCAATAATCTATGA
Found at i:1908532 original size:91 final size:91
Alignment explanation
Indices: 1908377--1908559 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
1908367 CCTAGAACAC
*
1908377 CCATGTGCCTTGCATATGACCAGCCCCCATGTGTCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1908442 AAGAGTTATCTCCCTATTCGGCCAAG
66 AAGAGTTATCTCCCTATTCGGCCAAG
** * * * *
1908468 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
*
1908533 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTATCTCCCTATTCGGCCAAG
1908559 C
1 C
1908560 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTATCTCCCTATTCGGCCAAG
Found at i:1914341 original size:21 final size:21
Alignment explanation
Indices: 1914315--1914358 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1914305 ATTCTGGGCT
* *
1914315 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1914336 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1914357 AG
1 AG
1914359 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1914429 original size:23 final size:22
Alignment explanation
Indices: 1914385--1914429 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1914375 AATGTCATGG
*
1914385 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1914407 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1914430 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1915766 original size:18 final size:18
Alignment explanation
Indices: 1915743--1915778 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1915733 AGGAATGATA
1915743 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1915761 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1915779 ATATGTATTC
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:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1915799 original size:121 final size:121
Alignment explanation
Indices: 1915640--1916003 Score: 656
Period size: 121 Copynumber: 3.0 Consensus size: 121
1915630 CGAGGGTCTA
*
1915640 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
1915705 GATCCGTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1915761 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
1915826 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
1915882 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
1915947 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1916003 T
1 T
1916004 ATTATATGGC
Statistics
Matches: 233, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 233 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:1915887 original size:18 final size:18
Alignment explanation
Indices: 1915864--1915899 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1915854 AGGAATGATA
1915864 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1915882 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1915900 ATATGTATTC
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:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1915901 original size:62 final size:62
Alignment explanation
Indices: 1915715--1915901 Score: 171
Period size: 62 Copynumber: 3.1 Consensus size: 62
1915705 GATCCGTAGT
1915715 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * *
1915777 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCTT-
1 ATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTC
1915833 -GG-C
58 GGGAC
1915836 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1915898 ATAT
1 ATAT
1915902 ATGTATTCTT
Statistics
Matches: 94, Mismatches: 12, Indels: 38
0.65 0.08 0.26
Matches are distributed among these distances:
57 6 0.06
58 7 0.07
59 20 0.21
60 12 0.13
61 12 0.13
62 24 0.26
63 7 0.07
64 6 0.06
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:1916067 original size:23 final size:23
Alignment explanation
Indices: 1916010--1916070 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1916000 CATTATTATA
*
1916010 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1916033 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
1916056 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
1916071 TTTATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1916078 original size:23 final size:23
Alignment explanation
Indices: 1916001--1916078 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1915991 CCTTATGGAC
* *
1916001 ATTATTATATGGCACTACAGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1916025 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
1916048 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1916071 TTTATATG
1 ATTATATG
1916079 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1919923 original size:23 final size:22
Alignment explanation
Indices: 1919879--1919923 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1919869 AATGTCATGG
*
1919879 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1919901 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1919924 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1921260 original size:18 final size:18
Alignment explanation
Indices: 1921237--1921272 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1921227 AGGAATGATA
1921237 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1921255 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1921273 ATATGTATTC
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:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1921292 original size:121 final size:121
Alignment explanation
Indices: 1921134--1921497 Score: 647
Period size: 121 Copynumber: 3.0 Consensus size: 121
1921124 CGAGGGTCTA
1921134 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1921199 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1921255 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * * * *
1921320 GATCCTTGGCATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
1921376 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
1921441 GATCACTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
1921497 T
1 T
1921498 ATTATATGGA
Statistics
Matches: 229, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 229 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:1921381 original size:18 final size:18
Alignment explanation
Indices: 1921358--1921393 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1921348 AGGAATAATA
*
1921358 TGTGGTCTTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1921376 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
1921394 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:1921395 original size:62 final size:62
Alignment explanation
Indices: 1921209--1921395 Score: 160
Period size: 62 Copynumber: 3.1 Consensus size: 62
1921199 GATCCCTAGT
* *
1921209 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * * *
1921271 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGTCTGGT-GAGACACATACT-TGATCCTT--
1 ATATGTATATGATTCTTAAGGAATAATATGTG--GTCT-TTCG-G-GACAT--TGTGGTCCTTCG
1921327 GG-C
59 GGAC
1921330 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
1921392 ATAT
1 ATAT
1921396 ATGTATTCTT
Statistics
Matches: 93, Mismatches: 15, Indels: 34
0.65 0.11 0.24
Matches are distributed among these distances:
57 6 0.06
58 5 0.05
59 21 0.23
60 12 0.13
61 12 0.13
62 26 0.28
63 5 0.05
64 6 0.06
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:1921538 original size:23 final size:23
Alignment explanation
Indices: 1921508--1921556 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1921498 ATTATATGGA
1921508 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGCGGC
* *
1921531 ACTACGGTGCAATTCTATGTGGC
1 ACTACGGTGCAATTCTACGCGGC
1921554 ACT
1 ACT
1921557 TCAGTGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGCGGC
Found at i:1921563 original size:23 final size:23
Alignment explanation
Indices: 1921508--1921564 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1921498 ATTATATGGA
*
1921508 ACTACGGTGCAATTCTACGCGGC
1 ACTACAGTGCAATTCTACGCGGC
* * *
1921531 ACTACGGTGCAATTCTATGTGGC
1 ACTACAGTGCAATTCTACGCGGC
*
1921554 ACTTCAGTGCA
1 ACTACAGTGCA
1921565 TTTATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
ACTACAGTGCAATTCTACGCGGC
Found at i:1921572 original size:23 final size:23
Alignment explanation
Indices: 1921508--1921572 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
1921498 ATTATATGGA
* * * *
1921508 ACTACGGTGCAATTCTACGCGGC
1 ACTACAGTGCAATTATATGTGGC
* *
1921531 ACTACGGTGCAATTCTATGTGGC
1 ACTACAGTGCAATTATATGTGGC
* *
1921554 ACTTCAGTGCATTTATATG
1 ACTACAGTGCAATTATATG
1921573 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
ACTACAGTGCAATTATATGTGGC
Found at i:1929238 original size:19 final size:21
Alignment explanation
Indices: 1929216--1929262 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1929206 AAAATTTATT
1929216 TAAATAATTAA-AT-ATAAAA
1 TAAATAATTAATATAATAAAA
1929235 TAAAT-A-TAATATAATAAAA
1 TAAATAATTAATATAATAAAA
*
1929254 AAAATAATT
1 TAAATAATT
1929263 TTACCTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.13
18 3 0.13
19 15 0.65
20 1 0.04
21 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAATAATTAATATAATAAAA
Found at i:1930292 original size:20 final size:20
Alignment explanation
Indices: 1930264--1930316 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1930254 GATTTTAGAT
*
1930264 AATCACAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
1930284 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
1930304 AATCGCAACGCGA
1 AATCGCAATGCGA
1930317 TAACACTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:1930330 original size:41 final size:41
Alignment explanation
Indices: 1930285--1930395 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
1930275 GAATATGTAA
*
1930285 ATCGCAATGCGAATATGTA-AATCGCAACGCGATAACACTTG
1 ATCGCAATGCGAATATG-ACAATCGCAACGCGATAACACGTG
* * * *
1930326 ATCGCAATGCGATTCTGACTATCGCAACGCGATAATACGTG
1 ATCGCAATGCGAATATGACAATCGCAACGCGATAACACGTG
* * * *
1930367 ATCGCAACGCGATTCTGACTATCGCAACG
1 ATCGCAATGCGAATATGACAATCGCAACG
1930396 AGATTCTGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 62 0.98
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGAATATGACAATCGCAACGCGATAACACGTG
Found at i:1930331 original size:21 final size:20
Alignment explanation
Indices: 1930305--1930379 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
1930295 GAATATGTAA
1930305 ATCGCAACGCGATAACACTTG
1 ATCGCAACGCGATAACAC-TG
* *
1930326 ATCGCAATGCGAT-TCTGACT-
1 ATCGCAACGCGATAAC--ACTG
*
1930346 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACAC-TG
1930367 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1930380 TCTGACTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 26 0.59
22 2 0.05
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAACACTG
Found at i:1930351 original size:20 final size:20
Alignment explanation
Indices: 1930326--1930411 Score: 111
Period size: 20 Copynumber: 4.2 Consensus size: 20
1930316 ATAACACTTG
*
1930326 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
1930346 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
1930366 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
1930387 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1930407 ATCGC
1 ATCGC
1930412 GTTATGATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 38 0.67
21 15 0.26
22 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1930611 original size:22 final size:22
Alignment explanation
Indices: 1930581--1930653 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1930571 CTACGGCGAC
*
1930581 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGGCAAA
* * *
1930603 ATCCATCCCCATTTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCAAA
1930625 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGGCAAA
1930647 ATCCGTC
1 ATCCGTC
1930654 TATCTCCATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGGCAAA
Found at i:1931071 original size:20 final size:20
Alignment explanation
Indices: 1931027--1931100 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1931017 GAGATAGCCA
*
1931027 TTTCGCGTTGCGATAGTCGA-
1 TTTCGCGTTGCGATAATC-AT
*
1931047 ATTCGCGTTGCGATAATCAT
1 TTTCGCGTTGCGATAATCAT
* **
1931067 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAATCAT
*
1931087 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
1931101 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAATCAT
Found at i:1931101 original size:20 final size:20
Alignment explanation
Indices: 1931048--1931103 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1931038 GATAGTCGAA
* **
1931048 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
1931068 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1931088 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1931104 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1931110 original size:20 final size:20
Alignment explanation
Indices: 1931067--1931110 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1931057 CGATAATCAT
* *
1931067 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1931087 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1931107 TTTC
1 TTTC
1931111 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1932985 original size:31 final size:31
Alignment explanation
Indices: 1932928--1932991 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 31
1932918 TTTGTCTTTG
*
1932928 TTTTGTCTTTTGGTTGAAGTTAGTAAATTCAT
1 TTTTGTCTTTTGGTTG-ACTTAGTAAATTCAT
1932960 TTTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTTGTCTTTTGG-TTGACTTAGTAAATTCAT
1932991 T
1 T
1932992 CGGTAGTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.47
32 13 0.43
33 3 0.10
ACGTcount: A:0.20, C:0.08, G:0.17, T:0.55
Consensus pattern (31 bp):
TTTTGTCTTTTGGTTGACTTAGTAAATTCAT
Found at i:1933140 original size:20 final size:20
Alignment explanation
Indices: 1933112--1933288 Score: 117
Period size: 20 Copynumber: 9.4 Consensus size: 20
1933102 AGAATAGTCA
* *
1933112 CAACACGAAAATGATTATCG
1 CAACGCGAAAATGACTATCG
**
1933132 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
* **
1933152 CAACGTGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
*
1933172 CAACG-G--GAT-A--ATCG
1 CAACGCGAAAATGACTATCG
* *
1933186 CAATGCGAAAACGACTATCG
1 CAACGCGAAAATGACTATCG
*
1933206 CAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCG
* **
1933226 CAACACGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
*
1933246 CAACG-G--GAT-A--ATCG
1 CAACGCGAAAATGACTATCG
*
1933260 CAATGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
1933280 CAATGCGAA
1 CAACGCGAA
1933289 TTTAGTTTCG
Statistics
Matches: 123, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
14 16 0.13
15 2 0.02
16 2 0.02
17 5 0.04
18 2 0.02
19 2 0.02
20 94 0.76
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:1933202 original size:34 final size:34
Alignment explanation
Indices: 1933163--1933282 Score: 141
Period size: 34 Copynumber: 3.4 Consensus size: 34
1933153 AACGTGAATT
1933163 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
* ** **
1933197 CGACTATCGCAACGCGGAAATGACTATCGCAACACGAATT
1 TGACTATCGCAACG-GG--AT-A--ATCGCAATGCGAAAA
1933237 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
1933271 TGACTATCGCAA
1 TGACTATCGCAA
1933283 TGCGAATTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
34 36 0.51
35 2 0.03
36 1 0.01
37 4 0.06
38 1 0.01
39 2 0.03
40 24 0.34
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (34 bp):
TGACTATCGCAACGGGATAATCGCAATGCGAAAA
Found at i:1933238 original size:74 final size:74
Alignment explanation
Indices: 1933117--1933289 Score: 276
Period size: 74 Copynumber: 2.3 Consensus size: 74
1933107 AGTCACAACA
* * **
1933117 CGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGGGATA
1 CGAAAATGACTATCGCAACGCGAATATGACTATCGCAACACGAATTTGACTATCGCAACGGGATA
1933182 ATCGCAATG
66 ATCGCAATG
*
1933191 CGAAAACGACTATCGCAACGCGGAA-ATGACTATCGCAACACGAATTTGACTATCGCAACGGGAT
1 CGAAAATGACTATCGCAACGC-GAATATGACTATCGCAACACGAATTTGACTATCGCAACGGGAT
1933255 AATCGCAATG
65 AATCGCAATG
*
1933265 CGAAAATGACTATCGCAATGCGAAT
1 CGAAAATGACTATCGCAACGCGAAT
1933290 TTAGTTTCGC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
73 3 0.03
74 84 0.93
75 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (74 bp):
CGAAAATGACTATCGCAACGCGAATATGACTATCGCAACACGAATTTGACTATCGCAACGGGATA
ATCGCAATG
Found at i:1933242 original size:40 final size:40
Alignment explanation
Indices: 1933112--1933282 Score: 125
Period size: 34 Copynumber: 4.6 Consensus size: 40
1933102 AGAATAGTCA
* *
1933112 CAACACGAAAATGATTATCGCAACGC-GAATTTGACTATCG
1 CAACACGAAAATGACTATCGCAACGCGGAA-ATGACTATCG
** **
1933152 CAACGTGAATTTGACTATCGCAACG-GG--AT-A--ATCG
1 CAACACGAAAATGACTATCGCAACGCGGAAATGACTATCG
** *
1933186 CAATGCGAAAACGACTATCGCAACGCGGAAATGACTATCG
1 CAACACGAAAATGACTATCGCAACGCGGAAATGACTATCG
**
1933226 CAACACGAATTTGACTATCGCAACG-GG--AT-A--ATCG
1 CAACACGAAAATGACTATCGCAACGCGGAAATGACTATCG
**
1933260 CAATGCGAAAATGACTATCGCAA
1 CAACACGAAAATGACTATCGCAA
1933283 TGCGAATTTA
Statistics
Matches: 104, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
34 47 0.45
35 2 0.02
36 2 0.02
37 5 0.05
38 1 0.01
39 2 0.02
40 45 0.43
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (40 bp):
CAACACGAAAATGACTATCGCAACGCGGAAATGACTATCG
Found at i:1933315 original size:19 final size:19
Alignment explanation
Indices: 1933283--1933329 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1933273 ACTATCGCAA
* *
1933283 TGCGAATTTAGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1933302 TGTGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1933321 TGCGATTTT
1 TGCGATTTT
1933330 CTCGTTGCGA
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:0.11, C:0.13, G:0.28, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1933369 original size:19 final size:20
Alignment explanation
Indices: 1933347--1933389 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1933337 CGATAATCAT
1933347 TTTCGT-TTGCAATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
*
1933366 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
1933386 TTTC
1 TTTC
1933390 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:1933958 original size:42 final size:42
Alignment explanation
Indices: 1933866--1933977 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
1933856 GCCCGACTCA
* * *
1933866 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGTC
* ** *
1933908 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGG-C
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGTC
*
1933949 CCTTGTCATCGTTGAAGAGGCCCCTCCCA
1 CC-TGTCATCGTTCAAGAGGCCCCTCCCA
1933978 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 3 0.05
42 54 0.95
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGTC
Found at i:1933961 original size:21 final size:21
Alignment explanation
Indices: 1933870--1933971 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
1933860 GACTCACCTG
*
1933870 TCATCGTTCAAGAGGCCTCTCC
1 TCATCGTTCAAGAGGCC-CTTC
*
1933892 T-ATCGTTCAAGAGGTCCC-TA
1 TCATCGTTCAAGAGG-CCCTTC
** * *
1933912 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCTTC
* * *
1933933 CCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCTTC
*
1933954 TCATCGTTGAAGAGGCCC
1 TCATCGTTCAAGAGGCCC
1933972 CTCCCAACAT
Statistics
Matches: 61, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.07
21 54 0.89
22 3 0.05
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCTTC
Found at i:1935559 original size:20 final size:20
Alignment explanation
Indices: 1935534--1935776 Score: 215
Period size: 20 Copynumber: 12.8 Consensus size: 20
1935524 CGATTTTCTT
*
1935534 GTTGCGATAGTCAAATTCCC
1 GTTGCGATAGTCAAATTCGC
* *
1935554 GTTGCGATAATCAAATTCGT
1 GTTGCGATAGTCAAATTCGC
*
1935574 GTTGCGATAGTC-ATTTCGC
1 GTTGCGATAGTCAAATTCGC
1935593 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
1935613 GTTGCGATAGTTAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
1935633 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
**
1935653 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
* *
1935673 ATTGCGAT--T---A-TCCC
1 GTTGCGATAGTCAAATTCGC
**
1935687 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
* * *
1935707 ATTACGAT--T---A-TCCC
1 GTTGCGATAGTCAAATTCGC
* **
1935721 GTTGCGATATTCAAATTCAA
1 GTTGCGATAGTCAAATTCGC
*
1935741 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCAAATTCGC
1935761 GTTGCGATAGTCAAAT
1 GTTGCGATAGTCAAAT
1935777 GAATGTGTAA
Statistics
Matches: 180, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
14 19 0.11
16 2 0.01
18 2 0.01
19 18 0.10
20 139 0.77
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:1935695 original size:34 final size:34
Alignment explanation
Indices: 1935652--1935729 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
1935642 GTCATTTTCG
*
1935652 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTACGATTATCC
1935686 CGTTGCGATAGTCATTTTCGCATTACGATTATCC
1 CGTTGCGATAGTCATTTTCGCATTACGATTATCC
1935720 CGTTGCGATA
1 CGTTGCGATA
1935730 TTCAAATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTACGATTATCC
Found at i:1935974 original size:18 final size:18
Alignment explanation
Indices: 1935951--1935985 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1935941 AAGCCGGTTG
*
1935951 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1935969 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1935986 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1939009 original size:20 final size:20
Alignment explanation
Indices: 1938979--1939084 Score: 158
Period size: 20 Copynumber: 5.3 Consensus size: 20
1938969 AATTCAGTGA
* *
1938979 TGCGTTAGTCAGAATCACGT
1 TGCGATAGTCAGAATCGCGT
** *
1938999 TATGATAGTCAAAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1939019 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
1939039 TGCGATAGTCTGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1939059 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1939079 TGCGAT
1 TGCGAT
1939085 CAAGTGTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1939224 original size:20 final size:19
Alignment explanation
Indices: 1939200--1939246 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1939190 TGGAAACTGA
*
1939200 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
1939220 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
1939239 ATTGCGAT
1 ATTGCGAT
1939247 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:1939236 original size:19 final size:19
Alignment explanation
Indices: 1939212--1939248 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1939202 TGCGATAATG
*
1939212 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1939231 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1939249 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1939558 original size:3 final size:3
Alignment explanation
Indices: 1939550--1939576 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1939540 CTTATATCGG
1939550 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1939577 CAAAATCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1957682 original size:23 final size:23
Alignment explanation
Indices: 1957654--1957718 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
1957644 GTGTCACATA
*
1957654 TTTGTCCTGAA-GAACCACATAGT
1 TTTGTCCCGAATG-ACCACATAGT
1957677 TTTGTCCCGAATGACCACATAGT
1 TTTGTCCCGAATGACCACATAGT
* *
1957700 TTTGTCCCAAAGGACCACA
1 TTTGTCCCGAATGACCACA
1957719 AAGAACCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (23 bp):
TTTGTCCCGAATGACCACATAGT
Found at i:1964738 original size:18 final size:18
Alignment explanation
Indices: 1964687--1964743 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1964677 GTGACTAATT
*
1964687 ATATTA-TAAAGTTATAAG
1 ATATTATTAAAGTTGT-AG
* *
1964705 GTATTATAAAAG-TGTAG
1 ATATTATTAAAGTTGTAG
*
1964722 ATATTATTAAAGTTGTAT
1 ATATTATTAAAGTTGTAG
1964740 ATAT
1 ATAT
1964744 AATTTGATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 12 0.39
18 15 0.48
19 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (18 bp):
ATATTATTAAAGTTGTAG
Found at i:1965046 original size:3 final size:3
Alignment explanation
Indices: 1965038--1965082 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1965028 TGATTCTAAC
1965038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1965083 TAAAAGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1970441 original size:17 final size:17
Alignment explanation
Indices: 1970419--1970452 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1970409 CAGGTTATTC
*
1970419 ATGAATTATATGTCAAA
1 ATGAATTATACGTCAAA
1970436 ATGAATTATACGTCAAA
1 ATGAATTATACGTCAAA
1970453 GAGTTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (17 bp):
ATGAATTATACGTCAAA
Found at i:1982629 original size:16 final size:17
Alignment explanation
Indices: 1982587--1982632 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1982577 TGTTTATGAC
1982587 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
1982605 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
*
1982621 GGGATTGGAATC
1 GGAATTGGAATC
1982633 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1983516 original size:38 final size:37
Alignment explanation
Indices: 1983439--1983523 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 37
1983429 TTTTCACCCT
* *
1983439 AAACCCGAATCCGACTAGACCTGAATATCACACTTAAAA
1 AAACCCG-ACCCGACTAGACCTGAATATAACACTT-AAA
*
1983478 AAACCCGACCCGACTCGACC-GAATATAACACTTAAA
1 AAACCCGACCCGACTAGACCTGAATATAACACTTAAA
1983514 AAACCCGACC
1 AAACCCGACC
1983524 AGACCCGAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 13 0.30
37 12 0.28
38 11 0.26
39 7 0.16
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (37 bp):
AAACCCGACCCGACTAGACCTGAATATAACACTTAAA
Found at i:1983589 original size:248 final size:239
Alignment explanation
Indices: 1983155--1983747 Score: 816
Period size: 250 Copynumber: 2.4 Consensus size: 239
1983145 TATAAGGTAA
* *
1983155 AATTATATATTTTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCG-ACCCGACCTGACC-C
1 AATTATATA-TATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CTGACCTG
* *
1983218 AATTATCACACTTAAAAAAACCCGATCCGAATCGACCCGAATATCACACTTAAAACCCCGACCCG
64 AA-TATCACACTTAAAAAAACCCGATCCGACTCGA-CCGAATATAACACTTAAAACCCCGACCCG
* *
1983283 AACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAA
127 AACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCCGAAA
** * *
1983348 TAATAAAAAATTATTTTTATTTAATGAAAACATTGACTTAAT-TCGACCTG
192 TAATAAAAAA--A-AATTATTTAATAAAAACATTGACTTAATCCCGACCTG
* * *
1983398 AATTATATATATATTCAGGTCGGTCTC-GTTTTTTTCACCCTAAACCCGAATCCGACTAGACCTG
1 AATTATATATATTTTCGGGTCGGTC-CGGTTTTTTTCACCCTAAACCCGAACCCGACT-GACCTG
*
1983462 AATATCACACTTAAAAAAACCCGACCCGACTCGACCGAATATAACACTTAAAAAACCCGACCAGA
64 AATATCACACTTAAAAAAACCCGATCCGACTCGACCGAATATAACACTT--AAAA-CC--CC-GA
1983527 CCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCC
123 CCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCC
1983592 GAAATAATAAAAAAAAATTATTTAATAAAAACATTGACTTAATCCGACCCGACCTG
188 GAAATAATAAAAAAAAATTATTTAATAAAAACATTGACTTAAT----CCCGACCTG
* * *
1983648 AATTATATATATTTTCGGGTTGGTCCGGGTTTTTTCACCCTAAACCCGAACCCGACCCGACCTGA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CTGACCTGA
*
1983713 ATATCACACTTAAAAAAACCCGATCCGACCCGACC
65 ATATCACACTTAAAAAAACCCGATCCGACTCGACC
1983748 AAAATAAAGT
Statistics
Matches: 311, Mismatches: 22, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
242 50 0.16
243 49 0.16
244 6 0.02
245 27 0.09
246 1 0.00
247 2 0.01
248 79 0.25
249 1 0.00
250 95 0.31
251 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (239 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACTGACCTGAA
TATCACACTTAAAAAAACCCGATCCGACTCGACCGAATATAACACTTAAAACCCCGACCCGAACA
AAATAAAGTTTCATCCGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCCGAAATAAT
AAAAAAAAATTATTTAATAAAAACATTGACTTAATCCCGACCTG
Found at i:1983936 original size:27 final size:27
Alignment explanation
Indices: 1983906--1983965 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
1983896 CTCCAACAAG
1983906 GGAATTGAATTCCATCCATTTTTGGAT
1 GGAATTGAATTCCATCCATTTTTGGAT
*
1983933 GGAATTGAATTCCATCCTTTTTTGGAT
1 GGAATTGAATTCCATCCATTTTTGGAT
1983960 GGAATT
1 GGAATT
1983966 CACTTTTCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (27 bp):
GGAATTGAATTCCATCCATTTTTGGAT
Found at i:1985656 original size:2 final size:2
Alignment explanation
Indices: 1985649--1985673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1985639 TAATGTTAGG
1985649 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1985674 TATTTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1987091 original size:19 final size:19
Alignment explanation
Indices: 1987067--1987122 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1987057 GAACGCTGGA
1987067 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
1987086 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1987107 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1987123 CACGACCCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1987102 original size:11 final size:11
Alignment explanation
Indices: 1987067--1987115 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
1987057 GAACGCTGGA
1987067 AACCGGTTTTG
1 AACCGGTTTTG
1987078 -ACCGG-TTT-
1 AACCGGTTTTG
1987086 AACCGGTTTTG
1 AACCGGTTTTG
1987097 AACCGGTTTTG
1 AACCGGTTTTG
1987108 -ACCGGTTT
1 AACCGGTTT
1987116 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1987118 original size:9 final size:10
Alignment explanation
Indices: 1987068--1987122 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
1987058 AACGCTGGAA
1987068 ACCGGTTTTG
1 ACCGGTTTTG
*
1987078 ACCGG-TTTA
1 ACCGGTTTTG
1987087 ACCGGTTTTG
1 ACCGGTTTTG
1987097 AACCGGTTTTG
1 -ACCGGTTTTG
1987108 ACCGG-TTTG
1 ACCGGTTTTG
1987117 ACCGGT
1 ACCGGT
1987123 CACGACCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1987144 original size:13 final size:13
Alignment explanation
Indices: 1987126--1987207 Score: 59
Period size: 13 Copynumber: 6.3 Consensus size: 13
1987116 GACCGGTCAC
1987126 GACCCGACCCGTT
1 GACCCGACCCGTT
1987139 GACCCGACCCGACTGTT
1 GACCCGA-CC--C-GTT
1987156 GACCCGACCC---
1 GACCCGACCCGTT
*
1987166 GACCGTTGACCCG--
1 GACC--CGACCCGTT
1987179 -ACCCGACCCGTT
1 GACCCGACCCGTT
1987191 GACCCGACCCGTT
1 GACCCGACCCGTT
1987204 GACC
1 GACC
1987208 GGTGCTATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
10 10 0.18
12 8 0.14
13 23 0.40
14 3 0.05
16 3 0.05
17 10 0.18
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1987158 original size:17 final size:18
Alignment explanation
Indices: 1987125--1987201 Score: 131
Period size: 17 Copynumber: 4.4 Consensus size: 18
1987115 TGACCGGTCA
1987125 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
1987143 CGACCCGA-CTGTTGACC
1 CGACCCGACCCGTTGACC
1987160 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
1987177 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
1987195 CGACCCG
1 CGACCCG
1987202 TTGACCGGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
17 32 0.57
18 24 0.43
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:1987269 original size:29 final size:28
Alignment explanation
Indices: 1987237--1987303 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1987227 ATTCGGTTTT
*
1987237 GGTGCTATTTTGGGAATTAATTCTAAAAG
1 GGTGCTATTTTGGGAATT-ATTCTAAAAA
* * *
1987266 GGTGCTATATTGGTAATTATTTTAAAAA
1 GGTGCTATTTTGGGAATTATTCTAAAAA
*
1987294 TGTGCTATTT
1 GGTGCTATTT
1987304 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTATTCTAAAAA
Found at i:1988038 original size:24 final size:24
Alignment explanation
Indices: 1988006--1988074 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
1987996 ATAGTTTATC
*
1988006 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
1988030 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
1988054 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
1988075 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:1988809 original size:16 final size:17
Alignment explanation
Indices: 1988776--1988812 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1988766 TTGTATTCCA
1988776 TAAAATATAAAATAAAT
1 TAAAATATAAAATAAAT
1988793 TAAAA-ATAATAAT-AAT
1 TAAAATATAA-AATAAAT
1988809 TAAA
1 TAAA
1988813 TTAAGCGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATAAAATAAAT
Found at i:1989262 original size:21 final size:22
Alignment explanation
Indices: 1989238--1989283 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1989228 TTAAAAAACT
1989238 AAAATTAT-TATATATTT-TTAA
1 AAAATTATGTAT-TATTTATTAA
*
1989259 AAAATTATGTATTTTTTATTAA
1 AAAATTATGTATTATTTATTAA
1989281 AAA
1 AAA
1989284 TGTATGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTATGTATTATTTATTAA
Found at i:1989283 original size:22 final size:20
Alignment explanation
Indices: 1989238--1989300 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1989228 TTAAAAAACT
*
1989238 AAAATTAT-TATATATTTTTAA
1 AAAATTATGTAT-T-TTTTTTA
1989259 AAAATTATGTATTTTTTATTA
1 AAAATTATGTATTTTTT-TTA
1989280 AAAATGTATGT-TTTTTCTTTA
1 AAAAT-TATGTATTTTT-TTTA
1989301 TAATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
20 4 0.11
21 24 0.65
22 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
AAAATTATGTATTTTTTTTA
Found at i:1990554 original size:13 final size:13
Alignment explanation
Indices: 1990536--1990561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1990526 ACAAAACAGG
1990536 TAAAAAATAATAA
1 TAAAAAATAATAA
1990549 TAAAAAATAATAA
1 TAAAAAATAATAA
1990562 AAATAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:1990582 original size:9 final size:9
Alignment explanation
Indices: 1990496--1990574 Score: 59
Period size: 10 Copynumber: 8.2 Consensus size: 9
1990486 ACGTGAGAAT
*
1990496 AATAAATAA
1 AATAAAAAA
1990505 AATAAGAAAA
1 AATAA-AAAA
1990515 AATAAAAAA
1 AATAAAAAA
* *
1990524 TAACAAAACA
1 -AATAAAAAA
**
1990534 GGTAAAAAA
1 AATAAAAAA
1990543 TAATAATAAAA
1 -AATAA-AAAA
*
1990554 AATAATAAA
1 AATAAAAAA
1990563 AATAAACAAA
1 AATAAA-AAA
1990573 AA
1 AA
1990575 GAATAAAATG
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
9 22 0.41
10 28 0.52
11 4 0.07
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:1990856 original size:40 final size:40
Alignment explanation
Indices: 1990763--1990858 Score: 94
Period size: 40 Copynumber: 2.5 Consensus size: 40
1990753 GATATACATG
1990763 ATATTAAGAAAATA-AT-AATAATAAAAAAATAAAGTAAA
1 ATATTAAGAAAATATATAAATAATAAAAAAATAAAGTAAA
* * * *
1990801 ATAATATA-TATATATATAAATAAATAAAAACAA-AAA-TAGA
1 ATATTA-AGAAAATATATAAAT-AATAAAAA-AATAAAGTAAA
1990841 ATATTAAGAAAATATATA
1 ATATTAAGAAAATATATA
1990859 TAAAAACGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
38 9 0.20
39 4 0.09
40 19 0.42
41 11 0.24
42 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (40 bp):
ATATTAAGAAAATATATAAATAATAAAAAAATAAAGTAAA
Found at i:1990993 original size:22 final size:22
Alignment explanation
Indices: 1990950--1991044 Score: 54
Period size: 22 Copynumber: 4.2 Consensus size: 22
1990940 ATATATAATG
*
1990950 ATATAAGATATATATAACAAAAATA
1 ATATAA-ATATAAAT-A-AAAAATA
1990975 ATATAAATATAAAT-AAAAA-A
1 ATATAAATATAAATAAAAAATA
* ** *
1990995 AGAGGAATAT-AGTAAATAAATA
1 ATATAAATATAAATAAA-AAATA
*
1991017 A-ATAAAATATAATTAAAAAATA
1 ATAT-AAATATAAATAAAAAATA
1991039 TATATA
1 -ATATA
1991045 TAGGGGACGA
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.04
20 10 0.18
21 9 0.16
22 12 0.22
23 7 0.13
24 9 0.16
25 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (22 bp):
ATATAAATATAAATAAAAAATA
Done.